BLASTP 2.2.22 [Sep-27-2009]


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


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


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

Query= gi|254780611|ref|YP_003065024.1| RNA polymerase factor sigma-32
[Candidatus Liberibacter asiaticus str. psy62]
         (302 letters)

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

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


Results from round 1


>gi|254780611|ref|YP_003065024.1| RNA polymerase factor sigma-32 [Candidatus Liberibacter asiaticus
           str. psy62]
 gi|254040288|gb|ACT57084.1| RNA polymerase factor sigma-32 [Candidatus Liberibacter asiaticus
           str. psy62]
          Length = 302

 Score =  618 bits (1594), Expect = e-175,   Method: Compositional matrix adjust.
 Identities = 302/302 (100%), Positives = 302/302 (100%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL
Sbjct: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS
Sbjct: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL
Sbjct: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER
Sbjct: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQKP 300
           RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQKP
Sbjct: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQKP 300

Query: 301 RY 302
           RY
Sbjct: 301 RY 302


>gi|315121811|ref|YP_004062300.1| RNA polymerase factor sigma-32 [Candidatus Liberibacter
           solanacearum CLso-ZC1]
 gi|313495213|gb|ADR51812.1| RNA polymerase factor sigma-32 [Candidatus Liberibacter
           solanacearum CLso-ZC1]
          Length = 300

 Score =  519 bits (1337), Expect = e-145,   Method: Compositional matrix adjust.
 Identities = 247/289 (85%), Positives = 269/289 (93%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+R+NMSI+++GEIGL RYIHEI+KIPMLEKQEEY+LAKRY EH DL+A H+LVTSHLRL
Sbjct: 1   MSRRNMSIMIDGEIGLRRYIHEIKKIPMLEKQEEYMLAKRYHEHHDLNAVHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VVKIAMGYRGYGLPISEV+SEGNIGLMQAVKKFDPERGFRLATY +WWIKAA+QEYILRS
Sbjct: 61  VVKIAMGYRGYGLPISEVISEGNIGLMQAVKKFDPERGFRLATYGIWWIKAAIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVKIGTTANQKRLFFNLRRLKG LQA+ D NLKPEQVV IA KLNVSE+EVISMNCRL
Sbjct: 121 WSLVKIGTTANQKRLFFNLRRLKGRLQAVNDTNLKPEQVVEIATKLNVSEAEVISMNCRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GDESLN L+NSSDK+SSQWQD LVY+HD QEQ LI+KEERKNRRNMLTRSMS LNPRER
Sbjct: 181 SGDESLNVLMNSSDKDSSQWQDLLVYNHDSQEQTLIDKEERKNRRNMLTRSMSTLNPRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           RIFEARRL ENP TLENLSSEF VSRER+RQIEARAF+KVQ S+QKQ E
Sbjct: 241 RIFEARRLNENPSTLENLSSEFAVSRERIRQIEARAFEKVQASVQKQTE 289


>gi|190893168|ref|YP_001979710.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CIAT
           652]
 gi|190698447|gb|ACE92532.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CIAT
           652]
          Length = 302

 Score =  449 bits (1156), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 213/288 (73%), Positives = 247/288 (85%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R  +  I  GE GL+RY+ EIRK PMLE Q+EY+LAKRY EHGD  AAH+LVTSHLRL
Sbjct: 1   MARNTLPSITAGEAGLNRYLDEIRKFPMLEPQQEYMLAKRYAEHGDRDAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EVVSEGN+GLMQAVKKFDPERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLRRLKG +QAI D +LKPE V  IA KLNVSE EVISMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKLNVSEEEVISMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA I +++ +S QWQDWLV DHD QE VLIE++E + RR ML+++MSVLN RER
Sbjct: 181 SGDASLNAPIKAAEGDSGQWQDWLVDDHDSQEDVLIEQDELETRRRMLSKAMSVLNERER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RIFEARRL E PVTLE+LS+EF++SRERVRQIE RAF+KVQ++++K+ 
Sbjct: 241 RIFEARRLAEEPVTLEDLSAEFDISRERVRQIEVRAFEKVQDAVRKEA 288


>gi|327190963|gb|EGE58017.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli
           CNPAF512]
          Length = 332

 Score =  449 bits (1155), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 213/288 (73%), Positives = 247/288 (85%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R  +  I  GE GL+RY+ EIRK PMLE Q+EY+LAKRY EHGD  AAH+LVTSHLRL
Sbjct: 31  MARNTLPSITAGEAGLNRYLDEIRKFPMLEPQQEYMLAKRYAEHGDRDAAHKLVTSHLRL 90

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EVVSEGN+GLMQAVKKFDPERGFRLATY+MWWIKA++QEYILRS
Sbjct: 91  VAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRS 150

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLRRLKG +QAI D +LKPE V  IA KLNVSE EVISMN RL
Sbjct: 151 WSLVKMGTTANQKRLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKLNVSEEEVISMNRRL 210

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA I +++ +S QWQDWLV DHD QE VLIE++E + RR ML+++MSVLN RER
Sbjct: 211 SGDASLNAPIKAAEGDSGQWQDWLVDDHDSQEDVLIEQDELETRRRMLSKAMSVLNERER 270

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RIFEARRL E PVTLE+LS+EF++SRERVRQIE RAF+KVQ++++K+ 
Sbjct: 271 RIFEARRLAEEPVTLEDLSAEFDISRERVRQIEVRAFEKVQDAVRKEA 318


>gi|222086841|ref|YP_002545375.1| alternative sigma factor RpoH [Agrobacterium radiobacter K84]
 gi|221724289|gb|ACM27445.1| alternative sigma factor RpoH [Agrobacterium radiobacter K84]
          Length = 302

 Score =  448 bits (1153), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 216/288 (75%), Positives = 242/288 (84%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R  +  I  GE GL+RY+ EIRK PMLE QEEY+LAKRY EH D  AAHRLVTSHLRL
Sbjct: 1   MARNTLPSIAAGEAGLNRYLDEIRKFPMLEPQEEYMLAKRYAEHADREAAHRLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EVVSEGN+GLMQAVKKFDPERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLRRLKG +QAI + +LKPE V  IA KL VSE EVISMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRRLKGRIQAIDEGDLKPEHVSEIATKLKVSEEEVISMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA I +S+  S QWQDWLV DH+ QE VLIE++E   RR ML R+MSVLN RER
Sbjct: 181 SGDASLNAPIKASEGESGQWQDWLVDDHESQEAVLIEQDELDTRRRMLARAMSVLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RIFEARRL E+PVTLE+LSSEF++SRERVRQIE RAF+KVQE++QK  
Sbjct: 241 RIFEARRLSEDPVTLEDLSSEFDISRERVRQIEVRAFEKVQEAVQKDA 288


>gi|74099847|gb|AAZ99132.1| RpoH [Rhizobium leguminosarum]
          Length = 302

 Score =  447 bits (1150), Expect = e-124,   Method: Compositional matrix adjust.
 Identities = 212/288 (73%), Positives = 245/288 (85%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R  +  I  GE GL+RY+ EIRK PMLE Q+EY+LAKRY EHGD  AAH+LVTSHLRL
Sbjct: 1   MARNTLPSITAGEAGLNRYLDEIRKFPMLEPQQEYMLAKRYAEHGDRDAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EVVSEGN+GLMQAVKKFD ERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDAERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLRRLKG +QAI D +LKPE V  IA KLNVSE EVISMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKLNVSEEEVISMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA I +++ +S QWQDWLV DHD QE VLIE++E   RR ML ++MSVLN RER
Sbjct: 181 SGDASLNAPIKAAEGDSGQWQDWLVDDHDSQEDVLIEQDELDTRRRMLAKAMSVLNERER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RIFEARRL E+PVTLE+LS+EF++SRERVRQIE RAF+KVQ++++K+ 
Sbjct: 241 RIFEARRLAEDPVTLEDLSTEFDISRERVRQIEVRAFEKVQDAVRKEA 288


>gi|15889716|ref|NP_355397.1| RNA polymerase factor sigma-32 [Agrobacterium tumefaciens str. C58]
 gi|15157628|gb|AAK88182.1| RNA polymerase sigma-32 factor [Agrobacterium tumefaciens str. C58]
          Length = 300

 Score =  446 bits (1147), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 214/288 (74%), Positives = 242/288 (84%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R ++  I  GE GL+RY+ EIRK PMLE QEEY+L KRY EHGD  AAH+LVTSHLRL
Sbjct: 1   MARNSLPTITAGEAGLNRYLDEIRKFPMLEPQEEYMLGKRYAEHGDRDAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EVVSEGN+GLMQAVKKFDPERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLRRLKG +QAI D +LKPE V  IA KL VSE EVISMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRRLKGRIQAIDDGDLKPEHVKEIATKLQVSEEEVISMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA I +S+  S QWQDWLV DH+ QE VLIE++E + RR ML ++M VLN RER
Sbjct: 181 HGDASLNAPIKASEGESGQWQDWLVDDHESQEAVLIEQDELETRRRMLAKAMGVLNERER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RIFEARRL E+PVTLE LSSEF++SRERVRQIE RAF+KVQE++QK+ 
Sbjct: 241 RIFEARRLAEDPVTLEELSSEFDISRERVRQIEVRAFEKVQEAVQKEA 288


>gi|325293796|ref|YP_004279660.1| RNA polymerase sigma-32 factor [Agrobacterium sp. H13-3]
 gi|1710644|sp|P50507|RP32_AGRTU RecName: Full=RNA polymerase sigma-32 factor
 gi|1143324|dbj|BAA09439.1| sigma-32 homolog [Agrobacterium tumefaciens]
 gi|325061649|gb|ADY65340.1| RNA polymerase sigma-32 factor [Agrobacterium sp. H13-3]
          Length = 300

 Score =  446 bits (1147), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 214/288 (74%), Positives = 242/288 (84%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R ++  I  GE GL+RY+ EIRK PMLE QEEY+L KRY EHGD  AAH+LVTSHLRL
Sbjct: 1   MARNSLPTITAGEAGLNRYLDEIRKFPMLEPQEEYMLGKRYAEHGDRDAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EVVSEGN+GLMQAVKKFDPERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLRRLKG +QAI D +LKPE V  IA KL VSE EVISMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRRLKGRIQAIDDGDLKPEHVKEIATKLQVSEEEVISMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA I +S+  S QWQDWLV DH+ QE VLIE++E + RR ML ++M VLN RER
Sbjct: 181 HGDASLNAPIKASEGESGQWQDWLVDDHESQEAVLIEQDELETRRRMLAKAMGVLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RIFEARRL E+PVTLE LSSEF++SRERVRQIE RAF+KVQE++QK+ 
Sbjct: 241 RIFEARRLAEDPVTLEELSSEFDISRERVRQIEVRAFEKVQEAVQKEA 288


>gi|86358940|ref|YP_470832.1| RNA polymerase factor sigma-32 [Rhizobium etli CFN 42]
 gi|86283042|gb|ABC92105.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CFN
           42]
          Length = 302

 Score =  446 bits (1147), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 211/288 (73%), Positives = 246/288 (85%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R  +  I  GE GL+RY+ EIRK PMLE Q+EY+LAKRY EHGD  AAH+LVTSHLRL
Sbjct: 1   MARNTLPSITAGEAGLNRYLDEIRKFPMLEPQQEYMLAKRYAEHGDRDAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EVVSEGN+GLMQAVKKFDPERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WS VK+GTTANQKRLFFNLRRLKG +QAI D +LKPE V  IA KLNVSE EVISMN RL
Sbjct: 121 WSAVKMGTTANQKRLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKLNVSEEEVISMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA I +++ +S QWQDWLV DH+ QE VLIE++E + RR ML ++MSVLN RER
Sbjct: 181 SGDASLNAPIKAAEGDSGQWQDWLVDDHESQEDVLIEQDELETRRRMLAKAMSVLNERER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RIFEARRL E+PVTLE+LS+EF++SRERVRQIE RAF+KVQ++++K+ 
Sbjct: 241 RIFEARRLAEDPVTLEDLSAEFDISRERVRQIEVRAFEKVQDAVRKEA 288


>gi|116253507|ref|YP_769345.1| RNA polymerase factor sigma-32 [Rhizobium leguminosarum bv. viciae
           3841]
 gi|115258155|emb|CAK09256.1| putative RNA polymerase sigma-32 factor [Rhizobium leguminosarum
           bv. viciae 3841]
          Length = 302

 Score =  446 bits (1146), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 211/288 (73%), Positives = 244/288 (84%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R  +  I  GE GL+RY+ EIRK PMLE Q+EY+LAKRY EHGD  AAH+LVTSHLRL
Sbjct: 1   MARNTLPSITAGEAGLNRYLDEIRKFPMLEPQQEYMLAKRYAEHGDRDAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EVVSEGN+GLMQAVKKFD ERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDAERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLRRLKG +QAI D +LKPE V  IA KLNVSE EVISMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKLNVSEEEVISMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA I +++ +  QWQDWLV DHD QE VLIE++E   RR ML ++MSVLN RER
Sbjct: 181 SGDASLNAPIKAAEGDGGQWQDWLVDDHDSQEDVLIEQDELDTRRRMLAKAMSVLNERER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RIFEARRL E+PVTLE+LS+EF++SRERVRQIE RAF+KVQ++++K+ 
Sbjct: 241 RIFEARRLAEDPVTLEDLSTEFDISRERVRQIEVRAFEKVQDAVRKEA 288


>gi|209550663|ref|YP_002282580.1| RNA polymerase factor sigma-32 [Rhizobium leguminosarum bv.
           trifolii WSM2304]
 gi|209536419|gb|ACI56354.1| RNA polymerase, sigma 32 subunit, RpoH [Rhizobium leguminosarum bv.
           trifolii WSM2304]
          Length = 302

 Score =  446 bits (1146), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 211/289 (73%), Positives = 245/289 (84%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R  +  I  GE GL+RY+ EIRK PMLE Q+EY+LAKRY EHGD  AAH+LVTSHLRL
Sbjct: 1   MARNTLPSITAGEAGLNRYLDEIRKFPMLEPQQEYMLAKRYAEHGDRDAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EVVSEGN+GLMQAVKKFD ERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDAERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLRRLKG +QAI D +LKPE V  IA KL VSE EVISMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKLKVSEEEVISMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA I +++ +S QWQDWLV DHD QE VLIE++E   RR ML ++MSVLN RER
Sbjct: 181 SGDASLNAPIKAAEGDSGQWQDWLVDDHDSQEDVLIEQDELDTRRRMLAKAMSVLNERER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           RIFEARRL E+PVTLE+LS+EF++SRERVRQIE RAF+KVQ++++K+ +
Sbjct: 241 RIFEARRLAEDPVTLEDLSTEFDISRERVRQIEVRAFEKVQDAVRKEAQ 289


>gi|222149598|ref|YP_002550555.1| RNA polymerase factor sigma-32 [Agrobacterium vitis S4]
 gi|221736580|gb|ACM37543.1| alternative sigma factor RpoH [Agrobacterium vitis S4]
          Length = 300

 Score =  445 bits (1145), Expect = e-123,   Method: Compositional matrix adjust.
 Identities = 214/288 (74%), Positives = 242/288 (84%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R ++  I  GE GL+RY+ EIRK PMLE Q EY+LAKRY EHGD  AAHRLVTSHLRL
Sbjct: 1   MARNSLPSITAGEGGLNRYLDEIRKFPMLEPQVEYMLAKRYAEHGDRDAAHRLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EVVSEGN+GLMQAVKKFDPERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLRRLKG +QAI + +LKP+QV  IA KL VSE EVISMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRRLKGKIQAIEEGDLKPDQVTEIATKLKVSEEEVISMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA I +S+  S QWQDWLV DHD QE  LIE++E + RRNML+R+M VLN RER
Sbjct: 181 SGDASLNAPIRASEGESGQWQDWLVDDHDSQEDTLIEQDELETRRNMLSRAMGVLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RIF ARRL E PVTLE LSSEF++SRERVRQIE RAF+KVQ+++QK  
Sbjct: 241 RIFAARRLAEEPVTLEELSSEFDISRERVRQIEVRAFEKVQDAVQKDA 288


>gi|241206034|ref|YP_002977130.1| RNA polymerase factor sigma-32 [Rhizobium leguminosarum bv.
           trifolii WSM1325]
 gi|240859924|gb|ACS57591.1| RNA polymerase, sigma 32 subunit, RpoH [Rhizobium leguminosarum bv.
           trifolii WSM1325]
          Length = 302

 Score =  443 bits (1140), Expect = e-122,   Method: Compositional matrix adjust.
 Identities = 210/288 (72%), Positives = 243/288 (84%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R  +  I  GE GL+RY+ EIRK PMLE Q+EY+LAKRY EHGD  AAH+LVTSHLRL
Sbjct: 1   MARNTLPSITAGEAGLNRYLDEIRKFPMLEPQQEYMLAKRYAEHGDRDAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EVVSEGN+GLMQAVKKFD ERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDAERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLRRLKG +QAI D +LKPE V  IA KL VSE EVISMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKLKVSEEEVISMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA I +++ +  QWQDWLV DHD QE VLIE++E   RR ML ++MSVLN RER
Sbjct: 181 SGDASLNAPIKAAEGDGGQWQDWLVDDHDSQEDVLIEQDELDTRRRMLAKAMSVLNERER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RIFEARRL E+PVTLE+LS+EF++SRERVRQIE RAF+KVQ++++K+ 
Sbjct: 241 RIFEARRLAEDPVTLEDLSTEFDISRERVRQIEVRAFEKVQDAVRKEA 288


>gi|10952458|gb|AAG24943.1|AF128845_2 RpoH [Sinorhizobium meliloti]
          Length = 301

 Score =  437 bits (1124), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 206/286 (72%), Positives = 244/286 (85%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R  +  I  GE GL+RY+ EIRK PMLE QEEY+LAKRY+EH D  AAH+LVTSHLRL
Sbjct: 1   MARNTLPTIAAGEGGLNRYLDEIRKFPMLEPQEEYMLAKRYQEHDDRKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVKKF+P+RGFRLATY+MWWIKAA+QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKKFEPDRGFRLATYAMWWIKAAIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLRRLKG +QA+ + +LKPEQV  IA  L VSE EV+SMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRRLKGRIQALDEGDLKPEQVKEIATTLKVSEEEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA I +S+ +S QWQDWLV DHD QEQ+LIE++E ++RR +L  +M VLN RER
Sbjct: 181 SGDASLNAPIKASEGDSGQWQDWLVDDHDNQEQILIEQDELESRRALLANAMKVLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           RIFEARRL E P+TLE+LS+EF++SRERVRQIE RAF+KVQE+++K
Sbjct: 241 RIFEARRLTEEPITLEDLSTEFDISRERVRQIEVRAFEKVQEAVRK 286


>gi|15966479|ref|NP_386832.1| RNA polymerase factor sigma-32 [Sinorhizobium meliloti 1021]
 gi|307300484|ref|ZP_07580264.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium meliloti
           BL225C]
 gi|307318349|ref|ZP_07597784.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium meliloti
           AK83]
 gi|15075750|emb|CAC47305.1| RNA polymerase sigma factor (Sigma-32) [Sinorhizobium meliloti
           1021]
 gi|306896031|gb|EFN26782.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium meliloti
           AK83]
 gi|306904650|gb|EFN35234.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium meliloti
           BL225C]
          Length = 301

 Score =  437 bits (1124), Expect = e-121,   Method: Compositional matrix adjust.
 Identities = 206/286 (72%), Positives = 244/286 (85%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R  +  I  GE GL+RY+ EIRK PMLE QEEY+LAKRY+EH D  AAH+LVTSHLRL
Sbjct: 1   MARNTLPTIAAGEGGLNRYLDEIRKFPMLEPQEEYMLAKRYQEHDDRKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVKKF+P+RGFRLATY+MWWIKAA+QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKKFEPDRGFRLATYAMWWIKAAIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLRRLKG +QA+ + +LKPEQV  IA  L VSE EV+SMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRRLKGRIQALDEGDLKPEQVKEIATTLKVSEEEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA I +S+ +S QWQDWLV DHD QEQ+LIE++E ++RR +L  +M VLN RER
Sbjct: 181 SGDASLNAPIKASEGDSGQWQDWLVDDHDNQEQILIEQDELESRRALLANAMKVLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           RIFEARRL E P+TLE+LS+EF++SRERVRQIE RAF+KVQE+++K
Sbjct: 241 RIFEARRLTEEPITLEDLSTEFDISRERVRQIEVRAFEKVQEAVRK 286


>gi|10129883|dbj|BAB13517.1| sigma factor [Sinorhizobium meliloti]
          Length = 301

 Score =  436 bits (1120), Expect = e-120,   Method: Compositional matrix adjust.
 Identities = 205/286 (71%), Positives = 244/286 (85%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R  +  I  GE GL+RY+ EIRK PMLE QEEY+LAKRY+EH D  AAH+LVTSHLRL
Sbjct: 1   MARNTLPTIAAGEGGLNRYLDEIRKFPMLEPQEEYMLAKRYQEHDDRKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVKKF+P+RGFRLATY+MWWIKAA+QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKKFEPDRGFRLATYAMWWIKAAIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLRRLKG +QA+ + +LKPEQV  IA  L VSE +V+SMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRRLKGRIQALDEGDLKPEQVKEIATTLKVSEEKVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA I +S+ +S QWQDWLV DHD QEQ+LIE++E ++RR +L  +M VLN RER
Sbjct: 181 SGDASLNAPIKASEGDSGQWQDWLVDDHDNQEQILIEQDELESRRGLLANAMKVLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           RIFEARRL E P+TLE+LS+EF++SRERVRQIE RAF+KVQE+++K
Sbjct: 241 RIFEARRLTEEPITLEDLSTEFDISRERVRQIEVRAFEKVQEAVRK 286


>gi|227823295|ref|YP_002827267.1| RNA polymerase factor sigma-32 [Sinorhizobium fredii NGR234]
 gi|227342296|gb|ACP26514.1| RNA polymerase sigma factor, sigma-70 family [Sinorhizobium fredii
           NGR234]
          Length = 301

 Score =  434 bits (1115), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 206/286 (72%), Positives = 243/286 (84%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R  +  I  GE GL+RY+ EIRK PMLE QEEY+LAKRY+EH D SAAH+LVTSHLRL
Sbjct: 1   MARSTLPSIAAGEGGLNRYLDEIRKFPMLEPQEEYMLAKRYQEHDDRSAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVKKF+P+RGFRLATY+MWWIKAA+QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVMSEGNVGLMQAVKKFEPDRGFRLATYAMWWIKAAIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLRRLKG +QA+ + +LKPEQV  IA  L VSE EV+SMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRRLKGRIQALDEGDLKPEQVKEIATTLKVSEDEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA I +S+ +S QWQDWLV +HD QE++LIE++E  +RR +L  +M VLN RER
Sbjct: 181 SGDASLNAPIKASEGDSGQWQDWLVDEHDNQEEILIEQDELDSRRALLASAMKVLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           RIFEARRL E PVTLE LS+EF++SRERVRQIE RAF+KVQE+++K
Sbjct: 241 RIFEARRLTEEPVTLEELSTEFDISRERVRQIEVRAFEKVQEAVRK 286


>gi|150397812|ref|YP_001328279.1| RNA polymerase factor sigma-32 [Sinorhizobium medicae WSM419]
 gi|150029327|gb|ABR61444.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium medicae
           WSM419]
          Length = 301

 Score =  434 bits (1115), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 205/286 (71%), Positives = 244/286 (85%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R  +  I  GE GL+RY+ EIRK PMLE QEEY+LAKRY+EH D  AAH+LVTSHLRL
Sbjct: 1   MARNTLPTIAAGEGGLNRYLDEIRKFPMLEPQEEYMLAKRYQEHDDRKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVKKF+P+RGFRLATY+MWWIKAA+QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKKFEPDRGFRLATYAMWWIKAAIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLRRLKG +QA+ + +LKPEQV  IA  L VSE EVISMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRRLKGRIQALDEGDLKPEQVKEIATTLKVSEDEVISMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA I +S+ +S QWQDWLV ++D QEQ+LIE++E  NRR +L  ++ VLN RER
Sbjct: 181 SGDASLNAPIKASEGDSGQWQDWLVDENDNQEQILIEQDELDNRRALLANALKVLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           RIFEARRL E+P+TLE+LS+EF++SRERVRQIE RAF+KVQE+++K
Sbjct: 241 RIFEARRLTEDPITLEDLSTEFDISRERVRQIEVRAFEKVQEAVRK 286


>gi|319781136|ref|YP_004140612.1| RNA polymerase sigma factor RpoH [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
 gi|317167024|gb|ADV10562.1| RNA polymerase sigma factor RpoH [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
          Length = 303

 Score =  433 bits (1113), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 200/282 (70%), Positives = 248/282 (87%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           +++  IV+GE GLSRY+ EIR+ PML+ QEEY+LAKRY EH D SAAH+LVTSHLRLV K
Sbjct: 3   QSLPSIVSGEGGLSRYLEEIRRFPMLQPQEEYMLAKRYAEHEDTSAAHKLVTSHLRLVAK 62

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IAMGYRGYGLPI EV+SEGN+GLMQAVKKF+PERGFRLATY+MWWIKA++QEYILRSWSL
Sbjct: 63  IAMGYRGYGLPIGEVISEGNVGLMQAVKKFEPERGFRLATYAMWWIKASIQEYILRSWSL 122

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VK+GTTANQKRLFFNLR++KG +QA+ D +LKP+Q+  IA +LNVSE+EV+SMN RL+GD
Sbjct: 123 VKMGTTANQKRLFFNLRKVKGKIQALDDGDLKPDQIAEIATRLNVSEAEVVSMNRRLSGD 182

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SLNA I +S+  S +WQDWLV DH+ QE++LIE++E +NRR ML+ +++VLN RERRIF
Sbjct: 183 ASLNAPIRASEGESGEWQDWLVDDHESQEEMLIEQDELENRRGMLSGALAVLNERERRIF 242

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           EARRL E P+TLE LSSEF++SRERVRQIE RAF+KVQ++++
Sbjct: 243 EARRLAEEPLTLEELSSEFDISRERVRQIEVRAFEKVQDAVK 284


>gi|260461535|ref|ZP_05809782.1| RNA polymerase, sigma 32 subunit, RpoH [Mesorhizobium opportunistum
           WSM2075]
 gi|259032605|gb|EEW33869.1| RNA polymerase, sigma 32 subunit, RpoH [Mesorhizobium opportunistum
           WSM2075]
          Length = 303

 Score =  431 bits (1107), Expect = e-119,   Method: Compositional matrix adjust.
 Identities = 198/282 (70%), Positives = 248/282 (87%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           +++  IV+GE GLSRY+ EIR+ PML+ QEEY+LAKRY EH D SAAH+LVTSHLRLV K
Sbjct: 3   QSLPSIVSGEGGLSRYLEEIRRFPMLQPQEEYMLAKRYAEHEDTSAAHKLVTSHLRLVAK 62

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IAMGYRGYGLPI EV+SEGN+GLMQAVKKF+PERGFRLATY+MWWIKA++QEYILRSWSL
Sbjct: 63  IAMGYRGYGLPIGEVISEGNVGLMQAVKKFEPERGFRLATYAMWWIKASIQEYILRSWSL 122

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VK+GTTANQKRLFFNLR++KG +QA+ D +LKP+Q+  IA +LNVSE+EV+SMN RL+GD
Sbjct: 123 VKMGTTANQKRLFFNLRKVKGKIQALDDGDLKPDQIAEIATRLNVSEAEVVSMNRRLSGD 182

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SLNA I +++  S +WQDWLV DH+ QE++LIE++E +NRR ML+ +++VLN RERRIF
Sbjct: 183 ASLNAPIRATEGESGEWQDWLVDDHESQEEMLIEQDELENRRGMLSGALAVLNDRERRIF 242

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           EARRL E P+TLE LS+EF++SRERVRQIE RAF+KVQ++++
Sbjct: 243 EARRLAEEPLTLEELSAEFDISRERVRQIEVRAFEKVQDAVK 284


>gi|13473215|ref|NP_104782.1| RNA polymerase factor sigma-32 [Mesorhizobium loti MAFF303099]
 gi|14023963|dbj|BAB50568.1| sigma factor [Mesorhizobium loti MAFF303099]
          Length = 303

 Score =  430 bits (1106), Expect = e-118,   Method: Compositional matrix adjust.
 Identities = 197/282 (69%), Positives = 248/282 (87%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           +++  IV+GE GLSRY+ EIR+ PML+ QEEY+LAKRY EH D SAAH+LVTSHLRLV K
Sbjct: 3   QSLPSIVSGEGGLSRYLEEIRRFPMLQPQEEYMLAKRYAEHEDTSAAHKLVTSHLRLVAK 62

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IAMGYRGYGLPI EV+SEGN+GLMQAVKKF+PERGFRLATY+MWWIKA++QEYILRSWSL
Sbjct: 63  IAMGYRGYGLPIGEVISEGNVGLMQAVKKFEPERGFRLATYAMWWIKASIQEYILRSWSL 122

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VK+GTTANQKRLFFNLR++KG +QA+ D +LKP+Q+  IA +LNV+E+EV+SMN RL+GD
Sbjct: 123 VKMGTTANQKRLFFNLRKVKGKIQALDDGDLKPDQIAEIATRLNVTEAEVVSMNRRLSGD 182

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SLNA I +++  S +WQDWLV DH+ QE++LIE++E +NRR ML+ +++VLN RERRIF
Sbjct: 183 ASLNAPIRATEGESGEWQDWLVDDHESQEEMLIEQDELENRRGMLSGALAVLNERERRIF 242

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           EARRL E P+TLE LS+EF++SRERVRQIE RAF+KVQ++++
Sbjct: 243 EARRLAEEPLTLEELSAEFDISRERVRQIEVRAFEKVQDAVK 284


>gi|110635485|ref|YP_675693.1| RNA polymerase factor sigma-32 [Mesorhizobium sp. BNC1]
 gi|110286469|gb|ABG64528.1| RNA polymerase, sigma 32 subunit, RpoH [Chelativorans sp. BNC1]
          Length = 308

 Score =  422 bits (1086), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 200/297 (67%), Positives = 248/297 (83%), Gaps = 4/297 (1%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           + +  IV+GE GL+RY+ EIR+ PML+ +EEY+LAKRYREH D  AAH+LVTSHLRLV K
Sbjct: 3   QTLPSIVSGEGGLTRYLEEIRRFPMLQPEEEYMLAKRYREHDDTDAAHKLVTSHLRLVAK 62

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IAMGYRGYGLPI EV+SEGN+GLMQAVKKF+PERGFRLATY+MWWIKAA+QEYILRSWSL
Sbjct: 63  IAMGYRGYGLPIGEVISEGNVGLMQAVKKFEPERGFRLATYAMWWIKAAIQEYILRSWSL 122

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VK+GTTANQKRLFFNLR++KG +QA+ + +L PEQV  IA +LNVSE EVISMN RL+GD
Sbjct: 123 VKMGTTANQKRLFFNLRKVKGKIQALDEGDLNPEQVSEIATRLNVSEEEVISMNRRLSGD 182

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SLNA I +++  S +WQDWLV +H+ QE++L+E++E ++RR ML  +M VLN RERRIF
Sbjct: 183 ASLNAPIRATEGESGEWQDWLVDEHENQEEMLVEQDELESRRRMLEDAMDVLNDRERRIF 242

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI----QKQVELSSSPPL 296
           EARRL + P+TLE LS EF++SRERVRQIE RAF+KVQE++    ++Q +   S PL
Sbjct: 243 EARRLSDEPMTLEELSGEFDISRERVRQIEVRAFEKVQEAVKASAKRQAQALRSAPL 299


>gi|163758761|ref|ZP_02165848.1| RNA polymerase sigma factor [Hoeflea phototrophica DFL-43]
 gi|162284051|gb|EDQ34335.1| RNA polymerase sigma factor [Hoeflea phototrophica DFL-43]
          Length = 300

 Score =  422 bits (1085), Expect = e-116,   Method: Compositional matrix adjust.
 Identities = 197/292 (67%), Positives = 244/292 (83%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M + ++  I  GE GL+RY+ EIR+ PMLE QEEY+LAKR+ +H D  AAH+LVTSHLRL
Sbjct: 1   MAQTSLPTISAGENGLNRYLAEIRRFPMLEPQEEYMLAKRFLQHEDTKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVKKFDPERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLR++K  +QA+ D +L+P+QV  IA KLNVSE EVISMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRKVKSKIQAVEDGDLRPDQVAEIATKLNVSEEEVISMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA I +S+  S QWQDWLV + D QE +L+E++E ++RR ML  ++ VLN RE+
Sbjct: 181 SGDASLNAPIKASEGESGQWQDWLVDESDSQEDMLVEQDELESRRAMLKSALEVLNEREK 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
           RIFEARRL+++P+TLE+LS EF++SRERVRQIE RAF+KVQ+++QK    S 
Sbjct: 241 RIFEARRLRDDPITLEDLSGEFDISRERVRQIEVRAFEKVQDAVQKAAAASD 292


>gi|90418989|ref|ZP_01226900.1| sigma factor [Aurantimonas manganoxydans SI85-9A1]
 gi|90337069|gb|EAS50774.1| sigma factor [Aurantimonas manganoxydans SI85-9A1]
          Length = 303

 Score =  413 bits (1062), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 194/292 (66%), Positives = 238/292 (81%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M + N+  I +GE GLSRY+ EIR+ PMLE QEEY+LAKRY EH D  AAHRLVTSHLRL
Sbjct: 1   MAQANLPSISSGEAGLSRYLEEIRRFPMLEPQEEYMLAKRYAEHDDRDAAHRLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EVVSEGN+GLMQAVK+FDPERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKRFDPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLR++K  +QA+ + +L+P+QV  IA  L VS+ EV+SMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRKMKSRIQALDEGDLRPDQVSQIATNLGVSDEEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA + +++  S +WQDWLV D + QE +L   +E   RR ML ++M VLN RER
Sbjct: 181 SGDASLNAPLRATEGESGEWQDWLVDDSETQEDLLARNDELDQRRGMLQQAMGVLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
           RIFEARRL E+P+TLE LS EFE+SRERVRQIE RAF+KVQ++++   + ++
Sbjct: 241 RIFEARRLAEDPLTLETLSGEFEISRERVRQIEVRAFEKVQKAVRDTADATN 292


>gi|254473077|ref|ZP_05086475.1| alternative sigma factor RpoH [Pseudovibrio sp. JE062]
 gi|211957798|gb|EEA93000.1| alternative sigma factor RpoH [Pseudovibrio sp. JE062]
          Length = 297

 Score =  413 bits (1061), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 195/283 (68%), Positives = 236/283 (83%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           +N+  +  GE GLSRY+ EIRK PML+ QEEY+LAKRYREH +  AA +LV SHLRLV K
Sbjct: 3   RNLPALTGGEGGLSRYLDEIRKFPMLQPQEEYMLAKRYREHDEPKAAEKLVNSHLRLVAK 62

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IAMGYRGYGLP+ EV+SEGN+GLMQAVK+F+P++GFRLATY+MWWIKA++QEYILR+WSL
Sbjct: 63  IAMGYRGYGLPLGEVISEGNVGLMQAVKRFEPDKGFRLATYAMWWIKASIQEYILRTWSL 122

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VK+GTTANQKRLFFNLRR+KG +QA  D +L+PEQV  IA  L V+E+EV+SMN RL GD
Sbjct: 123 VKMGTTANQKRLFFNLRRVKGKIQAFEDGDLRPEQVQQIATTLGVTENEVVSMNRRLGGD 182

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SLNA + SS+  SS+WQDWLV D + QE VL E+EE   RR+ML  +MSVLN RE RIF
Sbjct: 183 SSLNAPLRSSEGESSEWQDWLVDDSESQEAVLAEQEEYDVRRDMLKNAMSVLNERETRIF 242

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           EARRL ENP+TLE LS+EF VSRERVRQIE RAF+KVQ+++Q+
Sbjct: 243 EARRLSENPITLEELSTEFGVSRERVRQIEVRAFEKVQKAVQE 285


>gi|239832766|ref|ZP_04681095.1| alternative sigma factor RpoH [Ochrobactrum intermedium LMG 3301]
 gi|239825033|gb|EEQ96601.1| alternative sigma factor RpoH [Ochrobactrum intermedium LMG 3301]
          Length = 303

 Score =  413 bits (1061), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 193/278 (69%), Positives = 234/278 (84%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M + N+  I +G+ GL+RY+ EIR+ PMLE QEEY+LAKRY EH D  AAH+LVTSHLRL
Sbjct: 1   MAQMNLPSITSGDGGLTRYLEEIRRFPMLEPQEEYMLAKRYHEHTDPKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVK+F+PERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLR++K  +QA+ D +L P+QV  IA KLNVSE EV+SMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRKMKSKIQALDDGDLNPDQVKQIATKLNVSEDEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA + +S+  S +WQDWLV D   QEQ+LIE++E  NRR+ML ++M  LN RER
Sbjct: 181 SGDASLNAPLRASEGESGEWQDWLVDDSSSQEQILIEQDELDNRRSMLEQAMDTLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           RIFEARRL ++P+TLE+LSSEF +SRERVRQIE RAF+
Sbjct: 241 RIFEARRLSDDPMTLEDLSSEFSISRERVRQIEVRAFE 278


>gi|153008567|ref|YP_001369782.1| RNA polymerase factor sigma-32 [Ochrobactrum anthropi ATCC 49188]
 gi|151560455|gb|ABS13953.1| RNA polymerase, sigma 32 subunit, RpoH [Ochrobactrum anthropi ATCC
           49188]
          Length = 303

 Score =  412 bits (1059), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 194/278 (69%), Positives = 234/278 (84%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M + N+  I +G+ GL+RY+ EIR+ PMLE QEEY+LAKRY EH D  AAHRLVTSHLRL
Sbjct: 1   MAQMNLPSITSGDGGLTRYLEEIRRFPMLEPQEEYMLAKRYHEHTDPKAAHRLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVK+F+PERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLR++K  +QA+ D +L P+QV  IA KL VSE EV+SMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRKMKSKIQALDDGDLNPDQVKQIATKLKVSEDEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA + +S+  S +WQDWLV D   QEQVLIE++E +NRR+ML ++M  LN RER
Sbjct: 181 SGDASLNAPLRASEGESGEWQDWLVDDSSSQEQVLIEQDELENRRSMLEQAMDTLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           RIFEARRL ++P+TLE+LSSEF +SRERVRQIE RAF+
Sbjct: 241 RIFEARRLSDDPMTLEDLSSEFGISRERVRQIEVRAFE 278


>gi|114707401|ref|ZP_01440298.1| RNA polymerase sigma factor [Fulvimarina pelagi HTCC2506]
 gi|114537282|gb|EAU40409.1| RNA polymerase sigma factor [Fulvimarina pelagi HTCC2506]
          Length = 304

 Score =  412 bits (1058), Expect = e-113,   Method: Compositional matrix adjust.
 Identities = 192/288 (66%), Positives = 240/288 (83%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M + N+  I +GE GL+RY+ EIR+ PML+  EEY+LAKRY EH D +AAH+LVTSHLRL
Sbjct: 1   MAQMNLPSIASGEGGLNRYLEEIRRFPMLQPDEEYMLAKRYAEHDDRNAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EVVSEGN+GLMQAVK+FDPERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKRFDPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLR++K  +QA+ D +L P+QV  IA +L VS+ EVISMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRKMKSRIQALEDGDLNPDQVKQIATQLGVSDDEVISMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLN+ + +++  S +WQDWLV +++ QE VL +++E   RR ML R+M +LN RER
Sbjct: 181 SGDASLNSPLRATEGESGEWQDWLVDENESQEDVLAQQDELDQRRGMLKRAMGILNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RIFEARRL E+P+TLE LS EF++SRERVRQIE RAF+KVQ+++Q+ V
Sbjct: 241 RIFEARRLSEDPITLEALSGEFDISRERVRQIEVRAFEKVQKAVQENV 288


>gi|306844673|ref|ZP_07477258.1| alternative sigma factor RpoH [Brucella sp. BO1]
 gi|306274845|gb|EFM56615.1| alternative sigma factor RpoH [Brucella sp. BO1]
          Length = 303

 Score =  410 bits (1054), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 193/278 (69%), Positives = 234/278 (84%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M +  +  I +G+ GL+RY+ EIR+ PMLE QEEY+LAKRY EH D  AAH+LVTSHLRL
Sbjct: 1   MAQMKLPSITSGDGGLTRYLEEIRRFPMLEPQEEYMLAKRYHEHADPKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVK+F+PERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLR++K  +QA+ D +L P+QV  IA KLNVSE EV+SMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRKMKSKIQALDDGDLNPDQVKQIATKLNVSEDEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA + +S+  S +WQDWLV D + QEQVLIE++E ++RR+ML ++M  LN RER
Sbjct: 181 SGDASLNAPLRASEGESGEWQDWLVDDSNSQEQVLIEQDELESRRSMLEQAMETLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           RIFEARRL E P+TLE+LSSEF +SRERVRQIE RAF+
Sbjct: 241 RIFEARRLAEEPMTLEDLSSEFGISRERVRQIEVRAFE 278


>gi|306841398|ref|ZP_07474101.1| alternative sigma factor RpoH [Brucella sp. BO2]
 gi|306288583|gb|EFM59932.1| alternative sigma factor RpoH [Brucella sp. BO2]
          Length = 303

 Score =  408 bits (1049), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 192/278 (69%), Positives = 233/278 (83%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M +  +  I +G+ GL+RY+ EIR+ PMLE QEEY+LAKRY EH D  AAH+LVTSHLRL
Sbjct: 1   MAQMKLPSITSGDGGLTRYLEEIRRFPMLEPQEEYMLAKRYHEHADPKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVK+F+PERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLR++K  +QA+ D +L P+QV  IA KLNVSE EV+SMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRKMKSKIQALDDGDLNPDQVKQIATKLNVSEDEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA + +S+  S +WQDWLV D + QEQVLIE++E ++RR+ML ++M  LN RER
Sbjct: 181 SGDASLNAPLRASEGESGEWQDWLVDDSNSQEQVLIEQDELESRRSMLEQAMETLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           RIFEARRL E P+TLE+LS EF +SRERVRQIE RAF+
Sbjct: 241 RIFEARRLAEEPMTLEDLSGEFGISRERVRQIEVRAFE 278


>gi|218670385|ref|ZP_03520056.1| RNA polymerase factor sigma-32 [Rhizobium etli GR56]
          Length = 266

 Score =  408 bits (1048), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 192/252 (76%), Positives = 222/252 (88%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           +AKRY EHGD  AAH+LVTSHLRLV KIAMGYRGYGLPI EVVSEGN+GLMQAVKKFDPE
Sbjct: 1   MAKRYAEHGDRDAAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPE 60

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RGFRLATY+MWWIKA++QEYILRSWSLVK+GTTANQKRLFFNLRRLKG +QAI D +LKP
Sbjct: 61  RGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQKRLFFNLRRLKGRIQAIDDGDLKP 120

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           E V  IA KLNVSE EVISMN RL+GD SLNA I +++ +S QWQDWLV DHD QE VLI
Sbjct: 121 EHVSEIATKLNVSEEEVISMNRRLSGDASLNAPIKAAEGDSGQWQDWLVDDHDSQEDVLI 180

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           E++E + RR ML+++MSVLN RERRIFEARRL E PVTLE+LS+EF++SRERVRQIE RA
Sbjct: 181 EQDELETRRRMLSKAMSVLNERERRIFEARRLAEEPVTLEDLSAEFDISRERVRQIEVRA 240

Query: 277 FKKVQESIQKQV 288
           F+KVQ++++K+ 
Sbjct: 241 FEKVQDAVRKEA 252


>gi|254719685|ref|ZP_05181496.1| RNA polymerase factor sigma-32 [Brucella sp. 83/13]
 gi|265984700|ref|ZP_06097435.1| RNA polymerase factor sigma-32 [Brucella sp. 83/13]
 gi|306840038|ref|ZP_07472825.1| alternative sigma factor RpoH [Brucella sp. NF 2653]
 gi|264663292|gb|EEZ33553.1| RNA polymerase factor sigma-32 [Brucella sp. 83/13]
 gi|306404852|gb|EFM61144.1| alternative sigma factor RpoH [Brucella sp. NF 2653]
          Length = 303

 Score =  408 bits (1048), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 192/278 (69%), Positives = 233/278 (83%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M +  +  I +G+ GL+RY+ EIR+ PMLE QEEY+LAKRY EH D  AAH+LVTSHLRL
Sbjct: 1   MAQMKLPSITSGDGGLTRYLEEIRRFPMLEPQEEYMLAKRYHEHADPKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVK+F+PERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLR++K  +QA+ D +L P+QV  IA KLNVSE EV+SMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRKMKSKIQALDDGDLNPDQVKQIATKLNVSEDEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA + +S+  S +WQDWLV D + QEQVLIE++E ++RR+ML ++M  LN RER
Sbjct: 181 SGDASLNAPLRASEGESGEWQDWLVDDSNSQEQVLIEQDELESRRSMLEQAMETLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           RIFEARRL E P+TLE+LS EF +SRERVRQIE RAF+
Sbjct: 241 RIFEARRLAEEPMTLEDLSGEFGISRERVRQIEVRAFE 278


>gi|23502510|ref|NP_698637.1| RNA polymerase factor sigma-32 [Brucella suis 1330]
 gi|161619585|ref|YP_001593472.1| RNA polymerase factor sigma-32 [Brucella canis ATCC 23365]
 gi|163845234|ref|YP_001622889.1| RNA polymerase factor sigma-32 [Brucella suis ATCC 23445]
 gi|225628222|ref|ZP_03786256.1| alternative sigma factor RpoH [Brucella ceti str. Cudo]
 gi|254708479|ref|ZP_05170307.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M163/99/10]
 gi|254708670|ref|ZP_05170481.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis B2/94]
 gi|254714517|ref|ZP_05176328.1| RNA polymerase factor sigma-32 [Brucella ceti M644/93/1]
 gi|254717415|ref|ZP_05179226.1| RNA polymerase factor sigma-32 [Brucella ceti M13/05/1]
 gi|256030196|ref|ZP_05443810.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M292/94/1]
 gi|256061694|ref|ZP_05451831.1| RNA polymerase factor sigma-32 [Brucella neotomae 5K33]
 gi|256160370|ref|ZP_05458060.1| RNA polymerase factor sigma-32 [Brucella ceti M490/95/1]
 gi|256255578|ref|ZP_05461114.1| RNA polymerase factor sigma-32 [Brucella ceti B1/94]
 gi|260167873|ref|ZP_05754684.1| RNA polymerase factor sigma-32 [Brucella sp. F5/99]
 gi|260568745|ref|ZP_05839213.1| sigma-70 factor family protein [Brucella suis bv. 4 str. 40]
 gi|261219245|ref|ZP_05933526.1| RNA polymerase factor sigma-32 [Brucella ceti M13/05/1]
 gi|261222781|ref|ZP_05937062.1| RNA polymerase factor sigma-32 [Brucella ceti B1/94]
 gi|261315977|ref|ZP_05955174.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M163/99/10]
 gi|261316160|ref|ZP_05955357.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis B2/94]
 gi|261322306|ref|ZP_05961503.1| RNA polymerase factor sigma-32 [Brucella ceti M644/93/1]
 gi|261325699|ref|ZP_05964896.1| RNA polymerase factor sigma-32 [Brucella neotomae 5K33]
 gi|261757310|ref|ZP_06001019.1| sigma-70 factor family [Brucella sp. F5/99]
 gi|265987224|ref|ZP_06099781.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M292/94/1]
 gi|265998739|ref|ZP_06111296.1| RNA polymerase factor sigma-32 [Brucella ceti M490/95/1]
 gi|23348506|gb|AAN30552.1| RNA polymerase sigma-70 factor family protein [Brucella suis 1330]
 gi|161336396|gb|ABX62701.1| alternative sigma factor RpoH [Brucella canis ATCC 23365]
 gi|163675957|gb|ABY40067.1| alternative sigma factor RpoH [Brucella suis ATCC 23445]
 gi|225616068|gb|EEH13116.1| alternative sigma factor RpoH [Brucella ceti str. Cudo]
 gi|260154129|gb|EEW89211.1| sigma-70 factor family protein [Brucella suis bv. 4 str. 40]
 gi|260921365|gb|EEX88018.1| RNA polymerase factor sigma-32 [Brucella ceti B1/94]
 gi|260924334|gb|EEX90902.1| RNA polymerase factor sigma-32 [Brucella ceti M13/05/1]
 gi|261294996|gb|EEX98492.1| RNA polymerase factor sigma-32 [Brucella ceti M644/93/1]
 gi|261295383|gb|EEX98879.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis B2/94]
 gi|261301679|gb|EEY05176.1| RNA polymerase factor sigma-32 [Brucella neotomae 5K33]
 gi|261305003|gb|EEY08500.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M163/99/10]
 gi|261737294|gb|EEY25290.1| sigma-70 factor family [Brucella sp. F5/99]
 gi|262553428|gb|EEZ09197.1| RNA polymerase factor sigma-32 [Brucella ceti M490/95/1]
 gi|264659421|gb|EEZ29682.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M292/94/1]
          Length = 303

 Score =  408 bits (1048), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 192/278 (69%), Positives = 233/278 (83%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M +  +  I +G+ GL+RY+ EIR+ PMLE QEEY+LAKRY EH D  AAH+LVTSHLRL
Sbjct: 1   MAQMKLPSITSGDGGLTRYLEEIRRFPMLEPQEEYMLAKRYHEHADPKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVK+F+PERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLR++K  +QA+ D +L P+QV  IA KLNVSE EV+SMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRKMKSKIQALDDGDLNPDQVKQIATKLNVSEDEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA + +S+  S +WQDWLV D + QEQVLIE++E ++RR+ML ++M  LN RER
Sbjct: 181 SGDASLNAPLRASEGESGEWQDWLVDDSNSQEQVLIEQDELESRRSMLEQAMETLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           RIFEARRL E P+TLE+LS EF +SRERVRQIE RAF+
Sbjct: 241 RIFEARRLAEEPMTLEDLSGEFGISRERVRQIEVRAFE 278


>gi|328542558|ref|YP_004302667.1| RNA polymerase sigma factor [polymorphum gilvum SL003B-26A1]
 gi|326412304|gb|ADZ69367.1| RNA polymerase sigma factor [Polymorphum gilvum SL003B-26A1]
          Length = 296

 Score =  407 bits (1047), Expect = e-112,   Method: Compositional matrix adjust.
 Identities = 193/293 (65%), Positives = 238/293 (81%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           +N+ ++  GE GLSRY+ EIR+ PMLE QEEY+LAKRY+EH D +AA RLV SHLRLV K
Sbjct: 3   QNVPMLTAGEGGLSRYLDEIRRFPMLEPQEEYMLAKRYKEHDDPAAAERLVNSHLRLVAK 62

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IAMGYRGYGLP+ EVVSEGN+GLMQAVK+F+P++GFRLATY+MWWIKAA+QEYILRSWSL
Sbjct: 63  IAMGYRGYGLPLGEVVSEGNVGLMQAVKRFEPDKGFRLATYAMWWIKAAIQEYILRSWSL 122

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VK+GTTANQKRLFFNLRRLKG +QA+ + +LKPEQV  IA KL V E +V+SMN RLAGD
Sbjct: 123 VKMGTTANQKRLFFNLRRLKGRIQALEEGDLKPEQVQEIATKLGVPEEDVVSMNRRLAGD 182

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SLNA I +++ +S +WQDWLV + + QE +L  +EE   RR +L  +M +L  RERRIF
Sbjct: 183 ASLNAPIRAAEADSGEWQDWLVDESESQETLLANQEELDIRRKLLGDAMDILTERERRIF 242

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPL 296
           EARRL E+P+TLE LS+EF VSRERVRQIE RAF+K+Q++++K       P L
Sbjct: 243 EARRLAEDPITLEELSTEFGVSRERVRQIEVRAFEKIQKAVRKSARDLEQPSL 295


>gi|254703436|ref|ZP_05165264.1| RNA polymerase factor sigma-32 [Brucella suis bv. 3 str. 686]
 gi|261754065|ref|ZP_05997774.1| RNA polymerase factor sigma-32 [Brucella suis bv. 3 str. 686]
 gi|261743818|gb|EEY31744.1| RNA polymerase factor sigma-32 [Brucella suis bv. 3 str. 686]
          Length = 300

 Score =  407 bits (1045), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 191/270 (70%), Positives = 230/270 (85%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           I +G+ GL+RY+ EIR+ PMLE QEEY+LAKRY EH D  AAH+LVTSHLRLV KIAMGY
Sbjct: 6   ITSGDGGLTRYLEEIRRFPMLEPQEEYMLAKRYHEHADPKAAHKLVTSHLRLVAKIAMGY 65

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           RGYGLPI EV+SEGN+GLMQAVK+F+PERGFRLATY+MWWIKA++QEYILRSWSLVK+GT
Sbjct: 66  RGYGLPIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWWIKASIQEYILRSWSLVKMGT 125

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           TANQKRLFFNLR++K  +QA+ D +L P+QV  IA KLNVSE EV+SMN RL+GD SLNA
Sbjct: 126 TANQKRLFFNLRKMKSKIQALDDGDLNPDQVKQIATKLNVSEDEVVSMNRRLSGDASLNA 185

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            + +S+  S +WQDWLV D + QEQVLIE++E ++RR+ML ++M  LN RERRIFEARRL
Sbjct: 186 PLRASEGESGEWQDWLVDDSNSQEQVLIEQDELESRRSMLEQAMETLNDRERRIFEARRL 245

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFK 278
            E P+TLE+LS EF +SRERVRQIE RAF+
Sbjct: 246 AEEPMTLEDLSGEFGISRERVRQIEVRAFE 275


>gi|17986661|ref|NP_539295.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 1 str. 16M]
 gi|62290526|ref|YP_222319.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 1 str. 9-941]
 gi|82700442|ref|YP_415016.1| RNA polymerase factor sigma-32 [Brucella melitensis biovar Abortus
           2308]
 gi|189024748|ref|YP_001935516.1| RNA polymerase factor sigma-32 [Brucella abortus S19]
 gi|225853116|ref|YP_002733349.1| RNA polymerase factor sigma-32 [Brucella melitensis ATCC 23457]
 gi|237816032|ref|ZP_04595028.1| alternative sigma factor RpoH [Brucella abortus str. 2308 A]
 gi|254689824|ref|ZP_05153078.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 6 str. 870]
 gi|254694316|ref|ZP_05156144.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 3 str. Tulya]
 gi|254697972|ref|ZP_05159800.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 2 str.
           86/8/59]
 gi|254730858|ref|ZP_05189436.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 4 str. 292]
 gi|256045266|ref|ZP_05448160.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|256114225|ref|ZP_05454970.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 3 str.
           Ether]
 gi|256258077|ref|ZP_05463613.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 9 str. C68]
 gi|256263396|ref|ZP_05465928.1| sigma-70 factor [Brucella melitensis bv. 2 str. 63/9]
 gi|260547226|ref|ZP_05822964.1| sigma-70 factor family protein [Brucella abortus NCTC 8038]
 gi|260565841|ref|ZP_05836324.1| sigma-70 factor family protein [Brucella melitensis bv. 1 str. 16M]
 gi|260755355|ref|ZP_05867703.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 6 str. 870]
 gi|260758577|ref|ZP_05870925.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 4 str. 292]
 gi|260762409|ref|ZP_05874746.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 2 str.
           86/8/59]
 gi|260884371|ref|ZP_05895985.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 9 str. C68]
 gi|261214622|ref|ZP_05928903.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 3 str. Tulya]
 gi|265991691|ref|ZP_06104248.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|265995528|ref|ZP_06108085.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 3 str.
           Ether]
 gi|297248928|ref|ZP_06932636.1| alternative sigma factor RpoH [Brucella abortus bv. 5 str. B3196]
 gi|17982279|gb|AAL51559.1| RNA polymerase sigma-32 factor [Brucella melitensis bv. 1 str. 16M]
 gi|62196658|gb|AAX74958.1| RNA polymerase sigma-70 factor family protein [Brucella abortus bv.
           1 str. 9-941]
 gi|82616543|emb|CAJ11621.1| Sigma-70 factor family:Sigma-70 region 2:Sigma-70 region 4
           [Brucella melitensis biovar Abortus 2308]
 gi|189020320|gb|ACD73042.1| Sigma-70 factor family [Brucella abortus S19]
 gi|225641481|gb|ACO01395.1| alternative sigma factor RpoH [Brucella melitensis ATCC 23457]
 gi|237788695|gb|EEP62907.1| alternative sigma factor RpoH [Brucella abortus str. 2308 A]
 gi|260095591|gb|EEW79469.1| sigma-70 factor family protein [Brucella abortus NCTC 8038]
 gi|260151214|gb|EEW86309.1| sigma-70 factor family protein [Brucella melitensis bv. 1 str. 16M]
 gi|260668895|gb|EEX55835.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 4 str. 292]
 gi|260672835|gb|EEX59656.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 2 str.
           86/8/59]
 gi|260675463|gb|EEX62284.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 6 str. 870]
 gi|260873899|gb|EEX80968.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 9 str. C68]
 gi|260916229|gb|EEX83090.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 3 str. Tulya]
 gi|262766812|gb|EEZ12430.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 3 str.
           Ether]
 gi|263002647|gb|EEZ15050.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|263093393|gb|EEZ17462.1| sigma-70 factor [Brucella melitensis bv. 2 str. 63/9]
 gi|297174061|gb|EFH33418.1| alternative sigma factor RpoH [Brucella abortus bv. 5 str. B3196]
 gi|326409662|gb|ADZ66727.1| Sigma-70 factor family [Brucella melitensis M28]
 gi|326539369|gb|ADZ87584.1| alternative sigma factor RpoH [Brucella melitensis M5-90]
          Length = 303

 Score =  405 bits (1042), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 191/278 (68%), Positives = 232/278 (83%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M +  +  I +G+ GL+RY+ EIR+ PMLE QEEY+LAKRY EH D  AAH+LVTSHLRL
Sbjct: 1   MAQMKLPSITSGDGGLTRYLEEIRRFPMLEPQEEYMLAKRYHEHADPKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVK+F+PERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLR++K  +QA+ D +L P+QV  IA KLNVSE EV+SMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRKMKSKIQALDDGDLNPDQVKQIATKLNVSEDEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA + +S+  S +WQDWLV D + QEQVLIE++E ++RR+ML ++M  LN RER
Sbjct: 181 SGDASLNAPLRASEGESGEWQDWLVDDSNSQEQVLIEQDELESRRSMLEQAMETLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
            IFEARRL E P+TLE+LS EF +SRERVRQIE RAF+
Sbjct: 241 HIFEARRLAEEPMTLEDLSGEFGISRERVRQIEVRAFE 278


>gi|118588309|ref|ZP_01545718.1| RNA polymerase sigma factor [Stappia aggregata IAM 12614]
 gi|118439015|gb|EAV45647.1| RNA polymerase sigma factor [Stappia aggregata IAM 12614]
          Length = 294

 Score =  404 bits (1039), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 195/291 (67%), Positives = 233/291 (80%), Gaps = 1/291 (0%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           +N+  +  GE GLSRY+ EIRK PML+ QEEY+LAKRY+EH D  AA RLV SHLRLV K
Sbjct: 3   QNVPTLTAGEGGLSRYLDEIRKFPMLQPQEEYMLAKRYKEHEDPEAAERLVNSHLRLVAK 62

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IAMGYRGYGLPI EVVSEGN+GLMQAVK+F+P++GFRLATY+MWWIKAA+QEYILRSWSL
Sbjct: 63  IAMGYRGYGLPIGEVVSEGNVGLMQAVKRFEPDKGFRLATYAMWWIKAAIQEYILRSWSL 122

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VK+GTTANQKRLFFNLRRLKG +QA+ + +LKP QV  IA KL VSE EV+SMN RL GD
Sbjct: 123 VKMGTTANQKRLFFNLRRLKGKIQALDEGDLKPHQVSEIATKLGVSEEEVVSMNRRLGGD 182

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SLNA +  ++ ++ +WQDWLV + D QE +L  +EE   RR ML  +M VLN RERRIF
Sbjct: 183 ASLNAPVR-AEADAGEWQDWLVDESDSQETLLANQEELDMRRKMLNDAMDVLNERERRIF 241

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSP 294
           EARRL E+P+TLE+LS EF VSRERVRQIE RAF+KVQ++++        P
Sbjct: 242 EARRLSEDPMTLEDLSGEFGVSRERVRQIEVRAFEKVQKAVRNSARTMDQP 292


>gi|148560551|ref|YP_001259508.1| RNA polymerase factor sigma-32 [Brucella ovis ATCC 25840]
 gi|294850906|ref|ZP_06791582.1| alternative sigma factor RpoH [Brucella sp. NVSL 07-0026]
 gi|148371808|gb|ABQ61787.1| alternative sigma factor RpoH [Brucella ovis ATCC 25840]
 gi|294821549|gb|EFG38545.1| alternative sigma factor RpoH [Brucella sp. NVSL 07-0026]
          Length = 303

 Score =  404 bits (1039), Expect = e-111,   Method: Compositional matrix adjust.
 Identities = 191/278 (68%), Positives = 232/278 (83%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M +  +  I +G+ GL+RY+ EIR+ PMLE QEEY+LAKRY EH D  AAH+LVTSHLRL
Sbjct: 1   MAQMKLPSITSGDGGLTRYLEEIRRFPMLEPQEEYMLAKRYHEHADPKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGL I EV+SEGN+GLMQAVK+F+PERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLSIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLR++K  +QA+ D +L P+QV  IA KLNVSE EV+SMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRKMKSKIQALDDGDLNPDQVKQIATKLNVSEDEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA + +S+  S +WQDWLV D + QEQVLIE++E ++RR+ML ++M  LN RER
Sbjct: 181 SGDASLNAPLRASEGESGEWQDWLVDDSNSQEQVLIEQDELESRRSMLEQAMETLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           RIFEARRL E P+TLE+LS EF +SRERVRQIE RAF+
Sbjct: 241 RIFEARRLAEEPMTLEDLSGEFGISRERVRQIEVRAFE 278


>gi|256370062|ref|YP_003107573.1| RNA polymerase factor sigma-32 [Brucella microti CCM 4915]
 gi|256000225|gb|ACU48624.1| RNA polymerase factor sigma-32 [Brucella microti CCM 4915]
          Length = 303

 Score =  403 bits (1035), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 191/278 (68%), Positives = 232/278 (83%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M +  +  I +G+ GL+RY+ EIR+ PMLE QEEY+LAKRY EH D  AAH+LVTSHLRL
Sbjct: 1   MAQMKLPSITSGDGGLTRYLEEIRRFPMLEPQEEYMLAKRYHEHADPKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVK+F+PERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLR++K  +QA+ D +L P+QV  IA KLNVSE EV+SMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRKMKSKIQALDDGDLNPDQVKQIATKLNVSEDEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA + +S+  S +WQD LV D + QEQVLIE++E ++RR+ML ++M  LN RER
Sbjct: 181 SGDASLNAPLRASEGESGEWQDRLVDDSNSQEQVLIEQDELESRRSMLEQAMETLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           RIFEARRL E P+TLE+LS EF +SRERVRQIE RAF+
Sbjct: 241 RIFEARRLAEEPMTLEDLSGEFGISRERVRQIEVRAFE 278


>gi|49473931|ref|YP_031973.1| RNA polymerase factor sigma-32 [Bartonella quintana str. Toulouse]
 gi|49239434|emb|CAF25783.1| RNA polymerase sigma-32 factor [Bartonella quintana str. Toulouse]
          Length = 294

 Score =  401 bits (1030), Expect = e-110,   Method: Compositional matrix adjust.
 Identities = 191/285 (67%), Positives = 234/285 (82%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M   N+  +  G+ GL+RY+ E+R+ P+LE +EEY+LA+RYR+H DL AAHRLVTSHLRL
Sbjct: 1   MAHINLLSVTTGDGGLNRYLEEVRRFPILEPKEEYMLAQRYRQHNDLKAAHRLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVK+F+PERG RLATY++WWIKA++QEY+LRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKRFEPERGLRLATYAIWWIKASIQEYVLRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVKIGTTANQKRLFFNLR+LK  LQ +   +L  EQV  IA +LNV+E EVISMN RL
Sbjct: 121 WSLVKIGTTANQKRLFFNLRKLKSRLQVLDKGDLNAEQVKEIATQLNVTEDEVISMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA + + +  +S+WQDWLV D + QEQ LIE+ E +NRR+MLT +MS LN RE+
Sbjct: 181 CGDTSLNAPLRTQEGENSEWQDWLVDDSNNQEQTLIEQSELENRRSMLTYAMSNLNEREK 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           RIF+ARRL + P+TLE LSSEF +SRERVRQIE RAF+KVQ SI+
Sbjct: 241 RIFKARRLSDKPLTLEELSSEFNISRERVRQIEMRAFEKVQNSIK 285


>gi|307944600|ref|ZP_07659940.1| alternative sigma factor RpoH [Roseibium sp. TrichSKD4]
 gi|307772349|gb|EFO31570.1| alternative sigma factor RpoH [Roseibium sp. TrichSKD4]
          Length = 294

 Score =  400 bits (1028), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 191/291 (65%), Positives = 235/291 (80%), Gaps = 1/291 (0%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           +N+ ++  GE GLSRY+ EIRK P+L+ QEEY+LAKRY+EH D  AA RLV SHLRLV K
Sbjct: 3   QNVPMLTAGEGGLSRYLDEIRKFPLLQPQEEYMLAKRYKEHADPEAAERLVNSHLRLVAK 62

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IAMGYRGYGLPI EVVSEGN+GLMQAVK+F+P++GFRLATY+MWWIKAA+QEYILRSWSL
Sbjct: 63  IAMGYRGYGLPIGEVVSEGNVGLMQAVKRFEPDKGFRLATYAMWWIKAAIQEYILRSWSL 122

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VK+GTTANQKRLFFNLRRLKG +QA+ + +LKP QV  IA KL VSE EVISMN RL GD
Sbjct: 123 VKMGTTANQKRLFFNLRRLKGKIQALEEGDLKPHQVQEIATKLGVSEEEVISMNRRLGGD 182

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SLN+ +  ++ ++ +WQDWLV + D QE +L  +EE   RR +L+++M  LN RERRIF
Sbjct: 183 TSLNSPVR-AEADAGEWQDWLVDEADSQETLLANQEELDQRRELLSQAMDELNERERRIF 241

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSP 294
            ARRL E+P+TLE+LS+EF VSRERVRQIE RAF+KVQ++++        P
Sbjct: 242 TARRLSEDPITLEDLSTEFGVSRERVRQIEVRAFEKVQKAVKNSARAKELP 292


>gi|163867808|ref|YP_001609012.1| RNA polymerase factor sigma-32 [Bartonella tribocorum CIP 105476]
 gi|161017459|emb|CAK01017.1| RNA polymerase sigma-32 factor [Bartonella tribocorum CIP 105476]
          Length = 294

 Score =  399 bits (1025), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 192/285 (67%), Positives = 235/285 (82%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M   N+  I+ G+ GL+RY+ E+R+ PMLE +EEY+LA+RYREH DL AAHRLVTSHLRL
Sbjct: 1   MAHMNLLSIITGDGGLNRYLEEVRRFPMLEPKEEYMLAQRYREHNDLKAAHRLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V K+AMGYRGYGLPI EV+SEGNIGLMQAVK+F+PERGFRLATY++WWIKA++QEY+LRS
Sbjct: 61  VAKVAMGYRGYGLPIGEVISEGNIGLMQAVKRFEPERGFRLATYAIWWIKASIQEYVLRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLR+LK  LQA+   +L  EQV  IA +LNV+E EV+SMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRKLKNKLQALDSGDLNTEQVKEIATQLNVTEDEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA + + +  +S+ QDWLV + + QEQ+LIEK E +NRR ML  +M+ LN RER
Sbjct: 181 GGDTSLNAPLRTKEGENSELQDWLVDESNNQEQILIEKSELENRRFMLVNAMNNLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           RIF+ARRL + P+TLE LSSEF +SRERVRQIE RAF+KVQ SI+
Sbjct: 241 RIFKARRLNDIPLTLEELSSEFNISRERVRQIEMRAFEKVQNSIR 285


>gi|49475181|ref|YP_033222.1| RNA polymerase factor sigma-32 [Bartonella henselae str. Houston-1]
 gi|49237986|emb|CAF27191.1| RNA polymerase sigma-32 factor [Bartonella henselae str. Houston-1]
          Length = 294

 Score =  398 bits (1023), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 188/285 (65%), Positives = 236/285 (82%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M   N+  +  G+ GLSRY+ E+R+ PMLE QEEY+LA+RYR+H DL AAH+LVTSHLRL
Sbjct: 1   MAHMNLLSVTTGDGGLSRYLEEVRRFPMLEPQEEYMLAQRYRKHNDLKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIA+GYRGYGLPI EV+SEGN+GLM+AVK+F+PERGFRLATY++WWIKA++QEY+LRS
Sbjct: 61  VAKIAVGYRGYGLPIGEVISEGNVGLMKAVKRFEPERGFRLATYAIWWIKASIQEYVLRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLR+LK  LQA+ + +L  EQV  IA +LNV+E EV+SMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRKLKSRLQALDNGDLNAEQVKEIAIQLNVTEDEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA + + +  +S+WQDWLV D + QEQ LIE+ E +NRR+MLT ++  LN RE+
Sbjct: 181 GGDTSLNAPLRTKEGENSEWQDWLVDDSNNQEQTLIEQNELENRRSMLTNALDNLNEREK 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           RIF+ARRL + P+TLE LSSEF +SRERVRQIE RAF+K+Q SI+
Sbjct: 241 RIFKARRLSDIPLTLEELSSEFNISRERVRQIEMRAFEKIQNSIK 285


>gi|209886261|ref|YP_002290118.1| alternative sigma factor RpoH [Oligotropha carboxidovorans OM5]
 gi|209874457|gb|ACI94253.1| alternative sigma factor RpoH [Oligotropha carboxidovorans OM5]
          Length = 299

 Score =  397 bits (1021), Expect = e-109,   Method: Compositional matrix adjust.
 Identities = 193/288 (67%), Positives = 229/288 (79%), Gaps = 1/288 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R     I+NGE GLS Y+ EIRK PMLE QEEY+LAKR+REH D  AAH+LVTSHLRL
Sbjct: 1   MARTATLPILNGESGLSHYLAEIRKFPMLEPQEEYMLAKRWREHDDRDAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPISEVVSEGN+GLMQAVK+F+PE+GFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQK+LFFNLR+ K  + A+ D ++  +QV  IAK+L V+E +VI MN RL
Sbjct: 121 WSLVKMGTTANQKKLFFNLRKAKSKISALEDGDMHEDQVKLIAKRLGVTERDVIDMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA I   D    +WQDWLV     QE ++ E EE  +RRN LT +M VLNPRER
Sbjct: 181 GGDASLNAPIR-DDGEPGEWQDWLVDTSPNQETIMAESEEYDHRRNALTGAMGVLNPRER 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RIFEARRL E P+TLE+L++EF VSRERVRQIE RAF+KVQ +++  V
Sbjct: 240 RIFEARRLAEEPMTLEDLAAEFGVSRERVRQIEVRAFEKVQAAVKSTV 287


>gi|240850016|ref|YP_002971409.1| RNA polymerase sigma-32 factor [Bartonella grahamii as4aup]
 gi|240267139|gb|ACS50727.1| RNA polymerase sigma-32 factor [Bartonella grahamii as4aup]
          Length = 294

 Score =  397 bits (1020), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 191/285 (67%), Positives = 234/285 (82%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M   N+  +  G+ GL+RY+ E+R  PML+ +EEY+LA+RYREH DL AAHRLVTSHLRL
Sbjct: 1   MAHMNLLSVTAGDGGLNRYLEEVRHFPMLDPKEEYMLAQRYREHNDLKAAHRLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVK+F+PERGFRLATY++WWIKA++QEY+LRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKRFEPERGFRLATYAIWWIKASIQEYVLRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLR+LK  LQA+ + +L  EQV  IA +LNVSE EVISMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRKLKSKLQALDNGDLNAEQVKEIATQLNVSEDEVISMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA + + +  +S+ QDWLV + + QEQVLIEK E +NRR+ML  +M  LN RE+
Sbjct: 181 GGDTSLNAPLRTKEGENSELQDWLVDESNDQEQVLIEKSELENRRSMLINAMDNLNEREK 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           RIF+ARRL + P+TLE LS EF +SRERVRQIE RAF+KVQ+SI+
Sbjct: 241 RIFKARRLNDIPLTLEELSGEFNISRERVRQIEMRAFEKVQDSIR 285


>gi|299134310|ref|ZP_07027503.1| RNA polymerase, sigma 32 subunit, RpoH [Afipia sp. 1NLS2]
 gi|298591057|gb|EFI51259.1| RNA polymerase, sigma 32 subunit, RpoH [Afipia sp. 1NLS2]
          Length = 299

 Score =  397 bits (1019), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 192/288 (66%), Positives = 230/288 (79%), Gaps = 1/288 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R     ++NGE GLS Y+ EIRK PMLE QEEY+LAKR+REH D  AAHRLVTSHLRL
Sbjct: 1   MARTATLPVLNGESGLSHYLAEIRKFPMLEPQEEYMLAKRWREHDDRDAAHRLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPISEVVSEGN+GLMQAVK+F+PE+GFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQK+LFFNLR+ K  + A+ + +++ +QV  IAK+L V+E +VI MN RL
Sbjct: 121 WSLVKMGTTANQKKLFFNLRKAKSKISALEEGDMREDQVKLIAKRLGVTERDVIDMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA I   D    +WQDWLV     QE ++ E EE  +RRN LT +M VLNPRER
Sbjct: 181 GGDASLNAPIR-DDGEPGEWQDWLVDTSPNQEAIMAESEEYDHRRNALTGAMGVLNPRER 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RIFEARRL E P+TLE+L++EF VSRERVRQIE RAF+KVQ +++  V
Sbjct: 240 RIFEARRLAEEPMTLEDLAAEFGVSRERVRQIEVRAFEKVQAAVKSTV 287


>gi|27382448|ref|NP_773977.1| RNA polymerase factor sigma-32 [Bradyrhizobium japonicum USDA 110]
 gi|1834373|emb|CAA70697.1| rpoH2 [Bradyrhizobium japonicum]
 gi|27355619|dbj|BAC52602.1| sigma32-like transcription factor [Bradyrhizobium japonicum USDA
           110]
          Length = 299

 Score =  397 bits (1019), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 188/288 (65%), Positives = 233/288 (80%), Gaps = 1/288 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R     ++NGE GLSRY+ EIRK PMLE Q+EY+LAKR+REH D  AAH+LVTSHLRL
Sbjct: 1   MARTAALPVLNGESGLSRYLAEIRKFPMLEPQQEYMLAKRWREHDDRDAAHQLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPISEVVSEGN+GLMQAVK+F+PE+GFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQK+LFFNLR+ K  + A+ + +L+P+QV  IAK+L V++ +VI MN RL
Sbjct: 121 WSLVKMGTTANQKKLFFNLRKAKSKINALDEGDLRPDQVATIAKRLGVTDQDVIDMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA I   D  + +WQDWLV +   QE ++ E EE  +RR+ L  +M VLNPRER
Sbjct: 181 GGDASLNAPIR-DDGEAGEWQDWLVDNTPNQEAMMAEHEEYDHRRDALNGAMGVLNPRER 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RIFEARRL + P+TLE+L++EF VSRERVRQIE RAF+KVQ +++  +
Sbjct: 240 RIFEARRLADEPMTLEDLAAEFGVSRERVRQIEVRAFEKVQSAVKGTI 287


>gi|298292657|ref|YP_003694596.1| RNA polymerase, sigma 32 subunit, RpoH [Starkeya novella DSM 506]
 gi|296929168|gb|ADH89977.1| RNA polymerase, sigma 32 subunit, RpoH [Starkeya novella DSM 506]
          Length = 303

 Score =  396 bits (1018), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 189/296 (63%), Positives = 235/296 (79%), Gaps = 1/296 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R  MS+  + E GLSRY+ EIR+ PMLE QEEY+LAKR+REH D  AAH+LVTSHLRL
Sbjct: 1   MARSAMSL-PSAEGGLSRYLAEIRRFPMLEPQEEYMLAKRWREHEDPEAAHKLVTSHLRL 59

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPISEV+SEGN+GLMQAVK+F+P++GFRLATY+MWWIKA++QEYILRS
Sbjct: 60  VAKIAMGYRGYGLPISEVISEGNVGLMQAVKRFEPDKGFRLATYAMWWIKASIQEYILRS 119

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTA QK+LFFNLR+ K  + A+ D +L+P+QV  IA KL V+E EV+ MN RL
Sbjct: 120 WSLVKMGTTAAQKKLFFNLRKAKSQISALEDGDLRPDQVQQIATKLGVTEQEVVDMNRRL 179

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA +    +   +WQDWL  D D QE  L + EE  NRR+ L  ++SVLN RER
Sbjct: 180 SGDASLNAPLRGDVEGGGEWQDWLADDRDDQETTLADLEETDNRRSALAGALSVLNERER 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPL 296
           RIFEARRL ++P+TLE+L+SEF VSRERVRQIE RAF+KVQ+++  +V    + P+
Sbjct: 240 RIFEARRLSDDPMTLEDLASEFGVSRERVRQIEVRAFEKVQKAVIDRVHAMETAPM 295


>gi|158425877|ref|YP_001527169.1| RNA polymerase factor sigma-32 [Azorhizobium caulinodans ORS 571]
 gi|158332766|dbj|BAF90251.1| sigma-70 factor [Azorhizobium caulinodans ORS 571]
          Length = 300

 Score =  394 bits (1013), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 184/280 (65%), Positives = 228/280 (81%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           I + E GL+RY+ EIR+ PMLE QEEY+LAK +REHGD  AAH+LVTSHLRLV KIAMGY
Sbjct: 9   IPSAEGGLTRYLEEIRRFPMLEPQEEYMLAKSWREHGDRDAAHKLVTSHLRLVAKIAMGY 68

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           RGYGLPISEV+SEGN+GLMQAVK+F+PE+GFRLATY+MWWI+A++QEYILRSWSLVK+GT
Sbjct: 69  RGYGLPISEVISEGNVGLMQAVKRFEPEKGFRLATYAMWWIRASIQEYILRSWSLVKMGT 128

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           TA QK+LFFNLR+ K  + A+ + +L+P+QV  IA KL V+E +V+ MN RL+GD SLNA
Sbjct: 129 TAAQKKLFFNLRKAKSQISALEEGDLRPDQVKQIATKLGVTEQDVVDMNRRLSGDASLNA 188

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +        +WQDWL  DH  QE  L+E EE  NRR  L+ +++VLNPRERRIFEARRL
Sbjct: 189 PLREDGDGGGEWQDWLQDDHQDQETNLVESEELDNRRTALSSALAVLNPRERRIFEARRL 248

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            E+PVTLE L++EF VSRERVRQIE RAF+KVQ+++  +V
Sbjct: 249 SEDPVTLEELAAEFGVSRERVRQIEVRAFEKVQKAVVDKV 288


>gi|304393314|ref|ZP_07375242.1| alternative sigma factor RpoH [Ahrensia sp. R2A130]
 gi|303294321|gb|EFL88693.1| alternative sigma factor RpoH [Ahrensia sp. R2A130]
          Length = 300

 Score =  394 bits (1012), Expect = e-108,   Method: Compositional matrix adjust.
 Identities = 192/292 (65%), Positives = 233/292 (79%), Gaps = 2/292 (0%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           SI  +G  GL RY+ EIRK PML+  EEY+L KRY EH D  AAH++VTSHLRLV KIAM
Sbjct: 7   SISASGN-GLQRYMEEIRKFPMLKPDEEYMLGKRYSEHDDTEAAHKMVTSHLRLVAKIAM 65

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           GYRGYGLP+SEV+SEGN+GLMQAVKKFDPE+GFRLATY+MWWIKA++QEY+LRSWSLVK+
Sbjct: 66  GYRGYGLPVSEVISEGNVGLMQAVKKFDPEKGFRLATYAMWWIKASIQEYVLRSWSLVKM 125

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
           GTTANQKRLFFNLR+LKG L+A+ +  LK E V  IA  L VS  EV SMN RL+GD SL
Sbjct: 126 GTTANQKRLFFNLRKLKGKLKALEEGELKQENVEKIASTLGVSHDEVRSMNQRLSGDASL 185

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           NA I +++  S QWQDWLV D + QEQ+LI+++E   RR+ML  +M VLN RE+RIF AR
Sbjct: 186 NAPIKAAEGESGQWQDWLVDDSESQEQMLIKQDELDVRRDMLAEAMDVLNDREKRIFMAR 245

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES-IQKQVELSSSPPLL 297
           RL+E+P+TLE LS EF++SRERVRQIE RAF+KVQ++ +    EL+   P L
Sbjct: 246 RLEEDPLTLEVLSGEFDISRERVRQIEVRAFEKVQKAMVTANKELAKPAPQL 297


>gi|154245929|ref|YP_001416887.1| RNA polymerase factor sigma-32 [Xanthobacter autotrophicus Py2]
 gi|154160014|gb|ABS67230.1| RNA polymerase, sigma 32 subunit, RpoH [Xanthobacter autotrophicus
           Py2]
          Length = 300

 Score =  394 bits (1011), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 192/291 (65%), Positives = 234/291 (80%), Gaps = 2/291 (0%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           K+MSI  + E GLSRY+ EIR+ PMLE QEEY+LAK +REHGD  AAHRLVTSHLRLV K
Sbjct: 5   KSMSI-PSAEGGLSRYLEEIRRFPMLEPQEEYMLAKSWREHGDRDAAHRLVTSHLRLVAK 63

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IAMGYRGYGLPISEV+SEGN+GLMQAVK+F+PE+GFRLATY+MWWI+A++QEYILRSWSL
Sbjct: 64  IAMGYRGYGLPISEVISEGNVGLMQAVKRFEPEKGFRLATYAMWWIRASIQEYILRSWSL 123

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VK+GTTA QK+LFFNLR+ K  + A+ D +LKPE V  IA KL V+E +V+ MN RL+GD
Sbjct: 124 VKMGTTAAQKKLFFNLRKAKSQISALEDGDLKPEHVKQIATKLGVTEQDVVDMNRRLSGD 183

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SLN+ I   D    +WQDWLV +   QE+ L E EE  NRR  L+ ++SVLN RERRIF
Sbjct: 184 ASLNSPIR-EDSEGGEWQDWLVDERLDQEEQLAESEELDNRRAALSGALSVLNDRERRIF 242

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSP 294
           EARRL E+P+TLE+L+SEF VSRERVRQIE RAF+KVQ+++  +V    +P
Sbjct: 243 EARRLSEDPMTLEDLASEFGVSRERVRQIEVRAFEKVQKAVMDKVRQVEAP 293


>gi|170744871|ref|YP_001773526.1| RNA polymerase factor sigma-32 [Methylobacterium sp. 4-46]
 gi|168199145|gb|ACA21092.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium sp. 4-46]
          Length = 296

 Score =  393 bits (1010), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 188/280 (67%), Positives = 229/280 (81%), Gaps = 2/280 (0%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           ++  E GLSRY+ EIR+ PMLE  EEY+LAK +REHGD  AAH+LVTSHLRLV KIAMGY
Sbjct: 7   VLANEGGLSRYLDEIRRFPMLEPTEEYMLAKSWREHGDREAAHKLVTSHLRLVAKIAMGY 66

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           RGYGLPI EVVSEGN+GLMQAVK+FDP++GFRLATY+MWWIKAA+QEYILRSWSLVK+GT
Sbjct: 67  RGYGLPIGEVVSEGNVGLMQAVKRFDPDKGFRLATYAMWWIKAAIQEYILRSWSLVKMGT 126

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           TANQK+LFFNLR+ KG + A+ + +L+PEQV  IA +L V E +VI MN RL+GD SLNA
Sbjct: 127 TANQKKLFFNLRKAKGRISALDEGDLRPEQVKQIATRLGVPEQDVIEMNRRLSGDASLNA 186

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +   ++   +WQDWLV D   QE VL  +EE +NR   L  ++SVLNPRERRIFEARRL
Sbjct: 187 PLR--EEGEGEWQDWLVDDSPSQEAVLAREEEGQNRLAALRDALSVLNPRERRIFEARRL 244

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            E P+TLE+LSSEF VSRERVRQIE RAF+KVQ+++++ +
Sbjct: 245 AEEPITLEDLSSEFGVSRERVRQIEVRAFEKVQDAVKRNL 284


>gi|39933444|ref|NP_945720.1| RNA polymerase factor sigma-32 [Rhodopseudomonas palustris CGA009]
 gi|192288802|ref|YP_001989407.1| RNA polymerase factor sigma-32 [Rhodopseudomonas palustris TIE-1]
 gi|39647290|emb|CAE25811.1| RNA polymerase sigma 32 subunit, RpoH, stress response sigma factor
           [Rhodopseudomonas palustris CGA009]
 gi|192282551|gb|ACE98931.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodopseudomonas palustris
           TIE-1]
          Length = 299

 Score =  393 bits (1010), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 189/288 (65%), Positives = 228/288 (79%), Gaps = 1/288 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R     I+NGE GL+RY+ EIRK PMLE Q+EY+LAKR+REHGD  AAH+LVTSHLRL
Sbjct: 1   MARAATLPILNGESGLARYLAEIRKFPMLEPQQEYMLAKRWREHGDRDAAHQLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPISEVVSEGN+GLMQAVK+F+PE+GFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQK+LFFNLR+ K  + A+ + +L P+QV  IA +L V+E +V+ MN RL
Sbjct: 121 WSLVKMGTTANQKKLFFNLRKAKSKISALDEGDLHPDQVKLIATRLGVTEQDVVDMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA I   D    +WQDWLV     QE V+ E EE   RR  L  ++ VLNPRER
Sbjct: 181 GGDASLNAPIR-DDGEPGEWQDWLVDQSPSQEAVMAEHEELDQRRAALNGAIQVLNPRER 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RIFEARRL + P+TLE+L+SEF VSRERVRQIE RAF+KVQ +++  +
Sbjct: 240 RIFEARRLADEPMTLEDLASEFGVSRERVRQIEVRAFEKVQSAVKGTI 287


>gi|220927320|ref|YP_002502622.1| RNA polymerase factor sigma-32 [Methylobacterium nodulans ORS 2060]
 gi|219951927|gb|ACL62319.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium nodulans
           ORS 2060]
          Length = 296

 Score =  392 bits (1008), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 187/280 (66%), Positives = 229/280 (81%), Gaps = 2/280 (0%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           ++  E GLSRY+ EIR+ PMLE  EEY+LAK +REHGD  AAH+LVTSHLRLV KIAMGY
Sbjct: 7   VLANEGGLSRYLDEIRRFPMLEPTEEYMLAKSWREHGDREAAHKLVTSHLRLVAKIAMGY 66

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           RGYGLPI EVVSEGN+GLMQAVK+FDP++GFRLATY+MWWIKAA+QEYILRSWSLVK+GT
Sbjct: 67  RGYGLPIGEVVSEGNVGLMQAVKRFDPDKGFRLATYAMWWIKAAIQEYILRSWSLVKMGT 126

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           TANQK+LFFNLR+ KG + A+ + +L+PEQV  IA +L V E +VI MN RL+GD SLNA
Sbjct: 127 TANQKKLFFNLRKAKGRISALDEGDLRPEQVKQIATRLGVPEQDVIDMNRRLSGDASLNA 186

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +   ++   +WQDWLV D   QE VL  +EE +NR   L  ++SVLNPRERRIFEARRL
Sbjct: 187 PLR--EEGEGEWQDWLVDDSPSQEAVLAREEEGQNRLAALRDALSVLNPRERRIFEARRL 244

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            E P+TLE+LS+EF VSRERVRQIE RAF+KVQ+++++ +
Sbjct: 245 AEEPITLEDLSTEFGVSRERVRQIEVRAFEKVQDAVKRNL 284


>gi|75676615|ref|YP_319036.1| RNA polymerase factor sigma-32 [Nitrobacter winogradskyi Nb-255]
 gi|74421485|gb|ABA05684.1| RNA polymerase, sigma 32 subunit, RpoH [Nitrobacter winogradskyi
           Nb-255]
          Length = 299

 Score =  392 bits (1008), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 187/288 (64%), Positives = 228/288 (79%), Gaps = 1/288 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R     ++NGE GLSRY+ EIRK PMLE  EEY+ AKR REH D  AAH LVTSHLRL
Sbjct: 1   MARTATLPVLNGENGLSRYLSEIRKFPMLEPHEEYMFAKRLREHDDRDAAHHLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPISEVVSEGN+GLMQAVK+F+PE+GFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQK+LFFNLR+ K  + A+ + +++P+QV  IAK+L V+E +V+ MN RL
Sbjct: 121 WSLVKMGTTANQKKLFFNLRKAKSKISALDEGDMRPDQVKLIAKRLGVTEQDVVDMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA I   D  + +WQDWLV     QE ++ E EE  +RR  LT +M VLNPRER
Sbjct: 181 GGDASLNAPIR-DDGEAGEWQDWLVDQSPNQEAIMAEHEEFDHRRRALTGAMGVLNPRER 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RIFEARRL + P+TLE+L++EF VSRERVRQIE RAF+KVQ +++  +
Sbjct: 240 RIFEARRLADEPMTLEDLAAEFNVSRERVRQIEVRAFEKVQSAVKTTI 287


>gi|92118359|ref|YP_578088.1| RNA polymerase factor sigma-32 [Nitrobacter hamburgensis X14]
 gi|91801253|gb|ABE63628.1| RNA polymerase, sigma 32 subunit, RpoH [Nitrobacter hamburgensis
           X14]
          Length = 299

 Score =  392 bits (1008), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 187/288 (64%), Positives = 228/288 (79%), Gaps = 1/288 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R     I+NGE GLSRY+ EIRK PMLE  +EY+ AKR+REH D  AAH LVTSHLRL
Sbjct: 1   MARTATVPILNGESGLSRYLAEIRKFPMLEPHQEYMFAKRWREHDDREAAHHLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPISEVVSEGN+GLMQAVK+F+PE+GFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQK+LFFNLR+ K  + A+ + ++ P+QV  IAK+L V+E +V+ MN RL
Sbjct: 121 WSLVKMGTTANQKKLFFNLRKAKSKISALEEGDMHPDQVKLIAKRLGVTEQDVVDMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA I   D  + +WQDWLV     QE ++ E EE  +RR  LT +M VLNPRER
Sbjct: 181 GGDASLNAPIR-DDGEAGEWQDWLVDHSPTQEAIMAEHEELNHRRQALTGAMGVLNPRER 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RIFEARRL + P+TLE+L++EF VSRERVRQIE RAF+KVQ +++  +
Sbjct: 240 RIFEARRLADEPMTLEDLAAEFNVSRERVRQIEVRAFEKVQSAVKTTI 287


>gi|319898405|ref|YP_004158498.1| RNA polymerase sigma-32 factor [Bartonella clarridgeiae 73]
 gi|319402369|emb|CBI75908.1| RNA polymerase sigma-32 factor [Bartonella clarridgeiae 73]
          Length = 305

 Score =  392 bits (1006), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 187/285 (65%), Positives = 231/285 (81%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M   N+   +  + GLSRY+ E+R+ P+LE QEEY+LAKRY EH D  AAH+LVTSHLRL
Sbjct: 1   MAHINLPSFIANDSGLSRYLEEVRRFPVLEPQEEYMLAKRYHEHNDPKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGNIGLMQAVK+F+PERGFRLATY+MWWIKA++QEY+LRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVISEGNIGLMQAVKRFEPERGFRLATYAMWWIKASIQEYVLRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVKIGTTANQKRLFFNLR+LK  LQ     +L  EQV  IA +L V+E EV+SMN RL
Sbjct: 121 WSLVKIGTTANQKRLFFNLRKLKNKLQMFDSGDLNAEQVKEIATRLKVTEDEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA + ++   S +WQDWLV D + QEQ+LIE++E +NR +ML ++M  LN RE+
Sbjct: 181 SGDASLNAPLLTNKGESYEWQDWLVDDSNSQEQILIEQDELENRHSMLIQAMDNLNEREK 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           RIF+ARRL++ P+TLE LS+EF +SRERVRQIE RAF+K+Q SI+
Sbjct: 241 RIFKARRLRDEPMTLEELSNEFNISRERVRQIEMRAFEKIQNSIK 285


>gi|146338455|ref|YP_001203503.1| RNA polymerase factor sigma-32 [Bradyrhizobium sp. ORS278]
 gi|146191261|emb|CAL75266.1| sigma H (sigma 32) factor of RNA polymerase; transcription of heat
           shock and stress proteins [Bradyrhizobium sp. ORS278]
          Length = 299

 Score =  390 bits (1003), Expect = e-107,   Method: Compositional matrix adjust.
 Identities = 186/288 (64%), Positives = 230/288 (79%), Gaps = 1/288 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R     ++NGE GL+RY+ EIRK PMLE QEEY+LAKR+REH D  AAH+LVTSHLRL
Sbjct: 1   MARTATLPVLNGESGLARYLSEIRKFPMLEPQEEYMLAKRWREHDDSDAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPISEVVSEGN+GLMQAVK+F+PE+GFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQK+LFFNLR+ K  + A+ + +L+P+QV  IAK+L V++ +VI MN RL
Sbjct: 121 WSLVKMGTTANQKKLFFNLRKAKSKISALDEGDLRPDQVKLIAKRLGVTDQDVIDMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA I   D  + +WQDWLV     QE ++ E EE  +RR  L  ++ VLN RER
Sbjct: 181 GGDASLNAPIR-DDGEAGEWQDWLVDTSPNQEAIMAEHEEYDHRRQALNGAIGVLNARER 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RIFEARRL + P+TLE+L++EF VSRERVRQIE RAF+KVQ +++  +
Sbjct: 240 RIFEARRLADEPMTLEDLAAEFGVSRERVRQIEVRAFEKVQSAVKGAI 287


>gi|90422128|ref|YP_530498.1| RNA polymerase factor sigma-32 [Rhodopseudomonas palustris BisB18]
 gi|90104142|gb|ABD86179.1| sigma 32 (RpoH) [Rhodopseudomonas palustris BisB18]
          Length = 299

 Score =  390 bits (1003), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 186/288 (64%), Positives = 228/288 (79%), Gaps = 1/288 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R     ++NGE GLSRY+ EIRK PMLE Q+EY+ AKR+REH D  AAH LVTSHLRL
Sbjct: 1   MARAATLPVLNGESGLSRYLAEIRKFPMLEPQQEYMFAKRWREHDDRDAAHHLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPISEVVSEGN+GLMQAVK+F+PE+GFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQK+LFFNLR+ K  + A+ + ++ P+QV  IAK+L V+E +V+ MN RL
Sbjct: 121 WSLVKMGTTANQKKLFFNLRKAKSKISALDEGDMHPDQVKLIAKRLGVTEQDVVDMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA I   D    +WQDWLV     QE ++ E EE  +RR  LT ++ VLNPRER
Sbjct: 181 GGDASLNAPIR-DDGEPGEWQDWLVDHSPNQEAIMAEHEELDHRRAALTGAIGVLNPRER 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RIFEARRL + P+TLE+L++EF VSRERVRQIE RAF+KVQ +++  +
Sbjct: 240 RIFEARRLADEPMTLEDLAAEFGVSRERVRQIEVRAFEKVQSAVKGTI 287


>gi|319408110|emb|CBI81763.1| RNA polymerase sigma-32 factor [Bartonella schoenbuchensis R1]
          Length = 308

 Score =  390 bits (1002), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 185/288 (64%), Positives = 235/288 (81%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M   N+  I+ G+ GL+RY+ EIR+ PML+ +EEY+LAKRYREH D  AAH+LVTSHLRL
Sbjct: 1   MAHVNLPSIIAGDGGLNRYLEEIRRFPMLKPKEEYMLAKRYREHDDPKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIA+GYRGYGLPI EV+SEGNIGLMQAVK+F+PERGFRLATY+MWWIKA++QEY+LRS
Sbjct: 61  VAKIAIGYRGYGLPIGEVISEGNIGLMQAVKRFEPERGFRLATYAMWWIKASIQEYVLRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLR+LK  LQA+ + +L  EQV  IA +LNV+E EV+SMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRKLKNKLQALDNGDLNAEQVKEIATRLNVTEDEVVSMNHRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA + + +   ++WQDWLV D + QEQ+LIE++E +NRR+ML  ++  LN RE+
Sbjct: 181 SGDTSLNAPLRTKEGEKTEWQDWLVDDSNSQEQILIEQDELENRRSMLIHAIDNLNEREK 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            IF+ARRL +  +TLE LS+ F +SRERVRQIE RAF+KV+ SI+  +
Sbjct: 241 HIFKARRLSDESLTLEELSNTFNISRERVRQIEMRAFEKVRNSIKAAI 288


>gi|115522843|ref|YP_779754.1| RNA polymerase factor sigma-32 [Rhodopseudomonas palustris BisA53]
 gi|115516790|gb|ABJ04774.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodopseudomonas palustris
           BisA53]
          Length = 299

 Score =  389 bits (1000), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 186/288 (64%), Positives = 228/288 (79%), Gaps = 1/288 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R     ++NGE GLSRY+ EIRK PMLE Q+EY+LAKR+REH D  AAH LVTSHLRL
Sbjct: 1   MARAATLPVLNGESGLSRYLAEIRKFPMLEPQQEYMLAKRWREHDDRDAAHHLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPISEVVSEGN+GLMQAVK+F+PE+GFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQK+LFFNLR+ K  + A+ + ++ P+QV  IA +L V+E +V+ MN RL
Sbjct: 121 WSLVKMGTTANQKKLFFNLRKAKSKISALDEGDMHPDQVKLIATRLGVTEQDVVDMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA I   D    +WQDWLV     QE V+ E EE  +RR  L  ++ VLNPRER
Sbjct: 181 GGDASLNAPIR-DDGEPGEWQDWLVDHSPSQEAVMAEHEELDHRRAALNGAIGVLNPRER 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RIFEARRL ++P+TLE+L++EF VSRERVRQIE RAF+KVQ +++  +
Sbjct: 240 RIFEARRLADDPMTLEDLAAEFGVSRERVRQIEVRAFEKVQAAVKGTI 287


>gi|316931591|ref|YP_004106573.1| RNA polymerase sigma 32 subunit RpoH [Rhodopseudomonas palustris
           DX-1]
 gi|315599305|gb|ADU41840.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodopseudomonas palustris
           DX-1]
          Length = 299

 Score =  389 bits (998), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 186/288 (64%), Positives = 227/288 (78%), Gaps = 1/288 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R     ++NGE GL+RY+ EIRK PMLE ++EY+LAKR+REHGD  AAH+LVTSHLRL
Sbjct: 1   MARAATLPVLNGESGLARYLAEIRKFPMLEPEQEYMLAKRWREHGDRDAAHQLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPISEVVSEGN+GLMQAVK+F+PE+GFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQK+LFFNLR+ K  + A+ + +L P+ V  IA +L V+E +V+ MN RL
Sbjct: 121 WSLVKMGTTANQKKLFFNLRKAKSKISALDEGDLHPDHVKLIASRLGVTEQDVVDMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA I   D    +WQDWLV     QE VL E EE   RR  L  ++ VLNPRER
Sbjct: 181 GGDASLNAPIR-DDGEPGEWQDWLVDQSPSQEAVLAEHEELDQRRAALNGAIQVLNPRER 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RIFEARRL + P+TLE+L++EF VSRERVRQIE RAF+KVQ +++  +
Sbjct: 240 RIFEARRLADEPMTLEDLAAEFGVSRERVRQIEVRAFEKVQSAVKGTI 287


>gi|170752008|ref|YP_001758268.1| RNA polymerase factor sigma-32 [Methylobacterium radiotolerans JCM
           2831]
 gi|170658530|gb|ACB27585.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium
           radiotolerans JCM 2831]
          Length = 297

 Score =  387 bits (995), Expect = e-106,   Method: Compositional matrix adjust.
 Identities = 186/290 (64%), Positives = 230/290 (79%), Gaps = 3/290 (1%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
            + ++ N E GLSRY+ EIRK PMLE  EE+ LAK +R+ GD  AAHRLVTSHLRLV KI
Sbjct: 4   TLPVLAN-EGGLSRYLDEIRKFPMLEPSEEFTLAKAWRDAGDREAAHRLVTSHLRLVAKI 62

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           AMGYRGYGLPI EVVSEGN+GLMQAVK+FDP++GFRLATY+MWWIKAA+QEYILRSWSLV
Sbjct: 63  AMGYRGYGLPIGEVVSEGNVGLMQAVKRFDPDKGFRLATYAMWWIKAAIQEYILRSWSLV 122

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           K+GTTANQK+LFFNLR+ KG + A+ + +LKP+QV  IA +L V E +VI MN RL+GD 
Sbjct: 123 KMGTTANQKKLFFNLRKAKGKISALDEGDLKPDQVKQIATRLGVPEQDVIDMNRRLSGDT 182

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SLNA +   ++   +WQDWLV +   QE VL  ++E +NR + L  ++ VLNPRERRIFE
Sbjct: 183 SLNAPLR--EEGEGEWQDWLVDNSPSQETVLAREQEGQNRLSALKDALGVLNPRERRIFE 240

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSP 294
           ARRL E+P+TLE+LS EF VSRERVRQIE RAF+KVQE++++ +     P
Sbjct: 241 ARRLAEDPITLEDLSGEFGVSRERVRQIEVRAFEKVQEAVKRNIATRELP 290


>gi|86747581|ref|YP_484077.1| RNA polymerase factor sigma-32 [Rhodopseudomonas palustris HaA2]
 gi|86570609|gb|ABD05166.1| sigma 32 (RpoH) [Rhodopseudomonas palustris HaA2]
          Length = 299

 Score =  387 bits (994), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 185/288 (64%), Positives = 227/288 (78%), Gaps = 1/288 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R     ++NGE GL+RY+ EIRK PMLE Q+EY+ AKR+REH D  AAH LVTSHLRL
Sbjct: 1   MARAATLPVLNGESGLARYLAEIRKFPMLEPQQEYMFAKRWREHDDRDAAHHLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPISEVVSEGN+GLMQAVK+F+P++GFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPDKGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQK+LFFNLR+ K  + A+ + ++ P+QV  IAK+L V+E +VI MN RL
Sbjct: 121 WSLVKMGTTANQKKLFFNLRKAKSKISALDEGDMHPDQVKLIAKRLGVTEQDVIDMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA I   D    +WQDWLV     QE V+ E EE  +RR  L  ++ VLNPRER
Sbjct: 181 GGDASLNAPIR-DDGEPGEWQDWLVDQSPNQEAVMAEHEELDHRRAALNGAIGVLNPRER 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RIFEARRL + P+TLE+L++EF VSRERVRQIE RAF+KVQ +++  +
Sbjct: 240 RIFEARRLADEPMTLEDLAAEFGVSRERVRQIEVRAFEKVQSAVKGTI 287


>gi|300023529|ref|YP_003756140.1| RNA polymerase, sigma 32 subunit, RpoH [Hyphomicrobium
           denitrificans ATCC 51888]
 gi|299525350|gb|ADJ23819.1| RNA polymerase, sigma 32 subunit, RpoH [Hyphomicrobium
           denitrificans ATCC 51888]
          Length = 296

 Score =  387 bits (993), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 183/291 (62%), Positives = 227/291 (78%), Gaps = 1/291 (0%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           K +  +  G +GLSRY+ EIRK PML   EEY+LAKR+++H D  AA +LVTSHLRLV +
Sbjct: 5   KGLPTLAGGSLGLSRYLEEIRKFPMLAPNEEYMLAKRWQQHEDSDAAEKLVTSHLRLVAR 64

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IAMGYRGYGLPI EV+SEGN+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSWSL
Sbjct: 65  IAMGYRGYGLPIGEVISEGNVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSL 124

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VK+GTTA QK+LFFNLRR K  LQA+ D +L+PE V AIA KL V E +V+SMN RL GD
Sbjct: 125 VKMGTTAAQKKLFFNLRRAKSQLQALDDGDLRPEHVKAIATKLGVPEEDVVSMNRRLGGD 184

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SLNA I  ++  S +WQDWLV D   QE  L+E EE + R++ L+ ++SVLN RERR+F
Sbjct: 185 ASLNAPIR-AESESGEWQDWLVDDTPTQEDRLVEDEELRRRKSYLSSALSVLNDRERRVF 243

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSP 294
           E RRL E P TLE LS+EF VSRER+RQIE RAF+KVQ+++      + +P
Sbjct: 244 EQRRLAEEPATLEELSAEFGVSRERIRQIEVRAFEKVQKAVTSTARRAEAP 294


>gi|121602451|ref|YP_988610.1| RNA polymerase factor sigma-32 [Bartonella bacilliformis KC583]
 gi|120614628|gb|ABM45229.1| RNA polymerase sigma-32 factor [Bartonella bacilliformis KC583]
          Length = 303

 Score =  387 bits (993), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 188/288 (65%), Positives = 232/288 (80%), Gaps = 6/288 (2%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           I   + GLSRY+ EIR+ P+LE +EEY+L KRY EH DL AAH+LVTSHLRLV KIA+GY
Sbjct: 9   IAANDGGLSRYLEEIRRFPILEPKEEYMLVKRYNEHNDLKAAHKLVTSHLRLVAKIAIGY 68

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           RGYGLP+ EV+SEGNIGLMQAVK+F+PERGFRLATY+MWWIKA++QEY+LRSWSLVKIGT
Sbjct: 69  RGYGLPMGEVISEGNIGLMQAVKRFEPERGFRLATYAMWWIKASIQEYVLRSWSLVKIGT 128

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           T NQKRLFFNLR+LK  LQA+ +  L  EQV  IA +LNV+E EV+SMN RL+GD SLNA
Sbjct: 129 TTNQKRLFFNLRKLKSKLQALDNGELNTEQVKEIATRLNVTEDEVVSMNHRLSGDTSLNA 188

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            + +++   S+WQD LV +   QEQVLIEK+E +NRR++L  +M+ LN RE+RIFEARRL
Sbjct: 189 PLRTNEDEHSEWQDCLVDEASSQEQVLIEKDELENRRSLLIHAMANLNEREKRIFEARRL 248

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI------QKQVEL 290
            +  +TLE LSSEF +SRERVRQIE RAF+KVQ+ +      QKQ ++
Sbjct: 249 SDEVLTLEELSSEFNISRERVRQIEMRAFEKVQDFVRASALSQKQAQI 296


>gi|148257972|ref|YP_001242557.1| RNA polymerase factor sigma-32 [Bradyrhizobium sp. BTAi1]
 gi|146410145|gb|ABQ38651.1| RNA polymerase, sigma 32 subunit, RpoH [Bradyrhizobium sp. BTAi1]
          Length = 299

 Score =  386 bits (992), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 184/288 (63%), Positives = 228/288 (79%), Gaps = 1/288 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R     ++NGE GL+RY+ EIRK PMLE QEEY+LAKR+REH D  AA +LVTSHLRL
Sbjct: 1   MARTATLPVLNGESGLARYLAEIRKFPMLEPQEEYMLAKRWREHDDSDAAQKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPISEVVSEGN+GLMQAVK+F+PE+GFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQK+LFFNLR+ K  + A+ + +L P+QV  IAK+L V++ +V+ MN RL
Sbjct: 121 WSLVKMGTTANQKKLFFNLRKAKSRISALDEGDLHPDQVKLIAKRLGVTDQDVVDMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA I   D  + +WQDWLV     QE ++ E EE  +RR  L  ++ VLN RER
Sbjct: 181 GGDASLNAPIR-DDGEAGEWQDWLVDTSPNQEAIMAEHEEYDHRRQALNGAIGVLNARER 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RIFEARRL + P+TLE+L++EF VSRERVRQIE RAF+KVQ +++  +
Sbjct: 240 RIFEARRLADEPMTLEDLAAEFGVSRERVRQIEVRAFEKVQSAVKGAI 287


>gi|91974840|ref|YP_567499.1| RNA polymerase factor sigma-32 [Rhodopseudomonas palustris BisB5]
 gi|91681296|gb|ABE37598.1| RNA polymerase sigma factor RpoH [Rhodopseudomonas palustris BisB5]
          Length = 299

 Score =  386 bits (991), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 184/288 (63%), Positives = 226/288 (78%), Gaps = 1/288 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R     ++NGE GL+RY+ EIRK PMLE Q+EY+ AKR+REH D  AAH LVTSHLRL
Sbjct: 1   MARAATLPVLNGESGLARYLAEIRKFPMLEPQQEYMFAKRWREHDDRDAAHHLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPISEVVSEGN+GLMQAVK+F+P++GFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPDKGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQK+LFFNLR+ K  + A+ + ++ P+QV  IA +L V+E +VI MN RL
Sbjct: 121 WSLVKMGTTANQKKLFFNLRKAKSKISALDEGDMHPDQVKLIATRLGVTEQDVIDMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA I   D    +WQDWLV     QE V+ E EE  +RR  L  ++ VLNPRER
Sbjct: 181 GGDASLNAPIR-DDGEPGEWQDWLVDQSPSQEAVMAEHEELDHRRAALNGAIGVLNPRER 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RIFEARRL + P+TLE+L++EF VSRERVRQIE RAF+KVQ +++  +
Sbjct: 240 RIFEARRLADEPMTLEDLAAEFGVSRERVRQIEVRAFEKVQSAVKGTI 287


>gi|319405171|emb|CBI78776.1| RNA polymerase sigma-32 factor [Bartonella sp. AR 15-3]
          Length = 305

 Score =  385 bits (989), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 185/285 (64%), Positives = 232/285 (81%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M   N+   +  +  L+RY+ EIR+ P+LE QEEY+LAKRY EH D  AAH+LVTSHLRL
Sbjct: 1   MAHINLPSFIANDNSLNRYLEEIRRFPILEPQEEYMLAKRYHEHNDPKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIA+GYRGYGLPI EV+SEGNIGLMQAVK+F+PERGFRLATY+MWWIKA++QEY+LRS
Sbjct: 61  VAKIAIGYRGYGLPIGEVISEGNIGLMQAVKRFEPERGFRLATYAMWWIKASIQEYVLRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVKIGTTANQKRLFFNLR+LK  LQ +   +L  +QV  IA +L V+E EV+SMN RL
Sbjct: 121 WSLVKIGTTANQKRLFFNLRKLKNKLQMLDSGDLNAQQVKEIATRLKVTEDEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA + ++   S +WQDWLV D + QEQ+LIE++E +NR ++L ++M  LN RE+
Sbjct: 181 SGDASLNAPLLTNKGESYEWQDWLVDDSNNQEQILIEQDELENRYSLLIQAMDNLNEREK 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           RIF+ARRL++ P+TLE LS+EF +SRERVRQIEARAF+KVQ SI+
Sbjct: 241 RIFKARRLRDEPLTLEELSNEFNISRERVRQIEARAFEKVQNSIK 285


>gi|188580210|ref|YP_001923655.1| RNA polymerase factor sigma-32 [Methylobacterium populi BJ001]
 gi|179343708|gb|ACB79120.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium populi
           BJ001]
          Length = 297

 Score =  385 bits (988), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 184/286 (64%), Positives = 227/286 (79%), Gaps = 2/286 (0%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           ++  E GLSRY+ EIRK PMLE  EE+ LAK +R+ GD  AAHRLVTSHLRLV KIAMGY
Sbjct: 7   VLANEGGLSRYLDEIRKFPMLEPAEEFTLAKSWRDEGDREAAHRLVTSHLRLVAKIAMGY 66

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           RGYGLPISEVVSEGN+GLMQAVK+FDP++GFRLATY+MWWIKAA+QEYILRSWSLVK+GT
Sbjct: 67  RGYGLPISEVVSEGNVGLMQAVKRFDPDKGFRLATYAMWWIKAAIQEYILRSWSLVKMGT 126

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           TANQK+LFFNLR+ KG + A+ + +L+P+QV  IA  L V   +VI MN RL+GD SLNA
Sbjct: 127 TANQKKLFFNLRKAKGRISALDEGDLRPDQVQQIATSLGVPTQDVIDMNRRLSGDTSLNA 186

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +   ++   +WQDWLV +   QE VL  +EE +NR + L  ++ VLNPRERRIFEARRL
Sbjct: 187 PLR--EEGEGEWQDWLVDNSPSQETVLAREEEGRNRLSALRDALGVLNPRERRIFEARRL 244

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSP 294
            ++P+TLE+LS EF VSRERVRQIE RAF+KVQE++++ +     P
Sbjct: 245 ADDPITLEDLSGEFGVSRERVRQIEVRAFEKVQEAVKRNLATRELP 290


>gi|254700317|ref|ZP_05162145.1| RNA polymerase factor sigma-32 [Brucella suis bv. 5 str. 513]
 gi|261750811|ref|ZP_05994520.1| RNA polymerase factor sigma-32 [Brucella suis bv. 5 str. 513]
 gi|261740564|gb|EEY28490.1| RNA polymerase factor sigma-32 [Brucella suis bv. 5 str. 513]
          Length = 262

 Score =  384 bits (987), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 180/262 (68%), Positives = 219/262 (83%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M +  +  I +G+ GL+RY+ EIR+ PMLE QEEY+LAKRY EH D  AAH+LVTSHLRL
Sbjct: 1   MAQMKLPSITSGDGGLTRYLEEIRRFPMLEPQEEYMLAKRYHEHADPKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVK+F+PERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLR++K  +QA+ D +L P+QV  IA KLNVSE EV+SMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRKMKSKIQALDDGDLNPDQVKQIATKLNVSEDEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA + +S+  S +WQDWLV D + QEQVLIE++E ++RR+ML ++M  LN RER
Sbjct: 181 SGDASLNAPLRASEGESGEWQDWLVDDSNSQEQVLIEQDELESRRSMLEQAMETLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEF 262
           RIFEARRL E P+TLE+LS EF
Sbjct: 241 RIFEARRLAEEPMTLEDLSGEF 262


>gi|182677344|ref|YP_001831490.1| RNA polymerase, sigma 32 subunit, RpoH [Beijerinckia indica subsp.
           indica ATCC 9039]
 gi|182633227|gb|ACB94001.1| RNA polymerase, sigma 32 subunit, RpoH [Beijerinckia indica subsp.
           indica ATCC 9039]
          Length = 299

 Score =  384 bits (987), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 180/280 (64%), Positives = 229/280 (81%), Gaps = 2/280 (0%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +++GE GL+RY++EIR+ PMLE QEEY+LAKR+REH D  AA RLVTSHLRLV KIAMGY
Sbjct: 7   MISGESGLTRYLNEIRRFPMLEPQEEYMLAKRWREHEDPDAAQRLVTSHLRLVAKIAMGY 66

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           RGYGLPI EVVSEGN+GLMQAVK+F+P++GFRLATY+MWWI+A++QEYILRSWSLVK+GT
Sbjct: 67  RGYGLPIGEVVSEGNVGLMQAVKRFEPDKGFRLATYAMWWIRASIQEYILRSWSLVKMGT 126

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           TA+QK+LFFNLR+ K  + A+ + +L+P+QV  IA +L V+  EVI MN R++GD SLNA
Sbjct: 127 TASQKKLFFNLRKAKSQISALDEGDLRPDQVALIATRLGVTGQEVIDMNRRMSGDASLNA 186

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +   ++   +WQDWLV D   QE VL ++EE  NR   L +++ VLNPRERRIFEARRL
Sbjct: 187 PLR--EEGEGEWQDWLVDDQANQEHVLADQEESANRLGALRQALDVLNPRERRIFEARRL 244

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            ++PVTLE LS EF++SRERVRQIE RAF+KVQ +++  V
Sbjct: 245 ADDPVTLEALSDEFDISRERVRQIEVRAFEKVQAAVKAGV 284


>gi|218528993|ref|YP_002419809.1| RNA polymerase factor sigma-32 [Methylobacterium chloromethanicum
           CM4]
 gi|240137510|ref|YP_002961981.1| RNA polymerase sigma-32 (sigma H) factor [Methylobacterium
           extorquens AM1]
 gi|254559688|ref|YP_003066783.1| RNA polymerase sigma-32 [Methylobacterium extorquens DM4]
 gi|218521296|gb|ACK81881.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium
           chloromethanicum CM4]
 gi|240007478|gb|ACS38704.1| RNA polymerase sigma-32 (sigma H) factor [Methylobacterium
           extorquens AM1]
 gi|254266966|emb|CAX22766.1| RNA polymerase sigma-32 (sigma H) factor [Methylobacterium
           extorquens DM4]
          Length = 297

 Score =  384 bits (986), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 184/286 (64%), Positives = 227/286 (79%), Gaps = 2/286 (0%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           ++  E GLSRY+ EIRK PMLE  EE+ LAK +R+ GD  AAHRLVTSHLRLV KIAMGY
Sbjct: 7   VLANEGGLSRYLDEIRKFPMLEPAEEFTLAKSWRDDGDREAAHRLVTSHLRLVAKIAMGY 66

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           RGYGLPISEVVSEGN+GLMQAVK+FDP++GFRLATY+MWWIKAA+QEYILRSWSLVK+GT
Sbjct: 67  RGYGLPISEVVSEGNVGLMQAVKRFDPDKGFRLATYAMWWIKAAIQEYILRSWSLVKMGT 126

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           TANQK+LFFNLR+ KG + A+ + +L+P+QV  IA  L V   +VI MN RL+GD SLNA
Sbjct: 127 TANQKKLFFNLRKAKGRISALDEGDLRPDQVQHIATSLGVPAQDVIDMNRRLSGDTSLNA 186

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +   ++   +WQDWLV +   QE VL  +EE +NR + L  ++ VLNPRERRIFEARRL
Sbjct: 187 PLR--EEGEGEWQDWLVDNSPSQETVLAREEEGRNRLSALRDALGVLNPRERRIFEARRL 244

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSP 294
            ++P+TLE+LS EF VSRERVRQIE RAF+KVQE++++ +     P
Sbjct: 245 ADDPITLEDLSGEFGVSRERVRQIEVRAFEKVQEAVKRNLATRELP 290


>gi|163850434|ref|YP_001638477.1| RNA polymerase factor sigma-32 [Methylobacterium extorquens PA1]
 gi|163662039|gb|ABY29406.1| RNA polymerase sigma factor RpoH [Methylobacterium extorquens PA1]
          Length = 297

 Score =  384 bits (986), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 184/286 (64%), Positives = 227/286 (79%), Gaps = 2/286 (0%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           ++  E GLSRY+ EIRK PMLE  EE+ LAK +R+ GD  AAHRLVTSHLRLV KIAMGY
Sbjct: 7   VLANEGGLSRYLDEIRKFPMLEPAEEFTLAKSWRDDGDREAAHRLVTSHLRLVAKIAMGY 66

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           RGYGLPISEVVSEGN+GLMQAVK+FDP++GFRLATY+MWWIKAA+QEYILRSWSLVK+GT
Sbjct: 67  RGYGLPISEVVSEGNVGLMQAVKRFDPDKGFRLATYAMWWIKAAIQEYILRSWSLVKMGT 126

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           TANQK+LFFNLR+ KG + A+ + +L+P+QV  IA  L V   +VI MN RL+GD SLNA
Sbjct: 127 TANQKKLFFNLRKAKGRISALDEGDLRPDQVQHIATSLGVPAQDVIDMNRRLSGDTSLNA 186

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +   ++   +WQDWLV +   QE VL  +EE +NR + L  ++ VLNPRERRIFEARRL
Sbjct: 187 PLR--EEGEGEWQDWLVDNSPSQETVLAREEEGRNRLSALRDALGVLNPRERRIFEARRL 244

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSP 294
            ++P+TLE+LS EF VSRERVRQIE RAF+KVQE++++ +     P
Sbjct: 245 ADDPITLEDLSGEFGVSRERVRQIEVRAFEKVQEAVKRNLATRELP 290


>gi|217978453|ref|YP_002362600.1| RNA polymerase, sigma 32 subunit, RpoH [Methylocella silvestris
           BL2]
 gi|217503829|gb|ACK51238.1| RNA polymerase, sigma 32 subunit, RpoH [Methylocella silvestris
           BL2]
          Length = 303

 Score =  384 bits (986), Expect = e-105,   Method: Compositional matrix adjust.
 Identities = 178/280 (63%), Positives = 233/280 (83%), Gaps = 2/280 (0%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +++GE GL+RY++EIR+ PMLE Q+EY+LAKR+REH D  AAH+LVTSHLRLV KIAMGY
Sbjct: 7   MISGESGLARYLNEIRRFPMLEPQQEYMLAKRWREHADSDAAHKLVTSHLRLVAKIAMGY 66

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           RGYGLPISEVVSEGN+GLMQAVK+F+PE+GFRLATY+MWWI+A++QEYILRSWSLVK+GT
Sbjct: 67  RGYGLPISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWWIRASIQEYILRSWSLVKMGT 126

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           TA+QK+LFFNLR++K  + A+ + +L+PE V  IA +L VS+ +VI MN R++GD SLNA
Sbjct: 127 TASQKKLFFNLRKVKSQISALEEGDLRPEHVDKIAHRLGVSKQDVIDMNRRMSGDASLNA 186

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +   ++   +WQDWLV D   QE++L+++EE  NR   L  +++VLN RERRIFEARRL
Sbjct: 187 PLR--EEGEGEWQDWLVDDSASQEKLLVDREETDNRLGALHTALNVLNDRERRIFEARRL 244

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            ++P+TLE LS EF++SRERVRQIE RAF+KVQ +++  V
Sbjct: 245 ADDPMTLEALSDEFDISRERVRQIEVRAFEKVQSAVKAGV 284


>gi|319403703|emb|CBI77288.1| RNA polymerase sigma-32 factor [Bartonella rochalimae ATCC
           BAA-1498]
          Length = 305

 Score =  382 bits (982), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 183/281 (65%), Positives = 230/281 (81%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           N+   +  + GL+RY+ EIR+ P+LE QEEY+LAKRYRE+ D  AAH+LVTSHLRLV KI
Sbjct: 5   NLPSFIANDNGLNRYLEEIRRFPVLEPQEEYMLAKRYREYNDPKAAHKLVTSHLRLVAKI 64

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A+GYRGYGLPI EV+SEGNIGLMQAVK+F+PERGFRLATY+MWWIKA++QEY+LRSWSLV
Sbjct: 65  AIGYRGYGLPIGEVISEGNIGLMQAVKRFEPERGFRLATYAMWWIKASIQEYVLRSWSLV 124

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           KIGTTANQKRLFFNLR+LK  LQ + + +L  +QV  IA +L V+E EV+SMN RL GD 
Sbjct: 125 KIGTTANQKRLFFNLRKLKNKLQMLDNGDLNAQQVKEIATRLKVTEDEVVSMNRRLNGDA 184

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SLNA + ++   S +WQDWLV D + QEQ LIE+ E +NR ++L  +M  LN RE+RIF+
Sbjct: 185 SLNAPLLTNKGESYEWQDWLVDDSNNQEQTLIEQNELENRYSILIHAMDNLNEREKRIFK 244

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           ARRL+++P+TLE LS+EF +SRERVRQIEARAF+K+Q  I+
Sbjct: 245 ARRLRDDPLTLEELSNEFNISRERVRQIEARAFEKIQNFIK 285


>gi|296445492|ref|ZP_06887449.1| RNA polymerase, sigma 32 subunit, RpoH [Methylosinus trichosporium
           OB3b]
 gi|296257058|gb|EFH04128.1| RNA polymerase, sigma 32 subunit, RpoH [Methylosinus trichosporium
           OB3b]
          Length = 294

 Score =  381 bits (979), Expect = e-104,   Method: Compositional matrix adjust.
 Identities = 182/293 (62%), Positives = 235/293 (80%), Gaps = 5/293 (1%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           N    ++G+ GLSRY+ EIR+ PMLE ++EY+LAKR+REH D +AA +LVTSHLRLV KI
Sbjct: 3   NALPTLSGDSGLSRYLAEIRRFPMLEPEQEYMLAKRWREHEDPNAAQKLVTSHLRLVAKI 62

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           AMGYRGYGLPI E+VSEGN+GLMQAVK+F+PERGFRLATY+MWWI+A++QEYILRSWSLV
Sbjct: 63  AMGYRGYGLPIGEIVSEGNVGLMQAVKRFEPERGFRLATYAMWWIRASIQEYILRSWSLV 122

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           K+GTTA+QK+LFFNLR+ K  + A  D +L PE V  IA++L V+  +VI MN R++GD 
Sbjct: 123 KMGTTASQKKLFFNLRKAKSKISAFEDGDLTPEHVGEIARRLGVTNQDVIEMNRRMSGDA 182

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SLNA +   ++   +WQDWLV D   QE++L+++EE  NR + L  +++VLNPRERRIFE
Sbjct: 183 SLNAPLR--EEGEGEWQDWLVDDSSDQERILVDQEEAGNRLDALRGALTVLNPRERRIFE 240

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ---KQVELSSSP 294
           ARRL E+PVTLE+LS+EF VSRERVRQIE RAF+KVQ +++    Q+E   +P
Sbjct: 241 ARRLSEDPVTLEDLSTEFGVSRERVRQIEVRAFEKVQSAVRAGMAQLEALPAP 293


>gi|319406710|emb|CBI80343.1| RNA polymerase sigma-32 factor [Bartonella sp. 1-1C]
          Length = 305

 Score =  380 bits (975), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 183/295 (62%), Positives = 235/295 (79%), Gaps = 7/295 (2%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           N+   +  + GL+RY+ EIR+ P+LE QEEY+LAKRY E+ D  AAH+LVTSHLRLV KI
Sbjct: 5   NLPSFIANDNGLNRYLEEIRRFPVLEPQEEYMLAKRYHEYNDPKAAHKLVTSHLRLVAKI 64

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A+GYRGYGLPI EV+SEGNIGLMQAVK+F+PERGFRLATY+MWWIKA++QEY+LRSWSLV
Sbjct: 65  AIGYRGYGLPIGEVISEGNIGLMQAVKRFEPERGFRLATYAMWWIKASIQEYVLRSWSLV 124

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           KIGTTANQKRLFFNLR+LK  LQ + + +L  +QV  IA +L V+E EV+SMN RL GD 
Sbjct: 125 KIGTTANQKRLFFNLRKLKNKLQMLDNGDLNAQQVKEIATRLKVTEDEVVSMNRRLNGDA 184

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SLNA + ++   S +WQDWL+ D + QEQ LIE++E +NR ++L  +M  LN RE+RIF+
Sbjct: 185 SLNAPLLTNKGESYEWQDWLIDDSNNQEQTLIEQDELENRYSILIHAMDNLNEREKRIFK 244

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQK 299
           ARRL+++P+TLE LS+EF +SRERVRQIEARAF+K++  I+       + PL +K
Sbjct: 245 ARRLRDDPLTLEELSNEFNISRERVRQIEARAFEKIKNFIK-------TSPLFRK 292


>gi|312114652|ref|YP_004012248.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodomicrobium vannielii
           ATCC 17100]
 gi|311219781|gb|ADP71149.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodomicrobium vannielii
           ATCC 17100]
          Length = 308

 Score =  378 bits (970), Expect = e-103,   Method: Compositional matrix adjust.
 Identities = 181/288 (62%), Positives = 226/288 (78%), Gaps = 3/288 (1%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S+  +G  GL+RY+ EIR+ PMLE Q+EY+LAKR++EH D  AA +LVTSHLRLV +IAM
Sbjct: 6   SVAASG--GLARYLEEIRRFPMLEPQQEYMLAKRWQEHEDAKAAQKLVTSHLRLVARIAM 63

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           GYRGYGLPI EV+SEGN+GLMQAVK+FDP++GFRLATY+MWWI+AA+QEYILRSWSLVK+
Sbjct: 64  GYRGYGLPIGEVISEGNVGLMQAVKRFDPDKGFRLATYAMWWIRAAIQEYILRSWSLVKM 123

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
           GTTA+QK+LFFNLR+ K  LQA+ + +L+P+QV  IA  L V E +V+SMN RL GD SL
Sbjct: 124 GTTASQKKLFFNLRKAKSQLQALEEGDLRPDQVKTIATNLGVPEEDVVSMNRRLGGDASL 183

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           NA +  +D  S +WQDWLV +   QE  L E EE   RR  L  +M  LN RERRIF AR
Sbjct: 184 NAPLR-ADSESGEWQDWLVDEGPNQETQLAESEELSRRREYLGAAMDSLNERERRIFTAR 242

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSP 294
           RL ++P+TLE LSSEF VSRER+RQIE RAF+KVQ+++QK    + +P
Sbjct: 243 RLADDPLTLEELSSEFNVSRERIRQIEVRAFEKVQKAVQKAALKAEAP 290


>gi|254501465|ref|ZP_05113616.1| alternative sigma factor RpoH [Labrenzia alexandrii DFL-11]
 gi|222437536|gb|EEE44215.1| alternative sigma factor RpoH [Labrenzia alexandrii DFL-11]
          Length = 269

 Score =  375 bits (963), Expect = e-102,   Method: Compositional matrix adjust.
 Identities = 185/273 (67%), Positives = 223/273 (81%), Gaps = 6/273 (2%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           ML+ QEEY+LAKRY+EH D  AA RLV SHLRLV KIAMGYRGYGLPI EVVSEGN+GLM
Sbjct: 1   MLQPQEEYMLAKRYKEHEDPEAAERLVNSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLM 60

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           QAVK+F+P++GFRLATY+MWWIKAA+QEYILRSWSLVK+GTTANQKRLFFNLRRLKG +Q
Sbjct: 61  QAVKRFEPDKGFRLATYAMWWIKAAIQEYILRSWSLVKMGTTANQKRLFFNLRRLKGKIQ 120

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
           A+ + +LKP QV  IA +L VSE EV+SMN RL GD SLNA I  ++ ++ +WQDWLV +
Sbjct: 121 ALEEGDLKPHQVQEIATRLGVSEEEVVSMNRRLGGDASLNAPIR-AEADAGEWQDWLVDE 179

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            D QE +L  +EE   RR ML+ +M VLN RERRIFEARRL E+P+TLE+LS EF VSRE
Sbjct: 180 SDSQETLLANQEELDMRRKMLSDAMDVLNDRERRIFEARRLSEDPMTLEDLSGEFGVSRE 239

Query: 268 RVRQIEARAFKKVQESIQKQVELSSSPPLLQKP 300
           RVRQIE RAF+KVQ++++     +S+  L Q+P
Sbjct: 240 RVRQIEVRAFEKVQKAVR-----NSARTLDQQP 267


>gi|323137119|ref|ZP_08072198.1| RNA polymerase, sigma 32 subunit, RpoH [Methylocystis sp. ATCC
           49242]
 gi|322397477|gb|EFX99999.1| RNA polymerase, sigma 32 subunit, RpoH [Methylocystis sp. ATCC
           49242]
          Length = 294

 Score =  373 bits (957), Expect = e-101,   Method: Compositional matrix adjust.
 Identities = 177/284 (62%), Positives = 225/284 (79%), Gaps = 4/284 (1%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           N+ +I  G  GL+RY+ EIR+ PMLE Q+EY+LAKR+REH D  AA  LVTSHLRLV KI
Sbjct: 3   NLPVIAEG--GLARYLAEIRRFPMLEPQQEYMLAKRWREHEDPKAAQELVTSHLRLVAKI 60

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           AMGYRGYGLPI E++SEGN+GLMQAVK+F+P+RGFRLATY+MWWI+A++QEYILRSWSLV
Sbjct: 61  AMGYRGYGLPIGEIISEGNVGLMQAVKRFEPDRGFRLATYAMWWIRASIQEYILRSWSLV 120

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           K+GTTA+QK+LFFNLR+ K  + A  + +++PE V  IA +L VS+ +VI MN R+ GD 
Sbjct: 121 KMGTTASQKKLFFNLRKAKSRISAFEEGDMRPENVEKIATRLGVSQQDVIEMNRRMGGDA 180

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SLNA +   ++   +WQDWLV D + QE++L+ +EE  NR   L  ++ VLNPRERRIFE
Sbjct: 181 SLNAPLR--EEGEGEWQDWLVDDSEDQERILVAQEENNNRLKALRGALDVLNPRERRIFE 238

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           ARRL ++PVTLE LS EF VSRERVRQIE RAF+KVQ +++  V
Sbjct: 239 ARRLADDPVTLEQLSEEFGVSRERVRQIEVRAFEKVQAAVRSGV 282


>gi|154252606|ref|YP_001413430.1| RNA polymerase sigma-32 subunit RpoH [Parvibaculum lavamentivorans
           DS-1]
 gi|154156556|gb|ABS63773.1| RNA polymerase, sigma 32 subunit, RpoH [Parvibaculum
           lavamentivorans DS-1]
          Length = 340

 Score =  370 bits (951), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 180/276 (65%), Positives = 218/276 (78%), Gaps = 2/276 (0%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           N E  LSRY+ EIRK PMLE QEEY+LAKR+REH D  AAH+LVTSHLRLV KIAMGYRG
Sbjct: 49  NPEGSLSRYLQEIRKFPMLEPQEEYMLAKRWREHEDTEAAHQLVTSHLRLVAKIAMGYRG 108

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
           YGLPI EV+SEGN+GLMQAVK+F+PERGFRLATY+MWWI+A++QEYILRSWSLVK+GTTA
Sbjct: 109 YGLPIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWWIRASIQEYILRSWSLVKMGTTA 168

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNAL 189
            QK+LFFNLR++KG +QAI + +L PEQV  I+ +L V+E EVISMN RL+G D SLNA 
Sbjct: 169 AQKKLFFNLRKVKGQIQAIEEGDLHPEQVKVISDRLGVTEDEVISMNRRLSGPDNSLNAP 228

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           +   D    +WQDWLV D   QE  L E EE   RR ML  +M+ LN RE  I   RRL+
Sbjct: 229 LR-QDSEGGEWQDWLVDDTADQEATLGEAEELDQRREMLAAAMATLNEREMHILTERRLK 287

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + P TLE+LS E+ +SRERVRQIE RAF+K+Q++++
Sbjct: 288 DEPATLEDLSQEYGISRERVRQIEVRAFEKLQKAMK 323


>gi|163794484|ref|ZP_02188455.1| RNA polymerase sigma-32 factor [alpha proteobacterium BAL199]
 gi|159180208|gb|EDP64731.1| RNA polymerase sigma-32 factor [alpha proteobacterium BAL199]
          Length = 298

 Score =  368 bits (945), Expect = e-100,   Method: Compositional matrix adjust.
 Identities = 182/285 (63%), Positives = 225/285 (78%), Gaps = 6/285 (2%)

Query: 3   RKNM-SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           R N+ SI V G   LSRY+ EIRK PMLE  EEYVLAK +REH D+ +AH+LVTSHLRLV
Sbjct: 5   RANLPSISVEG--NLSRYLQEIRKFPMLEPGEEYVLAKSWREHDDVESAHKLVTSHLRLV 62

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            KIAMGYRGYGLP++E++SEGN+G+MQAVK+FDPERGFRLATY+MWWI+A++QEYIL SW
Sbjct: 63  AKIAMGYRGYGLPLAELISEGNVGMMQAVKRFDPERGFRLATYAMWWIRASIQEYILHSW 122

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
           SLVK+GTTA QK+LFFNLRRLKG +QAI D +L PE+V AIA+KL+VSE++V+SMN RLA
Sbjct: 123 SLVKMGTTAAQKKLFFNLRRLKGQMQAIEDGDLSPERVTAIAEKLDVSEADVVSMNRRLA 182

Query: 182 G-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
             D SLNA +        +WQDWLV +   QE    E EE   RR +L  +M  LN RER
Sbjct: 183 SPDHSLNAPLRQD--GEGEWQDWLVDEGQNQEVSFAEDEELSKRRRLLNVAMETLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            I   RRL++NP TLE+LS E+++SRERVRQIE RAF+K+Q++I+
Sbjct: 241 HILTERRLRDNPTTLEDLSQEYDISRERVRQIEVRAFEKLQKAIK 285


>gi|23015588|ref|ZP_00055360.1| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Magnetospirillum magnetotacticum
           MS-1]
          Length = 296

 Score =  366 bits (940), Expect = 2e-99,   Method: Compositional matrix adjust.
 Identities = 175/280 (62%), Positives = 222/280 (79%), Gaps = 3/280 (1%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S+ +  E  L+RY+ +IRK PML  +EEY+LAKR+REHGDL AA+RLVTSHLRLV KIAM
Sbjct: 7   SLSLAPEGNLTRYLQDIRKFPMLPPEEEYLLAKRFREHGDLPAANRLVTSHLRLVAKIAM 66

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           GYRGYGLP+ E++SEGN+G+MQAV++FDPERGFRLATY+MWWI+AA+QEYIL SWSLVK+
Sbjct: 67  GYRGYGLPLGELISEGNVGMMQAVRRFDPERGFRLATYAMWWIRAAIQEYILHSWSLVKM 126

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DES 185
           GTTA QK+LFFNLR+LKG +QAI + ++  E V  IA KL V+E EVI+MN RL+  D S
Sbjct: 127 GTTAAQKKLFFNLRKLKGQMQAIEEGDMSAENVAKIATKLEVTEDEVITMNRRLSSPDHS 186

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           LNA + +  +   +WQDWLV DH+ QE  L E+EE   RR MLT +++ LN RER I   
Sbjct: 187 LNAPVRT--EGEGEWQDWLVDDHEDQETELGEREEMGQRRGMLTSALAALNDRERAILIQ 244

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           RRL E+P TLE+LS  + +SRERVRQIE RAF+K+Q+S++
Sbjct: 245 RRLTEDPATLEDLSQRYGISRERVRQIEVRAFEKLQKSVK 284


>gi|83312286|ref|YP_422550.1| RNA polymerase factor sigma-32 [Magnetospirillum magneticum AMB-1]
 gi|82947127|dbj|BAE51991.1| DNA-directed RNA polymerase, sigma subunit [Magnetospirillum
           magneticum AMB-1]
          Length = 296

 Score =  364 bits (935), Expect = 8e-99,   Method: Compositional matrix adjust.
 Identities = 174/280 (62%), Positives = 221/280 (78%), Gaps = 3/280 (1%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S+ +  E  L+RY+ +IRK PML  +EEY+LAKR+REHGDL AA+RLVTSHLRLV KIAM
Sbjct: 7   SLSLAPEGNLTRYLQDIRKFPMLPPEEEYLLAKRFREHGDLPAANRLVTSHLRLVAKIAM 66

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           GYRGYGLP+ E++SEGN+G+MQAV++FDPERGFRLATY+MWWI+AA+QEYIL SWSLVK+
Sbjct: 67  GYRGYGLPLGELISEGNVGMMQAVRRFDPERGFRLATYAMWWIRAAIQEYILHSWSLVKM 126

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DES 185
           GTTA QK+LFFNLR+LKG +QAI + ++  E V  IA KL V+E EV++MN RL+  D S
Sbjct: 127 GTTAAQKKLFFNLRKLKGQMQAIEEGDMSAENVAKIATKLEVTEDEVVTMNRRLSSPDHS 186

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           LNA + +  +   +WQDWLV DH+ QE  L E+EE   RR MLT ++  LN RER I   
Sbjct: 187 LNAPVRA--EGEGEWQDWLVDDHEDQETELGEREELGQRRQMLTSALEALNDRERAILIQ 244

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           RRL E+P TLE+LS  + +SRERVRQIE RAF+K+Q+S++
Sbjct: 245 RRLTEDPATLEDLSQRYGISRERVRQIEVRAFEKLQKSVK 284


>gi|209965020|ref|YP_002297935.1| RNA polymerase sigma-32 factor [Rhodospirillum centenum SW]
 gi|209958486|gb|ACI99122.1| RNA polymerase sigma-32 factor [Rhodospirillum centenum SW]
          Length = 294

 Score =  364 bits (934), Expect = 1e-98,   Method: Compositional matrix adjust.
 Identities = 175/282 (62%), Positives = 222/282 (78%), Gaps = 3/282 (1%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           ++N E  L+RY+ EIRK PMLE +EEY+LAK +REHGD  AAHRLVTSHLRLV KIAMGY
Sbjct: 10  VINSESNLARYLQEIRKFPMLEAEEEYMLAKSWREHGDTDAAHRLVTSHLRLVAKIAMGY 69

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           RGYGLP+SE++SEGN+G+MQAVK+FDP+RGFRLATY+MWWI+AA+QEYIL SWSLVK+GT
Sbjct: 70  RGYGLPLSELISEGNVGMMQAVKRFDPDRGFRLATYAMWWIRAAIQEYILHSWSLVKMGT 129

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN 187
           TA QK+LFFNLR+LKG +QAI + +L PE V  IA+ L+V ES+V++MN RLA  D SLN
Sbjct: 130 TAAQKKLFFNLRKLKGQMQAIDEGDLHPETVRKIAETLDVPESDVVNMNRRLASPDHSLN 189

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           A +        +WQDWLV + + QE  L E+EE   R+ +L  +M  LN RER I   RR
Sbjct: 190 APLRVD--GEGEWQDWLVDESESQEIRLGEREELGKRKALLAEAMKTLNDRERHILVERR 247

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           L++NP TLE+LS ++ +SRERVRQIE RAF+K+Q++I+   E
Sbjct: 248 LRDNPTTLEDLSQQYGISRERVRQIEVRAFEKLQKAIRSAAE 289


>gi|294085881|ref|YP_003552641.1| RNA polymerase sigma-32 subunit RpoH [Candidatus Puniceispirillum
           marinum IMCC1322]
 gi|292665456|gb|ADE40557.1| RNA polymerase, sigma 32 subunit, RpoH [Candidatus Puniceispirillum
           marinum IMCC1322]
          Length = 312

 Score =  363 bits (933), Expect = 1e-98,   Method: Compositional matrix adjust.
 Identities = 169/274 (61%), Positives = 221/274 (80%), Gaps = 1/274 (0%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           LSRY+ +IR  PMLE ++EY+LAK ++E GD+ +AH+LVTSHLRLV KIAMGYRGYGLP+
Sbjct: 21  LSRYLEQIRAFPMLEPKQEYMLAKAWKEKGDVESAHQLVTSHLRLVAKIAMGYRGYGLPV 80

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++SEGN+G+M AVKKF+PE+GFRLATY+MWWIKAA+QEYILRSWSLVKIGTTA QK+L
Sbjct: 81  ADLISEGNLGMMHAVKKFEPEKGFRLATYAMWWIKAAIQEYILRSWSLVKIGTTAGQKKL 140

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLRR+KG +QAI + +LKPEQV  IA +LNV+E+EV+SMN R+AG D SLN  ++   
Sbjct: 141 FFNLRRIKGQIQAIDEGDLKPEQVTHIADELNVTEAEVMSMNQRMAGNDRSLNVPLSRDG 200

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
           + + +WQDWL  D   QE    E EE   R N++  +M  LN RE+RI +ARRL E P+T
Sbjct: 201 EGTGEWQDWLEDDTVDQETSFAEHEEYSARANLMMDAMKGLNEREQRILQARRLAEPPLT 260

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           LE+L+ EF VSRER+RQIE RAF+K+Q++++ + 
Sbjct: 261 LEDLAGEFNVSRERIRQIEVRAFEKLQKAVRDKA 294


>gi|85714568|ref|ZP_01045555.1| RNA polymerase sigma factor [Nitrobacter sp. Nb-311A]
 gi|85698453|gb|EAQ36323.1| RNA polymerase sigma factor [Nitrobacter sp. Nb-311A]
          Length = 272

 Score =  363 bits (931), Expect = 2e-98,   Method: Compositional matrix adjust.
 Identities = 172/261 (65%), Positives = 210/261 (80%), Gaps = 1/261 (0%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           MLE  EEY+ AKR REH D  AAH LVTSHLRLV KIAMGYRGYGLPISEVVSEGN+GLM
Sbjct: 1   MLEPHEEYMFAKRLREHDDRDAAHHLVTSHLRLVAKIAMGYRGYGLPISEVVSEGNVGLM 60

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           QAVK+F+PE+GFRLATY+MWWIKA++QEYILRSWSLVK+GTTANQK+LFFNLR+ K  + 
Sbjct: 61  QAVKRFEPEKGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQKKLFFNLRKAKSKIS 120

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
           A+ + +++P+QV  IA++L V+E +V+ MN RL GD SLNA I   D  + +WQDWLV  
Sbjct: 121 ALDEGDMRPDQVKLIARRLGVTEQDVVDMNRRLGGDASLNAPIR-DDGEAGEWQDWLVDQ 179

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
              QE V+ E EE  +RR  LT +M VLNPRERRIFEARRL + P+TLE+L++EF VSRE
Sbjct: 180 SPTQEAVMAEHEEFDHRRRALTGAMGVLNPRERRIFEARRLADEPMTLEDLAAEFNVSRE 239

Query: 268 RVRQIEARAFKKVQESIQKQV 288
           RVRQIE RAF+KVQ +++  +
Sbjct: 240 RVRQIEVRAFEKVQSAVKTTI 260


>gi|144897893|emb|CAM74757.1| RNA polymerase sigma-32 factor [Magnetospirillum gryphiswaldense
           MSR-1]
          Length = 288

 Score =  361 bits (927), Expect = 7e-98,   Method: Compositional matrix adjust.
 Identities = 175/283 (61%), Positives = 219/283 (77%), Gaps = 3/283 (1%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S+ +  E  LSRY+ EIRK PMLE  EEY LAKRYREHGD  AA RL+TSHLRLV KIAM
Sbjct: 7   SLSLAPEGNLSRYLQEIRKFPMLEPTEEYQLAKRYREHGDFEAADRLITSHLRLVAKIAM 66

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           GYRGYGLP+ E++SEGN+G+MQAVK+FDP+RGFRLATY+MWWI+AA+QEYIL SWSLVK+
Sbjct: 67  GYRGYGLPLGELISEGNVGMMQAVKRFDPDRGFRLATYAMWWIRAAVQEYILHSWSLVKM 126

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DES 185
           GTTA QK+LFFNLR+LKG +QA+ + +L  E V +IA KLNV E++VI+MN RLA  D S
Sbjct: 127 GTTAAQKKLFFNLRKLKGQMQAMDEGDLPQETVTSIATKLNVPENDVINMNRRLASPDHS 186

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           LNA +        +WQDWLV + D QE  L +++ER  R  +L+ ++  LN RER I   
Sbjct: 187 LNAPVRMD--GEGEWQDWLVDESDDQETELADRQERGIRSKLLSTALDTLNERERSILSQ 244

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RRL E+P TLE+LS ++ +SRERVRQIE RAF+K+Q+SI+  V
Sbjct: 245 RRLTEDPATLEDLSQQYGISRERVRQIEVRAFEKLQKSIRASV 287


>gi|296114957|ref|ZP_06833602.1| RNA polymerase factor sigma-32 [Gluconacetobacter hansenii ATCC
           23769]
 gi|295978475|gb|EFG85208.1| RNA polymerase factor sigma-32 [Gluconacetobacter hansenii ATCC
           23769]
          Length = 299

 Score =  361 bits (927), Expect = 7e-98,   Method: Compositional matrix adjust.
 Identities = 174/283 (61%), Positives = 219/283 (77%), Gaps = 3/283 (1%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           +I+   E  LS+Y+ +IRK PML  +EE  L++ ++E GD  AAH+LVTSHLRLV KIAM
Sbjct: 6   AILSGPENNLSKYLRDIRKFPMLSPEEELKLSRLWKEKGDTEAAHKLVTSHLRLVAKIAM 65

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           GYRGYGLP+ E++SEGNIG+MQAV++FDPERGFRLATY+MWWI+AA+QEYIL SWSLVKI
Sbjct: 66  GYRGYGLPVGELISEGNIGMMQAVRRFDPERGFRLATYAMWWIRAAIQEYILHSWSLVKI 125

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDES 185
           GTTA QK+LFFNLRRLKG +QAI D +L+PEQV  IAK L V E +V++MN RL A D S
Sbjct: 126 GTTAAQKKLFFNLRRLKGQMQAIDDGDLQPEQVDKIAKSLGVPEQDVVNMNRRLSAPDHS 185

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           LNA + +   +  +WQDWLV DHD QEQ L E EE   R+ +L  +M  LN RER I   
Sbjct: 186 LNAPLRTD--SEGEWQDWLVDDHDNQEQTLAENEEYSGRKALLANAMQSLNERERHILTE 243

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RRL+++P TLE+LS  + +SRERVRQIE RAF+KVQ +++ +V
Sbjct: 244 RRLKDDPATLEDLSHVYNISRERVRQIEVRAFEKVQNAMKAEV 286


>gi|315498780|ref|YP_004087584.1| RNA polymerase, sigma 32 subunit, rpoh [Asticcacaulis excentricus
           CB 48]
 gi|315416792|gb|ADU13433.1| RNA polymerase, sigma 32 subunit, RpoH [Asticcacaulis excentricus
           CB 48]
          Length = 344

 Score =  360 bits (923), Expect = 2e-97,   Method: Compositional matrix adjust.
 Identities = 175/278 (62%), Positives = 220/278 (79%), Gaps = 3/278 (1%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +++ + GL+RY+ EIRK PML K EE++LAKR+ EH D  AAH+LVTSHLRLV KIAMGY
Sbjct: 62  VLSPDGGLNRYLSEIRKFPMLAKDEEFMLAKRWAEHADPKAAHKLVTSHLRLVAKIAMGY 121

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           RGYGLPI EV+SEGN+GLMQAVKKFDP++GFRLATY+MWWIKAA+QEY+LRSWSLVK+GT
Sbjct: 122 RGYGLPIGEVISEGNVGLMQAVKKFDPDKGFRLATYAMWWIKAAIQEYVLRSWSLVKMGT 181

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN 187
           TA QK+LFFNLR++K  + A+ + +++ EQV  IA KL VSE +VISMN R++  D SLN
Sbjct: 182 TAAQKKLFFNLRKVKSEISALEEGDMRHEQVAQIATKLGVSEDDVISMNRRMSSPDSSLN 241

Query: 188 ALINSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           A +  S+ + S+WQDWL  D    QE VL + EE K R ++L  +M  LN RER I  AR
Sbjct: 242 APLRVSEGD-SEWQDWLADDSTPSQETVLADSEEYKLRMSLLEEAMGELNERERAILTAR 300

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           RLQENP TLE+L+  F VSRERVRQIE RAF+K+Q+++
Sbjct: 301 RLQENPTTLEDLADRFGVSRERVRQIEVRAFEKLQKAM 338


>gi|258543198|ref|YP_003188631.1| RNA polymerase factor sigma-32 [Acetobacter pasteurianus IFO
           3283-01]
 gi|256634276|dbj|BAI00252.1| DNA-directed RNA polymerase Heat shock sigma factor RpoH
           [Acetobacter pasteurianus IFO 3283-01]
 gi|256637336|dbj|BAI03305.1| DNA-directed RNA polymerase Heat shock sigma factor RpoH
           [Acetobacter pasteurianus IFO 3283-03]
 gi|256640388|dbj|BAI06350.1| DNA-directed RNA polymerase Heat shock sigma factor RpoH
           [Acetobacter pasteurianus IFO 3283-07]
 gi|256643445|dbj|BAI09400.1| DNA-directed RNA polymerase Heat shock sigma factor RpoH
           [Acetobacter pasteurianus IFO 3283-22]
 gi|256646500|dbj|BAI12448.1| DNA-directed RNA polymerase Heat shock sigma factor RpoH
           [Acetobacter pasteurianus IFO 3283-26]
 gi|256649553|dbj|BAI15494.1| DNA-directed RNA polymerase Heat shock sigma factor RpoH
           [Acetobacter pasteurianus IFO 3283-32]
 gi|256652539|dbj|BAI18473.1| DNA-directed RNA polymerase Heat shock sigma factor RpoH
           [Acetobacter pasteurianus IFO 3283-01-42C]
 gi|256655597|dbj|BAI21524.1| DNA-directed RNA polymerase Heat shock sigma factor RpoH
           [Acetobacter pasteurianus IFO 3283-12]
          Length = 319

 Score =  358 bits (920), Expect = 4e-97,   Method: Compositional matrix adjust.
 Identities = 177/283 (62%), Positives = 221/283 (78%), Gaps = 3/283 (1%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           I V  E  LSRY+ EIRK P+L  +EE  L++ +R+ GD+ AAH+LVTSHLRLV KIAMG
Sbjct: 29  INVGPENNLSRYLQEIRKYPLLTPEEELSLSRLWRDKGDVKAAHQLVTSHLRLVAKIAMG 88

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           YRGYGLPI+E++SEGNIG+MQAVK+FDPE+GFRLATY+MWWI+AA+QEYIL SWSLVK+G
Sbjct: 89  YRGYGLPINELISEGNIGMMQAVKRFDPEKGFRLATYAMWWIRAAIQEYILHSWSLVKMG 148

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESL 186
           TTA QK+LFFNLRRLKG +QAI D +LKPEQV  IA  L VSE +V+ MN R+A  D SL
Sbjct: 149 TTAAQKKLFFNLRRLKGQMQAIDDGDLKPEQVNKIATTLGVSEQDVVDMNRRMAAPDHSL 208

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           NA + +     S+WQD LV DH  QE V  E EE   R+ +L+ +M  LN RERRIF  R
Sbjct: 209 NAPMRAD--QDSEWQDRLVDDHTNQEDVYAENEELSGRKALLSSAMENLNERERRIFTER 266

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           RL+++P TLE L+ E+ +SRERVRQIE RAF+KVQ +++K+V+
Sbjct: 267 RLKDDPSTLEELAHEYGISRERVRQIEVRAFEKVQAAMKKEVQ 309


>gi|209542656|ref|YP_002274885.1| RNA polymerase factor sigma-32 [Gluconacetobacter diazotrophicus
           PAl 5]
 gi|209530333|gb|ACI50270.1| RNA polymerase, sigma 32 subunit, RpoH [Gluconacetobacter
           diazotrophicus PAl 5]
          Length = 295

 Score =  358 bits (920), Expect = 4e-97,   Method: Compositional matrix adjust.
 Identities = 173/281 (61%), Positives = 217/281 (77%), Gaps = 3/281 (1%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V  E  LSRY+ +IRK PML  ++E  L++R+++ GD  AAH LVTSHLRLV KIAMGYR
Sbjct: 8   VGPESNLSRYLQDIRKFPMLSPEDEQRLSRRWKDKGDTEAAHALVTSHLRLVAKIAMGYR 67

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYGLP+ E++SEGNIG+MQAV++FDP+RGFRLATY+MWWI+AA+QEYIL SWSLVK+GTT
Sbjct: 68  GYGLPLGELISEGNIGMMQAVRRFDPDRGFRLATYAMWWIRAAIQEYILHSWSLVKMGTT 127

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNA 188
           A QK+LFFNLRRLKG +QAI D +LKPEQV  IA+ L V E +VI+MN RL A D SLNA
Sbjct: 128 AAQKKLFFNLRRLKGQMQAIDDGDLKPEQVNKIAESLGVPEQDVINMNRRLSAPDHSLNA 187

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            + +   +  +WQDWLV +HD QEQ L E EE   R+ +L  +M  LN RER I   RRL
Sbjct: 188 PLRAD--SEGEWQDWLVDEHDNQEQTLAENEEFSGRKALLDNAMKTLNDRERHILTERRL 245

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           +++P TLE LS  + +SRERVRQIE RAF+KVQ +++ +VE
Sbjct: 246 KDDPATLEELSHTYNISRERVRQIEVRAFEKVQAAMKAEVE 286


>gi|329114085|ref|ZP_08242849.1| RNA polymerase sigma-32 factor [Acetobacter pomorum DM001]
 gi|326696624|gb|EGE48301.1| RNA polymerase sigma-32 factor [Acetobacter pomorum DM001]
          Length = 319

 Score =  358 bits (919), Expect = 5e-97,   Method: Compositional matrix adjust.
 Identities = 177/283 (62%), Positives = 221/283 (78%), Gaps = 3/283 (1%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           I V  E  LSRY+ EIRK P+L  +EE  L++ +R+ GD+ AAH+LVTSHLRLV KIAMG
Sbjct: 29  INVGPENNLSRYLQEIRKYPLLTPEEELSLSRLWRDKGDVKAAHQLVTSHLRLVAKIAMG 88

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           YRGYGLPI+E++SEGNIG+MQAVK+FDPE+GFRLATY+MWWI+AA+QEYIL SWSLVK+G
Sbjct: 89  YRGYGLPINELISEGNIGMMQAVKRFDPEKGFRLATYAMWWIRAAIQEYILHSWSLVKMG 148

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESL 186
           TTA QK+LFFNLRRLKG +QAI D +LKPEQV  IA  L VSE +V+ MN R+A  D SL
Sbjct: 149 TTAAQKKLFFNLRRLKGQMQAIDDGDLKPEQVNKIATTLGVSEQDVVDMNRRMAAPDHSL 208

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           NA + +     S+WQD LV DH  QE V  E EE   R+ +L+ +M  LN RERRIF  R
Sbjct: 209 NAPMRAD--QDSEWQDRLVDDHTNQEDVYAENEELSGRKALLSSAMENLNERERRIFTER 266

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           RL+++P TLE L+ E+ +SRERVRQIE RAF+KVQ +++K+V+
Sbjct: 267 RLKDDPSTLEELAHEYGISRERVRQIEVRAFEKVQAAMKKEVQ 309


>gi|162148038|ref|YP_001602499.1| RNA polymerase factor sigma-32 [Gluconacetobacter diazotrophicus
           PAl 5]
 gi|161786615|emb|CAP56197.1| putative RNA polymerase sigma-32 factor [Gluconacetobacter
           diazotrophicus PAl 5]
          Length = 325

 Score =  358 bits (919), Expect = 5e-97,   Method: Compositional matrix adjust.
 Identities = 173/281 (61%), Positives = 217/281 (77%), Gaps = 3/281 (1%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V  E  LSRY+ +IRK PML  ++E  L++R+++ GD  AAH LVTSHLRLV KIAMGYR
Sbjct: 38  VGPESNLSRYLQDIRKFPMLSPEDEQRLSRRWKDKGDTEAAHALVTSHLRLVAKIAMGYR 97

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYGLP+ E++SEGNIG+MQAV++FDP+RGFRLATY+MWWI+AA+QEYIL SWSLVK+GTT
Sbjct: 98  GYGLPLGELISEGNIGMMQAVRRFDPDRGFRLATYAMWWIRAAIQEYILHSWSLVKMGTT 157

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNA 188
           A QK+LFFNLRRLKG +QAI D +LKPEQV  IA+ L V E +VI+MN RL A D SLNA
Sbjct: 158 AAQKKLFFNLRRLKGQMQAIDDGDLKPEQVNKIAESLGVPEQDVINMNRRLSAPDHSLNA 217

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            + +   +  +WQDWLV +HD QEQ L E EE   R+ +L  +M  LN RER I   RRL
Sbjct: 218 PLRAD--SEGEWQDWLVDEHDNQEQTLAENEEFSGRKALLDNAMKTLNDRERHILTERRL 275

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           +++P TLE LS  + +SRERVRQIE RAF+KVQ +++ +VE
Sbjct: 276 KDDPATLEELSHTYNISRERVRQIEVRAFEKVQAAMKAEVE 316


>gi|58038976|ref|YP_190940.1| RNA polymerase factor sigma-32 [Gluconobacter oxydans 621H]
 gi|58001390|gb|AAW60284.1| Heat shock sigma factor RpoH [Gluconobacter oxydans 621H]
          Length = 297

 Score =  357 bits (917), Expect = 9e-97,   Method: Compositional matrix adjust.
 Identities = 176/283 (62%), Positives = 216/283 (76%), Gaps = 3/283 (1%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           I V  E  L+RY+ EIRK P+L  QEE  L++R+R+  D SAAHRLVTSHLRLV KIAMG
Sbjct: 7   ISVGPENNLTRYLQEIRKFPLLTPQEELDLSRRWRKDEDTSAAHRLVTSHLRLVAKIAMG 66

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           YRGYGLP++E++SEGNIG+MQAV++FDPERGFRLATY+MWWI+AAMQEYIL SWSLVK+G
Sbjct: 67  YRGYGLPVNELISEGNIGMMQAVRRFDPERGFRLATYAMWWIRAAMQEYILHSWSLVKMG 126

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESL 186
           TTA QK+LFFNLRRLKG +QAI D +LKPEQV +IA  L V E +V+SMN RLA  D SL
Sbjct: 127 TTAAQKKLFFNLRRLKGQMQAIDDGDLKPEQVNSIATTLGVPEQDVVSMNQRLAAPDHSL 186

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           NA +        +WQDWLV DH+ QEQ     EE   R+ +L +++  LN RER I   R
Sbjct: 187 NAPLRID--GEGEWQDWLVDDHENQEQTYAASEEFTGRKALLDQALMTLNERERHILSER 244

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           RL+E P TLE LS  + VSRER+RQIEARA +K+Q+++  +VE
Sbjct: 245 RLKEEPSTLEELSHHYNVSRERIRQIEARAMEKLQKAMAAEVE 287


>gi|197103875|ref|YP_002129252.1| heat shock sigma factor RpoH [Phenylobacterium zucineum HLK1]
 gi|196477295|gb|ACG76823.1| heat shock sigma factor RpoH [Phenylobacterium zucineum HLK1]
          Length = 295

 Score =  357 bits (915), Expect = 2e-96,   Method: Compositional matrix adjust.
 Identities = 178/287 (62%), Positives = 222/287 (77%), Gaps = 4/287 (1%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           N   +++ E GLSRY+ EIRK PML K EE++LAKR++EH D  AAHRLVTSHLRLV KI
Sbjct: 4   NALAVMSPEGGLSRYLTEIRKFPMLAKDEEFMLAKRWQEHQDPEAAHRLVTSHLRLVAKI 63

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           AMGYRGYGLPI EV+SEGN+GLMQAVKKFDP++GFRLATY+MWWI+A++QEYILRSWSLV
Sbjct: 64  AMGYRGYGLPIGEVISEGNVGLMQAVKKFDPDKGFRLATYAMWWIRASIQEYILRSWSLV 123

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GD 183
           K+GTTA QK+LFFNLR+ K  + A+ + +L+PEQV  IA KL V + EVISMN RLA GD
Sbjct: 124 KMGTTAAQKKLFFNLRKAKSEISALEEGDLRPEQVRQIATKLGVLDEEVISMNRRLAGGD 183

Query: 184 ESLNALINSSDKNSSQWQDWLV-YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
            SLN+ + +   + S+WQDWLV  D   QE V+ E EER  R  +L  +M+ L  RER I
Sbjct: 184 ASLNSPLRAD--SESEWQDWLVDEDTPSQESVVAEAEERGIRMELLQEAMAELTDRERHI 241

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
              RRL++ P TLE L+S++ VSRERVRQIE RAF+K+Q+S++   E
Sbjct: 242 LTERRLKDEPTTLEELASQYGVSRERVRQIEVRAFEKLQKSMRAAAE 288


>gi|288962535|ref|YP_003452830.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
 gi|288914801|dbj|BAI76286.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
          Length = 296

 Score =  355 bits (912), Expect = 3e-96,   Method: Compositional matrix adjust.
 Identities = 172/277 (62%), Positives = 221/277 (79%), Gaps = 3/277 (1%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           +  E  LSRY+ EIRK PMLE + EY+LAKR+++H D  AAH+LVTSHLRLV KIAMGYR
Sbjct: 10  IGSESNLSRYLQEIRKFPMLEPEREYMLAKRWQQHEDSGAAHQLVTSHLRLVAKIAMGYR 69

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYGLP+SE++SEGN+G+MQAVK+FDP+RGFRLATY+MWWI+AA+QEYIL SWSLVK+GTT
Sbjct: 70  GYGLPLSELISEGNVGMMQAVKRFDPDRGFRLATYAMWWIRAAIQEYILHSWSLVKMGTT 129

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNA 188
           A QK+LFFNLRRLKG +QAI + +L PEQV AIA KL+V E +V++MN RLA  D SLNA
Sbjct: 130 AAQKKLFFNLRRLKGQMQAIEEGDLSPEQVQAIATKLDVPEQDVVNMNRRLASPDHSLNA 189

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            + +  ++  +WQD+LV +   QE  L ++EE   RR +L  +M+ LN RER I   RRL
Sbjct: 190 PLRA--ESEGEWQDFLVDESASQEIALADREELGKRRKLLVEAMTGLNERERDILTERRL 247

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           +E P TLE+LS ++ +SRERVRQIE RAF+K+Q++I+
Sbjct: 248 REAPTTLEDLSQKYGISRERVRQIEVRAFEKLQKAIK 284


>gi|114797392|ref|YP_759060.1| RNA polymerase factor sigma-32 [Hyphomonas neptunium ATCC 15444]
 gi|114737566|gb|ABI75691.1| alternative sigma factor RpoH [Hyphomonas neptunium ATCC 15444]
          Length = 298

 Score =  355 bits (912), Expect = 3e-96,   Method: Compositional matrix adjust.
 Identities = 169/289 (58%), Positives = 221/289 (76%), Gaps = 3/289 (1%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S+ ++ E G+SRY+ EIRK PMLEK EE++LA+R+ EH D  AA ++VTSHLRLV KIAM
Sbjct: 9   SVALSPEQGMSRYLSEIRKFPMLEKNEEFMLARRWHEHEDTEAAEKMVTSHLRLVAKIAM 68

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           GYRGYGLP++EV+SEGN+GLMQAVKKFDP++GFRLATY+MWWI+AA+QEYILRSWSLVK+
Sbjct: 69  GYRGYGLPMAEVISEGNVGLMQAVKKFDPDKGFRLATYAMWWIRAAIQEYILRSWSLVKL 128

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DES 185
           GTTA QK+LFFNLRRLKG +QA+ + +LKPEQ   IA+KLNV+E+EV SMN R++G D S
Sbjct: 129 GTTAAQKKLFFNLRRLKGEMQALEEGDLKPEQARLIAEKLNVTETEVYSMNGRMSGSDAS 188

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           LN  + +      +WQDWL  D  G  +     +E   R  +LT++M  L+ RER I   
Sbjct: 189 LNVPMGTD--GDMEWQDWLADDEPGTAETFANSQELDARMTLLTQAMEDLSERERHILTE 246

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSP 294
           RRL + P TLE LS ++ VSRER+RQIE RAF+K+Q+++++  +    P
Sbjct: 247 RRLVDEPKTLEELSEQYNVSRERIRQIEVRAFEKLQKAMKRMAKEQGLP 295


>gi|329890478|ref|ZP_08268821.1| alternative sigma factor RpoH [Brevundimonas diminuta ATCC 11568]
 gi|328845779|gb|EGF95343.1| alternative sigma factor RpoH [Brevundimonas diminuta ATCC 11568]
          Length = 294

 Score =  354 bits (909), Expect = 7e-96,   Method: Compositional matrix adjust.
 Identities = 173/286 (60%), Positives = 216/286 (75%), Gaps = 3/286 (1%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           N   +++ E GLSRY+ EIRK PML K EE++LAKR+ EH D  AAHRLVTSHLRLV KI
Sbjct: 4   NTLTVMSPEQGLSRYLTEIRKFPMLTKDEEFMLAKRWSEHQDPEAAHRLVTSHLRLVAKI 63

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           AMGYRGYGLPI EV+SEGN+GLMQAVKKFDP++GFRLATY+MWWI+A++QEYILRSWSLV
Sbjct: 64  AMGYRGYGLPIGEVISEGNVGLMQAVKKFDPDKGFRLATYAMWWIRASIQEYILRSWSLV 123

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           K+GTTA QK+LFFNLR+ K  + A  + +L PE + AIA KL VSE EV +MN RL GD 
Sbjct: 124 KMGTTAAQKKLFFNLRKAKSQISAFEEGDLHPEHLTAIATKLGVSEEEVTNMNRRLGGDA 183

Query: 185 SLNALINSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           SLNA + +     S+WQDWL  D    QE  L E EE+  R ++L  +M  L  RE+ I 
Sbjct: 184 SLNAPLRAD--GESEWQDWLADDDAVSQETQLAENEEKSIRMSLLQEAMEELTDREKHIL 241

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
             RRL+++PVTLE L+ ++ VSRERVRQIE RAF+K+Q++++   E
Sbjct: 242 TERRLKDDPVTLEELAGQYGVSRERVRQIEVRAFEKLQKAMRAAAE 287


>gi|294678332|ref|YP_003578947.1| RNA polymerase sigma-32 factor [Rhodobacter capsulatus SB 1003]
 gi|294477152|gb|ADE86540.1| RNA polymerase sigma-32 factor-2 [Rhodobacter capsulatus SB 1003]
          Length = 299

 Score =  354 bits (909), Expect = 8e-96,   Method: Compositional matrix adjust.
 Identities = 171/271 (63%), Positives = 215/271 (79%), Gaps = 2/271 (0%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GL+RY+ EIRK P+LE +EEY+LAK + +H D  AAHRLVTSHLRL  KIAMGYRGYG
Sbjct: 13  EQGLNRYLQEIRKFPLLEPEEEYMLAKAWVDHQDPKAAHRLVTSHLRLAAKIAMGYRGYG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EV+SE N+GLMQAVK+FDPERGFRLATY+MWWI+AA+QEYILRSWSLVK+GTT+ Q
Sbjct: 73  LPQAEVISEANVGLMQAVKRFDPERGFRLATYAMWWIRAAIQEYILRSWSLVKLGTTSAQ 132

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALIN 191
           K+LFFNLR+ K  + A+ + +L+P+ V  IA  LNVSE +VI MN RLAG D SLNA + 
Sbjct: 133 KKLFFNLRKAKSKIGALDEGDLRPDAVAKIAHDLNVSEDDVIEMNRRLAGSDASLNAQVG 192

Query: 192 SSD-KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           +SD ++++QWQDWL  +   Q +   E +E + RR ML  +M VLN RER I  ARRL++
Sbjct: 193 ASDGESATQWQDWLEDEDADQAEAYAEADELQARRAMLVAAMDVLNERERDILMARRLRD 252

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            PVTLE LSS+++VSRER+RQIE RAF+K+Q
Sbjct: 253 EPVTLEELSSQYDVSRERIRQIEVRAFEKLQ 283


>gi|304320253|ref|YP_003853896.1| RNA polymerase sigma factor [Parvularcula bermudensis HTCC2503]
 gi|303299155|gb|ADM08754.1| RNA polymerase sigma factor [Parvularcula bermudensis HTCC2503]
          Length = 304

 Score =  353 bits (906), Expect = 2e-95,   Method: Compositional matrix adjust.
 Identities = 168/276 (60%), Positives = 218/276 (78%), Gaps = 2/276 (0%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GL+RY+ EIRK P+LE+ EEY+LAKR++EH D  AA RL+TSHLRLV KIAMGYRGYG
Sbjct: 16  EGGLNRYLAEIRKFPLLERDEEYMLAKRFKEHEDPDAAQRLITSHLRLVAKIAMGYRGYG 75

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP  EV+SEGN+GLMQAVKKFDP++GFRL+TY+MWWI+A++QEYILRSWSLVKIGTTA Q
Sbjct: 76  LPTGEVISEGNVGLMQAVKKFDPDKGFRLSTYAMWWIRASIQEYILRSWSLVKIGTTAAQ 135

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALIN 191
           K+LFFNLR+LKG + A+ + +++PE+V  IA +L V+E EVISMN R+AG D SLN+ + 
Sbjct: 136 KKLFFNLRKLKGQIDAVDEGDMRPEEVELIATRLGVTEDEVISMNRRMAGSDNSLNSPMR 195

Query: 192 SSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           S     ++WQDWLV ++    E  L++ +E + R  +L  +M  LN RER I   RRL E
Sbjct: 196 SDGDGGAEWQDWLVDENAVNAESQLVKDDEFETRMELLQEAMVDLNDRERHILTERRLTE 255

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           NP TLE LS E+ VSRER+RQIE RAF+K+Q+++++
Sbjct: 256 NPKTLEELSGEYGVSRERIRQIEVRAFEKLQKAMKR 291


>gi|114569135|ref|YP_755815.1| RNA polymerase factor sigma-32 [Maricaulis maris MCS10]
 gi|114339597|gb|ABI64877.1| RNA polymerase, sigma 32 subunit, RpoH [Maricaulis maris MCS10]
          Length = 295

 Score =  353 bits (905), Expect = 2e-95,   Method: Compositional matrix adjust.
 Identities = 171/282 (60%), Positives = 220/282 (78%), Gaps = 3/282 (1%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +S+ ++ E GLS Y+ EIR+ PMLEK EE++L KR+REH D  AA +LVTSHLRLV KIA
Sbjct: 5   VSMTLSPEQGLSSYLSEIRRFPMLEKDEEFMLGKRWREHEDGGAAEKLVTSHLRLVAKIA 64

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
           MGYRGYGLPI+EV+SEGN+GLMQAVKKFDP++GFRLATY+MWWI+A++QEYILRSWSLVK
Sbjct: 65  MGYRGYGLPIAEVISEGNVGLMQAVKKFDPDKGFRLATYAMWWIRASIQEYILRSWSLVK 124

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DE 184
           +GTTA QK+LFFNLRR+K  +QA+ + +LKP+QV AIA KL V+  EV+SMN RL+G D 
Sbjct: 125 MGTTAAQKKLFFNLRRMKSQMQALDEGDLKPDQVEAIATKLGVTNDEVMSMNGRLSGPDA 184

Query: 185 SLNALINSSDKNSSQWQDWLVYD-HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           SLNA +  ++    QWQDWL  D  + QE  L E +E   R  +L  +M  LN RE+ I 
Sbjct: 185 SLNAPLRGTE-GEGQWQDWLSDDTAESQEDELAESDEFDTRMQLLQSAMGELNEREQHIL 243

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + RRL E+P TLE L+  + VSRER+RQIE RAF+K+Q++++
Sbjct: 244 QERRLSEDPKTLEELAEHYGVSRERIRQIEVRAFEKLQKAMK 285


>gi|148261701|ref|YP_001235828.1| RNA polymerase factor sigma-32 [Acidiphilium cryptum JF-5]
 gi|326405194|ref|YP_004285276.1| RNA polymerase sigma factor RpoH [Acidiphilium multivorum AIU301]
 gi|146403382|gb|ABQ31909.1| RNA polymerase, sigma 32 subunit, RpoH [Acidiphilium cryptum JF-5]
 gi|325052056|dbj|BAJ82394.1| RNA polymerase sigma factor RpoH [Acidiphilium multivorum AIU301]
          Length = 296

 Score =  352 bits (903), Expect = 3e-95,   Method: Compositional matrix adjust.
 Identities = 170/277 (61%), Positives = 216/277 (77%), Gaps = 3/277 (1%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E  L+RY+ EIRK PML  +EE  LA+ +R++ D +AAH+LVTSHLRLV KIAMGYRGYG
Sbjct: 5   EGNLARYLQEIRKFPMLSPEEEDRLARAWRDNEDQAAAHKLVTSHLRLVAKIAMGYRGYG 64

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP+ E++SEGN+G+MQAVK+FDPERGFRLATY+MWWI+AA+QEYIL SWSLVK+GTTA Q
Sbjct: 65  LPLGELISEGNVGMMQAVKRFDPERGFRLATYAMWWIRAAIQEYILHSWSLVKMGTTAAQ 124

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALIN 191
           K+LFFNLRRLKG +QAI D +++PEQV  IA+ L V E +V+SMN RL A D SLNA I 
Sbjct: 125 KKLFFNLRRLKGQMQAIEDGDMQPEQVEKIARVLGVPEQDVVSMNRRLTAPDHSLNAPIR 184

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
                  +WQDWLV D D QE+ + + EE   RR +L  ++  LN RER I   RRL+++
Sbjct: 185 MD--GEGEWQDWLVDDADSQEEAIGDHEEMTGRRALLATALKTLNDRERHILIQRRLKDD 242

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           P TLE+LS ++ +SRERVRQIE RAF+K+Q+S++ QV
Sbjct: 243 PTTLEDLSQQYNISRERVRQIEVRAFEKLQKSMKAQV 279


>gi|302382389|ref|YP_003818212.1| RNA polymerase, sigma 32 subunit, RpoH [Brevundimonas subvibrioides
           ATCC 15264]
 gi|302193017|gb|ADL00589.1| RNA polymerase, sigma 32 subunit, RpoH [Brevundimonas subvibrioides
           ATCC 15264]
          Length = 295

 Score =  352 bits (903), Expect = 4e-95,   Method: Compositional matrix adjust.
 Identities = 170/282 (60%), Positives = 215/282 (76%), Gaps = 3/282 (1%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +++ E GLSRY+ EIRK PML K EE++LAKR+ EH D  +AHRLVTSHLRLV KIAMGY
Sbjct: 9   VMSPEQGLSRYLTEIRKFPMLTKDEEFMLAKRWSEHQDSESAHRLVTSHLRLVAKIAMGY 68

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           RGYGLPI EV+SEGN+GLMQAVKKFDP++GFRLATY+MWWI+A++QEYILRSWSLVK+GT
Sbjct: 69  RGYGLPIGEVISEGNVGLMQAVKKFDPDKGFRLATYAMWWIRASIQEYILRSWSLVKMGT 128

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           TA QK+LFFNLR+ K  + A  + +L+PE + AIA KL VSE EV +MN RL GD SLNA
Sbjct: 129 TAAQKKLFFNLRKAKSQISAFEEGDLRPEHLAAIATKLGVSEEEVTNMNRRLGGDASLNA 188

Query: 189 LINSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
            +       S+WQDWL  D+   QE  L + EE+  R  +L  +M  L  RE+ I   RR
Sbjct: 189 PLRVD--GESEWQDWLSDDNAVSQETALADSEEKSLRMGLLQEAMGELTEREKHILTERR 246

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           L+++PVTLE L+ ++ VSRERVRQIE RAF+K+Q++++   E
Sbjct: 247 LKDDPVTLEELAGQYGVSRERVRQIEVRAFEKLQKAMRAAAE 288


>gi|114327512|ref|YP_744669.1| RNA polymerase sigma-32 factor [Granulibacter bethesdensis CGDNIH1]
 gi|114315686|gb|ABI61746.1| RNA polymerase sigma-32 factor [Granulibacter bethesdensis CGDNIH1]
          Length = 375

 Score =  352 bits (903), Expect = 4e-95,   Method: Compositional matrix adjust.
 Identities = 169/282 (59%), Positives = 216/282 (76%), Gaps = 3/282 (1%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           I +  E  LSRY+ EIRK PML  +EE  L++R+R+  D+ AAHRLVTSHLRLV KIAMG
Sbjct: 76  IKIAPEGNLSRYLQEIRKYPMLTPEEELDLSRRWRDTEDMGAAHRLVTSHLRLVAKIAMG 135

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           YRGYGLP+ E++SEGN+G+MQAV++FDP+RGFRLATY+MWWI+AA+QEYIL SWSLVK+G
Sbjct: 136 YRGYGLPVGELISEGNVGMMQAVRRFDPDRGFRLATYAMWWIRAAIQEYILHSWSLVKMG 195

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESL 186
           TTA QK+LFFNLRRLKG +QAI D +LKPEQV  IA  LNV E +V+ MN R+ A D SL
Sbjct: 196 TTAAQKKLFFNLRRLKGQMQAIDDGDLKPEQVSKIATSLNVPEQDVVQMNRRMSAPDHSL 255

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           NA +    +   +WQDWLV D + QE VL + EE   R+ +L  ++  LN RER I   R
Sbjct: 256 NAPLRQ--EGEGEWQDWLVDDAETQETVLADTEELGGRKTLLANALKTLNDRERHILTER 313

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RL++ P TLE+LS  + +SRERVRQIE RAF+K+Q++++ +V
Sbjct: 314 RLKDEPTTLEDLSQHYNISRERVRQIEVRAFEKLQKAMKAEV 355


>gi|2384764|gb|AAC97123.1| heat shock sigma factor [Rhodobacter capsulatus]
          Length = 299

 Score =  352 bits (902), Expect = 5e-95,   Method: Compositional matrix adjust.
 Identities = 170/271 (62%), Positives = 213/271 (78%), Gaps = 2/271 (0%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GL+RY+ EIRK P+LE +EEY+LAK + +H D  AAHRLVTSHLRL  KIAMGYRGYG
Sbjct: 13  EQGLNRYLQEIRKFPLLEPEEEYMLAKAWVDHQDPKAAHRLVTSHLRLAAKIAMGYRGYG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EV+SE N+GLMQAVK+FDPERGFRLATY+MWWI+AA+QEYILRSWSLVK+GTT+ Q
Sbjct: 73  LPQAEVISEANVGLMQAVKRFDPERGFRLATYAMWWIRAAIQEYILRSWSLVKLGTTSAQ 132

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALIN 191
           K+LFFNLR+ K  + A  + +L+P+ V  IA  LNVSE +VI MN RLAG D SLNA + 
Sbjct: 133 KKLFFNLRKAKSKIGAFEEGDLRPDAVAKIAHDLNVSEGDVIEMNRRLAGSDASLNAQVG 192

Query: 192 SSD-KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           + D ++++QWQDWL  +   Q +   E +E + RR ML  +M VLN RER I  ARRL++
Sbjct: 193 AGDGESATQWQDWLEDEDADQAEAYAEADELQARRAMLVAAMDVLNERERDILMARRLRD 252

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            PVTLE LSS+++VSRER+RQIE RAF+K+Q
Sbjct: 253 EPVTLEELSSQYDVSRERIRQIEVRAFEKLQ 283


>gi|296536196|ref|ZP_06898318.1| DNA-directed RNA polymerase sigma subunit RpoH [Roseomonas
           cervicalis ATCC 49957]
 gi|296263478|gb|EFH09981.1| DNA-directed RNA polymerase sigma subunit RpoH [Roseomonas
           cervicalis ATCC 49957]
          Length = 295

 Score =  351 bits (901), Expect = 6e-95,   Method: Compositional matrix adjust.
 Identities = 167/282 (59%), Positives = 219/282 (77%), Gaps = 3/282 (1%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           I +  E  LSRY+ EIRK PML  +EE+ LAK ++EHGD  AAH+LVTSHLRLV KIAMG
Sbjct: 8   IPIAPEGNLSRYLQEIRKFPMLTPEEEFRLAKDWKEHGDQKAAHKLVTSHLRLVAKIAMG 67

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           YRGYGLP+ E++SEGN+G+MQAV++FDP+RGFRLATY+MWWI+AA+QEYIL SWSLVK+G
Sbjct: 68  YRGYGLPVGELISEGNVGMMQAVRRFDPDRGFRLATYAMWWIRAAIQEYILHSWSLVKMG 127

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESL 186
           TTA QK+LFFNLRRLKG + A+ + +L+PEQV  IA+ L V E +V+SMN RLA  D SL
Sbjct: 128 TTAAQKKLFFNLRRLKGQMAALEEGDLQPEQVEKIARVLQVPEQDVVSMNRRLASPDNSL 187

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           NA + +   +  +WQDWLV + + QE  + E+++  NRR +L  ++  LN RER I   R
Sbjct: 188 NAPVRAD--SEGEWQDWLVDESESQETEIAERQDMSNRRELLGEALKTLNERERHILIER 245

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RL++ P TLE LS ++ +SRERVRQIE RAF+K+Q+S++ Q+
Sbjct: 246 RLKDEPTTLEELSQQYNISRERVRQIEVRAFEKLQKSMKSQI 287


>gi|114763110|ref|ZP_01442536.1| RNA polymerase sigma factor [Pelagibaca bermudensis HTCC2601]
 gi|114544163|gb|EAU47172.1| RNA polymerase sigma factor [Roseovarius sp. HTCC2601]
          Length = 298

 Score =  351 bits (900), Expect = 9e-95,   Method: Compositional matrix adjust.
 Identities = 175/286 (61%), Positives = 217/286 (75%), Gaps = 5/286 (1%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GLSRY+ EIRK P+LE +EEY+LAKR+ E  D  +AHRLVTSHLRL  KIAMGYRGYG
Sbjct: 13  EAGLSRYLSEIRKFPLLEPEEEYMLAKRWVEDQDAESAHRLVTSHLRLAAKIAMGYRGYG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSWSLVK+GTT+ Q
Sbjct: 73  LPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQ 132

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALIN 191
           K+LFFNLR+ K  + A+ D +L+PE V  IA  L V+  EVISMN RL+ GD SLNA + 
Sbjct: 133 KKLFFNLRKAKSRIGALEDGDLRPEHVERIATDLGVTHDEVISMNRRLSGGDASLNATVG 192

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           S D++S QWQDWL  +   Q     E+ E + RR +LT +M VLN RER I   RRL E 
Sbjct: 193 SDDESSMQWQDWLEDESADQAGDYAERNELEARRELLTEAMDVLNERERDILTQRRLAEQ 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI----QKQVELSSS 293
           PVTLE LS  ++VSRER+RQIE RAF+K+Q+ +    Q+Q  LSS+
Sbjct: 253 PVTLEELSGVYDVSRERIRQIEVRAFEKLQKRMRDLAQEQGMLSSA 298


>gi|77462968|ref|YP_352472.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides 2.4.1]
 gi|126461842|ref|YP_001042956.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides ATCC 17029]
 gi|221638824|ref|YP_002525086.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides KD131]
 gi|332557843|ref|ZP_08412165.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides WS8N]
 gi|1769585|gb|AAC46050.1| RpoH [Rhodobacter sphaeroides]
 gi|77387386|gb|ABA78571.1| sigma factor RpoH1 (Sigma-32 group, heat shock) [Rhodobacter
           sphaeroides 2.4.1]
 gi|126103506|gb|ABN76184.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacter sphaeroides
           ATCC 17029]
 gi|221159605|gb|ACM00585.1| RNA polymerase sigma factor [Rhodobacter sphaeroides KD131]
 gi|332275555|gb|EGJ20870.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides WS8N]
          Length = 298

 Score =  351 bits (900), Expect = 9e-95,   Method: Compositional matrix adjust.
 Identities = 170/270 (62%), Positives = 212/270 (78%), Gaps = 1/270 (0%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GL+RY+ EIRK P+LE +EEY+LAKR+ +H D  AAH+LVTSHLRL  KIAMGYRGYG
Sbjct: 13  EQGLNRYMQEIRKFPLLEPEEEYMLAKRWVDHQDNRAAHKLVTSHLRLAAKIAMGYRGYG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSWSLVK+GTT+ Q
Sbjct: 73  LPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQ 132

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALIN 191
           K+LFFNLR+ K  L A+ + +L+PE V  IAK L VSE+EVI MN RL+G D SLNA I 
Sbjct: 133 KKLFFNLRKAKAKLGALEEGDLRPENVAQIAKDLGVSETEVIDMNRRLSGSDASLNATIG 192

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           S  + S+QWQDWL  +   Q     E++E + RR +L +SMSVLN RE+ I   RRL ++
Sbjct: 193 SDGEGSTQWQDWLEDEDSDQAADYAERDELEIRRELLAQSMSVLNDREKDILVQRRLTDD 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           PVTLE LS  + VSRER+RQIE RAF+K+Q
Sbjct: 253 PVTLEELSEGYGVSRERIRQIEVRAFEKLQ 282


>gi|254419521|ref|ZP_05033245.1| alternative sigma factor RpoH [Brevundimonas sp. BAL3]
 gi|196185698|gb|EDX80674.1| alternative sigma factor RpoH [Brevundimonas sp. BAL3]
          Length = 286

 Score =  350 bits (899), Expect = 1e-94,   Method: Compositional matrix adjust.
 Identities = 171/278 (61%), Positives = 212/278 (76%), Gaps = 3/278 (1%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GLSRY+ EIRK PML K EE++LAKR+ EH D  AAHRLVTSHLRLV KIAMGYRGYG
Sbjct: 4   EQGLSRYLTEIRKFPMLTKDEEFMLAKRWSEHQDPEAAHRLVTSHLRLVAKIAMGYRGYG 63

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LPI EV+SEGN+GLMQAVKKFDP++GFRLATY+MWWI+A++QEYILRSWSLVK+GTTA Q
Sbjct: 64  LPIGEVISEGNVGLMQAVKKFDPDKGFRLATYAMWWIRASIQEYILRSWSLVKMGTTAAQ 123

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
           K+LFFNLR+ K  + A  + +L PE + AIA KL VSE EV +MN RL GD SLNA + +
Sbjct: 124 KKLFFNLRKAKSQISAFEEGDLHPEHLAAIATKLGVSEEEVTNMNRRLGGDASLNAPLRA 183

Query: 193 SDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
                S+WQDWL  D    QE  L + EE+  R ++L  +M  L  RE+ I   RRL+++
Sbjct: 184 D--GESEWQDWLADDTAVSQETQLADDEEKGIRMSLLQEAMEELTDREKHILTERRLKDD 241

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           PVTLE L+ ++ VSRERVRQIE RAF+K+Q++++   E
Sbjct: 242 PVTLEELAGQYGVSRERVRQIEVRAFEKLQKAMRAAAE 279


>gi|103487228|ref|YP_616789.1| RNA polymerase factor sigma-32 [Sphingopyxis alaskensis RB2256]
 gi|98977305|gb|ABF53456.1| RNA polymerase sigma factor RpoH [Sphingopyxis alaskensis RB2256]
          Length = 300

 Score =  350 bits (899), Expect = 1e-94,   Method: Compositional matrix adjust.
 Identities = 172/290 (59%), Positives = 221/290 (76%), Gaps = 7/290 (2%)

Query: 2   NRKNMSIIV---NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHL 58
           N+ N+  +V    GE  L+RY+ EIRK P+L  ++EY+LAKR++EHGD  AA +LVTSHL
Sbjct: 3   NKSNVPAVVPALGGEASLNRYLAEIRKFPLLTPEQEYMLAKRFQEHGDNEAAAQLVTSHL 62

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLV KIAMGYRGYGLP+SE++SEGNIGLMQ VKKFDPERGFRLATY+MWWI+A++QE+IL
Sbjct: 63  RLVAKIAMGYRGYGLPVSELISEGNIGLMQGVKKFDPERGFRLATYAMWWIRASIQEFIL 122

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
           RSWSLVK+GTTA QK+LFFNLRR+K +L+A  D +L PE V  IA  L V+E EV+SMN 
Sbjct: 123 RSWSLVKMGTTAAQKKLFFNLRRMKNNLEAFEDGDLSPEHVAKIATDLGVTEDEVVSMNR 182

Query: 179 RLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
           R+A  GD SLN  +   +   SQWQD L  D   Q++ + E +ER  R ++LT ++  LN
Sbjct: 183 RMAMGGDTSLN--VPMGEDGDSQWQDLLGDDGPLQDERVAEAQERDVRHDLLTEALETLN 240

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            RER I   RRL ++P TLE+LS  ++VSRERVRQIE RAF+K+Q+++ K
Sbjct: 241 ERERHILTERRLTDDPKTLEDLSQLYDVSRERVRQIEVRAFEKLQKAMLK 290


>gi|330993273|ref|ZP_08317209.1| RNA polymerase sigma-32 factor [Gluconacetobacter sp. SXCC-1]
 gi|329759675|gb|EGG76183.1| RNA polymerase sigma-32 factor [Gluconacetobacter sp. SXCC-1]
          Length = 298

 Score =  350 bits (899), Expect = 1e-94,   Method: Compositional matrix adjust.
 Identities = 167/283 (59%), Positives = 217/283 (76%), Gaps = 3/283 (1%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           ++I   E  LS+Y+ +IRK PML  +EE  L++R+++ GD  AAH+LVTSHLRLV KIAM
Sbjct: 5   ALISGPENNLSKYLRDIRKFPMLSPEEELRLSRRWKDKGDTEAAHKLVTSHLRLVAKIAM 64

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           GYRGYGLP+ E++SEGNIG+MQAV++FDP+RGFRLATY+MWWI+AA+QEYIL SWSLVKI
Sbjct: 65  GYRGYGLPVGELISEGNIGMMQAVRRFDPDRGFRLATYAMWWIRAAIQEYILHSWSLVKI 124

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DES 185
           GTTA QK+LFFNLRRLKG +QAI D +L+PEQV  IA+ L V E +V++MN RLA  D S
Sbjct: 125 GTTAAQKKLFFNLRRLKGQMQAIDDGDLRPEQVNKIAQSLGVPEQDVVNMNRRLAAPDHS 184

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           LNA +        +WQDWLV D+D QE+ L + EE   R+ +L  ++  LN RER I   
Sbjct: 185 LNAPLRMD--GEGEWQDWLVDDNDNQEETLAQSEEYSGRQALLANALKTLNERERHILTE 242

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RRL++ P TLE+LS  + +SRERVRQIE RAF+K+Q +++ +V
Sbjct: 243 RRLKDEPATLEDLSHVYNISRERVRQIEVRAFEKLQAAMKAEV 285


>gi|260575497|ref|ZP_05843496.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacter sp. SW2]
 gi|259022417|gb|EEW25714.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacter sp. SW2]
          Length = 298

 Score =  350 bits (897), Expect = 2e-94,   Method: Compositional matrix adjust.
 Identities = 166/275 (60%), Positives = 217/275 (78%), Gaps = 1/275 (0%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GL+RY+ EIRK P+LE +EEY+LAKR+ +H D +AAH++VTSHLRL  KIAMGYRGYG
Sbjct: 13  EQGLNRYMQEIRKFPLLEPEEEYMLAKRWVDHQDATAAHKMVTSHLRLAAKIAMGYRGYG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSWSLVK+GTT+ Q
Sbjct: 73  LPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQ 132

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALIN 191
           K+LFFNLR+ K  + A+ + +L+PE V  IA  LNVSE+EVI MN RL+ GD SLNA + 
Sbjct: 133 KKLFFNLRKAKAKVGALEEGDLRPENVARIAHDLNVSETEVIDMNRRLSGGDASLNATVG 192

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           S  + S+QWQDWL  +   Q     E+ E + RR +L ++M+VLN RE+ I   RRL + 
Sbjct: 193 SDGEGSTQWQDWLEDEDSDQANDYAERNELEMRRALLVQAMAVLNDREKDILMQRRLADE 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           PVTLE+LS+ + VSRER+RQIE RAF+K+QE +++
Sbjct: 253 PVTLEDLSASYGVSRERIRQIEVRAFEKLQERMRE 287


>gi|218513990|ref|ZP_03510830.1| RNA polymerase factor sigma-32 [Rhizobium etli 8C-3]
          Length = 217

 Score =  350 bits (897), Expect = 2e-94,   Method: Compositional matrix adjust.
 Identities = 166/217 (76%), Positives = 184/217 (84%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R  +  I  GE GL+RY+ EIRK PMLE Q+EY+LAKRY EHGD  AAH+LVTSHLRL
Sbjct: 1   MARNTLPSITAGEAGLNRYLDEIRKFPMLEPQQEYMLAKRYAEHGDRDAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EVVSEGN+GLMQAVKKFDPERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLRRLKG +QAI D +LKPE V  IA KLNVSE EVISMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKLNVSEEEVISMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           +GD SLNA I +++ +S QWQDWLV DHD QE VLIE
Sbjct: 181 SGDASLNAPIKAAEGDSGQWQDWLVDDHDSQEDVLIE 217


>gi|167644630|ref|YP_001682293.1| RNA polymerase factor sigma-32 [Caulobacter sp. K31]
 gi|167347060|gb|ABZ69795.1| RNA polymerase, sigma 32 subunit, RpoH [Caulobacter sp. K31]
          Length = 295

 Score =  349 bits (895), Expect = 3e-94,   Method: Compositional matrix adjust.
 Identities = 169/280 (60%), Positives = 219/280 (78%), Gaps = 4/280 (1%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +++ + GLSRY+ EIRK PML K EE++LA+R++EH D  AAH++VTSHLRLV KIAMGY
Sbjct: 8   VMSPDGGLSRYLTEIRKFPMLPKDEEFMLAQRWKEHQDSEAAHKMVTSHLRLVAKIAMGY 67

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           RGYGLPI EV+SEGN+GLMQAVKKF+P++GFRLATY+MWWI+A++QEYILRSWSLVK+GT
Sbjct: 68  RGYGLPIGEVISEGNVGLMQAVKKFEPDKGFRLATYAMWWIRASIQEYILRSWSLVKMGT 127

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN 187
           TA QK+LFFNLR+ K  + A  D +L P+QV  IA KL V +SEVISMN RL G D SLN
Sbjct: 128 TAAQKKLFFNLRKAKSQIAAFQDGDLHPDQVSYIATKLGVLDSEVISMNRRLGGPDASLN 187

Query: 188 ALINSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           A + +     S+WQDWL  D+   QE V+ E +E+  R  +L  +M  L  RER I   R
Sbjct: 188 APLRAD--GESEWQDWLADDNQVSQETVVAENQEKSMRMTLLEEAMVELTDRERHILTER 245

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           RL+++P TLE+L++E+ VSRERVRQIE RAF+K+Q+S+++
Sbjct: 246 RLKDDPTTLEDLATEYGVSRERVRQIEVRAFEKLQKSMRE 285


>gi|329849869|ref|ZP_08264715.1| alternative sigma factor RpoH [Asticcacaulis biprosthecum C19]
 gi|328841780|gb|EGF91350.1| alternative sigma factor RpoH [Asticcacaulis biprosthecum C19]
          Length = 299

 Score =  348 bits (894), Expect = 5e-94,   Method: Compositional matrix adjust.
 Identities = 170/272 (62%), Positives = 215/272 (79%), Gaps = 3/272 (1%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           GL+RY+ EIRK PML K EE++LAKR++EH D  AAH+LVTSHLRLV KIAMGYRGYGLP
Sbjct: 23  GLNRYLSEIRKFPMLAKDEEFMLAKRWQEHQDPKAAHKLVTSHLRLVAKIAMGYRGYGLP 82

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + EV+SEGN+GLMQAVKKFD +RGFRLATY+MWWIKA++QEY+LRSWSLVK+GTTA QK+
Sbjct: 83  VGEVISEGNVGLMQAVKKFDADRGFRLATYAMWWIKASIQEYVLRSWSLVKMGTTAAQKK 142

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSS 193
           LFFNLR++K  + A+ + +L+ EQV  IA KL VSE++VI+MN R++  D SLNA I +S
Sbjct: 143 LFFNLRKVKSEISALEEGDLRHEQVEQIATKLGVSETDVINMNRRMSSPDSSLNAPIRAS 202

Query: 194 DKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
           +   S+WQDWLV D    QE VL + EE   R  +L  +M  LN RER I   RRL+++P
Sbjct: 203 E-GESEWQDWLVDDKQVSQETVLADSEEYSQRMGLLEAAMGELNAREREILTERRLKDSP 261

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TLE+L+  F VSRERVRQIE RAF+K+Q+++
Sbjct: 262 TTLEDLAERFGVSRERVRQIEVRAFEKLQKAM 293


>gi|260425792|ref|ZP_05779772.1| alternative sigma factor RpoH [Citreicella sp. SE45]
 gi|260423732|gb|EEX16982.1| alternative sigma factor RpoH [Citreicella sp. SE45]
          Length = 298

 Score =  348 bits (892), Expect = 7e-94,   Method: Compositional matrix adjust.
 Identities = 168/275 (61%), Positives = 214/275 (77%), Gaps = 1/275 (0%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GLSRY+ EIRK P+LE +EEY+LAKR+ E  D  +AH+LVTSHLRL  KIAMGYRGYG
Sbjct: 13  EAGLSRYLSEIRKFPLLEPEEEYMLAKRWVEDQDAPSAHKLVTSHLRLAAKIAMGYRGYG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSWSLVK+GTT+ Q
Sbjct: 73  LPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQ 132

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALIN 191
           K+LFFNLR+ K  + A+ + +L+PE V  IA  L VS+ EVISMN RL+ GD SLNA + 
Sbjct: 133 KKLFFNLRKAKSRIGALEEGDLRPEHVEKIATDLGVSKDEVISMNRRLSGGDASLNATVG 192

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           S D +S QWQDWL  +   Q     E+ E + RR +L ++M VLN RE+ I   RRL E 
Sbjct: 193 SDDDSSMQWQDWLEDEGADQASDYAERNELEARRALLAQAMDVLNDREKDILTQRRLAEQ 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           PVTLE+LSS ++VSRER+RQIE RAF+K+Q+ +++
Sbjct: 253 PVTLEDLSSVYDVSRERIRQIEVRAFEKLQKRMRE 287


>gi|146277611|ref|YP_001167770.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides ATCC 17025]
 gi|145555852|gb|ABP70465.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacter sphaeroides
           ATCC 17025]
          Length = 298

 Score =  348 bits (892), Expect = 7e-94,   Method: Compositional matrix adjust.
 Identities = 168/270 (62%), Positives = 211/270 (78%), Gaps = 1/270 (0%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GL+RY+ EIRK P+LE +EEY+LAKR+ +H D  AAHRLVTSHLRL  KIAMGYRGYG
Sbjct: 13  EQGLNRYMQEIRKFPLLEPEEEYMLAKRWVDHQDNRAAHRLVTSHLRLAAKIAMGYRGYG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSWSLVK+GTT+ Q
Sbjct: 73  LPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQ 132

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALIN 191
           K+LFFNLR+ K  L A+ + +L+PE V  IAK L+V+E+EVI MN RL A D SLNA I 
Sbjct: 133 KKLFFNLRKAKAKLGALEEGDLRPENVAQIAKDLSVTEAEVIDMNRRLSASDASLNATIG 192

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           S    ++QWQDWL  +   Q     E++E + RR +L ++MSVLN RE+ I   RRL ++
Sbjct: 193 SDGDGATQWQDWLEDEDSDQASDYAERDELEIRRELLAQAMSVLNDREKDILVQRRLTDD 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           PVTLE LS  + VSRER+RQIE RAF+K+Q
Sbjct: 253 PVTLEELSDGYGVSRERIRQIEVRAFEKLQ 282


>gi|84688065|ref|ZP_01015924.1| RNA polymerase sigma factor [Maritimibacter alkaliphilus HTCC2654]
 gi|84663915|gb|EAQ10420.1| RNA polymerase sigma factor [Rhodobacterales bacterium HTCC2654]
          Length = 298

 Score =  348 bits (892), Expect = 7e-94,   Method: Compositional matrix adjust.
 Identities = 165/275 (60%), Positives = 214/275 (77%), Gaps = 1/275 (0%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GL+RY+ +IRK PMLE +EEY+LAKR+ +H D  AAH+LVTSHLRL  KIAMGYRGYG
Sbjct: 13  EGGLNRYLQDIRKFPMLEPEEEYMLAKRWVDHQDTDAAHQLVTSHLRLAAKIAMGYRGYG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSWSLVK+GTT+ Q
Sbjct: 73  LPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQ 132

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALIN 191
           K+LFFNLR+ K  + A+ D +L+PE V  IA  LNV+E EVISMN R++ GD SLNA I 
Sbjct: 133 KKLFFNLRKAKARIGALEDGDLRPENVAQIAHDLNVTEEEVISMNRRMSGGDASLNATIT 192

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           +   ++ QWQDWL  +   Q     +++E   RR ML ++M VLN RE+ I   RRL + 
Sbjct: 193 NDGDSTMQWQDWLEDEDADQAGDYEQRDELTVRREMLAQAMDVLNDREKDILTQRRLSDE 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            VTLE+LS +++VSRER+RQIE RAF+K+Q+ +Q+
Sbjct: 253 TVTLEDLSGQYDVSRERIRQIEVRAFEKLQKRMQE 287


>gi|89067929|ref|ZP_01155373.1| RNA polymerase sigma factor [Oceanicola granulosus HTCC2516]
 gi|89046527|gb|EAR52583.1| RNA polymerase sigma factor [Oceanicola granulosus HTCC2516]
          Length = 297

 Score =  348 bits (892), Expect = 8e-94,   Method: Compositional matrix adjust.
 Identities = 166/275 (60%), Positives = 212/275 (77%), Gaps = 1/275 (0%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GL+RY+ EIR+ PMLE +EEY+LAKR+ +H D  AAH+LVTSHLRL  KIAMGYRGYG
Sbjct: 12  EQGLNRYLQEIRRFPMLEPEEEYMLAKRWVDHEDTDAAHKLVTSHLRLAAKIAMGYRGYG 71

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EV+SE N+GLMQAVK+FDPERGFRLATY+MWWI+A++QEYILRSWSLVK+GTT+ Q
Sbjct: 72  LPQAEVISEANVGLMQAVKRFDPERGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQ 131

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALIN 191
           K+LFFNLR+ K  + A+ + +L+PE V  IA  L V+E+EVISMN RL+ GD SLNA+I 
Sbjct: 132 KKLFFNLRKAKARIGALEEGDLRPENVAQIANDLGVTETEVISMNRRLSGGDASLNAMIG 191

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           +   +++QWQDWL  +   Q     E++E   RR +L  +M VLN RE+ I   RRLQ+ 
Sbjct: 192 TEGDSATQWQDWLEDESADQAGDYEERDELSTRRELLGEAMDVLNDREKDILTQRRLQDQ 251

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            VTLE LS ++ VSRER+RQIE RAF K+Q  +Q+
Sbjct: 252 AVTLEELSGQYGVSRERIRQIEVRAFDKLQARMQQ 286


>gi|254294740|ref|YP_003060763.1| RNA polymerase factor sigma-32 [Hirschia baltica ATCC 49814]
 gi|254043271|gb|ACT60066.1| RNA polymerase, sigma 32 subunit, RpoH [Hirschia baltica ATCC
           49814]
          Length = 295

 Score =  347 bits (890), Expect = 1e-93,   Method: Compositional matrix adjust.
 Identities = 170/288 (59%), Positives = 224/288 (77%), Gaps = 3/288 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M + + SI ++ E GLSRY+ EIRK P+LEK +E++LA R+R+H D  AA ++VTSHLRL
Sbjct: 1   MAQLSTSIALSPEQGLSRYLTEIRKYPLLEKDQEFMLANRWRDHEDPEAAEKMVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVKKFDP++GFRLATY+MWWI+A++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKKFDPDKGFRLATYAMWWIRASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTA QK+LFFNLRRLKG +QA+ + +L+PE V  IA +LNVSE+EVISMN R+
Sbjct: 121 WSLVKLGTTAAQKKLFFNLRRLKGEIQALEEGDLRPENVAEIATRLNVSETEVISMNRRM 180

Query: 181 -AGDESLNALINSSDKNSSQWQDWLVYDH-DGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
             GD SLNA I  +D +  +W DWL  D+   Q +   + +E   R ++L  +M  LN R
Sbjct: 181 TGGDASLNAPIGGADGD-GEWMDWLSDDNQQNQAEEYEQNDEFSTRMSLLETAMEGLNER 239

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E+ I   RRL++ P TLE LS+ + VSRER+RQIE RAF+K+Q+++++
Sbjct: 240 EKHIIAERRLKDEPSTLEELSAVYNVSRERIRQIEVRAFEKLQKAMKE 287


>gi|295688294|ref|YP_003591987.1| RNA polymerase sigma 32 factor subunit RpoH [Caulobacter segnis
           ATCC 21756]
 gi|295430197|gb|ADG09369.1| RNA polymerase, sigma 32 subunit, RpoH [Caulobacter segnis ATCC
           21756]
          Length = 295

 Score =  346 bits (887), Expect = 3e-93,   Method: Compositional matrix adjust.
 Identities = 168/280 (60%), Positives = 221/280 (78%), Gaps = 4/280 (1%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +++ + GLSRY+ EIRK PML K EE++LA+R++EH D  AAH++VTSHLRLV KIAMGY
Sbjct: 8   VMSPDGGLSRYLTEIRKFPMLSKDEEFMLAQRWKEHQDPQAAHKMVTSHLRLVAKIAMGY 67

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           RGYGLPI EV+SEGN+GLMQAVKKF+P++GFRLATY+MWWI+A++QEYILRSWSLVK+GT
Sbjct: 68  RGYGLPIGEVISEGNVGLMQAVKKFEPDKGFRLATYAMWWIRASIQEYILRSWSLVKMGT 127

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN 187
           TA QK+LFFNLR+ K  + A  + +L+PEQV AIA KL V +SEVISMN RL+G D SLN
Sbjct: 128 TAAQKKLFFNLRKAKSQIAAFQEGDLRPEQVSAIATKLGVLDSEVISMNRRLSGPDASLN 187

Query: 188 ALINSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           A + S   + S+WQDWL  +    QE  + E EE+  R ++L  +M  L  RER I   R
Sbjct: 188 APLRSD--SESEWQDWLADEEQVSQETRVAEDEEKSLRMSLLEEAMVELTDRERHILTER 245

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           RL+++P TLE L++++ VSRERVRQIE RAF+K+Q+++++
Sbjct: 246 RLKDDPTTLEELAAQYGVSRERVRQIEVRAFEKLQKTMRE 285


>gi|83592446|ref|YP_426198.1| RNA polymerase factor sigma-32 [Rhodospirillum rubrum ATCC 11170]
 gi|83575360|gb|ABC21911.1| Sigma 32 (RpoH) [Rhodospirillum rubrum ATCC 11170]
          Length = 299

 Score =  345 bits (886), Expect = 4e-93,   Method: Compositional matrix adjust.
 Identities = 166/277 (59%), Positives = 210/277 (75%), Gaps = 3/277 (1%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
            + +  E  L+RY+  IRK PML  +EEY LA+R R+ GD  AAHRLVTSHLRLV KIAM
Sbjct: 7   GLSIGPESNLTRYLQNIRKFPMLAPEEEYTLAQRLRDSGDSEAAHRLVTSHLRLVAKIAM 66

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           GYRGYGLP+ EV+SEGN+GLMQAVK+FDPERGFRLATY+MWWI+AA+QEYIL SWSLVK+
Sbjct: 67  GYRGYGLPMGEVISEGNVGLMQAVKRFDPERGFRLATYAMWWIRAAIQEYILHSWSLVKM 126

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DES 185
           GTTA QK+LFFNLR++KG LQ + + ++ P++V  IA KL V E +VI+MN RL+  D S
Sbjct: 127 GTTAAQKKLFFNLRKMKGQLQLMDEGDMHPDKVTQIATKLGVPEQDVINMNRRLSSPDHS 186

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           LNA +        +WQDWLV + D QE  L E +E   RR +L+ ++  LN RER I   
Sbjct: 187 LNAPVRMD--GDGEWQDWLVDESDDQETTLAESQEMGQRRALLSGALKSLNERERHILTQ 244

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           RRL+++PVTLE+LS  + +SRERVRQIE RAF+K+Q+
Sbjct: 245 RRLRDDPVTLEDLSQHYGISRERVRQIEVRAFEKLQK 281


>gi|126727088|ref|ZP_01742925.1| RNA polymerase sigma factor [Rhodobacterales bacterium HTCC2150]
 gi|126703516|gb|EBA02612.1| RNA polymerase sigma factor [Rhodobacterales bacterium HTCC2150]
          Length = 289

 Score =  345 bits (885), Expect = 5e-93,   Method: Compositional matrix adjust.
 Identities = 165/278 (59%), Positives = 211/278 (75%), Gaps = 1/278 (0%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GL+RY+ EIRK PMLE +EEY+LAK + EH D  AAHRLVTSHLRL  KIAMGYRGYG
Sbjct: 7   EQGLNRYMQEIRKFPMLEPEEEYMLAKNWVEHQDSGAAHRLVTSHLRLAAKIAMGYRGYG 66

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EVVSE N+GLMQAVKKFDPE+GFRL+TY+MWWI+A++QEY+LRSWSLVK+GTT+ Q
Sbjct: 67  LPQAEVVSEANVGLMQAVKKFDPEKGFRLSTYAMWWIRASIQEYVLRSWSLVKLGTTSAQ 126

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALIN 191
           K+LFFNLR+ K  + A+ + +L+PE V  IA  LNV+E+EVISMN R++ GD SLN  + 
Sbjct: 127 KKLFFNLRKAKNRIGALEEGDLRPENVAKIASDLNVTETEVISMNRRMSGGDASLNVQVG 186

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
              + ++QWQDWL  D   Q     +++E   RR ++ ++M+VLN RE+ I   RRLQ+ 
Sbjct: 187 GDGEGTAQWQDWLADDSADQAGDYEKQDELDTRRELMAQAMAVLNDREKEILMERRLQDK 246

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           P TLE LS  F VSRER+RQIE RAF+K+Q  ++   E
Sbjct: 247 PKTLEELSEVFSVSRERIRQIEVRAFEKLQTEMRSLAE 284


>gi|85373062|ref|YP_457124.1| RNA polymerase factor sigma-32 [Erythrobacter litoralis HTCC2594]
 gi|84786145|gb|ABC62327.1| RNA polymerase sigma-32 factor [Erythrobacter litoralis HTCC2594]
          Length = 301

 Score =  345 bits (884), Expect = 5e-93,   Method: Compositional matrix adjust.
 Identities = 164/279 (58%), Positives = 211/279 (75%), Gaps = 2/279 (0%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           + GE  L+RY+ EI+K P+L  ++EY+LAKRY+EH D  AA +LV+SHLRLV KIAMGYR
Sbjct: 12  LGGEQSLNRYLSEIKKYPVLTAEQEYMLAKRYQEHEDPEAAAQLVSSHLRLVAKIAMGYR 71

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYGLP+S+++SEGN+GLMQ VKKF+P+RGFRLATY+MWWIKA+MQE+ILRSWSLVK+GTT
Sbjct: 72  GYGLPVSDLISEGNVGLMQGVKKFEPDRGFRLATYAMWWIKASMQEFILRSWSLVKMGTT 131

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR--LAGDESLN 187
           A QK+LFFNLRR+K  L+A  D +L PE V  IA  L V E EVI+MN R  + GD SLN
Sbjct: 132 AAQKKLFFNLRRMKKQLEAYEDTDLSPEDVTKIATDLGVPEQEVINMNRRMMMGGDGSLN 191

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             + + +  S +WQDWL  D   Q++ +   EE + R  ML  +M  LN RE+ I   RR
Sbjct: 192 TPMRNGEDGSGEWQDWLTDDRPLQDETVANAEEAQVRHEMLVEAMDALNEREQHILTERR 251

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           L ENP TLE LS  ++VSRER+RQIE RAF+K+Q+++Q+
Sbjct: 252 LTENPQTLEELSQVYDVSRERIRQIEVRAFEKLQKAMQR 290


>gi|332185869|ref|ZP_08387616.1| alternative sigma factor RpoH [Sphingomonas sp. S17]
 gi|332014227|gb|EGI56285.1| alternative sigma factor RpoH [Sphingomonas sp. S17]
          Length = 301

 Score =  345 bits (884), Expect = 6e-93,   Method: Compositional matrix adjust.
 Identities = 167/279 (59%), Positives = 212/279 (75%), Gaps = 4/279 (1%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           + GE  L+RY+ EI+K P+L  ++EY+LAKR++EHGD  AA +LVTSHLRLV KIAMGYR
Sbjct: 14  LGGEQSLNRYLAEIKKFPILAPEQEYMLAKRFQEHGDPEAAAQLVTSHLRLVAKIAMGYR 73

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYGLP SE++SEGNIGLMQ VKKF+P+RGFRLATY+MWWI+A++QEYILRSWSLVK+GTT
Sbjct: 74  GYGLPTSELISEGNIGLMQGVKKFEPDRGFRLATYAMWWIRASIQEYILRSWSLVKMGTT 133

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
           A QK+LFFNLRR+K  L A  D +L+PE V  IA  L V+E EVISMN R+A  GD SLN
Sbjct: 134 AAQKKLFFNLRRMKSKLDAFEDGDLRPEDVTKIATDLGVNEDEVISMNRRMAMGGDTSLN 193

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             ++  +    QWQDWL  D   Q+ V+ E++E   R +ML  +M  LN RE+ I   RR
Sbjct: 194 --VSMREDGEGQWQDWLADDAPLQDSVVAEQQEADVRHDMLVSAMDDLNDREKHILTERR 251

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           L ++P TLE LS  + VSRERVRQIE RAF+K+Q+++ +
Sbjct: 252 LTDDPKTLEELSQVYGVSRERVRQIEVRAFEKLQKAMMR 290


>gi|84515395|ref|ZP_01002757.1| RNA polymerase sigma factor [Loktanella vestfoldensis SKA53]
 gi|84510678|gb|EAQ07133.1| RNA polymerase sigma factor [Loktanella vestfoldensis SKA53]
          Length = 303

 Score =  344 bits (883), Expect = 8e-93,   Method: Compositional matrix adjust.
 Identities = 167/270 (61%), Positives = 208/270 (77%), Gaps = 1/270 (0%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GL+RY+ EIRK PMLE +EEY+LAKR+ +H D  AAH++VTSHLRL  KIAMGYRGYG
Sbjct: 18  EGGLNRYMQEIRKFPMLEPEEEYMLAKRWVDHEDTEAAHKMVTSHLRLAAKIAMGYRGYG 77

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSWSLVK+GTT+ Q
Sbjct: 78  LPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKMGTTSAQ 137

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALIN 191
           K+LFFNLR+ K  + A+ + +L+PE V  IA  L V+E EVISMN RL+ GD SLNA I 
Sbjct: 138 KKLFFNLRKAKNRIGALEEGDLRPENVKQIANDLGVTEDEVISMNRRLSGGDASLNAQIG 197

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           S  + S QWQDWL  D         E +E   RR +L  +M++LNPRE+ I   RRL E 
Sbjct: 198 SDGEGSMQWQDWLEDDSANTAADYEEHDELDARRALLVEAMTLLNPREKDILVQRRLAEE 257

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            VTLE+LS+ +EVSRER+RQIE RAF+K+Q
Sbjct: 258 TVTLEDLSARYEVSRERIRQIEVRAFEKLQ 287


>gi|119384948|ref|YP_916004.1| RNA polymerase factor sigma-32 [Paracoccus denitrificans PD1222]
 gi|119374715|gb|ABL70308.1| RNA polymerase, sigma 32 subunit, RpoH [Paracoccus denitrificans
           PD1222]
          Length = 301

 Score =  344 bits (882), Expect = 1e-92,   Method: Compositional matrix adjust.
 Identities = 166/276 (60%), Positives = 214/276 (77%), Gaps = 2/276 (0%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GL+RY+ EIRK P+LE +EEY+LAK + +H D  AA RLVTSHLRL  KIAMGYRGYG
Sbjct: 13  EQGLNRYLQEIRKFPLLEPEEEYMLAKAWVDHQDAEAAQRLVTSHLRLAAKIAMGYRGYG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSWSLVK+GTT+ Q
Sbjct: 73  LPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKMGTTSAQ 132

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALIN 191
           K+LFFNLR+ K  L A+ + +L+PE V  IA  LNV+E EVI MN RL +GD SLNA + 
Sbjct: 133 KKLFFNLRKAKSKLGALEEGDLRPENVTQIAHDLNVTEQEVIDMNRRLSSGDASLNATVG 192

Query: 192 SSD-KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           S D ++++QWQDWL  +   Q +   E +E   RR ML  +M VLN RE+ I   RRL++
Sbjct: 193 SGDGESTAQWQDWLEDEDANQAEAFAEADELSARREMLIAAMDVLNDREKDILMERRLRD 252

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +P+TLE+LS+ + VSRER+RQIE RAF+K+Q  I++
Sbjct: 253 DPMTLEDLSTRYGVSRERIRQIEVRAFEKLQNRIRE 288


>gi|110679109|ref|YP_682116.1| RNA polymerase factor sigma-32 [Roseobacter denitrificans OCh 114]
 gi|109455225|gb|ABG31430.1| RNA polymerase sigma-32 factor [Roseobacter denitrificans OCh 114]
          Length = 298

 Score =  343 bits (881), Expect = 1e-92,   Method: Compositional matrix adjust.
 Identities = 166/283 (58%), Positives = 215/283 (75%), Gaps = 1/283 (0%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GL+RY+ EIRK P+LE QEEY+LAKR+ E  D  AAH++VTSHLRL  KIAMGYRGYG
Sbjct: 13  EGGLNRYMQEIRKFPLLEPQEEYMLAKRWVEEQDTEAAHKMVTSHLRLAAKIAMGYRGYG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSWSLVK+GTT+ Q
Sbjct: 73  LPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSGQ 132

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALIN 191
           K+LFFNLR+ K  + A+ + +L P+ V  IAK L V+E+EVISMN R++ GD SLNA + 
Sbjct: 133 KKLFFNLRKAKNKIGALEEGDLHPDNVARIAKDLGVTETEVISMNRRMSGGDASLNATVG 192

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           S  + + QWQDWL  +   Q      ++E + RR +L  +MSVLN RER I + RRL E 
Sbjct: 193 SEGEGTMQWQDWLEDEDADQAGDYEARDELEARRELLADAMSVLNDRERDILQQRRLSEQ 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSP 294
            VTLE+LS+E+ VSRER+RQIE RAF+K+Q+ ++   +    P
Sbjct: 253 TVTLEDLSAEYNVSRERIRQIEVRAFEKLQKKMRDLAKEKGMP 295


>gi|163747420|ref|ZP_02154772.1| RNA polymerase sigma factor [Oceanibulbus indolifex HEL-45]
 gi|161379273|gb|EDQ03690.1| RNA polymerase sigma factor [Oceanibulbus indolifex HEL-45]
          Length = 298

 Score =  343 bits (881), Expect = 1e-92,   Method: Compositional matrix adjust.
 Identities = 161/270 (59%), Positives = 211/270 (78%), Gaps = 1/270 (0%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GL+RY+ EIRK P+LE +EEY+LAKR+ E  D  AAHR+VTSHLRL  KIAMGYRGYG
Sbjct: 13  EGGLNRYMQEIRKFPLLEPEEEYMLAKRWVEEQDTEAAHRMVTSHLRLAAKIAMGYRGYG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSWSLVK+GTT+ Q
Sbjct: 73  LPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSGQ 132

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALIN 191
           K+LFFNLR+ K  + A+ + +L+PE V  IA +L V+E+EV+SMN R++ GD SLNA + 
Sbjct: 133 KKLFFNLRKAKNKIGALEEGDLRPENVTEIATQLGVTEAEVVSMNRRMSGGDASLNATVG 192

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           S  + + QWQDWL  +   Q     E++E + RR ML  ++ VLN RE+ I   RRL + 
Sbjct: 193 SEGEGTMQWQDWLEDEDADQAGDYAERDELETRREMLADALDVLNDREKDILTQRRLSDE 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            VTLE+LS++++VSRER+RQIE RAF+K+Q
Sbjct: 253 TVTLEDLSTQYDVSRERIRQIEVRAFEKLQ 282


>gi|89055891|ref|YP_511342.1| RNA polymerase factor sigma-32 [Jannaschia sp. CCS1]
 gi|88865440|gb|ABD56317.1| RNA polymerase, sigma 32 subunit, RpoH [Jannaschia sp. CCS1]
          Length = 298

 Score =  343 bits (881), Expect = 2e-92,   Method: Compositional matrix adjust.
 Identities = 163/275 (59%), Positives = 213/275 (77%), Gaps = 1/275 (0%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GL+RY+ EIRK PMLE +EEY+LAK + E  D  AAH++VTSHLRL  KIAMGYRGYG
Sbjct: 13  EGGLNRYLQEIRKFPMLEPEEEYMLAKAWAEKEDTEAAHKMVTSHLRLAAKIAMGYRGYG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EV+SE N+GLMQAVKKFDPE+GFRLATY+MWWI+AA+QEY+LRSWS+VK+GTT+ Q
Sbjct: 73  LPQAEVISEANVGLMQAVKKFDPEKGFRLATYAMWWIRAAIQEYVLRSWSMVKLGTTSAQ 132

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALIN 191
           K+LFFNLR+ K  + A+ + +L+PE V  IA  L V+E+EV+SMN R++ GD SLNA + 
Sbjct: 133 KKLFFNLRKAKARIGALEEGDLRPENVERIANDLGVTEAEVVSMNRRMSGGDASLNATVG 192

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           S D+ S+QWQDWL  +   Q     E++E ++R  ++  +M VLN RE+ I   RRLQE 
Sbjct: 193 SEDEGSAQWQDWLEDEDADQATDYAERDEFQSRMALMAEAMEVLNDREKDILTQRRLQEK 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            VTLE+LS  + VSRERVRQIE RAF+K+Q+ +++
Sbjct: 253 AVTLEDLSGVYNVSRERVRQIEVRAFEKLQKRMRE 287


>gi|163733965|ref|ZP_02141406.1| RNA polymerase sigma factor [Roseobacter litoralis Och 149]
 gi|161392501|gb|EDQ16829.1| RNA polymerase sigma factor [Roseobacter litoralis Och 149]
          Length = 298

 Score =  342 bits (878), Expect = 3e-92,   Method: Compositional matrix adjust.
 Identities = 165/283 (58%), Positives = 215/283 (75%), Gaps = 1/283 (0%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GL+RY+ EIRK P+LE QEEY+LAKR+ E  D  AAH++VTSHLRL  KIAMGYRGYG
Sbjct: 13  EGGLNRYMQEIRKFPLLEPQEEYMLAKRWVEEQDTEAAHKMVTSHLRLAAKIAMGYRGYG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSWSLVK+GTT+ Q
Sbjct: 73  LPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSGQ 132

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALIN 191
           K+LFFNLR+ K  + A+ + +L P+ V  IAK L V+E+EVISMN R++ GD SLNA + 
Sbjct: 133 KKLFFNLRKAKNKIGALEEGDLHPDNVARIAKDLGVTETEVISMNRRMSGGDASLNATVG 192

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           S  + + QWQDWL  +   Q      ++E + RR +L  +MSVLN RE+ I + RRL E 
Sbjct: 193 SEGEGTMQWQDWLEDEGADQAGDYEARDELEARRELLADAMSVLNDREKDILQQRRLSEK 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSP 294
            VTLE+LS+E+ VSRER+RQIE RAF+K+Q+ ++   +    P
Sbjct: 253 TVTLEDLSAEYNVSRERIRQIEVRAFEKLQKKMRDLAKEKGMP 295


>gi|326386899|ref|ZP_08208513.1| RNA polymerase factor sigma-32 [Novosphingobium nitrogenifigens DSM
           19370]
 gi|326208579|gb|EGD59382.1| RNA polymerase factor sigma-32 [Novosphingobium nitrogenifigens DSM
           19370]
          Length = 300

 Score =  342 bits (876), Expect = 5e-92,   Method: Compositional matrix adjust.
 Identities = 169/291 (58%), Positives = 220/291 (75%), Gaps = 7/291 (2%)

Query: 1   MNRKNMSIIV---NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSH 57
           M+ +N ++ V   +GE  L+RY+ EIRK P+L  ++EY+LAKRY+EHGD  AA +LVTSH
Sbjct: 1   MSEQNKALSVPALSGEASLNRYLTEIRKFPLLTAEQEYMLAKRYQEHGDPQAAAQLVTSH 60

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLV KIAMGYRGYGLP+SE++SEGNIGLMQ VKKFDP+RGFRLATY+MWWIKA++QE+I
Sbjct: 61  LRLVAKIAMGYRGYGLPVSELISEGNIGLMQGVKKFDPDRGFRLATYAMWWIKASIQEFI 120

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           LRSWSLVK+GTTA QK+LFFNLRR+K +L+A  D++L P+ V  IA  L V E++V+SMN
Sbjct: 121 LRSWSLVKMGTTAAQKKLFFNLRRMKKNLEAFEDSDLHPDDVKKIATDLGVPEADVVSMN 180

Query: 178 CR--LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
            R  + GD SLN  +    + S  WQDWL  +   Q++ + + EE + R ++L  +M  L
Sbjct: 181 RRMMMGGDASLNVPLREDGEGS--WQDWLADERPLQDEAVADAEEAQVRHDLLVEAMQDL 238

Query: 236 NPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           N RER I   RRL + P TLE LS  + VSRERVRQIE RAF+K+Q++IQ+
Sbjct: 239 NDRERHILIDRRLVDEPKTLEELSQVYHVSRERVRQIEVRAFEKLQKAIQR 289


>gi|16127328|ref|NP_421892.1| RNA polymerase factor sigma-32 [Caulobacter crescentus CB15]
 gi|221236131|ref|YP_002518568.1| RNA polymerase factor sigma-32 [Caulobacter crescentus NA1000]
 gi|13424754|gb|AAK25060.1| heat shock sigma factor RpoH [Caulobacter crescentus CB15]
 gi|220965304|gb|ACL96660.1| RNA polymerase sigma-32 factor [Caulobacter crescentus NA1000]
          Length = 298

 Score =  342 bits (876), Expect = 6e-92,   Method: Compositional matrix adjust.
 Identities = 166/280 (59%), Positives = 218/280 (77%), Gaps = 4/280 (1%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +++ + GLSRY+ EIRK PML K EE++LA+R++EH D  AAH++VTSHLRLV KIAMGY
Sbjct: 11  VMSPDGGLSRYLTEIRKFPMLSKDEEFMLAQRWKEHQDPQAAHKMVTSHLRLVAKIAMGY 70

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           RGYGLPI EV+SEGN+GLMQAVKKF+PE+GFRLATY+MWWI+A++QEYILRSWSLVK+GT
Sbjct: 71  RGYGLPIGEVISEGNVGLMQAVKKFEPEKGFRLATYAMWWIRASIQEYILRSWSLVKMGT 130

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN 187
           TA QK+LFFNLR+ K  + A  + +L P+QV  IA KL V +SEVISMN RL+G D SLN
Sbjct: 131 TAAQKKLFFNLRKAKSQIAAFQEGDLHPDQVSQIATKLGVLDSEVISMNRRLSGPDASLN 190

Query: 188 ALINSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           A + +     S+WQDWL  +    QE  + E EE+  R ++L  +M  L  RER I   R
Sbjct: 191 APLRAD--GESEWQDWLADEEQVSQETRVAEDEEKSLRMSLLEEAMVELTDRERHILTER 248

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           RL+++P TLE L++++ VSRERVRQIE RAF+K+Q+++++
Sbjct: 249 RLKDDPTTLEELAAQYGVSRERVRQIEVRAFEKLQKTMRE 288


>gi|310815299|ref|YP_003963263.1| alternative sigma factor RpoH [Ketogulonicigenium vulgare Y25]
 gi|308754034|gb|ADO41963.1| alternative sigma factor RpoH [Ketogulonicigenium vulgare Y25]
          Length = 298

 Score =  341 bits (875), Expect = 7e-92,   Method: Compositional matrix adjust.
 Identities = 162/275 (58%), Positives = 210/275 (76%), Gaps = 1/275 (0%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GLSRY+ EIRK PMLE ++EY+LA+ + +HGD  AAH+LVTSHLRL  KIAMGYRGYG
Sbjct: 13  EQGLSRYLQEIRKFPMLEPEQEYMLARNWVDHGDTQAAHKLVTSHLRLAAKIAMGYRGYG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSWSLVK+GTT+ Q
Sbjct: 73  LPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQ 132

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALIN 191
           K+LFFNLR+ K  + A+ + +L+PE V  IA  L V E EV++MN RL+ GD SLNA++ 
Sbjct: 133 KKLFFNLRKAKARIGALEEGDLRPEHVQRIAHDLGVPEEEVVNMNRRLSGGDASLNAMVG 192

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             D +S+QWQDWL  +   Q      ++E   RR +L  +M  LN RER +   RRLQ+ 
Sbjct: 193 GDDDSSTQWQDWLEDEDSDQAADFEARDELDARRVLLEAAMEDLNDRERDVLMMRRLQDP 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           PVTLE LS ++ VSRER+RQIE RAF+K+Q+ + +
Sbjct: 253 PVTLEELSEKYSVSRERIRQIEVRAFEKLQKRMTQ 287


>gi|254441831|ref|ZP_05055324.1| alternative sigma factor RpoH [Octadecabacter antarcticus 307]
 gi|198251909|gb|EDY76224.1| alternative sigma factor RpoH [Octadecabacter antarcticus 307]
          Length = 298

 Score =  341 bits (874), Expect = 8e-92,   Method: Compositional matrix adjust.
 Identities = 159/274 (58%), Positives = 211/274 (77%), Gaps = 1/274 (0%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GL+RY+ EIRK PMLE  EEY+LAKR+ +H D  AAH++VTSHLRL  KIAMGYRGYG
Sbjct: 13  EQGLNRYMQEIRKFPMLEPDEEYMLAKRWVDHEDTDAAHKMVTSHLRLAAKIAMGYRGYG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEY+LRSWS+VK+GTT+ Q
Sbjct: 73  LPTAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYVLRSWSMVKLGTTSAQ 132

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALIN 191
           K+LFFNLR+ K  + A+ + +L+PE V  IA  L V+E+EV+SMN R++ GD SLNA + 
Sbjct: 133 KKLFFNLRKAKNRIGALEEGDLRPENVQRIANDLGVTEAEVVSMNRRMSGGDASLNATVG 192

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           S  + + QWQDWL  +   Q     +++E + RR ++  +M VLN RE+ I   RRL E 
Sbjct: 193 SDGEGTMQWQDWLEDESADQAGDYEDRDELQQRRELMAEAMDVLNDREKDILMQRRLAEK 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            VTLE+LS ++ VSRER+RQIE RAF+K+Q+ +Q
Sbjct: 253 TVTLEDLSGQYSVSRERIRQIEVRAFEKLQKKMQ 286


>gi|239977584|sp|P0CAW9|RP32_CAUCR RecName: Full=RNA polymerase sigma-32 factor
 gi|239977655|sp|B8H3C3|RP32_CAUCN RecName: Full=RNA polymerase sigma-32 factor
 gi|1262200|gb|AAC43981.1| RpoH [Caulobacter vibrioides]
 gi|1588870|prf||2209377A heat shock sigma factor 32
          Length = 295

 Score =  341 bits (874), Expect = 8e-92,   Method: Compositional matrix adjust.
 Identities = 166/280 (59%), Positives = 218/280 (77%), Gaps = 4/280 (1%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +++ + GLSRY+ EIRK PML K EE++LA+R++EH D  AAH++VTSHLRLV KIAMGY
Sbjct: 8   VMSPDGGLSRYLTEIRKFPMLSKDEEFMLAQRWKEHQDPQAAHKMVTSHLRLVAKIAMGY 67

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           RGYGLPI EV+SEGN+GLMQAVKKF+PE+GFRLATY+MWWI+A++QEYILRSWSLVK+GT
Sbjct: 68  RGYGLPIGEVISEGNVGLMQAVKKFEPEKGFRLATYAMWWIRASIQEYILRSWSLVKMGT 127

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN 187
           TA QK+LFFNLR+ K  + A  + +L P+QV  IA KL V +SEVISMN RL+G D SLN
Sbjct: 128 TAAQKKLFFNLRKAKSQIAAFQEGDLHPDQVSQIATKLGVLDSEVISMNRRLSGPDASLN 187

Query: 188 ALINSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           A + +     S+WQDWL  +    QE  + E EE+  R ++L  +M  L  RER I   R
Sbjct: 188 APLRAD--GESEWQDWLADEEQVSQETRVAEDEEKSLRMSLLEEAMVELTDRERHILTER 245

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           RL+++P TLE L++++ VSRERVRQIE RAF+K+Q+++++
Sbjct: 246 RLKDDPTTLEELAAQYGVSRERVRQIEVRAFEKLQKTMRE 285


>gi|148552989|ref|YP_001260571.1| RNA polymerase factor sigma-32 [Sphingomonas wittichii RW1]
 gi|148498179|gb|ABQ66433.1| RNA polymerase sigma factor RpoH [Sphingomonas wittichii RW1]
          Length = 301

 Score =  341 bits (874), Expect = 8e-92,   Method: Compositional matrix adjust.
 Identities = 170/279 (60%), Positives = 210/279 (75%), Gaps = 4/279 (1%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           + GE  L+RY+ EIRK P+L  +EEY+LAKR++EHGD  AA RLVTSHLRLV KIAMGYR
Sbjct: 14  LGGEQSLNRYLAEIRKFPLLTAEEEYMLAKRFQEHGDPEAATRLVTSHLRLVAKIAMGYR 73

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYGLP SE++SEGNIGLMQ VKKF+P+RGFRLATY+MWWIKA++QEYILRSWSLVK+GTT
Sbjct: 74  GYGLPASELISEGNIGLMQGVKKFEPDRGFRLATYAMWWIKASIQEYILRSWSLVKMGTT 133

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
           A QK+LFFNLRR+K  L+A  D +LKPE +  IA  L VSE EV SMN R++  GD SLN
Sbjct: 134 AAQKKLFFNLRRMKSQLEAFEDGDLKPEDLKKIATDLGVSEEEVTSMNRRMSMGGDASLN 193

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             +N  +    +WQD LV     Q++ L E EE+  R NML  +++ LN RE+ I   RR
Sbjct: 194 VSMN--EDGEGEWQDMLVDQGPLQDERLAEVEEKSVRHNMLNEALAALNDREKHILVERR 251

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           L + P TLE LS  + VSRERVRQIE RAF K+Q+++ +
Sbjct: 252 LVDEPKTLEELSQVYGVSRERVRQIEVRAFDKLQKAMMR 290


>gi|159045149|ref|YP_001533943.1| RNA polymerase factor sigma-32 [Dinoroseobacter shibae DFL 12]
 gi|157912909|gb|ABV94342.1| RNA polymerase [Dinoroseobacter shibae DFL 12]
          Length = 298

 Score =  341 bits (874), Expect = 8e-92,   Method: Compositional matrix adjust.
 Identities = 164/274 (59%), Positives = 213/274 (77%), Gaps = 1/274 (0%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GL+RY+ EIRK PMLE +EEY+LAKR+ +H D  AAH++VTSHLRL  KIAMGYRGYG
Sbjct: 13  EQGLNRYLQEIRKFPMLEPEEEYMLAKRWVDHEDTEAAHKMVTSHLRLAAKIAMGYRGYG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSWSLVK+GTT+ Q
Sbjct: 73  LPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQ 132

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALIN 191
           K+LFFNLR+ K  + A+ + +L+PE V  IA  LNV+E EVISMN R++ GD SLNA+I 
Sbjct: 133 KKLFFNLRKAKNRIGALEEGDLRPENVARIANDLNVTEDEVISMNRRMSGGDASLNAMIG 192

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           S  + +++WQDWL  +   Q     EK+E   RR +L  +M VLN RE+ I   RRL++ 
Sbjct: 193 SDGEGATEWQDWLEDEDADQADDFAEKDELMVRRELLAEAMGVLNDREKDILMKRRLEDK 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           P TLE LS  + VSRER+RQIE RAF+K+Q++++
Sbjct: 253 PATLEELSEVYGVSRERIRQIEVRAFEKLQKAMR 286


>gi|126729201|ref|ZP_01745015.1| RNA polymerase sigma factor [Sagittula stellata E-37]
 gi|126710191|gb|EBA09243.1| RNA polymerase sigma factor [Sagittula stellata E-37]
          Length = 298

 Score =  341 bits (874), Expect = 9e-92,   Method: Compositional matrix adjust.
 Identities = 164/270 (60%), Positives = 207/270 (76%), Gaps = 1/270 (0%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GLSRY+ EIRK P+LE ++EY+LAKR+ E  D  AAH+LVTSHLRL  KIAMGYRGYG
Sbjct: 13  EAGLSRYLQEIRKFPLLEPEQEYMLAKRWVEDEDTQAAHQLVTSHLRLAAKIAMGYRGYG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSWSLVK+GTT+ Q
Sbjct: 73  LPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQ 132

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALIN 191
           K+LFFNLR+ K  + A+ D +L+PE V  IA  L V++ EVISMN RL+ GD SLNA + 
Sbjct: 133 KKLFFNLRKAKSRIGALEDGDLRPEHVEKIATDLGVTQDEVISMNRRLSGGDASLNATVG 192

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           S  + + QWQDWL  +   Q     E+ E + RR +L ++M VLN RER I   RRL + 
Sbjct: 193 SEGEGTMQWQDWLEDEDADQAGEYAERNELEARRALLEQAMDVLNDRERDILSQRRLSDQ 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            VTLE LS +++VSRER+RQIE RAF+K+Q
Sbjct: 253 AVTLEELSGQYDVSRERIRQIEVRAFEKLQ 282


>gi|254462386|ref|ZP_05075802.1| alternative sigma factor RpoH [Rhodobacterales bacterium HTCC2083]
 gi|206678975|gb|EDZ43462.1| alternative sigma factor RpoH [Rhodobacteraceae bacterium HTCC2083]
          Length = 298

 Score =  340 bits (873), Expect = 1e-91,   Method: Compositional matrix adjust.
 Identities = 163/271 (60%), Positives = 210/271 (77%), Gaps = 1/271 (0%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GL+RY+ EIRK PMLE +EEY+LAK + E  D +AAH++VTSHLRL  KIAMGYRGYG
Sbjct: 13  EGGLNRYMQEIRKFPMLEPEEEYMLAKSWVEKQDTAAAHKMVTSHLRLAAKIAMGYRGYG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EVVSE N+GLMQAVK+FDPE+GFRL+TY+MWWI+AA+QEYILRSWSLVK+GTT+ Q
Sbjct: 73  LPQAEVVSEANVGLMQAVKRFDPEKGFRLSTYAMWWIRAAIQEYILRSWSLVKLGTTSAQ 132

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALIN 191
           K+LFFNLR+ K  + A+ + +++PE V  IA  L V+E+EVISMN R++ GD SLNA + 
Sbjct: 133 KKLFFNLRKAKNRIGALEEGDMRPENVARIAHDLGVTETEVISMNRRMSGGDASLNAQVG 192

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           S  + + QWQDWL  +   Q      ++E + RR ML  +M VLN RE+ I   RRL + 
Sbjct: 193 SEGEGTMQWQDWLEDEDADQAGDYEARDELEARREMLADAMDVLNDREKDILVQRRLSDK 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           PVTLE+LS +++VSRER+RQIE RAF+K+QE
Sbjct: 253 PVTLEDLSGQYDVSRERIRQIEVRAFEKLQE 283


>gi|99080404|ref|YP_612558.1| RNA polymerase factor sigma-32 [Ruegeria sp. TM1040]
 gi|99036684|gb|ABF63296.1| RNA polymerase, sigma 32 subunit, RpoH [Ruegeria sp. TM1040]
          Length = 299

 Score =  340 bits (873), Expect = 1e-91,   Method: Compositional matrix adjust.
 Identities = 167/287 (58%), Positives = 216/287 (75%), Gaps = 4/287 (1%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GL+RY+ EIRK P+LE +EEY+LAKR+ E  D  AAH++VTSHLRL  KIAMGYRGYG
Sbjct: 13  EGGLNRYLQEIRKFPLLEPEEEYMLAKRWVEEQDTEAAHKMVTSHLRLAAKIAMGYRGYG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSWSLVK+GTT+ Q
Sbjct: 73  LPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQ 132

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALIN 191
           K+LFFNLR+ K  + A+ D +L+PE V  IA  L V+E EVISMN R++ GD SLNA++ 
Sbjct: 133 KKLFFNLRKAKARIGALEDGDLRPEVVKKIATDLGVTEDEVISMNRRMSGGDASLNAMVG 192

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           S   ++ QWQDWL  +   Q      ++E + RR +L  +MSVLN RE+ I   RRL E 
Sbjct: 193 SDGDSTMQWQDWLEDEDADQAGDYEARDELQARRELLAEAMSVLNDREKDILTQRRLAEQ 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQ 298
             TLE LS +++VSRER+RQIE RAF+K+Q   +K  EL++   +LQ
Sbjct: 253 AKTLEELSVQYDVSRERIRQIEVRAFEKLQ---KKMRELAAGKGMLQ 296


>gi|149202313|ref|ZP_01879286.1| RNA polymerase sigma factor [Roseovarius sp. TM1035]
 gi|149144411|gb|EDM32442.1| RNA polymerase sigma factor [Roseovarius sp. TM1035]
          Length = 298

 Score =  340 bits (873), Expect = 1e-91,   Method: Compositional matrix adjust.
 Identities = 162/270 (60%), Positives = 209/270 (77%), Gaps = 1/270 (0%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GL+RY+ EIRK P+LE +EEY+LAKR+ E  D  AAH++VTSHLRL  KIAMGYRGYG
Sbjct: 13  EGGLNRYMQEIRKFPLLEPEEEYMLAKRWAEEQDTEAAHKMVTSHLRLAAKIAMGYRGYG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EV+SE N+GLMQAVK+FDPERGFRLATY+MWWI+A++QEYILRSWSLVK+GTT+ Q
Sbjct: 73  LPQAEVISEANVGLMQAVKRFDPERGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQ 132

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALIN 191
           K+LFFNLR+ K  + A+ + +++P+ V  IA  L V+E+EVISMN R+AG D SLNA + 
Sbjct: 133 KKLFFNLRKAKAKIGALEEGDMRPDVVKKIATDLGVTEAEVISMNQRMAGADASLNATVG 192

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           +  + S QWQDWL  +   Q      ++E   RR +L ++M VLN RER I   RRL + 
Sbjct: 193 AEGEGSMQWQDWLEDEDADQAGDYERRDELDARRELLVQAMDVLNERERDILTQRRLSDE 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            VTLE+LS+E++VSRER+RQIE RAF+K+Q
Sbjct: 253 TVTLEDLSAEYDVSRERIRQIEVRAFEKLQ 282


>gi|85707639|ref|ZP_01038705.1| RNA polymerase sigma factor [Erythrobacter sp. NAP1]
 gi|85689173|gb|EAQ29176.1| RNA polymerase sigma factor [Erythrobacter sp. NAP1]
          Length = 298

 Score =  340 bits (872), Expect = 2e-91,   Method: Compositional matrix adjust.
 Identities = 161/279 (57%), Positives = 212/279 (75%), Gaps = 2/279 (0%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++GE  L+RY+ EI+K P+L  ++EY+LAKRY EH D  AA +LV+SHLRLV KIAMGYR
Sbjct: 9   LSGEQSLNRYLSEIKKYPVLTAEQEYMLAKRYAEHEDPEAASQLVSSHLRLVAKIAMGYR 68

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYGLP+S+++SEGN+GLMQ VKKF+P+RGFRLATY+MWWIKA++QEYILRSWSLVK+GTT
Sbjct: 69  GYGLPVSDLISEGNVGLMQGVKKFEPDRGFRLATYAMWWIKASIQEYILRSWSLVKMGTT 128

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR--LAGDESLN 187
           A QK+LFFNLRR+K  L+A  D++L P+ V  IA  L V E EV++MN R  + GD SLN
Sbjct: 129 AAQKKLFFNLRRMKKQLEAYEDSDLHPDDVTKIATDLGVPEQEVVNMNRRMMMGGDGSLN 188

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             + + +  S +WQDWL  D   Q++ + + EE + R  ML  +M  LN RE+ I   RR
Sbjct: 189 TPMRNGEDGSGEWQDWLTDDRPLQDETVADAEEAEVRHEMLVEAMDSLNEREQHILTERR 248

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           L E P TLE LS  ++VSRER+RQIE RAF+K+Q+++Q+
Sbjct: 249 LTEKPQTLEELSQVYDVSRERIRQIEVRAFEKLQKAMQR 287


>gi|83941135|ref|ZP_00953597.1| RNA polymerase sigma factor [Sulfitobacter sp. EE-36]
 gi|83846955|gb|EAP84830.1| RNA polymerase sigma factor [Sulfitobacter sp. EE-36]
          Length = 298

 Score =  340 bits (871), Expect = 2e-91,   Method: Compositional matrix adjust.
 Identities = 162/270 (60%), Positives = 209/270 (77%), Gaps = 1/270 (0%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GL+RY+ EIRK P+LE +EEY+LAKR+ E  D  AAHR+VTSHLRL  KIAMGYRGYG
Sbjct: 13  EGGLNRYMQEIRKFPLLEPEEEYMLAKRWVEEQDTEAAHRMVTSHLRLAAKIAMGYRGYG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSWSLVK+GTT+ Q
Sbjct: 73  LPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSGQ 132

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALIN 191
           K+LFFNLR+ K  + A+ + +L P+ V  IA  L V+E+EVISMN R++ GD SLNA + 
Sbjct: 133 KKLFFNLRKAKNRIGALEEGDLHPDNVKRIATDLGVTETEVISMNRRMSGGDASLNATVG 192

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           S  + + QWQDWL  +   Q     E++E + RR ML  ++ VLN RE+ I   RRL + 
Sbjct: 193 SEGEGTMQWQDWLEDEDADQATDYEERDELETRREMLAEALDVLNDREKDILTQRRLSDQ 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            VTLE+LSS+++VSRER+RQIE RAF+K+Q
Sbjct: 253 TVTLEDLSSQYDVSRERIRQIEVRAFEKLQ 282


>gi|1184690|gb|AAB01724.1| RNA polymerase sigma 32 subunit [Caulobacter crescentus CB15]
          Length = 295

 Score =  339 bits (870), Expect = 2e-91,   Method: Compositional matrix adjust.
 Identities = 166/280 (59%), Positives = 217/280 (77%), Gaps = 4/280 (1%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +++ + GLSRY+ EIRK PML K EE++LA+R++EH D  AAH++VTSHLRLV KIAMGY
Sbjct: 8   VMSPDGGLSRYLTEIRKFPMLSKDEEFMLAQRWKEHQDPQAAHKMVTSHLRLVAKIAMGY 67

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           RGYGLPI EV+SEGN+GLMQAVKKF+PE+GFRLATY+MWWI+A++QEYILRSWSLVK+GT
Sbjct: 68  RGYGLPIGEVISEGNVGLMQAVKKFEPEKGFRLATYAMWWIRASIQEYILRSWSLVKMGT 127

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN 187
           TA QK+LFFNLR+ K  + A  + +L P+QV  IA KL V +SEVISMN RL+G D SLN
Sbjct: 128 TAAQKKLFFNLRKAKSQIAAFQEGDLHPDQVSQIATKLGVLDSEVISMNRRLSGPDASLN 187

Query: 188 ALINSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           A +       S+WQDWL  +    QE  + E EE+  R ++L  +M  L  RER I   R
Sbjct: 188 APLRRD--GESEWQDWLADEEQVSQETRVAEDEEKSLRMSLLEEAMVELTDRERHILTER 245

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           RL+++P TLE L++++ VSRERVRQIE RAF+K+Q+++++
Sbjct: 246 RLKDDPTTLEELAAQYGVSRERVRQIEVRAFEKLQKTMRE 285


>gi|254453399|ref|ZP_05066836.1| alternative sigma factor RpoH [Octadecabacter antarcticus 238]
 gi|198267805|gb|EDY92075.1| alternative sigma factor RpoH [Octadecabacter antarcticus 238]
          Length = 298

 Score =  339 bits (869), Expect = 3e-91,   Method: Compositional matrix adjust.
 Identities = 159/274 (58%), Positives = 209/274 (76%), Gaps = 1/274 (0%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GL+RY+ EIRK PMLE  EEY+LAKR+ +H D  AAH++VTSHLRL  KIAMGYRGYG
Sbjct: 13  EQGLNRYMQEIRKFPMLEPDEEYMLAKRWVDHEDTEAAHKMVTSHLRLAAKIAMGYRGYG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEY+LRSWS+VK+GTT+ Q
Sbjct: 73  LPTAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYVLRSWSMVKLGTTSAQ 132

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALIN 191
           K+LFFNLR+ K  + A+ + +L+PE V  IA  L V+E+EV+SMN R++ GD SLNA + 
Sbjct: 133 KKLFFNLRKAKNRIGALEEGDLRPENVQRIATDLGVTEAEVVSMNRRMSGGDASLNATVG 192

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           S  + + QWQDWL  +   Q      ++E   RR ++  +M VLN RE+ I   RRL E 
Sbjct: 193 SDGEGTMQWQDWLEDESADQAGDYEARDELTQRRELMAEAMEVLNDREKDILMQRRLAEK 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            VTLE+LS ++ VSRER+RQIE RAF+K+Q+ +Q
Sbjct: 253 TVTLEDLSGQYSVSRERIRQIEVRAFEKLQKKMQ 286


>gi|126733180|ref|ZP_01748927.1| RNA polymerase sigma-32 factor [Roseobacter sp. CCS2]
 gi|126716046|gb|EBA12910.1| RNA polymerase sigma-32 factor [Roseobacter sp. CCS2]
          Length = 298

 Score =  339 bits (869), Expect = 3e-91,   Method: Compositional matrix adjust.
 Identities = 162/275 (58%), Positives = 210/275 (76%), Gaps = 1/275 (0%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GL+RY+ EIRK PMLE ++EY+LAKR+ +H D  AAH++VTSHLRL  KIAMGYRGYG
Sbjct: 13  EGGLNRYMQEIRKFPMLEPEQEYMLAKRWVDHEDTDAAHQMVTSHLRLAAKIAMGYRGYG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSWSLVK+GTT+ Q
Sbjct: 73  LPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQ 132

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALIN 191
           K+LFFNLR+ K  + A+ D +L+PE V  IA  L V+E EVISMN RL+ GD SLNA ++
Sbjct: 133 KKLFFNLRKAKNRIGALEDGDLRPENVERIANDLGVTEQEVISMNRRLSGGDASLNATVS 192

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           +  + ++QWQDWL  +           +E   RR +L  +M VLN RE+ I   RRL E 
Sbjct: 193 ADGEGAAQWQDWLEDESANTAADYEASDELTARRELLAEAMEVLNDREKDILMQRRLSEE 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            VTLE+LS +++VSRER+RQIE RAF+K+Q  +Q+
Sbjct: 253 TVTLEDLSGQYDVSRERIRQIEVRAFEKLQAKMQE 287


>gi|260434077|ref|ZP_05788048.1| alternative sigma factor RpoH [Silicibacter lacuscaerulensis
           ITI-1157]
 gi|260417905|gb|EEX11164.1| alternative sigma factor RpoH [Silicibacter lacuscaerulensis
           ITI-1157]
          Length = 298

 Score =  338 bits (868), Expect = 4e-91,   Method: Compositional matrix adjust.
 Identities = 166/286 (58%), Positives = 215/286 (75%), Gaps = 2/286 (0%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N KN+ +    E GL+RY+ EIRK P+LE +EEY+LAKR+ E  D  AAH+LVTSHLRL 
Sbjct: 3   NYKNLPVPTP-EGGLNRYLQEIRKFPLLEPEEEYMLAKRWVEDHDTEAAHKLVTSHLRLA 61

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            KIAMGYRGYGLP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSW
Sbjct: 62  AKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSW 121

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
           SLVK+GTT+ QK+LFFNLR+ K  + A+ D +L P+ V  IA  L V+E EVISMN R++
Sbjct: 122 SLVKLGTTSAQKKLFFNLRKAKARIGALEDGDLHPDNVKQIAHDLGVTEDEVISMNRRMS 181

Query: 182 -GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA + S  + + QWQDWL  +   Q      +EE + RR +L  ++ VLN RE+
Sbjct: 182 GGDASLNATVGSEGEGTMQWQDWLEDESADQAGDYETREELEVRRELLAEALEVLNDREK 241

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            I   RRL + PVTLE LSS++ VSRER+RQIE RAF+K+Q+ +++
Sbjct: 242 DILTQRRLMDQPVTLEELSSQYNVSRERIRQIEVRAFEKLQKKMRE 287


>gi|149187051|ref|ZP_01865358.1| RNA polymerase sigma factor [Erythrobacter sp. SD-21]
 gi|148829340|gb|EDL47784.1| RNA polymerase sigma factor [Erythrobacter sp. SD-21]
          Length = 319

 Score =  338 bits (867), Expect = 6e-91,   Method: Compositional matrix adjust.
 Identities = 161/278 (57%), Positives = 211/278 (75%), Gaps = 2/278 (0%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           + GE  L+RY+ EI+K P+L +++EY+LAKRY EHGD  AA +LVTSHLRLV KIAMGYR
Sbjct: 30  LGGEQSLNRYLSEIKKFPILTQEQEYMLAKRYEEHGDSEAAAQLVTSHLRLVSKIAMGYR 89

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYGLP+S+++SEGN+GLMQ VKKF+ +RGFRLATY+MWWIKA++QEYILRSWSLVK+GTT
Sbjct: 90  GYGLPVSDLISEGNVGLMQGVKKFEADRGFRLATYAMWWIKASIQEYILRSWSLVKMGTT 149

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR--LAGDESLN 187
           A QK+LFFNLRR+K +L A  D +L P+ V  IA  L V E EV++MN R  + GD SLN
Sbjct: 150 AAQKKLFFNLRRMKKNLDAYEDTDLHPDDVQKIATDLGVPEQEVVNMNRRMMMGGDGSLN 209

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             + + ++ S +W DWL  D   Q++ + + EE++ R  ML  +M  LN RE+ I   RR
Sbjct: 210 VPMRNGEEGSGEWMDWLTDDRPLQDETVADAEEKEVRHEMLGEAMEALNEREQHILTERR 269

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L ENP TLE LS  + VSRER+RQIE RAF+K+Q++++
Sbjct: 270 LTENPQTLEELSQVYNVSRERIRQIEVRAFEKLQKAMK 307


>gi|259417918|ref|ZP_05741837.1| alternative sigma factor RpoH [Silicibacter sp. TrichCH4B]
 gi|259346824|gb|EEW58638.1| alternative sigma factor RpoH [Silicibacter sp. TrichCH4B]
          Length = 298

 Score =  338 bits (866), Expect = 7e-91,   Method: Compositional matrix adjust.
 Identities = 165/287 (57%), Positives = 215/287 (74%), Gaps = 4/287 (1%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GL+RY+ EIRK P+LE +EEY+LAKR+ E  D  AAH++VTSHLRL  KIAMGYRGYG
Sbjct: 13  EGGLNRYLQEIRKFPLLEPEEEYMLAKRWVEEQDTEAAHKMVTSHLRLAAKIAMGYRGYG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSWSLVK+GTT+ Q
Sbjct: 73  LPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQ 132

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALIN 191
           K+LFFNLR+ K  + A+ D +L+PE V  IA  L V+E EVISMN R++ GD SLNA++ 
Sbjct: 133 KKLFFNLRKAKARIGALEDGDLRPEAVKKIATDLGVTEDEVISMNRRMSGGDASLNAMVG 192

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
               ++ QWQDWL  +   Q      ++E + RR +L  +MSVLN RE+ I   RRL + 
Sbjct: 193 GDGDSTMQWQDWLEDEGADQAGDYEAQDELQARRELLAEAMSVLNDREKDILTQRRLADQ 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQ 298
             TLE LS +++VSRER+RQIE RAF+K+Q   +K  EL++   +LQ
Sbjct: 253 AKTLEELSVQYDVSRERIRQIEVRAFEKLQ---KKMRELAAGKGMLQ 296


>gi|87201057|ref|YP_498314.1| RNA polymerase factor sigma-32 [Novosphingobium aromaticivorans DSM
           12444]
 gi|87136738|gb|ABD27480.1| RNA polymerase, sigma 32 subunit, RpoH [Novosphingobium
           aromaticivorans DSM 12444]
          Length = 299

 Score =  338 bits (866), Expect = 8e-91,   Method: Compositional matrix adjust.
 Identities = 164/279 (58%), Positives = 211/279 (75%), Gaps = 4/279 (1%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           + GE  L+RY+ EIRK P+L  ++EY+LAKR++EH D  AA +LVTSHLRLV KIAMGYR
Sbjct: 13  LGGEASLNRYLSEIRKFPVLTAEQEYMLAKRFQEHQDPEAAAQLVTSHLRLVAKIAMGYR 72

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYGLP+SE++SEGNIGLMQ VKKF+P+RGFRLATY+MWWIKA+MQE+ILRSWSLVK+GTT
Sbjct: 73  GYGLPVSELISEGNIGLMQGVKKFEPDRGFRLATYAMWWIKASMQEFILRSWSLVKMGTT 132

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR--LAGDESLN 187
           A QK+LFFNLRR+K +L+A  D++L P+ V  IA  L V E EV++MN R  + GD SLN
Sbjct: 133 AAQKKLFFNLRRMKKNLEAFEDSDLHPDDVRKIATDLGVPEQEVVNMNRRMMMGGDASLN 192

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             ++  +     WQDWL  D   Q++ + + EE + R  +L  +M  LN RER I   RR
Sbjct: 193 --VSMREDGEGSWQDWLTDDRPLQDETVADAEEAQYRHELLVEAMESLNERERHILTDRR 250

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           L ++P TLE LS  + VSRERVRQIE RAF+K+Q++IQ+
Sbjct: 251 LIDDPKTLEELSQVYNVSRERVRQIEVRAFEKLQKAIQR 289


>gi|85704966|ref|ZP_01036066.1| RNA polymerase sigma factor [Roseovarius sp. 217]
 gi|85670288|gb|EAQ25149.1| RNA polymerase sigma factor [Roseovarius sp. 217]
          Length = 279

 Score =  337 bits (865), Expect = 1e-90,   Method: Compositional matrix adjust.
 Identities = 161/263 (61%), Positives = 203/263 (77%), Gaps = 1/263 (0%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           + EIRK P+LE +EEY+LAKR+ E  D  AAH++VTSHLRL  KIAMGYRGYGLP +EV+
Sbjct: 1   MQEIRKFPLLEPEEEYMLAKRWVEEQDTEAAHKMVTSHLRLAAKIAMGYRGYGLPQAEVI 60

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
           SE N+GLMQAVK+FDPERGFRLATY+MWWI+A++QEYILRSWSLVK+GTT+ QK+LFFNL
Sbjct: 61  SEANVGLMQAVKRFDPERGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQKKLFFNL 120

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSS 198
           R+ K  + A+ D +++PE V  IA  L V+E+EVISMN R+AG D SLNA + S  + S 
Sbjct: 121 RKAKAKIGALEDGDMRPEVVKKIATDLGVTEAEVISMNQRMAGADASLNATVGSEGEGSM 180

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           QWQDWL  +   Q      ++E   RR +LT +M VLN RER I   RRL +  VTLE+L
Sbjct: 181 QWQDWLEDEDADQAGDYERRDEMDARRELLTMAMDVLNERERDILTQRRLSDETVTLEDL 240

Query: 259 SSEFEVSRERVRQIEARAFKKVQ 281
           S+E++VSRER+RQIE RAF+K+Q
Sbjct: 241 SAEYDVSRERIRQIEVRAFEKLQ 263


>gi|255263634|ref|ZP_05342976.1| alternative sigma factor RpoH [Thalassiobium sp. R2A62]
 gi|255105969|gb|EET48643.1| alternative sigma factor RpoH [Thalassiobium sp. R2A62]
          Length = 298

 Score =  337 bits (864), Expect = 1e-90,   Method: Compositional matrix adjust.
 Identities = 162/275 (58%), Positives = 212/275 (77%), Gaps = 1/275 (0%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GL+RY+ EIRK PMLE +EEY+LAK + E+ D  +AH+LVTSHLRL  KIAMGYRGYG
Sbjct: 13  EQGLNRYLQEIRKFPMLEPEEEYMLAKSWVENEDSKSAHKLVTSHLRLAAKIAMGYRGYG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EV+SE N+GLMQAVKKFDPE+GFRL+TY+MWWI+AA+QEY+LRSWS+VK+GTT+ Q
Sbjct: 73  LPQAEVISEANVGLMQAVKKFDPEKGFRLSTYAMWWIRAAIQEYVLRSWSMVKLGTTSAQ 132

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALIN 191
           K+LFFNLR+ K  + A+ D +L+PE V  IA  L V+E EVI+MN RL+ GD SLNA + 
Sbjct: 133 KKLFFNLRKAKSRIGALEDGDLRPEHVERIANDLGVNEQEVINMNRRLSGGDASLNAQVG 192

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           S  + + QWQDWL  +   Q      K+E  +RR +L  +MSVLN RE+ I   RRLQ+ 
Sbjct: 193 SEGEGTMQWQDWLEDEDADQAGDYEAKDELDSRRELLADAMSVLNDREKDILMQRRLQDK 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +TLE LS +++VSRER+RQIE RAF+K+Q+ +++
Sbjct: 253 AITLEELSGQYDVSRERIRQIEVRAFEKLQKKMRE 287


>gi|262277481|ref|ZP_06055274.1| alternative sigma factor RpoH [alpha proteobacterium HIMB114]
 gi|262224584|gb|EEY75043.1| alternative sigma factor RpoH [alpha proteobacterium HIMB114]
          Length = 300

 Score =  337 bits (864), Expect = 1e-90,   Method: Compositional matrix adjust.
 Identities = 164/281 (58%), Positives = 213/281 (75%), Gaps = 2/281 (0%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +++ +     Y+ +IRK PML+  EEY+LAK +RE GD  +AH+LVTSHLRLV KIA GY
Sbjct: 12  VLSPDGSFDSYLQKIRKFPMLDAAEEYILAKNWREKGDKESAHKLVTSHLRLVAKIATGY 71

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           RGYGLP+SE+VSEGNIGLM AVKKFDPERGFRLATY+MWWIKA+MQEYILRSWSLVKIGT
Sbjct: 72  RGYGLPMSELVSEGNIGLMTAVKKFDPERGFRLATYAMWWIKASMQEYILRSWSLVKIGT 131

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLN 187
           TA QK+LFFNLR++K  +      +L PEQV  IA +L+V+E EV SM+ R+ G E SLN
Sbjct: 132 TAAQKKLFFNLRKMKNQIMRSDQTDLLPEQVTEIANRLDVTEDEVNSMDQRMKGPEASLN 191

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           A I S ++  S+WQDW+V ++  QE  +  ++E   R+ +L ++MS+LN RE+ I   RR
Sbjct: 192 ATI-SGEEGESEWQDWVVDENADQELQIAHRQETNKRKALLDKAMSILNEREKEILFDRR 250

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           L E P TLE LS ++ +SRER+RQIE RAF+K+Q+ + +Q 
Sbjct: 251 LNEEPKTLEELSQKYNISRERIRQIENRAFEKLQKEMLEQA 291


>gi|94497521|ref|ZP_01304090.1| sigma 32 (RpoH) [Sphingomonas sp. SKA58]
 gi|94422938|gb|EAT07970.1| sigma 32 (RpoH) [Sphingomonas sp. SKA58]
          Length = 310

 Score =  336 bits (862), Expect = 2e-90,   Method: Compositional matrix adjust.
 Identities = 165/290 (56%), Positives = 216/290 (74%), Gaps = 6/290 (2%)

Query: 1   MNRKNMSII--VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHL 58
           M + N+  +  + GE  L+RY+ EIRK P+L  ++EY+LAKRY+EH D  AA +LVTSHL
Sbjct: 8   MAKSNVPAVPALGGEASLNRYLSEIRKFPLLTPEQEYMLAKRYQEHQDPEAAAQLVTSHL 67

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLV KIAMGYRGYGLP+SE++SEGNIGLMQ VKKF+ +RGFRLATY+MWWI+A++QE+IL
Sbjct: 68  RLVAKIAMGYRGYGLPVSELISEGNIGLMQGVKKFEADRGFRLATYAMWWIRASIQEFIL 127

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
           RSWSLVK+GTTA QK+LFFNLRR+K +++A  D +L+PE V  IA  L VSE +VISMN 
Sbjct: 128 RSWSLVKMGTTAAQKKLFFNLRRMKNNIEAFEDGDLRPEDVTKIATDLGVSEDDVISMNR 187

Query: 179 RLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
           R+A  GD SLN  +   +    QWQDWL      Q++ + +++E+  R +ML  +M  LN
Sbjct: 188 RMAMGGDTSLN--VPMREDGEGQWQDWLADTDPLQDERVADEQEKVQRHDMLVEAMDDLN 245

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            RE+ I   RRL E P TLE LS  + VSRERVRQIE RAF+K+Q+++ +
Sbjct: 246 DREKHILAERRLAEEPKTLEELSQVYGVSRERVRQIEVRAFEKLQKAMMR 295


>gi|330814385|ref|YP_004358624.1| RNA polymerase sigma factor RpoH [Candidatus Pelagibacter sp.
           IMCC9063]
 gi|327487480|gb|AEA81885.1| RNA polymerase sigma factor RpoH [Candidatus Pelagibacter sp.
           IMCC9063]
          Length = 300

 Score =  336 bits (861), Expect = 3e-90,   Method: Compositional matrix adjust.
 Identities = 163/273 (59%), Positives = 212/273 (77%), Gaps = 2/273 (0%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E   S Y+ +IRK PML+  EEYVLAK +RE GD  AAH+LVTSHLRLV KIAMGYRGYG
Sbjct: 16  EGSFSSYLSKIRKFPMLDAAEEYVLAKNWREQGDKDAAHKLVTSHLRLVAKIAMGYRGYG 75

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP+SE+VSEGNIGLMQAV+KFDPE+GFRLATY+MWWIKA++QEY+LRSWSLVKIGTT+ Q
Sbjct: 76  LPVSELVSEGNIGLMQAVRKFDPEKGFRLATYAMWWIKASIQEYVLRSWSLVKIGTTSAQ 135

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALIN 191
           K+LFFNL+++K  + A    N+ PE +  IA +L+V E EV+SMN RLAG E SLNA + 
Sbjct: 136 KKLFFNLKKIKNQIFAAEQGNMLPEHITEIATQLDVREDEVVSMNQRLAGHEHSLNAPVG 195

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             D + ++WQDW+V ++  QE  + +K+E   R+++L  ++ VL+ RE+ I   RRL + 
Sbjct: 196 GEDSD-AEWQDWVVDENADQELQISQKQELNQRQSLLKNALHVLDEREKEILHNRRLIDE 254

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           P TLE LS + +VSRER+RQIE RAF+KVQ+++
Sbjct: 255 PKTLEELSQKHKVSRERIRQIENRAFEKVQKAM 287


>gi|254464548|ref|ZP_05077959.1| alternative sigma factor RpoH [Rhodobacterales bacterium Y4I]
 gi|206685456|gb|EDZ45938.1| alternative sigma factor RpoH [Rhodobacterales bacterium Y4I]
          Length = 298

 Score =  336 bits (861), Expect = 3e-90,   Method: Compositional matrix adjust.
 Identities = 159/275 (57%), Positives = 212/275 (77%), Gaps = 1/275 (0%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GL+RY+ EIRK P+LE +EEY+LAKR+ E  D ++AH++VTSHLRL  KIAMGYRGYG
Sbjct: 13  EGGLNRYLQEIRKFPLLEPEEEYMLAKRWVEEQDAASAHKMVTSHLRLAAKIAMGYRGYG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSWSLVK+GTT+ Q
Sbjct: 73  LPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQ 132

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALIN 191
           K+LFFNLR+ K  + A+ D +L+PE V  IA  L V+E EVISMN R++ GD SLNA + 
Sbjct: 133 KKLFFNLRKAKARIGALEDGDLRPENVKRIATDLGVTEDEVISMNRRMSGGDASLNATVG 192

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           S  + + QWQDWL  +   Q      ++E + RR +L  ++ VLN RE+ I   RRL + 
Sbjct: 193 SEGEGTMQWQDWLEDEDADQAGDYEARDELEARRELLAEALDVLNDREKDILTQRRLMDQ 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            VTLE+LS+++ VSRER+RQIE RAF+K+Q+ +++
Sbjct: 253 AVTLEDLSAQYNVSRERIRQIEVRAFEKLQKKMRE 287


>gi|84500884|ref|ZP_00999119.1| RNA polymerase sigma factor [Oceanicola batsensis HTCC2597]
 gi|84390951|gb|EAQ03369.1| RNA polymerase sigma factor [Oceanicola batsensis HTCC2597]
          Length = 298

 Score =  335 bits (859), Expect = 5e-90,   Method: Compositional matrix adjust.
 Identities = 159/270 (58%), Positives = 208/270 (77%), Gaps = 1/270 (0%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GL+RY+ EIRK P+LE +EEY+LAKR+ E  D  AAH++VTSHLRL  KIAMGYRGYG
Sbjct: 13  EGGLNRYLQEIRKFPLLEPEEEYMLAKRWVEEQDTEAAHKMVTSHLRLAAKIAMGYRGYG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSWSLVK+GTT+ Q
Sbjct: 73  LPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQ 132

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALIN 191
           K+LFFNLR+ K  + A+ + +L P+ V  IA  L V+E+EVISMN R++ GD SLNA + 
Sbjct: 133 KKLFFNLRKAKARIGALEEGDLHPDNVKQIANDLGVTEAEVISMNRRMSGGDASLNATVG 192

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
              +++ +WQDWL  +   Q     E++E  +RR +L  +M+VLN RER I   RRL E 
Sbjct: 193 MDAESAMEWQDWLEDEEADQAGDYAERDEMDSRRELLAEAMAVLNDRERDILTQRRLSEE 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +TLE+LS ++ VSRER+RQIE RAF+K+Q
Sbjct: 253 TITLEDLSEQYGVSRERIRQIEVRAFEKLQ 282


>gi|83859148|ref|ZP_00952669.1| RNA polymerase sigma factor [Oceanicaulis alexandrii HTCC2633]
 gi|83852595|gb|EAP90448.1| RNA polymerase sigma factor [Oceanicaulis alexandrii HTCC2633]
          Length = 296

 Score =  334 bits (857), Expect = 7e-90,   Method: Compositional matrix adjust.
 Identities = 169/291 (58%), Positives = 221/291 (75%), Gaps = 4/291 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M     ++ ++ E GLSRY+ EIRK PMLEK +E++LAKR++EH D  AAH+LVTSHLRL
Sbjct: 1   MANMKTALTMSPEAGLSRYLAEIRKFPMLEKDQEFMLAKRWQEHEDSDAAHQLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI+EV+SEGN+GLMQAVKKFDP++GFRLATY+MWWI+A++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIAEVISEGNVGLMQAVKKFDPDKGFRLATYAMWWIRASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTA QK+LFFNLRR+K  ++A+ + +L+P+QV  IA KL V++ +VISMN RL
Sbjct: 121 WSLVKMGTTAAQKKLFFNLRRMKSQMRALDEGDLRPDQVEEIATKLGVTDDDVISMNRRL 180

Query: 181 AG-DESLNALINSSDKNSSQWQDW-LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           +G D SLNA + +     ++WQDW    D D  E  L E +E   R  +L  +M  LN R
Sbjct: 181 SGPDASLNAPMRAD--GEAEWQDWLADDDADDAEDELAESDEFSMRMTLLQEAMGALNER 238

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           E+ I + RRL E P TLE+L+  + VSRER+RQIE RAF+K+Q  +++  E
Sbjct: 239 EQNIIQERRLTEEPKTLEDLAQVYGVSRERIRQIEVRAFEKLQNEMKRLAE 289


>gi|307293092|ref|ZP_07572938.1| RNA polymerase, sigma 32 subunit, RpoH [Sphingobium
           chlorophenolicum L-1]
 gi|306881158|gb|EFN12374.1| RNA polymerase, sigma 32 subunit, RpoH [Sphingobium
           chlorophenolicum L-1]
          Length = 304

 Score =  333 bits (854), Expect = 2e-89,   Method: Compositional matrix adjust.
 Identities = 162/279 (58%), Positives = 210/279 (75%), Gaps = 4/279 (1%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           + GE  L+RY+ EIRK P+L  ++EY+LAKRY EH D  AA +LVTSHLRLV KIAMGYR
Sbjct: 13  LGGEASLNRYLSEIRKFPILTPEQEYMLAKRYAEHADSEAAAQLVTSHLRLVAKIAMGYR 72

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYGLP+SE++SEGNIGLMQ VKKF+P+RGFRLATY+MWWI+A++QE+ILRSWSLVK+GTT
Sbjct: 73  GYGLPVSELISEGNIGLMQGVKKFEPDRGFRLATYAMWWIRASIQEFILRSWSLVKMGTT 132

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
           A QK+LFFNLRR+K +++A  D +L P+ V  IA  L V+E +VISMN R+A  GD SLN
Sbjct: 133 AAQKKLFFNLRRMKNNIEAFEDGDLHPDDVKKIATDLGVTEEDVISMNRRMAMGGDTSLN 192

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             +   +    QWQDWL      Q++ + +++E + R +ML  +M  LN RE+ I   RR
Sbjct: 193 --VPMREDGEGQWQDWLADTDPLQDERVADRQESELRHDMLVEAMDDLNDREKHILAERR 250

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           L E P TLE LS  + VSRERVRQIE RAF+K+Q+++ +
Sbjct: 251 LAEEPKTLEELSQVYGVSRERVRQIEVRAFEKLQKAMMR 289


>gi|126738732|ref|ZP_01754428.1| RNA polymerase sigma factor [Roseobacter sp. SK209-2-6]
 gi|126719913|gb|EBA16620.1| RNA polymerase sigma factor [Roseobacter sp. SK209-2-6]
          Length = 298

 Score =  333 bits (854), Expect = 2e-89,   Method: Compositional matrix adjust.
 Identities = 163/288 (56%), Positives = 214/288 (74%), Gaps = 4/288 (1%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GL+RY+ EIRK P+LE +EEY+LAK + E  D  AAH++VTSHLRL  KIAMGYRGYG
Sbjct: 13  EGGLNRYMQEIRKFPLLEPEEEYMLAKAWVEKEDTGAAHKMVTSHLRLAAKIAMGYRGYG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSWSLVK+GTT+ Q
Sbjct: 73  LPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQ 132

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALIN 191
           K+LFFNLR+ K  + A+ + +L+PE V  IA  L V+E EVISMN R++ GD SLNA + 
Sbjct: 133 KKLFFNLRKAKARIGALEEGDLRPENVAQIAHDLGVTEEEVISMNRRMSGGDASLNATVG 192

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           S  + + QWQDWL  +   Q      ++E + RR +L ++M VLN RE+ I   RRL + 
Sbjct: 193 SEGEGTMQWQDWLEDEDADQAGDYEARDELEARRELLVQAMEVLNDREKDILTQRRLSDQ 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQK 299
             TLE+LS E+ VSRER+RQIE RAF+K+Q   +K  +L+S   +L +
Sbjct: 253 ATTLEDLSGEYGVSRERIRQIEVRAFEKLQ---KKMRDLASEKGMLAR 297


>gi|254511947|ref|ZP_05124014.1| alternative sigma factor RpoH [Rhodobacteraceae bacterium KLH11]
 gi|221535658|gb|EEE38646.1| alternative sigma factor RpoH [Rhodobacteraceae bacterium KLH11]
          Length = 298

 Score =  333 bits (854), Expect = 2e-89,   Method: Compositional matrix adjust.
 Identities = 158/275 (57%), Positives = 211/275 (76%), Gaps = 1/275 (0%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GL+RY+ EIRK P+LE +EEY+LAKR+ E  D  AAH++VTSHLRL  KIAMGYRGYG
Sbjct: 13  EGGLNRYMQEIRKFPLLEPEEEYMLAKRWVEEQDTEAAHKMVTSHLRLAAKIAMGYRGYG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EV+SE N+GLMQAVKKFDPE+GFRLATY+MWWI+A++QEY+LRSWS+VK+GTT+ Q
Sbjct: 73  LPQAEVISEANVGLMQAVKKFDPEKGFRLATYAMWWIRASIQEYVLRSWSMVKLGTTSAQ 132

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALIN 191
           K+LFFNLR+ K  + A+ + +L+PE V  IA+ L V+E EVISMN R++ GD SLNA + 
Sbjct: 133 KKLFFNLRKAKARIGALEEGDLRPENVARIAEDLGVTEEEVISMNRRMSGGDASLNATVG 192

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           S  + + QWQDWL  +   Q      ++E + RR +L  ++ VLN RE+ I   RRL + 
Sbjct: 193 SEGEGTMQWQDWLEDEDADQAGDYEARDELEARRELLAAALDVLNDREKDILTQRRLMDQ 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            VTLE LS+++ VSRER+RQIE RAF+K+Q+ +++
Sbjct: 253 VVTLEELSTQYNVSRERIRQIEVRAFEKLQKKMRE 287


>gi|86137868|ref|ZP_01056444.1| RNA polymerase sigma factor [Roseobacter sp. MED193]
 gi|85825460|gb|EAQ45659.1| RNA polymerase sigma factor [Roseobacter sp. MED193]
          Length = 298

 Score =  333 bits (854), Expect = 2e-89,   Method: Compositional matrix adjust.
 Identities = 163/286 (56%), Positives = 215/286 (75%), Gaps = 4/286 (1%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GL+RY+ EIRK P+LE +EEY+LAK + E  D  AAHR+VTSHLRL  KIAMGYRGYG
Sbjct: 13  EGGLNRYMQEIRKFPLLEPEEEYMLAKAWVEKEDSGAAHRMVTSHLRLAAKIAMGYRGYG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEY+LRSWS+VK+GTT+ Q
Sbjct: 73  LPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYVLRSWSMVKLGTTSAQ 132

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALIN 191
           K+LFFNLR+ K  + A+ + +L+PE V  IA  L V+E EVISMN R++ GD SLNA + 
Sbjct: 133 KKLFFNLRKAKARIGALEEGDLRPENVAKIAHDLGVTEDEVISMNRRMSGGDASLNATVG 192

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           S  + + QWQDWL  +   Q      ++E + RR +L +++ VLN RE+ I   RRL EN
Sbjct: 193 SEGEGTMQWQDWLEDEDADQAGDYEARDELEARRELLGQALEVLNDREKDILTKRRLAEN 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLL 297
             TLE LS+++ VSRER+RQIE RAF+K+Q   +K  EL+S+  +L
Sbjct: 253 VQTLEELSAQYSVSRERIRQIEVRAFEKLQ---KKMRELASAKGML 295


>gi|296284608|ref|ZP_06862606.1| RNA polymerase factor sigma-32 [Citromicrobium bathyomarinum JL354]
          Length = 280

 Score =  333 bits (853), Expect = 2e-89,   Method: Compositional matrix adjust.
 Identities = 158/269 (58%), Positives = 205/269 (76%), Gaps = 2/269 (0%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           + EI+K P+L  ++EY+LAKRY EH D  AA +LV+SHLRLV KIAMGYRGYGLP+S+++
Sbjct: 1   MSEIKKFPVLTAEQEYMLAKRYEEHEDPEAAAQLVSSHLRLVAKIAMGYRGYGLPVSDLI 60

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
           SEGN+GLMQ VKKF+P+RGFRLATY+MWWIKA++QEYILRSWSLVK+GTTA QK+LFFNL
Sbjct: 61  SEGNVGLMQGVKKFEPDRGFRLATYAMWWIKASIQEYILRSWSLVKMGTTAAQKKLFFNL 120

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR--LAGDESLNALINSSDKNS 197
           RR+K +L A  D +L P+ V  IA  L V E EVI+MN R  + GD SLN  +   ++N+
Sbjct: 121 RRMKKNLDAYEDTDLHPDDVKKIATDLGVPEQEVINMNRRMLMGGDSSLNVSMRGDEENA 180

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           SQWQDWL  D   Q++   + +E + R  ML  +M  LN RE+ I   RRL E+P TLE 
Sbjct: 181 SQWQDWLTDDRPLQDETTADTQEAQVRHAMLLEAMDSLNDREKHILTERRLTEDPQTLEE 240

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LS  ++VSRER+RQIE RAF+K+Q+++Q+
Sbjct: 241 LSKVYDVSRERIRQIEVRAFEKLQKAMQR 269


>gi|294011928|ref|YP_003545388.1| RNA polymerase sigma-32 factor [Sphingobium japonicum UT26S]
 gi|292675258|dbj|BAI96776.1| RNA polymerase sigma-32 factor [Sphingobium japonicum UT26S]
          Length = 304

 Score =  332 bits (852), Expect = 3e-89,   Method: Compositional matrix adjust.
 Identities = 162/279 (58%), Positives = 210/279 (75%), Gaps = 4/279 (1%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           + GE  L+RY+ EIRK P+L  ++EY+LAKRY EH D  AA +LVTSHLRLV KIAMGYR
Sbjct: 13  LGGEASLNRYLSEIRKFPILTPEQEYMLAKRYAEHQDSEAAAQLVTSHLRLVAKIAMGYR 72

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYGLP+SE++SEGNIGLMQ VKKF+P+RGFRLATY+MWWI+A++QE+ILRSWSLVK+GTT
Sbjct: 73  GYGLPVSELISEGNIGLMQGVKKFEPDRGFRLATYAMWWIRASIQEFILRSWSLVKMGTT 132

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
           A QK+LFFNLRR+K +++A  D +L P+ V  IA  L V+E +VISMN R+A  GD SLN
Sbjct: 133 AAQKKLFFNLRRMKNNIEAFEDGDLHPDDVKKIATDLGVTEEDVISMNRRMAMGGDTSLN 192

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             +   +    QWQDWL      Q++ + +++E + R +ML  +M  LN RE+ I   RR
Sbjct: 193 --VPMREDGEGQWQDWLADSDPLQDERVADRQESELRHDMLVEAMDDLNDREKHILAERR 250

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           L E P TLE LS  + VSRERVRQIE RAF+K+Q+++ +
Sbjct: 251 LAEEPKTLEELSQVYGVSRERVRQIEVRAFEKLQKAMMR 289


>gi|56696293|ref|YP_166650.1| RNA polymerase factor sigma-32 [Ruegeria pomeroyi DSS-3]
 gi|56678030|gb|AAV94696.1| RNA polymerase sigma-32 factor [Ruegeria pomeroyi DSS-3]
          Length = 298

 Score =  332 bits (852), Expect = 3e-89,   Method: Compositional matrix adjust.
 Identities = 160/276 (57%), Positives = 213/276 (77%), Gaps = 3/276 (1%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GL+RY+ EIRK P+LE +EEY+LAKR+ E  D  +AH++VTSHLRL  KIAMGYRGYG
Sbjct: 13  EGGLNRYMQEIRKFPLLEPEEEYMLAKRWVEEQDAESAHKMVTSHLRLAAKIAMGYRGYG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+AA+QEYILRSWSLVK+GTT+ Q
Sbjct: 73  LPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRAAIQEYILRSWSLVKLGTTSAQ 132

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALIN 191
           K+LFFNLR+ K  + A+ + +L+PE V  IA  L VSE +VISMN R++ GD SLNA + 
Sbjct: 133 KKLFFNLRKAKAKIGALEEGDLRPENVARIAHDLGVSEDDVISMNRRMSGGDASLNATVG 192

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIE-KEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           S  + + QWQDWL  D D  +    E ++E + RR +L  ++ VLN RE+ +   RRL +
Sbjct: 193 SEGEGTMQWQDWL-EDEDADQAADYEARDELEARRELLASALDVLNEREKDVLTQRRLLD 251

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             VTLE+LS+++ VSRER+RQIE RAF+K+Q+ +++
Sbjct: 252 QTVTLEDLSAQYNVSRERIRQIEVRAFEKLQKRMRE 287


>gi|83955694|ref|ZP_00964274.1| RNA polymerase sigma factor [Sulfitobacter sp. NAS-14.1]
 gi|83839988|gb|EAP79164.1| RNA polymerase sigma factor [Sulfitobacter sp. NAS-14.1]
          Length = 279

 Score =  331 bits (848), Expect = 1e-88,   Method: Compositional matrix adjust.
 Identities = 157/263 (59%), Positives = 203/263 (77%), Gaps = 1/263 (0%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           + EIRK P+LE +EEY+LAKR+ E  D  AAHR+VTSHLRL  KIAMGYRGYGLP +EV+
Sbjct: 1   MQEIRKFPLLEPEEEYMLAKRWVEEQDTEAAHRMVTSHLRLAAKIAMGYRGYGLPQAEVI 60

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
           SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSWSLVK+GTT+ QK+LFFNL
Sbjct: 61  SEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSGQKKLFFNL 120

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALINSSDKNSS 198
           R+ K  + A+ + +L P+ V  IA  L V+E+EVISMN R++ GD SLNA + S  + + 
Sbjct: 121 RKAKNRIGALEEGDLHPDNVKRIATDLGVTETEVISMNRRMSGGDASLNATVGSEGEGTM 180

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           QWQDWL  +   Q     E++E + RR ML  ++ VLN RE+ I   RRL +  VTLE+L
Sbjct: 181 QWQDWLEDEDADQATDYEERDELETRREMLAEALDVLNDREKDILTQRRLSDQTVTLEDL 240

Query: 259 SSEFEVSRERVRQIEARAFKKVQ 281
           SS+++VSRER+RQIE RAF+K+Q
Sbjct: 241 SSQYDVSRERIRQIEVRAFEKLQ 263


>gi|56551645|ref|YP_162484.1| RNA polymerase factor sigma-32 [Zymomonas mobilis subsp. mobilis
           ZM4]
 gi|241761228|ref|ZP_04759316.1| RNA polymerase, sigma 32 subunit, RpoH [Zymomonas mobilis subsp.
           mobilis ATCC 10988]
 gi|260752767|ref|YP_003225660.1| RNA polymerase factor sigma-32 [Zymomonas mobilis subsp. mobilis
           NCIMB 11163]
 gi|59803027|sp|P50512|RP32_ZYMMO RecName: Full=RNA polymerase sigma-32 factor
 gi|56543219|gb|AAV89373.1| RNA polymerase, sigma 32 subunit, RpoH [Zymomonas mobilis subsp.
           mobilis ZM4]
 gi|241374135|gb|EER63632.1| RNA polymerase, sigma 32 subunit, RpoH [Zymomonas mobilis subsp.
           mobilis ATCC 10988]
 gi|258552130|gb|ACV75076.1| RNA polymerase, sigma 32 subunit, RpoH [Zymomonas mobilis subsp.
           mobilis NCIMB 11163]
          Length = 302

 Score =  330 bits (847), Expect = 1e-88,   Method: Compositional matrix adjust.
 Identities = 172/290 (59%), Positives = 215/290 (74%), Gaps = 7/290 (2%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           + G+  L+ Y+ +IRK P+L+ +EEY+LAKR++EH D  AA RLVTSHLRLV KIAMGYR
Sbjct: 14  LGGDQSLNHYLADIRKFPILKPEEEYMLAKRFQEHQDPKAASRLVTSHLRLVAKIAMGYR 73

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYGLP+SE++SEGNIGLMQ VKKFDPERGFRLATY++WWIKA++QEYILRSWSLVK+GTT
Sbjct: 74  GYGLPVSELISEGNIGLMQGVKKFDPERGFRLATYAIWWIKASIQEYILRSWSLVKMGTT 133

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
           A QK+LFFNLRRLK ++ A  D +LKP++V +IA  L VS  EV++MN R+A  GD SLN
Sbjct: 134 AAQKKLFFNLRRLKSNMNAFEDGDLKPDEVDSIATNLGVSNEEVVNMNRRMAMGGDSSLN 193

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +    Q QDWLV     Q+Q + E+EE   R  +L  +M  LN RE+ I   RR
Sbjct: 194 --ITMREDGEGQMQDWLVDQEPLQDQQIEEEEESLVRHKLLIEAMDKLNDREKHILTERR 251

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLL 297
           L +NP TLE LS  + VSRERVRQIE RAF K+Q++I   +EL+    LL
Sbjct: 252 LSDNPKTLEELSQVYGVSRERVRQIEVRAFDKLQKAI---MELAGDRKLL 298


>gi|83949442|ref|ZP_00958175.1| RNA polymerase sigma factor [Roseovarius nubinhibens ISM]
 gi|83837341|gb|EAP76637.1| RNA polymerase sigma factor [Roseovarius nubinhibens ISM]
          Length = 298

 Score =  330 bits (847), Expect = 1e-88,   Method: Compositional matrix adjust.
 Identities = 161/271 (59%), Positives = 206/271 (76%), Gaps = 3/271 (1%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GL+RY+ EIRK P+LE +EEY+LAK + E  D  AAHR+VTSHLRL  KIAMGYRGYG
Sbjct: 13  EGGLNRYLQEIRKFPLLEPEEEYMLAKAWVEKQDTEAAHRMVTSHLRLAAKIAMGYRGYG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSWS+VK+GTT+ Q
Sbjct: 73  LPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSMVKLGTTSAQ 132

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALIN 191
           K+LFFNLR+ K  + A+ + ++ P+ V  IA  L V+E EVISMN R++ GD SLNA + 
Sbjct: 133 KKLFFNLRKAKARIGALEEGDMHPDNVKRIATDLGVTEDEVISMNRRMSGGDASLNATVG 192

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEK-EERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           S  + + QWQDWL  D D  +    EK  E + R  +LT +M VLN RE+ I   RRL +
Sbjct: 193 SEGEGTMQWQDWL-EDEDADQAGDYEKRNEMETRLELLTEAMDVLNDREKDILSQRRLND 251

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             VTLE+LS+E+ VSRER+RQIE RAF+K+Q
Sbjct: 252 ETVTLEDLSTEYGVSRERIRQIEVRAFEKLQ 282


>gi|1143379|dbj|BAA09444.1| sigma-32 homolog [Zymomonas mobilis]
          Length = 302

 Score =  330 bits (846), Expect = 1e-88,   Method: Compositional matrix adjust.
 Identities = 172/290 (59%), Positives = 215/290 (74%), Gaps = 7/290 (2%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           + G+  L+ Y+ +IRK P+L+ +EEY+LAKR++EH D  AA RLVTSHLRLV KIAMGYR
Sbjct: 14  LGGDQSLNHYLADIRKFPILKPEEEYMLAKRFQEHQDPKAASRLVTSHLRLVAKIAMGYR 73

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYGLP+SE++SEGNIGLMQ VKKFDPERGFRLATY++WWIKA++QEYILRSWSLVK+GTT
Sbjct: 74  GYGLPVSELISEGNIGLMQGVKKFDPERGFRLATYAIWWIKASIQEYILRSWSLVKMGTT 133

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
           A QK+LFFNLRRLK ++ A  D +LKP++V +IA  L VS  EV++MN R+A  GD SLN
Sbjct: 134 AAQKKLFFNLRRLKSNMNAFEDGDLKPDEVDSIATNLGVSNEEVVNMNRRMAMGGDSSLN 193

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +    Q QDWLV     Q+Q + E+EE   R  +L  +M  LN RE+ I   RR
Sbjct: 194 --ITMREDGEGQMQDWLVDQEPLQDQQIEEEEESLVRHKLLIEAMDRLNDREKHILTERR 251

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLL 297
           L +NP TLE LS  + VSRERVRQIE RAF K+Q++I   +EL+    LL
Sbjct: 252 LSDNPKTLEELSQVYGVSRERVRQIEVRAFDKLQKAI---MELAGDRKLL 298


>gi|163738663|ref|ZP_02146077.1| RNA polymerase, sigma 32 subunit, RpoH [Phaeobacter gallaeciensis
           BS107]
 gi|163742952|ref|ZP_02150335.1| RNA polymerase sigma factor [Phaeobacter gallaeciensis 2.10]
 gi|161383635|gb|EDQ08021.1| RNA polymerase sigma factor [Phaeobacter gallaeciensis 2.10]
 gi|161387991|gb|EDQ12346.1| RNA polymerase, sigma 32 subunit, RpoH [Phaeobacter gallaeciensis
           BS107]
          Length = 298

 Score =  330 bits (846), Expect = 2e-88,   Method: Compositional matrix adjust.
 Identities = 161/286 (56%), Positives = 215/286 (75%), Gaps = 4/286 (1%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GL+RY+ EIRK P+LE +EEY+LAKR+ E  D ++AH++VTSHLRL  KIAMGYRGYG
Sbjct: 13  EGGLNRYLQEIRKFPLLEPEEEYMLAKRWVEEQDSASAHKMVTSHLRLAAKIAMGYRGYG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSWSLVK+GTT+ Q
Sbjct: 73  LPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQ 132

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALIN 191
           K+LFFNLR+ K  + A+ + +L P+ V  IA  L V+E+EVISMN R++ GD SLNA + 
Sbjct: 133 KKLFFNLRKAKARIGALEEGDLHPDSVKKIATDLGVTETEVISMNRRMSGGDASLNATVG 192

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           S  + + QWQDWL  +   Q      ++E + RR +L  ++ VLN RE+ I   RRL + 
Sbjct: 193 SEGEGTMQWQDWLEDEDADQAGDYEARDELEARRELLASALEVLNDREKDILTQRRLADQ 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLL 297
             TLE+LS+++ VSRER+RQIE RAF+K+Q   +K  EL+S   +L
Sbjct: 253 AKTLEDLSTQYGVSRERIRQIEVRAFEKLQ---KKMRELASEKGML 295


>gi|254486865|ref|ZP_05100070.1| alternative sigma factor RpoH [Roseobacter sp. GAI101]
 gi|214043734|gb|EEB84372.1| alternative sigma factor RpoH [Roseobacter sp. GAI101]
          Length = 298

 Score =  329 bits (843), Expect = 3e-88,   Method: Compositional matrix adjust.
 Identities = 161/270 (59%), Positives = 210/270 (77%), Gaps = 1/270 (0%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GL+RY+ EIRK P+LE +EEY+LAKR+ E  D  AAHR+VTSHLRL  KIAMGYRGYG
Sbjct: 13  EGGLNRYMQEIRKFPLLEPEEEYMLAKRWVEEQDTEAAHRMVTSHLRLAAKIAMGYRGYG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSWSLVK+GTT+ Q
Sbjct: 73  LPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSGQ 132

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALIN 191
           K+LFFNLR+ K  + A+ + +++PE V  IA  L V+E+EV+SMN R++ GD SLNA + 
Sbjct: 133 KKLFFNLRKAKNRIGALEEGDMRPENVSRIATDLGVTEAEVVSMNRRMSGGDASLNATVG 192

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           S  + + QWQDWL  +   Q     E+EE + RR ML  ++ VLN RE+ I   RRL + 
Sbjct: 193 SEGEGTMQWQDWLEDEDADQAGDYEEREELETRREMLAEALEVLNDREKDILTQRRLSDE 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +TLE+LSS+++VSRER+RQIE RAF+K+Q
Sbjct: 253 TITLEDLSSQYDVSRERIRQIEVRAFEKLQ 282


>gi|254477747|ref|ZP_05091133.1| alternative sigma factor RpoH [Ruegeria sp. R11]
 gi|214031990|gb|EEB72825.1| alternative sigma factor RpoH [Ruegeria sp. R11]
          Length = 298

 Score =  327 bits (839), Expect = 1e-87,   Method: Compositional matrix adjust.
 Identities = 159/286 (55%), Positives = 214/286 (74%), Gaps = 4/286 (1%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GL+RY+ EIRK P+LE +EEY+LAKR+ E  D ++AH++VTSHLRL  KIAMGYRGYG
Sbjct: 13  EGGLNRYLQEIRKFPLLEPEEEYMLAKRWVEEQDANSAHKMVTSHLRLAAKIAMGYRGYG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSWSLVK+GTT+ Q
Sbjct: 73  LPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQ 132

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALIN 191
           K+LFFNLR+ K  + A+ + +L P+ V  IA  L V+E EVISMN R++ GD SLNA + 
Sbjct: 133 KKLFFNLRKAKARIGALEEGDLHPDSVKKIATDLGVTEDEVISMNRRMSGGDASLNATVG 192

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           +  + + QWQDWL  +   Q      ++E + RR +L  ++ VLN RE+ I   RRL + 
Sbjct: 193 TEGEGAMQWQDWLEDEDADQAGDYEARDELEARRELLASALEVLNDREKDILTQRRLADQ 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLL 297
             TLE+LS+++ VSRER+RQIE RAF+K+Q   +K  EL++   +L
Sbjct: 253 AKTLEDLSTQYGVSRERIRQIEVRAFEKLQ---KKMRELAAQKGML 295


>gi|254456610|ref|ZP_05070039.1| alternative sigma factor RpoH [Candidatus Pelagibacter sp.
           HTCC7211]
 gi|207083612|gb|EDZ61038.1| alternative sigma factor RpoH [Candidatus Pelagibacter sp.
           HTCC7211]
          Length = 297

 Score =  325 bits (833), Expect = 5e-87,   Method: Compositional matrix adjust.
 Identities = 160/284 (56%), Positives = 219/284 (77%), Gaps = 11/284 (3%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           N+  + N E GLS Y+ +I+K PML  +EEY+LAK ++  G++ AA +LVTSHLRLV KI
Sbjct: 8   NLPALTN-EGGLSAYLEQIKKFPMLAAEEEYMLAKNWKTTGNVKAAEKLVTSHLRLVAKI 66

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           AMGY+GYGLP++E++SEGN+GLMQAVKKF+PE+GFRLATY+MWWIKA++QEYILRSWSLV
Sbjct: 67  AMGYKGYGLPVNEMISEGNVGLMQAVKKFEPEKGFRLATYAMWWIKASIQEYILRSWSLV 126

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           KIGTT  QK+LFFNL+++K  +   T+ +L+ E V  IA KL+VS+ EV+SMN RL+G E
Sbjct: 127 KIGTTTAQKKLFFNLKKIKNQIAPQTEGDLRNEHVNEIANKLDVSKEEVVSMNRRLSGKE 186

Query: 185 -SLNALINSSDKNSSQWQDWLV---YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            SLNA +    ++  +WQDWLV    DHD +      +EE + R+++L  S+ VLN RER
Sbjct: 187 FSLNAQVG---EDGDEWQDWLVDKELDHDLK---FAHQEEMEQRKDLLKNSIKVLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            I  +RRL ++P TLE+LS ++++SRERVRQIE +AF+K+Q+ +
Sbjct: 241 EILYSRRLNDDPTTLEDLSKKYKISRERVRQIENKAFEKLQKHM 284


>gi|71083311|ref|YP_266030.1| RNA polymerase factor sigma-32 [Candidatus Pelagibacter ubique
           HTCC1062]
 gi|71062424|gb|AAZ21427.1| RNA polymerase sigma-32 factor (rpoH) RP303 [Candidatus
           Pelagibacter ubique HTCC1062]
          Length = 293

 Score =  325 bits (832), Expect = 7e-87,   Method: Compositional matrix adjust.
 Identities = 157/279 (56%), Positives = 216/279 (77%), Gaps = 10/279 (3%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ E GLS Y+ +I+K PML  +EEY+LAK ++  G++ AA +LVTSHLRLV KIAMGYR
Sbjct: 8   LSNEGGLSAYLEQIKKFPMLAAEEEYMLAKNWKATGNVKAAEKLVTSHLRLVAKIAMGYR 67

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYGLP++E++SEGN+GLMQAVKKF+PE+GFRLATY+MWWI+A++QEYILRSWSLVKIGTT
Sbjct: 68  GYGLPVNEMISEGNVGLMQAVKKFEPEKGFRLATYAMWWIRASIQEYILRSWSLVKIGTT 127

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNA 188
             QK+LFFNL+++K  +   ++ +L+PE V  IA KL+V++ EVISMN RL+G E SLNA
Sbjct: 128 TAQKKLFFNLKKIKNQIAPQSEGDLRPEHVTEIANKLDVNKDEVISMNRRLSGKEFSLNA 187

Query: 189 LINSSDKNSSQWQDWLV---YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
            +    ++  +WQDWLV    DHD +      +EE   R+N+L  S+ +LN RE+ I  +
Sbjct: 188 QVG---EDGDEWQDWLVDKELDHDLK---FAHQEEMGQRQNLLKDSIKILNEREKEILYS 241

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           RRL + P TLE+LS ++++SRERVRQIE +AF+K+Q+ +
Sbjct: 242 RRLNDEPTTLEDLSKKYKISRERVRQIENKAFEKLQKHM 280


>gi|91762259|ref|ZP_01264224.1| RNA polymerase sigma factor [Candidatus Pelagibacter ubique
           HTCC1002]
 gi|91718061|gb|EAS84711.1| RNA polymerase sigma factor [Candidatus Pelagibacter ubique
           HTCC1002]
          Length = 293

 Score =  324 bits (830), Expect = 1e-86,   Method: Compositional matrix adjust.
 Identities = 156/279 (55%), Positives = 216/279 (77%), Gaps = 10/279 (3%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ E GLS Y+ +I+K PML  +EEY+LAK ++  G++ AA +LVTSHLRLV KIAMGYR
Sbjct: 8   LSNEGGLSAYLEQIKKFPMLAAEEEYMLAKNWKATGNVKAAEKLVTSHLRLVAKIAMGYR 67

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYGLP++E++SEGN+GLMQAVKKF+PE+GFRLATY+MWWI+A++QEYILRSWSLVKIGTT
Sbjct: 68  GYGLPVNEMISEGNVGLMQAVKKFEPEKGFRLATYAMWWIRASIQEYILRSWSLVKIGTT 127

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNA 188
             QK+LFFNL+++K  +   ++ +L+PE V  IA KL+V++ EVISMN RL+G E SLNA
Sbjct: 128 TAQKKLFFNLKKIKNQIAPQSEGDLRPEHVTEIANKLDVNKDEVISMNRRLSGKEFSLNA 187

Query: 189 LINSSDKNSSQWQDWLV---YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
            +    ++  +WQDWLV    DHD +      +EE   R+N+L  S+ +LN RE+ I  +
Sbjct: 188 QVG---EDGDEWQDWLVDKELDHDLK---FAHQEEMGQRQNLLKDSIKILNEREKEILYS 241

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           RRL + P TLE+LS ++++SRER+RQIE +AF+K+Q+ +
Sbjct: 242 RRLNDEPTTLEDLSKKYKISRERIRQIENKAFEKLQKHM 280


>gi|197103427|ref|YP_002128805.1| RNA polymerase sigma 32 subunit(heat shock sigma factor)
           [Phenylobacterium zucineum HLK1]
 gi|196480703|gb|ACG80230.1| RNA polymerase sigma 32 subunit(heat shock sigma factor)
           [Phenylobacterium zucineum HLK1]
          Length = 316

 Score =  321 bits (822), Expect = 1e-85,   Method: Compositional matrix adjust.
 Identities = 167/279 (59%), Positives = 211/279 (75%), Gaps = 10/279 (3%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           + E GL RY+ EIRK P+L K EEY+LAKR+REH D  AAHRLVTSHLRL  KIA+ YRG
Sbjct: 9   SAEGGLRRYLTEIRKYPLLGKDEEYMLAKRWREHEDPEAAHRLVTSHLRLSAKIALSYRG 68

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
           YGLP+ EV+SEGN+GLM AVKKFDP++GFRLATY++WWI+AA+QEYILRSWSLVK+GT+A
Sbjct: 69  YGLPLGEVISEGNLGLMHAVKKFDPDKGFRLATYAIWWIRAAIQEYILRSWSLVKLGTSA 128

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNAL 189
            QK+LFFNLRR K  + A++D +LKP+QV AIA +L V+E EV++M+ RLA  D SLN+ 
Sbjct: 129 VQKKLFFNLRRAKARISALSDGDLKPDQVKAIASRLGVNEEEVVNMDRRLASRDASLNSP 188

Query: 190 INSSDKNSSQWQDWLVYDHD----GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           + +  +     Q+WL    D      E  + E EER  R ++L ++M  LN RERRIF A
Sbjct: 189 LAADAE-----QEWLDVLEDEAAVDPEAAVAEAEERALRMDLLAQAMQTLNARERRIFTA 243

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           RRLQ+ P  LE+L+ +F VSRERVRQIE RAF+KVQ  +
Sbjct: 244 RRLQDPPALLEDLAKDFGVSRERVRQIEVRAFEKVQAFV 282


>gi|288962386|ref|YP_003452681.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
 gi|288914652|dbj|BAI76137.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
          Length = 293

 Score =  318 bits (816), Expect = 5e-85,   Method: Compositional matrix adjust.
 Identities = 155/266 (58%), Positives = 204/266 (76%), Gaps = 2/266 (0%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           LSRYI++  + P+L  ++EY+LAK + EHGD+ AAHRLVTSHLRLVVKIA GYRGYGLP+
Sbjct: 16  LSRYINDTHRYPVLTAEDEYMLAKAWTEHGDVDAAHRLVTSHLRLVVKIAGGYRGYGLPL 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           S++++EGN+GLM AVKKF+PERGFRL+TY+MWWIKA++Q+YILRSWSLVKIGTTA QK+L
Sbjct: 76  SDLIAEGNLGLMTAVKKFEPERGFRLSTYAMWWIKASIQDYILRSWSLVKIGTTAAQKKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD-ESLNALINSSD 194
           FF+L RLK  L      +L P+ V +IA  L V E +V++MN RL+    SLNA + S++
Sbjct: 136 FFSLGRLKRKLGEYGGGDLHPDSVTSIATDLAVPEDDVVAMNRRLSAPVASLNAPM-SAE 194

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
            +S +WQD L  D    E+ L+E+ E + R  +L  +M VLN RER I  +RRL ++P+T
Sbjct: 195 GDSGEWQDLLADDRPSVEESLVERGEARQRSALLHEAMGVLNDRERDILTSRRLSDSPLT 254

Query: 255 LENLSSEFEVSRERVRQIEARAFKKV 280
           LE+LS  + VSRER+RQIE RAF+KV
Sbjct: 255 LEDLSVRYGVSRERIRQIEERAFEKV 280


>gi|83592357|ref|YP_426109.1| RNA polymerase factor sigma-32 [Rhodospirillum rubrum ATCC 11170]
 gi|83575271|gb|ABC21822.1| Sigma 32 (RpoH) [Rhodospirillum rubrum ATCC 11170]
          Length = 306

 Score =  315 bits (806), Expect = 6e-84,   Method: Compositional matrix adjust.
 Identities = 159/278 (57%), Positives = 204/278 (73%), Gaps = 3/278 (1%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V+ E GLSRY+ EI++ PML  +EE++LAKR ++ GD  AAHRLVTSHLRLV KIAMGYR
Sbjct: 11  VSDEGGLSRYLTEIKRFPMLTPEEEFMLAKRLQDEGDRDAAHRLVTSHLRLVAKIAMGYR 70

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
            YGLP+S++V+EGN+GLM+AVKKF+ +RGFRLATY+MWWIKA++ EYIL SWSLVK+GT 
Sbjct: 71  HYGLPVSDLVAEGNMGLMKAVKKFEADRGFRLATYAMWWIKASINEYILNSWSLVKVGTV 130

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNA 188
           A QK+LFFNLRRLK  L    + +L PE V  IA +L V+E++V+ MN RLAG D SLN 
Sbjct: 131 AAQKKLFFNLRRLKAKLGVYEEGDLSPEDVKTIATQLKVTEADVVMMNRRLAGPDASLNV 190

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +   +  S    D L+ + D QE+V    EE+     +L  ++S L  RER I  ARRL
Sbjct: 191 PVG--EDQSMDRMDLLMDEGDNQEEVYAAHEEQSLGNRLLKDALSTLTERERHIITARRL 248

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +  PVTLE L  E+ VSRERVRQIE RAF+K+Q +++K
Sbjct: 249 RSEPVTLEELGGEYGVSRERVRQIENRAFEKLQTAVRK 286


>gi|83311906|ref|YP_422170.1| RNA polymerase factor sigma-32 [Magnetospirillum magneticum AMB-1]
 gi|82946747|dbj|BAE51611.1| RNA polymerase sigma-32 factor [Magnetospirillum magneticum AMB-1]
          Length = 292

 Score =  309 bits (792), Expect = 3e-82,   Method: Compositional matrix adjust.
 Identities = 145/278 (52%), Positives = 210/278 (75%), Gaps = 4/278 (1%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +V G+ GL++Y+ +I++ P+L  +EE++LAKR+ ++ D  AAHRLVTSHLRLV KIA+GY
Sbjct: 8   VVAGDDGLAKYLRDIKEFPVLAPEEEFMLAKRWVDYEDTDAAHRLVTSHLRLVAKIALGY 67

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           R YGLP+++++SEGNIGLM+AVKKF+P+RGFRLATY+MWWIKA++ E++L SWS+VKIGT
Sbjct: 68  RHYGLPVADLISEGNIGLMRAVKKFEPDRGFRLATYAMWWIKASLNEFVLNSWSMVKIGT 127

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN 187
            A QK+LFFNLRR+K  L+ +   +L PE V  IA++L+V E +V++MN R+AG D SLN
Sbjct: 128 LAAQKKLFFNLRRIKSRLRLLEAGDLAPEHVATIARELDVDERDVVAMNRRMAGRDSSLN 187

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           A +    +  ++ QD +  + D QE    ++EE    R ++ R++  L  RER +F  RR
Sbjct: 188 APVG---EGGTEIQDLMADEADNQETAYGKREELSKGRVLIARALDSLTEREREVFVERR 244

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L+++PVTLE L   + VSRER+RQIE +AF+KV++ +Q
Sbjct: 245 LRDDPVTLEELGGRYGVSRERIRQIEVKAFEKVRDLVQ 282


>gi|23014972|ref|ZP_00054764.1| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Magnetospirillum magnetotacticum
           MS-1]
          Length = 292

 Score =  309 bits (791), Expect = 4e-82,   Method: Compositional matrix adjust.
 Identities = 143/278 (51%), Positives = 210/278 (75%), Gaps = 4/278 (1%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +V G+ GL++Y+ +I++ P+L  +EE++LAKR+ ++ D  AAH+LVTSHLRLV KIA+GY
Sbjct: 8   VVAGDDGLAKYLRDIKEFPVLAPEEEFMLAKRWVDYEDTEAAHKLVTSHLRLVAKIALGY 67

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           R YGLP+++++SEGNIGLM+AVKKF+P+RGFRLATY+MWWIKA++ E++L SWS+VKIGT
Sbjct: 68  RHYGLPVADLISEGNIGLMRAVKKFEPDRGFRLATYAMWWIKASLNEFVLNSWSMVKIGT 127

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN 187
            A QK+LFFNLRR+K  L+ +   +L PE V  IA++L+V E +V++MN R+AG D SLN
Sbjct: 128 LAAQKKLFFNLRRIKSRLRLLESGDLAPEHVTTIARELDVDERDVVAMNRRMAGRDSSLN 187

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             +    +  ++ QD +  + D QE  L ++EE    R ++ R++  L  RER +F  RR
Sbjct: 188 TPVG---EGGAEIQDLMADEADNQETSLAKREELSKGRTLIARALDSLTEREREVFVERR 244

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L+++P+TLE L   + VSRER+RQIE +AF+KV++ +Q
Sbjct: 245 LRDDPLTLEELGGRYGVSRERIRQIEVKAFEKVRDLVQ 282


>gi|91205341|ref|YP_537696.1| RNA polymerase factor sigma-32 [Rickettsia bellii RML369-C]
 gi|91068885|gb|ABE04607.1| RNA polymerase sigma-32 factor [Rickettsia bellii RML369-C]
          Length = 294

 Score =  305 bits (782), Expect = 4e-81,   Method: Compositional matrix adjust.
 Identities = 149/279 (53%), Positives = 202/279 (72%), Gaps = 1/279 (0%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           ++ ++ E G   Y+ +I KIP L ++EE++LAK Y E  DL AAH+LVTSHL+LV KIA 
Sbjct: 7   ALAISSESGFYSYLQKINKIPSLTQEEEFLLAKSYLEQNDLQAAHKLVTSHLKLVAKIAT 66

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           GYR YGLP++E+VSEGNIGLMQAVKKF+PE GFRL+TY+MWWIKAA+QEYIL+SWSLVK+
Sbjct: 67  GYRTYGLPVTELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKAAIQEYILKSWSLVKM 126

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DES 185
           GTTA QK+LFF+L ++K  +  +    +  +  V IA +L VS SEV  MN RL+G D S
Sbjct: 127 GTTAAQKKLFFSLSKIKNKITNLYSRAITSDDFVQIADELGVSVSEVSDMNIRLSGSDLS 186

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           LN  IN+ D +S +  + L       E + I KE+  ++R +L+ +M VLN RE RI   
Sbjct: 187 LNNTINNDDASSGELIELLPETRPSPEAIAISKEDMTHKRALLSSAMKVLNARELRILTE 246

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R+LQ+ P TL+ LSSE+ +S+ER+RQIE  AF+K+++ I
Sbjct: 247 RKLQDTPKTLDVLSSEYNISKERIRQIENTAFEKIKKFI 285


>gi|27380342|ref|NP_771871.1| RNA polymerase factor sigma-32 [Bradyrhizobium japonicum USDA 110]
 gi|1613784|gb|AAC44755.1| sigma32-like factor RpoH1 [Bradyrhizobium japonicum]
 gi|27353506|dbj|BAC50496.1| sigma32-like factor [Bradyrhizobium japonicum USDA 110]
          Length = 308

 Score =  305 bits (780), Expect = 8e-81,   Method: Compositional matrix adjust.
 Identities = 160/283 (56%), Positives = 208/283 (73%), Gaps = 1/283 (0%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           + GLS+Y+ EIRK P+L  ++E   A+R+REH D  AA+ LVTSHLRLV KIAM YRGYG
Sbjct: 13  DAGLSKYLVEIRKFPLLTPEQELAYARRWREHRDRDAAYHLVTSHLRLVAKIAMRYRGYG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LPI+E+VSEGNIGLMQAV++FDP+RG RLATY+MWWI+A++QEYILRSWSLVKI  +A+Q
Sbjct: 73  LPIAEIVSEGNIGLMQAVRRFDPDRGVRLATYAMWWIRASIQEYILRSWSLVKIAASASQ 132

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
           K+LFF LRR K  + A+ D +L+PEQV  IA++L V+E +V++M+ RL GD SLN  I+ 
Sbjct: 133 KKLFFKLRRAKSAISALQDGDLRPEQVRLIAERLKVAERDVVAMDRRLRGDASLNVPIHD 192

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            D+   Q  DWLV      E  L E++E K RR  L  +++ LN RER IF AR L E  
Sbjct: 193 EDEG-GQTLDWLVDPAPTCEITLAEEQEAKQRRLALANALANLNARERNIFTARWLNEES 251

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPP 295
            TLE L++E+ VSRERVRQIE RAF+KV+ ++      ++ PP
Sbjct: 252 TTLEELAAEYGVSRERVRQIEERAFQKVKAAMLTSRHEANGPP 294


>gi|288961334|ref|YP_003451673.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
 gi|288913642|dbj|BAI75129.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
          Length = 287

 Score =  302 bits (774), Expect = 4e-80,   Method: Compositional matrix adjust.
 Identities = 145/266 (54%), Positives = 195/266 (73%), Gaps = 2/266 (0%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ + RK   L  + E  LA R+ +H D +A  RLV SHLRLVVK+A GY GYGLP++++
Sbjct: 4   YLQDARKYQYLTPELELELAARWHDHQDPAALDRLVGSHLRLVVKMARGYLGYGLPLADL 63

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V+EGN+GLMQA +KFDP +GFR ATY+ WW++AA+QEY+L +WSLVKIGTTA QK+LFF+
Sbjct: 64  VAEGNVGLMQAAQKFDPGKGFRFATYASWWVRAAIQEYVLHNWSLVKIGTTAGQKKLFFS 123

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LRRLK  +Q +   +L PE V +IA +LNVS++EV+ MN RL  D SLN  +  S+   +
Sbjct: 124 LRRLKARMQELDSGDLSPEAVESIATELNVSKAEVVEMNRRLGNDRSLN--VGLSEDGDA 181

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           +WQD L  D   QE VL + EER+ R+  L   + VL+ RERRI  ARRL++ P+TLE L
Sbjct: 182 EWQDLLADDRPDQETVLADSEERRRRQQFLKLGLGVLDDRERRILVARRLRDEPLTLEEL 241

Query: 259 SSEFEVSRERVRQIEARAFKKVQESI 284
           S  F+VSRERVRQ+E RAF+K+Q+++
Sbjct: 242 SQTFQVSRERVRQLEVRAFEKLQKAV 267


>gi|144898533|emb|CAM75397.1| Sigma-70 region 2:Sigma-70 region 4 [Magnetospirillum
           gryphiswaldense MSR-1]
          Length = 290

 Score =  302 bits (773), Expect = 4e-80,   Method: Compositional matrix adjust.
 Identities = 149/280 (53%), Positives = 207/280 (73%), Gaps = 4/280 (1%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           R  +  I   + GLS+Y+ EIR  P+LE ++EY+LAKR+ ++ D +AAH+LVTSHLRLV 
Sbjct: 2   RATVPAISADDSGLSKYLREIRDFPVLEPEQEYMLAKRWVDYEDTAAAHQLVTSHLRLVA 61

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           KIAMGYR YGLP+++++SEGN+GLM+AVKKF+PERGFRL+TY+MWWIKA++ E++L SWS
Sbjct: 62  KIAMGYRHYGLPMADLISEGNLGLMRAVKKFEPERGFRLSTYAMWWIKASLNEFVLNSWS 121

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           LVKIGT A QK+LFFNLR++K  L+ +    L P  V AIAK+L VSE++V++MN R+ G
Sbjct: 122 LVKIGTLAAQKKLFFNLRKVKTKLRLLDATELAPADVRAIAKELGVSETDVVNMNRRMGG 181

Query: 183 -DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
            D SLN  +  S    ++  + L  + D QE  L + EE    R ++ ++++ LN RER 
Sbjct: 182 RDSSLNTPVGES---GTEIIELLPDETDNQETGLAKHEELSKGRKLIAQALTSLNERERE 238

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           IF  RRL++ P+TLE L + F VSRER+RQIE +AF+KV+
Sbjct: 239 IFVERRLRDEPLTLEELGARFGVSRERIRQIEVKAFEKVR 278


>gi|218680389|ref|ZP_03528286.1| RNA polymerase factor sigma-32 [Rhizobium etli CIAT 894]
          Length = 209

 Score =  298 bits (764), Expect = 5e-79,   Method: Compositional matrix adjust.
 Identities = 141/196 (71%), Positives = 168/196 (85%)

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D ERGFRLATY+MWWIKA++QEYILRSWSLVK+GTTANQKRLFFNLRRLKG +QAI D +
Sbjct: 1   DAERGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQKRLFFNLRRLKGRIQAIDDGD 60

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
           LKPE V  IA KL VSE EVISMN RL+GD SLNA I +++ +S QWQDWLV DHD QE 
Sbjct: 61  LKPEHVSEIATKLKVSEEEVISMNRRLSGDASLNAPIKAAEGDSGQWQDWLVDDHDSQED 120

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
           VLIE++E   RR ML ++MSVLN RERRIFEARRL E+PVTLE+LS+EF++SRERVRQIE
Sbjct: 121 VLIEQDELDTRRRMLAKAMSVLNERERRIFEARRLAEDPVTLEDLSTEFDISRERVRQIE 180

Query: 274 ARAFKKVQESIQKQVE 289
            RAF+KVQ++++K+ +
Sbjct: 181 VRAFEKVQDAVRKEAQ 196


>gi|67458885|ref|YP_246509.1| RNA polymerase factor sigma-32 [Rickettsia felis URRWXCal2]
 gi|67004418|gb|AAY61344.1| RNA polymerase sigma-32 factor [Rickettsia felis URRWXCal2]
          Length = 293

 Score =  297 bits (760), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 145/279 (51%), Positives = 200/279 (71%), Gaps = 1/279 (0%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           ++ ++ E G   Y+ +I KIP L ++EE++LAK Y E  DL AAH+LVTSHL+LV KIA 
Sbjct: 7   ALAISSESGFYSYLQKINKIPSLTQEEEFLLAKSYLEENDLQAAHKLVTSHLKLVAKIAS 66

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           GYR YGLPI+E+VSEGNIGLMQAVKKF+PE GFRL+TY+MWWIKAA+QEYIL+SWSLVK+
Sbjct: 67  GYRTYGLPITELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKAAIQEYILKSWSLVKM 126

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DES 185
           GTTA QK+LFF+L ++K  +  +    +  +  + IA +L VS +EV  MN R++G D S
Sbjct: 127 GTTAAQKKLFFSLNKIKHKITNLYSRAITADDFIQIADELGVSVNEVSEMNTRISGPDLS 186

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           LN  INS D  S +  + L       E + I K++   +R +L+ +M +LN RE RIF  
Sbjct: 187 LNNPINSDDAESGELIELLPETRPTPETIAINKQDSTGKRKLLSNAMKILNDRELRIFTE 246

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R+L + P TL+ LS+E+ +S+ER+RQIE  AF+K+++ I
Sbjct: 247 RKLTDTPKTLDILSNEYNISKERIRQIENTAFEKIKKFI 285


>gi|157803973|ref|YP_001492522.1| RNA polymerase factor sigma-32 [Rickettsia canadensis str. McKiel]
 gi|157785236|gb|ABV73737.1| hypothetical protein A1E_04050 [Rickettsia canadensis str. McKiel]
          Length = 296

 Score =  295 bits (755), Expect = 6e-78,   Method: Compositional matrix adjust.
 Identities = 146/282 (51%), Positives = 200/282 (70%), Gaps = 1/282 (0%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           ++ ++ E G   Y+ +I KIP L ++EE++LAK Y E  DL AAH+LVTSHL+LV KIA 
Sbjct: 7   ALAISSESGFYSYLQKINKIPSLTQEEEFLLAKSYLEENDLKAAHKLVTSHLKLVAKIAS 66

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           GYR YGLPI+E+VSEGNIGLMQAVKKF+PE GFRL+TY+MWWIKAA+QEYIL+SWSLVK+
Sbjct: 67  GYRTYGLPITELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKAAIQEYILKSWSLVKM 126

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DES 185
           GTTA QK+LFF+L ++K  +  +    +  +  V IA +L VS +EV  MN R++G D S
Sbjct: 127 GTTAAQKKLFFSLNKVKHKITNLYSRAITTDDFVQIADELGVSVNEVSEMNTRISGPDLS 186

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           LN  INS D  S +  + L       E + I K+    ++++L  +M +LN RE RI   
Sbjct: 187 LNNSINSDDTESGELIELLPETRPTPEAMAINKQNYTTKKHLLASAMKILNDRELRILTE 246

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           R+L++ P TL+ LSSE+ +S+ER+RQIE  AF+K+++ I K 
Sbjct: 247 RKLKDTPKTLDILSSEYNISKERIRQIENTAFEKIKKFILKH 288


>gi|239947881|ref|ZP_04699634.1| alternative sigma factor RpoH [Rickettsia endosymbiont of Ixodes
           scapularis]
 gi|239922157|gb|EER22181.1| alternative sigma factor RpoH [Rickettsia endosymbiont of Ixodes
           scapularis]
          Length = 293

 Score =  293 bits (749), Expect = 2e-77,   Method: Compositional matrix adjust.
 Identities = 145/279 (51%), Positives = 198/279 (70%), Gaps = 1/279 (0%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           ++ ++ E G   Y+ +I KIP L ++EE++LAK Y E  DL AAH+LVTSHL+LV KIA 
Sbjct: 7   ALAISSESGFYSYLQKINKIPSLTQEEEFLLAKSYLEENDLQAAHKLVTSHLKLVAKIAS 66

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           GYR YGLPI+E+VSEGNIGLMQAVKKF+PE GFRL+TY+MWWIKAA+QEYIL+SWSLVK+
Sbjct: 67  GYRTYGLPITELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKAAIQEYILKSWSLVKM 126

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DES 185
           GTTA QK+LFF+L ++K  +  +    +  +    IA +L VS +EV  MN R++G D S
Sbjct: 127 GTTAAQKKLFFSLNKVKHKITNLYSRAITTDDFAQIADELGVSINEVSEMNTRISGPDLS 186

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           LN  INS D  S +  + L       E + I K+   ++R +L+ +M +LN RE RI   
Sbjct: 187 LNNSINSDDAESGELIELLPETRPTPEAMAINKQNSTSKRKLLSNAMKILNDRELRILTE 246

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R+L + P TL+ LSSE+ +S+ER+RQIE  AF+K+++ I
Sbjct: 247 RKLTDTPKTLDILSSEYNISKERIRQIENTAFEKIKKFI 285


>gi|238650752|ref|YP_002916605.1| RNA polymerase factor sigma-32 [Rickettsia peacockii str. Rustic]
 gi|238624850|gb|ACR47556.1| RNA polymerase factor sigma-32 [Rickettsia peacockii str. Rustic]
          Length = 293

 Score =  291 bits (745), Expect = 9e-77,   Method: Compositional matrix adjust.
 Identities = 145/279 (51%), Positives = 198/279 (70%), Gaps = 1/279 (0%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           ++ ++ E G   Y+ +I KIP L ++EE +LAK Y E  DL AAH+LVTSHL+LV KIA 
Sbjct: 7   ALAISSESGFYSYLQKINKIPSLTQEEELLLAKSYLEGNDLQAAHKLVTSHLKLVAKIAS 66

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           GYR YGLPI+E+VSEGNIGLMQAVKKF+PE GFRL+TY+MWWIKAA+QEYIL+SWSLVK+
Sbjct: 67  GYRTYGLPITELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKAAIQEYILKSWSLVKM 126

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DES 185
           GTTA QK+LFF+L ++K  +  +    +  +  V IA +L VS +EV  MN R++G D S
Sbjct: 127 GTTAAQKKLFFSLNKVKHKITNLYSRAITTDDFVQIADELGVSVNEVSEMNTRISGPDLS 186

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           LN  INS D  S +  + L       E + I K+   ++R +L+ +M +LN RE RI   
Sbjct: 187 LNNSINSDDAESGELIELLPETRPTPEAMAINKQNSTSKRQLLSNAMKILNDRELRILTE 246

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R+L + P TL+ LS+E+ +S+ER+RQIE  AF+K+++ I
Sbjct: 247 RKLTDTPKTLDILSNEYNISKERIRQIENTAFEKIKKFI 285


>gi|15892330|ref|NP_360044.1| RNA polymerase factor sigma-32 [Rickettsia conorii str. Malish 7]
 gi|15619475|gb|AAL02945.1| RNA polymerase sigma-32 factor [Rickettsia conorii str. Malish 7]
          Length = 293

 Score =  291 bits (744), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 145/279 (51%), Positives = 198/279 (70%), Gaps = 1/279 (0%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           ++ ++ E G   Y+ +I KIP L ++EE +LAK Y E  DL AAH+LVTSHL+LV KIA 
Sbjct: 7   ALAISSESGFYSYLQKINKIPSLTQEEELLLAKSYLEGNDLQAAHKLVTSHLKLVAKIAS 66

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           GYR YGLPI+E+VSEGNIGLMQAVKKF+PE GFRL+TY+MWWIKAA+QEYIL+SWSLVK+
Sbjct: 67  GYRTYGLPITELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKAAIQEYILKSWSLVKM 126

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DES 185
           GTTA QK+LFF+L ++K  +  +    +  +  V IA +L VS +EV  MN R++G D S
Sbjct: 127 GTTAAQKKLFFSLNKVKHKITNLYSRAITTDDFVQIADELGVSVNEVSEMNTRISGPDLS 186

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           LN  INS D  S +  + L       E + I K+   ++R +L+ +M +LN RE RI   
Sbjct: 187 LNNSINSDDAESGELIELLPETRPTPEAMAINKQNSTSKRQLLSNAMKILNDRELRILTE 246

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R+L + P TL+ LS+E+ +S+ER+RQIE  AF+K+++ I
Sbjct: 247 RKLTDTPKTLDILSNEYNISKERIRQIENTAFEKIKKFI 285


>gi|229586560|ref|YP_002845061.1| RNA polymerase factor sigma-32 [Rickettsia africae ESF-5]
 gi|228021610|gb|ACP53318.1| RNA polymerase sigma-32 factor [Rickettsia africae ESF-5]
          Length = 293

 Score =  291 bits (744), Expect = 1e-76,   Method: Compositional matrix adjust.
 Identities = 144/279 (51%), Positives = 198/279 (70%), Gaps = 1/279 (0%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           ++ ++ E G   Y+ +I KIP L ++EE +LAK Y E  DL AAH+LVTSHL+LV KIA 
Sbjct: 7   ALAISSESGFYSYLQKINKIPSLTQEEELLLAKSYLEGNDLQAAHKLVTSHLKLVAKIAS 66

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           GYR YGLP++E+VSEGNIGLMQAVKKF+PE GFRL+TY+MWWIKAA+QEYIL+SWSLVK+
Sbjct: 67  GYRTYGLPMTELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKAAIQEYILKSWSLVKM 126

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DES 185
           GTTA QK+LFF+L ++K  +  +    +  +  V IA +L VS +EV  MN R++G D S
Sbjct: 127 GTTAAQKKLFFSLNKVKHKITNLYSRTITTDDFVQIADELGVSVNEVSEMNTRISGPDLS 186

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           LN  INS D  S +  + L       E + I K+   ++R +L+ +M +LN RE RI   
Sbjct: 187 LNNSINSDDAESGELIELLPETRPTPETMAINKQNSTSKRQLLSNAMKILNDRELRILTE 246

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R+L + P TL+ LS+E+ +S+ER+RQIE  AF+K+++ I
Sbjct: 247 RKLTDTPKTLDILSNEYNISKERIRQIENTAFEKIKKFI 285


>gi|51473499|ref|YP_067256.1| RNA polymerase factor sigma-32 [Rickettsia typhi str. Wilmington]
 gi|51459811|gb|AAU03774.1| RNA polymerase sigma 32 subunit (heat shock sigma factor)
           [Rickettsia typhi str. Wilmington]
          Length = 293

 Score =  290 bits (741), Expect = 3e-76,   Method: Compositional matrix adjust.
 Identities = 143/279 (51%), Positives = 198/279 (70%), Gaps = 1/279 (0%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           ++ ++ E G   Y+ +I KIP L ++EE++LAK Y E  DL AAH+LVTSHL+LV KIA 
Sbjct: 7   ALAISSESGFYSYLQKINKIPSLTQEEEFLLAKSYLEENDLQAAHKLVTSHLKLVAKIAS 66

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           GY+ YGLPI+E+VSEGNIGLMQAVKKF+PE GFRL+TY+MWWIKA++QEYIL+SWSLVK+
Sbjct: 67  GYKTYGLPITELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKASIQEYILKSWSLVKM 126

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DES 185
           GTTA QK+LFF+L ++K  +  +    +  +    IA +L VS  EV  MN R++G D S
Sbjct: 127 GTTAAQKKLFFSLNKVKHKITNLYSRAITTDDFAQIADELGVSVHEVSEMNTRISGPDLS 186

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           LN  INS D  S +  + L       E + I K+   ++R +L+ +M +LN RE RI + 
Sbjct: 187 LNNSINSDDVESGELIELLPETRPTPEAMAINKQNYTSKRKLLSNAMQILNDRELRILKD 246

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R+L + P TL+ LSSE+ +S+ER+RQIE  AF+K+++ I
Sbjct: 247 RKLTDTPKTLDILSSEYNISKERIRQIENTAFEKIKKFI 285


>gi|157964378|ref|YP_001499202.1| RNA polymerase factor sigma-32 [Rickettsia massiliae MTU5]
 gi|157844154|gb|ABV84655.1| RNA polymerase sigma-32 factor [Rickettsia massiliae MTU5]
          Length = 310

 Score =  290 bits (741), Expect = 3e-76,   Method: Compositional matrix adjust.
 Identities = 144/279 (51%), Positives = 197/279 (70%), Gaps = 1/279 (0%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           ++ ++ E G   Y+ +I KIP L ++EE +LAK Y E  DL AAH+LVTSHL+LV KIA 
Sbjct: 24  ALAISSESGFYSYLQKINKIPSLTQEEELLLAKSYLEGNDLQAAHKLVTSHLKLVAKIAS 83

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           GYR YGLPI+E+VSEGNIGLMQAVKKF+PE GFRL+TY+MWWIKAA+QEYIL+SWSLVK+
Sbjct: 84  GYRTYGLPITELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKAAIQEYILKSWSLVKM 143

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DES 185
           GTTA QK+LFF+L ++K  +  +    +  +    IA +L VS +EV  MN R++G D S
Sbjct: 144 GTTAAQKKLFFSLNKVKHKITNLYSRAITTDDFAQIADELGVSVNEVSEMNTRISGPDLS 203

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           LN  INS D  S +  + L       E + I K+   ++R +L+ +M +LN RE RI   
Sbjct: 204 LNNSINSDDAESGELIELLPETRPTPEAMAINKQNSTSKRQLLSNAMKILNDRELRILTE 263

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R+L + P TL+ LS+E+ +S+ER+RQIE  AF+K+++ I
Sbjct: 264 RKLTDTPKTLDILSNEYNISKERIRQIENTAFEKIKKFI 302


>gi|157825543|ref|YP_001493263.1| RNA polymerase factor sigma-32 [Rickettsia akari str. Hartford]
 gi|157799501|gb|ABV74755.1| RNA polymerase factor sigma-32 [Rickettsia akari str. Hartford]
          Length = 293

 Score =  289 bits (739), Expect = 4e-76,   Method: Compositional matrix adjust.
 Identities = 142/279 (50%), Positives = 196/279 (70%), Gaps = 1/279 (0%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           ++ ++ E G   Y+ +I  IP L ++EE++LAK Y E  DL AAH+LVTSHL+LV KIA 
Sbjct: 7   ALAISSESGFYNYLQKINNIPSLTQEEEFLLAKSYLEENDLQAAHKLVTSHLKLVAKIAS 66

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           GYR YG+PI+E+VSEGNIGLMQAVKKF+PE GFRL+TY+MWWIKAA+QEYIL+SWSLVK+
Sbjct: 67  GYRTYGIPITELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKAAIQEYILKSWSLVKM 126

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DES 185
           GTTA QK+LFF+L ++K  +  +    +  +    IA +L VS +EV  MN R++G D S
Sbjct: 127 GTTAAQKKLFFSLNKVKHKITNLYSRAITTDDFAKIADELGVSVNEVSEMNTRISGPDLS 186

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           LN  INS D  S +  + L       E + I K+   ++R +L  +M +LN RE RI   
Sbjct: 187 LNNSINSDDAASGELIELLPETRPTPEAMAINKQNFTSKRKLLANAMKILNDRELRILTE 246

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R+L + P TL+ LS+E+ +S+ER+RQIE  AF+K+++ I
Sbjct: 247 RKLTDTPTTLDILSNEYNISKERIRQIENTAFEKIKKFI 285


>gi|34580656|ref|ZP_00142136.1| RNA polymerase sigma-32 factor [Rickettsia sibirica 246]
 gi|28262041|gb|EAA25545.1| RNA polymerase sigma-32 factor [Rickettsia sibirica 246]
          Length = 293

 Score =  288 bits (737), Expect = 7e-76,   Method: Compositional matrix adjust.
 Identities = 143/279 (51%), Positives = 197/279 (70%), Gaps = 1/279 (0%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           ++ ++ E G   Y+ +I KIP L ++EE +LAK Y E  DL AAH+LVTSHL+LV KIA 
Sbjct: 7   ALAISSESGFYSYLQKINKIPSLTQEEELLLAKSYLEGNDLQAAHKLVTSHLKLVAKIAS 66

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           GYR YGLP++E+VSEGNIGLMQAVKKF+P  GFRL+TY+MWWIKAA+QEYIL+SWSLVK+
Sbjct: 67  GYRTYGLPMTELVSEGNIGLMQAVKKFNPALGFRLSTYAMWWIKAAIQEYILKSWSLVKM 126

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DES 185
           GTTA QK+LFF+L ++K  +  +    +  +  V IA +L VS +EV  MN R++G D S
Sbjct: 127 GTTAAQKKLFFSLNKVKHKITNLYSRAITTDDFVQIADELGVSVNEVSEMNTRISGPDLS 186

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           LN  INS D  S +  + L       E + I K+   ++R +L+ +M +LN RE RI   
Sbjct: 187 LNNSINSDDAESGELIELLPETRPTPETMAINKQNSTSKRQLLSNAMKILNDRELRILTE 246

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R+L + P TL+ LS+E+ +S+ER+RQIE  AF+K+++ I
Sbjct: 247 RKLTDTPKTLDILSNEYNISKERIRQIENTAFEKIKKFI 285


>gi|157828283|ref|YP_001494525.1| RNA polymerase factor sigma-32 [Rickettsia rickettsii str. 'Sheila
           Smith']
 gi|165932987|ref|YP_001649776.1| RNA polymerase factor sigma-32 [Rickettsia rickettsii str. Iowa]
 gi|157800764|gb|ABV76017.1| RNA polymerase factor sigma-32 [Rickettsia rickettsii str. 'Sheila
           Smith']
 gi|165908074|gb|ABY72370.1| RNA polymerase sigma-32 factor [Rickettsia rickettsii str. Iowa]
          Length = 293

 Score =  288 bits (736), Expect = 8e-76,   Method: Compositional matrix adjust.
 Identities = 143/279 (51%), Positives = 197/279 (70%), Gaps = 1/279 (0%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           ++ ++ E G   Y+ +I KIP L ++EE +LAK Y E  DL AAH+LVTSHL+LV KIA 
Sbjct: 7   ALAISSESGFYSYLQKINKIPSLTQEEELLLAKSYLEGNDLQAAHKLVTSHLKLVAKIAS 66

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           GYR YGLPI+E+VSEGNIGLMQAVKKF+PE GFRL+TY+MWWIKAA+QEYIL+SWSLVK+
Sbjct: 67  GYRTYGLPITELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKAAIQEYILKSWSLVKM 126

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DES 185
           GTT  QK+LFF+L ++K  +  +    +  +  V IA +L VS +EV  MN R++G D S
Sbjct: 127 GTTTAQKKLFFSLNKVKHKITNLYSRAITTDDFVQIADELGVSVNEVSEMNTRISGPDLS 186

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           LN  IN+ D  S +  + L       E + I K+   ++R +L+ +M +LN RE RI   
Sbjct: 187 LNNSINNDDAESGELIELLPETRPTPEAMAINKQNSTSKRQLLSNAMKILNDRELRILTE 246

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R+L + P TL+ LS+E+ +S+ER+RQIE  AF+K+++ I
Sbjct: 247 RKLTDTPKTLDILSNEYNISKERIRQIENTAFEKIKKFI 285


>gi|15604172|ref|NP_220687.1| RNA polymerase factor sigma-32 [Rickettsia prowazekii str. Madrid
           E]
 gi|3860864|emb|CAA14764.1| RNA POLYMERASE SIGMA-32 FACTOR (rpoH) [Rickettsia prowazekii]
 gi|292571903|gb|ADE29818.1| RNA polymerase sigma-32 factor [Rickettsia prowazekii Rp22]
          Length = 293

 Score =  287 bits (734), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 142/279 (50%), Positives = 198/279 (70%), Gaps = 1/279 (0%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           ++ ++ E G   Y+ +I KIP L ++EE++LAK Y E  DL AAH+LVTSHL+LV KIA 
Sbjct: 7   ALAISSESGFYSYLQKINKIPSLTQEEEFLLAKSYLEENDLQAAHKLVTSHLKLVAKIAS 66

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y+ YGLPI+E+VSEGNIGLMQAVKKF+PE GFRL+TY+MWWIKA++QEYIL+SWSLVK+
Sbjct: 67  SYKTYGLPITELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKASIQEYILKSWSLVKM 126

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DES 185
           GTTA QK+LFF+L ++K  +  +    +  +    IA +L VS +EV  MN R++G D S
Sbjct: 127 GTTAAQKKLFFSLNKVKHKITNLYSRAITTDDFAQIADELGVSVNEVSEMNTRISGPDLS 186

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           LN  INS D  S +  + L       E + I K+   ++R +L+ +M +LN RE RI + 
Sbjct: 187 LNNSINSDDVESGELIELLPELRPTPEAMAINKQNYTSKRKLLSNAMQILNDRELRILKD 246

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R+L + P TL+ LSSE+ +S+ER+RQIE  AF+K+++ I
Sbjct: 247 RKLTDTPKTLDILSSEYNISKERIRQIENTAFEKIKKFI 285


>gi|288958414|ref|YP_003448755.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
 gi|288910722|dbj|BAI72211.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
          Length = 323

 Score =  287 bits (734), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 143/278 (51%), Positives = 198/278 (71%), Gaps = 4/278 (1%)

Query: 9   IVNGE-IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++ GE   L+RYI E ++ P+L    E  LA  +RE G+  A  +LV SHLRLV+KIA G
Sbjct: 32  LLTGENASLTRYIEESKRFPILAPDVERDLAIAWRERGNPRALEQLVGSHLRLVIKIARG 91

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           + GYGL + ++V+EGN+GLMQA +KFDP+RGFR ATY+ WWI+AA+QEYIL SWSLVK+G
Sbjct: 92  FGGYGLSLVDLVAEGNVGLMQAAQKFDPQRGFRFATYATWWIRAAIQEYILHSWSLVKMG 151

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESL 186
           TTA QK+LFFNLRRLK  +  +   +L PE V  IA +L+V E+EV+ MN RLA  D SL
Sbjct: 152 TTAAQKKLFFNLRRLKSQMAELEQGDLSPETVATIAAELDVPETEVVEMNRRLAANDSSL 211

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           +A +++     + W + L  D   Q+ +L + +E   RR ++ +++  L+PRERRI   R
Sbjct: 212 DATLSTD--GETNWLELLADDRPTQDAMLADADELALRRRLVGQALDRLDPRERRILFER 269

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           RL+++P TLE LS +F VSRERVRQIE RAF+K+Q+++
Sbjct: 270 RLKDDPSTLEALSQQFSVSRERVRQIEVRAFEKLQKAV 307


>gi|218459714|ref|ZP_03499805.1| RNA polymerase factor sigma-32 [Rhizobium etli Kim 5]
          Length = 198

 Score =  278 bits (710), Expect = 1e-72,   Method: Compositional matrix adjust.
 Identities = 132/184 (71%), Positives = 159/184 (86%)

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +MWWIKA++QEYILRSWSLVK+GTTANQKRLFFNLRRLKG +QAI D +LKPE V  IA 
Sbjct: 1   AMWWIKASIQEYILRSWSLVKMGTTANQKRLFFNLRRLKGRIQAIDDGDLKPEHVSEIAT 60

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           KLNVSE EVISMN RL+GD SLNA I +++ +S QWQDWLV DHD QE VLIE++E + R
Sbjct: 61  KLNVSEEEVISMNRRLSGDASLNAPIKAAEGDSGQWQDWLVDDHDSQEDVLIEQDELETR 120

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R ML+++MSVLN RERRIFEARRL E PVTLE+LS+EF++SRERVRQIE RAF+KVQ+++
Sbjct: 121 RRMLSKAMSVLNERERRIFEARRLAEEPVTLEDLSAEFDISRERVRQIEVRAFEKVQDAV 180

Query: 285 QKQV 288
           +K+ 
Sbjct: 181 RKEA 184


>gi|190571331|ref|YP_001975689.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Culex
           quinquefasciatus Pel]
 gi|190357603|emb|CAQ55044.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Culex
           quinquefasciatus Pel]
          Length = 297

 Score =  263 bits (673), Expect = 2e-68,   Method: Compositional matrix adjust.
 Identities = 133/283 (46%), Positives = 197/283 (69%), Gaps = 2/283 (0%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           ++ VN    L +YI E+RK PML ++EE  LAK ++E+ D+S+AHRL+TSHL LVVKIAM
Sbjct: 7   NLCVNSSTNLMQYIAEVRKFPMLSQEEEVRLAKNWQEYQDISSAHRLITSHLNLVVKIAM 66

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            ++ YGL + ++V EGN+GLM AVKKF+P+ GFR +TY++WWI+A+M+++IL+SWSLVKI
Sbjct: 67  KFKNYGLLLMDLVMEGNMGLMHAVKKFNPDLGFRFSTYAVWWIEASMKDFILKSWSLVKI 126

Query: 127 GTTANQKRLFFNLRRLKGH-LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DE 184
           GTT  Q+RLFF+LR++K   LQ      L  E++ AI+ +L+VSE +V+ M+ RLA  D+
Sbjct: 127 GTTQAQRRLFFSLRKIKKRILQYTNRETLSKEEIKAISNELSVSEEDVVQMSYRLACKDQ 186

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SLN  I   D +  + QD +  +   QE      EE+  +  +L+ +++ LN R R IF 
Sbjct: 187 SLNNCIKIGDDSKKELQDMIPCNLVSQEVAYQNHEEKALKETILSNALASLNERSRDIFI 246

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +R L EN  TL+ LS ++ VSRER+RQ+  +A  KV++ I+ +
Sbjct: 247 SRYLSENTQTLDELSKKYCVSRERIRQLAEQAMSKVKQHIKSE 289


>gi|58584688|ref|YP_198261.1| DNA-directed RNA polymerase sigma 32 subunit [Wolbachia
           endosymbiont strain TRS of Brugia malayi]
 gi|58419004|gb|AAW71019.1| DNA-directed RNA polymerase sigma 32 subunit, RpoH subfamily
           [Wolbachia endosymbiont strain TRS of Brugia malayi]
          Length = 297

 Score =  261 bits (667), Expect = 1e-67,   Method: Compositional matrix adjust.
 Identities = 130/284 (45%), Positives = 197/284 (69%), Gaps = 2/284 (0%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +S+ +NG   L++YI E+RK PML ++EE  LAK + +  D+S+AH+L+TSHL LVVKIA
Sbjct: 6   VSLCINGSTNLTQYITEVRKFPMLSQEEEVRLAKSWNQCKDISSAHKLITSHLNLVVKIA 65

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
           M ++ YGL + +++ EGN+GL+ AVKKF+P+ GFR +TY++WWI+A+++++IL+SWS VK
Sbjct: 66  MKFKNYGLLLMDLIMEGNMGLIHAVKKFNPDLGFRFSTYAVWWIEASIKDFILKSWSFVK 125

Query: 126 IGTTANQKRLFFNLRRLKGH-LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-D 183
           IGTT  Q+RLFF+LR++K   LQ      L  E++ AI+ +L+VSE +VI MN RLA  D
Sbjct: 126 IGTTQAQRRLFFSLRKIKKRILQYTNRETLNNEEIKAISNELSVSEGDVIQMNYRLACKD 185

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           +SLN  I     +  + QD +  +   QE     +EE++ +  +L  +++ LN R R IF
Sbjct: 186 QSLNNCIKVGGDSKKELQDMIPCNSVNQEVTYQNREEKELKETILNNALASLNERSRDIF 245

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +R L EN  TL+ LS ++ VSRER+RQ+  +A  KV++ IQ +
Sbjct: 246 ISRYLSENTQTLDELSKKYCVSRERIRQLAEQAMSKVKQHIQSE 289


>gi|189184203|ref|YP_001937988.1| RNA polymerase factor sigma-32 [Orientia tsutsugamushi str. Ikeda]
 gi|189180974|dbj|BAG40754.1| heat shock sigma factor RpoH [Orientia tsutsugamushi str. Ikeda]
          Length = 299

 Score =  258 bits (659), Expect = 9e-67,   Method: Compositional matrix adjust.
 Identities = 130/269 (48%), Positives = 186/269 (69%), Gaps = 1/269 (0%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           G   Y+ +I +IP L  +EEY+LAK Y E  +L AAH LV SHL+LV KIA+ YRGYGLP
Sbjct: 18  GFYIYLQKINRIPSLTAEEEYMLAKSYFEQNNLKAAHSLVKSHLKLVAKIALSYRGYGLP 77

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++VSEGNIGL+QAVKK++PE GFRL+TY++WWIKAA+Q+YILRSWSLVK+GTTA QK+
Sbjct: 78  VVDLVSEGNIGLLQAVKKYNPELGFRLSTYAIWWIKAAIQDYILRSWSLVKLGTTAAQKK 137

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALINSS 193
           LFFNL ++K  +  +    +       IA +  VS +EV  +N RL+  D SLN  I+  
Sbjct: 138 LFFNLGKIKNKITKLHARAINSSDYKQIADESGVSIAEVSEVNQRLSNSDLSLNTPISYH 197

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           + ++++  + +      QE +L  +++   ++ +L  ++  L  RE  I  AR+LQ+ P 
Sbjct: 198 EDDATELVELVPEHRPNQEIILANQQDLNLKQEVLQNALQTLTQRELYIIRARKLQDEPD 257

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQE 282
           TLE LS  F VS+ER+RQIE++AF+K+Q+
Sbjct: 258 TLEKLSLHFNVSKERIRQIESKAFEKLQQ 286


>gi|148284686|ref|YP_001248776.1| RNA polymerase factor sigma-32 [Orientia tsutsugamushi str.
           Boryong]
 gi|146740125|emb|CAM80313.1| RNA polymerase sigma-32 factor [Orientia tsutsugamushi str.
           Boryong]
          Length = 299

 Score =  258 bits (658), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 134/274 (48%), Positives = 190/274 (69%), Gaps = 11/274 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           G   Y+ +I +IP L  +EEY+LAK Y E  +L AAH LV SHL+LV KIA+ YRGYGLP
Sbjct: 18  GFYIYLQKINRIPSLTAEEEYMLAKSYFEQNNLKAAHSLVKSHLKLVAKIALSYRGYGLP 77

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++VSEGNIGL+QAVKK++PE GFRL+TY++WWIKAA+Q+YILRSWSLVK+GTTA QK+
Sbjct: 78  VVDLVSEGNIGLLQAVKKYNPELGFRLSTYAIWWIKAAIQDYILRSWSLVKLGTTAAQKK 137

Query: 135 LFFNLRRLKG-----HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNA 188
           LFFNL ++K      H +AI  ++ K      IA +  VS +EV  +N RL+  D SLN 
Sbjct: 138 LFFNLGKIKNKITKMHARAINSSDYK-----QIADESGVSIAEVSEVNQRLSNSDLSLNT 192

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            I+  + ++++  + +      QE +L  +++   ++ +L  ++  L  RE  I  AR+L
Sbjct: 193 PISYHEDDATELVELVPEHRPNQEIILANQQDLNLKKEVLENALQTLTQRELYIIRARKL 252

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           Q+ P TLE LS  F VS+ER+RQIE++AF+K+Q+
Sbjct: 253 QDEPDTLEKLSLHFNVSKERIRQIESKAFEKLQQ 286


>gi|213018727|ref|ZP_03334535.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Culex
           quinquefasciatus JHB]
 gi|212995678|gb|EEB56318.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Culex
           quinquefasciatus JHB]
          Length = 281

 Score =  257 bits (657), Expect = 1e-66,   Method: Compositional matrix adjust.
 Identities = 130/272 (47%), Positives = 192/272 (70%), Gaps = 2/272 (0%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +YI E+RK PML ++EE  LAK ++E+ D+S+AHRL+TSHL LVVKIAM ++ YGL + +
Sbjct: 2   QYIAEVRKFPMLSQEEEVRLAKNWQEYQDISSAHRLITSHLNLVVKIAMKFKNYGLLLMD 61

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +V EGN+GLM AVKKF+P+ GFR +TY++WWI+A+M+++IL+SWSLVKIGTT  Q+RLFF
Sbjct: 62  LVMEGNMGLMHAVKKFNPDLGFRFSTYAVWWIEASMKDFILKSWSLVKIGTTQAQRRLFF 121

Query: 138 NLRRLKGH-LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDK 195
           +LR++K   LQ      L  E++ AI+ +L+VSE +V+ M+ RLA  D+SLN  I   D 
Sbjct: 122 SLRKIKKRILQYTNRETLSKEEIKAISNELSVSEEDVVQMSYRLACKDQSLNNCIKIGDD 181

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
           +  + QD +  +   QE      EE+  +  +L+ +++ LN R R IF +R L EN  TL
Sbjct: 182 SKKELQDMIPCNLVSQEVAYQNHEEKALKETILSNALASLNERSRDIFISRYLSENTQTL 241

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           + LS ++ VSRER+RQ+  +A  KV++ I+ +
Sbjct: 242 DELSKKYCVSRERIRQLAEQAMSKVKQHIKSE 273


>gi|197103189|ref|YP_002128567.1| RNA polymerase sigma 32 subunit(heat shock sigma factor)
           [Phenylobacterium zucineum HLK1]
 gi|196480465|gb|ACG79992.1| RNA polymerase sigma 32 subunit(heat shock sigma factor)
           [Phenylobacterium zucineum HLK1]
          Length = 310

 Score =  254 bits (648), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 130/275 (47%), Positives = 181/275 (65%), Gaps = 6/275 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+  +R+ P+L + EEY LA+R R+  DL+AAHRL+TSHLRL  KIA GYRGYGLP+
Sbjct: 19  LRQYLSAVRRYPVLTRDEEYALARRVRDEVDLAAAHRLMTSHLRLAAKIACGYRGYGLPL 78

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++SE N+GL+ A+ KFD ER  RL+TY+ WWI+AA+Q+YILR WS+VK+GT+A QKRL
Sbjct: 79  EDMISEANVGLLHAIYKFDLERDCRLSTYAAWWIRAALQDYILRHWSIVKLGTSATQKRL 138

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FF  RR +  ++A     L  + +  +A+  +V   ++  M  RL   D SL+AL    D
Sbjct: 139 FFGFRRARARVEACPSELLAGDSIAKMAELFHVPPGDITGMEARLGWRDLSLSAL--HGD 196

Query: 195 KNSSQWQDWLVYDHDGQ--EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
           +      + L  D + Q  E  L E +ER  R  +LT+++S L  RE RIF ARRL++ P
Sbjct: 197 EGEPDRLERLA-DENAQDPETALSEADERDYRTRLLTQALSPLGSREHRIFVARRLRDPP 255

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             L  L+ E+ VS ER+RQIE RAF+KVQ  +  Q
Sbjct: 256 APLAELAQEYGVSCERIRQIEMRAFEKVQRFVTDQ 290


>gi|73667010|ref|YP_303026.1| sigma-70 region 2:sigma-70 region 4 [Ehrlichia canis str. Jake]
 gi|72394151|gb|AAZ68428.1| RNA polymerase, sigma 32 subunit, RpoH [Ehrlichia canis str. Jake]
          Length = 300

 Score =  252 bits (643), Expect = 5e-65,   Method: Compositional matrix adjust.
 Identities = 133/280 (47%), Positives = 187/280 (66%), Gaps = 4/280 (1%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           SI    +  L  Y++E+   P+L  +EE  LAK + E+G +  AHRLVTSHLRLVVKIA+
Sbjct: 11  SIFSLTQDNLMSYMNEVHTFPILSPEEEDRLAKNWYENGIVEDAHRLVTSHLRLVVKIAL 70

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            ++ YGLP+ E++ EGNIGLMQAVKKF+P  GFRL+TY++WWIKA++++YIL+SWS +KI
Sbjct: 71  SFKNYGLPLIELIMEGNIGLMQAVKKFNPTLGFRLSTYAIWWIKASIKDYILKSWSCIKI 130

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DES 185
           GTT  Q++LFF+LR++K  L     NN+  + +  IA + + SE EV  MN      D S
Sbjct: 131 GTTQAQRKLFFSLRKIKQKL--FKYNNITQDDIKLIANECSTSEQEVEQMNRYFTYRDRS 188

Query: 186 LNALINSSDKNSS-QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           LN ++ S+D     + Q+ +  D   QE   +  EE   +  ++T+++S LN R R IF 
Sbjct: 189 LNEVVFSNDNQKGIELQEIIKCDTPNQEDTYLLNEEASLKETLITQALSTLNERYRDIFI 248

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            RRL ENP TL+ LS E+++S+ERVRQIE  AF KV+  I
Sbjct: 249 RRRLIENPDTLDTLSQEYKISKERVRQIEMHAFTKVKNFI 288


>gi|111035800|emb|CAL29427.1| RNA polymerase sigma-32 factor [Wolbachia endosymbiont of
           Onchocerca volvulus]
          Length = 297

 Score =  251 bits (642), Expect = 7e-65,   Method: Compositional matrix adjust.
 Identities = 124/284 (43%), Positives = 195/284 (68%), Gaps = 2/284 (0%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +++ +NG   L +YI E++K P+L ++EE  LAK + ++ ++S+AH+L+TSHL LVVKIA
Sbjct: 6   LNLCINGSASLMQYIAEVQKFPILSQEEETRLAKNWHQYKNISSAHKLITSHLNLVVKIA 65

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
           M ++ YGL + +++ EGNIGLM AVKKF+P  GFR +TY++WWI+A+++++IL+SWS +K
Sbjct: 66  MKFKNYGLLLMDLIMEGNIGLMHAVKKFNPNLGFRFSTYAVWWIEASIKDFILKSWSFIK 125

Query: 126 IGTTANQKRLFFNLRRLKGH-LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GD 183
           IGTT  Q++LFF+LR++K   LQ      L  E++ AI+ +L VSE +VI M+ RLA  D
Sbjct: 126 IGTTQAQRKLFFSLRKIKKRILQYTNRETLSNEEIKAISNELAVSEGDVIQMSYRLAYKD 185

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           +SLN+ +   D +  + QD +  +   QE      EE++ +  +L  +++ LN R R IF
Sbjct: 186 QSLNSCLKVGDGSKKELQDMIPCNSVSQEVTYQNHEEKELKETILNNALANLNERSRDIF 245

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +R L EN  TL+ L  ++ VSRER+RQ+  +A  KV++ IQ +
Sbjct: 246 ISRYLSENTQTLDELGKKYNVSRERIRQLAEQAMSKVKQYIQSE 289


>gi|42520871|ref|NP_966786.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Drosophila
           melanogaster]
 gi|42410611|gb|AAS14720.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Drosophila
           melanogaster]
          Length = 297

 Score =  251 bits (641), Expect = 9e-65,   Method: Compositional matrix adjust.
 Identities = 127/283 (44%), Positives = 194/283 (68%), Gaps = 2/283 (0%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           ++ V+    L +YI  ++K PML ++EE  LAK + ++ D+S+AH+L+TSHL LVVKIAM
Sbjct: 7   NLCVDSRTNLMQYIARVQKFPMLSQEEEVRLAKNWNQYKDVSSAHKLITSHLNLVVKIAM 66

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            ++ YGL + ++V EGN+GLM AVKKF+P+ GFR +TY++WWI+A+++++IL+SWS VKI
Sbjct: 67  KFKNYGLLLMDLVMEGNMGLMHAVKKFNPDLGFRFSTYAVWWIEASIKDFILKSWSFVKI 126

Query: 127 GTTANQKRLFFNLRRLKGH-LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DE 184
           GTT  Q+RLFF+LR++K   LQ      L  E++ AI+ +L+VSE +V+ MN R+A  D+
Sbjct: 127 GTTQAQRRLFFSLRKIKKRILQYTNRETLNNEEIKAISNELSVSEGDVLQMNYRMACKDQ 186

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SLN  I   D +  + QD +  +   QE      EE++ +  +L  +++ LN R R IF 
Sbjct: 187 SLNDCIKIGDDSKRELQDMIPCNLVSQEVTYQNHEEKELKETILNNALASLNERARDIFI 246

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +R L EN  TL+ LS ++ VSRER+RQ+  +A  KV++ IQ +
Sbjct: 247 SRYLSENIQTLDELSKKYCVSRERIRQLAEQAMAKVKQYIQSE 289


>gi|255003152|ref|ZP_05278116.1| RNA polymerase sigma-32 factor (rpoH) [Anaplasma marginale str.
           Puerto Rico]
 gi|255004281|ref|ZP_05279082.1| RNA polymerase sigma-32 factor (rpoH) [Anaplasma marginale str.
           Virginia]
          Length = 296

 Score =  250 bits (638), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 131/275 (47%), Positives = 188/275 (68%), Gaps = 4/275 (1%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           G   L  Y+ ++R  P+L ++EE  LA+ +   G ++ AHRLVTSHLRLVVKIAMG++ Y
Sbjct: 17  GSDDLVSYVAQVRTFPILSEEEEKRLAENWYRRGSVADAHRLVTSHLRLVVKIAMGFKSY 76

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GLPI E++ EGNIGLMQAVK+F+P+ GFRLATY++WWIKA++++YILRSWS +++GTT  
Sbjct: 77  GLPIMELIMEGNIGLMQAVKRFNPDLGFRLATYAVWWIKASIKDYILRSWSCIRVGTTQA 136

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALI 190
           QK+LFF+LR++K  L +   +  K E + AIA++   SE EV  M+   A  D SLN  +
Sbjct: 137 QKKLFFSLRKIKKRLLSCGSSMTKKE-IKAIAEECATSEEEVERMDRFFANRDVSLNEQV 195

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           +   ++S + QD +      QE + +  EE   +++M   +++ L+ R R IF  RRLQE
Sbjct: 196 HG--ESSVELQDLVPSSLPSQEIMYLADEESAIKKSMFDSALATLDDRHRDIFTRRRLQE 253

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            P TLE LS E+ VS+ERVRQIE +A  K++  I+
Sbjct: 254 RPDTLEKLSEEYGVSKERVRQIELQALCKIKSFIE 288


>gi|222475169|ref|YP_002563585.1| RNA polymerase sigma-32 factor (rpoH) [Anaplasma marginale str.
           Florida]
 gi|222419306|gb|ACM49329.1| RNA polymerase sigma-32 factor (rpoH) [Anaplasma marginale str.
           Florida]
          Length = 307

 Score =  250 bits (638), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 131/275 (47%), Positives = 188/275 (68%), Gaps = 4/275 (1%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           G   L  Y+ ++R  P+L ++EE  LA+ +   G ++ AHRLVTSHLRLVVKIAMG++ Y
Sbjct: 28  GSDDLVSYVAQVRTFPILSEEEEKRLAENWYRRGSVADAHRLVTSHLRLVVKIAMGFKSY 87

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GLPI E++ EGNIGLMQAVK+F+P+ GFRLATY++WWIKA++++YILRSWS +++GTT  
Sbjct: 88  GLPIMELIMEGNIGLMQAVKRFNPDLGFRLATYAVWWIKASIKDYILRSWSCIRVGTTQA 147

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALI 190
           QK+LFF+LR++K  L +   +  K E + AIA++   SE EV  M+   A  D SLN  +
Sbjct: 148 QKKLFFSLRKIKKRLLSCGSSMTKKE-IKAIAEECATSEEEVERMDRFFANRDVSLNEQV 206

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           +   ++S + QD +      QE + +  EE   +++M   +++ L+ R R IF  RRLQE
Sbjct: 207 HG--ESSVELQDLVPSSLPSQEIMYLADEESAIKKSMFDSALATLDDRHRDIFTRRRLQE 264

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            P TLE LS E+ VS+ERVRQIE +A  K++  I+
Sbjct: 265 RPDTLEKLSEEYGVSKERVRQIELQALCKIKSFIE 299


>gi|56416805|ref|YP_153879.1| RNA polymerase sigma-32 factor [Anaplasma marginale str. St.
           Maries]
 gi|56388037|gb|AAV86624.1| RNA polymerase sigma-32 factor [Anaplasma marginale str. St.
           Maries]
          Length = 290

 Score =  249 bits (637), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 131/275 (47%), Positives = 188/275 (68%), Gaps = 4/275 (1%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           G   L  Y+ ++R  P+L ++EE  LA+ +   G ++ AHRLVTSHLRLVVKIAMG++ Y
Sbjct: 11  GSDDLVSYVAQVRTFPILSEEEEKRLAENWYRRGSVADAHRLVTSHLRLVVKIAMGFKSY 70

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GLPI E++ EGNIGLMQAVK+F+P+ GFRLATY++WWIKA++++YILRSWS +++GTT  
Sbjct: 71  GLPIMELIMEGNIGLMQAVKRFNPDLGFRLATYAVWWIKASIKDYILRSWSCIRVGTTQA 130

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALI 190
           QK+LFF+LR++K  L +   +  K E + AIA++   SE EV  M+   A  D SLN  +
Sbjct: 131 QKKLFFSLRKIKKRLLSCGSSMTKKE-IKAIAEECATSEEEVERMDRFFANRDVSLNEQV 189

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           +   ++S + QD +      QE + +  EE   +++M   +++ L+ R R IF  RRLQE
Sbjct: 190 HG--ESSVELQDLVPSSLPSQEIMYLADEESAIKKSMFDSALATLDDRHRDIFTRRRLQE 247

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            P TLE LS E+ VS+ERVRQIE +A  K++  I+
Sbjct: 248 RPDTLEKLSEEYGVSKERVRQIELQALCKIKSFIE 282


>gi|88658518|ref|YP_507464.1| RNA polymerase sigma-32 factor [Ehrlichia chaffeensis str.
           Arkansas]
 gi|88599975|gb|ABD45444.1| RNA polymerase sigma-32 factor [Ehrlichia chaffeensis str.
           Arkansas]
          Length = 297

 Score =  248 bits (633), Expect = 7e-64,   Method: Compositional matrix adjust.
 Identities = 133/280 (47%), Positives = 189/280 (67%), Gaps = 3/280 (1%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           SI    +  L  YI+E+   P+L  +EE  LA+ + E+G ++ AHRLVTSHLRLVVK+A+
Sbjct: 5   SIFSLTQDNLMSYINEVHAFPILSPEEEDRLARNWYENGIVADAHRLVTSHLRLVVKVAL 64

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            ++ Y LP+ E++ EGNIGLMQAVKKF+P  GFRL+TY++WWIKA +++YIL+SWS +KI
Sbjct: 65  SFKNYELPLIELIMEGNIGLMQAVKKFNPTLGFRLSTYAIWWIKAFIKDYILKSWSCIKI 124

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN-CRLAGDES 185
           GTT  Q++LFF+LR++K  L    ++N+  E +  IA K + SE EV  MN   L  D S
Sbjct: 125 GTTQAQRKLFFSLRKIKKKLFKY-NHNITKEDIKLIANKCSTSEQEVEQMNRYFLYRDRS 183

Query: 186 LNALINSSD-KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           LN L+ S+D +N  + Q+ +  D   QE   +  EE   ++ ++++++S LN R R IF 
Sbjct: 184 LNELVFSNDNQNGVELQEIIKCDTPNQEDTYLLNEELNIKKALISQALSTLNERYRDIFI 243

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            RRL E P TL+ LS E+ +S+ERVRQIE  AF KV+  I
Sbjct: 244 RRRLIEEPDTLDKLSQEYNISKERVRQIEMHAFTKVKNFI 283


>gi|254995008|ref|ZP_05277198.1| RNA polymerase sigma-32 factor (rpoH) [Anaplasma marginale str.
           Mississippi]
          Length = 296

 Score =  248 bits (632), Expect = 9e-64,   Method: Compositional matrix adjust.
 Identities = 130/275 (47%), Positives = 188/275 (68%), Gaps = 4/275 (1%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           G   L  Y+ ++R  P+L ++EE  LA+ +   G ++ AHRLVTSHLRLVVKIAMG++ Y
Sbjct: 17  GSDDLVSYVAQVRTFPILSEEEEKRLAENWYRRGSVADAHRLVTSHLRLVVKIAMGFKSY 76

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GLPI E++ EGNIGLMQAVK+F+P+ GFRLATY++WWIKA++++YILRSWS +++GTT  
Sbjct: 77  GLPIMELIMEGNIGLMQAVKRFNPDLGFRLATYAVWWIKASIKDYILRSWSCIRVGTTQA 136

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALI 190
           QK+LFF+LR++K  L +   +  K E + AIA++   SE EV  M+   A  D SLN  +
Sbjct: 137 QKKLFFSLRKIKKRLLSCGSSMTKKE-IKAIAEECATSEEEVERMDRFFANRDVSLNEQV 195

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           +   ++S + QD +      QE + +  EE   +++M   +++ L+ R R IF  RRL+E
Sbjct: 196 HG--ESSVELQDLVPSSLPSQEIMYLADEESAIKKSMFDSALATLDDRHRDIFTRRRLRE 253

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            P TLE LS E+ VS+ERVRQIE +A  K++  I+
Sbjct: 254 RPDTLEKLSEEYGVSKERVRQIELQALCKIKSFIE 288


>gi|27375413|ref|NP_766942.1| RNA polymerase subunit [Bradyrhizobium japonicum USDA 110]
 gi|1834377|emb|CAA70861.1| RNA polymerase subunit [Bradyrhizobium japonicum]
 gi|27348550|dbj|BAC45567.1| RNA polymerase subunit [Bradyrhizobium japonicum USDA 110]
          Length = 307

 Score =  246 bits (627), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 129/269 (47%), Positives = 175/269 (65%), Gaps = 1/269 (0%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           LS Y   IR+  +LE  +E  LA+R+ E  D  AA  LVTSHLRL  K+A GY+GYGLP+
Sbjct: 25  LSAYSAAIRRYELLEPGQEQQLARRWHETRDRGAADALVTSHLRLAAKLARGYKGYGLPM 84

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++E N+GL+ A  +F+P RG R +TY++WWIKAA+ EYILRSWSLVKIGTTA QK+L
Sbjct: 85  VDLIAEANLGLVIAASRFEPGRGARFSTYAIWWIKAAIHEYILRSWSLVKIGTTAAQKKL 144

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FF LR           + L P+    IA KL+V+  EVI M+ RL GD SLNA +   ++
Sbjct: 145 FFKLRSEIRKATGSVMSGLTPDVAELIAGKLDVTAREVIEMDARLNGDMSLNARVG-GEE 203

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
           + ++ +  LV      E +L + E+ + R   L  ++  L  RER +FEARRL E PVTL
Sbjct: 204 SGTELEALLVDGAVDAETMLADHEQTERRAKALRVALGGLAARERHVFEARRLTECPVTL 263

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + L+ E  +S ERVRQIE RAF KV+ ++
Sbjct: 264 DQLARELSISSERVRQIEIRAFAKVKRAV 292


>gi|134096067|ref|YP_001101142.1| sigma H factor [Herminiimonas arsenicoxydans]
 gi|133739970|emb|CAL63021.1| RNA polymerase sigma-32 factor [Herminiimonas arsenicoxydans]
          Length = 298

 Score =  243 bits (620), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 135/285 (47%), Positives = 182/285 (63%), Gaps = 13/285 (4%)

Query: 6   MSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           MS+  +G +G +  YI  + ++PML  +EE  LAKR R+  DL AA +LV SHLRLVV I
Sbjct: 17  MSLGFSGALGNIDAYISAVNRLPMLTHEEEISLAKRLRDDNDLGAAQKLVLSHLRLVVSI 76

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A GY GYGLP ++++ EGNIGLM+AVK+FDP++G RL +YSM WIKA M EYIL++W LV
Sbjct: 77  ARGYLGYGLPHADLIQEGNIGLMKAVKRFDPDQGVRLVSYSMHWIKAEMHEYILKNWRLV 136

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           K+ TT  Q++LFFNLR  K  L A+T     P+QV A+AK LNV   EVI M  RL+G +
Sbjct: 137 KVATTKAQRKLFFNLRSHKTGLDAMT-----PDQVEALAKTLNVKREEVIEMETRLSGRD 191

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM--LTRSMSVLNPRERRI 242
              AL   +D    ++        D QE   + + +R +R     L+ ++  L+PR RRI
Sbjct: 192 I--ALEAPTDDEDDKFAPIAYLSSDSQEPTRVLESQRYDRLQTEGLSSALGKLDPRSRRI 249

Query: 243 FEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            EAR L  +     TL  L++EF VS ER+RQIE  A KK++ S+
Sbjct: 250 VEARWLANDDGSGATLHELANEFGVSAERIRQIETVALKKMKGSL 294


>gi|154252145|ref|YP_001412969.1| RNA polymerase sigma-32 subunit RpoH [Parvibaculum lavamentivorans
           DS-1]
 gi|154156095|gb|ABS63312.1| RNA polymerase, sigma 32 subunit, RpoH [Parvibaculum
           lavamentivorans DS-1]
          Length = 298

 Score =  243 bits (620), Expect = 2e-62,   Method: Compositional matrix adjust.
 Identities = 120/283 (42%), Positives = 185/283 (65%), Gaps = 3/283 (1%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           RY+ +   +P+L++Q E+ LA+R+++HGD  A H L  +++RLV+ +A  +R YGLP  +
Sbjct: 15  RYMKQAMTVPLLDEQHEFDLARRWKDHGDEQALHELTCAYMRLVISLATRFRNYGLPYGD 74

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGN+GLMQA  +F+PERG R +TY+ WWI+AA+Q+YILR+WS+V+ GTTA  K LFF
Sbjct: 75  LIQEGNVGLMQAAARFEPERGVRFSTYASWWIRAAIQDYILRNWSIVRTGTTAAHKSLFF 134

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALI--NSSD 194
           NLRRL+  +   T  NL  +  + IAK+L V  S+V +++ RL  GD SLNA +  ++S 
Sbjct: 135 NLRRLRALIANGTRQNLTEDDRIFIAKRLGVGASDVATIDARLMTGDRSLNATVSDSTSS 194

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
           +N ++WQD L  +    E+ ++E  + K R   +  ++  LN RE  I   RRL+++  T
Sbjct: 195 ENLTEWQDLLPCERPLPEEEVMENHDSKQRSRWIEGALESLNERELTIIRERRLRDDVAT 254

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLL 297
           LE L     +S+ERVRQIE  A KK++ ++  +V    +  LL
Sbjct: 255 LETLGVRLGISKERVRQIEHMALKKLRTALLDKVPDPEAAGLL 297


>gi|88607306|ref|YP_505338.1| RNA polymerase sigma-32 factor [Anaplasma phagocytophilum HZ]
 gi|88598369|gb|ABD43839.1| RNA polymerase sigma-32 factor [Anaplasma phagocytophilum HZ]
          Length = 289

 Score =  241 bits (615), Expect = 9e-62,   Method: Compositional matrix adjust.
 Identities = 121/270 (44%), Positives = 185/270 (68%), Gaps = 2/270 (0%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           G   L  Y+ ++R  PML ++EE   A+ + ++  ++ AH+LVTSHLRLVVK+AMG+R Y
Sbjct: 10  GADDLLAYMEQVRAFPMLTEREEKECAENWHKNRSVADAHKLVTSHLRLVVKVAMGFRSY 69

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GLP+ E++ EGNIGLMQAVKKF+PE GFRL+TY++WWIKA++++YILRSWS ++IGTT  
Sbjct: 70  GLPLMELIMEGNIGLMQAVKKFNPELGFRLSTYAIWWIKASIKDYILRSWSCMRIGTTQA 129

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
           QK+LFF+LR++K  +   + +  + + + AIA++   SE EV SM+ R   +  ++    
Sbjct: 130 QKKLFFSLRKIKRRILGCSASASQSD-IRAIAEECGTSEKEVESMD-RFFSNRDISLSDK 187

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
              ++ ++ QD +      QE + +  EE   +  M+  ++S L+ R R IF  R+L+E+
Sbjct: 188 VCCESGTELQDLIPCSSPNQEVMYLSHEESVMKDQMVKEALSTLDERHRDIFSRRKLKEH 247

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           P TLE LS E+ VS+ER+RQIE ++F KV+
Sbjct: 248 PDTLETLSEEYGVSKERIRQIELQSFSKVR 277


>gi|269958772|ref|YP_003328559.1| RNA polymerase sigma-32 factor [Anaplasma centrale str. Israel]
 gi|269848601|gb|ACZ49245.1| RNA polymerase sigma-32 factor [Anaplasma centrale str. Israel]
          Length = 307

 Score =  241 bits (614), Expect = 1e-61,   Method: Compositional matrix adjust.
 Identities = 126/275 (45%), Positives = 186/275 (67%), Gaps = 4/275 (1%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           G   L  YI ++R  P+L ++EE  LA+ +   G ++ AH+LVTSHLRLVVK+AMG++ Y
Sbjct: 28  GSGDLVSYIAQVRTFPVLSEEEEKRLAENWYRRGSVADAHKLVTSHLRLVVKVAMGFKNY 87

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GLP+ E++ EGNIGLMQAVK+F+P+ G RLATY++WWIKA++++YILRSWS +++GTT  
Sbjct: 88  GLPLMELIMEGNIGLMQAVKRFNPDLGSRLATYAVWWIKASIKDYILRSWSCIRVGTTQA 147

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALI 190
           QK+LFF+LR++K  L      ++  ++V  IA++   SE EV  M+   A  D SLN  +
Sbjct: 148 QKKLFFSLRKIKKRLLG-CGTSMTQKEVKTIAEECATSEEEVERMDRFFASRDVSLNEPV 206

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           +   ++S + QD +      QE + +  EE   +++M   ++S L+ R R IF  RRLQE
Sbjct: 207 HG--ESSVELQDLVPSSLPSQEAMYLADEESAIKKSMFDAALSTLDHRHRDIFTRRRLQE 264

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            P TLE LS ++ VS+ERVRQIE +A  K++  I+
Sbjct: 265 RPDTLEKLSEKYGVSKERVRQIELQALCKIKTFIE 299


>gi|58579073|ref|YP_197285.1| RNA polymerase sigma-32 factor [Ehrlichia ruminantium str.
           Welgevonden]
 gi|58417699|emb|CAI26903.1| RNA polymerase sigma-32 factor [Ehrlichia ruminantium str.
           Welgevonden]
          Length = 320

 Score =  239 bits (611), Expect = 3e-61,   Method: Compositional matrix adjust.
 Identities = 129/280 (46%), Positives = 191/280 (68%), Gaps = 3/280 (1%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           SI+   +  L  YI+E++   +L  +EE  LAK + EHG ++ AH+LVTSHLRLVVK+A+
Sbjct: 29  SILSLTQDNLMSYINEVQSFQVLSLEEEEKLAKNWYEHGVIADAHKLVTSHLRLVVKVAL 88

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            ++ YGLP+ E++ EGNIGLMQAVKKF+P  GFRL+TY++WWIKA++++YIL+SWS +KI
Sbjct: 89  SFKNYGLPLIELIMEGNIGLMQAVKKFNPNLGFRLSTYAIWWIKASIKDYILKSWSCIKI 148

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DES 185
           GTT  Q++LFF+LR++K  L     NN+  E +  IA + + SE EV  MN      D+S
Sbjct: 149 GTTQAQRKLFFSLRKIKKKLLK-YHNNITKEDIKMIANECSTSEQEVEQMNKYFTYRDKS 207

Query: 186 LNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           LN ++ S+  +N  Q QD +  +   QE   +  EE   +++++T++++ LN R R IF 
Sbjct: 208 LNDVVFSNGSQNGVQLQDMIKCEDPNQEDAYLLNEETDIKKSLITQALATLNERHRDIFI 267

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            R+L E P TLE LS ++ +S+ER+RQIE  AF KV+  +
Sbjct: 268 RRKLIEEPDTLEILSKKYNISKERIRQIETHAFLKVKNFV 307


>gi|58617131|ref|YP_196330.1| RNA polymerase sigma-32 factor [Ehrlichia ruminantium str. Gardel]
 gi|58416743|emb|CAI27856.1| RNA polymerase sigma-32 factor [Ehrlichia ruminantium str. Gardel]
          Length = 319

 Score =  239 bits (610), Expect = 3e-61,   Method: Compositional matrix adjust.
 Identities = 129/280 (46%), Positives = 191/280 (68%), Gaps = 3/280 (1%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           SI+   +  L  YI+E++   +L  +EE  LAK + EHG ++ AH+LVTSHLRLVVK+A+
Sbjct: 29  SILSLTQDNLMSYINEVQSFQVLSLEEEEKLAKNWYEHGVIADAHKLVTSHLRLVVKVAL 88

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            ++ YGLP+ E++ EGNIGLMQAVKKF+P  GFRL+TY++WWIKA++++YIL+SWS +KI
Sbjct: 89  SFKNYGLPLIELIMEGNIGLMQAVKKFNPNLGFRLSTYAIWWIKASIKDYILKSWSCIKI 148

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DES 185
           GTT  Q++LFF+LR++K  L     NN+  E +  IA + + SE EV  MN      D+S
Sbjct: 149 GTTQAQRKLFFSLRKIKKKLLK-YHNNITKEDIKMIANECSTSEQEVEQMNKYFTYRDKS 207

Query: 186 LNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           LN ++ S+  +N  Q QD +  +   QE   +  EE   +++++T++++ LN R R IF 
Sbjct: 208 LNDVVFSNGSQNGVQLQDMIKCEDPNQEDAYLLNEETDIKKSLITQALATLNERHRDIFI 267

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            R+L E P TLE LS ++ +S+ER+RQIE  AF KV+  +
Sbjct: 268 RRKLIEEPDTLEILSKKYNISKERIRQIETHAFLKVKNFV 307


>gi|57239125|ref|YP_180261.1| RNA polymerase sigma-32 factor [Ehrlichia ruminantium str.
           Welgevonden]
 gi|57161204|emb|CAH58118.1| RNA polymerase sigma-32 factor [Ehrlichia ruminantium str.
           Welgevonden]
          Length = 296

 Score =  239 bits (610), Expect = 4e-61,   Method: Compositional matrix adjust.
 Identities = 129/277 (46%), Positives = 190/277 (68%), Gaps = 3/277 (1%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           SI+   +  L  YI+E++   +L  +EE  LAK + EHG ++ AH+LVTSHLRLVVK+A+
Sbjct: 5   SILSLTQDNLMSYINEVQSFQVLSLEEEEKLAKNWYEHGVIADAHKLVTSHLRLVVKVAL 64

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            ++ YGLP+ E++ EGNIGLMQAVKKF+P  GFRL+TY++WWIKA++++YIL+SWS +KI
Sbjct: 65  SFKNYGLPLIELIMEGNIGLMQAVKKFNPNLGFRLSTYAIWWIKASIKDYILKSWSCIKI 124

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DES 185
           GTT  Q++LFF+LR++K  L     NN+  E +  IA + + SE EV  MN      D+S
Sbjct: 125 GTTQAQRKLFFSLRKIKKKLLKY-HNNITKEDIKMIANECSTSEQEVEQMNKYFTYRDKS 183

Query: 186 LNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           LN ++ S+  +N  Q QD +  +   QE   +  EE   +++++T++++ LN R R IF 
Sbjct: 184 LNDVVFSNGSQNGVQLQDMIKCEDPNQEDAYLLNEETDIKKSLITQALATLNERHRDIFI 243

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R+L E P TLE LS ++ +S+ER+RQIE  AF KV+
Sbjct: 244 RRKLIEEPDTLEILSKKYNISKERIRQIETHAFLKVK 280


>gi|209965510|ref|YP_002298425.1| RNA polymerase sigma-32 factor [Rhodospirillum centenum SW]
 gi|209958976|gb|ACI99612.1| RNA polymerase sigma-32 factor [Rhodospirillum centenum SW]
          Length = 295

 Score =  238 bits (607), Expect = 9e-61,   Method: Compositional matrix adjust.
 Identities = 125/273 (45%), Positives = 181/273 (66%), Gaps = 4/273 (1%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           +I    K P+L +  E+ LAKR+RE GD +A H LV S+ RLVV  A  +R YGLP+ ++
Sbjct: 16  FIKASMKEPLLSRDHEFDLAKRWRERGDEAALHELVRSYTRLVVATAARFRNYGLPMGDL 75

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GLMQA  +F+P+R  R +TY+ WWI++AMQ+YILR+WS+V+ GTTA QK LFFN
Sbjct: 76  VQEGNVGLMQAAARFEPDREVRFSTYAAWWIRSAMQDYILRNWSIVRTGTTAAQKALFFN 135

Query: 139 LRRLKGHLQ-AITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSSDKN 196
           LRRL+  ++ + + + L P+    IA++LNV ES+V SM  RL A D+SLN+ +  ++  
Sbjct: 136 LRRLRAKIEDSPSASALSPDGRRRIAEELNVDESDVESMEMRLAAADQSLNSPV--AEGG 193

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
             +WQD+L       E V+I   + + R   L  ++  L+PRER I   RRL+++  TLE
Sbjct: 194 DDEWQDFLSDQRPSPEDVVIGMRDGRMRSRWLAEALGELSPRERTIIAQRRLRDDGATLE 253

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
            L     VS+ERVRQ+E RA  K++ S+ ++VE
Sbjct: 254 ELGRVLGVSKERVRQLEHRALMKLRASMIRRVE 286


>gi|117925612|ref|YP_866229.1| RNA polymerase, sigma 32 subunit, RpoH [Magnetococcus sp. MC-1]
 gi|117609368|gb|ABK44823.1| RNA polymerase, sigma 32 subunit, RpoH [Magnetococcus sp. MC-1]
          Length = 290

 Score =  238 bits (606), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 127/278 (45%), Positives = 178/278 (64%), Gaps = 10/278 (3%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
            M +   GE  L+ Y+ ++   PML  +EE+ LA RYRE  DL AAH+LVTS+LR V  I
Sbjct: 4   TMLVPYKGENQLAGYMQQVDSYPMLSAEEEFELAVRYREQNDLEAAHKLVTSYLRYVASI 63

Query: 65  AMGYRGY-GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           A  Y+GY G+   ++V EG++GLMQAVK+FDP +GFRLATY+MWWIKA++QE++L  WSL
Sbjct: 64  AKEYQGYYGIKFMDLVQEGSVGLMQAVKRFDPHKGFRLATYAMWWIKASIQEFVLHHWSL 123

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG- 182
           VKIGTTA Q++LFFNLR+ K  L+      L   Q   + ++  VS   V+ M+ RL+G 
Sbjct: 124 VKIGTTAAQRKLFFNLRKSKDTLE-----RLDATQAEEMGQRFGVSGEAVLEMDARLSGP 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
           D+SLN  +    +   + Q+ L      QE  L+  E  + ++ M+ +++S L+ RE+ I
Sbjct: 179 DDSLNRCLV---EGGEEIQNMLADSAPNQEMRLLASESERLQQQMIKQALSFLSEREQMI 235

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             AR +   PVTLE L     VSRER+RQ+E RA KK+
Sbjct: 236 VRARIMCAEPVTLEVLGERLGVSRERIRQLETRALKKL 273


>gi|225630797|ref|YP_002727588.1| heat shock sigma factor RpoH [Wolbachia sp. wRi]
 gi|225592778|gb|ACN95797.1| heat shock sigma factor RpoH [Wolbachia sp. wRi]
          Length = 270

 Score =  236 bits (602), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 121/262 (46%), Positives = 182/262 (69%), Gaps = 2/262 (0%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           ML ++EE  LAK + ++ D+S+AH+L+TSHL LVVKIAM ++ YGL + ++V EGN+GLM
Sbjct: 1   MLSQEEEVRLAKNWNQYKDVSSAHKLITSHLNLVVKIAMKFKNYGLLLMDLVMEGNMGLM 60

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH-L 146
            AVKKF+P+ GFR +TY++WWI+A+++++IL+SWS VKIGTT  Q+RLFF+LR++K   L
Sbjct: 61  HAVKKFNPDLGFRFSTYAVWWIEASIKDFILKSWSFVKIGTTQAQRRLFFSLRKIKKRIL 120

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLV 205
           Q      L  E++ AI+ +L+VSE +V+ MN R+A  D+SLN  I   D +  + QD + 
Sbjct: 121 QYTNRETLNNEEIKAISNELSVSEGDVLQMNYRMACKDQSLNDCIKIGDDSKRELQDMIP 180

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            +   QE      EE++ +  +L  +++ LN R R IF +R L EN  TL+ LS ++ VS
Sbjct: 181 CNLVSQEVTYQNHEEKELKEAILNNALASLNERARDIFISRYLSENIQTLDELSKKYCVS 240

Query: 266 RERVRQIEARAFKKVQESIQKQ 287
           RER+RQ+  +A  KV++ IQ +
Sbjct: 241 RERIRQLAEQAMAKVKQYIQSE 262


>gi|256061796|ref|ZP_05451931.1| RNA polymerase factor sigma-32 [Brucella neotomae 5K33]
          Length = 311

 Score =  233 bits (595), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 116/267 (43%), Positives = 180/267 (67%), Gaps = 1/267 (0%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE++EE  LA R++E  D  A HR+ ++H+RLV+ +A  +R + LP+S+++ EG +GL
Sbjct: 42  PYLEREEERALAIRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGL 101

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +FDP+R  R +TY+ WWI+A+MQ+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 102 LEAAARFDPDRDVRFSTYAFWWIRASMQDYILRNWSIVRGGTSSAQKALFFNLRRLRSKL 161

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLV 205
               DN  K E    I+ +L VS S++  M+ RL+G D SL+A +N  +  +S+  D+LV
Sbjct: 162 AQTDDNMTKAEIYREISDQLGVSTSDIEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLV 221

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            DH  Q+++     + + R   LTR++  LN RE  I   RRL ++ VTLE L  +  +S
Sbjct: 222 DDHPLQDEIAESSIDMERRNRWLTRALDTLNERELHIIRERRLDDDGVTLEALGEKLGIS 281

Query: 266 RERVRQIEARAFKKVQESIQKQVELSS 292
           +ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 282 KERVRQIESRAMEKLKIALLSQHELAA 308


>gi|189024846|ref|YP_001935614.1| RNA polymerase factor sigma-32 [Brucella abortus S19]
 gi|189020418|gb|ACD73140.1| Sigma-70 factor family [Brucella abortus S19]
          Length = 306

 Score =  233 bits (594), Expect = 2e-59,   Method: Compositional matrix adjust.
 Identities = 117/267 (43%), Positives = 180/267 (67%), Gaps = 1/267 (0%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE++EE  LA R++E  D  A HR+ ++H+RLV+ +A  +R + LP+S+++ EG +GL
Sbjct: 37  PYLEREEERALAIRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGL 96

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +FDP+R  R +TY+ WWI+A+MQ+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 97  LEAAARFDPDRDVRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKALFFNLRRLRSKL 156

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLV 205
               DN  K E    I+ +L VS S+V  M+ RL+G D SL+A +N  +  +S+  D+LV
Sbjct: 157 AQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLV 216

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            DH  Q+++     + + R   LTR++  LN RE  I   RRL ++ VTLE L  +  +S
Sbjct: 217 DDHPLQDEIAESSIDMERRNRWLTRALDTLNERELHIIRERRLDDDGVTLEALGEKLGIS 276

Query: 266 RERVRQIEARAFKKVQESIQKQVELSS 292
           +ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 277 KERVRQIESRAMEKLKIALLSQHELAA 303


>gi|261325797|ref|ZP_05964994.1| RNA polymerase factor sigma-32 [Brucella neotomae 5K33]
 gi|261301777|gb|EEY05274.1| RNA polymerase factor sigma-32 [Brucella neotomae 5K33]
          Length = 293

 Score =  233 bits (594), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 116/267 (43%), Positives = 180/267 (67%), Gaps = 1/267 (0%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE++EE  LA R++E  D  A HR+ ++H+RLV+ +A  +R + LP+S+++ EG +GL
Sbjct: 24  PYLEREEERALAIRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGL 83

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +FDP+R  R +TY+ WWI+A+MQ+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 84  LEAAARFDPDRDVRFSTYAFWWIRASMQDYILRNWSIVRGGTSSAQKALFFNLRRLRSKL 143

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLV 205
               DN  K E    I+ +L VS S++  M+ RL+G D SL+A +N  +  +S+  D+LV
Sbjct: 144 AQTDDNMTKAEIYREISDQLGVSTSDIEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLV 203

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            DH  Q+++     + + R   LTR++  LN RE  I   RRL ++ VTLE L  +  +S
Sbjct: 204 DDHPLQDEIAESSIDMERRNRWLTRALDTLNERELHIIRERRLDDDGVTLEALGEKLGIS 263

Query: 266 RERVRQIEARAFKKVQESIQKQVELSS 292
           +ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 264 KERVRQIESRAMEKLKIALLSQHELAA 290


>gi|254694416|ref|ZP_05156244.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 3 str. Tulya]
          Length = 311

 Score =  233 bits (594), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 117/267 (43%), Positives = 180/267 (67%), Gaps = 1/267 (0%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE++EE  LA R++E  D  A HR+ ++H+RLV+ +A  +R + LP+S+++ EG +GL
Sbjct: 42  PYLEREEERALAIRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGL 101

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +FDP+R  R +TY+ WWI+A+MQ+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 102 LEAAARFDPDRDVRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKALFFNLRRLRSKL 161

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLV 205
               DN  K E    I+ +L VS S+V  M+ RL+G D SL+A +N  +  +S+  D+LV
Sbjct: 162 AQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLV 221

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            DH  Q+++     + + R   LTR++  LN RE  I   RRL ++ VTLE L  +  +S
Sbjct: 222 DDHPLQDEIAESSIDMERRNRWLTRALDTLNERELHIIRERRLDDDGVTLEALGEKLGIS 281

Query: 266 RERVRQIEARAFKKVQESIQKQVELSS 292
           +ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 282 KERVRQIESRAMEKLKIALLSQHELAA 308


>gi|62290634|ref|YP_222427.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 1 str. 9-941]
 gi|82700548|ref|YP_415122.1| RNA polymerase factor sigma-32 [Brucella melitensis biovar Abortus
           2308]
 gi|148559493|ref|YP_001259609.1| RNA polymerase factor sigma-32 [Brucella ovis ATCC 25840]
 gi|254689924|ref|ZP_05153178.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 6 str. 870]
 gi|254700417|ref|ZP_05162245.1| RNA polymerase factor sigma-32 [Brucella suis bv. 5 str. 513]
 gi|254719758|ref|ZP_05181569.1| RNA polymerase factor sigma-32 [Brucella sp. 83/13]
 gi|254730958|ref|ZP_05189536.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 4 str. 292]
 gi|256258178|ref|ZP_05463714.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 9 str. C68]
 gi|256370169|ref|YP_003107680.1| RNA polymerase factor sigma-32 [Brucella microti CCM 4915]
 gi|260547128|ref|ZP_05822866.1| sigma-70 factor family protein [Brucella abortus NCTC 8038]
 gi|297249027|ref|ZP_06932735.1| RNA polymerase sigma-32 factor [Brucella abortus bv. 5 str. B3196]
 gi|306839453|ref|ZP_07472261.1| RNA polymerase sigma factor, sigma-70 family [Brucella sp. NF 2653]
 gi|62196766|gb|AAX75066.1| RNA polymerase sigma-70 factor family protein [Brucella abortus bv.
           1 str. 9-941]
 gi|82616649|emb|CAJ11731.1| Sigma-70 factor family:Sigma-70 region 2:Sigma-70 region 4
           [Brucella melitensis biovar Abortus 2308]
 gi|148370750|gb|ABQ60729.1| RNA polymerase sigma-70 factor family protein [Brucella ovis ATCC
           25840]
 gi|256000332|gb|ACU48731.1| RNA polymerase factor sigma-32 [Brucella microti CCM 4915]
 gi|260095493|gb|EEW79371.1| sigma-70 factor family protein [Brucella abortus NCTC 8038]
 gi|297174160|gb|EFH33517.1| RNA polymerase sigma-32 factor [Brucella abortus bv. 5 str. B3196]
 gi|306405398|gb|EFM61669.1| RNA polymerase sigma factor, sigma-70 family [Brucella sp. NF 2653]
          Length = 311

 Score =  233 bits (594), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 117/267 (43%), Positives = 180/267 (67%), Gaps = 1/267 (0%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE++EE  LA R++E  D  A HR+ ++H+RLV+ +A  +R + LP+S+++ EG +GL
Sbjct: 42  PYLEREEERALAIRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGL 101

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +FDP+R  R +TY+ WWI+A+MQ+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 102 LEAAARFDPDRDVRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKALFFNLRRLRSKL 161

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLV 205
               DN  K E    I+ +L VS S+V  M+ RL+G D SL+A +N  +  +S+  D+LV
Sbjct: 162 AQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLV 221

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            DH  Q+++     + + R   LTR++  LN RE  I   RRL ++ VTLE L  +  +S
Sbjct: 222 DDHPLQDEIAESSIDMERRNRWLTRALDTLNERELHIIRERRLDDDGVTLEALGEKLGIS 281

Query: 266 RERVRQIEARAFKKVQESIQKQVELSS 292
           +ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 282 KERVRQIESRAMEKLKIALLSQHELAA 308


>gi|260755457|ref|ZP_05867805.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 6 str. 870]
 gi|260758679|ref|ZP_05871027.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 4 str. 292]
 gi|260884475|ref|ZP_05896089.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 9 str. C68]
 gi|261214728|ref|ZP_05929009.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 3 str. Tulya]
 gi|261750913|ref|ZP_05994622.1| RNA polymerase factor sigma-32 [Brucella suis bv. 5 str. 513]
 gi|265984775|ref|ZP_06097510.1| RNA polymerase factor sigma-32 [Brucella sp. 83/13]
 gi|294851008|ref|ZP_06791684.1| RNA polymerase sigma-32 factor [Brucella sp. NVSL 07-0026]
 gi|260668997|gb|EEX55937.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 4 str. 292]
 gi|260675565|gb|EEX62386.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 6 str. 870]
 gi|260874003|gb|EEX81072.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 9 str. C68]
 gi|260916335|gb|EEX83196.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 3 str. Tulya]
 gi|261740666|gb|EEY28592.1| RNA polymerase factor sigma-32 [Brucella suis bv. 5 str. 513]
 gi|264663367|gb|EEZ33628.1| RNA polymerase factor sigma-32 [Brucella sp. 83/13]
 gi|294821651|gb|EFG38647.1| RNA polymerase sigma-32 factor [Brucella sp. NVSL 07-0026]
          Length = 293

 Score =  233 bits (593), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 117/267 (43%), Positives = 180/267 (67%), Gaps = 1/267 (0%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE++EE  LA R++E  D  A HR+ ++H+RLV+ +A  +R + LP+S+++ EG +GL
Sbjct: 24  PYLEREEERALAIRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGL 83

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +FDP+R  R +TY+ WWI+A+MQ+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 84  LEAAARFDPDRDVRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKALFFNLRRLRSKL 143

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLV 205
               DN  K E    I+ +L VS S+V  M+ RL+G D SL+A +N  +  +S+  D+LV
Sbjct: 144 AQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLV 203

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            DH  Q+++     + + R   LTR++  LN RE  I   RRL ++ VTLE L  +  +S
Sbjct: 204 DDHPLQDEIAESSIDMERRNRWLTRALDTLNERELHIIRERRLDDDGVTLEALGEKLGIS 263

Query: 266 RERVRQIEARAFKKVQESIQKQVELSS 292
           +ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 264 KERVRQIESRAMEKLKIALLSQHELAA 290


>gi|306844750|ref|ZP_07477335.1| RNA polymerase sigma factor, sigma-70 family [Brucella sp. BO1]
 gi|306274922|gb|EFM56692.1| RNA polymerase sigma factor, sigma-70 family [Brucella sp. BO1]
          Length = 311

 Score =  233 bits (593), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 117/267 (43%), Positives = 180/267 (67%), Gaps = 1/267 (0%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE++EE  LA R++E  D  A HR+ ++H+RLV+ +A  +R + LP+S+++ EG +GL
Sbjct: 42  PYLEREEERALAIRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGL 101

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +FDP+R  R +TY+ WWI+A+MQ+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 102 LEAAARFDPDRDVRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKALFFNLRRLRSKL 161

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLV 205
               DN  K E    I+ +L VS S+V  M+ RL+G D SL+A +N  +  +S+  D+LV
Sbjct: 162 AQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEESGASRRMDFLV 221

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            DH  Q+++     + + R   LTR++  LN RE  I   RRL ++ VTLE L  +  +S
Sbjct: 222 DDHPLQDEIAESSIDMERRNRWLTRALDTLNERELHIIRERRLDDDGVTLEALGEKLGIS 281

Query: 266 RERVRQIEARAFKKVQESIQKQVELSS 292
           +ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 282 KERVRQIESRAMEKLKIALLSQHELAA 308


>gi|23502620|ref|NP_698747.1| RNA polymerase factor sigma-32 [Brucella suis 1330]
 gi|161619688|ref|YP_001593575.1| RNA polymerase factor sigma-32 [Brucella canis ATCC 23365]
 gi|254703536|ref|ZP_05165364.1| RNA polymerase factor sigma-32 [Brucella suis bv. 3 str. 686]
 gi|260568841|ref|ZP_05839309.1| sigma-70 factor family protein [Brucella suis bv. 4 str. 40]
 gi|23348625|gb|AAN30662.1| RNA polymerase sigma-70 factor family protein [Brucella suis 1330]
 gi|161336499|gb|ABX62804.1| RNA polymerase sigma factor, sigma-70 family [Brucella canis ATCC
           23365]
 gi|260154225|gb|EEW89307.1| sigma-70 factor family protein [Brucella suis bv. 4 str. 40]
          Length = 311

 Score =  233 bits (593), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 117/267 (43%), Positives = 180/267 (67%), Gaps = 1/267 (0%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE++EE  LA R++E  D  A HR+ ++H+RLV+ +A  +R + LP+S+++ EG +GL
Sbjct: 42  PYLEREEERALAIRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGL 101

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +FDP+R  R +TY+ WWI+A+MQ+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 102 LEAAARFDPDRDVRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKALFFNLRRLRSKL 161

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLV 205
               DN  K E    I+ +L VS S+V  M+ RL+G D SL+A +N  +  +S+  D+LV
Sbjct: 162 AQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLV 221

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            DH  Q+++     + + R   LTR++  LN RE  I   RRL ++ VTLE L  +  +S
Sbjct: 222 DDHPLQDEIAESSIDMERRNCWLTRALDTLNERELHIIRERRLDDDGVTLEALGEKLGIS 281

Query: 266 RERVRQIEARAFKKVQESIQKQVELSS 292
           +ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 282 KERVRQIESRAMEKLKIALLSQHELAA 308


>gi|237816135|ref|ZP_04595131.1| RNA polymerase sigma factor, sigma-70 family [Brucella abortus str.
           2308 A]
 gi|237788798|gb|EEP63010.1| RNA polymerase sigma factor, sigma-70 family [Brucella abortus str.
           2308 A]
          Length = 319

 Score =  233 bits (593), Expect = 3e-59,   Method: Compositional matrix adjust.
 Identities = 117/267 (43%), Positives = 180/267 (67%), Gaps = 1/267 (0%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE++EE  LA R++E  D  A HR+ ++H+RLV+ +A  +R + LP+S+++ EG +GL
Sbjct: 50  PYLEREEERALAIRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGL 109

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +FDP+R  R +TY+ WWI+A+MQ+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 110 LEAAARFDPDRDVRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKALFFNLRRLRSKL 169

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLV 205
               DN  K E    I+ +L VS S+V  M+ RL+G D SL+A +N  +  +S+  D+LV
Sbjct: 170 AQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLV 229

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            DH  Q+++     + + R   LTR++  LN RE  I   RRL ++ VTLE L  +  +S
Sbjct: 230 DDHPLQDEIAESSIDMERRNRWLTRALDTLNERELHIIRERRLDDDGVTLEALGEKLGIS 289

Query: 266 RERVRQIEARAFKKVQESIQKQVELSS 292
           +ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 290 KERVRQIESRAMEKLKIALLSQHELAA 316


>gi|261754167|ref|ZP_05997876.1| RNA polymerase factor sigma-32 [Brucella suis bv. 3 str. 686]
 gi|261743920|gb|EEY31846.1| RNA polymerase factor sigma-32 [Brucella suis bv. 3 str. 686]
          Length = 293

 Score =  233 bits (593), Expect = 4e-59,   Method: Compositional matrix adjust.
 Identities = 117/267 (43%), Positives = 180/267 (67%), Gaps = 1/267 (0%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE++EE  LA R++E  D  A HR+ ++H+RLV+ +A  +R + LP+S+++ EG +GL
Sbjct: 24  PYLEREEERALAIRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGL 83

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +FDP+R  R +TY+ WWI+A+MQ+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 84  LEAAARFDPDRDVRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKALFFNLRRLRSKL 143

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLV 205
               DN  K E    I+ +L VS S+V  M+ RL+G D SL+A +N  +  +S+  D+LV
Sbjct: 144 AQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLV 203

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            DH  Q+++     + + R   LTR++  LN RE  I   RRL ++ VTLE L  +  +S
Sbjct: 204 DDHPLQDEIAESSIDMERRNCWLTRALDTLNERELHIIRERRLDDDGVTLEALGEKLGIS 263

Query: 266 RERVRQIEARAFKKVQESIQKQVELSS 292
           +ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 264 KERVRQIESRAMEKLKIALLSQHELAA 290


>gi|152980759|ref|YP_001354832.1| RNA polymerase sigma-32 factor [Janthinobacterium sp. Marseille]
 gi|151280836|gb|ABR89246.1| RNA polymerase sigma-32 factor [Janthinobacterium sp. Marseille]
          Length = 298

 Score =  232 bits (592), Expect = 4e-59,   Method: Compositional matrix adjust.
 Identities = 131/288 (45%), Positives = 182/288 (63%), Gaps = 11/288 (3%)

Query: 2   NRKNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           N   +++  +G +G +  YI  + ++PML  +EE  LA+R R+  DL AA +LV SHLRL
Sbjct: 13  NSNMLALGFSGALGNIDAYISAVNRLPMLTHEEEMSLARRLRDENDLGAAQKLVLSHLRL 72

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA GY GYGLP ++++ EGNIGLM+AVK+FDP++G RL +YSM WIKA M EYIL++
Sbjct: 73  VVSIARGYLGYGLPHADLIQEGNIGLMKAVKRFDPDQGVRLVSYSMHWIKAEMHEYILKN 132

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W LVK+ TT  Q++LFFNLR  K  L ++T     P+QV  +AK LNV   EVI M  RL
Sbjct: 133 WRLVKVATTKAQRKLFFNLRSHKTGLDSMT-----PDQVDELAKTLNVKREEVIEMETRL 187

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D +L A  +  D   +    +L  D     +VL  ++  + +   L+ ++  L+ R 
Sbjct: 188 SGRDIALEAPTDDEDDKFAPIA-YLSSDMQEPTKVLESQQFDRLQTEGLSNALGKLDARS 246

Query: 240 RRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           RRI EAR L  +     TL  L+ EF VS ER+RQIEA A KK++ S+
Sbjct: 247 RRIVEARWLANDDGSGATLHELADEFGVSAERIRQIEAVALKKMKGSL 294


>gi|77919976|ref|YP_357791.1| RNA polymerase, sigma (32) factor [Pelobacter carbinolicus DSM
           2380]
 gi|77546059|gb|ABA89621.1| RNA polymerase, sigma 32 subunit, RpoH [Pelobacter carbinolicus DSM
           2380]
          Length = 286

 Score =  231 bits (590), Expect = 8e-59,   Method: Compositional matrix adjust.
 Identities = 127/295 (43%), Positives = 196/295 (66%), Gaps = 15/295 (5%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           N+ + V+ +  LS YI +IR   +L K+EE+ L + Y  + ++ AA +L+ ++LR VVKI
Sbjct: 3   NLPLPVSSD-NLSLYIAQIRAFELLTKEEEFRLTQDYHRNQNIEAAQQLICANLRFVVKI 61

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  YRGYGL + +++ EGNIGLM+AVKKFDP+RG R  TY++WWI+A +  +I+R+WSLV
Sbjct: 62  AHEYRGYGLKLLDIIQEGNIGLMKAVKKFDPDRGLRFITYAVWWIRAYIHNFIIRNWSLV 121

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-D 183
           KIGTT  QK+LFF L +++  +Q +T +    E   AIA++LNV + EV  M  R+AG D
Sbjct: 122 KIGTTQAQKKLFFKLNQVRSAIQRMTGS----EDTKAIARELNVRDDEVEDMARRMAGRD 177

Query: 184 ESLNA-LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
            SL+  L+   D       D L  + + QE++LI+++E++   + +  ++  LN RERRI
Sbjct: 178 TSLDMRLVEGEDFT---LLDSLADERESQEELLIKQQEKQITTSHIHGALQELNDRERRI 234

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLL 297
            E R LQE P TL+ L+ +F +SRERVRQ+E  A +K+++++      +++P LL
Sbjct: 235 VEERILQEEPRTLQALADDFGISRERVRQLEKNALEKIRKTLT-----ANAPCLL 284


>gi|254708375|ref|ZP_05170203.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M163/99/10]
 gi|254708771|ref|ZP_05170582.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis B2/94]
 gi|254714614|ref|ZP_05176425.1| RNA polymerase factor sigma-32 [Brucella ceti M644/93/1]
 gi|254717512|ref|ZP_05179323.1| RNA polymerase factor sigma-32 [Brucella ceti M13/05/1]
 gi|256030297|ref|ZP_05443911.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M292/94/1]
 gi|256160470|ref|ZP_05458159.1| RNA polymerase factor sigma-32 [Brucella ceti M490/95/1]
 gi|256255677|ref|ZP_05461213.1| RNA polymerase factor sigma-32 [Brucella ceti B1/94]
 gi|260167971|ref|ZP_05754782.1| RNA polymerase factor sigma-32 [Brucella sp. F5/99]
 gi|261757411|ref|ZP_06001120.1| sigma-70 factor family [Brucella sp. F5/99]
 gi|261737395|gb|EEY25391.1| sigma-70 factor family [Brucella sp. F5/99]
          Length = 311

 Score =  231 bits (589), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 116/267 (43%), Positives = 179/267 (67%), Gaps = 1/267 (0%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE++EE  LA R++E  D  A HR+ ++H+RLV+ +A  +R + LP+S+++ EG +GL
Sbjct: 42  PYLEREEERALAIRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGL 101

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +FDP+R  R +TY+ WWI+A+MQ+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 102 LEAAARFDPDRDVRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKALFFNLRRLRSKL 161

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLV 205
               DN  K E    I+ +L VS S+V  M+ RL+G D SL+  +N  +  +S+  D+LV
Sbjct: 162 AQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRLSGPDSSLSVPMNGEETGASRRMDFLV 221

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            DH  Q+++     + + R   LTR++  LN RE  I   RRL ++ VTLE L  +  +S
Sbjct: 222 DDHPLQDEIAESSIDMERRNRWLTRALDTLNERELHIIRERRLDDDGVTLEALGEKLGIS 281

Query: 266 RERVRQIEARAFKKVQESIQKQVELSS 292
           +ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 282 KERVRQIESRAMEKLKIALLSQHELAA 308


>gi|261219345|ref|ZP_05933626.1| RNA polymerase factor sigma-32 [Brucella ceti M13/05/1]
 gi|261222881|ref|ZP_05937162.1| RNA polymerase factor sigma-32 [Brucella ceti B1/94]
 gi|261315875|ref|ZP_05955072.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M163/99/10]
 gi|261316262|ref|ZP_05955459.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis B2/94]
 gi|261322406|ref|ZP_05961603.1| RNA polymerase factor sigma-32 [Brucella ceti M644/93/1]
 gi|265987326|ref|ZP_06099883.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M292/94/1]
 gi|265998840|ref|ZP_06111397.1| RNA polymerase factor sigma-32 [Brucella ceti M490/95/1]
 gi|260921465|gb|EEX88118.1| RNA polymerase factor sigma-32 [Brucella ceti B1/94]
 gi|260924434|gb|EEX91002.1| RNA polymerase factor sigma-32 [Brucella ceti M13/05/1]
 gi|261295096|gb|EEX98592.1| RNA polymerase factor sigma-32 [Brucella ceti M644/93/1]
 gi|261295485|gb|EEX98981.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis B2/94]
 gi|261304901|gb|EEY08398.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M163/99/10]
 gi|262553529|gb|EEZ09298.1| RNA polymerase factor sigma-32 [Brucella ceti M490/95/1]
 gi|264659523|gb|EEZ29784.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M292/94/1]
          Length = 293

 Score =  231 bits (588), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 116/267 (43%), Positives = 179/267 (67%), Gaps = 1/267 (0%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE++EE  LA R++E  D  A HR+ ++H+RLV+ +A  +R + LP+S+++ EG +GL
Sbjct: 24  PYLEREEERALAIRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGL 83

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +FDP+R  R +TY+ WWI+A+MQ+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 84  LEAAARFDPDRDVRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKALFFNLRRLRSKL 143

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLV 205
               DN  K E    I+ +L VS S+V  M+ RL+G D SL+  +N  +  +S+  D+LV
Sbjct: 144 AQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRLSGPDSSLSVPMNGEETGASRRMDFLV 203

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            DH  Q+++     + + R   LTR++  LN RE  I   RRL ++ VTLE L  +  +S
Sbjct: 204 DDHPLQDEIAESSIDMERRNRWLTRALDTLNERELHIIRERRLDDDGVTLEALGEKLGIS 263

Query: 266 RERVRQIEARAFKKVQESIQKQVELSS 292
           +ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 264 KERVRQIESRAMEKLKIALLSQHELAA 290


>gi|225628325|ref|ZP_03786359.1| RNA polymerase sigma factor, sigma-70 family protein [Brucella ceti
           str. Cudo]
 gi|225616171|gb|EEH13219.1| RNA polymerase sigma factor, sigma-70 family protein [Brucella ceti
           str. Cudo]
          Length = 278

 Score =  231 bits (588), Expect = 1e-58,   Method: Compositional matrix adjust.
 Identities = 116/267 (43%), Positives = 179/267 (67%), Gaps = 1/267 (0%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE++EE  LA R++E  D  A HR+ ++H+RLV+ +A  +R + LP+S+++ EG +GL
Sbjct: 9   PYLEREEERALAIRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGL 68

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +FDP+R  R +TY+ WWI+A+MQ+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 69  LEAAARFDPDRDVRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKALFFNLRRLRSKL 128

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLV 205
               DN  K E    I+ +L VS S+V  M+ RL+G D SL+  +N  +  +S+  D+LV
Sbjct: 129 AQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRLSGPDSSLSVPMNGEETGASRRMDFLV 188

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            DH  Q+++     + + R   LTR++  LN RE  I   RRL ++ VTLE L  +  +S
Sbjct: 189 DDHPLQDEIAESSIDMERRNRWLTRALDTLNERELHIIRERRLDDDGVTLEALGEKLGIS 248

Query: 266 RERVRQIEARAFKKVQESIQKQVELSS 292
           +ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 249 KERVRQIESRAMEKLKIALLSQHELAA 275


>gi|256114330|ref|ZP_05455068.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 3 str.
           Ether]
          Length = 311

 Score =  230 bits (586), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 116/267 (43%), Positives = 179/267 (67%), Gaps = 1/267 (0%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE++EE  LA R++E  D  A HR+ ++H+RLV+ +A  +R + LP+S+++ EG +GL
Sbjct: 42  PYLEREEERALAIRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGL 101

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++   +FDP+R  R +TY+ WWI+A+MQ+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 102 LEEAARFDPDRDVRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKVLFFNLRRLRSKL 161

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLV 205
               DN  K E    I+ +L VS S+V  M+ RL+G D SL+A +N  +  +S+  D+LV
Sbjct: 162 AQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLV 221

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            DH  Q+++     + + R   LTR++  LN RE  I   RRL ++ VTLE L  +  +S
Sbjct: 222 DDHPLQDEIAESSIDMERRNRWLTRALDTLNERELHIIRERRLDDDGVTLEALGEKLGIS 281

Query: 266 RERVRQIEARAFKKVQESIQKQVELSS 292
           +ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 282 KERVRQIESRAMEKLKIALLSQHELAA 308


>gi|225853213|ref|YP_002733446.1| RNA polymerase factor sigma-32 [Brucella melitensis ATCC 23457]
 gi|256263296|ref|ZP_05465828.1| sigma-70 factor [Brucella melitensis bv. 2 str. 63/9]
 gi|225641578|gb|ACO01492.1| RNA polymerase sigma factor, sigma-70 family protein [Brucella
           melitensis ATCC 23457]
 gi|263093265|gb|EEZ17362.1| sigma-70 factor [Brucella melitensis bv. 2 str. 63/9]
 gi|326409772|gb|ADZ66837.1| RNA polymerase factor sigma-32 [Brucella melitensis M28]
          Length = 311

 Score =  230 bits (586), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 116/267 (43%), Positives = 179/267 (67%), Gaps = 1/267 (0%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE++EE  LA R++E  D  A HR+ ++H+RLV+ +A  +R + LP+S+++ EG +GL
Sbjct: 42  PYLEREEERALAIRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGL 101

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++   +FDP+R  R +TY+ WWI+A+MQ+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 102 LEEAARFDPDRDVRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKVLFFNLRRLRSKL 161

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLV 205
               DN  K E    I+ +L VS S+V  M+ RL+G D SL+A +N  +  +S+  D+LV
Sbjct: 162 AQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLV 221

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            DH  Q+++     + + R   LTR++  LN RE  I   RRL ++ VTLE L  +  +S
Sbjct: 222 DDHPLQDEIAESSIDMERRNRWLTRALDTLNERELHIIRERRLDDDGVTLEALGEKLGIS 281

Query: 266 RERVRQIEARAFKKVQESIQKQVELSS 292
           +ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 282 KERVRQIESRAMEKLKIALLSQHELAA 308


>gi|265995632|ref|ZP_06108189.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 3 str.
           Ether]
 gi|262766916|gb|EEZ12534.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 3 str.
           Ether]
          Length = 293

 Score =  230 bits (586), Expect = 2e-58,   Method: Compositional matrix adjust.
 Identities = 116/267 (43%), Positives = 179/267 (67%), Gaps = 1/267 (0%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE++EE  LA R++E  D  A HR+ ++H+RLV+ +A  +R + LP+S+++ EG +GL
Sbjct: 24  PYLEREEERALAIRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGL 83

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++   +FDP+R  R +TY+ WWI+A+MQ+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 84  LEEAARFDPDRDVRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKVLFFNLRRLRSKL 143

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLV 205
               DN  K E    I+ +L VS S+V  M+ RL+G D SL+A +N  +  +S+  D+LV
Sbjct: 144 AQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLV 203

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            DH  Q+++     + + R   LTR++  LN RE  I   RRL ++ VTLE L  +  +S
Sbjct: 204 DDHPLQDEIAESSIDMERRNRWLTRALDTLNERELHIIRERRLDDDGVTLEALGEKLGIS 263

Query: 266 RERVRQIEARAFKKVQESIQKQVELSS 292
           +ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 264 KERVRQIESRAMEKLKIALLSQHELAA 290


>gi|326539488|gb|ADZ87703.1| RNA polymerase sigma factor, sigma-70 family protein [Brucella
           melitensis M5-90]
          Length = 293

 Score =  229 bits (585), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 116/267 (43%), Positives = 179/267 (67%), Gaps = 1/267 (0%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE++EE  LA R++E  D  A HR+ ++H+RLV+ +A  +R + LP+S+++ EG +GL
Sbjct: 24  PYLEREEERALAIRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGL 83

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++   +FDP+R  R +TY+ WWI+A+MQ+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 84  LEEAARFDPDRDVRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKVLFFNLRRLRSKL 143

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLV 205
               DN  K E    I+ +L VS S+V  M+ RL+G D SL+A +N  +  +S+  D+LV
Sbjct: 144 AQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLV 203

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            DH  Q+++     + + R   LTR++  LN RE  I   RRL ++ VTLE L  +  +S
Sbjct: 204 DDHPLQDEIAESSIDMERRNRWLTRALDTLNERELHIIRERRLDDDGVTLEALGEKLGIS 263

Query: 266 RERVRQIEARAFKKVQESIQKQVELSS 292
           +ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 264 KERVRQIESRAMEKLKIALLSQHELAA 290


>gi|88608622|ref|YP_506230.1| RNA polymerase sigma-32 factor [Neorickettsia sennetsu str.
           Miyayama]
 gi|88600791|gb|ABD46259.1| RNA polymerase sigma-32 factor [Neorickettsia sennetsu str.
           Miyayama]
          Length = 288

 Score =  229 bits (585), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 125/273 (45%), Positives = 182/273 (66%), Gaps = 11/273 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y  +I  IP+L+++EE  L  R+  H D+SAA RLV ++LRLVVK+ + +R YG P+ ++
Sbjct: 16  YARKILAIPILQEEEERELIDRWFVHRDISAAQRLVEAYLRLVVKVTVRFRNYGFPLMDL 75

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
            SEGNIGLM+A+K F+P  G  +ATY++WWIKAA+ EY++RSWS+VKIGTTA Q+RLFFN
Sbjct: 76  ASEGNIGLMKAIKNFNPTLGHGIATYAIWWIKAAINEYVIRSWSMVKIGTTAAQRRLFFN 135

Query: 139 LRRLK--GHLQAITDNNL--KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           LR+LK  G +  + +N +  +  +++A++K  +V E E I +N R   D SLN  +   D
Sbjct: 136 LRKLKNSGSVAGLDENQVVKRISEILAVSKN-DVEEMERI-LNAR---DVSLNMQLGEDD 190

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
             SS+  D + +    QE VL+E +ER+ +  +L  ++  L  R + IF AR L   P T
Sbjct: 191 --SSEVHDLVPFPEANQEAVLLETQERQMKSQLLYEAVEALEARHKEIFVARSLSAVPRT 248

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L+ L  +F +S+ERVRQI ARA KKV E ++K 
Sbjct: 249 LKELGEKFSISQERVRQIHARAMKKVTEYVEKH 281


>gi|329910210|ref|ZP_08275256.1| RNA polymerase sigma factor RpoH [Oxalobacteraceae bacterium
           IMCC9480]
 gi|327546240|gb|EGF31276.1| RNA polymerase sigma factor RpoH [Oxalobacteraceae bacterium
           IMCC9480]
          Length = 298

 Score =  229 bits (585), Expect = 3e-58,   Method: Compositional matrix adjust.
 Identities = 128/284 (45%), Positives = 182/284 (64%), Gaps = 11/284 (3%)

Query: 6   MSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +++   G +G +  YI  + ++PML  +EE  LA+R R+  DL AA  +V SHLRLVV I
Sbjct: 17  LALGFTGTLGNIDSYISAVNRLPMLTHEEEMSLARRLRDQNDLGAAQGMVLSHLRLVVSI 76

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A GY GYGLP ++++ EGNIGLM+AVK+FDP++G RL +Y+M WIKA M EYIL++W LV
Sbjct: 77  ARGYLGYGLPHADLIQEGNIGLMKAVKRFDPDQGVRLVSYAMHWIKAEMHEYILKNWRLV 136

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-D 183
           K+ TT  Q++LFFNLR  K  L ++T     P QV A+A+ LNV   EVI M  RL+G D
Sbjct: 137 KVATTKAQRKLFFNLRSHKTGLDSMT-----PAQVEALAQTLNVKREEVIEMETRLSGRD 191

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            +L A  +  D   +    +L  D +    VL  ++  + + + L+++++ L+ R RRI 
Sbjct: 192 IALEAPTDDEDDKFAPIA-YLSSDRNEPTNVLEAQQYDRLQSDGLSQALNKLDERSRRIV 250

Query: 244 EARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           EAR L  +     TL  L+ EF VS ER+RQIEA A KK++ S+
Sbjct: 251 EARWLANDDGSGATLHELAKEFGVSAERIRQIEAVALKKMKGSL 294


>gi|95929333|ref|ZP_01312076.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfuromonas acetoxidans
           DSM 684]
 gi|95134449|gb|EAT16105.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfuromonas acetoxidans
           DSM 684]
          Length = 282

 Score =  229 bits (584), Expect = 4e-58,   Method: Compositional matrix adjust.
 Identities = 123/279 (44%), Positives = 188/279 (67%), Gaps = 12/279 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           N+ ++++G      Y+ +I +   L+++ EY LA RYR++ DL AAH+LV ++LR VVKI
Sbjct: 3   NLPLVIDG---FDHYMAQISQFEPLDRETEYELANRYRKNNDLDAAHKLVCANLRFVVKI 59

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y+ YGL + ++V EGNIGLM+A+KKFDP+R  RL +Y++WWI+A +  YI+ +WSLV
Sbjct: 60  AYEYQAYGLKMIDLVQEGNIGLMKAIKKFDPDRNIRLISYAVWWIRAYIHNYIINAWSLV 119

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-D 183
           KIGTT  +K+LFF L++ +  LQ + ++    E    IA++LNVS  EV  M+ RL G D
Sbjct: 120 KIGTTQARKKLFFKLKQTRDALQKMGNDADHAE----IARQLNVSTDEVAEMSVRLGGRD 175

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
            SL+  + + D  +S   D LV DHD  QEQ LIE E      + + +++S LN RE+ I
Sbjct: 176 SSLDGQL-TPDSTTSHL-DTLV-DHDKDQEQRLIELEHESLTTHRVQQALSHLNEREQHI 232

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             +R LQ++  TL++L+ ++ +S+ERVRQ+E RA +K++
Sbjct: 233 VHSRILQDDKATLQDLADQYGISKERVRQLEKRALEKLK 271


>gi|78224050|ref|YP_385797.1| sigma 32 (RpoH) [Geobacter metallireducens GS-15]
 gi|78195305|gb|ABB33072.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter metallireducens
           GS-15]
          Length = 279

 Score =  229 bits (583), Expect = 5e-58,   Method: Compositional matrix adjust.
 Identities = 117/277 (42%), Positives = 178/277 (64%), Gaps = 9/277 (3%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           N+ ++ +     + Y+ EIRK P+L  +EE++ A ++ E  DL AAHRL+T++LR VVK+
Sbjct: 4   NLPVVADS---FTLYLAEIRKFPVLTPEEEHLYAVKFYEEKDLEAAHRLITANLRFVVKV 60

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y+ YG+ + +++ EGNIGLM AV+KFDP +G RL +Y++WWI+A +Q YI+ +WSL+
Sbjct: 61  AAEYKSYGMKMLDLIQEGNIGLMMAVRKFDPHKGIRLISYAVWWIRAYIQNYIISAWSLL 120

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           KIGTT  QK+LFF L + K  ++ +T  +       A A  L+V ESEVI M+ R+ GD 
Sbjct: 121 KIGTTQAQKKLFFKLNQAKNAIRRLTGGD----DTEATALSLHVKESEVIEMDQRMRGDY 176

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL+A +   D       D LV +   QE+ L E++E       +T+++  LN +ER + E
Sbjct: 177 SLDAEL--VDGEGLTMLDTLVDERQNQEEALAEQQEASRLHGQVTQALERLNEKERYVVE 234

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R   + P+TL+ ++  F +SRERVRQIE  A KK++
Sbjct: 235 NRVTADEPLTLQEIADHFAISRERVRQIEEGALKKIK 271


>gi|291613119|ref|YP_003523276.1| RNA polymerase, sigma 32 subunit, RpoH [Sideroxydans lithotrophicus
           ES-1]
 gi|291583231|gb|ADE10889.1| RNA polymerase, sigma 32 subunit, RpoH [Sideroxydans lithotrophicus
           ES-1]
          Length = 289

 Score =  229 bits (583), Expect = 5e-58,   Method: Compositional matrix adjust.
 Identities = 120/282 (42%), Positives = 183/282 (64%), Gaps = 10/282 (3%)

Query: 5   NMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           +MS+ +   +G L  Y+  + + P+L  +EE  LA R++ H DL AA +LV SHLR+VV 
Sbjct: 4   SMSLPIPSAVGSLESYVQAVNRFPVLSHEEELSLANRFKAHNDLDAARQLVLSHLRVVVS 63

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           +A GY GYGLP ++++ EGNIGLM+AVK++D  RG RL ++++ WI+A + EY++R+W L
Sbjct: 64  VARGYAGYGLPQADLIQEGNIGLMKAVKRYDATRGVRLVSFALHWIRAEIHEYVVRNWRL 123

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VKI TT +Q++LFFNLR +K  L+      LKP+QV  IA++LNVSE +V+ M  R AG 
Sbjct: 124 VKIATTKSQRKLFFNLRSMKQGLEP-----LKPQQVREIAQQLNVSERDVVEMEARFAGH 178

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRI 242
           E     ++  +  S     +L  + + +   ++E  ER++     L ++++ L+ R RRI
Sbjct: 179 EVALEPLSGEEDESYAPISYLADNAEHEPSYILEAAEREHLHTAGLAQALASLDERSRRI 238

Query: 243 FEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            EAR L   +E+  TL  L+ EF+VS ER+RQIE +A  K+Q
Sbjct: 239 VEARWLRDEEEHAATLHELADEFKVSAERIRQIEQKALSKMQ 280


>gi|265991792|ref|ZP_06104349.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|263002748|gb|EEZ15151.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 1 str.
           Rev.1]
          Length = 293

 Score =  229 bits (583), Expect = 5e-58,   Method: Compositional matrix adjust.
 Identities = 115/267 (43%), Positives = 179/267 (67%), Gaps = 1/267 (0%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE++EE  LA R++E  D  A HR+ ++H+RLV+ +A  +R + LP+S+++ EG +GL
Sbjct: 24  PYLEREEERALAIRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGL 83

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++   +FDP+R  R +TY+ WWI+A+MQ+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 84  LEEAARFDPDRDVRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKVLFFNLRRLRSKL 143

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLV 205
               DN  K E    I+ +L VS S+V  M+ RL+G D SL+A +N  +  +S+  D+LV
Sbjct: 144 AQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRLSGPDSSLSASMNGEETGASRRMDFLV 203

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            DH  Q+++     + + R   LTR++  LN RE  I   RRL ++ VTLE L  +  +S
Sbjct: 204 DDHPLQDEIAESSIDMERRNRWLTRALDTLNERELHIIRERRLDDDGVTLEALGEKLGIS 263

Query: 266 RERVRQIEARAFKKVQESIQKQVELSS 292
           ++RVRQIE+RA +K++ ++  Q EL++
Sbjct: 264 KQRVRQIESRAMEKLKIALLSQHELAA 290


>gi|256045366|ref|ZP_05448260.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|260565741|ref|ZP_05836224.1| sigma-70 factor family protein [Brucella melitensis bv. 1 str. 16M]
 gi|260151114|gb|EEW86209.1| sigma-70 factor family protein [Brucella melitensis bv. 1 str. 16M]
          Length = 311

 Score =  229 bits (583), Expect = 5e-58,   Method: Compositional matrix adjust.
 Identities = 115/267 (43%), Positives = 179/267 (67%), Gaps = 1/267 (0%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE++EE  LA R++E  D  A HR+ ++H+RLV+ +A  +R + LP+S+++ EG +GL
Sbjct: 42  PYLEREEERALAIRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGL 101

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++   +FDP+R  R +TY+ WWI+A+MQ+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 102 LEEAARFDPDRDVRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKVLFFNLRRLRSKL 161

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLV 205
               DN  K E    I+ +L VS S+V  M+ RL+G D SL+A +N  +  +S+  D+LV
Sbjct: 162 AQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRLSGPDSSLSASMNGEETGASRRMDFLV 221

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            DH  Q+++     + + R   LTR++  LN RE  I   RRL ++ VTLE L  +  +S
Sbjct: 222 DDHPLQDEIAESSIDMERRNRWLTRALDTLNERELHIIRERRLDDDGVTLEALGEKLGIS 281

Query: 266 RERVRQIEARAFKKVQESIQKQVELSS 292
           ++RVRQIE+RA +K++ ++  Q EL++
Sbjct: 282 KQRVRQIESRAMEKLKIALLSQHELAA 308


>gi|163845340|ref|YP_001622995.1| RNA polymerase factor sigma-32 [Brucella suis ATCC 23445]
 gi|163676063|gb|ABY40173.1| RNA polymerase sigma factor, sigma-70 family [Brucella suis ATCC
           23445]
          Length = 311

 Score =  228 bits (582), Expect = 6e-58,   Method: Compositional matrix adjust.
 Identities = 116/267 (43%), Positives = 178/267 (66%), Gaps = 1/267 (0%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE++EE  LA R++E  D  A HR+ ++H+RLV  +A  +R + LP+S+++ EG +GL
Sbjct: 42  PYLEREEERALAIRWKETKDQDALHRITSAHMRLVTSMAGRFRKFKLPMSDLIQEGYVGL 101

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +FDP+R  R +TY+ WWI+A+MQ+YILR+WS+V+ GT++ QK LFFNL RL+  L
Sbjct: 102 LEAAARFDPDRDVRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKALFFNLCRLRSKL 161

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLV 205
               DN  K E    I+ +L VS S+V  M+ RL+G D SL+A +N  +  +S+  D+LV
Sbjct: 162 AQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLV 221

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            DH  Q+++     + + R   LTR++  LN RE  I   RRL ++ VTLE L  +  +S
Sbjct: 222 DDHPLQDEIAESSIDMERRNCWLTRALDTLNERELHIIRERRLDDDGVTLEALGEKLGIS 281

Query: 266 RERVRQIEARAFKKVQESIQKQVELSS 292
           +ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 282 KERVRQIESRAMEKLKIALLSQHELAA 308


>gi|17986563|ref|NP_539197.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 1 str. 16M]
 gi|17982171|gb|AAL51461.1| RNA polymerase sigma-32 factor [Brucella melitensis bv. 1 str. 16M]
          Length = 319

 Score =  228 bits (582), Expect = 6e-58,   Method: Compositional matrix adjust.
 Identities = 115/267 (43%), Positives = 179/267 (67%), Gaps = 1/267 (0%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE++EE  LA R++E  D  A HR+ ++H+RLV+ +A  +R + LP+S+++ EG +GL
Sbjct: 50  PYLEREEERALAIRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGL 109

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++   +FDP+R  R +TY+ WWI+A+MQ+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 110 LEEAARFDPDRDVRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKVLFFNLRRLRSKL 169

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLV 205
               DN  K E    I+ +L VS S+V  M+ RL+G D SL+A +N  +  +S+  D+LV
Sbjct: 170 AQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRLSGPDSSLSASMNGEETGASRRMDFLV 229

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            DH  Q+++     + + R   LTR++  LN RE  I   RRL ++ VTLE L  +  +S
Sbjct: 230 DDHPLQDEIAESSIDMERRNRWLTRALDTLNERELHIIRERRLDDDGVTLEALGEKLGIS 289

Query: 266 RERVRQIEARAFKKVQESIQKQVELSS 292
           ++RVRQIE+RA +K++ ++  Q EL++
Sbjct: 290 KQRVRQIESRAMEKLKIALLSQHELAA 316


>gi|257095687|ref|YP_003169328.1| RNA polymerase sigma-32 subunit RpoH [Candidatus Accumulibacter
           phosphatis clade IIA str. UW-1]
 gi|257048211|gb|ACV37399.1| RNA polymerase, sigma 32 subunit, RpoH [Candidatus Accumulibacter
           phosphatis clade IIA str. UW-1]
          Length = 286

 Score =  228 bits (582), Expect = 6e-58,   Method: Compositional matrix adjust.
 Identities = 122/275 (44%), Positives = 175/275 (63%), Gaps = 9/275 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  YI   R+ PML ++EE+ LA R+R+  DL AA +LV SHLRLV+ IA GY GYGLP 
Sbjct: 16  IDAYIQAARQFPMLTQEEEFRLATRFRDDSDLDAARQLVLSHLRLVISIARGYLGYGLPH 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AVK+FDP  G RL ++++ WIKA + EY+L++W +VK+ TT  Q++L
Sbjct: 76  ADLIQEGNIGLMKAVKRFDPAHGVRLVSFAIHWIKAEIHEYVLKNWRMVKLATTKAQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR +K + +A     L P QV  IA +L+V   EV  M  RL G +   AL   SD 
Sbjct: 136 FFNLRSMKANSEA-----LSPGQVTDIAHRLSVKPEEVSEMEARLTGHDL--ALDGDSDD 188

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRN-MLTRSMSVLNPRERRIFEARRL-QENPV 253
           +        + DH  +   ++E   R+   N  L  +++ L+PR RRI EAR L  E+P 
Sbjct: 189 DEVFAPISYLADHSSEPVHVLEARARERLHNEGLQGALASLDPRSRRIVEARWLTDESPA 248

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           TL  L++EF VS ER+RQ+E +A +K++ S+   V
Sbjct: 249 TLHELAAEFGVSAERIRQVEVKAMQKMRASLAPLV 283


>gi|302877701|ref|YP_003846265.1| RNA polymerase, sigma 32 subunit, RpoH [Gallionella
           capsiferriformans ES-2]
 gi|302580490|gb|ADL54501.1| RNA polymerase, sigma 32 subunit, RpoH [Gallionella
           capsiferriformans ES-2]
          Length = 284

 Score =  228 bits (581), Expect = 9e-58,   Method: Compositional matrix adjust.
 Identities = 120/268 (44%), Positives = 176/268 (65%), Gaps = 7/268 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YIH +R+  +L ++EE+ LA R+R   DL AA +LV SHLR+VV +A GY GYGLP 
Sbjct: 16  LDSYIHLVRRYAVLSQEEEFDLATRFRNDNDLDAARQLVLSHLRVVVSVARGYAGYGLPQ 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AVK +DPE G RL ++++ WI+A + E+++R+W +VKI TT  Q++L
Sbjct: 76  ADLIQEGNIGLMKAVKHYDPEFGVRLVSFALHWIRAEINEFVVRNWRMVKIATTKAQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR LK  L++     LKP+Q+  IA++LNVSE +VI M  R AG E       S D 
Sbjct: 136 FFNLRSLKQGLES-----LKPKQISEIAEQLNVSEHDVIEMEARFAGHEVALDPAGSDDD 190

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENP-V 253
           ++     +L    + +   ++E  E  + R   L R+++ L+ R RRI EAR L E+   
Sbjct: 191 DTYAPIQYLADSEEHEPSNILESSEGLSLRTQGLARALASLDDRSRRIVEARWLSEDQNA 250

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TL +L++EF+VS ER+RQIE +A  K+ 
Sbjct: 251 TLHDLAAEFKVSAERIRQIEQKAMSKMH 278


>gi|86747323|ref|YP_483819.1| sigma 32 (RpoH) [Rhodopseudomonas palustris HaA2]
 gi|86570351|gb|ABD04908.1| sigma 32 (RpoH) [Rhodopseudomonas palustris HaA2]
          Length = 329

 Score =  227 bits (578), Expect = 2e-57,   Method: Compositional matrix adjust.
 Identities = 118/270 (43%), Positives = 166/270 (61%), Gaps = 1/270 (0%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+  I + P+LE  EE  L +R+ +H D +AA  L+TSHLRL  K+A  +R YG P+ ++
Sbjct: 25  YMRAIGRYPVLEPDEEARLWQRWLQHRDKAAADALITSHLRLAAKLARDFRRYGFPLGDL 84

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           ++E N+GLM A+ +FDPERG R +T ++WWI++A+ ++I+RSWSLV+IG T  QK+LFF 
Sbjct: 85  IAEANLGLMMALDRFDPERGARFSTCAVWWIRSAIYDHIIRSWSLVRIGRTPAQKKLFFR 144

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR     LQ      L  E    I+  L+V   EVI M  RL+GD SLN  ++  D+ S 
Sbjct: 145 LRGEIRRLQPDHHGTLTKELAEQISATLDVPLREVIEMEQRLSGDRSLNTPLSDLDE-SG 203

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           +WQD +  D    E VL   +E  ++R  L  ++  L+ RER IF AR L E P + E +
Sbjct: 204 EWQDLIADDAPNAEAVLAGHDELDHQRRALQDALVQLDARERYIFSARHLGERPASFETI 263

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQV 288
                +S ERVRQIEARAF KV  S ++  
Sbjct: 264 GQSLSISAERVRQIEARAFAKVANSARRTC 293


>gi|307943602|ref|ZP_07658946.1| RNA polymerase sigma-32 factor [Roseibium sp. TrichSKD4]
 gi|307773232|gb|EFO32449.1| RNA polymerase sigma-32 factor [Roseibium sp. TrichSKD4]
          Length = 291

 Score =  225 bits (574), Expect = 6e-57,   Method: Compositional matrix adjust.
 Identities = 114/265 (43%), Positives = 179/265 (67%), Gaps = 9/265 (3%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K P L ++EE+ LA R+R++ D  A  +L  SH RLV+ +A  +R +GLP+ +++ EG++
Sbjct: 17  KAPYLTREEEHDLAVRWRDNRDEKALEKLSLSHTRLVISVASKFRNFGLPLGDLIQEGHV 76

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK- 143
           GL++A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT+++QK LFFNLRRL+ 
Sbjct: 77  GLLEAAARFEPEREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSSQKALFFNLRRLRA 136

Query: 144 ---GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQ 199
              G+ Q +TD+ L  +    IA  + V  ++V +MN RL+G D SLNA +  S+ +SS 
Sbjct: 137 KLSGNQQNLTDSELHQK----IADAIGVKPADVATMNARLSGPDTSLNAPVTDSEGSSSD 192

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
            QD+LV D    + ++ E  + + RR  L  +M+VL  RE +I   RRL E   TLE+L 
Sbjct: 193 RQDFLVSDAPQPDDIVSESIDTERRRKWLASAMTVLTDRELKIVRERRLTEEGATLESLG 252

Query: 260 SEFEVSRERVRQIEARAFKKVQESI 284
            +  +S+ERVRQIE+RA +K++ ++
Sbjct: 253 QKLGISKERVRQIESRAMEKLKTAL 277


>gi|300313436|ref|YP_003777528.1| RNA polymerase sigma-32 factor protein [Herbaspirillum seropedicae
           SmR1]
 gi|300076221|gb|ADJ65620.1| RNA polymerase sigma-32 factor protein [Herbaspirillum seropedicae
           SmR1]
          Length = 299

 Score =  225 bits (573), Expect = 8e-57,   Method: Compositional matrix adjust.
 Identities = 128/285 (44%), Positives = 180/285 (63%), Gaps = 11/285 (3%)

Query: 6   MSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +++  +G +G +  YI  + ++PML  +EE  LA+  RE  DL AA ++V SHLRLVV I
Sbjct: 18  LALGFSGSLGNIDAYISAVNRLPMLTHEEEVKLARDLREKNDLGAAQKMVLSHLRLVVSI 77

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A GY GYGLP ++++ EGNIGLM+AVK+FDP +  RL +Y+M WIKA + EYIL++W LV
Sbjct: 78  ARGYLGYGLPHADLIQEGNIGLMKAVKRFDPAQNVRLVSYAMHWIKAEIHEYILKNWRLV 137

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-D 183
           K+ TT  Q++LFFNLR  K  L A+T     P QV A+AK L+V   EVI M  RL+G D
Sbjct: 138 KVATTKAQRKLFFNLRSHKEGLDAMT-----PAQVEALAKTLDVKREEVIEMETRLSGRD 192

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            +L +  +  D   +    +L  D+    +V+  K+  + +   L  ++S L+ R RRI 
Sbjct: 193 IALESPTDDEDDKFAPIA-YLSSDNSEPTRVIEAKQYDRLQSEGLEAALSKLDERSRRIV 251

Query: 244 EARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           EAR L  +     TL  L+ EF VS ER+RQIEA A KK++ S+Q
Sbjct: 252 EARWLANDDGSGATLHELADEFGVSAERIRQIEAVALKKMKTSLQ 296


>gi|297539272|ref|YP_003675041.1| RNA polymerase sigma-32 subunit RpoH [Methylotenera sp. 301]
 gi|297258619|gb|ADI30464.1| RNA polymerase, sigma 32 subunit, RpoH [Methylotenera sp. 301]
          Length = 285

 Score =  225 bits (573), Expect = 8e-57,   Method: Compositional matrix adjust.
 Identities = 127/277 (45%), Positives = 171/277 (61%), Gaps = 11/277 (3%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           ++     L  Y   I+  P+L  +EEY LA ++R   DL AA +L+ SHLRLV  IA GY
Sbjct: 9   VLTASDSLEHYSRVIKAYPVLSAEEEYSLAVKFRADNDLEAARQLIVSHLRLVASIARGY 68

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGLP S+++ EGNIGLM+AVK+FDPERG RL +++M WIKA M EYI+R+W +VKI T
Sbjct: 69  NGYGLPQSDLIQEGNIGLMKAVKRFDPERGVRLVSFAMHWIKAEMHEYIVRNWRMVKIAT 128

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLN 187
           T  Q++LFFNLR +K  L     N+L+P +V  IAK+LNV   EV+ M  RL G E SL 
Sbjct: 129 TKAQRKLFFNLRSMKTGL-----NSLQPAEVAHIAKELNVKPEEVLEMEARLNGHEISLE 183

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQE--QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           A  N  D +  Q+        +G E  + L  K+        L  ++  L+ R RR+ EA
Sbjct: 184 A--NIDDDSDEQYSPIAYLPDEGLEPLEALESKQIEIAETTGLANALQNLDDRSRRVVEA 241

Query: 246 RRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R LQ+    TL  L+ EF VS ER+RQIE +A +K++
Sbjct: 242 RWLQDQGGKTLHELADEFGVSAERIRQIEQKAMQKMK 278


>gi|153008471|ref|YP_001369686.1| RNA polymerase factor sigma-32 [Ochrobactrum anthropi ATCC 49188]
 gi|151560359|gb|ABS13857.1| RNA polymerase, sigma 32 subunit, RpoH [Ochrobactrum anthropi ATCC
           49188]
          Length = 311

 Score =  224 bits (572), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 114/267 (42%), Positives = 178/267 (66%), Gaps = 1/267 (0%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE++EE  LA R++E  D  A HR+ ++H+RLV+ +A  +R + LP+++++ EG +GL
Sbjct: 42  PYLEREEERALAIRWKELKDQDALHRITSAHMRLVISMAGRFRKFKLPMNDLIQEGYVGL 101

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +FDPER  R +TY+ WWI+A+MQ+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 102 LEAAARFDPEREVRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKALFFNLRRLRSKL 161

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLV 205
               DN  K E    I+ +L VS S+V  M+ RL+G D SL+A +N+ +  + +  D+LV
Sbjct: 162 AQSDDNMTKAEMYREISDQLGVSTSDVEIMDSRLSGPDSSLSAPVNNEESGAVRRMDFLV 221

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            DH  Q+++     + + R   L  ++  LN RE  I   RRL ++ VTLE L  +  +S
Sbjct: 222 DDHPLQDEIAESSIDMERRNQWLNVALDTLNERELHIIRERRLDDDGVTLEALGEKLGIS 281

Query: 266 RERVRQIEARAFKKVQESIQKQVELSS 292
           +ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 282 KERVRQIESRAMEKLKIALLSQHELAA 308


>gi|30248598|ref|NP_840668.1| RNA polymerase factor sigma-32 [Nitrosomonas europaea ATCC 19718]
 gi|30180193|emb|CAD84495.1| Sigma-70 factor family [Nitrosomonas europaea ATCC 19718]
          Length = 280

 Score =  224 bits (571), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 126/281 (44%), Positives = 178/281 (63%), Gaps = 9/281 (3%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M++ V     L  YI      P+L ++EE  LAKR RE GD++AAH+LV SHLR+VV IA
Sbjct: 5   MALPVMAGGDLDSYIRATSSFPVLSREEEASLAKRMREEGDVNAAHQLVLSHLRVVVTIA 64

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            GY GYGLP ++++ EGNIGLM+AV++FDPERG RL ++++ WI+A + E+I+R+W LVK
Sbjct: 65  RGYLGYGLPHADLIQEGNIGLMKAVRRFDPERGVRLISFAIHWIRAEIHEFIMRNWRLVK 124

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DE 184
           I TT  Q++LFFNLR +K  L     + +   +V ++A++L V   EV+ M  R +G D 
Sbjct: 125 IATTKQQRKLFFNLRSMKKGL-----DTMSQAEVASMAEQLGVKAEEVVEMETRFSGRDI 179

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL  + +S + + S    WL    D   ++  E+ ER      L  S+  L+ R RRI E
Sbjct: 180 SLEPVTDSDEDDFSPIA-WLTDGSDPSRELEKEQLERLTHAR-LKNSLDSLDERSRRIIE 237

Query: 245 ARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           AR L+E+   TL  L+ E  VS ERVRQIEA+A KK++  I
Sbjct: 238 ARWLREDKAATLHELADELGVSAERVRQIEAKAMKKMRAEI 278


>gi|239832848|ref|ZP_04681177.1| RNA polymerase sigma factor, sigma-70 family [Ochrobactrum
           intermedium LMG 3301]
 gi|239825115|gb|EEQ96683.1| RNA polymerase sigma factor, sigma-70 family [Ochrobactrum
           intermedium LMG 3301]
          Length = 278

 Score =  224 bits (571), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 116/267 (43%), Positives = 178/267 (66%), Gaps = 1/267 (0%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE++EE  LA R+RE  D  A HR+ ++H+RLV+ +A  +R + LP+++++ EG +GL
Sbjct: 9   PYLEREEERDLAIRWRELKDQEALHRITSAHMRLVISMAGRFRKFKLPMNDLIQEGYVGL 68

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +FDPER  R +TY+ WWI+A+MQ+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 69  LEAAARFDPEREVRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKALFFNLRRLRSKL 128

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLV 205
               D   K E    I+ +L VS S+V  M+ RL+G D SL+A +NS +  +S+  D+LV
Sbjct: 129 AQSDDTMSKAEIYREISDQLGVSTSDVEIMDSRLSGPDSSLSAPVNSEESGASRRMDFLV 188

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            DH  Q+++     + + R   L  ++  LN RE  I   RRL ++ VTLE L  +  +S
Sbjct: 189 DDHPLQDEIAESSIDMERRNQWLNVALDTLNERELHIIRERRLDDDGVTLEALGEKLGIS 248

Query: 266 RERVRQIEARAFKKVQESIQKQVELSS 292
           +ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 249 KERVRQIESRAMEKLKIALLSQHELAA 275


>gi|5911381|gb|AAD55771.1|AF177466_1 sigma-32 factor RpoH [Methylovorus sp. SS1]
          Length = 284

 Score =  224 bits (570), Expect = 1e-56,   Method: Compositional matrix adjust.
 Identities = 119/270 (44%), Positives = 174/270 (64%), Gaps = 11/270 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+  I+  P+L  +EEY LA R R+  D+ AA  L+ SHLRLV  IA GY GYGLP 
Sbjct: 16  LDQYLRTIKAFPVLSVEEEYDLATRLRKGTDIEAAKGLIVSHLRLVASIARGYSGYGLPQ 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGN+GLM+AV++FDP+RG RL +++M WIKA + EYI+R+W LVK+ TT  Q++L
Sbjct: 76  ADLIQEGNVGLMKAVRRFDPDRGVRLVSFAMHWIKAEIHEYIVRNWRLVKVATTKAQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR +K +      + L P +V  IA++L V   EV+ M  R+ G E   +L  +SD 
Sbjct: 136 FFNLRSMKKN-----SHTLSPAEVADIARELRVKPEEVVEMESRMGGHEI--SLEGNSDD 188

Query: 196 NSSQWQDWLVYDHDGQ---EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE-N 251
           ++      + Y  D Q    ++L E+E   N+   L  ++  L+ R RRI +AR LQE N
Sbjct: 189 DTEDNFSPIAYLEDQQPEPSELLAEREAEHNQTVGLAHALESLDERSRRIVQARWLQENN 248

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             TL +L++EF VS ER+RQIE +A +K++
Sbjct: 249 SATLHDLAAEFGVSAERIRQIEQKAMQKMK 278


>gi|118594538|ref|ZP_01551885.1| RNA polymerase sigma factor [Methylophilales bacterium HTCC2181]
 gi|118440316|gb|EAV46943.1| RNA polymerase sigma factor [Methylophilales bacterium HTCC2181]
          Length = 286

 Score =  223 bits (569), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 127/268 (47%), Positives = 172/268 (64%), Gaps = 13/268 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y   IRKIP L  +EEY LA R +   DL AA +L+ SHL+LV+KIA  Y GY LP +++
Sbjct: 18  YQETIRKIPSLTAEEEYELASRLKRDNDLEAAKKLILSHLKLVMKIARSYSGYNLPHADL 77

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGNIGLM+AVKKFDP+RG RL +Y+++WIKA +QEY++++W LVK  TT  Q++LFFN
Sbjct: 78  VQEGNIGLMKAVKKFDPDRGVRLVSYAIYWIKAEIQEYVVKNWRLVKTATTKAQRKLFFN 137

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR L+  LQ      LKPE++ +IA +LNV ESEV  M  RL G E+    I+ SD  S 
Sbjct: 138 LRSLRKTLQP-----LKPEEIKSIANELNVKESEVREMEFRLNGKET---TIDYSDDESE 189

Query: 199 QWQDWLVYDHDGQEQVLIEKEE----RKNRRNMLTRSMSVLNPRERRIFEARRLQENPV- 253
           +     +   + +    +EK E      N    L  ++S L+ R R + EAR L +N   
Sbjct: 190 EDHFRPISYLEDETPSPLEKIEMDQAESNVSAELQHALSELDSRSRSVVEARWLNDNKSE 249

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TL  L+S+F+VS ER+RQIE  AFKK++
Sbjct: 250 TLNELASKFKVSAERIRQIEKNAFKKIR 277


>gi|114798150|ref|YP_762122.1| putative alternative sigma factor RpoH [Hyphomonas neptunium ATCC
           15444]
 gi|114738324|gb|ABI76449.1| putative alternative sigma factor RpoH [Hyphomonas neptunium ATCC
           15444]
          Length = 295

 Score =  223 bits (568), Expect = 2e-56,   Method: Compositional matrix adjust.
 Identities = 109/270 (40%), Positives = 171/270 (63%), Gaps = 3/270 (1%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +++    K P+L+   E  LA+R+RE  D +A H L T+++RLV+ +A  +R YGLP+++
Sbjct: 14  QFVKTAMKAPLLDPAHEASLARRWREAEDEAALHELTTAYMRLVISMAAKFRHYGLPMAD 73

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +VSEGN+GLMQA  +F+PER  R +TY+ WWI++++Q+Y+LR+WS+V+ GTT+ QK LFF
Sbjct: 74  LVSEGNVGLMQAAARFEPEREVRFSTYASWWIRSSIQDYVLRNWSIVRTGTTSAQKSLFF 133

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKN 196
           NLRRL+  +  + D  +  E    ++  L V   +V  M+ RL+G D SLNA +      
Sbjct: 134 NLRRLRARISDLGDGTMTRENKQWVSTHLGVPLRDVEIMSARLSGSDRSLNAPLTM--DG 191

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
            ++WQD +  +    E+ ++   +   R   ++ +M  L PRE  I   RRL E P TLE
Sbjct: 192 DAEWQDMIADEGAPPEEAVMRSHDTARRHEWISEAMEALTPRETYIITRRRLSEEPQTLE 251

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L  E  VS+ERVRQIE +A  K++ ++++
Sbjct: 252 ALGHELGVSKERVRQIEHQALSKLKRALEQ 281


>gi|94309217|ref|YP_582427.1| RNA polymerase factor sigma-32 [Cupriavidus metallidurans CH34]
 gi|93353069|gb|ABF07158.1| RNA polymerase sigma 32 (sigma H) factor [Cupriavidus metallidurans
           CH34]
          Length = 311

 Score =  223 bits (568), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 123/286 (43%), Positives = 179/286 (62%), Gaps = 13/286 (4%)

Query: 6   MSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
            ++   G +G L  YI  + +IPML  +EE  LA+  R++  + AA R+V SHLRLVV I
Sbjct: 28  FALTFPGTLGNLDSYIQAVHRIPMLTPEEELSLARDLRDNDSVDAARRMVMSHLRLVVSI 87

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y GYGLP ++++ EGNIGLM+AVK+FDPE+G RL +Y+M WIKA + EY+L++W +V
Sbjct: 88  ARQYLGYGLPHADLIQEGNIGLMKAVKRFDPEQGVRLVSYAMHWIKAEIHEYVLKNWRMV 147

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GD 183
           K+ TT  Q++LFFNLR    H Q    +   PEQ+ A+A++LNV   EV+ M  R++ GD
Sbjct: 148 KVATTKAQRKLFFNLR---SHKQG--SHTFTPEQIEAVARELNVKPEEVMEMETRMSGGD 202

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            +L   I   ++  +    +L  +H+   QVL  K   + +   L  +++ L+PR RRI 
Sbjct: 203 MALEGQIEDGEEEFAPIA-YLADNHNEPTQVLEAKRHDRLQVEGLEEALTKLDPRSRRII 261

Query: 244 EARRLQENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           EAR L  N       TL  L+ EF VS ER+RQIE+ A KK++ ++
Sbjct: 262 EARWLDVNDDGSGGATLHELADEFGVSAERIRQIESAAMKKMKGAL 307


>gi|332286014|ref|YP_004417925.1| RNA polymerase sigma-32 factor [Pusillimonas sp. T7-7]
 gi|330429967|gb|AEC21301.1| RNA polymerase sigma-32 factor [Pusillimonas sp. T7-7]
          Length = 293

 Score =  223 bits (567), Expect = 3e-56,   Method: Compositional matrix adjust.
 Identities = 129/288 (44%), Positives = 187/288 (64%), Gaps = 14/288 (4%)

Query: 2   NRKNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           N+  M+I   G +G +  YI  + ++PML ++EE  L KR R+H DL AA +L+TSHLRL
Sbjct: 13  NQLAMAISNPGALGTIEAYISAVNRLPMLTQEEETSLGKRLRDHDDLDAARQLITSHLRL 72

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y GYGL  ++++ EGN+GLM+AVK+FDPERG RL ++++ WIKA + EYI+R+
Sbjct: 73  VVSIARQYLGYGLAHADLIQEGNVGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYIVRN 132

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W LVK+ TT  Q++LFFNLRR++   Q      L  EQV  IA++LNV   +V  M  R+
Sbjct: 133 WRLVKVATTKAQRKLFFNLRRMRPDGQ-----TLDTEQVNEIARELNVRPEDVSEMEVRM 187

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ---VLIEKEERKNRRNMLTRSMSVLNP 237
           +G E   AL ++ D++      +L    +GQ++   VL  +     + + L  ++ VL+ 
Sbjct: 188 SGREF--ALESNDDEDGYAPIAYL--SDEGQQEPSRVLERRAYDALQGSGLADALDVLDE 243

Query: 238 RERRIFEARRLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R RRI +AR LQ E   TL  L++EF VS ER+RQIEA AFKK++ ++
Sbjct: 244 RSRRIVQARWLQDEGGATLHELAAEFGVSAERIRQIEAAAFKKLRVAL 291


>gi|261855188|ref|YP_003262471.1| RNA polymerase, sigma 32 subunit, RpoH [Halothiobacillus
           neapolitanus c2]
 gi|261835657|gb|ACX95424.1| RNA polymerase, sigma 32 subunit, RpoH [Halothiobacillus
           neapolitanus c2]
          Length = 291

 Score =  223 bits (567), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 115/269 (42%), Positives = 177/269 (65%), Gaps = 8/269 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ E+R+IP+L   EE  LA++ +  GD+ AA +L+ SHLR VV IA GYRGYGLP
Sbjct: 19  SLQQYLAEVRRIPLLTADEEQKLAEQLKSTGDIDAAQKLIMSHLRFVVHIARGYRGYGLP 78

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           +++++ EGNIGLM+AVK+F+PE+  RL T+++ WI+A + EYIL++W +VKI TT  Q++
Sbjct: 79  LADLIQEGNIGLMKAVKRFEPEQKVRLVTFAVHWIRAEIHEYILKNWRIVKIATTKAQRK 138

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSS 193
           LFF +R++K  L  +T +  +     AIA +LNV E EV++M  RL + D +++A +  S
Sbjct: 139 LFFKMRQMKSGLGWLTADETR-----AIAAELNVPEREVVTMESRLYSHDIAIDAPVYDS 193

Query: 194 DKNSS--QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           ++  S   ++  LV  H    + +  + +  +R   +T ++  L+ R R I E R LQE 
Sbjct: 194 EQEGSGPSYEQILVDQHQVSVEDMTAQRDEDDRVTAMTHALHDLDARSRDILERRWLQEP 253

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             TL+ L+ E++VS ERVRQIE  A KK+
Sbjct: 254 KATLQTLADEYQVSAERVRQIENAALKKL 282


>gi|119776597|ref|YP_929337.1| RNA polymerase factor sigma-32 [Shewanella amazonensis SB2B]
 gi|119769097|gb|ABM01668.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella amazonensis
           SB2B]
          Length = 285

 Score =  222 bits (566), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 113/280 (40%), Positives = 175/280 (62%), Gaps = 7/280 (2%)

Query: 4   KNMSIIV-NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           ++M+++V  G   L  YIH +  +PMLE ++EY LAKR +E GDL AA +L+ SHLR VV
Sbjct: 6   QSMALMVPQGASSLEAYIHSVNSMPMLEAEQEYQLAKRLQETGDLQAAKQLIMSHLRFVV 65

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y GYGLP ++++ EGNIGLM+AVK+FDP+ G RL ++++ WIKA + EY+L++W 
Sbjct: 66  HVAKSYSGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYVLKNWR 125

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L   +D+     +V  +A+ L VS+ +V  M  R+A 
Sbjct: 126 IVKVATTKAQRKLFFNLRKAKQRLGWFSDD-----EVAMVAENLGVSKDDVTEMESRMAA 180

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERR 241
            +    L+N  D +        + DH       IE +    N +N L  ++  L+ R + 
Sbjct: 181 QDQAFDLVNDHDDDEGFAPVHYLEDHSSDLAANIENDNWESNAQNRLIAAIKTLDERSQH 240

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           I  AR L ++ VTL+ L+ +++VS ER+RQ+E  A  K++
Sbjct: 241 ILRARWLDDDKVTLQELAEQYQVSAERIRQLEKNAMNKLK 280


>gi|307728369|ref|YP_003905593.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. CCGE1003]
 gi|307582904|gb|ADN56302.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. CCGE1003]
          Length = 311

 Score =  222 bits (566), Expect = 4e-56,   Method: Compositional matrix adjust.
 Identities = 124/287 (43%), Positives = 177/287 (61%), Gaps = 13/287 (4%)

Query: 7   SIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           S ++ G++G +  YI  + +IPML   EE   A  +REH +L AA RLV SHLRLVV IA
Sbjct: 29  SSLLPGQLGNIDAYIQAVNRIPMLTPAEERQFATEFREHDNLEAARRLVLSHLRLVVSIA 88

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGLP ++++ EGNIGLM+AVK+FDPE+  RL +Y+M WIKA + EYILR+W +VK
Sbjct: 89  RNYLGYGLPHADLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHWIKAEIHEYILRNWRMVK 148

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDE 184
           + TT  Q++LFFNLR  K  L A T     P+++  +AK+LNV   EV  M  RL+ GD 
Sbjct: 149 VATTKAQRKLFFNLRSHKQGLGAFT-----PDEIDGLAKELNVKREEVAEMETRLSGGDV 203

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           +L   +   +++ +    +L   H     VL  ++  K + + +  ++  L+ R RRI E
Sbjct: 204 ALEGQVEDGEESYAPIA-YLADSHSEPTAVLASRQRDKLQSDGIATALEALDARSRRIIE 262

Query: 245 ARRLQ-----ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           AR L+         TL  L+ EF VS ER+RQIEA A KK++ ++ +
Sbjct: 263 ARWLKVQDDGSGGSTLHELADEFGVSAERIRQIEASAMKKMRGALSE 309


>gi|114570847|ref|YP_757527.1| RNA polymerase sigma 32 subunit RpoH [Maricaulis maris MCS10]
 gi|114341309|gb|ABI66589.1| RNA polymerase, sigma 32 subunit, RpoH [Maricaulis maris MCS10]
          Length = 305

 Score =  222 bits (566), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 111/277 (40%), Positives = 173/277 (62%), Gaps = 3/277 (1%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           + G  R++       +L +++E  LA+R+++  D  A H L  +H+RLV+ +A  ++ YG
Sbjct: 19  DAGEQRFVKSAMARDLLSREDEADLARRWKDDRDEKALHELTEAHMRLVIAVAAKFKRYG 78

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP S+++ EGNIGLM+A  +FDPER  R +TY  WWI++ +Q+Y+LR+WS+V+ GTT+ Q
Sbjct: 79  LPFSDLIQEGNIGLMKAADRFDPERDVRFSTYVTWWIRSCIQDYVLRNWSIVRTGTTSAQ 138

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALIN 191
           K LFFNLRR++ ++  +  +++ P+    IAK L V E +V +M  RL A D SLNA + 
Sbjct: 139 KSLFFNLRRIRANIGDLDGSSITPDNRQKIAKDLRVRERDVENMALRLSASDRSLNAPVG 198

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             D   SQWQD+LV D    E  ++ + + + R   L  ++  LN RE+ I   RRL+E+
Sbjct: 199 --DAEDSQWQDFLVDDTAAPETEVMNRTDSERRSAWLGLALDGLNSREQFIIRERRLRED 256

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
             TL +L     +S+ERVRQIE  A  K+++ +   V
Sbjct: 257 GSTLASLGDSLGISKERVRQIENAALAKLRDHLTANV 293


>gi|295675387|ref|YP_003603911.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. CCGE1002]
 gi|295435230|gb|ADG14400.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. CCGE1002]
          Length = 311

 Score =  222 bits (566), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 124/285 (43%), Positives = 176/285 (61%), Gaps = 13/285 (4%)

Query: 7   SIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           S ++ G++G +  YI  + +IPML   EE   A   REH +L AA RLV SHLRLVV IA
Sbjct: 29  SSLLPGQLGNIDAYIQAVNRIPMLTPAEERKFATELREHDNLEAARRLVLSHLRLVVSIA 88

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGLP ++++ EGNIGLM+AVK+FDPE+  RL +Y+M WIKA + EYILR+W +VK
Sbjct: 89  RNYLGYGLPHADLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHWIKAEIHEYILRNWRMVK 148

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDE 184
           + TT  Q++LFFNLR  K  L A T     P+++  +AK+LNV   EV  M  RL+ GD 
Sbjct: 149 VATTKAQRKLFFNLRSHKQGLGAFT-----PDEIEGLAKELNVKREEVAEMETRLSGGDI 203

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           +L   +   +++ +    +L   H     VL  ++  + + + +  ++  L+PR RRI E
Sbjct: 204 ALEGQVEDGEESYAPIA-YLADSHSEPTAVLASRQRDRLQSDGIASALDALDPRSRRIIE 262

Query: 245 ARRLQ-----ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           AR L+         TL  L+ EF VS ER+RQIEA A KK++ ++
Sbjct: 263 ARWLKVADDGSGGSTLHELADEFGVSAERIRQIEASAMKKMRGAL 307


>gi|332524130|ref|ZP_08400360.1| RNA polymerase sigma-32 factor [Rubrivivax benzoatilyticus JA2]
 gi|332107469|gb|EGJ08693.1| RNA polymerase sigma-32 factor [Rubrivivax benzoatilyticus JA2]
          Length = 306

 Score =  222 bits (566), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 119/283 (42%), Positives = 178/283 (62%), Gaps = 15/283 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + ++PML  QEE  L KR REHGDL AA RLV SHLRLVV ++  Y GYGLP 
Sbjct: 23  LDAYITAVNRLPMLSAQEEVALGKRLREHGDLEAAGRLVLSHLRLVVSVSRQYLGYGLPH 82

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM+AVK+FDP++G RL +Y++ WIKA + EYIL++W +VK+ TT  Q++L
Sbjct: 83  GDLIQEGNVGLMKAVKRFDPDQGVRLVSYALHWIKAEIHEYILKNWRMVKVATTKAQRKL 142

Query: 136 FFNLRRLKGHLQA------ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
           FFNLR +K  L+       +  + L P +V  +A++LNV   EV+ M  RLAG +   AL
Sbjct: 143 FFNLRSMKQGLKGEAAEADLHRSTLTPAEVETVARELNVKPDEVVEMETRLAGGDV--AL 200

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN--RRNMLTRSMSVLNPRERRIFEARR 247
              +D +   +        +  E   + +  R++    + + +++SVL+ R RRI E R 
Sbjct: 201 EPQTDDSEESFAPIAYLADEASEPTRLLEARRRDWLSGDGIAQALSVLDARSRRIVEERW 260

Query: 248 LQENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L+ N      +TL  L++E+ VS ER+RQIE  A KK++++++
Sbjct: 261 LKVNDDSSGGMTLHELAAEYGVSAERIRQIEVAAMKKMRKALE 303


>gi|115372678|ref|ZP_01459985.1| alternative sigma factor RpoH [Stigmatella aurantiaca DW4/3-1]
 gi|310823838|ref|YP_003956196.1| RNA polymerase sigma-c factor [Stigmatella aurantiaca DW4/3-1]
 gi|115370399|gb|EAU69327.1| alternative sigma factor RpoH [Stigmatella aurantiaca DW4/3-1]
 gi|309396910|gb|ADO74369.1| RNA polymerase sigma-C factor [Stigmatella aurantiaca DW4/3-1]
          Length = 293

 Score =  222 bits (566), Expect = 5e-56,   Method: Compositional matrix adjust.
 Identities = 121/269 (44%), Positives = 175/269 (65%), Gaps = 8/269 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           LS Y+ EI + P+L +QEE  LA+ +R+ GDL A HRLVTS+LR VVK+A  YR YGL +
Sbjct: 11  LSTYLSEINQYPLLTQQEEQALARSFRQ-GDLQAGHRLVTSNLRFVVKVAYEYRSYGLRM 69

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           S+++ E NIGLM+AV+KFDP++G RL +Y++WWI+A +Q Y+L++WSLVK+GTT  Q+RL
Sbjct: 70  SDLIQEANIGLMKAVQKFDPDKGIRLISYAVWWIRAYIQGYVLKNWSLVKLGTTQAQRRL 129

Query: 136 FFNLRRLKGHL--QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINS 192
           FF L R +  L  Q  TD N+   +   IA+KLNV  SEV  M  R+ G D SL+A +  
Sbjct: 130 FFALARTRRELEKQGNTDGNIVNAE--EIARKLNVKASEVREMEQRMGGRDLSLDAPMG- 186

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            +   +   D++  D   Q   + +++E    R  + +++  L+PRER I E R + ++ 
Sbjct: 187 -EDGDATHMDFVASDSVSQADEVADRQEADLARTRIQQALQRLDPRERFIIEKRVMSDSE 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +TL  L   F  SRER RQ+E RA  K++
Sbjct: 246 MTLSELGEHFGFSRERARQLEIRAKDKLK 274


>gi|323524659|ref|YP_004226812.1| RNA polymerase sigma-32 subunit RpoH [Burkholderia sp. CCGE1001]
 gi|323381661|gb|ADX53752.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. CCGE1001]
          Length = 311

 Score =  222 bits (565), Expect = 6e-56,   Method: Compositional matrix adjust.
 Identities = 124/285 (43%), Positives = 176/285 (61%), Gaps = 13/285 (4%)

Query: 7   SIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           S ++ G++G +  YI  + +IPML   EE   A  +REH +L AA RLV SHLRLVV IA
Sbjct: 29  SSLLPGQLGNIDAYIQAVNRIPMLTPAEERQFATEFREHDNLEAARRLVLSHLRLVVSIA 88

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGLP ++++ EGNIGLM+AVK+FDPE+  RL +Y+M WIKA + EYILR+W +VK
Sbjct: 89  RNYLGYGLPHADLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHWIKAEIHEYILRNWRMVK 148

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDE 184
           + TT  Q++LFFNLR  K  L A T     P+++  +AK+LNV   EV  M  RL+ GD 
Sbjct: 149 VATTKAQRKLFFNLRSHKQGLGAFT-----PDEIDGLAKELNVKREEVAEMETRLSGGDI 203

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           +L   +   +++ +    +L   H     VL  ++  K + + +  ++  L+ R RRI E
Sbjct: 204 ALEGQVEDGEESYAPIA-YLADSHSEPTAVLASRQRDKLQSDGIATALEALDARSRRIIE 262

Query: 245 ARRLQ-----ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           AR L+         TL  L+ EF VS ER+RQIEA A KK++ ++
Sbjct: 263 ARWLKVQDDGSGGSTLHELADEFGVSAERIRQIEASAMKKMRGAL 307


>gi|237749576|ref|ZP_04580056.1| RNA polymerase sigma-32 factor [Oxalobacter formigenes OXCC13]
 gi|229380938|gb|EEO31029.1| RNA polymerase sigma-32 factor [Oxalobacter formigenes OXCC13]
          Length = 299

 Score =  221 bits (564), Expect = 7e-56,   Method: Compositional matrix adjust.
 Identities = 124/289 (42%), Positives = 185/289 (64%), Gaps = 11/289 (3%)

Query: 1   MNRKNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLR 59
           ++R  ++ ++ G +G +  YI EI ++PML ++ E  LA+RY E+ DL+AA  LV SHLR
Sbjct: 13  VSRHALAPVLTGSLGNIEAYIAEINRLPMLTQERETELAQRYHENNDLAAAQELVLSHLR 72

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           LV  IA  Y GYGLP ++++ EGNIGLM+AVK+FDP+ G RL +Y++ WIKA + EYILR
Sbjct: 73  LVASIARNYLGYGLPHADLIQEGNIGLMKAVKRFDPKMGVRLVSYAIHWIKAEIHEYILR 132

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
           +W +VK+ TT  Q++LFFNLR  K   +A+T      EQ+ ++A+KLNV + EV  M  R
Sbjct: 133 NWRMVKVATTKAQRKLFFNLRSHKSGNEAMT-----REQIRSLAEKLNVKDEEVSEMETR 187

Query: 180 LAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           L+G D +L    +  D N +    +L  +     +VL  K+  + +   L  ++  L+ R
Sbjct: 188 LSGHDIALETQHDDDDDNFAPIA-YLSSEQTEPTRVLEAKQHDRLQSEGLAEALDKLDDR 246

Query: 239 ERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +RI EAR L+ +     TL +L+ EF VS ER+RQIEA A KK++ ++
Sbjct: 247 SKRIIEARWLKNDDGSGATLHDLAEEFGVSAERIRQIEAAALKKMKNTL 295


>gi|85859725|ref|YP_461927.1| RNA polymerase sigma-B factor [Syntrophus aciditrophicus SB]
 gi|85722816|gb|ABC77759.1| RNA polymerase sigma-B factor [Syntrophus aciditrophicus SB]
          Length = 289

 Score =  221 bits (564), Expect = 9e-56,   Method: Compositional matrix adjust.
 Identities = 116/267 (43%), Positives = 175/267 (65%), Gaps = 6/267 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI EI + P+L  +EE+  A  ++++ ++ AA +LV S+LR VVKIA  YR YG+ +
Sbjct: 10  LEVYIAEINRFPILTAEEEFRYAIEWKKNQNMEAAEKLVVSNLRFVVKIAHEYRNYGVKL 69

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM AVKKFDP +G+RL +Y++WWI+A +Q YI+++WSLVKIGTT  Q++L
Sbjct: 70  ADLIQEGNIGLMHAVKKFDPYKGYRLISYAVWWIRAYIQNYIIKTWSLVKIGTTQAQRKL 129

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FF L + K  +QA++   LK  +   IA+ L V E EV  M+ R++  D SL+  I   D
Sbjct: 130 FFKLNKTKKDIQALS---LKNPEFSEIAESLGVREGEVEEMDVRMSNRDLSLDMAI--GD 184

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
              S   D+L Y  + QE  LI KEE +  R  +T +++VLN +E  I   R + ++P T
Sbjct: 185 DGGSSHMDFLTYAGEDQETALIRKEEAELVRKNITGALAVLNEKEMYIIRNRVMADDPKT 244

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQ 281
           L+ +   + ++RER RQIE +A KK++
Sbjct: 245 LQEIGDIYNITRERARQIEKQALKKLR 271


>gi|313201748|ref|YP_004040406.1| RNA polymerase sigma-32 subunit RpoH [Methylovorus sp. MP688]
 gi|312441064|gb|ADQ85170.1| RNA polymerase, sigma 32 subunit, RpoH [Methylovorus sp. MP688]
          Length = 290

 Score =  221 bits (563), Expect = 9e-56,   Method: Compositional matrix adjust.
 Identities = 120/270 (44%), Positives = 175/270 (64%), Gaps = 11/270 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+  I+  P+L  +EEY LA R R+  D+ AA  L+ SHLRLV  IA GY GYGLP 
Sbjct: 22  LDQYLRTIKAFPVLSAEEEYDLATRLRKDNDIDAAKGLIVSHLRLVASIARGYSGYGLPQ 81

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGN+GLM+AV++FDP+RG RL +++M WIKA + EYI+R+W LVK+ TT  Q++L
Sbjct: 82  ADLIQEGNVGLMKAVRRFDPDRGVRLVSFAMHWIKAEIHEYIVRNWRLVKVATTKAQRKL 141

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR +K +      + L P++V  IA++L V   EV+ M  R+ G E   +L  +SD 
Sbjct: 142 FFNLRSMKKN-----SHTLSPDEVADIARELKVKPEEVVEMESRMGGHEI--SLEGNSDD 194

Query: 196 NSSQWQDWLVYDHDGQ---EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE-N 251
           +S      + Y  D Q    ++L E+E   N+   L  ++  L+ R RRI +AR LQE N
Sbjct: 195 DSEDSFSPIAYLEDQQPEPSELLAEREAEHNQTVGLAHALESLDDRSRRIVQARWLQENN 254

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             TL +L++EF VS ER+RQIE +A +K++
Sbjct: 255 SATLHDLAAEFGVSAERIRQIEQKAMQKMK 284


>gi|253999699|ref|YP_003051762.1| RNA polymerase sigma-32 subunit RpoH [Methylovorus sp. SIP3-4]
 gi|253986378|gb|ACT51235.1| RNA polymerase, sigma 32 subunit, RpoH [Methylovorus sp. SIP3-4]
          Length = 284

 Score =  221 bits (563), Expect = 9e-56,   Method: Compositional matrix adjust.
 Identities = 120/270 (44%), Positives = 175/270 (64%), Gaps = 11/270 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+  I+  P+L  +EEY LA R R+  D+ AA  L+ SHLRLV  IA GY GYGLP 
Sbjct: 16  LDQYLRTIKAFPVLSAEEEYDLATRLRKDNDIDAAKGLIVSHLRLVASIARGYSGYGLPQ 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGN+GLM+AV++FDP+RG RL +++M WIKA + EYI+R+W LVK+ TT  Q++L
Sbjct: 76  ADLIQEGNVGLMKAVRRFDPDRGVRLVSFAMHWIKAEIHEYIVRNWRLVKVATTKAQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR +K +      + L P++V  IA++L V   EV+ M  R+ G E   +L  +SD 
Sbjct: 136 FFNLRSMKKN-----SHTLSPDEVADIARELKVKPEEVVEMESRMGGHEI--SLEGNSDD 188

Query: 196 NSSQWQDWLVYDHDGQ---EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE-N 251
           +S      + Y  D Q    ++L E+E   N+   L  ++  L+ R RRI +AR LQE N
Sbjct: 189 DSEDSFSPIAYLEDQQPEPSELLAEREAEHNQTVGLAHALESLDDRSRRIVQARWLQENN 248

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             TL +L++EF VS ER+RQIE +A +K++
Sbjct: 249 SATLHDLAAEFGVSAERIRQIEQKAMQKMK 278


>gi|323138995|ref|ZP_08074055.1| RNA polymerase, sigma 32 subunit, RpoH [Methylocystis sp. ATCC
           49242]
 gi|322395749|gb|EFX98290.1| RNA polymerase, sigma 32 subunit, RpoH [Methylocystis sp. ATCC
           49242]
          Length = 294

 Score =  221 bits (563), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 116/262 (44%), Positives = 177/262 (67%), Gaps = 2/262 (0%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE+ EE  LA  +R+HGD  A H+L  +H+RLV+ +A  +R YGLPI+++V EG++GL
Sbjct: 19  PFLERDEEKALAVAWRDHGDRRALHKLTAAHMRLVIALAAKFRHYGLPIADLVQEGHVGL 78

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +F PER  R +TY+ WWI+A++Q+Y+LR+WS+V+ GT+++QK LFFNLRRL+  L
Sbjct: 79  LEAAARFAPERDVRFSTYATWWIRASIQDYVLRNWSIVRGGTSSSQKALFFNLRRLRARL 138

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNA-LINSSDKNSSQWQDWL 204
               D     +   AIAK L VS ++V  M+ RL+G D SLNA L++     S+Q  D+L
Sbjct: 139 ARDPDAYGSGDAYQAIAKALGVSRADVEMMDSRLSGSDVSLNAQLVDDDSSGSAQRMDFL 198

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           V DH   ++ + E  +   R   L  ++++L+ RE RI + RRL +N VTLE L  +  +
Sbjct: 199 VDDHPLPDEAVQETMDSDRRARWLKDALAILSERELRIVQERRLTDNLVTLETLGDKLGI 258

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+ERVRQIE+RA  K+++++ +
Sbjct: 259 SKERVRQIESRALIKLRKALSR 280


>gi|39995761|ref|NP_951712.1| RNA polymerase sigma-32 factor [Geobacter sulfurreducens PCA]
 gi|39982525|gb|AAR33985.1| RNA polymerase sigma-32 factor [Geobacter sulfurreducens PCA]
 gi|298504771|gb|ADI83494.1| RNA polymerase sigma-32 factor RpoH [Geobacter sulfurreducens
           KN400]
          Length = 284

 Score =  221 bits (562), Expect = 1e-55,   Method: Compositional matrix adjust.
 Identities = 117/277 (42%), Positives = 177/277 (63%), Gaps = 7/277 (2%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +MS+ V  +  L+ Y+ EIRK P+L  +EEY  A ++ E  DL AAH L+TS+LR VVKI
Sbjct: 2   SMSLPVVAD-SLTVYLREIRKFPVLTPEEEYRFAVKFYEDKDLEAAHSLITSNLRFVVKI 60

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  YR YGL + +++ EGN+GLM AV+KF+P +G RL +Y++WWI+A +Q +I+ +WSL+
Sbjct: 61  AAEYRSYGLKMLDLIQEGNVGLMMAVRKFNPYKGIRLISYAVWWIRAYIQNHIISAWSLL 120

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           KIGTT  QK+LFF L + K  ++ +T  +     + A A  L+V ESEV+ M+ R+ GD 
Sbjct: 121 KIGTTQAQKKLFFKLNQAKNAIKGLTGTD----DIEATATSLHVKESEVLEMDQRMRGDF 176

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
            L+A I + D  +    + L  +   QE  L E +E +  +  +  ++  LN +ER I E
Sbjct: 177 YLDAEIKNGDGLT--ILETLADERQNQEDTLAELQESELLKQHIAGALGKLNEKERFIVE 234

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R   + P+TL+ ++  F +SRERVRQIE  A +K++
Sbjct: 235 QRVTADTPLTLQEIADRFSISRERVRQIEEAALRKIK 271


>gi|1143832|gb|AAA84899.1| RNA polymerase sigma C subunit [Stigmatella aurantiaca DW4/3-1]
          Length = 293

 Score =  220 bits (561), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 121/269 (44%), Positives = 174/269 (64%), Gaps = 8/269 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           LS Y+ EI + P+L +QEE  LA+ +R+ GDL A HRLVTS+LR VVK+A  YR YGL +
Sbjct: 11  LSTYLSEINQYPLLTQQEEQALARSFRQ-GDLQAGHRLVTSNLRFVVKVAYEYRSYGLRM 69

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           S+++ E NIGLM+AV+KFDP++G RL +Y++WWI A +Q Y+L++WSLVK+GTT  Q+RL
Sbjct: 70  SDLIQEANIGLMKAVQKFDPDKGIRLISYAVWWILAYIQGYVLKNWSLVKLGTTQAQRRL 129

Query: 136 FFNLRRLKGHL--QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINS 192
           FF L R +  L  Q  TD N+   +   IA+KLNV  SEV  M  R+ G D SL+A +  
Sbjct: 130 FFALARTRRELEKQGNTDGNIVNAE--EIARKLNVKASEVREMEQRMGGRDLSLDAPMG- 186

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            +   +   D++  D   Q   + +++E    R  + +++  L+PRER I E R + ++ 
Sbjct: 187 -EDGDATHMDFVASDSVSQADEVADRQEADLARTRIQQALQRLDPRERFIIEKRVMSDSE 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +TL  L   F  SRER RQ+E RA  K++
Sbjct: 246 MTLSELGEHFGFSRERARQLEIRAKDKLK 274


>gi|188591091|ref|YP_001795691.1| RNA polymerase factor sigma-32 [Cupriavidus taiwanensis LMG 19424]
 gi|170937985|emb|CAP62969.1| RNA polymerase sigma H (sigma 32) factor; transcription of heat
           shock and stress proteins [Cupriavidus taiwanensis LMG
           19424]
          Length = 309

 Score =  220 bits (561), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 123/293 (41%), Positives = 181/293 (61%), Gaps = 17/293 (5%)

Query: 2   NRKNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           N  + ++     +G L  YI  + +IP+L  +EE  LA+  R+H  + AA RLV SHLRL
Sbjct: 22  NTGSFALTFPATVGNLDSYIQAVHRIPLLTAEEEQRLARELRDHDSVEAARRLVMSHLRL 81

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y GYGLP ++++ EGNIGLM+AVK+FDP++G RL +Y+M WIKA + EY+L++
Sbjct: 82  VVSIARQYLGYGLPHADLIQEGNIGLMKAVKRFDPDQGVRLVSYAMHWIKAEIHEYVLKN 141

Query: 121 WSLVKIGTTANQKRLFFNLRRLK--GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
           W +VK+ TT  Q++LFFNLR  K  GH          PEQV A+A++LNV   EV+ M  
Sbjct: 142 WRMVKVATTKAQRKLFFNLRSHKQGGH-------TFTPEQVEAVARELNVKPEEVMEMET 194

Query: 179 RLA-GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
           RL+ GD +L   ++  ++  +    +L  +H+   +V+  K + + +   L  +++ L+ 
Sbjct: 195 RLSGGDLALEGQVDDGEEEFAPIA-YLADNHNEPTRVMEAKRQDRMQVEGLEEALAKLDE 253

Query: 238 RERRIFEARRLQ-----ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           R RRI EAR L          TL  L+ EF VS ER+RQIEA A KK++ ++Q
Sbjct: 254 RSRRIIEARWLNVEDDGSGGATLHELADEFGVSAERIRQIEAAAMKKMKGALQ 306


>gi|170691517|ref|ZP_02882682.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia graminis
           C4D1M]
 gi|170143722|gb|EDT11885.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia graminis
           C4D1M]
          Length = 311

 Score =  220 bits (561), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 123/285 (43%), Positives = 176/285 (61%), Gaps = 13/285 (4%)

Query: 7   SIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           S ++ G++G +  YI  + +IPML   EE   A  +REH +L AA RLV SHLRLVV IA
Sbjct: 29  SSLLPGQLGNIDAYIQAVNRIPMLTPAEERQFATEFREHDNLEAARRLVLSHLRLVVSIA 88

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGLP ++++ EGNIGLM+AVK+FDPE+  RL +Y+M WIKA + EYILR+W +VK
Sbjct: 89  RNYLGYGLPHADLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHWIKAEIHEYILRNWRMVK 148

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDE 184
           + TT  Q++LFFNLR  K  L + T     P+++  +AK+LNV   EV  M  RL+ GD 
Sbjct: 149 VATTKAQRKLFFNLRSHKQGLGSFT-----PDEIEGLAKELNVKREEVAEMETRLSGGDI 203

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           +L   +   +++ +    +L   H     VL  ++  K + + +  ++  L+ R RRI E
Sbjct: 204 ALEGQVEDGEESYAPIA-YLADSHSEPTAVLASRQRDKLQSDGIATALEALDARSRRIIE 262

Query: 245 ARRLQ-----ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           AR L+         TL  L+ EF VS ER+RQIEA A KK++ ++
Sbjct: 263 ARWLKVQDDGSGGSTLHELADEFGVSAERIRQIEASAMKKMRGAL 307


>gi|237747428|ref|ZP_04577908.1| RNA polymerase sigma-32 factor [Oxalobacter formigenes HOxBLS]
 gi|229378779|gb|EEO28870.1| RNA polymerase sigma-32 factor [Oxalobacter formigenes HOxBLS]
          Length = 299

 Score =  220 bits (560), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 125/279 (44%), Positives = 175/279 (62%), Gaps = 11/279 (3%)

Query: 11  NGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
            G +G +  YI E+ ++P+L  ++E  LA RYRE  DLSAA  LV SHLRLVV IA  Y 
Sbjct: 23  TGSLGNIEAYIAEVNRLPILTLEQETDLALRYRERNDLSAAQELVLSHLRLVVSIARNYL 82

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYGLP ++++ EGNIGLM+AVK+FDP  G RL +Y++ WIKA + EYILR+W +VKI TT
Sbjct: 83  GYGLPHADLIQEGNIGLMKAVKRFDPGMGVRLVSYAIHWIKAEIHEYILRNWRMVKIATT 142

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNA 188
             Q++LFFNLR  K  L ++T       Q+ ++A+KLNV + EV  M  RL G D +L  
Sbjct: 143 KAQRKLFFNLRSHKNGLDSMT-----RAQIRSLAEKLNVKDEEVAEMETRLNGHDIALET 197

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
             +  D N +    +L  +      +L  ++  + +   L  +++ L+PR RRI EAR L
Sbjct: 198 QHDDDDDNFAPIA-YLSSEQTEPASILEARQNDRMQSEGLAEALAKLDPRSRRIVEARWL 256

Query: 249 QE---NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                N  TL  L++EF VS ER+RQIEA A KK++ ++
Sbjct: 257 NSDDGNSATLHALAAEFGVSAERIRQIEAAALKKMKNTL 295


>gi|328542017|ref|YP_004302126.1| RNA polymerase sigma factor [polymorphum gilvum SL003B-26A1]
 gi|326411767|gb|ADZ68830.1| RNA polymerase sigma factor [Polymorphum gilvum SL003B-26A1]
          Length = 289

 Score =  220 bits (560), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 112/261 (42%), Positives = 177/261 (67%), Gaps = 1/261 (0%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L ++EE  LA R+R+  D++A  RL  +H+RLV+ +A  +R +GLP+++++ EG++GL
Sbjct: 19  PYLTREEELELATRWRQDKDVAALERLSLAHMRLVIAVASRFRNFGLPMNDLIQEGHVGL 78

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 79  LEAAARFEPEREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSTQKALFFNLRRLRAKL 138

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLV 205
            +   +  + E    IA+ + V  ++V  MN RL+G D SLNA I  SD +S+  QD+L+
Sbjct: 139 SSNRVDLPETELHRQIAEAIGVKTADVDLMNARLSGPDTSLNAPIIDSDGSSADRQDFLI 198

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            D    ++ + E  + + +R  L  +M+VL  RER+I   RRL E   TLE L ++  +S
Sbjct: 199 SDAPLPDETVSENIDSERQRRWLRSAMNVLTERERKIVSERRLTEEGATLEALGAKMGIS 258

Query: 266 RERVRQIEARAFKKVQESIQK 286
           +ERVRQIE RA +K++E++ K
Sbjct: 259 KERVRQIENRALEKLREALLK 279


>gi|209519627|ref|ZP_03268417.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. H160]
 gi|209499913|gb|EDZ99978.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. H160]
          Length = 311

 Score =  220 bits (560), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 122/280 (43%), Positives = 172/280 (61%), Gaps = 13/280 (4%)

Query: 12  GEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           G++G +  YI  + +IPML   EE   A   REH +L AA RLV SHLRLVV IA  Y G
Sbjct: 34  GQLGNIDAYIQAVNRIPMLTPAEERQFATELREHDNLEAARRLVLSHLRLVVSIARNYLG 93

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
           YGLP ++++ EGNIGLM+AVK+FDPE+  RL +Y+M WIKA + EYILR+W +VK+ TT 
Sbjct: 94  YGLPHADLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHWIKAEIHEYILRNWRMVKVATTK 153

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNAL 189
            Q++LFFNLR  K  L A T     P+++  +A++LNV   EV  M  RL+ GD +L   
Sbjct: 154 AQRKLFFNLRSHKQGLGAFT-----PDEIDGLARELNVKREEVAEMETRLSGGDIALEGQ 208

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           +   +++ +    +L   H     VL  ++  +   + +  ++  L+PR RRI EAR L+
Sbjct: 209 VEDGEESYAPIA-YLADSHSEPTAVLASRQRDRLHSDGIASALDALDPRSRRIIEARWLK 267

Query: 250 -----ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                    TL  L+ EF VS ER+RQIEA A KK++ ++
Sbjct: 268 VADDGSGGSTLHELADEFGVSAERIRQIEASAMKKMRGAL 307


>gi|118578560|ref|YP_899810.1| RNA polymerase sigma-32 subunit RpoH [Pelobacter propionicus DSM
           2379]
 gi|118501270|gb|ABK97752.1| RNA polymerase, sigma 32 subunit, RpoH [Pelobacter propionicus DSM
           2379]
          Length = 292

 Score =  219 bits (558), Expect = 3e-55,   Method: Compositional matrix adjust.
 Identities = 121/296 (40%), Positives = 185/296 (62%), Gaps = 17/296 (5%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           N+ ++ +    L+ Y+ EIRK  +L ++EE   A R+ E  DL AAH LVTS+LR VVKI
Sbjct: 4   NLPVVADS---LTLYLAEIRKFNLLSEEEERSCAIRFYEEKDLEAAHTLVTSNLRYVVKI 60

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  YR YG+ + +++ EGNIGLM AV+KF+P R  RL +Y++WWI+A +Q YI+ +WSL+
Sbjct: 61  ASEYRNYGMKMLDLIQEGNIGLMMAVRKFNPYRKIRLISYAVWWIRAYIQNYIVSAWSLI 120

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           KIGTT  Q++LF+ LR+ K  L  +T ++        IA  L V + EVI M  RL G+ 
Sbjct: 121 KIGTTQAQRKLFYGLRKTKEALLRMTGSD---NDAAEIASMLQVPDHEVIDMEQRLKGEV 177

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL+  I  SD  +  + + +  D   QE++L E ++    +  + ++M  LN +ER I E
Sbjct: 178 SLDCQIVESDGLT--FLETIADDRMNQEELLGENQQELQVKQRVIKAMEGLNEKERYIVE 235

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQKP 300
            R   + P+TL++++S F +SRERVRQ+E RA  K+++ ++         PL++KP
Sbjct: 236 HRITSDEPLTLQDIASHFSISRERVRQLEERALAKLKKVLE---------PLMEKP 282


>gi|222053896|ref|YP_002536258.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter sp. FRC-32]
 gi|221563185|gb|ACM19157.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter sp. FRC-32]
          Length = 283

 Score =  219 bits (558), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 113/280 (40%), Positives = 183/280 (65%), Gaps = 8/280 (2%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +M ++V+    LS Y+ EI++ P+L  +EE+  A R+ E  DL AAH+L+TS+LR VVKI
Sbjct: 4   SMPVVVDN---LSLYLAEIKRFPVLSPEEEHECAVRFYEKKDLEAAHKLITSNLRFVVKI 60

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  YR YG+ + +++ EGN+GLM AV+KF+P +GFRL +Y++WWI+A +Q +I+ +WSL+
Sbjct: 61  AGEYRAYGMKMLDLIQEGNVGLMMAVRKFNPHKGFRLISYAVWWIRAYIQNHIISAWSLL 120

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           KIGTT  Q++LFF L + K  ++ +T      E   A A+ L+V E+EV  M+ R+ GD 
Sbjct: 121 KIGTTQAQRKLFFKLNQAKSAIRNMTGGG---EDFQATAEALDVKETEVAEMDQRMRGDF 177

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
            L+A + + +  +    + L  +   QE++L E +E       +  +++ LN +ER + E
Sbjct: 178 FLDAQVITGEGLT--MLESLPDERRNQEELLAEAQESALLEKQVASALTCLNEKERYVIE 235

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            R   E+P+TL+ ++  F +SRERVRQIE  A KK+++++
Sbjct: 236 QRVSAESPLTLQEIADHFSISRERVRQIEEGALKKMKQAL 275


>gi|83859721|ref|ZP_00953241.1| RNA polymerase sigma factor [Oceanicaulis alexandrii HTCC2633]
 gi|83852080|gb|EAP89934.1| RNA polymerase sigma factor [Oceanicaulis alexandrii HTCC2633]
          Length = 301

 Score =  219 bits (558), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 118/272 (43%), Positives = 174/272 (63%), Gaps = 3/272 (1%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           R++ +    P+LE++EE  LA  ++E GD  A H L T+++RLV+ IA  +R YGLP  +
Sbjct: 20  RFMKQAMDAPLLEREEELNLATAWKEKGDEEALHALTTAYMRLVISIAAKFRHYGLPFPD 79

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +VSEGNIGLMQA  +F+PER  R +TY+ WWI+A++Q+Y+LR+WS+V+ GTTA QK LFF
Sbjct: 80  LVSEGNIGLMQAAARFEPEREVRFSTYATWWIRASIQDYVLRNWSIVRTGTTAAQKSLFF 139

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKN 196
           NLRRL+  ++  +   L PE    +A+ L V E +V  M  RLA  D SLNA    S+  
Sbjct: 140 NLRRLRALIKDTSSGQLTPENRAYVAQALRVGEDDVEKMASRLAAVDRSLNAPF--SEDG 197

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
             +WQD L  ++   E  ++E  ++  R   L  ++S L+ RE+ I   RRL E+ VTLE
Sbjct: 198 EGEWQDLLADENPDPETQVMEDRDQAQRAQWLGEALSRLSEREQLIIRERRLGEDSVTLE 257

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            L     +S+ERVRQ+E +A  K+++ + + V
Sbjct: 258 KLGERLGISKERVRQVEHQALNKLKKYLTEVV 289


>gi|254796721|ref|YP_003081557.1| RNA polymerase sigma-32 factor (RpoH) [Neorickettsia risticii str.
           Illinois]
 gi|254589969|gb|ACT69331.1| RNA polymerase sigma-32 factor (RpoH) [Neorickettsia risticii str.
           Illinois]
          Length = 288

 Score =  219 bits (558), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 124/274 (45%), Positives = 177/274 (64%), Gaps = 13/274 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y  +I  IP+L+++EE  L  R+  H D+SAA RLV ++LRLVVK+ + +R YG P+ ++
Sbjct: 16  YARKILAIPILQEEEERDLIDRWFLHRDISAAQRLVEAYLRLVVKVTVRFRNYGFPLMDL 75

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
            SEGNIGLM+A+K F+P  G  +ATY++WWIKAA+ EY++RSWS+VKIGTTA Q++LFFN
Sbjct: 76  ASEGNIGLMKAIKNFNPTLGHGIATYAIWWIKAAINEYVIRSWSIVKIGTTAAQRKLFFN 135

Query: 139 LRRLKGHLQAITDNNLKPEQVVA-IAKKLNVSESEVISM----NCRLAGDESLNALINSS 193
           LR+LK    + +   L   QVV  I++ L VS+++V  M    N R   D SLN  +   
Sbjct: 136 LRKLK---NSGSVAGLDEHQVVGKISEMLEVSKNDVEEMERILNVR---DVSLN--MQLG 187

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           +  SS+  D + +    QE VL E  ER+ +  +L  ++  L  R + IF AR L   P 
Sbjct: 188 EDGSSEVHDLIPFPEANQEAVLSETRERQMKNRLLYEAVESLEARHKEIFVARSLSAVPR 247

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           TL+ L  +F +S+ERVRQI ARA KKV E +++ 
Sbjct: 248 TLKELGEKFSISQERVRQIHARAMKKVAEYVEEH 281


>gi|285019635|ref|YP_003377346.1| RNA polymerase sigma-32 factor protein [Xanthomonas albilineans GPE
           PC73]
 gi|283474853|emb|CBA17352.1| probable rna polymerase sigma-32 factor protein [Xanthomonas
           albilineans]
          Length = 292

 Score =  219 bits (558), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 117/269 (43%), Positives = 170/269 (63%), Gaps = 8/269 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + +IP+L  +EE+ LA RYR+  DL AA  LV SHLR VV +A GY GYGLP+
Sbjct: 24  LDAYIGAVHQIPVLTSEEEHALAVRYRDQEDLDAARELVHSHLRFVVHVARGYNGYGLPL 83

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++V EGNIGLM+AVK+FDP+ G RL ++++ WI+A M EYIL++W +VK+ TT  Q++L
Sbjct: 84  GDLVQEGNIGLMKAVKRFDPDMGVRLVSFAVHWIRAEMHEYILKNWRIVKVATTKAQRKL 143

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR+ K  L       +   +V A+AK LNVSE EV+ M  RL+G D   +A  +  D
Sbjct: 144 FFNLRKSKTRL-----GWMNAAEVTAVAKDLNVSEREVLEMESRLSGRDIGFDAPSDEDD 198

Query: 195 KNS-SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ-ENP 252
            ++      +L+ + +   Q     +   N+  +L   ++ L+ R R I E R L  ++ 
Sbjct: 199 DHAPPSPAAYLMANEEDPSQAYERADSDDNQLQLLREGLAELDARSRDIIERRWLDADSK 258

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +TL+ L+ E+ VS ER+RQIEA A KK++
Sbjct: 259 ITLQELADEYGVSAERIRQIEANALKKMK 287


>gi|325983562|ref|YP_004295964.1| RNA polymerase, sigma 32 subunit, RpoH [Nitrosomonas sp. AL212]
 gi|325533081|gb|ADZ27802.1| RNA polymerase, sigma 32 subunit, RpoH [Nitrosomonas sp. AL212]
          Length = 281

 Score =  219 bits (557), Expect = 4e-55,   Method: Compositional matrix adjust.
 Identities = 123/271 (45%), Positives = 173/271 (63%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           YI  +   P+L ++EE  LA+R    GD+ AA +L+ SHLR VV IA GY+GYGLP +++
Sbjct: 17  YIQSVNSFPILTQEEETSLARRLWNRGDIEAAQQLIMSHLRFVVAIARGYKGYGLPQADL 76

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM+AVK+FDPERG RL ++++ WIKA + E+I+R+W LVKI TT  Q++LFFN
Sbjct: 77  IQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEFIMRNWRLVKIATTKQQRKLFFN 136

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR +K  L     + + P++V A+A +L V   EVI M  R  G D SL  +    D   
Sbjct: 137 LRSMKHGL-----DTMNPQEVDAMAAQLGVKAEEVIEMEKRFNGSDISLEPVSEDEDDTF 191

Query: 198 SQWQDWLVYDHDGQE-QVLIEKEERKN-RRNMLTRSMSVLNPRERRIFEARRLQE-NPVT 254
           S     + Y  DG E   L+EKE+  + R   L +S+  L+ R R I EAR L+E +  T
Sbjct: 192 SP----INYLTDGTEPSQLLEKEQITHLREKGLQKSLDCLDKRSRHIIEARWLREKDTAT 247

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L +L+ E  VS ERVRQIE +A +K++ +I+
Sbjct: 248 LHDLADELGVSAERVRQIEVKALQKMRGAIK 278


>gi|189424394|ref|YP_001951571.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter lovleyi SZ]
 gi|189420653|gb|ACD95051.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter lovleyi SZ]
          Length = 285

 Score =  219 bits (557), Expect = 5e-55,   Method: Compositional matrix adjust.
 Identities = 118/275 (42%), Positives = 180/275 (65%), Gaps = 4/275 (1%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
            S+Y+ EI+  P+L++QEE+ LA R  E  DLSAA  L+TS+LR VVKIA  YR YGL +
Sbjct: 12  FSKYLSEIKSFPLLDEQEEHRLAVRLFEENDLSAAQTLITSNLRFVVKIAAEYRNYGLKM 71

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM AV+KF+P RGFRL TY++WWI+A +Q YI+ SWSL+KIGTT  Q++L
Sbjct: 72  LDLIQEGNIGLMLAVRKFNPYRGFRLITYAVWWIRAQIQSYIVSSWSLLKIGTTQAQRKL 131

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FF L++ K  +  ++ N      + A A  L+V E+EV  M  RL G+ SL+A   + + 
Sbjct: 132 FFKLKQAKNAI--LSMNGGDEGDLPATALSLDVREAEVEEMELRLMGEVSLDAEQVAGEG 189

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
            S    + LV D   QE  L + +E++  R ++  ++S L  +E+ + + R + ++P+TL
Sbjct: 190 GS--LLETLVDDRPNQESQLADLQEQQALRVVVADAVSRLGEKEQFVVKQRIVADDPMTL 247

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
           + ++  F +SRERVRQIE  A +K++  +   ++L
Sbjct: 248 QEIADHFSISRERVRQIEENALRKIKGFLGASMQL 282


>gi|311103433|ref|YP_003976286.1| alternative sigma factor RpoH [Achromobacter xylosoxidans A8]
 gi|310758122|gb|ADP13571.1| alternative sigma factor RpoH [Achromobacter xylosoxidans A8]
          Length = 294

 Score =  218 bits (556), Expect = 7e-55,   Method: Compositional matrix adjust.
 Identities = 125/288 (43%), Positives = 180/288 (62%), Gaps = 13/288 (4%)

Query: 2   NRKNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           N   ++I   G +G +  YI  + ++P+L  + E  L +R R+  DL AA  L+ SHLRL
Sbjct: 13  NALALAIANPGALGTIDAYISSVNRLPVLSAERETELGRRLRDQEDLGAARELILSHLRL 72

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y GYGLP ++++ EGN+GLM+AVK+FDPERG RL ++++ WIKA + EYI+R+
Sbjct: 73  VVSVARQYLGYGLPHADLIQEGNVGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYIIRN 132

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W LVK+ TT  Q++LFFNLR ++   Q      L P+QV  IA++LNV   +V  M  RL
Sbjct: 133 WRLVKVATTKAQRKLFFNLRSMRPDGQ-----TLDPDQVDHIARELNVRREDVSEMEVRL 187

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQV-LIEKEERKNRRNM-LTRSMSVLNP 237
           +G D SL    N  D + S      + D   QE   ++E+  R   ++  LT ++  L+P
Sbjct: 188 SGRDMSLE---NQDDDDDSYAPIAYLSDEGRQEPTRVLERAARDQLQSAGLTDALQALDP 244

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R RRI EAR LQ++   TL  L+ EF VS ER+RQIEA A KK++ ++
Sbjct: 245 RSRRIVEARWLQDDGGATLHELAQEFGVSAERIRQIEAAALKKMRGNL 292


>gi|192289929|ref|YP_001990534.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodopseudomonas palustris
           TIE-1]
 gi|192283678|gb|ACF00059.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodopseudomonas palustris
           TIE-1]
          Length = 326

 Score =  218 bits (556), Expect = 7e-55,   Method: Compositional matrix adjust.
 Identities = 116/270 (42%), Positives = 163/270 (60%), Gaps = 1/270 (0%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+  I + P+LE  EE  L +R+    D +AA  L+TSHLRL  K+A  YR YG PI ++
Sbjct: 25  YMRAIGRYPVLEPDEEARLWQRWHTARDKAAADVLITSHLRLAAKLARNYRRYGFPIGDL 84

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           ++E N+GLM A+ KFDP RG R AT ++WWI++A+ ++I+RSWSLV+IG T  QK+LFF 
Sbjct: 85  IAEANLGLMMALDKFDPTRGARFATCAVWWIRSAIYDHIVRSWSLVRIGRTPAQKKLFFR 144

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR     L+      L  +    I+  L+V   EVI M  RL+GD SLNA ++  D+ S 
Sbjct: 145 LRGEIRRLRPDHHGALTKDLAEQISTSLDVPLREVIEMEQRLSGDLSLNAPLSDLDE-SG 203

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           +WQD +  D    E +L   +E   +R  L  ++  L+ RER IF AR L + P + E +
Sbjct: 204 EWQDLIADDSPNAEAILAGHDELDRQRGALRDALVQLDARERYIFSARHLGDRPASFEAI 263

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQV 288
                +S ERVRQIEARAF KV  + ++  
Sbjct: 264 GQSLSLSAERVRQIEARAFAKVATAARRHC 293


>gi|114331030|ref|YP_747252.1| RNA polymerase factor sigma-32 [Nitrosomonas eutropha C91]
 gi|114308044|gb|ABI59287.1| RNA polymerase, sigma 32 subunit, RpoH [Nitrosomonas eutropha C91]
          Length = 280

 Score =  218 bits (555), Expect = 8e-55,   Method: Compositional matrix adjust.
 Identities = 126/284 (44%), Positives = 181/284 (63%), Gaps = 15/284 (5%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
            + +I  G   L  YI      P+L ++EE  LAK+ +E+GD++AAH+LV SHLR VV I
Sbjct: 6   TLPVISGG--NLESYIRAANSFPVLSREEEISLAKKMQENGDINAAHQLVLSHLRTVVMI 63

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A GY GYGLP ++++ EGNIGLM+AV++FDPERG RL ++++ WIKA + E+I+R+W LV
Sbjct: 64  ARGYLGYGLPHADLIQEGNIGLMKAVRRFDPERGVRLISFAIHWIKAEIHEFIMRNWRLV 123

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-D 183
           KI TT  Q++LFFNLR +K  L     + +   +V  +A++L V   EV+ M  R +G D
Sbjct: 124 KIATTKPQRKLFFNLRSMKEGL-----DTMNQAEVATMAEQLGVKAEEVVEMETRFSGRD 178

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVL-IEKEERKNRRNM-LTRSMSVLNPRERR 241
            SL  L +S +++ S     + Y  DG +    +EKE+ +   +  L  S+  L+ R RR
Sbjct: 179 ISLEPLTDSDEEDFSP----IAYLTDGSDPSRELEKEQLERLTHAKLKDSLDSLDERSRR 234

Query: 242 IFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           I EAR L+E+   TL  L+ E  VS ERVRQIEA+A KK++  I
Sbjct: 235 IIEARWLREDKAATLHELAKELGVSAERVRQIEAKAMKKMRAEI 278


>gi|127514531|ref|YP_001095728.1| RNA polymerase factor sigma-32 [Shewanella loihica PV-4]
 gi|126639826|gb|ABO25469.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella loihica PV-4]
          Length = 285

 Score =  218 bits (555), Expect = 9e-55,   Method: Compositional matrix adjust.
 Identities = 115/281 (40%), Positives = 175/281 (62%), Gaps = 9/281 (3%)

Query: 4   KNMSIIV-NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           ++M+++V      L  YIH    IPMLE  EEY LAKR +E GD+ AA +L+ SHLR V+
Sbjct: 6   QSMALMVPQSSSSLEAYIHSAHNIPMLEANEEYELAKRLQETGDIQAAKQLIMSHLRFVI 65

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A GY GYGLP ++++ EGNIGLM+AVK+FDP+ G RL ++++ WIKA + EY+L++W 
Sbjct: 66  HVAKGYAGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYVLKNWR 125

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L   +D     E+V  +A+ L VS+S+V  M  R+A 
Sbjct: 126 IVKVATTKAQRKLFFNLRKAKKRLGWFSD-----EEVTMVAENLGVSKSDVTEMESRMAA 180

Query: 183 DESLNALINSSDKNSSQWQDWLVYDH--DGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            +    L + +D +        + DH  D   QV  +  E  N+  +L  ++  L+ R +
Sbjct: 181 QDPAFDLASDNDDDQDYAPVHYLEDHSSDIASQVENDNFEADNQTRLLA-AIKTLDERSQ 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            I +AR L E   TL+ L++ ++VS ER+RQ+E  A  K++
Sbjct: 240 HILQARWLDEEKTTLQELAATYQVSAERIRQLEKNAMNKLK 280


>gi|317403164|gb|EFV83689.1| RNA polymerase sigma factor [Achromobacter xylosoxidans C54]
          Length = 294

 Score =  218 bits (555), Expect = 9e-55,   Method: Compositional matrix adjust.
 Identities = 126/288 (43%), Positives = 180/288 (62%), Gaps = 13/288 (4%)

Query: 2   NRKNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           N   ++I   G +G +  YI  + ++P+L  + E  L +R R+  DL AA  LV SHLRL
Sbjct: 13  NALALAIANPGALGTIDAYISAVNRLPVLSAERETELGRRLRDSEDLGAARELVLSHLRL 72

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y GYGLP ++++ EGN+GLM+AVK+FDPERG RL ++++ WIKA + EYI+R+
Sbjct: 73  VVSVARQYLGYGLPHADLIQEGNVGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYIIRN 132

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W LVK+ TT  Q++LFFNLR ++   Q      L PEQV  IA++LNV   +V  M  RL
Sbjct: 133 WRLVKVATTKAQRKLFFNLRSMRPDGQ-----TLDPEQVDHIARELNVRREDVSEMEVRL 187

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQV-LIEKEERKN-RRNMLTRSMSVLNP 237
           +G D SL    N  D + S      + D   QE   ++E+  R   + + L+ ++  L+P
Sbjct: 188 SGRDMSLE---NQDDDDDSYAPIAYLSDEGRQEPTRVLERAARDQLQSSGLSSALEALDP 244

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R RRI EAR LQ++   TL  L+ EF VS ER+RQIEA A KK++ ++
Sbjct: 245 RSRRIVEARWLQDDGGATLHELAQEFGVSAERIRQIEAAALKKMRGNL 292


>gi|329120658|ref|ZP_08249321.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Neisseria
           bacilliformis ATCC BAA-1200]
 gi|327460882|gb|EGF07216.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Neisseria
           bacilliformis ATCC BAA-1200]
          Length = 287

 Score =  218 bits (555), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 122/283 (43%), Positives = 183/283 (64%), Gaps = 9/283 (3%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           + +G   L +YIH +  IP+L  +EE+ LA+R +  GD+ AA RL+ SHLR+VV IA GY
Sbjct: 11  VPSGHGSLEQYIHTVNSIPLLTPEEEHNLAER-KMGGDVEAAKRLILSHLRVVVSIARGY 69

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGL  ++++ EGNIGLM+AVK+++P+RG RL ++++ WIKA + E+ILR+W LV++ T
Sbjct: 70  DGYGLNQADLIQEGNIGLMKAVKRYEPDRGARLFSFAVHWIKAEIHEFILRNWRLVRVAT 129

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           T  Q++LFFNLR ++  L A     L P++  AIA  L V  SEV+ M  R+ G +    
Sbjct: 130 TKPQRKLFFNLRSMRKSLSA-----LSPKEAQAIADDLGVKLSEVMEMEQRMTGRDIALL 184

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIE-KEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             NS D++S    DWL  DHD +    IE K     +   L  +++ L+ R RRI E R 
Sbjct: 185 ADNSDDEDSFAPIDWLA-DHDNEPTRQIERKAHHALQTEGLQNALAKLDERSRRIVETRW 243

Query: 248 LQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 244 LQDDGGLTLHELAAEYGVSAERIRQIEAKAMQKLRGFLAEEAE 286


>gi|241661869|ref|YP_002980229.1| RNA polymerase factor sigma-32 [Ralstonia pickettii 12D]
 gi|240863896|gb|ACS61557.1| RNA polymerase, sigma 32 subunit, RpoH [Ralstonia pickettii 12D]
          Length = 309

 Score =  218 bits (554), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 120/281 (42%), Positives = 179/281 (63%), Gaps = 12/281 (4%)

Query: 12  GEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           G +G +  YI  + ++PML  +EE  LA+ YR++ +L AA RLV SHLRLVV IA GY G
Sbjct: 31  GNLGNIDAYIQSVNRVPMLSAEEEQRLAREYRDNDNLDAARRLVLSHLRLVVSIARGYLG 90

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
           YGLP ++++ EGNIGLM+AVK+FDP++G RL +Y+M WIKA M EYIL++W +VK+ TT 
Sbjct: 91  YGLPHADLIQEGNIGLMKAVKRFDPDQGVRLVSYAMHWIKAEMHEYILKNWRMVKVATTK 150

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNAL 189
            Q++LFFNLR  K   QA        +++ A+A +LNV  +EV  M  RL+ GD +L   
Sbjct: 151 AQRKLFFNLRSHKQDAQA----TFTSDEIDAVAAELNVKGTEVREMETRLSGGDIALEGQ 206

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           ++  +++ +    +L   H+   +V+  +   + +   +  +++ L+ R RRI EAR L 
Sbjct: 207 MDDGEESYAPIA-YLADTHNEPTRVIEARSNDRMQSEGIEAALAKLDDRSRRIIEARWLN 265

Query: 250 ENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            N       TL  L+ EF VS ER+RQIE+ A KK++ ++Q
Sbjct: 266 VNDDGSGGSTLHELADEFGVSAERIRQIESAAMKKMKGALQ 306


>gi|187927337|ref|YP_001897824.1| RNA polymerase factor sigma-32 [Ralstonia pickettii 12J]
 gi|309779962|ref|ZP_07674716.1| alternative sigma factor RpoH [Ralstonia sp. 5_7_47FAA]
 gi|187724227|gb|ACD25392.1| RNA polymerase, sigma 32 subunit, RpoH [Ralstonia pickettii 12J]
 gi|308921321|gb|EFP66964.1| alternative sigma factor RpoH [Ralstonia sp. 5_7_47FAA]
          Length = 309

 Score =  218 bits (554), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 120/281 (42%), Positives = 179/281 (63%), Gaps = 12/281 (4%)

Query: 12  GEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           G +G +  YI  + ++PML  +EE  LA+ YR++ +L AA RLV SHLRLVV IA GY G
Sbjct: 31  GNLGNIDAYIQSVNRVPMLSAEEEQRLAREYRDNDNLDAARRLVLSHLRLVVSIARGYLG 90

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
           YGLP ++++ EGNIGLM+AVK+FDP++G RL +Y+M WIKA M EYIL++W +VK+ TT 
Sbjct: 91  YGLPHADLIQEGNIGLMKAVKRFDPDQGVRLVSYAMHWIKAEMHEYILKNWRMVKVATTK 150

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNAL 189
            Q++LFFNLR  K   QA        +++ A+A +LNV  +EV  M  RL+ GD +L   
Sbjct: 151 AQRKLFFNLRSHKQDAQA----TFTSDEIDAVAAELNVKGTEVREMETRLSGGDIALEGQ 206

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           ++  +++ +    +L   H+   +V+  +   + +   +  +++ L+ R RRI EAR L 
Sbjct: 207 MDDGEESFAPIA-YLADTHNEPTRVIEARSNDRMQSEGIEAALAKLDDRSRRIIEARWLN 265

Query: 250 ENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            N       TL  L+ EF VS ER+RQIE+ A KK++ ++Q
Sbjct: 266 VNDDGSGGSTLHELADEFGVSAERIRQIESAAMKKMKGALQ 306


>gi|3219168|dbj|BAA28784.1| sigma-32 homolog [Achromobacter xylosoxidans]
          Length = 306

 Score =  218 bits (554), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 125/288 (43%), Positives = 180/288 (62%), Gaps = 13/288 (4%)

Query: 2   NRKNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           N   ++I   G +G +  YI  + ++P+L  + E  L +R R+  DL AA  L+ SHLRL
Sbjct: 25  NALALAIANPGALGTIDAYISAVNRLPVLSAERETELGRRLRDQEDLGAARELILSHLRL 84

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y GYGLP ++++ EGN+GLM+AVK+FDPERG RL ++++ WIKA + EYI+R+
Sbjct: 85  VVSVARQYLGYGLPHADLIQEGNVGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYIIRN 144

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W LVK+ TT  Q++LFFNLR ++   Q      L PEQV  IA++LNV   +V  M  RL
Sbjct: 145 WRLVKVATTKAQRKLFFNLRSMRPDGQ-----TLDPEQVEHIARELNVRREDVSEMEVRL 199

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQV-LIEKEERKN-RRNMLTRSMSVLNP 237
           +G D SL    N  D + S      + D   QE   ++E+  R   + + L+ ++  L+P
Sbjct: 200 SGRDMSLE---NQDDDDDSYAPIAYLSDDGRQEPTRVLERAARDQLQGSGLSDALEALDP 256

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R RRI EAR LQ++   TL  L+ EF VS ER+RQIEA A KK++ ++
Sbjct: 257 RSRRIVEARWLQDDGGATLHELAQEFGVSAERIRQIEAAALKKMRGNL 304


>gi|33594607|ref|NP_882251.1| RNA polymerase factor sigma-32 [Bordetella pertussis Tohama I]
 gi|33598734|ref|NP_886377.1| RNA polymerase factor sigma-32 [Bordetella parapertussis 12822]
 gi|33603808|ref|NP_891368.1| RNA polymerase factor sigma-32 [Bordetella bronchiseptica RB50]
 gi|33564683|emb|CAE44005.1| RNA polymerase sigma-32 factor [Bordetella pertussis Tohama I]
 gi|33574864|emb|CAE39527.1| RNA polymerase sigma-32 factor [Bordetella parapertussis]
 gi|33577933|emb|CAE35198.1| RNA polymerase sigma-32 factor [Bordetella bronchiseptica RB50]
 gi|332384018|gb|AEE68865.1| RNA polymerase factor sigma-32 [Bordetella pertussis CS]
          Length = 307

 Score =  218 bits (554), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 124/289 (42%), Positives = 180/289 (62%), Gaps = 15/289 (5%)

Query: 2   NRKNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           N   +++   G +G +  YI  + ++P+L  ++E  LA+R R+ GDL AA  LV SHLRL
Sbjct: 25  NALALAVANPGALGTIDAYISAVNRLPILTAEQEGQLARRLRDEGDLEAARELVVSHLRL 84

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y GYGLP ++++ EGN+GLM+AVK+FDPERG RL ++++ WIKA + E+I+R+
Sbjct: 85  VVSVARQYLGYGLPHADLIQEGNVGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEFIIRN 144

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W LVK+ TT  Q++LFFNLR ++   Q      L PEQV  IA++LNV   +V  M  RL
Sbjct: 145 WRLVKVATTKAQRKLFFNLRSMRPDGQ-----TLDPEQVDHIARELNVRREDVSEMEVRL 199

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQ---VLIEKEERKNRRNMLTRSMSVLN 236
           +G D SL     S D +   +        +G+++   VL        +   L R++  L+
Sbjct: 200 SGRDLSL----ESQDDDDDSFAPIAYLSDEGRQEPSRVLDRMAHDDLQGAGLGRALEALD 255

Query: 237 PRERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            R RRI EAR LQ++  +TL  L+ EF VS ERVRQIEA A KK++ ++
Sbjct: 256 ARSRRIIEARWLQDDGGLTLHELAQEFGVSAERVRQIEAAALKKMRGAL 304


>gi|74316363|ref|YP_314103.1| sigma-70 factor [Thiobacillus denitrificans ATCC 25259]
 gi|74055858|gb|AAZ96298.1| sigma-70 factor [Thiobacillus denitrificans ATCC 25259]
          Length = 281

 Score =  218 bits (554), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 118/283 (41%), Positives = 182/283 (64%), Gaps = 8/283 (2%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           + MS+ +     L  YI  +   PML  +EE  LA+ + +  DL AA RLV SHLR+VV 
Sbjct: 3   QTMSLPIPAAYSLDSYIQTVSHYPMLSLEEEQKLARAWHDEQDLEAARRLVLSHLRVVVS 62

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y GYGLP ++++ EGN+GLM+AVK+FDP+RG RL ++++ WI+A + EY+L+++ +
Sbjct: 63  IARHYLGYGLPHADLIQEGNVGLMKAVKRFDPDRGVRLVSFALHWIRAEIHEYVLKNYRM 122

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG- 182
           VK+ TT  Q++LFFNLR LK  L A+T      +Q  A+A++LNVS  +V+ M  RL+G 
Sbjct: 123 VKLATTKAQRKLFFNLRSLKQSLNALT-----VQQADAMAQELNVSRKDVLEMETRLSGH 177

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
           D S++ +++  + + S    +L    +   Q L  ++  + R + LT ++  L+ R R I
Sbjct: 178 DVSIDPMVDDGEDDYSPIA-YLASAEENPAQRLEREQTERLRESGLTSALEELDERSRHI 236

Query: 243 FEARRLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +AR L E  V TL  L++++ VS ER+RQIEARA +K++ SI
Sbjct: 237 IQARWLSEGDVATLHELAAQYGVSAERIRQIEARALQKMRASI 279


>gi|167622231|ref|YP_001672525.1| RNA polymerase factor sigma-32 [Shewanella halifaxensis HAW-EB4]
 gi|167352253|gb|ABZ74866.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella halifaxensis
           HAW-EB4]
          Length = 285

 Score =  217 bits (553), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 115/285 (40%), Positives = 178/285 (62%), Gaps = 9/285 (3%)

Query: 4   KNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           + M+++V    G L  Y+H    IPMLE   EY LAKR +E GDL AA +L+ SHLR VV
Sbjct: 6   QTMALMVPQSSGSLESYVHSAHNIPMLEADTEYELAKRLQETGDLQAAKQLIMSHLRFVV 65

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A GY GYGLP ++++ EGNIGLM+AVK+FDP+ G RL ++++ WIKA + EY+L++W 
Sbjct: 66  HVAKGYSGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYVLKNWR 125

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L   +D+     +V  +A  L VS+++V  M  R+A 
Sbjct: 126 IVKVATTKAQRKLFFNLRKAKKRLGWFSDS-----EVGMVADSLGVSKADVTEMESRMAA 180

Query: 183 DESLNALINSSDKNSSQWQDWLVYDH--DGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            +    L + +D          + DH  D   QV  +  E+ N+  +L+ ++  L+ R +
Sbjct: 181 QDPAFDLASDNDDEHDYAPMHYLEDHSSDLASQVESDNWEQNNQARLLS-AIKTLDERSQ 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            I +AR L E+  TL++L+S ++VS ER+RQ+E  A  K++  ++
Sbjct: 240 HILKARWLDEDKTTLQDLASTYQVSAERIRQLEKNAMSKLKGCME 284


>gi|186475070|ref|YP_001856540.1| RNA polymerase factor sigma-32 [Burkholderia phymatum STM815]
 gi|184191529|gb|ACC69494.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia phymatum
           STM815]
          Length = 311

 Score =  217 bits (553), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 121/283 (42%), Positives = 173/283 (61%), Gaps = 13/283 (4%)

Query: 9   IVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++ G++G +  YI  + +IPML   EE   A  YRE  +L +A +LV SHLRLVV IA  
Sbjct: 31  LLPGQLGNIDAYIQAVNRIPMLTPAEERQFATEYREQNNLESARKLVLSHLRLVVSIARN 90

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y GYGLP ++++ EGNIGLM+AVK+FDPE+  RL +Y+M WIKA + EYILR+W +VK+ 
Sbjct: 91  YLGYGLPHADLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHWIKAEIHEYILRNWRMVKVA 150

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESL 186
           TT  Q++LFFNLR  K  LQ+ T     P+++  +AK+LNV   EV  M  RL+ GD +L
Sbjct: 151 TTKAQRKLFFNLRSHKQGLQSFT-----PDEIDGLAKELNVKREEVAEMETRLSGGDVAL 205

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              +   ++  +    +L   H     VL  ++  +   + +  ++  L+ R RRI EAR
Sbjct: 206 EGQVEDGEEAFAPIA-YLADSHSEPTAVLAARQRDRLHSDGIASALESLDSRSRRIIEAR 264

Query: 247 RLQ-----ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            LQ         TL  L+ EF VS ER+RQIEA A KK++ ++
Sbjct: 265 WLQVEDDGSGGSTLHELADEFGVSAERIRQIEASAMKKMRTAL 307


>gi|91775055|ref|YP_544811.1| sigma 32 (RpoH) [Methylobacillus flagellatus KT]
 gi|91709042|gb|ABE48970.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacillus flagellatus
           KT]
          Length = 285

 Score =  217 bits (553), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 119/270 (44%), Positives = 173/270 (64%), Gaps = 10/270 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+  I+  P+L  +EE  LA R +++ DL AA  LV SHLRLV  IA  Y GYGLP 
Sbjct: 16  LDQYLRAIKSFPVLSAEEELKLATRLKKYNDLEAAKTLVVSHLRLVASIARNYAGYGLPQ 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AV++FDP+RG RL +++M WIKA + EYI+R+W LVK+ TT  Q++L
Sbjct: 76  ADLIQEGNIGLMKAVRRFDPDRGVRLVSFAMHWIKAEIHEYIVRNWRLVKVATTKAQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
           FFNLR +K    A    +L  ++V  IA++LNV   EV+ M  R++G E SL    N+ D
Sbjct: 136 FFNLRSMKKGQTA----SLHSDEVAHIARELNVKPEEVLEMEARMSGHEISLEG--NADD 189

Query: 195 KNSSQWQ--DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE-N 251
            N   +    +L   H    ++L  +E  +     L+ +++ L+ R RRI EAR LQE +
Sbjct: 190 DNEDMFSPISYLQASHAEPSEILEAQEADQLHTTGLSTALAKLDDRSRRIVEARWLQEGH 249

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             TL +L+ EF VS ER+RQIE +A K+++
Sbjct: 250 NATLHDLAEEFGVSAERIRQIEQKAMKQMR 279


>gi|288957081|ref|YP_003447422.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
 gi|288909389|dbj|BAI70878.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
          Length = 298

 Score =  217 bits (553), Expect = 1e-54,   Method: Compositional matrix adjust.
 Identities = 124/280 (44%), Positives = 176/280 (62%), Gaps = 7/280 (2%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           +I    + P+L +  E+ LA+++RE  D  A H+LV ++ RLVV  A  +R YGLP+ ++
Sbjct: 16  FIKASMREPLLSRDHEFDLARKWREGSDERALHQLVRAYTRLVVATASRFRNYGLPMGDL 75

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GLMQA  +F+P+R  R +TY+ WWI++AMQ+YILR+WS+V+ GTTA QK LFFN
Sbjct: 76  VQEGNVGLMQAASRFEPDREVRFSTYAAWWIRSAMQDYILRNWSIVRTGTTAAQKSLFFN 135

Query: 139 LRRLKGHLQAITDNN----LKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSS 193
           LRRL+  + + T N     L  E    IA +L V  +EV +M  RL+G D+SLN  +  +
Sbjct: 136 LRRLRAKIDSATQNGSGAPLTKEGREWIAGELRVEVAEVEAMEMRLSGADQSLNTPV--A 193

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D +   WQD+L       E V+I   +   R   L  ++  L+PRER I   RRL+E   
Sbjct: 194 DGSDDDWQDFLADQRPSPEDVVIGMRDANTRSQWLAEALGELSPRERTIIRERRLREEGA 253

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           TLE L  E  VS+ERVRQ+E RA  K+++S+ K+VE S  
Sbjct: 254 TLEELGRELGVSKERVRQLEHRALLKLRQSMLKRVEDSDD 293


>gi|209965454|ref|YP_002298369.1| RNA polymerase sigma-32 factor [Rhodospirillum centenum SW]
 gi|209958920|gb|ACI99556.1| RNA polymerase sigma-32 factor [Rhodospirillum centenum SW]
          Length = 307

 Score =  217 bits (553), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 122/292 (41%), Positives = 176/292 (60%), Gaps = 4/292 (1%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           MS+       L  Y  +  + PML+  EE +LA+ + E  D  A  RLV SH+RL VKIA
Sbjct: 4   MSVFSESIDVLRAYTAQANRHPMLDPAEEQMLARAWAERQDRKAFDRLVRSHMRLAVKIA 63

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y   GLP+ +++SE NIGL++AV++FDP+RGFRLATY++WWI+A +Q Y+L +WS++K
Sbjct: 64  SKYARSGLPMGDLISEANIGLVKAVQRFDPDRGFRLATYALWWIRAEVQTYVLHNWSMLK 123

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD-E 184
            G TA  KRLFFNLR+ +  L  I D  +  E+   +A +L  S  EV  M  R A    
Sbjct: 124 GGNTAALKRLFFNLRQTQRRL-GIQDRIMSDEEADRVADELGASVDEVREMEHRFATPVT 182

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SLN  +     + +   D L  + +  E  L EK E   R+ ++  ++  L  RER IF 
Sbjct: 183 SLNVPVGEDGDHEA--LDLLADETETVEVRLAEKSELAVRKALMVDALGALGDRERHIFV 240

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPL 296
           +R L + PVTLE L+ ++ VS+ER+RQIE+ A+KKV   ++   E S++P L
Sbjct: 241 SRNLTDQPVTLETLAQQYGVSKERIRQIESGAYKKVARRVRGAAEASAAPIL 292


>gi|294670676|ref|ZP_06735551.1| hypothetical protein NEIELOOT_02398 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
 gi|291307564|gb|EFE48807.1| hypothetical protein NEIELOOT_02398 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
          Length = 287

 Score =  217 bits (553), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 119/283 (42%), Positives = 183/283 (64%), Gaps = 9/283 (3%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           + +G   L +YIH +  IP+L  +EE+ LA+R +  GD+ AA +L+ SHLR+VV IA GY
Sbjct: 11  VPSGHGSLDQYIHTVNSIPLLTPEEEHNLAER-KMRGDVEAAKQLILSHLRVVVSIARGY 69

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGL  ++++ EGNIGLM+AVK+++P+RG RL ++++ WIKA + E+ILR+W LV++ T
Sbjct: 70  DGYGLNQADLIQEGNIGLMKAVKRYEPDRGARLFSFAVHWIKAEIHEFILRNWRLVRVAT 129

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           T  Q++LFFNLR ++  L A     L P++  AIA  L V  SEV+ M  R+ G +    
Sbjct: 130 TKPQRKLFFNLRSMRKSLSA-----LSPKEAQAIADDLGVKLSEVLEMEQRMTGKDVALL 184

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFEARR 247
             NS D ++    DWL  DHD +    IE++     +   L  +++ L+ R RRI E R 
Sbjct: 185 ADNSDDDDNFAPIDWLA-DHDNEPTRQIERKAHYTLQTEGLQNALAKLDDRSRRIVETRW 243

Query: 248 LQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 244 LQDDGGLTLHELAAEYGVSAERIRQIEAKAMQKLRTFLAEETE 286


>gi|221199969|ref|ZP_03573012.1| alternative sigma factor RpoH [Burkholderia multivorans CGD2M]
 gi|221206876|ref|ZP_03579888.1| alternative sigma factor RpoH [Burkholderia multivorans CGD2]
 gi|221173531|gb|EEE05966.1| alternative sigma factor RpoH [Burkholderia multivorans CGD2]
 gi|221180208|gb|EEE12612.1| alternative sigma factor RpoH [Burkholderia multivorans CGD2M]
          Length = 311

 Score =  217 bits (553), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 119/283 (42%), Positives = 178/283 (62%), Gaps = 13/283 (4%)

Query: 9   IVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++ G++G +  YI  + +IP+L  +EE   A  YRE+ +L AA RLV SHLRLVV IA  
Sbjct: 31  MLPGQLGNIDAYIQAVNRIPLLTAEEERQYATEYRENNNLEAARRLVLSHLRLVVSIARN 90

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y GYGLP  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W +VK+ 
Sbjct: 91  YLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKVA 150

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESL 186
           TT  Q++LFFNLR  K  +QA+T     PE++  +A++LNV   EV  M  RL+ GD +L
Sbjct: 151 TTKAQRKLFFNLRSHKKGMQAMT-----PEEIDGLAQELNVKREEVTEMETRLSGGDIAL 205

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              +   +++ +    +L   H+    VL  ++    + + + +++  L+ R RRI EAR
Sbjct: 206 EGQVEDGEESYAPIA-YLADSHNEPTAVLAARQRDMLQTDGIAQALDALDARSRRIIEAR 264

Query: 247 RLQ-----ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L          TL +L++EF VS ER+RQIEA A KK++ ++
Sbjct: 265 WLHVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRTAL 307


>gi|15676610|ref|NP_273754.1| RNA polymerase factor sigma-32 [Neisseria meningitidis MC58]
 gi|7225940|gb|AAF41127.1| RNA polymerase sigma-32 factor [Neisseria meningitidis MC58]
          Length = 290

 Score =  217 bits (553), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 121/286 (42%), Positives = 186/286 (65%), Gaps = 9/286 (3%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +  I +G   L +YIH + +IPML ++EE  LA+R +  GDL+AA +L+ SHLR+VV IA
Sbjct: 10  LPAIQSGNGSLEQYIHTVNRIPMLTQEEETRLAER-QHKGDLNAAKQLILSHLRVVVSIA 68

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+ILR+W LV+
Sbjct: 69  RGYDGYGLNQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILRNWRLVR 128

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           + TT  Q++LFFNLR ++ +L     N L P++   IA  L V  SEV+ M  R+ G + 
Sbjct: 129 VATTKPQRKLFFNLRSMRKNL-----NALSPKEAQDIADDLGVKLSEVLEMEQRMTGHDI 183

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFE 244
                NS D++S    DWL  DHD +    + K+     +   L  +++ L+ R RRI E
Sbjct: 184 AIMADNSDDEDSFAPIDWLA-DHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRRIVE 242

Query: 245 ARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           +R LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 243 SRWLQDDGGLTLHQLAAEYGVSAERIRQIEAKAMQKLRGFLTEEAE 288


>gi|113866384|ref|YP_724873.1| RNA polymerase factor sigma-32 [Ralstonia eutropha H16]
 gi|113525160|emb|CAJ91505.1| DNA-directed RNA polymerase sigma subunit (RpoH) [Ralstonia
           eutropha H16]
          Length = 308

 Score =  217 bits (553), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 120/276 (43%), Positives = 172/276 (62%), Gaps = 12/276 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + +IP+L  +EE  LA+  R+H  + AA ++V SHLRLVV IA  Y GYGLP 
Sbjct: 36  LDSYIQAVHRIPLLTAEEEQRLARELRDHDSVDAARQMVMSHLRLVVSIARQYLGYGLPH 95

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AVK+FDP++G RL +Y+M WIKA + EY+L++W +VK+ TT  Q++L
Sbjct: 96  ADLIQEGNIGLMKAVKRFDPDQGVRLVSYAMHWIKAEIHEYVLKNWRMVKVATTKAQRKL 155

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALINSSD 194
           FFNLR  K      T     PEQV A+A++LNV   EV+ M  RL+ GD +L   I+  +
Sbjct: 156 FFNLRSHKQGAHTFT-----PEQVEAVARELNVKPEEVMEMETRLSGGDLALEGQIDDGE 210

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ----- 249
           +  +    +L  +H+   +VL  K   + +   L  ++  L+ R RRI EAR L      
Sbjct: 211 EEFAPIA-YLADNHNEPTRVLEAKRHDRMQVEGLEEALGKLDERSRRIIEARWLHVEDDG 269

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
               TL  L+ EF VS ER+RQIEA A KK++ ++Q
Sbjct: 270 SGGSTLHELADEFGVSAERIRQIEAAAMKKMKGALQ 305


>gi|220921709|ref|YP_002497010.1| RNA polymerase factor sigma-32 [Methylobacterium nodulans ORS 2060]
 gi|219946315|gb|ACL56707.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium nodulans
           ORS 2060]
          Length = 293

 Score =  217 bits (552), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 111/262 (42%), Positives = 173/262 (66%), Gaps = 1/262 (0%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE++EE  LA R+++  D  A HRL+++H+RLV+ +A  +R YGLP++++V EG++GL
Sbjct: 19  PFLEREEERGLAVRWKDERDEQALHRLISAHMRLVIALAGRFRHYGLPMADLVQEGHVGL 78

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 79  MEAAARFEPERDVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRARL 138

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLV 205
              TD  +  E    IA  + VS  +V  M+ RL+G D SLNA I      S++  D+LV
Sbjct: 139 MQSTDERVGDEIHSRIATAIGVSREDVALMDARLSGPDMSLNAPITDEGDASAERVDFLV 198

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
                 ++ + +  + + R   L ++++VL+ RE RI   RRL E+  TLE L     +S
Sbjct: 199 DTSPLPDEAVSDAVDGERRLTWLRQALTVLSERELRILHERRLAEDQATLEALGHRLGIS 258

Query: 266 RERVRQIEARAFKKVQESIQKQ 287
           +ERVRQIE RA +K++ ++ ++
Sbjct: 259 KERVRQIENRALEKLRRALAER 280


>gi|163748787|ref|ZP_02156039.1| RNA polymerase sigma factor [Shewanella benthica KT99]
 gi|161331561|gb|EDQ02366.1| RNA polymerase sigma factor [Shewanella benthica KT99]
          Length = 286

 Score =  217 bits (552), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 115/284 (40%), Positives = 178/284 (62%), Gaps = 10/284 (3%)

Query: 6   MSIIV-NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           M+++V +G   L  Y+H    I MLE  +EY LAKR +E GD+ AA +L+ SHLR VV +
Sbjct: 8   MALVVPHGSGSLEAYVHSAHNISMLEADQEYELAKRLQETGDIQAAKQLIMSHLRFVVHV 67

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A GY GYGLP ++++ EGNIGLM+AVK+FDP  G RL ++++ WIKA + EY+L++W +V
Sbjct: 68  AKGYAGYGLPQADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWIKAEIHEYVLKNWRIV 127

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           K+ TT  Q++LFFNLR+ K  L   +D      +V  +A+ L VS+++V  M  R+A  +
Sbjct: 128 KVATTKAQRKLFFNLRKAKKRLGWFSD-----AEVGMVAENLGVSKADVTEMESRMAAQD 182

Query: 185 SLNALINSSDKNSSQWQDWL-VYDH--DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
               L++ SD +   +   L + DH  D   QV  +  E  N+  +L  ++  L+ R + 
Sbjct: 183 PAFDLVSDSDDDIQDYAPALYLEDHSSDLASQVETDNLEASNQTRLLA-AIKTLDERSQH 241

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           I +AR L E+  TL+ L++ ++VS ER+RQ+E  A  K++  I+
Sbjct: 242 ILQARWLNEDKTTLQELAATYQVSAERIRQLEKNAMNKLKGCIE 285


>gi|255068324|ref|ZP_05320179.1| alternative sigma factor RpoH [Neisseria sicca ATCC 29256]
 gi|261365915|ref|ZP_05978798.1| alternative sigma factor RpoH [Neisseria mucosa ATCC 25996]
 gi|255047443|gb|EET42907.1| alternative sigma factor RpoH [Neisseria sicca ATCC 29256]
 gi|288565493|gb|EFC87053.1| alternative sigma factor RpoH [Neisseria mucosa ATCC 25996]
          Length = 287

 Score =  217 bits (552), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 120/286 (41%), Positives = 186/286 (65%), Gaps = 9/286 (3%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           + +I +G   L +YIH +  IPML  +EE  LA+R ++ GDL+AA +L+ SHLR+VV IA
Sbjct: 7   LPVIHSGNGSLEQYIHTVNSIPMLTPEEESQLAER-QQKGDLNAAKQLILSHLRVVVSIA 65

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+ILR+W LV+
Sbjct: 66  RGYDGYGLNQADLIQEGNIGLMKAVKRYEPSRGARLFSFAVHWIKAEIHEFILRNWRLVR 125

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           + TT  Q++LFFNLR ++ +L     N L P++   IA  L V  SEV+ M  R+ G + 
Sbjct: 126 VATTKPQRKLFFNLRSMRKNL-----NALSPKEAQDIADDLGVKLSEVMEMEQRMTGHDI 180

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFE 244
                N+ D++S    DWL  DHD +    + K+     +   L  +++ L+ R RRI E
Sbjct: 181 AIMADNNDDEDSFAPIDWLA-DHDAEPSRQLSKQAHYALQTEGLQNALAQLDDRSRRIVE 239

Query: 245 ARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           +R LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 240 SRWLQDDGGLTLHELAAEYGVSAERIRQIEAKAMQKLRGFLAEEAE 285


>gi|161869654|ref|YP_001598821.1| RNA polymerase factor sigma-32 [Neisseria meningitidis 053442]
 gi|161595207|gb|ABX72867.1| RNA polymerase sigma-32 factor [Neisseria meningitidis 053442]
 gi|316983693|gb|EFV62674.1| alternative sigma factor RpoH [Neisseria meningitidis H44/76]
 gi|325140133|gb|EGC62662.1| alternative sigma factor RpoH [Neisseria meningitidis CU385]
 gi|325200603|gb|ADY96058.1| alternative sigma factor RpoH [Neisseria meningitidis H44/76]
          Length = 287

 Score =  217 bits (552), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 121/286 (42%), Positives = 186/286 (65%), Gaps = 9/286 (3%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +  I +G   L +YIH + +IPML ++EE  LA+R +  GDL+AA +L+ SHLR+VV IA
Sbjct: 7   LPAIQSGNGSLEQYIHTVNRIPMLTQEEETRLAER-QHKGDLNAAKQLILSHLRVVVSIA 65

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+ILR+W LV+
Sbjct: 66  RGYDGYGLNQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILRNWRLVR 125

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           + TT  Q++LFFNLR ++ +L     N L P++   IA  L V  SEV+ M  R+ G + 
Sbjct: 126 VATTKPQRKLFFNLRSMRKNL-----NALSPKEAQDIADDLGVKLSEVLEMEQRMTGHDI 180

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFE 244
                NS D++S    DWL  DHD +    + K+     +   L  +++ L+ R RRI E
Sbjct: 181 AIMADNSDDEDSFAPIDWLA-DHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRRIVE 239

Query: 245 ARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           +R LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 240 SRWLQDDGGLTLHQLAAEYGVSAERIRQIEAKAMQKLRGFLTEEAE 285


>gi|297250602|ref|ZP_06934149.1| alternative sigma factor RpoH [Neisseria polysaccharea ATCC 43768]
 gi|296838520|gb|EFH22458.1| alternative sigma factor RpoH [Neisseria polysaccharea ATCC 43768]
          Length = 290

 Score =  217 bits (552), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 123/290 (42%), Positives = 186/290 (64%), Gaps = 9/290 (3%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N   +  I +G   L +YIH +  IPML ++EE  LA+R R  GDL+AA +L+ SHLR+V
Sbjct: 6   NAFALPAIQSGNGSLEQYIHTVNSIPMLSQEEETRLAER-RIKGDLNAAKQLILSHLRVV 64

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+ILR+W
Sbjct: 65  VSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILRNW 124

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            LV++ TT  Q++LFFNLR ++ +L     N L P++   IA  L V  SEV+ M  R+ 
Sbjct: 125 RLVRVATTKPQRKLFFNLRSMRKNL-----NALSPKEAQEIADDLGVKLSEVLEMEQRMT 179

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRER 240
           G +      NS D++S    DWL  DHD +    + K+     +   L  +++ L+ R R
Sbjct: 180 GHDIAIMADNSDDEDSFAPIDWLA-DHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSR 238

Query: 241 RIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           RI E+R LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 239 RIVESRWLQDDGGLTLHQLAAEYGVSAERIRQIEAKAMQKLRGFLAEEAE 288


>gi|325518946|gb|EGC98485.1| RNA polymerase factor sigma-32 [Burkholderia sp. TJI49]
          Length = 311

 Score =  217 bits (552), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 120/283 (42%), Positives = 177/283 (62%), Gaps = 13/283 (4%)

Query: 9   IVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++ G++G L  YI  + +IP+L  +EE   A ++RE  +L AA RLV SHLRLVV IA  
Sbjct: 31  MLPGQLGNLDAYIQAVNRIPLLTAEEERQYATQFREDNNLDAARRLVLSHLRLVVSIARN 90

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y GYGLP  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W  VK+ 
Sbjct: 91  YLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRTVKVA 150

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESL 186
           TT  Q++LFFNLR  K  +QA+T     PE++  +AK+LNV   EV  M  RL+ GD +L
Sbjct: 151 TTKAQRKLFFNLRSHKKGVQAMT-----PEEIDGLAKELNVKREEVTEMETRLSGGDIAL 205

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              +   +++ +    +L   H+    VL  ++    + + + +++  L+ R RRI EAR
Sbjct: 206 EGQVEDGEESYAPIA-YLADSHNEPTAVLAARQRDMLQTDGIAQALDALDARSRRIIEAR 264

Query: 247 RLQ-----ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L          TL +L++EF VS ER+RQIEA A KK++ ++
Sbjct: 265 WLHVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRTAL 307


>gi|296161515|ref|ZP_06844320.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. Ch1-1]
 gi|295888159|gb|EFG67972.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. Ch1-1]
          Length = 311

 Score =  217 bits (552), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 122/285 (42%), Positives = 175/285 (61%), Gaps = 13/285 (4%)

Query: 7   SIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           S ++ G++G +  YI  + +IPML   EE   A  +RE  +L +A RLV SHLRLVV IA
Sbjct: 29  SSLLPGQLGNIDAYIQAVNRIPMLTPAEERQFATEFREQDNLESARRLVLSHLRLVVSIA 88

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGLP ++++ EGNIGLM+AVK+FDPE+  RL +Y+M WIKA + EYILR+W +VK
Sbjct: 89  RNYLGYGLPHADLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHWIKAEIHEYILRNWRMVK 148

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDE 184
           + TT  Q++LFFNLR  K  L A T     P+++  +AK+LNV   EV  M  RL+ GD 
Sbjct: 149 VATTKAQRKLFFNLRSHKQGLGAFT-----PDEIEGLAKELNVKREEVSEMETRLSGGDI 203

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           +L   +   +++ +    +L   H     VL  ++  K + + +  ++  L+ R RRI E
Sbjct: 204 ALEGQVEDGEESYAPIA-YLADSHSEPTAVLASRQRDKLQSDGIASALDALDARSRRIIE 262

Query: 245 ARRLQ-----ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           AR L+         TL  L+ EF VS ER+RQIEA A KK++ ++
Sbjct: 263 ARWLKVEDDGSGGSTLHELADEFGVSAERIRQIEASAMKKMRGAL 307


>gi|254804595|ref|YP_003082816.1| RNA polymerase sigma subunit [Neisseria meningitidis alpha14]
 gi|254668137|emb|CBA04749.1| RNA polymerase sigma subunit [Neisseria meningitidis alpha14]
 gi|254669711|emb|CBA03845.1| RNA polymerase sigma-32 factor [Neisseria meningitidis alpha153]
 gi|308388900|gb|ADO31220.1| putative RNA polymerase sigma-32 factor [Neisseria meningitidis
           alpha710]
 gi|319410084|emb|CBY90418.1| RNA polymerase sigma factor RpoH (Sigma-32) [Neisseria meningitidis
           WUE 2594]
 gi|325127782|gb|EGC50690.1| alternative sigma factor RpoH [Neisseria meningitidis N1568]
 gi|325129864|gb|EGC52669.1| alternative sigma factor RpoH [Neisseria meningitidis OX99.30304]
 gi|325131835|gb|EGC54535.1| alternative sigma factor RpoH [Neisseria meningitidis M6190]
 gi|325133774|gb|EGC56430.1| alternative sigma factor RpoH [Neisseria meningitidis M13399]
 gi|325136066|gb|EGC58676.1| alternative sigma factor RpoH [Neisseria meningitidis M0579]
 gi|325137885|gb|EGC60460.1| alternative sigma factor RpoH [Neisseria meningitidis ES14902]
 gi|325141969|gb|EGC64407.1| alternative sigma factor RpoH [Neisseria meningitidis 961-5945]
 gi|325144085|gb|EGC66393.1| alternative sigma factor RpoH [Neisseria meningitidis M01-240013]
 gi|325197931|gb|ADY93387.1| alternative sigma factor RpoH [Neisseria meningitidis G2136]
 gi|325203799|gb|ADY99252.1| alternative sigma factor RpoH [Neisseria meningitidis M01-240355]
 gi|325206445|gb|ADZ01898.1| alternative sigma factor RpoH [Neisseria meningitidis M04-240196]
          Length = 287

 Score =  217 bits (552), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 122/286 (42%), Positives = 185/286 (64%), Gaps = 9/286 (3%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +  I +G   L +YIH +  IPML ++EE  LA+R R  GDL+AA +L+ SHLR+VV IA
Sbjct: 7   LPAIQSGNGSLEQYIHTVNSIPMLSQEEETRLAER-RIKGDLNAAKQLILSHLRVVVSIA 65

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+ILR+W LV+
Sbjct: 66  RGYDGYGLNQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILRNWRLVR 125

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           + TT  Q++LFFNLR ++ +L     N L P++   IA  L V  SEV+ M  R+ G + 
Sbjct: 126 VATTKPQRKLFFNLRSMRKNL-----NALSPKEAQDIADDLGVKLSEVLEMEQRMTGHDI 180

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFE 244
                NS D++S    DWL  DHD +    + K+     +   L  +++ L+ R RRI E
Sbjct: 181 AIMADNSDDEDSFAPIDWLA-DHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRRIVE 239

Query: 245 ARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           +R LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 240 SRWLQDDGGLTLHQLAAEYGVSAERIRQIEAKAMQKLRGFLTEEAE 285


>gi|34499661|ref|NP_903876.1| RNA polymerase factor sigma-32 [Chromobacterium violaceum ATCC
           12472]
 gi|34105511|gb|AAQ61866.1| RNA polymerase sigma-32 factor [Chromobacterium violaceum ATCC
           12472]
          Length = 287

 Score =  217 bits (552), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 116/276 (42%), Positives = 175/276 (63%), Gaps = 7/276 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +YI  +  IPML  ++E  LA R+++  DL AA ++V SHLR+VV ++ GY GYGL  
Sbjct: 16  LEQYIQAVNSIPMLTPEQETELATRFQQENDLEAARQMVLSHLRVVVSVSRGYAGYGLQQ 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AVK+F+P RG RL ++++ WIKA + E+ILR+W LV+I TT  Q++L
Sbjct: 76  ADLIQEGNIGLMKAVKRFEPGRGVRLFSFAIHWIKAEIHEFILRNWRLVRIATTKPQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR +K    A+++   K     +IA+ L V   EV  M  R+ G + ++ L +S D+
Sbjct: 136 FFNLRSMKSGFSALSEQEAK-----SIAEDLGVKPEEVREMEIRMTG-QDVSLLADSDDE 189

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP-VT 254
           +S    DWL   H    + L  +     +   L  ++S L+PR RRI EAR L ++   T
Sbjct: 190 DSYAPIDWLADSHSEPTRALERRAFDMLQSEGLEYALSTLDPRSRRIVEARWLADDSGAT 249

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
           L  L++EF VS ER+RQIEA+A  K++ ++ + V L
Sbjct: 250 LHELAAEFGVSAERIRQIEAKALSKMKAALSEGVVL 285


>gi|121634509|ref|YP_974754.1| RNA polymerase factor sigma-32 [Neisseria meningitidis FAM18]
 gi|218767834|ref|YP_002342346.1| RNA polymerase factor sigma-32 [Neisseria meningitidis Z2491]
 gi|120866215|emb|CAM09955.1| putative RNA polymerase sigma-32 factor [Neisseria meningitidis
           FAM18]
 gi|121051842|emb|CAM08148.1| putative RNA polymerase sigma-32 factor [Neisseria meningitidis
           Z2491]
 gi|261392916|emb|CAX50501.1| RNA polymerase sigma factor RpoH (Sigma-32) [Neisseria meningitidis
           8013]
          Length = 290

 Score =  217 bits (552), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 122/286 (42%), Positives = 185/286 (64%), Gaps = 9/286 (3%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +  I +G   L +YIH +  IPML ++EE  LA+R R  GDL+AA +L+ SHLR+VV IA
Sbjct: 10  LPAIQSGNGSLEQYIHTVNSIPMLSQEEETRLAER-RIKGDLNAAKQLILSHLRVVVSIA 68

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+ILR+W LV+
Sbjct: 69  RGYDGYGLNQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILRNWRLVR 128

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           + TT  Q++LFFNLR ++ +L     N L P++   IA  L V  SEV+ M  R+ G + 
Sbjct: 129 VATTKPQRKLFFNLRSMRKNL-----NALSPKEAQDIADDLGVKLSEVLEMEQRMTGHDI 183

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFE 244
                NS D++S    DWL  DHD +    + K+     +   L  +++ L+ R RRI E
Sbjct: 184 AIMADNSDDEDSFAPIDWLA-DHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRRIVE 242

Query: 245 ARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           +R LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 243 SRWLQDDGGLTLHQLAAEYGVSAERIRQIEAKAMQKLRGFLTEEAE 288


>gi|304387988|ref|ZP_07370160.1| DNA-directed RNA polymerase sigma subunit RpoH [Neisseria
           meningitidis ATCC 13091]
 gi|304337987|gb|EFM04125.1| DNA-directed RNA polymerase sigma subunit RpoH [Neisseria
           meningitidis ATCC 13091]
          Length = 290

 Score =  217 bits (552), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 122/286 (42%), Positives = 185/286 (64%), Gaps = 9/286 (3%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +  I +G   L +YIH +  IPML ++EE  LA+R R  GDL+AA +L+ SHLR+VV IA
Sbjct: 10  LPAIQSGNGSLEQYIHTVNSIPMLSQEEETRLAER-RIKGDLNAAKQLILSHLRVVVSIA 68

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+ILR+W LV+
Sbjct: 69  RGYDGYGLNQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILRNWRLVR 128

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           + TT  Q++LFFNLR ++ +L     N L P++   IA  L V  SEV+ M  R+ G + 
Sbjct: 129 VATTKPQRKLFFNLRSMRKNL-----NALSPKEAQDIADDLGVKLSEVLEMEQRMTGHDI 183

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFE 244
                NS D++S    DWL  DHD +    + K+     +   L  +++ L+ R RRI E
Sbjct: 184 AIMADNSDDEDSFAPIDWLA-DHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRRIVE 242

Query: 245 ARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           +R LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 243 SRWLQDDGGLTLHQLAAEYGVSAERIRQIEAKAMQKLRGFLTEKAE 288


>gi|83718896|ref|YP_441014.1| RNA polymerase factor sigma-32 [Burkholderia thailandensis E264]
 gi|167579742|ref|ZP_02372616.1| RNA polymerase factor sigma-32 [Burkholderia thailandensis TXDOH]
 gi|167617818|ref|ZP_02386449.1| RNA polymerase factor sigma-32 [Burkholderia thailandensis Bt4]
 gi|257140333|ref|ZP_05588595.1| RNA polymerase factor sigma-32 [Burkholderia thailandensis E264]
 gi|83652721|gb|ABC36784.1| RNA polymerase sigma-32 factor [Burkholderia thailandensis E264]
          Length = 311

 Score =  217 bits (552), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 121/283 (42%), Positives = 175/283 (61%), Gaps = 13/283 (4%)

Query: 9   IVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++ G++G +  YI  + +IP+L  +EE   A  YRE   L AA RLV SHLRLVV IA  
Sbjct: 31  MLPGQLGNIDAYIQAVNRIPLLTAEEERQYATEYREQNSLDAARRLVLSHLRLVVSIARN 90

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y GYGLP  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W +VK+ 
Sbjct: 91  YLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKVA 150

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESL 186
           TT  Q++LFFNLR  K   QA T     PE++  +A++LNV   EV  M  RL+ GD +L
Sbjct: 151 TTKAQRKLFFNLRSHKKGTQAFT-----PEEIDGLAQELNVKREEVAEMETRLSGGDIAL 205

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              I+  +++ +    +L   H+    VL  ++    + + + R++  L+ R RRI EAR
Sbjct: 206 EGQIDDGEESYAPIA-YLADSHNEPTAVLAARQRDMLQTDGIARALDSLDARSRRIIEAR 264

Query: 247 RLQ-----ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L          TL +L++EF VS ER+RQIEA A KK++ ++
Sbjct: 265 WLNVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRTAL 307


>gi|157963788|ref|YP_001503822.1| RNA polymerase factor sigma-32 [Shewanella pealeana ATCC 700345]
 gi|157848788|gb|ABV89287.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella pealeana ATCC
           700345]
          Length = 285

 Score =  217 bits (552), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 114/285 (40%), Positives = 181/285 (63%), Gaps = 9/285 (3%)

Query: 4   KNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           ++M+++V    G L  Y+H    IPMLE  +EY LAKR +E GDL AA +L+ SHLR VV
Sbjct: 6   QSMALMVPQSSGSLESYVHSAHNIPMLEADKEYELAKRLQETGDLQAAKQLIMSHLRFVV 65

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A GY GYGLP ++++ EGNIGLM+AVK+FDP+ G RL ++++ WIKA + EY+L++W 
Sbjct: 66  HVAKGYSGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYVLKNWR 125

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L   +D+     +V  +A+ L VS+++V  M  R+A 
Sbjct: 126 IVKVATTKAQRKLFFNLRKAKKRLGWFSDS-----EVGMVAESLGVSKADVTEMESRMAA 180

Query: 183 DESLNALINSSDKNSSQWQDWLVYDH--DGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            +    L + +D          + DH  D   QV  +  E+ N+  +L+ ++  L+ R +
Sbjct: 181 QDPAFDLASDNDDEQDYAPMHYLEDHSSDLASQVENDNWEQNNQARLLS-AIKTLDERSQ 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            I +AR L E+  TL++L++ ++VS ER+RQ+E  A  K++  ++
Sbjct: 240 HILKARWLDEDKTTLQDLAATYQVSAERIRQLEKNAMNKLKGCME 284


>gi|53724102|ref|YP_104622.1| RNA polymerase factor sigma-32 [Burkholderia mallei ATCC 23344]
 gi|121598782|ref|YP_991458.1| RNA polymerase factor sigma-32 [Burkholderia mallei SAVP1]
 gi|124383719|ref|YP_001027464.1| RNA polymerase factor sigma-32 [Burkholderia mallei NCTC 10229]
 gi|126449925|ref|YP_001082430.1| RNA polymerase factor sigma-32 [Burkholderia mallei NCTC 10247]
 gi|167001066|ref|ZP_02266867.1| alternative sigma factor RpoH [Burkholderia mallei PRL-20]
 gi|238561338|ref|ZP_00442201.2| alternative sigma factor RpoH [Burkholderia mallei GB8 horse 4]
 gi|254175044|ref|ZP_04881705.1| alternative sigma factor RpoH [Burkholderia mallei ATCC 10399]
 gi|254201710|ref|ZP_04908074.1| alternative sigma factor RpoH [Burkholderia mallei FMH]
 gi|254207043|ref|ZP_04913394.1| alternative sigma factor RpoH [Burkholderia mallei JHU]
 gi|254357524|ref|ZP_04973798.1| alternative sigma factor RpoH [Burkholderia mallei 2002721280]
 gi|52427525|gb|AAU48118.1| RNA polymerase sigma-32 factor [Burkholderia mallei ATCC 23344]
 gi|121227592|gb|ABM50110.1| alternative sigma factor RpoH [Burkholderia mallei SAVP1]
 gi|124291739|gb|ABN01008.1| RNA polymerase sigma-32 factor [Burkholderia mallei NCTC 10229]
 gi|126242795|gb|ABO05888.1| alternative sigma factor RpoH [Burkholderia mallei NCTC 10247]
 gi|147747604|gb|EDK54680.1| alternative sigma factor RpoH [Burkholderia mallei FMH]
 gi|147752585|gb|EDK59651.1| alternative sigma factor RpoH [Burkholderia mallei JHU]
 gi|148026588|gb|EDK84673.1| alternative sigma factor RpoH [Burkholderia mallei 2002721280]
 gi|160696089|gb|EDP86059.1| alternative sigma factor RpoH [Burkholderia mallei ATCC 10399]
 gi|238524810|gb|EEP88241.1| alternative sigma factor RpoH [Burkholderia mallei GB8 horse 4]
 gi|243063136|gb|EES45322.1| alternative sigma factor RpoH [Burkholderia mallei PRL-20]
          Length = 311

 Score =  217 bits (552), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 120/283 (42%), Positives = 175/283 (61%), Gaps = 13/283 (4%)

Query: 9   IVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++ G +G +  YI  + +IP+L  +EE   A  YRE  +L AA RLV SHLRLVV +A  
Sbjct: 31  MLPGHLGNIDAYIQAVNRIPLLSAEEERQYATEYREQNNLDAARRLVLSHLRLVVSVARN 90

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y GYGLP  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W +VK+ 
Sbjct: 91  YLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKVA 150

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESL 186
           TT  Q++LFFNLR  K   QA T     PE++  +A++LNV   EV  M  RL+ GD +L
Sbjct: 151 TTKAQRKLFFNLRSHKKGTQAFT-----PEEIDGLAQELNVKREEVAEMETRLSGGDIAL 205

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              I+  +++ +    +L   H+    VL  ++    + + + R++  L+ R RRI EAR
Sbjct: 206 EGQIDDGEESYAPIA-YLADSHNEPTAVLAARQRDMLQTDGIARALESLDARSRRIIEAR 264

Query: 247 RLQ-----ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L          TL +L++EF VS ER+RQIEA A KK++ ++
Sbjct: 265 WLNVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRTAL 307


>gi|53718144|ref|YP_107130.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei K96243]
 gi|76812253|ref|YP_332145.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei 1710b]
 gi|126441976|ref|YP_001057600.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei 668]
 gi|126453430|ref|YP_001064846.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei 1106a]
 gi|134279764|ref|ZP_01766476.1| alternative sigma factor RpoH [Burkholderia pseudomallei 305]
 gi|167717993|ref|ZP_02401229.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei DM98]
 gi|167737009|ref|ZP_02409783.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei 14]
 gi|167814118|ref|ZP_02445798.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei 91]
 gi|167822644|ref|ZP_02454115.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei 9]
 gi|167844214|ref|ZP_02469722.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei B7210]
 gi|167892724|ref|ZP_02480126.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei 7894]
 gi|167901220|ref|ZP_02488425.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei NCTC
           13177]
 gi|167909437|ref|ZP_02496528.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei 112]
 gi|167917468|ref|ZP_02504559.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei BCC215]
 gi|217419877|ref|ZP_03451383.1| alternative sigma factor RpoH [Burkholderia pseudomallei 576]
 gi|226199497|ref|ZP_03795054.1| alternative sigma factor RpoH [Burkholderia pseudomallei Pakistan
           9]
 gi|237810751|ref|YP_002895202.1| alternative sigma factor RpoH [Burkholderia pseudomallei MSHR346]
 gi|242316271|ref|ZP_04815287.1| alternative sigma factor RpoH [Burkholderia pseudomallei 1106b]
 gi|254181885|ref|ZP_04888482.1| alternative sigma factor RpoH [Burkholderia pseudomallei 1655]
 gi|254187820|ref|ZP_04894332.1| alternative sigma factor RpoH [Burkholderia pseudomallei Pasteur
           52237]
 gi|254196825|ref|ZP_04903249.1| alternative sigma factor RpoH [Burkholderia pseudomallei S13]
 gi|254260127|ref|ZP_04951181.1| alternative sigma factor RpoH [Burkholderia pseudomallei 1710a]
 gi|254296064|ref|ZP_04963521.1| alternative sigma factor RpoH [Burkholderia pseudomallei 406e]
 gi|52208558|emb|CAH34494.1| RNA polymerase sigma-32 factor [Burkholderia pseudomallei K96243]
 gi|76581706|gb|ABA51181.1| alternative sigma factor RpoH [Burkholderia pseudomallei 1710b]
 gi|126221469|gb|ABN84975.1| alternative sigma factor RpoH [Burkholderia pseudomallei 668]
 gi|126227072|gb|ABN90612.1| alternative sigma factor RpoH [Burkholderia pseudomallei 1106a]
 gi|134248964|gb|EBA49046.1| alternative sigma factor RpoH [Burkholderia pseudomallei 305]
 gi|157805888|gb|EDO83058.1| alternative sigma factor RpoH [Burkholderia pseudomallei 406e]
 gi|157935500|gb|EDO91170.1| alternative sigma factor RpoH [Burkholderia pseudomallei Pasteur
           52237]
 gi|169653568|gb|EDS86261.1| alternative sigma factor RpoH [Burkholderia pseudomallei S13]
 gi|184212423|gb|EDU09466.1| alternative sigma factor RpoH [Burkholderia pseudomallei 1655]
 gi|217397181|gb|EEC37197.1| alternative sigma factor RpoH [Burkholderia pseudomallei 576]
 gi|225928378|gb|EEH24408.1| alternative sigma factor RpoH [Burkholderia pseudomallei Pakistan
           9]
 gi|237503746|gb|ACQ96064.1| alternative sigma factor RpoH [Burkholderia pseudomallei MSHR346]
 gi|242139510|gb|EES25912.1| alternative sigma factor RpoH [Burkholderia pseudomallei 1106b]
 gi|254218816|gb|EET08200.1| alternative sigma factor RpoH [Burkholderia pseudomallei 1710a]
          Length = 311

 Score =  217 bits (552), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 120/283 (42%), Positives = 175/283 (61%), Gaps = 13/283 (4%)

Query: 9   IVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++ G +G +  YI  + +IP+L  +EE   A  YRE  +L AA RLV SHLRLVV +A  
Sbjct: 31  MLPGHLGNIDAYIQAVNRIPLLSAEEERQYATEYREQNNLDAARRLVLSHLRLVVSVARN 90

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y GYGLP  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W +VK+ 
Sbjct: 91  YLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKVA 150

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESL 186
           TT  Q++LFFNLR  K   QA T     PE++  +A++LNV   EV  M  RL+ GD +L
Sbjct: 151 TTKAQRKLFFNLRSHKKGTQAFT-----PEEIDGLAQELNVKREEVAEMETRLSGGDIAL 205

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              I+  +++ +    +L   H+    VL  ++    + + + R++  L+ R RRI EAR
Sbjct: 206 EGQIDDGEESYAPIA-YLADSHNEPTAVLAARQRDMLQTDGIARALESLDARSRRIIEAR 264

Query: 247 RLQ-----ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L          TL +L++EF VS ER+RQIEA A KK++ ++
Sbjct: 265 WLNVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRTAL 307


>gi|91781700|ref|YP_556906.1| RNA polymerase factor sigma-32 [Burkholderia xenovorans LB400]
 gi|91685654|gb|ABE28854.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia xenovorans
           LB400]
          Length = 307

 Score =  216 bits (551), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 122/285 (42%), Positives = 175/285 (61%), Gaps = 13/285 (4%)

Query: 7   SIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           S ++ G++G +  YI  + +IPML   EE   A  +RE  +L +A RLV SHLRLVV IA
Sbjct: 25  SSLLPGQLGNIDAYIQAVNRIPMLTPAEERQFATEFREQDNLESARRLVLSHLRLVVSIA 84

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGLP ++++ EGNIGLM+AVK+FDPE+  RL +Y+M WIKA + EYILR+W +VK
Sbjct: 85  RNYLGYGLPHADLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHWIKAEIHEYILRNWRMVK 144

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDE 184
           + TT  Q++LFFNLR  K  L A T     P+++  +AK+LNV   EV  M  RL+ GD 
Sbjct: 145 VATTKAQRKLFFNLRSHKQGLGAFT-----PDEIEGLAKELNVKREEVSEMETRLSGGDI 199

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           +L   +   +++ +    +L   H     VL  ++  K + + +  ++  L+ R RRI E
Sbjct: 200 ALEGQVEDGEESYAPIA-YLADSHSEPTAVLASRQRDKLQSDGIASALDALDARSRRIIE 258

Query: 245 ARRLQ-----ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           AR L+         TL  L+ EF VS ER+RQIEA A KK++ ++
Sbjct: 259 ARWLKVEDDGSGGSTLHELADEFGVSAERIRQIEASAMKKMRGAL 303


>gi|187922577|ref|YP_001894219.1| RNA polymerase factor sigma-32 [Burkholderia phytofirmans PsJN]
 gi|187713771|gb|ACD14995.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia phytofirmans
           PsJN]
          Length = 311

 Score =  216 bits (551), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 123/285 (43%), Positives = 173/285 (60%), Gaps = 13/285 (4%)

Query: 7   SIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           S ++ G++G +  YI  + +IPML   EE   A  +RE  +L +A RLV SHLRLVV IA
Sbjct: 29  SSLLPGQLGNIDAYIQAVNRIPMLTPAEERQFATEFREQDNLESARRLVLSHLRLVVSIA 88

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGLP ++++ EGNIGLM+AVK+FDPE+  RL +Y+M WIKA + EYILR+W +VK
Sbjct: 89  RNYLGYGLPHADLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHWIKAEIHEYILRNWRMVK 148

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDE 184
           + TT  Q++LFFNLR  K  L A T     P+Q+  +AK+LNV   EV  M  RL+ GD 
Sbjct: 149 VATTKAQRKLFFNLRSHKQGLGAFT-----PDQIDDLAKELNVKREEVSEMETRLSGGDI 203

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           +L   +   ++  +    +L   H     VL  ++  K   + +  ++  L+ R RRI E
Sbjct: 204 ALEGQVEDGEEAYAPIA-YLADSHSEPTAVLASRQRDKLHSDGIASALDALDARSRRIIE 262

Query: 245 ARRLQ-----ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           AR L+         TL  L+ EF VS ER+RQIEA A KK++ ++
Sbjct: 263 ARWLKVEDDGSGGSTLHELADEFGVSAERIRQIEASAMKKMRGAL 307


>gi|261377878|ref|ZP_05982451.1| alternative sigma factor RpoH [Neisseria cinerea ATCC 14685]
 gi|269145731|gb|EEZ72149.1| alternative sigma factor RpoH [Neisseria cinerea ATCC 14685]
          Length = 290

 Score =  216 bits (551), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 123/290 (42%), Positives = 185/290 (63%), Gaps = 9/290 (3%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N   +  I +G   L +YIH +  IPML   EE  LA+R R+ GDL+AA +L+ SHLR+V
Sbjct: 6   NAFALPAIQSGNGSLEQYIHTVNSIPMLTLDEETHLAERQRK-GDLNAAKQLILSHLRVV 64

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+ILR+W
Sbjct: 65  VSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILRNW 124

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            LV++ TT  Q++LFFNLR ++ +L     N L P++   IA  L V  SEV+ M  R+ 
Sbjct: 125 RLVRVATTKPQRKLFFNLRSMRKNL-----NALSPKEAQEIADDLGVKLSEVLEMEQRMT 179

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRER 240
           G +      NS D++S    DWL  DHD +    + K+     +   L  +++ L+ R R
Sbjct: 180 GHDIAIMADNSDDEDSFAPIDWLA-DHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSR 238

Query: 241 RIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           RI E+R LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 239 RIVESRWLQDDGGLTLHQLAAEYGVSAERIRQIEAKAMQKLRGFLAEEAE 288


>gi|170724574|ref|YP_001758600.1| RNA polymerase factor sigma-32 [Shewanella woodyi ATCC 51908]
 gi|169809921|gb|ACA84505.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella woodyi ATCC
           51908]
          Length = 283

 Score =  216 bits (551), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 115/284 (40%), Positives = 178/284 (62%), Gaps = 9/284 (3%)

Query: 1   MNRKNMSIIV-NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLR 59
           M  ++M++ V +G   L  Y+H    I MLE ++EY LAKR +E GDL AA +L+ SHLR
Sbjct: 1   MTNQSMALTVPHGSGSLEAYVHSAHNISMLEPEQEYELAKRLQETGDLQAAKQLIMSHLR 60

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
            VV +A GY GYGLP ++++ EGNIGLM+AVK+FDP+ G RL ++++ WIKA + EY+L+
Sbjct: 61  FVVHVAKGYSGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYVLK 120

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
           +W +VK+ TT  Q++LFFNLR+ K  L   +D     E+V  +A  L VS+++V  M  R
Sbjct: 121 NWRIVKVATTKAQRKLFFNLRKSKKRLGWFSD-----EEVGMVADNLGVSKADVTEMESR 175

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDH--DGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
           +A  +    L + +D +        + DH  D   QV  +  E  N+  +L+ ++  L+ 
Sbjct: 176 MAAQDPAFDLASDNDDDQDFSPVHYLEDHSSDLASQVENDNLESNNQARLLS-AIKTLDE 234

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R + I +AR L E+  TL+ L++ ++VS ER+RQ+E  A  K++
Sbjct: 235 RSQHILQARWLNEDKTTLQELAATYQVSAERIRQLEKNAMNKLK 278


>gi|221211178|ref|ZP_03584157.1| alternative sigma factor RpoH [Burkholderia multivorans CGD1]
 gi|221168539|gb|EEE01007.1| alternative sigma factor RpoH [Burkholderia multivorans CGD1]
          Length = 281

 Score =  216 bits (551), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 119/283 (42%), Positives = 178/283 (62%), Gaps = 13/283 (4%)

Query: 9   IVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++ G++G +  YI  + +IP+L  +EE   A  YRE+ +L AA RLV SHLRLVV IA  
Sbjct: 1   MLPGQLGNIDAYIQAVNRIPLLTAEEERQYATEYRENNNLEAARRLVLSHLRLVVSIARN 60

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y GYGLP  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W +VK+ 
Sbjct: 61  YLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKVA 120

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESL 186
           TT  Q++LFFNLR  K  +QA+T     PE++  +A++LNV   EV  M  RL+ GD +L
Sbjct: 121 TTKAQRKLFFNLRSHKKGMQAMT-----PEEIDGLAQELNVKREEVTEMETRLSGGDIAL 175

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              +   +++ +    +L   H+    VL  ++    + + + +++  L+ R RRI EAR
Sbjct: 176 EGQVEDGEESYAPIA-YLADSHNEPTAVLAARQRDMLQTDGIAQALDALDARSRRIIEAR 234

Query: 247 RLQ-----ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L          TL +L++EF VS ER+RQIEA A KK++ ++
Sbjct: 235 WLHVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRTAL 277


>gi|240013602|ref|ZP_04720515.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae DGI18]
 gi|240112396|ref|ZP_04726886.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae MS11]
 gi|240120672|ref|ZP_04733634.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID24-1]
 gi|268598456|ref|ZP_06132623.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae MS11]
 gi|268582587|gb|EEZ47263.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae MS11]
          Length = 290

 Score =  216 bits (551), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 122/286 (42%), Positives = 185/286 (64%), Gaps = 9/286 (3%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +  I +G   L +YIH +  IPML ++EE  LA+R R  GDL+AA +L+ SHLR+VV IA
Sbjct: 10  LPAIQSGNGSLEQYIHTVNSIPMLSQEEETRLAER-RIKGDLNAAKQLILSHLRVVVSIA 68

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+ILR+W LV+
Sbjct: 69  RGYDGYGLNQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILRNWRLVR 128

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           + TT  Q++LFFNLR ++ +L     N L P++   IA  L V  SEV+ M  R+ G + 
Sbjct: 129 VATTKPQRKLFFNLRSMRKNL-----NVLSPKEAQDIADDLGVKLSEVLEMEQRMTGHDI 183

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFE 244
                NS D++S    DWL  DHD +    + K+     +   L  +++ L+ R RRI E
Sbjct: 184 AIMTDNSDDEDSFAPIDWLA-DHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRRIVE 242

Query: 245 ARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           +R LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 243 SRWLQDDGGLTLHQLAAEYGVSAERIRQIEAKAMQKLRGFLTEEAE 288


>gi|317163755|gb|ADV07296.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae TCDC-NG08107]
          Length = 287

 Score =  216 bits (550), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 122/286 (42%), Positives = 185/286 (64%), Gaps = 9/286 (3%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +  I +G   L +YIH +  IPML ++EE  LA+R R  GDL+AA +L+ SHLR+VV IA
Sbjct: 7   LPAIQSGNGSLEQYIHTVNSIPMLSQEEETRLAER-RIKGDLNAAKQLILSHLRVVVSIA 65

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+ILR+W LV+
Sbjct: 66  RGYDGYGLNQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILRNWRLVR 125

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           + TT  Q++LFFNLR ++ +L     N L P++   IA  L V  SEV+ M  R+ G + 
Sbjct: 126 VATTKPQRKLFFNLRSMRKNL-----NVLSPKEAQDIADDLGVKLSEVLEMEQRMTGHDI 180

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFE 244
                NS D++S    DWL  DHD +    + K+     +   L  +++ L+ R RRI E
Sbjct: 181 AIMADNSDDEDSFAPIDWLA-DHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRRIVE 239

Query: 245 ARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           +R LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 240 SRWLQDDGGLTLHQLAAEYGVSAERIRQIEAKAMQKLRGFLTEEAE 285


>gi|161523666|ref|YP_001578678.1| RNA polymerase factor sigma-32 [Burkholderia multivorans ATCC
           17616]
 gi|189351565|ref|YP_001947193.1| RNA polymerase factor sigma-32 [Burkholderia multivorans ATCC
           17616]
 gi|160341095|gb|ABX14181.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia multivorans
           ATCC 17616]
 gi|189335587|dbj|BAG44657.1| RNA polymerase sigma-32 factor [Burkholderia multivorans ATCC
           17616]
          Length = 311

 Score =  216 bits (550), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 118/283 (41%), Positives = 178/283 (62%), Gaps = 13/283 (4%)

Query: 9   IVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++ G++G +  YI  + +IP+L  +EE   A  YRE+ +L AA RLV SHLRLVV IA  
Sbjct: 31  MLPGQLGNIDAYIQAVNRIPLLTAEEERQYATEYRENNNLEAARRLVLSHLRLVVSIARN 90

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y GYGLP  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W +VK+ 
Sbjct: 91  YLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKVA 150

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESL 186
           TT  Q++LFFNLR  K  +QA+T     PE++  +A++LNV   +V  M  RL+ GD +L
Sbjct: 151 TTKAQRKLFFNLRSHKKGMQAMT-----PEEIDGLAQELNVKREDVTEMETRLSGGDIAL 205

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              +   +++ +    +L   H+    VL  ++    + + + +++  L+ R RRI EAR
Sbjct: 206 EGQVEDGEESYAPIA-YLADSHNEPTAVLAARQRDMLQTDGIAQALDALDARSRRIIEAR 264

Query: 247 RLQ-----ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L          TL +L++EF VS ER+RQIEA A KK++ ++
Sbjct: 265 WLHVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRTAL 307


>gi|21233199|ref|NP_639116.1| RNA polymerase factor sigma-32 [Xanthomonas campestris pv.
           campestris str. ATCC 33913]
 gi|66770141|ref|YP_244903.1| RNA polymerase factor sigma-32 [Xanthomonas campestris pv.
           campestris str. 8004]
 gi|188993348|ref|YP_001905358.1| RNA polymerase factor sigma-32 [Xanthomonas campestris pv.
           campestris str. B100]
 gi|3046929|gb|AAC38329.1| heat shock sigma factor 32 [Xanthomonas campestris pv. campestris]
 gi|21115547|gb|AAM43471.1| RNA polymerase sigma-32 factor [Xanthomonas campestris pv.
           campestris str. ATCC 33913]
 gi|66575473|gb|AAY50883.1| RNA polymerase sigma-32 factor [Xanthomonas campestris pv.
           campestris str. 8004]
 gi|167735108|emb|CAP53320.1| RNA polymerase sigma-32 factor [Xanthomonas campestris pv.
           campestris]
          Length = 291

 Score =  216 bits (550), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 121/272 (44%), Positives = 170/272 (62%), Gaps = 14/272 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + +IP+L   EE  LA+R+R+  DL AA  LV SHLR VV +A GY GYGLP+
Sbjct: 23  LDAYIGAVHQIPVLSVDEEQNLARRFRDELDLDAARELVHSHLRFVVHVARGYNGYGLPL 82

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AVK+FDPE G RL ++++ WI+A M E+IL++W +VK+ TT  Q++L
Sbjct: 83  GDLIQEGNIGLMKAVKRFDPEMGVRLVSFAVHWIRAEMHEFILKNWRIVKVATTKAQRKL 142

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR+ K  L       L   +V A+AK LNVSE EV+ M  RL+G D   +A   SSD
Sbjct: 143 FFNLRKSKTRL-----GWLNASEVTAVAKDLNVSEREVMEMESRLSGRDIGFDA---SSD 194

Query: 195 KNSSQWQ----DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ- 249
           ++          +LV + +   Q     +   N+  +L   M+ L+ R R I + R L  
Sbjct: 195 EDDDHGPPSPVSYLVANEEDPSQAYERHDSEDNQLQLLREGMAGLDTRSRDIVKRRWLDS 254

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           E+ VTL+ L+ E+ VS ER+RQIEA A KK++
Sbjct: 255 ESKVTLQELADEYGVSAERIRQIEANALKKMK 286


>gi|59800736|ref|YP_207448.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae FA 1090]
 gi|194098013|ref|YP_002001061.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae NCCP11945]
 gi|239998477|ref|ZP_04718401.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae 35/02]
 gi|240016041|ref|ZP_04722581.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae FA6140]
 gi|240080183|ref|ZP_04724726.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae FA19]
 gi|240115137|ref|ZP_04729199.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID18]
 gi|240117420|ref|ZP_04731482.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID1]
 gi|240122976|ref|ZP_04735932.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID332]
 gi|240125228|ref|ZP_04738114.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae SK-92-679]
 gi|240127682|ref|ZP_04740343.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae SK-93-1035]
 gi|254493195|ref|ZP_05106366.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae 1291]
 gi|260441046|ref|ZP_05794862.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae DGI2]
 gi|268594335|ref|ZP_06128502.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae 35/02]
 gi|268596331|ref|ZP_06130498.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae FA19]
 gi|268600810|ref|ZP_06134977.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID18]
 gi|268603115|ref|ZP_06137282.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID1]
 gi|268681596|ref|ZP_06148458.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID332]
 gi|268683824|ref|ZP_06150686.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae SK-92-679]
 gi|268686066|ref|ZP_06152928.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae SK-93-1035]
 gi|291044379|ref|ZP_06570088.1| RNA polymerase sigma factor [Neisseria gonorrhoeae DGI2]
 gi|293399564|ref|ZP_06643717.1| alternative sigma factor RpoH [Neisseria gonorrhoeae F62]
 gi|59717631|gb|AAW89036.1| putative RNA polymerase sigma-32 [Neisseria gonorrhoeae FA 1090]
 gi|193933303|gb|ACF29127.1| RNA polymerase sigma factor [Neisseria gonorrhoeae NCCP11945]
 gi|226512235|gb|EEH61580.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae 1291]
 gi|268547724|gb|EEZ43142.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae 35/02]
 gi|268550119|gb|EEZ45138.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae FA19]
 gi|268584941|gb|EEZ49617.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID18]
 gi|268587246|gb|EEZ51922.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID1]
 gi|268621880|gb|EEZ54280.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID332]
 gi|268624108|gb|EEZ56508.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae SK-92-679]
 gi|268626350|gb|EEZ58750.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae SK-93-1035]
 gi|291011273|gb|EFE03269.1| RNA polymerase sigma factor [Neisseria gonorrhoeae DGI2]
 gi|291610133|gb|EFF39255.1| alternative sigma factor RpoH [Neisseria gonorrhoeae F62]
          Length = 290

 Score =  216 bits (550), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 122/286 (42%), Positives = 185/286 (64%), Gaps = 9/286 (3%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +  I +G   L +YIH +  IPML ++EE  LA+R R  GDL+AA +L+ SHLR+VV IA
Sbjct: 10  LPAIQSGNGSLEQYIHTVNSIPMLSQEEETRLAER-RIKGDLNAAKQLILSHLRVVVSIA 68

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+ILR+W LV+
Sbjct: 69  RGYDGYGLNQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILRNWRLVR 128

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           + TT  Q++LFFNLR ++ +L     N L P++   IA  L V  SEV+ M  R+ G + 
Sbjct: 129 VATTKPQRKLFFNLRSMRKNL-----NVLSPKEAQDIADDLGVKLSEVLEMEQRMTGHDI 183

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFE 244
                NS D++S    DWL  DHD +    + K+     +   L  +++ L+ R RRI E
Sbjct: 184 AIMADNSDDEDSFAPIDWLA-DHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRRIVE 242

Query: 245 ARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           +R LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 243 SRWLQDDGGLTLHQLAAEYGVSAERIRQIEAKAMQKLRGFLTEEAE 288


>gi|170742915|ref|YP_001771570.1| RNA polymerase factor sigma-32 [Methylobacterium sp. 4-46]
 gi|168197189|gb|ACA19136.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium sp. 4-46]
          Length = 293

 Score =  216 bits (550), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 111/262 (42%), Positives = 173/262 (66%), Gaps = 1/262 (0%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE++EE  LA R+++  D  A HRL+++H+RLV+ +A  +R YGLP++++V EG++GL
Sbjct: 19  PFLEREEERGLAVRWKDKRDEQALHRLISAHMRLVIALAGRFRHYGLPMADLVQEGHVGL 78

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 79  MEAAARFEPERDVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRARL 138

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLV 205
              TD  +  E    IA  + VS  +V  M+ RL+G D SLNA I      S++  D+LV
Sbjct: 139 MQSTDERVGDEIHRRIATAIGVSREDVALMDARLSGPDMSLNAPITDEGDASAERVDFLV 198

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
                 ++ + +  + + R   L ++++VL+ RE RI   RRL E+  TLE L     +S
Sbjct: 199 DTSPLPDEAVSDAVDGERRLTWLRQALTVLSERELRILHERRLAEDQATLEALGHRLGIS 258

Query: 266 RERVRQIEARAFKKVQESIQKQ 287
           +ERVRQIE RA +K++ ++ ++
Sbjct: 259 KERVRQIENRALEKLRRALAER 280


>gi|325913818|ref|ZP_08176177.1| RNA polymerase, sigma 32 subunit, RpoH [Xanthomonas vesicatoria
           ATCC 35937]
 gi|325539893|gb|EGD11530.1| RNA polymerase, sigma 32 subunit, RpoH [Xanthomonas vesicatoria
           ATCC 35937]
          Length = 291

 Score =  216 bits (550), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 121/272 (44%), Positives = 170/272 (62%), Gaps = 14/272 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + +IP+L   EE  LA+R+R+  DL AA  LV SHLR VV +A GY GYGLP+
Sbjct: 23  LDAYIGAVHQIPVLSVDEEQNLARRFRDELDLDAARELVHSHLRFVVHVARGYNGYGLPL 82

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AVK+FDPE G RL ++++ WI+A M E+IL++W +VK+ TT  Q++L
Sbjct: 83  GDLIQEGNIGLMKAVKRFDPEMGVRLVSFAVHWIRAEMHEFILKNWRIVKVATTKAQRKL 142

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR+ K  L       L   +V A+AK LNVSE EV+ M  RL+G D   +A   SSD
Sbjct: 143 FFNLRKSKTRL-----GWLNASEVTAVAKDLNVSEREVMEMESRLSGRDIGFDA---SSD 194

Query: 195 KNSSQWQ----DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ- 249
           ++          +LV + +   Q     +   N+  +L   M+ L+ R R I + R L  
Sbjct: 195 EDDDHGPPSPVSYLVANEEDPSQAYERHDSEDNQLQLLREGMAGLDTRSRDIVKRRWLDS 254

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           E+ VTL+ L+ E+ VS ER+RQIEA A KK++
Sbjct: 255 ESKVTLQELADEYGVSAERIRQIEANALKKMK 286


>gi|325202493|gb|ADY97947.1| alternative sigma factor RpoH [Neisseria meningitidis M01-240149]
 gi|325207756|gb|ADZ03208.1| alternative sigma factor RpoH [Neisseria meningitidis NZ-05/33]
          Length = 287

 Score =  216 bits (550), Expect = 3e-54,   Method: Compositional matrix adjust.
 Identities = 122/286 (42%), Positives = 184/286 (64%), Gaps = 9/286 (3%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +  I +G   L +YIH +  IPML ++EE  LA+R R  GDL+AA +L+ SHLR+VV IA
Sbjct: 7   LPAIQSGNGSLEQYIHTVNSIPMLSQEEETRLAER-RIKGDLNAAKQLILSHLRVVVSIA 65

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            GY GYGL  ++++ EGNIGLM+AVK++ P RG RL ++++ WIKA + E+ILR+W LV+
Sbjct: 66  RGYDGYGLNQADLIQEGNIGLMKAVKRYKPGRGARLFSFAVHWIKAEIHEFILRNWRLVR 125

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           + TT  Q++LFFNLR ++ +L     N L P++   IA  L V  SEV+ M  R+ G + 
Sbjct: 126 VATTKPQRKLFFNLRSMRKNL-----NALSPKEAQDIADDLGVKLSEVLEMEQRMTGHDI 180

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFE 244
                NS D++S    DWL  DHD +    + K+     +   L  +++ L+ R RRI E
Sbjct: 181 AIMADNSDDEDSFAPIDWLA-DHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRRIVE 239

Query: 245 ARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           +R LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 240 SRWLQDDGGLTLHQLAAEYGVSAERIRQIEAKAMQKLRGFLTEEAE 285


>gi|118579103|ref|YP_900353.1| RNA polymerase sigma-32 subunit RpoH [Pelobacter propionicus DSM
           2379]
 gi|118501813|gb|ABK98295.1| RNA polymerase, sigma 32 subunit, RpoH [Pelobacter propionicus DSM
           2379]
          Length = 282

 Score =  216 bits (549), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 117/273 (42%), Positives = 178/273 (65%), Gaps = 5/273 (1%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+ EIRK  +L ++EE+  A  + E  DL AAH L+TS+LR VV++A  YR YGL +
Sbjct: 12  LALYLAEIRKFTLLSEEEEHRTAIAFYEKKDLRAAHTLITSNLRFVVRVAYEYRHYGLKM 71

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM AVKK++P +G RL +Y++WWI+A +Q +++ +WSL+KIGTT  Q++L
Sbjct: 72  LDLIQEGNIGLMMAVKKYNPFKGVRLISYAVWWIRAYIQNHVISAWSLLKIGTTQAQRKL 131

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FF LR  +    AI   N   + + + A+ LNVS+SEV+ M  RL G+ SL+A +   + 
Sbjct: 132 FFKLREAR---NAIRHLNGGEDDLQSTARSLNVSDSEVVEMEQRLRGECSLDAELPGGEG 188

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
            +    D LV D   QE++L E + ++  R  +  ++S LN +ER + E R   + P+TL
Sbjct: 189 VTG--LDGLVDDRMNQEELLSECQLQRKLRTDVATAVSALNEKERFVIEHRVSADTPLTL 246

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           + ++S F +SRERVRQIE  A KK++ S+   V
Sbjct: 247 QEIASRFSISRERVRQIEEAALKKLKLSLVSAV 279


>gi|187479755|ref|YP_787780.1| RNA polymerase factor sigma-32 [Bordetella avium 197N]
 gi|115424342|emb|CAJ50895.1| RNA polymerase sigma-32 factor [Bordetella avium 197N]
          Length = 307

 Score =  216 bits (549), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 126/287 (43%), Positives = 181/287 (63%), Gaps = 22/287 (7%)

Query: 8   IIVN-GEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           ++ N G +G +  YI  + ++P+L  ++E  LA+R R+  DL +A  LV SHLRLVV +A
Sbjct: 30  VVANPGALGTIDAYITTVNRLPVLTAEQESTLARRLRDSDDLESARELVLSHLRLVVSVA 89

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGLP ++++ EGN+GLM+AVK+FDPERG RL ++++ WIKA + EYI+R+W LVK
Sbjct: 90  RQYLGYGLPHADLIQEGNVGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYIIRNWRLVK 149

Query: 126 IGTTANQKRLFFNLRRLK--GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG- 182
           + TT  Q++LFFNLR ++  GH        L  EQV  IA++LNV   +V  M  RL+G 
Sbjct: 150 VATTKAQRKLFFNLRSMRPDGH-------TLDTEQVDHIARELNVRREDVSEMEVRLSGR 202

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM----LTRSMSVLNPR 238
           D SL    N  D +        + D   +E   +   ERK R ++    L+ +++ L+PR
Sbjct: 203 DLSLE---NQDDDDDGYAPIAYLSDECREEPTRV--LERKARDDLQGKGLSDAITALDPR 257

Query: 239 ERRIFEARRLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            RRI EAR LQ E   TL  L++EF VS ER+RQIEA A KK++ ++
Sbjct: 258 SRRIVEARWLQDEGGATLHELAAEFGVSAERIRQIEAAALKKMRGAL 304


>gi|254251367|ref|ZP_04944685.1| hypothetical protein BDAG_00552 [Burkholderia dolosa AUO158]
 gi|124893976|gb|EAY67856.1| hypothetical protein BDAG_00552 [Burkholderia dolosa AUO158]
          Length = 311

 Score =  216 bits (549), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 118/283 (41%), Positives = 178/283 (62%), Gaps = 13/283 (4%)

Query: 9   IVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++ G++G +  YI  + +IP+L  +EE   A  +RE+ +L AA RLV SHLRLVV IA  
Sbjct: 31  MLPGQLGNIDAYIQAVNRIPLLTAEEERQYATEFRENNNLEAARRLVLSHLRLVVSIARN 90

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y GYGLP  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W +VK+ 
Sbjct: 91  YLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKVA 150

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESL 186
           TT  Q++LFFNLR  K  +QA+T     PE++  +A++LNV   EV  M  RL+ GD +L
Sbjct: 151 TTKAQRKLFFNLRSHKKSMQAMT-----PEEIDGLAQELNVKREEVAEMETRLSGGDVAL 205

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              +   +++ +    +L   H+    VL  ++    + + + +++  L+ R RRI EAR
Sbjct: 206 EGQVEDGEESYAPIA-YLADSHNEPTAVLAARQRDMLQTDGIAQALDALDARSRRIIEAR 264

Query: 247 RLQ-----ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L          TL +L++EF VS ER+RQIEA A KK++ ++
Sbjct: 265 WLNVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRTAL 307


>gi|107023748|ref|YP_622075.1| RNA polymerase factor sigma-32 [Burkholderia cenocepacia AU 1054]
 gi|116690835|ref|YP_836458.1| RNA polymerase factor sigma-32 [Burkholderia cenocepacia HI2424]
 gi|170734160|ref|YP_001766107.1| RNA polymerase factor sigma-32 [Burkholderia cenocepacia MC0-3]
 gi|254247164|ref|ZP_04940485.1| Sigma-70 region 2 [Burkholderia cenocepacia PC184]
 gi|105893937|gb|ABF77102.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia cenocepacia AU
           1054]
 gi|116648924|gb|ABK09565.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia cenocepacia
           HI2424]
 gi|124871940|gb|EAY63656.1| Sigma-70 region 2 [Burkholderia cenocepacia PC184]
 gi|169817402|gb|ACA91985.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia cenocepacia
           MC0-3]
          Length = 311

 Score =  216 bits (549), Expect = 4e-54,   Method: Compositional matrix adjust.
 Identities = 118/283 (41%), Positives = 177/283 (62%), Gaps = 13/283 (4%)

Query: 9   IVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++ G++G +  YI  + +IP+L  +EE   A  +RE  +L AA RLV SHLRLVV IA  
Sbjct: 31  MLPGQLGNIDAYIQAVNRIPLLTAEEERRYATEFREDNNLDAARRLVLSHLRLVVSIARN 90

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y GYGLP  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W +VK+ 
Sbjct: 91  YLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKVA 150

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESL 186
           TT  Q++LFFNLR  K  +QA+T     PE++  +A++LNV   EV  M  RL+ GD +L
Sbjct: 151 TTKAQRKLFFNLRSHKKSMQAMT-----PEEIDGLAQELNVKREEVTEMETRLSGGDIAL 205

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              +   +++ +    +L   H+    VL  ++    + + + +++  L+ R RRI EAR
Sbjct: 206 EGQVEDGEESYAPIA-YLADSHNEPTAVLAARQRDMLQTDGIAQALDALDARSRRIIEAR 264

Query: 247 RLQ-----ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L          TL +L++EF VS ER+RQIEA A KK++ ++
Sbjct: 265 WLHVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRTAL 307


>gi|167585406|ref|ZP_02377794.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ubonensis Bu]
          Length = 311

 Score =  216 bits (549), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 118/283 (41%), Positives = 177/283 (62%), Gaps = 13/283 (4%)

Query: 9   IVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++ G++G +  YI  + +IP+L  +EE   A  +RE  +L AA RLV SHLRLVV IA  
Sbjct: 31  MLPGQLGNIDAYIQAVNRIPLLTAEEERRYATEFREQNNLDAARRLVLSHLRLVVSIARN 90

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y GYGLP  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W +VK+ 
Sbjct: 91  YLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKVA 150

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESL 186
           TT  Q++LFFNLR  K  +QA+T     PE++  +A++LNV   EV  M  RL+ GD +L
Sbjct: 151 TTKAQRKLFFNLRSHKKGMQAMT-----PEEIDGLAQELNVKREEVTEMETRLSGGDIAL 205

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              +   +++ +    +L   H+    VL  ++    + + + +++  L+ R RRI EAR
Sbjct: 206 EGQVEDGEESYAPIA-YLADSHNEPTAVLAARQRDMLQTDGIAQALDALDARSRRIIEAR 264

Query: 247 RLQ-----ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L          TL +L++EF VS ER+RQIEA A KK++ ++
Sbjct: 265 WLHVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRTAL 307


>gi|319940794|ref|ZP_08015133.1| RNA polymerase sigma factor [Sutterella wadsworthensis 3_1_45B]
 gi|319805676|gb|EFW02457.1| RNA polymerase sigma factor [Sutterella wadsworthensis 3_1_45B]
          Length = 281

 Score =  216 bits (549), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 120/280 (42%), Positives = 177/280 (63%), Gaps = 13/280 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  ++    + PML  +EE  LA + R+  DL AA +LV SHLRLV+ IA G+ GYGLP 
Sbjct: 4   LDAFLRAAERAPMLTAEEEKTLALKLRDQNDLEAAQKLVLSHLRLVISIARGFLGYGLPY 63

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+A++++DP+RG RL T+++ WI++ +QEYI+R+W +VK+ TT NQ++L
Sbjct: 64  ADLIQEGNIGLMKAIRRYDPDRGARLMTFAVHWIRSEIQEYIIRNWRIVKLATTKNQRKL 123

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
           FFNLR+LK   QA   N    ++   IA  L+V   EV+ M  R+ G E S++   +S D
Sbjct: 124 FFNLRQLKEDSQAALTN----QEAQRIALTLDVKPKEVLDMEERMYGQETSIDGPADSDD 179

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN-MLTRSMSVLNPRERRIFEARRLQEN-- 251
            +     DWL    D Q + ++E E+R++     L  +++ L+PR RR+ EAR L  +  
Sbjct: 180 DDRFSPSDWLTRTSD-QPEAILEAEDRQHLEGEGLQTALAALDPRSRRVIEARYLTVDAD 238

Query: 252 ----PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
               PVTL+ L+ E  VS ERVRQIE  A KK+ E +  Q
Sbjct: 239 GTAKPVTLQALAHELGVSAERVRQIEKLAIKKMGEKLAGQ 278


>gi|71909448|ref|YP_287035.1| RNA polymerase factor sigma-32 [Dechloromonas aromatica RCB]
 gi|71849069|gb|AAZ48565.1| RNA polymerase, sigma 32 subunit, RpoH [Dechloromonas aromatica
           RCB]
          Length = 286

 Score =  215 bits (548), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 118/280 (42%), Positives = 172/280 (61%), Gaps = 8/280 (2%)

Query: 6   MSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +++ +   +G +  YI    + PML + EE  LA+R    GD+ AA +LV SHLRLV+ I
Sbjct: 5   LALPIPSSVGNIDAYIQAANRYPMLTEAEESRLAERLHNDGDVEAARQLVLSHLRLVISI 64

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A GY GYGLP ++++ EGNIGLM+AVK+FDP RG RL +++M WIKA + EYIL++W LV
Sbjct: 65  ARGYLGYGLPHADLIQEGNIGLMKAVKRFDPSRGVRLVSFAMHWIKAEIHEYILKNWRLV 124

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           K+ TT  Q++LFFNLR +K   + I  + L   Q   +A +L V + EV+ M  RL+G +
Sbjct: 125 KVATTKAQRKLFFNLRSMKSGYEGI--DTLSGTQAAEVAARLGVKQDEVVEMETRLSGRD 182

Query: 185 SLNALINSSDKNSSQWQ--DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
              AL  + D     +   D+L        +VL  K   + +   L  ++  L+PR RRI
Sbjct: 183 I--ALDGNPDDGEEAFAPIDYLADSRYEPTRVLENKAIARLQDEGLHEALEALDPRSRRI 240

Query: 243 FEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            EAR L +    TL +L+ EF+VS ER+RQIE +A +K++
Sbjct: 241 IEARWLHDGETATLHDLADEFDVSAERIRQIEVKALQKMR 280


>gi|300705271|ref|YP_003746874.1| RNA polymerase sigma h (sigma 32) factor; transcription of heat
           shock and stress proteins [Ralstonia solanacearum
           CFBP2957]
 gi|299072935|emb|CBJ44291.1| RNA polymerase sigma H (sigma 32) factor; transcription of heat
           shock and stress proteins [Ralstonia solanacearum
           CFBP2957]
          Length = 306

 Score =  215 bits (548), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 121/281 (43%), Positives = 176/281 (62%), Gaps = 12/281 (4%)

Query: 12  GEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           G +G L  YI  + ++PML  +EE  LA+ Y   GDL AA RLV SHLRLVV IA  Y G
Sbjct: 28  GSLGNLDAYIQSVNRVPMLTAEEEQQLARDYHATGDLDAARRLVLSHLRLVVSIARQYLG 87

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
           YGLP ++++ EGNIGLM+AVK+FDP++G RL +Y++ WIKA M EYIL++W +VK+ TT 
Sbjct: 88  YGLPHADLIQEGNIGLMKAVKRFDPDQGVRLVSYAIHWIKAEMHEYILKNWRMVKVATTK 147

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNAL 189
            Q++LFFNLR  K    A        +++ A+A++LNV  +EV  M  RL+ GD +L   
Sbjct: 148 AQRKLFFNLRSHKQDAHA----TFTSDEIDAVAQELNVKGAEVREMETRLSGGDIALEGH 203

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I+  +++ +    +L   H+   +VL  +   + +   +  +++ L+ R RRI EAR L 
Sbjct: 204 IDDGEESFAPIA-YLADTHNEPTRVLETRGHDRLQSEGIETALAKLDDRSRRIIEARWLN 262

Query: 250 ENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            N       TL  L+ EF VS ER+RQIE+ A KK++ ++Q
Sbjct: 263 VNDDGSGGATLHELADEFGVSAERIRQIESAAMKKMKGALQ 303


>gi|241206826|ref|YP_002977922.1| RNA polymerase factor sigma-32 [Rhizobium leguminosarum bv.
           trifolii WSM1325]
 gi|86450985|gb|ABC96760.1| putative RNA polymerase sigma factor [Rhizobium leguminosarum bv.
           trifolii TA1]
 gi|240860716|gb|ACS58383.1| RNA polymerase, sigma 32 subunit, RpoH [Rhizobium leguminosarum bv.
           trifolii WSM1325]
          Length = 287

 Score =  215 bits (548), Expect = 6e-54,   Method: Compositional matrix adjust.
 Identities = 116/263 (44%), Positives = 175/263 (66%), Gaps = 9/263 (3%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L +QEE+ LA R+++H D  A +++  +H+RLV+ +A  +R +GLP+S++V EG +GL
Sbjct: 18  PYLARQEEHDLATRWKDHDDRGARNQIAMAHMRLVISMAGKFRNFGLPMSDLVQEGYVGL 77

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 78  LEAAARFEPERDVRFSTYASWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRAKL 137

Query: 147 QAITDNNLKPEQV-VAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWL 204
            A  D  L  + +   IA  L VS S+V +M+ RL+G D SL A   S D  S++  D+L
Sbjct: 138 -AKGDTQLTLQSIHQEIAAALGVSLSDVQTMDARLSGNDASLQAPSVSGDAESAEKMDFL 196

Query: 205 VYDH---DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           V D    D Q   +I+ E    RR  L  ++  LN RE +I  ARRL E+  TLE L ++
Sbjct: 197 VSDDPLPDEQVSNMIDGE---RRRVWLASALKHLNEREMKIISARRLAEDGATLEELGAD 253

Query: 262 FEVSRERVRQIEARAFKKVQESI 284
             +S+ERVRQIE+RA +K++ ++
Sbjct: 254 LGISKERVRQIESRAMEKLRSAL 276


>gi|293602894|ref|ZP_06685333.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Achromobacter
           piechaudii ATCC 43553]
 gi|292818688|gb|EFF77730.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Achromobacter
           piechaudii ATCC 43553]
          Length = 294

 Score =  215 bits (547), Expect = 7e-54,   Method: Compositional matrix adjust.
 Identities = 123/287 (42%), Positives = 179/287 (62%), Gaps = 11/287 (3%)

Query: 2   NRKNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           N   ++I   G +G +  YI  + ++P+L  + E  L +R R+  DL AA  L+ SHLRL
Sbjct: 13  NALALAIANPGALGTIDAYISAVNRLPVLSAERETELGRRLRDQEDLGAARELILSHLRL 72

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y GYGLP ++++ EGN+GLM+AVK+FDPERG RL ++++ WIKA + EYI+R+
Sbjct: 73  VVSVARQYLGYGLPHADLIQEGNVGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYIIRN 132

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W LVK+ TT  Q++LFFNLR ++   Q      L P+QV  IA++LNV   +V  M  RL
Sbjct: 133 WRLVKVATTKAQRKLFFNLRSMRPDGQ-----TLDPDQVDHIARELNVRREDVSEMEVRL 187

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV-LIEKEERKNRRNM-LTRSMSVLNPR 238
           +G E   +L N  D + S      + D   QE   ++E+  R   ++  LT ++  L+ R
Sbjct: 188 SGREM--SLENQDDDDDSFAPIAYLSDDGRQEPTRVLERAARDELQSTGLTTALEALDAR 245

Query: 239 ERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            RRI EAR LQ++   TL  L+ EF VS ER+RQIEA A KK++ ++
Sbjct: 246 SRRIVEARWLQDDGGATLHELAQEFGVSAERIRQIEAAALKKMRGNL 292


>gi|325924311|ref|ZP_08185855.1| RNA polymerase, sigma 32 subunit, RpoH [Xanthomonas gardneri ATCC
           19865]
 gi|325545176|gb|EGD16486.1| RNA polymerase, sigma 32 subunit, RpoH [Xanthomonas gardneri ATCC
           19865]
          Length = 291

 Score =  215 bits (547), Expect = 8e-54,   Method: Compositional matrix adjust.
 Identities = 120/272 (44%), Positives = 170/272 (62%), Gaps = 14/272 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + +IP+L   EE  LA+R+R+  DL AA  LV SHLR VV +A GY GYGLP+
Sbjct: 23  LDAYIGAVHQIPVLSVDEEQNLARRFRDELDLDAARELVHSHLRFVVHVARGYNGYGLPL 82

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AVK+FDPE G RL ++++ WI+A M E+IL++W +VK+ TT  Q++L
Sbjct: 83  GDLIQEGNIGLMKAVKRFDPEMGVRLVSFAVHWIRAEMHEFILKNWRIVKVATTKAQRKL 142

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR+ K  L       L   +V A+AK LNVSE EV+ M  RL+G D   +A   SSD
Sbjct: 143 FFNLRKSKTRL-----GWLNASEVTAVAKDLNVSEREVMEMESRLSGRDIGFDA---SSD 194

Query: 195 KNSSQWQ----DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ- 249
           ++          +LV + +   Q     +   N+  +L   +S L+ R R I + R L  
Sbjct: 195 EDDDHGPPSPVSYLVANEEDPSQAYERHDSEDNQLQLLREGLSGLDTRSRDIVKRRWLDS 254

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++ VTL+ L+ E+ VS ER+RQIEA A KK++
Sbjct: 255 DSKVTLQELADEYGVSAERIRQIEANALKKMK 286


>gi|116254340|ref|YP_770178.1| RNA polymerase factor sigma-32 [Rhizobium leguminosarum bv. viciae
           3841]
 gi|115258988|emb|CAK10097.1| putative rpoH sigma factor [Rhizobium leguminosarum bv. viciae
           3841]
          Length = 304

 Score =  215 bits (547), Expect = 8e-54,   Method: Compositional matrix adjust.
 Identities = 116/263 (44%), Positives = 175/263 (66%), Gaps = 9/263 (3%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L +QEE+ LA R+++H D  A +++  +H+RLV+ +A  +R +GLP+S++V EG +GL
Sbjct: 35  PYLARQEEHDLATRWKDHDDRGARNQIAMAHMRLVISMAGKFRNFGLPMSDLVQEGYVGL 94

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 95  LEAAARFEPERDVRFSTYASWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRAKL 154

Query: 147 QAITDNNLKPEQV-VAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWL 204
            A  D  L  + +   IA  L VS S+V +M+ RL+G D SL A   S D  S++  D+L
Sbjct: 155 -AKGDTQLTLQSIHQEIAAALGVSLSDVQTMDARLSGNDASLQAPSVSGDAESAEKMDFL 213

Query: 205 VYDH---DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           V D    D Q   +I+ E    RR  L  ++  LN RE +I  ARRL E+  TLE L ++
Sbjct: 214 VSDDPLPDEQVSNMIDGE---RRRVWLASALKHLNEREMKIISARRLAEDGATLEELGAD 270

Query: 262 FEVSRERVRQIEARAFKKVQESI 284
             +S+ERVRQIE+RA +K++ ++
Sbjct: 271 LGISKERVRQIESRAMEKLRSAL 293


>gi|85710830|ref|ZP_01041891.1| RNA polymerase sigma factor [Idiomarina baltica OS145]
 gi|85695234|gb|EAQ33171.1| RNA polymerase sigma factor [Idiomarina baltica OS145]
          Length = 286

 Score =  215 bits (547), Expect = 8e-54,   Method: Compositional matrix adjust.
 Identities = 119/288 (41%), Positives = 184/288 (63%), Gaps = 15/288 (5%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           K M++ V    GL  YI  + +IPML  ++E  LAKR +E  DL AA  L+ SHLR VV 
Sbjct: 6   KTMALSVPQGGGLDGYIQSVNRIPMLSAEKEKALAKRLQEDKDLDAAKELIMSHLRFVVH 65

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W +
Sbjct: 66  IARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRV 125

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AG 182
           VK+ TT  Q++LFFNLR++K  L          ++V  +AK+L VS  EV+ M  R+ A 
Sbjct: 126 VKVATTKAQRKLFFNLRKMKKRL-----GWFNQDEVETVAKELGVSSKEVMEMEARMSAH 180

Query: 183 DESLNALINSSDKNSSQWQDW--LVYDHDGQ----EQVLIEKEERKNRRNMLTRSMSVLN 236
           D++    ++S D +S +   +   +Y  D +    E++  E  E   ++ + + +MS L+
Sbjct: 181 DQAFE--LSSDDDDSKEGSTYSPAMYLEDKRSDLAEEIETEDYEAHTQKKLFS-AMSELD 237

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            R + I ++R L E+ VTL +L++++EVS ERVRQ+E  A KK++ ++
Sbjct: 238 ERSQDIVQSRWLSESKVTLHDLAAKYEVSAERVRQLEQNAMKKLRAAM 285


>gi|226939164|ref|YP_002794235.1| RNA polymerase factor sigma-32 [Laribacter hongkongensis HLHK9]
 gi|226714088|gb|ACO73226.1| RpoH [Laribacter hongkongensis HLHK9]
          Length = 282

 Score =  214 bits (546), Expect = 9e-54,   Method: Compositional matrix adjust.
 Identities = 115/268 (42%), Positives = 174/268 (64%), Gaps = 9/268 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +YI  +  IPML + EE  LA+R ++  D+ AA +LV SHLR+VV IA GY GYGLP 
Sbjct: 16  LDQYIAAVNSIPMLSQDEEQALARRLQQDNDVEAARQLVMSHLRVVVSIARGYAGYGLPQ 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AVK+F+PERG RL ++++ WIKA + E+ILR+W LV++ TT  Q++L
Sbjct: 76  ADLIQEGNIGLMKAVKRFEPERGVRLFSFAIHWIKAEIHEFILRNWRLVRVATTKPQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR +K    A++D   +      IA  L V   EV  M  R++G + ++ L   +++
Sbjct: 136 FFNLRSMKQGFSALSDTEAR-----QIADDLGVKPEEVREMETRMSG-QDISLLAEDNEE 189

Query: 196 NSSQWQDWLVYDH-DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-PV 253
                 DWL     +  +Q+ ++  ER  R   + +++  L+PR RRI EAR L ++  +
Sbjct: 190 EGFAPIDWLADTRSEPTKQLEMQAYERLQREG-IEQALQALDPRSRRIIEARWLADDGGL 248

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TL +L++EF VS ER+RQIE +A KK++
Sbjct: 249 TLHDLAAEFGVSAERIRQIEVKALKKMK 276


>gi|206559184|ref|YP_002229944.1| RNA polymerase factor sigma-32 [Burkholderia cenocepacia J2315]
 gi|198035221|emb|CAR51095.1| RNA polymerase sigma-32 factor [Burkholderia cenocepacia J2315]
          Length = 311

 Score =  214 bits (546), Expect = 9e-54,   Method: Compositional matrix adjust.
 Identities = 117/283 (41%), Positives = 177/283 (62%), Gaps = 13/283 (4%)

Query: 9   IVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++ G++G +  YI  + +IP+L  +EE   A  +R+  +L AA RLV SHLRLVV IA  
Sbjct: 31  MLPGQLGNIDAYIQAVNRIPLLTAEEERRYATEFRDDNNLDAARRLVLSHLRLVVSIARN 90

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y GYGLP  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W +VK+ 
Sbjct: 91  YLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKVA 150

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESL 186
           TT  Q++LFFNLR  K  +QA+T     PE++  +A++LNV   EV  M  RL+ GD +L
Sbjct: 151 TTKAQRKLFFNLRSHKKSMQAMT-----PEEIDGLAQELNVKREEVTEMETRLSGGDIAL 205

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              +   +++ +    +L   H+    VL  ++    + + + +++  L+ R RRI EAR
Sbjct: 206 EGQVEDGEESYAPIA-YLADSHNEPTAVLAARQRDMLQTDGIAQALDALDARSRRIIEAR 264

Query: 247 RLQ-----ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L          TL +L++EF VS ER+RQIEA A KK++ ++
Sbjct: 265 WLHVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRTAL 307


>gi|21244548|ref|NP_644130.1| RNA polymerase factor sigma-32 [Xanthomonas axonopodis pv. citri
           str. 306]
 gi|21110222|gb|AAM38666.1| RNA polymerase sigma-32 factor [Xanthomonas axonopodis pv. citri
           str. 306]
          Length = 291

 Score =  214 bits (546), Expect = 9e-54,   Method: Compositional matrix adjust.
 Identities = 119/272 (43%), Positives = 170/272 (62%), Gaps = 14/272 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + +IP+L   EE  LA+R+R+  DL AA  LV SHLR VV +A GY GYGLP+
Sbjct: 23  LDAYIGAVHQIPVLSVDEEQDLARRFRDELDLDAARELVHSHLRFVVHVARGYNGYGLPL 82

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AVK+FDP+ G RL ++++ WI+A M E+IL++W +VK+ TT  Q++L
Sbjct: 83  GDLIQEGNIGLMKAVKRFDPDMGVRLVSFAVHWIRAEMHEFILKNWRIVKVATTKAQRKL 142

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR+ K  L       L   +V A+AK LNVSE EV+ M  RL+G D   +A   SSD
Sbjct: 143 FFNLRKSKTRL-----GWLNASEVTAVAKDLNVSEREVMEMESRLSGRDIGFDA---SSD 194

Query: 195 KNSSQWQ----DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ- 249
           ++          +LV + +   Q     +   N+  +L   M+ L+ R R I + R L  
Sbjct: 195 EDDDHGPPSPVSYLVANEEDPSQAYERHDSEDNQLQLLREGMAGLDARSRDIVKRRWLDS 254

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++ VTL+ L+ E+ VS ER+RQIEA A KK++
Sbjct: 255 DSKVTLQELADEYGVSAERIRQIEANALKKMK 286


>gi|261380105|ref|ZP_05984678.1| alternative sigma factor RpoH [Neisseria subflava NJ9703]
 gi|284797325|gb|EFC52672.1| alternative sigma factor RpoH [Neisseria subflava NJ9703]
          Length = 287

 Score =  214 bits (546), Expect = 9e-54,   Method: Compositional matrix adjust.
 Identities = 119/286 (41%), Positives = 186/286 (65%), Gaps = 9/286 (3%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           + +I +G   L +YIH +  IPML  +EE  LA+R ++ GDL+AA +L+ SHLR+VV IA
Sbjct: 7   LPVIHSGNGSLEQYIHTVNSIPMLTAEEETQLAER-QQKGDLNAAKQLILSHLRVVVSIA 65

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+ILR+W LV+
Sbjct: 66  RGYDGYGLNQADLIQEGNIGLMKAVKRYEPSRGARLFSFAVHWIKAEIHEFILRNWRLVR 125

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           + TT  Q++LFFNLR ++ +L     N L P++   IA  L V  SEV+ M  R+ G + 
Sbjct: 126 VATTKPQRKLFFNLRSMRKNL-----NALSPKEAQEIADDLGVKLSEVLEMEQRMTGHDI 180

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFE 244
                N+ D+++    DWL  DHD +    + K+     +   L  +++ L+ R RRI E
Sbjct: 181 GIMAENNDDEDNFAPIDWLA-DHDAEPSRQLSKQAHYALQTEGLQNALAQLDDRSRRIVE 239

Query: 245 ARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           +R LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 240 SRWLQDDGGLTLHELAAEYGVSAERIRQIEAKAMQKLRGFLAEEAE 285


>gi|241758558|ref|ZP_04756675.1| alternative sigma factor RpoH [Neisseria flavescens SK114]
 gi|241321301|gb|EER57461.1| alternative sigma factor RpoH [Neisseria flavescens SK114]
          Length = 287

 Score =  214 bits (546), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 119/286 (41%), Positives = 186/286 (65%), Gaps = 9/286 (3%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           + +I +G   L +YIH +  IPML  +EE  LA+R ++ GDL+AA +L+ SHLR+VV IA
Sbjct: 7   LPVIHSGNGSLEQYIHTVNSIPMLTAEEETQLAER-QQKGDLNAAKQLILSHLRVVVSIA 65

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+ILR+W LV+
Sbjct: 66  RGYDGYGLNQADLIQEGNIGLMKAVKRYEPSRGARLFSFAVHWIKAEIHEFILRNWRLVR 125

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           + TT  Q++LFFNLR ++ +L     N L P++   IA  L V  SEV+ M  R+ G + 
Sbjct: 126 VATTKPQRKLFFNLRSMRKNL-----NALSPKEAQEIANDLGVKLSEVLEMEQRMTGHDI 180

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFE 244
                N+ D+++    DWL  DHD +    + K+     +   L  +++ L+ R RRI E
Sbjct: 181 GIMAENNDDEDNFAPIDWLA-DHDAEPSRQLSKQAHYALQTEGLQNALAQLDDRSRRIVE 239

Query: 245 ARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           +R LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 240 SRWLQDDGGLTLHELAAEYGVSAERIRQIEAKAMQKLRGFLAEEAE 285


>gi|319945291|ref|ZP_08019553.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Lautropia
           mirabilis ATCC 51599]
 gi|319741861|gb|EFV94286.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Lautropia
           mirabilis ATCC 51599]
          Length = 298

 Score =  214 bits (546), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 114/275 (41%), Positives = 176/275 (64%), Gaps = 12/275 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + ++PML  +EE  LA+R++EH D+ AA  LVTSHLRLVV +A  Y GYGLP 
Sbjct: 26  LDAYISAVNRMPMLSAEEESSLARRFKEHQDVDAARTLVTSHLRLVVSVARQYLGYGLPH 85

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AVK+FDP+R  RL ++++ WIKA + EYIL++W LVK+ TT  Q++L
Sbjct: 86  ADLIQEGNIGLMKAVKRFDPDRSVRLVSFALHWIKAEIHEYILKNWRLVKVATTKAQRKL 145

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR +K  L  +T     PE V  IA++LNV E +V  M  R+ G E +       D+
Sbjct: 146 FFNLRSMKKDLDTLT-----PEAVTDIAEQLNVREKDVTEMETRMTGHE-IALEPQGDDE 199

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKN--RRNMLTRSMSVLNPRERRIFEARRLQE--- 250
             + +         G E   I ++ +++  +   L+ +++ L+ R R I ++R L++   
Sbjct: 200 EGAGFGPAAYLAAPGSEPTEIIEDRQRDWLQTEGLSNALATLDERSRNIVQSRWLRDEDE 259

Query: 251 -NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
               TL++L++E+ VS ER+RQIEA+A KK++ ++
Sbjct: 260 GGSRTLQDLANEYGVSAERIRQIEAQAMKKMKAAL 294


>gi|78049505|ref|YP_365680.1| RNA polymerase factor sigma-32 [Xanthomonas campestris pv.
           vesicatoria str. 85-10]
 gi|294626531|ref|ZP_06705130.1| RNA polymerase sigma factor [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 11122]
 gi|294665098|ref|ZP_06730402.1| RNA polymerase sigma factor [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 10535]
 gi|78037935|emb|CAJ25680.1| RNA polymerase sigma-32 factor [Xanthomonas campestris pv.
           vesicatoria str. 85-10]
 gi|292599221|gb|EFF43359.1| RNA polymerase sigma factor [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 11122]
 gi|292605140|gb|EFF48487.1| RNA polymerase sigma factor [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 10535]
          Length = 294

 Score =  214 bits (546), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 119/272 (43%), Positives = 170/272 (62%), Gaps = 14/272 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + +IP+L   EE  LA+R+R+  DL AA  LV SHLR VV +A GY GYGLP+
Sbjct: 26  LDAYIGAVHQIPVLSVDEEQDLARRFRDELDLDAARELVHSHLRFVVHVARGYNGYGLPL 85

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AVK+FDP+ G RL ++++ WI+A M E+IL++W +VK+ TT  Q++L
Sbjct: 86  GDLIQEGNIGLMKAVKRFDPDMGVRLVSFAVHWIRAEMHEFILKNWRIVKVATTKAQRKL 145

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR+ K  L       L   +V A+AK LNVSE EV+ M  RL+G D   +A   SSD
Sbjct: 146 FFNLRKSKTRL-----GWLNASEVTAVAKDLNVSEREVMEMESRLSGRDIGFDA---SSD 197

Query: 195 KNSSQWQ----DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ- 249
           ++          +LV + +   Q     +   N+  +L   M+ L+ R R I + R L  
Sbjct: 198 EDDDHGPPSPVSYLVANEEDPSQAYERHDSEDNQLQLLREGMAGLDARSRDIVKRRWLDS 257

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++ VTL+ L+ E+ VS ER+RQIEA A KK++
Sbjct: 258 DSKVTLQELADEYGVSAERIRQIEANALKKMK 289


>gi|253997181|ref|YP_003049245.1| RNA polymerase sigma-32 subunit RpoH [Methylotenera mobilis JLW8]
 gi|253983860|gb|ACT48718.1| RNA polymerase, sigma 32 subunit, RpoH [Methylotenera mobilis JLW8]
          Length = 285

 Score =  214 bits (545), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 118/277 (42%), Positives = 171/277 (61%), Gaps = 11/277 (3%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           ++     L +Y   I+  P+L  +EE  LA R+++  DL AA +L+ SHLRLV  IA GY
Sbjct: 9   VLTAADSLDQYTRAIKAYPILSAEEELTLANRFKKENDLEAARQLIVSHLRLVASIARGY 68

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGLP ++++ EGNIGLM+AVK+FDPERG RL +++M WIKA + EYI+R+W LVKI T
Sbjct: 69  MGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAMHWIKAEIHEYIVRNWRLVKIAT 128

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           T  Q++LFFNLR +K  +     N ++  ++  IA++LNV   EV+ M  RL G E   +
Sbjct: 129 TKAQRKLFFNLRSMKTGI-----NTMQTSEIDHIARELNVKPEEVLEMESRLNGHEI--S 181

Query: 189 LINSSDKNSSQWQDWLVYDHD---GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L ++ D +S +    + Y  D      + L  K+        L  +++ L+ R RR+ EA
Sbjct: 182 LESNIDDDSEEHYSPIAYLQDESLTPPEALEAKQFEMAETTGLASALNHLDERSRRVVEA 241

Query: 246 RRLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R LQE+   TL  L+ EF VS ER+RQIE +A  K++
Sbjct: 242 RWLQEDASKTLHELADEFGVSAERIRQIEQKAMLKMK 278


>gi|254503566|ref|ZP_05115717.1| RNA polymerase sigma factor, sigma-70 family [Labrenzia alexandrii
           DFL-11]
 gi|222439637|gb|EEE46316.1| RNA polymerase sigma factor, sigma-70 family [Labrenzia alexandrii
           DFL-11]
          Length = 287

 Score =  214 bits (545), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 108/265 (40%), Positives = 178/265 (67%), Gaps = 9/265 (3%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K P L ++EE  LA ++R++ D  A  +L  SH+RLV+ +A  ++ +GL I +++ EG++
Sbjct: 13  KAPYLTREEELELAIQWRDNKDEKALEKLSLSHMRLVIAVASRFKNFGLNIGDLIQEGHV 72

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT+++QK LFFNLRRL+ 
Sbjct: 73  GLLEAAARFEPEREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSSQKALFFNLRRLRA 132

Query: 145 HLQA----ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQ 199
            L +    +TD+ L  +    IA  + V +S+V  MN RL+G D SLNA +  ++ +S+ 
Sbjct: 133 KLSSNQTPLTDSELHQK----IADAIGVKQSDVAVMNARLSGPDTSLNAPVTDTEGSSAD 188

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
            QD+LV D    ++++ E  + + R   L  ++ VL+ RE +I   RRL E+  TLE+L 
Sbjct: 189 RQDFLVSDAPQPDEIVTENIDAERRNTWLASALDVLSERELKIVRERRLSEDGATLESLG 248

Query: 260 SEFEVSRERVRQIEARAFKKVQESI 284
            +  +S+ERVRQIE+RA +K++ ++
Sbjct: 249 KKLGISKERVRQIESRALQKLKSAL 273


>gi|110635708|ref|YP_675916.1| RNA polymerase factor sigma-32 [Mesorhizobium sp. BNC1]
 gi|110286692|gb|ABG64751.1| RNA polymerase, sigma 32 subunit, RpoH [Chelativorans sp. BNC1]
          Length = 284

 Score =  214 bits (545), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 110/271 (40%), Positives = 174/271 (64%), Gaps = 1/271 (0%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + I    K P L ++EE+ LA +++E  D  A HR++ +H+RLV+ +A  +R +GL +S+
Sbjct: 8   KLIKAAMKAPYLGREEEHELALQWKERQDQQALHRMIMAHMRLVIAMAGKFRNFGLSMSD 67

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EG++GL++A  +FDPER  R +TY+ WWI+A+MQ+YILR+WS+V+ GT++ QK LFF
Sbjct: 68  LIQEGHVGLLEAAARFDPEREVRFSTYATWWIRASMQDYILRNWSIVRGGTSSAQKALFF 127

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSSDKN 196
           NLRRL+  LQ         +    +A+ L VSES+V  M+ RL A D SLNA + S    
Sbjct: 128 NLRRLRMKLQKAGGTTPSEDVYREVAQALRVSESDVAMMDSRLAAADASLNAPLRSDSDP 187

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           +S+  D+L+ D    ++++ E  + + +   L +++  LN RE  I   RRL E   TLE
Sbjct: 188 TSERIDFLICDKPQPDELVREAIDGERKAQWLHQALGTLNGRELTIVRERRLSEEGATLE 247

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            L +   +S+ERVRQIE+RA +K++ ++ K 
Sbjct: 248 ALGASLGISKERVRQIESRALEKLRTALVKH 278


>gi|319639187|ref|ZP_07993938.1| RNA polymerase sigma-32 factor [Neisseria mucosa C102]
 gi|317399371|gb|EFV80041.1| RNA polymerase sigma-32 factor [Neisseria mucosa C102]
          Length = 287

 Score =  214 bits (545), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 119/286 (41%), Positives = 186/286 (65%), Gaps = 9/286 (3%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           + +I +G   L +YIH +  IPML  +EE  LA+R ++ GDL+AA +L+ SHLR+VV IA
Sbjct: 7   LPVIHSGNGSLEQYIHTVNSIPMLTAEEETQLAER-QQKGDLNAAKQLILSHLRVVVSIA 65

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+ILR+W LV+
Sbjct: 66  RGYDGYGLNQADLIQEGNIGLMKAVKRYEPSRGARLFSFAVHWIKAEIHEFILRNWRLVR 125

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           + TT  Q++LFFNLR ++ +L A     L P++   IA  L V  SEV+ M  R+ G + 
Sbjct: 126 VATTKPQRKLFFNLRSMRKNLSA-----LSPKEAQEIADDLGVKLSEVLEMEQRMTGHDI 180

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFE 244
                N+ D+++    DWL  DHD +    + K+     +   L  +++ L+ R RRI E
Sbjct: 181 GIMAENNDDEDNFAPIDWLA-DHDAEPSRQLSKQAHYALQTEGLQNALAQLDDRSRRIVE 239

Query: 245 ARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           +R LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 240 SRWLQDDGGLTLHELAAEYGVSAERIRQIEAKAMQKLRGFLAEEAE 285


>gi|84625707|ref|YP_453079.1| RNA polymerase factor sigma-32 [Xanthomonas oryzae pv. oryzae MAFF
           311018]
 gi|289664834|ref|ZP_06486415.1| RNA polymerase factor sigma-32 [Xanthomonas campestris pv.
           vasculorum NCPPB702]
 gi|289671390|ref|ZP_06492465.1| RNA polymerase factor sigma-32 [Xanthomonas campestris pv.
           musacearum NCPPB4381]
 gi|84369647|dbj|BAE70805.1| RNA polymerase sigma-32 factor [Xanthomonas oryzae pv. oryzae MAFF
           311018]
          Length = 291

 Score =  214 bits (545), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 119/272 (43%), Positives = 170/272 (62%), Gaps = 14/272 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + +IP+L   EE  LA+R+R+  DL AA  LV SHLR VV +A GY GYGLP+
Sbjct: 23  LDAYIGAVHQIPVLSVDEEQNLARRFRDELDLDAARELVHSHLRFVVHVARGYNGYGLPL 82

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AVK+FDP+ G RL ++++ WI+A M E+IL++W +VK+ TT  Q++L
Sbjct: 83  GDLIQEGNIGLMKAVKRFDPDMGVRLVSFAVHWIRAEMHEFILKNWRIVKVATTKAQRKL 142

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR+ K  L       L   +V A+AK LNVSE EV+ M  RL+G D   +A   SSD
Sbjct: 143 FFNLRKSKTRL-----GWLNASEVTAVAKDLNVSEREVMEMESRLSGRDIGFDA---SSD 194

Query: 195 KNSSQWQ----DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ- 249
           ++          +LV + +   Q     +   N+  +L   M+ L+ R R I + R L  
Sbjct: 195 EDDDHGPPSPVSYLVANEEDPSQAYERHDSEDNQLQLLREGMAGLDTRSRDIVKRRWLDS 254

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++ VTL+ L+ E+ VS ER+RQIEA A KK++
Sbjct: 255 DSKVTLQELADEYGVSAERIRQIEANALKKMK 286


>gi|325928799|ref|ZP_08189966.1| RNA polymerase, sigma 32 subunit, RpoH [Xanthomonas perforans
           91-118]
 gi|325540772|gb|EGD12347.1| RNA polymerase, sigma 32 subunit, RpoH [Xanthomonas perforans
           91-118]
          Length = 282

 Score =  214 bits (545), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 119/272 (43%), Positives = 170/272 (62%), Gaps = 14/272 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + +IP+L   EE  LA+R+R+  DL AA  LV SHLR VV +A GY GYGLP+
Sbjct: 14  LDAYIGAVHQIPVLSVDEEQDLARRFRDELDLDAARELVHSHLRFVVHVARGYNGYGLPL 73

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AVK+FDP+ G RL ++++ WI+A M E+IL++W +VK+ TT  Q++L
Sbjct: 74  GDLIQEGNIGLMKAVKRFDPDMGVRLVSFAVHWIRAEMHEFILKNWRIVKVATTKAQRKL 133

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR+ K  L       L   +V A+AK LNVSE EV+ M  RL+G D   +A   SSD
Sbjct: 134 FFNLRKSKTRL-----GWLNASEVTAVAKDLNVSEREVMEMESRLSGRDIGFDA---SSD 185

Query: 195 KNSSQWQ----DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ- 249
           ++          +LV + +   Q     +   N+  +L   M+ L+ R R I + R L  
Sbjct: 186 EDDDHGPPSPVSYLVANEEDPSQAYERHDSEDNQLQLLREGMAGLDARSRDIVKRRWLDS 245

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++ VTL+ L+ E+ VS ER+RQIEA A KK++
Sbjct: 246 DSKVTLQELADEYGVSAERIRQIEANALKKMK 277


>gi|153003975|ref|YP_001378300.1| RNA polymerase sigma-70 [Anaeromyxobacter sp. Fw109-5]
 gi|152027548|gb|ABS25316.1| RNA polymerase sigma-70 [Anaeromyxobacter sp. Fw109-5]
          Length = 299

 Score =  214 bits (545), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 122/276 (44%), Positives = 179/276 (64%), Gaps = 11/276 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ +L  +EE  LA+ +R+ G   AAH+LV ++LR VVK+A  YR YGL +
Sbjct: 11  LDQYLREINKVALLTVEEERRLAREFRDEGKTRAAHKLVEANLRFVVKVAFEYRSYGLRM 70

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AV+KFDP++  RL +Y++WWI+A +Q +IL+SWSLVKIGTT  Q++L
Sbjct: 71  ADLIQEGNIGLMKAVQKFDPDKEIRLISYAVWWIRAYIQNHILKSWSLVKIGTTQAQRKL 130

Query: 136 FFNLRRLKGHLQAITDN-NLKPE--QVVAIAKKLNVSESEVISMNCRLAG-DESLNALIN 191
           FF+L R +  ++ +T    L  E   V  +AKKL V  S+V+ M  R+ G D SL+A + 
Sbjct: 131 FFSLARTRHEIERVTPGAGLDSEGIDVNLVAKKLRVRASDVVEMQQRMEGRDLSLDAPV- 189

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERK--NRRNMLTRSMSVLNPRERRIFEARRLQ 249
            +D  S+  + +   D D Q+  L   EE    NRR  +  +MS L+PRER I EAR + 
Sbjct: 190 -ADGTSTHLE-FTPSDADPQDDELARAEEDAIVNRR--VNDAMSRLDPRERHIVEARIMG 245

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           +   TL +L   F  SRER RQ+E RA +K++  +Q
Sbjct: 246 DGKETLRDLGQHFGFSRERARQLEIRALEKLRRELQ 281


>gi|167835356|ref|ZP_02462239.1| RNA polymerase factor sigma-32 [Burkholderia thailandensis MSMB43]
          Length = 311

 Score =  214 bits (545), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 118/283 (41%), Positives = 176/283 (62%), Gaps = 13/283 (4%)

Query: 9   IVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++ G++G +  YI  + ++P+L  +EE   A  YRE  +L AA +LV SHLRLVV +A  
Sbjct: 31  MLPGQLGNIDAYIQAVNRVPLLTAEEERQYATEYREQNNLDAARQLVLSHLRLVVSVARN 90

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y GYGLP  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W +VK+ 
Sbjct: 91  YLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKVA 150

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESL 186
           TT  Q++LFFNLR  K   QA T     PE++  +A++LNV   EV  M  RL+ GD +L
Sbjct: 151 TTKAQRKLFFNLRSHKKGTQAFT-----PEEIDGLAQELNVKREEVAEMETRLSGGDIAL 205

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              I+  +++ +    +L   H+    VL  ++    + + + R++  L+ R RRI EAR
Sbjct: 206 EGQIDDGEESYAPIA-YLADSHNEPTAVLAARQRDMLQTDGIARALESLDARSRRIIEAR 264

Query: 247 RLQ-----ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L          TL +L++EF VS ER+RQIEA A KK++ ++
Sbjct: 265 WLNVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRTAL 307


>gi|58583919|ref|YP_202935.1| RNA polymerase factor sigma-32 [Xanthomonas oryzae pv. oryzae
           KACC10331]
 gi|58428513|gb|AAW77550.1| RNA polymerase sigma-32 factor [Xanthomonas oryzae pv. oryzae
           KACC10331]
          Length = 329

 Score =  214 bits (545), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 119/272 (43%), Positives = 170/272 (62%), Gaps = 14/272 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + +IP+L   EE  LA+R+R+  DL AA  LV SHLR VV +A GY GYGLP+
Sbjct: 61  LDAYIGAVHQIPVLSVDEEQNLARRFRDELDLDAARELVHSHLRFVVHVARGYNGYGLPL 120

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AVK+FDP+ G RL ++++ WI+A M E+IL++W +VK+ TT  Q++L
Sbjct: 121 GDLIQEGNIGLMKAVKRFDPDMGVRLVSFAVHWIRAEMHEFILKNWRIVKVATTKAQRKL 180

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR+ K  L       L   +V A+AK LNVSE EV+ M  RL+G D   +A   SSD
Sbjct: 181 FFNLRKSKTRL-----GWLNASEVTAVAKDLNVSEREVMEMESRLSGRDIGFDA---SSD 232

Query: 195 KNSSQWQ----DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ- 249
           ++          +LV + +   Q     +   N+  +L   M+ L+ R R I + R L  
Sbjct: 233 EDDDHGPPSPVSYLVANEEDPSQAYERHDSEDNQLQLLREGMAGLDTRSRDIVKRRWLDS 292

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++ VTL+ L+ E+ VS ER+RQIEA A KK++
Sbjct: 293 DSKVTLQELADEYGVSAERIRQIEANALKKMK 324


>gi|115378280|ref|ZP_01465448.1| RNA polymerase sigma-B factor [Stigmatella aurantiaca DW4/3-1]
 gi|310821082|ref|YP_003953440.1| RNA polymerase sigma-b factor [Stigmatella aurantiaca DW4/3-1]
 gi|401024|sp|Q01624|RPSB_STIAD RecName: Full=RNA polymerase sigma-B factor
 gi|46680|emb|CAA78693.1| sigma factor (SigB) [Stigmatella aurantiaca DW4/3-1]
 gi|115364722|gb|EAU63789.1| RNA polymerase sigma-B factor [Stigmatella aurantiaca DW4/3-1]
 gi|309394154|gb|ADO71613.1| RNA polymerase sigma-B factor [Stigmatella aurantiaca DW4/3-1]
          Length = 296

 Score =  214 bits (545), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 117/262 (44%), Positives = 168/262 (64%), Gaps = 4/262 (1%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+ EI +  +L  +EE  LA+++ + GDL+A HRLVTS+LR VVK++  YR YG+ +
Sbjct: 14  LTMYLSEINQYGLLSVEEEQALARKFVK-GDLAAGHRLVTSNLRFVVKVSYEYRSYGIKM 72

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           S+++ EGNIGLM+AV+KFDP++G RL +Y++WWI+A +Q YIL+SWSLVK+GTT  Q++L
Sbjct: 73  SDLIQEGNIGLMKAVQKFDPDKGIRLISYAVWWIRAYIQNYILKSWSLVKLGTTQAQRKL 132

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FF+L R +  L+     +     V  IA KLNV  SEV  M  R+ G D SL+A +    
Sbjct: 133 FFSLARTRRELEKFGAGDGAVVNVDEIANKLNVKASEVREMEQRMGGRDLSLDAPMGEDG 192

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
            NS    D++      Q+    +KEE     + +  ++  L+PRER I E R + E P+T
Sbjct: 193 GNSH--VDFVASAAAPQDDEFADKEEAGLINSRVHMALMRLDPRERFIIEQRVMNERPMT 250

Query: 255 LENLSSEFEVSRERVRQIEARA 276
           L+ L   F  SRER RQ+E RA
Sbjct: 251 LKELGEHFGFSRERARQLEIRA 272


>gi|188574757|ref|YP_001911686.1| RNA polymerase factor sigma-32 [Xanthomonas oryzae pv. oryzae
           PXO99A]
 gi|188519209|gb|ACD57154.1| alternative sigma factor RpoH [Xanthomonas oryzae pv. oryzae
           PXO99A]
          Length = 282

 Score =  214 bits (545), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 119/272 (43%), Positives = 170/272 (62%), Gaps = 14/272 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + +IP+L   EE  LA+R+R+  DL AA  LV SHLR VV +A GY GYGLP+
Sbjct: 14  LDAYIGAVHQIPVLSVDEEQNLARRFRDELDLDAARELVHSHLRFVVHVARGYNGYGLPL 73

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AVK+FDP+ G RL ++++ WI+A M E+IL++W +VK+ TT  Q++L
Sbjct: 74  GDLIQEGNIGLMKAVKRFDPDMGVRLVSFAVHWIRAEMHEFILKNWRIVKVATTKAQRKL 133

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR+ K  L       L   +V A+AK LNVSE EV+ M  RL+G D   +A   SSD
Sbjct: 134 FFNLRKSKTRL-----GWLNASEVTAVAKDLNVSEREVMEMESRLSGRDIGFDA---SSD 185

Query: 195 KNSSQWQ----DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ- 249
           ++          +LV + +   Q     +   N+  +L   M+ L+ R R I + R L  
Sbjct: 186 EDDDHGPPSPVSYLVANEEDPSQAYERHDSEDNQLQLLREGMAGLDTRSRDIVKRRWLDS 245

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++ VTL+ L+ E+ VS ER+RQIEA A KK++
Sbjct: 246 DSKVTLQELADEYGVSAERIRQIEANALKKMK 277


>gi|212637488|ref|YP_002314013.1| RNA polymerase factor sigma-32 [Shewanella piezotolerans WP3]
 gi|212558972|gb|ACJ31426.1| RNA polymerase sigma-32 factor [Shewanella piezotolerans WP3]
          Length = 285

 Score =  214 bits (544), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 114/281 (40%), Positives = 177/281 (62%), Gaps = 9/281 (3%)

Query: 4   KNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           + M+++V    G L  YIH    I ML+ ++E+ LAKR +E GDLSAA  L+ SHLR VV
Sbjct: 6   QTMALMVPQSSGSLESYIHSAHSISMLDAEKEHELAKRLQETGDLSAAKELIMSHLRFVV 65

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A GY GYGLP ++++ EGNIGLM+AVK+FDP+ G RL ++++ WIKA + EY+L++W 
Sbjct: 66  HVAKGYSGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYVLKNWR 125

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L   +DN     +V  +A+ L VS+++V  M  R+A 
Sbjct: 126 IVKVATTKAQRKLFFNLRKTKKRLGWFSDN-----EVGMVAESLGVSKADVTEMESRMAA 180

Query: 183 DESLNALINSSDKNSSQWQDWLVYDH--DGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            +    L + +D          + DH  D   QV  +  E+ N+  +L+ ++  L+ R +
Sbjct: 181 QDPAFDLASDNDDEQDYAPMHYLEDHSSDLASQVENDNWEQSNQTRLLS-AIKTLDERSQ 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            I +AR L E+  TL+ L++ ++VS ER+RQ+E  A  K++
Sbjct: 240 HILQARWLNEDKTTLQELAATYQVSAERIRQLEKNAMNKLK 280


>gi|86359605|ref|YP_471497.1| RNA polymerase factor sigma-32 [Rhizobium etli CFN 42]
 gi|86283707|gb|ABC92770.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CFN
           42]
          Length = 287

 Score =  214 bits (544), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 115/263 (43%), Positives = 175/263 (66%), Gaps = 9/263 (3%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L +QEE+ LA R+++H D  A +++  +H+RLV+ +A  +R +GLP+S++V EG +GL
Sbjct: 18  PYLARQEEHDLATRWKDHDDRGARNQIAMAHMRLVISMAGKFRNFGLPMSDLVQEGYVGL 77

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 78  LEAAARFEPERDVRFSTYASWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRAKL 137

Query: 147 QAITDNNLKPEQV-VAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWL 204
            A  D  L  + +   IA  L VS ++V +M+ RL+G D SL A   S D  S++  D+L
Sbjct: 138 -ARGDTQLTLQSIHQEIAAALGVSLADVQTMDARLSGNDASLQAPSVSGDAESAEKMDFL 196

Query: 205 VYDH---DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           V D    D Q   +I+ E    RR  L  ++  LN RE +I  ARRL E+  TLE L ++
Sbjct: 197 VSDDPLPDEQVSNMIDGE---RRRVWLASALKHLNEREMKIISARRLAEDGATLEELGAD 253

Query: 262 FEVSRERVRQIEARAFKKVQESI 284
             +S+ERVRQIE+RA +K++ ++
Sbjct: 254 LGISKERVRQIESRAMEKLRSAL 276


>gi|190893879|ref|YP_001980421.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CIAT
           652]
 gi|190699158|gb|ACE93243.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CIAT
           652]
          Length = 287

 Score =  214 bits (544), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 115/263 (43%), Positives = 175/263 (66%), Gaps = 9/263 (3%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L +QEE+ LA R+++H D  A +++  +H+RLV+ +A  +R +GLP+S++V EG +GL
Sbjct: 18  PYLARQEEHDLATRWKDHDDRGARNQIAMAHMRLVISMAGKFRNFGLPMSDLVQEGYVGL 77

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 78  LEAAARFEPERDVRFSTYASWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRAKL 137

Query: 147 QAITDNNLKPEQV-VAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWL 204
            A  D  L  + +   IA  L VS ++V +M+ RL+G D SL A   S D  S++  D+L
Sbjct: 138 -AKGDTQLTLQSIHQEIAAALGVSLADVQTMDARLSGNDASLQAPSVSGDAESAEKMDFL 196

Query: 205 VYDH---DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           V D    D Q   +I+ E    RR  L  ++  LN RE +I  ARRL E+  TLE L ++
Sbjct: 197 VSDDPLPDEQVSNMIDGE---RRRIWLASALKHLNEREMKIISARRLAEDGATLEELGAD 253

Query: 262 FEVSRERVRQIEARAFKKVQESI 284
             +S+ERVRQIE+RA +K++ ++
Sbjct: 254 LGISKERVRQIESRAMEKLRTAL 276


>gi|82703854|ref|YP_413420.1| RNA polymerase factor sigma-32 [Nitrosospira multiformis ATCC
           25196]
 gi|82411919|gb|ABB76028.1| RNA polymerase, sigma 32 subunit, RpoH [Nitrosospira multiformis
           ATCC 25196]
          Length = 281

 Score =  214 bits (544), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 121/280 (43%), Positives = 174/280 (62%), Gaps = 12/280 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
             ++ V     L  YI  + +  +L ++EE  LA+  R+ G + AA +LV SHLRLVV I
Sbjct: 2   TFALTVPSAGSLENYIQSVNQFRILTQEEELQLARSLRDEGSIDAARQLVLSHLRLVVAI 61

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A GY+GYGLP ++++ EGNIGLM+AVK+FDPERG RL ++++ WIKA + E+ILR+W LV
Sbjct: 62  ARGYKGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEFILRNWRLV 121

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-D 183
           KI TT  Q++LFFNLR LK  L     + +  ++V  +A++L V   EV+ M  R +G D
Sbjct: 122 KIATTKAQRKLFFNLRSLKQAL-----DTMSQKEVAEVAEQLGVKPEEVVEMETRFSGRD 176

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQE--QVLIEKEERKNRRNMLTRSMSVLNPRERR 241
            SL  L    D+ +      + Y  DG E   VL +++  + R   L +++  L+ R R 
Sbjct: 177 ISLEPLSEDDDEETFS---PIAYLTDGSEPSHVLEDEQTMRLRGEGLEQALESLDARSRH 233

Query: 242 IFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           I EAR L+E +  TL  L+ E  VS ERVRQIEA+A +K+
Sbjct: 234 IIEARWLREKDTATLHELADELGVSAERVRQIEAKAMQKL 273


>gi|312797371|ref|YP_004030293.1| RNA polymerase sigma-32 factor [Burkholderia rhizoxinica HKI 454]
 gi|312169146|emb|CBW76149.1| RNA polymerase sigma-32 factor [Burkholderia rhizoxinica HKI 454]
          Length = 319

 Score =  214 bits (544), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 123/288 (42%), Positives = 175/288 (60%), Gaps = 19/288 (6%)

Query: 9   IVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++ G +G L  YI  + +IP+L + +E  LA  YRE   L AA +LV SHLRLVV IA  
Sbjct: 39  MLPGTLGNLDAYIQAVNRIPLLSQADETRLAIEYREQNKLDAARQLVLSHLRLVVSIARN 98

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y GYGLP ++++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W +VK+ 
Sbjct: 99  YLGYGLPHADLIQEGNIGLMKAVKRFDPRQNVRLVSYAIHWIKAEIHEYILRNWRMVKVA 158

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESL 186
           TT  Q++LFFNLR  K  +QA T     P+++  +AK+LNV   EV  M  RLA GD +L
Sbjct: 159 TTKAQRKLFFNLRSHKQGMQAFT-----PDEIAGLAKELNVKREEVTEMETRLAGGDIAL 213

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQ---VLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
                  +++ +     + Y  D + +   VL  ++    +   L  ++  L+ R RRI 
Sbjct: 214 EGQFEDGEESFAP----IAYLADSRTEPTTVLASRQRDLLQTEGLAEALESLDARSRRII 269

Query: 244 EARRLQ-----ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           EAR LQ         TL  L+ EF VS ER+RQIEA A KK++ ++Q+
Sbjct: 270 EARWLQVQDDGSGGATLHELADEFGVSAERIRQIEASAMKKMRSALQQ 317


>gi|221065333|ref|ZP_03541438.1| RNA polymerase, sigma 32 subunit, RpoH [Comamonas testosteroni
           KF-1]
 gi|220710356|gb|EED65724.1| RNA polymerase, sigma 32 subunit, RpoH [Comamonas testosteroni
           KF-1]
          Length = 324

 Score =  214 bits (544), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 119/284 (41%), Positives = 174/284 (61%), Gaps = 15/284 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + ++PML  +EE   A++ +EH DL AA RLV SHLRLVV I+  Y GYGLP 
Sbjct: 37  LDAYISAVNRMPMLTLEEEQDYARKLKEHNDLDAAGRLVMSHLRLVVSISRQYLGYGLPH 96

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM+AVK+FDP++G RL +Y+M WIKA + EYIL++W +VK+ TT  Q++L
Sbjct: 97  GDLIQEGNVGLMKAVKRFDPDQGVRLVSYAMHWIKAEIHEYILKNWRMVKVATTKAQRKL 156

Query: 136 FFNLRRLKGHLQ---AITDN------NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
           FFNLR +K  L+   A+ D+       L   ++ A+A KLNV   EVI M  RLAG + L
Sbjct: 157 FFNLRSMKHELKSDAAMADDELALRETLTSNEIDAVAAKLNVKREEVIEMETRLAGGDVL 216

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFEA 245
                S D   +      + D   +   ++E  +R +   + L  ++  L+ R RRI E 
Sbjct: 217 LDPSPSDDGEQAFGPIAYLADASHEPTAMLESRQRDHLATDGLVMALEGLDDRSRRIVEE 276

Query: 246 RRLQENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R L+ N      +TL  L++E+ VS ER+RQIE  A KK+++++
Sbjct: 277 RWLKVNDDGSGGMTLHELAAEYGVSAERIRQIEVAAMKKMKKAL 320


>gi|115352926|ref|YP_774765.1| RNA polymerase factor sigma-32 [Burkholderia ambifaria AMMD]
 gi|170701101|ref|ZP_02892077.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           IOP40-10]
 gi|172061774|ref|YP_001809426.1| RNA polymerase factor sigma-32 [Burkholderia ambifaria MC40-6]
 gi|115282914|gb|ABI88431.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           AMMD]
 gi|170134002|gb|EDT02354.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           IOP40-10]
 gi|171994291|gb|ACB65210.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           MC40-6]
          Length = 311

 Score =  214 bits (544), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 116/283 (40%), Positives = 178/283 (62%), Gaps = 13/283 (4%)

Query: 9   IVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++ G++G +  YI  + +IP+L  +EE   A  +RE  +L +A RLV SHLRLVV IA  
Sbjct: 31  MLPGQLGNIDAYIQAVNRIPLLTAEEERRYATEFREDNNLDSARRLVLSHLRLVVSIARN 90

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y GYGLP  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W +VK+ 
Sbjct: 91  YLGYGLPHGDLIQEGNIGLMKAVKRFDPTQNVRLVSYAIHWIKAEIHEYILRNWRMVKVA 150

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESL 186
           TT  Q++LFFNLR  K  +QA+T     PE++  +A++LNV   +V  M  RL+ GD +L
Sbjct: 151 TTKAQRKLFFNLRSHKKSMQAMT-----PEEIDGLAQELNVKREDVTEMETRLSGGDIAL 205

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              ++  +++ +    +L   H+    VL  ++    + + + +++  L+ R RRI EAR
Sbjct: 206 EGQVDDGEESYAPIA-YLADSHNEPSAVLAARQRDMLQTDGIAQALEALDARSRRIIEAR 264

Query: 247 RLQ-----ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L          TL +L++EF VS ER+RQIEA A KK++ ++
Sbjct: 265 WLNVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRTAL 307


>gi|166710450|ref|ZP_02241657.1| RNA polymerase factor sigma-32 [Xanthomonas oryzae pv. oryzicola
           BLS256]
          Length = 282

 Score =  214 bits (544), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 119/272 (43%), Positives = 169/272 (62%), Gaps = 14/272 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + +IP+L   EE  LA+R+R+  DL AA  LV SHLR VV +A GY GYGLP+
Sbjct: 14  LDAYIGAVHQIPVLSVDEEQNLARRFRDELDLDAARELVHSHLRFVVHVARGYNGYGLPL 73

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AVK+FDP+ G RL ++++ WI+A M E+IL++W +VK+ TT  Q++L
Sbjct: 74  GDLIQEGNIGLMKAVKRFDPDMGVRLVSFAVHWIRAEMHEFILKNWRIVKVATTKAQRKL 133

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR+ K  L       L   +V A+AK LNVSE EV+ M  RL+G D   +A   SSD
Sbjct: 134 FFNLRKSKTRL-----GWLNASEVTAVAKDLNVSEREVMEMESRLSGRDIGFDA---SSD 185

Query: 195 KNSSQWQ----DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ- 249
           ++          +LV + +   Q     +   N   +L   M+ L+ R R I + R L  
Sbjct: 186 EDDDHGPPSPVSYLVANEEDPSQAYERHDSEDNHLQLLREGMAGLDTRSRDIVKRRWLDS 245

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++ VTL+ L+ E+ VS ER+RQIEA A KK++
Sbjct: 246 DSKVTLQELADEYGVSAERIRQIEANALKKMK 277


>gi|153004710|ref|YP_001379035.1| RNA polymerase sigma factor RpoH [Anaeromyxobacter sp. Fw109-5]
 gi|152028283|gb|ABS26051.1| RNA polymerase sigma factor RpoH [Anaeromyxobacter sp. Fw109-5]
          Length = 307

 Score =  214 bits (544), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 115/274 (41%), Positives = 173/274 (63%), Gaps = 6/274 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ EI + P+L   EE  LA+ +R+ GD  AAHRLVT++LR VVK++  YR YG  +
Sbjct: 13  LELYLSEINRFPLLTVDEEQRLARLFRDEGDTRAAHRLVTANLRFVVKVSYEYRSYGFKM 72

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AV+KFDP++G RL +Y++WWI+A +Q YIL+SWSLVK+GTT  Q++L
Sbjct: 73  ADLIQEGNIGLMKAVQKFDPDKGIRLISYAVWWIRAYIQNYILKSWSLVKLGTTQAQRKL 132

Query: 136 FFNLRRLKGHLQAIT---DNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALIN 191
           FF+L R K  L  ++     +   +    IAKKL V  +EV  M  R+ G D SL+A + 
Sbjct: 133 FFSLARTKRELDKMSVEHGRDSDAQDKGKIAKKLRVKPAEVEEMEQRMDGRDLSLDAPMG 192

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             D       D++      Q+  L + EE++     +T +++ L+ RER I E R + + 
Sbjct: 193 --DDGGYSHIDFVAAKSAAQDDELSDAEEQQIVSAKVTAALARLDQRERYIIEQRVMSDR 250

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           P+TL+ L   F  SRER RQ+E RA +K+++ + 
Sbjct: 251 PLTLKELGEHFGFSRERARQLEIRAKEKLKQELH 284


>gi|171320177|ref|ZP_02909239.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           MEX-5]
 gi|171094591|gb|EDT39643.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           MEX-5]
          Length = 311

 Score =  213 bits (543), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 116/283 (40%), Positives = 178/283 (62%), Gaps = 13/283 (4%)

Query: 9   IVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++ G++G +  YI  + +IP+L  +EE   A  +RE  +L +A RLV SHLRLVV IA  
Sbjct: 31  MLPGQLGNIDAYIQAVNRIPLLTAEEERRYATEFREDNNLDSARRLVLSHLRLVVSIARN 90

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y GYGLP  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W +VK+ 
Sbjct: 91  YLGYGLPHGDLIQEGNIGLMKAVKRFDPTQNVRLVSYAIHWIKAEIHEYILRNWRMVKVA 150

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESL 186
           TT  Q++LFFNLR  K  +QA+T     PE++  +A++LNV   +V  M  RL+ GD +L
Sbjct: 151 TTKAQRKLFFNLRSHKKSMQAMT-----PEEIDGLAQELNVKREDVTEMETRLSGGDIAL 205

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              ++  +++ +    +L   H+    VL  ++    + + + +++  L+ R RRI EAR
Sbjct: 206 EGQVDDGEESYAPIA-YLADSHNEPSAVLAARQRDMLQTDGIAQALEALDARSRRIIEAR 264

Query: 247 RLQ-----ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L          TL +L++EF VS ER+RQIEA A KK++ ++
Sbjct: 265 WLNVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRTAL 307


>gi|167561467|ref|ZP_02354383.1| RNA polymerase factor sigma-32 [Burkholderia oklahomensis EO147]
 gi|167568698|ref|ZP_02361572.1| RNA polymerase factor sigma-32 [Burkholderia oklahomensis C6786]
          Length = 311

 Score =  213 bits (543), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 119/283 (42%), Positives = 176/283 (62%), Gaps = 13/283 (4%)

Query: 9   IVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++ G++G +  YI  + +IP+L  +EE   A  YR+  +L AA +LV SHLRLVV IA  
Sbjct: 31  MLPGQLGNIDAYIQAVNRIPLLTPEEERQYATEYRDGNNLDAARQLVLSHLRLVVSIARN 90

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y GYGLP  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W +VK+ 
Sbjct: 91  YLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKVA 150

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESL 186
           TT  Q++LFFNLR  K   QA T     PE++  +A++LNV   EV  M  RL+ GD +L
Sbjct: 151 TTKAQRKLFFNLRSHKKGTQAFT-----PEEIDGLAQELNVKREEVAEMETRLSGGDIAL 205

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              I+  +++ +    +L   H+    VL  ++    + + + R++  L+ R RRI EAR
Sbjct: 206 EGQIDDGEESYAPIA-YLADSHNEPTAVLAARQRDMLQTDGIARALESLDARSRRIIEAR 264

Query: 247 RLQ-----ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L          TL +L++EF VS ER+RQIEA A KK++ ++
Sbjct: 265 WLNVGDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRTAL 307


>gi|327191758|gb|EGE58760.1| RNA polymerase factor sigma-32 [Rhizobium etli CNPAF512]
          Length = 319

 Score =  213 bits (543), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 115/263 (43%), Positives = 175/263 (66%), Gaps = 9/263 (3%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L +QEE+ LA R+++H D  A +++  +H+RLV+ +A  +R +GLP+S++V EG +GL
Sbjct: 50  PYLARQEEHDLATRWKDHDDRGARNQIAMAHMRLVISMAGKFRNFGLPMSDLVQEGYVGL 109

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 110 LEAAARFEPERDVRFSTYASWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRAKL 169

Query: 147 QAITDNNLKPEQV-VAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWL 204
            A  D  L  + +   IA  L VS ++V +M+ RL+G D SL A   S D  S++  D+L
Sbjct: 170 -AKGDTQLTLQSIHQEIAAALGVSLADVQTMDARLSGNDASLQAPSVSGDAESAEKMDFL 228

Query: 205 VYDH---DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           V D    D Q   +I+ E    RR  L  ++  LN RE +I  ARRL E+  TLE L ++
Sbjct: 229 VSDDPLPDEQVSNMIDGE---RRRIWLASALKHLNEREMKIISARRLAEDGATLEELGAD 285

Query: 262 FEVSRERVRQIEARAFKKVQESI 284
             +S+ERVRQIE+RA +K++ ++
Sbjct: 286 LGISKERVRQIESRAMEKLRTAL 308


>gi|83746847|ref|ZP_00943894.1| RNA polymerase sigma-32 factor [Ralstonia solanacearum UW551]
 gi|207727816|ref|YP_002256210.1| rna polymerase sigma h (sigma-32) factor protein [Ralstonia
           solanacearum MolK2]
 gi|207742220|ref|YP_002258612.1| rna polymerase sigma h (sigma-32) factor protein [Ralstonia
           solanacearum IPO1609]
 gi|83726432|gb|EAP73563.1| RNA polymerase sigma-32 factor [Ralstonia solanacearum UW551]
 gi|206591057|emb|CAQ56669.1| rna polymerase sigma h (sigma-32) factor protein [Ralstonia
           solanacearum MolK2]
 gi|206593608|emb|CAQ60535.1| rna polymerase sigma h (sigma-32) factor protein [Ralstonia
           solanacearum IPO1609]
          Length = 306

 Score =  213 bits (543), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 120/281 (42%), Positives = 176/281 (62%), Gaps = 12/281 (4%)

Query: 12  GEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           G +G L  YI  + ++PML  +EE  LA+ Y   G+L AA RLV SHLRLVV IA  Y G
Sbjct: 28  GSLGNLDAYIQSVNRVPMLTAEEEQQLARDYHATGNLDAARRLVLSHLRLVVSIARQYLG 87

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
           YGLP ++++ EGNIGLM+AVK+FDP++G RL +Y++ WIKA M EYIL++W +VK+ TT 
Sbjct: 88  YGLPHADLIQEGNIGLMKAVKRFDPDQGVRLVSYAIHWIKAEMHEYILKNWRMVKVATTK 147

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNAL 189
            Q++LFFNLR  K    A        +++ A+A++LNV  +EV  M  RL+ GD +L   
Sbjct: 148 AQRKLFFNLRSHKQDAHA----TFTSDEIDAVAQELNVKGAEVREMETRLSGGDIALEGQ 203

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I+  +++ +    +L   H+   +VL  +   + +   +  +++ L+ R RRI EAR L 
Sbjct: 204 IDDGEESFAPIA-YLADTHNEPTRVLETRGHDRLQSEGIETALAKLDDRSRRIIEARWLN 262

Query: 250 ENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            N       TL  L+ EF VS ER+RQIE+ A KK++ ++Q
Sbjct: 263 VNDDGSGGATLHELADEFGVSAERIRQIESAAMKKMKGALQ 303


>gi|148265963|ref|YP_001232669.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter uraniireducens
           Rf4]
 gi|146399463|gb|ABQ28096.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter uraniireducens
           Rf4]
          Length = 280

 Score =  213 bits (543), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 113/269 (42%), Positives = 175/269 (65%), Gaps = 5/269 (1%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           LS Y+ EIR+ P+L  +EE+ LA +  E  DL AAHRL+TS+LR VVKIA  YR YG+ +
Sbjct: 8   LSLYLAEIRRFPVLSAEEEHGLAVKLYEEKDLEAAHRLITSNLRFVVKIAGEYRSYGMKM 67

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM AV+KF+P +GFRL +Y++WWI+A +Q +I+ +WSL+KIGTT  Q++L
Sbjct: 68  LDLIQEGNIGLMMAVRKFNPYKGFRLISYAVWWIRAYIQNHIVSTWSLLKIGTTQAQRKL 127

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FF L + K  ++++T      + + A A  L+V ESE   M+ R+ GD  L+A + + + 
Sbjct: 128 FFKLNQAKSAIRSMTGGG---DDLQAAALSLDVKESEAQEMDQRMRGDYFLDAEVVTGEG 184

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
            +    + L  +   QE++L E EE       +  +++ LN +ER + E R   + P+TL
Sbjct: 185 LT--MLESLPDERRNQEELLGEAEESAILEREVAAALTCLNEKERYVIEQRVSSDEPLTL 242

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + ++  F +SRERVRQIE  A KK++ ++
Sbjct: 243 QEIADHFSISRERVRQIEEGALKKMKRAL 271


>gi|300692652|ref|YP_003753647.1| RNA polymerase sigma H (sigma 32) factor; transcription of heat
           shock and stress proteins [Ralstonia solanacearum PSI07]
 gi|299079712|emb|CBJ52389.1| RNA polymerase sigma H (sigma 32) factor; transcription of heat
           shock and stress proteins [Ralstonia solanacearum PSI07]
          Length = 306

 Score =  213 bits (543), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 120/281 (42%), Positives = 176/281 (62%), Gaps = 12/281 (4%)

Query: 12  GEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           G +G L  YI  + ++PML  +EE  LA+ Y   G+L AA RLV SHLRLVV IA  Y G
Sbjct: 28  GSLGNLDAYIQSVNRVPMLTAEEEQQLARDYHATGNLDAARRLVLSHLRLVVSIARQYLG 87

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
           YGLP ++++ EGNIGLM+AVK+FDP++G RL +Y++ WIKA M EYIL++W +VK+ TT 
Sbjct: 88  YGLPHADLIQEGNIGLMKAVKRFDPDQGVRLVSYAIHWIKAEMHEYILKNWRMVKVATTK 147

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNAL 189
            Q++LFFNLR  K    A        +++ A+A++LNV  +EV  M  RL+ GD +L   
Sbjct: 148 AQRKLFFNLRSHKQDAHA----TFTSDEIDAVAQELNVKGTEVREMETRLSGGDIALEGQ 203

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I+  +++ +    +L   H+   +VL  +   + +   +  +++ L+ R RRI EAR L 
Sbjct: 204 IDDGEESFAPIA-YLADAHNEPTRVLEARGHDRLQSEGIETALAKLDDRSRRIIEARWLN 262

Query: 250 ENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            N       TL  L+ EF VS ER+RQIE+ A KK++ ++Q
Sbjct: 263 VNDDGSGGATLHELADEFGVSAERIRQIESAAMKKMKGALQ 303


>gi|134297011|ref|YP_001120746.1| RNA polymerase factor sigma-32 [Burkholderia vietnamiensis G4]
 gi|134140168|gb|ABO55911.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia vietnamiensis
           G4]
          Length = 331

 Score =  213 bits (542), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 117/283 (41%), Positives = 176/283 (62%), Gaps = 13/283 (4%)

Query: 9   IVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++ G++G +  YI  + +IP+L  +EE   A  +RE  +L AA +LV SHLRLVV IA  
Sbjct: 51  LLPGQLGNIDAYIQAVNRIPLLSAEEERRYATEFREDNNLDAARKLVLSHLRLVVSIARN 110

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y GYGLP  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W +VK+ 
Sbjct: 111 YLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKVA 170

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESL 186
           TT  Q++LFFNLR  K  +QA+T     PE++  +A++LNV   EV  M  RL+ GD +L
Sbjct: 171 TTKAQRKLFFNLRSHKKSMQAMT-----PEEIDGLAQELNVKREEVTEMETRLSGGDIAL 225

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              +   ++  +    +L   H+    VL  ++    + + + +++  L+ R RRI EAR
Sbjct: 226 EGQVEDGEEAYAPIA-YLADSHNEPTAVLAARQRDMLQTDGIAQALEALDARSRRIIEAR 284

Query: 247 RLQ-----ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L          TL +L++EF VS ER+RQIEA A KK++ ++
Sbjct: 285 WLNVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRTAL 327


>gi|209551384|ref|YP_002283301.1| RNA polymerase factor sigma-32 [Rhizobium leguminosarum bv.
           trifolii WSM2304]
 gi|209537140|gb|ACI57075.1| RNA polymerase, sigma 32 subunit, RpoH [Rhizobium leguminosarum bv.
           trifolii WSM2304]
          Length = 287

 Score =  213 bits (542), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 115/263 (43%), Positives = 175/263 (66%), Gaps = 9/263 (3%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L +QEE+ LA R+++H D  A +++  +H+RLV+ +A  +R +GLP+S++V EG +GL
Sbjct: 18  PYLARQEEHDLAIRWKDHDDRGARNQIAMAHMRLVISMAGKFRNFGLPMSDLVQEGYVGL 77

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 78  LEAAARFEPERDVRFSTYASWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRAKL 137

Query: 147 QAITDNNLKPEQV-VAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWL 204
            A  D  L  + +   IA  L VS ++V +M+ RL+G D SL A   S D  S++  D+L
Sbjct: 138 -AKGDTQLTLQSIHQEIAAALGVSLADVQTMDARLSGNDASLQAPSVSGDAESAEKMDFL 196

Query: 205 VYDH---DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           V D    D Q   +I+ E    RR  L  ++  LN RE +I  ARRL E+  TLE L ++
Sbjct: 197 VSDDPLPDEQVSNMIDGE---RRRVWLASALKHLNEREMKIISARRLAEDGATLEELGAD 253

Query: 262 FEVSRERVRQIEARAFKKVQESI 284
             +S+ERVRQIE+RA +K++ ++
Sbjct: 254 LGISKERVRQIESRAMEKLRSAL 276


>gi|118591280|ref|ZP_01548678.1| RNA polymerase sigma factor [Stappia aggregata IAM 12614]
 gi|118435952|gb|EAV42595.1| RNA polymerase sigma factor [Stappia aggregata IAM 12614]
          Length = 287

 Score =  213 bits (541), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 109/265 (41%), Positives = 177/265 (66%), Gaps = 9/265 (3%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K P L ++EE  LA R+R+  D  A  +L  SH+RLV+ +A  +R +GL + +++ EG++
Sbjct: 15  KAPYLTREEELELAIRWRQERDEKALEKLSLSHMRLVIAVASRFRNFGLSLGDLIQEGHV 74

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT+++QK LFFNLRRL+ 
Sbjct: 75  GLLEAAARFEPEREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSSQKALFFNLRRLRA 134

Query: 145 HLQA----ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQ 199
            L      +TD+ L  +    IA  + V +S+V  MN RL+G D SLNA +  S+ +S+ 
Sbjct: 135 KLSGNQTPLTDSELHQK----IADAIGVKQSDVALMNARLSGPDTSLNAPVTDSEGSSAD 190

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
            QD+LV D    ++++    + + R+  L+ ++ VL+ RE +I   RRL E+  TLE+L 
Sbjct: 191 RQDFLVSDAPLPDEIVTVSIDTERRQRWLSSALEVLSERELKIVRERRLSEDGATLESLG 250

Query: 260 SEFEVSRERVRQIEARAFKKVQESI 284
            +  +S+ERVRQIE+RA +K++ ++
Sbjct: 251 VKLGISKERVRQIESRAMEKLKSAL 275


>gi|264680055|ref|YP_003279964.1| RNA polymerase, sigma 32 subunit, RpoH [Comamonas testosteroni
           CNB-2]
 gi|262210570|gb|ACY34668.1| RNA polymerase, sigma 32 subunit, RpoH [Comamonas testosteroni
           CNB-2]
          Length = 324

 Score =  213 bits (541), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 119/284 (41%), Positives = 173/284 (60%), Gaps = 15/284 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + ++PML  +EE   A++ +EH DL AA RLV SHLRLVV I+  Y GYGLP 
Sbjct: 37  LDAYISAVNRMPMLTLEEEQDYARKLKEHNDLDAAGRLVMSHLRLVVSISRQYLGYGLPH 96

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM+AVK+FDP++G RL +Y+M WIKA + EYIL++W +VK+ TT  Q++L
Sbjct: 97  GDLIQEGNVGLMKAVKRFDPDQGVRLVSYAMHWIKAEIHEYILKNWRMVKVATTKAQRKL 156

Query: 136 FFNLRRLKGHLQ---AITD------NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
           FFNLR +K  L+   A+ D        L   ++ A+A KLNV   EVI M  RLAG + L
Sbjct: 157 FFNLRSMKHDLKSDAAMADEELALRETLTSNEIDAVAAKLNVKREEVIEMETRLAGGDVL 216

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFEA 245
                S D   +      + D   +   ++E  +R +   + L  ++  L+ R RRI E 
Sbjct: 217 LDPSPSDDGEQAFGPIAYLADASHEPTAMLESRQRDHLATDGLVMALEGLDDRSRRIVEE 276

Query: 246 RRLQENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R L+ N      +TL  L++E+ VS ER+RQIE  A KK+++++
Sbjct: 277 RWLKVNDDGSGGMTLHELAAEYGVSAERIRQIEVAAMKKMKKAL 320


>gi|197121539|ref|YP_002133490.1| RNA polymerase, sigma 70 family subunit [Anaeromyxobacter sp. K]
 gi|196171388|gb|ACG72361.1| putative RNA polymerase, sigma 70 family subunit [Anaeromyxobacter
           sp. K]
          Length = 300

 Score =  213 bits (541), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 115/274 (41%), Positives = 178/274 (64%), Gaps = 7/274 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI ++ +L  +EE  LA+++R+ G+  A HRLV ++LR VVK+A  YR YGL +
Sbjct: 11  LDQYLREINRVALLTVEEERRLARQFRDEGNTRAGHRLVEANLRFVVKVAFEYRSYGLRM 70

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AV+KFDP++  RL +Y++WWI+A +Q +IL+SWSLVKIGTT  Q++L
Sbjct: 71  ADLIQEGNIGLMKAVQKFDPDKEIRLISYAVWWIRAYIQNHILKSWSLVKIGTTQAQRKL 130

Query: 136 FFNLRRLKGHLQAITDNNLKPEQ---VVAIAKKLNVSESEVISMNCRLAG-DESLNALIN 191
           FF+L R +  ++ +T      E+   V  +AKKL V  S+V+ M  R+ G D SL+A + 
Sbjct: 131 FFSLARTRHEIERLTPGAGLAEEGIDVALVAKKLRVRPSDVVEMTQRMEGRDLSLDAPV- 189

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
            +D  S+  + +   D + Q++ L   EE       ++ +M  L+PRER I EAR + E 
Sbjct: 190 -ADGTSTHLE-FTPADGEPQDEELARAEEDALLARRVSEAMGRLDPRERHIVEARIMGEG 247

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             TL +L   F  SRER RQ+E RA +K++  ++
Sbjct: 248 KETLRDLGHHFGFSRERARQLEIRALEKLRRDLE 281


>gi|17545093|ref|NP_518495.1| RNA polymerase factor sigma-32 [Ralstonia solanacearum GMI1000]
 gi|17427383|emb|CAD13902.1| probable rna polymerase sigma h (sigma-32) factor transcription
           regulator protein [Ralstonia solanacearum GMI1000]
          Length = 306

 Score =  213 bits (541), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 120/281 (42%), Positives = 176/281 (62%), Gaps = 12/281 (4%)

Query: 12  GEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           G +G L  YI  + ++PML  +EE  LA+ Y   G+L AA RLV SHLRLVV IA  Y G
Sbjct: 28  GSLGNLDAYIQSVNRVPMLTAEEEQQLARDYHATGNLDAARRLVLSHLRLVVSIARQYLG 87

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
           YGLP ++++ EGN+GLM+AVK+FDP++G RL +Y++ WIKA M EYIL++W +VK+ TT 
Sbjct: 88  YGLPHADLIQEGNVGLMKAVKRFDPDQGVRLVSYAIHWIKAEMHEYILKNWRMVKVATTK 147

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNAL 189
            Q++LFFNLR  K    A        ++V A+A++LNV  +EV  M  RL+ GD +L   
Sbjct: 148 AQRKLFFNLRSHKQDAHA----TFTSDEVDAVAQELNVKGAEVREMETRLSGGDIALEGQ 203

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I+  +++ +    +L   H+   +VL  +   + +   +  +++ L+ R RRI EAR L 
Sbjct: 204 IDDGEESFAPIA-YLADTHNEPTRVLEGRGRDRLQSEGIETALAKLDDRSRRIIEARWLH 262

Query: 250 ENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            N       TL  L+ EF VS ER+RQIE+ A KK++ ++Q
Sbjct: 263 VNDDGSGGATLHELADEFGVSAERIRQIESAAMKKMKGALQ 303


>gi|86157496|ref|YP_464281.1| RNA polymerase sigma-32 subunit RpoH [Anaeromyxobacter dehalogenans
           2CP-C]
 gi|85774007|gb|ABC80844.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter
           dehalogenans 2CP-C]
          Length = 300

 Score =  213 bits (541), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 119/289 (41%), Positives = 183/289 (63%), Gaps = 12/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           MNR + S        L +Y+ EI ++ +L  +EE  LA+++R+ G+  A HRLV ++LR 
Sbjct: 1   MNRPSTSSST-----LDQYLREINRVALLTVEEERRLARQFRDEGNTRAGHRLVEANLRF 55

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VVK+A  YR YGL +++++ EGNIGLM+AV+KFDP++  RL +Y++WWI+A +Q +IL+S
Sbjct: 56  VVKVAFEYRSYGLRMADLIQEGNIGLMKAVQKFDPDKEIRLISYAVWWIRAYIQNHILKS 115

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ---VVAIAKKLNVSESEVISMN 177
           WSLVKIGTT  Q++LFF+L R +  ++ +T      E+   V  +AKKL V  S+V+ M 
Sbjct: 116 WSLVKIGTTQAQRKLFFSLARTRHEIERLTPGAGLAEEGIDVALVAKKLRVRPSDVVEMT 175

Query: 178 CRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
            R+ G D SL+A +  +D  S+  + +   D + Q++ L   EE       ++ +M  L+
Sbjct: 176 QRMEGRDLSLDAPV--ADGTSTHLE-FTPADGEPQDEELARAEEDALLARRVSEAMGRLD 232

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           PRER I EAR + E   TL +L   F  SRER RQ+E RA +K++  ++
Sbjct: 233 PRERHIVEARIMGEGKETLRDLGHHFGFSRERARQLEIRALEKLRRDLE 281


>gi|299068068|emb|CBJ39282.1| RNA polymerase sigma H (sigma 32) factor; transcription of heat
           shock and stress proteins [Ralstonia solanacearum CMR15]
          Length = 306

 Score =  213 bits (541), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 119/281 (42%), Positives = 177/281 (62%), Gaps = 12/281 (4%)

Query: 12  GEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           G +G L  YI  + ++PML  +EE  LA+ Y   GDL AA RLV SHLRLVV IA  Y G
Sbjct: 28  GSLGNLDAYIQSVNRVPMLTAEEEQQLARDYHATGDLDAARRLVLSHLRLVVSIARQYLG 87

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
           YGLP ++++ EGN+GLM+AVK+FDP++G RL +Y++ WIKA M EYIL++W +VK+ TT 
Sbjct: 88  YGLPHADLIQEGNVGLMKAVKRFDPDQGVRLVSYAIHWIKAEMHEYILKNWRMVKVATTK 147

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNAL 189
            Q++LFFNLR  K +  A        +++ A+A++L+V  +EV  M  RL+ GD +L   
Sbjct: 148 AQRKLFFNLRSHKQNAHA----TFTSDEIDAVAQELDVKGAEVREMETRLSGGDIALEGQ 203

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I+  +++ +    +L   H+   +VL  +   + +   +  +++ L+ R RRI EAR L 
Sbjct: 204 IDDGEESFAPIA-YLADTHNEPTRVLEGRGLDRLQSEGIETALAKLDDRSRRIIEARWLH 262

Query: 250 ENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            N       TL  L+ EF VS ER+RQIE+ A KK++ ++Q
Sbjct: 263 VNDDGSGGATLHELADEFGVSAERIRQIESAAMKKMKGALQ 303


>gi|73540031|ref|YP_294551.1| RNA polymerase factor sigma-32 [Ralstonia eutropha JMP134]
 gi|72117444|gb|AAZ59707.1| Sigma-70 region 2 [Ralstonia eutropha JMP134]
          Length = 309

 Score =  212 bits (540), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 118/276 (42%), Positives = 171/276 (61%), Gaps = 12/276 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + +IPML  +EE  LA+  RE   + AA +LV SHLRLVV IA  Y GYGLP 
Sbjct: 37  LESYIQAVHRIPMLTAEEEQRLARELREDDSVDAARQLVMSHLRLVVSIARQYLGYGLPH 96

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AVK+FDP +G RL +Y+M WIKA + EY+L++W +VK+ TT  Q++L
Sbjct: 97  ADLIQEGNIGLMKAVKRFDPNQGVRLVSYAMHWIKAEIHEYVLKNWRMVKVATTKAQRKL 156

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALINSSD 194
           FFNLR    H Q    +   PEQ+ A+A+ LNV   EV+ M  R++ GD +L   ++  +
Sbjct: 157 FFNLR---SHKQG--SHTFTPEQIEAVARDLNVKPEEVMEMETRMSGGDLALEGQVDDGE 211

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ----- 249
           +  +    +L  +H+   +VL  K + + +   L  +++ L+ R RRI EAR L      
Sbjct: 212 EEFAPIA-YLADNHNEPTRVLEAKRQDRMQVEGLEEALARLDERSRRIIEARWLNVEDDG 270

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
               TL  L+ EF VS ER+RQIE  A KK++ ++Q
Sbjct: 271 SGGATLHELADEFGVSAERIRQIEVAAMKKMKGALQ 306


>gi|330818365|ref|YP_004362070.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia gladioli BSR3]
 gi|327370758|gb|AEA62114.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia gladioli BSR3]
          Length = 311

 Score =  212 bits (540), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 115/283 (40%), Positives = 179/283 (63%), Gaps = 13/283 (4%)

Query: 9   IVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++ G++G +  YI  + +IPML  +EE   A  +R+  +L +A RLV SHLRLVV IA  
Sbjct: 31  MLPGQLGNIDAYIQSVNRIPMLTLEEERQYATEFRDQNNLESARRLVLSHLRLVVSIARN 90

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y GYGLP  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W +VK+ 
Sbjct: 91  YLGYGLPHGDLIQEGNIGLMKAVKRFDPNQNVRLVSYAIHWIKAEIHEYILRNWRMVKVA 150

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESL 186
           TT  Q++LFFNLR  K  +QA+T     PE++  +A++LNV   +V  M  RL+ GD +L
Sbjct: 151 TTKAQRKLFFNLRSHKKGMQAMT-----PEEIDGLAQELNVKREDVAEMETRLSGGDIAL 205

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              ++  +++ +    +L   H+    V+  ++  + + + ++ ++  L+ R RRI EAR
Sbjct: 206 EGQVDDGEESFAPIA-YLADSHNEPTAVIASRQRDRLQTDGISEALESLDARSRRIIEAR 264

Query: 247 RLQ-----ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L          TL +L++EF VS ER+RQIEA A KK++ ++
Sbjct: 265 WLNVEDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRAAL 307


>gi|238028681|ref|YP_002912912.1| RNA polymerase factor sigma-32 [Burkholderia glumae BGR1]
 gi|237877875|gb|ACR30208.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia glumae BGR1]
          Length = 311

 Score =  212 bits (540), Expect = 4e-53,   Method: Compositional matrix adjust.
 Identities = 116/283 (40%), Positives = 178/283 (62%), Gaps = 13/283 (4%)

Query: 9   IVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++ G++G +  YI  + +IPML  +EE   A  +R+  +L +A RLV SHLRLVV IA  
Sbjct: 31  MLPGQLGNIDAYIQAVNRIPMLTPEEERQYATEFRDQQNLESARRLVLSHLRLVVSIARN 90

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y GYGLP  +++ EGNIGLM+AVK+FDP++  RL +Y++ WIKA + EYILR+W +VK+ 
Sbjct: 91  YLGYGLPHGDLIQEGNIGLMKAVKRFDPDQNVRLVSYAIHWIKAEIHEYILRNWRMVKVA 150

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESL 186
           TT  Q++LFFNLR  K  +QA+T     PE++  +A++LNV   +V  M  RL+ GD +L
Sbjct: 151 TTKAQRKLFFNLRSHKKGMQAMT-----PEEIDGLAQELNVKREDVAEMETRLSGGDIAL 205

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              +   +++ +    +L   H+    VL  ++  + +   ++ ++  L+ R RRI EAR
Sbjct: 206 EGQVEDGEESFAPIA-YLADSHNEPTAVLASRQRDRLQTEGISEALDSLDTRSRRIIEAR 264

Query: 247 RLQ-----ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L          TL +L++EF VS ER+RQIEA A KK++ ++
Sbjct: 265 WLNVGDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRAAL 307


>gi|220916304|ref|YP_002491608.1| RNA polymerase, sigma 70 family subunit [Anaeromyxobacter
           dehalogenans 2CP-1]
 gi|219954158|gb|ACL64542.1| putative RNA polymerase, sigma 70 family subunit [Anaeromyxobacter
           dehalogenans 2CP-1]
          Length = 300

 Score =  212 bits (540), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 115/274 (41%), Positives = 178/274 (64%), Gaps = 7/274 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI ++ +L  +EE  LA+++R+ G+  A HRLV ++LR VVK+A  YR YGL +
Sbjct: 11  LDQYLREINRVALLTVEEERRLARQFRDEGNTRAGHRLVEANLRFVVKVAFEYRSYGLRM 70

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AV+KFDP++  RL +Y++WWI+A +Q +IL+SWSLVKIGTT  Q++L
Sbjct: 71  ADLIQEGNIGLMKAVQKFDPDKEIRLISYAVWWIRAYIQNHILKSWSLVKIGTTQAQRKL 130

Query: 136 FFNLRRLKGHLQAITDNNLKPEQ---VVAIAKKLNVSESEVISMNCRLAG-DESLNALIN 191
           FF+L R +  ++ +T      E+   V  +AKKL V  S+V+ M  R+ G D SL+A + 
Sbjct: 131 FFSLARTRHEIERLTPGAGLAEEGIDVALVAKKLRVRPSDVVEMTQRMEGRDLSLDAPV- 189

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
            +D  S+  + +   D + Q++ L   EE       ++ +M  L+PRER I EAR + E 
Sbjct: 190 -ADGTSTHLE-FTPADGEPQDEELARAEEDALLARRVSEAMGRLDPRERHIVEARIMGEG 247

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             TL +L   F  SRER RQ+E RA +K++  ++
Sbjct: 248 KETLRDLGHHFGFSRERARQLEIRALEKLRRDLE 281


>gi|78067614|ref|YP_370383.1| RNA polymerase factor sigma-32 [Burkholderia sp. 383]
 gi|77968359|gb|ABB09739.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. 383]
          Length = 311

 Score =  212 bits (540), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 117/283 (41%), Positives = 176/283 (62%), Gaps = 13/283 (4%)

Query: 9   IVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++ G++G +  YI  + +IP+L  +EE   A  +RE  +L +A RLV SHLRLVV I+  
Sbjct: 31  MLPGQLGNIDAYIQAVNRIPLLTVEEERQYATEFREGNNLDSARRLVLSHLRLVVSISRN 90

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y GYGLP  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W  VK+ 
Sbjct: 91  YLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRTVKVA 150

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESL 186
           TT  Q++LFFNLR  K  LQA+T     PE++  +AK+LNV   +V  M  RL+ GD +L
Sbjct: 151 TTKAQRKLFFNLRSHKKGLQAMT-----PEEIDGLAKELNVKREDVTEMETRLSGGDIAL 205

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              +   +++ +    +L   H+    VL  ++    + + + +++  L+ R RRI EAR
Sbjct: 206 EGQVEDGEESYAPIA-YLADSHNEPTAVLAARQRDTLQTDGIAQALDALDARSRRIIEAR 264

Query: 247 RLQ-----ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L          TL +L++EF VS ER+RQIEA A KK++ ++
Sbjct: 265 WLHVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRTAL 307


>gi|299534115|ref|ZP_07047467.1| RNA polymerase, sigma 32 subunit, RpoH [Comamonas testosteroni S44]
 gi|298718024|gb|EFI59029.1| RNA polymerase, sigma 32 subunit, RpoH [Comamonas testosteroni S44]
          Length = 314

 Score =  212 bits (540), Expect = 5e-53,   Method: Compositional matrix adjust.
 Identities = 119/284 (41%), Positives = 173/284 (60%), Gaps = 15/284 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + ++PML  +EE   A++ +EH DL AA RLV SHLRLVV I+  Y GYGLP 
Sbjct: 27  LDAYISAVNRMPMLTLEEEQDYARKLKEHNDLDAAGRLVMSHLRLVVSISRQYLGYGLPH 86

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM+AVK+FDP++G RL +Y+M WIKA + EYIL++W +VK+ TT  Q++L
Sbjct: 87  GDLIQEGNVGLMKAVKRFDPDQGVRLVSYAMHWIKAEIHEYILKNWRMVKVATTKAQRKL 146

Query: 136 FFNLRRLKGHLQ---AITD------NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
           FFNLR +K  L+   A+ D        L   ++ A+A KLNV   EVI M  RLAG + L
Sbjct: 147 FFNLRSMKHDLKSDAAMADEELALRETLTSNEIDAVAAKLNVKREEVIEMETRLAGGDVL 206

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFEA 245
                S D   +      + D   +   ++E  +R +   + L  ++  L+ R RRI E 
Sbjct: 207 LDPSPSDDGEQAFGPIAYLADASHEPTAMLESRQRDHLATDGLVMALEGLDDRSRRIVEE 266

Query: 246 RRLQENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R L+ N      +TL  L++E+ VS ER+RQIE  A KK+++++
Sbjct: 267 RWLKVNDDGSGGMTLHELAAEYGVSAERIRQIEVAAMKKMKKAL 310


>gi|157373363|ref|YP_001471963.1| RNA polymerase factor sigma-32 [Shewanella sediminis HAW-EB3]
 gi|157315737|gb|ABV34835.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella sediminis
           HAW-EB3]
          Length = 285

 Score =  212 bits (539), Expect = 6e-53,   Method: Compositional matrix adjust.
 Identities = 113/281 (40%), Positives = 176/281 (62%), Gaps = 9/281 (3%)

Query: 4   KNMSIIV-NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           ++M++ V +G   L  Y+H    I ML+ ++EY LAKR +E GDL AA +L+ SHLR VV
Sbjct: 6   QSMALTVPHGSGSLEAYVHSAHNISMLQPEQEYELAKRLQETGDLQAAKQLIMSHLRFVV 65

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A GY GYGLP ++++ EGNIGLM+AVK+FDP  G RL ++++ WIKA + EY+L++W 
Sbjct: 66  HVAKGYSGYGLPQADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWIKAEIHEYVLKNWR 125

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L   +D     E+V  +A  L VS+++V  M  R+A 
Sbjct: 126 IVKVATTKAQRKLFFNLRKSKKRLGWFSD-----EEVGMVADNLGVSKADVTEMESRMAA 180

Query: 183 DESLNALINSSDKNSSQWQDWLVYDH--DGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            +    L + +D +        + DH  D   QV  +  E  N+  +L+ ++  L+ R +
Sbjct: 181 QDPAFDLASDNDDDHDFAPMHYLEDHSSDLASQVENDNLEASNQARLLS-AIKTLDERSQ 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            I +AR L E+  TL+ L++ ++VS ER+RQ+E  A  K++
Sbjct: 240 HILQARWLNEDKTTLQELAATYQVSAERIRQLEKNAMNKLK 280


>gi|319778863|ref|YP_004129776.1| RNA polymerase sigma factor RpoH [Taylorella equigenitalis MCE9]
 gi|317108887|gb|ADU91633.1| RNA polymerase sigma factor RpoH [Taylorella equigenitalis MCE9]
          Length = 292

 Score =  212 bits (539), Expect = 6e-53,   Method: Compositional matrix adjust.
 Identities = 117/288 (40%), Positives = 182/288 (63%), Gaps = 10/288 (3%)

Query: 4   KNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           K+M +I    +G +  YI E+ +IP+L  ++E   A+R ++ GDL AA  L+  HLRLVV
Sbjct: 12  KSMDLINPSALGTIEAYIQEVNRIPILTAEQERDYAERLQKSGDLKAAQALILPHLRLVV 71

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y GYGLP ++++ EGNIGLM+AVK+FD  RG RL T++M WIKA + EY++R+W 
Sbjct: 72  SVARQYLGYGLPHADLIQEGNIGLMKAVKRFDVSRGVRLVTFAMHWIKAEIHEYVIRNWR 131

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           LVKI TT  Q++LFFNL  L+   +++ +++     +V IAKKLNV   +V+ M  R++G
Sbjct: 132 LVKIATTKAQRKLFFNLNSLRPEGKSLDNDD-----IVGIAKKLNVRPEDVVEMEKRMSG 186

Query: 183 -DESLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            D +L+ L++  D  +     +L  D   + E V++ +E  K     L  ++  L+ R R
Sbjct: 187 HDIALDTLMDEDDDYAP--IQYLADDEAYEPENVMLAQEHDKLENQGLKSALDQLDDRSR 244

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            I E+R L E+  TL +L++++ VS ER+RQIE  A KK++  ++  V
Sbjct: 245 HIIESRWLSEDKPTLHDLAAQYNVSAERIRQIENAAIKKMRSYLEDYV 292


>gi|120600694|ref|YP_965268.1| RNA polymerase factor sigma-32 [Shewanella sp. W3-18-1]
 gi|146291400|ref|YP_001181824.1| RNA polymerase factor sigma-32 [Shewanella putrefaciens CN-32]
 gi|120560787|gb|ABM26714.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella sp. W3-18-1]
 gi|145563090|gb|ABP74025.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella putrefaciens
           CN-32]
 gi|319428373|gb|ADV56447.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella putrefaciens
           200]
          Length = 285

 Score =  211 bits (538), Expect = 7e-53,   Method: Compositional matrix adjust.
 Identities = 110/284 (38%), Positives = 172/284 (60%), Gaps = 7/284 (2%)

Query: 4   KNMSIIV-NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           ++M++ V  G   L  YIH +  I ML+ + EY LAKR +E GDL AA +L+ SHLR VV
Sbjct: 6   QSMALTVPQGSSSLEAYIHSVTSISMLDAEAEYELAKRLQETGDLQAAKQLIMSHLRFVV 65

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A GY GYGLP ++++ EGNIGLM+AVK+FDP+ G RL ++++ WIKA + EY+L++W 
Sbjct: 66  HVAKGYSGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYVLKNWR 125

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFN+R+ K  L   +D     E+V  +A+ L VS+++V  M  R+A 
Sbjct: 126 IVKVATTKAQRKLFFNIRKAKKRLGWFSD-----EEVTMVAENLGVSKADVTEMESRMAA 180

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERR 241
            +    L + +D          + DH       IE +    N +  L  ++  L+ R + 
Sbjct: 181 QDPAFDLTSDNDDEQDFAPVHYLEDHSSDLAENIENDNWESNAQGRLLSAIKTLDERSQH 240

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           I  AR L ++  TL+ L+  ++VS ER+RQ+E  A  K++  ++
Sbjct: 241 ILRARWLDDDKTTLQELAETYQVSAERIRQLEKNAMNKLKACME 284


>gi|160877394|ref|YP_001556710.1| RNA polymerase factor sigma-32 [Shewanella baltica OS195]
 gi|160862916|gb|ABX51450.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella baltica OS195]
 gi|315269598|gb|ADT96451.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella baltica OS678]
          Length = 285

 Score =  211 bits (538), Expect = 7e-53,   Method: Compositional matrix adjust.
 Identities = 110/284 (38%), Positives = 171/284 (60%), Gaps = 7/284 (2%)

Query: 4   KNMSIIV-NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           ++M++ V  G   L  YIH +  I ML+ + EY LAKR +E GDL AA +L+ SHLR VV
Sbjct: 6   QSMALTVPQGASSLEAYIHSVTSISMLDAEAEYELAKRLQETGDLQAAKQLIMSHLRFVV 65

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A GY GYGLP ++++ EGNIGLM+AVK+FDP+ G RL ++++ WIKA + EY+L++W 
Sbjct: 66  HVAKGYSGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYVLKNWR 125

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFN+R+ K  L   +D      +V  +A+ L VS+++V  M  R+A 
Sbjct: 126 IVKVATTKAQRKLFFNIRKAKKRLGWFSD-----AEVTMVAENLGVSKADVTEMESRMAA 180

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERR 241
            +    L N  D+         + DH       IE +    N +  L  ++  L+ R + 
Sbjct: 181 QDPAFDLTNDQDEEHDFAPVHYLEDHSSDLAENIENDNWESNAQGRLLSAIKTLDERSQH 240

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           I  AR L ++  TL+ L+  ++VS ER+RQ+E  A  K++  ++
Sbjct: 241 ILHARWLDDDKTTLQELAETYQVSAERIRQLEKNAMNKLKACME 284


>gi|189423258|ref|YP_001950435.1| RNA polymerase, sigma 70 family subunit [Geobacter lovleyi SZ]
 gi|189419517|gb|ACD93915.1| putative RNA polymerase, sigma 70 family subunit [Geobacter lovleyi
           SZ]
          Length = 280

 Score =  211 bits (538), Expect = 8e-53,   Method: Compositional matrix adjust.
 Identities = 116/284 (40%), Positives = 178/284 (62%), Gaps = 8/284 (2%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           N+ II +    L+ Y+ EIRK  +L + EE   A ++ E  DL AAH L+TS+LR VVK+
Sbjct: 4   NLPIISDS---LTLYLSEIRKFNLLTEDEERDYAVKFFEEKDLEAAHTLITSNLRYVVKV 60

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  YR YGL + +++ EGNIGLM AV+KF+P RG RL +Y++WWI+A +Q YI+ +WSLV
Sbjct: 61  ASEYRHYGLKMLDLIQEGNIGLMMAVRKFNPYRGVRLISYAVWWIRAYIQNYIVSAWSLV 120

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           KIGTT  Q++LF+ LR+ K  L  +T    +      ++  L+V + EV+ M  RL G+ 
Sbjct: 121 KIGTTQAQRKLFYGLRKTKEALLKLTG---RDSDAFEVSSMLHVPDHEVVEMEQRLKGEV 177

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SLN  I   D  +    + +  D   QE++L E ++  + +  +  ++  LN +E+ I E
Sbjct: 178 SLNEEIIEGDGLT--ILETIADDRMNQEEMLGEYQQEHSLKKAIAHALQGLNEKEKYIVE 235

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            R   ++P+TL++++  F +SRERVRQIE RA  K++  +Q Q+
Sbjct: 236 HRITNDDPLTLQDIADHFSISRERVRQIEERALVKLKNVLQPQL 279


>gi|224827256|ref|ZP_03700350.1| RNA polymerase, sigma 32 subunit, RpoH [Lutiella nitroferrum 2002]
 gi|224600545|gb|EEG06734.1| RNA polymerase, sigma 32 subunit, RpoH [Lutiella nitroferrum 2002]
          Length = 287

 Score =  211 bits (538), Expect = 9e-53,   Method: Compositional matrix adjust.
 Identities = 116/279 (41%), Positives = 174/279 (62%), Gaps = 9/279 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +YI  +  +P+L  +EE  LA R     DL AA +LV SHLR+VV IA GY GYGLP 
Sbjct: 16  LEQYIQIVNSVPLLSAEEENELANRLHAQNDLEAAKKLVLSHLRVVVSIARGYAGYGLPQ 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AVK+F+P RG RL ++++ WIKA + E+ILR+W LV++ TT  Q++L
Sbjct: 76  ADLIQEGNIGLMKAVKRFEPNRGVRLFSFAVHWIKAEIHEFILRNWRLVRVATTKPQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR +K    A+TD+  +      IA  L V   EV  M  R++G + +  L + +D 
Sbjct: 136 FFNLRSMKKSFAALTDSEAR-----VIADDLGVKPEEVREMETRMSG-QDVALLADDNDD 189

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENP-V 253
                 DWL  D D +    +EK+   + +   L +++S L+ R RRI EAR L ++   
Sbjct: 190 EGFAPIDWLA-DSDHEPTRQLEKKAFDHLQTAGLEQALSSLDARSRRIIEARWLADDSGA 248

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
           TL  L++EF VS ER+RQIEA+A  K++ ++ ++  + +
Sbjct: 249 TLHELAAEFGVSAERIRQIEAKALTKMKAALSERAAIEA 287


>gi|257453679|ref|ZP_05618966.1| RNA polymerase factor sigma-32 [Enhydrobacter aerosaccus SK60]
 gi|257448913|gb|EEV23869.1| RNA polymerase factor sigma-32 [Enhydrobacter aerosaccus SK60]
          Length = 393

 Score =  211 bits (537), Expect = 9e-53,   Method: Compositional matrix adjust.
 Identities = 111/278 (39%), Positives = 167/278 (60%), Gaps = 7/278 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + L  YI+ + +IP+L  ++E  LA RY + GD+ AA  LV SHLR V+ IA  Y GYGL
Sbjct: 119 VNLGAYINAVHQIPILTAEQEQELAHRYTDEGDVEAARLLVMSHLRFVIHIARSYSGYGL 178

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P  +++ EGN+GLM+AVK+FDP +G RL ++++ WIKA + E+++R+W +VK+ TT   +
Sbjct: 179 PQGDLIQEGNVGLMKAVKRFDPNKGVRLVSFAVHWIKAEIHEFVIRNWRIVKVATTKAHR 238

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINS 192
           +LFFNLR LK      T+N L  E+  AIAK LNV+  +V+ M  RL   D S  A  + 
Sbjct: 239 KLFFNLRSLKK-----TNNQLTLEEAEAIAKDLNVTVKQVLEMESRLTSYDASFEAQSDD 293

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            D+     Q + + D      ++ + +  +N  + L  +M  L+ R R I + R L E  
Sbjct: 294 EDEGRYAPQ-YFLEDAADPADMVEDADWEENNNSALMEAMEDLDDRSRDIVQQRWLNEQK 352

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
            TL  L++E+ +S ERVRQIE  A  K++E++     L
Sbjct: 353 ATLHELAAEYNISAERVRQIEKNAMDKIKEAMLANTHL 390


>gi|298369543|ref|ZP_06980860.1| alternative sigma factor RpoH [Neisseria sp. oral taxon 014 str.
           F0314]
 gi|298282100|gb|EFI23588.1| alternative sigma factor RpoH [Neisseria sp. oral taxon 014 str.
           F0314]
          Length = 287

 Score =  211 bits (537), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 119/281 (42%), Positives = 177/281 (62%), Gaps = 9/281 (3%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N   +  + +G   L +YIH +  IPML  +EE  LA+R ++ GDL AA +L+ SHLR+V
Sbjct: 3   NAFALPAVHSGNGSLEQYIHTVNSIPMLSAEEESSLAER-QQKGDLEAAKQLILSHLRVV 61

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+ILR+W
Sbjct: 62  VSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPSRGARLFSFAVHWIKAEIHEFILRNW 121

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            LV++ TT  Q++LFFNLR ++  L     N L P++   IA  L V  SEV+ M  R+ 
Sbjct: 122 RLVRVATTKPQRKLFFNLRSMRKSL-----NALSPKEAQEIADDLGVKLSEVLEMEQRMT 176

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRER 240
             +      NS D++S    DWL  DHD +    + K+     +   L  +++ L+ R R
Sbjct: 177 SHDIGIMADNSDDEDSFAPIDWLA-DHDAEPSRQLAKQAHYALQTEGLQNALAQLDDRSR 235

Query: 241 RIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKV 280
           RI E+R LQ++  +TL  L+ E+ VS ER+RQIEA+A +K+
Sbjct: 236 RIVESRWLQDDGGLTLHELADEYGVSAERIRQIEAKAMQKL 276


>gi|259416055|ref|ZP_05739975.1| RNA polymerase sigma-32 factor [Silicibacter sp. TrichCH4B]
 gi|259347494|gb|EEW59271.1| RNA polymerase sigma-32 factor [Silicibacter sp. TrichCH4B]
          Length = 292

 Score =  211 bits (537), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 111/270 (41%), Positives = 183/270 (67%), Gaps = 10/270 (3%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K  +L+ + E  LA  +R+H D+ A HRL+T+++RL V +A  +R YG P+++++ E  +
Sbjct: 17  KAELLDAETELALAYAWRDHQDVQALHRLITAYMRLAVSMASKFRRYGAPMNDLIQEAGL 76

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A +KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFN+RR++ 
Sbjct: 77  GLMKAAEKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQA 136

Query: 145 HL--QAITD----NNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
            L  +A +D    +  K  Q+V  A+++ V   +V  M+ RLAG D SLNA + S+D++ 
Sbjct: 137 QLEREAESDGVELDRHKLHQMV--AEEIGVPLRDVEMMDGRLAGADFSLNA-VQSADEDG 193

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
            +W D L  D +   + +    +R+  R  L  +++ LN RER I   R+L+E   TLE+
Sbjct: 194 REWIDALEDDSEQAAERVAADHDRRQLREWLVTALNGLNERERFIVRERKLREESRTLES 253

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L +E  +S+ERVRQ+EA AF K+++S++ Q
Sbjct: 254 LGNELGLSKERVRQLEAAAFLKMRKSLEGQ 283


>gi|126172428|ref|YP_001048577.1| RNA polymerase factor sigma-32 [Shewanella baltica OS155]
 gi|153002659|ref|YP_001368340.1| RNA polymerase factor sigma-32 [Shewanella baltica OS185]
 gi|217975235|ref|YP_002359986.1| RNA polymerase factor sigma-32 [Shewanella baltica OS223]
 gi|304412289|ref|ZP_07393897.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella baltica OS183]
 gi|307306073|ref|ZP_07585818.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella baltica BA175]
 gi|125995633|gb|ABN59708.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella baltica OS155]
 gi|151367277|gb|ABS10277.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella baltica OS185]
 gi|217500370|gb|ACK48563.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella baltica OS223]
 gi|304349324|gb|EFM13734.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella baltica OS183]
 gi|306910946|gb|EFN41373.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella baltica BA175]
          Length = 285

 Score =  211 bits (537), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 110/284 (38%), Positives = 171/284 (60%), Gaps = 7/284 (2%)

Query: 4   KNMSIIV-NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           ++M++ V  G   L  YIH +  I ML+ + EY LAKR +E GDL AA +L+ SHLR VV
Sbjct: 6   QSMALTVPQGASSLEAYIHSVTSISMLDAEAEYELAKRLQETGDLQAAKQLIMSHLRFVV 65

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A GY GYGLP ++++ EGNIGLM+AVK+FDP+ G RL ++++ WIKA + EY+L++W 
Sbjct: 66  HVAKGYSGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYVLKNWR 125

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFN+R+ K  L   +D      +V  +A+ L VS+++V  M  R+A 
Sbjct: 126 IVKVATTKAQRKLFFNIRKAKKRLGWFSD-----AEVTMVAENLGVSKADVTEMESRMAA 180

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERR 241
            +    L N  D+         + DH       IE +    N +  L  ++  L+ R + 
Sbjct: 181 QDPAFDLTNDQDEEHDFAPVHYLEDHSSDLAENIENDNWESNAQGRLLSAIKTLDERSQH 240

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           I  AR L ++  TL+ L+  ++VS ER+RQ+E  A  K++  ++
Sbjct: 241 ILRARWLDDDKTTLQELAETYQVSAERIRQLEKNAMNKLKACME 284


>gi|294138987|ref|YP_003554965.1| RNA polymerase sigma-32 factor [Shewanella violacea DSS12]
 gi|293325456|dbj|BAJ00187.1| RNA polymerase sigma-32 factor [Shewanella violacea DSS12]
          Length = 286

 Score =  211 bits (537), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 112/282 (39%), Positives = 178/282 (63%), Gaps = 10/282 (3%)

Query: 4   KNMSIIV-NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           ++M+++V +G   L  Y+H    I MLE ++E+ LAKR +E GD+ AA +L+ SHLR VV
Sbjct: 6   QSMALVVPHGSGSLEAYVHSAHNISMLEAKQEHELAKRLQETGDIQAAKQLIMSHLRFVV 65

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A GY GYGLP ++++ EGNIGLM+AVK+FDP  G RL ++++ WIKA + EY+L++W 
Sbjct: 66  HVAKGYSGYGLPQADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWIKAEIHEYVLKNWR 125

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L   +D      +V  +A+ L VS+++V  M  R+A 
Sbjct: 126 IVKVATTKAQRKLFFNLRKSKKRLGWFSD-----AEVGMVAENLGVSKADVTEMESRMAA 180

Query: 183 DESLNALINSSDKNSSQWQDWL-VYDH--DGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            +    L + +D +   +   L + DH  D   QV  +  E  N+  +L  ++  L+ R 
Sbjct: 181 QDPAFDLASDNDDDIQDYAPALYLEDHSSDLANQVETDNFEADNQTRLLA-AIKTLDERS 239

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           + I +AR L E+  TL+ L++ ++VS ER+RQ+E  A  K++
Sbjct: 240 QHILQARWLNEDKTTLQELAATYQVSAERIRQLEKNAMNKLK 281


>gi|254468686|ref|ZP_05082092.1| alternative sigma factor RpoH [beta proteobacterium KB13]
 gi|207087496|gb|EDZ64779.1| alternative sigma factor RpoH [beta proteobacterium KB13]
          Length = 281

 Score =  211 bits (537), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 120/267 (44%), Positives = 168/267 (62%), Gaps = 11/267 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y  +++ IP+L + EE  LAK+  E  DL+AA +L+ SHLRLV+KIA  Y GYGL  +++
Sbjct: 19  YQQQVQAIPLLTEHEEMNLAKKLHEENDLNAARQLIMSHLRLVIKIARSYSGYGLNQADL 78

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGNIGLM+AVK+FDP RG RL +++M+WIKA +QE+++R+W LVK  TT  Q++LFFN
Sbjct: 79  VQEGNIGLMKAVKRFDPSRGVRLVSFAMYWIKAEIQEFVVRNWRLVKTATTKAQRKLFFN 138

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR +K  LQ      LK E++  IAK+LNV ES+V  M  R  G+E   AL    + N  
Sbjct: 139 LRSMKKTLQP-----LKQEEIKEIAKELNVKESDVKEMEYRFNGNEI--ALDYQDEDNED 191

Query: 199 QWQDWLVYDHDGQE---QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-QENPVT 254
           +    + Y  D      + LI KE   N  + L+ ++  ++ R R I E+R L +E   T
Sbjct: 192 EVFRPISYLQDENADPVKQLISKESESNNLSALSNAIKSIDERSRYILESRWLNEEKSKT 251

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQ 281
           L  L+ E  VS ER+RQIE  A KK++
Sbjct: 252 LHELADELGVSAERIRQIEQNALKKLK 278


>gi|114561466|ref|YP_748979.1| RNA polymerase factor sigma-32 [Shewanella frigidimarina NCIMB 400]
 gi|114332759|gb|ABI70141.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella frigidimarina
           NCIMB 400]
          Length = 285

 Score =  211 bits (537), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 111/274 (40%), Positives = 171/274 (62%), Gaps = 9/274 (3%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  YI  +  I ML+   EY +AKR +E+GDL AA +L+ SHLR VV +A GY GYGLP
Sbjct: 18  SLEAYIQSVTSINMLDADTEYDIAKRLQENGDLQAAKQLIMSHLRFVVHVAKGYSGYGLP 77

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGNIGLM+AVK+FDP+ G RL ++++ WIKA + EY+L++W +VK+ TT  Q++
Sbjct: 78  QADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYVLKNWRIVKVATTKAQRK 137

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           LFFN+R+ K  L   +D      +V  +A+ L VS+++V  M  R+A  +    L N SD
Sbjct: 138 LFFNIRKSKKRLGWFSD-----AEVTMVAENLGVSKADVTEMESRMAAQDPAFDLTNDSD 192

Query: 195 KNSSQWQDWL-VYDH--DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
            +   +   L + DH  D  +QV     E  ++  +L+ ++  L+ R + I  AR L + 
Sbjct: 193 DDHHDFAPALYLEDHSSDVADQVEHANWEADSQTRLLS-AIKTLDERSQHILRARWLDDT 251

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            VTL+ L+S +EVS ER+RQ+E  A  K++  ++
Sbjct: 252 KVTLQELASTYEVSAERIRQLEKNAMNKLKSCME 285


>gi|222150148|ref|YP_002551105.1| RNA polymerase factor sigma-32 [Agrobacterium vitis S4]
 gi|221737130|gb|ACM38093.1| alternative sigma factor RpoH [Agrobacterium vitis S4]
          Length = 285

 Score =  211 bits (536), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 111/263 (42%), Positives = 173/263 (65%), Gaps = 9/263 (3%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE+QEE+ LA R++   D  A +++  +H+RLV+ +A  +RG+GLP+ +++ EG IGL
Sbjct: 18  PYLERQEEHDLAVRWKHGNDQVARNQIAHAHMRLVIAMASKFRGFGLPLGDLIQEGYIGL 77

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +F+P R  R +TY+ WWI+A+MQ+YILR+WS+V+ GT+++QK LFFNLRRL+  L
Sbjct: 78  LEAAARFEPTRDVRFSTYAGWWIRASMQDYILRNWSIVRGGTSSSQKALFFNLRRLRAKL 137

Query: 147 ----QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQ 201
               Q +TD  +  E    IA  L VS ++V SM+ RL+  D SL A I+++ +  ++  
Sbjct: 138 AQGDQRLTDQAIHQE----IATALGVSLADVQSMDARLSSNDTSLQAPISNNGEEGAERL 193

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           D L  D    ++ + +  + + R + L  +M+ LN RE RI  ARRL E+  TLE L  E
Sbjct: 194 DMLASDEPTPDEQVTDMIDTERRLDWLRGAMAHLNEREMRIIRARRLSEDGATLEELGCE 253

Query: 262 FEVSRERVRQIEARAFKKVQESI 284
             +S+ERVRQIE RA +K++ ++
Sbjct: 254 LGISKERVRQIETRAMEKLKVAL 276


>gi|90420276|ref|ZP_01228184.1| RNA polymerase major sigma-32 factor [Aurantimonas manganoxydans
           SI85-9A1]
 gi|90335610|gb|EAS49360.1| RNA polymerase major sigma-32 factor [Aurantimonas manganoxydans
           SI85-9A1]
          Length = 289

 Score =  210 bits (535), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 105/260 (40%), Positives = 173/260 (66%), Gaps = 2/260 (0%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L+++EEY LA R++E  D  A H++ ++H+RLV+ +A  +R +GL +++++ EG++GL
Sbjct: 18  PYLQREEEYELAVRWKEKRDQEALHKITSAHMRLVISMAAKFRHFGLAMNDLIQEGHVGL 77

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 78  LEAAARFEPEREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRARL 137

Query: 147 QAITDNNLKPEQVVA-IAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWL 204
               D  +    +   IA  L VSE +V  M+ RL+G D SLNA +   +  S+  QD+L
Sbjct: 138 SQGADGGVTGSAMYKEIATALKVSEGDVALMDSRLSGPDSSLNAPLMEDESGSADRQDFL 197

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           V +    ++++    + + R   L  ++ VL+ RE +I   RRLQ++  TLE L ++  +
Sbjct: 198 VSNSPLPDEMVSVSIDDERRVTWLHSALDVLSERELKIIRERRLQDDGATLEALGTKLGI 257

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ERVRQIE RA +K++ ++
Sbjct: 258 SKERVRQIETRALEKLRAAL 277


>gi|13473307|ref|NP_104874.1| RNA polymerase factor sigma-32 [Mesorhizobium loti MAFF303099]
 gi|14024055|dbj|BAB50660.1| RpoH-like sigma factor C [Mesorhizobium loti MAFF303099]
          Length = 287

 Score =  210 bits (535), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 112/268 (41%), Positives = 174/268 (64%), Gaps = 10/268 (3%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K P LE+ EE+ LA  +++  D +A H +  +H+RLV+ +A  +R YGLP+ +++ EG++
Sbjct: 16  KAPYLERDEEHRLALLWKQDNDQNALHSITVAHMRLVISMASKFRHYGLPLGDLIQEGHV 75

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A  +F+PER  R +TY+ WWI+A+MQ+YILR+WS+V+ GT++ QK LFFNLRRL+ 
Sbjct: 76  GLLEAAARFEPEREVRFSTYATWWIRASMQDYILRNWSIVRGGTSSAQKALFFNLRRLRA 135

Query: 145 HL----QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSSDKNSSQ 199
            L    + +++  L  E  VA    L VSE++V  M+ RL A D SLN  + + D  +++
Sbjct: 136 RLANGAEPLSNTTLYREVSVA----LGVSEADVAMMDSRLSAPDSSLNMPL-ADDAGATE 190

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
             D+LV D    ++++ +K +   R   L  ++  LN RE RI E RRL +   TLE L 
Sbjct: 191 RMDFLVSDDPLPDEIVGDKIDVARRSLWLKEALHALNARELRIIEERRLNDEGATLEALG 250

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQ 287
               +S+ERVRQIEARA +K++ ++ KQ
Sbjct: 251 ETLGISKERVRQIEARAMEKLKVALVKQ 278


>gi|332977407|gb|EGK14184.1| DNA-directed RNA polymerase sigma subunit RpoH [Psychrobacter sp.
           1501(2011)]
          Length = 362

 Score =  210 bits (534), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 112/273 (41%), Positives = 164/273 (60%), Gaps = 9/273 (3%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           I L  Y++ + +IP+L  ++E  LA RY + GD+ AA  LV SHLR V+ IA  Y GYGL
Sbjct: 84  INLGAYMNSVHQIPILTTEQEQELAHRYYDEGDVEAARILVMSHLRFVIHIARSYSGYGL 143

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P ++++ EGN+GLM+AVK+FDP +G RL ++++ WIKA + E+++R+W +VK+ TT   +
Sbjct: 144 PQADLIQEGNLGLMKAVKRFDPNKGVRLVSFAVHWIKAEIHEFVIRNWRIVKVATTKAHR 203

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINS 192
           +LFFNLR LK      T+N L  E+  AIA  LNV+  +V+ M  RL   D S  A   S
Sbjct: 204 KLFFNLRSLKK-----TNNQLTLEEADAIAADLNVTRKQVLEMESRLTSYDASFEA--QS 256

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           SD     +   L  +       ++E  +  +N  N L  +M  L+ R R I E R L E 
Sbjct: 257 SDDEDGHYAPQLFLEDGVDPAEMVEDADWEENNTNALMDAMDTLDDRSRDIVEQRWLSEQ 316

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL  L++ + +S ERVRQIE  A  K++E++
Sbjct: 317 KSTLHELAAVYNISAERVRQIEKNAMDKIREAM 349


>gi|322421263|ref|YP_004200486.1| RNA polymerase sigma 32 subunit RpoH [Geobacter sp. M18]
 gi|320127650|gb|ADW15210.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter sp. M18]
          Length = 284

 Score =  210 bits (534), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 114/266 (42%), Positives = 167/266 (62%), Gaps = 6/266 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+ EI + P+L   EE  LA R+R+ GDL AAH+L+TS+LR VVKIA  YR YG+ +
Sbjct: 12  LTLYLTEINRFPLLSADEEMDLAYRFRDEGDLQAAHKLITSNLRFVVKIAGEYRSYGMKM 71

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM AV+KFDP +G RL +Y++WWI+A +Q +I+ +WSL+KIGTT  Q++L
Sbjct: 72  LDLIQEGNIGLMMAVRKFDPAKGVRLISYAVWWIRAYIQNHIISAWSLLKIGTTQAQRKL 131

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FF L + K   QAI  N      + A A  L+V ++E   M  RL G+ SL+  +   D 
Sbjct: 132 FFKLNQAK---QAII-NMTGEGDLHAAAISLDVKDTEAREMEQRLRGELSLD--VEMFDG 185

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
               + + L      QE++L E++E       +  ++  LN +ER + E R   E P+TL
Sbjct: 186 EGGTFLETLPDLRQNQEEMLAERQETTILEQGVASALGHLNEKERFVIERRVAAEEPLTL 245

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           + ++  F +SRERVRQIE  A KK++
Sbjct: 246 QEIADHFSISRERVRQIEEGALKKMK 271


>gi|217969486|ref|YP_002354720.1| RNA polymerase factor sigma-32 [Thauera sp. MZ1T]
 gi|217506813|gb|ACK53824.1| RNA polymerase, sigma 32 subunit, RpoH [Thauera sp. MZ1T]
          Length = 283

 Score =  210 bits (534), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 116/279 (41%), Positives = 177/279 (63%), Gaps = 8/279 (2%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           + ++  V     L +YI  + ++PML +Q+E  LA R R+ GD+ AA +LV SHLR+VV 
Sbjct: 3   QALTFPVPAAGSLDQYIQSVNRMPMLSEQQEVELATRLRDEGDVDAARQLVMSHLRVVVA 62

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA GY GYGLP ++++ EGNIGLM+AVK+FDP RG RL ++++ WIKA + EYIL++W L
Sbjct: 63  IARGYLGYGLPHADLIQEGNIGLMKAVKRFDPTRGVRLVSFAIHWIKAEIHEYILKNWRL 122

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG- 182
           VKI TT  Q++LFFNLR +K        + L+P +V +IA +L V   EV+ M  RL+G 
Sbjct: 123 VKIATTKAQRKLFFNLRGMKQ-----DSSTLQPAEVRSIAAQLGVKPEEVVEMETRLSGR 177

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
           D  L+A  +  D+  +    +L   H    + + + +  + + + L  +++ L+ R R I
Sbjct: 178 DIPLDAGSDDEDERFAPIA-YLPDPHAEPSEQVEQAQLARLQDSGLRDALASLDERSRAI 236

Query: 243 FEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            + R L E +  TL  L++E+ VS ER+RQIEA+A +K+
Sbjct: 237 VQRRWLAEGDSATLHELAAEYGVSAERIRQIEAKAMQKM 275


>gi|319781051|ref|YP_004140527.1| RNA polymerase sigma factor, sigma-70 family [Mesorhizobium ciceri
           biovar biserrulae WSM1271]
 gi|317166939|gb|ADV10477.1| RNA polymerase sigma factor, sigma-70 family [Mesorhizobium ciceri
           biovar biserrulae WSM1271]
          Length = 287

 Score =  210 bits (534), Expect = 2e-52,   Method: Compositional matrix adjust.
 Identities = 112/268 (41%), Positives = 175/268 (65%), Gaps = 10/268 (3%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K P LE+ EE+ LA  ++E  D +A H +  +H+RLV+ +A  +R YGLP+ ++V EG++
Sbjct: 16  KAPYLERDEEHRLALLWKEDNDQNALHSITVAHMRLVISMASKFRHYGLPLGDLVQEGHV 75

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A  +F+PER  R +TY+ WWI+A+MQ+YILR+WS+V+ GT++ QK LFFNLRRL+ 
Sbjct: 76  GLLEAAARFEPEREVRFSTYATWWIRASMQDYILRNWSIVRGGTSSAQKALFFNLRRLRA 135

Query: 145 HL----QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSSDKNSSQ 199
            L    + +++  L  E    +++ L VSE++V  M+ RL A D SLN  + + D  S++
Sbjct: 136 RLANGAEPLSNATLYRE----VSEALGVSEADVAMMDSRLSAPDSSLNMPV-ADDAGSTE 190

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
             ++LV D    ++++ +K +   R   L  ++  LN RE RI E RRL +   TLE L 
Sbjct: 191 RMEFLVSDDPLPDEIVGDKIDVARRSLWLREALRALNARELRIIEERRLNDEGATLEALG 250

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQ 287
               +S+ERVRQIEARA +K++ ++ KQ
Sbjct: 251 ETLGISKERVRQIEARAMEKLKVALVKQ 278


>gi|225024603|ref|ZP_03713795.1| hypothetical protein EIKCOROL_01480 [Eikenella corrodens ATCC
           23834]
 gi|224942617|gb|EEG23826.1| hypothetical protein EIKCOROL_01480 [Eikenella corrodens ATCC
           23834]
          Length = 283

 Score =  210 bits (534), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 118/282 (41%), Positives = 176/282 (62%), Gaps = 8/282 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           MN      I +G   L +YIH +  IP+L  +EE+ LA R  + GDL AA +L+ SHLR+
Sbjct: 1   MNNAFALPIPSGHGSLEQYIHTVNSIPLLTAEEEHSLAVRQLQ-GDLEAAKKLILSHLRV 59

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+ILR+
Sbjct: 60  VVSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPNRGARLFSFAVHWIKAEIHEFILRN 119

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +V++ TT  Q++LFFNLR ++  +     N L PE+   IA  L V   EV+ M  R+
Sbjct: 120 WRMVRVATTKPQRKLFFNLRSMRKSM-----NALSPEEAQTIADDLGVKMDEVLEMEQRM 174

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            G D +L    + SD++S    DWL        Q + +K     +   L  +++ L+ R 
Sbjct: 175 TGKDIALLPDNSDSDEDSYAPIDWLADTRSEPTQQIAQKARYAMQTEGLQNALAQLDDRS 234

Query: 240 RRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKV 280
           RRI E+R LQ++  +TL  L++E+ VS ER+RQIEA+A +K+
Sbjct: 235 RRIVESRWLQDDGGLTLHELAAEYGVSAERIRQIEAKAIQKL 276


>gi|56477835|ref|YP_159424.1| RNA polymerase factor sigma-32 [Aromatoleum aromaticum EbN1]
 gi|56313878|emb|CAI08523.1| Sigma-32 factor RpoH (RNA polymerase sigma factor) [Aromatoleum
           aromaticum EbN1]
          Length = 283

 Score =  209 bits (533), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 120/280 (42%), Positives = 175/280 (62%), Gaps = 11/280 (3%)

Query: 6   MSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +S  V   +G + +YI  + +IP+L +QEE  LA R R  GDL AA  LV SHLRLVV I
Sbjct: 5   LSFPVPFAVGSIDQYIQSVNRIPLLTEQEEVSLATRLRNEGDLEAARGLVMSHLRLVVAI 64

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           + GY GYGLP ++++ EGNIGLM+AVK+FDP+RG RL ++++ WIKA + EYIL++W LV
Sbjct: 65  SRGYLGYGLPHADLIQEGNIGLMKAVKRFDPDRGVRLVSFAIHWIKAEIHEYILKNWRLV 124

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           KI TT  Q++LFFNLR LK          L  ++VVA+AK+L V   EV+ M  RL G +
Sbjct: 125 KIATTKAQRKLFFNLRSLKQ-----DTGTLNRDEVVAVAKQLGVKPEEVVEMETRLTGRD 179

Query: 185 SLNALINSSDKNSSQWQD--WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
               L    D +   +    +L   +    +VL + +  + +   L+ +++ L+ R R I
Sbjct: 180 I--QLEGGPDDDEHHFAPIAYLPDPNAEPSEVLEQAQLARLQDEGLSDALASLDDRSRTI 237

Query: 243 FEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            + R L E +  TL  L++E+ VS ER+RQIEA+A +K++
Sbjct: 238 VKRRWLTEGDSATLHELAAEYGVSAERIRQIEAKAMQKMR 277


>gi|239817346|ref|YP_002946256.1| RNA polymerase, sigma 32 subunit, RpoH [Variovorax paradoxus S110]
 gi|239803923|gb|ACS20990.1| RNA polymerase, sigma 32 subunit, RpoH [Variovorax paradoxus S110]
          Length = 313

 Score =  209 bits (533), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 115/283 (40%), Positives = 172/283 (60%), Gaps = 14/283 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI    ++PML  +EE   A+R R+H DL AA  L+ SHLRLVV I+  Y GYGLP 
Sbjct: 27  LDAYISAANRLPMLTLEEEQGFARRLRDHNDLEAAGALILSHLRLVVSISRQYLGYGLPH 86

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM+AVK+FDP++G RL +Y+M WIKA + EYIL++W +VK+ TT  Q++L
Sbjct: 87  GDLIQEGNVGLMKAVKRFDPDQGVRLVSYAMHWIKAEIHEYILKNWRMVKVATTKAQRKL 146

Query: 136 FFNLRRLKGHLQ---AITDNN-----LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
           FFNLR +K   +   A  DN      L P++V  +A +LNV   EV+ M  RL+G + L 
Sbjct: 147 FFNLRSMKQGFKADSAAADNGTHRDTLSPDEVSQMATRLNVKPEEVLEMETRLSGGDVLL 206

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFEAR 246
               S D + +      + D   +   L+E ++R     + +  ++  L+ R RRI E R
Sbjct: 207 DPGPSDDGDEAFGPIAYLADATQEPTALLESQQRDRLSSDGIATALEALDDRSRRIVEER 266

Query: 247 RLQENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L+ N      +TL +L++ + VS ER+RQIE  A KK+++++
Sbjct: 267 WLKVNDDGSGGMTLHDLAAVYGVSAERIRQIEVAAMKKMKKAL 309


>gi|71064787|ref|YP_263514.1| RNA polymerase factor sigma-32 [Psychrobacter arcticus 273-4]
 gi|71037772|gb|AAZ18080.1| putative Sigma 32 (RpoH) [Psychrobacter arcticus 273-4]
          Length = 341

 Score =  209 bits (533), Expect = 3e-52,   Method: Compositional matrix adjust.
 Identities = 113/274 (41%), Positives = 169/274 (61%), Gaps = 11/274 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + L  YI+ + +IP+L   +E  LA RY + GD+ AA  LV SHLR V+ IA  Y GYGL
Sbjct: 64  VNLGAYINTVHQIPILTPTQEQELAHRYYDEGDVEAARLLVMSHLRFVIHIARSYSGYGL 123

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P ++++ EGN+GLM+AVK+FDP +G RL ++++ WIKA + E+++R+W +VK+ TT   +
Sbjct: 124 PQADLIQEGNLGLMKAVKRFDPNKGVRLVSFAVHWIKAEIHEFVIRNWRIVKVATTKAHR 183

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINS 192
           +LFFNLR LK      T+N L  E+  AIA  LNV+  +V+ M  RL   D S  A   S
Sbjct: 184 KLFFNLRSLKK-----TNNQLTIEEADAIANDLNVTRKQVLEMESRLTSYDASFEA--QS 236

Query: 193 SDKNSSQWQDWLVYDHDGQE--QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           SD +  ++   L  + DG +  +++ E +  +N  + L  +M  L+ R R I E R L E
Sbjct: 237 SDDDDGRYAPQLFLE-DGIDPAEIVEESDWEENNSSALIAAMETLDDRSRDIVEQRWLSE 295

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              TL  L++ + +S ERVRQIE  A  K++E++
Sbjct: 296 QKSTLHELAAVYSISAERVRQIEKNAMDKIREAM 329


>gi|253699229|ref|YP_003020418.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter sp. M21]
 gi|251774079|gb|ACT16660.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter sp. M21]
          Length = 285

 Score =  209 bits (532), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 115/266 (43%), Positives = 168/266 (63%), Gaps = 5/266 (1%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+ EI + P+L   EE  LA R+R  GDL AAHRL+TS+LR VVKIA  YR YG+ +
Sbjct: 12  LTLYLTEINRFPLLTADEEMDLACRFRREGDLEAAHRLITSNLRFVVKIAGEYRSYGMKM 71

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM AV+KFDP++G RL +Y++WWI+A +Q +I+ +WSL+KIGTT  Q++L
Sbjct: 72  LDLIQEGNIGLMMAVRKFDPDKGVRLISYAVWWIRAYIQNHIISAWSLLKIGTTQAQRKL 131

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FF L + K   QAI  N      + A A  L+V + E   M  RL G+ SL+  +   + 
Sbjct: 132 FFKLNQAK---QAIV-NMTGEGDLHAAAISLDVKDHEAQEMEQRLRGELSLDVEMFEGEG 187

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
             + + + L      QE++L E++E       +  ++  LN +ER + E R   ENP+TL
Sbjct: 188 GGT-FLESLPDLRQNQEEMLAERQETTILERNVASALEDLNEKERFVIEQRVAAENPMTL 246

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           + ++  F +SRERVRQIE  A KK++
Sbjct: 247 QEIADHFSISRERVRQIEEGALKKMK 272


>gi|93005058|ref|YP_579495.1| RNA polymerase factor sigma-32 [Psychrobacter cryohalolentis K5]
 gi|92392736|gb|ABE74011.1| sigma 32 (RpoH) [Psychrobacter cryohalolentis K5]
          Length = 287

 Score =  209 bits (532), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 113/274 (41%), Positives = 169/274 (61%), Gaps = 11/274 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + L  YI+ + +IP+L   +E  LA RY + GD+ AA  LV SHLR V+ IA  Y GYGL
Sbjct: 10  VNLGAYINTVHQIPILTPTQEQELAHRYYDEGDVEAARLLVMSHLRFVIHIARSYSGYGL 69

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P ++++ EGN+GLM+AVK+FDP +G RL ++++ WIKA + E+++R+W +VK+ TT   +
Sbjct: 70  PQADLIQEGNLGLMKAVKRFDPNKGVRLVSFAVHWIKAEIHEFVIRNWRIVKVATTKAHR 129

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINS 192
           +LFFNLR LK      T+N L  E+  AIA  LNV+  +V+ M  RL   D S  A   S
Sbjct: 130 KLFFNLRSLKK-----TNNQLTLEEADAIANDLNVTRKQVLEMESRLTSYDASFEA--QS 182

Query: 193 SDKNSSQWQDWLVYDHDGQE--QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           SD +  ++   L  + DG +  +++ E +  +N  + L  +M  L+ R R I E R L E
Sbjct: 183 SDDDDGRYAPQLFLE-DGIDPAEIVEESDWEENNSSALIAAMETLDDRSRDIVEQRWLSE 241

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              TL  L++ + +S ERVRQIE  A  K++E++
Sbjct: 242 QKSTLHELAAVYSISAERVRQIEKNAMDKIREAM 275


>gi|163736875|ref|ZP_02144293.1| RNA polymerase, sigma 32 subunit, RpoH [Phaeobacter gallaeciensis
           BS107]
 gi|161389479|gb|EDQ13830.1| RNA polymerase, sigma 32 subunit, RpoH [Phaeobacter gallaeciensis
           BS107]
          Length = 292

 Score =  209 bits (532), Expect = 4e-52,   Method: Compositional matrix adjust.
 Identities = 109/266 (40%), Positives = 178/266 (66%), Gaps = 6/266 (2%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K  +L+ + E  LA  +R+  D+ A HRL+ +++RL + +A  +R YG P+++++ E  +
Sbjct: 17  KAELLDAETELQLAYAWRDERDVQALHRLINAYMRLAISMASKFRRYGAPMNDLIQEAGL 76

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFN+RR++ 
Sbjct: 77  GLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQA 136

Query: 145 HL--QAITDN-NLKPEQV-VAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQ 199
            L  QA +D   L   Q+   IA ++ V   +V  M+ RLAG D SLNA + SS+    +
Sbjct: 137 QLERQAQSDGARLDKHQLHQQIATEIGVPLRDVQMMDGRLAGSDFSLNA-VQSSEDEGRE 195

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
           W + L  D     +++ E  + +  R+ L  +M  LN RER I   R+L+E P TLE+L 
Sbjct: 196 WIEALEDDSAQAAELVEESHDTRQLRDWLVEAMQALNERERFIITERKLREKPRTLESLG 255

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQ 285
           +E ++S+ERVRQ+EA AF+K+++S++
Sbjct: 256 NELDLSKERVRQLEAGAFQKMRKSLE 281


>gi|113972098|ref|YP_735891.1| RNA polymerase factor sigma-32 [Shewanella sp. MR-4]
 gi|114049328|ref|YP_739878.1| RNA polymerase factor sigma-32 [Shewanella sp. MR-7]
 gi|117922401|ref|YP_871593.1| RNA polymerase factor sigma-32 [Shewanella sp. ANA-3]
 gi|113886782|gb|ABI40834.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella sp. MR-4]
 gi|113890770|gb|ABI44821.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella sp. MR-7]
 gi|117614733|gb|ABK50187.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella sp. ANA-3]
          Length = 285

 Score =  209 bits (531), Expect = 5e-52,   Method: Compositional matrix adjust.
 Identities = 112/286 (39%), Positives = 175/286 (61%), Gaps = 11/286 (3%)

Query: 4   KNMSIIV-NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           ++M++ V  G   L  YIH +  + ML+ + EY LAKR +E GDL AA +L+ SHLR VV
Sbjct: 6   QSMALTVPQGSSSLEAYIHSVTSMTMLDAETEYELAKRLQETGDLQAAKQLIMSHLRFVV 65

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A GY GYGLP ++++ EGNIGLM+AVK+FDP+ G RL ++++ WIKA + EY+L++W 
Sbjct: 66  HVAKGYSGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYVLKNWR 125

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFN+R+ K  L   +D+     +V  +A+ L VS+++V  M  R+A 
Sbjct: 126 IVKVATTKAQRKLFFNIRKAKTRLGWFSDD-----EVAMVAENLGVSKADVTEMESRMAA 180

Query: 183 DESLNALINSSDKNSSQWQDWLVY--DHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRE 239
            +   A   SSD +  Q    + Y  DH       IE +    N +  L  ++  L+ R 
Sbjct: 181 QDP--AFDLSSDNDDEQDFAPVHYLEDHSSDLAENIENDNWESNAQGRLLSAIKTLDERS 238

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + I  AR L ++  TL+ L+  ++VS ER+RQ+E  A  K++  ++
Sbjct: 239 QHILRARWLDDDKTTLQELAETYQVSAERIRQLEKNAMNKLKACME 284


>gi|160897140|ref|YP_001562722.1| RNA polymerase sigma 32 subunit RpoH [Delftia acidovorans SPH-1]
 gi|160362724|gb|ABX34337.1| RNA polymerase, sigma 32 subunit, RpoH [Delftia acidovorans SPH-1]
          Length = 314

 Score =  209 bits (531), Expect = 5e-52,   Method: Compositional matrix adjust.
 Identities = 118/286 (41%), Positives = 175/286 (61%), Gaps = 19/286 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + ++PML  +EE   A++ +EH DL AA RLV SHLRLVV I+  Y GYGLP 
Sbjct: 27  LDAYISAVNRLPMLTLEEEQDYARKLKEHSDLDAAGRLVMSHLRLVVSISRQYLGYGLPH 86

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM+AVK+FDP++  RL +Y+M WIKA + EYIL++W +VK+ TT  Q++L
Sbjct: 87  GDLIQEGNVGLMKAVKRFDPDQNVRLVSYAMHWIKAEIHEYILKNWRMVKVATTKAQRKL 146

Query: 136 FFNLRRLKGHLQ---------AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
           FFNLR +K  L+         A+  + L   ++ A+A+KLNV   EV+ M  RLAG + L
Sbjct: 147 FFNLRSMKQGLKSDAAMAEDGAMLRDTLTSGEIDAVAEKLNVKREEVMEMETRLAGGDVL 206

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQ--VLIEKEERKN-RRNMLTRSMSVLNPRERRIF 243
             L  S   +  Q    + Y  DG  +   +IE  +R +   + +  ++  L+ R RRI 
Sbjct: 207 --LDPSPSDDGEQAFGPIAYLADGAHEPTAMIESRQRDHLATDGIAMALDSLDDRSRRIV 264

Query: 244 EARRLQENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           E R L+ N      +TL  L++ + VS ER+RQIE  A KK+++++
Sbjct: 265 EERWLKVNDDGSGGMTLHELAAVYGVSAERIRQIEVAAMKKMKKAL 310


>gi|319788352|ref|YP_004147827.1| RNA polymerase, sigma 32 subunit, RpoH [Pseudoxanthomonas
           suwonensis 11-1]
 gi|317466864|gb|ADV28596.1| RNA polymerase, sigma 32 subunit, RpoH [Pseudoxanthomonas
           suwonensis 11-1]
          Length = 292

 Score =  209 bits (531), Expect = 6e-52,   Method: Compositional matrix adjust.
 Identities = 114/269 (42%), Positives = 171/269 (63%), Gaps = 8/269 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + +IP+L  +EE  LA+RYR+  DL AA  LV SHLR VV +A GY GYGL +
Sbjct: 24  LEAYIGAVHQIPVLSVEEEQALARRYRDQEDLDAARELVHSHLRFVVHVARGYNGYGLQL 83

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AVK+FDP+ G RL ++++ WI+A + E+IL++W +VK+ TT  Q++L
Sbjct: 84  GDLIQEGNIGLMKAVKRFDPDLGVRLVSFAVHWIRAEIHEFILKNWRIVKVATTKAQRKL 143

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR+ K  L       +   +V A+AK LNVSE EV+ M  RL+G D   +A  +  +
Sbjct: 144 FFNLRKAKTRL-----GWMNAAEVSAVAKDLNVSEREVLEMESRLSGRDIGFDAPADEDE 198

Query: 195 KNS-SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-QENP 252
           +++      +LV   +   Q L  ++   ++ ++L   ++ L+ R R I   R L  E+ 
Sbjct: 199 EHAPPSPAAYLVSMDEDPSQALEREDSEGHKLDLLRDGLASLDARSRDIIARRWLDDESK 258

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           VTL+ L+ E+ VS ER+RQIEA A KK++
Sbjct: 259 VTLQELADEYGVSAERIRQIEANAMKKMR 287


>gi|148652168|ref|YP_001279261.1| RNA polymerase factor sigma-32 [Psychrobacter sp. PRwf-1]
 gi|148571252|gb|ABQ93311.1| RNA polymerase, sigma 32 subunit, RpoH [Psychrobacter sp. PRwf-1]
          Length = 372

 Score =  209 bits (531), Expect = 6e-52,   Method: Compositional matrix adjust.
 Identities = 111/273 (40%), Positives = 164/273 (60%), Gaps = 9/273 (3%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           I L  Y++ + +IP+L  ++E  LA RY + GD+ AA  LV SHLR V+ IA  Y GYGL
Sbjct: 94  INLGAYMNSVHQIPILTTEQEQELAHRYYDDGDVEAARILVMSHLRFVIHIARSYSGYGL 153

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P ++++ EGN+GLM+AVK+FDP +G RL ++++ WIKA + E+++R+W +VK+ TT   +
Sbjct: 154 PQADLIQEGNLGLMKAVKRFDPNKGVRLVSFAVHWIKAEIHEFVIRNWRIVKVATTKAHR 213

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINS 192
           +LFFNLR LK      T+N L  E+  AIA  LNV+  +V+ M  RL   D S  A   S
Sbjct: 214 KLFFNLRSLKK-----TNNQLTLEEADAIAADLNVTRKQVLEMESRLTSYDASFEA--QS 266

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           +D     +   L  +       ++E  +  +N  N L  +M  L+ R R I E R L E 
Sbjct: 267 TDDEDGHYAPQLFLEDGVDPAEMVEDADWEENNTNALMDAMDTLDERSRDIVEQRWLSEQ 326

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL  L++ + +S ERVRQIE  A  K++E++
Sbjct: 327 KSTLHELAAVYNISAERVRQIEKNAMDKIREAM 359


>gi|296448000|ref|ZP_06889906.1| RNA polymerase, sigma 32 subunit, RpoH [Methylosinus trichosporium
           OB3b]
 gi|296254510|gb|EFH01631.1| RNA polymerase, sigma 32 subunit, RpoH [Methylosinus trichosporium
           OB3b]
          Length = 289

 Score =  208 bits (530), Expect = 6e-52,   Method: Compositional matrix adjust.
 Identities = 109/261 (41%), Positives = 175/261 (67%), Gaps = 3/261 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE++EE  LA  +++  D  A H+L ++H+RLV+ +A+ +R YGLP++++V EG++GL
Sbjct: 19  PFLEREEEKQLAIAWKDRRDGVALHKLASAHMRLVIALAVRFRHYGLPVADLVQEGHVGL 78

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +F PER  R +TY+ WWI+A++Q+Y+LR+WS+V+ GT+++QK LFFNLRRL+  L
Sbjct: 79  LEAAARFAPERDVRFSTYATWWIRASIQDYVLRNWSIVRGGTSSSQKALFFNLRRLRAKL 138

Query: 147 -QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNA-LINSSDKNSSQWQDW 203
             A        +   AIA  + VS ++V  MN RLAG D SLN+ LI     +S++  D+
Sbjct: 139 AHAPQTAAESGDAFDAIAGAIGVSRADVELMNSRLAGSDVSLNSQLIEDDSASSAERMDF 198

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           LV D    ++++ ++ +   R   L  ++ +L+ RE RI + RRL E+ VTLE+L     
Sbjct: 199 LVDDRPLPDEIVEDRLDSDRRARWLADALKLLSERELRIVQERRLSESLVTLESLGDRLG 258

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ERVRQIE RA  K+++++
Sbjct: 259 ISKERVRQIENRALCKLRKAL 279


>gi|241764416|ref|ZP_04762441.1| RNA polymerase, sigma 32 subunit, RpoH [Acidovorax delafieldii 2AN]
 gi|241366206|gb|EER60777.1| RNA polymerase, sigma 32 subunit, RpoH [Acidovorax delafieldii 2AN]
          Length = 312

 Score =  208 bits (530), Expect = 7e-52,   Method: Compositional matrix adjust.
 Identities = 113/282 (40%), Positives = 170/282 (60%), Gaps = 13/282 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + ++P+L  +EE   A++ R+H D+ AA RLV SHLRLVV IA  Y GYGLP 
Sbjct: 27  LDAYISAVNRLPLLTHEEEQTYARKLRDHNDVDAAGRLVMSHLRLVVSIARQYLGYGLPH 86

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM+AVK+FDP++G RL +Y+M WIKA + EYIL++W +VK+ TT  Q++L
Sbjct: 87  GDLIQEGNVGLMKAVKRFDPDQGVRLVSYAMHWIKAEIHEYILKNWRMVKVATTKAQRKL 146

Query: 136 FFNLRRLKGHLQAITD-------NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           FFNLR +K   +A          + L  +++ A+A +LNV   EVI M  R+AG + L  
Sbjct: 147 FFNLRSMKQGFKADAAVDAATHRDTLSEQEIDAVATQLNVKREEVIEMETRMAGGDVLLD 206

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFEARR 247
              S D   +      + D   +   +IE  +R     + +  +++ L+ R RRI E R 
Sbjct: 207 PAPSDDGEQAFGPIGYLADASHEPTAMIESRQRDALATDGIAMALARLDDRSRRIVEERW 266

Query: 248 LQENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L+ N      +TL  L++ + VS ER+RQIE  A KK++ ++
Sbjct: 267 LKVNDDGTGGMTLHELAAVYGVSAERIRQIEVAAMKKMKTAL 308


>gi|12744861|gb|AAK06822.1|AF326688_1 RNA polymerase sigma-32 factor [Burkholderia pseudomallei]
          Length = 281

 Score =  208 bits (530), Expect = 8e-52,   Method: Compositional matrix adjust.
 Identities = 117/283 (41%), Positives = 171/283 (60%), Gaps = 13/283 (4%)

Query: 9   IVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++ G +G +  YI  + +IP+L  +EE   A  YRE  +L AA RLV SHLRLVV +A  
Sbjct: 1   MLPGHLGNIDAYIQAVNRIPLLSAEEERQYATEYREQNNLDAARRLVLSHLRLVVSVARN 60

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y GYGLP  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W +VK+G
Sbjct: 61  YLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKVG 120

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESL 186
                 + FFNLR  K   QA T     PE++  +A++LNV   EV  M  RL+ GD +L
Sbjct: 121 DDEGAAQAFFNLRSHKKGTQAFT-----PEEIDGLAQELNVKREEVAEMETRLSGGDIAL 175

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              I+  +++ +    +L   H+    VL  ++    + + + R++  L+ R RRI EAR
Sbjct: 176 EGQIDDGEESYAPIA-YLADSHNEPTAVLAARQRDMLQTDGIARALESLDARSRRIIEAR 234

Query: 247 RLQ-----ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L          TL +L++EF VS ER+RQIEA A KK++ ++
Sbjct: 235 WLNVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRTAL 277


>gi|24376056|ref|NP_720099.1| RNA polymerase factor sigma-32 [Shewanella oneidensis MR-1]
 gi|24351072|gb|AAN57543.1|AE015890_4 RNA polymerase sigma-32 factor [Shewanella oneidensis MR-1]
          Length = 285

 Score =  208 bits (529), Expect = 9e-52,   Method: Compositional matrix adjust.
 Identities = 108/284 (38%), Positives = 172/284 (60%), Gaps = 7/284 (2%)

Query: 4   KNMSIIV-NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           ++M++ V  G   L  YIH +  + ML+ + EY LAKR +E GDL AA +L+ SHLR VV
Sbjct: 6   QSMALTVPQGSSSLEAYIHSVTSMNMLDAETEYELAKRLQETGDLQAAKQLIMSHLRFVV 65

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A GY GYGLP ++++ EGNIGLM+AVK+FDP+ G RL ++++ WIKA + EY+L++W 
Sbjct: 66  HVAKGYAGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYVLKNWR 125

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFN+R+ K  L   +D+     +V  +A+ L VS+++V  M  R+A 
Sbjct: 126 IVKVATTKAQRKLFFNIRKAKTRLGWFSDD-----EVTMVAENLGVSKADVTEMESRMAA 180

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERR 241
            +    L + +D          + DH       IE +    N +  L  ++  L+ R + 
Sbjct: 181 QDPAFDLSSDNDDEHDFAPVHYLEDHSSDLAENIENDNWESNAQGRLLSAIKTLDERSQH 240

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           I  AR L ++  TL+ L+  ++VS ER+RQ+E  A  K++  ++
Sbjct: 241 ILRARWLDDDKTTLQELAETYQVSAERIRQLEKNAMNKLKACME 284


>gi|15839280|ref|NP_299968.1| RNA polymerase factor sigma-32 [Xylella fastidiosa 9a5c]
 gi|9107932|gb|AAF85488.1|AE004075_3 RNA polymerase sigma-32 factor [Xylella fastidiosa 9a5c]
          Length = 293

 Score =  207 bits (528), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 113/268 (42%), Positives = 166/268 (61%), Gaps = 9/268 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + +I +L   EE +LA+RYR+  DL AA  LV SHLR VV++A GY GYGL +
Sbjct: 28  LEAYISAVHQISVLSVDEEQLLARRYRDQQDLDAARELVHSHLRFVVRVARGYSGYGLSL 87

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AVK+FDP+ G RL +++M WI+A M E+IL++W +VK+ TT  Q++L
Sbjct: 88  GDLIQEGNIGLMKAVKRFDPDMGVRLVSFAMHWIRAEMHEFILKNWRIVKVATTKAQRKL 147

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR+ +  L       +  E+V A+A+ LNVSE EV+ M  RL+G D   +A     D
Sbjct: 148 FFNLRKSRTRL-----GWMNAEEVSAVARDLNVSEREVLEMESRLSGRDIGFDA--PEED 200

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ-ENPV 253
                   +L+ +     Q        + +  +L   +SVL+ R R I + R L+ +  +
Sbjct: 201 NAPPSPVGYLIANDGDPSQAYERGNSEETKLRLLQEGLSVLDTRSRDIIQRRWLETDKKI 260

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TL+ L+ E+ VS ER+RQIEA A KK++
Sbjct: 261 TLQELAEEYGVSAERIRQIEANALKKMK 288


>gi|91787153|ref|YP_548105.1| sigma 32 (RpoH) [Polaromonas sp. JS666]
 gi|91696378|gb|ABE43207.1| RNA polymerase, sigma 32 subunit, RpoH [Polaromonas sp. JS666]
          Length = 322

 Score =  207 bits (527), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 114/278 (41%), Positives = 171/278 (61%), Gaps = 11/278 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + ++PML  ++E   AK+ +E+ DL +A +LV SHLRLVV I+  Y GYGLP 
Sbjct: 39  LDAYISAVNRLPMLTLEQEQEFAKKLKENNDLDSAGKLVLSHLRLVVSISRKYLGYGLPH 98

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AVK+FDPE+  RL +Y+M WIKA + EYIL++W +VK+ TT  Q++L
Sbjct: 99  GDLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHWIKAEIHEYILKNWRMVKVATTKAQRKL 158

Query: 136 FFNLRRLKGHLQAITD-----NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
           FFNLR +K   +   D     + L   Q+ ++AK LNV   EVI M  R++G + L    
Sbjct: 159 FFNLRSMKQGFKDDADVATHRDTLTEGQIDSMAKTLNVKREEVIEMEQRMSGGDVLLDPS 218

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFEARRLQ 249
            S D   +      + D   +   L+E  +R +   + ++ ++  L+PR RRI E R L+
Sbjct: 219 PSDDGEDAFGPIAYLADATQEPTALMESRQRDSLASDGISAALQELDPRSRRIVEERWLK 278

Query: 250 ENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            N      +TL +L+ E++VS ER+RQIE  A KK+++
Sbjct: 279 VNDDGSGGMTLHDLADEYQVSAERIRQIEVSAMKKMKK 316


>gi|108762657|ref|YP_634340.1| RNA polymerase sigma-C factor [Myxococcus xanthus DK 1622]
 gi|585929|sp|Q07083|RPSC_MYXXA RecName: Full=RNA polymerase sigma-C factor
 gi|293866|gb|AAA25408.1| sigma factor [Myxococcus xanthus]
 gi|108466537|gb|ABF91722.1| RNA polymerase sigma-C factor [Myxococcus xanthus DK 1622]
          Length = 295

 Score =  207 bits (527), Expect = 1e-51,   Method: Compositional matrix adjust.
 Identities = 113/267 (42%), Positives = 173/267 (64%), Gaps = 4/267 (1%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           LS Y+ EI + P+L + +E  L+KR+R  GDL+A H+LVT++LR VVK+A  YR YGL +
Sbjct: 13  LSTYLSEINQYPLLTQPQEQELSKRFR-AGDLAAGHQLVTANLRFVVKVAYEYRSYGLKM 71

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           S+++ E NIGLM+AV+KFDP++G RL +Y++WWI+A +Q  IL++WSLVK+GTT  Q+RL
Sbjct: 72  SDLIQEANIGLMKAVQKFDPDKGIRLISYAVWWIRAYIQNCILKNWSLVKLGTTQAQRRL 131

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FF+L R +  L+ +   +        IA+KLNV  SEV  M  R+ G D SL+A +   D
Sbjct: 132 FFSLARTRRELEKMGAGDANVVNAEEIARKLNVKASEVREMEQRMGGRDLSLDAPMG-ED 190

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
            +++   D++  +       + ++++    R ++ R++  L+PRER I E R + +  +T
Sbjct: 191 GDATHL-DFVESESVSAVDEVADRQQANLTRELVQRALRRLDPRERFIIEQRVMGDAEMT 249

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQ 281
           L  L   F  SRER RQ+E RA  K++
Sbjct: 250 LSELGEHFGFSRERARQLEIRAKDKLK 276


>gi|28199909|ref|NP_780223.1| RNA polymerase factor sigma-32 [Xylella fastidiosa Temecula1]
 gi|28058040|gb|AAO29872.1| RNA polymerase sigma-32 factor [Xylella fastidiosa Temecula1]
          Length = 293

 Score =  207 bits (526), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 113/268 (42%), Positives = 166/268 (61%), Gaps = 9/268 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + +I +L   EE +LA+RYR+  DL AA  LV SHLR VV++A GY GYGL +
Sbjct: 28  LEAYISAVHQISVLSVDEEQLLARRYRDQQDLDAARELVHSHLRFVVRVARGYSGYGLSL 87

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AVK+FDP+ G RL +++M WI+A M E+IL++W +VK+ TT  Q++L
Sbjct: 88  GDLIQEGNIGLMKAVKRFDPDMGVRLVSFAMHWIRAEMHEFILKNWRIVKVATTKAQRKL 147

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR+ +  L       +  E+V A+A+ LNVSE EV+ M  RL+G D   +A     D
Sbjct: 148 FFNLRKSRTRL-----GWMNAEEVSAVARDLNVSEREVLEMESRLSGRDIGFDA--PEED 200

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ-ENPV 253
                   +L+ +     Q        + +  +L   +SVL+ R R I + R L+ +  +
Sbjct: 201 NAPPSPVGYLIANDGDPSQAYERGNSEETQLRLLQEGLSVLDTRSRDIIQRRWLETDKKI 260

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TL+ L+ E+ VS ER+RQIEA A KK++
Sbjct: 261 TLQELAEEYGVSAERIRQIEANALKKMK 288


>gi|182682661|ref|YP_001830821.1| RNA polymerase factor sigma-32 [Xylella fastidiosa M23]
 gi|182632771|gb|ACB93547.1| RNA polymerase, sigma 32 subunit, RpoH [Xylella fastidiosa M23]
          Length = 288

 Score =  207 bits (526), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 113/268 (42%), Positives = 166/268 (61%), Gaps = 9/268 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + +I +L   EE +LA+RYR+  DL AA  LV SHLR VV++A GY GYGL +
Sbjct: 23  LEAYISAVHQISVLSVDEEQLLARRYRDQQDLDAARELVHSHLRFVVRVARGYSGYGLSL 82

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AVK+FDP+ G RL +++M WI+A M E+IL++W +VK+ TT  Q++L
Sbjct: 83  GDLIQEGNIGLMKAVKRFDPDMGVRLVSFAMHWIRAEMHEFILKNWRIVKVATTKAQRKL 142

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR+ +  L       +  E+V A+A+ LNVSE EV+ M  RL+G D   +A     D
Sbjct: 143 FFNLRKSRTRL-----GWMNAEEVSAVARDLNVSEREVLEMESRLSGRDIGFDA--PEED 195

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ-ENPV 253
                   +L+ +     Q        + +  +L   +SVL+ R R I + R L+ +  +
Sbjct: 196 NAPPSPVGYLIANDGDPSQAYERGNSEETQLRLLQEGLSVLDTRSRDIIQRRWLETDKKI 255

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TL+ L+ E+ VS ER+RQIEA A KK++
Sbjct: 256 TLQELAEEYGVSAERIRQIEANALKKMK 283


>gi|71901711|ref|ZP_00683785.1| Sigma-70 region 2:Sigma-70 region 4 [Xylella fastidiosa Ann-1]
 gi|71728528|gb|EAO30685.1| Sigma-70 region 2:Sigma-70 region 4 [Xylella fastidiosa Ann-1]
          Length = 288

 Score =  207 bits (526), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 113/268 (42%), Positives = 166/268 (61%), Gaps = 9/268 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + +I +L   EE +LA+RYR+  DL AA  LV SHLR VV++A GY GYGL +
Sbjct: 23  LEAYISAVHQISVLSVDEEQLLARRYRDQQDLDAARELVHSHLRFVVRVARGYSGYGLSL 82

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AVK+FDP+ G RL +++M WI+A M E+IL++W +VK+ TT  Q++L
Sbjct: 83  GDLIQEGNIGLMKAVKRFDPDMGVRLVSFAMHWIRAEMHEFILKNWRIVKVATTKAQRKL 142

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR+ +  L       +  E+V A+A+ LNVSE EV+ M  RL+G D   +A     D
Sbjct: 143 FFNLRKSRTRL-----GWMNAEEVSAVARDLNVSEREVLEMESRLSGRDIGFDA--PEED 195

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ-ENPV 253
                   +L+ +     Q        + +  +L   +SVL+ R R I + R L+ +  +
Sbjct: 196 NAPPSPVGYLIANDGDPSQAYERGNSEETQLRLLQEGLSVLDTRSRDIIQRRWLETDKKI 255

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TL+ L+ E+ VS ER+RQIEA A KK++
Sbjct: 256 TLQELAEEYGVSAERIRQIEANALKKMK 283


>gi|294676015|ref|YP_003576630.1| RNA polymerase sigma-32 factor [Rhodobacter capsulatus SB 1003]
 gi|294474835|gb|ADE84223.1| RNA polymerase sigma-32 factor-1 [Rhodobacter capsulatus SB 1003]
          Length = 292

 Score =  207 bits (526), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 106/268 (39%), Positives = 178/268 (66%), Gaps = 10/268 (3%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L+ + E  LA+ +R+H D +A HRLV++++RL + +A  +R YG P+++++ E ++GLM+
Sbjct: 21  LDAETEAALARAWRDHRDEAALHRLVSAYMRLAISMASKFRRYGAPMNDLIQEASLGLMK 80

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ- 147
           A  KFDP+RG R +TY++WWIKA++QE+++R+WS+V+ G+T++QK LFFNL+R++  +Q 
Sbjct: 81  AADKFDPDRGVRFSTYAVWWIKASIQEFVMRNWSMVRTGSTSSQKALFFNLKRVQAQIQR 140

Query: 148 -----AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQ 201
                 +  +  +  + VAI+  + VS ++V  M  RL+G D SLNA   S D++  +W 
Sbjct: 141 EAEAEGVVLDGAQLREKVAIS--IGVSMADVEMMEGRLSGSDLSLNA-PQSHDEDGREWV 197

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           D L  +    E  + E  +    R+ L ++M  L+ RER I   RRL + P TLE+L  E
Sbjct: 198 DTLEDEGGSPETRVTEAHDGAKMRDWLGQAMGQLSARERYIVAQRRLIDEPRTLESLGEE 257

Query: 262 FEVSRERVRQIEARAFKKVQESIQKQVE 289
             +S+ER+RQ+EA+AF K+++S++ + E
Sbjct: 258 LGLSKERIRQLEAQAFSKMRKSLESRSE 285


>gi|319764144|ref|YP_004128081.1| RNA polymerase sigma factor rpoh [Alicycliphilus denitrificans BC]
 gi|330826499|ref|YP_004389802.1| RNA polymerase sigma-32 subunit RpoH [Alicycliphilus denitrificans
           K601]
 gi|317118705|gb|ADV01194.1| RNA polymerase sigma factor RpoH [Alicycliphilus denitrificans BC]
 gi|329311871|gb|AEB86286.1| RNA polymerase, sigma 32 subunit, RpoH [Alicycliphilus
           denitrificans K601]
          Length = 311

 Score =  207 bits (526), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 114/281 (40%), Positives = 172/281 (61%), Gaps = 12/281 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + ++P+L  +EE   A+++++  DL AA RLV SHLRLVV I+  Y GYGLP 
Sbjct: 27  LDAYISAVNRLPLLTLEEEQRYAQQFKKDNDLEAAGRLVLSHLRLVVSISRQYLGYGLPH 86

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM+AVK+FDP++G RL +Y+M WIKA + EYIL++W +VK+ TT  Q++L
Sbjct: 87  GDLIQEGNVGLMKAVKRFDPDQGVRLVSYAMHWIKAEIHEYILKNWRMVKVATTKAQRKL 146

Query: 136 FFNLRRLKGHLQAITDN------NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
           FFNLR +K   +A   +       L   ++  +A++LNV   EVI M  RLAG + L   
Sbjct: 147 FFNLRSMKQGFKADAIDADTHRETLSDHEIDMVAEQLNVKREEVIEMETRLAGGDVLLDP 206

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFEARRL 248
             S D   +      + D   +   +IE  +R     + +T +++ L+ R RRI E R L
Sbjct: 207 APSDDGEQAFGPIAYLADTAHEPTAMIESRQRDALATDGITSALASLDARSRRIVEQRWL 266

Query: 249 QENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           Q N      +TL  L++E+ VS ER+RQIE  A KK+++++
Sbjct: 267 QVNDDGSGGMTLHELAAEYGVSAERIRQIEVAAMKKMKKAL 307


>gi|238021049|ref|ZP_04601475.1| hypothetical protein GCWU000324_00946 [Kingella oralis ATCC 51147]
 gi|237868029|gb|EEP69035.1| hypothetical protein GCWU000324_00946 [Kingella oralis ATCC 51147]
          Length = 290

 Score =  207 bits (526), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 123/282 (43%), Positives = 175/282 (62%), Gaps = 8/282 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           MN      + +G   L +YIH +  IPML  +EE  LA+R +  GDL AA +L+ SHLR+
Sbjct: 1   MNNAFALSVPSGHGSLEQYIHTVNSIPMLTLEEETSLAQR-QLRGDLEAAKQLILSHLRV 59

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA GY GYGL  ++++ EGN+GLM+AVK+F+P  G RL ++++ WIKA + E+ILR+
Sbjct: 60  VVSIARGYDGYGLNQADLIQEGNVGLMKAVKRFEPTHGARLFSFAVHWIKAEIHEFILRN 119

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W LV+I TT  Q++LFFNLR ++  L A     L P++   IA  L V  S+V+ M  R+
Sbjct: 120 WRLVRIATTKPQRKLFFNLRSMRKSLSA-----LSPKEAQDIADDLGVKLSDVLEMEQRM 174

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            G D +L A  +  D N+    DWL  D     Q L +K     +   L  ++S L+ R 
Sbjct: 175 TGNDVALLADNSDDDDNNFAPIDWLSDDSSEPSQQLAKKAHYALQTEGLRNALSQLDERS 234

Query: 240 RRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKV 280
           RRI E R LQ++  +TL  L++EF VS ER+RQIEA+A +K+
Sbjct: 235 RRIVETRWLQDDGGLTLHELAAEFGVSAERIRQIEAKAMQKL 276


>gi|71275285|ref|ZP_00651572.1| Sigma-70 region 2:Sigma-70 region 4 [Xylella fastidiosa Dixon]
 gi|71902025|ref|ZP_00684069.1| Sigma-70 region 2:Sigma-70 region 4 [Xylella fastidiosa Ann-1]
 gi|71164094|gb|EAO13809.1| Sigma-70 region 2:Sigma-70 region 4 [Xylella fastidiosa Dixon]
 gi|71728204|gb|EAO30391.1| Sigma-70 region 2:Sigma-70 region 4 [Xylella fastidiosa Ann-1]
          Length = 288

 Score =  207 bits (526), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 113/268 (42%), Positives = 166/268 (61%), Gaps = 9/268 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + +I +L   EE +LA+RYR+  DL AA  LV SHLR VV++A GY GYGL +
Sbjct: 23  LEAYISAVHQISVLSVDEEQLLARRYRDQQDLDAARELVHSHLRFVVRVARGYSGYGLSL 82

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AVK+FDP+ G RL +++M WI+A M E+IL++W +VK+ TT  Q++L
Sbjct: 83  GDLIQEGNIGLMKAVKRFDPDMGVRLVSFAMHWIRAEMHEFILKNWRIVKVATTKAQRKL 142

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR+ +  L       +  E+V A+A+ LNVSE EV+ M  RL+G D   +A     D
Sbjct: 143 FFNLRKSRTRL-----GWMNAEEVSAVARDLNVSEREVLEMESRLSGRDIGFDA--PEED 195

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ-ENPV 253
                   +L+ +     Q        + +  +L   +SVL+ R R I + R L+ +  +
Sbjct: 196 NAPPSPVGYLIANDGDPSQAYERGNSEETQLRLLQEGLSVLDTRSRDIIQRRWLETDKKI 255

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TL+ L+ E+ VS ER+RQIEA A KK++
Sbjct: 256 TLQELAEEYGVSAERIRQIEANALKKMK 283


>gi|222087729|ref|YP_002546266.1| alternative sigma factor RpoH [Agrobacterium radiobacter K84]
 gi|221725177|gb|ACM28333.1| alternative sigma factor RpoH [Agrobacterium radiobacter K84]
          Length = 286

 Score =  207 bits (526), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 115/275 (41%), Positives = 176/275 (64%), Gaps = 15/275 (5%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           R I      P L + EE+ LA R+++H D  A +++ T+H+RLV+ +A  +R +GLP+S+
Sbjct: 8   RMIKMAMAAPYLARDEEHDLAIRWKDHEDRGARNKIATAHMRLVISMAGKFRNFGLPMSD 67

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +V EG +GL++A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFF
Sbjct: 68  LVQEGYVGLLEAAARFEPEREVRFSTYASWWIRASIQDYILRNWSIVRGGTSSAQKALFF 127

Query: 138 NLRRLKGHL----QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINS 192
           NLRRL+  L      +T  ++  E    IA  L VS S+V +M+ RL+  D SL A   S
Sbjct: 128 NLRRLRAKLARGNTGVTVQSIHEE----IAVALGVSLSDVQTMDARLSSNDASLQAPSIS 183

Query: 193 SDKNSSQWQDWLVYDH---DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
            D  S++  D+L+ D    D Q   +I+ E    RR  L  ++  LN RE +I  ARRL 
Sbjct: 184 GDAESAERMDFLISDEPLPDEQVSNMIDGE---RRRVWLASALKHLNEREMKIIRARRLV 240

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           E+  TLE L ++  +S+ERVRQIE+RA +K++ ++
Sbjct: 241 EDGATLEELGADLGISKERVRQIESRAMEKLRSAL 275


>gi|307578942|gb|ADN62911.1| RNA polymerase factor sigma-32 [Xylella fastidiosa subsp.
           fastidiosa GB514]
          Length = 282

 Score =  207 bits (526), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 113/268 (42%), Positives = 166/268 (61%), Gaps = 9/268 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + +I +L   EE +LA+RYR+  DL AA  LV SHLR VV++A GY GYGL +
Sbjct: 17  LEAYISAVHQISVLSVDEEQLLARRYRDQQDLDAARELVHSHLRFVVRVARGYSGYGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AVK+FDP+ G RL +++M WI+A M E+IL++W +VK+ TT  Q++L
Sbjct: 77  GDLIQEGNIGLMKAVKRFDPDMGVRLVSFAMHWIRAEMHEFILKNWRIVKVATTKAQRKL 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR+ +  L       +  E+V A+A+ LNVSE EV+ M  RL+G D   +A     D
Sbjct: 137 FFNLRKSRTRL-----GWMNAEEVSAVARDLNVSEREVLEMESRLSGRDIGFDA--PEED 189

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ-ENPV 253
                   +L+ +     Q        + +  +L   +SVL+ R R I + R L+ +  +
Sbjct: 190 NAPPSPVGYLIANDGDPSQAYERGNSEETQLRLLQEGLSVLDTRSRDIIQRRWLETDKKI 249

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TL+ L+ E+ VS ER+RQIEA A KK++
Sbjct: 250 TLQELAEEYGVSAERIRQIEANALKKMK 277


>gi|298293645|ref|YP_003695584.1| RNA polymerase, sigma 32 subunit, RpoH [Starkeya novella DSM 506]
 gi|296930156|gb|ADH90965.1| RNA polymerase, sigma 32 subunit, RpoH [Starkeya novella DSM 506]
          Length = 293

 Score =  206 bits (525), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 118/273 (43%), Positives = 174/273 (63%), Gaps = 12/273 (4%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+L++ EEY LA+R+ E  D  A H L+ +H+RL + IA  +R YGLP+ +++ EG+IGL
Sbjct: 19  PLLDRTEEYELARRWAEQHDEKALHALIHAHMRLAIAIARRFRNYGLPMPDLIQEGHIGL 78

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+A  +F+     R ATY+ WWI+AA+Q+Y+LR+WS+V+ GT++ QK LFFNLRR++  L
Sbjct: 79  MEAASRFETTHEVRFATYASWWIRAAIQDYVLRNWSIVRGGTSSGQKALFFNLRRVRARL 138

Query: 147 Q---AITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSSDKNSSQWQD 202
           +          + E   +IA+KL VSE EV  M+ RL   D SLNA ++  +++ ++  D
Sbjct: 139 ERANGGAGETTREEMHRSIAEKLGVSEIEVARMDARLNVPDLSLNAPLSFGEEDGAERMD 198

Query: 203 WLV-YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
            LV  D    EQV +E +  + RR  L  ++  LN RE RI EARRL E+  TLE L   
Sbjct: 199 QLVAADPLPDEQVSMEIDGER-RRRWLQGALRGLNEREFRIIEARRLTEDSETLEVLGER 257

Query: 262 FEVSRERVRQIEARAFKKVQESIQKQVELSSSP 294
             +S+ERVRQIE+RA +K+      ++ L+ SP
Sbjct: 258 LGISKERVRQIESRAIEKL------RIALTRSP 284


>gi|52842873|ref|YP_096672.1| RNA polymerase factor sigma-32 [Legionella pneumophila subsp.
           pneumophila str. Philadelphia 1]
 gi|52629984|gb|AAU28725.1| RNA polymerase sigma-32 factor RpoH [Legionella pneumophila subsp.
           pneumophila str. Philadelphia 1]
          Length = 292

 Score =  206 bits (525), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 110/272 (40%), Positives = 177/272 (65%), Gaps = 7/272 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YIH + +IPML  +EE   A+R+   GD+ AA +LV +HLR VV++A GY GYGLP+
Sbjct: 25  LDSYIHRVNQIPMLTLEEEIAYAERFHSEGDIEAARQLVLAHLRYVVRVARGYLGYGLPL 84

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           S+++ EGN+GLM+AVK+FDP+ G RL ++++ WIKA + E++LR+W +VK+ TT  Q++L
Sbjct: 85  SDLIQEGNVGLMKAVKRFDPKMGVRLVSFAVHWIKAEIHEFVLRNWRIVKVATTKAQRKL 144

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSSD 194
           FFNLR++K  L   ++     E+V A+AK L VS  +V+ M  RL   D S +A     +
Sbjct: 145 FFNLRQMKNRLGWFSN-----EEVDAVAKDLGVSREDVLLMEQRLNVMDSSYDAPDVDDN 199

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPRERRIFEARRLQENPV 253
            ++ +  +  +++ +    VL+E E+  ++ R  L  +M  L+ R + I + R L E  +
Sbjct: 200 DDAYKAPERYLFNVNDDPAVLLENEDTGDQGREKLLFAMEQLDERSQDILQQRWLAEEKL 259

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           TL +L+ ++ VS ERVRQ+E  A KK+++ ++
Sbjct: 260 TLHDLAEKYGVSAERVRQLEKNAMKKIRQYME 291


>gi|54295507|ref|YP_127922.1| RNA polymerase factor sigma-32 [Legionella pneumophila str. Lens]
 gi|53755339|emb|CAH16835.1| RNA polymerase sigma-32 factor [Legionella pneumophila str. Lens]
          Length = 284

 Score =  206 bits (525), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 110/272 (40%), Positives = 177/272 (65%), Gaps = 7/272 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YIH + +IPML  +EE   A+R+   GD+ AA +LV +HLR VV++A GY GYGLP+
Sbjct: 17  LDSYIHRVNQIPMLTLEEEIAYAERFHSEGDIEAARQLVLAHLRYVVRVARGYLGYGLPL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           S+++ EGN+GLM+AVK+FDP+ G RL ++++ WIKA + E++LR+W +VK+ TT  Q++L
Sbjct: 77  SDLIQEGNVGLMKAVKRFDPKMGVRLVSFAVHWIKAEIHEFVLRNWRIVKVATTKAQRKL 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSSD 194
           FFNLR++K  L   ++     E+V A+AK L VS  +V+ M  RL   D S +A     +
Sbjct: 137 FFNLRQMKNRLGWFSN-----EEVDAVAKDLGVSREDVLLMEQRLNVMDSSYDAPDVDDN 191

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPRERRIFEARRLQENPV 253
            ++ +  +  +++ +    VL+E E+  ++ R  L  +M  L+ R + I + R L E  +
Sbjct: 192 DDAYKAPERYLFNVNDDPAVLLENEDTGDQGREKLLFAMEQLDERSQDILQQRWLAEEKL 251

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           TL +L+ ++ VS ERVRQ+E  A KK+++ ++
Sbjct: 252 TLHDLAEKYGVSAERVRQLEKNAMKKIRQYME 283


>gi|307611543|emb|CBX01223.1| RNA polymerase sigma-32 factor [Legionella pneumophila 130b]
          Length = 284

 Score =  206 bits (525), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 110/272 (40%), Positives = 177/272 (65%), Gaps = 7/272 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YIH + +IPML  +EE   A+R+   GD+ AA +LV +HLR VV++A GY GYGLP+
Sbjct: 17  LDSYIHRVNQIPMLTLEEEIAYAERFHSEGDIEAARQLVLAHLRYVVRVARGYLGYGLPL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           S+++ EGN+GLM+AVK+FDP+ G RL ++++ WIKA + E++LR+W +VK+ TT  Q++L
Sbjct: 77  SDLIQEGNVGLMKAVKRFDPKMGVRLVSFAVHWIKAEIHEFVLRNWRIVKVATTKAQRKL 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSSD 194
           FFNLR++K  L   ++     E+V A+AK L VS  +V+ M  RL   D S +A     +
Sbjct: 137 FFNLRQMKNRLGWFSN-----EEVDAVAKDLGVSREDVLLMEQRLNVMDSSYDAPDVDDN 191

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPRERRIFEARRLQENPV 253
            ++ +  +  +++ +    VL+E E+  ++ R  L  +M  L+ R + I + R L E  +
Sbjct: 192 DDAYKAPERYLFNVNDDPAVLLENEDTGDQGREKLLFAMEQLDERSQDILQQRWLAEEKL 251

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           TL +L+ ++ VS ERVRQ+E  A KK+++ ++
Sbjct: 252 TLHDLAEKYGVSAERVRQLEKNAMKKIRQYME 283


>gi|297180174|gb|ADI16396.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [uncultured bacterium HF130_12L15]
          Length = 288

 Score =  206 bits (525), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 118/279 (42%), Positives = 184/279 (65%), Gaps = 3/279 (1%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           +N E   S  I   RK P L++ EE+ LA R+R+  D  A HR+  +H+RLV+ +A  +R
Sbjct: 1   MNAEPAGSSMISAARKAPYLDRVEEHDLAVRWRDDRDQEALHRITMAHMRLVISMAGKFR 60

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
            +GLP+S++V EG++GL++A  +F+PER  R +TY+ WWI+A+MQ++ILR+WS+V+ GT+
Sbjct: 61  YFGLPMSDLVQEGHVGLLEAAARFEPERDVRFSTYATWWIRASMQDHILRNWSIVRGGTS 120

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-AIAKKLNVSESEVISMNCRLAG-DESLN 187
           + QK LFFNLRRL+  L   T+  LK   V   IA  + VS ++V  M+ RL+G D SLN
Sbjct: 121 SAQKALFFNLRRLRARLAQGTE-PLKGAAVYQEIADAIGVSVADVALMDSRLSGPDSSLN 179

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           A +    +++S+  D+LV +    ++V+    + + R   L R++ VLN RE RI   RR
Sbjct: 180 APVADGGESTSERMDFLVSEDPTPDEVVSASIDDERRTMWLNRALGVLNDRELRIIRERR 239

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           L++   TLE+L ++  +S+ERVRQIE RA +K++ ++ K
Sbjct: 240 LRDEGATLESLGAKLGISKERVRQIENRALEKLRSALLK 278


>gi|170731288|ref|YP_001776721.1| RNA polymerase factor sigma-32 [Xylella fastidiosa M12]
 gi|167966081|gb|ACA13091.1| RNA polymerase sigma-32 factor [Xylella fastidiosa M12]
          Length = 288

 Score =  206 bits (525), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 113/268 (42%), Positives = 166/268 (61%), Gaps = 9/268 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + +I +L   EE +LA+RYR+  DL AA  LV SHLR VV++A GY GYGL +
Sbjct: 23  LEAYISAVHQISVLSVDEEQLLARRYRDQQDLDAARELVHSHLRFVVRVARGYSGYGLSL 82

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AVK+FDP+ G RL +++M WI+A M E+IL++W +VK+ TT  Q++L
Sbjct: 83  GDLIQEGNIGLMKAVKRFDPDMGVRLVSFAMHWIRAEMHEFILKNWRIVKVATTKAQRKL 142

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR+ +  L       +  E+V A+A+ LNVSE EV+ M  RL+G D   +A     D
Sbjct: 143 FFNLRKSRTRL-----GWMNAEEVSAVARDLNVSEREVLEMESRLSGRDIGFDA--PEED 195

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ-ENPV 253
                   +L+ +     Q        + +  +L   +SVL+ R R I + R L+ +  +
Sbjct: 196 NAPLSPVGYLIANDGDPSQAYERGNSEETQLRLLQEGLSVLDTRSRDIIQRRWLETDKKI 255

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TL+ L+ E+ VS ER+RQIEA A KK++
Sbjct: 256 TLQELAEEYGVSAERIRQIEANALKKMK 283


>gi|221133912|ref|ZP_03560217.1| RNA polymerase, sigma 32 subunit, RpoH [Glaciecola sp. HTCC2999]
          Length = 283

 Score =  206 bits (525), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 113/281 (40%), Positives = 169/281 (60%), Gaps = 7/281 (2%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M++ +     +  YI  +  IPML   EE  LA+R    GDL+AA  LV SHLR VV IA
Sbjct: 7   MALTIPQSGSIESYIQSVSNIPMLSADEEKSLAERLFNEGDLTAARELVMSHLRFVVHIA 66

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGL  +++V EGNIGLM+AVK+FDP  G RL ++++ WIKA + E++L++W +VK
Sbjct: 67  KSYSGYGLAQADLVQEGNIGLMKAVKRFDPNVGVRLVSFAVHWIKAEIHEFVLKNWRIVK 126

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DE 184
           + TT  Q++LFFNLR+ K  L   T      ++V  +A++L VSE EV+ M  R+   D 
Sbjct: 127 VATTKAQRKLFFNLRKSKKRLGWFT-----HKEVQKVAEELGVSEKEVLQMEARMGSQDT 181

Query: 185 SLNALINSSDKNSS-QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           + +   +  D NS+     +L    +  E  +I  +   N    L  ++  L+ R + I 
Sbjct: 182 AFDLSSDDGDDNSNFSPAQYLEDKSENVEAAVINADYDSNASARLYSAIKTLDERSQYII 241

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           E R L +N +TL++L++++EVS ERVRQIE  A KK+Q ++
Sbjct: 242 ETRWLNDNKMTLQDLAAKYEVSAERVRQIEKNAMKKIQAAM 282


>gi|56695321|ref|YP_165669.1| RNA polymerase factor sigma-32 [Ruegeria pomeroyi DSS-3]
 gi|56677058|gb|AAV93724.1| RNA polymerase sigma-32 factor [Ruegeria pomeroyi DSS-3]
          Length = 292

 Score =  206 bits (525), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 106/266 (39%), Positives = 177/266 (66%), Gaps = 6/266 (2%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K  +L+ + E  LA  +R+H D +A HRL+T+++RL + +A  ++ YG P+++++ E  +
Sbjct: 17  KAELLDAETELALAYAWRDHRDEAALHRLITAYMRLAISMAAKFKRYGAPMNDLIQEAGL 76

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFN+RR++ 
Sbjct: 77  GLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQA 136

Query: 145 HL--QAITDN-NLKPEQV-VAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQ 199
            L  +A TD   L   Q+   IA ++ V   +V  M  RL+G D SLNA   +SD+   +
Sbjct: 137 RLEREAATDGLALDRHQLHQMIASEIGVPLRDVEMMEGRLSGSDFSLNA-TQASDEEGRE 195

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
           W + L  + +   +++  + + +  R+ L  +M  LN RER I   R+L++ P TLE+L 
Sbjct: 196 WIEALEDESEQAAELVAHRHDTEQLRDWLIEAMQALNERERFIVRERKLRDEPRTLESLG 255

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQ 285
            E  +S+ERVRQ+EA AF K+++S++
Sbjct: 256 DELGLSKERVRQLEAAAFAKMRKSLE 281


>gi|148358598|ref|YP_001249805.1| hypothetical protein LPC_0471 [Legionella pneumophila str. Corby]
 gi|148280371|gb|ABQ54459.1| hypothetical protein LPC_0471 [Legionella pneumophila str. Corby]
          Length = 284

 Score =  206 bits (525), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 110/272 (40%), Positives = 177/272 (65%), Gaps = 7/272 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YIH + +IPML  +EE   A+R+   GD+ AA +LV +HLR VV++A GY GYGLP+
Sbjct: 17  LDSYIHRVNQIPMLTLEEEIAYAERFHSEGDIEAARQLVLAHLRYVVRVARGYLGYGLPL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           S+++ EGN+GLM+AVK+FDP+ G RL ++++ WIKA + E++LR+W +VK+ TT  Q++L
Sbjct: 77  SDLIQEGNVGLMKAVKRFDPKMGVRLVSFAVHWIKAEIHEFVLRNWRIVKVATTKAQRKL 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSSD 194
           FFNLR++K  L   ++     E+V A+AK L VS  +V+ M  RL   D S +A     +
Sbjct: 137 FFNLRQMKNRLGWFSN-----EEVDAVAKDLGVSREDVLLMEQRLNVMDSSYDAPDVDDN 191

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPRERRIFEARRLQENPV 253
            ++ +  +  +++ +    VL+E E+  ++ R  L  +M  L+ R + I + R L E  +
Sbjct: 192 DDAYKAPERYLFNVNDDPAVLLENEDTGDQGREKLLFAMEQLDERSQDILQQRWLAEEKL 251

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           TL +L+ ++ VS ERVRQ+E  A KK+++ ++
Sbjct: 252 TLHDLAEKYGVSAERVRQLEKNAMKKIRQYME 283


>gi|54298657|ref|YP_125026.1| RNA polymerase factor sigma-32 [Legionella pneumophila str. Paris]
 gi|296108313|ref|YP_003620014.1| RNA polymerase sigma-32 factor [Legionella pneumophila 2300/99
           Alcoy]
 gi|53752442|emb|CAH13874.1| RNA polymerase sigma-32 factor [Legionella pneumophila str. Paris]
 gi|295650215|gb|ADG26062.1| RNA polymerase sigma-32 factor [Legionella pneumophila 2300/99
           Alcoy]
          Length = 284

 Score =  206 bits (525), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 110/272 (40%), Positives = 177/272 (65%), Gaps = 7/272 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YIH + +IPML  +EE   A+R+   GD+ AA +LV +HLR VV++A GY GYGLP+
Sbjct: 17  LDSYIHRVNQIPMLTLEEEIAYAERFHSEGDIEAARQLVLAHLRYVVRVARGYLGYGLPL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           S+++ EGN+GLM+AVK+FDP+ G RL ++++ WIKA + E++LR+W +VK+ TT  Q++L
Sbjct: 77  SDLIQEGNVGLMKAVKRFDPKMGVRLVSFAVHWIKAEIHEFVLRNWRIVKVATTKAQRKL 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSSD 194
           FFNLR++K  L   ++     E+V A+AK L VS  +V+ M  RL   D S +A     +
Sbjct: 137 FFNLRQMKNRLGWFSN-----EEVDAVAKDLGVSREDVLLMEQRLNVMDSSYDAPDVDDN 191

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPRERRIFEARRLQENPV 253
            ++ +  +  +++ +    VL+E E+  ++ R  L  +M  L+ R + I + R L E  +
Sbjct: 192 DDAYKAPERYLFNVNDDPAVLLENEDTGDQGREKLLFAMEQLDERSQDILQQRWLAEEKL 251

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           TL +L+ ++ VS ERVRQ+E  A KK+++ ++
Sbjct: 252 TLHDLAEKYGVSAERVRQLEKNAMKKIRQYME 283


>gi|190576084|ref|YP_001973929.1| RNA polymerase factor sigma-32 [Stenotrophomonas maltophilia K279a]
 gi|190014006|emb|CAQ47646.1| putative RNA polymerase sigma-32 factor [Stenotrophomonas
           maltophilia K279a]
          Length = 291

 Score =  206 bits (525), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 111/269 (41%), Positives = 169/269 (62%), Gaps = 8/269 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + +IP+L   +E  LA+R+R+  DL AA  LV SHLR VV +A GY GYGL +
Sbjct: 23  LDAYIGAVHQIPVLSVDDEQDLARRFRDGNDLDAARELVHSHLRFVVHVARGYNGYGLAL 82

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AVK+FDP+ G RL ++++ WI+A M E+IL++W +VK+ TT  Q++L
Sbjct: 83  GDLIQEGNIGLMKAVKRFDPDMGVRLVSFAVHWIRAEMHEFILKNWRIVKVATTKAQRKL 142

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR+ K  L       +   +V A+AK LNVSE EV+ M  RL+G D   +A  +  +
Sbjct: 143 FFNLRKSKTRL-----GWMNAAEVSAVAKDLNVSEREVMEMESRLSGRDIGFDAPTDEDN 197

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLNPRERRIFEARRLQ-ENP 252
           +++       +   D    +  E+E+ + N+  +L   ++ L+ R R I   R L  ++ 
Sbjct: 198 EHAPPSPAAFLVADDEDPSMAYEREDSEDNQMQLLREGLAELDARSRDIIRRRWLDADSK 257

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           VTL+ L+ E+ VS ER+RQ+EA A KK++
Sbjct: 258 VTLQELADEYGVSAERIRQVEANALKKMK 286


>gi|47028349|gb|AAT09107.1| RpoH-like sigma factor [Rhizobium sp. TAL11145]
          Length = 289

 Score =  206 bits (524), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 119/292 (40%), Positives = 182/292 (62%), Gaps = 22/292 (7%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+ KNMS          R I      P L + EE+ LA R+++H D  A +++ T+H+RL
Sbjct: 1   MHMKNMS-------ADRRMIKIAMAAPYLGRDEEHDLAIRWKDHDDRGARNKIATAHMRL 53

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A  +R +GLP+S++V EG +GL++A  +F+PER  R +TY+ WWI+A++Q+YILR+
Sbjct: 54  VISMAGKFRNFGLPMSDLVQEGYVGLLEAAARFEPEREVRFSTYASWWIRASIQDYILRN 113

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHL----QAITDNNLKPEQVVAIAKKLNVSESEVISM 176
           WS+V+ GT++ QK LFFNLRRL+  L      +T  ++  E    IA  L VS ++V +M
Sbjct: 114 WSIVRGGTSSAQKALFFNLRRLRAKLARGNTGVTVQSIHEE----IAVALGVSLADVQTM 169

Query: 177 NCRLAG-DESLNALINSSDKNSSQWQDWLVYDH---DGQEQVLIEKEERKNRRNMLTRSM 232
           + RL+  D SL A   S D  S++  D+L+ D    D Q   +I+ E    RR  L  ++
Sbjct: 170 DARLSSNDASLQAPSISGDAESAERMDFLISDEPLPDEQVSNMIDGE---RRRVWLASAL 226

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             LN RE +I  ARRL E+  TLE L ++  +S+ERVRQIE+RA +K++ ++
Sbjct: 227 KHLNEREMKIIRARRLVEDGATLEELGADLGISKERVRQIESRAMEKLRSAL 278


>gi|254465185|ref|ZP_05078596.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacterales bacterium
           Y4I]
 gi|206686093|gb|EDZ46575.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacterales bacterium
           Y4I]
          Length = 292

 Score =  206 bits (524), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 104/268 (38%), Positives = 176/268 (65%), Gaps = 6/268 (2%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K  +L+   E  LA  +R+  D+ + HRL+ +++RL + +A  ++ YG P+++++ E  +
Sbjct: 17  KAELLDADTERRLAYAWRDDRDVESLHRLINAYMRLAISMAAKFKRYGAPMNDLIQEAGL 76

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFN+RR++ 
Sbjct: 77  GLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQA 136

Query: 145 HLQAITDNNLKP----EQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQ 199
            L+    ++  P    +    IA ++ V   +V  M  RL+G D SLNA + S+D+   +
Sbjct: 137 QLEREARSSGVPLDQHQLHQKIATEIGVPLRDVEMMEGRLSGADFSLNA-VQSTDEEGRE 195

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
           W D L  D    E ++ E+ +R+  R  L  ++  LN RER I   R+L++ P TLE+L 
Sbjct: 196 WIDALEDDASQAEDLVQERHDRRQLRKWLVTALQALNDRERFIITERKLRDRPRTLESLG 255

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +E  +S+ERVRQ+EA AF+K+++S++ Q
Sbjct: 256 TELGLSKERVRQLEAGAFQKMRKSLESQ 283


>gi|197116970|ref|YP_002137397.1| RNA polymerase sigma-32 factor RpoH [Geobacter bemidjiensis Bem]
 gi|197086330|gb|ACH37601.1| RNA polymerase sigma-32 factor RpoH [Geobacter bemidjiensis Bem]
          Length = 285

 Score =  206 bits (524), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 112/266 (42%), Positives = 169/266 (63%), Gaps = 5/266 (1%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+ EI + P+L   EE  LA R+R  GDL AAHRL+T++LR VVKIA  YR YG+ +
Sbjct: 12  LTLYLAEINRFPLLTADEEMDLAGRFRREGDLEAAHRLITANLRFVVKIAGEYRSYGMKM 71

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM AV+KFDP++G RL +Y++WWI+A +Q +I+ +WSL+KIGTT  Q++L
Sbjct: 72  LDLIQEGNIGLMMAVRKFDPDKGVRLISYAVWWIRAYIQNHIISAWSLLKIGTTQAQRKL 131

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FF L + K   QAI  N      + A A  L+V ++E   M  RL G+ SL+  +   + 
Sbjct: 132 FFKLNQAK---QAIV-NMTGEGDLHAAAISLDVKDNEAREMEQRLRGELSLDVEMFEGEG 187

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
             + + + L      QE++L E++E       +  ++  LN +E+ + E R   E+P+TL
Sbjct: 188 GGT-FLESLPDLRQNQEEMLAERQETTILERNVASALENLNEKEKFVIEQRVAAEDPMTL 246

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           + ++  F +SRERVRQIE  A KK++
Sbjct: 247 QEIADHFSISRERVRQIEEGALKKMK 272


>gi|99080297|ref|YP_612451.1| RNA polymerase factor sigma-32 [Ruegeria sp. TM1040]
 gi|99036577|gb|ABF63189.1| RNA polymerase, sigma 32 subunit, RpoH [Ruegeria sp. TM1040]
          Length = 292

 Score =  206 bits (524), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 108/270 (40%), Positives = 179/270 (66%), Gaps = 10/270 (3%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K  +L+ + E  LA  +R+  D+ A HRL+T+++RL V +A  +R YG P+++++ E  +
Sbjct: 17  KAELLDAETELALAYAWRDEKDVQALHRLITAYMRLAVSMASKFRRYGAPMNDLIQEAGL 76

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A +KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFN+RR++ 
Sbjct: 77  GLMKAAEKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQA 136

Query: 145 HL------QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
            L      + +  +  K  Q+V  A+++ V   +V  M+ RLAG D SLNA + S+D++ 
Sbjct: 137 QLEREAAGEGVELDRHKLMQMV--AEEIGVPLRDVEMMDGRLAGADFSLNA-VQSADEDG 193

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
            +W D L  D +     +    +R+  R  L  +++ LN RER I   R+L+E   TLE+
Sbjct: 194 REWIDALEDDSEQAADRVEADHDRRQLREWLLSALNGLNERERFIVRERKLREEARTLES 253

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L +E  +S+ERVRQ+EA AF K+++S++ Q
Sbjct: 254 LGNELGLSKERVRQLEAAAFSKMRKSLEGQ 283


>gi|303256291|ref|ZP_07342307.1| alternative sigma factor RpoH [Burkholderiales bacterium 1_1_47]
 gi|330998988|ref|ZP_08322713.1| alternative sigma factor RpoH [Parasutterella excrementihominis YIT
           11859]
 gi|302861020|gb|EFL84095.1| alternative sigma factor RpoH [Burkholderiales bacterium 1_1_47]
 gi|329575730|gb|EGG57256.1| alternative sigma factor RpoH [Parasutterella excrementihominis YIT
           11859]
          Length = 306

 Score =  206 bits (524), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 116/280 (41%), Positives = 166/280 (59%), Gaps = 13/280 (4%)

Query: 9   IVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           I +  +G L  YI    K P+L  + E+ LA R +EHGD+ AA  LV SHLRLV+ IA  
Sbjct: 24  IPDASLGSLEEYIRAANKAPILSAEREHELAVRLQEHGDMEAAGELVMSHLRLVISIARQ 83

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y+GYGLP  +++ EGNIGLM+AVK+F+P  G RL T++M WIK+ +QEY+LR+W LVK+ 
Sbjct: 84  YQGYGLPFGDLIQEGNIGLMKAVKRFNPNNGARLVTFAMTWIKSEIQEYVLRNWRLVKVA 143

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESL 186
           TT +Q++LFFNLR+LK   +      L   +   IA+ L+V  SEV  M  R+ G D  +
Sbjct: 144 TTKSQRKLFFNLRKLKDDTKL-----LGTSEAEKIAETLDVKPSEVFEMEKRMLGSDVEI 198

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           +     +D+  +   +WL  + D  E  +          N L  ++  L+ R RRI EAR
Sbjct: 199 DEPSGGTDEGMAP-SEWLTDERDTPENTIARGAYENTIENRLPEAVKKLDDRSRRIIEAR 257

Query: 247 RLQEN-----PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L  +       TL +L+ E  VS+ERVRQ+E +AF  ++
Sbjct: 258 WLYNDQDGSKGATLADLAKEMGVSQERVRQLEKKAFATLK 297


>gi|119899581|ref|YP_934794.1| RNA polymerase factor sigma-32 [Azoarcus sp. BH72]
 gi|119671994|emb|CAL95908.1| RNA polymerase sigma-32 factor [Azoarcus sp. BH72]
          Length = 284

 Score =  206 bits (524), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 115/283 (40%), Positives = 178/283 (62%), Gaps = 13/283 (4%)

Query: 4   KNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           + +S  V   +G + +YI  + ++P+L +Q+E  LA R R+ GD+ AA +LV SHLR+VV
Sbjct: 3   QALSFPVPSVVGSIDQYIQAVNRVPLLTEQQEVELATRLRDDGDVDAARQLVMSHLRVVV 62

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA GY GYGLP ++++ EGNIGLM+AVK+FDP RG RL ++++ WIKA + EYIL++W 
Sbjct: 63  AIARGYLGYGLPHADLIQEGNIGLMKAVKRFDPTRGVRLVSFAIHWIKAEIHEYILKNWR 122

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           LVKI TT  Q++LFFNLR LK          L  ++V A+A +L V   EV+ M  RL+G
Sbjct: 123 LVKIATTKAQRKLFFNLRSLKQDT-----GTLNRDEVEAVATQLGVKPEEVVEMETRLSG 177

Query: 183 DESLNALINSSDKNSSQWQDWLVY--DHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRE 239
               +  I+  + +  +    + Y      +   ++E+ ER + ++  L +++  L+ R 
Sbjct: 178 R---DIPIDGGNDDEDERFAPIAYLPAPAAEPSEVLERAERAHLQDTGLKQALGALDERS 234

Query: 240 RRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R I E R L + +  TL  L++E+ VS ER+RQIEA+A +K++
Sbjct: 235 RTIVERRWLTDGDSATLHELAAEYGVSAERIRQIEAKAMQKMR 277


>gi|326318574|ref|YP_004236246.1| RNA polymerase sigma-32 subunit RpoH [Acidovorax avenae subsp.
           avenae ATCC 19860]
 gi|323375410|gb|ADX47679.1| RNA polymerase, sigma 32 subunit, RpoH [Acidovorax avenae subsp.
           avenae ATCC 19860]
          Length = 313

 Score =  206 bits (524), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 113/285 (39%), Positives = 174/285 (61%), Gaps = 18/285 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + ++PML  +EE   A+R +EH D+ AA R+V SHLRLVV IA  Y GYGLP 
Sbjct: 27  LDAYISAVNRLPMLTAEEERTYARRLKEHNDVEAAGRMVMSHLRLVVSIARQYLGYGLPH 86

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM+AVK+FDP++  RL +Y+M WIKA + EYIL++W +VK+ TT +Q++L
Sbjct: 87  GDLIQEGNVGLMKAVKRFDPDQNVRLVSYAMHWIKAEIHEYILKNWRMVKVATTKSQRKL 146

Query: 136 FFNLRRLKGHLQAITD--------NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
           FFNLR +K   +A +           L  +++  +A++LNV   EVI M  RL+G + + 
Sbjct: 147 FFNLRSMKQGFKADSAAGNTGTHRETLSEQEIDVVAQQLNVKREEVIEMETRLSGGDVM- 205

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQ--VLIEKEERKN-RRNMLTRSMSVLNPRERRIFE 244
            L  +   +  Q    + Y  DG  +   +IE  +R     + +  +++ L+ R RRI E
Sbjct: 206 -LDPAPSDDGEQAYGPIAYLADGTHEPTAMIESRQRDVLATDGIANALATLDDRSRRIVE 264

Query: 245 ARRLQENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            R L+ N      +TL  L++ + VS ER+RQIE  A KK+++++
Sbjct: 265 ERWLKVNDDGSGGMTLHELAAVYGVSAERIRQIEVAAMKKMKKAL 309


>gi|121611388|ref|YP_999195.1| RNA polymerase sigma-32 subunit RpoH [Verminephrobacter eiseniae
           EF01-2]
 gi|121556028|gb|ABM60177.1| RNA polymerase, sigma 32 subunit, RpoH [Verminephrobacter eiseniae
           EF01-2]
          Length = 313

 Score =  206 bits (523), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 113/285 (39%), Positives = 174/285 (61%), Gaps = 14/285 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + ++P+L  ++E   A++++EH DL AA RLV SHLRLVV IA  Y GYGLP 
Sbjct: 27  LDAYIAAVNRLPLLTYEQEQSYARQFKEHNDLDAAGRLVLSHLRLVVSIARQYLGYGLPH 86

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AVK+FDP++G RL +Y+M WIKA + EYIL++W +VK+ TT  Q++L
Sbjct: 87  GDLIQEGNIGLMKAVKRFDPDQGVRLVSYAMHWIKAEIHEYILKNWRMVKVATTKAQRKL 146

Query: 136 FFNLRRLKGHLQAITD--------NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
           FFNLR +K   +A           + L   ++ A+A +L+V   EVI M  R++G + L 
Sbjct: 147 FFNLRSMKQGFKADAGATDAATYRDTLSEHEIDAVAAQLHVKREEVIEMETRMSGGDVLL 206

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFEAR 246
               S D   +      + D   +   LIE  +R     + + ++++ L+ R RRI + R
Sbjct: 207 DPAPSDDGEQAFGPIAYLADASHEPTALIESRQRDALATDGIAKALASLDERSRRIVQER 266

Query: 247 RLQENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L+ N      +TL +L++ + VS ER+RQIE  A KK+++++ K
Sbjct: 267 WLKVNDDGTGGMTLHDLAAIYGVSAERIRQIEVAAMKKMKQALVK 311


>gi|254490572|ref|ZP_05103758.1| alternative sigma factor RpoH [Methylophaga thiooxidans DMS010]
 gi|224464316|gb|EEF80579.1| alternative sigma factor RpoH [Methylophaga thiooxydans DMS010]
          Length = 287

 Score =  206 bits (523), Expect = 5e-51,   Method: Compositional matrix adjust.
 Identities = 112/272 (41%), Positives = 171/272 (62%), Gaps = 10/272 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y   +  IP+L  +EEY LA R ++ GDL AA RLV SHLR VV+IA GY GYGLP+
Sbjct: 18  LDAYTSLVHTIPVLTAEEEYDLATRLQQDGDLEAAQRLVLSHLRFVVRIAKGYSGYGLPV 77

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AVK+F+PE+G RL ++++ W++A + EY++R+W +VKI TT  Q++L
Sbjct: 78  ADLIQEGNIGLMKAVKRFNPEKGVRLVSFAVHWVRAEIHEYVIRNWRIVKIATTKAQRKL 137

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALINSSD 194
           FFNLR  K  L       L  E+V A+A+ L V+ + V+ M  RLA  D S +   +S+D
Sbjct: 138 FFNLRSAKQRL-----GWLNQEEVEAVAEDLGVTPANVMDMERRLAQPDASFDLPADSND 192

Query: 195 KNSSQWQD--WLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFEARRLQEN 251
              + +    +L    +      +E+E   + ++  LT +++ L+ R R I   R L E+
Sbjct: 193 DEETHFSPVAYLAGPENSDPSQQLEQENYSDYQQQKLTNALATLDDRSRDIIMQRWLNED 252

Query: 252 P-VTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              TL  L+ +++VS ER+RQIE  A KK+++
Sbjct: 253 DKATLHTLADQYQVSAERIRQIENNAMKKLKK 284


>gi|319407753|emb|CBI81400.1| RNA polymerase sigma-32 factor [Bartonella sp. 1-1C]
          Length = 303

 Score =  205 bits (522), Expect = 6e-51,   Method: Compositional matrix adjust.
 Identities = 109/277 (39%), Positives = 180/277 (64%), Gaps = 4/277 (1%)

Query: 11  NGEIGLSR-YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           N +  L R  +   ++ P LE+++E+ LA R++   D +A H++  +H+RLV+ IA  ++
Sbjct: 17  NTDTSLGRNMMRSAKQAPYLERKKEHDLALRWKNKRDDNAMHQIAAAHMRLVISIASRFK 76

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
            + +P+ ++V EG +GL++A  +FDP+RG R +TY+ WWI+A++Q+YILR+WS+V+ GT+
Sbjct: 77  RFKMPLGDLVQEGYVGLLEAAARFDPDRGVRFSTYATWWIRASIQDYILRNWSIVRGGTS 136

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-AIAKKLNVSESEVISMNCRLAG-DESLN 187
           ++QK LFFNLRRL+  L A  DN L  +++  AI++KL VS ++V  M+ R +G D SL+
Sbjct: 137 SSQKALFFNLRRLRAKL-AQDDNTLTKQEIFRAISEKLGVSVNDVEKMDFRFSGTDNSLS 195

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I+ + +      D L+ DH   + V+ +  + + R   L  ++ +LN RE  I   RR
Sbjct: 196 LSISENGETPIAKMDSLIDDHPLPDSVIEQAIDGQRRAQWLHEALQILNERELEIIRFRR 255

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L E   TLE L  +  +S+ERVRQIEARA +K++ ++
Sbjct: 256 LNEEGTTLEVLGEKLGISKERVRQIEARALQKLRCAL 292


>gi|121603798|ref|YP_981127.1| RNA polymerase sigma-32 subunit RpoH [Polaromonas naphthalenivorans
           CJ2]
 gi|120592767|gb|ABM36206.1| RNA polymerase, sigma 32 subunit, RpoH [Polaromonas
           naphthalenivorans CJ2]
          Length = 322

 Score =  205 bits (522), Expect = 6e-51,   Method: Compositional matrix adjust.
 Identities = 112/278 (40%), Positives = 172/278 (61%), Gaps = 11/278 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + ++PML  ++E   +K+ +E+ DL +A +LV SHLRLVV I+  Y GYGLP 
Sbjct: 39  LDAYISAVNRLPMLTLEQEQEFSKKLKENNDLDSAGKLVLSHLRLVVSISRKYLGYGLPH 98

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AVK+FDP++  RL +Y+M WIKA + EYIL++W +VK+ TT  Q++L
Sbjct: 99  GDLIQEGNIGLMKAVKRFDPDQNVRLVSYAMHWIKAEIHEYILKNWRMVKVATTKAQRKL 158

Query: 136 FFNLRRLKGHLQAITD-----NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
           FFNLR +K   +   D     + L   Q+ ++A+ LNV   EVI M  R++G + L    
Sbjct: 159 FFNLRSMKQGYKDDADVATHRDTLTESQIDSMARTLNVKREEVIEMEQRMSGGDVLLDPS 218

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFEARRLQ 249
            + D + +      + D   +   L+E  ER +   + L+ ++  L+PR RRI E R L 
Sbjct: 219 PNDDGDDAFGPIAYLADAAQEPTALMESRERDDLMTDGLSTALQELDPRARRIVEERWLN 278

Query: 250 ENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            N      +TL +L++E++VS ER+RQIE  A KK+++
Sbjct: 279 VNDDGSGGMTLHDLAAEYKVSAERIRQIEVAAMKKMKK 316


>gi|163740703|ref|ZP_02148097.1| RNA polymerase sigma factor [Phaeobacter gallaeciensis 2.10]
 gi|161386561|gb|EDQ10936.1| RNA polymerase sigma factor [Phaeobacter gallaeciensis 2.10]
          Length = 292

 Score =  205 bits (522), Expect = 6e-51,   Method: Compositional matrix adjust.
 Identities = 107/266 (40%), Positives = 177/266 (66%), Gaps = 6/266 (2%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K  +L+ + E  LA  +R+  D+ A HRL+ +++RL + +A  +R YG P+++++ E  +
Sbjct: 17  KAELLDAETELQLAYAWRDERDVQALHRLINAYMRLAISMASKFRRYGAPMNDLIQEAGL 76

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFN+RR++ 
Sbjct: 77  GLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQA 136

Query: 145 HL--QAITDNN-LKPEQV-VAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQ 199
            L  QA ++   L   Q+   IA ++ V   +V  M+ RLAG D SLNA + S+++   +
Sbjct: 137 QLERQAQSEGTRLDQHQLHQQIATEIGVPLRDVQMMDGRLAGADFSLNA-VQSAEEEGRE 195

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
           W + L  D     +++ E  + +  R  L  +M  LN RER I   R+L+E P TLE+L 
Sbjct: 196 WIEALEDDSAQAAELVEESHDTRQLRTWLVEAMQALNDRERFIITERKLREKPRTLESLG 255

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQ 285
           +E  +S+ERVRQ+EA AF+K+++S++
Sbjct: 256 TELGLSKERVRQLEAGAFQKMRKSLE 281


>gi|270158013|ref|ZP_06186670.1| RNA polymerase sigma-32 factor RpoH [Legionella longbeachae D-4968]
 gi|289163720|ref|YP_003453858.1| RNA polymerase sigma-32 factor [Legionella longbeachae NSW150]
 gi|269990038|gb|EEZ96292.1| RNA polymerase sigma-32 factor RpoH [Legionella longbeachae D-4968]
 gi|288856893|emb|CBJ10704.1| RNA polymerase sigma-32 factor [Legionella longbeachae NSW150]
          Length = 284

 Score =  205 bits (521), Expect = 7e-51,   Method: Compositional matrix adjust.
 Identities = 110/279 (39%), Positives = 175/279 (62%), Gaps = 8/279 (2%)

Query: 10  VNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +N  +G +  YIH + +IPML  +EE   A+R+   GDL AA RLV +HLR VV++A GY
Sbjct: 10  INLPVGSIDAYIHRVNQIPMLSLEEEIACAERFHSEGDLEAARRLVLAHLRYVVRVARGY 69

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGLP+++++ EGN+GLM+AVK+FDP+ G RL ++++ WIKA + E++LR+W +VKI T
Sbjct: 70  LGYGLPLNDLIQEGNVGLMKAVKRFDPKMGVRLVSFAVHWIKAEIHEFVLRNWRIVKIAT 129

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLN 187
           T  Q++LFFNLR++K  L  ++      E+V A+A  L VS  +V+ M  RL A D   +
Sbjct: 130 TKAQRKLFFNLRQMKNRLGWMSH-----EEVSAVANDLGVSREDVLVMEQRLNAMDTPYD 184

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPRERRIFEAR 246
           A             +  +++ +    V++E +   ++ R  L  ++  L+ R + I + R
Sbjct: 185 APDADDHDEFYTAPERYLFNTNDDPSVMLENDSASDQGREKLMFALEQLDERSQDILQQR 244

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            L E  +TL +L+ ++ VS ERVRQ+E  A KK+++ I+
Sbjct: 245 WLSEEKLTLHDLAKKYGVSAERVRQLEKNAMKKLKQYIE 283


>gi|170750108|ref|YP_001756368.1| RNA polymerase factor sigma-32 [Methylobacterium radiotolerans JCM
           2831]
 gi|170656630|gb|ACB25685.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium
           radiotolerans JCM 2831]
          Length = 291

 Score =  205 bits (521), Expect = 7e-51,   Method: Compositional matrix adjust.
 Identities = 112/278 (40%), Positives = 179/278 (64%), Gaps = 1/278 (0%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           +I    + P L ++EE  LA R+++  D  A HRL+++H+RLV+ +A  +R YGLP++++
Sbjct: 11  FIRTAMEAPFLAREEERGLAVRWKDERDERALHRLISAHMRLVIALAGRFRHYGLPMADL 70

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EG++GLM+A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFFN
Sbjct: 71  VQEGHVGLMEAAARFEPERDVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKALFFN 130

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LRRL+  L   T+ ++  E    IA  + VS  +V  M+ RL+G D SLNA +      S
Sbjct: 131 LRRLRARLMQSTEEHVGDEIHRRIASAIGVSRDDVALMDARLSGPDMSLNAPVGEDSDAS 190

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           S+  D+LV   D  ++ +    + + R + L ++++VL+ RE RI   RRL E+  TLE 
Sbjct: 191 SERMDFLVDGADLPDETVSATVDGERRLSWLQQALTVLSERELRILRERRLAEDQATLEA 250

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPP 295
           L     +S+ERVRQIE RA +K++ ++  +   ++  P
Sbjct: 251 LGQRLGISKERVRQIENRALEKLRRALADRFPAATGSP 288


>gi|325266382|ref|ZP_08133060.1| DNA-directed RNA polymerase sigma subunit RpoH [Kingella
           denitrificans ATCC 33394]
 gi|324982175|gb|EGC17809.1| DNA-directed RNA polymerase sigma subunit RpoH [Kingella
           denitrificans ATCC 33394]
          Length = 332

 Score =  205 bits (521), Expect = 7e-51,   Method: Compositional matrix adjust.
 Identities = 119/284 (41%), Positives = 174/284 (61%), Gaps = 9/284 (3%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           + +G   L +YIH +  IPML  +EE  LA+R  + GDL AA +L+ SHLR+VV IA GY
Sbjct: 50  VPSGHGNLEQYIHTVNNIPMLSAEEETRLAERQIK-GDLEAAKQLILSHLRVVVSIARGY 108

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGL  ++++ EGNIGLM+AVK+F+P  G RL ++++ WIKA + E+ILR+W LV++ T
Sbjct: 109 DGYGLNQADLIQEGNIGLMKAVKRFEPHHGARLFSFAVHWIKAEIHEFILRNWRLVRVAT 168

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN 187
           T  Q++LFFNLR ++  L+A     L P++   IA  L V  SEV+ M  R+ G D  L 
Sbjct: 169 TKPQRKLFFNLRSMRNSLKA-----LSPKEAQDIADDLGVKVSEVMEMEQRMTGHDIGLL 223

Query: 188 ALINSSDKNSSQWQ-DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           A     D+N++    DWL          L +K     +   L  +++ L+ R RRI E R
Sbjct: 224 ADNQDDDENNAFAPIDWLSDSQHEPSHQLAQKAHYALQTEGLQAALAQLDERSRRIVETR 283

Query: 247 RLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
            L +    TL  L++EF VS ER+RQIEA+A +K++  ++ Q +
Sbjct: 284 WLHDGQAATLHELAAEFGVSAERIRQIEAKAIQKLRAIMENQAD 327


>gi|319795672|ref|YP_004157312.1| RNA polymerase, sigma 32 subunit, rpoh [Variovorax paradoxus EPS]
 gi|315598135|gb|ADU39201.1| RNA polymerase, sigma 32 subunit, RpoH [Variovorax paradoxus EPS]
          Length = 313

 Score =  205 bits (521), Expect = 8e-51,   Method: Compositional matrix adjust.
 Identities = 112/283 (39%), Positives = 172/283 (60%), Gaps = 14/283 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI    ++P+L  +EE   A++ R+  DL AA  L+ SHLRLVV I+  Y GYGLP 
Sbjct: 27  LDAYISAANRLPLLTLEEEQGFARKLRDQNDLDAAGALILSHLRLVVSISRQYLGYGLPH 86

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM+AVK+FDP++G RL +Y+M WIKA + EYIL++W +VK+ TT  Q++L
Sbjct: 87  GDLIQEGNVGLMKAVKRFDPDQGVRLVSYAMHWIKAEIHEYILKNWRMVKVATTKAQRKL 146

Query: 136 FFNLRRLKGHLQ---AITDNN-----LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
           FFNLR +K   +   A +DN      L P++V  +A +LNV   EV+ M  RL+G + L 
Sbjct: 147 FFNLRSMKQGFKADSAASDNGTHRETLSPDEVSQMATRLNVKPEEVLEMETRLSGGDVLL 206

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFEAR 246
               S D + +      + D   +   L+E ++R     + +  ++  L+ R RRI E R
Sbjct: 207 DPGPSDDGDEAFGPIAYLADATQEPTALLESQQRDRLSSDGIATALEALDARSRRIVEER 266

Query: 247 RLQENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L+ N      +TL +L++ + VS ER+RQIE  A KK+++++
Sbjct: 267 WLKVNDDGSGGMTLHDLAAVYGVSAERIRQIEVAAMKKMKKAL 309


>gi|294788977|ref|ZP_06754217.1| alternative sigma factor RpoH [Simonsiella muelleri ATCC 29453]
 gi|294483079|gb|EFG30766.1| alternative sigma factor RpoH [Simonsiella muelleri ATCC 29453]
          Length = 289

 Score =  205 bits (521), Expect = 8e-51,   Method: Compositional matrix adjust.
 Identities = 116/284 (40%), Positives = 177/284 (62%), Gaps = 10/284 (3%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           I +G   L +YIH +  IPML  +EE  LA+R +  GD+ AA +L+ SHLR+VV IA GY
Sbjct: 9   IPSGHGSLEQYIHTVNAIPMLSLEEETKLAER-QLRGDIEAAKQLILSHLRVVVSIARGY 67

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGL  ++++ EGNIGLM+AVK+F+P  G RL ++++ WIKA + E+ILR+W LV+I T
Sbjct: 68  DGYGLNQADLIQEGNIGLMKAVKRFEPVHGARLFSFAVHWIKAEIHEFILRNWRLVRIAT 127

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           T  Q++LFFNLR ++  L     N L P++   IA  L V  +EV+ M  R+ G++ +  
Sbjct: 128 TKPQRKLFFNLRSMRKSL-----NALSPKEAQEIADDLGVKLTEVMEMEQRMTGND-VAL 181

Query: 189 LINSSDKNSSQWQ--DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           L  S D N   +   DWL  +     Q + ++     +   L  +++ L+ R RRI E R
Sbjct: 182 LAESDDDNEDSFAPIDWLADNDSEPSQQIAKQAHYALQTEGLQNALAQLDERSRRIVETR 241

Query: 247 RLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
            L ++  +TL +L++E+ VS ER+RQIEA+A +K++  +  + E
Sbjct: 242 WLADDGGLTLHDLAAEYGVSAERIRQIEAKAMQKLRGFLASEAE 285


>gi|194367438|ref|YP_002030048.1| RNA polymerase factor sigma-32 [Stenotrophomonas maltophilia
           R551-3]
 gi|194350242|gb|ACF53365.1| RNA polymerase, sigma 32 subunit, RpoH [Stenotrophomonas
           maltophilia R551-3]
          Length = 291

 Score =  204 bits (520), Expect = 9e-51,   Method: Compositional matrix adjust.
 Identities = 111/269 (41%), Positives = 167/269 (62%), Gaps = 8/269 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + +IP+L   +E  LA+R+R+  DL AA  LV SHLR VV +A GY GYGL +
Sbjct: 23  LDAYIGAVHQIPVLSVDDEQDLARRFRDGNDLDAARELVHSHLRFVVHVARGYNGYGLAL 82

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AVK+FDPE G RL ++++ WI+A M E+IL++W +VK+ TT  Q++L
Sbjct: 83  GDLIQEGNIGLMKAVKRFDPEMGVRLVSFAVHWIRAEMHEFILKNWRIVKVATTKAQRKL 142

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR+ K  L       +   +V A+AK LNVSE EV+ M  RL+G D   +A  +  +
Sbjct: 143 FFNLRKSKTRL-----GWMNAAEVSAVAKDLNVSEREVMEMESRLSGRDIGFDAPTDEDN 197

Query: 195 KNS-SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ-ENP 252
           +++      +LV + +         +   N+  +L   ++ L+ R R I   R L  ++ 
Sbjct: 198 EHAPPSPAAYLVANDEDPSMAYERADSEDNQMQLLREGLAELDARSRDIIRRRWLDADSK 257

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           VTL+ L+ E+ VS ER+RQ+EA A KK++
Sbjct: 258 VTLQELADEYGVSAERIRQVEANALKKMK 286


>gi|254525091|ref|ZP_05137146.1| alternative sigma factor RpoH [Stenotrophomonas sp. SKA14]
 gi|219722682|gb|EED41207.1| alternative sigma factor RpoH [Stenotrophomonas sp. SKA14]
          Length = 291

 Score =  204 bits (520), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 110/269 (40%), Positives = 168/269 (62%), Gaps = 8/269 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + +IP+L   +E  LA+R+R+  DL AA  LV SHLR VV +A GY GYGL +
Sbjct: 23  LDAYIGAVHQIPVLSVDDEQDLARRFRDGNDLDAARELVHSHLRFVVHVARGYNGYGLAL 82

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AVK+FDP+ G RL ++++ WI+A M E+IL++W +VK+ TT  Q++L
Sbjct: 83  GDLIQEGNIGLMKAVKRFDPDMGVRLVSFAVHWIRAEMHEFILKNWRIVKVATTKAQRKL 142

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR+ K  L       +   +V A+AK LNVSE EV+ M  RL+G D   +A  +  +
Sbjct: 143 FFNLRKSKTRL-----GWMNAAEVSAVAKDLNVSEREVMEMESRLSGRDIGFDAPTDEDN 197

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEK-EERKNRRNMLTRSMSVLNPRERRIFEARRLQ-ENP 252
           +++       +  +D    +  E+ +   N+  +L   ++ L+ R R I   R L  ++ 
Sbjct: 198 EHAPPSPAAFLVANDEDPSMAYERADSEDNQMQLLREGLAELDARSRDIIRRRWLDADSK 257

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           VTL+ L+ E+ VS ER+RQ+EA A KK++
Sbjct: 258 VTLQELADEYGVSAERIRQVEANALKKMK 286


>gi|171060212|ref|YP_001792561.1| RNA polymerase sigma-32 subunit RpoH [Leptothrix cholodnii SP-6]
 gi|170777657|gb|ACB35796.1| RNA polymerase, sigma 32 subunit, RpoH [Leptothrix cholodnii SP-6]
          Length = 313

 Score =  204 bits (520), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 116/282 (41%), Positives = 171/282 (60%), Gaps = 15/282 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + ++P+L  +EE   A+R R+  D+ AA RLV SHLRLVV +A  Y GYGLP 
Sbjct: 30  LDAYISAVNRLPLLTHEEEVSFARRLRDSQDVEAAGRLVLSHLRLVVSVARQYLGYGLPH 89

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM+AVK+FDPE+G RL +Y+M WIKA + EY+L++W +VK+ TT  Q++L
Sbjct: 90  GDLIQEGNVGLMKAVKRFDPEQGVRLVSYAMHWIKAEIHEYVLKNWRVVKLATTKAQRKL 149

Query: 136 FFNLRRLKGHLQA-ITDNN-----LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
           FFNLR +K  L+    D +     L   ++  +A++LNV   EVI M  R AG +   AL
Sbjct: 150 FFNLRSMKRQLKGEAADGDTHRSSLTEAEIDTVARELNVKREEVIEMEARFAGGDV--AL 207

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQV-LIEKEERKNRRN-MLTRSMSVLNPRERRIFEARR 247
              SD++   +        + QE    +E   R       L R++  L+ R RRI E R 
Sbjct: 208 EPGSDEDDESYTPIAYLADERQEPTRALEAAHRDELAGPGLLRALDALDARSRRIVEERW 267

Query: 248 LQENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L+ N      +TL +L++E+ VS ER+RQIE  A KK+++++
Sbjct: 268 LKVNDDGSGGLTLHDLAAEYGVSAERIRQIEVAAMKKMRKAL 309


>gi|163759996|ref|ZP_02167080.1| RNA polymerase sigma-32 factor [Hoeflea phototrophica DFL-43]
 gi|162282954|gb|EDQ33241.1| RNA polymerase sigma-32 factor [Hoeflea phototrophica DFL-43]
          Length = 278

 Score =  204 bits (520), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 113/268 (42%), Positives = 169/268 (63%), Gaps = 10/268 (3%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE+ EE+ LA  ++ + D  A H++  +H+RLV+ +A  +R +GLP+ ++V EG++GL
Sbjct: 9   PYLERDEEHDLAVAWKNNKDQDALHKITMAHMRLVISMAAKFRNFGLPMGDLVQEGHVGL 68

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +FDPER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 69  LEAAARFDPEREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRARL 128

Query: 147 QAITDNNLKPEQV-VAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKN-SSQWQDW 203
            A  D  L    + + IA  L V   +V  M+ RL+G D SLNA ++  +   SS   D+
Sbjct: 129 -AQDDPTLTDSAIHIQIADSLGVHVKDVAVMDARLSGPDSSLNAPMSDGESGASSDRMDF 187

Query: 204 LVYDH---DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
           L  D    D Q   +I+ EER+N    L  +++ LNPRE  I   RRL E   TLE L +
Sbjct: 188 LKSDEPLPDEQVSTIID-EERRN--TWLGDALNTLNPRELLIIRKRRLAEEGATLEALGA 244

Query: 261 EFEVSRERVRQIEARAFKKVQESIQKQV 288
              +S+ERVRQIE RA +K++  +  + 
Sbjct: 245 TLGISKERVRQIENRALEKLRAVLSSET 272


>gi|254476880|ref|ZP_05090266.1| RNA polymerase, sigma 32 subunit, RpoH [Ruegeria sp. R11]
 gi|214031123|gb|EEB71958.1| RNA polymerase, sigma 32 subunit, RpoH [Ruegeria sp. R11]
          Length = 292

 Score =  204 bits (520), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 104/266 (39%), Positives = 174/266 (65%), Gaps = 6/266 (2%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K  +L+ + E  LA  +R+  D+ A HRL+ +++RL + +A  +R YG P+++++ E  +
Sbjct: 17  KAELLDAETELKLAYAWRDERDVQALHRLINAYMRLAISMASKFRRYGAPMNDLIQEAGL 76

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFN+RR++ 
Sbjct: 77  GLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQA 136

Query: 145 HLQ---AITDNNLKPEQV-VAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQ 199
            L+   A +   L   Q+   IA ++ V   +V  M+ RL+G D SLNA + S++    +
Sbjct: 137 QLEREAAASGEQLDQHQLHQKIATEIGVPLRDVQMMDGRLSGADFSLNA-VQSAEDEGRE 195

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
           W + L  D     +++ E  + +  R  L  +M  LN RER I   R+L++ P TLE+L 
Sbjct: 196 WIEALEDDSAQAAELVEESHDTRQLRTWLVEAMQALNDRERFIITERKLRDKPRTLESLG 255

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQ 285
            E  +S+ERVRQ+EA AF+K+++S++
Sbjct: 256 DELGLSKERVRQLEAAAFQKMRKSLE 281


>gi|146329254|ref|YP_001209773.1| RNA polymerase sigma-32 factor [Dichelobacter nodosus VCS1703A]
 gi|146232724|gb|ABQ13702.1| RNA polymerase sigma-32 factor [Dichelobacter nodosus VCS1703A]
          Length = 297

 Score =  204 bits (519), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 107/272 (39%), Positives = 178/272 (65%), Gaps = 9/272 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           + +YI ++R+IP+L+  EE+ LA   +++  L+AA  L+  HL+ VV IA G+ GYGLP+
Sbjct: 27  IDQYIAKVRQIPILDADEEFRLATELQQNHSLAAAQTLIVHHLKFVVHIARGFLGYGLPL 86

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AVK+F+P+RG RL ++++ WIK+ + EY++R+W LVKI TT  Q++L
Sbjct: 87  GDLIQEGNIGLMKAVKRFEPQRGVRLVSFAVHWIKSEIHEYVIRNWRLVKIATTKAQRKL 146

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR +K ++  ++D   +      IA+ LNVS  +V+ M  R+ G D + + L  + D
Sbjct: 147 FFNLRSMKKNMHWLSDAEAQ-----TIAEDLNVSVKDVLEMESRIHGQDIAFDPLDENDD 201

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFEARRLQEN-P 252
           + +     WL  D      +  E  E+K+  ++ LT+ ++ L+ R R I E+R L E+  
Sbjct: 202 EENVAPAAWLT-DESVDPALSTEHHEQKHLLQHQLTQGLNQLDARSREIIESRWLNEHEK 260

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           VTL+ L+S++ +S ER+RQIE +A  +++ S+
Sbjct: 261 VTLQTLASKYHISAERIRQIEQQALLQLKNSM 292


>gi|120612533|ref|YP_972211.1| RNA polymerase sigma-32 subunit RpoH [Acidovorax citrulli AAC00-1]
 gi|120590997|gb|ABM34437.1| RNA polymerase, sigma 32 subunit, RpoH [Acidovorax citrulli
           AAC00-1]
          Length = 313

 Score =  204 bits (519), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 113/285 (39%), Positives = 173/285 (60%), Gaps = 18/285 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + ++PML  +EE   A+R +EH D+ AA R+V SHLRLVV IA  Y GYGLP 
Sbjct: 27  LDAYISAVNRLPMLTAEEERTYARRLKEHNDVEAAGRMVMSHLRLVVSIARQYLGYGLPH 86

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM+AVK+FDP++  RL +Y+M WIKA + EYIL++W +VK+ TT +Q++L
Sbjct: 87  GDLIQEGNVGLMKAVKRFDPDQNVRLVSYAMHWIKAEIHEYILKNWRMVKVATTKSQRKL 146

Query: 136 FFNLRRLKGHLQAITD--------NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
           FFNLR +K   +A             L  +++  +A++LNV   EVI M  RL+G + + 
Sbjct: 147 FFNLRSMKQGFKADAAAGDAGTHRETLSEQEIDVVAQQLNVKREEVIEMETRLSGGDVM- 205

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQ--VLIEKEERKN-RRNMLTRSMSVLNPRERRIFE 244
            L  +   +  Q    + Y  DG  +   +IE  +R     + +  +++ L+ R RRI E
Sbjct: 206 -LDPAPSDDGEQAYGPIAYLADGMHEPTAMIESRQRDVLATDGIANALATLDDRSRRIVE 264

Query: 245 ARRLQENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            R L+ N      +TL  L++ + VS ER+RQIE  A KK+++++
Sbjct: 265 ERWLKVNDDGSGGMTLHELAAVYGVSAERIRQIEVAAMKKMKKAL 309


>gi|149925644|ref|ZP_01913908.1| RNA polymerase sigma factor [Limnobacter sp. MED105]
 gi|149825761|gb|EDM84969.1| RNA polymerase sigma factor [Limnobacter sp. MED105]
          Length = 308

 Score =  204 bits (519), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 119/288 (41%), Positives = 176/288 (61%), Gaps = 9/288 (3%)

Query: 3   RKNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           R   +++  G +G L  YI    +IPML  +EE  L +R +   DL AA RLV SHLRLV
Sbjct: 20  RDPWALVARGPLGNLDAYISATHQIPMLSPEEEVELGERLQRDNDLEAARRLVLSHLRLV 79

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V +A  Y GYGLP ++++ EGNIGLM+AVK+FDP RG RL ++++ WIKA + EYI+R+W
Sbjct: 80  VAVARQYLGYGLPHADLIQEGNIGLMKAVKRFDPTRGVRLVSFALHWIKAEIHEYIIRNW 139

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            +VK+ TT   ++LFFNL   K + Q      L P+Q+  +A +LNV   +V  M  R+A
Sbjct: 140 RMVKMITTKAHRKLFFNLNSFKKYGQ-----TLSPDQINEVASELNVRPEDVYDMERRMA 194

Query: 182 GDE-SLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           G E SL+ +++  S++NS     +L  +     +VL      +     L  +++ L+ R 
Sbjct: 195 GHEFSLDPVVDVDSEENSYNPVRYLAAEGAEPTEVLEGANMERLHSEGLDMALASLDERS 254

Query: 240 RRIFEARRLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +RI  +R L  EN  TL +L++E  VS ERVRQIE +A KK++ ++ K
Sbjct: 255 QRIISSRWLAGENAKTLHDLAAELGVSAERVRQIETQAMKKMKTALLK 302


>gi|54307376|ref|YP_128396.1| RNA polymerase factor sigma-32 [Photobacterium profundum SS9]
 gi|46911796|emb|CAG18594.1| putative RNA polymerase sigma-32 factor [Photobacterium profundum
           SS9]
          Length = 282

 Score =  204 bits (519), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 113/283 (39%), Positives = 173/283 (61%), Gaps = 10/283 (3%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +M++I  G   L  YI  + + PML  ++E  LA+R    GD+ AA  LV SH+R VV +
Sbjct: 3   SMALIFAG--SLDSYIQTVNRHPMLSAEQEKELAERLHYDGDIEAAKGLVMSHMRFVVHV 60

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A GY GYGLPI++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W +V
Sbjct: 61  ARGYSGYGLPIADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIV 120

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           K+ TT  Q++LFFNLR+ K  L     NN + E V   A++L V+ SEV  M  RLA  +
Sbjct: 121 KVATTKAQRKLFFNLRKSKKRLGWF--NNAEVEMV---AEQLGVNPSEVREMESRLAAQD 175

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNPRERR 241
               L N  D   + +   + +  D    V +  EE     +  N L+ +++ L+ R + 
Sbjct: 176 PAFELPNEDDDRDAGYTAPVYFLEDKSSDVALSYEENNWENHTNNRLSNALAGLDERSQH 235

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           I  +R L +   TL++L++ + +S ERVRQ+E  A KK++E++
Sbjct: 236 IVRSRWLDDEKTTLQDLANHYGISAERVRQLEKNAMKKLKEAV 278


>gi|50262051|gb|AAT72766.1| putative sigma factor 32 [Dichelobacter nodosus]
          Length = 283

 Score =  204 bits (519), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 107/272 (39%), Positives = 178/272 (65%), Gaps = 9/272 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           + +YI ++R+IP+L+  EE+ LA   +++  L+AA  L+  HL+ VV IA G+ GYGLP+
Sbjct: 13  IDQYIAKVRQIPILDADEEFRLATELQQNHSLAAAQTLIVHHLKFVVHIARGFLGYGLPL 72

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AVK+F+P+RG RL ++++ WIK+ + EY++R+W LVKI TT  Q++L
Sbjct: 73  GDLIQEGNIGLMKAVKRFEPQRGVRLVSFAVHWIKSEIHEYVIRNWRLVKIATTKAQRKL 132

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR +K ++  ++D   +      IA+ LNVS  +V+ M  R+ G D + + L  + D
Sbjct: 133 FFNLRSMKKNMHWLSDAEAQ-----TIAEDLNVSVKDVLEMESRIHGQDIAFDPLDENDD 187

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFEARRLQEN-P 252
           + +     WL  D      +  E  E+K+  ++ LT+ ++ L+ R R I E+R L E+  
Sbjct: 188 EENVAPAAWLT-DESVDPALSTEHHEQKHLLQHQLTQGLNQLDARSREIIESRWLNEHEK 246

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           VTL+ L+S++ +S ER+RQIE +A  +++ S+
Sbjct: 247 VTLQTLASKYHISAERIRQIEQQALLQLKNSM 278


>gi|319406278|emb|CBI79915.1| RNA polymerase sigma-32 factor [Bartonella sp. AR 15-3]
          Length = 303

 Score =  204 bits (519), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 111/277 (40%), Positives = 180/277 (64%), Gaps = 4/277 (1%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V+  +G S     +R  P LE+++E+ LA R+++  D  A H++  +H+RLV+ IA  ++
Sbjct: 18  VDASLGRSMMRSAMRA-PYLERKKEHDLALRWKDKRDDDAMHQIAAAHMRLVISIASRFK 76

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
            + +P+ ++V EG +GL++A  +FDPER  R +TY+ WWI+A++Q+YILR+WS+V+ GT+
Sbjct: 77  RFKMPLGDLVQEGYVGLLEAAARFDPEREVRFSTYATWWIRASIQDYILRNWSIVRGGTS 136

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-AIAKKLNVSESEVISMNCRLAG-DESLN 187
           ++QK LFFNLRRL+  L A  DN L  +++  AI++KL VS ++V  M+ R +G D SL+
Sbjct: 137 SSQKALFFNLRRLRAKL-AQDDNTLTKQEIFSAISEKLGVSVNDVEKMDFRFSGTDNSLS 195

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I+ S +      D L+ DH   + V+ +  + + R   L  ++ +LN RE  I   RR
Sbjct: 196 LSISESGETPIAKMDSLIDDHPLPDAVIEQVIDGQRRAQWLYEALQILNERELEIIRFRR 255

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L+E   TLE L  +  +S+ERVRQIEARA +K++ ++
Sbjct: 256 LKEEGATLEVLGEKLGISKERVRQIEARALQKLRCAL 292


>gi|115374575|ref|ZP_01461855.1| sigma-E factor [Stigmatella aurantiaca DW4/3-1]
 gi|310823765|ref|YP_003956123.1| RNA polymerase sigma factor [Stigmatella aurantiaca DW4/3-1]
 gi|115368445|gb|EAU67400.1| sigma-E factor [Stigmatella aurantiaca DW4/3-1]
 gi|309396837|gb|ADO74296.1| RNA polymerase sigma factor [Stigmatella aurantiaca DW4/3-1]
          Length = 366

 Score =  204 bits (518), Expect = 1e-50,   Method: Compositional matrix adjust.
 Identities = 114/283 (40%), Positives = 184/283 (65%), Gaps = 12/283 (4%)

Query: 13  EIGLSR------YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           + GL+R      Y+ E+ + P+L+++EEY LAK+Y++ GD+ AA+RLV S+LRLVVK+A 
Sbjct: 78  DTGLARKDPLQAYMAEVTRHPLLKREEEYALAKQYQQTGDVRAAYRLVASNLRLVVKLAH 137

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y    L + ++V EGNIGLMQAVKK+DPERG +L++Y+ WWI+A +  YI+ +W +VK+
Sbjct: 138 EYHRNPLSLLDLVQEGNIGLMQAVKKYDPERGVKLSSYAAWWIRAYILRYIMDNWKMVKL 197

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-S 185
           GTT  Q++LFF LR+ +  L A      +P   + +A++LNV+E +V+ M+ RL  DE S
Sbjct: 198 GTTEAQRKLFFKLRQEQDKLIA---QGFEPNPKL-LAERLNVTEQDVVEMDQRLGHDEVS 253

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           ++A +    + +S+    L     G E+ L  +E ++  R  L      L  +ER IFE+
Sbjct: 254 IDAPVGDESR-ASRADRLLPSSAVGAEERLGNEELKELFREKLAEFAQTLEGKERFIFES 312

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           R   + P+TL+++  ++ VSRER RQIEA    +++E +++++
Sbjct: 313 RLTADEPLTLQDIGDKYGVSRERARQIEAALINRMREFMRERI 355


>gi|254498663|ref|ZP_05111381.1| RNA polymerase factor sigma-32 [Legionella drancourtii LLAP12]
 gi|254352111|gb|EET10928.1| RNA polymerase factor sigma-32 [Legionella drancourtii LLAP12]
          Length = 280

 Score =  204 bits (518), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 110/272 (40%), Positives = 176/272 (64%), Gaps = 7/272 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YIH + +IPML  +EE   A+R+   GD+ AA RLV +HLR VV++A GY GYGLP+
Sbjct: 13  LDAYIHRVNQIPMLTMEEEIACAERFHSEGDIEAARRLVLAHLRYVVRVARGYLGYGLPL 72

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGN+GLM+AVK+FDP+ G RL ++++ WIKA + E++LR+W +VKI TT  Q++L
Sbjct: 73  NDLIQEGNVGLMKAVKRFDPKMGVRLVSFAVHWIKAEIHEFVLRNWRIVKIATTKAQRKL 132

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSSD 194
           FFNLR++K  L   ++     E+V A+AK L VS  EV+ M  RL A D   +A     +
Sbjct: 133 FFNLRQMKNRLGWFSN-----EEVAAVAKDLGVSTDEVLVMEQRLNAMDAPYDAPDADDN 187

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPRERRIFEARRLQENPV 253
            +     +  +++ +    +++EKE   +R R  L  ++  L+ R + I + R L ++ +
Sbjct: 188 DDFHMAPERYLFNVNDDPALVLEKESTGDRGREQLLLALEQLDERSQDILQQRWLADDKL 247

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           TL +L+ ++ +S ERVRQ+E  A KK+++ I+
Sbjct: 248 TLHDLAEKYAISAERVRQLEKNAMKKLRQFIE 279


>gi|308051462|ref|YP_003915028.1| RNA polymerase, sigma 32 subunit, RpoH [Ferrimonas balearica DSM
           9799]
 gi|307633652|gb|ADN77954.1| RNA polymerase, sigma 32 subunit, RpoH [Ferrimonas balearica DSM
           9799]
          Length = 286

 Score =  204 bits (518), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 112/288 (38%), Positives = 170/288 (59%), Gaps = 10/288 (3%)

Query: 2   NRKNMSIIV--NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLR 59
            R NM+++V   G   L  YI  +  IPML  +EE  LA++  E GDL AA  L+ +HLR
Sbjct: 4   TRPNMALMVVPQGHGTLESYIQAVNAIPMLSAEEEQYLARQV-EQGDLDAAKHLIMAHLR 62

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
            VV +A  Y GYGLP ++++ EGNIGLM+AVK+FDP  G RL ++++ WIKA + EY+L+
Sbjct: 63  FVVHVARSYAGYGLPQADLIQEGNIGLMKAVKRFDPNIGVRLVSFAVHWIKAEIHEYVLK 122

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
           +W +VK+ TT  Q++LFFNLR+ K  L          E+V  +A +L VSESEV+ M  R
Sbjct: 123 NWRIVKVATTKAQRKLFFNLRKAKKRL-----GWFSAEEVSTVADELGVSESEVMEMEAR 177

Query: 180 LAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNP 237
           +A  D + +      D   +      + D        +E+E+  +  +  L  +++ L+ 
Sbjct: 178 MAAVDAAFDIAPERDDDEGAFAPALFLEDKQSDHAEALEQEDWDRQSQQRLHAALNTLDE 237

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           R R I  AR L E   TL+ L+  ++VS ER+RQ+E  A KK++ +++
Sbjct: 238 RSRDILMARWLDEPKATLQELADRYQVSAERIRQLEKNAIKKLKSAME 285


>gi|90407357|ref|ZP_01215542.1| RpoD protein [Psychromonas sp. CNPT3]
 gi|90311508|gb|EAS39608.1| RpoD protein [Psychromonas sp. CNPT3]
          Length = 282

 Score =  204 bits (518), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 115/283 (40%), Positives = 169/283 (59%), Gaps = 10/283 (3%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +M ++  G I    YI  + K  ML   EE  LA+R    GDL AA +LV SHLR V  I
Sbjct: 7   SMGLVPQGSI--EAYIQSVNKFAMLSASEEKALAERLFYEGDLDAAKKLVMSHLRFVAYI 64

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y GYGL I++++ EGN+GLM+AVK+FDP  G RL ++++ WIKA + EY++R+W +V
Sbjct: 65  AKSYAGYGLAIADLIQEGNVGLMKAVKRFDPTVGVRLVSFAVHWIKAEIHEYVIRNWRVV 124

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-D 183
           KI TT  Q++LFFNLR+ K  L   +      ++V  +A  LNVS  +V+ M  RL G D
Sbjct: 125 KIATTKAQRKLFFNLRKAKKRLGWFS-----KDEVENVANNLNVSTKDVLEMESRLNGHD 179

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE-ERKNRRNMLTRSMSVLNPRERRI 242
            S +   +  D+N      +L  D +    +L+E E  + N +  L  ++S L+ R + I
Sbjct: 180 YSFDLTGDDDDENCFAPVQYL-EDKNADVALLVEVENSQSNMKRQLHSALSSLDERSQDI 238

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             +R L E   TL +L++ + +S ERVRQ+EA A KK+Q ++Q
Sbjct: 239 ISSRWLNEPKATLHDLAARYSISAERVRQLEANAIKKLQSNMQ 281


>gi|56459340|ref|YP_154621.1| RNA polymerase factor sigma-32 [Idiomarina loihiensis L2TR]
 gi|56178350|gb|AAV81072.1| DNA-directed RNA polymerase sigma 32 subunit [Idiomarina loihiensis
           L2TR]
          Length = 286

 Score =  204 bits (518), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 113/282 (40%), Positives = 173/282 (61%), Gaps = 13/282 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
            M++ V    GL  YI  + +IPML  ++E  LA R  E+ DL AA  L+ SHLR VV +
Sbjct: 7   TMALSVPQGAGLDGYIQSVNRIPMLTAEKEKALATRLYENSDLDAAKELIMSHLRFVVHV 66

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y GYGLP ++++ EGNIGLM+AVK+FDP  G RL ++++ WIKA + EY+LR+W +V
Sbjct: 67  ARSYSGYGLPQADLIQEGNIGLMKAVKRFDPSVGVRLVSFAVHWIKAEIHEYVLRNWRVV 126

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGD 183
           K+ TT  Q++LFFNLR++K  L   +      ++V  +A +L VS  EV+ M  R+ A D
Sbjct: 127 KVATTKAQRKLFFNLRKMKKRLGWFS-----QKEVETVANELGVSTKEVLEMETRMSAHD 181

Query: 184 ESLNALINSSDKNSSQWQDW--LVYDHDGQEQVLIE---KEERKNRRNMLTRSMSVLNPR 238
           ++    ++S D +S +   +   +Y  D +  +  E   K+   + +  L  +MS L+ R
Sbjct: 182 QAFE--LSSDDDDSKEGSAYSPAMYLEDKRSDLAAEIEAKDYENHTQQKLLGAMSHLDER 239

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            + I ++R L E+  TL +L+ ++EVS ERVRQ+E  A KK+
Sbjct: 240 SQDIVQSRWLSEDKTTLHDLAEKYEVSAERVRQLEQNAMKKL 281


>gi|146276534|ref|YP_001166693.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides ATCC 17025]
 gi|145554775|gb|ABP69388.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacter sphaeroides
           ATCC 17025]
          Length = 292

 Score =  204 bits (518), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 110/270 (40%), Positives = 174/270 (64%), Gaps = 10/270 (3%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           +  +L+ Q E  LA  +R+  D  A HRL+T+++RL + +A  YR YG P+++++ E ++
Sbjct: 17  RAELLDAQTELRLAYAWRDQRDERALHRLITAYMRLAISMASKYRRYGAPMNDLIQEASL 76

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WSLV+ G+T++QK LFFN+RR++ 
Sbjct: 77  GLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSLVRTGSTSSQKALFFNMRRVQA 136

Query: 145 HLQAITDNNLKPEQVVA------IAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
            L+   + + + EQ+ A      +A  + V  S+V  M  RL+G D SLNA   S+D   
Sbjct: 137 RLE--REASQRGEQLDAHQLRELVAHDVGVPLSDVEMMEGRLSGSDFSLNA-TQSADDEG 193

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
            +W D L  D     +V+    + +  R  L  +M  LN RER I   R+L++ P TLE+
Sbjct: 194 REWIDALEDDSAQASEVVEGSLDAERLRGWLVVAMQQLNARERFIVTERKLRDVPRTLES 253

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L  E ++S+ERVRQ+EA AF K++ S++ Q
Sbjct: 254 LGEELKLSKERVRQLEAAAFAKMRRSLEAQ 283


>gi|156972625|ref|YP_001443532.1| RNA polymerase factor sigma-32 [Vibrio harveyi ATCC BAA-1116]
 gi|156524219|gb|ABU69305.1| hypothetical protein VIBHAR_00277 [Vibrio harveyi ATCC BAA-1116]
          Length = 285

 Score =  204 bits (518), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 111/272 (40%), Positives = 164/272 (60%), Gaps = 8/272 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  +   PML  +EE  LA+R    G++ AA  L+ SHLR VV +A GY GYGLP+
Sbjct: 16  LDSYIRSVNSYPMLTPEEERGLAERLHYKGEIDAAKGLILSHLRFVVHVARGYSGYGLPM 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           +++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W +VKI TT  Q++L
Sbjct: 76  ADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR+ K  L    +      +V  +A++L V  SEV  M  RLA  +S   +    D 
Sbjct: 136 FFNLRKSKKRLGWFNNG-----EVETVARELGVEPSEVREMESRLAAVDSTFDMPMDDDD 190

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
           NS+ +   + Y  D    V    E      +  N L  +++ L+ R +RI  +R L ++ 
Sbjct: 191 NSNSYTAPMFYLEDKSSDVADNIEAANWETHTNNRLGHALASLDERSQRIVRSRWLDDDK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL++L+ EF VS ER+RQ+E  A KK++ ++
Sbjct: 251 ATLQDLADEFGVSAERIRQLEKNAMKKLKLAV 282


>gi|304311558|ref|YP_003811156.1| RNA polymerase sigma factor [gamma proteobacterium HdN1]
 gi|301797291|emb|CBL45511.1| RNA polymerase sigma factor [gamma proteobacterium HdN1]
          Length = 285

 Score =  203 bits (517), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 111/269 (41%), Positives = 171/269 (63%), Gaps = 9/269 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+RY+  +  + +L   EE  LA+RY  + D+ AA +LV +HLR VV +A GY GYGL +
Sbjct: 17  LNRYLSAVNSVAILSADEERALAERYYYNEDVDAARQLVLAHLRFVVHVARGYNGYGLQL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           S++V EGN+GLM+AVK+FDP  G RL ++++ WIKA + E+ILR+W +VKI TT +Q++L
Sbjct: 77  SDLVQEGNVGLMKAVKRFDPTMGVRLVSFAVHWIKAEIHEFILRNWRIVKIATTKSQRKL 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR  K  L       L  ++V  IA +LNVS  +V  M  RLA  D + +A +++ D
Sbjct: 137 FFNLRSHKRRLGV-----LSGDEVNMIATELNVSPEDVREMEGRLAAHDTAFDAPVDADD 191

Query: 195 KNSSQWQDWLVYDH--DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
           +++SQ   + + D   D   Q L + +   N  + L  +M+ L+ R R I + R   ++ 
Sbjct: 192 ESASQAPVYYLEDASMDPAHQ-LEDAQWTDNTTDRLQLAMNSLDERSRDILQQRWFNDDK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TL +L++++ VS ER+RQ+EA A KK++
Sbjct: 251 ATLHDLAAQYSVSAERIRQLEANAMKKIK 279


>gi|296135250|ref|YP_003642492.1| RNA polymerase, sigma 32 subunit, RpoH [Thiomonas intermedia K12]
 gi|294339349|emb|CAZ87705.1| RNA polymerase sigma-32 factor (Heat shock regulatory protein
           F33.4) [Thiomonas sp. 3As]
 gi|295795372|gb|ADG30162.1| RNA polymerase, sigma 32 subunit, RpoH [Thiomonas intermedia K12]
          Length = 302

 Score =  203 bits (517), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 115/278 (41%), Positives = 169/278 (60%), Gaps = 18/278 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + ++PML  +EE  LA+ +RE GD  AA +LV SHLRLVV  A  Y GYGLP 
Sbjct: 30  LDAYISAVNRLPMLSAEEEARLARTWREQGDKDAAGKLVLSHLRLVVSTARQYLGYGLPH 89

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AVK+FDP  G RL +Y++ WIKA + EYILR+W LVK+ TT +Q++L
Sbjct: 90  ADLIQEGNIGLMKAVKRFDPAHGVRLVSYALHWIKAEIHEYILRNWRLVKVATTKSQRKL 149

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR +K       +  +   Q+  +A+ LNV   +VI M  R+ G D +L+  +   +
Sbjct: 150 FFNLRSMK-----TANAGMNEAQIDDMAQALNVKREDVIEMESRMGGADIALDPTVEDGE 204

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRR---NMLTRSMSVLNPRERRIFEARRLQEN 251
           ++ +     + Y  D  ++ +   E R + R     L  ++ +L+ R R I E R LQ N
Sbjct: 205 ESYAP----ISYLADNTQEPMAVLEARSHDRLQVEGLENALELLDARSRAIVEQRWLQVN 260

Query: 252 P-----VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                  TL  L++E+ VS ER+RQIE  A KK+++S+
Sbjct: 261 DDGSGGKTLHELAAEYGVSAERIRQIEVAAMKKMRKSL 298


>gi|163803403|ref|ZP_02197278.1| RNA polymerase sigma factor [Vibrio sp. AND4]
 gi|159172807|gb|EDP57652.1| RNA polymerase sigma factor [Vibrio sp. AND4]
          Length = 285

 Score =  203 bits (517), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 113/287 (39%), Positives = 170/287 (59%), Gaps = 8/287 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  S+ +  +  L  YI      PML   EE  LA+R    G++ AA  L+ SHLR 
Sbjct: 1   MTKEAYSMALVTQDSLDSYIRSANSYPMLTADEERGLAERLHYKGEIDAAKGLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A GY GYGLP++++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L    +      +V  +A++L V  SEV  M  RL
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKSKKRLGWFNNG-----EVETVARELGVEPSEVREMESRL 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNP 237
           A  +S   +    D NS+ +   +VY  D    V    E      +  N L  +++ L+ 
Sbjct: 176 AAVDSTFDMPMDDDDNSNSYTAPMVYLEDKSSDVADNIEAANWEAHTNNRLGHALASLDE 235

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R +RI  +R L ++  TL++L+ EF VS ER+RQ+E  A KK++ ++
Sbjct: 236 RSQRIVRSRWLDDDKSTLQDLADEFGVSAERIRQLEKNAMKKLKLAV 282


>gi|260425737|ref|ZP_05779717.1| RNA polymerase sigma-32 factor [Citreicella sp. SE45]
 gi|260423677|gb|EEX16927.1| RNA polymerase sigma-32 factor [Citreicella sp. SE45]
          Length = 292

 Score =  203 bits (517), Expect = 2e-50,   Method: Compositional matrix adjust.
 Identities = 108/268 (40%), Positives = 174/268 (64%), Gaps = 6/268 (2%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K  +L+ + E  LA  +R+  D ++ HRL+ +++RL + +A  ++ YG P+ ++V E  +
Sbjct: 17  KAELLDAETELRLAYAWRDQRDEASLHRLINAYMRLAISMASKFKRYGAPMGDLVQEAGL 76

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFN+RR++ 
Sbjct: 77  GLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQA 136

Query: 145 HLQ---AITDNNLKPEQV-VAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQ 199
            L+   A     L+   +  AIA+++ V  S+V  M  RL+G D SLNA   SSD++  +
Sbjct: 137 RLEREAAAEGKTLERHMLHAAIAQEIGVPLSDVEMMEGRLSGSDFSLNA-TQSSDEDGRE 195

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
           W D L  D +    V+  + +    R  L  +MS LN RER I   R+L++   TLE+L 
Sbjct: 196 WIDTLEDDGEQGSSVVEGRLDNAQLREWLVVAMSALNDRERFIVRERKLRDETRTLESLG 255

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQ 287
            E  +S+ERVRQ+EA AF K+++S++ Q
Sbjct: 256 QELGLSKERVRQLEAAAFAKMRKSLEAQ 283


>gi|195970121|ref|NP_387362.2| RNA polymerase factor sigma-32 [Sinorhizobium meliloti 1021]
 gi|307302477|ref|ZP_07582234.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium meliloti
           BL225C]
 gi|307316193|ref|ZP_07595637.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium meliloti
           AK83]
 gi|8131943|gb|AAF73147.1|AF149031_2 sigma factor RpoH2 [Sinorhizobium meliloti]
 gi|10129889|dbj|BAB13518.1| sigma factor [Sinorhizobium meliloti]
 gi|187904236|emb|CAC47835.2| RNA polymerase sigma factor (Sigma-32) [Sinorhizobium meliloti
           1021]
 gi|306898033|gb|EFN28775.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium meliloti
           AK83]
 gi|306903147|gb|EFN33737.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium meliloti
           BL225C]
          Length = 288

 Score =  203 bits (516), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 113/276 (40%), Positives = 171/276 (61%), Gaps = 9/276 (3%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           R I    + P LE+ EE+ LA+ +R   D  A +++  SH+RLV+ +A  +R +GLP+ +
Sbjct: 9   RMIKIAMEAPYLERDEEHALAQAWRNDNDQEARNKIAMSHMRLVISMAAKFRSFGLPMGD 68

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +V EG+IGL++A  +F+P R  R +TY+ WWI+A+MQ+Y+LR+WS+V+ GT++ QK LFF
Sbjct: 69  LVQEGHIGLLEAAARFEPSREVRFSTYATWWIRASMQDYVLRNWSIVRGGTSSAQKALFF 128

Query: 138 NLRRLKGHLQAITDNNLKPEQV-VAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDK 195
           NLRRL+  L A  D  L  + +   IA  L VS ++V +M+ RL+G D SL A I S D 
Sbjct: 129 NLRRLRARL-AQGDRQLTSQAMHEEIAAALGVSLADVQTMDARLSGNDASLQAPIGSGDP 187

Query: 196 NSSQWQDWLVYDH---DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
           ++    D+L  +    D Q   LI+ E     R  L  ++  L+ RE +I  ARRL E+ 
Sbjct: 188 DAGARLDFLASEAPLPDEQVSDLIDGE---RARRWLQVALGELSEREMKIIRARRLTEDG 244

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            TLE L     +S+ERVRQIE RA +K++ ++  + 
Sbjct: 245 ATLEELGVALGISKERVRQIETRALEKLRAALTAKA 280


>gi|260461453|ref|ZP_05809700.1| RNA polymerase, sigma 32 subunit, RpoH [Mesorhizobium opportunistum
           WSM2075]
 gi|259032523|gb|EEW33787.1| RNA polymerase, sigma 32 subunit, RpoH [Mesorhizobium opportunistum
           WSM2075]
          Length = 287

 Score =  203 bits (516), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 113/268 (42%), Positives = 175/268 (65%), Gaps = 10/268 (3%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K P LE+ EE+ LA  ++E  D +A H +  +H+RLV+ +A  +R YGLP+ +++ EG++
Sbjct: 16  KAPYLERDEEHRLALLWKEDNDQNALHSITVAHMRLVISMASKFRHYGLPLGDLIQEGHV 75

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A  +F+PER  R +TY+ WWI+A+MQ+YILR+WS+V+ GT++ QK LFFNLRRL+ 
Sbjct: 76  GLLEAAARFEPERDVRFSTYATWWIRASMQDYILRNWSIVRGGTSSAQKALFFNLRRLRA 135

Query: 145 HL----QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSSDKNSSQ 199
            L    + +++  L  E  VA    L VSE++V  M+ RL A D SLN  + + D  +++
Sbjct: 136 RLANGAEPLSNETLYREVSVA----LGVSEADVAMMDSRLSAPDSSLNVPL-ADDAGATE 190

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
             D+LV D    ++V+ ++ +   R   L  +++ LN RE RI E RRL +   TLE L 
Sbjct: 191 RMDFLVSDDPLPDEVVSDRIDVARRSVWLKAALAALNARELRIIEERRLSDEGATLEALG 250

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQ 287
               +S+ERVRQIEARA +K++ ++ KQ
Sbjct: 251 ETLGISKERVRQIEARAMEKLKVALVKQ 278


>gi|86158413|ref|YP_465198.1| RNA polymerase sigma factor RpoH [Anaeromyxobacter dehalogenans
           2CP-C]
 gi|85774924|gb|ABC81761.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter
           dehalogenans 2CP-C]
          Length = 307

 Score =  203 bits (516), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 114/274 (41%), Positives = 165/274 (60%), Gaps = 6/274 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ EI + P+L   EE  LA+++    D  AAHRLVT++LR VVK+A  YR YG  +
Sbjct: 13  LELYLSEINRFPLLTVDEEQRLARQFCADRDTRAAHRLVTANLRFVVKVAYEYRSYGFRM 72

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AV+KFDP++G RL +Y++WWI+A +Q YIL+SWSLVK+GTT  Q++L
Sbjct: 73  ADLIQEGNIGLMKAVQKFDPDKGIRLISYAVWWIRAYIQNYILKSWSLVKLGTTQAQRKL 132

Query: 136 FFNLRRLKGHLQAITDN---NLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALIN 191
           FF+L R K  L   +     +        +AKKL V   EV  M  R+ G D SL+A + 
Sbjct: 133 FFSLARTKRELDKRSQEQGADSDGHDANKVAKKLRVKPGEVREMEQRMEGRDLSLDAPMG 192

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             D       D+L      Q+  L   +E+K     +  ++  L+ RER I E R + + 
Sbjct: 193 --DDGGYSHVDFLASGSTSQDDELSGVQEQKVVSGRIVEALGRLDQRERYIIEMRVMSDR 250

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           P+TL+ L   F  SRER RQ+E RA  K++E ++
Sbjct: 251 PLTLKELGEHFGFSRERARQLEIRAKDKLKEELR 284


>gi|242281118|ref|YP_002993247.1| RNA polymerase, sigma 70 family subunit [Desulfovibrio salexigens
           DSM 2638]
 gi|242124012|gb|ACS81708.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio
           salexigens DSM 2638]
          Length = 322

 Score =  203 bits (516), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 120/283 (42%), Positives = 177/283 (62%), Gaps = 12/283 (4%)

Query: 12  GEIG----LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           GE+     L  Y+ EI + P+LE  EE+ LAK+ +E+GD  AA RLV+SHLRLVVKIAM 
Sbjct: 34  GEVATKDPLHLYLQEISRFPLLEPDEEFRLAKQVQENGDQQAAFRLVSSHLRLVVKIAMD 93

Query: 68  Y-RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           + R +   + +++ EGN+GLM+AV KFDP++G + + Y+ +WIKA + +YI+ +W +VKI
Sbjct: 94  FQRRWMQNVLDLIQEGNVGLMKAVNKFDPDKGIKFSYYAAFWIKAYILKYIMDNWRMVKI 153

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDES 185
           GTT  Q++LF+NL + +  LQA+  +    E    ++KKLNVSE E+  M+ RLA  D S
Sbjct: 154 GTTQTQRKLFYNLNKERQRLQALGFDPTTSE----LSKKLNVSEEEITEMDQRLAKNDLS 209

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           LN  +   + + +   D+L     G E+ L  KE      + L   +  LN +E+ I   
Sbjct: 210 LN--LKFGEDSEATRMDFLPDLGPGVEETLANKEISTLLLDQLRAIVPNLNEKEQVILND 267

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           R L ++P TL  +  EF V+RERVRQIEAR  KK++E + + V
Sbjct: 268 RLLSDSPRTLREIGEEFGVTRERVRQIEARLLKKLREHLAESV 310


>gi|3219170|dbj|BAA28785.1| sigma-32 homolog [Hydrogenophilus thermoluteolus]
          Length = 309

 Score =  203 bits (516), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 116/276 (42%), Positives = 167/276 (60%), Gaps = 12/276 (4%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           RYI  + + P+L + EE+ LA+R+ E  DL AA +LV ++LR VV IA  Y GYGLP ++
Sbjct: 39  RYIQAVNRFPVLSEAEEHELARRFHETNDLDAARKLVLANLRYVVMIARQYFGYGLPEAD 98

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGN+GL++AV++FDP +G R  T++ +WIKA + +YILR+W LVKI TT  QK+LFF
Sbjct: 99  LIQEGNVGLLKAVRRFDPYKGVRFITFAAYWIKAEIHDYILRNWRLVKIATTKAQKKLFF 158

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALINSSDKN 196
           NLR+L G         L   +  AIA+ L V   EV  M+ R A GD +L A I+S ++ 
Sbjct: 159 NLRKLLG------SEPLTRAKADAIAETLAVKPEEVAEMHARFAGGDVALEAPIDSDEE- 211

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRR---NMLTRSMSVLNPRERRIFEARRLQENPV 253
            + W+  L Y  D          E +  R     L ++++ L+ R R I   R L E P 
Sbjct: 212 -ADWRAPLAYLPDPSGTPEEAVAEAEAERLSHEGLQQALTQLDERSRAIVTRRWLTEKPA 270

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           TL  L++E+ +S ERVRQIEA A KK++  +  Q +
Sbjct: 271 TLHELAAEYGISAERVRQIEAAALKKLRVWLSPQAD 306


>gi|254510133|ref|ZP_05122200.1| RNA polymerase sigma-32 factor [Rhodobacteraceae bacterium KLH11]
 gi|221533844|gb|EEE36832.1| RNA polymerase sigma-32 factor [Rhodobacteraceae bacterium KLH11]
          Length = 292

 Score =  202 bits (515), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 107/268 (39%), Positives = 177/268 (66%), Gaps = 6/268 (2%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K  +L+ + E  LA  +R++ D  A HRL+T+++RL + +A  ++ YG P+++++ E  +
Sbjct: 17  KAELLDAETELQLAYAWRDNRDEQALHRLITAYMRLAISMAAKFKRYGAPMNDLIQEAGL 76

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFN+RR++ 
Sbjct: 77  GLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQA 136

Query: 145 HL--QAITDN-NLKPEQV-VAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQ 199
            L  +A T+  +L   Q+   IA ++ V   +V  M  RLAG D SLNA + S+D++  +
Sbjct: 137 RLEREAATEGLDLDRHQLHQMIAAEIGVPLRDVEMMEGRLAGSDFSLNA-VQSADEDGRE 195

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
           W D L  D +   + +    + +  R+ L  +M  LN RER I   R+L+E   TLE+L 
Sbjct: 196 WIDALEDDREQAAESVEHSHDTQQLRDWLVTAMQALNDRERFIVRERKLREPARTLESLG 255

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQ 287
            E  +S+ERVRQ+EA AF K++++++ Q
Sbjct: 256 QELGLSKERVRQLEAAAFTKMRKNLEAQ 283


>gi|208779746|ref|ZP_03247090.1| alternative sigma factor RpoH [Francisella novicida FTG]
 gi|208744201|gb|EDZ90501.1| alternative sigma factor RpoH [Francisella novicida FTG]
          Length = 292

 Score =  202 bits (515), Expect = 3e-50,   Method: Compositional matrix adjust.
 Identities = 105/284 (36%), Positives = 176/284 (61%), Gaps = 7/284 (2%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           K  ++ V  +  LS Y++ +  +P+L  ++E  LA+RY+   DL AA +LV SHLR V K
Sbjct: 11  KTKTLPVVSDNNLSAYLNFVNTLPVLSLEQEQELARRYKYKKDLDAAQQLVLSHLRFVTK 70

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  + GYGL I++++ EGNIGLM+AV KFDP++G RL ++++ WIKA M +Y+L++W +
Sbjct: 71  IARNFSGYGLSIADLIQEGNIGLMKAVSKFDPDQGVRLVSFAVHWIKAEMHDYVLKNWKI 130

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-G 182
           VK+ TT  Q++LFFNLR +K  +  ++  ++K      +A++L V E  VI M  R+  G
Sbjct: 131 VKVATTKAQRKLFFNLRSIKDKIGWLSSEDIKE-----LAEELGVKEETVIEMEKRMCQG 185

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           D SL+      D   +  Q   + D     E  +++++   N + ++   +S  + R + 
Sbjct: 186 DASLDLPYTDDDGEQTSQQSLYLEDKSSNIEHQVVQQDYYDNFKAIVKDVLSGFDTRTKD 245

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           I  +R L +N  TL++L++++ +S ERVRQIE  A  K++++I+
Sbjct: 246 IIMSRYLLDNKATLQDLAAKYNISAERVRQIEEDALAKLKKAIK 289


>gi|114764201|ref|ZP_01443439.1| RNA polymerase sigma factor [Pelagibaca bermudensis HTCC2601]
 gi|114543353|gb|EAU46369.1| RNA polymerase sigma factor [Roseovarius sp. HTCC2601]
          Length = 292

 Score =  202 bits (515), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 106/268 (39%), Positives = 175/268 (65%), Gaps = 6/268 (2%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K  +L+ + E  LA  +R+H D +A HRL+ +++RL + +A  ++ YG P+ +++ E  +
Sbjct: 17  KAELLDAETELQLAYAWRDHRDEAALHRLINAYMRLAISMAAKFKRYGAPMGDLIQEAGL 76

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFN+RR++ 
Sbjct: 77  GLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQA 136

Query: 145 HLQ---AITDNNLKPEQV-VAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQ 199
            L+   A     L+   +  AIAK++ V   +V  M+ RL+G D SLNA   S+D++  +
Sbjct: 137 RLEREAAAEGRALERHSLHAAIAKEVGVPLHDVEMMDGRLSGSDFSLNA-TQSTDEDGRE 195

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
           W D L  D +    ++  K +    R  L  +++ LN RER I   R+L++   TLE+L 
Sbjct: 196 WIDTLEDDGEQSASLVEGKLDNDQLREWLVVALTGLNDRERFIVRERKLRDETRTLESLG 255

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQ 287
            E  +S+ERVRQ+EA AF K+++S++ Q
Sbjct: 256 QELGLSKERVRQLEAAAFVKMRKSLEAQ 283


>gi|91794849|ref|YP_564500.1| RNA polymerase factor sigma-32 [Shewanella denitrificans OS217]
 gi|91716851|gb|ABE56777.1| RNA polymerase sigma factor RpoH [Shewanella denitrificans OS217]
          Length = 284

 Score =  202 bits (515), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 106/284 (37%), Positives = 171/284 (60%), Gaps = 7/284 (2%)

Query: 4   KNMSIIV-NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           ++MS+ V  G   L  YI  +  I ML  ++E  LAKR +E GDL AA +L+ SHLR VV
Sbjct: 6   QSMSLTVPRGSSSLEAYIQSVTSINMLGAEDEQALAKRLQETGDLQAAKQLIMSHLRFVV 65

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A GY GYGLP ++++ EGNIGLM+AVK+FDP+ G RL ++++ WIKA + EY+L++W 
Sbjct: 66  HVAKGYAGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYVLKNWR 125

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFN+R+ K  L   +D      +V  +A+ L VS+++V  M  R+A 
Sbjct: 126 IVKVATTKAQRKLFFNIRKSKKRLGWFSD-----AEVTMVAENLGVSKADVTEMESRMAA 180

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERR 241
            +    + + +D  +       + DH       +E      N ++ L  ++  L+ R + 
Sbjct: 181 QDPAFDIASDNDDETDFSPVHYLEDHSSDVAQQVENANWESNSQSRLFSAIKTLDERSQH 240

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           I +AR L ++  TL+ L+  ++VS ER+RQ+E  A  K++  ++
Sbjct: 241 ILQARWLDDDKTTLQELAETYQVSAERIRQLEKNAMNKLKACME 284


>gi|260574108|ref|ZP_05842113.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacter sp. SW2]
 gi|259023574|gb|EEW26865.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacter sp. SW2]
          Length = 292

 Score =  202 bits (515), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 108/277 (38%), Positives = 177/277 (63%), Gaps = 6/277 (2%)

Query: 17  SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
           +R   +  K  +L+ + E  LA  +R+  D +A HRL+T+++RL + +A  +R YG P++
Sbjct: 9   ARLSRQAMKAELLDAETELRLAYAWRDQRDEAALHRLITAYMRLAISMAAKFRRYGAPMN 68

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++ E ++GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LF
Sbjct: 69  DLIQEASLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLF 128

Query: 137 FNLRRLKGHLQ---AITDNNLKPEQV-VAIAKKLNVSESEVISMNCRLAG-DESLNALIN 191
           FNL+R++  L+   A    +L   Q+   +A+++ V  ++V  M  RLAG D SLNA   
Sbjct: 129 FNLKRVQAKLEREAAQRGESLDGHQLREMVAREVGVPLADVEMMEGRLAGSDFSLNA-TQ 187

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           SS+    +W D L  D     + +    +    R  L  +M+ LNPRER I   R+L+ +
Sbjct: 188 SSEDEGREWIDALEDDGVQAAEAVEGAHDAARLRGWLVVAMAALNPRERFIVTERKLRGD 247

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
             TLE+L +E  +S+ERVRQ+EA AF K++ S++ Q 
Sbjct: 248 GRTLESLGAELGLSKERVRQLEAAAFAKLRRSLEGQT 284


>gi|89256211|ref|YP_513573.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           holarctica LVS]
 gi|115314678|ref|YP_763401.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           holarctica OSU18]
 gi|156502270|ref|YP_001428335.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           holarctica FTNF002-00]
 gi|167009752|ref|ZP_02274683.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           holarctica FSC200]
 gi|254367537|ref|ZP_04983563.1| RNA polymerase sigma-32 factor [Francisella tularensis subsp.
           holarctica 257]
 gi|290952961|ref|ZP_06557582.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           holarctica URFT1]
 gi|295313833|ref|ZP_06804405.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           holarctica URFT1]
 gi|89144042|emb|CAJ79290.1| RNA polymerase sigma-32 factor [Francisella tularensis subsp.
           holarctica LVS]
 gi|115129577|gb|ABI82764.1| DNA-directed RNA polymerase [Francisella tularensis subsp.
           holarctica OSU18]
 gi|134253353|gb|EBA52447.1| RNA polymerase sigma-32 factor [Francisella tularensis subsp.
           holarctica 257]
 gi|156252873|gb|ABU61379.1| alternative sigma factor RpoH [Francisella tularensis subsp.
           holarctica FTNF002-00]
          Length = 292

 Score =  202 bits (514), Expect = 4e-50,   Method: Compositional matrix adjust.
 Identities = 106/284 (37%), Positives = 175/284 (61%), Gaps = 7/284 (2%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           K  ++ V  +  LS Y++ +  +P+L  ++E  LA+RY+   DL AA +LV SHLR V K
Sbjct: 11  KTKTLPVVSDNNLSAYLNFVNTLPVLSLEQEQELARRYKYKKDLDAAQQLVLSHLRFVTK 70

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  + GYGL I++++ EGNIGLM+AV KFDP++G RL ++++ WIKA M +Y+L++W +
Sbjct: 71  IARNFSGYGLSIADLIQEGNIGLMKAVSKFDPDQGVRLLSFAVHWIKAEMHDYVLKNWKI 130

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-G 182
           VK+ TT  Q++LFFNLR  K  +  ++  N+K      +A++L V E  VI M  R+  G
Sbjct: 131 VKVATTKAQRKLFFNLRSSKDKIGWLSSENIKE-----LAEELGVKEETVIEMEKRMCQG 185

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           D SL+      D   +  Q   + D     E  +++++   N + ++   +S  + R + 
Sbjct: 186 DASLDLSYTDDDGEQTSQQSLYLEDKSSNIEHQVVQQDYYDNFKAIVKDVLSGFDTRTKD 245

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           I  +R L +N  TL++L++++ +S ERVRQIE  A  K++++I+
Sbjct: 246 IIMSRYLLDNKATLQDLAAKYNISAERVRQIEEDALAKLKKAIK 289


>gi|220917075|ref|YP_002492379.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter
           dehalogenans 2CP-1]
 gi|219954929|gb|ACL65313.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter
           dehalogenans 2CP-1]
          Length = 307

 Score =  202 bits (514), Expect = 5e-50,   Method: Compositional matrix adjust.
 Identities = 114/274 (41%), Positives = 167/274 (60%), Gaps = 6/274 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ EI + P+L  ++E  LA++Y    D  AAHRLVT++LR VVK+A  YR YG  +
Sbjct: 13  LEVYLSEINRFPLLTVEDEQRLARQYCADRDTRAAHRLVTANLRFVVKVAYEYRSYGFRM 72

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AV+KFDP++G RL +Y++WWI+A +Q YIL+SWSLVK+GTT  Q++L
Sbjct: 73  ADLIQEGNIGLMKAVQKFDPDKGIRLISYAVWWIRAYIQNYILKSWSLVKLGTTQAQRKL 132

Query: 136 FFNLRRLKGHLQAITDN---NLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALIN 191
           FF+L R K  L   +     +        +AKKL V   EV  M  R+ G D SL+A + 
Sbjct: 133 FFSLARTKRELDKRSQEHGADSDGHDANKVAKKLRVKPGEVREMEQRMEGRDLSLDAPMG 192

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             D       D+L      Q+  L   +E+K     +  ++  L+ RER I E R + + 
Sbjct: 193 --DDGGYSHVDFLPSGTASQDDELSGVQEQKVVSGRVVEALGRLDQRERYIIEMRVMSDR 250

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           P+TL+ L   F  SRER RQ+E RA +K++E ++
Sbjct: 251 PLTLKELGEHFGFSRERARQLEIRAKEKLKEELR 284


>gi|56708190|ref|YP_170086.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           tularensis SCHU S4]
 gi|110670661|ref|YP_667218.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           tularensis FSC198]
 gi|134302102|ref|YP_001122071.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           tularensis WY96-3418]
 gi|187931929|ref|YP_001891914.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           mediasiatica FSC147]
 gi|224457293|ref|ZP_03665766.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|254370677|ref|ZP_04986682.1| RNA polymerase sigma-32 factor [Francisella tularensis subsp.
           tularensis FSC033]
 gi|254875002|ref|ZP_05247712.1| alternative sigma factor rpoH [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|56604682|emb|CAG45745.1| RNA polymerase sigma-32 factor [Francisella tularensis subsp.
           tularensis SCHU S4]
 gi|110320994|emb|CAL09128.1| RNA polymerase sigma-32 factor [Francisella tularensis subsp.
           tularensis FSC198]
 gi|134049879|gb|ABO46950.1| alternative sigma factor RpoH [Francisella tularensis subsp.
           tularensis WY96-3418]
 gi|151568920|gb|EDN34574.1| RNA polymerase sigma-32 factor [Francisella tularensis subsp.
           tularensis FSC033]
 gi|187712838|gb|ACD31135.1| RNA polymerase sigma-32 factor [Francisella tularensis subsp.
           mediasiatica FSC147]
 gi|254841001|gb|EET19437.1| alternative sigma factor rpoH [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|282159406|gb|ADA78797.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           tularensis NE061598]
          Length = 292

 Score =  202 bits (514), Expect = 5e-50,   Method: Compositional matrix adjust.
 Identities = 106/284 (37%), Positives = 175/284 (61%), Gaps = 7/284 (2%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           K  ++ V  +  LS Y++ +  +P+L  ++E  LA+RY+   DL AA +LV SHLR V K
Sbjct: 11  KTKTLPVVSDNNLSAYLNFVNTLPVLSLEQEQELARRYKYKKDLDAAQQLVLSHLRFVTK 70

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  + GYGL I++++ EGNIGLM+AV KFDP++G RL ++++ WIKA M +Y+L++W +
Sbjct: 71  IARNFSGYGLSIADLIQEGNIGLMKAVSKFDPDQGVRLLSFAVHWIKAEMHDYVLKNWKI 130

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-G 182
           VK+ TT  Q++LFFNLR  K  +  ++  N+K      +A++L V E  VI M  R+  G
Sbjct: 131 VKVATTKAQRKLFFNLRSSKDKIGWLSSENIKE-----LAEELGVKEETVIEMEKRMCQG 185

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           D SL+      D   +  Q   + D     E  +++++   N + ++   +S  + R + 
Sbjct: 186 DASLDLPYTDDDGEQTSQQSLYLEDKSSNIEHQVVQQDYYDNFKAIVKDVLSGFDTRTKD 245

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           I  +R L +N  TL++L++++ +S ERVRQIE  A  K++++I+
Sbjct: 246 IIMSRYLLDNKATLQDLAAKYNISAERVRQIEEDALAKLKKAIK 289


>gi|328675965|gb|AEB28640.1| RNA polymerase sigma factor RpoH [Francisella cf. novicida 3523]
          Length = 292

 Score =  202 bits (514), Expect = 5e-50,   Method: Compositional matrix adjust.
 Identities = 106/284 (37%), Positives = 175/284 (61%), Gaps = 7/284 (2%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           K  ++ V  +  LS Y++ +  +P+L  ++E  LA+RY+   DL AA +LV SHLR V K
Sbjct: 11  KTKTLPVVSDNNLSAYLNFVNTLPVLSLEQEQELARRYKYKKDLDAAQQLVLSHLRFVTK 70

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  + GYGL I++++ EGNIGLM+AV KFDPE+G RL ++++ WIKA M +Y+L++W +
Sbjct: 71  IARNFSGYGLSIADLIQEGNIGLMKAVSKFDPEQGVRLVSFAVHWIKAEMHDYVLKNWKI 130

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-G 182
           VK+ TT  Q++LFFNLR  K  +  ++  ++K      +A++L V E  VI M  R+  G
Sbjct: 131 VKVATTKAQRKLFFNLRSSKDKIGWLSSEDIKE-----LAEELGVKEETVIEMEKRMCQG 185

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           D SL+      D   +  Q   + D     E  +++++   N + ++   +S  + R + 
Sbjct: 186 DASLDLPYTDDDGEQTSQQSLYLEDKSSNIEHQVVQQDYYDNFKAIVKDVLSGFDTRTKD 245

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           I  +R L +N  TL++L++++ +S ERVRQIE  A  K++++I+
Sbjct: 246 IIMSRYLLDNKATLQDLAAKYNISAERVRQIEEDALAKLKKAIK 289


>gi|62258694|gb|AAX77814.1| unknown protein [synthetic construct]
          Length = 327

 Score =  202 bits (514), Expect = 5e-50,   Method: Compositional matrix adjust.
 Identities = 106/284 (37%), Positives = 175/284 (61%), Gaps = 7/284 (2%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           K  ++ V  +  LS Y++ +  +P+L  ++E  LA+RY+   DL AA +LV SHLR V K
Sbjct: 37  KTKTLPVVSDNNLSAYLNFVNTLPVLSLEQEQELARRYKYKKDLDAAQQLVLSHLRFVTK 96

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  + GYGL I++++ EGNIGLM+AV KFDP++G RL ++++ WIKA M +Y+L++W +
Sbjct: 97  IARNFSGYGLSIADLIQEGNIGLMKAVSKFDPDQGVRLLSFAVHWIKAEMHDYVLKNWKI 156

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-G 182
           VK+ TT  Q++LFFNLR  K  +  ++  N+K      +A++L V E  VI M  R+  G
Sbjct: 157 VKVATTKAQRKLFFNLRSSKDKIGWLSSENIKE-----LAEELGVKEETVIEMEKRMCQG 211

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           D SL+      D   +  Q   + D     E  +++++   N + ++   +S  + R + 
Sbjct: 212 DASLDLPYTDDDGEQTSQQSLYLEDKSSNIEHQVVQQDYYDNFKAIVKDVLSGFDTRTKD 271

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           I  +R L +N  TL++L++++ +S ERVRQIE  A  K++++I+
Sbjct: 272 IIMSRYLLDNKATLQDLAAKYNISAERVRQIEEDALAKLKKAIK 315


>gi|90412724|ref|ZP_01220725.1| RNA polymerase sigma factor [Photobacterium profundum 3TCK]
 gi|90326299|gb|EAS42718.1| RNA polymerase sigma factor [Photobacterium profundum 3TCK]
          Length = 286

 Score =  202 bits (514), Expect = 5e-50,   Method: Compositional matrix adjust.
 Identities = 111/283 (39%), Positives = 173/283 (61%), Gaps = 10/283 (3%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +M+++  G   L  YI  + + PML  ++E  LA+R    GD+ AA  LV SH+R VV +
Sbjct: 7   SMALVSTG--SLDSYIQTVNRHPMLTVEQEKELAERLHYDGDIEAAKGLVMSHMRFVVHV 64

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A GY GYGLP+++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W +V
Sbjct: 65  ARGYSGYGLPMADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIV 124

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           K+ TT  Q++LFFNLR+ K  L     NN + E V   A++L V+ SEV  M  RLA  +
Sbjct: 125 KVATTKAQRKLFFNLRKSKKRLGWF--NNAEVEMV---AEQLGVNPSEVREMESRLAAQD 179

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNPRERR 241
               L N  D   + +   + +  D    V +  EE     +  N L+ +++ L+ R + 
Sbjct: 180 PAFELPNEDDDRDAGYTAPVYFLEDKASDVALSYEENNWENHTNNRLSNALAGLDERSQH 239

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           I  +R L +   TL++L++ + +S ERVRQ+E  A KK++E++
Sbjct: 240 IVRSRWLDDEKTTLQDLANHYGISAERVRQLEKNAMKKLKEAV 282


>gi|254369205|ref|ZP_04985217.1| DNA-directed RNA polymerase [Francisella tularensis subsp.
           holarctica FSC022]
 gi|157122155|gb|EDO66295.1| DNA-directed RNA polymerase [Francisella tularensis subsp.
           holarctica FSC022]
          Length = 292

 Score =  202 bits (514), Expect = 6e-50,   Method: Compositional matrix adjust.
 Identities = 106/284 (37%), Positives = 175/284 (61%), Gaps = 7/284 (2%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           K  ++ V  +  LS Y++ +  +P+L  ++E  LA+RY+   DL AA +LV SHLR V K
Sbjct: 11  KTKTLPVVSDNNLSAYLNFVNTLPVLSLEQEQELARRYKYKKDLDAAQQLVLSHLRFVTK 70

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  + GYGL I++++ EGNIGLM+AV KFDP++G RL ++++ WIKA M +Y+L++W +
Sbjct: 71  IARNFSGYGLSIADLIQEGNIGLMKAVSKFDPDQGVRLLSFAVHWIKAEMHDYVLKNWKI 130

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-G 182
           VK+ TT  Q++LFFNLR  K  +  ++  N+K      +A++L V E  VI M  R+  G
Sbjct: 131 VKVATTKAQRKLFFNLRSSKDKIGWLSSENIKE-----LAEELGVKEETVIEMEKRMCQG 185

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           D SL+      D   +  Q   + D     E  +++++   N + ++   +S  + R + 
Sbjct: 186 DASLDLPYTDDDGEQTSQQSLYLEDKSSNIEHQVVQQDYYDNFKAIVKDVLSGFDTRTKD 245

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           I  +R L +N  TL++L++++ +S ERVRQIE  A  K++++I+
Sbjct: 246 IIMSRYLLDNKATLQDLAAKYNISAERVRQIEEDALAKLKKAIK 289


>gi|114705882|ref|ZP_01438785.1| RNA polymerase sigma factor [Fulvimarina pelagi HTCC2506]
 gi|114538728|gb|EAU41849.1| RNA polymerase sigma factor [Fulvimarina pelagi HTCC2506]
          Length = 300

 Score =  202 bits (513), Expect = 6e-50,   Method: Compositional matrix adjust.
 Identities = 104/252 (41%), Positives = 169/252 (67%), Gaps = 9/252 (3%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A R++E+ D  A H++ ++H+RLV+ +A  +R +GL +++++ EG++GL++A  +F+PER
Sbjct: 42  AVRWKENRDQEALHKITSAHMRLVISMASKFRHFGLAMNDLIQEGHVGLLEAAARFEPER 101

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL----QAITDNN 153
             R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFFNLRRL+  L    + I+ N 
Sbjct: 102 EVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRARLSQGAEPISGNA 161

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +  E    IA  L VSES+V  M+ RL+G D SLNA +   +  S+  QD+LV D    +
Sbjct: 162 MYRE----IAGALKVSESDVALMDSRLSGPDSSLNAPLLDDESGSADRQDFLVADDPLPD 217

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           + +    + + R   LT ++ VL+ RE +I   RRLQ++  TLE L ++  +S+ERVRQI
Sbjct: 218 ETVSVSIDDERRVTWLTSALDVLSERELKIIRERRLQDDGATLEALGTKLGISKERVRQI 277

Query: 273 EARAFKKVQESI 284
           E RA +K++ ++
Sbjct: 278 ETRALEKLRSAL 289


>gi|326563747|gb|EGE13998.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis 46P47B1]
          Length = 371

 Score =  202 bits (513), Expect = 6e-50,   Method: Compositional matrix adjust.
 Identities = 108/273 (39%), Positives = 162/273 (59%), Gaps = 9/273 (3%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + L  YI+ + +IP+L  +EE  LA+RY   GD+ AA  LV SHLR V+ IA  Y GYGL
Sbjct: 97  VNLGAYINTVHQIPILTPEEERALAERYYHDGDVEAARLLVMSHLRFVIHIARSYSGYGL 156

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
             ++++ EGN+GLM+AVK+FDP +G RL ++++ WIKA + E+++++W +VK+ TT   +
Sbjct: 157 SQADLIQEGNLGLMKAVKRFDPNKGVRLVSFAVHWIKAEIHEFVIKNWRIVKVATTKAHR 216

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINS 192
           +LFFNLR LK      + N L  ++  AIA  LNV+  +V+ M  RL   D S  A    
Sbjct: 217 KLFFNLRSLKK-----SSNQLTLDEATAIANDLNVTVKQVLEMESRLTSYDASFEA--QD 269

Query: 193 SDKNSSQWQDWLVY-DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           SD +  ++   L   D      V+ E +  +N    L  +M +L+ R R I   R L + 
Sbjct: 270 SDDDEGRYAPQLFLEDAVNPADVVEEADWEENTTTALKDAMEILDERSRDIITQRWLADQ 329

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL  L++ + +S ERVRQIE  A  K++E+I
Sbjct: 330 KSTLHELAATYNISAERVRQIEKNAMNKIKEAI 362


>gi|197122293|ref|YP_002134244.1| RNA polymerase, sigma 70 family subunit [Anaeromyxobacter sp. K]
 gi|196172142|gb|ACG73115.1| putative RNA polymerase, sigma 70 family subunit [Anaeromyxobacter
           sp. K]
          Length = 307

 Score =  202 bits (513), Expect = 6e-50,   Method: Compositional matrix adjust.
 Identities = 116/278 (41%), Positives = 169/278 (60%), Gaps = 14/278 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ EI + P+L  ++E  LA++Y    D  AAHRLVT++LR VVK+A  YR YG  +
Sbjct: 13  LEVYLSEINRFPLLTVEDEQRLARQYCADRDTRAAHRLVTANLRFVVKVAYEYRSYGFRM 72

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AV+KFDP++G RL +Y++WWI+A +Q YIL+SWSLVK+GTT  Q++L
Sbjct: 73  ADLIQEGNIGLMKAVQKFDPDKGIRLISYAVWWIRAYIQNYILKSWSLVKLGTTQAQRKL 132

Query: 136 FFNLRRLKGHLQ-------AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN 187
           FF+L R K  L        A +D +        +AKKL V   EV  M  R+ G D SL+
Sbjct: 133 FFSLARTKRELDKRSQEHGADSDGH----DANKVAKKLRVKPGEVREMEQRMEGRDLSLD 188

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           A +   D       D+L      Q+  L   +E+K     +  ++  L+ RER I E R 
Sbjct: 189 APMG--DDGGYSHVDFLPSGTASQDDELSGVQEQKVVSGRVGEALGRLDQRERYIIEMRV 246

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + + P+TL+ L   F  SRER RQ+E RA +K++E ++
Sbjct: 247 MSDRPLTLKELGEHFGFSRERARQLEIRAKEKLKEELR 284


>gi|269961508|ref|ZP_06175871.1| RNA polymerase sigma -32 factor [Vibrio harveyi 1DA3]
 gi|269833737|gb|EEZ87833.1| RNA polymerase sigma -32 factor [Vibrio harveyi 1DA3]
          Length = 285

 Score =  202 bits (513), Expect = 7e-50,   Method: Compositional matrix adjust.
 Identities = 110/272 (40%), Positives = 165/272 (60%), Gaps = 8/272 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  +   PML  +EE  LA+R   +G++ AA  L+ SHLR VV +A GY GYGLP+
Sbjct: 16  LDSYIRSVNSYPMLTPEEERGLAERLHYNGEIDAAKGLILSHLRFVVHVARGYSGYGLPM 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           +++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W +VKI TT  Q++L
Sbjct: 76  ADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR+ K  L    +      +V  +A++L V  SEV  M  RLA  +S   +    D 
Sbjct: 136 FFNLRKSKKRLGWFNNG-----EVETVARELGVEPSEVREMESRLAAVDSTFDMPMDDDD 190

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
           +++ +   +VY  D    V    E      +  N L  +++ L+ R +RI  +R L +  
Sbjct: 191 SANSYTAPMVYLEDKSSDVADNIEAANWETHTNNRLGHALASLDERSQRIVRSRWLDDEK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL++L+ EF VS ER+RQ+E  A KK++ ++
Sbjct: 251 ATLQDLADEFGVSAERIRQLEKNAMKKLKLAV 282


>gi|309378784|emb|CBX22610.1| unnamed protein product [Neisseria lactamica Y92-1009]
          Length = 287

 Score =  202 bits (513), Expect = 7e-50,   Method: Compositional matrix adjust.
 Identities = 119/290 (41%), Positives = 185/290 (63%), Gaps = 9/290 (3%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N   +  I +G   L +YI  +  IPML ++EE  LA+R R  GDL+AA +L+ SHLR+V
Sbjct: 3   NTFALPAIQSGNGSLEQYIRTVNSIPMLSQEEETRLAER-RIKGDLNAAKQLILSHLRVV 61

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+IL++W
Sbjct: 62  VSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILKNW 121

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            LV++ TT  Q++LFFNLR ++ +L     N L P++  +IA  L V  SEV+ M  R+ 
Sbjct: 122 RLVRVATTKPQRKLFFNLRSMRKNL-----NALSPKEAQSIADDLGVKLSEVLEMEQRMT 176

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRER 240
           G +      N+ D ++    DWL  DHD +    + K+     +   L  +++ L+ R R
Sbjct: 177 GRDIAIMADNNDDDDNFAPIDWLA-DHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSR 235

Query: 241 RIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           RI E+R LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 236 RIVESRWLQDDGGLTLHQLAAEYGVSAERIRQIEAKAMQKLRGFLTEEAE 285


>gi|332529979|ref|ZP_08405929.1| RNA polymerase sigma-32 subunit RpoH [Hylemonella gracilis ATCC
           19624]
 gi|332040452|gb|EGI76828.1| RNA polymerase sigma-32 subunit RpoH [Hylemonella gracilis ATCC
           19624]
          Length = 326

 Score =  202 bits (513), Expect = 7e-50,   Method: Compositional matrix adjust.
 Identities = 113/290 (38%), Positives = 169/290 (58%), Gaps = 21/290 (7%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + ++PML  +EE   A+++R++ DL AA +LV SHLRLVV  A  Y GYGLP 
Sbjct: 33  LDAYITAVNRMPMLTAEEEQEFARKFRDNNDLEAAGKLVLSHLRLVVATARQYMGYGLPH 92

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM+AVK+FDP++G RL +Y++ WIKA + EYIL++W +VK+ TT  Q++L
Sbjct: 93  GDLIQEGNVGLMKAVKRFDPDQGVRLVSYALHWIKAEIHEYILKNWRMVKVATTKAQRKL 152

Query: 136 FFNLR--------------RLKGHLQAITD-NNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           FFNLR               L   L A T    L   ++  +A++LNV   EVI M  RL
Sbjct: 153 FFNLRSKKQGYKAASAADSSLHDGLDAATHRETLSEHEIDQMARELNVKREEVIEMETRL 212

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRE 239
           +G + +       D   S      + D   +   +IE  +R     + + +++  L+PR 
Sbjct: 213 SGGDVMLDPGPGEDGEDSFGPIAYLTDAGHEPTAMIEARQRDRLATDGIAKALDALDPRS 272

Query: 240 RRIFEARRLQENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           RRI E R L+ N      +TL  L++E+ VS ER+RQIE  A KK++ ++
Sbjct: 273 RRIVEERWLKVNDDASGGMTLHELAAEYGVSAERIRQIEVAAMKKMKTAL 322


>gi|261400394|ref|ZP_05986519.1| alternative sigma factor RpoH [Neisseria lactamica ATCC 23970]
 gi|313668808|ref|YP_004049092.1| RNA polymerase sigma-32 factor [Neisseria lactamica ST-640]
 gi|269209833|gb|EEZ76288.1| alternative sigma factor RpoH [Neisseria lactamica ATCC 23970]
 gi|313006270|emb|CBN87733.1| putative RNA polymerase sigma-32 factor [Neisseria lactamica
           020-06]
          Length = 290

 Score =  202 bits (513), Expect = 7e-50,   Method: Compositional matrix adjust.
 Identities = 119/290 (41%), Positives = 185/290 (63%), Gaps = 9/290 (3%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N   +  I +G   L +YI  +  IPML ++EE  LA+R R  GDL+AA +L+ SHLR+V
Sbjct: 6   NAFALPAIQSGNGSLEQYIRTVNSIPMLSQEEETRLAER-RIKGDLNAAKQLILSHLRVV 64

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+IL++W
Sbjct: 65  VSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILKNW 124

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            LV++ TT  Q++LFFNLR ++ +L     N L P++  +IA  L V  SEV+ M  R+ 
Sbjct: 125 RLVRVATTKPQRKLFFNLRSMRKNL-----NALSPKEAQSIADDLGVKLSEVLEMEQRMT 179

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRER 240
           G +      N+ D ++    DWL  DHD +    + K+     +   L  +++ L+ R R
Sbjct: 180 GRDIAIMADNNDDDDNFAPIDWLA-DHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSR 238

Query: 241 RIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           RI E+R LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 239 RIVESRWLQDDGGLTLHQLAAEYGVSAERIRQIEAKAMQKLRGFLTEEAE 288


>gi|58699726|ref|ZP_00374383.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Drosophila
           ananassae]
 gi|58533758|gb|EAL58100.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Drosophila
           ananassae]
          Length = 216

 Score =  201 bits (512), Expect = 8e-50,   Method: Compositional matrix adjust.
 Identities = 98/208 (47%), Positives = 148/208 (71%), Gaps = 2/208 (0%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           ++ V+    L +YI  ++K PML ++EE  LAK + ++ D+S+AH+L+TSHL LVVKIAM
Sbjct: 3   NLCVDSRTNLMQYIARVQKFPMLSQEEEVRLAKNWNQYKDVSSAHKLITSHLNLVVKIAM 62

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            ++ YGL + ++V EGN+GLM AVKKF+P+ GFR +TY++WWI+A+++++IL+SWS VKI
Sbjct: 63  KFKNYGLLLMDLVMEGNMGLMHAVKKFNPDLGFRFSTYAVWWIEASIKDFILKSWSFVKI 122

Query: 127 GTTANQKRLFFNLRRLKGH-LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DE 184
           GTT  Q+RLFF+LR++K   LQ      L  E++ AI+ +L+VSE +V+ MN R+A  D+
Sbjct: 123 GTTQAQRRLFFSLRKIKKRILQYTNRETLNNEEIKAISNELSVSEGDVLQMNYRMACKDQ 182

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQE 212
           SLN  I   D +  + QD +  +   QE
Sbjct: 183 SLNDCIKIGDDSKRELQDMIPCNLVSQE 210


>gi|292492240|ref|YP_003527679.1| RNA polymerase sigma factor RpoH [Nitrosococcus halophilus Nc4]
 gi|291580835|gb|ADE15292.1| RNA polymerase sigma factor RpoH [Nitrosococcus halophilus Nc4]
          Length = 287

 Score =  201 bits (512), Expect = 8e-50,   Method: Compositional matrix adjust.
 Identities = 115/285 (40%), Positives = 174/285 (61%), Gaps = 14/285 (4%)

Query: 3   RKNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           R +   +V   +G L  Y   +  IP+L   +E+ LA R R+H DL AA +LV SHLR V
Sbjct: 6   RNSNGFLVPVAVGDLDTYCQTVHSIPILSADQEHNLALRLRDHHDLDAARQLVLSHLRFV 65

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V+IA GY GYGLP+++++ EGNIGLM+AVK+FDPE+G RL ++++ WI+A + E+ILR+W
Sbjct: 66  VRIARGYSGYGLPLADLIQEGNIGLMKAVKRFDPEQGVRLVSFAVHWIRAEIHEFILRNW 125

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            +VK+ TT  Q++LFFNLR  K  L       L  ++V  +A+ L VS  +V+ M  RL+
Sbjct: 126 RIVKVATTKAQRKLFFNLRSAKKRL-----GWLNRKEVDEVARDLGVSPKQVLEMEARLS 180

Query: 182 GD----ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLN 236
                 E  NA  NS D   +      ++D        +E+ +++N     L +++  L+
Sbjct: 181 SQDTPFEGPNAE-NSEDDIPAPIA--YLFDPTTDPARQMERLDQENHYGQRLQQALEALD 237

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           PR R I   R LQE+  TL  L++E+++S ER+RQ+E  A KK++
Sbjct: 238 PRSRAIIHRRWLQESKSTLHELAAEYQISAERIRQLENNAIKKLR 282


>gi|319409355|emb|CBI82999.1| RNA polymerase sigma-32 factor [Bartonella schoenbuchensis R1]
          Length = 303

 Score =  201 bits (511), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 110/262 (41%), Positives = 173/262 (66%), Gaps = 7/262 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LEK++E+ LA R+++  D  A H++  +H+RLV+ IA  ++ + +P+S++V EG +GL
Sbjct: 34  PYLEKKKEHDLALRWKDKRDDKAMHQIAAAHMRLVISIASRFKRFKMPLSDLVQEGYVGL 93

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +F+P+R  R +TY+ WWI+A++Q+YILR+WS+V+ GT+++QK LFFNLRRL+  L
Sbjct: 94  LEAAARFEPDRDVRFSTYATWWIRASIQDYILRNWSIVRGGTSSSQKALFFNLRRLRAQL 153

Query: 147 QAITDNNLKPEQVV--AIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDW 203
             + D++   +Q +   I++KL VS S+V +M+ R +G D SL+  ++ +D NS    D 
Sbjct: 154 --VQDDSTMSKQDIFRVISEKLGVSVSDVETMDFRFSGTDNSLSMSVSENDDNSVTKLDT 211

Query: 204 LVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
           LV D       LIEK     RR   L  ++ +LN RE  I   RRL E   TLE L  + 
Sbjct: 212 LV-DEKPLPDSLIEKVIDGQRRTQWLYDALQILNERELEIIRFRRLNEESATLEFLGEKL 270

Query: 263 EVSRERVRQIEARAFKKVQESI 284
            +S+ERVRQIEARA +K++ ++
Sbjct: 271 GISKERVRQIEARALQKLRCAL 292


>gi|124268355|ref|YP_001022359.1| RNA polymerase sigma-32 factor [Methylibium petroleiphilum PM1]
 gi|124261130|gb|ABM96124.1| RNA polymerase sigma-32 factor [Methylibium petroleiphilum PM1]
          Length = 319

 Score =  201 bits (511), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 114/281 (40%), Positives = 173/281 (61%), Gaps = 13/281 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ YI  + ++PML  +EE  L +R R+  DL AA RLV SHLRLVV ++  Y GYGLP 
Sbjct: 36  LNAYIAAVNRLPMLTLEEEQSLGQRLRDEHDLEAAGRLVLSHLRLVVSVSRQYLGYGLPH 95

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM+AVK+FDP +G RL +Y++ WIKA + EY+LR+W +VK+ TT  Q++L
Sbjct: 96  GDLIQEGNVGLMKAVKRFDPSQGVRLVSYALHWIKAEIHEYVLRNWRMVKLATTKAQRKL 155

Query: 136 FFNLRRLK-GHLQAITDNN-----LKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNA 188
           FFNLR +K G     TD++     L   ++  +A +L V   EVI M  RL+ GD +L+ 
Sbjct: 156 FFNLRSMKQGFKGDATDSDLHRSTLTDAEIDIVASELKVKREEVIEMETRLSGGDVALDP 215

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
             +  D++ +    +L  D     +VL  +       + +  ++ VL+ R RRI E R L
Sbjct: 216 QTDDGDESYAPIA-YLADDRHEPTRVLDAQRRDALAGDGIGEALDVLDARSRRIVEERWL 274

Query: 249 QENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + N      +TL  L++E+ VS ER+RQIE  A KK+++++
Sbjct: 275 KVNDNGSGGMTLHELAAEYGVSAERIRQIEVAAMKKMRKAL 315


>gi|150398305|ref|YP_001328772.1| RNA polymerase factor sigma-32 [Sinorhizobium medicae WSM419]
 gi|150029820|gb|ABR61937.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium medicae
           WSM419]
          Length = 288

 Score =  201 bits (511), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 112/272 (41%), Positives = 169/272 (62%), Gaps = 9/272 (3%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           R I    + P LE+ EE+ LA+ +R   D  A +++  SH+RLV+ +A  +R +GLP+ +
Sbjct: 9   RMIKIAMEAPYLERDEEHALAEAWRNDNDQEARNKIAMSHMRLVISMAAKFRSFGLPMGD 68

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +V EG+IGL++A  +F+P R  R +TY+ WWI+A+MQ+Y+LR+WS+V+ GT++ QK LFF
Sbjct: 69  LVQEGHIGLLEAAARFEPSREVRFSTYATWWIRASMQDYVLRNWSIVRGGTSSAQKALFF 128

Query: 138 NLRRLKGHLQAITDNNLKPEQV-VAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDK 195
           NLRRL+  L A  D  L  + V   IA  + VS ++V +M+ RL+G D SL A I   D 
Sbjct: 129 NLRRLRARL-AQGDRQLTSQAVHEEIAAAIGVSLADVQTMDARLSGNDASLQAPIGGGDP 187

Query: 196 NSSQWQDWLVYDH---DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
           ++    D+L  +    D Q   LI+ E     R  L  ++  L+ RE +I  ARRL E+ 
Sbjct: 188 DAGARLDFLASEAPLPDEQVSDLIDGE---RARRWLHVALGELSEREMKIIRARRLSEDG 244

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TLE L     +S+ERVRQIE RA +K++ ++
Sbjct: 245 ATLEELGVALGISKERVRQIETRALEKLRAAL 276


>gi|260431476|ref|ZP_05785447.1| RNA polymerase sigma-32 factor [Silicibacter lacuscaerulensis
           ITI-1157]
 gi|260415304|gb|EEX08563.1| RNA polymerase sigma-32 factor [Silicibacter lacuscaerulensis
           ITI-1157]
          Length = 292

 Score =  201 bits (511), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 107/268 (39%), Positives = 175/268 (65%), Gaps = 6/268 (2%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K  +L+ + E  LA  +R+  D  A HRL+T+++RL + +A  ++ YG P+++++ E  +
Sbjct: 17  KAELLDAETELRLAYAWRDERDEQALHRLITAYMRLAISMAAKFKRYGAPMNDLIQEAGL 76

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFN+RR++ 
Sbjct: 77  GLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQA 136

Query: 145 HL--QAITDN-NLKPEQV-VAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQ 199
            L  +A +D   L   Q+   IA ++ V   +V  M+ RLAG D SLNA + S+D++  +
Sbjct: 137 RLEREAASDGVELDRHQLHQMIAAEIGVPLRDVEMMHGRLAGSDFSLNA-VQSADEDGRE 195

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
           W D L  D     +++    + +  R  L  +M  LN RER I   R+L++   TLE+L 
Sbjct: 196 WIDALEDDSAQAAELVEHGHDTRQLREWLITAMQALNERERFIVRERKLRDPARTLESLG 255

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQ 287
            E  +S+ERVRQ+EA AF K+++S++ Q
Sbjct: 256 QELGLSKERVRQLEAAAFAKMRKSLEGQ 283


>gi|118497682|ref|YP_898732.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           novicida U112]
 gi|194323654|ref|ZP_03057430.1| alternative sigma factor RpoH [Francisella tularensis subsp.
           novicida FTE]
 gi|254373048|ref|ZP_04988537.1| RNA polymerase sigma-32 factor [Francisella tularensis subsp.
           novicida GA99-3549]
 gi|254374500|ref|ZP_04989981.1| RNA polymerase sigma-32 factor [Francisella novicida GA99-3548]
 gi|118423588|gb|ABK89978.1| RNA polymerase sigma-32 factor [Francisella novicida U112]
 gi|151570775|gb|EDN36429.1| RNA polymerase sigma-32 factor [Francisella novicida GA99-3549]
 gi|151572219|gb|EDN37873.1| RNA polymerase sigma-32 factor [Francisella novicida GA99-3548]
 gi|194322018|gb|EDX19500.1| alternative sigma factor RpoH [Francisella tularensis subsp.
           novicida FTE]
 gi|332678395|gb|AEE87524.1| RNA polymerase sigma factor RpoH [Francisella cf. novicida Fx1]
          Length = 292

 Score =  201 bits (511), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 105/284 (36%), Positives = 175/284 (61%), Gaps = 7/284 (2%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           K  ++ V  +  LS Y++ +  +P+L  ++E  LA+RY+   DL AA +LV SHLR V K
Sbjct: 11  KTKTLPVVSDNNLSAYLNFVNTLPVLSLEQEQELARRYKYKKDLDAAQQLVLSHLRFVTK 70

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  + GYGL I++++ EGNIGLM+AV KFDP++G RL ++++ WIKA M +Y+L++W +
Sbjct: 71  IARNFSGYGLSIADLIQEGNIGLMKAVSKFDPDQGVRLVSFAVHWIKAEMHDYVLKNWKI 130

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-G 182
           VK+ TT  Q++LFFNLR  K  +  ++  ++K      +A++L V E  VI M  R+  G
Sbjct: 131 VKVATTKAQRKLFFNLRSSKDKIGWLSSEDIKE-----LAEELGVKEETVIEMEKRMCQG 185

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           D SL+      D   +  Q   + D     E  +++++   N + ++   +S  + R + 
Sbjct: 186 DASLDLPYTDDDGEQTSQQSLYLEDKSSNIEHQVVQQDYYDNFKAIVKDVLSGFDTRTKD 245

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           I  +R L +N  TL++L++++ +S ERVRQIE  A  K++++I+
Sbjct: 246 IIMSRYLLDNKATLQDLAAKYNISAERVRQIEEDALAKLKKAIK 289


>gi|198284457|ref|YP_002220778.1| RNA polymerase sigma-32 subunit RpoH [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218667652|ref|YP_002427124.1| RNA polymerase sigma-32 factor [Acidithiobacillus ferrooxidans ATCC
           23270]
 gi|198248978|gb|ACH84571.1| RNA polymerase, sigma 32 subunit, RpoH [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218519865|gb|ACK80451.1| RNA polymerase sigma-32 factor [Acidithiobacillus ferrooxidans ATCC
           23270]
          Length = 286

 Score =  201 bits (511), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 109/272 (40%), Positives = 173/272 (63%), Gaps = 10/272 (3%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           GL+ Y+  +   P+L  +EE  LA+R R+HGD+ AA  LV SHLR VV++A GYRGYGL 
Sbjct: 16  GLAGYLRFVNAQPLLRPEEERDLARRLRDHGDVDAAKDLVLSHLRFVVRVARGYRGYGLQ 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGNIGLM+AVK++DP+ G RL ++++ W+KA + E+ILR+W +VK+ TT  Q++
Sbjct: 76  EADLIQEGNIGLMKAVKRYDPDHGVRLVSFAVHWVKAEIHEFILRNWRIVKVATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSS 193
           LFFNLR  + H   ++      E+  A+A  L V++++V+ M  R++G D SLN L    
Sbjct: 136 LFFNLRSSRSHTGWMSG-----EESAAMADDLGVTQAQVLEMEGRMSGYDYSLN-LEPDE 189

Query: 194 DKNSSQWQDWLVYDHDGQE-QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
           ++   +  D  + D  G   + L+E++  + +   L  ++S L  R+R I E R L ++P
Sbjct: 190 EREGGRAPD--LADPTGSPIEQLVERDWDQQQHRALHTALSALPQRDRYIIENRWLSDDP 247

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL+ L  E  VS ERVRQ+E  +  K+++ +
Sbjct: 248 KTLQVLGDELGVSAERVRQLEKSSMGKLRQQM 279


>gi|222112015|ref|YP_002554279.1| RNA polymerase sigma-32 subunit RpoH [Acidovorax ebreus TPSY]
 gi|221731459|gb|ACM34279.1| RNA polymerase, sigma 32 subunit, RpoH [Acidovorax ebreus TPSY]
          Length = 311

 Score =  201 bits (511), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 111/281 (39%), Positives = 170/281 (60%), Gaps = 12/281 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + +IP+L ++EE   A++ ++  ++ AA RLV SHLRLVV I+  Y GYGLP 
Sbjct: 27  LDAYISAVNRIPLLTQEEEQRYARQLKDDNNVEAAGRLVLSHLRLVVSISRQYLGYGLPH 86

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM+AVK+FDP++G RL +Y+M WIKA + EYIL++W +VK+ TT  Q++L
Sbjct: 87  GDLIQEGNVGLMKAVKRFDPDQGVRLVSYAMHWIKAEIHEYILKNWRMVKVATTKAQRKL 146

Query: 136 FFNLRRLKGHLQAITDN------NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
           FFNLR +K   +A   +       L   ++  +A++LNV   EVI M  RL+G + L   
Sbjct: 147 FFNLRSMKQGFKADALDADTHRETLSDHEIDLVAEQLNVKREEVIEMETRLSGGDVLLDP 206

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFEARRL 248
             S D   +      + D   +   +IE  +R     + +  ++  L+ R RRI E R L
Sbjct: 207 APSDDGEQAFGPIAYLADAGHEPTAMIESRQRDALATDGIATALDSLDARSRRIVEQRWL 266

Query: 249 QENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           Q N      +TL  L++E+ VS ER+RQIE  A KK+++++
Sbjct: 267 QVNDDGSGGMTLHELAAEYGVSAERIRQIEVAAMKKMKKAL 307


>gi|326571483|gb|EGE21498.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis BC7]
          Length = 371

 Score =  201 bits (510), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 108/273 (39%), Positives = 161/273 (58%), Gaps = 9/273 (3%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + L  YI+ + +IP+L  +EE  LA+RY   GD+ AA  LV SHLR V+ IA  Y GYGL
Sbjct: 97  VNLGAYINTVHQIPILTPEEERALAERYYHDGDVEAARLLVMSHLRFVIHIARSYSGYGL 156

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
             ++++ EGN+GLM+AVK+FDP +G RL ++++ WIKA + E+++++W +VK+ TT   +
Sbjct: 157 SQADLIQEGNLGLMKAVKRFDPNKGVRLVSFAVHWIKAEIHEFVIKNWRIVKVATTKAHR 216

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINS 192
           +LFFNLR LK      + N L  ++  AIA  LNV+  +V+ M  RL   D S  A    
Sbjct: 217 KLFFNLRSLKK-----SSNQLTLDEATAIANDLNVTVKQVLEMESRLTSYDASFEA--QD 269

Query: 193 SDKNSSQWQDWLVY-DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           SD +  ++   L   D      V+ E +  +N    L  +M  L+ R R I   R L + 
Sbjct: 270 SDDDEGRYAPQLFLEDAVNPADVVEEADWEENTTTALKDAMETLDERSRDIITQRWLADQ 329

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL  L++ + +S ERVRQIE  A  K++E+I
Sbjct: 330 KSTLHELAATYNISAERVRQIEKNAMNKIKEAI 362


>gi|77464172|ref|YP_353676.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides 2.4.1]
 gi|126463015|ref|YP_001044129.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides ATCC 17029]
 gi|221640041|ref|YP_002526303.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides KD131]
 gi|332559048|ref|ZP_08413370.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides WS8N]
 gi|77388590|gb|ABA79775.1| sigma factor RpoH2 (Sigma-32 group [Rhodobacter sphaeroides 2.4.1]
 gi|126104679|gb|ABN77357.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacter sphaeroides
           ATCC 17029]
 gi|221160822|gb|ACM01802.1| RNA polymerase, sigma 32 subunit, RpoH precursor [Rhodobacter
           sphaeroides KD131]
 gi|332276760|gb|EGJ22075.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides WS8N]
          Length = 292

 Score =  201 bits (510), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 108/272 (39%), Positives = 171/272 (62%), Gaps = 14/272 (5%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           +  +L+ + E  LA  +R+  D  A HRL+T+++RL + +A  YR YG P+++++ E ++
Sbjct: 17  RAELLDAETELRLAYAWRDQRDERALHRLITAYMRLAISMASKYRRYGAPMNDLIQEASL 76

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WSLV+ G+T++QK LFFN+RR++ 
Sbjct: 77  GLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSLVRTGSTSSQKALFFNMRRVQA 136

Query: 145 HL--------QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDK 195
            L        +A+  + L+      +A  + V  S+V  M  RL+G D SLNA   S+D 
Sbjct: 137 RLEREASQRGEALDAHQLRE----MVAHDVGVPLSDVEMMEGRLSGSDFSLNA-TQSADD 191

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
              +W D L  D     +V+    +    R  L  +M  LN RER I   R+L++ P TL
Sbjct: 192 EGREWIDALEDDSAQAAEVVEGSLDAARLRGWLVSAMQQLNARERFIVTERKLRDVPRTL 251

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+L  E ++S+ERVRQ+EA AF K++ S++ Q
Sbjct: 252 ESLGEELKLSKERVRQLEAAAFAKMRRSLEAQ 283


>gi|296112758|ref|YP_003626696.1| RNA polymerase sigma factor 32 [Moraxella catarrhalis RH4]
 gi|295920452|gb|ADG60803.1| RNA polymerase sigma factor 32 [Moraxella catarrhalis RH4]
 gi|326561004|gb|EGE11369.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis 7169]
 gi|326566767|gb|EGE16906.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis 103P14B1]
 gi|326567391|gb|EGE17506.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis BC1]
 gi|326575234|gb|EGE25162.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis CO72]
 gi|326576679|gb|EGE26586.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis 101P30B1]
 gi|326577646|gb|EGE27523.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis O35E]
          Length = 371

 Score =  201 bits (510), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 108/273 (39%), Positives = 161/273 (58%), Gaps = 9/273 (3%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + L  YI+ + +IP+L  +EE  LA+RY   GD+ AA  LV SHLR V+ IA  Y GYGL
Sbjct: 97  VNLGAYINTVHQIPILTPEEERALAERYYHDGDVEAARLLVMSHLRFVIHIARSYSGYGL 156

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
             ++++ EGN+GLM+AVK+FDP +G RL ++++ WIKA + E+++++W +VK+ TT   +
Sbjct: 157 SQADLIQEGNLGLMKAVKRFDPNKGVRLVSFAVHWIKAEIHEFVIKNWRIVKVATTKAHR 216

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINS 192
           +LFFNLR LK      + N L  ++  AIA  LNV+  +V+ M  RL   D S  A    
Sbjct: 217 KLFFNLRSLKK-----SSNQLTLDEATAIANDLNVTVKQVLEMESRLTSYDASFEA--QD 269

Query: 193 SDKNSSQWQDWLVY-DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           SD +  ++   L   D      V+ E +  +N    L  +M  L+ R R I   R L + 
Sbjct: 270 SDDDEGRYAPQLFLEDAVNPADVVEEADWEENTTTALKDAMETLDERSRDIITQRWLADQ 329

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL  L++ + +S ERVRQIE  A  K++E+I
Sbjct: 330 KSTLHELAATYNISAERVRQIEKNAMNKIKEAI 362


>gi|121595815|ref|YP_987711.1| RNA polymerase sigma-32 subunit RpoH [Acidovorax sp. JS42]
 gi|120607895|gb|ABM43635.1| RNA polymerase, sigma 32 subunit, RpoH [Acidovorax sp. JS42]
          Length = 321

 Score =  201 bits (510), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 111/281 (39%), Positives = 170/281 (60%), Gaps = 12/281 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + ++P+L ++EE   A++ ++  ++ AA RLV SHLRLVV I+  Y GYGLP 
Sbjct: 37  LDAYISAVNRLPLLTQEEEQRYARQLKDDNNVEAAGRLVLSHLRLVVSISRQYLGYGLPH 96

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM+AVK+FDP++G RL +Y+M WIKA + EYIL++W +VK+ TT  Q++L
Sbjct: 97  GDLIQEGNVGLMKAVKRFDPDQGVRLVSYAMHWIKAEIHEYILKNWRMVKVATTKAQRKL 156

Query: 136 FFNLRRLKGHLQAITDN------NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
           FFNLR +K   +A   +       L   ++  +A++LNV   EVI M  RL+G + L   
Sbjct: 157 FFNLRSMKQGFKADALDADTHRETLSDHEIDLVAEQLNVKREEVIEMETRLSGGDVLLDP 216

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFEARRL 248
             S D   +      + D   +   LIE  +R     + +  ++  L+ R RRI E R L
Sbjct: 217 APSDDGEQAFGPIAYLADAGHEPTALIESRQRDALATDGIATALDSLDARSRRIVEQRWL 276

Query: 249 QENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           Q N      +TL  L++E+ VS ER+RQIE  A KK+++++
Sbjct: 277 QVNDDGSGGMTLHELATEYGVSAERIRQIEVAAMKKMKKAL 317


>gi|319899398|ref|YP_004159495.1| RNA polymerase sigma-32 factor [Bartonella clarridgeiae 73]
 gi|319403366|emb|CBI76925.1| RNA polymerase sigma-32 factor [Bartonella clarridgeiae 73]
          Length = 303

 Score =  201 bits (510), Expect = 1e-49,   Method: Compositional matrix adjust.
 Identities = 105/260 (40%), Positives = 172/260 (66%), Gaps = 3/260 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE+++E+ LA R+++  D +A H++  +H+RLV+ IA  ++ + +P+ ++V EG +GL
Sbjct: 34  PYLERKKEHDLALRWKDKRDDNAMHQIAAAHMRLVISIASRFKRFKMPLGDLVQEGYVGL 93

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +FDP+R  R +TY+ WWI+A++Q+YILR+WS+V+ GT+++QK LFFNLRRL+  L
Sbjct: 94  LEAAARFDPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSSQKALFFNLRRLRAKL 153

Query: 147 QAITDNNLKPEQVV-AIAKKLNVSESEVISMNCRL-AGDESLNALINSSDKNSSQWQDWL 204
            A  D+ L  +++   I++KL VS S+V  M+ R  A D SL+  ++ + +N     D L
Sbjct: 154 -AQDDSTLTKQEIFRTISEKLGVSVSDVEKMDFRFSAADNSLSLSVSENGENPIAKMDSL 212

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           V DH   + V+ +  + + R   L  ++ +LN RE  I   RRL E   TLE L  +  +
Sbjct: 213 VDDHPLPDAVIEQAIDGQRRTKWLYEALKILNERELEIIRFRRLNEEGATLEVLGQKLGI 272

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ERVRQIEARA +K++ ++
Sbjct: 273 SKERVRQIEARALQKLRCAL 292


>gi|326564381|gb|EGE14609.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis 12P80B1]
          Length = 371

 Score =  201 bits (510), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 108/273 (39%), Positives = 161/273 (58%), Gaps = 9/273 (3%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + L  YI+ + +IP+L  +EE  LA+RY   GD+ AA  LV SHLR V+ IA  Y GYGL
Sbjct: 97  VNLGAYINTVHQIPILTPEEERALAERYYHDGDVEAARLLVMSHLRFVIHIARSYSGYGL 156

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
             ++++ EGN+GLM+AVK+FDP +G RL ++++ WIKA + E+++++W +VK+ TT   +
Sbjct: 157 SQADLIQEGNLGLMKAVKRFDPNKGVRLVSFAVHWIKAEIHEFVIKNWRIVKVATTKAHR 216

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINS 192
           +LFFNLR LK      + N L  ++  AIA  LNV+  +V+ M  RL   D S  A    
Sbjct: 217 KLFFNLRSLKK-----SSNQLTLDEATAIANDLNVTVKQVLEMESRLTSYDASFEA--QD 269

Query: 193 SDKNSSQWQDWLVY-DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           SD +  ++   L   D      V+ E +  +N    L  +M  L+ R R I   R L + 
Sbjct: 270 SDDDEGRYAPQLFLEDAVNPADVVEEADWEENTTTALKDAMETLDERSRDIITQRWLADQ 329

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL  L++ + +S ERVRQIE  A  K++E+I
Sbjct: 330 KSTLHELAATYNISAERVRQIEKNAMNKIKEAI 362


>gi|269103879|ref|ZP_06156576.1| RNA polymerase sigma factor RpoH [Photobacterium damselae subsp.
           damselae CIP 102761]
 gi|268163777|gb|EEZ42273.1| RNA polymerase sigma factor RpoH [Photobacterium damselae subsp.
           damselae CIP 102761]
          Length = 287

 Score =  200 bits (509), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 111/276 (40%), Positives = 165/276 (59%), Gaps = 8/276 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + + PML  ++E  LA+R    GD+ AA  LV SHLR VV IA GY GYGLP+
Sbjct: 16  LDSYIQAVNRYPMLTAEQEKELAERLHFDGDIDAAKALVMSHLRFVVHIARGYSGYGLPM 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + E++LR+W +VK+ TT  Q++L
Sbjct: 76  ADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEFVLRNWRIVKVATTKAQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR+ K  L     NN   E++  +A +L V  SEV  M  RLA  ++   + N  D 
Sbjct: 136 FFNLRKSKKRLGWF--NN---EEINMVADQLGVEPSEVREMESRLAAQDATFEMSNDDDD 190

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
                     Y  D    V    EE     +  N L+++++ L+ R + I  +R L E+ 
Sbjct: 191 RDFTPTAPAYYLEDKSSDVARSYEESNWETHATNRLSQALAGLDERSQFIVRSRWLDEDK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            TL++L+  F VS ER+RQ+E  A KK++E++   +
Sbjct: 251 STLQDLADRFGVSAERIRQLEKNAMKKLKEAVGDDI 286


>gi|114321809|ref|YP_743492.1| RNA polymerase, sigma 32 subunit, RpoH [Alkalilimnicola ehrlichii
           MLHE-1]
 gi|114228203|gb|ABI58002.1| RNA polymerase, sigma 32 subunit, RpoH [Alkalilimnicola ehrlichii
           MLHE-1]
          Length = 285

 Score =  200 bits (509), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 105/267 (39%), Positives = 162/267 (60%), Gaps = 6/267 (2%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           YIH + +IP+L  +EE+ LA+RYR  GDL AA  LV SHLR VV IA  YRGYGLP+ ++
Sbjct: 23  YIHAVNQIPVLSAEEEHELAERYRLQGDLDAARALVLSHLRFVVHIARSYRGYGLPLGDI 82

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AVK+FDP +G RL ++++ WI+A + EY+LR+W +VK+ TT  Q++LFFN
Sbjct: 83  IQEGNVGLMKAVKRFDPAQGVRLVSFAVHWIRAEIHEYVLRNWRIVKVATTKAQRKLFFN 142

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  + HL  +T      E+V A+A+ L V    V  M  R+ G D + +      D+  
Sbjct: 143 LRSGRKHLGWLTS-----EEVDAMARDLGVKPETVREMEARMTGNDTTFDPTPGQDDEGI 197

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
                +L          + E +  ++R   L ++++ L+ R + I   R L E   TL+ 
Sbjct: 198 HAPVAYLEDKRYDPATAVEEADWEQHRDQNLHQALAGLDERSQDILARRWLSERKATLKE 257

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESI 284
           L+  ++VS ER+RQ+E  A  +++ ++
Sbjct: 258 LAEHYQVSAERIRQLEKNAMGRLKTAL 284


>gi|254230128|ref|ZP_04923524.1| alternative sigma factor RpoH [Vibrio sp. Ex25]
 gi|151937373|gb|EDN56235.1| alternative sigma factor RpoH [Vibrio sp. Ex25]
          Length = 284

 Score =  200 bits (509), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 110/272 (40%), Positives = 163/272 (59%), Gaps = 8/272 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  +   PML   EE  LA+R    G++ AA  L+ SHLR VV +A GY GYGLP+
Sbjct: 16  LDSYIRSVNSYPMLTADEERELAERLHYKGEIEAAKGLILSHLRFVVHVARGYSGYGLPM 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           +++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W +VKI TT  Q++L
Sbjct: 76  ADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR+ K  L    +      +V  +A++L V  SEV  M  RLA  +S   +    D 
Sbjct: 136 FFNLRKSKKRLGWFNNG-----EVETVARELGVEPSEVREMESRLAAVDSTFDMPTDEDD 190

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERK---NRRNMLTRSMSVLNPRERRIFEARRLQENP 252
           +S+ +   ++Y  D    V    E      +  N L  +++ L+ R +RI  +R L +  
Sbjct: 191 SSNAYTAPMLYLEDKSSDVADNIEAANWEMHTNNRLGHALASLDERSQRIVRSRWLDDEK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL++L+ EF VS ER+RQ+E  A KK++ ++
Sbjct: 251 ATLQDLADEFGVSAERIRQLEKNAMKKLKLAV 282


>gi|28899727|ref|NP_799332.1| RNA polymerase factor sigma-32 [Vibrio parahaemolyticus RIMD
           2210633]
 gi|260879104|ref|ZP_05891459.1| alternative sigma factor RpoH [Vibrio parahaemolyticus AN-5034]
 gi|28807979|dbj|BAC61216.1| RNA polymerase sigma-32 factor [Vibrio parahaemolyticus RIMD
           2210633]
 gi|308089656|gb|EFO39351.1| alternative sigma factor RpoH [Vibrio parahaemolyticus AN-5034]
 gi|328472446|gb|EGF43312.1| RNA polymerase factor sigma-32 [Vibrio parahaemolyticus 10329]
          Length = 286

 Score =  200 bits (509), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 110/273 (40%), Positives = 163/273 (59%), Gaps = 9/273 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  +   PML   EE  LA+R    G++ AA  L+ SHLR VV +A GY GYGLP+
Sbjct: 16  LDSYIRSVNSYPMLTADEERELAERLHYKGEIEAAKGLILSHLRFVVHVARGYSGYGLPM 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           +++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W +VKI TT  Q++L
Sbjct: 76  ADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR+ K  L    +      +V  +A++L V  SEV  M  RLA  D + +   +  D
Sbjct: 136 FFNLRKSKKRLGWFNNG-----EVETVARELGVEPSEVREMESRLAAVDSTFDMPTDDDD 190

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERK---NRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             +S +   ++Y  D    V    E      +  N L  +++ L+ R +RI  +R L + 
Sbjct: 191 SATSSYTAPMLYLEDKSSDVADNIEAANWEMHTNNRLGHALASLDERSQRIVRSRWLDDE 250

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL++L+ EF VS ER+RQ+E  A KK++ ++
Sbjct: 251 KATLQDLADEFGVSAERIRQLEKNAMKKLKLAV 283


>gi|91227498|ref|ZP_01261835.1| RNA polymerase sigma factor [Vibrio alginolyticus 12G01]
 gi|262392915|ref|YP_003284769.1| RNA polymerase sigma factor RpoH [Vibrio sp. Ex25]
 gi|269968648|ref|ZP_06182645.1| RNA polymerase sigma -32 factor [Vibrio alginolyticus 40B]
 gi|91188522|gb|EAS74814.1| RNA polymerase sigma factor [Vibrio alginolyticus 12G01]
 gi|262336509|gb|ACY50304.1| RNA polymerase sigma factor RpoH [Vibrio sp. Ex25]
 gi|269826735|gb|EEZ81072.1| RNA polymerase sigma -32 factor [Vibrio alginolyticus 40B]
          Length = 285

 Score =  200 bits (509), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 110/272 (40%), Positives = 163/272 (59%), Gaps = 8/272 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  +   PML   EE  LA+R    G++ AA  L+ SHLR VV +A GY GYGLP+
Sbjct: 16  LDSYIRSVNSYPMLTADEERELAERLHYKGEIEAAKGLILSHLRFVVHVARGYSGYGLPM 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           +++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W +VKI TT  Q++L
Sbjct: 76  ADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR+ K  L    +      +V  +A++L V  SEV  M  RLA  +S   +    D 
Sbjct: 136 FFNLRKSKKRLGWFNNG-----EVETVARELGVEPSEVREMESRLAAVDSTFDMPTDEDD 190

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERK---NRRNMLTRSMSVLNPRERRIFEARRLQENP 252
           +S+ +   ++Y  D    V    E      +  N L  +++ L+ R +RI  +R L +  
Sbjct: 191 SSNAYTAPMLYLEDKSSDVADNIEAANWEMHTNNRLGHALASLDERSQRIVRSRWLDDEK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL++L+ EF VS ER+RQ+E  A KK++ ++
Sbjct: 251 ATLQDLADEFGVSAERIRQLEKNAMKKLKLAV 282


>gi|323144379|ref|ZP_08078987.1| alternative sigma factor RpoH [Succinatimonas hippei YIT 12066]
 gi|322415832|gb|EFY06558.1| alternative sigma factor RpoH [Succinatimonas hippei YIT 12066]
          Length = 295

 Score =  200 bits (509), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 115/272 (42%), Positives = 164/272 (60%), Gaps = 8/272 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y+  I K PMLE+++E  LAKR R++GDL AA +LV SHLRLVV IA GY GYGLPI
Sbjct: 20  IDAYVKAINKFPMLEEEDERTLAKRLRDYGDLDAARKLVLSHLRLVVSIARGYLGYGLPI 79

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           S+++ EGNIGLM+AVK FDP+ G RLA +++ WIKA + +Y++++W +VK+ TT  Q++L
Sbjct: 80  SDLIQEGNIGLMKAVKHFDPDVGGRLAAFAVHWIKAEIHDYVIKNWRVVKVATTKAQRKL 139

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FF LR+ K  L   +D+         +A  L VS  +V  M  RLAG +      +  D 
Sbjct: 140 FFKLRQNKQRLGWFSDSERNK-----VADDLGVSADDVAEMETRLAGQDIGFDADSDDDS 194

Query: 196 NSSQWQDWLVY--DHDGQEQVLIEKEERKNRR-NMLTRSMSVLNPRERRIFEARRLQENP 252
           +         Y  D +       E  + +N   + L +++  L+ R R I + R L EN 
Sbjct: 195 DKGSSFSPSAYLEDENSNFANTFENIDYENYELSSLRKALDSLDERSRYIVQRRWLDENK 254

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL+ LS +  VS ERVRQIE +A KK++ +I
Sbjct: 255 ATLQELSEKLNVSIERVRQIENQALKKIKSNI 286


>gi|77359323|ref|YP_338898.1| RNA polymerase factor sigma-32 [Pseudoalteromonas haloplanktis
           TAC125]
 gi|76874234|emb|CAI85455.1| RNA polymerase sigma-32 factor (Heat shock regulatory protein
           F33.4) [Pseudoalteromonas haloplanktis TAC125]
          Length = 287

 Score =  200 bits (508), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 108/273 (39%), Positives = 166/273 (60%), Gaps = 9/273 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y+  +  IPML+ ++E  LA R +E GDLSAA +L+ SHLR V  IA GY GYGLP 
Sbjct: 19  MDGYLQAVSTIPMLKVEQEQELATRLQEEGDLSAAKQLIMSHLRFVAHIAKGYSGYGLPQ 78

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + E++L++W +VK+ TT  Q++L
Sbjct: 79  ADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEFVLKNWRIVKVATTKAQRKL 138

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR+ K  L           +V  +A +L VSE EV  M  R++G D   +   +  D
Sbjct: 139 FFNLRKNKKRL-----GWFNQAEVSTVASELGVSEKEVREMESRMSGQDMGFDLTGDDDD 193

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR---SMSVLNPRERRIFEARRLQEN 251
              S     + Y  DG   +  + E+++ +    TR   ++  L+ R + I  AR L ++
Sbjct: 194 SAPSSTYSPVQYLTDGTADLADDIEQQQWQEQSHTRLFSALKTLDERSQDIVSARWLTDD 253

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL+ L+ ++ VS ERVRQ+E  A KK+Q ++
Sbjct: 254 KATLQELAEKYSVSAERVRQLEKTAMKKLQAAM 286


>gi|89053397|ref|YP_508848.1| RNA polymerase factor sigma-32 [Jannaschia sp. CCS1]
 gi|88862946|gb|ABD53823.1| RNA polymerase, sigma 32 subunit, RpoH [Jannaschia sp. CCS1]
          Length = 292

 Score =  200 bits (508), Expect = 2e-49,   Method: Compositional matrix adjust.
 Identities = 109/281 (38%), Positives = 179/281 (63%), Gaps = 9/281 (3%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           G+  LSR      K  +L+ + E  LA  +R+     + HRLVT+++RL + +A  ++ Y
Sbjct: 6   GDQSLSR---RAMKAELLDAETELRLAYAWRDDRCEESLHRLVTAYMRLAISMAAKFKRY 62

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           G P+++++ E  +GLM+A  KFDP+RG R +TY++WWIKA++Q++++R+WS+V+ G+T++
Sbjct: 63  GAPMNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDHVMRNWSMVRTGSTSS 122

Query: 132 QKRLFFNLRRLKGHLQ---AITDNNLKPEQV-VAIAKKLNVSESEVISMNCRLAG-DESL 186
           QK LFFN+RR++  L+     + + L   Q+   IA ++ V   +V  M  RLAG D SL
Sbjct: 123 QKSLFFNMRRVQARLEREAMKSGDTLDKHQLRQMIATEVGVPLHDVEMMEGRLAGSDYSL 182

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           NA   S++    +W D L  D +  E ++    +    R+ L  SM+ LN RER I   R
Sbjct: 183 NA-TQSAEDEGREWIDTLEDDGEQAEHIVEHFHDTAQLRDWLIASMNALNDRERFIVRER 241

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +L+E+P TLE+L +E  +S+ERVRQ+EA AF K++++++ Q
Sbjct: 242 KLREDPRTLESLGTELGLSKERVRQLEAAAFGKMRKTLEAQ 282


>gi|260774824|ref|ZP_05883726.1| RNA polymerase sigma factor [Vibrio coralliilyticus ATCC BAA-450]
 gi|260609249|gb|EEX35404.1| RNA polymerase sigma factor [Vibrio coralliilyticus ATCC BAA-450]
          Length = 285

 Score =  200 bits (508), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 110/287 (38%), Positives = 169/287 (58%), Gaps = 8/287 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  +   + V  +  L  YI  +   PML  +EE  LA+R   +G++ AA  L+ SHLR 
Sbjct: 1   MTNQAYPMAVVTQDSLDSYIRTVNGYPMLTAEEERGLAERLHYNGEIEAAKGLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A GY GYGLP++++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VKI TT  Q++LFFNLR+ K  L    +      +V  +A++L V  SEV  M  RL
Sbjct: 121 WRIVKIATTKAQRKLFFNLRKSKKRLGWFNNG-----EVETVARELGVEPSEVREMESRL 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNP 237
           A  ++   + N  D +   +   ++Y  D    V    E      +  N L+ ++S L+ 
Sbjct: 176 AAQDAAFEMQNDDDDSGVSYTAPMLYLEDKASDVADNVEAANWEAHTNNRLSLALSSLDE 235

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R + I  +R L++N  TL+ L+  + VS ER+RQ+E  A KK++ ++
Sbjct: 236 RSQHIVRSRWLEDNKSTLQELAETYSVSAERIRQLEKNAMKKLKAAV 282


>gi|149202416|ref|ZP_01879389.1| RNA polymerase sigma-32 factor [Roseovarius sp. TM1035]
 gi|149144514|gb|EDM32545.1| RNA polymerase sigma-32 factor [Roseovarius sp. TM1035]
          Length = 277

 Score =  200 bits (508), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 107/268 (39%), Positives = 173/268 (64%), Gaps = 6/268 (2%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K  ML+ + E  LA  +R+  D  A HRL+ +++RL + +A  +R YG P+++++ E  +
Sbjct: 2   KAEMLDAETELALAYAWRDQRDEEALHRLINAYMRLAISMASKFRRYGAPMNDLIQEAGL 61

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFN+RR++ 
Sbjct: 62  GLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQA 121

Query: 145 HL--QAITDN-NLKPEQV-VAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQ 199
            L  +A+ +   L   Q+   IA ++ V   +V  M  RL+G D SLNA   SS+    Q
Sbjct: 122 RLEREALANGEQLDGYQLREMIAHEVGVPLRDVEMMEGRLSGSDFSLNA-TQSSEDEGRQ 180

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
           W D L  D    ++++    +    R  L  ++S LN RER I   R+L+++P TLE+L 
Sbjct: 181 WIDTLEDDGARGDEIVERDHDMHALRTWLADALSRLNDRERFIVRERKLRDDPRTLESLG 240

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQ 287
            E  +S+ERVRQ+EA AF+K+++ ++K 
Sbjct: 241 EELNLSKERVRQLEAAAFQKMRKHLEKH 268


>gi|258546170|ref|ZP_05706404.1| deoxyuridine 5`-triphosphate nucleotidohydrolase [Cardiobacterium
           hominis ATCC 15826]
 gi|258518595|gb|EEV87454.1| deoxyuridine 5`-triphosphate nucleotidohydrolase [Cardiobacterium
           hominis ATCC 15826]
          Length = 287

 Score =  199 bits (507), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 113/274 (41%), Positives = 169/274 (61%), Gaps = 11/274 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           + +YI +IR+IP L+ +EE  LA   +E  D++AA  L+  HL+ VV IA G+ GYGLP+
Sbjct: 20  IDQYIAKIRQIPALDAEEERKLAIALQETNDINAAQTLIVHHLKFVVHIARGFTGYGLPL 79

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM+AVK+F+P+RG RL ++++ WIK+ + EYI+R+W +VKI TT  Q++L
Sbjct: 80  GDLIQEGNVGLMKAVKRFEPQRGVRLVSFAVHWIKSEIHEYIIRNWRMVKIATTKAQRKL 139

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR +K  L     N L   +  AIA +LNVS  +V  M  R+ G D +     +  D
Sbjct: 140 FFNLRSMKKSL-----NWLNEAEAKAIADELNVSTKDVFEMESRIHGQDIAFELNDDDED 194

Query: 195 KNSSQWQDWLVYDH-DGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFEARRLQENP 252
            +      WL  D  D  E    E  E +N  +  L + +  L+PR R I +AR L E+ 
Sbjct: 195 NDHFSPSQWLADDSIDPAEHT--EHAEHENLMQRKLAKGLQALDPRSRAIVQARWLNEDS 252

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             TL+ L+SE+ VS ER+RQIE +A  +++  I+
Sbjct: 253 KATLQTLASEYNVSAERIRQIEQQAMHQLRAHIE 286


>gi|159045518|ref|YP_001534312.1| RNA polymerase factor sigma-32 [Dinoroseobacter shibae DFL 12]
 gi|157913278|gb|ABV94711.1| RNA polymerase sigma 32 factor [Dinoroseobacter shibae DFL 12]
          Length = 293

 Score =  199 bits (507), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 112/283 (39%), Positives = 179/283 (63%), Gaps = 11/283 (3%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           +GE+ LSR      +  +L+ + E  LA  +R+  D  A HRL+T+++RL + +A  ++ 
Sbjct: 7   SGEMSLSR---RAMQAELLDAETELRLAYAWRDQRDEEALHRLITAYMRLAISMAAKFKR 63

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
           YG P+++++ E  +GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T+
Sbjct: 64  YGAPMNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTS 123

Query: 131 NQKRLFFNLRRLKGHLQ---AITDNNLKPEQV-VAIAKKLNVSESEVISMNCRLAG-DES 185
           +QK LFFN+RR++  L+   A     L   Q+   IA ++ V   +V  M  RLAG D S
Sbjct: 124 SQKSLFFNMRRVQARLEREAASAGEPLDRHQLRQMIATEVGVPLHDVEMMEGRLAGSDYS 183

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE-ERKNRRNMLTRSMSVLNPRERRIFE 244
           LNA   S++    +W D L  D   Q   L+E++ + +  R  L  +M  LN RER I  
Sbjct: 184 LNA-TQSTEDEGREWIDTL-EDTGAQAAELVEQDHDIETLRGWLITAMDALNERERFIVR 241

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R+L++ P TLE+L  E  +S+ERVRQ+EA AF K+++++  Q
Sbjct: 242 ERKLRDQPRTLESLGQELGLSKERVRQLEAAAFGKMRKNLMNQ 284


>gi|332531759|ref|ZP_08407644.1| RNA polymerase sigma factor RpoH [Pseudoalteromonas haloplanktis
           ANT/505]
 gi|332038735|gb|EGI75177.1| RNA polymerase sigma factor RpoH [Pseudoalteromonas haloplanktis
           ANT/505]
          Length = 287

 Score =  199 bits (507), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 107/273 (39%), Positives = 165/273 (60%), Gaps = 9/273 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y+  +  IPML+ ++E  LAKR +E GDLSAA +L+ SHLR V  IA  Y GYGLP 
Sbjct: 19  MDGYLQAVSTIPMLKVEQEQELAKRLQEEGDLSAAKQLIMSHLRFVAHIAKSYSGYGLPQ 78

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AVK+FDP  G RL ++++ WIKA + E++L++W +VK+ TT  Q++L
Sbjct: 79  ADLIQEGNIGLMKAVKRFDPTVGVRLVSFAVHWIKAEIHEFVLKNWRIVKVATTKAQRKL 138

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR+ K  L           +V  +A +L VSE EV  M  R++G D   +   + +D
Sbjct: 139 FFNLRKNKKRL-----GWFNQAEVSTVASELGVSEKEVREMESRMSGQDMGFDLTGDDND 193

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR---SMSVLNPRERRIFEARRLQEN 251
              +     + Y  DG   +  + E+ + +    TR   ++  L+ R + I  AR L ++
Sbjct: 194 DAPTSTYSPVQYLTDGAADLADDVEQEQWKEQAHTRLFSALKTLDERSQDIVSARWLSDD 253

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL+ L+ ++ VS ERVRQ+E  A KK+Q ++
Sbjct: 254 KATLQELAQKYSVSAERVRQLEKTAMKKLQSAM 286


>gi|167627742|ref|YP_001678242.1| RNA polymerase factor sigma-32 [Francisella philomiragia subsp.
           philomiragia ATCC 25017]
 gi|167597743|gb|ABZ87741.1| RNA polymerase sigma-32 factor [Francisella philomiragia subsp.
           philomiragia ATCC 25017]
          Length = 292

 Score =  199 bits (507), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 105/284 (36%), Positives = 175/284 (61%), Gaps = 7/284 (2%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           K  S+ V  +  L+ Y++ +  +P+L  +EE  LA+RY+   DL AA +LV SHLR V K
Sbjct: 11  KGKSLPVVSDNNLNSYLNFVNSLPILSVEEEQELARRYKYQKDLDAAQQLVLSHLRFVTK 70

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  + GYGL I++++ EGNIGLM+AV KFDP++G RL ++++ WIKA M +Y+L++W +
Sbjct: 71  IARNFSGYGLSIADLIQEGNIGLMKAVSKFDPDQGVRLVSFAVHWIKAEMHDYVLKNWKI 130

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-G 182
           VK+ TT  Q++LFFNLR  K  +  ++  ++K      +A++L V E  VI M  R+  G
Sbjct: 131 VKVATTKAQRKLFFNLRSSKDKIGWLSSEDIKQ-----LAEELGVKEETVIEMEKRMCQG 185

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           D SL+      +   S  Q + + D     E  +++++   N + ++   +S  + R + 
Sbjct: 186 DASLDLPYTDDEGGQSNQQSFYLEDKSSDIEHQIVQQDYYDNFKAIVKDVISGFDTRTKD 245

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           I  +R L +   TL++L++++ +S ERVRQIE  A  K++++I+
Sbjct: 246 IIMSRYLLDTKATLQDLAAKYNISAERVRQIEEEALVKLRKAIK 289


>gi|84499725|ref|ZP_00998013.1| RNA polymerase sigma factor [Oceanicola batsensis HTCC2597]
 gi|84392869|gb|EAQ05080.1| RNA polymerase sigma factor [Oceanicola batsensis HTCC2597]
          Length = 292

 Score =  199 bits (507), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 108/270 (40%), Positives = 172/270 (63%), Gaps = 10/270 (3%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K  +L+ + E  LA  +R+  D  A HRLVT+++RL + +A  YR YG P+++++ E  +
Sbjct: 17  KAELLDAETELSLAYSWRDDRDERALHRLVTAYMRLAISMASKYRRYGAPMNDLIQEAGL 76

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFN+RR++ 
Sbjct: 77  GLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQA 136

Query: 145 HLQ------AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
            L+        T +  +  Q+VA+  ++ V   +V  M+ RL+G D SLNA   S D+  
Sbjct: 137 KLEREALGRGETLDKHQLHQLVAM--EVGVPLRDVQMMDGRLSGSDFSLNA-TQSVDEEG 193

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
            +W D +  D     + +    +R+  R  L  +MS LN RE  I   R+L++ P TLE+
Sbjct: 194 REWIDTIEDDGVQAAEAVEADHDRETLRLWLAEAMSDLNDRETLIVTERKLRDAPRTLES 253

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L  E  +S+ERVRQ+EA AFKK++  ++ Q
Sbjct: 254 LGQELGLSKERVRQLEAAAFKKMRRHLESQ 283


>gi|77165402|ref|YP_343927.1| RpoH [Nitrosococcus oceani ATCC 19707]
 gi|254433859|ref|ZP_05047367.1| alternative sigma factor RpoH [Nitrosococcus oceani AFC27]
 gi|76883716|gb|ABA58397.1| RNA polymerase, sigma 32 subunit, RpoH [Nitrosococcus oceani ATCC
           19707]
 gi|207090192|gb|EDZ67463.1| alternative sigma factor RpoH [Nitrosococcus oceani AFC27]
          Length = 287

 Score =  199 bits (506), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 116/286 (40%), Positives = 176/286 (61%), Gaps = 18/286 (6%)

Query: 3   RKNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           R +   +V   +G L+ Y      IP+L  ++E  LA R R+H DL AA +LV SHLR V
Sbjct: 6   RNDNGALVPVAVGNLNTYCQNAHSIPVLSAEQERSLALRLRQHNDLEAARQLVLSHLRFV 65

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           ++IA GY GYGLP+++++ EGNIGLM+AVK+FDPE+G RL ++++ WI+A + E+ILR+W
Sbjct: 66  IRIARGYNGYGLPLADLIQEGNIGLMKAVKRFDPEQGVRLVSFAVHWIRAEIHEFILRNW 125

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            +VK+ TT  Q++LFFNLR  K  L       L  ++V  +A+ L VS  +V+ M  RL+
Sbjct: 126 RIVKVATTKAQRKLFFNLRSAKKRL-----GWLNRKEVDEVAQDLGVSPKQVMEMEARLS 180

Query: 182 GDESLNALINSSDKNSSQ--WQDWLVYDHD-----GQEQVLIEKEERKNRRNMLTRSMSV 234
              S +A  + S+   S+      + Y  D      Q+  L+++E    +R  L +++ V
Sbjct: 181 ---SQDAPFDGSNAEESENGIPAPMAYLADPSADPAQKMELLDQENYYGQR--LQQALEV 235

Query: 235 LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           L+ R R I   R LQEN  TL  L++E+++S ER+RQ+E  A KK+
Sbjct: 236 LDLRSRTIINRRWLQENKSTLHELAAEYQISAERIRQLENNAIKKM 281


>gi|332995320|gb|AEF05375.1| RNA polymerase sigma factor [Alteromonas sp. SN2]
          Length = 284

 Score =  199 bits (506), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 107/267 (40%), Positives = 162/267 (60%), Gaps = 6/267 (2%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+  + +I ML  +EE  LA R RE  DL AA +LV SHLR VV IA  Y GYGLP +++
Sbjct: 21  YVQAVSRIDMLTAEEERALAVRLREDEDLEAARKLVMSHLRFVVHIAKSYSGYGLPQADL 80

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM+AVK+FDP  G RL ++++ WIKA + E++L++W +VK+ TT  Q++LFFN
Sbjct: 81  IQEGNIGLMKAVKRFDPTVGVRLVSFAVHWIKAEIHEFVLKNWRIVKVATTKAQRKLFFN 140

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR+ K  L   T      E+V  +A +L VS  EV+ M  R++  D++ +   +  +  +
Sbjct: 141 LRKAKKRLGWFT-----HEEVQTVASELGVSTKEVLQMEARMSSQDQAFDLSADEDETGN 195

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
                +L       E  +I  +   N    L  ++  L+ R + I E R L ++ +TL++
Sbjct: 196 FAPVQFLEDKSTDVEMDVINNDWDTNASKRLYSAIKTLDDRSQDIIETRWLADSKITLQD 255

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESI 284
           L+ ++EVS ERVRQIE  A KK+Q ++
Sbjct: 256 LADKYEVSAERVRQIEKNAMKKLQAAM 282


>gi|126739146|ref|ZP_01754840.1| RNA polymerase sigma-32 factor [Roseobacter sp. SK209-2-6]
 gi|126719763|gb|EBA16471.1| RNA polymerase sigma-32 factor [Roseobacter sp. SK209-2-6]
          Length = 292

 Score =  199 bits (506), Expect = 4e-49,   Method: Compositional matrix adjust.
 Identities = 111/266 (41%), Positives = 173/266 (65%), Gaps = 8/266 (3%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K  +L+ + E  LA  +R+  D+ A HRL  +++RL + +A  +  YG P+++++ E  +
Sbjct: 17  KAELLDAETERALAYAWRDQRDVKALHRLTNAYMRLAISMAAKFNRYGAPMNDLIQEAGL 76

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFNLRR++ 
Sbjct: 77  GLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKTLFFNLRRVQA 136

Query: 145 HLQ--AITDNN-LKPEQV-VAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQ 199
            L+  A  D + L   Q+   IA ++ V   +V  M+ RL+G D SLNA   +SD +  +
Sbjct: 137 QLERRAYADGHRLDRHQLHQKIASEIGVPLRDVEMMDGRLSGSDFSLNA-NQASDNDGRE 195

Query: 200 WQDWLVYDH-DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           W D L  +H +G EQV     +R+  R  L  +M  L  RER I  AR+LQE   TLE+L
Sbjct: 196 WIDALEDEHAEGAEQV-EGTHDRRQLRQWLVEAMQSLTERERFIIVARKLQEPFRTLEDL 254

Query: 259 SSEFEVSRERVRQIEARAFKKVQESI 284
             E  +S+ERVRQ+EA A KK+++++
Sbjct: 255 GQELNLSKERVRQLEAAALKKMRKAL 280


>gi|326569916|gb|EGE19966.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis BC8]
          Length = 371

 Score =  199 bits (505), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 107/273 (39%), Positives = 161/273 (58%), Gaps = 9/273 (3%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + L  YI+ + +IP+L  +EE  LA+RY   GD+ A   LV SHLR V+ IA  Y GYGL
Sbjct: 97  VNLGAYINTVHQIPILTPEEERALAERYYHDGDVEATRLLVMSHLRFVIHIARSYSGYGL 156

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
             ++++ EGN+GLM+AVK+FDP +G RL ++++ WIKA + E+++++W +VK+ TT   +
Sbjct: 157 SQADLIQEGNLGLMKAVKRFDPNKGVRLVSFAVHWIKAEIHEFVIKNWRIVKVATTKAHR 216

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINS 192
           +LFFNLR LK      + N L  ++  AIA  LNV+  +V+ M  RL   D S  A    
Sbjct: 217 KLFFNLRSLKK-----SSNQLTLDEATAIANDLNVTVKQVLEMESRLTSYDASFEA--QD 269

Query: 193 SDKNSSQWQDWL-VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           SD +  ++   L + D      V+ E +  +N    L  +M  L+ R R I   R L + 
Sbjct: 270 SDDDEGRYAPQLFLEDAVNPADVVEEADWEENTTTALKDAMETLDERSRDIITQRWLADQ 329

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL  L++ + +S ERVRQIE  A  K++E+I
Sbjct: 330 KSTLHELAATYNISAERVRQIEKNAMNKIKEAI 362


>gi|307824539|ref|ZP_07654764.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacter tundripaludum
           SV96]
 gi|307734523|gb|EFO05375.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacter tundripaludum
           SV96]
          Length = 285

 Score =  199 bits (505), Expect = 5e-49,   Method: Compositional matrix adjust.
 Identities = 104/283 (36%), Positives = 176/283 (62%), Gaps = 8/283 (2%)

Query: 6   MSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +++ +N  +G    Y++ +R++P L  ++E  LA ++R+ GDL AA  LV ++LR V+ +
Sbjct: 5   LALPINLSVGTFDAYLNVVRQMPKLTVEQERELALKFRDDGDLEAARELVMTNLRFVIHV 64

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A GY GYGL + +++ EGNIGLM+AVK+FDP+ G RL ++++ WIKA + EY++++W +V
Sbjct: 65  ARGYSGYGLSMPDIIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYVIKNWGIV 124

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-D 183
           K+ TT  Q++LFFNLR+ K  L  ++++     + VAIAK L+V  S V  M  RL   D
Sbjct: 125 KVATTKAQRKLFFNLRKSKQDLGWLSND-----EAVAIAKDLDVDVSTVYEMEKRLGSRD 179

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERRI 242
            S +  ++ S + S       ++ H G   VL+E  +   + +++L  +M+ L+ R   I
Sbjct: 180 MSFDMPVDESTEESYVAPASYLHQHGGDPAVLLENSDWEGHEQDLLADAMAELDERSLDI 239

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             +R L +   TL  L+  + VS ER+RQ+E  A KK++ +++
Sbjct: 240 LSSRWLMDKKATLHELAERYNVSAERIRQLEQNAMKKLRAAVE 282


>gi|258404985|ref|YP_003197727.1| putative RNA polymerase, sigma 70 family subunit [Desulfohalobium
           retbaense DSM 5692]
 gi|257797212|gb|ACV68149.1| putative RNA polymerase, sigma 70 family subunit [Desulfohalobium
           retbaense DSM 5692]
          Length = 350

 Score =  199 bits (505), Expect = 6e-49,   Method: Compositional matrix adjust.
 Identities = 112/276 (40%), Positives = 175/276 (63%), Gaps = 8/276 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLP 74
           L  Y+ E+ + P+LE  EE  LA+R R+  D SAA RL++SHLRLVVKIAM + R +   
Sbjct: 71  LKLYLREVNRFPLLEPDEEVELARRVRDENDQSAAFRLISSHLRLVVKIAMEFQRRWMKN 130

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++V EGN+GLM+AV+KFDPERG + + Y+ +WI+A + ++I+ +W +VK+GTT  Q++
Sbjct: 131 VLDLVQEGNVGLMKAVQKFDPERGIKFSYYASFWIRAYILKFIMDNWRMVKLGTTQAQRK 190

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSS 193
           LF+NL R K  LQA       P+    +++ L+VSE  V+ M  RL G D SL+A +   
Sbjct: 191 LFYNLSREKQRLQA---QGFDPD-ASTLSENLDVSEESVVEMTQRLGGHDLSLDAPLG-- 244

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           + +SS   D+L     G E+ L ++E     R  L   +  LN +E+ I E R L ++PV
Sbjct: 245 EDSSSSRMDFLPALGAGIEESLAQQEMGSALRQHLQTILPKLNDKEKEILEHRLLTDSPV 304

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           TL  +  ++ ++RERVRQIE+R  +K++  +  +++
Sbjct: 305 TLREIGEKYGITRERVRQIESRLLQKLKTHLSSEIQ 340


>gi|303248805|ref|ZP_07335056.1| RNA polymerase sigma factor, sigma-70 family [Desulfovibrio
           fructosovorans JJ]
 gi|302489817|gb|EFL49747.1| RNA polymerase sigma factor, sigma-70 family [Desulfovibrio
           fructosovorans JJ]
          Length = 344

 Score =  199 bits (505), Expect = 6e-49,   Method: Compositional matrix adjust.
 Identities = 109/279 (39%), Positives = 179/279 (64%), Gaps = 6/279 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLP 74
           L  Y+ EI K PML+ +EE  LA+R R+ GD  AA RL++SHLRLVVKIAM + R +   
Sbjct: 64  LQLYLREIGKFPMLKPEEEQELARRVRDSGDEKAAFRLISSHLRLVVKIAMDFQRRWMQN 123

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++ EGN+GLM+AV KFDP++G + + Y+ +WIKA + +YI+ +W +VKIGTT  Q++
Sbjct: 124 VLDLIQEGNVGLMRAVTKFDPDKGIKFSYYAAYWIKAYILKYIMDNWRMVKIGTTQAQRK 183

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           LF+NL + +  LQ +      P     +++ LNV+ES+++ M+ RL+G++ L+  ++  +
Sbjct: 184 LFYNLNKERNRLQTL---GFDP-SASQLSEALNVTESDIVEMDQRLSGND-LSLDVSLGE 238

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
            ++S   D+L     G E++L   E        +      LN +E  + + R L ++PVT
Sbjct: 239 DSTSTRLDFLPALTPGIEEILAGDEISHQLEKHIQTIRPSLNEKELDLLDNRILSDSPVT 298

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           L  + +++ ++RERVRQIEAR  +K++E + K++E  SS
Sbjct: 299 LREIGAKYGITRERVRQIEARLLEKLKEHLSKRIEDFSS 337


>gi|323498063|ref|ZP_08103069.1| RNA polymerase factor sigma-32 [Vibrio sinaloensis DSM 21326]
 gi|323316871|gb|EGA69876.1| RNA polymerase factor sigma-32 [Vibrio sinaloensis DSM 21326]
          Length = 285

 Score =  199 bits (505), Expect = 6e-49,   Method: Compositional matrix adjust.
 Identities = 110/287 (38%), Positives = 167/287 (58%), Gaps = 8/287 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  +   + V  +  L  YI ++   PML   EE  LA+R    G++ AA  L+ SHLR 
Sbjct: 1   MTNQAYPMAVVTQDSLDSYIRKVNSYPMLTADEERELAERLHYDGEIEAAKGLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A GY GYGLP++++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VKI TT  Q++LFFNLR+ K  L    +      +V  +AK+L V  +EV  M  RL
Sbjct: 121 WRIVKIATTKAQRKLFFNLRKSKKRLGWFNNG-----EVETVAKELGVEPAEVREMESRL 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNP 237
           A  +S   +    D + S +   ++Y  D    V    E      +  N L+ +++ L+ 
Sbjct: 176 AAQDSTFEMPTDDDDSVSSYTAPVLYLEDKASDVADNVEAANWEAHTNNRLSLALASLDE 235

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R + I  +R L +N  TL+ L+  + VS ER+RQ+E  A KK++ ++
Sbjct: 236 RSQHIVRSRWLDDNKSTLQELAETYSVSAERIRQLEKNAMKKLKTAV 282


>gi|241668310|ref|ZP_04755888.1| RNA polymerase factor sigma-32 [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
 gi|254876843|ref|ZP_05249553.1| RNA polymerase sigma-32 factor [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
 gi|254842864|gb|EET21278.1| RNA polymerase sigma-32 factor [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
          Length = 292

 Score =  198 bits (504), Expect = 7e-49,   Method: Compositional matrix adjust.
 Identities = 105/284 (36%), Positives = 174/284 (61%), Gaps = 7/284 (2%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           K  S+ V  +  L+ Y++ +  +P+L  +EE  LA+RY+   DL AA +LV SHLR V K
Sbjct: 11  KGKSLPVVSDNNLNSYLNFVNSLPILSVEEEQELARRYKYQKDLDAAQQLVLSHLRFVTK 70

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  + GYGL I++++ EGNIGLM+AV KFDP++G RL ++++ WIKA M +Y+L++W +
Sbjct: 71  IARNFSGYGLSIADLIQEGNIGLMKAVSKFDPDQGVRLVSFAVHWIKAEMHDYVLKNWKI 130

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-G 182
           VK+ TT  Q++LFFNLR  K  +  ++  ++K      +A++L V E  VI M  R+  G
Sbjct: 131 VKVATTKAQRKLFFNLRSSKDKIGWLSSEDIKQ-----LAEELGVKEETVIEMEKRMCQG 185

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           D SL+      +   S  Q   + D     E  +++++   N + ++   +S  + R + 
Sbjct: 186 DASLDLPYTDDEGGQSNQQSLYLEDKSSDIEHQIVQQDYYDNFKAIVKDVISGFDTRTKD 245

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           I  +R L +   TL++L++++ +S ERVRQIE  A  K++++I+
Sbjct: 246 IIMSRYLLDTKATLQDLATKYNISAERVRQIEEEALVKLRKAIK 289


>gi|254487022|ref|ZP_05100227.1| RNA polymerase sigma-32 factor [Roseobacter sp. GAI101]
 gi|214043891|gb|EEB84529.1| RNA polymerase sigma-32 factor [Roseobacter sp. GAI101]
          Length = 277

 Score =  198 bits (504), Expect = 7e-49,   Method: Compositional matrix adjust.
 Identities = 105/268 (39%), Positives = 171/268 (63%), Gaps = 6/268 (2%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K  +L+ + E  LA  +R+  D  A HRL+T+++RL + +A  ++ YG P+++++ E  +
Sbjct: 2   KAELLDAETELKLAYAWRDERDEEALHRLITAYMRLAISMAGKFKRYGAPMNDLIQEAGL 61

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A  KFDP+RG R +TY++WWIKA++Q++++R+WS+V+ G+T++QK LFFN+RR++ 
Sbjct: 62  GLMKAADKFDPDRGVRFSTYAVWWIKASIQDHVMRNWSMVRTGSTSSQKSLFFNMRRVQA 121

Query: 145 HL----QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQ 199
            L    QA  +   K +    I+ ++ V   +V  M  RL+G D SLNA   SS+    +
Sbjct: 122 RLEREAQAAGETLDKHQLRQMISTEIGVPMHDVEMMEGRLSGSDYSLNA-TQSSEDEGRE 180

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
           W D LV D     + + E  +    RN L  +M  LN RE+ I   R+L++ P TLE+L 
Sbjct: 181 WIDALVDDTAQAAERVEESHDIVTLRNWLLGAMQALNDREQFIVRERKLRDQPRTLESLG 240

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQ 287
            E  +S+ERVRQ+EA AF K++++++ Q
Sbjct: 241 QELNLSKERVRQLEAAAFAKMRKTLETQ 268


>gi|46579995|ref|YP_010803.1| sigma 70 family protein [Desulfovibrio vulgaris str. Hildenborough]
 gi|120602593|ref|YP_966993.1| sigma-70 region 2 domain-containing protein [Desulfovibrio vulgaris
           DP4]
 gi|46449411|gb|AAS96062.1| sigma 70 family protein [Desulfovibrio vulgaris str. Hildenborough]
 gi|120562822|gb|ABM28566.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfovibrio vulgaris DP4]
 gi|311234006|gb|ADP86860.1| RNA polymerase sigma factor, sigma-70 family [Desulfovibrio
           vulgaris RCH1]
          Length = 356

 Score =  198 bits (504), Expect = 8e-49,   Method: Compositional matrix adjust.
 Identities = 114/289 (39%), Positives = 180/289 (62%), Gaps = 7/289 (2%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           + +  G+  L  Y+ EI + PML+ +EEY LAKR RE GD  AA RLV+SHLRLVVKIAM
Sbjct: 68  ATVSTGKDSLHLYLREISRFPMLKPEEEYELAKRVRETGDGDAAFRLVSSHLRLVVKIAM 127

Query: 67  GY-RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            + R +   + +++ EGN+GLM+AV KFDPE+G + + Y+ +WIKA + ++I+ +W +VK
Sbjct: 128 DFQRRWMQNVLDLIQEGNVGLMRAVNKFDPEKGIKFSYYAAFWIKAYILKFIMDNWRMVK 187

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDE 184
           IGTT  Q++LF+NL + +   Q +      P+    ++++LNV++ +V+ M  RL A D 
Sbjct: 188 IGTTQAQRKLFYNLNKER---QKLILQGYDPD-AATLSERLNVTKEQVVEMEQRLDASDV 243

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL+  +      +S+  D+L     G E  L   E     +N L   +  L+ +E  I +
Sbjct: 244 SLDIPVGDEGGGASR-MDFLPALGPGIEDALSNHEIASMVQNRLQSIIPKLSDKEVDILQ 302

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
            R L E PVTL  +  +++++RERVRQIEAR  +K+++ + K+++  SS
Sbjct: 303 NRLLSEEPVTLREIGEKYDITRERVRQIEARLLQKIRDHLFKEIKDFSS 351


>gi|15603449|ref|NP_246523.1| RNA polymerase factor sigma-32 [Pasteurella multocida subsp.
           multocida str. Pm70]
 gi|12721979|gb|AAK03668.1| RpoH [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 281

 Score =  198 bits (504), Expect = 8e-49,   Method: Compositional matrix adjust.
 Identities = 109/288 (37%), Positives = 171/288 (59%), Gaps = 13/288 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           MN+   ++++  +  +  YI    + PML  +EE  LA+R     DL AA +L+ SHLR 
Sbjct: 1   MNKDTQTMMLVPQGSIEAYIRAANEYPMLTAEEEKELAERLYYQEDLEAAKKLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L    +N     +V  +A +L VS ++V+ M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNEN-----EVEMVANELGVSPADVMEMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV----LN 236
            G +   A    +D N   +   L  +  G       + E +N     T  +SV    L+
Sbjct: 176 TGADV--AFDLPTDDNEETYSPSLYLEDKGSN--FAAELENENYEAQATEQLSVALEGLD 231

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            R   I +AR L EN  TL++L++++ +S ERVRQ+E  A KK++ ++
Sbjct: 232 ERSLDIIKARWLDENKATLQDLAAKYNISAERVRQLETNALKKLKSAV 279


>gi|315127793|ref|YP_004069796.1| RNA polymerase factor sigma-32 [Pseudoalteromonas sp. SM9913]
 gi|315016307|gb|ADT69645.1| RNA polymerase factor sigma-32 [Pseudoalteromonas sp. SM9913]
          Length = 287

 Score =  198 bits (503), Expect = 8e-49,   Method: Compositional matrix adjust.
 Identities = 106/273 (38%), Positives = 166/273 (60%), Gaps = 9/273 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y+  +  IPML+ ++E  LAK+ +E GDLSAA +L+ SHLR V  IA  Y GYGLP 
Sbjct: 19  MDGYLQAVSTIPMLKVEQEQELAKKLQEEGDLSAAKQLIMSHLRFVAHIAKSYSGYGLPQ 78

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AVK+FDP  G RL ++++ WIKA + E++L++W +VK+ TT  Q++L
Sbjct: 79  ADLIQEGNIGLMKAVKRFDPSVGVRLVSFAVHWIKAEIHEFVLKNWRIVKVATTKAQRKL 138

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR+ K  L           +V  +A +L VSE EV  M  R++G D   +   + +D
Sbjct: 139 FFNLRKNKKRL-----GWFNQAEVSTVASELGVSEKEVREMESRMSGQDMGFDLTGDDND 193

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR---SMSVLNPRERRIFEARRLQEN 251
              +     + Y  DG   +  + E+++ +    TR   ++  L+ R + I  AR L ++
Sbjct: 194 DAPTSTYSPVQYLTDGSADLADDIEQQQWQEQSHTRLFSALKTLDERSQDIVSARWLSDD 253

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL+ L+ ++ VS ERVRQ+E  A KK+Q ++
Sbjct: 254 KATLQELAEKYSVSAERVRQLEKTAMKKLQSAM 286


>gi|239994826|ref|ZP_04715350.1| RNA polymerase sigma factor [Alteromonas macleodii ATCC 27126]
          Length = 284

 Score =  198 bits (503), Expect = 8e-49,   Method: Compositional matrix adjust.
 Identities = 109/284 (38%), Positives = 168/284 (59%), Gaps = 6/284 (2%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N ++M++ V     +  YI  +  I ML  +EE  LA R RE  DL AA +LV SHLR V
Sbjct: 4   NLQSMALSVPHSGSIEGYIQAVSSIDMLSAEEERELAVRLREDEDLQAARKLVMSHLRFV 63

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA  Y GYGLP ++++ EGNIGLM+AVK+FDP  G RL ++++ WIKA + E++L++W
Sbjct: 64  VHIAKSYSGYGLPQADLIQEGNIGLMKAVKRFDPTVGVRLVSFAVHWIKAEIHEFVLKNW 123

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            +VK+ TT  Q++LFFNLR+ K  L   T      ++V  +A +L VS  EV+ M  R++
Sbjct: 124 RIVKVATTKAQRKLFFNLRKAKKRLGWFT-----HDEVQTVANELGVSTKEVLQMEARMS 178

Query: 182 G-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
             D++ +   +  +  +     +L       E  +I  +        L  ++  L+ R +
Sbjct: 179 SQDQAFDLTADEDETGNFAPVQYLEDKSSDVETDVINNDWDTAASKRLYSAIKTLDERSQ 238

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            I E R L +N +TL++L+ +++VS ERVRQIE  A KK+Q ++
Sbjct: 239 DIIETRWLADNKITLQDLADKYQVSAERVRQIEKNAMKKLQAAM 282


>gi|320353914|ref|YP_004195253.1| RNA polymerase sigma 32 subunit RpoH [Desulfobulbus propionicus DSM
           2032]
 gi|320122416|gb|ADW17962.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfobulbus propionicus
           DSM 2032]
          Length = 328

 Score =  198 bits (503), Expect = 8e-49,   Method: Compositional matrix adjust.
 Identities = 111/276 (40%), Positives = 180/276 (65%), Gaps = 8/276 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L RY+ EI +  +L ++E   LA R++E GD  AA+RLV+S+LRLVVK+AM ++ Y + 
Sbjct: 36  ALHRYLQEISQYELLSREETEELAVRFQETGDPDAAYRLVSSNLRLVVKVAMDFQKYWMQ 95

Query: 75  -ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL+QA KKFDP RG + + Y+ +WI+A + ++I+ +W LVKIGTT  Q+
Sbjct: 96  NFMDLIQEGNVGLVQATKKFDPYRGVKFSYYAAYWIRAYILKFIMDNWRLVKIGTTQAQR 155

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINS 192
           +LFF+L + K  L++      KPE V  +A++LNV ESEVI M  R+   D SL A + S
Sbjct: 156 KLFFSLNKEKKLLES---QGFKPE-VKLLAERLNVKESEVIEMGQRMDNWDVSLEAPVRS 211

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
             ++  + +++L ++  G E+++  +E R+    +L    + LN +E+ I   R L + P
Sbjct: 212 DSED--EQKNFLPHEGPGIEEMVASQEMRERLAGILADLSTRLNEKEQVILTTRLLSDEP 269

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            TL+ ++ EF +SRERVRQIE+   KK+++  +K++
Sbjct: 270 KTLQTIADEFNISRERVRQIESNLLKKLRKQFEKEM 305


>gi|94265020|ref|ZP_01288789.1| Sigma-70 region 2 [delta proteobacterium MLMS-1]
 gi|94270029|ref|ZP_01291635.1| Sigma-70 region 2 [delta proteobacterium MLMS-1]
 gi|93450968|gb|EAT01953.1| Sigma-70 region 2 [delta proteobacterium MLMS-1]
 gi|93454509|gb|EAT04794.1| Sigma-70 region 2 [delta proteobacterium MLMS-1]
          Length = 337

 Score =  197 bits (502), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 117/288 (40%), Positives = 183/288 (63%), Gaps = 10/288 (3%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           ++N+ ++  G   L RY+ EI +  +L ++E   LA+R++E GD  AA++LVT++LRLVV
Sbjct: 39  QENLPVV--GNAALHRYLQEISQYRLLSREETDELARRFQESGDPDAAYQLVTANLRLVV 96

Query: 63  KIAMGYRGYGLP-ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           K+AM ++ Y +    +++ EGNIGL+QAVKKFDP R  + + Y+ +WI+A + ++I+ +W
Sbjct: 97  KVAMDFQKYWMQNFLDLIQEGNIGLVQAVKKFDPYRQVKFSYYAAYWIRAYILKFIMDNW 156

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            LVKIGTT  Q++LFFNL + K  L+A      +PE  + +A++LNV ESE+I M  RL 
Sbjct: 157 RLVKIGTTQAQRKLFFNLNKEKKLLEA---QGFEPEPKL-LAQRLNVKESEIIEMGQRLE 212

Query: 182 -GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SL + +     +  Q +D+L     G EQ + E E R+    ML +    LN +E 
Sbjct: 213 HGDMSLESPLRED--SDEQRKDFLPMLGPGVEQRVAEDEIRQWMAAMLDKLRLTLNEKEL 270

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            I + R L ++P TL+ ++  F +SRERVRQIEA   KK++  ++ +V
Sbjct: 271 AILDQRLLNDDPRTLQEIADRFTISRERVRQIEANLLKKMRLYLENEV 318


>gi|332142899|ref|YP_004428637.1| RNA polymerase sigma factor [Alteromonas macleodii str. 'Deep
           ecotype']
 gi|332143056|ref|YP_004428794.1| RNA polymerase sigma factor [Alteromonas macleodii str. 'Deep
           ecotype']
 gi|327552921|gb|AEA99639.1| RNA polymerase sigma factor [Alteromonas macleodii str. 'Deep
           ecotype']
 gi|327553078|gb|AEA99796.1| RNA polymerase sigma factor [Alteromonas macleodii str. 'Deep
           ecotype']
          Length = 284

 Score =  197 bits (502), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 110/284 (38%), Positives = 166/284 (58%), Gaps = 6/284 (2%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N ++M++ V     +  YI  +  I ML  +EE  LA R RE  DL AA +LV SHLR V
Sbjct: 4   NLQSMALSVPHSGSIEGYIQAVSSIDMLSAEEERELAVRLREDEDLQAARKLVMSHLRFV 63

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA  Y GYGLP ++++ EGNIGLM+AVK+FDP  G RL ++++ WIKA + E++L++W
Sbjct: 64  VHIAKSYSGYGLPQADLIQEGNIGLMKAVKRFDPTVGVRLVSFAVHWIKAEIHEFVLKNW 123

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            +VK+ TT  Q++LFFNLR+ K  L   T      ++V  +A +L VS  EV+ M  R++
Sbjct: 124 RIVKVATTKAQRKLFFNLRKAKKRLGWFT-----HDEVQTVANELGVSTKEVLQMEARMS 178

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRER 240
             +    L    D+  +      + D     E  +I  +        L  ++  L+ R +
Sbjct: 179 SQDQAFDLSADEDETGNFAPVQFLEDKSSDVETDVINNDWDTAASKRLYSAIKTLDDRSQ 238

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            I E R L +N +TL++L+ +++VS ERVRQIE  A KK+Q ++
Sbjct: 239 DIIETRWLADNKITLQDLADKYQVSAERVRQIEKNAMKKLQAAM 282


>gi|126734879|ref|ZP_01750625.1| RNA polymerase sigma-32 factor [Roseobacter sp. CCS2]
 gi|126715434|gb|EBA12299.1| RNA polymerase sigma-32 factor [Roseobacter sp. CCS2]
          Length = 277

 Score =  197 bits (501), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 104/268 (38%), Positives = 173/268 (64%), Gaps = 6/268 (2%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K  +L+ + E  LA  +R+  D  A HRL+T+++RL + +A  ++ YG P+++++ E ++
Sbjct: 2   KAELLDAETELALAYAWRDERDEKALHRLITAYMRLAISMASKFKRYGAPMNDLIQEASV 61

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFN+RR++ 
Sbjct: 62  GLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQA 121

Query: 145 HL--QAITDNNLKPEQVV--AIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQ 199
            L  +A  +  +  +Q +   IA ++ V   +V  M  RL+G D SLNA   S +    +
Sbjct: 122 RLEREAAAEGRVMDKQEMRELIAIEVGVPLHDVEMMEGRLSGSDFSLNA-TQSVEDEGRE 180

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
           W D L  D     + +    +    R  L  ++S LN RE+ I   R+L+E+P TLE+L 
Sbjct: 181 WIDALEDDGPQAAETVEHTHDNDTLRQWLLTALSNLNDREQFIVRERKLREDPRTLESLG 240

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +E  +S+ERVRQ+EA AF K+++S++ Q
Sbjct: 241 TELGLSKERVRQLEAAAFGKMRKSLESQ 268


>gi|149924702|ref|ZP_01913051.1| sigma 32 (RpoH) [Plesiocystis pacifica SIR-1]
 gi|149814429|gb|EDM74021.1| sigma 32 (RpoH) [Plesiocystis pacifica SIR-1]
          Length = 371

 Score =  197 bits (501), Expect = 1e-48,   Method: Compositional matrix adjust.
 Identities = 114/275 (41%), Positives = 178/275 (64%), Gaps = 6/275 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           ++ Y+ E+R+ P+L +++E+ LA R+ EHGD  AA RLVTS+LRLVVKIA  YR     +
Sbjct: 90  MAAYMAEVRRHPLLTREQEHELAVRWVEHGDQEAAKRLVTSNLRLVVKIANEYRRGYQNL 149

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++V EGN+GL++AV+KFDP RG +L+TYS WWI+A + ++IL +W LVKIGTT NQ++L
Sbjct: 150 LDLVQEGNVGLLKAVQKFDPYRGVKLSTYSGWWIRAYVLKHILNNWRLVKIGTTQNQRKL 209

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSSD 194
           FFNLR+ +   +A+    + P     IAK+L+VS  EV+ M  R+ A D SLNA + S +
Sbjct: 210 FFNLRKQR---EALIRAGIDP-TAENIAKELDVSTEEVVEMQKRMGAPDASLNAPLGSGE 265

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQENPV 253
           +  ++ +  ++ D     +  +  EE K   +   R+  + L+ RE  IF  R + + P+
Sbjct: 266 EPGARTRLDMLEDETTDPEGEVSGEEFKRLLHDKLRTFGATLSGREAEIFGERLIADEPI 325

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           TL+ L   + VSRER RQ+E R   ++++ +Q ++
Sbjct: 326 TLQALGERWGVSRERARQVEKRMVLRLRKYLQAEL 360


>gi|261250002|ref|ZP_05942579.1| RNA polymerase sigma factor RpoH [Vibrio orientalis CIP 102891]
 gi|260939506|gb|EEX95491.1| RNA polymerase sigma factor RpoH [Vibrio orientalis CIP 102891]
          Length = 285

 Score =  197 bits (501), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 107/272 (39%), Positives = 160/272 (58%), Gaps = 8/272 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI      PML  +EE  LA+R    G++ AA  L+ SHLR VV +A GY GYGLP+
Sbjct: 16  LDSYIRSANSYPMLTPEEERDLAERLHYDGEIEAAKGLILSHLRFVVHVARGYSGYGLPM 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           +++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W +VKI TT  Q++L
Sbjct: 76  ADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR+ K  L    +      +V  +A++L V  SEV  M  RLA  ++   +    D+
Sbjct: 136 FFNLRKSKKRLGWFNNG-----EVETVARELGVEPSEVREMESRLAAQDATFEMPTDDDE 190

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
             + +   +VY  D    V    E      +  N L+ ++  L+ R + I  +R L +N 
Sbjct: 191 TGTSYTAPMVYLEDKASDVADHVEASNWEAHTNNRLSLALKSLDDRSQHIVRSRWLDDNK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL+ L+  + VS ER+RQ+E  A KK++ ++
Sbjct: 251 STLQELAETYSVSAERIRQLEKNAMKKLKAAV 282


>gi|319775860|ref|YP_004138348.1| RNA polymerase sigma-32 factor [Haemophilus influenzae F3047]
 gi|317450451|emb|CBY86667.1| RNA polymerase sigma-32 factor [Haemophilus influenzae F3047]
          Length = 281

 Score =  197 bits (501), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 111/283 (39%), Positives = 170/283 (60%), Gaps = 14/283 (4%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M ++  G I    YI    + PML  +EE  LA+R   H DL AA +L+ SHLR V+ +A
Sbjct: 7   MMLVPQGSI--EGYIRAANEYPMLTAEEEKELAERLYYHEDLDAAKKLILSHLRFVIHVA 64

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            GY GYGLP ++++ EGNIGLM+AVK+F+PE G RLA++++ WIKA + EY+LR+W +VK
Sbjct: 65  RGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLASFAVHWIKAEIHEYVLRNWRIVK 124

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           + TT  Q++LFFNLR+ K  L    +N     +V  +A +L VS+ +VI M  R++G + 
Sbjct: 125 VATTKAQRKLFFNLRKTKQRLGWFNEN-----EVDMVANELGVSKEDVIEMESRMSGADV 179

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV----LNPRERR 241
              L   +D   ++     +Y  D       E  E +N  +  T  + V    L+ R + 
Sbjct: 180 GFDL--PTDDAETETYSPALYLEDKSSNFAAEL-ENENFESQATEQLGVALQSLDARSQD 236

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           I +AR L +N  TL +L++++ VS ER+RQ+E  A KK++ ++
Sbjct: 237 IIKARWLDDNKATLHDLAAKYNVSAERIRQLETNALKKLKSAV 279


>gi|254673642|emb|CBA09200.1| RNA polymerase sigma-32 factor [Neisseria meningitidis alpha275]
          Length = 268

 Score =  197 bits (501), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 112/262 (42%), Positives = 167/262 (63%), Gaps = 9/262 (3%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +  I +G   L +YIH +  IPML ++EE  LA+R R  GDL+AA +L+ SHLR+VV IA
Sbjct: 7   LPAIQSGNGSLEQYIHTVNSIPMLSQEEETRLAER-RIKGDLNAAKQLILSHLRVVVSIA 65

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+ILR+W LV+
Sbjct: 66  RGYDGYGLNQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILRNWRLVR 125

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           + TT  Q++LFFNLR ++ +L     N L P++   IA  L V  SEV+ M  R+ G + 
Sbjct: 126 VATTKPQRKLFFNLRSMRKNL-----NALSPKEAQDIADDLGVKLSEVLEMEQRMTGHDI 180

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFE 244
                NS D++S    DWL  DHD +    + K+     +   L  +++ L+ R RRI E
Sbjct: 181 AIMADNSDDEDSFAPIDWLA-DHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRRIVE 239

Query: 245 ARRLQEN-PVTLENLSSEFEVS 265
           +R LQ++  +TL  L++E+ VS
Sbjct: 240 SRWLQDDGGLTLHQLAAEYGVS 261


>gi|170718627|ref|YP_001783826.1| RNA polymerase factor sigma-32 [Haemophilus somnus 2336]
 gi|168826756|gb|ACA32127.1| RNA polymerase, sigma 32 subunit, RpoH [Haemophilus somnus 2336]
          Length = 280

 Score =  197 bits (500), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 105/287 (36%), Positives = 171/287 (59%), Gaps = 12/287 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           MN++  ++++  +  +  YIH     PML  +EE  LA+R   H DL AA  L+ SHLR 
Sbjct: 1   MNKETQAMMLVPQGSIEGYIHAAYDYPMLTAEEEKELAERLYYHQDLDAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L   +D     ++V  +A +L VS+ +V+ M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFSD-----KEVDMVANELGVSKEDVLEMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNP 237
            G +    L    D++ +      +Y  D       E E         + +  +++ L+ 
Sbjct: 176 TGSDVGFDLPVDDDESYAP----ALYLEDKSSNFAAELENENFETQAADQVANALAELDE 231

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R R I ++R L +   TL +L++++ +S ERVRQ+E  A KK++ ++
Sbjct: 232 RSRDIIKSRWLDDEKATLHDLAAKYNISAERVRQLETNALKKLKSAV 278


>gi|332969043|gb|EGK08083.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Kingella kingae
           ATCC 23330]
          Length = 287

 Score =  197 bits (500), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 119/283 (42%), Positives = 174/283 (61%), Gaps = 8/283 (2%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           I +G   L +YIH +  IPML  +EE  LA+R +  GDL AA +L+ SHLR+VV IA GY
Sbjct: 7   IPSGHGSLEQYIHTVNNIPMLSLEEEVGLAER-QIKGDLEAAKKLILSHLRVVVSIARGY 65

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGL  ++++ EGNIGLM+AVK+++P  G RL ++++ WIKA + E+ILR+W LV++ T
Sbjct: 66  DGYGLNQADLIQEGNIGLMKAVKRYEPNHGARLFSFAVHWIKAEIHEFILRNWRLVRVAT 125

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN 187
           T  Q++LFFNLR ++  L A     L P++  +IA  L V  SEV+ M  R+ G D  L 
Sbjct: 126 TKPQRKLFFNLRSMRSSLSA-----LSPKEAQSIADDLGVKLSEVMEMEQRMTGRDIGLL 180

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           A  N  D  +    +WL        Q L  K     + + L  +++ L+ R RRI E R 
Sbjct: 181 ADNNDDDDAAFAPIEWLSDASHEPSQQLERKAHYALQTDGLQAALAQLDERSRRIVETRW 240

Query: 248 LQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           LQ E  +TL  L++E+ VS ER+RQIE +A +K++  + +Q +
Sbjct: 241 LQDEGALTLHELAAEYGVSAERIRQIEVKAMQKLKALLAEQAD 283


>gi|330447179|ref|ZP_08310829.1| alternative sigma factor RpoH [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
 gi|328491370|dbj|GAA05326.1| alternative sigma factor RpoH [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
          Length = 286

 Score =  197 bits (500), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 108/273 (39%), Positives = 164/273 (60%), Gaps = 8/273 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  YI  + + PML  + E  LA+R     D++AA  LV SHLR VV IA GY GYGLP
Sbjct: 15  SLDSYIQTVNRYPMLTPEREKELAERLHYDDDINAAKALVMSHLRFVVHIARGYSGYGLP 74

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           I++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W +VK+ TT  Q++
Sbjct: 75  IADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRK 134

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           LFFNLR+ K  L     NN   E+V  +A++L V   EV  M  RLA  +    + N  D
Sbjct: 135 LFFNLRKSKKRLGWF--NN---EEVNMVAEQLGVEPEEVREMESRLAAQDPTFEMQNDDD 189

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
              +       +  D    V +  EE     +  N L+++++ L+ R + I  +R L ++
Sbjct: 190 DRDAAPMAPAYFLEDKSSDVALTYEENNWENHANNRLSQALASLDERSQHIVRSRWLDDD 249

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL++L+  + VS ER+RQ+E  A KK+++++
Sbjct: 250 KSTLQDLADSYGVSAERIRQLEKNAMKKLKDAV 282


>gi|108757418|ref|YP_634007.1| RNA polymerase sigma-E factor [Myxococcus xanthus DK 1622]
 gi|108461298|gb|ABF86483.1| RNA polymerase sigma-E factor [Myxococcus xanthus DK 1622]
          Length = 278

 Score =  197 bits (500), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 111/280 (39%), Positives = 184/280 (65%), Gaps = 9/280 (3%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           + E+++ P+L ++EE  LA+ Y+E GD++AA+RLV S+LRLVVK+A  Y    L + ++V
Sbjct: 1   MAEVQRHPLLTREEELQLARHYKESGDVNAAYRLVASNLRLVVKLAHEYHRNPLSLLDLV 60

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EGNIGLMQAVKK+DPERG +L++Y+ WWI+A +  YI+ +W +VK+GTT  Q++LFF L
Sbjct: 61  QEGNIGLMQAVKKYDPERGVKLSSYAAWWIRAYILRYIMDNWKMVKLGTTEAQRKLFFKL 120

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNA-LINSSDKNS 197
           R+ +  L A       P+    +A++LNV+E +V+ M+ RL  DE S++A L N  D  +
Sbjct: 121 RQEQEKLIA-QGFEASPK---LLAERLNVTEQDVVEMDQRLGHDEMSIDAPLGNDDDSRT 176

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           ++   +L  +    ++ L  ++ +   R  L+     L  +ER IFE+R + + P+TL++
Sbjct: 177 TRADRYLPSNSMPADERLGAEQLKALFREKLSEFARTLEGKERFIFESRLVSDEPLTLQD 236

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQV---ELSSSP 294
           +  ++ VSRER RQIEA    ++++ +++Q+   +L +SP
Sbjct: 237 IGDKYGVSRERARQIEAALINRMRDFMREQIPDFDLVASP 276


>gi|172087778|ref|YP_205833.2| RNA polymerase, sigma-32 (sigma-H) factor [Vibrio fischeri ES114]
 gi|197336399|ref|YP_002157235.1| alternative sigma factor RpoH [Vibrio fischeri MJ11]
 gi|171902364|gb|AAW86945.2| RNA polymerase, sigma-32 (sigma-H) factor [Vibrio fischeri ES114]
 gi|197317889|gb|ACH67336.1| alternative sigma factor RpoH [Vibrio fischeri MJ11]
          Length = 286

 Score =  197 bits (500), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 107/287 (37%), Positives = 167/287 (58%), Gaps = 8/287 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+++  S+ V  +  +  Y+  +   PML   EE  LA+R     ++ AA  L+ SHLR 
Sbjct: 1   MSKEMYSMAVVSQDSIDSYLRSVNSYPMLTVAEERELAERLHYKEEIEAAKELILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A GY GYGLP+++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARGYSGYGLPLADLIQEGNVGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L    +      +V A+AK L V+ SEV  M  RL
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKNKKRLGWFNNG-----EVEAVAKDLGVAPSEVREMEARL 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNP 237
           A  +S        D     +   + Y  D Q  V    EE        N L  +++ L+ 
Sbjct: 176 AAQDSTFEAPAEDDDRDMAFTAPVYYLEDKQSDVAYSLEEDNWEDYTNNRLANAIATLDE 235

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R + I ++R L +   TL+ L+  ++VS ER+RQ+E  A KK+++++
Sbjct: 236 RSQHIVQSRWLADEKATLQELADTYQVSAERIRQLEKNAMKKLKDAV 282


>gi|227823777|ref|YP_002827750.1| RNA polymerase factor sigma-32 [Sinorhizobium fredii NGR234]
 gi|227342779|gb|ACP26997.1| RNA polymerase sigma factor, sigma-70 family [Sinorhizobium fredii
           NGR234]
          Length = 288

 Score =  197 bits (500), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 106/269 (39%), Positives = 166/269 (61%), Gaps = 3/269 (1%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           R I      P LE+ EE+ LA+ +R   D  A +++  SH+RLV+ +A  +R +GLP+ +
Sbjct: 9   RLIKIAMDAPYLERDEEHALAEAWRNDHDQEARNKIAMSHMRLVIAMAAKFRSFGLPMGD 68

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +V EG+IGL++A  +F+P R  R +TY+ WWI+A+MQ+++LR+WS+V+ GT++ QK LFF
Sbjct: 69  LVQEGHIGLLEAAARFEPSREVRFSTYATWWIRASMQDFVLRNWSIVRGGTSSAQKALFF 128

Query: 138 NLRRLKGHLQAITDNNLKPEQV-VAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDK 195
           NLRRL+  L A  D  L    +   IA  L VS ++V +M+ RL+G D SL A +   D 
Sbjct: 129 NLRRLRARL-AQGDRQLTSLAMHQEIAAALGVSLADVQTMDARLSGNDASLQAPVGHGDS 187

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
           +     D+L  D    ++ + +  + +  R  L  +++ L  RE +I  ARRL E+  TL
Sbjct: 188 DGGARLDFLPSDAPLPDEQVSDMIDGERARRWLQVALTQLTEREMKIIRARRLSEDGATL 247

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESI 284
           E L     +S+ERVRQIE RA +K++ ++
Sbjct: 248 EELGLALGISKERVRQIETRALEKLRTAL 276


>gi|323699411|ref|ZP_08111323.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio sp.
           ND132]
 gi|323459343|gb|EGB15208.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio
           desulfuricans ND132]
          Length = 375

 Score =  196 bits (499), Expect = 2e-48,   Method: Compositional matrix adjust.
 Identities = 114/278 (41%), Positives = 171/278 (61%), Gaps = 14/278 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR----GY 71
           L  Y+ EI + PMLE +EEY LAKR +E  D  AA +LV+SHLRLVVKIAM ++      
Sbjct: 95  LQLYLKEIARFPMLEPEEEYALAKRVQEDNDQDAAFKLVSSHLRLVVKIAMDFQRRWMQN 154

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL   +++ EGN+GL++AV KFDPE+G + + Y+ +WIKA + +YI+ +W +VKIGTT  
Sbjct: 155 GL---DLIQEGNVGLLKAVTKFDPEKGIKFSYYAAFWIKAYILKYIMDNWRMVKIGTTQT 211

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALI 190
           Q++LF+NL + +  LQ +      P    A++++L VSE+E+  M+ RL+  D SLN  +
Sbjct: 212 QRKLFYNLNKERQRLQTL---GFDP-STEALSERLGVSEAEIDEMDQRLSKNDMSLNTPL 267

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
              D + +   D+L     G E+ +   +      N +    + LN +E  I + R L +
Sbjct: 268 --GDDSDTTRMDFLPSLAPGVEESIANDQIVDLLLNNIREIRASLNDKEVAILDRRLLSD 325

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +PVTL  +  EF V+RERVRQIEAR   K++E +  +V
Sbjct: 326 DPVTLREIGEEFGVTRERVRQIEARLMAKIREHLTDKV 363


>gi|223041647|ref|ZP_03611844.1| RNA polymerase sigma-32 factor [Actinobacillus minor 202]
 gi|223017511|gb|EEF15925.1| RNA polymerase sigma-32 factor [Actinobacillus minor 202]
          Length = 321

 Score =  196 bits (499), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 104/270 (38%), Positives = 163/270 (60%), Gaps = 6/270 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI    + P+L   +E  LA+RY    D+ AA +L+ SH+R V+ IA GY GYGLP+
Sbjct: 53  LESYIRMANQYPILTADQEKELAERYYYDEDVEAAKQLILSHMRFVIHIARGYLGYGLPL 112

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AVK+FDP  G RL ++++ W+KA + EY+LR+W +VK+ TT  Q++L
Sbjct: 113 ADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWVKAEIHEYVLRNWRIVKVATTKAQRKL 172

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR+ K  L    +     E++  +A  L VSE EV  M  R+ G +    L +  D+
Sbjct: 173 FFNLRKNKNRLAWFNE-----EEIKRVAHDLGVSEEEVREMESRMTGQDLGFDLPSGDDE 227

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENPVT 254
           + +      + D+       +E EE        L  ++S L+ R + I + R L EN +T
Sbjct: 228 DEAYTPSMYLEDNSSNFADELEDEEHTGEATAQLAYALSTLDERSQDIIKTRWLDENKLT 287

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L +L++++++S ERVRQ+E  A KK++ +I
Sbjct: 288 LHDLAAKYQISAERVRQLENAALKKIKNAI 317


>gi|121999080|ref|YP_001003867.1| RNA polymerase sigma-32 subunit RpoH [Halorhodospira halophila SL1]
 gi|121590485|gb|ABM63065.1| RNA polymerase, sigma 32 subunit, RpoH [Halorhodospira halophila
           SL1]
          Length = 287

 Score =  196 bits (499), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 106/268 (39%), Positives = 167/268 (62%), Gaps = 7/268 (2%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           YI  + +IP+L+  EEY LA+R +  GDL AA +LV SHLR VV +A GYRGYGL + ++
Sbjct: 23  YIQAVSQIPVLDADEEYELARRCQYEGDLDAARQLVLSHLRFVVHVARGYRGYGLALGDL 82

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM+AVK+FDP+ G RL ++++ WI+A + E+ILR+W +VK+ TT  Q++LFFN
Sbjct: 83  IQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIRAEIHEFILRNWRIVKVATTKAQRKLFFN 142

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  K  L  +T      E+V A+A+ L V    V+ M  RL+G D   + L++  D+  
Sbjct: 143 LRGAKKRLGWMT-----REEVNAVAEDLGVQPETVLEMESRLSGQDLGFDPLVSEEDEEQ 197

Query: 198 SQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           ++     + D       ++E  +   ++ + L +++  L+ R + I  AR L+E   TL+
Sbjct: 198 ARAPVAYLEDRRFDPAEVVESSDWGTHQDDSLHQALGQLDERSQNILRARWLEEERQTLQ 257

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
            L+  + VS ER+RQ+E  A  K++ ++
Sbjct: 258 ELAERYGVSAERIRQLEKNAISKLRGAV 285


>gi|262273588|ref|ZP_06051402.1| RNA polymerase sigma-32 factor [Grimontia hollisae CIP 101886]
 gi|262222566|gb|EEY73877.1| RNA polymerase sigma-32 factor [Grimontia hollisae CIP 101886]
          Length = 287

 Score =  196 bits (499), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 112/276 (40%), Positives = 164/276 (59%), Gaps = 15/276 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ ++   PML   EE  LA+R     DL AA  L+ SHLR VV IA GY GYGLPI
Sbjct: 16  LDSYLQQVNSYPMLTADEERELAERLHYEEDLDAAKSLILSHLRFVVHIARGYSGYGLPI 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           S++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W +VK+ TT  Q++L
Sbjct: 76  SDLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR+ K  L          E+V  +A++L V  +EV  M  RLA  D   +A +   +
Sbjct: 136 FFNLRKSKKRL-----GWFNAEEVNMVAEQLGVDAAEVREMESRLAAQDAGFDAGVGDDE 190

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEK-----EERKNRRNMLTRSMSVLNPRERRIFEARRL- 248
           +        + Y  D    +         E+  NRR  L ++MS L+ R + I  +R L 
Sbjct: 191 REGGAVAP-VFYLEDKSSDIATNLESQNWEDHTNRR--LAQAMSGLDARSQHIIRSRWLD 247

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +N VTL+ L+  ++VS ER+RQ+E  A +K+++++
Sbjct: 248 DDNKVTLQELADHYQVSAERIRQLEKNAMRKLKDAV 283


>gi|240948113|ref|ZP_04752523.1| RNA polymerase factor sigma-32 [Actinobacillus minor NM305]
 gi|240297593|gb|EER48085.1| RNA polymerase factor sigma-32 [Actinobacillus minor NM305]
          Length = 321

 Score =  196 bits (499), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 104/270 (38%), Positives = 163/270 (60%), Gaps = 6/270 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI    + P+L   +E  LA+RY    D+ AA +L+ SH+R V+ IA GY GYGLP+
Sbjct: 53  LESYIRMANQYPILTADQEKELAERYYYDEDVEAAKQLILSHMRFVIHIARGYLGYGLPL 112

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AVK+FDP  G RL ++++ W+KA + EY+LR+W +VK+ TT  Q++L
Sbjct: 113 ADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWVKAEIHEYVLRNWRIVKVATTKAQRKL 172

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR+ K  L    +     E++  +A  L VSE EV  M  R+ G +    L +  D+
Sbjct: 173 FFNLRKNKNRLAWFNE-----EEIKRVAHDLGVSEEEVREMESRMTGQDLGFDLPSGDDE 227

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENPVT 254
           + +      + D+       +E EE        L  ++S L+ R + I + R L EN +T
Sbjct: 228 DEAYTPSMYLEDNSSNFADELEDEEHTGEATAQLAYALSTLDERSQDIIKTRWLDENKLT 287

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L +L++++++S ERVRQ+E  A KK++ +I
Sbjct: 288 LHDLAAKYQISAERVRQLENAALKKIKNAI 317


>gi|300114350|ref|YP_003760925.1| RNA polymerase sigma 32 subunit RpoH [Nitrosococcus watsonii C-113]
 gi|299540287|gb|ADJ28604.1| RNA polymerase, sigma 32 subunit, RpoH [Nitrosococcus watsonii
           C-113]
          Length = 287

 Score =  196 bits (499), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 109/271 (40%), Positives = 169/271 (62%), Gaps = 13/271 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y      IP+L   +E  LA R R++ DL AA +LV SHLR V++IA GY GYGLP+
Sbjct: 20  LNTYCQNAHSIPVLSADQERSLALRLRQYNDLEAARQLVLSHLRFVIRIARGYNGYGLPL 79

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AVK+FDPE+G RL ++++ WI+A + E+ILR+W +VK+ TT  Q++L
Sbjct: 80  ADLIQEGNIGLMKAVKRFDPEQGVRLVSFAVHWIRAEIHEFILRNWRIVKVATTKAQRKL 139

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR  K  L       L  ++V  +A+ L +S  +V+ M  RL+  ++     N+ + 
Sbjct: 140 FFNLRSAKKRL-----GWLNRKEVNEVAQDLGISPKQVMEMEARLSSQDTPFDGTNTEES 194

Query: 196 NSSQWQDWLVYDHD-----GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
            +S     + Y  D      Q+  L+++E    +R  L +++ VL+ R R I   R LQE
Sbjct: 195 ENSLPAP-MAYLADPSADPAQKMELLDQENYYGQR--LRQALEVLDLRSRTIINRRWLQE 251

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           N  TL  L++E+++S ER+RQ+E  A KK++
Sbjct: 252 NKSTLHELAAEYQISAERIRQLENNAIKKMR 282


>gi|329123705|ref|ZP_08252265.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Haemophilus
           aegyptius ATCC 11116]
 gi|327469904|gb|EGF15369.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Haemophilus
           aegyptius ATCC 11116]
          Length = 281

 Score =  196 bits (499), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 107/280 (38%), Positives = 168/280 (60%), Gaps = 8/280 (2%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M ++  G I    YI    + PML  +EE  LA+R   H DL AA +L+ SHLR V+ +A
Sbjct: 7   MMLVPQGSI--EGYIRAANEYPMLTAEEEKELAERLYYHEDLDAAKKLILSHLRFVIHVA 64

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            GY GYGLP ++++ EGNIGLM+AVK+F+PE G RLA++++ WIKA + EY+LR+W +VK
Sbjct: 65  RGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLASFAVHWIKAEIHEYVLRNWRIVK 124

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           + TT  Q++LFFNLR+ K  L    +N     +V  +A +L VS+ +VI M  R++G + 
Sbjct: 125 VATTKAQRKLFFNLRKTKQRLGWFNEN-----EVDMVANELGVSKEDVIEMESRMSGADV 179

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN-MLTRSMSVLNPRERRIFE 244
              L     +  +      + D        +E E  +++    L  ++  L+ R + I +
Sbjct: 180 GFDLPTDDAETETYSPALYLEDKSSNFAAELENENFESQATEQLGAALQSLDARSQDIIK 239

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           AR L +N  TL +L++++ VS ER+RQ+E  A KK++ ++
Sbjct: 240 ARWLDDNKATLHDLAAKYNVSAERIRQLETNALKKLKSAV 279


>gi|283852956|ref|ZP_06370215.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio sp.
           FW1012B]
 gi|283571646|gb|EFC19647.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio sp.
           FW1012B]
          Length = 342

 Score =  196 bits (499), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 108/279 (38%), Positives = 177/279 (63%), Gaps = 6/279 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLP 74
           L  Y+ EI K PML+ +EE  LA+R R+ GD  AA RL++SHLRLVVKIAM + R +   
Sbjct: 62  LHLYLREIGKFPMLKPEEEQELARRVRDLGDQKAAFRLISSHLRLVVKIAMDFQRRWMQN 121

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++ EGN+GLM+AV KFDP++G + + Y+ +WIKA + +YI+ +W +VKIGTT  Q++
Sbjct: 122 VLDLIQEGNVGLMRAVTKFDPDKGIKFSYYAAYWIKAYILKYIMDNWRMVKIGTTQAQRK 181

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           LF+NL + +  LQ +      P     +++ LNV+ES+++ M+ RL+G++ L+  +   D
Sbjct: 182 LFYNLNKERHRLQTL---GFDP-SASQLSQALNVTESDIVEMDQRLSGND-LSLDMTLGD 236

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
            ++S   D+L     G E++L   E        +      LN +E  + + R L ++P T
Sbjct: 237 DSTSTRLDFLPALTPGIEEILAGDEISHQLDKHIQTIRPKLNEKELDLLDNRILSDSPAT 296

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           L  + +++ ++RERVRQIEAR  +K++E + +++E  SS
Sbjct: 297 LREIGAKYGITRERVRQIEARLLEKLKEHLSRRIEDFSS 335


>gi|226952985|ref|ZP_03823449.1| sigma H (sigma 32) factor of RNA polymerase [Acinetobacter sp. ATCC
           27244]
 gi|294650567|ref|ZP_06727924.1| RNA polymerase factor sigma-32 [Acinetobacter haemolyticus ATCC
           19194]
 gi|226836306|gb|EEH68689.1| sigma H (sigma 32) factor of RNA polymerase [Acinetobacter sp. ATCC
           27244]
 gi|292823564|gb|EFF82410.1| RNA polymerase factor sigma-32 [Acinetobacter haemolyticus ATCC
           19194]
          Length = 289

 Score =  196 bits (498), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 109/273 (39%), Positives = 162/273 (59%), Gaps = 7/273 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + L  YI  + +IP+L  ++E  LA+RY    DL AA  LV SHLR VV IA  Y GYGL
Sbjct: 19  VNLGAYISTVNQIPILTAEQEKELAERYYYDQDLDAAKLLVMSHLRFVVHIARSYAGYGL 78

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P  +++ EGN+GLM+AVK+FDP  G RL ++++ WIKA + EY++R+W +VKI TT  Q+
Sbjct: 79  PQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVKIATTKAQR 138

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINS 192
           +LFFNLR LK      +   L  E+  AIA  LNV+  +V+ M  RL A D +  A  + 
Sbjct: 139 KLFFNLRSLKK-----SSKRLTLEEAQAIANDLNVTAEQVLEMEGRLTAYDAAFEAQGDD 193

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN-MLTRSMSVLNPRERRIFEARRLQEN 251
            D          + D+      L E+E+ + +    L ++M  L+ R R I + R L ++
Sbjct: 194 DDDTPHTAPALYLEDNRYDPARLAEEEDYEAQSTAALHQAMDQLDDRSRNILQRRWLDDD 253

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL  L++E+ VS ER+RQ+E  A +K++ ++
Sbjct: 254 KSTLHELAAEYNVSAERIRQLEKNAMEKIKTAM 286


>gi|145639818|ref|ZP_01795419.1| RNA polymerase sigma factor [Haemophilus influenzae PittII]
 gi|145271036|gb|EDK10952.1| RNA polymerase sigma factor [Haemophilus influenzae PittII]
 gi|309750314|gb|ADO80298.1| RNA polymerase sigma-32 factor [Haemophilus influenzae R2866]
          Length = 281

 Score =  196 bits (498), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 106/280 (37%), Positives = 168/280 (60%), Gaps = 8/280 (2%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M ++  G I    YI    + PML  +EE  LA+R   H DL AA +L+ SHLR V+ +A
Sbjct: 7   MMLVPQGSI--EGYIRAANEYPMLTAEEEKELAERLYYHEDLDAAKKLILSHLRFVIHVA 64

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W +VK
Sbjct: 65  RGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVK 124

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           + TT  Q++LFFNLR+ K  L    +N     +V  +A +L VS+ +VI M  R++G + 
Sbjct: 125 VATTKAQRKLFFNLRKTKQRLGWFNEN-----EVDMVANELGVSKEDVIEMESRMSGADV 179

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN-MLTRSMSVLNPRERRIFE 244
              L     +  +      + D        +E E  +++    L+ ++  L+ R + I +
Sbjct: 180 GFDLPTDDAETETYSPSLYLEDKSSNFAAELENENFESQATEQLSAALQSLDARSQDIIK 239

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           AR L +N  TL +L++++ VS ER+RQ+E  A KK++ ++
Sbjct: 240 ARWLDDNKATLHDLAAKYNVSAERIRQLETNALKKLKSAV 279


>gi|239906748|ref|YP_002953489.1| RNA polymerase sigma factor [Desulfovibrio magneticus RS-1]
 gi|239796614|dbj|BAH75603.1| RNA polymerase sigma factor [Desulfovibrio magneticus RS-1]
          Length = 348

 Score =  196 bits (498), Expect = 3e-48,   Method: Compositional matrix adjust.
 Identities = 107/279 (38%), Positives = 178/279 (63%), Gaps = 6/279 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLP 74
           L  Y+ EI K PML+ +EE  LA+R R+  D  AA RL++SHLRLVVKIAM + R +   
Sbjct: 68  LQLYLREIGKFPMLKPEEEQELARRVRDANDQKAAFRLISSHLRLVVKIAMDFQRRWMQN 127

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++ EGN+GLM+AV KFDP++G + + Y+ +WIKA + +YI+ +W +VKIGTT  Q++
Sbjct: 128 VLDLIQEGNVGLMRAVTKFDPDKGIKFSYYAAYWIKAYILKYIMDNWRMVKIGTTQAQRK 187

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           LF+NL + +  LQ++      P     +++ LNV+ES+++ M+ RL+G++ L+  ++  D
Sbjct: 188 LFYNLNKERQRLQSL---GFDP-SAAQLSQALNVTESDIVEMDQRLSGND-LSLDVSLGD 242

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
             +S   D+L     G E++L   E        +      LN +E  + + R L ++PVT
Sbjct: 243 DTTSTRLDFLPALTPGIEEILAGDEISHQLDKHIQSIRPKLNEKEIELLDNRILSDSPVT 302

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           L  + +++ ++RERVRQIE+R  +K+++ + K++E  SS
Sbjct: 303 LREIGAKYGITRERVRQIESRLLEKLKDHLSKRIEDFSS 341


>gi|262372449|ref|ZP_06065728.1| alternative sigma factor RpoH [Acinetobacter junii SH205]
 gi|262312474|gb|EEY93559.1| alternative sigma factor RpoH [Acinetobacter junii SH205]
          Length = 289

 Score =  196 bits (498), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 109/270 (40%), Positives = 161/270 (59%), Gaps = 7/270 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + L  YI  + +IP+L  ++E  LA+RY    DL AA  LV SHLR VV IA  Y GYGL
Sbjct: 19  VNLGAYISTVNQIPILTAEQEKELAERYYYDQDLDAAKLLVMSHLRFVVHIARSYAGYGL 78

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P  +++ EGN+GLM+AVK+FDP  G RL ++++ WIKA + EY++R+W +VKI TT  Q+
Sbjct: 79  PQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVKIATTKAQR 138

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINS 192
           +LFFNLR LK      +   L  E+  +IA  LNV+  +V+ M  RL A D +  A  + 
Sbjct: 139 KLFFNLRSLKK-----SSKRLTLEEAQSIANDLNVTPEQVLEMEGRLTAYDAAFEAQGDD 193

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPRERRIFEARRLQEN 251
            D          + D+      LIE+E+ + +  + L  +M  L+ R R I + R L ++
Sbjct: 194 DDDTPHTAPALYLEDNRYDPARLIEEEDYEEQSTSALHEAMDQLDDRSRNILQRRWLDDD 253

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             TL  L++E+ VS ER+RQ+E  A +K++
Sbjct: 254 KSTLHELAAEYNVSAERIRQLEKNAMEKIK 283


>gi|332289156|ref|YP_004420008.1| RNA polymerase factor sigma-32 [Gallibacterium anatis UMN179]
 gi|330432052|gb|AEC17111.1| RNA polymerase factor sigma-32 [Gallibacterium anatis UMN179]
          Length = 281

 Score =  196 bits (498), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 109/285 (38%), Positives = 168/285 (58%), Gaps = 15/285 (5%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           +NM ++  G   L  YI    + PML  +EE  LA+R   H D+ AA +L+ SHLR V+ 
Sbjct: 6   QNMMLVPQG--SLEGYIRAANEYPMLTAEEEKELAERLYYHQDVDAAKKLILSHLRFVIH 63

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA GY GYGLP ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W +
Sbjct: 64  IARGYSGYGLPQADLIQEGNVGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRI 123

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG- 182
           VK+ TT  Q++LFFNLR+ K  L     N     +V  +A +L VS  +V  M  R++G 
Sbjct: 124 VKVATTKAQRKLFFNLRKTKQRLGWFNAN-----EVDMVANELGVSAEDVQEMESRMSGI 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNPRE 239
           D + +   + S++  S      +Y  D       E EE        + L+ ++  L+ R 
Sbjct: 179 DMAFDLPTDDSEETYSP----ALYLEDKSSNFAAELEEENFENQATDQLSEALEQLDERS 234

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R I + R L +N  TL+ L+  + VS ER+RQ+E+ A KK++ ++
Sbjct: 235 RHIIQTRWLDDNKATLQELADHYGVSAERIRQLESNALKKLRNAV 279


>gi|209696299|ref|YP_002264230.1| RNA polymerase factor sigma-32 [Aliivibrio salmonicida LFI1238]
 gi|208010253|emb|CAQ80584.1| RNA polymerase sigma-32 factor [Aliivibrio salmonicida LFI1238]
          Length = 286

 Score =  196 bits (497), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 106/287 (36%), Positives = 169/287 (58%), Gaps = 8/287 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+++  S+ V  +  +  Y+  + + PML  ++E  LA+R     ++ AA  L+ SHLR 
Sbjct: 1   MSKEMYSMAVVSQDSIDSYLRSVNRYPMLTVEKERDLAERLHYKEEIEAAKELILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A GY GYGLP+++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARGYSGYGLPLADLIQEGNVGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L    +      +V A+AK L VS SEV  M  RL
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKNKKRLGWFNNG-----EVEAVAKDLGVSPSEVREMESRL 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNP 237
           A  +S        D     +   + Y  D Q  +    EE        N L  +++ L+ 
Sbjct: 176 AAQDSTFEAPTEDDDRDMAFTAPVYYLEDKQSDIAHSLEEDNWEDYTNNRLANAIATLDD 235

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R + I ++R L +   TL+ L++ + VS ER+RQ+E  A KK+++++
Sbjct: 236 RSQHIVQSRWLTDEKTTLQELANTYSVSAERIRQLEKNAMKKLKDAV 282


>gi|293609550|ref|ZP_06691852.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|292828002|gb|EFF86365.1| conserved hypothetical protein [Acinetobacter sp. SH024]
          Length = 288

 Score =  196 bits (497), Expect = 4e-48,   Method: Compositional matrix adjust.
 Identities = 108/273 (39%), Positives = 162/273 (59%), Gaps = 7/273 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + L  YI  + +IP+L  ++E  LA+RY    DL AA  LV SHLR VV IA  Y GYGL
Sbjct: 18  VNLGAYISTVNQIPILTAEQEKELAERYYYDQDLDAAKMLVMSHLRFVVHIARSYAGYGL 77

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P  +++ EGN+GLM+AVK+FDP  G RL ++++ WIKA + EY++R+W +VKI TT  Q+
Sbjct: 78  PQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVKIATTKAQR 137

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINS 192
           +LFFNLR LK   + +T      E+  +IA  LNV+  +V+ M  RL A D +  A  + 
Sbjct: 138 KLFFNLRSLKKSSKKLT-----LEEAQSIANDLNVTPEQVLEMEGRLTAYDAAFEAQGDD 192

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
            D          + D+      L+E E+  +   + L  +M  L+ R R I + R L ++
Sbjct: 193 DDDTPHTAPALYLEDNRYDPARLVENEDWEEQSTSALHDAMDQLDDRSRNILQRRWLDDD 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL  L++E+ VS ER+RQ+E  A +K++ ++
Sbjct: 253 KSTLHELAAEYNVSAERIRQLEKNAMEKIKTAM 285


>gi|27364575|ref|NP_760103.1| RNA polymerase factor sigma-32 [Vibrio vulnificus CMCP6]
 gi|37678299|ref|NP_932908.1| RNA polymerase factor sigma-32 [Vibrio vulnificus YJ016]
 gi|320154977|ref|YP_004187356.1| RNA polymerase sigma factor RpoH [Vibrio vulnificus MO6-24/O]
 gi|29611852|sp|Q8DD54|RP32_VIBVU RecName: Full=RNA polymerase sigma-32 factor
 gi|27360694|gb|AAO09630.1| alternative sigma factor RpoH [Vibrio vulnificus CMCP6]
 gi|37197038|dbj|BAC92879.1| RNA polymerase sigma-32 factor [Vibrio vulnificus YJ016]
 gi|319930289|gb|ADV85153.1| RNA polymerase sigma factor RpoH [Vibrio vulnificus MO6-24/O]
          Length = 285

 Score =  196 bits (497), Expect = 5e-48,   Method: Compositional matrix adjust.
 Identities = 109/272 (40%), Positives = 163/272 (59%), Gaps = 8/272 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  +   PML   EE  LA+R    G++ AA  L+ SHLR VV +A GY GYGLP+
Sbjct: 16  LDGYIRSVNSYPMLTADEERDLAERLHYKGEIEAAKGLILSHLRFVVHVARGYSGYGLPM 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           +++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W +VKI TT  Q++L
Sbjct: 76  ADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR+ K  L    +      +V  +A++L V  +EV  M  RLA  +S   L N  D 
Sbjct: 136 FFNLRKSKKRLGWFNNG-----EVETVARELGVEPAEVREMESRLAAVDSTFDLPNEEDD 190

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERK---NRRNMLTRSMSVLNPRERRIFEARRLQENP 252
           +SS     ++Y  D    V    E +    +  N L  +++ L+ R + I  +R L ++ 
Sbjct: 191 SSSVSTAPVLYLEDKSSDVADNLEAQNWEAHTNNRLAMALASLDERSQHIVRSRWLDDDK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL++L+  + VS ER+RQ+E  A KK++ ++
Sbjct: 251 ATLQDLAEMYGVSAERIRQLEKNAMKKLKMAV 282


>gi|126728120|ref|ZP_01743936.1| RNA polymerase sigma-32 factor [Sagittula stellata E-37]
 gi|126711085|gb|EBA10135.1| RNA polymerase sigma-32 factor [Sagittula stellata E-37]
          Length = 277

 Score =  196 bits (497), Expect = 5e-48,   Method: Compositional matrix adjust.
 Identities = 105/269 (39%), Positives = 173/269 (64%), Gaps = 8/269 (2%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K  +L+ + E  LA  +R+  D +A HRL+ +++RL + +A  ++ YG P+++++ E  +
Sbjct: 2   KAELLDAETELRLAYAWRDEKDEAALHRLIQAYMRLAISMAAKFKRYGAPMNDLIQEAGL 61

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFN+RR++ 
Sbjct: 62  GLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKALFFNMRRVQA 121

Query: 145 HL----QAITDNNLKPEQV-VAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSS 198
            L    QAI    L   Q+   IA ++ V   +V  M  RL+G D SLNA   S +    
Sbjct: 122 RLEREAQAIG-AQLDSHQLRHMIASEIGVPLRDVEMMEGRLSGSDFSLNA-TQSVEDEGR 179

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           +W D L  D     +++    + +  R+ L ++M  LN RER I   R+L++ P TLE+L
Sbjct: 180 EWIDTLEDDSAHGAEIVENSHDTECLRDWLVQAMGSLNERERFIVRERKLRDEPRTLESL 239

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +E  +S+ERVRQ+EA AF K++++++ Q
Sbjct: 240 GNELGLSKERVRQLEAAAFGKMRKALEAQ 268


>gi|145631055|ref|ZP_01786830.1| RNA polymerase factor sigma-32 [Haemophilus influenzae R3021]
 gi|148827424|ref|YP_001292177.1| RNA polymerase factor sigma-32 [Haemophilus influenzae PittGG]
 gi|144983340|gb|EDJ90822.1| RNA polymerase factor sigma-32 [Haemophilus influenzae R3021]
 gi|148718666|gb|ABQ99793.1| RNA polymerase sigma factor [Haemophilus influenzae PittGG]
 gi|301168923|emb|CBW28517.1| RNA polymerase, sigma 32 (sigma H) factor [Haemophilus influenzae
           10810]
          Length = 281

 Score =  196 bits (497), Expect = 5e-48,   Method: Compositional matrix adjust.
 Identities = 106/280 (37%), Positives = 168/280 (60%), Gaps = 8/280 (2%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M ++  G I    YI    + PML  +EE  LA+R   H DL AA +L+ SHLR V+ +A
Sbjct: 7   MMLVPQGSI--EGYIRAANEYPMLTAEEEKELAERLYYHEDLDAAKKLILSHLRFVIHVA 64

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W +VK
Sbjct: 65  RGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVK 124

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           + TT  Q++LFFNLR+ K  L    +N     +V  +A +L VS+ +VI M  R++G + 
Sbjct: 125 VATTKAQRKLFFNLRKTKQRLGWFNEN-----EVDMVANELGVSKEDVIEMESRMSGADV 179

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN-MLTRSMSVLNPRERRIFE 244
              L     +  +      + D        +E E  +++    L+ ++  L+ R + I +
Sbjct: 180 GFDLPTDDAETETYSPALYLEDKSSNFAAELENENFESQATEQLSAALQSLDARSQDIIK 239

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           AR L +N  TL +L++++ VS ER+RQ+E  A KK++ ++
Sbjct: 240 ARWLDDNKATLHDLAAKYNVSAERIRQLETNALKKLKSAV 279


>gi|113461681|ref|YP_719750.1| RNA polymerase factor sigma-32 [Haemophilus somnus 129PT]
 gi|112823724|gb|ABI25813.1| RNA polymerase, sigma 32 subunit, RpoH [Haemophilus somnus 129PT]
          Length = 280

 Score =  195 bits (496), Expect = 5e-48,   Method: Compositional matrix adjust.
 Identities = 104/287 (36%), Positives = 171/287 (59%), Gaps = 12/287 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           MN++  ++++  +  +  YIH     PML  +EE  LA+R   H DL AA  L+ SHLR 
Sbjct: 1   MNKETQAMMLVPQGSIEGYIHAAYDYPMLTAEEEKELAERLYYHQDLDAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L   +D     ++V  +A +L VS+ +V+ M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFSD-----KEVDMVANELGVSKEDVLEMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNP 237
            G +    L    D++ +      +Y  D       E E         + +  +++ L+ 
Sbjct: 176 TGSDVGFDLPVDDDESYAP----ALYLEDKSSNFAAELENENFETQAADQVANALAELDE 231

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R + I ++R L +   TL +L++++ +S ERVRQ+E  A KK++ ++
Sbjct: 232 RSQDIIKSRWLDDEKATLHDLAAKYNISAERVRQLETNALKKLKSAV 278


>gi|154707560|ref|YP_001423635.1| RNA polymerase factor sigma-32 [Coxiella burnetii Dugway 5J108-111]
 gi|154356846|gb|ABS78308.1| RNA polymerase sigma-32 factor [Coxiella burnetii Dugway 5J108-111]
          Length = 288

 Score =  195 bits (496), Expect = 5e-48,   Method: Compositional matrix adjust.
 Identities = 109/277 (39%), Positives = 169/277 (61%), Gaps = 11/277 (3%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           G IG   YI  + +IP+L  +EE+ LA ++R+  DL AA +LV SHLR VV+IA GY GY
Sbjct: 16  GSIG--SYISWVNRIPLLSAEEEHDLANKFRQSNDLEAARKLVLSHLRFVVRIARGYSGY 73

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL  ++++ EGNIGLM+AVK+FDP+ G RLA++++ WI+A + E+IL++W +VKI TT  
Sbjct: 74  GLSQADLIQEGNIGLMKAVKRFDPQVGVRLASFAVHWIRAEIHEFILKNWRIVKIATTKA 133

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALI 190
           Q++LFFNLR+        +D+     +  A+A++LNVS  +V  M  RL + DE+ +   
Sbjct: 134 QRKLFFNLRKHAKKRGWFSDH-----EAFALAEELNVSTKDVRQMEERLNSYDEAFDGAD 188

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEER---KNRRNMLTRSMSVLNPRERRIFEARR 247
             SD  +  W     Y  D +    ++ E      ++ + L  +M  L+ R R I   R 
Sbjct: 189 EESDSGTPSWGAPAHYLEDKRYNPALQLERSNWADDQEHRLHNAMQSLDDRSRDILYQRW 248

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L E   TL  L++++ VS ER+RQ+E  A +K++ ++
Sbjct: 249 LSEKKSTLHELAAQYAVSAERIRQLEKNAMQKIRTAM 285


>gi|325122820|gb|ADY82343.1| RNA polymerase factor sigma-32 [Acinetobacter calcoaceticus PHEA-2]
          Length = 276

 Score =  195 bits (496), Expect = 6e-48,   Method: Compositional matrix adjust.
 Identities = 108/273 (39%), Positives = 162/273 (59%), Gaps = 7/273 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + L  YI  + +IP+L  ++E  LA+RY    DL AA  LV SHLR VV IA  Y GYGL
Sbjct: 6   VNLGAYISTVNQIPILTAEQEKELAERYYYDQDLDAAKMLVMSHLRFVVHIARSYAGYGL 65

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P  +++ EGN+GLM+AVK+FDP  G RL ++++ WIKA + EY++R+W +VKI TT  Q+
Sbjct: 66  PQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVKIATTKAQR 125

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINS 192
           +LFFNLR LK   + +T      E+  +IA  LNV+  +V+ M  RL A D +  A  + 
Sbjct: 126 KLFFNLRSLKKSSKKLT-----LEEAQSIANDLNVTPEQVLEMEGRLTAYDAAFEAQGDD 180

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
            D          + D+      L+E E+  +   + L  +M  L+ R R I + R L ++
Sbjct: 181 DDDTPHTAPALYLEDNRYDPARLVENEDWEEQSTSALHDAMDQLDDRSRNILQRRWLDDD 240

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL  L++E+ VS ER+RQ+E  A +K++ ++
Sbjct: 241 KSTLHELAAEYNVSAERIRQLEKNAMEKIKTAM 273


>gi|145637130|ref|ZP_01792792.1| RNA polymerase sigma factor [Haemophilus influenzae PittHH]
 gi|145640200|ref|ZP_01795784.1| RNA polymerase sigma factor [Haemophilus influenzae R3021]
 gi|229846357|ref|ZP_04466465.1| RNA polymerase factor sigma-32 [Haemophilus influenzae 7P49H1]
 gi|145269575|gb|EDK09516.1| RNA polymerase sigma factor [Haemophilus influenzae PittHH]
 gi|145274786|gb|EDK14648.1| RNA polymerase sigma factor [Haemophilus influenzae 22.4-21]
 gi|229810450|gb|EEP46168.1| RNA polymerase factor sigma-32 [Haemophilus influenzae 7P49H1]
 gi|309972570|gb|ADO95771.1| RNA polymerase sigma-32 factor [Haemophilus influenzae R2846]
          Length = 281

 Score =  195 bits (496), Expect = 6e-48,   Method: Compositional matrix adjust.
 Identities = 106/280 (37%), Positives = 167/280 (59%), Gaps = 8/280 (2%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M ++  G I    YI    + PML  +EE  LA+R   H DL AA +L+ SHLR V+ +A
Sbjct: 7   MMLVPQGSI--EGYIRAANEYPMLTAEEEKELAERLYYHEDLDAAKKLILSHLRFVIHVA 64

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W +VK
Sbjct: 65  RGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVK 124

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           + TT  Q++LFFNLR+ K  L    +N     +V  +A +L VS+ +VI M  R++G + 
Sbjct: 125 VATTKAQRKLFFNLRKTKQRLGWFNEN-----EVDMVANELGVSKEDVIEMESRMSGADV 179

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN-MLTRSMSVLNPRERRIFE 244
              L     +  +      + D        +E E  +++    L  ++  L+ R + I +
Sbjct: 180 GFDLPTDDAETETYSPALYLEDKSSNFAAALENENFESQATEQLGAALQSLDARSQDIIK 239

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           AR L +N  TL +L++++ VS ER+RQ+E  A KK++ ++
Sbjct: 240 ARWLDDNKATLHDLAAKYNVSAERIRQLETNALKKLKSAV 279


>gi|299769389|ref|YP_003731415.1| RNA polymerase factor sigma-32 [Acinetobacter sp. DR1]
 gi|298699477|gb|ADI90042.1| RNA polymerase factor sigma-32 [Acinetobacter sp. DR1]
          Length = 288

 Score =  195 bits (496), Expect = 6e-48,   Method: Compositional matrix adjust.
 Identities = 108/270 (40%), Positives = 159/270 (58%), Gaps = 7/270 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + L  YI  + +IP+L  ++E  LA+RY    DL AA  LV SHLR VV IA  Y GYGL
Sbjct: 18  VNLGAYISTVNQIPILTAEQEKELAERYYYDQDLDAAKMLVMSHLRFVVHIARSYAGYGL 77

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P  +++ EGN+GLM+AVK+FDP  G RL ++++ WIKA + EY++R+W +VKI TT  Q+
Sbjct: 78  PQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVKIATTKAQR 137

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINS 192
           +LFFNLR LK      +   L  E+  +IA  LNV+  +V+ M  RL A D +  A  + 
Sbjct: 138 KLFFNLRSLKK-----SSKKLTLEEAQSIANDLNVTAEQVLEMEGRLTAYDAAFEAQGDD 192

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
            D          + D+      L+E E+  +   + L  +M  L+ R R I + R L ++
Sbjct: 193 DDDTPHTAPALYLEDNRYDPARLVENEDWEEQSTSALHDAMDQLDDRSRNILQRRWLDDD 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             TL  L++E+ VS ER+RQ+E  A +K++
Sbjct: 253 KSTLHELAAEYNVSAERIRQLEKNAMEKIK 282


>gi|89076088|ref|ZP_01162448.1| RNA polymerase sigma factor [Photobacterium sp. SKA34]
 gi|89048240|gb|EAR53822.1| RNA polymerase sigma factor [Photobacterium sp. SKA34]
          Length = 286

 Score =  195 bits (496), Expect = 6e-48,   Method: Compositional matrix adjust.
 Identities = 105/273 (38%), Positives = 165/273 (60%), Gaps = 8/273 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  YI  + + PML  + E  LA+R     D+++A  LV SHLR VV IA GY GYGLP
Sbjct: 15  SLDSYIQTVNRYPMLTPEREKELAERLHYDDDINSAKALVMSHLRFVVHIARGYSGYGLP 74

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           I++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W +VK+ TT  Q++
Sbjct: 75  IADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRK 134

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           LFFNLR+ K  L    +     ++V  +A++L V  S+V  M  RLA  +    + N  D
Sbjct: 135 LFFNLRKSKKRLGWFNN-----DEVNMVAEQLGVEPSDVREMESRLAAQDPTFEMQNDDD 189

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           +  +       Y  D    V +  EE     +  N L+++++ L+ R + I  +R L + 
Sbjct: 190 ERDTTPVAPAYYLEDKSSDVALTYEENNWENHANNRLSQALASLDERSQHIVRSRWLDDE 249

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL++L++ + VS ER+RQ+E  A KK+++++
Sbjct: 250 KSTLQDLANNYGVSAERIRQLEKNAMKKLKDAV 282


>gi|262278444|ref|ZP_06056229.1| EsvH [Acinetobacter calcoaceticus RUH2202]
 gi|262258795|gb|EEY77528.1| EsvH [Acinetobacter calcoaceticus RUH2202]
          Length = 288

 Score =  195 bits (496), Expect = 6e-48,   Method: Compositional matrix adjust.
 Identities = 108/270 (40%), Positives = 160/270 (59%), Gaps = 7/270 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + L  YI  + +IP+L  ++E  LA+RY    DL AA  LV SHLR VV IA  Y GYGL
Sbjct: 18  VNLGAYISTVNQIPILTAEQEKELAERYYYDQDLDAAKMLVMSHLRFVVHIARSYAGYGL 77

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P  +++ EGN+GLM+AVK+FDP  G RL ++++ WIKA + EY++R+W +VKI TT  Q+
Sbjct: 78  PQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVKIATTKAQR 137

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINS 192
           +LFFNLR LK   + +T      E+  +IA  LNV+  +V+ M  RL A D +  A  + 
Sbjct: 138 KLFFNLRSLKKSSKKLT-----LEEAQSIANDLNVTAEQVLEMEGRLTAYDAAFEAQGDD 192

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
            D          + D+      L+E E+  +   + L  +M  L+ R R I + R L ++
Sbjct: 193 DDDTPHTAPALYLEDNRYDPARLVENEDWEEQSTSALHNAMDQLDDRSRNILQRRWLDDD 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             TL  L++E+ VS ER+RQ+E  A +K++
Sbjct: 253 KSTLHELAAEYNVSAERIRQLEKNAMEKIK 282


>gi|145628599|ref|ZP_01784399.1| RNA polymerase sigma factor [Haemophilus influenzae 22.1-21]
 gi|145632513|ref|ZP_01788247.1| RNA polymerase sigma factor [Haemophilus influenzae 3655]
 gi|148825451|ref|YP_001290204.1| RNA polymerase factor sigma-32 [Haemophilus influenzae PittEE]
 gi|144979069|gb|EDJ88755.1| RNA polymerase sigma factor [Haemophilus influenzae 22.1-21]
 gi|144986708|gb|EDJ93260.1| RNA polymerase sigma factor [Haemophilus influenzae 3655]
 gi|148715611|gb|ABQ97821.1| RNA polymerase sigma factor [Haemophilus influenzae PittEE]
          Length = 281

 Score =  195 bits (496), Expect = 6e-48,   Method: Compositional matrix adjust.
 Identities = 110/283 (38%), Positives = 170/283 (60%), Gaps = 14/283 (4%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M ++  G I    YI    + PML  +EE  LA+R   H DL AA +L+ SHLR V+ +A
Sbjct: 7   MMLVPQGSI--EGYIRAANEYPMLTAEEEKELAERLYYHEDLDAAKKLILSHLRFVIHVA 64

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W +VK
Sbjct: 65  RGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVK 124

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           + TT  Q++LFFNLR+ K  L    +N     +V  +A +L VS+ +VI M  R++G + 
Sbjct: 125 VATTKAQRKLFFNLRKTKQRLGWFNEN-----EVDMVANELGVSKEDVIEMESRMSGAD- 178

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV----LNPRERR 241
           +   + + D  +  +   L Y  D       E  E +N  +  T  + V    L+ R + 
Sbjct: 179 VGFDLPTDDAETETYSPSL-YLEDKSSNFAAEL-ENENFESQATEQLGVALQSLDARSQD 236

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           I +AR L +N  TL +L++++ VS ER+RQ+E  A KK++ ++
Sbjct: 237 IIKARWLDDNKATLHDLAAKYNVSAERIRQLETNALKKLKSAV 279


>gi|260582846|ref|ZP_05850631.1| alternative sigma factor RpoH [Haemophilus influenzae NT127]
 gi|260094059|gb|EEW77962.1| alternative sigma factor RpoH [Haemophilus influenzae NT127]
          Length = 281

 Score =  195 bits (496), Expect = 6e-48,   Method: Compositional matrix adjust.
 Identities = 110/283 (38%), Positives = 170/283 (60%), Gaps = 14/283 (4%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M ++  G I    YI    + PML  +EE  LA+R   H DL AA +L+ SHLR V+ +A
Sbjct: 7   MMLVPQGSI--EGYIRAANEYPMLTAEEEKELAERLYYHEDLDAAKKLILSHLRFVIHVA 64

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W +VK
Sbjct: 65  RGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVK 124

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           + TT  Q++LFFNLR+ K  L    +N     +V  +A +L VS+ +VI M  R++G + 
Sbjct: 125 VATTKAQRKLFFNLRKTKQRLGWFNEN-----EVDMVANELGVSKEDVIEMESRMSGAD- 178

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV----LNPRERR 241
           +   + + D  +  +   L Y  D       E  E +N  +  T  + V    L+ R + 
Sbjct: 179 VGFDLPTDDAETETYSPSL-YLEDKSSNFAAEL-ENENFESQATEQLGVALQSLDARSQD 236

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           I +AR L +N  TL +L++++ VS ER+RQ+E  A KK++ ++
Sbjct: 237 IIKARWLDDNKATLHDLAAKYNVSAERIRQLETNALKKLKSAV 279


>gi|114770145|ref|ZP_01447683.1| RNA polymerase sigma factor [alpha proteobacterium HTCC2255]
 gi|114548982|gb|EAU51865.1| RNA polymerase sigma factor [alpha proteobacterium HTCC2255]
          Length = 294

 Score =  195 bits (496), Expect = 7e-48,   Method: Compositional matrix adjust.
 Identities = 98/263 (37%), Positives = 174/263 (66%), Gaps = 6/263 (2%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K  ML+   EY LA  +R+H D  A HRL+ +++RL + +A  +R YG+   +++ E  +
Sbjct: 17  KAEMLDVDTEYKLAIAWRDHKDEDALHRLINAYMRLAISMASKFRRYGVSQQDLIQEAGM 76

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A  KFDP++G R +TY+ WW+KA++Q++++R++S+V+ G+T NQK LFFN++R+K 
Sbjct: 77  GLMKAADKFDPDKGVRFSTYAQWWVKASIQDFVMRNYSMVRTGSTTNQKSLFFNIKRVKA 136

Query: 145 HLQ--AITDN-NLKPEQVV-AIAKKLNVSESEVISMNCRLA-GDESLNALINSSDKNSSQ 199
            L+  A+ +N  + P Q++  ++ +L V   +V+ MN R++ GD SLNA I S+D    +
Sbjct: 137 QLERDAVQNNQTVTPAQILEQVSTELGVPMRDVMMMNGRMSGGDMSLNA-IQSNDDEGRE 195

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
           W + L  +  G  +++ +  + +  +  + +SM VLN RE+ I   R++ ++P TLE++ 
Sbjct: 196 WIETLADEAPGGAEIVEQSFDEEKLKIWIGQSMEVLNEREKYIVIQRKMIDSPRTLESIG 255

Query: 260 SEFEVSRERVRQIEARAFKKVQE 282
            E ++S+ER+RQIE  A +K+++
Sbjct: 256 VELKLSKERIRQIENAALEKLKK 278


>gi|83953376|ref|ZP_00962098.1| RNA polymerase sigma factor [Sulfitobacter sp. NAS-14.1]
 gi|83842344|gb|EAP81512.1| RNA polymerase sigma factor [Sulfitobacter sp. NAS-14.1]
          Length = 295

 Score =  195 bits (495), Expect = 7e-48,   Method: Compositional matrix adjust.
 Identities = 106/287 (36%), Positives = 179/287 (62%), Gaps = 9/287 (3%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M++  + E  L+R      K  +L+ + E  LA  +R+  D  A HRL+T+++RL + +A
Sbjct: 4   MTLAQSREFSLTRTAM---KAELLDAETELKLAYAWRDERDEEALHRLITAYMRLAISMA 60

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             ++ YG  +++++ E  +GLM+A  KFDP+RG R +TY++WWIKA++Q++++R+WS+V+
Sbjct: 61  GKFKRYGASMNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDHVMRNWSMVR 120

Query: 126 IGTTANQKRLFFNLRRLKGHL----QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            G+T++QK LFFN+RR++  L    QA  +   K +    I+ ++ V   +V  M  RL+
Sbjct: 121 TGSTSSQKSLFFNMRRVQARLEREAQAAGETLDKHQLRQMISTEIGVPMHDVEMMEGRLS 180

Query: 182 G-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           G D SLNA   S++    +W D LV D     + + E  +    R+ L  +M  LN RE+
Sbjct: 181 GSDFSLNA-TQSAEDEGREWIDALVDDSAQAAERIEESHDTLTLRSWLLSAMQALNEREQ 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            I   R+L++ P TLE+L +E  +S+ERVRQ+EA AF K++++++ Q
Sbjct: 240 FIVRERKLRDQPRTLESLGAELSLSKERVRQLEAAAFGKMRKTLETQ 286


>gi|86139299|ref|ZP_01057869.1| RNA polymerase sigma factor [Roseobacter sp. MED193]
 gi|85824143|gb|EAQ44348.1| RNA polymerase sigma factor [Roseobacter sp. MED193]
          Length = 292

 Score =  195 bits (495), Expect = 7e-48,   Method: Compositional matrix adjust.
 Identities = 104/266 (39%), Positives = 173/266 (65%), Gaps = 8/266 (3%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K  ML+ + E  LA  +R+H D+ A HRL  +++RL + +A+ ++ YG P+++++ E  +
Sbjct: 17  KAEMLDAETEKRLAYAWRDHRDVEALHRLTNAYMRLAISMAVKFKRYGAPMNDLIQEAGL 76

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFN+RR++ 
Sbjct: 77  GLMKAADKFDPDRGVRFSTYAIWWIKASVQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQT 136

Query: 145 HLQAITD---NNLKPEQV-VAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQ 199
            L+   +     L   Q+   IA ++ V   +V  M+ RL+G D SLNA   S++    +
Sbjct: 137 QLERQANAQGQRLDKHQLHQQIASEIGVPIRDVEMMDGRLSGADFSLNA-ARSTEAEGQE 195

Query: 200 WQDWLVYDHDGQEQVLIEK-EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           W + ++ D   Q   L+E+  + +  R  L  +M  L+ RE+RI  AR+L   P TLE L
Sbjct: 196 WIE-ILEDDSAQAAELVERSHDHRKLRKWLVEAMQGLSGREQRIVVARKLSNPPRTLEAL 254

Query: 259 SSEFEVSRERVRQIEARAFKKVQESI 284
             E  +S+ERVRQ+EA AF+K+++++
Sbjct: 255 GRELSLSKERVRQLEAGAFQKMRKTL 280


>gi|260550924|ref|ZP_05825130.1| alternative sigma factor RpoH [Acinetobacter sp. RUH2624]
 gi|260406051|gb|EEW99537.1| alternative sigma factor RpoH [Acinetobacter sp. RUH2624]
          Length = 288

 Score =  195 bits (495), Expect = 7e-48,   Method: Compositional matrix adjust.
 Identities = 108/270 (40%), Positives = 160/270 (59%), Gaps = 7/270 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + L  YI  + +IP+L  ++E  LA+RY    DL AA  LV SHLR VV IA  Y GYGL
Sbjct: 18  VNLGAYISTVNQIPILTAEQEKELAERYYYDQDLDAAKMLVMSHLRFVVHIARSYAGYGL 77

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P  +++ EGN+GLM+AVK+FDP  G RL ++++ WIKA + EY++R+W +VKI TT  Q+
Sbjct: 78  PQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVKIATTKAQR 137

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINS 192
           +LFFNLR LK   + +T      E+  +IA  LNV+  +V+ M  RL A D +  A  + 
Sbjct: 138 KLFFNLRSLKKSSKKLT-----LEEAQSIANDLNVTPEQVLEMEGRLTAYDAAFEAQGDD 192

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
            D          + D+      L+E E+  +   + L  +M  L+ R R I + R L ++
Sbjct: 193 DDDTPHTAPALYLEDNRYDPARLVENEDWEEQSTSALHDAMDQLDDRSRNILQRRWLDDD 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             TL  L++E+ VS ER+RQ+E  A +K++
Sbjct: 253 KSTLHELAAEYNVSAERIRQLEKNAMEKIK 282


>gi|188583534|ref|YP_001926979.1| RNA polymerase factor sigma-32 [Methylobacterium populi BJ001]
 gi|179347032|gb|ACB82444.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium populi
           BJ001]
          Length = 290

 Score =  195 bits (495), Expect = 7e-48,   Method: Compositional matrix adjust.
 Identities = 110/270 (40%), Positives = 175/270 (64%), Gaps = 1/270 (0%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           +I    + P L ++EE  LA  ++E  D  A HRL+++H+RLV+ +A  +R YGLP++++
Sbjct: 11  FIRTAMEAPFLAREEERGLAVAWKEARDERALHRLISAHMRLVIALAGRFRHYGLPMADL 70

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EG++GLM+A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFFN
Sbjct: 71  VQEGHVGLMEAAARFEPERDVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKALFFN 130

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LRRL+  L   T+  +  E    IA  + VS  +V  M+ RL+G D SLNA +    + S
Sbjct: 131 LRRLRARLMQSTEEQVGSEIHGRIASAIGVSREDVALMDARLSGPDMSLNAPVGEESEAS 190

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           S+  D+LV +    ++ +    + + R   L ++++VL+ RE RI   RRL E+  TLE 
Sbjct: 191 SERMDFLVDNAALPDETVSALVDGERRLVWLRQALTVLSERELRILRERRLAEDQATLEA 250

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L     +S+ERVRQIE RA +K++ ++ ++
Sbjct: 251 LGHRLGISKERVRQIENRALEKLRRALAEK 280


>gi|258622821|ref|ZP_05717838.1| RNA polymerase sigma -32 factor [Vibrio mimicus VM573]
 gi|258584882|gb|EEW09614.1| RNA polymerase sigma -32 factor [Vibrio mimicus VM573]
          Length = 286

 Score =  195 bits (495), Expect = 8e-48,   Method: Compositional matrix adjust.
 Identities = 110/274 (40%), Positives = 164/274 (59%), Gaps = 11/274 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  +   PML   EE  LA+R    GD+ AA  L+ SHLR VV +A GY GYGLP+
Sbjct: 16  LDSYIRSVNGYPMLSADEERELAERLHYKGDIDAAKGLILSHLRFVVHVARGYSGYGLPM 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           +++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W +VKI TT  Q++L
Sbjct: 76  ADLVQEGNIGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR+ K  L    +      +V  +A++L V  SEV  M  RLA  ++   +    D+
Sbjct: 136 FFNLRKSKKRLGWFNNG-----EVETVARELGVEPSEVREMESRLAAQDAAFEMSAEDDE 190

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV----LNPRERRIFEARRL-QE 250
           N   +   ++Y  D     L +  E +N     T+ +S+    L+ R + I  AR L  +
Sbjct: 191 NGMAYTAPVLYLEDKHSD-LADNLEAENWEAHTTQRLSMALASLDERSQHIVRARWLDDD 249

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           N  TL++L+  + VS ER+RQ+E  A +K++E++
Sbjct: 250 NKTTLQDLAEMYGVSAERIRQLEKNAMRKLKEAV 283


>gi|153840380|ref|ZP_01993047.1| alternative sigma factor RpoH [Vibrio parahaemolyticus AQ3810]
 gi|149745954|gb|EDM57084.1| alternative sigma factor RpoH [Vibrio parahaemolyticus AQ3810]
          Length = 274

 Score =  195 bits (495), Expect = 8e-48,   Method: Compositional matrix adjust.
 Identities = 107/262 (40%), Positives = 156/262 (59%), Gaps = 9/262 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  +   PML   EE  LA+R    G++ AA  L+ SHLR VV +A GY GYGLP+
Sbjct: 16  LDSYIRSVNSYPMLTADEERELAERLHYKGEIEAAKGLILSHLRFVVHVARGYSGYGLPM 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           +++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W +VKI TT  Q++L
Sbjct: 76  ADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR+ K  L    +      +V  +A++L V  SEV  M  RLA  D + +   +  D
Sbjct: 136 FFNLRKSKKRLGWFNNG-----EVETVARELGVEPSEVREMESRLAAVDSTFDMPTDDDD 190

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERK---NRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             +S +   ++Y  D    V    E      +  N L  +++ L+ R +RI  +R L + 
Sbjct: 191 SATSSYTAPMLYLEDKSSDVADNIEAANWEMHTNNRLGHALASLDERSQRIVRSRWLDDE 250

Query: 252 PVTLENLSSEFEVSRERVRQIE 273
             TL++L+ EF VS ER+RQ+E
Sbjct: 251 KATLQDLADEFGVSAERIRQLE 272


>gi|83944334|ref|ZP_00956789.1| RNA polymerase sigma factor [Sulfitobacter sp. EE-36]
 gi|83844878|gb|EAP82760.1| RNA polymerase sigma factor [Sulfitobacter sp. EE-36]
          Length = 295

 Score =  195 bits (495), Expect = 8e-48,   Method: Compositional matrix adjust.
 Identities = 106/287 (36%), Positives = 179/287 (62%), Gaps = 9/287 (3%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M++  + E  L+R      K  +L+ + E  LA  +R+  D  A HRL+T+++RL + +A
Sbjct: 4   MTLAQSREFSLTRTAM---KAELLDAETELKLAYAWRDERDEEALHRLITAYMRLAISMA 60

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             ++ YG  +++++ E  +GLM+A  KFDP+RG R +TY++WWIKA++Q++++R+WS+V+
Sbjct: 61  GKFKRYGASMNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDHVMRNWSMVR 120

Query: 126 IGTTANQKRLFFNLRRLKGHL----QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            G+T++QK LFFN+RR++  L    QA  +   K +    I+ ++ V   +V  M  RL+
Sbjct: 121 TGSTSSQKSLFFNMRRVQARLEREAQAAGETLDKHQLRQMISTEIGVPMHDVEMMEGRLS 180

Query: 182 G-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           G D SLNA   S++    +W D LV D     + + E  +    R+ L  +M  LN RE+
Sbjct: 181 GSDFSLNA-TQSAEDEGREWIDALVDDSAQAAERVEESHDTLTLRSWLLSAMQALNEREQ 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            I   R+L++ P TLE+L +E  +S+ERVRQ+EA AF K++++++ Q
Sbjct: 240 FIVRERKLRDQPRTLESLGAELSLSKERVRQLEAAAFGKMRKTLETQ 286


>gi|301155494|emb|CBW14960.1| RNA polymerase, sigma 32 (sigma H) factor [Haemophilus
           parainfluenzae T3T1]
          Length = 280

 Score =  194 bits (494), Expect = 9e-48,   Method: Compositional matrix adjust.
 Identities = 108/287 (37%), Positives = 173/287 (60%), Gaps = 10/287 (3%)

Query: 1   MNRKN-MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLR 59
           MN++  M ++  G I    YI    + PML  +EE  LA+R    GD+ AA +LV SHLR
Sbjct: 1   MNKETQMMLVPQGSI--EGYIRAANEYPMLTAEEEKSLAERLYYDGDIEAAKKLVLSHLR 58

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
            V+ +A GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR
Sbjct: 59  FVIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLR 118

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
           +W +VK+ TT  Q++LFFNLR+ K  L    +N     +V  +A +L VS+ +VI M  R
Sbjct: 119 NWRIVKVATTKAQRKLFFNLRKTKQRLGWFNEN-----EVDMVANELGVSKEDVIEMESR 173

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN-MLTRSMSVLNPR 238
           + G + +   + + D + +      + D        +E E  + +    L  +++ L+ R
Sbjct: 174 MTGAD-VGFDLPTDDDDEAYVPSLYLEDKSSNFAAELESENFEEQATEKLGTALANLDER 232

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            + I +AR L +   TL +L++++ VS ER+RQ+EA A KK++ ++ 
Sbjct: 233 SQEIIKARWLDDEKATLHDLAAKYNVSAERIRQLEANALKKLKSAVD 279


>gi|229844972|ref|ZP_04465109.1| RNA polymerase factor sigma-32 [Haemophilus influenzae 6P18H1]
 gi|229812106|gb|EEP47798.1| RNA polymerase factor sigma-32 [Haemophilus influenzae 6P18H1]
          Length = 281

 Score =  194 bits (494), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 110/283 (38%), Positives = 170/283 (60%), Gaps = 14/283 (4%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M ++  G I    YI    + PML  +EE  LA+R   H DL AA +L+ SHLR V+ +A
Sbjct: 7   MMLVPQGSI--EGYIRAANEYPMLTAEEEKELAERLYYHEDLDAAKKLILSHLRFVIHVA 64

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W +VK
Sbjct: 65  RGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVK 124

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           + TT  Q++LFFNLR+ K  L    +N     +V  +A +L VS+ +VI M  R++G + 
Sbjct: 125 VATTKAQRKLFFNLRKTKQRLGWFNEN-----EVDMVANELGVSKEDVIEMESRMSGAD- 178

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV----LNPRERR 241
           +   + + D  +  +   L Y  D       E  E +N  +  T  + V    L+ R + 
Sbjct: 179 VGFDLPTDDAETETYSPSL-YLEDKSSNFAAEL-ENENFESQATEQLGVALQSLDVRSQD 236

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           I +AR L +N  TL +L++++ VS ER+RQ+E  A KK++ ++
Sbjct: 237 IIKARWLDDNKATLHDLAAKYNVSAERIRQLETNALKKLKSAV 279


>gi|332703233|ref|ZP_08423321.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio
           africanus str. Walvis Bay]
 gi|332553382|gb|EGJ50426.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio
           africanus str. Walvis Bay]
          Length = 398

 Score =  194 bits (494), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 110/276 (39%), Positives = 172/276 (62%), Gaps = 8/276 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLP 74
           L  Y+ EI + P+L+ +EE  LA+R R+ GD  AA RLVTSHLRLVVKIAM + R +   
Sbjct: 118 LHMYMQEISRFPILKPEEEVELARRVRDTGDQDAAFRLVTSHLRLVVKIAMDFQRRWMQN 177

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++V EGN+GLM+AV+KFDPE+G + + Y+ +WIKA + ++I+ +W +VKIGTT  Q++
Sbjct: 178 VLDLVQEGNVGLMRAVQKFDPEKGIKFSYYAAFWIKAYILKFIMDNWRMVKIGTTQTQRK 237

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALINSS 193
           LF+NL + +  LQ+       P     ++K L VS  ++  M+ RL+  D SL+  I   
Sbjct: 238 LFYNLNKERQRLQS---QGFDPTSST-LSKSLGVSVEDIEEMDQRLSRSDMSLDITIG-- 291

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D  ++   D+L     G E+ L   E     R  L   + +L+ +E+ I + R L ++PV
Sbjct: 292 DDTTATRMDFLPALGPGIEETLANSEISALLREHLASIVPMLSDKEQDILQKRLLSDSPV 351

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           TL  +  ++ ++RERVRQIEAR  +K++E +  ++E
Sbjct: 352 TLREIGDQYGITRERVRQIEARLLQKIREHLTDKIE 387


>gi|260913469|ref|ZP_05919947.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Pasteurella
           dagmatis ATCC 43325]
 gi|260632409|gb|EEX50582.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Pasteurella
           dagmatis ATCC 43325]
          Length = 281

 Score =  194 bits (494), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 108/289 (37%), Positives = 174/289 (60%), Gaps = 15/289 (5%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           MN++  ++++  +  L  YI    + PML  +EE  LA+R     DL AA +L+ SHLR 
Sbjct: 1   MNKETQTMMLVPQGSLEGYIRAANEYPMLTAEEEKELAERLYYQEDLEAAKKLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L    +N     +V  +A +L V+  +V+ M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNEN-----EVEMVANELGVTPEDVMEMESRM 175

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV----L 235
            G D + +   + S++  S      +Y  D       E E+ +N     T  +SV    L
Sbjct: 176 TGSDVAFDLPTDDSEETYSP----ALYLEDKGSNFAAELED-ENYETQATEQLSVALEGL 230

Query: 236 NPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + R   I ++R L +N  TL++L++++ +S ERVRQ+E  A KK++ ++
Sbjct: 231 DERSLDIIKSRWLDDNKATLQDLAAKYNISAERVRQLETNALKKLKSAV 279


>gi|84515923|ref|ZP_01003284.1| RNA polymerase sigma factor [Loktanella vestfoldensis SKA53]
 gi|84510365|gb|EAQ06821.1| RNA polymerase sigma factor [Loktanella vestfoldensis SKA53]
          Length = 277

 Score =  194 bits (494), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 102/268 (38%), Positives = 174/268 (64%), Gaps = 6/268 (2%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           +  +L+ + E  LA  +R+  D  A HRL+T+++RL + +A  ++ YG P+++++ E ++
Sbjct: 2   RAELLDAETELRLAYAWRDQRDEEALHRLITAYMRLAISMASKFKRYGAPMNDLIQEASV 61

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFN+RR++ 
Sbjct: 62  GLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQA 121

Query: 145 HLQ---AITDNNLKPEQV-VAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQ 199
            L+   A    +L+  ++   IA ++ V   +V  M+ RL+G D SLNA   S +    +
Sbjct: 122 RLEREAAAEGLHLETHELHEKIAIEVGVPLHDVQMMDGRLSGSDFSLNA-TQSMEDEGRE 180

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
           W D L  D     + +    +    R  L  +++ LN RE+ I   R+L+++P TLE+L 
Sbjct: 181 WIDALEDDAPQAAEKVENSHDTDTLRQWLVTALTALNDREQFIVRERKLRDDPRTLESLG 240

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQ 287
           SE  +S+ERVRQ+EA AF K+++S++ Q
Sbjct: 241 SELGLSKERVRQLEAAAFGKMRKSLEAQ 268


>gi|325579283|ref|ZP_08149239.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Haemophilus
           parainfluenzae ATCC 33392]
 gi|325159518|gb|EGC71652.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Haemophilus
           parainfluenzae ATCC 33392]
          Length = 293

 Score =  194 bits (494), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 108/287 (37%), Positives = 173/287 (60%), Gaps = 10/287 (3%)

Query: 1   MNRKN-MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLR 59
           MN++  M ++  G I    YI    + PML  +EE  LA+R    GD+ AA +LV SHLR
Sbjct: 14  MNKETQMMLVPQGSI--EAYIRAANEYPMLTAEEEKSLAERLYYDGDIEAAKKLVLSHLR 71

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
            V+ +A GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR
Sbjct: 72  FVIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLR 131

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
           +W +VK+ TT  Q++LFFNLR+ K  L    +N     +V  +A +L VS+ +VI M  R
Sbjct: 132 NWRIVKVATTKAQRKLFFNLRKTKQRLGWFNEN-----EVDMVANELGVSKEDVIEMESR 186

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN-MLTRSMSVLNPR 238
           + G + +   + + D + +      + D        +E E  + +    L  +++ L+ R
Sbjct: 187 MTGAD-VGFDLPTDDDDEAYVPSLYLEDKSSNFAAELESENFEEQATEKLGTALANLDER 245

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            + I +AR L +   TL +L++++ VS ER+RQ+EA A KK++ ++ 
Sbjct: 246 SQDIIKARWLDDEKATLHDLAAKYNVSAERIRQLEANALKKLKSAVD 292


>gi|52424080|ref|YP_087217.1| RNA polymerase factor sigma-32 [Mannheimia succiniciproducens
           MBEL55E]
 gi|52306132|gb|AAU36632.1| RpoD protein [Mannheimia succiniciproducens MBEL55E]
          Length = 282

 Score =  194 bits (494), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 103/285 (36%), Positives = 168/285 (58%), Gaps = 6/285 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++++  +  +  YI    + PML  +EE  LA+R     DL AA +L+ SHLR 
Sbjct: 1   MTKETQTMMLVPQGSIEAYIRAANEYPMLSAEEEKELAERLYYQEDLEAAKKLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L   +DN L       +A +L V++ +VI M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFSDNELD-----LVANELGVTKEDVIEMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR-NMLTRSMSVLNPRE 239
            G +    L     +  +      + D        +E E  + +  + L+ +M  L+ R 
Sbjct: 176 TGADVGFDLPTDDSEEETFAPSMYLEDKSSNFAAELESENFETQAIDQLSNAMENLDERS 235

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + I +AR L +   TL  L++++ +S ERVRQ+E  A KK++ ++
Sbjct: 236 KDIIQARWLDDTKATLHELAAKYNISAERVRQLETNALKKLKSAV 280


>gi|169632997|ref|YP_001706733.1| RNA polymerase factor sigma-32 [Acinetobacter baumannii SDF]
 gi|169795347|ref|YP_001713140.1| RNA polymerase factor sigma-32 [Acinetobacter baumannii AYE]
 gi|184158784|ref|YP_001847123.1| RNA polymerase factor sigma-32 [Acinetobacter baumannii ACICU]
 gi|213158666|ref|YP_002319964.1| alternative sigma factor RpoH (EsvH) [Acinetobacter baumannii
           AB0057]
 gi|215482881|ref|YP_002325084.1| alternative sigma factor RpoH [Acinetobacter baumannii AB307-0294]
 gi|239502880|ref|ZP_04662190.1| RNA polymerase factor sigma-32 [Acinetobacter baumannii AB900]
 gi|301346949|ref|ZP_07227690.1| RNA polymerase factor sigma-32 [Acinetobacter baumannii AB056]
 gi|301513493|ref|ZP_07238730.1| RNA polymerase factor sigma-32 [Acinetobacter baumannii AB058]
 gi|301596794|ref|ZP_07241802.1| RNA polymerase factor sigma-32 [Acinetobacter baumannii AB059]
 gi|332850459|ref|ZP_08432779.1| alternative sigma factor RpoH [Acinetobacter baumannii 6013150]
 gi|332871911|ref|ZP_08440323.1| alternative sigma factor RpoH [Acinetobacter baumannii 6013113]
 gi|169148274|emb|CAM86139.1| sigma H (sigma 32) factor of RNA polymerase [Acinetobacter
           baumannii AYE]
 gi|169151789|emb|CAP00610.1| sigma H (sigma 32) factor of RNA polymerase [Acinetobacter
           baumannii]
 gi|183210378|gb|ACC57776.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Acinetobacter baumannii ACICU]
 gi|193077812|gb|ABO12685.2| EsvH [Acinetobacter baumannii ATCC 17978]
 gi|213057826|gb|ACJ42728.1| alternative sigma factor RpoH (EsvH) [Acinetobacter baumannii
           AB0057]
 gi|213986534|gb|ACJ56833.1| alternative sigma factor RpoH [Acinetobacter baumannii AB307-0294]
 gi|322507403|gb|ADX02857.1| rpoH [Acinetobacter baumannii 1656-2]
 gi|323518699|gb|ADX93080.1| RNA polymerase factor sigma-32 [Acinetobacter baumannii
           TCDC-AB0715]
 gi|332730730|gb|EGJ62041.1| alternative sigma factor RpoH [Acinetobacter baumannii 6013150]
 gi|332731125|gb|EGJ62426.1| alternative sigma factor RpoH [Acinetobacter baumannii 6013113]
          Length = 288

 Score =  194 bits (494), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 108/270 (40%), Positives = 161/270 (59%), Gaps = 7/270 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + L  YI  + +IP+L  ++E  LA+RY    DL AA  LV SHLR VV IA  Y GYGL
Sbjct: 18  VNLGAYISTVNQIPILTAEQEKELAERYYYDQDLDAAKMLVMSHLRFVVHIARSYAGYGL 77

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P  +++ EGN+GLM+AVK+FDP  G RL ++++ WIKA + EY++R+W +VKI TT  Q+
Sbjct: 78  PQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVKIATTKAQR 137

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINS 192
           +LFFNLR LK   + +T      E+  +IA  LNV+  +V+ M  RL A D +  A  + 
Sbjct: 138 KLFFNLRSLKKSSKKLT-----LEEAQSIANDLNVTPEQVLEMEGRLTAYDAAFEAQGDD 192

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
            D          + D+      L+E E+  +   + L  +M+ L+ R R I + R L ++
Sbjct: 193 DDDTPHTAPVLYLEDNRYDPARLVENEDWEEQSTSALHDAMNQLDDRSRNILQRRWLDDD 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             TL  L++E+ VS ER+RQ+E  A +K++
Sbjct: 253 KSTLHELAAEYNVSAERIRQLEKNAMEKIK 282


>gi|16272227|ref|NP_438438.1| RNA polymerase factor sigma-32 [Haemophilus influenzae Rd KW20]
 gi|68248876|ref|YP_247988.1| RNA polymerase factor sigma-32 [Haemophilus influenzae 86-028NP]
 gi|260580848|ref|ZP_05848673.1| alternative sigma factor RpoH [Haemophilus influenzae RdAW]
 gi|319896604|ref|YP_004134797.1| RNA polymerase sigma-32 factor [Haemophilus influenzae F3031]
 gi|1173123|sp|P44404|RP32_HAEIN RecName: Full=RNA polymerase sigma-32 factor
 gi|1573235|gb|AAC21935.1| RNA polymerase sigma-32 factor (rpoH) [Haemophilus influenzae Rd
           KW20]
 gi|68057075|gb|AAX87328.1| RNA polymerase sigma-32 factor [Haemophilus influenzae 86-028NP]
 gi|260092471|gb|EEW76409.1| alternative sigma factor RpoH [Haemophilus influenzae RdAW]
 gi|317432106|emb|CBY80457.1| RNA polymerase sigma-32 factor [Haemophilus influenzae F3031]
          Length = 281

 Score =  194 bits (494), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 106/280 (37%), Positives = 167/280 (59%), Gaps = 8/280 (2%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M ++  G I    YI    + PML  +EE  LA+R   H DL AA +L+ SHLR V+ +A
Sbjct: 7   MMLVPQGSI--EGYIRAANEYPMLTAEEEKELAERLYYHEDLDAAKKLILSHLRFVIHVA 64

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W +VK
Sbjct: 65  RGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVK 124

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           + TT  Q++LFFNLR+ K  L    +N     +V  +A +L VS+ +VI M  R++G + 
Sbjct: 125 VATTKAQRKLFFNLRKTKQRLGWFNEN-----EVDMVANELGVSKEDVIEMESRMSGADV 179

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN-MLTRSMSVLNPRERRIFE 244
              L     +  +      + D        +E E  +++    L  ++  L+ R + I +
Sbjct: 180 GFDLPTDDAETETYSPALYLEDKSSNFAAELENENFESQATEQLGAALQSLDARSQDIIK 239

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           AR L +N  TL +L++++ VS ER+RQ+E  A KK++ ++
Sbjct: 240 ARWLDDNKATLHDLAAKYNVSAERIRQLETNALKKLKSAV 279


>gi|260554461|ref|ZP_05826682.1| alternative sigma factor RpoH [Acinetobacter baumannii ATCC 19606]
 gi|260411003|gb|EEX04300.1| alternative sigma factor RpoH [Acinetobacter baumannii ATCC 19606]
          Length = 288

 Score =  194 bits (494), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 108/270 (40%), Positives = 161/270 (59%), Gaps = 7/270 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + L  YI  + +IP+L  ++E  LA+RY    DL AA  LV SHLR VV IA  Y GYGL
Sbjct: 18  VNLGAYISTVNQIPILTAEQEKELAERYYYDQDLDAAKMLVMSHLRFVVHIARSYAGYGL 77

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P  +++ EGN+GLM+AVK+FDP  G RL ++++ WIKA + EY++R+W +VKI TT  Q+
Sbjct: 78  PQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVKIATTKAQR 137

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINS 192
           +LFFNLR LK   + +T      E+  +IA  LNV+  +V+ M  RL A D +  A  + 
Sbjct: 138 KLFFNLRSLKKSSKKLT-----LEEAQSIANDLNVTPEQVMEMEGRLTAYDAAFEAQGDD 192

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
            D          + D+      L+E E+  +   + L  +M+ L+ R R I + R L ++
Sbjct: 193 DDDTPHTAPVLYLEDNRYDPARLVENEDWEEQSTSALHDAMNQLDDRSRNILQRRWLDDD 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             TL  L++E+ VS ER+RQ+E  A +K++
Sbjct: 253 KSTLHELAAEYNVSAERIRQLEKNAMEKIK 282


>gi|85704163|ref|ZP_01035266.1| RNA polymerase sigma-32 factor [Roseovarius sp. 217]
 gi|85671483|gb|EAQ26341.1| RNA polymerase sigma-32 factor [Roseovarius sp. 217]
          Length = 277

 Score =  194 bits (494), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 103/268 (38%), Positives = 174/268 (64%), Gaps = 6/268 (2%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K  ML+ + E  LA  +R+  D  A HRL+ +++RL + +A  +R YG P+++++ E  +
Sbjct: 2   KAEMLDAETELALAYAWRDQRDEEALHRLINAYMRLAISMASKFRRYGAPMNDLIQEAGL 61

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFN+RR++ 
Sbjct: 62  GLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQA 121

Query: 145 HL--QAITDN-NLKPEQV-VAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQ 199
            L  +A+ +   L   Q+   IA ++ V   +V  M  RL+G D SLNA   S++    +
Sbjct: 122 RLEREAMANGQQLDGYQLREMIAHEVGVPLRDVEMMEGRLSGSDFSLNA-TQSAEDEGRE 180

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
           W D L  +    ++++    +    R+ L  +++ LN RER I   R+L+++P TLE+L 
Sbjct: 181 WIDTLEDEGARGDEIVERHHDMHALRDWLADALARLNERERFIVRERKLRDDPRTLESLG 240

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQ 287
            E  +S+ERVRQ+EA AF+K+++ ++K 
Sbjct: 241 EELNLSKERVRQLEAAAFQKMRKHLEKH 268


>gi|116749546|ref|YP_846233.1| sigma-70 region 2 domain-containing protein [Syntrophobacter
           fumaroxidans MPOB]
 gi|116698610|gb|ABK17798.1| sigma-70 region 2 domain protein [Syntrophobacter fumaroxidans
           MPOB]
          Length = 326

 Score =  194 bits (493), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 109/273 (39%), Positives = 178/273 (65%), Gaps = 8/273 (2%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP-ISE 77
           Y+ EI++ P+L ++EE  LA RYRE GD+ A ++L+T++LRLVVKIAM ++ Y +  + +
Sbjct: 48  YLDEIKRYPLLSREEETDLAIRYREKGDIEAGYKLITANLRLVVKIAMDFQRYWMQNLMD 107

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGN+GLMQAVKKFDP RG++ + Y+ +WIKA + ++I+ +W LVKIGTT  Q++LFF
Sbjct: 108 LIQEGNVGLMQAVKKFDPYRGYKFSYYASFWIKAYIIKFIMDNWKLVKIGTTQAQRKLFF 167

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKN 196
           NLR+ K  L+A       P+    ++ +L+V ESE+I M+ RL   E SL++ +    ++
Sbjct: 168 NLRKEKERLEA-QGIEASPK---LLSHRLDVKESEIIEMDQRLNSWEISLDSPLKEDSED 223

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           +   + +L  D    +  + ++E +    + L      L  +E  IF+ R L E P+TL+
Sbjct: 224 TH--KSFLPSDDLPVDDQIADREAKAILHDKLLLFREQLKGKEAVIFDKRLLTEEPMTLQ 281

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
            +   F +SRERVRQIE+R  KK++  +++++E
Sbjct: 282 EIGDRFGISRERVRQIESRLKKKLKAYLEEEIE 314


>gi|145635177|ref|ZP_01790882.1| RNA polymerase sigma factor [Haemophilus influenzae PittAA]
 gi|145267598|gb|EDK07597.1| RNA polymerase sigma factor [Haemophilus influenzae PittAA]
          Length = 281

 Score =  194 bits (493), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 108/282 (38%), Positives = 166/282 (58%), Gaps = 12/282 (4%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M ++  G I    YI    + PML  +EE  LA+R   H DL AA +L+ SHLR V+ +A
Sbjct: 7   MMLVPQGSI--EGYIRAANEYPMLTAEEEKELAERLYYHEDLDAAKKLILSHLRFVIHVA 64

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W +VK
Sbjct: 65  RGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVK 124

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           + TT  Q++LFFNLR+ K  L    +N     +V  +A +L VS+ +VI M  R++G + 
Sbjct: 125 VATTKAQRKLFFNLRKTKQRLGWFNEN-----EVDMVANELGVSKEDVIEMESRMSGADV 179

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNPRERRI 242
              L   +D   ++     +Y  D       E E           L  ++  L+ R + I
Sbjct: 180 GFDL--PTDDAETEIYSPSLYLEDKSSNFAAELENENFESQATEQLNTALQSLDARSQDI 237

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +AR L +N  TL +L++++ VS ER+RQ+E  A KK++ ++
Sbjct: 238 IKARWLDDNKATLHDLAAKYNVSAERIRQLETNALKKLKSAV 279


>gi|332875153|ref|ZP_08442986.1| alternative sigma factor RpoH [Acinetobacter baumannii 6014059]
 gi|332736597|gb|EGJ67591.1| alternative sigma factor RpoH [Acinetobacter baumannii 6014059]
          Length = 280

 Score =  194 bits (493), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 108/270 (40%), Positives = 160/270 (59%), Gaps = 7/270 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + L  YI  + +IP+L  ++E  LA+RY    DL AA  LV SHLR VV IA  Y GYGL
Sbjct: 10  VNLGAYISTVNQIPILTAEQEKELAERYYYDQDLDAAKMLVMSHLRFVVHIARSYAGYGL 69

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P  +++ EGN+GLM+AVK+FDP  G RL ++++ WIKA + EY++R+W +VKI TT  Q+
Sbjct: 70  PQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVKIATTKAQR 129

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINS 192
           +LFFNLR LK      +   L  E+  +IA  LNV+  +V+ M  RL A D +  A  + 
Sbjct: 130 KLFFNLRSLKK-----SSKKLTLEEAQSIANDLNVTPEQVLEMEGRLTAYDAAFEAQGDD 184

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
            D          + D+      L+E E+  +   + L  +M+ L+ R R I + R L ++
Sbjct: 185 DDDTPHTAPVLYLEDNRYDPARLVENEDWEEQSTSALHDAMNQLDDRSRNILQRRWLDDD 244

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             TL  L++E+ VS ER+RQ+E  A +K++
Sbjct: 245 KSTLHELAAEYNVSAERIRQLEKNAMEKIK 274


>gi|90581423|ref|ZP_01237218.1| RNA polymerase sigma factor [Vibrio angustum S14]
 gi|90437400|gb|EAS62596.1| RNA polymerase sigma factor [Vibrio angustum S14]
          Length = 286

 Score =  194 bits (493), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 106/273 (38%), Positives = 165/273 (60%), Gaps = 8/273 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  YI  + + PML  + E  LA+R     D+++A  LV SHLR VV IA GY GYGLP
Sbjct: 15  SLDSYIQTVNRYPMLTPEREKELAERLHYDDDINSAKALVMSHLRFVVHIARGYSGYGLP 74

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           I++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W +VK+ TT  Q++
Sbjct: 75  IADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRK 134

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           LFFNLR+ K  L     NN   ++V  +A++L V  S+V  M  RLA  +    + N  D
Sbjct: 135 LFFNLRKSKKRLGWF--NN---DEVNMVAEQLGVEPSDVREMESRLAAQDPTFEMQNDDD 189

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           +  +       Y  D    + +  EE     +  N L+++++ L+ R + I  +R L + 
Sbjct: 190 ERDTTPVAPAYYLEDKSSDLALTYEENNWENHANNRLSQALASLDERSQHIVRSRWLDDE 249

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL++L+  + VS ER+RQ+E  A KK+++++
Sbjct: 250 KSTLQDLADNYGVSAERIRQLEKNAMKKLKDAV 282


>gi|13377878|gb|AAK20883.1|AF334761_4 RNA polymerase sigma-32 [Aeromonas hydrophila]
          Length = 284

 Score =  194 bits (493), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 111/288 (38%), Positives = 175/288 (60%), Gaps = 15/288 (5%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           ++ M++I  G   L  YI  +  IP+L   EE  LA+R ++ GDL AA +LV SHLR VV
Sbjct: 6   QRTMALIPQG--SLEGYIQAVNSIPVLTADEERELAERLQQGGDLEAARQLVMSHLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y GYGLP +++V EGNIGLM+AVK+FDP  G RL ++++ WIKA + EY+LR+W 
Sbjct: 64  HVAKSYAGYGLPQADLVQEGNIGLMKAVKRFDPTVGVRLVSFAVHWIKADIHEYVLRNWR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L   + +     +V A+A +L VS ++V  M  R++ 
Sbjct: 124 MVKVATTKAQRKLFFNLRKSKKRLGWFSHD-----EVQAVAAELGVSPTDVTEMEARMSN 178

Query: 183 -DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK---EERKNRRNMLTRSMSVLNPR 238
            D++ + + +  D+       +L  D        IE    ++   RR  L+ +++ L+ R
Sbjct: 179 YDQAFDLVGDDEDEGGFAPVHYL-EDKSSDLAATIENDNWDDHATRR--LSSALATLDER 235

Query: 239 ERRIFEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            + I  AR L ++   TL+ L+  + VS ERVRQ+E  A KK++++++
Sbjct: 236 SQHIIRARWLDDDSKTTLQELADTYGVSAERVRQLEKNALKKLKDAME 283


>gi|254453216|ref|ZP_05066653.1| sigma 32 [Octadecabacter antarcticus 238]
 gi|198267622|gb|EDY91892.1| sigma 32 [Octadecabacter antarcticus 238]
          Length = 292

 Score =  194 bits (492), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 101/272 (37%), Positives = 172/272 (63%), Gaps = 14/272 (5%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K  +L+ + E  LA  +R+  D  A HRL+T+++RL + +A  +R YG P+++++ E ++
Sbjct: 17  KAELLDAETELALAYAWRDERDEQALHRLITAYMRLAISMASKFRRYGAPMNDLIQEASL 76

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A  KFDP+RG R +TY++WWIKA++Q++++R+WS+V+ G+T++QK LFFNLRR++ 
Sbjct: 77  GLMKAADKFDPDRGVRFSTYAVWWIKASIQDHVMRNWSMVRTGSTSSQKSLFFNLRRVQA 136

Query: 145 HL--------QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDK 195
            L        + +  ++++      IA ++ V   +V  M  RL+G D SLNA   SS+ 
Sbjct: 137 RLEREAMKRGETLDRHDMRQ----MIATEVGVPLRDVEMMEGRLSGSDFSLNA-TQSSED 191

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
              +W D L  D +     +    +    R  L  +++ L+ RE+ I   R+L++ P TL
Sbjct: 192 EGREWIDALEDDGEQAADAVQNSHDTDTLRQWLLTALTALSDREQFIVRERKLRDAPRTL 251

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+L +E  +S+ERVRQ+EA AF K+++S++ Q
Sbjct: 252 ESLGTELSLSKERVRQLEAAAFGKMRKSLEGQ 283


>gi|171464209|ref|YP_001798322.1| RNA polymerase, sigma 32 subunit, RpoH [Polynucleobacter
           necessarius subsp. necessarius STIR1]
 gi|171193747|gb|ACB44708.1| RNA polymerase, sigma 32 subunit, RpoH [Polynucleobacter
           necessarius subsp. necessarius STIR1]
          Length = 307

 Score =  194 bits (492), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 115/277 (41%), Positives = 165/277 (59%), Gaps = 14/277 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + ++PML   EE  LA+ +R   ++ AA  LV SHLRLVV +A  Y GYG+P 
Sbjct: 36  LDSYIAYVNRVPMLSAAEELHLAQEFRCTENVDAAKTLVLSHLRLVVSVARQYLGYGIPH 95

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AVK++DP  G RLA+Y++ WIKA + EYIL++W LVK  TT  Q++L
Sbjct: 96  ADLIQEGNIGLMKAVKRYDPSNGARLASYAIHWIKAEIHEYILKNWRLVKTATTKAQRKL 155

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALINSSD 194
           FFNLR  K  L A+T     P +V A+AK L+V  S+V  M  RLA GD +L    + SD
Sbjct: 156 FFNLRSNKPTLSALT-----PNEVDALAKTLDVKGSDVKEMEMRLAGGDVALEG--DDSD 208

Query: 195 KNSSQWQ-DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           ++S+     WL          +   E    +   L +++  L+ R R I ++R L  +  
Sbjct: 209 EDSAYAPIQWLADSSQEPTARIASAEANALQGPKLDQALMALDERSRNIVQSRWLAMDAE 268

Query: 253 ----VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
                TL +L+ E+ +S ERVRQIE  A KK++  +Q
Sbjct: 269 GNGTKTLHDLADEYGISAERVRQIETAALKKMRGLLQ 305


>gi|121602584|ref|YP_988464.1| RNA polymerase factor sigma-32 [Bartonella bacilliformis KC583]
 gi|120614761|gb|ABM45362.1| RNA polymerase sigma-32 factor [Bartonella bacilliformis KC583]
          Length = 303

 Score =  194 bits (492), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 107/278 (38%), Positives = 178/278 (64%), Gaps = 6/278 (2%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
            +G +G    +    + P LE+++EY LA R+++  D  A H++  +H+RLV+ IA  ++
Sbjct: 18  TDGSLGRD-MVRSAMQAPYLERKKEYDLALRWKDKRDDEAMHQIAAAHMRLVISIASRFK 76

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
            + +P+ ++V EG +GL++A  +F+P+R  R +TY+ WWI+A++Q+YILR+WS+V+ GT+
Sbjct: 77  RFKMPLGDLVQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTS 136

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-AIAKKLNVSESEVISMNCRLAG-DESLN 187
           ++QK LFFNLRRL+  L    D+ L  + +  +IA+KL+V  S+V  M+ R +G D SL+
Sbjct: 137 SSQKALFFNLRRLRAQL-VQEDSTLTKQDIFRSIAEKLSVPVSDVERMDFRFSGADNSLS 195

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEAR 246
             I+ ++++     D LV +H   + +LIEK     RR   L  ++ +LN RE  I   R
Sbjct: 196 VSISENEESPVTKIDNLVDEHPLPD-ILIEKAIDGQRRTQWLYDALQILNEREMEIIRFR 254

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           RL +   TLE+L     +S+ERVRQIE RA +K++ ++
Sbjct: 255 RLNDESATLESLGERLGISKERVRQIEVRALQKLRRAL 292


>gi|145590108|ref|YP_001156705.1| RNA polymerase, sigma 32 subunit, RpoH [Polynucleobacter
           necessarius subsp. asymbioticus QLW-P1DMWA-1]
 gi|145048514|gb|ABP35141.1| RNA polymerase, sigma 32 subunit, RpoH [Polynucleobacter
           necessarius subsp. asymbioticus QLW-P1DMWA-1]
          Length = 309

 Score =  194 bits (492), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 111/278 (39%), Positives = 164/278 (58%), Gaps = 10/278 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + ++PML   EE  LA+ +R   ++ AA  LV SHLRLVV +A  Y GYG+P 
Sbjct: 36  LDSYIAYVNRVPMLSAAEELHLAQEFRRTENVDAAKTLVLSHLRLVVSVARQYLGYGIPH 95

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AVK++DP  G RL +Y++ WIKA + EYIL++W LVK  TT  Q++L
Sbjct: 96  ADLIQEGNIGLMKAVKRYDPNNGARLVSYAIHWIKAEIHEYILKNWRLVKTATTKAQRKL 155

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR  K  L A+T     P +V A+AK L+V  S+V  M  RLAG +      +S D+
Sbjct: 156 FFNLRSNKPTLSALT-----PSEVDALAKALDVKGSDVKEMEMRLAGGDIALEGDDSDDE 210

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--- 252
           ++     WL  +       +   E    +   L +++  L+ R R I ++R L  +    
Sbjct: 211 SAYAPIQWLADNTQEPTARIASAEADALQGPRLDQALMSLDERSRNIVQSRWLAMDAEGN 270

Query: 253 --VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
              TL +L++E+ +S ERVRQIE  A KK++  ++ Q 
Sbjct: 271 GTKTLHDLAAEYGISAERVRQIETAALKKMRGLLEAQA 308


>gi|15640181|ref|NP_229808.1| RNA polymerase factor sigma-32 [Vibrio cholerae O1 biovar El Tor
           str. N16961]
 gi|121591866|ref|ZP_01679036.1| RNA polymerase sigma-32 factor [Vibrio cholerae 2740-80]
 gi|147674371|ref|YP_001218271.1| RNA polymerase factor sigma-32 [Vibrio cholerae O395]
 gi|153214854|ref|ZP_01949662.1| RNA polymerase sigma-32 factor [Vibrio cholerae 1587]
 gi|153803613|ref|ZP_01958199.1| RNA polymerase sigma-32 factor [Vibrio cholerae MZO-3]
 gi|153818953|ref|ZP_01971620.1| RNA polymerase sigma-32 factor [Vibrio cholerae NCTC 8457]
 gi|153824136|ref|ZP_01976803.1| RNA polymerase sigma-32 factor [Vibrio cholerae B33]
 gi|153826296|ref|ZP_01978963.1| RNA polymerase sigma-32 factor [Vibrio cholerae MZO-2]
 gi|153830006|ref|ZP_01982673.1| RNA polymerase sigma-32 factor [Vibrio cholerae 623-39]
 gi|227080385|ref|YP_002808936.1| RNA polymerase sigma-32 factor [Vibrio cholerae M66-2]
 gi|229508425|ref|ZP_04397929.1| RNA polymerase sigma factor RpoH [Vibrio cholerae BX 330286]
 gi|229508894|ref|ZP_04398384.1| RNA polymerase sigma factor RpoH [Vibrio cholerae B33]
 gi|229515820|ref|ZP_04405278.1| RNA polymerase sigma factor RpoH [Vibrio cholerae TMA 21]
 gi|229517008|ref|ZP_04406454.1| RNA polymerase sigma factor RpoH [Vibrio cholerae RC9]
 gi|229520061|ref|ZP_04409489.1| RNA polymerase sigma factor RpoH [Vibrio cholerae TM 11079-80]
 gi|229527110|ref|ZP_04416504.1| RNA polymerase sigma factor RpoH [Vibrio cholerae 12129(1)]
 gi|229606698|ref|YP_002877346.1| RNA polymerase factor sigma-32 [Vibrio cholerae MJ-1236]
 gi|254291956|ref|ZP_04962737.1| RNA polymerase sigma-32 factor [Vibrio cholerae AM-19226]
 gi|254851536|ref|ZP_05240886.1| RNA polymerase sigma-32 factor [Vibrio cholerae MO10]
 gi|255743901|ref|ZP_05417856.1| RNA polymerase sigma factor RpoH [Vibrio cholera CIRS 101]
 gi|262163699|ref|ZP_06031440.1| RNA polymerase sigma factor RpoH [Vibrio mimicus VM223]
 gi|262172906|ref|ZP_06040584.1| RNA polymerase sigma factor RpoH [Vibrio mimicus MB-451]
 gi|262190731|ref|ZP_06048960.1| RNA polymerase sigma factor RpoH [Vibrio cholerae CT 5369-93]
 gi|262404885|ref|ZP_06081439.1| RNA polymerase sigma factor RpoH [Vibrio sp. RC586]
 gi|297581813|ref|ZP_06943734.1| RNA polymerase sigma-32 factor [Vibrio cholerae RC385]
 gi|298501088|ref|ZP_07010888.1| alternative sigma factor RpoH [Vibrio cholerae MAK 757]
 gi|12644296|sp|P50511|RP32_VIBCH RecName: Full=RNA polymerase sigma-32 factor
 gi|9654552|gb|AAF93327.1| RNA polymerase sigma-32 factor [Vibrio cholerae O1 biovar El Tor
           str. N16961]
 gi|121546267|gb|EAX56564.1| RNA polymerase sigma-32 factor [Vibrio cholerae 2740-80]
 gi|124115097|gb|EAY33917.1| RNA polymerase sigma-32 factor [Vibrio cholerae 1587]
 gi|124120852|gb|EAY39595.1| RNA polymerase sigma-32 factor [Vibrio cholerae MZO-3]
 gi|126510515|gb|EAZ73109.1| RNA polymerase sigma-32 factor [Vibrio cholerae NCTC 8457]
 gi|126518343|gb|EAZ75566.1| RNA polymerase sigma-32 factor [Vibrio cholerae B33]
 gi|146316254|gb|ABQ20793.1| RNA polymerase sigma-32 factor [Vibrio cholerae O395]
 gi|148874491|gb|EDL72626.1| RNA polymerase sigma-32 factor [Vibrio cholerae 623-39]
 gi|149739964|gb|EDM54143.1| RNA polymerase sigma-32 factor [Vibrio cholerae MZO-2]
 gi|150422166|gb|EDN14132.1| RNA polymerase sigma-32 factor [Vibrio cholerae AM-19226]
 gi|227008273|gb|ACP04485.1| RNA polymerase sigma-32 factor [Vibrio cholerae M66-2]
 gi|227011849|gb|ACP08059.1| RNA polymerase sigma-32 factor [Vibrio cholerae O395]
 gi|229335341|gb|EEO00824.1| RNA polymerase sigma factor RpoH [Vibrio cholerae 12129(1)]
 gi|229342849|gb|EEO07839.1| RNA polymerase sigma factor RpoH [Vibrio cholerae TM 11079-80]
 gi|229346071|gb|EEO11043.1| RNA polymerase sigma factor RpoH [Vibrio cholerae RC9]
 gi|229347083|gb|EEO12044.1| RNA polymerase sigma factor RpoH [Vibrio cholerae TMA 21]
 gi|229354011|gb|EEO18944.1| RNA polymerase sigma factor RpoH [Vibrio cholerae B33]
 gi|229354698|gb|EEO19620.1| RNA polymerase sigma factor RpoH [Vibrio cholerae BX 330286]
 gi|229369353|gb|ACQ59776.1| RNA polymerase sigma factor RpoH [Vibrio cholerae MJ-1236]
 gi|254847241|gb|EET25655.1| RNA polymerase sigma-32 factor [Vibrio cholerae MO10]
 gi|255738384|gb|EET93774.1| RNA polymerase sigma factor RpoH [Vibrio cholera CIRS 101]
 gi|261893982|gb|EEY39968.1| RNA polymerase sigma factor RpoH [Vibrio mimicus MB-451]
 gi|262027915|gb|EEY46579.1| RNA polymerase sigma factor RpoH [Vibrio mimicus VM223]
 gi|262033375|gb|EEY51884.1| RNA polymerase sigma factor RpoH [Vibrio cholerae CT 5369-93]
 gi|262348969|gb|EEY98108.1| RNA polymerase sigma factor RpoH [Vibrio sp. RC586]
 gi|297533907|gb|EFH72747.1| RNA polymerase sigma-32 factor [Vibrio cholerae RC385]
 gi|297540122|gb|EFH76183.1| alternative sigma factor RpoH [Vibrio cholerae MAK 757]
 gi|327483048|gb|AEA77455.1| RNA polymerase sigma factor RpoH [Vibrio cholerae LMA3894-4]
          Length = 286

 Score =  194 bits (492), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 109/274 (39%), Positives = 164/274 (59%), Gaps = 11/274 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  +   PML   EE  LA+R    GD+ AA  L+ SHLR VV +A GY GYGLP+
Sbjct: 16  LDSYIRSVNGYPMLSADEERELAERLHYKGDIDAAKGLILSHLRFVVHVARGYSGYGLPM 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           +++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W +VKI TT  Q++L
Sbjct: 76  ADLVQEGNIGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR+ K  L    +      +V  +A++L V  +EV  M  RLA  ++   +    D+
Sbjct: 136 FFNLRKSKKRLGWFNNG-----EVETVARELGVEPAEVREMESRLAAQDAAFEMSAEDDE 190

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV----LNPRERRIFEARRL-QE 250
           N   +   ++Y  D     L +  E +N     T+ +S+    L+ R + I  AR L  +
Sbjct: 191 NGMAYTAPVLYLEDKHSD-LADNLEAENWEAHTTQRLSMALASLDERSQHIVRARWLDDD 249

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           N  TL++L+  + VS ER+RQ+E  A +K++E++
Sbjct: 250 NKTTLQDLAEMYGVSAERIRQLEKNAMRKLKEAV 283


>gi|218710915|ref|YP_002418536.1| RNA polymerase factor sigma-32 [Vibrio splendidus LGP32]
 gi|218323934|emb|CAV20295.1| RNA polymerase sigma-32 factor [Vibrio splendidus LGP32]
          Length = 303

 Score =  194 bits (492), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 110/274 (40%), Positives = 162/274 (59%), Gaps = 12/274 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI      PML   EE  LA+R    G++ AA  L+ SHLR VV +A GY GYGLP+
Sbjct: 34  LDSYIRSANSYPMLTPDEERGLAERLHYKGEIDAAKGLILSHLRFVVHVARGYSGYGLPM 93

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           +++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W +VKI TT  Q++L
Sbjct: 94  ADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKL 153

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR+ K  L    +      +V  +A++L V  SEV  M  RLA  D +  A ++  D
Sbjct: 154 FFNLRKSKKRLGWFNNG-----EVETVARELGVEPSEVREMESRLAAQDATFEAPMDDDD 208

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKN----RRNMLTRSMSVLNPRERRIFEARRLQE 250
             S+      VY  + +   + E  E  N      N L  ++  L+ R + I  +R L +
Sbjct: 209 GGSAYTAP--VYYLEDKASDVAETVEAANWESHTNNRLGLALKSLDERSQHIVRSRWLDD 266

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           N  TL++L+  + +S ERVRQ+E  A KK+++++
Sbjct: 267 NKATLQDLADTYSISAERVRQLEKNAMKKLKQAV 300


>gi|254439883|ref|ZP_05053377.1| RNA polymerase sigma factor, sigma-70 family [Octadecabacter
           antarcticus 307]
 gi|198255329|gb|EDY79643.1| RNA polymerase sigma factor, sigma-70 family [Octadecabacter
           antarcticus 307]
          Length = 292

 Score =  194 bits (492), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 102/268 (38%), Positives = 172/268 (64%), Gaps = 6/268 (2%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K  +L+ + E  LA  +R+  D  A HRL+T+++RL + +A  +R YG P+++++ E ++
Sbjct: 17  KAELLDAETELALAYAWRDERDEQALHRLITAYMRLAISMASKFRRYGAPMNDLIQEASL 76

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A  KFDP+RG R +TY++WWIKA++Q++++R+WS+V+ G+T++QK LFFNLRR++ 
Sbjct: 77  GLMKAADKFDPDRGVRFSTYAVWWIKASIQDHVMRNWSMVRTGSTSSQKSLFFNLRRVQA 136

Query: 145 HL--QAITDNNL--KPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQ 199
            L  +A+       + +    IA ++ V   +V  M  RL+G D SLNA   SS+    +
Sbjct: 137 RLEREAMKRGETLDRHDMRQMIATEVGVPLRDVEMMEGRLSGSDFSLNA-TQSSEDEGRE 195

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
           W D L  D +   + +    +    R  L  +++ L+ RE+ I   R+L++ P TLE+L 
Sbjct: 196 WIDALEDDGEQAAETVQNSHDTDTLRQWLLTALTALSDREQFIVRERKLRDAPRTLESLG 255

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +E  +S+ERVRQ+EA AF K+++S++ Q
Sbjct: 256 TELGLSKERVRQLEAAAFGKMRKSLEGQ 283


>gi|165922507|ref|ZP_02219678.1| alternative sigma factor RpoH [Coxiella burnetii RSA 334]
 gi|212211687|ref|YP_002302623.1| RNA polymerase factor sigma-32 [Coxiella burnetii CbuG_Q212]
 gi|165916712|gb|EDR35316.1| alternative sigma factor RpoH [Coxiella burnetii RSA 334]
 gi|212010097|gb|ACJ17478.1| RNA polymerase sigma-32 factor [Coxiella burnetii CbuG_Q212]
          Length = 288

 Score =  194 bits (492), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 108/277 (38%), Positives = 168/277 (60%), Gaps = 11/277 (3%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           G IG   YI  + +IP+L  +EE+ LA ++R+  DL AA +LV SHLR VV+IA GY GY
Sbjct: 16  GSIG--SYISWVNRIPLLSAEEEHDLANKFRQSNDLEAARKLVLSHLRFVVRIARGYSGY 73

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL  ++++ EGNIGLM+AVK+FDP+ G RL ++++ WI+A + E+IL++W +VKI TT  
Sbjct: 74  GLSQADLIQEGNIGLMKAVKRFDPQVGVRLVSFAVHWIRAEIHEFILKNWRIVKIATTKA 133

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALI 190
           Q++LFFNLR+        +D+     +  A+A++LNVS  +V  M  RL + DE+ +   
Sbjct: 134 QRKLFFNLRKHAKKRGWFSDH-----EAFALAEELNVSTKDVRQMEERLNSYDEAFDGAD 188

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEER---KNRRNMLTRSMSVLNPRERRIFEARR 247
             SD  +  W     Y  D +    ++ E      ++ + L  +M  L+ R R I   R 
Sbjct: 189 EESDSGTPSWGAPAHYLEDKRYNPALQLERSNWADDQEHRLHNAMQSLDDRSRDILYQRW 248

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L E   TL  L++++ VS ER+RQ+E  A +K++ ++
Sbjct: 249 LSEKKSTLHELAAQYAVSAERIRQLEKNAMQKIRTAM 285


>gi|163853281|ref|YP_001641324.1| RNA polymerase factor sigma-32 [Methylobacterium extorquens PA1]
 gi|218532097|ref|YP_002422913.1| RNA polymerase factor sigma-32 [Methylobacterium chloromethanicum
           CM4]
 gi|254563204|ref|YP_003070299.1| RNA polymerase sigma-32 [Methylobacterium extorquens DM4]
 gi|163664886|gb|ABY32253.1| RNA polymerase sigma factor, sigma-70 family [Methylobacterium
           extorquens PA1]
 gi|218524400|gb|ACK84985.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium
           chloromethanicum CM4]
 gi|254270482|emb|CAX26482.1| RNA polymerase sigma-32 (sigma H) factor [Methylobacterium
           extorquens DM4]
          Length = 290

 Score =  194 bits (492), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 110/270 (40%), Positives = 174/270 (64%), Gaps = 1/270 (0%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           +I    + P L + EE  LA  ++E  D  A HRL+++H+RLV+ +A  +R YGLP++++
Sbjct: 11  FIRTAMEAPFLARDEERGLAVAWKEARDERALHRLISAHMRLVIALAGRFRHYGLPMADL 70

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EG++GLM+A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFFN
Sbjct: 71  VQEGHVGLMEAAARFEPEREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKALFFN 130

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LRRL+  L   T+  +  E    IA  + VS  +V  M+ RL+G D SLNA +    + S
Sbjct: 131 LRRLRARLMQSTEEQVGSEIHGRIATAIGVSREDVALMDARLSGPDMSLNAPVGEESEAS 190

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           S+  D+LV +    ++ +    + + R   L ++++VL+ RE RI   RRL E+  TLE 
Sbjct: 191 SERMDFLVDNAALPDETVSALVDGERRLIWLRQALTVLSERELRILRERRLAEDQATLEA 250

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L     +S+ERVRQIE RA +K++ ++ ++
Sbjct: 251 LGHRLGISKERVRQIENRALEKLRRALAEK 280


>gi|229525043|ref|ZP_04414448.1| RNA polymerase sigma factor RpoH [Vibrio cholerae bv. albensis
           VL426]
 gi|229338624|gb|EEO03641.1| RNA polymerase sigma factor RpoH [Vibrio cholerae bv. albensis
           VL426]
          Length = 286

 Score =  194 bits (492), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 106/273 (38%), Positives = 163/273 (59%), Gaps = 9/273 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  +   PML   EE  LA+R    GD+ AA  L+ SHLR VV +A GY GYGLP+
Sbjct: 16  LDSYIRSVNGYPMLSADEERELAERLHYKGDIDAAKGLILSHLRFVVHVARGYSGYGLPM 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           +++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W +VKI TT  Q++L
Sbjct: 76  ADLVQEGNIGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR+ K  L    +      +V  +A++L V  +EV  M  RLA  ++   +    D+
Sbjct: 136 FFNLRKSKKRLGWFNNG-----EVETVARELGVEPAEVREMESRLAAQDAAFEMSAEDDE 190

Query: 196 NSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-QEN 251
           N   +   ++Y  D    +   L  +    +    L+ +++ L+ R + I  AR L  +N
Sbjct: 191 NGMAYTAPVLYLEDKHSDLADNLAAENWEAHTTQRLSMALASLDERSQHIVRARWLDDDN 250

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL++L+  + VS ER+RQ+E  A +K++E++
Sbjct: 251 KTTLQDLAEMYGVSAERIRQLEKNAMRKLKEAV 283


>gi|153209360|ref|ZP_01947367.1| alternative sigma factor RpoH [Coxiella burnetii 'MSU Goat Q177']
 gi|212217703|ref|YP_002304490.1| RNA polymerase factor sigma-32 [Coxiella burnetii CbuK_Q154]
 gi|120575393|gb|EAX32017.1| alternative sigma factor RpoH [Coxiella burnetii 'MSU Goat Q177']
 gi|212011965|gb|ACJ19345.1| RNA polymerase sigma-32 factor [Coxiella burnetii CbuK_Q154]
          Length = 288

 Score =  193 bits (491), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 108/277 (38%), Positives = 168/277 (60%), Gaps = 11/277 (3%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           G IG   YI  + +IP+L  +EE+ LA ++R+  DL AA +LV SHLR VV+IA GY GY
Sbjct: 16  GSIG--SYISLVNRIPLLSAEEEHDLANKFRQSNDLEAARKLVLSHLRFVVRIARGYSGY 73

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL  ++++ EGNIGLM+AVK+FDP+ G RL ++++ WI+A + E+IL++W +VKI TT  
Sbjct: 74  GLSQADLIQEGNIGLMKAVKRFDPQVGVRLVSFAVHWIRAEIHEFILKNWRIVKIATTKA 133

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALI 190
           Q++LFFNLR+        +D+     +  A+A++LNVS  +V  M  RL + DE+ +   
Sbjct: 134 QRKLFFNLRKHAKKRGWFSDH-----EAFALAEELNVSTKDVRQMEERLNSYDEAFDGAD 188

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEER---KNRRNMLTRSMSVLNPRERRIFEARR 247
             SD  +  W     Y  D +    ++ E      ++ + L  +M  L+ R R I   R 
Sbjct: 189 EESDSGTPSWGAPAHYLEDKRYNPALQLERSNWADDQEHRLHNAMQSLDDRSRDILYQRW 248

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L E   TL  L++++ VS ER+RQ+E  A +K++ ++
Sbjct: 249 LSEKKSTLHELAAQYAVSAERIRQLEKNAMQKIRTAM 285


>gi|118602568|ref|YP_903783.1| RNA polymerase, sigma 32 subunit, RpoH [Candidatus Ruthia magnifica
           str. Cm (Calyptogena magnifica)]
 gi|118567507|gb|ABL02312.1| RNA polymerase, sigma 32 subunit, RpoH [Candidatus Ruthia magnifica
           str. Cm (Calyptogena magnifica)]
          Length = 280

 Score =  193 bits (491), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 99/262 (37%), Positives = 171/262 (65%), Gaps = 7/262 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+L  ++E+ LA +  E+ DLSAA +LV SH+R V  IA GY+GYGL  +++V EG IGL
Sbjct: 23  PILNSEQEHELAVKLYENHDLSAARKLVLSHMRFVAFIAHGYKGYGLEQADLVQEGTIGL 82

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AVK+F+P R  RLA+++++WI+A + E+I ++W +VK+ TT  Q++LFF L++ K H+
Sbjct: 83  MKAVKRFNPNRNVRLASFAVYWIRAEIHEFIFKNWKIVKVATTKAQRKLFFKLKQAKAHI 142

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
            +    +L  EQ   IA  L V   +V+ M  RL  ++    +  S D++S   + +L  
Sbjct: 143 YS----SLNEEQADKIANDLGVRRKDVLEMESRLQFNDVTFEV--SDDEDSLAPEQYLTN 196

Query: 207 DH-DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
           ++    EQ+L+  + ++N++  L +++S L+ R   I ++R L+E   TL  L+ ++ +S
Sbjct: 197 ENVQTPEQLLLINDSKQNQQQQLYKALSSLDERSLDILQSRYLKEEKTTLHTLADKYGIS 256

Query: 266 RERVRQIEARAFKKVQESIQKQ 287
           +ERVRQ+E +A +K++ ++Q+Q
Sbjct: 257 KERVRQLETKAMQKLKSNLQEQ 278


>gi|50084493|ref|YP_046003.1| RNA polymerase factor sigma-32 [Acinetobacter sp. ADP1]
 gi|49530469|emb|CAG68181.1| sigma H (sigma 32) factor of RNA polymerase [Acinetobacter sp.
           ADP1]
          Length = 289

 Score =  193 bits (491), Expect = 2e-47,   Method: Compositional matrix adjust.
 Identities = 107/271 (39%), Positives = 162/271 (59%), Gaps = 8/271 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + L  YI  + +IP+L  ++E  LA+RY    DL AA  LV SHLR VV IA  Y GYGL
Sbjct: 18  VNLGAYISTVNQIPILTAEQEKELAERYYYDQDLDAAKMLVMSHLRFVVHIARSYAGYGL 77

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P  +++ EGN+GLM+AVK+FDP  G RL ++++ WIKA + EY++R+W +VKI TT  Q+
Sbjct: 78  PQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVKIATTKAQR 137

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
           +LFFNLR LK   + +T      E+  +IA  LNV+  +V+ M  RL   ++        
Sbjct: 138 KLFFNLRSLKKSSKKLT-----LEEAQSIANDLNVTPEQVLEMEGRLTAYDAAFETQGDD 192

Query: 194 DKNSSQWQDWLVYDHDGQEQV--LIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQE 250
           D +SS      +Y  D +     L E ++ + + +  L  +M+ L+ R R I + R L +
Sbjct: 193 DDDSSTHVAPALYLEDNRYDPARLAENDDYEEQSSTALHEAMNQLDDRSRNILQRRWLDD 252

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +  TL  L++E+ VS ER+RQ+E  A +K++
Sbjct: 253 DKSTLHELAAEYNVSAERIRQLEKNAMEKIK 283


>gi|254515828|ref|ZP_05127888.1| alternative sigma factor RpoH [gamma proteobacterium NOR5-3]
 gi|219675550|gb|EED31916.1| alternative sigma factor RpoH [gamma proteobacterium NOR5-3]
          Length = 303

 Score =  193 bits (490), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 104/269 (38%), Positives = 160/269 (59%), Gaps = 7/269 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+  + ++P+L  + E++LA++    GD+ AA  LV SHLR V  IA  YRGYGL  
Sbjct: 36  LAAYVQAVARVPVLSPEREHMLAEKLFYDGDVQAARELVMSHLRFVAHIARSYRGYGLSE 95

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGN+GLM+AVK+FDP +G RL ++++ WIKA + EYILR+W +VKI TT  Q++L
Sbjct: 96  ADLIQEGNVGLMKAVKRFDPTKGVRLVSFAVHWIKAEIHEYILRNWRIVKIATTKAQRKL 155

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR  K  L       L  ++  A+A  L V   EV  M  RL+  D + +A   S D
Sbjct: 156 FFNLRSAKKSLAW-----LSADEAQAVANDLGVDVQEVHRMEGRLSSHDVAFDAPAGSDD 210

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
               Q   + + D      + +E  E + + +  L  +++ L+ R R I   R L ++  
Sbjct: 211 DEGWQAPQYYLEDRSADPAIDVEDSEWQADSQAQLHAAIADLDERSRNILAQRWLTDDKA 270

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQE 282
           TL  L++E+ VS ER+RQ+E  A KK+++
Sbjct: 271 TLHELAAEYGVSAERIRQLEQAAMKKIRQ 299


>gi|88705470|ref|ZP_01103181.1| RNA polymerase sigma-32 factor [Congregibacter litoralis KT71]
 gi|88700560|gb|EAQ97668.1| RNA polymerase sigma-32 factor [Congregibacter litoralis KT71]
          Length = 338

 Score =  193 bits (490), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 104/267 (38%), Positives = 159/267 (59%), Gaps = 7/267 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+  + K+P+L    E+ LA++    GD+ AA  LV SHLR V  IA  YRGYGL  
Sbjct: 71  LAAYVQAVAKVPVLSADREHELAEKLFYDGDVQAARELVMSHLRFVAHIARSYRGYGLAE 130

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGN+GLM+AVK+FDP +G RL ++++ WIKA + EYILR+W +VKI TT  Q++L
Sbjct: 131 ADLIQEGNVGLMKAVKRFDPTKGVRLVSFAVHWIKAEIHEYILRNWRIVKIATTKAQRKL 190

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR  K  L  ++ +  K     A+A  L V   EV  M  RL+  D + +A + + D
Sbjct: 191 FFNLRSAKKSLAWLSADEAK-----AVADDLGVDVQEVHRMEGRLSSHDVAFDAPVGADD 245

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           +   Q   + + D        +E  E + + +  L  +++ L+ R R I   R L ++  
Sbjct: 246 EEGWQAPQYYLEDQSVDPATNVENSEWQADSQAQLHAAIAELDERSRNILAQRWLTDDKA 305

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKV 280
           TL  L++E++VS ER+RQ+E  A KK+
Sbjct: 306 TLHELAAEYDVSAERIRQLEQAAMKKI 332


>gi|1163231|gb|AAC45341.1| DNA polymerase sigma 32 subunit [Vibrio cholerae]
          Length = 286

 Score =  193 bits (490), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 108/274 (39%), Positives = 165/274 (60%), Gaps = 11/274 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  +   PML   EE  LA+R    GD+ AA  L+ SHLR VV +A GY GYGLP+
Sbjct: 16  LDSYIRSVNGYPMLSADEERELAERLHYKGDIDAAKGLILSHLRFVVHVARGYSGYGLPM 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           +++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W +VKI TT  Q++L
Sbjct: 76  ADLVQEGNIGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR+ K  L    +      +V  +A++L V  +EV  M  RLA  ++   +    D+
Sbjct: 136 FFNLRKSKKRLGWFNNG-----EVETVARELGVEPAEVREMESRLAAQDAAFEMSAEDDE 190

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV----LNPRERRIFEARRL-QE 250
           N   +   ++Y  D     L +  E +N     T+ +S+    L+   + I  AR L  +
Sbjct: 191 NGMAYTAPVLYLEDKHSD-LADNLEAENWEAHTTQRLSMALASLDDGSQHIVRARWLDDD 249

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           N  TL++L++++ VS ER+RQ+E  A +K++E++
Sbjct: 250 NKTTLQDLAAKYGVSAERIRQLEKNAMRKLKEAV 283


>gi|315635212|ref|ZP_07890490.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Aggregatibacter
           segnis ATCC 33393]
 gi|315476174|gb|EFU66928.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Aggregatibacter
           segnis ATCC 33393]
          Length = 283

 Score =  193 bits (490), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 105/287 (36%), Positives = 176/287 (61%), Gaps = 10/287 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+++  ++++  +  L  YI    + PML  +EE  LA+R   + D+ AA +LV SHLR 
Sbjct: 2   MDKETQTMMLVPQGSLEAYIRAANEYPMLTAEEEKELAERLYYNEDIEAAKKLVLSHLRF 61

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 62  VIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 121

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L    +N     +V  +A +L VS  +V+ M  R+
Sbjct: 122 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNEN-----EVDMVANELGVSPQDVVEMESRM 176

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQE-QVLIEKEERKNR-RNMLTRSMSVLNP 237
            G D + +  + + D +   +   L  +  G      +E E  + +  + L  +++ L+ 
Sbjct: 177 TGADVAFD--LPTDDHDEETYAPALYLEDKGSNFAAELENENYEAQATDQLVVALNNLDA 234

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R + I +AR L E   TL++L++++ +S ERVRQ+E  A KK++ ++
Sbjct: 235 RSQDIIKARWLDETKATLQDLAAKYNISAERVRQLETNALKKLKSAV 281


>gi|258625092|ref|ZP_05720011.1| RNA polymerase sigma -32 factor [Vibrio mimicus VM603]
 gi|258582643|gb|EEW07473.1| RNA polymerase sigma -32 factor [Vibrio mimicus VM603]
          Length = 286

 Score =  193 bits (490), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 108/274 (39%), Positives = 164/274 (59%), Gaps = 11/274 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  +   PML   EE  LA+R    GD+ AA  L+ SHLR VV +A GY GYGLP+
Sbjct: 16  LDSYIRSVNGYPMLSADEERELAERLHYKGDIDAAKGLILSHLRFVVHVARGYSGYGLPM 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           +++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W +VK+ TT  Q++L
Sbjct: 76  ADLVQEGNIGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR+ K  L    +      +V  +A++L V  +EV  M  RLA  ++   +    D+
Sbjct: 136 FFNLRKSKKRLGWFNNG-----EVETVARELGVEPAEVREMESRLAAQDAAFEMSAEDDE 190

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV----LNPRERRIFEARRL-QE 250
           N   +   ++Y  D     L +  E +N     T+ +S+    L+ R + I  AR L  +
Sbjct: 191 NGMAYTAPVLYLEDKHSD-LADNLEAENWEAHTTQRLSMALASLDERSQHIVRARWLDDD 249

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           N  TL++L+  + VS ER+RQ+E  A +K++E++
Sbjct: 250 NKTTLQDLAEMYGVSAERIRQLEKNAMRKLKEAV 283


>gi|284008659|emb|CBA75293.1| RNA polymerase sigma-32 factor [Arsenophonus nasoniae]
          Length = 292

 Score =  193 bits (490), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 109/282 (38%), Positives = 170/282 (60%), Gaps = 11/282 (3%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           +++++I  G I    Y+      PML  +EE   AKR   HGDL+AA +L+ SHLR V+ 
Sbjct: 13  QSLALIPQGSI--EAYVRSANAYPMLTAEEEQEYAKRLHYHGDLNAAKQLILSHLRFVIH 70

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W +
Sbjct: 71  IARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRI 130

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VK+ TT  Q++LFFNLR+ K  +     N     +V  +AK+L V+  +V  M  R+A  
Sbjct: 131 VKVATTKAQRKLFFNLRKNKKRIGWFNQN-----EVDMVAKELGVTSKDVREMESRMAAQ 185

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVL--IEKEERKNR-RNMLTRSMSVLNPRER 240
           +    + +  D   +     ++Y  D        IE++  +N   + LT+++S L+ R +
Sbjct: 186 DMAFDMNDDDDSGENTTIAPVLYLQDKSSDFADSIEEDNWENHATDKLTQALSTLDERSQ 245

Query: 241 RIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            I  AR L  EN  TL++L+ ++ VS ERVRQ+E  A KK++
Sbjct: 246 DIIRARWLDDENKTTLQDLADKYSVSAERVRQLEKNAMKKLR 287


>gi|89092456|ref|ZP_01165410.1| RNA polymerase sigma factor [Oceanospirillum sp. MED92]
 gi|89083544|gb|EAR62762.1| RNA polymerase sigma factor [Oceanospirillum sp. MED92]
          Length = 284

 Score =  193 bits (490), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 108/274 (39%), Positives = 165/274 (60%), Gaps = 11/274 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+  +  IP+L  +EE  LA+R    GD+ AA +LV SHLR VV +A  Y GYGLP+
Sbjct: 17  LDAYVQNVTAIPVLSVEEERSLAERLHFDGDVEAARQLVMSHLRFVVHVAKTYSGYGLPL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM+AVK+FDP  G RL ++++ W+KA M E+ILR+W +VK+ TT  Q++L
Sbjct: 77  GDLIQEGNVGLMKAVKRFDPTMGVRLVSFAVHWVKAEMHEFILRNWRIVKVATTKAQRKL 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR  K  L  +T++     +V AIA+ L V    V  M  R+A  D + +A   + D
Sbjct: 137 FFNLRSKKKSLSWMTND-----EVNAIAEDLGVEAKVVRQMEGRMASVDTAFDAPEGADD 191

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEK---EERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           + ++      + D      + +E+   E+   RR  L  +MS L+ R + I   R L ++
Sbjct: 192 EQAAWAPAHYLEDKSADPSMQLEEANWEQDSQRR--LMSAMSELDERSKDILARRWLTDD 249

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             TL  L++E+ VS ER+RQ+E  A KK++ S++
Sbjct: 250 KATLHELAAEYGVSAERIRQLEKNAMKKIRVSME 283


>gi|161829709|ref|YP_001597727.1| RNA polymerase factor sigma-32 [Coxiella burnetii RSA 331]
 gi|161761576|gb|ABX77218.1| alternative sigma factor RpoH [Coxiella burnetii RSA 331]
          Length = 288

 Score =  193 bits (490), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 107/277 (38%), Positives = 168/277 (60%), Gaps = 11/277 (3%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           G IG   YI  + +IP+L  +EE+ LA ++R+  DL AA +LV SHLR VV+IA GY GY
Sbjct: 16  GSIG--SYISWVNRIPLLSAEEEHDLANKFRQSNDLEAARKLVLSHLRFVVRIARGYSGY 73

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL  ++++ EGNIGLM+AVK+FDP+ G RL ++++ WI+A + E+IL++W +VKI TT  
Sbjct: 74  GLSQADLIQEGNIGLMKAVKRFDPQVGVRLVSFAVHWIRAEIHEFILKNWRIVKIATTKA 133

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALI 190
           Q++LFFNLR+        +D+     +  A+A++LNVS  +V  M  RL + DE+ +   
Sbjct: 134 QRKLFFNLRKHAKKRGWFSDH-----EAFALAEELNVSTKDVRQMEERLNSYDEAFDGAD 188

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEER---KNRRNMLTRSMSVLNPRERRIFEARR 247
             SD  +  W     Y  D +    ++ E      ++ + L  +M  ++ R R I   R 
Sbjct: 189 EESDSGTPSWGAPAHYLEDKRYNPALQLERSNWADDQEHRLHNAMQSMDDRSRDILYQRW 248

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L E   TL  L++++ VS ER+RQ+E  A +K++ ++
Sbjct: 249 LSEKKSTLHELAAQYSVSAERIRQLEKNAMQKIRTAM 285


>gi|110678526|ref|YP_681533.1| RNA polymerase factor sigma-32 [Roseobacter denitrificans OCh 114]
 gi|109454642|gb|ABG30847.1| RNA polymerase sigma-32 factor [Roseobacter denitrificans OCh 114]
          Length = 292

 Score =  192 bits (489), Expect = 3e-47,   Method: Compositional matrix adjust.
 Identities = 106/287 (36%), Positives = 180/287 (62%), Gaps = 9/287 (3%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M++    ++ LSR   +  K  +L+ + E  LA  +R+     + HRL+T+++RL + +A
Sbjct: 1   MALDSTRDMALSR---KAMKAELLDAETELELAYAWRDERCEKSLHRLITAYMRLAISMA 57

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             ++ YG P+++++ E  +GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+
Sbjct: 58  SKFKRYGAPMNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVR 117

Query: 126 IGTTANQKRLFFNLRRLKGHLQ---AITDNNLKPEQV-VAIAKKLNVSESEVISMNCRLA 181
            G+T++QK LFFN+RR++  L+   A +   L   Q+   I+ ++ V   +V  M  RL+
Sbjct: 118 TGSTSSQKSLFFNMRRVQARLERESAASGEPLDRHQLRQMISTEIGVPLHDVEMMEGRLS 177

Query: 182 G-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           G D SLNA   S++    +W D L  D     + +    + +  R  L ++M+ LN RER
Sbjct: 178 GSDYSLNA-TQSTEDEGREWIDALEDDSAQAAETVEHHHDTEQLRAWLLQAMNDLNERER 236

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            I   R+L++ P TLE+L  E  +S+ERVRQ+EA AF K+++S++ Q
Sbjct: 237 FIVRERKLRDAPRTLESLGQELNLSKERVRQLEAAAFGKMRKSLENQ 283


>gi|256823783|ref|YP_003147746.1| RNA polymerase sigma-32 subunit RpoH [Kangiella koreensis DSM
           16069]
 gi|256797322|gb|ACV27978.1| RNA polymerase, sigma 32 subunit, RpoH [Kangiella koreensis DSM
           16069]
          Length = 283

 Score =  192 bits (489), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 107/268 (39%), Positives = 164/268 (61%), Gaps = 7/268 (2%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+  +  IP+L  ++E  LA  + ++ DL AA +LV +HLR VV IA  Y GYGLP +++
Sbjct: 20  YVSTVSAIPVLSVEQEQKLAHEFHDNNDLEAARQLVMAHLRFVVYIARSYSGYGLPQADL 79

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM+AVK+FDP  G RL ++++ WIKA + EY+LR+W +VKI TT  Q++LFFN
Sbjct: 80  IQEGNIGLMKAVKRFDPTVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKLFFN 139

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSSDKNS 197
           LR  K  L     N L  ++V A+A+ L VSE EV  M  RL A D S +A   S D ++
Sbjct: 140 LRSKKKTL-----NWLNNDEVNAVAQDLGVSEEEVRRMEGRLNAHDASFDAPNASDDDDA 194

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENPVTLE 256
                  +   +      IE+E+ +++R + L  ++  L+ R + I + R L +   TL 
Sbjct: 195 VYAPIHYLESPNSDPAQAIEQEDWQDQREVRLMSALKTLDERSQDILQQRWLSDQKATLH 254

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
           +L+ ++ +S ER+RQ+E  A  K++ +I
Sbjct: 255 DLADKYGISAERIRQLEKNAMNKIKNAI 282


>gi|29655194|ref|NP_820886.1| RNA polymerase factor sigma-32 [Coxiella burnetii RSA 493]
 gi|6716381|gb|AAF26609.1|AF120928_1 heat-shock sigma factor [Coxiella burnetii]
 gi|29542466|gb|AAO91400.1| RNA polymerase sigma-32 factor [Coxiella burnetii RSA 493]
          Length = 288

 Score =  192 bits (489), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 107/277 (38%), Positives = 168/277 (60%), Gaps = 11/277 (3%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           G IG   YI  + +IP+L  +EE+ LA ++R+  DL AA +LV SHLR VV+IA GY GY
Sbjct: 16  GSIG--SYISWVNRIPLLSAEEEHDLANKFRQSNDLEAARKLVLSHLRFVVRIARGYSGY 73

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL  ++++ EGNIGLM+AVK+FDP+ G RL ++++ WI+A + E+IL++W +VKI TT  
Sbjct: 74  GLSQADLIQEGNIGLMKAVKRFDPQVGVRLVSFAVHWIRAEIHEFILKNWRIVKIATTKA 133

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALI 190
           Q++LFFNLR+        +D+     +  A+A++LNVS  +V  M  RL + DE+ +   
Sbjct: 134 QRKLFFNLRKHAKKRGWFSDH-----EAFALAEELNVSTKDVRQMEERLNSYDEAFDGAD 188

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEER---KNRRNMLTRSMSVLNPRERRIFEARR 247
             SD  +  W     Y  D +    ++ E      ++ + L  +M  ++ R R I   R 
Sbjct: 189 EESDSGTPSWGAPAHYLEDKRYNPALQLERSNWADDQEHRLHNAMQSMDDRSRDILYQRW 248

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L E   TL  L++++ VS ER+RQ+E  A +K++ ++
Sbjct: 249 LSEKKSTLHELAAQYAVSAERIRQLEKNAMQKIRTAM 285


>gi|88813090|ref|ZP_01128332.1| RpoH [Nitrococcus mobilis Nb-231]
 gi|88789723|gb|EAR20848.1| RpoH [Nitrococcus mobilis Nb-231]
          Length = 292

 Score =  192 bits (489), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 109/266 (40%), Positives = 160/266 (60%), Gaps = 8/266 (3%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           YI  + ++P L  +EEY LA+RYR+H DL AA  LV SHLR VV IA GY+GYGLP++++
Sbjct: 25  YIQAVNRLPTLSAEEEYQLARRYRDHNDLKAARGLVLSHLRFVVHIARGYKGYGLPLTDL 84

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM+AVK+FDP  G RL ++++ WI+A + E+ILR+W +VK+ TT  Q++LFFN
Sbjct: 85  IQEGNIGLMKAVKRFDPAVGVRLVSFAVHWIRAEIHEFILRNWRIVKVATTKAQRKLFFN 144

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSS-DKN 196
           LR  K  L       L   +V A+A  L V    V  M  RL+G E S +   +++ D +
Sbjct: 145 LRGAKKRL-----GWLNRAEVDAVANDLGVKPETVQEMELRLSGQEVSFDPGPDAAEDDD 199

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
             +     + D        IE  + + ++   L  +++ L+ R R I   R L E   TL
Sbjct: 200 IVRAPAAYLRDQRPNPAEEIESHDWQTHQSESLATALAHLDERSRAIVHERWLNEPKATL 259

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           + L+  + VS ER+RQ+E  A KK++
Sbjct: 260 QELAERYAVSAERIRQLEKNALKKLR 285


>gi|293391201|ref|ZP_06635535.1| alternative sigma factor RpoH [Aggregatibacter
           actinomycetemcomitans D7S-1]
 gi|290951735|gb|EFE01854.1| alternative sigma factor RpoH [Aggregatibacter
           actinomycetemcomitans D7S-1]
          Length = 282

 Score =  192 bits (489), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 105/287 (36%), Positives = 170/287 (59%), Gaps = 10/287 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+++  ++++  +  +  YI    + PML  +EE  LA+R     D+ AA +LV SHLR 
Sbjct: 1   MDKETQTMMLVPQGSIEAYIRAANEYPMLTAEEEKELAERLYYKEDIEAAKKLVLSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L    +N     +V  +A +L VS  +V+ M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNEN-----EVDMVANELGVSPQDVMEMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK---NRRNMLTRSMSVLNP 237
            G +   A     D++  +     +Y  D       E E         + L  ++  L+ 
Sbjct: 176 TGADV--AFDLPGDEHDEETYAPALYLEDKSSNFAAELENENYEAQATDQLAVALDNLDA 233

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R + I +AR L E   TL++L++++ +S ERVRQ+EA A KK++ ++
Sbjct: 234 RSQDIIKARWLDETKATLQDLAAKYNISAERVRQLEANALKKLKSAV 280


>gi|322513377|ref|ZP_08066496.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Actinobacillus
           ureae ATCC 25976]
 gi|322120867|gb|EFX92727.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Actinobacillus
           ureae ATCC 25976]
          Length = 318

 Score =  192 bits (489), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 101/270 (37%), Positives = 161/270 (59%), Gaps = 6/270 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI    + P+L  ++E  LA+RY    DL AA +L+ SH+R V+ IA GY GYGLP+
Sbjct: 51  LDSYIRMANQYPILSAEQEKELAERYYYDEDLEAAKQLILSHMRFVIHIARGYLGYGLPL 110

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AVK+FDP  G RL ++++ W+KA + EY+L++W +VK+ TT  Q++L
Sbjct: 111 ADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWVKAEIHEYVLKNWRIVKVATTKAQRKL 170

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR+ K  L    ++ +K      +A+ L VS  EV  M  R+ G +    L    D 
Sbjct: 171 FFNLRKNKNRLAWFNEDEIKK-----VAEDLGVSVEEVREMESRMTGQDLGFDLPAGEDD 225

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENPVT 254
           + +      + D+       +E EE        L  +++ L+ R + I + R L E+  T
Sbjct: 226 DEAYAPSMYIEDNSSNFADELEDEEHTGEATAQLAYALATLDERSQDIIKTRWLDEDKAT 285

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L++L+ ++ +S ERVRQ+E  A KK++++I
Sbjct: 286 LQDLADKYGISAERVRQLENAALKKIKDAI 315


>gi|251793696|ref|YP_003008426.1| RNA polymerase factor sigma-32 [Aggregatibacter aphrophilus NJ8700]
 gi|247535093|gb|ACS98339.1| alternative sigma factor RpoH [Aggregatibacter aphrophilus NJ8700]
          Length = 282

 Score =  192 bits (489), Expect = 4e-47,   Method: Compositional matrix adjust.
 Identities = 105/289 (36%), Positives = 172/289 (59%), Gaps = 14/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+++  ++++  +  L  YI    + PML  +EE  LA+R     D+ AA +LV SHLR 
Sbjct: 1   MDKETQTMMLVPQGSLEAYIRAANEYPMLTAEEEKELAERLYYQEDIDAAKKLVLSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K      ++N     +V  +A +L VS  +V+ M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRFGWFSEN-----EVDMVANELGVSPQDVVEMESRM 175

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV----L 235
            G D + +  + + D +   +   L  +  G       + E +N     T  ++V    L
Sbjct: 176 TGADVAFD--LPTDDHDEETYAPALYLEDKGSN--FAAELENENYEAQATDRLAVALDNL 231

Query: 236 NPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + R + I +AR L E   TL++L+ ++ +S ERVRQ+E  A KK++ ++
Sbjct: 232 DARSQDIIKARWLDETKATLQDLAEKYNISAERVRQLETNALKKLKSAV 280


>gi|89900482|ref|YP_522953.1| sigma 32 (RpoH) [Rhodoferax ferrireducens T118]
 gi|89345219|gb|ABD69422.1| sigma 32 (RpoH) [Rhodoferax ferrireducens T118]
          Length = 313

 Score =  192 bits (488), Expect = 5e-47,   Method: Compositional matrix adjust.
 Identities = 108/283 (38%), Positives = 170/283 (60%), Gaps = 14/283 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI    ++PML  +EE   ++++R+  DL+AA +LV SHLRLVV ++  Y GYGLP 
Sbjct: 27  LDAYISAANRLPMLTLEEEQEFSRKFRQDNDLAAAGKLVLSHLRLVVSVSRQYLGYGLPH 86

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM+AVK+FDP+ G RL +Y++ WIKA + EYIL++W +VK+ TT  Q++L
Sbjct: 87  GDLIQEGNVGLMKAVKRFDPDHGVRLVSYALHWIKAEIHEYILKNWRMVKVATTKAQRKL 146

Query: 136 FFNLRRLKGHLQ---AITD-----NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
           FFNLR +K   +   A  D     + L  +Q+ A+A +L V   EV+ M  RL+G + L 
Sbjct: 147 FFNLRSMKQRYKSDDAAADLGTHRDTLNEDQIDAMALELRVKREEVMEMETRLSGGDVLL 206

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLNPRERRIFEAR 246
               + D + +      + D   +   +IE  +R     + +  ++  L+ R RRI E R
Sbjct: 207 DPSPTDDGDDAFGPIAYLTDTRHEPTEMIEAHQRDLLASDGIATALEALDERSRRIVEER 266

Query: 247 RLQENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L+ N      +TL  L++ + VS ER+RQIE  A KK+++++
Sbjct: 267 WLKVNDDNSGGMTLHELAAVYGVSAERIRQIEVAAMKKMKKTL 309


>gi|84393530|ref|ZP_00992284.1| RNA polymerase sigma factor [Vibrio splendidus 12B01]
 gi|84375809|gb|EAP92702.1| RNA polymerase sigma factor [Vibrio splendidus 12B01]
          Length = 291

 Score =  192 bits (488), Expect = 5e-47,   Method: Compositional matrix adjust.
 Identities = 111/273 (40%), Positives = 161/273 (58%), Gaps = 12/273 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI      PML  +EE  LA+R    G++ AA  L+ SHLR VV +A GY GYGLP+
Sbjct: 16  LDSYIRSANSYPMLTPEEERGLAERLHYKGEIDAAKGLILSHLRFVVHVARGYSGYGLPM 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           +++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W +VKI TT  Q++L
Sbjct: 76  ADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR+ K  L    +      +V  +A++L V  SEV  M  RLA  D +  A ++  D
Sbjct: 136 FFNLRKSKKRLGWFNNG-----EVETVARELGVEPSEVREMESRLAAQDATFEAPMDDDD 190

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKN----RRNMLTRSMSVLNPRERRIFEARRLQE 250
             S+      VY  + +   + E  E  N      N L  ++  L+ R + I  +R L +
Sbjct: 191 GGSAYTAP--VYYLEDKASDVAETVEAANWESHTNNRLGLALKSLDERSQHIVRSRWLDD 248

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           N  TL++L+  + +S ERVRQ+E  A KK++ S
Sbjct: 249 NKSTLQDLADTYSISAERVRQLEKNAMKKLKAS 281


>gi|153005405|ref|YP_001379730.1| RNA polymerase sigma-70 [Anaeromyxobacter sp. Fw109-5]
 gi|152028978|gb|ABS26746.1| RNA polymerase sigma-70 [Anaeromyxobacter sp. Fw109-5]
          Length = 357

 Score =  192 bits (487), Expect = 6e-47,   Method: Compositional matrix adjust.
 Identities = 116/289 (40%), Positives = 184/289 (63%), Gaps = 14/289 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ EI + P+L ++EE+ LA RYRE GD+ AA+RLV S+LRLVVKIA  YR     +
Sbjct: 71  LRAYMAEIARHPLLSREEEHELAVRYRETGDVDAAYRLVASNLRLVVKIAHEYRRTAFQL 130

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++V EGN+GLMQAVKK+DP +G +L++Y+ WWI+A +  +I+ +W +VK+GTT  Q++L
Sbjct: 131 LDLVQEGNMGLMQAVKKYDPWKGVKLSSYAAWWIRAYIIRFIMENWRMVKLGTTQAQRKL 190

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNL + +  L A     ++P   + +AK L+V E +V  M  R+AG D SL+A +   +
Sbjct: 191 FFNLAKEREKLLA---RGIEPTPRL-LAKNLDVEEKDVEEMTARMAGEDLSLDAPLRGDE 246

Query: 195 KNSSQWQ-DWLVYDH-DGQEQVLIEKEERKNRRNML-TRSMSVLNPRERRIFEARRLQ-- 249
             S Q + D +  D  D  ++ L +++ R+  R  L T S ++ + +ER IF+ R L   
Sbjct: 247 DGSRQTRLDRVAGDGADAPDERLGDEQLRRLFREKLETFSKTIRDEKERYIFDKRLLPAG 306

Query: 250 -ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV---ELSSSP 294
            E P+TL+ +   F+++RER RQIEA+   ++++ ++ ++   EL   P
Sbjct: 307 GEAPLTLQEIGDRFKLTRERARQIEAKLTARLRDYLRAEIPDFELLGPP 355


>gi|110835430|ref|YP_694289.1| RNA polymerase sigma-32 factor [Alcanivorax borkumensis SK2]
 gi|110648541|emb|CAL18017.1| RNA polymerase sigma-32 factor [Alcanivorax borkumensis SK2]
          Length = 289

 Score =  192 bits (487), Expect = 6e-47,   Method: Compositional matrix adjust.
 Identities = 106/281 (37%), Positives = 164/281 (58%), Gaps = 8/281 (2%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +++ V G   L  Y+  +  +P+L  +EE  L +R     DL AA  LV SHLR V  IA
Sbjct: 13  LTLAVPGH-DLDAYMRAVNAVPVLSAEEEQRLGERLYYDQDLDAARSLVLSHLRFVAHIA 71

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGLP+ ++V EGN+GLM+AVK+FDP +G RL ++++ WIKA + EY++++W +VK
Sbjct: 72  RSYTGYGLPLGDLVQEGNVGLMKAVKRFDPTKGVRLVSFAVHWIKAEIHEYVIKNWRIVK 131

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDE 184
           + TT  Q++LFFNLR  K  L       L  E+   +A  L V+ ++V  M  RL A D 
Sbjct: 132 VATTKAQRKLFFNLRGQKKRL-----GRLTLEEAQRVADDLGVTAAQVKEMEGRLGAYDA 186

Query: 185 SLNALINSSDKNS-SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           S +   N  D ++      +L  D+     +L E+++++     L+ ++  L+ R R I 
Sbjct: 187 SFDGPTNDDDDSTVVSPAAYLHSDNSDPADLLAEQDQQQRESRQLSSALMALDERSRDIL 246

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           E R L +   TL+ L+ E+ VS ER+RQ+E  A KK++ +I
Sbjct: 247 ERRWLADQKSTLQELADEYSVSAERIRQLENNAIKKLRNAI 287


>gi|254363063|ref|ZP_04979122.1| DNA-directed RNA polymerase sigma subunit RpoH [Mannheimia
           haemolytica PHL213]
 gi|261492837|ref|ZP_05989384.1| DNA-directed RNA polymerase sigma subunit RpoH [Mannheimia
           haemolytica serotype A2 str. BOVINE]
 gi|261494798|ref|ZP_05991276.1| DNA-directed RNA polymerase sigma subunit RpoH [Mannheimia
           haemolytica serotype A2 str. OVINE]
 gi|153094728|gb|EDN75518.1| DNA-directed RNA polymerase sigma subunit RpoH [Mannheimia
           haemolytica PHL213]
 gi|261309509|gb|EEY10734.1| DNA-directed RNA polymerase sigma subunit RpoH [Mannheimia
           haemolytica serotype A2 str. OVINE]
 gi|261311519|gb|EEY12675.1| DNA-directed RNA polymerase sigma subunit RpoH [Mannheimia
           haemolytica serotype A2 str. BOVINE]
          Length = 319

 Score =  192 bits (487), Expect = 6e-47,   Method: Compositional matrix adjust.
 Identities = 101/270 (37%), Positives = 159/270 (58%), Gaps = 6/270 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI    + P+L  ++E  LA+RY    D+ AA +L+ SH+R V+ IA GY GYGLP+
Sbjct: 51  LDSYIRMANQYPILTAEQEKELAERYYYDEDVEAAKQLILSHMRFVIHIARGYLGYGLPL 110

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AVK+FDP  G RL ++++ W+KA + EY+L++W +VK+ TT  Q++L
Sbjct: 111 ADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWVKAEIHEYVLKNWRIVKVATTKAQRKL 170

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR+ K  L    +     E++  +A  L VS  EV  M  R+ G +    L    D 
Sbjct: 171 FFNLRKNKNRLAWFNE-----EEIKKVADDLGVSVEEVREMESRMTGQDLGFDLPAGDDD 225

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENPVT 254
             S      + D        +E E+   +    L  +++ L+ R + I + R L +N  T
Sbjct: 226 EDSYAPSMYIEDSSSNFADDLEDEQHNGQATAQLAYALATLDERSQDIIKTRWLDDNKAT 285

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L++L+ ++ +S ERVRQ+E  A KK++E+I
Sbjct: 286 LQDLADKYNISAERVRQLENAALKKIKEAI 315


>gi|218885581|ref|YP_002434902.1| RNA polymerase, sigma 70 family subunit [Desulfovibrio vulgaris
           str. 'Miyazaki F']
 gi|218756535|gb|ACL07434.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio
           vulgaris str. 'Miyazaki F']
          Length = 474

 Score =  192 bits (487), Expect = 6e-47,   Method: Compositional matrix adjust.
 Identities = 110/280 (39%), Positives = 175/280 (62%), Gaps = 7/280 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLP 74
           L  Y+ EI + P+L+  EE+ LA+R +E GD  AA RLVTSHLRLVVKIAM + R +   
Sbjct: 195 LHLYLREISRFPLLKPDEEFDLARRVQEQGDSDAAFRLVTSHLRLVVKIAMDFQRRWMQN 254

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++ EGN+GLM+AV KFDPE+G + + Y+ +WIKA + ++I+ +W +VKIGTT  Q++
Sbjct: 255 VLDLIQEGNVGLMRAVNKFDPEKGIKFSYYAAFWIKAYILKFIMDNWRMVKIGTTQAQRK 314

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSS 193
           LF+NL + +  L A       P+  + +++KLNV+  +VI M  RL + D SL+  +   
Sbjct: 315 LFYNLNKERQRLIA---QGYDPDATI-LSEKLNVTVEQVIEMEQRLDSSDMSLDITVG-E 369

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D   +   D+L     G E+ L   E  +  ++ +   +  L+ +E  I + R L E PV
Sbjct: 370 DSGGATRMDFLPALGPGIEETLANSEIARMVQDRVQTILPKLSDKEAYILQHRLLSEQPV 429

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           TL  +  +++++RERVRQIEAR  +K+++ + K++   SS
Sbjct: 430 TLREIGEKYDITRERVRQIEARLLQKLRDHLFKEIRDFSS 469


>gi|212703179|ref|ZP_03311307.1| hypothetical protein DESPIG_01221 [Desulfovibrio piger ATCC 29098]
 gi|212673445|gb|EEB33928.1| hypothetical protein DESPIG_01221 [Desulfovibrio piger ATCC 29098]
          Length = 364

 Score =  192 bits (487), Expect = 6e-47,   Method: Compositional matrix adjust.
 Identities = 109/277 (39%), Positives = 170/277 (61%), Gaps = 7/277 (2%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY- 68
             G   L  Y+ E+ + PML+ +EE+ LA R R+H D  AA RLV+SHLRLVV+IAM + 
Sbjct: 80  TGGRDSLQLYLREVSRFPMLKPEEEHELAVRVRDHNDPDAAFRLVSSHLRLVVRIAMDFQ 139

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           R +   + ++V EGN+GLM+AV KFDP++G + + Y+ +WIKA + ++I+ +W +VKIGT
Sbjct: 140 RRWMQNVLDLVQEGNVGLMRAVNKFDPDKGIKFSYYASFWIKAYILKFIMDNWRMVKIGT 199

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN 187
           T  Q++LF+NL R +   Q +      P+  + ++++L VSE ++  M+ RLA  D SLN
Sbjct: 200 TQVQRKLFYNLNRER---QKLIAQGFDPDAAM-LSERLGVSEEQITEMDQRLAANDLSLN 255

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           A +   D   +   D+L     G E  L + E  +  R  L   +  LN +E  I + R 
Sbjct: 256 AQV-GEDAGGATRMDFLPALGPGIEDSLGDSEVAELLREKLKTILPKLNEKELYILQNRL 314

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L ++PVTL  +   + V+RERVRQ+EAR  +K+++ +
Sbjct: 315 LTDDPVTLREIGERYNVTRERVRQLEARLLEKIRQHL 351


>gi|317494584|ref|ZP_07952997.1| alternative sigma factor RpoH [Enterobacteriaceae bacterium
           9_2_54FAA]
 gi|316917514|gb|EFV38860.1| alternative sigma factor RpoH [Enterobacteriaceae bacterium
           9_2_54FAA]
          Length = 283

 Score =  192 bits (487), Expect = 7e-47,   Method: Compositional matrix adjust.
 Identities = 107/287 (37%), Positives = 168/287 (58%), Gaps = 7/287 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  Y+      PML  +EE  L +R    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLTLVPQGSLEAYVRAANTYPMLTAEEEKELGERLHYEGDLDAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEMGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VSE +V+ M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVELVARELGVSEKDVLEMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRE 239
           A  +    + N  D++S       + D        IE +    +  + LT +M  L+ R 
Sbjct: 176 AAQDMAFDMSNDDDESSPAAPVLFLQDKSSDFANDIEDDNWDSHAADKLTLAMEGLDERS 235

Query: 240 RRIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + I  AR L  +N  TL+ L+ ++ VS ERVRQ+E  A KK++ +I+
Sbjct: 236 QHIIRARWLDDDNKATLQELADQYGVSAERVRQLEKNAMKKLRAAIE 282


>gi|260771645|ref|ZP_05880565.1| RNA polymerase sigma-32 factor [Vibrio metschnikovii CIP 69.14]
 gi|260613422|gb|EEX38621.1| RNA polymerase sigma-32 factor [Vibrio metschnikovii CIP 69.14]
          Length = 285

 Score =  192 bits (487), Expect = 7e-47,   Method: Compositional matrix adjust.
 Identities = 111/272 (40%), Positives = 166/272 (61%), Gaps = 8/272 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  +   PML  +EE  LA+R    GD+ AA  L+ SHLR VV +A GY GYGLPI
Sbjct: 16  LDSYIRSVSSYPMLTAEEERELAERLHYSGDIEAAKTLILSHLRFVVHVARGYSGYGLPI 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           +++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W +VKI TT  Q++L
Sbjct: 76  ADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR+ K  L    +      +V  +A++L V  +EV  M  RLA  +S        D 
Sbjct: 136 FFNLRKSKKRLGWFNNG-----EVETVARELGVEPAEVREMESRLAALDSTFEFSAEDDD 190

Query: 196 NSSQWQDWLVYDHDGQEQVL--IEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENP 252
           N + +   ++Y  D Q  +   IE +  +N  N  L+ +++ L+ R + I  +R L +  
Sbjct: 191 NPNAYTAPVLYLEDKQSDLAENIEAQNWENHTNHRLSLALASLDERSQHIVRSRWLDDQK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL+ L+  ++VS ER+RQ+E  A KK++E++
Sbjct: 251 ATLQELADLYQVSAERIRQLEKNAMKKLKEAV 282


>gi|160871836|ref|ZP_02061968.1| alternative sigma factor RpoH [Rickettsiella grylli]
 gi|159120635|gb|EDP45973.1| alternative sigma factor RpoH [Rickettsiella grylli]
          Length = 290

 Score =  192 bits (487), Expect = 7e-47,   Method: Compositional matrix adjust.
 Identities = 107/277 (38%), Positives = 172/277 (62%), Gaps = 14/277 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           YI  +++IP+L  +EE  LA+RY +H DL AA +L+ ++LR VV IA  Y GYGL ++++
Sbjct: 20  YITRLKQIPVLSAEEEIELAERYYQHHDLDAAKKLIITNLRFVVHIAQTYMGYGLALADL 79

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM+AVK+FDP+ G RL ++++ WIKA +QE+ILR+W +VKI TT  Q++LFFN
Sbjct: 80  IQEGNIGLMKAVKRFDPKVGVRLISFAVHWIKAEIQEFILRNWRIVKIATTKAQRKLFFN 139

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR++K  L     N     ++ A+A  L V    V  M  RLA  D SL+  I+  D N 
Sbjct: 140 LRKMKKRLGWFNQN-----EIEAVAHDLGVKPETVREMEFRLASNDMSLD--ISHDDPNE 192

Query: 198 SQWQDWLVYDHDGQE------QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           ++   + + D   ++      ++L      ++  + L ++++ L+ RE+ I   R L E 
Sbjct: 193 AKSTRYPLLDIHFEDNRYDPARLLEASNSTESNHDNLYKALTQLDEREQNIIRDRWLMEP 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +TL+ L+  + VS ER+RQ+E +A K ++ ++ +Q 
Sbjct: 253 KMTLQELAQRYHVSAERIRQLEQKAMKALRHTLLQQT 289


>gi|163854463|ref|YP_001628761.1| RNA polymerase factor sigma-32 [Bordetella petrii DSM 12804]
 gi|163258191|emb|CAP40490.1| RNA polymerase sigma-32 factor [Bordetella petrii]
          Length = 295

 Score =  192 bits (487), Expect = 7e-47,   Method: Compositional matrix adjust.
 Identities = 119/289 (41%), Positives = 179/289 (61%), Gaps = 15/289 (5%)

Query: 2   NRKNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           N   ++I   G +G +  YI  + ++P+L  + E  L +R R+  DL AA  LV SHLRL
Sbjct: 13  NALALAIANPGSLGTIEAYISAVNRLPVLTAERETELGRRLRDRDDLDAARELVLSHLRL 72

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y GYGLP ++++ EGN+GLM+AVK+FDPERG RL ++++ WIKA + E+I+R+
Sbjct: 73  VVSVARQYLGYGLPHADLIQEGNVGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEFIIRN 132

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR ++   Q      L PEQV  IA++LNV   +V  M  RL
Sbjct: 133 WRMVKVATTKAQRKLFFNLRSMRPDGQ-----TLDPEQVDRIAQELNVRREDVSEMEVRL 187

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQ---VLIEKEERKNRRNMLTRSMSVLN 236
           +G D SL       D +   +        +G+++   VL  ++  + +   L  ++  L+
Sbjct: 188 SGRDLSL----EKQDDDEEAFAPISYLSDEGRQEPTRVLDRRDHDELQGAGLAHALQALD 243

Query: 237 PRERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            R RRI EAR LQ++  VTL+ L+ EF VS ER+RQIE+ A KK++ ++
Sbjct: 244 ARSRRIIEARWLQDDGGVTLQELAQEFGVSAERIRQIESAALKKMRGAL 292


>gi|78357159|ref|YP_388608.1| sigma 70 family protein [Desulfovibrio desulfuricans subsp.
           desulfuricans str. G20]
 gi|78219564|gb|ABB38913.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfovibrio desulfuricans
           subsp. desulfuricans str. G20]
          Length = 360

 Score =  191 bits (486), Expect = 8e-47,   Method: Compositional matrix adjust.
 Identities = 108/281 (38%), Positives = 177/281 (62%), Gaps = 7/281 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGL 73
            L  Y+ EI + PML+  EE+ LA+R + H D  AA RLV+SHLRLVVKIAM + R +  
Sbjct: 80  SLHLYLREISRFPMLKPDEEFELARRVQLHNDSDAAFRLVSSHLRLVVKIAMDFQRRWMQ 139

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++ EGN+GLM+AV KFDP++G + + Y+ +WIKA + ++I+ +W LVKIGTT  Q+
Sbjct: 140 NVLDLIQEGNVGLMRAVNKFDPDKGIKFSYYAAFWIKAYILKFIMDNWRLVKIGTTQAQR 199

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINS 192
           +LF+NL + +  L A       P+  + ++++L+V+  +V+ M  RL A D SL+  +  
Sbjct: 200 KLFYNLNKERQKLIA---QGYDPDAAM-LSERLDVTTEQVVEMEQRLDASDMSLDVQVGD 255

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            + ++S+  D+L     G E  L   E     +  +   + +LN +E  I  +R L E+P
Sbjct: 256 ENGSASR-MDFLPALGPGIEDTLANNEIAAMVQERIRDIVPLLNDKELDILNSRLLSEDP 314

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           VTL  +  +++++RERVRQIEAR  +K+++ + K+++  SS
Sbjct: 315 VTLREIGEKYDITRERVRQIEARLLQKIRDHLFKEIKDFSS 355


>gi|307546422|ref|YP_003898901.1| RNA polymerase factor sigma-32 [Halomonas elongata DSM 2581]
 gi|307218446|emb|CBV43716.1| RNA polymerase factor sigma-32 [Halomonas elongata DSM 2581]
          Length = 288

 Score =  191 bits (486), Expect = 9e-47,   Method: Compositional matrix adjust.
 Identities = 112/273 (41%), Positives = 161/273 (58%), Gaps = 11/273 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ YI  +  IPML   EE  LA R  + GDL AA RLV SHLR VV IA  Y GYGL  
Sbjct: 17  LNGYIQAVNGIPMLTVDEERELAFRLHDEGDLEAARRLVMSHLRFVVHIARSYSGYGLAQ 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGN+GLM+AVK+FDP +G RL ++++ WIKA + E++LR+W +VK+ TT  Q++L
Sbjct: 77  ADLIQEGNVGLMKAVKRFDPNQGVRLVSFAVHWIKAEIHEFVLRNWRIVKVATTKAQRKL 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSSD 194
           FFNLR  K  L  +  N     +V AIAK L+V    V  M  RL A D   +A     +
Sbjct: 137 FFNLRGAKKRLAWLNSN-----EVEAIAKDLDVKPEVVREMEGRLSAHDAGFDAA--PGE 189

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
              S +Q  + Y  D  +    + E+    ++    L  ++S L+ R R I + R L ++
Sbjct: 190 DEESAYQAPVHYLDDASQDPATQLEDSDWEEDSTQRLQAALSELDERSRDILQRRWLSDD 249

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL +L+  + VS ER+RQ+E  A KK+++SI
Sbjct: 250 KSTLHDLADVYGVSAERIRQLEKNAMKKIRQSI 282


>gi|323492929|ref|ZP_08098069.1| RNA polymerase factor sigma-32 [Vibrio brasiliensis LMG 20546]
 gi|323312822|gb|EGA65946.1| RNA polymerase factor sigma-32 [Vibrio brasiliensis LMG 20546]
          Length = 285

 Score =  191 bits (486), Expect = 9e-47,   Method: Compositional matrix adjust.
 Identities = 109/287 (37%), Positives = 167/287 (58%), Gaps = 8/287 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  +   + V  +  L  YI  +   PML   EE  LA+R    G++ AA  L+ SHLR 
Sbjct: 1   MTNQAYPMAVVTQDSLDSYIRSVNSYPMLTADEERELAERLHYDGEIEAAKGLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A GY GYGLP++++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VKI TT  Q++LFFNLR+ K  L    +      +V  +A++L V  +EV  M  RL
Sbjct: 121 WRIVKIATTKAQRKLFFNLRKSKKRLGWFNNG-----EVETVARELGVEPAEVREMESRL 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNP 237
           A  ++   + +  D ++S +   +VY  D    V    E      +  N L+ ++  L+ 
Sbjct: 176 AAQDATFEMPSDDDDSASSYTAPMVYLEDKASDVADNVEAANWEAHTNNRLSLALKTLDD 235

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R + I  +R L +N  TL+ L+  + VS ER+RQ+E  A KK++ ++
Sbjct: 236 RSQHIVRSRWLDDNKSTLQELAETYSVSAERIRQLEKNAMKKLKAAV 282


>gi|317154823|ref|YP_004122871.1| sigma-70 family RNA polymerase sigma factor [Desulfovibrio
           aespoeensis Aspo-2]
 gi|316945074|gb|ADU64125.1| RNA polymerase sigma factor, sigma-70 family [Desulfovibrio
           aespoeensis Aspo-2]
          Length = 397

 Score =  191 bits (486), Expect = 9e-47,   Method: Compositional matrix adjust.
 Identities = 109/275 (39%), Positives = 173/275 (62%), Gaps = 8/275 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLP 74
           L  Y+ EI + P+L+ +EEY LAKR ++  D  AA +LV+SHLRLVV+IAM + R +   
Sbjct: 117 LQLYLKEIARFPLLDPEEEYALAKRVQDENDQDAAFKLVSSHLRLVVRIAMDFQRRWMQN 176

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
             +++ EGN+GL++AV KFDPE+G + + Y+ +W+KA + +YI+ +W +VK+GTT  Q++
Sbjct: 177 ALDLIQEGNVGLLKAVTKFDPEKGIKFSYYAAFWVKAYILKYIMDNWRMVKVGTTQTQRK 236

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALINSS 193
           LF+NL + +  LQA+      P    A++K L VSE+E+  M+ RL+  D SLNA +   
Sbjct: 237 LFYNLNKERQRLQAM---GFDP-TTEALSKSLGVSEAEIDEMDQRLSRNDMSLNAPLG-E 291

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D ++++  D+L     G E+ L   +  +     L      LN +E  I + R L ++P+
Sbjct: 292 DSDATR-MDFLPSLGPGIEESLASDQIVELLLENLKAIRPTLNDKELAILDHRLLSDDPM 350

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           TL  +   FEV+RERVRQIEAR   K++E + +++
Sbjct: 351 TLREIGERFEVTRERVRQIEARLIAKIREHMTEKI 385


>gi|153873537|ref|ZP_02002087.1| RNA polymerase sigma-32 factor [Beggiatoa sp. PS]
 gi|152069997|gb|EDN67913.1| RNA polymerase sigma-32 factor [Beggiatoa sp. PS]
          Length = 288

 Score =  191 bits (485), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 112/283 (39%), Positives = 172/283 (60%), Gaps = 9/283 (3%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           N  + V G   +  Y   I+ IP+L  + E  LA+R+    D+ AA  LV SHLR V+ I
Sbjct: 8   NQQLAVPG-TSIEGYAQAIKAIPLLSIEAERKLAERFIGEDDIEAARTLVMSHLRFVMHI 66

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  YRGYGLP ++++ EGNIGLM+AVK+FDP  G RL ++++ WI+A + EYILR+W +V
Sbjct: 67  AHNYRGYGLPQADLIQEGNIGLMKAVKRFDPTVGVRLVSFAVHWIRAEIHEYILRNWRIV 126

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGD 183
           K+ TT +Q++LFFNLR  K  L  +T      ++V  +AK L VS  +V  M  RL + D
Sbjct: 127 KVATTKSQRKLFFNLRSAKKRLGWLTQ-----DEVETVAKDLGVSPKDVREMELRLNSYD 181

Query: 184 ESLNALINSSDKNSSQWQD-WLVYDHDGQEQVLIEKEERKNRRN-MLTRSMSVLNPRERR 241
            S +  +++ D N+        + D+      L+E+ E K   +  L ++++ L+ R + 
Sbjct: 182 LSFDMPVDADDDNAEILSPVGYLEDNRYDPADLVEQSEWKTHGHRQLHQALAKLDVRSQD 241

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           I + R L EN  TL+ L++ ++VS ER+RQIE  A KK++++I
Sbjct: 242 ILQKRWLSENKTTLQELANHYKVSAERIRQIENNALKKLKKNI 284


>gi|148244663|ref|YP_001219357.1| DNA-directed RNA polymerase sigma-32 factor [Candidatus
           Vesicomyosocius okutanii HA]
 gi|146326490|dbj|BAF61633.1| DNA-directed RNA polymerase sigma-32 factor [Candidatus
           Vesicomyosocius okutanii HA]
          Length = 277

 Score =  191 bits (485), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 97/261 (37%), Positives = 167/261 (63%), Gaps = 7/261 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+L  +EE+ LA +  E+ +LSAA +LV SH+R V  IA  Y+GYGL  +++V EG IGL
Sbjct: 23  PILSSEEEHELAVQLYENHNLSAARKLVLSHMRFVAFIAHSYKGYGLEQADLVQEGTIGL 82

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AVK+F+P R  RLA+++++WI+A + E+I ++W +VK+ TT  Q++LFF L++ K H+
Sbjct: 83  MKAVKRFNPHRNVRLASFAVYWIRAEIHEFIFKNWKIVKVATTKAQRKLFFKLKQAKAHI 142

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                N+L  EQ   IAK L V   +V+ M  RL   +    + +  D ++   + +L  
Sbjct: 143 Y----NSLNEEQADKIAKDLGVRRKDVLEMESRLQFSDVTFEVFDEEDSHAP--EQYLTN 196

Query: 207 DH-DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
           ++    EQ+L+  + +K ++  L +++S L+ R   I ++R L+E   TL  L+ ++ +S
Sbjct: 197 ENIQTPEQLLLTDDSKKTQQQRLYKALSSLDERSLDILQSRYLKEEKTTLYTLADKYSIS 256

Query: 266 RERVRQIEARAFKKVQESIQK 286
           +ERVRQ+E +A +K++ ++Q+
Sbjct: 257 KERVRQLETKAMQKLKSNLQE 277


>gi|304320154|ref|YP_003853797.1| RNA polymerase sigma-70 factor family protein [Parvularcula
           bermudensis HTCC2503]
 gi|303299057|gb|ADM08656.1| RNA polymerase sigma-70 factor family protein [Parvularcula
           bermudensis HTCC2503]
          Length = 283

 Score =  191 bits (485), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 97/283 (34%), Positives = 172/283 (60%), Gaps = 7/283 (2%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++++ +  L   I +    P+L  +EE  L +R+ +  D  A  +L  +H+R+ V  A+ 
Sbjct: 1   MVIDNDEYLKATIRQAMSAPLLSIEEERSLMRRWVDDQDERALGKLTRAHMRMAVSTAIK 60

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           +RGYGLP+++++ EG IGL++A K+FDP+R  R  TY+ WWI+A+MQ+YILR+WS+V++G
Sbjct: 61  FRGYGLPLADLIQEGAIGLLEAAKRFDPDREVRFCTYAGWWIRASMQDYILRNWSIVRVG 120

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQV-VAIAKKLNVSESEVISMNCRLA-GDES 185
           + +  K +FFNL R++  ++   D +  P    +  A++ NVSES++  M  RL   D+S
Sbjct: 121 SKSAHKTIFFNLSRIRSMIE---DADTAPRTARIKAAERFNVSESDIEFMTSRLGRRDQS 177

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           LNA++  +D    + QD +  + +G + +     ++  R++ + +++  L+ RER I E 
Sbjct: 178 LNAML--TDDGDIERQDLIPDEREGPDSLAEGTLDQARRKSWIGKALKTLSNRERMIIEH 235

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           R   E  +TL  L  +  +S+ERVRQIE +A  K++  +  + 
Sbjct: 236 RFFTEEKMTLSRLGDDLSLSKERVRQIEKQAMGKLKACLAAEA 278


>gi|261866928|ref|YP_003254850.1| RNA polymerase factor sigma-32 [Aggregatibacter
           actinomycetemcomitans D11S-1]
 gi|261412260|gb|ACX81631.1| alternative sigma factor RpoH [Aggregatibacter
           actinomycetemcomitans D11S-1]
          Length = 282

 Score =  191 bits (484), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 104/287 (36%), Positives = 169/287 (58%), Gaps = 10/287 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+++  ++++  +  +  YI    + PML  +EE  LA+R     D+ AA +LV SHLR 
Sbjct: 1   MDKETQTMMLVPQGSIEAYIRAANEYPMLTAEEEKELAERLYYKEDIEAAKKLVLSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L    +N     +V  +A +L VS  +V+ M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNEN-----EVDMVANELGVSPQDVMEMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK---NRRNMLTRSMSVLNP 237
            G +   A     D++  +     +Y  D       E E         + L  ++  L+ 
Sbjct: 176 TGADV--AFDLPGDEHDEETYAPALYLEDKSSNFAAELENENYEAQATDQLAVALDNLDA 233

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R + I +AR L E   TL++L++++ +S ERVRQ+E  A KK++ ++
Sbjct: 234 RSQDIIKARWLDETKATLQDLAAKYNISAERVRQLETNALKKLKSAV 280


>gi|149915381|ref|ZP_01903908.1| RNA polymerase sigma factor [Roseobacter sp. AzwK-3b]
 gi|149810670|gb|EDM70511.1| RNA polymerase sigma factor [Roseobacter sp. AzwK-3b]
          Length = 292

 Score =  191 bits (484), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 102/270 (37%), Positives = 172/270 (63%), Gaps = 10/270 (3%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           +  +L+ + E  LA  +R+  D  A HRL+T+++RL + +A  +R YG P+++++ E  +
Sbjct: 17  RAELLDAETELKLAYAWRDQRDEEALHRLITAYMRLAISMASKFRRYGAPMNDLIQEAGL 76

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFN+RR++ 
Sbjct: 77  GLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQA 136

Query: 145 HLQAITDNNLKPEQVVA------IAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
            ++   +   K EQ+        IA ++ V   +V  M  RL+G D SLNA   S +   
Sbjct: 137 RIE--REAMAKGEQLDGHQLREMIAHEVGVPLRDVEMMEGRLSGTDFSLNA-TQSVEDEG 193

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
            +W D +  +    +Q++ +  +    R  L  +MS LN RER I   R+L++ P TLE+
Sbjct: 194 REWIDTIEDEGPRGDQLVEQDHDLMALREWLGDAMSKLNDRERFIVRERKLRDVPRTLES 253

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L  E  +S+ERVRQ+EA AF+K+++ +++ 
Sbjct: 254 LGEELNLSKERVRQLEAAAFQKMRKHLERH 283


>gi|261210147|ref|ZP_05924444.1| RNA polymerase sigma-32 factor [Vibrio sp. RC341]
 gi|260840687|gb|EEX67236.1| RNA polymerase sigma-32 factor [Vibrio sp. RC341]
          Length = 286

 Score =  191 bits (484), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 109/274 (39%), Positives = 163/274 (59%), Gaps = 11/274 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  +   PML   EE  LA+R     D+ AA  L+ SHLR VV +A GY GYGLP+
Sbjct: 16  LDSYIRSVNGYPMLTADEERELAERLHYKEDIEAAKGLILSHLRFVVHVARGYSGYGLPM 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           +++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W +VKI TT  Q++L
Sbjct: 76  ADLVQEGNIGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR+ K  L    +      +V  +A++L V  SEV  M  RLA  ++   +    D+
Sbjct: 136 FFNLRKSKKRLGWFNNG-----EVETVARELGVEPSEVREMESRLAAQDAAFEMSAEDDE 190

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV----LNPRERRIFEARRL-QE 250
           N   +   ++Y  D     L +  E +N     T+ +S+    L+ R + I  AR L  +
Sbjct: 191 NGMAYTAPVLYLEDKHSD-LADNLEAENWEAHTTQRLSMALASLDERSQHIVRARWLDDD 249

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           N  TL++L+  + VS ER+RQ+E  A +K++E++
Sbjct: 250 NKTTLQDLAEMYGVSAERIRQLEKNAMRKLKEAV 283


>gi|254428104|ref|ZP_05041811.1| alternative sigma factor RpoH [Alcanivorax sp. DG881]
 gi|196194273|gb|EDX89232.1| alternative sigma factor RpoH [Alcanivorax sp. DG881]
          Length = 287

 Score =  191 bits (484), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 106/281 (37%), Positives = 165/281 (58%), Gaps = 8/281 (2%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +++ V G   L  Y+  +  +P+L  +EE  L +R     DL AA  LV SHLR V  IA
Sbjct: 11  LTLAVPGN-DLDAYMRAVNAVPVLSAEEEQRLGERLYYDQDLDAARSLVLSHLRFVAHIA 69

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGLP+ ++V EGN+GLM+AVK+FDP +G RL ++++ WIKA + EY++++W +VK
Sbjct: 70  RSYTGYGLPLGDLVQEGNVGLMKAVKRFDPTKGVRLVSFAVHWIKAEIHEYVIKNWRIVK 129

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDE 184
           + TT  Q++LFFNLR  K  L  +T      E+   +A  L V+ ++V  M  RL A D 
Sbjct: 130 VATTKAQRKLFFNLRGQKKRLGRLT-----MEEAQRVADDLGVTATQVKEMEGRLGAYDA 184

Query: 185 SLNALINSSDKNS-SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           S +   N  D ++      +L  D+     +L E+++++     L+ ++  L+ R R I 
Sbjct: 185 SFDGPTNDDDDSTVVSPAAYLHSDNSDPADLLAEQDKQQRESRQLSSALMALDERSRDIL 244

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           E R L +   TL+ L+ E+ VS ER+RQ+E  A KK++ +I
Sbjct: 245 ERRWLADQKSTLQELADEYGVSAERIRQLENNAIKKLRNAI 285


>gi|83950005|ref|ZP_00958738.1| RNA polymerase sigma factor [Roseovarius nubinhibens ISM]
 gi|83837904|gb|EAP77200.1| RNA polymerase sigma factor [Roseovarius nubinhibens ISM]
          Length = 277

 Score =  190 bits (483), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 101/268 (37%), Positives = 169/268 (63%), Gaps = 6/268 (2%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           +  +L+ + E  LA  +R+  D  A HRL+ +++RL + +A  YR YG P+++++ E  +
Sbjct: 2   RAELLDAETELALAYAWRDQRDEEALHRLINAYMRLAISMASKYRRYGAPLNDLIQEAGL 61

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A  KFDP+RG R +TY++WWIKA +Q+Y++R+WS+V+ G+T++QK LFFN+RR++ 
Sbjct: 62  GLMKAADKFDPDRGVRFSTYAVWWIKAGIQDYVMRNWSMVRTGSTSSQKALFFNMRRVRA 121

Query: 145 HLQ---AITDNNLKPEQV-VAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQ 199
            ++     +   L   Q+   IA ++ V   +V  M  RL+G D SLNA   S++    +
Sbjct: 122 QIEREAEASGTRLDGHQLREMIATEVGVPLRDVEMMEGRLSGSDLSLNA-TQSTEDEGRE 180

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
           W D L  D    E+++ E  +++  R  L  +++ LN RER I   R+L E   TLE+L 
Sbjct: 181 WIDALEDDGPRAEEMVEEDHDQRVLRLWLRDALAALNDRERFILRHRKLSEEVRTLESLG 240

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQ 287
            E  +S+ERVRQ+EA A  K+++ ++++
Sbjct: 241 EELGLSKERVRQLEAAALVKMRKRLERE 268


>gi|163735266|ref|ZP_02142701.1| RNA polymerase sigma-32 factor [Roseobacter litoralis Och 149]
 gi|161391480|gb|EDQ15814.1| RNA polymerase sigma-32 factor [Roseobacter litoralis Och 149]
          Length = 284

 Score =  190 bits (483), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 101/268 (37%), Positives = 171/268 (63%), Gaps = 6/268 (2%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K  +L+ + E  LA  +R+     + HRL+T+++RL + +A  ++ YG P+++++ E  +
Sbjct: 9   KAELLDAETELRLAYAWRDERCEKSLHRLITAYMRLAISMASKFKRYGAPMNDLIQEAGL 68

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFN+RR++ 
Sbjct: 69  GLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQA 128

Query: 145 HLQ---AITDNNLKPEQV-VAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQ 199
            L+   A +   L   Q+   I+ ++ V   +V  M  RL+G D SLNA   S++    +
Sbjct: 129 RLERESAASGEPLDRHQLRQMISTEIGVPLHDVEMMEGRLSGSDYSLNA-TQSTEDEGRE 187

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
           W D L  D     + +    + +  R  L ++M+ LN RER I   R+L++ P TLE+L 
Sbjct: 188 WIDALEDDSAQAAETVEHHHDTEQLRAWLLQAMNDLNERERFIVRERKLRDAPRTLESLG 247

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQ 287
            E  +S+ERVRQ+EA AF K++++++ Q
Sbjct: 248 QELSLSKERVRQLEAAAFGKMRKNLENQ 275


>gi|89068061|ref|ZP_01155478.1| RNA polymerase sigma factor [Oceanicola granulosus HTCC2516]
 gi|89046300|gb|EAR52357.1| RNA polymerase sigma factor [Oceanicola granulosus HTCC2516]
          Length = 281

 Score =  190 bits (483), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 104/270 (38%), Positives = 175/270 (64%), Gaps = 16/270 (5%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           +L+ + E  LA  +R+  D  A HRL+T+++RL + +A  +R YG P+++++ E ++GLM
Sbjct: 10  LLDAETELRLAYAWRDQRDERALHRLITAYMRLAISMAAKFRRYGAPMNDLIQEASLGLM 69

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFNLRR++  L+
Sbjct: 70  KAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNLRRVQARLE 129

Query: 148 AITDNNLKP----EQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQD 202
                +  P    +    IA ++ V   +V  M  RL+G D SLNA  ++ D+     ++
Sbjct: 130 REAAASGAPIDRQKMREMIAAEVGVPLHDVEMMEGRLSGSDYSLNATQSAEDEG----RE 185

Query: 203 WL-VYDHDGQEQVLIEKEERKNR----RNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           W+   + DG +    EK E  +     R+ L  ++S LN RER I + R+L+++P TLE+
Sbjct: 186 WIEALEDDGMQAA--EKVENSHDIDTLRHWLLNALSQLNERERFIVKERKLRDDPRTLES 243

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L  E  +S+ERVRQ+EA AF K+++ ++ +
Sbjct: 244 LGDELGLSKERVRQLEAAAFGKMRKMLETE 273


>gi|109900247|ref|YP_663502.1| RNA polymerase, sigma 32 subunit, RpoH [Pseudoalteromonas atlantica
           T6c]
 gi|109702528|gb|ABG42448.1| RNA polymerase, sigma 32 subunit, RpoH [Pseudoalteromonas atlantica
           T6c]
          Length = 289

 Score =  190 bits (482), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 103/284 (36%), Positives = 165/284 (58%), Gaps = 6/284 (2%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           + + +++ V     +  Y+  +  I ML  +EE  LA+R ++  DL AA +L+ SHLR V
Sbjct: 10  DMRALTLTVPQTGSIETYVQAVSSINMLTAEEERGLAERLQQEDDLLAARKLIMSHLRFV 69

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA  Y GYGLP ++++ EGNIGLM+AV++FDP  G RL ++++ WIKA + E++LR+W
Sbjct: 70  VHIAKSYSGYGLPQADLIQEGNIGLMKAVRRFDPTVGVRLVSFAVHWIKAEIHEFVLRNW 129

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            +VK+ TT  Q++LFFNLR+ K  L   T       +V  +A  L VSE EV+ M  R++
Sbjct: 130 RIVKVATTKAQRKLFFNLRKNKKRLGWFT-----HAEVQKVASDLGVSEKEVLQMEARMS 184

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRER 240
             +    L    D++ S      + D     E  ++  +        L  ++  L+ R +
Sbjct: 185 SHDQAFDLSADDDESGSFAPVQFLEDKSADVETDVVNADWDATASQKLYSAIKTLDERSQ 244

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            I + R L ++  TL++L+ +++VS ERVRQIE  A KK+Q ++
Sbjct: 245 HIIQTRWLSDDKTTLQDLADKYQVSAERVRQIEKNAMKKLQSAM 288


>gi|33151352|ref|NP_872705.1| RNA polymerase factor sigma-32 [Haemophilus ducreyi 35000HP]
 gi|33147572|gb|AAP95094.1| RNA polymerase sigma-32 factor [Haemophilus ducreyi 35000HP]
          Length = 319

 Score =  190 bits (482), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 101/272 (37%), Positives = 164/272 (60%), Gaps = 10/272 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI    + P+L  ++E  LA+RY    D+ AA +L+ SH+R V+ IA GY GYGLP+
Sbjct: 51  LDSYIRMANQYPILTAEQEKTLAERYYYDEDVDAAKQLILSHMRFVIHIARGYMGYGLPL 110

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AVK+FDP  G RL ++++ W+KA + EY+L++W +VK+ TT  Q++L
Sbjct: 111 ADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWVKAEIHEYVLKNWRIVKVATTKAQRKL 170

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR+ K  L    ++ ++      +A+ L VS  EV  M  R+ G +       S+++
Sbjct: 171 FFNLRKNKHRLAWFNEDEIQQ-----VAQDLGVSTEEVREMESRMTGQDV--GFDISANE 223

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM---LTRSMSVLNPRERRIFEARRLQENP 252
           + S+     +Y  D       E EE ++       L  +++ L+ R + I + R L EN 
Sbjct: 224 DESEVYVPSMYLEDNSSNFADELEEEQHTGEATAKLAYALATLDERSQDIIKTRWLDENK 283

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL  L++++ +S ERVRQ+E  A KK++++I
Sbjct: 284 ATLHELAAKYSISAERVRQLENAALKKIKDTI 315


>gi|332308280|ref|YP_004436131.1| RNA polymerase, sigma 32 subunit, RpoH [Glaciecola agarilytica
           4H-3-7+YE-5]
 gi|332175609|gb|AEE24863.1| RNA polymerase, sigma 32 subunit, RpoH [Glaciecola agarilytica
           4H-3-7+YE-5]
          Length = 283

 Score =  190 bits (482), Expect = 2e-46,   Method: Compositional matrix adjust.
 Identities = 102/284 (35%), Positives = 166/284 (58%), Gaps = 6/284 (2%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           + + +++ V     +  Y+  +  I ML  +EE  LA+R ++  DL AA +L+ SHLR V
Sbjct: 4   DMRALTLTVPQTGSIETYVQAVSSIDMLSAEEEKGLAERLQQEDDLLAARKLIMSHLRFV 63

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA  Y GYGLP ++++ EGNIGLM+AV++FDP  G RL ++++ WIKA + E++LR+W
Sbjct: 64  VHIAKSYSGYGLPQADLIQEGNIGLMKAVRRFDPTVGVRLVSFAVHWIKAEIHEFVLRNW 123

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            +VK+ TT  Q++LFFNLR+ K  L   T       +V  +A  L VSE EV+ M  R++
Sbjct: 124 RIVKVATTKAQRKLFFNLRKNKKRLGWFT-----HAEVQKVASDLGVSEKEVLQMEARMS 178

Query: 182 G-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
             D++ +   +  +  S     +L       E  ++  +        L  ++  L+ R +
Sbjct: 179 SHDQAFDLSADDDESGSFAPVQFLEDKSPDVETEVVNADWDATASQKLYSAIKTLDERSQ 238

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            I + R L ++  TL++L+ +++VS ERVRQIE  A KK+Q ++
Sbjct: 239 HIIQTRWLSDDKTTLQDLADKYQVSAERVRQIEKNAMKKLQSAM 282


>gi|254459542|ref|ZP_05072958.1| sigma 32 [Rhodobacterales bacterium HTCC2083]
 gi|206676131|gb|EDZ40618.1| sigma 32 [Rhodobacteraceae bacterium HTCC2083]
          Length = 292

 Score =  190 bits (482), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 101/280 (36%), Positives = 176/280 (62%), Gaps = 14/280 (5%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           G +R+     K  ML+ + E  LA  +R+    ++ HRL+ +++RL + +A  +R YG P
Sbjct: 7   GDARFSRRAMKAEMLDAETELKLAYAWRDERCEASLHRLINAYMRLAISMASKFRRYGAP 66

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           +++++ E  +GLM+A  KFDP+RG R +TY++WWIKA++Q++++R+WS+V+ G+T++QK 
Sbjct: 67  LNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDHVMRNWSMVRTGSTSSQKS 126

Query: 135 LFFNLRRLKGHL--------QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DES 185
           LFFN+RR++  L        +A+  + L       I+ ++ V  ++V  M+ RL+G D S
Sbjct: 127 LFFNMRRVQARLEREAQQRGEALDRHQLHQ----MISTEIGVPLNDVEMMHGRLSGSDFS 182

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           LNA   S +    +W D L  D    E+++  + +    R  L  +M+ LN RER I   
Sbjct: 183 LNA-TQSVEDEGREWIDALEDDGAQAEEIVENEHDTAQMREWLLGAMNALNERERFIVRE 241

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           R+L + P TLE+L +E  +S+ER+RQ+EA AF+K++++++
Sbjct: 242 RKLLDEPRTLESLGNELGLSKERIRQLEAAAFQKMRKTLE 281


>gi|119944398|ref|YP_942078.1| RNA polymerase sigma-32 factor RpoH [Psychromonas ingrahamii 37]
 gi|119863002|gb|ABM02479.1| RNA polymerase sigma-32 factor RpoH [Psychromonas ingrahamii 37]
          Length = 283

 Score =  190 bits (482), Expect = 3e-46,   Method: Compositional matrix adjust.
 Identities = 110/281 (39%), Positives = 167/281 (59%), Gaps = 8/281 (2%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +MS++  G IG   Y+  + +  ML  + E  LA+R    GDL+AA +LV SHLR VV I
Sbjct: 7   SMSLVPQGSIG--AYVQSVNQFSMLSAEAEKELAERLFHEGDLAAAKKLVMSHLRFVVYI 64

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y GYGL  ++++ EGNIGLM+AVK+FDP  G RL ++++ WIKA + EY++R+W +V
Sbjct: 65  AKSYAGYGLAQADLIQEGNIGLMKAVKRFDPSVGVRLVSFAVHWIKAEIHEYVIRNWRMV 124

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           KI TT  Q++LFFNLRR K  L   +      ++V  +A+ LNVS  +V+ M  RL   +
Sbjct: 125 KIATTKAQRKLFFNLRRAKKRLGWFSH-----DEVATVAENLNVSTKDVLEMESRLNAQD 179

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQE-QVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
               L +S D  S       + D      QV+  +  + + +N L  ++S L+ R + I 
Sbjct: 180 QSFDLSDSDDDESGFAPVQYLEDKSADVFQVVATENTQLHTKNKLYSALSTLDERSQDIV 239

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +R L E   TL +L++ + +S ER+RQ+E  A KK+Q ++
Sbjct: 240 SSRWLSEPKATLHDLAARYGISAERIRQLEENAMKKLQSNM 280


>gi|163744692|ref|ZP_02152052.1| RNA polymerase sigma-32 factor [Oceanibulbus indolifex HEL-45]
 gi|161381510|gb|EDQ05919.1| RNA polymerase sigma-32 factor [Oceanibulbus indolifex HEL-45]
          Length = 292

 Score =  189 bits (480), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 104/287 (36%), Positives = 178/287 (62%), Gaps = 9/287 (3%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           MS+    E  L+R      K  +L+   E  LA  +R+  D +A HRL+T+++RL + +A
Sbjct: 1   MSLQTAREFSLTRTAM---KAELLDADTELKLAYAWRDQRDEAALHRLITAYMRLAISMA 57

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             ++ YG P+++++ E  +GLM+A  KFDP+RG R +TY++WWIKA++Q++++R+WS+V+
Sbjct: 58  GKFKRYGAPMNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDHVMRNWSMVR 117

Query: 126 IGTTANQKRLFFNLRRLKGHLQ----AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            G+T++QK LFFN+RR++  L+    A+ +   K +    I+ ++ V   +V  M  RL+
Sbjct: 118 TGSTSSQKSLFFNMRRVQARLEREASAVGETLDKHQLRQMISTEIGVPLHDVEMMEGRLS 177

Query: 182 G-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           G D SLNA   S++    +W + L  +     + + E+ +    RN L  +M  L+ RE+
Sbjct: 178 GSDYSLNA-TQSAEDEGREWIEALADESAQAAERVEEQHDTAQLRNWLLTAMQGLSDREQ 236

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            I   R+L++   TLE+L  E  +S+ERVRQ+EA AF K+++S++ Q
Sbjct: 237 FIVRERKLRDPSRTLESLGDELSLSKERVRQLEAAAFGKMRKSLEMQ 283


>gi|152978131|ref|YP_001343760.1| RNA polymerase factor sigma-32 [Actinobacillus succinogenes 130Z]
 gi|150839854|gb|ABR73825.1| RNA polymerase, sigma 32 subunit, RpoH [Actinobacillus succinogenes
           130Z]
          Length = 281

 Score =  189 bits (480), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 105/286 (36%), Positives = 169/286 (59%), Gaps = 9/286 (3%)

Query: 1   MNRK-NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLR 59
           MN++  M ++  G   L  YI    + PML  ++E   A+R     DL AA  L+ SHLR
Sbjct: 1   MNKEAQMMLVPQG--NLEGYIRAANEYPMLTAEQEKDYAERLYYQDDLDAAKALILSHLR 58

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
            V+ +A GY GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+L+
Sbjct: 59  FVIHVARGYAGYGLPQADLIQEGNIGLMKAVRRFNPEMGVRLVSFAVHWIKAEIHEYVLK 118

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
           +W +VK+ TT  Q++LFFNLR+ K  L   ++N     +V  +A +L VS+ +VI M  R
Sbjct: 119 NWRIVKVATTKAQRKLFFNLRKTKQRLGWFSEN-----EVDLVANELGVSKEDVIEMESR 173

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR-NMLTRSMSVLNPR 238
           + G +    L     +  +      + D        +E E  + +  + LT +M  L+ R
Sbjct: 174 MTGADIGFDLPADDAEEETFAPSMYLEDKSSNFAAELENENFETQAVDQLTVAMETLDAR 233

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + I + R L EN  TL +L++++ +S ERVRQ+E+ A KK++ ++
Sbjct: 234 SQDIIKTRWLDENKATLHDLAAKYNISAERVRQLESNALKKLKSAV 279


>gi|32423705|gb|AAP81248.1| sigma-32 subunit of RNA polymerase [Candidatus Portiera
           aleyrodidarum]
          Length = 280

 Score =  189 bits (480), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 110/276 (39%), Positives = 163/276 (59%), Gaps = 12/276 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E  +  YI  +   P++  Q+EY LA+R R  GDL AA  LV S+LR V+ IA  Y GYG
Sbjct: 7   ETNIEGYIKTVLGFPIISAQDEYDLARRLRNKGDLDAARCLVISNLRFVIHIARSYSGYG 66

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L  S+++ EGN+GLM+AVK+FDP  G RL ++++ WIKA + EY+LR+W +VKI TT +Q
Sbjct: 67  LQNSDIIQEGNVGLMKAVKRFDPAHGVRLVSFAIHWIKAEIHEYVLRNWRIVKIATTKSQ 126

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
           ++LFF+LR  K  L     N L  E++ +IAK LNV  + V  M CRL+  +      N 
Sbjct: 127 RKLFFSLRCAKTSL-----NWLNREEIKSIAKDLNVKPTVVREMECRLSSTDY--GFDNK 179

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKE----ERKNRRNMLTRSMSVLNPRERRIFEARRL 248
             +  + +++   Y  D +    ++ E    ER + R +   +++ L+ R R I + R L
Sbjct: 180 QKEEKNNYKNPSNYLEDSRFDPALQFENFDFERYSYRRLYV-ALNKLDERVRDILKQRWL 238

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            E   TL  L+  + VS ER+RQ+E RA KK++  I
Sbjct: 239 NEPKATLHELADIYGVSAERIRQLEQRAIKKIKNYI 274


>gi|144899360|emb|CAM76224.1| Sigma-70 region 2:Sigma-70 region 4:Sigma-70 region 1.2
           [Magnetospirillum gryphiswaldense MSR-1]
          Length = 291

 Score =  189 bits (480), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 105/277 (37%), Positives = 162/277 (58%), Gaps = 4/277 (1%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           MSI+       S Y   +R+  +L  ++E  L +R+++ GD  A  RL+++HLRLVVK A
Sbjct: 1   MSILRPASDTASAYYKAMRETALLSGEDEAELIRRWKDEGDEKARTRLLSAHLRLVVKTA 60

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             ++GYGL  +++V+EGN+GL++A++ FDP R  R +TY+ WW++AAM EY+L+  + V 
Sbjct: 61  GQFKGYGLSGADLVAEGNLGLVRALESFDPGRNLRFSTYAQWWVRAAMFEYVLKFSTPVN 120

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDE 184
            G +A +K+LFF LR +K  L   + N L   +   +A +L V +  V  M   L     
Sbjct: 121 FGLSAERKKLFFKLRGIKARLTGPSGNALSVAETAQVADELGVRDQRVAEMERLLTQSPR 180

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL+A +  S      + + L  D    E+ L E++E   RR +L  +   L  RER I  
Sbjct: 181 SLDAPVGES---GIPFGELLADDRPSVEETLGERQELMYRRELLKHAWEGLTERERDIVA 237

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R L+ENP+ LE+L+  + +SRERVRQIE  A  K++
Sbjct: 238 QRTLRENPLRLEDLAQRYSISRERVRQIEGSALTKLK 274


>gi|84872788|gb|ABC67485.1| RpoH2 [Sinorhizobium sp. BL3]
          Length = 286

 Score =  189 bits (480), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 105/259 (40%), Positives = 159/259 (61%), Gaps = 3/259 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE+ EE+ LA+ +R   D  A +++  SH+RLVV +A  +R +GLP+ ++V EG+IGL
Sbjct: 18  PYLERDEEHALAEAWRYDHDQEARNKIAMSHMRLVVAMAAKFRSFGLPMGDLVQEGHIGL 77

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +F+P R  R +TY+ WWI+A+MQ+Y+LR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 78  LEAAARFEPSREVRFSTYATWWIRASMQDYVLRNWSIVRGGTSSAQKALFFNLRRLRARL 137

Query: 147 QAITDNNLKPEQV-VAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWL 204
            A  D  L  + +   IA  L VS ++V +M+ RL+G D SL A +   D  S    D+L
Sbjct: 138 -AQGDRQLTSQAMHEEIAAALGVSLADVQTMDARLSGNDASLQAPVGHGDAESGARLDFL 196

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             D    ++ + E  + +  R  L  ++  L+ RE +I  ARRL E+  TLE L     +
Sbjct: 197 PSDAPLPDEQVSEMIDGERARRWLHSALRELSEREMKIIRARRLSEDGATLEELGVALGI 256

Query: 265 SRERVRQIEARAFKKVQES 283
           S+ERVR    R+   V+ S
Sbjct: 257 SKERVRSKRGRSKSCVRRS 275


>gi|255262130|ref|ZP_05341472.1| RNA polymerase sigma-32 factor [Thalassiobium sp. R2A62]
 gi|255104465|gb|EET47139.1| RNA polymerase sigma-32 factor [Thalassiobium sp. R2A62]
          Length = 292

 Score =  189 bits (479), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 100/268 (37%), Positives = 171/268 (63%), Gaps = 6/268 (2%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           +  +L+ + E  LA  +R+     + HRL+T+++RL + +A  ++ YG P+++++ E ++
Sbjct: 17  RAELLDAETELKLAYAWRDERCEQSLHRLITAYMRLAISMASKFKRYGAPMNDLIQEASL 76

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFNLRR++ 
Sbjct: 77  GLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNLRRVQA 136

Query: 145 HLQ---AITDNNLKPEQV-VAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQ 199
            L+   A     L   Q+   IA ++ V   +V  M  RL+G D SLNA   SS+    +
Sbjct: 137 RLEREAATAGEELDRHQMRQMIATEVGVPLHDVEMMEGRLSGSDYSLNA-TQSSEDEGRE 195

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
           W D L  D D   + +    + +  R+ L  ++S L+ RE+ I   R++++   TLE+L 
Sbjct: 196 WIDALEDDSDQAAENVENDHDTETLRSWLVTALSALSHREQYIVTERKIKDQTRTLESLG 255

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQ 287
            E  +S+ER+RQ+EA AF K+++S++ Q
Sbjct: 256 HELGLSKERIRQLEAAAFIKMRKSLEGQ 283


>gi|237809745|ref|YP_002894185.1| RNA polymerase, sigma 32 subunit, RpoH [Tolumonas auensis DSM 9187]
 gi|237502006|gb|ACQ94599.1| RNA polymerase, sigma 32 subunit, RpoH [Tolumonas auensis DSM 9187]
          Length = 284

 Score =  189 bits (479), Expect = 5e-46,   Method: Compositional matrix adjust.
 Identities = 108/285 (37%), Positives = 168/285 (58%), Gaps = 9/285 (3%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           ++N+ ++  G   L  YI  +  IPML  ++E  LA++ +  GDL AA +LV SHLR VV
Sbjct: 6   QRNLVLVPQG--SLEGYIQAVNSIPMLTAEKERALAEQLQNDGDLEAARQLVMSHLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA  Y GYGLP ++++ EGNIGLM+AVK+FDP  G RL ++++ WIKA + EY+LR+W 
Sbjct: 64  HIARTYSGYGLPQADLIQEGNIGLMKAVKRFDPTVGVRLVSFAVHWIKAEIHEYVLRNWR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L          ++V A+A++L VS  +V  M  R++G
Sbjct: 124 MVKVATTKAQRKLFFNLRKTKKRL-----GWFNQDEVRAVAEELGVSPEDVTEMESRMSG 178

Query: 183 -DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
            D S +   +   +++     +L         V        +  + L  ++  L+ R ++
Sbjct: 179 LDHSFDGYDDDDSESNFAPAQYLEDKSSDLATVYENNNWDTHAEHRLAYALQGLDERSQQ 238

Query: 242 IFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           I  AR L E N  TL+ L+  + VS ERVRQ+E  A KK+++ ++
Sbjct: 239 IVRARWLDEDNKQTLQELADRYGVSAERVRQLEKNALKKLKDVLE 283


>gi|304415276|ref|ZP_07395971.1| RNA polymerase sigma 32 (sigma H) factor [Candidatus Regiella
           insecticola LSR1]
 gi|304282866|gb|EFL91334.1| RNA polymerase sigma 32 (sigma H) factor [Candidatus Regiella
           insecticola LSR1]
          Length = 285

 Score =  189 bits (479), Expect = 6e-46,   Method: Compositional matrix adjust.
 Identities = 109/286 (38%), Positives = 168/286 (58%), Gaps = 11/286 (3%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           + +++I  G  GL  YI      PML  +EE  LA+R   HGDLSAA +L+ SHLR V  
Sbjct: 6   RTLALISQG--GLDAYIRTSNTYPMLTAEEEQELAERLHYHGDLSAAKQLILSHLRFVTH 63

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           +A  Y GYGLP ++++ EGNIGLM+AV++F+P  G RL ++++ WIKA + EY+LR+W +
Sbjct: 64  VARNYSGYGLPQADLIQEGNIGLMKAVRRFNPAIGVRLVSFAVHWIKAEIHEYVLRNWRI 123

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VK+ TT  Q++LFFNLR+ K  L          ++V  +AK+L VS+ +V  M  R++  
Sbjct: 124 VKVATTKAQRKLFFNLRKSKQRL-----GWFNQDEVEMVAKELGVSKKDVHEMESRMSAQ 178

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNPRER 240
           +    L    D    Q    ++Y  D       + EE     +  + L+ ++  L+ R +
Sbjct: 179 DMTFDLSPDDDTRDGQLVAPVLYLQDRNSDFAGDVEEDNWDNHAVDKLSFALEKLDERSQ 238

Query: 241 RIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            I  AR L  +N  TL+ L++++ VS ERVRQ+E  A KK++ +I+
Sbjct: 239 HIIRARWLNDDNKATLQELANQYGVSAERVRQLEKNAMKKLRLAIE 284


>gi|30424475|dbj|BAC76410.1| heat shock sigma-32 factor [Colwellia maris]
          Length = 285

 Score =  189 bits (479), Expect = 6e-46,   Method: Compositional matrix adjust.
 Identities = 103/273 (37%), Positives = 164/273 (60%), Gaps = 15/273 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+     IPML  ++E+ LA R     DLSAA  L+ SHLR V+ +A GY GYGLP +++
Sbjct: 18  YMRSAYSIPMLTAEKEHNLATRLYNENDLSAAQELIMSHLRFVIHVAKGYSGYGLPHADL 77

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GLM+AVK+F+PE G RL ++++ WIKA + EY+L++W +VK+ TT  Q++LFFN
Sbjct: 78  VQEGNVGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLKNWRIVKVATTKAQRKLFFN 137

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN-- 196
           LR+ K  L   +      E+V  +A+ L V+  +V+ M  R++  +    L    D N  
Sbjct: 138 LRKNKKRLGWFS-----TEEVNTVAENLGVTTKDVMEMESRMSSYDQAFELSKDDDDNLG 192

Query: 197 SSQWQDWLVYDHDGQEQVLIEKE-----ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           +S +     Y  D Q  + +E E        N+R  L+ ++  L+ R + I + R L E+
Sbjct: 193 ASNFSP-AQYLQDKQSDLAVEVENDNWDNHANKR--LSTALVTLDERSQDIIKTRWLTED 249

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL+ L++++++S ERVRQ+E  A  K++ ++
Sbjct: 250 KTTLQELANKYQISAERVRQLEKNALSKLKNTM 282


>gi|156936376|ref|YP_001440292.1| RNA polymerase factor sigma-32 [Cronobacter sakazakii ATCC BAA-894]
 gi|260599762|ref|YP_003212333.1| RNA polymerase factor sigma-32 [Cronobacter turicensis z3032]
 gi|156534630|gb|ABU79456.1| hypothetical protein ESA_04276 [Cronobacter sakazakii ATCC BAA-894]
 gi|260218939|emb|CBA34294.1| RNA polymerase sigma-32 factor [Cronobacter turicensis z3032]
          Length = 285

 Score =  189 bits (479), Expect = 6e-46,   Method: Compositional matrix adjust.
 Identities = 111/287 (38%), Positives = 166/287 (57%), Gaps = 10/287 (3%)

Query: 4   KNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           K M  +    +G L  YI      PML   EE  LA++    GDL AA +L+ SHLR VV
Sbjct: 3   KEMQTLALAPVGNLDSYIRAANAWPMLSADEERALAEKLHYQGDLEAAKKLILSHLRFVV 62

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W 
Sbjct: 63  HIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWR 122

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+A 
Sbjct: 123 IVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVEMVARELGVSSKDVREMESRMAA 177

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVL--IEKEE-RKNRRNMLTRSMSVLNPRE 239
            +    +    D   SQ    +++  D        IE +   ++  + LT +M  L+ R 
Sbjct: 178 QDMTFDMSPDDDAGDSQPMAPVLFLQDKSSNFADGIEDDNWEEHAADKLTDAMQGLDERS 237

Query: 240 RRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           ++I  AR L E N  TL+ L++ + VS ERVRQ+E  A KK++ +I+
Sbjct: 238 QQIIRARWLDEDNKSTLQELANRYGVSAERVRQLEKNAMKKLRAAIE 284


>gi|88858433|ref|ZP_01133075.1| RNA polymerase sigma factor [Pseudoalteromonas tunicata D2]
 gi|88820050|gb|EAR29863.1| RNA polymerase sigma factor [Pseudoalteromonas tunicata D2]
          Length = 288

 Score =  189 bits (479), Expect = 6e-46,   Method: Compositional matrix adjust.
 Identities = 102/267 (38%), Positives = 162/267 (60%), Gaps = 9/267 (3%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+  +  I ML  ++E  LA + ++ GDL AA +L+ SHLR V  IA GY GYGLP +++
Sbjct: 22  YLQAVSGIAMLSAEDEQALAVKLQQDGDLDAARQLIMSHLRFVAHIAKGYSGYGLPQADL 81

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM+AVK+FDP  G RL ++++ WIKA + EY+L++W +VK+ TT  Q++LFFN
Sbjct: 82  IQEGNIGLMKAVKRFDPTVGVRLVSFAVHWIKAEIHEYVLKNWRIVKVATTKAQRKLFFN 141

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR+ K  L         PE+V  +A +L V+E +V  M  R++  + +  L    D ++S
Sbjct: 142 LRKNKKRL-----GWFNPEEVSTVANELGVTEKDVREMEARMSSQDMVFDLTTDDDDSTS 196

Query: 199 QWQ----DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
             Q     +L  +       + E++  +   N L  ++  L+ R + I + R L ++  T
Sbjct: 197 ATQYSPVQYLTDNSVDLADKIEEEQWEEQTHNRLFHALKSLDERSQDIVQTRWLSDDKAT 256

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQ 281
           L++L+ +++VS ERVRQ+E  A KK+Q
Sbjct: 257 LQDLAVKYDVSAERVRQLEKTAMKKLQ 283


>gi|255319457|ref|ZP_05360671.1| alternative sigma factor RpoH [Acinetobacter radioresistens SK82]
 gi|262378519|ref|ZP_06071676.1| alternative sigma factor RpoH [Acinetobacter radioresistens SH164]
 gi|255303397|gb|EET82600.1| alternative sigma factor RpoH [Acinetobacter radioresistens SK82]
 gi|262299804|gb|EEY87716.1| alternative sigma factor RpoH [Acinetobacter radioresistens SH164]
          Length = 289

 Score =  188 bits (478), Expect = 7e-46,   Method: Compositional matrix adjust.
 Identities = 109/271 (40%), Positives = 162/271 (59%), Gaps = 8/271 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + L  YI  + +IP+L  ++E  LA+RY    DL AA  LV SHLR VV IA  Y GYGL
Sbjct: 18  VNLGAYISTVNQIPILTAEQEKELAERYYYDQDLDAAKMLVMSHLRFVVHIARSYAGYGL 77

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P  +++ EGN+GLM+AVK+FDP  G RL ++++ WIKA + EY++R+W +VKI TT  Q+
Sbjct: 78  PQGDLIQEGNLGLMKAVKRFDPSMGVRLVSFAVHWIKAEIHEYVIRNWRIVKIATTKAQR 137

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
           +LFFNLR LK      +   L  E+  +IA  LNV+  +V+ M  RL   ++        
Sbjct: 138 KLFFNLRSLKK-----SSKKLTLEEARSIANDLNVTPEQVLEMEGRLTAYDAAFEAQGDD 192

Query: 194 DKNSSQWQDWLVYDHDGQEQV--LIEKEERKNRRN-MLTRSMSVLNPRERRIFEARRLQE 250
           D +SS     ++Y  D +     L+E E+ + + N  L  +M  L+ R R I + R L +
Sbjct: 193 DDDSSSHVAPVLYLEDSRYDPARLVEDEDWEEQSNSALHNAMDQLDDRSRNILQRRWLDD 252

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +  TL  L++E+ VS ER+RQ+E  A +K++
Sbjct: 253 DKSTLHELAAEYNVSAERIRQLEKNAMEKIK 283


>gi|90415296|ref|ZP_01223230.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2207]
 gi|90332619|gb|EAS47789.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2207]
          Length = 278

 Score =  188 bits (478), Expect = 7e-46,   Method: Compositional matrix adjust.
 Identities = 107/269 (39%), Positives = 160/269 (59%), Gaps = 8/269 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ YI     +P+L   EE  L +      DL AA R+V +HLR VV IA  Y GYGLP+
Sbjct: 10  LNAYIQGTATVPILTIDEERALGESLYYQEDLDAARRMVMAHLRFVVHIARSYNGYGLPL 69

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGN+GLM+AV++F+PE+G RL ++++ WIKA + E+ILR+W +VKI TT  Q++L
Sbjct: 70  ADLIQEGNVGLMKAVRRFNPEKGVRLVSFAVHWIKAEIHEFILRNWRIVKIATTKAQRKL 129

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR  K  LQ ++ +  K     A+A  L V   +V+ M  RL   D + +A     D
Sbjct: 130 FFNLRSAKKQLQWLSADEAK-----AVADDLGVQVKDVMEMEMRLTSRDPAFDAPAGEDD 184

Query: 195 KNSS-QWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENP 252
           ++SS Q   + + D       L E ++ +   N  L  ++S L+ R R I + R L +  
Sbjct: 185 ESSSFQAPVYFLEDKSMDPAQLAENDDWEVDNNTRLIAAVSDLDDRSRDILQRRWLNDAK 244

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TL  L++E+ VS ER+RQ+E  A KKV+
Sbjct: 245 ATLHELAAEYGVSAERIRQLEKNAMKKVR 273


>gi|317046493|ref|YP_004114141.1| RNA polymerase,sigma 32 subunit,RpoH [Pantoea sp. At-9b]
 gi|316948110|gb|ADU67585.1| RNA polymerase, sigma 32 subunit, RpoH [Pantoea sp. At-9b]
          Length = 285

 Score =  188 bits (478), Expect = 7e-46,   Method: Compositional matrix adjust.
 Identities = 111/287 (38%), Positives = 164/287 (57%), Gaps = 10/287 (3%)

Query: 4   KNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           K M  +    +G L  YI      PML  +EE  LA+R    GDL AA  L+ SHLR VV
Sbjct: 3   KEMQTLAIAPLGNLESYIRAANVWPMLSAEEEKALAERLHYQGDLDAAKTLILSHLRFVV 62

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W 
Sbjct: 63  HIARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWR 122

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+A 
Sbjct: 123 IVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVEMVARELGVSSKDVREMESRMAA 177

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK---NRRNMLTRSMSVLNPRE 239
            +    +    +   S+    ++Y  D         EE     +  + LT +M  L+ R 
Sbjct: 178 QDMTFDMSADDENGESKTMAPVLYLQDKTSDFADGIEEDNWDAHAADKLTDAMQGLDERS 237

Query: 240 RRIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + I  AR L +EN  TL+ L+ ++ VS ERVRQ+E  A KK++ +I+
Sbjct: 238 QHIIRARWLDEENKTTLQELADQYGVSAERVRQLEKNAMKKLRMAIE 284


>gi|288942274|ref|YP_003444514.1| RNA polymerase sigma-32 subunit RpoH [Allochromatium vinosum DSM
           180]
 gi|288897646|gb|ADC63482.1| RNA polymerase, sigma 32 subunit, RpoH [Allochromatium vinosum DSM
           180]
          Length = 279

 Score =  188 bits (478), Expect = 7e-46,   Method: Compositional matrix adjust.
 Identities = 113/280 (40%), Positives = 170/280 (60%), Gaps = 10/280 (3%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           K+ SI+  G I    YI+   +IP+L  +EE  LA R R+  D+ AA RLVTSHLR V++
Sbjct: 3   KDFSILPTGTI--EAYINSAYQIPVLTLEEERSLAVRLRDQNDMEAAKRLVTSHLRFVIR 60

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA GY GYGLP+ +++ EG +GLM+AV++F+P+ G RL ++++ WI+A + EYILR+W +
Sbjct: 61  IARGYLGYGLPLPDLIQEGTVGLMKAVRRFEPDMGVRLVSFAVHWIRAEIHEYILRNWRI 120

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG- 182
           VK+ TT  Q++LFFNLR  K  L  +T      ++V  +A  L V    V+ M  RL+  
Sbjct: 121 VKVATTKAQRKLFFNLRSSKKRLGWLT-----KQEVDEVAADLGVKPEVVLQMESRLSNQ 175

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER-KNRRNMLTRSMSVLNPRERR 241
           D S + L +  D + +    +L  D   +   L+E E+  +++R  L  +++ L+ R + 
Sbjct: 176 DLSFDGLEDDDDDSPAAPSTYLP-DVRMEPSRLLEHEDTDRDQRERLYAALADLDERSKT 234

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           I   R L E   TL  L+ +F VS ER+RQIE  A KKV+
Sbjct: 235 ILFERWLSEKKQTLHELAEKFGVSAERIRQIEKNAMKKVR 274


>gi|51246044|ref|YP_065928.1| RNA polymerase sigma-B factor [Desulfotalea psychrophila LSv54]
 gi|50877081|emb|CAG36921.1| probable RNA polymerase sigma-B factor [Desulfotalea psychrophila
           LSv54]
          Length = 332

 Score =  188 bits (478), Expect = 7e-46,   Method: Compositional matrix adjust.
 Identities = 111/289 (38%), Positives = 179/289 (61%), Gaps = 10/289 (3%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           + +N+  + N    L RY+ EI +  +L ++E   LA RY+E GD  AA+ LV+S+LRLV
Sbjct: 35  DNENLPAVSNP--ALHRYLQEISQYELLTREETDALATRYKESGDQDAAYTLVSSNLRLV 92

Query: 62  VKIAMGYRGYGLP-ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VK+AM ++ Y +    +++ EGN+GL+QA KKFDP RG + + Y+ +WI+A + ++I+ +
Sbjct: 93  VKVAMDFQKYWMQNFMDLIQEGNVGLVQATKKFDPYRGVKFSYYAAYWIRAYVLKFIMDN 152

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W LVKIGTT  Q++LFF+L + K  L++       P+  + +A++LNV E EVI M  R+
Sbjct: 153 WRLVKIGTTQAQRKLFFSLNKEKKLLES---QGFDPKPKL-LAERLNVREKEVIEMGQRM 208

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
              D SL + +  SD +  Q + +L  +  G E V+  KE +     ++      LN +E
Sbjct: 209 DNWDVSLESPVR-SDSDDEQ-KSFLPSNGPGIESVVAGKEIKVKLTELIDVLKVNLNDKE 266

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           R I E R L + P+TL+N++ +F +SRERVRQIE    KK+++  + ++
Sbjct: 267 RMILEKRLLTDEPLTLQNIADKFGISRERVRQIEVNLLKKMKKYFEAEM 315


>gi|330719751|gb|EGG98273.1| RNA polymerase sigma factor RpoH [gamma proteobacterium IMCC2047]
          Length = 283

 Score =  188 bits (478), Expect = 7e-46,   Method: Compositional matrix adjust.
 Identities = 114/285 (40%), Positives = 170/285 (59%), Gaps = 12/285 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
            M  +V G+  L+ Y+  +  IP+L  ++E  LA+R     DL AA +L+ SHLR VV I
Sbjct: 6   TMDNMVPGQ-NLAAYVTSVSSIPVLTAEQEKELAERLYYQEDLEAARQLIMSHLRFVVHI 64

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y GYGLP  +++ EGN+GLM+AVK+FDPERG RL ++++ WIKA + EYILR+W +V
Sbjct: 65  AKSYSGYGLPQGDLIQEGNVGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRIV 124

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGD 183
           K+ TT  Q++LFFNLR  K  L  ++++     +V AIA+ L V    V  M  RL A D
Sbjct: 125 KVATTKAQRKLFFNLRGAKKSLAWLSND-----EVDAIAEDLGVDAKVVRQMEGRLSAHD 179

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK---EERKNRRNMLTRSMSVLNPRER 240
              +   +  D ++ Q     + D       L+E+   +E  NR+  L  +M+ L+ R +
Sbjct: 180 APFDMGADDDDDSAYQAPANYLEDKRCDPVDLLEQQNWQETSNRK--LFEAMADLDERSK 237

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            I  AR L E   TL +L+ ++ VS ER+RQ+E  A KK++ ++Q
Sbjct: 238 DILNARWLSEQKSTLHDLADKYGVSAERIRQLEKNAMKKIKVAMQ 282


>gi|4103482|gb|AAD01786.1| sigma-E factor [Myxococcus xanthus]
          Length = 280

 Score =  188 bits (477), Expect = 8e-46,   Method: Compositional matrix adjust.
 Identities = 110/282 (39%), Positives = 183/282 (64%), Gaps = 11/282 (3%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           + E+++ P+L ++EE  LA+ Y+E GD++AA+RLV  +LRLVVK+A  Y    L + ++V
Sbjct: 1   MAEVQRHPLLTREEELQLARHYKESGDVNAAYRLVAWNLRLVVKLAHEYHRNPLSLLDLV 60

Query: 80  --SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
              EGNIGLMQAVKK+DPERG +L++Y+ WWI+A +  YI+ +W +VK+GTT  Q++LFF
Sbjct: 61  LVQEGNIGLMQAVKKYDPERGVKLSSYAAWWIRAYILRYIMDNWKMVKLGTTEAQRKLFF 120

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNA-LINSSDK 195
            LR+ +  L A       P+    +A++LNV+E +V+ M+ RL  DE S++A L N  D 
Sbjct: 121 KLRQEQEKLIA-QGFEASPK---LLAERLNVTEQDVVEMDQRLGHDEMSIDAPLGNDDDS 176

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
            +++   +L  +    ++ L  ++ +   R  L+     L  +ER IFE+R + + P+TL
Sbjct: 177 RTTRADRYLPSNSMPADERLGAEQLKALFREKLSEFARTLEGKERFIFESRLVSDEPLTL 236

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQV---ELSSSP 294
           +++  ++ VSRER RQIEA    ++++ +++Q+   +L +SP
Sbjct: 237 QDIGDKYGVSRERARQIEAALINRMRDFMREQIPDFDLVASP 278


>gi|71280363|ref|YP_266929.1| RNA polymerase factor sigma-32 [Colwellia psychrerythraea 34H]
 gi|71146103|gb|AAZ26576.1| RNA polymerase sigma-32 factor [Colwellia psychrerythraea 34H]
          Length = 285

 Score =  188 bits (477), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 102/273 (37%), Positives = 163/273 (59%), Gaps = 15/273 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+     IPML  ++E+ LA R     DL AA  L+ SHLR V+ +A GY GYGLP +++
Sbjct: 18  YMQSAYSIPMLTAEKEHDLATRLYNENDLQAAQELIMSHLRFVIHVAKGYSGYGLPHADL 77

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GLM+AVK+F+PE G RL ++++ WIKA + E++L++W +VK+ TT  Q++LFFN
Sbjct: 78  VQEGNVGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEFVLKNWRIVKVATTKAQRKLFFN 137

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN-- 196
           LR+ K  L   +      E+V  +A+ L V+  +V+ M  R++  +    L    D N  
Sbjct: 138 LRKNKKRLGWFS-----TEEVNTVAENLGVTTKDVMEMESRMSSHDQAFELSKDDDDNLG 192

Query: 197 SSQWQDWLVYDHDGQEQVLIEKE-----ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           SS +     Y  D Q  + +E E        N+R  L+ ++  L+ R + I + R L E+
Sbjct: 193 SSSFSP-AQYLQDKQSDLAVEVENDNWDNHANKR--LSTALVTLDERSQDIIKTRWLTED 249

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL+ L++++++S ERVRQ+E  A  K++ ++
Sbjct: 250 KTTLQELANKYQISAERVRQLEKNALSKLKNTM 282


>gi|311277614|ref|YP_003939845.1| RNA polymerase, sigma 32 subunit, RpoH [Enterobacter cloacae SCF1]
 gi|308746809|gb|ADO46561.1| RNA polymerase, sigma 32 subunit, RpoH [Enterobacter cloacae SCF1]
          Length = 285

 Score =  188 bits (477), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 113/287 (39%), Positives = 162/287 (56%), Gaps = 10/287 (3%)

Query: 4   KNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           K M  +    +G L  YI      PML   EE  LA++    GDL AA +L+ SHLR VV
Sbjct: 3   KEMQNLALAPVGNLESYIRAANAWPMLSADEERALAEKLHYQGDLEAAKKLILSHLRFVV 62

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W 
Sbjct: 63  HIARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWR 122

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+A 
Sbjct: 123 IVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVEMVARELGVSSKDVREMESRMAA 177

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVL--IEKEE-RKNRRNMLTRSMSVLNPRE 239
            +    L    D    Q    ++Y  D        IE +   +   N LT +M  L+ R 
Sbjct: 178 QDMTFDLGPDDDAQDGQPMAPVLYLQDKSSNFADGIEDDNWEEQAANKLTDAMQGLDERS 237

Query: 240 RRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + I  AR L E N  TL+ L+  + VS ERVRQ+E  A KK++ +I+
Sbjct: 238 QDIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIE 284


>gi|262369666|ref|ZP_06062994.1| RNA polymerase factor sigma-32 [Acinetobacter johnsonii SH046]
 gi|262315734|gb|EEY96773.1| RNA polymerase factor sigma-32 [Acinetobacter johnsonii SH046]
          Length = 289

 Score =  188 bits (477), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 108/271 (39%), Positives = 162/271 (59%), Gaps = 8/271 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + L  YI  + +IP+L  ++E  LA+RY    DL AA  LV SHLR VV IA  Y GYGL
Sbjct: 18  VNLGAYISTVNQIPILTAEQEKELAERYYYDQDLDAAKLLVMSHLRFVVHIARSYAGYGL 77

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P  +++ EGN+GLM+AVK+FDP  G RL ++++ WIKA + EY++R+W +VKI TT  Q+
Sbjct: 78  PQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVKIATTKAQR 137

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINS 192
           +LFFNLR LK   + +T      ++  +IA  LNV+  +V+ M  RL A D +  A  + 
Sbjct: 138 KLFFNLRSLKKSSKKLT-----LKEAQSIANDLNVTPEQVLEMEGRLTAYDAAFEAQGDD 192

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEE--RKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
            D+ S+     L  + +  +   + +EE   +   N L  +M  L+ R R I + R L +
Sbjct: 193 DDEGSTHVAPALYLEDNRYDPARLAEEEDYEEQSTNALHDAMEQLDDRSRNILQRRWLDD 252

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              TL  L++E+ VS ER+RQ+E  A +K++
Sbjct: 253 EKSTLHELAAEYNVSAERIRQLEKNAMEKIK 283


>gi|114776846|ref|ZP_01451889.1| RNA polymerase sigma factor [Mariprofundus ferrooxydans PV-1]
 gi|114552932|gb|EAU55363.1| RNA polymerase sigma factor [Mariprofundus ferrooxydans PV-1]
          Length = 274

 Score =  187 bits (476), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 102/277 (36%), Positives = 163/277 (58%), Gaps = 29/277 (10%)

Query: 22  EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           E+RK P L++ EE  LA+ + + GD  AA +LV ++L  V  IA  YR +GLP  +++ E
Sbjct: 16  EMRKTPRLDRAEETRLARLWHDQGDREAARQLVVANLGGVAAIAREYRHFGLPEMDLIQE 75

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           G +GLM AVK+FDPERGFRL TY+ WW++AA+ ++IL SWS+VK+GT   Q+R+F  L++
Sbjct: 76  GTLGLMHAVKRFDPERGFRLMTYASWWVRAAIHDFILHSWSIVKLGTNKLQRRVFAGLQK 135

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEV-----------ISMNCRLAGDESLNALI 190
            K  + A   +         +A    ++  E            +S++C  A DE  +A++
Sbjct: 136 AKNAIAAFDGSRADD-----VAADFGITAGEYQEAAGAFLQRDLSLDC--ACDEGGDAMV 188

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           ++ +   +             EQ++ +    ++R+  L  ++S L  R+R I + R L +
Sbjct: 189 HNLESMDAS-----------PEQIVTDNNWSEHRQAGLYHALSTLPERDRLILQRRHLSD 237

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            P TL++LS EF VS ER+RQ+EARA K+++ES+  Q
Sbjct: 238 EPATLKDLSEEFGVSMERIRQLEARAMKQLRESLVNQ 274


>gi|220904711|ref|YP_002480023.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio
           desulfuricans subsp. desulfuricans str. ATCC 27774]
 gi|219869010|gb|ACL49345.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio
           desulfuricans subsp. desulfuricans str. ATCC 27774]
          Length = 433

 Score =  187 bits (476), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 107/276 (38%), Positives = 169/276 (61%), Gaps = 7/276 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLP 74
           L  Y+ E+ + PML+ +EE+ LA R R+H D  AA RLV+SHLRLVV+IAM + R +   
Sbjct: 154 LHLYLREVSRFPMLKPEEEHELAVRVRDHNDADAAFRLVSSHLRLVVRIAMDFQRRWMQN 213

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++V EGN+GLM+AV KFDP++G + + Y+ +WIKA + ++I+ +W +VKIGTT  Q++
Sbjct: 214 VLDLVQEGNVGLMRAVNKFDPDKGIKFSYYASFWIKAYILKFIMDNWRMVKIGTTQVQRK 273

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSS 193
           LF+NL R +   Q +      P+  + ++++L V+E ++  M+ RLA  D SLNA +   
Sbjct: 274 LFYNLNRER---QKLIMQGYDPDAAM-LSERLGVTEEQINEMDQRLASTDMSLNAQVG-E 328

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D   +   D+L     G E  L   E     R+ L   M  LN +E+ I   R L + P+
Sbjct: 329 DSGGATRMDFLPALGPGIEDSLASTEIAGIVRSKLKTIMPKLNEKEQYILHNRLLSDEPI 388

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           TL  +   + ++RERVRQ+EAR  +K+ + ++  +E
Sbjct: 389 TLREIGERYNITRERVRQLEARLVEKIGQHMKNDIE 424


>gi|197123044|ref|YP_002134995.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter sp. K]
 gi|196172893|gb|ACG73866.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter sp. K]
          Length = 322

 Score =  187 bits (476), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 112/289 (38%), Positives = 176/289 (60%), Gaps = 14/289 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ E+ + P+L + EE+ LA +YRE GD+ AA+RLV S+LRLVVKIA  YR     +
Sbjct: 36  LRAYMAEVARHPVLSRDEEHALAVQYRETGDVDAAYRLVASNLRLVVKIAHEYRRTAFQL 95

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++V EGN+GLMQAVKK+DP +G +L++Y+ WWI+A +  +I+ +W LVK+GTT  Q++L
Sbjct: 96  LDLVQEGNLGLMQAVKKYDPWKGVKLSSYAAWWIRAYIIRFIMENWRLVKLGTTQAQRKL 155

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
           FFNL + +  L A     ++P   + +AK L V E +V  M+ R+A D+ SL+A + +  
Sbjct: 156 FFNLSKEREKLLA---RGIEPTPRL-LAKNLQVEEKDVEEMSARMAADDLSLDAPVGTEG 211

Query: 195 KNSSQWQ-DWLVYDHDGQEQVLIEKEE--RKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
            +  Q + D L  D        +  E+  R  R  +   S ++ + +ER IFE R L  +
Sbjct: 212 DDGRQNRLDRLADDGGPSPDAALGDEQLRRIFREKLDAFSGTLTDEKERYIFEHRLLPPD 271

Query: 252 ---PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV---ELSSSP 294
              P+TL+ +   F ++RER RQIEA+   +++E ++ ++   EL   P
Sbjct: 272 GTPPLTLQEVGDHFRLTRERARQIEAKLTGRLREFLRAEIPDFELLGPP 320


>gi|90023234|ref|YP_529061.1| RNA polymerase factor sigma-32 [Saccharophagus degradans 2-40]
 gi|89952834|gb|ABD82849.1| CheW protein [Saccharophagus degradans 2-40]
          Length = 284

 Score =  187 bits (475), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 105/272 (38%), Positives = 164/272 (60%), Gaps = 7/272 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ YI  +  + +L  +EE  LA+      +L AA ++V +HLR VV IA  Y GYGL  
Sbjct: 17  LNAYIQTVNGVAVLTAEEEKALAEDLYYRDNLDAARKMVMAHLRFVVHIAKSYSGYGLSQ 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           S+++ EGN+GLM+AVK+F+PE+G RL ++++ WIKA + E+ILR+W +VKI TT  Q++L
Sbjct: 77  SDLIQEGNVGLMKAVKRFNPEKGVRLVSFAVHWIKAEIHEFILRNWRIVKIATTKAQRKL 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR  K  L  +T++     +  A+A+ LNV    V  M  RLA  D + +A  +  D
Sbjct: 137 FFNLRGQKKRLAWLTNS-----EAEAVAQDLNVDVKHVREMEGRLASFDATFDAGADEDD 191

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
             + Q     + D       L+E E+  +N  + LT ++  L+ R R I + R L ++  
Sbjct: 192 DTAYQAPANYLEDRRYDPSTLLEDEDWTENSVSGLTTALESLDDRSRDILQQRWLSDDKS 251

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           TL +L++++ VS ER+RQ+E  A KKV+  ++
Sbjct: 252 TLHDLAAQYGVSAERIRQLEKNAMKKVKTYLE 283


>gi|220917834|ref|YP_002493138.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter
           dehalogenans 2CP-1]
 gi|219955688|gb|ACL66072.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter
           dehalogenans 2CP-1]
          Length = 322

 Score =  187 bits (475), Expect = 1e-45,   Method: Compositional matrix adjust.
 Identities = 112/289 (38%), Positives = 176/289 (60%), Gaps = 14/289 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ E+ + P+L + EE+ LA +YRE GD+ AA+RLV S+LRLVVKIA  YR     +
Sbjct: 36  LRAYMAEVARHPVLSRDEEHALAVQYRETGDVDAAYRLVASNLRLVVKIAHEYRRTAFQL 95

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++V EGN+GLMQAVKK+DP +G +L++Y+ WWI+A +  +I+ +W LVK+GTT  Q++L
Sbjct: 96  LDLVQEGNLGLMQAVKKYDPWKGVKLSSYAAWWIRAYIIRFIMENWRLVKLGTTQAQRKL 155

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
           FFNL + +  L A     ++P   + +AK L V E +V  M+ R+A D+ SL+A + +  
Sbjct: 156 FFNLSKEREKLLA---RGIEPTPRL-LAKNLQVEEKDVEEMSARMAADDLSLDAPVGTEG 211

Query: 195 KNSSQWQ-DWLVYDHDGQEQVLIEKEE--RKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
            +  Q + D L  D        +  E+  R  R  +   S ++ + +ER IFE R L  +
Sbjct: 212 DDGRQNRLDRLADDGGPSPDAALGDEQLRRIFREKLDAFSGTLTDEKERYIFEHRLLPPD 271

Query: 252 ---PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV---ELSSSP 294
              P+TL+ +   F ++RER RQIEA+   +++E ++ ++   EL   P
Sbjct: 272 GTPPLTLQEVGDHFRLTRERARQIEAKLTGRLREFLRAEIPDFELLGPP 320


>gi|319404792|emb|CBI78393.1| RNA polymerase sigma-32 factor [Bartonella rochalimae ATCC
           BAA-1498]
          Length = 247

 Score =  187 bits (475), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 96/236 (40%), Positives = 156/236 (66%), Gaps = 3/236 (1%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           H++  +H+RLV+ IA  ++ + +P+ ++V EG +GL++A  +FDP+RG R +TY+ WWI+
Sbjct: 2   HQIAAAHMRLVISIASRFKRFKMPLGDLVQEGYVGLLEAAARFDPDRGVRFSTYATWWIR 61

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-AIAKKLNVS 169
           A++Q+YILR+WS+V+ GT+++QK LFFNLRRL+  L A  DN L  +++  AI++KL VS
Sbjct: 62  ASIQDYILRNWSIVRGGTSSSQKALFFNLRRLRAKL-AQDDNTLTKQEIFRAISEKLGVS 120

Query: 170 ESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            ++V  M+ R +G D SL+  I+ + +      D L+ DH   + V+ +  + + R   L
Sbjct: 121 VNDVEKMDFRFSGTDNSLSLSISENGETPIAKMDSLIDDHPLPDSVIEQAIDGQRRAQWL 180

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             ++ +LN RE  I   RRL E   TLE L  +  +S+ERVRQIE RA +K++ ++
Sbjct: 181 HEALQILNERELEIIRFRRLNEEGTTLEVLGEKLGISKERVRQIEVRALQKLRCAL 236


>gi|283787904|ref|YP_003367769.1| RNA polymerase sigma-32 factor [Citrobacter rodentium ICC168]
 gi|282951358|emb|CBG91057.1| RNA polymerase sigma-32 factor [Citrobacter rodentium ICC168]
          Length = 284

 Score =  187 bits (475), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 113/287 (39%), Positives = 169/287 (58%), Gaps = 11/287 (3%)

Query: 4   KNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           K M  +    +G L  YI      PML   EE  LA+R    GDL AA  L+ SHLR VV
Sbjct: 3   KEMQNLALAPVGNLESYIRAANAWPMLSADEERALAERLHYQGDLEAAKTLILSHLRFVV 62

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W 
Sbjct: 63  HIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWR 122

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+A 
Sbjct: 123 IVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVEMVARELGVSSKDVREMESRMAA 177

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVL--IEKEERKNR-RNMLTRSMSVLNPRE 239
            + +   ++  D++ SQ    ++Y  D        IE++  +++  + LT +M  L+ R 
Sbjct: 178 -QDMTFDMSPDDESDSQPMAPVLYLQDKTSNFADGIEEDNWEDQAASKLTHAMEGLDERS 236

Query: 240 RRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + I  AR L E N  TL+ L+  + VS ERVRQ+E  A KK++ +I+
Sbjct: 237 QAIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIE 283


>gi|86157650|ref|YP_464435.1| sigma 32 (RpoH) [Anaeromyxobacter dehalogenans 2CP-C]
 gi|85774161|gb|ABC80998.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter
           dehalogenans 2CP-C]
          Length = 322

 Score =  187 bits (475), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 112/289 (38%), Positives = 180/289 (62%), Gaps = 14/289 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ E+ + P+L + EE+ LA +YRE GD+ AA++LV S+LRLVVKIA  YR     +
Sbjct: 36  LRAYMAEVARHPVLSRDEEHALAVQYRETGDVDAAYKLVASNLRLVVKIAHEYRRTAFQL 95

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++V EGN+GLMQAVKK+DP +G +L++Y+ WWI+A +  +I+ +W LVK+GTT  Q++L
Sbjct: 96  LDLVQEGNLGLMQAVKKYDPWKGVKLSSYAAWWIRAYIIRFIMENWRLVKLGTTQAQRKL 155

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
           FFNL + +  L A     ++P   + +AK L V E +V  M+ R+A D+ SL+A + +  
Sbjct: 156 FFNLSKEREKLLA---RGIEPTPRL-LAKNLQVEEKDVEEMSARMAADDLSLDAPVGTEG 211

Query: 195 KNSSQWQDWLVYDHDGQ--EQVLIEKEERKNRRNMLTR-SMSVLNPRERRIFEARRLQEN 251
            +  Q +   + D  GQ  +  L +++ R+  R  L   S ++ + +ER IFE R L  +
Sbjct: 212 DDGRQNRLDRLADDGGQAPDAALGDEQLRRIFREKLDAFSGTLTDEKERYIFEHRLLPPD 271

Query: 252 ---PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV---ELSSSP 294
              P+TL+ +   F ++RER RQIEA+   +++E ++ ++   EL   P
Sbjct: 272 GTPPLTLQEVGDHFRLTRERARQIEAKLTGRLREFLRAEIPDFELLGPP 320


>gi|330831381|ref|YP_004394333.1| RNA polymerase sigma factor [Aeromonas veronii B565]
 gi|328806517|gb|AEB51716.1| RNA polymerase sigma factor [Aeromonas veronii B565]
          Length = 284

 Score =  187 bits (475), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 112/287 (39%), Positives = 171/287 (59%), Gaps = 13/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           ++ M++I  G   L  YI  +  IP+L  +EE  LA+R ++ GDL AA +LV SHLR VV
Sbjct: 6   QRTMALIPQG--SLEGYIQAVNSIPVLSAEEERELAERLQQDGDLEAARQLVMSHLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y GYGLP +++V EGNIGLM+AVK+FDP  G RL ++++ WIKA + EY+LR+W 
Sbjct: 64  HVAKSYAGYGLPQADLVQEGNIGLMKAVKRFDPTVGVRLVSFAVHWIKAEIHEYVLRNWR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L       L  E+V A+A  L VS ++V  M  R+A 
Sbjct: 124 MVKVATTKAQRKLFFNLRKSKKRL-----GWLNHEEVQAVAADLGVSAADVTEMEARMAN 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK---EERKNRRNMLTRSMSVLNPRE 239
            +    L+   ++         + D        IE    ++   RR  L+ +++ L+ R 
Sbjct: 179 YDQAFDLVGDDEEEGGFAPVHYLEDKSSDLAATIENDNWDDHATRR--LSSALATLDERS 236

Query: 240 RRIFEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + I  AR L ++   TL+ L+  + VS ERVRQ+E  A KK++++++
Sbjct: 237 QHIIRARWLDDDSKTTLQELADTYGVSAERVRQLEKNALKKLKDAME 283


>gi|167854819|ref|ZP_02477597.1| RNA polymerase factor sigma-32 [Haemophilus parasuis 29755]
 gi|219871694|ref|YP_002476069.1| RNA polymerase factor sigma-32 [Haemophilus parasuis SH0165]
 gi|167854117|gb|EDS25353.1| RNA polymerase factor sigma-32 [Haemophilus parasuis 29755]
 gi|219691898|gb|ACL33121.1| RNA polymerase factor sigma-32 [Haemophilus parasuis SH0165]
          Length = 315

 Score =  187 bits (474), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 107/286 (37%), Positives = 168/286 (58%), Gaps = 30/286 (10%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI    + P+L  ++E  LA+R+    DL AA +L+ SHLR VV IA GY GYGLP+
Sbjct: 46  LDSYIRMANQYPVLTAEQEKELAERFYYDEDLDAAKQLIMSHLRFVVYIARGYLGYGLPL 105

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AVK+F+PE G RLA++++ W+KA + EY+L++W +VK+ TT +Q++L
Sbjct: 106 ADLIQEGNIGLMKAVKRFNPEIGVRLASFAVHWVKAEIHEYVLKNWRIVKVATTKSQRKL 165

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-----DESLNALI 190
           FFNLR+ K  L    +     E++  +A++L VS  +V  M  R+ G     D S+    
Sbjct: 166 FFNLRKNKQRLAWFNE-----EEIRKVAEELGVSTDDVKEMESRMVGQDIGFDTSVGDDD 220

Query: 191 NSS-------DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRI 242
           + +       +  SS + D L Y            EE   R    L  +++ L+ R + I
Sbjct: 221 DDNYVPSMYLEDESSNFVDELEY------------EEYSGRATAQLAYALAQLDERSQNI 268

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            + R L EN  TL  L++++ +S ERVRQ+E +A KK+++ I   +
Sbjct: 269 IKTRWLDENKATLHELAAQYNISAERVRQLENQALKKIKDVITYDI 314


>gi|92115102|ref|YP_575030.1| RNA polymerase factor sigma-32 [Chromohalobacter salexigens DSM
           3043]
 gi|91798192|gb|ABE60331.1| RNA polymerase, sigma 32 subunit, RpoH [Chromohalobacter salexigens
           DSM 3043]
          Length = 288

 Score =  186 bits (473), Expect = 2e-45,   Method: Compositional matrix adjust.
 Identities = 113/274 (41%), Positives = 162/274 (59%), Gaps = 13/274 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ YI  + +I +L  +EE  L  R  E GDL AA RLV SHLR VV IA  Y GYGLP 
Sbjct: 17  LNGYIQAVNRIAVLSSEEERELGFRLYEQGDLEAARRLVMSHLRFVVHIARSYSGYGLPQ 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGN+GLM+AVK+FDP +G RL ++++ WIKA + EY+LR+W +VKI TT  Q++L
Sbjct: 77  ADLIQEGNVGLMKAVKRFDPTQGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKL 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSSD 194
           FFNLR  K  L  +  NN   ++V AIAK L+V    V  M  RL A D   +A  +  +
Sbjct: 137 FFNLRGAKKRLAWL--NN---DEVDAIAKDLDVKPQVVREMEGRLSAFDAGYDATPSEEE 191

Query: 195 KNSSQ----WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
               Q    + D   +D   Q +    +E+  +R   L  ++  L+ R R I + R L E
Sbjct: 192 DQGYQAPAHYLDDERFDPAAQLEAADWEEDSTHR---LQAALGELDERSRDILQRRWLAE 248

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +  TL  L+  + VS ER+RQ+E  A KK+++ +
Sbjct: 249 SKATLHELADVYGVSAERIRQLEKNAMKKIKQQL 282


>gi|83643468|ref|YP_431903.1| RNA polymerase factor sigma-32 [Hahella chejuensis KCTC 2396]
 gi|83631511|gb|ABC27478.1| RNA polymerase sigma-32 factor RpoH [Hahella chejuensis KCTC 2396]
          Length = 284

 Score =  186 bits (473), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 113/270 (41%), Positives = 165/270 (61%), Gaps = 11/270 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+H +  IP+L  +EE  LA+R+ ++ DL AA +LV +HLR VV IA  Y GYGL  
Sbjct: 17  LEGYVHAVNSIPVLSAEEERELAERFHQNEDLYAARQLVMAHLRFVVHIAKSYSGYGLSQ 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           +++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++L
Sbjct: 77  ADLVQEGNIGLMKAVKRFNPEFGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRKL 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR  K  L  +T++  K     A+A+ L V    V  M  RLAG D S +A  +  D
Sbjct: 137 FFNLRSAKKRLAWLTNDEAK-----AVAEDLGVDTHVVREMESRLAGQDTSFDAGADEDD 191

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEK---EERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           + + +     + D      +++E    EE  N R  L  +++ L+ R + I + R L EN
Sbjct: 192 ETAFKAPANYLEDRRYDPAMMLENENWEEDSNSR--LHDALTQLDERSKDIIQKRWLAEN 249

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             TL  L+ E+ VS ER+RQ+E  A KKV+
Sbjct: 250 KATLHELADEYGVSAERIRQLEKNAMKKVK 279


>gi|307251409|ref|ZP_07533324.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 4 str. M62]
 gi|306856577|gb|EFM88718.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 4 str. M62]
          Length = 316

 Score =  186 bits (473), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 99/270 (36%), Positives = 160/270 (59%), Gaps = 6/270 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI    + P+L  ++E  LA+RY    D+ AA +L+ SH+R V+ IA GY GYGLP+
Sbjct: 49  LDSYIRMANQYPILTAEQEKELAERYYYDEDVEAAKQLILSHMRFVIHIARGYLGYGLPL 108

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AVK+FDP  G RL ++++ W+KA + EY+L++W +VK+ TT  Q++L
Sbjct: 109 ADLIQEGNIGLMKAVKRFDPNVGVRLVSFAIHWVKAEIHEYVLKNWRIVKVATTKAQRKL 168

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR+ K  L    +     E++  +A+ L VS  EV  M  R+ G +    L    D 
Sbjct: 169 FFNLRKNKNRLAWFNE-----EEIQKVAEDLGVSPEEVREMESRMTGQDLGFDLPVGEDD 223

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENPVT 254
           +        + D+       +E E+   +    L  +++ L+ R + I + R L E   T
Sbjct: 224 DEVYTPSMYLEDNSSNFADDLEDEQYNGQATAQLAYALATLDERSQDIIKTRWLDEEKAT 283

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L++L+ ++ +S ERVRQ+E  A KK++++I
Sbjct: 284 LQDLAEKYGISAERVRQLENAALKKIKDAI 313


>gi|303251140|ref|ZP_07337324.1| RNA polymerase factor sigma-32 [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|307253519|ref|ZP_07535389.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|302649991|gb|EFL80163.1| RNA polymerase factor sigma-32 [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|306859020|gb|EFM91063.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
          Length = 316

 Score =  186 bits (473), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 99/270 (36%), Positives = 160/270 (59%), Gaps = 6/270 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI    + P+L  ++E  LA+RY    D+ AA +L+ SH+R V+ IA GY GYGLP+
Sbjct: 49  LDSYIRMANQYPILTAEQEKELAERYYYDEDVEAAKQLILSHMRFVIHIARGYLGYGLPL 108

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AVK+FDP  G RL ++++ W+KA + EY+L++W +VK+ TT  Q++L
Sbjct: 109 ADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWVKAEIHEYVLKNWRIVKVATTKAQRKL 168

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR+ K  L    +     E++  +A+ L VS  EV  M  R+ G +    L    D 
Sbjct: 169 FFNLRKNKNRLAWFNE-----EEIQKVAEDLGVSPEEVREMESRMTGQDLGFDLPVGEDD 223

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENPVT 254
           +        + D+       +E E+   +    L  +++ L+ R + I + R L E   T
Sbjct: 224 DEVYTPSMYLEDNSSNFADDLEDEQYNGQATAQLAYALATLDKRSQDIIKTRWLDEEKAT 283

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L++L+ ++ +S ERVRQ+E  A KK++++I
Sbjct: 284 LQDLAEKYGISAERVRQLENAALKKIKDAI 313


>gi|162457339|ref|YP_001619706.1| RNA polymerase sigma factor rpoD [Sorangium cellulosum 'So ce 56']
 gi|161167921|emb|CAN99226.1| RNA polymerase sigma factor rpoD [Sorangium cellulosum 'So ce 56']
          Length = 443

 Score =  186 bits (473), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 110/285 (38%), Positives = 174/285 (61%), Gaps = 11/285 (3%)

Query: 11  NGEIGLSR------YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +G++ LSR      Y+ E+++  +L   EE  L  +Y +  D++ A RLVT++LRLVVK+
Sbjct: 156 SGDVALSRTDPLQAYLREVQRHALLTPDEEKELTIKYTKTQDVATAARLVTANLRLVVKL 215

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  YR     I +++ EGNIGLMQAVK++DP RG +L++Y+ WWI+A +  +IL +W LV
Sbjct: 216 AYEYRRAYKNIMDLIQEGNIGLMQAVKRYDPYRGVKLSSYAAWWIRAYILRFILNNWRLV 275

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GD 183
           K+GTT  Q++LFFNL + K  L A+    ++P     IAK+L+V E EV+ M+ RLA G+
Sbjct: 276 KLGTTQAQRKLFFNLNKEKAKLSAM---GIEP-TAAEIAKRLSVEEKEVVDMDRRLASGE 331

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SL+A +   +  +    + LV      +      E      + L++    L  ++  IF
Sbjct: 332 ASLDAPVGDLEGRTIPRVELLVSSGASPDTAFEASEMGMLVHDRLSKFRETLKGKDVIIF 391

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           + R   E+P+TL+ L +EF +SRERVRQ+EAR   K++  +Q+++
Sbjct: 392 DKRMAAEDPLTLQELGNEFGISRERVRQLEARLQSKLRTYLQEEL 436


>gi|46143484|ref|ZP_00135165.2| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|126209296|ref|YP_001054521.1| RNA polymerase factor sigma-32 [Actinobacillus pleuropneumoniae
           L20]
 gi|126098088|gb|ABN74916.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 5b str. L20]
          Length = 316

 Score =  186 bits (473), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 99/270 (36%), Positives = 160/270 (59%), Gaps = 6/270 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI    + P+L  ++E  LA+RY    D+ AA +L+ SH+R V+ IA GY GYGLP+
Sbjct: 49  LDSYIRMANQYPILTAEQEKELAERYYYDEDVEAAKQLILSHMRFVIHIARGYLGYGLPL 108

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AVK+FDP  G RL ++++ W+KA + EY+L++W +VK+ TT  Q++L
Sbjct: 109 ADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWVKAEIHEYVLKNWRIVKVATTKAQRKL 168

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR+ K  L    +     E++  +A+ L VS  EV  M  R+ G +    L    D 
Sbjct: 169 FFNLRKNKNRLAWFNE-----EEIQKVAEDLGVSPEEVREMESRMTGQDLGFDLPVGEDD 223

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENPVT 254
           +        + D+       +E E+   +    L  +++ L+ R + I + R L E   T
Sbjct: 224 DEVYTPSMYLEDNSSNFADDLEDEQYNGQATAQLAYALATLDERSQDIIKTRWLDEEKAT 283

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L++L+ ++ +S ERVRQ+E  A KK++++I
Sbjct: 284 LQDLAEKYGISAERVRQLENAALKKIKDAI 313


>gi|165977273|ref|YP_001652866.1| RNA polymerase factor sigma-32 [Actinobacillus pleuropneumoniae
           serovar 3 str. JL03]
 gi|190151190|ref|YP_001969715.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 7 str. AP76]
 gi|303252711|ref|ZP_07338873.1| RNA polymerase factor sigma-32 [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|307248906|ref|ZP_07530917.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 2 str. S1536]
 gi|307262328|ref|ZP_07543976.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 12 str. 1096]
 gi|307264539|ref|ZP_07546123.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 13 str. N273]
 gi|165877374|gb|ABY70422.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 3 str. JL03]
 gi|189916321|gb|ACE62573.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 7 str. AP76]
 gi|302648450|gb|EFL78644.1| RNA polymerase factor sigma-32 [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|306854601|gb|EFM86793.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 2 str. S1536]
 gi|306867991|gb|EFM99819.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 12 str. 1096]
 gi|306870138|gb|EFN01898.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 13 str. N273]
          Length = 316

 Score =  186 bits (472), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 99/270 (36%), Positives = 160/270 (59%), Gaps = 6/270 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI    + P+L  ++E  LA+RY    D+ AA +L+ SH+R V+ IA GY GYGLP+
Sbjct: 49  LDSYIRMANQYPILTAEQEKELAERYYYDEDVEAAKQLILSHMRFVIHIARGYLGYGLPL 108

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AVK+FDP  G RL ++++ W+KA + EY+L++W +VK+ TT  Q++L
Sbjct: 109 ADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWVKAEIHEYVLKNWRIVKVATTKAQRKL 168

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR+ K  L    +     E++  +A+ L VS  EV  M  R+ G +    L    D 
Sbjct: 169 FFNLRKNKNRLAWFNE-----EEIQKVAEDLGVSPEEVREMESRMTGQDLGFDLPVGEDD 223

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENPVT 254
           +        + D+       +E E+   +    L  +++ L+ R + I + R L E   T
Sbjct: 224 DEVYTPSMYLEDNSSNFADDLEDEQYNGQATAQLAYALATLDERSQDIIKTRWLDEEKAT 283

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L++L+ ++ +S ERVRQ+E  A KK++++I
Sbjct: 284 LQDLAEKYGISAERVRQLENAALKKIKDAI 313


>gi|294638156|ref|ZP_06716412.1| alternative sigma factor RpoH [Edwardsiella tarda ATCC 23685]
 gi|291088723|gb|EFE21284.1| alternative sigma factor RpoH [Edwardsiella tarda ATCC 23685]
          Length = 284

 Score =  186 bits (472), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 105/289 (36%), Positives = 169/289 (58%), Gaps = 10/289 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+++  ++ +  +  L  Y+      PML  +EE  L +R    GDL AA +L+ SHLR 
Sbjct: 1   MSKEMQTLTLVPQGSLEAYVRAANAYPMLTAEEERALGERLHYQGDLDAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEMGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VSE +V+ M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVELVARELGVSEKDVLEMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNP 237
           A  +    L N  ++  +     +++  D       E E+     +  + L+ ++  L+ 
Sbjct: 176 AAQDMAFDLPNDDEQEGAPAAP-VLFLQDKSSDFANEIEDDNWESHAADKLSVALEGLDE 234

Query: 238 RERRIFEARRLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           R + I  AR L  EN  TL+ L+  + VS ERVRQ+E  A KK++ +I+
Sbjct: 235 RSQHIIRARWLDSENKATLQELADRYGVSAERVRQLEKNAMKKLRAAIE 283


>gi|303327038|ref|ZP_07357480.1| deoxyuridine 5`-triphosphate nucleotidohydrolase [Desulfovibrio sp.
           3_1_syn3]
 gi|302863026|gb|EFL85958.1| deoxyuridine 5`-triphosphate nucleotidohydrolase [Desulfovibrio sp.
           3_1_syn3]
          Length = 352

 Score =  186 bits (472), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 107/271 (39%), Positives = 166/271 (61%), Gaps = 7/271 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLP 74
           L  Y+ E+ + PML+ +EE+ LA R R+H D  AA RLV+SHLRLVV+IAM + R +   
Sbjct: 73  LHLYLREVSRFPMLKPEEEHELALRVRDHNDPDAAFRLVSSHLRLVVRIAMDFQRRWMQN 132

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++V EGN+GLM+AV KFDP++G + + Y+ +WIKA + ++I+ +W +VKIGTT  Q++
Sbjct: 133 VLDLVQEGNVGLMRAVNKFDPDKGIKFSYYASFWIKAYILKFIMDNWRMVKIGTTQVQRK 192

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSS 193
           LF+NL R +   Q +      P+  + ++++L V+E ++  M+ RLA  D SLN  +   
Sbjct: 193 LFYNLNRER---QKLIAQGYDPDAAM-LSERLGVTEDQINEMDQRLASTDLSLNVQV-GE 247

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D   +   D+L     G E  L   E     R+ L   M  LN +E  I + R L + PV
Sbjct: 248 DSGGASRMDFLPALGPGIEDTLASDEIAGLVRSRLKTIMPKLNEKEVYILQNRLLTDEPV 307

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           TL  +   + V+RERVRQ+EAR  +K+++ +
Sbjct: 308 TLREIGERYNVTRERVRQLEARLLEKIRQHL 338


>gi|304397877|ref|ZP_07379753.1| RNA polymerase, sigma 32 subunit, RpoH [Pantoea sp. aB]
 gi|308188475|ref|YP_003932606.1| RNA polymerase sigma-32 factor [Pantoea vagans C9-1]
 gi|304354588|gb|EFM18959.1| RNA polymerase, sigma 32 subunit, RpoH [Pantoea sp. aB]
 gi|308058985|gb|ADO11157.1| RNA polymerase sigma-32 factor [Pantoea vagans C9-1]
          Length = 285

 Score =  186 bits (472), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 113/289 (39%), Positives = 167/289 (57%), Gaps = 14/289 (4%)

Query: 4   KNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           K M  +    +G L  Y+      PML  +EE  LA+R    GDL AA  L+ SHLR VV
Sbjct: 3   KEMQTLAIAPLGNLESYVRAANTWPMLSAEEEKALAERLHYQGDLEAAKTLILSHLRFVV 62

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA  Y GYGLP +++V EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W 
Sbjct: 63  HIARNYSGYGLPQADLVQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWR 122

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+A 
Sbjct: 123 IVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVEMVARELGVSSKDVREMESRMAA 177

Query: 183 DESLNALINSSDKNSSQWQDW--LVYDHDGQEQVLIEKEERK---NRRNMLTRSMSVLNP 237
            +    +  S+D  SS+ +    ++Y  D         EE     +  + L+ +M  L+ 
Sbjct: 178 QDMTFDM--SADDESSEGRSMAPVLYLQDKTSDFADGIEEDNWDAHAADKLSYAMEGLDE 235

Query: 238 RERRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           R + I  AR L E N  TL+ L+ ++ VS ERVRQ+E  A KK++ +I+
Sbjct: 236 RSQHIIRARWLDEDNKTTLQELADQYGVSAERVRQLEKNAMKKLRMAIE 284


>gi|119503515|ref|ZP_01625598.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2080]
 gi|119460577|gb|EAW41669.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2080]
          Length = 282

 Score =  186 bits (472), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 108/273 (39%), Positives = 158/273 (57%), Gaps = 11/273 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+  +  IP+L    E  LA++    G + +A  LV +HLR VV IA  Y GYGL  
Sbjct: 15  LPAYVQAVSGIPILSVDREQALAEKLYYEGCVDSARELVLAHLRFVVHIARSYSGYGLAE 74

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM+AVK+FDP +G RL ++++ WIKA M E+ILR+W +VK+ TT  Q++L
Sbjct: 75  GDLIQEGNVGLMKAVKRFDPNKGVRLVSFAVHWIKAEMHEFILRNWRIVKVATTKAQRKL 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR  K  L       L  E+  AIA  L V E+EV  M  RL+  D + +   ++ D
Sbjct: 135 FFNLRSAKKSL-----GWLNAEETQAIAADLGVDEAEVQRMEGRLSSRDIAFDLPTDADD 189

Query: 195 KNSSQWQDWLVY--DHDGQEQVLIEKEER-KNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           +++  WQ    Y  D        IE E+  ++  N L  ++S L+ R R I   R L E 
Sbjct: 190 EDA--WQSPQAYLDDISTDPARCIEAEDSARDGENRLRAALSDLDERSRNIVTQRWLAEQ 247

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL  L++E+ VS ER+RQ+E  A KK++ ++
Sbjct: 248 KATLHELAAEYGVSAERIRQLEVNAMKKLKNTL 280


>gi|289207353|ref|YP_003459419.1| RNA polymerase, sigma 32 subunit, RpoH [Thioalkalivibrio sp.
           K90mix]
 gi|288942984|gb|ADC70683.1| RNA polymerase, sigma 32 subunit, RpoH [Thioalkalivibrio sp.
           K90mix]
          Length = 289

 Score =  186 bits (472), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 101/273 (36%), Positives = 169/273 (61%), Gaps = 9/273 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+  + +I +L+ + E  LA+   E  DL AA +L+  +LR VV +A GY+GYGLP+
Sbjct: 20  LDHYMQAVSRIEVLDPEHERELARSLHERNDLDAARQLILHNLRFVVHVARGYQGYGLPL 79

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM+AV++FDP +G RL ++++ WI+A + E+ILR+W +VK+ TT  Q++L
Sbjct: 80  GDLIQEGNVGLMKAVRRFDPNQGVRLVSFAVHWIRAEIHEFILRNWRIVKVATTKAQRKL 139

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR  K  L  ++++     +V A+A+ L VSE++V  M  RL+  D S +   +S D
Sbjct: 140 FFNLRSAKQRLGWMSND-----EVSAVARDLGVSENDVWEMERRLSSQDASFDPAPDSDD 194

Query: 195 KNS--SQWQDWLVYD-HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           +++  +  Q   + D  D   QV  +++  ++ +  L  ++  L+ R R I   R + E 
Sbjct: 195 EHTYLAPAQRLSIEDMSDDPAQVAEDEDWDRHYQERLASTLGELDERSRDILARRYMSEP 254

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL  L++E+ VS ER+RQIE  A K+++ + 
Sbjct: 255 KATLHELAAEYGVSAERIRQIENNAIKRIRTAF 287


>gi|119475401|ref|ZP_01615754.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2143]
 gi|119451604|gb|EAW32837.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2143]
          Length = 282

 Score =  186 bits (471), Expect = 4e-45,   Method: Compositional matrix adjust.
 Identities = 108/272 (39%), Positives = 164/272 (60%), Gaps = 8/272 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+  +   P+L  + E+ LA+    H +L +A  LV +HLR VV IA  Y GYGLP+
Sbjct: 16  LNAYMQTVNNFPVLTAEREHELAEALYYHENLESARELVMAHLRFVVHIARSYNGYGLPL 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AVK+F+PE+G RL ++++ W+KA M EYILR+W +VK+ TT  Q++L
Sbjct: 76  ADLIQEGNIGLMKAVKRFNPEKGVRLVSFAVHWVKAEMHEYILRNWRIVKVATTKAQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSSD 194
           FFNLR  K  L  + +     ++  AIA+ LNV   EV  M  RL A D   +A  +  D
Sbjct: 136 FFNLRGAKKKLAWLNE-----KEAHAIAEDLNVDVKEVRRMESRLTASDLGFDAGADDED 190

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
                   +L  DH     +L+E  +  +N    L  ++  L+ R R I +AR L ++  
Sbjct: 191 DGFVAPAHYL-EDHSANPAMLLEDADWEQNSNQHLQLALEQLDERSRDIIQARWLSDSKS 249

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           TL +L+ ++ VS ERVRQ+E  A KKV+ +++
Sbjct: 250 TLHDLAGKYGVSAERVRQLEKNAMKKVRATME 281


>gi|262376306|ref|ZP_06069536.1| alternative sigma factor RpoH [Acinetobacter lwoffii SH145]
 gi|262308907|gb|EEY90040.1| alternative sigma factor RpoH [Acinetobacter lwoffii SH145]
          Length = 289

 Score =  186 bits (471), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 107/271 (39%), Positives = 158/271 (58%), Gaps = 8/271 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + L  YI  + +IP+L  ++E  LA+RY    DL AA  LV SHLR VV IA  Y GYGL
Sbjct: 18  VNLGAYISTVNQIPILTAEQEKELAERYYYDQDLDAAKMLVMSHLRFVVHIARSYAGYGL 77

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P  +++ EGN+GLM+AVK+FDP  G RL ++++ WIKA + EY++R+W +VKI TT  Q+
Sbjct: 78  PQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVKIATTKAQR 137

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
           +LFFNLR LK      +   L   +  +IA  LNV+  +V+ M  RL   ++     +  
Sbjct: 138 KLFFNLRSLKK-----SSKKLTLAEAQSIANDLNVTPEQVLEMEGRLTAYDAAFDASSDD 192

Query: 194 DKNSSQWQDWLVYDHDGQEQV--LIEKEERKNR-RNMLTRSMSVLNPRERRIFEARRLQE 250
           D   S      +Y  D +     LIE E+ + +  + L  +M  L+ R R I + R L +
Sbjct: 193 DDEGSTHVAPALYLEDNRYDPARLIENEDYEEQSTSALHEAMDQLDDRSRNILQRRWLDD 252

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              TL  L++E+ VS ER+RQ+E  A +K++
Sbjct: 253 EKSTLHELAAEYNVSAERIRQLEKNAMEKIK 283


>gi|117618742|ref|YP_854903.1| alternative sigma factor RpoH [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
 gi|117560149|gb|ABK37097.1| alternative sigma factor RpoH [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
          Length = 284

 Score =  186 bits (471), Expect = 5e-45,   Method: Compositional matrix adjust.
 Identities = 112/287 (39%), Positives = 171/287 (59%), Gaps = 13/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           ++ M++I  G   L  YI  +  IP+L  +EE  LA+R ++ GDL AA +LV SHLR VV
Sbjct: 6   QRTMALIPQGS--LEGYIQAVNSIPVLSAEEERELAERLQQGGDLEAARQLVMSHLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y GYGLP +++V EGNIGLM+AVK+FDP  G RL ++++ WIKA + EY+LR+W 
Sbjct: 64  HVAKSYAGYGLPQADLVQEGNIGLMKAVKRFDPSVGVRLVSFAVHWIKAEIHEYVLRNWR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L       L  E+V A+A  L VS ++V  M  R++ 
Sbjct: 124 MVKVATTKAQRKLFFNLRKSKKRL-----GWLNHEEVQAVAADLGVSAADVTEMEARMSN 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK---EERKNRRNMLTRSMSVLNPRE 239
            +    L+   ++         + D        IE    ++   RR  L+ +++ L+ R 
Sbjct: 179 YDQAFDLVGDDEEEGGFAPVHYLEDKSSDLAATIENDNWDDHATRR--LSSALATLDERS 236

Query: 240 RRIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + I  AR L  E+  TL+ L+  + VS ERVRQ+E  A KK++++++
Sbjct: 237 QHIIRARWLDDESKTTLQELADTYGVSAERVRQLEKNALKKLKDAME 283


>gi|291619275|ref|YP_003522017.1| RpoH [Pantoea ananatis LMG 20103]
 gi|291154305|gb|ADD78889.1| RpoH [Pantoea ananatis LMG 20103]
 gi|327395604|dbj|BAK13026.1| RNA polymerase sigma-32 factor RpoH [Pantoea ananatis AJ13355]
          Length = 285

 Score =  185 bits (470), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 109/287 (37%), Positives = 161/287 (56%), Gaps = 10/287 (3%)

Query: 4   KNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           K M  +    +G L  Y+      PML  +EE  LA+R    GDL AA  L+ SHLR VV
Sbjct: 3   KEMQTLAIAPLGNLESYVRAANTWPMLSAEEEKALAERLHYQGDLDAAKTLILSHLRFVV 62

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W 
Sbjct: 63  HIARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWR 122

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+A 
Sbjct: 123 IVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVEMVARELGVSSKDVREMESRMAA 177

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNPRE 239
            +    +    +    +    ++Y  D         EE     +  + LT +M  L+ R 
Sbjct: 178 QDMTFDMSADDESGEGKSMAPVLYLQDKTSDFADGIEEDNWESHAADKLTYAMEGLDERS 237

Query: 240 RRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + I  AR L E N  TL+ L+  + VS ERVRQ+E  A KK++ +I+
Sbjct: 238 QHIIRARWLDEDNKTTLQELADRYGVSAERVRQLEKNAMKKLRMAIE 284


>gi|307246764|ref|ZP_07528832.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|307255748|ref|ZP_07537551.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 9 str. CVJ13261]
 gi|307257933|ref|ZP_07539687.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 10 str. D13039]
 gi|307260200|ref|ZP_07541909.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 11 str. 56153]
 gi|306852339|gb|EFM84576.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|306861308|gb|EFM93299.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 9 str. CVJ13261]
 gi|306863580|gb|EFM95509.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 10 str. D13039]
 gi|306865745|gb|EFM97624.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 11 str. 56153]
          Length = 316

 Score =  185 bits (470), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 99/270 (36%), Positives = 160/270 (59%), Gaps = 6/270 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI    + P+L  ++E  LA+RY    D+ AA +L+ SH+R V+ IA GY GYGLP+
Sbjct: 49  LDSYIRMANQYPILTAEQEKELAERYYYDEDVEAAKQLILSHMRFVIHIARGYLGYGLPL 108

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AVK+FDP  G RL ++++ W+KA + EY+L++W +VK+ TT  Q++L
Sbjct: 109 ADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWVKAEIHEYVLKNWRIVKVATTKAQRKL 168

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR+ K  L    +     E++  +A+ L VS  EV  M  R+ G +    L    D 
Sbjct: 169 FFNLRKNKNRLAWFNE-----EEIQKVAEDLGVSLEEVREMESRMTGQDLGFDLPVGEDD 223

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRN-MLTRSMSVLNPRERRIFEARRLQENPVT 254
           +        + D+       +E E+   +    L  +++ L+ R + I + R L E   T
Sbjct: 224 DEVYTPSMYLEDNSSNFADDLEDEQYNGQATAQLAYALATLDERSQDIIKTRWLDEEKAT 283

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L++L+ ++ +S ERVRQ+E  A KK++++I
Sbjct: 284 LQDLAEKYGISAERVRQLENAALKKIKDAI 313


>gi|1710646|sp|P50509|RP32_PROMI RecName: Full=RNA polymerase sigma-32 factor
 gi|1143374|dbj|BAA09441.1| sigma-32 homolog [Proteus mirabilis]
          Length = 284

 Score =  185 bits (470), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 110/285 (38%), Positives = 169/285 (59%), Gaps = 10/285 (3%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           ++++++  G I    YI      PML  +EE  LA+R    GDL AA  L+ SHLR V+ 
Sbjct: 6   QSLALVPQGSI--EAYIRAANSYPMLTAEEEKELAERLHYEGDLEAAKTLILSHLRFVIH 63

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           +A  Y GYGLP ++++ EGNIGLM+AV+ F+PE G RL ++++ WIKA + EY+LR+W +
Sbjct: 64  VARSYSGYGLPQADLIQEGNIGLMKAVRHFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRI 123

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AG 182
           VK+ TT +Q++LFFNLR+ K  L          ++V  +AK+L VSES+V  M  R+ A 
Sbjct: 124 VKVATTKSQRKLFFNLRKNKKRL-----GWFNQDEVELVAKELGVSESDVREMESRMSAQ 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPRERR 241
           D + +   + SD          + D        IE++   N   + LT ++  L+ R + 
Sbjct: 179 DMAFDMSADDSDDPHPVAPVLFLEDKSSDFADGIEEDNWDNHAADRLTLAIKTLDERSQD 238

Query: 242 IFEARRLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           I  AR L+ +N  TL+ L+ ++ VS ERVRQ+E  A KK++ +I+
Sbjct: 239 IIRARWLEDDNKSTLQELADKYGVSAERVRQLEKNAMKKLRLAIE 283


>gi|307128894|ref|YP_003880910.1| RNA polymerase sigma-32 (sigma H) factor [Dickeya dadantii 3937]
 gi|306526423|gb|ADM96353.1| RNA polymerase, sigma 32 (sigma H) factor [Dickeya dadantii 3937]
          Length = 285

 Score =  185 bits (470), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 105/274 (38%), Positives = 157/274 (57%), Gaps = 9/274 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI      PML  +EE  LA+R   HGDL AA +L+ SHLR V+ +A  Y GYGLP 
Sbjct: 16  LEGYIRAANAYPMLTAEEERALAERLHYHGDLDAAKQLILSHLRFVIHVARNYSGYGLPQ 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W +VK+ TT  Q++L
Sbjct: 76  ADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR+ K  L          ++V  +A++L V+  +V  M  R+A  +         D 
Sbjct: 136 FFNLRKTKQRL-----GWFNQDEVELVARELGVTSKDVREMESRMAAQDMTFDPSPEDDA 190

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNPRERRIFEARRL-QEN 251
              Q    ++Y  D         EE     +  + LT ++  L+ R + I  AR L  +N
Sbjct: 191 QPGQPMAPMLYLQDKSSDFADGIEEDNWETHAADKLTYALEGLDERSQHIIRARWLDDDN 250

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             TL+ L+  + VS ERVRQ+E  A KK++ +I+
Sbjct: 251 KSTLQELADHYGVSAERVRQLEKNAMKKLRAAIE 284


>gi|149909450|ref|ZP_01898105.1| RNA polymerase sigma factor [Moritella sp. PE36]
 gi|149807560|gb|EDM67509.1| RNA polymerase sigma factor [Moritella sp. PE36]
          Length = 287

 Score =  185 bits (470), Expect = 6e-45,   Method: Compositional matrix adjust.
 Identities = 107/289 (37%), Positives = 171/289 (59%), Gaps = 13/289 (4%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           + ++M+++  G I    YI  +  IPML  ++E  L +R +  GD+ AA +L+ SHLR V
Sbjct: 4   DMQSMALVPQGSI--EAYIQGVNNIPMLTAEQEKELGERLQNEGDVDAARQLIMSHLRFV 61

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V +A GY GYGL  ++++ EGNIGLM+AVK+F+PE G RL ++++ W+KA + E++LR+W
Sbjct: 62  VHVARGYAGYGLAQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWVKAEIHEFVLRNW 121

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            +VK+ TT  Q++LFFNLR+ K  L   T   +K      +A+ L VS  +V+ M  R++
Sbjct: 122 RVVKVATTKAQRKLFFNLRKSKKRLGWFTSAEVKT-----VAETLGVSTKDVVEMESRMS 176

Query: 182 -GDESLNALINSSDKNSSQWQDW--LVYDHDGQEQVLIEKEER---KNRRNMLTRSMSVL 235
             D++ +   +      S    +    Y  D    V ++ E     K+    LT ++S L
Sbjct: 177 YSDQAFDLYADDDSDKDSGSTSFSPAQYLEDNASDVALQVERENWDKSASLSLTNAISEL 236

Query: 236 NPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + R + I ++R L E+  TL+ L+  + VS ERVRQ+E  A KK++E I
Sbjct: 237 DERSQDIVKSRWLAEDKATLQYLADRYGVSAERVRQLEKNAMKKLREFI 285


>gi|317486415|ref|ZP_07945242.1| alternative sigma factor RpoH [Bilophila wadsworthia 3_1_6]
 gi|316922325|gb|EFV43584.1| alternative sigma factor RpoH [Bilophila wadsworthia 3_1_6]
          Length = 403

 Score =  185 bits (470), Expect = 7e-45,   Method: Compositional matrix adjust.
 Identities = 104/290 (35%), Positives = 178/290 (61%), Gaps = 7/290 (2%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           +++++  + + +  L  Y+ E+ + PML+  EE+ LA+R ++ GD  AA RLV+SHLRLV
Sbjct: 110 SQQHLPSLSSSKDSLHLYLREVSRFPMLKPDEEFDLARRVQKTGDSDAAFRLVSSHLRLV 169

Query: 62  VKIAMGY-RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VKIAM + R +   + +++ EGN+GLM+AV KFDP++G + + Y+ +WI+A + ++I+ +
Sbjct: 170 VKIAMDFQRRWMQNVLDLIQEGNVGLMRAVNKFDPDKGIKFSYYAAFWIRAYILKFIMDN 229

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VKIGTT  Q++LF+NL R +  L A       P+    +A++L V E +++ M  RL
Sbjct: 230 WRMVKIGTTQAQRKLFYNLNRERQKLIA---EGFDPD-AATLAERLGVGEDQIVEMQQRL 285

Query: 181 -AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            A D SL+A +   +  S+   D+L     G E+ L   E  +  ++ +   +  L+ +E
Sbjct: 286 DASDMSLDATVG-DESGSATRMDFLPALGPGIEESLAGMEIAELLQSKIRDILPSLSEKE 344

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
             I E R L ++PVTL  +   + V+RERVRQ+EAR  +K++  +   ++
Sbjct: 345 AYILEHRLLTDDPVTLREIGERYNVTRERVRQLEARLLQKLKTHLSTDIQ 394


>gi|312884403|ref|ZP_07744108.1| RNA polymerase factor sigma-32 [Vibrio caribbenthicus ATCC
           BAA-2122]
 gi|309367925|gb|EFP95472.1| RNA polymerase factor sigma-32 [Vibrio caribbenthicus ATCC
           BAA-2122]
          Length = 285

 Score =  185 bits (469), Expect = 8e-45,   Method: Compositional matrix adjust.
 Identities = 105/272 (38%), Positives = 162/272 (59%), Gaps = 8/272 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+  +   PML  +EE  LA+R    G++ AA  L+ SHLR VV +A GY GYGLP+
Sbjct: 16  LDSYVRSVNSYPMLTAEEERELAERLHYDGEIDAAKGLILSHLRFVVHVARGYSGYGLPM 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           +++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W +VKI TT  Q++L
Sbjct: 76  ADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR+ K  L           +V  +A++L V  SEV  M  RLA  ++   + +  D 
Sbjct: 136 FFNLRKSKKRLGWFNQG-----EVETVARELGVEPSEVREMESRLAAQDATFEVPSDDDD 190

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
             + +   +VY  D    +    E      +  N L+ ++  L+ R + I  +R L +N 
Sbjct: 191 AHTSYVAPMVYLEDKASDIADNIEAANWEAHTNNRLSLALKSLDERSQHIVRSRWLDDNK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL+ L+  ++VS ER+RQ+E  A KK+++++
Sbjct: 251 STLQELAETYQVSAERIRQLEKNAMKKLKDAV 282


>gi|121730259|ref|ZP_01682638.1| RNA polymerase sigma-32 factor [Vibrio cholerae V52]
 gi|121627991|gb|EAX60548.1| RNA polymerase sigma-32 factor [Vibrio cholerae V52]
          Length = 259

 Score =  184 bits (468), Expect = 9e-45,   Method: Compositional matrix adjust.
 Identities = 105/262 (40%), Positives = 159/262 (60%), Gaps = 11/262 (4%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           ML   EE  LA+R    GD+ AA  L+ SHLR VV +A GY GYGLP++++V EGNIGLM
Sbjct: 1   MLSADEERELAERLHYKGDIDAAKGLILSHLRFVVHVARGYSGYGLPMADLVQEGNIGLM 60

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AVK+F+PE G RL ++++ WIKA + EY+LR+W +VKI TT  Q++LFFNLR+ K  L 
Sbjct: 61  KAVKRFNPEMGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKLFFNLRKSKKRLG 120

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
              +      +V  +A++L V  +EV  M  RLA  ++   +    D+N   +   ++Y 
Sbjct: 121 WFNNG-----EVETVARELGVEPAEVREMESRLAAQDAAFEMSAEDDENGMAYTAPVLYL 175

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSV----LNPRERRIFEARRL-QENPVTLENLSSEF 262
            D     L +  E +N     T+ +S+    L+ R + I  AR L  +N  TL++L+  +
Sbjct: 176 EDKHSD-LADNLEAENWEAHTTQRLSMALASLDERSQHIVRARWLDDDNKTTLQDLAEMY 234

Query: 263 EVSRERVRQIEARAFKKVQESI 284
            VS ER+RQ+E  A +K++E++
Sbjct: 235 GVSAERIRQLEKNAMRKLKEAV 256


>gi|120556648|ref|YP_960999.1| RNA polymerase factor sigma-32 [Marinobacter aquaeolei VT8]
 gi|120326497|gb|ABM20812.1| RNA polymerase, sigma 32 subunit, RpoH [Marinobacter aquaeolei VT8]
          Length = 286

 Score =  184 bits (468), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 104/268 (38%), Positives = 157/268 (58%), Gaps = 7/268 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI    +IP+L   EE  LA+R   HGD+ AA +LV SHLR V+ IA  Y GYGL  
Sbjct: 17  LESYIQAASRIPVLSVDEERELAERLHYHGDVEAARQLVLSHLRFVIHIARSYAGYGLAQ 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++L
Sbjct: 77  ADLIQEGNVGLMKAVKRFNPEYGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRKL 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR  K  L  +  + LK     A+A  L V    V  M  RLA  D + +  ++  +
Sbjct: 137 FFNLRSQKKKLAWLNHDELK-----AVANDLGVEPHVVREMEGRLASQDTAFDGPMDDDE 191

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
            N+ Q   + + D      V +E  +  ++    L +++  L+ R + I   R L E+  
Sbjct: 192 DNAYQAPAYYLEDRRSDPAVQLENADWSEDSNGRLMQALEQLDERSQDILRERWLSESKS 251

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TL  L+ ++ VS ER+RQ+E  A KK++
Sbjct: 252 TLHELADKYGVSAERIRQLEKNAMKKIR 279


>gi|251791618|ref|YP_003006339.1| RNA polymerase factor sigma-32 [Dickeya zeae Ech1591]
 gi|247540239|gb|ACT08860.1| RNA polymerase, sigma 32 subunit, RpoH [Dickeya zeae Ech1591]
          Length = 285

 Score =  184 bits (468), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 104/274 (37%), Positives = 157/274 (57%), Gaps = 9/274 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI      PML  +EE  LA+R   HGDL AA +L+ SHLR V+ +A  Y GYGLP 
Sbjct: 16  LEGYIRAANAYPMLTAEEERALAERLHYHGDLDAAKQLILSHLRFVIHVARNYSGYGLPQ 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AV++F+P+ G RL ++++ WIKA + EY+LR+W +VK+ TT  Q++L
Sbjct: 76  ADLIQEGNIGLMKAVRRFNPDVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR+ K  L          ++V  +A++L V+  +V  M  R+A  +         D 
Sbjct: 136 FFNLRKTKQRL-----GWFNQDEVEMVARELGVTSKDVREMESRMAAQDMTFDPSPEDDA 190

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNPRERRIFEARRL-QEN 251
              Q    ++Y  D         EE     +  + LT ++  L+ R + I  AR L  +N
Sbjct: 191 QPGQPMAPMLYLQDKSSDFADGIEEDNWETHAADKLTYALEGLDERSQHIIRARWLDDDN 250

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             TL+ L+  + VS ERVRQ+E  A KK++ +I+
Sbjct: 251 KSTLQELADHYGVSAERVRQLEKNAMKKLRAAIE 284


>gi|117926357|ref|YP_866974.1| RNA polymerase, sigma 32 subunit, RpoH [Magnetococcus sp. MC-1]
 gi|117610113|gb|ABK45568.1| RNA polymerase, sigma 32 subunit, RpoH [Magnetococcus sp. MC-1]
          Length = 297

 Score =  184 bits (468), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 114/291 (39%), Positives = 163/291 (56%), Gaps = 35/291 (12%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
            GE G  R++ +  + PML   EEY LA  YR H DL AAHRLV +HLRLV+KIA  Y  
Sbjct: 18  QGEEGFQRFLKQAAQAPMLSADEEYQLATNYRRHNDLEAAHRLVHAHLRLVLKIAREYLY 77

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
           Y   + ++V EG+IGLM AVKKFD +RG RLATY++WWI+AA+ ++IL +  +VK+ TT 
Sbjct: 78  YRSSLPDLVQEGSIGLMHAVKKFDAQRGNRLATYAVWWIRAAIHDFILNTAHMVKVATTK 137

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNAL 189
            ++ LFF LR+ K  L  +  N  + E+   +A K       ++ M+ RLAG D SLN  
Sbjct: 138 LKRHLFFKLRQAKSSLAPL--NQQEAEE---LAVKFATDAQTILEMDSRLAGADSSLNQP 192

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR-------------NMLTRSMSVLN 236
           +               +D  G+   L+E +ER N+               ++ + +  LN
Sbjct: 193 L---------------FDEGGELIELLE-DERPNQELQLQSAQQQQRLGRLVKQGLKQLN 236

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            RE+ I  +R + E+    E L+  F++S ERVRQIE RA  K++   Q Q
Sbjct: 237 EREQAIIISRFMGEHAEPREQLAQRFQISGERVRQIEQRAMAKLRSYFQSQ 287


>gi|53802588|ref|YP_112675.1| RNA polymerase factor sigma-32 [Methylococcus capsulatus str. Bath]
 gi|53756349|gb|AAU90640.1| RNA polymerase sigma-32 factor [Methylococcus capsulatus str. Bath]
          Length = 286

 Score =  184 bits (468), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 107/272 (39%), Positives = 168/272 (61%), Gaps = 8/272 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y   + ++P L+  EE  LA R+R+  DL AA RLV ++LR V  IA GY GYGLP+
Sbjct: 16  IDDYFAAVNRLPRLDADEERELAIRFRDEQDLEAARRLVLANLRFVAYIARGYLGYGLPL 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AVK++DP+ G RL ++++ WI+A + E+I+++W +VKI TT  Q++L
Sbjct: 76  ADLIQEGNIGLMKAVKRYDPDVGVRLVSFAVHWIRAEIHEFIIQNWRIVKIATTKAQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALI-NSS 193
           FFNLR++K  L  +T     PE+  A+A +L V   +V  M  RL   D +L A   +  
Sbjct: 136 FFNLRKMKNRLGWLT-----PEEAAAVAAELGVDVEDVYKMENRLNNPDMALEAHGEDDG 190

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN-MLTRSMSVLNPRERRIFEARRLQENP 252
           D   S      +    G   +LIE  E +NR+   L  ++  L+ R R I  +R L E+ 
Sbjct: 191 DDRESHAPIHYLQQEGGDPALLIEHSEWENRQQEKLQEAIGQLDERSRDIVASRWLSEDK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +TL +L++ + VS ER+RQ+E+ A KK++ ++
Sbjct: 251 LTLHDLAARYNVSAERIRQLESSAMKKLRNAL 282


>gi|300718824|ref|YP_003743627.1| RNA polymerase sigma-32 factor [Erwinia billingiae Eb661]
 gi|299064660|emb|CAX61780.1| RNA polymerase sigma-32 factor [Erwinia billingiae Eb661]
          Length = 284

 Score =  184 bits (468), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 108/287 (37%), Positives = 164/287 (57%), Gaps = 11/287 (3%)

Query: 4   KNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           K M  +    +G L  YI      PML  +EE  LA+R    GDL AA  L+ SHLR VV
Sbjct: 3   KEMQTLAIAPLGNLDSYIRAANVWPMLTAEEEKALAERLHYQGDLEAAKTLILSHLRFVV 62

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W 
Sbjct: 63  HVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWR 122

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L          E+V  +A++L V+  +V+ M  R+A 
Sbjct: 123 IVKVATTKAQRKLFFNLRKAKQRL-----GWFNQEEVEMVARELGVTSKDVLEMESRMAA 177

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNPRE 239
            + +       D+   +    ++Y  D         EE     +  + L+ +M  L+ R 
Sbjct: 178 -QDMTFDPTPDDEGEGRSMAPMLYLQDKSSDFADGIEEDNWESHAADKLSDAMQGLDERS 236

Query: 240 RRIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + I  AR L  +N  TL+ L+ ++ VS ERVRQ+E  A KK++ +I+
Sbjct: 237 QNIIRARWLDDDNKTTLQELADQYGVSAERVRQLEKNAMKKLRVAIE 283


>gi|163869170|ref|YP_001610422.1| RNA polymerase factor sigma-32 [Bartonella tribocorum CIP 105476]
 gi|161018869|emb|CAK02427.1| RNA polymerase sigma-32 factor [Bartonella tribocorum CIP 105476]
          Length = 303

 Score =  184 bits (467), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 101/263 (38%), Positives = 169/263 (64%), Gaps = 5/263 (1%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K P LE+Q+E+ LA R+++  D  A H++  +H+RLV+ IA  ++ + +P+ ++V EG +
Sbjct: 32  KAPYLERQKEHDLALRWKDKRDDDAMHQIAAAHMRLVIAIANRFKRFKMPLGDLVQEGYV 91

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A  +F+P+R  R +TY+ WWI+A++Q+YILR+WS+V+ GT+++QK LFFNLRRL+ 
Sbjct: 92  GLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSSQKALFFNLRRLRA 151

Query: 145 HLQAITDNNLKPEQVV--AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
            L  + D++   +Q +   IA+KL VS  +V +M+ R +  ++  ++  S + +S   + 
Sbjct: 152 KL--VQDDSALSKQDIFRTIAEKLGVSVRDVETMDFRFSSSDNSLSVSVSENSDSPVAKM 209

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
            ++ D       LIE+     RR   L  ++ +LN RE  I   RRL E   TLE L  +
Sbjct: 210 DVLVDESPLPDALIEQVIDGQRRTQWLYDALQILNERELEIIRFRRLNEEGATLEVLGEK 269

Query: 262 FEVSRERVRQIEARAFKKVQESI 284
             +S+ERVRQIEARA +K++ ++
Sbjct: 270 LGISKERVRQIEARALQKLRSAL 292


>gi|254482649|ref|ZP_05095887.1| alternative sigma factor RpoH [marine gamma proteobacterium
           HTCC2148]
 gi|214037008|gb|EEB77677.1| alternative sigma factor RpoH [marine gamma proteobacterium
           HTCC2148]
          Length = 284

 Score =  184 bits (467), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 106/272 (38%), Positives = 163/272 (59%), Gaps = 9/272 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+  +  IP+L  + E  LA+    + +L+AA  LV SHLR VV IA  Y GYGL  
Sbjct: 17  LAAYVQAVGSIPVLSPERERELAEDLFYNDNLTAARELVMSHLRFVVHIARSYSGYGLAE 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGN+GLM+A+K+FDPE+G RL ++++ WIKA M EYILR+W +VK+ TT  Q++L
Sbjct: 77  ADLIQEGNVGLMKAIKRFDPEKGVRLVSFAVHWIKAEMHEYILRNWRIVKVATTKAQRKL 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR  K  L  ++ +  K     A+A+ L V   EV  M  RL   + L   +++   
Sbjct: 137 FFNLRSKKKSLSWLSADEAK-----AVAEDLGVDVKEVHRMEGRLTSRD-LAYDMSTDSD 190

Query: 196 NSSQWQ--DWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
           +   WQ   + + DH     Q + E + ++N +  L  +++ L+ R R I   R L E+ 
Sbjct: 191 DDDAWQAPQYYLEDHSSDPAQTVEEGDWKQNSQAQLHSALADLDERSRNILAQRWLAEDK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL  L+ ++ VS ER+RQ+EA A KK++ +I
Sbjct: 251 STLHELADQYGVSAERIRQLEANAMKKLKVAI 282


>gi|260767580|ref|ZP_05876516.1| RNA polymerase sigma-32 factor [Vibrio furnissii CIP 102972]
 gi|260617480|gb|EEX42663.1| RNA polymerase sigma-32 factor [Vibrio furnissii CIP 102972]
 gi|315178774|gb|ADT85688.1| RNA polymerase sigma-32 factor [Vibrio furnissii NCTC 11218]
          Length = 258

 Score =  184 bits (467), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 100/244 (40%), Positives = 150/244 (61%), Gaps = 10/244 (4%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD+ AA  L+ SHLR VV +A GY GYGLP++++V EGNIGLM+AVK+F+PE G RL ++
Sbjct: 18  GDIEAAKGLILSHLRFVVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVRLVSF 77

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           ++ WIKA + EY+LR+W +VKI TT  Q++LFFNLR+ K  L    +      +V  +A+
Sbjct: 78  AVHWIKAEIHEYVLRNWRIVKIATTKAQRKLFFNLRKSKKRLGWFNNG-----EVETVAR 132

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN- 223
           +L V  SEV  M  RLA  ++   + N  D N + +   ++Y  D Q   L E  E +N 
Sbjct: 133 ELGVEPSEVREMESRLAAQDATFEMSNDDDDNPNAYTAPVLYLEDKQSD-LAENVEAQNW 191

Query: 224 ---RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                  L  ++S L+ R + I  +R L +   TL+ L+  + VS ER+RQ+E  A KK+
Sbjct: 192 EAHTNQRLALALSSLDERSQHIVRSRWLDDQKATLQELAEMYNVSAERIRQLEKNAMKKL 251

Query: 281 QESI 284
           ++++
Sbjct: 252 KDAV 255


>gi|146410|gb|AAA23991.1| heat shock regulatory protein [Escherichia coli]
          Length = 284

 Score =  184 bits (467), Expect = 1e-44,   Method: Compositional matrix adjust.
 Identities = 114/300 (38%), Positives = 167/300 (55%), Gaps = 32/300 (10%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  K  S+ +     L  YI      PML   EE  LA++   HGDL AA  L+ SHLR 
Sbjct: 1   MTDKMQSLALAPVGNLDSYIRAANAWPMLSADEERALAEKLHYHGDLEAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVEMVARELGVTSKDVREMESRM 175

Query: 181 AGDE--------------SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           A  +              ++  ++   DK SS + D  + D + +EQ            N
Sbjct: 176 AAQDMTFDLASDDDSDSHAMAPVLYLQDK-SSNFADG-IEDDNWEEQAA----------N 223

Query: 227 MLTRSMSVLNPRERRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            LT +M  L+ R + I  AR L E N  TL+ L+  + VS ERVRQ+E  A KK++ +I+
Sbjct: 224 RLTDAMQGLDERSQDIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIE 283


>gi|240140689|ref|YP_002965169.1| RNA polymerase sigma-32 (sigma H) factor [Methylobacterium
           extorquens AM1]
 gi|240010666|gb|ACS41892.1| RNA polymerase sigma-32 (sigma H) factor [Methylobacterium
           extorquens AM1]
          Length = 262

 Score =  184 bits (466), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 104/252 (41%), Positives = 166/252 (65%), Gaps = 1/252 (0%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           +A  ++E  D  A HRL+++H+RLV+ +A  +R YGLP++++V EG++GLM+A  +F+PE
Sbjct: 1   MAVAWKEARDERALHRLISAHMRLVIALAGRFRHYGLPMADLVQEGHVGLMEAAARFEPE 60

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           R  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFFNLRRL+  L   T+  +  
Sbjct: 61  REVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRARLMQSTEEQVGS 120

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
           E    IA  + VS  +V  M+ RL+G D SLNA +    + SS+  D+LV +    ++ +
Sbjct: 121 EIHGRIATAIGVSREDVALMDARLSGPDMSLNAPVGEESEASSERMDFLVDNAALPDETV 180

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
               + + R   L ++++VL+ RE RI   RRL E+  TLE L     +S+ERVRQIE R
Sbjct: 181 SALVDGERRLIWLRQALTVLSERELRILRERRLAEDQATLEALGHRLGISKERVRQIENR 240

Query: 276 AFKKVQESIQKQ 287
           A +K++ ++ ++
Sbjct: 241 ALEKLRRALAEK 252


>gi|329295846|ref|ZP_08253182.1| RNA polymerase factor sigma-32 [Plautia stali symbiont]
          Length = 285

 Score =  184 bits (466), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 107/286 (37%), Positives = 164/286 (57%), Gaps = 11/286 (3%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           +N++I   G   L  Y+      P+L  +EE  LA+R    GDL AA  L+ SHLR VV 
Sbjct: 6   QNLAIAPLG--NLESYVRAANNWPVLTAEEEKALAERLHYQGDLDAAKTLILSHLRFVVH 63

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W +
Sbjct: 64  IARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRI 123

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VK  TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V+ M  R+A  
Sbjct: 124 VKAATTKAQRKLFFNLRKTKQRL-----GWFNQDEVEMVARELGVSSKDVLEMESRMAAQ 178

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK---NRRNMLTRSMSVLNPRER 240
           +    + +  D    +    ++Y  D         EE     +  + L+ +M  L+ R +
Sbjct: 179 DMTFDMSSDDDAGEGKPMAPVLYLQDKTSDFADGIEEDNWDAHAADKLSDAMLSLDERSQ 238

Query: 241 RIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            I  AR L  +N  TL+ L+ ++ VS ERVRQ+E  A KK++ +I+
Sbjct: 239 HIIRARWLDDDNKTTLQELADQYGVSAERVRQLEKNAMKKLRMAIE 284


>gi|271502546|ref|YP_003335572.1| RNA polymerase sigma-32 subunit RpoH [Dickeya dadantii Ech586]
 gi|270346101|gb|ACZ78866.1| RNA polymerase, sigma 32 subunit, RpoH [Dickeya dadantii Ech586]
          Length = 285

 Score =  184 bits (466), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 104/274 (37%), Positives = 156/274 (56%), Gaps = 9/274 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI      PML   EE  LA+R   HGDL AA +L+ SHLR V+ +A  Y GYGLP 
Sbjct: 16  LEGYIRAANAYPMLTADEERALAERLHYHGDLDAAKQLILSHLRFVIHVARNYSGYGLPQ 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AV++F+P+ G RL ++++ WIKA + EY+LR+W +VK+ TT  Q++L
Sbjct: 76  ADLIQEGNIGLMKAVRRFNPDVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR+ K  L          ++V  +A++L V+  +V  M  R+A  +         D 
Sbjct: 136 FFNLRKTKQRL-----GWFNQDEVELVARELGVTSKDVREMESRMAAQDMTFDPSPEDDA 190

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNPRERRIFEARRL-QEN 251
              Q    ++Y  D         EE     +  + LT ++  L+ R + I  AR L  +N
Sbjct: 191 QPGQPMAPMLYLQDKSSDFADGIEEDNWETHAADKLTYALEGLDERSQHIIRARWLDDDN 250

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             TL+ L+  + VS ERVRQ+E  A KK++ +I+
Sbjct: 251 KSTLQELADHYGVSAERVRQLEKNAMKKLRAAIE 284


>gi|145300817|ref|YP_001143658.1| RNA polymerase sigma-32 factor [Aeromonas salmonicida subsp.
           salmonicida A449]
 gi|142853589|gb|ABO91910.1| RNA polymerase sigma-32 factor [Aeromonas salmonicida subsp.
           salmonicida A449]
          Length = 284

 Score =  184 bits (466), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 111/288 (38%), Positives = 176/288 (61%), Gaps = 15/288 (5%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           ++ M++I  G   L  YI  +  IP+L  +EE  LA+R ++ GDL AA +LV SHLR VV
Sbjct: 6   QRTMALIPQGS--LEGYIQAVNSIPVLTAEEERELAERLQQGGDLEAARQLVMSHLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y GYGLP +++V EGNIGLM+AVK+FDP  G RL ++++ WIKA + EY+LR+W 
Sbjct: 64  HVAKSYAGYGLPQADLVQEGNIGLMKAVKRFDPTVGVRLVSFAVHWIKAEIHEYVLRNWR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L   + +     +V A+A +L VS ++V  M  R++ 
Sbjct: 124 MVKVATTKAQRKLFFNLRKSKKRLGWFSHD-----EVQAVAAELGVSPTDVTEMEARMSN 178

Query: 183 -DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK---EERKNRRNMLTRSMSVLNPR 238
            D++ + + +  D+       +L  D        IE    ++   RR  L+ +++ L+ R
Sbjct: 179 YDQAFDLVGDDEDEGGFAPVHYL-EDKSSDLAATIENDNWDDHATRR--LSSALATLDER 235

Query: 239 ERRIFEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            + I  AR L ++   TL+ L+  + VS ERVRQ+E  A KK++++++
Sbjct: 236 SQHIIRARWLDDDSKTTLQELADTYGVSAERVRQLEKNALKKLKDAME 283


>gi|290473624|ref|YP_003466496.1| sigma H (sigma 32) factor of RNA polymerase; transcription of heat
           shock and stress proteins [Xenorhabdus bovienii SS-2004]
 gi|289172929|emb|CBJ79700.1| sigma H (sigma 32) factor of RNA polymerase; transcription of heat
           shock and stress proteins [Xenorhabdus bovienii SS-2004]
          Length = 285

 Score =  184 bits (466), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 106/289 (36%), Positives = 172/289 (59%), Gaps = 9/289 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  Y+      PML  +EE  LA+R    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLALVPQGSLEGYVRASNAYPMLSAEEEKELAERLHYQGDLDAAKKLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARSYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +AK+L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKAKQRL-----GWFNQDEVDLVAKELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL--IEKEERKNR-RNMLTRSMSVLNP 237
           +  +    + ++ D + SQ    ++Y  D        IE++  +N   + L+ ++  L+ 
Sbjct: 176 SAQDMAFDMSSNDDSHDSQPVAPVLYLQDKASDFADGIEEDNWENHAADKLSMAIEGLDE 235

Query: 238 RERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           R + I  AR L  +N  TL+ L+ ++ VS ERVRQ+E  A KK++ +I+
Sbjct: 236 RSQDIIRARWLDDDNKSTLQELADKYGVSAERVRQLEKNAMKKLRLAIE 284


>gi|262195735|ref|YP_003266944.1| RNA polymerase, sigma 70 family subunit [Haliangium ochraceum DSM
           14365]
 gi|262079082|gb|ACY15051.1| putative RNA polymerase, sigma 70 family subunit [Haliangium
           ochraceum DSM 14365]
          Length = 389

 Score =  183 bits (465), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 105/276 (38%), Positives = 173/276 (62%), Gaps = 7/276 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           LS YI E ++ P+L ++EE+ LA +  E+ D  AA RL+ ++LRLVVKI+  YR     +
Sbjct: 106 LSAYIQETKRYPLLSREEEHDLAVKLVENEDADAARRLIEANLRLVVKISYEYRRAYRNL 165

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLMQAV+K+DP RG +L++Y+ WWI+A + ++IL +W LVKIGTT  Q++L
Sbjct: 166 LDLIQEGNIGLMQAVRKYDPYRGVKLSSYAAWWIRAYILKFILNNWRLVKIGTTQAQRKL 225

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSSD 194
           FFNLR+ +  L+ +      P   + +A+ L+V+E EV+ M  RL A D SL+A +   +
Sbjct: 226 FFNLRKERERLEQL---GFTPTPAL-LAENLDVTEKEVVEMEKRLSAPDASLDAPMQGEE 281

Query: 195 KNSSQWQ-DWL-VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
             + + + D+L   + D  ++ + + + ++  R  L R    L  RE  IF  R L + P
Sbjct: 282 DGAPRTRMDYLPTEETDRPDRQVAQSQFQELLREKLERFAETLEGREETIFRERWLTDTP 341

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            TL+ +  ++ VSRER RQ+E R   ++++ ++ ++
Sbjct: 342 STLQQIGDQYGVSRERARQLEKRLLGRLRKYLEAEL 377


>gi|253686510|ref|YP_003015700.1| RNA polymerase, sigma 32 subunit, RpoH [Pectobacterium carotovorum
           subsp. carotovorum PC1]
 gi|251753088|gb|ACT11164.1| RNA polymerase, sigma 32 subunit, RpoH [Pectobacterium carotovorum
           subsp. carotovorum PC1]
          Length = 285

 Score =  183 bits (465), Expect = 2e-44,   Method: Compositional matrix adjust.
 Identities = 103/274 (37%), Positives = 157/274 (57%), Gaps = 9/274 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI      PML  +EE  LA+R    GDL AA  L+ SHLR V+ +A  Y GYGLP 
Sbjct: 16  LEGYIRAANAYPMLTAEEERALAERLHYQGDLDAAKHLILSHLRFVIHVARNYSGYGLPQ 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W +VK+ TT  Q++L
Sbjct: 76  ADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR+ K  L          ++V  +A++L V+  +V  M  R+A  +         D 
Sbjct: 136 FFNLRKTKTRL-----GWFNQDEVELVARELGVTSKDVREMESRMAAQDMTFDPTPEEDS 190

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNPRERRIFEARRL-QEN 251
           +  +    ++Y  D         EE     +  + LT ++  L+ R + I  AR L  +N
Sbjct: 191 HDGKAMSPMLYLQDKSSDFADGIEEDNWDTHAADKLTYALEGLDERSQHIIRARWLDDDN 250

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             TL+ L+ ++ VS ERVRQ+E  A KK++ +I+
Sbjct: 251 KSTLQELADQYGVSAERVRQLEKNAMKKLRAAIE 284


>gi|15803973|ref|NP_290009.1| RNA polymerase factor sigma-32 [Escherichia coli O157:H7 EDL933]
 gi|15833564|ref|NP_312337.1| RNA polymerase factor sigma-32 [Escherichia coli O157:H7 str.
           Sakai]
 gi|16131333|ref|NP_417918.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli str.
           K-12 substr. MG1655]
 gi|26250076|ref|NP_756116.1| RNA polymerase factor sigma-32 [Escherichia coli CFT073]
 gi|74314061|ref|YP_312480.1| RNA polymerase factor sigma-32 [Shigella sonnei Ss046]
 gi|82545824|ref|YP_409771.1| RNA polymerase factor sigma-32 [Shigella boydii Sb227]
 gi|82778725|ref|YP_405074.1| RNA polymerase factor sigma-32 [Shigella dysenteriae Sd197]
 gi|89110551|ref|AP_004331.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli str.
           K-12 substr. W3110]
 gi|91212950|ref|YP_542936.1| RNA polymerase factor sigma-32 [Escherichia coli UTI89]
 gi|110643701|ref|YP_671431.1| RNA polymerase factor sigma-32 [Escherichia coli 536]
 gi|117625739|ref|YP_859062.1| RNA polymerase factor sigma-32 [Escherichia coli APEC O1]
 gi|157158396|ref|YP_001464926.1| RNA polymerase factor sigma-32 [Escherichia coli E24377A]
 gi|157162938|ref|YP_001460256.1| RNA polymerase factor sigma-32 [Escherichia coli HS]
 gi|168747045|ref|ZP_02772067.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4113]
 gi|168753229|ref|ZP_02778236.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4401]
 gi|168759499|ref|ZP_02784506.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4501]
 gi|168765824|ref|ZP_02790831.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4486]
 gi|168772630|ref|ZP_02797637.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4196]
 gi|168779560|ref|ZP_02804567.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4076]
 gi|168785282|ref|ZP_02810289.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str. EC869]
 gi|168797247|ref|ZP_02822254.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str. EC508]
 gi|170018307|ref|YP_001723261.1| RNA polymerase factor sigma-32 [Escherichia coli ATCC 8739]
 gi|170082975|ref|YP_001732295.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli str.
           K-12 substr. DH10B]
 gi|170683649|ref|YP_001745710.1| RNA polymerase factor sigma-32 [Escherichia coli SMS-3-5]
 gi|170766775|ref|ZP_02901228.1| alternative sigma factor RpoH [Escherichia albertii TW07627]
 gi|187730400|ref|YP_001882152.1| RNA polymerase factor sigma-32 [Shigella boydii CDC 3083-94]
 gi|188495507|ref|ZP_03002777.1| alternative sigma factor RpoH [Escherichia coli 53638]
 gi|191169502|ref|ZP_03031234.1| alternative sigma factor RpoH [Escherichia coli B7A]
 gi|191170346|ref|ZP_03031899.1| alternative sigma factor RpoH [Escherichia coli F11]
 gi|193061907|ref|ZP_03043004.1| alternative sigma factor RpoH [Escherichia coli E22]
 gi|193068783|ref|ZP_03049743.1| alternative sigma factor RpoH [Escherichia coli E110019]
 gi|194427076|ref|ZP_03059628.1| alternative sigma factor RpoH [Escherichia coli B171]
 gi|194431093|ref|ZP_03063386.1| alternative sigma factor RpoH [Shigella dysenteriae 1012]
 gi|194435828|ref|ZP_03067931.1| alternative sigma factor RpoH [Escherichia coli 101-1]
 gi|195934955|ref|ZP_03080337.1| RNA polymerase factor sigma-32 [Escherichia coli O157:H7 str.
           EC4024]
 gi|208806017|ref|ZP_03248354.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4206]
 gi|208814463|ref|ZP_03255792.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4045]
 gi|208821158|ref|ZP_03261478.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4042]
 gi|209398124|ref|YP_002272905.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4115]
 gi|209920920|ref|YP_002295004.1| RNA polymerase factor sigma-32 [Escherichia coli SE11]
 gi|215488736|ref|YP_002331167.1| RNA polymerase factor sigma-32 [Escherichia coli O127:H6 str.
           E2348/69]
 gi|217325718|ref|ZP_03441802.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           TW14588]
 gi|218550723|ref|YP_002384514.1| RNA polymerase factor sigma-32 [Escherichia fergusonii ATCC 35469]
 gi|218556012|ref|YP_002388925.1| RNA polymerase factor sigma-32 [Escherichia coli IAI1]
 gi|218560529|ref|YP_002393442.1| RNA polymerase factor sigma-32 [Escherichia coli S88]
 gi|218691746|ref|YP_002399958.1| RNA polymerase factor sigma-32 [Escherichia coli ED1a]
 gi|218697144|ref|YP_002404811.1| RNA polymerase factor sigma-32 [Escherichia coli 55989]
 gi|218702206|ref|YP_002409835.1| RNA polymerase factor sigma-32 [Escherichia coli IAI39]
 gi|218707055|ref|YP_002414574.1| RNA polymerase factor sigma-32 [Escherichia coli UMN026]
 gi|227883607|ref|ZP_04001412.1| RNA polymerase factor sigma-32 [Escherichia coli 83972]
 gi|237703208|ref|ZP_04533689.1| alternative sigma factor RpoH [Escherichia sp. 3_2_53FAA]
 gi|238902552|ref|YP_002928348.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli BW2952]
 gi|253771710|ref|YP_003034541.1| RNA polymerase factor sigma-32 [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254038629|ref|ZP_04872685.1| alternative sigma factor RpoH [Escherichia sp. 1_1_43]
 gi|254163385|ref|YP_003046493.1| RNA polymerase factor sigma-32 [Escherichia coli B str. REL606]
 gi|254795381|ref|YP_003080218.1| RNA polymerase factor sigma-32 [Escherichia coli O157:H7 str.
           TW14359]
 gi|256020809|ref|ZP_05434674.1| RNA polymerase factor sigma-32 [Shigella sp. D9]
 gi|256025815|ref|ZP_05439680.1| RNA polymerase factor sigma-32 [Escherichia sp. 4_1_40B]
 gi|260846245|ref|YP_003224023.1| RNA polymerase, sigma 32 factor [Escherichia coli O103:H2 str.
           12009]
 gi|260857567|ref|YP_003231458.1| RNA polymerase, sigma 32 factor [Escherichia coli O26:H11 str.
           11368]
 gi|260870186|ref|YP_003236588.1| RNA polymerase, sigma 32 factor [Escherichia coli O111:H- str.
           11128]
 gi|261224744|ref|ZP_05939025.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli O157:H7
           str. FRIK2000]
 gi|261254361|ref|ZP_05946894.1| RNA polymerase, sigma 32 factor [Escherichia coli O157:H7 str.
           FRIK966]
 gi|291284801|ref|YP_003501619.1| RNA polymerase sigma factor [Escherichia coli O55:H7 str. CB9615]
 gi|293407042|ref|ZP_06650966.1| RNA polymerase factor sigma-32 [Escherichia coli FVEC1412]
 gi|293412884|ref|ZP_06655552.1| alternative sigma factor RpoH [Escherichia coli B354]
 gi|293416865|ref|ZP_06659502.1| alternative sigma factor RpoH [Escherichia coli B185]
 gi|293453766|ref|ZP_06664185.1| alternative sigma factor RpoH [Escherichia coli B088]
 gi|297517521|ref|ZP_06935907.1| RNA polymerase factor sigma-32 [Escherichia coli OP50]
 gi|298382788|ref|ZP_06992383.1| RNA polymerase sigma-32 factor [Escherichia coli FVEC1302]
 gi|300815334|ref|ZP_07095559.1| alternative sigma factor RpoH [Escherichia coli MS 107-1]
 gi|300822733|ref|ZP_07102870.1| alternative sigma factor RpoH [Escherichia coli MS 119-7]
 gi|300898837|ref|ZP_07117141.1| alternative sigma factor RpoH [Escherichia coli MS 198-1]
 gi|300907388|ref|ZP_07125036.1| alternative sigma factor RpoH [Escherichia coli MS 84-1]
 gi|300917205|ref|ZP_07133887.1| alternative sigma factor RpoH [Escherichia coli MS 115-1]
 gi|300930998|ref|ZP_07146356.1| alternative sigma factor RpoH [Escherichia coli MS 187-1]
 gi|300936478|ref|ZP_07151398.1| alternative sigma factor RpoH [Escherichia coli MS 21-1]
 gi|300946790|ref|ZP_07161034.1| alternative sigma factor RpoH [Escherichia coli MS 116-1]
 gi|300956796|ref|ZP_07169063.1| alternative sigma factor RpoH [Escherichia coli MS 175-1]
 gi|300985247|ref|ZP_07177344.1| alternative sigma factor RpoH [Escherichia coli MS 45-1]
 gi|300987360|ref|ZP_07178168.1| alternative sigma factor RpoH [Escherichia coli MS 200-1]
 gi|301018548|ref|ZP_07182926.1| alternative sigma factor RpoH [Escherichia coli MS 69-1]
 gi|301021811|ref|ZP_07185775.1| alternative sigma factor RpoH [Escherichia coli MS 196-1]
 gi|301050314|ref|ZP_07197203.1| alternative sigma factor RpoH [Escherichia coli MS 185-1]
 gi|301302348|ref|ZP_07208480.1| alternative sigma factor RpoH [Escherichia coli MS 124-1]
 gi|301645904|ref|ZP_07245818.1| alternative sigma factor RpoH [Escherichia coli MS 146-1]
 gi|306816195|ref|ZP_07450333.1| RNA polymerase factor sigma-32 [Escherichia coli NC101]
 gi|307140144|ref|ZP_07499500.1| RNA polymerase factor sigma-32 [Escherichia coli H736]
 gi|307311872|ref|ZP_07591510.1| RNA polymerase, sigma 32 subunit, RpoH [Escherichia coli W]
 gi|309794740|ref|ZP_07689162.1| alternative sigma factor RpoH [Escherichia coli MS 145-7]
 gi|312968227|ref|ZP_07782437.1| alternative sigma factor RpoH [Escherichia coli 2362-75]
 gi|331644161|ref|ZP_08345290.1| alternative sigma factor RpoH [Escherichia coli H736]
 gi|331649268|ref|ZP_08350354.1| alternative sigma factor RpoH [Escherichia coli M605]
 gi|331655044|ref|ZP_08356043.1| alternative sigma factor RpoH [Escherichia coli M718]
 gi|331659757|ref|ZP_08360695.1| alternative sigma factor RpoH [Escherichia coli TA206]
 gi|331665070|ref|ZP_08365971.1| alternative sigma factor RpoH [Escherichia coli TA143]
 gi|331670287|ref|ZP_08371126.1| alternative sigma factor RpoH [Escherichia coli TA271]
 gi|331674946|ref|ZP_08375703.1| alternative sigma factor RpoH [Escherichia coli TA280]
 gi|331679529|ref|ZP_08380199.1| alternative sigma factor RpoH [Escherichia coli H591]
 gi|331685107|ref|ZP_08385693.1| alternative sigma factor RpoH [Escherichia coli H299]
 gi|332282016|ref|ZP_08394429.1| RNA polymerase sigma 32 (sigma H) factor [Shigella sp. D9]
 gi|84028120|sp|P0AGB5|RP32_ECO57 RecName: Full=RNA polymerase sigma-32 factor; AltName: Full=Heat
           shock regulatory protein F33.4
 gi|84028121|sp|P0AGB4|RP32_ECOL6 RecName: Full=RNA polymerase sigma-32 factor; AltName: Full=Heat
           shock regulatory protein F33.4
 gi|84028122|sp|P0AGB3|RP32_ECOLI RecName: Full=RNA polymerase sigma-32 factor; AltName: Full=Heat
           shock regulatory protein F33.4
 gi|12518117|gb|AAG58570.1|AE005569_10 RNA polymerase, sigma(32) factor; regulation of proteins induced at
           high temperatures [Escherichia coli O157:H7 str. EDL933]
 gi|26110505|gb|AAN82690.1|AE016768_108 RNA polymerase sigma-32 factor [Escherichia coli CFT073]
 gi|147732|gb|AAA24587.1| RNA polymerase sigma-32 subunit [Escherichia coli]
 gi|466597|gb|AAB18436.1| RNA polymerase sigma-32 subunit [Escherichia coli str. K-12 substr.
           MG1655]
 gi|1789871|gb|AAC76486.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli str.
           K-12 substr. MG1655]
 gi|13363784|dbj|BAB37733.1| RNA polymerase sigma32 factor [Escherichia coli O157:H7 str. Sakai]
 gi|73671328|gb|AAZ80075.1| RpoH [Escherichia coli LW1655F+]
 gi|73857538|gb|AAZ90245.1| RNA polymerase, sigma(32) factor [Shigella sonnei Ss046]
 gi|81242873|gb|ABB63583.1| RNA polymerase, sigma(32) factor [Shigella dysenteriae Sd197]
 gi|81247235|gb|ABB67943.1| RNA polymerase sigma(32) factor [Shigella boydii Sb227]
 gi|85676582|dbj|BAE77832.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli str.
           K12 substr. W3110]
 gi|91074524|gb|ABE09405.1| component of RNA polymerase, sigma 32 factor [Escherichia coli
           UTI89]
 gi|110345293|gb|ABG71530.1| RNA polymerase sigma-32 factor [Escherichia coli 536]
 gi|115514863|gb|ABJ02938.1| RNA polymerase sigma factor [Escherichia coli APEC O1]
 gi|157068618|gb|ABV07873.1| alternative sigma factor RpoH [Escherichia coli HS]
 gi|157080426|gb|ABV20134.1| alternative sigma factor RpoH [Escherichia coli E24377A]
 gi|169753235|gb|ACA75934.1| RNA polymerase, sigma 32 subunit, RpoH [Escherichia coli ATCC 8739]
 gi|169890810|gb|ACB04517.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli str.
           K-12 substr. DH10B]
 gi|170124213|gb|EDS93144.1| alternative sigma factor RpoH [Escherichia albertii TW07627]
 gi|170521367|gb|ACB19545.1| alternative sigma factor RpoH [Escherichia coli SMS-3-5]
 gi|187427392|gb|ACD06666.1| alternative sigma factor RpoH [Shigella boydii CDC 3083-94]
 gi|187771635|gb|EDU35479.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4196]
 gi|188018405|gb|EDU56527.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4113]
 gi|188490706|gb|EDU65809.1| alternative sigma factor RpoH [Escherichia coli 53638]
 gi|189002511|gb|EDU71497.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4076]
 gi|189359084|gb|EDU77503.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4401]
 gi|189364663|gb|EDU83082.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4486]
 gi|189369524|gb|EDU87940.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4501]
 gi|189374649|gb|EDU93065.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str. EC869]
 gi|189380077|gb|EDU98493.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str. EC508]
 gi|190900463|gb|EDV60280.1| alternative sigma factor RpoH [Escherichia coli B7A]
 gi|190909154|gb|EDV68740.1| alternative sigma factor RpoH [Escherichia coli F11]
 gi|192932697|gb|EDV85294.1| alternative sigma factor RpoH [Escherichia coli E22]
 gi|192957859|gb|EDV88302.1| alternative sigma factor RpoH [Escherichia coli E110019]
 gi|194415037|gb|EDX31307.1| alternative sigma factor RpoH [Escherichia coli B171]
 gi|194420548|gb|EDX36624.1| alternative sigma factor RpoH [Shigella dysenteriae 1012]
 gi|194425371|gb|EDX41355.1| alternative sigma factor RpoH [Escherichia coli 101-1]
 gi|208725818|gb|EDZ75419.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4206]
 gi|208735740|gb|EDZ84427.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4045]
 gi|208741281|gb|EDZ88963.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4042]
 gi|209159524|gb|ACI36957.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4115]
 gi|209756038|gb|ACI76331.1| RNA polymerase sigma32 factor [Escherichia coli]
 gi|209756040|gb|ACI76332.1| RNA polymerase sigma32 factor [Escherichia coli]
 gi|209756042|gb|ACI76333.1| RNA polymerase sigma32 factor [Escherichia coli]
 gi|209756044|gb|ACI76334.1| RNA polymerase sigma32 factor [Escherichia coli]
 gi|209756046|gb|ACI76335.1| RNA polymerase sigma32 factor [Escherichia coli]
 gi|209914179|dbj|BAG79253.1| RNA polymerase sigma-32 factor [Escherichia coli SE11]
 gi|215266808|emb|CAS11249.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli O127:H6
           str. E2348/69]
 gi|217321939|gb|EEC30363.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           TW14588]
 gi|218353876|emb|CAV00268.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli 55989]
 gi|218358264|emb|CAQ90911.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia fergusonii
           ATCC 35469]
 gi|218362780|emb|CAR00406.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli IAI1]
 gi|218367298|emb|CAR05076.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli S88]
 gi|218372192|emb|CAR20054.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli IAI39]
 gi|218429310|emb|CAR10124.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli ED1a]
 gi|218434152|emb|CAR15069.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli UMN026]
 gi|222035167|emb|CAP77912.1| RNA polymerase sigma-32 factor [Escherichia coli LF82]
 gi|226839135|gb|EEH71158.1| alternative sigma factor RpoH [Escherichia sp. 1_1_43]
 gi|226902472|gb|EEH88731.1| alternative sigma factor RpoH [Escherichia sp. 3_2_53FAA]
 gi|227839486|gb|EEJ49952.1| RNA polymerase factor sigma-32 [Escherichia coli 83972]
 gi|238863499|gb|ACR65497.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli BW2952]
 gi|242378982|emb|CAQ33780.1| RNA polymerase, sigma 32 (sigma H) factor, subunit of RNA
           polymerase sigma 32 [Escherichia coli BL21(DE3)]
 gi|253322754|gb|ACT27356.1| RNA polymerase, sigma 32 subunit, RpoH [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|253975286|gb|ACT40957.1| RNA polymerase sigma factor [Escherichia coli B str. REL606]
 gi|253979442|gb|ACT45112.1| RNA polymerase sigma factor [Escherichia coli BL21(DE3)]
 gi|254594781|gb|ACT74142.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli O157:H7
           str. TW14359]
 gi|257756216|dbj|BAI27718.1| RNA polymerase, sigma 32 factor [Escherichia coli O26:H11 str.
           11368]
 gi|257761392|dbj|BAI32889.1| RNA polymerase, sigma 32 factor [Escherichia coli O103:H2 str.
           12009]
 gi|257766542|dbj|BAI38037.1| RNA polymerase, sigma 32 factor [Escherichia coli O111:H- str.
           11128]
 gi|260447523|gb|ACX37945.1| RNA polymerase, sigma 32 subunit, RpoH [Escherichia coli DH1]
 gi|281180490|dbj|BAI56820.1| RNA polymerase sigma-32 factor [Escherichia coli SE15]
 gi|284923451|emb|CBG36546.1| RNA polymerase sigma-32 factor [Escherichia coli 042]
 gi|290764674|gb|ADD58635.1| RNA polymerase sigma factor [Escherichia coli O55:H7 str. CB9615]
 gi|291321892|gb|EFE61323.1| alternative sigma factor RpoH [Escherichia coli B088]
 gi|291425853|gb|EFE98887.1| RNA polymerase factor sigma-32 [Escherichia coli FVEC1412]
 gi|291431441|gb|EFF04426.1| alternative sigma factor RpoH [Escherichia coli B185]
 gi|291468531|gb|EFF11024.1| alternative sigma factor RpoH [Escherichia coli B354]
 gi|294492777|gb|ADE91533.1| alternative sigma factor RpoH [Escherichia coli IHE3034]
 gi|298276624|gb|EFI18142.1| RNA polymerase sigma-32 factor [Escherichia coli FVEC1302]
 gi|299881444|gb|EFI89655.1| alternative sigma factor RpoH [Escherichia coli MS 196-1]
 gi|300297943|gb|EFJ54328.1| alternative sigma factor RpoH [Escherichia coli MS 185-1]
 gi|300306228|gb|EFJ60748.1| alternative sigma factor RpoH [Escherichia coli MS 200-1]
 gi|300316435|gb|EFJ66219.1| alternative sigma factor RpoH [Escherichia coli MS 175-1]
 gi|300357522|gb|EFJ73392.1| alternative sigma factor RpoH [Escherichia coli MS 198-1]
 gi|300399667|gb|EFJ83205.1| alternative sigma factor RpoH [Escherichia coli MS 69-1]
 gi|300400897|gb|EFJ84435.1| alternative sigma factor RpoH [Escherichia coli MS 84-1]
 gi|300408118|gb|EFJ91656.1| alternative sigma factor RpoH [Escherichia coli MS 45-1]
 gi|300415544|gb|EFJ98854.1| alternative sigma factor RpoH [Escherichia coli MS 115-1]
 gi|300453547|gb|EFK17167.1| alternative sigma factor RpoH [Escherichia coli MS 116-1]
 gi|300458400|gb|EFK21893.1| alternative sigma factor RpoH [Escherichia coli MS 21-1]
 gi|300461176|gb|EFK24669.1| alternative sigma factor RpoH [Escherichia coli MS 187-1]
 gi|300524733|gb|EFK45802.1| alternative sigma factor RpoH [Escherichia coli MS 119-7]
 gi|300532226|gb|EFK53288.1| alternative sigma factor RpoH [Escherichia coli MS 107-1]
 gi|300842511|gb|EFK70271.1| alternative sigma factor RpoH [Escherichia coli MS 124-1]
 gi|301075893|gb|EFK90699.1| alternative sigma factor RpoH [Escherichia coli MS 146-1]
 gi|305850591|gb|EFM51048.1| RNA polymerase factor sigma-32 [Escherichia coli NC101]
 gi|306908016|gb|EFN38516.1| RNA polymerase, sigma 32 subunit, RpoH [Escherichia coli W]
 gi|307555555|gb|ADN48330.1| component of RNA polymerase [Escherichia coli ABU 83972]
 gi|307628534|gb|ADN72838.1| RNA polymerase factor sigma-32 [Escherichia coli UM146]
 gi|308121790|gb|EFO59052.1| alternative sigma factor RpoH [Escherichia coli MS 145-7]
 gi|309703867|emb|CBJ03208.1| RNA polymerase sigma-32 factor [Escherichia coli ETEC H10407]
 gi|312287052|gb|EFR14962.1| alternative sigma factor RpoH [Escherichia coli 2362-75]
 gi|312948014|gb|ADR28841.1| RNA polymerase factor sigma-32 [Escherichia coli O83:H1 str. NRG
           857C]
 gi|315062740|gb|ADT77067.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli W]
 gi|315138035|dbj|BAJ45194.1| RNA polymerase sigma factor [Escherichia coli DH1]
 gi|315256058|gb|EFU36026.1| alternative sigma factor RpoH [Escherichia coli MS 85-1]
 gi|315286128|gb|EFU45566.1| alternative sigma factor RpoH [Escherichia coli MS 110-3]
 gi|315291684|gb|EFU51040.1| alternative sigma factor RpoH [Escherichia coli MS 153-1]
 gi|315295969|gb|EFU55278.1| alternative sigma factor RpoH [Escherichia coli MS 16-3]
 gi|320175708|gb|EFW50796.1| RNA polymerase sigma factor RpoH [Shigella dysenteriae CDC 74-1112]
 gi|320187771|gb|EFW62446.1| RNA polymerase sigma factor RpoH [Shigella flexneri CDC 796-83]
 gi|320191521|gb|EFW66171.1| RNA polymerase sigma factor RpoH [Escherichia coli O157:H7 str.
           EC1212]
 gi|320194037|gb|EFW68670.1| RNA polymerase sigma factor RpoH [Escherichia coli WV_060327]
 gi|320199638|gb|EFW74228.1| RNA polymerase sigma factor RpoH [Escherichia coli EC4100B]
 gi|320639745|gb|EFX09339.1| RNA polymerase factor sigma-32 [Escherichia coli O157:H7 str.
           G5101]
 gi|320645244|gb|EFX14260.1| RNA polymerase factor sigma-32 [Escherichia coli O157:H- str.
           493-89]
 gi|320650555|gb|EFX19021.1| RNA polymerase factor sigma-32 [Escherichia coli O157:H- str. H
           2687]
 gi|320655748|gb|EFX23671.1| RNA polymerase factor sigma-32 [Escherichia coli O55:H7 str.
           3256-97 TW 07815]
 gi|320661531|gb|EFX28946.1| RNA polymerase factor sigma-32 [Escherichia coli O55:H7 str. USDA
           5905]
 gi|320666554|gb|EFX33537.1| RNA polymerase factor sigma-32 [Escherichia coli O157:H7 str.
           LSU-61]
 gi|323154300|gb|EFZ40503.1| alternative sigma factor RpoH [Escherichia coli EPECa14]
 gi|323174100|gb|EFZ59728.1| alternative sigma factor RpoH [Escherichia coli LT-68]
 gi|323376672|gb|ADX48940.1| RNA polymerase, sigma 32 subunit, RpoH [Escherichia coli KO11]
 gi|323934553|gb|EGB30953.1| sigma protein RpoH [Escherichia coli E1520]
 gi|323939321|gb|EGB35532.1| sigma proteinRpoH [Escherichia coli E482]
 gi|323944315|gb|EGB40390.1| sigma protein RpoH [Escherichia coli H120]
 gi|323950129|gb|EGB46012.1| sigma proteinRpoH [Escherichia coli H252]
 gi|323954785|gb|EGB50566.1| sigma proteinRpoH [Escherichia coli H263]
 gi|323959687|gb|EGB55338.1| sigma proteinRpoH [Escherichia coli H489]
 gi|323966125|gb|EGB61562.1| sigma proteinRpoH [Escherichia coli M863]
 gi|323970059|gb|EGB65334.1| sigma proteinRpoH [Escherichia coli TA007]
 gi|323974898|gb|EGB70009.1| sigma proteinRpoH [Escherichia coli TW10509]
 gi|324009349|gb|EGB78568.1| alternative sigma factor RpoH [Escherichia coli MS 57-2]
 gi|324014559|gb|EGB83778.1| alternative sigma factor RpoH [Escherichia coli MS 60-1]
 gi|324018638|gb|EGB87857.1| alternative sigma factor RpoH [Escherichia coli MS 117-3]
 gi|324111782|gb|EGC05762.1| sigma proteinRpoH [Escherichia fergusonii B253]
 gi|324116341|gb|EGC10260.1| sigma proteinRpoH [Escherichia coli E1167]
 gi|325499010|gb|EGC96869.1| RNA polymerase factor sigma-32 [Escherichia fergusonii ECD227]
 gi|326337569|gb|EGD61404.1| RNA polymerase sigma factor RpoH [Escherichia coli O157:H7 str.
           1044]
 gi|326344680|gb|EGD68429.1| RNA polymerase sigma factor RpoH [Escherichia coli O157:H7 str.
           1125]
 gi|330909502|gb|EGH38016.1| RNA polymerase sigma factor RpoH [Escherichia coli AA86]
 gi|331036455|gb|EGI08681.1| alternative sigma factor RpoH [Escherichia coli H736]
 gi|331041766|gb|EGI13910.1| alternative sigma factor RpoH [Escherichia coli M605]
 gi|331047059|gb|EGI19137.1| alternative sigma factor RpoH [Escherichia coli M718]
 gi|331052972|gb|EGI25005.1| alternative sigma factor RpoH [Escherichia coli TA206]
 gi|331057580|gb|EGI29566.1| alternative sigma factor RpoH [Escherichia coli TA143]
 gi|331062349|gb|EGI34269.1| alternative sigma factor RpoH [Escherichia coli TA271]
 gi|331067855|gb|EGI39253.1| alternative sigma factor RpoH [Escherichia coli TA280]
 gi|331072701|gb|EGI44026.1| alternative sigma factor RpoH [Escherichia coli H591]
 gi|331077478|gb|EGI48690.1| alternative sigma factor RpoH [Escherichia coli H299]
 gi|332085344|gb|EGI90516.1| alternative sigma factor RpoH [Shigella boydii 5216-82]
 gi|332085690|gb|EGI90854.1| alternative sigma factor RpoH [Shigella dysenteriae 155-74]
 gi|332090225|gb|EGI95323.1| alternative sigma factor RpoH [Shigella boydii 3594-74]
 gi|332104368|gb|EGJ07714.1| RNA polymerase sigma 32 (sigma H) factor [Shigella sp. D9]
 gi|332345416|gb|AEE58750.1| alternative sigma factor RpoH [Escherichia coli UMNK88]
          Length = 284

 Score =  183 bits (464), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 114/300 (38%), Positives = 166/300 (55%), Gaps = 32/300 (10%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  K  S+ +     L  YI      PML   EE  LA++   HGDL AA  L+ SHLR 
Sbjct: 1   MTDKMQSLALAPVGNLDSYIRAANAWPMLSADEERALAEKLHYHGDLEAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVEMVARELGVTSKDVREMESRM 175

Query: 181 AGDE--------------SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           A  +               +  ++   DK SS + D  + D + +EQ            N
Sbjct: 176 AAQDMTFDLSSDDDSDSQPMAPVLYLQDK-SSNFADG-IEDDNWEEQAA----------N 223

Query: 227 MLTRSMSVLNPRERRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            LT +M  L+ R + I  AR L E N  TL+ L+  + VS ERVRQ+E  A KK++ +I+
Sbjct: 224 RLTDAMQGLDERSQDIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIE 283


>gi|301059188|ref|ZP_07200126.1| putative alternative sigma factor RpoH [delta proteobacterium
           NaphS2]
 gi|300446678|gb|EFK10505.1| putative alternative sigma factor RpoH [delta proteobacterium
           NaphS2]
          Length = 329

 Score =  183 bits (464), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 110/279 (39%), Positives = 177/279 (63%), Gaps = 16/279 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP- 74
           L  Y+ EI++  +L ++EE  LA R +E+ D  AA RLVTS+LRLVVKIAM +  Y    
Sbjct: 49  LQIYLLEIKQYHLLTREEEIELATRIQENNDDDAAFRLVTSNLRLVVKIAMDFHRYWTKN 108

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++ EGN+GL+QAV+KFDP RG + + Y+ +WIKA + ++I+ +W +VKIGTT +Q++
Sbjct: 109 LLDLIQEGNLGLLQAVRKFDPYRGIKFSYYASFWIKAYILKFIMDNWKMVKIGTTQSQRK 168

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSS 193
           LFFNL + +  L A       PE  + +A+KL+V ESEV+ M  RL G E SL+A +   
Sbjct: 169 LFFNLAKERDKLIA---QGFTPEPRL-LAEKLDVKESEVVEMTQRLGGWEISLSAPVGED 224

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM----SVLNPRERRIFEARRLQ 249
            + S       + D       L+  +E K   N+LT+S+      L+ +E  IF+ R L 
Sbjct: 225 SRES---YGSFLPDPAMAADDLLSNDESK---NVLTKSLQEFRKTLSGKEADIFDNRILA 278

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           E P+TL++L  ++++SRER+RQI+ +  K +++ +++++
Sbjct: 279 EKPLTLQDLGDKYKISRERIRQIQEKIIKNIRKWLKEKI 317


>gi|300926841|ref|ZP_07142609.1| alternative sigma factor RpoH [Escherichia coli MS 182-1]
 gi|301329786|ref|ZP_07222521.1| alternative sigma factor RpoH [Escherichia coli MS 78-1]
 gi|300417191|gb|EFK00502.1| alternative sigma factor RpoH [Escherichia coli MS 182-1]
 gi|300844135|gb|EFK71895.1| alternative sigma factor RpoH [Escherichia coli MS 78-1]
          Length = 284

 Score =  183 bits (464), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 114/300 (38%), Positives = 166/300 (55%), Gaps = 32/300 (10%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  K  S+ +     L  YI      PML   EE  LA++   HGDL AA  L+ SHLR 
Sbjct: 1   MTDKMQSLALAPVGNLDSYIRAANAWPMLSADEERALAEKLHYHGDLEAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVEMVARELGVTSKDVREMESRM 175

Query: 181 AGDE--------------SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           A  +               +  ++   DK SS + D  + D + +EQ            N
Sbjct: 176 AAQDMTFDQSSDDDSDSQPMAPVLYLQDK-SSNFADG-IEDDNWEEQAA----------N 223

Query: 227 MLTRSMSVLNPRERRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            LT +M  L+ R + I  AR L E N  TL+ L+  + VS ERVRQ+E  A KK++ +I+
Sbjct: 224 RLTDAMQGLDERSQDIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIE 283


>gi|94676476|ref|YP_588537.1| alternative sigma factor RpoH [Baumannia cicadellinicola str. Hc
           (Homalodisca coagulata)]
 gi|94219626|gb|ABF13785.1| alternative sigma factor RpoH [Baumannia cicadellinicola str. Hc
           (Homalodisca coagulata)]
          Length = 286

 Score =  183 bits (464), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 103/283 (36%), Positives = 163/283 (57%), Gaps = 8/283 (2%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           +I++ +  L  Y+      PML  +EE  LA++    GD+ AA  L+ SHLR V+ IA  
Sbjct: 9   VIIDKKGSLEDYVKAANAYPMLTAEEELKLAEKLHYQGDIEAAKLLILSHLRFVINIART 68

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y GY LP ++++ EGNIGLM+AV+KF+PE G RL ++++ WIKA + EY+LR+W +VK+ 
Sbjct: 69  YSGYNLPQADLIQEGNIGLMKAVRKFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVA 128

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
           TT  Q+RLFFNLR++K  L          E+V  +AK+L V+  +V  M  R+A  +   
Sbjct: 129 TTKAQRRLFFNLRKIKQRL-----GWFNQEEVEMVAKELGVTSKDVREMESRMAAQDIAF 183

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK---NRRNMLTRSMSVLNPRERRIFE 244
             I + +         ++Y  D         EE+    +  + L  ++  L+ R + I  
Sbjct: 184 DPIPNDEVPDKLLMAPILYLQDKGSDFADRIEEQNWEYHAADKLNIALDKLDERSKNIIA 243

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           AR L     TL++L++++ VS ER+RQ+E  A KK++ +I+ Q
Sbjct: 244 ARWLDNKKSTLQDLANKYGVSAERIRQLEKNAMKKIRMAIEAQ 286


>gi|24114721|ref|NP_709231.1| RNA polymerase factor sigma-32 [Shigella flexneri 2a str. 301]
 gi|30065262|ref|NP_839433.1| RNA polymerase factor sigma-32 [Shigella flexneri 2a str. 2457T]
 gi|110807289|ref|YP_690809.1| RNA polymerase factor sigma-32 [Shigella flexneri 5 str. 8401]
 gi|24053937|gb|AAN44938.1| sigma(32) factor of RNA polymerase [Shigella flexneri 2a str. 301]
 gi|30043524|gb|AAP19244.1| sigma(32) factor of RNA polymerase [Shigella flexneri 2a str.
           2457T]
 gi|110616837|gb|ABF05504.1| RNA polymerase sigma factor [Shigella flexneri 5 str. 8401]
 gi|281602809|gb|ADA75793.1| Sigma(32) factor of RNA polymerase [Shigella flexneri 2002017]
 gi|313647240|gb|EFS11692.1| alternative sigma factor RpoH [Shigella flexneri 2a str. 2457T]
 gi|332749439|gb|EGJ79856.1| alternative sigma factor RpoH [Shigella flexneri K-671]
 gi|332750286|gb|EGJ80697.1| alternative sigma factor RpoH [Shigella flexneri 4343-70]
 gi|332751371|gb|EGJ81774.1| alternative sigma factor RpoH [Shigella flexneri 2747-71]
 gi|332996248|gb|EGK15875.1| alternative sigma factor RpoH [Shigella flexneri VA-6]
 gi|332996590|gb|EGK16215.1| alternative sigma factor RpoH [Shigella flexneri K-272]
 gi|332997356|gb|EGK16972.1| alternative sigma factor RpoH [Shigella flexneri K-218]
 gi|333012512|gb|EGK31893.1| alternative sigma factor RpoH [Shigella flexneri K-304]
 gi|333012998|gb|EGK32374.1| alternative sigma factor RpoH [Shigella flexneri K-227]
          Length = 284

 Score =  183 bits (464), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 114/300 (38%), Positives = 166/300 (55%), Gaps = 32/300 (10%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  K  S+ +     L  YI      PML   EE  LA++   HGDL AA  L+ SHLR 
Sbjct: 1   MTDKMQSLALAPVGNLDSYIRAANAWPMLSADEERALAEKLHYHGDLEAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVEMVARELGVTSKDVREMESRM 175

Query: 181 AGDE--------------SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           A  +               +  ++   DK SS + D  + D + +EQ            N
Sbjct: 176 AAQDMTFDLSSDDDSDSQPMAPVLYLQDK-SSNFADG-IEDDNWEEQAA----------N 223

Query: 227 MLTRSMSVLNPRERRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            LT +M  L+ R + I  AR L E N  TL+ L+  + VS ERVRQ+E  A KK++ +I+
Sbjct: 224 RLTDAMHGLDERSQDIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIE 283


>gi|261819465|ref|YP_003257571.1| RNA polymerase factor sigma-32 [Pectobacterium wasabiae WPP163]
 gi|261603478|gb|ACX85964.1| RNA polymerase, sigma 32 subunit, RpoH [Pectobacterium wasabiae
           WPP163]
          Length = 285

 Score =  183 bits (464), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 103/274 (37%), Positives = 157/274 (57%), Gaps = 9/274 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI      PML  +EE  LA+R    GDL AA  L+ SHLR V+ +A  Y GYGLP 
Sbjct: 16  LEGYIRAANAYPMLTAEEERALAERLHYQGDLEAAKHLILSHLRFVIHVARNYSGYGLPQ 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W +VK+ TT  Q++L
Sbjct: 76  ADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR+ K  L          ++V  +A++L V+  +V  M  R+A  +         D 
Sbjct: 136 FFNLRKTKTRL-----GWFNQDEVELVARELGVTSKDVREMESRMAAQDMTFDPTPEEDS 190

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNPRERRIFEARRL-QEN 251
           +  +    ++Y  D         EE     +  + LT ++  L+ R + I  AR L  +N
Sbjct: 191 HDGKAMSPMLYLQDKSSDFAGGIEEDNWDTHAADKLTYALEGLDERSQHIIRARWLDDDN 250

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             TL+ L+ ++ VS ERVRQ+E  A KK++ +I+
Sbjct: 251 KSTLQELADQYGVSAERVRQLEKNAMKKLRAAIE 284


>gi|50123263|ref|YP_052430.1| RNA polymerase factor sigma-32 [Pectobacterium atrosepticum
           SCRI1043]
 gi|49613789|emb|CAG77240.1| RNA polymerase sigma-32 factor [Pectobacterium atrosepticum
           SCRI1043]
          Length = 285

 Score =  183 bits (464), Expect = 3e-44,   Method: Compositional matrix adjust.
 Identities = 103/274 (37%), Positives = 157/274 (57%), Gaps = 9/274 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI      PML  +EE  LA+R    GDL AA  L+ SHLR V+ +A  Y GYGLP 
Sbjct: 16  LEGYIRAANAYPMLTAEEERALAERLHYQGDLEAAKHLILSHLRFVIHVARNYSGYGLPQ 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W +VK+ TT  Q++L
Sbjct: 76  ADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR+ K  L          ++V  +A++L V+  +V  M  R+A  +         D 
Sbjct: 136 FFNLRKAKTRL-----GWFNQDEVELVARELGVTTKDVREMESRMAAQDMTFDPTPEEDS 190

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNPRERRIFEARRL-QEN 251
           +  +    ++Y  D         EE     +  + LT ++  L+ R + I  AR L  +N
Sbjct: 191 HDGKAMSPMLYLQDKSSDFADGIEEDNWDTHAADKLTYALEGLDERSQHIIRARWLDDDN 250

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             TL+ L+ ++ VS ERVRQ+E  A KK++ +I+
Sbjct: 251 KSTLQELADQYGVSAERVRQLEKNAMKKLRAAIE 284


>gi|108760621|ref|YP_631554.1| RNA polymerase sigma-B factor [Myxococcus xanthus DK 1622]
 gi|108464501|gb|ABF89686.1| RNA polymerase sigma-B factor [Myxococcus xanthus DK 1622]
          Length = 246

 Score =  182 bits (463), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 100/233 (42%), Positives = 147/233 (63%), Gaps = 4/233 (1%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           +VT++LR VVK+A  YR YG+ +S+++ EGNIGLM+AV+KFDP++G RL +Y++WWI+A 
Sbjct: 1   MVTANLRFVVKVAYEYRSYGIKMSDLIQEGNIGLMKAVQKFDPDKGIRLISYAVWWIRAY 60

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +Q YIL+SWSLVK+GTT  Q++LFF+L R +  L+     +     V  IA++L+V   E
Sbjct: 61  IQNYILKSWSLVKLGTTQAQRKLFFSLARTRRELEKFGSGD-AAVNVDDIARRLHVKPGE 119

Query: 173 VISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           V  M  R+ G D SL+A +     NS    D++V     Q+    +KEE       +  +
Sbjct: 120 VREMEQRMGGRDLSLDAPMGEDGGNSH--VDFVVSAAAPQDDEFADKEEAGLINARVRTA 177

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +  L+PRER I E R + E P+TL+ L   F  SRER RQ+E RA  K++  +
Sbjct: 178 LMRLDPRERFIIEQRVMNERPMTLKELGEHFGFSRERARQLEIRAKDKLKSEL 230


>gi|292489953|ref|YP_003532845.1| RNA polymerase sigma-32 factor [Erwinia amylovora CFBP1430]
 gi|292900984|ref|YP_003540353.1| RNA polymerase sigma-32 factor [Erwinia amylovora ATCC 49946]
 gi|291200832|emb|CBJ47966.1| RNA polymerase sigma-32 factor [Erwinia amylovora ATCC 49946]
 gi|291555392|emb|CBA23800.1| RNA polymerase sigma-32 factor [Erwinia amylovora CFBP1430]
 gi|312174141|emb|CBX82394.1| RNA polymerase sigma-32 factor [Erwinia amylovora ATCC BAA-2158]
          Length = 284

 Score =  182 bits (463), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 108/286 (37%), Positives = 165/286 (57%), Gaps = 9/286 (3%)

Query: 4   KNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           K M  +    +G L  YI      PML  +EE  LA+R    GDL AA  L+ SHLR VV
Sbjct: 3   KEMQTLAIAPLGNLDSYIRAANAWPMLTAEEEKALAERLHYQGDLEAAKTLILSHLRFVV 62

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W 
Sbjct: 63  HVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWR 122

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+A 
Sbjct: 123 IVKVATTKAQRKLFFNLRKAKQRL-----GWFNQDEVEMVARELGVSSKDVREMESRMAA 177

Query: 183 -DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPRER 240
            D + +   +   +  S      + D        IE++  ++   + L+ +M  L+ R +
Sbjct: 178 QDMTFDPTPDDEGEGRSMAPMLYLQDKSSDFANGIEEDNWEDHAADKLSDAMQGLDERSQ 237

Query: 241 RIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            I  AR L  +N  TL+ L+ ++ VS ERVRQ+E  A KK++ +I+
Sbjct: 238 HIIRARWLDDDNKTTLQELADQYGVSAERVRQLEKNAMKKLRVAIE 283


>gi|149916583|ref|ZP_01905097.1| RNA polymerase sigma factor [Roseobacter sp. AzwK-3b]
 gi|149809510|gb|EDM69370.1| RNA polymerase sigma factor [Roseobacter sp. AzwK-3b]
          Length = 189

 Score =  182 bits (463), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 95/189 (50%), Positives = 134/189 (70%), Gaps = 4/189 (2%)

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           +A++QEYILRSWS+VK+GTT+ QK+LFFNLR+ K  + A+ + +L+PE V  IA  L V+
Sbjct: 1   RASIQEYILRSWSMVKLGTTSAQKKLFFNLRKAKAKIGALEEGDLRPENVKQIAHDLGVT 60

Query: 170 ESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           E+EVISMN R++G D SLNA I S  + S +WQDWL  +   Q      ++E + RR ML
Sbjct: 61  ETEVISMNRRMSGGDASLNAQIGSDGEGSMEWQDWLEDEDADQASDYERRDELEARREML 120

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
             +M VLN RER I   RRL +  VTLE+LS++++VSRER+RQIE RAF+K+Q+ ++   
Sbjct: 121 ALAMDVLNERERDILTQRRLSDETVTLEDLSTQYDVSRERIRQIEVRAFEKLQDRMR--- 177

Query: 289 ELSSSPPLL 297
           EL++   +L
Sbjct: 178 ELAAEKGML 186


>gi|298529795|ref|ZP_07017198.1| putative RNA polymerase, sigma 70 family subunit
           [Desulfonatronospira thiodismutans ASO3-1]
 gi|298511231|gb|EFI35134.1| putative RNA polymerase, sigma 70 family subunit
           [Desulfonatronospira thiodismutans ASO3-1]
          Length = 336

 Score =  182 bits (463), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 95/272 (34%), Positives = 173/272 (63%), Gaps = 6/272 (2%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISE 77
           Y+ ++   P +  +EE+ LA+++R+ G+  AA  L+TS+LRLVVKIAM + R +   + +
Sbjct: 60  YLRQVGNFPTMSAEEEFELARKFRDEGNQDAAFMLITSNLRLVVKIAMEFQRKWMKNVLD 119

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGN+GLM+A+KKFDP++G + + Y+ +WI+A + ++I+ +W +VK+GTT  Q++LF+
Sbjct: 120 LIQEGNVGLMKALKKFDPDKGIKFSYYASFWIRAYILKFIMDNWRMVKVGTTQAQRKLFY 179

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
           NL + K  L+++           AI++ L+VSE++V+ M  RL G   L+  +  ++ + 
Sbjct: 180 NLSKEKQRLESMGIT----ADADAISQSLDVSETDVVEMGQRL-GQHDLSLDMPYNEDSD 234

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
               + +    DG E++L++ E  +  +  +   M  L+ +E+ I E R L E+PVTL  
Sbjct: 235 VTPMNVIPALGDGAEEILLQGETAQLLQQNIKELMPKLSDKEKDIIEMRLLAESPVTLRE 294

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           +  ++ ++RERVRQIE+R   K++  IQ+ ++
Sbjct: 295 IGEKYGITRERVRQIESRLLGKIKAHIQENID 326


>gi|70733139|ref|YP_262912.1| RNA polymerase factor sigma-32 [Pseudomonas fluorescens Pf-5]
 gi|68347438|gb|AAY95044.1| transcription initiation factor sigma 32 [Pseudomonas fluorescens
           Pf-5]
          Length = 284

 Score =  182 bits (463), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 106/272 (38%), Positives = 159/272 (58%), Gaps = 7/272 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+H +  IP+L  ++E  LA+      DL AA ++V +HLR VV IA  Y GYGL 
Sbjct: 16  NLEAYVHTVNSIPLLTPEQERELAESLYYEQDLEAARQMVLAHLRFVVHIARSYSGYGLA 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++
Sbjct: 76  QADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSS 193
           LFFNLR  K  L  +  NN   E+V  +A+ L V   EV  M  RL G D + +    + 
Sbjct: 136 LFFNLRSQKKRLAWL--NN---EEVHRVAESLGVEPREVREMESRLTGQDMAFDPAAEAD 190

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
           D ++ Q     + DH     + +E  +   N  + L  ++ VL+ R R I   R L E  
Sbjct: 191 DDSAFQSPANYLEDHRYDPALQLEDADWSDNSTSNLHEALEVLDERSRDILYQRWLAEEK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL +L+ ++ VS ER+RQ+E  A  K++ SI
Sbjct: 251 ATLHDLAQKYNVSAERIRQLEKSAMNKLKLSI 282


>gi|255020686|ref|ZP_05292748.1| RNA polymerase sigma factor RpoH [Acidithiobacillus caldus ATCC
           51756]
 gi|254969922|gb|EET27422.1| RNA polymerase sigma factor RpoH [Acidithiobacillus caldus ATCC
           51756]
          Length = 285

 Score =  182 bits (463), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 110/268 (41%), Positives = 167/268 (62%), Gaps = 10/268 (3%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           G++ Y+  +   P+L  +EE  LA+R R+  D+ AA +LV SHLR VV++A  YRGYGLP
Sbjct: 16  GMAAYLRFVHAQPVLSVEEERRLARRLRDEDDVDAAKQLVLSHLRFVVRVARAYRGYGLP 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGNIGLM+AVK+FDPE+G RL ++++ WIKA M E+ILR+W +VK+ TT  Q++
Sbjct: 76  EADLIQEGNIGLMKAVKRFDPEQGVRLVSFAVHWIKAEMHEFILRNWRIVKVATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           LFFNLR  +      +   L  E+  AIA+ L VS+  V+ M  R+AG +   +L   SD
Sbjct: 136 LFFNLRSARQ-----SSGWLGQEESAAIAEDLGVSQEAVLEMEGRMAGQD--YSLQYESD 188

Query: 195 KNSSQWQDWLVYDHDGQEQV--LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
                 +  L  +  G+  V  LI+++  + R+  L  ++  L+ R+R I + R L ++P
Sbjct: 189 DEEGHGRT-LELEDPGESSVEALIDRDWDQQRQRGLRAALQSLSERDRYIIQNRWLSDDP 247

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKV 280
            TL+ L  E  VS ERVRQ+E    +K+
Sbjct: 248 KTLQALGEELGVSAERVRQLEKSGMEKL 275


>gi|227113845|ref|ZP_03827501.1| RNA polymerase factor sigma-32 [Pectobacterium carotovorum subsp.
           brasiliensis PBR1692]
          Length = 285

 Score =  182 bits (463), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 103/274 (37%), Positives = 157/274 (57%), Gaps = 9/274 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI      PML  +EE  LA+R    GDL AA  L+ SHLR V+ +A  Y GYGLP 
Sbjct: 16  LEGYIRAANAYPMLTAEEERALAERLHYQGDLEAAKHLILSHLRFVIHVARNYSGYGLPQ 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W +VK+ TT  Q++L
Sbjct: 76  ADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR+ K  L          ++V  +A++L V+  +V  M  R+A  +         D 
Sbjct: 136 FFNLRKSKTRL-----GWFNQDEVELVARELGVTSKDVREMESRMAAQDMTFDPTPEEDS 190

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNPRERRIFEARRL-QEN 251
           +  +    ++Y  D         EE     +  + LT ++  L+ R + I  AR L  +N
Sbjct: 191 HDGKAMSPMLYLQDKSSDFADGIEEDNWETHAADKLTYALEGLDERSQHIIRARWLDDDN 250

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             TL+ L+ ++ VS ERVRQ+E  A KK++ +I+
Sbjct: 251 KSTLQELADQYGVSAERVRQLEKNAMKKLRAAIE 284


>gi|328952031|ref|YP_004369365.1| putative RNA polymerase, sigma 70 family subunit [Desulfobacca
           acetoxidans DSM 11109]
 gi|328452355|gb|AEB08184.1| putative RNA polymerase, sigma 70 family subunit [Desulfobacca
           acetoxidans DSM 11109]
          Length = 328

 Score =  182 bits (463), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 113/290 (38%), Positives = 178/290 (61%), Gaps = 11/290 (3%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL- 73
            L RY+ EI + P+L+ +EE  LA  Y E  D  AA+ L+TS+LRLVVKIA+ ++ + + 
Sbjct: 45  ALQRYMGEINRYPLLQPEEEKRLATLYHETADQDAAYTLITSNLRLVVKIALDFQKFWMR 104

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++ EGNIGLMQA+KKFDP RG +L+ Y+ +WIKA + ++I+ +W LVKIGTT  Q+
Sbjct: 105 NLLDLIQEGNIGLMQAIKKFDPYRGIKLSYYASFWIKAYILKFIMDNWKLVKIGTTQAQR 164

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINS 192
           +LFF+L++ K  L+A       P+    I+ +LNV E+EVI M+ RL   E SL+A + S
Sbjct: 165 KLFFSLKKEKERLRA-QGYEADPK---LISTRLNVKEAEVIEMDQRLGSWEFSLDAPLKS 220

Query: 193 SDKNSSQWQ-DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
              +S +   ++L       ++ L  +E +      L    + L   ER I + R L E+
Sbjct: 221 ---DSEELHINFLTSGETAADEHLAREEMKDIFLMRLAEFRNTLKDNERDILDLRLLAEH 277

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV-ELSSSPPLLQKP 300
           P+TL+ + +   +SRERVRQIE R  KK+++ +  ++ +  S   L+ +P
Sbjct: 278 PLTLQEIGARHNISRERVRQIEERLLKKLRQFMHNEIPDFQSYQTLVNEP 327


>gi|322834883|ref|YP_004214910.1| RNA polymerase, sigma 32 subunit, RpoH [Rahnella sp. Y9602]
 gi|321170084|gb|ADW75783.1| RNA polymerase, sigma 32 subunit, RpoH [Rahnella sp. Y9602]
          Length = 285

 Score =  182 bits (463), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 103/286 (36%), Positives = 168/286 (58%), Gaps = 11/286 (3%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           + ++++  G   L  Y+      PML  +EE  LA+R   +GDL AA  L+ SHLR V  
Sbjct: 6   RTLALVPQG--SLEAYVRAANAYPMLTAEEERALAERLHYNGDLEAAKELILSHLRFVAH 63

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W +
Sbjct: 64  IARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRI 123

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG- 182
           VK+ TT  Q++LFFNLR+ K  L   + +     +V  +A++L V+  +V+ M  R+A  
Sbjct: 124 VKVATTKAQRKLFFNLRKNKQRLGWFSHD-----EVEHVARELGVTSKDVLEMESRMAAQ 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQE--QVLIEKEERKNRRNMLTRSMSVLNPRER 240
           D + +   +   ++ +     L       +  + + E    ++  + L+ +M  L+ R +
Sbjct: 179 DMTFDPTPDDEPRDGAAMAPMLYLQDKSSDFAETIEEDNWDQDATDKLSSAMEGLDERSQ 238

Query: 241 RIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            I  AR L  EN  TL+ L+ ++ VS ERVRQ+E  A KK++ +I+
Sbjct: 239 DIIRARWLDDENKSTLQELADKYGVSAERVRQLEKNAMKKLRMAIE 284


>gi|126664542|ref|ZP_01735526.1| RNA polymerase sigma factor [Marinobacter sp. ELB17]
 gi|126630868|gb|EBA01482.1| RNA polymerase sigma factor [Marinobacter sp. ELB17]
          Length = 286

 Score =  182 bits (463), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 109/285 (38%), Positives = 163/285 (57%), Gaps = 12/285 (4%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M  +V G   L  YI    +IP+L   EE  L++R    GD+ AA +L+ SHLR V+ IA
Sbjct: 8   MDKLVPG-ANLESYIQAASRIPILTVDEERALSERLYYEGDVDAARQLILSHLRFVIHIA 66

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGL  S++V EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK
Sbjct: 67  RSYSGYGLNQSDLVQEGNVGLMKAVKRFNPEYGVRLVSFAVHWIKAEIHEFILRNWRIVK 126

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DE 184
           + TT  Q++LFFNLR  K  L  ++ + L      A+A  L V    V  M  RL+  D 
Sbjct: 127 VATTKAQRKLFFNLRGQKKKLAWLSHDELN-----AVAADLGVEARVVREMEGRLSSHDT 181

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE---ERKNRRNMLTRSMSVLNPRERR 241
           + +  +N  + ++ Q   + + DH       +E+    E  N R  L +++S L+ R + 
Sbjct: 182 AFDGPMNDDEDSAYQAPAYYLEDHRSNPATQLERSNWTEDSNGR--LMQALSSLDDRSQD 239

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           I   R L E   TL  L+  + VS ER+RQ+E  A KK++  +Q+
Sbjct: 240 ILRERWLSETKSTLHQLADRYGVSAERIRQLEKNAMKKIRLQMQE 284


>gi|227329284|ref|ZP_03833308.1| RNA polymerase factor sigma-32 [Pectobacterium carotovorum subsp.
           carotovorum WPP14]
          Length = 285

 Score =  182 bits (463), Expect = 4e-44,   Method: Compositional matrix adjust.
 Identities = 103/274 (37%), Positives = 157/274 (57%), Gaps = 9/274 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI      PML  +EE  LA+R    GDL AA  L+ SHLR V+ +A  Y GYGLP 
Sbjct: 16  LEGYIRAANAYPMLTAEEERALAERLHYQGDLDAAKHLILSHLRFVIHVARNYSGYGLPQ 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W +VK+ TT  Q++L
Sbjct: 76  ADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR+ K  L          ++V  +A++L V+  +V  M  R+A  +         D 
Sbjct: 136 FFNLRKSKTRL-----GWFNQDEVELVARELGVTSKDVREMESRMAAQDMTFDPTPEEDS 190

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNPRERRIFEARRL-QEN 251
           +  +    ++Y  D         EE     +  + LT ++  L+ R + I  AR L  +N
Sbjct: 191 HDGKAMSPMLYLQDKSSDFADGIEEDNWETHAADKLTYALEGLDERSQHIIRARWLDDDN 250

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             TL+ L+ ++ VS ERVRQ+E  A KK++ +I+
Sbjct: 251 KSTLQELADKYGVSAERVRQLEKNAMKKLRAAIE 284


>gi|269140667|ref|YP_003297368.1| RNA polymerase factor sigma-32 [Edwardsiella tarda EIB202]
 gi|267986328|gb|ACY86157.1| RNA polymerase factor sigma-32 [Edwardsiella tarda EIB202]
 gi|304560452|gb|ADM43116.1| RNA polymerase sigma factor RpoH [Edwardsiella tarda FL6-60]
          Length = 284

 Score =  182 bits (463), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 103/289 (35%), Positives = 167/289 (57%), Gaps = 10/289 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  Y+      PML  +EE  L +R    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLTLVPQGSLEAYVRAANAYPMLTAEEERALGERLHYKGDLDAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEMGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VSE +V+ M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVELVARELGVSEKDVLEMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNP 237
           A  +    L    ++  +     +++  D       E E+     +  + L+ ++  L+ 
Sbjct: 176 AAQDMAFDLPGDDEQEGAPTAP-VLFLQDKSSDFANEIEDDNWESHAADKLSVALEGLDE 234

Query: 238 RERRIFEARRLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           R + I  AR L  +N  TL+ L+  + VS ERVRQ+E  A KK++ +I+
Sbjct: 235 RSQHIIRARWLDSDNKATLQELADRYGVSAERVRQLEKNAMKKLRAAIE 283


>gi|242241268|ref|YP_002989449.1| RNA polymerase factor sigma-32 [Dickeya dadantii Ech703]
 gi|242133325|gb|ACS87627.1| RNA polymerase, sigma 32 subunit, RpoH [Dickeya dadantii Ech703]
          Length = 285

 Score =  182 bits (462), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 103/274 (37%), Positives = 156/274 (56%), Gaps = 9/274 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI      PML  +EE  LA+R   HGDL AA +L+ SHLR V+ +A  Y GYGLP 
Sbjct: 16  LEGYIRAANAYPMLTAEEERALAERLHYHGDLDAAKQLILSHLRFVIHVARNYAGYGLPQ 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AV++F+P+ G RL ++++ WIKA + EY+LR+W +VK+ TT  Q++L
Sbjct: 76  ADLIQEGNIGLMKAVRRFNPDVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR+ K  L          ++V  +A++L V+  +V  M  R+A  +         D 
Sbjct: 136 FFNLRKTKRRL-----GWFNQDEVELVARELGVTSKDVREMESRMAAQDMTYDPTPDDDA 190

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNPRERRIFEARRL-QEN 251
              Q    ++Y  D         EE     +  + L  ++  L+ R + I  AR L  +N
Sbjct: 191 QPGQPMAPMLYLQDKSSDFADGIEEDNWETHAADKLAYALEGLDERSQHIIRARWLDDDN 250

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             TL+ L+  + VS ERVRQ+E  A KK++ +I+
Sbjct: 251 KSTLQELADYYGVSAERVRQLEKNAMKKLRAAIE 284


>gi|332763556|gb|EGJ93795.1| alternative sigma factor RpoH [Shigella flexneri 2930-71]
          Length = 280

 Score =  182 bits (462), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 111/285 (38%), Positives = 161/285 (56%), Gaps = 32/285 (11%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI      PML   EE  LA++   HGDL AA  L+ SHLR VV IA  Y GYGLP 
Sbjct: 12  LDSYIRAANAWPMLSADEERALAEKLHYHGDLEAAKTLILSHLRFVVHIARNYAGYGLPQ 71

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W +VK+ TT  Q++L
Sbjct: 72  ADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKL 131

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE----------- 184
           FFNLR+ K  L          ++V  +A++L V+  +V  M  R+A  +           
Sbjct: 132 FFNLRKTKQRL-----GWFNQDEVEMVARELGVTSKDVREMESRMAAQDMTFDLSSDDDS 186

Query: 185 ---SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
               +  ++   DK SS + D  + D + +EQ            N LT +M  L+ R + 
Sbjct: 187 DSQPMAPVLYLQDK-SSNFADG-IEDDNWEEQAA----------NRLTDAMHGLDERSQD 234

Query: 242 IFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           I  AR L E N  TL+ L+  + VS ERVRQ+E  A KK++ +I+
Sbjct: 235 IIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIE 279


>gi|297569322|ref|YP_003690666.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfurivibrio
           alkaliphilus AHT2]
 gi|296925237|gb|ADH86047.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfurivibrio
           alkaliphilus AHT2]
          Length = 363

 Score =  182 bits (462), Expect = 5e-44,   Method: Compositional matrix adjust.
 Identities = 109/284 (38%), Positives = 175/284 (61%), Gaps = 8/284 (2%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           ++ V G   L RY+ EI +  +L + E   LA+ ++E GD  AA++LVT++LRLVVK+AM
Sbjct: 71  NLPVVGNAALHRYLQEISQYRLLSRAETDELARLFKETGDPEAAYKLVTANLRLVVKVAM 130

Query: 67  GYRGYGLP-ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            ++ Y +    +++ EGNIGL+QAVKKFDP R  + + Y+ +WI+A + ++I+ +W LVK
Sbjct: 131 DFQKYWMQNFLDLIQEGNIGLVQAVKKFDPYRQVKFSYYAAYWIRAYILKFIMDNWRLVK 190

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DE 184
           IGTT  Q++LFF+L + K  L++      KPE  + +A++LNV ESEVI M+ R+   D 
Sbjct: 191 IGTTQAQRKLFFSLNKEKKLLES---QGFKPEPKL-LAQRLNVKESEVIEMSQRMDNWDM 246

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL + +   + +  + +D+L       E+ +   E R+    +L +    LN +E  I  
Sbjct: 247 SLESPMR--EDSGDERKDFLPVAGPSVEERVAADEVREWMAGILDKMRRTLNEKELAILR 304

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            R L + P TL+ ++  F +SRERVRQIEA   KK++  ++ +V
Sbjct: 305 ERLLSDEPATLQEIADRFAISRERVRQIEANLLKKMRTYLENEV 348


>gi|240851254|ref|YP_002972657.1| RNA polymerase sigma-32 factor [Bartonella grahamii as4aup]
 gi|240268377|gb|ACS51965.1| RNA polymerase sigma-32 factor [Bartonella grahamii as4aup]
          Length = 303

 Score =  182 bits (461), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 100/261 (38%), Positives = 168/261 (64%), Gaps = 5/261 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE+Q+E+ LA R+++  D  A H++  +H+RLV+ IA  ++ + +P+ ++V EG +GL
Sbjct: 34  PYLERQKEHDLALRWKDKRDDDAMHQIAAAHMRLVIAIANRFKRFKMPLGDLVQEGYVGL 93

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +F+P+R  R +TY+ WWI+A++Q+YILR+WS+V+ GT+++QK LFFNLRRL+  L
Sbjct: 94  LEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSSQKALFFNLRRLRAKL 153

Query: 147 QAITDNNLKPEQVV--AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             I D++   +Q +   IA+KL VS  +V +M+ R +  ++  ++  S + ++   +  +
Sbjct: 154 --IQDDSALSKQDIFRTIAEKLGVSVRDVETMDFRFSSSDNSLSVSVSENSDNPIAKMDV 211

Query: 205 VYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           + D       LIE+     RR   L  ++ +LN RE  I   RRL E   TLE L  +  
Sbjct: 212 LVDDSPLPDALIEQVIDGQRRTQWLYDALQILNERELEIIRFRRLNEEGATLEVLGEKLG 271

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ERVRQIEARA +K++ ++
Sbjct: 272 ISKERVRQIEARALQKLRSAL 292


>gi|229593148|ref|YP_002875267.1| RNA polymerase factor sigma-32 [Pseudomonas fluorescens SBW25]
 gi|312963636|ref|ZP_07778117.1| RNA polymerase sigma-32 factor [Pseudomonas fluorescens WH6]
 gi|229365014|emb|CAY53168.1| RNA polymerase sigma-32 factor [Pseudomonas fluorescens SBW25]
 gi|311282145|gb|EFQ60745.1| RNA polymerase sigma-32 factor [Pseudomonas fluorescens WH6]
          Length = 284

 Score =  182 bits (461), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 108/272 (39%), Positives = 160/272 (58%), Gaps = 9/272 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+H +  IP+L  ++E  LA+      DL AA ++V +HLR VV IA  Y GYGL  
Sbjct: 17  LEAYVHTVNSIPLLTPEQERELAESLYYEQDLGAARQMVLAHLRFVVHIARSYSGYGLAQ 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++L
Sbjct: 77  ADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRKL 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR  K  L  +  NN   E+V  +A+ L V   EV  M  RL G D + +    + D
Sbjct: 137 FFNLRSQKKRLAWL--NN---EEVHRVAESLGVEPREVREMESRLTGHDMAFDPAAEADD 191

Query: 195 KNSSQWQDWLVYDH--DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            ++ Q     + DH  D   Q L + +   N  + L  ++ VL+ R R I   R L E  
Sbjct: 192 DSAFQSPANYLEDHRYDPARQ-LEDADWSDNSNHNLHEALEVLDDRSRDILYQRWLAEEK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL +L+ ++ VS ER+RQ+E  A  K++ SI
Sbjct: 251 ATLHDLAQKYNVSAERIRQLEKSAMNKLKLSI 282


>gi|114776576|ref|ZP_01451621.1| RNA polymerase sigma factor [Mariprofundus ferrooxydans PV-1]
 gi|114553406|gb|EAU55804.1| RNA polymerase sigma factor [Mariprofundus ferrooxydans PV-1]
          Length = 281

 Score =  182 bits (461), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 104/268 (38%), Positives = 164/268 (61%), Gaps = 11/268 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L R+  E+R+IP L+++EE  LA++++   DL++  +L+ ++L +V  IA  YR +GLP 
Sbjct: 13  LDRFYQELRRIPKLDREEEDALARKWQRDHDLASVQQLINANLHVVAAIAREYRHFGLPE 72

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EG +GLMQAVK+FDP+RGFRL TY+ +WI+A++ ++ILRSWS+VK+GT   Q+R+
Sbjct: 73  EDLIQEGTLGLMQAVKRFDPDRGFRLKTYAAYWIRASIHDFILRSWSIVKMGTNKLQRRI 132

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS-ESEVISMNCRLAGDESLNALINSSD 194
           F  L++ +  + A+    L+      +A +  VS ES        L  D S+++   + D
Sbjct: 133 FAGLQKAECAIAALEGRGLE-----GVASQYGVSGESYQQIAASFLRRDYSIDS-DATED 186

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
            N  +    L    D  EQ L+ K+ +      L ++M  L+ R+R I   R L E P T
Sbjct: 187 GNIIE----LPAPGDTPEQALVAKDWQSFTTMQLKQAMEALSERDRNIIRQRYLVEPPST 242

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQE 282
           L+ LS +  +S ERVRQ+EARA KK+ E
Sbjct: 243 LKELSEDLGISIERVRQLEARAMKKIGE 270


>gi|71737989|ref|YP_276878.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv.
           phaseolicola 1448A]
 gi|257482996|ref|ZP_05637037.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. tabaci
           ATCC 11528]
 gi|289624653|ref|ZP_06457607.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. aesculi
           str. NCPPB3681]
 gi|289648492|ref|ZP_06479835.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. aesculi
           str. 2250]
 gi|289672442|ref|ZP_06493332.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. syringae
           FF5]
 gi|298485264|ref|ZP_07003357.1| RNA polymerase sigma factor RpoH [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
 gi|302187226|ref|ZP_07263899.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. syringae
           642]
 gi|71558542|gb|AAZ37753.1| RNA polymerase sigma-32 factor [Pseudomonas syringae pv.
           phaseolicola 1448A]
 gi|298160252|gb|EFI01280.1| RNA polymerase sigma factor RpoH [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
 gi|320326376|gb|EFW82429.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. glycinea
           str. B076]
 gi|320331634|gb|EFW87572.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. glycinea
           str. race 4]
 gi|330871135|gb|EGH05844.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. aesculi
           str. 0893_23]
 gi|330872356|gb|EGH06505.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. glycinea
           str. race 4]
 gi|330891333|gb|EGH23994.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. mori str.
           301020]
 gi|330898959|gb|EGH30378.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. japonica
           str. M301072PT]
 gi|330954977|gb|EGH55237.1| RNA polymerase factor sigma-32 [Pseudomonas syringae Cit 7]
 gi|330982560|gb|EGH80663.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. aptata
           str. DSM 50252]
 gi|330985905|gb|EGH84008.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. lachrymans
           str. M301315]
 gi|331011765|gb|EGH91821.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. tabaci
           ATCC 11528]
          Length = 284

 Score =  182 bits (461), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 107/273 (39%), Positives = 160/273 (58%), Gaps = 9/273 (3%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+H +  IP+L  ++E  LA+      DL AA ++V +HLR VV IA  Y GYGL 
Sbjct: 16  NLEAYVHTVNSIPLLTPEQERELAESLYYEQDLDAARQMVLAHLRFVVHIARSYSGYGLA 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++
Sbjct: 76  QADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSS 193
           LFFNLR  K  L  +  NN   ++V  +A+ L V   EV  M  RL G D + +    + 
Sbjct: 136 LFFNLRSQKKRLAWL--NN---DEVHRVAESLGVEPREVREMESRLTGHDMAFDPAAEAD 190

Query: 194 DKNSSQWQDWLVYDH--DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           D ++ Q     + DH  D   Q L + +   N    L +++ VL+ R R I   R L E 
Sbjct: 191 DDSAFQSPANYLEDHRYDPARQ-LEDSDWTDNSTANLHQALDVLDERSRDILYQRWLAEE 249

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL +L+ ++ VS ER+RQ+E  A  K++ SI
Sbjct: 250 KATLHDLAQKYNVSAERIRQLEKSAMNKLKTSI 282


>gi|16762736|ref|NP_458353.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. CT18]
 gi|16766854|ref|NP_462469.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhimurium str. LT2]
 gi|29144223|ref|NP_807565.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. Ty2]
 gi|62182067|ref|YP_218484.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Choleraesuis str. SC-B67]
 gi|161616616|ref|YP_001590580.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Paratyphi B str. SPB7]
 gi|167549215|ref|ZP_02342974.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA29]
 gi|167990783|ref|ZP_02571882.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar 4,[5],12:i:- str. CVM23701]
 gi|168232714|ref|ZP_02657772.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Kentucky str. CDC 191]
 gi|168241719|ref|ZP_02666651.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL486]
 gi|168260704|ref|ZP_02682677.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Hadar str. RI_05P066]
 gi|168465152|ref|ZP_02699044.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Newport str. SL317]
 gi|168818616|ref|ZP_02830616.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Weltevreden str. HI_N05-537]
 gi|194443524|ref|YP_002042813.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Newport str. SL254]
 gi|194449082|ref|YP_002047593.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL476]
 gi|194469731|ref|ZP_03075715.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Kentucky str. CVM29188]
 gi|197250526|ref|YP_002148491.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Agona str. SL483]
 gi|197265856|ref|ZP_03165930.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA23]
 gi|198244039|ref|YP_002217526.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Dublin str. CT_02021853]
 gi|200387614|ref|ZP_03214226.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Virchow str. SL491]
 gi|204928638|ref|ZP_03219837.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Javiana str. GA_MM04042433]
 gi|205354814|ref|YP_002228615.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 287/91]
 gi|207858806|ref|YP_002245457.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Enteritidis str. P125109]
 gi|213426834|ref|ZP_03359584.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. E02-1180]
 gi|213619347|ref|ZP_03373173.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-2068]
 gi|213649997|ref|ZP_03380050.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. J185]
 gi|213857359|ref|ZP_03384330.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. M223]
 gi|224585360|ref|YP_002639159.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
 gi|238910431|ref|ZP_04654268.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Tennessee str. CDC07-0191]
 gi|289829445|ref|ZP_06547057.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-3139]
 gi|25288476|pir||AB0992 RNA polymerase sigma-32 factor [imported] - Salmonella enterica
           subsp. enterica serovar Typhi (strain CT18)
 gi|16422128|gb|AAL22428.1| sigma H factor of RNA polymerase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|16505042|emb|CAD08062.1| RNA polymerase sigma-32 factor [Salmonella enterica subsp. enterica
           serovar Typhi]
 gi|29139860|gb|AAO71425.1| RNA polymerase sigma-32 factor [Salmonella enterica subsp. enterica
           serovar Typhi str. Ty2]
 gi|62129700|gb|AAX67403.1| sigma H (sigma 32) factor of RNA polymerase; transcription of heat
           shock proteins induced by cytoplasmic stress [Salmonella
           enterica subsp. enterica serovar Choleraesuis str.
           SC-B67]
 gi|161365980|gb|ABX69748.1| hypothetical protein SPAB_04433 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|194402187|gb|ACF62409.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Newport str. SL254]
 gi|194407386|gb|ACF67605.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL476]
 gi|194456095|gb|EDX44934.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Kentucky str. CVM29188]
 gi|195632472|gb|EDX50956.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Newport str. SL317]
 gi|197214229|gb|ACH51626.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Agona str. SL483]
 gi|197244111|gb|EDY26731.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA23]
 gi|197938555|gb|ACH75888.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Dublin str. CT_02021853]
 gi|199604712|gb|EDZ03257.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Virchow str. SL491]
 gi|204322071|gb|EDZ07269.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Javiana str. GA_MM04042433]
 gi|205274595|emb|CAR39645.1| RNA polymerase sigma-32 factor [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 287/91]
 gi|205325609|gb|EDZ13448.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA29]
 gi|205330694|gb|EDZ17458.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar 4,[5],12:i:- str. CVM23701]
 gi|205333102|gb|EDZ19866.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Kentucky str. CDC 191]
 gi|205338892|gb|EDZ25656.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL486]
 gi|205344405|gb|EDZ31169.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Weltevreden str. HI_N05-537]
 gi|205350317|gb|EDZ36948.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Hadar str. RI_05P066]
 gi|206710609|emb|CAR34967.1| RNA polymerase sigma-32 factor [Salmonella enterica subsp. enterica
           serovar Enteritidis str. P125109]
 gi|224469888|gb|ACN47718.1| RNA polymerase sigma factor [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
 gi|261248721|emb|CBG26559.1| RNA polymerase sigma-32 factor [Salmonella enterica subsp. enterica
           serovar Typhimurium str. D23580]
 gi|267995798|gb|ACY90683.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhimurium str. 14028S]
 gi|301160107|emb|CBW19627.1| RNA polymerase sigma-32 factor [Salmonella enterica subsp. enterica
           serovar Typhimurium str. SL1344]
 gi|312914591|dbj|BAJ38565.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhimurium str. T000240]
 gi|320087978|emb|CBY97740.1| RNA polymerase sigma-32 factor Heat shock regulatory protein F33.4
           [Salmonella enterica subsp. enterica serovar Weltevreden
           str. 2007-60-3289-1]
 gi|321226618|gb|EFX51668.1| RNA polymerase sigma factor RpoH [Salmonella enterica subsp.
           enterica serovar Typhimurium str. TN061786]
 gi|322614066|gb|EFY11002.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 315996572]
 gi|322617958|gb|EFY14851.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-1]
 gi|322625428|gb|EFY22254.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-3]
 gi|322629893|gb|EFY26666.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-4]
 gi|322632218|gb|EFY28969.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 515920-1]
 gi|322636431|gb|EFY33138.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 515920-2]
 gi|322643092|gb|EFY39666.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 531954]
 gi|322644713|gb|EFY41249.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. NC_MB110209-0054]
 gi|322651265|gb|EFY47649.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. OH_2009072675]
 gi|322652822|gb|EFY49161.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. CASC_09SCPH15965]
 gi|322659124|gb|EFY55376.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 19N]
 gi|322663174|gb|EFY59378.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 81038-01]
 gi|322668661|gb|EFY64814.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. MD_MDA09249507]
 gi|322674536|gb|EFY70629.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 414877]
 gi|322678259|gb|EFY74320.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 366867]
 gi|322682485|gb|EFY78506.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 413180]
 gi|322684198|gb|EFY80204.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 446600]
 gi|322716555|gb|EFZ08126.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Choleraesuis str. A50]
 gi|323131927|gb|ADX19357.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhimurium str. 4/74]
 gi|323192247|gb|EFZ77479.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 609458-1]
 gi|323196326|gb|EFZ81478.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 556150-1]
 gi|323201872|gb|EFZ86935.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 609460]
 gi|323206415|gb|EFZ91376.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 507440-20]
 gi|323212008|gb|EFZ96835.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 556152]
 gi|323216913|gb|EGA01636.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB101509-0077]
 gi|323222313|gb|EGA06696.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB102109-0047]
 gi|323224327|gb|EGA08616.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB110209-0055]
 gi|323228255|gb|EGA12386.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB111609-0052]
 gi|323233477|gb|EGA17570.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 2009083312]
 gi|323237061|gb|EGA21128.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 2009085258]
 gi|323243724|gb|EGA27740.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 315731156]
 gi|323246034|gb|EGA30021.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2009159199]
 gi|323250810|gb|EGA34688.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008282]
 gi|323255821|gb|EGA39571.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008283]
 gi|323261903|gb|EGA45470.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008284]
 gi|323267705|gb|EGA51187.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008285]
 gi|323268585|gb|EGA52052.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008287]
 gi|326625307|gb|EGE31652.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Dublin str. 3246]
 gi|326629958|gb|EGE36301.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 9]
 gi|332990419|gb|AEF09402.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhimurium str. UK-1]
          Length = 284

 Score =  182 bits (461), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 115/298 (38%), Positives = 165/298 (55%), Gaps = 33/298 (11%)

Query: 4   KNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           K M  +    +G L  YI      PML   EE  LA+R    GDL AA  L+ SHLR VV
Sbjct: 3   KEMQNLALAPVGNLESYIRAANAWPMLSADEERALAERLHYQGDLEAAKTLILSHLRFVV 62

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W 
Sbjct: 63  HIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWR 122

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+A 
Sbjct: 123 IVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVEMVARELGVSSKDVREMESRMAA 177

Query: 183 DE--------------SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            +               +  ++   DK SS + D  + D + +EQ            N L
Sbjct: 178 QDMTFDMSSDDESDSQPMAPVLYLQDK-SSNFADG-IEDDNWEEQAA----------NRL 225

Query: 229 TRSMSVLNPRERRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           T +M  L+ R + I  AR L E N  TL+ L+  + VS ERVRQ+E  A KK++ +I+
Sbjct: 226 TDAMQGLDERSQDIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIE 283


>gi|161505889|ref|YP_001573001.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. arizonae
           serovar 62:z4,z23:-- str. RSK2980]
 gi|160867236|gb|ABX23859.1| hypothetical protein SARI_04068 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 284

 Score =  182 bits (461), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 115/298 (38%), Positives = 165/298 (55%), Gaps = 33/298 (11%)

Query: 4   KNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           K M  +    +G L  YI      PML   EE  LA+R    GDL AA  L+ SHLR VV
Sbjct: 3   KEMQNLALAPVGNLESYIRAANAWPMLSADEERALAERLHYQGDLEAAKTLILSHLRFVV 62

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W 
Sbjct: 63  HIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWR 122

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+A 
Sbjct: 123 IVKVATTKAQRKLFFNLRKAKQRL-----GWFNQDEVEMVARELGVSSKDVREMESRMAA 177

Query: 183 DE--------------SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            +               +  ++   DK SS + D  + D + +EQ            N L
Sbjct: 178 QDMTFDMSSDDESDSQPMAPVLYLQDK-SSNFADG-IEDDNWEEQAA----------NRL 225

Query: 229 TRSMSVLNPRERRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           T +M  L+ R + I  AR L E N  TL+ L+  + VS ERVRQ+E  A KK++ +I+
Sbjct: 226 TDAMQGLDERSQDIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIE 283


>gi|170719544|ref|YP_001747232.1| RNA polymerase factor sigma-32 [Pseudomonas putida W619]
 gi|169757547|gb|ACA70863.1| RNA polymerase, sigma 32 subunit, RpoH [Pseudomonas putida W619]
          Length = 284

 Score =  182 bits (461), Expect = 7e-44,   Method: Compositional matrix adjust.
 Identities = 106/271 (39%), Positives = 158/271 (58%), Gaps = 7/271 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+H +  IP+L  ++E  LA+R     DL AA ++V +HLR VV IA  Y GYGL  
Sbjct: 17  LEAYVHTVNSIPLLTVEQERDLAERLYYEQDLEAARQMVMAHLRFVVHIARSYAGYGLAQ 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++L
Sbjct: 77  ADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRKL 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR  K  L  +  NN   ++V  +A+ L V   EV  M  RL+G D + +    + D
Sbjct: 137 FFNLRSQKKRLAWL--NN---DEVHRVAESLGVEPREVREMESRLSGQDMAFDPAAEADD 191

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
            ++ Q     + DH     V +E  +   N  + L  ++  L+ R R I   R L E   
Sbjct: 192 DSAFQSPAHYLEDHRYDPAVQLEDADWSDNSTSNLHEALQGLDERSRDILYQRWLAEEKA 251

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           TL  L+ ++ VS ER+RQ+E  A  KV+  I
Sbjct: 252 TLHELADKYSVSAERIRQLEKNAMNKVKALI 282


>gi|77461555|ref|YP_351062.1| RNA polymerase factor sigma-32 [Pseudomonas fluorescens Pf0-1]
 gi|77385558|gb|ABA77071.1| RNA polymerase, sigma 32 subunit, RpoH [Pseudomonas fluorescens
           Pf0-1]
          Length = 284

 Score =  182 bits (461), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 106/272 (38%), Positives = 159/272 (58%), Gaps = 9/272 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+H +  IP+L  ++E  LA+      DL AA ++V +HLR VV IA  Y GYGL  
Sbjct: 17  LEAYVHTVNSIPLLTPEQERELAESLYYEQDLGAARQMVLAHLRFVVHIARSYSGYGLAQ 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++L
Sbjct: 77  ADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRKL 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR  K  L  + +     E+V  +A+ L V   EV  M  RL G D + +    + D
Sbjct: 137 FFNLRSQKKRLAWLNN-----EEVHRVAESLGVEPREVREMESRLTGHDMAFDPAAEADD 191

Query: 195 KNSSQWQDWLVYDH--DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            ++ Q     + DH  D   Q L + +   N  + L  ++ VL+ R R I   R L E  
Sbjct: 192 DSAFQSPANYLEDHRYDPARQ-LEDADWSDNSNHNLHEALEVLDERSRDILYQRWLAEEK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL +L+ ++ VS ER+RQ+E  A  K++ SI
Sbjct: 251 ATLHDLAQKYNVSAERIRQLEKSAMNKLKLSI 282


>gi|330812379|ref|YP_004356841.1| RNA polymerase sigma factor [Pseudomonas brassicacearum subsp.
           brassicacearum NFM421]
 gi|327380487|gb|AEA71837.1| RNA polymerase sigma factor [Pseudomonas brassicacearum subsp.
           brassicacearum NFM421]
          Length = 284

 Score =  181 bits (460), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 108/273 (39%), Positives = 159/273 (58%), Gaps = 9/273 (3%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+H +  IP+L  ++E  LA+      DL AA ++V +HLR VV IA  Y GYGL 
Sbjct: 16  NLEAYVHTVNSIPLLTPEQERELAESLYYEQDLEAARQMVLAHLRFVVHIARSYSGYGLA 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++
Sbjct: 76  QADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSS 193
           LFFNLR  K  L  +  NN   E+V  +A+ L V   EV  M  RL G D + +    + 
Sbjct: 136 LFFNLRSQKKRLAWL--NN---EEVHRVAESLGVEPREVREMESRLTGHDMAFDPAAEAD 190

Query: 194 DKNSSQWQDWLVYDH--DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           D ++ Q     + DH  D   Q L + +   N    L  ++ VL+ R R I   R L E 
Sbjct: 191 DDSAFQSPANYLEDHRYDPARQ-LEDADWSDNSNTNLHEALEVLDERSRDILYQRWLAEE 249

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL +L+ ++ VS ER+RQ+E  A  K++ SI
Sbjct: 250 KATLHDLAQKYNVSAERIRQLEKSAMNKLKVSI 282


>gi|330944706|gb|EGH46637.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. pisi str.
           1704B]
          Length = 284

 Score =  181 bits (460), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 107/273 (39%), Positives = 160/273 (58%), Gaps = 9/273 (3%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+H +  IP+L  ++E  LA+      DL AA ++V +HLR VV IA  Y GYGL 
Sbjct: 16  NLEAYVHTVNSIPLLTPEQERELAESLYYEQDLDAARQMVLAHLRFVVHIARSYSGYGLA 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++
Sbjct: 76  QADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSS 193
           LFFNLR  K  L  +  NN   ++V  +A+ L V   EV  M  RL G D + +    + 
Sbjct: 136 LFFNLRSQKKRLAWL--NN---DEVHRVAESLGVEPREVREMESRLTGHDMAFDPAAEAD 190

Query: 194 DKNSSQWQDWLVYDH--DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           D ++ Q     + DH  D   Q L + +   N    L +++ VL+ R R I   R L E 
Sbjct: 191 DDSAFQSPANYLEDHRYDPARQ-LEDSDWTDNSPANLHQALDVLDERSRDILYQRWLAEE 249

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL +L+ ++ VS ER+RQ+E  A  K++ SI
Sbjct: 250 KATLHDLAQKYNVSAERIRQLEKSAMNKLKTSI 282


>gi|238921550|ref|YP_002935065.1| RNA polymerase factor sigma-32 [Edwardsiella ictaluri 93-146]
 gi|238871119|gb|ACR70830.1| alternative sigma factor RpoH, putative [Edwardsiella ictaluri
           93-146]
          Length = 284

 Score =  181 bits (460), Expect = 8e-44,   Method: Compositional matrix adjust.
 Identities = 103/289 (35%), Positives = 167/289 (57%), Gaps = 10/289 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  Y+      PML  +EE  L +R    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLTLVPQGSLEAYVRAANAYPMLTAEEERALGERLHYKGDLDAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEMGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VSE +V+ M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVELVARELGVSEKDVLEMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNP 237
           A  +    L    ++  +     +++  D       E E+     +  + L+ ++  L+ 
Sbjct: 176 AAQDMAFDLPGDDEQEGAPAAP-VLFLQDKSSDFANEIEDDNWESHAADKLSVALEGLDE 234

Query: 238 RERRIFEARRLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           R + I  AR L  +N  TL+ L+  + VS ERVRQ+E  A KK++ +I+
Sbjct: 235 RSQHIIRARWLDSDNKATLQELADRYGVSAERVRQLEKNAMKKLRMAIE 283


>gi|146313497|ref|YP_001178571.1| RNA polymerase factor sigma-32 [Enterobacter sp. 638]
 gi|145320373|gb|ABP62520.1| RNA polymerase, sigma 32 subunit, RpoH [Enterobacter sp. 638]
          Length = 285

 Score =  181 bits (460), Expect = 9e-44,   Method: Compositional matrix adjust.
 Identities = 113/287 (39%), Positives = 167/287 (58%), Gaps = 10/287 (3%)

Query: 4   KNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           K M  +    +G L  YI      PML  +EE  LA++    GDL AA  L+ SHLR VV
Sbjct: 3   KEMQTLALAPVGNLESYIRAANTWPMLTAEEEKELAEKLHYQGDLEAAKTLILSHLRFVV 62

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W 
Sbjct: 63  HVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWR 122

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L          E+V  +A++L VS  +V  M  R+A 
Sbjct: 123 IVKVATTKAQRKLFFNLRKAKQRL-----GWFNQEEVEMVARELGVSSKDVREMESRMAA 177

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVL--IEKEERKNR-RNMLTRSMSVLNPRE 239
            +    + +  D   SQ    ++Y  D        IE++  +++  N LT +M  L+ R 
Sbjct: 178 QDMTFDMSSDDDAQDSQPMAPVLYLQDKTSNFADGIEEDNWEDQAANKLTHAMEGLDERS 237

Query: 240 RRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + I  AR L E N  TL+ L+  + VS ERVRQ+E  A KK++ +I+
Sbjct: 238 QAIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIE 284


>gi|152972335|ref|YP_001337481.1| RNA polymerase factor sigma-32 [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|206580698|ref|YP_002236168.1| alternative sigma factor RpoH [Klebsiella pneumoniae 342]
 gi|238896924|ref|YP_002921669.1| RNA polymerase factor sigma-32 [Klebsiella pneumoniae NTUH-K2044]
 gi|262040527|ref|ZP_06013768.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Klebsiella
           pneumoniae subsp. rhinoscleromatis ATCC 13884]
 gi|288933158|ref|YP_003437217.1| RNA polymerase, sigma 32 subunit, RpoH [Klebsiella variicola At-22]
 gi|290511960|ref|ZP_06551328.1| alternative sigma factor RpoH [Klebsiella sp. 1_1_55]
 gi|329999131|ref|ZP_08303332.1| alternative sigma factor RpoH [Klebsiella sp. MS 92-3]
 gi|150957184|gb|ABR79214.1| RNA polymerase sigma factor [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|206569756|gb|ACI11532.1| alternative sigma factor RpoH [Klebsiella pneumoniae 342]
 gi|238549251|dbj|BAH65602.1| RNA polymerase sigma factor [Klebsiella pneumoniae subsp.
           pneumoniae NTUH-K2044]
 gi|259042120|gb|EEW43150.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Klebsiella
           pneumoniae subsp. rhinoscleromatis ATCC 13884]
 gi|288887887|gb|ADC56205.1| RNA polymerase, sigma 32 subunit, RpoH [Klebsiella variicola At-22]
 gi|289775750|gb|EFD83750.1| alternative sigma factor RpoH [Klebsiella sp. 1_1_55]
 gi|328538425|gb|EGF64546.1| alternative sigma factor RpoH [Klebsiella sp. MS 92-3]
          Length = 284

 Score =  181 bits (459), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 113/298 (37%), Positives = 166/298 (55%), Gaps = 33/298 (11%)

Query: 4   KNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           K M  +    +G L  YI      PML   EE  LA++    GDL AA +L+ SHLR VV
Sbjct: 3   KEMQTLALAPVGNLESYIRAANTWPMLSADEERELAEKLHYQGDLEAAKKLILSHLRFVV 62

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W 
Sbjct: 63  HIARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWR 122

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+A 
Sbjct: 123 IVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVEMVARELGVSSKDVREMESRMAA 177

Query: 183 DE--------------SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            +               +  ++   DK +S + D  + D + +EQ            N L
Sbjct: 178 QDMTFDMSSDDESDSQPMAPVLYLQDK-TSNFADG-IEDDNWEEQAA----------NKL 225

Query: 229 TRSMSVLNPRERRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           T +M  L+ R + I  AR L E N  TL+ L+  + VS ERVRQ+E  A KK++ +I+
Sbjct: 226 TDAMQGLDERSQDIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIE 283


>gi|326797246|ref|YP_004315066.1| RNA polymerase, sigma 32 subunit, RpoH [Marinomonas mediterranea
           MMB-1]
 gi|326548010|gb|ADZ93230.1| RNA polymerase, sigma 32 subunit, RpoH [Marinomonas mediterranea
           MMB-1]
          Length = 288

 Score =  181 bits (459), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 112/271 (41%), Positives = 161/271 (59%), Gaps = 13/271 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+  +  IP+L  +EE  LA+R    GDL AA  LV SHLR VV IA  Y GYGL  
Sbjct: 17  LESYVQGVSTIPILTAEEEQKLAERLYYDGDLEAARALVMSHLRFVVHIAKSYSGYGLSQ 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++V EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+IL++W +VK+ TT  Q+++
Sbjct: 77  GDLVQEGNVGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEFILKNWRIVKVATTKAQRKM 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR  K  L  + ++     +V A+A  L VS   V  M  R++  + +     + D 
Sbjct: 137 FFNLRSAKKTLSWLNNS-----EVDAVANDLGVSPDVVRQMEGRMSSTD-MAFDATTDDD 190

Query: 196 NSSQWQDWLVYDHDGQ--EQVLIEK---EERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           + S +Q    Y  DG+    +L+E    E   NRR  L ++MS L+ R R I   R L E
Sbjct: 191 DDSAFQAPASYLEDGRYDPAMLLEDGNWEADSNRR--LQQAMSDLDERSRNILVQRWLSE 248

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           N  TL +L+ E+ VS ER+RQ+E  A KK++
Sbjct: 249 NKSTLHDLADEYGVSAERIRQLEKNAMKKIR 279


>gi|56415467|ref|YP_152542.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. ATCC 9150]
 gi|197364396|ref|YP_002144033.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. AKU_12601]
 gi|56129724|gb|AAV79230.1| RNA polymerase sigma-32 factor [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. ATCC 9150]
 gi|197095873|emb|CAR61447.1| RNA polymerase sigma-32 factor [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. AKU_12601]
          Length = 284

 Score =  181 bits (459), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 115/298 (38%), Positives = 165/298 (55%), Gaps = 33/298 (11%)

Query: 4   KNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           K M  +    +G L  YI      PML   EE  LA+R    GDL AA  L+ SHLR VV
Sbjct: 3   KEMQNLALAPVGNLESYIRAANAWPMLSADEERALAERLHYQGDLEAAKTLILSHLRFVV 62

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W 
Sbjct: 63  HIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWR 122

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+A 
Sbjct: 123 IVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVEMVARELGVSSKDVREMESRMAA 177

Query: 183 DE--------------SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            +               +  ++   DK SS + D  + D + +EQ            N L
Sbjct: 178 QDMTFDMSSDDESDSQPMAPVLYLQDK-SSNFADG-IEDDNWEEQAA----------NRL 225

Query: 229 TRSMSVLNPRERRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           T +M  L+ R + I  AR L E N  TL+ L+  + VS ERVRQ+E  A KK++ +I+
Sbjct: 226 TDAMQGLDERSQDIIRARWLDEDNKSTLQELADRYGVSVERVRQLEKNAMKKLRAAIE 283


>gi|49476176|ref|YP_034217.1| RNA polymerase factor sigma-32 [Bartonella henselae str. Houston-1]
 gi|49238984|emb|CAF28284.1| RNA polymerase sigma-32 factor [Bartonella henselae str. Houston-1]
          Length = 303

 Score =  181 bits (458), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 99/261 (37%), Positives = 169/261 (64%), Gaps = 5/261 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE+Q+E+ LA R+++  D  A H++  +H+RLV+ IA  ++ + +P+ ++V EG +GL
Sbjct: 34  PYLERQKEHDLALRWKDKRDDEAMHQIAAAHMRLVIAIANRFKRFKMPLGDLVQEGYVGL 93

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +F+P+R  R +TY+ WWI+A++Q+YILR+WS+V+ GT+++QK LFFNLRRL+  L
Sbjct: 94  LEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSSQKALFFNLRRLRAKL 153

Query: 147 QAITDNNLKPEQVV--AIAKKLNVSESEVISMNCRLAGDESLNALINSSD-KNSSQWQDW 203
             + D++   +Q +  +IA+KL VS  +V +M+ R +  ++  ++  S +  N     D 
Sbjct: 154 --VQDDSALSKQDIFRSIAEKLGVSVRDVETMDFRFSSSDNSLSVSVSENSDNPVAKMDA 211

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           LV D    + ++ +  + + R   L  ++ +LN RE  I   RRL E   TLE L  +  
Sbjct: 212 LVDDSPLPDALIEQVIDGQRRTQWLYDALQILNERELEIIRFRRLNEEGATLEVLGEKLG 271

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ERVRQIEARA +K++ ++
Sbjct: 272 ISKERVRQIEARALQKLRSAL 292


>gi|85058065|ref|YP_453767.1| RNA polymerase factor sigma-32 [Sodalis glossinidius str.
           'morsitans']
 gi|84778585|dbj|BAE73362.1| RNA polymerase sigma-32 factor RpoH [Sodalis glossinidius str.
           'morsitans']
          Length = 285

 Score =  181 bits (458), Expect = 1e-43,   Method: Compositional matrix adjust.
 Identities = 108/287 (37%), Positives = 161/287 (56%), Gaps = 10/287 (3%)

Query: 4   KNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           KNM ++     G L  Y+      PML  +EE  LA+R    GDL AA +L+ SHLR VV
Sbjct: 3   KNMQVLAYVPQGSLEAYVRAANAYPMLTAEEERALAERLHYQGDLEAAKKLILSHLRFVV 62

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W 
Sbjct: 63  HIARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWR 122

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L          ++V  +AK+L V+  +V  M  R+A 
Sbjct: 123 IVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVEMVAKELGVTSKDVREMESRMAA 177

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNPRE 239
            +         +    Q    ++Y  D         EE     +  + L+ ++  L+ R 
Sbjct: 178 QDMTFDPTPEDEAREGQPMAPMLYLQDKSSDFADGIEEDNWDDHAADKLSAALEGLDERS 237

Query: 240 RRIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + I  AR L  +N  TL+ L+  + VS ERVRQ+E  A KK++  I+
Sbjct: 238 QDIIRARWLDDDNKSTLQELADRYGVSAERVRQLEKNAMKKMRLVIE 284


>gi|28867660|ref|NP_790279.1| RNA polymerase sigma-32 factor [Pseudomonas syringae pv. tomato
           str. DC3000]
 gi|213967796|ref|ZP_03395943.1| RNA polymerase sigma-32 factor [Pseudomonas syringae pv. tomato T1]
 gi|301382433|ref|ZP_07230851.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. tomato
           Max13]
 gi|302061175|ref|ZP_07252716.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. tomato
           K40]
 gi|302132032|ref|ZP_07258022.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. tomato
           NCPPB 1108]
 gi|28850895|gb|AAO53974.1| RNA polymerase sigma-32 factor [Pseudomonas syringae pv. tomato
           str. DC3000]
 gi|213927572|gb|EEB61120.1| RNA polymerase sigma-32 factor [Pseudomonas syringae pv. tomato T1]
 gi|330965442|gb|EGH65702.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. actinidiae
           str. M302091]
 gi|331014973|gb|EGH95029.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. lachrymans
           str. M302278PT]
          Length = 284

 Score =  181 bits (458), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 107/273 (39%), Positives = 159/273 (58%), Gaps = 9/273 (3%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+H +  IP+L  + E  LA+      DL AA ++V +HLR VV IA  Y GYGL 
Sbjct: 16  NLEAYVHTVNSIPLLTPERERELAESLYYEQDLDAARQMVLAHLRFVVHIARSYSGYGLA 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++
Sbjct: 76  QADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSS 193
           LFFNLR  K  L  +  NN   ++V  +A+ L V   EV  M  RL G D + +    + 
Sbjct: 136 LFFNLRSQKKRLAWL--NN---DEVHRVAESLGVEPREVREMESRLTGHDMAFDPAAEAD 190

Query: 194 DKNSSQWQDWLVYDH--DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           D ++ Q     + DH  D   Q L + +   N    L +++ VL+ R R I   R L E 
Sbjct: 191 DDSAFQSPANYLEDHRYDPARQ-LEDADWTDNSTANLHQALDVLDERSRDILYQRWLAEE 249

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL +L+ ++ VS ER+RQ+E  A  K++ SI
Sbjct: 250 KATLHDLAQKYNVSAERIRQLEKSAMNKLKTSI 282


>gi|188535384|ref|YP_001909181.1| RNA polymerase factor sigma-32 [Erwinia tasmaniensis Et1/99]
 gi|188030426|emb|CAO98320.1| RNA polymerase sigma-32 factor [Erwinia tasmaniensis Et1/99]
          Length = 284

 Score =  180 bits (457), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 108/286 (37%), Positives = 163/286 (56%), Gaps = 9/286 (3%)

Query: 4   KNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           K M  +    +G L  YI      PML  +EE  LA+R    GDL AA  L+ SHLR VV
Sbjct: 3   KEMQTLAIAPLGNLDSYIRAANARPMLTAEEEKALAERLHYQGDLEAAKTLILSHLRFVV 62

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W 
Sbjct: 63  HVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWR 122

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+A 
Sbjct: 123 IVKVATTKAQRKLFFNLRKAKQRL-----GWFNQDEVEMVARELGVSSKDVREMESRMAA 177

Query: 183 -DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPRER 240
            D + +   +   +  S      + D        IE++  ++   + L  +M  L+ R +
Sbjct: 178 QDMTFDPAPDDEGEGRSMAPMLYLQDKSSDFANGIEEDNWEDHAADKLNDAMQGLDERSQ 237

Query: 241 RIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            I  AR L  +N  TL+ L+  + VS ERVRQ+E  A KK++ +I+
Sbjct: 238 HIIRARWLDDDNKTTLQELADRYGVSAERVRQLEKNAMKKLRVAIE 283


>gi|168235161|ref|ZP_02660219.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. SL480]
 gi|194737973|ref|YP_002116503.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. CVM19633]
 gi|194713475|gb|ACF92696.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. CVM19633]
 gi|197291332|gb|EDY30684.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. SL480]
          Length = 284

 Score =  180 bits (457), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 114/298 (38%), Positives = 165/298 (55%), Gaps = 33/298 (11%)

Query: 4   KNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           K M  +    +G L  YI      PML   EE  LA+R    GDL AA  L+ SHLR VV
Sbjct: 3   KEMQNLALAPVGNLESYIRAANAWPMLSADEERALAERLHYQGDLEAAKTLILSHLRFVV 62

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W 
Sbjct: 63  HIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWR 122

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+A 
Sbjct: 123 IVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVEMVARELGVSSKDVREMESRMAA 177

Query: 183 DE--------------SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            +               +  ++   DK SS + D  + D + +EQ            N L
Sbjct: 178 QDMTFDMSSDDESDSQPMAPVLYLQDK-SSNFADG-IEDDNWEEQAA----------NRL 225

Query: 229 TRSMSVLNPRERRIFEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           T +M  L+ R + I  AR L E+   TL+ L+  + VS ERVRQ+E  A KK++ +I+
Sbjct: 226 TDAMQGLDERSQDIIRARWLDEDTKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIE 283


>gi|49474699|ref|YP_032741.1| RNA polymerase factor sigma-32 [Bartonella quintana str. Toulouse]
 gi|49240203|emb|CAF26671.1| RNA polymerase sigma-32 factor [Bartonella quintana str. Toulouse]
          Length = 303

 Score =  180 bits (457), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 99/261 (37%), Positives = 167/261 (63%), Gaps = 5/261 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE+Q+E+ LA R+++  D  A H++  +H+RLV+ IA  ++ + +P+ ++V EG +GL
Sbjct: 34  PYLERQKEHDLALRWKDKRDDDAMHQIAAAHMRLVIAIANRFKRFKMPLGDLVQEGYVGL 93

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +F+P+R  R +TY+ WWI+A++Q+YILR+WS+V+ GT+++QK LFFNLRRL+  L
Sbjct: 94  LEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSSQKALFFNLRRLRAKL 153

Query: 147 QAITDNNLKPEQVV--AIAKKLNVSESEVISMNCRLAGDESLNALINSSD-KNSSQWQDW 203
             + D+N   +Q +   IA++L VS  +V +M+ R +  ++  ++  S +  N     D 
Sbjct: 154 --VQDDNALTKQDIFRTIAERLGVSVRDVETMDFRFSSSDNSLSVSVSENSDNPIAKMDA 211

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           LV D    + ++ +  + + R   L  ++  LN RE  I   RRL E   TLE L  +  
Sbjct: 212 LVDDSPLPDALIEQVIDSQRRTQWLHDALQSLNERELEIIRFRRLNEEGATLEVLGEKLG 271

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ERVRQIEARA +K++ ++
Sbjct: 272 ISKERVRQIEARALQKLRSAL 292


>gi|288287|emb|CAA39117.1| unnamed protein product [Myxococcus xanthus]
          Length = 246

 Score =  180 bits (456), Expect = 2e-43,   Method: Compositional matrix adjust.
 Identities = 99/233 (42%), Positives = 145/233 (62%), Gaps = 4/233 (1%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           +VT++LR VVK+A  YR YG+ +S+++ EGNIGLM+AV+KFDP++G RL +Y++WWI+A 
Sbjct: 1   MVTANLRFVVKVAYEYRSYGIKMSDLIQEGNIGLMKAVQKFDPDKGIRLISYAVWWIRAY 60

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +Q YIL+SWSLVK+GTT    +LFF+L R +  L+     +     V  IA++L+V   E
Sbjct: 61  IQNYILKSWSLVKLGTTQAHGKLFFSLARTRRELEKFGSGD-AAVNVDDIARRLHVKPGE 119

Query: 173 VISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           V  M  R+ G D SL+A +     NS    D++V     Q+    +KEE       +  +
Sbjct: 120 VREMEQRMGGRDLSLDAPMGEDGGNSH--VDFVVSAAAPQDDEFADKEEAGLINARVRTA 177

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +  L+PRER I E R + E P+TL+ L   F  SRER RQ+E RA  K++  +
Sbjct: 178 LMRLDPRERFIIEQRVMNERPMTLKELGEHFGFSRERARQLEIRAKDKLKSEL 230


>gi|320539367|ref|ZP_08039036.1| RNA polymerase, sigma 32 (sigma H) factor [Serratia symbiotica str.
           Tucson]
 gi|320030492|gb|EFW12502.1| RNA polymerase, sigma 32 (sigma H) factor [Serratia symbiotica str.
           Tucson]
          Length = 285

 Score =  180 bits (456), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 104/289 (35%), Positives = 163/289 (56%), Gaps = 9/289 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  YI      PML  +EE  LA+R    GDL AA +L+ +HLR 
Sbjct: 1   MTKEMQTLALVPQGSLEAYIRAANTYPMLTAEEERDLAERLHYQGDLGAAKQLILAHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VAHIARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVELVARELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNP 237
           A  +         +    Q    ++Y  D       + EE     N  + L  ++  L+ 
Sbjct: 176 AAQDMTFDPAPDDETRDGQSLAPVLYLQDKSSDFAEDIEEDNWESNAADKLAYALEGLDE 235

Query: 238 RERRIFEARRLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           R + I  AR L  +N  TL+ L+ ++ VS ERVRQ+E  A KK++ +I+
Sbjct: 236 RSQHIIRARWLDNDNKSTLQELADQYGVSAERVRQLEKNAMKKLKMAIE 284


>gi|237728776|ref|ZP_04559257.1| RNA polymerase factor sigma-32 [Citrobacter sp. 30_2]
 gi|283835854|ref|ZP_06355595.1| alternative sigma factor RpoH [Citrobacter youngae ATCC 29220]
 gi|226909398|gb|EEH95316.1| RNA polymerase factor sigma-32 [Citrobacter sp. 30_2]
 gi|291068027|gb|EFE06136.1| alternative sigma factor RpoH [Citrobacter youngae ATCC 29220]
          Length = 284

 Score =  180 bits (456), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 113/287 (39%), Positives = 170/287 (59%), Gaps = 11/287 (3%)

Query: 4   KNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           K M  +    +G L  YI      PML   EE  LA++    GDL AA  L+ SHLR VV
Sbjct: 3   KEMQNLALAPVGNLESYIRAANAWPMLSADEERALAEKLHYQGDLEAAKTLILSHLRFVV 62

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W 
Sbjct: 63  HVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWR 122

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+A 
Sbjct: 123 IVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVEMVARELGVSSKDVREMESRMAA 177

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVL--IEKEERKNR-RNMLTRSMSVLNPRE 239
            + +   ++S D++ SQ    ++Y  D        IE++  +++  N LT +M  L+ R 
Sbjct: 178 -QDMTFDMSSDDESDSQPMAPVLYLQDKSSNFADGIEEDNWEDQAANKLTHAMEGLDERS 236

Query: 240 RRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + I  AR L E N  TL+ L+  + VS ERVRQ+E  A KK++ +I+
Sbjct: 237 QDIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIE 283


>gi|253991200|ref|YP_003042556.1| RNA polymerase factor sigma-32 [Photorhabdus asymbiotica subsp.
           asymbiotica ATCC 43949]
 gi|253782650|emb|CAQ85814.1| component of rna polymerase, sigma 32 factor [Photorhabdus
           asymbiotica]
          Length = 285

 Score =  179 bits (455), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 105/286 (36%), Positives = 166/286 (58%), Gaps = 11/286 (3%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           + ++++  G   L  YI      PML  +EE  LA+R    GDL AA +L+ SHLR VV 
Sbjct: 6   QTLALVPQG--SLEGYIRASNAYPMLTAEEEKELAERLHYQGDLDAAKKLILSHLRFVVH 63

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W +
Sbjct: 64  VARSYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRI 123

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VK+ TT  Q++LFFNLR+ K  L          ++V  +AK+L V+  +V  M  R++  
Sbjct: 124 VKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVEMVAKELGVTSKDVREMESRMSAQ 178

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVL--IEKEERKNR-RNMLTRSMSVLNPRER 240
           +    +    D    Q    ++Y  D        IE++  +N   + L+ ++  L+ R +
Sbjct: 179 DMAFDMSADDDNQEGQSVAPVLYLQDKASDFAGGIEEDNWENHAADKLSVAIEGLDERSQ 238

Query: 241 RIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            I   R L  +N  TL+ L+ ++ VS ERVRQ+E  A KK++ +I+
Sbjct: 239 DIIRCRWLDDDNKSTLQELADKYGVSAERVRQLEKNAMKKLRVAIE 284


>gi|37527948|ref|NP_931293.1| RNA polymerase factor sigma-32 [Photorhabdus luminescens subsp.
           laumondii TTO1]
 gi|36787384|emb|CAE16473.1| RNA polymerase sigma-32 factor [Photorhabdus luminescens subsp.
           laumondii TTO1]
          Length = 285

 Score =  179 bits (455), Expect = 3e-43,   Method: Compositional matrix adjust.
 Identities = 107/288 (37%), Positives = 171/288 (59%), Gaps = 15/288 (5%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           + ++++  G   L  Y+      PML  +EE  LA+R    GDL AA +L+ SHLR VV 
Sbjct: 6   QTLALVPQG--SLEGYVRASNTYPMLTAEEEKELAERLHYQGDLDAAKKLILSHLRFVVH 63

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W +
Sbjct: 64  VARSYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRI 123

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VK+ TT  Q++LFFNLR+ K  L          ++V  +AK+L V+  +V  M  R++  
Sbjct: 124 VKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVEMVAKELGVTSKDVREMESRMSAQ 178

Query: 184 ESLNALINSSDKNSSQWQDW--LVYDHDGQEQVL--IEKEERKNR-RNMLTRSMSVLNPR 238
           +   A   S+D +S + Q    ++Y  D        IE++  +N   + L+ ++  L+ R
Sbjct: 179 DM--AFDMSADDDSQEGQPVAPVLYLQDKASDFADGIEEDNWENHAADKLSVAIESLDER 236

Query: 239 ERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            + I   R L  +N  TL+ L+ ++ VS ERVRQ+E  A KK++ +I+
Sbjct: 237 SQDIIRCRWLDDDNKSTLQELADKYGVSAERVRQLEKNAMKKLRVAIE 284


>gi|197287411|ref|YP_002153283.1| RNA polymerase factor sigma-32 [Proteus mirabilis HI4320]
 gi|227358346|ref|ZP_03842687.1| RNA polymerase sigma-32 factor [Proteus mirabilis ATCC 29906]
 gi|194684898|emb|CAR47059.1| RNA polymerase sigma-32 factor [Proteus mirabilis HI4320]
 gi|227161682|gb|EEI46719.1| RNA polymerase sigma-32 factor [Proteus mirabilis ATCC 29906]
          Length = 284

 Score =  179 bits (455), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 110/288 (38%), Positives = 171/288 (59%), Gaps = 8/288 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  S+ +  +  +  YI      PML  +EE  LA+R    GDL AA  L+ SHLR 
Sbjct: 1   MTKEMQSLALVPQGSIEAYIRAANSYPMLTAEEEKELAERLHYEGDLEAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VIHVARSYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT +Q++LFFNLR+ K  L          ++V  +AK+L VSES+V  M  R+
Sbjct: 121 WRIVKVATTKSQRKLFFNLRKNKKRL-----GWFNQDEVELVAKELGVSESDVREMESRM 175

Query: 181 -AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPR 238
            A D + +   + SD +        + D        IE++   N   + LT ++  L+ R
Sbjct: 176 SAQDMAFDMSADDSDDSHPVAPVLFLEDKSSDFADGIEEDNWDNHAADRLTLAIKTLDER 235

Query: 239 ERRIFEARRLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            + I  AR L+ +N  TL+ L+ ++ VS ERVRQ+E  A KK++ +I+
Sbjct: 236 SQDIIRARWLEDDNKSTLQELADKYGVSAERVRQLEKNAMKKLRLAIE 283


>gi|302343327|ref|YP_003807856.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfarculus baarsii DSM
           2075]
 gi|301639940|gb|ADK85262.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfarculus baarsii DSM
           2075]
          Length = 346

 Score =  179 bits (455), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 109/276 (39%), Positives = 168/276 (60%), Gaps = 8/276 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL- 73
            L RY+ E R+ P+L ++EE  LA+R+ E  D  AA  LVTS+LRLVVKIAM ++ Y + 
Sbjct: 63  ALQRYLWEARQYPLLSREEEDALARRFVEEQDPEAAAMLVTSNLRLVVKIAMEHQRYWMR 122

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++ EGN+GL+QAV+KFDP RG + + Y+ +WIKA + ++I+ +W LV++GTT  Q+
Sbjct: 123 NLLDLIQEGNMGLLQAVQKFDPFRGIKFSYYASFWIKAYILKFIMDNWRLVRVGTTQAQR 182

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINS 192
           +LF+ LRR K  LQA     + P   + + ++L VSE +V+ M  RL   E SL+A +  
Sbjct: 183 KLFYKLRREKEKLQA---QGVTPGPRL-LGQRLGVSEKDVVDMEQRLDSWELSLDAPVR- 237

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            D +    ++ L       EQ L + E R+     L      L+ +E+ I + R L ENP
Sbjct: 238 -DDSDDTHKNLLPSPRPTAEQDLADSELRQLFHRKLMEFRQTLDDKEQDILDNRLLAENP 296

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            TL  +     VSRER+RQ++ R  +K+ E +Q+Q+
Sbjct: 297 QTLSEVGDRHGVSRERIRQLQVRLMEKLGEFMQEQI 332


>gi|87121174|ref|ZP_01077065.1| sigma factor RpoH [Marinomonas sp. MED121]
 gi|86163666|gb|EAQ64940.1| sigma factor RpoH [Marinomonas sp. MED121]
          Length = 291

 Score =  179 bits (454), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 109/273 (39%), Positives = 161/273 (58%), Gaps = 11/273 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  +  IP+L  ++E  LA+R    GDL AA +LV SHLR VV IA  Y GYGL  
Sbjct: 17  LESYIQAVSTIPILTAEDENKLAERLYYDGDLEAARQLVMSHLRFVVHIAKSYSGYGLNQ 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+IL++W +VK+ TT  Q+++
Sbjct: 77  GDLIQEGNVGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEFILKNWRIVKVATTKAQRKM 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSSD 194
           FFNLR  K  L   ++     ++V ++A  L VS   V  M  R+ + D + +A  +  D
Sbjct: 137 FFNLRSAKKTLSWFSN-----DEVESVAGDLGVSPEVVRQMEGRMSSSDTTFDASSDDDD 191

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEK---EERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
            ++ Q     + DH      L E    EE  NRR  L  +MS L+ R R I   R L ++
Sbjct: 192 DSAYQAPANYLEDHRYDPASLTENGNWEEDSNRR--LQEAMSELDERSRNILVQRWLSDS 249

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL +L+ E+ VS ER+RQ+E  A  K++ S+
Sbjct: 250 KSTLHDLADEYGVSAERIRQLEKNAMAKIRTSM 282


>gi|162454145|ref|YP_001616512.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
 gi|161164727|emb|CAN96032.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
          Length = 283

 Score =  179 bits (454), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 103/274 (37%), Positives = 166/274 (60%), Gaps = 7/274 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            +SRYI  +R+IP L ++EE  LA+R+R+HGD  AA  L  ++LR VV IA+ YR YG+P
Sbjct: 10  AVSRYITHVRQIPELSREEEVELARRWRDHGDEQAAAALALANLRHVVSIAISYRRYGIP 69

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           ++++++EGN G++ A++K+DP+RG R  TY+ +WI+A +  +++ SWSLV +G+   + +
Sbjct: 70  LADLIAEGNFGIVHAIRKYDPDRGNRFVTYAAYWIRAYILNHVIHSWSLVGVGSGPLRSK 129

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSS 193
           +FF LRR +  +  +     + +++  +A+K      +V+ M  RL A D SL+  +   
Sbjct: 130 MFFRLRRERARIAGLVGEGEEGDRL--LAEKFGAPAEKVLEMAHRLEARDVSLDTKVFED 187

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--EN 251
              S    D L  D   QE+     EE    R  LT+++  L+PRER I E R +   E 
Sbjct: 188 GARS--LVDTLPADDQDQEERFSRAEEGALLRERLTQAVENLDPRERYIVETRMMADPEE 245

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            ++L  +     VSRER RQ+EARA KK+++ +Q
Sbjct: 246 ELSLAEIGRRLGVSRERARQLEARAKKKLRDRLQ 279


>gi|192362020|ref|YP_001983950.1| RNA polymerase factor sigma-32 [Cellvibrio japonicus Ueda107]
 gi|190688185|gb|ACE85863.1| alternative sigma factor RpoH [Cellvibrio japonicus Ueda107]
          Length = 286

 Score =  179 bits (454), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 103/267 (38%), Positives = 158/267 (59%), Gaps = 6/267 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+  +    +L  +EE  LA+   ++G+L AA +LV +HLR VV IA  Y GYGLP+
Sbjct: 19  LNAYVQAVSSFAILSVEEEQQLARDLHDNGNLDAARKLVMAHLRFVVHIARSYNGYGLPL 78

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM+AVK+FDP++G RL ++++ WIKA + E+ILR+W +VKI TT  Q++L
Sbjct: 79  GDLIQEGNVGLMKAVKRFDPDKGVRLVSFAVHWIKAEIHEFILRNWRIVKIATTKAQRKL 138

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR  K  L  +++     ++  A+A  L V   +V  M  RLA  D   +A  +  D
Sbjct: 139 FFNLRGAKKRLAWLSN-----DEAEAVALDLGVDVKQVREMEGRLASYDAGFDASDDDED 193

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
            N     ++L  +       L E    +   N L  +M  L+ R R I + R L ++  T
Sbjct: 194 DNYVAPANYLEDNRYDPAARLEEANWEEASVNGLEMAMEKLDDRSRVILQRRWLNDDKAT 253

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQ 281
           L +L++E+ VS ER+RQ+E  A  KV+
Sbjct: 254 LHDLAAEYGVSAERIRQLEKNAMNKVK 280


>gi|325275633|ref|ZP_08141532.1| RNA polymerase factor sigma-32 [Pseudomonas sp. TJI-51]
 gi|313501084|gb|ADR62450.1| RpoH [Pseudomonas putida BIRD-1]
 gi|324099220|gb|EGB97167.1| RNA polymerase factor sigma-32 [Pseudomonas sp. TJI-51]
          Length = 284

 Score =  179 bits (454), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 104/271 (38%), Positives = 157/271 (57%), Gaps = 7/271 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+H +  IP+L  ++E  L +R     D+ AA ++V +HLR VV IA  Y GYGL  
Sbjct: 17  LEAYVHTVNSIPLLTVEQERDLGERLYYQQDVEAARQMVMAHLRFVVHIARSYAGYGLAQ 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++L
Sbjct: 77  ADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRKL 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR  K  L  +  NN   ++V  +A+ L V   EV  M  RL+G D + +    + D
Sbjct: 137 FFNLRSQKKRLAWL--NN---DEVHRVAESLGVEPREVREMESRLSGQDMAFDPAAEADD 191

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
            ++ Q     + DH     V +E  +   N  + L  ++  L+ R R I   R L E   
Sbjct: 192 DSAFQSPAHYLEDHRYDPAVQLEDADWSDNSTSNLHEALQGLDERSRDILYQRWLAEEKA 251

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           TL  L+ ++ VS ER+RQ+E  A  KV+  I
Sbjct: 252 TLHELADKYSVSAERIRQLEKNAMNKVKALI 282


>gi|157149048|ref|YP_001456366.1| RNA polymerase factor sigma-32 [Citrobacter koseri ATCC BAA-895]
 gi|157086253|gb|ABV15931.1| hypothetical protein CKO_04887 [Citrobacter koseri ATCC BAA-895]
          Length = 284

 Score =  179 bits (454), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 112/287 (39%), Positives = 170/287 (59%), Gaps = 11/287 (3%)

Query: 4   KNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           K M  +    +G L  YI      PML   EE  LA++    GDL AA  L+ SHLR VV
Sbjct: 3   KEMQNLALAPVGNLESYIRAANAWPMLSADEERALAEKLHYQGDLEAAKTLILSHLRFVV 62

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W 
Sbjct: 63  HVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWR 122

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L V+  +V  M  R+A 
Sbjct: 123 IVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVEMVARELGVTSKDVREMESRMAA 177

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVL--IEKEERKNR-RNMLTRSMSVLNPRE 239
            + +   ++S D++ SQ    ++Y  D        IE++  +++  N LT +M  L+ R 
Sbjct: 178 -QDMTFDMSSDDESDSQPMAPVLYLQDKTSNFADGIEEDNWEDQAANKLTHAMEGLDERS 236

Query: 240 RRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + I  AR L E N  TL+ L+  + VS ERVRQ+E  A KK++ +I+
Sbjct: 237 QDIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIE 283


>gi|104779584|ref|YP_606082.1| RNA polymerase factor sigma-32 [Pseudomonas entomophila L48]
 gi|95108571|emb|CAK13265.1| sigma H (sigma 32) factor of RNA polymerase RpoH [Pseudomonas
           entomophila L48]
          Length = 284

 Score =  179 bits (453), Expect = 5e-43,   Method: Compositional matrix adjust.
 Identities = 104/271 (38%), Positives = 157/271 (57%), Gaps = 7/271 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+H +  IP+L  ++E  L +R     DL AA ++V +HLR VV IA  Y GYGL  
Sbjct: 17  LEAYVHTVNSIPLLTPEQERDLGERLYYEQDLEAARQMVMAHLRFVVHIARSYAGYGLAQ 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++L
Sbjct: 77  ADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRKL 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR  K  L  +  NN   ++V  +A+ L V   EV  M  RL+G D + +    + D
Sbjct: 137 FFNLRSQKKRLAWL--NN---DEVHRVAESLGVEPREVREMESRLSGQDMAFDPASEADD 191

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
            ++ Q     + DH     + +E  +   N  + L  ++  L+ R R I   R L E   
Sbjct: 192 DSAFQSPAHYLEDHRYDPALQLEDADWSDNSSSNLHEALQGLDDRSRDILYQRWLAEEKA 251

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           TL  L+ ++ VS ER+RQ+E  A  KV+  I
Sbjct: 252 TLHELAEKYSVSAERIRQLEKNAMNKVKALI 282


>gi|148550183|ref|YP_001270285.1| RNA polymerase factor sigma-32 [Pseudomonas putida F1]
 gi|148514241|gb|ABQ81101.1| RNA polymerase, sigma 32 subunit, RpoH [Pseudomonas putida F1]
          Length = 284

 Score =  179 bits (453), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 104/271 (38%), Positives = 157/271 (57%), Gaps = 7/271 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+H +  IP+L  ++E  L +R     D+ AA ++V +HLR VV IA  Y GYGL  
Sbjct: 17  LEAYVHTVNSIPLLTVEQERDLGERLYYEQDVEAARQMVMAHLRFVVHIARSYAGYGLAQ 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++L
Sbjct: 77  ADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRKL 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR  K  L  +  NN   ++V  +A+ L V   EV  M  RL+G D + +    + D
Sbjct: 137 FFNLRSQKKRLAWL--NN---DEVHRVAESLGVEPREVREMESRLSGQDMAFDPAAEADD 191

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
            ++ Q     + DH     V +E  +   N  + L  ++  L+ R R I   R L E   
Sbjct: 192 DSAFQSPAHYLEDHRYDPAVQLEDADWSDNSTSNLHEALQGLDERSRDILYQRWLAEEKA 251

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           TL  L+ ++ VS ER+RQ+E  A  KV+  I
Sbjct: 252 TLHELADKYSVSAERIRQLEKNAMNKVKALI 282


>gi|167036147|ref|YP_001671378.1| RNA polymerase factor sigma-32 [Pseudomonas putida GB-1]
 gi|166862635|gb|ABZ01043.1| RNA polymerase, sigma 32 subunit, RpoH [Pseudomonas putida GB-1]
          Length = 284

 Score =  179 bits (453), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 104/271 (38%), Positives = 157/271 (57%), Gaps = 7/271 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+H +  IP+L  ++E  L +R     D+ AA ++V +HLR VV IA  Y GYGL  
Sbjct: 17  LEAYVHTVNSIPLLTVEQERDLGERLYYEQDVEAARQMVMAHLRFVVHIARSYAGYGLAQ 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++L
Sbjct: 77  ADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRKL 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR  K  L  +  NN   ++V  +A+ L V   EV  M  RL+G D + +    + D
Sbjct: 137 FFNLRSQKKRLAWL--NN---DEVHRVAESLGVEPREVREMESRLSGQDMAFDPAAEADD 191

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
            ++ Q     + DH     V +E  +   N  + L  ++  L+ R R I   R L E   
Sbjct: 192 DSAFQSPAHYLEDHRYDPAVQLEDADWSDNSASNLHEALQGLDERSRDILYQRWLAEEKA 251

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           TL  L+ ++ VS ER+RQ+E  A  KV+  I
Sbjct: 252 TLHELADKYSVSAERIRQLEKNAMNKVKALI 282


>gi|26991784|ref|NP_747209.1| RNA polymerase factor sigma-32 [Pseudomonas putida KT2440]
 gi|8885996|gb|AAF80334.1|AF157048_1 heat shock sigma factor RpoH [Pseudomonas putida]
 gi|24986895|gb|AAN70673.1|AE016711_1 RNA polymerase sigma-32 factor [Pseudomonas putida KT2440]
          Length = 284

 Score =  179 bits (453), Expect = 6e-43,   Method: Compositional matrix adjust.
 Identities = 104/271 (38%), Positives = 157/271 (57%), Gaps = 7/271 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+H +  IP+L  ++E  L +R     D+ AA ++V +HLR VV IA  Y GYGL  
Sbjct: 17  LEAYVHTVNSIPLLTVEQERDLGERLYYEQDVEAARQMVMAHLRFVVHIARSYAGYGLAQ 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++L
Sbjct: 77  ADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRKL 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR  K  L  +  NN   ++V  +A+ L V   EV  M  RL+G D + +    + D
Sbjct: 137 FFNLRSQKKRLAWL--NN---DEVHRVAESLGVEPREVREMESRLSGQDMAFDPAAEADD 191

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
            ++ Q     + DH     V +E  +   N  + L  ++  L+ R R I   R L E   
Sbjct: 192 DSAFQSPAHYLEDHRYDPAVQLEDADWSDNSTSNLHEALQGLDERSRDILYQRWLAEEKA 251

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           TL  L+ ++ VS ER+RQ+E  A  KV+  I
Sbjct: 252 TLHELADKYSVSAERIRQLEKNAMNKVKALI 282


>gi|94987055|ref|YP_594988.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Lawsonia intracellularis PHE/MN1-00]
 gi|94731304|emb|CAJ54667.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Lawsonia intracellularis PHE/MN1-00]
          Length = 385

 Score =  178 bits (452), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 102/276 (36%), Positives = 171/276 (61%), Gaps = 7/276 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGL 73
            L  Y+ E+ + PML+ +EE  LA+  ++ G   AA RL++SHLRLVVKIAM + R +  
Sbjct: 105 SLQLYLREVSRFPMLKPEEELRLAQDVQKKGCSKAAFRLISSHLRLVVKIAMDFQRRWMQ 164

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++ EGN+GLM+AV KFDP++G + + Y+ +WI+A + ++I+ +W +VKIGTT  Q+
Sbjct: 165 NVLDLIQEGNVGLMRAVNKFDPDKGIKFSYYAAFWIRAYILKFIMDNWRMVKIGTTQAQR 224

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINS 192
           +LF+NL R +  L A       P+   ++A +L V E ++I M  RL A D SL+  +  
Sbjct: 225 KLFYNLNRERQKLLA---EGFDPD-TSSLALRLGVGEEQIIEMQQRLDASDMSLDVTVGE 280

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
              N+S+  D+L   + G E+ L  +E     ++ +   + +L+ +E  I   R L ++P
Sbjct: 281 ETGNASRI-DFLPAINPGIEESLAGQEIAILLQDRIKDILPLLSEKEVYILHNRLLTDDP 339

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           VTL  +  ++ V+RERVRQ+EAR  +K++  + +Q+
Sbjct: 340 VTLREIGEKYSVTRERVRQLEARLLQKLRTHLSRQI 375


>gi|259910110|ref|YP_002650466.1| RNA polymerase factor sigma-32 [Erwinia pyrifoliae Ep1/96]
 gi|224965732|emb|CAX57264.1| RNA polymerase sigma-32 factor [Erwinia pyrifoliae Ep1/96]
 gi|283480207|emb|CAY76123.1| RNA polymerase sigma-32 factor [Erwinia pyrifoliae DSM 12163]
 gi|310765698|gb|ADP10648.1| RNA polymerase factor sigma-32 [Erwinia sp. Ejp617]
          Length = 284

 Score =  178 bits (452), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 107/286 (37%), Positives = 163/286 (56%), Gaps = 9/286 (3%)

Query: 4   KNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           K M  +    +G L  YI      PML  +EE  LA+R    G L AA  L+ SHLR VV
Sbjct: 3   KEMQTLAIAPLGNLDSYIRAANAWPMLTAEEEKALAERLHYQGCLEAAKTLILSHLRFVV 62

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W 
Sbjct: 63  HVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWR 122

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+A 
Sbjct: 123 IVKVATTKAQRKLFFNLRKAKQRL-----GWFNQDEVEMVARELGVSSKDVREMESRMAA 177

Query: 183 -DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPRER 240
            D + +   +   +  S      + D        IE++  ++   + L  +M  L+ R +
Sbjct: 178 QDMTFDPTPDDEGEGRSMAPMLYLQDKSSDFANGIEEDNWEDHAADKLNDAMQGLDERSQ 237

Query: 241 RIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            I  AR L  +N  TL+ L+ ++ VS ERVRQ+E  A KK++ +I+
Sbjct: 238 HIIRARWLDDDNKTTLQELADQYGVSAERVRQLEKNAMKKLRVAIE 283


>gi|301644085|ref|ZP_07244098.1| alternative sigma factor RpoH [Escherichia coli MS 146-1]
 gi|301077566|gb|EFK92372.1| alternative sigma factor RpoH [Escherichia coli MS 146-1]
          Length = 283

 Score =  178 bits (452), Expect = 7e-43,   Method: Compositional matrix adjust.
 Identities = 103/286 (36%), Positives = 164/286 (57%), Gaps = 12/286 (4%)

Query: 4   KNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           K MS++    +G L  YI      PML ++EE  LA   + H DL AA +L+ SHLR V+
Sbjct: 3   KEMSVL--APVGNLDSYIRAAYACPMLSQEEEQQLASNLQIHDDLDAAKQLILSHLRFVI 60

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA  Y GYGLP ++++ EGNIGLM+AV++F+P+ G RL ++++ W+K+ + EY+LR+W 
Sbjct: 61  HIARQYSGYGLPQADLIQEGNIGLMKAVRRFNPDVGVRLVSFAVHWVKSEIHEYVLRNWR 120

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R++ 
Sbjct: 121 IVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVDMVARELGVSVKDVREMESRMSA 175

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQV--LIEKEE-RKNRRNMLTRSMSVLNPRE 239
            +    +    + ++       +Y  D       +IE++       + L  +M  L+PR 
Sbjct: 176 QDMAYDIYPDDETDTHHPVSPSLYLQDKSSDFAGMIEEDNWDAQATDHLVAAMETLDPRS 235

Query: 240 RRIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + I  AR L  +N  TL  L+  + +S ERVRQ+E  A KK++ +I
Sbjct: 236 QDIIRARWLDDDNKATLHELAERYGISAERVRQLENNAMKKLRSAI 281


>gi|94499830|ref|ZP_01306366.1| RNA polymerase sigma-32 factor RpoH [Oceanobacter sp. RED65]
 gi|94428031|gb|EAT13005.1| RNA polymerase sigma-32 factor RpoH [Oceanobacter sp. RED65]
          Length = 288

 Score =  177 bits (450), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 105/272 (38%), Positives = 156/272 (57%), Gaps = 7/272 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y++ I  I +L  +EE  LA R     DL AA RLV SHLR VV IA  Y GYGL  
Sbjct: 19  LDGYLNAIGGIAVLSAEEERELADRLYYESDLEAARRLVLSHLRFVVHIAKSYNGYGLNQ 78

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           S+++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+IL++W +VK+ TT  Q++L
Sbjct: 79  SDLIQEGNVGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEFILKNWRIVKVATTKAQRKL 138

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR  K       +  L   +   IA+ L VS  EV  M  RL+  D + ++ +   +
Sbjct: 139 FFNLRSAKKR-----NGWLNEAEAHKIAEDLGVSAKEVYEMEGRLSSHDSTFDSPVADDE 193

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
            ++ Q     + DH     + +E E   ++    L  ++  L+ R + I   R L E+  
Sbjct: 194 DSAYQAPANYLEDHSFDPALAVENENYEQDSTARLQDALVQLDDRSKDILMRRWLGEHKA 253

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           TL  L+ E+ VS ER+RQ+E  A KK++  I+
Sbjct: 254 TLHELADEYGVSAERIRQLEKNAMKKIKGMIE 285


>gi|256829638|ref|YP_003158366.1| RNA polymerase sigma-32 subunit RpoH [Desulfomicrobium baculatum
           DSM 4028]
 gi|256578814|gb|ACU89950.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfomicrobium baculatum
           DSM 4028]
          Length = 356

 Score =  177 bits (450), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 102/279 (36%), Positives = 168/279 (60%), Gaps = 6/279 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLP 74
           L  Y+ EI+K   LE+ EE+ LA+RYR+  +  AA  L+TS+LRLVVKIAM + R +   
Sbjct: 76  LHIYLQEIKKFKPLEQDEEFDLARRYRDEKEEQAAFILITSNLRLVVKIAMDFQRRWMKN 135

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++ EGN+GLM+AV+KFDP++G + + Y+ +WIKA + ++I+ +W +VKIGTT  Q++
Sbjct: 136 VLDLIQEGNVGLMKAVQKFDPDKGIKFSYYASFWIKAYILKFIMDNWRMVKIGTTQAQRK 195

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           LF+NL + +  LQA       P     ++K L VSE++++ M  RL G   ++  +   D
Sbjct: 196 LFYNLGKERQRLQA---QGFDP-TTSTLSKNLQVSEADIVEMGQRL-GQHDVSLDMKIGD 250

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
            +S    D++     G E+ +   E      + +      LN +E  I E R L ++P+T
Sbjct: 251 DSSFTPMDFIPALEAGIEEQMAADEISVLIHDNIDAIRDGLNEKELDILEQRLLADSPIT 310

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           L  +  ++ ++RERVRQIEAR  +K++  +   ++  SS
Sbjct: 311 LREIGDKYGITRERVRQIEARLLQKIKAQMSSTIQDFSS 349


>gi|66047972|ref|YP_237813.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. syringae
           B728a]
 gi|237802354|ref|ZP_04590815.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. oryzae
           str. 1_6]
 gi|63258679|gb|AAY39775.1| Sigma-70 region 2:Sigma-70 region 4 [Pseudomonas syringae pv.
           syringae B728a]
 gi|330957082|gb|EGH57342.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. maculicola
           str. ES4326]
 gi|330970950|gb|EGH71016.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. aceris
           str. M302273PT]
 gi|331025211|gb|EGI05267.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. oryzae
           str. 1_6]
          Length = 284

 Score =  177 bits (450), Expect = 1e-42,   Method: Compositional matrix adjust.
 Identities = 106/273 (38%), Positives = 158/273 (57%), Gaps = 9/273 (3%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+  +  IP+L  + E  LA+      DL AA ++V +HLR VV IA  Y GYGL 
Sbjct: 16  NLEAYVQTVNSIPLLTPERERELAESLYYEQDLDAARQMVLAHLRFVVHIARSYSGYGLA 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++
Sbjct: 76  QADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSS 193
           LFFNLR  K  L  +  NN   ++V  +A+ L V   EV  M  RL G D + +    + 
Sbjct: 136 LFFNLRSQKKRLAWL--NN---DEVHRVAESLGVEPREVREMESRLTGHDMAFDPAAEAD 190

Query: 194 DKNSSQWQDWLVYDH--DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           D ++ Q     + DH  D   Q L + +   N    L +++ VL+ R R I   R L E 
Sbjct: 191 DDSAFQSPANYLEDHRYDPARQ-LEDSDWTDNSTANLHQALDVLDERSRDILYQRWLAEE 249

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL +L+ ++ VS ER+RQ+E  A  K++ SI
Sbjct: 250 KATLHDLAQKYNVSAERIRQLEKSAMNKLKTSI 282


>gi|5821404|dbj|BAA83808.1| sigma factor 32 [Pseudomonas putida]
          Length = 284

 Score =  177 bits (449), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 104/271 (38%), Positives = 156/271 (57%), Gaps = 7/271 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+H +  IP+L  ++E  L +R     D+ AA ++V +HLR VV IA  Y GYGL  
Sbjct: 17  LEAYVHTVNSIPLLTVEQERDLGERLYYEQDVEAARQMVMAHLRFVVHIARSYAGYGLAQ 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++L
Sbjct: 77  ADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIPEFILRNWRIVKVATTKAQRKL 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR  K  L  +  NN   ++V  +A+ L V   EV  M  RL+G D + +    + D
Sbjct: 137 FFNLRSQKKRLAWL--NN---DEVHRVAESLGVEPREVREMESRLSGQDMAFDPAAEADD 191

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
            ++ Q     + DH     V +E  +   N  + L  ++   N R R I   R L E   
Sbjct: 192 DSAFQSPAHYLEDHRYDPAVQLEDADWSDNSTSNLHEALQGWNERSRDILYQRWLAEEKA 251

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           TL  L+ ++ VS ER+RQ+E  A  KV+  I
Sbjct: 252 TLHELADKYSVSAERIRQLEKNAMNKVKALI 282


>gi|133470|sp|P19433|RPSB_MYXXA RecName: Full=RNA polymerase sigma-B factor
          Length = 246

 Score =  177 bits (449), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 98/233 (42%), Positives = 144/233 (61%), Gaps = 4/233 (1%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           +VT++LR VVK+A  YR YG+ +S+++ EGNIGLM+AV+KFDP++G RL +Y++WWI+A 
Sbjct: 1   MVTANLRFVVKVAYEYRSYGIKMSDLIQEGNIGLMKAVQKFDPDKGIRLISYAVWWIRAY 60

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +Q YIL+SWSLVK+GTT    +LFF+L R +  L+     +     V  IA++L+V   E
Sbjct: 61  IQNYILKSWSLVKLGTTQAHGKLFFSLARTRRELEKFGSGD-AAVNVDDIARRLHVKPGE 119

Query: 173 VISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           V  M  R+ G D SL+A +     NS    D++V     Q+    +KEE       +  +
Sbjct: 120 VREMEQRMGGRDLSLDAPMGEDGGNSH--VDFVVSAAAPQDDEFADKEEAGLINARVRAA 177

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +  L+PRE  I E R + E P+TL+ L   F  SRER RQ+E RA  K++  +
Sbjct: 178 LMRLDPREPFIIEQRVMNERPMTLKELGEHFGFSRERARQLEIRAKDKLKSEL 230


>gi|146344240|ref|YP_001202096.1| putative RNA polymerase sigma-32 factor [Pseudomonas fluorescens
           SBW25]
 gi|146188052|emb|CAM96382.1| putative RNA polymerase sigma-32 factor [Pseudomonas fluorescens
           SBW25]
          Length = 291

 Score =  177 bits (448), Expect = 2e-42,   Method: Compositional matrix adjust.
 Identities = 106/281 (37%), Positives = 159/281 (56%), Gaps = 13/281 (4%)

Query: 1   MNRKNMSIIVNGEI------GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLV 54
           MN   +S     +I       L  Y+  I  IP +  +EE  L++R  EH D+ AA  LV
Sbjct: 1   MNTSTLSTKAAAQIPMVPGSNLDAYLTVIHSIPNMSAEEERRLSERLVEHNDMDAARELV 60

Query: 55  TSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114
           TS LR VV IA  Y GYGLP+S+++ EGNIGL++AVK+F+P    RL T+ + WI+A + 
Sbjct: 61  TSQLRFVVHIARSYSGYGLPLSDLIQEGNIGLIKAVKRFNPAAQVRLITFGVHWIRAEIN 120

Query: 115 EYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVI 174
           E+I+R+  +V++ TT  Q++LFFNLR+     Q  + N L  ++   IA  LNVS  +V 
Sbjct: 121 EFIIRNGRMVRLATTKAQRKLFFNLRK-----QPRSRNWLTADETRHIADTLNVSVLDVK 175

Query: 175 SMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE-ERKNRRNMLTRSM 232
            M  R+AG D S +   ++ D+++       + DH        E E +     + L  ++
Sbjct: 176 EMETRMAGNDTSFDPAADADDESAYITPSHQIGDHRYDPAYQYETEADAGTSTDDLHAAL 235

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
           + L+ R R I   R L E+  TL +L+S++ VS ER+RQIE
Sbjct: 236 NNLDERSRDILAQRFLSESKATLNDLASKYNVSAERIRQIE 276


>gi|309785782|ref|ZP_07680413.1| alternative sigma factor RpoH [Shigella dysenteriae 1617]
 gi|308926902|gb|EFP72378.1| alternative sigma factor RpoH [Shigella dysenteriae 1617]
 gi|315614730|gb|EFU95370.1| alternative sigma factor RpoH [Escherichia coli 3431]
 gi|323162701|gb|EFZ48540.1| alternative sigma factor RpoH [Escherichia coli E128010]
 gi|323164790|gb|EFZ50582.1| alternative sigma factor RpoH [Shigella sonnei 53G]
 gi|323179012|gb|EFZ64586.1| alternative sigma factor RpoH [Escherichia coli 1180]
 gi|323182926|gb|EFZ68327.1| alternative sigma factor RpoH [Escherichia coli 1357]
 gi|323188948|gb|EFZ74232.1| alternative sigma factor RpoH [Escherichia coli RN587/1]
 gi|327251097|gb|EGE62790.1| alternative sigma factor RpoH [Escherichia coli STEC_7v]
          Length = 257

 Score =  176 bits (447), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 107/273 (39%), Positives = 157/273 (57%), Gaps = 32/273 (11%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           ML   EE  LA++   HGDL AA  L+ SHLR VV IA  Y GYGLP ++++ EGNIGLM
Sbjct: 1   MLSADEERALAEKLHYHGDLEAAKTLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLM 60

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV++F+PE G RL ++++ WIKA + EY+LR+W +VK+ TT  Q++LFFNLR+ K  L 
Sbjct: 61  KAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRL- 119

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--------------SLNALINSS 193
                    ++V  +A++L V+  +V  M  R+A  +               +  ++   
Sbjct: 120 ----GWFNQDEVEMVARELGVTSKDVREMESRMAAQDMTFDLSSDDDSDSQPMAPVLYLQ 175

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE-NP 252
           DK SS + D  + D + +EQ            N LT +M  L+ R + I  AR L E N 
Sbjct: 176 DK-SSNFADG-IEDDNWEEQAA----------NRLTDAMQGLDERSQDIIRARWLDEDNK 223

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            TL+ L+  + VS ERVRQ+E  A KK++ +I+
Sbjct: 224 STLQELADRYGVSAERVRQLEKNAMKKLRAAIE 256


>gi|226946813|ref|YP_002801886.1| RNA polymerase factor sigma-32 [Azotobacter vinelandii DJ]
 gi|226721740|gb|ACO80911.1| RNA polymerase sigma-32 factor [Azotobacter vinelandii DJ]
          Length = 284

 Score =  176 bits (447), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 111/284 (39%), Positives = 165/284 (58%), Gaps = 14/284 (4%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +S +V G   L  Y+H +  IP+L  ++E  LA R     DL AA ++V +HLR VV IA
Sbjct: 8   VSALVPG-ANLEAYVHAVNSIPLLTAEQERELADRLYYQQDLDAARQMVLAHLRFVVHIA 66

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGL  S+++ EGN+GLM+AVK+F+PE G RL ++++ WI+A + E+ILR+W +VK
Sbjct: 67  RSYSGYGLAQSDLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIRAEIHEFILRNWRIVK 126

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           I TT  Q++LFFNLR  K  L  +  NN   E+V A+A+ L V   EV  M  RL+G + 
Sbjct: 127 IATTKAQRKLFFNLRSQKKRLAWL--NN---EEVDAVAESLGVEPHEVREMESRLSGQDM 181

Query: 186 LNALINSSDKNS-----SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
                  +D +S     + + +   YD   Q   L E +   +    L  ++  L+ R R
Sbjct: 182 AFDPAADADDDSVFQAPAHYLEDQRYDPARQ---LEEADWSDSAAANLHEALEGLDERSR 238

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            I   R L E   TL +L+++++VS ER+RQ+E  A  K++ SI
Sbjct: 239 DILYQRWLAEEKATLHDLAAKYKVSAERIRQLEKSALNKLKGSI 282


>gi|220936149|ref|YP_002515048.1| RNA polymerase, sigma 32 subunit, RpoH [Thioalkalivibrio sp.
           HL-EbGR7]
 gi|219997459|gb|ACL74061.1| RNA polymerase, sigma 32 subunit, RpoH [Thioalkalivibrio sp.
           HL-EbGR7]
          Length = 281

 Score =  176 bits (446), Expect = 3e-42,   Method: Compositional matrix adjust.
 Identities = 109/271 (40%), Positives = 161/271 (59%), Gaps = 7/271 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  I ++P+L+ +EE  LA+  R+  DL AA +LV  +LR VV IA GY GYGL +
Sbjct: 14  LDGYIQAITRLPVLDAEEEQRLARDLRDRQDLEAARKLVMHNLRFVVHIARGYSGYGLGL 73

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AVK+FDPE G RL ++++ WI+A + E+ILR+W +VK+ TT  Q++L
Sbjct: 74  GDLIQEGNIGLMKAVKRFDPEMGVRLISFAVHWIRAEIHEFILRNWRIVKVATTKAQRKL 133

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR  K  L          E+V A+A  L V+ ++V+ M  RLAG D S +    S +
Sbjct: 134 FFNLRSAKQRL-----GWFNSEEVNAVADDLGVTPAQVLEMESRLAGQDVSFDPAPASDE 188

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
              S      + D  G     +E ++   +    L   +  L+PR R I   R L E   
Sbjct: 189 DGPSLSPAETLIDESGDPAERLEADDWAAHHETRLHSGLEALDPRSRDIVARRWLTEQKA 248

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           TL  L++E+ +S ERVRQ+E+ A +K++ S+
Sbjct: 249 TLHELAAEYGISAERVRQLESNAMRKLRASL 279


>gi|15616654|ref|NP_239866.1| RNA polymerase factor sigma-32 [Buchnera aphidicola str. APS
           (Acyrthosiphon pisum)]
 gi|219681412|ref|YP_002467797.1| RNA polymerase sigma factor [Buchnera aphidicola str. 5A
           (Acyrthosiphon pisum)]
 gi|219681968|ref|YP_002468352.1| RNA polymerase sigma factor [Buchnera aphidicola str. Tuc7
           (Acyrthosiphon pisum)]
 gi|257471086|ref|ZP_05635085.1| RNA polymerase factor sigma-32 [Buchnera aphidicola str. LSR1
           (Acyrthosiphon pisum)]
 gi|7994684|sp|O05385|RP32_BUCAI RecName: Full=RNA polymerase sigma-32 factor
 gi|25288470|pir||H84932 DNA-directed RNA polymerase (EC 2.7.7.6) sigma-32 factor [imported]
           - Buchnera sp. (strain APS)
 gi|1929472|gb|AAB51433.1| heat shock sigma factor 32 [Buchnera aphidicola]
 gi|10038717|dbj|BAB12752.1| RNA polymerase sigma-32 factor [Buchnera aphidicola str. APS
           (Acyrthosiphon pisum)]
 gi|219621701|gb|ACL29857.1| RNA polymerase sigma factor [Buchnera aphidicola str. Tuc7
           (Acyrthosiphon pisum)]
 gi|219624255|gb|ACL30410.1| RNA polymerase sigma factor [Buchnera aphidicola str. 5A
           (Acyrthosiphon pisum)]
 gi|311085774|gb|ADP65856.1| RNA polymerase factor sigma-32 [Buchnera aphidicola str. LL01
           (Acyrthosiphon pisum)]
 gi|311086927|gb|ADP67007.1| RNA polymerase factor sigma-32 [Buchnera aphidicola str. JF99
           (Acyrthosiphon pisum)]
          Length = 284

 Score =  176 bits (446), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 110/277 (39%), Positives = 166/277 (59%), Gaps = 16/277 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI      PML  +EE  L KR R +GDL AA  L+ SHLR V+ I+  Y GYGL  
Sbjct: 16  LDAYIRIANLWPMLSIEEEKKLTKRLRYNGDLDAAKTLILSHLRFVIHISRNYSGYGLLQ 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           S+++ EGNIGLM+AV++F+PE G RL ++++ WIK+ + EY+LR+W +VK+ TT +Q++L
Sbjct: 76  SDLIQEGNIGLMKAVRRFNPEIGVRLVSFAVHWIKSEIHEYVLRNWRIVKVATTKSQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNAL----I 190
           FFNLR+ K  L    +     E++  +A++L VS  +V  M  R+ A D + N       
Sbjct: 136 FFNLRKTKKRLGWFNE-----EEIQIVARELGVSSRDVREMESRMSAQDVAFNPSPEEHC 190

Query: 191 NSSDKNSSQW-QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           +S   +S Q+ QD      +G EQ   E+       N L+ ++  L+ R R I  AR L 
Sbjct: 191 DSKTNSSIQYLQDKTSNFANGVEQDNWEEHA----ANKLSSALLRLDERSRHIIHARWLD 246

Query: 250 ENPV-TLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           +N   TL+N+++ + +S ERVRQ+E  A KK++ +I+
Sbjct: 247 KNKKNTLQNIANNYGISAERVRQLEKNAMKKLKLAIE 283


>gi|312972274|ref|ZP_07786448.1| alternative sigma factor RpoH [Escherichia coli 1827-70]
 gi|310334651|gb|EFQ00856.1| alternative sigma factor RpoH [Escherichia coli 1827-70]
          Length = 257

 Score =  176 bits (446), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 107/273 (39%), Positives = 157/273 (57%), Gaps = 32/273 (11%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           ML   EE  LA++   HGDL AA  L+ SHLR VV IA  Y GYGLP ++++ EGNIGLM
Sbjct: 1   MLSADEERALAEKLHYHGDLEAAKTLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLM 60

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV++F+PE G RL ++++ WIKA + EY+LR+W +VK+ TT  Q++LFFNLR+ K  L 
Sbjct: 61  KAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRL- 119

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--------------SLNALINSS 193
                    ++V  +A++L V+  +V  M  R+A  +               +  ++   
Sbjct: 120 ----GWFNQDEVEMVARELGVTSKDVREMESRMAAQDMTFDLSSNDDSDSQPMAPVLYLQ 175

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE-NP 252
           DK SS + D  + D + +EQ            N LT +M  L+ R + I  AR L E N 
Sbjct: 176 DK-SSNFADG-IEDDNWEEQAA----------NRLTDAMQGLDERSQDIIRARWLDEDNK 223

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            TL+ L+  + VS ERVRQ+E  A KK++ +I+
Sbjct: 224 STLQELADRYGVSAERVRQLEKNAMKKLRAAIE 256


>gi|183598031|ref|ZP_02959524.1| hypothetical protein PROSTU_01387 [Providencia stuartii ATCC 25827]
 gi|188022810|gb|EDU60850.1| hypothetical protein PROSTU_01387 [Providencia stuartii ATCC 25827]
          Length = 292

 Score =  176 bits (446), Expect = 4e-42,   Method: Compositional matrix adjust.
 Identities = 108/307 (35%), Positives = 172/307 (56%), Gaps = 36/307 (11%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           + ++++++  G I    Y+      PML  +EE  LA+R   HGDL AA +L+ SHLR V
Sbjct: 4   DMQSLALVPQGSI--EAYMRAANAYPMLTAEEEKELAERLHYHGDLDAAKQLILSHLRFV 61

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           + +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W
Sbjct: 62  IHVARSYAGYGLPQADLIQEGNIGLMKAVRRFNPEIGVRLVSFAVHWIKAEIHEYVLRNW 121

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            +VKI TT +Q++LFFNLR+ K  L          ++V  +AK+L VS  +V  M  R+A
Sbjct: 122 RIVKIATTKSQRKLFFNLRKNKKRL-----GWFNQDEVDMVAKELGVSTKDVREMESRMA 176

Query: 182 GD----------------ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
                             + +  ++   DK+S         D  G    + E     +  
Sbjct: 177 AQDMAFDMSDDDDSGDLGQPIAPVLFLQDKSS---------DFAGS---IEEDNWESHAT 224

Query: 226 NMLTRSMSVLNPRERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + L  ++  L+ R + I  AR L  +N  TL+ L+ ++ VS ERVRQ+E  A KK++ ++
Sbjct: 225 DRLADALDSLDERSQDIIRARWLDDDNKTTLQELADKYGVSAERVRQLEKNAMKKLRAAM 284

Query: 285 QKQVELS 291
           ++  E S
Sbjct: 285 EEGEEES 291


>gi|71892394|ref|YP_278128.1| RNA polymerase factor sigma-32 [Candidatus Blochmannia
           pennsylvanicus str. BPEN]
 gi|71796500|gb|AAZ41251.1| RNA polymerase sigma-32 factor [Candidatus Blochmannia
           pennsylvanicus str. BPEN]
          Length = 282

 Score =  176 bits (445), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 107/292 (36%), Positives = 168/292 (57%), Gaps = 25/292 (8%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +KN+++I  G   L  YI       ML  +EE  LAKR   +GDL AA +L+ SHLR VV
Sbjct: 6   QKNVTLIPQG--NLEAYIKVANAYTMLTAEEEKTLAKRLYYNGDLDAAKKLIVSHLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            ++  Y GYGLP ++++ EGNIGLM+AV++F+PE   RL ++++ WIK+ + EY+L++W 
Sbjct: 64  HVSRNYSGYGLPQADLIQEGNIGLMKAVRRFNPELDVRLVSFAVHWIKSEIHEYVLKNWR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VKI TT  Q++LFFNLR+ K  L           ++  +AK LNV+  +V  M  R++ 
Sbjct: 124 IVKIATTKAQRKLFFNLRKTKQRLGW-----FNAGEIEIVAKALNVTSKDVREMESRMSA 178

Query: 183 DESLNALINSSDKNSS--------QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV 234
            +       SSD+++           QD +V  ++ +E +           + L  ++  
Sbjct: 179 QDM--TFEQSSDEDNRGITIAPILYLQDKIVSSNEEEEWI-------DQVSDKLNAAIKT 229

Query: 235 LNPRERRIFEARRLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L+ R + I  AR L  +N  TL+ L++++ VS ERVRQ+E  A KK++  IQ
Sbjct: 230 LDERSQHIIRARWLNVDNKSTLQELANQYGVSAERVRQLEKNAMKKMKLIIQ 281


>gi|133286|sp|P11539|RP32_CITFR RecName: Full=RNA polymerase sigma-32 factor; AltName: Full=Heat
           shock regulatory protein
 gi|40469|emb|CAA33083.1| unnamed protein product [Citrobacter freundii]
          Length = 284

 Score =  176 bits (445), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 112/287 (39%), Positives = 169/287 (58%), Gaps = 11/287 (3%)

Query: 4   KNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           K M  +    +G L  YI      PML   EE  LA++    GDL AA  L+ SHLR VV
Sbjct: 3   KEMQNLALAPVGNLESYIRAANAWPMLSADEERALAEKLHYQGDLEAAKTLILSHLRFVV 62

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y GYGL  ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W 
Sbjct: 63  HVARNYAGYGLRQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWR 122

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+A 
Sbjct: 123 IVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVEMVARELGVSSKDVREMESRMAA 177

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVL--IEKEERKNR-RNMLTRSMSVLNPRE 239
            + +   ++S D++ SQ    ++Y  D        IE++  +++  N LT +M  L+ R 
Sbjct: 178 -QDMTFDMSSDDESDSQPMAPVLYLQDKSSNFADGIEEDNWEDQAANKLTHAMEGLDERS 236

Query: 240 RRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + I  AR L E N  TL+ L+  + VS ERVRQ+E  A KK++ +I+
Sbjct: 237 QDIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIE 283


>gi|146284301|ref|YP_001174454.1| RNA polymerase factor sigma-32 [Pseudomonas stutzeri A1501]
 gi|145572506|gb|ABP81612.1| sigma factor RpoH [Pseudomonas stutzeri A1501]
 gi|327482685|gb|AEA85995.1| RNA polymerase factor sigma-32 [Pseudomonas stutzeri DSM 4166]
          Length = 284

 Score =  175 bits (444), Expect = 6e-42,   Method: Compositional matrix adjust.
 Identities = 106/274 (38%), Positives = 162/274 (59%), Gaps = 11/274 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+  +  +P+L  ++E  LA+R   H DL AA ++V +HLR VV IA  Y GYGL  
Sbjct: 17  LEAYVQTVNSLPLLTVEQERELAERLFYHQDLEAARQMVLAHLRFVVHIARSYSGYGLAQ 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGN+GLM+AVK+F+PE G RL ++++ WI+A + E+ILR+W +VK+ TT  Q++L
Sbjct: 77  ADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIRAEIHEFILRNWRIVKVATTKAQRKL 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR  K  L  +  NN   ++V A+A  L V   EV  M  RL G   +     +   
Sbjct: 137 FFNLRSQKKRLAWL--NN---DEVTAVADSLGVEPHEVREMESRLTG-HDMAFDPAADAD 190

Query: 196 NSSQWQDWLVY--DH--DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           + S +Q    Y  DH  D   Q L + +   +  + L  ++  L+ R R I + R L E+
Sbjct: 191 DDSAYQSPAHYLEDHRYDPARQ-LEDADWSDSSTSSLHAALEGLDERSRDILQQRWLNED 249

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             TL +L++++ VS ER+RQ+E  A  K++ SIQ
Sbjct: 250 KATLHDLAAKYNVSAERIRQLEKNAMNKLKGSIQ 283


>gi|152998320|ref|YP_001343155.1| RNA polymerase factor sigma-32 [Marinomonas sp. MWYL1]
 gi|150839244|gb|ABR73220.1| RNA polymerase, sigma 32 subunit, RpoH [Marinomonas sp. MWYL1]
          Length = 288

 Score =  175 bits (444), Expect = 7e-42,   Method: Compositional matrix adjust.
 Identities = 107/269 (39%), Positives = 156/269 (57%), Gaps = 11/269 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + +IP+L   EE  LA+R     DL AA  LV SHLR VV IA  Y GYGL  
Sbjct: 17  LESYIQAVSRIPILTADEEKALAERLYYQEDLEAARTLVMSHLRFVVHIAKSYSGYGLAQ 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+IL++W +VK+ TT  Q+++
Sbjct: 77  GDLIQEGNVGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEFILKNWRIVKVATTKAQRKM 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSSD 194
           FFNLR  K  L   +++     +V ++A  L V+   V  M  RL + D + +A  +  D
Sbjct: 137 FFNLRSAKKSLSWFSNS-----EVESVASDLGVTPEVVRQMEGRLSSSDMAFDASADDDD 191

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEK---EERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
            ++ Q     + DH      L+E    EE  N+R  L  +M+ L+ R R I   R L + 
Sbjct: 192 DSAFQAPSQYLEDHRSDPATLLENGNWEEDSNQR--LEVAMADLDERSRNILVQRWLSDA 249

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             TL  L+ E+ VS ER+RQ+E  A KK+
Sbjct: 250 KSTLHELADEYGVSAERIRQLEKNAMKKI 278


>gi|42524684|ref|NP_970064.1| RNA polymerase sigma-32 factor [Bdellovibrio bacteriovorus HD100]
 gi|39576894|emb|CAE78123.1| RNA polymerase sigma-32 factor [Bdellovibrio bacteriovorus HD100]
          Length = 373

 Score =  175 bits (444), Expect = 7e-42,   Method: Compositional matrix adjust.
 Identities = 99/278 (35%), Positives = 170/278 (61%), Gaps = 14/278 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y++EIR+  +L ++EE  LAK+Y E  D  AA  LV ++LR VVK+A  Y  +G  +
Sbjct: 103 LVMYLNEIRRYKVLTREEEMALAKKYFESKDPEAAQALVKANLRFVVKVAAEYSKFGSKM 162

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM AV++F+P +G RL TY++WWI+  +QE+++R +S+V+IGTT NQ++L
Sbjct: 163 IDLIQEGNVGLMHAVREFNPYKGARLITYAVWWIRGYIQEFLMRQYSMVRIGTTQNQRKL 222

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           F+ L++ K  L A+    ++P  +  I+ +L + E EV  M  R++G D SL+  ++  D
Sbjct: 223 FYQLQKEKEALDAM---GIEP-NIGLISSRLGIPEDEVRDMTMRMSGRDVSLDRPVD--D 276

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP----RERRIFEARRLQE 250
           ++ +   D      D   Q L E      +  +L + +  + P    RE+ I + R L +
Sbjct: 277 ESGTTLGDLQRGPSD---QPLDEALAHNEQLEILKQKIEEIRPELSEREKIILDERILND 333

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +P+TL+ +  +  ++RE VRQ+EAR  KK++  +++  
Sbjct: 334 DPLTLQEIGEKHGITREAVRQMEARLMKKIKAKMEEDA 371


>gi|300721688|ref|YP_003710964.1| sigma H (sigma 32) factor of RNA polymerase [Xenorhabdus
           nematophila ATCC 19061]
 gi|297628181|emb|CBJ88736.1| sigma H (sigma 32) factor of RNA polymerase; transcription of heat
           shock and stress proteins [Xenorhabdus nematophila ATCC
           19061]
          Length = 285

 Score =  175 bits (443), Expect = 8e-42,   Method: Compositional matrix adjust.
 Identities = 108/289 (37%), Positives = 170/289 (58%), Gaps = 9/289 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  YI      PML  +EE  LA+R    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLALVPQGSLEGYIRASNTYPMLSAEEERELAERLHYQGDLDAAKKLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARSYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          +++  +AK+L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKAKQRL-----GWFNQDEIELVAKELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL--IEKEERKNR-RNMLTRSMSVLNP 237
           +  +    +    D + SQ    ++Y  D        IE++  +N   + L+ +M  L+ 
Sbjct: 176 SAQDMAFDMSADDDNHDSQPVAPVLYLQDKASDFADGIEEDNWENHAADKLSVAMEGLDE 235

Query: 238 RERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           R + I  AR L  EN  TL+ L+ ++ VS ERVRQ+E  A KK++ +I+
Sbjct: 236 RSQDIIRARWLDDENKTTLQELADKYGVSAERVRQLEKNAMKKLRLAIE 284


>gi|27904539|ref|NP_777665.1| RNA polymerase factor sigma-32 [Buchnera aphidicola str. Bp
           (Baizongia pistaciae)]
 gi|31340406|sp|Q89B27|RP32_BUCBP RecName: Full=RNA polymerase sigma-32 factor
 gi|27903936|gb|AAO26770.1| RNA polymerase sigma-32 factor [Buchnera aphidicola str. Bp
           (Baizongia pistaciae)]
          Length = 287

 Score =  174 bits (442), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 98/276 (35%), Positives = 161/276 (58%), Gaps = 10/276 (3%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  YI E    PML  QEE  L+++   HGDL+AA  L+ SHLR V+ ++  Y GYGL 
Sbjct: 16  NLDSYIREANSWPMLSSQEEKYLSEKLFYHGDLNAAKTLILSHLRFVIHVSRNYSGYGLL 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGNIGLM+AV++F+P+ G RL ++++ WIK+ + EY+LR+W +VK+ TT +Q++
Sbjct: 76  QADLIQEGNIGLMKAVRRFNPKIGVRLVSFAVHWIKSEIHEYVLRNWRIVKVATTKSQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           LFFNLR+ K  L    D+ L+      +A++L V   +V  M  R++  +     +  + 
Sbjct: 136 LFFNLRKTKQRLGWFNDHELE-----LVAQELGVKREDVREMESRMSAQDIALHHVPDNF 190

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNPRERRIFEARRLQ-- 249
           +    +   + Y  D         EE     ++ N L+ ++S L+ R R I  AR L   
Sbjct: 191 REEQNFSYTIPYLKDSLSDFANHVEEDNWEAHKTNKLSNALSSLDERSRNIIHARWLDDS 250

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           ++ +TL  ++  + +S ERVRQ+E  A KK++ +I+
Sbjct: 251 DHKMTLREIAHNYGISAERVRQLEKNAMKKLKVAIE 286


>gi|311696378|gb|ADP99251.1| RNA polymerase, sigma 32 subunit, RpoH [marine bacterium HP15]
          Length = 286

 Score =  174 bits (441), Expect = 1e-41,   Method: Compositional matrix adjust.
 Identities = 103/267 (38%), Positives = 153/267 (57%), Gaps = 7/267 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI    +IP+L   EE  LA+R    GD+ AA +LV SHLR V+ IA  Y GYGL  
Sbjct: 17  LESYIQAASRIPVLTVDEERELAERLHYEGDVEAARQLVMSHLRFVIHIARSYSGYGLAQ 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++L
Sbjct: 77  ADLIQEGNVGLMKAVKRFNPEYGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRKL 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR  K  L  ++ + L      A+A+ L V    V  M  RLA  D + +   +  D
Sbjct: 137 FFNLRSQKKKLAWLSHDELN-----AVAEDLGVEPRVVREMEGRLASQDTAFDGPQDDDD 191

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN-MLTRSMSVLNPRERRIFEARRLQENPV 253
            N+ Q   + + D        +E  +  +  N  L +++  L+ R + I   R L E+  
Sbjct: 192 DNAYQAPAYYLEDARSNPATQLENADWSDDSNGRLMQALGQLDERSQDILRERWLSESKS 251

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKV 280
           TL  L+  + VS ER+RQ+E  A KK+
Sbjct: 252 TLHELADRYGVSAERIRQLEKNAMKKI 278


>gi|301166786|emb|CBW26363.1| RNA polymerase sigma-32 factor [Bacteriovorax marinus SJ]
          Length = 350

 Score =  174 bits (440), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 110/280 (39%), Positives = 167/280 (59%), Gaps = 17/280 (6%)

Query: 11  NGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           + +IG  L+ Y+ EI K  +L  +EE  L ++  E GD+  A +LV ++LRLVVKIAM Y
Sbjct: 71  DSKIGDPLTAYLREISKYELLTIEEERELTQKLVETGDIEVAKKLVAANLRLVVKIAMEY 130

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           R     + +++ EGNIGLM+AV K+DP++G +L+ Y+ WWIK+ + +YIL ++ LVKIGT
Sbjct: 131 RSSFQNVMDLIQEGNIGLMKAVSKYDPDKGAKLSYYASWWIKSYILKYILDNFRLVKIGT 190

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA---GDES 185
           T  QK+LF+NL + K  L       ++P+  + +++ L VSE  V  M+ R++   G+ S
Sbjct: 191 TNEQKKLFYNLMKEKDRLAK---QGIEPDHKL-LSENLGVSEKAVALMDGRMSSSGGELS 246

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM----SVLNPRERR 241
           L   +   D  S    D LV   D  E  + EK        +L  ++    S L  R+R 
Sbjct: 247 LETPL-GHDSGSGVLSDILV---DQDESDISEKIADAQGLEILQENLRDFVSGLKERDRD 302

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           IF+ R L E P +L+N++ E+ VSRER+RQIE R  K ++
Sbjct: 303 IFKKRLLSEVPPSLQNIADEYGVSRERIRQIEERLLKNLK 342


>gi|33520062|ref|NP_878894.1| RNA polymerase factor sigma-32 [Candidatus Blochmannia floridanus]
 gi|33504408|emb|CAD83301.1| RNA polymerase sigma-32 factor [Candidatus Blochmannia floridanus]
          Length = 283

 Score =  173 bits (438), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 103/282 (36%), Positives = 167/282 (59%), Gaps = 12/282 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           RKN+++   G   L  YI      PML  +EE  LAK    +GDL+AA +L+ SHLR V+
Sbjct: 6   RKNVTLASQG--TLEAYIRAANLYPMLTVEEEQKLAKNLYYNGDLNAAKKLIVSHLRFVI 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y GYGL  ++++ EGNIGLM+++++F+PE   RL ++++ WIK+ + EY+L++W 
Sbjct: 64  HVARNYSGYGLSQADLIQEGNIGLMKSIRRFNPELDVRLVSFAVHWIKSEIHEYVLKNWR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VKI TT  Q++LFFNLR+ K  L    +      ++  +AK L+V+  +V  M  R+A 
Sbjct: 124 IVKIATTKAQRKLFFNLRKTKQRLGWFNEG-----EIEMVAKTLHVTCKDVREMESRMAA 178

Query: 183 -DESL-NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            D +L    ++  DKN       ++Y  D    +  E+E      N L  +++ L+ R +
Sbjct: 179 QDMTLEQPYLDEDDKNILSIP--MLYLQDKITIIDDEEEWIDQVSNKLNIALNTLDKRSQ 236

Query: 241 RIFEARRLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            I  AR L  +N  TL+ L++++ +S ER+RQ+E  A KK++
Sbjct: 237 HIIRARWLNADNKTTLQELANQYGISAERIRQLEKNAMKKMK 278


>gi|158522485|ref|YP_001530355.1| RNA polymerase sigma 70 family subunit [Desulfococcus oleovorans
           Hxd3]
 gi|158511311|gb|ABW68278.1| putative RNA polymerase, sigma 70 family subunit [Desulfococcus
           oleovorans Hxd3]
          Length = 321

 Score =  173 bits (438), Expect = 3e-41,   Method: Compositional matrix adjust.
 Identities = 102/275 (37%), Positives = 169/275 (61%), Gaps = 7/275 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLP 74
           L RY+ E+ +  +L +++E  L KR +E GD  AA+ L TS+LRLVVKIA+ + R +   
Sbjct: 41  LQRYLKEVSRYNLLTREQEIELGKRVQEEGDEEAAYILATSNLRLVVKIALEFQRVWMQN 100

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++ EGNIGLM AV+KFDP +  + + Y+ +WIKA + ++++ +W LVKIGTT NQ++
Sbjct: 101 LLDLIQEGNIGLMHAVQKFDPYKNVKFSYYASFWIKAYILKFVMDNWRLVKIGTTQNQRK 160

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSS 193
           LFF   RLK   QA+ D   +P   + +A++L V + EVI+M  RL   D SL+  + S 
Sbjct: 161 LFF---RLKKEKQALIDQGFEPRPKL-LAERLGVPQKEVINMEQRLDMWDLSLDEPV-SH 215

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D ++ +     + +    ++ + +K  R+     L      L PRER IF+ R   + P+
Sbjct: 216 DSDTQKGDLLDINNTQPVDEQVGDKALRQLVGEHLVEFKKTLTPRERDIFKTRIYTDQPM 275

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           TL+++   + +SRERVRQ+E    KK+++  ++++
Sbjct: 276 TLQDIGERYAISRERVRQLEVNIIKKMRDFFKEKI 310


>gi|261344963|ref|ZP_05972607.1| alternative sigma factor RpoH [Providencia rustigianii DSM 4541]
 gi|282567106|gb|EFB72641.1| alternative sigma factor RpoH [Providencia rustigianii DSM 4541]
          Length = 291

 Score =  173 bits (438), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 105/303 (34%), Positives = 173/303 (57%), Gaps = 38/303 (12%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           + ++++++  G I    YI      PML  +EE  LA+R    GDL AA +L+ SHLR V
Sbjct: 4   DMQSLALVPQGSI--EAYIRAANTYPMLSAEEEKELAERLHYDGDLEAAKQLILSHLRFV 61

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           + IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W
Sbjct: 62  IHIARSYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNW 121

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            +VK+ TT +Q++LFFNLR+ K  L          ++V  +A++L VS  +V+ M  R+A
Sbjct: 122 RIVKVATTKSQRKLFFNLRKNKKRL-----GWFNQDEVDMVAQELGVSTKDVLEMESRMA 176

Query: 182 GDES----------------LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE-RKNR 224
             +                 +  ++   DK+S         D  G     IE +    + 
Sbjct: 177 AQDMAFDMSDDDDSGDFGGPIAPVLYLQDKSS---------DFAGS----IEDDNWESHA 223

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            + L+ +++ L+ R + I  AR L ++   TL+ L+ ++ VS ERVRQ+E  A KK++ +
Sbjct: 224 TDRLSDALASLDERSQDIIRARWLDDDSKTTLQELADKYGVSAERVRQLEKNAMKKLRLA 283

Query: 284 IQK 286
           +++
Sbjct: 284 MEE 286


>gi|78486471|ref|YP_392396.1| sigma 32 (RpoH) [Thiomicrospira crunogena XCL-2]
 gi|78364757|gb|ABB42722.1| sigma 32 (RpoH) [Thiomicrospira crunogena XCL-2]
          Length = 283

 Score =  172 bits (437), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 96/267 (35%), Positives = 157/267 (58%), Gaps = 7/267 (2%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+  ++ +P L   EE  LA++     DL+AA +L+ S LR VV IA  Y GYGLP++++
Sbjct: 21  YLRTVQTLPQLSADEERELAEKLYHDKDLNAARQLILSSLRYVVPIARSYNGYGLPLNDL 80

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM+AVK+F+P    RL T+++ W++A + EY++++W +VK  TT  Q++LFF 
Sbjct: 81  IQEGNIGLMKAVKRFNPAEKVRLMTFAVHWVRAEINEYVIKNWRIVKTATTKAQRKLFFK 140

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  K  L+ + D +        IAK+L V+  +V+ M  RL G D S++   +  + NS
Sbjct: 141 LRSTKKSLEWLGDKDAD-----TIAKELGVTRKDVLEMETRLYGQDMSVDLSPDEEEANS 195

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
             +   +  + D + Q L    +  +    + +++  L+ R R I + R L E+   L+ 
Sbjct: 196 KTYPVLVSQELDPETQ-LANDSQSDHELGKMHQALKQLDQRSRDILQQRWLSEDKTGLKA 254

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESI 284
           LS ++ VS ER+RQIE +A K +  S+
Sbjct: 255 LSEKYGVSMERIRQIEQQAIKTLHASM 281


>gi|296105152|ref|YP_003615298.1| RNA polymerase factor sigma-32 [Enterobacter cloacae subsp. cloacae
           ATCC 13047]
 gi|295059611|gb|ADF64349.1| RNA polymerase factor sigma-32 [Enterobacter cloacae subsp. cloacae
           ATCC 13047]
          Length = 285

 Score =  172 bits (437), Expect = 4e-41,   Method: Compositional matrix adjust.
 Identities = 112/287 (39%), Positives = 169/287 (58%), Gaps = 10/287 (3%)

Query: 4   KNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           K M  +    +G L  YI      PML  +EE  LA++    GDL AA +L+ SHLR VV
Sbjct: 3   KEMQTLALAPVGNLESYIRAANTWPMLTAEEEKELAEKLHYQGDLEAAKKLILSHLRFVV 62

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W 
Sbjct: 63  HIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWR 122

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+A 
Sbjct: 123 IVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVEMVARELGVSSKDVREMESRMAA 177

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVL--IEKEERKNR-RNMLTRSMSVLNPRE 239
            +    + +  D + SQ    ++Y  D        IE++  +++  N L+ +M  L+ R 
Sbjct: 178 QDMTFDMSSDDDASDSQPMAPVLYLQDKTSNFADGIEEDNWEDQAANKLSYAMEGLDERS 237

Query: 240 RRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + I  AR L E N  TL+ L+  + VS ERVRQ+E  A KK++ +I+
Sbjct: 238 QDIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIE 284


>gi|149378434|ref|ZP_01896128.1| RNA polymerase sigma-32 factor RpoH [Marinobacter algicola DG893]
 gi|149357284|gb|EDM45812.1| RNA polymerase sigma-32 factor RpoH [Marinobacter algicola DG893]
          Length = 289

 Score =  172 bits (437), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 102/268 (38%), Positives = 154/268 (57%), Gaps = 7/268 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI    +IP+L  +EE  LA+R    GD+ AA  LV SHLR V+ IA  Y GYGL  
Sbjct: 17  LESYIQAASRIPVLSVEEERKLAERLHYDGDVDAARELVLSHLRFVIHIARSYAGYGLSQ 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++L
Sbjct: 77  ADLIQEGNVGLMKAVKRFNPEYGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRKL 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR  K  L  ++ +     +V A+A  L V    V  M  RLA  D + +   +  D
Sbjct: 137 FFNLRSQKKRLAWLSHD-----EVNAVASDLGVEPRVVREMEGRLASHDTAFDGPQDDDD 191

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN-MLTRSMSVLNPRERRIFEARRLQENPV 253
            N+ Q   + + D        +E+ +  +  N  L  ++  L+ R + I   R L ++  
Sbjct: 192 DNAYQAPAYYLEDKRSNPATQLEQSDWTDDSNGRLMAALEQLDERSQDILRERWLSDSKS 251

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TL  L+  + VS ER+RQ+E  A KK++
Sbjct: 252 TLHELADRYGVSAERIRQLEKNAMKKIR 279


>gi|157368473|ref|YP_001476462.1| RNA polymerase factor sigma-32 [Serratia proteamaculans 568]
 gi|157320237|gb|ABV39334.1| RNA polymerase, sigma 32 subunit, RpoH [Serratia proteamaculans
           568]
          Length = 285

 Score =  172 bits (436), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 107/289 (37%), Positives = 162/289 (56%), Gaps = 9/289 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  YI      PML  +EE  LA+R    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLALVPQGSLEAYIRAANTYPMLTAEEERELAERLHYQGDLEAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VAHIARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVELVARELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNP 237
           A  +         D    Q    ++Y  D         EE     N  + L  +M  L+ 
Sbjct: 176 AAQDMTFDPTPDDDAREGQSMAPVLYLQDKSSDFAEGIEEDNWESNAADKLAYAMEGLDE 235

Query: 238 RERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           R + I  AR L  +N  TL+ L+ ++ VS ERVRQ+E  A KK++ +I+
Sbjct: 236 RSQHIIRARWLDDDNKSTLQELADQYGVSAERVRQLEKNAMKKLKMAIE 284


>gi|268590799|ref|ZP_06125020.1| alternative sigma factor RpoH [Providencia rettgeri DSM 1131]
 gi|291313578|gb|EFE54031.1| alternative sigma factor RpoH [Providencia rettgeri DSM 1131]
          Length = 292

 Score =  172 bits (436), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 105/303 (34%), Positives = 170/303 (56%), Gaps = 38/303 (12%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           + ++++++  G I    Y+      PML  +EE  LA+R   HGDL AA +L+ SHLR V
Sbjct: 4   DMQSLALVPQGSI--EAYVRAANSYPMLTAEEEKELAERLHYHGDLDAAKQLILSHLRFV 61

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           + +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W
Sbjct: 62  IHVARSYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNW 121

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            +VK+ TT +Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+A
Sbjct: 122 RIVKVATTKSQRKLFFNLRKNKKRL-----GWFNQDEVDMVAQELGVSTKDVREMESRMA 176

Query: 182 GDES----------------LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE-RKNR 224
             +                 +  ++   DK S         D  G     IE +    + 
Sbjct: 177 AQDMAFDMSDDDDSSDFGGPVAPVLYLQDKAS---------DFAGS----IEDDNWESHA 223

Query: 225 RNMLTRSMSVLNPRERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            + L  ++  L+ R + I  AR L  +N  TL+ L+ ++ VS ERVRQ+E  A KK++ +
Sbjct: 224 TDRLADALDSLDERSQDIIRARWLDDDNKTTLQELADKYGVSAERVRQLEKNAMKKLRLA 283

Query: 284 IQK 286
           +++
Sbjct: 284 MEE 286


>gi|224369499|ref|YP_002603663.1| RpoH [Desulfobacterium autotrophicum HRM2]
 gi|223692216|gb|ACN15499.1| RpoH [Desulfobacterium autotrophicum HRM2]
          Length = 322

 Score =  172 bits (436), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 105/276 (38%), Positives = 166/276 (60%), Gaps = 10/276 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLP 74
           L  Y+ EI +  +L ++EE  L  + +E  D  AA+ +VTS+LRLVVKIA+ + R +   
Sbjct: 43  LQSYLAEINRYRLLTREEEVNLGTKIQEENDSDAAYVMVTSNLRLVVKIALDFQRIWMQN 102

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++ EGNIGL++AVKKFDP +  + + Y+ +WIKA + ++I+ +W LVKIGTT  Q++
Sbjct: 103 LLDLIQEGNIGLVKAVKKFDPYKNVKFSYYASFWIKAYILKFIMDNWRLVKIGTTQGQRK 162

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN-ALINS 192
           LFF   RLK   Q + D    P   + +++++ VSE E+I M+ RL G D SL+  L N 
Sbjct: 163 LFF---RLKKEKQKLIDEGFDPGPKL-LSERMGVSEQEIIEMDQRLDGWDLSLDEPLRND 218

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
           SD   ++  +++  + D  E  +  KE        + +  + LNPRE  IF  R   + P
Sbjct: 219 SD---TERIEFINVESDSTEDRVARKEIEDILHVRVKKFTATLNPREMEIFSKRIFSDEP 275

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            TL+ +  E+ +SRERVRQIE    KK++E  + ++
Sbjct: 276 RTLQEIGEEYNISRERVRQIENNIIKKMKEYFKNEM 311


>gi|260220134|emb|CBA27368.1| RNA polymerase sigma-32 factor [Curvibacter putative symbiont of
           Hydra magnipapillata]
          Length = 354

 Score =  172 bits (435), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 87/180 (48%), Positives = 119/180 (66%), Gaps = 10/180 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI    ++PML  +EE   A++++   DL AA +LV SHLRLVV +A  Y GYGLP 
Sbjct: 36  LDAYISAANRLPMLTLEEEQEFARKFKNENDLEAAGKLVLSHLRLVVSVARQYLGYGLPH 95

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM+AVK+FDPE+G RL +Y++ WIKA + EYIL++W +VK+ TT  Q++L
Sbjct: 96  GDLIQEGNVGLMKAVKRFDPEQGVRLVSYALHWIKAEIHEYILKNWRMVKVATTKAQRKL 155

Query: 136 FFNLR----RLKGHLQAITD-----NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
           FFNLR    R KG   A  D     + L  EQV  +A++LNV   EV+ M  RLAG + L
Sbjct: 156 FFNLRSMKQRFKGE-DAAADLDTHRDTLNSEQVNTMARELNVKPEEVLEMEARLAGGDVL 214


>gi|146309186|ref|YP_001189651.1| RNA polymerase factor sigma-32 [Pseudomonas mendocina ymp]
 gi|145577387|gb|ABP86919.1| RNA polymerase, sigma 32 subunit, RpoH [Pseudomonas mendocina ymp]
          Length = 284

 Score =  172 bits (435), Expect = 6e-41,   Method: Compositional matrix adjust.
 Identities = 102/272 (37%), Positives = 159/272 (58%), Gaps = 9/272 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+H +  IP+L  ++E  LA+      DL AA ++V +HLR VV IA  Y GYGL  
Sbjct: 17  LEAYVHAVNSIPLLTPEQERELAESLYYQQDLEAARQMVLAHLRFVVHIARSYSGYGLAQ 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGN+GLM+AVK+F+PE G RL ++++ WI+A + E+IL++W +VK+ TT  Q++L
Sbjct: 77  ADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIRAEIHEFILKNWRIVKVATTKAQRKL 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR  K  L  + ++     +V A+A+ L V   EV  M  RL G D + +   ++ D
Sbjct: 137 FFNLRSQKKRLAWLNND-----EVTAVAESLGVEPHEVREMESRLTGQDMAFDPASDADD 191

Query: 195 KNSSQWQDWLVYDH--DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            ++ Q     + DH  D   Q+        +  N L  ++  L+ R R I   R L E  
Sbjct: 192 DSAFQSPAHYLEDHRYDPARQLEDADWSDSSSSN-LHEALESLDERSRDILYQRWLAEEK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL +L++++ VS ER+RQ+E  A  K++ SI
Sbjct: 251 ATLHDLAAKYNVSAERIRQLEKNAMNKLKGSI 282


>gi|329896515|ref|ZP_08271573.1| RNA polymerase sigma factor RpoH [gamma proteobacterium IMCC3088]
 gi|328921732|gb|EGG29105.1| RNA polymerase sigma factor RpoH [gamma proteobacterium IMCC3088]
          Length = 286

 Score =  172 bits (435), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 104/267 (38%), Positives = 158/267 (59%), Gaps = 8/267 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ YI  +  IP+L  + E  LA+    + +L AA +LV SHLR VV IA  Y GYGL  
Sbjct: 17  LAAYIQTVSSIPVLSVERERELAEDLYYNDNLEAARQLVMSHLRFVVHIARSYSGYGLAE 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGN+GLM+AVK+F+PE+G RL ++++ WIKA M E+ILR+W +VK+ TT  Q++L
Sbjct: 77  ADLIQEGNVGLMKAVKRFNPEKGVRLVSFAVHWIKAEMHEFILRNWRIVKVATTKAQRKL 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR  K  L       L  E+  A+A  L V   EV +M  R++  D + +A  +S D
Sbjct: 137 FFNLRSSKKALAW-----LSAEEAQAVADDLGVDVREVATMEARMSSRDVAFDAPSDSDD 191

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
            +    Q +L  DH       +E    +++  + L  ++  L+ R R I   R L +   
Sbjct: 192 DDVYAPQYYL-EDHRADPAQQVESTNWQEDSESRLHYALEQLDERSRDILAQRWLNDEKA 250

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKV 280
           TL +L++++ VS ER+RQ+E  A +KV
Sbjct: 251 TLHDLAAQYGVSAERIRQLEQNAMQKV 277


>gi|254449115|ref|ZP_05062567.1| alternative sigma factor RpoH [gamma proteobacterium HTCC5015]
 gi|198261307|gb|EDY85600.1| alternative sigma factor RpoH [gamma proteobacterium HTCC5015]
          Length = 227

 Score =  172 bits (435), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 87/193 (45%), Positives = 122/193 (63%), Gaps = 5/193 (2%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           NM+ +      L  Y+ ++  IP+L  +EE  LA+R    GDL AA +LV SHLR V  I
Sbjct: 34  NMAPVALSNDTLDAYMQQVSSIPVLGAEEEQELAQRLHREGDLDAARQLVFSHLRFVTHI 93

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A GY+GYGLP+++V+ EGNIGLM+AVK+FDP  G RL ++++ WI+A + EYILR+W +V
Sbjct: 94  ARGYKGYGLPLADVIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWIRAEIHEYILRNWRIV 153

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           K+ TT  Q++LFF LR  K  L       L  E+V  +AK L V  S+V+ M  RLAG +
Sbjct: 154 KVATTKAQRKLFFKLRSNKKSL-----GWLNHEEVKTVAKDLGVEASDVMEMESRLAGSD 208

Query: 185 SLNALINSSDKNS 197
               L  + D ++
Sbjct: 209 MAYDLPGNDDDDA 221


>gi|195940831|ref|ZP_03086213.1| RNA polymerase factor sigma-32 [Escherichia coli O157:H7 str.
           EC4024]
 gi|1710645|sp|P50508|RP32_ENTCL RecName: Full=RNA polymerase sigma-32 factor
 gi|1143326|dbj|BAA09440.1| sigma-32 homolog [Enterobacter cloacae]
 gi|295097059|emb|CBK86149.1| RNA polymerase, sigma 32 subunit, RpoH [Enterobacter cloacae subsp.
           cloacae NCTC 9394]
          Length = 285

 Score =  172 bits (435), Expect = 7e-41,   Method: Compositional matrix adjust.
 Identities = 112/287 (39%), Positives = 167/287 (58%), Gaps = 10/287 (3%)

Query: 4   KNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           K M  +    +G L  YI      PML  +EE  LA++    GDL AA  L+ SHLR VV
Sbjct: 3   KEMQTLALAPVGNLESYIRAANTWPMLTAEEEKELAEKLHYQGDLEAAKTLILSHLRFVV 62

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W 
Sbjct: 63  HVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWR 122

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+A 
Sbjct: 123 IVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVEMVARELGVSSKDVREMESRMAA 177

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVL--IEKEERKNR-RNMLTRSMSVLNPRE 239
            +    +    D + SQ    ++Y  D        IE++  +++  N LT +M  L+ R 
Sbjct: 178 QDMTFDMSADDDASDSQPMAPVLYLQDKTSNFADGIEEDNWEDQAANKLTFAMEGLDERS 237

Query: 240 RRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + I  AR L E N  TL+ L+  + VS ERVRQ+E  A KK++ +I+
Sbjct: 238 QDIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIE 284


>gi|262195942|ref|YP_003267151.1| RNA polymerase, sigma 32 subunit, RpoH [Haliangium ochraceum DSM
           14365]
 gi|262079289|gb|ACY15258.1| RNA polymerase, sigma 32 subunit, RpoH [Haliangium ochraceum DSM
           14365]
          Length = 298

 Score =  172 bits (435), Expect = 8e-41,   Method: Compositional matrix adjust.
 Identities = 108/299 (36%), Positives = 169/299 (56%), Gaps = 13/299 (4%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M+  ++ E G   Y+  + +I  LE++EE  LA+R+REHGD +AA  LV+S LR V+KIA
Sbjct: 1   MARYISEEPGFQTYVDSVERIAALEREEELALARRWREHGDRAAADALVSSQLRSVLKIA 60

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             YRGYG+ +S++V+EGN+GL++AV +F+PERG R  TY+  W++A +  ++L+ WS+V 
Sbjct: 61  RKYRGYGIYLSDLVAEGNLGLLEAVNRFEPERGLRFFTYARHWVRAFILAHVLKHWSIVD 120

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-AIAKKLNVSESEVISMNCRLA-GD 183
           +GTTA Q ++FF L+    H + +T    + +QV   +A     S  +V +   RLA  D
Sbjct: 121 LGTTAQQSKMFFRLQ--SEHARLLTTLGDQSDQVERQLADTFKTSPEQVRANLQRLARRD 178

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SL+  +         + D L  D   QE      E     RN ++     L+ RER I 
Sbjct: 179 ASLDVPVVD---GGITFLDMLQADTTDQETQTAAAELSSVVRNAVSELWPTLDCRERLIV 235

Query: 244 EARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK----QVELSSSPPL 296
           + R L    +P TL  L  +  ++RERVRQ+EA    +++  + +    +VE +   PL
Sbjct: 236 DERLLPADGDPRTLAALGRQLGLTRERVRQLEAGVKDRLRAVLDRLLGGEVEHAQPAPL 294


>gi|270264290|ref|ZP_06192557.1| RNA polymerase sigma-32 factor [Serratia odorifera 4Rx13]
 gi|270041939|gb|EFA15036.1| RNA polymerase sigma-32 factor [Serratia odorifera 4Rx13]
          Length = 285

 Score =  171 bits (433), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 106/289 (36%), Positives = 162/289 (56%), Gaps = 9/289 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  YI      PML  +EE  LA+R    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLALVPQGSLEAYIRAANTYPMLTAEEERELAERLHYQGDLEAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VAHIARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVELVARELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNP 237
           A  +         D    Q    ++Y  D         EE     N  + L  ++  L+ 
Sbjct: 176 AAQDMTFDPTPDDDARDGQSMAPVLYLQDKSSDFAEGIEEDNWESNAADKLAYALEGLDE 235

Query: 238 RERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           R + I  AR L  +N  TL+ L+ ++ VS ERVRQ+E  A KK++ +I+
Sbjct: 236 RSQHIIRARWLDDDNKSTLQELADQYGVSAERVRQLEKNAMKKLKMAIE 284


>gi|212711019|ref|ZP_03319147.1| hypothetical protein PROVALCAL_02088 [Providencia alcalifaciens DSM
           30120]
 gi|212686187|gb|EEB45715.1| hypothetical protein PROVALCAL_02088 [Providencia alcalifaciens DSM
           30120]
          Length = 291

 Score =  171 bits (433), Expect = 1e-40,   Method: Compositional matrix adjust.
 Identities = 103/291 (35%), Positives = 170/291 (58%), Gaps = 12/291 (4%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           + ++++++  G I    Y+      PML  +EE  LA+R    GDL AA +L+ SHLR V
Sbjct: 4   DMQSLALVPQGSI--EAYMRAANAYPMLTAEEEKELAERLHYDGDLEAAKQLILSHLRFV 61

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           + IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W
Sbjct: 62  IHIARSYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNW 121

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            +VK+ TT +Q++LFFNLR+ K  L          ++V  +A++L VS  +V+ M  R+A
Sbjct: 122 RIVKVATTKSQRKLFFNLRKNKKRL-----GWFNQDEVNMVAQELGVSTKDVLEMESRMA 176

Query: 182 GDESLNALINSSDKNSSQWQ-DWLVYDHDGQEQV--LIEKEE-RKNRRNMLTRSMSVLNP 237
             +    + +  D          ++Y  D        IE +    +  + L  +++ L+ 
Sbjct: 177 AQDMAFDMSDDDDSGDFGGPVAPVLYLQDKASDFANTIEDDNWESHATDRLADALASLDE 236

Query: 238 RERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           R + I  AR L  +N  TL+ L+ ++ VS ERVRQ+E  A KK++ +++ +
Sbjct: 237 RSQDIIRARWLDDDNKTTLQELADKYGVSAERVRQLEKNAMKKLRLAMEDE 287


>gi|254283645|ref|ZP_04958613.1| alternative sigma factor RpoH [gamma proteobacterium NOR51-B]
 gi|219679848|gb|EED36197.1| alternative sigma factor RpoH [gamma proteobacterium NOR51-B]
          Length = 291

 Score =  171 bits (432), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 104/271 (38%), Positives = 158/271 (58%), Gaps = 7/271 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  +  IPML  + E  LA++      +++A  LV +HLR VV IA  Y GYGL  
Sbjct: 24  LPAYIQAVGTIPMLSAEREQALAEKLYYGECVASARELVLAHLRFVVHIARSYSGYGLAE 83

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGN+GLM+AVK+FDP +G RL ++++ WIKA M E+ILR+W +VK+ TT  Q++L
Sbjct: 84  ADLIQEGNVGLMKAVKRFDPNKGVRLVSFAVHWIKAEMHEFILRNWRIVKVATTKAQRKL 143

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR  K +L  +T +  +     AIA+ L V E+EV  M  RL+  D + +A  ++ D
Sbjct: 144 FFNLRSAKKNLSWLTHSETQ-----AIAEDLGVPEAEVQRMEGRLSCRDMAFDAPSDADD 198

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKE-ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
            ++ Q     + D      V +E      +    L  +++ L+ R + I   R L E   
Sbjct: 199 DDAWQAPQHYLQDLSSDPAVAVEAANSSADDETRLHAALAQLDARSQDILARRWLAEKKA 258

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           TL  L++E  VS ER+RQ+EA A KK++  +
Sbjct: 259 TLHELAAEHGVSAERIRQLEANAMKKLRTGL 289


>gi|254473016|ref|ZP_05086414.1| RNA polymerase sigma factor [Pseudovibrio sp. JE062]
 gi|211957737|gb|EEA92939.1| RNA polymerase sigma factor [Pseudovibrio sp. JE062]
          Length = 289

 Score =  171 bits (432), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 102/266 (38%), Positives = 163/266 (61%), Gaps = 10/266 (3%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           RK P L K+EEY L + +    D  A  +L  SH RLV+  A+ ++ YG+P+S+++ EG+
Sbjct: 18  RKAPYLSKEEEYKLLEGWITKRDHRALDKLSLSHSRLVIAQALRFKSYGVPLSDLIQEGH 77

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+A  +F   +  R +TY+ WWIK+ +Q+Y+LR+ S+V+ GT++ QK LFF  +R++
Sbjct: 78  IGLMEAANRFKLSKDVRFSTYASWWIKSFIQDYVLRNQSIVRGGTSSRQKMLFFGFKRMR 137

Query: 144 GHLQAITDNNLKPEQV-VAIAKKLNVSESEVISMNCRLA-GDESLNALINSSDKNSSQWQ 201
             L A     L  +Q+   I+ +   +  ++  M+ RL   D SLNA +  S+ N  Q Q
Sbjct: 138 AEL-ASKHPELSEDQLHQQISNQTGANMRDIKMMSSRLGRSDTSLNATLKGSETN-LQLQ 195

Query: 202 DWLVYDHDGQEQVLIE---KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           D L  D    +++ +E     ER  RR  L  ++  L PRE+R+   R+L+E+ VTLE L
Sbjct: 196 DTLAADEPLPDEI-VEVHLDSERAERR--LFDAIKTLPPREQRVIRDRKLREDGVTLEAL 252

Query: 259 SSEFEVSRERVRQIEARAFKKVQESI 284
             +  VS+ERVRQIE+RA +K+++++
Sbjct: 253 GKKLGVSKERVRQIESRAMQKLKDAM 278


>gi|261341953|ref|ZP_05969811.1| alternative sigma factor RpoH [Enterobacter cancerogenus ATCC
           35316]
 gi|288315861|gb|EFC54799.1| alternative sigma factor RpoH [Enterobacter cancerogenus ATCC
           35316]
          Length = 285

 Score =  170 bits (431), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 111/287 (38%), Positives = 168/287 (58%), Gaps = 10/287 (3%)

Query: 4   KNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           K M  +    +G L  YI      PML  +EE  LA++    GDL AA  L+ SHLR VV
Sbjct: 3   KEMQTLALAPVGNLESYIRAANTWPMLTAEEEKELAEKLHYQGDLEAAKTLILSHLRFVV 62

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W 
Sbjct: 63  HVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWR 122

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+A 
Sbjct: 123 IVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVEMVARELGVSSKDVREMESRMAA 177

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVL--IEKEERKNR-RNMLTRSMSVLNPRE 239
            +    + +  D + SQ    ++Y  D        IE++  +++  N L+ +M  L+ R 
Sbjct: 178 QDMTFDMSSDDDASDSQPMAPVLYLQDKTSNFADGIEEDNWEDQAANKLSFAMEGLDERS 237

Query: 240 RRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + I  AR L E N  TL+ L+  + VS ERVRQ+E  A KK++ +I+
Sbjct: 238 QDIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIE 284


>gi|238755238|ref|ZP_04616583.1| RNA polymerase sigma-32 factor [Yersinia ruckeri ATCC 29473]
 gi|238706579|gb|EEP98951.1| RNA polymerase sigma-32 factor [Yersinia ruckeri ATCC 29473]
          Length = 285

 Score =  170 bits (431), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 105/289 (36%), Positives = 163/289 (56%), Gaps = 9/289 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  YI      PML  +EE  LA+R    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLALVPQGSLEAYIRAANAYPMLTAEEERELAERLHYQGDLGAAKKLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VAHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          E+V  +AK+L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRL-----GWFNQEEVELVAKELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNP 237
           +  +         D    Q    ++Y  D         EE     +  + L+ ++  L+ 
Sbjct: 176 SAQDMTFDPTPDDDVRDGQSMAPVLYLQDKTSDFADGIEEDNWESHAADKLSYALEGLDE 235

Query: 238 RERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           R + I  AR L  +N  TL+ L+ ++ VS ERVRQ+E  A KK++ +I+
Sbjct: 236 RSQHIIRARWLDDDNKTTLQELADQYGVSAERVRQLEKNAMKKLRIAIE 284


>gi|308273291|emb|CBX29894.1| RNA polymerase sigma-32 factor [uncultured Desulfobacterium sp.]
          Length = 298

 Score =  170 bits (431), Expect = 2e-40,   Method: Compositional matrix adjust.
 Identities = 100/275 (36%), Positives = 169/275 (61%), Gaps = 8/275 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLP 74
           L RY+ E+    +L ++ EY LA +  +H D  AA+ +VTS+LRLVVKIA+ + R +   
Sbjct: 22  LQRYMMEVSNHNLLSREREYALAVKVFDHDDKDAAYEIVTSNLRLVVKIALEFQRIWMQN 81

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++ EGNIGLMQAV+KFDP +  + + Y+ +WIKA + ++I+ +W LVKIGTT  Q++
Sbjct: 82  LLDLIQEGNIGLMQAVRKFDPYKNVKFSYYASFWIKAYILKFIMDNWRLVKIGTTQGQRK 141

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSS 193
                 +LK   Q + D    P+  + ++++L V+E E++ M+ RL G D SLN  +  S
Sbjct: 142 ---LFFKLKKEKQDLIDQGFDPKPKL-LSERLGVTEKEIVDMDQRLDGWDVSLNTPL--S 195

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D + S+  +++ YD D  E+ + +K+      + +     ++  RE  IF+ R   +NPV
Sbjct: 196 DDSDSEKIEFISYDSDSAEEQVAKKQMDNLIYSKIDEFRKLMTKRENEIFDLRIFSDNPV 255

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           TL+ +   + +SRERVRQ+E     K++E I++++
Sbjct: 256 TLQEIGDRYGISRERVRQLEKNIITKMREFIKEEL 290


>gi|88797598|ref|ZP_01113187.1| RNA polymerase sigma factor [Reinekea sp. MED297]
 gi|88779770|gb|EAR10956.1| RNA polymerase sigma factor [Reinekea sp. MED297]
          Length = 290

 Score =  170 bits (430), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 101/269 (37%), Positives = 149/269 (55%), Gaps = 7/269 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  +    +L  +EE  LA+R   H DL +A RLV SHLR VV IA  Y GYGL  
Sbjct: 21  LEAYITTVNGFELLSAEEEKDLAERLYYHDDLESARRLVMSHLRFVVHIAKSYSGYGLNQ 80

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM+A+++F+PE G RL ++++ WIKA + EYIL++W +VKI TT  Q++L
Sbjct: 81  GDLIQEGNVGLMKAIRRFNPEVGVRLVSFAVHWIKAEIHEYILKNWRIVKIATTKAQRKL 140

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR  K  L       L   +  AIA  L V +  V  M  RL   ++     N  D 
Sbjct: 141 FFNLRSSKKRL-----GWLNEREAQAIADDLGVEKKIVYDMEGRLTASDAAFDGFNDDDD 195

Query: 196 NSSQWQ--DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           + + +   D+L+ + D     + +     +    L  ++  L+ R R I + R L E   
Sbjct: 196 DGAAFHPSDYLMNEADDPAAAVEQANYTDDAHGQLFSALEDLDDRSRDIIQQRWLNEEKA 255

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQE 282
           TL  L+ ++ VS ER+RQ+E  A  KV++
Sbjct: 256 TLHELADKYGVSAERIRQLEKNAMNKVKK 284


>gi|15595573|ref|NP_249067.1| RNA polymerase factor sigma-32 [Pseudomonas aeruginosa PAO1]
 gi|116054106|ref|YP_788549.1| RNA polymerase factor sigma-32 [Pseudomonas aeruginosa UCBPP-PA14]
 gi|152989115|ref|YP_001345866.1| RNA polymerase factor sigma-32 [Pseudomonas aeruginosa PA7]
 gi|218889117|ref|YP_002437981.1| RNA polymerase factor sigma-32 [Pseudomonas aeruginosa LESB58]
 gi|254243475|ref|ZP_04936797.1| sigma factor RpoH [Pseudomonas aeruginosa 2192]
 gi|296386874|ref|ZP_06876373.1| RNA polymerase factor sigma-32 [Pseudomonas aeruginosa PAb1]
 gi|313112005|ref|ZP_07797792.1| RNA polymerase sigma-32 factor [Pseudomonas aeruginosa 39016]
 gi|2507390|sp|P42378|RP32_PSEAE RecName: Full=RNA polymerase sigma-32 factor
 gi|9946228|gb|AAG03765.1|AE004475_7 sigma factor RpoH [Pseudomonas aeruginosa PAO1]
 gi|765096|dbj|BAA08769.1| heat-shock sigma factor [Pseudomonas aeruginosa]
 gi|998760|gb|AAB33935.1| heat-shock sigma factor sigma 32 [Pseudomonas aeruginosa]
 gi|115589327|gb|ABJ15342.1| RNA polymerase sigma-32 factor [Pseudomonas aeruginosa UCBPP-PA14]
 gi|126196853|gb|EAZ60916.1| sigma factor RpoH [Pseudomonas aeruginosa 2192]
 gi|150964273|gb|ABR86298.1| alternative sigma factor RpoH [Pseudomonas aeruginosa PA7]
 gi|218769340|emb|CAW25100.1| sigma factor RpoH [Pseudomonas aeruginosa LESB58]
 gi|310884294|gb|EFQ42888.1| RNA polymerase sigma-32 factor [Pseudomonas aeruginosa 39016]
          Length = 284

 Score =  170 bits (430), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 102/272 (37%), Positives = 156/272 (57%), Gaps = 9/272 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+H +  IP+L  ++E  LA+R     DL AA ++V +HLR VV IA  Y GYGL  
Sbjct: 17  LEAYVHSVNSIPLLSPEQERELAERLFYQQDLEAARQMVLAHLRFVVHIAKSYSGYGLAQ 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++L
Sbjct: 77  ADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRKL 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR  K  L  + +     E+V  +A+ L V   EV  M  RL G + +     +   
Sbjct: 137 FFNLRSQKKRLAWLNN-----EEVHRVAESLGVEPREVREMESRLTG-QDMAFDPAADAD 190

Query: 196 NSSQWQDWLVY--DHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENP 252
           + S +Q    Y  DH       +E  +  +  +  L  ++  L+ R R I + R L E  
Sbjct: 191 DESAYQSPAHYLEDHRYDPARQLEDADWSDSSSANLHEALEGLDERSRDILQQRWLSEEK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL +L+ ++ VS ER+RQ+E  A  K++  I
Sbjct: 251 ATLHDLAEKYNVSAERIRQLEKNAMSKLKGRI 282


>gi|493078|gb|AAA92723.1| RpoH (sigma 32) [Pseudomonas aeruginosa]
          Length = 284

 Score =  169 bits (429), Expect = 3e-40,   Method: Compositional matrix adjust.
 Identities = 102/272 (37%), Positives = 156/272 (57%), Gaps = 9/272 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+H +  IP+L  ++E  LA+R     DL AA ++V +HLR VV IA  Y GYGL  
Sbjct: 17  LEAYVHSVNSIPLLSPEQERELAERLFYQQDLEAARQMVLAHLRFVVHIAKSYSGYGLAQ 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++L
Sbjct: 77  ADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRKL 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR  K  L  + +     E+V  +A+ L V   EV  M  RL G + +     +   
Sbjct: 137 FFNLRSQKKRLAWLNN-----EEVHRVAESLGVEPREVREMESRLTG-QDMAFDPAADAD 190

Query: 196 NSSQWQDWLVY--DHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENP 252
           + S +Q    Y  DH       +E  +  +  +  L  ++  L+ R R I + R L E  
Sbjct: 191 DESAYQSPAHYLEDHRYDPARQLEDADWSDSSSANLHEALEGLDERSRDILQQRWLSEEK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL +L+ ++ VS ER+RQ+E  A  K++  I
Sbjct: 251 ATLHDLAEKYNVSAERIRQLEKNAMSKLKGRI 282


>gi|107099361|ref|ZP_01363279.1| hypothetical protein PaerPA_01000373 [Pseudomonas aeruginosa PACS2]
          Length = 274

 Score =  169 bits (429), Expect = 4e-40,   Method: Compositional matrix adjust.
 Identities = 102/272 (37%), Positives = 156/272 (57%), Gaps = 9/272 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+H +  IP+L  ++E  LA+R     DL AA ++V +HLR VV IA  Y GYGL  
Sbjct: 7   LEAYVHSVNSIPLLSPEQERELAERLFYQQDLEAARQMVLAHLRFVVHIAKSYSGYGLAQ 66

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++L
Sbjct: 67  ADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRKL 126

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR  K  L  + +     E+V  +A+ L V   EV  M  RL G + +     +   
Sbjct: 127 FFNLRSQKKRLAWLNN-----EEVHRVAESLGVEPREVREMESRLTG-QDMAFDPAADAD 180

Query: 196 NSSQWQDWLVY--DHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENP 252
           + S +Q    Y  DH       +E  +  +  +  L  ++  L+ R R I + R L E  
Sbjct: 181 DESAYQSPAHYLEDHRYDPARQLEDADWSDSSSANLHEALEGLDERSRDILQQRWLSEEK 240

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL +L+ ++ VS ER+RQ+E  A  K++  I
Sbjct: 241 ATLHDLAEKYNVSAERIRQLEKNAMSKLKGRI 272


>gi|1710647|sp|P50510|RP32_SERMA RecName: Full=RNA polymerase sigma-32 factor
 gi|1143376|dbj|BAA09442.1| sigma-32 homolog [Serratia marcescens]
          Length = 285

 Score =  169 bits (428), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 105/289 (36%), Positives = 162/289 (56%), Gaps = 9/289 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  YI      PML  +EE  LA+R    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLALVPQGSLEAYIRAANAYPMLTAEEERELAERLHYQGDLDAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VAHIARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVELVARELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNP 237
           A  +         +    Q    ++Y  D         EE     N  + L  ++  L+ 
Sbjct: 176 AAQDMTFDPTPDDEARDGQSMAPVLYLQDKSSDFAEGIEEDNWESNAADKLAYALEGLDE 235

Query: 238 RERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           R + I  AR L  +N  TL+ L+ ++ VS ERVRQ+E  A KK++ +I+
Sbjct: 236 RSQHIIRARWLDDDNKSTLQELADQYGVSAERVRQLEKNAMKKLKMAIE 284


>gi|293393954|ref|ZP_06638260.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Serratia
           odorifera DSM 4582]
 gi|291423514|gb|EFE96737.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Serratia
           odorifera DSM 4582]
          Length = 285

 Score =  169 bits (427), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 105/289 (36%), Positives = 162/289 (56%), Gaps = 9/289 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  YI      PML  +EE  LA+R    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLALVPQGSLEAYIRAANAYPMLTAEEERELAERLHYQGDLEAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VAHIARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVELVARELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNP 237
           A  +         +    Q    ++Y  D         EE     N  + L  ++  L+ 
Sbjct: 176 AAQDMTFDPTPDDEARDGQSMAPVLYLQDKTSDFAEGIEEDNWESNAADKLAYALEGLDE 235

Query: 238 RERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           R + I  AR L  +N  TL+ L+ ++ VS ERVRQ+E  A KK++ +I+
Sbjct: 236 RSQHIIRARWLDDDNKSTLQELADQYGVSAERVRQLEKNAMKKLKMAIE 284


>gi|22124334|ref|NP_667757.1| RNA polymerase factor sigma-32 [Yersinia pestis KIM 10]
 gi|45442990|ref|NP_994529.1| RNA polymerase factor sigma-32 [Yersinia pestis biovar Microtus
           str. 91001]
 gi|51594579|ref|YP_068770.1| RNA polymerase factor sigma-32 [Yersinia pseudotuberculosis IP
           32953]
 gi|108806209|ref|YP_650125.1| RNA polymerase factor sigma-32 [Yersinia pestis Antiqua]
 gi|108810319|ref|YP_646086.1| RNA polymerase factor sigma-32 [Yersinia pestis Nepal516]
 gi|145600678|ref|YP_001164754.1| RNA polymerase factor sigma-32 [Yersinia pestis Pestoides F]
 gi|153997132|ref|ZP_02022265.1| RNA polymerase sigma-32 factor [Yersinia pestis CA88-4125]
 gi|162418961|ref|YP_001605171.1| RNA polymerase factor sigma-32 [Yersinia pestis Angola]
 gi|165926363|ref|ZP_02222195.1| alternative sigma factor RpoH [Yersinia pestis biovar Orientalis
           str. F1991016]
 gi|165939186|ref|ZP_02227737.1| alternative sigma factor RpoH [Yersinia pestis biovar Orientalis
           str. IP275]
 gi|166011667|ref|ZP_02232565.1| alternative sigma factor RpoH [Yersinia pestis biovar Antiqua str.
           E1979001]
 gi|166213537|ref|ZP_02239572.1| alternative sigma factor RpoH [Yersinia pestis biovar Antiqua str.
           B42003004]
 gi|167401873|ref|ZP_02307361.1| alternative sigma factor RpoH [Yersinia pestis biovar Antiqua str.
           UG05-0454]
 gi|167420986|ref|ZP_02312739.1| alternative sigma factor RpoH [Yersinia pestis biovar Orientalis
           str. MG05-1020]
 gi|167426241|ref|ZP_02317994.1| alternative sigma factor RpoH [Yersinia pestis biovar Mediaevalis
           str. K1973002]
 gi|170026187|ref|YP_001722692.1| RNA polymerase factor sigma-32 [Yersinia pseudotuberculosis YPIII]
 gi|186893581|ref|YP_001870693.1| RNA polymerase factor sigma-32 [Yersinia pseudotuberculosis PB1/+]
 gi|218930813|ref|YP_002348688.1| RNA polymerase factor sigma-32 [Yersinia pestis CO92]
 gi|229837138|ref|ZP_04457303.1| RNA polymerase, sigma 32 (sigma H) factor [Yersinia pestis
           Pestoides A]
 gi|229839498|ref|ZP_04459657.1| RNA polymerase, sigma 32 (sigma H) factor [Yersinia pestis biovar
           Orientalis str. PEXU2]
 gi|229900061|ref|ZP_04515198.1| RNA polymerase, sigma 32 (sigma H) factor [Yersinia pestis biovar
           Orientalis str. India 195]
 gi|229900493|ref|ZP_04515622.1| RNA polymerase, sigma 32 (sigma H) factor [Yersinia pestis
           Nepal516]
 gi|270488848|ref|ZP_06205922.1| alternative sigma factor RpoH [Yersinia pestis KIM D27]
 gi|294505476|ref|YP_003569538.1| RNA polymerase sigma factor [Yersinia pestis Z176003]
 gi|21957109|gb|AAM84008.1|AE013642_9 RNA polymerase, sigma(32) factor [Yersinia pestis KIM 10]
 gi|45437857|gb|AAS63406.1| RNA polymerase sigma-32 factor [Yersinia pestis biovar Microtus
           str. 91001]
 gi|51587861|emb|CAH19464.1| RNA polymerase sigma-32 factor [Yersinia pseudotuberculosis IP
           32953]
 gi|108773967|gb|ABG16486.1| RNA polymerase sigma-32 factor [Yersinia pestis Nepal516]
 gi|108778122|gb|ABG12180.1| RNA polymerase sigma-32 factor [Yersinia pestis Antiqua]
 gi|115349424|emb|CAL22397.1| RNA polymerase sigma-32 factor [Yersinia pestis CO92]
 gi|145212374|gb|ABP41781.1| RNA polymerase sigma-32 factor [Yersinia pestis Pestoides F]
 gi|149289438|gb|EDM39516.1| RNA polymerase sigma-32 factor [Yersinia pestis CA88-4125]
 gi|162351776|gb|ABX85724.1| alternative sigma factor RpoH [Yersinia pestis Angola]
 gi|165912959|gb|EDR31585.1| alternative sigma factor RpoH [Yersinia pestis biovar Orientalis
           str. IP275]
 gi|165921887|gb|EDR39084.1| alternative sigma factor RpoH [Yersinia pestis biovar Orientalis
           str. F1991016]
 gi|165989436|gb|EDR41737.1| alternative sigma factor RpoH [Yersinia pestis biovar Antiqua str.
           E1979001]
 gi|166205210|gb|EDR49690.1| alternative sigma factor RpoH [Yersinia pestis biovar Antiqua str.
           B42003004]
 gi|166961115|gb|EDR57136.1| alternative sigma factor RpoH [Yersinia pestis biovar Orientalis
           str. MG05-1020]
 gi|167048766|gb|EDR60174.1| alternative sigma factor RpoH [Yersinia pestis biovar Antiqua str.
           UG05-0454]
 gi|167054760|gb|EDR64564.1| alternative sigma factor RpoH [Yersinia pestis biovar Mediaevalis
           str. K1973002]
 gi|169752721|gb|ACA70239.1| RNA polymerase, sigma 32 subunit, RpoH [Yersinia pseudotuberculosis
           YPIII]
 gi|186696607|gb|ACC87236.1| RNA polymerase, sigma 32 subunit, RpoH [Yersinia pseudotuberculosis
           PB1/+]
 gi|229682512|gb|EEO78599.1| RNA polymerase, sigma 32 (sigma H) factor [Yersinia pestis
           Nepal516]
 gi|229686841|gb|EEO78920.1| RNA polymerase, sigma 32 (sigma H) factor [Yersinia pestis biovar
           Orientalis str. India 195]
 gi|229695864|gb|EEO85911.1| RNA polymerase, sigma 32 (sigma H) factor [Yersinia pestis biovar
           Orientalis str. PEXU2]
 gi|229706081|gb|EEO92090.1| RNA polymerase, sigma 32 (sigma H) factor [Yersinia pestis
           Pestoides A]
 gi|262363541|gb|ACY60262.1| RNA polymerase sigma factor [Yersinia pestis D106004]
 gi|262367470|gb|ACY64027.1| RNA polymerase sigma factor [Yersinia pestis D182038]
 gi|270337352|gb|EFA48129.1| alternative sigma factor RpoH [Yersinia pestis KIM D27]
 gi|294355935|gb|ADE66276.1| RNA polymerase sigma factor [Yersinia pestis Z176003]
 gi|320013591|gb|ADV97162.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Medievalis
           str. Harbin 35]
          Length = 285

 Score =  169 bits (427), Expect = 5e-40,   Method: Compositional matrix adjust.
 Identities = 104/289 (35%), Positives = 164/289 (56%), Gaps = 9/289 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  YI      PML  +EE  LA+R    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLALVPQGSLEAYIRAANAYPMLTAEEERELAERLHYQGDLGAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VAHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +AK+L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVELVAKELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNP 237
           +  +         +    Q+   ++Y  D         EE     +  + L+ ++  L+ 
Sbjct: 176 SAQDMTFDPSPDDEARDGQFMAPVLYLQDKTSDFADGIEEDNWDSHAADKLSYALEGLDE 235

Query: 238 RERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           R + I  AR L  EN  TL+ L+ ++ VS ERVRQ+E  A KK++ +I+
Sbjct: 236 RSQHIIRARWLDDENKSTLQELADQYGVSAERVRQLEKNAMKKLRMAIE 284


>gi|330959691|gb|EGH59951.1| putative RNA polymerase sigma-32 factor [Pseudomonas syringae pv.
           maculicola str. ES4326]
          Length = 291

 Score =  169 bits (427), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 109/292 (37%), Positives = 165/292 (56%), Gaps = 13/292 (4%)

Query: 1   MNRKNMSIIVNGEI------GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLV 54
           MN   +S     +I       L  Y+  I  +P +  +EE  L++R+ EH D+ AA +LV
Sbjct: 1   MNTPTLSTKAAAQIPMAPGSNLDAYLTVIHSLPKMSAEEERRLSERHFEHNDMDAARQLV 60

Query: 55  TSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114
           TS LR VV IA  Y GYGLP+S+++ EGNIGL++AVK+F+P    RL T+++  IKA + 
Sbjct: 61  TSQLRFVVHIARRYSGYGLPLSDLIQEGNIGLIKAVKRFNPAAQVRLITFAVHGIKAEIN 120

Query: 115 EYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVI 174
           EYILR+  +V++ TT  Q++L FNLR+     Q  +   L  ++   IA  LNVS  +V 
Sbjct: 121 EYILRNCRMVRMATTKAQRKLLFNLRK-----QPRSRTWLTADETKHIADILNVSVRDVK 175

Query: 175 SMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSM 232
            M  R+AG D S +   ++ D ++       + DH      L E E   +  +  L  ++
Sbjct: 176 EMETRMAGNDTSFDPAADADDDSALLTPAHQLGDHRYDPAHLYETENDADTSSYDLHTAL 235

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + L+ R R I   R L E   TL +L+++++VS ER+RQIE  A  K++ SI
Sbjct: 236 NSLDERSRDILAQRFLSERKATLHDLATKYKVSAERIRQIEKLALAKLKVSI 287


>gi|153947554|ref|YP_001399239.1| RNA polymerase factor sigma-32 [Yersinia pseudotuberculosis IP
           31758]
 gi|152959049|gb|ABS46510.1| alternative sigma factor RpoH [Yersinia pseudotuberculosis IP
           31758]
          Length = 285

 Score =  169 bits (427), Expect = 6e-40,   Method: Compositional matrix adjust.
 Identities = 104/289 (35%), Positives = 164/289 (56%), Gaps = 9/289 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  YI      PML  +EE  LA+R    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLALVPQGSLEAYIRAANAYPMLTAEEERELAERLHYQGDLGAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VAHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +AK+L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVELVAKELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNP 237
           +  +         +    Q+   ++Y  D         EE     +  + L+ ++  L+ 
Sbjct: 176 SAQDMTFDPSPDDEARDGQFMAPVLYLQDKTSDFADGIEEDNWDTHAADKLSYALEGLDE 235

Query: 238 RERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           R + I  AR L  EN  TL+ L+ ++ VS ERVRQ+E  A KK++ +I+
Sbjct: 236 RSQHIIRARWLDDENKSTLQELADQYGVSAERVRQLEKNAMKKLRMAIE 284


>gi|123440620|ref|YP_001004614.1| RNA polymerase factor sigma-32 [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|332159850|ref|YP_004296427.1| RNA polymerase factor sigma-32 [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|122087581|emb|CAL10362.1| RNA polymerase sigma-32 factor [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|318607604|emb|CBY29102.1| RNA polymerase sigma factor RpoH [Yersinia enterocolitica subsp.
           palearctica Y11]
 gi|325664080|gb|ADZ40724.1| RNA polymerase factor sigma-32 [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|330862604|emb|CBX72757.1| RNA polymerase sigma-32 factor [Yersinia enterocolitica W22703]
          Length = 285

 Score =  168 bits (425), Expect = 9e-40,   Method: Compositional matrix adjust.
 Identities = 105/289 (36%), Positives = 165/289 (57%), Gaps = 9/289 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  YI      PML  +EE  LA+R    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLALVPQGSLEAYIRAANAYPMLTAEEERELAERLHYQGDLEAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VAHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +AK+L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVELVAKELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL--IEKEERKNR-RNMLTRSMSVLNP 237
           +  +         +    Q    ++Y  D        IE++   N   + LT ++  L+ 
Sbjct: 176 SAQDMTFDPTPDDEVRDGQSMAPVLYLQDKTSDFADGIEEDNWDNHAADKLTYALEGLDE 235

Query: 238 RERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           R + I  AR L  +N  TL+ L+ ++ VS ERVRQ+E  A KK++ +I+
Sbjct: 236 RSQHIIRARWLDDDNKSTLQELADQYGVSAERVRQLEKNAMKKLRMAIE 284


>gi|330505413|ref|YP_004382282.1| RNA polymerase factor sigma-32 [Pseudomonas mendocina NK-01]
 gi|328919699|gb|AEB60530.1| RNA polymerase factor sigma-32 [Pseudomonas mendocina NK-01]
          Length = 284

 Score =  168 bits (425), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 101/273 (36%), Positives = 156/273 (57%), Gaps = 11/273 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+H +  IP+L  ++E  LA+      DL AA ++V +HLR VV IA  Y GYGL  
Sbjct: 17  LEAYVHAVNSIPLLTPEQERELAENLFYQQDLEAARQMVLAHLRFVVHIARSYSGYGLAQ 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGN+GLM+AVK+F+PE G RL ++++ WI+A + E+IL++W +VK+ TT  Q++L
Sbjct: 77  ADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIRAEIHEFILKNWRIVKVATTKAQRKL 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR  K  L  + ++     +V A+A+ L V   EV  M  RL G + +     +   
Sbjct: 137 FFNLRSQKKRLAWLNND-----EVTAVAESLGVEPHEVREMESRLTG-QDMAFDPAADAD 190

Query: 196 NSSQWQDWLVY--DH--DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           + S +Q    Y  DH  D   Q+        +  N L  ++  L+ R R I   R L E 
Sbjct: 191 DDSAFQSPAHYLEDHRYDPARQLEDADWSDSSSSN-LHEALESLDERSRDILYQRWLAEE 249

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL +L++++ VS ER+RQ+E  A  K++  I
Sbjct: 250 KATLHDLAAKYNVSAERIRQLEKNAMNKLKGCI 282


>gi|295698248|ref|YP_003602903.1| alternative sigma factor RpoH [Candidatus Riesia pediculicola USDA]
 gi|295698251|ref|YP_003602906.1| alternative sigma factor RpoH [Candidatus Riesia pediculicola USDA]
 gi|291157186|gb|ADD79631.1| alternative sigma factor RpoH [Candidatus Riesia pediculicola USDA]
 gi|291157289|gb|ADD79734.1| alternative sigma factor RpoH [Candidatus Riesia pediculicola USDA]
          Length = 286

 Score =  168 bits (425), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 103/291 (35%), Positives = 165/291 (56%), Gaps = 18/291 (6%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           KN S  +     LS YI      P+L  +EE      +  H DL AA +L+ SHLR V+ 
Sbjct: 3   KNKSFSLAISNNLSAYIKTAYSYPVLTMEEEKKYINLFYHHQDLRAAKKLILSHLRFVIH 62

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           I+  Y GYGL  ++++ EGN+GLM+AV+KF+P    RL ++++ WIKA + EYILR+W +
Sbjct: 63  ISKNYSGYGLLQADLIQEGNVGLMKAVQKFNPNASVRLVSFAIHWIKAEIHEYILRNWRI 122

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VK+ TT  Q++LFFNLRR K  +           ++ ++AKKL VS+ +V  M  R+   
Sbjct: 123 VKVATTKAQRKLFFNLRRNKKKIGWFDQT-----EIDSVAKKLGVSKKDVREMESRMVAK 177

Query: 184 ESLNALINSSDKNSSQWQDWL----VYDHDGQEQVLIEKEERKNRRNM----LTRSMSVL 235
           +    + + +++ +    D+     +Y  D +     E  E+ N  N     LT+++S L
Sbjct: 178 D---MVFDINEEENRMKDDFFLIPALYLED-KSSTFFESLEKDNWENHTIKRLTQALSKL 233

Query: 236 NPRERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + R + I + R L Q    TL++L+ +++VS ER+RQ+E  A KK++  I+
Sbjct: 234 DKRSQEIIKKRWLNQSGRETLQDLAKQYKVSAERIRQLEKNAMKKIRSLIE 284


>gi|126642303|ref|YP_001085287.1| EsvH [Acinetobacter baumannii ATCC 17978]
          Length = 233

 Score =  167 bits (424), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 93/231 (40%), Positives = 138/231 (59%), Gaps = 7/231 (3%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV SHLR VV IA  Y GYGLP  +++ EGN+GLM+AVK+FDP  G RL ++++ WIKA 
Sbjct: 2   LVMSHLRFVVHIARSYAGYGLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAE 61

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           + EY++R+W +VKI TT  Q++LFFNLR LK      +   L  E+  +IA  LNV+  +
Sbjct: 62  IHEYVIRNWRIVKIATTKAQRKLFFNLRSLKK-----SSKKLTLEEAQSIANDLNVTPEQ 116

Query: 173 VISMNCRL-AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTR 230
           V+ M  RL A D +  A  +  D          + D+      L+E E+  +   + L  
Sbjct: 117 VLEMEGRLTAYDAAFEAQGDDDDDTPHTAPVLYLEDNRYDPARLVENEDWEEQSTSALHD 176

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +M+ L+ R R I + R L ++  TL  L++E+ VS ER+RQ+E  A +K++
Sbjct: 177 AMNQLDDRSRNILQRRWLDDDKSTLHELAAEYNVSAERIRQLEKNAMEKIK 227


>gi|32490821|ref|NP_871075.1| RNA polymerase factor sigma-32 [Wigglesworthia glossinidia
           endosymbiont of Glossina brevipalpis]
 gi|25166027|dbj|BAC24218.1| rpoH [Wigglesworthia glossinidia endosymbiont of Glossina
           brevipalpis]
          Length = 281

 Score =  167 bits (424), Expect = 1e-39,   Method: Compositional matrix adjust.
 Identities = 101/289 (34%), Positives = 167/289 (57%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M + N+   VN +  L  YI +     ML  +EE +L +R   +GDL AA +L+ SHLR 
Sbjct: 1   MKKINILTCVN-QSSLESYIKKANSYSMLSIEEEKILTERLHYNGDLLAAKKLILSHLRF 59

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV I+  Y GYGL  ++++ EGN+GLM+AVK+F+P  G RL ++++ WIKA + EY+LR+
Sbjct: 60  VVHISRNYSGYGLQRADLIQEGNVGLMKAVKRFNPAIGVRLVSFAVHWIKAEIHEYVLRN 119

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L           +V  +AK L V+  +V  M  R+
Sbjct: 120 WRIVKVATTKAQRKLFFNLRKAKKKLGWFN-----QYEVDMLAKSLGVTSKDVREMESRM 174

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK---NRRNMLTRSMSVLNP 237
           +  +      +  DK+ +   + ++Y  D         EE     +  + L+ ++S L+ 
Sbjct: 175 SAKDMAFDFNSEEDKHKN---NAILYLKDKTSDFADTIEEDNWDIHATDKLSAALSNLDL 231

Query: 238 RERRIFEARRLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           R + I  +R L+ +N  TL+ L+ ++ +S ER+RQ+E  A KK++ +++
Sbjct: 232 RSQEIIRSRWLRYDNKSTLKELAKKYGISAERIRQLEKNAMKKIRFAVE 280


>gi|238763647|ref|ZP_04624607.1| RNA polymerase sigma-32 factor [Yersinia kristensenii ATCC 33638]
 gi|238789414|ref|ZP_04633200.1| RNA polymerase sigma-32 factor [Yersinia frederiksenii ATCC 33641]
 gi|238793542|ref|ZP_04637166.1| RNA polymerase sigma-32 factor [Yersinia intermedia ATCC 29909]
 gi|238698125|gb|EEP90882.1| RNA polymerase sigma-32 factor [Yersinia kristensenii ATCC 33638]
 gi|238722557|gb|EEQ14211.1| RNA polymerase sigma-32 factor [Yersinia frederiksenii ATCC 33641]
 gi|238727132|gb|EEQ18662.1| RNA polymerase sigma-32 factor [Yersinia intermedia ATCC 29909]
          Length = 285

 Score =  167 bits (422), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 104/289 (35%), Positives = 165/289 (57%), Gaps = 9/289 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  YI      PML  +EE  LA+R    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLALVPQGSLEAYIRAANAYPMLTAEEERELAERLHYQGDLGAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VAHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +AK+L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVELVAKELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL--IEKEERKNR-RNMLTRSMSVLNP 237
           +  +         +    Q    ++Y  D        IE++   N   + L+ ++  L+ 
Sbjct: 176 SAQDMTFDPSPDDEARDGQSMAPVLYLQDKTSDFADGIEEDNWDNHAADKLSYALEGLDE 235

Query: 238 RERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           R + I  AR L  +N  TL+ L+ ++ VS ERVRQ+E  A KK++ +I+
Sbjct: 236 RSQHIIRARWLDDDNKSTLQELADQYGVSAERVRQLEKNAMKKLRMAIE 284


>gi|238750715|ref|ZP_04612214.1| RNA polymerase sigma-32 factor [Yersinia rohdei ATCC 43380]
 gi|238711105|gb|EEQ03324.1| RNA polymerase sigma-32 factor [Yersinia rohdei ATCC 43380]
          Length = 285

 Score =  167 bits (422), Expect = 2e-39,   Method: Compositional matrix adjust.
 Identities = 103/289 (35%), Positives = 163/289 (56%), Gaps = 9/289 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  YI      PML  +EE  LA+R    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLALVPQGSLEAYIRAANAYPMLTAEEERELAERLHYQGDLGAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VAHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +AK+L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVELVAKELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNP 237
           +  +         +    Q    ++Y  D         EE     +  + L+ ++  L+ 
Sbjct: 176 SAQDMTFDPSPDDEARDGQSMAPVLYLQDKTSDFADSIEEDNWDDHAADKLSYALEGLDE 235

Query: 238 RERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           R + I  AR L  +N  TL+ L+ ++ VS ERVRQ+E  A KK++ +I+
Sbjct: 236 RSQHIIRARWLDDDNKSTLQELADQYGVSAERVRQLEKNAMKKLRMAIE 284


>gi|254784503|ref|YP_003071931.1| RNA polymerase factor sigma-32 [Teredinibacter turnerae T7901]
 gi|237687248|gb|ACR14512.1| alternative sigma factor RpoH [Teredinibacter turnerae T7901]
          Length = 284

 Score =  166 bits (421), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 102/283 (36%), Positives = 161/283 (56%), Gaps = 10/283 (3%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           + ++  G+  L+ Y+  +    +L  +EE  LA+      DL AA RLV +HLR VV IA
Sbjct: 8   LDVLAPGQ-NLNAYMQAVNNFAVLSAEEEKQLAEDLYYRQDLDAARRLVMAHLRFVVHIA 66

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGL   +++ EGN+GLM+AVK+F+PE+G RL ++++ WIKA + E+ILR+W +VK
Sbjct: 67  KSYAGYGLAQGDLIQEGNVGLMKAVKRFNPEKGVRLVSFAVHWIKAEIHEFILRNWRIVK 126

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           + TT  Q++LFFNLR  K  L  +T+     ++  A+A+ LNV    V  M  RL+    
Sbjct: 127 VATTKAQRKLFFNLRGQKKRLAWLTN-----DEANAVAQDLNVDVKNVREMESRLSA-YD 180

Query: 186 LNALINSSDKNSSQWQDWLVYDHD---GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
                 + D + + +Q    Y  D       +L   +  +N    L R+M  L+ R R I
Sbjct: 181 AAFDAGADDDDETAYQAPANYLEDRRYDPSTMLENADWTENSVAGLERAMDQLDDRSRDI 240

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            + R L ++  TL  L+ ++ VS ER+RQ+E  A KK++ +++
Sbjct: 241 LQQRWLSDSKATLHELADKYGVSAERIRQLEKNAMKKMRVAME 283


>gi|21672319|ref|NP_660386.1| RNA polymerase factor sigma-32 [Buchnera aphidicola str. Sg
           (Schizaphis graminum)]
 gi|25091196|sp|Q8KA76|RP32_BUCAP RecName: Full=RNA polymerase sigma-32 factor
 gi|21622919|gb|AAM67597.1| RNA polymerase sigma-32 factor [Buchnera aphidicola str. Sg
           (Schizaphis graminum)]
          Length = 285

 Score =  166 bits (421), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 98/274 (35%), Positives = 157/274 (57%), Gaps = 9/274 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI      PML  +EE +L KR R H DL AA  L+ SHLR V+ I+  Y GYGL  
Sbjct: 16  LDAYIRIANLWPMLSIKEEKLLTKRLRYHDDLDAAKTLILSHLRFVIHISRNYSGYGLLQ 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+AV++F+P+ G RL ++++ WIK+ + EY+LR+W +VK+ TT +Q++L
Sbjct: 76  ADLIQEGNIGLMKAVRRFNPDIGVRLVSFAVHWIKSEIHEYVLRNWRIVKVATTKSQRKL 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR+ K  L          E++  +A++L VS  +V  M  R++  +         D 
Sbjct: 136 FFNLRKNKKRLGWFN-----QEEIEIVARELGVSSEDVREMESRMSAQDITFNPFPEEDL 190

Query: 196 NSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-QEN 251
              +    + Y  D        L +    K+  + L+ ++  L+ R R I  AR L ++ 
Sbjct: 191 KDGKINGNMFYLQDKTSNFANGLEQDNWNKHTTSKLSNALLRLDERSRNIIRARWLDKKE 250

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             TL+ +++ + +S ERVRQ+E  A KK++ +I+
Sbjct: 251 KNTLQKIANNYGISAERVRQLEKNAMKKLKIAIE 284


>gi|238784413|ref|ZP_04628423.1| RNA polymerase sigma-32 factor [Yersinia bercovieri ATCC 43970]
 gi|238714705|gb|EEQ06707.1| RNA polymerase sigma-32 factor [Yersinia bercovieri ATCC 43970]
          Length = 285

 Score =  166 bits (421), Expect = 3e-39,   Method: Compositional matrix adjust.
 Identities = 104/289 (35%), Positives = 164/289 (56%), Gaps = 9/289 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  YI      PML  +EE  LA+R    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLALVPQGSLEAYIRAANAYPMLTAEEERELAERLHYQGDLGAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VAHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +AK+L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVELVAKELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL--IEKEERKNR-RNMLTRSMSVLNP 237
           +  +         +    Q    ++Y  D        IE++   N   + L  ++  L+ 
Sbjct: 176 SAQDMTFDPSPDDEARDGQSMAPVLYLQDKTSDFADGIEEDNWDNHAADKLAYALEGLDE 235

Query: 238 RERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           R + I  AR L  +N  TL+ L+ ++ VS ERVRQ+E  A KK++ +I+
Sbjct: 236 RSQHIIRARWLDDDNKSTLQELADQYGVSAERVRQLEKNAMKKLRMAIE 284


>gi|319760734|ref|YP_004124672.1| RNA polymerase sigma-32 factor [Candidatus Blochmannia vafer str.
           BVAF]
 gi|318039448|gb|ADV33998.1| RNA polymerase sigma-32 factor [Candidatus Blochmannia vafer str.
           BVAF]
          Length = 284

 Score =  166 bits (420), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 106/284 (37%), Positives = 168/284 (59%), Gaps = 10/284 (3%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           KN+S++  G   L  YI      PML  +EE  LA+R   + DL+AA +L+ SHLR VV 
Sbjct: 8   KNISLVPQG--TLEAYIRATNLYPMLTAEEERELAERLYYNSDLNAAKKLIVSHLRFVVH 65

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y GYGL  ++++ EGNIGLM++V++F+PE   RL ++++ WIK+ + EY+L++W +
Sbjct: 66  IARNYSGYGLAQADLIQEGNIGLMKSVRRFNPELDVRLVSFAVHWIKSEIHEYVLKNWRI 125

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VKI TT  Q++LFFNLR+ K  L    +     E++  +AK L+V+  +V  M  R+A  
Sbjct: 126 VKIATTKAQRKLFFNLRKTKQRLGWFNE-----EEIEMVAKTLHVTCKDVREMESRMAA- 179

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           + +    +S D   +     ++Y  D    +  E+E      N L  +++ L+ R + I 
Sbjct: 180 QDMTFEQSSDDDEKNILSIPMLYLQDKVTMIDEEEEWINQVSNKLNIALNSLDKRSQHII 239

Query: 244 EARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            AR L   +N  TL+ L++++ VS ER+RQ+E  A KK++  IQ
Sbjct: 240 RARWLNTNDNKTTLQELANQYGVSAERIRQLEKNAMKKMKLIIQ 283


>gi|14530750|emb|CAC42416.1| RpoH protein [Ralstonia metallidurans CH34]
          Length = 317

 Score =  166 bits (420), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 97/248 (39%), Positives = 142/248 (57%), Gaps = 9/248 (3%)

Query: 6   MSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
            ++   G +G L  YI  + +IPML  +EE  LA+  R++  + AA R+V SHLRLVV I
Sbjct: 47  FALTFPGTLGNLDSYIQAVHRIPMLTPEEELSLARDLRDNDSVDAARRMVMSHLRLVVSI 106

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y GYGLP ++++ EGNIGLM+AVK+FDPE+            +  + EY+L++W +V
Sbjct: 107 ARQYLGYGLPHADLIQEGNIGLMKAVKRFDPEQACAWCRTRCTGSRPEIHEYVLKNWRMV 166

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GD 183
           K+ TT  Q++LFFNLR    H Q    +   PEQ+ A+A++LNV   EV+ M  R++ GD
Sbjct: 167 KVATTKAQRKLFFNLR---SHKQG--SHTFTPEQIEAVARELNVKPEEVMEMETRMSGGD 221

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            +L   I   ++  +    +L  +H+   QVL E + R +      R      P +RRI 
Sbjct: 222 MALEGQIEDGEEEFAPIA-YLADNHNEPTQVL-EAKRRPSAGRGPGRGADEAGPAQRRII 279

Query: 244 EARRLQEN 251
           EAR L  N
Sbjct: 280 EARWLDVN 287


>gi|238798006|ref|ZP_04641495.1| RNA polymerase sigma-32 factor [Yersinia mollaretii ATCC 43969]
 gi|238718109|gb|EEQ09936.1| RNA polymerase sigma-32 factor [Yersinia mollaretii ATCC 43969]
          Length = 285

 Score =  166 bits (420), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 103/289 (35%), Positives = 162/289 (56%), Gaps = 9/289 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  YI      PML  +EE  LA+R    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLALVPQGSLEAYIRAANAYPMLTAEEERELAERLHYQGDLGAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VAHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +AK+L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVELVAKELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK---NRRNMLTRSMSVLNP 237
           +  +         +    Q    ++Y  D         EE     +  + L  ++  L+ 
Sbjct: 176 SAQDMTFDPSPDDEARDGQSMAPVLYLQDKTSDFADSIEEDNWDGHAADKLAYALEGLDE 235

Query: 238 RERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           R + I  AR L  +N  TL+ L+ ++ VS ERVRQ+E  A KK++ +I+
Sbjct: 236 RSQHIIRARWLDDDNKSTLQELADQYGVSAERVRQLEKNAMKKLRMAIE 284


>gi|331007677|ref|ZP_08330813.1| RNA polymerase sigma factor RpoH [gamma proteobacterium IMCC1989]
 gi|330418520|gb|EGG93050.1| RNA polymerase sigma factor RpoH [gamma proteobacterium IMCC1989]
          Length = 288

 Score =  166 bits (420), Expect = 4e-39,   Method: Compositional matrix adjust.
 Identities = 104/277 (37%), Positives = 160/277 (57%), Gaps = 10/277 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           ++ Y+  +    +L  +EE  L +R   H DL AA  LV +HLR VV IA  Y GYGL  
Sbjct: 17  INAYMQAVNSFAVLTVEEEKDLGERLYYHEDLDAARGLVMAHLRFVVHIAKSYAGYGLSQ 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           S+++ EGN+GLM+AVK+F+PE+G RL ++++ WIKA M E+ILR+W +VK+ TT  Q++L
Sbjct: 77  SDLIQEGNVGLMKAVKRFNPEKGVRLVSFAVHWIKAEMHEFILRNWRIVKVATTKAQRKL 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR  K  L       L  ++  A+A  LNV    V  M  RL+     +   ++ D 
Sbjct: 137 FFNLRGQKKRL-----GWLSYDEATAVAADLNVEVKHVHEMESRLSA-YDASFDADNDDD 190

Query: 196 NSSQWQDWLVYDHDGQ---EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-QEN 251
           + S ++    Y  D +    Q L   +   +  + L  +++ L+ R + I + R L  +N
Sbjct: 191 DESAYKAPANYLEDHRYNPAQELEASDWSDDNASRLRTALATLDERSQVIIQRRWLNDDN 250

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
             TL  L++EF VS ER+RQ+E  A KKV+ +++ +V
Sbjct: 251 KSTLHELAAEFGVSAERIRQLEKNAMKKVKTAMETEV 287


>gi|238759635|ref|ZP_04620796.1| RNA polymerase sigma-32 factor [Yersinia aldovae ATCC 35236]
 gi|238702178|gb|EEP94734.1| RNA polymerase sigma-32 factor [Yersinia aldovae ATCC 35236]
          Length = 285

 Score =  166 bits (419), Expect = 5e-39,   Method: Compositional matrix adjust.
 Identities = 105/290 (36%), Positives = 166/290 (57%), Gaps = 11/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  YI      PML  +EE  LA+R    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLALVPQGSLEAYIRAANAYPMLTAEEERELAERLHYQGDLGAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VAHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +AK+L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVELVAKELGVTSKDVREMESRM 175

Query: 181 -AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLN 236
            A D + +   +   ++       ++Y  D         EE     +  + L+ +M  L+
Sbjct: 176 SAQDMTFDPSPDDEARDGHSMAP-VLYLQDKSSDFADGIEEDNWDSHAADKLSYAMEGLD 234

Query: 237 PRERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            R + I  AR L  +N  TL+ L+ ++ VS ERVRQ+E  A KK++ +I+
Sbjct: 235 ERSQHIIRARWLDDDNKSTLQELADQYGVSAERVRQLEKNAMKKLRMAIE 284


>gi|149923127|ref|ZP_01911542.1| RNA polymerase sigma-C factor [Plesiocystis pacifica SIR-1]
 gi|149816035|gb|EDM75549.1| RNA polymerase sigma-C factor [Plesiocystis pacifica SIR-1]
          Length = 304

 Score =  166 bits (419), Expect = 6e-39,   Method: Compositional matrix adjust.
 Identities = 99/281 (35%), Positives = 152/281 (54%), Gaps = 25/281 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
             RY+  +     ++ + E  LA+ Y E GD  A  RL+ +HLR VV IA GYR YG P+
Sbjct: 21  FERYVAHVSSFEEIDGERERELARAYHE-GDRLAGQRLIEAHLRDVVAIARGYRNYGHPM 79

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           +E+V+EGN+GL++A++ FDPERG R  TY  +W++A +  ++ RSWSLV++G+++   RL
Sbjct: 80  AELVAEGNVGLVRALESFDPERGLRFMTYGRYWVRARILAHVQRSWSLVRVGSSSAHTRL 139

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN-----AL 189
           F+ L R +G  QA         +  A+A+    SE+ V +M  R+ G D SL+     AL
Sbjct: 140 FYGLHRARGRFQATAGERDGAAERAALAEYFGCSEAHVEAMAARIDGRDLSLDHPSSAAL 199

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           ++ S                  E  + E+E  +  R  +   +  L+PRER I   R L 
Sbjct: 200 VSESTV----------------EATIFEREVGELVRERIAAVIRELDPRERVILRRRLLD 243

Query: 250 E--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           E  +P +L  +  E  +SRER RQ+E R   K++  +   V
Sbjct: 244 ESGSPPSLVEVGRELGLSRERTRQLEQRVKTKLRRRLHDVV 284


>gi|149188340|ref|ZP_01866634.1| RNA polymerase sigma factor [Vibrio shilonii AK1]
 gi|148837929|gb|EDL54872.1| RNA polymerase sigma factor [Vibrio shilonii AK1]
          Length = 285

 Score =  164 bits (414), Expect = 2e-38,   Method: Compositional matrix adjust.
 Identities = 100/286 (34%), Positives = 164/286 (57%), Gaps = 12/286 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+  N +I  N    LS Y+  +    +L++ EE  LA     + +     +LV  HLR 
Sbjct: 1   MSHSNAAISFNNSQNLSYYMQYVNSHSILKECEERQLANDLYYNNNEDVISKLVLPHLRY 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA G+ GYGLP+ +++  GNIGL++AVKKF+PE GFRL ++++ WIK+ + ++I+++
Sbjct: 61  VVYIAKGFAGYGLPLVDMIQSGNIGLLKAVKKFNPELGFRLVSFAVHWIKSEITDFIIKN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WS+VKI TT +Q++LFFNL++ K   + ++++     +   +A KL VS+ +V+SM+ RL
Sbjct: 121 WSIVKIATTKSQRKLFFNLKKYKQSQEWMSES-----EAENLASKLKVSKKDVLSMDGRL 175

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM---LTRSMSVLN 236
           +  D  ++  I   +       +      + Q  V IE E +   R++   L   ++ L+
Sbjct: 176 SARDSYIDPKIGEDEDQVISTGEVFA---EPQLDVAIEYETQDWDRHINDELNAGLAKLD 232

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            R R I  +R L    VTL  L+    VS ERVRQIE    +K+++
Sbjct: 233 ARSRDIIVSRWLLSEKVTLNELAERHRVSAERVRQIELMTLEKLKD 278


>gi|153876074|ref|ZP_02003579.1| RNA polymerase sigma-32 factor [Beggiatoa sp. PS]
 gi|152067462|gb|EDN66421.1| RNA polymerase sigma-32 factor [Beggiatoa sp. PS]
          Length = 242

 Score =  163 bits (412), Expect = 4e-38,   Method: Compositional matrix adjust.
 Identities = 93/240 (38%), Positives = 150/240 (62%), Gaps = 7/240 (2%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L    +LV SHLR V+ IA GYRGYGLP+++++ EGNIGLM+AVK+F+P  G RL ++++
Sbjct: 4   LKPPKKLVISHLRFVLYIAHGYRGYGLPLADLIQEGNIGLMKAVKRFNPNVGVRLVSFAV 63

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            WI+A + E+ILR+W +VK+ TT  Q++LFFNLR +K  L       L   +V  +A+ L
Sbjct: 64  HWIRAEIHEFILRNWRIVKVVTTKAQRKLFFNLRSMKKRL-----GWLSQAEVDKVAQDL 118

Query: 167 NVSESEVISMNCRLA-GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE-RKNR 224
            VS  +V+ M  RL+  D + +A ++S D +        + D+      L+E++E   + 
Sbjct: 119 GVSSKDVLEMEKRLSMQDVAFDAPVDSDDDDEVFAPAAYLEDNRYDPAALVEQDEWEAHG 178

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              L  +   L+ R + I + R L E+  TL+ L++ ++VS ER+RQIE+ A KK+++++
Sbjct: 179 HKQLLHAFKKLDVRSQDILQQRWLSEDKATLQELANHYKVSAERIRQIESNALKKLKKNM 238


>gi|238899138|ref|YP_002924820.1| sigma H (sigma 32) factor of RNA polymerase; transcription of heat
           shock and stress proteins [Candidatus Hamiltonella
           defensa 5AT (Acyrthosiphon pisum)]
 gi|229466898|gb|ACQ68672.1| sigma H (sigma 32) factor of RNA polymerase; transcription of heat
           shock and stress proteins [Candidatus Hamiltonella
           defensa 5AT (Acyrthosiphon pisum)]
          Length = 285

 Score =  162 bits (411), Expect = 5e-38,   Method: Compositional matrix adjust.
 Identities = 96/246 (39%), Positives = 144/246 (58%), Gaps = 11/246 (4%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           HGDL+AA +L+ SHLR V  IA  Y GYGLP ++++ EGNIGLM+AV++F+P  G RL +
Sbjct: 44  HGDLNAARQLILSHLRFVAHIARHYSGYGLPQADLIQEGNIGLMKAVRRFNPNMGVRLVS 103

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           +++ WIKA + EY+LR+W +VK+ TT  Q++LFFNLR+ K  L   + N     +V  +A
Sbjct: 104 FAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKAKQRLGWFSQN-----EVDMVA 158

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           K+L V+  +V  M  R++  +    L    +    Q    ++Y  D       +  E+ N
Sbjct: 159 KELGVTSKDVREMESRMSAQDMAFELPLEDESREGQSPAPVMYLEDKNSD-FADNIEKNN 217

Query: 224 RRNMLTRSMSV----LNPRERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFK 278
             +    S+ V    L+ R + I  AR L  +N  TL+ L+  + VS ERVRQ+E  A K
Sbjct: 218 WGDHAADSLWVALKGLDERSQDIIRARWLDDDNKSTLQELADRYGVSAERVRQLEKNAMK 277

Query: 279 KVQESI 284
           K++ SI
Sbjct: 278 KLRLSI 283


>gi|46204236|ref|ZP_00050286.2| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Magnetospirillum magnetotacticum
           MS-1]
          Length = 182

 Score =  161 bits (407), Expect = 1e-37,   Method: Compositional matrix adjust.
 Identities = 77/166 (46%), Positives = 115/166 (69%), Gaps = 1/166 (0%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L + EE  LA  ++E  D  A HRL+++H+RLV+ +A  +R YGLP++++V EG++GL
Sbjct: 4   PFLARDEERGLAVAWKEERDERALHRLISAHMRLVIALAGRFRHYGLPMADLVQEGHVGL 63

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 64  MEAAARFEPEREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRARL 123

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALIN 191
              T+  +  E    IA  + VS  +V  M+ RL+G D SLNA + 
Sbjct: 124 MQSTEEQVGSEIHGRIATAIGVSREDVALMDARLSGPDMSLNAPVG 169


>gi|218777994|ref|YP_002429312.1| RNA polymerase, sigma 70 family subunit [Desulfatibacillum
           alkenivorans AK-01]
 gi|218759378|gb|ACL01844.1| putative RNA polymerase, sigma 70 family subunit [Desulfatibacillum
           alkenivorans AK-01]
          Length = 328

 Score =  160 bits (406), Expect = 2e-37,   Method: Compositional matrix adjust.
 Identities = 104/275 (37%), Positives = 162/275 (58%), Gaps = 8/275 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLP 74
           L RY+ EI K P+L ++EE  LA R +E  D  AA+RLVT++LRLVVKIA+ + R +   
Sbjct: 42  LQRYLSEISKYPLLTREEERELAVRVQEFDDPDAAYRLVTANLRLVVKIALEFQRVWMQN 101

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++ EGNIGLMQA +KFDP +  + + YS +WIKA + ++I+ +W LVKIGTT  Q R
Sbjct: 102 LLDLIQEGNIGLMQAARKFDPYKNVKFSYYSSFWIKAYILKFIMDNWRLVKIGTTQAQ-R 160

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSS 193
             F   + +         + KP+    +++KL VSE ++I M+ RL   D SL+A +   
Sbjct: 161 KLFFKLKKEKQKLLEEGFDPKPK---LLSEKLGVSERDIIDMDQRLNNWDLSLDAPVK-- 215

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D + S+  ++L    +  E  +  KE     R  +      L  RE  IF+ R   ++PV
Sbjct: 216 DDSDSERIEFLSTPSESAEDQVARKEMETILREKIDIFRKTLKERELEIFDERVFSDSPV 275

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           TL+ +     +SRERVRQ+E+   KK++  ++K++
Sbjct: 276 TLQQIGDRHGISRERVRQVESGVVKKLKAFLEKEI 310


>gi|306841478|ref|ZP_07474178.1| RNA polymerase factor sigma-32 [Brucella sp. BO2]
 gi|306288442|gb|EFM59798.1| RNA polymerase factor sigma-32 [Brucella sp. BO2]
          Length = 198

 Score =  159 bits (402), Expect = 4e-37,   Method: Compositional matrix adjust.
 Identities = 86/195 (44%), Positives = 128/195 (65%), Gaps = 1/195 (0%)

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
            R +TY+ WWI+A+MQ+YILR+WS+V+ GT++ QK LFFNLRRL+  L    DN  K E 
Sbjct: 1   MRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKALFFNLRRLRSKLAQTDDNMTKAEI 60

Query: 159 VVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
              I+ +L VS S+V  M+ RL+G D SL+A +N  +  +S+  D+LV DH  Q+++   
Sbjct: 61  YREISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIAES 120

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
             + + R   LTR++  LN RE  I   RRL ++ VTLE L  +  +S+ERVRQIE+RA 
Sbjct: 121 SIDMERRNRWLTRALDTLNERELHIIRERRLDDDGVTLEALGEKLGISKERVRQIESRAM 180

Query: 278 KKVQESIQKQVELSS 292
           +K++ ++  Q EL++
Sbjct: 181 EKLKIALLSQHELAA 195


>gi|213027483|ref|ZP_03341930.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. 404ty]
          Length = 253

 Score =  157 bits (398), Expect = 1e-36,   Method: Compositional matrix adjust.
 Identities = 99/263 (37%), Positives = 142/263 (53%), Gaps = 32/263 (12%)

Query: 4   KNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           K M  +    +G L  YI      PML   EE  LA+R    GDL AA  L+ SHLR VV
Sbjct: 3   KEMQNLALAPVGNLESYIRAANAWPMLSADEERALAERLHYQGDLEAAKTLILSHLRFVV 62

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W 
Sbjct: 63  HIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWR 122

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+A 
Sbjct: 123 IVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVEMVARELGVSSKDVREMESRMAA 177

Query: 183 DE--------------SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            +               +  ++   DK SS + D  + D + +EQ            N L
Sbjct: 178 QDMTFDMSSDDESDSQPMAPVLYLQDK-SSNFAD-GIEDDNWEEQAA----------NRL 225

Query: 229 TRSMSVLNPRERRIFEARRLQEN 251
           T +M  L+ R + I  AR L E+
Sbjct: 226 TDAMQGLDERSQDIIRARWLDED 248


>gi|308273000|emb|CBX29604.1| hypothetical protein N47_J05850 [uncultured Desulfobacterium sp.]
          Length = 326

 Score =  157 bits (397), Expect = 2e-36,   Method: Compositional matrix adjust.
 Identities = 96/275 (34%), Positives = 166/275 (60%), Gaps = 14/275 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY-GLPISE 77
           Y+ EI +  +L ++EE  LA   ++  D  +A +L+TS+LRLVVKIA  ++ Y    + +
Sbjct: 49  YLREISQYRLLSREEEIELAINVKDKDDKESASKLITSNLRLVVKIAFNFQHYLANNVPD 108

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGL+ AVKK+DP +G + + Y+ +WI+A + ++I+ +W ++KIGTT  Q++LFF
Sbjct: 109 LIQEGNIGLIHAVKKYDPYKGVKFSYYAAFWIRAYIFKFIMNNWDMLKIGTTQKQRKLFF 168

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
           NL + +   + IT   L PE  + +A++L V E++++ M  RL  D S  +L     ++S
Sbjct: 169 NLNKER---RQITAEGLNPEPKL-LAERLGVQENDIVQMIPRL--DYSPLSLNQPLSEDS 222

Query: 198 SQWQDWLVYDHDG----QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
            +  +  V D +     Q  VL   E + N    L +   +L   +  IF+ R + ENPV
Sbjct: 223 KECLEERVQDKNASTIDQLSVL---ESKTNLERELKKFRKLLKGIKADIFDMRIMAENPV 279

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +L+++   +++SRERVRQI+     K+ + ++KQ+
Sbjct: 280 SLQSIGDRYQISRERVRQIQEMIINKIGKWLKKQI 314


>gi|218677311|ref|ZP_03525208.1| RNA polymerase factor sigma-32 [Rhizobium etli CIAT 894]
          Length = 171

 Score =  156 bits (394), Expect = 4e-36,   Method: Compositional matrix adjust.
 Identities = 77/170 (45%), Positives = 119/170 (70%), Gaps = 3/170 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L +QEE+ LA R+++H D  A +++  +H+RLV+ +A  +R +GLP+S++V EG +GL
Sbjct: 3   PYLARQEEHDLAIRWKDHDDRGARNQIAMAHMRLVISMAGKFRNFGLPMSDLVQEGYVGL 62

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +F+P+R  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 63  LEAAARFEPDRDVRFSTYASWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRAKL 122

Query: 147 QAITDNNLKPEQV-VAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
            A  D  L  + +   IA  L VS ++V +M+ RL+G D SL A   S D
Sbjct: 123 -AKGDTQLTLQSIHQEIAAALGVSLADVQTMDARLSGNDASLQAPSVSGD 171


>gi|68171972|ref|ZP_00545278.1| Sigma-70 region 4 [Ehrlichia chaffeensis str. Sapulpa]
 gi|67998602|gb|EAM85349.1| Sigma-70 region 4 [Ehrlichia chaffeensis str. Sapulpa]
          Length = 205

 Score =  155 bits (392), Expect = 6e-36,   Method: Compositional matrix adjust.
 Identities = 87/192 (45%), Positives = 125/192 (65%), Gaps = 3/192 (1%)

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P  GFRL+TY++WWIKA +++YIL+SWS +KIGTT  Q++LFF+LR++K  L    ++N+
Sbjct: 1   PTLGFRLSTYAIWWIKAFIKDYILKSWSCIKIGTTQAQRKLFFSLRKIKKKLFKY-NHNI 59

Query: 155 KPEQVVAIAKKLNVSESEVISMN-CRLAGDESLNALINSSD-KNSSQWQDWLVYDHDGQE 212
             E +  IA K + SE EV  MN   L  D SLN L+ S+D +N  + Q+ +  D   QE
Sbjct: 60  TKEDIKLIANKCSTSEQEVEQMNRYFLYRDRSLNELVFSNDNQNGVELQEIIKCDTPNQE 119

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
              +  EE   ++ ++++++S LN R R IF  RRL E P TL+ LS E+ +S+ERVRQI
Sbjct: 120 DTYLLNEELNIKKALISQALSTLNERYRDIFIRRRLIEEPDTLDKLSQEYNISKERVRQI 179

Query: 273 EARAFKKVQESI 284
           E  AF KV+  I
Sbjct: 180 EMHAFTKVKNFI 191


>gi|116514965|ref|YP_802594.1| RNA polymerase sigma-32 factor [Buchnera aphidicola str. Cc (Cinara
           cedri)]
 gi|116256819|gb|ABJ90501.1| RNA polymerase sigma-32 factor [Buchnera aphidicola str. Cc (Cinara
           cedri)]
          Length = 291

 Score =  155 bits (391), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 92/284 (32%), Positives = 162/284 (57%), Gaps = 24/284 (8%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  YI       +L  ++E  LAK+   + D+ +A  L+ S+LR V+ +A  Y GYGLP
Sbjct: 18  SLEAYIRLANSFSILTSEKEKSLAKKLFFYSDIESAKLLILSNLRFVIHVAKNYSGYGLP 77

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGNIGLM+A+++F+P    RL ++++ WIK+ + EY+LR+W +VKI TT  Q++
Sbjct: 78  QADLIQEGNIGLMKAIRRFNPNINVRLVSFAVHWIKSEIHEYVLRNWRIVKIATTKAQRK 137

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL----------AGDE 184
           LFFNLR+ K  L           ++  ++++L VS  EV  M  R+          A D 
Sbjct: 138 LFFNLRKSKKRLGW-----FNRHEIDTVSQELGVSTQEVKEMEARMSAQDITFDLSAKDS 192

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLNPRERRIF 243
            L+++ N+   +      + + D      + IEK+    +  N LT ++ +L+ R ++I 
Sbjct: 193 HLDSITNNLRTS------FHLEDKKSNFSIKIEKDNWALHATNKLTNALLILDKRSQQII 246

Query: 244 EARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + R L ++   +TL+ ++ ++ +S ERVRQ+E  A KK++ +I+
Sbjct: 247 KRRWLDDDKPKITLQAIARDYGISAERVRQLEKNAMKKLKIAIE 290


>gi|213421295|ref|ZP_03354361.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. E01-6750]
          Length = 191

 Score =  154 bits (390), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 80/182 (43%), Positives = 112/182 (61%), Gaps = 6/182 (3%)

Query: 4   KNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           K M  +    +G L  YI      PML   EE  LA+R    GDL AA  L+ SHLR VV
Sbjct: 3   KEMQNLALAPVGNLESYIRAANAWPMLSADEERALAERLHYQGDLEAAKTLILSHLRFVV 62

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W 
Sbjct: 63  HIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWR 122

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+A 
Sbjct: 123 IVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDEVEMVARELGVSSKDVREMESRMAA 177

Query: 183 DE 184
            +
Sbjct: 178 QD 179


>gi|302036735|ref|YP_003797057.1| RNA polymerase, sigma 32 (sigma H) factor [Candidatus Nitrospira
           defluvii]
 gi|300604799|emb|CBK41131.1| RNA polymerase, sigma 32 (sigma H) factor [Candidatus Nitrospira
           defluvii]
          Length = 340

 Score =  154 bits (389), Expect = 2e-35,   Method: Compositional matrix adjust.
 Identities = 97/274 (35%), Positives = 159/274 (58%), Gaps = 7/274 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EIR+ P L K+EE  L + Y+  G   AA +L+ ++LR+ V IA  Y   G   
Sbjct: 65  LQQYLTEIRRYPYLSKEEELRLFEEYQLRGSRDAAMKLILANLRVSVSIASEYLHTGADH 124

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GL+QA+KKFDP +  R   Y+ WW +A +  Y+L ++ L+K+GTT +Q++L
Sbjct: 125 MDLIQEGNVGLLQAIKKFDPTKNVRFYAYAAWWARAYILRYLLNTYRLIKVGTTQDQRKL 184

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
           F+NL++ K  L+        P+  + +A +LNV E +VI M+ RL   E SL+  I    
Sbjct: 185 FYNLKKEKAKLER---EGFAPDSKL-LADRLNVRERDVIEMDQRLGSWELSLDQPIGQ-- 238

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
           +N     D L       ++ L + + +   R  L      L+ RE  I   R L E P+T
Sbjct: 239 ENDGTLMDILPAHEQPADERLADTQLKALFRRKLAEFTKTLDEREEDILRNRILSETPLT 298

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           LE++ +++ +++ER RQ+EAR  K++++ I+K V
Sbjct: 299 LEDMGAKYGITKERTRQLEARIIKRLRDYIKKDV 332


>gi|330980004|gb|EGH78270.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. aptata
           str. DSM 50252]
          Length = 214

 Score =  149 bits (377), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 80/194 (41%), Positives = 119/194 (61%), Gaps = 6/194 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+H +  IP+L  ++E  LA+      DL AA ++V +HLR VV IA  Y GYGL  
Sbjct: 17  LEAYVHTVNSIPLLTPEQERELAESLYYEQDLDAARQMVLAHLRFVVHIARSYSGYGLAQ 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++L
Sbjct: 77  ADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRKL 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR  K  L  +  NN   ++V  +A+ L V   EV  M  RL G D + +    + D
Sbjct: 137 FFNLRSQKKRLAWL--NN---DEVHRVAESLGVEPREVREMESRLTGHDMAFDPAAEADD 191

Query: 195 KNSSQWQDWLVYDH 208
            ++ Q     + DH
Sbjct: 192 DSAFQSPANYLEDH 205


>gi|149188355|ref|ZP_01866649.1| RNA polymerase sigma factor [Vibrio shilonii AK1]
 gi|148837944|gb|EDL54887.1| RNA polymerase sigma factor [Vibrio shilonii AK1]
          Length = 290

 Score =  149 bits (375), Expect = 6e-34,   Method: Compositional matrix adjust.
 Identities = 88/272 (32%), Positives = 147/272 (54%), Gaps = 13/272 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            LS Y+  I K P+L +++E  LA +        + + L+  HLR V  IA  + GYG+ 
Sbjct: 15  SLSHYLGSISKYPLLSEEKERTLANKVVTENCSQSLNELILPHLRYVAYIAKNFVGYGMS 74

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
             +++  GN+GL++A+KKF+P RG RL ++++ WIK+ + EYI+++WS+VK+ TT  Q++
Sbjct: 75  TLDIIQAGNVGLIKAIKKFNPARGIRLVSFAIHWIKSEINEYIIKNWSMVKVATTKEQRK 134

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSS 193
           LFFNLR+ K     +++     EQ   IAK L V   +V  M+ RL+  D+ L +     
Sbjct: 135 LFFNLRKHKNDSGWVSE-----EQAKDIAKNLKVRVRDVFVMDGRLSNKDKQLESHNYDE 189

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV----LNPRERRIFEARRLQ 249
           + +    +D    +H        +  E +N  N L+  + +    L+ R + I   R L 
Sbjct: 190 EFHCPYTEDNYFREHRDD---FADNHEEENWSNHLSSELKIAIQKLDERSKDIIFHRWLT 246

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
               TL  L+ + ++S ER+RQIE     K++
Sbjct: 247 NEKATLSELADKHQLSAERIRQIEVATLAKLK 278


>gi|251771333|gb|EES51914.1| RNA polymerase, sigma 70 subunit, RpoD family [Leptospirillum
           ferrodiazotrophum]
          Length = 307

 Score =  149 bits (375), Expect = 7e-34,   Method: Compositional matrix adjust.
 Identities = 98/294 (33%), Positives = 158/294 (53%), Gaps = 15/294 (5%)

Query: 10  VNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           V+G+IG L+ Y+  +R  P+L   EE  LA+R    GD  A  R++ S+LRLVV IA  Y
Sbjct: 23  VSGDIGSLALYLRTLRDYPLLSASEEVDLARRI-ATGDAEARERMILSNLRLVVMIAKRY 81

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            G GLP  +++ EGN+GLM+AV ++DPE+GFR +TY+ WWI+ +++  ++    ++++  
Sbjct: 82  AGRGLPFPDLIEEGNLGLMKAVDRYDPEKGFRFSTYASWWIRQSIERAVINLGHMIRLPV 141

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
              +K     + R    ++ +     +P+   A A+K  ++  E  S+   +A   SL+A
Sbjct: 142 HMREK-----VNRYLAAVEQMVSTGREPDPSEA-ARKAGLTVEEFESLYPLIAATISLDA 195

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-- 246
            +   D+N+   +D L    D +    +E   R+     L  ++SVL PRER I   R  
Sbjct: 196 PVGEQDENT--LKDVL---GDPEADSPLEVVSRREEGRELEAALSVLRPRERDILFLRFG 250

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQKP 300
              E+P TL+ +     ++RERVRQIEA A  K++  I      +S    L  P
Sbjct: 251 LSGEDPKTLDEIGRRLGITRERVRQIEAVALSKMRAYIDDARPFASHHSPLPPP 304


>gi|330874700|gb|EGH08849.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv.
           morsprunorum str. M302280PT]
          Length = 202

 Score =  147 bits (372), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 78/185 (42%), Positives = 115/185 (62%), Gaps = 6/185 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+H +  IP+L  + E  LA+      DL AA ++V +HLR VV IA  Y GYGL  
Sbjct: 17  LEAYVHTVNSIPLLTPERERELAESLYYEQDLDAARQMVLAHLRFVVHIARSYSGYGLAQ 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++L
Sbjct: 77  ADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRKL 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR  K  L  +  NN   ++V  +A+ L V   EV  M  RL G D + +    + D
Sbjct: 137 FFNLRSQKKRLAWL--NN---DEVHRVAESLGVEPREVREMESRLTGHDMAFDPAAEADD 191

Query: 195 KNSSQ 199
            ++ Q
Sbjct: 192 DSAFQ 196


>gi|260361298|ref|ZP_05774403.1| RNA polymerase sigma-32 factor [Vibrio parahaemolyticus K5030]
 gi|308111826|gb|EFO49366.1| RNA polymerase sigma-32 factor [Vibrio parahaemolyticus K5030]
          Length = 158

 Score =  147 bits (370), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 69/131 (52%), Positives = 93/131 (70%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  +   PML   EE  LA+R    G++ AA  L+ SHLR VV +A GY GYGLP+
Sbjct: 16  LDSYIRSVNSYPMLTADEERELAERLHYKGEIEAAKGLILSHLRFVVHVARGYSGYGLPM 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           +++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W +VKI TT  Q++L
Sbjct: 76  ADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKL 135

Query: 136 FFNLRRLKGHL 146
           FFNLR+ K  L
Sbjct: 136 FFNLRKSKKRL 146


>gi|223936758|ref|ZP_03628668.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [bacterium
           Ellin514]
 gi|223894609|gb|EEF61060.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [bacterium
           Ellin514]
          Length = 352

 Score =  145 bits (365), Expect = 8e-33,   Method: Compositional matrix adjust.
 Identities = 97/278 (34%), Positives = 148/278 (53%), Gaps = 13/278 (4%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           +G+  +  Y+ EI ++ +L  Q+E  LA R ++ GD  A   ++ ++LRLVVKIA  Y G
Sbjct: 80  DGDTAIKLYLREIGQVQLLTPQQEIELAARIKK-GDKKARELMIKANLRLVVKIARDYEG 138

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            GLP+ +++SEGNIGLM+AV++FDP +G +L+TY  WWIK +++  +      +++    
Sbjct: 139 IGLPLLDLISEGNIGLMKAVERFDPAKGGKLSTYGSWWIKQSIKRALANQSKTIRLPVHL 198

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
             K     +RR    LQ I       E+   +A +LN+S   V  M        SL+A I
Sbjct: 199 VDK--ISKMRRTALKLQEILGREPSDEE---LADELNISAMRVSQMRTAAIRPASLDAPI 253

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
              D N     ++     D       E+ E K    ML   +  L+PRE  I  AR   +
Sbjct: 254 GDEDSN-----NFAEVVQDENADTPYEQLEEKTVTKMLQELVKTLDPREATILRARFGLD 308

Query: 251 --NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             N  TLE +  +F V+RERVRQI+  A KK+++ I+K
Sbjct: 309 GGNQKTLEEVGQKFGVTRERVRQIQNIALKKLRKMIEK 346


>gi|189218244|ref|YP_001938886.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Methylacidiphilum infernorum V4]
 gi|189185102|gb|ACD82287.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Methylacidiphilum infernorum V4]
          Length = 287

 Score =  144 bits (364), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 92/281 (32%), Positives = 161/281 (57%), Gaps = 16/281 (5%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           N +  L  Y+ EI +IP+L K++E  LAKR  + GD  A  +++ ++LRLVVKIA  Y  
Sbjct: 3   NNDSALKLYLREISQIPLLTKEKEVELAKRI-QQGDQEARRQMIQANLRLVVKIAHDYAN 61

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            GLP+ +++SEGNIGLM+AV +FDP +G +L+TY+ WWIK +++  +      +++    
Sbjct: 62  SGLPLPDLISEGNIGLMKAVDRFDPSKGGKLSTYAAWWIKQSIKRALANQSKTIRLPVHL 121

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
             K     +RR+   L  I   +   E+   +A++L +S ++V  +        SL+A +
Sbjct: 122 VDK--IAKMRRVAMQLSEILGRDPTDEE---LAEELGMSTTKVAELRTIAIRPASLDATV 176

Query: 191 NSSDKNSSQWQDWLVYDHDGQ--EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-R 247
              +  ++  +  LV D      +Q +++    +N +N +   +  L+ RER+I   R  
Sbjct: 177 GEEEDGTALGE--LVKDESAASPDQSVLD----QNLKNTIMELLPKLDERERKILSLRFG 230

Query: 248 LQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L+ N  +TLE +  EF V+RER+RQ++  A +K+++ ++KQ
Sbjct: 231 LEGNEQMTLEEIGKEFHVTRERIRQLQNIALRKIRKELEKQ 271


>gi|213580121|ref|ZP_03361947.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-0664]
          Length = 143

 Score =  144 bits (362), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 70/141 (49%), Positives = 94/141 (66%), Gaps = 1/141 (0%)

Query: 4   KNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           K M  +    +G L  YI      PML   EE  LA+R    GDL AA  L+ SHLR VV
Sbjct: 3   KEMQNLALAPVGNLESYIRAANAWPMLSADEERALAERLHYQGDLEAAKTLILSHLRFVV 62

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W 
Sbjct: 63  HIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWR 122

Query: 123 LVKIGTTANQKRLFFNLRRLK 143
           +VK+ TT  Q++LFFNLR+ K
Sbjct: 123 IVKVATTKAQRKLFFNLRKTK 143


>gi|162449128|ref|YP_001611495.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
 gi|161159710|emb|CAN91015.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
          Length = 275

 Score =  144 bits (362), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 92/273 (33%), Positives = 150/273 (54%), Gaps = 17/273 (6%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
             S Y  E+     L  + E  LA R+R  GD  A  RL+ + L  V+ IA+ YR +GLP
Sbjct: 9   AFSAYRTELANYATLSPEAERELALRWR-AGDRDAGRRLIEACLPFVMTIALEYRRWGLP 67

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++V EGNIGL++A ++FDP+RG RLATY+ +WI+A ++E++ R + +V++G++ +++R
Sbjct: 68  MEDIVQEGNIGLLKAAERFDPDRGCRLATYAAYWIRAEIREHVARGYRIVRLGSSKSERR 127

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS-MNCRLAGDESLNALINSS 193
                R+      A+            +A+   +SE      +   +A D SL     S 
Sbjct: 128 ALRIYRKTHEKDPAV------------LAELSGLSEERAAELLPLLMARDVSLE---RSP 172

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
            ++     + L       E    + +ER      L + ++ L+PRER I   R L ++PV
Sbjct: 173 TEDGIAPVERLASSAHTPEDEACDADERAQLSRALLQVVNELSPRERSIMNQRWLTDSPV 232

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TLE L ++F VS+ERVRQIE RA K+++  I++
Sbjct: 233 TLEQLGADFGVSKERVRQIEERAKKRMRARIEE 265


>gi|254698073|ref|ZP_05159901.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 2 str.
           86/8/59]
          Length = 188

 Score =  143 bits (360), Expect = 4e-32,   Method: Compositional matrix adjust.
 Identities = 80/185 (43%), Positives = 121/185 (65%), Gaps = 1/185 (0%)

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           ++A+MQ+YILR+WS+V+ GT++ QK LFFNLRRL+  L    DN  K E    I+ +L V
Sbjct: 1   MRASMQDYILRNWSIVRGGTSSAQKALFFNLRRLRSKLAQTDDNMTKAEIYREISDQLGV 60

Query: 169 SESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           S S+V  M+ RL+G D SL+A +N  +  +S+  D+LV DH  Q+++     + + R   
Sbjct: 61  STSDVEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIAESSIDMERRNRW 120

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           LTR++  LN RE  I   RRL ++ VTLE L  +  +S+ERVRQIE+RA +K++ ++  Q
Sbjct: 121 LTRALDTLNERELHIIRERRLDDDGVTLEALGEKLGISKERVRQIESRAMEKLKIALLSQ 180

Query: 288 VELSS 292
            EL++
Sbjct: 181 HELAA 185


>gi|257126034|ref|YP_003164148.1| RNA polymerase, sigma 32 subunit, RpoH [Leptotrichia buccalis
           C-1013-b]
 gi|257049973|gb|ACV39157.1| RNA polymerase, sigma 32 subunit, RpoH [Leptotrichia buccalis
           C-1013-b]
          Length = 273

 Score =  142 bits (358), Expect = 6e-32,   Method: Compositional matrix adjust.
 Identities = 91/273 (33%), Positives = 159/273 (58%), Gaps = 15/273 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +S Y+ +I+K  +L K+EEY L +R RE  D  A   L+ S+LRLV+  A    G GLP+
Sbjct: 9   MSLYLSDIQKFDLLSKEEEYELLRRIREDNDEQARQLLILSNLRLVISTAKKSLGNGLPL 68

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++SEGNIGL++A+ KFD E+G R +TY++WWIK A+++ I+     ++I +       
Sbjct: 69  IDLISEGNIGLIKAINKFDYEKGHRFSTYAVWWIKQAIKKAIINIGRDIRIPSYK----- 123

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           +  L ++   ++  T  + +      IAKK+++ ES++I +        SLN  I     
Sbjct: 124 YEQLSKVNKAIKDYTAIHGEAPSTEYIAKKVDLKESKIILLLGEFQDIMSLNETI----- 178

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPV- 253
             + + + ++  +D  E  +I++++    R +L R   +LN RER+I E R  L +N + 
Sbjct: 179 GDNIYLEDVIGKNDDVEDKIIKEDQLLEMRELLER---ILNERERKILEYRYGLYDNKIH 235

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TL+ +  +  ++RERVRQIE +A  K++E +++
Sbjct: 236 TLKEIGEQMGITRERVRQIEKKAITKLKEHLEE 268


>gi|260889708|ref|ZP_05900971.1| RNA polymerase sigma factor RpoD [Leptotrichia hofstadii F0254]
 gi|260860314|gb|EEX74814.1| RNA polymerase sigma factor RpoD [Leptotrichia hofstadii F0254]
          Length = 273

 Score =  140 bits (352), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 91/273 (33%), Positives = 159/273 (58%), Gaps = 15/273 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +S Y+ +I+K  +L K+EEY L KR RE  D  A   L+ S+LRLV+  A    G GLP+
Sbjct: 9   MSLYLSDIQKFDLLSKEEEYELLKRIREDDDEQARQLLILSNLRLVISTAKKSLGNGLPL 68

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++SEGNIGL++A+ KFD E+G R +TY++WWIK ++++ I+     ++I +       
Sbjct: 69  IDLISEGNIGLIKAINKFDYEKGHRFSTYAVWWIKQSIKKAIINIGRDIRIPSYK----- 123

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           +  L ++   ++  T  + +      IAK++++ ES+VI +        SLN  I     
Sbjct: 124 YEQLSKVNKVIKDYTAIHGEAPSTEYIAKEVDLKESKVILLLGEFQDIMSLNETI----- 178

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPV- 253
             + + + ++  +D  E  +I++++    +++L R   VLN RER I E R  L +N + 
Sbjct: 179 GDNIYLEDIIGKNDDVEDKIIKEDQLIEMKDLLER---VLNERERAILEYRYGLYDNKIH 235

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TL+ +  +  ++RERVRQIE +A  K++E +++
Sbjct: 236 TLKEIGEQMGITRERVRQIEKKAITKLKEHLEE 268


>gi|260762513|ref|ZP_05874850.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 2 str.
           86/8/59]
 gi|260672939|gb|EEX59760.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 2 str.
           86/8/59]
          Length = 184

 Score =  139 bits (351), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 79/181 (43%), Positives = 117/181 (64%), Gaps = 1/181 (0%)

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           MQ+YILR+WS+V+ GT++ QK LFFNLRRL+  L    DN  K E    I+ +L VS S+
Sbjct: 1   MQDYILRNWSIVRGGTSSAQKALFFNLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTSD 60

Query: 173 VISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           V  M+ RL+G D SL+A +N  +  +S+  D+LV DH  Q+++     + + R   LTR+
Sbjct: 61  VEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTRA 120

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           +  LN RE  I   RRL ++ VTLE L  +  +S+ERVRQIE+RA +K++ ++  Q EL+
Sbjct: 121 LDTLNERELHIIRERRLDDDGVTLEALGEKLGISKERVRQIESRAMEKLKIALLSQHELA 180

Query: 292 S 292
           +
Sbjct: 181 A 181


>gi|222832154|gb|EEE70631.1| predicted protein [Populus trichocarpa]
          Length = 299

 Score =  138 bits (348), Expect = 8e-31,   Method: Compositional matrix adjust.
 Identities = 87/239 (36%), Positives = 136/239 (56%), Gaps = 29/239 (12%)

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AVK+FDP++  RL +Y+M WIKA + EYIL++W +VK+ TT  Q++LFFNLR +K  L
Sbjct: 1   MKAVKRFDPDQNVRLVSYAMHWIKAEIHEYILKNWRMVKVATTKAQRKLFFNLRSMKQGL 60

Query: 147 Q---------AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
           +         A+  + L   ++ A+A+KLNV   EV+ M  RLAG + L  L  S   + 
Sbjct: 61  KSDAAMAEDGAMLRDTLTSGEIDAVAEKLNVKREEVMEMETRLAGGDVL--LDPSPSDDG 118

Query: 198 SQWQDWLVYDHDGQEQ--VLIEKEERKN-RRNMLTRSMSVLNPRERRIFEARRLQENP-- 252
            Q    + Y  DG  +   +IE  +R +   + +  ++  L+ R RRI E R L+ N   
Sbjct: 119 EQAFGPIAYLADGAHEPTAMIESRQRDHLATDGIAMALDSLDDRSRRIVEERWLKVNDDG 178

Query: 253 ---VTLENLSSEFEVSRERVRQIEARAFKKVQESI----------QKQVELSSSPPLLQ 298
              +TL  L++ + VS ER+RQIE  A KK+++++           +Q  L+++PPL Q
Sbjct: 179 SGGMTLHELAAVYGVSAERIRQIEVAAMKKMKKALADLCGPHAPHARQRHLATTPPLRQ 237


>gi|225159269|ref|ZP_03725570.1| RNA polymerase, sigma 70 subunit, RpoD family [Opitutaceae
           bacterium TAV2]
 gi|224802166|gb|EEG20437.1| RNA polymerase, sigma 70 subunit, RpoD family [Opitutaceae
           bacterium TAV2]
          Length = 373

 Score =  137 bits (345), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 91/276 (32%), Positives = 154/276 (55%), Gaps = 16/276 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ EI K P+L   EE  LA+R R  GD +A   +++++LRLVVKIAM Y+ +GLP+
Sbjct: 61  LQLYLQEIGKTPLLTLDEEVTLARRIR-RGDKAARDHMISANLRLVVKIAMDYKDFGLPL 119

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++SEGNIGL++AV++FDP +G +L+TY+ WWIK +++  +      +++        L
Sbjct: 120 LDLISEGNIGLVKAVERFDPRKGGKLSTYAAWWIKQSIKRALANQSKTIRLPV-----HL 174

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + R++    A+T+   +      IA +L +  S+V  +        SL+A +   D 
Sbjct: 175 VDKIARMRRTAMALTEQLGREPSDEEIAMELQIPTSKVAHLKSVSVRPASLDAPVG-EDG 233

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSM-SVLNPRERRIFEARRLQE--N 251
           +SS + + +     G E  +   E  K R RN   + M   L PRE  I   R   +  +
Sbjct: 234 DSSTFGELV-----GDENAVSPFESLKERSRNADLKEMVDSLEPREAEIIRYRFGLDGRD 288

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +TLE +  +F+V+RERVRQ++  A  K+++++ + 
Sbjct: 289 ELTLEEVGQKFKVTRERVRQLQNLALSKMRKAMSRH 324


>gi|223937956|ref|ZP_03629855.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [bacterium
           Ellin514]
 gi|223893357|gb|EEF59819.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [bacterium
           Ellin514]
          Length = 353

 Score =  137 bits (345), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 90/278 (32%), Positives = 151/278 (54%), Gaps = 13/278 (4%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           +G    + Y+ E+ +  +L  QEE  LAKR ++ GD  A  +++ ++LRLVVKIA  Y  
Sbjct: 79  DGNTAFNLYLREVGQTKLLTPQEEVDLAKRIKK-GDKKAREQMIKANLRLVVKIAREYED 137

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
           YG+P+ ++++EGN+GLM+AV++FDP +G +L+TYS WWIK +++  +      +++    
Sbjct: 138 YGMPLLDLINEGNMGLMKAVERFDPAKGAKLSTYSAWWIKQSIKRALANQSKTIRLPVHV 197

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
             K   F++R+    LQ +       E+   +  +L  S  +V  +        SL A +
Sbjct: 198 VDK--LFHMRQASVKLQEVLGREPTDEE---LGDELGFSAQKVAQLRTAAIRPASLEAPL 252

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQ 249
              D  +S+  D +    D       E+ E K   +ML   ++ L+PRE  I   R  L 
Sbjct: 253 G--DDETSRIADVV---RDETADTPYEQLEEKTNTSMLRELVATLDPREAEILRYRFGLD 307

Query: 250 ENPV-TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +P  TLE +  +F V+RER+RQI+  A  K+++ I+K
Sbjct: 308 GDPERTLEEVGQKFGVTRERIRQIQNVALNKLRKQIEK 345


>gi|108803849|ref|YP_643786.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108765092|gb|ABG03974.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 289

 Score =  136 bits (343), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 95/267 (35%), Positives = 144/267 (53%), Gaps = 12/267 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y   I K  +L  QEE  L++R ++ GD  A  +L+  +LRLVV +A  YRGYGLP  ++
Sbjct: 22  YFARIDKGELLTHQEEIELSRRAKK-GDRKARQKLIEKNLRLVVSVAKKYRGYGLPFEDL 80

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM+AV+KFDPERGFR +TY+ WWI+ A+Q  +      +++     +K     
Sbjct: 81  IQEGNIGLMKAVEKFDPERGFRFSTYATWWIRQAVQRAVADKGRTIRVPVHMTEK--IRK 138

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           + R    L A  +     E+V   A+ L  +  EV  +   +    SLN  + SSD++SS
Sbjct: 139 MARTYNELSAQLEREPTDEEV---AEALGWTPEEVREVKGAMPDATSLNQPL-SSDEDSS 194

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
           +  ++ V D    +       + +N    L +++  L  R R +   R   ++  P TL 
Sbjct: 195 EIGEF-VEDERASDTAGAVARDIEN--AALRKAIERLPERNRHVLVRRYGLDDREPATLA 251

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQES 283
            LS E  VSRERVRQ++  A + +QES
Sbjct: 252 ELSEELGVSRERVRQLQREAERMIQES 278


>gi|226329393|ref|ZP_03804911.1| hypothetical protein PROPEN_03298 [Proteus penneri ATCC 35198]
 gi|225202579|gb|EEG84933.1| hypothetical protein PROPEN_03298 [Proteus penneri ATCC 35198]
          Length = 137

 Score =  136 bits (342), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 62/134 (46%), Positives = 93/134 (69%), Gaps = 2/134 (1%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           ++++++  G I    YI      PML  +EE  LA+R    GDL AA  L+ SHLR V+ 
Sbjct: 6   QSLALVPQGSI--EAYIRAANSYPMLTAEEEKELAERLHYEGDLDAARTLILSHLRFVIH 63

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W +
Sbjct: 64  VARSYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRI 123

Query: 124 VKIGTTANQKRLFF 137
           VK+ TT +Q++LFF
Sbjct: 124 VKVATTKSQRKLFF 137


>gi|221134005|ref|ZP_03560310.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Glaciecola sp. HTCC2999]
          Length = 326

 Score =  136 bits (342), Expect = 5e-30,   Method: Compositional matrix adjust.
 Identities = 100/275 (36%), Positives = 155/275 (56%), Gaps = 20/275 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE VL  R    GD  A  R++ S+LRLVVKIA  Y+  GL + ++
Sbjct: 53  YLNEIGFSPLLSAEEE-VLHGRKALKGDKDARERMIVSNLRLVVKIARRYKDRGLALLDL 111

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     V++      K L   
Sbjct: 112 VEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTVRLPIHV-VKELNIY 170

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV---ISMNCRLAGDESLNALINSSDK 195
           LR  +   Q + D+    E+   IA KL+VS  +V   + +N R+   +S   L + SD 
Sbjct: 171 LRTARNLAQEL-DHEPTAEE---IADKLDVSTEDVNKMLRLNERIKSVDSY--LSHESDG 224

Query: 196 NSSQWQDWLV-YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENP 252
           NS    D L   +H G E    EK +  + +N +   +  LNP++R +   R   +   P
Sbjct: 225 NS--LLDILPDSNHSGPE----EKNQEDDIKNNIVMWLQELNPKQREVLSRRFGLMGFEP 278

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            TLEN+ +E  ++RERVRQI+  A +++++ +  Q
Sbjct: 279 DTLENVGAEIGLTRERVRQIQVEALRRLKDMLGLQ 313


>gi|298244288|ref|ZP_06968094.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297551769|gb|EFH85634.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 334

 Score =  135 bits (340), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 95/275 (34%), Positives = 150/275 (54%), Gaps = 29/275 (10%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           + +Y+ EI   P+L  ++E  LA+R    GD  A  RL+ ++LRLVV IA  Y   GLP+
Sbjct: 64  VKQYLKEIGMYPLLTAEQELQLAERV-ARGDQYARQRLIEANLRLVVSIAKRYSNQGLPL 122

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+A +KFD +RGFR +TY+ WWI+ A+   I      + I     +  L
Sbjct: 123 LDLIQEGNIGLMRATQKFDYKRGFRFSTYATWWIRQAISRAIAEHSRSIHIPVHVVE--L 180

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLN 187
            + ++R+   L         PEQV A        + + LNVSE + IS++  +A DE  +
Sbjct: 181 IYKIKRITRRLYQEQGVEPLPEQVAAELGLPRERVVELLNVSE-QPISLDAPMADDEEYH 239

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
                         D L    D      I+   ++ +R  + ++M+VLNPRER I E R 
Sbjct: 240 ------------LSDML---EDTSMAPTIDVVSQQLQREHIEQAMTVLNPRERTIIEMRY 284

Query: 248 -LQE-NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            L++ + ++L+ +S  F ++RER+RQIE +A +K+
Sbjct: 285 GLKDGHSLSLDEVSVLFHLTRERIRQIEVKALRKL 319


>gi|171909626|ref|ZP_02925096.1| RNA polymerase sigma factor [Verrucomicrobium spinosum DSM 4136]
          Length = 298

 Score =  135 bits (340), Expect = 8e-30,   Method: Compositional matrix adjust.
 Identities = 95/280 (33%), Positives = 160/280 (57%), Gaps = 23/280 (8%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           G+  Y+ EI K  +L  Q+E  LA+R ++ GD  A   ++ ++LRLVVKIA  Y  YGLP
Sbjct: 9   GIKIYLREIGKTDLLTPQQEVELAERIKK-GDPEARSHMIRANLRLVVKIAQDYANYGLP 67

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++SEGNIGLM+AV++FDP +G +L+TY+ WWIK +++  +      +++      K 
Sbjct: 68  LLDLISEGNIGLMKAVERFDPNKGGKLSTYAAWWIKQSIKRALANQSKTIRLPVHMVDK- 126

Query: 135 LFFNLRRLKGHL-----QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
               +RR+   +     +  TD+ L  E  +   K   +S+ +V SM        SL+A 
Sbjct: 127 -ISKMRRVAMAMSEELGREPTDDELSEEIGIDRGK---LSQLKVASMRP-----ASLDAP 177

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL- 248
           I+  D  S+++ + +V D +   Q   +    KN  + L   ++VL+ RER+I +AR   
Sbjct: 178 ISEDD--STEFGE-IVGDENA--QTPFDLLSHKNMHSQLDGLLTVLDERERKIIDARFGL 232

Query: 249 -QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             +   TLE +  EF V+RER+RQ++  A +K++ ++QK+
Sbjct: 233 NGQKARTLEEVGQEFGVTRERIRQLQNIALRKLRRALQKK 272


>gi|46204564|ref|ZP_00049813.2| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Magnetospirillum magnetotacticum
           MS-1]
          Length = 132

 Score =  134 bits (337), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 69/127 (54%), Positives = 92/127 (72%), Gaps = 2/127 (1%)

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + E +VI MN RL+GD SLNA +   ++   +WQDWLV +   QE VL  +EE +NR + 
Sbjct: 1   MPEQDVIDMNRRLSGDTSLNAPLR--EEGEGEWQDWLVDNSPSQETVLAREEEGRNRLSA 58

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L  ++ VLNPRERRIFEARRL ++P+TLE+LS EF VSRERVRQIE RAF+KVQE++++ 
Sbjct: 59  LRDALGVLNPRERRIFEARRLADDPITLEDLSGEFGVSRERVRQIEVRAFEKVQEAVKRN 118

Query: 288 VELSSSP 294
           +     P
Sbjct: 119 LATRELP 125


>gi|269104472|ref|ZP_06157168.1| RNA polymerase sigma factor RpoS [Photobacterium damselae subsp.
           damselae CIP 102761]
 gi|268161112|gb|EEZ39609.1| RNA polymerase sigma factor RpoS [Photobacterium damselae subsp.
           damselae CIP 102761]
          Length = 294

 Score =  134 bits (337), Expect = 2e-29,   Method: Compositional matrix adjust.
 Identities = 90/273 (32%), Positives = 147/273 (53%), Gaps = 15/273 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ +I   P+L K EE +L  R    GD  +   ++ S+LRLVV IA  YRG G+ +S++
Sbjct: 21  YLKDIALKPLLTKDEE-ILYSRKALVGDAKSKKVMIESNLRLVVSIAKKYRGSGMQLSDM 79

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGL+ AV+KFDPERGFR +TY+ WWIK  ++  I      +++    +++     
Sbjct: 80  IDEGNIGLITAVEKFDPERGFRFSTYATWWIKQTIERAIHNQARTIRLPVHVSKEINTI- 138

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
              L+ H Q +  NN +P     +A +L+ S  ++ ++    A   S +  I+S D NS 
Sbjct: 139 ---LRTHKQLMKTNNSEPTH-EEVADELDKSVEDISALLSYDAPVMSFDQTISSEDSNSQ 194

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARR---LQENPVT 254
               ++  D D      I+    KN    LT +M   LNPR+R I   RR   +     T
Sbjct: 195 TMASFISDDSDNGPDAQID----KNDIQKLTLTMLEGLNPRDREIL-CRRFGLMGYEAQT 249

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L+ ++ E  ++RER+RQ++  +  K++  +Q++
Sbjct: 250 LQQVAEEVGLTRERIRQLQVSSLNKLKNVLQRE 282


>gi|260219679|emb|CBA26524.1| RNA polymerase sigma factor rpoS [Curvibacter putative symbiont of
           Hydra magnipapillata]
          Length = 340

 Score =  133 bits (335), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 89/293 (30%), Positives = 153/293 (52%), Gaps = 32/293 (10%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           ++ S +  G   LS Y+  +R+ P+   ++E+ +A R R  GD +A   ++  +LRLV+ 
Sbjct: 51  EDPSTLEQGPDALSVYLRGVRRTPLFTPEQEFEVATRAR-AGDFAARQSMIEHNLRLVIS 109

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA GY G G+P+S+++ EGN+GLM A+ KF+PERGFR +TY+ WWI+ ++   ++     
Sbjct: 110 IAKGYAGRGVPMSDLIEEGNLGLMHAIDKFEPERGFRFSTYATWWIRQSVDRALMYQGRA 169

Query: 124 VKIGT-TANQKRLFFNLRRL---KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM--- 176
           V++      + +     RRL      L A     ++ E + A+  +  V  +++++M   
Sbjct: 170 VRLPVNVVREVQQVLRARRLLENDAVLLAQRPEGIRVEDIAALLGRDAVDVTDLLAMAEA 229

Query: 177 ----NCR--LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
               + R    GDE  ++L +S     +   D     H+                 +L +
Sbjct: 230 PRSLDARNDAGGDE--HSLGDSLADTLAAAPDSTALAHEVDA--------------LLEQ 273

Query: 231 SMSVLNPRERRIFEAR-RLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            ++ LNPRE+ + EAR  L + +P TLE LS    ++RERVRQI+  A  K++
Sbjct: 274 WIATLNPREQEVLEARFGLHDRDPETLETLSERLGLTRERVRQIQNEALFKLK 326


>gi|257438255|ref|ZP_05614010.1| RNA polymerase sigma factor RpoD [Faecalibacterium prausnitzii
           A2-165]
 gi|257199332|gb|EEU97616.1| RNA polymerase sigma factor RpoD [Faecalibacterium prausnitzii
           A2-165]
          Length = 359

 Score =  133 bits (334), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 88/266 (33%), Positives = 146/266 (54%), Gaps = 15/266 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  ++E  LA R  + GD  A  +L  ++LRLVV +A  Y G GLP  ++
Sbjct: 92  YLKEIGRVPLLTMEQELELA-RAAQAGDADARRKLSEANLRLVVSVAKRYAGRGLPFLDL 150

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+A +KF+P+RGFR +TY+ WWI+ ++   I     +++I        L  +
Sbjct: 151 IQEGNLGLMKAAEKFEPDRGFRFSTYATWWIRQSITRAIADQGRVIRIPV-----HLVES 205

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           + R+K     +   N +      IA +L++    V  +  +LA D  SL   +   ++  
Sbjct: 206 INRVKKTAGELLRKNGREPTAEEIAVRLDMEPDRVREL-LQLAQDPISLETPVG--EEED 262

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTL 255
           +  +D++    D +  V +++  R+  R  L   +  L PRE R+   R   E+    TL
Sbjct: 263 AHLEDFI---QDEEAGVPVDEAGRELLRRELANVLKSLTPREERVLTLRFGLEDGQARTL 319

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           E L  EF V+RER+RQIEA+A +K++
Sbjct: 320 EELGKEFNVTRERIRQIEAKALRKLR 345


>gi|56459854|ref|YP_155135.1| DNA-directed RNA polymerase sigma 38 subunit [Idiomarina loihiensis
           L2TR]
 gi|56178864|gb|AAV81586.1| DNA-directed RNA polymerase sigma 38 subunit [Idiomarina loihiensis
           L2TR]
          Length = 322

 Score =  133 bits (334), Expect = 3e-29,   Method: Compositional matrix adjust.
 Identities = 99/278 (35%), Positives = 150/278 (53%), Gaps = 27/278 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   ++R  + GD +A  R++ S+LRLVVKIA  Y   GLP+ ++
Sbjct: 52  YLGEIGFSPLLTAEEEVFYSRRALK-GDKAARRRMIESNLRLVVKIARRYSNRGLPLLDL 110

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 111 VEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 169

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD---- 194
           LR  +  L    D+    E    IAK LN    ++  M         LN  I S D    
Sbjct: 170 LRAAR-ELAHKLDHEPTAED---IAKSLNKPVGDITKML-------RLNERIGSVDTPIG 218

Query: 195 -KNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR---LQ 249
             N     D L  D D G E VL    + +N +  +T  +  LN ++R +  ARR   + 
Sbjct: 219 GDNDKALLDILTDDADTGPEGVL----QDENLKGNITEWLQSLNQKQREVL-ARRFGLMG 273

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             P TLE++  E  ++RERVRQI+  A +K+++S+++Q
Sbjct: 274 YEPSTLEDVGREIGLTRERVRQIQVEALRKLRDSLKQQ 311


>gi|298242664|ref|ZP_06966471.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297555718|gb|EFH89582.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 394

 Score =  132 bits (333), Expect = 5e-29,   Method: Compositional matrix adjust.
 Identities = 84/273 (30%), Positives = 152/273 (55%), Gaps = 13/273 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            + +Y+ EI + P+L  ++E  +A R   +GD+ A  RLV ++LRLVV IA  Y   G+ 
Sbjct: 125 AIRQYLAEIGRFPLLTSEQELTIAWRV-ANGDMEAQKRLVEANLRLVVSIAKRYNNQGIS 183

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++ EGN+GL++AV+KFDP+RGFR +TY+ WWI+ A+   +      + +     +  
Sbjct: 184 LLDLIQEGNLGLIRAVQKFDPQRGFRFSTYATWWIRQAISRAVAEHTRTIHVPVHVVE-- 241

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           L + ++R+   L      +  PE+   IA+ +N+++  V+ +        SL+A +   +
Sbjct: 242 LIYKMKRITRQLYQDLGRDPFPEE---IAQAINLTKERVVELQSIAEAPISLDAPLIEDE 298

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPV 253
           +      D L   H      ++  +     R+ ++R++  L+ RER++ E R  L +   
Sbjct: 299 QY--HLADMLEDTHAAAPAEVVTHQ---VLRDHISRALETLSQRERQVIELRYGLYDGYC 353

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            TLE LS+ F+++RER+RQIE +A + ++  IQ
Sbjct: 354 HTLEELSAYFKLTRERIRQIEVKALRTLRHPIQ 386


>gi|225849737|ref|YP_002729971.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Persephonella marina EX-H1]
 gi|225645950|gb|ACO04136.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Persephonella marina EX-H1]
          Length = 285

 Score =  131 bits (330), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 96/277 (34%), Positives = 149/277 (53%), Gaps = 19/277 (6%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E G++ Y++ I KIP+L  +EE  +AK+ +E GD  A  +L+ S+LR VV +A  Y GYG
Sbjct: 7   EEGITYYLNSISKIPLLSPEEEKEIAKKAKE-GDKEALEKLIKSNLRFVVNVAKNYTGYG 65

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +P  E++S GNIGL++A K+FDPERG R  +Y++WWIK ++ + I     ++KI     Q
Sbjct: 66  IPFQELISAGNIGLIEAAKRFDPERGVRFISYAIWWIKQSILQTIQSQKDIIKIP----Q 121

Query: 133 KRLFFNLRRLKGHLQAITDNNLKP---EQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
           K    +++    +L+     N +P   E    + +  N+   E    N  L    S+ +L
Sbjct: 122 KTQNLSMKIDTAYLELKERLNREPKYSEIKEYLKEHENIDIDEETIENYLLIKRHSV-SL 180

Query: 190 INSSDKNSSQWQDWLVYDH---DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
               D +   +   L+  H   D +E ++ E  E++     +   +S L+ RER I   R
Sbjct: 181 DTPVDMDEGTFFIDLISKHSTKDIEENIVRESIEKE-----IEYILSHLSERERFIIVNR 235

Query: 247 RL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                E P TL  +  E  +SRERVRQIE RA KK++
Sbjct: 236 FGLNGEEPKTLREIGKELGISRERVRQIEIRALKKIR 272


>gi|85712119|ref|ZP_01043172.1| DNA-directed RNA polymerase sigma 38 subunit [Idiomarina baltica
           OS145]
 gi|85694109|gb|EAQ32054.1| DNA-directed RNA polymerase sigma 38 subunit [Idiomarina baltica
           OS145]
          Length = 333

 Score =  131 bits (330), Expect = 1e-28,   Method: Compositional matrix adjust.
 Identities = 94/283 (33%), Positives = 153/283 (54%), Gaps = 37/283 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   ++R  + GD++A  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 63  YLSEIGFSPLLTAEEEIFYSRRALK-GDIAARKRMIESNLRLVVKIARRYCNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 122 VEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 180

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDES---LN 187
           LR  +  L    D+    E + A        I K L ++E  V S++  + GD     L+
Sbjct: 181 LRAAR-ELAHKLDHEPTAEDIAASLNKPVEDITKMLRLNE-RVTSVDTPIGGDNDKALLD 238

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
            L + +D              DG E VL    +  + +  +T  +  LNP+++ +  ARR
Sbjct: 239 ILTDEAD--------------DGPEGVL----QDGDLKERITEWLDALNPKQKEVL-ARR 279

Query: 248 ---LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              L   P TLE++  E  ++RERVRQI+  A +K+++ +++Q
Sbjct: 280 FGLLGYEPSTLEDVGHEIGLTRERVRQIQVEALRKLRDFLRQQ 322


>gi|262038022|ref|ZP_06011434.1| RNA polymerase sigma factor RpoD [Leptotrichia goodfellowii F0264]
 gi|261747975|gb|EEY35402.1| RNA polymerase sigma factor RpoD [Leptotrichia goodfellowii F0264]
          Length = 258

 Score =  130 bits (328), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 90/267 (33%), Positives = 152/267 (56%), Gaps = 25/267 (9%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +S Y+ +I+K  +L K+EEY L +R RE  D  A   L+ S+LRLV+  A    G GLP+
Sbjct: 9   ISLYLSDIQKFNLLSKEEEYELLRRIREENDEQARQLLILSNLRLVISTAKKLLGNGLPL 68

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++SEGNIGL++A+ KFD E+G R +TY++WWIK ++++ I+ +   ++I +       
Sbjct: 69  IDLISEGNIGLIKAINKFDYEKGHRFSTYAVWWIKQSIKKAIINTGRDIRIPS------- 121

Query: 136 FFNLRRLKGHLQAITDNNLK-----PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
            +   +L    + ITD   K     P +   IAK++++ ES+VI +        SLN  I
Sbjct: 122 -YKYEQLSKVNKVITDYVAKYGESPPTE--YIAKEVDLKESKVILLLNEFQDVISLNETI 178

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQ 249
                  + + + +V + D  E+ +I++++    R +L    ++L  RER I E R  L 
Sbjct: 179 -----GDNIYLEDIVGNTDDVEEKIIKEDQLSEMRELLE---NILTDREREILELRYGLY 230

Query: 250 ENPV-TLENLSSEFEVSRERVRQIEAR 275
            N + TL+ + ++  ++RERVRQIE +
Sbjct: 231 NNKIHTLKEIGAKLNITRERVRQIEKK 257


>gi|313113550|ref|ZP_07799138.1| RNA polymerase sigma factor RpoD [Faecalibacterium cf. prausnitzii
           KLE1255]
 gi|310624065|gb|EFQ07432.1| RNA polymerase sigma factor RpoD [Faecalibacterium cf. prausnitzii
           KLE1255]
          Length = 377

 Score =  130 bits (327), Expect = 2e-28,   Method: Compositional matrix adjust.
 Identities = 90/266 (33%), Positives = 145/266 (54%), Gaps = 15/266 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  ++E  LA R  + GD  A  +L  ++LRLVV +A  Y G GLP  ++
Sbjct: 110 YLKEIGRVPLLTAEQETELA-RAAQAGDEDARRKLSEANLRLVVSVAKRYAGRGLPFLDL 168

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+A +KF+PERGF+ +TY+ WWI+ ++   I      ++I        L  +
Sbjct: 169 IQEGNLGLMKAAEKFEPERGFKFSTYATWWIRQSITRAIADQGRTIRIPV-----HLVES 223

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           + R+K     +   N +      IA +L++    V  +  +LA D  SL   +   ++  
Sbjct: 224 INRVKKMTGDLLRKNGREPTAEEIAVQLDMEPDRVREL-LQLAQDPISLETPVG--EEED 280

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTL 255
           +  +D+ + D D    V +++  R+  R  L   +  L PRE R+   R   E+    TL
Sbjct: 281 AHLEDF-IQDEDA--GVPVDEAGRQLLRRELFSVLKSLTPREERVIALRFGLEDGRAHTL 337

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           E L  EF V+RERVRQIEA+A +K++
Sbjct: 338 EELGKEFNVTRERVRQIEAKALRKLR 363


>gi|297614550|gb|ADI48581.1| putative DNA-directed RNA polymerase sigma 38 subunit [uncultured
           bacterium fss6]
          Length = 322

 Score =  130 bits (326), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 94/279 (33%), Positives = 158/279 (56%), Gaps = 28/279 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   ++  R+ GD  A  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 51  YLSEIGYSPLLSAEEEVHFSRLARK-GDAKARARMIESNLRLVVKIARRYTNRGLALLDL 109

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++            
Sbjct: 110 VEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-------- 161

Query: 139 LRRLKGHLQAITD--NNLKPEQVVA-IAKKLNVSESEV---ISMNCRLAGDESLNALINS 192
           ++ L  +L+A  +  + L  E     IA+KL+VS ++V   + +N R+    S++  +  
Sbjct: 162 VKELNSYLRAARELAHTLDHEPTAEDIAEKLDVSVADVSRMLRLNERVT---SVDTPMGG 218

Query: 193 SDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR---L 248
           SD N     D L  D+D G E  + E    ++ R+ +   +  LN ++R +  ARR   L
Sbjct: 219 SD-NDKTLVDMLTDDNDYGPEGDMQE----EDVRDHIMTWLENLNEKQREVL-ARRFGLL 272

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              P TLE++  E  ++RERVRQI+  A +++++ +++Q
Sbjct: 273 GYEPATLEDVGREIGLTRERVRQIQVEALRRLRDMLRQQ 311


>gi|269120610|ref|YP_003308787.1| RNA polymerase, sigma 32 subunit, RpoH [Sebaldella termitidis ATCC
           33386]
 gi|268614488|gb|ACZ08856.1| RNA polymerase, sigma 32 subunit, RpoH [Sebaldella termitidis ATCC
           33386]
          Length = 270

 Score =  130 bits (326), Expect = 3e-28,   Method: Compositional matrix adjust.
 Identities = 87/265 (32%), Positives = 150/265 (56%), Gaps = 15/265 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ +I+K  +L ++EEY L +R +E     A H L+ S+LRLV+ IA    G GLP+ ++
Sbjct: 11  YLKDIQKYELLNREEEYELFRRIKEDDSQDARHELILSNLRLVISIAKKSLGNGLPLIDL 70

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           +SEGNIGL++A+ KFD  +G R +TY++WWIK ++++ I+     ++I +   ++    N
Sbjct: 71  ISEGNIGLIKAINKFDYTKGHRFSTYAVWWIKQSIKKAIINKGRDIRIPSYKYEQLAKVN 130

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
               K  +  I D+   P  V  IA++L + E +V  +        SLN +I       +
Sbjct: 131 ----KVMVNYINDHGETP-SVAYIAEQLEIKEYKVSLLINEFQDIISLNDVI-----GDN 180

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPV-TLE 256
            + + ++ + D  E+ +I+ ++    R +L    ++L+ RER I E R  L  N + TL+
Sbjct: 181 IFLEDVIGNEDNIEEKIIKNDQINKMRELLD---NILSEREREIIELRYGLYNNKMHTLK 237

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  E  ++RERVRQIE +A  K++
Sbjct: 238 EIGDELNITRERVRQIEKKAITKLK 262


>gi|124266448|ref|YP_001020452.1| RNA polymerase sigma S (sigma-38) factor transcription regulator
           protein [Methylibium petroleiphilum PM1]
 gi|124259223|gb|ABM94217.1| RNA polymerase sigma S (sigma-38) factor transcription regulator
           protein [Methylibium petroleiphilum PM1]
          Length = 343

 Score =  129 bits (325), Expect = 4e-28,   Method: Compositional matrix adjust.
 Identities = 90/278 (32%), Positives = 144/278 (51%), Gaps = 15/278 (5%)

Query: 12  GEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           GE+G  L  Y+ EIR+ P+    EE+ +A R R  GD +A  +++  +LRLVV IA  Y 
Sbjct: 59  GEVGNTLQTYLREIRRAPLFTPDEEFAMATRARA-GDFAARQQMIERNLRLVVSIAKSYL 117

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
             GLP+++++ EGN+GLM A+ KF+PERGFR +TY+ WWI+ +++  I+    LV++   
Sbjct: 118 SRGLPMTDLIEEGNLGLMHAIGKFEPERGFRFSTYASWWIRQSIERAIMHQARLVRLPVH 177

Query: 130 ANQK--RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
             ++  ++    R L+G   A  D   +  +V  IA  L    +EV  +        SL+
Sbjct: 178 VVRELNQVLKARRALEGEAAASADG--RTVRVDEIAAALGRPVTEVSELLRFAEQPTSLD 235

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR--NMLTRSMSVLNPRERRIFEA 245
           A +     N ++    +V D    EQ         N     +L   +  L+ RER +   
Sbjct: 236 APLERQAGNGAETLGDMVAD----EQATDPLGHTLNHELDVLLEHGLGELSEREREVLAG 291

Query: 246 RRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R    +  P TLE L+    ++RER+RQI+  A  K++
Sbjct: 292 RYGLHDREPETLEVLAERLGLTRERIRQIQQEALLKLK 329


>gi|124514327|gb|EAY55841.1| RNA polymerase, sigma 70 subunit, RpoD family [Leptospirillum
           rubarum]
          Length = 499

 Score =  129 bits (323), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 93/283 (32%), Positives = 149/283 (52%), Gaps = 23/283 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ +++K  +L  +EE  LAKR R  GD SA   ++ S+LRLVV IA  Y G GL +
Sbjct: 49  LGSYLKKLQKSHLLTFEEEQDLAKRVRA-GDESARQAMIQSNLRLVVSIAKRYIGRGLLL 107

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM+AV KFDP++GFR +TY+ WWI+ A++  I+    ++++     +K  
Sbjct: 108 EDLIEEGNLGLMKAVSKFDPDKGFRFSTYASWWIRQAIERGIINQGHMIRLPVHMMEK-- 165

Query: 136 FFNLRRLKGHLQAI---TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 +  +L AI     +  +P+ +  +A+K  +   ++  +   L    SL+  I  
Sbjct: 166 ------VNAYLNAIERQVADGQQPD-IETLARKNGLKVRDLQEIQALLKNTVSLDTPIG- 217

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-----R 247
            D+  S  +D LV          IE  E  +R   L  S+++L  +ERR+   R      
Sbjct: 218 -DREDSTLKDILVDPTSFSPISTIESREEGDR---LRESLALLKDKERRVIHLRFGLPGE 273

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
             E  +TLE +     V+RERVRQIEA A  K++  ++   E 
Sbjct: 274 GPEEGMTLEAIGQMLGVTRERVRQIEASAMAKLRAYMEDPSEF 316


>gi|268315720|ref|YP_003289439.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhodothermus
           marinus DSM 4252]
 gi|262333254|gb|ACY47051.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhodothermus
           marinus DSM 4252]
          Length = 279

 Score =  129 bits (323), Expect = 7e-28,   Method: Compositional matrix adjust.
 Identities = 88/278 (31%), Positives = 158/278 (56%), Gaps = 31/278 (11%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI KIP+L  +EE  LA+R ++ GD  A H+L  ++LR VV +A  Y+G GL +
Sbjct: 10  LDQYLQEIGKIPLLTPEEEVELARRIKQ-GDEEALHKLTRANLRFVVSVAKKYQGQGLSL 68

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV-----KIGTTA 130
           +++++EGN GL++A ++FD  RGF+  +Y++WWI+ A+ + +     +V     +IGT +
Sbjct: 69  ADLINEGNYGLIKAAQRFDETRGFKFISYAVWWIRQAILQALAEQSRVVRLPLNRIGTIS 128

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
             +++  + R  + H +A +   L        A++LN+   ++           S++A  
Sbjct: 129 KIRKV--SARLAQEHERAPSAEEL--------AEELNIDVEKIREALQHTGRALSMDAPF 178

Query: 191 NSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL- 248
              D NS    D L  + D   ++ L+E+  + +    + R++S L+PRE  I    RL 
Sbjct: 179 TDDDDNS--LLDVLPNEEDTSPDEGLMEESLKID----IERALSTLHPREAEII---RLY 229

Query: 249 ----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
               +E+P+TLE +   F ++RERVRQI+ +A +K+++
Sbjct: 230 FGIGREHPLTLEEIGQRFGLTRERVRQIKEKALRKLRQ 267


>gi|294055548|ref|YP_003549206.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Coraliomargarita
           akajimensis DSM 45221]
 gi|293614881|gb|ADE55036.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Coraliomargarita
           akajimensis DSM 45221]
          Length = 342

 Score =  128 bits (322), Expect = 8e-28,   Method: Compositional matrix adjust.
 Identities = 87/269 (32%), Positives = 153/269 (56%), Gaps = 13/269 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           GL  Y+ EI K  +L  QEE  LAKR ++ G+ +A   +++++LRLVVKIA  Y  +GLP
Sbjct: 46  GLRAYMQEIGKTALLTPQEEVELAKRIQK-GNKAARDHMISANLRLVVKIAHDYNNFGLP 104

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++SEGNIGL++AV++FDP +G +L+TY+ WWIK +++  +      +++      K 
Sbjct: 105 LMDLISEGNIGLVKAVERFDPSKGGKLSTYAAWWIKQSIKRALANQSKTIRLPVHLVDKI 164

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
            +  +R++   L    D     E+   IA  + +  ++V  +        SL+A +   D
Sbjct: 165 AY--MRKITAELADELDREPTDEE---IAYTMGMPVNKVAHLKSVSVRPSSLDAPVG-ED 218

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENP 252
            ++S  +  LV D +  +   +E  + K+  N +   +++L+ RE  I   R     E+P
Sbjct: 219 GDTSFGE--LVGDEN--QATPLENLQEKSLSNDMHSMIALLDQREAEIIRLRFGLDGEHP 274

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +TLE +  +F+++RERVRQI+  A  K++
Sbjct: 275 LTLEEVGEQFKITRERVRQIQNIAIHKMR 303


>gi|206602787|gb|EDZ39268.1| RNA polymerase, RpoD-like sigma subunit [Leptospirillum sp. Group
           II '5-way CG']
          Length = 499

 Score =  128 bits (321), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 93/283 (32%), Positives = 149/283 (52%), Gaps = 23/283 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ +++K  +L  +EE  LAKR R  GD SA   ++ S+LRLVV IA  Y G GL +
Sbjct: 49  LGSYLKKLQKSHLLTFEEEQDLAKRVRA-GDESARQAMIQSNLRLVVSIAKRYIGRGLLL 107

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM+AV KFDP++GFR +TY+ WWI+ A++  I+    ++++     +K  
Sbjct: 108 EDLIEEGNLGLMKAVSKFDPDKGFRFSTYASWWIRQAIERGIINQGHMIRLPVHMMEK-- 165

Query: 136 FFNLRRLKGHLQAI---TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 +  +L AI     +  +P+ +  +A+K  +   ++  +   L    SL+  I  
Sbjct: 166 ------VNAYLNAIERQVADGQQPD-IENLARKNGLKVRDLQEIQALLKNTVSLDTPIG- 217

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-----R 247
            D+  S  +D LV          IE  E  +R   L  S+++L  +ERR+   R      
Sbjct: 218 -DREDSTLKDILVDPTSFSPISTIESREEGDR---LRESLALLKDKERRVIHLRFGLPGE 273

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
             E  +TLE +     V+RERVRQIEA A  K++  ++   E 
Sbjct: 274 GPEEGMTLEAIGQMLGVTRERVRQIEASAMAKLRAYMEDPSEF 316


>gi|254455073|ref|ZP_05068509.1| RNA polymerase, sigma 32 subunit, RpoH [Octadecabacter antarcticus
           238]
 gi|198263775|gb|EDY88046.1| RNA polymerase, sigma 32 subunit, RpoH [Octadecabacter antarcticus
           238]
          Length = 249

 Score =  128 bits (321), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 80/210 (38%), Positives = 124/210 (59%), Gaps = 15/210 (7%)

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
            NIGL++A  +FDP++GFR +TY+ WWI+A +Q+Y L+ WSLVK+  +A  ++LF+NL+R
Sbjct: 4   ANIGLLKAADRFDPDKGFRFSTYAAWWIRAEIQDYKLQGWSLVKLPNSAFGRKLFYNLKR 63

Query: 142 LKGHLQAITDNNLKPEQVVA-IAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQ 199
           ++  L  + +  + PE +V  IA  L V+  +V+ M  RLA  D SLN  + S D  ++Q
Sbjct: 64  VETRL--VAEGEVPPEHLVDRIATDLGVTPEQVVLMQQRLAAPDGSLNRPV-SDDGGTAQ 120

Query: 200 WQDWLVYDHDGQEQVLIEKE--ERKNRR---NMLTRSMSVLNPRERRIFEARRLQENPVT 254
            QD L+ D D      +EKE   R + R     L+  ++ L+ RE+ I     + + P T
Sbjct: 121 LQD-LLEDPDAD----VEKEVSARLDSRAFWTTLSFHLNRLSKREQEIIIEIYVSDTPKT 175

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L  L  +F VS ER+RQI   A  +++ S 
Sbjct: 176 LYELGEQFSVSHERIRQIREAALTRLRASF 205


>gi|196232822|ref|ZP_03131672.1| RNA polymerase, sigma 70 subunit, RpoD family [Chthoniobacter
           flavus Ellin428]
 gi|196223021|gb|EDY17541.1| RNA polymerase, sigma 70 subunit, RpoD family [Chthoniobacter
           flavus Ellin428]
          Length = 296

 Score =  128 bits (321), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 88/284 (30%), Positives = 162/284 (57%), Gaps = 23/284 (8%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           + + G+  Y+ EI +IP+L  ++E  LA + ++ GD +A   ++ S+LRLVVKIA  Y  
Sbjct: 8   DSDSGIKIYLREIGQIPLLTPEQEIELAAKIKK-GDKAARSLMIRSNLRLVVKIAHDYAN 66

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK----- 125
            GLP+ +++SEGNIGLM+AV++FDP +G +L+TY+ WWIK +++  +      ++     
Sbjct: 67  LGLPLLDLISEGNIGLMKAVERFDPAKGGKLSTYAAWWIKQSIKRALANQSKTIRLPVHL 126

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           +   +  +R+   +    G  +  TD+ L  E  ++  K   +S+ + +S+        S
Sbjct: 127 VDKISKMRRVALQMSEELG--REPTDDELAEEVGLSSGK---ISQLKTVSIRP-----AS 176

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L+A I  SD +S+++ + +    D +     E+   KN R+ +   + VL+ RE++I  +
Sbjct: 177 LDAPI--SDDDSTEFGEIV---GDLEALTPFERLRDKNLRDEVGDLLEVLDEREKKIIFS 231

Query: 246 RRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           R   +     TLE +  +F V+RER+RQ++  A  K++ ++QK+
Sbjct: 232 RFGLDGGKAKTLEEVGKKFGVTRERIRQLQNIALMKLRRALQKK 275


>gi|54302639|ref|YP_132632.1| DNA-directed RNA polymerase sigma factor [Photobacterium profundum
           SS9]
 gi|90412658|ref|ZP_01220660.1| hypothetical DNA-directed RNA polymerase, sigma subunit
           [Photobacterium profundum 3TCK]
 gi|46916063|emb|CAG22832.1| hypothetical DNA-directed RNA polymerase, sigma subunit
           [Photobacterium profundum SS9]
 gi|90326466|gb|EAS42878.1| hypothetical DNA-directed RNA polymerase, sigma subunit
           [Photobacterium profundum 3TCK]
          Length = 291

 Score =  127 bits (320), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 87/271 (32%), Positives = 149/271 (54%), Gaps = 14/271 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L K EE +L  R    GD  A   ++ S+LRLVV IA  YRG G+ +S++
Sbjct: 19  YLREIALKPLLTKHEE-ILYSRKSLTGDKEAKKVMIESNLRLVVSIAKKYRGSGMQLSDL 77

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGL+ +V+KFDPERGFR +TY+ WWIK  ++  I      +++    +++     
Sbjct: 78  IDEGNIGLITSVEKFDPERGFRFSTYATWWIKQTIERCIHNQARTIRLPVHVSKEINTI- 136

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
              ++ H Q +  NN +P +   +A+KL  S  ++ S+    A   S +  IN  D NS 
Sbjct: 137 ---IRTHKQLMKKNNQEPTR-EEVAEKLERSVDDISSVLAYDAPIVSFDQTIN-DDANSQ 191

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR---LQENPVTL 255
               ++  D   + +  ++K++ K    +    +  LN R+R I   RR   L     TL
Sbjct: 192 SISVFIADDSSDKPESQVDKDDIK---GLALAMLENLNQRDREIL-CRRFGLLGYEVQTL 247

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           + +++E  ++RER+RQ++  + KK++ ++++
Sbjct: 248 QQVANEVGLTRERIRQLQVSSLKKLKNTLER 278


>gi|325971114|ref|YP_004247305.1| RNA polymerase, sigma 70 family subunit [Spirochaeta sp. Buddy]
 gi|324026352|gb|ADY13111.1| putative RNA polymerase, sigma 70 family subunit [Spirochaeta sp.
           Buddy]
          Length = 293

 Score =  127 bits (320), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 84/277 (30%), Positives = 163/277 (58%), Gaps = 13/277 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           LS Y+ EI +IP+L  QEE VLAKR ++ GD  A  R++ S+LR VV +A  Y+  G+P+
Sbjct: 23  LSMYLKEINQIPLLTPQEELVLAKRAQK-GDEFARKRMIESNLRFVVNVAKKYQNQGMPL 81

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGNIGLM A++KFDP++G+   +Y++WWI+ ++ + I      V++      + L
Sbjct: 82  VDLINEGNIGLMTALEKFDPDKGYHFISYAVWWIRQSIMKAINEKSRAVRLPLNRTNELL 141

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
             + +  +  ++ ++ ++   E++  +        S ++S++  L    SL+A +  +D 
Sbjct: 142 QMH-KAQRSLMKDLSTDDPSMEEIGTLTGFDPKHVSNLLSISRDLI---SLDAPV-FTDG 196

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPV 253
           ++S   D++  +    EQ L++   +++ R++L    + L+ +ER I E R   E   P+
Sbjct: 197 SASNIGDFIEDESQNPEQSLLDASLKEDVRSLL----ATLSDKERDIIELRFGLEGKTPM 252

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQE-SIQKQVE 289
           +L+ +   + +++ER+RQIE +A ++++  S  K VE
Sbjct: 253 SLKEIGELYNLTKERIRQIEKKALERLRNPSKSKMVE 289


>gi|237809473|ref|YP_002893913.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Tolumonas auensis
           DSM 9187]
 gi|237501734|gb|ACQ94327.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Tolumonas auensis
           DSM 9187]
          Length = 324

 Score =  127 bits (320), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 91/281 (32%), Positives = 146/281 (51%), Gaps = 34/281 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +E Y   +  R  GD +A +R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 55  YLGEIGFSPLLTAEEVYFARRALR--GDDAARNRMIESNLRLVVKIARRYNNRGLALLDL 112

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 113 VEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTVERAIMNQTRTIRLPIHV-VKELNVY 171

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA---------GDESLNAL 189
           LR  +   Q + D+    E + ++  K     S ++ +N R+          GD+SL  +
Sbjct: 172 LRTARELAQRL-DHEPTAEDIASLLDKPVEEVSRMLKLNERICSVDTPIAGDGDKSLIDI 230

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-- 247
           +     N  + Q     D D Q  ++I  E+              LNP++R +  ARR  
Sbjct: 231 LTDDRINCPEDQ---TQDDDMQHSIVIWLEQ--------------LNPKQREVL-ARRFG 272

Query: 248 -LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            L   P TLE +  E  ++RERVRQI+    ++++E + +Q
Sbjct: 273 LLGYEPATLEEVGEEIGLTRERVRQIQVEGLRRMKEMLTQQ 313


>gi|91792562|ref|YP_562213.1| RNA polymerase sigma factor RpoS [Shewanella denitrificans OS217]
 gi|91714564|gb|ABE54490.1| RNA polymerase sigma factor RpoS [Shewanella denitrificans OS217]
          Length = 327

 Score =  127 bits (320), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 95/282 (33%), Positives = 148/282 (52%), Gaps = 35/282 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE V   R    G   + +R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 58  YLGEIGFSPLLSAEEE-VFFSRKALKGCEKSRNRMIESNLRLVVKIARRYNNRGLALLDL 116

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 117 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 175

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRLAGDESLNA 188
           LR  +   Q + D+    E+   IA KL+VS S+V           S++  L GD    A
Sbjct: 176 LRTARQLAQKL-DHEPTAEE---IAAKLDVSTSDVSRMLKLNEKITSVDTPLGGDNE-KA 230

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR- 247
           L++    + S   D+ V D D                N +   ++ LN ++R +  ARR 
Sbjct: 231 LLDVIADDDSVGPDYQVQDED--------------LSNSIVGWLNELNTKQREVL-ARRF 275

Query: 248 --LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             L   P TLEN+ +E  ++RERVRQI+  A K++++ +  Q
Sbjct: 276 GLLGYEPSTLENVGAEIGLTRERVRQIQVEALKRLKDLLSSQ 317


>gi|255282119|ref|ZP_05346674.1| RNA polymerase sigma factor RpoD [Bryantella formatexigens DSM
           14469]
 gi|255267438|gb|EET60643.1| RNA polymerase sigma factor RpoD [Bryantella formatexigens DSM
           14469]
          Length = 374

 Score =  127 bits (319), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 97/284 (34%), Positives = 151/284 (53%), Gaps = 33/284 (11%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V+ E  +  Y+ EI  +P+L  +EE  LAKR  E GD  A  RL+ ++LRLVV IA  Y 
Sbjct: 99  VSTEDPVRMYLKEIGNVPLLTTEEEVELAKRV-EAGDEEAKKRLIEANLRLVVSIAKKYV 157

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT- 128
           G G+P  +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I  +   +++   
Sbjct: 158 GRGMPFLDLIQEGNMGLMKAVDKFDYAKGFKFSTYATWWIRQAITRGIADTGRTIRVPVH 217

Query: 129 ---TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE- 184
              T N+      LR  +  LQ +      PE+V   A++LNV  S V  +  +++ D  
Sbjct: 218 MVETINK-----TLRMTRTLLQELG-REPTPEEV---AERLNVPVSRVREV-LKISRDPV 267

Query: 185 SLNALINSSDKNSSQWQDWLVYD-----HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           SL+  I   D   S   D++  D      D     ++ +E        L  ++  L  RE
Sbjct: 268 SLDTPIGEED--DSHLGDFIEDDSALSPSDSAAFSMLREE--------LGTALESLTDRE 317

Query: 240 RRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R++ + R   +     TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 318 RQVVQLRFGLIDGRARTLEEVGKEFNVTRERIRQIEAKALRKLR 361


>gi|164688099|ref|ZP_02212127.1| hypothetical protein CLOBAR_01744 [Clostridium bartlettii DSM
           16795]
 gi|164602512|gb|EDQ95977.1| hypothetical protein CLOBAR_01744 [Clostridium bartlettii DSM
           16795]
          Length = 385

 Score =  127 bits (319), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 94/266 (35%), Positives = 147/266 (55%), Gaps = 15/266 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L+  EE   AKR  E GD  A  RLV ++LRLVV IA  Y G G+   ++
Sbjct: 119 YLKEIGKIPLLKPHEEIEYAKRMLE-GDEIAKQRLVEANLRLVVSIAKRYVGRGMLFLDL 177

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD ERGF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 178 IQEGNLGLIKAVEKFDYERGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 235

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R+   L      + KPE+   IAK++++SE +V  +  ++A D  SL   I   ++  
Sbjct: 236 LIRVSRQLLQELGRDPKPEE---IAKEMDMSEEKVREI-MKIAQDPVSLETPI--GEEED 289

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTL 255
           S   D++    D       E       ++ +   +  LN RE+++ + R   E+    TL
Sbjct: 290 SHLGDFI---PDEDALAPAEAAAYSLLKDQIEEVLGSLNEREQKVLKLRFGLEDGRARTL 346

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           E +  EF+V+RER+RQIEA+A +K++
Sbjct: 347 EEVGKEFDVTRERIRQIEAKALRKLR 372


>gi|225388598|ref|ZP_03758322.1| hypothetical protein CLOSTASPAR_02334 [Clostridium asparagiforme
           DSM 15981]
 gi|225045346|gb|EEG55592.1| hypothetical protein CLOSTASPAR_02334 [Clostridium asparagiforme
           DSM 15981]
          Length = 405

 Score =  127 bits (319), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 90/276 (32%), Positives = 149/276 (53%), Gaps = 23/276 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  I +L  +EE  LAKR  E GD  A  RLV ++LRLVV IA  Y G G+   ++
Sbjct: 139 YLKEIGAIALLTPEEEAGLAKRCAE-GDEEAGKRLVEANLRLVVSIAKRYTGRGMSFLDL 197

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGNIGLM+AV+KFD E+G+RL+TY+ WW+K A+   +      +++    +       
Sbjct: 198 VQEGNIGLMKAVEKFDYEKGYRLSTYATWWVKQAITRALADQARTIRL--PVHMVEAVNK 255

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           +RR +  L      +    +   +A+ + ++E  V  +  + +GD +++      D++ S
Sbjct: 256 IRRTQRDLSVQLGRDPSNRE---LAEAVGMTEKRVEEL-IQTSGD-TVSLETPVGDEDGS 310

Query: 199 QWQDWLVYD-----HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-- 251
              D++  +      D  E VL+ +E        +   +  LN RER++ + R   EN  
Sbjct: 311 SLGDFVADNAGDSTEDQAENVLLREE--------IDSMLQGLNERERQVIKLRFGLENGR 362

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           P+TLE +  +F V+RER+RQIE  A +K++  ++ +
Sbjct: 363 PLTLEEVGRQFNVTRERIRQIETAALRKLRNPVRSK 398


>gi|109900163|ref|YP_663418.1| RNA polymerase, sigma 28 subunit [Pseudoalteromonas atlantica T6c]
 gi|109702444|gb|ABG42364.1| RNA polymerase, sigma 38 subunit, RpoS [Pseudoalteromonas atlantica
           T6c]
          Length = 327

 Score =  127 bits (318), Expect = 3e-27,   Method: Compositional matrix adjust.
 Identities = 88/269 (32%), Positives = 151/269 (56%), Gaps = 19/269 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   ++R  + GD ++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 56  YLGEIGFSPLLSAEEEVYFSRRALK-GDEASRQRMIVSNLRLVVKIARRYNNRGLALLDL 114

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 115 VEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 173

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +   Q + D+    E++    +K     ++++ +N R+    S++  I S  +N +
Sbjct: 174 LRTSRELAQKL-DHEPTAEEIAEAVQKPVADVTKMLRLNERIT---SVDTPIGS--ENDN 227

Query: 199 QWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR---LQENPV 253
              D +  D  HD +E +     + KN +  +   +  LNP++R +  ARR   L   P 
Sbjct: 228 VLLDIIADDNGHDPEEDL-----QDKNVKLSIVGWLEDLNPKQREVL-ARRFGLLGYEPS 281

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQE 282
           TLE++  E  ++RERVRQI+  A +++++
Sbjct: 282 TLEDVGVEIGLTRERVRQIQVEALRRLKD 310


>gi|108804071|ref|YP_644008.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108765314|gb|ABG04196.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 294

 Score =  126 bits (317), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 86/265 (32%), Positives = 144/265 (54%), Gaps = 16/265 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L++Y+  I +  +L  QEE  L++R ++ GD  A  +L+  +LRLVV +A  YRGYGLP 
Sbjct: 24  LAKYLAHIGQGELLTHQEEIELSRRAKK-GDRKARQKLIEKNLRLVVSVAKKYRGYGLPF 82

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AV+KFDPERGFR +TY+ WWI+ A+Q  +      +++     +K  
Sbjct: 83  EDLIQEGNIGLMKAVEKFDPERGFRFSTYATWWIRQAVQRAVADKGRTIRVPVHMTEK-- 140

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              +R++      ++    +      IA++L     +V      +    SL+  + SS++
Sbjct: 141 ---IRKVSRTFNELSLELEREPTDEEIARRLEWDVEDVRLTISAMPDATSLDQPV-SSEE 196

Query: 196 NSSQWQDWLVYDH--DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-- 251
           ++S+  D++  +   D  + VL E E      + L  ++  L  R R +   R   ++  
Sbjct: 197 SASELGDFIEDERTSDTPDTVLKELES-----SQLKEAIERLPERARYVLVRRYGLDDRE 251

Query: 252 PVTLENLSSEFEVSRERVRQIEARA 276
           P TL  L  E ++SRERVRQ++  A
Sbjct: 252 PATLAELGDELKISRERVRQLQREA 276


>gi|281357500|ref|ZP_06243988.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Victivallis
           vadensis ATCC BAA-548]
 gi|281316103|gb|EFB00129.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Victivallis
           vadensis ATCC BAA-548]
          Length = 432

 Score =  126 bits (316), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 92/272 (33%), Positives = 149/272 (54%), Gaps = 21/272 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHR-----LVTSHLRLVVKIAMGYRGYGL 73
           Y+ EI +IP++ K+EE  LA     HGD    H      L+ ++LRLVVKIA  ++G GL
Sbjct: 163 YMGEIARIPLVNKKEEAELADAI--HGDNEDRHEDARSTLIKANLRLVVKIAHDFKGLGL 220

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++SEGNIGLM+AV+KFDP +G + ++Y+ WWIK +M+  +      ++I   +  K
Sbjct: 221 PLLDLISEGNIGLMRAVEKFDPAKGAKFSSYAAWWIKQSMRRALANQSRTIRIPVQSAGK 280

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                + ++K     + +   +      IA+ L+ SE  V  +        SL+  I   
Sbjct: 281 -----INKIKSVRMKLAEELGREPSDAEIAEHLDFSERTVAGLRLADLRTFSLHDPIQQG 335

Query: 194 DKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN 251
           ++   ++QD +   H    +Q+L + E      ++L +    L  RERRI E R  L+ N
Sbjct: 336 EEG--EFQDIIPDRHAMTPDQILGDVESVFRLMDLLEK----LEERERRILEMRFGLRGN 389

Query: 252 -PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            P+TLE +S E   +RERVRQI+ +A  K+++
Sbjct: 390 RPLTLEEVSQEIGRTRERVRQIQNQALAKLKQ 421


>gi|212634213|ref|YP_002310738.1| RNA polymerase sigma-38 factor [Shewanella piezotolerans WP3]
 gi|212555697|gb|ACJ28151.1| RNA polymerase sigma-38 factor [Shewanella piezotolerans WP3]
          Length = 322

 Score =  126 bits (316), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 94/281 (33%), Positives = 150/281 (53%), Gaps = 33/281 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE V   R    G   + +R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 53  YLGEIGFSPLLSAEEE-VFFSRKSLKGCEKSRNRMIESNLRLVVKIARRYNNRGLALLDL 111

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 112 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 170

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV---ISMNCRLA------GDESLNAL 189
           LR  +  L    D+    E+   IA+KL++S S+V   + +N R+       G ES  AL
Sbjct: 171 LRTAR-ELAHKLDHEPTAEE---IAEKLDLSSSDVSRMLKLNERITSVDTPLGGESDKAL 226

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-- 247
           ++    + +   D+ V D D  + V+              + +  LN ++R +  ARR  
Sbjct: 227 LDVLADDDNVGPDYKVQDEDMSKSVV--------------KWLDELNTKQREVL-ARRFG 271

Query: 248 -LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            L   P TLEN+  E  ++RERVRQI+  A K++++ +  Q
Sbjct: 272 LLGYEPSTLENVGKEIGLTRERVRQIQVEALKRLKDLLGAQ 312


>gi|256425191|ref|YP_003125844.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chitinophaga
           pinensis DSM 2588]
 gi|256040099|gb|ACU63643.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chitinophaga
           pinensis DSM 2588]
          Length = 285

 Score =  126 bits (316), Expect = 5e-27,   Method: Compositional matrix adjust.
 Identities = 84/276 (30%), Positives = 149/276 (53%), Gaps = 25/276 (9%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            + +Y+ EI KIP+L  +EE VLA+R +  GD  A  RL T +LR VV +A  Y+  GL 
Sbjct: 17  AVEKYLQEISKIPLLTPEEETVLAQRIK-MGDQKALERLTTGNLRFVVSVAKQYQHQGLS 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV-----KIGTT 129
           +S++++EGN+GL++A ++FD  +GF+  +Y++WWI+ ++ + +     LV     KIGT 
Sbjct: 76  LSDLINEGNLGLIKAAQRFDETKGFKFISYAVWWIRQSILQALAEQGRLVRLPQNKIGTY 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
               + +           A    N +      +A+ L +SESE+ ++        SL+A 
Sbjct: 136 NKANKAYM----------AFEQENEREPSTEELAEILEMSESEINNIFQSNTRHMSLDAP 185

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA--RR 247
           ++ ++  +    D L       + V+     R + R  + R +  L+PRE  I  A    
Sbjct: 186 VHEAEDVA--MGDLLEGGDITDDDVM-----RDSLREEIRRVLKSLSPREAEIVNAYFGL 238

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             EN  T+E +  ++++++ER+RQI+ RA K++Q++
Sbjct: 239 DGENGATIEQIGQKYDLTKERIRQIKERAIKRLQKA 274


>gi|332308186|ref|YP_004436037.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Glaciecola
           agarilytica 4H-3-7+YE-5]
 gi|332175515|gb|AEE24769.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Glaciecola
           agarilytica 4H-3-7+YE-5]
          Length = 327

 Score =  125 bits (315), Expect = 6e-27,   Method: Compositional matrix adjust.
 Identities = 87/269 (32%), Positives = 150/269 (55%), Gaps = 19/269 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   ++R  + GD ++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 56  YLGEIGFSPLLSAEEEVYFSRRALK-GDEASRQRMIVSNLRLVVKIARRYNNRGLALLDL 114

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 115 VEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 173

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +   Q + D+    E++    ++     ++++ +N R+    S++  I S + N  
Sbjct: 174 LRTSRELAQKL-DHEPTAEEIAEAVQRPVADVTKMLRLNERIT---SVDTPIGSDNDNV- 228

Query: 199 QWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR---LQENPV 253
              D +  D  HD +E +     + KN +  +   +  LNP++R +  ARR   L   P 
Sbjct: 229 -LLDIIADDNGHDPEEDL-----QDKNVKLSIVGWLEDLNPKQREVL-ARRFGLLGYEPS 281

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQE 282
           TLE++  E  ++RERVRQI+  A +++++
Sbjct: 282 TLEDVGVEIGLTRERVRQIQVEALRRLKD 310


>gi|149911320|ref|ZP_01899941.1| DNA-directed RNA polymerase, sigma subunit [Moritella sp. PE36]
 gi|149805635|gb|EDM65637.1| DNA-directed RNA polymerase, sigma subunit [Moritella sp. PE36]
          Length = 294

 Score =  125 bits (314), Expect = 7e-27,   Method: Compositional matrix adjust.
 Identities = 84/273 (30%), Positives = 145/273 (53%), Gaps = 12/273 (4%)

Query: 15  GLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
            L  Y  E+++   +L KQEEY  A     +GD +A   ++ S+LRLV+ +A  Y+ Y L
Sbjct: 8   ALDVYFDELQRFSQLLSKQEEYDTAVA-AANGDKAARDTMIQSNLRLVLMVAKKYQNYSL 66

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
             +E++ EGN GLM AV KFDPERG R +TY++WWI+  +++YI+     ++I       
Sbjct: 67  DWAEIIQEGNTGLMHAVDKFDPERGCRFSTYAVWWIRNNIEQYIMNHSRTIRIPIHVT-- 124

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
           R++  + +    L    D N   E +  IA++L +S  +V+++      + SL+  I+S 
Sbjct: 125 RVYKQILKASSELGLDVDTN---EGITKIAQELKISPRKVLNILGHYFNEGSLDKEIHSG 181

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQEN 251
           D   +  +D +  + D Q  +  EK +     + L   + V   R + I   R     ++
Sbjct: 182 DNLLATLKDLVAAEVDCQPDIRYEKCDYYEYMDALLEYLPV---RSQNIIRLRFGFKGQD 238

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           P++L+ ++   ++SRERVRQI      +V+E +
Sbjct: 239 PMSLQAIAQLMDISRERVRQIIRNGLSQVREQL 271


>gi|210620870|ref|ZP_03292287.1| hypothetical protein CLOHIR_00230 [Clostridium hiranonis DSM 13275]
 gi|210155082|gb|EEA86088.1| hypothetical protein CLOHIR_00230 [Clostridium hiranonis DSM 13275]
          Length = 388

 Score =  125 bits (314), Expect = 9e-27,   Method: Compositional matrix adjust.
 Identities = 92/266 (34%), Positives = 146/266 (54%), Gaps = 15/266 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L+  EE   AKR  E GD  A  RLV ++LRLVV IA  Y G G+   ++
Sbjct: 122 YLKEIGKIPLLKPHEEVEYAKRMHE-GDELAKQRLVEANLRLVVSIAKRYVGRGMLFLDL 180

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD E+GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 181 IQEGNLGLIKAVEKFDYEKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 238

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R+   L      + KPE+   IAK++++S  +V  +  ++A D  SL   I   ++  
Sbjct: 239 LMRVSRQLLQELGRDAKPEE---IAKEMDLSVEKVREI-MKIAQDPVSLETPI--GEEED 292

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTL 255
           S   D++  D      +       K +   +   +  LN RE+++ + R   E+    TL
Sbjct: 293 SHLGDFIPDDDAPAPDISAAYSLLKEQ---IDEVLGSLNEREQKVLKLRFGLEDGRARTL 349

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           E +  EF+V+RER+RQIEA+A +K++
Sbjct: 350 EEVGKEFDVTRERIRQIEAKALRKLR 375


>gi|160947542|ref|ZP_02094709.1| hypothetical protein PEPMIC_01477 [Parvimonas micra ATCC 33270]
 gi|158446676|gb|EDP23671.1| hypothetical protein PEPMIC_01477 [Parvimonas micra ATCC 33270]
          Length = 382

 Score =  125 bits (314), Expect = 9e-27,   Method: Compositional matrix adjust.
 Identities = 89/270 (32%), Positives = 141/270 (52%), Gaps = 23/270 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L   EE +LA+   E GD+ A  +L  ++LRLVV IA  Y G G+   ++
Sbjct: 116 YLKEIGKIPLLSADEERILAENM-EAGDIEAKKKLAETNLRLVVSIAKRYVGRGMQFLDL 174

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT--TANQKRLF 136
           + EGN+GLM+AV+KFD  RGF+ +TY+ WWI+ A+   I      ++I         +L 
Sbjct: 175 IQEGNMGLMKAVEKFDFRRGFKFSTYATWWIRQAITRSIADQARTIRIPVHMVETINKLV 234

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
              R+L   L     N    E +     K+N           R    E ++      +++
Sbjct: 235 RIERQLVQELGREPTNEEISEHMGIEVDKVN---------EIRKIAQEPVSLETPIGEED 285

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKN---RRNMLTRSMSVLNPRERRIFEAR-RLQE-N 251
            S   D++      +++  I  +E  N    +  L + +S L+ RE+++ E R  L +  
Sbjct: 286 DSHLGDFI------EDETAIAPDEAANFSMLKEQLNQVLSTLSDREKKVLELRFGLNDGT 339

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           P TLE +  EFEV+RER+RQIEA+A +K++
Sbjct: 340 PRTLEEVGKEFEVTRERIRQIEAKALRKLK 369


>gi|149911458|ref|ZP_01900075.1| sigma S (sigma 38) factor of RNA polymerase, major
           sigmafactorduring stationary phase [Moritella sp. PE36]
 gi|149805489|gb|EDM65496.1| sigma S (sigma 38) factor of RNA polymerase, major
           sigmafactorduring stationary phase [Moritella sp. PE36]
          Length = 319

 Score =  125 bits (313), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 89/280 (31%), Positives = 148/280 (52%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD S+  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 50  YLGEIGFSPLLTAEEEVFYARRAL-RGDASSRKRMIESNLRLVVKIARRYNNRGLALLDL 108

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 109 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYL 168

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I D   KP  V  ++K L ++E  + S++  + GD     L 
Sbjct: 169 RAARELAHELDHEPTAEDIADKLDKP--VADVSKMLRLNE-RISSVDTPIGGDSEKALLD 225

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
             SD+             DG E     + +  + +  + R +  LNP++R +  ARR   
Sbjct: 226 IISDEKG-----------DGPES----RTQNDDIKFSIIRWLEELNPKQREVL-ARRFGL 269

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L  +  TLE++  E  ++RERVRQI+  A ++++E + +Q
Sbjct: 270 LGYDASTLEDVGREIGLTRERVRQIQVEALRRLREVLAQQ 309


>gi|225011103|ref|ZP_03701566.1| RNA polymerase, sigma 70 subunit, RpoD family [Flavobacteria
           bacterium MS024-3C]
 gi|225004737|gb|EEG42696.1| RNA polymerase, sigma 70 subunit, RpoD family [Flavobacteria
           bacterium MS024-3C]
          Length = 287

 Score =  125 bits (313), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 93/287 (32%), Positives = 152/287 (52%), Gaps = 47/287 (16%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ +I KI ++  QEE  LA+R +  GD  A  RL T++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQDISKIDLINAQEEVELAQRIKA-GDAVALERLTTANLRFVVSVAKQYQNQGLTL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
            ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ A+      Q  I+R   L KIG+ 
Sbjct: 77  PDLINEGNVGLVKAAKRFDETRGFKFISYAVWWIRQAILQALAEQARIVR-LPLNKIGSI 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCR 179
               + F        +L+        PE+   IAK+L ++ S+V          +SM+  
Sbjct: 136 NKINKAF-------SYLEQAHQRPPSPEE---IAKELEMTVSDVKQSLKNSGRHVSMDAP 185

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVY-DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           L   E           NSS + D L Y D    +Q LI+     +    +TR++  L+PR
Sbjct: 186 LIDGE-----------NSSLY-DVLDYGDSPRPDQALIQ----SSLHTEITRALDTLSPR 229

Query: 239 ERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           E  + +      ++ P+TL  +   F+++RERVRQI  +A +K++ S
Sbjct: 230 EADVIKLFYGIGEQPPMTLAEIGLTFDLTRERVRQIREKAIRKLRHS 276


>gi|89901551|ref|YP_524022.1| sigma-70 region 2 [Rhodoferax ferrireducens T118]
 gi|89346288|gb|ABD70491.1| sigma-70 region 2 [Rhodoferax ferrireducens T118]
          Length = 350

 Score =  125 bits (313), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 87/283 (30%), Positives = 152/283 (53%), Gaps = 26/283 (9%)

Query: 12  GEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           GE G  L+ Y+ ++R+  +   QEE+ LA R R  GD +A   ++  +LRLVV IA  Y 
Sbjct: 67  GESGDALTVYLRQVRRTTLFTPQEEFELAGRARA-GDFAARQSMIEHNLRLVVSIAKAYM 125

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+P+ +++ EGN+GLM A+ KF+PERGFR +TY+ WWI+ ++   ++    +V++   
Sbjct: 126 GRGVPLLDLIEEGNLGLMHAIDKFEPERGFRFSTYATWWIRQSVDRALMCQGRVVRL--P 183

Query: 130 ANQKRLFFNLRRLKGHLQAIT------DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
            N  R    + R +  L++         + ++ E V A+  +  V  ++++ +       
Sbjct: 184 VNVVRELQQVLRARRALESDAAFVVSRPDGIRVEDVAALLGRDPVHVADLLGLA---EAP 240

Query: 184 ESLNALINSSDKNSS---QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            SL+A ++ S +  +      D +  D  G  QV   + ER     +L   +  L+ RE+
Sbjct: 241 RSLDAALDRSGETQTFGDSLVDEITADPSGVTQV--HEVER-----LLEEWVGTLSEREK 293

Query: 241 RIFEAR-RLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            + E R  L +  P TL+ LS+  +++RERVRQ++  A  K++
Sbjct: 294 EVLEGRFGLHDREPETLDVLSARLDLTRERVRQVQNEALAKLK 336


>gi|182415180|ref|YP_001820246.1| RpoD family RNA polymerase sigma factor [Opitutus terrae PB90-1]
 gi|177842394|gb|ACB76646.1| RNA polymerase, sigma 70 subunit, RpoD family [Opitutus terrae
           PB90-1]
          Length = 353

 Score =  124 bits (312), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 85/280 (30%), Positives = 152/280 (54%), Gaps = 12/280 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ EI K  +L   EE  LAKR R+ GD +A   ++ ++LRLVVKIAM Y+ +GLP+
Sbjct: 51  LQLYLQEIGKTALLTIDEEISLAKRIRK-GDKAARDHMIKANLRLVVKIAMDYKDFGLPL 109

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++SEGNIGL++AV++FDP +G +L+TY+ WWIK +++  +      +++        L
Sbjct: 110 LDLISEGNIGLIKAVERFDPRKGGKLSTYAAWWIKQSIKRALANQSKTIRLPV-----HL 164

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + +++    A+T+   +      +A +L +  S+V  +        SL+A +     
Sbjct: 165 VDKISKMRRTAMALTEELGREPTDEELAIELQIPTSKVAHLKSVSVRPASLDAPVGEEGD 224

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPV 253
           +++  +  +V D +       E    KN  + L   ++ L+ RE  I   R   +  + +
Sbjct: 225 SATFGE--IVGDDNAVSP--FEGLREKNLNSDLHAMVASLDEREAEIIRLRFGLDGKDEL 280

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           TLE +   F V+RER+RQ+E  A  K+++++ K   + +S
Sbjct: 281 TLEEVGRRFHVTRERIRQLEYLALSKMRKAMAKHEAIRTS 320


>gi|218961053|ref|YP_001740828.1| putative RNA polymerase, sigma S (sigma 38) factor [Candidatus
           Cloacamonas acidaminovorans]
 gi|167729710|emb|CAO80622.1| putative RNA polymerase, sigma S (sigma 38) factor [Candidatus
           Cloacamonas acidaminovorans]
          Length = 292

 Score =  124 bits (312), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 84/282 (29%), Positives = 154/282 (54%), Gaps = 18/282 (6%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V  +  L  Y++EI K   L ++EE+ LA + + +GD+ A ++L+ ++L+ VVKIA  Y+
Sbjct: 7   VFADKALQNYLNEISKFKTLSREEEHDLAIKAK-NGDMDAMNKLIQANLKFVVKIASRYQ 65

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI--G 127
             GL +SE++SEGNIGL++A++KFDP++  +L +Y++WWIK  +   +    SL+++  G
Sbjct: 66  NRGLSLSELISEGNIGLIKAIEKFDPDKDIKLISYAIWWIKQRIMLAVSEKSSLIRVPMG 125

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
            ++   R+     R       I      P++   +++K+N++E  +  +  +L    S +
Sbjct: 126 KSSAAHRVKLTQDRYFTETGKIA----TPDE---LSEKMNIAEKTIEQLQNKLPETSSFD 178

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE----RRIF 243
            +I +SD      +D L+ D D  +   +  +ER   +  +  ++S L+ RE    R  F
Sbjct: 179 DIITTSDSQDFTAKD-LLEDKDTLDPQSLYYQERMQEK--IQNAISKLDAREAEIIRNYF 235

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
                 E+      ++ +  +SRERVRQI+  A KK+   I+
Sbjct: 236 GLNESHESR-NFAQIAEKLGLSRERVRQIQKEALKKIMREIK 276


>gi|304439790|ref|ZP_07399688.1| DNA-directed RNA polymerase sigma subunit RpoD [Peptoniphilus
           duerdenii ATCC BAA-1640]
 gi|304371777|gb|EFM25385.1| DNA-directed RNA polymerase sigma subunit RpoD [Peptoniphilus
           duerdenii ATCC BAA-1640]
          Length = 370

 Score =  124 bits (312), Expect = 1e-26,   Method: Compositional matrix adjust.
 Identities = 93/276 (33%), Positives = 138/276 (50%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L   EE V+AKR  E GD  AA  L  ++LRLVV IA  Y G G+   ++
Sbjct: 104 YLKEIGKIPLLTADEEVVIAKRM-EKGDREAARELAEANLRLVVSIAKRYVGRGMSFLDL 162

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 163 IQEGNLGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLV 222

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES--LN 187
             Q++L  +L R     +   + N+  E+V  I K       E +S+   +  +E   L 
Sbjct: 223 RIQRQLVQDLGRDPSPEEIAEEMNIDVERVREIQK----IAQEPVSLETPIGEEEDSHLG 278

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S Q         D     L+        R  L   +  L  RE+++   R 
Sbjct: 279 DFIPDEEIQSPQ---------DAATFTLL--------REQLGDVLDTLTDREKKVLTLRF 321

Query: 248 LQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             E+    TLE +  EF+V+RER+RQIEA+A +K++
Sbjct: 322 GLEDGRNRTLEEVGKEFDVTRERIRQIEAKALRKLR 357


>gi|323144152|ref|ZP_08078788.1| RNA polymerase sigma factor [Succinatimonas hippei YIT 12066]
 gi|322416060|gb|EFY06758.1| RNA polymerase sigma factor [Succinatimonas hippei YIT 12066]
          Length = 311

 Score =  124 bits (311), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 87/264 (32%), Positives = 147/264 (55%), Gaps = 17/264 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  +R+ P+L +++E  L  R  + GD+ A + ++TS+LRLV+K+A  YR  G+P+
Sbjct: 43  LVSYISSVRRYPLLSQEDEVRLG-RLVQQGDVKARNSMITSNLRLVIKVARDYRTRGVPM 101

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI--GTTANQK 133
            +++ EGN+GL+ AV KFDPERGFR +TY+ WWI+  ++  ++    LV++      +  
Sbjct: 102 LDLIEEGNLGLIHAVNKFDPERGFRFSTYATWWIRQGIEHAVMNQSRLVRLPFHVIKDLN 161

Query: 134 RLFFNLRRL--KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
           ++    ++L  K H QA+         V  IAK+L++ E +V SM   +A   S++ L N
Sbjct: 162 QVLKVKKKLQEKAHGQAVA--------VKDIAKELDIDEDKVRSM-LVVAEGISISDL-N 211

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQE 250
             +K+S +    L    D +   L E+        +L   +  LN R++ I   R  + +
Sbjct: 212 VKNKDSEKNVSLLDLLADEKTPTLEEQFGNTEIEKLLRSWIDSLNERQKIIVIHRFGIND 271

Query: 251 NPV-TLENLSSEFEVSRERVRQIE 273
           N + TLE +     ++RERVRQ++
Sbjct: 272 NDIKTLEEIGEMLHLTRERVRQLQ 295


>gi|160941150|ref|ZP_02088487.1| hypothetical protein CLOBOL_06043 [Clostridium bolteae ATCC
           BAA-613]
 gi|158435711|gb|EDP13478.1| hypothetical protein CLOBOL_06043 [Clostridium bolteae ATCC
           BAA-613]
          Length = 406

 Score =  124 bits (311), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 87/265 (32%), Positives = 143/265 (53%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  I +L  +EE  LA+R  E GD+ A  +LV ++LRLVV IA  Y G G+   ++
Sbjct: 140 YLKEIGSIALLTPEEESDLARRKSE-GDVEAGRKLVEANLRLVVSIAKRYTGRGMSFLDL 198

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GLM+AV+KFD  +G+RL+TY+ WW+K ++   +      +++    +       
Sbjct: 199 VQEGNLGLMKAVEKFDYAKGYRLSTYATWWVKQSITRSLADQSRTIRL--PVHMVEAVNK 256

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           +RR +  L          E+V   A+++N+S   V  +  + +GD +++      D+  S
Sbjct: 257 IRRAQRSLSVKLGREPSMEEV---AEEVNMSGKRVAEL-IQASGD-TVSLETPVGDEEGS 311

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLE 256
              D++  D +   +   +K E    R  +   +  LNPRER +   R   E  +P+TLE
Sbjct: 312 NLGDFVADDANASTE---DKAESFLLREEIDSMLQGLNPREREVIILRFGLETGHPLTLE 368

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +   F V+RER+RQIE  A +K++
Sbjct: 369 EVGKRFNVTRERIRQIETAALRKLR 393


>gi|261345855|ref|ZP_05973499.1| RNA polymerase sigma factor RpoS [Providencia rustigianii DSM 4541]
 gi|282566345|gb|EFB71880.1| RNA polymerase sigma factor RpoS [Providencia rustigianii DSM 4541]
          Length = 328

 Score =  124 bits (311), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 86/280 (30%), Positives = 152/280 (54%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 59  YLSEIGFSPLLTAEEEVFYARRAL-RGDIASRQRMIESNLRLVVKISRRYNNRGLALLDL 117

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPE+GFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 118 IEEGNLGLIRAVEKFDPEKGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI-VKELNIY 176

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +   Q + D+   PE++          +++ L ++E  + S++  +AGD   + L 
Sbjct: 177 LRTARELAQKL-DHEPSPEEIAEQLDKPVEDVSRMLRLNER-ITSVDTPIAGDSEKSLLE 234

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
             SD N S           G E  + + + ++N    + + +  LNP++R +  ARR   
Sbjct: 235 VLSDDNDS-----------GPENTIQDNDLKEN----IVKWLYELNPKQREVL-ARRFGL 278

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L     TLE +  E  ++RERVRQI+    +++++ +Q +
Sbjct: 279 LGYEAETLEEVGREIGLTRERVRQIQVEGLRRLKDILQGE 318


>gi|227872476|ref|ZP_03990816.1| DNA-directed RNA polymerase sigma subunit SigA [Oribacterium sinus
           F0268]
 gi|227841677|gb|EEJ51967.1| DNA-directed RNA polymerase sigma subunit SigA [Oribacterium sinus
           F0268]
          Length = 385

 Score =  124 bits (311), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 88/283 (31%), Positives = 146/283 (51%), Gaps = 43/283 (15%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EEY LA + +E GD  A  RL+ ++LRLVV IA  Y G G+   ++
Sbjct: 119 YLKEIGTVPLLTAEEEYALAMKKQE-GDEYAKQRLIEANLRLVVSIAKRYTGRGMSFLDL 177

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           V EGN+GL++ V+KFDPE+GF+L+TY+ WWI+ ++   +      +++      T N   
Sbjct: 178 VQEGNLGLIKGVEKFDPEKGFKLSTYATWWIRQSVTRALADQARTIRVPVHMVETINKMS 237

Query: 132 --QKRLFFNL------RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
             Q++L   L      + L  HL    +   K ++++ IA++    E+ +   +    GD
Sbjct: 238 KMQRKLTLELGYEPSVKELAEHLDMTEE---KVQEIMQIAREPASLETPIGEEDDSNLGD 294

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
              +  + S + N               E V++        R  +   +  L  RER++ 
Sbjct: 295 FVADTNVLSPEGNV--------------ESVML--------REHIDTLLGDLKERERQVI 332

Query: 244 EARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             R   E+  P TLE +  EF V+RER+RQIEA+A +K++  +
Sbjct: 333 VLRFGLEDGHPRTLEEVGKEFNVTRERIRQIEAKALRKLRNPV 375


>gi|291458966|ref|ZP_06598356.1| RNA polymerase sigma factor RpoD [Oribacterium sp. oral taxon 078
           str. F0262]
 gi|291418220|gb|EFE91939.1| RNA polymerase sigma factor RpoD [Oribacterium sp. oral taxon 078
           str. F0262]
          Length = 388

 Score =  124 bits (310), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 88/286 (30%), Positives = 149/286 (52%), Gaps = 43/286 (15%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  + +L  +EEY LA R ++ GD +A  RL+ ++LRLVV IA  Y G G+   ++
Sbjct: 122 YLKEIGTVSLLSAEEEYALAIR-KQQGDEAAKQRLIEANLRLVVSIAKRYTGRGMSFLDL 180

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           V EGN+GL++ V+KFDPE+GF+L+TY+ WWI+ ++   +      +++      T N   
Sbjct: 181 VQEGNLGLIKGVEKFDPEKGFKLSTYATWWIRQSVTRALADQARTIRVPVHMVETINKMS 240

Query: 132 --QKRLFFNL------RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
             Q++L   L      + L  HL    D   K ++++ IA++    E+ +   +    GD
Sbjct: 241 KMQRKLTLELGYEPSVKELAEHLDMSED---KVQEIMQIAREPASLETPIGEEDDSNLGD 297

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
              +A + + + N               E V++        R  +   +  L  RER++ 
Sbjct: 298 FVADANVLTPESNV--------------EAVML--------REHIDSLLGDLKERERQVI 335

Query: 244 EARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             R   E+  P TLE +  EF V+RER+RQIEA+A +K++  ++ +
Sbjct: 336 VLRFGLEDGHPRTLEEVGKEFNVTRERIRQIEAKALRKLRNPVRSK 381


>gi|149200267|ref|ZP_01877288.1| RNA polymerase sigma-A factor [Lentisphaera araneosa HTCC2155]
 gi|149136631|gb|EDM25063.1| RNA polymerase sigma-A factor [Lentisphaera araneosa HTCC2155]
          Length = 274

 Score =  124 bits (310), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 88/271 (32%), Positives = 143/271 (52%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+H I    ++ K+EE  LA   +   D  A  +L+ S+LRLVVKIA  ++G GLP+S++
Sbjct: 11  YMHNISDYSLVTKEEEVDLAADIKLGSD-KAREKLIVSNLRLVVKIAHDFKGLGLPLSDL 69

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           +SEGNIGLM+AV+KFDP +G + ++Y+ WWIK +M+  +      ++I   +  K     
Sbjct: 70  ISEGNIGLMRAVEKFDPAKGAKFSSYAAWWIKQSMRRGLANQSRTIRIPVQSAGK----- 124

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           + +++     + +  ++      IA  L  S+  V  ++       SL A +   D    
Sbjct: 125 INKIRNARIELKEKLMREPTDQEIATYLEFSKRTVSGLSTVGGSTISLQAKLQ--DGEDG 182

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLE 256
           + QD +V D   Q    I  E      N + + +  L  RE+ + E R   L   P TLE
Sbjct: 183 EIQD-IVADKASQTASDIIGEAESI--NSMMKFIVYLTDREKLVLELRFGLLSGRPKTLE 239

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +S     +RERVRQI+ +A KK++E +Q++
Sbjct: 240 EVSQAIGRTRERVRQIQNQALKKLRERMQRE 270


>gi|325103187|ref|YP_004272841.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pedobacter
           saltans DSM 12145]
 gi|324972035|gb|ADY51019.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pedobacter
           saltans DSM 12145]
          Length = 286

 Score =  124 bits (310), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 81/275 (29%), Positives = 155/275 (56%), Gaps = 14/275 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+HEI K+ ++  +EE +LA++ RE GD +A  RL  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLHEIGKVDLITAEEEVILAQKIRE-GDQAALERLTKTNLRFVVSVAKQYQNQGLTL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A K+FD  +GF+  +Y++WWI+ ++ + I     +V++    NQ   
Sbjct: 77  GDLINEGNLGLIKAAKRFDETKGFKFISYAVWWIRQSILQAIAEQSRIVRL--PLNQVGS 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + +    L+   +    PE++  I +      S+ +S + R     S++A     ++
Sbjct: 135 LSKISKAFSKLEQEYEREPSPEELADILETTVDKISDTLSNSGRHV---SMDAPFVQGEE 191

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA-RRLQEN-PV 253
           N+    D L  D+   + +LI++   +     + RS+S L  RER I      L  N P+
Sbjct: 192 NT--LLDVLENDNPNTDSMLIDESLSEE----IKRSLSTLTEREREIIVLFFGLGSNHPL 245

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +LE +  +F ++RERVRQI+ +A ++++ + + ++
Sbjct: 246 SLEEIGEKFNLTRERVRQIKDKALQRLRHTSRSKI 280


>gi|169838629|ref|ZP_02871817.1| RNA polymerase sigma factor RpoD [candidate division TM7
           single-cell isolate TM7a]
          Length = 323

 Score =  124 bits (310), Expect = 2e-26,   Method: Compositional matrix adjust.
 Identities = 91/270 (33%), Positives = 146/270 (54%), Gaps = 22/270 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L  +EE  LA R  + GD  A  ++  +++RLVV IA  Y G GL   ++
Sbjct: 54  YLREIGKIPLLSAEEEMELAHRVVQ-GDKKAKDKMAEANMRLVVSIAKRYSGRGLDFLDL 112

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN GL++AV+KFDP++GF+ +TY+ WWI+ A+   I     +++I      T N  +
Sbjct: 113 IQEGNTGLLRAVEKFDPDKGFKFSTYATWWIRQAITRAIADQARVIRIPVHMVETIN--K 170

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD-ESLNALIN-S 192
           L    RR+   L      N +P  +  ++K+L++ E + I    ++  D  SL+A +   
Sbjct: 171 LLRTQRRMTQEL------NREP-TIEELSKELDM-EPDKIEYVMKIKQDIHSLDAGVGRD 222

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN- 251
            D+  S   D++    D       E    +  +  +   +S L+ RE++I + R   EN 
Sbjct: 223 GDEEDSVLGDFI---EDEDTATPEESASSQLLKEQVQGILSSLSDREQKIIKMRFGLENG 279

Query: 252 -PVTLENLSSEFEVSRERVRQIEARAFKKV 280
              TLE +  EF V+RER+RQIEA+A  K+
Sbjct: 280 KSHTLEEVGQEFAVTRERIRQIEAKALAKL 309


>gi|170727680|ref|YP_001761706.1| RpoD family RNA polymerase sigma factor [Shewanella woodyi ATCC
           51908]
 gi|169813027|gb|ACA87611.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella woodyi
           ATCC 51908]
          Length = 322

 Score =  123 bits (309), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 90/282 (31%), Positives = 149/282 (52%), Gaps = 35/282 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   +++  +  D S  +R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 53  YLSEIGFSPLLSAEEEVYFSRKALKGCDKSR-NRMIESNLRLVVKIARRYNNRGLALLDL 111

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 112 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 170

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRLAGDESLNA 188
           LR  +  L    D+    E+   IA+KL++  ++V           S++  L GD    A
Sbjct: 171 LRTAR-ELAHKLDHEPTAEE---IAEKLDLPSADVSRMLKLNERITSVDTPLGGDND-KA 225

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR- 247
           L++    + +   D+ V D D  + V+              + +  LN ++R +  ARR 
Sbjct: 226 LLDVLADDDNVGPDYKVQDEDMSKSVV--------------KWLDELNTKQREVL-ARRF 270

Query: 248 --LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             L   P TLEN+  E  ++RERVRQI+  A K++++ +  Q
Sbjct: 271 GLLGYEPSTLENVGKEIGLTRERVRQIQVEALKRLKDLLSAQ 312


>gi|167469361|ref|ZP_02334065.1| RNA polymerase sigma factor RpoS [Yersinia pestis FV-1]
          Length = 277

 Score =  123 bits (309), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 88/277 (31%), Positives = 141/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+S+  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 8   YLGEIGYSPLLSAEEEVYFARRAL-RGDVSSRRRMIESNLRLVVKIARRYSNRGLALLDL 66

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 67  IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 126

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 127 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 183

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             SD+N +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 184 ILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 232

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 233 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 267


>gi|253583872|ref|ZP_04861070.1| RpoD family RNA polymerase sigma factor [Fusobacterium varium ATCC
           27725]
 gi|251834444|gb|EES63007.1| RpoD family RNA polymerase sigma factor [Fusobacterium varium ATCC
           27725]
          Length = 260

 Score =  123 bits (309), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 80/273 (29%), Positives = 146/273 (53%), Gaps = 16/273 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + +S YI +I   P+L  +EE  +A + R  GD  A  +LVTS+LRLV+ IA  Y   G+
Sbjct: 2   LDISEYIKDISTYPLLTPKEEREIAVKAR-SGDREAQEKLVTSNLRLVISIARKYTNMGI 60

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           PI +++ EGN+GL++AV+K++P++  R +TYS +WIK ++  YI  S  L++  +     
Sbjct: 61  PILDLIQEGNMGLIRAVEKYEPDKNIRFSTYSTFWIKQSILRYITSSRGLIRFPSY---- 116

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            ++  + R+K ++Q   + N     +  I + L++ + E       L   E  N + N  
Sbjct: 117 -VYDGISRMKKYVQDYKNKNSHCPSIDEICRSLDMKKKEAERYIDVL---EKGNGIGNEM 172

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQEN 251
                ++   ++YD   +++V+      K+    L + ++ L PRER +   R   L E 
Sbjct: 173 YGEMVEYCSSIIYDDTFEDEVIA-----KSSNIDLMKKVNKLPPREREVLIYRYGLLDEK 227

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +TL  +     +++ER+RQI+  A  +++E +
Sbjct: 228 VLTLGEIGQRMNLTKERIRQIQLEAIDRLREKL 260


>gi|149191506|ref|ZP_01869755.1| RNA polymerase sigma factor [Vibrio shilonii AK1]
 gi|148834694|gb|EDL51682.1| RNA polymerase sigma factor [Vibrio shilonii AK1]
          Length = 125

 Score =  123 bits (309), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 57/110 (51%), Positives = 78/110 (70%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  +   PML   EE  LA+R    G++ AA  L+ SHLR VV +A GY GYGLP+
Sbjct: 16  LDGYIRSVNSYPMLTADEERELAERLHYDGEIEAAKGLILSHLRFVVHVARGYSGYGLPM 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
           +++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W +VK
Sbjct: 76  ADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVK 125


>gi|153001641|ref|YP_001367322.1| RpoD family RNA polymerase sigma factor [Shewanella baltica OS185]
 gi|160876377|ref|YP_001555693.1| RpoD family RNA polymerase sigma factor [Shewanella baltica OS195]
 gi|217972427|ref|YP_002357178.1| RNA polymerase sigma 70 subunit RpoD subfamily [Shewanella baltica
           OS223]
 gi|151366259|gb|ABS09259.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella baltica
           OS185]
 gi|160861899|gb|ABX50433.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella baltica
           OS195]
 gi|217497562|gb|ACK45755.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Shewanella
           baltica OS223]
 gi|315268567|gb|ADT95420.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Shewanella
           baltica OS678]
          Length = 326

 Score =  123 bits (309), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 90/282 (31%), Positives = 151/282 (53%), Gaps = 35/282 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   +++  + G   + +R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 57  YLGEIGFSPLLSAEEEVYFSRKALK-GCAKSRNRMIESNLRLVVKIARRYNNRGLALLDL 115

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 116 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 174

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRLAGDESLNA 188
           LR  +   Q + D+    E+   IA+KL VS ++V           S++  L GD    A
Sbjct: 175 LRTARELAQKL-DHEPTAEE---IAEKLQVSSADVSRMLKLNEKITSVDTPLGGDND-KA 229

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR- 247
           L++    + +   D+ V D D                N + + ++ LN ++R +  ARR 
Sbjct: 230 LLDILADDDNVGPDYKVQDEDIS--------------NSVVKWLNELNTKQREVL-ARRF 274

Query: 248 --LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             L   P TLE++ +E  ++RERVRQI+  A K++++ +  Q
Sbjct: 275 GLLGYEPSTLEDVGAEIGLTRERVRQIQVEALKRLRDLLGSQ 316


>gi|167623164|ref|YP_001673458.1| RpoD family RNA polymerase sigma factor [Shewanella halifaxensis
           HAW-EB4]
 gi|167353186|gb|ABZ75799.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella
           halifaxensis HAW-EB4]
          Length = 321

 Score =  123 bits (309), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 91/281 (32%), Positives = 152/281 (54%), Gaps = 33/281 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   +++  + G   + +R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 52  YLGEIGFSPLLSAEEEVYFSRKSLK-GCEKSRNRMIESNLRLVVKIARRYNNRGLALLDL 110

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 111 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 169

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV---ISMNCRLA------GDESLNAL 189
           LR  +  L    D+    E+   IA++L++S S+V   + +N R+       G ES  AL
Sbjct: 170 LRTAR-ELAHKLDHEPTAEE---IAEQLDLSSSDVSRMLKLNERITSVDTPLGGESDKAL 225

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-- 247
           ++    + +   D+ V D D  + V+              + +  LN ++R +  ARR  
Sbjct: 226 LDVLADDDNVGPDYKVQDEDISKSVV--------------KWLDELNTKQREVL-ARRFG 270

Query: 248 -LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            L   P TLEN+  E  ++RERVRQI+  A K++++ +  Q
Sbjct: 271 LLGYEPSTLENVGKEIGLTRERVRQIQVEALKRLKDLLGAQ 311


>gi|268591356|ref|ZP_06125577.1| RNA polymerase sigma factor RpoS [Providencia rettgeri DSM 1131]
 gi|291313333|gb|EFE53786.1| RNA polymerase sigma factor RpoS [Providencia rettgeri DSM 1131]
          Length = 328

 Score =  123 bits (309), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 86/275 (31%), Positives = 149/275 (54%), Gaps = 31/275 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 59  YLSEIGFSPLLTAEEEVFYARRAL-RGDIASRQRMIESNLRLVVKISRRYNNRGLALLDL 117

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPE+GFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 118 IEEGNLGLIRAVEKFDPEKGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI-VKELNIY 176

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +   Q + D+   PE++          +++ L ++E  + S++  +AGD   + L 
Sbjct: 177 LRTARELAQKL-DHEPSPEEIAEQLDKPVEDVSRMLRLNER-ITSVDTPIAGDSEKSLLE 234

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
             SD N S           G E  + + + ++N    + + +  LNP++R +  ARR   
Sbjct: 235 VLSDDNDS-----------GPENTIQDNDLKEN----IVKWLYELNPKQREVL-ARRFGL 278

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           L     TLE +  E  ++RERVRQI+    K++++
Sbjct: 279 LGYEAETLEEVGREIGLTRERVRQIQVEGLKRLKD 313


>gi|261749591|ref|YP_003257277.1| RNA polymerase sigma factor rpoD [Blattabacterium sp. (Periplaneta
           americana) str. BPLAN]
 gi|261497684|gb|ACX84134.1| RNA polymerase sigma factor rpoD [Blattabacterium sp. (Periplaneta
           americana) str. BPLAN]
          Length = 287

 Score =  123 bits (309), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 90/278 (32%), Positives = 149/278 (53%), Gaps = 19/278 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+HEI KIP+L  +EE   A+R RE GD SA  +LV ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLHEIGKIPLLTPEEEVEYARRARE-GDSSAIEKLVNANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT--ANQK 133
            ++++EGN+GL++ + +FD  RGF+  +Y +WWI+ A+ + I      ++  T   A   
Sbjct: 77  CDLINEGNLGLIKGILRFDETRGFKCISYVVWWIRQAILQAIAEQSRSIRQPTNKLALLN 136

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA-LINS 192
           ++   L +L+  LQ       +      IA+ L+++E +V           S++A LI  
Sbjct: 137 KILKTLAQLEQELQ-------RTPSAREIAEHLDMNEKDVEESIKNSGRHVSMDAPLIEG 189

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR--IFEARRLQE 250
            D N     D +  D   +     E  ER++ R  + R +  L+ RERR  I        
Sbjct: 190 EDSN---LYDLVRSDESPRPD---EHLERESLRKDIKRILETLSERERRVIILHFGLNGS 243

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            P+TLE +    +++RERVRQIE+ A K+++ S + ++
Sbjct: 244 PPMTLEEVGQSCDLTRERVRQIESIALKRLKHSSRSKI 281


>gi|22124745|ref|NP_668168.1| RNA polymerase sigma factor RpoS [Yersinia pestis KIM 10]
 gi|45440189|ref|NP_991728.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Microtus
           str. 91001]
 gi|108808779|ref|YP_652695.1| RNA polymerase sigma factor RpoS [Yersinia pestis Antiqua]
 gi|108810903|ref|YP_646670.1| RNA polymerase sigma factor RpoS [Yersinia pestis Nepal516]
 gi|145600262|ref|YP_001164338.1| RNA polymerase sigma factor RpoS [Yersinia pestis Pestoides F]
 gi|153997601|ref|ZP_02022701.1| RNA polymerase sigma factor RpoS [Yersinia pestis CA88-4125]
 gi|162420853|ref|YP_001605522.1| RNA polymerase sigma factor RpoS [Yersinia pestis Angola]
 gi|165925871|ref|ZP_02221703.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Orientalis
           str. F1991016]
 gi|165936700|ref|ZP_02225267.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Orientalis
           str. IP275]
 gi|166010016|ref|ZP_02230914.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Antiqua
           str. E1979001]
 gi|166212931|ref|ZP_02238966.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Antiqua
           str. B42003004]
 gi|167398742|ref|ZP_02304266.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Antiqua
           str. UG05-0454]
 gi|167421704|ref|ZP_02313457.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Orientalis
           str. MG05-1020]
 gi|167423190|ref|ZP_02314943.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar
           Mediaevalis str. K1973002]
 gi|218930373|ref|YP_002348248.1| RNA polymerase sigma factor RpoS [Yersinia pestis CO92]
 gi|229838982|ref|ZP_04459141.1| RNA polymerase, sigma S (sigma 38) factor [Yersinia pestis biovar
           Orientalis str. PEXU2]
 gi|229896462|ref|ZP_04511630.1| RNA polymerase, sigma S (sigma 38) factor [Yersinia pestis
           Pestoides A]
 gi|229899549|ref|ZP_04514690.1| RNA polymerase, sigma S (sigma 38) factor [Yersinia pestis biovar
           Orientalis str. India 195]
 gi|229901116|ref|ZP_04516239.1| RNA polymerase, sigma S (sigma 38) factor [Yersinia pestis
           Nepal516]
 gi|270489294|ref|ZP_06206368.1| RNA polymerase sigma factor RpoS [Yersinia pestis KIM D27]
 gi|294505063|ref|YP_003569125.1| RNA polymerase sigma factor [Yersinia pestis Z176003]
 gi|21957564|gb|AAM84419.1|AE013686_2 RNA polymerase, sigma S (sigma38) factor [Yersinia pestis KIM 10]
 gi|45435045|gb|AAS60605.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Microtus
           str. 91001]
 gi|108774551|gb|ABG17070.1| RNA polymerase sigma factor RpoS [Yersinia pestis Nepal516]
 gi|108780692|gb|ABG14750.1| RNA polymerase sigma factor RpoS [Yersinia pestis Antiqua]
 gi|115348984|emb|CAL21944.1| RNA polymerase sigma factor RpoS [Yersinia pestis CO92]
 gi|145211958|gb|ABP41365.1| RNA polymerase sigma factor RpoS [Yersinia pestis Pestoides F]
 gi|149289238|gb|EDM39318.1| RNA polymerase sigma factor RpoS [Yersinia pestis CA88-4125]
 gi|162353668|gb|ABX87616.1| RNA polymerase sigma factor RpoS [Yersinia pestis Angola]
 gi|165915349|gb|EDR33959.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Orientalis
           str. IP275]
 gi|165922483|gb|EDR39660.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Orientalis
           str. F1991016]
 gi|165990923|gb|EDR43224.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Antiqua
           str. E1979001]
 gi|166205718|gb|EDR50198.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Antiqua
           str. B42003004]
 gi|166960623|gb|EDR56644.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Orientalis
           str. MG05-1020]
 gi|167051246|gb|EDR62654.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Antiqua
           str. UG05-0454]
 gi|167057360|gb|EDR67106.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar
           Mediaevalis str. K1973002]
 gi|224483372|gb|ACN50513.1| RpoS [Yersinia pestis]
 gi|229681841|gb|EEO77934.1| RNA polymerase, sigma S (sigma 38) factor [Yersinia pestis
           Nepal516]
 gi|229687041|gb|EEO79116.1| RNA polymerase, sigma S (sigma 38) factor [Yersinia pestis biovar
           Orientalis str. India 195]
 gi|229695348|gb|EEO85395.1| RNA polymerase, sigma S (sigma 38) factor [Yersinia pestis biovar
           Orientalis str. PEXU2]
 gi|229700536|gb|EEO88567.1| RNA polymerase, sigma S (sigma 38) factor [Yersinia pestis
           Pestoides A]
 gi|262363123|gb|ACY59844.1| RNA polymerase sigma factor [Yersinia pestis D106004]
 gi|262367053|gb|ACY63610.1| RNA polymerase sigma factor [Yersinia pestis D182038]
 gi|270337798|gb|EFA48575.1| RNA polymerase sigma factor RpoS [Yersinia pestis KIM D27]
 gi|294355522|gb|ADE65863.1| RNA polymerase sigma factor [Yersinia pestis Z176003]
 gi|320016550|gb|ADW00122.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Medievalis
           str. Harbin 35]
          Length = 332

 Score =  123 bits (309), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 88/277 (31%), Positives = 141/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+S+  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 63  YLGEIGYSPLLTAEEEVYFARRAL-RGDVSSRRRMIESNLRLVVKIARRYSNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 181

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 182 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 238

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             SD+N +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 239 ILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 287

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 288 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 322


>gi|260767191|ref|ZP_05876133.1| RNA polymerase sigma factor RpoS [Vibrio furnissii CIP 102972]
 gi|260617799|gb|EEX42976.1| RNA polymerase sigma factor RpoS [Vibrio furnissii CIP 102972]
 gi|315181178|gb|ADT88092.1| RNA polymerase sigma factor RpoS [Vibrio furnissii NCTC 11218]
          Length = 329

 Score =  123 bits (309), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 89/284 (31%), Positives = 148/284 (52%), Gaps = 39/284 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 57  YLSEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 115

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 116 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 174

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA---------GDESLNAL 189
           LR  +   Q +       E  V + K ++   S+++ +N R++         GD++L  +
Sbjct: 175 LRTARELSQKLDHEPTAEEIAVELDKPVD-DVSKMLRLNERISSVDTPIGGDGDKALLDI 233

Query: 190 ---INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              IN+SD   S   D +                    R+ L   +  LNP+++ +  AR
Sbjct: 234 IPDINNSDPEVSTQDDDI--------------------RDSLVAWLDELNPKQKEVL-AR 272

Query: 247 R---LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 273 RFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILMKQ 316


>gi|120598086|ref|YP_962660.1| RpoD family RNA polymerase sigma factor [Shewanella sp. W3-18-1]
 gi|146293843|ref|YP_001184267.1| RpoD family RNA polymerase sigma factor [Shewanella putrefaciens
           CN-32]
 gi|120558179|gb|ABM24106.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella sp.
           W3-18-1]
 gi|145565533|gb|ABP76468.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella
           putrefaciens CN-32]
          Length = 326

 Score =  123 bits (309), Expect = 3e-26,   Method: Compositional matrix adjust.
 Identities = 91/282 (32%), Positives = 150/282 (53%), Gaps = 35/282 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   +++  + G   + +R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 57  YLGEIGFSPLLSAEEEVYFSRKALK-GCEKSRNRMIESNLRLVVKIARRYNNRGLALLDL 115

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 116 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 174

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRLAGDESLNA 188
           LR  +   Q + D+    E+   IA+KL V  ++V           S++  L GD    A
Sbjct: 175 LRTARELAQKL-DHEPTAEE---IAEKLQVPSADVSRMLKLNEKITSVDTPLGGDND-KA 229

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR- 247
           LI+    + S   D+ V D D                N + + ++ LN ++R +  ARR 
Sbjct: 230 LIDILADDDSVGPDYKVQDEDIS--------------NSVVKWLNELNTKQREVL-ARRF 274

Query: 248 --LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             L   P TLE++ +E  ++RERVRQI+  A K++++ +  Q
Sbjct: 275 GLLGYEPSTLEDVGAEIGLTRERVRQIQVEALKRLRDLLGSQ 316


>gi|315185379|gb|EFU19152.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           thermophila DSM 6578]
          Length = 292

 Score =  123 bits (308), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 82/277 (29%), Positives = 157/277 (56%), Gaps = 16/277 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           LS Y+ EI +IP+L ++EE   A R    GD  A  +LVT++LR VV +A  Y+  GLP+
Sbjct: 21  LSLYLKEINRIPLLSREEEDHYA-RLAAQGDQDAKEKLVTANLRFVVNVAKKYQNQGLPL 79

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT-ANQKR 134
           ++++SEGNIGL+ A+++FDP++G+   +Y++WWI+ A+ + I     ++++    AN+  
Sbjct: 80  ADLISEGNIGLLNAIERFDPDKGYHFISYAVWWIRQAILKAISEKSRMIRLPLNRANELV 139

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
                R+L      +   + +  ++  +A+ L+  E  V ++        SL+  +   D
Sbjct: 140 QIEKARKL------VQTESGEHNEIKKVAETLDYDEDHVANLLNLSKEYVSLDTPV-YED 192

Query: 195 KNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QEN 251
           ++S+   D+L  +     E V++EK  ++  + +L    + L  +E  I + R      +
Sbjct: 193 RDSAMLGDYLKDEASRPPEDVVLEKTLQEEIQEVL----ATLTEKEAEIIQYRFGLNGRH 248

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           P++L+ +   + +++ER+RQIE +A KK+Q+S + +V
Sbjct: 249 PMSLKEIGDMYNLTKERIRQIEKKALKKIQQSEKAKV 285


>gi|15606622|ref|NP_214002.1| RNA polymerase sigma factor RpoS [Aquifex aeolicus VF5]
 gi|2983844|gb|AAC07398.1| RNA polymerase sigma factor RpoS [Aquifex aeolicus VF5]
          Length = 310

 Score =  123 bits (308), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 91/299 (30%), Positives = 157/299 (52%), Gaps = 44/299 (14%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +++Y+ +I KIP+L  +EE  LA+R ++ GD  A  +LV S+LR VV +A  Y GYGLP 
Sbjct: 10  INQYLKKISKIPLLTPEEEKELARRAKQ-GDKEALKKLVESNLRFVVSVAKQYIGYGLPF 68

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           SE+++ GN+GL++A K+FDP+RG +  +Y++WWI+ A+ + + +    V+I     Q  +
Sbjct: 69  SELIAAGNLGLLEAAKRFDPDRGVKFISYAVWWIRQAIMQALSQQTGAVRI--PLKQSHI 126

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVV------AIAK------------------------K 165
              +  + G L    +    PE++        IAK                        K
Sbjct: 127 INKISHIYGELSKKLEREPSPEEIAEELSKQMIAKELEKELGREPTEEEIEERFKKEGYK 186

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNR 224
           +   E E     CR+    SL+A +  ++   + + D+L      + E+ +I++  +K  
Sbjct: 187 ITPEEVEKYLQVCRVPL--SLDAPVGENE--DTFFIDFLSKHGTAEVEEKVIQEVIQKEI 242

Query: 225 RNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            ++L++    L  +ER++ E R  L+ N P TL  +     +SRERVRQ+E RA +K++
Sbjct: 243 DDLLSK----LTDKERKVIELRFGLKGNEPKTLREIGEILGLSRERVRQLETRALRKLR 297


>gi|294141938|ref|YP_003557916.1| RNA polymerase sigma-38 factor [Shewanella violacea DSS12]
 gi|293328407|dbj|BAJ03138.1| RNA polymerase sigma-38 factor [Shewanella violacea DSS12]
          Length = 328

 Score =  123 bits (308), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 91/282 (32%), Positives = 148/282 (52%), Gaps = 35/282 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   +++  + G   + +R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 59  YLGEIGFSPLLSAEEEVYFSRKSLK-GCGKSRNRMIESNLRLVVKIARRYNNRGLALLDL 117

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 118 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 176

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRLAGDESLNA 188
           LR  +  L    D+    E+   IA KL++  S+V           S++  L GD    A
Sbjct: 177 LRTAR-ELAHKLDHEPTAEE---IAAKLDLPSSDVSRMLKLNERITSVDTPLGGDND-KA 231

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR- 247
           L++    + S   D+ V D D  + V+              + +  LN ++R +  ARR 
Sbjct: 232 LLDVLAADDSVGPDYKVQDEDMSKSVV--------------KWLDELNTKQREVL-ARRF 276

Query: 248 --LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             L   P TLEN+  E  ++RERVRQI+  A K++++ +  Q
Sbjct: 277 GLLGYEPSTLENVGKEIGLTRERVRQIQVEALKRLKDLLGAQ 318


>gi|297617785|ref|YP_003702944.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Syntrophothermus
           lipocalidus DSM 12680]
 gi|297145622|gb|ADI02379.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Syntrophothermus
           lipocalidus DSM 12680]
          Length = 361

 Score =  123 bits (308), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 89/276 (32%), Positives = 137/276 (49%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LAKR  E+GD  A  +LV ++LRLVV IA  Y G G+   ++
Sbjct: 95  YLKEIGRVPLLSAEEEIELAKRI-ENGDEDAKRKLVEANLRLVVSIAKRYVGRGMLFLDL 153

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 154 IQEGNLGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLS 213

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q+ L   L R     +   + ++  E+V+ I K       E +S+   +    D  L 
Sbjct: 214 RIQRALLQKLGREPTPAEVAEEMDIPVERVMEIMK----VAQEPVSLETPIGEEDDSHLG 269

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S +     V                   R  L   +S L  RE ++   R 
Sbjct: 270 DFITDEDAESPEESASFVL-----------------LREHLDGILSTLTDREEKVLRLRF 312

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++  P TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 313 GLDDGRPRTLEEVGQEFGVTRERIRQIEAKALRKLR 348


>gi|300812193|ref|ZP_07092635.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus PB2003/044-T3-4]
 gi|300496829|gb|EFK31909.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus PB2003/044-T3-4]
          Length = 378

 Score =  123 bits (308), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 93/272 (34%), Positives = 144/272 (52%), Gaps = 22/272 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG--LPIS 76
           Y+ EI K+P+L + EE  +AKR  E+GD SA   L  ++LRLVV IA  Y  +   + I 
Sbjct: 107 YLKEIGKVPLLSRDEEVEVAKRI-ENGDESAKDELAAANLRLVVSIAKRYAKHNGKMGIL 165

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++ EGNIGLM+AV KFD  +GF+ +TY+ WWI+ A+   +     +++I     +    
Sbjct: 166 DLIQEGNIGLMKAVDKFDYSKGFKFSTYATWWIRQAITRALADQDRMIRIPVHVVES--I 223

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
             + R++  LQ   D + KPE++ A   +      E+I++      D SL+  +   ++ 
Sbjct: 224 NKMNRIQRTLQQDLDRDAKPEELAAEMNEPLQKVQEIITVAKNQETD-SLDKPV--GEEG 280

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV-----LNPRERRIFEARRLQEN 251
            SQ  D L      ++   I  EE      ML   +S+     L  RE ++ + R   EN
Sbjct: 281 DSQLGDLL------EDNKAINPEEY-TASEMLKDQLSIMMGEFLTDREAKVLKLRFGLEN 333

Query: 252 --PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             P TLE +     V+RERVRQIEA+A KK++
Sbjct: 334 DEPHTLEEVGRSLGVTRERVRQIEAKAVKKLK 365


>gi|262340892|ref|YP_003283747.1| RNA polymerase sigma-70 factor [Blattabacterium sp. (Blattella
           germanica) str. Bge]
 gi|262272229|gb|ACY40137.1| RNA polymerase sigma-70 factor [Blattabacterium sp. (Blattella
           germanica) str. Bge]
          Length = 287

 Score =  123 bits (308), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 90/278 (32%), Positives = 149/278 (53%), Gaps = 19/278 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+HEI KIP+L  +EE   A+R RE GD SA  +LV ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLHEIGKIPLLTPEEEVEYARRARE-GDASAIDKLVNANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT--ANQK 133
            ++++EGN+GL++ + +FD  RGF+  +Y +WWI+ A+ + I      ++  T   A   
Sbjct: 77  CDLINEGNLGLIKGILRFDETRGFKCISYVVWWIRQAILQAIAEQSRSIRQPTNKLALLN 136

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA-LINS 192
           ++   L +L+  LQ       +      IA+ L+++E +V           S++A LI  
Sbjct: 137 KILKTLAQLEQELQ-------RTPSAREIAEYLDMNEKDVEESIKNSGRHVSMDAPLIEG 189

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR--IFEARRLQE 250
            D N     D +  D   +    +EKE   + R  + R +  L+ RERR  I        
Sbjct: 190 EDSN---LYDLVRSDESPRPDEHLEKE---SLRKDIKRILETLSERERRVIILHFGLNGS 243

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            P+TLE +    +++RERVRQIE+ A K+++ S + ++
Sbjct: 244 PPMTLEEVGQSCDLTRERVRQIESIALKRLKHSSRSKI 281


>gi|330836598|ref|YP_004411239.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           coccoides DSM 17374]
 gi|329748501|gb|AEC01857.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           coccoides DSM 17374]
          Length = 293

 Score =  123 bits (308), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 79/269 (29%), Positives = 155/269 (57%), Gaps = 13/269 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           LS Y+ EI +IPML  +EEY +AK   E G+  A +RLV S+LR VV IA  Y+  GLP+
Sbjct: 24  LSIYLKEINRIPMLTHEEEYKVAKLAAE-GNQKARNRLVESNLRFVVNIAKKYQNQGLPL 82

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGNIGLM A++KFD ++G+   +Y++WWI+ A+ + I      V++    N+   
Sbjct: 83  GDLINEGNIGLMNAIEKFDVDKGYHFISYAVWWIRQAILKAISEKSRTVRL--PLNRANE 140

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              +++ +  L   +      E++  + +      +++I+++  +    SL+A + +   
Sbjct: 141 LMQIQKAQKSLMNESGAEPTMEEIGRLTQLDPSHVADLIAISKEMV---SLDAPVFTDSG 197

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPV 253
           NSS   D++    D  + V+I+   +++    + + ++ L+ +E  I E R     ++P+
Sbjct: 198 NSS-VGDFIQDGADSPDDVIIDSALKED----INKVLATLSEKEMEILEFRFGLNGQHPM 252

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +L+ +   + +++ER+RQIE +A +++Q+
Sbjct: 253 SLKEIGELYNLTKERIRQIEKKAIERLQQ 281


>gi|304410159|ref|ZP_07391778.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Shewanella
           baltica OS183]
 gi|307302130|ref|ZP_07581888.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Shewanella
           baltica BA175]
 gi|304351568|gb|EFM15967.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Shewanella
           baltica OS183]
 gi|306914168|gb|EFN44589.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Shewanella
           baltica BA175]
          Length = 326

 Score =  123 bits (308), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 90/282 (31%), Positives = 151/282 (53%), Gaps = 35/282 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   +++  + G   + +R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 57  YLGEIGFSPLLSAEEEVYFSRKALK-GCAKSRNRMIESNLRLVVKIARRYNNRGLALLDL 115

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 116 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 174

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRLAGDESLNA 188
           LR  +   Q + D+    E+   IA+KL VS ++V           S++  L GD    A
Sbjct: 175 LRTARELAQKL-DHEPTAEE---IAEKLQVSSADVSRMLKLNEKITSVDMPLGGDND-KA 229

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR- 247
           L++    + +   D+ V D D                N + + ++ LN ++R +  ARR 
Sbjct: 230 LLDILADDDNVGPDYKVQDEDIS--------------NSVVKWLNELNTKQREVL-ARRF 274

Query: 248 --LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             L   P TLE++ +E  ++RERVRQI+  A K++++ +  Q
Sbjct: 275 GLLGYEPSTLEDVGAEIGLTRERVRQIQVEALKRLRDLLGSQ 316


>gi|157374437|ref|YP_001473037.1| RpoD family RNA polymerase sigma factor [Shewanella sediminis
           HAW-EB3]
 gi|157316811|gb|ABV35909.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella sediminis
           HAW-EB3]
          Length = 323

 Score =  123 bits (308), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 90/282 (31%), Positives = 149/282 (52%), Gaps = 35/282 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   +++  + G   + +R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 54  YLSEIGFSPLLSAEEEVYFSRKALK-GCGKSRNRMIESNLRLVVKIARRYNNRGLALLDL 112

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 113 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 171

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRLAGDESLNA 188
           LR  +  L    D+    E+   IA+KL++  ++V           S++  L GD    A
Sbjct: 172 LRTAR-ELAHKLDHEPTAEE---IAEKLDLPSADVSRMLKLNERITSVDTPLGGDND-KA 226

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR- 247
           L++    + S   D+ V D D  + V+              + +  LN ++R +  ARR 
Sbjct: 227 LLDVLADDDSVGPDYKVQDEDMSKSVV--------------KWLDELNTKQREVL-ARRF 271

Query: 248 --LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             L   P TLEN+  E  ++RERVRQI+  A K++++ +  Q
Sbjct: 272 GLLGYEPSTLENVGKEIGLTRERVRQIQVEALKRLKDLLGSQ 313


>gi|326794473|ref|YP_004312293.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Marinomonas
           mediterranea MMB-1]
 gi|326545237|gb|ADZ90457.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Marinomonas
           mediterranea MMB-1]
          Length = 329

 Score =  122 bits (307), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 90/275 (32%), Positives = 151/275 (54%), Gaps = 20/275 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 57  YLSEIGFSPLLTAEEEVYFA-RLALKGDEAARKRMIESNLRLVVKISRRYLNRGLSLLDL 115

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 116 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 174

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV---ISMNCRLAGDESLNALINSSDK 195
           LR  +   Q + D+   PE+   IA KL+    +V   +S+N R++   S+++ +  S+ 
Sbjct: 175 LRAARELTQQL-DHEPSPEE---IADKLDRPVEDVQKMLSLNERIS---SIDSPLGGSEG 227

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENP 252
           + S  +      H   E    ++ +  +  N +   +  LN ++R +  ARR       P
Sbjct: 228 DKSLVEVIPDTQHSNPE----DERQEGDVLNSIDGWLDALNEKQREVI-ARRFGLRGYEP 282

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            TLE++ +E  ++RERVRQI+  A +K++  + KQ
Sbjct: 283 STLEDVGAEIGLTRERVRQIQVEALRKLRLMLDKQ 317


>gi|237738339|ref|ZP_04568820.1| RNA polymerase [Fusobacterium mortiferum ATCC 9817]
 gi|229420219|gb|EEO35266.1| RNA polymerase [Fusobacterium mortiferum ATCC 9817]
          Length = 273

 Score =  122 bits (307), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 89/274 (32%), Positives = 153/274 (55%), Gaps = 17/274 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +S Y+ +IRK  +LEK EE  L K+ +  GD+ A ++L+  +LRLVV IA  Y   GL +
Sbjct: 8   ISYYLEDIRKYKVLEKDEETELLKKAK-AGDIEAKNKLILCNLRLVVNIAKNYVNRGLSL 66

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++SEGN GL+ A++KFD ++GFR +TY++WWIK ++ + I+     ++I   + +  L
Sbjct: 67  IDLISEGNFGLIYAIEKFDMKKGFRFSTYAVWWIKQSITKAIICKGRGIRI--PSYKYDL 124

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + R    L  + +  + P  V  I++ LNV++ ++  +        SL+A I     
Sbjct: 125 LSKVNRY--VLNRVREEGIYP-TVEEISEDLNVNKEKIEEIMVAFQDPMSLSASIG---- 177

Query: 196 NSSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENP 252
           +  Q +D +  + +   E  +IE+  R+  R +    + VL+ RE++I + R     E  
Sbjct: 178 DDIQLEDIIANNSETSIEDDIIEEMGREQVRQI----VKVLDEREKQILKLRFGLDGEEI 233

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            TLE +   F ++RERVRQIE +  KK++   +K
Sbjct: 234 HTLEEIGQTFNITRERVRQIEKKTLKKLKMQCEK 267


>gi|163783667|ref|ZP_02178655.1| RNA polymerase sigma factor RpoS [Hydrogenivirga sp. 128-5-R1-1]
 gi|159881072|gb|EDP74588.1| RNA polymerase sigma factor RpoS [Hydrogenivirga sp. 128-5-R1-1]
          Length = 309

 Score =  122 bits (307), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 94/298 (31%), Positives = 153/298 (51%), Gaps = 44/298 (14%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +++Y+  I KIP+L  +EE  LA++ +E GD  +  +LV S+LR VV +A  Y GYGLP 
Sbjct: 9   INQYLKRISKIPLLSPEEEKELARKAKE-GDEESLKKLVESNLRFVVSVAKQYIGYGLPF 67

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           SE+++ GN+GL++A K+FDPERG +  +Y++WWI+ A+ + + +    V+I     Q  L
Sbjct: 68  SELIAAGNLGLLEAAKRFDPERGVKFISYAVWWIRQAIMQALSQQTGAVRI--PLKQSHL 125

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVV------AIAK------------------------K 165
              +  +   L    +    PE+V        IAK                        K
Sbjct: 126 ISKIGTIYAELAKELEREPTPEEVAEQLSKEMIAKELTKELGREPTDEEVQKKFKKEGYK 185

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNR 224
           ++  E E     CR+    SL+A +  ++   + + D+L      + E+ +I++   K  
Sbjct: 186 ISPEEVEKYLQVCRIPL--SLDAPVGENE--DTFFVDFLSKHGTAEVEESVIQEVLEKEI 241

Query: 225 RNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKV 280
            ++L +    L  +ERR+ E R  L+ N P TL  +     VSRERVRQ+E RA +K+
Sbjct: 242 YDLLDK----LPEKERRVVELRFGLKGNEPKTLREIGDILGVSRERVRQLETRALRKL 295


>gi|262164038|ref|ZP_06031777.1| RNA polymerase sigma factor RpoS [Vibrio mimicus VM223]
 gi|262027566|gb|EEY46232.1| RNA polymerase sigma factor RpoS [Vibrio mimicus VM223]
          Length = 336

 Score =  122 bits (307), Expect = 5e-26,   Method: Compositional matrix adjust.
 Identities = 90/280 (32%), Positives = 148/280 (52%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 62  YLSEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 120

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 121 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 179

Query: 139 LRRLKGHLQAITDNNLKPEQVV--------AIAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +  L    D+   PE++          + K L ++E  + S++  + GD     L 
Sbjct: 180 LRTAR-ELSQRLDHEPTPEEIALELDKPVDDVTKMLRLNER-ISSVDTPIGGDGDKALLD 237

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
              D N++   ++   D D +E +L          N L      LNP+++ +  ARR   
Sbjct: 238 ILPDSNNAD-PEFSTQDDDIRESLL----------NWLDE----LNPKQKEVL-ARRFGL 281

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 282 LGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREVLVKQ 321


>gi|89073765|ref|ZP_01160279.1| hypothetical DNA-directed RNA polymerase, sigma subunit
           [Photobacterium sp. SKA34]
 gi|89050540|gb|EAR56032.1| hypothetical DNA-directed RNA polymerase, sigma subunit
           [Photobacterium sp. SKA34]
          Length = 291

 Score =  122 bits (306), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 90/303 (29%), Positives = 161/303 (53%), Gaps = 41/303 (13%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           MN+K       G+I +  Y+ +I + P+L K +E +L  R    GD  + + L+ S+LRL
Sbjct: 3   MNKKEEQFSHGGDI-VHLYLKDISEKPLLTKDDE-ILYSRKSLSGDAYSKNVLIESNLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  YRG  + IS+++ EGNIGLM AV+KFDPE+GFR +TY+ WWIK  ++  I   
Sbjct: 61  VVSIAKKYRGSSIHISDLIDEGNIGLMTAVEKFDPEKGFRFSTYATWWIKQTIERAIHNQ 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS----------E 170
              +++    +++        ++ H Q +  NN +P   + +A+ LN +          +
Sbjct: 121 GRTIRLPVHVSKEINTI----IRTHKQLVKKNNQEPSTEL-VAEVLNKTLDDISTTLSYD 175

Query: 171 SEVISMNCRL---AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + ++S +  +   A  +S+  LI  +D+NS++  D +       + + I+K        +
Sbjct: 176 TPIVSYDQSITSEASSQSIAVLI--ADENSAKPDDLV-------DDLAIQK--------I 218

Query: 228 LTRSMSVLNPRERRIFEARR---LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            T  ++ LN R++ I   RR   L     TL+ ++ E  ++RER+RQ++  +  K++ S+
Sbjct: 219 TTNVLNCLNNRDKEII-CRRFGLLGYEAQTLQEVADEVGLTRERIRQLQVTSLAKLKNSL 277

Query: 285 QKQ 287
            + 
Sbjct: 278 SRD 280


>gi|258623793|ref|ZP_05718750.1| RNA polymerase sigma-38 factor [Vibrio mimicus VM603]
 gi|258583916|gb|EEW08708.1| RNA polymerase sigma-38 factor [Vibrio mimicus VM603]
          Length = 336

 Score =  122 bits (306), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 90/280 (32%), Positives = 148/280 (52%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 62  YLSEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 120

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 121 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 179

Query: 139 LRRLKGHLQAITDNNLKPEQVV--------AIAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +  L    D+   PE++          + K L ++E  + S++  + GD     L 
Sbjct: 180 LRTAR-ELSQRLDHEPTPEEIALELDKPVDDVTKMLRLNER-ISSVDTPIGGDGDKALLD 237

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
              D N++   ++   D D +E +L          N L      LNP+++ +  ARR   
Sbjct: 238 ILPDSNNAD-PEFSTQDDDIRESLL----------NWLDE----LNPKQKEVL-ARRFGL 281

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 282 LGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVKQ 321


>gi|261210105|ref|ZP_05924403.1| RNA polymerase sigma factor RpoS [Vibrio sp. RC341]
 gi|260840870|gb|EEX67412.1| RNA polymerase sigma factor RpoS [Vibrio sp. RC341]
          Length = 336

 Score =  122 bits (306), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 90/280 (32%), Positives = 148/280 (52%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 62  YLSEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 120

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 121 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 179

Query: 139 LRRLKGHLQAITDNNLKPEQVV--------AIAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +  L    D+   PE++          + K L ++E  + S++  + GD     L 
Sbjct: 180 LRTAR-ELSQRLDHEPTPEEIALELDRPVDDVTKMLRLNER-ISSVDTPIGGDGDKALLD 237

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
              D N++   ++   D D +E +L          N L      LNP+++ +  ARR   
Sbjct: 238 ILPDSNNAD-PEFSTQDDDIRESLL----------NWLDE----LNPKQKEVL-ARRFGL 281

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 282 LGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVKQ 321


>gi|262401766|ref|ZP_06078332.1| RNA polymerase sigma factor RpoS [Vibrio sp. RC586]
 gi|262352183|gb|EEZ01313.1| RNA polymerase sigma factor RpoS [Vibrio sp. RC586]
          Length = 336

 Score =  122 bits (306), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 88/280 (31%), Positives = 148/280 (52%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 62  YLSEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 120

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 121 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 179

Query: 139 LRRLKGHLQAITDNNLKPEQVV--------AIAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +  L    D+   PE++          + K L ++E  + S++  + GD    AL+
Sbjct: 180 LRTAR-ELSQRLDHEPTPEEIALELDRPVDDVTKMLRLNER-ISSVDTPIGGDGD-KALL 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
           +    + +   ++   D D +E +L                M  LNP+++ +  ARR   
Sbjct: 237 DILPDSHNADPEFSTQDDDIRESLL--------------GWMDELNPKQKEVL-ARRFGL 281

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 282 LGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVKQ 321


>gi|319792729|ref|YP_004154369.1| RNA polymerase, sigma 70 family subunit [Variovorax paradoxus EPS]
 gi|315595192|gb|ADU36258.1| putative RNA polymerase, sigma 70 family subunit [Variovorax
           paradoxus EPS]
          Length = 340

 Score =  122 bits (306), Expect = 6e-26,   Method: Compositional matrix adjust.
 Identities = 81/281 (28%), Positives = 142/281 (50%), Gaps = 13/281 (4%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           G   L+ Y+ ++R+  +    EE+  A   R  GD +A   ++  +LRLVV IA GY G 
Sbjct: 58  GADALTIYLRQVRRTELFTPDEEFQAACAAR-SGDFAARQSMIEHNLRLVVNIAKGYLGR 116

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK--IGTT 129
           G+P+S+++ EGN+GLM A+ KF+PERGFR +TY+ WWI+ +++  ++     ++  +   
Sbjct: 117 GVPLSDLIEEGNLGLMHAITKFEPERGFRFSTYATWWIRQSVERAVMTQARAIRLPVHVV 176

Query: 130 ANQKRLFFNLRRLKGHLQAIT--DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              +++    R L+G  + +    + ++ E + A+   L     EV  +        SL+
Sbjct: 177 RELQQVLRARRALEGDAEFVARRPDGVRVEDIAAL---LGRDVQEVADLLALSEAPRSLD 233

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           A     D+  +        D  G    + +  E +    +L + +  L+ RER + E R 
Sbjct: 234 AGDARGDEGFTLADTVASDDEQGNPSGVTQAHEVE---RLLDQWIHALDAREREVLEGRY 290

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +  P TLE LS    ++RERVRQI+  A  K++  + +
Sbjct: 291 GLHDREPETLEVLSVRLGLTRERVRQIQNEALAKMRRQLAR 331


>gi|1350861|sp|P47765|RPOS_YEREN RecName: Full=RNA polymerase sigma factor rpoS
 gi|687583|gb|AAC43391.1| RpoS [Yersinia enterocolitica]
          Length = 331

 Score =  122 bits (306), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 88/287 (30%), Positives = 143/287 (49%), Gaps = 25/287 (8%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           + +G      Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y
Sbjct: 52  VTSGADATQLYLGEIGYSPLLTAEEEVYFARRAL-RGDVPSRRRMIESNLRLVVKIARRY 110

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
              GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++  
Sbjct: 111 SNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPI 170

Query: 129 -TANQKRLFFNLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
               +  ++    R   H        + I +   KP   V+   +LN     + S++  L
Sbjct: 171 HIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPL 227

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD     L   SD+N +  +D    D   Q  V    E    +R +L R   +L     
Sbjct: 228 GGDSEKALLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG---- 283

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             +EA        TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 284 --YEA-------ATLEDVGREIGLTRERVRQIQVEGLRRLREILQAQ 321


>gi|212711364|ref|ZP_03319492.1| hypothetical protein PROVALCAL_02436 [Providencia alcalifaciens DSM
           30120]
 gi|212686093|gb|EEB45621.1| hypothetical protein PROVALCAL_02436 [Providencia alcalifaciens DSM
           30120]
          Length = 328

 Score =  122 bits (306), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 86/280 (30%), Positives = 151/280 (53%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 59  YLSEIGFSPLLTAEEEVFYARRAL-RGDVASRQRMIESNLRLVVKISRRYNNRGLALLDL 117

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPE+GFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 118 IEEGNLGLIRAVEKFDPEKGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI-VKELNIY 176

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +   Q + D+   PE++          +++ L ++E  + S++  +AGD   + L 
Sbjct: 177 LRTARELAQKL-DHEPSPEEIAERLDKPVEDVSRMLRLNER-ITSVDTPIAGDSEKSLLE 234

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
             SD N S           G E  + +   ++N    + + +  LNP++R +  ARR   
Sbjct: 235 VLSDDNES-----------GPENTIQDNNLKEN----IVKWLYELNPKQREVL-ARRFGL 278

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L     TLE +  E  ++RERVRQI+    +++++ +Q +
Sbjct: 279 LGYEAETLEEVGREIGLTRERVRQIQVEGLRRLKDILQGE 318


>gi|7416823|dbj|BAA94072.1| rpoS [Rubrivivax gelatinosus]
          Length = 322

 Score =  122 bits (306), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 90/283 (31%), Positives = 147/283 (51%), Gaps = 29/283 (10%)

Query: 12  GEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           GE G  L  Y+ +IR+ P++  +EE+  A R R  GD +A   ++  +LRLVV IA  Y 
Sbjct: 42  GEHGNTLQSYLRDIRRAPLMSAEEEHATAVRARA-GDFAARQAMIERNLRLVVSIAKHYV 100

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+P+ +++ EGN+GLM A  KF+PERGFR +TY+ WWI+ +++  I+    L+++   
Sbjct: 101 GRGMPMIDLIEEGNLGLMHATGKFEPERGFRFSTYASWWIRQSIERAIMHQARLIRLPVH 160

Query: 130 A----NQ----KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
                NQ    +R   + RR +           +P  V  +A  L     EV  +  +LA
Sbjct: 161 VVRELNQVLKARRALESARRGEAE---------RPVSVDEVAAALQRPVEEVAEL-LKLA 210

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
             E   +L    ++ S +     V D D  + + +     +   ++L   ++ LN RER 
Sbjct: 211 --EQPTSLDMPLERESGESMLDTVADEDAIDPLGLTLS--REAVHLLDNGLAELNERERE 266

Query: 242 IFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   R   R +E P TLE L++   ++RER+RQI+  A  K++
Sbjct: 267 VLAGRFGLRDRE-PETLEELAARLGLTRERIRQIQQEALLKLK 308


>gi|258623525|ref|ZP_05718526.1| RNA polymerase sigma-38 factor [Vibrio mimicus VM573]
 gi|262172378|ref|ZP_06040056.1| RNA polymerase sigma factor RpoS [Vibrio mimicus MB-451]
 gi|258584187|gb|EEW08935.1| RNA polymerase sigma-38 factor [Vibrio mimicus VM573]
 gi|261893454|gb|EEY39440.1| RNA polymerase sigma factor RpoS [Vibrio mimicus MB-451]
          Length = 336

 Score =  122 bits (306), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 90/280 (32%), Positives = 148/280 (52%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 62  YLSEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 120

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 121 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 179

Query: 139 LRRLKGHLQAITDNNLKPEQVV--------AIAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +  L    D+   PE++          + K L ++E  + S++  + GD     L 
Sbjct: 180 LRTAR-ELSQRLDHEPTPEEIALELDKPVDDVTKMLRLNER-ISSVDTPIGGDGDKALLD 237

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
              D N++   ++   D D +E +L          N L      LNP+++ +  ARR   
Sbjct: 238 ILPDSNNAD-PEFSTQDDDIRESLL----------NWLDE----LNPKQKEVL-ARRFGL 281

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 282 LGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVKQ 321


>gi|37524720|ref|NP_928064.1| RNA polymerase sigma factor RpoS [Photorhabdus luminescens subsp.
           laumondii TTO1]
 gi|36784145|emb|CAE13014.1| RNA polymerase sigma factor (sigma-38) [Photorhabdus luminescens
           subsp. laumondii TTO1]
          Length = 332

 Score =  122 bits (306), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 88/280 (31%), Positives = 150/280 (53%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 63  YLGEIGFSPLLTAEEEVFFARRAL-RGDVLARQRMIESNLRLVVKISRRYSNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI-VKELNVY 180

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +  L    D+   PE++          +++ L ++E  +IS++  ++GD     L 
Sbjct: 181 LRTAR-ELAHKLDHEPSPEEIAEQLDKPVDDVSRMLRLNER-IISVDTPISGDSDKALLD 238

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
             SD+N +           G E    E + +K+    + + +  LN ++R +  ARR   
Sbjct: 239 VLSDENET-----------GPEGTTQEDDMKKS----IVKWLFELNSKQREVL-ARRFGL 282

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L     TLE++  E  ++RERVRQI+    +++++ +Q Q
Sbjct: 283 LGYEAETLEDVGKEIGLTRERVRQIQVEGLRRLKDIMQTQ 322


>gi|222100016|ref|YP_002534584.1| RNA polymerase sigma factor rpoD [Thermotoga neapolitana DSM 4359]
 gi|221572406|gb|ACM23218.1| RNA polymerase sigma factor rpoD [Thermotoga neapolitana DSM 4359]
          Length = 392

 Score =  122 bits (306), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 89/275 (32%), Positives = 140/275 (50%), Gaps = 33/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L   +E  LA+R  + GD  A  +L+TS+LRLVV IA  Y G GL   ++
Sbjct: 119 YLKEIGKIPLLTPAQERELARRA-QMGDKKAKEKLITSNLRLVVSIAKRYMGRGLSFQDL 177

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-- 132
           + EGNIGL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 178 IQEGNIGLLKAVEKFDWRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLN 237

Query: 133 --KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
             +R ++     +  ++ +     KP + +   K++  +  E IS+   +  DE      
Sbjct: 238 RLRREYYQKYGEEPSVEELAKMMGKPPEKI---KEILEAAKETISLESPIGEDE------ 288

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEE--RKNRRNMLTRSMSVLNPRERRIFEARR- 247
                      D  + D    E V   K+E  R   R  L + +  L+PRE  +   R  
Sbjct: 289 -----------DSSIEDFVADESVPSPKKEAMRMLMREELEKVLKTLSPREAMVLRMRYG 337

Query: 248 -LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L   P TLE +   F V+RER+RQIE +A +K++
Sbjct: 338 LLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKLR 372


>gi|108804647|ref|YP_644584.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108765890|gb|ABG04772.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 304

 Score =  122 bits (305), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 85/275 (30%), Positives = 147/275 (53%), Gaps = 16/275 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+  I +  +L +  E  L++R +  GD  A  +L+  +LRLVV +A  YRGYGLP 
Sbjct: 35  LAGYLDRIGRWRLLTRDGEIELSRRAK-KGDRKARQKLIEKNLRLVVSVAKKYRGYGLPF 93

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AV+KFDPERGFR +TY+ WWI+ A+Q  +      +++     +K  
Sbjct: 94  EDLIQEGNIGLMKAVEKFDPERGFRFSTYATWWIRQAVQRAVADKGRTIRVPVHMTEK-- 151

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              +R++      ++    +      IA++L     +V      +    SL+  + SS++
Sbjct: 152 ---IRKVSRTFNELSLELEREPTDEEIARRLEWDVEDVRLTISAMPDATSLDQPV-SSEE 207

Query: 196 NSSQWQDWLVYDH--DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-- 251
           ++S+  D++  +   D  + VL E E      + L  ++  L  R R +   R   ++  
Sbjct: 208 SASELGDFIEDERTSDTPDTVLKELES-----SQLKEAIERLPERARYVLVRRYGLDDRE 262

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           P TL  L  E ++SRERVRQ++  A + ++  I++
Sbjct: 263 PATLAELGDELKISRERVRQLQREAERLLKAGIRR 297


>gi|238761664|ref|ZP_04622639.1| RNA polymerase sigma factor rpoS [Yersinia kristensenii ATCC 33638]
 gi|238700178|gb|EEP92920.1| RNA polymerase sigma factor rpoS [Yersinia kristensenii ATCC 33638]
          Length = 332

 Score =  122 bits (305), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 87/277 (31%), Positives = 141/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+S+  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 63  YLGEIGYSPLLTAEEEVYFARRAL-RGDVSSRRRMIESNLRLVVKIARRYSNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 181

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   +P   V+   +LN     + S++  L GD     L 
Sbjct: 182 RTARELSHKLDHEPSAEEIAEQLDRPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 238

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             SD+N +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 239 ILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 287

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 288 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQAQ 322


>gi|157961021|ref|YP_001501055.1| RpoD family RNA polymerase sigma factor [Shewanella pealeana ATCC
           700345]
 gi|157846021|gb|ABV86520.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella pealeana
           ATCC 700345]
          Length = 322

 Score =  122 bits (305), Expect = 7e-26,   Method: Compositional matrix adjust.
 Identities = 90/281 (32%), Positives = 150/281 (53%), Gaps = 33/281 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   +++  + G   + +R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 53  YLGEIGFSPLLSAEEEVYFSRKSLK-GCEKSRNRMIESNLRLVVKIARRYNNRGLALLDL 111

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 112 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 170

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV---ISMNCRLA------GDESLNAL 189
           LR  +  L    D+    E+   IA KL++  ++V   + +N R+       G ES  AL
Sbjct: 171 LRTAR-ELAHKLDHEPTAEE---IADKLDLPSADVSRMLKLNERITSVDTPLGGESDKAL 226

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-- 247
           ++    + +   D+ V D D  + V+              + +  LN ++R +  ARR  
Sbjct: 227 LDVLADDDNVGPDYKVQDEDMSKSVV--------------KWLDELNTKQREVL-ARRFG 271

Query: 248 -LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            L   P TLEN+  E  ++RERVRQI+  A K++++ +  Q
Sbjct: 272 LLGYEPSTLENVGKEIGLTRERVRQIQVEALKRLKDLLGAQ 312


>gi|127512145|ref|YP_001093342.1| RpoD family RNA polymerase sigma factor [Shewanella loihica PV-4]
 gi|126637440|gb|ABO23083.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella loihica
           PV-4]
          Length = 324

 Score =  122 bits (305), Expect = 8e-26,   Method: Compositional matrix adjust.
 Identities = 90/282 (31%), Positives = 148/282 (52%), Gaps = 35/282 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   +++  + G   + +R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 55  YLSEIGFSPLLSAEEEVYFSRKALK-GCEKSRNRMIESNLRLVVKIARRYNNRGLALLDL 113

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 114 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 172

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRLAGDESLNA 188
           LR  +  L    D+    E+   IA++L++  S+V           S++  L GD    A
Sbjct: 173 LRTAR-ELAHKLDHEPTAEE---IAEQLDLPSSDVSKMLKLNERITSVDTPLGGDND-KA 227

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR- 247
           L++    +     D+ V D D  + V+              R +  LN ++R +  ARR 
Sbjct: 228 LLDVLADDDCVGPDYKVQDDDMSKSVV--------------RWLDELNSKQREVL-ARRF 272

Query: 248 --LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             L   P TLEN+  E  ++RERVRQI+  A K++++ +  Q
Sbjct: 273 GLLGYEPSTLENVGKEIGLTRERVRQIQVEALKRLRDLLSAQ 314


>gi|15644200|ref|NP_229250.1| RNA polymerase sigma-A factor [Thermotoga maritima MSB8]
 gi|6831649|sp|P77994|RPOD_THEMA RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A
 gi|4982015|gb|AAD36519.1|AE001796_11 RNA polymerase sigma-A factor [Thermotoga maritima MSB8]
          Length = 399

 Score =  122 bits (305), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 86/273 (31%), Positives = 141/273 (51%), Gaps = 29/273 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L   +E  LA+R  + GD  A  +L+TS+LRLVV IA  Y G GL   ++
Sbjct: 126 YLKEIGKIPLLTPAQERELARRA-QMGDKKAKEKLITSNLRLVVSIAKRYMGRGLSFQDL 184

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-- 132
           + EGNIGL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 185 IQEGNIGLLKAVEKFDWRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLN 244

Query: 133 --KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
             +R ++     +  ++ +     KP + +   K++  +  E IS+   +  DE      
Sbjct: 245 RLRREYYQKHGEEPSIEELAKMMGKPPEKI---KEILEAAKETISLESPIGEDE------ 295

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--L 248
                  S  +D++  D     +   ++  R   R  L + +  L+PRE  +   R   L
Sbjct: 296 ------DSSIEDFVADDSIASPK---KEAMRMLMREELEKVLKTLSPREAMVLRMRYGLL 346

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              P TLE +   F V+RER+RQIE +A +K++
Sbjct: 347 DGKPKTLEEVGQYFNVTRERIRQIEVKALRKLR 379


>gi|226328647|ref|ZP_03804165.1| hypothetical protein PROPEN_02542 [Proteus penneri ATCC 35198]
 gi|225203380|gb|EEG85734.1| hypothetical protein PROPEN_02542 [Proteus penneri ATCC 35198]
          Length = 327

 Score =  122 bits (305), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 84/280 (30%), Positives = 149/280 (53%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 58  YLGEIGYSPLLTAEEEVFFARRAL-RGDIPSRQRMIESNLRLVVKISRRYTNRGLALLDL 116

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPE+GFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 117 IEEGNLGLIRAVEKFDPEKGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 176

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H       ++ I ++  KP  V  ++K L ++E  + S++  + GD     L 
Sbjct: 177 RTARELAHKLDHEPSVEEIAESLDKP--VEDVSKMLRLNER-ITSVDTPIGGDSDKALLD 233

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
             SD+N            +G E  +    +  N +  + + +  LNP++R +  ARR   
Sbjct: 234 IISDEN-----------EEGPEATI----QNNNLKENIIKWLFELNPKQREVL-ARRFGL 277

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L     TLE++  E  ++RERVRQI+    +++++ +Q Q
Sbjct: 278 LGYEAETLEDVGREIGLTRERVRQIQVEGLRRLKDILQSQ 317


>gi|281412780|ref|YP_003346859.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermotoga
           naphthophila RKU-10]
 gi|281373883|gb|ADA67445.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermotoga
           naphthophila RKU-10]
          Length = 407

 Score =  122 bits (305), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 86/273 (31%), Positives = 141/273 (51%), Gaps = 29/273 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L   +E  LA+R  + GD  A  +L+TS+LRLVV IA  Y G GL   ++
Sbjct: 134 YLKEIGKIPLLTPAQERELARRA-QMGDKKAKEKLITSNLRLVVSIAKRYMGRGLSFQDL 192

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-- 132
           + EGNIGL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 193 IQEGNIGLLKAVEKFDWRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLN 252

Query: 133 --KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
             +R ++     +  ++ +     KP + +   K++  +  E IS+   +  DE      
Sbjct: 253 RLRREYYQKHGEEPSIEELAKMMGKPPEKI---KEILEAAKETISLESPIGEDE------ 303

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--L 248
                  S  +D++  D     +   ++  R   R  L + +  L+PRE  +   R   L
Sbjct: 304 ------DSSIEDFVADDSIASPK---KEAMRMLMREELEKVLKTLSPREAMVLRMRYGLL 354

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              P TLE +   F V+RER+RQIE +A +K++
Sbjct: 355 DGKPKTLEEVGQYFNVTRERIRQIEVKALRKLR 387


>gi|149177995|ref|ZP_01856592.1| RNA polymerase sigma factor rpoS [Planctomyces maris DSM 8797]
 gi|148843188|gb|EDL57554.1| RNA polymerase sigma factor rpoS [Planctomyces maris DSM 8797]
          Length = 279

 Score =  122 bits (305), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 89/277 (32%), Positives = 143/277 (51%), Gaps = 25/277 (9%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ EI +  +L  +EE  L+ R  EHGD  A  R+V ++LRLVV IA  Y G GLP+
Sbjct: 17  LETYLKEINETALLSAEEERELSNRI-EHGDKEARDRMVRANLRLVVNIARAYSGKGLPL 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GL++AV+ FDPE G R +TY+ +WIK +++  ++ S   ++I   A    L
Sbjct: 76  QDLIEEGNLGLLRAVEGFDPEMGTRFSTYASYWIKQSIKRALVNSAKTIRI--PAYMVEL 133

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
               RR    LQ   D     E+V   A++L++   ++  +   +        L NSS +
Sbjct: 134 LTKWRRATAQLQDTLDRTPTTEEV---ARELDLPPKKLKIVKKAI-------QLYNSSPQ 183

Query: 196 NSSQWQDW----LVYDH--DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--R 247
           +      W    ++ D    G +  L+E +  K+    + R +  +  RE  I   R   
Sbjct: 184 SEQHDAGWSLGEMIPDDRLKGPDDELVENDNLKH----VFRLLKEIPEREANILRMRFGL 239

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             + P TL+ +     ++RERVRQIE+ A KK+ + I
Sbjct: 240 DGDEPKTLKEIGQALGLTRERVRQIESEALKKLAKEI 276


>gi|2618586|dbj|BAA23365.1| sigma factor [Vibrio cholerae]
          Length = 335

 Score =  122 bits (305), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 89/280 (31%), Positives = 149/280 (53%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 62  YLSEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 120

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 121 IEEGNLGLIRAVEKFDPERGFRFSTYTTWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 179

Query: 139 LRRLKGHLQAITDNNLKPEQVV--------AIAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +  L    D+   PE++          + K L ++E  + S++  + GD    AL+
Sbjct: 180 LRTAR-ELSQRLDHEPTPEEIALELDRPVDDVTKMLRLNER-ISSVDTPIGGDGD-KALL 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
           +    + +   ++   D D +E +L          N L      LNP+++ +  ARR   
Sbjct: 237 DILPDSHNADPEFSTQDDDIRESLL----------NWLDE----LNPKQKEVL-ARRFGL 281

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 282 LGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVKQ 321


>gi|114562238|ref|YP_749751.1| RNA polymerase, sigma 28 subunit [Shewanella frigidimarina NCIMB
           400]
 gi|114333531|gb|ABI70913.1| RNA polymerase, sigma 28 subunit [Shewanella frigidimarina NCIMB
           400]
          Length = 323

 Score =  122 bits (305), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 92/282 (32%), Positives = 149/282 (52%), Gaps = 35/282 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE V   R    G   + +R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 54  YLGEIGFSPLLTAEEE-VFFSRKSLKGCEKSRNRMIESNLRLVVKISRRYNNRGLALLDL 112

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 113 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI-VKELNVY 171

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRLAGDESLNA 188
           LR  +   Q + D+    E+   IA+KL+VS  +V           S++  L+GD    A
Sbjct: 172 LRTARQLAQKL-DHEPTAEE---IAEKLDVSTGDVSRMLKLNERITSVDSPLSGDNE-KA 226

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR- 247
           L++    + S   D+ V + D                N +   ++ LN ++R +  ARR 
Sbjct: 227 LLDVIADDDSVGPDYRVQNED--------------LSNSIVGWLNELNTKQREVL-ARRF 271

Query: 248 --LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             L   P TLEN+ +E  ++RERVRQI+  A K++++ +  Q
Sbjct: 272 GLLGYEPSTLENVGAEIGLTRERVRQIQVEALKRLKDLLGSQ 313


>gi|309389374|gb|ADO77254.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Halanaerobium
           praevalens DSM 2228]
          Length = 310

 Score =  122 bits (305), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 89/273 (32%), Positives = 149/273 (54%), Gaps = 29/273 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ E+ K+ +L+K+EE  LAKR  E GD  A  +L  ++LRLVV IA  Y G G+   ++
Sbjct: 41  YLKEMGKVDLLDKEEEVELAKRI-EQGDQRAREQLTEANLRLVVSIAKKYIGQGMSFLDL 99

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN GLM+AV+KFD  +G++ +TY+ WWI+ ++   +      ++I      T N   
Sbjct: 100 IQEGNKGLMKAVEKFDYTKGYKFSTYATWWIRQSITRALADQARTIRIPVHMVETMNKLR 159

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +KRL  +L R     +   + N++PE+V+ I K         ++MN +     SL+  
Sbjct: 160 RIEKRLKKDLEREPTLEEIGEEMNMEPEKVLEIQK---------LAMNQQPT---SLDTP 207

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S  +D+ + D D     ++   E    ++ L   +  L  RE+RI + R   
Sbjct: 208 IG--EEKDSHLKDF-IEDQDAPAPEMLASSEL--LKDQLETVLDTLTDREKRIIKLRFGL 262

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
           E+    TL+ + S+F V+RER+RQI+A+A +K+
Sbjct: 263 EDGRQRTLKEVGSQFGVTRERIRQIQAKALRKL 295


>gi|153802558|ref|ZP_01957144.1| RNA polymerase sigma factor RpoS [Vibrio cholerae MZO-3]
 gi|124121921|gb|EAY40664.1| RNA polymerase sigma factor RpoS [Vibrio cholerae MZO-3]
          Length = 335

 Score =  122 bits (305), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 89/280 (31%), Positives = 149/280 (53%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 62  YLSEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 120

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 121 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 179

Query: 139 LRRLKGHLQAITDNNLKPEQVV--------AIAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +  L    D+   PE++          + K L ++E  + S++  + GD    AL+
Sbjct: 180 LRTAR-ELSQRLDHEPTPEEIALELDRPVDDVTKMLRLNER-ISSVDTPIGGDGD-KALL 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
           +    + +   ++   D D +E +L          N L      LNP+++ +  ARR   
Sbjct: 237 DILPDSHNADPEFSTQDDDIRESLL----------NWLDE----LNPKQKEVL-ARRFGL 281

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 282 LGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVKQ 321


>gi|297184127|gb|ADI20246.1| hypothetical protein [uncultured Sphingobacterium sp. EB080_L08E11]
          Length = 287

 Score =  122 bits (305), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 87/296 (29%), Positives = 157/296 (53%), Gaps = 55/296 (18%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ ++  +EE  LA+R +  GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGKVELITAEEEVELAQRIKA-GDQIALEKLTKANLRFVVSVAKQYQNQGLTL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
            ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++      Q  I+R   L KIG+ 
Sbjct: 77  PDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVR-LPLNKIGSI 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCR 179
               + +  L +           + +P     I+K L +SES+V          +SM+  
Sbjct: 136 NKINKAYAYLEQ----------EHERPPSAAEISKHLEMSESDVKESMRNSGRHVSMDAP 185

Query: 180 L--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
           L    D +L  ++NSSD  S    + L+ D               + R  + RS++ L P
Sbjct: 186 LVEGEDSNLYDVLNSSD--SPHPDEDLMMD---------------SLRTEIERSLATLTP 228

Query: 238 RERRIFEARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RE  +    RL      ++P+TLE +  +F+++RERVRQI+ +A ++++ + + ++
Sbjct: 229 REGDVI---RLYFGLGGQHPMTLEEIGEKFDLTRERVRQIKEKAIRRMKHTSRSKI 281


>gi|307718169|ref|YP_003873701.1| RNA polymerase sigma-70 factor family protein [Spirochaeta
           thermophila DSM 6192]
 gi|306531894|gb|ADN01428.1| RNA polymerase sigma-70 factor family protein [Spirochaeta
           thermophila DSM 6192]
          Length = 303

 Score =  122 bits (305), Expect = 9e-26,   Method: Compositional matrix adjust.
 Identities = 81/272 (29%), Positives = 154/272 (56%), Gaps = 16/272 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           LS Y+ EI +IP+L ++EE   A R    GD  A  +LVT++LR VV +A  Y+  GLP+
Sbjct: 32  LSLYLKEINRIPLLTREEEDHYA-RLAAQGDQHAKEKLVTANLRFVVNVAKKYQNQGLPL 90

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT-ANQKR 134
           ++++SEGNIGL+ A+++FDP++G+   +Y++WWI+ A+ + I     ++++    AN+  
Sbjct: 91  ADLISEGNIGLLNAIERFDPDKGYHFISYAVWWIRQAILKAISEKSRMIRLPLNRANELV 150

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
                R+L      +   + +  ++  +A+ L+  E  V ++        SL+  +   D
Sbjct: 151 QIEKARKL------VQTESGEHNEIKKVAETLDYDEDHVANLLNLSKEYVSLDTPV-YED 203

Query: 195 KNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QEN 251
           ++S+   D+L  +     E V++EK  ++  + +L    + L  +E  I + R      +
Sbjct: 204 RDSAMLGDYLKDEASRPPEDVVLEKTLQEEIQEVL----ATLTEKEAEIIQYRFGLNGRH 259

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           P++L+ +   + +++ER+RQIE +A KK+Q+S
Sbjct: 260 PMSLKEIGDLYNLTKERIRQIEKKALKKIQQS 291


>gi|147674644|ref|YP_001216035.1| RNA polymerase sigma factor RpoS [Vibrio cholerae O395]
 gi|262169845|ref|ZP_06037535.1| RNA polymerase sigma factor RpoS [Vibrio cholerae RC27]
 gi|146316527|gb|ABQ21066.1| RNA polymerase sigma factor RpoS [Vibrio cholerae O395]
 gi|227012360|gb|ACP08570.1| RNA polymerase sigma factor RpoS [Vibrio cholerae O395]
 gi|262021579|gb|EEY40290.1| RNA polymerase sigma factor RpoS [Vibrio cholerae RC27]
          Length = 335

 Score =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 89/280 (31%), Positives = 149/280 (53%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 62  YLSEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 120

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 121 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 179

Query: 139 LRRLKGHLQAITDNNLKPEQVV--------AIAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +  L    D+   PE++          + K L ++E  + S++  + GD    AL+
Sbjct: 180 LRTAR-ELSQRLDHEPTPEEIALELDRPVDDVTKMLRLNER-ISSVDTPIGGDGD-KALL 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
           +    + +   ++   D D +E +L          N L      LNP+++ +  ARR   
Sbjct: 237 DILPDSHNADPEFSTQDDDIRESLL----------NWLDE----LNPKQKEVL-ARRFGL 281

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 282 LGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVKQ 321


>gi|148270473|ref|YP_001244933.1| RpoD family RNA polymerase sigma factor [Thermotoga petrophila
           RKU-1]
 gi|170289132|ref|YP_001739370.1| RpoD family RNA polymerase sigma factor [Thermotoga sp. RQ2]
 gi|147736017|gb|ABQ47357.1| RNA polymerase, sigma 70 subunit, RpoD family [Thermotoga
           petrophila RKU-1]
 gi|170176635|gb|ACB09687.1| RNA polymerase, sigma 70 subunit, RpoD family [Thermotoga sp. RQ2]
          Length = 407

 Score =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 86/273 (31%), Positives = 141/273 (51%), Gaps = 29/273 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L   +E  LA+R  + GD  A  +L+TS+LRLVV IA  Y G GL   ++
Sbjct: 134 YLKEIGKIPLLTPAQERELARRA-QMGDKKAKEKLITSNLRLVVSIAKRYMGRGLSFQDL 192

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-- 132
           + EGNIGL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 193 IQEGNIGLLKAVEKFDWRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLN 252

Query: 133 --KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
             +R ++     +  ++ +     KP + +   K++  +  E IS+   +  DE      
Sbjct: 253 RLRREYYQKHGEEPSIEELAKMMGKPPEKI---KEILEAAKETISLESPIGEDE------ 303

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--L 248
                  S  +D++  D     +   ++  R   R  L + +  L+PRE  +   R   L
Sbjct: 304 ------DSSIEDFVADDSIASPK---KEAMRMLMREELEKVLKTLSPREAMVLRMRYGLL 354

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              P TLE +   F V+RER+RQIE +A +K++
Sbjct: 355 DGKPKTLEEVGQYFNVTRERIRQIEVKALRKLR 387


>gi|5030433|gb|AAC44889.2| sigma 70-type sigma factor SigA [Thermotoga maritima]
          Length = 407

 Score =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 86/273 (31%), Positives = 141/273 (51%), Gaps = 29/273 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L   +E  LA+R  + GD  A  +L+TS+LRLVV IA  Y G GL   ++
Sbjct: 134 YLKEIGKIPLLTPAQERELARRA-QMGDKKAKEKLITSNLRLVVSIAKRYMGRGLSFQDL 192

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-- 132
           + EGNIGL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 193 IQEGNIGLLKAVEKFDWRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLN 252

Query: 133 --KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
             +R ++     +  ++ +     KP + +   K++  +  E IS+   +  DE      
Sbjct: 253 RLRREYYQKHGEEPSIEELAKMMGKPPEKI---KEILEAAKETISLESPIGEDE------ 303

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--L 248
                  S  +D++  D     +   ++  R   R  L + +  L+PRE  +   R   L
Sbjct: 304 ------DSSIEDFVADDSIASPK---KEAMRMLMREELEKVLKTLSPREAMVLRMRYGLL 354

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              P TLE +   F V+RER+RQIE +A +K++
Sbjct: 355 DGKPKTLEEVGQYFNVTRERIRQIEVKALRKLR 387


>gi|229512804|ref|ZP_04402271.1| RNA polymerase sigma factor RpoS [Vibrio cholerae TMA 21]
 gi|229350053|gb|EEO15006.1| RNA polymerase sigma factor RpoS [Vibrio cholerae TMA 21]
 gi|327483355|gb|AEA77762.1| RNA polymerase sigma factor RpoS [Vibrio cholerae LMA3894-4]
          Length = 335

 Score =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 89/280 (31%), Positives = 149/280 (53%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 62  YLSEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 120

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 121 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 179

Query: 139 LRRLKGHLQAITDNNLKPEQVV--------AIAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +  L    D+   PE++          + K L ++E  + S++  + GD    AL+
Sbjct: 180 LRTAR-ELSQRLDHEPTPEEIALELDRPVDDVTKMLRLNER-ISSVDTPIGGDGD-KALL 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
           +    + +   ++   D D +E +L          N L      LNP+++ +  ARR   
Sbjct: 237 DILPDSHNADPEFSTQDDDIRESLL----------NWLDE----LNPKQKEVL-ARRFGL 281

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 282 LGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVKQ 321


>gi|153214922|ref|ZP_01949705.1| RNA polymerase sigma factor RpoS [Vibrio cholerae 1587]
 gi|153826929|ref|ZP_01979596.1| RNA polymerase sigma factor RpoS [Vibrio cholerae MZO-2]
 gi|153829928|ref|ZP_01982595.1| RNA polymerase sigma factor RpoS [Vibrio cholerae 623-39]
 gi|229530348|ref|ZP_04419736.1| RNA polymerase sigma factor RpoS [Vibrio cholerae 12129(1)]
 gi|254226840|ref|ZP_04920411.1| RNA polymerase sigma factor RpoS [Vibrio cholerae V51]
 gi|254291219|ref|ZP_04962015.1| RNA polymerase sigma factor RpoS [Vibrio cholerae AM-19226]
 gi|262190768|ref|ZP_06048995.1| RNA polymerase sigma factor RpoS [Vibrio cholerae CT 5369-93]
 gi|124114995|gb|EAY33815.1| RNA polymerase sigma factor RpoS [Vibrio cholerae 1587]
 gi|125620637|gb|EAZ49000.1| RNA polymerase sigma factor RpoS [Vibrio cholerae V51]
 gi|148874616|gb|EDL72751.1| RNA polymerase sigma factor RpoS [Vibrio cholerae 623-39]
 gi|149739232|gb|EDM53500.1| RNA polymerase sigma factor RpoS [Vibrio cholerae MZO-2]
 gi|150422913|gb|EDN14864.1| RNA polymerase sigma factor RpoS [Vibrio cholerae AM-19226]
 gi|229332121|gb|EEN97609.1| RNA polymerase sigma factor RpoS [Vibrio cholerae 12129(1)]
 gi|262033353|gb|EEY51864.1| RNA polymerase sigma factor RpoS [Vibrio cholerae CT 5369-93]
          Length = 335

 Score =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 89/280 (31%), Positives = 149/280 (53%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 62  YLSEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 120

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 121 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 179

Query: 139 LRRLKGHLQAITDNNLKPEQVV--------AIAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +  L    D+   PE++          + K L ++E  + S++  + GD    AL+
Sbjct: 180 LRTAR-ELSQRLDHEPTPEEIALELDRPVDDVTKMLRLNER-ISSVDTPIGGDGD-KALL 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
           +    + +   ++   D D +E +L          N L      LNP+++ +  ARR   
Sbjct: 237 DILPDSHNADPEFSTQDDDIRESLL----------NWLDE----LNPKQKEVL-ARRFGL 281

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 282 LGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVKQ 321


>gi|15640556|ref|NP_230185.1| RNA polymerase sigma-38 factor [Vibrio cholerae O1 biovar El Tor
           str. N16961]
 gi|121590676|ref|ZP_01678009.1| RNA polymerase sigma factor RpoS [Vibrio cholerae 2740-80]
 gi|121728563|ref|ZP_01681585.1| RNA polymerase sigma factor RpoS [Vibrio cholerae V52]
 gi|153819103|ref|ZP_01971770.1| RNA polymerase sigma factor RpoS [Vibrio cholerae NCTC 8457]
 gi|153823615|ref|ZP_01976282.1| RNA polymerase sigma factor RpoS [Vibrio cholerae B33]
 gi|227080717|ref|YP_002809268.1| RNA polymerase sigma factor RpoS [Vibrio cholerae M66-2]
 gi|229507145|ref|ZP_04396651.1| RNA polymerase sigma factor RpoS [Vibrio cholerae BX 330286]
 gi|229508992|ref|ZP_04398480.1| RNA polymerase sigma factor RpoS [Vibrio cholerae B33]
 gi|229519660|ref|ZP_04409103.1| RNA polymerase sigma factor RpoS [Vibrio cholerae RC9]
 gi|229606176|ref|YP_002876824.1| RNA polymerase sigma factor RpoS [Vibrio cholerae MJ-1236]
 gi|254850774|ref|ZP_05240124.1| RNA polymerase sigma factor rpoS [Vibrio cholerae MO10]
 gi|255744238|ref|ZP_05418191.1| RNA polymerase sigma factor RpoS [Vibrio cholera CIRS 101]
 gi|262149032|ref|ZP_06028176.1| RNA polymerase sigma factor RpoS [Vibrio cholerae INDRE 91/1]
 gi|6094129|sp|O51804|RPOS_VIBCH RecName: Full=RNA polymerase sigma factor rpoS; AltName:
           Full=Sigma-38 factor
 gi|2897902|gb|AAC38175.1| sigma S [Vibrio cholerae]
 gi|9654961|gb|AAF93702.1| RNA polymerase sigma-38 factor [Vibrio cholerae O1 biovar El Tor
           str. N16961]
 gi|121547462|gb|EAX57570.1| RNA polymerase sigma factor RpoS [Vibrio cholerae 2740-80]
 gi|121629175|gb|EAX61616.1| RNA polymerase sigma factor RpoS [Vibrio cholerae V52]
 gi|126510335|gb|EAZ72929.1| RNA polymerase sigma factor RpoS [Vibrio cholerae NCTC 8457]
 gi|126518864|gb|EAZ76087.1| RNA polymerase sigma factor RpoS [Vibrio cholerae B33]
 gi|227008605|gb|ACP04817.1| RNA polymerase sigma factor RpoS [Vibrio cholerae M66-2]
 gi|229344349|gb|EEO09324.1| RNA polymerase sigma factor RpoS [Vibrio cholerae RC9]
 gi|229353917|gb|EEO18851.1| RNA polymerase sigma factor RpoS [Vibrio cholerae B33]
 gi|229355890|gb|EEO20810.1| RNA polymerase sigma factor RpoS [Vibrio cholerae BX 330286]
 gi|229368831|gb|ACQ59254.1| RNA polymerase sigma factor RpoS [Vibrio cholerae MJ-1236]
 gi|254846479|gb|EET24893.1| RNA polymerase sigma factor rpoS [Vibrio cholerae MO10]
 gi|255738178|gb|EET93570.1| RNA polymerase sigma factor RpoS [Vibrio cholera CIRS 101]
 gi|262031177|gb|EEY49797.1| RNA polymerase sigma factor RpoS [Vibrio cholerae INDRE 91/1]
          Length = 335

 Score =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 89/280 (31%), Positives = 149/280 (53%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 62  YLSEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 120

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 121 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 179

Query: 139 LRRLKGHLQAITDNNLKPEQVV--------AIAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +  L    D+   PE++          + K L ++E  + S++  + GD    AL+
Sbjct: 180 LRTAR-ELSQRLDHEPTPEEIALELDRPVDDVTKMLRLNER-ISSVDTPIGGDGD-KALL 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
           +    + +   ++   D D +E +L          N L      LNP+++ +  ARR   
Sbjct: 237 DILPDSHNADPEFSTQDDDIRESLL----------NWLDE----LNPKQKEVL-ARRFGL 281

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 282 LGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVKQ 321


>gi|317493947|ref|ZP_07952364.1| RNA polymerase sigma factor RpoS [Enterobacteriaceae bacterium
           9_2_54FAA]
 gi|316918274|gb|EFV39616.1| RNA polymerase sigma factor RpoS [Enterobacteriaceae bacterium
           9_2_54FAA]
          Length = 328

 Score =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 86/277 (31%), Positives = 143/277 (51%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD ++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 59  YLGEIGYSPLLTAEEEVFFARRAL-RGDDASRRRMIESNLRLVVKIARRYSNRGLALLDL 117

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 118 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 177

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   +P  V  +++ L ++E  + S++  L GD     L 
Sbjct: 178 RTARELSHKLDHEPSAEEIAEQLDRP--VTDVSRMLRLNER-ITSVDTPLGGDSEKALLD 234

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+N S  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 235 ILTDENESGPEDTTQSDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 283

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 284 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQAQ 318


>gi|238797130|ref|ZP_04640632.1| RNA polymerase sigma factor rpoS [Yersinia mollaretii ATCC 43969]
 gi|238718977|gb|EEQ10791.1| RNA polymerase sigma factor rpoS [Yersinia mollaretii ATCC 43969]
          Length = 332

 Score =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 87/277 (31%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 63  YLGEIGYSPLLTAEEEVYFARRAL-RGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 181

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 182 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 238

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             SD+N +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 239 ILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 287

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 288 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 322


>gi|239626174|ref|ZP_04669205.1| DNA-directed RNA polymerase sigma subunit [Clostridiales bacterium
           1_7_47_FAA]
 gi|239520404|gb|EEQ60270.1| DNA-directed RNA polymerase sigma subunit [Clostridiales bacterium
           1_7_47FAA]
          Length = 409

 Score =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 86/265 (32%), Positives = 141/265 (53%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  I +L  +EE  LA+R  E GD  A  +LV ++LRLVV IA  Y G G+   ++
Sbjct: 142 YLKEIGSISLLTPEEETDLARRKSE-GDAEAGRQLVEANLRLVVSIAKRYTGRGMGFLDL 200

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GLM+AV+KFD  +G+RL+TY+ WW+K ++   +      +++    +       
Sbjct: 201 VQEGNLGLMKAVEKFDYSKGYRLSTYATWWVKQSITRSLADQSRTIRL--PVHMVEAVNK 258

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           +RR +  L          E+   IA+++ + E  V  +  + +GD +++      D+  S
Sbjct: 259 IRRAQRSLSVRLGREPSTEE---IAEEVGMPEKRVTEL-IQASGD-TVSLETPVGDEEGS 313

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLE 256
              D++  D +   +   +K E    R  +   +  LNPRER +   R   E  +P+TLE
Sbjct: 314 NLGDFVADDANASTE---DKAESFLLREEIDAMLQGLNPREREVIILRFGLETGHPLTLE 370

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +   F V+RER+RQIE  A +K++
Sbjct: 371 EVGRRFNVTRERIRQIETAALRKLR 395


>gi|238754524|ref|ZP_04615879.1| RNA polymerase sigma factor rpoS [Yersinia ruckeri ATCC 29473]
 gi|238707353|gb|EEP99715.1| RNA polymerase sigma factor rpoS [Yersinia ruckeri ATCC 29473]
          Length = 332

 Score =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 87/277 (31%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 63  YLGEIGYSPLLTAEEEVYFARRAL-RGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 181

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 182 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 238

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             SD+N +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 239 ILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 287

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 288 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 322


>gi|51595126|ref|YP_069317.1| RNA polymerase sigma factor RpoS [Yersinia pseudotuberculosis IP
           32953]
 gi|153948385|ref|YP_001402250.1| RNA polymerase sigma factor RpoS [Yersinia pseudotuberculosis IP
           31758]
 gi|170025640|ref|YP_001722145.1| RNA polymerase sigma factor RpoS [Yersinia pseudotuberculosis
           YPIII]
 gi|186894139|ref|YP_001871251.1| RNA polymerase sigma factor RpoS [Yersinia pseudotuberculosis
           PB1/+]
 gi|51588408|emb|CAH20016.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Yersinia pseudotuberculosis IP
           32953]
 gi|152959880|gb|ABS47341.1| RNA polymerase sigma factor RpoS [Yersinia pseudotuberculosis IP
           31758]
 gi|169752174|gb|ACA69692.1| RNA polymerase, sigma 70 subunit, RpoD family [Yersinia
           pseudotuberculosis YPIII]
 gi|186697165|gb|ACC87794.1| RNA polymerase, sigma 70 subunit, RpoD family [Yersinia
           pseudotuberculosis PB1/+]
          Length = 332

 Score =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 87/277 (31%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 63  YLGEIGYSPLLTAEEEVYFARRAL-RGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 181

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 182 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 238

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             SD+N +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 239 ILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 287

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 288 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 322


>gi|119774181|ref|YP_926921.1| RNA polymerase sigma-38 factor [Shewanella amazonensis SB2B]
 gi|119766681|gb|ABL99251.1| RNA polymerase sigma-38 factor [Shewanella amazonensis SB2B]
          Length = 327

 Score =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 93/282 (32%), Positives = 145/282 (51%), Gaps = 35/282 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE V   R    G   + +R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 58  YLSEIGFSPLLTAEEE-VYYSRKALRGCEKSRNRMIESNLRLVVKIARRYNNRGLALLDL 116

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 117 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 175

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRLAGDESLNA 188
           LR  +  L    D+    E+   IA KLN+   EV           S++  L GD    A
Sbjct: 176 LRTAR-ELAHKLDHEPTAEE---IAAKLNLPSVEVSRMLKLNEKITSVDVPLGGDND-KA 230

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR- 247
           L++    + S   D+ V D D                N +   ++ LN ++R +  ARR 
Sbjct: 231 LLDVLPDDDSVGPDYKVQDEDIS--------------NSVVNWLNELNTKQREVL-ARRF 275

Query: 248 --LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             L   P TLE++ +E  ++RERVRQI+  A K++++ +  Q
Sbjct: 276 GLLGYEPSTLEDVGAEIGLTRERVRQIQVEALKRLRDILSAQ 317


>gi|24374942|ref|NP_718985.1| RNA polymerase sigma-38 factor [Shewanella oneidensis MR-1]
 gi|24349657|gb|AAN56429.1|AE015779_6 RNA polymerase sigma-38 factor [Shewanella oneidensis MR-1]
          Length = 326

 Score =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 90/282 (31%), Positives = 150/282 (53%), Gaps = 35/282 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   +++  + G   + +R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 57  YLGEIGFSPLLSAEEEVYFSRKALK-GCEKSRNRMIESNLRLVVKIARRYNNRGLALLDL 115

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 116 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 174

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRLAGDESLNA 188
           LR  +   Q + D+    E+   IA+KL VS  +V           S++  L GD    A
Sbjct: 175 LRTARELAQKL-DHEPTAEE---IAEKLQVSSVDVSRMLKLNEKITSVDVPLGGDND-KA 229

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR- 247
           L++    + +   D+ V D D                N + + ++ LN ++R +  ARR 
Sbjct: 230 LLDVLADDDNVGPDYKVQDEDIS--------------NSVVKWLNELNTKQREVL-ARRF 274

Query: 248 --LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             L   P TLE++ +E  ++RERVRQI+  A K++++ +  Q
Sbjct: 275 GLLGYEPSTLEDVGAEIGLTRERVRQIQVEALKRLRDLLGAQ 316


>gi|238791265|ref|ZP_04634904.1| RNA polymerase sigma factor rpoS [Yersinia intermedia ATCC 29909]
 gi|238729398|gb|EEQ20913.1| RNA polymerase sigma factor rpoS [Yersinia intermedia ATCC 29909]
          Length = 332

 Score =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 87/277 (31%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 63  YLGEIGYSPLLTAEEEVYFARRAL-RGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 181

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 182 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 238

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             SD+N +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 239 ILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 287

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 288 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 322


>gi|332667453|ref|YP_004450241.1| RpoD subfamily RNA polymerase sigma-70 subunit [Haliscomenobacter
           hydrossis DSM 1100]
 gi|332336267|gb|AEE53368.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Haliscomenobacter
           hydrossis DSM 1100]
          Length = 288

 Score =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 82/285 (28%), Positives = 152/285 (53%), Gaps = 38/285 (13%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + L +Y+++I KIPML   +E  LA+R R+ GD  A  +L  ++LR VV +A  Y+  GL
Sbjct: 16  LALDKYLNDIGKIPMLTADDEAELARRIRQ-GDDDAMAKLTRANLRFVVSVAKQYQNQGL 74

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            +S++++EGN+GLM+A K+FD  +GF+  +Y++WWI+ ++ + I+    +V++       
Sbjct: 75  SLSDLINEGNVGLMKAAKRFDETKGFKFISYAVWWIRQSILQAIVEYSRIVRL------- 127

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL-----NVSESEVISMNCRLAGDE---- 184
                       L  +   N   E  +A  ++      N    E++ MN R  G+     
Sbjct: 128 -----------PLNKVGSYNKVNEAYLAFIQQFEREPSNEELGELLEMNPREVGNMLKGN 176

Query: 185 ----SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               S++A ++  + +S+        D  G +  L+E    ++ ++ + + +S+LN RE 
Sbjct: 177 GRHVSVDAPLSGEEGDSTMLDVITDEDDMGPDFRLME----QSLKDEVKQGLSILNIREV 232

Query: 241 RIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +  A    E   P+TLE +   + ++RERVRQI+ RA +++++S
Sbjct: 233 EVLSAYYGLEGQKPLTLEEIGEMYGLTRERVRQIKERAIRRLRKS 277


>gi|126175320|ref|YP_001051469.1| RpoD family RNA polymerase sigma factor [Shewanella baltica OS155]
 gi|125998525|gb|ABN62600.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella baltica
           OS155]
          Length = 326

 Score =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 90/282 (31%), Positives = 151/282 (53%), Gaps = 35/282 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   +++  + G   + +R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 57  YLGEIGFSPLLSAEEEVYFSRKALK-GCAKSRNRMIESNLRLVVKIARRYNNRGLALLDL 115

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 116 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 174

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRLAGDESLNA 188
           LR  +   Q + D+    E+   IA+KL VS ++V           S++  L GD    A
Sbjct: 175 LRTARELAQKL-DHEPTAEE---IAEKLQVSSADVSRMLKLNEKITSVDTPLWGDND-KA 229

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR- 247
           L++    + +   D+ V D D                N + + ++ LN ++R +  ARR 
Sbjct: 230 LLDILADDDNVGPDYKVQDEDIS--------------NSVVKWLNELNTKQREVL-ARRF 274

Query: 248 --LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             L   P TLE++ +E  ++RERVRQI+  A K++++ +  Q
Sbjct: 275 GLLGYEPSTLEDVGAEIGLTRERVRQIQVEALKRLRDLLGSQ 316


>gi|238786006|ref|ZP_04629967.1| RNA polymerase sigma factor rpoS [Yersinia bercovieri ATCC 43970]
 gi|238713067|gb|EEQ05118.1| RNA polymerase sigma factor rpoS [Yersinia bercovieri ATCC 43970]
          Length = 332

 Score =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 87/277 (31%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 63  YLGEIGYSPLLTAEEEVYFARRAL-RGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 181

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 182 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 238

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             SD+N +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 239 ILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 287

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 288 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 322


>gi|238750591|ref|ZP_04612091.1| RNA polymerase sigma factor rpoS [Yersinia rohdei ATCC 43380]
 gi|238711239|gb|EEQ03457.1| RNA polymerase sigma factor rpoS [Yersinia rohdei ATCC 43380]
          Length = 332

 Score =  121 bits (304), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 87/277 (31%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 63  YLGEIGYSPLLTAEEEVYFARRAL-RGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 181

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 182 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 238

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             SD+N +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 239 ILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 287

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 288 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQGQ 322


>gi|238758207|ref|ZP_04619386.1| RNA polymerase sigma factor rpoS [Yersinia aldovae ATCC 35236]
 gi|238703537|gb|EEP96075.1| RNA polymerase sigma factor rpoS [Yersinia aldovae ATCC 35236]
          Length = 332

 Score =  121 bits (303), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 87/277 (31%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 63  YLGEIGYSPLLTAEEEVYFARRAL-RGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 181

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 182 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 238

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             SD+N +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 239 ILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 287

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 288 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 322


>gi|123441128|ref|YP_001005116.1| RNA polymerase sigma factor RpoS [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|332160357|ref|YP_004296934.1| RNA polymerase sigma factor RpoS [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|122088089|emb|CAL10877.1| RNA polymerase sigma factor RpoS [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|318604409|emb|CBY25907.1| RNA polymerase sigma factor RpoS [Yersinia enterocolitica subsp.
           palearctica Y11]
 gi|325664587|gb|ADZ41231.1| RNA polymerase sigma factor RpoS [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|330859888|emb|CBX70219.1| RNA polymerase sigma factor rpoS [Yersinia enterocolitica W22703]
          Length = 332

 Score =  121 bits (303), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 87/277 (31%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 63  YLGEIGYSPLLTAEEEVYFARRAL-RGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 181

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 182 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 238

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             SD+N +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 239 ILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 287

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 288 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQAQ 322


>gi|113969467|ref|YP_733260.1| RNA polymerase, sigma 28 subunit [Shewanella sp. MR-4]
 gi|114046700|ref|YP_737250.1| RNA polymerase, sigma 28 subunit [Shewanella sp. MR-7]
 gi|117919573|ref|YP_868765.1| RNA polymerase, sigma 38 subunit, RpoS [Shewanella sp. ANA-3]
 gi|113884151|gb|ABI38203.1| RNA polymerase, sigma 28 subunit [Shewanella sp. MR-4]
 gi|113888142|gb|ABI42193.1| RNA polymerase, sigma 28 subunit [Shewanella sp. MR-7]
 gi|117611905|gb|ABK47359.1| RNA polymerase, sigma 38 subunit, RpoS [Shewanella sp. ANA-3]
          Length = 326

 Score =  121 bits (303), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 90/282 (31%), Positives = 150/282 (53%), Gaps = 35/282 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   +++  + G   + +R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 57  YLGEIGFSPLLSAEEEVYFSRKALK-GCEKSRNRMIESNLRLVVKIARRYNNRGLALLDL 115

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 116 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 174

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRLAGDESLNA 188
           LR  +   Q + D+    E+   IA+KL VS  +V           S++  L GD    A
Sbjct: 175 LRTARELAQKL-DHEPTAEE---IAEKLQVSSVDVSRMLKLNEKITSVDIPLGGDND-KA 229

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR- 247
           L++    + +   D+ V D D                N + + ++ LN ++R +  ARR 
Sbjct: 230 LLDVLADDDNVGPDYKVQDEDIS--------------NSVVKWLNELNTKQREVL-ARRF 274

Query: 248 --LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             L   P TLE++ +E  ++RERVRQI+  A K++++ +  Q
Sbjct: 275 GLLGYEPSTLEDVGAEIGLTRERVRQIQVEALKRLRDLLGAQ 316


>gi|197302434|ref|ZP_03167489.1| hypothetical protein RUMLAC_01162 [Ruminococcus lactaris ATCC
           29176]
 gi|197298332|gb|EDY32877.1| hypothetical protein RUMLAC_01162 [Ruminococcus lactaris ATCC
           29176]
          Length = 283

 Score =  121 bits (303), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 89/267 (33%), Positives = 146/267 (54%), Gaps = 18/267 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI +IP+L+ +EE  L +R  + GD  A  RL   +LRLVV IA  Y G G+P+ ++
Sbjct: 24  YLNEIGQIPLLDAEEEKELGRRSVD-GDEEARRRLEEGNLRLVVSIAKHYTGRGIPLMDL 82

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM+AV+K+D  +  R +TY+ WWIK A+Q  I +    +++     +      
Sbjct: 83  IQEGNIGLMRAVEKYDFTKENRFSTYASWWIKEAIQRAIDQQSREIRVPVHVAEA--MKK 140

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKL-NVSESEVISMNCRLAGDESLNALINSSDKNS 197
           ++R+   LQ        PE+   IA+KL + S  +V ++   L    SL   +    +N+
Sbjct: 141 VQRISKELQQSLGREATPEE---IAEKLGDKSTEDVKNILSYLQNPVSLETPVGEDGENN 197

Query: 198 --SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV-- 253
                +D      +    +L++KEE       ++  ++ LN RE+++   R   E+    
Sbjct: 198 LGDMVEDKASPTPEEAMNLLVQKEE-------VSELLNALNDREKQVIRLRYGLEDGKTH 250

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKV 280
           TLE +  E +V+RERVRQIE+RA +K+
Sbjct: 251 TLEEIGEELKVTRERVRQIESRAMEKL 277


>gi|225026959|ref|ZP_03716151.1| hypothetical protein EUBHAL_01215 [Eubacterium hallii DSM 3353]
 gi|224955724|gb|EEG36933.1| hypothetical protein EUBHAL_01215 [Eubacterium hallii DSM 3353]
          Length = 422

 Score =  121 bits (303), Expect = 1e-25,   Method: Compositional matrix adjust.
 Identities = 90/276 (32%), Positives = 146/276 (52%), Gaps = 21/276 (7%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           N E  +  Y+ EI +IP+L  +EE  LAKR  E GD  A  +L  ++LRL V IA  Y G
Sbjct: 147 NAEDPVRMYLKEIGRIPLLSSEEEIELAKRM-EEGDEEAKKKLSEANLRLTVSIAKRYSG 205

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-- 128
            G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ ++   I      ++I    
Sbjct: 206 RGMQFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQSITRAIADQARTIRIPVHM 265

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
                R+    RRL   LQ        PE+   IA+ +N+    V+ ++       SL  
Sbjct: 266 VETMNRVNRTSRRL---LQEYG-REPTPEE---IAEAMNLPVERVLEISKISQEPVSLET 318

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR--RNMLTRSMSVLNPRERRIFEAR 246
            I   ++  S   D++  +H     + +  +E  +   R  L + M  L+ RE+++   R
Sbjct: 319 PI--GEEEDSHLGDFIQDEH-----IPVPADEAAHTLLREQLEKVMDTLSEREQKVLALR 371

Query: 247 RLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
              E+  P TLE +  EF+V+RER+RQIEA+A +K+
Sbjct: 372 FGLEDGKPHTLEEVGREFQVTRERIRQIEAKALRKL 407


>gi|289549268|ref|YP_003474256.1| RNA polymerase, sigma 70 family subunit [Thermocrinis albus DSM
           14484]
 gi|289182885|gb|ADC90129.1| putative RNA polymerase, sigma 70 family subunit [Thermocrinis
           albus DSM 14484]
          Length = 310

 Score =  121 bits (303), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 96/296 (32%), Positives = 150/296 (50%), Gaps = 40/296 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L++Y+ ++ KIP+L  +EE  LA+R +E GD  A  +LV S+LR V+ IA  Y+GYGLP+
Sbjct: 10  LAQYLKKVSKIPLLTPEEEKELARRAKE-GDTEALRKLVESNLRFVISIAKQYQGYGLPL 68

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG-------- 127
           SE+++ GN GL++A K+FDP+RG +  +Y++WWI+ A+ + + +    V+I         
Sbjct: 69  SELIAAGNYGLVEAAKRFDPDRGVKFISYAVWWIRQAIMQALSQQSGAVRIPLKQSHVIN 128

Query: 128 ----------------TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK--LNVS 169
                            TA +    +    L+  ++         E++    KK  L +S
Sbjct: 129 RIASIYSKLYKEQEKEPTAEEVAYEYTKEILQKEMERELGRPPTEEEIERRIKKEGLKIS 188

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH---DGQEQVLIEKEERKNRRN 226
             EV           SL+A I   +   + + D L+  H   D +E+VL E  E K    
Sbjct: 189 PQEVEKCLQICKAPLSLDAPIGEDE--DTFFVD-LLSKHGSADVEEKVLTEFLE-KEIEE 244

Query: 227 MLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           ML +    L  +ERR+ E R     E P TL  +     +SRERVRQ+E RA +K+
Sbjct: 245 MLDK----LPEKERRVIELRFGLRGEEPRTLREIGEILNISRERVRQLETRALRKL 296


>gi|284046131|ref|YP_003396471.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Conexibacter
           woesei DSM 14684]
 gi|283950352|gb|ADB53096.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Conexibacter
           woesei DSM 14684]
          Length = 367

 Score =  121 bits (303), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 87/275 (31%), Positives = 144/275 (52%), Gaps = 15/275 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  ++ +I K+ +L  QEE  LAKR  E GDL A  ++V S+LRLVV IA  YR  GLP 
Sbjct: 99  LQLFLKDIGKVRLLTAQEEVDLAKRI-ERGDLDAKQKMVESNLRLVVSIAKNYRNQGLPF 157

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EG +GL++A +KFD  +GF+ +TY+ WWI+ A+   +      ++I     +K  
Sbjct: 158 LDLIQEGTLGLVRAAEKFDYRKGFKFSTYATWWIRQAIARALADKARTIRIPVHVVEK-- 215

Query: 136 FFNLRRL-KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
              L ++ +   + +T+   +P     IA    +   EV S+        SL   +   D
Sbjct: 216 ---LNKIGRAERKLVTELGREP-TAEEIADVTGIDPEEVDSIKRSAQAPVSLEKPVG--D 269

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENP 252
           +  S++  ++    D + +   E+      +  L  ++  L+ RERR+ E R     E+P
Sbjct: 270 EEESEFGQFIA---DERAESPYERAAEILTKEALREALENLSYRERRVLELRYGLGGEHP 326

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            TL+ +   F V+RER+RQIE ++ KK+Q   + Q
Sbjct: 327 RTLDEVGRTFNVTRERIRQIENQSLKKLQSLAEAQ 361


>gi|297588502|ref|ZP_06947145.1| DNA-directed RNA polymerase sigma subunit RpoD [Finegoldia magna
           ATCC 53516]
 gi|297573875|gb|EFH92596.1| DNA-directed RNA polymerase sigma subunit RpoD [Finegoldia magna
           ATCC 53516]
          Length = 389

 Score =  120 bits (302), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 88/278 (31%), Positives = 143/278 (51%), Gaps = 21/278 (7%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           +N +  +  Y+ EI KIP+L  +EE  LA+   E+G   A  +L  ++LRLVV IA  Y 
Sbjct: 114 INVDDPVKMYLKEIGKIPLLSAEEEVKLAQEM-ENGSKRAKKKLAEANLRLVVSIAKRYV 172

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GLM+AV KFD  RGF+ +TY+ WWI+ A+   I      ++I   
Sbjct: 173 GRGMSFLDLIQEGNLGLMKAVDKFDYTRGFKFSTYATWWIRQAITRAIADQARTIRIPV- 231

Query: 130 ANQKRLFFNLRRL-KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
                +   + RL +   Q + D    P     IAK++ +   +V     R    E ++ 
Sbjct: 232 ----HMVETINRLVRIERQLLQDLGRDPTN-EEIAKEMGIEVEKV--REVRKIAQEPVSL 284

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN---RRNMLTRSMSVLNPRERRIFEA 245
                ++  S   D++      ++   I  +E  N    R  L   ++ LN RER++   
Sbjct: 285 ETPIGEEEDSHLGDFI------EDDTAIAPDEAANFTMLREELEGILNTLNERERKVLAL 338

Query: 246 R--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   +   P TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 339 RFGLVDGTPRTLEEVGKDFDVTRERIRQIEAKALRKLK 376


>gi|166078602|gb|ABY81278.1| alternative sigma factor S [Listonella anguillarum]
          Length = 332

 Score =  120 bits (302), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 90/284 (31%), Positives = 146/284 (51%), Gaps = 40/284 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  QEE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 61  YLSEIGFSPLLTAQEEVLYARRSL-RGDEAARKRMIESNLRLVVKISRRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA---------GDESLNAL 189
           LR  +   Q +       E    + K  +V  S+++ +N R++         GD++L  +
Sbjct: 179 LRTARELSQKLDHEPTAEEIAFQLDKPEDV--SKMLRLNERISSVDTPIGGDGDKALLDI 236

Query: 190 I---NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           I   N+SD   S   D +                    R  L   +  LNP+++ +  AR
Sbjct: 237 IPDTNNSDPEISTQDDDI--------------------RESLLNWLDELNPKQKEVL-AR 275

Query: 247 R---LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 276 RFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVKQ 319


>gi|323493642|ref|ZP_08098763.1| RNA polymerase sigma factor RpoS [Vibrio brasiliensis LMG 20546]
 gi|323312165|gb|EGA65308.1| RNA polymerase sigma factor RpoS [Vibrio brasiliensis LMG 20546]
          Length = 326

 Score =  120 bits (302), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 89/285 (31%), Positives = 147/285 (51%), Gaps = 41/285 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 54  YLGEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 112

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 113 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 171

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNAL- 189
           LR  +   Q + D+    E++          ++K L ++E  + S++  + GD     L 
Sbjct: 172 LRTARELSQKL-DHEPTAEEIATQLDKPVDDVSKMLRLNE-RISSVDTPIGGDGEKALLD 229

Query: 190 ----INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
               IN+SD   S   D +                    +N L   +  LNP+++ +  A
Sbjct: 230 IIPDINNSDPEVSTQDDDI--------------------KNSLIHWLDELNPKQKEVL-A 268

Query: 246 RR---LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           RR   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 269 RRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILIKQ 313


>gi|225174152|ref|ZP_03728151.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dethiobacter
           alkaliphilus AHT 1]
 gi|225169937|gb|EEG78732.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dethiobacter
           alkaliphilus AHT 1]
          Length = 372

 Score =  120 bits (302), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 90/266 (33%), Positives = 137/266 (51%), Gaps = 15/266 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L   EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 106 YLKEIGKIPLLSSDEEIALAKRM-EAGDEEAKRRLAEANLRLVVSIAKKYVGRGMLFLDL 164

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 165 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 222

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R+   L         P++   IA  +N+SE  V  +  ++A +  SL   I   D   
Sbjct: 223 LIRVSRQLVQELGREPAPDE---IAHVMNISEERVREI-LKIAQEPVSLETPIGEED--D 276

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTL 255
           S   D++    D   Q   E    +  +  L   +  L PRE+++   R   E+    TL
Sbjct: 277 SHLGDFI---EDQDVQAPAEAAAFELLKEQLDDVLETLTPREKKVLTLRFGLEDGRSRTL 333

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           E +   F V+RER+RQIEA+A +K++
Sbjct: 334 EEVGQVFGVTRERIRQIEAKALRKLR 359


>gi|291459241|ref|ZP_06598631.1| RNA polymerase sigma factor RpoD [Oribacterium sp. oral taxon 078
           str. F0262]
 gi|291418495|gb|EFE92214.1| RNA polymerase sigma factor RpoD [Oribacterium sp. oral taxon 078
           str. F0262]
          Length = 398

 Score =  120 bits (302), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 92/279 (32%), Positives = 141/279 (50%), Gaps = 43/279 (15%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  IP+L  +EE  LA+R +E GD  A  RLV ++LRLVV IA  Y G G+ I ++
Sbjct: 130 YLKEIGTIPLLSPEEEKELARRSKE-GDPLARQRLVEANLRLVVSIAKRYTGRGMSILDL 188

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI---------GTT 129
           + EGN+GLM+ V+KF+P++GF+L+TY+ WWI+  +   +      +++           T
Sbjct: 189 IQEGNLGLMKGVEKFEPDKGFKLSTYATWWIRQGITRALADQSRTIRVPVHMVESINKVT 248

Query: 130 ANQKRLFFNL------RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
             Q+RL   L      + L   L  +T+  LK  +++ ++K+    E+ V        GD
Sbjct: 249 RTQRRLTLELGYEPSPKELAASLN-MTEEKLK--EILDVSKQPTSLETPV--------GD 297

Query: 184 ESLNALINSSDKNSSQW--QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           E         D N S +   + ++        V++ +E  K   N+  R   VL      
Sbjct: 298 E--------EDSNLSDFVADEKMISPEQNAANVMLREEIDKLLENLKDRERDVL------ 343

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           I       E   TLE +   F V+RERVRQIEA+A KK+
Sbjct: 344 IHRFGLHGEESHTLEEVGQMFGVTRERVRQIEAKALKKI 382


>gi|269123355|ref|YP_003305932.1| RNA polymerase, sigma 32 subunit, RpoH [Streptobacillus
           moniliformis DSM 12112]
 gi|268314681|gb|ACZ01055.1| RNA polymerase, sigma 32 subunit, RpoH [Streptobacillus
           moniliformis DSM 12112]
          Length = 280

 Score =  120 bits (302), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 83/283 (29%), Positives = 148/283 (52%), Gaps = 35/283 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +S YI +++   +L  +EE  L KR RE  D  A H L+ S+LRLVV  A    G G+P+
Sbjct: 16  ISLYISDLQNHELLTSEEEVELFKRVREENDEQAKHLLILSNLRLVVSEAKKLLGNGMPL 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++SEGN+GL++++ KFD  +G R +TY++WWIK  +++ I+     ++I +   ++  
Sbjct: 76  IDLISEGNLGLIKSIDKFDYTKGLRFSTYAVWWIKQTIKKSIVNLGRDIRIPSYKYEQLS 135

Query: 136 FFNLRRLKGHLQAITDN----------NLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
             N + ++ +     D            +KP +VV +  +      E+IS+N  +  +  
Sbjct: 136 KVN-KVIESYQNEFGDIPTAEYIAEVLGMKPSKVVLLQNEF----QEIISLNDAIGDNIF 190

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L  +I  S               D  E  +I  ++     N+  ++   LNPRE+ I E 
Sbjct: 191 LEDVIGQS---------------DNVEDDIIRNDQLSEMYNLFDKT---LNPREKEILEL 232

Query: 246 RR-LQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R  L  N + TL+ +  +  ++RERVRQIE +A  K+++++++
Sbjct: 233 RYGLANNKIHTLKEIGEKLSITRERVRQIEKKAITKLKKNLEE 275


>gi|283797719|ref|ZP_06346872.1| RNA polymerase sigma factor RpoD [Clostridium sp. M62/1]
 gi|291074616|gb|EFE11980.1| RNA polymerase sigma factor RpoD [Clostridium sp. M62/1]
 gi|295092057|emb|CBK78164.1| RNA polymerase, sigma 70 subunit, RpoD [Clostridium cf.
           saccharolyticum K10]
          Length = 372

 Score =  120 bits (302), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 90/268 (33%), Positives = 143/268 (53%), Gaps = 19/268 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  +EE  LAKR  E GD SA  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 106 YLKEIGKVPLLTPEEEIDLAKRM-EMGDESAKKRLAEANLRLVVSIAKRYVGRGMQFLDL 164

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT--TANQKRLF 136
           + EGN+GL++AV+K+D  +GF+ +TY+ WWI+ A+   I      ++I         RL 
Sbjct: 165 IQEGNLGLIKAVEKYDYSKGFKFSTYATWWIRQAITRSIADQARTIRIPVHMVETINRLI 224

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDK 195
              R+L   LQ +     +      +A+KL++    V  +  +++ D  SL   I   ++
Sbjct: 225 RTSRQL---LQELG----REPSAEELAEKLDMPVERVREI-MKISQDPVSLETPI--GEE 274

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PV 253
             S   D++  DH    QV ++          L   +  L  RE+++   R   ++  P 
Sbjct: 275 EDSHLGDFIQDDH---VQVPVDAATYTLLHEQLMEVLDTLTDREQKVLRLRFGLDDGRPR 331

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 332 TLEEVGREFNVTRERIRQIEAKALRKLR 359


>gi|104774138|ref|YP_619118.1| RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
 gi|103423219|emb|CAI98047.1| RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
 gi|325125917|gb|ADY85247.1| RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           bulgaricus 2038]
          Length = 378

 Score =  120 bits (302), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 92/274 (33%), Positives = 145/274 (52%), Gaps = 24/274 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG--LPIS 76
           Y+ EI K+P+L + EE  +AKR + +GD SA   L  ++LRLVV IA  Y  +   + I 
Sbjct: 107 YLKEIGKVPLLSRDEEVEVAKRIK-NGDESAKDELAAANLRLVVSIAKRYAKHNGKMGIL 165

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++ EGNIGLM+AV KFD  +GF+ +TY+ WWI+ A+   +     +++I     +    
Sbjct: 166 DLIQEGNIGLMKAVDKFDYSKGFKFSTYATWWIRQAITRALADQDRMIRIPVHVVES--I 223

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS-SDK 195
             + R++  LQ   D N KPE++ A   +      E+I+    +A ++  ++L  S  ++
Sbjct: 224 NKMNRIQRTLQQDLDRNAKPEELAAEMNEPLQKVQEIIT----VAKNQETDSLDKSVGEE 279

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS-----VLNPRERRIFEARRLQE 250
             SQ  D L      ++   I  EE      ML   +S      L  RE ++ + R   E
Sbjct: 280 GDSQLGDLL------EDNKAINPEEY-TAFEMLKDQLSGMMGEFLTDREAKVLKLRFGLE 332

Query: 251 N--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           N  P TLE +     V+RERVRQIE +A KK+++
Sbjct: 333 NYEPHTLEEVGRSLGVTRERVRQIEDKAVKKLKQ 366


>gi|188996015|ref|YP_001930266.1| RNA polymerase, sigma 32 subunit, RpoH [Sulfurihydrogenibium sp.
           YO3AOP1]
 gi|188931082|gb|ACD65712.1| RNA polymerase, sigma 32 subunit, RpoH [Sulfurihydrogenibium sp.
           YO3AOP1]
          Length = 285

 Score =  120 bits (302), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 87/270 (32%), Positives = 140/270 (51%), Gaps = 17/270 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+  I KIP+L K+EE  L K+ +E GD  A  +L+ S+LR V+ IA  Y GYG+P S++
Sbjct: 13  YLKSIYKIPLLSKEEEESLLKKVKE-GDKEALQKLIISNLRFVINIAKRYAGYGIPFSDL 71

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           +S GNIGL++A KKFD  RG R  +Y++WWI+ ++   I     ++K        R++  
Sbjct: 72  ISAGNIGLIEAAKKFDTSRGVRFISYAVWWIRQSIINTIQHESEIIK-----KPNRMYAY 126

Query: 139 LRRLKGHLQAITDN-NLKP--EQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSS 193
             ++      + D  N +P  +++++  K   +   + +  N  L      SL+  I  +
Sbjct: 127 ASKINNAYSYLKDTLNREPSIDEIISFLKTQGIKVEKEMVENYFLFKSVFLSLDTPIEGT 186

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QEN 251
           D +        VY+    E+ + E++ ++    +L      L+PRER I   R     E 
Sbjct: 187 DNDLVLEDTISVYNTLDIEKDINEEDLKRAIEALL----DTLSPRERTILIHRFGLNGEE 242

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           P TL  +     +SRERVRQIE R  KK++
Sbjct: 243 PKTLNEVGEMVGLSRERVRQIENRILKKLR 272


>gi|77359643|ref|YP_339218.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Pseudoalteromonas haloplanktis
           TAC125]
 gi|76874554|emb|CAI85775.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Pseudoalteromonas haloplanktis
           TAC125]
          Length = 324

 Score =  120 bits (302), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 88/273 (32%), Positives = 151/273 (55%), Gaps = 17/273 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE V   R    G  ++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 53  YLGEIGFSPLLSAEEE-VFFSRKSLKGCEASRKRMIESNLRLVVKIARRYNNRGLALLDL 111

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 112 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 170

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +   Q + D+    E++ A   K     ++++ +N ++A   S++  I    +N +
Sbjct: 171 LRTARELTQKL-DHEPTAEEIAACLDKPVEDVTKMLRLNEKIA---SVDMPIGG--ENDT 224

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRN-MLTRSMSVLNPRERRIFEARR---LQENPVT 254
              D +  D++    V  E E + N  N  +   +  LNP++R +  ARR   L   P T
Sbjct: 225 ALLDIIADDNN----VGPEGEVQNNDMNKHIVDWLGELNPKQREVL-ARRFGLLGYEPST 279

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           LE++  E  ++RERVRQI+  A +++++ +Q++
Sbjct: 280 LEDVGREIGLTRERVRQIQVEALRRLKDILQQE 312


>gi|56267933|gb|AAV85439.1| RpoS [Listonella anguillarum]
 gi|56267935|gb|AAV85440.1| RpoS [Listonella anguillarum]
 gi|167987243|gb|ACA13292.1| RpoS [Listonella anguillarum]
 gi|222101826|gb|ACM44037.1| RNA polymerase sigma factor [Listonella anguillarum]
          Length = 333

 Score =  120 bits (302), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 90/284 (31%), Positives = 147/284 (51%), Gaps = 39/284 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  QEE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 61  YLSEIGFSPLLTAQEEVLYARRSL-RGDEAARKRMIESNLRLVVKISRRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA---------GDESLNAL 189
           LR  +   Q + D+    E++     K     S+++ +N R++         GD++L  +
Sbjct: 179 LRTARELSQKL-DHEPTAEEIAFQLDKPVEDVSKMLRLNERISSVDTPIGGDGDKALLDI 237

Query: 190 I---NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           I   N+SD   S   D +                    R  L   +  LNP+++ +  AR
Sbjct: 238 IPDTNNSDPEISTQDDDI--------------------RESLLNWLDELNPKQKEVL-AR 276

Query: 247 R---LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 277 RFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVKQ 320


>gi|83747939|ref|ZP_00944970.1| RpoS [Ralstonia solanacearum UW551]
 gi|83725357|gb|EAP72504.1| RpoS [Ralstonia solanacearum UW551]
          Length = 381

 Score =  120 bits (301), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 87/276 (31%), Positives = 144/276 (52%), Gaps = 21/276 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++ I   P+L   EE   + R +  G+ +A   ++  +LRLVV IA GY   G+P+ ++
Sbjct: 112 YLNRISIKPLLTPAEELHFSTRAKA-GEFAARQVMIERNLRLVVSIAKGYLNRGVPLLDL 170

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM A++KFDPERGFR +TY+ WWI+ +++  I+     V++    +  R    
Sbjct: 171 IEEGNLGLMHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRELNQ 228

Query: 139 LRRLKGHLQ--AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
           + R K HL+   I   +   E +  +  K      +V+S+N      E   +L    D +
Sbjct: 229 VLRAKRHLEKSGIDGRDASIEDIAHLLGKTTEEVQDVLSLN------EHTTSLDTPFDLD 282

Query: 197 S-SQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--- 251
           S +   D+L  +H    +Q +  +E  +  ++ L R    L+ + R + E RR   N   
Sbjct: 283 SGTSLLDFLSDEHGASPDQEVAHRELSQLMKSWLAR----LSDKHRYVVE-RRFGLNHIE 337

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           P TLE L++E  ++RERVRQI+  A  K++     Q
Sbjct: 338 PATLEELAAEMGLTRERVRQIQQEALVKLKRHFASQ 373


>gi|294634769|ref|ZP_06713298.1| RNA polymerase sigma factor RpoS [Edwardsiella tarda ATCC 23685]
 gi|291091828|gb|EFE24389.1| RNA polymerase sigma factor RpoS [Edwardsiella tarda ATCC 23685]
          Length = 328

 Score =  120 bits (301), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 86/277 (31%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD ++  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 60  YLGEIGYAPLLTAEEEVFFARRAL-RGDEASRKRMIESNLRLVVKISRRYSNRGLALLDL 118

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 119 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 178

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 179 RTARELSHKLDHEPSAEEIAEQLEKPVHDVSRMLRLN---ERITSVDTPLGGDSEKALLD 235

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+N S  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 236 ILTDENESGPEDCTQNDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 284

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 285 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQGQ 319


>gi|168768834|ref|ZP_02793841.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4486]
 gi|189362139|gb|EDU80558.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4486]
          Length = 329

 Score =  120 bits (301), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 84/277 (30%), Positives = 143/277 (51%), Gaps = 26/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D D ++ ++    E   +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPED-TTQDDDMKQSIVKWLFENAKQREVLARRFGLLG------YEA----- 284

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 285 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 319


>gi|116514228|ref|YP_813134.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Lactobacillus delbrueckii subsp. bulgaricus ATCC
           BAA-365]
 gi|116093543|gb|ABJ58696.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Lactobacillus delbrueckii subsp. bulgaricus ATCC
           BAA-365]
          Length = 378

 Score =  120 bits (301), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 92/274 (33%), Positives = 145/274 (52%), Gaps = 24/274 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG--LPIS 76
           Y+ EI K+P+L + EE  +AKR + +GD SA   L  ++LRLVV IA  Y  +   + I 
Sbjct: 107 YLKEIGKVPLLSRDEEVEVAKRIK-NGDESAKDELAAANLRLVVSIAKRYAKHNGKMGIL 165

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++ EGNIGLM+AV KFD  +GF+ +TY+ WWI+ A+   +     +++I     +    
Sbjct: 166 DLIQEGNIGLMKAVDKFDYSKGFKFSTYATWWIRQAITRALADQDRMIRIPVHVVES--I 223

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS-SDK 195
             + R++  LQ   D N KPE++ A   +      E+I+    +A ++  ++L  S  ++
Sbjct: 224 NKMNRIQRTLQQDLDRNAKPEELAAEMNEPLQKVQEIIT----VAKNQETDSLDKSVGEE 279

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS-----VLNPRERRIFEARRLQE 250
             SQ  D L      ++   I  EE      ML   +S      L  RE ++ + R   E
Sbjct: 280 GDSQLGDLL------EDNKAINPEEY-TAFEMLKDQLSGMMGEFLTDREAKVLKLRFGLE 332

Query: 251 N--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           N  P TLE +     V+RERVRQIE +A KK+++
Sbjct: 333 NYEPHTLEEVGRSLGVTRERVRQIEDKAVKKLKQ 366


>gi|300724640|ref|YP_003713965.1| sigma S (sigma 38) factor of RNA polymerase [Xenorhabdus
           nematophila ATCC 19061]
 gi|6643920|gb|AAF20816.1|AF198628_2 RpoS [Xenorhabdus nematophila]
 gi|297631182|emb|CBJ91877.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Xenorhabdus nematophila ATCC
           19061]
          Length = 331

 Score =  120 bits (301), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 83/277 (29%), Positives = 144/277 (51%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD++A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 62  YLGEIGFSPLLTAEEEVLFARRAL-RGDIAARQRMIESNLRLVVKISRRYSNRGLALLDL 120

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 121 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 180

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H       ++ I +   KP + ++   +LN     + S++  ++GD     L 
Sbjct: 181 RTARELAHKLDHEPTVEEIAERLDKPVEDISRMMRLN---ERITSVDTPISGDSDKALLD 237

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             SD+N S  +  +  D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 238 ILSDENDSGPETTIQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEAE---- 287

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    +++++ +  Q
Sbjct: 288 ---TLEDVGREIGLTRERVRQIQVEGLRRLRDILHTQ 321


>gi|90407885|ref|ZP_01216060.1| putative RNA polymerase sigma-38 factor [Psychromonas sp. CNPT3]
 gi|90310976|gb|EAS39086.1| putative RNA polymerase sigma-38 factor [Psychromonas sp. CNPT3]
          Length = 313

 Score =  120 bits (301), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 91/274 (33%), Positives = 153/274 (55%), Gaps = 19/274 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  QEE   A+R    GD  A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 44  YLGEIGFSPLLTAQEEVYYARRSL-RGDDVARKRMIESNLRLVVKISRRYTNRGLSLLDL 102

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPE+GFR +TY+ WWI+  ++  I+     +++      K+L   
Sbjct: 103 VEEGNLGLIRAVEKFDPEKGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI-VKKLNVY 161

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE-SEVISMNCRLAGDESLNALI-NSSDKN 196
           LR  +    ++T      +  +A+A  +   + S+++ +N R++   S++  I N+SDK 
Sbjct: 162 LRTARELSHSLTHEPTAED--IALALDIPAKDVSKILKLNERIS---SVDIPIGNNSDK- 215

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR---LQENPV 253
                + L    D +E +   + E ++ +  +   +  LNP++R +  ARR   L     
Sbjct: 216 -----ELLDIIPDRKEIIPENELENEDMKLRIVEWLEDLNPKQREVL-ARRFGLLGYEAA 269

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           TLEN+  E  ++RERVRQI+  A K ++E + +Q
Sbjct: 270 TLENVGKEIGLTRERVRQIQVEALKCLREVLSQQ 303


>gi|2624188|emb|CAA05499.1| rpoS gene [Kluyvera cryocrescens]
          Length = 345

 Score =  120 bits (301), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 86/277 (31%), Positives = 141/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 76  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 134

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 135 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 194

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 195 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 251

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+N +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 252 ILADENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 300

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 301 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQGQ 335


>gi|238898782|ref|YP_002924464.1| RNA polymerase, sigma S (sigma 38) factor [Candidatus Hamiltonella
           defensa 5AT (Acyrthosiphon pisum)]
 gi|229466542|gb|ACQ68316.1| RNA polymerase, sigma S (sigma 38) factor [Candidatus Hamiltonella
           defensa 5AT (Acyrthosiphon pisum)]
          Length = 335

 Score =  120 bits (301), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 86/272 (31%), Positives = 147/272 (54%), Gaps = 15/272 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L   EE   A+R    GD S+  R++ S+LRLVVKI+  Y   GLP+ ++
Sbjct: 70  YLGEIGYSPLLTAAEEIYFARRVL-CGDESSRRRMIESNLRLVVKISRRYINRGLPLLDL 128

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 129 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 187

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +  L    D++  PE++     K     S ++ +N R++  ++  +  N+++K   
Sbjct: 188 LRAAR-ELSHKLDHDPSPEEIAEQLNKPVDYVSRMLRLNERISSVDT--SFGNAAEKG-- 242

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR---LQENPVTL 255
              D L  + D   +   + ++ K     + + +  L+ ++R +  ARR   L   P TL
Sbjct: 243 -LLDVLSDETDNDPENTTQNDDMKKS---VVKWLFELSTKQREVL-ARRFGLLGYEPATL 297

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +  E  ++RERVRQI+     +++E +Q Q
Sbjct: 298 EEVGCEIGLTRERVRQIQVEGLLRLKEMLQTQ 329


>gi|169830688|ref|YP_001716670.1| RNA polymerase sigma factor RpoD [Candidatus Desulforudis
           audaxviator MP104C]
 gi|169637532|gb|ACA59038.1| RNA polymerase, sigma 70 subunit, RpoD family [Candidatus
           Desulforudis audaxviator MP104C]
          Length = 360

 Score =  120 bits (301), Expect = 2e-25,   Method: Compositional matrix adjust.
 Identities = 87/265 (32%), Positives = 140/265 (52%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI +IP+L  +EE  LA+R  E GD  A  RL+ ++LRLVV IA  Y G G+   ++
Sbjct: 94  YLKEIGRIPLLTPEEEVSLARRM-EAGDDEAKRRLIEANLRLVVSIAKRYVGRGMLFLDL 152

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD ++G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 153 IQEGNLGLIKAVEKFDYKKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 210

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L         PE+   IA+++++SE +V  +        SL   I   ++  S
Sbjct: 211 LIRISRQLLQELGREPLPEE---IAREMDISEDKVREIQKIAQEPVSLETPIG--EEEDS 265

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D+ + D D Q     E+      R  L   +  L  RE+R+   R   ++    TLE
Sbjct: 266 HLGDF-IEDQDAQAPA--EEASFTLLREQLDDVLKTLTEREQRVLRLRFGLDDGRARTLE 322

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF V+RER+RQIEA+  +K++
Sbjct: 323 EVGQEFGVTRERIRQIEAKTLRKLR 347


>gi|238921111|ref|YP_002934626.1| RNA polymerase sigma factor RpoS [Edwardsiella ictaluri 93-146]
 gi|238870680|gb|ACR70391.1| RNA polymerase sigma factor RpoS, putative [Edwardsiella ictaluri
           93-146]
          Length = 328

 Score =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 86/277 (31%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD ++  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 60  YLSEIGYAPLLTAEEEVFFARRAL-RGDEASRKRMIESNLRLVVKISRRYSNRGLALLDL 118

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 119 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 178

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 179 RTARELAHKLDHEPSAEEIAERLEKPVHDVSRMLRLN---ERITSVDTPLGGDSEKALLD 235

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+N S  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 236 ILTDENESGPEDCTQNDDMKQSIVNWLFELNAKQREVLARRFGLLG------YEA----- 284

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 285 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQMQ 319


>gi|169824520|ref|YP_001692131.1| RNA polymerase sigma A factor [Finegoldia magna ATCC 29328]
 gi|302380672|ref|ZP_07269137.1| RNA polymerase sigma factor RpoD [Finegoldia magna ACS-171-V-Col3]
 gi|303233690|ref|ZP_07320344.1| RNA polymerase sigma factor RpoD [Finegoldia magna BVS033A4]
 gi|167831325|dbj|BAG08241.1| RNA polymerase sigma A factor [Finegoldia magna ATCC 29328]
 gi|302311615|gb|EFK93631.1| RNA polymerase sigma factor RpoD [Finegoldia magna ACS-171-V-Col3]
 gi|302495124|gb|EFL54876.1| RNA polymerase sigma factor RpoD [Finegoldia magna BVS033A4]
          Length = 388

 Score =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 88/278 (31%), Positives = 142/278 (51%), Gaps = 21/278 (7%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           +N +  +  Y+ EI KIP+L   EE  LA+   E+G   A  +L  ++LRLVV IA  Y 
Sbjct: 113 INVDDPVKMYLKEIGKIPLLSADEEVQLAQEM-ENGSKRAKKKLAEANLRLVVSIAKRYV 171

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GLM+AV KFD  RGF+ +TY+ WWI+ A+   I      ++I   
Sbjct: 172 GRGMSFLDLIQEGNLGLMKAVDKFDYTRGFKFSTYATWWIRQAITRAIADQARTIRIPV- 230

Query: 130 ANQKRLFFNLRRL-KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
                +   + RL +   Q + D    P     IAK++ +   +V     R    E ++ 
Sbjct: 231 ----HMVETINRLVRIERQLLQDLGRDPTN-EEIAKEMGIEVEKV--REVRKIAQEPVSL 283

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN---RRNMLTRSMSVLNPRERRIFEA 245
                ++  S   D++      ++   I  +E  N    R  L   ++ LN RER++   
Sbjct: 284 ETPIGEEEDSHLGDFI------EDDTAIAPDEAANFTMLREELEGILNTLNERERKVLAL 337

Query: 246 R--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   +   P TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 338 RFGLVDGTPRTLEEVGKDFDVTRERIRQIEAKALRKLK 375


>gi|145300341|ref|YP_001143182.1| RNA polymerase, sigma factor RpoS [Aeromonas salmonicida subsp.
           salmonicida A449]
 gi|142853113|gb|ABO91434.1| RNA polymerase, sigma factor RpoS [Aeromonas salmonicida subsp.
           salmonicida A449]
          Length = 327

 Score =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 93/274 (33%), Positives = 144/274 (52%), Gaps = 19/274 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD +A  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 57  YLGEIGFSPLLTAEEEVYYARRAL-RGDKAARKRMIESNLRLVVKIACRYNNRGLVLLDL 115

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 116 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 174

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +  L    D+    E    IA  L+ S  +V  M         LN  I S D    
Sbjct: 175 LRTAR-ELSHRLDHEPTAED---IAFALDRSVDDVNRML-------KLNEKITSVDTPIG 223

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNR--RNMLTRSMSVLNPRERRIFEARR---LQENPV 253
             +D  + D    E+ +  + E ++   R  +   +  LNP++R +  ARR   L   P 
Sbjct: 224 GDRDKALLDVLSDERGMGPELESQDDDMRASIVHWLEELNPKQREVL-ARRFGLLGYEPA 282

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           TLE++ SE  ++RERVRQI+    ++++E +  Q
Sbjct: 283 TLEDVGSEIGLTRERVRQIQVEGLRRLREILLGQ 316


>gi|229520830|ref|ZP_04410252.1| RNA polymerase sigma factor RpoS [Vibrio cholerae TM 11079-80]
 gi|229342063|gb|EEO07059.1| RNA polymerase sigma factor RpoS [Vibrio cholerae TM 11079-80]
          Length = 335

 Score =  120 bits (301), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 88/280 (31%), Positives = 149/280 (53%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 62  YLSEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 120

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 121 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 179

Query: 139 LRRLKGHLQAITDNNLKPEQVV--------AIAKKLNVSESEVISMNCRLAGDESLNALI 190
           +R  +  L    D+   PE++          + K L ++E  + S++  + GD    AL+
Sbjct: 180 VRTAR-ELSQRLDHEPTPEEIALELDRPVDDVTKMLRLNER-ISSVDTPIGGDGD-KALL 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
           +    + +   ++   D D +E +L          N L      LNP+++ +  ARR   
Sbjct: 237 DILPDSHNADPEFSTQDDDIRESLL----------NWLDE----LNPKQKEVL-ARRFGL 281

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 282 LGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVKQ 321


>gi|269140216|ref|YP_003296917.1| RNA polymerase sigma factor [Edwardsiella tarda EIB202]
 gi|228204742|gb|ACP74149.1| RNA polymerase sigma factor [Edwardsiella tarda]
 gi|267985877|gb|ACY85706.1| RNA polymerase sigma factor [Edwardsiella tarda EIB202]
 gi|304560047|gb|ADM42711.1| RNA polymerase sigma factor RpoS [Edwardsiella tarda FL6-60]
          Length = 328

 Score =  120 bits (300), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 86/277 (31%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD ++  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 60  YLGEIGYAPLLTAEEEVFFARRAL-RGDEASRKRMIESNLRLVVKISRRYSNRGLALLDL 118

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 119 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 178

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 179 RTARELSHKLDHEPSAEEIAERLEKPVHDVSRMLRLN---ERITSVDTPLGGDSEKALLD 235

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+N S  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 236 ILTDENESGPEDCTQNDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 284

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 285 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQMQ 319


>gi|37680992|ref|NP_935601.1| DNA-directed RNA polymerase, sigma subunit [Vibrio vulnificus
           YJ016]
 gi|37199742|dbj|BAC95572.1| DNA-directed RNA polymerase, sigma subunit [Vibrio vulnificus
           YJ016]
          Length = 330

 Score =  120 bits (300), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 90/280 (32%), Positives = 148/280 (52%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 58  YLGEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 116

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 117 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 175

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +   Q + D+    E++ A        ++K L ++E  + S++  + GD     L 
Sbjct: 176 LRTARELSQKL-DHEPTAEEIAAQLDIPVDDVSKMLRLNER-ISSVDTPIGGDGEKALLD 233

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
              D N+S   D  V   D            ++ R  L   +  LNP+++ +  ARR   
Sbjct: 234 IIPDANNS---DPEVSTQD------------EDMRVSLIHWLEELNPKQKEVL-ARRFGL 277

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 278 LGYEPSTLEEVGQEIGLTRERVRQIQVEGLRRLREVLIKQ 317


>gi|269925789|ref|YP_003322412.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
 gi|269789449|gb|ACZ41590.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
          Length = 363

 Score =  120 bits (300), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 87/269 (32%), Positives = 141/269 (52%), Gaps = 21/269 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LAKR  E GD  A  R V ++LRLVV IA  Y G GLP+ ++
Sbjct: 95  YLREIGSVPLLTPKEEVELAKRI-EKGDTEALQRFVLANLRLVVSIAKRYVGRGLPLLDL 153

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM+AV+KFD  +G R +TY+ WWI+ A+   I      +++    N++     
Sbjct: 154 IQEGNIGLMRAVQKFDWRKGHRFSTYATWWIRQAITRAIGDKSREIRLPAHINEE--LNR 211

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN-SSDKNS 197
           + R++  L    +    PE+   IA+K   S   V  +   L    SL+  +   +D   
Sbjct: 212 INRIRQQLSQTVNREPTPEE---IAEKAGTSPERVRELLGYLQQPVSLDTPVGEEADSTL 268

Query: 198 SQWQDWLVY--DHDGQEQVLIEKEERKNRRNMLTRSMS-VLNPRERRIFEARR--LQENP 252
            ++   +    + +  ++VL         +  + R +  VL PRE+R+ + R      + 
Sbjct: 269 GEFVPDVRANPEEEATDEVL---------KTEMDRVLDEVLTPREKRVLQLRYGLGDGHT 319

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +LE +  E  V+RERVRQ+E +A +K++
Sbjct: 320 YSLEKVGRELGVTRERVRQLEKQALEKLR 348


>gi|239814806|ref|YP_002943716.1| RNA polymerase, sigma 70 family subunit [Variovorax paradoxus S110]
 gi|239801383|gb|ACS18450.1| putative RNA polymerase, sigma 70 family subunit [Variovorax
           paradoxus S110]
          Length = 331

 Score =  120 bits (300), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 82/279 (29%), Positives = 138/279 (49%), Gaps = 13/279 (4%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           G   L+ Y+ ++R+  +   +EEY  A   R  GD +A   ++  +LRLVV IA  Y G 
Sbjct: 49  GADALTIYLRQVRRTELFTPEEEYQAACAARA-GDFAARQSMIEHNLRLVVNIAKAYLGR 107

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK--IGTT 129
           G+P+S+++ EGN+GLM A+ KF+PERGFR +TY+ WWI+ +++  +L     ++  +   
Sbjct: 108 GVPLSDLIEEGNLGLMHAITKFEPERGFRFSTYATWWIRQSVERAVLTQARAIRLPVHVV 167

Query: 130 ANQKRLFFNLRRLKGHLQAIT--DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              +++    R L+G  + +    + ++ E V A    L +    V  +        SL+
Sbjct: 168 RELQQVLRARRTLEGDAEFLAHRPDGVRVEDVAAF---LGLEVQAVAELLALAEAPRSLD 224

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           A     D+  +        D  G    +    E      +L + +  L+ RER + E R 
Sbjct: 225 AGDAHGDEGFTLADTVASEDEQGDPTDVTHTHEVA---RLLDQWVHALDAREREVLEGRY 281

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              +  P TLE LS    ++RERVRQI+  A  K++  +
Sbjct: 282 GLHDREPETLEVLSVRLGLTRERVRQIQNEALAKMRRQL 320


>gi|323495851|ref|ZP_08100919.1| RNA polymerase sigma factor RpoS [Vibrio sinaloensis DSM 21326]
 gi|323319067|gb|EGA72010.1| RNA polymerase sigma factor RpoS [Vibrio sinaloensis DSM 21326]
          Length = 331

 Score =  120 bits (300), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 88/285 (30%), Positives = 147/285 (51%), Gaps = 41/285 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 59  YLGEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 117

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 118 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 176

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNAL- 189
           LR  +   Q + D+    E++          ++K L ++E  + S++  + GD     L 
Sbjct: 177 LRTARELSQKL-DHEPTAEEIATKLDKPVDDVSKMLRLNE-RISSVDTPIGGDGEKALLD 234

Query: 190 ----INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
               +N+SD   S   D +                    +N L   +  LNP+++ +  A
Sbjct: 235 IIPDVNNSDPEVSTQDDDI--------------------KNSLIHWLDELNPKQKEVL-A 273

Query: 246 RR---LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           RR   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 274 RRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILIKQ 318


>gi|163802977|ref|ZP_02196864.1| protein-L-isoaspartate O-methyltransferase [Vibrio sp. AND4]
 gi|159173267|gb|EDP58095.1| protein-L-isoaspartate O-methyltransferase [Vibrio sp. AND4]
          Length = 328

 Score =  120 bits (300), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 89/280 (31%), Positives = 149/280 (53%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 56  YLGEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 114

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 115 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 173

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +   Q + D+    E++ A        ++K L ++E  + S++  + GD     L 
Sbjct: 174 LRTARELSQKL-DHEPTAEEIAAQLDIPVEDVSKMLRLNE-RISSVDTPIGGDGEKALLD 231

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
              D N+S   +    D D +  +++  EE              LNP+++ +  ARR   
Sbjct: 232 IIPDANNSD-PEVSTQDDDIKSSLILWLEE--------------LNPKQKEVL-ARRFGL 275

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 276 LGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLREILIKQ 315


>gi|147677242|ref|YP_001211457.1| RNA polymerase sigma factor RpoD [Pelotomaculum thermopropionicum
           SI]
 gi|146273339|dbj|BAF59088.1| DNA-directed RNA polymerase, sigma subunit [Pelotomaculum
           thermopropionicum SI]
          Length = 363

 Score =  120 bits (300), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 85/265 (32%), Positives = 144/265 (54%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 97  YLKEIGRVPLLTPEEEVELAKRM-EKGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 155

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 156 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 213

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R++  L      +  PE+   IAK++N++E +V  +  ++A  E ++      ++  S
Sbjct: 214 LVRVQRQLLQELGRDPSPEE---IAKEMNITEDKVREI-LKIA-QEPVSLETPIGEEEDS 268

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D+ + DH+ +     E+      R  L   +  L  RE+R+   R   ++    TLE
Sbjct: 269 HLGDF-IEDHEARAPA--EEASFTLLREQLDEVLKTLTEREQRVLRLRFGLDDGRARTLE 325

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  +F V+RER+RQIEA+  +K++
Sbjct: 326 EVGQKFGVTRERIRQIEAKTLRKLR 350


>gi|330828425|ref|YP_004391377.1| RNA polymerase sigma factor [Aeromonas veronii B565]
 gi|328803561|gb|AEB48760.1| RNA polymerase sigma factor [Aeromonas veronii B565]
          Length = 327

 Score =  120 bits (300), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 93/275 (33%), Positives = 146/275 (53%), Gaps = 21/275 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD +A  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 57  YLGEIGFSPLLTAEEEVYYARRAL-RGDKAARKRMIESNLRLVVKIARRYNNRGLVLLDL 115

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 116 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 174

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +  L    D+    E    IA  L+ S  +V  M         LN  I S D    
Sbjct: 175 LRTAR-ELSHRLDHEPTAED---IAFALDRSVDDVNRML-------KLNEKITSVDTPIG 223

Query: 199 QWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEARR---LQENP 252
             +D  + D    E+ +   +E +E  + R+ +   +  LNP++R +  ARR   L   P
Sbjct: 224 GDRDKALLDVLSDERGMGPELESQE-DDMRSSIVHWLEELNPKQREVL-ARRFGLLGYEP 281

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            TLE++ +E  ++RERVRQI+    ++++E +  Q
Sbjct: 282 ATLEDVGAEIGLTRERVRQIQVEGLRRLREILLSQ 316


>gi|297518365|ref|ZP_06936751.1| RNA polymerase sigma factor RpoS [Escherichia coli OP50]
          Length = 327

 Score =  120 bits (300), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 86/274 (31%), Positives = 141/274 (51%), Gaps = 22/274 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF- 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++     ++   + 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 -NLRRLKGH---LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
              R L  H    + I +   KP   V+   +LN     + S++  L GD     L   +
Sbjct: 180 RTARELSDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLDILA 236

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D+  +  +D    D   Q  V    E    +R +L R   +L       +EA        
Sbjct: 237 DEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA-------A 283

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 284 TLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 317


>gi|197286082|ref|YP_002151954.1| RNA polymerase sigma factor RpoS [Proteus mirabilis HI4320]
 gi|227356592|ref|ZP_03840979.1| RNA polymerase sigma factor RpoS [Proteus mirabilis ATCC 29906]
 gi|194683569|emb|CAR44440.1| RNA polymerase sigma factor RpoS [Proteus mirabilis HI4320]
 gi|227163348|gb|EEI48275.1| RNA polymerase sigma factor RpoS [Proteus mirabilis ATCC 29906]
          Length = 329

 Score =  120 bits (300), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 84/280 (30%), Positives = 147/280 (52%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 59  YLGEIGYSPLLSAEEEVFFARRAL-RGDIPSRQRMIESNLRLVVKISRRYTNRGLALLDL 117

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPE+GFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 118 IEEGNLGLIRAVEKFDPEKGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 177

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H       ++ I     KP  V  ++K L ++E  + S++  + GD     L 
Sbjct: 178 RTARELAHKLDHEPSVEEIAQTLDKP--VDDVSKMLRLNER-ISSVDTPIGGDSDKALLD 234

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
             SD+N            +G E  +    +  N +  + + +  LNP++R +  ARR   
Sbjct: 235 IISDEN-----------EEGPEATI----QNNNLKENIVKWLFELNPKQREVL-ARRFGL 278

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L     TLE++  E  ++RERVRQI+    +++++ +Q Q
Sbjct: 279 LGYEAETLEDVGREIGLTRERVRQIQVEGLRRLKDILQGQ 318


>gi|291522892|emb|CBK81185.1| RNA polymerase, sigma 70 subunit, RpoD [Coprococcus catus GD/7]
          Length = 366

 Score =  120 bits (300), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 88/281 (31%), Positives = 146/281 (51%), Gaps = 45/281 (16%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  + +L  +EE  L+KR  E GD  A  R++ ++LRLVV IA  Y G G+P  ++
Sbjct: 99  YLKEIGSVKLLSPEEEVELSKRA-EAGDQKAKDRIIEANLRLVVSIAKKYVGRGIPFLDL 157

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ ++   I      +++      T N+  
Sbjct: 158 IQEGNMGLIKAVEKFDYAKGFKFSTYATWWIRQSITRGIADKGKTIRVPVHMVETINK-- 215

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRLA--G 182
               LR  +  LQ +       E    IA++L  ++ +V          +SM+  +    
Sbjct: 216 ---TLRMSRNLLQELGREPTSEE----IAERLGTTKQKVEEALEISRDPVSMDSPIGEEE 268

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
           D SL   I   D+N       ++   D  +  +++KE        L  ++  L  RER++
Sbjct: 269 DSSLGDFI--EDEN-------MLSPSDSADYQMLKKE--------LVNALDTLTDRERKV 311

Query: 243 FEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            E R   +     TLE +  EF+V+RER+RQIEA+A +K++
Sbjct: 312 IELRFGLIDGQARTLEEVGKEFKVTRERIRQIEAKALRKLR 352


>gi|27364956|ref|NP_760484.1| RNA polymerase sigma factor RpoS [Vibrio vulnificus CMCP6]
 gi|320155343|ref|YP_004187722.1| RNA polymerase sigma factor RpoS [Vibrio vulnificus MO6-24/O]
 gi|27361102|gb|AAO10011.1| RNA polymerase sigma factor RpoS [Vibrio vulnificus CMCP6]
 gi|319930655|gb|ADV85519.1| RNA polymerase sigma factor RpoS [Vibrio vulnificus MO6-24/O]
          Length = 330

 Score =  120 bits (300), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 90/280 (32%), Positives = 148/280 (52%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 58  YLGEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 116

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 117 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 175

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +   Q + D+    E++ A        ++K L ++E  + S++  + GD     L 
Sbjct: 176 LRTARELSQKL-DHEPTAEEIAAQLDIPVDDVSKMLRLNER-ISSVDTPIGGDGEKALLD 233

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
              D N+S   D  V   D            ++ R  L   +  LNP+++ +  ARR   
Sbjct: 234 IIPDANNS---DPEVSTQD------------EDMRVSLIHWLEELNPKQKEVL-ARRFGL 277

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 278 LGYEPSTLEEVGQEIGLTRERVRQIQVEGLRRLREVLIKQ 317


>gi|82778108|ref|YP_404457.1| RNA polymerase sigma factor RpoS [Shigella dysenteriae Sd197]
 gi|81242256|gb|ABB62966.1| RNA polymerase, sigma S factor [Shigella dysenteriae Sd197]
          Length = 330

 Score =  120 bits (300), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 141/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E +++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIDLTRERVRQIQVEGLRRLREILQTQ 320


>gi|209695924|ref|YP_002263854.1| RNA polymerase sigma subunit RpoS (sigma-38) [Aliivibrio
           salmonicida LFI1238]
 gi|208009877|emb|CAQ80190.1| RNA polymerase sigma subunit RpoS (sigma-38) [Aliivibrio
           salmonicida LFI1238]
          Length = 321

 Score =  120 bits (300), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 96/276 (34%), Positives = 151/276 (54%), Gaps = 23/276 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE V   R    GD++A  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 49  YLSEIGFSPLLTAEEE-VYFSRLALKGDVAARSRMIESNLRLVVKIARRYNHRGLALLDL 107

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 108 VEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 166

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV---ISMNCRLAGDESLNALINSSDK 195
           LR  +   Q + D+   PE+   IA+KL+   S+V   + +N R+A  +S+ A    SDK
Sbjct: 167 LRAARELSQKL-DHEPTPEE---IAEKLDKPVSDVSRMLRLNERVASVDSMVA--GDSDK 220

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRN-MLTRSMSVLNPRERRIFEARR---LQEN 251
                   ++ D    +    E E + N  N  L   +  LNP+++ +  ARR   L   
Sbjct: 221 ALLD----IIPDTKHADP---ESETQTNDINESLVGWLGQLNPKQKEVV-ARRFGLLGYE 272

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +  E  ++RERVRQI+    ++++E + +Q
Sbjct: 273 ASTLEQVGREIGLTRERVRQIQVEGLRRLREIMTQQ 308


>gi|28200488|gb|AAO31615.1| RNA polymerase subunit sigma factor S [Vibrio vulnificus]
          Length = 343

 Score =  120 bits (300), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 90/280 (32%), Positives = 148/280 (52%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 58  YLGEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 116

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 117 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 175

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +   Q + D+    E++ A        ++K L ++E  + S++  + GD     L 
Sbjct: 176 LRTARELSQKL-DHEPTAEEIAAQLDIPVDDVSKMLRLNER-ISSVDTPIGGDGEKALLD 233

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
              D N+S   D  V   D            ++ R  L   +  LNP+++ +  ARR   
Sbjct: 234 IIPDANNS---DPEVSTQD------------EDMRVSLIHWLEELNPKQKEVL-ARRFGL 277

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 278 LGYEPSTLEEVGQEIGLTRERVRQIQVEGLRRLREVLIKQ 317


>gi|86146341|ref|ZP_01064665.1| DNA-directed RNA polymerase, sigma subunit [Vibrio sp. MED222]
 gi|85835820|gb|EAQ53954.1| DNA-directed RNA polymerase, sigma subunit [Vibrio sp. MED222]
          Length = 326

 Score =  119 bits (299), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 90/280 (32%), Positives = 148/280 (52%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 54  YLGEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 112

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 113 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 171

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +   Q + D+    E++ +        ++K L ++E  V S++  + GD     L 
Sbjct: 172 LRTARELSQKL-DHEPTAEEIASKLDKPVGDVSKMLRLNE-RVSSVDTPIGGDGEKALLD 229

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
              D N+S   D  V   D             + +N L   +  LNP+++ +  ARR   
Sbjct: 230 IIPDINNS---DPEVSTQDS------------DIKNSLIFWLDELNPKQKEVL-ARRFGL 273

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 274 LGYEPSTLEEVGREISLTRERVRQIQVEGLRRLREILIKQ 313


>gi|148978207|ref|ZP_01814737.1| DNA-directed RNA polymerase, sigma subunit [Vibrionales bacterium
           SWAT-3]
 gi|145962629|gb|EDK27905.1| DNA-directed RNA polymerase, sigma subunit [Vibrionales bacterium
           SWAT-3]
          Length = 326

 Score =  119 bits (299), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 90/280 (32%), Positives = 148/280 (52%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 54  YLGEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 112

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 113 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 171

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +   Q + D+    E++ +        ++K L ++E  V S++  + GD     L 
Sbjct: 172 LRTARELSQKL-DHEPTAEEIASKLDKPVGDVSKMLRLNE-RVSSVDTPIGGDGEKALLD 229

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
              D N+S   D  V   D             + +N L   +  LNP+++ +  ARR   
Sbjct: 230 IIPDINNS---DPEVSTQDS------------DIKNSLIFWLDELNPKQKEVL-ARRFGL 273

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 274 LGYEPSTLEEVGREISLTRERVRQIQVEGLRRLREILIKQ 313


>gi|332999494|gb|EGK19079.1| RNA polymerase sigma factor RpoS [Shigella flexneri VA-6]
          Length = 359

 Score =  119 bits (299), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 89/290 (30%), Positives = 146/290 (50%), Gaps = 26/290 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ-VELSSSPPLLQK 299
              TLE++  E  ++RERVRQI+    ++++E +Q Q  E  S+ P + K
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQGAEYRSAVPRVSK 333


>gi|84390122|ref|ZP_00991384.1| DNA-directed RNA polymerase, sigma subunit [Vibrio splendidus
           12B01]
 gi|84376776|gb|EAP93651.1| DNA-directed RNA polymerase, sigma subunit [Vibrio splendidus
           12B01]
          Length = 326

 Score =  119 bits (299), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 90/280 (32%), Positives = 148/280 (52%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 54  YLGEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 112

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 113 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 171

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +   Q + D+    E++ +        ++K L ++E  V S++  + GD     L 
Sbjct: 172 LRTARELSQKL-DHEPTAEEIASKLDKPVGDVSKMLRLNE-RVSSVDTPIGGDGEKALLD 229

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
              D N+S   D  V   D             + +N L   +  LNP+++ +  ARR   
Sbjct: 230 IIPDINNS---DPEVSTQDS------------DIKNSLIFWLDELNPKQKEVL-ARRFGL 273

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 274 LGYEPSTLEEVGREISLTRERVRQIQVEGLRRLREILIKQ 313


>gi|183600216|ref|ZP_02961709.1| hypothetical protein PROSTU_03759 [Providencia stuartii ATCC 25827]
 gi|188022512|gb|EDU60552.1| hypothetical protein PROSTU_03759 [Providencia stuartii ATCC 25827]
          Length = 328

 Score =  119 bits (299), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 88/284 (30%), Positives = 154/284 (54%), Gaps = 32/284 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 59  YLSEIGFSPLLTAEEEVFYARRAL-RGDVASRQRMIESNLRLVVKISRRYNNRGLALLDL 117

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPE+GFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 118 IEEGNLGLIRAVEKFDPEKGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI-VKELNIY 176

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +   Q + D+    E++          +++ L ++E  + S++  +AGD   + L 
Sbjct: 177 LRTARELAQKL-DHEPSAEEIAEQLDKPVEDVSRMLRLNER-ITSVDTPIAGDSEKSLLE 234

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
             SD+N S           G E  + +   ++N    + + +  LNP++R +  ARR   
Sbjct: 235 VLSDENES-----------GPEHTIQDNNLKEN----IVKWLFELNPKQREVL-ARRFGL 278

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           L     TLE +  E  ++RERVRQI+    +++++ +Q + ELS
Sbjct: 279 LGYEAETLEEVGREIGLTRERVRQIQVEGLRRLKDILQGE-ELS 321


>gi|282882556|ref|ZP_06291177.1| RNA polymerase sigma factor RpoD [Peptoniphilus lacrimalis 315-B]
 gi|281297698|gb|EFA90173.1| RNA polymerase sigma factor RpoD [Peptoniphilus lacrimalis 315-B]
          Length = 361

 Score =  119 bits (299), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 88/267 (32%), Positives = 140/267 (52%), Gaps = 17/267 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L   EE  +AKR  E+GD SA   L  ++LRLVV IA  Y G G+   ++
Sbjct: 95  YLKEIGKIPLLTGDEEVEIAKRM-ENGDNSAKKELAEANLRLVVSIAKRYVGRGMSFLDL 153

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 154 IQEGNLGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 211

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R++  L      +  PE+   IAK++N+   +V  +        SL   I   ++  S
Sbjct: 212 LVRVQRQLVQELGRDPLPEE---IAKEMNIEVEKVREIQKIAQEPVSLETPI--GEEEDS 266

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNR--RNMLTRSMSVLNPRERRIFEARRLQEN--PVT 254
              D++       E++L  ++       R  L+  +  L  RE+++   R   ++    T
Sbjct: 267 HLGDFI-----PDEEILSPQDAATFTLLREQLSTVLETLTDREKKVLTLRFGLDDGRART 321

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQ 281
           LE +  EF V+RER+RQIEA+A +K++
Sbjct: 322 LEEVGKEFAVTRERIRQIEAKAIRKLR 348


>gi|251788478|ref|YP_003003199.1| RNA polymerase sigma factor RpoS [Dickeya zeae Ech1591]
 gi|247537099|gb|ACT05720.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dickeya zeae
           Ech1591]
          Length = 330

 Score =  119 bits (299), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 90/281 (32%), Positives = 146/281 (51%), Gaps = 33/281 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GDLS+  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDLSSRRRMIESNLRLVVKIARRYNNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V    +LN     + S++  L GD S  AL+
Sbjct: 180 RTARELSHKLDHEPSAEEIAERLDKPVDDVNRMLRLN---ERITSVDTPLGGD-SEKALL 235

Query: 191 NSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-- 247
                      D L  + D G E    + + ++N    + + +  LN ++R +  ARR  
Sbjct: 236 -----------DILADEKDNGPEDTTQDNDMKQN----IVKWLFELNAKQREVL-ARRFG 279

Query: 248 -LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            L     TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 280 LLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQVQ 320


>gi|218710550|ref|YP_002418171.1| RNA polymerase sigma factor RpoS [Vibrio splendidus LGP32]
 gi|218323569|emb|CAV19793.1| RNA polymerase sigma factor rpoS (Sigma-38 factor) [Vibrio
           splendidus LGP32]
          Length = 335

 Score =  119 bits (299), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 90/280 (32%), Positives = 148/280 (52%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 63  YLGEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 180

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +   Q + D+    E++ +        ++K L ++E  V S++  + GD     L 
Sbjct: 181 LRTARELSQKL-DHEPTAEEIASKLDKPVGDVSKMLRLNE-RVSSVDTPIGGDGEKALLD 238

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
              D N+S   D  V   D             + +N L   +  LNP+++ +  ARR   
Sbjct: 239 IIPDINNS---DPEVSTQD------------SDIKNSLIFWLDELNPKQKEVL-ARRFGL 282

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 283 LGYEPSTLEEVGREISLTRERVRQIQVEGLRRLREILIKQ 322


>gi|283795510|ref|ZP_06344663.1| RNA polymerase sigma factor RpoD [Clostridium sp. M62/1]
 gi|291077175|gb|EFE14539.1| RNA polymerase sigma factor RpoD [Clostridium sp. M62/1]
          Length = 377

 Score =  119 bits (299), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 84/271 (30%), Positives = 141/271 (52%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LAKR  E GD+SA  RL+ ++LRLVV IA  Y G G+   ++
Sbjct: 112 YLKEIGTVPLLSAEEELRLAKRKAE-GDVSAKERLIEANLRLVVSIAKRYTGRGMSFLDL 170

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++ V+KFD  +G++L+TY+ WWI+ ++   +      +++        +   
Sbjct: 171 VQEGNLGLIKGVEKFDYTKGYKLSTYATWWIRQSVTRALADQARTIRVPV-----HMVET 225

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           + ++    + +T        V  ++  L++SE +V+ +        SL   I   D   S
Sbjct: 226 INKMSKMQRKLTLELGYEPSVAELSAALDMSEDKVMEIMQIAREPASLETPIGEED--DS 283

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++    DG         E    R  +   +  L  RER++   R   E+  P TLE
Sbjct: 284 NLGDFVA---DGNVVTPEGNVESVMLREHIDALLGDLKERERQVIVLRFGLEDGHPRTLE 340

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +  EF V+RER+RQIEA+A +K++  ++ +
Sbjct: 341 EVGKEFNVTRERIRQIEAKALRKLRNPVRSK 371


>gi|41855|emb|CAA78689.1| KatF [Escherichia coli]
          Length = 377

 Score =  119 bits (299), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 88/290 (30%), Positives = 145/290 (50%), Gaps = 26/290 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 73  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 131

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 132 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 191

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 192 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 248

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 249 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 297

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQKP 300
              TLE++  E  ++RERVRQI+    ++++E +Q Q  L+   P  + P
Sbjct: 298 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ-GLNIEAPFARNP 344


>gi|90577776|ref|ZP_01233587.1| hypothetical DNA-directed RNA polymerase, sigma subunit [Vibrio
           angustum S14]
 gi|90440862|gb|EAS66042.1| hypothetical DNA-directed RNA polymerase, sigma subunit [Vibrio
           angustum S14]
          Length = 291

 Score =  119 bits (299), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 92/300 (30%), Positives = 156/300 (52%), Gaps = 35/300 (11%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N+K       G+I +  Y+ EI + P+L K++E +L  R    GD  + + L+ S+LRL
Sbjct: 3   INKKEEQFSHGGDI-VHLYLKEISEKPLLTKEDE-ILYSRKSLCGDACSKNVLIESNLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  YRG  + IS+++ EGNIGLM AV+KFDPE+GFR +TY+ WWIK  ++  I   
Sbjct: 61  VVSIAKKYRGSSIHISDLIDEGNIGLMTAVEKFDPEKGFRFSTYATWWIKQTIERAIHNQ 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP--EQVVAIAKKLNVSESEVISMNC 178
              +++    +++        ++ H Q +  NN +P  E V  +  K     S  +S + 
Sbjct: 121 GRTIRLPVHVSKEINTI----IRTHKQLVKKNNQEPSTELVAEVLNKTLDDVSTTLSYDT 176

Query: 179 RLAG-DESLNALINS-------SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            +   D+S+ +   S       +D+NS++  D LV D      + I+K        +   
Sbjct: 177 PIVSYDQSITSEATSQSIAVLIADENSAK-PDELVDD------LAIQK--------ITAN 221

Query: 231 SMSVLNPRERRIFEARR---LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +  LN R++ I   RR   L     TL+ ++ E  ++RER+RQ++  +  K++ S+ + 
Sbjct: 222 VLKCLNNRDKEII-CRRFGLLGYEAQTLQEVAEEVGLTRERIRQLQVTSLAKLKNSLSRD 280


>gi|158320313|ref|YP_001512820.1| RpoD family RNA polymerase sigma factor [Alkaliphilus oremlandii
           OhILAs]
 gi|158140512|gb|ABW18824.1| RNA polymerase, sigma 70 subunit, RpoD family [Alkaliphilus
           oremlandii OhILAs]
          Length = 372

 Score =  119 bits (299), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 87/274 (31%), Positives = 148/274 (54%), Gaps = 13/274 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           VN +  +  Y+ EI K+P+L  +EE  LAKR  + GD  A  RLV ++LRLVV IA  Y 
Sbjct: 97  VNIDDPVRMYLKEIGKVPLLSAEEEIELAKRM-DAGDEEAKKRLVEANLRLVVSIAKRYV 155

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ WWI+ A+   I      ++I   
Sbjct: 156 GRGMLFLDLIQEGNLGLIKAVEKFDYKKGFKFSTYATWWIRQAITRAIADQARTIRI--P 213

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
            +       L R+   L      + KPE+   IA ++++SE +V  +  ++A  E ++  
Sbjct: 214 VHMVETINKLIRVSRQLLQELGRDPKPEE---IAAEMDLSEEKVREI-LKIA-QEPVSLE 268

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
               ++  S   D++  +              K +   L   +  L PRE+++   R   
Sbjct: 269 TPIGEEEDSHLGDFIPDEDAPAPAEAAAFSLLKEQ---LVEVLDTLTPREQKVLRLRFGL 325

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 326 DDGRARTLEEVGKKFDVTRERIRQIEAKALRKLR 359


>gi|225412271|ref|ZP_03761460.1| hypothetical protein CLOSTASPAR_05493 [Clostridium asparagiforme
           DSM 15981]
 gi|225042189|gb|EEG52435.1| hypothetical protein CLOSTASPAR_05493 [Clostridium asparagiforme
           DSM 15981]
          Length = 376

 Score =  119 bits (298), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 87/270 (32%), Positives = 138/270 (51%), Gaps = 23/270 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L+ + E  LA R  E GD  AA RL  S+LRLVV IA  Y G G+   ++
Sbjct: 109 YLKEIGKIPLLDMEAEIRLA-RQMEEGDREAAKRLAESNLRLVVSIAKRYVGRGMQFLDL 167

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT--TANQKRLF 136
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      N  RL 
Sbjct: 168 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRSIADQARTIRIPVHMVENINRLV 227

Query: 137 FNLRRL---KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
              R+L    G      +   + E  V    ++     E +S+   +  +E  +      
Sbjct: 228 RTSRQLLQELGREPTTEEIAARAEMSVERVSEILKMSQEPVSLETPIGEEEDSHLGDFIQ 287

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-- 251
           D N +  QD   Y        L+ ++        L   ++ L  RE+++   R   ++  
Sbjct: 288 DDNVTVPQDAATY-------TLLHEQ--------LMEVLTTLTEREQKVLRLRFGLDDGR 332

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           P TLE +  EF+V+RER+RQIEA+A +K++
Sbjct: 333 PRTLEEVGREFKVTRERIRQIEAKALRKLR 362


>gi|325686024|gb|EGD28082.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           delbrueckii subsp. lactis DSM 20072]
          Length = 378

 Score =  119 bits (298), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 91/268 (33%), Positives = 143/268 (53%), Gaps = 14/268 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG--LPIS 76
           Y+ EI K+P+L + EE  +AKR  E+GD SA   L  ++LRLVV IA  Y  +   + I 
Sbjct: 107 YLKEIGKVPLLSRDEEVEVAKRI-ENGDESAKDELAAANLRLVVSIAKRYAKHNGKMGIL 165

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++ EGNIGLM+AV KFD  +GF+ +TY+ WWI+ A+   +     +++I     +    
Sbjct: 166 DLIQEGNIGLMKAVDKFDYSKGFKFSTYATWWIRQAITRALADQDRMIRIPVHVVES--I 223

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
             + R++  LQ   D + KPE++ A   +      E+I++      D SL+  +   ++ 
Sbjct: 224 NKMNRIQRILQQDLDRDAKPEELAAEMNEPLQKVQEIITVAKNQETD-SLDKPV--GEEG 280

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS-VLNPRERRIFEARRLQEN--PV 253
            SQ  D L    D +     E    +  ++ L+  M   L  RE ++ + R   EN  P 
Sbjct: 281 DSQLGDLL---EDNKATNPEEYTAFEMLKDQLSSMMGEFLTNREAKVLKLRFGLENDEPH 337

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TLE +     V+RERVRQIEA+A KK++
Sbjct: 338 TLEEVGRSLGVTRERVRQIEAKAVKKLK 365


>gi|254794681|ref|YP_003079518.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           TW14359]
 gi|254594081|gb|ACT73442.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O157:H7
           str. TW14359]
          Length = 330

 Score =  119 bits (298), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWPFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|260893571|ref|YP_003239668.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ammonifex
           degensii KC4]
 gi|260865712|gb|ACX52818.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ammonifex
           degensii KC4]
          Length = 369

 Score =  119 bits (298), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 86/264 (32%), Positives = 137/264 (51%), Gaps = 13/264 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI +IP+L  +EE  LAKR  E GD  A  RL+ ++LRLVV IA  Y G G+   ++
Sbjct: 103 YLKEIGRIPLLTPEEEIELAKRM-EQGDEEAKRRLIEANLRLVVSIAKRYVGRGMLFLDL 161

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 162 IQEGNLGLIKAVEKFDWRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 219

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L         PE+   IA+K+ +S  +V  +        SL   I   ++  S
Sbjct: 220 LVRVSRQLVQELGREPTPEE---IAEKMGISPEKVREIMKVAQEPVSLETPIG--EEEDS 274

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++    D + Q   E+      R  L   +  L PRE+++   R   ++    TLE
Sbjct: 275 HLGDFI---EDQEAQAPAEEASYALLREQLNEVLQSLTPREQKVLRLRFGLDDGRARTLE 331

Query: 257 NLSSEFEVSRERVRQIEARAFKKV 280
            +  +F V+RER+RQIEA+  +K+
Sbjct: 332 EVGQKFGVTRERIRQIEAKTLRKL 355


>gi|6010724|gb|AAF01228.1|AF184097_1 mutant RpoS [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
          Length = 326

 Score =  119 bits (298), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 87/276 (31%), Positives = 139/276 (50%), Gaps = 27/276 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     + I    N   ++  
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIHIVKELN---VYLR 176

Query: 139 LRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
             R   H        + I +   KP   V+   +LN     + S++  L GD     L  
Sbjct: 177 TARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLDI 233

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
            +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA      
Sbjct: 234 LADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA------ 281

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 282 -ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 316


>gi|298244164|ref|ZP_06967970.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297551645|gb|EFH85510.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 316

 Score =  119 bits (298), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 86/265 (32%), Positives = 146/265 (55%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI +IP+L    E  LA+R  E+G+  A + L+ ++LRLVV IA  Y G GL + ++
Sbjct: 50  YLREISRIPLLSAVSESRLAERA-ENGEKEARNHLIEANLRLVVSIAKKYVGQGLSLEDL 108

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGL++AV KFD  +GFR +TY+ WWIK A+   IL    +V++     ++     
Sbjct: 109 IGEGNIGLIRAVTKFDYRKGFRFSTYATWWIKQAITRAILEGTRVVRLPVYIMEE--VMR 166

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           ++R    L         PE    I ++L ++   V  +        SL+A ++  ++N+ 
Sbjct: 167 VKRTTRQLYQELGREPTPE---IIGERLGMTAERVSELLIWAEKVFSLDAPLSEEEENT- 222

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLE 256
              D +    D +E+  +E  +++  R  + + +  L  RER++ E R   + ++  TLE
Sbjct: 223 -LGDII---EDVRERGPMEITDQQLLREEIRKVLGQLTVRERQVIELRFGLIDDHDHTLE 278

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  + +V+RERVRQIE RA +K++
Sbjct: 279 EVGKKLKVTRERVRQIEERAIRKLR 303


>gi|289805024|ref|ZP_06535653.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. AG3]
          Length = 145

 Score =  119 bits (298), Expect = 5e-25,   Method: Compositional matrix adjust.
 Identities = 53/95 (55%), Positives = 74/95 (77%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RL+ SHLR VV IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA
Sbjct: 40  RLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKA 99

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
            + EY+LR+W +VK+ TT  Q++LFFNLR+ K  L
Sbjct: 100 EIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRL 134


>gi|315652381|ref|ZP_07905370.1| RNA polymerase sigma factor rpoD [Eubacterium saburreum DSM 3986]
 gi|315485355|gb|EFU75748.1| RNA polymerase sigma factor rpoD [Eubacterium saburreum DSM 3986]
          Length = 410

 Score =  119 bits (298), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 89/285 (31%), Positives = 149/285 (52%), Gaps = 41/285 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L   EE  LAKR ++ GD  A  RL+ ++LRLVV IA  Y G G+   ++
Sbjct: 144 YLKEIGTVPLLTANEELELAKR-KQDGDEYAKQRLIEANLRLVVSIAKRYTGRGMSFLDL 202

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           V EGN+GL++ V+KFD  +GF+L+TY+ WWI+ ++   +      +++      T N   
Sbjct: 203 VQEGNLGLIKGVEKFDYTKGFKLSTYATWWIRQSVTRALADQARTIRVPVHMVETINKMS 262

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             Q++L   L    G+  ++T+          +A  L+++E +V+ +        SL   
Sbjct: 263 KMQRKLTLEL----GYEPSVTE----------LANALDMTEEKVMEIMQIAREPASLETP 308

Query: 190 INSSDKNSSQWQDWL----VYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           I   D   S   D++    V   +G  E V++        R  +   +  L  RER++  
Sbjct: 309 IGEED--DSNLGDFVADSNVLTPEGNVESVML--------REHIDTLLGDLKERERQVIV 358

Query: 245 ARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R   E+  P TLE +  EF+V+RER+RQIEA+A +K++  ++ +
Sbjct: 359 LRFGLEDGHPRTLEEVGKEFKVTRERIRQIEAKALRKLRNPVRSK 403


>gi|253988173|ref|YP_003039529.1| RNA polymerase sigma factor RpoS [Photorhabdus asymbiotica subsp.
           asymbiotica ATCC 43949]
 gi|253779623|emb|CAQ82784.1| rna polymerase sigma factor (sigma-38) [Photorhabdus asymbiotica]
          Length = 332

 Score =  119 bits (298), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 87/280 (31%), Positives = 149/280 (53%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 63  YLGEIGFSPLLTAEEEVFFARRAL-RGDVLARRRMIESNLRLVVKISRRYSNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI-VKELNVY 180

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +  L    D+   PE++          +++ L ++E  +IS++  ++ D     L 
Sbjct: 181 LRTAR-ELAHKLDHEPSPEEIAEQLDKPVDDVSRMLRLNER-IISVDTPISSDSDKALLD 238

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
             SD+N +           G E    E + +K+    + + +  LN ++R +  ARR   
Sbjct: 239 VLSDENET-----------GPEGTTQEDDMKKS----IVKWLFELNSKQREVL-ARRFGL 282

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L     TLE++  E  ++RERVRQI+    +++++ +Q Q
Sbjct: 283 LGYEAETLEDVGKEIGLTRERVRQIQVEGLRRLKDIMQTQ 322


>gi|289450258|ref|YP_003475183.1| RNA polymerase sigma factor RpoD [Clostridiales genomosp. BVAB3
           str. UPII9-5]
 gi|289184805|gb|ADC91230.1| RNA polymerase sigma factor RpoD [Clostridiales genomosp. BVAB3
           str. UPII9-5]
          Length = 353

 Score =  119 bits (298), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 92/293 (31%), Positives = 145/293 (49%), Gaps = 35/293 (11%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  + S ++N +  +  Y+ EI K+P+L  +EE  LA+  +E G   A  RL  ++LRL
Sbjct: 69  LNIDDSSDVMNVDDPVRMYLKEIGKVPLLNAEEEKDLARAMKE-GSQEAKDRLCEANLRL 127

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV KFD E+GF+ +TY+ WWI+ A+   I   
Sbjct: 128 VVSIAKRYVGRGMQFLDLIQEGNLGLIKAVDKFDYEKGFKFSTYATWWIRQAITRAIADQ 187

Query: 121 WSLVKIGT----TAN-----QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
              ++I      T N     Q++L   L R     +   +  + PE+V  I K   +S+ 
Sbjct: 188 ARTIRIPVHMVETINKLIRVQRQLLQELGREPEVEELAQEMGISPEKVREIQK---ISQ- 243

Query: 172 EVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E +S+   +  +E   L   I   D  S   Q                       +  L 
Sbjct: 244 EPVSLEKPIGEEEDSHLGDFIPDDDAPSPADQAAFTL-----------------LKEQLL 286

Query: 230 RSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             +S L PRE ++   R   ++    TLE +  EF V+RER+RQIEA+A +K+
Sbjct: 287 EILSGLTPREEKVLRLRFGLDDGRSRTLEEVGREFNVTRERIRQIEAKALRKM 339


>gi|91227834|ref|ZP_01262007.1| DNA-directed RNA polymerase, sigma subunit [Vibrio alginolyticus
           12G01]
 gi|269965239|ref|ZP_06179373.1| RNA polymerase sigma-38 factor [Vibrio alginolyticus 40B]
 gi|91188344|gb|EAS74640.1| DNA-directed RNA polymerase, sigma subunit [Vibrio alginolyticus
           12G01]
 gi|269830225|gb|EEZ84452.1| RNA polymerase sigma-38 factor [Vibrio alginolyticus 40B]
          Length = 328

 Score =  119 bits (298), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 89/280 (31%), Positives = 148/280 (52%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 56  YLGEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 114

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 115 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 173

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +   Q + D+    E++ A        ++K L ++E  + S++  + GD     L 
Sbjct: 174 LRTARELSQKL-DHEPTAEEIAAQLDIPVEDVSKMLRLNE-RISSVDTPIGGDGEKALLD 231

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
              D N+S   D  V   D             + ++ L   +  LNP+++ +  ARR   
Sbjct: 232 IIPDANNS---DPEVSTQD------------DDIKSSLIHWLEELNPKQKEVL-ARRFGL 275

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 276 LGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLREVLIKQ 315


>gi|329296050|ref|ZP_08253386.1| RNA polymerase sigma factor RpoS [Plautia stali symbiont]
          Length = 330

 Score =  119 bits (298), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 139/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVFFARRAL-RGDIPSRRRMIESNLRLVVKIARRYSNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|310779070|ref|YP_003967403.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ilyobacter
           polytropus DSM 2926]
 gi|309748393|gb|ADO83055.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ilyobacter
           polytropus DSM 2926]
          Length = 275

 Score =  119 bits (298), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 88/280 (31%), Positives = 145/280 (51%), Gaps = 25/280 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +S Y+ +IR   +L K+EE  L  R +  G   A H+L+ S+LRLVV IA  Y   G+  
Sbjct: 8   VSLYLEDIRSYNILTKEEELDLLIRAK-SGCEDAKHKLILSNLRLVVNIAKSYVHKGMGF 66

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN 131
            +++SEGN GLM A++KFD E+GFR +TY++WWIK ++ + I+     ++I +      N
Sbjct: 67  IDLISEGNFGLMHAIEKFDVEKGFRFSTYAVWWIKQSISKAIISKGREIRIPSYKHDLLN 126

Query: 132 QKRLFFNLRRLKGHLQA-ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
           +   F     +K  +   I D  L  E      +K+ +   +++S+N  +  D  L   I
Sbjct: 127 KVNKFIMEFVMKNSVYPNIEDIALGLEITPKKVQKVMLEFQDLLSLNASIGDDIFLEDTI 186

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQ 249
           +  D+ S             +++VL E       RN +   + VL PRE+ I + R  L 
Sbjct: 187 SQPDEESL------------EDEVLGEI-----GRNEINDILEVLKPREKEILKLRYGLD 229

Query: 250 ENPV-TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
              + TLE +   F ++RERVRQIE +  +K++    +++
Sbjct: 230 GYEIHTLEEIGKSFSITRERVRQIEKKTLQKLRNKFSEEL 269


>gi|291618595|ref|YP_003521337.1| RpoS [Pantoea ananatis LMG 20103]
 gi|291153625|gb|ADD78209.1| RpoS [Pantoea ananatis LMG 20103]
 gi|327394975|dbj|BAK12397.1| RNA polymerase sigma factor RpoS [Pantoea ananatis AJ13355]
          Length = 330

 Score =  119 bits (298), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVLFARRAL-RGDIPSRRRMIESNLRLVVKIARRYSNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQGQ 320


>gi|119944449|ref|YP_942129.1| RNA polymerase sigma-38 factor RpoS [Psychromonas ingrahamii 37]
 gi|119863053|gb|ABM02530.1| RNA polymerase sigma-38 factor RpoS [Psychromonas ingrahamii 37]
          Length = 322

 Score =  119 bits (298), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 92/276 (33%), Positives = 152/276 (55%), Gaps = 23/276 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD  +  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 53  YLGEIGFSPLLTAEEEVYYARRLL-RGDQVSRKRMIESNLRLVVKISRRYNNRGLSLLDL 111

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPE+GFR +TY+ WWI+  ++  I+     +++      K+L   
Sbjct: 112 VEEGNLGLIRAVEKFDPEKGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI-VKKLNVY 170

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV---ISMNCRLAGDESLNALI-NSSD 194
           LR  +     +T      E    IA+ L VS  EV   + +N R++   S++  I N+SD
Sbjct: 171 LRTARELTHTLTHEPTAEE----IAEVLGVSAKEVSKILKLNERIS---SVDIPIGNNSD 223

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR---LQEN 251
           K   +  D +    +   +  +++ + K R   + + +  LNP++R +  ARR   L   
Sbjct: 224 K---ELLDIIPDRKEASPENELQEADMKLR---IVKWLEDLNPKQREVL-ARRFGLLGYE 276

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLEN+  E  ++RERVRQI+  A K +++ + +Q
Sbjct: 277 AATLENVGKEIGLTRERVRQIQVEALKYLRDVLSEQ 312


>gi|300704422|ref|YP_003746025.1| RNA polymerase sigma factor rpos [Ralstonia solanacearum CFBP2957]
 gi|299072086|emb|CBJ43418.1| RNA polymerase sigma factor rpoS [Ralstonia solanacearum CFBP2957]
          Length = 376

 Score =  119 bits (297), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 86/276 (31%), Positives = 143/276 (51%), Gaps = 21/276 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++ I   P+L   EE   + R +  G+ +A   ++  +LRLVV IA GY   G+P+ ++
Sbjct: 107 YLNRISIKPLLTPAEELHFSTRAKA-GEFAARQVMIERNLRLVVSIAKGYLNRGVPLLDL 165

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM A++KFDPERGFR +TY+ WWI+ +++  I+     V++    +  R    
Sbjct: 166 IEEGNLGLMHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRELNQ 223

Query: 139 LRRLKGHLQ--AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
           + R K HL+   I   +   E +  +  K      +V+S+N      E   +L    D +
Sbjct: 224 VLRAKRHLEKSGIDGRDASIEDIAHLLGKTTDEVQDVLSLN------EHTTSLDTPFDLD 277

Query: 197 -SSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--- 251
             +   D+L  +H    +Q +  +E  +  ++ L R    L+ + R + E RR   N   
Sbjct: 278 PGTSLLDFLSDEHGASPDQEVAHRELSQLMKSWLAR----LSDKHRYVVE-RRFGLNHIE 332

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           P TLE L++E  ++RERVRQI+  A  K++     Q
Sbjct: 333 PATLEELAAEMGLTRERVRQIQQEALVKLKRHFASQ 368


>gi|145284374|gb|ABP51953.1| RpoS [Vibrio alginolyticus]
          Length = 328

 Score =  119 bits (297), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 89/280 (31%), Positives = 148/280 (52%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 56  YLGEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 114

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 115 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 173

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +   Q + D+    E++ A        ++K L ++E  + S++  + GD     L 
Sbjct: 174 LRTARELSQKL-DHEPTAEEIAAQLDIPVEDVSKMLRLNE-RISSVDTPIGGDGEKALLD 231

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
              D N+S   D  V   D             + ++ L   +  LNP+++ +  ARR   
Sbjct: 232 IIPDANNS---DPEVSTQD------------DDIKSSLIHWLEELNPKQKEVL-ARRFGL 275

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 276 LGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLREVLIKQ 315


>gi|260878982|ref|ZP_05891337.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus AN-5034]
 gi|260895455|ref|ZP_05903951.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus Peru-466]
 gi|157674653|gb|ABV60415.1| RpoS [Vibrio parahaemolyticus]
 gi|308088215|gb|EFO37910.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus Peru-466]
 gi|308090442|gb|EFO40137.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus AN-5034]
 gi|328474140|gb|EGF44945.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus 10329]
          Length = 329

 Score =  119 bits (297), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 89/280 (31%), Positives = 148/280 (52%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 57  YLGEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 115

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 116 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 174

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +   Q + D+    E++ A        ++K L ++E  + S++  + GD     L 
Sbjct: 175 LRTARELSQKL-DHEPTAEEIAAQLDIPVEDVSKMLRLNE-RISSVDTPIGGDGEKALLD 232

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
              D N+S   D  V   D             + ++ L   +  LNP+++ +  ARR   
Sbjct: 233 IIPDANNS---DPEVSTQD------------DDIKSSLIHWLEELNPKQKEVL-ARRFGL 276

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 277 LGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLREILIKQ 316


>gi|260902364|ref|ZP_05910759.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus AQ4037]
 gi|308110564|gb|EFO48104.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus AQ4037]
          Length = 329

 Score =  119 bits (297), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 89/280 (31%), Positives = 148/280 (52%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 57  YLGEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 115

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 116 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 174

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +   Q + D+    E++ A        ++K L ++E  + S++  + GD     L 
Sbjct: 175 LRTARELSQKL-DHEPTAEEIAAQLDIPVEDVSKMLRLNE-RISSVDTPIGGDGEKALLD 232

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
              D N+S   D  V   D             + ++ L   +  LNP+++ +  ARR   
Sbjct: 233 IIPDANNS---DPEVSTQD------------DDIKSSLIHWLEELNPKQKEVL-ARRFGL 276

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 277 LGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLREILIKQ 316


>gi|254230502|ref|ZP_04923875.1| RNA polymerase sigma factor RpoS [Vibrio sp. Ex25]
 gi|262393289|ref|YP_003285143.1| RNA polymerase sigma factor RpoS [Vibrio sp. Ex25]
 gi|151936974|gb|EDN55859.1| RNA polymerase sigma factor RpoS [Vibrio sp. Ex25]
 gi|262336883|gb|ACY50678.1| RNA polymerase sigma factor RpoS [Vibrio sp. Ex25]
          Length = 328

 Score =  119 bits (297), Expect = 6e-25,   Method: Compositional matrix adjust.
 Identities = 89/280 (31%), Positives = 148/280 (52%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 56  YLGEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 114

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 115 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 173

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +   Q + D+    E++ A        ++K L ++E  + S++  + GD     L 
Sbjct: 174 LRTARELSQKL-DHEPTAEEIAAQLDIPVEDVSKMLRLNE-RISSVDTPIGGDGEKALLD 231

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
              D N+S   D  V   D             + ++ L   +  LNP+++ +  ARR   
Sbjct: 232 IIPDANNS---DPEVSTQD------------DDIKSSLIHWLEELNPKQKEVL-ARRFGL 275

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 276 LGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLREVLIKQ 315


>gi|317049278|ref|YP_004116926.1| RpoD subfamily RNA polymerase sigma-70 factor [Pantoea sp. At-9b]
 gi|316950895|gb|ADU70370.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pantoea sp.
           At-9b]
          Length = 330

 Score =  119 bits (297), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 139/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVFFARRAL-RGDIPSRRRMIESNLRLVVKIARRYSNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|300718097|ref|YP_003742900.1| RNA polymerase sigma factor [Erwinia billingiae Eb661]
 gi|299063933|emb|CAX61053.1| RNA polymerase sigma factor [Erwinia billingiae Eb661]
          Length = 330

 Score =  119 bits (297), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVFFARRAL-RGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP + V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELTHKLDHEPSAEEIAEQLDKPVEDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQAQ 320


>gi|290476558|ref|YP_003469463.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Xenorhabdus bovienii SS-2004]
 gi|289175896|emb|CBJ82699.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Xenorhabdus bovienii SS-2004]
          Length = 331

 Score =  119 bits (297), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 83/277 (29%), Positives = 143/277 (51%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD++A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 62  YLGEIGFSPLLTAEEEVLFARRAL-RGDIAARQRMIESNLRLVVKISRRYSNRGLALLDL 120

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 121 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 180

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H       ++ I +   +P   V+   +LN     + S++  ++GD     L 
Sbjct: 181 RTARELAHKLDHEPSVEEIAEKLDRPIDDVSRMMRLN---ERITSVDTPISGDSDKALLD 237

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             SD+N S  +  +  D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 238 ILSDENDSGPETTIQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEAE---- 287

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    +++++ +  Q
Sbjct: 288 ---TLEDVGREIGLTRERVRQIQVEGLRRLRDILHTQ 321


>gi|225849654|ref|YP_002729888.1| RNA polymerase sigma-70 factor [Persephonella marina EX-H1]
 gi|225646208|gb|ACO04394.1| RNA polymerase sigma-70 factor [Persephonella marina EX-H1]
          Length = 281

 Score =  119 bits (297), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 84/268 (31%), Positives = 147/268 (54%), Gaps = 12/268 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ YI ++ + P+L  +EE  LAKR ++ GD  A  +LV  +LR VV +A  + G+G+P+
Sbjct: 11  LNLYIQKMAEHPLLTPEEEKELAKRAKK-GDKEALKKLVEGNLRFVVNVAKNFMGWGVPL 69

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           +++++ GN+GL++A K+FDPER  +  +Y++WWI+ A+ + I +    V+I     ++ L
Sbjct: 70  TDLIAAGNLGLIEAAKRFDPERDVKFISYAVWWIRQAIMQTIFQQTGAVRIPV---KESL 126

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           F +  ++K   + + +   +   +  IA+K+  S  +V +    +    SL+  +    +
Sbjct: 127 FIS--KVKETYEKLKEELKREPTIEEIAEKVGASPKKVKNALQVVRMPYSLDKPLGEEGE 184

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPV 253
           + +      V    G E V  E  E    + + T  ++VL+ RER I E R     E P 
Sbjct: 185 DLTLLD---VLSKKGTEDVEKEIVEESLHKELNT-LLNVLDERERAIIEHRFGLNGEEPK 240

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TL  +     +SRERVRQ+E RA KK++
Sbjct: 241 TLTEVGEILGISRERVRQLEQRALKKLR 268


>gi|2792523|gb|AAC38577.1| alternative RNA sigma factor RpoS [Ralstonia solanacearum]
          Length = 376

 Score =  119 bits (297), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 86/276 (31%), Positives = 143/276 (51%), Gaps = 21/276 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++ I   P+L   EE   + R +  G+ +A   ++  +LRLVV IA GY   G+P+ ++
Sbjct: 107 YLNRISIKPLLTPAEELHFSTRAKA-GEFAARQVMIERNLRLVVSIAKGYLNRGVPLLDL 165

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM A++KFDPERGFR +TY+ WWI+ +++  I+     V++    +  R    
Sbjct: 166 IEEGNLGLMHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRELNQ 223

Query: 139 LRRLKGHLQ--AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
           + R K HL+   I   +   E +  +  K      +V+S+N      E   +L    D +
Sbjct: 224 VLRAKRHLEKSGIDGRDASIEDIAHLLGKTTEEVQDVLSLN------EHTTSLDTPFDLD 277

Query: 197 -SSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--- 251
             +   D+L  +H    +Q +  +E  +  ++ L R    L+ + R + E RR   N   
Sbjct: 278 PGTSLLDFLSDEHGASPDQEVAHRELSQLMKSWLAR----LSDKHRYVVE-RRFGLNHIE 332

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           P TLE L++E  ++RERVRQI+  A  K++     Q
Sbjct: 333 PATLEELAAEMGLTRERVRQIQQEALVKLKRHFASQ 368


>gi|331003577|ref|ZP_08327074.1| hypothetical protein HMPREF0491_01936 [Lachnospiraceae oral taxon
           107 str. F0167]
 gi|330412418|gb|EGG91809.1| hypothetical protein HMPREF0491_01936 [Lachnospiraceae oral taxon
           107 str. F0167]
          Length = 409

 Score =  119 bits (297), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 89/285 (31%), Positives = 149/285 (52%), Gaps = 41/285 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L   EE  LAKR ++ GD  A  RL+ ++LRLVV IA  Y G G+   ++
Sbjct: 143 YLKEIGTVPLLTANEELELAKR-KQDGDEYAKQRLIEANLRLVVSIAKRYTGRGMSFLDL 201

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           V EGN+GL++ V+KFD  +GF+L+TY+ WWI+ ++   +      +++      T N   
Sbjct: 202 VQEGNLGLIKGVEKFDYTKGFKLSTYATWWIRQSVTRALADQARTIRVPVHMVETINKMS 261

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             Q++L   L    G+  ++T+          +A +L ++E +V+ +        SL   
Sbjct: 262 KMQRKLTLEL----GYEPSVTE----------LANELGMTEEKVMEIMQIAREPASLETP 307

Query: 190 INSSDKNSSQWQDWL----VYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           I   D   S   D++    V   +G  E V++        R  +   +  L  RER++  
Sbjct: 308 IGEED--DSNLGDFVADANVLTPEGNVESVML--------REHIDTLLGDLKERERQVIV 357

Query: 245 ARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R   E+  P TLE +  EF+V+RER+RQIEA+A +K++  ++ +
Sbjct: 358 LRFGLEDGHPRTLEEVGKEFKVTRERIRQIEAKALRKLRNPVRSK 402


>gi|308187918|ref|YP_003932049.1| RNA polymerase sigma factor rpoD [Pantoea vagans C9-1]
 gi|308058428|gb|ADO10600.1| RNA polymerase sigma factor rpoD [Pantoea vagans C9-1]
          Length = 330

 Score =  119 bits (297), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 139/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVFFARRAL-RGDIPSRRRMIESNLRLVVKIARRYSNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQAQ 320


>gi|12958587|gb|AAK09363.1|AF321124_1 RpoS [Vibrio harveyi]
          Length = 327

 Score =  119 bits (297), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 89/280 (31%), Positives = 147/280 (52%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 55  YLGEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 113

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 114 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 172

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +  L    D+    E++ A        ++K L ++E  + S++  + GD     L 
Sbjct: 173 LRTAR-ELSQKLDHEPTAEEIAAQLDIPVEDVSKMLRLNE-RISSVDTPIGGDGEKALLD 230

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
              D N+S   D  V   D             + ++ L   +  LNP+++ +  ARR   
Sbjct: 231 IIPDANNS---DPEVSTQD------------DDIKSSLIHWLEELNPKQKEVL-ARRFGL 274

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 275 LGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLREILIKQ 314


>gi|82545186|ref|YP_409133.1| RNA polymerase sigma factor RpoS [Shigella boydii Sb227]
 gi|81246597|gb|ABB67305.1| RNA polymerase sigma S factor [Shigella boydii Sb227]
 gi|332092174|gb|EGI97252.1| RNA polymerase sigma factor RpoS [Shigella boydii 3594-74]
          Length = 331

 Score =  119 bits (297), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 139/277 (50%), Gaps = 24/277 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE V   R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 120

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 121 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 180

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 181 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 237

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 238 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 286

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 287 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 321


>gi|218133123|ref|ZP_03461927.1| hypothetical protein BACPEC_00985 [Bacteroides pectinophilus ATCC
           43243]
 gi|217991996|gb|EEC58000.1| hypothetical protein BACPEC_00985 [Bacteroides pectinophilus ATCC
           43243]
          Length = 448

 Score =  119 bits (297), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 87/267 (32%), Positives = 140/267 (52%), Gaps = 17/267 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  +EE  LAKR  E+GD+ A +RL  ++LRLVV IA  Y G G+   ++
Sbjct: 182 YLKEIGKVPLLSAEEEIELAKRM-ENGDVEAKNRLAEANLRLVVSIAKRYVGRGMLFLDL 240

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 241 IQEGNLGLIKAVDKFDFRKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 298

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L         PE+   IAK++++    V  +        SL   I   ++  S
Sbjct: 299 LLRVSRQLLQELGREPTPEE---IAKEMDIPVERVREIQKISQEPVSLETPI--GEEEDS 353

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNR--RNMLTRSMSVLNPRERRIFEARRLQEN--PVT 254
              D++  D+     V +  EE  +   +  L   +  L  RE+++   R   ++    T
Sbjct: 354 HLGDFIQDDN-----VPVPAEEAASTILKEQLVEVLGTLTEREQKVLRLRFGLDDGRART 408

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQ 281
           LE +  EF V+RER+RQIEA+A +K++
Sbjct: 409 LEEVGREFNVTRERIRQIEAKALRKLR 435


>gi|160945279|ref|ZP_02092505.1| hypothetical protein FAEPRAM212_02798 [Faecalibacterium prausnitzii
           M21/2]
 gi|158443010|gb|EDP20015.1| hypothetical protein FAEPRAM212_02798 [Faecalibacterium prausnitzii
           M21/2]
 gi|295105509|emb|CBL03053.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii SL3/3]
          Length = 360

 Score =  119 bits (297), Expect = 7e-25,   Method: Compositional matrix adjust.
 Identities = 88/265 (33%), Positives = 142/265 (53%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   +E  LAK  R   D  A   L  ++LRLVV +A  Y G GLP  ++
Sbjct: 93  YLKEIGRVPLLTAGQEMALAKAARAG-DADARRALSEANLRLVVSVAKRYAGRGLPFLDL 151

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+A +KF+PERGF+ +TY+ WWI+ ++   I      ++I        L  +
Sbjct: 152 IQEGNLGLMKAAEKFEPERGFKFSTYATWWIRQSITRAIADQGRTIRIPV-----HLVES 206

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           + R+K     +   N +   V  IA  L++   +V  +  +L+  E ++      ++  +
Sbjct: 207 INRVKKTAGDLLHKNGREPTVEEIAAALDMEPDKVREL-LQLS-QEPISLETPVGEEEDA 264

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
             +D+ + D D    V +++  R+  R  L   +  L PRE R+   R   E+    TLE
Sbjct: 265 HLEDF-IQDEDA--GVPVDEAGRQLLRRELLHVLKSLTPREERVITLRFGLEDGRARTLE 321

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            L  EF V+RERVRQIEA+A +K++
Sbjct: 322 ELGKEFNVTRERVRQIEAKALRKLR 346


>gi|197335185|ref|YP_002156867.1| RNA polymerase sigma factor RpoS [Vibrio fischeri MJ11]
 gi|197316675|gb|ACH66122.1| RNA polymerase sigma factor RpoS [Vibrio fischeri MJ11]
          Length = 321

 Score =  119 bits (297), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 97/276 (35%), Positives = 149/276 (53%), Gaps = 23/276 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE V   R    GD +A  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 49  YLGEIGFSPLLTAEEE-VYFSRLALKGDEAARARMIESNLRLVVKIARRYNHRGLALLDL 107

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 108 VEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 166

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV---ISMNCRLAGDESLNALINSSDK 195
           LR  +   Q + D+   PE+   IA+KL+   S+V   + +N R+A  +S+ A    SDK
Sbjct: 167 LRAARELSQKL-DHEPTPEE---IAEKLDKPVSDVSRMLRLNERVASVDSMVA--GESDK 220

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARR---LQEN 251
                 D L    +       E E +K+  N  L   +  LNP+++ +  ARR   L   
Sbjct: 221 ---ALLDILPDTKNSDP----ESETQKDDINTSLVGWLGQLNPKQKEVV-ARRFGLLGYE 272

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +  E  ++RERVRQI+    ++++E +  Q
Sbjct: 273 AATLEQVGVEIGLTRERVRQIQVEGLRRLREIMTNQ 308


>gi|195938492|ref|ZP_03083874.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4024]
          Length = 279

 Score =  119 bits (297), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 10  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 68

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 69  IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 128

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 129 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 185

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 186 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 234

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 235 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 269


>gi|153835750|ref|ZP_01988417.1| RNA polymerase sigma factor RpoS [Vibrio harveyi HY01]
 gi|156975773|ref|YP_001446680.1| hypothetical protein VIBHAR_03517 [Vibrio harveyi ATCC BAA-1116]
 gi|148867581|gb|EDL66895.1| RNA polymerase sigma factor RpoS [Vibrio harveyi HY01]
 gi|156527367|gb|ABU72453.1| hypothetical protein VIBHAR_03517 [Vibrio harveyi ATCC BAA-1116]
          Length = 328

 Score =  119 bits (297), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 89/280 (31%), Positives = 148/280 (52%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 56  YLGEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 114

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 115 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 173

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +   Q + D+    E++ A        ++K L ++E  + S++  + GD     L 
Sbjct: 174 LRTARELSQKL-DHEPTAEEIAAQLDIPVEDVSKMLRLNE-RISSVDTPIGGDGEKALLD 231

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
              D N+S   D  V   D             + ++ L   +  LNP+++ +  ARR   
Sbjct: 232 IIPDANNS---DPEVSTQD------------DDIKSSLIHWLEELNPKQKEVL-ARRFGL 275

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 276 LGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLREILIKQ 315


>gi|254444043|ref|ZP_05057519.1| RNA polymerase sigma factor, sigma-70 family [Verrucomicrobiae
           bacterium DG1235]
 gi|198258351|gb|EDY82659.1| RNA polymerase sigma factor, sigma-70 family [Verrucomicrobiae
           bacterium DG1235]
          Length = 377

 Score =  119 bits (297), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 80/265 (30%), Positives = 143/265 (53%), Gaps = 12/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI +I +L   +E  LA+R  + G+  A   ++ S+LRLVVKIA  Y+ +GLP+ ++
Sbjct: 84  YLQEIGRIDLLTPAQEVTLARRI-QAGEKEARDLMIKSNLRLVVKIAHDYKDFGLPVLDL 142

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           +SEGNIGL++AV++FDP++G +L+TY+ WWIK +++  +      +++        L   
Sbjct: 143 ISEGNIGLVKAVERFDPDKGGKLSTYAAWWIKQSIKRALANQSKTIRLPV-----HLVDK 197

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           + R++     +T+   +      +A+ L +  ++V  +        SLNA +   D NS+
Sbjct: 198 ISRMRKMALMLTEELGREPTDQELAEMLEMPVNKVSHLKSVSVRPTSLNAPV-GEDGNST 256

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
           ++ + +    D       E    K+ R  L   +  L  RE  I   R     ++P+TLE
Sbjct: 257 EFGEIV---GDDNAPTPYENLHEKSLRGDLHEMIDGLEDREAEIIRLRFGLNGDSPLTLE 313

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +   F+++RERVRQ++  A  K++
Sbjct: 314 EVGQVFDITRERVRQLQNIALSKMR 338


>gi|89109528|ref|AP_003308.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli str.
           K-12 substr. W3110]
 gi|218547743|ref|YP_002381534.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia fergusonii
           ATCC 35469]
 gi|85675562|dbj|BAE76818.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli str.
           K12 substr. W3110]
 gi|218355284|emb|CAQ87891.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia fergusonii
           ATCC 35469]
 gi|320645931|gb|EFX14912.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H- str.
           493-89]
          Length = 291

 Score =  119 bits (297), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 22  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 80

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 81  IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 140

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 141 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 197

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 198 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 246

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 247 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 281


>gi|311278284|ref|YP_003940515.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Enterobacter
           cloacae SCF1]
 gi|308747479|gb|ADO47231.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Enterobacter
           cloacae SCF1]
          Length = 330

 Score =  118 bits (296), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYSNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQGQ 320


>gi|261250229|ref|ZP_05942805.1| RNA polymerase sigma factor RpoS [Vibrio orientalis CIP 102891]
 gi|260939345|gb|EEX95331.1| RNA polymerase sigma factor RpoS [Vibrio orientalis CIP 102891]
          Length = 323

 Score =  118 bits (296), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 88/285 (30%), Positives = 147/285 (51%), Gaps = 41/285 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 51  YLGEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 109

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 110 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 168

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNAL- 189
           LR  +   Q + D+    E++          ++K L ++E  + S++  + GD     L 
Sbjct: 169 LRTARELSQKL-DHEPTAEEIATQLDKPVDDVSKMLRLNER-ISSVDTPIGGDGEKALLD 226

Query: 190 ----INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
               IN+SD   S   D +                    ++ L   +  LNP+++ +  A
Sbjct: 227 IIPDINNSDPEVSTQDDDI--------------------KSSLIHWLDELNPKQKEVL-A 265

Query: 246 RR---LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           RR   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 266 RRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILIKQ 310


>gi|2961260|emb|CAA73683.1| rpoS [Enterobacter cloacae]
          Length = 346

 Score =  118 bits (296), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 77  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 135

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 136 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 195

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 196 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 252

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 253 ILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 301

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 302 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQGQ 336


>gi|23306706|gb|AAN15274.1| N-terminal truncated RNA polymerase sigma factor S [Escherichia
           coli]
 gi|23306708|gb|AAN15270.1| N-terminal truncated RNA polymerase sigma factor S [Escherichia
           coli]
 gi|23306710|gb|AAN15272.1| N-terminal truncated RNA polymerase sigma factor S [Escherichia
           coli]
          Length = 277

 Score =  118 bits (296), Expect = 8e-25,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 8   YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 66

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 67  IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 126

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 127 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 183

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 184 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 232

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 233 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 267


>gi|163749990|ref|ZP_02157234.1| RNA polymerase sigma-38 factor [Shewanella benthica KT99]
 gi|161330264|gb|EDQ01245.1| RNA polymerase sigma-38 factor [Shewanella benthica KT99]
          Length = 323

 Score =  118 bits (296), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 86/280 (30%), Positives = 149/280 (53%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   +++  + G   + +R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 54  YLGEIGFSPLLSAEEEVYFSRKSLK-GCGKSRNRMIESNLRLVVKIARRYNNRGLALLDL 112

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 113 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 171

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +  L    D+    E++ A        +++ L ++E  + S++  L GD    AL+
Sbjct: 172 LRTAR-ELAHKLDHEPTAEEIAAKLDLPCSDVSRMLKLNE-RITSVDTPLGGDND-KALL 228

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
           +    + +   D+ V + D  + V+              + +  LN ++R +  ARR   
Sbjct: 229 DVLAADDNVGPDYKVQNEDMSKSVV--------------KWLDELNTKQREVL-ARRFGL 273

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   P TLEN+  E  ++RERVRQI+  A K++++ +  Q
Sbjct: 274 LGYEPSTLENVGKEIGLTRERVRQIQVEALKRLKDLLGAQ 313


>gi|146312853|ref|YP_001177927.1| RNA polymerase sigma factor RpoS [Enterobacter sp. 638]
 gi|145319729|gb|ABP61876.1| RNA polymerase, sigma 38 subunit, RpoS [Enterobacter sp. 638]
          Length = 330

 Score =  118 bits (296), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYSNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQGQ 320


>gi|298209056|ref|YP_003717235.1| RNA polymerase sigma factor rpoD (Sigma-A) [Croceibacter atlanticus
           HTCC2559]
 gi|83848983|gb|EAP86852.1| RNA polymerase sigma factor rpoD (Sigma-A) [Croceibacter atlanticus
           HTCC2559]
          Length = 287

 Score =  118 bits (296), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 85/287 (29%), Positives = 157/287 (54%), Gaps = 37/287 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ ++  +EE  LA+R R  GD  A  +L  ++LR VV ++  Y+  GL +
Sbjct: 18  LDKYLQEIGKVDLITAEEEVELAQRIR-AGDNRALEKLTKANLRFVVSVSKQYQNQGLTL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
            ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++      Q  I+R   L KIG+ 
Sbjct: 77  PDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVR-LPLNKIGSI 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA- 188
               +++  L +          +N +P     IA++L ++ SEV           S++A 
Sbjct: 136 NKINKMYAYLEQ----------SNQRPPTPEEIAQELEMTISEVKESLKNSGRHLSMDAP 185

Query: 189 LINSSDKNSSQWQDWLVYDH--DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           L++  D N     D L +    + ++ +L+E     + +  + R++  L PRE  +    
Sbjct: 186 LVDGEDSN---LYDVLKFGESPNPEKDLLVE-----SLQTEIDRALETLTPREADVI--- 234

Query: 247 RL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RL     Q+ P+TLE +   FE++RERVRQI+ +A ++++ + + ++
Sbjct: 235 RLYFGLGQQQPLTLEEIGETFELTRERVRQIKEKATRRLKHTSRSKI 281


>gi|307128696|ref|YP_003880726.1| RNA polymerase sigma factor rpoD [Candidatus Sulcia muelleri CARI]
 gi|306483158|gb|ADM90028.1| RNA polymerase sigma factor rpoD [Candidatus Sulcia muelleri CARI]
          Length = 288

 Score =  118 bits (296), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 81/276 (29%), Positives = 146/276 (52%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y++EI KIP+L  +EE   AK  R+  ++ A + L+ ++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLYEIGKIPLLNNEEEIQFAKFARKTYNIKAINFLIKANLRFVVSVAKQYQNQGLN 76

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           +S++++EGN+GL++ + +FD  +GF+  +YS+WWI+ ++ + I      V+  T    K 
Sbjct: 77  LSDLINEGNLGLIKGIFRFDERKGFKCISYSVWWIRQSILQAIADKSRCVRCPTN---KL 133

Query: 135 LFFN-LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            F+N + +    L+ I      P  +  I + LN +E E+           SL+A I   
Sbjct: 134 AFYNKVNKKYSELEQIYQ---IPPSIKQIGEYLNSNEKEIEEALKNSVKHTSLDAPIIEG 190

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENP 252
           +  +S   D + YD      + +EKE  K     + R +  L+ +E +I      L+ + 
Sbjct: 191 E--NSNLYDIIKYDESPHPDLDLEKESLKKD---IKRLLDTLSEKEAQIITLHYGLESST 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           + LE +S    ++RER RQIE    +++++S +K +
Sbjct: 246 INLEEISFLLNLTRERCRQIEIYGLRRLKQSSRKNI 281


>gi|27735253|sp|P35540|RPOS_SHIFL RecName: Full=RNA polymerase sigma factor rpoS
 gi|332753598|gb|EGJ83977.1| RNA polymerase sigma factor RpoS [Shigella flexneri K-671]
 gi|333000355|gb|EGK19938.1| RNA polymerase sigma factor RpoS [Shigella flexneri K-218]
 gi|333015759|gb|EGK35097.1| RNA polymerase sigma factor RpoS [Shigella flexneri K-304]
          Length = 330

 Score =  118 bits (296), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|149278388|ref|ZP_01884525.1| RNA polymerase sigma-70 factor [Pedobacter sp. BAL39]
 gi|255532892|ref|YP_003093264.1| sigma-70 family RNA polymerase sigma factor [Pedobacter heparinus
           DSM 2366]
 gi|149230758|gb|EDM36140.1| RNA polymerase sigma-70 factor [Pedobacter sp. BAL39]
 gi|255345876|gb|ACU05202.1| RNA polymerase sigma factor, sigma-70 family [Pedobacter heparinus
           DSM 2366]
          Length = 286

 Score =  118 bits (296), Expect = 9e-25,   Method: Compositional matrix adjust.
 Identities = 80/275 (29%), Positives = 151/275 (54%), Gaps = 14/275 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+HEI K+ ++  +EE +LA++ RE GD +A  RL  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLHEIGKVDLITAEEEVILARKIRE-GDQAALERLTKTNLRFVVSVAKQYQNQGLTL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A K+FD  +GF+  +Y++WWI+ ++ + I     +V++    NQ   
Sbjct: 77  GDLINEGNLGLIKAAKRFDETKGFKFISYAVWWIRQSILQAIAEQSRIVRL--PLNQVGS 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + +    L+   +    PE++  I +      S+ +S + R     S++A     ++
Sbjct: 135 LSKISKAFSKLEQEYEREPSPEELADILETTVDKISDTLSNSGRHV---SMDAPFVQGEE 191

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA-RRLQEN-PV 253
           N+    D L       +  LI     ++    + RS+S L  RER I      L  N P+
Sbjct: 192 NT--LLDVLENHEPNTDSSLI----NESLSEEIKRSLSTLTEREREIIVLFFGLSTNHPL 245

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +LE +  +F ++RERVRQI+ +A ++++ + + ++
Sbjct: 246 SLEEIGEKFNLTRERVRQIKDKALQRLRHTSRSKI 280


>gi|188534815|ref|YP_001908612.1| RNA polymerase sigma factor RpoS [Erwinia tasmaniensis Et1/99]
 gi|188029857|emb|CAO97741.1| RNA polymerase sigma factor RpoS [Erwinia tasmaniensis Et1/99]
          Length = 330

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 139/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVFFARRAL-RGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEKLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQGQ 320


>gi|312888769|ref|ZP_07748333.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Mucilaginibacter
           paludis DSM 18603]
 gi|311298769|gb|EFQ75874.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Mucilaginibacter
           paludis DSM 18603]
          Length = 286

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 81/285 (28%), Positives = 151/285 (52%), Gaps = 34/285 (11%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+HEI K+ ++  +EE +LA++ RE GD +A  RL  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLHEIGKVDLITAEEEVILAQKIRE-GDQAALERLTKTNLRFVVSVAKQYQNQGLTL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A K+FD  +GF+  +Y++WWI+ ++ + I     +V++    NQ   
Sbjct: 77  GDLINEGNLGLIKAAKRFDETKGFKFISYAVWWIRQSILQAIAEQSRIVRL--PLNQVGS 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR--------LAGDESLN 187
              + +    L+   +    PE++  I +      S+ +S + R        + G+E  N
Sbjct: 135 LSKISKAFSKLEQEYEREPSPEELADILETTVDKISDTLSNSGRHVSMDAPFVQGEE--N 192

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI---FE 244
            L++  D +       L+ +   +E               + RS+S L  RER I   F 
Sbjct: 193 TLLDVLDNHEPNTDFHLINESLAEE---------------IKRSLSTLTEREREIVVLFF 237

Query: 245 ARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
              L  N P +LE +  +F ++RERVRQI+ +A ++++ + + ++
Sbjct: 238 G--LGSNSPFSLEEIGEKFNLTRERVRQIKDKALQRLRHTSRSKI 280


>gi|283786707|ref|YP_003366572.1| RNA polymerase sigma factor (sigma-38) [Citrobacter rodentium
           ICC168]
 gi|282950161|emb|CBG89797.1| RNA polymerase sigma factor (sigma-38) [Citrobacter rodentium
           ICC168]
          Length = 330

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|238896221|ref|YP_002920957.1| RNA polymerase sigma factor RpoS [Klebsiella pneumoniae NTUH-K2044]
 gi|238548539|dbj|BAH64890.1| RNA polymerase sigma factor [Klebsiella pneumoniae subsp.
           pneumoniae NTUH-K2044]
          Length = 366

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 97  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYSNRGLALLDL 155

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 156 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 215

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 216 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 272

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 273 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 321

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 322 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQGQ 356


>gi|73671310|gb|AAZ80066.1| RpoS variant [Escherichia coli LW1655F+]
          Length = 330

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|83272624|gb|ABC00797.1| RpoS [Escherichia coli]
          Length = 330

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNPTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|225026302|ref|ZP_03715494.1| hypothetical protein EUBHAL_00543 [Eubacterium hallii DSM 3353]
 gi|224956366|gb|EEG37575.1| hypothetical protein EUBHAL_00543 [Eubacterium hallii DSM 3353]
          Length = 367

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 91/274 (33%), Positives = 146/274 (53%), Gaps = 31/274 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  IP+L  +EE  LA+R  E GD  A  +L+ ++LRLVV IA  Y G G+   ++
Sbjct: 101 YLKEIGNIPLLTAEEEVFLAQRI-EKGDEQARKQLIEANLRLVVSIAKKYVGRGMSFLDL 159

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GLM+AV+KFD ++G + +TYS WWI+ A+   I  +   +++      T N+  
Sbjct: 160 IQEGNMGLMKAVEKFDYKKGNKFSTYSTWWIRQAITRGIADTAKTIRVPVHMVETINK-- 217

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               LR  +  LQ +       E    IAKK+N+  +++  +        SL+  I   +
Sbjct: 218 ---TLRTSRMLLQELGREPTNEE----IAKKMNMPVAKIDEILKTSRDPVSLDTPI--GE 268

Query: 195 KNSSQWQDW-----LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RL 248
           +  SQ  D+     L+   D     ++++E        L  +M+ L  RER + + R  L
Sbjct: 269 EEDSQLGDFIEDESLLSPVDSASFSMLKEE--------LEEAMASLTERERNVIKLRFGL 320

Query: 249 QENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +    TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 321 DDGKTRTLEEVGKEFNVTRERIRQIEAKALRKLR 354


>gi|59712674|ref|YP_205450.1| RNA polymerase, sigma-S (sigma-38) factor [Vibrio fischeri ES114]
 gi|59480775|gb|AAW86562.1| RNA polymerase, sigma-S (sigma-38) factor [Vibrio fischeri ES114]
          Length = 321

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 97/276 (35%), Positives = 149/276 (53%), Gaps = 23/276 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE V   R    GD +A  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 49  YLGEIGFSPLLTAEEE-VYFSRLALKGDEAARARMIESNLRLVVKIARRYNHRGLALLDL 107

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 108 VEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 166

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV---ISMNCRLAGDESLNALINSSDK 195
           LR  +   Q + D+   PE+   IA+KL+   S+V   + +N R+A  +S+ A    SDK
Sbjct: 167 LRAARELSQKL-DHEPTPEE---IAEKLDKPVSDVSRMLRLNERVASVDSMVA--GESDK 220

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARR---LQEN 251
                 D L    +       E E +K+  N  L   +  LNP+++ +  ARR   L   
Sbjct: 221 ---ALLDILPDTKNSDP----ESETQKDDINTSLVGWLGQLNPKQKEVV-ARRFGLLGYE 272

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +  E  ++RERVRQI+    ++++E +  Q
Sbjct: 273 AATLEQVGIEIGLTRERVRQIQVEGLRRLREIMTNQ 308


>gi|292487251|ref|YP_003530123.1| RNA polymerase sigma factor rpoS [Erwinia amylovora CFBP1430]
 gi|292900377|ref|YP_003539746.1| RNA polymerase sigma subunit RpoS (sigma-38) [Erwinia amylovora
           ATCC 49946]
 gi|3183703|emb|CAA10959.1| RpoS [Erwinia amylovora]
 gi|291200225|emb|CBJ47353.1| RNA polymerase sigma subunit RpoS (sigma-38) [Erwinia amylovora
           ATCC 49946]
 gi|291552670|emb|CBA19715.1| RNA polymerase sigma factor rpoS [Erwinia amylovora CFBP1430]
          Length = 330

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 139/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVFFARRAL-RGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEKLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQGQ 320


>gi|290511076|ref|ZP_06550445.1| RNA polymerase sigma factor RpoS [Klebsiella sp. 1_1_55]
 gi|289776069|gb|EFD84068.1| RNA polymerase sigma factor RpoS [Klebsiella sp. 1_1_55]
          Length = 347

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 78  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYSNRGLALLDL 136

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 137 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 196

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 197 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 253

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 254 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 302

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 303 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQGQ 337


>gi|41861|emb|CAA78692.1| KatF [Escherichia coli]
          Length = 342

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 73  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 131

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 132 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 191

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 192 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 248

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 249 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 297

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 298 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 332


>gi|332765694|gb|EGJ95907.1| RNA polymerase sigma factor RpoS [Shigella flexneri 2930-71]
          Length = 330

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 84/277 (30%), Positives = 141/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EG++GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGDLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E++Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLRETLQTQ 320


>gi|216659|dbj|BAA02747.1| RNA polymerase sigma subunit, sigma-38 [Escherichia coli]
 gi|23306698|gb|AAN15268.1| RNA polymerase sigma factor S variant [Escherichia coli]
 gi|260448208|gb|ACX38630.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Escherichia coli
           DH1]
          Length = 330

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|320640384|gb|EFX09923.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           G5101]
          Length = 330

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHQLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|117617733|ref|YP_855373.1| RNA polymerase sigma factor RpoS [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
 gi|117559140|gb|ABK36088.1| RNA polymerase sigma factor RpoS [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
          Length = 327

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 92/274 (33%), Positives = 144/274 (52%), Gaps = 19/274 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD +A  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 57  YLGEIGFSPLLTAEEEVYYARRAL-RGDKAARKRMIESNLRLVVKIARRYNNRGLVLLDL 115

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 116 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 174

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +  L    D+    E    IA  L+ S  +V  M         LN  I S D    
Sbjct: 175 LRTAR-ELSHRLDHEPTAED---IAFALDRSVDDVNRML-------KLNEKITSVDTPIG 223

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNR--RNMLTRSMSVLNPRERRIFEARR---LQENPV 253
             +D  + D    E+ +  + E ++   R  +   +  LNP++R +  ARR   L   P 
Sbjct: 224 GDRDKALLDVLSDERGMGPELESQDDDMRASIVHWLEELNPKQREVL-ARRFGLLGYEPA 282

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           TLE++ +E  ++RERVRQI+    ++++E +  Q
Sbjct: 283 TLEDVGAEIGLTRERVRQIQVEGLRRLREILLGQ 316


>gi|23306702|gb|AAN15269.1| RNA polymerase sigma factor S variant [Escherichia coli]
          Length = 330

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|322831414|ref|YP_004211441.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rahnella sp.
           Y9602]
 gi|321166615|gb|ADW72314.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rahnella sp.
           Y9602]
          Length = 328

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 139/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 59  YLGEIGYSPLLTAEEEVYFARRAL-RGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 117

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 118 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 177

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 178 RTARELAHKLDHEPSAEEIAEQLDKPVHDVSRMLRLN---ERITSVDTPLGGDSEKALLD 234

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 235 ILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 283

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 284 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQGQ 318


>gi|307243281|ref|ZP_07525452.1| RNA polymerase sigma factor RpoD [Peptostreptococcus stomatis DSM
           17678]
 gi|306493409|gb|EFM65391.1| RNA polymerase sigma factor RpoD [Peptostreptococcus stomatis DSM
           17678]
          Length = 384

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 88/266 (33%), Positives = 146/266 (54%), Gaps = 15/266 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L+  EE   AKR  E GD  A  +LV ++LRLVV IA  Y G G+   ++
Sbjct: 118 YLKEIGKIPLLKPHEEVEYAKRMAE-GDEFAKQKLVEANLRLVVSIAKRYVGRGMLFLDL 176

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD ++G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 177 IQEGNLGLIKAVEKFDYKKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 234

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R+   L      + KP++   IAK++N++E +V  +  ++A D  SL   I   ++  
Sbjct: 235 LIRVSRQLLQELGRDPKPDE---IAKEMNMTEEKVREI-MKIAQDPVSLETPI--GEEED 288

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTL 255
           S   D++  +              K +   +   ++ LN RE+ + + R   E+    TL
Sbjct: 289 SHLGDFIPDEDAPAPAEAAAYSLLKEQ---IEDVLNTLNDREQNVLKLRFGLEDGRARTL 345

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           E +  EF+V+RER+RQIEA+A +K++
Sbjct: 346 EEVGKEFDVTRERIRQIEAKALRKLR 371


>gi|15803258|ref|NP_289290.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 EDL933]
 gi|12517195|gb|AAG57848.1|AE005502_2 RNA polymerase, sigma S (sigma38) factor; synthesis of many growth
           phase related proteins [Escherichia coli O157:H7 str.
           EDL933]
          Length = 330

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|260599105|ref|YP_003211676.1| RNA polymerase sigma factor RpoS [Cronobacter turicensis z3032]
 gi|260218282|emb|CBA33240.1| RNA polymerase sigma factor rpoS [Cronobacter turicensis z3032]
          Length = 351

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 82  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYSNRGLALLDL 140

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 141 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 200

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 201 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 257

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 258 ILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 306

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 307 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQGQ 341


>gi|157364824|ref|YP_001471591.1| RpoD family RNA polymerase sigma factor [Thermotoga lettingae TMO]
 gi|157315428|gb|ABV34527.1| RNA polymerase, sigma 70 subunit, RpoD family [Thermotoga lettingae
           TMO]
          Length = 400

 Score =  118 bits (296), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 90/275 (32%), Positives = 140/275 (50%), Gaps = 33/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L   +E  LA+R  + G+  A  +L+ S+LRLVV IA  Y G GLP  ++
Sbjct: 128 YLREIGKIPLLTPSQERELARRA-QIGNKRAKEKLIESNLRLVVSIAKRYIGRGLPFLDL 186

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-- 132
           + EGNIGL++AV+KFD ++G++ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 187 IQEGNIGLLKAVEKFDWKKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLN 246

Query: 133 --KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R ++     +  L+ +     KP  V  + + L  S+ E +S+   +  DE      
Sbjct: 247 RITREYYQKHGEQPSLEELAKLMDKP--VDKVEEILQASK-ETVSLEAPVGEDE------ 297

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEE--RKNRRNMLTRSMSVLNPRERRIFEARR- 247
                      D  V D    E +   K+E  R   R  L + +  LNPRE  + + R  
Sbjct: 298 -----------DSTVGDFVADENITSPKKEAMRMLMREELEKVLKTLNPREAMVLKMRYG 346

Query: 248 -LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L     TLE +   F V+RER+RQIE +A +K++
Sbjct: 347 LLDGKAKTLEEVGQYFNVTRERIRQIEVKALRKLR 381


>gi|152971625|ref|YP_001336734.1| RNA polymerase sigma factor RpoS [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|206580660|ref|YP_002236889.1| RNA polymerase sigma factor RpoS [Klebsiella pneumoniae 342]
 gi|262041489|ref|ZP_06014687.1| RNA polymerase sigma factor [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|288933843|ref|YP_003437902.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Klebsiella
           variicola At-22]
 gi|330008320|ref|ZP_08306195.1| RNA polymerase sigma factor RpoS [Klebsiella sp. MS 92-3]
 gi|150956474|gb|ABR78504.1| RNA polymerase sigma factor [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|206569718|gb|ACI11494.1| RNA polymerase sigma factor RpoS [Klebsiella pneumoniae 342]
 gi|259041148|gb|EEW42221.1| RNA polymerase sigma factor [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|288888572|gb|ADC56890.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Klebsiella
           variicola At-22]
 gi|328535178|gb|EGF61679.1| RNA polymerase sigma factor RpoS [Klebsiella sp. MS 92-3]
          Length = 330

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYSNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQGQ 320


>gi|15832849|ref|NP_311622.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           Sakai]
 gi|74313307|ref|YP_311726.1| RNA polymerase sigma factor RpoS [Shigella sonnei Ss046]
 gi|110642882|ref|YP_670612.1| RNA polymerase sigma factor RpoS [Escherichia coli 536]
 gi|110806628|ref|YP_690148.1| RNA polymerase sigma factor RpoS [Shigella flexneri 5 str. 8401]
 gi|157157336|ref|YP_001464064.1| RNA polymerase sigma factor RpoS [Escherichia coli E24377A]
 gi|157162189|ref|YP_001459507.1| RNA polymerase sigma factor RpoS [Escherichia coli HS]
 gi|168749933|ref|ZP_02774955.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4113]
 gi|168755487|ref|ZP_02780494.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4401]
 gi|168778725|ref|ZP_02803732.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4076]
 gi|168787997|ref|ZP_02813004.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC869]
 gi|170019013|ref|YP_001723967.1| RNA polymerase sigma factor RpoS [Escherichia coli ATCC 8739]
 gi|170684160|ref|YP_001744890.1| RNA polymerase sigma factor RpoS [Escherichia coli SMS-3-5]
 gi|191166775|ref|ZP_03028601.1| RNA polymerase sigma factor RpoS [Escherichia coli B7A]
 gi|191171134|ref|ZP_03032684.1| RNA polymerase sigma factor RpoS [Escherichia coli F11]
 gi|193065048|ref|ZP_03046123.1| RNA polymerase sigma factor RpoS [Escherichia coli E22]
 gi|193069671|ref|ZP_03050623.1| RNA polymerase sigma factor RpoS [Escherichia coli E110019]
 gi|194431745|ref|ZP_03064036.1| RNA polymerase sigma factor RpoS [Shigella dysenteriae 1012]
 gi|194438995|ref|ZP_03071079.1| RNA polymerase sigma factor RpoS [Escherichia coli 101-1]
 gi|208812039|ref|ZP_03253368.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4045]
 gi|209395891|ref|YP_002272204.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4115]
 gi|209920184|ref|YP_002294268.1| RNA polymerase sigma factor RpoS [Escherichia coli SE11]
 gi|217326648|ref|ZP_03442731.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           TW14588]
 gi|218559734|ref|YP_002392647.1| RNA polymerase sigma factor RpoS [Escherichia coli S88]
 gi|218696339|ref|YP_002404006.1| RNA polymerase sigma factor RpoS [Escherichia coli 55989]
 gi|218706235|ref|YP_002413754.1| RNA polymerase sigma factor RpoS [Escherichia coli UMN026]
 gi|253772403|ref|YP_003035234.1| RNA polymerase sigma factor RpoS [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254162672|ref|YP_003045780.1| RNA polymerase sigma factor RpoS [Escherichia coli B str. REL606]
 gi|256019474|ref|ZP_05433339.1| RNA polymerase sigma factor RpoS [Shigella sp. D9]
 gi|256024751|ref|ZP_05438616.1| RNA polymerase sigma factor RpoS [Escherichia sp. 4_1_40B]
 gi|260845388|ref|YP_003223166.1| RNA polymerase, sigma S factor [Escherichia coli O103:H2 str.
           12009]
 gi|260869420|ref|YP_003235822.1| RNA polymerase, sigma S factor [Escherichia coli O111:H- str.
           11128]
 gi|261226035|ref|ZP_05940316.1| RNA polymerase sigma factor [Escherichia coli O157:H7 str.
           FRIK2000]
 gi|261256708|ref|ZP_05949241.1| RNA polymerase, sigma S factor [Escherichia coli O157:H7 str.
           FRIK966]
 gi|291284068|ref|YP_003500886.1| RNA polymerase sigma factor [Escherichia coli O55:H7 str. CB9615]
 gi|293406233|ref|ZP_06650159.1| RNA polymerase sigma factor RpoS [Escherichia coli FVEC1412]
 gi|293412096|ref|ZP_06654819.1| RNA polymerase sigma factor RpoS [Escherichia coli B354]
 gi|293415987|ref|ZP_06658627.1| RNA polymerase sigma factor RpoS [Escherichia coli B185]
 gi|293449062|ref|ZP_06663483.1| RNA polymerase sigma factor RpoS [Escherichia coli B088]
 gi|298381970|ref|ZP_06991567.1| RNA polymerase sigma factor rpoS [Escherichia coli FVEC1302]
 gi|300899982|ref|ZP_07118185.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 198-1]
 gi|301027336|ref|ZP_07190677.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 196-1]
 gi|306812377|ref|ZP_07446575.1| RNA polymerase sigma factor RpoS [Escherichia coli NC101]
 gi|307139429|ref|ZP_07498785.1| RNA polymerase sigma factor RpoS [Escherichia coli H736]
 gi|307312831|ref|ZP_07592461.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Escherichia coli
           W]
 gi|312973048|ref|ZP_07787221.1| RNA polymerase sigma factor RpoS [Escherichia coli 1827-70]
 gi|331658855|ref|ZP_08359797.1| RNA polymerase sigma factor RpoS [Escherichia coli TA206]
 gi|331664297|ref|ZP_08365203.1| RNA polymerase sigma factor RpoS [Escherichia coli TA143]
 gi|331669480|ref|ZP_08370326.1| RNA polymerase sigma factor RpoS [Escherichia coli TA271]
 gi|331684360|ref|ZP_08384952.1| RNA polymerase sigma factor RpoS [Escherichia coli H299]
 gi|10197692|gb|AAG14975.1|AF242208_8 alternative sigma factor [Escherichia coli]
 gi|10197707|gb|AAG14988.1|AF242210_7 alternative sigma factor [Escherichia coli]
 gi|10197712|gb|AAG14992.1|AF242211_4 alternative sigma factor [Escherichia coli]
 gi|15529697|gb|AAL01412.1|AF410776_1 RpoS [Escherichia coli]
 gi|15529700|gb|AAL01414.1|AF410777_1 RpoS [Escherichia coli]
 gi|4887559|emb|CAB43502.1| alternative sigma factor, sigma 38 [Escherichia coli]
 gi|13363066|dbj|BAB37018.1| sigma factor RpoS [Escherichia coli O157:H7 str. Sakai]
 gi|37924617|gb|AAP59881.1| sigma S [Shigella boydii]
 gi|73856784|gb|AAZ89491.1| RNA polymerase, sigma S (sigma38) factor [Shigella sonnei Ss046]
 gi|83272618|gb|ABC00794.1| RpoS [Escherichia coli]
 gi|83272620|gb|ABC00795.1| RpoS [Escherichia coli]
 gi|83272622|gb|ABC00796.1| RpoS [Escherichia coli]
 gi|83272626|gb|ABC00798.1| RpoS [Escherichia coli]
 gi|110344474|gb|ABG70711.1| RNA polymerase sigma factor RpoS [Escherichia coli 536]
 gi|110616176|gb|ABF04843.1| RNA polymerase sigma factor [Shigella flexneri 5 str. 8401]
 gi|134036992|gb|ABO47833.1| sigma 38 factor [Escherichia coli]
 gi|134037004|gb|ABO47841.1| sigma 38 factor [Escherichia coli]
 gi|134037007|gb|ABO47843.1| sigma 38 factor [Escherichia coli]
 gi|134037010|gb|ABO47845.1| sigma 38 factor [Escherichia coli]
 gi|134037013|gb|ABO47847.1| sigma 38 factor [Escherichia coli]
 gi|157067869|gb|ABV07124.1| RNA polymerase sigma factor RpoS [Escherichia coli HS]
 gi|157079366|gb|ABV19074.1| RNA polymerase sigma factor RpoS [Escherichia coli E24377A]
 gi|169753941|gb|ACA76640.1| RNA polymerase, sigma 70 subunit, RpoD family [Escherichia coli
           ATCC 8739]
 gi|170521878|gb|ACB20056.1| RNA polymerase sigma factor RpoS [Escherichia coli SMS-3-5]
 gi|188015788|gb|EDU53910.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4113]
 gi|189003307|gb|EDU72293.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4076]
 gi|189357252|gb|EDU75671.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4401]
 gi|189372241|gb|EDU90657.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC869]
 gi|190903146|gb|EDV62869.1| RNA polymerase sigma factor RpoS [Escherichia coli B7A]
 gi|190908434|gb|EDV68023.1| RNA polymerase sigma factor RpoS [Escherichia coli F11]
 gi|192927345|gb|EDV81964.1| RNA polymerase sigma factor RpoS [Escherichia coli E22]
 gi|192957034|gb|EDV87485.1| RNA polymerase sigma factor RpoS [Escherichia coli E110019]
 gi|194420101|gb|EDX36179.1| RNA polymerase sigma factor RpoS [Shigella dysenteriae 1012]
 gi|194422116|gb|EDX38119.1| RNA polymerase sigma factor RpoS [Escherichia coli 101-1]
 gi|208733316|gb|EDZ82003.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4045]
 gi|209157291|gb|ACI34724.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4115]
 gi|209747660|gb|ACI72137.1| sigma factor RpoS [Escherichia coli]
 gi|209747662|gb|ACI72138.1| sigma factor RpoS [Escherichia coli]
 gi|209747664|gb|ACI72139.1| sigma factor RpoS [Escherichia coli]
 gi|209913443|dbj|BAG78517.1| RNA polymerase sigma factor S RpoS [Escherichia coli SE11]
 gi|217319015|gb|EEC27440.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           TW14588]
 gi|218353071|emb|CAU98896.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli 55989]
 gi|218366503|emb|CAR04255.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli S88]
 gi|218433332|emb|CAR14232.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli UMN026]
 gi|222034438|emb|CAP77180.1| RNA polymerase sigma factor rpoS [Escherichia coli LF82]
 gi|242378296|emb|CAQ33073.1| RNA polymerase, sigma S (sigma 38) factor, subunit of RNA
           polymerase sigma 38 [Escherichia coli BL21(DE3)]
 gi|253323447|gb|ACT28049.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|253974573|gb|ACT40244.1| RNA polymerase sigma factor [Escherichia coli B str. REL606]
 gi|253978740|gb|ACT44410.1| RNA polymerase sigma factor [Escherichia coli BL21(DE3)]
 gi|257760535|dbj|BAI32032.1| RNA polymerase, sigma S factor [Escherichia coli O103:H2 str.
           12009]
 gi|257765776|dbj|BAI37271.1| RNA polymerase, sigma S factor [Escherichia coli O111:H- str.
           11128]
 gi|281179747|dbj|BAI56077.1| RNA polymerase sigma factor S RpoS [Escherichia coli SE15]
 gi|290763941|gb|ADD57902.1| RNA polymerase sigma factor [Escherichia coli O55:H7 str. CB9615]
 gi|291322152|gb|EFE61581.1| RNA polymerase sigma factor RpoS [Escherichia coli B088]
 gi|291426239|gb|EFE99271.1| RNA polymerase sigma factor RpoS [Escherichia coli FVEC1412]
 gi|291432176|gb|EFF05158.1| RNA polymerase sigma factor RpoS [Escherichia coli B185]
 gi|291468867|gb|EFF11358.1| RNA polymerase sigma factor RpoS [Escherichia coli B354]
 gi|298277110|gb|EFI18626.1| RNA polymerase sigma factor rpoS [Escherichia coli FVEC1302]
 gi|299879329|gb|EFI87540.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 196-1]
 gi|300356491|gb|EFJ72361.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 198-1]
 gi|305854415|gb|EFM54853.1| RNA polymerase sigma factor RpoS [Escherichia coli NC101]
 gi|306907266|gb|EFN37772.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Escherichia coli
           W]
 gi|307554720|gb|ADN47495.1| sigma factor RpoS [Escherichia coli ABU 83972]
 gi|307625683|gb|ADN69987.1| RNA polymerase sigma factor RpoS [Escherichia coli UM146]
 gi|309703100|emb|CBJ02432.1| RNA polymerase sigma factor (sigma-38) [Escherichia coli ETEC
           H10407]
 gi|310332990|gb|EFQ00204.1| RNA polymerase sigma factor RpoS [Escherichia coli 1827-70]
 gi|312947273|gb|ADR28100.1| RNA polymerase sigma factor RpoS [Escherichia coli O83:H1 str. NRG
           857C]
 gi|315062022|gb|ADT76349.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli W]
 gi|315615130|gb|EFU95767.1| RNA polymerase sigma factor RpoS [Escherichia coli 3431]
 gi|320186525|gb|EFW61253.1| RNA polymerase sigma factor RpoS [Shigella flexneri CDC 796-83]
 gi|320189070|gb|EFW63729.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC1212]
 gi|320194880|gb|EFW69509.1| RNA polymerase sigma factor RpoS [Escherichia coli WV_060327]
 gi|320202392|gb|EFW76962.1| RNA polymerase sigma factor RpoS [Escherichia coli EC4100B]
 gi|320651231|gb|EFX19666.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H- str. H
           2687]
 gi|320656781|gb|EFX24669.1| RNA polymerase sigma factor RpoS [Escherichia coli O55:H7 str.
           3256-97 TW 07815]
 gi|320667375|gb|EFX34333.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           LSU-61]
 gi|323159951|gb|EFZ45921.1| RNA polymerase sigma factor RpoS [Escherichia coli E128010]
 gi|323167243|gb|EFZ52960.1| RNA polymerase sigma factor RpoS [Shigella sonnei 53G]
 gi|323172966|gb|EFZ58597.1| RNA polymerase sigma factor RpoS [Escherichia coli LT-68]
 gi|323180167|gb|EFZ65719.1| RNA polymerase sigma factor RpoS [Escherichia coli 1180]
 gi|323183273|gb|EFZ68670.1| RNA polymerase sigma factor RpoS [Escherichia coli 1357]
 gi|323188842|gb|EFZ74127.1| RNA polymerase sigma factor RpoS [Escherichia coli RN587/1]
 gi|323935702|gb|EGB32016.1| RNA polymerase sigma protein RpoS [Escherichia coli E1520]
 gi|323941428|gb|EGB37611.1| RNA polymerase sigma proteinRpoS [Escherichia coli E482]
 gi|323946373|gb|EGB42401.1| RNA polymerase sigma protein RpoS [Escherichia coli H120]
 gi|323951037|gb|EGB46913.1| RNA polymerase sigma proteinRpoS [Escherichia coli H252]
 gi|323957044|gb|EGB52769.1| RNA polymerase sigma proteinRpoS [Escherichia coli H263]
 gi|323960599|gb|EGB56225.1| RNA polymerase sigma proteinRpoS [Escherichia coli H489]
 gi|323966893|gb|EGB62322.1| RNA polymerase sigma proteinRpoS [Escherichia coli M863]
 gi|323971530|gb|EGB66763.1| RNA polymerase sigma proteinRpoS [Escherichia coli TA007]
 gi|323978651|gb|EGB73733.1| RNA polymerase sigma proteinRpoS [Escherichia coli TW10509]
 gi|324111374|gb|EGC05356.1| RNA polymerase sigma proteinRpoS [Escherichia fergusonii B253]
 gi|324119995|gb|EGC13873.1| RNA polymerase sigma proteinRpoS [Escherichia coli E1167]
 gi|325496210|gb|EGC94069.1| sigma factor RpoS [Escherichia fergusonii ECD227]
 gi|326339191|gb|EGD63006.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           1044]
 gi|326342926|gb|EGD66694.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           1125]
 gi|330908777|gb|EGH37291.1| RNA polymerase sigma factor RpoS [Escherichia coli AA86]
 gi|331053437|gb|EGI25466.1| RNA polymerase sigma factor RpoS [Escherichia coli TA206]
 gi|331058228|gb|EGI30209.1| RNA polymerase sigma factor RpoS [Escherichia coli TA143]
 gi|331063148|gb|EGI35061.1| RNA polymerase sigma factor RpoS [Escherichia coli TA271]
 gi|331077975|gb|EGI49181.1| RNA polymerase sigma factor RpoS [Escherichia coli H299]
 gi|332344623|gb|AEE57957.1| RNA polymerase sigma factor RpoS [Escherichia coli UMNK88]
          Length = 330

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|260775503|ref|ZP_05884400.1| RNA polymerase sigma factor RpoS [Vibrio coralliilyticus ATCC
           BAA-450]
 gi|260608684|gb|EEX34849.1| RNA polymerase sigma factor RpoS [Vibrio coralliilyticus ATCC
           BAA-450]
          Length = 327

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 87/285 (30%), Positives = 147/285 (51%), Gaps = 41/285 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 55  YLGEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 113

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 114 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 172

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNAL- 189
           LR  +   Q + D+    E++          ++K L ++E  + S++  + GD     L 
Sbjct: 173 LRTARELSQKL-DHEPTAEEIATQLDKPVDDVSKMLRLNE-RISSVDTPIGGDGEKALLD 230

Query: 190 ----INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
               +N+SD   S   D +                    ++ L   +  LNP+++ +  A
Sbjct: 231 IIPDVNNSDPEVSTQDDDI--------------------KSSLIHWLDELNPKQKEVL-A 269

Query: 246 RR---LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           RR   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 270 RRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILIKQ 314


>gi|87118598|ref|ZP_01074497.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Marinomonas sp. MED121]
 gi|86166232|gb|EAQ67498.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Marinomonas sp. MED121]
          Length = 330

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 83/272 (30%), Positives = 151/272 (55%), Gaps = 14/272 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A++  + GD S+  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 58  YLSEIGFSPLLSAEEEVYYARKSLK-GDESSRKRMIESNLRLVVKISRRYLNRGLSLLDL 116

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 117 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 175

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +   Q + D+    E +  +  +      +++S+N R++   S+++ +   D + S
Sbjct: 176 LRAARELTQKL-DHEPSAEDIADMLDRPVEDVQKMLSLNERIS---SIDSPVGGMDTDKS 231

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTL 255
             +      H G E    ++ +  +  + +   ++ LN ++R +  ARR       P TL
Sbjct: 232 LVEIIADEQHAGPE----DERQFSDVVHNIDHWLNDLNEKQREVI-ARRFGLRGYEPSTL 286

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E++ +E  ++RERVRQI+  A +K++  ++KQ
Sbjct: 287 EDVGAEIGLTRERVRQIQVEALRKLKLMMEKQ 318


>gi|320662323|gb|EFX29720.1| RNA polymerase sigma factor RpoS [Escherichia coli O55:H7 str. USDA
           5905]
          Length = 330

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|320180825|gb|EFW55748.1| RNA polymerase sigma factor RpoS [Shigella boydii ATCC 9905]
          Length = 330

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|271501815|ref|YP_003334841.1| RpoD subfamily RNA polymerase sigma-70 subunit [Dickeya dadantii
           Ech586]
 gi|270345370|gb|ACZ78135.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dickeya dadantii
           Ech586]
          Length = 330

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 89/281 (31%), Positives = 146/281 (51%), Gaps = 33/281 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+S+  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVSSRRRMIESNLRLVVKIARRYNNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V    +LN     + S++  L GD S  AL+
Sbjct: 180 RTARELSHKLDHEPSAEEIAERLDKPVDDVNRMLRLN---ERITSVDTPLGGD-SEKALL 235

Query: 191 NSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-- 247
                      D L  + D G E    + + ++N    + + +  LN ++R +  ARR  
Sbjct: 236 -----------DILADEKDNGPEDTTQDNDMKQN----IVKWLFELNAKQREVL-ARRFG 279

Query: 248 -LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            L     TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 280 LLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQVQ 320


>gi|6010726|gb|AAF01229.1|AF184098_1 mutant RpoS [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
          Length = 330

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVQKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|220932077|ref|YP_002508985.1| RNA polymerase, sigma 70 subunit, RpoD family [Halothermothrix
           orenii H 168]
 gi|219993387|gb|ACL69990.1| RNA polymerase, sigma 70 subunit, RpoD family [Halothermothrix
           orenii H 168]
          Length = 358

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/265 (32%), Positives = 136/265 (51%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  +EE  LAKR  E GD  A   LV ++LRLVV IA  Y G G+   ++
Sbjct: 92  YLKEIGKVPLLTAEEEVDLAKRI-EQGDEQAKRELVEANLRLVVSIAKKYVGRGMSFLDL 150

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 151 IQEGNMGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 208

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L         PE+   I +++ +  +E +    ++A  E ++      ++  S
Sbjct: 209 LIRVSRQLLQEKGREPTPEE---IGEEMGMP-AEKVREILKIA-QEPVSLETPIGEEEDS 263

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++    D               R  L   +  L  RE+R+ E R   E+  P TLE
Sbjct: 264 HLGDFI---EDEDAPAPASAASFTLLREQLDDVLDTLTDREKRVLELRFGLEDGRPRTLE 320

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF V+RER+RQIEA+A +K++
Sbjct: 321 EVGKEFGVTRERIRQIEAKALRKLR 345


>gi|170765845|ref|ZP_02900656.1| RNA polymerase sigma factor RpoS [Escherichia albertii TW07627]
 gi|170124991|gb|EDS93922.1| RNA polymerase sigma factor RpoS [Escherichia albertii TW07627]
          Length = 434

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 165 YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 223

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 224 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 283

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 284 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 340

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 341 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 389

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 390 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 424



 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 60/156 (38%), Positives = 101/156 (64%), Gaps = 13/156 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL---RSWSLVKIGTT---ANQ 132
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+   R++ L +IG +     +
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTY-LGEIGYSPLLTAE 178

Query: 133 KRLFFNLRRLKGHLQA---ITDNNLKPEQVVAIAKK 165
           + ++F  R L+G + +   + ++NL+   VV IA++
Sbjct: 179 EEVYFARRALRGDVASRRRMIESNLR--LVVKIARR 212


>gi|312171353|emb|CBX79612.1| RNA polymerase sigma factor rpoS [Erwinia amylovora ATCC BAA-2158]
          Length = 330

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 139/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVFFARRAL-RGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEKLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQGQ 320


>gi|192358973|ref|YP_001982681.1| RNA polymerase sigma factor RpoS [Cellvibrio japonicus Ueda107]
 gi|190685138|gb|ACE82816.1| RNA polymerase sigma factor RpoS [Cellvibrio japonicus Ueda107]
          Length = 335

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 91/277 (32%), Positives = 153/277 (55%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L   EE   A++  + GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 66  YLNEIGFSPLLLSAEEVFFARKALK-GDEAARKRMIESNLRLVVKISRRYVNRGLALLDL 124

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 125 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 183

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN-SSDKNS 197
           LR  +   Q + D+   PE++  + +K       ++S+N R+    S++A I  SSD+  
Sbjct: 184 LRAARELSQKL-DHEPTPEEIANLLEKPVADVEHMLSLNERVT---SIDAPIGASSDRTV 239

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS----VLNPRERRIFEARR--LQEN 251
           +   D +   H      L++  +       LT S+      L  ++R +  ARR  L+  
Sbjct: 240 A---DTIADTHVSDPAALLQDSD-------LTASLDHWLEELTEKQREVL-ARRFGLRGY 288

Query: 252 PV-TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            V TLE +  E  ++RERVRQI+  A K++++ ++KQ
Sbjct: 289 EVSTLEEVGHEIGLTRERVRQIQVEALKRLRDIMEKQ 325


>gi|91212108|ref|YP_542094.1| RNA polymerase sigma factor RpoS [Escherichia coli UTI89]
 gi|117624976|ref|YP_853964.1| RNA polymerase sigma factor RpoS [Escherichia coli APEC O1]
 gi|227888284|ref|ZP_04006089.1| RNA polymerase sigma factor RpoS [Escherichia coli 83972]
 gi|237706630|ref|ZP_04537111.1| sigma factor RpoS [Escherichia sp. 3_2_53FAA]
 gi|254037782|ref|ZP_04871840.1| sigma factor RpoS [Escherichia sp. 1_1_43]
 gi|300815849|ref|ZP_07096073.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 107-1]
 gi|300820522|ref|ZP_07100673.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 119-7]
 gi|300906754|ref|ZP_07124436.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 84-1]
 gi|300919222|ref|ZP_07135745.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 115-1]
 gi|300922264|ref|ZP_07138390.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 182-1]
 gi|300930600|ref|ZP_07145992.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 187-1]
 gi|300941124|ref|ZP_07155636.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 21-1]
 gi|300946980|ref|ZP_07161206.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 116-1]
 gi|300954984|ref|ZP_07167395.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 175-1]
 gi|300976231|ref|ZP_07173328.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 200-1]
 gi|300976795|ref|ZP_07173612.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 45-1]
 gi|301027157|ref|ZP_07190526.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 69-1]
 gi|301306156|ref|ZP_07212232.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 124-1]
 gi|301326219|ref|ZP_07219602.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 78-1]
 gi|301645276|ref|ZP_07245227.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 146-1]
 gi|309795208|ref|ZP_07689627.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 145-7]
 gi|331643427|ref|ZP_08344558.1| RNA polymerase sigma factor RpoS [Escherichia coli H736]
 gi|331648464|ref|ZP_08349552.1| RNA polymerase sigma factor RpoS [Escherichia coli M605]
 gi|331654219|ref|ZP_08355219.1| RNA polymerase sigma factor RpoS [Escherichia coli M718]
 gi|331674247|ref|ZP_08375007.1| RNA polymerase sigma factor RpoS [Escherichia coli TA280]
 gi|331678721|ref|ZP_08379395.1| RNA polymerase sigma factor RpoS [Escherichia coli H591]
 gi|332280596|ref|ZP_08393009.1| sigma factor RpoS [Shigella sp. D9]
 gi|11036547|gb|AAG27177.1|AF270497_2 RpoS [Escherichia coli]
 gi|91073682|gb|ABE08563.1| sigma factor RpoS [Escherichia coli UTI89]
 gi|115514100|gb|ABJ02175.1| sigma factor RpoS [Escherichia coli APEC O1]
 gi|120538764|emb|CAM07120.1| sigma factor S [Escherichia coli]
 gi|226839406|gb|EEH71427.1| sigma factor RpoS [Escherichia sp. 1_1_43]
 gi|226899670|gb|EEH85929.1| sigma factor RpoS [Escherichia sp. 3_2_53FAA]
 gi|227834553|gb|EEJ45019.1| RNA polymerase sigma factor RpoS [Escherichia coli 83972]
 gi|300308576|gb|EFJ63096.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 200-1]
 gi|300318076|gb|EFJ67860.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 175-1]
 gi|300395189|gb|EFJ78727.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 69-1]
 gi|300401448|gb|EFJ84986.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 84-1]
 gi|300409981|gb|EFJ93519.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 45-1]
 gi|300413667|gb|EFJ96977.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 115-1]
 gi|300421394|gb|EFK04705.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 182-1]
 gi|300453367|gb|EFK16987.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 116-1]
 gi|300454167|gb|EFK17660.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 21-1]
 gi|300461542|gb|EFK25035.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 187-1]
 gi|300526786|gb|EFK47855.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 119-7]
 gi|300531778|gb|EFK52840.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 107-1]
 gi|300838588|gb|EFK66348.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 124-1]
 gi|300847064|gb|EFK74824.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 78-1]
 gi|301076441|gb|EFK91247.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 146-1]
 gi|308121179|gb|EFO58441.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 145-7]
 gi|315254525|gb|EFU34493.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 85-1]
 gi|315289257|gb|EFU48652.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 110-3]
 gi|315293697|gb|EFU53049.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 153-1]
 gi|315298766|gb|EFU58020.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 16-3]
 gi|323377395|gb|ADX49663.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Escherichia coli
           KO11]
 gi|324005707|gb|EGB74926.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 57-2]
 gi|324015519|gb|EGB84738.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 60-1]
 gi|324017012|gb|EGB86231.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 117-3]
 gi|331036898|gb|EGI09122.1| RNA polymerase sigma factor RpoS [Escherichia coli H736]
 gi|331042211|gb|EGI14353.1| RNA polymerase sigma factor RpoS [Escherichia coli M605]
 gi|331047601|gb|EGI19678.1| RNA polymerase sigma factor RpoS [Escherichia coli M718]
 gi|331068341|gb|EGI39736.1| RNA polymerase sigma factor RpoS [Escherichia coli TA280]
 gi|331073551|gb|EGI44872.1| RNA polymerase sigma factor RpoS [Escherichia coli H591]
 gi|332102948|gb|EGJ06294.1| sigma factor RpoS [Shigella sp. D9]
          Length = 342

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 73  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 131

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 132 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 191

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 192 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 248

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 249 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 297

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 298 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 332


>gi|307132339|ref|YP_003884355.1| RNA polymerase sigma-S (sigma 38) factor [Dickeya dadantii 3937]
 gi|306529868|gb|ADM99798.1| RNA polymerase, sigma S (sigma 38) factor [Dickeya dadantii 3937]
          Length = 330

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 89/281 (31%), Positives = 146/281 (51%), Gaps = 33/281 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+S+  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVSSRRRMIESNLRLVVKIARRYNNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V    +LN     + S++  L GD S  AL+
Sbjct: 180 RTARELSHKLDHEPSAEEIAERLDKPVDDVNRMLRLN---ERITSVDTPLGGD-SEKALL 235

Query: 191 NSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-- 247
                      D L  + D G E    + + ++N    + + +  LN ++R +  ARR  
Sbjct: 236 -----------DILADEKDNGPEDTTQDNDMKQN----IVKWLFELNAKQREVL-ARRFG 279

Query: 248 -LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            L     TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 280 LLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQVQ 320


>gi|254509205|ref|ZP_05121302.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus 16]
 gi|219547863|gb|EED24891.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus 16]
          Length = 331

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 87/285 (30%), Positives = 147/285 (51%), Gaps = 41/285 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 59  YLGEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 117

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 118 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 176

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNAL- 189
           LR  +   Q + D+    E++          ++K L ++E  + S++  + GD     L 
Sbjct: 177 LRTARELSQKL-DHEPTAEEIATQLDKPVDDVSKMLRLNE-RISSVDTPIGGDGEKALLD 234

Query: 190 ----INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
               +N+SD   S   D +                    ++ L   +  LNP+++ +  A
Sbjct: 235 IIPDVNNSDPEVSTQDDDI--------------------KSSLVHWLDELNPKQKEVL-A 273

Query: 246 RR---LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           RR   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 274 RRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILIKQ 318


>gi|205353865|ref|YP_002227666.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 287/91]
 gi|205273646|emb|CAR38635.1| RNA polymerase sigma subunit RpoS (sigma-38) [Salmonella enterica
           subsp. enterica serovar Gallinarum str. 287/91]
 gi|326628975|gb|EGE35318.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 9]
          Length = 330

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|16130648|ref|NP_417221.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli str.
           K-12 substr. MG1655]
 gi|170082316|ref|YP_001731636.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli str.
           K-12 substr. DH10B]
 gi|238901878|ref|YP_002927674.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli BW2952]
 gi|1710676|sp|P13445|RPOS_ECOLI RecName: Full=RNA polymerase sigma factor rpoS; AltName:
           Full=Sigma-38
 gi|882634|gb|AAA69251.1| RNA polymerase sigma subunit RpoS (sigma-38) [Escherichia coli str.
           K-12 substr. MG1655]
 gi|1789098|gb|AAC75783.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli str.
           K-12 substr. MG1655]
 gi|23306700|gb|AAN15267.1| RNA polymerase sigma factor S [Escherichia coli]
 gi|23306712|gb|AAN15273.1| RNA polymerase sigma factor S [Escherichia coli]
 gi|169890151|gb|ACB03858.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli str.
           K-12 substr. DH10B]
 gi|238863502|gb|ACR65500.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli BW2952]
          Length = 330

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|24114036|ref|NP_708546.1| RNA polymerase sigma factor RpoS [Shigella flexneri 2a str. 301]
 gi|24053158|gb|AAN44253.1| similar to sigmaD(70) factor of RNA polymerase [Shigella flexneri
           2a str. 301]
 gi|281602111|gb|ADA75095.1| RNA polymerase sigma factor [Shigella flexneri 2002017]
          Length = 342

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 73  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 131

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 132 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 191

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 192 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 248

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 249 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 297

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 298 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 332


>gi|312143990|ref|YP_003995436.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Halanaerobium sp.
           'sapolanicus']
 gi|311904641|gb|ADQ15082.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Halanaerobium sp.
           'sapolanicus']
          Length = 360

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 86/274 (31%), Positives = 139/274 (50%), Gaps = 33/274 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+ +L   EE +LAKR  E GD  A  +LV ++LRLVV IA  Y G G+   ++
Sbjct: 94  YLKEIGKVDLLTADEEVMLAKRM-EQGDEWAKQQLVEANLRLVVSIAKKYVGRGMLFLDL 152

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV+KFD  +G++ +TY+ WWI+ A+   I      +++    +       
Sbjct: 153 IQEGNMGLMKAVEKFDYTKGYKFSTYATWWIRQAITRSIADQARTIRV--PVHMVETINK 210

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRLAGDESLNA 188
           L R+   L        KPE+   I +++++S  +V          +S+   +  +E  + 
Sbjct: 211 LIRVSRQLLQEKGREPKPEE---IGEEMDISAEKVREIMKIAQEPVSLETPIGEEEDSHL 267

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
                D++S        Y       +L+        +  L   +  L  RE+R+ E R  
Sbjct: 268 GDFIEDEDSPAPASAASY-------ILL--------KEQLDGVLDTLTEREKRVLELRFG 312

Query: 249 QEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
            E+  P TLE +  EF V+RER+RQIEA+A +K+
Sbjct: 313 IEDGRPRTLEEVGKEFGVTRERIRQIEAKALRKL 346


>gi|313123887|ref|YP_004034146.1| RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           bulgaricus ND02]
 gi|312280450|gb|ADQ61169.1| RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           bulgaricus ND02]
          Length = 378

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 92/272 (33%), Positives = 142/272 (52%), Gaps = 22/272 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG--LPIS 76
           Y+ EI K+P+L + EE  +AKR  E+GD  A   L  ++LRLVV IA  Y  +   + I 
Sbjct: 107 YLKEIGKVPLLSRDEEVEVAKRI-ENGDELAKDELAAANLRLVVSIAKRYAKHNGKMGIL 165

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++ EGNIGLM+AV KFD  +GF+ +TY+ WWI+ A+   +     +++I     +    
Sbjct: 166 DLIQEGNIGLMKAVDKFDYSKGFKFSTYATWWIRQAITRALADQDRMIRIPVHVVES--I 223

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
             + R++  LQ   D + KPE++ A   +      E+I++      D SL+  +   ++ 
Sbjct: 224 NKMNRIQRILQQDLDRDAKPEELAAEMNEPLQKVQEIITVAKNQETD-SLDKPV--GEEG 280

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS-----VLNPRERRIFEARRLQEN 251
            SQ  D L      ++   I  EE      ML   +S      L  RE ++ + R   EN
Sbjct: 281 DSQLGDLL------EDNKAINPEEY-TASEMLKDQLSSMMGEFLTDREAKVLKLRFGLEN 333

Query: 252 --PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             P TLE +     V+RERVRQIEA+A KK++
Sbjct: 334 DEPHTLEEVGRSLGVTRERVRQIEAKAVKKLK 365


>gi|296104425|ref|YP_003614571.1| RNA polymerase nonessential primary-like sigma factor [Enterobacter
           cloacae subsp. cloacae ATCC 13047]
 gi|295058884|gb|ADF63622.1| RNA polymerase nonessential primary-like sigma factor [Enterobacter
           cloacae subsp. cloacae ATCC 13047]
 gi|295097322|emb|CBK86412.1| RNA polymerase sigma factor RpoS [Enterobacter cloacae subsp.
           cloacae NCTC 9394]
          Length = 330

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQGQ 320


>gi|289805538|ref|ZP_06536167.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. AG3]
          Length = 321

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|126699059|ref|YP_001087956.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile 630]
 gi|115250496|emb|CAJ68320.1| RNA polymerase sigma factor SigA1 (sigma-43) [Clostridium
           difficile]
          Length = 390

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 89/266 (33%), Positives = 144/266 (54%), Gaps = 15/266 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L+  EE   A+R  E GD  A  RLV ++LRLVV IA  Y G G+   ++
Sbjct: 124 YLKEIGKIPLLKPHEEVEFARRMHE-GDEIAKQRLVEANLRLVVSIAKRYVGRGMLFLDL 182

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 183 IQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 240

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R+   L      + KPE+   IAK++ ++E +V  +  ++A D  SL   I   ++  
Sbjct: 241 LIRVSRQLLQELGRDPKPEE---IAKEMEMTEDKVREI-MKIAQDPVSLETPIG--EEED 294

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTL 255
           S   D++  D              K +   +   +  LN RE+++ + R   E+    TL
Sbjct: 295 SHLGDFIPDDDAPAPAEAAAYSLLKEQ---IEDVLGSLNDREQKVLKLRFGLEDGRARTL 351

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           E +  EF+V+RER+RQIEA+A +K++
Sbjct: 352 EEVGKEFDVTRERIRQIEAKALRKLR 377


>gi|320173409|gb|EFW48608.1| RNA polymerase sigma factor RpoS [Shigella dysenteriae CDC 74-1112]
          Length = 342

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 73  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 131

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 132 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 191

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 192 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 248

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 249 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 297

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 298 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 332


>gi|10197699|gb|AAG14981.1|AF242209_6 alternative sigma factor [Escherichia coli]
          Length = 360

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|16761696|ref|NP_457313.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. CT18]
 gi|16766230|ref|NP_461845.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|56414872|ref|YP_151947.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. ATCC 9150]
 gi|62181426|ref|YP_217843.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|157148284|ref|YP_001455603.1| RNA polymerase sigma factor RpoS [Citrobacter koseri ATCC BAA-895]
 gi|167550225|ref|ZP_02343982.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Saintpaul str. SARA29]
 gi|168230998|ref|ZP_02656056.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Kentucky str. CDC 191]
 gi|168235962|ref|ZP_02661020.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. SL480]
 gi|168242664|ref|ZP_02667596.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL486]
 gi|168261948|ref|ZP_02683921.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Hadar str. RI_05P066]
 gi|168463936|ref|ZP_02697853.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Newport str. SL317]
 gi|168820376|ref|ZP_02832376.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Weltevreden str. HI_N05-537]
 gi|194442500|ref|YP_002042165.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Newport str. SL254]
 gi|194451079|ref|YP_002046882.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL476]
 gi|194470798|ref|ZP_03076782.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Kentucky str. CVM29188]
 gi|194738113|ref|YP_002115873.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. CVM19633]
 gi|197263839|ref|ZP_03163913.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Saintpaul str. SARA23]
 gi|197363800|ref|YP_002143437.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. AKU_12601]
 gi|198243199|ref|YP_002216890.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Dublin str. CT_02021853]
 gi|200388856|ref|ZP_03215468.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Virchow str. SL491]
 gi|204928102|ref|ZP_03219302.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Javiana str. GA_MM04042433]
 gi|207858184|ref|YP_002244835.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Enteritidis str. P125109]
 gi|213052392|ref|ZP_03345270.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. E00-7866]
 gi|213648321|ref|ZP_03378374.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. J185]
 gi|224584701|ref|YP_002638499.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Paratyphi C strain RKS4594]
 gi|237729723|ref|ZP_04560204.1| RNA polymerase sigma factor RpoS [Citrobacter sp. 30_2]
 gi|238909692|ref|ZP_04653529.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Tennessee str. CDC07-0191]
 gi|283835495|ref|ZP_06355236.1| RNA polymerase sigma factor RpoS [Citrobacter youngae ATCC 29220]
 gi|61236740|sp|P0A2E5|RPOS_SALTY RecName: Full=RNA polymerase sigma factor rpoS; AltName:
           Full=Sigma-38
 gi|61236751|sp|P0A2E6|RPOS_SALTI RecName: Full=RNA polymerase sigma factor rpoS; AltName:
           Full=Sigma-38
 gi|61236761|sp|P0A2E7|RPOS_SALDU RecName: Full=RNA polymerase sigma factor rpoS; AltName:
           Full=Sigma-38
 gi|1073666|pir||S49471 transcription initiation factor sigma kaltF - Salmonella
           choleraesuis
 gi|6010738|gb|AAF01235.1|AF184104_1 mutant RpoS [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
 gi|558645|emb|CAA57640.1| katF (rpoS) [Salmonella enterica]
 gi|602087|emb|CAA54798.1| KatF [Salmonella enterica subsp. enterica serovar Typhimurium]
 gi|16421473|gb|AAL21804.1| sigma S (sigma 38) factor of RNA polymerase [Salmonella enterica
           subsp. enterica serovar Typhimurium str. LT2]
 gi|16503997|emb|CAD06030.1| RNA polymerase sigma subunit RpoS (sigma-38) [Salmonella enterica
           subsp. enterica serovar Typhi]
 gi|56129129|gb|AAV78635.1| RNA polymerase sigma subunit RpoS (sigma-38) [Salmonella enterica
           subsp. enterica serovar Paratyphi A str. ATCC 9150]
 gi|62129059|gb|AAX66762.1| sigma S (sigma 38) factor of RNA polymerase, major sigmafactor
           during stationary phase [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|157085489|gb|ABV15167.1| hypothetical protein CKO_04101 [Citrobacter koseri ATCC BAA-895]
 gi|194401163|gb|ACF61385.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Newport str. SL254]
 gi|194409383|gb|ACF69602.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL476]
 gi|194457162|gb|EDX46001.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Kentucky str. CVM29188]
 gi|194713615|gb|ACF92836.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. CVM19633]
 gi|195633598|gb|EDX52012.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Newport str. SL317]
 gi|197095277|emb|CAR60830.1| RNA polymerase sigma subunit RpoS (sigma-38) [Salmonella enterica
           subsp. enterica serovar Paratyphi A str. AKU_12601]
 gi|197242094|gb|EDY24714.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Saintpaul str. SARA23]
 gi|197290706|gb|EDY30060.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. SL480]
 gi|197937715|gb|ACH75048.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Dublin str. CT_02021853]
 gi|199605954|gb|EDZ04499.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Virchow str. SL491]
 gi|204322424|gb|EDZ07621.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Javiana str. GA_MM04042433]
 gi|205324779|gb|EDZ12618.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Saintpaul str. SARA29]
 gi|205334505|gb|EDZ21269.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Kentucky str. CDC 191]
 gi|205338030|gb|EDZ24794.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL486]
 gi|205342988|gb|EDZ29752.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Weltevreden str. HI_N05-537]
 gi|205349304|gb|EDZ35935.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Hadar str. RI_05P066]
 gi|206709987|emb|CAR34342.1| RNA polymerase sigma subunit RpoS (sigma-38) [Salmonella enterica
           subsp. enterica serovar Enteritidis str. P125109]
 gi|224469228|gb|ACN47058.1| RNA polymerase sigma factor [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
 gi|226908329|gb|EEH94247.1| RNA polymerase sigma factor RpoS [Citrobacter sp. 30_2]
 gi|261248060|emb|CBG25894.1| RNA polymerase sigma subunit RpoS (sigma-38) [Salmonella enterica
           subsp. enterica serovar Typhimurium str. D23580]
 gi|267995054|gb|ACY89939.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 14028S]
 gi|291068697|gb|EFE06806.1| RNA polymerase sigma factor RpoS [Citrobacter youngae ATCC 29220]
 gi|301159483|emb|CBW19002.1| RNA polymerase sigma subunit RpoS (sigma-38) [Salmonella enterica
           subsp. enterica serovar Typhimurium str. SL1344]
 gi|312913942|dbj|BAJ37916.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhimurium str. T000240]
 gi|320087327|emb|CBY97092.1| RNA polymerase sigma factor rpoS [Salmonella enterica subsp.
           enterica serovar Weltevreden str. 2007-60-3289-1]
 gi|321225598|gb|EFX50652.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhimurium str. TN061786]
 gi|322614255|gb|EFY11186.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315996572]
 gi|322621681|gb|EFY18534.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-1]
 gi|322624542|gb|EFY21375.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-3]
 gi|322628873|gb|EFY25656.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-4]
 gi|322633400|gb|EFY30142.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-1]
 gi|322636024|gb|EFY32732.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-2]
 gi|322639617|gb|EFY36303.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 531954]
 gi|322646916|gb|EFY43419.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. NC_MB110209-0054]
 gi|322652217|gb|EFY48576.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. OH_2009072675]
 gi|322654704|gb|EFY51023.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. CASC_09SCPH15965]
 gi|322658925|gb|EFY55178.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 19N]
 gi|322664508|gb|EFY60702.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 81038-01]
 gi|322668243|gb|EFY64400.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. MD_MDA09249507]
 gi|322673777|gb|EFY69878.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 414877]
 gi|322677838|gb|EFY73901.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 366867]
 gi|322681332|gb|EFY77364.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 413180]
 gi|322683734|gb|EFY79744.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 446600]
 gi|322715910|gb|EFZ07481.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. A50]
 gi|323131276|gb|ADX18706.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 4/74]
 gi|323193878|gb|EFZ79081.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609458-1]
 gi|323200347|gb|EFZ85429.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556150-1]
 gi|323202369|gb|EFZ87413.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609460]
 gi|323205603|gb|EFZ90568.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 507440-20]
 gi|323210115|gb|EFZ95018.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556152]
 gi|323216417|gb|EGA01144.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB101509-0077]
 gi|323220766|gb|EGA05207.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB102109-0047]
 gi|323226390|gb|EGA10598.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB110209-0055]
 gi|323230730|gb|EGA14848.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB111609-0052]
 gi|323234919|gb|EGA19005.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009083312]
 gi|323238958|gb|EGA23008.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009085258]
 gi|323241658|gb|EGA25689.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315731156]
 gi|323248195|gb|EGA32131.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2009159199]
 gi|323251221|gb|EGA35094.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008282]
 gi|323257395|gb|EGA41091.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008283]
 gi|323263241|gb|EGA46779.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008284]
 gi|323264257|gb|EGA47763.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008285]
 gi|323271083|gb|EGA54511.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008287]
 gi|326624653|gb|EGE30998.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Dublin str. 3246]
 gi|332989795|gb|AEF08778.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhimurium str. UK-1]
          Length = 330

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|261883762|ref|ZP_06007801.1| RNA polymerase factor sigma-32 [Campylobacter fetus subsp.
           venerealis str. Azul-94]
          Length = 165

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 67/156 (42%), Positives = 97/156 (62%), Gaps = 1/156 (0%)

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           +MQ+YILR+WS+V+ GT++ QK LFFNLRRL+  L    DN  K E    I+ +L VS S
Sbjct: 1   SMQDYILRNWSIVRGGTSSAQKALFFNLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTS 60

Query: 172 EVISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           +V  M+ RL+G D SL+A +N  +  +S+  D+LV DH  Q+++     + + R   LTR
Sbjct: 61  DVEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTR 120

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           ++  LN RE  I   RRL ++ VTLE L  +  +SR
Sbjct: 121 ALDTLNERELHIIRERRLDDDGVTLEALGEKLGISR 156


>gi|259909441|ref|YP_002649797.1| RNA polymerase sigma factor [Erwinia pyrifoliae Ep1/96]
 gi|224965063|emb|CAX56595.1| RNA polymerase sigma factor [Erwinia pyrifoliae Ep1/96]
          Length = 277

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 138/277 (49%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 8   YLGEIGYSPLLTAEEEVFFARRAL-RGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 66

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 67  IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 126

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I     KP   V+   +LN     + S++  L GD     L 
Sbjct: 127 RTARELSHKLDHEPSAEEIAQKLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 183

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 184 ILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 232

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 233 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQGQ 267


>gi|320538977|ref|ZP_08038652.1| RNA polymerase, sigma S (sigma 38) factor [Serratia symbiotica str.
           Tucson]
 gi|320030910|gb|EFW12914.1| RNA polymerase, sigma S (sigma 38) factor [Serratia symbiotica str.
           Tucson]
          Length = 332

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 84/280 (30%), Positives = 143/280 (51%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA+ Y   GL + ++
Sbjct: 63  YLGEIGYSPLLTAEEEVYFARRAL-RGDVLSRRRMIESNLRLVVKIALRYSNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 181

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD S  AL+
Sbjct: 182 RTARELSHRLDHEPSAEEIAEQLDKPVGDVSHMLRLN---ERITSVDTPLGGD-SEKALL 237

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
           +          +    D D ++ ++              + +  LN ++R +  ARR   
Sbjct: 238 DILADEKDNGPEGTTQDDDMKQSIV--------------KWLFELNAKQREVL-ARRFGL 282

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L     TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 283 LGYESATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 322


>gi|332799075|ref|YP_004460574.1| RpoD subfamily RNA polymerase sigma-70 [Tepidanaerobacter sp. Re1]
 gi|332696810|gb|AEE91267.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Tepidanaerobacter
           sp. Re1]
          Length = 374

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 82/265 (30%), Positives = 141/265 (53%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  +EE +L+KR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 108 YLKEIGKVPLLSAEEEIMLSKRI-EEGDKEAKRRLAEANLRLVVSIAKKYVGRGMLFLDL 166

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV+KFD ++G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 167 IQEGNLGLMKAVEKFDYKKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 224

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R++  L      +  PE+   IA+++ +   +V  +  ++A  E ++      ++  S
Sbjct: 225 LIRIQRQLLQELGRDPLPEE---IAEEMELPVEKVREI-MKIA-QEPVSLATPIGEEEDS 279

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++    D +     +       +  L   +  L PRE ++   R   ++  P TLE
Sbjct: 280 FLGDFI---PDDEALAPADAAAYLLLKEQLEDVLETLTPREEKVLRLRFGLDDGRPRTLE 336

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +   F V+RER+RQIEA+A +K++
Sbjct: 337 EVGQVFGVTRERIRQIEAKALRKLR 361


>gi|315127432|ref|YP_004069435.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Pseudoalteromonas sp. SM9913]
 gi|315015946|gb|ADT69284.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Pseudoalteromonas sp. SM9913]
          Length = 323

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 91/274 (33%), Positives = 147/274 (53%), Gaps = 19/274 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A++  + G  ++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 52  YLGEIGFSPLLSAEEEVFFARKSLK-GCEASRKRMIESNLRLVVKIARRYNNRGLALLDL 110

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 111 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 169

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +   Q + D+    E+   IA+ L+    +V  M         LN  I S D    
Sbjct: 170 LRTARELTQKL-DHEPTAEE---IAESLDRPVEDVTKML-------RLNEKIASVDMPIG 218

Query: 199 QWQDWLVYDHDGQEQ-VLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARR---LQENPV 253
              D  + D    E+ V  E E + N  N  +   +  LNP++R +  ARR   L   P 
Sbjct: 219 SENDSALLDVIADEKNVGPEGEVQNNDMNTHIIDWLGELNPKQREVL-ARRFGLLGYEPS 277

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           TLE++  E  ++RERVRQI+  A +++++ +Q++
Sbjct: 278 TLEDVGREIGLTRERVRQIQVEALRRLKDILQQE 311


>gi|6010728|gb|AAF01230.1|AF184099_1 mutant RpoS [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
          Length = 330

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|4100838|gb|AAD01001.1| RpoS [Escherichia coli]
 gi|4100840|gb|AAD01002.1| RpoS [Escherichia coli]
 gi|4100842|gb|AAD01003.1| RpoS [Escherichia coli]
          Length = 328

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|188997117|ref|YP_001931368.1| RNA polymerase, sigma 70 subunit, RpoD family [Sulfurihydrogenibium
           sp. YO3AOP1]
 gi|188932184|gb|ACD66814.1| RNA polymerase, sigma 70 subunit, RpoD family [Sulfurihydrogenibium
           sp. YO3AOP1]
          Length = 281

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 87/274 (31%), Positives = 143/274 (52%), Gaps = 35/274 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ ++ K PML  +EE  LA R +  GD  A  +LV  +LR VV IA  + G+G+P+
Sbjct: 10  LQLYMQQMGKHPMLSPEEEKELAIRAK-QGDKEALKKLVEGNLRFVVSIAKNFMGWGVPL 68

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           +++++ GN+GL++A K+FDP++  +  +Y++WWI+ A+ + I +    V+I     ++ L
Sbjct: 69  TDLIAAGNLGLIEAAKRFDPDKNVKFISYAVWWIRQAIMQTIFQQTGAVRIPV---KESL 125

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRL--AGD 183
           F  + ++K   + + +   +      IAK+LN S  +V          IS++  L   G+
Sbjct: 126 F--IAKVKETYEKLKEELGREPTEEEIAKRLNTSVKKVKNALSIVRLPISLDMPLGEGGE 183

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           E    L   S K +              E+ LIE+   K   +ML     VL+ RE+ I 
Sbjct: 184 EDFTLLDVLSKKGTEDI-----------EKELIEETIHKELESML----DVLDEREKEII 228

Query: 244 EARRL--QENPVTLENLSSEFEVSRERVRQIEAR 275
           + R     E P TLE +  +  +SRERVRQ+E R
Sbjct: 229 KMRYGLDGEEPKTLEEVGEKLGISRERVRQLEQR 262


>gi|255655465|ref|ZP_05400874.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           QCD-23m63]
 gi|296451458|ref|ZP_06893195.1| DNA-directed RNA polymerase sigma subunit RpoD [Clostridium
           difficile NAP08]
 gi|296880193|ref|ZP_06904159.1| DNA-directed RNA polymerase sigma subunit RpoD [Clostridium
           difficile NAP07]
 gi|296259725|gb|EFH06583.1| DNA-directed RNA polymerase sigma subunit RpoD [Clostridium
           difficile NAP08]
 gi|296428782|gb|EFH14663.1| DNA-directed RNA polymerase sigma subunit RpoD [Clostridium
           difficile NAP07]
          Length = 388

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 89/266 (33%), Positives = 144/266 (54%), Gaps = 15/266 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L+  EE   A+R  E GD  A  RLV ++LRLVV IA  Y G G+   ++
Sbjct: 122 YLKEIGKIPLLKPHEEVEFARRMHE-GDEIAKQRLVEANLRLVVSIAKRYVGRGMLFLDL 180

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 181 IQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 238

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R+   L      + KPE+   IAK++ ++E +V  +  ++A D  SL   I   ++  
Sbjct: 239 LIRVSRQLLQELGRDPKPEE---IAKEMEMTEDKVREI-MKIAQDPVSLETPIG--EEED 292

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTL 255
           S   D++  D              K +   +   +  LN RE+++ + R   E+    TL
Sbjct: 293 SHLGDFIPDDDAPAPAEAAAYSLLKEQ---IEDVLGSLNDREQKVLKLRFGLEDGRARTL 349

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           E +  EF+V+RER+RQIEA+A +K++
Sbjct: 350 EEVGKEFDVTRERIRQIEAKALRKLR 375


>gi|153839213|ref|ZP_01991880.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus AQ3810]
 gi|149747278|gb|EDM58264.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus AQ3810]
          Length = 274

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 89/280 (31%), Positives = 146/280 (52%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 2   YLGEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 60

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++      ++      K L   
Sbjct: 61  IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTTRLPIHV-VKELNIY 119

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +  L    D+    E++ A        ++K L ++E  + S++  + GD     L 
Sbjct: 120 LRTAR-ELSQKLDHEPTAEEIAAQLDIPVEDVSKMLRLNER-ISSVDTPIGGDGEKALLD 177

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
              D N+S   D  V   D             + ++ L   +  LNP+++ +  ARR   
Sbjct: 178 IIPDANNS---DPEVSTQD------------DDIKSSLIHWLEELNPKQKEVL-ARRFGL 221

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 222 LGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLREILIKQ 261


>gi|441116|gb|AAA61628.1| RNA polymerase sigma factor [Salmonella enterica subsp. enterica
           serovar Typhimurium]
 gi|1090521|prf||2019251A RNA polymerase sigma factor
          Length = 330

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRDL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|301049496|ref|ZP_07196454.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 185-1]
 gi|300298727|gb|EFJ55112.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 185-1]
          Length = 342

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 73  YLGEIGYSPLLTAKEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 131

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 132 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 191

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 192 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 248

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 249 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 297

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 298 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 332


>gi|12483895|gb|AAG53883.1|AF275947_2 sigma factor RpoS [Escherichia coli]
          Length = 366

 Score =  118 bits (295), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 73  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 131

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 132 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 191

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 192 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 248

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 249 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 297

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 298 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 332


>gi|302391478|ref|YP_003827298.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acetohalobium
           arabaticum DSM 5501]
 gi|302203555|gb|ADL12233.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acetohalobium
           arabaticum DSM 5501]
          Length = 358

 Score =  117 bits (294), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 85/265 (32%), Positives = 138/265 (52%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+ +L  +EE  LAKR  E GD+ A   LV ++LRLVV IA  Y G G+   ++
Sbjct: 92  YLKEIGKVDLLTAEEEVELAKRM-EEGDMEAKRMLVEANLRLVVSIAKKYVGRGMLFLDL 150

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 151 IQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRSIADQARTIRI--PVHMVETINK 208

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           + R+  HL         PE+   IA+++++SE +V          E ++      ++  S
Sbjct: 209 VIRVSRHLLQELGREPTPEE---IAEEMDLSEEKV--REVLKISQEPVSLETPIGEEEDS 263

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++  D      V          +  L   +  L+ RE+R+ E R   E+    TLE
Sbjct: 264 HLGDFIEDDDAPAPSV---AASHMMLQEQLDEVLDTLSDREKRVLELRFGVEDGRSRTLE 320

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF V+RER+RQIEA+A +K++
Sbjct: 321 EVGKEFGVTRERIRQIEAKALRKLR 345


>gi|254975009|ref|ZP_05271481.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           QCD-66c26]
 gi|255092397|ref|ZP_05321875.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile CIP
           107932]
 gi|255100481|ref|ZP_05329458.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           QCD-63q42]
 gi|255306421|ref|ZP_05350592.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile ATCC
           43255]
 gi|255314137|ref|ZP_05355720.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           QCD-76w55]
 gi|255516815|ref|ZP_05384491.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           QCD-97b34]
 gi|255649917|ref|ZP_05396819.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           QCD-37x79]
 gi|260683071|ref|YP_003214356.1| RNA polymerase factor sigma-43 [Clostridium difficile CD196]
 gi|260686669|ref|YP_003217802.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           R20291]
 gi|306520001|ref|ZP_07406348.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           QCD-32g58]
 gi|260209234|emb|CBA62522.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           CD196]
 gi|260212685|emb|CBE03759.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           R20291]
          Length = 388

 Score =  117 bits (294), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 89/266 (33%), Positives = 144/266 (54%), Gaps = 15/266 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L+  EE   A+R  E GD  A  RLV ++LRLVV IA  Y G G+   ++
Sbjct: 122 YLKEIGKIPLLKPHEEVEFARRMHE-GDEIAKQRLVEANLRLVVSIAKRYVGRGMLFLDL 180

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 181 IQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 238

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R+   L      + KPE+   IAK++ ++E +V  +  ++A D  SL   I   ++  
Sbjct: 239 LIRVSRQLLQELGRDPKPEE---IAKEMEMTEDKVREI-MKIAQDPVSLETPIG--EEED 292

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTL 255
           S   D++  D              K +   +   +  LN RE+++ + R   E+    TL
Sbjct: 293 SHLGDFIPDDDAPAPAEAAAYSLLKEQ---IEDVLGSLNDREQKVLKLRFGLEDGRARTL 349

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           E +  EF+V+RER+RQIEA+A +K++
Sbjct: 350 EEVGKEFDVTRERIRQIEAKALRKLR 375


>gi|300813859|ref|ZP_07094164.1| RNA polymerase sigma factor RpoD [Peptoniphilus sp. oral taxon 836
           str. F0141]
 gi|300512046|gb|EFK39241.1| RNA polymerase sigma factor RpoD [Peptoniphilus sp. oral taxon 836
           str. F0141]
          Length = 361

 Score =  117 bits (294), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 87/267 (32%), Positives = 140/267 (52%), Gaps = 17/267 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L   EE  +AKR  E+GD SA   L  ++LRLVV IA  Y G G+   ++
Sbjct: 95  YLKEIGKIPLLTGDEEVEIAKRM-ENGDNSAKKELAEANLRLVVSIAKRYVGRGMSFLDL 153

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 154 IQEGNLGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 211

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R++  L      +  PE+   IAK++++   +V  +        SL   I   ++  S
Sbjct: 212 LVRVQRQLVQELGRDPLPEE---IAKEMSIDVEKVREIQKIAQEPVSLETPI--GEEEDS 266

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNR--RNMLTRSMSVLNPRERRIFEARRLQEN--PVT 254
              D++       E++L  ++       R  L+  +  L  RE+++   R   ++    T
Sbjct: 267 HLGDFI-----PDEEILSPQDAATFTLLREQLSTVLETLTDREKKVLTLRFGLDDGRART 321

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQ 281
           LE +  EF V+RER+RQIEA+A +K++
Sbjct: 322 LEEVGKEFAVTRERIRQIEAKAIRKLR 348


>gi|266625476|ref|ZP_06118411.1| RNA polymerase sigma factor RpoD [Clostridium hathewayi DSM 13479]
 gi|288862622|gb|EFC94920.1| RNA polymerase sigma factor RpoD [Clostridium hathewayi DSM 13479]
          Length = 381

 Score =  117 bits (294), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 88/285 (30%), Positives = 145/285 (50%), Gaps = 41/285 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L   EE  LAKR +  GD  A  RL+ ++LRLVV IA  Y G G+   ++
Sbjct: 116 YLKEIGTVPLLSADEELRLAKR-KADGDEDAKERLIEANLRLVVSIAKRYTGRGMSFLDL 174

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           V EGN+GL++ V+KFD  +G++L+TY+ WWI+ ++   +      +++      T N   
Sbjct: 175 VQEGNLGLIKGVEKFDYTKGYKLSTYATWWIRQSVTRALADQARTIRVPVHMVETINKMS 234

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             Q++L   L    G+  ++T+          +A  L++SE +V+ +        SL   
Sbjct: 235 KMQRKLTLEL----GYEPSVTE----------LADALDMSEDKVMEIMQIAREPASLETP 280

Query: 190 INSSDKNSSQWQDW-----LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           I   D   S   D+     +V      E V++        R  +   +  L  RER++  
Sbjct: 281 IGEED--DSNLGDFVADNNVVTPEGNVESVML--------REHIDALLGDLKERERQVIV 330

Query: 245 ARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R   E+  P TLE +  EF V+RER+RQIEA+A +K++  ++ +
Sbjct: 331 LRFGLEDGHPRTLEEVGKEFNVTRERIRQIEAKALRKLRNPVRSK 375


>gi|168704138|ref|ZP_02736415.1| RNA polymerase sigma factor rpoS [Gemmata obscuriglobus UQM 2246]
          Length = 280

 Score =  117 bits (294), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 89/297 (29%), Positives = 143/297 (48%), Gaps = 37/297 (12%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           K M I   G   +S Y+ EI + P+L   EE  L  R  + GD +A  R+V ++LRLVV 
Sbjct: 9   KPMGISAPGGTAMSAYLREIDRTPLLSATEERELGGRILD-GDPAARDRMVRANLRLVVN 67

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           +A GY G GL + ++V+EGN+GL++AV+ FDP    R +TY+ +WIK ++Q  I+ +   
Sbjct: 68  LARGYTGRGLSLDDLVAEGNMGLLRAVEGFDPGMSTRFSTYASFWIKQSIQRAIVNTART 127

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV--ISMNCRLA 181
           +++ T      L    RR    L         PE+V   A  L +S  ++  + +  ++A
Sbjct: 128 IRVPT--YMAALVARWRRATAALGDELGRAPAPEEV---AGHLGLSRRKLAMVQLALKVA 182

Query: 182 G--------DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
           G        +  L  LI  +  + S        D D  EQ+ +  E+           + 
Sbjct: 183 GAGTQADDAEGGLEGLIPDTRDSGS--------DADAAEQLKLVFEQ-----------LD 223

Query: 234 VLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            LNPR+  +   R     E P TL+ +     +++ERVRQIE+ A   +   +  +V
Sbjct: 224 RLNPRDADVLRLRFGLSGEEPKTLKEVGEALGLTKERVRQIESAALSALATGLVDRV 280


>gi|333001093|gb|EGK20663.1| RNA polymerase sigma factor RpoS [Shigella flexneri K-272]
 gi|333015402|gb|EGK34741.1| RNA polymerase sigma factor RpoS [Shigella flexneri K-227]
          Length = 330

 Score =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 140/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTVRELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|83589488|ref|YP_429497.1| RNA polymerase sigma factor RpoD [Moorella thermoacetica ATCC
           39073]
 gi|83572402|gb|ABC18954.1| RNA polymerase, sigma 70 subunit, RpoD [Moorella thermoacetica ATCC
           39073]
          Length = 361

 Score =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 87/264 (32%), Positives = 136/264 (51%), Gaps = 13/264 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 95  YLKEIGRVPLLTPEEEIELAKRM-EAGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 153

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 154 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 211

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R++  L         PE+   IA ++++    V  +        SL   I   ++  S
Sbjct: 212 LIRVQRQLLQELGREPTPEE---IAHEMDIPVERVREIQKIAQEPVSLETPIG--EEEDS 266

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D+ + D D Q     E       R  L   ++ L PRE+R+   R   ++    TLE
Sbjct: 267 HLGDF-IEDEDAQAPA--EAASFMLLREQLEEVLNSLTPREKRVLRLRFGLDDGRARTLE 323

Query: 257 NLSSEFEVSRERVRQIEARAFKKV 280
            +  EF V+RER+RQIEA+A +K+
Sbjct: 324 EVGQEFGVTRERIRQIEAKALRKL 347


>gi|315137348|dbj|BAJ44507.1| RNA polymerase sigma factor RpoS [Escherichia coli DH1]
          Length = 330

 Score =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 139/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL +AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLTRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|71278347|ref|YP_267823.1| RNA polymerase sigma factor RpoS [Colwellia psychrerythraea 34H]
 gi|71144087|gb|AAZ24560.1| RNA polymerase sigma factor RpoS [Colwellia psychrerythraea 34H]
          Length = 296

 Score =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 92/280 (32%), Positives = 149/280 (53%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE V   R    GD  +  R++ S+LRLVVKIA  Y   GLP+ ++
Sbjct: 27  YLSEIGFSPLLTAEEE-VYFSRLALKGDEPSRKRMIESNLRLVVKIARRYNNRGLPLLDL 85

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 86  IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNIY 144

Query: 139 LRRLKGHLQAITDNNLKPEQV-------VAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
           LR  +  +Q + D+    E +       VA   K+      + S++   AG ES  AL++
Sbjct: 145 LRASRELIQKL-DHEPTAEDIAQHLDRPVADVNKMLRLNERIASVDTPFAG-ESDKALLD 202

Query: 192 S-SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
             +D+ S+           G E  L    + ++  N +   ++ LN ++R +  ARR   
Sbjct: 203 VIADEKST-----------GPESDL----QSEDMSNNIIHWLNELNTKQREVL-ARRFGL 246

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L     TLEN+  E  ++RERVRQI+  A K++++ + +Q
Sbjct: 247 LGYEASTLENVGREIGLTRERVRQIQVEALKRLRDILSQQ 286


>gi|332140079|ref|YP_004425817.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Alteromonas macleodii str.
           'Deep ecotype']
 gi|332143123|ref|YP_004428861.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Alteromonas macleodii str.
           'Deep ecotype']
 gi|327550101|gb|AEA96819.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Alteromonas macleodii str.
           'Deep ecotype']
 gi|327553145|gb|AEA99863.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Alteromonas macleodii str.
           'Deep ecotype']
          Length = 330

 Score =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 86/275 (31%), Positives = 147/275 (53%), Gaps = 21/275 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R  + G  ++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 59  YLGEIGFSPLLTAEEEVYFARRSLK-GCEASRKRMIVSNLRLVVKIARRYNNRGLALLDL 117

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 118 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 176

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +  L    D+    E++ A   K     ++++ +N R          I S D    
Sbjct: 177 LRASR-ELSQKLDHEPTAEEIAAALDKPVEDVTKMLRLNER----------ITSVDTPIG 225

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKN---RRNMLTRSMSVLNPRERRIFEARR---LQENP 252
              D  + D    E+    +E  ++   + N++T  +  LNP++R +  ARR   +   P
Sbjct: 226 GENDKALLDIIADEKEFSPEESLQDSDIKSNIIT-WLEELNPKQREVL-ARRFGLMGYEP 283

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            TLE++ +E  ++RERVRQI+  A +++++ +  Q
Sbjct: 284 STLEDVGAEIGLTRERVRQIQVEALRRLRDMLGHQ 318


>gi|295101750|emb|CBK99295.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii L2-6]
          Length = 359

 Score =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 80/240 (33%), Positives = 128/240 (53%), Gaps = 14/240 (5%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A  RL  ++LRLVV +A  Y G GLP  +++ EGN+GLM+A +KF+P+RGF+ +TY
Sbjct: 117 GDEDARRRLSEANLRLVVSVAKRYAGRGLPFLDLIQEGNLGLMKAAEKFEPDRGFKFSTY 176

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + WWI+ ++   I      ++I        L  ++ R+K     +     +      IA 
Sbjct: 177 ATWWIRQSITRAIADQGRTIRIPV-----HLVESINRVKKTAGELLRRTGREPTAEEIAA 231

Query: 165 KLNVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           +L++  + V  +  +LA D  SL   +   ++  +  +D++  D  G   V  ++  R+ 
Sbjct: 232 QLDMEPARVREL-IQLAQDPISLETPVG--EEEDAHLEDFIQDDEAG---VPADEAGRQL 285

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R  L   +  L PRE R+   R   E+    TLE L  EF V+RERVRQIEA+A +K++
Sbjct: 286 LRRELMNVLKSLTPREERVIALRFGLEDGRARTLEELGREFNVTRERVRQIEAKALRKLR 345


>gi|242238323|ref|YP_002986504.1| RNA polymerase sigma factor RpoS [Dickeya dadantii Ech703]
 gi|242130380|gb|ACS84682.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dickeya dadantii
           Ech703]
          Length = 330

 Score =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 91/276 (32%), Positives = 149/276 (53%), Gaps = 23/276 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+S+  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVSSRRRMIESNLRLVVKIARRYNNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI-VKELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV---ISMNCRLAGDESLNALINSSDK 195
           LR  +  L    D+    E+   IA++L+    +V   + +N R+   ++   L   SDK
Sbjct: 179 LRTAR-ELSHKLDHEPSAEE---IAERLDRPVDDVNRMLRLNERITSVDT--PLGGDSDK 232

Query: 196 NSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR---LQEN 251
                 D L  + D G E      + ++N    + + +  LN ++R +  ARR   L   
Sbjct: 233 ---ALLDILADEKDNGPEDTTQNNDMKQN----IVKWLFELNAKQREVL-ARRFGLLGYE 284

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 285 AATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|312883942|ref|ZP_07743659.1| hypothetical protein VIBC2010_01628 [Vibrio caribbenthicus ATCC
           BAA-2122]
 gi|309368400|gb|EFP95935.1| hypothetical protein VIBC2010_01628 [Vibrio caribbenthicus ATCC
           BAA-2122]
          Length = 325

 Score =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 87/285 (30%), Positives = 147/285 (51%), Gaps = 41/285 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 53  YLGEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 111

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 112 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 170

Query: 139 LRRLKGHLQAITDNNLKPEQVV--------AIAKKLNVSESEVISMNCRLAGDESLNAL- 189
           LR  +   Q + D+    E++          ++K L ++E  + S++  + GD     L 
Sbjct: 171 LRTARELSQKL-DHEPTAEEIALQLDKPVDDVSKMLRLNE-RISSVDTPIGGDGEKALLD 228

Query: 190 ----INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
               +N+SD   S   D +                    ++ L   +  LNP+++ +  A
Sbjct: 229 IIPDVNNSDPEVSTQDDDI--------------------KSSLIDWLDELNPKQKEVL-A 267

Query: 246 RR---LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           RR   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 268 RRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVKQ 312


>gi|288819153|ref|YP_003433501.1| RNA polymerase sigma factor RpoS [Hydrogenobacter thermophilus
           TK-6]
 gi|288788553|dbj|BAI70300.1| RNA polymerase sigma factor RpoS [Hydrogenobacter thermophilus
           TK-6]
 gi|308752737|gb|ADO46220.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Hydrogenobacter
           thermophilus TK-6]
          Length = 310

 Score =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 95/298 (31%), Positives = 153/298 (51%), Gaps = 42/298 (14%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +++Y+ ++ KIP+L  +EE  +A+R +E GD  A  +LV S+LR V+ IA  Y GYGLP+
Sbjct: 10  INQYLKKVAKIPLLTPEEEKEVARRAKE-GDQEAFRKLVESNLRFVINIAKQYLGYGLPL 68

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ--- 132
           SE+++ GN GL++A K+FDP+RG +  +Y++WWI+ A+ + + +    V+I         
Sbjct: 69  SELIAAGNHGLIEAAKRFDPDRGVKFISYAVWWIRQAIMQALSQQTGAVRIPLKQAHVIN 128

Query: 133 ------KRLFFNLRR---------------LKGHLQAITDNNLKPEQVVAIAK----KLN 167
                  RLF  L R               L   L+         ++V    K    K++
Sbjct: 129 RIGSIYSRLFRELEREPTPEEVAIEYSKEILSRELERELGRKPTKDEVEQRFKKEGFKIS 188

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY--DHDGQEQVLIEKEERKNRR 225
             E E     CR+    SL+A +  ++   + + D+L      D +E+++ E  E K   
Sbjct: 189 PEEVEKCLQVCRIPL--SLDAPVGENE--DTFFVDFLSQHGTADVEERIINEVLE-KEIG 243

Query: 226 NMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +ML R    L  +ERR+ E R     E P TL  +     +SRERVRQ+E RA +K++
Sbjct: 244 DMLDR----LPEKERRVIELRFGLRGEEPRTLREIGDILNISRERVRQLETRALRKLR 297


>gi|260361829|ref|ZP_05774845.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus K5030]
 gi|308114475|gb|EFO52015.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus K5030]
          Length = 329

 Score =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 89/280 (31%), Positives = 147/280 (52%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R+  S+LRLVVKI+  Y   GL + ++
Sbjct: 57  YLGEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMFESNLRLVVKISRRYSNRGLALLDL 115

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 116 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 174

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +   Q + D+    E++ A        ++K L ++E  + S++  + GD     L 
Sbjct: 175 LRTARELSQKL-DHEPTAEEIAAQLDIPVEDVSKMLRLNE-RISSVDTPIGGDGEKALLD 232

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
              D N+S   D  V   D             + ++ L   +  LNP+++ +  ARR   
Sbjct: 233 IIPDANNS---DPEVSTQD------------DDIKSSLIHWLEELNPKQKEVL-ARRFGL 276

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 277 LGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLREILIKQ 316


>gi|319955411|ref|YP_004166678.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Cellulophaga
           algicola DSM 14237]
 gi|319424071|gb|ADV51180.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cellulophaga
           algicola DSM 14237]
          Length = 286

 Score =  117 bits (294), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 93/298 (31%), Positives = 150/298 (50%), Gaps = 59/298 (19%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y  EI K+ M+   EE  LA + RE GD  A + LV ++LR VV +A  Y+G GL +
Sbjct: 18  LEKYFQEISKLDMITANEEVELAIKIRE-GDQVALNTLVNANLRFVVSVAKQYQGSGLRL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI-----LRSWSLVKIGTTA 130
           S++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + I     +    L KIG   
Sbjct: 77  SDLINEGNVGLVKAAKRFDETRGFKFISYAVWWIRQSILQAISELSRMVRLPLNKIGEIG 136

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRL 180
              ++F  L +    LQ       +P   + IA++L++S S+V          +SM+   
Sbjct: 137 KINKVFSYLEQ---SLQ-------RPPNAIEIARELDMSTSQVKLAMKNTGKHLSMDAPF 186

Query: 181 AGDESLNA--LINSSDKNSSQ---WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
           A  ES N   ++ S + NS      Q+ L  D                    +   +S L
Sbjct: 187 AEGESSNLYNVVQSKEANSPDTNLMQESLSSD--------------------IGDLLSTL 226

Query: 236 NPRERRIFEARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
             RE  I    RL     ++ P++L  +   F++SRERVRQI  +A + ++   QK+V
Sbjct: 227 PSRESDII---RLYYGIGEKAPMSLTEIGEIFDISRERVRQIREKAIRVLRRKSQKEV 281


>gi|157369077|ref|YP_001477066.1| RNA polymerase sigma factor RpoS [Serratia proteamaculans 568]
 gi|157320841|gb|ABV39938.1| RNA polymerase, sigma 70 subunit, RpoD family [Serratia
           proteamaculans 568]
          Length = 332

 Score =  117 bits (293), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 139/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 63  YLGEIGYSPLLTAEEEVYFARRAL-RGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 181

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 182 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 238

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 239 ILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 287

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 288 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQMQ 322


>gi|221633247|ref|YP_002522472.1| RNA polymerase sigma factor rpoD [Thermomicrobium roseum DSM 5159]
 gi|221156052|gb|ACM05179.1| RNA polymerase sigma factor rpoD [Thermomicrobium roseum DSM 5159]
          Length = 340

 Score =  117 bits (293), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 93/266 (34%), Positives = 140/266 (52%), Gaps = 15/266 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ +I + P+L  +EE  LAKR +E GD  A  R V S+LRLVV IA  Y G GL + ++
Sbjct: 73  YLRDIAEAPLLTPEEEVELAKRIKE-GDTEALQRFVRSNLRLVVSIAKRYVGRGLSLLDL 131

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM+AV+KFD  RG+R +TY+ WWI+ A+   I      +++          ++
Sbjct: 132 IQEGNIGLMRAVEKFDWRRGYRFSTYATWWIRQAITRAIADQGRTIRLPVHMTDSITRYH 191

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
             R    L         PE+   IA+ ++V + E I+   R A    SL+  ++  D+ S
Sbjct: 192 --RTTTQLAQELGRQPTPEE---IAEAMSV-QPEKIAQIVRAAQRAVSLDQPLSEEDETS 245

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTL 255
               D L+ D   Q    +  EE   RR+ +   + +L PRER + + R    +  P TL
Sbjct: 246 --LGD-LIADELAQSPEEL-AEESLMRRD-IAEILEMLTPRERLVLQLRYGLSDGEPRTL 300

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
             +     +SRERVRQIE  A +K++
Sbjct: 301 AEVGDLLGISRERVRQIENEALRKLR 326


>gi|310766652|gb|ADP11602.1| RNA polymerase sigma factor RpoS [Erwinia sp. Ejp617]
          Length = 330

 Score =  117 bits (293), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 138/277 (49%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVFFARRAL-RGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I     KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAQKLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQGQ 320


>gi|54294183|ref|YP_126598.1| RNA polymerase sigma factor RpoS [Legionella pneumophila str. Lens]
 gi|54297202|ref|YP_123571.1| RNA polymerase sigma factor RpoS [Legionella pneumophila str.
           Paris]
 gi|53750987|emb|CAH12398.1| RNA polymerase sigma factor RpoS [Legionella pneumophila str.
           Paris]
 gi|53754015|emb|CAH15486.1| RNA polymerase sigma factor RpoS [Legionella pneumophila str. Lens]
 gi|307609996|emb|CBW99528.1| RNA polymerase sigma factor RpoS [Legionella pneumophila 130b]
          Length = 341

 Score =  117 bits (293), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 82/275 (29%), Positives = 147/275 (53%), Gaps = 23/275 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A    + GD+ A  +++ S+LRLVVKIA  Y   GLP+ ++
Sbjct: 74  YLGEIGFSPLLTAEEEIHYATLALK-GDMEARKKMIESNLRLVVKIARRYLNRGLPLLDL 132

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM++V+KFDP+RGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 133 IEEGNLGLMKSVEKFDPKRGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 191

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-------DESLNALIN 191
           LR  +   Q + D+   PE++  +  K      +++ +N ++A        DE+ + L  
Sbjct: 192 LRAARQLTQKL-DHEPSPEEIAEMVDKPLEDVQKLLGLNDKVASVDTPIGFDETKSLLDT 250

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
            +D+NS    + L  ++  Q    +  +  +N++ ++ R   +      R FE       
Sbjct: 251 IADENSLNPAELLTNENLRQHIESLLDKLTENQQQVIARRFGL------RGFEK------ 298

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             TLE++  E +++RERVRQI+  A K ++  +++
Sbjct: 299 -ATLEDVGKEIDLTRERVRQIQVEALKTLRTLLER 332


>gi|5771430|gb|AAD51396.1|AF117715_5 stationary phase specific sigma factor homolog [Legionella
           pneumophila]
          Length = 341

 Score =  117 bits (293), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 82/275 (29%), Positives = 147/275 (53%), Gaps = 23/275 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A    + GD+ A  +++ S+LRLVVKIA  Y   GLP+ ++
Sbjct: 74  YLGEIGFSPLLTAEEEIHYATLALK-GDMEARKKMIESNLRLVVKIARRYLNRGLPLLDL 132

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM++V+KFDP+RGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 133 IEEGNLGLMKSVEKFDPKRGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 191

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-------DESLNALIN 191
           LR  +   Q + D+   PE++  +  K      +++ +N ++A        DE+ + L  
Sbjct: 192 LRAARQLTQKL-DHEPSPEEIAEMVDKPLEDVQKLLGLNDKVASVDTPIGFDETKSLLDT 250

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
            +D+NS    + L  ++  Q    +  +  +N++ ++ R   +      R FE       
Sbjct: 251 IADENSLNPAELLTNENLRQHIESLLDKLTENQQQVIARRFGL------RGFEK------ 298

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             TLE++  E +++RERVRQI+  A K ++  +++
Sbjct: 299 -ATLEDVGKEIDLTRERVRQIQVEALKTLRTLLER 332


>gi|327399101|ref|YP_004339970.1| putative RNA polymerase, sigma 70 family subunit [Hippea maritima
           DSM 10411]
 gi|327181730|gb|AEA33911.1| putative RNA polymerase, sigma 70 family subunit [Hippea maritima
           DSM 10411]
          Length = 289

 Score =  117 bits (293), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 91/298 (30%), Positives = 149/298 (50%), Gaps = 44/298 (14%)

Query: 4   KNMSIIVNGEI------GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSH 57
           KN  + +N E+       L+ Y+ EI KIP+L  +EE  L +R ++ GD  A  +LV  +
Sbjct: 8   KNEQLAINDEVDLAESSALTSYLKEISKIPVLSAEEEKELGRRIKK-GDKEALKKLVKHN 66

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LR VV +A  Y+  G+P+ ++++EGN+GL++A KKFDP+R  +  +Y+ WWIK ++ +YI
Sbjct: 67  LRFVVSVAKKYKNLGIPLLDLINEGNLGLIKAAKKFDPDRNTKFISYAAWWIKQSIMKYI 126

Query: 118 ----------LRSWSLV-KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
                     L++ S + KI T     R  F+   + G +  I+D               
Sbjct: 127 TEQSTPIRIPLKAKSRISKIDTIKEDYRQKFDEEPMNGEISEISD--------------- 171

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRR 225
            +SE E+   N  LA         +S D   S  +D L  D    ++  IE E  +K+  
Sbjct: 172 -LSEREI--KNAELA-----RFYFDSLDDYVSDDKDILKGDLISLKEQSIEDEHIQKSLI 223

Query: 226 NMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             + + +S L  RE+ I + R       P TL  +  ++ +S+ERVRQ+E     K++
Sbjct: 224 EEVNKFLSELPEREQDIIKLRYGLYDGRPRTLREIGEKYGISKERVRQLENNILNKLK 281


>gi|302871329|ref|YP_003839965.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor obsidiansis OB47]
 gi|302574188|gb|ADL41979.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor obsidiansis OB47]
          Length = 417

 Score =  117 bits (293), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 89/265 (33%), Positives = 139/265 (52%), Gaps = 15/265 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 151 YLKEIGKIPLLTPEEEIELAKRI-EQGDEEAKKRLAEANLRLVVSIAKRYVGRGMLFLDL 209

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 210 IQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 267

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R+   L         PE+   IAK++N+   +V  +  ++A +  SL   I   ++  
Sbjct: 268 LVRVSRQLLQEKGREPTPEE---IAKEMNMPVEKVREI-LKIAQEPVSLETPI--GEEED 321

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTL 255
           S   D++    D       E       +  L   +  LN RE+++ + R   E+    TL
Sbjct: 322 SHLGDFI---PDDDALAPSEAAAYSMLKEQLLEVLDSLNEREKKVLKLRFGLEDGRARTL 378

Query: 256 ENLSSEFEVSRERVRQIEARAFKKV 280
           E +  EF V+RER+RQIEA+A +K+
Sbjct: 379 EEVGKEFNVTRERIRQIEAKALRKL 403


>gi|226226116|ref|YP_002760222.1| RNA polymerase sigma factor [Gemmatimonas aurantiaca T-27]
 gi|226089307|dbj|BAH37752.1| RNA polymerase sigma factor [Gemmatimonas aurantiaca T-27]
          Length = 295

 Score =  117 bits (293), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 85/276 (30%), Positives = 147/276 (53%), Gaps = 25/276 (9%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y++E+   P+L+  EE  LAK+ R  GD  A   LV  +LR V+ +A  Y+  GLP+
Sbjct: 26  LDQYLYEVSTYPLLKAAEEIELAKKIR-AGDQDALQELVKRNLRFVISVAKKYQNRGLPL 84

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI--GTTANQK 133
            +++ EGN+GL+ A +KFDP++G +  +Y++WWI+ A+   + R    V++    TA+  
Sbjct: 85  IDLIGEGNVGLLTAARKFDPDQGVKFISYAVWWIRQAILSSLARQGRTVRVPLNRTADLS 144

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
           R+      L+  L+        PE+   +A+   +S   V S+     GD  L+A ++  
Sbjct: 145 RIIKASEILRQKLR----REPSPEE---LAQVTGLSVDVVQSLAALNTGDVRLDAPMD-P 196

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNR--RNMLTRSMSVLNPRERRI----FEARR 247
           D + S  + ++  +    E      EE  NR   + + +++S L PR+ ++    F    
Sbjct: 197 DGDRSLIERFVADEMPDTE------EEAMNRFLTDEIEQALSTLPPRDAKVLRLYFGLEG 250

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +E+  TLE + S   V+RERVRQ+  RA K+++E 
Sbjct: 251 GREH--TLEEIGSMLGVTRERVRQLRDRALKRLREG 284


>gi|134094484|ref|YP_001099559.1| RNA polymerase sigma factor RpoS [Herminiimonas arsenicoxydans]
 gi|133738387|emb|CAL61432.1| RNA polymerase sigma factor rpoS (Sigma-38) [Herminiimonas
           arsenicoxydans]
          Length = 344

 Score =  117 bits (293), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 86/272 (31%), Positives = 145/272 (53%), Gaps = 15/272 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+++I   P+L   EE   A   ++ G+ +A  +++  +LRLVV IA  Y   G+ + ++
Sbjct: 75  YLNQIGARPLLTVPEEVHFATLAKQ-GNFAARQKMIEHNLRLVVSIAKHYINRGVVLLDL 133

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+A+ KF+PERGFR +TY+ WWI+ +++  I+     V++    +  R    
Sbjct: 134 IEEGNLGLMRAIDKFEPERGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVVRELNQ 191

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
             R K HL+A   ++ K      IA  +  S  +V  +        SL+A ++   ++S 
Sbjct: 192 TLRAKFHLEA-QHHDGKDATAEDIAHLVERSVEDVQDILALSEHASSLDAPLDGDPQSS- 249

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS-MSVLNPRERRIFEARRL---QENPVT 254
              D L  DH     VL E +E      +L R  +  L+ ++R +   RR     ++P T
Sbjct: 250 -LMDLLQGDHANDPDVLAEHQEMI----VLVRDWLDKLSDKQRLVI-TRRFGLDNDDPAT 303

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE L++E  V+RERVRQI+  A  K++ S+ +
Sbjct: 304 LEELATEMHVTRERVRQIQQEALVKLKRSLAR 335


>gi|23428544|gb|AAL11451.1| RNA polymerase sigma-38 subunit [Serratia plymuthica]
          Length = 331

 Score =  117 bits (293), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 139/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 62  YLGEIGYSPLLTAEEEVYFARRAL-RGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 120

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 121 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 180

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 181 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 237

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 238 ILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 286

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 287 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQLQ 321


>gi|91217671|ref|ZP_01254628.1| putative sigma factor A [Psychroflexus torquis ATCC 700755]
 gi|91184175|gb|EAS70561.1| putative sigma factor A [Psychroflexus torquis ATCC 700755]
          Length = 288

 Score =  117 bits (293), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 79/284 (27%), Positives = 152/284 (53%), Gaps = 44/284 (15%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ +I K+ ++  +EE  LA+R RE GD +A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQDISKVDLITAEEEVELAQRIRE-GDQAALEKLTNANLRFVVSVAKQYQNQGLKL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + +     +V++    N+  +
Sbjct: 77  PDLINEGNVGLVKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRVVRL--PLNKIGV 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRLA---G 182
              + +   HL+ +   N +P   + IAK+L++SE++V          +SM+        
Sbjct: 135 INKINKTFSHLEQV---NERPPSAIEIAKELDMSEAQVKVALKNSGRHLSMDAPFKEGEN 191

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
           D +L  +++S++  S    D L+ D    E               + R++  L+ RE  +
Sbjct: 192 DSNLYDVLSSAE--SPTPDDQLMRDSLSIE---------------INRALETLSQREADV 234

Query: 243 FEARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
               RL      +  +TL+ +   F++SRERVRQI  +  ++++
Sbjct: 235 I---RLNYGIGNQPAMTLQEIGDTFDLSRERVRQIREKGIRRLK 275


>gi|330447824|ref|ZP_08311472.1| RNA polymerase sigma factor, sigma-70 family protein
           [Photobacterium leiognathi subsp. mandapamensis
           svers.1.1.]
 gi|328492015|dbj|GAA05969.1| RNA polymerase sigma factor, sigma-70 family protein
           [Photobacterium leiognathi subsp. mandapamensis
           svers.1.1.]
          Length = 286

 Score =  117 bits (293), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 88/284 (30%), Positives = 146/284 (51%), Gaps = 38/284 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+++I   P+L K++E   ++++   GD +A   LV S+LRLVV IA  YR   L +S++
Sbjct: 14  YLNDISNKPLLTKEDEIQYSRKFL-MGDTNAKKILVESNLRLVVSIAKKYRASKLSLSDL 72

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM AV KFDPE+GFR +TY+ WWIK  ++  I      +++    +++     
Sbjct: 73  IDEGNIGLMTAVDKFDPEKGFRFSTYASWWIKQTIERAIHNQNRTIRLPVHVSKEINTL- 131

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLN----------VSESEVISMNCRLAGDESLNA 188
              L+ H + +  NN +P Q   IA+ LN           SE  V+S+   L  DE+ N 
Sbjct: 132 ---LRTHRELMKVNNNEPTQ-DDIARVLNRDINEISSLLASEVNVVSLEQTLGDDENSNT 187

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV--LNPRERRIFEAR 246
           +             +LV D    EQ+     E  +   M   +M +  L  R+R I   R
Sbjct: 188 VA------------YLVAD----EQIASPSAEVDSDDIMKVTNMILHKLPSRDREIM-CR 230

Query: 247 R---LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           R   +   P TL+ ++    ++RER+RQ++ +    ++ S++++
Sbjct: 231 RYGLMGYEPHTLQEVADSVGLTRERIRQLQIKTLNTLKRSLERE 274


>gi|326324968|dbj|BAJ84180.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Oranienburg]
          Length = 330

 Score =  117 bits (293), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 139/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL +  +
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLNL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|167993163|ref|ZP_02574258.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar 4,[5],12:i:- str. CVM23701]
 gi|205328726|gb|EDZ15490.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar 4,[5],12:i:- str. CVM23701]
          Length = 330

 Score =  117 bits (293), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 139/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    + ++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRPLREILQTQ 320


>gi|146295919|ref|YP_001179690.1| RpoD family RNA polymerase sigma factor [Caldicellulosiruptor
           saccharolyticus DSM 8903]
 gi|145409495|gb|ABP66499.1| RNA polymerase, sigma 70 subunit, RpoD [Caldicellulosiruptor
           saccharolyticus DSM 8903]
          Length = 411

 Score =  117 bits (293), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 89/265 (33%), Positives = 139/265 (52%), Gaps = 15/265 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 145 YLKEIGKIPLLTPEEEIELAKRI-EQGDEEAKKRLAEANLRLVVSIAKRYVGRGMLFLDL 203

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 204 IQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 261

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R+   L         PE+   IAK++N+   +V  +  ++A +  SL   I   ++  
Sbjct: 262 LVRVSRQLLQEKGREPTPEE---IAKEMNMPVEKVREI-LKIAQEPVSLETPI--GEEED 315

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTL 255
           S   D++    D       E       +  L   +  LN RE+++ + R   E+    TL
Sbjct: 316 SHLGDFI---PDDDALAPSEAAAYSMLKEQLLEVLDSLNEREKKVLKLRFGLEDGRARTL 372

Query: 256 ENLSSEFEVSRERVRQIEARAFKKV 280
           E +  EF V+RER+RQIEA+A +K+
Sbjct: 373 EEVGKEFNVTRERIRQIEAKALRKL 397


>gi|52841515|ref|YP_095314.1| stationary phase specific sigma factor RpoS [Legionella pneumophila
           subsp. pneumophila str. Philadelphia 1]
 gi|52628626|gb|AAU27367.1| stationary phase specific sigma factor RpoS [Legionella pneumophila
           subsp. pneumophila str. Philadelphia 1]
          Length = 359

 Score =  117 bits (292), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 82/275 (29%), Positives = 147/275 (53%), Gaps = 23/275 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A    + GD+ A  +++ S+LRLVVKIA  Y   GLP+ ++
Sbjct: 92  YLGEIGFSPLLTAEEEIHYATLALK-GDMEARKKMIESNLRLVVKIARRYLNRGLPLLDL 150

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM++V+KFDP+RGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 151 IEEGNLGLMKSVEKFDPKRGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 209

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-------DESLNALIN 191
           LR  +   Q + D+   PE++  +  K      +++ +N ++A        DE+ + L  
Sbjct: 210 LRAARQLTQKL-DHEPSPEEIAEMVDKPLEDVQKLLGLNDKVASVDTPIGFDETKSLLDT 268

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
            +D+NS    + L  ++  Q    +  +  +N++ ++ R   +      R FE       
Sbjct: 269 IADENSLNPAELLTNENLRQHIESLLDKLTENQQQVIARRFGL------RGFEK------ 316

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             TLE++  E +++RERVRQI+  A K ++  +++
Sbjct: 317 -ATLEDVGKEIDLTRERVRQIQVEALKTLRTLLER 350


>gi|148358826|ref|YP_001250033.1| stationary phase specific sigma factor RpoS [Legionella pneumophila
           str. Corby]
 gi|296106871|ref|YP_003618571.1| stationary phase specific sigma factor RpoS [Legionella pneumophila
           2300/99 Alcoy]
 gi|148280599|gb|ABQ54687.1| stationary phase specific sigma factor RpoS [Legionella pneumophila
           str. Corby]
 gi|295648772|gb|ADG24619.1| stationary phase specific sigma factor RpoS [Legionella pneumophila
           2300/99 Alcoy]
          Length = 341

 Score =  117 bits (292), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 82/275 (29%), Positives = 147/275 (53%), Gaps = 23/275 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A    + GD+ A  +++ S+LRLVVKIA  Y   GLP+ ++
Sbjct: 74  YLGEIGFSPLLTAEEEIHYATLALK-GDMEARKKMIESNLRLVVKIARRYLNRGLPLLDL 132

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM++V+KFDP+RGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 133 IEEGNLGLMKSVEKFDPKRGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 191

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-------DESLNALIN 191
           LR  +   Q + D+   PE++  +  K      +++ +N ++A        DE+ + L  
Sbjct: 192 LRAARQLTQKL-DHEPSPEEIAEMVDKPLEDVQKLLGLNDKVASVDTPIGFDETKSLLDT 250

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
            +D+NS    + L  ++  Q    +  +  +N++ ++ R   +      R FE       
Sbjct: 251 IADENSLNPAELLTNENLRQHIESLLDKLTENQQQVIARRFGL------RGFEK------ 298

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             TLE++  E +++RERVRQI+  A K ++  +++
Sbjct: 299 -ATLEDVGKEIDLTRERVRQIQVEALKTLRTLLER 332


>gi|270264030|ref|ZP_06192298.1| RNA polymerase sigma factor RpoS [Serratia odorifera 4Rx13]
 gi|270042223|gb|EFA15319.1| RNA polymerase sigma factor RpoS [Serratia odorifera 4Rx13]
          Length = 332

 Score =  117 bits (292), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 139/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 63  YLGEIGYSPLLTAEEEVYFARRAL-RGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 181

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 182 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 238

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 239 ILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 287

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 288 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQLQ 322


>gi|312128161|ref|YP_003993035.1| RNA polymerase, sigma 70 subunit, rpod subfamily
           [Caldicellulosiruptor hydrothermalis 108]
 gi|312134621|ref|YP_004001959.1| RNA polymerase, sigma 70 subunit, rpod subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|312792985|ref|YP_004025908.1| RNA polymerase, sigma 70 subunit, rpod subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
 gi|311774672|gb|ADQ04159.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|311778180|gb|ADQ07666.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor hydrothermalis 108]
 gi|312180125|gb|ADQ40295.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
          Length = 417

 Score =  117 bits (292), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 89/265 (33%), Positives = 139/265 (52%), Gaps = 15/265 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 151 YLKEIGKIPLLTPEEEIELAKRI-EQGDEEAKKRLAEANLRLVVSIAKRYVGRGMLFLDL 209

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 210 IQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 267

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R+   L         PE+   IAK++N+   +V  +  ++A +  SL   I   ++  
Sbjct: 268 LVRVSRQLLQEKGREPTPEE---IAKEMNMPVEKVREI-LKIAQEPVSLETPI--GEEED 321

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTL 255
           S   D++    D       E       +  L   +  LN RE+++ + R   E+    TL
Sbjct: 322 SHLGDFI---PDDDALAPSEAAAYSMLKEQLLEVLDSLNEREKKVLKLRFGLEDGRARTL 378

Query: 256 ENLSSEFEVSRERVRQIEARAFKKV 280
           E +  EF V+RER+RQIEA+A +K+
Sbjct: 379 EEVGKEFNVTRERIRQIEAKALRKL 403


>gi|261822742|ref|YP_003260848.1| RNA polymerase sigma factor RpoS [Pectobacterium wasabiae WPP163]
 gi|5912456|emb|CAB56153.1| RpoS protein [Pectobacterium carotovorum]
 gi|261606755|gb|ACX89241.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pectobacterium
           wasabiae WPP163]
          Length = 330

 Score =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 88/281 (31%), Positives = 145/281 (51%), Gaps = 33/281 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDIPSRRRMIESNLRLVVKIARRYNNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V    +LN     + S++  L GD S  AL+
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVNRMLRLN---ERITSVDTPLGGD-SEKALL 235

Query: 191 NSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-- 247
                      D L  + D G E    + + ++N    + + +  LN ++R +  ARR  
Sbjct: 236 -----------DILADEKDNGPEDTTQDNDMKQN----IVKWLFELNAKQREVL-ARRFG 279

Query: 248 -LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            L     TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 280 LLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQVQ 320


>gi|312876451|ref|ZP_07736435.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
 gi|311796809|gb|EFR13154.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
          Length = 419

 Score =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 89/265 (33%), Positives = 139/265 (52%), Gaps = 15/265 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 153 YLKEIGKIPLLTPEEEIELAKRI-EQGDEEAKKRLAEANLRLVVSIAKRYVGRGMLFLDL 211

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 212 IQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 269

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R+   L         PE+   IAK++N+   +V  +  ++A +  SL   I   ++  
Sbjct: 270 LVRVSRQLLQEKGREPTPEE---IAKEMNMPVEKVREI-LKIAQEPVSLETPI--GEEED 323

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTL 255
           S   D++    D       E       +  L   +  LN RE+++ + R   E+    TL
Sbjct: 324 SHLGDFI---PDDDALAPSEAAAYSMLKEQLLEVLDSLNEREKKVLKLRFGLEDGRARTL 380

Query: 256 ENLSSEFEVSRERVRQIEARAFKKV 280
           E +  EF V+RER+RQIEA+A +K+
Sbjct: 381 EEVGKEFNVTRERIRQIEAKALRKL 405


>gi|302386858|ref|YP_003822680.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           saccharolyticum WM1]
 gi|302197486|gb|ADL05057.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           saccharolyticum WM1]
          Length = 380

 Score =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 87/285 (30%), Positives = 147/285 (51%), Gaps = 41/285 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LAKR +  GD  A  RL+ ++LRLVV IA  Y G G+   ++
Sbjct: 115 YLKEIGTVPLLNAEEELRLAKR-KADGDDDAKERLIEANLRLVVSIAKRYTGRGMSFLDL 173

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           V EGN+GL++ V+KFD  +G++L+TY+ WWI+ ++   +      +++      T N   
Sbjct: 174 VQEGNLGLIKGVEKFDYTKGYKLSTYATWWIRQSVTRALADQARTIRVPVHMVETINKMS 233

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             Q++L   L    G+  ++++          +A+ L++SE +V+ +        SL   
Sbjct: 234 KMQRKLTLEL----GYEPSVSE----------LAEALDMSEDKVMEIMQIAREPASLETP 279

Query: 190 INSSDKNSSQWQDW-----LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           I   D   S   D+     +V      E V++        R  +   +  L  RER++  
Sbjct: 280 IGEED--DSNLGDFVADNNVVTPEGNVESVML--------REHIDALLGDLKERERQVIV 329

Query: 245 ARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R   E+  P TLE +  EF V+RER+RQIEA+A +K++  ++ +
Sbjct: 330 LRFGLEDGHPRTLEEVGKEFNVTRERIRQIEAKALRKLRNPVRSK 374


>gi|299140647|ref|ZP_07033785.1| RNA polymerase sigma-70 factor [Prevotella oris C735]
 gi|298577613|gb|EFI49481.1| RNA polymerase sigma-70 factor [Prevotella oris C735]
          Length = 287

 Score =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 83/274 (30%), Positives = 148/274 (54%), Gaps = 28/274 (10%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI    ++  +EE  LA++ +  GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGHEDLISVEEEVELAQKIK-RGDRRALEKLTRANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK-----IGTTA 130
            ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V+     +G+  
Sbjct: 77  PDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGSVN 136

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLK---PEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
             KR+   L +       I +   K   PE  VA A K   S    +S++  LA  E  N
Sbjct: 137 KIKRVLNKLEQENEQFPTIEEIAAKVDIPEDKVADAIK---SNGRHVSVDAPLAEGEE-N 192

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA-R 246
           +L++    N++Q  D ++     QE +          R+ +  ++  LN RER I EA  
Sbjct: 193 SLLDILPNNNAQMADSMLV----QESL----------RDEVANALQSLNERERNIIEAFF 238

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            + ++ +TLE +  +F ++RERVRQI+ +A +++
Sbjct: 239 GINQSEMTLEEIGDKFGLTRERVRQIKEKAIRRL 272


>gi|326800649|ref|YP_004318468.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphingobacterium
           sp. 21]
 gi|326551413|gb|ADZ79798.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphingobacterium
           sp. 21]
          Length = 286

 Score =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 79/275 (28%), Positives = 151/275 (54%), Gaps = 14/275 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+HEI K+ ++  +EE +LA++ RE GD +A  RL  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLHEIGKVDLITAEEEVILAQKIRE-GDQAALERLTKTNLRFVVSVAKQYQNQGLTL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A K+FD  +GF+  +Y++WWI+ ++ + I     +V++    NQ   
Sbjct: 77  GDLINEGNLGLIKAAKRFDETKGFKFISYAVWWIRQSILQAIAEQSRIVRL--PLNQVGS 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + +    L+   +    PE++  I +      S+ +S + R     S++A     ++
Sbjct: 135 LSKISKAFSRLEQEYEREPSPEELADILETTVDKISDTLSNSGRHV---SMDAPFVQGEE 191

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA-RRLQEN-PV 253
           N+    D L       +  LI++   +     + RS++ L  RER I      L  N P+
Sbjct: 192 NT--LLDVLENHDPNTDSNLIDESLSEE----IKRSLATLTEREREIIVLFFGLGSNHPL 245

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +LE +   F ++RERVRQI+ +A ++++ + + ++
Sbjct: 246 SLEEIGETFNLTRERVRQIKDKALQRLRHTSRSKI 280


>gi|317502748|ref|ZP_07960858.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella salivae
           DSM 15606]
 gi|315666141|gb|EFV05698.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella salivae
           DSM 15606]
          Length = 287

 Score =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 85/282 (30%), Positives = 153/282 (54%), Gaps = 29/282 (10%)

Query: 9   IVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           I N E   L +Y+ EI    ++  +EE  LA++ +  GD  A  +L  ++LR VV +A  
Sbjct: 10  ITNRECASLDKYLQEIGHEDLISVEEEVELAQKIK-RGDRRALEKLTRANLRFVVSVAKQ 68

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK-- 125
           Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V+  
Sbjct: 69  YQNQGLSLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLP 128

Query: 126 ---IGTTANQKRLFFNLRRLKGHLQAITDNNLK---PEQVVAIAKKLNVSESEVISMNCR 179
              +G+    KR+   L +   H   I +   K   PE+ VA A K   S    +S++  
Sbjct: 129 LNQVGSVNKIKRVLNKLEQENEHFPTIEEIAAKVDIPEEKVADAIK---SNGRHVSVDAP 185

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            A  E  N+L++    +++Q  D           VL++    ++ R+ ++ ++  LN RE
Sbjct: 186 FAEGEE-NSLLDVLPNSNAQMAD----------NVLVQ----ESLRDEISSALKSLNERE 230

Query: 240 RRIFEA-RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           R I EA   + +  +TLE +  +F ++RERVRQI+ +A +++
Sbjct: 231 RNIIEAFFGINQAEMTLEEIGDKFGLTRERVRQIKEKAIRRL 272


>gi|300777898|ref|ZP_07087756.1| DNA-directed RNA polymerase sigma subunit RpoD [Chryseobacterium
           gleum ATCC 35910]
 gi|57471279|gb|AAW50925.1| RpoD [Chryseobacterium indologenes]
 gi|300503408|gb|EFK34548.1| DNA-directed RNA polymerase sigma subunit RpoD [Chryseobacterium
           gleum ATCC 35910]
          Length = 288

 Score =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 81/289 (28%), Positives = 157/289 (54%), Gaps = 41/289 (14%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ ++   EE  LA+R R  GD +A  +L+ ++LR VV ++  Y+  GL +
Sbjct: 18  LDKYLQEIGKVELITADEEVELAQRIR-AGDRAALEKLIKANLRFVVSVSKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GLM+A K++D  RGF+  +Y++WWI+ ++ + +     +V++    N+   
Sbjct: 77  PDLINEGNLGLMKAAKRYDETRGFKFISYAVWWIRQSILQALAEQSRIVRL--PLNKIGS 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRLAGDES 185
              + +   HL+   +    PE+   +A+ L++SE ++          +SM+  L   E 
Sbjct: 135 INKINKAYAHLEQENERPPSPEE---LAEVLDMSEEDIKESMKNSGRHLSMDAPLVEGED 191

Query: 186 LNAL-INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
            N   +  S ++ S  +D ++      E + IE E          R+++ L PRE  +  
Sbjct: 192 SNLYDVLRSGESPSPDKDLML------ESLQIEIE----------RALNTLTPREADLV- 234

Query: 245 ARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
             RL      ++P+TLE +   F+++RERVRQI+ +A K+++ + + ++
Sbjct: 235 --RLYFGLNGKHPMTLEEIGETFDLTRERVRQIKEKAIKRLKHNTRSKI 281


>gi|291531112|emb|CBK96697.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Eubacterium siraeum 70/3]
          Length = 358

 Score =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 87/271 (32%), Positives = 140/271 (51%), Gaps = 25/271 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LA R  + GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 92  YLKEIGRVPLLTAEEEIELATRMAQ-GDKYARKRLSEANLRLVVSIAKRYVGRGMQFLDL 150

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG-----TTANQK 133
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T    K
Sbjct: 151 IQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRSIADQARTIRIPVHMVETITKVK 210

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINS 192
           ++   L    GH          P++   IA +L ++   V  +  R++ D  SL   I  
Sbjct: 211 KVSSQLLHENGH-------EPTPQE---IADRLGITVDRVREI-LRISQDPVSLETPIG- 258

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN- 251
            ++  S   D++            E   R   +  L+  +  L PRE ++   R   E+ 
Sbjct: 259 -EEEDSHLGDFIPD---EDAPAPAEAASRTLLKEQLSEILGTLTPREEKVLRLRFGLEDG 314

Query: 252 -PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            P TLE +  EF+V+RER+RQIEA+A +K++
Sbjct: 315 RPRTLEEVGKEFDVTRERIRQIEAKALRKLR 345


>gi|167750934|ref|ZP_02423061.1| hypothetical protein EUBSIR_01919 [Eubacterium siraeum DSM 15702]
 gi|167656113|gb|EDS00243.1| hypothetical protein EUBSIR_01919 [Eubacterium siraeum DSM 15702]
 gi|291557421|emb|CBL34538.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Eubacterium siraeum
           V10Sc8a]
          Length = 358

 Score =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 87/271 (32%), Positives = 140/271 (51%), Gaps = 25/271 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LA R  + GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 92  YLKEIGRVPLLTAEEEIELATRMAQ-GDKYARKRLSEANLRLVVSIAKRYVGRGMQFLDL 150

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG-----TTANQK 133
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T    K
Sbjct: 151 IQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRSIADQARTIRIPVHMVETITKVK 210

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINS 192
           ++   L    GH          P++   IA +L ++   V  +  R++ D  SL   I  
Sbjct: 211 KVSSQLLHENGH-------EPTPQE---IADRLGITVDRVREI-LRISQDPVSLETPIG- 258

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN- 251
            ++  S   D++            E   R   +  L+  +  L PRE ++   R   E+ 
Sbjct: 259 -EEEDSHLGDFIPD---EDAPAPAEAASRTLLKEQLSEILGTLTPREEKVLRLRFGLEDG 314

Query: 252 -PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            P TLE +  EF+V+RER+RQIEA+A +K++
Sbjct: 315 RPRTLEEVGKEFDVTRERIRQIEAKALRKLR 345


>gi|50122451|ref|YP_051618.1| RNA polymerase sigma factor RpoS [Pectobacterium atrosepticum
           SCRI1043]
 gi|227114060|ref|ZP_03827716.1| RNA polymerase sigma factor RpoS [Pectobacterium carotovorum subsp.
           brasiliensis PBR1692]
 gi|227327750|ref|ZP_03831774.1| RNA polymerase sigma factor RpoS [Pectobacterium carotovorum subsp.
           carotovorum WPP14]
 gi|49612977|emb|CAG76428.1| RNA polymerase sigma factor [Pectobacterium atrosepticum SCRI1043]
          Length = 330

 Score =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 88/281 (31%), Positives = 145/281 (51%), Gaps = 33/281 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVPSRRRMIESNLRLVVKIARRYNNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V    +LN     + S++  L GD S  AL+
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVNRMLRLN---ERITSVDTPLGGD-SEKALL 235

Query: 191 NSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-- 247
                      D L  + D G E    + + ++N    + + +  LN ++R +  ARR  
Sbjct: 236 -----------DILADEKDNGPEDTTQDNDMKQN----IVKWLFELNAKQREVL-ARRFG 279

Query: 248 -LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            L     TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 280 LLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQVQ 320


>gi|157169065|ref|YP_258338.2| RNA polymerase sigma factor RpoS [Pseudomonas fluorescens Pf-5]
 gi|1000294|gb|AAB02846.1| RpoS [Pseudomonas fluorescens Pf-5]
 gi|157061761|gb|AAY90494.2| RNA polymerase sigma factor RpoS [Pseudomonas fluorescens Pf-5]
          Length = 335

 Score =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 87/272 (31%), Positives = 146/272 (53%), Gaps = 17/272 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + +K       ++ +N R++  D SL      SDK  
Sbjct: 185 LRAARELTQKL-DHEPSPEEIANLLEKPVAEVKRMLGLNERVSSVDVSLGP---DSDKT- 239

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++       + + +S L  ++R +   R   R  E+  T
Sbjct: 240 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTEKQREVVVRRFGLRGHESS-T 293

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE++  E  ++RERVRQI+    K+++E ++K
Sbjct: 294 LEDVGLEIGLTRERVRQIQVEGLKRLREILEK 325


>gi|152980760|ref|YP_001353824.1| RNA polymerase sigma factor RpoS [Janthinobacterium sp. Marseille]
 gi|151280837|gb|ABR89247.1| RNA polymerase nonessential primary-like sigma factor
           [Janthinobacterium sp. Marseille]
          Length = 345

 Score =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 84/271 (30%), Positives = 141/271 (52%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+++I   P+L   EE   A   ++ G+ +A  +++  +LRLVV IA  Y   G+ + ++
Sbjct: 76  YLNQIGTRPLLTVPEEVHFATLAKQ-GNFAARQKMIEHNLRLVVSIAKHYINRGVILLDL 134

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+A+ KF+PERGFR +TY+ WWI+ +++  I+     V++    +  R    
Sbjct: 135 IEEGNLGLMRAIDKFEPERGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVVRELNQ 192

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
             R K HL+A   ++ K      IA  ++ S  +V  +        SL+A ++   ++S 
Sbjct: 193 TLRAKFHLEA-QHHDGKDATAEDIAHLVDRSVEDVQDILALSEHATSLDAPLDGDPQSS- 250

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTL 255
              D L  DH      L E     N   +L        P ++R+   RR     ++P TL
Sbjct: 251 -LMDLLQGDHANDPDALAE----HNEMTVLVHDWLEKLPDKQRLVITRRFGLDNDDPATL 305

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E L++E  V+RERVRQI+  A  K++ S+ +
Sbjct: 306 EALAAEMHVTRERVRQIQQEALVKLKRSLMR 336


>gi|41853|emb|CAA34435.1| katF [Escherichia coli K-12]
          Length = 362

 Score =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 139/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 73  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 131

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 132 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 191

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H          I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 192 RTARELSHKLDHEPSAVEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 248

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 249 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 297

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 298 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 332


>gi|253689710|ref|YP_003018900.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pectobacterium
           carotovorum subsp. carotovorum PC1]
 gi|251756288|gb|ACT14364.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pectobacterium
           carotovorum subsp. carotovorum PC1]
          Length = 330

 Score =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 88/281 (31%), Positives = 145/281 (51%), Gaps = 33/281 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVPSRRRMIESNLRLVVKIARRYNNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V    +LN     + S++  L GD S  AL+
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVNRMLRLN---ERITSVDTPLGGD-SEKALL 235

Query: 191 NSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-- 247
                      D L  + D G E    + + ++N    + + +  LN ++R +  ARR  
Sbjct: 236 -----------DILADEKDNGPEDTTQDNDMKQN----IVKWLFELNAKQREVL-ARRFG 279

Query: 248 -LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            L     TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 280 LLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQVQ 320


>gi|78044024|ref|YP_359316.1| RNA polymerase sigma factor RpoD [Carboxydothermus hydrogenoformans
           Z-2901]
 gi|77996139|gb|ABB15038.1| RNA polymerase sigma factor RpoD [Carboxydothermus hydrogenoformans
           Z-2901]
          Length = 370

 Score =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 87/265 (32%), Positives = 140/265 (52%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LAKR +E GD  A  +L  ++LRLVV IA  Y G G+   ++
Sbjct: 104 YLKEIGRVPLLTPEEEIELAKR-KEEGDEEAKRKLAEANLRLVVSIAKRYVGRGMLFLDL 162

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 163 IQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 220

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+  +L         PE+   IAK++ +SE +V  +        SL   I   ++  S
Sbjct: 221 LIRVSRNLLQELGREPTPEE---IAKEMGISEDKVREIMKIAQEPVSLETPI--GEEEDS 275

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D+ V D D +  V  E+      R  L   +  L  RE+++   R   ++    TLE
Sbjct: 276 HLGDF-VEDPDAKAPV--EEASYTLLREQLDEVLKTLTEREQKVLRLRFGLDDGRARTLE 332

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +   F V+RER+RQIEA+A +K++
Sbjct: 333 EVGQIFGVTRERIRQIEAKALRKLR 357


>gi|222528719|ref|YP_002572601.1| RpoD subfamily RNA polymerase sigma-70 factor [Caldicellulosiruptor
           bescii DSM 6725]
 gi|222455566|gb|ACM59828.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor bescii DSM 6725]
          Length = 417

 Score =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 89/265 (33%), Positives = 139/265 (52%), Gaps = 15/265 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 151 YLKEIGKIPLLTPEEEIELAKRI-EQGDEEAKKRLAEANLRLVVSIAKRYVGRGMLFLDL 209

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 210 IQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 267

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R+   L         PE+   IAK++N+   +V  +  ++A +  SL   I   ++  
Sbjct: 268 LVRVSRQLLQEKGREPTPEE---IAKEMNMPVEKVREI-LKIAQEPVSLETPI--GEEED 321

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTL 255
           S   D++    D       E       +  L   +  LN RE+++ + R   E+    TL
Sbjct: 322 SHLGDFI---PDDDALAPSEAAAYSMLKEQLLEVLDSLNEREKKVLKLRFGLEDGRARTL 378

Query: 256 ENLSSEFEVSRERVRQIEARAFKKV 280
           E +  EF V+RER+RQIEA+A +K+
Sbjct: 379 EEVGKEFNVTRERIRQIEAKALRKL 403


>gi|160881641|ref|YP_001560609.1| RpoD family RNA polymerase sigma factor [Clostridium
           phytofermentans ISDg]
 gi|160430307|gb|ABX43870.1| RNA polymerase, sigma 70 subunit, RpoD family [Clostridium
           phytofermentans ISDg]
          Length = 372

 Score =  117 bits (292), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 87/274 (31%), Positives = 140/274 (51%), Gaps = 13/274 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ E  +  Y+ EI K+P+L   EE VLA+R  E GD +A  RL  ++LRLVV IA  Y 
Sbjct: 97  ISTEDPVRMYLKEIGKVPLLSADEEIVLAQRM-EQGDKNAKKRLAEANLRLVVSIAKRYV 155

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 156 GRGMQFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--P 213

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
            +       L R++  L         PE+V   AK++N+    V  +        SL   
Sbjct: 214 VHMVETINKLIRVQRQLLQELGREPFPEEV---AKEMNIPVERVREIQKISQEPVSLETP 270

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++    D    V  E       +  L   +  L  RE+++   R   
Sbjct: 271 I--GEEEDSHLGDFI---QDDNVPVPAEAAAFTLLKEQLMEVLGTLTDREQKVLRLRFGL 325

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 326 DDGRARTLEEVGKEFNVTRERIRQIEAKALRKLR 359


>gi|304413872|ref|ZP_07395289.1| RNA polymerase sigma S (sigma 38) factor [Candidatus Regiella
           insecticola LSR1]
 gi|304283592|gb|EFL91987.1| RNA polymerase sigma S (sigma 38) factor [Candidatus Regiella
           insecticola LSR1]
          Length = 332

 Score =  116 bits (291), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 84/280 (30%), Positives = 141/280 (50%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD  +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 63  YLGEIGYSPLLTAEEEVYFARRAL-CGDQQSRRRMIESNLRLVVKIARRYGNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 181

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   +P   V+   +LN     + S++  L GD     L 
Sbjct: 182 RTARELAHKLDHEPSAEEIAEQLDRPVDDVSRMLRLN---ERITSVDSPLGGDSEKALLD 238

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
             SD + +  +D    D               + ++ + + +  LN ++R +  ARR   
Sbjct: 239 ILSDDSENGPEDTTQND---------------DMKHSIVKWLFELNAKQREVL-ARRFGL 282

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L     TLEN+  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 283 LGYEAATLENVGKEIGLTRERVRQIQVEGLRRLREILQTQ 322


>gi|225388546|ref|ZP_03758270.1| hypothetical protein CLOSTASPAR_02282 [Clostridium asparagiforme
           DSM 15981]
 gi|225045391|gb|EEG55637.1| hypothetical protein CLOSTASPAR_02282 [Clostridium asparagiforme
           DSM 15981]
          Length = 381

 Score =  116 bits (291), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 87/285 (30%), Positives = 147/285 (51%), Gaps = 41/285 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L   EE  LA+R  E GD +A  RL+ ++LRLVV IA  Y G G+   ++
Sbjct: 116 YLKEIGTVPLLTADEELQLAQRKAE-GDEAAKERLIEANLRLVVSIAKRYTGRGMSFLDL 174

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           V EGN+GL++ V+KFD  +G++L+TY+ WWI+ ++   +      +++      T N   
Sbjct: 175 VQEGNLGLIKGVEKFDYTKGYKLSTYATWWIRQSVTRALADQARTIRVPVHMVETINKMS 234

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             Q++L   L    G+  ++T+          +A+ L+++E +V+ +        SL   
Sbjct: 235 KMQRKLTLEL----GYEPSVTE----------LAEALDMTEDKVMEIMQIAREPASLETP 280

Query: 190 INSSDKNSSQWQDW-----LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           I   D   S   D+     +V      E V++        R  +   +  L  RER++  
Sbjct: 281 IGEED--DSNLGDFVADNNVVTPEGNVESVML--------REHIDALLGDLKERERQVIV 330

Query: 245 ARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R   E+  P TLE +  EF V+RER+RQIEA+A +K++  ++ +
Sbjct: 331 LRFGLEDGHPRTLEEVGKEFNVTRERIRQIEAKALRKLRNPVRSK 375


>gi|237757189|ref|ZP_04585608.1| RNA polymerase sigma-70 factor [Sulfurihydrogenibium yellowstonense
           SS-5]
 gi|237690651|gb|EEP59840.1| RNA polymerase sigma-70 factor [Sulfurihydrogenibium yellowstonense
           SS-5]
          Length = 285

 Score =  116 bits (291), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 86/278 (30%), Positives = 142/278 (51%), Gaps = 17/278 (6%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           N E  +  Y+  I KIP+L K+EE  L K+ +E GD  A  +L+ S+LR V+ IA  Y G
Sbjct: 5   NHEENVDFYLKSIYKIPLLSKEEEESLLKKVKE-GDKEALQKLIISNLRFVINIAKRYAG 63

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
           YG+P S+++S GN+GL++A KKFD  +G R  +Y++WWI+ ++   I     ++K     
Sbjct: 64  YGIPFSDLISAGNVGLIEAAKKFDTSKGVRFISYAVWWIRQSIINTIQHESEIIK----- 118

Query: 131 NQKRLFFNLRRLKGHLQAITDN-NLKP--EQVVAIAKKLNVSESEVISMNCRLAGDE--S 185
              R++    ++      + D  N +P  +++++  K   +   + +  N  L      S
Sbjct: 119 KPNRMYAYASKINNAYSYLKDTLNREPSIDEIISFLKTQGIKVEKEMVENYFLFKSVFLS 178

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L+  I  +D +        VY+    E+ + E++ ++    +L      L+ RER I   
Sbjct: 179 LDTPIEGTDNDLVLEDTISVYNTLDIEKDINEEDLKRAIETLL----DTLSQRERTILIH 234

Query: 246 RRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R     E P TL  +     +SRERVRQIE R  KK++
Sbjct: 235 RFGLNGEEPKTLNEVGEIVGLSRERVRQIENRVLKKLR 272


>gi|213859421|ref|ZP_03385125.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. M223]
          Length = 319

 Score =  116 bits (291), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 84/275 (30%), Positives = 139/275 (50%), Gaps = 25/275 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              TLE++  E  ++RERVRQI+    ++++E +Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQ 318


>gi|332087476|gb|EGI92604.1| RNA polymerase sigma factor RpoS [Shigella boydii 5216-82]
          Length = 330

 Score =  116 bits (291), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 84/280 (30%), Positives = 144/280 (51%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
             +D+  +  +D    D D ++ ++              + +  LN ++R +  ARR   
Sbjct: 237 ILADEKENGPED-TTQDDDMKQSIV--------------KWLFELNSKQREV-PARRFGL 280

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L     TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 281 LGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|104783164|ref|YP_609662.1| RNA polymerase sigma factor RpoS [Pseudomonas entomophila L48]
 gi|95112151|emb|CAK16878.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Pseudomonas entomophila L48]
          Length = 335

 Score =  116 bits (291), Expect = 3e-24,   Method: Compositional matrix adjust.
 Identities = 86/272 (31%), Positives = 146/272 (53%), Gaps = 17/272 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++ ++ +K       ++ +N R++  D SL      SDK  
Sbjct: 185 LRAARELTQKL-DHEPSPEEIASLLEKPVAEVKRMLGLNERVSSVDVSLGP---DSDKT- 239

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++       + + +  L  ++R +   R   R  E+  T
Sbjct: 240 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLGELTDKQREVVVRRFGLRGHESS-T 293

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE++  E  ++RERVRQI+    K+++E ++K
Sbjct: 294 LEDVGLEIGLTRERVRQIQVEGLKRLREILEK 325


>gi|312622967|ref|YP_004024580.1| RNA polymerase, sigma 70 subunit, rpod subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
 gi|312203434|gb|ADQ46761.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
          Length = 417

 Score =  116 bits (291), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 89/265 (33%), Positives = 139/265 (52%), Gaps = 15/265 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 151 YLKEIGKIPLLTPEEEIELAKRI-EQGDEEAKKRLAEANLRLVVSIAKRYVGRGMLFLDL 209

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 210 IQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 267

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R+   L         PE+   IAK++N+   +V  +  ++A +  SL   I   ++  
Sbjct: 268 LVRVSRQLLQEKGREPTPEE---IAKEMNMPVEKVREI-LKIAQEPVSLETPI--GEEED 321

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTL 255
           S   D++    D       E       +  L   +  LN RE+++ + R   E+    TL
Sbjct: 322 SHLGDFI---PDDDALAPSEAAAYSMLKEQLLEVLDSLNEREKKVLKLRFGLEDGRARTL 378

Query: 256 ENLSSEFEVSRERVRQIEARAFKKV 280
           E +  EF V+RER+RQIEA+A +K+
Sbjct: 379 EEVGREFNVTRERIRQIEAKALRKL 403


>gi|153840560|ref|ZP_01993227.1| RpoS [Vibrio parahaemolyticus AQ3810]
 gi|149745777|gb|EDM56907.1| RpoS [Vibrio parahaemolyticus AQ3810]
          Length = 415

 Score =  116 bits (291), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 88/280 (31%), Positives = 146/280 (52%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 2   YLGEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 60

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++      ++      K L   
Sbjct: 61  IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTTRLPIHV-VKELNIY 119

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +  L    D+    E++ A        ++K L ++E  + S++  + GD     L 
Sbjct: 120 LRTAR-ELSQKLDHEPTAEEIAAQLDIPVEDVSKMLRLNE-RISSVDTPIGGDGEKALLD 177

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
              D N+S   D  V   D             + ++ L   +  LNP+++ +  ARR   
Sbjct: 178 IIPDANNS---DPEVSTQD------------DDIKSSLIHWLEELNPKQKEVL-ARRFGL 221

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   P TLE +  E  ++RERVRQI+    ++++E  +K+
Sbjct: 222 LGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLREMKEKK 261


>gi|289423762|ref|ZP_06425557.1| RNA polymerase sigma factor RpoD [Peptostreptococcus anaerobius
           653-L]
 gi|289155801|gb|EFD04471.1| RNA polymerase sigma factor RpoD [Peptostreptococcus anaerobius
           653-L]
          Length = 385

 Score =  116 bits (291), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 87/266 (32%), Positives = 144/266 (54%), Gaps = 15/266 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L+  EE   A R    GD  +  +LV ++LRLVV IA  Y G G+   ++
Sbjct: 119 YLKEIGKIPLLKPHEEVEFA-RLMSEGDERSKQKLVEANLRLVVSIAKRYVGRGMLFLDL 177

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD ++G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 178 IQEGNLGLIKAVEKFDYKKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 235

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R+   L      + KPE+   IAK +N+SE +V  +  ++A D  SL   I   ++  
Sbjct: 236 LIRVSRQLLQELGRDPKPEE---IAKVMNMSEDKVREI-MKIAQDPVSLETPI--GEEED 289

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTL 255
           S   D++  +              K +   +   ++ LN RE+++ + R   E+    TL
Sbjct: 290 SHLGDFIPDEDAPAPAEAAAYSLLKEQ---IEEVLNTLNDREQKVLKLRFGLEDGRARTL 346

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           E +  EF+V+RER+RQIEA+A +K++
Sbjct: 347 EEVGKEFDVTRERIRQIEAKALRKLR 372


>gi|260899647|ref|ZP_05908042.1| RNA polymerase sigma-C factor [Vibrio parahaemolyticus AQ4037]
 gi|308106738|gb|EFO44278.1| RNA polymerase sigma-C factor [Vibrio parahaemolyticus AQ4037]
          Length = 120

 Score =  116 bits (291), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 54/105 (51%), Positives = 74/105 (70%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  +   PML   EE  LA+R    G++ AA  L+ SHLR VV +A GY GYGLP+
Sbjct: 16  LDSYIRSVNSYPMLTADEERELAERLHYKGEIEAAKGLILSHLRFVVHVARGYSGYGLPM 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           +++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 76  ADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120


>gi|239995277|ref|ZP_04715801.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Alteromonas macleodii ATCC
           27126]
          Length = 330

 Score =  116 bits (291), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 87/275 (31%), Positives = 146/275 (53%), Gaps = 21/275 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R  + G  ++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 59  YLGEIGFSPLLTAEEEVYFARRSLK-GCEASRKRMIVSNLRLVVKIARRYNNRGLALLDL 117

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 118 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 176

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +   Q +       E  +A+ K +     E ++   R      LN  I S D    
Sbjct: 177 LRASRELSQKLDHEPTAEEIALALDKPV-----EDVTKMLR------LNERITSVDTPIG 225

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKN---RRNMLTRSMSVLNPRERRIFEARR---LQENP 252
              D  + D    E+    +E  ++   + N++T  +  LNP++R +  ARR   +   P
Sbjct: 226 GENDKALLDIIADEKEFSPEESLQDSDIKSNIVT-WLEELNPKQREVL-ARRFGLMGYEP 283

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            TLE++ +E  ++RERVRQI+  A +++++ +  Q
Sbjct: 284 STLEDVGAEIGLTRERVRQIQVEALRRLRDMLGHQ 318


>gi|116668483|gb|ABK15514.1| sigma factor [Pseudomonas alkylphenolia]
          Length = 335

 Score =  116 bits (291), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 87/272 (31%), Positives = 147/272 (54%), Gaps = 17/272 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++ ++ +K       ++ +N R++  D SL      SDK  
Sbjct: 185 LRAARELTQKL-DHEPSPEEIASLLEKPVGEVKRMLGLNERVSSVDVSLGP---DSDKT- 239

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++       + + +S L  ++R +   R   R  E+  T
Sbjct: 240 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTDKQREVVIRRFGLRGHESS-T 293

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE++  E  ++RERVRQI+    K+++E ++K
Sbjct: 294 LEDVGLEIGLTRERVRQIQVEGLKRLREILEK 325


>gi|18073320|emb|CAC81021.1| mutant RpoS sigma factor [Escherichia coli]
          Length = 302

 Score =  116 bits (291), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 139/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 33  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 91

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 92  IEEGNQGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 151

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 152 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 208

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 209 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 257

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 258 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 292


>gi|149370109|ref|ZP_01889960.1| RNA polymerase sigma-70 factor [unidentified eubacterium SCB49]
 gi|149356600|gb|EDM45156.1| RNA polymerase sigma-70 factor [unidentified eubacterium SCB49]
          Length = 287

 Score =  116 bits (291), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 85/286 (29%), Positives = 150/286 (52%), Gaps = 45/286 (15%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ E+ KI ++  +EE  LA++ +  GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEVGKIDLITAEEEVELAQKIK-AGDQRALEKLTNANLRFVVSVAKQYQNQGLTL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
            ++++EGN+GL++A  +FD  RGF+  +Y++WWI+ A+      Q  I+R   L KIG+ 
Sbjct: 77  PDLINEGNVGLIKAASRFDETRGFKFISYAVWWIRQAILQALAEQSRIVR-LPLNKIGSI 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCR 179
               + F        HL+        PE+   IAK+L+++ ++V          ISM+  
Sbjct: 136 NKINKAF-------THLEQAHQRPPSPEE---IAKELDMTINDVKESIKNSGRSISMDAP 185

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           L   E  N L +  +   S   D         + +L+E     + R  + R++  L PRE
Sbjct: 186 LTEGEDYN-LYDVLNTGESPNPD---------QALLLE-----SLRTEIERALETLTPRE 230

Query: 240 RRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             + +       + P+TLE + S F+++RERVRQI+ +A ++++ +
Sbjct: 231 SDVIKLYFGLSDQRPMTLEEIGSTFDLTRERVRQIKEKAVRRLKHT 276


>gi|90577256|ref|ZP_01233067.1| hypothetical DNA-directed RNA polymerase, sigma subunit [Vibrio
           angustum S14]
 gi|90440342|gb|EAS65522.1| hypothetical DNA-directed RNA polymerase, sigma subunit [Vibrio
           angustum S14]
          Length = 286

 Score =  116 bits (291), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 86/275 (31%), Positives = 147/275 (53%), Gaps = 20/275 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+++I   P+L K +E +   R    GDL++   L+ S+LRLVV IA  YR   L +S++
Sbjct: 14  YLNDISNKPLLNKDDE-IQYSRKSLTGDLASKKILIESNLRLVVSIAKKYRASNLSLSDL 72

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM AV+KFDPE+GFR +TY+ WWIK  ++  I      +++    +++     
Sbjct: 73  IDEGNIGLMTAVEKFDPEKGFRFSTYASWWIKQTIERAIHNQNRTIRLPVHISKEINTL- 131

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
              L+ H + +  NN +P     IA+ LN    E+ ++        SL+  I  ++K  S
Sbjct: 132 ---LRTHRELMKLNNNEPTH-EDIAQALNKDSKEISALFSNEVNVISLDQTIGDTEK--S 185

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL---NPRERRIFEARR---LQENP 252
           Q   +LV D    EQ+     E  N  +M+  +  +L   N R++ I   RR   +   P
Sbjct: 186 QTIAYLVAD----EQITSPSAEVDN-DDMVKITNLILNGINARDKEII-CRRFGLMGYEP 239

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            TL+ ++    ++RER+RQ++ ++   ++ S+ ++
Sbjct: 240 HTLQEVADAVGLTRERIRQLQIKSLSSLKRSLARE 274


>gi|229588834|ref|YP_002870953.1| RNA polymerase sigma factor RpoS [Pseudomonas fluorescens SBW25]
 gi|229360700|emb|CAY47558.1| RNA polymerase sigma factor [Pseudomonas fluorescens SBW25]
          Length = 334

 Score =  116 bits (291), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 87/272 (31%), Positives = 146/272 (53%), Gaps = 17/272 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 66  YLNEIGFSPLLTPEEEVHFA-RLSQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 124

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 125 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 183

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + +K       ++ +N R++  D SL      SDK  
Sbjct: 184 LRAARELTQKL-DHEPSPEEIANLLEKPVAEVKRMLGLNERVSSVDVSLGP---DSDKT- 238

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++       + + +S L  ++R +   R   R  E+  T
Sbjct: 239 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTDKQREVVIRRFGLRGHESS-T 292

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE++  E  ++RERVRQI+    K+++E ++K
Sbjct: 293 LEDVGLEIGLTRERVRQIQVEGLKRLREILEK 324


>gi|332532870|ref|ZP_08408743.1| RNA polymerase sigma factor RpoS [Pseudoalteromonas haloplanktis
           ANT/505]
 gi|332037716|gb|EGI74167.1| RNA polymerase sigma factor RpoS [Pseudoalteromonas haloplanktis
           ANT/505]
          Length = 324

 Score =  116 bits (291), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 83/278 (29%), Positives = 148/278 (53%), Gaps = 27/278 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE V   R    G  ++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 53  YLGEIGFSPLLSAEEE-VFFSRKSLRGCEASRKRMIESNLRLVVKIARRYNNRGLALLDL 111

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 112 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 170

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA------GDESLNALINS 192
           LR  +   Q + D+    +++ A   +     ++++ +N R+A      G E+ + L++ 
Sbjct: 171 LRTARELTQKL-DHEPTADEIAACLDRPVEDVTKMLRLNERIASVDMPIGGENDSVLLDI 229

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR---LQ 249
                S   +  V ++D  + ++                +  LNP++R +  ARR   L 
Sbjct: 230 IPDEKSAGPEGEVQNNDINKHIV--------------DWLGELNPKQREVL-ARRFGLLG 274

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             P TLE++  E  ++RERVRQI+  A +++++ +Q++
Sbjct: 275 YEPSTLEDVGREIGLTRERVRQIQVEALRRLKDILQQE 312


>gi|94311053|ref|YP_584263.1| RNA polymerase sigma factor RpoS [Cupriavidus metallidurans CH34]
 gi|93354905|gb|ABF08994.1| RNA polymerase sigma 38 (sigma S) factor [Cupriavidus metallidurans
           CH34]
          Length = 386

 Score =  116 bits (291), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 91/277 (32%), Positives = 142/277 (51%), Gaps = 23/277 (8%)

Query: 19  YIHEIRKIPMLEKQEEY---VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           Y++ I   P+L   EE     LAK     GD SA   ++  +LRLVV IA GY   G+P+
Sbjct: 117 YLNRISIKPLLSAPEELHFSTLAK----GGDFSARQVMIERNLRLVVSIAKGYLNRGVPL 172

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++    +  R 
Sbjct: 173 LDLIEEGNLGLMHAIEKFDPSRGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRE 230

Query: 136 FFNLRRLKGHLQ-AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
              + R K HL+   TD   +   +  IA  L  +  EV  +   LA +E   +L    D
Sbjct: 231 LNQVLRAKRHLEKGGTDG--RDASLEDIAHLLGKTPDEVQDV---LALNEHTTSLDTPFD 285

Query: 195 KN-SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-- 251
            +  S   D+L  +H+      +   E +   N++   ++ L+ + R + E RR   N  
Sbjct: 286 LDPGSSLLDFLSDEHNAAPDQEVAHRELE---NLMKLWLARLSEKHRYVVE-RRFGLNHI 341

Query: 252 -PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            P TLE L+ E  ++RERVRQI+  A  K++     Q
Sbjct: 342 EPATLEELAEEMGLTRERVRQIQQEALVKLKRHFASQ 378


>gi|1519382|gb|AAC46141.1| RNA polymerase subunit sigma 38 [Pectobacterium carotovorum]
          Length = 330

 Score =  116 bits (290), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 88/281 (31%), Positives = 148/281 (52%), Gaps = 33/281 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVPSRRRMIESNLRLVVKIARRYNNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP  V  + + L ++E  + S++  L GD S  AL+
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKP--VDDVNRMLALNER-ITSVDTPLGGD-SEKALL 235

Query: 191 NSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-- 247
                      D L  + D G E    + + ++N    + + +  LN ++R +  ARR  
Sbjct: 236 -----------DILADEKDNGPEDTTQDNDMKQN----IVKWLFELNAKQREVL-ARRFG 279

Query: 248 -LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            L     TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 280 LLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQVQ 320


>gi|332994558|gb|AEF04613.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Alteromonas sp. SN2]
          Length = 330

 Score =  116 bits (290), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 84/273 (30%), Positives = 149/273 (54%), Gaps = 17/273 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A++    G  ++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 59  YLGEIGFSPLLSAEEEVFFARKAL-RGCEASRKRMIVSNLRLVVKIARRYNNRGLALLDL 117

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 118 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 176

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +   Q +       E  +A+ K +    ++++ +N R+    S++  I    +N  
Sbjct: 177 LRAARELSQKLDHEPTAEEIALALDKPVE-DVTKMLRLNERIT---SVDTPIGG--ENDK 230

Query: 199 QWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR---LQENPVT 254
              D L  + + G E+ L + + + N    +   +  LNP++R +  ARR   +   P T
Sbjct: 231 ALLDILADEKEFGPEENLQDSDIKSN----IVGWLEELNPKQREVL-ARRFGLMGYEPST 285

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           LE++ +E  ++RERVRQI+  A +++++ +  Q
Sbjct: 286 LEDVGAEIGLTRERVRQIQVEALRRLRDILGHQ 318


>gi|310778262|ref|YP_003966595.1| RNA polymerase sigma factor, sigma-70 family [Ilyobacter polytropus
           DSM 2926]
 gi|309747585|gb|ADO82247.1| RNA polymerase sigma factor, sigma-70 family [Ilyobacter polytropus
           DSM 2926]
          Length = 263

 Score =  116 bits (290), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 80/282 (28%), Positives = 149/282 (52%), Gaps = 38/282 (13%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + +S Y+ EI   P+L K+EE   A +  ++GD SA  +LVTS+LRLVV IA  Y   G+
Sbjct: 1   MNISNYLKEISHYPLLTKEEEIEFALK-AQNGDESAHEKLVTSNLRLVVSIAKKYINIGI 59

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGNIGL++AV KFD     R +TY+ +WIK ++  YI  +  +++  T     
Sbjct: 60  PVLDLIQEGNIGLIKAVSKFDTTMDKRFSTYATFWIKQSILRYISSNKGVIRYPT----- 114

Query: 134 RLFFNLRRLKGHLQAITD--NNLKPEQVVA---------IAKKLNVSESEVISMNCRLAG 182
            ++ N+ ++   ++   +   ++   +V+A         + K LN+ E  + S+      
Sbjct: 115 YIYDNISKINKFIRDYKNKYGSVPSIEVIATGLEFKKKDVEKYLNIFEQSLNSLEESYGE 174

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
           +  L+++I S D     +++ ++ D   +E               L  ++ +LN +ER +
Sbjct: 175 NGDLHSIIPSDD----LFEEQIITDSVNEE---------------LISNLKILNSKERDV 215

Query: 243 FEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              R     +N +TLE + +   ++RER+RQI+ +A  K+++
Sbjct: 216 IIHRFGLFNKNVLTLEEIGNHLNLTRERIRQIQLKAIDKLRD 257


>gi|226324578|ref|ZP_03800096.1| hypothetical protein COPCOM_02362 [Coprococcus comes ATCC 27758]
 gi|225207026|gb|EEG89380.1| hypothetical protein COPCOM_02362 [Coprococcus comes ATCC 27758]
          Length = 371

 Score =  116 bits (290), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 85/273 (31%), Positives = 138/273 (50%), Gaps = 29/273 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  +EE  LAKR  + GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 105 YLKEIGKVPLLSAEEEIELAKRMAD-GDEEAKKRLAEANLRLVVSIAKRYVGRGMLFLDL 163

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD ++GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 164 IQEGNLGLIKAVEKFDYQKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 221

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALI 190
           L R+   L         PE++ A        + + L +S+ E +S+   +  +E      
Sbjct: 222 LIRVSRQLLQELGREPTPEEIAAELDMPVDRVREILKISQ-EPVSLETPIGEEE------ 274

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
                  S   D++    D    V  E   +   +  L   +S L  RE+++   R    
Sbjct: 275 ------DSHLGDFI---QDDNVPVPAEAAAQTLLKEQLDEVLSTLTEREQKVLRLRFGMS 325

Query: 251 N--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +    TLE +  EF+V+RER+RQIEA+A +K++
Sbjct: 326 DGRARTLEEVGKEFDVTRERIRQIEAKALRKLR 358


>gi|194334634|ref|YP_002016494.1| RNA polymerase sigma-32 subunit RpoH [Prosthecochloris aestuarii
           DSM 271]
 gi|194312452|gb|ACF46847.1| RNA polymerase, sigma 32 subunit, RpoH [Prosthecochloris aestuarii
           DSM 271]
          Length = 299

 Score =  116 bits (290), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 94/305 (30%), Positives = 160/305 (52%), Gaps = 47/305 (15%)

Query: 9   IVNGE-IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS-----------AAHRLVTS 56
           I N E + L RY+ EI K  +L  ++E  L    +E  D+            A  +L+  
Sbjct: 10  ITNRESLSLDRYLQEIGKYELLTAEDEVKLTMAIKEGYDMPVDTPEYKRAKRALDKLIKG 69

Query: 57  HLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM--- 113
           +LR VV +A  Y+  GL + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++   
Sbjct: 70  NLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQA 129

Query: 114 ---QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
              Q  I+R   L ++GT     + +  L +     +   D N K      +A  L++ +
Sbjct: 130 LAEQSRIVR-LPLNRVGTLNKISKAYSQLEQ-----EFERDPNTK-----ELATVLDM-D 177

Query: 171 SEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           S+ ++   ++AG   S++A     D N  +  D  V  HDGQ      K +    R+ LT
Sbjct: 178 SQDVADTLKIAGRHVSVDAPFAQGDDN--RLLD--VLQHDGQ------KPDHGLTRDSLT 227

Query: 230 ----RSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               RS+SVL PRE  +  +      ENP+TLE +  +F+++RERVRQI+ +A +++++S
Sbjct: 228 LEVERSLSVLAPREADVIRSYFGIGMENPLTLEEIGEKFKLTRERVRQIKEKAIRRLRQS 287

Query: 284 IQKQV 288
              +V
Sbjct: 288 AYSKV 292


>gi|281425773|ref|ZP_06256686.1| RNA polymerase sigma-70 factor [Prevotella oris F0302]
 gi|281400034|gb|EFB30865.1| RNA polymerase sigma-70 factor [Prevotella oris F0302]
          Length = 287

 Score =  116 bits (290), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 83/274 (30%), Positives = 148/274 (54%), Gaps = 28/274 (10%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI    ++  +EE  LA++ +  GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGHEDLISVEEEVELAQKIK-RGDRRALEKLTRANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK-----IGTTA 130
            ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V+     +G+  
Sbjct: 77  PDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGSVN 136

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLK---PEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
             KR+   L +       I +   K   PE  VA A K   S    +S++  LA  E  N
Sbjct: 137 KIKRVLNKLEQENEQFPTIEEIAAKVDIPEDKVADAIK---SNGRHVSVDAPLAEGEE-N 192

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA-R 246
           +L++    N++Q  D ++     QE +          R+ +  ++  LN RER I EA  
Sbjct: 193 SLLDILPNNNAQMADSVLV----QESL----------RDEVANALQSLNERERNIVEAFF 238

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            + ++ +TLE +  +F ++RERVRQI+ +A +++
Sbjct: 239 GINQSEMTLEEIGDKFGLTRERVRQIKEKAIRRL 272


>gi|330448286|ref|ZP_08311934.1| RNA polymerase sigma factor RpoS [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
 gi|328492477|dbj|GAA06431.1| RNA polymerase sigma factor RpoS [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
          Length = 291

 Score =  116 bits (290), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 83/275 (30%), Positives = 143/275 (52%), Gaps = 20/275 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ +I +  +L K++E VL  R    GD ++   L+ S+LRLVV IA  YRG  + IS++
Sbjct: 20  YLKDIAEKDLLTKEDE-VLYSRKSLAGDENSKKVLIESNLRLVVSIAKKYRGSPMHISDL 78

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGL+ AV+KFDPE+GFR +TY+ WWIK  ++  I      +++    +++     
Sbjct: 79  IDEGNIGLITAVEKFDPEKGFRFSTYATWWIKQTIERAIHNQGRTIRLPVHVSKEINTI- 137

Query: 139 LRRLKGHLQAITDNNLKP--EQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDK 195
              ++ H Q +  NN +P  EQ+  I  K     S  +S    +   D+S+N  +N+   
Sbjct: 138 ---VRAHKQLVKKNNEEPSKEQIANILNKSLHDVSTTLSYETPIISYDQSVNGEVNAQSM 194

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR---LQENP 252
                 + +       + + IEK        + T  ++ LN R++ I   RR   L    
Sbjct: 195 AVLIADETMAKPDQHVDDLAIEK--------ITTNVLNCLNKRDKEII-CRRFGLLGYEA 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            TL+ ++ E  ++RER+RQ++  +  K++ S+ + 
Sbjct: 246 QTLQEVAEEVGLTRERIRQLQVTSLSKLKNSLTRD 280


>gi|170723213|ref|YP_001750901.1| RNA polymerase sigma factor RpoS [Pseudomonas putida W619]
 gi|169761216|gb|ACA74532.1| RNA polymerase, sigma 70 subunit, RpoD family [Pseudomonas putida
           W619]
          Length = 335

 Score =  116 bits (290), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 86/272 (31%), Positives = 145/272 (53%), Gaps = 17/272 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + +K       ++ +N R++  D SL      SDK  
Sbjct: 185 LRAARELTQKL-DHEPSPEEIATLLEKPVAEVKRMLGLNERVSSVDVSLGP---DSDKT- 239

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++       + + +  L  ++R +   R   R  E+  T
Sbjct: 240 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLGELTDKQREVVVRRFGLRGHESS-T 293

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE++  E  ++RERVRQI+    K+++E ++K
Sbjct: 294 LEDVGLEIGLTRERVRQIQVEGLKRLREILEK 325


>gi|5305130|emb|CAB46191.1| RNA polymerase sigma factor [Pseudomonas putida]
          Length = 335

 Score =  116 bits (290), Expect = 4e-24,   Method: Compositional matrix adjust.
 Identities = 86/272 (31%), Positives = 145/272 (53%), Gaps = 17/272 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + +K       ++ +N R++  D SL      SDK  
Sbjct: 185 LRAARELTQKL-DHEPSPEEIATLLEKPVAEVKRMLGLNERVSSVDVSLGP---DSDKT- 239

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++       + + +  L  ++R +   R   R  E+  T
Sbjct: 240 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLGELTDKQREVVVRRFGLRGHESS-T 293

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE++  E  ++RERVRQI+    K+++E ++K
Sbjct: 294 LEDVGLEIGLTRERVRQIQVEGLKRLREILEK 325


>gi|311694174|gb|ADP97047.1| RNA polymerase, sigma 70 subunit, RpoD family [marine bacterium
           HP15]
          Length = 331

 Score =  116 bits (290), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 86/280 (30%), Positives = 148/280 (52%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A+  R  G+ S   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 63  YLNEIGFSPLLTPEEEVYFARLAR-KGEESGRKRMIESNLRLVVKIARRYVNRGLTLLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNLY 180

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA---------GDESLNAL 189
           LR  +   Q + D+    E++  +  K       ++ +N R+A         G++SL  L
Sbjct: 181 LRAARELTQKL-DHEPSAEEIARMVDKPVADVKRMLGLNERVASMDTPIGAGGEKSL--L 237

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RL 248
              +D+ +S   D L               +  N  + L + +  L+ +++ +   R  L
Sbjct: 238 DTVADEGASDPADLL---------------QDNNMCSCLEKWIDQLSDKQQEVLSRRFGL 282

Query: 249 QENPV-TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +  PV TLE +  E  ++RERVRQI+  A ++++E ++K+
Sbjct: 283 RGYPVSTLEEVGQEIGLTRERVRQIQVEALRRLREILEKE 322


>gi|208821597|ref|ZP_03261917.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4042]
 gi|218690868|ref|YP_002399080.1| RNA polymerase sigma factor RpoS [Escherichia coli ED1a]
 gi|260856852|ref|YP_003230743.1| RNA polymerase, sigma S factor [Escherichia coli O26:H11 str.
           11368]
 gi|208741720|gb|EDZ89402.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4042]
 gi|218428432|emb|CAR09358.2| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli ED1a]
 gi|257755501|dbj|BAI27003.1| RNA polymerase, sigma S factor [Escherichia coli O26:H11 str.
           11368]
 gi|284922677|emb|CBG35765.1| RNA polymerase sigma factor (sigma-38) [Escherichia coli 042]
          Length = 330

 Score =  116 bits (290), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 87/277 (31%), Positives = 143/277 (51%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI-VKELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQ--------VVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +  L    D+    E+        V  +++ L ++E  + S++  L GD     L 
Sbjct: 179 LRTAR-ELSHKLDHEPSAEESAEQLDKPVDDVSRMLRLNER-ITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|300691814|ref|YP_003752809.1| RNA polymerase sigma factor rpoS [Ralstonia solanacearum PSI07]
 gi|299078874|emb|CBJ51535.1| RNA polymerase sigma factor rpoS [Ralstonia solanacearum PSI07]
          Length = 377

 Score =  116 bits (290), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 88/279 (31%), Positives = 143/279 (51%), Gaps = 27/279 (9%)

Query: 19  YIHEIRKIPMLEKQEEY---VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           Y++ I   P+L   EE     LAK     G+ +A   ++  +LRLVV IA GY   G+P+
Sbjct: 108 YLNRISIKPLLTPAEELHFSTLAKA----GEFAARQVMIERNLRLVVSIAKGYLNRGVPL 163

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A++KFDPERGFR +TY+ WWI+ +++  I+     V++    +  R 
Sbjct: 164 LDLIEEGNLGLMHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRE 221

Query: 136 FFNLRRLKGHLQ--AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
              + R K HL+   I   +   E +  +  K      +V+S+N      E   +L    
Sbjct: 222 LNQVLRAKRHLEKSGIDGRDASIEDIAHLLGKTTDEVQDVLSLN------EHTTSLDTPF 275

Query: 194 DKN-SSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           D +  +   D+L  +H    +Q +  +E  +  ++ L R    L+ + R + E RR   N
Sbjct: 276 DLDPGTSLLDFLSDEHGASPDQEVAHRELSQLMKSWLAR----LSDKHRYVVE-RRFGLN 330

Query: 252 ---PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              P TLE L++E  ++RERVRQI+  A  K++     Q
Sbjct: 331 HIEPATLEELAAEMGLTRERVRQIQQEALVKLKRHFASQ 369


>gi|330446961|ref|ZP_08310612.1| RNA polymerase sigma factor RpoS [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
 gi|328491152|dbj|GAA05109.1| RNA polymerase sigma factor RpoS [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
          Length = 333

 Score =  116 bits (290), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 87/272 (31%), Positives = 148/272 (54%), Gaps = 15/272 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD  A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 62  YLGEIGYSPLLTAEEEVLYARRAL-RGDEVARKRMIESNLRLVVKISRRYSNRGLALLDL 120

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 121 VEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 179

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +   Q + D+    E    IA++L   E  V  +N  L  +E ++++ N    +S 
Sbjct: 180 LRTARELAQKL-DHEPTAED---IAQQL---EKPVDDVNRMLRLNERVSSVDNPIGGDSE 232

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR---LQENPVTL 255
           +    ++ D  G       +++  + +N +   +  LNP++R +  ARR   L     TL
Sbjct: 233 KALLDIIPDEKGGSPESSTQDD--DIKNSIVHWLQELNPKQREVL-ARRFGLLGYEASTL 289

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E++  E  ++RERVRQI+    +++++ +  Q
Sbjct: 290 EDVGREIGLTRERVRQIQVEGLRRLRDMLTHQ 321


>gi|166030947|ref|ZP_02233776.1| hypothetical protein DORFOR_00628 [Dorea formicigenerans ATCC
           27755]
 gi|166029214|gb|EDR47971.1| hypothetical protein DORFOR_00628 [Dorea formicigenerans ATCC
           27755]
          Length = 382

 Score =  116 bits (290), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 85/273 (31%), Positives = 136/273 (49%), Gaps = 29/273 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L   EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 116 YLKEIGKVPLLSADEEVELAKRMAE-GDEDAKKRLAEANLRLVVSIAKRYVGRGMLFLDL 174

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 175 IQEGNLGLIKAVEKFDYHKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 232

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALI 190
           L R+   L         PE++ A        + + L +S+ E +S+   +  +E      
Sbjct: 233 LIRVSRQLLQELGREPTPEEIAAELDMPVERVREILKISQ-EPVSLETPIGEEE------ 285

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
                  S   D++    D    V  E   +   +  L   +  L  RE+++   R   +
Sbjct: 286 ------DSHLGDFI---QDDNVPVPAEAAAQTLLKEQLDEVLDTLTEREQKVLRLRFGMD 336

Query: 251 N--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +    TLE +  EF+V+RER+RQIEA+A +K++
Sbjct: 337 DGRARTLEEVGKEFDVTRERIRQIEAKALRKLR 369


>gi|325277035|ref|ZP_08142696.1| RNA polymerase sigma factor RpoS [Pseudomonas sp. TJI-51]
 gi|324097832|gb|EGB96017.1| RNA polymerase sigma factor RpoS [Pseudomonas sp. TJI-51]
          Length = 335

 Score =  116 bits (290), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 86/272 (31%), Positives = 145/272 (53%), Gaps = 17/272 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + +K       ++ +N R++  D SL      SDK  
Sbjct: 185 LRAARELTQKL-DHEPSPEEIATLLEKPVAEVKRMLGLNERVSSVDVSLGP---DSDKT- 239

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++       + + +  L  ++R +   R   R  E+  T
Sbjct: 240 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLGELTDKQREVVVRRFGLRGHESS-T 293

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE++  E  ++RERVRQI+    K+++E ++K
Sbjct: 294 LEDVGLEIGLTRERVRQIQVEGLKRLREILEK 325


>gi|269837876|ref|YP_003320104.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphaerobacter
           thermophilus DSM 20745]
 gi|269787139|gb|ACZ39282.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphaerobacter
           thermophilus DSM 20745]
          Length = 341

 Score =  116 bits (290), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 84/272 (30%), Positives = 139/272 (51%), Gaps = 31/272 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ +I + P+L  +EE  LAKR  E GD+ A  R V S+LRLVV IA  Y G GL + ++
Sbjct: 75  YLRDIAQAPLLTAEEEVELAKRI-EEGDVEALQRFVRSNLRLVVSIAKRYVGRGLSLLDL 133

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+K+D  RG+R +TY+ WWI+ A+   I      +++        +  +
Sbjct: 134 IQEGNLGLIRAVQKYDWRRGYRFSTYATWWIRQAITRAIADQGRTIRLPV-----HMIDS 188

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           + R +  +  +T    +P +   +A+ ++V               E +   I ++ +  S
Sbjct: 189 ITRYRRTVMQLTQELGRPPRAEEVAEAMSVPP-------------EKVEQFIRAAQRTIS 235

Query: 199 QWQDWLVYDHDGQEQVLIEKE-----ERKNRRNMLTRSMS----VLNPRERRIFEARRLQ 249
             +  +  D +G    LI  E     E +    +L R ++     L PRER + + R   
Sbjct: 236 -LEKPIGEDEEGTLADLIADEVARSPEEEAVETLLQRDVAEVLEELTPRERLVLQLRFGL 294

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKK 279
            N  P TL  +  + ++SRERVRQIE+ A +K
Sbjct: 295 GNGSPHTLSEVGQQLDISRERVRQIESEALRK 326


>gi|325109992|ref|YP_004271060.1| RNA polymerase, sigma 38 subunit, RpoS [Planctomyces brasiliensis
           DSM 5305]
 gi|324970260|gb|ADY61038.1| RNA polymerase, sigma 38 subunit, RpoS [Planctomyces brasiliensis
           DSM 5305]
          Length = 286

 Score =  116 bits (290), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 84/277 (30%), Positives = 135/277 (48%), Gaps = 25/277 (9%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ EI +  +L   EE  LA R    GDL A  R+V ++LRLVV IA GY   GLP+
Sbjct: 24  LETYLREINETSLLSADEEKELANRI-AMGDLEARDRMVRANLRLVVNIARGYASKGLPL 82

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GL++AV+ FDP    R +TY+ +WIK +++  ++     ++I   A    L
Sbjct: 83  QDLIEEGNLGLLRAVEGFDPNMNTRFSTYASYWIKQSIKRSLVNCAKTIRI--PAYMVEL 140

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVA----IAKKLNVSESEVISMNCRLAGDESLNALIN 191
               R+    LQ   +     E+V A      KKLN+ +  +               L N
Sbjct: 141 LSKWRKATARLQDELNRTPTAEEVAAELGLPKKKLNIVKKAI--------------QLYN 186

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM--LTRSMSVLNPRERRIFEAR--R 247
           S+ ++  +   W + +    E+ +  +EE  N  N+  + R +  ++ RE  I   R   
Sbjct: 187 STPQSDDEESGWSLGEMVADERAIGPEEELVNNDNLNHVYRMLDDMDDRESTILRMRFGL 246

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             E P TL+ +     ++RERVRQIE  A  ++   +
Sbjct: 247 DHEEPKTLKEIGESLGLTRERVRQIEQEALNRLNRGL 283


>gi|26988355|ref|NP_743780.1| RNA polymerase sigma factor RpoS [Pseudomonas putida KT2440]
 gi|148549360|ref|YP_001269462.1| RNA polymerase sigma factor RpoS [Pseudomonas putida F1]
 gi|167032190|ref|YP_001667421.1| RNA polymerase sigma factor RpoS [Pseudomonas putida GB-1]
 gi|24983106|gb|AAN67244.1|AE016351_6 RNA polymerase sigma factor RpoS [Pseudomonas putida KT2440]
 gi|148513418|gb|ABQ80278.1| RNA polymerase, sigma 70 subunit, RpoD family [Pseudomonas putida
           F1]
 gi|166858678|gb|ABY97085.1| RNA polymerase, sigma 70 subunit, RpoD family [Pseudomonas putida
           GB-1]
 gi|313500209|gb|ADR61575.1| RpoS [Pseudomonas putida BIRD-1]
          Length = 335

 Score =  116 bits (290), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 86/272 (31%), Positives = 145/272 (53%), Gaps = 17/272 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + +K       ++ +N R++  D SL      SDK  
Sbjct: 185 LRAARELTQKL-DHEPSPEEIATLLEKPVAEVKRMLGLNERVSSVDVSLGP---DSDKT- 239

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++       + + +  L  ++R +   R   R  E+  T
Sbjct: 240 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLGELTDKQREVVVRRFGLRGHESS-T 293

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE++  E  ++RERVRQI+    K+++E ++K
Sbjct: 294 LEDVGLEIGLTRERVRQIQVEGLKRLREILEK 325


>gi|319790059|ref|YP_004151692.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermovibrio
           ammonificans HB-1]
 gi|317114561|gb|ADU97051.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermovibrio
           ammonificans HB-1]
          Length = 318

 Score =  116 bits (290), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 85/269 (31%), Positives = 146/269 (54%), Gaps = 13/269 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  ++  I KIP+L ++EE  LAKR +  GD  A  +LV S+LR VV +A  Y G GLP+
Sbjct: 49  LDAFLKSISKIPLLSREEEIELAKRAK-AGDKEALKKLVESNLRFVVSVAKKYLGCGLPL 107

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EG +GL++A ++FDP++G +  +Y++WWI+ ++ + + +    VKI     Q  L
Sbjct: 108 HDLIAEGILGLIEAARRFDPDKGVKFISYAVWWIRQSIMQALAQQTGAVKI--PVKQAVL 165

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + R  G L  +     +P  +  +A  + +   EV  +        SL+  I   D+
Sbjct: 166 VNKITRSYGEL--LKKLGREP-TIEELADYVGMEPKEVERLLSICQVPLSLDTPIG--DE 220

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PV 253
             + ++D+L  +   + +  + +EE K     +   +  L P+E++I   R  L  N P 
Sbjct: 221 EDTTFKDFLKGEGTAEVEEKVVQEELKQS---IQEMLEQLTPQEKKIIIMRFGLDGNEPK 277

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQE 282
           TL  +  +  +SRERVRQ+E RA KK++E
Sbjct: 278 TLREIGEKLGISRERVRQLETRAKKKMKE 306


>gi|149190125|ref|ZP_01868401.1| RNA polymerase sigma-38 factor [Vibrio shilonii AK1]
 gi|148836014|gb|EDL52975.1| RNA polymerase sigma-38 factor [Vibrio shilonii AK1]
          Length = 325

 Score =  116 bits (290), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 88/275 (32%), Positives = 155/275 (56%), Gaps = 21/275 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R  + GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 53  YLGEIGFSPLLTAEEEVLYARRALK-GDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 111

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 112 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 170

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLN--VSE-SEVISMNCRLAGDESLNALINSSDK 195
           LR  +   Q + D+    E+   IA+KL+  VS+ S+++ +N R++   S++  I    +
Sbjct: 171 LRTARELSQKL-DHEPTAEE---IAQKLDKPVSDVSKMLRLNERIS---SVDTPIGGDGE 223

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR---LQENP 252
            +    D +        +V  + ++ K+    L   +  LNP+++ +  ARR   L   P
Sbjct: 224 KA--LLDIIPDSTHSDPEVSTQDDDIKSS---LIHWLDELNPKQKEVL-ARRFGLLGYEP 277

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            TLE +  E  ++RERVRQI+    +++++ + KQ
Sbjct: 278 STLEEVGREINLTRERVRQIQVEGLRRLRDILIKQ 312


>gi|258516189|ref|YP_003192411.1| RNA polymerase sigma factor RpoD [Desulfotomaculum acetoxidans DSM
           771]
 gi|257779894|gb|ACV63788.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfotomaculum
           acetoxidans DSM 771]
          Length = 359

 Score =  115 bits (289), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 85/265 (32%), Positives = 139/265 (52%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LAKR  E G+  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 93  YLKEIGRVPLLSSEEEVELAKRM-EMGEEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 151

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 152 IQEGNMGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 209

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L         PE+   IAK++N++E +V  +        SL   I   ++  S
Sbjct: 210 LIRVSRQLLQELGREPMPEE---IAKEMNITEDKVREIMKIAQEPVSLETPIG--EEEDS 264

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D+ + DHD +     E+      R  L   +  L  RE+++   R   ++    TLE
Sbjct: 265 HLGDF-IEDHDARAPA--EEASFTLLREQLDDVLKTLTDREQKVLRLRFGLDDGRARTLE 321

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  +F V+RER+RQIEA+  +K++
Sbjct: 322 EVGQKFGVTRERIRQIEAKTLRKLR 346


>gi|125973412|ref|YP_001037322.1| RNA polymerase sigma factor RpoD [Clostridium thermocellum ATCC
           27405]
 gi|125713637|gb|ABN52129.1| RNA polymerase, sigma 38 subunit, RpoS [Clostridium thermocellum
           ATCC 27405]
          Length = 358

 Score =  115 bits (289), Expect = 5e-24,   Method: Compositional matrix adjust.
 Identities = 86/265 (32%), Positives = 133/265 (50%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  +EE  LA R  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 92  YLKEIGKVPLLTAEEEIELAHRI-EQGDAEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 150

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 151 IQEGNLGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 208

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L         PE+   IAK++N+   +V  +        SL   I   ++  S
Sbjct: 209 LIRVSRQLLQELGREPHPEE---IAKEMNMPVEKVREIMKISQEPVSLETPIG--EEEDS 263

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++    D       E       +  L   +  L PRE ++   R   ++    TLE
Sbjct: 264 HLGDFI---PDDDAPAPSEAAAFTLLKEQLVDVLDTLTPREEKVLRLRFGLDDGRARTLE 320

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF V+RER+RQIEA+A +K++
Sbjct: 321 EVGKEFNVTRERIRQIEAKALRKLR 345


>gi|218458675|ref|ZP_03498766.1| RNA polymerase factor sigma-32 [Rhizobium etli Kim 5]
          Length = 138

 Score =  115 bits (289), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 46/99 (46%), Positives = 77/99 (77%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L +QEE+ LA R+++H D  A +++  +H+RLV+ +A  +R +GLP+S++V EG +GL
Sbjct: 39  PYLARQEEHDLATRWKDHDDRGARNQIAMAHMRLVISMAGKFRNFGLPMSDLVQEGYVGL 98

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
           ++A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+
Sbjct: 99  LEAAARFEPERDVRFSTYASWWIRASIQDYILRNWSIVR 137


>gi|17545926|ref|NP_519328.1| RNA polymerase sigma factor RpoS [Ralstonia solanacearum GMI1000]
 gi|17428221|emb|CAD14909.1| rna polymerase sigma s (sigma-38) factor transcription regulator
           protein [Ralstonia solanacearum GMI1000]
          Length = 377

 Score =  115 bits (289), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 88/279 (31%), Positives = 143/279 (51%), Gaps = 27/279 (9%)

Query: 19  YIHEIRKIPMLEKQEEY---VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           Y++ I   P+L   EE     LAK     G+ +A   ++  +LRLVV IA GY   G+P+
Sbjct: 108 YLNRISIKPLLTPAEELHFSTLAKA----GEFAARQVMIERNLRLVVSIAKGYLNRGVPL 163

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A++KFDPERGFR +TY+ WWI+ +++  I+     V++    +  R 
Sbjct: 164 LDLIEEGNLGLMHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRE 221

Query: 136 FFNLRRLKGHLQ--AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
              + R K HL+   I   +   E +  +  K      +V+S+N      E   +L    
Sbjct: 222 LNQVLRAKRHLEKSGIDGRDASIEDIAHLLGKTTEEVQDVLSLN------EHTTSLDTPF 275

Query: 194 DKN-SSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           D +  +   D+L  +H    +Q +  +E  +  ++ L R    L+ + R + E RR   N
Sbjct: 276 DLDPGTSLLDFLSDEHGASPDQEVAHRELSQLMKSWLAR----LSDKHRYVVE-RRFGLN 330

Query: 252 ---PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              P TLE L++E  ++RERVRQI+  A  K++     Q
Sbjct: 331 HIEPATLEELAAEMGLTRERVRQIQQEALVKLKRHFASQ 369


>gi|89075068|ref|ZP_01161509.1| putative RNA polymerase sigma-38 factor [Photobacterium sp. SKA34]
 gi|89049155|gb|EAR54720.1| putative RNA polymerase sigma-38 factor [Photobacterium sp. SKA34]
          Length = 337

 Score =  115 bits (289), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 87/272 (31%), Positives = 148/272 (54%), Gaps = 15/272 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD  A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 66  YLGEIGYSPLLTAEEEVLYARRAL-RGDEVARKRMIESNLRLVVKISRRYSNRGLALLDL 124

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 125 VEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 183

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +   Q + D+    E    IA++L   E  V  +N  L  +E ++++ N    +S 
Sbjct: 184 LRTARELAQKL-DHEPTAED---IAQQL---EKPVDDVNRMLRLNERVSSVDNPIGGDSE 236

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR---LQENPVTL 255
           +    ++ D  G       +++  + +N +   +  LNP++R +  ARR   L     TL
Sbjct: 237 KALLDIIPDEKGGSPESSTQDD--DIKNSIVHWLQELNPKQREVL-ARRFGLLGYEASTL 293

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E++  E  ++RERVRQI+    +++++ +  Q
Sbjct: 294 EDVGREIGLTRERVRQIQVEGLRRLRDMLTHQ 325


>gi|291533682|emb|CBL06795.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Megamonas hypermegale
           ART12/1]
          Length = 329

 Score =  115 bits (289), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 86/265 (32%), Positives = 137/265 (51%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   EE  LAKR  E GDL A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 69  YLKEIGRVPLLSADEEIKLAKRM-EDGDLEAQKRLAEANLRLVVSIAKRYVGRGMLFLDL 127

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 128 IQEGNLGLIKAVEKFDYNKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 185

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L         PE+   IAK+++VS   V  +  ++A  E ++      ++  S
Sbjct: 186 LIRVSRQLLQSLGREPSPEE---IAKEMDVSVDRVREI-MKIA-QEPVSLETPIGEEEDS 240

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D+ + DHD       E       +  L   +  L  RE ++   R   ++    TLE
Sbjct: 241 HLGDF-IEDHDAPAPA--EAASFVLLKEQLEDVLDTLTEREEKVLRLRFGLDDGRARTLE 297

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +   F V+RER+RQIEA+A +K++
Sbjct: 298 EVGQNFGVTRERIRQIEAKALRKLR 322


>gi|89895793|ref|YP_519280.1| RNA polymerase sigma factor RpoD [Desulfitobacterium hafniense Y51]
 gi|89335241|dbj|BAE84836.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 367

 Score =  115 bits (289), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 86/277 (31%), Positives = 135/277 (48%), Gaps = 37/277 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LAKR  E GD SA  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 101 YLKEIGRVPLLTAEEEIELAKRM-EQGDESAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 159

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 160 IQEGNLGLIKAVEKFDYVKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 217

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVS----------ESEVISMNCRLAGDES--L 186
           L R+   L         PE+   IA ++++S            E +S+   +  +E   L
Sbjct: 218 LIRVSRQLLQELGREPTPEE---IAVQMDISVERVREIMKIAQEPVSLETPIGEEEDSHL 274

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              I   D  +       +   +  E+VL                   L PRE ++   R
Sbjct: 275 GDFIPDEDAPAPSEAASFILLKEQLEEVL-----------------ETLTPREEKVLRLR 317

Query: 247 RLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              ++    TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 318 FGLDDGRTRTLEEVGQEFGVTRERIRQIEAKALRKLR 354


>gi|323703334|ref|ZP_08114984.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfotomaculum
           nigrificans DSM 574]
 gi|323531697|gb|EGB21586.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfotomaculum
           nigrificans DSM 574]
          Length = 367

 Score =  115 bits (289), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 83/265 (31%), Positives = 139/265 (52%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 101 YLKEIGRVPLLSPEEEVELAKRM-EQGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 159

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 160 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 217

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L         PE+   IAK++N+S  +V  +  ++A  E ++      ++  S
Sbjct: 218 LIRVSRQLLQELGREPTPEE---IAKEMNISGDKVREI-MKIA-QEPVSLETPIGEEEDS 272

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++    D   +   E+      R  L   +  L  RE+++   R   ++    TLE
Sbjct: 273 HLGDFI---EDADARAPAEEASFTLLREQLDEVLKTLTDREQKVLRLRFGLDDGRARTLE 329

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  +F V+RER+RQIEA+  +K++
Sbjct: 330 EVGQKFGVTRERIRQIEAKTLRKLR 354


>gi|291278687|ref|YP_003495522.1| DNA-directed RNA polymerase sigma 70 factor [Deferribacter
           desulfuricans SSM1]
 gi|290753389|dbj|BAI79766.1| DNA-directed RNA polymerase sigma 70 factor [Deferribacter
           desulfuricans SSM1]
          Length = 298

 Score =  115 bits (289), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 79/273 (28%), Positives = 146/273 (53%), Gaps = 12/273 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            ++ Y++EI K P L K+EE  L+KR  E GD  A + ++  +L+LVV IA  Y   GL 
Sbjct: 26  SITIYLNEIIKYPTLSKEEEIELSKRI-EQGDEEAKNLMINCNLKLVVSIAKKYNNRGLQ 84

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGNIGL++AV+KFD  +GF+ +TY+ WWI+ A++  ++    +V+I    N+  
Sbjct: 85  LIDLINEGNIGLIKAVEKFDYRKGFKFSTYATWWIRQAIERALVNQTKMVRIPVHMNE-- 142

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
              N+ ++K   + +     +   +  ++ + N+S   +      +  + S++  IN  D
Sbjct: 143 ---NINKVKKATEKLRRKLKREPTLFELSTECNMSLLTIQKTIDAMQQNISIDGTINEDD 199

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
             +S   D ++ D + +     +  + KNR  ++   +  LN  E+ +   R   +   P
Sbjct: 200 --NSTLHD-ILPDPESKADPFKKIVQEKNRE-LIMNWIECLNENEKELIIKRFGLDGKEP 255

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            TL+ +     V+RERVRQIE R   K++  ++
Sbjct: 256 ETLDKIGKRLGVTRERVRQIEKRILTKLRNHLK 288


>gi|237800176|ref|ZP_04588637.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. oryzae
           str. 1_6]
 gi|331023033|gb|EGI03090.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. oryzae
           str. 1_6]
          Length = 335

 Score =  115 bits (289), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 87/272 (31%), Positives = 146/272 (53%), Gaps = 17/272 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVYFA-RLSQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + +K       ++ +N R++  D SL      SDK  
Sbjct: 185 LRAARELTQKL-DHEPTPEEIANLLEKPVGEVKRMLGLNERVSSVDVSLGP---DSDKT- 239

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++       + + +S L  ++R +   R   R  E+  T
Sbjct: 240 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTEKQREVVIRRFGLRGHESS-T 293

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE++  E  ++RERVRQI+    K+++E ++K
Sbjct: 294 LEDVGLEIGLTRERVRQIQVEGLKRLREILEK 325


>gi|269121540|ref|YP_003309717.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sebaldella
           termitidis ATCC 33386]
 gi|268615418|gb|ACZ09786.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sebaldella
           termitidis ATCC 33386]
          Length = 387

 Score =  115 bits (289), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 83/270 (30%), Positives = 140/270 (51%), Gaps = 23/270 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI +IP+L  +EE  LA++  E+ D  A  +L+ S+LRLVV IA  +   GL + ++
Sbjct: 121 YLREIGQIPLLTYEEEIALAQKVLEN-DEEAKQKLIESNLRLVVSIAKKHTNRGLKMLDL 179

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV+KF+ E+GF+ +TY+ WWI+ A+   I      ++I        +   
Sbjct: 180 IQEGNMGLMKAVEKFEYEKGFKFSTYATWWIRQAITRAIADQGRTIRIPV-----HMIET 234

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           + ++K   + I     K      +AKKL +   +V S+        SL   + S +   S
Sbjct: 235 INKIKKESRIILQETGKEATAEELAKKLEIPVDKVKSILEMNQDPISLETPVGSEE--DS 292

Query: 199 QWQDWLVYD-----HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-- 251
           +  D++  D     +D   +VL+        +  L   +  L+ RE  +   R   ++  
Sbjct: 293 ELGDFVEDDKFLNPYDATTRVLL--------KEQLDGVLKTLSEREEMVLRYRYGLDDGS 344

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           P TLE +   F V+RER+RQIE +A +K++
Sbjct: 345 PKTLEEVGKIFNVTRERIRQIEVKALRKLR 374


>gi|90580346|ref|ZP_01236153.1| putative RNA polymerase sigma-38 factor [Vibrio angustum S14]
 gi|90438648|gb|EAS63832.1| putative RNA polymerase sigma-38 factor [Vibrio angustum S14]
          Length = 337

 Score =  115 bits (289), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 87/272 (31%), Positives = 148/272 (54%), Gaps = 15/272 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD  A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 66  YLGEIGYSPLLTAEEEVLYARRAL-RGDEVARKRMIESNLRLVVKISRRYSNRGLALLDL 124

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 125 VEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 183

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +   Q + D+    E    IA++L   E  V  +N  L  +E ++++ N    +S 
Sbjct: 184 LRTARELAQKL-DHEPTAED---IAQQL---EKPVDDVNRMLRLNERVSSVDNPIGGDSE 236

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR---LQENPVTL 255
           +    ++ D  G       +++  + +N +   +  LNP++R +  ARR   L     TL
Sbjct: 237 KALLDIIPDEKGGSPESSTQDD--DIKNSIVHWLQELNPKQREVL-ARRFGLLGYEASTL 293

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E++  E  ++RERVRQI+    +++++ +  Q
Sbjct: 294 EDVGREIGLTRERVRQIQVEGLRRLRDMLTHQ 325


>gi|261367093|ref|ZP_05979976.1| RNA polymerase sigma factor RpoD [Subdoligranulum variabile DSM
           15176]
 gi|282571217|gb|EFB76752.1| RNA polymerase sigma factor RpoD [Subdoligranulum variabile DSM
           15176]
          Length = 364

 Score =  115 bits (289), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 86/272 (31%), Positives = 142/272 (52%), Gaps = 24/272 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
           Y+ EI ++P+L  +EE  LA + +  G     A  RL  ++LRLVV IA  Y G G+   
Sbjct: 95  YLKEIGRVPLLTPEEEIDLALKIQAGGPEGEKAKQRLSEANLRLVVSIAKRYVGRGMQFL 154

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ 132
           +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N+
Sbjct: 155 DLIQEGNLGLIKAVEKFDHTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINK 214

Query: 133 -KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
            K++   L    GH  +  +          IA++L++S  +V  +  R+A  E ++    
Sbjct: 215 VKKVSSQLLHEYGHDPSAEE----------IAERLDMSVDKVREI-MRVA-QEPVSLETP 262

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             ++  S   D++    D    V  E   +   +  L   +  L PRE ++   R   E+
Sbjct: 263 IGEEEDSHLGDFI---PDDDAPVPAEAASQTLLKEQLADVLKTLTPREEKVLRLRFGLED 319

Query: 252 --PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             P TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 320 GRPRTLEEVGKEFNVTRERIRQIEAKALRKLR 351


>gi|48727551|gb|AAT46075.1| RNA polymerase sigma factor [Pseudomonas chlororaphis]
          Length = 334

 Score =  115 bits (289), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 87/272 (31%), Positives = 146/272 (53%), Gaps = 17/272 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 66  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 124

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 125 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 183

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + +K       ++ +N R++  D SL      SDK  
Sbjct: 184 LRAARELTQKL-DHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSLGP---DSDKT- 238

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++       + + +S L  ++R +   R   R  E+  T
Sbjct: 239 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTDKQREVVVRRFGLRGHESS-T 292

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE++  E  ++RERVRQI+    K+++E ++K
Sbjct: 293 LEDVGLEIGLTRERVRQIQVEGLKRLREILEK 324


>gi|323127013|gb|ADX24310.1| RNA polymerase sigma factor RpoD [Streptococcus dysgalactiae subsp.
           equisimilis ATCC 12394]
          Length = 369

 Score =  115 bits (289), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 88/269 (32%), Positives = 142/269 (52%), Gaps = 21/269 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE VLA    E GDL A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLTSEEEKVLAVAVAE-GDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 218

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L      +  PEQ   IA+++ ++  +V  +  ++A +  SL   I   D   
Sbjct: 219 LVREQRNLLQELGQDPTPEQ---IAERMEMTPDKVREI-LKIAQEPVSLETPIGEED--D 272

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 273 SHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 326

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE++   F V+RER+RQIEA+A +K++
Sbjct: 327 RTLEDVGKVFNVTRERIRQIEAKALRKLR 355


>gi|219670224|ref|YP_002460659.1| RNA polymerase sigma factor RpoD [Desulfitobacterium hafniense
           DCB-2]
 gi|219540484|gb|ACL22223.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Desulfitobacterium hafniense DCB-2]
          Length = 372

 Score =  115 bits (289), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 86/277 (31%), Positives = 135/277 (48%), Gaps = 37/277 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LAKR  E GD SA  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 106 YLKEIGRVPLLTAEEEIELAKRM-EQGDESAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 164

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 165 IQEGNLGLIKAVEKFDYVKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 222

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVS----------ESEVISMNCRLAGDES--L 186
           L R+   L         PE+   IA ++++S            E +S+   +  +E   L
Sbjct: 223 LIRVSRQLLQELGREPTPEE---IAVQMDISVERVREIMKIAQEPVSLETPIGEEEDSHL 279

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              I   D  +       +   +  E+VL                   L PRE ++   R
Sbjct: 280 GDFIPDEDAPAPSEAASFILLKEQLEEVL-----------------ETLTPREEKVLRLR 322

Query: 247 RLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              ++    TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 323 FGLDDGRTRTLEEVGQEFGVTRERIRQIEAKALRKLR 359


>gi|33150232|gb|AAP97086.1| RNA polymerase sigma factor [Pseudomonas chlororaphis]
 gi|103488976|gb|ABF71881.1| RpoS [Pseudomonas chlororaphis]
          Length = 334

 Score =  115 bits (289), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 87/272 (31%), Positives = 146/272 (53%), Gaps = 17/272 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 66  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 124

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 125 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 183

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + +K       ++ +N R++  D SL      SDK  
Sbjct: 184 LRAARELTQKL-DHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSLGP---DSDKT- 238

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++       + + +S L  ++R +   R   R  E+  T
Sbjct: 239 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTDKQREVVVRRFGLRGHESS-T 292

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE++  E  ++RERVRQI+    K+++E ++K
Sbjct: 293 LEDVGLEIGLTRERVRQIQVEGLKRLREILEK 324


>gi|77457359|ref|YP_346864.1| RNA polymerase sigma factor RpoS [Pseudomonas fluorescens Pf0-1]
 gi|77381362|gb|ABA72875.1| RNA polymerase, sigma 38 subunit, RpoS [Pseudomonas fluorescens
           Pf0-1]
          Length = 335

 Score =  115 bits (289), Expect = 6e-24,   Method: Compositional matrix adjust.
 Identities = 87/272 (31%), Positives = 146/272 (53%), Gaps = 17/272 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + +K       ++ +N R++  D SL      SDK  
Sbjct: 185 LRAARELTQKL-DHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSLGP---DSDKT- 239

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++       + + +S L  ++R +   R   R  E+  T
Sbjct: 240 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTDKQREVVVRRFGLRGHESS-T 293

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE++  E  ++RERVRQI+    K+++E ++K
Sbjct: 294 LEDVGLEIGLTRERVRQIQVEGLKRLREILEK 325


>gi|1017750|gb|AAA79182.1| RpoS [Serratia entomophila]
          Length = 332

 Score =  115 bits (289), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 139/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 63  YLGEIGYSPLLTAEEEVYFARRAL-RGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 181

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 182 RTARELSHKLDHEPSAEEIAEQLDKPVHDVSRMLRLN---ERMPSVDTPLGGDSEKALLD 238

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 239 ILADEKDNGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 287

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 288 --ATLEDVGREIVLTRERVRQIQVEGLRRLREILQMQ 322


>gi|256004390|ref|ZP_05429371.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           thermocellum DSM 2360]
 gi|255991674|gb|EEU01775.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           thermocellum DSM 2360]
 gi|316940353|gb|ADU74387.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           thermocellum DSM 1313]
          Length = 358

 Score =  115 bits (289), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 86/265 (32%), Positives = 133/265 (50%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  +EE  LA R  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 92  YLKEIGKVPLLTAEEEIELAHRM-EQGDAEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 150

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 151 IQEGNLGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 208

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L         PE+   IAK++N+   +V  +        SL   I   ++  S
Sbjct: 209 LIRVSRQLLQELGREPHPEE---IAKEMNMPVEKVREIMKISQEPVSLETPIG--EEEDS 263

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++    D       E       +  L   +  L PRE ++   R   ++    TLE
Sbjct: 264 HLGDFI---PDDDAPAPSEAAAFTLLKEQLVDVLDTLTPREEKVLRLRFGLDDGRARTLE 320

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF V+RER+RQIEA+A +K++
Sbjct: 321 EVGKEFNVTRERIRQIEAKALRKLR 345


>gi|281417615|ref|ZP_06248635.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           thermocellum JW20]
 gi|281409017|gb|EFB39275.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           thermocellum JW20]
          Length = 358

 Score =  115 bits (289), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 86/265 (32%), Positives = 133/265 (50%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  +EE  LA R  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 92  YLKEIGKVPLLTAEEEIELAHRI-EQGDAEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 150

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 151 IQEGNLGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 208

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L         PE+   IAK++N+   +V  +        SL   I   ++  S
Sbjct: 209 LIRVSRQLLQELGREPHPEE---IAKEMNMPVEKVREIMKISQEPVSLETPIG--EEEDS 263

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++    D       E       +  L   +  L PRE ++   R   ++    TLE
Sbjct: 264 HLGDFI---PDDDAPAPSEAAAFTLLKEQLVDVLDTLTPREEKVLRLRFGLDDGRARTLE 320

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF V+RER+RQIEA+A +K++
Sbjct: 321 EVGKEFNVTRERIRQIEAKALRKLR 345


>gi|253580849|ref|ZP_04858112.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251847919|gb|EES75886.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 375

 Score =  115 bits (289), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 87/270 (32%), Positives = 142/270 (52%), Gaps = 23/270 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  +EE  LAKR  E+GD +A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 109 YLKEIGKVPLLSAEEEIELAKRM-ENGDEAAKKRLAEANLRLVVSIAKRYVGRGMLFLDL 167

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 168 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 225

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L         PE+   IAK++++S   V  +        SL   I   ++  S
Sbjct: 226 LIRVSRQLLQELGREPTPEE---IAKEMDMSVERVREILKISQEPVSLETPI--GEEEDS 280

Query: 199 QWQDWLVYDH-----DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-- 251
              D++  D+     D     L++++        L   +S L  RE+++   R   ++  
Sbjct: 281 HLGDFIQDDNVPVPADAAAFTLLKEQ--------LVEVLSTLTDREQKVLRLRFGLDDGR 332

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 333 ARTLEEVGKEFNVTRERIRQIEAKALRKLR 362


>gi|152985831|ref|YP_001346901.1| RNA polymerase sigma factor RpoS [Pseudomonas aeruginosa PA7]
 gi|150960989|gb|ABR83014.1| RNA polymerase sigma factor RpoS [Pseudomonas aeruginosa PA7]
          Length = 344

 Score =  115 bits (289), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 143/277 (51%), Gaps = 27/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 76  YLNEIGFSPLLTPEEEVHFA-RLAQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 134

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 135 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 193

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA------GDESLNALINS 192
           LR  +  L    D+   PE++  + +K       ++ +N R+       G +S   L+++
Sbjct: 194 LRAAR-ELTHKLDHEPSPEEIANLLEKPVAEVKRMLGLNERVTSVDVSLGPDSDKTLLDT 252

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQ 249
              +       L+ D D  E +               + +S L  ++R +   R   R  
Sbjct: 253 LTDDRPTDPCELLQDDDLSESI--------------DQWLSELTDKQREVVIRRFGLRGH 298

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E+  TLE +  E  ++RERVRQI+  A K+++E ++K
Sbjct: 299 ESS-TLEEVGQEIGLTRERVRQIQVEALKRLREILEK 334


>gi|186702713|gb|ACC91623.1| RNA polymerase sigma factor [Pseudomonas sp. CT07]
          Length = 336

 Score =  115 bits (288), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 87/272 (31%), Positives = 146/272 (53%), Gaps = 17/272 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 68  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 126

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 127 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 185

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + +K       ++ +N R++  D SL      SDK  
Sbjct: 186 LRAARELTQKL-DHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSLGP---DSDKT- 240

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++       + + +S L  ++R +   R   R  E+  T
Sbjct: 241 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTDKQREVVVRRFGLRGHESS-T 294

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE++  E  ++RERVRQI+    K+++E ++K
Sbjct: 295 LEDVGLEIGLTRERVRQIQVEGLKRLREILEK 326


>gi|218701232|ref|YP_002408861.1| RNA polymerase sigma factor RpoS [Escherichia coli IAI39]
 gi|218371218|emb|CAR19049.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli IAI39]
 gi|327251469|gb|EGE63155.1| RNA polymerase sigma factor RpoS [Escherichia coli STEC_7v]
          Length = 330

 Score =  115 bits (288), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 84/277 (30%), Positives = 139/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGF  +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFSFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|322411497|gb|EFY02405.1| RNA polymerase sigma factor RpoD [Streptococcus dysgalactiae subsp.
           dysgalactiae ATCC 27957]
          Length = 369

 Score =  115 bits (288), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 88/269 (32%), Positives = 142/269 (52%), Gaps = 21/269 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE VLA    E GDL A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLTSEEEKVLAVAVAE-GDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 218

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L      +  PEQ   IA+++ ++  +V  +  ++A +  SL   I   D   
Sbjct: 219 LVREQRNLLQELGQDPTPEQ---IAERMEMTPDKVREI-LKIAQEPVSLETPIGEED--D 272

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 273 SHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 326

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE++   F V+RER+RQIEA+A +K++
Sbjct: 327 RTLEDVGKVFNVTRERIRQIEAKALRKLR 355


>gi|225848787|ref|YP_002728951.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Sulfurihydrogenibium azorense Az-Fu1]
 gi|225643846|gb|ACN98896.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Sulfurihydrogenibium azorense Az-Fu1]
          Length = 282

 Score =  115 bits (288), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 87/274 (31%), Positives = 143/274 (52%), Gaps = 35/274 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ ++ K PML  +EE  LA R +  GD  A  +LV  +LR VV IA  + G+G+P+
Sbjct: 11  LQLYMQQMGKYPMLTPEEERELAIRAK-KGDKEALKKLVEGNLRFVVNIAKNFMGWGVPL 69

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           +++++ GN+GL++A K+FDP++  +  +Y++WWI+ A+ + I +    V+I     ++ L
Sbjct: 70  TDLIAAGNLGLIEAAKRFDPDKNVKFISYAVWWIRQAIMQTIFQQTGAVRIPI---KESL 126

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRL--AGD 183
           F +  ++K   + + ++  +      IAK+L  S  +V          IS++  L   G+
Sbjct: 127 FIS--KVKNAYEKLKESLGREPTEEEIAKELKTSVKKVKNALAIVRQPISLDMPLGEGGE 184

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           E    L   S K +   +  LV      E  L E+ E         R ++VL+ RER I 
Sbjct: 185 EDFTLLDILSKKGTEDVEKDLV------ESTLKEEFE---------RLLNVLDEREREII 229

Query: 244 EARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
           + R   E   P TLE +     +SRERVRQ+E R
Sbjct: 230 KLRYGLEGLEPKTLEEVGEMLGISRERVRQLEQR 263


>gi|161502017|ref|YP_001569129.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:-- str. RSK2980]
 gi|160863364|gb|ABX19987.1| hypothetical protein SARI_00033 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 330

 Score =  115 bits (288), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 84/277 (30%), Positives = 139/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGF  +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFSFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|20808174|ref|NP_623345.1| RNA polymerase sigma factor RpoD [Thermoanaerobacter tengcongensis
           MB4]
 gi|20516766|gb|AAM24949.1| DNA-directed RNA polymerase sigma subunits (sigma70/sigma32)
           [Thermoanaerobacter tengcongensis MB4]
          Length = 372

 Score =  115 bits (288), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 84/265 (31%), Positives = 139/265 (52%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L  +EE  LAKR  E GD  A  RL+ ++LRLVV IA  Y G G+   ++
Sbjct: 106 YLKEIGKIPLLTPEEEIELAKRI-EQGDEEAKKRLIEANLRLVVSIAKRYVGRGMLFLDL 164

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 165 IQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 222

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R++  L         PE+   +AK++ + E +V  +  ++A  E ++      ++  S
Sbjct: 223 LIRVQRQLLQELGREPTPEE---LAKEMGMPEEKVREI-LKIA-QEPVSLETPIGEEEDS 277

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++  +              K +   L   +  L PRE ++   R   ++    TLE
Sbjct: 278 HLGDFIPDEDAPAPAEAAAYTMLKEQ---LMDVLDTLTPREEKVLRLRFGLDDGRARTLE 334

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF V+RER+RQIEA+A +K++
Sbjct: 335 EVGKEFNVTRERIRQIEAKALRKLR 359


>gi|330807812|ref|YP_004352274.1| RNA polymerase sigma factor [Pseudomonas brassicacearum subsp.
           brassicacearum NFM421]
 gi|327375920|gb|AEA67270.1| RNA polymerase sigma factor [Pseudomonas brassicacearum subsp.
           brassicacearum NFM421]
          Length = 335

 Score =  115 bits (288), Expect = 7e-24,   Method: Compositional matrix adjust.
 Identities = 87/272 (31%), Positives = 146/272 (53%), Gaps = 17/272 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + +K       ++ +N R++  D SL      SDK  
Sbjct: 185 LRAARELTQKL-DHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSLGP---DSDKT- 239

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++       + + +S L  ++R +   R   R  E+  T
Sbjct: 240 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTDKQREVVIRRFGLRGHESS-T 293

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE++  E  ++RERVRQI+    K+++E ++K
Sbjct: 294 LEDVGLEIGLTRERVRQIQVEGLKRLREILEK 325


>gi|241662747|ref|YP_002981107.1| RNA polymerase sigma factor RpoS [Ralstonia pickettii 12D]
 gi|240864774|gb|ACS62435.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ralstonia
           pickettii 12D]
          Length = 378

 Score =  115 bits (288), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 87/279 (31%), Positives = 143/279 (51%), Gaps = 27/279 (9%)

Query: 19  YIHEIRKIPMLEKQEEY---VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           Y++ I   P+L   EE     LAK     G+ +A   ++  +LRLVV IA GY   G+P+
Sbjct: 109 YLNRISIKPLLTPAEELHFSTLAKA----GEFAARQVMIERNLRLVVSIAKGYLNRGVPL 164

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A++KFDPERGFR +TY+ WWI+ +++  I+     V++    +  R 
Sbjct: 165 LDLIEEGNLGLMHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRE 222

Query: 136 FFNLRRLKGHLQ--AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
              + R K HL+   +   +   E +  +  K      +V+S+N      E   +L    
Sbjct: 223 LNQVLRAKRHLEKSGVDGRDASLEDIAHLLGKTTEEVQDVLSLN------EHTTSLDTPF 276

Query: 194 DKN-SSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           D +  +   D+L  +H    +Q +  +E  +  ++ L R    L+ + R + E RR   N
Sbjct: 277 DLDPGTSLLDFLSDEHGASPDQEVAHRELSQLMKSWLAR----LSDKHRYVVE-RRFGLN 331

Query: 252 ---PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              P TLE L++E  ++RERVRQI+  A  K++     Q
Sbjct: 332 YIEPATLEELAAEMGLTRERVRQIQQEALVKLKRHFASQ 370


>gi|268610742|ref|ZP_06144469.1| RNA polymerase sigma factor RpoD [Ruminococcus flavefaciens FD-1]
          Length = 360

 Score =  115 bits (288), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 90/271 (33%), Positives = 142/271 (52%), Gaps = 25/271 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LA+R  + GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 94  YLKEIGRVPLLTTEEEIELAQRMAK-GDRYAKKRLSEANLRLVVSIAKKYVGRGMQFLDL 152

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG-----TTANQK 133
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T    K
Sbjct: 153 IQEGNLGLIKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETITKVK 212

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINS 192
           ++   L    GH       +  PE+   IA KLN+   +V  +  R+A D  SL   I  
Sbjct: 213 KVSSQLLHENGH-------DPSPEE---IADKLNMPVDKVREI-MRVAQDPVSLETPI-- 259

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN- 251
            ++  S   D++  D              K + N +   +S L  RE ++ + R   E+ 
Sbjct: 260 GEEEDSHLGDFIPDDDAPAPAEAASHTLLKEQLNEV---LSTLTDREAKVLKLRFGLEDG 316

Query: 252 -PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              TLE +   F+V+RER+RQIEA+A +K++
Sbjct: 317 KSRTLEEVGQRFDVTRERIRQIEAKALRKLR 347


>gi|153814577|ref|ZP_01967245.1| hypothetical protein RUMTOR_00791 [Ruminococcus torques ATCC 27756]
 gi|317501262|ref|ZP_07959466.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|331089991|ref|ZP_08338881.1| hypothetical protein HMPREF1025_02464 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|145848071|gb|EDK24989.1| hypothetical protein RUMTOR_00791 [Ruminococcus torques ATCC 27756]
 gi|316897329|gb|EFV19396.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|330402905|gb|EGG82471.1| hypothetical protein HMPREF1025_02464 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 273

 Score =  115 bits (288), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 86/278 (30%), Positives = 146/278 (52%), Gaps = 38/278 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI +IP+L++ EE  L +R  + GD SA  RL   +LRLVV IA  Y G GLP+ ++
Sbjct: 15  YLNEIGEIPLLDETEEKELGRRISD-GDESARARLEEGNLRLVVSIAKHYTGRGLPLMDL 73

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM A +K+D  +  R +TY+ WWIK A+   I +    +++     +     N
Sbjct: 74  IQEGNIGLMHAAEKYDYTKDNRFSTYASWWIKEAITRAIDQQSREIRVPVHVAE-----N 128

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKL-NVSESEV----------ISMNCRLA--GDES 185
           ++R++   + +     +  +   IAKKL + +E EV          +S+   +   G++S
Sbjct: 129 IKRVQKAAKELQQEFGREAEPGEIAKKLGDRTEEEVKNILSYIRNPVSLETPVGEDGEDS 188

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L   +   D++ +  +D +         VL+ KEE       +   +  LN RE+ +   
Sbjct: 189 LGDFV--EDRSETTPEDAM--------DVLVRKEE-------VQELLETLNDREKEVISL 231

Query: 246 R--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R    ++   TLE +     ++RERVRQIE++A +K++
Sbjct: 232 RFGLGKDRTYTLEEIGESLGITRERVRQIESKAMEKLR 269


>gi|309782329|ref|ZP_07677056.1| RNA polymerase sigma factor RpoS [Ralstonia sp. 5_7_47FAA]
 gi|308918947|gb|EFP64617.1| RNA polymerase sigma factor RpoS [Ralstonia sp. 5_7_47FAA]
          Length = 378

 Score =  115 bits (288), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 87/279 (31%), Positives = 143/279 (51%), Gaps = 27/279 (9%)

Query: 19  YIHEIRKIPMLEKQEEY---VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           Y++ I   P+L   EE     LAK     G+ +A   ++  +LRLVV IA GY   G+P+
Sbjct: 109 YLNRISIKPLLTPAEELHFSTLAKA----GEFAARQVMIERNLRLVVSIAKGYLNRGVPL 164

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A++KFDPERGFR +TY+ WWI+ +++  I+     V++    +  R 
Sbjct: 165 LDLIEEGNLGLMHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRE 222

Query: 136 FFNLRRLKGHLQ--AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
              + R K HL+   +   +   E +  +  K      +V+S+N      E   +L    
Sbjct: 223 LNQVLRAKRHLEKSGVDGRDASLEDIAHLLGKTTEEVQDVLSLN------EHTTSLDTPF 276

Query: 194 DKN-SSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           D +  +   D+L  +H    +Q +  +E  +  ++ L R    L+ + R + E RR   N
Sbjct: 277 DLDPGTSLLDFLSDEHGASPDQEVAHRELSQLMKSWLAR----LSDKHRYVVE-RRFGLN 331

Query: 252 ---PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              P TLE L++E  ++RERVRQI+  A  K++     Q
Sbjct: 332 YIEPATLEELAAEMGLTRERVRQIQQEALVKLKRHFASQ 370


>gi|253573701|ref|ZP_04851044.1| LOW QUALITY PROTEIN: DNA-directed RNA polymerase [Paenibacillus sp.
           oral taxon 786 str. D14]
 gi|251847229|gb|EES75234.1| LOW QUALITY PROTEIN: DNA-directed RNA polymerase [Paenibacillus sp.
           oral taxon 786 str. D14]
          Length = 325

 Score =  115 bits (288), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 86/265 (32%), Positives = 137/265 (51%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LA+R  E+GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 59  YLKEIGRVPLLSAEEEIELAQRI-ENGDEEAKRRLAEANLRLVVSIARRYVGRGMVFLDL 117

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 118 IQEGNMGLIKAVEKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 175

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L         PE+   IAK+++++  +V  +        SL   I   ++N S
Sbjct: 176 LIRVSRQLLQEIGREPTPEE---IAKEMDLTPDKVREIMKIAQEPVSLETPI--GEENDS 230

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D+ + DHD          E    +  L   +  L  RE  +   R   ++    TLE
Sbjct: 231 NLGDF-IEDHDAPAPAEAAAYEL--LKEQLEEVLDTLTEREENVLRLRFGMDDGRTRTLE 287

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF V+RER+RQIEA+A +K++
Sbjct: 288 EVGKEFGVTRERIRQIEAKALRKLR 312


>gi|2289784|dbj|BAA21674.1| rpoS sigma factor [Pseudomonas tolaasii]
          Length = 336

 Score =  115 bits (288), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 87/272 (31%), Positives = 146/272 (53%), Gaps = 17/272 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 68  YLNEIGFSPLLTPEEEVHFA-RLSQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 126

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 127 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 185

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + +K       ++ +N R++  D SL      SDK  
Sbjct: 186 LRAARELTQKL-DHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSLGP---DSDKT- 240

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++       + + +S L  ++R +   R   R  E+  T
Sbjct: 241 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTDKQREVVIRRFGLRGHESS-T 294

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE++  E  ++RERVRQI+    K+++E ++K
Sbjct: 295 LEDVGLEIGLTRERVRQIQVEGLKRLREILEK 326


>gi|24379277|ref|NP_721232.1| RNA polymerase sigma factor RpoD [Streptococcus mutans UA159]
 gi|290580718|ref|YP_003485110.1| DNA-dependent RNA polymerase sigma subunit [Streptococcus mutans
           NN2025]
 gi|18202024|sp|O33662|RPOD_STRMU RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-42
 gi|24377195|gb|AAN58538.1|AE014923_2 DNA-dependent RNA polymerase sigma subunit; major sigma factor
           (sigma 70/42) [Streptococcus mutans UA159]
 gi|2258087|dbj|BAA21507.1| sigma 42 protein [Streptococcus mutans]
 gi|254997617|dbj|BAH88218.1| DNA-dependent RNA polymerase sigma subunit [Streptococcus mutans
           NN2025]
          Length = 371

 Score =  115 bits (288), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 89/273 (32%), Positives = 147/273 (53%), Gaps = 29/273 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E+GDL A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 104 YLKEIGVVPLLTNEEEKELAIAV-ENGDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 162

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 163 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKL- 221

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSS 193
               +R  +  LQ +   +  PEQ   IA++++++  +V  +  ++A +  SL   I   
Sbjct: 222 ----VREQRNLLQELG-QDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEE 272

Query: 194 DKNSSQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQ 249
           D   S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L 
Sbjct: 273 D--DSHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLD 324

Query: 250 ENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +  + TLE++   F+V+RER+RQIEA+A +K++
Sbjct: 325 DGKMRTLEDVGKVFDVTRERIRQIEAKALRKLR 357


>gi|289578734|ref|YP_003477361.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter italicus Ab9]
 gi|289528447|gb|ADD02799.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter italicus Ab9]
          Length = 357

 Score =  115 bits (288), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 84/265 (31%), Positives = 139/265 (52%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L  +EE  LAKR  E GD  A  RL+ ++LRLVV IA  Y G G+   ++
Sbjct: 91  YLKEIGKIPLLTPEEEIELAKRI-EQGDEEAKKRLIEANLRLVVSIAKRYVGRGMLFLDL 149

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 150 IQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 207

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R++  L         PE+   +AK++ + E +V  +  ++A  E ++      ++  S
Sbjct: 208 LIRIQRQLLQELGREPTPEE---LAKEMGMPEEKVREI-MKIA-QEPVSLETPIGEEEDS 262

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++  +              K +   L   +  L PRE ++   R   ++    TLE
Sbjct: 263 HLGDFIPDEDAPAPAEAAAFTMLKEQ---LMDVLDTLTPREEKVLRLRFGLDDGRARTLE 319

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF V+RER+RQIEA+A +K++
Sbjct: 320 EVGKEFNVTRERIRQIEAKALRKLR 344


>gi|86141299|ref|ZP_01059845.1| putative sigma factor A [Leeuwenhoekiella blandensis MED217]
 gi|85831858|gb|EAQ50313.1| putative sigma factor A [Leeuwenhoekiella blandensis MED217]
          Length = 287

 Score =  115 bits (288), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 90/294 (30%), Positives = 155/294 (52%), Gaps = 51/294 (17%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ ++   EE  LA+R +  GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGKVDLITADEEVELAQRIK-AGDQRALEKLTKANLRFVVSVAKQYQNQGLTL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
            ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++      Q  I+R   L KIG+ 
Sbjct: 77  PDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVR-LPLNKIGSI 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNA 188
               + F  L +           N +P     IAK+L+++ +EV   + + AG   S++A
Sbjct: 136 NKINKTFAFLEQ----------ANERPPSPEEIAKELDMTVNEV-KESLKNAGRHVSMDA 184

Query: 189 -LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS--------VLNPRE 239
            LI   D N        +YD      VL   E     R +L+ S+S         L PRE
Sbjct: 185 PLIEGEDSN--------LYD------VLRSGESPNPDRELLSESLSTEIERALETLTPRE 230

Query: 240 RRIFEARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
             +    RL      ++P+TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 231 ADVV---RLYFGLGHQHPMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|157688389|gb|ABV64841.1| RpoS [Pseudomonas sp. 122]
          Length = 334

 Score =  115 bits (288), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 87/272 (31%), Positives = 146/272 (53%), Gaps = 17/272 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 66  YLNEIGFSPLLTPEEEVHFA-RLSQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 124

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 125 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 183

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + +K       ++ +N R++  D SL      SDK  
Sbjct: 184 LRAARELTQKL-DHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSLGP---DSDKT- 238

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++       + + +S L  ++R +   R   R  E+  T
Sbjct: 239 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTDKQREVVIRRFGLRGHESS-T 292

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE++  E  ++RERVRQI+    K+++E ++K
Sbjct: 293 LEDVGLEIGLTRERVRQIQVEGLKRLREILEK 324


>gi|323484375|ref|ZP_08089742.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323692387|ref|ZP_08106623.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
 gi|323402369|gb|EGA94700.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323503527|gb|EGB19353.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
          Length = 372

 Score =  115 bits (288), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 90/276 (32%), Positives = 147/276 (53%), Gaps = 19/276 (6%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           VN +  +  Y+ EI K+P+L  +EE  LAK+  E G+  A  RL  ++LRLVV IA  Y 
Sbjct: 97  VNIDDPVRMYLKEIGKVPLLSPEEEIELAKQM-EMGNEYAKKRLAEANLRLVVSIAKRYV 155

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT- 128
           G G+   +++ EGN+GL++AV+K+D  +GF+ +TY+ WWI+ A+   I      ++I   
Sbjct: 156 GRGMQFLDLIQEGNLGLIKAVEKYDYSKGFKFSTYATWWIRQAITRSIADQARTIRIPVH 215

Query: 129 -TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SL 186
                 RL    R+L   LQ +      PE+V   A+++++    V  +  +++ D  SL
Sbjct: 216 MVETINRLIRTSRQL---LQELG-REPHPEEV---AERMDMPVERVREI-MKISQDPVSL 267

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              I   ++  S   D++  DH    QV ++          L   +  L  RE+++   R
Sbjct: 268 ETPI--GEEEDSHLGDFIQDDH---VQVPLDAATFTLLHEQLMEVLDTLTDREQKVLRLR 322

Query: 247 RLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
              ++  P TLE +  EF V+RER+RQIEA+A +K+
Sbjct: 323 FGLDDGRPRTLEEVGKEFNVTRERIRQIEAKALRKL 358


>gi|299067258|emb|CBJ38455.1| RNA polymerase sigma factor rpoS [Ralstonia solanacearum CMR15]
          Length = 376

 Score =  115 bits (288), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 88/279 (31%), Positives = 142/279 (50%), Gaps = 27/279 (9%)

Query: 19  YIHEIRKIPMLEKQEEY---VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           Y++ I   P+L   EE     LAK     G+  A   ++  +LRLVV IA GY   G+P+
Sbjct: 107 YLNRISIKPLLTPAEELHFSTLAKA----GEFPARQVMIERNLRLVVSIAKGYLNRGVPL 162

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A++KFDPERGFR +TY+ WWI+ +++  I+     V++    +  R 
Sbjct: 163 LDLIEEGNLGLMHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRE 220

Query: 136 FFNLRRLKGHLQ--AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
              + R K HL+   I   +   E +  +  K      +V+S+N      E   +L    
Sbjct: 221 LNQVLRAKRHLEKSGIDGRDASIEDIAHLLGKTTDEVQDVLSLN------EHTTSLDTPF 274

Query: 194 DKN-SSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           D +  +   D+L  +H    +Q +  +E  +  ++ L R    L+ + R + E RR   N
Sbjct: 275 DLDPGTSLLDFLSDEHGASPDQEVAHRELSQLMKSWLAR----LSDKHRYVVE-RRFGLN 329

Query: 252 ---PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              P TLE L++E  ++RERVRQI+  A  K++     Q
Sbjct: 330 HIEPATLEELAAEMGLTRERVRQIQQEALVKLKRHFASQ 368


>gi|114567027|ref|YP_754181.1| sigma 38 (RpoS) [Syntrophomonas wolfei subsp. wolfei str.
           Goettingen]
 gi|114337962|gb|ABI68810.1| sigma 38 (RpoS) [Syntrophomonas wolfei subsp. wolfei str.
           Goettingen]
          Length = 358

 Score =  115 bits (288), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 85/265 (32%), Positives = 138/265 (52%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   +E  LA+R  E GD  A  +LV ++LRLVV IA  Y G G+   ++
Sbjct: 92  YLKEIGRVPLLIAAQEIDLAQRI-EEGDEEAKRQLVEANLRLVVSIAKRYVGRGMLFLDL 150

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 151 IQEGNLGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 208

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R++  L  I      P +V   A++++++   VI +        SL   I   D   S
Sbjct: 209 LSRVQRSLLQILGREPTPAEV---AEEMDIAVDRVIEIMKVAQEPVSLETPIGEED--DS 263

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++    D + +   E       R  L   ++ L  RE ++   R   ++  P TLE
Sbjct: 264 HLGDFIT---DEEAESPEESASFVLLREHLDGILNTLTEREEKVLRLRFGLDDGRPRTLE 320

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF V+RER+RQIEA+A +K++
Sbjct: 321 EVGQEFGVTRERIRQIEAKALRKLR 345


>gi|226945910|ref|YP_002800983.1| RNA polymerase sigma factor RpoS [Azotobacter vinelandii DJ]
 gi|16226165|gb|AAL16091.1|AF421351_3 stationary phase sigma factor [Azotobacter vinelandii]
 gi|226720837|gb|ACO80008.1| RNA polymerase sigma factor [Azotobacter vinelandii DJ]
          Length = 334

 Score =  115 bits (288), Expect = 8e-24,   Method: Compositional matrix adjust.
 Identities = 89/277 (32%), Positives = 141/277 (50%), Gaps = 27/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L   EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 66  YLNEIGFSPLLTPAEEVHFA-RLAQRGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 124

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 125 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 183

Query: 139 LRRLKGHLQAITDN-------NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
           LR  +   Q +          NL  + V  + + L ++E  V S++  L  D     L  
Sbjct: 184 LRAARELTQKLDHEPSAEEIANLLEKPVAEVKRMLGLNE-RVTSVDVSLGPDSDKTLLDV 242

Query: 192 SSDKNSSQWQDWLVYDHDGQ--EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
            +D   S   D L  D   Q  +Q L +  E++  R ++ R   +            R  
Sbjct: 243 LTDDRPSDPCDLLQDDDLSQSIDQWLFDLTEKQ--REVVVRRFGL------------RGH 288

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E+  TLE +  E  ++RERVRQI+  A K+++E ++K
Sbjct: 289 ES-CTLEEVGQEIGLTRERVRQIQVEALKRLREILEK 324


>gi|325294741|ref|YP_004281255.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Desulfurobacterium thermolithotrophum DSM 11699]
 gi|325065189|gb|ADY73196.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Desulfurobacterium thermolithotrophum DSM 11699]
          Length = 322

 Score =  115 bits (288), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 84/269 (31%), Positives = 144/269 (53%), Gaps = 13/269 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  ++  I KIP+L ++EE   AKR +  GD  A  +LV S+LR VV +A  Y G GLP+
Sbjct: 53  LDAFLKSISKIPLLSREEEIEYAKRAK-AGDKEALKKLVESNLRFVVSVAKKYLGCGLPL 111

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EG +GL++A ++FDP++G +  +Y++WWI+ ++ + + +    VKI     Q  L
Sbjct: 112 HDLIAEGILGLIEAARRFDPDKGVKFISYAVWWIRQSIMQALAQQTGAVKI--PVKQAVL 169

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + R  G L          E++      +   E E +   C++    SL+  I   D+
Sbjct: 170 VNKITRSYGELLKKLGREPTTEELAEYV-GMEPKEIERLLTVCQVP--LSLDTPIG--DE 224

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PV 253
             + ++D+L  +   + +  + +EE K     +   +  L P+E++I   R  L  N P 
Sbjct: 225 EDTTFKDFLKGEGTAEVEEKVVQEELKQS---IQEMLEQLTPQEKKIIIMRFGLDGNEPK 281

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQE 282
           TL  +  +  +SRERVRQ+E RA KK++E
Sbjct: 282 TLREIGEKLGISRERVRQLETRAKKKMKE 310


>gi|104774139|ref|YP_619119.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
 gi|103423220|emb|CAI98048.1| RNA polymerase sigma factor RpoD (Sigma-A) [Lactobacillus
           delbrueckii subsp. bulgaricus ATCC 11842]
          Length = 372

 Score =  115 bits (288), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 87/275 (31%), Positives = 133/275 (48%), Gaps = 33/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI +  +L  +EE  LAKR  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 106 YLKEIGRFNLLTSEEEVALAKRI-EAGDEEAKQELAEANLRLVVSIAKRYVGRGMNFLDL 164

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 165 IQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 222

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLA--GDESLNA 188
           L R++  L      + +PE++ A        + + L V++ E +S+   +    D  L  
Sbjct: 223 LIRIQRQLLQDLGRDPEPEEIAAEMDLPVKKVREALKVAQ-EPVSLETPIGEEDDSHLGD 281

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-R 247
            I   D  S +        H   E +          R+ L   +  L  RE  +   R  
Sbjct: 282 FIEDKDTTSPEQ-------HAASEML----------RDQLAEVLDTLTDREENVLRLRFG 324

Query: 248 LQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           L + NP TLE +   F V+RER+RQIEA+A +K++
Sbjct: 325 LDDGNPRTLEEVGRVFGVTRERIRQIEAKALRKLR 359


>gi|312959424|ref|ZP_07773941.1| sigma-28 (flagella/sporulation) [Pseudomonas fluorescens WH6]
 gi|311286141|gb|EFQ64705.1| sigma-28 (flagella/sporulation) [Pseudomonas fluorescens WH6]
          Length = 335

 Score =  115 bits (288), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 87/272 (31%), Positives = 146/272 (53%), Gaps = 17/272 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLTPEEEVHFA-RLSQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + +K       ++ +N R++  D SL      SDK  
Sbjct: 185 LRAARELTQKL-DHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSLGP---DSDKT- 239

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++       + + +S L  ++R +   R   R  E+  T
Sbjct: 240 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTDKQREVVIRRFGLRGHESS-T 293

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE++  E  ++RERVRQI+    K+++E ++K
Sbjct: 294 LEDVGLEIGLTRERVRQIQVEGLKRLREILEK 325


>gi|158969744|gb|ABW86844.1| RpoS [Vibrio alginolyticus]
          Length = 330

 Score =  115 bits (288), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 90/281 (32%), Positives = 146/281 (51%), Gaps = 31/281 (11%)

Query: 19  YIHEIRKIPML-EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           Y+ EI   P+L    EE VL  R    GD +A  R++ S+LRLVVKI+  Y   GL + +
Sbjct: 56  YLGEIGFSPLLILTAEEEVLYARRALRGDEAARKRMIESNLRLVVKISRRYSNRGLALLD 115

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L  
Sbjct: 116 LIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNI 174

Query: 138 NLRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNAL 189
            LR  +   Q + D+    E++ A        ++K L ++E  + S++  + GD     L
Sbjct: 175 YLRTARELSQKL-DHEPTAEEIAAQLDIPVEDVSKMLRLNE-RISSVDTPIGGDGEKALL 232

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-- 247
               D N+S   D  V   D             + ++ L   +  LNP+++ +  ARR  
Sbjct: 233 DIIPDANNS---DPEVSTQD------------DDIKSSLIHWLEELNPKQKEVL-ARRFG 276

Query: 248 -LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 277 LLGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLREVLIKQ 317


>gi|187928144|ref|YP_001898631.1| RNA polymerase sigma factor RpoS [Ralstonia pickettii 12J]
 gi|187725034|gb|ACD26199.1| RNA polymerase, sigma 70 subunit, RpoD family [Ralstonia pickettii
           12J]
          Length = 378

 Score =  115 bits (288), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 87/279 (31%), Positives = 143/279 (51%), Gaps = 27/279 (9%)

Query: 19  YIHEIRKIPMLEKQEEY---VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           Y++ I   P+L   EE     LAK     G+ +A   ++  +LRLVV IA GY   G+P+
Sbjct: 109 YLNRISIKPLLTPAEELHFSTLAKA----GEFAARQVMIERNLRLVVSIAKGYLNRGVPL 164

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A++KFDPERGFR +TY+ WWI+ +++  I+     V++    +  R 
Sbjct: 165 LDLIEEGNLGLMHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRE 222

Query: 136 FFNLRRLKGHLQ--AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
              + R K HL+   +   +   E +  +  K      +V+S+N      E   +L    
Sbjct: 223 LNQVLRAKRHLEKSGVDGRDASLEDIAHLLGKTTEEVQDVLSLN------EHTTSLDTPF 276

Query: 194 DKN-SSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           D +  +   D+L  +H    +Q +  +E  +  ++ L R    L+ + R + E RR   N
Sbjct: 277 DLDPGTSLLDFLSDEHGASPDQEVAHRELSQLMKSWLAR----LSDKHRYVVE-RRFGLN 331

Query: 252 ---PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              P TLE L++E  ++RERVRQI+  A  K++     Q
Sbjct: 332 YIEPATLEELAAEMGLTRERVRQIQQEALVKLKRHFASQ 370


>gi|298488362|ref|ZP_07006394.1| RNA polymerase sigma factor RpoS [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
 gi|298157184|gb|EFH98272.1| RNA polymerase sigma factor RpoS [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
          Length = 335

 Score =  115 bits (288), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 87/272 (31%), Positives = 147/272 (54%), Gaps = 17/272 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + +K       ++ +N R++  D SL      SDK  
Sbjct: 185 LRAARELTQKL-DHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSLGP---DSDKT- 239

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++  +    + + +S L  ++R +   R   R  E+  T
Sbjct: 240 --LLDTLTDDRPTDPCELLQDDDLSHS---IDQWLSELTEKQREVVIRRFGLRGHESS-T 293

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE++  E  ++RERVRQI+    K+++E ++K
Sbjct: 294 LEDVGLEIGLTRERVRQIQVEGLKRLREILEK 325


>gi|292670109|ref|ZP_06603535.1| DNA-directed RNA polymerase sigma subunit RpoD [Selenomonas noxia
           ATCC 43541]
 gi|292648297|gb|EFF66269.1| DNA-directed RNA polymerase sigma subunit RpoD [Selenomonas noxia
           ATCC 43541]
          Length = 382

 Score =  115 bits (288), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 87/275 (31%), Positives = 139/275 (50%), Gaps = 25/275 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   EE  LA+R  E GD SA HRL  ++LRLVV IA  Y G G+   ++
Sbjct: 115 YLKEIGRVPLLTADEEIELARRM-EAGDESARHRLEEANLRLVVSIAKRYVGRGMLFLDL 173

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 174 IQEGNLGLLKAVEKFDYSKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINK-- 231

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
            +  + R     Q + D    P     +AK++ +S   V  +        SL   I   +
Sbjct: 232 -YIRISR-----QLLQDLGRDP-TAEEVAKEMGLSTLRVREIMKIAQEPVSLETPIGEEE 284

Query: 195 KN--SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN- 251
            +      +D    D      V++ KE+       +T  +  L PRE  +   R   E+ 
Sbjct: 285 DSHLGDFIEDEAALDPADAASVMLLKEQ-------ITEVLQTLAPREAEVLRLRFGLEDG 337

Query: 252 -PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              TLE +   F V+RER+RQIEA+A +K++  ++
Sbjct: 338 RSRTLEEVGQSFGVTRERIRQIEAKALRKLRHPVR 372


>gi|71736784|ref|YP_275947.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv.
           phaseolicola 1448A]
 gi|71557337|gb|AAZ36548.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv.
           phaseolicola 1448A]
          Length = 335

 Score =  115 bits (288), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 86/273 (31%), Positives = 146/273 (53%), Gaps = 19/273 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + +K       ++ +N R++  D SL      SDK  
Sbjct: 185 LRAARELTQKL-DHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSLGP---DSDKT- 239

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI----FEARRLQENPV 253
               D L  D       L++ ++       + + +S L  ++R +    F  R  + +  
Sbjct: 240 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTEKQREVVIRRFGLRGYESS-- 292

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TLE++  E  ++RERVRQI+    K+++E ++K
Sbjct: 293 TLEDVGLEIGLTRERVRQIQVEGLKRLREILEK 325


>gi|302389497|ref|YP_003825318.1| RNA polymerase, sigma 70 subunit, RpoD [Thermosediminibacter oceani
           DSM 16646]
 gi|302200125|gb|ADL07695.1| RNA polymerase, sigma 70 subunit, RpoD [Thermosediminibacter oceani
           DSM 16646]
          Length = 367

 Score =  115 bits (288), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 86/265 (32%), Positives = 137/265 (51%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 101 YLKEIGKIPLLTPEEEIELAKRI-EKGDKEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 159

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 160 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 217

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L      +  PE+   IA+++ +   +V  +        SL   I   ++  S
Sbjct: 218 LIRVSRQLLQELGRDPTPEE---IAEEMELPVEKVREIMKIAQEPVSLETPIG--EEEDS 272

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++    D + Q   +    +  R  L   +  L PRE ++   R   ++  P TLE
Sbjct: 273 HLGDFI---PDEEAQAPADAAAYRLLREQLEDVLETLTPREEKVLRLRFGLDDGKPRTLE 329

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +   F V+RER+RQIEA+A +K++
Sbjct: 330 EVGQVFGVTRERIRQIEAKALRKLR 354


>gi|150026087|ref|YP_001296913.1| RNA polymerase sigma-70 factor RpoD [Flavobacterium psychrophilum
           JIP02/86]
 gi|149772628|emb|CAL44111.1| RNA polymerase sigma-70 factor RpoD [Flavobacterium psychrophilum
           JIP02/86]
          Length = 287

 Score =  115 bits (287), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 83/292 (28%), Positives = 155/292 (53%), Gaps = 47/292 (16%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ ++   EE  LA+R +  GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGKVDLITADEEVELAQRIK-AGDQRALEKLTKANLRFVVSVAKQYQNQGLTL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
            ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++      Q  I+R   L KIG+ 
Sbjct: 77  PDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVR-LPLNKIGSI 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA- 188
               +++  L +          +N +P     IAK+L+++ ++V           S++A 
Sbjct: 136 NKINKMYALLEQ----------SNERPPSAEEIAKELDMTVNDVKESMKNSGRHLSMDAP 185

Query: 189 LINSSDKNSSQWQDWLVYD-------HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           L+   D N        +YD        +   +++IE     + R  + RS+  L PRE  
Sbjct: 186 LVEGEDSN--------LYDVLRSGESPNPDRELIIE-----SLRTEIERSLETLTPREAD 232

Query: 242 IFEARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +    RL      ++P+TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 233 VV---RLYFGLADQHPMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|88798286|ref|ZP_01113872.1| RNA polymerase sigma factor RpoS [Reinekea sp. MED297]
 gi|88779062|gb|EAR10251.1| RNA polymerase sigma factor RpoS [Reinekea sp. MED297]
          Length = 344

 Score =  115 bits (287), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 84/279 (30%), Positives = 149/279 (53%), Gaps = 29/279 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A+  R+ G+ +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 75  YLNEIGFSPLLSPEEEVYFARLARK-GEPAGRKRMIESNLRLVVKIARRYLNRGLTLLDL 133

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 134 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 192

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA------GDESLNALINS 192
           LR  +   Q + D+   PE +  + +K      +++++N R+       G  S  +L+ +
Sbjct: 193 LRAARELAQKL-DHEPTPEDIAQLLEKPVEDVKKMLALNERVTSIDTPIGPSSEKSLLET 251

Query: 193 -SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--- 248
            SD  +S   D L  D               + +  + R +  L+ ++R +  ARR    
Sbjct: 252 ISDDRASDPSDTLQDD---------------DLKASIDRWLDELSEKQREVV-ARRFGLR 295

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
                TLE++  E  ++RERVRQI+  + +++++ ++KQ
Sbjct: 296 GYETSTLEDVGREIGLTRERVRQIQVESLRRLRDIMEKQ 334


>gi|28210583|ref|NP_781527.1| RNA polymerase sigma factor rpoD [Clostridium tetani E88]
 gi|28203021|gb|AAO35464.1| RNA polymerase sigma factor rpoD [Clostridium tetani E88]
          Length = 282

 Score =  115 bits (287), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 94/279 (33%), Positives = 139/279 (49%), Gaps = 41/279 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI +  +L  +EE  LAKR  E GD  A   L+ S+LRLVV IA  Y G GL   ++
Sbjct: 16  YLKEIGQSDLLTAEEEIDLAKRI-EKGDERAKSELIKSNLRLVVSIAKKYIGRGLSFLDL 74

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GLM+AV K+D ++G+R +TY+ WWIK A+   I      ++I    N+  +   
Sbjct: 75  VQEGNLGLMKAVDKYDYKKGYRFSTYATWWIKQAVTRSIADQSRTIRIPVHMNE--VISK 132

Query: 139 LRRLKGHLQAITDNN--------LKPEQVVAIAKKLNVSESEVISMNCRLAGDES--LNA 188
           + R K  L+   D               +  I +  NVS+  V S+   +  +E   L  
Sbjct: 133 MIRTKKKLEQELDREPTEEEIAETAEISIEKIKRIYNVSQDPV-SLETPVGENEDTILQN 191

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            I+          D  + +    EQ+L          + L+  +S L+PRE RI    RL
Sbjct: 192 FISD---------DRYLPEDKVTEQML---------GDTLSNVLSTLSPREERIV---RL 230

Query: 249 QENPV------TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   V      TLE +  EF ++RER+RQIEARA +K++
Sbjct: 231 RYGLVGDGESRTLEEIGREFNLTRERIRQIEARAIRKLR 269


>gi|187764347|gb|ACD36026.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
          Length = 322

 Score =  115 bits (287), Expect = 9e-24,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 144/277 (51%), Gaps = 27/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 60  YLNEIGFSPLLTPEEEVHFA-RLAQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 118

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 119 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 177

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA------GDESLNALINS 192
           LR  +  L    D+   PE++  + +K       ++ +N R+       G +S   L+++
Sbjct: 178 LRAAR-ELTHKLDHEPSPEEIANLLEKPVAEVKRMLGLNERVTSVDVSLGPDSDKTLLDT 236

Query: 193 SDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
              +       L+ D D  E +   L E  +++  R ++ R   +      R  E+    
Sbjct: 237 LTDDRPTDPCELLQDDDLSESIDQWLTELTDKQ--REVVIRRFGL------RGHESS--- 285

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
               TLE +  E  ++RERVRQI+  A K+++E ++K
Sbjct: 286 ----TLEEVGQEIGLTRERVRQIQVEALKRLREILEK 318


>gi|56421017|ref|YP_148335.1| RNA polymerase sigma factor RpoD [Geobacillus kaustophilus HTA426]
 gi|261417657|ref|YP_003251339.1| RNA polymerase sigma factor RpoD [Geobacillus sp. Y412MC61]
 gi|297529352|ref|YP_003670627.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus sp.
           C56-T3]
 gi|319767537|ref|YP_004133038.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus sp.
           Y412MC52]
 gi|56380859|dbj|BAD76767.1| DNA-directed RNA polymerase major sigma-43 factor (sigma-A)
           [Geobacillus kaustophilus HTA426]
 gi|261374114|gb|ACX76857.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus sp.
           Y412MC61]
 gi|297252604|gb|ADI26050.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus sp.
           C56-T3]
 gi|317112403|gb|ADU94895.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus sp.
           Y412MC52]
          Length = 375

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 87/275 (31%), Positives = 137/275 (49%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 109 YLKEIGRVPLLSAEEEIELAKRI-EQGDEEAKRRLTEANLRLVVSIAKRYVGRGMLFLDL 167

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 168 IQEGNMGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 227

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I   L +++ E +S+   +    D  L 
Sbjct: 228 RVQRQLLQDLGREPTPEEIAEEMDLTPEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 283

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S         +H   E +          +  L   +  L  RE  +   R 
Sbjct: 284 DFIEDQDATSPS-------EHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 326

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 327 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 361


>gi|257487049|ref|ZP_05641090.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. tabaci
           ATCC 11528]
 gi|320323089|gb|EFW79178.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. glycinea
           str. B076]
 gi|320329639|gb|EFW85628.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. glycinea
           str. race 4]
 gi|330878042|gb|EGH12191.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. glycinea
           str. race 4]
 gi|330985141|gb|EGH83244.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv.
           lachrymans str. M301315]
 gi|331009312|gb|EGH89368.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. tabaci
           ATCC 11528]
          Length = 335

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 87/272 (31%), Positives = 146/272 (53%), Gaps = 17/272 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + +K       ++ +N R++  D SL      SDK  
Sbjct: 185 LRAARELTQKL-DHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSLGP---DSDKT- 239

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++       + + +S L  ++R +   R   R  E+  T
Sbjct: 240 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTEKQREVVIRRFGLRGHESS-T 293

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE++  E  ++RERVRQI+    K+++E ++K
Sbjct: 294 LEDVGLEIGLTRERVRQIQVEGLKRLREILEK 325


>gi|167037157|ref|YP_001664735.1| RNA polymerase sigma factor RpoD [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|167039957|ref|YP_001662942.1| RNA polymerase sigma factor RpoD [Thermoanaerobacter sp. X514]
 gi|256751255|ref|ZP_05492135.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter ethanolicus CCSD1]
 gi|300915505|ref|ZP_07132817.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter sp. X561]
 gi|307266219|ref|ZP_07547761.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|307724719|ref|YP_003904470.1| RpoD subfamily RNA polymerase sigma-70 subunit [Thermoanaerobacter
           sp. X513]
 gi|320115576|ref|YP_004185735.1| RNA polymerase sigma factor RpoD [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
 gi|326390577|ref|ZP_08212133.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter ethanolicus JW 200]
 gi|166854197|gb|ABY92606.1| RNA polymerase, sigma 70 subunit, RpoD family [Thermoanaerobacter
           sp. X514]
 gi|166855991|gb|ABY94399.1| RNA polymerase, sigma 70 subunit, RpoD family [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|256749810|gb|EEU62834.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter ethanolicus CCSD1]
 gi|300888457|gb|EFK83607.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter sp. X561]
 gi|306918749|gb|EFN48981.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|307581780|gb|ADN55179.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter sp. X513]
 gi|319928667|gb|ADV79352.1| RNA polymerase sigma factor RpoD [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
 gi|325993402|gb|EGD51838.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter ethanolicus JW 200]
          Length = 357

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 84/265 (31%), Positives = 139/265 (52%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L  +EE  LAKR  E GD  A  RL+ ++LRLVV IA  Y G G+   ++
Sbjct: 91  YLKEIGKIPLLTPEEEIELAKRI-EQGDEEAKKRLIEANLRLVVSIAKRYVGRGMLFLDL 149

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 150 IQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 207

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R++  L         PE+   +AK++ + E +V  +  ++A  E ++      ++  S
Sbjct: 208 LIRVQRQLLQELGREPTPEE---LAKEMGMPEEKVREI-MKIA-QEPVSLETPIGEEEDS 262

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++  +              K +   L   +  L PRE ++   R   ++    TLE
Sbjct: 263 HLGDFIPDEDAPAPAEAAAFTMLKEQ---LMDVLDTLTPREEKVLRLRFGLDDGRARTLE 319

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF V+RER+RQIEA+A +K++
Sbjct: 320 EVGKEFNVTRERIRQIEAKALRKLR 344


>gi|6010736|gb|AAF01234.1|AF184103_1 mutant RpoS [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
          Length = 330

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 84/277 (30%), Positives = 139/277 (50%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++ ERVRQI+    ++++E +Q Q
Sbjct: 286 --ATLEDVGREIGLTCERVRQIQVEGLRRLREILQTQ 320


>gi|330968927|gb|EGH68993.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. aceris
           str. M302273PT]
          Length = 335

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 87/272 (31%), Positives = 146/272 (53%), Gaps = 17/272 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + +K       ++ +N R++  D SL      SDK  
Sbjct: 185 LRAARELTQKL-DHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSLGP---DSDKT- 239

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++       + + +S L  ++R +   R   R  E+  T
Sbjct: 240 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTEKQREVVIRRFGLRGHESS-T 293

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE++  E  ++RERVRQI+    K+++E ++K
Sbjct: 294 LEDVGLEIGLTRERVRQIQVEGLKRLREILEK 325


>gi|304312494|ref|YP_003812092.1| RNA sigma factor RpoS [gamma proteobacterium HdN1]
 gi|301798227|emb|CBL46449.1| RNA sigma factor RpoS [gamma proteobacterium HdN1]
          Length = 342

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 86/272 (31%), Positives = 144/272 (52%), Gaps = 15/272 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A+R    G+  A  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 73  YLNEIGFSPLLTPEEEVYYARRAL-RGNADARKRMIESNLRLVVKIARRYVNRGLSLLDL 131

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 132 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 190

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +   Q + D+   PE++ A+  K       ++ +N R++  +S       SDK+  
Sbjct: 191 LRAARELTQKL-DHEPTPEEISALLDKPLEDVKRMLGLNERISSVDSPVGF--DSDKS-- 245

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV---TL 255
              D +    +     L++  + KN  +     +    P ++R   ARR         TL
Sbjct: 246 -LLDTIADTKNTDPAELLQDADLKNSIDYWLDQL----PGKQREVIARRFGLRGFEMSTL 300

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +  E  ++RERVRQI+  A K++++ ++KQ
Sbjct: 301 EEVGREIGLTRERVRQIQVEALKRLRDLLEKQ 332


>gi|55821465|ref|YP_139907.1| RNA polymerase sigma factor RpoD [Streptococcus thermophilus LMG
           18311]
 gi|55737450|gb|AAV61092.1| DNA directed RNA polymerase sigma 42 protein [Streptococcus
           thermophilus LMG 18311]
          Length = 369

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 87/269 (32%), Positives = 143/269 (53%), Gaps = 21/269 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E+GDL A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLSNEEEKKLAIAV-ENGDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 218

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L      +  PEQ   IA++++++  +V  +  ++A +  SL   I   D   
Sbjct: 219 LVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEED--D 272

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 273 SHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 326

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE++   F V+RER+RQIEA+A +K++
Sbjct: 327 RTLEDVGKVFNVTRERIRQIEAKALRKLR 355


>gi|296387874|ref|ZP_06877349.1| RNA polymerase sigma factor RpoS [Pseudomonas aeruginosa PAb1]
          Length = 334

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 144/277 (51%), Gaps = 27/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 66  YLNEIGFSPLLTPEEEVHFA-RLAQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 124

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 125 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 183

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA------GDESLNALINS 192
           LR  +  L    D+   PE++  + +K       ++ +N R+       G +S   L+++
Sbjct: 184 LRAAR-ELTHKLDHEPSPEEIANLLEKPVAEVKRMLGLNERVTSVDVSLGPDSDKTLLDT 242

Query: 193 SDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
              +       L+ D D  E +   L E  +++  R ++ R   +      R  E+    
Sbjct: 243 LTDDRPTDPCELLQDDDLSESIDQWLTELTDKQ--REVVIRRFGL------RGHESS--- 291

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
               TLE +  E  ++RERVRQI+  A K+++E ++K
Sbjct: 292 ----TLEEVGQEIGLTRERVRQIQVEALKRLREILEK 324


>gi|92114749|ref|YP_574677.1| sigma 28 (flagella/sporulation) [Chromohalobacter salexigens DSM
           3043]
 gi|91797839|gb|ABE59978.1| RNA polymerase, sigma 38 subunit, RpoS [Chromohalobacter salexigens
           DSM 3043]
          Length = 325

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 87/280 (31%), Positives = 148/280 (52%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE V   R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 57  YLNEIGFSPLLTPEEE-VHYGRLAQKGDPAGRQRMIESNLRLVVKIARRYLNRGLSLLDL 115

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 116 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 174

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA------GDESLNALINS 192
           LR  +   Q + D+    E++     K   +  +++ +N R++      G ES   LI++
Sbjct: 175 LRAARELTQRL-DHEATAEEIAEFLDKPVGTVKKMLGLNERVSSVDYPMGGESDKPLIDT 233

Query: 193 -SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT----RSMSVLNPRERRIFEARR 247
            +D+N +           G E +L+  + +++  + L     + M V+  R    F  R 
Sbjct: 234 LADENEA-----------GPESLLVGNDVKQHVDDWLAELTDKQMEVVVRR----FGLR- 277

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
                 TLE +  E  ++RERVRQI+  A KK++  ++KQ
Sbjct: 278 -GHEAATLEEVGEEIGLTRERVRQIQVEALKKLRRVLEKQ 316


>gi|391964|gb|AAA03294.1| RNA polymerase sigma factor [Shigella flexneri]
          Length = 362

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 84/277 (30%), Positives = 142/277 (51%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ +I   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 73  YLGKIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 131

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF- 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++     ++   + 
Sbjct: 132 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 191

Query: 138 -NLRRLKGHLQ------AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
             +R L   L        I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 192 RTVRELSHKLDYEPSAVEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 248

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R ++ R   +L       +EA     
Sbjct: 249 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVIARRFGLLG------YEA----- 297

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+ +  ++++E +Q Q
Sbjct: 298 --ATLEDVGREIGLTRERVRQIQVQGLRRLREILQTQ 332


>gi|297544972|ref|YP_003677274.1| RpoD subfamily RNA polymerase sigma-70 subunit [Thermoanaerobacter
           mathranii subsp. mathranii str. A3]
 gi|296842747|gb|ADH61263.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
          Length = 357

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 84/265 (31%), Positives = 139/265 (52%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L  +EE  LAKR  E GD  A  RL+ ++LRLVV IA  Y G G+   ++
Sbjct: 91  YLKEIGKIPLLTPEEEIELAKRI-EQGDEEAKKRLIEANLRLVVSIAKRYVGRGMLFLDL 149

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 150 IQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 207

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R++  L         PE+   +AK++ + E +V  +  ++A  E ++      ++  S
Sbjct: 208 LIRVQRQLLQELGREPTPEE---LAKEMGMPEEKVREI-MKIA-QEPVSLETPIGEEEDS 262

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++  +              K +   L   +  L PRE ++   R   ++    TLE
Sbjct: 263 HLGDFIPDEDAPAPAEAAAFTMLKEQ---LMDVLDTLTPREEKVLRLRFGLDDGRARTLE 319

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF V+RER+RQIEA+A +K++
Sbjct: 320 EVGKEFNVTRERIRQIEAKALRKLR 344


>gi|15598818|ref|NP_252312.1| RNA polymerase sigma factor RpoS [Pseudomonas aeruginosa PAO1]
 gi|116051619|ref|YP_789542.1| RNA polymerase sigma factor RpoS [Pseudomonas aeruginosa
           UCBPP-PA14]
 gi|218890153|ref|YP_002439017.1| RNA polymerase sigma factor RpoS [Pseudomonas aeruginosa LESB58]
 gi|254242320|ref|ZP_04935642.1| sigma factor RpoS [Pseudomonas aeruginosa 2192]
 gi|1173167|sp|P45684|RPOS_PSEAE RecName: Full=RNA polymerase sigma factor rpoS
 gi|9949780|gb|AAG07010.1|AE004782_8 sigma factor RpoS [Pseudomonas aeruginosa PAO1]
 gi|440378|dbj|BAA05131.1| RNA polymerase principal sigma factor [Pseudomonas aeruginosa]
 gi|52632371|gb|AAU85546.1| RNA polymerase sigma factor [Pseudomonas sp. M18]
 gi|115586840|gb|ABJ12855.1| sigma factor RpoS [Pseudomonas aeruginosa UCBPP-PA14]
 gi|126195698|gb|EAZ59761.1| sigma factor RpoS [Pseudomonas aeruginosa 2192]
 gi|218770376|emb|CAW26141.1| sigma factor RpoS [Pseudomonas aeruginosa LESB58]
          Length = 334

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 84/277 (30%), Positives = 143/277 (51%), Gaps = 27/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 66  YLNEIGFSPLLTPEEEVHFA-RLAQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 124

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 125 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 183

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA------GDESLNALINS 192
           LR  +  L    D+   PE++  + +K       ++ +N R+       G +S   L+++
Sbjct: 184 LRAAR-ELTHKLDHEPSPEEIANLLEKPVAEVKRMLGLNERVTSVDVSLGPDSDKTLLDT 242

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQ 249
              +       L+ D D  E +               + ++ L  ++R +   R   R  
Sbjct: 243 LTDDRPTDPCELLQDDDLSESI--------------DQWLTELTDKQREVVIRRFGLRGH 288

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E+  TLE +  E  ++RERVRQI+  A K+++E ++K
Sbjct: 289 ES-STLEEVGQEIGLTRERVRQIQVEALKRLREILEK 324


>gi|326791438|ref|YP_004309259.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           lentocellum DSM 5427]
 gi|326542202|gb|ADZ84061.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           lentocellum DSM 5427]
          Length = 363

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 83/264 (31%), Positives = 139/264 (52%), Gaps = 13/264 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  ++E +LA+R ++ GD  A  +L  ++LRLVV IA  Y G G+   ++
Sbjct: 97  YLKEIGKVPLLSAEQEIILAQRMQD-GDQEAKKKLAEANLRLVVSIAKRYVGRGMLFLDL 155

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 156 IQEGNLGLIKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 213

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L      + +PE+   IAK++++  S+V  +        SL   I   ++  S
Sbjct: 214 LMRVSRQLLQELGRDPQPEE---IAKRMDMPVSKVREIMKISQEPVSLETPI--GEEEDS 268

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++    D    V  E       +  L   +  L  RE+++   R   ++    TLE
Sbjct: 269 HLGDFI---PDEDIPVPAEAAAFTLLKEQLIEVLDTLTEREQKVLRLRFGLDDGRARTLE 325

Query: 257 NLSSEFEVSRERVRQIEARAFKKV 280
            +  EF V+RER+RQIEA+A +K+
Sbjct: 326 EVGKEFSVTRERIRQIEAKALRKL 349


>gi|54310169|ref|YP_131189.1| putative RNA polymerase sigma-38 factor [Photobacterium profundum
           SS9]
 gi|46914610|emb|CAG21387.1| putative RNA polymerase sigma-38 factor [Photobacterium profundum
           SS9]
          Length = 342

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 88/272 (32%), Positives = 147/272 (54%), Gaps = 15/272 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD  A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 70  YLGEIGFSPLLTAEEEVLYARRAL-RGDEIARKRMIESNLRLVVKISRRYSNRGLALLDL 128

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 129 VEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 187

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +   Q + D+    E    IA KL   E  V  +N  L  +E ++++ N    +S 
Sbjct: 188 LRTARELAQKL-DHEPTAED---IALKL---EKPVDDVNRMLRLNERVSSVDNPIGGDSE 240

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR---LQENPVTL 255
           +    ++ D  G       +++  + +N +   +  LNP++R +  ARR   L     TL
Sbjct: 241 KALLDIIPDEKGGSPESSTQDD--DIKNSIVHWLQELNPKQREVL-ARRFGLLGYEASTL 297

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E++  E  ++RERVRQI+    +++++ +  Q
Sbjct: 298 EDVGREIGLTRERVRQIQVEGLRRLRDMLTHQ 329


>gi|319955596|ref|YP_004166863.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Cellulophaga
           algicola DSM 14237]
 gi|319424256|gb|ADV51365.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cellulophaga
           algicola DSM 14237]
          Length = 287

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 88/286 (30%), Positives = 148/286 (51%), Gaps = 49/286 (17%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ +I KI ++   EE  LA+R RE GD  A  +L T++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQDISKIDLITANEEVDLAQRIRE-GDQLALEKLTTANLRFVVSVAKQYQNQGLTL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
            ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ A+      Q  I+R   L KIG+ 
Sbjct: 77  PDLINEGNVGLVKAAKRFDETRGFKFISYAVWWIRQAILQALAEQSRIVR-LPLNKIGSI 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCR 179
              K+ F  L +           + +P     IAK+L ++ SEV          +SM+  
Sbjct: 136 NKIKKAFSYLEQA----------HERPPSAEEIAKELEMTVSEVQQSLKNTGRHVSMDAP 185

Query: 180 L--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
           L    D +L  +I S +  +   Q         Q+ + IE          + R++  L+ 
Sbjct: 186 LKEGEDSNLYNVIGSGESPNPDKQLL-------QQSLNIE----------INRALETLSQ 228

Query: 238 RERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           RE  + +       ++ +TLE +   F+++RERVRQI  +A +K++
Sbjct: 229 READVVKLYYGIGDQHSMTLEEIGQTFDLTRERVRQIREKAIRKLK 274


>gi|323484891|ref|ZP_08090246.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323693741|ref|ZP_08107938.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
 gi|323401772|gb|EGA94115.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323502192|gb|EGB18057.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
          Length = 374

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 83/276 (30%), Positives = 141/276 (51%), Gaps = 23/276 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L   EE  LAKR  E GD +A  RL+ ++LRLVV IA  Y G G+   ++
Sbjct: 109 YLKEIGTVPLLSADEELRLAKRKAE-GDDNAKERLIEANLRLVVSIAKRYTGRGMSFLDL 167

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++ V+KFD  +G++L+TY+ WWI+ ++   +      +++        +   
Sbjct: 168 VQEGNLGLIKGVEKFDYTKGYKLSTYATWWIRQSVTRALADQARTIRVPV-----HMVET 222

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           + ++    + +T        V  +++ L +SE +V+ +        SL   I   D   S
Sbjct: 223 INKMSKMQRKLTLELGYEPSVAELSEALEMSEDKVMEIMQIAREPASLETPIGEED--DS 280

Query: 199 QWQDW-----LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-- 251
              D+     +V      E V++        R  +   +  L  RER++   R   E+  
Sbjct: 281 NLGDFVADSNVVTPEGNVESVML--------REHIDALLGDLKERERQVIVLRFGLEDGH 332

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           P TLE +  EF V+RER+RQIEA+A +K++  ++ +
Sbjct: 333 PRTLEEVGKEFNVTRERIRQIEAKALRKLRNPVRSK 368


>gi|66044622|ref|YP_234463.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. syringae
           B728a]
 gi|289675304|ref|ZP_06496194.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. syringae
           FF5]
 gi|6644290|gb|AAF20993.1|AF208000_1 RpoS [Pseudomonas syringae pv. syringae]
 gi|24415296|gb|AAN59882.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. aptata]
 gi|24415299|gb|AAN59884.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. aptata]
 gi|63255329|gb|AAY36425.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Pseudomonas syringae pv. syringae B728a]
 gi|330896091|gb|EGH28312.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. japonica
           str. M301072PT]
          Length = 335

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 87/272 (31%), Positives = 146/272 (53%), Gaps = 17/272 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + +K       ++ +N R++  D SL      SDK  
Sbjct: 185 LRAARELTQKL-DHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSLGP---DSDKT- 239

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++       + + +S L  ++R +   R   R  E+  T
Sbjct: 240 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTEKQREVVIRRFGLRGHESS-T 293

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE++  E  ++RERVRQI+    K+++E ++K
Sbjct: 294 LEDVGLEIGLTRERVRQIQVEGLKRLREILEK 325


>gi|28868771|ref|NP_791390.1| RNA polymerase sigma-38 factor [Pseudomonas syringae pv. tomato
           str. DC3000]
 gi|301383956|ref|ZP_07232374.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. tomato
           Max13]
 gi|302064158|ref|ZP_07255699.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. tomato
           K40]
 gi|302134085|ref|ZP_07260075.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. tomato
           NCPPB 1108]
 gi|3132688|gb|AAC16326.1| sigma factor [Pseudomonas syringae pv. tomato]
 gi|28852010|gb|AAO55085.1| RNA polymerase sigma-38 factor [Pseudomonas syringae pv. tomato
           str. DC3000]
 gi|331016398|gb|EGH96454.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv.
           lachrymans str. M302278PT]
          Length = 335

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 87/272 (31%), Positives = 146/272 (53%), Gaps = 17/272 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + +K       ++ +N R++  D SL      SDK  
Sbjct: 185 LRAARELTQKL-DHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSLGP---DSDKT- 239

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++       + + +S L  ++R +   R   R  E+  T
Sbjct: 240 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTEKQREVVIRRFGLRGHESS-T 293

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE++  E  ++RERVRQI+    K+++E ++K
Sbjct: 294 LEDVGLEIGLTRERVRQIQVEGLKRLREILEK 325


>gi|308048570|ref|YP_003912136.1| RNA polymerase, sigma 38 subunit, RpoS [Ferrimonas balearica DSM
           9799]
 gi|307630760|gb|ADN75062.1| RNA polymerase, sigma 38 subunit, RpoS [Ferrimonas balearica DSM
           9799]
          Length = 328

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 89/273 (32%), Positives = 148/273 (54%), Gaps = 17/273 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R +      + +R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 59  YLSEIGFSPLLTAEEEVYYARRAQRDC-AKSRNRMIESNLRLVVKIARRYNNRGLALLDL 117

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 118 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 176

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +  L    D+    E+   IA KL+    +V  M   L  +E ++++      +S 
Sbjct: 177 LRTAR-ELAHTLDHEPTAEE---IAMKLDKPVEDVSRM---LKLNEKISSVDTPIGGDSD 229

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRN-MLTRSMSVLNPRERRIFEARR---LQENPVT 254
           +    ++ D D   +V  E + + +  N  + R +  LN ++R +  ARR   L   P T
Sbjct: 230 KALLDVIADDD---RVCPEVQAQDDDINGSVVRWLGELNSKQREVL-ARRFGLLGYEPST 285

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           LE++  E  ++RERVRQI+  A ++++E I  Q
Sbjct: 286 LEDVGREIGLTRERVRQIQVEALRRLRELIGAQ 318


>gi|289626003|ref|ZP_06458957.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. aesculi
           str. NCPPB3681]
 gi|289651481|ref|ZP_06482824.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. aesculi
           str. 2250]
 gi|330868573|gb|EGH03282.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. aesculi
           str. 0893_23]
          Length = 335

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 87/272 (31%), Positives = 146/272 (53%), Gaps = 17/272 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + +K       ++ +N R++  D SL      SDK  
Sbjct: 185 LRAARELTQKL-DHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSLGP---DSDKT- 239

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++       + + +S L  ++R +   R   R  E+  T
Sbjct: 240 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTEKQREVVIRRFGLRGHESS-T 293

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE++  E  ++RERVRQI+    K+++E ++K
Sbjct: 294 LEDVGLEIGLTRERVRQIQVEGLKRLREILEK 325


>gi|88858314|ref|ZP_01132956.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Pseudoalteromonas tunicata D2]
 gi|88819931|gb|EAR29744.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Pseudoalteromonas tunicata D2]
          Length = 339

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 86/280 (30%), Positives = 148/280 (52%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   +++  + G  ++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 71  YLGEIGFSPLLSAEEEVYFSRKSLK-GCEASRKRMIESNLRLVVKIARRYNNRGLALLDL 129

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 130 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 188

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +   Q + D+    E++          + K L ++E ++ S++  + GD S  AL+
Sbjct: 189 LRTARELTQKL-DHEPTAEEIAEKLDRPVEDVTKMLRLNE-KITSVDTPIGGD-SEKALL 245

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
           +          +  + D D +E ++   EE              LN ++R +  ARR   
Sbjct: 246 DILADEKGGGPESCIQDEDIRENIVHWLEE--------------LNAKQREVL-ARRFGL 290

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   P TLE++  E  ++RERVRQI+  A ++++E +  Q
Sbjct: 291 LGYEPSTLEDVGKEIGLTRERVRQIQVEALRRLKEILMHQ 330


>gi|160941160|ref|ZP_02088497.1| hypothetical protein CLOBOL_06053 [Clostridium bolteae ATCC
           BAA-613]
 gi|158435721|gb|EDP13488.1| hypothetical protein CLOBOL_06053 [Clostridium bolteae ATCC
           BAA-613]
          Length = 381

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 86/285 (30%), Positives = 146/285 (51%), Gaps = 41/285 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L   EE  LA+R +  GD  A  RL+ ++LRLVV IA  Y G G+   ++
Sbjct: 116 YLKEIGTVPLLTADEELDLAQR-KADGDEFAKERLIEANLRLVVSIAKRYTGRGMSFLDL 174

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           V EGN+GL++ V+KFD  +G++L+TY+ WWI+ ++   +      +++      T N   
Sbjct: 175 VQEGNLGLIKGVEKFDYTKGYKLSTYATWWIRQSVTRALADQARTIRVPVHMVETINKMS 234

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             Q++L   L    G+  ++T+          +A+ L+++E +V+ +        SL   
Sbjct: 235 KMQRKLTLEL----GYEPSVTE----------LAEALDMTEDKVMEIMQIAREPASLETP 280

Query: 190 INSSDKNSSQWQDW-----LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           I   D   S   D+     +V      E V++        R  +   +  L  RER++  
Sbjct: 281 IGEED--DSNLGDFVADNNVVTPEGNVESVML--------REHIDALLGDLKERERQVIV 330

Query: 245 ARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R   E+  P TLE +  EF V+RER+RQIEA+A +K++  ++ +
Sbjct: 331 LRFGLEDGHPRTLEEVGKEFNVTRERIRQIEAKALRKLRNPVRSK 375


>gi|291542495|emb|CBL15605.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Ruminococcus bromii
           L2-63]
          Length = 367

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 82/269 (30%), Positives = 136/269 (50%), Gaps = 23/269 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   EE  LA R  + GD++A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 100 YLKEIGRVPLLSSDEEINLAIRIAD-GDVAAKQRLSEANLRLVVSIAKRYLGRGMQFLDL 158

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-K 133
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N+ K
Sbjct: 159 IQEGNLGLIKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKVK 218

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
           ++   L    GH  +  +   + +  V   +++     E +S+   +  +E         
Sbjct: 219 KVQSQLLHQNGHEPSADEIAAEIDMPVDKVREIMRVAQEPVSLETPIGEEE--------- 269

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-- 251
               S   D++            +       R  L+  +S L PRE ++ + R   E+  
Sbjct: 270 ---DSHLGDFIPD---NDAPAPADAASHTMLREQLSDVLSTLTPREAKVLKLRFGLEDGR 323

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             TLE +  EF V+RER+RQIEA+A +K+
Sbjct: 324 SRTLEEVGKEFNVTRERIRQIEAKALRKL 352


>gi|167772125|ref|ZP_02444178.1| hypothetical protein ANACOL_03499 [Anaerotruncus colihominis DSM
           17241]
 gi|167665923|gb|EDS10053.1| hypothetical protein ANACOL_03499 [Anaerotruncus colihominis DSM
           17241]
          Length = 361

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 84/272 (30%), Positives = 136/272 (50%), Gaps = 27/272 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   EE  LA R  + GD+ A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 95  YLKEIGRVPLLSADEEIDLAVRMAQ-GDIDARKRLSEANLRLVVSIAKRYVGRGMQFLDL 153

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-K 133
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N+ K
Sbjct: 154 IQEGNLGLIKAVEKFDHTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKVK 213

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES--LNALIN 191
           ++   L    GH     + + + +  V   +++     E +S+   +  +E   L   I 
Sbjct: 214 KVSSLLLHKNGHEPTAEEISAELDMPVDKVREIMRVAQEPVSLETPIGEEEDSHLGDFIP 273

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             D  +         D      +L         R  L+  +  L PRE ++   R   E+
Sbjct: 274 DEDAPAP--------DTAASHTLL---------REQLSEVLQTLTPREEKVLRLRFGLED 316

Query: 252 --PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
               TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 317 GRSRTLEEVGREFNVTRERIRQIEAKALRKLR 348


>gi|330894625|gb|EGH27286.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. mori
           str. 301020]
          Length = 335

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 87/272 (31%), Positives = 146/272 (53%), Gaps = 17/272 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + +K       ++ +N R++  D SL      SDK  
Sbjct: 185 LRAARELTQKL-DHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSLGP---DSDKT- 239

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++       + + +S L  ++R +   R   R  E+  T
Sbjct: 240 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTEKQREVVIRRFGLRGHESS-T 293

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE++  E  ++RERVRQI+    K+++E ++K
Sbjct: 294 LEDVGLEIGLTRERVRQIQVEGLKRLREILEK 325


>gi|302187929|ref|ZP_07264602.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. syringae
           642]
          Length = 335

 Score =  115 bits (287), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 87/272 (31%), Positives = 146/272 (53%), Gaps = 17/272 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + +K       ++ +N R++  D SL      SDK  
Sbjct: 185 LRAARELTQKL-DHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSLGP---DSDKT- 239

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++       + + +S L  ++R +   R   R  E+  T
Sbjct: 240 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTEKQREVVIRRFGLRGHESS-T 293

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE++  E  ++RERVRQI+    K+++E ++K
Sbjct: 294 LEDVGLEIGLTRERVRQIQVEGLKRLREILEK 325


>gi|312863004|ref|ZP_07723242.1| RNA polymerase sigma factor RpoD [Streptococcus vestibularis F0396]
 gi|311100540|gb|EFQ58745.1| RNA polymerase sigma factor RpoD [Streptococcus vestibularis F0396]
          Length = 369

 Score =  114 bits (286), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 89/273 (32%), Positives = 146/273 (53%), Gaps = 29/273 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E+GDL A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLSNEEEKELAIAV-ENGDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKL- 219

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSS 193
               +R  +  LQ +   +  PEQ   IA++++++  +V  +  ++A +  SL   I   
Sbjct: 220 ----VREQRNLLQELG-QDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEE 270

Query: 194 DKNSSQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQ 249
           D   S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L 
Sbjct: 271 D--DSHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLD 322

Query: 250 ENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +  + TLE++   F V+RER+RQIEA+A +K++
Sbjct: 323 DGKMRTLEDVGKVFNVTRERIRQIEAKALRKLR 355


>gi|330872696|gb|EGH06845.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv.
           morsprunorum str. M302280PT]
          Length = 335

 Score =  114 bits (286), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 87/272 (31%), Positives = 146/272 (53%), Gaps = 17/272 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTVERAIMNQTRTIRLPIHV-VKELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + +K       ++ +N R++  D SL      SDK  
Sbjct: 185 LRAARELTQKL-DHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSLGP---DSDKT- 239

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++       + + +S L  ++R +   R   R  E+  T
Sbjct: 240 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTEKQREVVIRRFGLRGHESS-T 293

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE++  E  ++RERVRQI+    K+++E ++K
Sbjct: 294 LEDVGLEIGLTRERVRQIQVEGLKRLREILEK 325


>gi|239626154|ref|ZP_04669185.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47_FAA]
 gi|239520384|gb|EEQ60250.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47FAA]
          Length = 381

 Score =  114 bits (286), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 86/285 (30%), Positives = 146/285 (51%), Gaps = 41/285 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L   EE  LA+R +  GD  A  RL+ ++LRLVV IA  Y G G+   ++
Sbjct: 116 YLKEIGTVPLLTADEELNLAQR-KADGDDYAKERLIEANLRLVVSIAKRYTGRGMSFLDL 174

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           V EGN+GL++ V+KFD  +G++L+TY+ WWI+ ++   +      +++      T N   
Sbjct: 175 VQEGNLGLIKGVEKFDYTKGYKLSTYATWWIRQSVTRALADQARTIRVPVHMVETINKMS 234

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             Q++L   L    G+  ++T+          +A+ L+++E +V+ +        SL   
Sbjct: 235 KMQRKLTLEL----GYEPSVTE----------LAEALDMTEDKVMEIMQIAREPASLETP 280

Query: 190 INSSDKNSSQWQDW-----LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           I   D   S   D+     +V      E V++        R  +   +  L  RER++  
Sbjct: 281 IGEED--DSNLGDFVADNNVVTPEGNVESVML--------REHIDALLGDLKERERQVIV 330

Query: 245 ARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R   E+  P TLE +  EF V+RER+RQIEA+A +K++  ++ +
Sbjct: 331 LRFGLEDGHPRTLEEVGKEFNVTRERIRQIEAKALRKLRNPVRSK 375


>gi|55823393|ref|YP_141834.1| RNA polymerase sigma factor RpoD [Streptococcus thermophilus
           CNRZ1066]
 gi|116628187|ref|YP_820806.1| RNA polymerase sigma factor RpoD [Streptococcus thermophilus LMD-9]
 gi|55739378|gb|AAV63019.1| DNA directed RNA polymerase sigma 42 protein [Streptococcus
           thermophilus CNRZ1066]
 gi|116101464|gb|ABJ66610.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Streptococcus thermophilus LMD-9]
 gi|312278801|gb|ADQ63458.1| RNA polymerase sigma factor [Streptococcus thermophilus ND03]
          Length = 369

 Score =  114 bits (286), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 87/269 (32%), Positives = 143/269 (53%), Gaps = 21/269 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E+GDL A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLSNEEEKELAIAV-ENGDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 218

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L      +  PEQ   IA++++++  +V  +  ++A +  SL   I   D   
Sbjct: 219 LVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEED--D 272

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 273 SHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 326

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE++   F V+RER+RQIEA+A +K++
Sbjct: 327 RTLEDVGKVFNVTRERIRQIEAKALRKLR 355


>gi|289578595|ref|YP_003477222.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter italicus Ab9]
 gi|289528308|gb|ADD02660.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter italicus Ab9]
          Length = 273

 Score =  114 bits (286), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 87/269 (32%), Positives = 142/269 (52%), Gaps = 14/269 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y+ EI  IP+L  +EE  L KR  E GD  A  R + S+LRLVV IA GY G G+  
Sbjct: 4   IGMYLREISHIPLLTPEEENELLKRI-EEGDEEAKKRFIESNLRLVVSIAKGYVGKGISF 62

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GL++AV++FD  +G++ +TY+ WWIK  +   I      ++I     +   
Sbjct: 63  PDLIQEGNLGLLKAVERFDYRKGYKFSTYATWWIKQTITRAIADQARTIRIPVHMVES-- 120

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
             N + LK   Q +     +P  +  IA+++N+SE +   +   + G  SL   +   D+
Sbjct: 121 -VN-KLLKIQKQFLQKLGREP-SIEEIAEEMNISEKKAKVLLEIVQGIVSLEEPVG-EDE 176

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV- 253
           N       ++ D +  + V  E+ E    +  +   +S L PRE ++   R  L +  + 
Sbjct: 177 NGKLGD--IIADKEAVDPV--EELESMLLKEQVDEVLSTLAPREEKVLRLRFGLDDGKIR 232

Query: 254 TLENLSSEF-EVSRERVRQIEARAFKKVQ 281
           TLE +  E   +SRERVRQIE +A K+++
Sbjct: 233 TLEEVGKELGGISRERVRQIETKALKRLR 261


>gi|120553862|ref|YP_958213.1| RpoD family RNA polymerase sigma factor [Marinobacter aquaeolei
           VT8]
 gi|120323711|gb|ABM18026.1| RNA polymerase, sigma 38 subunit, RpoS [Marinobacter aquaeolei VT8]
          Length = 332

 Score =  114 bits (286), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 84/278 (30%), Positives = 150/278 (53%), Gaps = 27/278 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A+  R+ G+ S   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 64  YLNEIGFSPLLTPEEEVYFARLARK-GEESGRKRMIESNLRLVVKIARRYVNRGLTLLDL 122

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 123 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNLY 181

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA------GDESLNALINS 192
           LR  +   Q + D+    E++  +  K       ++ +N R+A      G  S  +L+++
Sbjct: 182 LRAARELTQKL-DHEPTAEEIARMVDKPVDDVKRMLGLNERVASMDTPIGAGSDKSLMDT 240

Query: 193 -SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQE 250
            +D+ +S   D L               +  N  + L + +  L+ +++ +   R  L+ 
Sbjct: 241 VADEGASDPADLL---------------QDNNMCSCLEKWIDQLSDKQQEVLSRRFGLRG 285

Query: 251 NPV-TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            P+ TLE +  E  ++RERVRQI+  A ++++E ++K+
Sbjct: 286 YPISTLEEVGQEIGLTRERVRQIQVEALRRLREILEKE 323


>gi|311747140|ref|ZP_07720925.1| RNA polymerase sigma-70 factor [Algoriphagus sp. PR1]
 gi|126578848|gb|EAZ83012.1| RNA polymerase sigma-70 factor [Algoriphagus sp. PR1]
          Length = 287

 Score =  114 bits (286), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 82/274 (29%), Positives = 152/274 (55%), Gaps = 21/274 (7%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ +L   EE VLAKR RE GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGKVDLLTADEEVVLAKRIRE-GDQLALEKLTKANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     +V++    N+   
Sbjct: 77  GDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL--PLNRVGS 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
              + +    L+   +    PE+   +A+ L V+ +EV+    +++G   S++A     +
Sbjct: 135 LNKISKTFSELEQRFEREPSPEE---LAEVLEVTANEVVD-TMKISGRHVSMDAPFVQGE 190

Query: 195 KNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--Q 249
           +NS       V ++DG E+    L+    RK     + R++S L  RE  +         
Sbjct: 191 ENSL----LDVLENDGDEKPDDGLMNDSLRKE----VQRALSTLTQREADVITLYFGLNG 242

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           E+ +TLE +  +F ++RERVRQI+ +A ++++ +
Sbjct: 243 EHAMTLEEIGEKFNLTRERVRQIKEKAIRRLRHT 276


>gi|212638699|ref|YP_002315219.1| RNA polymerase sigma factor RpoD [Anoxybacillus flavithermus WK1]
 gi|212560179|gb|ACJ33234.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Anoxybacillus flavithermus WK1]
          Length = 372

 Score =  114 bits (286), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 87/276 (31%), Positives = 135/276 (48%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 106 YLKEIGRVPLLSAEEEIELAKRI-EQGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 164

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 165 IQEGNMGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 224

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I K       E +S+   +    D  L 
Sbjct: 225 RVQRQLLQDLGREPSPEEIAEEMDLTPEKVREILK----IAQEPVSLETPIGEEDDSHLG 280

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S         +H   E +          +  L   +  L  RE  +   R 
Sbjct: 281 DFIEDQDATSPA-------EHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 323

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 324 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 359


>gi|288940519|ref|YP_003442759.1| RNA polymerase sigma-70 subunit RpoD subfamily [Allochromatium
           vinosum DSM 180]
 gi|288895891|gb|ADC61727.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Allochromatium
           vinosum DSM 180]
          Length = 338

 Score =  114 bits (286), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 88/275 (32%), Positives = 147/275 (53%), Gaps = 21/275 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI +  +L  +EE   A R  + GD +A  R++  +LRLVVKIA  Y   GLP+ ++
Sbjct: 70  YLNEIGESRLLTAEEEIRFA-RLAQAGDNAARQRMIVCNLRLVVKIARRYLNRGLPLLDL 128

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     V++      +  ++ 
Sbjct: 129 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTVRLPIHVVKEINIYL 188

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
              R    L    D++   E    IA+ L+   +EV     R+ G   LN  I S D   
Sbjct: 189 KASR---QLAQSLDHDPTSED---IAQLLDRPINEV----KRMLG---LNERITSVDTPY 235

Query: 198 SQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENP 252
           S+  D  + D   D       E+ +  +    +   + +LN ++R + E R      EN 
Sbjct: 236 SKDADKPLVDMLQDDGSSDPTERIQDDDIHVNIEHWLGLLNDKQREVVERRFGLHGHENS 295

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            TLE+++ E  V+RERVRQI+  A +++++ ++ +
Sbjct: 296 -TLESVARELGVTRERVRQIQMDALRRLRDILESE 329


>gi|73541783|ref|YP_296303.1| RNA polymerase sigma factor RpoS [Ralstonia eutropha JMP134]
 gi|72119196|gb|AAZ61459.1| Sigma-70 region 1.2 [Ralstonia eutropha JMP134]
          Length = 391

 Score =  114 bits (286), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 87/274 (31%), Positives = 141/274 (51%), Gaps = 17/274 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++ I   P+L   EE   +   ++ GD SA   ++  +LRLVV IA GY   G+P+ ++
Sbjct: 122 YLNRISIKPLLSAPEELHFSTLAKD-GDFSARQVMIERNLRLVVSIAKGYLNRGVPLLDL 180

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++    +  R    
Sbjct: 181 IEEGNLGLMHAIEKFDPSRGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRELNQ 238

Query: 139 LRRLKGHLQ-AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN- 196
           + R K HL+   TD   +   +  IA  L  +  EV  +   LA +E   +L    D + 
Sbjct: 239 VLRAKRHLEKGGTDG--RDASLEDIAHLLGKTPDEVQDV---LALNEHTTSLDTPFDLDP 293

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN---PV 253
            S   D+L  +H+      +   E +    ++   ++ L+ + R + E RR   N   P 
Sbjct: 294 GSSLLDFLSDEHNAAPDQEVAHRELE---GLMKLWLARLSEKHRYVVE-RRFGLNHIEPA 349

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           TLE L+ E  ++RERVRQI+  A  K++     Q
Sbjct: 350 TLEELAEEMGLTRERVRQIQQEALVKLKRHFASQ 383


>gi|313109026|ref|ZP_07794999.1| sigma factor RpoS [Pseudomonas aeruginosa 39016]
 gi|310881501|gb|EFQ40095.1| sigma factor RpoS [Pseudomonas aeruginosa 39016]
          Length = 344

 Score =  114 bits (286), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 144/277 (51%), Gaps = 27/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 76  YLNEIGFSPLLTPEEEVHFA-RLAQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 134

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 135 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 193

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA------GDESLNALINS 192
           LR  +  L    D+   PE++  + +K       ++ +N R+       G +S   L+++
Sbjct: 194 LRAAR-ELTHKLDHEPSPEEIANLLEKPVAEVKRMLGLNERVTSVDVSLGPDSDKTLLDT 252

Query: 193 SDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
              +       L+ D D  E +   L E  +++  R ++ R   +      R  E+    
Sbjct: 253 LTDDRPTDPCELLQDDDLSESIDQWLTELTDKQ--REVVIRRFGL------RGHESS--- 301

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
               TLE +  E  ++RERVRQI+  A K+++E ++K
Sbjct: 302 ----TLEEVGQEIGLTRERVRQIQVEALKRLREILEK 334


>gi|88705821|ref|ZP_01103530.1| RNA polymerase sigma-38 subunit [Congregibacter litoralis KT71]
 gi|88699892|gb|EAQ97002.1| RNA polymerase sigma-38 subunit [Congregibacter litoralis KT71]
          Length = 331

 Score =  114 bits (286), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 91/288 (31%), Positives = 149/288 (51%), Gaps = 25/288 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI  +P+L   EE   A R  + GD +A  R++ S+LRLVVKIA  Y   G+ + ++
Sbjct: 62  YLNEIGFVPLLTADEEKHYA-RLTQKGDEAARKRMIESNLRLVVKIARRYLHRGMSLLDL 120

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV+KFDPERGFR +TY+ WWI+  ++  I+     +++            
Sbjct: 121 IEEGNLGLMRAVEKFDPERGFRFSTYATWWIRQTIERGIMNQARTIRLP--------IHV 172

Query: 139 LRRLKGHLQAITD--NNLKPEQVV-AIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           ++ L G L+A  +    L  E     IA + + S  EV     RL G   LN  ++S D 
Sbjct: 173 VKDLNGCLRAARELTQQLDHEPTTQEIASRTHKSAKEV----SRLMG---LNERVSSVDA 225

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNR--RNMLTRSMSVLNPRERRIFEAR--RLQEN 251
                 D  V +    + +    E+ +N    + +   ++ L  ++R +   R   L   
Sbjct: 226 PLGPDSDSSVVETIADDHLCDPSEQLQNDDVHDSVADWLNELTDKQREVVMRRFGLLGHE 285

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQK 299
             TLE +  E  ++RERVRQI+  A K+++  +++Q    S+  LLQ+
Sbjct: 286 SSTLEEVGQEIGLTRERVRQIQVEALKRLRRILERQG--LSADALLQR 331


>gi|125717671|ref|YP_001034804.1| RNA polymerase sigma factor RpoD [Streptococcus sanguinis SK36]
 gi|125497588|gb|ABN44254.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32),
           putative [Streptococcus sanguinis SK36]
 gi|324990502|gb|EGC22438.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK353]
 gi|324995458|gb|EGC27370.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK678]
 gi|325688386|gb|EGD30405.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK72]
 gi|325690016|gb|EGD32020.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK115]
 gi|325693940|gb|EGD35858.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK150]
 gi|327461509|gb|EGF07840.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK1]
 gi|327468857|gb|EGF14329.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK330]
 gi|327489365|gb|EGF21158.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK1058]
 gi|332361594|gb|EGJ39398.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK1056]
 gi|332363116|gb|EGJ40903.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK355]
 gi|332365901|gb|EGJ43657.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK1059]
          Length = 370

 Score =  114 bits (286), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 87/268 (32%), Positives = 141/268 (52%), Gaps = 21/268 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E GDL A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 103 YLKEIGVVPLLSNEEEQELAILV-EQGDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 161

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 162 IQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 219

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L      +  PEQ   IA++++++  +V  +  ++A +  SL   I   D   
Sbjct: 220 LVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEED--D 273

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 274 SHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 327

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKV 280
            TLE++   F V+RER+RQIEA+A +K+
Sbjct: 328 RTLEDVGKVFNVTRERIRQIEAKALRKL 355


>gi|325662013|ref|ZP_08150632.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|331085863|ref|ZP_08334946.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|325471676|gb|EGC74895.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|330406786|gb|EGG86291.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 370

 Score =  114 bits (286), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 90/269 (33%), Positives = 140/269 (52%), Gaps = 21/269 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  +EE  LA+R  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 104 YLKEIGKVPLLSAEEEIELARRM-EEGDEDAKKRLAEANLRLVVSIAKRYVGRGMLFLDL 162

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 163 IQEGNLGLIKAVEKFDYNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKL- 221

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               +R  +  LQ +    L PE+   IAK+L++    V  +        SL   I   +
Sbjct: 222 ----IRVSRQLLQELGREPL-PEE---IAKELDMPVDRVREILKISQEPVSLETPI--GE 271

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
           +  S   D++    D    V  E       +  L   +S L  RE+++   R    +   
Sbjct: 272 EEDSHLGDFI---QDDNVPVPAEAAAATLLKEQLDEVLSTLTDREQKVLRLRFGMNDGRA 328

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE +  EF+V+RER+RQIEA+A +K++
Sbjct: 329 RTLEEVGKEFDVTRERIRQIEAKALRKLR 357


>gi|228476995|ref|ZP_04061633.1| RNA polymerase sigma factor RpoD [Streptococcus salivarius SK126]
 gi|322516348|ref|ZP_08069273.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           vestibularis ATCC 49124]
 gi|228251014|gb|EEK10185.1| RNA polymerase sigma factor RpoD [Streptococcus salivarius SK126]
 gi|322125081|gb|EFX96474.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           vestibularis ATCC 49124]
          Length = 369

 Score =  114 bits (286), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 87/269 (32%), Positives = 143/269 (53%), Gaps = 21/269 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E+GDL A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLSNEEEKELAIAV-ENGDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 218

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L      +  PEQ   IA++++++  +V  +  ++A +  SL   I   D   
Sbjct: 219 LVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEED--D 272

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 273 SHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 326

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE++   F V+RER+RQIEA+A +K++
Sbjct: 327 RTLEDVGKVFNVTRERIRQIEAKALRKLR 355


>gi|330964173|gb|EGH64433.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv.
           actinidiae str. M302091]
          Length = 335

 Score =  114 bits (286), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 87/272 (31%), Positives = 145/272 (53%), Gaps = 17/272 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE +  + +K       ++ +N R++  D SL      SDK  
Sbjct: 185 LRAARELTQKL-DHEPSPEDIANLLEKPVGEVKRMLGLNERVSSVDVSLGP---DSDKT- 239

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++       + + +S L  ++R +   R   R  E+  T
Sbjct: 240 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTEKQREVVIRRFGLRGHESS-T 293

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE++  E  ++RERVRQI+    K+++E ++K
Sbjct: 294 LEDVGLEIGLTRERVRQIQVEGLKRLREILEK 325


>gi|294338839|emb|CAZ87173.1| RNA polymerase sigma factor rpoS [Thiomonas sp. 3As]
          Length = 351

 Score =  114 bits (286), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 85/278 (30%), Positives = 142/278 (51%), Gaps = 21/278 (7%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           +G   L  Y++ IR  P+   ++E+  A R +  GD  A   +V  +LRLVV IA  Y G
Sbjct: 74  SGVSALQAYLNHIRAKPLFTPEQEFETATRAK-AGDFEARQAMVEHNLRLVVSIAKAYVG 132

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            G  + +++ EGN+GL+ A++KF+PERGFR +TY+ WWI+ +++  +++    +++    
Sbjct: 133 RGAALGDLIEEGNLGLIHAIEKFEPERGFRFSTYASWWIRQSIERALMQQVRTIRL--PV 190

Query: 131 NQKRLFFNLRRLKGHLQAITD--NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           +  R    + R + HL+   D       E V A+   L  S  EV  +        SL+A
Sbjct: 191 HVIRELNQVLRARKHLEQAADYRGQTSDEDVAAL---LGRSTEEVTDLLALAEQPTSLDA 247

Query: 189 L--INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS-MSVLNPRERRIFEA 245
           L    S +  + Q+ D        Q  + +E++ +      L  S +  L  RER + EA
Sbjct: 248 LRETQSGESYADQFAD--------QNALSMEEQTQTREVEALVDSWVGELAEREREVIEA 299

Query: 246 R-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R  L    + TLE+L+    ++RERVRQI+  +  K++
Sbjct: 300 RFGLHGRELETLESLAQRLGLTRERVRQIQQESLLKLK 337


>gi|288555754|ref|YP_003427689.1| RNA polymerase sigma factor RpoD [Bacillus pseudofirmus OF4]
 gi|288546914|gb|ADC50797.1| RNA polymerase sigma factor SigD [Bacillus pseudofirmus OF4]
          Length = 372

 Score =  114 bits (286), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 90/275 (32%), Positives = 137/275 (49%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  QEE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 106 YLKEIGRVPLLSAQEEIELAKRI-EQGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 164

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD E+G++ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 165 IQEGNMGLIKAVEKFDYEKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 224

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +  R     +   +  L PE+V  I K       E +S+   +    D  L 
Sbjct: 225 RVQRQLLQDFGREPTPEEVAEEMELTPEKVREILK----IAQEPVSLETPIGEEDDSHLG 280

Query: 188 ALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
             I   D+ +    D   Y+   +  E VL    +R+   N+L     + + R R     
Sbjct: 281 DFIE--DQEALAPSDAAAYELLKEQLEDVLDTLTDREE--NVLRLRFGLDDGRTR----- 331

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                   TLE +   F V+RER+RQIEA+A +K+
Sbjct: 332 --------TLEEVGKVFGVTRERIRQIEAKALRKL 358


>gi|323352412|ref|ZP_08087547.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis VMC66]
 gi|322121844|gb|EFX93585.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis VMC66]
 gi|325696737|gb|EGD38625.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK160]
 gi|328945882|gb|EGG40032.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK1087]
          Length = 370

 Score =  114 bits (286), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 87/268 (32%), Positives = 141/268 (52%), Gaps = 21/268 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E GDL A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 103 YLKEIGVVPLLSNEEEQELAILV-EQGDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 161

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 162 IQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 219

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L      +  PEQ   IA++++++  +V  +  ++A +  SL   I   D   
Sbjct: 220 LVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEED--D 273

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 274 SHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 327

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKV 280
            TLE++   F V+RER+RQIEA+A +K+
Sbjct: 328 RTLEDVGKVFNVTRERIRQIEAKALRKL 355


>gi|119773417|ref|YP_926157.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)-like
           protein [Shewanella amazonensis SB2B]
 gi|119765917|gb|ABL98487.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)-like
           protein [Shewanella amazonensis SB2B]
          Length = 969

 Score =  114 bits (286), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 72/238 (30%), Positives = 135/238 (56%), Gaps = 20/238 (8%)

Query: 46  DLSAA-HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           D+SAA   ++T +LRLV+ +A  Y G GL ++++V EGNIGLM+AV+KFD  +GF+ +TY
Sbjct: 729 DISAARDEMITFNLRLVLSVANKYLGRGLELADLVQEGNIGLMKAVEKFDHRKGFKFSTY 788

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + WWI+ A+   I     +++I    N+     +L +L    + +T    +  ++  ++ 
Sbjct: 789 ATWWIRQAITRAIADQARIIRIPVHVNE-----SLNKLISASKVLTHKFGRGPKISELSL 843

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            L++ E++V ++   L  +      +  +D N++ + DW        E+ +I+ +   N 
Sbjct: 844 ILSMPETKVENLKQILVMEP-----VAEADHNTNGYVDWAAM---SPEEEIIDDDRDTNI 895

Query: 225 RNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           +++L      L  +E+++ E R        +TLE +  +F+V+RER+RQIEA++ KK+
Sbjct: 896 KDLLKG----LTDKEKKVLELRFGINAATELTLEEVGQQFDVTRERIRQIEAKSLKKL 949


>gi|291563082|emb|CBL41898.1| RNA polymerase, sigma 70 subunit, RpoD [butyrate-producing
           bacterium SS3/4]
          Length = 374

 Score =  114 bits (286), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 89/270 (32%), Positives = 143/270 (52%), Gaps = 23/270 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L   EE  LAK+  E GD  A  +L  S+LRLVV IA  Y G G+ + ++
Sbjct: 107 YLKEIGKVPLLSPDEEIELAKKI-ELGDEEAKKKLAESNLRLVVSIAKRYAGRGMQLLDL 165

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N  R
Sbjct: 166 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETIN--R 223

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSS 193
           L    R+L   L         PE+   +AK+L++    V  +  +++ D  SL   I   
Sbjct: 224 LVRTQRQLVQKLG----REATPEE---LAKELDMPVERVREI-MKISQDPVSLETPIG-- 273

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-- 251
           ++  S   D++    D   +V  +          L   +S L  RE+++   R   ++  
Sbjct: 274 EEEDSHLGDFI---QDNNVEVPADAATYTLLHEQLMDVLSTLTEREQKVLRLRFGLDDGR 330

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           P TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 331 PRTLEEVGRQFNVTRERIRQIEAKALRKLR 360


>gi|296134902|ref|YP_003642144.1| RNA polymerase sigma factor RpoS [Thiomonas intermedia K12]
 gi|295795024|gb|ADG29814.1| RNA polymerase sigma factor RpoS [Thiomonas intermedia K12]
          Length = 351

 Score =  114 bits (286), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 85/278 (30%), Positives = 142/278 (51%), Gaps = 21/278 (7%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           +G   L  Y++ IR  P+   ++E+  A R +  GD  A   +V  +LRLVV IA  Y G
Sbjct: 74  SGVSALQSYLNHIRAKPLFTPEQEFETATRAK-AGDFEARQAMVEHNLRLVVSIAKAYVG 132

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            G  + +++ EGN+GL+ A++KF+PERGFR +TY+ WWI+ +++  +++    +++    
Sbjct: 133 RGAALGDLIEEGNLGLIHAIEKFEPERGFRFSTYASWWIRQSIERALMQQVRTIRL--PV 190

Query: 131 NQKRLFFNLRRLKGHLQAITD--NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           +  R    + R + HL+   D       E V A+   L  S  EV  +        SL+A
Sbjct: 191 HVIRELNQVLRARKHLEQAADYRGQTSDEDVAAL---LGRSTEEVADLLALAEQPTSLDA 247

Query: 189 L--INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS-MSVLNPRERRIFEA 245
           L    S +  + Q+ D        Q  + +E++ +      L  S +  L  RER + EA
Sbjct: 248 LRETQSGESYADQFAD--------QNALSMEEQTQTREVEALVDSWVGELAEREREVIEA 299

Query: 246 R-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R  L    + TLE+L+    ++RERVRQI+  +  K++
Sbjct: 300 RFGLHGRELETLESLAQRLGLTRERVRQIQQESLLKLK 337


>gi|206895369|ref|YP_002247042.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Coprothermobacter proteolyticus DSM 5265]
 gi|206737986|gb|ACI17064.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Coprothermobacter proteolyticus DSM 5265]
          Length = 360

 Score =  114 bits (286), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 93/276 (33%), Positives = 150/276 (54%), Gaps = 36/276 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+H++ +  +L  ++E +LA+R  E  D +A   L+  +LRLV+ IA  Y   GL   E+
Sbjct: 91  YLHDVGQYDLLTAEQERILAQRI-EKNDAAAREELIKRNLRLVISIAKKYTNKGLSFMEL 149

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGL++AV+KFD  +G++ +TY+ WWIK A+   +            A+Q RL   
Sbjct: 150 IQEGNIGLIKAVEKFDWRKGYKFSTYATWWIKQAITRAL------------ADQSRL--- 194

Query: 139 LRRLKGHLQAITD---------NNLKPEQVV-AIAKKLNVSESEVISMNCRLAGDE--SL 186
           +RR    ++A            N L  E  V  +A+ L  SE +V+++  +++  E  SL
Sbjct: 195 IRRPVHMVEAYHQFQKKLNELYNQLGREPTVQELAEALGFSEDKVLALK-QMSNPEPQSL 253

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           +A I   D++ S+ QD++    +G       +   + RR +L   +S LN RER I E R
Sbjct: 254 DATI--GDQDDSRVQDFVPDTGEGAADKYFWE---EERRRVLEEVLSTLNKREREIIEMR 308

Query: 247 RLQENPV--TLENLSSEFEVSRERVRQIEARAFKKV 280
               + V  TLE + + F ++RERVRQIE +A +K+
Sbjct: 309 YGLVDGVEHTLEEVGASFNITRERVRQIETKALRKL 344


>gi|332362696|gb|EGJ40494.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK49]
          Length = 370

 Score =  114 bits (286), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 89/272 (32%), Positives = 144/272 (52%), Gaps = 29/272 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E GDL A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 103 YLKEIGVVPLLSNEEEQELAILV-EQGDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 161

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 162 IQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKL- 220

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSS 193
               +R  +  LQ +   +  PEQ   IA++++++  +V  +  ++A +  SL   I   
Sbjct: 221 ----VREQRNLLQELG-QDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEE 271

Query: 194 DKNSSQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQ 249
           D   S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L 
Sbjct: 272 D--DSHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLD 323

Query: 250 ENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
           +  + TLE++   F V+RER+RQIEA+A +K+
Sbjct: 324 DGKMRTLEDVGKVFNVTRERIRQIEAKALRKL 355


>gi|331001843|ref|ZP_08325365.1| hypothetical protein HMPREF0491_00227 [Lachnospiraceae oral taxon
           107 str. F0167]
 gi|330412817|gb|EGG92200.1| hypothetical protein HMPREF0491_00227 [Lachnospiraceae oral taxon
           107 str. F0167]
          Length = 389

 Score =  114 bits (286), Expect = 1e-23,   Method: Compositional matrix adjust.
 Identities = 88/286 (30%), Positives = 150/286 (52%), Gaps = 23/286 (8%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL---SAAHRLVTSHLRLV 61
           +++  V+ E  +  Y+ EI KIP+L   +E  LAK+  +  +     AA R+  S+LRLV
Sbjct: 105 DLNDYVSIEDPIKMYLKEIGKIPLLNVDDEMDLAKKISDPDESIRKEAAKRMAESNLRLV 164

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA  Y G G+ + +++ EGN+GL++AV+KFD ++GF+ +TY+ WWI+ A+   I    
Sbjct: 165 VSIAKRYMGRGMQLLDLIQEGNLGLLRAVEKFDYKKGFKFSTYATWWIRQAITRSIADQA 224

Query: 122 SLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
             ++I      T N+      L + +  L  I      PE+V   AK++N+S  +V  + 
Sbjct: 225 RTIRIPVHMVETINR------LIKTQRKLVQILGREPSPEEV---AKEMNISVPKVREIM 275

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                  S+   I   D++ S   D+L    D   +V +         + L   + +L  
Sbjct: 276 SFALEPVSMETPI--GDEDDSHLGDFL---QDYNAKVPVNFAMDVLLHDQLMDVIKLLTE 330

Query: 238 RERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           RE+++   R   E+  P TLE +   F ++RER+RQIEA++ +K++
Sbjct: 331 REQKVILLRFGLEDGKPRTLEEVGKVFGITRERIRQIEAKSLRKLR 376


>gi|324993240|gb|EGC25160.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK405]
          Length = 370

 Score =  114 bits (286), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 87/268 (32%), Positives = 141/268 (52%), Gaps = 21/268 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E GDL A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 103 YLKEIGVVPLLSNEEEQELAILV-EQGDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 161

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 162 IQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 219

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L      +  PEQ   IA++++++  +V  +  ++A +  SL   I   D   
Sbjct: 220 LVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEED--D 273

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 274 SHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 327

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKV 280
            TLE++   F V+RER+RQIEA+A +K+
Sbjct: 328 RTLEDVGKVFNVTRERIRQIEAKALRKL 355


>gi|312867612|ref|ZP_07727818.1| RNA polymerase sigma factor RpoD [Streptococcus parasanguinis
           F0405]
 gi|311096675|gb|EFQ54913.1| RNA polymerase sigma factor RpoD [Streptococcus parasanguinis
           F0405]
          Length = 369

 Score =  114 bits (286), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 89/272 (32%), Positives = 144/272 (52%), Gaps = 29/272 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E GDL A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLTNEEEQELAILV-EQGDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 161 IQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKL- 219

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSS 193
               +R  +  LQ +   +  PEQ   IA++++++  +V  +  ++A +  SL   I   
Sbjct: 220 ----VREQRNLLQELG-QDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEE 270

Query: 194 DKNSSQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQ 249
           D   S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L 
Sbjct: 271 D--DSHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLD 322

Query: 250 ENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
           +  + TLE++   F V+RER+RQIEA+A +K+
Sbjct: 323 DGKMRTLEDVGKVFNVTRERIRQIEAKALRKL 354


>gi|6175878|gb|AAF05319.1|AF178851_2 sigma factor 38 [Pseudomonas putida]
          Length = 335

 Score =  114 bits (286), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 83/272 (30%), Positives = 143/272 (52%), Gaps = 17/272 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     + +     ++   ++
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIPLPIHVVKELNVYS 185

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
             R    L    D+   PE++  + +K       ++ +N R++  D SL      SDK  
Sbjct: 186 --RAARELTQKLDHEPSPEEIATLLEKPVAEVKRMLGLNERVSSVDVSLGP---DSDKT- 239

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++       + + +  L  ++R +   R   R  E+  T
Sbjct: 240 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLGELTDKQREVVVRRFGLRGHESS-T 293

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE++  E  ++RERVRQI+    K+++E ++K
Sbjct: 294 LEDVGLEIGLTRERVRQIQVEGLKRLREILEK 325


>gi|310659059|ref|YP_003936780.1| RNA polymerase sigma factor rpod [Clostridium sticklandii DSM 519]
 gi|308825837|emb|CBH21875.1| RNA polymerase sigma factor RpoD [Clostridium sticklandii]
          Length = 376

 Score =  114 bits (286), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 84/265 (31%), Positives = 145/265 (54%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L  +EE  LA++   +GD  A  +LV ++LRLVV IA  Y G G+   ++
Sbjct: 110 YLKEIGKIPLLSAEEEIDLAEKMG-YGDEIAKKKLVEANLRLVVSIAKRYVGRGMLFLDL 168

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD ++GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 169 IQEGNLGLIKAVEKFDYKKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 226

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L      + KPE+   +AK++++ E ++  +  ++A  E ++      ++  S
Sbjct: 227 LIRVHRQLLQEYGRDPKPEE---LAKEMDMPEEKIREI-MKIA-QEPVSLETPIGEEEDS 281

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++  D              K +   L   +  LN RE+++ + R   E+    TLE
Sbjct: 282 HLGDFIPDDDAPAPAEAAAYSLLKEQ---LEDVLCTLNEREQKVLKLRFGLEDGRARTLE 338

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF+V+RER+RQIEA+A +K++
Sbjct: 339 EVGKEFDVTRERIRQIEAKALRKLR 363


>gi|322385457|ref|ZP_08059101.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           cristatus ATCC 51100]
 gi|321270195|gb|EFX53111.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           cristatus ATCC 51100]
          Length = 370

 Score =  114 bits (286), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 87/268 (32%), Positives = 141/268 (52%), Gaps = 21/268 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E GDL A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 103 YLKEIGVVPLLSNEEEQELAILV-EQGDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 161

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 162 IQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 219

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L      +  PEQ   IA++++++  +V  +  ++A +  SL   I   D   
Sbjct: 220 LVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEED--D 273

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 274 SHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 327

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKV 280
            TLE++   F V+RER+RQIEA+A +K+
Sbjct: 328 RTLEDVGKVFNVTRERIRQIEAKALRKL 355


>gi|89072392|ref|ZP_01158971.1| hypothetical DNA-directed RNA polymerase, sigma subunit
           [Photobacterium sp. SKA34]
 gi|89051924|gb|EAR57376.1| hypothetical DNA-directed RNA polymerase, sigma subunit
           [Photobacterium sp. SKA34]
          Length = 286

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 89/282 (31%), Positives = 148/282 (52%), Gaps = 21/282 (7%)

Query: 13  EIGLSR-YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           EI + R Y+++I   P+L K +E +   R    GD ++   L+ S+LRLVV IA  YR  
Sbjct: 7   EIDVVRLYLNDISNKPLLSKDDE-IQYSRKSLTGDPASKKILIESNLRLVVSIAKKYRAA 65

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
            L +S+++ EGNIGLM AV+KFDPE+GFR +TY+ WWIK  ++  I      +++    +
Sbjct: 66  NLSLSDLIDEGNIGLMTAVEKFDPEKGFRFSTYASWWIKQTIERAIHNQNRTIRLPVNIS 125

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
           ++        L+ H + +  NN +P     IA+ LN    E+ ++        SL+  I 
Sbjct: 126 KEINTL----LRTHRELMKLNNNEPTH-EDIAQALNKESKEISALFSNEVNVVSLDQTI- 179

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL---NPRERRIFEARR- 247
             D  +S    +LV D    EQ+     E  N  +M+  +  VL   N R+R I   RR 
Sbjct: 180 -GDNENSHTIAYLVAD----EQITSPSAEVDN-DDMIKITNLVLNGINKRDREII-CRRF 232

Query: 248 --LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             +   P TL+ ++    ++RER+RQ++ ++   ++ S+ ++
Sbjct: 233 GLMGYEPHTLQEVADAVGLTRERIRQLQIKSLNSLKRSLARE 274


>gi|322389216|ref|ZP_08062777.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           parasanguinis ATCC 903]
 gi|321144121|gb|EFX39538.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           parasanguinis ATCC 903]
          Length = 369

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 89/272 (32%), Positives = 144/272 (52%), Gaps = 29/272 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E GDL A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLTNEEEQELAILV-EQGDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 161 IQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKL- 219

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSS 193
               +R  +  LQ +   +  PEQ   IA++++++  +V  +  ++A +  SL   I   
Sbjct: 220 ----VREQRNLLQELG-QDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEE 270

Query: 194 DKNSSQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQ 249
           D   S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L 
Sbjct: 271 D--DSHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLD 322

Query: 250 ENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
           +  + TLE++   F V+RER+RQIEA+A +K+
Sbjct: 323 DGKMRTLEDVGKVFNVTRERIRQIEAKALRKL 354


>gi|315223009|ref|ZP_07864888.1| RNA polymerase sigma factor RpoD [Streptococcus anginosus F0211]
 gi|319939161|ref|ZP_08013525.1| RNA polymerase sigma factor rpoD [Streptococcus anginosus 1_2_62CV]
 gi|315187959|gb|EFU21695.1| RNA polymerase sigma factor RpoD [Streptococcus anginosus F0211]
 gi|319812211|gb|EFW08477.1| RNA polymerase sigma factor rpoD [Streptococcus anginosus 1_2_62CV]
          Length = 370

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 87/268 (32%), Positives = 141/268 (52%), Gaps = 21/268 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E GDL A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 103 YLKEIGVVPLLTNEEEQELAVLV-EQGDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 161

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 162 IQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 219

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L      +  PEQ   IA++++++  +V  +  ++A +  SL   I   D   
Sbjct: 220 LVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEED--D 273

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 274 SHLGDFI------EDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 327

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKV 280
            TLE++   F V+RER+RQIEA+A +K+
Sbjct: 328 RTLEDVGKVFNVTRERIRQIEAKALRKL 355


>gi|270157097|ref|ZP_06185754.1| RNA polymerase sigma factor RpoS [Legionella longbeachae D-4968]
 gi|289164492|ref|YP_003454630.1| RNA polymerase sigma factor RpoS [Legionella longbeachae NSW150]
 gi|269989122|gb|EEZ95376.1| RNA polymerase sigma factor RpoS [Legionella longbeachae D-4968]
 gi|288857665|emb|CBJ11508.1| RNA polymerase sigma factor RpoS [Legionella longbeachae NSW150]
          Length = 341

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 82/275 (29%), Positives = 146/275 (53%), Gaps = 23/275 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A    + GD++A  +++ S+LRLVVKI+  Y   GLP+ ++
Sbjct: 74  YLSEIGFSPLLSAEEEVHYATLALK-GDVAARKKMIESNLRLVVKISRRYLNRGLPLLDL 132

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM++V+KFDP+RGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 133 IEEGNLGLMKSVEKFDPKRGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 191

Query: 139 LRRLKGHLQAITDNNLKPEQVVAI-------AKKLNVSESEVISMNCRLAGDESLNALIN 191
           LR  +   Q + D+   PE++  +        +KL     +V S++  +  DE+ + L  
Sbjct: 192 LRAARQLTQKL-DHEPSPEEIAEMVDKPLEDVQKLLGLNDKVTSVDTPIGFDENKSLLDT 250

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             D+NS    + L  ++       +  +  +N++ ++ R   +      R FE       
Sbjct: 251 IPDENSVNPAELLTNENLRLHIESLLDKLTENQQQVIARRFGL------RGFEK------ 298

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             TLE++  E +++RERVRQI+  A K ++  ++K
Sbjct: 299 -ATLEDVGKEIDLTRERVRQIQVEALKTLRSLLEK 332


>gi|331082069|ref|ZP_08331197.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|330405664|gb|EGG85194.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 374

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 88/275 (32%), Positives = 145/275 (52%), Gaps = 33/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  +EE  LA+R  E GD SA  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 108 YLKEIGKVPLLSAEEEITLAQRM-EEGDESAKKRLAEANLRLVVSIAKRYVGRGMLFLDL 166

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-- 132
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 167 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 226

Query: 133 ---KRLFFNLRRLKGHLQAITDN-NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
              ++L   L R + H + I +  N+  E+V  I   L +S+ E +S+   +  +E  + 
Sbjct: 227 RVSRQLLQELGR-EPHPEEIAEEMNMSVERVREI---LKISQ-EPVSLETPIGEEEDSHL 281

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
                D N     D   +        L++++        L   +  L  RE+++   R  
Sbjct: 282 GDFIQDDNVPVPADAAAF-------TLLKEQ--------LVEVLGTLTEREQKVLRLRFG 326

Query: 249 QEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            ++    TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 327 LDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLR 361


>gi|296876770|ref|ZP_06900818.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           parasanguinis ATCC 15912]
 gi|296432272|gb|EFH18071.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           parasanguinis ATCC 15912]
          Length = 369

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 89/272 (32%), Positives = 144/272 (52%), Gaps = 29/272 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E GDL A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLTNEEEQELAILV-EQGDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 161 IQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKL- 219

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSS 193
               +R  +  LQ +   +  PEQ   IA++++++  +V  +  ++A +  SL   I   
Sbjct: 220 ----VREQRNLLQELG-QDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEE 270

Query: 194 DKNSSQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQ 249
           D   S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L 
Sbjct: 271 D--DSHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLD 322

Query: 250 ENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
           +  + TLE++   F V+RER+RQIEA+A +K+
Sbjct: 323 DGKMRTLEDVGKVFNVTRERIRQIEAKALRKL 354


>gi|327458597|gb|EGF04945.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK1057]
          Length = 370

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 87/268 (32%), Positives = 141/268 (52%), Gaps = 21/268 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E GDL A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 103 YLKEIGVVPLLSNEEEQELAILV-EQGDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 161

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 162 IQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 219

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L      +  PEQ   IA++++++  +V  +  ++A +  SL   I   D   
Sbjct: 220 LVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEED--D 273

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 274 SHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 327

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKV 280
            TLE++   F V+RER+RQIEA+A +K+
Sbjct: 328 RTLEDVGKVFNVTRERIRQIEAKALRKL 355


>gi|299144149|ref|ZP_07037229.1| RNA polymerase sigma factor RpoD [Peptoniphilus sp. oral taxon 386
           str. F0131]
 gi|298518634|gb|EFI42373.1| RNA polymerase sigma factor RpoD [Peptoniphilus sp. oral taxon 386
           str. F0131]
          Length = 383

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 85/269 (31%), Positives = 135/269 (50%), Gaps = 23/269 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L   EE  +A+R  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 117 YLKEIGKIPLLTGDEEIDIAQRM-EVGDEDAKQELAEANLRLVVSIAKRYVGRGMSFLDL 175

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 176 IQEGNLGLMKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 233

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R++  L      +  PE+   I K++N+   +V  +        SL   I   ++  S
Sbjct: 234 LVRVQRQLVQELGRDPLPEE---IGKEMNLEVEKVREIQKIAQEPVSLETPI--GEEEDS 288

Query: 199 QWQDWLVYDH-----DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-- 251
              D++  D      D     L+        +  L   +  L  RE+++   R   ++  
Sbjct: 289 HLGDFIPDDEILSPSDAATFTLL--------KEQLEDVLQTLTDREKKVLTLRFGLDDGR 340

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             TLE +  EF+V+RER+RQIEA+A +K+
Sbjct: 341 ARTLEEVGKEFDVTRERIRQIEAKALRKL 369


>gi|229825188|ref|ZP_04451257.1| hypothetical protein GCWU000182_00540 [Abiotrophia defectiva ATCC
           49176]
 gi|229790560|gb|EEP26674.1| hypothetical protein GCWU000182_00540 [Abiotrophia defectiva ATCC
           49176]
          Length = 372

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 84/266 (31%), Positives = 139/266 (52%), Gaps = 13/266 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L+  EE  LAK   E GD  A  +L  ++LRLVV IA  Y G G+   ++
Sbjct: 106 YLKEIGKVPLLDMDEEIKLAKSMAE-GDDEARKKLTEANLRLVVSIAKRYLGRGMQFLDL 164

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWIK ++   I      ++I    +       
Sbjct: 165 IQEGNMGLIKAVEKFDYTKGYKFSTYATWWIKQSITRAIADQARTIRI--PVHMVETINK 222

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R +  L        +PE+   I K+LN+   +V S+  ++A  E ++      ++  S
Sbjct: 223 LIRAQRQLTQTLGREPQPEE---IGKELNMEPEKVRSI-MKIA-QEPVSFETPIGEEEDS 277

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++    D      +E       +  L   +  L  RE R+ + R   E+    TLE
Sbjct: 278 HIGDFI---PDDSNMAPVEAATHAILKEQLEEVLDSLTEREARVIKLRFGLEDGRTRTLE 334

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQE 282
            +  EF V+RER+RQIE++A +K+++
Sbjct: 335 EVGKEFNVTRERIRQIESKALRKLRQ 360


>gi|319947289|ref|ZP_08021522.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           australis ATCC 700641]
 gi|319746531|gb|EFV98791.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           australis ATCC 700641]
          Length = 370

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 87/268 (32%), Positives = 141/268 (52%), Gaps = 21/268 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E GDL A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 103 YLKEIGVVPLLTNEEEQELAILV-EQGDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 161

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 162 IQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 219

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L      +  PEQ   IA++++++  +V  +  ++A +  SL   I   D   
Sbjct: 220 LVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEED--D 273

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 274 SHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 327

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKV 280
            TLE++   F V+RER+RQIEA+A +K+
Sbjct: 328 RTLEDVGKVFNVTRERIRQIEAKALRKL 355


>gi|251782161|ref|YP_002996463.1| RNA polymerase sigma factor RpoD [Streptococcus dysgalactiae subsp.
           equisimilis GGS_124]
 gi|242390790|dbj|BAH81249.1| RNA polymerase sigma factor [Streptococcus dysgalactiae subsp.
           equisimilis GGS_124]
          Length = 369

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 87/269 (32%), Positives = 141/269 (52%), Gaps = 21/269 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE V A    E GDL A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLTSEEEKVFAVAVAE-GDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 218

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L      +  PEQ   IA+++ ++  +V  +  ++A +  SL   I   D   
Sbjct: 219 LVREQRNLLQELGQDPTPEQ---IAERMEMTPDKVREI-LKIAQEPVSLETPIGEED--D 272

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 273 SHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 326

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE++   F V+RER+RQIEA+A +K++
Sbjct: 327 RTLEDVGKVFNVTRERIRQIEAKALRKLR 355


>gi|146299193|ref|YP_001193784.1| RpoD family RNA polymerase sigma factor [Flavobacterium johnsoniae
           UW101]
 gi|57471283|gb|AAW50927.1| RpoD [Flavobacterium johnsoniae]
 gi|146153611|gb|ABQ04465.1| RNA polymerase, sigma 70 subunit, RpoD family [Flavobacterium
           johnsoniae UW101]
          Length = 287

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 82/287 (28%), Positives = 153/287 (53%), Gaps = 37/287 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ ++   EE  LA+R +  GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGKVDLITADEEVELAQRIK-AGDQRALEKLTKANLRFVVSVAKQYQNQGLTL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
            ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++      Q  I+R   L KIG+ 
Sbjct: 77  PDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVR-LPLNKIGSI 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA- 188
               +++  L +          +N +P     IAK+L+++ ++V           S++A 
Sbjct: 136 NKINKMYALLEQ----------SNERPPSAEEIAKELDMTVNDVKESMKNSGRHLSMDAP 185

Query: 189 LINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           L+   D N        +YD    G+      +   ++ R  + RS+  L PRE  +    
Sbjct: 186 LVEGEDSN--------LYDVLRSGESPNPDRELIHESLRTEIERSLETLTPREADVV--- 234

Query: 247 RL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RL      ++P+TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 235 RLYFGLGDQHPMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|254786794|ref|YP_003074223.1| RNA polymerase sigma factor RpoS [Teredinibacter turnerae T7901]
 gi|237685659|gb|ACR12923.1| RNA polymerase sigma factor RpoS [Teredinibacter turnerae T7901]
          Length = 337

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 85/274 (31%), Positives = 148/274 (54%), Gaps = 19/274 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L   EE   A+R  + GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSADEEVYFARRALK-GDEAARKRMIESNLRLVVKISRRYVNRGLALLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +   Q + D+    E++  + +K       ++++N R+    S++A I  + + + 
Sbjct: 185 LRAARELSQKL-DHEPSAEEIAELLEKPVEDVERMLALNERVT---SMDAPIGPASEKT- 239

Query: 199 QWQDWLVYDHDGQEQVL--IEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPV 253
                 V D    +QV   +E  E  +    L   +  L+ ++R +  ARR         
Sbjct: 240 ------VVDTVPDQQVSDPVELLEDSDLSTSLNSWLDELSEKQREVV-ARRFGLRGHETS 292

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           TLE +  E  ++RERVRQI+  A +++++ ++KQ
Sbjct: 293 TLEEVGREIGLTRERVRQIQVEALRRLRDILEKQ 326


>gi|254514875|ref|ZP_05126936.1| RNA polymerase sigma factor RpoS [gamma proteobacterium NOR5-3]
 gi|219677118|gb|EED33483.1| RNA polymerase sigma factor RpoS [gamma proteobacterium NOR5-3]
          Length = 367

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 81/272 (29%), Positives = 147/272 (54%), Gaps = 15/272 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI  +P+L   EE   A R  + GD +A  R++ S+LRLVV IA  Y   G+ + ++
Sbjct: 98  YLNEIGFVPLLSADEEKHYA-RLVQKGDEAARKRMIESNLRLVVNIARRYLHRGMSLLDL 156

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 157 IEEGNLGLMRAVEKFDPERGFRFSTYATWWIRQTIERGIMNQARTIRLPIHV-VKDLNGC 215

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +   Q + D++   +++ +   K     S ++ +N R++   S++A +  +  +S 
Sbjct: 216 LRAARELTQQL-DHDPTTQEIASRTHKTATEVSRLMGLNERVS---SMDAPLGPNSDSSV 271

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR---LQENPVTL 255
                  +  D  EQ+     +  +  + +   +  L+ ++R +   RR   L  +  TL
Sbjct: 272 AETIADEHGCDPSEQI-----QDDDVHDSVAHWLDELSEKQREVV-VRRFGLLGYDSCTL 325

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +  E  ++RERVRQI+  A K+++  +++Q
Sbjct: 326 EEVGQEIGLTRERVRQIQVEALKRLRRILERQ 357


>gi|329769784|ref|ZP_08261185.1| RNA polymerase sigma factor rpoD [Gemella sanguinis M325]
 gi|328838146|gb|EGF87764.1| RNA polymerase sigma factor rpoD [Gemella sanguinis M325]
          Length = 362

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 88/269 (32%), Positives = 142/269 (52%), Gaps = 17/269 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAK---RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           Y+ EI K+P+L K++E  L+K      E     A   L  ++LRLVV IA  Y G G+  
Sbjct: 92  YLKEIGKVPLLSKEKELELSKIIENGTEEEKEQAKKDLAEANLRLVVSIAKRYVGRGMLF 151

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GL++AV+KFD E+GF+ +TY+ WWI+ A+   I      ++I    +    
Sbjct: 152 LDLIQEGNMGLIKAVEKFDYEKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVET 209

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
              L R++  L        KPE+   IAKK+N++  +V  +  ++A +  SL   I   D
Sbjct: 210 INRLIRVQRQLLQDLGREPKPEE---IAKKMNMTPDKVREI-LKIAQEPVSLETPIGEED 265

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
              S   D++    D + Q  +E    +  +  L   +  L  RE  + + R  L++   
Sbjct: 266 --DSHLGDFI---EDKEAQSPVEHAANELLKEQLEEILETLTDREENVLKLRFGLKDGKT 320

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE + S F V+RER+RQIEA+A +K++
Sbjct: 321 HTLEEVGSAFGVTRERIRQIEAKAIRKLK 349


>gi|331090835|ref|ZP_08339681.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           2_1_46FAA]
 gi|330399694|gb|EGG79356.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           2_1_46FAA]
          Length = 370

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 87/265 (32%), Positives = 136/265 (51%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 104 YLKEIGKVPLLSAEEEIELAKRMAE-GDEDAKKRLAEANLRLVVSIAKRYVGRGMLFLDL 162

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD E+GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 163 IQEGNLGLIKAVEKFDYEKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 220

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L         PE+   IA++L++    V  +        SL   I   ++  S
Sbjct: 221 LIRVSRQLLQELGREPSPEE---IAEELDMPVERVREILKISQEPVSLETPI--GEEEDS 275

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++    D    V  E       +  L   ++ L  RE+++   R    +    TLE
Sbjct: 276 HLGDFI---QDDNVPVPAEAAAATLLKEQLGEVLNTLTDREQKVLRLRFGMNDGRARTLE 332

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF+V+RER+RQIEA+A +K++
Sbjct: 333 EVGKEFDVTRERIRQIEAKALRKLR 357


>gi|153853334|ref|ZP_01994743.1| hypothetical protein DORLON_00730 [Dorea longicatena DSM 13814]
 gi|149754120|gb|EDM64051.1| hypothetical protein DORLON_00730 [Dorea longicatena DSM 13814]
          Length = 369

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 84/273 (30%), Positives = 136/273 (49%), Gaps = 29/273 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  +EE  LAKR  + GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 103 YLKEIGKVPLLSAEEEVELAKRMAD-GDEEAKKRLAEANLRLVVSIAKRYVGRGMLFLDL 161

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 162 IQEGNLGLIKAVEKFDYHKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 219

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALI 190
           L R+   L         PE++ A        + + L +S+ E +S+   +  +E      
Sbjct: 220 LIRVSRQLLQELGREPTPEEIAAELDMPVERVREILKISQ-EPVSLETPIGEEE------ 272

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
                  S   D++    D    V  E   +   +  L   +  L  RE+++   R    
Sbjct: 273 ------DSHLGDFI---QDDNVPVPAEAAAQTLLKEQLDEVLDTLTEREQKVLRLRFGMN 323

Query: 251 N--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +    TLE +  EF+V+RER+RQIEA+A +K++
Sbjct: 324 DGRARTLEEVGKEFDVTRERIRQIEAKALRKLR 356


>gi|260588574|ref|ZP_05854487.1| RNA polymerase sigma factor RpoD [Blautia hansenii DSM 20583]
 gi|260541049|gb|EEX21618.1| RNA polymerase sigma factor RpoD [Blautia hansenii DSM 20583]
          Length = 330

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 86/270 (31%), Positives = 140/270 (51%), Gaps = 23/270 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  +EE  LA+R  E GD SA  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 64  YLKEIGKVPLLSAEEEITLAQRM-EEGDESAKKRLAEANLRLVVSIAKRYVGRGMLFLDL 122

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 123 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 180

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L         PE+   IA+++N+S   V  +        SL   I   ++  S
Sbjct: 181 LIRVSRQLLQELGREPHPEE---IAEEMNMSVERVREILKISQEPVSLETPI--GEEEDS 235

Query: 199 QWQDWLVYDH-----DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-- 251
              D++  D+     D     L++++        L   +  L  RE+++   R   ++  
Sbjct: 236 HLGDFIQDDNVPVPADAAAFTLLKEQ--------LVEVLGTLTEREQKVLRLRFGLDDGR 287

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 288 ARTLEEVGKEFNVTRERIRQIEAKALRKLR 317


>gi|307546200|ref|YP_003898679.1| RNA polymerase sigma factor RpoS [Halomonas elongata DSM 2581]
 gi|307218224|emb|CBV43494.1| RNA polymerase sigma factor RpoS [Halomonas elongata DSM 2581]
          Length = 330

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 87/279 (31%), Positives = 143/279 (51%), Gaps = 29/279 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE    +  R+ GD     R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 62  YLNEIGFSPLLTPEEEVHYGRLARQ-GDPQGRSRMIESNLRLVVKIARRYLNRGLTLLDL 120

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 121 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 179

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA------GDESLNALINS 192
           LR  +   Q + D+    E++     K   S   ++ +N R++      G ES   LI +
Sbjct: 180 LRAARELTQKL-DHEATAEEIADHLDKPVASVKRMMGLNERVSSVDYPVGSESDKPLIET 238

Query: 193 SDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--- 248
                      L  D+D G E  L++ + +++  + L      L  ++R +   RR    
Sbjct: 239 -----------LTDDNDLGPESTLVDGDVKQHVDDWLAE----LTDKQREVV-VRRFGLR 282

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
                TLE +  E  ++RERVRQI+  A KK++  + KQ
Sbjct: 283 GHEASTLEQVGEEIGLTRERVRQIQVEALKKLRRMLDKQ 321


>gi|83644704|ref|YP_433139.1| nonessential primary sigma factor [Hahella chejuensis KCTC 2396]
 gi|83632747|gb|ABC28714.1| nonessential primary sigma factor [Hahella chejuensis KCTC 2396]
          Length = 332

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 85/278 (30%), Positives = 147/278 (52%), Gaps = 27/278 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A+  R  GD     R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 64  YLNEIGFSPLLTPEEEVHFARMAR-RGDEKGRKRMIESNLRLVVKIARRYVNRGLSLLDL 122

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 123 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 181

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA------GDESLNALINS 192
           LR  +   Q + D+    E++  + +K       ++ +N R+       G  +  +L+++
Sbjct: 182 LRASRELTQKL-DHEPSAEEIADLLEKPVKDVKRMLGLNERITSVDSPIGGNAEKSLLDT 240

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQE 250
               +S     L+ D D               +  L R +  L+ +++ +  ARR  L+ 
Sbjct: 241 VADEASNDPAELLQDSD--------------LKGCLDRWLDQLSDKQQEVI-ARRFGLRG 285

Query: 251 NPV-TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            P+ TLE +  E  ++RERVRQI+  A K+++E ++K+
Sbjct: 286 YPMSTLEEVGQEIGLTRERVRQIQVEALKRMRELLEKE 323


>gi|327473233|gb|EGF18653.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK408]
          Length = 370

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 87/268 (32%), Positives = 141/268 (52%), Gaps = 21/268 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E GDL A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 103 YLKEIGVVPLLSNEEEQELAILV-EKGDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 161

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 162 IQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 219

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L      +  PEQ   IA++++++  +V  +  ++A +  SL   I   D   
Sbjct: 220 LVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEED--D 273

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 274 SHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 327

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKV 280
            TLE++   F V+RER+RQIEA+A +K+
Sbjct: 328 RTLEDVGKVFNVTRERIRQIEAKALRKL 355


>gi|311031650|ref|ZP_07709740.1| RNA polymerase sigma factor RpoD [Bacillus sp. m3-13]
          Length = 374

 Score =  114 bits (285), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 87/275 (31%), Positives = 135/275 (49%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 108 YLKEIGRVDLLSAEEEISLANRI-EEGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 166

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 167 IQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 226

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   D +L P++V  I   L +++ E +S+   +    D  L 
Sbjct: 227 RVQRQLLQDLGREPSPEEIAEDMDLTPDKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 282

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 283 DFIEDQDATSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 325

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 326 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 360


>gi|149378178|ref|ZP_01895895.1| nonessential primary sigma factor [Marinobacter algicola DG893]
 gi|149357540|gb|EDM46045.1| nonessential primary sigma factor [Marinobacter algicola DG893]
          Length = 333

 Score =  114 bits (284), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 84/280 (30%), Positives = 149/280 (53%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A+  R+ G+ S   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 65  YLNEIGFSPLLTPEEEVYFARLARK-GEESGRKRMIESNLRLVVKIARRYVNRGLTLLDL 123

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 124 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNLY 182

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA---------GDESLNAL 189
           LR  +   Q + D+    E++  +  K       ++ +N R+A         G++SL  L
Sbjct: 183 LRAARELTQKL-DHEPSAEEIARMVDKPVADVKRMLGLNERVASMDTPIGTGGEKSL--L 239

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RL 248
              +D+ +S   D L               +  N  + + + +  L+ +++ +   R  L
Sbjct: 240 DTVADEGASDPADLL---------------QDNNMCSCVEKWIDQLSDKQQEVLSRRFGL 284

Query: 249 QENPV-TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +  P+ TLE +  E  ++RERVRQI+  A ++++E ++K+
Sbjct: 285 RGYPISTLEEVGQEIGLTRERVRQIQVEALRRLREILEKE 324


>gi|322373396|ref|ZP_08047932.1| RNA polymerase sigma factor RpoD [Streptococcus sp. C150]
 gi|321278438|gb|EFX55507.1| RNA polymerase sigma factor RpoD [Streptococcus sp. C150]
          Length = 369

 Score =  114 bits (284), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 87/269 (32%), Positives = 142/269 (52%), Gaps = 21/269 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E+GDL A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLSNEEEKELAIAV-ENGDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 218

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L      +  PEQ   IA+++ ++  +V  +  ++A +  SL   I   D   
Sbjct: 219 LVREQRNLLQELGQDPTPEQ---IAERMGMTPDKVREI-LKIAQEPVSLETPIGEED--D 272

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 273 SHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 326

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE++   F V+RER+RQIEA+A +K++
Sbjct: 327 RTLEDVGKVFNVTRERIRQIEAKALRKLR 355


>gi|167745452|ref|ZP_02417579.1| hypothetical protein ANACAC_00143 [Anaerostipes caccae DSM 14662]
 gi|317472996|ref|ZP_07932299.1| sigma-70 family RNA polymerase sigma factor [Anaerostipes sp.
           3_2_56FAA]
 gi|167655173|gb|EDR99302.1| hypothetical protein ANACAC_00143 [Anaerostipes caccae DSM 14662]
 gi|316899541|gb|EFV21552.1| sigma-70 family RNA polymerase sigma factor [Anaerostipes sp.
           3_2_56FAA]
          Length = 347

 Score =  114 bits (284), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 84/278 (30%), Positives = 145/278 (52%), Gaps = 38/278 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR-GYGLPISE 77
           Y+H I +IP+L K +E  LAK   E G  SA  +++ S+LRLVV +A  Y  G G+ + +
Sbjct: 79  YLHRIGRIPLLSKDQEERLAKEI-EAGSQSAKDKMINSNLRLVVSVAKRYAAGSGMALLD 137

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KFD  RG++ +TY+MWWI+ ++   I      ++I     +K    
Sbjct: 138 LIQEGNIGLMKAVDKFDYRRGYKFSTYAMWWIRQSVTRAIADQARTIRIPVHMKEK---- 193

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE----------SEVISMNCRLAGDESLN 187
            + ++ G  +   + N +      +A+ + +S           S+ +S++  + G+E   
Sbjct: 194 -MGKVSGAARKFLEENGREPNADELAELMEISRDQMDEIMRLYSDTVSLDSPV-GEEEDA 251

Query: 188 ALIN--SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
            L+N  + +    Q+Q         ++ +L E+         +   +S L  RE+ I   
Sbjct: 252 MLMNFVADESMPEQYQ-------TAEQGILSEQ---------INEILSELTEREQTILRL 295

Query: 246 R-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R    EN + TLE +  E+ V+RER+RQIE +A +K++
Sbjct: 296 RFGFVENRIWTLEEVGREYHVTRERIRQIEGKALRKLK 333


>gi|284036901|ref|YP_003386831.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirosoma
           linguale DSM 74]
 gi|283816194|gb|ADB38032.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirosoma
           linguale DSM 74]
          Length = 287

 Score =  114 bits (284), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 79/274 (28%), Positives = 152/274 (55%), Gaps = 21/274 (7%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ +L   EE  LA++ RE GD  +  RL  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGKVDLLTPDEEVTLAQKIRE-GDQLSLERLTKANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     +V++    N+   
Sbjct: 77  GDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL--PLNRVGS 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
              + +    L+   +    PE++ A+   L +S +EV+    +++G   S++A     +
Sbjct: 135 LNKISKTFSDLEQKFEREPSPEELAAV---LEISAAEVVD-TLKISGRHVSMDAPFVQGE 190

Query: 195 KNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--Q 249
           +NS       V ++DG+++    LI    RK     + R++S L  RE  +         
Sbjct: 191 ENSL----LDVLENDGEDKPDSGLINDSLRKE----VQRALSTLTQREADVITLYFGLNG 242

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           E+ +TLE +  +F ++RERVRQI+ +A ++++ +
Sbjct: 243 EHAMTLEEIGEKFNLTRERVRQIKEKAIRRLRHT 276


>gi|294673737|ref|YP_003574353.1| RNA polymerase sigma factor RpoD [Prevotella ruminicola 23]
 gi|294473567|gb|ADE82956.1| putative RNA polymerase sigma factor RpoD [Prevotella ruminicola
           23]
          Length = 286

 Score =  114 bits (284), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 83/278 (29%), Positives = 145/278 (52%), Gaps = 28/278 (10%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI K  M+  +EE  LA+R +  GD  A  RL  ++LR VV +A  Y+  GL 
Sbjct: 17  ALEKYLQEISKETMISAEEEVELAQRIK-KGDTKALERLTKANLRFVVSVAKQYQNQGLS 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK-----IGTT 129
           + ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + I     +V+     +G+ 
Sbjct: 76  LPDLINEGNLGLLKAAERFDETRGFKFISYAVWWIRQSILQAISEQSRIVRLPLNQVGSV 135

Query: 130 ANQKR---LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
               R    F  L   +  +  I +    P++ +  A  +N  +  V +       +  L
Sbjct: 136 NKINREINRFEQLNERRPSVDEIAEKVDLPQEKIDEAMAINGHQISVDAPFVEGEDNSLL 195

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           + + NS         D  + D+   E+ L  K E +N       ++S LN RER + EA 
Sbjct: 196 DVMANS---------DAPLADNQLVEESL--KSEIQN-------ALSALNERERNVVEAS 237

Query: 247 RLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
                P +TLE + ++F ++RERVRQI+ +A +K++ S
Sbjct: 238 YGINQPELTLEEIGTKFGLTRERVRQIKEKAIRKLRNS 275


>gi|330950646|gb|EGH50906.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae Cit 7]
          Length = 335

 Score =  114 bits (284), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 86/272 (31%), Positives = 146/272 (53%), Gaps = 17/272 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + ++       ++ +N R++  D SL      SDK  
Sbjct: 185 LRAARELTQKL-DHEPSPEEIANLLERPVGEVKRMLGLNERVSSVDVSLGP---DSDKT- 239

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++       + + +S L  ++R +   R   R  E+  T
Sbjct: 240 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTEKQREVVIRRFGLRGHESS-T 293

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE++  E  ++RERVRQI+    K+++E ++K
Sbjct: 294 LEDVGLEIGLTRERVRQIQVEGLKRLREILEK 325


>gi|296133798|ref|YP_003641045.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermincola sp.
           JR]
 gi|296032376|gb|ADG83144.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermincola
           potens JR]
          Length = 366

 Score =  114 bits (284), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 85/265 (32%), Positives = 136/265 (51%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G GL   ++
Sbjct: 100 YLKEIGRVPLLTAEEEVELAKRM-ETGDEEAKRRLAEANLRLVVSIAKRYVGRGLLFLDL 158

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 159 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 216

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L         PE+   IA ++++    V  +  ++A  E ++      ++  S
Sbjct: 217 LIRVSRQLLQELGREPTPEE---IAAEMDIPVDRVREI-MKIA-QEPVSLETPIGEEEDS 271

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D+ + D D       E       R  L   +  L PRE ++   R   ++    TLE
Sbjct: 272 HLGDF-IEDQDAPAPA--EAASFILLREQLEEVLETLTPREEKVLRLRFGLDDGRSRTLE 328

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF V+RER+RQIEA+A +K++
Sbjct: 329 EVGQEFGVTRERIRQIEAKALRKLR 353


>gi|302386569|ref|YP_003822391.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           saccharolyticum WM1]
 gi|302197197|gb|ADL04768.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           saccharolyticum WM1]
          Length = 401

 Score =  114 bits (284), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 86/268 (32%), Positives = 140/268 (52%), Gaps = 21/268 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  ++E  LAK+  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 134 YLKEIGKVPLLSSEDEIELAKKI-ELGDDDAKQRLTEANLRLVVSIAKRYVGRGMQFLDL 192

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N  R
Sbjct: 193 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETIN--R 250

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           L    R+L   LQ +    + PE++ A A        E++ ++      E ++      +
Sbjct: 251 LVRVSRQL---LQELGREPV-PEEIAARADMQVDRVREIMKVSQ-----EPVSLETPIGE 301

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
           +  S   D++    D Q  V  +          L   +  L  RE+++ + R   ++  P
Sbjct: 302 EEDSHLGDFI---QDEQVAVPADAATFTMLHEQLMEVLDTLTEREQKVLKLRFGLDDGRP 358

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKV 280
            TLE +  EF V+RER+RQIEA+A +K+
Sbjct: 359 RTLEEVGKEFNVTRERIRQIEAKALRKL 386


>gi|306820486|ref|ZP_07454120.1| DNA-directed RNA polymerase sigma subunit RpoD [Eubacterium yurii
           subsp. margaretiae ATCC 43715]
 gi|304551472|gb|EFM39429.1| DNA-directed RNA polymerase sigma subunit RpoD [Eubacterium yurii
           subsp. margaretiae ATCC 43715]
          Length = 538

 Score =  114 bits (284), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 82/265 (30%), Positives = 144/265 (54%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KI +L  +EE+ L++     GD  A  ++V ++LRLVV IA  Y G G+   ++
Sbjct: 272 YLKEIGKIQLLTVEEEHRLSE-LMVKGDEYAKMKIVEANLRLVVSIAKRYVGRGMLFLDL 330

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 331 IQEGNLGLIKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 388

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L      + +PE+   IA+++ +S+ ++  +  ++A  E ++      ++  S
Sbjct: 389 LIRINRQLVQELGRDPRPEE---IAEQMGMSQDKIREI-MKIA-QEPVSLETPIGEEEDS 443

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++    D   Q   E       R  + + +  L  RERR+ + R   ++  P TLE
Sbjct: 444 HLGDFI---PDDDAQAPSEAAAYSLLREQIEQVLCTLTDRERRVLKLRFGLDDGRPRTLE 500

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF+V+RER+RQIEA+A +K++
Sbjct: 501 EVGKEFDVTRERIRQIEAKALRKLR 525


>gi|194290015|ref|YP_002005922.1| RNA polymerase sigma factor rpos [Cupriavidus taiwanensis LMG
           19424]
 gi|193223850|emb|CAQ69859.1| RNA polymerase sigma factor rpoS [Cupriavidus taiwanensis LMG
           19424]
          Length = 395

 Score =  114 bits (284), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 86/274 (31%), Positives = 141/274 (51%), Gaps = 17/274 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++ I   P+L   EE   +   ++ GD +A   ++  +LRLVV IA GY   G+P+ ++
Sbjct: 126 YLNRISIKPLLSAPEELHFSTLAKD-GDFAARQVMIERNLRLVVSIAKGYLNRGVPLLDL 184

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++    +  R    
Sbjct: 185 IEEGNLGLMHAIEKFDPSRGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRELNQ 242

Query: 139 LRRLKGHLQ-AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN- 196
           + R K HL+   TD   +   +  IA  L  +  EV  +   LA +E   +L    D + 
Sbjct: 243 VLRAKRHLEKGGTDG--RDASLEDIAHLLGKTPDEVQDV---LALNEHTTSLDTPFDLDP 297

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN---PV 253
            S   D+L  +H+      +   E +    ++   ++ L+ + R + E RR   N   P 
Sbjct: 298 GSSLLDFLSDEHNAAPDQEVAHRELE---GLMKLWLARLSEKHRYVVE-RRFGLNHIEPA 353

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           TLE L+ E  ++RERVRQI+  A  K++     Q
Sbjct: 354 TLEELAEEMGLTRERVRQIQQEALVKLKRHFASQ 387


>gi|325287834|ref|YP_004263624.1| RpoD subfamily RNA polymerase sigma 70 subunit [Cellulophaga lytica
           DSM 7489]
 gi|324323288|gb|ADY30753.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cellulophaga
           lytica DSM 7489]
          Length = 287

 Score =  114 bits (284), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 83/274 (30%), Positives = 144/274 (52%), Gaps = 25/274 (9%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ +I KI ++   EE  LA++ R  GD +A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQDISKIDLITANEEVELAQKIRA-GDEAALEKLTNANLRFVVSVAKQYQNQGLKL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
            ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++      Q  I+R   L KIG+ 
Sbjct: 77  PDLINEGNVGLVKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVR-LPLNKIGSI 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
              K+ F  L +           + +P     IAK+L +S SEV           S++A 
Sbjct: 136 NKIKKAFSYLEQ----------THERPPSAEEIAKELELSVSEVKQSMKNSGRHVSMDAP 185

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-- 247
               +   S   D + Y   G+     EK   ++    + R++  L+PRE  + +     
Sbjct: 186 FKEGE--DSNLYDVIKY---GESPNPDEKLMHQSLNTEINRALETLSPREADVVKLYYGI 240

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++ +TLE +   F+++RERVRQI  +A +K++
Sbjct: 241 GDKHSMTLEEIGQIFDLTRERVRQIREKAIRKLK 274


>gi|300812189|ref|ZP_07092631.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus PB2003/044-T3-4]
 gi|300496825|gb|EFK31905.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus PB2003/044-T3-4]
          Length = 373

 Score =  114 bits (284), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 85/275 (30%), Positives = 134/275 (48%), Gaps = 33/275 (12%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +Y+  I ++ +L   EE  LAKR  E GD  A   L +++LRLVV IA  Y G G+   +
Sbjct: 106 QYLKRIGRVSLLSGDEEVQLAKRI-EAGDQEAKDELTSANLRLVVSIAKRYVGRGMSFLD 164

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGN+GLM+AV KFD + GF+ +TY+ WWI+ A+   I      ++I    +      
Sbjct: 165 LIQEGNMGLMKAVDKFDYQLGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETIN 222

Query: 138 NLRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLA--GDESLN 187
            L R++  L      + +PE++ A        + + L V++ E +S+   +    D  L 
Sbjct: 223 KLIRIQRQLLQDLGRDPEPEEIAAEMDLPVKKVREVLKVAQ-EPVSLETPIGEEDDSHLG 281

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR- 246
             I   D  S +        H   E +          ++ L   +  L  RE  +   R 
Sbjct: 282 DFIEDKDATSPEQ-------HAASEML----------KDQLAEVLDTLTDREENVLRLRF 324

Query: 247 RLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            L + NP TLE +   F V+RER+RQIEA+A +K+
Sbjct: 325 GLDDGNPRTLEEVGRVFGVTRERIRQIEAKALRKL 359


>gi|257092978|ref|YP_003166619.1| RNA polymerase sigma factor RpoS [Candidatus Accumulibacter
           phosphatis clade IIA str. UW-1]
 gi|257045502|gb|ACV34690.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Candidatus
           Accumulibacter phosphatis clade IIA str. UW-1]
          Length = 319

 Score =  114 bits (284), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 80/274 (29%), Positives = 150/274 (54%), Gaps = 19/274 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++ I   P+L   EE   A+R R  G+  A  +++  +LRLVV IA  Y   G+P+ ++
Sbjct: 52  YLNAIGAKPLLSPAEEVNWARRARA-GEFPARQKMIEHNLRLVVNIAKHYLNRGIPLLDL 110

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL+ A++K+DPERGFR +TY+ WWI+ +++  I+     +++      K +   
Sbjct: 111 IEEGNLGLIHAIEKYDPERGFRFSTYATWWIRQSIERAIMNQSRTIRLPVHV-VKDINLV 169

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR ++ HL++ +   + P+++  +  +       V+++N R+A   SL+A +     + S
Sbjct: 170 LRAIR-HLESASGREICPDRIAHLIDRPVEDVRRVMALNERIA---SLDAPLQV---DPS 222

Query: 199 QWQDWLVYDHDGQEQVLIEKEE--RKNRRNMLTRS-MSVLNPRERRIFEARR--LQENPV 253
           Q    L+ D     + L++ +E  + N    L R+ +  L  + R++ E R       P 
Sbjct: 223 QTVGDLIAD-----ESLLDPDELLQSNELGELLRNWLGQLAGKHRQVLERRYGLGGSEPS 277

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           TLE ++ +  ++RERVRQI+  A   ++  I+++
Sbjct: 278 TLEEIAFDLNLTRERVRQIQIEALDHLRRIIRRR 311


>gi|327480191|gb|AEA83501.1| RNA polymerase sigma factor RpoS [Pseudomonas stutzeri DSM 4166]
          Length = 332

 Score =  114 bits (284), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 85/276 (30%), Positives = 142/276 (51%), Gaps = 25/276 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 64  YLNEIGFSPLLTPEEEVHFA-RLAQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 122

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 123 VEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 181

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKK--------LNVSESEVISMNCRLAGDESLNALI 190
           LR  +   Q + D+   PE++  + +K        L ++E  V S++  L  D     L 
Sbjct: 182 LRAARELTQKL-DHEPSPEEIANLLEKPVGEVKRMLGLNE-RVTSVDVSLGPDTDKTLLD 239

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D   +   + L+ D       L   +  + +R ++ R   +      R  EA     
Sbjct: 240 TLTDDRPTDPCELLLDDDLSNSIDLWLSDLSEKQREVVIRRFGL------RGHEAS---- 289

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              TLE +  E  ++RERVRQI+  A ++++E +++
Sbjct: 290 ---TLEEVGQEIGLTRERVRQIQVEALRRLREILER 322


>gi|239616750|ref|YP_002940072.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Kosmotoga olearia
           TBF 19.5.1]
 gi|239505581|gb|ACR79068.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Kosmotoga olearia
           TBF 19.5.1]
          Length = 405

 Score =  114 bits (284), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 89/279 (31%), Positives = 139/279 (49%), Gaps = 41/279 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L   +E  LA+R ++ GD  A   L+T++LRLVV IA  Y G GL   ++
Sbjct: 131 YLKEIGKIPLLTPSKERELARRAQK-GDKKAREELITANLRLVVSIAKRYIGRGLSFLDL 189

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGNIGL++AV+KFD ++G++ +TY+ WWI+ A+   I      +++      T N+  
Sbjct: 190 IQEGNIGLIKAVEKFDWKKGYKFSTYATWWIRQAITRAIADQARTIRVPVHMVETINKVN 249

Query: 135 LFFNLRRLKGHLQAITDNNL------KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
                  L+ H +  T   L       PE++  I      +  E +S+   ++GDE    
Sbjct: 250 KVIR-EHLQEHGEYPTVEELGKLTGKTPEKIEEIL----AASKETVSLESPISGDE---- 300

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN----RRNMLTRSMSVLNPRERRIFE 244
                    S   D++   HD      IEK E        R  +   +  L+PRE  + +
Sbjct: 301 --------ESTMGDFV---HDES----IEKPEEAAIKMLLREQIDEVLDTLSPREAMVLK 345

Query: 245 ARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R   L     TLE +   F V+RER+RQIE +A +K++
Sbjct: 346 MRYGLLDGKTKTLEEVGQFFNVTRERIRQIEVKALRKLR 384


>gi|220927994|ref|YP_002504903.1| RNA polymerase sigma factor RpoD [Clostridium cellulolyticum H10]
 gi|219998322|gb|ACL74923.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           cellulolyticum H10]
          Length = 359

 Score =  114 bits (284), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 86/265 (32%), Positives = 135/265 (50%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L   EE  LA R  E+GD+ A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 93  YLKEIGKVPLLTADEEIDLAHRM-ENGDIEAKRRLAEANLRLVVSIAKRYVGRGMQFLDL 151

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  RGF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 152 IQEGNLGLIKAVEKFDYRRGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 209

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L        +P++   IAK++ +S  +V  +        SL   I   ++  S
Sbjct: 210 LIRVSRQLLQELGREPQPDE---IAKEIGMSVDKVREIMKISQEPVSLETPIG--EEEDS 264

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++  D              K +   L   +  L PRE ++   R   ++    TLE
Sbjct: 265 HLGDFIPDDDAPAPAEAAAFTLLKEQ---LIDVLDTLTPREEKVLRLRFGLDDGRARTLE 321

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF V+RER+RQIEA+A +K++
Sbjct: 322 EVGKEFNVTRERIRQIEAKALRKLR 346


>gi|90412104|ref|ZP_01220111.1| putative RNA polymerase sigma-38 factor [Photobacterium profundum
           3TCK]
 gi|90327082|gb|EAS43461.1| putative RNA polymerase sigma-38 factor [Photobacterium profundum
           3TCK]
          Length = 334

 Score =  114 bits (284), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 87/272 (31%), Positives = 147/272 (54%), Gaps = 15/272 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD  A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 62  YLGEIGFSPLLTAEEEVLYARRAL-RGDEIARKRMIESNLRLVVKISRRYSNRGLALLDL 120

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 121 VEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 179

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +   Q + D+    E    IA +L   E  V  +N  L  +E ++++ N    +S 
Sbjct: 180 LRTARELAQKL-DHEPTAED---IALQL---EKPVDDVNRMLRLNERVSSVDNPIGGDSE 232

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR---LQENPVTL 255
           +    ++ D  G       +++  + +N +   +  LNP++R +  ARR   L     TL
Sbjct: 233 KALLDIIPDEKGGSPESSTQDD--DIKNSIVHWLQELNPKQREVL-ARRFGLLGYEASTL 289

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E++  E  ++RERVRQI+    +++++ +  Q
Sbjct: 290 EDVGREIGLTRERVRQIQVEGLRRLRDMLTHQ 321


>gi|330959229|gb|EGH59489.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv.
           maculicola str. ES4326]
          Length = 336

 Score =  114 bits (284), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 86/272 (31%), Positives = 146/272 (53%), Gaps = 17/272 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 68  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 126

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 127 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 185

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + ++       ++ +N R++  D SL      SDK  
Sbjct: 186 LRAARELTQKL-DHEPSPEEIANLLERPVGEVKRMLGLNERVSSVDVSLGP---DSDKT- 240

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++       + + +S L  ++R +   R   R  E+  T
Sbjct: 241 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTEKQREVVIRRFGLRGHESS-T 294

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE++  E  ++RERVRQI+    K+++E ++K
Sbjct: 295 LEDVGLEIGLTRERVRQIQVEGLKRLREILEK 326


>gi|313123888|ref|YP_004034147.1| RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           bulgaricus ND02]
 gi|312280451|gb|ADQ61170.1| RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           bulgaricus ND02]
          Length = 373

 Score =  114 bits (284), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 85/275 (30%), Positives = 134/275 (48%), Gaps = 33/275 (12%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +Y+  I ++ +L   EE  LAKR  E GD  A   L +++LRLVV IA  Y G G+   +
Sbjct: 106 QYLKRIGRVSLLSGDEEVQLAKRI-EAGDQEAKDELTSANLRLVVSIAKRYVGRGMSFLD 164

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGN+GLM+AV KFD + GF+ +TY+ WWI+ A+   I      ++I    +      
Sbjct: 165 LIQEGNMGLMKAVDKFDYQLGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETIN 222

Query: 138 NLRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLA--GDESLN 187
            L R++  L      + +PE++ A        + + L V++ E +S+   +    D  L 
Sbjct: 223 KLIRIQRQLLQDLGRDPEPEEIAAEMDLPVKKVREVLKVAQ-EPVSLETPIGEEDDSHLG 281

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR- 246
             I   D  S +        H   E +          ++ L   +  L  RE  +   R 
Sbjct: 282 DFIEDKDATSPEQ-------HAASEML----------KDQLAEVLDTLTDREENVLRLRF 324

Query: 247 RLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            L + NP TLE +   F V+RER+RQIEA+A +K+
Sbjct: 325 GLDDGNPRTLEEVGRVFGVTRERIRQIEAKALRKL 359


>gi|304317433|ref|YP_003852578.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacterium thermosaccharolyticum DSM 571]
 gi|302778935|gb|ADL69494.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacterium thermosaccharolyticum DSM 571]
          Length = 357

 Score =  114 bits (284), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 90/269 (33%), Positives = 144/269 (53%), Gaps = 21/269 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L   EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 91  YLKEIGKIPLLSPDEEIELAKRI-EKGDEEAKKRLTEANLRLVVSIAKRYVGRGMQFLDL 149

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GL++AV+KF+  +GF+ +TY+ WWI+ A+   I      ++I      T N  +
Sbjct: 150 IQEGNLGLLKAVEKFNYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETIN--K 207

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           L    R+L   LQ +  + L PE+   IAK++++S  +V  +  ++A  E ++      +
Sbjct: 208 LIRVSRQL---LQELGRDPL-PEE---IAKEMDMSVDKVREI-MKIA-QEPVSLETPIGE 258

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
           +  S   D++  +              K +   L   +  L PRE ++   R   ++   
Sbjct: 259 EEDSHLGDFIPDEDAPAPAEAAAFTMLKEQ---LIDVLDTLTPREEKVLRLRFGLDDGRA 315

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 316 RTLEEVGKEFNVTRERIRQIEAKALRKLR 344


>gi|188585841|ref|YP_001917386.1| RNA polymerase, sigma 70 subunit, RpoD family [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|179350528|gb|ACB84798.1| RNA polymerase, sigma 70 subunit, RpoD family [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 360

 Score =  114 bits (284), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 85/265 (32%), Positives = 139/265 (52%), Gaps = 15/265 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L   +E  LAK+  E GD  A  +L  ++LRLVV IA  Y G G+   ++
Sbjct: 94  YLKEIGKIPLLSPDDEIELAKKI-EEGDEGAKRKLAEANLRLVVSIAKKYVGRGMLFLDL 152

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 153 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 210

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R+   L         PE+   IA+++++SE +V  +  ++A +  SL   I   D   
Sbjct: 211 LIRVSRQLVQELGREPLPEE---IAEQMDMSEDKVREI-LKIAQEPVSLETPIGEED--D 264

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TL 255
           S   D++    D   +   +    +  +  L   +  L PRE+++   R  L +    TL
Sbjct: 265 SHLGDFI---EDQDAKPPADAAAFELLKGQLEEVLDSLTPREQKVLRLRFGLDDGKTRTL 321

Query: 256 ENLSSEFEVSRERVRQIEARAFKKV 280
           E +   F V+RER+RQIEA+A +K+
Sbjct: 322 EEVGKHFGVTRERIRQIEAKALRKL 346


>gi|88801442|ref|ZP_01116970.1| putative sigma factor A [Polaribacter irgensii 23-P]
 gi|88782100|gb|EAR13277.1| putative sigma factor A [Polaribacter irgensii 23-P]
          Length = 287

 Score =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 84/287 (29%), Positives = 154/287 (53%), Gaps = 31/287 (10%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ ++   EE  LA+  +  GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGKVDLITADEEVELAQLIK-AGDQRALEKLTKANLRFVVSVAKQYQNQGLTL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
            ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++      Q  I+R   L KIG+ 
Sbjct: 77  PDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVR-LPLNKIGSI 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA- 188
               +++  L +           N +P     IAKKL+++ ++V           S++A 
Sbjct: 136 NKINKMYAFLEQ----------ENERPPSAEEIAKKLDMTVNDVKESMKNSGRHVSMDAP 185

Query: 189 LINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           LI   D N        +YD  + G+      K   ++ R  + R++  L PRE  + +  
Sbjct: 186 LIEGEDSN--------LYDVLNSGESPNPDRKLLHESLRIEIDRALETLTPREADVVKLY 237

Query: 247 -RLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
             L E+ P+TLE +   F+++RERVRQI+ +A ++++ + + ++ ++
Sbjct: 238 FGLGEHQPMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKILMT 284


>gi|25900789|emb|CAD57977.1| RNA polymerase sigma factor [Pseudomonas oleovorans]
          Length = 335

 Score =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 85/272 (31%), Positives = 145/272 (53%), Gaps = 17/272 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMSQTRTIRLPFHV-VKELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + +K       ++ +N R++  D SL      SDK  
Sbjct: 185 LRAARELTQKL-DHEPSPEEIATLLEKPVAEVKRMLGLNERVSSVDVSLGP---DSDKT- 239

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++       + + +  L  ++R +   R   R  E+  T
Sbjct: 240 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLGELTDKQREVVVRRFGLRGHESS-T 293

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE++  E  ++RERVRQI+    ++++E ++K
Sbjct: 294 LEDVGLEIGLTRERVRQIQVEGLERLREILEK 325


>gi|332295554|ref|YP_004437477.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermodesulfobium
           narugense DSM 14796]
 gi|332178657|gb|AEE14346.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermodesulfobium
           narugense DSM 14796]
          Length = 356

 Score =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 89/278 (32%), Positives = 145/278 (52%), Gaps = 27/278 (9%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E  + +Y+ EI KIP+L+  EE  LA+R   HGD +A  +L  ++LRLVV IA  Y   G
Sbjct: 84  EDPVRQYLKEIGKIPLLKHSEEKYLAERAF-HGDEAAKKKLAEANLRLVVSIAKKYTKRG 142

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT---- 128
           L   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      
Sbjct: 143 LLFLDLIQEGNMGLLRAVEKFDYRKGYKFSTYATWWIRQAVTRAIADQARTIRIPVHMVE 202

Query: 129 TANQKRLFFNLRRLKGHL-QAITDNNLKPEQVVAIAK--KLNVSESEVISMNCRLAGDES 185
           T N+ +    +R L   L +  TD  +  +  V + K  ++     E IS+   +  DE 
Sbjct: 203 TINKYKK--TVRNLSQQLSRKPTDEEIAEKMEVNVEKIHEIKRISQEPISIETPIGKDED 260

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
            +     +D++ S   + + Y      ++L E          L   +  L PRER +   
Sbjct: 261 SHLGDFIADESISSPMEAVTY------RLLKED---------LEEVIKDLQPRERDVVRL 305

Query: 246 R--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   +  +  TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 306 RFGLVDGHARTLEEVGKEFGVTRERIRQIEAKALRKLR 343


>gi|120434745|ref|YP_860432.1| RNA polymerase sigma-70 factor [Gramella forsetii KT0803]
 gi|117576895|emb|CAL65364.1| RNA polymerase sigma-70 factor [Gramella forsetii KT0803]
          Length = 287

 Score =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 82/287 (28%), Positives = 153/287 (53%), Gaps = 37/287 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ ++   EE  LA+R +  GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGKVDLITADEEVELAQRIK-AGDDRALEKLTKANLRFVVSVAKQYQNQGLTL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
            ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++      Q  I+R   L KIG+ 
Sbjct: 77  PDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVR-LPLNKIGSI 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA- 188
               + F  L +          ++ +P     IAK+L+++ ++V           S++A 
Sbjct: 136 NKINKTFAFLEQ----------SHERPPSAEEIAKELDMTINDVKESMKNSGRHVSMDAP 185

Query: 189 LINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           L+   D N        +YD    G+     ++   ++ R  + R++  L PRE  +    
Sbjct: 186 LVEGEDSN--------LYDVLRSGESPNPDKELLHESLRTEIERALETLTPREADVI--- 234

Query: 247 RL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RL      ++P+TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 235 RLYFGLGDQHPMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|14970557|emb|CAC44359.1| RpoS protein [Erwinia chrysanthemi]
          Length = 332

 Score =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 89/283 (31%), Positives = 147/283 (51%), Gaps = 35/283 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+S+  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVSSRRRMIESNLRLVVKIARRYNNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V    +LN     + S++  L GD S  AL+
Sbjct: 180 RTARELSHKLDHEPSAEEIAERLDKPVDDVNRMLRLN---ERITSVDTPLGGD-SEKALL 235

Query: 191 NSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-- 247
                      D L  + D G E    + + ++N    + + +  LN ++R +  ARR  
Sbjct: 236 -----------DILADEKDNGPEDTTQDNDMKQN----IVKWLFELNAKQREVL-ARRFG 279

Query: 248 -LQENPVTLENLSSEFEVSRERVRQIEAR--AFKKVQESIQKQ 287
            L     TLE++  E  ++RERVRQI+ +    ++++E +Q Q
Sbjct: 280 LLGYEAATLEDVGREIGLTRERVRQIQVQVEGLRRLREILQVQ 322


>gi|167758408|ref|ZP_02430535.1| hypothetical protein CLOSCI_00748 [Clostridium scindens ATCC 35704]
 gi|167664305|gb|EDS08435.1| hypothetical protein CLOSCI_00748 [Clostridium scindens ATCC 35704]
          Length = 371

 Score =  114 bits (284), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 84/273 (30%), Positives = 136/273 (49%), Gaps = 29/273 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  +EE  LAKR  + GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 105 YLKEIGKVPLLTAEEEVDLAKRMAD-GDEEAKKRLAEANLRLVVSIAKRYVGRGMLFLDL 163

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 164 IQEGNLGLIKAVEKFDYHKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 221

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALI 190
           L R+   L         PE++ A        + + L +S+ E +S+   +  +E      
Sbjct: 222 LIRVSRQLLQELGREPTPEEIAAQLDMPVERVREILKISQ-EPVSLETPIGEEE------ 274

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
                  S   D++    D    V  E   +   +  L   +  L  RE+++   R    
Sbjct: 275 ------DSHLGDFI---QDDNVPVPAEAAAQTLLKEQLDEVLDTLTEREQKVLRLRFGMN 325

Query: 251 N--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +    TLE +  EF+V+RER+RQIEA+A +K++
Sbjct: 326 DGRARTLEEVGKEFDVTRERIRQIEAKALRKLR 358


>gi|15613939|ref|NP_242242.1| RNA polymerase sigma factor RpoD [Bacillus halodurans C-125]
 gi|12643264|sp|O66381|RPOD_BACHD RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-43; AltName: Full=Sigma-A
 gi|10173992|dbj|BAB05095.1| RNA polymerase major sigma factor [Bacillus halodurans C-125]
          Length = 372

 Score =  113 bits (283), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 89/275 (32%), Positives = 138/275 (50%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LA R  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 106 YLKEIGRVPLLTAEEEIELATRI-EQGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 164

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 165 IQEGNMGLIKAVEKFDYNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 224

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I K       E +S+   +    D  L 
Sbjct: 225 RVQRQLLQDLGREPSPEEVAEEMDLTPEKVREILK----IAQEPVSLETPIGEEDDSHLG 280

Query: 188 ALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
             I   D+++    D   Y+   +  E VL    +R+   N+L     + + R R     
Sbjct: 281 DFI--EDQDALAPSDAAAYELLKEQLEDVLDTLTDREE--NVLRLRFGLDDGRTR----- 331

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                   TLE +   F V+RER+RQIEA+A +K+
Sbjct: 332 --------TLEEVGKVFGVTRERIRQIEAKALRKL 358


>gi|113868347|ref|YP_726836.1| RNA polymerase sigma factor RpoS [Ralstonia eutropha H16]
 gi|113527123|emb|CAJ93468.1| DNA-directed RNA polymerase sigma subunit (sigma38) [Ralstonia
           eutropha H16]
          Length = 392

 Score =  113 bits (283), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 86/274 (31%), Positives = 141/274 (51%), Gaps = 17/274 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++ I   P+L   EE   +   ++ GD +A   ++  +LRLVV IA GY   G+P+ ++
Sbjct: 123 YLNRISIKPLLSAPEELHFSTLAKD-GDFAARQVMIERNLRLVVSIAKGYLNRGVPLLDL 181

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++    +  R    
Sbjct: 182 IEEGNLGLMHAIEKFDPSRGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRELNQ 239

Query: 139 LRRLKGHLQ-AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN- 196
           + R K HL+   TD   +   +  IA  L  +  EV  +   LA +E   +L    D + 
Sbjct: 240 VLRAKRHLEKGGTDG--RDASLEDIAHLLGKTPDEVQDV---LALNEHTTSLDTPFDLDP 294

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN---PV 253
            S   D+L  +H+      +   E +    ++   ++ L+ + R + E RR   N   P 
Sbjct: 295 GSSLLDFLSDEHNAAPDQEVAHRELE---GLMKLWLARLSEKHRYVVE-RRFGLNHIEPA 350

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           TLE L+ E  ++RERVRQI+  A  K++     Q
Sbjct: 351 TLEELAEEMGLTRERVRQIQQEALVKLKRHFASQ 384


>gi|330504211|ref|YP_004381080.1| RNA polymerase sigma factor RpoS [Pseudomonas mendocina NK-01]
 gi|328918497|gb|AEB59328.1| RNA polymerase sigma factor RpoS [Pseudomonas mendocina NK-01]
          Length = 335

 Score =  113 bits (283), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 87/272 (31%), Positives = 145/272 (53%), Gaps = 17/272 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLTPEEEVHFA-RLAQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+    E++  + +K       ++ +N R++  D SL      SDK  
Sbjct: 185 LRAARELTQKL-DHEPSAEEIANLLEKPVGEVKRMLGLNERVSSVDVSLGP---DSDKT- 239

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++       + + +S L  ++R +   R   R  E+  T
Sbjct: 240 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSDLTDKQREVVVRRFGLRGHES-CT 293

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE +  E  ++RERVRQI+  A K+++E ++K
Sbjct: 294 LEEVGQEIGLTRERVRQIQVEALKRLREILEK 325


>gi|163815580|ref|ZP_02206953.1| hypothetical protein COPEUT_01755 [Coprococcus eutactus ATCC 27759]
 gi|158449217|gb|EDP26212.1| hypothetical protein COPEUT_01755 [Coprococcus eutactus ATCC 27759]
          Length = 399

 Score =  113 bits (283), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 85/269 (31%), Positives = 139/269 (51%), Gaps = 21/269 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ +I K+P+L  +EE  LAKR  E GD +A  +L  S+LRLVV IA  Y G G+   ++
Sbjct: 132 YLKDIGKVPLLSAEEEIELAKRM-EAGDEAAKKKLAESNLRLVVSIAKRYVGRGMLFLDL 190

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 191 IQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKV- 249

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
                R  +  LQ +    L PE+V  +         E++ +       E ++      +
Sbjct: 250 ----TRVSRDLLQKLGREPL-PEEVGEVMGLPKERVQEIMKI-----AQEPVSLETPIGE 299

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
           +  S   D++    D      +E   +      L   +S L  RE+R+ + R   ++  P
Sbjct: 300 EEDSHLGDFI---QDESIPTPVEATNQTLLHEQLDDVVSTLTEREQRVIKLRFGWDDGRP 356

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 357 RTLEEVGKEFNVTRERIRQIEAKALRKLR 385


>gi|254496518|ref|ZP_05109389.1| stationary phase specific sigma factor RpoS [Legionella drancourtii
           LLAP12]
 gi|254354257|gb|EET12921.1| stationary phase specific sigma factor RpoS [Legionella drancourtii
           LLAP12]
          Length = 342

 Score =  113 bits (283), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 81/275 (29%), Positives = 146/275 (53%), Gaps = 23/275 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A    + GD++A  +++ S+LRLVVKI+  Y   GLP+ ++
Sbjct: 75  YLSEIGFSPLLSAEEEVHYATLALK-GDVAARKKMIESNLRLVVKISRRYLNRGLPLLDL 133

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM++V+KFDP RGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 134 IEEGNLGLMKSVEKFDPNRGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 192

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-------DESLNALIN 191
           LR  +   Q + D+   PE++  +  K      +++ +N ++A        DE+ + L  
Sbjct: 193 LRAARQLTQKL-DHEPSPEEIAEMVDKPLEDVQKLLGLNDKVASVDTPIGFDENKSLLDT 251

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
            +D+NS    + L  ++       +  +  +N++ ++ R   +      R FE       
Sbjct: 252 IADENSVNPAELLTNENLRLHIESLLDKLTENQQQVIARRFGL------RGFEK------ 299

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             TLE++  E +++RERVRQI+  A K ++  ++K
Sbjct: 300 -ATLEDVGKEIDLTRERVRQIQVEALKTLRGLLEK 333


>gi|300727119|ref|ZP_07060538.1| RNA polymerase sigma-70 factor [Prevotella bryantii B14]
 gi|299775663|gb|EFI72254.1| RNA polymerase sigma-70 factor [Prevotella bryantii B14]
          Length = 295

 Score =  113 bits (283), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 84/283 (29%), Positives = 148/283 (52%), Gaps = 30/283 (10%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L RY+ EI    ++   EE  LA+R ++ GD  A  RL  ++LR VV +A  Y+  GL 
Sbjct: 25  ALDRYLQEIGHEDLISVDEEVELAQRIKK-GDKRALERLTKANLRFVVSVAKQYQNQGLS 83

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK-----IGTT 129
           + ++++EGN+GL++A KKFD  RGF+  +Y++WWI+ ++ + I     +V+     +G+ 
Sbjct: 84  LPDLINEGNLGLIKAAKKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGSV 143

Query: 130 ANQKRL---FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV-ISMNCRLAGDES 185
               RL   F      +  +  I DN   PE    IA  LNV+   V +    +   D S
Sbjct: 144 NKINRLVNSFEQENERRPSVDEIADNIDLPED--KIADALNVNTHHVSVDAPFQEGEDNS 201

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L  ++ ++D  S+  +  LV++               + R  + R +  LN RER + EA
Sbjct: 202 LLDVLPNTDIPSADSE--LVHE---------------SLREEIARVLETLNQRERNVVEA 244

Query: 246 -RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              + +  +TLE +  ++ ++RERVRQI+ +A ++++ + + +
Sbjct: 245 FFGIGQAEMTLEEIGDKYGLTRERVRQIKEKAIRRLRHNTKNK 287


>gi|289208462|ref|YP_003460528.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thioalkalivibrio
           sp. K90mix]
 gi|288944093|gb|ADC71792.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thioalkalivibrio
           sp. K90mix]
          Length = 359

 Score =  113 bits (283), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 89/274 (32%), Positives = 141/274 (51%), Gaps = 31/274 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ +I   P+L  +EE   A+  R+ GD S   R++  +LRLVVKIA  Y   GLP+ ++
Sbjct: 89  YLRDIEYRPLLTPEEERKYARLARD-GDESGRRRMIECNLRLVVKIARRYLNRGLPLLDL 147

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM AV+KFDPERGFR +TY+ WWI+  ++  ++     ++I    + K L  +
Sbjct: 148 IEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERALMNQGRTIRIPVHVS-KELRMH 206

Query: 139 LRRLKGHLQAITDNNLKPE------QVVAIAKKLNVSESEVISMNCRLA--GDESLNALI 190
            R  +   Q +  +  + E      + VA  +KL        SM+      G+ SL  ++
Sbjct: 207 ARIARNLTQELGRDPTEEELAQRLGKPVADIQKLRAMSEPSTSMDLPPGPDGERSLTDIL 266

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEK---EERKNRRNMLTRSMSVLNPRERRIFEARR 247
             +D N +Q    L+ D D Q   L+++   E    +R +L R   +        FE   
Sbjct: 267 --ADVN-AQEPSSLLEDQDIQH--LVDEWLGELDYKQREVLVRRFGLHG------FER-- 313

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                 TLE + +E  V+RERVRQI+  A K+++
Sbjct: 314 -----STLEQVGAEIGVTRERVRQIQMDALKRLR 342


>gi|77406972|ref|ZP_00783989.1| RNA polymerase sigma-70 factor [Streptococcus agalactiae H36B]
 gi|77174413|gb|EAO77265.1| RNA polymerase sigma-70 factor [Streptococcus agalactiae H36B]
          Length = 369

 Score =  113 bits (283), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 87/269 (32%), Positives = 142/269 (52%), Gaps = 21/269 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E GDL A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLTNEEEKELAVAVAE-GDLMAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 218

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L      +  PEQ   IA++++++  +V  +  ++A +  SL   I   D   
Sbjct: 219 LVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEED--D 272

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 273 SHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 326

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE++   F V+RER+RQIEA+A +K++
Sbjct: 327 RTLEDVGKVFNVTRERIRQIEAKALRKLR 355


>gi|237740231|ref|ZP_04570712.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. 2_1_31]
 gi|229422248|gb|EEO37295.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. 2_1_31]
          Length = 269

 Score =  113 bits (283), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 84/275 (30%), Positives = 144/275 (52%), Gaps = 21/275 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   EE   AKR  E GD  A+ +L+ S+LRLVV IA  +   GL + ++
Sbjct: 2   YLREIGQVPLLTHDEEIEYAKRAYE-GDEEASQKLIESNLRLVVSIAKKHTNRGLKLLDL 60

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM+AV+KF+  +G++ +TY+ WWI+ A+   I      ++I        +   
Sbjct: 61  IQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPV-----HMIET 115

Query: 139 LRRLKG----HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           + ++K     +LQ  T  +  PE    +A++L +   ++ ++        SL   + S +
Sbjct: 116 INKIKKESRIYLQE-TGKDASPE---ILAERLGMEVEKIKAIQEMNQEPISLETPVGSEE 171

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
              S+  D++    D +     E   R   R  L   +  L+PRE ++   R   ++  P
Sbjct: 172 --DSELGDFV---EDQKTTSPYEATNRAILREELDGVLKTLSPREEKVLRYRYGLDDSSP 226

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            TLE +   F V+RER+RQIE +A +K++   +K+
Sbjct: 227 KTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRKK 261


>gi|257453204|ref|ZP_05618503.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. 3_1_5R]
 gi|317059738|ref|ZP_07924223.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. 3_1_5R]
 gi|313685414|gb|EFS22249.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. 3_1_5R]
          Length = 436

 Score =  113 bits (283), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 87/272 (31%), Positives = 147/272 (54%), Gaps = 27/272 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI +IP+L  +EE  LAK+  E GD  A  RL+ ++LRLVV IA  +   GL + ++
Sbjct: 169 YLREIGQIPLLTHKEELELAKKALE-GDEFANKRLIEANLRLVVSIAKKHTNRGLKLLDL 227

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGNIGLM+AV+KF+  +G++ +TY+ WWI+ A+   I      ++I      T N+ +
Sbjct: 228 IQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPVHMIETINKIK 287

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
                +  + +LQ  T  +  PE    +A++L +   +V S+        SL   + S +
Sbjct: 288 -----KEARIYLQE-TGKDATPE---ILAERLGMEVEKVKSIQEMNQDPISLETPVGSEE 338

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNR---RNMLTRSMSVLNPRERRIFEARRLQEN 251
              S+  D++      ++Q ++   E  NR   R  L   +  L+ RE ++   R   ++
Sbjct: 339 --DSELGDFV------EDQKMLTPYELTNRSLLREQLDSVLGSLSSREEKVLRYRYGLDD 390

Query: 252 --PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             P TLE +   F+V+RER+RQIE +A +K++
Sbjct: 391 GSPKTLEEVGKIFKVTRERIRQIEVKALRKLR 422


>gi|304437691|ref|ZP_07397643.1| DNA-directed RNA polymerase sigma subunit SigA [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
 gi|304369324|gb|EFM22997.1| DNA-directed RNA polymerase sigma subunit SigA [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
          Length = 370

 Score =  113 bits (283), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 86/272 (31%), Positives = 137/272 (50%), Gaps = 13/272 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA+R  E GD  A HRL  ++LRLVV IA  Y G G+   ++
Sbjct: 104 YLKEIGHVPLLTAEEEVALAQRM-EAGDEEARHRLEEANLRLVVSIAKRYVGRGMLFLDL 162

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 163 IQEGNLGLLKAVEKFDYSKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 220

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L      + +PE+   IAK++ +S + V  +        SL   I   ++  S
Sbjct: 221 LVRISRQLLQELGRDPRPEE---IAKEMGISVARVHEIMKIAQEPVSLETPIG--EEEDS 275

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++    D       E       R  L   +  L  RE+ +   R   E+    TLE
Sbjct: 276 HLGDFI---EDEAAPAPAEAASFMLLREQLEEVLETLTDREKNVLRLRFGLEDGRSRTLE 332

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +   F V+RER+RQIEA+A +K++   + +V
Sbjct: 333 EVGQSFGVTRERIRQIEAKALRKLRHPSRSKV 364


>gi|89100479|ref|ZP_01173341.1| RNA polymerase sigma factor [Bacillus sp. NRRL B-14911]
 gi|89084822|gb|EAR63961.1| RNA polymerase sigma factor [Bacillus sp. NRRL B-14911]
          Length = 374

 Score =  113 bits (283), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 87/276 (31%), Positives = 137/276 (49%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  QEE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 108 YLKEIGRVDLLSAQEEISLAKRI-EEGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 166

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 167 IQEGNMGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 226

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   D +L P++V  I   L +++ E +S+   +    D  L 
Sbjct: 227 RVQRQLLQDLGREPTPEEIAEDMDLTPDKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 282

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S         +H   E +          +  L   +  L  RE  +   R 
Sbjct: 283 DFIEDQDATSPS-------EHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 325

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 326 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 361


>gi|229825330|ref|ZP_04451399.1| hypothetical protein GCWU000182_00684 [Abiotrophia defectiva ATCC
           49176]
 gi|229790702|gb|EEP26816.1| hypothetical protein GCWU000182_00684 [Abiotrophia defectiva ATCC
           49176]
          Length = 409

 Score =  113 bits (283), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 87/281 (30%), Positives = 138/281 (49%), Gaps = 45/281 (16%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L   EE  LAK+  E GD  A  RL  S+LRLVV IA  Y G GL   ++
Sbjct: 142 YLKEIGNYPLLSMDEEVELAKKIAE-GDQYATDRLTESNLRLVVSIAKKYVGRGLSFLDL 200

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV KFD  +G++ +TY+ WWI+ A+   I            A+Q R    
Sbjct: 201 IQEGNLGLIKAVDKFDYSKGYKFSTYATWWIRQAITRSI------------ADQSRTI-- 246

Query: 139 LRRLKGHLQAITDNNLKPEQVV-----------AIAKKLNVSESEVISMNCRLAGDESLN 187
             R+  H+  + +   +  + +            IAK++N+   +V  +    A   SL+
Sbjct: 247 --RIPVHMSEVINKAYRISRSLLQELGREPTEEEIAKEMNLPVEKVREIMKISADPISLD 304

Query: 188 ALINSSDKNSSQWQDWLVYD-----HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             I   D   S   D++  D      D     +++        + + + ++ L+ RE+R+
Sbjct: 305 TPIGEED--DSHLGDFIKDDTIMGPEDAAAYTMLQ--------DQIQKLLTTLSEREQRV 354

Query: 243 FEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              R   L     TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 355 LILRFGLLDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLR 395


>gi|160935059|ref|ZP_02082445.1| hypothetical protein CLOLEP_03935 [Clostridium leptum DSM 753]
 gi|156866512|gb|EDO59884.1| hypothetical protein CLOLEP_03935 [Clostridium leptum DSM 753]
          Length = 365

 Score =  113 bits (283), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 84/272 (30%), Positives = 136/272 (50%), Gaps = 27/272 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LA R  E GD SA  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 99  YLKEIGRVPLLSPEEEIDLAIRISE-GDESAKKRLSEANLRLVVSIAKRYLGRGMQFLDL 157

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-K 133
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N+ K
Sbjct: 158 IQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKVK 217

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES--LNALIN 191
           ++   L    GH     +  L+ +  V   +++     E +S+   +  +E   L   I 
Sbjct: 218 KVSSQLLHTNGHEPTADEIALELDMPVDKVREIMRVAQEPVSLETPIGEEEDSHLGDFIP 277

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             D  +                +L+        +  L   +  L PRE ++   R   E+
Sbjct: 278 DDDAPAPADA---------ASHILL--------KEQLAEVLDTLTPREEKVLRLRFGLED 320

Query: 252 --PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
               TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 321 GRSRTLEEVGKEFNVTRERIRQIEAKALRKLR 352


>gi|257470234|ref|ZP_05634325.1| RpoD family RNA polymerase sigma factor [Fusobacterium ulcerans
           ATCC 49185]
 gi|317064448|ref|ZP_07928933.1| RNA polymerase sigma-A factor [Fusobacterium ulcerans ATCC 49185]
 gi|313690124|gb|EFS26959.1| RNA polymerase sigma-A factor [Fusobacterium ulcerans ATCC 49185]
          Length = 260

 Score =  113 bits (283), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 75/273 (27%), Positives = 146/273 (53%), Gaps = 16/273 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + +S YI +I + P+L  +EE  ++ + +  GD  A  +LVTS+LRLV+ IA  Y   G+
Sbjct: 2   LDISEYIKDISRYPLLTPEEEKDISIKAK-AGDKDAQEKLVTSNLRLVISIARKYTNMGI 60

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGN+GL++AV+K++PE+  R +TYS +WIK ++  YI  S  L++  +     
Sbjct: 61  PLLDLIQEGNMGLIRAVEKYEPEKNIRFSTYSTFWIKQSILRYITSSRGLIRFPSY---- 116

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            ++  + R+K ++Q   + N     +  I   L++ + E       L   E  + + N  
Sbjct: 117 -VYDGISRMKKYVQDYKNKNSHLPSIEEICSSLDMRKKEAERYIEVL---EKGSCIGNEM 172

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQEN 251
               +++   +++D   +++V+      KN    L + ++ L  +ER +   R   L E 
Sbjct: 173 YGEIAEYCSSIIFDDTFEDKVI-----AKNSTIDLMKKVNKLPSKEREVLIYRYGLLDEK 227

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +TL  +     +++ER+RQI+  A  K++ ++
Sbjct: 228 VLTLGEIGERMNLTKERIRQIQLEAIDKLRGTL 260


>gi|1514627|emb|CAA62840.1| starvation sigma factor [Pseudomonas putida]
          Length = 335

 Score =  113 bits (283), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 87/279 (31%), Positives = 146/279 (52%), Gaps = 17/279 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A    + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFAPLV-QKGDPAGRKRMMQSNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + +K       ++ +N R++  D SL      SDK  
Sbjct: 185 LRAARELTQKL-DHEPSPEEIATLLEKPVAEVKRMLGLNERVSSVDVSLGP---DSDKT- 239

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++       + + +  L  ++R +   R   R  E+  T
Sbjct: 240 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLGELTDKQREVVVRRFGLRGHESS-T 293

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           LE++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 294 LEDVGLEIGLTRERVRQIQVEGLKRLREILEKNGHTSES 332


>gi|294507979|ref|YP_003572037.1| RNA polymerase sigma-70 factor [Salinibacter ruber M8]
 gi|294344307|emb|CBH25085.1| RNA polymerase sigma-70 factor [Salinibacter ruber M8]
          Length = 279

 Score =  113 bits (283), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 92/285 (32%), Positives = 155/285 (54%), Gaps = 35/285 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI KI +LE +EE  LA+R  E GD  A H+L  ++LR VV +A  Y+G GL +
Sbjct: 10  LDQYLQEIGKIDLLEPEEEVELARRI-EDGDEEALHKLCRANLRFVVSVAKKYQGQGLSL 68

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV-----KIGTTA 130
           +++++EGN GL++A K+FD  RGF+  +Y++WWI+ A+ + +     +V     +IGT +
Sbjct: 69  ADLINEGNYGLIKAAKRFDETRGFKFISYAVWWIRQAILQALAEQSRVVRLPLNRIGTIS 128

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES--EVISMNCRLAGDESLNA 188
                   +R+    LQ   D + KP       +     +   E +    R     S++A
Sbjct: 129 -------KIRKASARLQ--QDLDRKPNIEELAEELEIDVQKVREAMKHTSRHL---SMDA 176

Query: 189 LINSSDKNSSQWQDWLV-YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             N  D NS    D L   D+D  ++ ++ +  + +    + R++S L+ RE  I    R
Sbjct: 177 PFNEEDDNS--LLDVLPDEDNDSPDEEMLSESVKID----IERALSALHDREAEIT---R 227

Query: 248 L-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L     +E+P+TLE +   F+++RERVRQI+ +A +K+++   KQ
Sbjct: 228 LYFGIGREHPLTLEEIGKRFDLTRERVRQIKEKALRKLRQRHSKQ 272


>gi|326803636|ref|YP_004321454.1| RNA polymerase sigma factor RpoD [Aerococcus urinae
           ACS-120-V-Col10a]
 gi|326651510|gb|AEA01693.1| RNA polymerase sigma factor RpoD [Aerococcus urinae
           ACS-120-V-Col10a]
          Length = 401

 Score =  113 bits (283), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 90/276 (32%), Positives = 137/276 (49%), Gaps = 37/276 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LAKR  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 134 YLKEIGRVDLLTADEEVALAKRI-EAGDPVAKQELAEANLRLVVSIAKRYVGRGMSFLDL 192

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 193 IQEGNMGLMKAVEKFDYTKGFKFSTYATWWIRQAITRSIADQARTIRIPVHMVETINKLV 252

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             Q++L   L R     +   + +L  E+V  I K   +S+  V           SL   
Sbjct: 253 RIQRQLLQELGREPTPEEIGAEMDLPTEKVRNIMK---ISQEPV-----------SLETP 298

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR---RNMLTRSMSVLNPRERRIFEAR 246
           I   D   S   D+ + D+D      ++ +E  N+   +  L   +  L  RE  +   R
Sbjct: 299 IGEED--DSHLGDF-IEDNDA-----MQPDEYTNQELLKEQLNEVLDTLTDREENVLRLR 350

Query: 247 RLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
              E+    TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 351 FGLEDGQTKTLEQVGQQFGVTRERIRQIEAKALRKL 386


>gi|291543225|emb|CBL16334.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Ruminococcus sp. 18P13]
          Length = 360

 Score =  113 bits (283), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 89/275 (32%), Positives = 142/275 (51%), Gaps = 33/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LA+R  + GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 94  YLKEIGRVPLLSAEEEIELAQRMSK-GDSYAKKRLSEANLRLVVSIAKKYVGRGMQFLDL 152

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG-----TTANQK 133
           + EGN+GL++AV KFD  +GF+ +TY+ WWI+ A+   I      ++I      T    K
Sbjct: 153 IQEGNLGLIKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETITKVK 212

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINS 192
           ++   L    GH +   D          IA++L +   +V  +  R+A D  SL   I  
Sbjct: 213 KIISQLLHETGH-EPTADE---------IAERLEMPVEKVREI-MRIAQDPVSLETPIG- 260

Query: 193 SDKNSSQWQDWL----VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            ++  S   D++             +++ KE+       L   +S L  RE ++ + R  
Sbjct: 261 -EEEDSHLGDFIPDDDAPAPAEAASLILLKEQ-------LNEVLSTLTEREAKVLKLRFG 312

Query: 249 QEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            E+    TLE +  EFEV+RER+RQIEA+A +K++
Sbjct: 313 LEDGRSRTLEEVGREFEVTRERIRQIEAKALRKLR 347


>gi|22537572|ref|NP_688423.1| RNA polymerase sigma factor RpoD [Streptococcus agalactiae 2603V/R]
 gi|25011538|ref|NP_735933.1| RNA polymerase sigma factor RpoD [Streptococcus agalactiae NEM316]
 gi|76788342|ref|YP_330069.1| RNA polymerase sigma factor RpoD [Streptococcus agalactiae A909]
 gi|77409561|ref|ZP_00786243.1| RNA polymerase sigma-70 factor [Streptococcus agalactiae COH1]
 gi|77412516|ref|ZP_00788814.1| RNA polymerase sigma-70 factor [Streptococcus agalactiae CJB111]
 gi|77414847|ref|ZP_00790961.1| RNA polymerase sigma-70 factor [Streptococcus agalactiae 515]
 gi|22534455|gb|AAN00296.1|AE014257_3 RNA polymerase sigma-70 factor [Streptococcus agalactiae 2603V/R]
 gi|24413077|emb|CAD47155.1| RNA polymerase major sigma factor RpoD [Streptococcus agalactiae
           NEM316]
 gi|76563399|gb|ABA45983.1| RNA polymerase sigma factor RpoD [Streptococcus agalactiae A909]
 gi|77159097|gb|EAO70294.1| RNA polymerase sigma-70 factor [Streptococcus agalactiae 515]
 gi|77161430|gb|EAO72443.1| RNA polymerase sigma-70 factor [Streptococcus agalactiae CJB111]
 gi|77171826|gb|EAO75013.1| RNA polymerase sigma-70 factor [Streptococcus agalactiae COH1]
          Length = 369

 Score =  113 bits (283), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 87/269 (32%), Positives = 142/269 (52%), Gaps = 21/269 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E GDL A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLTNEEEKELAVAVAE-GDLMAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 218

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L      +  PEQ   IA++++++  +V  +  ++A +  SL   I   D   
Sbjct: 219 LVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEED--D 272

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 273 SHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 326

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE++   F V+RER+RQIEA+A +K++
Sbjct: 327 RTLEDVGKVFNVTRERIRQIEAKALRKLR 355


>gi|309800318|ref|ZP_07694490.1| RNA polymerase sigma factor RpoD [Streptococcus infantis SK1302]
 gi|308116065|gb|EFO53569.1| RNA polymerase sigma factor RpoD [Streptococcus infantis SK1302]
          Length = 369

 Score =  113 bits (283), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 86/270 (31%), Positives = 143/270 (52%), Gaps = 21/270 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E GD+ A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLTNEEEKELALAV-EAGDIEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 218

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L      +  PEQ   IA++++++  +V  +  ++A +  SL   I   D   
Sbjct: 219 LVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEED--D 272

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 273 SHLGDFI------EDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 326

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKVQE 282
            TLE++   F V+RER+RQIEA+A +K+++
Sbjct: 327 RTLEDVGKVFNVTRERIRQIEAKALRKLRQ 356


>gi|313888947|ref|ZP_07822607.1| RNA polymerase sigma factor RpoD [Peptoniphilus harei
           ACS-146-V-Sch2b]
 gi|312845120|gb|EFR32521.1| RNA polymerase sigma factor RpoD [Peptoniphilus harei
           ACS-146-V-Sch2b]
          Length = 362

 Score =  113 bits (282), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 88/276 (31%), Positives = 136/276 (49%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KI +L  +EE  +AKR  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 96  YLKEIGKISLLTAEEEVEIAKRM-EEGDELAKKELAEANLRLVVSIAKRYVGRGMSFLDL 154

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 155 IQEGNLGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLV 214

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES--LN 187
             Q++L  +L R     +   + NL  E+V  I K       E +S+   +  +E   L 
Sbjct: 215 RVQRQLVQDLGRDPLPEEIAAEMNLDVERVREIQK----IAQEPVSLETPIGEEEDSHLG 270

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I           D ++   D     L+        +  L   +  L  RE+++   R 
Sbjct: 271 DFIPD---------DEILSPQDAATFTLL--------KEQLNTVLETLTDREKKVLTLRF 313

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +  EF+V+RER+RQIEA+A +K++
Sbjct: 314 GLDDGRARTLEEVGKEFDVTRERIRQIEAKALRKLR 349


>gi|257464031|ref|ZP_05628416.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. D12]
          Length = 436

 Score =  113 bits (282), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 87/272 (31%), Positives = 147/272 (54%), Gaps = 27/272 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI +IP+L  +EE  LAK+  E GD  A  RL+ ++LRLVV IA  +   GL + ++
Sbjct: 169 YLREIGQIPLLTHKEELELAKKALE-GDEFANKRLIEANLRLVVSIAKKHTNRGLKLLDL 227

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGNIGLM+AV+KF+  +G++ +TY+ WWI+ A+   I      ++I      T N+ +
Sbjct: 228 IQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPVHMIETINKIK 287

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
                +  + +LQ  T  +  PE    +A++L +   +V S+        SL   + S +
Sbjct: 288 -----KEARIYLQE-TGKDATPE---ILAERLGMEVEKVKSIQEMNQDPISLETPVGSEE 338

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNR---RNMLTRSMSVLNPRERRIFEARRLQEN 251
              S+  D++      ++Q ++   E  NR   R  L   +  L+ RE ++   R   ++
Sbjct: 339 --DSELGDFV------EDQKMLTPYELTNRSLLREQLDSVLGSLSSREEKVLRYRYGLDD 390

Query: 252 --PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             P TLE +   F+V+RER+RQIE +A +K++
Sbjct: 391 GSPKTLEEVGKIFKVTRERIRQIEVKALRKLR 422


>gi|148469868|gb|ABQ65863.1| stationary sigma factor [Pseudomonas fluorescens]
          Length = 335

 Score =  113 bits (282), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 86/272 (31%), Positives = 145/272 (53%), Gaps = 17/272 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPE GFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPEHGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + +K       ++ +N R++  D SL      SDK  
Sbjct: 185 LRAARELTQKL-DHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSLGP---DSDKT- 239

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++       + + +S L  ++R +   R   R  E+  T
Sbjct: 240 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTDKQREVVIRRFGLRGHESS-T 293

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE++  E  ++RERVRQI+    K+++E ++K
Sbjct: 294 LEDVGLEIGLTRERVRQIQVEGLKRLREILEK 325


>gi|323704675|ref|ZP_08116253.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
 gi|323536137|gb|EGB25910.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
          Length = 357

 Score =  113 bits (282), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 90/269 (33%), Positives = 144/269 (53%), Gaps = 21/269 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L   EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 91  YLKEIGKIPLLSPDEEIELAKRI-EKGDEEAKKRLTEANLRLVVSIAKRYVGRGMLFLDL 149

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GL++AV+KF+  +GF+ +TY+ WWI+ A+   I      ++I      T N  +
Sbjct: 150 IQEGNLGLLKAVEKFNYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETIN--K 207

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           L    R+L   LQ +  + L PE+   IAK++++S  +V  +  ++A  E ++      +
Sbjct: 208 LIRVSRQL---LQELGRDPL-PEE---IAKEMDMSVDKVREI-MKIA-QEPVSLETPIGE 258

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
           +  S   D++  +              K +   L   +  L PRE ++   R   ++   
Sbjct: 259 EEDSHLGDFIPDEDAPAPAEAAAFTMLKEQ---LIDVLDTLTPREEKVLRLRFGLDDGRA 315

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 316 RTLEEVGKEFNVTRERIRQIEAKALRKLR 344


>gi|257467207|ref|ZP_05631518.1| RNA polymerase sigma factor rpoD [Fusobacterium gonidiaformans ATCC
           25563]
 gi|315918337|ref|ZP_07914577.1| RNA polymerase sigma factor rpoD [Fusobacterium gonidiaformans ATCC
           25563]
 gi|313692212|gb|EFS29047.1| RNA polymerase sigma factor rpoD [Fusobacterium gonidiaformans ATCC
           25563]
          Length = 352

 Score =  113 bits (282), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 87/272 (31%), Positives = 147/272 (54%), Gaps = 27/272 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI +IP+L  +EE  LAK+  E GD  A  RL+ ++LRLVV IA  +   GL + ++
Sbjct: 85  YLREIGQIPLLTHKEELELAKKALE-GDEFANKRLIEANLRLVVSIAKKHTNRGLKLLDL 143

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGNIGLM+AV+KF+  +G++ +TY+ WWI+ A+   I      ++I      T N+ +
Sbjct: 144 IQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPVHMIETINKIK 203

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
                +  + +LQ  T  +  PE    +A++L +   +V S+        SL   + S +
Sbjct: 204 -----KEARIYLQE-TGKDATPE---ILAERLGMEVEKVKSIQEMNQDPISLETPVGSEE 254

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNR---RNMLTRSMSVLNPRERRIFEARRLQEN 251
              S+  D++      ++Q ++   E  NR   R  L   +  L+ RE ++   R   ++
Sbjct: 255 --DSELGDFV------EDQKMLTPYELTNRSLLREQLDSVLGSLSSREEKVLRYRYGLDD 306

Query: 252 --PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             P TLE +   F+V+RER+RQIE +A +K++
Sbjct: 307 GSPKTLEEVGKIFKVTRERIRQIEVKALRKLR 338


>gi|307705133|ref|ZP_07642010.1| RNA polymerase sigma factor rpoD [Streptococcus mitis SK597]
 gi|307621329|gb|EFO00389.1| RNA polymerase sigma factor rpoD [Streptococcus mitis SK597]
          Length = 369

 Score =  113 bits (282), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 86/270 (31%), Positives = 143/270 (52%), Gaps = 21/270 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E GD+ A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLTNEEEKELALAV-EAGDIEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 218

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L      +  PEQ   IA++++++  +V  +  ++A +  SL   I   D   
Sbjct: 219 LVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEED--D 272

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 273 SHLGDFI------EDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 326

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKVQE 282
            TLE++   F V+RER+RQIEA+A +K+++
Sbjct: 327 RTLEDVGKVFNVTRERIRQIEAKALRKLRQ 356


>gi|74316856|ref|YP_314596.1| RNA polymerase sigma factor RpoS [Thiobacillus denitrificans ATCC
           25259]
 gi|74056351|gb|AAZ96791.1| RNA polymerase sigma-70 factor [Thiobacillus denitrificans ATCC
           25259]
          Length = 316

 Score =  113 bits (282), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 84/258 (32%), Positives = 138/258 (53%), Gaps = 15/258 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI + P+L   EE  LA+R    GD  A   ++  +LRLVV IA  Y   GL + ++
Sbjct: 49  YLNEIGQAPLLTAAEEVALARRTV-LGDFEARQTMIERNLRLVVNIAKHYANRGLTLLDL 107

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL+ A++KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 108 VEEGNLGLIHALEKFDPERGFRFSTYATWWIRQNIERAIMNQSRTIRLPVHI-IKELNIY 166

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  + HL+     +   + + A+          ++ +N R+A   SL+A ++     S 
Sbjct: 167 LRAQR-HLETHGVTDATSDDIAALTGHPVADVRRIMQLNERIA---SLDAPLDVDPTLS- 221

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN---PVTL 255
              + +  D+      +++ EE +N    +   ++ LN ++R + E RR   N     TL
Sbjct: 222 -LGEAIADDNAHLPDEMLQLEEIENH---VQEWLTQLNDKQRWVIE-RRFGLNGCEACTL 276

Query: 256 ENLSSEFEVSRERVRQIE 273
           E+L+ E EV+RERVRQI+
Sbjct: 277 EDLALELEVTRERVRQIQ 294


>gi|283769573|ref|ZP_06342469.1| RNA polymerase sigma factor RpoD [Bulleidia extructa W1219]
 gi|283103841|gb|EFC05227.1| RNA polymerase sigma factor RpoD [Bulleidia extructa W1219]
          Length = 413

 Score =  113 bits (282), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 84/270 (31%), Positives = 139/270 (51%), Gaps = 22/270 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L+  EE  +AK+  E GD  A + L++S+LRLVV IA  Y G G+   ++
Sbjct: 145 YLKEIGRVPLLKASEEIEIAKKI-EQGDEEARNVLISSNLRLVVSIAKKYVGRGMQFLDL 203

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 204 IQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 261

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDK-- 195
           L R++  L         PE++ A  + ++  +   I    ++A D  SL   I   D   
Sbjct: 262 LTRVERSLVQELSREPTPEEISACLEGISADKVREIK---KIALDPVSLETPIGEEDDSH 318

Query: 196 --NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQEN 251
             +  + +D L  D     Q+L         ++ +   +S L  RE ++   R       
Sbjct: 319 LGDFIEDKDALSPDQYASNQLL---------KDEINDVLSGLTEREEKVLRLRFGLYDGR 369

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 370 TRTLEEVGREFNVTRERIRQIEAKALRKLK 399


>gi|83815083|ref|YP_446059.1| RNA polymerase sigma-70 factor [Salinibacter ruber DSM 13855]
 gi|83756477|gb|ABC44590.1| RNA polymerase sigma-70 factor [Salinibacter ruber DSM 13855]
          Length = 313

 Score =  113 bits (282), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 94/286 (32%), Positives = 156/286 (54%), Gaps = 37/286 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI KI +LE +EE  LA+R  E GD  A H+L  ++LR VV +A  Y+G GL +
Sbjct: 44  LDQYLQEIGKIDLLEPEEEVELARRI-EDGDEEALHKLCRANLRFVVSVAKKYQGQGLSL 102

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
           +++++EGN GL++A K+FD  RGF+  +Y++WWI+ A+      Q  ++R   L +IGT 
Sbjct: 103 ADLINEGNYGLIKAAKRFDETRGFKFISYAVWWIRQAILQALAEQSRVVR-LPLNRIGTI 161

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES--EVISMNCRLAGDESLN 187
           +        +R+    LQ   D + KP       +     +   E +    R     S++
Sbjct: 162 S-------KIRKASARLQ--QDLDRKPNIEELAEELEIDVQKVREAMKHTSRHL---SMD 209

Query: 188 ALINSSDKNSSQWQDWLV-YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           A  N  D NS    D L   D+D  ++ ++ +  + +    + R++S L+ RE  I    
Sbjct: 210 APFNEEDDNS--LLDVLPDEDNDSPDEEMLSESVKID----IERALSALHDREAEIT--- 260

Query: 247 RL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           RL     +E+P+TLE +   F+++RERVRQI+ +A +K+++   KQ
Sbjct: 261 RLYFGIGREHPLTLEEIGKRFDLTRERVRQIKEKALRKLRQRHSKQ 306


>gi|295132793|ref|YP_003583469.1| RNA polymerase sigma-70 factor [Zunongwangia profunda SM-A87]
 gi|294980808|gb|ADF51273.1| RNA polymerase sigma-70 factor [Zunongwangia profunda SM-A87]
          Length = 287

 Score =  113 bits (282), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 82/287 (28%), Positives = 152/287 (52%), Gaps = 37/287 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ ++   EE  LA+R +  GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGKVDLITADEEVELAQRIK-AGDNRALEKLTKANLRFVVSVAKQYQNQGLTL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
            ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++      Q  I+R   L KIG+ 
Sbjct: 77  PDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVR-LPLNKIGSI 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA- 188
               + F  L +          ++ +P     IAK+L+++ ++V           S++A 
Sbjct: 136 NKINKTFAFLEQ----------SHERPPSAEEIAKELDMTINDVKESMKNSGRHVSMDAP 185

Query: 189 LINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           L+   D N        +YD    G+     +    ++ R  + R++  L PRE  +    
Sbjct: 186 LVEGEDSN--------LYDVLRSGESPNPDKDLLHESLRTEIERALETLTPREADVI--- 234

Query: 247 RL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RL      ++P+TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 235 RLYFGLGDQHPMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|307706485|ref|ZP_07643293.1| RNA polymerase sigma factor rpoD [Streptococcus mitis SK321]
 gi|307708623|ref|ZP_07645087.1| RNA polymerase sigma factor RpoD [Streptococcus mitis NCTC 12261]
 gi|307615372|gb|EFN94581.1| RNA polymerase sigma factor RpoD [Streptococcus mitis NCTC 12261]
 gi|307618125|gb|EFN97284.1| RNA polymerase sigma factor rpoD [Streptococcus mitis SK321]
          Length = 369

 Score =  113 bits (282), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 88/274 (32%), Positives = 146/274 (53%), Gaps = 29/274 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E GD+ A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLTNEEEKELALAV-EAGDIEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKL- 219

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSS 193
               +R  +  LQ +   +  PEQ   IA++++++  +V  +  ++A +  SL   I   
Sbjct: 220 ----VREQRNLLQELG-QDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEE 270

Query: 194 DKNSSQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQ 249
           D   S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L 
Sbjct: 271 D--DSHLGDFI------EDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLRFGLD 322

Query: 250 ENPV-TLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +  + TLE++   F V+RER+RQIEA+A +K+++
Sbjct: 323 DGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRQ 356


>gi|270292885|ref|ZP_06199096.1| RNA polymerase sigma-70 factor [Streptococcus sp. M143]
 gi|306825379|ref|ZP_07458719.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus sp.
           oral taxon 071 str. 73H25AP]
 gi|315613017|ref|ZP_07887928.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis ATCC 49296]
 gi|322374450|ref|ZP_08048964.1| RNA polymerase sigma-70 factor [Streptococcus sp. C300]
 gi|331266528|ref|YP_004326158.1| RNA polymerase sigma factor RpoD (sigma-70 factor, Sigma-A)
           [Streptococcus oralis Uo5]
 gi|270278864|gb|EFA24710.1| RNA polymerase sigma-70 factor [Streptococcus sp. M143]
 gi|304432317|gb|EFM35293.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus sp.
           oral taxon 071 str. 73H25AP]
 gi|315315127|gb|EFU63168.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis ATCC 49296]
 gi|321279950|gb|EFX56989.1| RNA polymerase sigma-70 factor [Streptococcus sp. C300]
 gi|326683200|emb|CBZ00818.1| RNA polymerase sigma factor RpoD (sigma-70 factor, Sigma-A)
           [Streptococcus oralis Uo5]
          Length = 369

 Score =  113 bits (282), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 88/274 (32%), Positives = 146/274 (53%), Gaps = 29/274 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E GD+ A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLTNEEEKELALAV-EAGDIEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKL- 219

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSS 193
               +R  +  LQ +   +  PEQ   IA++++++  +V  +  ++A +  SL   I   
Sbjct: 220 ----VREQRNLLQELG-QDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEE 270

Query: 194 DKNSSQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQ 249
           D   S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L 
Sbjct: 271 D--DSHLGDFI------EDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLRFGLD 322

Query: 250 ENPV-TLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +  + TLE++   F V+RER+RQIEA+A +K+++
Sbjct: 323 DGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRQ 356


>gi|225570457|ref|ZP_03779482.1| hypothetical protein CLOHYLEM_06558 [Clostridium hylemonae DSM
           15053]
 gi|225160654|gb|EEG73273.1| hypothetical protein CLOHYLEM_06558 [Clostridium hylemonae DSM
           15053]
          Length = 370

 Score =  113 bits (282), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 84/273 (30%), Positives = 135/273 (49%), Gaps = 29/273 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L   EE  LAKR  + GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 104 YLKEIGKVPLLTADEEVDLAKRMAD-GDEEAKKRLAEANLRLVVSIAKRYVGRGMLFLDL 162

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 163 IQEGNLGLIKAVEKFDYHKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 220

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALI 190
           L R+   L         PE++ A        + + L +S+ E +S+   +  +E      
Sbjct: 221 LIRVSRQLLQELGREPTPEEIAAELDMPVERVREILKISQ-EPVSLETPIGEEE------ 273

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
                  S   D++    D    V  E   +   +  L   +  L  RE+++   R    
Sbjct: 274 ------DSHLGDFI---QDDNVPVPAEAAAQTLLKEQLDEVLDTLTEREQKVLRLRFGMN 324

Query: 251 N--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +    TLE +  EF+V+RER+RQIEA+A +K++
Sbjct: 325 DGRARTLEEVGKEFDVTRERIRQIEAKALRKLR 357


>gi|255535549|ref|YP_003095920.1| RNA polymerase sigma factor RpoD [Flavobacteriaceae bacterium
           3519-10]
 gi|255341745|gb|ACU07858.1| RNA polymerase sigma factor RpoD [Flavobacteriaceae bacterium
           3519-10]
          Length = 294

 Score =  113 bits (282), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 80/290 (27%), Positives = 154/290 (53%), Gaps = 43/290 (14%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ ++   EE  LA++ R  GD  A  +L+ ++LR VV ++  Y+  GL +
Sbjct: 24  LDKYLQEIGKVDLITADEEVDLAQKIR-AGDRVALEKLIKANLRFVVSVSKQYQNQGLSL 82

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GLM+A K++D  RGF+  +Y++WWI+ ++ + +     +V++    N+   
Sbjct: 83  PDLINEGNLGLMKAAKRYDETRGFKFISYAVWWIRQSILQALAEQSRIVRL--PLNKIGS 140

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRL--AGD 183
              + +   HL+   +    PE+   +A+ L++SE ++          +SM+  L    D
Sbjct: 141 INKINKAYAHLEQENERPPSPEE---LAEVLDMSEDDIKESMKNSGRHLSMDAPLVEGED 197

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            +L  ++ S +  S   +  L       E + IE E          R++  L PRE  + 
Sbjct: 198 SNLYDVLRSGESPSPDKELML-------ESLQIEIE----------RALQTLTPREADLV 240

Query: 244 EARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
              RL      ++P+TLE +   F+++RERVRQI+ +A K+++ + + ++
Sbjct: 241 ---RLYFGLNGKHPMTLEEIGETFDLTRERVRQIKEKAIKRLKHNTRSKI 287


>gi|319745370|gb|EFV97681.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           agalactiae ATCC 13813]
          Length = 380

 Score =  113 bits (282), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 87/269 (32%), Positives = 142/269 (52%), Gaps = 21/269 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E GDL A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 113 YLKEIGVVPLLTNEEEKELAVAVAE-GDLMAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 171

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 172 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 229

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L      +  PEQ   IA++++++  +V  +  ++A +  SL   I   D   
Sbjct: 230 LVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEED--D 283

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 284 SHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 337

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE++   F V+RER+RQIEA+A +K++
Sbjct: 338 RTLEDVGKVFNVTRERIRQIEAKALRKLR 366


>gi|293365255|ref|ZP_06611972.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           oralis ATCC 35037]
 gi|306829363|ref|ZP_07462553.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus mitis
           ATCC 6249]
 gi|291316705|gb|EFE57141.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           oralis ATCC 35037]
 gi|304428449|gb|EFM31539.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus mitis
           ATCC 6249]
          Length = 369

 Score =  113 bits (282), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 88/274 (32%), Positives = 146/274 (53%), Gaps = 29/274 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E GD+ A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLTNEEEKELALAV-EAGDIEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKL- 219

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSS 193
               +R  +  LQ +   +  PEQ   IA++++++  +V  +  ++A +  SL   I   
Sbjct: 220 ----VREQRNLLQELG-QDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEE 270

Query: 194 DKNSSQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQ 249
           D   S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L 
Sbjct: 271 D--DSHLGDFI------EDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLRFGLD 322

Query: 250 ENPV-TLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +  + TLE++   F V+RER+RQIEA+A +K+++
Sbjct: 323 DGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRQ 356


>gi|227536516|ref|ZP_03966565.1| RNA polymerase sigma-70 factor [Sphingobacterium spiritivorum ATCC
           33300]
 gi|300773589|ref|ZP_07083458.1| DNA-directed RNA polymerase sigma subunit RpoD [Sphingobacterium
           spiritivorum ATCC 33861]
 gi|227243593|gb|EEI93608.1| RNA polymerase sigma-70 factor [Sphingobacterium spiritivorum ATCC
           33300]
 gi|300759760|gb|EFK56587.1| DNA-directed RNA polymerase sigma subunit RpoD [Sphingobacterium
           spiritivorum ATCC 33861]
          Length = 286

 Score =  113 bits (282), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 79/276 (28%), Positives = 151/276 (54%), Gaps = 16/276 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+HEI K+ ++  +EE +LA+R RE GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLHEIGKVDLITAEEEVILAQRIRE-GDQVALEKLTKTNLRFVVSVAKQYQNQGLTL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A K+FD  +GF+  +Y++WWI+ ++ + I     +V++    NQ   
Sbjct: 77  GDLINEGNLGLIKAAKRFDETKGFKFISYAVWWIRQSILQAIAEQSRIVRL--PLNQVGS 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + +    L+   +    PE++  I +      S+ +S + R     S++A     ++
Sbjct: 135 LSKISKAFSKLEQEYEREPSPEELADILETTVDKVSDTLSNSGRHV---SMDAPFVQGEE 191

Query: 196 NSSQWQDWLV-YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA-RRLQEN-P 252
           N+    D L  +D D    ++ E    +     + RS++ L  RER I      L  N  
Sbjct: 192 NT--LLDVLENHDPDTDSSLIDESLSEE-----IKRSLATLTEREREIIVLFFGLGSNHQ 244

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           ++LE +  +F ++RERVRQI+ +A ++++ + + ++
Sbjct: 245 LSLEEIGEKFNLTRERVRQIKDKALQRLRHTSRSKI 280


>gi|213029652|ref|ZP_03344099.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. 404ty]
          Length = 322

 Score =  113 bits (282), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 83/270 (30%), Positives = 134/270 (49%), Gaps = 25/270 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
              TLE++  E  ++RERVRQI+    + V
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRAV 313


>gi|307709167|ref|ZP_07645626.1| RNA polymerase sigma factor rpoD [Streptococcus mitis SK564]
 gi|307620113|gb|EFN99230.1| RNA polymerase sigma factor rpoD [Streptococcus mitis SK564]
          Length = 369

 Score =  113 bits (282), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 88/274 (32%), Positives = 146/274 (53%), Gaps = 29/274 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E GD+ A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLTNEEEKELALAV-EAGDIEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKL- 219

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSS 193
               +R  +  LQ +   +  PEQ   IA++++++  +V  +  ++A +  SL   I   
Sbjct: 220 ----VREQRNLLQELG-QDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEE 270

Query: 194 DKNSSQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQ 249
           D   S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L 
Sbjct: 271 D--DSHLGDFI------EDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLRFGLD 322

Query: 250 ENPV-TLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +  + TLE++   F V+RER+RQIEA+A +K+++
Sbjct: 323 DGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRQ 356


>gi|307703796|ref|ZP_07640737.1| RNA polymerase sigma factor RpoD [Streptococcus oralis ATCC 35037]
 gi|307622631|gb|EFO01627.1| RNA polymerase sigma factor RpoD [Streptococcus oralis ATCC 35037]
          Length = 318

 Score =  113 bits (282), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 86/270 (31%), Positives = 143/270 (52%), Gaps = 21/270 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E GD+ A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 51  YLKEIGVVPLLTNEEEKELALAV-EAGDIEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 109

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 110 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 167

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L      +  PEQ   IA++++++  +V  +  ++A +  SL   I   D   
Sbjct: 168 LVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEED--D 221

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 222 SHLGDFI------EDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 275

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKVQE 282
            TLE++   F V+RER+RQIEA+A +K+++
Sbjct: 276 RTLEDVGKVFNVTRERIRQIEAKALRKLRQ 305


>gi|6175921|gb|AAF05336.1|AF182103_2 RNA polymerase sigma subunit [Escherichia coli]
          Length = 313

 Score =  113 bits (282), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 82/270 (30%), Positives = 135/270 (50%), Gaps = 25/270 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLPAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
              TLE++  E  ++RERVRQI+    +++
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRL 313


>gi|237744142|ref|ZP_04574623.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. 7_1]
 gi|229431371|gb|EEO41583.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. 7_1]
          Length = 417

 Score =  113 bits (282), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 85/278 (30%), Positives = 146/278 (52%), Gaps = 27/278 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   EE   AKR  E GD  A+ +L+ S+LRLVV IA  +   GL + ++
Sbjct: 150 YLREIGQVPLLTHDEEIEYAKRAYE-GDEEASKKLIESNLRLVVSIAKKHTNRGLKLLDL 208

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM+AV+KF+  +G++ +TY+ WWI+ A+   I      ++I        +   
Sbjct: 209 IQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPV-----HMIET 263

Query: 139 LRRLKG----HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           + ++K     +LQ  T  +  PE    +A++L +   ++ ++        SL   + S +
Sbjct: 264 INKIKKESRIYLQE-TGKDASPE---ILAERLGMEVDKIKAIQEMNQEPISLETPVGSEE 319

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNR---RNMLTRSMSVLNPRERRIFEARRLQEN 251
              S+  D++      ++Q      E  NR   R  L   +  L+PRE ++   R   ++
Sbjct: 320 --DSELGDFV------EDQKTTSPYEATNRAILREELDAVLKTLSPREEKVLRYRYGLDD 371

Query: 252 --PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             P TLE +   F V+RER+RQIE +A +K++   +K+
Sbjct: 372 SSPKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRKK 409


>gi|322376488|ref|ZP_08050981.1| RNA polymerase sigma-70 factor [Streptococcus sp. M334]
 gi|321282295|gb|EFX59302.1| RNA polymerase sigma-70 factor [Streptococcus sp. M334]
          Length = 369

 Score =  113 bits (282), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 88/274 (32%), Positives = 146/274 (53%), Gaps = 29/274 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E GD+ A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLTNEEEKELALAV-EAGDIEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKL- 219

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSS 193
               +R  +  LQ +   +  PEQ   IA++++++  +V  +  ++A +  SL   I   
Sbjct: 220 ----VREQRNLLQELG-QDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEE 270

Query: 194 DKNSSQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQ 249
           D   S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L 
Sbjct: 271 D--DSHLGDFI------EDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLRFGLD 322

Query: 250 ENPV-TLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +  + TLE++   F V+RER+RQIEA+A +K+++
Sbjct: 323 DGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRQ 356


>gi|294501280|ref|YP_003564980.1| RNA polymerase sigma factor [Bacillus megaterium QM B1551]
 gi|295706627|ref|YP_003599702.1| RNA polymerase sigma factor [Bacillus megaterium DSM 319]
 gi|294351217|gb|ADE71546.1| RNA polymerase sigma factor [Bacillus megaterium QM B1551]
 gi|294804286|gb|ADF41352.1| RNA polymerase sigma factor [Bacillus megaterium DSM 319]
          Length = 377

 Score =  113 bits (282), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 87/275 (31%), Positives = 136/275 (49%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 111 YLKEIGRVDLLSAEEEINLAKRI-EEGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 169

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 170 IQEGNMGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 229

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   D +L PE+V  I   L +++ E +S+   +    D  L 
Sbjct: 230 RVQRQLLQDLGREPSPEEIAEDMDLTPEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 285

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S         +H   E +          +  L   +  L  RE  +   R 
Sbjct: 286 DFIEDQDATSPS-------EHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 328

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 329 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 363


>gi|256027745|ref|ZP_05441579.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. D11]
 gi|260494274|ref|ZP_05814405.1| RNA polymerase sigma factor RpoS [Fusobacterium sp. 3_1_33]
 gi|289765702|ref|ZP_06525080.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. D11]
 gi|260198420|gb|EEW95936.1| RNA polymerase sigma factor RpoS [Fusobacterium sp. 3_1_33]
 gi|289717257|gb|EFD81269.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. D11]
          Length = 416

 Score =  113 bits (282), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 85/278 (30%), Positives = 146/278 (52%), Gaps = 27/278 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   EE   AKR  E GD  A+ +L+ S+LRLVV IA  +   GL + ++
Sbjct: 149 YLREIGQVPLLTHDEEIEYAKRAYE-GDEEASKKLIESNLRLVVSIAKKHTNRGLKLLDL 207

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM+AV+KF+  +G++ +TY+ WWI+ A+   I      ++I        +   
Sbjct: 208 IQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPV-----HMIET 262

Query: 139 LRRLKG----HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           + ++K     +LQ  T  +  PE    +A++L +   ++ ++        SL   + S +
Sbjct: 263 INKIKKESRIYLQE-TGKDASPE---ILAERLGMEVDKIKAIQEMNQEPISLETPVGSEE 318

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNR---RNMLTRSMSVLNPRERRIFEARRLQEN 251
              S+  D++      ++Q      E  NR   R  L   +  L+PRE ++   R   ++
Sbjct: 319 --DSELGDFV------EDQKTTSPYEATNRAILREELDAVLKTLSPREEKVLRYRYGLDD 370

Query: 252 --PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             P TLE +   F V+RER+RQIE +A +K++   +K+
Sbjct: 371 SSPKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRKK 408


>gi|15900942|ref|NP_345546.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae TIGR4]
 gi|15903023|ref|NP_358573.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae R6]
 gi|111657922|ref|ZP_01408632.1| hypothetical protein SpneT_02000898 [Streptococcus pneumoniae
           TIGR4]
 gi|116516638|ref|YP_816435.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae D39]
 gi|148985044|ref|ZP_01818287.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP3-BS71]
 gi|148989116|ref|ZP_01820506.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP6-BS73]
 gi|148994179|ref|ZP_01823494.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae
           SP9-BS68]
 gi|148998339|ref|ZP_01825781.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP11-BS70]
 gi|149003984|ref|ZP_01828792.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP14-BS69]
 gi|149006254|ref|ZP_01829966.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae
           SP18-BS74]
 gi|149013172|ref|ZP_01833989.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP19-BS75]
 gi|149019675|ref|ZP_01834994.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP23-BS72]
 gi|168483147|ref|ZP_02708099.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae CDC1873-00]
 gi|168487460|ref|ZP_02711968.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae CDC1087-00]
 gi|168488915|ref|ZP_02713114.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae SP195]
 gi|168494506|ref|ZP_02718649.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae CDC3059-06]
 gi|168576202|ref|ZP_02722096.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae MLV-016]
 gi|169833634|ref|YP_001694498.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae
           Hungary19A-6]
 gi|182684177|ref|YP_001835924.1| RNA polymerase sigma factor [Streptococcus pneumoniae CGSP14]
 gi|221231817|ref|YP_002510969.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae ATCC
           700669]
 gi|225854569|ref|YP_002736081.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae JJA]
 gi|225856717|ref|YP_002738228.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae P1031]
 gi|225858886|ref|YP_002740396.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae 70585]
 gi|225861039|ref|YP_002742548.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae
           Taiwan19F-14]
 gi|237650028|ref|ZP_04524280.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae CCRI
           1974]
 gi|237821736|ref|ZP_04597581.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae CCRI
           1974M2]
 gi|298230104|ref|ZP_06963785.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae str.
           Canada MDR_19F]
 gi|298255542|ref|ZP_06979128.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae str.
           Canada MDR_19A]
 gi|298502915|ref|YP_003724855.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           pneumoniae TCH8431/19A]
 gi|303256088|ref|ZP_07342108.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae BS455]
 gi|303260611|ref|ZP_07346576.1| RNA polymerase sigma factor [Streptococcus pneumoniae SP-BS293]
 gi|303263023|ref|ZP_07348956.1| RNA polymerase sigma factor [Streptococcus pneumoniae SP14-BS292]
 gi|303264870|ref|ZP_07350786.1| RNA polymerase sigma factor [Streptococcus pneumoniae BS397]
 gi|303266910|ref|ZP_07352787.1| RNA polymerase sigma factor [Streptococcus pneumoniae BS457]
 gi|303269116|ref|ZP_07354896.1| RNA polymerase sigma factor [Streptococcus pneumoniae BS458]
 gi|307067745|ref|YP_003876711.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Streptococcus pneumoniae AP200]
 gi|307127396|ref|YP_003879427.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae 670-6B]
 gi|61234224|sp|P0A4I9|RPOD_STRPN RecName: Full=RNA polymerase sigma factor rpoD
 gi|61234230|sp|P0A4J0|RPOD_STRR6 RecName: Full=RNA polymerase sigma factor rpoD
 gi|2108331|emb|CAA72252.1| rpoD [Streptococcus pneumoniae]
 gi|14972548|gb|AAK75186.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae TIGR4]
 gi|15458593|gb|AAK99783.1| RNA polymerase sigmA FACTOR 70 [Streptococcus pneumoniae R6]
 gi|116077214|gb|ABJ54934.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae D39]
 gi|147755736|gb|EDK62781.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP11-BS70]
 gi|147758043|gb|EDK65049.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP14-BS69]
 gi|147762031|gb|EDK68993.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae
           SP18-BS74]
 gi|147763023|gb|EDK69967.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP19-BS75]
 gi|147922742|gb|EDK73859.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP3-BS71]
 gi|147925339|gb|EDK76417.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP6-BS73]
 gi|147927422|gb|EDK78452.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae
           SP9-BS68]
 gi|147931050|gb|EDK82030.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP23-BS72]
 gi|168996136|gb|ACA36748.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae Hungary19A-6]
 gi|172043392|gb|EDT51438.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae CDC1873-00]
 gi|182629511|gb|ACB90459.1| RNA polymerase sigma factor [Streptococcus pneumoniae CGSP14]
 gi|183569691|gb|EDT90219.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae CDC1087-00]
 gi|183572434|gb|EDT92962.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae SP195]
 gi|183575600|gb|EDT96128.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae CDC3059-06]
 gi|183577989|gb|EDT98517.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae MLV-016]
 gi|220674277|emb|CAR68818.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae ATCC
           700669]
 gi|225720127|gb|ACO15981.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae 70585]
 gi|225722225|gb|ACO18078.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae JJA]
 gi|225725305|gb|ACO21157.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae P1031]
 gi|225728137|gb|ACO23988.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae Taiwan19F-14]
 gi|298238510|gb|ADI69641.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           pneumoniae TCH8431/19A]
 gi|301794192|emb|CBW36610.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae INV104]
 gi|301800046|emb|CBW32640.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae OXC141]
 gi|301802035|emb|CBW34765.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae INV200]
 gi|302596935|gb|EFL64061.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae BS455]
 gi|302635850|gb|EFL66352.1| RNA polymerase sigma factor [Streptococcus pneumoniae SP14-BS292]
 gi|302638261|gb|EFL68731.1| RNA polymerase sigma factor [Streptococcus pneumoniae SP-BS293]
 gi|302641365|gb|EFL71732.1| RNA polymerase sigma factor [Streptococcus pneumoniae BS458]
 gi|302643543|gb|EFL73813.1| RNA polymerase sigma factor [Streptococcus pneumoniae BS457]
 gi|302645558|gb|EFL75789.1| RNA polymerase sigma factor [Streptococcus pneumoniae BS397]
 gi|306409282|gb|ADM84709.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Streptococcus pneumoniae AP200]
 gi|306484458|gb|ADM91327.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae 670-6B]
 gi|327389372|gb|EGE87717.1| RNA polymerase sigma factor rpoD [Streptococcus pneumoniae GA04375]
 gi|332073431|gb|EGI83910.1| RNA polymerase sigma factor rpoD [Streptococcus pneumoniae GA17570]
 gi|332075028|gb|EGI85499.1| RNA polymerase sigma factor rpoD [Streptococcus pneumoniae GA17545]
 gi|332075404|gb|EGI85873.1| RNA polymerase sigma factor rpoD [Streptococcus pneumoniae GA41301]
 gi|332200548|gb|EGJ14620.1| RNA polymerase sigma factor rpoD [Streptococcus pneumoniae GA41317]
 gi|332201555|gb|EGJ15625.1| RNA polymerase sigma factor rpoD [Streptococcus pneumoniae GA47368]
 gi|332202930|gb|EGJ16998.1| RNA polymerase sigma factor rpoD [Streptococcus pneumoniae GA47901]
          Length = 369

 Score =  113 bits (282), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 88/274 (32%), Positives = 146/274 (53%), Gaps = 29/274 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E GD+ A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLTNEEEKELALAV-EAGDIEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKL- 219

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSS 193
               +R  +  LQ +   +  PEQ   IA++++++  +V  +  ++A +  SL   I   
Sbjct: 220 ----VREQRNLLQELG-QDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEE 270

Query: 194 DKNSSQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQ 249
           D   S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L 
Sbjct: 271 D--DSHLGDFI------EDEVIENPVDYTTRIVLREQLDEILDTLTDREENVLRLRFGLD 322

Query: 250 ENPV-TLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +  + TLE++   F V+RER+RQIEA+A +K+++
Sbjct: 323 DGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRQ 356


>gi|317061552|ref|ZP_07926037.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. D12]
 gi|313687228|gb|EFS24063.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. D12]
          Length = 363

 Score =  113 bits (282), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 87/272 (31%), Positives = 147/272 (54%), Gaps = 27/272 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI +IP+L  +EE  LAK+  E GD  A  RL+ ++LRLVV IA  +   GL + ++
Sbjct: 96  YLREIGQIPLLTHKEELELAKKALE-GDEFANKRLIEANLRLVVSIAKKHTNRGLKLLDL 154

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGNIGLM+AV+KF+  +G++ +TY+ WWI+ A+   I      ++I      T N+ +
Sbjct: 155 IQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPVHMIETINKIK 214

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
                +  + +LQ  T  +  PE    +A++L +   +V S+        SL   + S +
Sbjct: 215 -----KEARIYLQE-TGKDATPE---ILAERLGMEVEKVKSIQEMNQDPISLETPVGSEE 265

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNR---RNMLTRSMSVLNPRERRIFEARRLQEN 251
              S+  D++      ++Q ++   E  NR   R  L   +  L+ RE ++   R   ++
Sbjct: 266 --DSELGDFV------EDQKMLTPYELTNRSLLREQLDSVLGSLSSREEKVLRYRYGLDD 317

Query: 252 --PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             P TLE +   F+V+RER+RQIE +A +K++
Sbjct: 318 GSPKTLEEVGKIFKVTRERIRQIEVKALRKLR 349


>gi|58257340|gb|AAK30051.2| RpoS sigma factor [Pseudomonas fluorescens]
          Length = 335

 Score =  113 bits (282), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 83/273 (30%), Positives = 146/273 (53%), Gaps = 19/273 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVVKELNVYL 185

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKN 196
              R    L    D+   PE++  + +K       ++ +N R++  D SL+     SDK 
Sbjct: 186 GAAR---ELTQKLDHEPSPEEIANMLEKPVTEVKRMLGLNERVSSVDVSLDP---DSDKT 239

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPV 253
                D L  D       ++++++       + + +S L  ++R +   R   R  E+  
Sbjct: 240 V---LDTLTDDRPTDRCEVLQEDDLSQG---IDQWLSELTEKQREVVVRRFGLRGHESS- 292

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TLE++  E  ++RERVRQI+    K+++E ++K
Sbjct: 293 TLEDVGLEIGLTRERVRQIQIEGLKRLREILEK 325


>gi|240147091|ref|ZP_04745692.1| RNA polymerase sigma factor RpoD [Roseburia intestinalis L1-82]
 gi|257200737|gb|EEU99021.1| RNA polymerase sigma factor RpoD [Roseburia intestinalis L1-82]
 gi|291536629|emb|CBL09741.1| RNA polymerase, sigma 70 subunit, RpoD [Roseburia intestinalis
           M50/1]
          Length = 397

 Score =  113 bits (282), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 88/279 (31%), Positives = 141/279 (50%), Gaps = 41/279 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 131 YLKEIGKVPLLSAEEEIELAKRM-ELGDQEAKKRLAEANLRLVVSIAKRYVGRGMLFLDL 189

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-- 132
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 190 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 249

Query: 133 ---KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
              ++L   L R     +   + N+  E+V  I   L +S+ E +S+   +  +E     
Sbjct: 250 RVSRQLLQELGREPTPEEIAAEMNMPVERVREI---LKISQ-EPVSLETPIGEEE----- 300

Query: 190 INSSDKNSSQWQDWLVYDH-----DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
                   S   D++  D+     D     L+        +  L   +  L  RE+++  
Sbjct: 301 -------DSHLGDFIQDDNVPVPADAAAFTLL--------KEQLEEVLGTLTEREQKVLT 345

Query: 245 ARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R   E+    TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 346 LRFGLEDGRARTLEEVGREFNVTRERIRQIEAKALRKLR 384


>gi|269101863|ref|ZP_06154560.1| RNA polymerase sigma factor RpoS [Photobacterium damselae subsp.
           damselae CIP 102761]
 gi|268161761|gb|EEZ40257.1| RNA polymerase sigma factor RpoS [Photobacterium damselae subsp.
           damselae CIP 102761]
          Length = 333

 Score =  113 bits (282), Expect = 4e-23,   Method: Compositional matrix adjust.
 Identities = 83/267 (31%), Positives = 144/267 (53%), Gaps = 15/267 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD  A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 61  YLGEIGFSPLLTAEEEVLYARRAL-RGDDVARKRMIESNLRLVVKISRRYSNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 VEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +   Q + D+    E +    +K     + ++ +N R++  +  N +   +DK   
Sbjct: 179 LRTARELAQKL-DHEPTAEDIAIQLEKPVDDVNRMLRLNERVSSVD--NPISGDADK--- 232

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR---LQENPVTL 255
              D +  +  G  +V  + ++ K+    +   +  LNP++R +  ARR   L     TL
Sbjct: 233 ALLDIIPDEKGGTPEVSTQTDDIKSS---IVDWLDELNPKQREVL-ARRFGLLGYEASTL 288

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQE 282
           E++  E  ++RERVRQI+    +++++
Sbjct: 289 EDVGREIGLTRERVRQIQVEGLRRLRD 315


>gi|19704653|ref|NP_604215.1| RNA polymerase sigma factor rpoD [Fusobacterium nucleatum subsp.
           nucleatum ATCC 25586]
 gi|19714957|gb|AAL95514.1| RNA polymerase sigma factor rpoD [Fusobacterium nucleatum subsp.
           nucleatum ATCC 25586]
          Length = 331

 Score =  112 bits (281), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 84/278 (30%), Positives = 147/278 (52%), Gaps = 27/278 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE   AK+  E GD  A+ +L+ S+LRLVV IA  +   GL + ++
Sbjct: 64  YLREIGQVPLLTHEEEIDYAKKAYE-GDEEASKKLIESNLRLVVSIAKKHTNRGLKLLDL 122

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM+AV+KF+  +G++ +TY+ WWI+ A+   I      ++I        +   
Sbjct: 123 IQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPV-----HMIET 177

Query: 139 LRRLKG----HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           + ++K     +LQ  T  +  PE    +A++L +   ++ ++        SL   + S +
Sbjct: 178 INKIKKESRIYLQE-TGKDASPE---ILAERLGMEVDKIKAIQEMNQEPISLETPVGSEE 233

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNR---RNMLTRSMSVLNPRERRIFEARRLQEN 251
              S+  D++      ++Q      E  NR   R  L   +  L+PRE ++   R   ++
Sbjct: 234 --DSELGDFV------EDQKTTSPYEATNRAILREELDAVLKTLSPREEKVLRYRYGLDD 285

Query: 252 --PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             P TLE +   F V+RER+RQIE +A +K++   +K+
Sbjct: 286 SSPKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRKK 323


>gi|289167835|ref|YP_003446104.1| DNA-dependent RNA Polymerase sigma factor rpoD [Streptococcus mitis
           B6]
 gi|288907402|emb|CBJ22239.1| DNA-dependent RNA Polymerase sigma factor rpoD [Streptococcus mitis
           B6]
          Length = 369

 Score =  112 bits (281), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 87/270 (32%), Positives = 142/270 (52%), Gaps = 21/270 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E GD+ A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLTNEEEKELALAV-EAGDIEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 218

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L         PEQ   IA+K++++  +V  +  ++A +  SL   I   D   
Sbjct: 219 LVREQRNLLQEYGQEPTPEQ---IAEKMDMTPDKVREI-LKIAQEPVSLETPIGEED--D 272

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 273 SHLGDFI------EDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 326

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKVQE 282
            TLE++   F V+RER+RQIEA+A +K+++
Sbjct: 327 RTLEDVGKVFNVTRERIRQIEAKALRKLRQ 356


>gi|257064907|ref|YP_003144579.1| RNA polymerase sigma factor, sigma-70 family [Slackia
           heliotrinireducens DSM 20476]
 gi|256792560|gb|ACV23230.1| RNA polymerase sigma factor, sigma-70 family [Slackia
           heliotrinireducens DSM 20476]
          Length = 314

 Score =  112 bits (281), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 85/291 (29%), Positives = 142/291 (48%), Gaps = 42/291 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR------------------------------EHGDLS 48
           Y+ +I K+ +L   EE  LAK+Y+                              +     
Sbjct: 20  YLRDIGKVDLLTPAEEVELAKKYQTGLAAEAALAQMNEGSVEVDRRECRKLLRVQRAGQE 79

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +LV ++LRLVV IA  YRG GLP+ ++V EGN+GL++AV+KFD  +GF+L+TY+ WW
Sbjct: 80  AKDKLVAANLRLVVSIAKKYRGRGLPLLDLVQEGNLGLIRAVEKFDYTKGFKLSTYATWW 139

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      +++    +   L   + R++  L    + +  P +   IA +L +
Sbjct: 140 IRQAVTRAIADKARTIRL--PVHVVGLMNKVVRVQHELADELERDPSPAE---IADRLGI 194

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SE  V+ +  +L G E L+      D  +S+  D++    D   +   +       R+ +
Sbjct: 195 SEQCVVEL-LKL-GSEPLSLETPVGDDKTSEIGDFI---EDRNSEDAFDAAAEAMLRDDV 249

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAF 277
             ++S L  RER+I E R   +   P TL  +  +  V+RER+RQIE++  
Sbjct: 250 ASALSRLPERERKIIELRFGIVDGEPRTLAQIGDQLGVTRERIRQIESKTL 300


>gi|329117418|ref|ZP_08246135.1| RNA polymerase sigma factor RpoD [Streptococcus parauberis NCFD
           2020]
 gi|326907823|gb|EGE54737.1| RNA polymerase sigma factor RpoD [Streptococcus parauberis NCFD
           2020]
          Length = 369

 Score =  112 bits (281), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 87/269 (32%), Positives = 141/269 (52%), Gaps = 21/269 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E GDL A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLTGEEEKELAVAVDE-GDLEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 218

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L      +  PEQ   IA+++ ++  +V  +  ++A +  SL   I   D   
Sbjct: 219 LVREQRNLLQELGQDPTPEQ---IAERMEMTPDKVREI-LKIAQEPVSLETPIGEED--D 272

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 273 SHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 326

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE++   F V+RER+RQIEA+A +K++
Sbjct: 327 RTLEDVGKVFNVTRERIRQIEAKALRKLR 355


>gi|138896056|ref|YP_001126509.1| RNA polymerase sigma factor RpoD [Geobacillus thermodenitrificans
           NG80-2]
 gi|196248949|ref|ZP_03147649.1| RNA polymerase, sigma 70 subunit, RpoD family [Geobacillus sp.
           G11MC16]
 gi|134267569|gb|ABO67764.1| RNA polymerase sigma factor RpoD [Geobacillus thermodenitrificans
           NG80-2]
 gi|196211825|gb|EDY06584.1| RNA polymerase, sigma 70 subunit, RpoD family [Geobacillus sp.
           G11MC16]
          Length = 375

 Score =  112 bits (281), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 86/275 (31%), Positives = 137/275 (49%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 109 YLKEIGRVPLLSAEEEIELAKRI-EQGDEEAKRRLTEANLRLVVSIAKRYVGRGMLFLDL 167

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 168 IQEGNMGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 227

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I   L +++ E +S+   +    D  L 
Sbjct: 228 RVQRQLLQDLGREPTPEEIAEEMDLTPEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 283

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         +H   E +          +  L   +  L  RE  +   R 
Sbjct: 284 DFIEDQEATSPS-------EHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 326

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 327 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 361


>gi|291541030|emb|CBL14141.1| RNA polymerase, sigma 70 subunit, RpoD [Roseburia intestinalis
           XB6B4]
          Length = 397

 Score =  112 bits (281), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 88/279 (31%), Positives = 141/279 (50%), Gaps = 41/279 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 131 YLKEIGKVPLLSAEEEIELAKRM-ELGDQEAKKRLAEANLRLVVSIAKRYVGRGMLFLDL 189

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-- 132
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 190 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 249

Query: 133 ---KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
              ++L   L R     +   + N+  E+V  I   L +S+ E +S+   +  +E     
Sbjct: 250 RVSRQLLQELGREPTPEEIAAEMNMPVERVREI---LKISQ-EPVSLETPIGEEE----- 300

Query: 190 INSSDKNSSQWQDWLVYDH-----DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
                   S   D++  D+     D     L+        +  L   +  L  RE+++  
Sbjct: 301 -------DSHLGDFIQDDNVPVPADAAAFTLL--------KEQLEEVLGTLTEREQKVLT 345

Query: 245 ARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R   E+    TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 346 LRFGLEDGRARTLEEVGREFNVTRERIRQIEAKALRKLR 384


>gi|146308041|ref|YP_001188506.1| RNA polymerase sigma factor RpoS [Pseudomonas mendocina ymp]
 gi|145576242|gb|ABP85774.1| RNA polymerase, sigma 38 subunit, RpoS [Pseudomonas mendocina ymp]
          Length = 335

 Score =  112 bits (281), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 87/272 (31%), Positives = 145/272 (53%), Gaps = 17/272 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLTPEEEVHFA-RLAQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+    E++  + +K       ++ +N R++  D SL      SDK  
Sbjct: 185 LRAARELTQKL-DHEPSAEEIANLLEKPVGEVKRMLGLNERVSSVDVSLGP---DSDKT- 239

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++       + + +S L  ++R +   R   R  E+  T
Sbjct: 240 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSDLTDKQREVVVRRFGLRGHESS-T 293

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE +  E  ++RERVRQI+  A K+++E ++K
Sbjct: 294 LEEVGQEIGLTRERVRQIQVEALKRLREILEK 325


>gi|239827752|ref|YP_002950376.1| RNA polymerase sigma factor RpoD [Geobacillus sp. WCH70]
 gi|239808045|gb|ACS25110.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus sp.
           WCH70]
          Length = 374

 Score =  112 bits (281), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 86/276 (31%), Positives = 138/276 (50%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 108 YLKEIGRVPLLSAEEEIELAKRI-EQGDEEAKRRLTEANLRLVVSIAKRYVGRGMLFLDL 166

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 167 IQEGNMGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 226

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I   L +++ E +S+   +    D  L 
Sbjct: 227 RVQRQLLQDLGREPTPEEIAEEMDLTPEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 282

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         +H   E +          +  L   +  L  RE  +   R 
Sbjct: 283 DFIEDQEATSPS-------EHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 325

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 326 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 361


>gi|6175918|gb|AAF05334.1|AF182102_2 RNA polymerase sigma subunit [Escherichia coli]
 gi|6175933|gb|AAF05344.1|AF182107_2 RNA polymerase sigma subunit [Escherichia coli]
          Length = 313

 Score =  112 bits (281), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 82/270 (30%), Positives = 135/270 (50%), Gaps = 25/270 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
              TLE++  E  ++RERVRQI+    +++
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRL 313


>gi|327404710|ref|YP_004345548.1| RpoD subfamily RNA polymerase sigma-70 subunit [Fluviicola
           taffensis DSM 16823]
 gi|327320218|gb|AEA44710.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Fluviicola
           taffensis DSM 16823]
          Length = 289

 Score =  112 bits (281), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 81/278 (29%), Positives = 147/278 (52%), Gaps = 27/278 (9%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI ++ ++  +EE  LAKR +  GD  A  RL  ++LR VV ++  Y+  GL +
Sbjct: 18  LDKYLQEIGRVELITAEEEVELAKRIK-AGDKRALERLTKANLRFVVSVSKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV-----KIGTTA 130
            ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     +V     KIGT  
Sbjct: 77  PDLINEGNLGLIKAAERFDETRGFKFISYAVWWIRQSILQALAEQARIVRLPLNKIGTIN 136

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R +  L ++            +P     +A+ L  S  +V       A   S++A +
Sbjct: 137 KINRAYSELEQVYE----------RPPSADELAEFLECSVEDVRQSLANTARHLSMDAPL 186

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-- 248
              D++SS   D L  D     +  + KE   + R  + RS+S L+ RE  +    RL  
Sbjct: 187 VDGDESSSSMYDVLPNDALPSPENELNKE---SLRKEIERSLSSLSGREGDVV---RLYY 240

Query: 249 ---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               ++ +TLE +   F+++RERVRQI+ +A ++++ +
Sbjct: 241 GLNGKHALTLEEIGDLFDLTRERVRQIKEKAIRRLKHT 278


>gi|319892618|ref|YP_004149493.1| RNA polymerase sigma factor RpoD [Staphylococcus pseudintermedius
           HKU10-03]
 gi|317162314|gb|ADV05857.1| RNA polymerase sigma factor RpoD [Staphylococcus pseudintermedius
           HKU10-03]
 gi|323464344|gb|ADX76497.1| RNA polymerase sigma factor SigA [Staphylococcus pseudintermedius
           ED99]
          Length = 369

 Score =  112 bits (281), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 88/275 (32%), Positives = 133/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  QEE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 103 YLKEIGRVDLLSAQEEIELAKRI-EQGDEVAKARLAEANLRLVVSIAKRYVGRGMLFLDL 161

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 162 IQEGNMGLIKAVEKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 221

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I K       E +S+   +    D  L 
Sbjct: 222 RVQRQLLQDLGRDPAPEEIGEEMDLPPEKVREILK----IAQEPVSLETPIGEEDDSHLG 277

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 278 DFIEDQEAQSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 320

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 321 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 355


>gi|269123266|ref|YP_003305843.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptobacillus
           moniliformis DSM 12112]
 gi|268314592|gb|ACZ00966.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptobacillus
           moniliformis DSM 12112]
          Length = 379

 Score =  112 bits (281), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 89/273 (32%), Positives = 143/273 (52%), Gaps = 38/273 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI +IP+L+ +EE+ LA+R  E GD  A  +L+ S+LRLVV IA  +   GL + ++
Sbjct: 112 YLREIGQIPLLKSEEEFELARRIGE-GDERAKQQLMESNLRLVVSIAKKHTNRGLKLLDL 170

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM+AV+KF+ ++GF+ +TY+ WWI+ A+   I      ++I        +   
Sbjct: 171 IQEGNIGLMKAVEKFESDKGFKFSTYATWWIRQAITRAIADQGRTIRIPV-----HMIET 225

Query: 139 LRRLKG----HLQAI----TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
           + ++K     HLQ      TD+ L     + + K  N+ E     MN       SL   +
Sbjct: 226 INKIKKASRIHLQETGKEPTDDYLAEIVEMPVEKVKNILE-----MNQDPI---SLETPV 277

Query: 191 NSSDKNSSQWQDWLVYD-----HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
            S D   S+  D++  D     H+   + ++     K + N + R    LN RE ++   
Sbjct: 278 GSED--DSELGDFVEDDKFLNPHEATVRSVL-----KEKLNDVLRKE--LNEREEQVLRL 328

Query: 246 RRLQEN--PVTLENLSSEFEVSRERVRQIEARA 276
           R   ++  P TLE +   F+V+RER+RQIE +A
Sbjct: 329 RYGLDDGAPKTLEEVGKIFDVTRERIRQIEVKA 361


>gi|168491966|ref|ZP_02716109.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae CDC0288-04]
 gi|183573791|gb|EDT94319.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae CDC0288-04]
          Length = 369

 Score =  112 bits (281), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 88/274 (32%), Positives = 146/274 (53%), Gaps = 29/274 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E GD+ A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLTNEEEKELALAV-EAGDIEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKL- 219

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSS 193
               +R  +  LQ +   +  PEQ   IA++++++  +V  +  ++A +  SL   I   
Sbjct: 220 ----VREQRNLLQELG-QDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEE 270

Query: 194 DKNSSQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQ 249
           D   S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L 
Sbjct: 271 D--DSHLGDFI------EDEVIENPVDYTTRIVLREQLDEILDTLTDREENVLRLRFGLD 322

Query: 250 ENPV-TLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +  + TLE++   F V+RER+RQIEA+A +K+++
Sbjct: 323 DGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRQ 356


>gi|322391830|ref|ZP_08065295.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           peroris ATCC 700780]
 gi|321145310|gb|EFX40706.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           peroris ATCC 700780]
          Length = 381

 Score =  112 bits (281), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 86/270 (31%), Positives = 143/270 (52%), Gaps = 21/270 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E GD+ A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 114 YLKEIGVVPLLTNEEEKELALAV-EAGDVEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 172

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 173 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 230

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L      +  PEQ   IA++++++  +V  +  ++A +  SL   I   D   
Sbjct: 231 LVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEED--D 284

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 285 SHLGDFI------EDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 338

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKVQE 282
            TLE++   F V+RER+RQIEA+A +K+++
Sbjct: 339 RTLEDVGKVFNVTRERIRQIEAKALRKLRQ 368


>gi|193212077|ref|YP_001998030.1| RNA polymerase sigma 32 subunit RpoH [Chlorobaculum parvum NCIB
           8327]
 gi|193085554|gb|ACF10830.1| RNA polymerase, sigma 32 subunit, RpoH [Chlorobaculum parvum NCIB
           8327]
          Length = 299

 Score =  112 bits (281), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 91/304 (29%), Positives = 159/304 (52%), Gaps = 45/304 (14%)

Query: 9   IVNGE-IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS-----------AAHRLVTS 56
           I N E + L RY+ EI K  +L  ++E  L    +E  D+            A  +L+  
Sbjct: 10  ITNRESLSLDRYLQEIGKYDLLTAEDEVKLTMAIKEGYDMPVDTVEYKRAKRALDKLIKG 69

Query: 57  HLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM--- 113
           +LR VV +A  Y+  GL + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++   
Sbjct: 70  NLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQA 129

Query: 114 ---QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
              Q  I+R   L ++GT     + +  L +     +   D N K      +A  L++ +
Sbjct: 130 LAEQSRIVR-LPLNRVGTLNKISKAYSQLEQ-----EYERDPNTKE-----LANLLDM-D 177

Query: 171 SEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-- 227
           S+ ++   ++AG   S++A     D N  +  D L  D    +  L       NR ++  
Sbjct: 178 SQDVADTLKIAGRHVSVDAPFAQGDDN--RLLDVLQNDGHMPDHTL-------NRDSLTL 228

Query: 228 -LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + RS+SVL PRE  +  +      ENP+TLE +  +F+++RERVRQI+ +A +++++S 
Sbjct: 229 EVERSLSVLAPREADVIRSYFGIGMENPLTLEEIGEKFKLTRERVRQIKEKAIRRLRQSA 288

Query: 285 QKQV 288
            K+V
Sbjct: 289 YKEV 292


>gi|322387734|ref|ZP_08061343.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           infantis ATCC 700779]
 gi|321141601|gb|EFX37097.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           infantis ATCC 700779]
          Length = 369

 Score =  112 bits (281), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 87/270 (32%), Positives = 142/270 (52%), Gaps = 21/270 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E GD+ A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLTNEEEKELALAV-EAGDVEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 218

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L         PEQ   IA+K++++  +V  +  ++A +  SL   I   D   
Sbjct: 219 LVREQRNLLQEYGQEPTPEQ---IAEKMDMTPDKVREI-LKIAQEPVSLETPIGEED--D 272

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 273 SHLGDFI------EDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 326

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKVQE 282
            TLE++   F V+RER+RQIEA+A +K+++
Sbjct: 327 RTLEDVGKVFNVTRERIRQIEAKALRKLRQ 356


>gi|261879347|ref|ZP_06005774.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           bergensis DSM 17361]
 gi|270334050|gb|EFA44836.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           bergensis DSM 17361]
          Length = 290

 Score =  112 bits (281), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 82/277 (29%), Positives = 141/277 (50%), Gaps = 12/277 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYG 72
            L RY+ EI ++PM+   EE  LA+  R+ G     A  +LV ++LR VV +A  Y+  G
Sbjct: 17  ALDRYLVEIGRVPMITVDEEIELAQAIRKGGKEGERAKEKLVKANLRFVVSVAKQYQHQG 76

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V++    NQ
Sbjct: 77  LGLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRL--PLNQ 134

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 L ++   +      N +P  V  +A+  N+ E+++           S++A    
Sbjct: 135 ---VGALSKINAEISKFEQENHRPPSVQELARLTNIEEAKIEQTMKADNHHMSIDAPFQE 191

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF-EARRLQEN 251
            D NS    D L    D +    ++ E     + + T   +VL  RER I  E   +  +
Sbjct: 192 DDDNS--MADVLSSGDDSRADRQVDYESMS--KELDTVLCNVLKERERTIVRECFGIGCH 247

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
              LE +  +  ++RERVRQI  ++  K++ES   Q+
Sbjct: 248 EKGLEEIGDQLGLTRERVRQIREKSIVKLRESGHAQL 284


>gi|295399207|ref|ZP_06809189.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|312110191|ref|YP_003988507.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus sp.
           Y4.1MC1]
 gi|294978673|gb|EFG54269.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|311215292|gb|ADP73896.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus sp.
           Y4.1MC1]
          Length = 377

 Score =  112 bits (281), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 86/276 (31%), Positives = 138/276 (50%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 111 YLKEIGRVPLLSAEEEIELAKRI-EQGDEEAKRRLTEANLRLVVSIAKRYVGRGMLFLDL 169

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 170 IQEGNMGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 229

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I   L +++ E +S+   +    D  L 
Sbjct: 230 RVQRQLLQDLGREPTPEEIAEEMDLTPEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 285

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         +H   E +          +  L   +  L  RE  +   R 
Sbjct: 286 DFIEDQEATSPS-------EHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 328

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 329 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 364


>gi|312865945|ref|ZP_07726166.1| RNA polymerase sigma factor RpoD [Streptococcus downei F0415]
 gi|311098349|gb|EFQ56572.1| RNA polymerase sigma factor RpoD [Streptococcus downei F0415]
          Length = 338

 Score =  112 bits (281), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 87/269 (32%), Positives = 142/269 (52%), Gaps = 21/269 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E GDL A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 71  YLKEIGIVPLLTNEEEKELAIAAAE-GDLMAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 129

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 130 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 187

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L      +  PEQ   IA++++++  +V  +  ++A +  SL   I   D   
Sbjct: 188 LVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEED--D 241

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 242 SHLGDFI------EDEVIENPVDYTTRIVLREQLNEVLDTLTDREENVLRLRFGLDDGKM 295

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE++   F V+RER+RQIEA+A +K++
Sbjct: 296 RTLEDVGKVFNVTRERIRQIEAKALRKLR 324


>gi|254302832|ref|ZP_04970190.1| DNA-directed RNA polymerase sigma subunit RpoD [Fusobacterium
           nucleatum subsp. polymorphum ATCC 10953]
 gi|148323024|gb|EDK88274.1| DNA-directed RNA polymerase sigma subunit RpoD [Fusobacterium
           nucleatum subsp. polymorphum ATCC 10953]
          Length = 418

 Score =  112 bits (281), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 85/278 (30%), Positives = 146/278 (52%), Gaps = 27/278 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   EE   AKR  E GD  A+ +L+ S+LRLVV IA  +   GL + ++
Sbjct: 151 YLREIGQVPLLTHDEEIEYAKRAYE-GDEEASKKLIESNLRLVVSIAKKHTNRGLKLLDL 209

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM+AV+KF+  +G++ +TY+ WWI+ A+   I      ++I        +   
Sbjct: 210 IQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPV-----HMIET 264

Query: 139 LRRLKG----HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           + ++K     +LQ  T  +  PE    +A++L +   ++ ++        SL   + S +
Sbjct: 265 INKIKKESRIYLQE-TGKDASPE---ILAERLGMEVEKIKAIQEMNQEPISLETPVGSEE 320

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNR---RNMLTRSMSVLNPRERRIFEARRLQEN 251
              S+  D++      ++Q      E  NR   R  L   +  L+PRE ++   R   ++
Sbjct: 321 --DSELGDFV------EDQKTTSPYEATNRAILREELDAVLKTLSPREEKVLRYRYGLDD 372

Query: 252 --PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             P TLE +   F V+RER+RQIE +A +K++   +K+
Sbjct: 373 SSPKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRKK 410


>gi|282858973|ref|ZP_06268111.1| sigma-70 region 2 [Prevotella bivia JCVIHMP010]
 gi|282588253|gb|EFB93420.1| sigma-70 region 2 [Prevotella bivia JCVIHMP010]
          Length = 286

 Score =  112 bits (281), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 81/293 (27%), Positives = 155/293 (52%), Gaps = 40/293 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           NR++MS        L +Y+ EI    +L  +EE  LA+R R+ GD  A  RL  ++LR V
Sbjct: 12  NRESMS--------LDKYLQEIGNEELLTPEEEVELAQRIRK-GDKKALERLTRANLRFV 62

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V +A  Y+  G+ + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + I    
Sbjct: 63  VSVAKQYQTQGIDLPDLINEGNMGLIKAAKRFDETRGFKFISYAVWWIRQSILQAIAAQG 122

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV-------- 173
            L+++   ANQ  +   + R+   L      N +   +  +A+++++SE  +        
Sbjct: 123 RLIRL--PANQIGVVNKITRI---LNKFEQENERIPNIDELAREVDLSEEHIEDALSLSF 177

Query: 174 --ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
             +SM+     DE ++ L      N       LV D   +E++              +R+
Sbjct: 178 RQVSMDSPFKDDEGVSLLDVMPSTNVPSTDKSLV-DESLKEEI--------------SRA 222

Query: 232 MSVLNPRERRIFEARR-LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           + +L+ RE+++  A   + +  ++LE +  +F +SRERVRQI+ +A + ++++
Sbjct: 223 LKILSEREQKVLCAYYGIGQLEMSLEEIGDKFGLSRERVRQIKEKAIRNLRKA 275


>gi|288574624|ref|ZP_06392981.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dethiosulfovibrio
           peptidovorans DSM 11002]
 gi|288570365|gb|EFC91922.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dethiosulfovibrio
           peptidovorans DSM 11002]
          Length = 381

 Score =  112 bits (281), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 86/279 (30%), Positives = 138/279 (49%), Gaps = 41/279 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  IP+L + +E  LAKR  E GD  A  +L+ ++LRLVV IA  Y G G+   ++
Sbjct: 115 YLREIGTIPLLNQPQEVELAKRV-EMGDDEAKSQLIEANLRLVVSIAKKYMGRGMLFLDL 173

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-- 132
           + EGN+GL++AV+KFD  RG++ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 174 IQEGNLGLIRAVEKFDYSRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKVM 233

Query: 133 ---KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
              + L  +L R     +   +  ++P +VV I K       E IS+   +    D  L 
Sbjct: 234 RASRNLVQSLGREPTDEEIAAEMGIEPAKVVQIRK----VAQEPISLESPVGEEDDSELG 289

Query: 188 ALINSSD---KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
             I   D    + S   ++L                    R+ L   +  L  RE+++  
Sbjct: 290 DFIEDKDMISPDDSTSMEFL--------------------RDQLDDVLEGLTDREKQVLR 329

Query: 245 ARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R   ++    TLE++   F V+RER+RQIEA+A +K++
Sbjct: 330 LRFGFDDGQCYTLEDVGRRFGVTRERIRQIEAKALRKLR 368


>gi|156975281|ref|YP_001446188.1| hypothetical protein VIBHAR_03010 [Vibrio harveyi ATCC BAA-1116]
 gi|156526875|gb|ABU71961.1| hypothetical protein VIBHAR_03010 [Vibrio harveyi ATCC BAA-1116]
          Length = 287

 Score =  112 bits (281), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 89/278 (32%), Positives = 144/278 (51%), Gaps = 19/278 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y ++I K  +L   +E   A+R +  GD  A  R++ S+LRLVV IA  Y+G GL   ++
Sbjct: 21  YFNDIGKYALLSADDEREYARRAK-MGDADARTRMINSNLRLVVNIAKRYKGRGLTFLDL 79

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ--KRLF 136
           +SEGNIGLM+AV+KFDPE+GFR +TY+  WI+ +++  ++     V++    N+  KR  
Sbjct: 80  ISEGNIGLMRAVEKFDPEKGFRFSTYATHWIRQSIERELMNQARTVRLPVHINKELKRYV 139

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
              + L    Q IT  +        IA  L +  S V+     L  D+S  +L +  DK 
Sbjct: 140 KATKELSQKTQTITPRD--------IADHLEIPVSSVLK---HLEFDKSTISLDSYQDKE 188

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQEN-PVT 254
            ++     +  H  +   L  + E  N   ML + +  L P  + I   R  L  N P +
Sbjct: 189 EAKPLAETMACHRLRCPEL--ELEEDNAFLMLLQWIEELEPDLKLILTRRYGLDGNTPTS 246

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
           L+ + +E   SRER+R ++ +  KK+Q ++ K + +S 
Sbjct: 247 LDTVGTELGYSRERIRHLQMQGIKKLQ-NLAKNIPVSG 283


>gi|121998209|ref|YP_001002996.1| RpoD family RNA polymerase sigma factor [Halorhodospira halophila
           SL1]
 gi|121589614|gb|ABM62194.1| RNA polymerase, sigma 38 subunit, RpoS [Halorhodospira halophila
           SL1]
          Length = 336

 Score =  112 bits (280), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 87/274 (31%), Positives = 144/274 (52%), Gaps = 21/274 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI    +L  +EE  LA+R  + GD +A  R++ S+LRLVVKIA  Y   GL   ++
Sbjct: 68  YLNEIGHASLLTAEEEVALARRV-QQGDAAARARMIESNLRLVVKIARRYMNRGLAFLDL 126

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK--IGTTANQKRLF 136
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     ++  I       +  
Sbjct: 127 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERGIMNQTRTIRLPIHVIKEINQYL 186

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
              RRL   L      + +P  V  IA  +  S  +V  M     G  S++  I    K+
Sbjct: 187 RTQRRLTQTL------DHEP-TVDEIADAMGRSPEDVRRMRGLNEGTTSVDVPIG---KD 236

Query: 197 SSQ-WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--- 252
           S +   D +  +  G  + ++E ++       L   +  L  ++R + E RR   N    
Sbjct: 237 SDRVLLDAIPDETQGMPENVLEDDDVVRH---LQDWLGFLTDKQRAVLE-RRFGLNGHER 292

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            TLE + ++  V+RERVRQI+  A ++++E +++
Sbjct: 293 YTLEQVGTQVGVTRERVRQIQIDALRRLRELMER 326


>gi|320547037|ref|ZP_08041336.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           equinus ATCC 9812]
 gi|320448322|gb|EFW89066.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           equinus ATCC 9812]
          Length = 369

 Score =  112 bits (280), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 87/269 (32%), Positives = 141/269 (52%), Gaps = 21/269 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA      GDL A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLSSEEEKELAVAV-AAGDLQAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 218

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L      +  PEQ   IA+++++S  +V  +  ++A +  SL   I   D   
Sbjct: 219 LVREQRNLLQELGQDPTPEQ---IAERMDMSPDKVREI-LKIAQEPVSLETPIGEED--D 272

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 273 SHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 326

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE++   F V+RER+RQIEA+A +K++
Sbjct: 327 RTLEDVGKVFNVTRERIRQIEAKALRKLR 355


>gi|149908704|ref|ZP_01897365.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region
           4:Sigma-70region 1.2 [Moritella sp. PE36]
 gi|149808246|gb|EDM68185.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region
           4:Sigma-70region 1.2 [Moritella sp. PE36]
          Length = 284

 Score =  112 bits (280), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 86/287 (29%), Positives = 146/287 (50%), Gaps = 29/287 (10%)

Query: 15  GLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
            L  Y++++ +   +L K+EEY  A    E GD  A  R++ S+LRLV+ IA  Y+   L
Sbjct: 9   ALDVYMYQVNQSSKLLTKEEEYETAMASNE-GDEKARQRMIQSNLRLVINIAKRYQHTSL 67

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ- 132
           P+ +++ EGN GL+ AV+KFD  +GFR +TY++WWIK  ++ +I+     +++     + 
Sbjct: 68  PLVDIIQEGNTGLIHAVEKFDATKGFRFSTYAVWWIKNNIERFIMNQSRTIRVPIHIGKV 127

Query: 133 -KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
            KR+    R  +  LQ   D       V+ +A+ L +  ++V  +      + SL+  I 
Sbjct: 128 YKRILKTAREQELDLQCNHD-------VMTLAEFLEMQYAQVNEVLSYYFNEASLDKTIV 180

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKE----ERKNRRNMLTRSMSVLNPRERRIFEAR- 246
           +   +S+   D L       E   I K     E  +    L   +  L+ R+R+I E R 
Sbjct: 181 TDRDSSTALVDML-------EDYSICKPNDELEDADTLCYLNEVLGHLSERDRKIIELRF 233

Query: 247 -RLQENPVTLENLSSEFEVSRERVRQIEARAFKKV-----QESIQKQ 287
              +E+P+TL  +     +SRER+RQI   + +K+     Q ++QKQ
Sbjct: 234 GLGEEDPLTLHVIGERLSMSRERIRQIINLSLQKIQPELLQNTVQKQ 280


>gi|313608766|gb|EFR84582.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           F2-208]
          Length = 374

 Score =  112 bits (280), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 88/276 (31%), Positives = 135/276 (48%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LAKR  E GD+ A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 108 YLKEIGRVDLLTADEEIALAKRI-EAGDIEAKGRLAEANLRLVVSIAKRYVGRGMLFLDL 166

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 167 IQEGNMGLMKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 226

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q+ L  +L R     +   + +L  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 227 RVQRSLLQDLGRDPSPEEIGEEMDLPTEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 282

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 283 DFIEDQDATSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 325

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 326 GLDDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLR 361


>gi|119468990|ref|ZP_01612015.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Alteromonadales bacterium TW-7]
 gi|119447642|gb|EAW28909.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Alteromonadales bacterium TW-7]
          Length = 324

 Score =  112 bits (280), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 85/273 (31%), Positives = 151/273 (55%), Gaps = 17/273 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A++  + G  ++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 53  YLGEIGFSPLLSAEEEVFFARKSLK-GCEASRKRMIESNLRLVVKIARRYNNRGLALLDL 111

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 112 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 170

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +   Q + D+    E++     K     ++++ +N ++A   S++  I    +N S
Sbjct: 171 LRTARELTQKL-DHEPTAEEIAECLDKPVEDVTKMLRLNEKIA---SVDMPIGG--ENDS 224

Query: 199 QWQDWLVYDH-DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR---LQENPVT 254
              D L  +  +G E  + + E  K+    +   +  LN ++R +  ARR   L   P T
Sbjct: 225 VLLDILPDEKGNGPEGEVQDTEINKH----IVDWLGELNLKQREVL-ARRFGLLGYEPST 279

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           LE++  E  ++RERVRQI+  A +++++ +Q++
Sbjct: 280 LEDVGREIGLTRERVRQIQVEALRRLKDILQQE 312


>gi|257869538|ref|ZP_05649191.1| RNA polymerase sigma-43 factor [Enterococcus gallinarum EG2]
 gi|257803702|gb|EEV32524.1| RNA polymerase sigma-43 factor [Enterococcus gallinarum EG2]
          Length = 368

 Score =  112 bits (280), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 87/273 (31%), Positives = 135/273 (49%), Gaps = 31/273 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGRVPLLTAEEEVALALKI-EEGDQEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 161 IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 220

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 221 RIQRQLLQDLGREPTPEEIGAEMDLPTEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 276

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S           +  E VL    +R+   N+L     + + R R       
Sbjct: 277 DFIEDQDATSPAEHAAYELLKEQLEDVLDTLTDREE--NVLRLRFGIDDGRTR------- 327

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                 TLE +   F V+RER+RQIEA+A +K+
Sbjct: 328 ------TLEEVGKVFGVTRERIRQIEAKALRKL 354


>gi|257867642|ref|ZP_05647295.1| RNA polymerase sigma-43 factor [Enterococcus casseliflavus EC30]
 gi|257873971|ref|ZP_05653624.1| RNA polymerase sigma-43 factor [Enterococcus casseliflavus EC10]
 gi|257876550|ref|ZP_05656203.1| RNA polymerase sigma-43 factor [Enterococcus casseliflavus EC20]
 gi|325571155|ref|ZP_08146727.1| DNA-directed RNA polymerase sigma subunit RpoD [Enterococcus
           casseliflavus ATCC 12755]
 gi|257801725|gb|EEV30628.1| RNA polymerase sigma-43 factor [Enterococcus casseliflavus EC30]
 gi|257808135|gb|EEV36957.1| RNA polymerase sigma-43 factor [Enterococcus casseliflavus EC10]
 gi|257810716|gb|EEV39536.1| RNA polymerase sigma-43 factor [Enterococcus casseliflavus EC20]
 gi|325156240|gb|EGC68426.1| DNA-directed RNA polymerase sigma subunit RpoD [Enterococcus
           casseliflavus ATCC 12755]
          Length = 368

 Score =  112 bits (280), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 87/273 (31%), Positives = 135/273 (49%), Gaps = 31/273 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGRVPLLTAEEEVALALKI-EEGDQEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 161 IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 220

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 221 RIQRQLLQDLGREPTPEEIGAEMDLPTEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 276

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S           +  E VL    +R+   N+L     + + R R       
Sbjct: 277 DFIEDQDATSPAEHAAYELLKEQLEDVLDTLTDREE--NVLRLRFGIDDGRTR------- 327

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                 TLE +   F V+RER+RQIEA+A +K+
Sbjct: 328 ------TLEEVGKVFGVTRERIRQIEAKALRKL 354


>gi|262282856|ref|ZP_06060623.1| RNA polymerase sigma factor RpoD [Streptococcus sp. 2_1_36FAA]
 gi|262261108|gb|EEY79807.1| RNA polymerase sigma factor RpoD [Streptococcus sp. 2_1_36FAA]
          Length = 370

 Score =  112 bits (280), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 86/268 (32%), Positives = 140/268 (52%), Gaps = 21/268 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 103 YLKEIGVVPLLTNEEEQELAILV-EQGDTEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 161

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 162 IQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 219

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L      +  PEQ   IA++++++  +V  +  ++A +  SL   I   D   
Sbjct: 220 LVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEED--D 273

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 274 SHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 327

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKV 280
            TLE++   F V+RER+RQIEA+A +K+
Sbjct: 328 RTLEDVGKVFNVTRERIRQIEAKALRKL 355


>gi|304383342|ref|ZP_07365808.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella marshii
           DSM 16973]
 gi|304335510|gb|EFM01774.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella marshii
           DSM 16973]
          Length = 287

 Score =  112 bits (280), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 89/286 (31%), Positives = 160/286 (55%), Gaps = 21/286 (7%)

Query: 9   IVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           I N E   L +Y+ EI    +L  +EE  LA+R R  GD  A  +L  ++LR VV +A  
Sbjct: 10  ITNRETASLEKYLQEIGHEELLTVEEEVELAQRIR-RGDRQALEKLTKANLRFVVSVAKQ 68

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V++ 
Sbjct: 69  YQNQGLSLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRL- 127

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE---SEVISMNCRLAGDE 184
              NQ     ++ R+   L      N +   +  IA K+N+S+   ++V+ +N R     
Sbjct: 128 -PLNQ---IGSVNRINKMLNRFEQENERRPSMEEIADKVNLSQEKVADVLKVNSRQV--- 180

Query: 185 SLNALINSSDKNSSQWQDWLV-YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           S++A     D+ S    D L   D    ++ L+    R++ R  + R++ VLN RER I 
Sbjct: 181 SVDAPFTEGDETS--LLDVLCNNDSPMADRELV----RESLREEINRTLQVLNERERNIV 234

Query: 244 EA-RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           EA   + +   TLE + ++F ++RERVRQI+ +A ++++++ + ++
Sbjct: 235 EAFFGINQGEKTLEEIGNKFGLTRERVRQIKEKAIRRLRQNTKSRL 280


>gi|300765597|ref|ZP_07075576.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           N1-017]
 gi|300513698|gb|EFK40766.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           N1-017]
          Length = 374

 Score =  112 bits (280), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 88/276 (31%), Positives = 135/276 (48%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LAKR  E GD+ A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 108 YLKEIGRVDLLTADEEIALAKRI-EAGDIEAKGRLAEANLRLVVSIAKRYVGRGMLFLDL 166

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 167 IQEGNMGLMKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 226

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q+ L  +L R     +   + +L  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 227 RVQRSLLQDLGRDPSPEEIGEEMDLPTEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 282

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 283 DFIEDQDATSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 325

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 326 GLDDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLR 361


>gi|116514229|ref|YP_813135.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC BAA-365]
 gi|116093544|gb|ABJ58697.1| RNA polymerase, sigma 70 subunit, RpoD [Lactobacillus delbrueckii
           subsp. bulgaricus ATCC BAA-365]
          Length = 372

 Score =  112 bits (280), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 85/275 (30%), Positives = 132/275 (48%), Gaps = 33/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI +  +L  +EE  LAKR  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 106 YLKEIGRFNLLTSEEEVALAKRI-EAGDEEAKQELAEANLRLVVSIAKRYVGRGMNFLDL 164

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 165 IQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 222

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLA--GDESLNA 188
           L R++         + +PE++ A        + + L V++ E +S+   +    D  L  
Sbjct: 223 LIRIQRQFLQDLGRDPEPEEIAAEMDLPVKKVREALKVAQ-EPVSLETPIGEEDDSHLGD 281

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-R 247
            I   D  S +        H   E +          ++ L   +  L  RE  +   R  
Sbjct: 282 FIEDKDATSPEQ-------HAASEML----------KDQLAEVLDTLTDREENVLRLRFG 324

Query: 248 LQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           L + NP TLE +   F V+RER+RQIEA+A +K++
Sbjct: 325 LDDGNPRTLEEVGRVFGVTRERIRQIEAKALRKLR 359


>gi|160872453|ref|ZP_02062585.1| RNA polymerase sigma factor RpoS [Rickettsiella grylli]
 gi|159121252|gb|EDP46590.1| RNA polymerase sigma factor RpoS [Rickettsiella grylli]
          Length = 330

 Score =  112 bits (280), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 94/277 (33%), Positives = 142/277 (51%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R    GD  A  R++ S+LRLVVKIA  Y   GL   ++
Sbjct: 62  YLNEIGFSPLLSAEEEVYYA-RLIAKGDQDARKRMIESNLRLVVKIARHYNNRGLQFLDL 120

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM AV+KFDPERGFR +TY+ WW++ A++  I+     V++            
Sbjct: 121 IEEGNLGLMHAVEKFDPERGFRFSTYATWWVRQAIERAIMNQARTVRLPIHV-------- 172

Query: 139 LRRLKGHLQAITDNNLKPEQVVA---IAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           ++ L  +LQA  +   K +       IAK L+    EV     R+ G   LN  I S D 
Sbjct: 173 VKELNVYLQAARELTQKLDHKPTSDEIAKWLDRPFEEV----ERMLG---LNEHITSVDA 225

Query: 196 NSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR---LQE 250
            +S   D  + +   D +E       E +N R  L   +  L+  +R +  ARR   L  
Sbjct: 226 PASSEADKPLLETLSDNRENDPEHILEGENLRKRLEGWLKQLSTNQREVI-ARRYGLLGC 284

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           + +TLE +     ++RERVRQI+    K +++ ++KQ
Sbjct: 285 DRMTLEEVGEVIGLTRERVRQIQVEGLKTLRKIMEKQ 321


>gi|254495200|ref|ZP_05108124.1| RNA polymerase sigma-70 factor RpoD [Polaribacter sp. MED152]
 gi|85819552|gb|EAQ40709.1| RNA polymerase sigma-70 factor RpoD [Polaribacter sp. MED152]
          Length = 287

 Score =  112 bits (280), Expect = 6e-23,   Method: Compositional matrix adjust.
 Identities = 83/296 (28%), Positives = 158/296 (53%), Gaps = 49/296 (16%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ ++   EE  LA+  +  GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGKVDLITADEEVELAQLIK-AGDQRALEKLTKANLRFVVSVAKQYQNQGLTL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
            ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++      Q  I+R   L KIG+ 
Sbjct: 77  PDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVR-LPLNKIGSI 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCR 179
               +++  L +           N +P     IAKKL+++ ++V          +SM+  
Sbjct: 136 NKINKMYAFLEQ----------ENERPPSPEEIAKKLDMTVNDVKESMKNSGRHVSMDAP 185

Query: 180 L--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
           L    D +L  ++NS +  +              ++VL+     ++ R  + R++  L P
Sbjct: 186 LIEGEDSNLYDVLNSGESPNP-------------DRVLL----HESLRIEINRALETLTP 228

Query: 238 RERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           RE  + +    L E+ P+TLE +   F+++RERVRQI+ +A ++++ + + ++ ++
Sbjct: 229 READVVKLYFGLGEHQPMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKILMT 284


>gi|16800559|ref|NP_470827.1| RNA polymerase sigma factor RpoD [Listeria innocua Clip11262]
 gi|116872885|ref|YP_849666.1| RNA polymerase sigma factor RpoD [Listeria welshimeri serovar 6b
           str. SLCC5334]
 gi|217964400|ref|YP_002350078.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43) [Listeria
           monocytogenes HCC23]
 gi|290894216|ref|ZP_06557185.1| rpoD protein [Listeria monocytogenes FSL J2-071]
 gi|20140102|sp|Q92BQ6|RPOD_LISIN RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-43
 gi|16413964|emb|CAC96722.1| RNA polymerase sigma factor RpoD [Listeria innocua Clip11262]
 gi|116741763|emb|CAK20887.1| RNA polymerase sigma factor RpoD (Sigma-A) [Listeria welshimeri
           serovar 6b str. SLCC5334]
 gi|217333670|gb|ACK39464.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43) [Listeria
           monocytogenes HCC23]
 gi|290556213|gb|EFD89758.1| rpoD protein [Listeria monocytogenes FSL J2-071]
 gi|307571035|emb|CAR84214.1| RNA polymerase sigma factor [Listeria monocytogenes L99]
 gi|313623755|gb|EFR93895.1| RNA polymerase sigma factor RpoD [Listeria innocua FSL J1-023]
          Length = 374

 Score =  112 bits (280), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 88/276 (31%), Positives = 135/276 (48%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LAKR  E GD+ A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 108 YLKEIGRVDLLTADEEIALAKRI-EAGDIEAKGRLAEANLRLVVSIAKRYVGRGMLFLDL 166

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 167 IQEGNMGLMKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 226

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q+ L  +L R     +   + +L  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 227 RVQRSLLQDLGRDPSPEEIGEEMDLPTEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 282

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 283 DFIEDQDATSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 325

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 326 GLDDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLR 361


>gi|90020900|ref|YP_526727.1| RNA polymerase sigma factor RpoS [Saccharophagus degradans 2-40]
 gi|89950500|gb|ABD80515.1| RNA polymerase sigma factor RpoS [Saccharophagus degradans 2-40]
          Length = 333

 Score =  112 bits (280), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 85/273 (31%), Positives = 149/273 (54%), Gaps = 17/273 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A++  + G  ++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 63  YLNEIGFSPLLSAEEEVFFARKALK-GCEASRKRMIESNLRLVVKIARRYVNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 180

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN-SSDKNS 197
           LR  +   Q + D+   PE++  + +K       ++++N R+    S++  I  SS+K  
Sbjct: 181 LRAARELSQKL-DHEPSPEEIATLLEKPLEDVERMLALNERVT---SMDVPIGPSSEKTV 236

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVT 254
                  V D D  + V + +E   +    L   +  L+ ++R +  ARR         T
Sbjct: 237 VD----TVADQDVSDPVELLQE--SDLSQSLDGWLDELSEKQREVV-ARRFGLRGHETST 289

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           LE +  E  ++RERVRQI+  A +++++ ++KQ
Sbjct: 290 LEEVGKEIGLTRERVRQIQVEALRRLRDILEKQ 322


>gi|317495391|ref|ZP_07953760.1| RNA polymerase sigma factor RpoD [Gemella moribillum M424]
 gi|316914450|gb|EFV35927.1| RNA polymerase sigma factor RpoD [Gemella moribillum M424]
          Length = 361

 Score =  112 bits (280), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 91/270 (33%), Positives = 143/270 (52%), Gaps = 19/270 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS----AAHRLVTSHLRLVVKIAMGYRGYGLP 74
           Y+ EI K+P+L K++E  L+K   E G  S    A   L  ++LRLVV IA  Y G G+ 
Sbjct: 91  YLKEIGKVPLLSKEKELELSKII-ESGTESEKEQAKKDLAEANLRLVVSIAKRYVGRGML 149

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
             +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I    +   
Sbjct: 150 FLDLIQEGNMGLIKAVEKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVE 207

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSS 193
               L R++  L        KPE+   IAKK+N++  +V  +  ++A +  SL   I   
Sbjct: 208 TINRLIRVQRQLLQDLGREPKPEE---IAKKMNMTPDKVREI-LKIAQEPVSLETPIGEE 263

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENP 252
           D   S   D+ + D D Q  V  E    +  +  L   +  L  RE  + + R  L++  
Sbjct: 264 D--DSHLGDF-IEDKDAQSPV--EHAANELLKEQLEEILETLTDREENVLKLRFGLKDGK 318

Query: 253 V-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
             TLE + S F V+RER+RQIEA+A +K++
Sbjct: 319 THTLEEVGSAFGVTRERIRQIEAKAIRKLK 348


>gi|149370424|ref|ZP_01890113.1| RNA polymerase sigma-70 factor [unidentified eubacterium SCB49]
 gi|149355975|gb|EDM44532.1| RNA polymerase sigma-70 factor [unidentified eubacterium SCB49]
          Length = 288

 Score =  112 bits (280), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 81/277 (29%), Positives = 146/277 (52%), Gaps = 32/277 (11%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+ ++ KI M+  +EE  LA+R RE GD  A  +L  ++LR V+ +A  Y+  GL +
Sbjct: 18  LNSYLQDVSKIDMITAEEEVELAQRIRE-GDKRALDKLTRANLRFVISVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + I     +V++    N+   
Sbjct: 77  PDLINEGNVGLVKAAKRFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRL--PLNKIGD 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRLAGDES 185
              +++   HLQ + +     ++   IA +L+++ S V          ISM+      E+
Sbjct: 135 INKVKKASIHLQQVYERVPTAQE---IANELDITVSSVKSSMKNSNRSISMDAPFQEGEN 191

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
            N L +      S   D      +G  Q  ++ E        + R++  L+ RE  + + 
Sbjct: 192 DNNLYDVISSGESPNPD------NGLMQESLKTE--------IDRALDTLSQREADVVKL 237

Query: 246 R-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              L  NPV TL+ +   F++SRERVRQI  +A +++
Sbjct: 238 NFGLSGNPVMTLQEIGDTFDLSRERVRQIREKAIRRL 274


>gi|3062909|dbj|BAA25730.1| SigA [Bacillus sp.]
          Length = 372

 Score =  112 bits (280), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 88/275 (32%), Positives = 138/275 (50%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LA R  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 106 YLKEIGRVPLLTAEEEIELATRI-EQGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 164

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 165 IQEGNMGLIKAVEKFDYNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 224

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  ++ R     +   + +L PE+V  I K       E +S+   +    D  L 
Sbjct: 225 RVQRQLLQDVGREPSPEEVAEEMDLTPEKVREILK----IAQEPVSLETPIGEEDDSHLG 280

Query: 188 ALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
             I   D+++    D   Y+   +  E VL    +R+   N+L     + + R R     
Sbjct: 281 DFI--EDQDALAPSDAAAYELLKEQLEDVLDTLTDREE--NVLRLRFGLDDGRTR----- 331

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                   TLE +   F V+RER+RQIEA+A +K+
Sbjct: 332 --------TLEEVGKVFGVTRERIRQIEAKALRKL 358


>gi|313206169|ref|YP_004045346.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Riemerella
           anatipestifer DSM 15868]
 gi|312445485|gb|ADQ81840.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Riemerella
           anatipestifer DSM 15868]
 gi|315023147|gb|EFT36160.1| RNA polymerase sigma factor RpoD [Riemerella anatipestifer RA-YM]
 gi|325336386|gb|ADZ12660.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Riemerella anatipestifer RA-GD]
          Length = 288

 Score =  112 bits (280), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 80/283 (28%), Positives = 150/283 (53%), Gaps = 43/283 (15%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ ++   EE  LA++ R  GD  A  +L+ ++LR VV ++  Y+  GL +
Sbjct: 18  LDKYLQEIGKVDLITADEEVELAQKIR-AGDKVALEKLIKANLRFVVSVSKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GLM+A K++D  RGF+  +Y++WWI+ ++ + +     +V++    N+   
Sbjct: 77  PDLINEGNLGLMKAAKRYDETRGFKFISYAVWWIRQSILQALAEQSRIVRL--PLNKIGS 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRL--AGD 183
              + +   HL+   +    PE+   +A+ L++SE ++          +SM+  L    D
Sbjct: 135 INKINKAYAHLEQENERPPSPEE---LAEVLDMSEEDIKESMKNSGRHLSMDAPLVEGED 191

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            +L  ++ S +  S   +  L       E + IE E          R++  L PRE  + 
Sbjct: 192 SNLYDVLRSGESPSPDKELML-------ESLQIEIE----------RALQTLTPREADLV 234

Query: 244 EARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              RL      ++P+TLE +   F+++RERVRQI+ +A K+++
Sbjct: 235 ---RLYFGLNGKHPMTLEEIGETFDLTRERVRQIKEKAIKRLK 274


>gi|284104060|ref|ZP_06386126.1| RNA polymerase, sigma 70 subunit, RpoD family [Candidatus
           Poribacteria sp. WGA-A3]
 gi|283830219|gb|EFC34468.1| RNA polymerase, sigma 70 subunit, RpoD family [Candidatus
           Poribacteria sp. WGA-A3]
          Length = 271

 Score =  112 bits (280), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 85/273 (31%), Positives = 147/273 (53%), Gaps = 21/273 (7%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI +I ++   EE  LA+R ++ GD  A  +L  ++LR VV +A  ++G GL +
Sbjct: 2   LDQYLKEIGQIDLVTPAEEAELARRIKQ-GDEEALLKLTRANLRFVVSVAKKFQGQGLHL 60

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           +++++EGN GL++A K+FD  RGF+  +Y++WWI+ ++ + +     +V++    NQ   
Sbjct: 61  TDLINEGNYGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQGRVVRL--PLNQIGT 118

Query: 136 FFNLRRLKGHL--QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
              +R+    L  +   D NL+      +A  L +   +V S   R A   S++A  N  
Sbjct: 119 ISKIRKSSARLAQEHERDPNLE-----ELATDLQIDIEKVRSAMQRTARHLSMDAPFNEE 173

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI----FEARRLQ 249
           D+NS    D L  +        +  E  K     +  ++S L PRE  I    F   R  
Sbjct: 174 DENS--LLDVLPSNEIAPPDEPLRGESLKID---IEVALSSLCPREAEITRLYFGVGR-- 226

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           E+P+TLE +   F+++RERVRQI+ +A +K+++
Sbjct: 227 EHPLTLEEIGLRFDLTRERVRQIKEKALRKLRQ 259


>gi|146281946|ref|YP_001172099.1| RNA polymerase sigma factor RpoS [Pseudomonas stutzeri A1501]
 gi|145570151|gb|ABP79257.1| sigma factor RpoS [Pseudomonas stutzeri A1501]
          Length = 332

 Score =  112 bits (280), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 87/278 (31%), Positives = 145/278 (52%), Gaps = 29/278 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 64  YLNEIGFSPLLTPEEEVHFA-RLAQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 122

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 123 VEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 181

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKK--------LNVSESEVISMNCRLAGDESLNALI 190
           LR  +   Q + D+   PE++  + +K        L ++E  V S++  L  D     L 
Sbjct: 182 LRAARELTQKL-DHEPSPEEIANLLEKPVGEVKRMLGLNE-RVTSVDVSLGPDTDKTLLD 239

Query: 191 NSSDKNSSQWQDWLVYDHDGQ--EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
             +D   +   + L+ D      +Q L +  E++  R ++ R   +      R  EA   
Sbjct: 240 TLTDDRPTDPCELLLDDDLSASIDQWLSDLSEKQ--REVVIRRFGL------RGHEAS-- 289

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                TLE +  E  ++RERVRQI+  A ++++E +++
Sbjct: 290 -----TLEEVGQEIGLTRERVRQIQVEALRRLREILER 322


>gi|296327931|ref|ZP_06870466.1| DNA-directed RNA polymerase sigma subunit RpoD [Fusobacterium
           nucleatum subsp. nucleatum ATCC 23726]
 gi|296154887|gb|EFG95669.1| DNA-directed RNA polymerase sigma subunit RpoD [Fusobacterium
           nucleatum subsp. nucleatum ATCC 23726]
          Length = 418

 Score =  112 bits (280), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 84/278 (30%), Positives = 147/278 (52%), Gaps = 27/278 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE   AK+  E GD  A+ +L+ S+LRLVV IA  +   GL + ++
Sbjct: 151 YLREIGQVPLLTHEEEIDYAKKAYE-GDEEASKKLIESNLRLVVSIAKKHTNRGLKLLDL 209

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM+AV+KF+  +G++ +TY+ WWI+ A+   I      ++I        +   
Sbjct: 210 IQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPV-----HMIET 264

Query: 139 LRRLKG----HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           + ++K     +LQ  T  +  PE    +A++L +   ++ ++        SL   + S +
Sbjct: 265 INKIKKESRIYLQE-TGKDASPE---ILAERLGMEVDKIKAIQEMNQEPISLETPVGSEE 320

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNR---RNMLTRSMSVLNPRERRIFEARRLQEN 251
              S+  D++      ++Q      E  NR   R  L   +  L+PRE ++   R   ++
Sbjct: 321 --DSELGDFV------EDQKTTSPYEATNRAILREELDAVLKTLSPREEKVLRYRYGLDD 372

Query: 252 --PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             P TLE +   F V+RER+RQIE +A +K++   +K+
Sbjct: 373 SSPKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRKK 410


>gi|16803494|ref|NP_464979.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes EGD-e]
 gi|46907682|ref|YP_014071.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes serotype
           4b str. F2365]
 gi|47092744|ref|ZP_00230530.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes str. 4b
           H7858]
 gi|47095405|ref|ZP_00233015.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes str. 1/2a
           F6854]
 gi|224499695|ref|ZP_03668044.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes Finland
           1988]
 gi|224501605|ref|ZP_03669912.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           R2-561]
 gi|226224055|ref|YP_002758162.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes Clip81459]
 gi|254824487|ref|ZP_05229488.1| RNA polymerase subunit sigma [Listeria monocytogenes FSL J1-194]
 gi|254827742|ref|ZP_05232429.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           N3-165]
 gi|254829787|ref|ZP_05234442.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes 10403S]
 gi|254852080|ref|ZP_05241428.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           R2-503]
 gi|254898380|ref|ZP_05258304.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes J0161]
 gi|254912128|ref|ZP_05262140.1| sigma 43 subunit of RNA polymerase [Listeria monocytogenes J2818]
 gi|254932639|ref|ZP_05265998.1| RNA polymerase subunit sigma [Listeria monocytogenes HPB2262]
 gi|254936456|ref|ZP_05268153.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes F6900]
 gi|254994146|ref|ZP_05276336.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           J2-064]
 gi|255029176|ref|ZP_05301127.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes LO28]
 gi|255522085|ref|ZP_05389322.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           J1-175]
 gi|284801841|ref|YP_003413706.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes 08-5578]
 gi|284994983|ref|YP_003416751.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes 08-5923]
 gi|315282349|ref|ZP_07870778.1| RNA polymerase sigma factor RpoD [Listeria marthii FSL S4-120]
 gi|1710684|sp|P52331|RPOD_LISMO RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-43
 gi|664756|gb|AAC43306.1| sigma 43 subunit of RNA polymerase [Listeria monocytogenes]
 gi|16410883|emb|CAC99532.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes EGD-e]
 gi|46880950|gb|AAT04248.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes serotype
           4b str. F2365]
 gi|47016226|gb|EAL07149.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes str. 1/2a
           F6854]
 gi|47018932|gb|EAL09679.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes str. 4b
           H7858]
 gi|225876517|emb|CAS05226.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes serotype
           4b str. CLIP 80459]
 gi|258600121|gb|EEW13446.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           N3-165]
 gi|258605378|gb|EEW17986.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           R2-503]
 gi|258609048|gb|EEW21656.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes F6900]
 gi|284057403|gb|ADB68344.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes 08-5578]
 gi|284060450|gb|ADB71389.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes 08-5923]
 gi|293584198|gb|EFF96230.1| RNA polymerase subunit sigma [Listeria monocytogenes HPB2262]
 gi|293590099|gb|EFF98433.1| sigma 43 subunit of RNA polymerase [Listeria monocytogenes J2818]
 gi|293593725|gb|EFG01486.1| RNA polymerase subunit sigma [Listeria monocytogenes FSL J1-194]
 gi|313614010|gb|EFR87725.1| RNA polymerase sigma factor RpoD [Listeria marthii FSL S4-120]
 gi|328465497|gb|EGF36726.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes 1816]
 gi|332311895|gb|EGJ24990.1| RNA polymerase sigma factor rpoD [Listeria monocytogenes str. Scott
           A]
 gi|1093602|prf||2104269C RNA polymerase:SUBUNIT=sigma
          Length = 374

 Score =  112 bits (280), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 88/276 (31%), Positives = 135/276 (48%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LAKR  E GD+ A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 108 YLKEIGRVDLLTADEEIALAKRI-EAGDIEAKGRLAEANLRLVVSIAKRYVGRGMLFLDL 166

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 167 IQEGNMGLMKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 226

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q+ L  +L R     +   + +L  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 227 RVQRSLLQDLGRDPSPEEIGEEMDLPTEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 282

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 283 DFIEDQDATSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 325

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 326 GLDDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLR 361


>gi|326335966|ref|ZP_08202143.1| RNA polymerase sigma-70 factor [Capnocytophaga sp. oral taxon 338
           str. F0234]
 gi|325691930|gb|EGD33892.1| RNA polymerase sigma-70 factor [Capnocytophaga sp. oral taxon 338
           str. F0234]
          Length = 287

 Score =  112 bits (280), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 82/284 (28%), Positives = 152/284 (53%), Gaps = 31/284 (10%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ ++   EE  LA+R +  GD  A  RL  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGKVDLISADEEVELAQRIK-AGDKVALERLTKANLRFVVSVAKQYQNQGLTL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
            ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++      Q  I+R   L KIG+ 
Sbjct: 77  PDLINEGNMGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVR-LPLNKIGSI 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA- 188
               +++  L +    + +  +          IA++L++S S+V           S++A 
Sbjct: 136 NKINKMYAYLEQTHERIPSAEE----------IARELDMSVSDVKESMKNSGRHISMDAP 185

Query: 189 LINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           L+   D N        +YD    G+     ++   ++ +  + R++  L PRE  +    
Sbjct: 186 LVEGEDSN--------LYDVLRSGESPNPDKELMHESLKTEIERALETLTPREADVIRLY 237

Query: 247 -RLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
             L EN P+TLE +   FE++RERVRQI+ +A ++++ + + ++
Sbjct: 238 FGLGENYPMTLEEIGETFELTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|194397936|ref|YP_002037704.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae G54]
 gi|194357603|gb|ACF56051.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae G54]
          Length = 369

 Score =  112 bits (280), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 88/271 (32%), Positives = 143/271 (52%), Gaps = 29/271 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E GD+ A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLTNEEEKELALAV-EAGDIEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKL- 219

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSS 193
               +R  +  LQ +   +  PEQ   IA++++++  +V  +  ++A +  SL   I   
Sbjct: 220 ----VREQRNLLQELG-QDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEE 270

Query: 194 DKNSSQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQ 249
           D   S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L 
Sbjct: 271 D--DSHLGDFI------EDEVIENPVDYTTRIVLREQLDEILDTLTDREENVLRLRFGLD 322

Query: 250 ENPV-TLENLSSEFEVSRERVRQIEARAFKK 279
           +  + TLE++   F V+RER+RQIEA+A +K
Sbjct: 323 DGKMRTLEDVGKVFNVTRERIRQIEAKALRK 353


>gi|323490072|ref|ZP_08095293.1| RNA polymerase sigma factor RpoD [Planococcus donghaensis MPA1U2]
 gi|323396368|gb|EGA89193.1| RNA polymerase sigma factor RpoD [Planococcus donghaensis MPA1U2]
          Length = 384

 Score =  112 bits (280), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 88/276 (31%), Positives = 138/276 (50%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L+ +EE  LAK   E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 118 YLKEIGRVDLLKAEEEVRLAKLI-EQGDEEAKKRLAEANLRLVVSIAKRYVGRGMLFLDL 176

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 177 IQEGNMGLIKAVEKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 236

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I   L +++ E +S+   +    D  L 
Sbjct: 237 RVQRQLLQDLGRDPSPEEIGEEMDLLPEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 292

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I  SD  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 293 DFIEDSDAQSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 335

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 336 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 371


>gi|319651585|ref|ZP_08005712.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
 gi|317396652|gb|EFV77363.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
          Length = 374

 Score =  112 bits (280), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 86/276 (31%), Positives = 133/276 (48%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 108 YLKEIGRVDLLSAEEEIALANRI-EEGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 166

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 167 IQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 226

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   D +L P++V  I K       E +S+   +    D  L 
Sbjct: 227 RVQRQLLQDLGREPTPEEIAEDMDLTPDKVREILK----IAQEPVSLETPIGEEDDSHLG 282

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S         +H   E +          +  L   +  L  RE  +   R 
Sbjct: 283 DFIEDQDATSPS-------EHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 325

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 326 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 361


>gi|255026189|ref|ZP_05298175.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           J2-003]
          Length = 361

 Score =  112 bits (280), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 88/276 (31%), Positives = 135/276 (48%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LAKR  E GD+ A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 95  YLKEIGRVDLLTADEEIALAKRI-EAGDIEAKGRLAEANLRLVVSIAKRYVGRGMLFLDL 153

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 154 IQEGNMGLMKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 213

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q+ L  +L R     +   + +L  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 214 RVQRSLLQDLGRDPSPEEIGEEMDLPTEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 269

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 270 DFIEDQDATSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 312

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 313 GLDDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLR 348


>gi|302874342|ref|YP_003842975.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           cellulovorans 743B]
 gi|307689391|ref|ZP_07631837.1| RNA polymerase sigma factor RpoD [Clostridium cellulovorans 743B]
 gi|302577199|gb|ADL51211.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           cellulovorans 743B]
          Length = 363

 Score =  112 bits (280), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 82/265 (30%), Positives = 136/265 (51%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  + E  LA+R  E GD +A  +L  ++LRLVV IA  Y G G+   ++
Sbjct: 97  YLKEIGKVPLLSPETEIELAERI-EAGDPAAKKKLAEANLRLVVSIAKRYVGRGMLFLDL 155

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 156 IQEGNLGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 213

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L      +  PE+   +A+K+ +   +VI +  R    E ++      ++  S
Sbjct: 214 LLRITRQLVQELGRDPLPEE---LAEKMEMPVDKVIEI--RKIAQEPVSLETPIGEEEDS 268

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++  D              K +   L   +  L PRE ++   R   ++    TLE
Sbjct: 269 HLGDFIPDDDAPAPAEAAAFTMLKEQ---LINVLDTLTPREEKVLRLRFGLDDGRARTLE 325

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF V+RER+RQIEA+A +K++
Sbjct: 326 EVGREFNVTRERIRQIEAKALRKLR 350


>gi|86143196|ref|ZP_01061598.1| putative sigma factor A [Leeuwenhoekiella blandensis MED217]
 gi|85830101|gb|EAQ48561.1| putative sigma factor A [Leeuwenhoekiella blandensis MED217]
          Length = 288

 Score =  112 bits (280), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 81/280 (28%), Positives = 144/280 (51%), Gaps = 22/280 (7%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+ ++ K+ M+   EE  LA+R RE GD  A  RL  ++LR VV +A  Y+  GL +
Sbjct: 18  LNTYLQDVSKLDMITADEEVELAQRIRE-GDQVALERLTKANLRFVVSVAKQYQNQGLKL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV-----KIGTTA 130
            ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + I      V     KIGT +
Sbjct: 77  PDLINEGNVGLVKAAKRFDETRGFKFISYAVWWIRQSILQAISEHSRTVRLPLNKIGTIS 136

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              + F  L       Q++     +P     IAK+L+++ ++V         + S++A  
Sbjct: 137 KINKAFSYLE------QSLE----RPPSAEEIAKELDMTVAKVKLAMKNSGRNLSMDAPF 186

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--L 248
              + N S   D L           + +E        + R++  L+PRE  + +      
Sbjct: 187 KEGE-NDSNLYDVLKSGESPNPDADLMQESLGTE---IERALETLSPRESDVIKLNYGLG 242

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            E P TL+ +   F++SRERVRQI  +  ++++ + + +V
Sbjct: 243 GEQPHTLQEIGEMFDLSRERVRQIREKGIRRLRHTSRSKV 282


>gi|196034883|ref|ZP_03102290.1| RNA polymerase sigma-43 factor [Bacillus cereus W]
 gi|195992422|gb|EDX56383.1| RNA polymerase sigma-43 factor [Bacillus cereus W]
          Length = 373

 Score =  112 bits (280), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 87/276 (31%), Positives = 134/276 (48%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 107 YLKEIGRVDLLSAEEEIRLATRI-EEGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 165

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 166 IQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 225

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I K       E +S+   +   GD  L 
Sbjct: 226 RVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILK----IAQEPVSLETPIGEEGDSHLG 281

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 282 DFIEDQEATSPA-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 324

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 325 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 360


>gi|239637627|ref|ZP_04678599.1| RNA polymerase sigma factor RpoD [Staphylococcus warneri L37603]
 gi|239596845|gb|EEQ79370.1| RNA polymerase sigma factor RpoD [Staphylococcus warneri L37603]
 gi|330686029|gb|EGG97652.1| RNA polymerase sigma factor RpoD [Staphylococcus epidermidis
           VCU121]
          Length = 367

 Score =  112 bits (280), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 88/275 (32%), Positives = 133/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  QEE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 101 YLKEIGRVDLLSAQEEIELAKRI-EQGDEIAKSRLAEANLRLVVSIAKRYVGRGMLFLDL 159

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 160 IQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 219

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I K       E +S+   +    D  L 
Sbjct: 220 RVQRQLLQDLGRDPAPEEIGEEMDLPPEKVREILK----IAQEPVSLETPIGEEDDSHLG 275

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 276 DFIEDQEAQSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 318

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 319 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 353


>gi|182416213|ref|YP_001821279.1| RpoD family RNA polymerase sigma factor [Opitutus terrae PB90-1]
 gi|177843427|gb|ACB77679.1| RNA polymerase, sigma 70 subunit, RpoD family [Opitutus terrae
           PB90-1]
          Length = 347

 Score =  112 bits (280), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 82/277 (29%), Positives = 145/277 (52%), Gaps = 16/277 (5%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           +G   L  Y+ +I + P+L  +EE+ LA+R R  GD  A   ++ ++LRLVV+IA  Y  
Sbjct: 30  DGRSSLQIYLQDIGQTPLLTAREEFALAERVR-RGDAGARDHMIRANLRLVVRIAKDYAQ 88

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
           YGLP+++++SEGN+GL+ AV +FDP  G +L+TY+ WWI+ A++         +++    
Sbjct: 89  YGLPLADLISEGNVGLIHAVDRFDPRIGGKLSTYAAWWIRQAIRRAFAHHARAIRLPV-- 146

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNA 188
               +   + RL+    ++++   +      +A +L  +  E I++  + AGD   SL+A
Sbjct: 147 ---HMLDRIARLRRAQASLSEQFGREATTDELAAELQ-APVEKIAL-WKSAGDAPFSLDA 201

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            + +   + S+     + D          ++    R   L   ++ L+ RE  I   R  
Sbjct: 202 AVGTG--SESRRLSETIRDERAPTAFTQLRDATTARD--LRAIIATLDVREATILRLRFG 257

Query: 249 --QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
              + P TL  +S  F ++RERVRQ+E RA + V+ +
Sbjct: 258 LDGDEPQTLHAVSLRFGITRERVRQLERRALQNVRNA 294


>gi|29143180|ref|NP_806522.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
 gi|695759|emb|CAA57298.1| sigma S [Salmonella enterica subsp. enterica serovar Typhi]
 gi|3820469|emb|CAA76807.1| RNA polymerase sigma subunit [Salmonella enterica subsp. enterica
           serovar Typhi str. Ty2]
 gi|29138813|gb|AAO70382.1| RNA polymerase sigma subunit RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
          Length = 384

 Score =  112 bits (279), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 86/286 (30%), Positives = 139/286 (48%), Gaps = 26/286 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFK-KVQESIQKQVELSSSPP 295
              TLE++  E  ++RERVRQI+    +   + S     E  S+ P
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRPSARNSADAGAEYRSAVP 329


>gi|323345452|ref|ZP_08085675.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella oralis
           ATCC 33269]
 gi|323093566|gb|EFZ36144.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella oralis
           ATCC 33269]
          Length = 295

 Score =  112 bits (279), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 77/268 (28%), Positives = 149/268 (55%), Gaps = 14/268 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI    ++  +EE  LA+R R+ GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 27  LDKYLQEIGHEELISVEEEVELAQRIRK-GDRKALEKLTKANLRFVVSVAKQYQNQGLSL 85

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V++    NQ   
Sbjct: 86  PDLINEGNVGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRL--PLNQ--- 140

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
             ++ ++   L      N +   +  IA ++++ E ++I    ++ G   S++A     +
Sbjct: 141 VGSVNKINRALNKFEQENERHPSIEEIADRIDLPEEKIIDA-MKINGKHISVDAPFAEGE 199

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA-RRLQENPV 253
            NS      L    + +     E+   ++ R+ ++R + +LN RER I EA   + +  +
Sbjct: 200 DNS-----LLDIMPNTESPTADERLVSESLRDEISRVLLLLNERERMIIEAFFGINQQDM 254

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TLE +  +F ++RERVRQI+ +A ++++
Sbjct: 255 TLEEIGDKFGLTRERVRQIKEKAIRRLR 282


>gi|228476045|ref|ZP_04060753.1| RNA polymerase sigma factor RpoD [Staphylococcus hominis SK119]
 gi|314936318|ref|ZP_07843665.1| RNA polymerase sigma factor RpoD [Staphylococcus hominis subsp.
           hominis C80]
 gi|228269868|gb|EEK11348.1| RNA polymerase sigma factor RpoD [Staphylococcus hominis SK119]
 gi|313654937|gb|EFS18682.1| RNA polymerase sigma factor RpoD [Staphylococcus hominis subsp.
           hominis C80]
          Length = 368

 Score =  112 bits (279), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 88/275 (32%), Positives = 133/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  QEE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGRVNLLSAQEEIELAKRI-EQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 161 IQEGNMGLIKAVEKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 220

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I K       E +S+   +    D  L 
Sbjct: 221 RVQRQLLQDLGRDPAPEEIGEEMDLPPEKVREILK----IAQEPVSLETPIGEEDDSHLG 276

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 277 DFIEDQEAQSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 319

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 320 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 354


>gi|315303191|ref|ZP_07873849.1| RNA polymerase sigma factor RpoD [Listeria ivanovii FSL F6-596]
 gi|313628434|gb|EFR96909.1| RNA polymerase sigma factor RpoD [Listeria ivanovii FSL F6-596]
          Length = 386

 Score =  112 bits (279), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 88/276 (31%), Positives = 135/276 (48%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LAKR  E GD+ A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 120 YLKEIGRVDLLTADEEIALAKRI-EAGDIEAKGRLAEANLRLVVSIAKRYVGRGMLFLDL 178

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 179 IQEGNMGLMKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 238

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q+ L  +L R     +   + +L  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 239 RVQRSLLQDLGRDPSPEEIGEEMDLPTEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 294

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 295 DFIEDQDATSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 337

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 338 GLDDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLR 373


>gi|284009102|emb|CBA76093.1| RNA polymerase sigma factor RpoS [Arsenophonus nasoniae]
          Length = 329

 Score =  112 bits (279), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 83/272 (30%), Positives = 144/272 (52%), Gaps = 15/272 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD ++  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 60  YLGEIGYSPLLTAEEEVFYARRAL-RGDAASLQRMIESNLRLVVKISRRYSNRGLALLDL 118

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPE+GFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 119 IEEGNLGLIRAVEKFDPEKGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI-VKELNVY 177

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +   Q + D+    E++     K     S ++ +N R++  ++   +   SDK   
Sbjct: 178 LRIARELAQKL-DHEPSAEEIAERLDKPVDDVSRMLRLNERISSVDT--PIGGDSDK--- 231

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR---LQENPVTL 255
              D L  D+D   +  I+     N +  + + +  LN ++R +  ARR   L     TL
Sbjct: 232 ALLDVLSDDNDSGPEGTIQA---NNMKESIVKWLFELNAKQREVL-ARRFGLLGYESETL 287

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +  E  ++RERVRQI+    +++++ +  Q
Sbjct: 288 EEVGREIGLTRERVRQIQVEGLRRLKDILHNQ 319


>gi|34763652|ref|ZP_00144580.1| RNA polymerase sigma factor rpoD [Fusobacterium nucleatum subsp.
           vincentii ATCC 49256]
 gi|237742311|ref|ZP_04572792.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. 4_1_13]
 gi|27886661|gb|EAA23826.1| RNA polymerase sigma factor rpoD [Fusobacterium nucleatum subsp.
           vincentii ATCC 49256]
 gi|229429959|gb|EEO40171.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. 4_1_13]
          Length = 340

 Score =  112 bits (279), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 84/278 (30%), Positives = 146/278 (52%), Gaps = 27/278 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   EE   AK+  E GD  A+ +L+ S+LRLVV IA  +   GL + ++
Sbjct: 73  YLREIGQVPLLTHDEEIEYAKKAYE-GDEEASKKLIESNLRLVVSIAKKHTNRGLKLLDL 131

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM+AV+KF+  +G++ +TY+ WWI+ A+   I      ++I        +   
Sbjct: 132 IQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPV-----HMIET 186

Query: 139 LRRLKG----HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           + ++K     +LQ  T  +  PE    +A++L +   ++ ++        SL   + S +
Sbjct: 187 INKIKKESRIYLQE-TGKDASPE---ILAERLGMEVDKIKAIQEMNQEPISLETPVGSEE 242

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNR---RNMLTRSMSVLNPRERRIFEARRLQEN 251
              S+  D++      ++Q      E  NR   R  L   +  L+PRE ++   R   ++
Sbjct: 243 --DSELGDFV------EDQKTTSPYEATNRAILREELDAVLKTLSPREEKVLRYRYGLDD 294

Query: 252 --PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             P TLE +   F V+RER+RQIE +A +K++   +K+
Sbjct: 295 SSPKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRKK 332


>gi|294782673|ref|ZP_06747999.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. 1_1_41FAA]
 gi|294481314|gb|EFG29089.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. 1_1_41FAA]
          Length = 500

 Score =  112 bits (279), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 83/275 (30%), Positives = 144/275 (52%), Gaps = 21/275 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   EE   AK+  E GD  A+ +L+ S+LRLVV IA  +   GL + ++
Sbjct: 233 YLREIGQVPLLTHDEEIEYAKKAYE-GDEEASQKLIESNLRLVVSIAKKHTNRGLKLLDL 291

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM+AV+KF+  +G++ +TY+ WWI+ A+   I      ++I        +   
Sbjct: 292 IQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPV-----HMIET 346

Query: 139 LRRLKG----HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           + ++K     +LQ  T  +  PE    +A++L +   ++ ++        SL   + S +
Sbjct: 347 INKIKKESRIYLQE-TGKDASPE---ILAERLGMEVEKIKAIQEMNQEPISLETPVGSEE 402

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
              S+  D++    D +     E   R   R  L   +  L+PRE ++   R   ++  P
Sbjct: 403 --DSELGDFV---EDQKTTSPYEATNRAILREELDGVLKTLSPREEKVLRYRYGLDDSSP 457

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            TLE +   F V+RER+RQIE +A +K++   +K+
Sbjct: 458 KTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRKK 492


>gi|225868705|ref|YP_002744653.1| RNA polymerase sigma factor RpoD [Streptococcus equi subsp.
           zooepidemicus]
 gi|225701981|emb|CAW99541.1| RNA polymerase sigma factor RpoD [Streptococcus equi subsp.
           zooepidemicus]
          Length = 369

 Score =  112 bits (279), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 86/269 (31%), Positives = 140/269 (52%), Gaps = 21/269 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L   EE VLA      GD+ A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLTSDEEKVLAVAV-AAGDMEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 218

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L      +  PEQ   IA+++ ++  +V  +  ++A +  SL   I   D   
Sbjct: 219 LVREQRNLLQELGQDPTPEQ---IAERMEMTPDKVREI-LKIAQEPVSLETPIGEED--D 272

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 273 SHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 326

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE++   F V+RER+RQIEA+A +K++
Sbjct: 327 RTLEDVGKVFNVTRERIRQIEAKALRKLR 355


>gi|108805426|ref|YP_645363.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108766669|gb|ABG05551.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 282

 Score =  112 bits (279), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 86/275 (31%), Positives = 138/275 (50%), Gaps = 26/275 (9%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L++Y+  IR+  +L   EE  L++R R  GD +A  RL+ S+LRLVV IA  YRG G+P 
Sbjct: 9   LTQYLGRIREGRLLTAGEEVELSRRAR-AGDGAARRRLIESNLRLVVAIAKRYRGRGVPF 67

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN GL++AV+KFDPE G R +TY+ WWI+ A+   +      V++   A+    
Sbjct: 68  EDLIQEGNAGLIRAVEKFDPEMGNRFSTYATWWIRQAVTRAVADQGRAVRL--PAHVVDS 125

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAI-------AKKLNVSESEVISMNCRLAGDESLNA 188
            + LRR +  L          E+V          A++L      + S++ RL GDE    
Sbjct: 126 VYRLRRAESALSVELGREPTDEEVAGRLGTSPEEARRLREVSQPISSISARL-GDE---- 180

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
                 ++ ++  D L  +   +E   +E       R +L  ++  L  RE R+   R  
Sbjct: 181 ------EDGAELGDLLPDEAASEEYARVEA---GPWRGVLREAVGSLPEREARVLRLRHG 231

Query: 249 --QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              E   TL  +S    +S+ER RQ+E +A + ++
Sbjct: 232 LDGERARTLREVSEILGISQERARQVELKALRTLR 266


>gi|332526107|ref|ZP_08402245.1| RNA polymerase sigma S (sigma-38) factor transcription regulator
           protein [Rubrivivax benzoatilyticus JA2]
 gi|332109950|gb|EGJ10578.1| RNA polymerase sigma S (sigma-38) factor transcription regulator
           protein [Rubrivivax benzoatilyticus JA2]
          Length = 320

 Score =  112 bits (279), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 81/285 (28%), Positives = 146/285 (51%), Gaps = 31/285 (10%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ +IR+ P++  +EE+  A R R  GD +A   ++  +LRLVV IA  Y G G+P+
Sbjct: 46  LQSYLRDIRRAPLMSAEEEHATAVRARA-GDFAARQTMIERNLRLVVSIAKHYVGRGMPM 104

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK-- 133
            +++ EGN+GLM A  KF+PERGFR +TY+ WWI+ +++  I+    L+++     ++  
Sbjct: 105 IDLIEEGNLGLMHATGKFEPERGFRFSTYASWWIRQSIERAIMHQARLIRLPVHVVRELN 164

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEV-ISMNCRLAGDE 184
           ++    R L+       +  +  ++V A        +A+ L ++E    + M     G E
Sbjct: 165 QVLKARRALESSRHGEAERPVSVDEVAAALGRPVDEVAELLKLAEQPTSLDMPLEREGGE 224

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           S   ++++   + +     L      +E V           ++L   ++ LN RER +  
Sbjct: 225 S---MLDTVADDDAVDPLGLTLS---REAV-----------HLLDHGLAELNEREREVLA 267

Query: 245 AR-RLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R  L +  P TLE L+    ++RER+RQI+  A  K++  + ++
Sbjct: 268 GRFGLHDREPETLEELAVRLGLTRERIRQIQQEALLKLKRRMMRR 312


>gi|210615118|ref|ZP_03290449.1| hypothetical protein CLONEX_02663 [Clostridium nexile DSM 1787]
 gi|210150426|gb|EEA81435.1| hypothetical protein CLONEX_02663 [Clostridium nexile DSM 1787]
          Length = 370

 Score =  112 bits (279), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 91/269 (33%), Positives = 141/269 (52%), Gaps = 21/269 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 104 YLKEIGKVPLLSAEEEIELAKRMAE-GDEDAKKRLAEANLRLVVSIAKRYVGRGMLFLDL 162

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GL++AV+KFD ++GF+ +TY+ WWI+ A+   I      ++I      T N  +
Sbjct: 163 IQEGNLGLIKAVEKFDYQKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETIN--K 220

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           L    R+L   LQ +    L PE+   IA++L++    V  +        SL   I   +
Sbjct: 221 LIRVSRQL---LQELGREPL-PEE---IAEELDMPVERVREILKISQEPVSLETPIG--E 271

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
           +  S   D++    D    V  E       +  L   +  L  RE+++   R    +   
Sbjct: 272 EEDSHLGDFI---QDDNVPVPAEAAAATLLKEQLGEVLDTLTDREQKVLRLRFGMNDGRA 328

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE +  EF+V+RER+RQIEA+A +K++
Sbjct: 329 RTLEEVGKEFDVTRERIRQIEAKALRKLR 357


>gi|310827637|ref|YP_003959994.1| RNA polymerase [Eubacterium limosum KIST612]
 gi|308739371|gb|ADO37031.1| RNA polymerase [Eubacterium limosum KIST612]
          Length = 395

 Score =  112 bits (279), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 88/278 (31%), Positives = 141/278 (50%), Gaps = 17/278 (6%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S+ VN  + L  Y+ EI K+P+L  ++E  +AKR  E GD  A   L  ++LRLVV IA 
Sbjct: 119 SVSVNDPVRL--YLKEIGKVPLLTAEQEMGIAKRM-EAGDDEAKKELAEANLRLVVSIAK 175

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I
Sbjct: 176 RYVGRGMSFLDLIQEGNLGLIKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRI 235

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-S 185
               +       L R+   L         P +   I K++  SE +V  +  ++A D  S
Sbjct: 236 --PVHMVETINKLIRVSRQLLQELGREPTPAE---IGKEMGFSEEKVREIQ-KIAQDPVS 289

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L   I   ++  S   D++    D       E       +  L   ++ L  RE ++   
Sbjct: 290 LETPIG--EEEDSHLGDFI---EDDNAPAPSEAASYALLKEQLMEVLNTLTEREEKVLRL 344

Query: 246 RRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   ++    TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 345 RFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLR 382


>gi|260436706|ref|ZP_05790676.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 8109]
 gi|260414580|gb|EEX07876.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 8109]
          Length = 377

 Score =  112 bits (279), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 76/238 (31%), Positives = 121/238 (50%), Gaps = 17/238 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLVV +A  Y+  G+ I ++V EG +GL +AV+KFDP RGFR +TY+ WW
Sbjct: 137 AKDHMIQANLRLVVAVAKKYQQRGMEILDLVQEGTLGLERAVEKFDPTRGFRFSTYAYWW 196

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   I      +++     +K     L R+K   Q I  N  +   +  +A++L +
Sbjct: 197 IRQGITRAIATQSRTIRLPVHVTEK-----LNRIKRVQQEIASNEGRIASIADLARELGI 251

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SE  V     R+    SL+  +    +  +Q  D +   H   EQ L   E   +  ++L
Sbjct: 252 SEDTVRQTLARVPRSVSLDTRVGR--EQDTQLGDLIEDGHATPEQTLTHDELHNDLEDLL 309

Query: 229 ----TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
               +R  +VL    RR F      + P TL  +  E ++SRERVRQIE RA  K+++
Sbjct: 310 DELTSREAAVL----RRRFGLE--DDTPQTLAQIGEELKLSRERVRQIETRALLKLRQ 361


>gi|225870339|ref|YP_002746286.1| RNA polymerase sigma factor RpoD [Streptococcus equi subsp. equi
           4047]
 gi|225699743|emb|CAW93506.1| RNA polymerase sigma factor RpoD [Streptococcus equi subsp. equi
           4047]
          Length = 369

 Score =  112 bits (279), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 86/269 (31%), Positives = 140/269 (52%), Gaps = 21/269 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L   EE VLA      GD+ A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLTSDEEKVLAVAV-AAGDMEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 218

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L      +  PEQ   IA+++ ++  +V  +  ++A +  SL   I   D   
Sbjct: 219 LVREQRNLLQELGQDPTPEQ---IAERMEMTPDKVREI-LKIAQEPVSLETPIGEED--D 272

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 273 SHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 326

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE++   F V+RER+RQIEA+A +K++
Sbjct: 327 RTLEDVGKVFNVTRERIRQIEAKALRKLR 355


>gi|254449272|ref|ZP_05062719.1| RNA polymerase sigma factor RpoS [gamma proteobacterium HTCC5015]
 gi|198261127|gb|EDY85425.1| RNA polymerase sigma factor RpoS [gamma proteobacterium HTCC5015]
          Length = 308

 Score =  112 bits (279), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 86/277 (31%), Positives = 147/277 (53%), Gaps = 25/277 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  ++E +   R  + GD +A  +++ S+LRLVVKI+  Y   GLP+ ++
Sbjct: 40  YLKEIEFSPLLTAEQE-IHYGRLVQEGDEAARRKMIESNLRLVVKISRRYMNRGLPLLDL 98

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPE+GFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 99  IEEGNLGLIRAVEKFDPEKGFRFSTYATWWIRQTIERGLMNQTRTIRLPIHVI-KELNVY 157

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +   Q        PE+V   AK L+    +V    CR+ G   LN  + S D    
Sbjct: 158 LRAARAMQQEFA-REPTPEEV---AKHLDKPVDDV----CRMYG---LNERVASVDVPIG 206

Query: 199 QWQDWLVYDHDGQEQV-----LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QE 250
           +  D L+ D    + V     L++ EE       +   +  L+ +++ + E RR     +
Sbjct: 207 KEGDSLLLDLIADDSVPDPTALLQSEEVA---AYVDHWLEELDAKQKAVVE-RRFGLHGQ 262

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +  TLE +  E  V+RERVRQI+  + KK+++ ++ +
Sbjct: 263 DYATLEVIGHELGVTRERVRQIQMESLKKLRKILEAE 299


>gi|313897024|ref|ZP_07830571.1| RNA polymerase sigma factor RpoD [Selenomonas sp. oral taxon 137
           str. F0430]
 gi|312974471|gb|EFR39939.1| RNA polymerase sigma factor RpoD [Selenomonas sp. oral taxon 137
           str. F0430]
          Length = 381

 Score =  112 bits (279), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 146/277 (52%), Gaps = 29/277 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LA+R  E GD SA HRL  ++LRLVV IA  Y G G+   ++
Sbjct: 114 YLKEIGRVPLLTAEEEVELARRM-EAGDASARHRLEEANLRLVVSIAKRYVGRGMLFLDL 172

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I      T N+  
Sbjct: 173 IQEGNLGLLKAVEKFDYSKGYKFSTYATWWIRQAITRALADQARTIRIPVHMVETINKL- 231

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               +R  +  LQ +  +    E    IAK++ +S   V  +  ++A  E ++      +
Sbjct: 232 ----VRVSRSLLQELGRDATAEE----IAKEMGLSVVRVREI-MKIA-QEPVSLETPVGE 281

Query: 195 KNSSQWQDWL----VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           +  S   D++      D      +++ KE+       ++  +  L PRE  +   R   E
Sbjct: 282 EEDSHLGDFIEDEAALDPADAASMMLLKEQ-------ISEVLKTLAPREAEVLRLRFGLE 334

Query: 251 N--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           +    TLE +   F V+RER+RQIEA+A +K++  ++
Sbjct: 335 DGRSRTLEEVGQSFGVTRERIRQIEAKALRKLRHPVR 371


>gi|163787530|ref|ZP_02181977.1| RNA polymerase sigma-70 factor [Flavobacteriales bacterium ALC-1]
 gi|159877418|gb|EDP71475.1| RNA polymerase sigma-70 factor [Flavobacteriales bacterium ALC-1]
          Length = 287

 Score =  112 bits (279), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 84/293 (28%), Positives = 152/293 (51%), Gaps = 49/293 (16%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ ++   EE  LA+R +  GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGKVDLITADEEVELAQRIKA-GDQIALEKLTKANLRFVVSVAKQYQNQGLTL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
            ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++      Q  I+R   L KIG+ 
Sbjct: 77  PDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVR-LPLNKIGSI 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA- 188
               + F  L +          ++ +P     IAK+L+++ ++V           S++A 
Sbjct: 136 NKINKTFAFLEQ----------SHERPPSAEEIAKELDMTINDVKESMKNSGRHVSMDAP 185

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML--------TRSMSVLNPRER 240
           L+   D N        +YD      VL   E     R++L         R++  L PRE 
Sbjct: 186 LVEGEDSN--------LYD------VLRSGESPNPDRDLLHESLRTEIERALETLTPREA 231

Query: 241 RIFEARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +    RL      ++P+TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 232 DVI---RLYFGLGNQHPMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|157151547|ref|YP_001450555.1| RNA polymerase sigma factor RpoD [Streptococcus gordonii str.
           Challis substr. CH1]
 gi|157076341|gb|ABV11024.1| RNA polymerase sigma factor [Streptococcus gordonii str. Challis
           substr. CH1]
          Length = 370

 Score =  112 bits (279), Expect = 8e-23,   Method: Compositional matrix adjust.
 Identities = 88/272 (32%), Positives = 143/272 (52%), Gaps = 29/272 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 103 YLKEIGVVPLLTNEEEQELAILV-EQGDTEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 161

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 162 IQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKL- 220

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSS 193
               +R  +  LQ +   +  PEQ   IA++++++  +V  +  ++A +  SL   I   
Sbjct: 221 ----VREQRNLLQELG-QDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEE 271

Query: 194 DKNSSQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQ 249
           D   S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L 
Sbjct: 272 D--DSHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLD 323

Query: 250 ENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
           +  + TLE++   F V+RER+RQIEA+A +K+
Sbjct: 324 DGKMRTLEDVGKVFNVTRERIRQIEAKALRKL 355


>gi|305666839|ref|YP_003863126.1| RNA polymerase sigma factor rpoD (Sigma-A) [Maribacter sp.
           HTCC2170]
 gi|88709063|gb|EAR01297.1| RNA polymerase sigma factor rpoD (Sigma-A) [Maribacter sp.
           HTCC2170]
          Length = 287

 Score =  112 bits (279), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 82/279 (29%), Positives = 148/279 (53%), Gaps = 37/279 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ +I KI ++  QEE  LA+R R  GD  A  +L T++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQDISKIELINAQEEVELAQRIR-AGDQVALEKLTTANLRFVVSVAKQYQNQGLKL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
            ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++      Q  ++R   L KIG+ 
Sbjct: 77  PDLINEGNLGLVKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRVVR-LPLNKIGSI 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
              K+ F  L +           + +P     IAK+L ++ +EV           S++A 
Sbjct: 136 NKIKKTFSYLEQ----------AHERPPSAEEIAKELEMTVTEVKQSLKNTGRHVSMDAP 185

Query: 190 INSSDKNSSQWQDWLVYD--HDGQ----EQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           +        Q +D  +YD    G+    +++L++    ++    + R++  L+PRE  + 
Sbjct: 186 LR-------QGEDSNLYDVLRSGESPRPDKILLQ----QSLNTEINRALETLSPREADVV 234

Query: 244 EARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           +       +  +TL  +   F+++RERVRQI  +A +K+
Sbjct: 235 KLYYGIGDQQSMTLAEIGQTFDLTRERVRQIREKAIRKL 273


>gi|303238871|ref|ZP_07325402.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302593504|gb|EFL63221.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 359

 Score =  112 bits (279), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 83/265 (31%), Positives = 134/265 (50%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L   EE  LA++  E GD  +  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 93  YLKEIGKVPLLSADEEIQLAQKM-EKGDSESKRRLAEANLRLVVSIAKRYVGRGMLFLDL 151

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 152 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 209

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L        +PE+   IAK++N+   +V  +        SL   I   ++  S
Sbjct: 210 LIRVSRQLLQELGKEPQPEE---IAKEMNMPVEKVREIMKISQEPVSLETPIG--EEEDS 264

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++    D       E       +  L   +  L PRE ++   R   ++    TLE
Sbjct: 265 HLGDFI---PDDDAPAPSEAAAFTLLKEQLIDVLDTLTPREEKVLRLRFGLDDGRARTLE 321

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF V+RER+RQIEA+A +K++
Sbjct: 322 EVGKEFNVTRERIRQIEAKALRKLR 346


>gi|134300301|ref|YP_001113797.1| RNA polymerase sigma factor RpoD [Desulfotomaculum reducens MI-1]
 gi|134053001|gb|ABO50972.1| RNA polymerase, sigma 70 subunit, RpoD [Desulfotomaculum reducens
           MI-1]
          Length = 367

 Score =  112 bits (279), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 81/265 (30%), Positives = 139/265 (52%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LAKR  E G+  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 101 YLKEIGRVPLLSPEEEVDLAKRM-EQGEEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 159

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 160 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 217

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L         PE+   IAK++++S  +V  +  ++A  E ++      ++  S
Sbjct: 218 LIRVSRQLLQELGREPSPEE---IAKEMDISGEKVREI-LKIA-QEPVSLETPIGEEEDS 272

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++    D   +   E+      R  L   +  L  RE+++   R   ++    TLE
Sbjct: 273 HLGDFI---EDADARAPAEEASFTLLREQLDEVLKTLTDREQKVLRLRFGLDDGRARTLE 329

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  +F V+RER+RQIEA+  +K++
Sbjct: 330 EVGQKFGVTRERIRQIEAKTLRKLR 354


>gi|320530862|ref|ZP_08031899.1| RNA polymerase sigma factor RpoD [Selenomonas artemidis F0399]
 gi|320136896|gb|EFW28841.1| RNA polymerase sigma factor RpoD [Selenomonas artemidis F0399]
          Length = 381

 Score =  112 bits (279), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 146/277 (52%), Gaps = 29/277 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LA+R  E GD SA HRL  ++LRLVV IA  Y G G+   ++
Sbjct: 114 YLKEIGRVPLLTAEEEVELARRM-EAGDASARHRLEEANLRLVVSIAKRYVGRGMLFLDL 172

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I      T N+  
Sbjct: 173 IQEGNLGLLKAVEKFDYSKGYKFSTYATWWIRQAITRALADQARTIRIPVHMVETINKL- 231

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               +R  +  LQ +  +    E    IAK++ +S   V  +  ++A  E ++      +
Sbjct: 232 ----VRVSRSLLQELGRDATAEE----IAKEMGLSVVRVREI-MKIA-QEPVSLETPVGE 281

Query: 195 KNSSQWQDWL----VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           +  S   D++      D      +++ KE+       ++  +  L PRE  +   R   E
Sbjct: 282 EEDSHLGDFIEDEAALDPADAASMMLLKEQ-------ISEVLKTLAPREAEVLRLRFGLE 334

Query: 251 N--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           +    TLE +   F V+RER+RQIEA+A +K++  ++
Sbjct: 335 DGRSRTLEEVGQSFGVTRERIRQIEAKALRKLRHPVR 371


>gi|332666643|ref|YP_004449431.1| RpoD subfamily RNA polymerase sigma-70 subunit [Haliscomenobacter
           hydrossis DSM 1100]
 gi|332335457|gb|AEE52558.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Haliscomenobacter
           hydrossis DSM 1100]
          Length = 289

 Score =  112 bits (279), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 84/290 (28%), Positives = 152/290 (52%), Gaps = 52/290 (17%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ +L  +EE  LAKR ++ GD +A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LEKYLQEIGKVDLLTPEEEVELAKRIKQ-GDQAALEKLTKANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
           S++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++      Q  I+R   L K+G+ 
Sbjct: 77  SDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVR-LPLNKVGSL 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCR 179
               + F         L+   +    PE+   +A+ L +   EV          +SM+  
Sbjct: 136 NKINKAF-------SELEQEFEREPSPEE---LAEMLEIPTEEVETTLGVAARHVSMDAP 185

Query: 180 LAGDESLNALINSSDKNSSQWQD-WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
               E  N+L++  + N++   D  L Y+               + R  + RS+S L  R
Sbjct: 186 FVEGED-NSLLDVLENNTTPSTDAGLDYNE--------------SLRREIERSLSTLTDR 230

Query: 239 ERRIFEARRLQ-----ENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +  +    +L      E+P++LE++  +F ++RERVRQI+ +A  K++ +
Sbjct: 231 QCDVI---KLYFGIGVEHPMSLEDIGEKFGLTRERVRQIKDKAINKLRSA 277


>gi|241889518|ref|ZP_04776817.1| RNA polymerase sigma factor RpoD [Gemella haemolysans ATCC 10379]
 gi|241863825|gb|EER68208.1| RNA polymerase sigma factor RpoD [Gemella haemolysans ATCC 10379]
          Length = 361

 Score =  112 bits (279), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 87/269 (32%), Positives = 141/269 (52%), Gaps = 17/269 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAK---RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           Y+ EI K+P+L K++E  L+K      E     A   L  ++LRLVV IA  Y G G+  
Sbjct: 91  YLKEIGKVPLLSKEKELELSKIIETGTEEEKEQAKKDLAEANLRLVVSIAKRYVGRGMLF 150

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I    +    
Sbjct: 151 LDLIQEGNMGLIKAVEKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVET 208

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
              L R++  L        KPE+   IAKK+N++  +V  +  ++A +  SL   I   D
Sbjct: 209 INRLIRIQRQLLQDLGREPKPEE---IAKKMNMTPEKVREI-LKIAQEPVSLETPIGEED 264

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
              S   D++    D + Q  +E    +  +  L   +  L  RE  + + R  L++   
Sbjct: 265 --DSHLGDFI---EDKEAQSPVEHAANELLKEQLEEILETLTDREENVLKLRFGLKDGKT 319

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE + S F V+RER+RQIEA+A +K++
Sbjct: 320 HTLEEVGSAFGVTRERIRQIEAKAIRKLK 348


>gi|27468166|ref|NP_764803.1| RNA polymerase sigma factor RpoD [Staphylococcus epidermidis ATCC
           12228]
 gi|57867102|ref|YP_188703.1| RNA polymerase sigma factor RpoD [Staphylococcus epidermidis RP62A]
 gi|251810978|ref|ZP_04825451.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           epidermidis BCM-HMP0060]
 gi|282876013|ref|ZP_06284880.1| RNA polymerase sigma factor RpoD [Staphylococcus epidermidis SK135]
 gi|293366478|ref|ZP_06613155.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           epidermidis M23864:W2(grey)]
 gi|47606037|sp|Q8CP24|RPOD_STAES RecName: Full=RNA polymerase sigma factor rpoD
 gi|81674470|sp|Q5HNY7|RPOD_STAEQ RecName: Full=RNA polymerase sigma factor rpoD
 gi|27315712|gb|AAO04847.1|AE016748_81 RNA polymerase sigma factor [Staphylococcus epidermidis ATCC 12228]
 gi|57637760|gb|AAW54548.1| RNA polymerase sigma-70 factor [Staphylococcus epidermidis RP62A]
 gi|251805488|gb|EES58145.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           epidermidis BCM-HMP0060]
 gi|281295038|gb|EFA87565.1| RNA polymerase sigma factor RpoD [Staphylococcus epidermidis SK135]
 gi|291319247|gb|EFE59616.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           epidermidis M23864:W2(grey)]
 gi|319400897|gb|EFV89116.1| RNA polymerase sigma factor rpoD [Staphylococcus epidermidis
           FRI909]
 gi|329725345|gb|EGG61828.1| RNA polymerase sigma factor RpoD [Staphylococcus epidermidis
           VCU144]
 gi|329735301|gb|EGG71593.1| RNA polymerase sigma factor RpoD [Staphylococcus epidermidis
           VCU045]
 gi|329737328|gb|EGG73582.1| RNA polymerase sigma factor RpoD [Staphylococcus epidermidis
           VCU028]
          Length = 368

 Score =  112 bits (279), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 88/275 (32%), Positives = 133/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  QEE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGRVNLLSAQEEIELAKRI-EQGDEIAKSRLAEANLRLVVSIAKRYVGRGMLFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 161 IQEGNMGLIKAVEKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 220

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I K       E +S+   +    D  L 
Sbjct: 221 RVQRQLLQDLGRDPAPEEIGEEMDLPPEKVREILK----IAQEPVSLETPIGEEDDSHLG 276

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 277 DFIEDQEAQSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 319

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 320 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 354


>gi|87306425|ref|ZP_01088572.1| RNA polymerase sigma factor rpoS [Blastopirellula marina DSM 3645]
 gi|87290604|gb|EAQ82491.1| RNA polymerase sigma factor rpoS [Blastopirellula marina DSM 3645]
          Length = 296

 Score =  112 bits (279), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 88/286 (30%), Positives = 142/286 (49%), Gaps = 19/286 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ EI +  +L  ++E  LAK   E GD++A  R+V ++LRLVV IA GY G GL +
Sbjct: 18  LETYLREINETALLSAKDEKDLAKLIGE-GDVNARDRMVRANLRLVVNIARGYTGKGLGL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GL++AV+ FDP  G R +TY+ +WIK +++  ++     ++I   A    L
Sbjct: 77  QDLIEEGNLGLLRAVEGFDPAMGTRFSTYASYWIKQSIKRALINCAKTIRI--PAYMVEL 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
               RR    L         PE+   IA+ L + + ++  +   +    S       +D+
Sbjct: 135 LSKWRRATNRLTEELGRTPTPEE---IARVLGLPKKKLPIIKKAIKIYNS----TPQTDQ 187

Query: 196 NSSQWQ-DWLVYDH--DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE-- 250
             S W    +V D      E  ++E ++ KN   ML      ++ RE  +   R   E  
Sbjct: 188 ADSGWSLGEMVMDDRLKNPEDEMVEHDDLKNVMQML----KTMDGREATVLRMRFGLEGM 243

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPL 296
           +P TL+ +  +  ++RERVRQIE  A  K+ E +Q   E     P 
Sbjct: 244 DPHTLKEIGEKLGLTRERVRQIETEALGKLAEGLQDPRERELEGPF 289


>gi|313618909|gb|EFR90770.1| RNA polymerase sigma factor RpoD [Listeria innocua FSL S4-378]
          Length = 374

 Score =  112 bits (279), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 88/276 (31%), Positives = 132/276 (47%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LAKR  E GD+ A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 108 YLKEIGRVDLLTADEEIALAKRI-EVGDIEAKGRLAEANLRLVVSIAKRYVGRGMLFLDL 166

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 167 IQEGNMGLMKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 226

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q+ L  +L R     +   + +L  E+V  I K       E +S+   +    D  L 
Sbjct: 227 RVQRSLLQDLGRDPSPEEIGEEMDLPTEKVREILK----IAQEPVSLETPIGEEDDSHLG 282

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 283 DFIEDQDATSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 325

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 326 GLDDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLR 361


>gi|195977963|ref|YP_002123207.1| RNA polymerase sigma factor RpoD [Streptococcus equi subsp.
           zooepidemicus MGCS10565]
 gi|195974668|gb|ACG62194.1| RNA polymerase sigma factor RpoD [Streptococcus equi subsp.
           zooepidemicus MGCS10565]
          Length = 369

 Score =  112 bits (279), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 86/269 (31%), Positives = 140/269 (52%), Gaps = 21/269 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L   EE VLA      GD+ A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLTSDEEKVLAVAVA-AGDMEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 218

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L      +  PEQ   IA+++ ++  +V  +  ++A +  SL   I   D   
Sbjct: 219 LVREQRNLLQELGQDPTPEQ---IAERMEMTPDKVREI-LKIAQEPVSLETPIGEED--D 272

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 273 SHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 326

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE++   F V+RER+RQIEA+A +K++
Sbjct: 327 RTLEDVGKVFNVTRERIRQIEAKALRKLR 355


>gi|213969149|ref|ZP_03397288.1| RNA polymerase sigma-38 factor [Pseudomonas syringae pv. tomato T1]
 gi|213926147|gb|EEB59703.1| RNA polymerase sigma-38 factor [Pseudomonas syringae pv. tomato T1]
          Length = 334

 Score =  112 bits (279), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 86/272 (31%), Positives = 145/272 (53%), Gaps = 18/272 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +E  V   R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEE--VHFARLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 124

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 125 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 183

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + +K       ++ +N R++  D SL      SDK  
Sbjct: 184 LRAARELTQKL-DHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSLGP---DSDKT- 238

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++       + + +S L  ++R +   R   R  E+  T
Sbjct: 239 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTEKQREVVIRRFGLRGHESS-T 292

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE++  E  ++RERVRQI+    K+++E ++K
Sbjct: 293 LEDVGLEIGLTRERVRQIQVEGLKRLREILEK 324


>gi|284046806|ref|YP_003397146.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Conexibacter
           woesei DSM 14684]
 gi|283951027|gb|ADB53771.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Conexibacter
           woesei DSM 14684]
          Length = 380

 Score =  112 bits (279), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 86/266 (32%), Positives = 139/266 (52%), Gaps = 15/266 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+  I ++ +L  ++E  LA+R  E GD+ A  +++ ++LRLVV IA GY G GL   ++
Sbjct: 115 YLRSIGRVNLLTAEQEVHLAQRI-ERGDMRAKQQMIEANLRLVVSIAKGYLGRGLTFLDL 173

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EG++GL++AV+KFD  RGF+ +TY+ WWI+ A+   I      ++I     +K     
Sbjct: 174 IQEGSLGLIRAVEKFDHRRGFKFSTYATWWIRQAVTRAIADKGRTIRIPVHMVEK--LNK 231

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           +  ++  L         PE+   IA +L  +  EV  +  R+A    SL   I   ++  
Sbjct: 232 VVHVERQLVQSLGREPTPEE---IAAELECTVREVRDI-LRMAQQPVSLEKPIG--EEEE 285

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTL 255
           S+  D+ V D   +    +  E    RR+ + R++  L  RER + E R       P TL
Sbjct: 286 SELGDF-VEDQTAESPFELASE--NLRRDNVRRALQALPQREREVIEMRFGLGGGRPRTL 342

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           E +   F V+RER+RQIE    KK++
Sbjct: 343 EEVGRAFNVTRERIRQIENHTLKKLE 368


>gi|193216316|ref|YP_001997515.1| RpoD family RNA polymerase, sigma 70 subunit [Chloroherpeton
           thalassium ATCC 35110]
 gi|193089793|gb|ACF15068.1| RNA polymerase, sigma 70 subunit, RpoD family [Chloroherpeton
           thalassium ATCC 35110]
          Length = 299

 Score =  112 bits (279), Expect = 9e-23,   Method: Compositional matrix adjust.
 Identities = 89/290 (30%), Positives = 152/290 (52%), Gaps = 42/290 (14%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVL-------------AKRYREHGDLSAAHRLVTSHLRLVV 62
           L RY+ EI K  +L  QEE  L             +K YRE     A  +L+ ++LR VV
Sbjct: 18  LDRYLQEIGKFDLLTAQEEIELTRQIKKGDGQPIDSKEYREA--RRALEKLIKANLRFVV 75

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEY 116
            +A  Y+  GL + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++      Q  
Sbjct: 76  SVAKQYQNQGLSLGDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSR 135

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
           I+R   L ++GT     + F         L+   + +   E+   +A  L+++ SE I+ 
Sbjct: 136 IVR-LPLNRVGTLNKIGKAF-------SQLEQEYERDPSTEE---LAHLLDMNSSE-ITD 183

Query: 177 NCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
             ++AG   S++A     D N  +  D L  D    +  L+++  R      + RS+S L
Sbjct: 184 TLKIAGRHISVDAPFAQGDDN--RLLDVLQNDSQRPDHGLLQESLRLE----VERSLSAL 237

Query: 236 NPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +PRE  +  +      ENP+TLE +   F+++RERVRQI+ +A ++++ S
Sbjct: 238 SPREADVIRSYFGIGMENPLTLEEIGERFKLTRERVRQIKEKAIRRLRHS 287


>gi|126663248|ref|ZP_01734246.1| RNA polymerase sigma-70 factor [Flavobacteria bacterium BAL38]
 gi|126624906|gb|EAZ95596.1| RNA polymerase sigma-70 factor [Flavobacteria bacterium BAL38]
          Length = 287

 Score =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 83/293 (28%), Positives = 152/293 (51%), Gaps = 49/293 (16%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ ++   EE  LA+R +  GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGKVDLITADEEVELAQRIK-AGDQRALEKLTKANLRFVVSVAKQYQNQGLTL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
            ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++      Q  I+R   L KIG+ 
Sbjct: 77  PDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVR-LPLNKIGSI 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA- 188
               +++  L +          +N +P     IAK+L+++ ++V           S++A 
Sbjct: 136 NKINKMYALLEQ----------SNERPPSAEEIAKELDMTVNDVKESMKNSGRHLSMDAP 185

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM--------LTRSMSVLNPRER 240
           L+   D N        +YD      VL   E     R +        + R++  L PRE 
Sbjct: 186 LVEGEDSN--------LYD------VLRSGESPNPDRELIHESLQTEIERALETLTPREA 231

Query: 241 RIFEARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +    RL      ++P+TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 232 DVV---RLYFGLGDQHPMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|70726356|ref|YP_253270.1| RNA polymerase sigma factor RpoD [Staphylococcus haemolyticus
           JCSC1435]
 gi|68447080|dbj|BAE04664.1| RNA polymerase sigma factor [Staphylococcus haemolyticus JCSC1435]
          Length = 368

 Score =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 88/275 (32%), Positives = 133/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  QEE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGRVNLLSAQEEIELAKRI-EQGDEIAKSRLAEANLRLVVSIAKRYVGRGMLFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 161 IQEGNMGLIKAVEKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 220

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I K       E +S+   +    D  L 
Sbjct: 221 RVQRQLLQDLGRDPAPEEIGEEMDLPPEKVREILK----IAQEPVSLETPIGEEDDSHLG 276

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 277 DFIEDQEAQSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 319

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 320 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 354


>gi|148240795|ref|YP_001226182.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp. WH
           7803]
 gi|147849334|emb|CAK24885.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 7803]
          Length = 376

 Score =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 78/233 (33%), Positives = 116/233 (49%), Gaps = 13/233 (5%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ ++LRLVV +A  Y+  G+ + ++V EG +GL +AV+KFDP RGFR +TY+ WWI+ 
Sbjct: 139 RMIQANLRLVVAVAKKYQQRGMELLDLVQEGTLGLERAVEKFDPTRGFRFSTYAYWWIRQ 198

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            +   I      +++     +K     L R+K   Q I     +   V  +AK+L VSE 
Sbjct: 199 GITRAIATQSRTIRLPVHITEK-----LNRIKRVQQEIASEQGRLASVSDLAKELGVSED 253

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
            V     R+    SL   +       +Q  D L   H   EQ L     R    + L   
Sbjct: 254 TVRQTLARVPRSVSLETRVGKD--QDTQLGDLLEDGHATPEQTLT----RDALHDDLEHL 307

Query: 232 MSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +  LNPRE  +  +R   E+  P TL  +     +SRERVRQIE RA  K+++
Sbjct: 308 LDELNPREAEVIRSRFGLEDDTPRTLAEIGEAMALSRERVRQIETRALLKLRQ 360


>gi|121534199|ref|ZP_01666024.1| RNA polymerase, sigma 70 subunit, RpoD family [Thermosinus
           carboxydivorans Nor1]
 gi|121307302|gb|EAX48219.1| RNA polymerase, sigma 70 subunit, RpoD family [Thermosinus
           carboxydivorans Nor1]
          Length = 368

 Score =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 84/265 (31%), Positives = 134/265 (50%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGRVPLLTAEEEIQLAKRM-EQGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 161 IQEGNLGLIKAVEKFDYNKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 218

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L         PE+   IA+++++S   V  +        SL   I   ++  S
Sbjct: 219 LIRVSRQLLQEKGREPTPEE---IAREMDISVERVREIMKIAQEPVSLETPIG--EEEDS 273

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D+ + D D       E       +  L   +  L PRE ++   R   ++    TLE
Sbjct: 274 HLGDF-IEDQDAPAPA--EAASFMLLKEQLEEVLETLTPREEKVLRLRFGLDDGRARTLE 330

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +   F V+RER+RQIEA+A +K++
Sbjct: 331 EVGQYFGVTRERIRQIEAKALRKLR 355


>gi|262068176|ref|ZP_06027788.1| RNA polymerase sigma factor RpoD [Fusobacterium periodonticum ATCC
           33693]
 gi|291378119|gb|EFE85637.1| RNA polymerase sigma factor RpoD [Fusobacterium periodonticum ATCC
           33693]
          Length = 502

 Score =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 83/275 (30%), Positives = 144/275 (52%), Gaps = 21/275 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   EE   AK+  E GD  A+ +L+ S+LRLVV IA  +   GL + ++
Sbjct: 235 YLREIGQVPLLTHDEEIEYAKKAYE-GDEEASQKLIESNLRLVVSIAKKHTNRGLKLLDL 293

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM+AV+KF+  +G++ +TY+ WWI+ A+   I      ++I        +   
Sbjct: 294 IQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPV-----HMIET 348

Query: 139 LRRLKG----HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           + ++K     +LQ  T  +  PE    +A++L +   ++ ++        SL   + S +
Sbjct: 349 INKIKKESRIYLQE-TGKDASPE---ILAERLGMEVEKIKAIQEMNQEPISLETPVGSEE 404

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
              S+  D++    D +     E   R   R  L   +  L+PRE ++   R   ++  P
Sbjct: 405 --DSELGDFV---EDQKTTSPYEATNRAILREELDGVLKTLSPREEKVLRYRYGLDDSSP 459

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            TLE +   F V+RER+RQIE +A +K++   +K+
Sbjct: 460 KTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRKK 494


>gi|225848935|ref|YP_002729099.1| RNA polymerase sigma-70 factor [Sulfurihydrogenibium azorense
           Az-Fu1]
 gi|225644026|gb|ACN99076.1| RNA polymerase sigma-70 factor [Sulfurihydrogenibium azorense
           Az-Fu1]
          Length = 285

 Score =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 83/285 (29%), Positives = 145/285 (50%), Gaps = 31/285 (10%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           N E G+  YI  I KIP+L  ++E  + ++ +  GD  A  +L+ S+LR V+ IA  Y G
Sbjct: 5   NYEEGVEYYIRSIYKIPLLTPEQEKEILEKIK-LGDKEAFQKLILSNLRFVINIAKRYAG 63

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
           YG+P+ +++S GNIGL++A K+FDP +G +  +Y++WWIK ++            I T +
Sbjct: 64  YGIPLQDLISAGNIGLIEAAKRFDPSKGVKFISYAIWWIKQSI------------INTLS 111

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL- 189
            +  +     +++   Q I++     +  +     ++   S ++     +  D   N L 
Sbjct: 112 QEGDIIRKPTKIQSLFQKISNAYFYLKDSLNREPSVDEIHSFLLREGLEVEKDTIENYLF 171

Query: 190 -----INSSDKNSSQWQDWLVYD---HDGQEQV---LIEKEERKNRRNMLTRSMSVLNPR 238
                I+  +   SQ +D  + D   + G E +   LI+++  K     +   +  L+PR
Sbjct: 172 FNQHFISLDEPILSQDEDIHLSDTISNSGTEDIERKLIDEDILK----FIDELLDTLSPR 227

Query: 239 ERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           E++I   R     E P TL+ + +   +SRERVRQIE R  KK++
Sbjct: 228 EKQILIHRFGLYGEEPKTLKEVGNIVGISRERVRQIEIRLLKKLR 272


>gi|238927758|ref|ZP_04659518.1| DNA-directed RNA polymerase sigma subunit SigA [Selenomonas
           flueggei ATCC 43531]
 gi|238884474|gb|EEQ48112.1| DNA-directed RNA polymerase sigma subunit SigA [Selenomonas
           flueggei ATCC 43531]
          Length = 383

 Score =  112 bits (279), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 85/272 (31%), Positives = 136/272 (50%), Gaps = 13/272 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA+R  E GD  A HRL  ++LRLVV IA  Y G G+   ++
Sbjct: 117 YLKEIGHVPLLTAEEEVALAQRM-EAGDEEARHRLEEANLRLVVSIAKRYVGRGMLFLDL 175

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 176 IQEGNLGLLKAVEKFDYSKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 233

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L      +  PE+   IAK++ ++ + V  +        SL   I   ++  S
Sbjct: 234 LVRISRQLLQELGRDPHPEE---IAKEMGITVARVHEIMKIAQEPVSLETPIG--EEEDS 288

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++    D       E       R  L   +  L  RE+ +   R   E+    TLE
Sbjct: 289 HLGDFI---EDEAAPAPAEAASFMLLREQLEEVLETLTDREKNVLRLRFGLEDGRSRTLE 345

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +   F V+RER+RQIEA+A +K++   + +V
Sbjct: 346 EVGQSFGVTRERIRQIEAKALRKLRHPSRSKV 377


>gi|171779914|ref|ZP_02920818.1| hypothetical protein STRINF_01701 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
 gi|171281262|gb|EDT46697.1| hypothetical protein STRINF_01701 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
          Length = 369

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 86/269 (31%), Positives = 141/269 (52%), Gaps = 21/269 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA      GDL A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLSSEEEKELAVAV-AAGDLQAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 218

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L      +  PEQ   IA++++++  +V  +  ++A +  SL   I   D   
Sbjct: 219 LVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEED--D 272

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 273 SHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 326

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE++   F V+RER+RQIEA+A +K++
Sbjct: 327 RTLEDVGKVFNVTRERIRQIEAKALRKLR 355


>gi|150390747|ref|YP_001320796.1| RpoD family RNA polymerase sigma factor [Alkaliphilus
           metalliredigens QYMF]
 gi|149950609|gb|ABR49137.1| RNA polymerase, sigma 70 subunit, RpoD family [Alkaliphilus
           metalliredigens QYMF]
          Length = 372

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 84/265 (31%), Positives = 140/265 (52%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L   EE  LA R  E GD  A  +LV ++LRLVV IA  Y G G+   ++
Sbjct: 106 YLKEIGKVPLLTGPEEIDLATRM-EAGDELAKKKLVEANLRLVVSIAKRYVGRGMLFLDL 164

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 165 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 222

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L        KPE+   IAK++++ E +V  +  ++A  E ++      ++  S
Sbjct: 223 LIRVSRQLLQEFGREPKPEE---IAKEMDLPEEKVREI-LKIA-QEPVSLETPIGEEEDS 277

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++  D              K +   L   +  L PRE+++   R   ++    TLE
Sbjct: 278 HLGDFIPDDDAPAPAEAAAFSLLKEQ---LIEVLDTLTPREQKVLRLRFGLDDGRARTLE 334

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  +F+V+RER+RQIEA+A +K++
Sbjct: 335 EVGKKFDVTRERIRQIEAKALRKLR 359


>gi|288803307|ref|ZP_06408740.1| RNA polymerase sigma-70 factor [Prevotella melaninogenica D18]
 gi|288334127|gb|EFC72569.1| RNA polymerase sigma-70 factor [Prevotella melaninogenica D18]
          Length = 287

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 80/279 (28%), Positives = 146/279 (52%), Gaps = 32/279 (11%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI    M+  +EE  LA++ R +GD  A  RL  ++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQEIGHEEMISIEEEVELAQKIR-NGDRKALERLTKANLRFVVSVAKQYQNQGLS 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG----TTA 130
           + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + I     ++++     ++ 
Sbjct: 76  LPDLINEGNVGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIIRLPLNQVSSV 135

Query: 131 NQKRLFF------NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           N+           N RR    +  I  N   PE  +  A K+N   S  +S++     DE
Sbjct: 136 NKINKILTQFEQENERR--PSIDEIAQNTDIPEDKIVDAMKVN---SRHVSVDAPFYDDE 190

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
             + L    + N+      LV      E+ L         R  + R++ +L  RE+ + E
Sbjct: 191 QSSLLDVIPNDNTPSTDKELV------EESL---------REEIGRALQILEDREKVVIE 235

Query: 245 AR-RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           A   + +  +TLE + S++ ++RERVRQI+ +A +++++
Sbjct: 236 AYFGINQREMTLEEIGSKYNLTRERVRQIKEKAIRRLRQ 274


>gi|88608313|ref|YP_506202.1| RNA polymerase sigma factor RpoD [Neorickettsia sennetsu str.
           Miyayama]
 gi|88600482|gb|ABD45950.1| RNA polymerase sigma factor RpoD [Neorickettsia sennetsu str.
           Miyayama]
          Length = 620

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 96/313 (30%), Positives = 155/313 (49%), Gaps = 62/313 (19%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQE--EY----VLAKRYREHGDLS--AAHRLVTSHLRL 60
           I +    L  ++  IR+   LEK E  +Y     L ++   H D +  A HR+V ++LRL
Sbjct: 316 ICDTHFSLEEFLSPIRE---LEKNEGMDYRSISFLTRKVATHLDNANAAKHRMVEANLRL 372

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ IA  Y   G+P  +++ EGNIGLM+AV KFD  RG + +TY+ WW + A+   I   
Sbjct: 373 VISIAKKYTNRGMPFPDLIQEGNIGLMKAVDKFDHRRGHKFSTYATWWCRQAITRAIADC 432

Query: 121 WSLVK----IGTTANQ----KRLFFNLRRLKGHLQAITDNNLK--PEQVVAIAKKLNVSE 170
            S+V+    I  TAN+    +R  +NL   +  ++ I  N LK  P++V    K L V++
Sbjct: 433 GSIVRKPVHIHETANKVMRTRRRLYNLNGREPTVEEIA-NLLKISPDKV---KKSLKVNQ 488

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
             +           SL + +   D NS  + D+ + D +   QV +     KN R +L  
Sbjct: 489 DPI-----------SLESPV-GDDSNSGSFGDF-IEDKNAVSQVDVVLS--KNLRKVLDE 533

Query: 231 SMSVLNPRERRIFEARRLQENPV----------------------TLENLSSEFEVSRER 268
           ++++L+PRE +I   R    N V                      TLE +   + V+RER
Sbjct: 534 ALAMLSPREEKILRYRFGLCNSVHSPEDEHYLKSLKIDLNRGTNLTLEQVGILYNVTRER 593

Query: 269 VRQIEARAFKKVQ 281
           +RQIE+++ +K++
Sbjct: 594 IRQIESKSLRKMR 606


>gi|289434736|ref|YP_003464608.1| RNA polymerase sigma factor RpoD [Listeria seeligeri serovar 1/2b
           str. SLCC3954]
 gi|289170980|emb|CBH27522.1| RNA polymerase sigma factor RpoD [Listeria seeligeri serovar 1/2b
           str. SLCC3954]
 gi|313633237|gb|EFS00106.1| RNA polymerase sigma factor RpoD [Listeria seeligeri FSL N1-067]
          Length = 374

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 88/276 (31%), Positives = 135/276 (48%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LAKR  E GD+ A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 108 YLKEIGRVNLLTADEEIALAKRI-EAGDIEAKGRLAEANLRLVVSIAKRYVGRGMLFLDL 166

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 167 IQEGNMGLMKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 226

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q+ L  +L R     +   + +L  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 227 RVQRSLLQDLGRDPSPEEIGEEMDLPTEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 282

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 283 DFIEDQDATSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 325

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 326 GLDDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLR 361


>gi|254796694|ref|YP_003081530.1| RNA polymerase sigma-70 factor (RpoD) [Neorickettsia risticii str.
           Illinois]
 gi|254589929|gb|ACT69291.1| RNA polymerase sigma-70 factor (RpoD) [Neorickettsia risticii str.
           Illinois]
          Length = 620

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 96/313 (30%), Positives = 155/313 (49%), Gaps = 62/313 (19%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQE--EY----VLAKRYREHGDLS--AAHRLVTSHLRL 60
           I +    L  ++  IR+   LEK E  +Y     L ++   H D +  A HR+V ++LRL
Sbjct: 316 ICDTHFSLEEFLSPIRE---LEKNEGMDYESISFLTRKVATHLDNANAAKHRMVEANLRL 372

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ IA  Y   G+P  +++ EGNIGLM+AV KFD  RG + +TY+ WW + A+   I   
Sbjct: 373 VISIAKKYTNRGMPFPDLIQEGNIGLMKAVDKFDHRRGHKFSTYATWWCRQAITRAIADC 432

Query: 121 WSLVK----IGTTANQ----KRLFFNLRRLKGHLQAITDNNLK--PEQVVAIAKKLNVSE 170
            S+V+    I  TAN+    +R  +NL   +  ++ I  N LK  P++V    K L V++
Sbjct: 433 GSIVRKPVHIHETANKVMRTRRRLYNLNGREPTVEEIA-NLLKISPDKV---KKSLKVNQ 488

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
             +           SL + +   D NS  + D+ + D +   QV +     KN R +L  
Sbjct: 489 DPI-----------SLESPV-GDDSNSGSFGDF-IEDKNAVSQVDVVLS--KNLRKVLDE 533

Query: 231 SMSVLNPRERRIFEARRLQENPV----------------------TLENLSSEFEVSRER 268
           ++++L+PRE +I   R    N V                      TLE +   + V+RER
Sbjct: 534 ALAMLSPREEKILRYRFGLCNSVHSPEDEHYLKSLKIDLNRGTNLTLEQVGILYNVTRER 593

Query: 269 VRQIEARAFKKVQ 281
           +RQIE+++ +K++
Sbjct: 594 IRQIESKSLRKMR 606


>gi|37522577|ref|NP_925954.1| group 2 sigma 70-type sigma factor [Gloeobacter violaceus PCC 7421]
 gi|35213578|dbj|BAC90949.1| group 2 sigma 70-type sigma factor [Gloeobacter violaceus PCC 7421]
          Length = 305

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 89/284 (31%), Positives = 148/284 (52%), Gaps = 36/284 (12%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRG 70
           E  + +++ E+ + P+L  ++E  LA+     G  +  A  RLV ++LRLVV IA  Y  
Sbjct: 29  EDSVGQFLREMSRYPLLTSEQEVELAQVIATGGSEAEAAKRRLVRANLRLVVSIAKKYLN 88

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            G+P  +++ EG IGLM+A +KFD ERGF+ +TY+ WWI+  +   I      V++    
Sbjct: 89  RGVPFLDLIQEGAIGLMRAAEKFDFERGFKFSTYAYWWIRQGITRAIASQSRTVRLPVHM 148

Query: 131 NQKRLFFNLRRLKGHL-QAITDNNLKPEQVVAIAKKLNVSESE--------VISMNCRLA 181
            +K     ++R++  L Q +     KPE  +A A +L++ + +         +S++ ++ 
Sbjct: 149 VEK--LNQVKRVRRQLTQELARKPTKPE--MAEALELDIDKLDEILDAGRRTLSLHVKVG 204

Query: 182 GDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            +E   L  LI  SD  S       V DH+    +L+E+ E           + +L PRE
Sbjct: 205 KEEDTELLQLIEDSDTISPSE----VLDHN----LLVEQIE---------SLLHLLTPRE 247

Query: 240 RRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R I E R      N  TL ++   + +SRERVRQI+A+A +K++
Sbjct: 248 RDIIELRFGLADGNSYTLADIGEMYNLSRERVRQIQAKAMRKLR 291


>gi|306833811|ref|ZP_07466936.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus bovis
           ATCC 700338]
 gi|304424005|gb|EFM27146.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus bovis
           ATCC 700338]
          Length = 369

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 86/269 (31%), Positives = 141/269 (52%), Gaps = 21/269 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA      GDL A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLTSEEEKELAVAV-ATGDLQAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 218

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L      +  PEQ   IA++++++  +V  +  ++A +  SL   I   D   
Sbjct: 219 LVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEED--D 272

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 273 SHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 326

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE++   F V+RER+RQIEA+A +K++
Sbjct: 327 RTLEDVGKVFNVTRERIRQIEAKALRKLR 355


>gi|56963455|ref|YP_175186.1| RNA polymerase sigma factor RpoD [Bacillus clausii KSM-K16]
 gi|56909698|dbj|BAD64225.1| DNA-directed RNA polymerase major sigma-43 factor sigma-A [Bacillus
           clausii KSM-K16]
          Length = 373

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 90/274 (32%), Positives = 145/274 (52%), Gaps = 33/274 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 107 YLKEIGRVPLLSAEEEIDLAKRI-EQGDEEAKKRLAEANLRLVVSIAKRYVGRGMLFLDL 165

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD ++GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 166 IQEGNMGLIKAVEKFDYDKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 225

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +  R     +   + +L P++V  I   L +++ E +S+   +    D  L 
Sbjct: 226 RVQRQLLQDYGREPTPEEVGKEMDLSPDKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 281

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT-RSMSVLNPRERRIFEAR 246
             I   D+ +    D   Y+        + KE+ ++  + LT R  +VL  R R   +  
Sbjct: 282 DFIE--DQEALAPSDAAAYE--------LLKEQLEDVLDTLTDREENVL--RLRFGLDDG 329

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           R +    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 330 RTR----TLEEVGKVFGVTRERIRQIEAKALRKL 359


>gi|289550668|ref|YP_003471572.1| RNA polymerase sigma factor RpoD [Staphylococcus lugdunensis
           HKU09-01]
 gi|315658163|ref|ZP_07911035.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           lugdunensis M23590]
 gi|289180200|gb|ADC87445.1| RNA polymerase sigma factor RpoD [Staphylococcus lugdunensis
           HKU09-01]
 gi|315496492|gb|EFU84815.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           lugdunensis M23590]
          Length = 368

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 88/275 (32%), Positives = 133/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  QEE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGRVNLLNAQEEIELAKRI-EQGDEIAKSRLAEANLRLVVSIAKRYVGRGMLFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 161 IQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 220

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I K       E +S+   +    D  L 
Sbjct: 221 RVQRQLLQDLGRDPAPEEIGEEMDLPPEKVREILK----IAQEPVSLETPIGEEDDSHLG 276

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 277 DFIEDQEAQSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 319

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 320 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 354


>gi|163786482|ref|ZP_02180930.1| RNA polymerase sigma-70 factor [Flavobacteriales bacterium ALC-1]
 gi|159878342|gb|EDP72398.1| RNA polymerase sigma-70 factor [Flavobacteriales bacterium ALC-1]
          Length = 287

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 84/294 (28%), Positives = 151/294 (51%), Gaps = 51/294 (17%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ +I KIP++  +EE  LA+  ++ GD  A  +L T++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQDISKIPLITAEEEVELAQLIKK-GDQVALDKLTTANLRFVVSVAKQYQNQGLKL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
            ++++EGN GL++A K+FD  RGF+  +Y++WWI+ A+      Q  I+R   L KIGT 
Sbjct: 77  PDLINEGNAGLVKAAKRFDETRGFKFISYAVWWIRQAILQALAEQSRIVR-LPLNKIGTI 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCR 179
               + F +L +L          + +P     IA++L++S  EV          +SM+  
Sbjct: 136 NKINKAFSHLEQL----------HQRPPNAEEIARELDISAREVKQSMKNSGRHLSMDAP 185

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           L   E+ +     S   S +    L+     +E + +E E          R++  L  +E
Sbjct: 186 LKDGETFSLYDVVSATESPRPDKNLM-----KESLNLEVE----------RALETLTQKE 230

Query: 240 RRIFEARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
             +    RL      + P+TLE +   ++++RERVRQI  +  ++++ + + ++
Sbjct: 231 SDVI---RLNFGIGDQPPMTLEEIGGIYDLTRERVRQIREKGIRRLRHASKSKI 281


>gi|160893000|ref|ZP_02073788.1| hypothetical protein CLOL250_00537 [Clostridium sp. L2-50]
 gi|156865083|gb|EDO58514.1| hypothetical protein CLOL250_00537 [Clostridium sp. L2-50]
          Length = 377

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 80/270 (29%), Positives = 137/270 (50%), Gaps = 23/270 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  +EE  LAKR  E GD  A  +L  ++LRLVV IA  Y G G+   ++
Sbjct: 111 YLKEIGKVPLLSAEEEIELAKRM-EEGDEQAKQKLAEANLRLVVSIAKRYVGRGMLFLDL 169

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 170 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 227

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L        +PE++  +         E++ ++      E ++      ++  S
Sbjct: 228 LIRVSRQLLQELGREPQPEEIADVMDIPVERVREILKIS-----QEPVSLETPIGEEEDS 282

Query: 199 QWQDWLVYDH-----DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-- 251
              D++  D+     D     L++++        L   +  L  RE+++   R   E+  
Sbjct: 283 HLGDFIPDDNMPVPADAAAFTLLKEQ--------LVEVLDTLTEREKKVLTLRFGLEDGR 334

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 335 ARTLEEVGKEFNVTRERIRQIEAKALRKLR 364


>gi|256845590|ref|ZP_05551048.1| RNA polymerase sigma factor RpoS [Fusobacterium sp. 3_1_36A2]
 gi|294785121|ref|ZP_06750409.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. 3_1_27]
 gi|256719149|gb|EEU32704.1| RNA polymerase sigma factor RpoS [Fusobacterium sp. 3_1_36A2]
 gi|294486835|gb|EFG34197.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. 3_1_27]
          Length = 418

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 84/278 (30%), Positives = 146/278 (52%), Gaps = 27/278 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   EE   AK+  E GD  A+ +L+ S+LRLVV IA  +   GL + ++
Sbjct: 151 YLREIGQVPLLTHDEEIEYAKKAYE-GDEEASKKLIESNLRLVVSIAKKHTNRGLKLLDL 209

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM+AV+KF+  +G++ +TY+ WWI+ A+   I      ++I        +   
Sbjct: 210 IQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPV-----HMIET 264

Query: 139 LRRLKG----HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           + ++K     +LQ  T  +  PE    +A++L +   ++ ++        SL   + S +
Sbjct: 265 INKIKKESRIYLQE-TGKDASPE---ILAERLGMEVDKIKAIQEMNQEPISLETPVGSEE 320

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNR---RNMLTRSMSVLNPRERRIFEARRLQEN 251
              S+  D++      ++Q      E  NR   R  L   +  L+PRE ++   R   ++
Sbjct: 321 --DSELGDFV------EDQKTTSPYEATNRAILREELDAVLKTLSPREEKVLRYRYGLDD 372

Query: 252 --PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             P TLE +   F V+RER+RQIE +A +K++   +K+
Sbjct: 373 SSPKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRKK 410


>gi|224476669|ref|YP_002634275.1| RNA polymerase sigma factor RpoD [Staphylococcus carnosus subsp.
           carnosus TM300]
 gi|222421276|emb|CAL28090.1| RNA polymerase sigma factor SigA [Staphylococcus carnosus subsp.
           carnosus TM300]
          Length = 369

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 88/275 (32%), Positives = 133/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  QEE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 103 YLKEIGRVDLLNAQEEIELAKRI-EQGDEVAKARLAEANLRLVVSIAKRYVGRGMLFLDL 161

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 162 IQEGNMGLIKAVEKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 221

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I K       E +S+   +    D  L 
Sbjct: 222 RVQRQLLQDLGRDPAPEEIGEEMDLPPEKVREILK----IAQEPVSLETPIGEEDDSHLG 277

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 278 DFIEDQEVQSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 320

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 321 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 355


>gi|302345330|ref|YP_003813683.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           melaninogenica ATCC 25845]
 gi|302149662|gb|ADK95924.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           melaninogenica ATCC 25845]
          Length = 284

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 80/279 (28%), Positives = 146/279 (52%), Gaps = 32/279 (11%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI    M+  +EE  LA++ R +GD  A  RL  ++LR VV +A  Y+  GL 
Sbjct: 14  SLDKYLQEIGHEEMISIEEEVELAQKIR-NGDRKALERLTKANLRFVVSVAKQYQNQGLS 72

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG----TTA 130
           + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + I     ++++     ++ 
Sbjct: 73  LPDLINEGNVGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIIRLPLNQVSSV 132

Query: 131 NQKRLFF------NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           N+           N RR    +  I  N   PE  +  A K+N   S  +S++     DE
Sbjct: 133 NKINKILTQFEQENERR--PSIDEIAQNTDIPEDKIVDAMKVN---SRHVSVDAPFYDDE 187

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
             + L    + N+      LV      E+ L         R  + R++ +L  RE+ + E
Sbjct: 188 QSSLLDVIPNDNTPSTDKELV------EESL---------REEIGRALQILEDREKVVIE 232

Query: 245 AR-RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           A   + +  +TLE + S++ ++RERVRQI+ +A +++++
Sbjct: 233 AYFGINQREMTLEEIGSKYNLTRERVRQIKEKAIRRLRQ 271


>gi|302036606|ref|YP_003796928.1| RNA polymerase, sigma S (sigma 38) factor [Candidatus Nitrospira
           defluvii]
 gi|300604670|emb|CBK41002.1| RNA polymerase, sigma S (sigma 38) factor [Candidatus Nitrospira
           defluvii]
          Length = 332

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 87/289 (30%), Positives = 145/289 (50%), Gaps = 13/289 (4%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           NR   S    G   +  Y+ E+RK  +L  +EE  L KR    GD +A   ++ ++LRLV
Sbjct: 48  NRPAESGRAEGLDTIKSYLREVRKSTLLNFKEEQALGKRVM-AGDEAARQEMIEANLRLV 106

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           + I   Y   G P +++V EGN+GL++AV+KF+ +RGFR +TY+ WWI+  ++  I+   
Sbjct: 107 ISIGKRYMNRGFPFADIVEEGNLGLIKAVEKFNYKRGFRFSTYASWWIRQFIERAIINQG 166

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            LV++     ++     L R  G ++ +     +  +   +A KL  S +EV  +   + 
Sbjct: 167 KLVRLPVHVVER-----LNRYLGKVEQLVHELGREPRADEVAAKLKTSVAEVDDLKQLVR 221

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              SL++ I  SD+  +  +D +    D       E  E   RR  L   +  L  +ER 
Sbjct: 222 TTCSLDSPI--SDRQDTFLRDVI---EDPLCLTPAETTEGVMRRAELMAWVKELPEKERT 276

Query: 242 IFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +  AR   +     TLE +  E  ++RERVRQIE  A  +++  I+++ 
Sbjct: 277 VILARFGLDGAESRTLEEIGQEMGLTRERVRQIETAALARLRGIIERKT 325


>gi|108803721|ref|YP_643658.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108764964|gb|ABG03846.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 365

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 84/267 (31%), Positives = 137/267 (51%), Gaps = 13/267 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K P+L K +E  LAKR  E GD  A   L  ++LRLVV IA  Y G G+ + ++
Sbjct: 99  YLDEIGKTPLLSKAQEVYLAKRI-ERGDRRAKAHLTRANLRLVVSIAKKYAGRGVSLLDL 157

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM+AV+KFD  +G++ +TY+ WWI+ A+   I      +++     +K     
Sbjct: 158 IQEGNIGLMRAVEKFDYRKGYKFSTYATWWIRQAVTRAIADKGRTIRVPVHMVEK--INK 215

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
             R++  L +  + +   E+V   A+++ V   E      R     S++      + +SS
Sbjct: 216 YYRVQRTLASELNRDPTDEEV---AREMGVEVEE--VERIRQVSRRSISLETPVGEDHSS 270

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLE 256
           +  D++  +       L +    K R   +  +++ L  RER + E R       P TLE
Sbjct: 271 ELGDFIADEESESPHDLAKSSLLKAR---MREALNGLPERERMVLEYRFGLTGGQPKTLE 327

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQES 283
            +   F+V+RER+RQI+  A  K++ S
Sbjct: 328 EVGERFDVTRERIRQIQLTALAKIKSS 354


>gi|332518972|ref|ZP_08395439.1| RNA polymerase sigma factor, sigma-70 family [Lacinutrix algicola
           5H-3-7-4]
 gi|332044820|gb|EGI81013.1| RNA polymerase sigma factor, sigma-70 family [Lacinutrix algicola
           5H-3-7-4]
          Length = 287

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 81/287 (28%), Positives = 152/287 (52%), Gaps = 37/287 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ ++   EE  LA+R +  GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGKVDLITADEEVELAQRIK-AGDQVALEKLTKANLRFVVSVAKQYQNQGLTL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
            ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++      Q  I+R   L KIG+ 
Sbjct: 77  PDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVR-LPLNKIGSI 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA- 188
               + F  L +           + +P     IAK+L+++ ++V           S++A 
Sbjct: 136 NKINKTFAFLEQA----------HERPPSAEEIAKELDMTINDVKESMKNSGRHVSMDAP 185

Query: 189 LINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           L+   D N        +YD  + G+      +   ++ R  + R++  L PRE  +    
Sbjct: 186 LVEGEDSN--------LYDVLNSGESPNPDRELLHESLRTEIERALETLTPREADVI--- 234

Query: 247 RL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RL      ++P+TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 235 RLYFGLGNQHPMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|291520418|emb|CBK75639.1| RNA polymerase, sigma 70 subunit, RpoD [Butyrivibrio fibrisolvens
           16/4]
          Length = 376

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 85/273 (31%), Positives = 136/273 (49%), Gaps = 29/273 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  +EE  LA++  E GD  A ++L  ++LRLVV IA  Y G G+   ++
Sbjct: 109 YLKEIGKVPLLSAEEEVELAQKM-EDGDQEAKNKLAEANLRLVVSIAKRYVGRGMLFLDL 167

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 168 IQEGNLGLMKAVEKFDYHKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 225

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALI 190
           L R+   L         PE++ A        + + L +S+ E +S+   +  +E      
Sbjct: 226 LIRVSRQLLQEYGREPTPEEIAAAMGITVDRVHEILKISQ-EPVSLETPIGEEE------ 278

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
                  S   D+L    D    V  E       +  L   +  L  RE+R+   R   E
Sbjct: 279 ------DSHLGDFL---PDENVPVPAEAATFTLLKEQLHEVLDTLTEREQRVLILRFGLE 329

Query: 251 N--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +    TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 330 DGKARTLEEVGKEFNVTRERIRQIEAKALRKLR 362


>gi|82701632|ref|YP_411198.1| RNA polymerase sigma factor RpoS [Nitrosospira multiformis ATCC
           25196]
 gi|82409697|gb|ABB73806.1| RNA polymerase, sigma 38 subunit, RpoS [Nitrosospira multiformis
           ATCC 25196]
          Length = 317

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 83/265 (31%), Positives = 141/265 (53%), Gaps = 15/265 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y +EI    +L  +EE  L +R R++ D +A  +++  +LRLVV IA  Y  +G+ + ++
Sbjct: 50  YFNEIGHNALLTPKEEAELTRRVRQN-DFAARQKMIECNLRLVVNIAKHYTNHGVALLDL 108

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+G+M A+ KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 109 IEEGNMGMMHALDKFDPERGFRFSTYATWWIRQNIERCIMNQSRTIRLPVHV-IKDLNII 167

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L+  + HL+A T  + K E V  +  +       ++S+N  +    SL+A ++     S 
Sbjct: 168 LQAAR-HLEAHTGKDPKAEDVAHLLGRTVKEVQRMLSLNQSMM---SLDAPLDVDPLLS- 222

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPRERRIFEARRLQEN--PVTL 255
              D +  D      ++ E+ E K R ++ L R    LN ++R I E R         TL
Sbjct: 223 -IGDAIADDQSPGPDLMWEQSEIKGRVQDWLNR----LNDKQRYIIEQRYGLNGYETQTL 277

Query: 256 ENLSSEFEVSRERVRQIEARAFKKV 280
           E L++  +++RERVRQI+  A + +
Sbjct: 278 EQLAASLDLTRERVRQIQLEALQTL 302


>gi|329766845|ref|ZP_08258374.1| hypothetical protein HMPREF0428_00071 [Gemella haemolysans M341]
 gi|328838571|gb|EGF88177.1| hypothetical protein HMPREF0428_00071 [Gemella haemolysans M341]
          Length = 361

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 89/269 (33%), Positives = 141/269 (52%), Gaps = 17/269 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAK---RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           Y+ EI K+P+L K++E  L+K      E     A   L  ++LRLVV IA  Y G G+  
Sbjct: 91  YLKEIGKVPLLSKEKELELSKIIETGTEAEKEQAKKDLAEANLRLVVSIAKRYVGRGMLF 150

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I    +    
Sbjct: 151 LDLIQEGNMGLIKAVEKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVET 208

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
              L R++  L        KPE+   IAKK+N++  +V  +  ++A +  SL   I   D
Sbjct: 209 INRLIRIQRQLLQDLGREPKPEE---IAKKMNMTPEKVREI-LKIAQEPVSLETPIGEED 264

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
              S   D+ + D D Q  V  E    +  +  L   +  L  RE  + + R  L++   
Sbjct: 265 --DSHLGDF-IEDKDAQSPV--EHAANELLKEQLEEILETLTDREENVLKLRFGLKDGKT 319

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE + S F V+RER+RQIEA+A +K++
Sbjct: 320 HTLEEVGSAFGVTRERIRQIEAKAIRKLK 348


>gi|300854008|ref|YP_003778992.1| putative RNA polymerase sigma factor [Clostridium ljungdahlii DSM
           13528]
 gi|300434123|gb|ADK13890.1| predicted RNA polymerase sigma factor [Clostridium ljungdahlii DSM
           13528]
          Length = 354

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 86/286 (30%), Positives = 139/286 (48%), Gaps = 17/286 (5%)

Query: 2   NRKNMSIIVNGEIGLSR----YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSH 57
           N KN+ + V   I +      Y+ EI K+P+L  +EE  LAKR  E GD  A  +L  ++
Sbjct: 67  NEKNLDLSVPDGIAIDDPVRMYLKEIGKVPLLLPEEEISLAKRI-EEGDQIAKKKLAEAN 125

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I
Sbjct: 126 LRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAI 185

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
                 ++I    +       L R+   L         PE+V  I +       E++ + 
Sbjct: 186 ADQARTIRI--PVHMVETINKLVRVSRQLLQELGREPHPEEVAQIMEMPVDKVREIMKI- 242

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                 E ++      ++  S   D++  D              K +   L   +  L P
Sbjct: 243 ----AQEPVSLETPIGEEEDSHLGDFIPDDEAPAPAEAAAFTMLKEQ---LINVLDTLTP 295

Query: 238 RERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           RE ++   R   ++    TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 296 REEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLR 341


>gi|78214100|ref|YP_382879.1| type II alternative RNA polymerase sigma factor [Synechococcus sp.
           CC9605]
 gi|78198559|gb|ABB36324.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. CC9605]
          Length = 377

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 76/238 (31%), Positives = 121/238 (50%), Gaps = 17/238 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLVV +A  Y+  G+ I ++V EG +GL +AV+KFDP RGFR +TY+ WW
Sbjct: 137 AKDHMIQANLRLVVAVAKKYQQRGMEILDLVQEGTLGLERAVEKFDPTRGFRFSTYAYWW 196

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   I      +++     +K     L R+K   Q I  N  +   +  +A++L +
Sbjct: 197 IRQGITRAIATQSRTIRLPVHVTEK-----LNRIKRVQQEIASNEGRIASIADLARELGI 251

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SE  V     R+    SL+  +    +  +Q  D +   H   EQ L   E   +  ++L
Sbjct: 252 SEDTVRQTLARVPRSVSLDTRVGR--EQDTQLGDLIEDGHATPEQTLTHDELHNDLEHLL 309

Query: 229 ----TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
               +R  +VL    RR F      + P TL  +  E ++SRERVRQIE RA  K+++
Sbjct: 310 DELTSREAAVL----RRRFGLE--DDTPQTLAQIGEELKLSRERVRQIETRALLKLRQ 361


>gi|325125918|gb|ADY85248.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus 2038]
          Length = 373

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 85/275 (30%), Positives = 131/275 (47%), Gaps = 33/275 (12%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +Y+  I ++ +L   EE  LAKR    GD  A   L  ++LRLVV IA  Y G G+   +
Sbjct: 106 QYLKRIGRVSLLSGDEEVQLAKRIG-AGDQEAKDELTNANLRLVVSIAKRYVGRGMSFLD 164

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      ++I    +      
Sbjct: 165 LIQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETIN 222

Query: 138 NLRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLA--GDESLN 187
            L R++  L      + +PE++ A        + + L V++ E +S+   +    D  L 
Sbjct: 223 KLIRIQRQLLQDLGRDPEPEEIAAEMDLPVKKVREALKVAQ-EPVSLETPIGEEDDSHLG 281

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR- 246
             I   D  S +        H   E +          R+ L   +  L  RE  +   R 
Sbjct: 282 DFIEDKDATSPEQ-------HAASEML----------RDQLAEVLDTLTDREENVLRLRF 324

Query: 247 RLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            L + NP TLE +   F V+RER+RQIEA+A +K+
Sbjct: 325 GLDDGNPRTLEEVGRVFGVTRERIRQIEAKALRKL 359


>gi|288905580|ref|YP_003430802.1| RNA polymerase major sigma factor [Streptococcus gallolyticus
           UCN34]
 gi|306831670|ref|ZP_07464827.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           gallolyticus subsp. gallolyticus TX20005]
 gi|325978609|ref|YP_004288325.1| RNA polymerase sigma factor rpoD [Streptococcus gallolyticus subsp.
           gallolyticus ATCC BAA-2069]
 gi|288732306|emb|CBI13876.1| RNA polymerase major sigma factor [Streptococcus gallolyticus
           UCN34]
 gi|304426095|gb|EFM29210.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           gallolyticus subsp. gallolyticus TX20005]
 gi|325178537|emb|CBZ48581.1| RNA polymerase sigma factor rpoD [Streptococcus gallolyticus subsp.
           gallolyticus ATCC BAA-2069]
          Length = 369

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 86/269 (31%), Positives = 141/269 (52%), Gaps = 21/269 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA      GDL A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLTSEEEKELAVAV-AAGDLQAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 218

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L      +  PEQ   IA++++++  +V  +  ++A +  SL   I   D   
Sbjct: 219 LVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREI-LKIAQEPVSLETPIGEED--D 272

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 273 SHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 326

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE++   F V+RER+RQIEA+A +K++
Sbjct: 327 RTLEDVGKVFNVTRERIRQIEAKALRKLR 355


>gi|119897381|ref|YP_932594.1| RNA polymerase sigma factor RpoS [Azoarcus sp. BH72]
 gi|119669794|emb|CAL93707.1| putative RNA polymerase sigma factor [Azoarcus sp. BH72]
          Length = 311

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 87/281 (30%), Positives = 143/281 (50%), Gaps = 33/281 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE  LA+R R  GD  A   ++  +LRLVV IA  Y   G+P+ ++
Sbjct: 44  YLNEIGANPLLSAEEEAALARRVRA-GDFDARQTMIERNLRLVVNIAKHYLNRGIPLLDL 102

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GLM A++KFDPERGFR +TY+ WWI+  ++  I+            NQ R    
Sbjct: 103 VEEGNLGLMHALEKFDPERGFRFSTYATWWIRQNIERAIM------------NQSRTI-- 148

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVI--------SMNCRLAGDESLNALI 190
             RL  H+    +  L+ ++VV  A   + S  E+          +   LA  E   +L 
Sbjct: 149 --RLPVHVVKELNQVLRAQRVVEAASNGDFSLDEIARRLDKPIEEVRAILALSEHTASLD 206

Query: 191 NSSDKNSS-QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS-MSVLNPRERRIFEARR- 247
              D + +    + L  +H    +  I   E +     L R+ + +LN ++R +   R  
Sbjct: 207 APLDIDPTLSIGESLADEHAETPESQIHNAEIEG----LIRAWIDMLNDKQRLVIRHRYG 262

Query: 248 -LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             +   +TLE L++  E++RERVRQI+  A  +++  ++++
Sbjct: 263 IGECELMTLEELAARLELTRERVRQIQLEALGQLRRILKRR 303


>gi|238916620|ref|YP_002930137.1| RNA polymerase primary sigma factor [Eubacterium eligens ATCC
           27750]
 gi|238871980|gb|ACR71690.1| RNA polymerase primary sigma factor [Eubacterium eligens ATCC
           27750]
          Length = 434

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 83/265 (31%), Positives = 132/265 (49%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L   EE   AKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 168 YLKEIGKVPLLSADEEIEYAKRM-EEGDEEAKKRLAEANLRLVVSIAKRYVGRGMQFLDL 226

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+K+D  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 227 IQEGNLGLIKAVEKYDYRKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 284

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R++  L         PE+   IA+ +++    V  +        SL   I   ++  S
Sbjct: 285 LVRVQRQLLQELGREPSPEE---IAENMDIPVERVREIQKISQEPVSLETPI--GEEEDS 339

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++    D    V  E       +  L   +  L  RE+++   R   ++    TLE
Sbjct: 340 HLGDFI---QDDNVPVPAEAAASTLLKEQLVEVLGTLTEREQKVLRLRFGMDDGRARTLE 396

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF V+RER+RQIEA+A +K++
Sbjct: 397 EVGKEFNVTRERIRQIEAKALRKLR 421


>gi|228472793|ref|ZP_04057551.1| RNA polymerase sigma factor RpoD [Capnocytophaga gingivalis ATCC
           33624]
 gi|228275844|gb|EEK14610.1| RNA polymerase sigma factor RpoD [Capnocytophaga gingivalis ATCC
           33624]
          Length = 287

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 82/284 (28%), Positives = 152/284 (53%), Gaps = 31/284 (10%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ ++   EE  LA+R +  GD  A  RL  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGKVDLISADEEVELAQRIK-AGDKIALERLTKANLRFVVSVAKQYQNQGLTL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
            ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++      Q  I+R   L KIG+ 
Sbjct: 77  PDLINEGNMGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVR-LPLNKIGSI 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA- 188
               +++  L +    + +  +          IAK+L++S ++V           S++A 
Sbjct: 136 NKINKMYAYLEQTHERVPSAEE----------IAKELDMSVNDVKESMKNSGRHISMDAP 185

Query: 189 LINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           L+   D N        +YD    G+     ++   ++ +  + R++  L PRE  +    
Sbjct: 186 LVEGEDSN--------LYDVLRSGESPNPDKELMHESLKTEIERALETLTPREADVIRLY 237

Query: 247 -RLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
             L EN P+TLE +   FE++RERVRQI+ +A ++++ + + ++
Sbjct: 238 FGLGENYPMTLEEIGETFELTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|317122932|ref|YP_004102935.1| RNA polymerase, sigma 70 subunit, RpoD [Thermaerobacter marianensis
           DSM 12885]
 gi|315592912|gb|ADU52208.1| RNA polymerase, sigma 70 subunit, RpoD [Thermaerobacter marianensis
           DSM 12885]
          Length = 433

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 85/275 (30%), Positives = 137/275 (49%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI +IP+L  ++E  LAKR  E GD  A  +L+ ++LRLVV IA  Y G G+   ++
Sbjct: 167 YLKEIGRIPLLTPEQEIELAKRI-EQGDEEAKRKLIQANLRLVVSIAKRYVGRGMLFLDL 225

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++A +KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 226 IQEGNLGLIKAAEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 285

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES--LN 187
             Q++L   L R     +   +  ++PE+V  I K       E +S+   +  +E   L 
Sbjct: 286 RVQRQLVQELGREPTPEEIAKEMGIEPEKVREIMKIAQ----EPVSLETPIGEEEDSHLG 341

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D          +   +   Q+L+        R  L   +  L  RE+++   R 
Sbjct: 342 DFIEDEDA---------LAPAEAASQLLL--------REQLEDVLHTLTDREQKVLRLRF 384

Query: 248 LQENP--VTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 385 GLDDGRQRTLEEVGQVFGVTRERIRQIEAKALRKL 419


>gi|313673100|ref|YP_004051211.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Calditerrivibrio
           nitroreducens DSM 19672]
 gi|312939856|gb|ADR19048.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Calditerrivibrio
           nitroreducens DSM 19672]
          Length = 327

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 80/280 (28%), Positives = 146/280 (52%), Gaps = 38/280 (13%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            +  +I++I K   L ++EEY L KR  + GD  A ++L+ S+++ VV +A  Y+  G+ 
Sbjct: 58  SIKDFINKIDKFKPLTREEEYELGKRI-QQGDQEALNKLILSNIKFVVSMANRYKNTGVS 116

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           +S+++++GN+GL++A K+FDP++G +  +Y++WWI+ AM + +      VK+     Q  
Sbjct: 117 LSDLINQGNLGLVEAAKRFDPDKGVKFISYAVWWIRQAMIQLLAEQSGTVKL--PIKQAS 174

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN-VSESEVISMNCRLAGDESLNALINSS 193
           L + +                 E +  ++KK +    SE IS    +  +   N L+ S 
Sbjct: 175 LLYKIN----------------EAIETLSKKYHREPTSEEISEYLNIPKENIENILMVS- 217

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERK-----------NRRNMLTRSMSVLNPRERRI 242
            KN   ++  +    DG+++  ++  E +             ++ L   +  L+ RE +I
Sbjct: 218 -KNYLSFESPI---KDGEDRTFLDLMESRTIKVEDEVINHTLKDTLQSLIQELDEREAKI 273

Query: 243 FEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            + R     ENP+TLE + +   +SRERVRQIE+RA  K+
Sbjct: 274 LKMRYGLDGENPMTLEEVGNILNISRERVRQIESRALSKL 313


>gi|291280296|ref|YP_003497131.1| DNA-directed RNA polymerase sigma 70 factor [Deferribacter
           desulfuricans SSM1]
 gi|290754998|dbj|BAI81375.1| DNA-directed RNA polymerase sigma 70 factor [Deferribacter
           desulfuricans SSM1]
          Length = 313

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 86/270 (31%), Positives = 138/270 (51%), Gaps = 24/270 (8%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GL  Y++ I +   L ++EEY L KR +  GD  A  +LV S+L+ VV IA  Y+  G
Sbjct: 42  EDGLKNYLNRISQFQPLSREEEYELGKRIQ-QGDKKALEKLVLSNLKFVVSIANRYKNTG 100

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP+++++++GN+GL++A K+FDPERG +  +Y++WWI+ A+ + +      VK+     Q
Sbjct: 101 LPLADIINQGNLGLLEAAKRFDPERGVKFISYAVWWIRQAIIQALAEQSGTVKL--PLKQ 158

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV-----ISMNCRLAGDESLN 187
             + + +      L         P++   IA  L++  +++     +S N       SL 
Sbjct: 159 ASILYKINEAIEVLSKELGREPTPDE---IAVYLDMDPADIENVLRVSRNYL-----SLE 210

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR- 246
           A I   D     + D L       E+ +     + N   ++      LN RE +I + R 
Sbjct: 211 API--KDGEDRAFIDLLESGGKSVEEEIFLNTLKANIEEIVDE----LNEREAQIIKWRF 264

Query: 247 RLQ-ENPVTLENLSSEFEVSRERVRQIEAR 275
            L+ E P TLE +     +SRERVRQIEAR
Sbjct: 265 GLEGETPKTLEEIGEILNISRERVRQIEAR 294


>gi|6175927|gb|AAF05340.1|AF182105_2 RNA polymerase sigma subunit [Escherichia coli]
          Length = 313

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 82/270 (30%), Positives = 134/270 (49%), Gaps = 25/270 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL +AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLNRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
              TLE++  E  ++RERVRQI+    +++
Sbjct: 286 --ATLEDVGREIGLTRERVRQIQVEGLRRL 313


>gi|71908137|ref|YP_285724.1| RNA polymerase sigma factor RpoS [Dechloromonas aromatica RCB]
 gi|71847758|gb|AAZ47254.1| RNA polymerase, sigma 38 subunit, RpoS [Dechloromonas aromatica
           RCB]
          Length = 309

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 77/270 (28%), Positives = 145/270 (53%), Gaps = 13/270 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L   EE   ++  RE GD SA  R++  +LRLVV IA  Y   G+P+ ++
Sbjct: 42  YLSEIGAKPLLTPAEELATSRLVRE-GDFSARQRMIEHNLRLVVNIAKHYLNRGIPLLDL 100

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL+ A++KFDPERGFR +TY+ WWI+  ++  I+     +++      K +   
Sbjct: 101 IEEGNLGLIHALEKFDPERGFRFSTYATWWIRQNIERGIMNQSRTIRLPVHI-VKEINVV 159

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR ++ HL++    +   E++  +  +       ++S+N  +A   SL+A +   D N +
Sbjct: 160 LRAMR-HLESADKRDSTVERIALLIDRPVADVRRILSLNEHIA---SLDAPLE-IDPNHT 214

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
             +  +  D +   + L++  E     +++   +  L  R+R + E R      +  TL+
Sbjct: 215 MAE-VIADDGESDPESLLQSSEVG---SLVDDWLEQLTERQRSVIERRYGLSGADLATLD 270

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            ++ +  ++RERVRQI+     ++++ I++
Sbjct: 271 VIACDLGLTRERVRQIQMEGLDRLRKIIKR 300


>gi|332292552|ref|YP_004431161.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Krokinobacter
           diaphorus 4H-3-7-5]
 gi|332170638|gb|AEE19893.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Krokinobacter
           diaphorus 4H-3-7-5]
          Length = 287

 Score =  111 bits (278), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 82/296 (27%), Positives = 154/296 (52%), Gaps = 55/296 (18%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ ++   EE  LA+R +  GD  A  +L  ++LR VV ++  Y+  GL +
Sbjct: 18  LDKYLQEIGKVDLITADEEVELAQRIK-AGDHRALEKLTKANLRFVVSVSKQYQNQGLTL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
            ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++      Q  I+R   L KIG+ 
Sbjct: 77  PDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVR-LPLNKIGSI 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCR 179
               + F  L +           N +P     IAK+L++S ++V          ISM+  
Sbjct: 136 NKINKTFAFLEQA----------NERPPSPEEIAKELDMSINDVKESLKNSGRHISMDAP 185

Query: 180 L--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
           L    D +L  ++NS +  +   +  L+++               + +  + R++  L P
Sbjct: 186 LVEGEDSNLYDVLNSGESPNPDRE--LLHE---------------SLKTEIERALETLTP 228

Query: 238 RERRIFEARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RE  +    RL      + P+TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 229 READVV---RLYFGLGDQQPMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|313890499|ref|ZP_07824127.1| RNA polymerase sigma factor RpoD [Streptococcus pseudoporcinus SPIN
           20026]
 gi|332523157|ref|ZP_08399409.1| RNA polymerase sigma factor RpoD [Streptococcus porcinus str.
           Jelinkova 176]
 gi|313121016|gb|EFR44127.1| RNA polymerase sigma factor RpoD [Streptococcus pseudoporcinus SPIN
           20026]
 gi|332314421|gb|EGJ27406.1| RNA polymerase sigma factor RpoD [Streptococcus porcinus str.
           Jelinkova 176]
          Length = 369

 Score =  111 bits (277), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 86/269 (31%), Positives = 141/269 (52%), Gaps = 21/269 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E GD+ A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLTGEEEKELAIAVAE-GDVDAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 218

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L      +  PEQ   IA+++ ++  +V  +  ++A +  SL   I   D   
Sbjct: 219 LVREQRNLLQELGQDPTPEQ---IAERMEMTPDKVREI-LKIAQEPVSLETPIGEED--D 272

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 273 SHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 326

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE++   F V+RER+RQIEA+A +K++
Sbjct: 327 RTLEDVGKVFNVTRERIRQIEAKALRKLR 355


>gi|292670108|ref|ZP_06603534.1| DNA-directed RNA polymerase sigma subunit RpoD [Selenomonas noxia
           ATCC 43541]
 gi|292648296|gb|EFF66268.1| DNA-directed RNA polymerase sigma subunit RpoD [Selenomonas noxia
           ATCC 43541]
          Length = 370

 Score =  111 bits (277), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 84/272 (30%), Positives = 139/272 (51%), Gaps = 13/272 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA+R  E GD  A HRL  ++LRLVV IA  Y G G+   ++
Sbjct: 104 YLKEIGHVPLLTAEEEVALAQRM-EAGDEEARHRLEEANLRLVVSIAKRYVGRGMLFLDL 162

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 163 IQEGNLGLLKAVEKFDYSKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 220

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L      +  PE+V   A+++ +S + V  +  ++A  E ++      ++  S
Sbjct: 221 LVRISRQLLQELGRDPHPEEV---AREMGISVARVHEI-MKIA-QEPVSLETPIGEEEDS 275

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++    D       E       R  L   +  L  RE+ +   R   E+    TLE
Sbjct: 276 HLGDFI---EDEAAPAPAEAASFMLLREQLEEVLETLTDREKNVLRLRFGLEDGRSRTLE 332

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +   F V+RER+RQIEA+A +K++   + +V
Sbjct: 333 EVGQSFGVTRERIRQIEAKALRKLRHPSRSKV 364


>gi|302338230|ref|YP_003803436.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           smaragdinae DSM 11293]
 gi|301635415|gb|ADK80842.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           smaragdinae DSM 11293]
          Length = 291

 Score =  111 bits (277), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 76/285 (26%), Positives = 159/285 (55%), Gaps = 20/285 (7%)

Query: 11  NGEIG----LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           +G+ G    +S Y+ EI K+P+L +++E   A R    GD  A   L+ S+LR VV +A 
Sbjct: 11  SGDFGNENVISIYLKEINKVPLLSREDEDRYA-RLAADGDEHAKEMLIKSNLRFVVNVAK 69

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y+  GLP++++++EGNIGLM A++++D ++G+   +Y++WWI+ A+ + I     ++++
Sbjct: 70  KYQNQGLPLADLINEGNIGLMNAIERYDVDKGYHFISYAVWWIRQAILKAISEKARMIRL 129

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD-ES 185
               N+      + + K  LQ       +  +   IA+ + +    V S+   ++ D  S
Sbjct: 130 --PLNRANELVQIEKAKKGLQLEG---KEEPEFEEIARVVGMDAEHVASL-VNISRDLVS 183

Query: 186 LNALINSSDKNSSQWQDWL-VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           L + I  +D++ S+  D++   D+   ++ L+E+  +++    + + +  L+ +E  I  
Sbjct: 184 LESPI-YTDRSQSELGDFIEDVDYKSPDETLMEQSLKED----IAKVLDTLSEKEADIIR 238

Query: 245 ARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R   +   P++L+++   + +++ER+RQIE +A K++Q   ++Q
Sbjct: 239 HRFGLDGRAPLSLKDIGDRYNLTKERIRQIEKKAIKRLQHPSRRQ 283


>gi|312891071|ref|ZP_07750594.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Mucilaginibacter
           paludis DSM 18603]
 gi|311296379|gb|EFQ73525.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Mucilaginibacter
           paludis DSM 18603]
          Length = 285

 Score =  111 bits (277), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 77/280 (27%), Positives = 144/280 (51%), Gaps = 34/280 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ ++   EE +LA++ RE GD +A  RL  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLTEIGKVDLITADEEVILAQKIRE-GDQAALERLTKTNLRFVVSVAKQYQNQGLTL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A K+FD  +GF+  +Y++WWI+ ++   +     +V++    NQ   
Sbjct: 77  GDLINEGNLGLIKAAKRFDETKGFKFISYAVWWIRQSILSAVAEQSRIVRL--PLNQIGS 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRLAGDES 185
              +R+    L+   +   +P Q   +A  L  +E ++          +SM+      E 
Sbjct: 135 LNKIRQAFSKLEQQYER--EPSQ-AELADILETTEDKICDSLSNSGRHVSMDAPFVQGEE 191

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
            N L++    N     D+L+ +   QE               + RS+  L  RER +   
Sbjct: 192 -NTLLDVLQNNEPTTDDYLMEESLSQE---------------IMRSLVTLAEREREVIVL 235

Query: 246 RRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
                N  P++LE +  ++ ++RERVRQI+ +A ++++ +
Sbjct: 236 FFGLGNNYPLSLEEIGEKYNLTRERVRQIKDKALQRLRHT 275


>gi|260591639|ref|ZP_05857097.1| RNA polymerase sigma-70 factor [Prevotella veroralis F0319]
 gi|260536439|gb|EEX19056.1| RNA polymerase sigma-70 factor [Prevotella veroralis F0319]
          Length = 287

 Score =  111 bits (277), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 76/276 (27%), Positives = 152/276 (55%), Gaps = 14/276 (5%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI    M+  +EE  LA++ R+ GD  A  RL  ++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQEIGHEEMISIEEEVELAQQIRK-GDRKALERLTKANLRFVVSVAKQYQNQGLS 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           +S++++EGN GL++A +KFD  RGF+  +Y++WWI+ ++ + I     ++++    NQ  
Sbjct: 76  LSDLINEGNFGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIIRL--PLNQ-- 131

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
              ++ ++   L      N +   +  IA+  ++ E ++I          S++A  +  D
Sbjct: 132 -VSSVNKINKVLNKFEQENERRPSIDEIAQDTDIPEEKIIEAFKINTHHISVDAPFHDDD 190

Query: 195 KNSSQWQDWLVYDH-DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENP 252
           ++S    D +  D     ++ L+E    ++ R  + R + +L  RE+++ EA   + +  
Sbjct: 191 ESS--LLDVIPNDAIPSTDKSLVE----ESLRAEIGRVLDILEDREKKVIEAYFGINQRE 244

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TLE + S++ ++RERVRQI+ +A +++++    ++
Sbjct: 245 MTLEEIGSKYGLTRERVRQIKEKAIRRLRQQTNSKI 280


>gi|94500747|ref|ZP_01307276.1| nonessential primary sigma factor [Oceanobacter sp. RED65]
 gi|94427069|gb|EAT12050.1| nonessential primary sigma factor [Oceanobacter sp. RED65]
          Length = 331

 Score =  111 bits (277), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 88/281 (31%), Positives = 143/281 (50%), Gaps = 33/281 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  QEE   A+  R+ GD     R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 58  YLNEIGFSPLLTPQEEVHFARLARK-GDEKGRKRMIESNLRLVVKIARRYVNRGLTLLDL 116

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 117 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 175

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA------GDESLNALINS 192
           LR  +   Q + D+    E++  + +K       ++ +N R+       G  S  A++++
Sbjct: 176 LRAARELTQKL-DHEPTAEEIADLLEKPVDDVKRMLGLNERVTSVDTPLGYNSDKAILDT 234

Query: 193 ------SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
                 SD       D +    DG    L EK+     R ++ R   +      R +E  
Sbjct: 235 IADEAVSDPCQVLQDDDISSSLDGWLDELTEKQ-----REVIARRFGL------RGYEIS 283

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
                  TLE +  E  ++RERVRQI+  A K+++E ++KQ
Sbjct: 284 -------TLEEVGFEIGLTRERVRQIQVEALKRLREIMEKQ 317


>gi|229916320|ref|YP_002884966.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Exiguobacterium
           sp. AT1b]
 gi|229467749|gb|ACQ69521.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Exiguobacterium
           sp. AT1b]
          Length = 364

 Score =  111 bits (277), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 88/276 (31%), Positives = 141/276 (51%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  ++E  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 98  YLKEIGRVDLLSAKDETELAKRI-EQGDEEAKKRLAEANLRLVVSIAKRYVGRGMLFLDL 156

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 157 IQEGNMGLIKAVEKFDYMKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 216

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   +  L PE+V  I   L +++ E +S+   +    D  L 
Sbjct: 217 RVQRQLLQDLGREPSPEEIAKEMELTPEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 272

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D+++   QD   Y      ++L E+         L   +  L  RE  +   R 
Sbjct: 273 DFI--EDQDAMAPQDAAAY------ELLKEQ---------LEDVLDTLTDREENVLRLRF 315

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 316 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 351


>gi|299535819|ref|ZP_07049140.1| RNA polymerase sigma factor [Lysinibacillus fusiformis ZC1]
 gi|298729019|gb|EFI69573.1| RNA polymerase sigma factor [Lysinibacillus fusiformis ZC1]
          Length = 375

 Score =  111 bits (277), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 86/276 (31%), Positives = 138/276 (50%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  ++E  LA+R  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 109 YLKEIGRVDLLSAEQEIALAERI-EQGDEEARKRLAEANLRLVVSIAKRYVGRGMLFLDL 167

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 168 IQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 227

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I   L +++ E +S+   +    D  L 
Sbjct: 228 RVQRQLLQDLGREPSPEEIGEEMDLTPEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 283

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I  S+  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 284 DFIEDSEAQSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 326

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 327 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 362


>gi|167630065|ref|YP_001680564.1| RNA polymerase sigma factor rpod [Heliobacterium modesticaldum
           Ice1]
 gi|167592805|gb|ABZ84553.1| RNA polymerase sigma factor rpod [Heliobacterium modesticaldum
           Ice1]
          Length = 371

 Score =  111 bits (277), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 86/275 (31%), Positives = 136/275 (49%), Gaps = 33/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LAKR  E GD +A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 105 YLKEIGRVPLLSAEEEIELAKRM-EEGDEAAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 163

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 164 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 221

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVS----------ESEVISMNCRLAGDES--L 186
           L R+   L         PE+   IAK++++             E +S+   +  +E   L
Sbjct: 222 LIRVSRQLLQEYGREPMPEE---IAKEMDIPVERVREIMKIAQEPVSLETPIGEEEDSHL 278

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              I   D  +       +   +  E+VL           +  R M VL  R R   +  
Sbjct: 279 GDFIEDQDAPAPAEAASFILLKEQLEEVL---------ETLTAREMKVL--RLRFGLDDG 327

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R +    TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 328 RSR----TLEEVGQEFGVTRERIRQIEAKALRKLR 358


>gi|1519632|gb|AAC44890.1| sigma 70-type sigma factor SigA [Heliobacillus mobilis]
          Length = 333

 Score =  111 bits (277), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 86/275 (31%), Positives = 135/275 (49%), Gaps = 33/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 67  YLKEIGRVPLLSAEEEIELAKRM-EDGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 126 IQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 183

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVS----------ESEVISMNCRLAGDES--L 186
           L R+   L         PE+   IAK++++             E +S+   +  +E   L
Sbjct: 184 LIRVSRQLLQEFGREPNPEE---IAKEMDIPVDRVREIMKIAQEPVSLETPIGEEEDSHL 240

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              I   D  +       +   +  E+VL           +  R M VL  R R   +  
Sbjct: 241 GDFIEDQDAPAPAEAASFILLKEQLEEVL---------ETLTAREMKVL--RLRFGLDDG 289

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R +    TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 290 RSR----TLEEVGQEFGVTRERIRQIEAKALRKLR 320


>gi|160937106|ref|ZP_02084469.1| hypothetical protein CLOBOL_01996 [Clostridium bolteae ATCC
           BAA-613]
 gi|158440007|gb|EDP17755.1| hypothetical protein CLOBOL_01996 [Clostridium bolteae ATCC
           BAA-613]
          Length = 378

 Score =  111 bits (277), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 87/271 (32%), Positives = 141/271 (52%), Gaps = 27/271 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L  ++E  LAK+  E GD  A  RL  S+LRLVV IA  Y G G+   ++
Sbjct: 111 YLKEIGKIPLLGMEDEVELAKKM-ELGDPEARKRLAESNLRLVVSIAKRYVGRGMQFLDL 169

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT--TANQKRLF 136
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I         RL 
Sbjct: 170 IQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINRLV 229

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS---ESEVISMNCRLAGDESLNALINSS 193
              R+L   LQ +       E    IA +L++     SE++ M+      E ++      
Sbjct: 230 RTSRQL---LQELGREPTTEE----IAARLDLPVERVSEIMKMS-----QEPVSLETPIG 277

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNR--RNMLTRSMSVLNPRERRIFEARRLQEN 251
           ++  S   D++  D+     VL+ ++          L   +  L  RE+++   R   ++
Sbjct: 278 EEEDSHLGDFIQDDN-----VLVPQDAAAFTLLHEQLMEVLLTLTEREQKVLRLRFGLDD 332

Query: 252 --PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             P TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 333 GRPRTLEEVGKQFNVTRERIRQIEAKALRKL 363


>gi|146319082|ref|YP_001198794.1| RNA polymerase sigma factor RpoD [Streptococcus suis 05ZYH33]
 gi|146321288|ref|YP_001200999.1| RNA polymerase sigma factor RpoD [Streptococcus suis 98HAH33]
 gi|223932503|ref|ZP_03624504.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptococcus
           suis 89/1591]
 gi|253752138|ref|YP_003025279.1| RNA polymerase sigma factor RpoD [Streptococcus suis SC84]
 gi|253753963|ref|YP_003027104.1| RNA polymerase sigma factor RpoD [Streptococcus suis P1/7]
 gi|253755898|ref|YP_003029038.1| RNA polymerase sigma factor RpoD [Streptococcus suis BM407]
 gi|330833083|ref|YP_004401908.1| RNA polymerase sigma factor RpoD [Streptococcus suis ST3]
 gi|145689888|gb|ABP90394.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Streptococcus suis 05ZYH33]
 gi|145692094|gb|ABP92599.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Streptococcus suis 98HAH33]
 gi|223898774|gb|EEF65134.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptococcus
           suis 89/1591]
 gi|251816427|emb|CAZ52060.1| RNA polymerase sigma factor RpoD [Streptococcus suis SC84]
 gi|251818362|emb|CAZ56188.1| RNA polymerase sigma factor RpoD [Streptococcus suis BM407]
 gi|251820209|emb|CAR46610.1| RNA polymerase sigma factor RpoD [Streptococcus suis P1/7]
 gi|292558723|gb|ADE31724.1| RNA polymerase sigma factor rpoD [Streptococcus suis GZ1]
 gi|319758521|gb|ADV70463.1| RNA polymerase sigma factor RpoD [Streptococcus suis JS14]
 gi|329307306|gb|AEB81722.1| RNA polymerase sigma factor RpoD [Streptococcus suis ST3]
          Length = 372

 Score =  111 bits (277), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 88/272 (32%), Positives = 143/272 (52%), Gaps = 29/272 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 105 YLKEIGVVPLLTNEEEQELALAV-EAGDPEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 163

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 164 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKL- 222

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSS 193
               +R  +  LQ +   +  PEQ   IA++++++  +V  +  ++A +  SL   I   
Sbjct: 223 ----VREQRNLLQELG-QDPTPEQ---IAERMDMTPEKVREI-LKIAQEPVSLETPIGEE 273

Query: 194 DKNSSQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQ 249
           D   S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L 
Sbjct: 274 D--DSHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLD 325

Query: 250 ENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
           +  + TLE++   F V+RER+RQIEA+A +K+
Sbjct: 326 DGKMRTLEDVGKVFNVTRERIRQIEAKALRKL 357


>gi|255531368|ref|YP_003091740.1| sigma-70 family RNA polymerase sigma factor [Pedobacter heparinus
           DSM 2366]
 gi|255344352|gb|ACU03678.1| RNA polymerase sigma factor, sigma-70 family [Pedobacter heparinus
           DSM 2366]
          Length = 286

 Score =  111 bits (277), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 84/304 (27%), Positives = 155/304 (50%), Gaps = 67/304 (22%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           SI    +  L+RY+ EI K P+L+ +EE VL KR +E GD  A  RLV+S+LR VV +A 
Sbjct: 9   SITNRSQDSLARYLQEISKYPLLDAEEEIVLGKRIKE-GDWDALQRLVSSNLRFVVTVAK 67

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y    L +++++S+GNIGL++A ++FD +RGF+  +Y++WWI+ ++ +           
Sbjct: 68  KYESPDLSLADLISDGNIGLIKAAERFDEKRGFKFISYAVWWIRQSILQ----------- 116

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
           G   +++ +   + ++ G ++ +  + +K EQ             E+  + CR    E L
Sbjct: 117 GMNTSKRMVHLPMSQISG-IRQVKRSEIKLEQ-------------ELQRIPCR----EEL 158

Query: 187 NALINSSDKNSSQWQDWLVYDH--------------DGQEQVLI-------------EKE 219
              + ++++        +VYD+              +GQ+ VLI                
Sbjct: 159 AGFMKTAEE--------VVYDYLYISGSQVSLDAPTEGQDGVLIPCIVQYDKGPAPDASL 210

Query: 220 ERKNRRNMLTRSMSVLNPRERRI-FEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAF 277
           ER++    + R M +L+PRER I F A  +  N P+  +++S+   +S E +R+ + +A 
Sbjct: 211 ERESLEKDVQRMMDILSPRERSILFLAYGMGNNRPLQNDDISTLLGLSTETIRRSKNKAL 270

Query: 278 KKVQ 281
            +++
Sbjct: 271 DRLR 274


>gi|330721381|gb|EGG99448.1| RNA polymerase sigma factor RpoS [gamma proteobacterium IMCC2047]
          Length = 321

 Score =  111 bits (277), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 84/279 (30%), Positives = 141/279 (50%), Gaps = 29/279 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R    GD +   R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 52  YLNEIGFSPLLSAEEEVYYA-RLALKGDEAGRKRMIESNLRLVVKISRRYVNRGLTLLDL 110

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 111 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNVY 169

Query: 139 LRRLKGHLQAITDNNLKPEQVVAI-------AKKLNVSESEVISMNCRLAGDESLNALIN 191
           LR  +   Q + D+    E++  +        K++      V S++  + GD   +   N
Sbjct: 170 LRAARELTQKL-DHEPSAEEIAEMLDRPVENVKRMLKLNERVTSIDAPMGGDSERSMAEN 228

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR---L 248
            + +N     + L  D               N    LT  +  L+ ++R +  ARR   L
Sbjct: 229 ITGENVDDPSELLQND---------------NLHGNLTHWLGELSEKQREVI-ARRFGLL 272

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
                TLE + SE  ++RERVRQI+  A K+++  ++K+
Sbjct: 273 GYEMSTLEQVGSEIGLTRERVRQIQVEALKRLRAVMEKE 311


>gi|313903305|ref|ZP_07836697.1| RNA polymerase, sigma 70 subunit, RpoD [Thermaerobacter
           subterraneus DSM 13965]
 gi|313466393|gb|EFR61915.1| RNA polymerase, sigma 70 subunit, RpoD [Thermaerobacter
           subterraneus DSM 13965]
          Length = 432

 Score =  111 bits (277), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 85/275 (30%), Positives = 137/275 (49%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI +IP+L  ++E  LAKR  E GD  A  +L+ ++LRLVV IA  Y G G+   ++
Sbjct: 166 YLKEIGRIPLLTPEQEIELAKRI-EQGDEEAKRKLIQANLRLVVSIAKRYVGRGMLFLDL 224

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++A +KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 225 IQEGNLGLIKAAEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 284

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES--LN 187
             Q++L   L R     +   +  ++PE+V  I K       E +S+   +  +E   L 
Sbjct: 285 RVQRQLVQELGREPTPEEIAKEMGIEPEKVREIMK----IAQEPVSLETPIGEEEDSHLG 340

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  +           +   Q+L+        R  L   +  L  RE+++   R 
Sbjct: 341 DFIEDEDALAP---------AEAASQLLL--------REQLEDVLHTLTDREQKVLRLRF 383

Query: 248 LQENP--VTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 384 GLDDGRQRTLEEVGQIFGVTRERIRQIEAKALRKL 418


>gi|154484558|ref|ZP_02027006.1| hypothetical protein EUBVEN_02272 [Eubacterium ventriosum ATCC
           27560]
 gi|149734406|gb|EDM50323.1| hypothetical protein EUBVEN_02272 [Eubacterium ventriosum ATCC
           27560]
          Length = 429

 Score =  111 bits (277), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 82/280 (29%), Positives = 145/280 (51%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V  E  +  Y+ EI  +P+L   EE  LAKR  E GD+ A  +L+ ++LRLVV IA  Y 
Sbjct: 153 VGTEDPVRMYLKEIGTVPLLTADEELELAKRKTE-GDIVAKEKLIEANLRLVVSIAKRYT 211

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   ++V EGN+GL++ V+KFD  +G++L+TY+ WWI+ ++   +      +++   
Sbjct: 212 GRGMSFLDLVQEGNLGLIKGVEKFDYTKGYKLSTYATWWIRQSVTRALADHARTIRVPV- 270

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
                +   + R+    + +T           +A  L+++E +V+ +        SL   
Sbjct: 271 ----HMVETINRMSKMQRKLTLELGYEPSTKELATALDMTEEKVLEIMQIAREPASLETP 326

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RL 248
           I   D   S   D++  ++    +  IE    +   ++L +    L  RER +   R  L
Sbjct: 327 IGEED--DSNLGDFVADNNTVTPEANIESVMLREHIDVLLQD---LKDREREVIILRFGL 381

Query: 249 QE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++ +P TLE +   F V+RER+RQIEA+A +K++  ++ +
Sbjct: 382 RDGHPRTLEEVGKIFNVTRERIRQIEAKALRKLRNPVRSK 421


>gi|295397565|ref|ZP_06807644.1| RNA polymerase sigma factor rpoD [Aerococcus viridans ATCC 11563]
 gi|294974189|gb|EFG49937.1| RNA polymerase sigma factor rpoD [Aerococcus viridans ATCC 11563]
          Length = 374

 Score =  111 bits (277), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 86/275 (31%), Positives = 134/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LA+R  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 108 YLKEIGRVELLTADEEVSLAQRI-EQGDPVAKQELAEANLRLVVSIAKRYVGRGMSFLDL 166

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 167 IQEGNMGLMKAVEKFDYHKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLV 226

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 227 RIQRQLLQDLGREPTPEEIGAEMDLPTEKVRDI---LKIAQ-EPVSLETPIGEEDDSHLG 282

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S         D+   E +          +  L   +  L  RE  +   R 
Sbjct: 283 DFIEDHDATSPD-------DYTSAELL----------KEQLNEVLDTLTDREENVLRLRF 325

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             E+    TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 326 GLEDGQSKTLEQVGQQFGVTRERIRQIEAKALRKL 360


>gi|42526449|ref|NP_971547.1| RNA polymerase sigma-70 factor family protein [Treponema denticola
           ATCC 35405]
 gi|41816642|gb|AAS11428.1| RNA polymerase sigma-70 factor family protein [Treponema denticola
           ATCC 35405]
 gi|325473389|gb|EGC76584.1| RNA polymerase sigma factor [Treponema denticola F0402]
          Length = 286

 Score =  111 bits (277), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 81/274 (29%), Positives = 146/274 (53%), Gaps = 12/274 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+ EI +IP+L  +EE   AK   E GD  A + LV S+LR VV +A  Y+  GLP+
Sbjct: 16  LATYLKEINQIPLLTAEEEIKYAK-LAEKGDEDAKNMLVNSNLRFVVNVAKKYQNQGLPL 74

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++SEGNIGLM A ++FD  +G++  +Y++WWIK ++ + I     ++++    N+   
Sbjct: 75  MDLISEGNIGLMNAAERFDVSKGYKFISYAVWWIKQSILKAICEKSRMIRL--PLNRANE 132

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + + K  +   + N  K  ++  IA  LN+  S V ++        S++A +   + 
Sbjct: 133 LVQIEKAKKEID-FSGNETK--ELNEIAGILNMDNSMVHTIMNAAREPISIDAPV-FDEP 188

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PV 253
            SS   D+L    D   Q+  +     + R+ +   +  L+ RE  I   R       P+
Sbjct: 189 GSSSVNDFL---QDETHQMPEDYAMDMSLRDEVNELLKNLDDREAEIIRYRFGLGGYAPL 245

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +L+ +   F +++ER+RQIE +A +++++  +KQ
Sbjct: 246 SLKEVGLIFNLTKERIRQIEKKALQQLKKPAEKQ 279


>gi|145219258|ref|YP_001129967.1| RNA polymerase, sigma 32 subunit, RpoH [Prosthecochloris
           vibrioformis DSM 265]
 gi|145205422|gb|ABP36465.1| RNA polymerase, sigma 32 subunit, RpoH [Chlorobium phaeovibrioides
           DSM 265]
          Length = 299

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 89/305 (29%), Positives = 158/305 (51%), Gaps = 47/305 (15%)

Query: 9   IVNGE-IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS-----------AAHRLVTS 56
           I N E + L RY+ EI K  +L   +E  L K  +E  D+            A  +L+  
Sbjct: 10  ITNRESLSLDRYLQEIGKYDLLTADDEVRLTKAIKEGFDMPLDTTEYKRAKRALDKLIKG 69

Query: 57  HLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM--- 113
           +LR VV +A  Y+  GL + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++   
Sbjct: 70  NLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQA 129

Query: 114 ---QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
              Q  I+R   L ++GT     + +  L +     +   D N K      +A  L++ +
Sbjct: 130 LAEQSRIVR-LPLNRVGTLNKISKAYSQLEQ-----EYERDPNTKE-----LANLLDM-D 177

Query: 171 SEVISMNCRLAGDE-SLNALINSSDKN---SSQWQDWLVYDHD-GQEQVLIEKEERKNRR 225
           S+ ++   ++AG   S++A     D N        D  + DH   ++ + +E E      
Sbjct: 178 SQDVADTLKIAGRHVSVDAPFAQGDDNRLLDVLQNDGHLPDHGLNRDSLTLEVE------ 231

Query: 226 NMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               RS+SVL PRE  + ++      +NP+TLE +  +F+++RERVRQI+ +A +++++S
Sbjct: 232 ----RSLSVLAPREADVIKSYFGIGMDNPLTLEEIGEKFKLTRERVRQIKEKAIRRLRQS 287

Query: 284 IQKQV 288
              +V
Sbjct: 288 AYSKV 292


>gi|297170837|gb|ADI21856.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [uncultured verrucomicrobium HF0130_25O04]
          Length = 303

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 97/291 (33%), Positives = 153/291 (52%), Gaps = 44/291 (15%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ +I  +P+L  +EE  LA R + +GD  A   ++T++LRLVVKIA  Y   GL +
Sbjct: 9   LDIYLRQISTVPLLTVEEEIELASRIK-NGDEKARETMITANLRLVVKIAKEYSNIGLSL 67

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGNIGLM+AV++FDP +G +L+TY  WWIK A++  +            ANQ + 
Sbjct: 68  LDLINEGNIGLMKAVERFDPSKGGKLSTYGAWWIKQAIKRAL------------ANQSKT 115

Query: 136 FFNLRRLKGHLQAITDNNLKPEQV-VAIAKKLN---VSESEVISMNCRLAGDESLNALIN 191
                RL  H+    D   +  +  V +A+KL      E     MN  +A    +  L +
Sbjct: 116 I----RLPVHM---VDRVTQIRRTSVQLAEKLGREPTDEELAAEMNLPVA---RITLLKS 165

Query: 192 SSDKNSSQWQDWLVYDHDGQ---EQVLIEKE----ERKNRRNMLTRSMSV---LNPRERR 241
            S K +S   D  + ++DG    E V  EK     E    ++++    SV   L PRE  
Sbjct: 166 VSRKPAS--LDSPLGENDGSTLGEMVADEKSANPYEHLQSKSLVGDVNSVLAQLEPREAD 223

Query: 242 IFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE---SIQKQ 287
           I   R   E   P+TLE +  +  V+RERVRQ++ +A +++++   S++KQ
Sbjct: 224 IIRLRFGLEGLEPLTLEEVGEKIGVTRERVRQLQEQALRQLRKNMASMEKQ 274


>gi|154706690|ref|YP_001423754.1| RNA polymerase sigma factor [Coxiella burnetii Dugway 5J108-111]
 gi|154355976|gb|ABS77438.1| RNA polymerase sigma factor [Coxiella burnetii Dugway 5J108-111]
          Length = 352

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 86/269 (31%), Positives = 141/269 (52%), Gaps = 13/269 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ E+   P+L  +EE  +A+R  + GD  A  +++ ++LRLVVKIA  Y   GLP  ++
Sbjct: 84  YLRELGFQPLLNAKEELKIARRVHK-GDPKARKQMIEANLRLVVKIARHYVNRGLPFLDL 142

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM AV+KFDPERGFR +TY+ WWI+  ++  I+     V++      K L   
Sbjct: 143 IEEGNLGLMSAVEKFDPERGFRFSTYATWWIRQTIERAIMNQSRTVRLPIHV-IKELNVY 201

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  K   Q + D+   PE V  +  K      E+  +        S++  I+   + S 
Sbjct: 202 LRTAKKLTQEV-DHEATPEDVAHLIDK---PVQEIRRIMDLAPSATSIDVPISEDGQKS- 256

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLE 256
              D L  D++     LI+  + ++    + R ++ L+ R R +   R  L EN   TLE
Sbjct: 257 -LVDTLADDNNIDPARLIQNVDLQDH---IERWLAQLDERHREVVILRFGLHENEKGTLE 312

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            +     ++RERVRQI+  A ++++  ++
Sbjct: 313 AVGKAVGLTRERVRQIQIDALQQLRHILE 341


>gi|325686025|gb|EGD28083.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           delbrueckii subsp. lactis DSM 20072]
          Length = 373

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 84/275 (30%), Positives = 133/275 (48%), Gaps = 33/275 (12%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +Y+  I ++ +L   EE  LAKR  E GD  A   L +++LRLVV IA  Y G G+   +
Sbjct: 106 QYLKRIGRVSLLSGDEEVQLAKRI-EAGDQEAKDELTSANLRLVVSIAKRYVGRGMSFLD 164

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGN+GLM+AV KFD + GF+ +TY+ WWI+ A+   I      ++I    +      
Sbjct: 165 LIQEGNMGLMKAVGKFDYQLGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETIN 222

Query: 138 NLRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLA--GDESLN 187
            L R++  L      + +PE++ A        + + L V++ E +S+   +    D  L 
Sbjct: 223 KLIRIQRQLLQDLGRDPEPEEIAAEMDLPVKKVREVLKVAQ-EPVSLETPIGEEDDSHLG 281

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR- 246
             I   D  S +        H   E +          ++ L   +  L   E  +   R 
Sbjct: 282 DFIEDKDATSPEQ-------HAASEML----------KDQLAEVLDTLTDSEENVLRLRF 324

Query: 247 RLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            L + NP TLE +   F V+RER+RQIEA+A +K+
Sbjct: 325 GLDDGNPRTLEEVGRVFGVTRERIRQIEAKALRKL 359


>gi|153207564|ref|ZP_01946247.1| RNA polymerase sigma factor RpoS [Coxiella burnetii 'MSU Goat
           Q177']
 gi|161829847|ref|YP_001597499.1| RNA polymerase sigma factor RpoS [Coxiella burnetii RSA 331]
 gi|165918356|ref|ZP_02218442.1| RNA polymerase sigma factor RpoS [Coxiella burnetii RSA 334]
 gi|212211994|ref|YP_002302930.1| RNA polymerase sigma factor [Coxiella burnetii CbuG_Q212]
 gi|212218001|ref|YP_002304788.1| RNA polymerase sigma factor [Coxiella burnetii CbuK_Q154]
 gi|120576532|gb|EAX33156.1| RNA polymerase sigma factor RpoS [Coxiella burnetii 'MSU Goat
           Q177']
 gi|161761714|gb|ABX77356.1| RNA polymerase sigma factor RpoS [Coxiella burnetii RSA 331]
 gi|165918006|gb|EDR36610.1| RNA polymerase sigma factor RpoS [Coxiella burnetii RSA 334]
 gi|212010404|gb|ACJ17785.1| RNA polymerase sigma factor [Coxiella burnetii CbuG_Q212]
 gi|212012263|gb|ACJ19643.1| RNA polymerase sigma factor [Coxiella burnetii CbuK_Q154]
          Length = 352

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 86/269 (31%), Positives = 141/269 (52%), Gaps = 13/269 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ E+   P+L  +EE  +A+R  + GD  A  +++ ++LRLVVKIA  Y   GLP  ++
Sbjct: 84  YLRELGFQPLLNAKEELKIARRVHK-GDPKARKQMIEANLRLVVKIARHYVNRGLPFLDL 142

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM AV+KFDPERGFR +TY+ WWI+  ++  I+     V++      K L   
Sbjct: 143 IEEGNLGLMTAVEKFDPERGFRFSTYATWWIRQTIERAIMNQSRTVRLPIHV-IKELNVY 201

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  K   Q + D+   PE V  +  K      E+  +        S++  I+   + S 
Sbjct: 202 LRTAKKLTQEV-DHEATPEDVAHLIDK---PVQEIRRIMDLAPSATSIDVPISEDGQKS- 256

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLE 256
              D L  D++     LI+  + ++    + R ++ L+ R R +   R  L EN   TLE
Sbjct: 257 -LVDTLADDNNIDPARLIQNVDLQDH---IERWLAQLDERHREVVILRFGLHENEKGTLE 312

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            +     ++RERVRQI+  A ++++  ++
Sbjct: 313 AVGKAVGLTRERVRQIQIDALQQLRHILE 341


>gi|88809466|ref|ZP_01124974.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 7805]
 gi|88786685|gb|EAR17844.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 7805]
          Length = 376

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 78/236 (33%), Positives = 118/236 (50%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R++ ++LRLVV +A  Y+  G+ + ++V EG +GL +AV+KFDP RGFR +TY+ WW
Sbjct: 136 ARDRMIQANLRLVVAVAKKYQQRGMELLDLVQEGTLGLERAVEKFDPTRGFRFSTYAYWW 195

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   I      +++     +K     L R+K   Q I     +   V  +AK+L V
Sbjct: 196 IRQGITRAIATQSRTIRLPVHITEK-----LNRIKRVQQEIASEKGRLASVSDLAKELGV 250

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SE  V     R+    SL   +       +Q  D L   H   EQ L     R +  + L
Sbjct: 251 SEETVRQTLARVPRSVSLETRVGKD--QDTQLGDLLEDGHATPEQTLT----RDSLHDDL 304

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              +  L+PRE  +  +R   E+  P TL  +     +SRERVRQIE RA  K+++
Sbjct: 305 EHLLEELSPREAEVIRSRFGLEDDTPRTLAEIGEAMALSRERVRQIETRALLKLRQ 360


>gi|229543825|ref|ZP_04432884.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacillus
           coagulans 36D1]
 gi|229324964|gb|EEN90640.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacillus
           coagulans 36D1]
          Length = 377

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 85/276 (30%), Positives = 133/276 (48%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 111 YLKEIGRVDLLSADEEIELAKRI-EQGDEEAKRRLAEANLRLVVSIAKRYVGRGMQFLDL 169

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD ++G++ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 170 IQEGNMGLIKAVEKFDYKKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 229

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q+ L  +L R     +   + ++ P++V  I K       E +S+   +    D  L 
Sbjct: 230 RVQRSLLQDLGREPTPEEIAEEMDISPDKVREIIKIAQ----EPVSLETPIGEEDDSHLG 285

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 286 DFIEDQDATSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 328

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 329 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 364


>gi|107029001|ref|YP_626096.1| RNA polymerase sigma factor RpoS [Burkholderia cenocepacia AU 1054]
 gi|105898165|gb|ABF81123.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia cenocepacia AU
           1054]
          Length = 362

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 83/278 (29%), Positives = 142/278 (51%), Gaps = 25/278 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+P+
Sbjct: 84  IQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGVPL 142

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++    +  R 
Sbjct: 143 LDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRE 200

Query: 136 FFNLRRLKGHL--------QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              + R K HL        +A        + +  +  K     ++++++N   A   SL+
Sbjct: 201 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTA---SLD 257

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS-MSVLNPRERRIFEAR 246
           A ++     +S   D L  D        ++  E +     LTR+ +S L+ + R + E R
Sbjct: 258 APLDPD--PASSLLDLLPDDQSQSPDAEVQHRELET----LTRAWLSRLSDKHRHVIE-R 310

Query: 247 RLQEN---PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   N   P TLE L+ E  ++RERVRQI+  A  +++
Sbjct: 311 RFGLNHIEPATLEELADEMGLTRERVRQIQQEALVRLK 348


>gi|325269188|ref|ZP_08135807.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           multiformis DSM 16608]
 gi|324988417|gb|EGC20381.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           multiformis DSM 16608]
          Length = 287

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 80/283 (28%), Positives = 146/283 (51%), Gaps = 28/283 (9%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI    M+  +EE  LA+R R+ GD  A  RL  ++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQEIGHEEMISIEEEVELAQRIRK-GDRKALERLTKANLRFVVSVAKQYQNQGLS 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG----TTA 130
           + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + I     ++++     ++ 
Sbjct: 76  LPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIIRLPLNQVSSV 135

Query: 131 NQKRLFFNL----RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
           N+     N        +  +  I  +   PE  +A A K N   S  +S++     DE  
Sbjct: 136 NKINKILNRFEQENERRPSIDEIAQSTDLPEDKIADAMKAN---SRHVSVDAPFYDDEQS 192

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           + L    + N+      LV      E+ L         R  + R + +L  RE+ + EA 
Sbjct: 193 SLLDVIPNDNAPSTDRGLV------EESL---------REEIGRVLQILEDREKMVVEAY 237

Query: 247 -RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
             + +  +TLE + S++ ++RERVRQI+ +A +++++    +V
Sbjct: 238 FGINQREMTLEEIGSKYNLTRERVRQIKEKAIRRLRQQTNSKV 280


>gi|195953303|ref|YP_002121593.1| putative RNA polymerase, sigma 70 family subunit [Hydrogenobaculum
           sp. Y04AAS1]
 gi|195932915|gb|ACG57615.1| putative RNA polymerase, sigma 70 family subunit [Hydrogenobaculum
           sp. Y04AAS1]
          Length = 311

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 83/300 (27%), Positives = 145/300 (48%), Gaps = 45/300 (15%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +++Y+  +  + +L  QEE   AKR +  GD  A   LV ++LR VV +A  Y GYG+P+
Sbjct: 10  INQYMKRVSSVKLLTPQEEKEFAKRAK-AGDKEALKALVEANLRFVVSVAKQYMGYGIPL 68

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK---------- 125
           SE+++ GN+GL++A  +FDP++  +  +Y++WW++ A+ + + +    V+          
Sbjct: 69  SELIAAGNLGLLEAATRFDPDKNVKFISYAVWWVRQAIMQALSQQTGAVRIPVKHSHLIS 128

Query: 126 ---------------------IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
                                I    N+K +    ++  G   A T+  L  EQ +    
Sbjct: 129 AVGLAYNELLKELEREPTYKEIADYINKKNIIREFKKETGF--APTEEEL--EQSMTQEH 184

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL-VYDHDGQEQVLIEKEERKN 223
           K  V+E +V    C       L+      D   + + D L + D D  E+ +I+    K 
Sbjct: 185 KYTVTEEDV--KKCLQICKTPLSLDTPVGDNPDTLFVDLLSISDTDEIEEGVIKDVLEKE 242

Query: 224 RRNMLTRSMSVLNPRERRIFEARR-LQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             +++++    L  +ER++ E R  L  N P+TL  +     +SRERVRQ+E RA KK++
Sbjct: 243 LHDIISK----LPEKERKVLELRYGLNGNEPLTLREIGDALGISRERVRQLETRAIKKLR 298


>gi|309388945|gb|ADO76825.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Halanaerobium
           praevalens DSM 2228]
          Length = 364

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 87/272 (31%), Positives = 144/272 (52%), Gaps = 27/272 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+ +L  +EE  LAKR  E G+  A  +LV ++LRLVV IA  Y G G+   ++
Sbjct: 98  YLKEIGKVDLLTAEEEVELAKRM-EQGEEWAKQQLVQANLRLVVSIAKKYVGRGMLFLDL 156

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +G++ +TY+ WWI+ A+   I      +++    +       
Sbjct: 157 IQEGNMGLMKAVDKFDYTKGYKFSTYATWWIRQAITRSIADQARTIRV--PVHMVETINK 214

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R+   L        K E++ A   ++++S  +V  +  +++ D  SL   I   ++  
Sbjct: 215 LIRVSRQLLQEKGREPKDEEIGA---EMDISAEKVREI-MKISQDPVSLETPIG--EEED 268

Query: 198 SQWQDWLVYDHD------GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           S   D+ + D D          +L++++        L   +  L  RE+R+ E R   E+
Sbjct: 269 SHLGDF-IEDVDSPAPASAASYILLKEQ--------LNDVLDTLTDREKRVLELRFGIED 319

Query: 252 --PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             P TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 320 GRPRTLEEVGKEFGVTRERIRQIEAKALRKLR 351


>gi|262038195|ref|ZP_06011589.1| RNA polymerase sigma factor RpoD [Leptotrichia goodfellowii F0264]
 gi|261747776|gb|EEY35221.1| RNA polymerase sigma factor RpoD [Leptotrichia goodfellowii F0264]
          Length = 393

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 83/272 (30%), Positives = 137/272 (50%), Gaps = 29/272 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI +IP+L  +EE   A+R    GD  A  +L+ S+LRLVV IA  +   GL + ++
Sbjct: 127 YLREIGQIPLLSYEEEIDYAQRVL-KGDEEAKQKLIESNLRLVVSIAKKHTNRGLKMLDL 185

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV+KF+ E+GF+ +TY+ WWI+ A+   I      ++I        +   
Sbjct: 186 IQEGNMGLMKAVEKFEYEKGFKFSTYATWWIRQAITRAIADQGRTIRIPV-----HMIET 240

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV---ISMNCRLAGDESLNALINSSDK 195
           + ++K   + I     K      ++KKL +   +V   + MN       SL   + S + 
Sbjct: 241 INKIKKESRIILQETGKEPTAEELSKKLEIPVDKVKNILEMNQDPI---SLETPVGSEE- 296

Query: 196 NSSQWQDWLVYD-----HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             S+  D++  D     +D   +VL+        +  L   +  LN RE  +   R   +
Sbjct: 297 -DSELGDFVEDDKFLNPYDATTRVLL--------KEQLDEILKTLNEREEMVLRYRYGLD 347

Query: 251 NPV--TLENLSSEFEVSRERVRQIEARAFKKV 280
           +    TLE +   F V+RER+RQIE +A +K+
Sbjct: 348 DGSQKTLEEVGKIFNVTRERIRQIEVKALRKL 379


>gi|319953761|ref|YP_004165028.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Cellulophaga
           algicola DSM 14237]
 gi|319422421|gb|ADV49530.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cellulophaga
           algicola DSM 14237]
          Length = 287

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 83/288 (28%), Positives = 157/288 (54%), Gaps = 39/288 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ ++   EE  LA+R ++ GD +A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGKVDLITADEEVELAQRIKK-GDQAALEKLTKANLRFVVSVAKQYQNQGLTL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
            ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++      Q  I+R   L KIG+ 
Sbjct: 77  PDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVR-LPLNKIGSI 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNA 188
               + F         L+   +    PE+   IAK+L+++  E +  + + +G   S++A
Sbjct: 136 NKINKTF-------AFLEQAHERQPSPEE---IAKELDMT-VEDVKQSLKNSGRHVSMDA 184

Query: 189 -LINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
            LI+  D N        +YD    G+      +   ++ R  + R++  L PRE  +   
Sbjct: 185 PLIDGEDSN--------LYDVLRSGESPNPDRELLHESLRTEIERALETLTPREADVI-- 234

Query: 246 RRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            RL      ++ +TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 235 -RLYFGLAGQHSMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|226226576|ref|YP_002760682.1| RNA polymerase sigma factor [Gemmatimonas aurantiaca T-27]
 gi|226089767|dbj|BAH38212.1| RNA polymerase sigma factor [Gemmatimonas aurantiaca T-27]
          Length = 286

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 83/285 (29%), Positives = 146/285 (51%), Gaps = 41/285 (14%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E  L +Y+ +I   P++ ++EE  LA+R R+ GD  A  +LV S+LR VV +A  Y+  G
Sbjct: 14  EGSLDQYLRDISAYPLISREEEAELARRIRQ-GDQEALDKLVRSNLRFVVSVAKKYQNQG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-----------RSW 121
           + +S++++EGN+GL++A +KFD  +G +  +Y++WWI+ A+ + +            R+ 
Sbjct: 73  VSLSDLINEGNLGLIRAARKFDETKGIKFISYAVWWIRQAILQALAEQSRIVRVPLNRAG 132

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
           +L +IG  AN   L   L R   H +     ++  E+V   AK +++S+  +        
Sbjct: 133 TLHRIGKRANA--LLQELGREATHAEIAHGMDITEEEV---AKTMSISQVHL-------- 179

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              SL+A +   + N       L Y  D       ++   K     +  S+  L  RE +
Sbjct: 180 ---SLDAPLTPGEDNR-----LLDYLPDTVHPTPEDQTFDKALTEAIEESLGGLKEREAK 231

Query: 242 IFEARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           I    RL       +P+TLE + S+  ++RERVRQI+ +A  +++
Sbjct: 232 IL---RLYFGIDGADPMTLEEIGSQLGITRERVRQIKEKALSRLR 273


>gi|160902085|ref|YP_001567666.1| RpoD family RNA polymerase sigma factor [Petrotoga mobilis SJ95]
 gi|160359729|gb|ABX31343.1| RNA polymerase, sigma 70 subunit, RpoD family [Petrotoga mobilis
           SJ95]
          Length = 424

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 80/280 (28%), Positives = 145/280 (51%), Gaps = 26/280 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K  +L    E  LA+R  + GD  A   L+ ++LRLV+ IA  Y G+GL   ++
Sbjct: 153 YLKEISKSKLLTPSRERKLARR-AQMGDKRAREELIKANLRLVISIAKRYVGHGLGFLDL 211

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG-----TTANQK 133
           + EGNIGLM+AV KFD ++G++ +TYS WWI+ A+   I      V+I      T     
Sbjct: 212 IQEGNIGLMKAVAKFDWKKGYKFSTYSYWWIRQAITRAIADQGRTVRIPVHLVETINRMN 271

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD---ESLNALI 190
           R+     +  G +  + + ++  ++ V   K++ +S   + S+N  ++ D   E  + ++
Sbjct: 272 RVVNKYIQENGEVPDLEELSVLMDKPVDKMKEVLISAKNIFSLNAPISNDVDAEGESEVL 331

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--L 248
           +  D +S         D +G++ ++         R  +   +  L+P+E  I + R   +
Sbjct: 332 DFIDSDSP------TPDEEGRKMII---------RQKMEMIIDTLSPKEAMILKMRYGFV 376

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
                TLE +   F V+RER+RQIE+++ +K++   +K++
Sbjct: 377 DGKQKTLEEVGEFFNVTRERIRQIESKSIRKLKHPARKKM 416


>gi|313672395|ref|YP_004050506.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Calditerrivibrio
           nitroreducens DSM 19672]
 gi|312939151|gb|ADR18343.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Calditerrivibrio
           nitroreducens DSM 19672]
          Length = 337

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 77/265 (29%), Positives = 138/265 (52%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ E+ K P+L K+EE  LA+R  E GD  A   ++  +LRLVV IA  Y   G+P+ ++
Sbjct: 70  YLKELSKCPVLSKEEECELARRI-EEGDEKAKETMINCNLRLVVSIAKKYANKGVPLEDL 128

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           +SEGNIGL++AV+KFD  +GF+ +TY+ WWI+ A++  I+ +  +V++     +      
Sbjct: 129 ISEGNIGLIRAVEKFDYRKGFKFSTYATWWIRQAIERAIIANTKIVRVPVHVLE--YIKK 186

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           + + K  LQ     N        ++    ++ S +      +  D S++A I+  ++ + 
Sbjct: 187 ILKAKSELQETLGRN---PTYTELSTYTGITLSNIYKAVEAMRHDVSIDAPISEDEQENM 243

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
                L+ D+   +    +     N + ++++ M  LN  E+ I   R   +     TL+
Sbjct: 244 H---NLIPDNIHTDP--FDHAFELNIQKLVSKWMGYLNETEKLIITLRYGLDGKRSRTLD 298

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  E  ++RER+RQIE R   K++
Sbjct: 299 EVGKELNLTRERIRQIEKRVLNKLR 323


>gi|126667564|ref|ZP_01738534.1| nonessential primary sigma factor [Marinobacter sp. ELB17]
 gi|126627990|gb|EAZ98617.1| nonessential primary sigma factor [Marinobacter sp. ELB17]
          Length = 333

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 91/284 (32%), Positives = 154/284 (54%), Gaps = 39/284 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A+  R+ G+ S   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 65  YLNEIGFSPLLTPEEEVYFARLARK-GEESGRKRMIESNLRLVVKIARRYVNRGLTLLDL 123

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 124 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERGIMNQTRTIRLPIHV-VKELNLY 182

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV---ISMNCRLA---------GDESL 186
           LR  +   Q + D+    E+   IA+K++    +V   + +N R+A         G++SL
Sbjct: 183 LRAARELTQQL-DHEPTAEE---IARKVDKPVKDVKRMLGLNERVASMDTPIGAGGEKSL 238

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
             L   +D+ +S   D L               +  N    L + +  L+ +++ +  AR
Sbjct: 239 --LDTVADEGASDPADVL---------------QDNNISVCLQQWIDQLSEKQQEVL-AR 280

Query: 247 R--LQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           R  L+  PV TLE +  E  ++RERVRQI+  A ++++E ++K+
Sbjct: 281 RFGLRGYPVSTLEEVGQEIGLTRERVRQIQVEALRRLREILEKE 324


>gi|314933733|ref|ZP_07841098.1| RNA polymerase sigma factor RpoD [Staphylococcus caprae C87]
 gi|313653883|gb|EFS17640.1| RNA polymerase sigma factor RpoD [Staphylococcus caprae C87]
          Length = 368

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 87/275 (31%), Positives = 133/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  QEE  LAK+  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGRVNLLSAQEEIELAKKI-EQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 161 IQEGNMGLIKAVEKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 220

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I K       E +S+   +    D  L 
Sbjct: 221 RVQRQLLQDLGRDPAPEEIGEEMDLPPEKVREILK----IAQEPVSLETPIGEEDDSHLG 276

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 277 DFIEDQEAQSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 319

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 320 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 354


>gi|302024138|ref|ZP_07249349.1| RNA polymerase sigma factor RpoD [Streptococcus suis 05HAS68]
          Length = 372

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 85/268 (31%), Positives = 140/268 (52%), Gaps = 21/268 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 105 YLKEIGVVPLLTNEEEQELALAV-EAGDPEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 163

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 164 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 221

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L      +  PEQ   IA++++++  +V  +  ++A +  SL   I   D   
Sbjct: 222 LVREQRNLLQELGQDPTPEQ---IAERMDMTPEKVREI-LKIAQEPVSLETPIGEED--D 275

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++++   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 276 SHLGDFI------EDEIIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 329

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKV 280
            TLE++   F V+RER+RQIEA+A +K+
Sbjct: 330 RTLEDVGKVFNVTRERIRQIEAKALRKL 357


>gi|253581343|ref|ZP_04858569.1| DNA-directed RNA polymerase sigma subunit RpoD [Fusobacterium
           varium ATCC 27725]
 gi|251836707|gb|EES65241.1| DNA-directed RNA polymerase sigma subunit RpoD [Fusobacterium
           varium ATCC 27725]
          Length = 414

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 87/272 (31%), Positives = 145/272 (53%), Gaps = 27/272 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI +IP+L   EE   AKR  E GD  A+ +L+ ++LRLVV IA  +   GL + ++
Sbjct: 148 YLREIGQIPLLSHDEELEYAKRALE-GDEWASKQLIEANLRLVVSIAKKHTNRGLKLLDL 206

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGNIGLM+AV+KF+  +G++ +TY+ WWI+ A+   I      ++I      T N+ +
Sbjct: 207 IQEGNIGLMKAVEKFEYSKGYKFSTYATWWIRQAITRAIADQGRTIRIPVHMIETINKIK 266

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
                +  + +LQ  T  +  PE    + ++L +   +V ++        SL   + S +
Sbjct: 267 -----KEARIYLQE-TGKDATPE---VLGERLGMEVDKVKAIQEMNQDPISLETPVGSEE 317

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNR---RNMLTRSMSVLNPRERRIFEARRLQEN 251
              S+  D+ V DH      ++   E  NR   R  L   ++ L+ RE R+   R   ++
Sbjct: 318 --DSELGDF-VEDHK-----MLNPYELTNRSLLREQLNGVLNTLSSREERVLRYRYGLDD 369

Query: 252 --PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             P TLE +   F+V+RER+RQIE +A +K++
Sbjct: 370 GSPKTLEEVGKIFKVTRERIRQIEVKALRKLR 401


>gi|73662504|ref|YP_301285.1| RNA polymerase sigma factor RpoD [Staphylococcus saprophyticus
           subsp. saprophyticus ATCC 15305]
 gi|72495019|dbj|BAE18340.1| RNA polymerase sigma factor A [Staphylococcus saprophyticus subsp.
           saprophyticus ATCC 15305]
          Length = 368

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 87/275 (31%), Positives = 133/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  QEE  LAK+  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGRVNLLNAQEEIELAKKI-EQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 161 IQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 220

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I K       E +S+   +    D  L 
Sbjct: 221 RVQRQLLQDLGRDPAPEEIGEEMDLPPEKVREILK----IAQEPVSLETPIGEEDDSHLG 276

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 277 DFIEDQEAQSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 319

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 320 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 354


>gi|126652263|ref|ZP_01724442.1| RNA polymerase sigma factor RpoD [Bacillus sp. B14905]
 gi|126590995|gb|EAZ85107.1| RNA polymerase sigma factor RpoD [Bacillus sp. B14905]
          Length = 375

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 86/276 (31%), Positives = 138/276 (50%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  ++E  LA+R  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 109 YLKEIGRVDLLSAEQEIALAERI-EQGDEEARKRLAEANLRLVVSIAKRYVGRGMLFLDL 167

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 168 IQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 227

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I   L +++ E +S+   +    D  L 
Sbjct: 228 RVQRQLLQDLGREPSPEEIGEEMDLTPEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 283

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I  S+  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 284 DFIEDSEAQSPS-------DHAAYELL----------KEQLEDVIDTLTDREENVLRLRF 326

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 327 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 362


>gi|223044379|ref|ZP_03614413.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Staphylococcus capitis SK14]
 gi|222442248|gb|EEE48359.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Staphylococcus capitis SK14]
          Length = 368

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 87/275 (31%), Positives = 133/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  QEE  LAK+  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGRVNLLSAQEEIELAKKI-EQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 161 IQEGNMGLIKAVEKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 220

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I K       E +S+   +    D  L 
Sbjct: 221 RVQRQLLQDLGRDPAPEEIGEEMDLPPEKVREILK----IAQEPVSLETPIGEEDDSHLG 276

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 277 DFIEDQEAQSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 319

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 320 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 354


>gi|307298746|ref|ZP_07578549.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermotogales
           bacterium mesG1.Ag.4.2]
 gi|306915911|gb|EFN46295.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermotogales
           bacterium mesG1.Ag.4.2]
          Length = 416

 Score =  110 bits (276), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 84/275 (30%), Positives = 138/275 (50%), Gaps = 33/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KI +L    E  LA+R  + G+  A   L+T++LRLVV IA  Y G GL   ++
Sbjct: 142 YLKEIGKISLLTPSRERELARRA-QKGEPKAKEELITANLRLVVSIAKRYIGRGLTFLDL 200

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGL++AV+KFD ++G++ +TY+ WWI+ A+   I      +++     +     N
Sbjct: 201 IQEGNIGLIKAVEKFDWKKGYKFSTYATWWIRQAITRAIADQARTIRVPVHMVETINKLN 260

Query: 139 LRRLKGHLQAITD-------NNL---KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
            + ++ HLQ   +        NL    PE++  I      +  E +S+   ++GDE    
Sbjct: 261 -KVIREHLQDHGEYPTIEELGNLTGKTPEKIEEIL----AASKETVSLESPISGDE---- 311

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR- 247
                    S   D++   HD   +   E   +   R  + + +  L+PRE  + + R  
Sbjct: 312 --------ESTMGDFI---HDDSMEQPEEAAMKMLLREQIDQILDTLSPREAMVLKMRYG 360

Query: 248 -LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L     TLE +   F V+RER+RQIE +A +K++
Sbjct: 361 LLDGKTKTLEEVGQFFNVTRERIRQIEVKALRKLR 395


>gi|255034849|ref|YP_003085470.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dyadobacter
           fermentans DSM 18053]
 gi|254947605|gb|ACT92305.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dyadobacter
           fermentans DSM 18053]
          Length = 287

 Score =  110 bits (275), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 79/269 (29%), Positives = 147/269 (54%), Gaps = 17/269 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ +L   EE  LA++ R+ GD  A  RL  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGKVDLLTPDEEVTLAQKIRD-GDQLALERLTKANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     +V++    N+   
Sbjct: 77  GDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL--PLNRVGS 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
              + +    L+   +    PE+   +A+ L +S SEV+    +++G   S++A     +
Sbjct: 135 LNKISKTFSELEQRFEREPSPEE---LAEVLEISSSEVVD-TMKISGRHVSMDAPFVQGE 190

Query: 195 KNSSQWQDWLVYD-HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QEN 251
           +NS    D L  D  D  +  L+ +  RK     + R++  L  RE  +         E+
Sbjct: 191 ENS--LLDVLENDLEDKPDSGLVNESLRKE----VQRALCTLTQREADVIALYFGLNGEH 244

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKV 280
            +TLE +  +F ++RERVRQI+ +A +++
Sbjct: 245 AMTLEEIGEKFNLTRERVRQIKEKAIRRL 273


>gi|327313374|ref|YP_004328811.1| putative RNA polymerase sigma factor RpoD [Prevotella denticola
           F0289]
 gi|326944913|gb|AEA20798.1| putative RNA polymerase sigma factor RpoD [Prevotella denticola
           F0289]
          Length = 327

 Score =  110 bits (275), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 77/275 (28%), Positives = 152/275 (55%), Gaps = 14/275 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI    M+  +EE  LA+R R+ GD  A  RL  ++LR VV +A  Y+  GL +
Sbjct: 58  LDKYLQEIGHEEMISIEEEVELAQRIRK-GDRKALERLTKANLRFVVSVAKQYQNQGLSL 116

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + I     ++++    NQ   
Sbjct: 117 PDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIIRL--PLNQ--- 171

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
             ++ ++   L      N +   +  IA+  ++ E ++       +   S++A     D+
Sbjct: 172 VSSVNKINKILNQFEQENERRPSIGEIAQSTDIPEEKIADAIKVSSRHVSVDAPFYDDDQ 231

Query: 196 NSSQWQDWLVYDH-DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           +S    D +  D+    ++ L+E+  R+     + R + VL  RE+++ EA   + +  +
Sbjct: 232 SS--LLDVIPNDNVPSTDRGLVEESLREE----IGRVLQVLEDREKKVVEAYFGINQREM 285

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           TLE + S++ ++RERVRQI+ +A +++++    +V
Sbjct: 286 TLEEIGSKYNLTRERVRQIKEKAIRRLRQQTNSKV 320


>gi|218288616|ref|ZP_03492893.1| RNA polymerase, sigma 70 subunit, RpoD family [Alicyclobacillus
           acidocaldarius LAA1]
 gi|258511944|ref|YP_003185378.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
 gi|218241273|gb|EED08448.1| RNA polymerase, sigma 70 subunit, RpoD family [Alicyclobacillus
           acidocaldarius LAA1]
 gi|257478670|gb|ACV58989.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
          Length = 368

 Score =  110 bits (275), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 87/273 (31%), Positives = 133/273 (48%), Gaps = 31/273 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  QEE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGRVPLLSAQEEIELAKRI-EQGDEEAKQRLAEANLRLVVSIAKRYVGRGMLFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-- 132
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 161 IQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 220

Query: 133 ---KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
              ++L   L R     +   + +L PE+V  I K       E +S+   +    D  L 
Sbjct: 221 RVSRQLLQELGREPTPEEIAAEMDLTPEKVREIQK----IAQEPVSLETPIGEEDDSHLG 276

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  +           +  E VL    ER+   N+L     + + R R       
Sbjct: 277 DFIPDDEAPAPADAAAYELLKEQLEDVLDTLTEREE--NVLRLRFGLDDGRTR------- 327

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                 TLE +   F V+RER+RQIEA+A +K+
Sbjct: 328 ------TLEEVGKVFGVTRERIRQIEAKALRKL 354


>gi|325857152|ref|ZP_08172442.1| putative RNA polymerase sigma factor RpoD [Prevotella denticola
           CRIS 18C-A]
 gi|325483215|gb|EGC86193.1| putative RNA polymerase sigma factor RpoD [Prevotella denticola
           CRIS 18C-A]
          Length = 327

 Score =  110 bits (275), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 77/275 (28%), Positives = 152/275 (55%), Gaps = 14/275 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI    M+  +EE  LA+R R+ GD  A  RL  ++LR VV +A  Y+  GL +
Sbjct: 58  LDKYLQEIGHEEMISIEEEVELAQRIRK-GDRKALERLTKANLRFVVSVAKQYQNQGLSL 116

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + I     ++++    NQ   
Sbjct: 117 PDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIIRL--PLNQ--- 171

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
             ++ ++   L      N +   +  IA+  ++ E ++       +   S++A     D+
Sbjct: 172 VSSVNKINKILNQFEQENERRPSIGEIAQSTDIPEEKIADAIKVSSRHVSVDAPFYDDDQ 231

Query: 196 NSSQWQDWLVYDH-DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           +S    D +  D+    ++ L+E+  R+     + R + VL  RE+++ EA   + +  +
Sbjct: 232 SS--LLDVIPNDNVPSTDRGLVEESLREE----IGRVLQVLEDREKKVVEAYFGINQREM 285

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           TLE + S++ ++RERVRQI+ +A +++++    +V
Sbjct: 286 TLEEIGSKYNLTRERVRQIKEKAIRRLRQQTNSKV 320


>gi|257470878|ref|ZP_05634968.1| RNA polymerase sigma factor rpoD [Fusobacterium ulcerans ATCC
           49185]
 gi|317065080|ref|ZP_07929565.1| RNA polymerase sigma factor rpoD [Fusobacterium ulcerans ATCC
           49185]
 gi|313690756|gb|EFS27591.1| RNA polymerase sigma factor rpoD [Fusobacterium ulcerans ATCC
           49185]
          Length = 418

 Score =  110 bits (275), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 87/272 (31%), Positives = 145/272 (53%), Gaps = 27/272 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI +IP+L   EE   AKR  E GD  A+ +L+ ++LRLVV IA  +   GL + ++
Sbjct: 152 YLREIGQIPLLSHDEELEYAKRALE-GDDWASKQLIEANLRLVVSIAKKHTNRGLKLLDL 210

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGNIGLM+AV+KF+  +G++ +TY+ WWI+ A+   I      ++I      T N+ +
Sbjct: 211 IQEGNIGLMKAVEKFEYSKGYKFSTYATWWIRQAITRAIADQGRTIRIPVHMIETINKIK 270

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
                +  + +LQ  T  +  PE    + ++L +   +V ++        SL   + S +
Sbjct: 271 -----KEARIYLQE-TGKDATPE---VLGERLGMEVDKVKAIQEMNQDPISLETPVGSEE 321

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNR---RNMLTRSMSVLNPRERRIFEARRLQEN 251
              S+  D+ V DH      ++   E  NR   R  L   ++ L+ RE R+   R   ++
Sbjct: 322 --DSELGDF-VEDHK-----MLNPYELTNRSLLREQLNGVLNTLSSREERVLRYRYGLDD 373

Query: 252 --PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             P TLE +   F+V+RER+RQIE +A +K++
Sbjct: 374 GSPKTLEEVGKIFKVTRERIRQIEVKALRKLR 405


>gi|242242833|ref|ZP_04797278.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           epidermidis W23144]
 gi|242233734|gb|EES36046.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           epidermidis W23144]
          Length = 368

 Score =  110 bits (275), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 87/275 (31%), Positives = 133/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  QEE  LAK+  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGRVNLLSAQEEIELAKKI-EQGDEIAKSRLAEANLRLVVSIAKRYVGRGMLFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 161 IQEGNMGLIKAVEKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 220

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I K       E +S+   +    D  L 
Sbjct: 221 RVQRQLLQDLGRDPAPEEIGEEMDLPPEKVREILK----IAQEPVSLETPIGEEDDSHLG 276

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 277 DFIEDQEAQSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 319

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 320 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 354


>gi|205374117|ref|ZP_03226917.1| RNA polymerase sigma factor RpoD [Bacillus coahuilensis m4-4]
          Length = 337

 Score =  110 bits (275), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 87/274 (31%), Positives = 137/274 (50%), Gaps = 31/274 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE  LA+R  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 71  YLKEIGRVDLLSAEEEISLAERI-EQGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 129

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 130 IQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 189

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             Q++L  +L R     +   + +L PE+V  I   L +++  V           SL   
Sbjct: 190 RVQRQLLQDLGREPSPEEIGEEMDLPPEKVREI---LKIAQEPV-----------SLETP 235

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   D   S   D++    D + Q   E    +  +  L   +  L  RE  +   R   
Sbjct: 236 IGEED--DSHLGDFI---EDSEAQSPSEHAAYELLKEQLEDVLDTLTDREENVLRLRFGL 290

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 291 DDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 324


>gi|182438860|ref|YP_001826579.1| putative RNA polymerase principal sigma factor [Streptomyces
           griseus subsp. griseus NBRC 13350]
 gi|326779516|ref|ZP_08238781.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces cf.
           griseus XylebKG-1]
 gi|178467376|dbj|BAG21896.1| putative RNA polymerase principal sigma factor [Streptomyces
           griseus subsp. griseus NBRC 13350]
 gi|326659849|gb|EGE44695.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces cf.
           griseus XylebKG-1]
          Length = 363

 Score =  110 bits (275), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 91/295 (30%), Positives = 146/295 (49%), Gaps = 44/295 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRY------------------REHGDL--------SAAHR 52
           Y+ EI +IP+L   EE  LA+R                   R  GDL        +A  R
Sbjct: 70  YLREIGRIPLLTAAEEVELARRVEAGLFAEERLAGTPDLDSRLAGDLDRLVVMGRTAKRR 129

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY+ WWI+ A
Sbjct: 130 LIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIRQA 189

Query: 113 MQEYILRSWSLVKIGTTANQ--KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
           M   +      +++     +   R+    RRL      + +  ++P     IA  L+++ 
Sbjct: 190 MSRALADQARTIRVPVHVVELINRVVRVQRRL------LQERGVEP-TAEDIAVDLDLTP 242

Query: 171 SEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             V  +  RLA +  SL+A +   D  S  + D +    DG     +E       R  L 
Sbjct: 243 ERVTDI-LRLAQEPVSLHAPVGEEDDVS--FGDLI---EDGDAASPVESAAFLLLREHLE 296

Query: 230 RSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             +S L  RER++ + R   E+  P TLE +   F V+RER+RQIE++   ++++
Sbjct: 297 AVLSTLGERERKVVQLRYGLEDGRPRTLEEIGRIFGVTRERIRQIESKTLSRLRD 351


>gi|227878689|ref|ZP_03996603.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus JV-V01]
 gi|256843283|ref|ZP_05548771.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus
           125-2-CHN]
 gi|256850360|ref|ZP_05555788.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus MV-1A-US]
 gi|262046492|ref|ZP_06019454.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus MV-3A-US]
 gi|293380134|ref|ZP_06626221.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus 214-1]
 gi|295693058|ref|YP_003601668.1| RNA polymerase sigma factor [Lactobacillus crispatus ST1]
 gi|312978174|ref|ZP_07789918.1| RNA polymerase sigma-43 factor [Lactobacillus crispatus CTV-05]
 gi|227861704|gb|EEJ69309.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus JV-V01]
 gi|256614703|gb|EEU19904.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus
           125-2-CHN]
 gi|256712757|gb|EEU27750.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus MV-1A-US]
 gi|260573363|gb|EEX29921.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus MV-3A-US]
 gi|290923304|gb|EFE00220.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus 214-1]
 gi|295031164|emb|CBL50643.1| RNA polymerase sigma factor [Lactobacillus crispatus ST1]
 gi|310894892|gb|EFQ43962.1| RNA polymerase sigma-43 factor [Lactobacillus crispatus CTV-05]
          Length = 370

 Score =  110 bits (275), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 87/273 (31%), Positives = 133/273 (48%), Gaps = 31/273 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   +E  LAKR  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 104 YLKEIGRVPLLTADQEIALAKRI-ESGDEEAKQELAEANLRLVVSIAKRYVGRGMSFLDL 162

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 163 IQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 222

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + N+   +V  I   L +++ E +S+   +    D  L 
Sbjct: 223 RIQRQLLQDLGREPTPEEIGAEMNMPTNKVRDI---LKIAQ-EPVSLETPIGEEDDSHLG 278

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S +         +  EQVL    +R+   N+L     + + R R       
Sbjct: 279 DFIEDKDATSPEQHASYEMLKEQLEQVLETLTDREE--NVLRLRFGLDDGRTR------- 329

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                 TLE +   F V+RER+RQIEA+A +K+
Sbjct: 330 ------TLEEVGKVFGVTRERIRQIEAKALRKL 356


>gi|114320976|ref|YP_742659.1| RNA polymerase, sigma 28 subunit [Alkalilimnicola ehrlichii MLHE-1]
 gi|114227370|gb|ABI57169.1| RNA polymerase, sigma 38 subunit, RpoS [Alkalilimnicola ehrlichii
           MLHE-1]
          Length = 342

 Score =  110 bits (275), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 87/278 (31%), Positives = 146/278 (52%), Gaps = 27/278 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   ++R  + GD +A  R++ S+LRLVVKIA  Y   GL   ++
Sbjct: 74  YLNEIGYSPLLSAEEEVYFSRRA-QRGDAAARARMIESNLRLVVKIARRYMNRGLAFLDL 132

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK--IGTTANQKRLF 136
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     ++  I       +  
Sbjct: 133 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVIKEINQYL 192

Query: 137 FNLRRLKGHL------QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R+L   L      + I D+  +  + V   + LN   + V     R A    L+A+ 
Sbjct: 193 RAARKLTQELDHEPSVEEIADHMGRDVEDVRRMRGLNEGTTSVDVPIGRDADRVLLDAIP 252

Query: 191 NSSDKNS-SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           + ++ +  S  QD  V+ +   E  L E  E++  R ++ R    LN  +R         
Sbjct: 253 DENNVDPVSALQDGDVFGN--LEAWLGELTEKQ--RAVVERRFG-LNGHDR--------- 298

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
               TLE + +E  V+RERVRQI+  A ++++E ++++
Sbjct: 299 ---ATLEQVGNEIGVTRERVRQIQIDALRRLREVMERE 333


>gi|124006216|ref|ZP_01691051.1| RpoD [Microscilla marina ATCC 23134]
 gi|123988140|gb|EAY27798.1| RpoD [Microscilla marina ATCC 23134]
          Length = 287

 Score =  110 bits (275), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 78/272 (28%), Positives = 151/272 (55%), Gaps = 17/272 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ +L   EE  LAKR RE GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGKVDLLTPDEEVELAKRIRE-GDQVALEKLTKANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     +V++    N+   
Sbjct: 77  GDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL--PLNRVGS 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
              + +    L+   +    P++   +A+ L+V+ SEV+    +++G   S++A     +
Sbjct: 135 LNKISKTFSELEQKYEREPSPDE---LAEVLDVTTSEVVD-TLKISGRHVSMDAPFVQGE 190

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPRERRIFEARRL--QEN 251
           +NS      L+   + + +V  + E   +  R  + R++S L  RE  +         E+
Sbjct: 191 ENS------LLDVLENESEVKPDSELMNDSLRKEVQRALSTLTQREADVITLYFGLNGEH 244

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +TLE +  +F ++RERVRQI+ +A ++++ +
Sbjct: 245 AMTLEEIGEKFNLTRERVRQIKEKAIRRLRHT 276


>gi|242373866|ref|ZP_04819440.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           epidermidis M23864:W1]
 gi|242348420|gb|EES40022.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           epidermidis M23864:W1]
          Length = 368

 Score =  110 bits (275), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 87/275 (31%), Positives = 133/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  QEE  LAK+  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGRVNLLSAQEEIELAKKI-EQGDEIAKSRLAEANLRLVVSIAKRYVGRGMLFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 161 IQEGNMGLIKAVEKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 220

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I K       E +S+   +    D  L 
Sbjct: 221 RVQRQLLQDLGRDPAPEEIGEEMDLPPEKVREILK----IAQEPVSLETPIGEEDDSHLG 276

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 277 DFIEDQEAQSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 319

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 320 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 354


>gi|253582113|ref|ZP_04859337.1| RNA polymerase [Fusobacterium varium ATCC 27725]
 gi|251836462|gb|EES64999.1| RNA polymerase [Fusobacterium varium ATCC 27725]
          Length = 275

 Score =  110 bits (275), Expect = 2e-22,   Method: Compositional matrix adjust.
 Identities = 86/279 (30%), Positives = 147/279 (52%), Gaps = 23/279 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +S Y+ +IRK  +L+K EE  L  + +  GD  + ++L+ S+LRLVV IA GY   GL  
Sbjct: 9   ISLYLADIRKYKILDKDEELNLLIKAK-AGDEESKNQLILSNLRLVVNIAKGYINKGLSF 67

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ--- 132
            +++SEGN+GL+ A++KFD  +GFR +TY++WWIK ++ + ++     ++I +       
Sbjct: 68  IDLISEGNLGLIYAIEKFDITKGFRFSTYAVWWIKQSISKAVIVKGREIRIPSYKYDLLN 127

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
           K   + + RLK       + N  P  V  IA +LN+   ++  +        SL+  I  
Sbjct: 128 KVNRYVMSRLK------DEGNYPP--VEEIAAELNIDVDKIQDIIMDFQDPMSLSTQIG- 178

Query: 193 SDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQE 250
              +    +D L    D   E+ +  +  RK  R+M+ +    L  RE+ I + R  L  
Sbjct: 179 ---DDIYLEDTLAQQEDFSMEEEIFNEMGRKQVRDMVNQ----LEEREKEILKLRYGLDG 231

Query: 251 NPV-TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
             + TLE + +   ++RERVRQIE +  +K++    K++
Sbjct: 232 YEIHTLEEIGNTLNITRERVRQIEKKTLQKLRSKYTKEL 270


>gi|58337478|ref|YP_194063.1| RNA polymerase sigma factor RpoD [Lactobacillus acidophilus NCFM]
 gi|58254795|gb|AAV43032.1| RNA polymerase sigma factor [Lactobacillus acidophilus NCFM]
          Length = 356

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 87/273 (31%), Positives = 133/273 (48%), Gaps = 31/273 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   +E  LAKR  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 90  YLKEIGRVPLLTADQEIALAKRI-ESGDEEAKQELAEANLRLVVSIAKRYVGRGMSFLDL 148

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 149 IQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 208

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + N+   +V  I   L +++ E +S+   +    D  L 
Sbjct: 209 RIQRQLLQDLGREPTPEEIGAEMNMPTNKVRDI---LKIAQ-EPVSLETPIGEEDDSHLG 264

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S +         +  EQVL    +R+   N+L     + + R R       
Sbjct: 265 DFIEDKDATSPEQHASYEMLKEQLEQVLETLTDREE--NVLRLRFGLDDGRTR------- 315

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                 TLE +   F V+RER+RQIEA+A +K+
Sbjct: 316 ------TLEEVGKVFGVTRERIRQIEAKALRKL 342


>gi|323466388|gb|ADX70075.1| RNA polymerase sigma factor [Lactobacillus helveticus H10]
          Length = 370

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 87/273 (31%), Positives = 133/273 (48%), Gaps = 31/273 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   +E  LAKR  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 104 YLKEIGRVPLLTADQEIALAKRI-EEGDEEAKQELAEANLRLVVSIAKRYVGRGMSFLDL 162

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 163 IQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 222

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + N+   +V  I   L +++ E +S+   +    D  L 
Sbjct: 223 RIQRQLLQDLGREPTPEEIGAEMNMPTNKVRNI---LKIAQ-EPVSLETPIGEEDDSHLG 278

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S +         +  EQVL    +R+   N+L     + + R R       
Sbjct: 279 DFIEDKDATSPEQHASYEMLKEQLEQVLETLTDREE--NVLRLRFGLDDGRTR------- 329

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                 TLE +   F V+RER+RQIEA+A +K+
Sbjct: 330 ------TLEEVGKVFGVTRERIRQIEAKALRKL 356


>gi|227904114|ref|ZP_04021919.1| RNA polymerase sigma factor RpoD [Lactobacillus acidophilus ATCC
           4796]
 gi|227868133|gb|EEJ75554.1| RNA polymerase sigma factor RpoD [Lactobacillus acidophilus ATCC
           4796]
          Length = 370

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 87/273 (31%), Positives = 133/273 (48%), Gaps = 31/273 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   +E  LAKR  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 104 YLKEIGRVPLLTADQEIALAKRI-ESGDEEAKQELAEANLRLVVSIAKRYVGRGMSFLDL 162

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 163 IQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 222

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + N+   +V  I   L +++ E +S+   +    D  L 
Sbjct: 223 RIQRQLLQDLGREPTPEEIGAEMNMPTNKVRDI---LKIAQ-EPVSLETPIGEEDDSHLG 278

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S +         +  EQVL    +R+   N+L     + + R R       
Sbjct: 279 DFIEDKDATSPEQHASYEMLKEQLEQVLETLTDREE--NVLRLRFGLDDGRTR------- 329

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                 TLE +   F V+RER+RQIEA+A +K+
Sbjct: 330 ------TLEEVGKVFGVTRERIRQIEAKALRKL 356


>gi|21910055|ref|NP_664323.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS315]
 gi|28896247|ref|NP_802597.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes SSI-1]
 gi|21904246|gb|AAM79126.1| putative RNA polymerase sigma 42 protein RpoD [Streptococcus
           pyogenes MGAS315]
 gi|28811498|dbj|BAC64430.1| putative RNA polymerase sigma 42 protein [Streptococcus pyogenes
           SSI-1]
          Length = 369

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 86/269 (31%), Positives = 141/269 (52%), Gaps = 21/269 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    + GDL A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLTSEEEKELAVAVAK-GDLMAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 218

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L      +  PEQ   IA+++ ++  +V  +  ++A +  SL   I   D   
Sbjct: 219 LVREQRNLLQELGQDPTPEQ---IAERMEMTPDKVREI-LKIAQEPVSLETPIGEED--D 272

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 273 SHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 326

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE++   F V+RER+RQIEA+A +K++
Sbjct: 327 RTLEDVGKVFNVTRERIRQIEAKALRKLR 355


>gi|257457314|ref|ZP_05622485.1| RNA polymerase sigma factor RpoD [Treponema vincentii ATCC 35580]
 gi|257445236|gb|EEV20308.1| RNA polymerase sigma factor RpoD [Treponema vincentii ATCC 35580]
          Length = 286

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 86/282 (30%), Positives = 152/282 (53%), Gaps = 17/282 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
            + Y+ EI KIP+L  ++E   AK     GD  A   L+ S+LR VV +A  Y+   +PI
Sbjct: 14  FATYLREINKIPLLSVEDEVKYAKAA-AAGDEKAKKILIESNLRFVVNVAKKYQNKNIPI 72

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT-ANQKR 134
            +++SEGNIGLM A  +FDP++G++  +Y++WWI+ A+ + I     ++++    AN+  
Sbjct: 73  MDLISEGNIGLMNAADRFDPDKGYKFISYAVWWIRQAILKAICEKSRMIRLPLNRANELV 132

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSS 193
                R+L G     T    + +++ AIA+ L + E E++      A D  SL+A    +
Sbjct: 133 QIEKARKLTGK----TGTEPEDKELTAIAQDLRI-EPEMVRTIMNAARDPVSLDA-PQFN 186

Query: 194 DKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN- 251
           D +++   D++      Q E   ++ + R+N   +L    + L+ RE  I   R      
Sbjct: 187 DNSAASTGDFIEDTRYMQPESYALDIDLRENVDALL----ASLSEREAEILRYRFGLNGY 242

Query: 252 -PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
             ++L+ + + F +++ER+RQIE +A +++Q S+  Q EL S
Sbjct: 243 EQLSLKEVGTRFNLTKERIRQIEKKALERLQ-SVGHQHELES 283


>gi|256420372|ref|YP_003121025.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chitinophaga
           pinensis DSM 2588]
 gi|256035280|gb|ACU58824.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chitinophaga
           pinensis DSM 2588]
          Length = 291

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 78/281 (27%), Positives = 147/281 (52%), Gaps = 34/281 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ ++  +EE  LA R ++ GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 20  LEKYLQEIGKVDLITPEEEVNLAIRIKQ-GDQRALEKLTKANLRFVVSVAKQYQNQGLSL 78

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           S++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     +V++    N+  L
Sbjct: 79  SDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL--PLNKVGL 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV--------ISMNCRLAGDES-- 185
              + +    L+   +    P+++  I  ++N  E E         +SM+      E   
Sbjct: 137 SNKISKAYSQLEQEFEREPSPDELATIL-EINTEEVEATLGVAARHVSMDAPFIDGEDNS 195

Query: 186 -LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR--I 242
            L+ L N +  N+ +  D     HD             + R  + RS+S L  R++   I
Sbjct: 196 LLDVLANPNAVNADEELDH----HD-------------SLRREIERSLSTLTDRQKDVII 238

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
                  E+P++LE++  +F ++RERVRQI+ +A  K++ +
Sbjct: 239 LYFGIAVEHPMSLEDIGEKFGLTRERVRQIKDKAITKLRTT 279


>gi|195939453|ref|ZP_03084835.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4024]
          Length = 305

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 82/262 (31%), Positives = 131/262 (50%), Gaps = 25/262 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVRQI 272
              TLE++  E  ++RERVRQI
Sbjct: 286 --ATLEDVGREIGLTRERVRQI 305


>gi|259046798|ref|ZP_05737199.1| RNA polymerase sigma-43 factor [Granulicatella adiacens ATCC 49175]
 gi|259036566|gb|EEW37821.1| RNA polymerase sigma-43 factor [Granulicatella adiacens ATCC 49175]
          Length = 374

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 88/276 (31%), Positives = 138/276 (50%), Gaps = 36/276 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   EE  LA R +E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 107 YLKEIGRVPLLSADEEVALALRIQE-GDTEAKQELAEANLRLVVSIAKRYVGRGMQFLDL 165

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+ V+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 166 IQEGNMGLMKTVEKFDHTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLV 225

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 226 RVQRQLLQDLGREPTPEEIGAEMDLPTEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 281

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR- 246
             I   D N++   D   Y        L++++        L   +  L  RE  +   R 
Sbjct: 282 DFIE--DDNATSPADHTAY-------ALLKEQ--------LDEVLEQLTDREENVLRLRF 324

Query: 247 RLQENPV--TLENLSSEFEVSRERVRQIEARAFKKV 280
            L +N    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 325 GLDKNGEIRTLEQVGQVFGVTRERIRQIEAKALRKL 360


>gi|19745866|ref|NP_607002.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS8232]
 gi|19748016|gb|AAL97501.1| putative RNA polymerase sigma 42 protein [Streptococcus pyogenes
           MGAS8232]
          Length = 369

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 86/269 (31%), Positives = 141/269 (52%), Gaps = 21/269 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    + GDL A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLTSEEEKELAVAVAK-GDLMAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 218

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L      +  PEQ   IA+++ ++  +V  +  ++A +  SL   I   D   
Sbjct: 219 LVREQRNLLQELGQDPTPEQ---IAERMEMTPDKVREI-LKIAQEPVSLETPIGEED--D 272

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 273 SHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 326

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE++   F V+RER+RQIEA+A +K++
Sbjct: 327 RTLEDVGKVFNVTRERIRQIEAKALRKLR 355


>gi|313903914|ref|ZP_07837294.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Eubacterium
           cellulosolvens 6]
 gi|313471063|gb|EFR66385.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Eubacterium
           cellulosolvens 6]
          Length = 373

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 86/265 (32%), Positives = 133/265 (50%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L   EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 107 YLKEIGKVPLLSADEEIELAKRM-EEGDEVAKKRLAEANLRLVVSIAKRYVGRGMLFLDL 165

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 166 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 223

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L         PE+   IAK +N+S   V  +        SL   I   ++  S
Sbjct: 224 LIRVSRQLLQEYGREPTPEE---IAKNMNMSVERVREILKISQEPVSLETPI--GEEEDS 278

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++    D    V  +       +  L   +  L  RE+++   R   ++    TLE
Sbjct: 279 HLGDFI---QDENVPVPADAAAFTMLKEQLEEVLGTLAEREQKVLRLRFGLDDGRARTLE 335

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF V+RER+RQIEA+A +K++
Sbjct: 336 EVGKEFNVTRERIRQIEAKALRKLR 360


>gi|15674827|ref|NP_269001.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes M1 GAS]
 gi|50913963|ref|YP_059935.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS10394]
 gi|71903245|ref|YP_280048.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS6180]
 gi|71910413|ref|YP_281963.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS5005]
 gi|94988285|ref|YP_596386.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS9429]
 gi|94990164|ref|YP_598264.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS10270]
 gi|94992161|ref|YP_600260.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS2096]
 gi|94994083|ref|YP_602181.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS10750]
 gi|139474032|ref|YP_001128748.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes str.
           Manfredo]
 gi|209559154|ref|YP_002285626.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes NZ131]
 gi|306827613|ref|ZP_07460893.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           pyogenes ATCC 10782]
 gi|13621959|gb|AAK33722.1| putative RNA polymerase sigma 42 protein [Streptococcus pyogenes M1
           GAS]
 gi|50903037|gb|AAT86752.1| RNA polymerase sigma factor rpoD [Streptococcus pyogenes MGAS10394]
 gi|71802340|gb|AAX71693.1| RNA polymerase sigma factor [Streptococcus pyogenes MGAS6180]
 gi|71853195|gb|AAZ51218.1| RNA polymerase sigma factor [Streptococcus pyogenes MGAS5005]
 gi|94541793|gb|ABF31842.1| RNA polymerase sigma factor [Streptococcus pyogenes MGAS9429]
 gi|94543672|gb|ABF33720.1| RNA polymerase sigma factor rpoD [Streptococcus pyogenes MGAS10270]
 gi|94545669|gb|ABF35716.1| RNA polymerase sigma factor rpoD [Streptococcus pyogenes MGAS2096]
 gi|94547591|gb|ABF37637.1| RNA polymerase sigma factor rpoD [Streptococcus pyogenes MGAS10750]
 gi|134272279|emb|CAM30532.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes str.
           Manfredo]
 gi|209540355|gb|ACI60931.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes NZ131]
 gi|304430176|gb|EFM33205.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           pyogenes ATCC 10782]
          Length = 369

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 86/269 (31%), Positives = 141/269 (52%), Gaps = 21/269 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    + GDL A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLTSEEEKELAVAVAK-GDLMAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 218

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R + +L      +  PEQ   IA+++ ++  +V  +  ++A +  SL   I   D   
Sbjct: 219 LVREQRNLLQELGQDPTPEQ---IAERMEMTPDKVREI-LKIAQEPVSLETPIGEED--D 272

Query: 198 SQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV 253
           S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L +  +
Sbjct: 273 SHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGKM 326

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE++   F V+RER+RQIEA+A +K++
Sbjct: 327 RTLEDVGKVFNVTRERIRQIEAKALRKLR 355


>gi|326204489|ref|ZP_08194346.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           papyrosolvens DSM 2782]
 gi|325985282|gb|EGD46121.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           papyrosolvens DSM 2782]
          Length = 359

 Score =  110 bits (275), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 85/265 (32%), Positives = 134/265 (50%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L   EE  LA R  E+GD+ A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 93  YLKEIGKVPLLSADEEIDLAHRM-ENGDIEAKRRLAEANLRLVVSIAKRYVGRGMQFLDL 151

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  RGF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 152 IQEGNLGLIKAVEKFDYRRGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 209

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L        +P++   IAK++ +S  +V  +        SL   I   ++  S
Sbjct: 210 LIRVSRQLLQELGREPQPDE---IAKEIGMSVDKVREIMKISQEPVSLETPIG--EEEDS 264

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++  D              K +   L   +  L  RE ++   R   ++    TLE
Sbjct: 265 HLGDFIPDDDAPAPAEAAAFTLLKEQ---LIDVLDTLTAREEKVLRLRFGLDDGRARTLE 321

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF V+RER+RQIEA+A +K++
Sbjct: 322 EVGKEFNVTRERIRQIEAKALRKLR 346


>gi|224824776|ref|ZP_03697883.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Lutiella
           nitroferrum 2002]
 gi|224603269|gb|EEG09445.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Lutiella
           nitroferrum 2002]
          Length = 316

 Score =  110 bits (274), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 87/265 (32%), Positives = 137/265 (51%), Gaps = 15/265 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+++I    +L  QEE  LA R    GD  A  +++  +LRLVV IA  Y   GL + ++
Sbjct: 49  YLNDIGNNALLSPQEEQSLA-RLVVQGDFEARQKMIEHNLRLVVNIAKRYINRGLALLDL 107

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM A++KFDPERGFR +TY+ WWI+ +++  I+     +++      K L   
Sbjct: 108 IEEGNIGLMHALEKFDPERGFRFSTYATWWIRQSIERAIMNQSRTIRLPVHV-IKELNVY 166

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  + HL++        E++  +  K       V+++N R+A   SL+A ++  D   S
Sbjct: 167 LRASR-HLESQIGREPSVEEIAQLVDKPVEDVRRVMNLNERMA---SLDAPLD-IDPMLS 221

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP---VTL 255
             +      HD  E  L          N +   M+ LN ++R + E RR   N     TL
Sbjct: 222 IGESIPDDQHDEPEIQL----HNTQLENFVHEWMAQLNDKQRMVIE-RRYGLNGHEICTL 276

Query: 256 ENLSSEFEVSRERVRQIEARAFKKV 280
           E L+S   ++RERVRQI+    +++
Sbjct: 277 EELASTLSLTRERVRQIQIEGLEQL 301


>gi|78185801|ref|YP_378235.1| type II alternative RNA polymerase sigma factor [Synechococcus sp.
           CC9902]
 gi|78170095|gb|ABB27192.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. CC9902]
          Length = 377

 Score =  110 bits (274), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 75/236 (31%), Positives = 118/236 (50%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLVV +A  Y+  G+ I ++V EG +GL +AV+KFDP RGFR +TY+ WW
Sbjct: 137 AKDHMIQANLRLVVAVAKKYQQRGMEILDLVQEGTLGLERAVEKFDPTRGFRFSTYAYWW 196

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  M   I      +++     +K     L R+K   Q I  N  +   +  +A++L +
Sbjct: 197 IRQGMTRAIATQSRTIRLPVHVTEK-----LNRIKRVQQEIASNEGRIASIADLARELGI 251

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SE  V     R+    SL++ +       +Q  D +       E+ L   E   +   +L
Sbjct: 252 SEDTVRQTLERVPRSVSLDSRVGKD--QDTQLGDLIEDGKATPEETLTHDELHNDLEGLL 309

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
                 L PRE  +   R   E+  P TL  +  E ++SRERVRQIE RA  K+++
Sbjct: 310 DE----LTPREASVLRRRFGLEDDTPQTLAQIGEELKLSRERVRQIETRALLKLRQ 361


>gi|134295851|ref|YP_001119586.1| RNA polymerase sigma factor RpoS [Burkholderia vietnamiensis G4]
 gi|134139008|gb|ABO54751.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia vietnamiensis
           G4]
          Length = 361

 Score =  110 bits (274), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 83/278 (29%), Positives = 142/278 (51%), Gaps = 25/278 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+P+
Sbjct: 83  IQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFDARQVMIERNLRLVVSIAKGYLNRGVPL 141

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++    +  R 
Sbjct: 142 LDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRE 199

Query: 136 FFNLRRLKGHLQ--------AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              + R K HL+        A        + +  +  K     ++++++N   A   SL+
Sbjct: 200 LNQVLRAKRHLEKNSMSTGDAAERREASIDDIAYLTGKTAEEVTDILALNEHTA---SLD 256

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS-MSVLNPRERRIFEAR 246
           A ++     +S   D L  D        ++  E +     LTR+ +S L+ + R + E R
Sbjct: 257 APLDLD--PASSLLDLLPDDQSQSPDAEVQHRELET----LTRAWLSRLSDKHRHVIE-R 309

Query: 247 RLQEN---PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   N   P TLE L+ E  ++RERVRQI+  A  +++
Sbjct: 310 RFGLNHIEPATLEELADEMGLTRERVRQIQQEALVRLK 347


>gi|315038507|ref|YP_004032075.1| RNA polymerase sigma factor RpoD [Lactobacillus amylovorus GRL
           1112]
 gi|325956923|ref|YP_004292335.1| RNA polymerase sigma factor RpoD [Lactobacillus acidophilus 30SC]
 gi|312276640|gb|ADQ59280.1| RNA polymerase sigma factor RpoD [Lactobacillus amylovorus GRL
           1112]
 gi|325333488|gb|ADZ07396.1| RNA polymerase sigma factor RpoD [Lactobacillus acidophilus 30SC]
 gi|327183703|gb|AEA32150.1| RNA polymerase sigma factor RpoD [Lactobacillus amylovorus GRL
           1118]
          Length = 370

 Score =  110 bits (274), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 87/273 (31%), Positives = 133/273 (48%), Gaps = 31/273 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   +E  LAKR  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 104 YLKEIGRVPLLTADQEIALAKRI-EAGDEEAKQELAEANLRLVVSIAKRYVGRGMSFLDL 162

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 163 IQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 222

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + N+   +V  I   L +++ E +S+   +    D  L 
Sbjct: 223 RIQRQLLQDLGREPTPEEIGAEMNMPTNKVRDI---LKIAQ-EPVSLETPIGEEDDSHLG 278

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S +         +  EQVL    +R+   N+L     + + R R       
Sbjct: 279 DFIEDKDATSPEQHASYEMLKEQLEQVLETLTDREE--NVLRLRFGLDDGRTR------- 329

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                 TLE +   F V+RER+RQIEA+A +K+
Sbjct: 330 ------TLEEVGKVFGVTRERIRQIEAKALRKL 356


>gi|226309754|ref|YP_002769648.1| RNA polymerase sigma factor [Brevibacillus brevis NBRC 100599]
 gi|226092702|dbj|BAH41144.1| RNA polymerase sigma factor [Brevibacillus brevis NBRC 100599]
          Length = 314

 Score =  110 bits (274), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 82/273 (30%), Positives = 138/273 (50%), Gaps = 20/273 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           ++  +   PML+K+EE     RY+  GDL A   +V ++LR VV  A+ +   G+P  ++
Sbjct: 39  FLESVAATPMLDKEEELACLIRYQRDGDLEARETIVRAYLRYVVSTALRHLKRGMPFLDL 98

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EG IGL  A+ KFD  RG RL  YS WWI  A+   I    +L++I    +++   + 
Sbjct: 99  IQEGTIGLFTAIDKFDVGRGVRLYHYSHWWISQAITRAINDKATLIRIPVHMHEQIRQYQ 158

Query: 139 LRRLKGHLQAITDNNLKPE-QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
               K  L  +   N  P+ Q +A+   + + + E I +   +   ES++A     + +S
Sbjct: 159 ----KQVLHLVHALNRTPDRQEIAVLLDIPLEKVEAIELALMMKM-ESIDA-----ELDS 208

Query: 198 SQWQDW-----LVYDH--DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQ 249
            +WQ W     L Y    D     L +  E+ + R+ +  ++  L+PR + I   R  L 
Sbjct: 209 EKWQTWHEDESLSYAEIMDDGLSSLDDWIEKVDLRSQMRAALDRLSPRAQEIISMRYGLY 268

Query: 250 ENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++ V TLE +   F ++RER+RQIEA    +++
Sbjct: 269 DDQVYTLEEVGKMFGLTRERIRQIEATTIDRLR 301


>gi|113953359|ref|YP_732042.1| RNA polymerase sigma-70 factor family protein [Synechococcus sp.
           CC9311]
 gi|113880710|gb|ABI45668.1| RNA polymerase sigma-70 factor family protein [Synechococcus sp.
           CC9311]
          Length = 376

 Score =  110 bits (274), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 76/236 (32%), Positives = 120/236 (50%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R++ ++LRLVV +A  Y+  G+ + ++V EG +GL +AV+KFD  RGFR +TYS WW
Sbjct: 136 ARDRMIQANLRLVVAVAKKYQHRGMELLDLVQEGTLGLERAVEKFDSTRGFRFSTYSYWW 195

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   I      +++     +K     L R+K   Q I  N  +   +  +A++L+V
Sbjct: 196 IRQGITRAIATQSRTIRLPVHITEK-----LNRIKRVQQEIASNEGRTASMTDLARELSV 250

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SE  V     R+    SL   +       +Q  + L  +H   EQ L     R +  + L
Sbjct: 251 SEDTVRQTLARVPRSVSLETKVGRD--QDTQLGELLEDEHATPEQTLT----RDSLHDDL 304

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              ++ L PRE  +   R   E+  P TL  +  +  +SRERVRQIE RA  K+++
Sbjct: 305 EHLLNELTPREATVIRCRFGLEDDTPRTLAQIGEDMNLSRERVRQIETRALLKLRQ 360


>gi|312129690|ref|YP_003997030.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Leadbetterella
           byssophila DSM 17132]
 gi|311906236|gb|ADQ16677.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Leadbetterella
           byssophila DSM 17132]
          Length = 287

 Score =  110 bits (274), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 82/278 (29%), Positives = 154/278 (55%), Gaps = 29/278 (10%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ +L   EE +LA++ R+ GD  +  RL  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGKVDLLTPDEEVILAQKIRD-GDQLSLERLTKANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
            ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++      Q  I+R   L ++G+ 
Sbjct: 77  GDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVR-LPLNRVGSL 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNA 188
               + F         L+   +    PE+   +A+ L +S +EV+    +++G   S++A
Sbjct: 136 NKISKTF-------SELEQRFEREPSPEE---LAEVLEISANEVVD-TMKISGRHVSVDA 184

Query: 189 LINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERRI--FEA 245
                ++NS    D L  D + + +Q L+    R+     + R++S L  RE  +  F  
Sbjct: 185 PFVQGEENS--LLDVLENDTEIRPDQELMNDSLRRE----VLRALSTLTQREAEVIMFYF 238

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               E  +TLE +  +F ++RERVRQI+ +A ++++++
Sbjct: 239 GLNGEQAMTLEEIGEKFNLTRERVRQIKEKAIRRLRQT 276


>gi|255659373|ref|ZP_05404782.1| RNA polymerase sigma factor RpoD [Mitsuokella multacida DSM 20544]
 gi|260848459|gb|EEX68466.1| RNA polymerase sigma factor RpoD [Mitsuokella multacida DSM 20544]
          Length = 373

 Score =  110 bits (274), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 81/265 (30%), Positives = 134/265 (50%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 107 YLKEIGRVPLLTAEEEVALAKRM-EAGDEEAQKRLAEANLRLVVSIAKRYVGRGMLFLDL 165

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 166 IQEGNLGLIKAVEKFDYNKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 223

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L         PE+   IAK++ +    V  +  ++A  E ++      ++  S
Sbjct: 224 LIRVSRQLLQQLGREPTPEE---IAKEMEIGVDRVREI-MKIA-QEPVSLETPIGEEEDS 278

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++    D       +       +  L   +  L PRE ++   R   ++    TLE
Sbjct: 279 HLGDFI---EDQDAPAPADAASFMLLKEQLEDVLDTLTPREEKVLRLRFGLDDGRARTLE 335

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +   F V+RER+RQIEA+A +K++
Sbjct: 336 EVGQNFGVTRERIRQIEAKALRKLR 360


>gi|317500513|ref|ZP_07958736.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|331089388|ref|ZP_08338287.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|316898102|gb|EFV20150.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|330404756|gb|EGG84294.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 370

 Score =  110 bits (274), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 87/267 (32%), Positives = 137/267 (51%), Gaps = 17/267 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  + E  LAKR  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 104 YLKEIGKVPLLSAEREIELAKRM-EEGDEDAKKELAEANLRLVVSIAKRYVGRGMLFLDL 162

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT--TANQKRLF 136
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I         +L 
Sbjct: 163 IQEGNLGLIKAVEKFDYHKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 222

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
              R+L   LQ +    L PE+   IAK+L++    V  +        SL   I   ++ 
Sbjct: 223 RVSRQL---LQELGREPL-PEE---IAKELDMPVERVREILKISQEPVSLETPI--GEEE 273

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVT 254
            S   D++    D    V  E   +   +  L   +  L  RE+++   R    +    T
Sbjct: 274 DSHLGDFI---QDDNVPVPAEAAAQTLLKEQLDEVLDTLTEREQKVLRLRFGMNDGRART 330

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQ 281
           LE +  EF+V+RER+RQIEA+A +K++
Sbjct: 331 LEEVGKEFDVTRERIRQIEAKALRKLR 357


>gi|291484966|dbj|BAI86041.1| RNA polymerase sigma factor [Bacillus subtilis subsp. natto
           BEST195]
          Length = 371

 Score =  110 bits (274), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 85/275 (30%), Positives = 135/275 (49%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE   AK+  E GD  +  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 105 YLKEIGRVNLLSAKEEIAYAKKI-EEGDEESKRRLAEANLRLVVSIAKRYVGRGMLFLDL 163

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 164 IQEGNMGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 223

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   D +L PE+V  I   L +++ E +S+   +    D  L 
Sbjct: 224 RVQRQLLQDLGREPTPEEIAEDMDLTPEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 279

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 280 DFIEDQEATSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 322

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 323 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 357


>gi|332878128|ref|ZP_08445857.1| putative RNA polymerase sigma factor RpoD [Capnocytophaga sp. oral
           taxon 329 str. F0087]
 gi|332683866|gb|EGJ56734.1| putative RNA polymerase sigma factor RpoD [Capnocytophaga sp. oral
           taxon 329 str. F0087]
          Length = 287

 Score =  110 bits (274), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 82/294 (27%), Positives = 155/294 (52%), Gaps = 51/294 (17%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI ++ ++   EE  LA+R +E GD++A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGRVDLITADEEVELAQRIKE-GDVAALEKLTKANLRFVVSVAKQYQNQGLTL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
            ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++      Q  I+R   L KIG+ 
Sbjct: 77  PDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVR-LPLNKIGSI 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCR 179
               +++  L +    + +  +          IA++L++S ++V          ISM+  
Sbjct: 136 NKINKMYAYLEQANERVPSAEE----------IARELDMSVNDVKESMKNSGRHISMDAP 185

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           L   E  N L +    N S   D        +E +L       + R  + R++  L PRE
Sbjct: 186 LVEGEDSN-LYDVIRSNESPNPD--------KELIL------ASLRTEIERALETLTPRE 230

Query: 240 RRIFEARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
             +    RL      ++ +TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 231 ADVI---RLYFGLGDQHAMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|169829158|ref|YP_001699316.1| RNA polymerase sigma factor rpoD [Lysinibacillus sphaericus C3-41]
 gi|168993646|gb|ACA41186.1| RNA polymerase sigma factor rpoD (Sigma-A) (Sigma-43)
           [Lysinibacillus sphaericus C3-41]
          Length = 375

 Score =  110 bits (274), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 86/276 (31%), Positives = 138/276 (50%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  ++E  LA+R  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 109 YLKEIGRVDLLSAEQEIKLAERI-EQGDEEARKRLAEANLRLVVSIAKRYVGRGMLFLDL 167

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 168 IQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 227

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I   L +++ E +S+   +    D  L 
Sbjct: 228 RVQRQLLQDLGREPSPEEIGEEMDLTPEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 283

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I  S+  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 284 DFIEDSEAQSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 326

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 327 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 362


>gi|315640587|ref|ZP_07895693.1| RNA polymerase sigma factor rpoD [Enterococcus italicus DSM 15952]
 gi|315483615|gb|EFU74105.1| RNA polymerase sigma factor rpoD [Enterococcus italicus DSM 15952]
          Length = 368

 Score =  110 bits (274), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 87/273 (31%), Positives = 134/273 (49%), Gaps = 31/273 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGRVPLLTAAEEVELALKI-EEGDQEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 161 IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 220

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 221 RIQRQLLQDLGREPTPEEIGAEMDLSTEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 276

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S           +  E VL    +R+   N+L     + + R R       
Sbjct: 277 DFIEDQDATSPAEHAAYELLKEQLEDVLDTLTDREE--NVLRLRFGIDDGRTR------- 327

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                 TLE +   F V+RER+RQIEA+A +K+
Sbjct: 328 ------TLEEVGKVFGVTRERIRQIEAKALRKL 354


>gi|266623970|ref|ZP_06116905.1| RNA polymerase sigma factor RpoD [Clostridium hathewayi DSM 13479]
 gi|288864209|gb|EFC96507.1| RNA polymerase sigma factor RpoD [Clostridium hathewayi DSM 13479]
          Length = 345

 Score =  110 bits (274), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 85/274 (31%), Positives = 139/274 (50%), Gaps = 31/274 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L   +E  LAK+  E GD  A  +L  ++LRLVV IA  Y G G+   ++
Sbjct: 78  YLKEIGKVPLLSSDDEIELAKKI-ELGDELAKEKLTEANLRLVVSIAKRYVGRGMQFLDL 136

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-- 132
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 137 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINRLV 196

Query: 133 ---KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
              ++L   L R     +  +  ++  E+V  I K   VS+ E +S+   +  +E     
Sbjct: 197 RVSRQLLQELGREPSPEEVASRVDMPVERVREIMK---VSQ-EPVSLETPIGEEE----- 247

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
                   S   D++    D Q  V  +          L   +  L  RE+++   R   
Sbjct: 248 -------DSHLGDFI---QDDQVAVPADAATFTMLHEQLMEVLDTLTEREQKVLRLRFGL 297

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++  P TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 298 DDGRPRTLEEVGREFNVTRERIRQIEAKALRKLR 331


>gi|261856530|ref|YP_003263813.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Halothiobacillus
           neapolitanus c2]
 gi|261836999|gb|ACX96766.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Halothiobacillus
           neapolitanus c2]
          Length = 343

 Score =  110 bits (274), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 85/279 (30%), Positives = 145/279 (51%), Gaps = 31/279 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ ++    +L  +EE + ++R  + GD SA  +++  +LRLV+KIA  Y   GL + ++
Sbjct: 74  YLRDVETERLLTAEEEVIYSRRA-QSGDESARQKMIVCNLRLVIKIARRYMNRGLDLLDL 132

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM+AV+KFDPERGFR +TY+ WWI+  ++  ++     V++     ++   FN
Sbjct: 133 IEEGNIGLMRAVEKFDPERGFRFSTYATWWIRQTIERGLMNQSRTVRLPVHVVKEVHTFN 192

Query: 139 --LRRLKGHLQA------ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R++  +  A      I D+  +P   V      N  +S   S +  L GD   + L 
Sbjct: 193 RAARKIAQNQNAEVTAEQIADHLDRPVNEVLKIMAFNERQS---SFDSPLKGDGEFSLLD 249

Query: 191 NSSDKNSSQWQDWLVYD---HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
              D+ S+Q  D L+ D   H   +Q++ + E ++  R +L R   +      R +E   
Sbjct: 250 LIPDQESNQ-PDELLQDAGVHGFLDQLIAQLESKQ--REVLVRRYGL------RGYETH- 299

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                 TLE + +   V+RERVRQI+  A ++++   +K
Sbjct: 300 ------TLEEVGNHLGVTRERVRQIQLEAVRRLKSLAKK 332


>gi|167562539|ref|ZP_02355455.1| RNA polymerase sigma factor RpoS [Burkholderia oklahomensis EO147]
 gi|167569723|ref|ZP_02362597.1| RNA polymerase sigma factor RpoS [Burkholderia oklahomensis C6786]
          Length = 362

 Score =  110 bits (274), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 83/278 (29%), Positives = 142/278 (51%), Gaps = 25/278 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+P+
Sbjct: 84  IQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFDARQVMIERNLRLVVSIAKGYLNRGVPL 142

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++    +  R 
Sbjct: 143 LDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRE 200

Query: 136 FFNLRRLKGHL--------QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              + R K HL        +A        + +  +  K     ++++++N   A   SL+
Sbjct: 201 LNQVLRAKRHLEKNSLSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTA---SLD 257

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS-MSVLNPRERRIFEAR 246
           A ++     +S   D L  D        ++  E +     LTR+ +S L+ + R + E R
Sbjct: 258 APLDLD--PASSLLDLLPDDQSQSPDAEVQHRELET----LTRAWLSRLSDKHRHVIE-R 310

Query: 247 RLQEN---PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   N   P TLE L+ E  ++RERVRQI+  A  +++
Sbjct: 311 RFGLNHIEPATLEELADEMGLTRERVRQIQQEALVRLK 348


>gi|219847152|ref|YP_002461585.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus
           aggregans DSM 9485]
 gi|219541411|gb|ACL23149.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus
           aggregans DSM 9485]
          Length = 398

 Score =  110 bits (274), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 79/290 (27%), Positives = 138/290 (47%), Gaps = 39/290 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLA--------------------------KRYREHGDLSAAHR 52
           Y+ EI ++P+L  ++E  LA                          +R +E GD  A  +
Sbjct: 104 YLREIGQVPLLTAEQEKQLAQMIERGQAAERKLATLPPDSPEAAKLRRIKEQGD-EARQK 162

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           +  ++LRLVV IA  YR  GLP+ +++ EG++GL++A++KFD  +G++ +TY+ WWIK A
Sbjct: 163 MAAANLRLVVSIAKRYRDRGLPLLDLIQEGSLGLLRAIEKFDHTKGYKFSTYATWWIKQA 222

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +     LV++        L   L R++   + +T +  +      +A  L +SE +
Sbjct: 223 LSRALADQSRLVRLPV-----HLGETLNRIQSARRQLTQSLGREPTDTELANHLGMSEEK 277

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           +     R    + ++      ++  S   D++   H        +       R  +  ++
Sbjct: 278 L--RELRRTAQDPVSLATPVGEEADSTLADFIPDPH---ALDADDAAASGMLRQQIAAAL 332

Query: 233 SVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             L+ RERR+ E R       P TLE +   F V+RERVRQIE +A +K+
Sbjct: 333 DQLSERERRVLELRYGLADGQPRTLEEVGKAFGVTRERVRQIEVKALRKL 382


>gi|78066590|ref|YP_369359.1| RNA polymerase sigma factor RpoS [Burkholderia sp. 383]
 gi|77967335|gb|ABB08715.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia sp. 383]
          Length = 362

 Score =  110 bits (274), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 83/278 (29%), Positives = 142/278 (51%), Gaps = 25/278 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+P+
Sbjct: 84  IQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGVPL 142

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++    +  R 
Sbjct: 143 LDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRE 200

Query: 136 FFNLRRLKGHL--------QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              + R K HL        +A        + +  +  K     ++++++N   A   SL+
Sbjct: 201 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTA---SLD 257

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS-MSVLNPRERRIFEAR 246
           A ++     +S   D L  D        ++  E +     LTR+ +S L+ + R + E R
Sbjct: 258 APLDLD--PASSLLDLLPDDQSQSPDAEVQHRELET----LTRAWLSRLSDKHRHVIE-R 310

Query: 247 RLQEN---PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   N   P TLE L+ E  ++RERVRQI+  A  +++
Sbjct: 311 RFGLNHIEPATLEELADEMGLTRERVRQIQQEALVRLK 348


>gi|153816193|ref|ZP_01968861.1| hypothetical protein RUMTOR_02441 [Ruminococcus torques ATCC 27756]
 gi|145846528|gb|EDK23446.1| hypothetical protein RUMTOR_02441 [Ruminococcus torques ATCC 27756]
          Length = 383

 Score =  110 bits (274), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 85/270 (31%), Positives = 140/270 (51%), Gaps = 23/270 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  + E  LAKR  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 117 YLKEIGKVPLLSAEREIELAKRM-EEGDEDAKKELAEANLRLVVSIAKRYVGRGMLFLDL 175

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT--TANQKRLF 136
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I         +L 
Sbjct: 176 IQEGNLGLIKAVEKFDYHKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 235

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES---EVISMNCRLAGDESLNALINSS 193
              R+L   LQ +    L PE+   IAK+L++      E++ ++      E ++      
Sbjct: 236 RVSRQL---LQELGREPL-PEE---IAKELDMPVERVREILKIS-----QEPVSLETPIG 283

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-- 251
           ++  S   D++    D    V  E   +   +  L   +  L  RE+++   R    +  
Sbjct: 284 EEEDSHLGDFI---QDDNVPVPAEAAAQTLLKEQLDEVLDTLTEREQKVLRLRFGMNDGR 340

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             TLE +  EF+V+RER+RQIEA+A +K++
Sbjct: 341 ARTLEEVGKEFDVTRERIRQIEAKALRKLR 370


>gi|1519642|gb|AAB07554.1| SigD [Chloroflexus aurantiacus J-10-fl]
          Length = 398

 Score =  110 bits (274), Expect = 3e-22,   Method: Compositional matrix adjust.
 Identities = 83/290 (28%), Positives = 142/290 (48%), Gaps = 39/290 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLA--------------------------KRYREHGDLSAAHR 52
           Y+ EI ++P+L  ++E  LA                          K+ +  G+  A H 
Sbjct: 104 YLREIGQVPLLTAEQEKRLAQLIEQGQEAERKLATLPPDSPEAARLKQLKAKGE-EARHE 162

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           +  ++LRLVV IA  YR  GLP+ +++ EG++GL++A++KFD  +G++ +TY+ WWIK A
Sbjct: 163 MAAANLRLVVSIAKRYRDRGLPLLDLIQEGSLGLLRAIEKFDYTKGYKFSTYATWWIKQA 222

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +     LV++        L   L R++   + +T +  +      +A  L +SE +
Sbjct: 223 LSRALADQSRLVRLPV-----HLGETLNRIQSARRQLTQSLGREPTDTELANHLGMSEEK 277

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           + ++  R A D    A     + NS+   D++   H        +       R  +T ++
Sbjct: 278 LATVR-RTAQDPVSLATPVGEEANST-LADFIPDPH---ALDADDAAASGIVRQQITAAL 332

Query: 233 SVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             L+ RERR+ E R   +   P TLE +   F V+RERVRQIE +A +K+
Sbjct: 333 DQLSERERRVLELRYGLVDGQPRTLEEVGKAFGVTRERVRQIEVKALRKL 382


>gi|53719139|ref|YP_108125.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei K96243]
 gi|53723558|ref|YP_103014.1| RNA polymerase sigma factor RpoS [Burkholderia mallei ATCC 23344]
 gi|67639892|ref|ZP_00438721.1| RNA polymerase sigma factor RpoS [Burkholderia mallei GB8 horse 4]
 gi|76810144|ref|YP_333760.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1710b]
 gi|121600326|ref|YP_993163.1| RNA polymerase sigma factor RpoS [Burkholderia mallei SAVP1]
 gi|124385284|ref|YP_001026062.1| RNA polymerase sigma factor RpoS [Burkholderia mallei NCTC 10229]
 gi|126440772|ref|YP_001059233.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 668]
 gi|126450398|ref|YP_001080670.1| RNA polymerase sigma factor RpoS [Burkholderia mallei NCTC 10247]
 gi|126452489|ref|YP_001066500.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1106a]
 gi|134277449|ref|ZP_01764164.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 305]
 gi|167002252|ref|ZP_02268042.1| RNA polymerase sigma factor RpoS [Burkholderia mallei PRL-20]
 gi|167719257|ref|ZP_02402493.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei DM98]
 gi|167738254|ref|ZP_02411028.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 14]
 gi|167815444|ref|ZP_02447124.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 91]
 gi|167823855|ref|ZP_02455326.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 9]
 gi|167845396|ref|ZP_02470904.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei B7210]
 gi|167893937|ref|ZP_02481339.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 7894]
 gi|167902387|ref|ZP_02489592.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei NCTC
           13177]
 gi|167910629|ref|ZP_02497720.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 112]
 gi|167918658|ref|ZP_02505749.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei BCC215]
 gi|217421435|ref|ZP_03452939.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 576]
 gi|226197238|ref|ZP_03792815.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei
           Pakistan 9]
 gi|237812557|ref|YP_002897008.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei
           MSHR346]
 gi|242315690|ref|ZP_04814706.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1106b]
 gi|254178572|ref|ZP_04885227.1| RNA polymerase sigma factor RpoS [Burkholderia mallei ATCC 10399]
 gi|254179542|ref|ZP_04886141.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1655]
 gi|254189067|ref|ZP_04895578.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei Pasteur
           52237]
 gi|254197294|ref|ZP_04903716.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei S13]
 gi|254199960|ref|ZP_04906326.1| RNA polymerase sigma factor RpoS [Burkholderia mallei FMH]
 gi|254206293|ref|ZP_04912645.1| RNA polymerase sigma factor RpoS [Burkholderia mallei JHU]
 gi|254261861|ref|ZP_04952915.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1710a]
 gi|254297419|ref|ZP_04964872.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 406e]
 gi|254358292|ref|ZP_04974565.1| RNA polymerase sigma factor RpoS [Burkholderia mallei 2002721280]
 gi|28394113|gb|AAO34104.1| rpoS [Burkholderia pseudomallei]
 gi|52209553|emb|CAH35506.1| RNA polymerase sigma factor [Burkholderia pseudomallei K96243]
 gi|52426981|gb|AAU47574.1| RNA polymerase sigma factor [Burkholderia mallei ATCC 23344]
 gi|76579597|gb|ABA49072.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1710b]
 gi|121229136|gb|ABM51654.1| RNA polymerase sigma factor RpoS [Burkholderia mallei SAVP1]
 gi|124293304|gb|ABN02573.1| RNA polymerase sigma factor RpoS [Burkholderia mallei NCTC 10229]
 gi|126220265|gb|ABN83771.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 668]
 gi|126226131|gb|ABN89671.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1106a]
 gi|126243268|gb|ABO06361.1| RNA polymerase sigma factor RpoS [Burkholderia mallei NCTC 10247]
 gi|134251099|gb|EBA51178.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 305]
 gi|147749556|gb|EDK56630.1| RNA polymerase sigma factor RpoS [Burkholderia mallei FMH]
 gi|147753736|gb|EDK60801.1| RNA polymerase sigma factor RpoS [Burkholderia mallei JHU]
 gi|148027419|gb|EDK85440.1| RNA polymerase sigma factor RpoS [Burkholderia mallei 2002721280]
 gi|157807858|gb|EDO85028.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 406e]
 gi|157936746|gb|EDO92416.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei Pasteur
           52237]
 gi|160699611|gb|EDP89581.1| RNA polymerase sigma factor RpoS [Burkholderia mallei ATCC 10399]
 gi|169654035|gb|EDS86728.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei S13]
 gi|184210082|gb|EDU07125.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1655]
 gi|217395177|gb|EEC35195.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 576]
 gi|225930617|gb|EEH26627.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei
           Pakistan 9]
 gi|237506433|gb|ACQ98751.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei
           MSHR346]
 gi|238520504|gb|EEP83963.1| RNA polymerase sigma factor RpoS [Burkholderia mallei GB8 horse 4]
 gi|242138929|gb|EES25331.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1106b]
 gi|243062069|gb|EES44255.1| RNA polymerase sigma factor RpoS [Burkholderia mallei PRL-20]
 gi|254220550|gb|EET09934.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1710a]
          Length = 359

 Score =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 83/278 (29%), Positives = 142/278 (51%), Gaps = 25/278 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+P+
Sbjct: 81  IQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGVPL 139

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++    +  R 
Sbjct: 140 LDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRE 197

Query: 136 FFNLRRLKGHL--------QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              + R K HL        +A        + +  +  K     ++++++N   A   SL+
Sbjct: 198 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTA---SLD 254

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS-MSVLNPRERRIFEAR 246
           A ++     +S   D L  D        ++  E +     LTR+ +S L+ + R + E R
Sbjct: 255 APLDLD--PASSLLDLLPDDQSQSPDAEVQHRELET----LTRAWLSRLSDKHRHVIE-R 307

Query: 247 RLQEN---PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   N   P TLE L+ E  ++RERVRQI+  A  +++
Sbjct: 308 RFGLNHIEPATLEELADEMGLTRERVRQIQQEALVRLK 345


>gi|221632805|ref|YP_002522027.1| sigma factor MysA [Thermomicrobium roseum DSM 5159]
 gi|221156346|gb|ACM05473.1| sigma factor MysA [Thermomicrobium roseum DSM 5159]
          Length = 369

 Score =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 97/300 (32%), Positives = 152/300 (50%), Gaps = 56/300 (18%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRY---------------------------REHGDLSAAH 51
           Y+ EI +  +L  QEE  LA+R                            +E G+ + AH
Sbjct: 76  YLQEIGETALLTPQEEVWLAQRIERGKIAKVRLERGDYKSEDERLALVADKEDGERARAH 135

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G GL   +++ EGNIGLM+A +KFD +RG++ +TY+ WWI+ 
Sbjct: 136 -LIQANLRLVVSVAKKYVGRGLSFLDLIQEGNIGLMKATEKFDYKRGYKFSTYATWWIRQ 194

Query: 112 AMQEYI---LRSWSL-VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           A+   I    R+  L V +G T N+      ++++   LQ I +   +P Q + +A+ L+
Sbjct: 195 AITRAISDQSRTIRLPVHVGETINR------IKKISHRLQQILER--EPTQ-LEVARALD 245

Query: 168 VSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKN 223
           + E ++  I    RL    SL A I        Q  D  + D   D  +   +E   ++ 
Sbjct: 246 MPEEKIRQILEAARLP--VSLEAPIG-------QDGDAFLGDFIEDETQPAPLEIASQQL 296

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R  L  ++S L  RERRI   R   E+    TLE +  EF ++RER+RQIEA+A +K++
Sbjct: 297 LRQQLEEALSRLTERERRIIILRYGLEDGQFRTLEEVGREFGITRERIRQIEAKALRKLR 356


>gi|261407775|ref|YP_003244016.1| RpoD subfamily RNA polymerase sigma-70 factor [Paenibacillus sp.
           Y412MC10]
 gi|329927238|ref|ZP_08281536.1| RNA polymerase sigma factor RpoD [Paenibacillus sp. HGF5]
 gi|261284238|gb|ACX66209.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Paenibacillus sp.
           Y412MC10]
 gi|328938638|gb|EGG35021.1| RNA polymerase sigma factor RpoD [Paenibacillus sp. HGF5]
          Length = 316

 Score =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 88/274 (32%), Positives = 138/274 (50%), Gaps = 31/274 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   EE  L+KR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 50  YLKEIGRVPLLSADEEVELSKRI-EEGDEEAKRRLAEANLRLVVSIARRYAGRGMQFLDL 108

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-- 132
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 109 IQEGNMGLIKAVEKFDYSKGFKFSTYATWWIRQAITRSIADQARTIRIPVHMVETINKLV 168

Query: 133 ---KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
              ++L   L R     +   + ++ PE+V  I K   VS+ E +S+   +    D +L 
Sbjct: 169 RVSRQLLQELGREPTPEEIGKEMDISPEKVREIQK---VSQ-EPVSLETPVGEESDSNLG 224

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  +           +  E+VL    ER+   N+L     + + R R       
Sbjct: 225 DFIEDQDALAPADAAAFELLKEQLEEVLDTLTEREE--NVLRLRFGLEDGRTR------- 275

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                 TLE +   F V+RER+RQIEA+A +K++
Sbjct: 276 ------TLEEVGQVFGVTRERIRQIEAKALRKLR 303


>gi|325125919|gb|ADY85249.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus 2038]
          Length = 372

 Score =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 83/274 (30%), Positives = 131/274 (47%), Gaps = 33/274 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI +  +L  +EE  LAKR  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 106 YLKEIGRFNLLTSEEEVALAKRI-EAGDEEAKQELAEANLRLVVSIAKRYVGRGMNFLDL 164

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 165 IQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 222

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLA--GDESLNA 188
           L R++  L      + +PE++ A        + + L + + E +S+   +    D +L  
Sbjct: 223 LIRIQRQLLQDLGRDPEPEEIAAEMDLPVKKVREILKICQ-EPVSLETPIGEEDDSNLGD 281

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            I   D  S +        H   E +          +  L   +  L+ RE  +   R  
Sbjct: 282 FIEDKDAMSPEQ-------HAANEML----------KEQLAEVLDTLSDREEEVLRLRFG 324

Query: 249 QEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
            ++    TLE +   FEV+RER+RQIEA+A +K+
Sbjct: 325 LDDGKSRTLEEVGQHFEVTRERIRQIEAKALRKL 358


>gi|83721572|ref|YP_442747.1| RNA polymerase sigma factor RpoS [Burkholderia thailandensis E264]
 gi|167581696|ref|ZP_02374570.1| RNA polymerase sigma factor RpoS [Burkholderia thailandensis TXDOH]
 gi|167619812|ref|ZP_02388443.1| RNA polymerase sigma factor RpoS [Burkholderia thailandensis Bt4]
 gi|257138958|ref|ZP_05587220.1| RNA polymerase sigma factor RpoS [Burkholderia thailandensis E264]
 gi|83655397|gb|ABC39460.1| RpoS [Burkholderia thailandensis E264]
          Length = 363

 Score =  110 bits (274), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 83/278 (29%), Positives = 142/278 (51%), Gaps = 25/278 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+P+
Sbjct: 85  IQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGVPL 143

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++    +  R 
Sbjct: 144 LDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRE 201

Query: 136 FFNLRRLKGHL--------QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              + R K HL        +A        + +  +  K     ++++++N   A   SL+
Sbjct: 202 LNQVLRAKRHLEKNSLSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTA---SLD 258

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS-MSVLNPRERRIFEAR 246
           A ++     +S   D L  D        ++  E +     LTR+ +S L+ + R + E R
Sbjct: 259 APLDLD--PASSLLDLLPDDQSQSPDAEVQHRELET----LTRAWLSRLSDKHRHVIE-R 311

Query: 247 RLQEN---PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   N   P TLE L+ E  ++RERVRQI+  A  +++
Sbjct: 312 RFGLNHIEPATLEELADEMGLTRERVRQIQQEALVRLK 349


>gi|116689841|ref|YP_835464.1| RNA polymerase sigma factor RpoS [Burkholderia cenocepacia HI2424]
 gi|170733180|ref|YP_001765127.1| RNA polymerase sigma factor RpoS [Burkholderia cenocepacia MC0-3]
 gi|116647930|gb|ABK08571.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia cenocepacia
           HI2424]
 gi|169816422|gb|ACA91005.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia cenocepacia
           MC0-3]
          Length = 362

 Score =  109 bits (273), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 83/278 (29%), Positives = 142/278 (51%), Gaps = 25/278 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+P+
Sbjct: 84  IQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGVPL 142

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++    +  R 
Sbjct: 143 LDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRE 200

Query: 136 FFNLRRLKGHL--------QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              + R K HL        +A        + +  +  K     ++++++N   A   SL+
Sbjct: 201 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTA---SLD 257

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS-MSVLNPRERRIFEAR 246
           A ++     +S   D L  D        ++  E +     LTR+ +S L+ + R + E R
Sbjct: 258 APLDLD--PASSLLDLLPDDQSQSPDAEVQHRELET----LTRAWLSRLSDKHRHVIE-R 310

Query: 247 RLQEN---PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   N   P TLE L+ E  ++RERVRQI+  A  +++
Sbjct: 311 RFGLNHIEPATLEELADEMGLTRERVRQIQQEALVRLK 348


>gi|171321354|ref|ZP_02910311.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia ambifaria
           MEX-5]
 gi|171093372|gb|EDT38562.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia ambifaria
           MEX-5]
          Length = 361

 Score =  109 bits (273), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 83/278 (29%), Positives = 142/278 (51%), Gaps = 25/278 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+P+
Sbjct: 83  IQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGVPL 141

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++    +  R 
Sbjct: 142 LDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRE 199

Query: 136 FFNLRRLKGHL--------QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              + R K HL        +A        + +  +  K     ++++++N   A   SL+
Sbjct: 200 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTA---SLD 256

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS-MSVLNPRERRIFEAR 246
           A ++     +S   D L  D        ++  E +     LTR+ +S L+ + R + E R
Sbjct: 257 APLDLD--PASSLLDLLPDDQSQSPDAEVQHRELET----LTRAWLSRLSDKHRHVIE-R 309

Query: 247 RLQEN---PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   N   P TLE L+ E  ++RERVRQI+  A  +++
Sbjct: 310 RFGLNHIEPATLEELADEMGLTRERVRQIQQEALVRLK 347


>gi|206560255|ref|YP_002231019.1| RNA polymerase sigma factor RpoS [Burkholderia cenocepacia J2315]
 gi|198036296|emb|CAR52192.1| RNA polymerase sigma factor [Burkholderia cenocepacia J2315]
          Length = 362

 Score =  109 bits (273), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 83/278 (29%), Positives = 142/278 (51%), Gaps = 25/278 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+P+
Sbjct: 84  IQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGVPL 142

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++    +  R 
Sbjct: 143 LDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRE 200

Query: 136 FFNLRRLKGHL--------QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              + R K HL        +A        + +  +  K     ++++++N   A   SL+
Sbjct: 201 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTA---SLD 257

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS-MSVLNPRERRIFEAR 246
           A ++     +S   D L  D        ++  E +     LTR+ +S L+ + R + E R
Sbjct: 258 APLDLD--PASSLLDLLPDDQSQSPDAEVQHRELET----LTRAWLSRLSDKHRHVIE-R 310

Query: 247 RLQEN---PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   N   P TLE L+ E  ++RERVRQI+  A  +++
Sbjct: 311 RFGLNHIEPATLEELADEMGLTRERVRQIQQEALVRLK 348


>gi|167587040|ref|ZP_02379428.1| RNA polymerase sigma factor RpoS [Burkholderia ubonensis Bu]
          Length = 360

 Score =  109 bits (273), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 83/278 (29%), Positives = 142/278 (51%), Gaps = 25/278 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+P+
Sbjct: 82  IQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGVPL 140

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++    +  R 
Sbjct: 141 LDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRE 198

Query: 136 FFNLRRLKGHL--------QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              + R K HL        +A        + +  +  K     ++++++N   A   SL+
Sbjct: 199 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTA---SLD 255

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS-MSVLNPRERRIFEAR 246
           A ++     +S   D L  D        ++  E +     LTR+ +S L+ + R + E R
Sbjct: 256 APLDLD--PASSLLDLLPDDQSQSPDAEVQHRELET----LTRAWLSRLSDKHRHVIE-R 308

Query: 247 RLQEN---PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   N   P TLE L+ E  ++RERVRQI+  A  +++
Sbjct: 309 RFGLNHIEPATLEELADEMGLTRERVRQIQQEALVRLK 346


>gi|227892546|ref|ZP_04010351.1| RNA polymerase sigma factor RpoD [Lactobacillus ultunensis DSM
           16047]
 gi|227865667|gb|EEJ73088.1| RNA polymerase sigma factor RpoD [Lactobacillus ultunensis DSM
           16047]
          Length = 370

 Score =  109 bits (273), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 87/273 (31%), Positives = 133/273 (48%), Gaps = 31/273 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   +E  LAKR  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 104 YLKEIGRVPLLTADQEIALAKRI-EAGDEEAKQELAEANLRLVVSIAKRYVGRGMSFLDL 162

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 163 IQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 222

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + N+   +V  I   L +++ E +S+   +    D  L 
Sbjct: 223 KIQRQLLQDLGREPTPEEIGAEMNVPTNKVRDI---LKIAQ-EPVSLETPIGEEDDSHLG 278

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S +         +  EQVL    +R+   N+L     + + R R       
Sbjct: 279 DFIEDKDATSPEQHASYEMLKEQLEQVLETLTDREE--NVLRLRFGLDDGRTR------- 329

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                 TLE +   F V+RER+RQIEA+A +K+
Sbjct: 330 ------TLEEVGKVFGVTRERIRQIEAKALRKL 356


>gi|153875311|ref|ZP_02003170.1| RNA polymerase subunit sigma-38 [Beggiatoa sp. PS]
 gi|152068225|gb|EDN66830.1| RNA polymerase subunit sigma-38 [Beggiatoa sp. PS]
          Length = 314

 Score =  109 bits (273), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 90/295 (30%), Positives = 149/295 (50%), Gaps = 61/295 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI K  +L  +EE   A+R  + G+ +A +R++  +LRLVVKIA  Y   GL + ++
Sbjct: 45  YLNEIGKSKLLTAEEEIKYARRA-QQGNEAARNRMIEGNLRLVVKIARNYMNRGLALLDL 103

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFDPE+GFR +TY+ WWI+  ++  I+            NQ R    
Sbjct: 104 IEEGNLGLMRAVNKFDPEKGFRFSTYATWWIRQTIERAIM------------NQNRTI-- 149

Query: 139 LRRLKGHLQAITDNNLKPEQVVA-----------IAKKLNVSESEVISMNCRLAGDESLN 187
             RL  H+    +  L+   V++           IAK L  S+ EV              
Sbjct: 150 --RLPIHVLKEINQCLRTNHVLSQTLDHEPTSEEIAKTLKKSKQEV-------------E 194

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIE---KEERKNRRNMLTRS---------MSVL 235
            L+  +++  S    W+ Y     E+ LI+    E   + R +L  +         +S L
Sbjct: 195 KLLEVNERAISMDSPWMNY----SEKSLIDNIPDELNPDPRLILEDADIIKCLHLWLSQL 250

Query: 236 NPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             ++R + E RR      +  TLE + +E E++RERVRQI+  A ++++E ++++
Sbjct: 251 TDKQRLVVE-RRFGIGNGDEATLEEIGAELELTRERVRQIQITATERLKEILERE 304


>gi|317056182|ref|YP_004104649.1| RpoD subfamily RNA polymerase sigma-70 subunit [Ruminococcus albus
           7]
 gi|315448451|gb|ADU22015.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ruminococcus
           albus 7]
          Length = 366

 Score =  109 bits (273), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 88/278 (31%), Positives = 146/278 (52%), Gaps = 35/278 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGD---LSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           Y+ EI ++P+L  +EE  LA+      D   + A  RL  ++LRLVV IA  Y G G+  
Sbjct: 96  YLKEIGRVPLLTSEEEIQLAEMMSGDNDREAVKARKRLAEANLRLVVSIAKRYVGRGMSF 155

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG-----TTA 130
            +++ EGN+GL++AV+KFD ++GF+ +TY+ WWI+ A+   I      ++I      T  
Sbjct: 156 LDLIQEGNMGLIKAVEKFDYKKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETIT 215

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNAL 189
             K++   L    GH       +  PE+   IA++L++S   V  +  R+A D  SL   
Sbjct: 216 KVKKVSSQLLHKNGH-------DPSPEE---IAEELDMSVERVREI-MRIAQDPVSLETP 264

Query: 190 INSSDKNSSQWQDWL----VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           I   ++  S   D++             +++ KE+       + + +S L  RE ++   
Sbjct: 265 I--GEEEDSHLGDFIPDDDAPAPAEAASLVLLKEQ-------IDQVLSTLTEREEKVLRL 315

Query: 246 R-RLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R  LQ+    TLE +  EF+V+RER+RQIEA+A +K++
Sbjct: 316 RFGLQDGRSRTLEEVGQEFKVTRERIRQIEAKALRKLR 353


>gi|221198089|ref|ZP_03571135.1| RNA polymerase sigma factor RpoS [Burkholderia multivorans CGD2M]
 gi|221204352|ref|ZP_03577369.1| RNA polymerase sigma factor RpoS [Burkholderia multivorans CGD2]
 gi|221175209|gb|EEE07639.1| RNA polymerase sigma factor RpoS [Burkholderia multivorans CGD2]
 gi|221182021|gb|EEE14422.1| RNA polymerase sigma factor RpoS [Burkholderia multivorans CGD2M]
          Length = 338

 Score =  109 bits (273), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 83/278 (29%), Positives = 142/278 (51%), Gaps = 25/278 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+P+
Sbjct: 60  IQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGVPL 118

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++    +  R 
Sbjct: 119 LDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRE 176

Query: 136 FFNLRRLKGHL--------QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              + R K HL        +A        + +  +  K     ++++++N   A   SL+
Sbjct: 177 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTA---SLD 233

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS-MSVLNPRERRIFEAR 246
           A ++     +S   D L  D        ++  E +     LTR+ +S L+ + R + E R
Sbjct: 234 APLDLD--PASSLLDLLPDDQSQSPDAEVQHRELET----LTRAWLSRLSDKHRHVIE-R 286

Query: 247 RLQEN---PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   N   P TLE L+ E  ++RERVRQI+  A  +++
Sbjct: 287 RFGLNHIEPATLEELADEMGLTRERVRQIQQEALVRLK 324


>gi|161524626|ref|YP_001579638.1| RNA polymerase sigma factor RpoS [Burkholderia multivorans ATCC
           17616]
 gi|189350618|ref|YP_001946246.1| RNA polymerase sigma factor RpoS [Burkholderia multivorans ATCC
           17616]
 gi|221212761|ref|ZP_03585737.1| RNA polymerase sigma factor RpoS [Burkholderia multivorans CGD1]
 gi|160342055|gb|ABX15141.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia multivorans
           ATCC 17616]
 gi|189334640|dbj|BAG43710.1| RNA polymerase sigma factor RpoS [Burkholderia multivorans ATCC
           17616]
 gi|221166974|gb|EED99444.1| RNA polymerase sigma factor RpoS [Burkholderia multivorans CGD1]
          Length = 361

 Score =  109 bits (273), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 83/278 (29%), Positives = 142/278 (51%), Gaps = 25/278 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+P+
Sbjct: 83  IQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGVPL 141

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++    +  R 
Sbjct: 142 LDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRE 199

Query: 136 FFNLRRLKGHL--------QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              + R K HL        +A        + +  +  K     ++++++N   A   SL+
Sbjct: 200 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTA---SLD 256

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS-MSVLNPRERRIFEAR 246
           A ++     +S   D L  D        ++  E +     LTR+ +S L+ + R + E R
Sbjct: 257 APLDLD--PASSLLDLLPDDQSQSPDAEVQHRELET----LTRAWLSRLSDKHRHVIE-R 309

Query: 247 RLQEN---PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   N   P TLE L+ E  ++RERVRQI+  A  +++
Sbjct: 310 RFGLNHIEPATLEELADEMGLTRERVRQIQQEALVRLK 347


>gi|170703618|ref|ZP_02894360.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia ambifaria
           IOP40-10]
 gi|170131475|gb|EDT00061.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia ambifaria
           IOP40-10]
          Length = 361

 Score =  109 bits (273), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 83/278 (29%), Positives = 142/278 (51%), Gaps = 25/278 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+P+
Sbjct: 83  IQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGVPL 141

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++    +  R 
Sbjct: 142 LDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRE 199

Query: 136 FFNLRRLKGHL--------QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              + R K HL        +A        + +  +  K     ++++++N   A   SL+
Sbjct: 200 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTA---SLD 256

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS-MSVLNPRERRIFEAR 246
           A ++     +S   D L  D        ++  E +     LTR+ +S L+ + R + E R
Sbjct: 257 APLDLD--PASSLLDLLPDDQSQSPDAEVQHRELET----LTRAWLSRLSDKHRHVIE-R 309

Query: 247 RLQEN---PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   N   P TLE L+ E  ++RERVRQI+  A  +++
Sbjct: 310 RFGLNHIEPATLEELADEMGLTRERVRQIQQEALVRLK 347


>gi|20330084|emb|CAD30008.1| RNA polymerase sigma factor [Burkholderia cepacia]
          Length = 362

 Score =  109 bits (273), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 83/278 (29%), Positives = 142/278 (51%), Gaps = 25/278 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+P+
Sbjct: 84  IQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGVPL 142

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++    +  R 
Sbjct: 143 LDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRE 200

Query: 136 FFNLRRLKGHL--------QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              + R K HL        +A        + +  +  K     ++++++N   A   SL+
Sbjct: 201 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTA---SLD 257

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS-MSVLNPRERRIFEAR 246
           A ++     +S   D L  D        ++  E +     LTR+ +S L+ + R + E R
Sbjct: 258 APLDLD--PASSLLDLLPDDQSQSPDAEVQHRELET----LTRAWLSRLSDKHRHVIE-R 310

Query: 247 RLQEN---PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   N   P TLE L+ E  ++RERVRQI+  A  +++
Sbjct: 311 RFGLNHIEPATLEELADEMGLTRERVRQIQQEALVRLK 348


>gi|89092114|ref|ZP_01165069.1| RNA polymerase sigma factor RpoS [Oceanospirillum sp. MED92]
 gi|89083849|gb|EAR63066.1| RNA polymerase sigma factor RpoS [Oceanospirillum sp. MED92]
          Length = 339

 Score =  109 bits (273), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 85/278 (30%), Positives = 142/278 (51%), Gaps = 29/278 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE V   R    GD +A  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 70  YLNEIGFSPLLSAEEE-VYFSRLALKGDEAARKRMIESNLRLVVKIARRYINRGLTLLDL 128

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 129 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 187

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA------GDESLNALINS 192
           LR  +   Q + D+   PE++  +  K   +   ++ +N R++      G +S  +L+++
Sbjct: 188 LRAARELAQKL-DHEPSPEEIAELVDKPVENVERMLGLNERVSSVDTPMGKDSDKSLLDT 246

Query: 193 -SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             D  SS     L               +  N    L R +  L  +   +  +RR    
Sbjct: 247 IPDTVSSDPATLL---------------QNSNISGNLDRWLDALPEKHAEVL-SRRFGLR 290

Query: 252 PV---TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                TLE +  E  ++RERVRQI+  A +K+++ ++K
Sbjct: 291 GYEMSTLEEVGKEIGLTRERVRQIQVEALRKLRDIVEK 328


>gi|331006084|ref|ZP_08329420.1| RNA polymerase sigma factor RpoS [gamma proteobacterium IMCC1989]
 gi|330420121|gb|EGG94451.1| RNA polymerase sigma factor RpoS [gamma proteobacterium IMCC1989]
          Length = 342

 Score =  109 bits (273), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 89/280 (31%), Positives = 144/280 (51%), Gaps = 31/280 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A++  + G+ +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 71  YLNEIGFSPLLSAEEEVFFARKSLK-GEEAARKRMIESNLRLVVKISRRYVNRGLALLDL 129

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 130 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 188

Query: 139 LR-------RLKGHLQAITDNNLKPEQVVAIAKKLNVSES-EVISMNCRLAGDESLNALI 190
           LR       +L     A    NL  + V  + K L ++E    I +N    GD++L+  I
Sbjct: 189 LRAARELSQKLDHEPSAEEIANLLDKPVADVEKMLGLNERVNSIDVNIGPQGDKTLSDTI 248

Query: 191 ---NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
              + SD  S      +    DG    L EK+     R +L R   +      R +E   
Sbjct: 249 PDQHVSDPVSLLQDSDMSASIDGWLTELTEKQ-----REVLCRRFGL------RGYETS- 296

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
                 TLE +  E  ++RERVRQI+  A K++++ ++ Q
Sbjct: 297 ------TLEEVGREIGLTRERVRQIQVEALKRLKDIMELQ 330


>gi|254252249|ref|ZP_04945567.1| Sigma-70 region 2 [Burkholderia dolosa AUO158]
 gi|124894858|gb|EAY68738.1| Sigma-70 region 2 [Burkholderia dolosa AUO158]
          Length = 361

 Score =  109 bits (273), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 83/278 (29%), Positives = 142/278 (51%), Gaps = 25/278 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+P+
Sbjct: 83  IQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGVPL 141

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++    +  R 
Sbjct: 142 LDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRE 199

Query: 136 FFNLRRLKGHLQ--------AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              + R K HL+        A        + +  +  K     ++++++N   A   SL+
Sbjct: 200 LNQVLRAKRHLEKNSMSTGDAAERREASIDDIAYLTGKTAEEVTDILALNEHTA---SLD 256

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS-MSVLNPRERRIFEAR 246
           A ++     +S   D L  D        ++  E +     LTR+ +S L+ + R + E R
Sbjct: 257 APLDLD--PASSLLDLLPDDQSQSPDAEVQHRELET----LTRAWLSRLSDKHRHVIE-R 309

Query: 247 RLQEN---PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   N   P TLE L+ E  ++RERVRQI+  A  +++
Sbjct: 310 RFGLNHIEPATLEELADEMGLTRERVRQIQQEALVRLK 347


>gi|28211633|ref|NP_782577.1| RNA polymerase sigma factor RpoD [Clostridium tetani E88]
 gi|28204075|gb|AAO36514.1| RNA polymerase sigma factor rpoD [Clostridium tetani E88]
          Length = 366

 Score =  109 bits (273), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 84/265 (31%), Positives = 134/265 (50%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  +EE  LA+R  E G+L A  +L  ++LRLVV IA  Y G G+   ++
Sbjct: 100 YLKEIGKVPLLTSEEEVDLAQRI-EAGELKARKKLAEANLRLVVSIAKRYVGRGMLFLDL 158

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 159 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 216

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L         PE+   IAK++ +S   V  +        SL   I   ++  S
Sbjct: 217 LIRVSRQLLQELGREPTPEE---IAKEMEISVDRVREIMKIAQEPVSLETPIG--EEEDS 271

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++  D              K +   L   +  L PRE ++   R   ++    TLE
Sbjct: 272 HLGDFIPDDDALAPAEAAAFTMLKEQ---LINVLDTLTPREEKVLRLRFGLDDGRARTLE 328

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF V+RER+RQIEA+A +K++
Sbjct: 329 EVGKEFNVTRERIRQIEAKALRKLR 353


>gi|315647917|ref|ZP_07901018.1| RNA polymerase, sigma 70 subunit, RpoD subfamily protein
           [Paenibacillus vortex V453]
 gi|315276563|gb|EFU39906.1| RNA polymerase, sigma 70 subunit, RpoD subfamily protein
           [Paenibacillus vortex V453]
          Length = 316

 Score =  109 bits (273), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 88/274 (32%), Positives = 138/274 (50%), Gaps = 31/274 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   EE  L+KR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 50  YLKEIGRVPLLSADEEVELSKRI-EEGDEEAKRRLAEANLRLVVSIARRYAGRGMQFLDL 108

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-- 132
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 109 IQEGNMGLIKAVEKFDYSKGFKFSTYATWWIRQAITRSIADQARTIRIPVHMVETINKLV 168

Query: 133 ---KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
              ++L   L R     +   + ++ PE+V  I K   VS+ E +S+   +    D +L 
Sbjct: 169 RVSRQLLQELGREPTPEEIGKEMDITPEKVREIQK---VSQ-EPVSLETPVGEESDSNLG 224

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  +           +  E+VL    ER+   N+L     + + R R       
Sbjct: 225 DFIEDQDALAPADAAAFELLKEQLEEVLDTLTEREE--NVLRLRFGLEDGRTR------- 275

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                 TLE +   F V+RER+RQIEA+A +K++
Sbjct: 276 ------TLEEVGQVFGVTRERIRQIEAKALRKLR 303


>gi|299822900|ref|ZP_07054786.1| DNA-directed RNA polymerase sigma subunit RpoD [Listeria grayi DSM
           20601]
 gi|299816429|gb|EFI83667.1| DNA-directed RNA polymerase sigma subunit RpoD [Listeria grayi DSM
           20601]
          Length = 389

 Score =  109 bits (273), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 87/276 (31%), Positives = 132/276 (47%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LAKR  E GD+ A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 123 YLKEIGRVNLLTADEEVALAKRI-ETGDIEAKGRLAEANLRLVVSIAKRYVGRGMLFLDL 181

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 182 IQEGNMGLMKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 241

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q+ L  +L R     +   + +L  E+V  I K       E +S+   +    D  L 
Sbjct: 242 RVQRSLLQDLGRDPSPEEIGEEMDLPTEKVREILK----IAQEPVSLETPIGEEDDSHLG 297

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 298 DFIEDQEATSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 340

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 341 GLDDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLR 376


>gi|189500956|ref|YP_001960426.1| RNA polymerase, sigma 70 subunit, RpoD family [Chlorobium
           phaeobacteroides BS1]
 gi|189496397|gb|ACE04945.1| RNA polymerase, sigma 70 subunit, RpoD family [Chlorobium
           phaeobacteroides BS1]
          Length = 299

 Score =  109 bits (273), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 89/301 (29%), Positives = 156/301 (51%), Gaps = 39/301 (12%)

Query: 9   IVNGE-IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS-----------AAHRLVTS 56
           I N E + L RY+ EI K  +L  ++E  L K  +   D+            A  +L+  
Sbjct: 10  ITNRESLSLDRYLQEIGKYELLTAEDEVKLTKAIKAGYDMPVDTTEYKRAKRALDKLIKG 69

Query: 57  HLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM--- 113
           +LR VV +A  Y+  GL + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++   
Sbjct: 70  NLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQA 129

Query: 114 ---QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
              Q  I+R   L ++GT     + +  L +     +   D N K      +A  L++ +
Sbjct: 130 LAEQSRIVR-LPLNRVGTLNKISKAYSQLEQ-----EYERDPNTKE-----LANLLDM-D 177

Query: 171 SEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           S+ ++   ++AG   S++A     D N  +  D L  D    +  L     R +    + 
Sbjct: 178 SQDVADTLKIAGRHVSVDAPFAQGDDN--RLLDVLQNDGHKPDHGLT----RDSLNLEVE 231

Query: 230 RSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           RS+SVL PRE  +  +      +NP+TLE +  +F+++RERVRQI+ +A K++++S   +
Sbjct: 232 RSLSVLAPREADVIRSYFGIGMDNPLTLEEIGEKFKLTRERVRQIKEKAIKRLRQSAYSK 291

Query: 288 V 288
           V
Sbjct: 292 V 292


>gi|253682266|ref|ZP_04863063.1| RNA polymerase sigma factor RpoD [Clostridium botulinum D str.
           1873]
 gi|253561978|gb|EES91430.1| RNA polymerase sigma factor RpoD [Clostridium botulinum D str.
           1873]
          Length = 368

 Score =  109 bits (273), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 79/265 (29%), Positives = 132/265 (49%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L   EE  LA+R  E GD+ A  +L  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGKVPLLSPDEEISLAQRI-EDGDMYAKKKLAEANLRLVVSIAKRYVGRGMLFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 161 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 218

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L        +PE++  I +       E++ +       E ++      ++  S
Sbjct: 219 LIRVSRQLLQELGREPQPEEIAKIMEMPVDKVREIMKI-----AQEPVSLETPIGEEEDS 273

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++  D              K +   L   +  L PRE ++   R   ++    TLE
Sbjct: 274 HLGDFIPDDEAPAPAEAAAFTMLKEQ---LINVLDTLTPREEKVLRLRFGLDDGRARTLE 330

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF V+RER+RQIEA+A +K++
Sbjct: 331 EVGKEFNVTRERIRQIEAKALRKLR 355


>gi|115351809|ref|YP_773648.1| RNA polymerase sigma factor RpoS [Burkholderia ambifaria AMMD]
 gi|115281797|gb|ABI87314.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia ambifaria
           AMMD]
          Length = 361

 Score =  109 bits (273), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 83/278 (29%), Positives = 142/278 (51%), Gaps = 25/278 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+P+
Sbjct: 83  IQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGVPL 141

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++    +  R 
Sbjct: 142 LDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRE 199

Query: 136 FFNLRRLKGHL--------QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              + R K HL        +A        + +  +  K     ++++++N   A   SL+
Sbjct: 200 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTA---SLD 256

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS-MSVLNPRERRIFEAR 246
           A ++     +S   D L  D        ++  E +     LTR+ +S L+ + R + E R
Sbjct: 257 APLDLD--PASSLLDLLPDDQSQSPDAEVQHRELET----LTRAWLSRLSDKHRHVIE-R 309

Query: 247 RLQEN---PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   N   P TLE L+ E  ++RERVRQI+  A  +++
Sbjct: 310 RFGLNHIEPATLEELADEMGLTRERVRQIQQEALVRLK 347


>gi|29654959|ref|NP_820651.1| RNA polymerase sigma factor [Coxiella burnetii RSA 493]
 gi|81788312|sp|Q9KI19|RPOS_COXBU RecName: Full=RNA polymerase sigma factor rpoS
 gi|7340285|gb|AAF61172.1|AF244357_1 stress response sigma factor RpoS [Coxiella burnetii]
 gi|29542228|gb|AAO91165.1| RNA polymerase sigma factor [Coxiella burnetii RSA 493]
          Length = 352

 Score =  109 bits (273), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 85/269 (31%), Positives = 141/269 (52%), Gaps = 13/269 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ E+   P+L  +EE  +A+R  + GD  A  +++ ++LRLVVKIA  Y   GLP  ++
Sbjct: 84  YLRELGFQPLLNAKEELKIARRVHK-GDPKARKQMIEANLRLVVKIARHYVNRGLPFLDL 142

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL+ AV+KFDPERGFR +TY+ WWI+  ++  I+     V++      K L   
Sbjct: 143 IEEGNLGLLTAVEKFDPERGFRFSTYATWWIRQTIERAIMNQSRTVRLPIHV-IKELNVY 201

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  K   Q + D+   PE V  +  K      E+  +        S++  I+   + S 
Sbjct: 202 LRTAKKLTQEV-DHEATPEDVAHLIDK---PVQEIRRIMDLAPSATSIDVPISEDGQKS- 256

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLE 256
              D L  D++     LI+  + ++    + R ++ L+ R R +   R  L EN   TLE
Sbjct: 257 -LVDTLADDNNIDPARLIQNVDLQDH---IERWLAQLDERHREVVILRFGLHENEKGTLE 312

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            +     ++RERVRQI+  A ++++  ++
Sbjct: 313 AVGKAVGLTRERVRQIQIDALQQLRHILE 341


>gi|330817175|ref|YP_004360880.1| Stationary phase sigma factor [Burkholderia gladioli BSR3]
 gi|327369568|gb|AEA60924.1| Stationary phase sigma factor [Burkholderia gladioli BSR3]
          Length = 366

 Score =  109 bits (273), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 83/278 (29%), Positives = 142/278 (51%), Gaps = 25/278 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+P+
Sbjct: 88  IQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGVPL 146

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++    +  R 
Sbjct: 147 LDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRE 204

Query: 136 FFNLRRLKGHL--------QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              + R K HL        +A        + +  +  K     ++++++N   A   SL+
Sbjct: 205 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTA---SLD 261

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS-MSVLNPRERRIFEAR 246
           A ++     +S   D L  D        ++  E +     LTR+ +S L+ + R + E R
Sbjct: 262 APLDLD--PASSLLDLLPDDQSQSPDAEVQHRELET----LTRAWLSRLSDKHRHVIE-R 314

Query: 247 RLQEN---PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   N   P TLE L+ E  ++RERVRQI+  A  +++
Sbjct: 315 RFGLNNIEPATLEELADEMGLTRERVRQIQQEALVRLK 352


>gi|296269171|ref|YP_003651803.1| RpoD subfamily RNA polymerase sigma-70 [Thermobispora bispora DSM
           43833]
 gi|296091958|gb|ADG87910.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobispora
           bispora DSM 43833]
          Length = 367

 Score =  109 bits (273), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 91/298 (30%), Positives = 146/298 (48%), Gaps = 40/298 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR--------------------EHGDL-----SAAHRL 53
           Y+ EI K+P+L  +EE  LAK                       E  DL      A  RL
Sbjct: 76  YLREIGKVPLLTAEEEVELAKAIEAGLFAEDKLCEKKAAGIECPELEDLVWEGIRAKQRL 135

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           + ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+
Sbjct: 136 IEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAI 195

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
              I      ++I    +       L R++  L         PE+   IAK++++    V
Sbjct: 196 TRAIADQARTIRI--PVHMVETINKLVRVQRQLHQDLGREPTPEE---IAKEMDLPVERV 250

Query: 174 ISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           + +  R+A +  SL + I   D   S   D++    D    V +E       ++ L   +
Sbjct: 251 VEIQ-RIAQEPVSLQSPIGEED---SDLGDFI---EDADAVVPLEAAAFILLQDHLDDIL 303

Query: 233 SVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           S L+ RE+RI + R      +P TLE +  EF V+RER+RQIE++   K++   + QV
Sbjct: 304 STLSEREQRIIQLRFGLADGHPRTLEEVGREFGVTRERIRQIESKTLAKLRHPTRAQV 361


>gi|320530863|ref|ZP_08031900.1| RNA polymerase sigma factor RpoD [Selenomonas artemidis F0399]
 gi|320136897|gb|EFW28842.1| RNA polymerase sigma factor RpoD [Selenomonas artemidis F0399]
          Length = 370

 Score =  109 bits (273), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 85/272 (31%), Positives = 136/272 (50%), Gaps = 13/272 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA+   E GD  A HRL  ++LRLVV IA  Y G G+   ++
Sbjct: 104 YLKEIGHVPLLTAEEEVELAQ-LMEAGDEEARHRLEEANLRLVVSIAKRYVGRGMLFLDL 162

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 163 IQEGNLGLLKAVEKFDYSKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 220

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L      + +PE+   IAK++ +S + V  +        SL   I   ++  S
Sbjct: 221 LVRISRQLLQELGRDPRPEE---IAKEMGISVARVHEIMKIAQEPVSLETPIG--EEEDS 275

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++    D       E       R  L   +  L  RE+ +   R   E+    TLE
Sbjct: 276 HLGDFI---EDEAAPAPAEAASFMLLREQLEEVLETLTDREKNVLRLRFGLEDGRSRTLE 332

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +   F V+RER+RQIEA+A +K++   + +V
Sbjct: 333 EVGQSFGVTRERIRQIEAKALRKLRHPSRSKV 364


>gi|313897089|ref|ZP_07830636.1| RNA polymerase sigma factor RpoD [Selenomonas sp. oral taxon 137
           str. F0430]
 gi|312974536|gb|EFR40004.1| RNA polymerase sigma factor RpoD [Selenomonas sp. oral taxon 137
           str. F0430]
          Length = 370

 Score =  109 bits (273), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 85/272 (31%), Positives = 136/272 (50%), Gaps = 13/272 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA+   E GD  A HRL  ++LRLVV IA  Y G G+   ++
Sbjct: 104 YLKEIGHVPLLTAEEEVELAQ-LMEAGDEEARHRLEEANLRLVVSIAKRYVGRGMLFLDL 162

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 163 IQEGNLGLLKAVEKFDYSKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 220

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L      + +PE+   IAK++ +S + V  +        SL   I   ++  S
Sbjct: 221 LVRISRQLLQELGRDPRPEE---IAKEMGISVARVHEIMKIAQEPVSLETPIG--EEEDS 275

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++    D       E       R  L   +  L  RE+ +   R   E+    TLE
Sbjct: 276 HLGDFI---EDEAAPAPAEAASFMLLREQLEEVLETLTDREKNVLRLRFGLEDGRSRTLE 332

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +   F V+RER+RQIEA+A +K++   + +V
Sbjct: 333 EVGQSFGVTRERIRQIEAKALRKLRHPSRSKV 364


>gi|163784595|ref|ZP_02179438.1| RNA polymerase sigma factor RpoS [Hydrogenivirga sp. 128-5-R1-1]
 gi|159880134|gb|EDP73795.1| RNA polymerase sigma factor RpoS [Hydrogenivirga sp. 128-5-R1-1]
          Length = 154

 Score =  109 bits (273), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 50/116 (43%), Positives = 80/116 (68%), Gaps = 1/116 (0%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           N E G++ Y+ +I  IP++  +EE  LAK+ +E GD  A  +LV ++LR V+ +A  Y G
Sbjct: 5   NYEEGVTYYLKQIADIPLISPEEEKNLAKKIKE-GDKQALDKLVKANLRFVINVAKNYIG 63

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           YG+P  E++S GNIGL++A K+FDP+RG R  +Y++WWIK ++ + I +   L++I
Sbjct: 64  YGVPFQELISAGNIGLIEAAKRFDPDRGVRFISYAIWWIKQSIFQTIQQQKDLIRI 119


>gi|199598416|ref|ZP_03211835.1| RNA polymerase sigma factor RpoD [Lactobacillus rhamnosus HN001]
 gi|258508506|ref|YP_003171257.1| RNA polymerase sigma factor RpoD [Lactobacillus rhamnosus GG]
 gi|199590735|gb|EDY98822.1| RNA polymerase sigma factor RpoD [Lactobacillus rhamnosus HN001]
 gi|257148433|emb|CAR87406.1| RNA polymerase sigma factor [Lactobacillus rhamnosus GG]
 gi|259649816|dbj|BAI41978.1| RNA polymerase sigma factor RpoD [Lactobacillus rhamnosus GG]
          Length = 416

 Score =  109 bits (273), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 85/275 (30%), Positives = 134/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 150 YLKEIGRVSLLTADEEVALALKI-EQGDQEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 208

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 209 IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 268

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + ++  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 269 RIQRQLLQDLGREPTPEEIGAEMDMPTEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 324

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S +       DH   E +          +  L   +  L  RE  +   R 
Sbjct: 325 DFIEDQDATSPE-------DHASYELL----------KEQLESVLDTLTDREENVLRLRF 367

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 368 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 402


>gi|167836384|ref|ZP_02463267.1| RNA polymerase sigma factor RpoS [Burkholderia thailandensis
           MSMB43]
          Length = 366

 Score =  109 bits (273), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 83/278 (29%), Positives = 142/278 (51%), Gaps = 25/278 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+P+
Sbjct: 84  IQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGVPL 142

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++    +  R 
Sbjct: 143 LDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRE 200

Query: 136 FFNLRRLKGHLQ--------AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              + R K HL+        A        + +  +  K     ++++++N   A   SL+
Sbjct: 201 LNQVLRAKRHLEKNSLSTGAAAERREASIDDIAYLTGKTAEEVTDILALNEHTA---SLD 257

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS-MSVLNPRERRIFEAR 246
           A ++     +S   D L  D        ++  E +     LTR+ +S L+ + R + E R
Sbjct: 258 APLDLD--PASSLLDLLPDDQSQSPDAEVQHRELET----LTRAWLSRLSDKHRHVIE-R 310

Query: 247 RLQEN---PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   N   P TLE L+ E  ++RERVRQI+  A  +++
Sbjct: 311 RFGLNHIEPATLEELADEMGLTRERVRQIQQEALVRLK 348


>gi|116071891|ref|ZP_01469159.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. BL107]
 gi|116065514|gb|EAU71272.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. BL107]
          Length = 355

 Score =  109 bits (273), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 79/248 (31%), Positives = 124/248 (50%), Gaps = 37/248 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLVV +A  Y+  G+ I ++V EG +GL +AV+KFDP RGFR +TY+ WW
Sbjct: 115 AKDHMIQANLRLVVAVAKKYQQRGMEILDLVQEGTLGLERAVEKFDPTRGFRFSTYAYWW 174

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  M   I      +++     +K     L R+K   Q I  N  +   +  +A++L +
Sbjct: 175 IRQGMTRAIATQSRTIRLPVHVTEK-----LNRIKRVQQEIASNEGRIASIADLARELGI 229

Query: 169 SESEV----------ISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYD--HDGQEQV 214
           SE  V          +S++ R+  D+   L  LI          ++ L +D  H+  E +
Sbjct: 230 SEDTVRQTLERVPRSVSLDSRVGKDQDTQLGDLIEDGKATP---EETLTHDELHNDLEGL 286

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
           L E         + TR  +VL    RR F      + P TL  +  E ++SRERVRQIE 
Sbjct: 287 LDE---------LTTREAAVL----RRRFGLE--DDTPQTLAQIGEELKLSRERVRQIET 331

Query: 275 RAFKKVQE 282
           RA  K+++
Sbjct: 332 RALLKLRQ 339


>gi|78186275|ref|YP_374318.1| RNA polymerase sigma-70 factor [Chlorobium luteolum DSM 273]
 gi|78166177|gb|ABB23275.1| RNA polymerase sigma-70 factor [Chlorobium luteolum DSM 273]
          Length = 299

 Score =  109 bits (273), Expect = 4e-22,   Method: Compositional matrix adjust.
 Identities = 88/300 (29%), Positives = 155/300 (51%), Gaps = 47/300 (15%)

Query: 9   IVNGE-IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS-----------AAHRLVTS 56
           I N E + L RY+ EI K  +L   +E  L K  +E  D+            A  +L+  
Sbjct: 10  ITNRESLSLDRYLQEIGKYDLLTADDEVRLTKAIKEGFDMPVDTTEYKRAKRALDKLIKG 69

Query: 57  HLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM--- 113
           +LR VV +A  Y+  GL + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++   
Sbjct: 70  NLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQA 129

Query: 114 ---QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
              Q  I+R   L ++GT     + +  L +     +   D N K      +A  L++ +
Sbjct: 130 LAEQSRIVR-LPLNRVGTLNKISKAYSQLEQ-----EFERDPNTKE-----LANLLDM-D 177

Query: 171 SEVISMNCRLAGDE-SLNALINSSDKN---SSQWQDWLVYDHD-GQEQVLIEKEERKNRR 225
           S+ ++   ++AG   S++A     D N        D  + DH   ++ + +E E      
Sbjct: 178 SQDVADTLKIAGRHVSVDAPFAQGDDNRLLDVLQNDGHLPDHGLNRDSLTLEVE------ 231

Query: 226 NMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               RS+SVL PRE  + ++      +NP+TLE +  +F+++RERVRQI+ +A ++++ S
Sbjct: 232 ----RSLSVLAPREADVIKSYFGIGMDNPLTLEEIGEKFKLTRERVRQIKEKAIRRLRTS 287


>gi|258539717|ref|YP_003174216.1| RNA polymerase sigma factor RpoD [Lactobacillus rhamnosus Lc 705]
 gi|257151393|emb|CAR90365.1| RNA polymerase sigma factor [Lactobacillus rhamnosus Lc 705]
          Length = 416

 Score =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 85/275 (30%), Positives = 134/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 150 YLKEIGRVSLLTTDEEVALALKI-EQGDQEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 208

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 209 IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 268

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + ++  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 269 RIQRQLLQDLGREPTPEEIGAEMDMPTEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 324

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S +       DH   E +          +  L   +  L  RE  +   R 
Sbjct: 325 DFIEDQDATSPE-------DHASYELL----------KEQLESVLDTLTDREENVLRLRF 367

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 368 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 402


>gi|116494985|ref|YP_806719.1| RNA polymerase sigma factor RpoD [Lactobacillus casei ATCC 334]
 gi|191638497|ref|YP_001987663.1| RNA polymerase sigma factor RpoD [Lactobacillus casei BL23]
 gi|227535009|ref|ZP_03965058.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           paracasei subsp. paracasei ATCC 25302]
 gi|301066553|ref|YP_003788576.1| DNA-directed RNA polymerase sigma70/sigma32 subunit [Lactobacillus
           casei str. Zhang]
 gi|116105135|gb|ABJ70277.1| RNA polymerase, sigma 70 subunit, RpoD [Lactobacillus casei ATCC
           334]
 gi|190712799|emb|CAQ66805.1| RNA polymerase sigma factor [Lactobacillus casei BL23]
 gi|227187324|gb|EEI67391.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           paracasei subsp. paracasei ATCC 25302]
 gi|300438960|gb|ADK18726.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Lactobacillus casei str. Zhang]
 gi|327382532|gb|AEA54008.1| RNA polymerase, sigma 70 subunit, RpoD [Lactobacillus casei LC2W]
 gi|327385729|gb|AEA57203.1| RNA polymerase, sigma 70 subunit, RpoD [Lactobacillus casei BD-II]
          Length = 422

 Score =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 85/275 (30%), Positives = 134/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 156 YLKEIGRVSLLTADEEVALALKI-EQGDQEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 214

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 215 IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 274

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + ++  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 275 RIQRQLLQDLGREPTPEEIGAEMDMPTEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 330

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S +       DH   E +          +  L   +  L  RE  +   R 
Sbjct: 331 DFIEDQDATSPE-------DHASYELL----------KEQLESVLDTLTDREENVLRLRF 373

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 374 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 408


>gi|172060780|ref|YP_001808432.1| RNA polymerase sigma factor RpoS [Burkholderia ambifaria MC40-6]
 gi|171993297|gb|ACB64216.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia ambifaria
           MC40-6]
          Length = 361

 Score =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 83/278 (29%), Positives = 142/278 (51%), Gaps = 25/278 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+P+
Sbjct: 83  IQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGVPL 141

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++    +  R 
Sbjct: 142 LDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRE 199

Query: 136 FFNLRRLKGHL--------QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              + R K HL        +A        + +  +  K     ++++++N   A   SL+
Sbjct: 200 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTA---SLD 256

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS-MSVLNPRERRIFEAR 246
           A ++     +S   D L  D        ++  E +     LTR+ +S L+ + R + E R
Sbjct: 257 APLDLD--PASSLLDLLPDDQSQSPDAEVQHRELET----LTRAWLSRLSDKHRHVIE-R 309

Query: 247 RLQEN---PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   N   P TLE L+ E  ++RERVRQI+  A  +++
Sbjct: 310 RFGLNHIEPATLEELADEMGLTRERVRQIQQEALVRLK 347


>gi|327440913|dbj|BAK17278.1| DNA-directed RNA polymerase, sigma subunit [Solibacillus silvestris
           StLB046]
          Length = 375

 Score =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 86/276 (31%), Positives = 137/276 (49%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   +E  LA+R  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 109 YLKEIGRVDLLSADQEIRLAERI-EQGDEEARKRLAEANLRLVVSIAKRYVGRGMLFLDL 167

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 168 IQEGNMGLIKAVEKFDHRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 227

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I   L +++ E +S+   +    D  L 
Sbjct: 228 RVQRQLLQDLGREPSPEEIGEEMDLTPEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 283

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I  S+  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 284 DFIEDSEAQSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 326

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 327 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 362


>gi|320527310|ref|ZP_08028495.1| RNA polymerase sigma factor RpoD [Solobacterium moorei F0204]
 gi|320132334|gb|EFW24879.1| RNA polymerase sigma factor RpoD [Solobacterium moorei F0204]
          Length = 468

 Score =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 85/282 (30%), Positives = 141/282 (50%), Gaps = 46/282 (16%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L+ ++E  +AKR  E GD  A + L++S+LRLVV IA  Y G G+   ++
Sbjct: 200 YLKEIGRVPLLKPEDEPEIAKRI-EEGDEEARNILISSNLRLVVSIAKKYVGRGMLFLDL 258

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT---------T 129
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I           T
Sbjct: 259 IQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLT 318

Query: 130 ANQKRLFFNLRR------LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-- 181
             Q++L   L R      +   ++ I+   ++  Q +A+         E +S+   +   
Sbjct: 319 RVQRQLVQELGRDPSAEEISQRMEGISPEKVREIQKIAL---------EPVSLETPIGEE 369

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
            D  L   I   DK +      L  D     Q+L         ++ +   +S L  RE +
Sbjct: 370 DDSHLGDFIE--DKEA------LSPDQYASNQLL---------KDEINSVLSGLTEREEK 412

Query: 242 IFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   R         TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 413 VLRLRFGLYDGRTRTLEEVGREFSVTRERIRQIEAKALRKLK 454


>gi|291166412|gb|EFE28458.1| RNA polymerase sigma factor RpoD [Filifactor alocis ATCC 35896]
          Length = 372

 Score =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 83/264 (31%), Positives = 139/264 (52%), Gaps = 13/264 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KI +L  +EE  LA++  +  +L A  +LV ++LRLVV IA  Y G G+   ++
Sbjct: 106 YLKEIGKISLLSAEEEIELAQKMDQGSEL-AKKKLVEANLRLVVSIAKRYVGRGMLFLDL 164

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 165 IQEGNLGLIKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 222

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R++  L        +PE+   I+K +++S  ++  +        SL   I   ++  S
Sbjct: 223 LIRVQRQLLQELGREPRPEE---ISKVMDMSVEKIREIQKISQEPVSLETPI--GEEEDS 277

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++    D       E       +  L   +S LN RE+++ + R   E+    TLE
Sbjct: 278 HLGDFI---PDDDALAPSEAAAYSLLKEQLEEVLSTLNEREQKVLKLRFGLEDGRTRTLE 334

Query: 257 NLSSEFEVSRERVRQIEARAFKKV 280
            +  EF+V+RER+RQIEA+A +K+
Sbjct: 335 EVGKEFDVTRERIRQIEAKALRKL 358


>gi|170017101|ref|YP_001728020.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Leuconostoc citreum KM20]
 gi|169803958|gb|ACA82576.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Leuconostoc citreum KM20]
          Length = 432

 Score =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 86/274 (31%), Positives = 136/274 (49%), Gaps = 31/274 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L+  EE  +AKR  E GD+ A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 162 YLKEIGRVNLLKGDEEINIAKRI-EDGDVEAKQELAEANLRLVVSIAKRYVGRGMQFLDL 220

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 221 IQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 280

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             Q++L  +L R     +   + +L P++V  I   L +++  V           SL   
Sbjct: 281 RIQRQLLQDLGREPLPEEIGAEMDLTPDKVREI---LKIAQEPV-----------SLETP 326

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   D   S   D++    D +     +    +  R+ L   +  L  RE  +   R   
Sbjct: 327 IGEED--DSHLGDFI---EDNEAISPADSAAYEMLRDQLESVLETLTDREENVLRLRFGL 381

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           E+    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 382 EDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLR 415


>gi|325521809|gb|EGD00541.1| RNA polymerase sigma factor RpoS [Burkholderia sp. TJI49]
          Length = 339

 Score =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 83/278 (29%), Positives = 142/278 (51%), Gaps = 25/278 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+P+
Sbjct: 61  IQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGVPL 119

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++    +  R 
Sbjct: 120 LDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRE 177

Query: 136 FFNLRRLKGHL--------QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              + R K HL        +A        + +  +  K     ++++++N   A   SL+
Sbjct: 178 LNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTA---SLD 234

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS-MSVLNPRERRIFEAR 246
           A ++     +S   D L  D        ++  E +     LTR+ +S L+ + R + E R
Sbjct: 235 APLDLD--PASSLLDLLPDDQSQSPDAEVQHRELET----LTRAWLSRLSDKHRHVIE-R 287

Query: 247 RLQEN---PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   N   P TLE L+ E  ++RERVRQI+  A  +++
Sbjct: 288 RFGLNHIEPATLEELADEMGLTRERVRQIQQEALVRLK 325


>gi|323345487|ref|ZP_08085710.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella oralis
           ATCC 33269]
 gi|323093601|gb|EFZ36179.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella oralis
           ATCC 33269]
          Length = 290

 Score =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 81/273 (29%), Positives = 144/273 (52%), Gaps = 16/273 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGL 73
           L +Y+ EI ++PM+   EE  LA+  R+ G     A  +L+ ++LR VV +A  Y+  GL
Sbjct: 18  LDKYLLEIGRLPMVSIDEETELAQLIRKGGKEGERAKEKLINANLRFVVSVAKQYQHQGL 77

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V++    NQ 
Sbjct: 78  SLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRL--PLNQ- 134

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINS 192
                L ++   +      + +      +A   N+ E++ IS   R      S++A  + 
Sbjct: 135 --VGALSKINSEVAKFEQEHQRRPSTQELASLTNIDENK-ISQTMRADNHHMSIDAPFSD 191

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS-VLNPRERRIF-EARRLQE 250
            D+NS    D L    D +   ++++E   +    L  +M+  L PRE  I  E+  +  
Sbjct: 192 DDENS--MADVLASGDDSRADRIVDRESMNSD---LDDAMANALKPREVAILKESFGIGC 246

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               LE +  EF ++RERVRQI  ++ +K++ES
Sbjct: 247 TEKGLEEIGEEFGLTRERVRQIREKSIQKLRES 279


>gi|239631415|ref|ZP_04674446.1| DNA-directed RNA polymerase [Lactobacillus paracasei subsp.
           paracasei 8700:2]
 gi|239525880|gb|EEQ64881.1| DNA-directed RNA polymerase [Lactobacillus paracasei subsp.
           paracasei 8700:2]
          Length = 352

 Score =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 85/275 (30%), Positives = 134/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 86  YLKEIGRVSLLTADEEVALALKI-EQGDQEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 144

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 145 IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 204

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + ++  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 205 RIQRQLLQDLGREPTPEEIGAEMDMPTEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 260

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S +       DH   E +          +  L   +  L  RE  +   R 
Sbjct: 261 DFIEDQDATSPE-------DHASYELL----------KEQLESVLDTLTDREENVLRLRF 303

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 304 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 338


>gi|149907981|ref|ZP_01896649.1| sigma S (sigma 38) factor of RNA polymerase, major sigma
           factorduring stationary phase [Moritella sp. PE36]
 gi|149808987|gb|EDM68918.1| sigma S (sigma 38) factor of RNA polymerase, major sigma
           factorduring stationary phase [Moritella sp. PE36]
          Length = 284

 Score =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 84/280 (30%), Positives = 144/280 (51%), Gaps = 20/280 (7%)

Query: 9   IVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           + N    L  Y+ ++ K   +L K++EY  A    E GD  A  R++ S+LRLV+ IA  
Sbjct: 3   LFNESSALDLYMQQVNKTSVLLTKEQEYDTAIAVHE-GDQKARQRMIQSNLRLVINIAKR 61

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK-- 125
           Y+   L + +++ EGN GL+ AV+KFD  +GFR +TY++WWIK  ++ +I+     ++  
Sbjct: 62  YQHTSLSLVDIIQEGNTGLIHAVEKFDATKGFRFSTYAVWWIKNNIERFIMNQSRTIRVP 121

Query: 126 --IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
             IG T   KR+  N R     L+   +N+LK      IA  L +   +V+++      +
Sbjct: 122 IHIGKTY--KRILKNAREKVLDLKC--NNDLKK-----IAINLELEFDDVVNVLSYYFTE 172

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SL+  I + + +++   D +    D       ++ E+ +  + L   ++ L  R+R I 
Sbjct: 173 ASLDKTIATKNDSNTALVDLI---EDSSICKPNDEIEKTDTSSYLITVLNHLCDRDREII 229

Query: 244 EAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           E R    +E P TL  +     +SRERVRQI   + +K++
Sbjct: 230 ELRFGLGREEPQTLNAIGERLFMSRERVRQIITASLQKIK 269


>gi|5804831|emb|CAB53534.1| RpoS protein [Escherichia coli O157:H7]
 gi|332087634|gb|EGI92761.1| RNA polymerase sigma factor RpoS [Shigella dysenteriae 155-74]
          Length = 298

 Score =  109 bits (273), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 80/263 (30%), Positives = 131/263 (49%), Gaps = 24/263 (9%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE V   R    GD+++  R++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+K
Sbjct: 42  EEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEK 101

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFFNLRRLKGH------ 145
           FDPERGFR +TY+ WWI+  ++  I+     +++      +  ++    R   H      
Sbjct: 102 FDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEP 161

Query: 146 -LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + I +   KP   V+   +LN     + S++  L GD     L   +D+  +  +D  
Sbjct: 162 SAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLDILADEKENGPEDTT 218

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             D   Q  V    E    +R +L R   +L       +EA        TLE++  E  +
Sbjct: 219 QDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA-------ATLEDVGREIGL 265

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RERVRQI+    ++++E +Q Q
Sbjct: 266 TRERVRQIQVEGLRRLREILQTQ 288


>gi|229552308|ref|ZP_04441033.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           rhamnosus LMS2-1]
 gi|229314290|gb|EEN80263.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           rhamnosus LMS2-1]
          Length = 416

 Score =  109 bits (272), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 85/275 (30%), Positives = 134/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 150 YLKEIGRVSLLTADEEVALALKI-EQGDQEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 208

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 209 IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 268

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + ++  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 269 RIQRQLLQDLGREPTPEEIGAEMDMPTEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 324

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S +       DH   E +          +  L   +  L  RE  +   R 
Sbjct: 325 DFIEDQDATSPE-------DHASYELL----------KEQLESVLDTLTDREENVLRLRF 367

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 368 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 402


>gi|225575013|ref|ZP_03783623.1| hypothetical protein RUMHYD_03093 [Blautia hydrogenotrophica DSM
           10507]
 gi|225037764|gb|EEG48010.1| hypothetical protein RUMHYD_03093 [Blautia hydrogenotrophica DSM
           10507]
          Length = 374

 Score =  109 bits (272), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 88/274 (32%), Positives = 138/274 (50%), Gaps = 31/274 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+ +L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 108 YLKEIGKVNLLTAEEEIELAKRM-EEGDEDAKKRLAEANLRLVVSIAKRYVGRGMLFLDL 166

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 167 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINK-- 224

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               L R+   L         PE+   IAK++ +S   V  +        SL   I   +
Sbjct: 225 ----LIRVSRQLLQELGREPTPEE---IAKEMEMSVDRVREILKISQEPVSLETPIG--E 275

Query: 195 KNSSQWQDWLVYDH-----DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           +  S   D++  D+     D     L+        +  L   +S L  RE+++   R   
Sbjct: 276 EEDSHLGDFIQDDNVPVPADAAAFTLL--------KEQLVEVLSTLTDREQKVLRLRFGL 327

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 328 DDGRARTLEEVGKEFNVTRERIRQIEAKALRKLR 361


>gi|4929285|gb|AAD33933.1|AF144608_2 RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus]
          Length = 321

 Score =  109 bits (272), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 84/265 (31%), Positives = 139/265 (52%), Gaps = 31/265 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 57  YLGEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 115

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 116 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 174

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +   Q + D+    E++ A        ++K L ++E  + S++  + GD     L 
Sbjct: 175 LRTARELSQKL-DHEPTAEEIAAQLDIPVEDVSKMLRLNE-RISSVDTPIGGDGEKALLD 232

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
              D N+S   D  V   D             + ++ L   +  LNP+++ +  ARR   
Sbjct: 233 IIPDANNS---DPEVSTQD------------DDIKSSLIHWLEELNPKQKEVL-ARRFGL 276

Query: 248 LQENPVTLENLSSEFEVSRERVRQI 272
           L   P TLE +  E  ++RERVR++
Sbjct: 277 LGYEPSTLEEVGREIGLTRERVRRL 301


>gi|320104603|ref|YP_004180194.1| RNA polymerase sigma-38 subunit RpoS [Isosphaera pallida ATCC
           43644]
 gi|319751885|gb|ADV63645.1| RNA polymerase, sigma 38 subunit, RpoS [Isosphaera pallida ATCC
           43644]
          Length = 277

 Score =  109 bits (272), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 82/274 (29%), Positives = 143/274 (52%), Gaps = 19/274 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ EI ++ +L  +EE  LA R    GD +A  R+V ++LRLVV IA GY G GL +
Sbjct: 16  LETYLREINEMALLSAEEEKELAARI-AKGDKTARERMVRANLRLVVNIARGYVGKGLAL 74

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GL++AV+ FDP+ G R +TY+ +WIK +++  ++ +   ++I   A    L
Sbjct: 75  QDLIEEGNLGLLRAVEGFDPKVGTRFSTYASYWIKQSIKRALVNTAKPIRI--PAYMVEL 132

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
               RR    LQ   D   +      IA +L + + ++  +   +     +  L+  SD+
Sbjct: 133 LCKWRRAAIELQ---DRLGRTPTTDEIAHELRIPKKKLAIVKKAI----KVYNLVPQSDQ 185

Query: 196 NSSQWQ--DWLVYDHDGQEQV-LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN- 251
             S W   D L+ +      V ++E +  K    ++ R +  ++ RE  +   R   ++ 
Sbjct: 186 PESGWSLGDMLMDERTRPPDVEMVEADNLK----LVMRRLEEMDKREATVLRMRFGLDDQ 241

Query: 252 -PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            P TL+ +  +  ++RERVRQIE  A  K+  ++
Sbjct: 242 PPCTLKEIGEQLGLTRERVRQIENEALNKLSATL 275


>gi|75761907|ref|ZP_00741832.1| RNA polymerase sigma factor rpoD [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|74490615|gb|EAO53906.1| RNA polymerase sigma factor rpoD [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
          Length = 268

 Score =  109 bits (272), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 86/276 (31%), Positives = 133/276 (48%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 2   YLKEIGRVDLLSAEEEIRLATRI-EEGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 60

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 61  IQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 120

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I K       E +S+   +    D  L 
Sbjct: 121 RVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILK----IAQEPVSLETPIGEEDDSHLG 176

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 177 DFIEDQEATSPA-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 219

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 220 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 255


>gi|291444398|ref|ZP_06583788.1| RNA polymerase principal sigma factor hrdA [Streptomyces
           roseosporus NRRL 15998]
 gi|291347345|gb|EFE74249.1| RNA polymerase principal sigma factor hrdA [Streptomyces
           roseosporus NRRL 15998]
          Length = 395

 Score =  109 bits (272), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 90/295 (30%), Positives = 147/295 (49%), Gaps = 44/295 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRY------------------REHGDL--------SAAHR 52
           Y+ EI +IP+L   EE  LA+R                   R  GDL        +A  R
Sbjct: 102 YLREIGRIPLLTAAEEVELARRVEAGLFAEERLTGTPDLDSRLAGDLDRLVVMGRTAKRR 161

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY+ WWI+ A
Sbjct: 162 LIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIRQA 221

Query: 113 MQEYILRSWSLVKIGTTANQ--KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
           M   +      +++     +   R+    RRL      + +  ++P     IA +L+++ 
Sbjct: 222 MSRALADQARTIRVPVHVVELINRVVRVQRRL------LQERGVEP-TAEDIAVELDLTP 274

Query: 171 SEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             V  +  RLA +  SL+A +   D  S  + D +    DG     +E       R  L 
Sbjct: 275 ERVTEV-LRLAQEPVSLHAPVGEEDDVS--FGDLI---EDGDAASPVESAAFLLLRQHLE 328

Query: 230 RSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             +S L  RER++ + R   ++  P TLE +   F V+RER+RQIE++   ++++
Sbjct: 329 AVLSTLGERERKVVQLRYGLDDGRPRTLEEIGRIFGVTRERIRQIESKTLSRLRD 383


>gi|260890619|ref|ZP_05901882.1| RNA polymerase sigma factor RpoD [Leptotrichia hofstadii F0254]
 gi|260859664|gb|EEX74164.1| RNA polymerase sigma factor RpoD [Leptotrichia hofstadii F0254]
          Length = 392

 Score =  109 bits (272), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 81/269 (30%), Positives = 137/269 (50%), Gaps = 23/269 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI +IP+L  +EE   A+R   +G+  A  +L+ S+LRLVV IA  +   GL + ++
Sbjct: 126 YLREIGQIPLLSYEEEIDYAQRVL-NGEEEAKQKLIESNLRLVVSIAKKHTNRGLKMLDL 184

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV+KF+ E+GF+ +TY+ WWI+ A+   I      ++I        +   
Sbjct: 185 IQEGNMGLMKAVEKFEYEKGFKFSTYATWWIRQAITRAIADQGRTIRIPV-----HMIET 239

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           + ++K   + I     K      +A+KL +   +V S+        SL   + S +   S
Sbjct: 240 INKIKKESRIILQETGKEPTAEELAEKLELPVEKVKSILEMNQDPISLETPVGSEE--DS 297

Query: 199 QWQDWLVYD-----HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           +  D++  D     +D   +VL+        +  L   +  LN RE  +   R   ++  
Sbjct: 298 ELGDFVEDDKFANPYDATTRVLL--------KEQLDEVLKTLNEREEMVLRYRYGLDDGS 349

Query: 254 --TLENLSSEFEVSRERVRQIEARAFKKV 280
             TLE +   F V+RER+RQIE +A +K+
Sbjct: 350 QKTLEEVGKIFNVTRERIRQIEVKALRKL 378


>gi|239626722|ref|ZP_04669753.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47_FAA]
 gi|239516868|gb|EEQ56734.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47FAA]
          Length = 374

 Score =  109 bits (272), Expect = 5e-22,   Method: Compositional matrix adjust.
 Identities = 87/275 (31%), Positives = 136/275 (49%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L  +EE  LAK   E G   A  RL  S+LRLVV IA  Y G G+   ++
Sbjct: 107 YLKEIGKIPLLSMEEEIELAKSM-ELGSEDARKRLAESNLRLVVSIAKRYVGRGMQFLDL 165

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-- 132
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 166 IQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINRLV 225

Query: 133 ---KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
              ++L   L R     +     +L  E+V  I K       E +S+   +  +E  +  
Sbjct: 226 RTSRQLLQELGREPTTEEIAARADLPVERVSEIMKMAQ----EPVSLETPIGEEEDSHLG 281

Query: 190 INSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
               D N    QD   +   H+   +VL+                  L  RE+++ + R 
Sbjct: 282 DFIQDDNVMVPQDAAAFTLLHEQLMEVLL-----------------TLTEREQKVLKLRF 324

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++  P TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 325 GLDDGRPRTLEEVGRQFNVTRERIRQIEAKALRKL 359


>gi|229086862|ref|ZP_04219022.1| RNA polymerase sigma factor [Bacillus cereus Rock3-44]
 gi|228696437|gb|EEL49262.1| RNA polymerase sigma factor [Bacillus cereus Rock3-44]
          Length = 373

 Score =  109 bits (272), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 86/276 (31%), Positives = 133/276 (48%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 107 YLKEIGRVDLLSAEEEIRLATRI-EEGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 165

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 166 IQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 225

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I K       E +S+   +    D  L 
Sbjct: 226 RVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILK----IAQEPVSLETPIGEEDDSHLG 281

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 282 DFIEDQEATSPA-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 324

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 325 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 360


>gi|239940961|ref|ZP_04692898.1| putative RNA polymerase principal sigma factor [Streptomyces
           roseosporus NRRL 15998]
 gi|239987439|ref|ZP_04708103.1| putative RNA polymerase principal sigma factor [Streptomyces
           roseosporus NRRL 11379]
          Length = 363

 Score =  109 bits (272), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 90/295 (30%), Positives = 147/295 (49%), Gaps = 44/295 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRY------------------REHGDL--------SAAHR 52
           Y+ EI +IP+L   EE  LA+R                   R  GDL        +A  R
Sbjct: 70  YLREIGRIPLLTAAEEVELARRVEAGLFAEERLTGTPDLDSRLAGDLDRLVVMGRTAKRR 129

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY+ WWI+ A
Sbjct: 130 LIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIRQA 189

Query: 113 MQEYILRSWSLVKIGTTANQ--KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
           M   +      +++     +   R+    RRL      + +  ++P     IA +L+++ 
Sbjct: 190 MSRALADQARTIRVPVHVVELINRVVRVQRRL------LQERGVEP-TAEDIAVELDLTP 242

Query: 171 SEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             V  +  RLA +  SL+A +   D  S  + D +    DG     +E       R  L 
Sbjct: 243 ERVTEV-LRLAQEPVSLHAPVGEEDDVS--FGDLI---EDGDAASPVESAAFLLLRQHLE 296

Query: 230 RSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             +S L  RER++ + R   ++  P TLE +   F V+RER+RQIE++   ++++
Sbjct: 297 AVLSTLGERERKVVQLRYGLDDGRPRTLEEIGRIFGVTRERIRQIESKTLSRLRD 351


>gi|30022370|ref|NP_834001.1| RNA polymerase sigma factor RpoD [Bacillus cereus ATCC 14579]
 gi|218232261|ref|YP_002369099.1| RNA polymerase sigma factor RpoD [Bacillus cereus B4264]
 gi|228923044|ref|ZP_04086337.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228960557|ref|ZP_04122206.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|229048011|ref|ZP_04193587.1| RNA polymerase sigma factor [Bacillus cereus AH676]
 gi|229111765|ref|ZP_04241313.1| RNA polymerase sigma factor [Bacillus cereus Rock1-15]
 gi|229129569|ref|ZP_04258539.1| RNA polymerase sigma factor [Bacillus cereus BDRD-Cer4]
 gi|229146877|ref|ZP_04275242.1| RNA polymerase sigma factor [Bacillus cereus BDRD-ST24]
 gi|229152492|ref|ZP_04280684.1| RNA polymerase sigma factor [Bacillus cereus m1550]
 gi|296504786|ref|YP_003666486.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis BMB171]
 gi|29897928|gb|AAP11202.1| RNA polymerase sigma factor rpoD [Bacillus cereus ATCC 14579]
 gi|218160218|gb|ACK60210.1| RNA polymerase sigma-43 factor [Bacillus cereus B4264]
 gi|228631100|gb|EEK87737.1| RNA polymerase sigma factor [Bacillus cereus m1550]
 gi|228636705|gb|EEK93170.1| RNA polymerase sigma factor [Bacillus cereus BDRD-ST24]
 gi|228653886|gb|EEL09754.1| RNA polymerase sigma factor [Bacillus cereus BDRD-Cer4]
 gi|228671759|gb|EEL27055.1| RNA polymerase sigma factor [Bacillus cereus Rock1-15]
 gi|228723468|gb|EEL74837.1| RNA polymerase sigma factor [Bacillus cereus AH676]
 gi|228799157|gb|EEM46125.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228836677|gb|EEM82025.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|296325838|gb|ADH08766.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis BMB171]
          Length = 375

 Score =  109 bits (272), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 86/276 (31%), Positives = 133/276 (48%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 109 YLKEIGRVDLLSAEEEIRLATRI-EEGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 167

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 168 IQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 227

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I K       E +S+   +    D  L 
Sbjct: 228 RVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILK----IAQEPVSLETPIGEEDDSHLG 283

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 284 DFIEDQEATSPA-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 326

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 327 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 362


>gi|206971344|ref|ZP_03232295.1| RNA polymerase sigma-43 factor [Bacillus cereus AH1134]
 gi|218899458|ref|YP_002447869.1| RNA polymerase sigma-43 factor [Bacillus cereus G9842]
 gi|228902815|ref|ZP_04066960.1| RNA polymerase sigma factor [Bacillus thuringiensis IBL 4222]
 gi|228910126|ref|ZP_04073946.1| RNA polymerase sigma factor [Bacillus thuringiensis IBL 200]
 gi|228941457|ref|ZP_04104008.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228954576|ref|ZP_04116601.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228967357|ref|ZP_04128392.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228974388|ref|ZP_04134957.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228980981|ref|ZP_04141284.1| RNA polymerase sigma factor [Bacillus thuringiensis Bt407]
 gi|229071795|ref|ZP_04205010.1| RNA polymerase sigma factor [Bacillus cereus F65185]
 gi|229081552|ref|ZP_04214050.1| RNA polymerase sigma factor [Bacillus cereus Rock4-2]
 gi|229180570|ref|ZP_04307912.1| RNA polymerase sigma factor [Bacillus cereus 172560W]
 gi|229192502|ref|ZP_04319465.1| RNA polymerase sigma factor [Bacillus cereus ATCC 10876]
 gi|206734116|gb|EDZ51287.1| RNA polymerase sigma-43 factor [Bacillus cereus AH1134]
 gi|218541635|gb|ACK94029.1| RNA polymerase sigma-43 factor [Bacillus cereus G9842]
 gi|228591079|gb|EEK48935.1| RNA polymerase sigma factor [Bacillus cereus ATCC 10876]
 gi|228602994|gb|EEK60473.1| RNA polymerase sigma factor [Bacillus cereus 172560W]
 gi|228701757|gb|EEL54245.1| RNA polymerase sigma factor [Bacillus cereus Rock4-2]
 gi|228711390|gb|EEL63350.1| RNA polymerase sigma factor [Bacillus cereus F65185]
 gi|228778772|gb|EEM27036.1| RNA polymerase sigma factor [Bacillus thuringiensis Bt407]
 gi|228785438|gb|EEM33448.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228792392|gb|EEM39959.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228805233|gb|EEM51827.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228818238|gb|EEM64312.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228849643|gb|EEM94477.1| RNA polymerase sigma factor [Bacillus thuringiensis IBL 200]
 gi|228856824|gb|EEN01339.1| RNA polymerase sigma factor [Bacillus thuringiensis IBL 4222]
 gi|326942074|gb|AEA17970.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 375

 Score =  109 bits (272), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 86/276 (31%), Positives = 133/276 (48%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 109 YLKEIGRVDLLSAEEEIRLATRI-EEGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 167

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 168 IQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 227

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I K       E +S+   +    D  L 
Sbjct: 228 RVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILK----IAQEPVSLETPIGEEDDSHLG 283

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 284 DFIEDQEATSPA-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 326

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 327 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 362


>gi|238027063|ref|YP_002911294.1| RNA polymerase sigma factor RpoS [Burkholderia glumae BGR1]
 gi|76057940|emb|CAJ30487.1| stationary phase sigma factor [Burkholderia plantarii]
 gi|121663602|emb|CAM12359.1| stationary phase sigma factor [Burkholderia glumae]
 gi|237876257|gb|ACR28590.1| Stationary phase sigma factor [Burkholderia glumae BGR1]
          Length = 364

 Score =  109 bits (272), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 83/278 (29%), Positives = 142/278 (51%), Gaps = 25/278 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+P+
Sbjct: 86  IQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGVPL 144

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++    +  R 
Sbjct: 145 LDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRE 202

Query: 136 FFNLRRLKGHL--------QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              + R K HL        +A        + +  +  K     ++++++N   A   SL+
Sbjct: 203 LNQVLRAKRHLEKNSMSTGEAAERREAGIDDIAYLTGKTAEEVTDILALNEHTA---SLD 259

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS-MSVLNPRERRIFEAR 246
           A ++     +S   D L  D        ++  E +     LTR+ +S L+ + R + E R
Sbjct: 260 APLDLD--PASSLLDLLPDDQSQSPDAEVQHRELET----LTRAWLSRLSDKHRHVIE-R 312

Query: 247 RLQEN---PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   N   P TLE L+ E  ++RERVRQI+  A  +++
Sbjct: 313 RFGLNHIEPATLEELADEMGLTRERVRQIQQEALVRLK 350


>gi|300173322|ref|YP_003772488.1| RNA polymerase sigma factor RpoD [Leuconostoc gasicomitatum LMG
           18811]
 gi|299887701|emb|CBL91669.1| RNA polymerase sigma factor RpoD [Leuconostoc gasicomitatum LMG
           18811]
          Length = 432

 Score =  109 bits (272), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 86/274 (31%), Positives = 135/274 (49%), Gaps = 31/274 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L+  EE  +AKR  E GD+ A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 162 YLKEIGRVNLLKGDEEINIAKRI-EDGDIEAKQELAEANLRLVVSIAKRYVGRGMQFLDL 220

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 221 IQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 280

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             Q++L  +L R     +   + +L P++V  I   L +++  V           SL   
Sbjct: 281 RIQRQLLQDLGREPLPEEIGAEMDLTPDKVREI---LKIAQEPV-----------SLETP 326

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   D   S   D++    D +     +    +  R  L   +  L  RE  +   R   
Sbjct: 327 IGEED--DSHLGDFI---EDNEAVSPADSAAYEMLREQLESVLETLTDREENVLRLRFGL 381

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           E+    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 382 EDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLR 415


>gi|317128328|ref|YP_004094610.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacillus
           cellulosilyticus DSM 2522]
 gi|315473276|gb|ADU29879.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacillus
           cellulosilyticus DSM 2522]
          Length = 372

 Score =  109 bits (272), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 87/275 (31%), Positives = 137/275 (49%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   EE  LAK+  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 106 YLKEIGRVPLLSASEEIDLAKKI-EDGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 164

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 165 IQEGNMGLIKAVEKFDYNKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 224

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L P++V  I K       E +S+   +    D  L 
Sbjct: 225 RVQRQLLQDLGREPSPEEVSKEMDLTPDKVREILK----IAQEPVSLETPIGEEDDSHLG 280

Query: 188 ALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
             I   D+ +    D   Y+   +  E VL    +R+   N+L     + + R R     
Sbjct: 281 DFIE--DQEALAPSDAAAYELLKEQLEDVLDTLTDREE--NVLRLRFGLDDGRTR----- 331

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                   TLE +   F V+RER+RQIEA+A +K+
Sbjct: 332 --------TLEEVGKVFGVTRERIRQIEAKALRKL 358


>gi|331269992|ref|YP_004396484.1| RpoD family RNA polymerase sigma-70 subunit [Clostridium botulinum
           BKT015925]
 gi|329126542|gb|AEB76487.1| RNA polymerase, sigma 70 subunit, RpoD family [Clostridium
           botulinum BKT015925]
          Length = 368

 Score =  109 bits (272), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 79/265 (29%), Positives = 132/265 (49%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L   EE  LA+R  E GD+ A  +L  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGKVPLLSPDEEINLAQRI-EDGDMYAKKKLAEANLRLVVSIAKRYVGRGMLFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 161 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 218

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L        +PE++  I +       E++ +       E ++      ++  S
Sbjct: 219 LIRVSRQLLQELGREPQPEEIAKIMEMPVDKVREIMKI-----AQEPVSLETPIGEEEDS 273

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++  D              K +   L   +  L PRE ++   R   ++    TLE
Sbjct: 274 HLGDFIPDDEAPAPAEAAAFTMLKEQ---LINVLDTLTPREEKVLRLRFGLDDGRARTLE 330

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF V+RER+RQIEA+A +K++
Sbjct: 331 EVGKEFNVTRERIRQIEAKALRKLR 355


>gi|255525304|ref|ZP_05392244.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           carboxidivorans P7]
 gi|296188172|ref|ZP_06856564.1| RNA polymerase sigma factor RpoD [Clostridium carboxidivorans P7]
 gi|255510976|gb|EET87276.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           carboxidivorans P7]
 gi|296047298|gb|EFG86740.1| RNA polymerase sigma factor RpoD [Clostridium carboxidivorans P7]
          Length = 361

 Score =  109 bits (272), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 80/265 (30%), Positives = 133/265 (50%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  +EE  LA+R  E+GD  A  +L  ++LRLVV IA  Y G G+   ++
Sbjct: 95  YLKEIGKVPLLAPEEEISLAQRI-ENGDQIAKKKLAEANLRLVVSIAKRYVGRGMLFLDL 153

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 154 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 211

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L        +PE+V  I +       E++ +       E ++      ++  S
Sbjct: 212 LIRVSRQLLQELGREPQPEEVAKIMEMPVDKVREIMKI-----AQEPVSLETPIGEEEDS 266

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++  D              K +   L   +  L PRE ++   R   ++    TLE
Sbjct: 267 HLGDFIPDDEAPAPAEAAAFTMLKEQ---LINVLDTLTPREEKVLRLRFGLDDGRARTLE 323

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF V+RER+RQIEA+A +K++
Sbjct: 324 EVGKEFNVTRERIRQIEAKALRKLR 348


>gi|229174966|ref|ZP_04302486.1| RNA polymerase sigma factor [Bacillus cereus MM3]
 gi|228608634|gb|EEK65936.1| RNA polymerase sigma factor [Bacillus cereus MM3]
          Length = 375

 Score =  109 bits (272), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 86/276 (31%), Positives = 133/276 (48%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 109 YLKEIGRVDLLSAEEEIRLATRI-EEGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 167

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 168 IQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 227

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I K       E +S+   +    D  L 
Sbjct: 228 RVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILK----IAQEPVSLETPIGEEDDSHLG 283

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 284 DFIEDQEATSPA-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 326

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 327 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 362


>gi|30264362|ref|NP_846739.1| RNA polymerase sigma factor RpoD [Bacillus anthracis str. Ames]
 gi|47529811|ref|YP_021160.1| RNA polymerase sigma factor RpoD [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49187190|ref|YP_030442.1| RNA polymerase sigma factor RpoD [Bacillus anthracis str. Sterne]
 gi|49481307|ref|YP_038350.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|52141207|ref|YP_085621.1| RNA polymerase sigma factor RpoD [Bacillus cereus E33L]
 gi|65321666|ref|ZP_00394625.1| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Bacillus anthracis str. A2012]
 gi|118479464|ref|YP_896615.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis str. Al
           Hakam]
 gi|165872043|ref|ZP_02216683.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0488]
 gi|167634513|ref|ZP_02392833.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0442]
 gi|167638663|ref|ZP_02396939.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0193]
 gi|170687516|ref|ZP_02878733.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0465]
 gi|170707362|ref|ZP_02897816.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0389]
 gi|196046412|ref|ZP_03113638.1| RNA polymerase sigma-43 factor [Bacillus cereus 03BB108]
 gi|218905429|ref|YP_002453263.1| RNA polymerase sigma-43 factor [Bacillus cereus AH820]
 gi|225866273|ref|YP_002751651.1| RNA polymerase sigma-43 factor [Bacillus cereus 03BB102]
 gi|228929335|ref|ZP_04092360.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228935612|ref|ZP_04098427.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228948006|ref|ZP_04110292.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|229093361|ref|ZP_04224468.1| RNA polymerase sigma factor [Bacillus cereus Rock3-42]
 gi|229123831|ref|ZP_04253025.1| RNA polymerase sigma factor [Bacillus cereus 95/8201]
 gi|229186532|ref|ZP_04313694.1| RNA polymerase sigma factor [Bacillus cereus BGSC 6E1]
 gi|229601154|ref|YP_002868581.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0248]
 gi|254684050|ref|ZP_05147910.1| RNA polymerase sigma factor RpoD [Bacillus anthracis str.
           CNEVA-9066]
 gi|254736399|ref|ZP_05194105.1| RNA polymerase sigma factor RpoD [Bacillus anthracis str. Western
           North America USA6153]
 gi|254741437|ref|ZP_05199124.1| RNA polymerase sigma factor RpoD [Bacillus anthracis str. Kruger B]
 gi|254757799|ref|ZP_05209826.1| RNA polymerase sigma factor RpoD [Bacillus anthracis str. Australia
           94]
 gi|30259020|gb|AAP28225.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. Ames]
 gi|47504959|gb|AAT33635.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49181117|gb|AAT56493.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. Sterne]
 gi|49332863|gb|AAT63509.1| RNA polymerase sigma-43 factor [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|51974676|gb|AAU16226.1| RNA polymerase sigma-43 factor [Bacillus cereus E33L]
 gi|118418689|gb|ABK87108.1| RNA polymerase sigma-43 factor [Bacillus thuringiensis str. Al
           Hakam]
 gi|164712174|gb|EDR17711.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0488]
 gi|167513511|gb|EDR88881.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0193]
 gi|167529965|gb|EDR92700.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0442]
 gi|170127606|gb|EDS96479.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0389]
 gi|170668711|gb|EDT19457.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0465]
 gi|196022882|gb|EDX61563.1| RNA polymerase sigma-43 factor [Bacillus cereus 03BB108]
 gi|218536133|gb|ACK88531.1| RNA polymerase sigma-43 factor [Bacillus cereus AH820]
 gi|225787167|gb|ACO27384.1| RNA polymerase sigma-43 factor [Bacillus cereus 03BB102]
 gi|228596963|gb|EEK54621.1| RNA polymerase sigma factor [Bacillus cereus BGSC 6E1]
 gi|228659652|gb|EEL15298.1| RNA polymerase sigma factor [Bacillus cereus 95/8201]
 gi|228690017|gb|EEL43818.1| RNA polymerase sigma factor [Bacillus cereus Rock3-42]
 gi|228811696|gb|EEM58031.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228824052|gb|EEM69869.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228830349|gb|EEM75961.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|229265562|gb|ACQ47199.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0248]
          Length = 373

 Score =  109 bits (272), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 86/276 (31%), Positives = 133/276 (48%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 107 YLKEIGRVDLLSAEEEIRLATRI-EEGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 165

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 166 IQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 225

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I K       E +S+   +    D  L 
Sbjct: 226 RVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILK----IAQEPVSLETPIGEEDDSHLG 281

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 282 DFIEDQEATSPA-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 324

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 325 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 360


>gi|229098765|ref|ZP_04229703.1| RNA polymerase sigma factor [Bacillus cereus Rock3-29]
 gi|229104924|ref|ZP_04235581.1| RNA polymerase sigma factor [Bacillus cereus Rock3-28]
 gi|229117789|ref|ZP_04247154.1| RNA polymerase sigma factor [Bacillus cereus Rock1-3]
 gi|228665652|gb|EEL21129.1| RNA polymerase sigma factor [Bacillus cereus Rock1-3]
 gi|228678498|gb|EEL32718.1| RNA polymerase sigma factor [Bacillus cereus Rock3-28]
 gi|228684609|gb|EEL38549.1| RNA polymerase sigma factor [Bacillus cereus Rock3-29]
          Length = 375

 Score =  109 bits (272), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 86/276 (31%), Positives = 133/276 (48%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 109 YLKEIGRVDLLSAEEEIRLATRI-EEGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 167

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 168 IQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 227

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I K       E +S+   +    D  L 
Sbjct: 228 RVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILK----IAQEPVSLETPIGEEDDSHLG 283

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 284 DFIEDQEATSPA-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 326

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 327 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 362


>gi|163942050|ref|YP_001646934.1| RNA polymerase sigma factor RpoD [Bacillus weihenstephanensis
           KBAB4]
 gi|229013514|ref|ZP_04170648.1| RNA polymerase sigma factor [Bacillus mycoides DSM 2048]
 gi|229019517|ref|ZP_04176334.1| RNA polymerase sigma factor [Bacillus cereus AH1273]
 gi|229025758|ref|ZP_04182158.1| RNA polymerase sigma factor [Bacillus cereus AH1272]
 gi|229061987|ref|ZP_04199313.1| RNA polymerase sigma factor [Bacillus cereus AH603]
 gi|229135118|ref|ZP_04263920.1| RNA polymerase sigma factor [Bacillus cereus BDRD-ST196]
 gi|229169042|ref|ZP_04296758.1| RNA polymerase sigma factor [Bacillus cereus AH621]
 gi|163864247|gb|ABY45306.1| RNA polymerase, sigma 70 subunit, RpoD family [Bacillus
           weihenstephanensis KBAB4]
 gi|228614451|gb|EEK71560.1| RNA polymerase sigma factor [Bacillus cereus AH621]
 gi|228648347|gb|EEL04380.1| RNA polymerase sigma factor [Bacillus cereus BDRD-ST196]
 gi|228717296|gb|EEL68969.1| RNA polymerase sigma factor [Bacillus cereus AH603]
 gi|228735541|gb|EEL86136.1| RNA polymerase sigma factor [Bacillus cereus AH1272]
 gi|228741773|gb|EEL91956.1| RNA polymerase sigma factor [Bacillus cereus AH1273]
 gi|228747751|gb|EEL97620.1| RNA polymerase sigma factor [Bacillus mycoides DSM 2048]
          Length = 375

 Score =  109 bits (272), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 86/276 (31%), Positives = 133/276 (48%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 109 YLKEIGRVDLLSAEEEIRLATRI-EEGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 167

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 168 IQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 227

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I K       E +S+   +    D  L 
Sbjct: 228 RVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILK----IAQEPVSLETPIGEEDDSHLG 283

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 284 DFIEDQEATSPA-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 326

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 327 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 362


>gi|326693497|ref|ZP_08230502.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Leuconostoc argentinum KCTC 3773]
          Length = 432

 Score =  109 bits (272), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 86/274 (31%), Positives = 136/274 (49%), Gaps = 31/274 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L+  EE  +AKR  E GD+ A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 162 YLKEIGRVNLLKGDEEINIAKRI-EAGDVEAKQELAEANLRLVVSIAKRYVGRGMQFLDL 220

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 221 IQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 280

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             Q++L  +L R     +   + +L P++V  I   L +++  V           SL   
Sbjct: 281 RIQRQLLQDLGREPLPEEIGAEMDLTPDKVREI---LKIAQEPV-----------SLETP 326

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   D   S   D++    D +     +    +  R+ L   +  L  RE  +   R   
Sbjct: 327 IGEED--DSHLGDFI---EDNEAISPADSAAYEMLRDQLESVLETLTDREENVLRLRFGL 381

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           E+    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 382 EDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLR 415


>gi|228993035|ref|ZP_04152958.1| RNA polymerase sigma factor [Bacillus pseudomycoides DSM 12442]
 gi|228999085|ref|ZP_04158667.1| RNA polymerase sigma factor [Bacillus mycoides Rock3-17]
 gi|229006633|ref|ZP_04164267.1| RNA polymerase sigma factor [Bacillus mycoides Rock1-4]
 gi|228754494|gb|EEM03905.1| RNA polymerase sigma factor [Bacillus mycoides Rock1-4]
 gi|228760702|gb|EEM09666.1| RNA polymerase sigma factor [Bacillus mycoides Rock3-17]
 gi|228766683|gb|EEM15323.1| RNA polymerase sigma factor [Bacillus pseudomycoides DSM 12442]
          Length = 373

 Score =  109 bits (272), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 86/276 (31%), Positives = 133/276 (48%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 107 YLKEIGRVDLLSAEEEIRLATRI-EEGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 165

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 166 IQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 225

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I K       E +S+   +    D  L 
Sbjct: 226 RVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILK----IAQEPVSLETPIGEEDDSHLG 281

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 282 DFIEDQEATSPA-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 324

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 325 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 360


>gi|161507646|ref|YP_001577600.1| RNA polymerase sigma factor RpoD [Lactobacillus helveticus DPC
           4571]
 gi|160348635|gb|ABX27309.1| RNA polymerase sigma factor [Lactobacillus helveticus DPC 4571]
          Length = 356

 Score =  109 bits (272), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 86/273 (31%), Positives = 130/273 (47%), Gaps = 31/273 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P++   +E  LAKR  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 90  YLKEIGRVPLITADQEIALAKRI-EEGDEEAKQELAEANLRLVVSIAKRYVGRGMSFLDL 148

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 149 IQEGNMGLMKAVDKFDYCLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 208

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + N+   +V  I K       E +S+   +    D  L 
Sbjct: 209 RIQRQLLQDLGREPTPEEIGAEMNMPTNKVRDILK----IAQEPVSLETPIGEEDDSHLG 264

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S +         +  EQVL    +R+   N+L     + + R R       
Sbjct: 265 DFIEDKDATSPEQHASYEMLKEQLEQVLETLTDREE--NVLRLRFGLDDGRTR------- 315

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                 TLE +   F V+RER+RQIEA+A +K+
Sbjct: 316 ------TLEEVGKVFGVTRERIRQIEAKALRKL 342


>gi|325677627|ref|ZP_08157279.1| RNA polymerase sigma factor RpoD [Ruminococcus albus 8]
 gi|324110595|gb|EGC04759.1| RNA polymerase sigma factor RpoD [Ruminococcus albus 8]
          Length = 366

 Score =  109 bits (272), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 87/278 (31%), Positives = 144/278 (51%), Gaps = 35/278 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAH---RLVTSHLRLVVKIAMGYRGYGLPI 75
           Y+ EI ++P+L  +EE  LA+      D  A+    RL  ++LRLVV IA  Y G G+  
Sbjct: 96  YLKEIGRVPLLTSEEEIQLAEMMSGDNDRDASKARKRLAEANLRLVVSIAKRYVGRGMSF 155

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG-----TTA 130
            +++ EGN+GL++AV+KFD ++GF+ +TY+ WWI+ A+   I      ++I      T  
Sbjct: 156 LDLIQEGNMGLIKAVEKFDYKKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETIT 215

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNAL 189
             K+    L    GH       +  PE+   IA+ L++S  +V  +  R+A D  SL   
Sbjct: 216 KVKKASSQLLHKNGH-------DPSPEE---IAEDLDMSVEKVREI-MRIAQDPVSLETP 264

Query: 190 INSSDKNSSQWQDWL----VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           I   ++  S   D++             +++ KE+       + + +S L  RE ++   
Sbjct: 265 I--GEEEDSHLGDFIPDDDAPAPAEAASLVLLKEQ-------IDQVLSTLTEREEKVLRL 315

Query: 246 RRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   E+    TLE +  EF+V+RER+RQIEA+A +K++
Sbjct: 316 RFGLEDGRSRTLEEVGQEFKVTRERIRQIEAKALRKLR 353


>gi|227817068|ref|YP_002817077.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. CDC 684]
 gi|227007300|gb|ACP17043.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. CDC 684]
          Length = 373

 Score =  109 bits (272), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 86/276 (31%), Positives = 133/276 (48%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 107 YLKEIGRVDLLSAEEEIRLATRI-EEGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 165

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 166 IQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 225

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I K       E +S+   +    D  L 
Sbjct: 226 RVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILK----IAQEPVSLETPIGEEDDSHLG 281

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 282 DFIEDQEATSPA-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 324

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 325 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 360


>gi|51599021|ref|YP_073209.1| RNA polymerase sigma factor [Borrelia garinii PBi]
 gi|51573592|gb|AAU07617.1| RNA polymerase sigma factor [Borrelia garinii PBi]
          Length = 266

 Score =  109 bits (272), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 83/282 (29%), Positives = 149/282 (52%), Gaps = 20/282 (7%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M+I  N ++ +  Y+  +R+  ++  +EE  LA +  + G+  A ++++ ++LRLV+KI 
Sbjct: 1   MNIFSNEDLNI--YLKSVREHKLITHEEEIKLASQI-QRGNAQAKNKMINANLRLVLKII 57

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y G GL I +++ EGN+GL++A +K+DP +  + +TY+ +WIK ++Q  +     LVK
Sbjct: 58  KRYAGKGLKIEDLIQEGNLGLIRAAEKYDPNKNTKFSTYASFWIKQSLQRALNTKTRLVK 117

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           +          +    L   +        K  +   I K+ N+S ++ I +   L  + S
Sbjct: 118 VP---------YRKENLILQINKYLTEEEKSPKKEEIMKRFNLSPAQYIKIIPYLEKEYS 168

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L+  I  S+ NS+     L  D+    ++ +E++      N +  +   LN +ER I + 
Sbjct: 169 LDKEIEGSE-NSTLLN--LYEDNSFNPEITLEQDSTIKHLNYVLETK--LNEKERYIIKK 223

Query: 246 R-RLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L  NP   TL+++S+E  +S E VRQIE R  KK++E I
Sbjct: 224 RYNLDNNPKKSTLKDISTELGISSETVRQIEKRVLKKLKEEI 265


>gi|254750874|ref|ZP_05202913.1| RNA polymerase sigma factor RpoD [Bacillus anthracis str. Vollum]
          Length = 359

 Score =  109 bits (272), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 86/275 (31%), Positives = 132/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 107 YLKEIGRVDLLSAEEEIRLATRI-EEGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 165

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 166 IQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 225

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I K       E +S+   +    D  L 
Sbjct: 226 RVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILK----IAQEPVSLETPIGEEDDSHLG 281

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 282 DFIEDQEATSPA-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 324

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 325 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 359


>gi|42783418|ref|NP_980665.1| RNA polymerase sigma factor RpoD [Bacillus cereus ATCC 10987]
 gi|47567855|ref|ZP_00238563.1| RNA polymerase sigma factor rpoD [Bacillus cereus G9241]
 gi|217961783|ref|YP_002340353.1| RNA polymerase sigma factor RpoD [Bacillus cereus AH187]
 gi|228916924|ref|ZP_04080486.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228987542|ref|ZP_04147661.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|229141030|ref|ZP_04269573.1| RNA polymerase sigma factor [Bacillus cereus BDRD-ST26]
 gi|229157906|ref|ZP_04285980.1| RNA polymerase sigma factor [Bacillus cereus ATCC 4342]
 gi|229163237|ref|ZP_04291192.1| RNA polymerase sigma factor [Bacillus cereus R309803]
 gi|229198419|ref|ZP_04325125.1| RNA polymerase sigma factor [Bacillus cereus m1293]
 gi|301055785|ref|YP_003793996.1| RNA polymerase sigma factor [Bacillus anthracis CI]
 gi|42739347|gb|AAS43273.1| RNA polymerase sigma-43 factor [Bacillus cereus ATCC 10987]
 gi|47555532|gb|EAL13875.1| RNA polymerase sigma factor rpoD [Bacillus cereus G9241]
 gi|217066780|gb|ACJ81030.1| RNA polymerase sigma-43 factor [Bacillus cereus AH187]
 gi|228585119|gb|EEK43231.1| RNA polymerase sigma factor [Bacillus cereus m1293]
 gi|228620300|gb|EEK77171.1| RNA polymerase sigma factor [Bacillus cereus R309803]
 gi|228625565|gb|EEK82318.1| RNA polymerase sigma factor [Bacillus cereus ATCC 4342]
 gi|228642463|gb|EEK98751.1| RNA polymerase sigma factor [Bacillus cereus BDRD-ST26]
 gi|228772274|gb|EEM20721.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228842748|gb|EEM87834.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|300377954|gb|ADK06858.1| RNA polymerase sigma factor [Bacillus cereus biovar anthracis str.
           CI]
 gi|324328197|gb|ADY23457.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis serovar
           finitimus YBT-020]
          Length = 375

 Score =  109 bits (272), Expect = 6e-22,   Method: Compositional matrix adjust.
 Identities = 86/276 (31%), Positives = 136/276 (49%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 109 YLKEIGRVDLLSAEEEIRLATRI-EEGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 167

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 168 IQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 227

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I   L +++ E +S+   +    D  L 
Sbjct: 228 RVQRQLLQDLGREPSPEEIGEEMDLAPEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 283

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 284 DFIEDQEATSPA-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 326

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 327 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 362


>gi|254721884|ref|ZP_05183673.1| RNA polymerase sigma factor RpoD [Bacillus anthracis str. A1055]
          Length = 373

 Score =  108 bits (271), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 86/276 (31%), Positives = 133/276 (48%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 107 YLKEIGRVDLLSAEEEIRLATRI-EEGDEEAKRRLAEANLRLVVSIAKRYVGRGILFLDL 165

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 166 IQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 225

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I K       E +S+   +    D  L 
Sbjct: 226 RVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILK----IAQEPVSLETPIGEEDDSHLG 281

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 282 DFIEDQEATSPA-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 324

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 325 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 360


>gi|229031941|ref|ZP_04187928.1| RNA polymerase sigma factor [Bacillus cereus AH1271]
 gi|228729405|gb|EEL80395.1| RNA polymerase sigma factor [Bacillus cereus AH1271]
          Length = 375

 Score =  108 bits (271), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 86/276 (31%), Positives = 133/276 (48%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 109 YLKEIGRVDLLSAEEEIRLATRI-EDGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 167

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 168 IQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 227

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I K       E +S+   +    D  L 
Sbjct: 228 RVQRQLLQDLGREPSPEEIGEEMDLAPEKVREILK----IAQEPVSLETPIGEEDDSHLG 283

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 284 DFIEDQEATSPA-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 326

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 327 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 362


>gi|332297439|ref|YP_004439361.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           brennaborense DSM 12168]
 gi|332180542|gb|AEE16230.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           brennaborense DSM 12168]
          Length = 287

 Score =  108 bits (271), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 78/270 (28%), Positives = 151/270 (55%), Gaps = 15/270 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+ EI KIP+L ++EE  LA +       +A  R+V ++LR VV +A  Y+ +GL +
Sbjct: 16  LALYLKEINKIPLLSREEETDLAVKAAAGD-KAAKDRIVNANLRFVVNVAKKYQNHGLDL 74

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT-ANQKR 134
            +++SEGNIGLM A+++FD  +G+   +Y++WWI+ ++ + I     ++++    AN+  
Sbjct: 75  VDLISEGNIGLMTAIERFDVSKGYHFISYAVWWIRQSILKAICEKSRMIRLPLNRANELV 134

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSS 193
              + R+L      +  +  + E++  +A  LN+  S V  M   ++ D  SL+A I SS
Sbjct: 135 QIEHARKL------VAQDKTEEEEITEVADMLNMDVSHVREM-LNISRDMISLDASIRSS 187

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN- 251
           D++S+   ++L    D + +   +     + ++ +   +  L  +E  +   R  L  N 
Sbjct: 188 DQDSASIGEFL---EDSRYEDPADTVLNASMQDDIDGVLGTLTDKEADVLRYRFGLNGNK 244

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            ++L+ +  +F +++ER+RQIE +A K++Q
Sbjct: 245 SMSLKEVGDKFNLTKERIRQIEKKAIKRLQ 274


>gi|282880271|ref|ZP_06288987.1| putative RNA polymerase sigma factor RpoD [Prevotella timonensis
           CRIS 5C-B1]
 gi|281305866|gb|EFA97910.1| putative RNA polymerase sigma factor RpoD [Prevotella timonensis
           CRIS 5C-B1]
          Length = 292

 Score =  108 bits (271), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 78/275 (28%), Positives = 147/275 (53%), Gaps = 18/275 (6%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI +  +L  +EE  LA+R ++ GD  A  +L  ++LR VV +A  Y+  GL 
Sbjct: 22  ALDKYLQEIGREDLLSTEEEIELAQRIKK-GDRKALDKLTKANLRFVVSVAKQYQNQGLS 80

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V++    NQ  
Sbjct: 81  LPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRL--PLNQVG 138

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               + +L+   +   +      +   IA+++++ E +VI          S++A  +  D
Sbjct: 139 SVNKINQLQNKFEQEFERRPNSSE---IAERIDIPEDKVIDAMKANGKHVSVDAPFSDGD 195

Query: 195 KNSSQWQDWLVYDHD---GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
            NS    D L  D D      ++++E     + R  +  ++  LN RER + E       
Sbjct: 196 DNS--LIDVLP-DSDIPMADNELVME-----SLRKEIADALHTLNERERNVIECFYGINQ 247

Query: 252 P-VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           P +TLE +   + ++RERVRQI  +A +K++++ +
Sbjct: 248 PEMTLEEIGDRYGLTRERVRQIREKALRKLRKNTK 282


>gi|154506043|ref|ZP_02042781.1| hypothetical protein RUMGNA_03585 [Ruminococcus gnavus ATCC 29149]
 gi|153793542|gb|EDN75962.1| hypothetical protein RUMGNA_03585 [Ruminococcus gnavus ATCC 29149]
          Length = 297

 Score =  108 bits (271), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 93/284 (32%), Positives = 150/284 (52%), Gaps = 41/284 (14%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ EI +IP+L  +EE  L ++  E GD  A  ++  ++LRLVV +A  Y G G+  
Sbjct: 34  LKIYLKEIGRIPLLTAEEELELGRQIAE-GDTEARRKMEEANLRLVVAVAKHYAGKGMQF 92

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AV+KFD  +G + +TY++WWIK A    ILR+          +Q R 
Sbjct: 93  MDLIQEGNIGLMRAVEKFDYTKGSKFSTYAVWWIKEA----ILRALD--------SQSRE 140

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVA-------IAKKLNVSESEVISMNCRLAGDESLNA 188
                R+  ++  I+    K EQ +        IAK+L+++  EV  M   +    SL  
Sbjct: 141 IRVPVRVAQNMNKISKTERKMEQTLGREVAAEEIAKELHMTTEEVERMQSYIKNPVSLET 200

Query: 189 LINSSDKNSSQWQDWLVYDHDGQE-------QVLIEKEERKNRRNMLTRSMSVLNPRERR 241
            +   D+ +S  +D++    D QE         L++KEE       +   +S L  +E++
Sbjct: 201 PVG--DEENSNLEDFI---EDTQEPTPEEAVAALVQKEE-------VQEMLSTLTEKEQK 248

Query: 242 IFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQES 283
           I   R  L++  V TLE       V+RER+RQ+E+RA +K+++S
Sbjct: 249 ILRLRYGLEDGNVHTLEETGQILGVTRERIRQLESRALEKLRKS 292


>gi|152976724|ref|YP_001376241.1| RNA polymerase sigma factor RpoD [Bacillus cereus subsp. cytotoxis
           NVH 391-98]
 gi|152025476|gb|ABS23246.1| RNA polymerase, sigma 70 subunit, RpoD family [Bacillus cytotoxicus
           NVH 391-98]
          Length = 373

 Score =  108 bits (271), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 86/275 (31%), Positives = 132/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 107 YLKEIGRVDLLSAEEEIQLATRI-EEGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 165

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 166 IQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 225

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I K       E +S+   +    D  L 
Sbjct: 226 RVQRQLLQDLGREPTPEEIGEEMDLAPEKVREILK----IAQEPVSLETPIGEEDDSHLG 281

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 282 DFIEDQEATSPA-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 324

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 325 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 359


>gi|260101316|ref|ZP_05751553.1| RNA polymerase sigma factor rpoD [Lactobacillus helveticus DSM
           20075]
 gi|260084901|gb|EEW69021.1| RNA polymerase sigma factor rpoD [Lactobacillus helveticus DSM
           20075]
          Length = 370

 Score =  108 bits (271), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 86/273 (31%), Positives = 133/273 (48%), Gaps = 31/273 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P++   +E  LAKR  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 104 YLKEIGRVPLITADQEIALAKRI-EEGDEEAKQELAEANLRLVVSIAKRYVGRGMSFLDL 162

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 163 IQEGNMGLMKAVDKFDYCLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 222

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + N+   +V  I   L +++ E +S+   +    D  L 
Sbjct: 223 RIQRQLLQDLGREPTPEEIGAEMNMPTNKVRDI---LKIAQ-EPVSLETPIGEEDDSHLG 278

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S +         +  EQVL    +R+   N+L     + + R R       
Sbjct: 279 DFIEDKDATSPEQHASYEMLKEQLEQVLETLTDREE--NVLRLRFGLDDGRTR------- 329

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                 TLE +   F V+RER+RQIEA+A +K+
Sbjct: 330 ------TLEEVGKVFGVTRERIRQIEAKALRKL 356


>gi|332975851|gb|EGK12729.1| DNA-directed RNA polymerase sigma subunit SigA [Desmospora sp.
           8437]
          Length = 372

 Score =  108 bits (271), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 88/274 (32%), Positives = 136/274 (49%), Gaps = 31/274 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 106 YLKEIGRVPLLSAEEEVELAKRI-EEGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 164

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-- 132
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 165 IQEGNMGLIKAVEKFDFRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 224

Query: 133 ---KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
              ++L   L R     +   + +L PE+V  I K   +++  V           SL   
Sbjct: 225 RVSRQLLQELGREPSPEEIAEEMDLSPEKVREIMK---IAQEPV-----------SLETP 270

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   D   S   D++  D           E  K +   L   +  L+ RE  +   R   
Sbjct: 271 IGEED--DSHLGDFIPDDDAQAPADAAAYELLKEQ---LKDVLDTLSDREENVLRLRFGL 325

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 326 DDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 359


>gi|164687939|ref|ZP_02211967.1| hypothetical protein CLOBAR_01584 [Clostridium bartlettii DSM
           16795]
 gi|164602352|gb|EDQ95817.1| hypothetical protein CLOBAR_01584 [Clostridium bartlettii DSM
           16795]
          Length = 294

 Score =  108 bits (271), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 81/280 (28%), Positives = 146/280 (52%), Gaps = 33/280 (11%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            +  Y+ EI +  ML   EE  LAK+  E     A    + ++ RLVV IA  YR   + 
Sbjct: 23  AMKMYLKEIEEYKMLSAVEEVELAKKVNEEIP-EAKEDFINANYRLVVSIAKKYRKENVD 81

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           I +++  GNIGL++AV+K+D  +G++ +TY+ WWIK ++  YI    + ++I    +Q+ 
Sbjct: 82  ILDLIQAGNIGLIKAVEKYDYTKGYKFSTYATWWIKQSITRYIDDCENTIRIPVHLHQRI 141

Query: 135 LFF--------NLRRLKGHLQAITD-NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE- 184
            F         N+ + +  L+ + D  ++  ++V+ I K+    +  V+S++  +  DE 
Sbjct: 142 NFVKRKKQELSNVLQREPSLEELADICDMDVDKVIEILKR----DKNVVSLDTPIKEDED 197

Query: 185 -SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SL   I  SD N S               V++ + E+ N +  +   ++ L+ +E+++ 
Sbjct: 198 SSLVEFI-PSDANFS--------------DVVMHEVEQHNLKEKINELLTGLSEQEQKVL 242

Query: 244 EAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             R     ++P TLE +   F V+RER+RQIEA+A +K++
Sbjct: 243 RMRFGLDDDDPKTLEEIGKVFGVTRERIRQIEAKAIRKLR 282


>gi|88802114|ref|ZP_01117642.1| RNA polymerase sigma-70 factor [Polaribacter irgensii 23-P]
 gi|88782772|gb|EAR13949.1| RNA polymerase sigma-70 factor [Polaribacter irgensii 23-P]
          Length = 287

 Score =  108 bits (271), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 82/296 (27%), Positives = 151/296 (51%), Gaps = 55/296 (18%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y  EI KI ++   EE  LA + +  GD  A   LV+++LR VV +A  Y+G GL +
Sbjct: 18  LDKYFQEISKIGLITADEEVELALKIK-VGDSKALDALVSANLRFVVSVAKQYQGQGLKL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV-----KIGTTA 130
           S++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + +     +V     KIG+  
Sbjct: 77  SDLINEGNLGLVKAAKRFDETRGFKFISYAVWWIRQSIMQALAEQSRIVRLPLNKIGSIN 136

Query: 131 NQKRLFFNL----RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISM 176
             K+++  L    +R+  H +              IAK+L+++E+EV          +SM
Sbjct: 137 KIKKIYARLEQNEQRMPTHKE--------------IAKQLDMTEAEVEQSLKNSGRHVSM 182

Query: 177 NC--RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV 234
           +   +   D +L  ++ S D      Q          + + IE E          R++  
Sbjct: 183 DAPFKEGEDSNLYNVLQSGDSPRPDSQLM-------AQSLKIEIE----------RALGT 225

Query: 235 LNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           L  +E ++ +       E   +LE +  +F+++RERVRQ++ +A +++Q   + Q+
Sbjct: 226 LTYKEAKVIKMYYGIGNEAMASLEEIGEKFDLTRERVRQVKQKAIRRLQSGSKTQM 281


>gi|52786447|ref|YP_092276.1| RNA polymerase sigma factor RpoD [Bacillus licheniformis ATCC
           14580]
 gi|163119552|ref|YP_079858.2| RNA polymerase sigma factor RpoD [Bacillus licheniformis ATCC
           14580]
 gi|319644974|ref|ZP_07999207.1| RNA polymerase sigma factor rpoD [Bacillus sp. BT1B_CT2]
 gi|52348949|gb|AAU41583.1| SigA [Bacillus licheniformis ATCC 14580]
 gi|145903060|gb|AAU24220.2| RNA polymerase major sigma-43 factor (sigma-A) [Bacillus
           licheniformis ATCC 14580]
 gi|317392783|gb|EFV73577.1| RNA polymerase sigma factor rpoD [Bacillus sp. BT1B_CT2]
          Length = 373

 Score =  108 bits (271), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 85/275 (30%), Positives = 135/275 (49%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE   AK+  E GD  +  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 107 YLKEIGRVNLLSAKEEIEYAKKI-EEGDEESKRRLAEANLRLVVSIAKRYVGRGMLFLDL 165

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 166 IQEGNMGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 225

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   D +L PE+V  I   L +++ E +S+   +    D  L 
Sbjct: 226 RVQRQLLQDLGREPTPEEIAEDMDLTPEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 281

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 282 DFIEDQEATSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 324

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 325 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 359


>gi|311069121|ref|YP_003974044.1| RNA polymerase sigma factor RpoD [Bacillus atrophaeus 1942]
 gi|310869638|gb|ADP33113.1| RNA polymerase sigma factor RpoD [Bacillus atrophaeus 1942]
          Length = 373

 Score =  108 bits (271), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 84/275 (30%), Positives = 135/275 (49%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE   A++  E GD  +  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 107 YLKEIGRVNLLSAKEEITYAQKI-EEGDEESKRRLAEANLRLVVSIAKRYVGRGMLFLDL 165

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 166 IQEGNMGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 225

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   D +L PE+V  I   L +++ E +S+   +    D  L 
Sbjct: 226 RVQRQLLQDLGREPTPEEIAEDMDLTPEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 281

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 282 DFIEDQEATSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 324

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 325 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 359


>gi|256532390|gb|ACU81353.1| RpoH [Rhizobium leguminosarum bv. trifolii]
          Length = 148

 Score =  108 bits (271), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 67/152 (44%), Positives = 95/152 (62%), Gaps = 9/152 (5%)

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFFNLRRL+  L A  D 
Sbjct: 1   FEPERDVRFSTYASWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRAKL-AKGDT 59

Query: 153 NLKPEQV-VAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDH-- 208
            L  + +   IA  L VS ++V +M+ RL+G D SL A   S D  S++  D+LV D   
Sbjct: 60  QLTLQSIHQEIAAALGVSLADVQTMDARLSGNDASLQAPSVSGDAESAEKMDFLVSDDPL 119

Query: 209 -DGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            D Q   +I+ E    RR +L  ++  LN RE
Sbjct: 120 PDEQVSNMIDGER---RRVLLASALKHLNERE 148


>gi|222152854|ref|YP_002562031.1| RNA polymerase sigma factor RpoD [Streptococcus uberis 0140J]
 gi|222113667|emb|CAR41594.1| RNA polymerase sigma factor RpoD [Streptococcus uberis 0140J]
          Length = 369

 Score =  108 bits (271), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 87/273 (31%), Positives = 142/273 (52%), Gaps = 29/273 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L   EE  LA      GD+ A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLTSDEEKELAIAV-AAGDVDAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKL- 219

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSS 193
               +R  +  LQ +   +  PEQ   IA+++ ++  +V  +  ++A +  SL   I   
Sbjct: 220 ----VREQRNLLQELG-QDPTPEQ---IAERMEMTPDKVREI-LKIAQEPVSLETPIGEE 270

Query: 194 DKNSSQWQDWLVYDHDGQEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQ 249
           D   S   D++      +++V+   ++   R   R  L   +  L  RE  +   R  L 
Sbjct: 271 D--DSHLGDFI------EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLD 322

Query: 250 ENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +  + TLE++   F V+RER+RQIEA+A +K++
Sbjct: 323 DGKMRTLEDVGKVFNVTRERIRQIEAKALRKLR 355


>gi|291550766|emb|CBL27028.1| RNA polymerase, sigma 70 subunit, RpoD [Ruminococcus torques L2-14]
          Length = 280

 Score =  108 bits (271), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 88/286 (30%), Positives = 142/286 (49%), Gaps = 38/286 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y++EI +IP+L ++EE  L  +    GD  A  +L   +LRLVV +A  Y G G+ +
Sbjct: 17  LKIYLNEIGQIPLLSEEEERDLGCKSA-SGDEDARRKLEEGNLRLVVSLAKHYTGRGITL 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--TTANQK 133
            +++ EGNIGLM A +K+D  +  R +TY+ WWIK AMQ  I +    +++      N K
Sbjct: 76  MDLIQEGNIGLMHAAEKYDYTKENRFSTYASWWIKEAMQRAIDQQSREIRVPVHVAENMK 135

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV-----------ISMNCRLAG 182
           +    ++++   LQ        PE+   IA+++     E            +S+   +  
Sbjct: 136 K----VQKISKDLQQKFGREATPEE---IAEEMKDKSPEFVKEILSYLQNPVSLETPVGE 188

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
           D   N      DK+++  +D +          L++KEE       +   +  LN RER++
Sbjct: 189 DGENNLGDMVEDKDATTPEDAM--------NQLVQKEE-------VQELLESLNDRERQV 233

Query: 243 FEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              R  L++    TLE +  E  V+RERVRQIEARA +K++    K
Sbjct: 234 IRLRFGLEDGKTHTLEEIGDELNVTRERVRQIEARAMEKLRSKATK 279


>gi|325263837|ref|ZP_08130570.1| RNA polymerase sigma factor RpoD [Clostridium sp. D5]
 gi|324030875|gb|EGB92157.1| RNA polymerase sigma factor RpoD [Clostridium sp. D5]
          Length = 369

 Score =  108 bits (271), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 83/265 (31%), Positives = 133/265 (50%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  + E  LA+R  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 103 YLKEIGKVPLLSAEREIELAQRM-EDGDEDAKKELAEANLRLVVSIAKRYVGRGMLFLDL 161

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 162 IQEGNLGLIKAVEKFDYHKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 219

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L         PE+   IAK+L++    V  +        SL   I   ++  S
Sbjct: 220 LIRVSRQLLQELGREPTPEE---IAKELDMPVERVREILKISQEPVSLETPI--GEEEDS 274

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++    D    V  E   +   +  L   +  L  RE+++   R    +    TLE
Sbjct: 275 HLGDFI---QDDNVPVPAEAAAQTLLKEQLDEVLDTLTEREQKVLRLRFGMNDGRARTLE 331

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF+V+RER+RQIEA+A +K++
Sbjct: 332 EVGKEFDVTRERIRQIEAKALRKLR 356


>gi|149278736|ref|ZP_01884871.1| RNA polymerase sigma-70 factor [Pedobacter sp. BAL39]
 gi|149230355|gb|EDM35739.1| RNA polymerase sigma-70 factor [Pedobacter sp. BAL39]
          Length = 286

 Score =  108 bits (271), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 73/273 (26%), Positives = 150/273 (54%), Gaps = 13/273 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           + +Y+ +I +I +L  +EE  LA+R ++ GD +A  +LV ++LR VV +A  Y+  GL +
Sbjct: 18  IDKYLTDIGRIGLLSVEEELGLARRIKK-GDEAALDKLVKTNLRFVVSVAKKYQNKGLQL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++SEGN+GL++A ++FD  +GF+  ++++WWI+ ++ + +     ++++    NQ   
Sbjct: 77  ADLISEGNLGLIKAAQRFDDTKGFKFISFAVWWIRQSIMQALADQKRMIRL--PGNQVLG 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + +    L+ + +     E+   +A     SE++V           SL+  + + ++
Sbjct: 135 IIKINKAADELEQVLERAPTYEE---LAMATEFSEAKVADYLDSAPLSYSLD--MTTHEE 189

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER--RIFEARRLQENPV 253
           +     D LV ++      L+ KE        + RS+S+L  RE+   IF         +
Sbjct: 190 SDFSLMDTLVNENTPDTDELMMKESMSED---VRRSLSILPEREKWIIIFFFGLDNHTAL 246

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TL++++  F++S+ER+RQ++ RA K ++ S +K
Sbjct: 247 TLDDMTDVFQLSKERIRQLKDRALKTLKTSCRK 279


>gi|328465879|gb|EGF37062.1| RNA polymerase sigma factor RpoD [Lactobacillus helveticus MTCC
           5463]
          Length = 370

 Score =  108 bits (271), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 86/273 (31%), Positives = 133/273 (48%), Gaps = 31/273 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P++   +E  LAKR  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 104 YLKEIGRVPLITADQEIALAKRI-EEGDEEAKQELAEANLRLVVSIAKRYVGRGMSFLDL 162

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 163 IQEGNMGLMKAVDKFDYCLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 222

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + N+   +V  I   L +++ E +S+   +    D  L 
Sbjct: 223 RIQRQLLQDLGREPTPEEIGAEMNMPTNKVRDI---LKIAQ-EPVSLETPIGEEDDSHLG 278

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S +         +  EQVL    +R+   N+L     + + R R       
Sbjct: 279 DFIEDKDATSPEQHASYEMLKEQLEQVLETLTDREE--NVLRLRFGLDDGRTR------- 329

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                 TLE +   F V+RER+RQIEA+A +K+
Sbjct: 330 ------TLEEVGKVFGVTRERIRQIEAKALRKL 356


>gi|226311661|ref|YP_002771555.1| RNA polymerase sigma factor [Brevibacillus brevis NBRC 100599]
 gi|226094609|dbj|BAH43051.1| RNA polymerase sigma factor [Brevibacillus brevis NBRC 100599]
          Length = 376

 Score =  108 bits (271), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 87/275 (31%), Positives = 138/275 (50%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LA+R  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 110 YLKEIGRVPLLSAEEEIKLAQRI-EQGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 168

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-- 132
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 169 IQEGNMGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 228

Query: 133 ---KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
              ++L   L R     +     +L PE+V  I K       E +S+   +    D  L 
Sbjct: 229 RVSRQLLQELGREPMPEEIAEKMDLTPEKVREIMK----IAQEPVSLETPIGEEDDSHLG 284

Query: 188 ALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
             I   D+++ +  D   Y+   +  E VL    +R+   N+L     + + R R     
Sbjct: 285 DFIE--DQDALEPSDAAAYELLKEQLEDVLDTLTDREE--NVLRLRFGLDDGRTR----- 335

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                   TLE +   F V+RER+RQIEA+A +K+
Sbjct: 336 --------TLEEVGKVFGVTRERIRQIEAKALRKL 362


>gi|222151460|ref|YP_002560616.1| RNA polymerase sigma factor SigA [Macrococcus caseolyticus
           JCSC5402]
 gi|222120585|dbj|BAH17920.1| RNA polymerase sigma factor SigA [Macrococcus caseolyticus
           JCSC5402]
          Length = 366

 Score =  108 bits (271), Expect = 7e-22,   Method: Compositional matrix adjust.
 Identities = 87/275 (31%), Positives = 132/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 100 YLKEIGRVNLLSAEEEIELAKRI-EQGDEEAKARLAEANLRLVVSIAKRYVGRGMLFLDL 158

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 159 IQEGNMGLIKAVEKFDFTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 218

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L  E+V  I K       E +S+   +    D  L 
Sbjct: 219 RVQRQLLQDLGRDPSPEEIGEEMDLPAEKVREILK----IAQEPVSLETPIGEEDDSHLG 274

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 275 DFIEDQDAQSP-------ADHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 317

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 318 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 352


>gi|260655747|ref|ZP_05861216.1| RNA polymerase major sigma factor [Jonquetella anthropi E3_33 E1]
 gi|260629363|gb|EEX47557.1| RNA polymerase major sigma factor [Jonquetella anthropi E3_33 E1]
          Length = 969

 Score =  108 bits (271), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 86/273 (31%), Positives = 142/273 (52%), Gaps = 31/273 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ +I K+ +L+  EE  LAKR  E GD +A   ++ ++LRLVV IA  Y G G+   ++
Sbjct: 703 YLRDIGKVSLLDAAEEVALAKRV-EAGDETAKDEIINANLRLVVSIAKKYIGRGMQFLDL 761

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-- 132
           + EGN+GL++AV+KFD  RGF+ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 762 IQEGNLGLIRAVEKFDYRRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKMV 821

Query: 133 ---KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
              ++L   L R     +   +  ++PE+V  I +   +     +S+   + G+E  + L
Sbjct: 822 RISRQLVQKLGREPSDEEIAAEMKIEPERVEEIKRISQMP----VSLETPI-GEEEDSQL 876

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
            +  +  S    + +  D+  QEQ+            ML    + L+ RER +   R   
Sbjct: 877 GDFIEDRSLPSPEDVAADNLLQEQI----------EEML----NALSDREREVLRYRFGL 922

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
           E+    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 923 EDGRSYTLEEVGRRFGVTRERIRQIEAKALRKL 955


>gi|114776318|ref|ZP_01451363.1| RpoS [Mariprofundus ferrooxydans PV-1]
 gi|114553148|gb|EAU55546.1| RpoS [Mariprofundus ferrooxydans PV-1]
          Length = 282

 Score =  108 bits (271), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 80/276 (28%), Positives = 139/276 (50%), Gaps = 22/276 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI +  +L   EE  LAKR    GD  A H +V ++LRLVVKI+  Y   G+ ++++
Sbjct: 14  YMREISRYELLTAAEEIALAKRIGA-GDKEAHHYMVQANLRLVVKISRRYMNRGVALADL 72

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD   G R +TY+ WWI+ A++  I+     +++     ++     
Sbjct: 73  IEEGNLGLIRAVEKFDVTHGCRFSTYATWWIRQAVERAIMNQSRTIRVPVHVGKE----- 127

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI--NSSDKN 196
           L  L  H   +     +    V IA+ + VS   +          E + A +  +S+D  
Sbjct: 128 LYALTKHTNRLRSELERDPTDVEIAEAMGVSVQRI---------QELMGAAVRTDSADDM 178

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKN--RRNMLTRSMSVLNPRERRIFEARRLQE---N 251
                D+ +YD    E      ++ +   R  +L   MS L  +ER +   R   +   +
Sbjct: 179 LHDDSDFTLYDVTADEAAESPGDQMQTVLRNEILQVWMSKLEKKEREVVRLRYGLDDAGD 238

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           P TLE +  +  V+RER+RQI+ +A +K++  + ++
Sbjct: 239 PWTLEMIGEQLGVTRERIRQIQVQALQKLRRIVSQE 274


>gi|308174309|ref|YP_003921014.1| RpoD [Bacillus amyloliquefaciens DSM 7]
 gi|307607173|emb|CBI43544.1| RpoD [Bacillus amyloliquefaciens DSM 7]
 gi|328554255|gb|AEB24747.1| RNA polymerase sigma factor RpoD [Bacillus amyloliquefaciens TA208]
 gi|328912652|gb|AEB64248.1| RNA polymerase sigma factor rpoD [Bacillus amyloliquefaciens LL3]
          Length = 373

 Score =  108 bits (271), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 84/275 (30%), Positives = 135/275 (49%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE   A++  E GD  +  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 107 YLKEIGRVNLLSAKEEITYAQKI-EEGDEESKRRLAEANLRLVVSIAKRYVGRGMLFLDL 165

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 166 IQEGNMGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 225

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   D +L PE+V  I   L +++ E +S+   +    D  L 
Sbjct: 226 RVQRQLLQDLGREPTPEEIAEDMDLTPEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 281

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 282 DFIEDQEATSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 324

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 325 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 359


>gi|281355585|ref|ZP_06242079.1| RNA polymerase, sigma 32 subunit, RpoH [Victivallis vadensis ATCC
           BAA-548]
 gi|281318465|gb|EFB02485.1| RNA polymerase, sigma 32 subunit, RpoH [Victivallis vadensis ATCC
           BAA-548]
          Length = 248

 Score =  108 bits (271), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 79/239 (33%), Positives = 131/239 (54%), Gaps = 17/239 (7%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +LRLV KIA  + G GLP  ++VSEGN GLM A +++DP RG R +TYS WWIK A
Sbjct: 18  LIEENLRLVQKIANDFLGRGLPWEDLVSEGNRGLMTAARRYDPSRGARFSTYSAWWIKQA 77

Query: 113 MQEYILRSWSLVK--IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
           +++ I     +V+  IGT  + ++    +RR+   L     +    E+V   A+  N+  
Sbjct: 78  IRQAIAEQAQMVRVPIGTQTHWRK----IRRIVNELTEALGHAPSDEEV---AEAANLPL 130

Query: 171 SEVISM-NCRLAGDESLNALINSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNML 228
           + V  +   R    +SLNA I+  D +  ++QD+   D +   +Q LI+ E+ +N  ++L
Sbjct: 131 ATVNRLRGSRQIDVQSLNAPISDGDPDGGEFQDFFQDDTEPAPDQQLIKLEDVENLLSLL 190

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
                    RE+++   R  L   P+ TL+ + +E   + ERVRQI+ +A +K+   ++
Sbjct: 191 ETLTE----REQKVLRLRFGLDGEPIRTLDEVGTELNCTNERVRQIQNQALRKLHAQLE 245


>gi|325290508|ref|YP_004266689.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Syntrophobotulus
           glycolicus DSM 8271]
 gi|324965909|gb|ADY56688.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Syntrophobotulus
           glycolicus DSM 8271]
          Length = 392

 Score =  108 bits (271), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 86/270 (31%), Positives = 135/270 (50%), Gaps = 23/270 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LAK   E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 126 YLKEIGRVPLLTAEEEIELAKSM-EAGDEMAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 184

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 185 IQEGNLGLIKAVEKFDFRKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 242

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L      +  PE+    AK +++ E  V  +        SL   I   ++  S
Sbjct: 243 LIRVNRQLLQELGRDPTPEET---AKVMDIPEERVREIMKIAQEPVSLETPIG--EEEDS 297

Query: 199 QWQDWLVYDHDG-----QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-- 251
              D+ + D D          L+ KE+       L   +  L  RE ++   R   ++  
Sbjct: 298 HLGDF-IPDEDAPAPSEAASFLLLKEQ-------LEEVLETLTSREEKVLRLRFGLDDGR 349

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 350 TRTLEEVGQEFGVTRERIRQIEAKALRKLR 379


>gi|154686781|ref|YP_001421942.1| RNA polymerase sigma factor RpoD [Bacillus amyloliquefaciens FZB42]
 gi|154352632|gb|ABS74711.1| RpoD [Bacillus amyloliquefaciens FZB42]
          Length = 373

 Score =  108 bits (271), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 84/275 (30%), Positives = 132/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE   A++  E GD  +  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 107 YLKEIGRVNLLSAKEEITYAQKI-EEGDEESKRRLAEANLRLVVSIAKRYVGRGMLFLDL 165

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 166 IQEGNMGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 225

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   D +L PE+V  I K       E +S+   +    D  L 
Sbjct: 226 RVQRQLLQDLGREPTPEEIAEDMDLTPEKVREILKIAQ----EPVSLETPIGEEDDSHLG 281

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 282 DFIEDQEATSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 324

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 325 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 359


>gi|110638185|ref|YP_678394.1| RNA polymerase sigma-70 factor [Cytophaga hutchinsonii ATCC 33406]
 gi|110280866|gb|ABG59052.1| RNA polymerase sigma-70 factor [Cytophaga hutchinsonii ATCC 33406]
          Length = 287

 Score =  108 bits (271), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 83/285 (29%), Positives = 148/285 (51%), Gaps = 43/285 (15%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ +L   EE  LAKR RE GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGKVDLLTPDEEVDLAKRIRE-GDQLALEKLTKANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     +V++    N+   
Sbjct: 77  GDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL--PLNRVGS 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRLA-GDE 184
              + +    L+   +    P++   +A+ L VS +EV          +SM+     G+E
Sbjct: 135 LNKISKTFSELEQKYEREPSPDE---LAEVLEVSTAEVVDTLKISGRHVSMDAPFVQGEE 191

Query: 185 S--LNALINSSDK--NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +  L+ L NSS+   +SS   D L                    R  + R++S L  RE 
Sbjct: 192 NSLLDVLENSSESAPDSSLMNDSL--------------------RREVQRALSTLTQREA 231

Query: 241 RIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +         E+ +TLE +  +F ++RERVRQI+ +A ++++ +
Sbjct: 232 DVISLYFGLNGEHSMTLEEIGEKFNLTRERVRQIKEKAIRRLRHT 276


>gi|223985702|ref|ZP_03635749.1| hypothetical protein HOLDEFILI_03055 [Holdemania filiformis DSM
           12042]
 gi|223962313|gb|EEF66778.1| hypothetical protein HOLDEFILI_03055 [Holdemania filiformis DSM
           12042]
          Length = 408

 Score =  108 bits (271), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 88/281 (31%), Positives = 142/281 (50%), Gaps = 44/281 (15%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  ++E  +A+R  + GD  A   L++S+LRLVV IA  Y G G+   ++
Sbjct: 139 YLKEIGRVPLLNPEDEPEIARRI-QAGDEEAKRILISSNLRLVVSIAKKYVGRGMLFLDL 197

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT---------T 129
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I           T
Sbjct: 198 IQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLT 257

Query: 130 ANQKRLFFNLRR------LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-- 181
             Q++L  +L R      +   ++ IT + ++  Q +A+         E +S+   +   
Sbjct: 258 RVQRQLVQDLGREPTAEEIAEKMENITPDKVREIQKIAL---------EPVSLETPIGEE 308

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT-RSMSVLNPRER 240
            D  L   I   D  S         D     Q+L  K+E  N    LT R   VL  R  
Sbjct: 309 DDSHLGDFIEDKDAMSP--------DQYANNQLL--KDEINNVLQGLTEREEKVLRLR-F 357

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +++ R       TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 358 GLYDGRTR-----TLEEVGKEFNVTRERIRQIEAKALRKLK 393


>gi|89074640|ref|ZP_01161105.1| hypothetical DNA-directed RNA polymerase, sigma subunit
           [Photobacterium sp. SKA34]
 gi|89049578|gb|EAR55138.1| hypothetical DNA-directed RNA polymerase, sigma subunit
           [Photobacterium sp. SKA34]
          Length = 284

 Score =  108 bits (271), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 82/282 (29%), Positives = 145/282 (51%), Gaps = 30/282 (10%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           IGL  Y+ +I   P+L K +E   +++Y   GD  A  +L+ S+LRLVV IA  YR   L
Sbjct: 9   IGL--YMKDISSKPLLTKMDEIHYSRKYLR-GDNKAKEKLIESNLRLVVSIAKKYRAAHL 65

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++ EGN+GL+ AV+KFDPE+GFR +TY+ WWIK  ++  I      +++    +++
Sbjct: 66  LLGDMIDEGNLGLITAVEKFDPEKGFRFSTYATWWIKQNIERAIHNQNRAIRLPVHVSKE 125

Query: 134 -----RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
                R   +L + + H     D  L+  +       L   E  ++S++  +  DES   
Sbjct: 126 INALLRTHRDLMKKQNHEPTHEDIALQLNKETQDISTLLSYELNIVSLDQTIGDDESKGT 185

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKE--ERKNRRNMLTRSMSVLNPRERRIFEAR 246
           + +            LV D    EQ+       E  +  N+    ++ + PRER I   R
Sbjct: 186 IAS------------LVVD----EQIPSPSHIVEENSMVNLAEGLLNKIKPREREIL-CR 228

Query: 247 R---LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           R   +   P TL+ ++S   ++RERVRQ++ ++ ++++ +++
Sbjct: 229 RFGMMGYEPQTLQEVASALGLTRERVRQLQMKSLERLKMNLK 270


>gi|300812183|ref|ZP_07092625.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus PB2003/044-T3-4]
 gi|300496819|gb|EFK31899.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus PB2003/044-T3-4]
          Length = 372

 Score =  108 bits (271), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 83/274 (30%), Positives = 132/274 (48%), Gaps = 33/274 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE  LAKR  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 106 YLKEIGRVNLLTSEEEVALAKRI-EAGDEEAKQELAEANLRLVVSIAKRYVGRGMNFLDL 164

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD   G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 165 IQEGNMGLMKAVDKFDYRLGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 222

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLA--GDESLNA 188
           L R++  L      + +PE++ A        + + L + + E +S+   +    D +L  
Sbjct: 223 LIRIQRQLLQDLGRDPEPEEIGAEMDLPVKKVREILKICQ-EPVSLETPIGEEDDSNLGD 281

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-R 247
            I   D  S +        H   E +          +  L   +  L+ RE  +   R  
Sbjct: 282 FIEDKDAMSPEQ-------HAANEML----------KEQLAEVLDTLSDREEEVLRLRFG 324

Query: 248 LQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
           L +    TLE +   FEV+RER+RQIEA+A +K+
Sbjct: 325 LDDGKARTLEEVGQHFEVTRERIRQIEAKALRKL 358


>gi|282877766|ref|ZP_06286579.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           buccalis ATCC 35310]
 gi|281300082|gb|EFA92438.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           buccalis ATCC 35310]
          Length = 298

 Score =  108 bits (271), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 78/280 (27%), Positives = 144/280 (51%), Gaps = 28/280 (10%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI    ++  +EE  LA+R ++ GD  A  +L  ++LR VV +A  Y+  GL 
Sbjct: 28  ALDKYLQEIGHEDLISIEEEIELAQRIKK-GDRKALEKLTKANLRFVVSVAKQYQNQGLS 86

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK-----IGTT 129
           + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V+     +G+ 
Sbjct: 87  LPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGSV 146

Query: 130 ANQKRL---FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
               R+   F      + ++  I D    PE  +  A K+N     V +     A    L
Sbjct: 147 NKINRILNKFEQEHERRPNVDEIADQIDLPEDKIVEAMKVNGKHISVDAPIMEGADSSLL 206

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA- 245
           + L N+    S    + LV +               + R  +  +++VLN RER I E  
Sbjct: 207 DVLPNTE---SPMADNELVME---------------SLREEVASALNVLNERERNIIECF 248

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             + +  +TLE +  +F ++RERVRQI+ +A ++++++ +
Sbjct: 249 YGINQREMTLEEIGDKFGLTRERVRQIKEKALRRLRQNTK 288


>gi|257126628|ref|YP_003164742.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Leptotrichia
           buccalis C-1013-b]
 gi|257050567|gb|ACV39751.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Leptotrichia
           buccalis C-1013-b]
          Length = 392

 Score =  108 bits (271), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 80/269 (29%), Positives = 137/269 (50%), Gaps = 23/269 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI +IP+L  +EE   A+R  + G+  A  +L+ S+LRLVV IA  +   GL + ++
Sbjct: 126 YLREIGQIPLLSYEEEIDYAQRVLD-GEEEAKQKLIESNLRLVVSIAKKHTNRGLKMLDL 184

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV+KF+ E+GF+ +TY+ WWI+ A+   I      ++I        +   
Sbjct: 185 IQEGNMGLMKAVEKFEYEKGFKFSTYATWWIRQAITRAIADQGRTIRIPV-----HMIET 239

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           + ++K   + I     K      +A+KL +   +V S+        SL   + S +   S
Sbjct: 240 INKIKKESRIILQETGKEPTAEELAEKLELPVEKVKSILEMNQDPISLETPVGSEE--DS 297

Query: 199 QWQDWLVYD-----HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           +  D++  D     +D   ++L+        +  L   +  LN RE  +   R   ++  
Sbjct: 298 ELGDFVEDDKFANPYDATTRILL--------KEQLDEVLKTLNEREEMVLRYRYGLDDGS 349

Query: 254 --TLENLSSEFEVSRERVRQIEARAFKKV 280
             TLE +   F V+RER+RQIE +A +K+
Sbjct: 350 QKTLEEVGKIFNVTRERIRQIEVKALRKL 378


>gi|157693020|ref|YP_001487482.1| RNA polymerase sigma factor RpoD [Bacillus pumilus SAFR-032]
 gi|157681778|gb|ABV62922.1| DNA-directed RNA polymerase sigma subunit SigA [Bacillus pumilus
           SAFR-032]
          Length = 373

 Score =  108 bits (271), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 84/275 (30%), Positives = 135/275 (49%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE   A++  E GD  +  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 107 YLKEIGRVNLLSAKEEITYAQKI-EEGDEESKRRLAEANLRLVVSIAKRYVGRGMLFLDL 165

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 166 IQEGNMGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 225

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   D +L PE+V  I   L +++ E +S+   +    D  L 
Sbjct: 226 RVQRQLLQDLGREPTPEEIAEDMDLTPEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 281

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 282 DFIEDQEATSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 324

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 325 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 359


>gi|238927759|ref|ZP_04659519.1| possible DNA-directed RNA polymerase sigma subunit SigA
           [Selenomonas flueggei ATCC 43531]
 gi|238884475|gb|EEQ48113.1| possible DNA-directed RNA polymerase sigma subunit SigA
           [Selenomonas flueggei ATCC 43531]
          Length = 382

 Score =  108 bits (271), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 82/273 (30%), Positives = 141/273 (51%), Gaps = 21/273 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LA+R  E GD +A HRL  ++LRLVV IA  Y G G+   ++
Sbjct: 115 YLKEIGRVPLLTAEEEVELARRM-EAGDEAARHRLEEANLRLVVSIAKRYAGRGMMFLDL 173

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 174 IQEGNLGLLKAVEKFDYSKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 231

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
             R+   L      +  PE+   IA ++ +S + V  +        SL   I   ++  +
Sbjct: 232 YIRISRQLLQELGRDPTPEE---IAHRMGLSVARVREIMKISQEPVSLETPIG--EEEDT 286

Query: 199 QWQDWL----VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENP 252
           +  D++      D      +L+ KE+       ++  ++ L PRE  +   R   +    
Sbjct: 287 RLSDFIEDEAAPDPADAASMLLLKEQ-------ISEVLTTLAPREAEVLRLRFGLVDGRS 339

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            TLE +   F V+RER+RQIEA+A +K++  ++
Sbjct: 340 RTLEEVGQNFGVTRERIRQIEAKALRKLRHPVR 372


>gi|298208827|ref|YP_003717006.1| putative sigma factor A [Croceibacter atlanticus HTCC2559]
 gi|83848754|gb|EAP86623.1| putative sigma factor A [Croceibacter atlanticus HTCC2559]
          Length = 288

 Score =  108 bits (271), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 76/275 (27%), Positives = 145/275 (52%), Gaps = 28/275 (10%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+ ++ K+ ++  +EE  LA+R RE GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LNNYLQDVSKLDLITAEEEVELAQRIRE-GDQIALEKLTKANLRFVVSVAKQYQNQGLRL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + +     +V++    N+  +
Sbjct: 77  PDLINEGNVGLVKAAKRFDETRGFKFISYAVWWIRQSILQALAEHSRVVRL--PLNKIGV 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + +   +L+   +   +P     IAK+L++  S+V +         S++A     + 
Sbjct: 135 INKINKTFSYLEQAYE---RPPSAAEIAKELDMPVSKVKTAMKNSGRSLSMDAPFQEGEN 191

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV-----LNPRERRIFEARRLQ- 249
           +S+      +YD      VL   E      N++  S+SV     L+    R  +  RL  
Sbjct: 192 DSN------LYD------VLKSGESPSPDNNLMQDSLSVEIERALDTLTEREADVIRLNY 239

Query: 250 ----ENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
               + P+TL+ +   F++SRERVRQI  +  +++
Sbjct: 240 GLGGQQPLTLQEIGETFDLSRERVRQIREKGIRRL 274


>gi|1943995|dbj|BAA19494.1| sigA=sigma70 [Staphylococcus aureus]
          Length = 368

 Score =  108 bits (271), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 87/275 (31%), Positives = 132/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  QEE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGRVNLLSAQEEIELAKRI-EQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 161 IQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIAHQARTIRIPVHMVETINKLI 220

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L  E+V  I K       E +S+   +    D  L 
Sbjct: 221 RVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREILK----IAQEPVSLETPIGEEDDSHLG 276

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 277 DFIEDQEAQSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 319

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 320 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 354


>gi|28378605|ref|NP_785497.1| RNA polymerase sigma factor RpoD [Lactobacillus plantarum WCFS1]
 gi|300768133|ref|ZP_07078038.1| RNA polymerase sigma factor rpoD [Lactobacillus plantarum subsp.
           plantarum ATCC 14917]
 gi|308180761|ref|YP_003924889.1| RNA polymerase sigma factor RpoD [Lactobacillus plantarum subsp.
           plantarum ST-III]
 gi|28271441|emb|CAD64346.1| DNA-directed RNA polymerase, sigma factor 42 [Lactobacillus
           plantarum WCFS1]
 gi|300494197|gb|EFK29360.1| RNA polymerase sigma factor rpoD [Lactobacillus plantarum subsp.
           plantarum ATCC 14917]
 gi|308046252|gb|ADN98795.1| RNA polymerase sigma factor RpoD [Lactobacillus plantarum subsp.
           plantarum ST-III]
          Length = 368

 Score =  108 bits (271), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 87/279 (31%), Positives = 140/279 (50%), Gaps = 41/279 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LA R  E GD SA   L  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGRVDLLTADEEVALALRI-EQGDESAKQELAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 161 IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 220

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + ++  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 221 RIQRQLLQDLGREPTPEEIGAEMDMPTEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 276

Query: 188 ALINSSDKNSSQWQDWLVYD-----HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             I   D++++   D   Y+      +G    L ++EE     N+L     + + R R  
Sbjct: 277 DFIE--DQDATSPADAAAYELLKEQLEGVLDTLTDREE-----NVLRLRFGLDDGRTR-- 327

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                      TLE +   F V+RER+RQIEA+A +K++
Sbjct: 328 -----------TLEEVGKVFGVTRERIRQIEAKALRKLR 355


>gi|254519856|ref|ZP_05131912.1| transcription initiation factor sigma A [Clostridium sp. 7_2_43FAA]
 gi|226913605|gb|EEH98806.1| transcription initiation factor sigma A [Clostridium sp. 7_2_43FAA]
          Length = 370

 Score =  108 bits (270), Expect = 8e-22,   Method: Compositional matrix adjust.
 Identities = 83/265 (31%), Positives = 134/265 (50%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  +EE  LA R  E GD  A  +L  ++LRLVV IA  Y G G+   ++
Sbjct: 104 YLKEIGKVPLLSSEEEIELANRI-EQGDQRAKKKLAEANLRLVVSIAKRYVGRGMLFLDL 162

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 163 IQEGNLGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 220

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R++  L      +  PE+   I+K +++   +V  +        SL   I   ++  S
Sbjct: 221 LIRVQRQLLQELGRDPFPEE---ISKVMDLPVDKVREIQKIAQEPVSLETPI--GEEEDS 275

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++  D              K +   L   +  L PRE ++   R   ++    TLE
Sbjct: 276 HLGDFIPDDDALAPAEAAAFTMLKEQ---LINVLDTLTPREEKVLRLRFGLDDGRARTLE 332

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF V+RER+RQIEA+A +K++
Sbjct: 333 EVGKEFNVTRERIRQIEAKALRKLR 357


>gi|260062909|ref|YP_003195989.1| putative sigma factor A [Robiginitalea biformata HTCC2501]
 gi|88784477|gb|EAR15647.1| putative sigma factor A [Robiginitalea biformata HTCC2501]
          Length = 287

 Score =  108 bits (270), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 82/281 (29%), Positives = 146/281 (51%), Gaps = 41/281 (14%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ +I KI ++   EE  LA+R ++ GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQDISKIDLITANEEVELAQRIKQ-GDQLALEKLTKANLRFVVSVAKQYQNQGLKL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
            ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++      Q  ++R   L KIG+ 
Sbjct: 77  PDLINEGNVGLVKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRVVR-LPLNKIGSI 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
              K+ F  L +           + +P     IAK+L+++ SEV   + + +G       
Sbjct: 136 NKIKKTFSYLEQ----------AHERPPSAEEIAKELDMTVSEV-KQSIKNSGRHV---- 180

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML--------TRSMSVLNPRERR 241
             S D    + +D  +YD      VL   E  K  ++++         R++  L+PRE  
Sbjct: 181 --SMDAPLREGEDSNLYD------VLRSGESPKPDKSLMLQSLNTEINRALETLSPREAD 232

Query: 242 IFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + +       +  +TL  +   F+++RERVRQI  +A +K+
Sbjct: 233 VVKLYYGIGDQQSMTLAEIGQTFDLTRERVRQIREKAIRKL 273


>gi|221310444|ref|ZP_03592291.1| RNA polymerase sigma factor RpoD [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221314767|ref|ZP_03596572.1| RNA polymerase sigma factor RpoD [Bacillus subtilis subsp. subtilis
           str. NCIB 3610]
 gi|221319690|ref|ZP_03600984.1| RNA polymerase sigma factor RpoD [Bacillus subtilis subsp. subtilis
           str. JH642]
 gi|221323967|ref|ZP_03605261.1| RNA polymerase sigma factor RpoD [Bacillus subtilis subsp. subtilis
           str. SMY]
 gi|255767573|ref|NP_390399.2| RNA polymerase sigma factor RpoD [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|296333322|ref|ZP_06875775.1| RNA polymerase sigma factor RpoD [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305675173|ref|YP_003866845.1| RNA polymerase major sigma-43 factor (sigma-A) [Bacillus subtilis
           subsp. spizizenii str. W23]
 gi|321312003|ref|YP_004204290.1| RNA polymerase sigma factor RpoD [Bacillus subtilis BSn5]
 gi|251757327|sp|P06224|RPOD_BACSU RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-43; AltName: Full=Sigma-A
 gi|225185201|emb|CAB14450.2| RNA polymerase major sigma-43 factor (sigma-A) [Bacillus subtilis
           subsp. subtilis str. 168]
 gi|296149520|gb|EFG90416.1| RNA polymerase sigma factor RpoD [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305413417|gb|ADM38536.1| RNA polymerase major sigma-43 factor (sigma-A) [Bacillus subtilis
           subsp. spizizenii str. W23]
 gi|320018277|gb|ADV93263.1| RNA polymerase sigma factor RpoD [Bacillus subtilis BSn5]
          Length = 371

 Score =  108 bits (270), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 84/275 (30%), Positives = 135/275 (49%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE   A++  E GD  +  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 105 YLKEIGRVNLLSAKEEIAYAQKI-EEGDEESKRRLAEANLRLVVSIAKRYVGRGMLFLDL 163

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 164 IQEGNMGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 223

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   D +L PE+V  I   L +++ E +S+   +    D  L 
Sbjct: 224 RVQRQLLQDLGREPTPEEIAEDMDLTPEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 279

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 280 DFIEDQEATSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 322

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 323 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 357


>gi|149277811|ref|ZP_01883951.1| RNA polymerase sigma-70 factor [Pedobacter sp. BAL39]
 gi|149231499|gb|EDM36878.1| RNA polymerase sigma-70 factor [Pedobacter sp. BAL39]
          Length = 288

 Score =  108 bits (270), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 82/281 (29%), Positives = 149/281 (53%), Gaps = 12/281 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           R + SI   G   L +Y+ EI KI +L  +EE  LA   RE GD +A  +LV+++LR VV
Sbjct: 5   RISKSITDRGGDSLEKYLSEISKIELLNVEEEVRLASIVRE-GDRAALDKLVSANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL +++++SEGN+GL++A  ++D  +GF+  ++++WWI+ ++   I     
Sbjct: 64  SVAKNYQDMGLRLADLISEGNLGLIKAASRYDHTKGFKFISFAVWWIRQSITYAIADQHR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           ++++    NQ      L R    L+   +     E+V   A+ L++ E++V+        
Sbjct: 124 MIRL--PGNQIVGITRLNRTSDLLEQKLERRPSLEEV---AEALDLPETKVVDYQMSALK 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             SL+  I   +  ++        + +  + VL  +   +N R +L    S+L PRE++I
Sbjct: 179 TTSLDMPILLGEPGTTFGHMIRNSEVEAADAVLDRQSLAENVRRLL----SILPPREQKI 234

Query: 243 FEARR-LQENPVT-LENLSSEFEVSRERVRQIEARAFKKVQ 281
                 L   P T LE++   F +S+ER+RQ++ +A K ++
Sbjct: 235 LSLYYGLGGMPQTRLEDMVPVFHLSKERLRQLKDKAVKTLK 275


>gi|51891726|ref|YP_074417.1| RNA polymerase sigma factor RpoD [Symbiobacterium thermophilum IAM
           14863]
 gi|51855415|dbj|BAD39573.1| RNA polymerase major sigma factor [Symbiobacterium thermophilum IAM
           14863]
          Length = 388

 Score =  108 bits (270), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 79/273 (28%), Positives = 130/273 (47%), Gaps = 31/273 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE + A+R  E GD  A  +L  ++LRLVV IA  Y G G+   ++
Sbjct: 122 YLKEIGRVPLLTAEEEIMYAERI-EKGDEEAKRKLAEANLRLVVSIAKRYVGRGMQFLDL 180

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 181 IQEGNLGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 238

Query: 139 LRRLKGHLQAITDNNLKPEQVVAI-------AKKLNVSESEVISMNCRLAGDES--LNAL 189
           L R+   L         PE++ A+        +++     E +S+   +  +E   L   
Sbjct: 239 LIRVTRQLVQELGREPTPEEIAAVMDIPVERVREIQKIAQEPVSLETPIGEEEDSHLGDF 298

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   D  +           +  E+VL                   L PRE ++   R   
Sbjct: 299 IEDQDAPAPAEAASFTLLKEQLEEVL-----------------ESLTPREEKVLRLRFGL 341

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
           ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 342 DDGRARTLEEVGQVFGVTRERIRQIEAKALRKL 374


>gi|219684379|ref|ZP_03539323.1| RNA polymerase sigma factor [Borrelia garinii PBr]
 gi|219685569|ref|ZP_03540385.1| RNA polymerase sigma factor [Borrelia garinii Far04]
 gi|219672368|gb|EED29421.1| RNA polymerase sigma factor [Borrelia garinii PBr]
 gi|219672847|gb|EED29870.1| RNA polymerase sigma factor [Borrelia garinii Far04]
          Length = 266

 Score =  108 bits (270), Expect = 9e-22,   Method: Compositional matrix adjust.
 Identities = 83/282 (29%), Positives = 149/282 (52%), Gaps = 20/282 (7%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M+I  N ++ +  Y+  +R+  ++  +EE  LA +  + G+  A ++++ ++LRLV+KI 
Sbjct: 1   MNIFSNEDLNI--YLKSVREHKLITHEEEIKLAGQI-QRGNAQAKNKMINANLRLVLKII 57

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y G GL I +++ EGN+GL++A +K+DP +  + +TY+ +WIK ++Q  +     LVK
Sbjct: 58  KRYAGKGLKIEDLIQEGNLGLIRAAEKYDPNKNTKFSTYASFWIKQSLQRALNTKTRLVK 117

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           +          +    L   +        K  +   I K+ N+S ++ I +   L  + S
Sbjct: 118 VP---------YRKENLILQINKYLTEEEKSPKKEEIMKRFNLSPAQYIKIIPYLEKEYS 168

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L+  I  S+ NS+     L  D+    ++ +E++      N +  +   LN +ER I + 
Sbjct: 169 LDKEIEGSE-NSTLLN--LYEDNSFNPEITLEQDSTIKHLNYVLETK--LNEKERYIIKK 223

Query: 246 R-RLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L  NP   TL+++S+E  +S E VRQIE R  KK++E I
Sbjct: 224 RYNLDNNPKKSTLKDISTELGISSETVRQIEKRVLKKLKEEI 265


>gi|296112139|ref|YP_003622521.1| RNA polymerase sigma factor [Leuconostoc kimchii IMSNU 11154]
 gi|295833671|gb|ADG41552.1| RNA polymerase sigma factor [Leuconostoc kimchii IMSNU 11154]
          Length = 432

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 86/274 (31%), Positives = 135/274 (49%), Gaps = 31/274 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L+  EE  +AKR  E GD+ A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 162 YLKEIGRVNLLKGDEEINIAKRI-EDGDVEAKQELAEANLRLVVSIAKRYVGRGMQFLDL 220

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 221 IQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 280

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             Q++L  +L R     +   + +L P++V  I   L +++  V           SL   
Sbjct: 281 RIQRQLLQDLGREPLPEEIGAEMDLTPDKVREI---LKIAQEPV-----------SLETP 326

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   D   S   D++    D +     +    +  R  L   +  L  RE  +   R   
Sbjct: 327 IGEED--DSHLGDFI---EDNEAISPADSAAYEMLREQLESVLETLTDREENVLRLRFGL 381

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           E+    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 382 EDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLR 415


>gi|163754266|ref|ZP_02161389.1| RNA polymerase sigma-70 factor [Kordia algicida OT-1]
 gi|161326480|gb|EDP97806.1| RNA polymerase sigma-70 factor [Kordia algicida OT-1]
          Length = 287

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 79/287 (27%), Positives = 153/287 (53%), Gaps = 37/287 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ ++   EE  LA+R +  GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGKVDLITADEEVELAQRIKA-GDQIALEKLTKANLRFVVSVAKQYQNQGLTL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
            ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++      Q  I+R   L KIG+ 
Sbjct: 77  PDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVR-LPLNKIGSI 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA- 188
               + F  L +    + +  +          IAK+L+++ ++V           S++A 
Sbjct: 136 NKINKTFAYLEQSHERIPSAEE----------IAKELDMTVNDVKESMKNSGRHVSMDAP 185

Query: 189 LINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           L+   D N        +YD  + G+     ++   ++ +  + R++  L PRE  +    
Sbjct: 186 LVEGEDSN--------LYDVLNSGESPNPDKELLHESLKTEIERALETLTPREADVI--- 234

Query: 247 RL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RL      ++P+TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 235 RLYFGLGNQHPMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|90416198|ref|ZP_01224130.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2207]
 gi|90331923|gb|EAS47137.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2207]
          Length = 306

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 85/275 (30%), Positives = 150/275 (54%), Gaps = 18/275 (6%)

Query: 17  SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
           S Y+ EI   P+L   EE   A++  + GD SA  R++ S+LRLVVKIA  Y   GL + 
Sbjct: 32  SLYLKEIGYAPLLTAAEEVFYARKLLK-GDESARKRMIESNLRLVVKIARRYVNRGLELL 90

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++ EGNIGLM+AV+KFDPE G+R +TY+ WWI+  ++  ++     +++      K L 
Sbjct: 91  DLIEEGNIGLMRAVEKFDPELGYRFSTYATWWIRQTIERGLMNQTRTIRLPVHI-VKELN 149

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
             +R  +   Q + D+   PE+   IA++++    +V+ +        SL+  I+S D  
Sbjct: 150 VYVRASRKLAQRL-DHTPTPEE---IAEEVDKPVEDVLKIF-------SLSERISSIDIP 198

Query: 197 SSQWQDWLVYDHDGQEQVLIEKE-ERKNRRNMLTRSMSVLNPRERRIFEARR---LQENP 252
            ++ +  L+     +     E++ E +N   +L + ++ L  ++R +   RR   L    
Sbjct: 199 VAENEKSLIETISAEGASSPERQVEGENLSEVLNKWLAQLPEKQREVL-VRRFGLLHHQE 257

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            TLE +  E  ++RERVRQI+  A +++++ ++K 
Sbjct: 258 ETLEQVGREIGLTRERVRQIQVDALRRLRDVLRKH 292


>gi|325686026|gb|EGD28084.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           delbrueckii subsp. lactis DSM 20072]
          Length = 372

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 86/275 (31%), Positives = 132/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE  LAKR  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 106 YLKEIGRVNLLTSEEEVALAKRI-EAGDEEAKQELAEANLRLVVSIAKRYVGRGMNFLDL 164

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV KFD   G++ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 165 IQEGNMGLMKAVDKFDYRLGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 224

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L  ++V  I K       E +S+   +    D +L 
Sbjct: 225 RIQRQLLQDLGRDPEPEEIGAEMDLPVKKVREILKLCQ----EPVSLETPIGEEDDSNLG 280

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR- 246
             I   D  S +        H   E +          +  L   +  L+ RE  +   R 
Sbjct: 281 DFIEDKDAMSPEQ-------HAANEML----------KEQLAEVLDTLSDREEEVLRLRF 323

Query: 247 RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
            L +    TLE +   FEV+RER+RQIEA+A +K+
Sbjct: 324 GLDDGKARTLEEVGQHFEVTRERIRQIEAKALRKL 358


>gi|296121869|ref|YP_003629647.1| RNA polymerase sigma factor, sigma-70 family [Planctomyces
           limnophilus DSM 3776]
 gi|296014209|gb|ADG67448.1| RNA polymerase sigma factor, sigma-70 family [Planctomyces
           limnophilus DSM 3776]
          Length = 290

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 77/273 (28%), Positives = 142/273 (52%), Gaps = 17/273 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ EI +  +L  ++E  LA R   +G+  A  R+V ++LRLVV IA  Y G GLP+
Sbjct: 28  LETYLREINETALLTARDERELANRI-ANGEKEARDRMVRANLRLVVNIARAYVGKGLPL 86

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GL++AV+ FDP+   R +TY+ +WIK +++  ++     ++I   A    L
Sbjct: 87  QDLIEEGNLGLLRAVEGFDPDMNTRFSTYASYWIKQSIKRALINCGKTIRI--PAYMVEL 144

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
               R+    L+   D   +P     +A +L + + ++  +   +        L +S+ +
Sbjct: 145 LSKWRKATAKLE---DQFKRPPTQEEVAIELGLPKKKLSIVKKAI-------HLYSSTPQ 194

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM--LTRSMSVLNPRERRIFEARRLQEN-- 251
              +   W++ D    E+V    +E  +  N+  +   +  ++ RE +I   R   ++  
Sbjct: 195 TDDEESGWMMSDMVADERVKGPDDELLDVDNLKHVYAMLETMDEREAKILRLRFGLDDSE 254

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           P TL+ +  E  ++RERVRQIE+ A K++ + I
Sbjct: 255 PKTLKEIGEEMGLTRERVRQIESEALKRIAKRI 287


>gi|169334166|ref|ZP_02861359.1| hypothetical protein ANASTE_00560 [Anaerofustis stercorihominis DSM
           17244]
 gi|169258883|gb|EDS72849.1| hypothetical protein ANASTE_00560 [Anaerofustis stercorihominis DSM
           17244]
          Length = 403

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 87/269 (32%), Positives = 142/269 (52%), Gaps = 21/269 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+ +L  +EE  LA++  E GD+ A  +L  ++LRLVV IA  Y   G+   ++
Sbjct: 138 YLKEIGKVDLLSAEEELDLAQKI-ESGDVEARKKLCEANLRLVVSIAKRYVNRGMSFLDL 196

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 197 IQEGNLGLLKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 254

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L+R++  L  I D    P     IAK++ + E +V  +  +++ D  SL   I   ++  
Sbjct: 255 LKRVQRML--IQDLGRDPNS-HEIAKEMGLPEEKVRDI-MKISQDPVSLETPI--GEEED 308

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNR---RNMLTRSMSVLNPRERRIFEARRLQEN--P 252
           S   D+ + D D      +  EE  +    R  L   +  L  RE ++   R   E+  P
Sbjct: 309 SHLGDF-IPDDDA-----VAPEEAASYMLLRTQLFEVLKTLTDREAKVLILRFGLEDGRP 362

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE +   F V+RER+RQIEA+A +K++
Sbjct: 363 RTLEEVGDIFCVTRERIRQIEAKALRKLR 391


>gi|40143|emb|CAA27538.1| unnamed protein product [Bacillus subtilis]
 gi|143454|gb|AAA22709.1| RNA polymerase sigma-43 factor [Bacillus subtilis]
 gi|1303833|dbj|BAA12489.1| RpoD [Bacillus subtilis]
          Length = 371

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 84/275 (30%), Positives = 135/275 (49%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE   A++  E GD  +  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 105 YLKEIGRVNLLSAKEEIAYAQKI-EEGDEESKRRLAEANLRLVVSIAKRYVGRGMLFLDL 163

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 164 IHEGNMGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 223

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   D +L PE+V  I   L +++ E +S+   +    D  L 
Sbjct: 224 RVQRQLLQDLGREPTPEEIAEDMDLTPEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 279

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 280 DFIEDQEATSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 322

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 323 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 357


>gi|258446806|ref|ZP_05694960.1| transcription initiation factor sigma plaC [Staphylococcus aureus
           A6300]
 gi|257854381|gb|EEV77330.1| transcription initiation factor sigma plaC [Staphylococcus aureus
           A6300]
          Length = 368

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 87/275 (31%), Positives = 132/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  QEE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGRVNLLSAQEEIELAKRI-EQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 161 IQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 220

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L  E+V  I K       E +S+   +    D  L 
Sbjct: 221 RVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREILK----IAQEPVSLETPIGEEDDSHLG 276

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 277 DFIEDQEAQSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 319

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 320 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 354


>gi|258437393|ref|ZP_05689377.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A9299]
 gi|257848598|gb|EEV72586.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A9299]
          Length = 368

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 87/275 (31%), Positives = 132/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  QEE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGRVNLLSAQEEIELAKRI-EQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 161 IQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 220

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L  E+V  I K       E +S+   +    D  L 
Sbjct: 221 RVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREILK----IAQEPVSLETPIGEEDDSHLG 276

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 277 DFIEDQEAQSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 319

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 320 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 354


>gi|312134852|ref|YP_004002190.1| RNA polymerase, sigma 70 subunit, rpod subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|311774903|gb|ADQ04390.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor owensensis OL]
          Length = 273

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 82/273 (30%), Positives = 148/273 (54%), Gaps = 37/273 (13%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           +L  +EE  LAKR  E GD  A  +L  ++ RLV  IA  YRG+GL   +++ EG IGLM
Sbjct: 17  LLTPEEEIELAKRI-EQGDEKAKEKLFRANKRLVANIAKRYRGFGLDYEDLMQEGFIGLM 75

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
            AV K+D  +G+R ATY+ WWI+ A+ + I  +   +++    +++   F +R++  + +
Sbjct: 76  NAVNKYDYRQGYRFATYATWWIRQAITKAIYNTGRNIRVPIHLHEQ--MFKIRKV--YRK 131

Query: 148 AITDNNLKPEQVVAIAKKLNVSE----------SEVISMNCRLAGDESLNALINS--SDK 195
            + +NN +P  +  IAK++N S           +E++S++  + G++ L  + +    DK
Sbjct: 132 LLQENNREP-TIREIAKEMNWSTKKVQKMLDLFNEIVSLDTPI-GEDGLATIGDFMIDDK 189

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPV 253
             S       Y  + ++Q+L+E+         LT+    L+ +E+R+   R         
Sbjct: 190 AFS-------YFENVEKQLLVEQ---------LTKYFDKLSEKEKRVIVLRYGLADGKGR 233

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TLE + +   ++RER+RQIE +A +K++ ++ K
Sbjct: 234 TLEEVGNALNLTRERIRQIEIKALRKIRYNLLK 266


>gi|329733136|gb|EGG69473.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus 21193]
          Length = 314

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 87/276 (31%), Positives = 133/276 (48%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  QEE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 48  YLKEIGRVNLLSAQEEIELAKRI-EQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDL 106

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 107 IQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 166

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L  E+V  I K       E +S+   +    D  L 
Sbjct: 167 RVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREILK----IAQEPVSLETPIGEEDDSHLG 222

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 223 DFIEDQEAQSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 265

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 266 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 301


>gi|304437692|ref|ZP_07397644.1| DNA-directed RNA polymerase sigma subunit SigA [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
 gi|304369325|gb|EFM22998.1| DNA-directed RNA polymerase sigma subunit SigA [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
          Length = 381

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 82/273 (30%), Positives = 140/273 (51%), Gaps = 21/273 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LA+R  E GD +A HRL  ++LRLVV IA  Y G G+   ++
Sbjct: 114 YLKEIGRVPLLTAEEEVDLARRM-EAGDETARHRLEEANLRLVVSIAKRYVGRGMMFLDL 172

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 173 IQEGNLGLLKAVEKFDYSKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 230

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
             R+   L      +  PE+   IA ++ +S + V  +        SL   I   ++  +
Sbjct: 231 YIRVSRQLLQELGRDPTPEE---IAHRMGLSVARVREIMKISQEPVSLETPIG--EEEDT 285

Query: 199 QWQDWL----VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENP 252
              D++      D      +L+ KE+       ++  ++ L PRE  +   R   +    
Sbjct: 286 HLSDFIEDEAAPDPADAASMLLLKEQ-------ISEVLTTLAPREAEVLRLRFGLVDGRS 338

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            TLE +   F V+RER+RQIEA+A +K++  ++
Sbjct: 339 RTLEEVGQNFGVTRERIRQIEAKALRKLRHPVR 371


>gi|261879259|ref|ZP_06005686.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           bergensis DSM 17361]
 gi|270334090|gb|EFA44876.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           bergensis DSM 17361]
          Length = 291

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 82/277 (29%), Positives = 145/277 (52%), Gaps = 21/277 (7%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYG 72
            L RY+ EI + PML   EE +LA+   + G     A  RLV+ +LR VV +A  Y+  G
Sbjct: 17  ALDRYLSEIAREPMLSPDEEAMLAQAIHKGGPEGDRARDRLVSGNLRFVVSVAKQYQHQG 76

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           + + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ E +     +V        
Sbjct: 77  ISLIDLINEGNMGLVKAAEKFDETRGFKFISYAVWWIRQSIMEALAVKSRIV-------- 128

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVA----IAKKLNVSESEVISMNCRLAGDESLNA 188
            R+  N   + G +   T++ L+    V     +A+ L V E+++ +     A   S++A
Sbjct: 129 -RMPLNQVGIYGKVIRTTESFLQEHGRVPSNHELAEILQVEEAQITAAMSAGARATSIDA 187

Query: 189 LINSSDKNSSQWQDWLVYDHDG-QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF-EAR 246
            + + +  S    D L  D  G +    ++KE      N L R   VL+ RE+RI  E+ 
Sbjct: 188 PLGNDEDGS--MADMLASDDSGMKSDSSLDKESMNQFINDLLR--EVLSAREQRIIKESF 243

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +     +LE ++    ++RER+RQ+  +A +K++ S
Sbjct: 244 GIGVMEKSLEEIADSMGMTRERIRQVREKALRKIRFS 280


>gi|237736224|ref|ZP_04566705.1| RNA polymerase sigma factor rpoD [Fusobacterium mortiferum ATCC
           9817]
 gi|229421777|gb|EEO36824.1| RNA polymerase sigma factor rpoD [Fusobacterium mortiferum ATCC
           9817]
          Length = 351

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 84/272 (30%), Positives = 146/272 (53%), Gaps = 27/272 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI +IP+L   EE   AKR  E GD  A+ +L+ ++LRLVV IA  +   GL + ++
Sbjct: 85  YLREIGQIPLLSHDEELEYAKRALE-GDEWASQQLIEANLRLVVSIAKKHTNRGLKLLDL 143

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGNIGLM+AV+KF+  +G++ +TY+ WWI+ A+   I      ++I      T N+ +
Sbjct: 144 IQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPVHMIETINKIK 203

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
                +  + +LQ  T  +  PE    +A++L +   +V ++        SL   + S +
Sbjct: 204 -----KEARIYLQE-TGKDATPE---VLAERLGMEVEKVKAIQEMNQDPISLETPVGSEE 254

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNR---RNMLTRSMSVLNPRERRIFEARRLQEN 251
              S+  D++      ++  ++   E  NR   R  L   ++ L+ RE ++   R   ++
Sbjct: 255 --DSELGDFV------EDNKMLNPYELTNRSLLREQLDGVLNSLSSREEKVLRYRYGLDD 306

Query: 252 --PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             P TLE +   F+V+RER+RQIE +A +K++
Sbjct: 307 GSPKTLEEVGKIFKVTRERIRQIEVKALRKLR 338


>gi|167768032|ref|ZP_02440085.1| hypothetical protein CLOSS21_02575 [Clostridium sp. SS2/1]
 gi|317498375|ref|ZP_07956670.1| RNA polymerase sigma factor RpoD [Lachnospiraceae bacterium
           5_1_63FAA]
 gi|167710361|gb|EDS20940.1| hypothetical protein CLOSS21_02575 [Clostridium sp. SS2/1]
 gi|291561030|emb|CBL39830.1| RNA polymerase, sigma 70 subunit, RpoD [butyrate-producing
           bacterium SSC/2]
 gi|316894269|gb|EFV16456.1| RNA polymerase sigma factor RpoD [Lachnospiraceae bacterium
           5_1_63FAA]
          Length = 363

 Score =  108 bits (270), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 83/274 (30%), Positives = 142/274 (51%), Gaps = 31/274 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L   EE  LA+R  E GD +A  +L  ++LRLVV IA  Y G G+   ++
Sbjct: 97  YLKEIGKVPLLSADEEIKLAQRM-EEGDEAAKKKLAEANLRLVVSIAKRYVGRGMLFLDL 155

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-- 132
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 156 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 215

Query: 133 ---KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
              ++L   L R     +   + ++  E+V  I   L +S+ E +S+   +  +E  +  
Sbjct: 216 RVSRQLLQELGREPSPEEIAEEMDIPVERVREI---LKISQ-EPVSLETPIGEEEDSHLG 271

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
               D+N     D   +        L++++        L   +  L  RE+++   R   
Sbjct: 272 DFIQDENVPVPADAAAF-------TLLKEQ--------LDEVLGTLTEREQKVLRLRFGL 316

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 317 DDSRARTLEEVGKEFNVTRERIRQIEAKALRKLR 350


>gi|257425686|ref|ZP_05602110.1| transcription initiation factor sigma plaC [Staphylococcus aureus
           subsp. aureus 55/2053]
 gi|257271380|gb|EEV03526.1| transcription initiation factor sigma plaC [Staphylococcus aureus
           subsp. aureus 55/2053]
          Length = 368

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 87/275 (31%), Positives = 132/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  QEE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGRVNLLSAQEEIELAKRI-EQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 161 IQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 220

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L  E+V  I K       E +S+   +    D  L 
Sbjct: 221 RVQRQLLQDLGREPAPEEIGEEMDLPAEKVREILK----IAQEPVSLETPIGEEDDSHLG 276

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 277 DFIEDQEAQSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 319

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 320 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 354


>gi|119357820|ref|YP_912464.1| RNA polymerase, sigma 32 subunit, RpoH [Chlorobium phaeobacteroides
           DSM 266]
 gi|119355169|gb|ABL66040.1| RNA polymerase, sigma 32 subunit, RpoH [Chlorobium phaeobacteroides
           DSM 266]
          Length = 299

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 87/305 (28%), Positives = 157/305 (51%), Gaps = 47/305 (15%)

Query: 9   IVNGE-IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS-----------AAHRLVTS 56
           I N E + L RY+ EI K  +L  ++E  L K  +E  D             A  +L+  
Sbjct: 10  ITNRESLSLDRYLQEIGKYDLLTAEDEVKLTKAIKEGYDTPVDTVEYRRAKRALDKLIKG 69

Query: 57  HLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM--- 113
           +LR VV +A  Y+  GL + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++   
Sbjct: 70  NLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQA 129

Query: 114 ---QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
              Q  I+R   L ++GT     + +  L +     +   D N +      +A  L++ +
Sbjct: 130 LAEQSRIVR-LPLNRVGTLNKISKAYSQLEQ-----EFERDPNTRE-----LANLLDM-D 177

Query: 171 SEVISMNCRLAGDE-SLNALINSSDKN---SSQWQDWLVYDHD-GQEQVLIEKEERKNRR 225
           S+ ++   ++AG   S++A     D N        D  + DH   ++ + +E E      
Sbjct: 178 SQDVADTLKIAGRHVSVDAPFAQGDDNRLLDVLQNDGHLPDHGLNKDSLTLEVE------ 231

Query: 226 NMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               RS+SVL PRE  +  +      +NP+TLE +  +F+++RERVRQI+ +A +++++S
Sbjct: 232 ----RSLSVLAPREADVIRSYFGIGMDNPLTLEEIGEKFKLTRERVRQIKEKAIRRLRQS 287

Query: 284 IQKQV 288
              ++
Sbjct: 288 AYSKI 292


>gi|309775524|ref|ZP_07670524.1| RNA polymerase sigma factor RpoD [Erysipelotrichaceae bacterium
           3_1_53]
 gi|308916618|gb|EFP62358.1| RNA polymerase sigma factor RpoD [Erysipelotrichaceae bacterium
           3_1_53]
          Length = 397

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 82/272 (30%), Positives = 140/272 (51%), Gaps = 26/272 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L+ +EE  +A+R ++ GD  A  +L++++LRLVV IA  Y G G+   ++
Sbjct: 128 YLKEIGRVELLDPKEEPEIAQRIQD-GDEEAKKKLISANLRLVVSIAKKYVGRGMLFLDL 186

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 187 IQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINK-- 244

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               L R++  L  + D    P      AK  N+S  +V  +        SL   I   D
Sbjct: 245 ----LTRIQRQL--VQDLGRDPSAEEIAAKMENISPEKVREIQKIALEPVSLETPIGEED 298

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNR---RNMLTRSMSVLNPRERRIFEAR--RLQ 249
              S   D++      +++  +  +E  N    ++ +   +  L  RE ++   R     
Sbjct: 299 --DSHLGDFI------EDKEALSPDEYANNQLLKDEINTVLQGLTEREEKVLRLRFGLYD 350

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
               TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 351 GRTRTLEEVGKEFNVTRERIRQIEAKALRKLK 382


>gi|302391919|ref|YP_003827739.1| RNA polymerase, sigma 70 subunit, RpoD [Acetohalobium arabaticum
           DSM 5501]
 gi|302203996|gb|ADL12674.1| RNA polymerase, sigma 70 subunit, RpoD [Acetohalobium arabaticum
           DSM 5501]
          Length = 273

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 81/259 (31%), Positives = 145/259 (55%), Gaps = 18/259 (6%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           +L K+EE  LAK   ++GD  A   L+  +LRLVV IA  YRG G+   +++ EGN+GLM
Sbjct: 14  LLSKKEEAKLAKGA-QNGDQEARKELIEHNLRLVVSIAKKYRGKGMEFEDMIQEGNLGLM 72

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL-VKIGTTANQKRLFFNLRRLKGHL 146
           +A+ KFDP++G+R +TY+ WWI+ ++   +  + ++ V +       ++F    +L   L
Sbjct: 73  KAIDKFDPDKGYRFSTYATWWIRQSITRALPEAKTIRVPVHVWEKTTKVFKAKEKLYNQL 132

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN--SSDKNSSQWQDWL 204
                 N +P     I+++  + +SE +    R++ D++L +L N    D+N+   +  L
Sbjct: 133 ------NREP-TFEEISEETGI-DSEKVKEIIRISSDQNLASLNNLVGDDENTELGE--L 182

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEF 262
           + D D +E +      R+  +  L   +  L  RE  I   R  L++N P TL+ ++  F
Sbjct: 183 IADDDVEEPMT--DLNRQFLQEDLEEVLEELTDREAEIIRLRFGLKDNWPKTLQEVADRF 240

Query: 263 EVSRERVRQIEARAFKKVQ 281
           ++SRER+RQI+ +A ++++
Sbjct: 241 KLSRERIRQIQEKALRRLR 259


>gi|15924551|ref|NP_372085.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus Mu50]
 gi|21283242|ref|NP_646330.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus MW2]
 gi|49483810|ref|YP_041034.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus MRSA252]
 gi|49486397|ref|YP_043618.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus MSSA476]
 gi|57651954|ref|YP_186458.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus COL]
 gi|82751164|ref|YP_416905.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus RF122]
 gi|87162254|ref|YP_494216.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus USA300_FPR3757]
 gi|88195369|ref|YP_500173.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus NCTC 8325]
 gi|148268045|ref|YP_001246988.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus JH9]
 gi|150394113|ref|YP_001316788.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus JH1]
 gi|151221676|ref|YP_001332498.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus str. Newman]
 gi|156979879|ref|YP_001442138.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus Mu3]
 gi|161509790|ref|YP_001575449.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus USA300_TCH1516]
 gi|221140019|ref|ZP_03564512.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus str. JKD6009]
 gi|253314932|ref|ZP_04838145.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus str. CF-Marseille]
 gi|253732214|ref|ZP_04866379.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus USA300_TCH959]
 gi|253733189|ref|ZP_04867354.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus TCH130]
 gi|255006347|ref|ZP_05144948.2| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus Mu50-omega]
 gi|257428347|ref|ZP_05604745.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus 65-1322]
 gi|257433672|ref|ZP_05610030.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus E1410]
 gi|257436586|ref|ZP_05612630.1| transcription initiation factor sigma plaC [Staphylococcus aureus
           subsp. aureus M876]
 gi|257793637|ref|ZP_05642616.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus A9781]
 gi|258411063|ref|ZP_05681343.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus A9763]
 gi|258420133|ref|ZP_05683088.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A9719]
 gi|258423989|ref|ZP_05686871.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus A9635]
 gi|258443599|ref|ZP_05691938.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A8115]
 gi|258448720|ref|ZP_05696832.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus A6224]
 gi|258450610|ref|ZP_05698672.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A5948]
 gi|258453537|ref|ZP_05701515.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A5937]
 gi|262049137|ref|ZP_06022014.1| RNA polymerase sigma factor [Staphylococcus aureus D30]
 gi|262051223|ref|ZP_06023447.1| RNA polymerase sigma factor [Staphylococcus aureus 930918-3]
 gi|269203189|ref|YP_003282458.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus ED98]
 gi|282893062|ref|ZP_06301296.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A8117]
 gi|282904143|ref|ZP_06312031.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus C160]
 gi|282905970|ref|ZP_06313825.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus Btn1260]
 gi|282908880|ref|ZP_06316698.1| RNA polymerase sigma factor RpoS [Staphylococcus aureus subsp.
           aureus WW2703/97]
 gi|282911199|ref|ZP_06319001.1| RNA polymerase sigma factor RpoS [Staphylococcus aureus subsp.
           aureus WBG10049]
 gi|282914368|ref|ZP_06322154.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus M899]
 gi|282916831|ref|ZP_06324589.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus D139]
 gi|282919337|ref|ZP_06327072.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus C427]
 gi|282920110|ref|ZP_06327835.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A9765]
 gi|282924662|ref|ZP_06332330.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus C101]
 gi|282928194|ref|ZP_06335799.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A10102]
 gi|283770637|ref|ZP_06343529.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus H19]
 gi|283958325|ref|ZP_06375776.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus A017934/97]
 gi|284024620|ref|ZP_06379018.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus 132]
 gi|293503442|ref|ZP_06667289.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus 58-424]
 gi|293510459|ref|ZP_06669165.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus M809]
 gi|293530999|ref|ZP_06671681.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus M1015]
 gi|294848592|ref|ZP_06789338.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A9754]
 gi|295406684|ref|ZP_06816489.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A8819]
 gi|295428139|ref|ZP_06820771.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus EMRSA16]
 gi|296275817|ref|ZP_06858324.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus MR1]
 gi|297207720|ref|ZP_06924155.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus ATCC 51811]
 gi|297245734|ref|ZP_06929599.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A8796]
 gi|297590895|ref|ZP_06949533.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus MN8]
 gi|300911801|ref|ZP_07129244.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus TCH70]
 gi|304380850|ref|ZP_07363510.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus ATCC BAA-39]
 gi|60390420|sp|Q6G905|RPOD_STAAS RecName: Full=RNA polymerase sigma factor rpoD
 gi|60390434|sp|Q6GGD8|RPOD_STAAR RecName: Full=RNA polymerase sigma factor rpoD
 gi|60393872|sp|P0A0I8|RPOD_STAAM RecName: Full=RNA polymerase sigma factor rpoD
 gi|60393873|sp|P0A0I9|RPOD_STAAW RecName: Full=RNA polymerase sigma factor rpoD
 gi|60393874|sp|P0A0J0|RPOD_STAA8 RecName: Full=RNA polymerase sigma factor rpoD
 gi|81694388|sp|Q5HFJ9|RPOD_STAAC RecName: Full=RNA polymerase sigma factor rpoD
 gi|153069|gb|AAB59090.1| sigma factor [Staphylococcus aureus]
 gi|14247332|dbj|BAB57723.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           Mu50]
 gi|21204682|dbj|BAB95378.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           MW2]
 gi|49241939|emb|CAG40633.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           MRSA252]
 gi|49244840|emb|CAG43300.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           MSSA476]
 gi|57286140|gb|AAW38234.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus COL]
 gi|82656695|emb|CAI81122.1| RNA polymerase sigma factor [Staphylococcus aureus RF122]
 gi|87128228|gb|ABD22742.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus USA300_FPR3757]
 gi|87202927|gb|ABD30737.1| RNA polymerase sigma factor, putative [Staphylococcus aureus subsp.
           aureus NCTC 8325]
 gi|147741114|gb|ABQ49412.1| RNA polymerase, sigma 70 subunit, RpoD family [Staphylococcus
           aureus subsp. aureus JH9]
 gi|149946565|gb|ABR52501.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus JH1]
 gi|150374476|dbj|BAF67736.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           str. Newman]
 gi|156722014|dbj|BAF78431.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           Mu3]
 gi|160368599|gb|ABX29570.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus USA300_TCH1516]
 gi|253724003|gb|EES92732.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus USA300_TCH959]
 gi|253728729|gb|EES97458.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus TCH130]
 gi|257275188|gb|EEV06675.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus 65-1322]
 gi|257281765|gb|EEV11902.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus E1410]
 gi|257283937|gb|EEV14060.1| transcription initiation factor sigma plaC [Staphylococcus aureus
           subsp. aureus M876]
 gi|257787609|gb|EEV25949.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus A9781]
 gi|257840213|gb|EEV64677.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus A9763]
 gi|257843844|gb|EEV68238.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A9719]
 gi|257845610|gb|EEV69642.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus A9635]
 gi|257851005|gb|EEV74948.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A8115]
 gi|257857998|gb|EEV80887.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus A6224]
 gi|257861768|gb|EEV84567.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A5948]
 gi|257864268|gb|EEV87018.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A5937]
 gi|259160860|gb|EEW45880.1| RNA polymerase sigma factor [Staphylococcus aureus 930918-3]
 gi|259162806|gb|EEW47371.1| RNA polymerase sigma factor [Staphylococcus aureus D30]
 gi|262075479|gb|ACY11452.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus ED98]
 gi|269941051|emb|CBI49435.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           TW20]
 gi|282313497|gb|EFB43892.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus C101]
 gi|282317147|gb|EFB47521.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus C427]
 gi|282319318|gb|EFB49670.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus D139]
 gi|282321549|gb|EFB51874.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus M899]
 gi|282324894|gb|EFB55204.1| RNA polymerase sigma factor RpoS [Staphylococcus aureus subsp.
           aureus WBG10049]
 gi|282327144|gb|EFB57439.1| RNA polymerase sigma factor RpoS [Staphylococcus aureus subsp.
           aureus WW2703/97]
 gi|282331262|gb|EFB60776.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus Btn1260]
 gi|282590001|gb|EFB95083.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A10102]
 gi|282594458|gb|EFB99443.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A9765]
 gi|282595761|gb|EFC00725.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus C160]
 gi|282764380|gb|EFC04506.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A8117]
 gi|283460784|gb|EFC07874.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus H19]
 gi|283470839|emb|CAQ50050.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Staphylococcus aureus subsp. aureus ST398]
 gi|283790474|gb|EFC29291.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus A017934/97]
 gi|285817243|gb|ADC37730.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus 04-02981]
 gi|290920267|gb|EFD97333.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus M1015]
 gi|291095108|gb|EFE25373.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus 58-424]
 gi|291466823|gb|EFF09343.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus M809]
 gi|294824618|gb|EFG41041.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A9754]
 gi|294968431|gb|EFG44455.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A8819]
 gi|295128497|gb|EFG58131.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus EMRSA16]
 gi|296887737|gb|EFH26635.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus ATCC 51811]
 gi|297177385|gb|EFH36637.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A8796]
 gi|297575781|gb|EFH94497.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus MN8]
 gi|298694843|gb|ADI98065.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           ED133]
 gi|300886047|gb|EFK81249.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus TCH70]
 gi|302333237|gb|ADL23430.1| RNA polymerase sigma-70 factor RpoD [Staphylococcus aureus subsp.
           aureus JKD6159]
 gi|302751392|gb|ADL65569.1| RNA polymerase sigma-70 factor RpoD [Staphylococcus aureus subsp.
           aureus str. JKD6008]
 gi|304340577|gb|EFM06511.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus ATCC BAA-39]
 gi|312437970|gb|ADQ77041.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus TCH60]
 gi|312829949|emb|CBX34791.1| RNA polymerase sigma factor rpoD (Sigma-A) (Sigma-43)
           [Staphylococcus aureus subsp. aureus ECT-R 2]
 gi|315129839|gb|EFT85829.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus CGS03]
 gi|315195463|gb|EFU25850.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus CGS00]
 gi|315198744|gb|EFU29072.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus CGS01]
 gi|320140554|gb|EFW32408.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus MRSA131]
 gi|320144091|gb|EFW35860.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus MRSA177]
 gi|323440459|gb|EGA98171.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus O11]
 gi|323443233|gb|EGB00851.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus O46]
 gi|329314237|gb|AEB88650.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus T0131]
 gi|329727416|gb|EGG63872.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus 21172]
 gi|329728458|gb|EGG64895.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus 21189]
          Length = 368

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 87/275 (31%), Positives = 132/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  QEE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGRVNLLSAQEEIELAKRI-EQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 161 IQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 220

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L  E+V  I K       E +S+   +    D  L 
Sbjct: 221 RVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREILK----IAQEPVSLETPIGEEDDSHLG 276

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 277 DFIEDQEAQSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 319

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 320 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 354


>gi|257452079|ref|ZP_05617378.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. 3_1_5R]
 gi|257466122|ref|ZP_05630433.1| RNA polymerase sigma factor RpoD [Fusobacterium gonidiaformans ATCC
           25563]
 gi|315917279|ref|ZP_07913519.1| RNA polymerase sigma factor RpoD [Fusobacterium gonidiaformans ATCC
           25563]
 gi|317058628|ref|ZP_07923113.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. 3_1_5R]
 gi|313684304|gb|EFS21139.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. 3_1_5R]
 gi|313691154|gb|EFS27989.1| RNA polymerase sigma factor RpoD [Fusobacterium gonidiaformans ATCC
           25563]
          Length = 272

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 85/279 (30%), Positives = 147/279 (52%), Gaps = 24/279 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           LS Y+ +IR+   LEK+EE  L  +  + GD  A ++L+  +LRLVV +A GYR  G+ +
Sbjct: 7   LSLYLKDIRQYRTLEKEEELDLVIK-AQSGDEEAKNQLILCNLRLVVNVAKGYRSKGMNL 65

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++SEGN+GL++A++KFD  +GFR +TY++WWIK ++ + I+     ++I +       
Sbjct: 66  IDLISEGNLGLIRAIEKFDVGKGFRFSTYAVWWIKQSISKAIIFKGREIRIPSYR----- 120

Query: 136 FFNLRRLKGHL-QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +  L ++  ++ + +    + P  V  +A+ L +  ++V  +        SL+  I    
Sbjct: 121 YDILNKINKYVTETVKLCGIYP-TVEEVAEYLKMPVNKVEEVMIEFQEPMSLSTEIGED- 178

Query: 195 KNSSQWQDWLVYDHD---GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQE 250
                     +Y  D   G E+   EK   K  +  L   +S L  RE+ I + R  L  
Sbjct: 179 ----------IYLEDTLSGAEEHFEEKVYYKMMQQRLKDILSRLESREQEILKLRFGLDG 228

Query: 251 NPV-TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
             + TLE++   F ++RERVRQIE    KK++    K++
Sbjct: 229 YEIHTLEDIGKNFNITRERVRQIEKNTLKKLKRKYTKEL 267


>gi|257430984|ref|ZP_05607364.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus 68-397]
 gi|257278414|gb|EEV09050.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus 68-397]
          Length = 342

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 87/276 (31%), Positives = 133/276 (48%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  QEE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 76  YLKEIGRVNLLSAQEEIELAKRI-EQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDL 134

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 135 IQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 194

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L  E+V  I K       E +S+   +    D  L 
Sbjct: 195 RVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREILK----IAQEPVSLETPIGEEDDSHLG 250

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 251 DFIEDQEAQSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 293

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 294 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 329


>gi|89890814|ref|ZP_01202323.1| DNA-directed RNA polymerase major sigma-43 factor (sigma-A) rpoD
           [Flavobacteria bacterium BBFL7]
 gi|89516959|gb|EAS19617.1| DNA-directed RNA polymerase major sigma-43 factor (sigma-A) rpoD
           [Flavobacteria bacterium BBFL7]
          Length = 287

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 81/291 (27%), Positives = 152/291 (52%), Gaps = 45/291 (15%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ +I KI ++  +EE  LA+  ++ GD  A  +L T++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQDISKIDLITAEEEVELAQLIKK-GDQRALEKLTTANLRFVVSVAKQYQNQGLKL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
            ++++EGN GL++A K+FD  RGF+  +Y++WWI+ ++      Q  I+R   L KIG+ 
Sbjct: 77  PDLINEGNAGLVKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVR-LPLNKIGSI 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCR 179
               + F        HL+ + +    PE+   +AK+L+++ S+V          +SM+  
Sbjct: 136 NKINKAF-------SHLEQLHERPPSPEE---LAKELDMTVSDVKQSLKNAGRHVSMDAP 185

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           L   E+ N         S      L++     E + +E          +TR++  L+ +E
Sbjct: 186 LKEGETSNLYDVVRSGESPNPDRELMH-----ESLTLE----------ITRALETLSQKE 230

Query: 240 RRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
             +        N  P++LE +   F+++RERVRQI+ +  K+++++ + ++
Sbjct: 231 ADVISLYFGIGNQQPMSLEEIGETFDLTRERVRQIKEKGIKRLRQNSRSKI 281


>gi|297584635|ref|YP_003700415.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacillus
           selenitireducens MLS10]
 gi|297143092|gb|ADH99849.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacillus
           selenitireducens MLS10]
          Length = 371

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 88/275 (32%), Positives = 139/275 (50%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LAKR  E  D  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 105 YLKEIGRVPLLSAKEEVELAKRI-EEDDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 163

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 164 IQEGNMGLIKAVEKFDYNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 223

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   +  L P++V  I   L +++ E +S+   +    D  L 
Sbjct: 224 RVQRQLLQDLGREPTPEEVSKEMELTPDKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 279

Query: 188 ALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
             I   D+ +    D   Y+   +  E VL    +R+   N+L     + + R R     
Sbjct: 280 DFIE--DQEALAPSDAAAYELLKEQLEDVLDTLTDREE--NVLRLRFGLDDGRTR----- 330

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                   TLE +   F V+RER+RQIEA+A +K+
Sbjct: 331 --------TLEEVGKVFGVTRERIRQIEAKALRKL 357


>gi|315924365|ref|ZP_07920587.1| DNA-directed RNA polymerase sigma subunit RpoD [Pseudoramibacter
           alactolyticus ATCC 23263]
 gi|315622244|gb|EFV02203.1| DNA-directed RNA polymerase sigma subunit RpoD [Pseudoramibacter
           alactolyticus ATCC 23263]
          Length = 396

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 83/266 (31%), Positives = 134/266 (50%), Gaps = 15/266 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  +AKR    GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 130 YLKEIGRVSLLTADEEMAIAKRMA-AGDEDAKKELAEANLRLVVSIAKRYVGRGMSFLDL 188

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 189 IQEGNLGLIKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 246

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R+   L         P +   I K++  SE +V  +  ++A D  SL   I   ++  
Sbjct: 247 LIRVSRQLLQEYGREPTPAE---IGKEMGFSEDKVREIQ-KIAQDPVSLETPIG--EEED 300

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTL 255
           S   D++    D +     E       +  L   +S L  RE ++   R   ++    TL
Sbjct: 301 SHLGDFI---PDDEAPAPSEAASYALLKEQLIDVLSTLTDREEKVLRLRFGLDDGRARTL 357

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           E +  EF+V+RER+RQIEA+A +K++
Sbjct: 358 EEVGKEFDVTRERIRQIEAKALRKLR 383


>gi|325285575|ref|YP_004261365.1| RpoD subfamily RNA polymerase sigma 70 subunit [Cellulophaga lytica
           DSM 7489]
 gi|324321029|gb|ADY28494.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cellulophaga
           lytica DSM 7489]
          Length = 287

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 85/293 (29%), Positives = 157/293 (53%), Gaps = 49/293 (16%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ ++   EE  LA+R +  GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGKVDLITADEEVELAQRIK-AGDQVALEKLTKANLRFVVSVAKQYQNQGLTL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
            ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++      Q  I+R   L KIG+ 
Sbjct: 77  PDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVR-LPLNKIGSI 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNA 188
               + F  L +          +  KP     IAK+L+++  E +  + + +G   S++A
Sbjct: 136 NKINKTFAFLEQA---------HERKP-SAEEIAKELDMT-IEDVKQSLKNSGRHVSMDA 184

Query: 189 -LINSSDKNSSQWQDWLVYD-------HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            LI+  D N        +YD        +   ++LIE     + R  + R++  L PRE 
Sbjct: 185 PLIDGEDSN--------LYDVLRSGESPNPDRELLIE-----SLRTEIERALETLTPREA 231

Query: 241 RIFEARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +    RL     +++ +TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 232 DVI---RLYFGLAEQHSMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|260438482|ref|ZP_05792298.1| RNA polymerase sigma factor RpoD [Butyrivibrio crossotus DSM 2876]
 gi|292809071|gb|EFF68276.1| RNA polymerase sigma factor RpoD [Butyrivibrio crossotus DSM 2876]
          Length = 370

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 85/274 (31%), Positives = 138/274 (50%), Gaps = 31/274 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L   EE  LAKR  E GD  A  +L  ++LRLVV IA  Y G G+   ++
Sbjct: 104 YLKEIGKVPLLSADEEIELAKRM-ELGDEEAKKKLAEANLRLVVSIAKRYVGRGMLFLDL 162

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-- 132
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 163 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 222

Query: 133 ---KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
              ++L   L R     +   + ++  E+V  I   L +S+ E +S+   +  +E     
Sbjct: 223 RVSRQLLQELGREPSPQEIADEMDIPVERVREI---LKISQ-EPVSLETPIGEEE----- 273

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
                   S   D++    D    V  E       +  L   +  L  RE+++ + R   
Sbjct: 274 -------DSHLGDFI---QDDNVPVPAEAAAFTLLKEQLNEVLGTLTEREQKVLKLRFGL 323

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           E+    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 324 EDGRARTLEEVGKVFNVTRERIRQIEAKALRKLR 357


>gi|213963182|ref|ZP_03391440.1| RNA polymerase sigma factor RpoD [Capnocytophaga sputigena Capno]
 gi|213954266|gb|EEB65590.1| RNA polymerase sigma factor RpoD [Capnocytophaga sputigena Capno]
          Length = 287

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 74/288 (25%), Positives = 149/288 (51%), Gaps = 39/288 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI ++ ++   EE  LA+R +  GD++A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGRVDLITADEEVELAQRIK-AGDVAALEKLTKANLRFVVSVAKQYQNQGLTL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     +V++    N+   
Sbjct: 77  PDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL--PLNKIGS 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRLAGDES 185
              + ++  +L+   +     E+   IA++L++S ++V          ISM+  L   E 
Sbjct: 135 INKINKMYAYLEQANERVPSAEE---IARELDMSVNDVKESMKNAGRHISMDAPLVEGED 191

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
            N         S      L+ D               + R  + R++  L PRE  +   
Sbjct: 192 SNLYDVIRSNESPNPDKSLILD---------------SLRTEIERALETLTPREADVI-- 234

Query: 246 RRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            RL      ++ +TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 235 -RLYFGLGDQHAMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|189424151|ref|YP_001951328.1| RNA polymerase, sigma 70 subunit, RpoD family [Geobacter lovleyi
           SZ]
 gi|189420410|gb|ACD94808.1| RNA polymerase, sigma 70 subunit, RpoD family [Geobacter lovleyi
           SZ]
          Length = 320

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 78/274 (28%), Positives = 139/274 (50%), Gaps = 31/274 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ +I++ P+L  + E  LA+R  E GD +A ++++ ++LRLVVKIA  Y   GLP  ++
Sbjct: 60  YLRDIQRTPLLNAEAEKELARRV-EQGDKAARNQMIEANLRLVVKIAKRYLNRGLPFLDL 118

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK--IGTTANQKRLF 136
           + EGN+GLM+AV++F  E+  R +TY+ WWI+ +++  ++     ++  +  + +  R+ 
Sbjct: 119 IEEGNLGLMKAVERFSLEKECRFSTYATWWIRQSIERALVNQSRTIRLPVHVSDDISRML 178

Query: 137 FNLRRLKGHL------QAITDN-NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
              R+L   L      Q + D   +KP  +    +KL +      SM+  +        +
Sbjct: 179 KVSRQLSQELHREPSVQELADAMQIKPLHI----RKLMILLRRTCSMDVPIGEGNDFFLV 234

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RL 248
               D N+    D L               E  +R  ++      L+  ER I   R  L
Sbjct: 235 DTIEDTNAVSPADLL---------------ENIDRYELIAEHFDQLSENERTILGLRFGL 279

Query: 249 QE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            + +P TL+ +   F V+RER+RQIEA++ +K++
Sbjct: 280 DDRDPQTLDTIGQSFGVTRERIRQIEAKSLEKLK 313


>gi|86132636|ref|ZP_01051229.1| RNA polymerase sigma-70 factor RpoD [Dokdonia donghaensis MED134]
 gi|85816878|gb|EAQ38063.1| RNA polymerase sigma-70 factor RpoD [Dokdonia donghaensis MED134]
          Length = 287

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 81/296 (27%), Positives = 153/296 (51%), Gaps = 55/296 (18%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ ++  +EE  LA+R +  GD  A  +L  ++LR VV ++  Y+  GL +
Sbjct: 18  LDKYLQEIGKVDLITAEEEVELAQRIK-AGDHRALEQLTKANLRFVVSVSKQYQNQGLTL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
            ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++      Q  I+R   L KIG+ 
Sbjct: 77  PDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVR-LPLNKIGSI 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCR 179
               + F  L +           N +P     IAK+L+++  +V          ISM+  
Sbjct: 136 NKINKTFAFLEQA----------NERPPSPEEIAKELDMTIKDVKESLKNSGRHISMDAP 185

Query: 180 L--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
           L    D +L  ++NS +  S      L+++               + +  + R++  L P
Sbjct: 186 LVEGEDSNLYDVLNSGE--SPNPDRALLHE---------------SLKTEIERALETLTP 228

Query: 238 RERRIFEARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RE  +    RL      + P++LE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 229 READVV---RLYFGLGDQRPMSLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|322383680|ref|ZP_08057431.1| RNA polymerase sigma factor RpoD-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321151892|gb|EFX44835.1| RNA polymerase sigma factor RpoD-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 354

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 82/265 (30%), Positives = 132/265 (49%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  ++E  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 88  YLKEIGRVPLLSAEDEVELAKRI-EQGDEEAKRRLTEANLRLVVSIAKRYVGRGMLFLDL 146

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 147 IQEGNMGLIKAVEKFDHTKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 204

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L         PE+   IAK++ +S  +V  +        SL   I   D   S
Sbjct: 205 LIRVSRQLLQELGREPTPEE---IAKEMELSTDKVREIMKIAQEPVSLETPIGEED--DS 259

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++    D +     +    +  +  L   +  L  RE  +   R   ++    TLE
Sbjct: 260 HLGDFI---EDQEALAPADAAAYELLKEQLEDVLDTLTEREENVLRLRFGLDDGRTRTLE 316

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +   F V+RER+RQIEA+A +K++
Sbjct: 317 EVGKVFGVTRERIRQIEAKALRKLR 341


>gi|315224630|ref|ZP_07866455.1| DNA-directed RNA polymerase sigma subunit RpoD [Capnocytophaga
           ochracea F0287]
 gi|314945415|gb|EFS97439.1| DNA-directed RNA polymerase sigma subunit RpoD [Capnocytophaga
           ochracea F0287]
          Length = 287

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 76/290 (26%), Positives = 155/290 (53%), Gaps = 43/290 (14%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI ++ ++   EE  LA+R +  GD++A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGRVDLITADEEVELAQRIK-AGDVAALEKLTKANLRFVVSVAKQYQNQGLTL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     +V++    N+   
Sbjct: 77  PDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL--PLNKIGS 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRL--AGD 183
              + ++  +L+   +     E+   IA++L++S ++V          ISM+  L    D
Sbjct: 135 INKINKMYAYLEQANERVPSAEE---IARELDMSVNDVKESMKNAGRHISMDAPLVEGED 191

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            +L  +I S++  S      L+ D               + R  + R++  L PRE  + 
Sbjct: 192 SNLYDVIRSNE--SPNPDKALILD---------------SLRTEIERALETLTPREADVV 234

Query: 244 EARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
              RL      ++ +TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 235 ---RLYFGLSDQHAMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|313123889|ref|YP_004034148.1| RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           bulgaricus ND02]
 gi|312280452|gb|ADQ61171.1| RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           bulgaricus ND02]
          Length = 372

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 86/275 (31%), Positives = 131/275 (47%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE  LAKR  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 106 YLKEIGRVNLLTSEEEVALAKRI-EAGDEEAKQELAEANLRLVVSIAKRYVGRGMNFLDL 164

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV KFD   G++ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 165 IQEGNMGLMKAVDKFDYRLGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 224

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L   +V  I K       E +S+   +    D +L 
Sbjct: 225 RIQRQLLQDLGRDPEPEEIGAEMDLPVNKVREILKLCQ----EPVSLETPIGEEDDSNLG 280

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR- 246
             I   D  S +        H   E +          +  L   +  L+ RE  +   R 
Sbjct: 281 DFIEDKDAMSPEQ-------HAANEML----------KEQLAEVLDTLSDREEEVLRLRF 323

Query: 247 RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
            L +    TLE +   FEV+RER+RQIEA+A +K+
Sbjct: 324 GLDDGKARTLEEVGQHFEVTRERIRQIEAKALRKL 358


>gi|193089925|gb|ACF15191.1| RpoS [Pseudomonas sp. DF41]
          Length = 335

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 85/272 (31%), Positives = 144/272 (52%), Gaps = 17/272 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERG R +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGSRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + +K       ++ +N R++  D SL      SDK  
Sbjct: 185 LRAARELTQKL-DHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSLGP---DSDKT- 239

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++       + + +S L  ++  +   R   R  E+  T
Sbjct: 240 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTDKQWEVVIRRFGLRGHESS-T 293

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE++  E  ++RERVRQI+    K+++E ++K
Sbjct: 294 LEDVGLEIGLTRERVRQIQVEGLKRLREILEK 325


>gi|160878392|ref|YP_001557360.1| RpoD family RNA polymerase sigma factor [Clostridium
           phytofermentans ISDg]
 gi|160427058|gb|ABX40621.1| RNA polymerase, sigma 70 subunit, RpoD family [Clostridium
           phytofermentans ISDg]
          Length = 371

 Score =  108 bits (269), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 87/279 (31%), Positives = 138/279 (49%), Gaps = 35/279 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           + +Y+ EI   P+L   EE  LAK+  E GD  A   L  S+LRLVV IA  Y G GL  
Sbjct: 101 VKQYLKEIGSYPLLSVAEEIELAKKI-EAGDNMAKQILAESNLRLVVSIAKRYVGRGLSF 159

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ--- 132
            +++ EGN+GL++AV KFD  +G++ +TY+ WWI+ A+   I      ++I    ++   
Sbjct: 160 LDLIQEGNLGLIKAVDKFDYNKGYKFSTYATWWIRQAITRSIADQSRTIRIPVHMSEVIN 219

Query: 133 ------KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDE 184
                 + L   L R     +     NL  E+V  I   L VS ++ IS++  +    D 
Sbjct: 220 KTYRVSRNLLQELGREPSEQELADAMNLPIEKVREI---LKVS-ADPISLDTPIGEEDDS 275

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
            L   I           D ++   D     +++        + +++ +  L  RE+R+  
Sbjct: 276 HLGDFIKD---------DTIMGPEDAASYAVLQ--------DQISKLLDTLTEREQRVLI 318

Query: 245 AR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R  LQ+    TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 319 LRFGLQDGRSRTLEEVGKEFNVTRERIRQIEAKALRKLR 357


>gi|312796084|ref|YP_004029006.1| RNA polymerase sigma factor rpoS [Burkholderia rhizoxinica HKI 454]
 gi|312167859|emb|CBW74862.1| RNA polymerase sigma factor rpoS [Burkholderia rhizoxinica HKI 454]
          Length = 358

 Score =  107 bits (268), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 85/279 (30%), Positives = 141/279 (50%), Gaps = 26/279 (9%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+P+
Sbjct: 79  IQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFDARQMMIERNLRLVVSIAKGYLNRGVPL 137

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++    +  R 
Sbjct: 138 LDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRE 195

Query: 136 FFNLRRLKGHLQ---------AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
              + R K HL+         A    +   + +  +  K     ++++++N   A   SL
Sbjct: 196 LNQVLRAKRHLERNASAPASGADEHRDASVDDIAYLIGKTPEEVADILALNEHTA---SL 252

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS-MSVLNPRERRIFEA 245
           +A +   D  SS     L+ D   Q     + E +      LTR  +S L  + R + E 
Sbjct: 253 DAPLE-LDPASSLLD--LLSDEQSQSP---DAEAQHRELETLTRVWLSRLPDKHRHVIE- 305

Query: 246 RRLQEN---PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           RR   N   P TLE L+ E  ++RERVRQI+  A  +++
Sbjct: 306 RRFGLNNIEPATLEELADEMGLTRERVRQIQQEALARLK 344


>gi|154502790|ref|ZP_02039850.1| hypothetical protein RUMGNA_00604 [Ruminococcus gnavus ATCC 29149]
 gi|153796673|gb|EDN79093.1| hypothetical protein RUMGNA_00604 [Ruminococcus gnavus ATCC 29149]
          Length = 371

 Score =  107 bits (268), Expect = 1e-21,   Method: Compositional matrix adjust.
 Identities = 88/269 (32%), Positives = 138/269 (51%), Gaps = 21/269 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L    E  LA+R  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 105 YLKEIGKVPLLSADREIELAQRM-EEGDEDAKKELAEANLRLVVSIAKRYVGRGMLFLDL 163

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N  +
Sbjct: 164 IQEGNLGLIKAVEKFDYHKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETIN--K 221

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           L    R+L   LQ +    L PE+   IAK+L++    V  +        SL   I   +
Sbjct: 222 LIRVSRQL---LQELGREPL-PEE---IAKELDMPVERVREILKISQEPVSLETPI--GE 272

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
           +  S   D++    D    V  E   +   +  L   +  L  RE+++   R    +   
Sbjct: 273 EEDSHLGDFI---QDDNVPVPAEAAAQTLLKEQLDEVLDTLTEREQKVLRLRFGMNDGRA 329

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE +  EF+V+RER+RQIEA+A +K++
Sbjct: 330 RTLEEVGKEFDVTRERIRQIEAKALRKLR 358


>gi|291522137|emb|CBK80430.1| RNA polymerase, sigma 70 subunit, RpoD [Coprococcus catus GD/7]
          Length = 365

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 80/268 (29%), Positives = 141/268 (52%), Gaps = 15/268 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  IP+L  +EE  LAK  +E G   AA ++  ++LRLVV IA  Y G G+   ++
Sbjct: 98  YLKEIGNIPLLTPEEEVELAKEMKE-GSKQAAKKMAEANLRLVVSIAKRYVGRGMQFLDL 156

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++A++K+D  +G++ +TY+ WWI+ A+   I      ++I        +   
Sbjct: 157 IQEGNVGLIKAIEKYDYTKGYKFSTYATWWIRQAITRSIADQARTIRIPV-----HMVET 211

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           + +L    +++T    +   V  IA+ +++  + V  +   +    SL   + S ++  S
Sbjct: 212 MNKLTKVQRSLTQELGREPSVEEIAENVHMDVNRVREILKLVQETVSLETPVGSEEE--S 269

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS-MSVLNPRERRIFEARRLQENPV--TL 255
              D++  DH      L   E    +     RS +  LN RE+++   R   ++    TL
Sbjct: 270 HLADFIEDDH----TPLPSDEAAFGQLKDDIRSVLDKLNEREQKVLRMRFGLDDGKEHTL 325

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQES 283
           E +  E  V+RER+RQIEA+A +K+++S
Sbjct: 326 EEVGQELHVTRERIRQIEAKALRKLRQS 353


>gi|88812406|ref|ZP_01127656.1| RNA polymerase sigma factor [Nitrococcus mobilis Nb-231]
 gi|88790413|gb|EAR21530.1| RNA polymerase sigma factor [Nitrococcus mobilis Nb-231]
          Length = 356

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 86/282 (30%), Positives = 143/282 (50%), Gaps = 37/282 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A+R  + GD SA  R++ S+LRLVVKIA  Y   GL   ++
Sbjct: 88  YLNEIGYSPLLTAKEEVYYARRA-QGGDESARKRMIESNLRLVVKIARRYMNRGLAFLDL 146

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K +   
Sbjct: 147 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-IKEINQY 205

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKK-------LNVSESEVISMNCRLAGDES---LNA 188
           LR  +  +Q +       E  +A+ +        + ++E  V S++  +  D     L+A
Sbjct: 206 LRVARQLVQRLDHEPTLEEIAIAMDRSIEDVRHMMGLNEG-VTSVDIPIGRDADRVLLDA 264

Query: 189 LINSSDKNS-SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           + +  + +  +  QD  V  H                   L   ++ L  ++R + E RR
Sbjct: 265 IPDEVNPDPFAALQDEDVVSH-------------------LDAWLNELTEKQRAVVE-RR 304

Query: 248 L---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                    TLE +  E  V+RERVRQI+  A KK++E +++
Sbjct: 305 FGLHGHEKATLEEVGDEIGVTRERVRQIQIDALKKLREVMER 346


>gi|254556820|ref|YP_003063237.1| RNA polymerase sigma factor RpoD [Lactobacillus plantarum JDM1]
 gi|254045747|gb|ACT62540.1| RNA polymerase sigma factor RpoD [Lactobacillus plantarum JDM1]
          Length = 368

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 87/279 (31%), Positives = 139/279 (49%), Gaps = 41/279 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LA R  E GD SA   L  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGRVDLLTADEEVALALRI-EQGDESAKQELAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 161 IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 220

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + ++  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 221 RIQRQLLQDLGREPTPEEIGAEMDMPTEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 276

Query: 188 ALINSSDKNSSQWQDWLVYD-----HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             I   D++++   D   Y+      +G    L  +EE     N+L     + + R R  
Sbjct: 277 DFIE--DQDATSPADAAAYELLKEQLEGVLDTLTNREE-----NVLRLRFGLDDGRTR-- 327

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                      TLE +   F V+RER+RQIEA+A +K++
Sbjct: 328 -----------TLEEVGKVFGVTRERIRQIEAKALRKLR 355


>gi|256819198|ref|YP_003140477.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Capnocytophaga
           ochracea DSM 7271]
 gi|256580781|gb|ACU91916.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Capnocytophaga
           ochracea DSM 7271]
          Length = 287

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 78/294 (26%), Positives = 149/294 (50%), Gaps = 51/294 (17%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI ++ ++   EE  LA+R +  GD++A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGRVDLITADEEVELAQRIK-AGDVAALEKLTKANLRFVVSVAKQYQNQGLTL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
            ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++      Q  I+R   L KIG+ 
Sbjct: 77  PDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVR-LPLNKIGSI 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCR 179
               +++  L +    + +  +          IA++L++S ++V          ISM+  
Sbjct: 136 NKINKMYAYLEQANERVPSAEE----------IARELDMSVNDVKESMKNAGRHISMDAP 185

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           L   E  N         S      L+ D               + R  + R++  L PRE
Sbjct: 186 LVEGEDSNLYDVIRSNESPNPDKSLILD---------------SLRTEIERALETLTPRE 230

Query: 240 RRIFEARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
             +    RL      ++ +TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 231 ADVV---RLYFGLSDQHAMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|327405377|ref|YP_004346215.1| RpoD subfamily RNA polymerase sigma-70 subunit [Fluviicola
           taffensis DSM 16823]
 gi|327320885|gb|AEA45377.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Fluviicola
           taffensis DSM 16823]
          Length = 288

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 75/274 (27%), Positives = 149/274 (54%), Gaps = 20/274 (7%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ +I K  ++  +EE  LA++ ++ GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQDIGKEELITAEEEVELARKIKQ-GDQRALEKLTRANLRFVVSVAKQYQNQGLTL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     +V++    NQ   
Sbjct: 77  PDLINEGNLGLIKAAQKFDETRGFKFISYAVWWIRQSILQALAEQARIVRL--PLNQ--- 131

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
             +L ++      +     +P     +A+ L V E + I  +  ++G   S++A ++SS+
Sbjct: 132 VGSLNKINKAFSRLEQEFERPPSAEELAEALEVPEDK-IKESLNVSGRHVSMDAPLSSSE 190

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-----Q 249
              +        D    +  L+ +  +K     + RS+S L  +ER I    RL      
Sbjct: 191 DGGTLMDVMANADSPKADHALMAESLQKE----IERSLSTLTDKEREII---RLFFGIGM 243

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            + +TLE + ++F ++RERVRQI+ +A ++++ +
Sbjct: 244 NHGLTLEEIGAKFNLTRERVRQIKEKAIRRLRHT 277


>gi|33862253|ref|NP_893814.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus subsp. pastoris str. CCMP1986]
 gi|33634471|emb|CAE20156.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus subsp. pastoris str. CCMP1986]
          Length = 339

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 81/278 (29%), Positives = 151/278 (54%), Gaps = 26/278 (9%)

Query: 13  EIGLSRYIHEIRK---IPMLEKQEEYV----LAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           EI L+ ++  ++K   IP +E+  +++    + KR R+        R+++++LRLVV +A
Sbjct: 70  EIELAHHVQNMKKMLEIPEIERSSKHLRLIKIGKRARD--------RMMSANLRLVVSVA 121

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+  M   I  S   ++
Sbjct: 122 KKYQNQGLDLLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIR 181

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           +    ++K     +RR+   L     +  +P + + +A  + + + ++  +  + A   S
Sbjct: 182 LPIHISEK--LSKMRRVSRELS--QKSGRQPTR-LEMATAMGIEQKDLEDLISQSAPCAS 236

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L+A     +  S+  +  L+ D +G+E   +E  +R  ++  L   ++ LN RE++I + 
Sbjct: 237 LDAHARGEEDRSTLGE--LIPDPNGEEP--MEGMDRTIQKEHLGTWLTQLNEREQKIMKL 292

Query: 246 R--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R     E P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 293 RFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 330


>gi|227510293|ref|ZP_03940342.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           brevis subsp. gravesensis ATCC 27305]
 gi|227524444|ref|ZP_03954493.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           hilgardii ATCC 8290]
 gi|227088403|gb|EEI23715.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           hilgardii ATCC 8290]
 gi|227189945|gb|EEI70012.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           brevis subsp. gravesensis ATCC 27305]
          Length = 389

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 86/276 (31%), Positives = 134/276 (48%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LAKR  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 123 YLKEIGRVSLLSADEEINLAKRI-ESGDEEAKQELAEANLRLVVSIAKRYVGRGMQFLDL 181

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 182 IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 241

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + ++  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 242 RIQRQLLQDLGREPLPEEIGAEMDMPTEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 297

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 298 DFIEDQDATSPA-------DHAAYELL----------KEQLESVLDTLTDREENVLRLRF 340

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 341 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 376


>gi|227513300|ref|ZP_03943349.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           buchneri ATCC 11577]
 gi|227083501|gb|EEI18813.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           buchneri ATCC 11577]
          Length = 389

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 86/276 (31%), Positives = 134/276 (48%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LAKR  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 123 YLKEIGRVSLLSADEEINLAKRI-ESGDEEAKQELAEANLRLVVSIAKRYVGRGMQFLDL 181

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 182 IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 241

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + ++  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 242 RIQRQLLQDLGREPLPEEIGAEMDMPTEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 297

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 298 DFIEDQDATSP-------ADHAAYELL----------KEQLESVLDTLTDREENVLRLRF 340

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 341 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 376


>gi|167463432|ref|ZP_02328521.1| RNA polymerase sigma factor RpoD [Paenibacillus larvae subsp.
           larvae BRL-230010]
          Length = 375

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 82/265 (30%), Positives = 132/265 (49%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  ++E  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 109 YLKEIGRVPLLSAEDEVELAKRI-EQGDEEAKRRLTEANLRLVVSIAKRYVGRGMLFLDL 167

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 168 IQEGNMGLIKAVEKFDHTKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 225

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L         PE+   IAK++ +S  +V  +        SL   I   D   S
Sbjct: 226 LIRVSRQLLQELGREPTPEE---IAKEMELSTDKVREIMKIAQEPVSLETPIGEED--DS 280

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++    D +     +    +  +  L   +  L  RE  +   R   ++    TLE
Sbjct: 281 HLGDFI---EDQEALAPADAAAYELLKEQLEDVLDTLTEREENVLRLRFGLDDGRTRTLE 337

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +   F V+RER+RQIEA+A +K++
Sbjct: 338 EVGKVFGVTRERIRQIEAKALRKLR 362


>gi|78188365|ref|YP_378703.1| RNA polymerase sigma factor rpoD (sigma-A) [Chlorobium
           chlorochromatii CaD3]
 gi|78170564|gb|ABB27660.1| RNA polymerase sigma factor rpoD (Sigma-A) [Chlorobium
           chlorochromatii CaD3]
          Length = 299

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 82/299 (27%), Positives = 154/299 (51%), Gaps = 35/299 (11%)

Query: 9   IVNGE-IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS-----------AAHRLVTS 56
           I N E + L RY+ EI K  +L  ++E  L K  +E  D+            A  +L+  
Sbjct: 10  ITNRESLSLDRYLQEIGKYDLLTAEDEVRLTKAIKEGFDMPVDTPEYKRAKRALDKLIKG 69

Query: 57  HLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           +LR VV +A  Y+  GL + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + 
Sbjct: 70  NLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQA 129

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
           +     +V++    N+      + +    L+   + +    ++ ++ +     +S+ ++ 
Sbjct: 130 LAEQSRIVRL--PLNRVGTLNKISKAYSQLEQEYERDPNTRELASLLE----MDSQDVAD 183

Query: 177 NCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT----RS 231
             ++AG   S++A     D N  +  D L  D    +  L         R+ LT    RS
Sbjct: 184 TLKIAGRHVSVDAPFAQGDDN--RLLDVLQNDGHMPDYGLT--------RDSLTLEVERS 233

Query: 232 MSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +SVL PRE  +  +      +NP+TLE +  +F ++RERVRQI+ +A +++++S   +V
Sbjct: 234 LSVLAPREADVIRSYFGIGMDNPLTLEEIGEKFRLTRERVRQIKEKAIRRLRQSAYSKV 292


>gi|15927141|ref|NP_374674.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus N315]
 gi|20178083|sp|Q99TT5|RPOD_STAAN RecName: Full=RNA polymerase sigma factor rpoD
 gi|13701359|dbj|BAB42653.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           N315]
          Length = 368

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 86/275 (31%), Positives = 132/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  QEE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGRVNLLSAQEEIELAKRI-EQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 161 IQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 220

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L  E+V  + K       E +S+   +    D  L 
Sbjct: 221 RVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREVLK----IAQEPVSLETPIGEEDDSHLG 276

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 277 DFIEDQEAQSPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 319

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 320 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 354


>gi|227529171|ref|ZP_03959220.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           vaginalis ATCC 49540]
 gi|227350896|gb|EEJ41187.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           vaginalis ATCC 49540]
          Length = 380

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 86/276 (31%), Positives = 133/276 (48%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LA R  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 114 YLKEIGRVNLLSADEEVALALRI-EQGDEEAKQELAEANLRLVVSIAKRYVGRGMQFLDL 172

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  RGF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 173 IQEGNMGLMKAVEKFDYRRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 232

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + ++  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 233 RIQRQLLQDLGREPLPEEIGAEMDMPTEKVRNI---LKIAQ-EPVSLETPIGEEDDSHLG 288

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 289 DFIEDQDATSPA-------DHAAYEMM----------KKQLENVLDTLTDREENVLRLRF 331

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 332 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 367


>gi|256532384|gb|ACU81350.1| RpoH [Rhizobium leguminosarum bv. trifolii]
 gi|256532396|gb|ACU81356.1| RpoH [Rhizobium leguminosarum bv. trifolii]
          Length = 148

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 68/152 (44%), Positives = 94/152 (61%), Gaps = 9/152 (5%)

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFFNLRRL+  L A  D 
Sbjct: 1   FEPERDVRFSTYASWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRAKL-AKGDT 59

Query: 153 NLKPEQV-VAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDH-- 208
            L  + +   IA  L VS S+V +M+ RL+G D SL A   S D  S++  D+LV D   
Sbjct: 60  QLTLQSIHQEIAAALGVSLSDVQTMDARLSGNDASLQAPSVSGDAESAEKMDFLVSDDPL 119

Query: 209 -DGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            D Q   +I+ E    RR  L  ++  LN RE
Sbjct: 120 PDEQVSNMIDGER---RRVWLASALKHLNERE 148


>gi|163790450|ref|ZP_02184881.1| RNA polymerase sigma factor RpoD [Carnobacterium sp. AT7]
 gi|159874354|gb|EDP68427.1| RNA polymerase sigma factor RpoD [Carnobacterium sp. AT7]
          Length = 373

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 87/274 (31%), Positives = 136/274 (49%), Gaps = 31/274 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 107 YLKEIGRVNLLTAAEEVELAIKI-EEGDQEARQRLAEANLRLVVSIAKRYVGRGMQFLDL 165

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD ++GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 166 IQEGNMGLMKAVEKFDYKKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 225

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             Q++L  +L R     +   + +L  E+V  I   L +++  V           SL   
Sbjct: 226 RIQRQLLQDLGREPTPEEIGAEMDLPTEKVREI---LKIAQEPV-----------SLETP 271

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   D   S   D+ + DHD       E    +  +  L   +  L  RE  +   R   
Sbjct: 272 IGEED--DSHLGDF-IEDHDATSPA--ENAAYELLKEQLEDVLDTLTDREENVLRLRFGL 326

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    TLE++   F V+RER+RQIEA+A +K++
Sbjct: 327 DDGRNRTLEDVGKVFGVTRERIRQIEAKALRKLR 360


>gi|260063687|ref|YP_003196767.1| putative sigma factor A [Robiginitalea biformata HTCC2501]
 gi|88783132|gb|EAR14305.1| putative sigma factor A [Robiginitalea biformata HTCC2501]
          Length = 287

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 81/288 (28%), Positives = 156/288 (54%), Gaps = 39/288 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ ++   EE  LA+R +  GD +A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGKVDLITADEEVELAQRIK-AGDQAALEKLTKANLRFVVSVAKQYQNQGLTL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
            ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++      Q  I+R   L KIG+ 
Sbjct: 77  PDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVR-LPLNKIGSI 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNA 188
               + F  L +    + +  +          IAK+L+++  E +  + + +G   S++A
Sbjct: 136 NKINKTFAFLEQAHERVPSAEE----------IAKELDMT-VEDVKQSLKNSGRHVSMDA 184

Query: 189 -LINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
            LI+  D N        +YD    G+     ++   ++ R  + R++  L PRE  +   
Sbjct: 185 PLIDGEDSN--------LYDVLRSGESPNPDKELLHESLRTEIERALETLTPREADVI-- 234

Query: 246 RRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            RL      ++ +TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 235 -RLYFGLAGQHSMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|81428494|ref|YP_395494.1| RNA polymerase sigma factor RpoD [Lactobacillus sakei subsp. sakei
           23K]
 gi|78610136|emb|CAI55185.1| DNA-directed RNA polymerase sigma factor, sigma A (Primary sigma
           factor) [Lactobacillus sakei subsp. sakei 23K]
          Length = 369

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 85/275 (30%), Positives = 135/275 (49%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  Q+E  LA R  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 103 YLKEIGRVSLLNAQQEVDLALRI-EQGDQEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 161

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 162 IQEGNMGLMKAVEKFDHRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 221

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + ++  ++V  I   L +++ E +S+   +    D  L 
Sbjct: 222 RIQRQLLQDLGREPTPEEIGAEMDMNTDKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 277

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR- 246
             I   D  S +       +H   E +          +  L   +  L  RE  +   R 
Sbjct: 278 DFIEDQDATSPE-------EHASYELL----------KEQLESVLDTLTDREENVLRLRF 320

Query: 247 RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
            L +    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 321 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 355


>gi|308804840|ref|XP_003079732.1| SigA (ISS) [Ostreococcus tauri]
 gi|116058189|emb|CAL53378.1| SigA (ISS) [Ostreococcus tauri]
          Length = 525

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 76/271 (28%), Positives = 138/271 (50%), Gaps = 15/271 (5%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           V A R R H   +A + ++ ++LRLVV IA  Y    +   +++ EG +GL++  +KFD 
Sbjct: 264 VSALRQRLHDGKAAKNEMIQANLRLVVSIAKKYANTNMSFQDLIQEGCVGLIRGAEKFDF 323

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           +RG++ +TY+ WWI+ A+   I      +++        LF  + R+    Q     N +
Sbjct: 324 QRGYKFSTYAHWWIRQAVTRSISDQSRTIRLPV-----HLFEIISRISKMEQKFALYNGR 378

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
           P  +  IA ++ +S  ++  +        SL   +   +K  +     +  + +G E+V 
Sbjct: 379 PPTLEEIASEMEMSVEKITQIKKAAQAPVSLAQTMGGENKGRTIEDTLIDANAEGPEKVS 438

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIE 273
            +   +++  N+L    + LNPRER +   R  L +  V TLE + + F V+RER+RQIE
Sbjct: 439 GKSLLKEDLENVL----NTLNPRERDVLRLRYGLDDGRVKTLEEIGTVFSVTRERIRQIE 494

Query: 274 ARAFKKVQESIQKQVE----LSSSPPLLQKP 300
           A+A +K+++  + QV     +  +PP   +P
Sbjct: 495 AKALRKLKQPSRNQVLQEYFVDDAPPNTHRP 525


>gi|291546785|emb|CBL19893.1| RNA polymerase, sigma 70 subunit, RpoD [Ruminococcus sp. SR1/5]
          Length = 375

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 84/274 (30%), Positives = 141/274 (51%), Gaps = 31/274 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+ +L   EE  LAKR  E GD +A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 109 YLKEIGKVSLLSADEEIELAKRM-EKGDEAAKKRLAEANLRLVVSIAKRYVGRGMLFLDL 167

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-- 132
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 168 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 227

Query: 133 ---KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
              ++L   L R     +   + ++  ++V  I   L +S+ E +S+   +  +E  +  
Sbjct: 228 RVSRQLLQELGREPTPEEIAEEMDMPVDRVREI---LKISQ-EPVSLETPIGEEEDSHLG 283

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
               D N     D   +        L++++        L   +S L  RE+++   R   
Sbjct: 284 DFIQDDNVPVPADAAAF-------TLLKEQ--------LVEVLSTLTDREQKVLRLRFGL 328

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 329 DDGRARTLEEVGKEFNVTRERIRQIEAKALRKLR 362


>gi|110596913|ref|ZP_01385203.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4 [Chlorobium
           ferrooxidans DSM 13031]
 gi|110341600|gb|EAT60060.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4 [Chlorobium
           ferrooxidans DSM 13031]
          Length = 299

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 88/304 (28%), Positives = 159/304 (52%), Gaps = 45/304 (14%)

Query: 9   IVNGE-IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS-----------AAHRLVTS 56
           I N E + L RY+ EI K  +L  ++E  L K  ++  D+            A  +L+  
Sbjct: 10  ITNRESLSLDRYLQEIGKYDLLTAEDEVKLTKAIKDGFDMPVDTTEYKRAKRALDKLIKG 69

Query: 57  HLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM--- 113
           +LR VV +A  Y+  GL + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++   
Sbjct: 70  NLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQA 129

Query: 114 ---QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
              Q  I+R   L ++GT     + +  L +     +   D N +      +A  L++ +
Sbjct: 130 LAEQSRIVR-LPLNRVGTLNKISKAYSQLEQ-----EFERDPNTRE-----LATLLDM-D 177

Query: 171 SEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-- 227
           S+ ++   ++AG   S++A     D N  +  D L  D    +  L       NR ++  
Sbjct: 178 SQDVADTLKIAGRHVSVDAPFAQGDDN--RLLDVLQNDGHLPDYGL-------NRDSLTL 228

Query: 228 -LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + RS+SVL PRE  +  +      +NP+TLE +  +F+++RERVRQI+ +A +++++S 
Sbjct: 229 EVERSLSVLAPREADVIRSYFGIGMDNPLTLEEIGEKFKLTRERVRQIKEKAIRRLRQSA 288

Query: 285 QKQV 288
             +V
Sbjct: 289 YSKV 292


>gi|313897367|ref|ZP_07830910.1| RNA polymerase sigma factor RpoD [Clostridium sp. HGF2]
 gi|312957737|gb|EFR39362.1| RNA polymerase sigma factor RpoD [Clostridium sp. HGF2]
          Length = 398

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 82/272 (30%), Positives = 139/272 (51%), Gaps = 26/272 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L+ +EE  +A+R  + GD  A  +L++++LRLVV IA  Y G G+   ++
Sbjct: 129 YLKEIGRVELLDPKEEPEIARRI-QAGDEEAKKKLISANLRLVVSIAKKYVGRGMLFLDL 187

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 188 IQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINK-- 245

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               L R++  L  + D    P      AK  N+S  +V  +        SL   I   D
Sbjct: 246 ----LTRIQRQL--VQDLGRDPSAEEIAAKMENISPEKVREIQKIALEPVSLETPIGEED 299

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNR---RNMLTRSMSVLNPRERRIFEAR--RLQ 249
              S   D++      +++  +  +E  N    ++ +   +  L  RE ++   R     
Sbjct: 300 --DSHLGDFI------EDKEALSPDEYANNQLLKDEINTVLQGLTEREEKVLRLRFGLYD 351

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
               TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 352 GRTRTLEEVGKEFNVTRERIRQIEAKALRKLK 383


>gi|296532040|ref|ZP_06894819.1| DNA-directed RNA polymerase sigma subunit RpoD [Roseomonas
           cervicalis ATCC 49957]
 gi|296267655|gb|EFH13501.1| DNA-directed RNA polymerase sigma subunit RpoD [Roseomonas
           cervicalis ATCC 49957]
          Length = 640

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 81/238 (34%), Positives = 119/238 (50%), Gaps = 14/238 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L  ++LRLVV IA  YR  GL   +++ EGNIGLM+AV KFD  RGF+ ATY+ WW
Sbjct: 403 AKEELTRANLRLVVHIAKRYRNRGLMFGDLIQEGNIGLMRAVDKFDWRRGFKFATYATWW 462

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           ++ A+   +      +++    +       + R+             PE+   +A +L +
Sbjct: 463 VRQAITRSLADQARTIRV--PVHMTETVGKVARMSRRFAQKAGREPTPEE---LAGELGM 517

Query: 169 SESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           S  +V ++  RLA +  SL   I   D    +  D++    D    +  +   R   R+ 
Sbjct: 518 SVDKVRAVQ-RLAREPVSLENPIGEDD--DGRLGDFI---EDENAVMPFDAASRSAMRDA 571

Query: 228 LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             R +S L PRE RI   R     EN  TLE +   F V+RER+RQIEA+A KK+Q S
Sbjct: 572 TMRILSDLTPREERILRMRFGIGGENDHTLEEVGKTFNVTRERIRQIEAKALKKLQVS 629


>gi|328957491|ref|YP_004374877.1| RNA polymerase sigma factor RpoD [Carnobacterium sp. 17-4]
 gi|328673815|gb|AEB29861.1| RNA polymerase sigma factor RpoD [Carnobacterium sp. 17-4]
          Length = 373

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 87/274 (31%), Positives = 136/274 (49%), Gaps = 31/274 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 107 YLKEIGRVNLLTAAEEVELAIKI-EEGDQEARQRLAEANLRLVVSIAKRYVGRGMQFLDL 165

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD ++GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 166 IQEGNMGLMKAVEKFDYKKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 225

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             Q++L  +L R     +   + +L  E+V  I   L +++  V           SL   
Sbjct: 226 RIQRQLLQDLGREPTPEEIGAEMDLPTEKVREI---LKIAQEPV-----------SLETP 271

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   D   S   D+ + DHD       E    +  +  L   +  L  RE  +   R   
Sbjct: 272 IGEED--DSHLGDF-IEDHDATSPA--ENAAYELLKEQLEDVLDTLTDREENVLRLRFGL 326

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    TLE++   F V+RER+RQIEA+A +K++
Sbjct: 327 DDGRNRTLEDVGKVFGVTRERIRQIEAKALRKLR 360


>gi|325478784|gb|EGC81895.1| RNA polymerase sigma factor RpoD [Anaerococcus prevotii
           ACS-065-V-Col13]
          Length = 604

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 79/248 (31%), Positives = 125/248 (50%), Gaps = 36/248 (14%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  +L  ++LRLVV IA  Y G G+   +++ EGN+GLM+AV K+D  RGF+ +TY+ W
Sbjct: 367 AAKQKLAETNLRLVVSIAKKYVGRGMSFLDLIQEGNMGLMKAVDKYDYNRGFKFSTYATW 426

Query: 108 WIKAAMQEYILRSWSLVKIGT----TAN-----QKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           WI+ A+   I      ++I      T N     Q++L  +L R   + +      ++ E+
Sbjct: 427 WIRQAITRAIADQARTIRIPVHMVETINKLVRIQRQLVQDLGRDPSNEEIAEQMGIEVEK 486

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           V  I K   +S+  V           SL   I   D   S   D++      ++   I+ 
Sbjct: 487 VQEIRK---ISQEPV-----------SLETPIGEED--DSHLGDFI------EDDTAIDP 524

Query: 219 EERKNR---RNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIE 273
            E  N    R  L   +S L  RE+R+ + R   +   P TLE +  EF+V+RER+RQIE
Sbjct: 525 GEAANYTMLREQLNDVLSCLGAREKRVLQLRFGLIDGTPRTLEEVGKEFDVTRERIRQIE 584

Query: 274 ARAFKKVQ 281
           A+A +K++
Sbjct: 585 AKALRKLK 592


>gi|118444745|ref|YP_878546.1| RNA polymerase sigma factor RpoD [Clostridium novyi NT]
 gi|118135201|gb|ABK62245.1| RNA polymerase sigma-70 factor [Clostridium novyi NT]
          Length = 368

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 78/265 (29%), Positives = 132/265 (49%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L   EE  LA+R  E G++ A  +L  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGKVPLLTPDEEIDLAQRI-EEGEMYAKKKLAEANLRLVVSIAKRYVGRGMLFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 161 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 218

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L        +PE++  I +       E++ +       E ++      ++  S
Sbjct: 219 LIRVSRQLLQELGREPQPEEIAKIMEMPVDKVREIMKI-----AQEPVSLETPIGEEEDS 273

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++  D              K +   L   +  L PRE ++   R   ++    TLE
Sbjct: 274 HLGDFIPDDEAPAPAEAAAFTMLKEQ---LINVLDTLTPREEKVLRLRFGLDDGRARTLE 330

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF V+RER+RQIEA+A +K++
Sbjct: 331 EVGKEFNVTRERIRQIEAKALRKLR 355


>gi|403013|emb|CAA50594.1| major sigma factor [Lactococcus lactis]
          Length = 340

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 85/271 (31%), Positives = 141/271 (52%), Gaps = 22/271 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
           Y+ EI + P++   EE  LA+     G+ +  A   L  ++LRLVV IA  Y G G+   
Sbjct: 72  YLKEIGRYPLISLDEETKLAEAIIAGGEGAEFAKQMLAEANLRLVVSIAKRYSGRGMQFL 131

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +     
Sbjct: 132 DLIQEGNMGLMKAVDKFDQTKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETI 189

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDK 195
             L R++ +L      +  PE+   I K+L+++  +V  +  ++A +  SL   I   D 
Sbjct: 190 NKLIRVQRNLLQELGRDPSPEE---IGKELHMAPDKVREV-LKIAQEPVSLETPIGEED- 244

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNR---RNMLTRSMSVLNPRERRIFEAR-RLQEN 251
             S   D++      ++ V+    +  NR   R  L   M  L  RE  +   R  L + 
Sbjct: 245 -DSHLGDFI------EDDVIESPVDYTNRILLREQLDEVMDTLTDREENVLRMRFGLDDG 297

Query: 252 PV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            + TLE++  +F+V+RER+RQIEA+A KK++
Sbjct: 298 RMHTLEDVGKQFKVTRERIRQIEAKAIKKLR 328


>gi|116511352|ref|YP_808568.1| RNA polymerase sigma factor RpoD [Lactococcus lactis subsp.
           cremoris SK11]
 gi|125623388|ref|YP_001031871.1| RNA polymerase sigma factor RpoD [Lactococcus lactis subsp.
           cremoris MG1363]
 gi|116107006|gb|ABJ72146.1| RNA polymerase, sigma 70 subunit, RpoD [Lactococcus lactis subsp.
           cremoris SK11]
 gi|124492196|emb|CAL97125.1| RNA polymerase sigma factor rpoD (Sigma-42) [Lactococcus lactis
           subsp. cremoris MG1363]
 gi|300070136|gb|ADJ59536.1| RNA polymerase sigma factor RpoD [Lactococcus lactis subsp.
           cremoris NZ9000]
          Length = 447

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 85/271 (31%), Positives = 141/271 (52%), Gaps = 22/271 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
           Y+ EI + P++   EE  LA+     G+ +  A   L  ++LRLVV IA  Y G G+   
Sbjct: 179 YLKEIGRYPLISLDEETKLAEAIIAGGEGAEFAKQMLAEANLRLVVSIAKRYSGRGMQFL 238

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +     
Sbjct: 239 DLIQEGNMGLMKAVDKFDHTKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETI 296

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDK 195
             L R++ +L      +  PE+   I K+L+++  +V  +  ++A +  SL   I   D 
Sbjct: 297 NKLIRVQRNLLQELGRDPSPEE---IGKELHMAPDKVREV-LKIAQEPVSLETPIGEED- 351

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNR---RNMLTRSMSVLNPRERRIFEAR-RLQEN 251
             S   D++      ++ V+    +  NR   R  L   M  L  RE  +   R  L + 
Sbjct: 352 -DSHLGDFI------EDDVIESPVDYTNRILLREQLDEVMDTLTDREENVLRMRFGLDDG 404

Query: 252 PV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            + TLE++  +F+V+RER+RQIEA+A KK++
Sbjct: 405 RMHTLEDVGKQFKVTRERIRQIEAKAIKKLR 435


>gi|297570260|ref|YP_003691604.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfurivibrio
           alkaliphilus AHT2]
 gi|296926175|gb|ADH86985.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfurivibrio
           alkaliphilus AHT2]
          Length = 555

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 82/257 (31%), Positives = 127/257 (49%), Gaps = 42/257 (16%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +RLV S+LRLVV +A  Y G GL + ++V EGNIGLM+AV+KF+  RG++ +TY+ WW
Sbjct: 316 AKNRLVQSNLRLVVSVAKKYAGRGLQLLDLVQEGNIGLMKAVEKFEYRRGYKFSTYATWW 375

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKG-------HLQAITDNNLKPE 157
           I+ A+   I      ++I      T N        R LKG       H +  T   +   
Sbjct: 376 IRQAVTRAIADQGRTIRIPVHMIDTIN--------RMLKGAKEYQRQHGREPTPEEMAEH 427

Query: 158 QVVAIAKKLNVSE--SEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQ 213
             V IAK  ++ +   E +S++  +   E   L+  I  +D  S    +  +YD      
Sbjct: 428 LGVDIAKVKSILKIAKEPLSLDTPVGSGEDSFLSDFIEDADSTSP--DEATIYD------ 479

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQ 271
                    + ++ L R +  L PRE  +   R   +    +TLE +   F V+RER+RQ
Sbjct: 480 ---------SLQDNLARVLKTLTPREEMVLRLRFGIDTATDLTLEEVGENFSVTRERIRQ 530

Query: 272 IEARAFKKVQESIQKQV 288
           IEA+A KK++   +K +
Sbjct: 531 IEAKALKKLKHPTRKSI 547


>gi|293400669|ref|ZP_06644814.1| RNA polymerase sigma factor RpoD [Erysipelotrichaceae bacterium
           5_2_54FAA]
 gi|291305695|gb|EFE46939.1| RNA polymerase sigma factor RpoD [Erysipelotrichaceae bacterium
           5_2_54FAA]
          Length = 396

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 80/268 (29%), Positives = 137/268 (51%), Gaps = 18/268 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L+ +EE  +A+R  + GD  A  +L++++LRLVV IA  Y G G+   ++
Sbjct: 127 YLKEIGRVELLDPKEEPEIARRI-QAGDEEAKKKLISANLRLVVSIAKKYVGRGMLFLDL 185

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 186 IQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 243

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R++  L  + D    P      AK  N+S  +V  +        SL   I   D   S
Sbjct: 244 LTRIQRQL--VQDLGRDPSAEEIAAKMENISPEKVREIQKIALEPVSLETPIGEED--DS 299

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNR---RNMLTRSMSVLNPRERRIFEAR--RLQENPV 253
              D++      +++  +  +E  N    ++ +   +  L  RE ++   R         
Sbjct: 300 HLGDFI------EDKEALSPDEYANNQLLKDEINTVLQGLTEREEKVLRLRFGLYDGRTR 353

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 354 TLEEVGKEFNVTRERIRQIEAKALRKLK 381


>gi|189345950|ref|YP_001942479.1| RNA polymerase, sigma 32 subunit, RpoH [Chlorobium limicola DSM
           245]
 gi|189340097|gb|ACD89500.1| RNA polymerase, sigma 32 subunit, RpoH [Chlorobium limicola DSM
           245]
          Length = 299

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 87/305 (28%), Positives = 156/305 (51%), Gaps = 47/305 (15%)

Query: 9   IVNGE-IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS-----------AAHRLVTS 56
           I N E + L RY+ EI K  +L   +E  L    +E  D+            A  +L+  
Sbjct: 10  ITNRESLSLDRYLQEIGKYDLLTADDEVKLTMAIKEGYDMPVDTVEYKRAKRALDKLIKG 69

Query: 57  HLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM--- 113
           +LR VV +A  Y+  GL + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++   
Sbjct: 70  NLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQA 129

Query: 114 ---QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
              Q  I+R   L ++GT     + +  L +     +   D N +      +A  L++ +
Sbjct: 130 LAEQSRIVR-LPLNRVGTLNKISKAYSQLEQ-----EFERDPNTRE-----LANLLDM-D 177

Query: 171 SEVISMNCRLAGDE-SLNALINSSDKN---SSQWQDWLVYDHD-GQEQVLIEKEERKNRR 225
           S+ ++   ++AG   S++A     D N        D  + DH   ++ + +E E      
Sbjct: 178 SQDVADTLKIAGRHVSVDAPFAQGDDNRLLDVLQNDGHLPDHGLNKDSLTLEVE------ 231

Query: 226 NMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               RS+SVL PRE  +  +      +NP+TLE +  +F+++RERVRQI+ +A +++++S
Sbjct: 232 ----RSLSVLAPREADVIRSYFGIGMDNPLTLEEIGEKFKLTRERVRQIKEKAIRRLRQS 287

Query: 284 IQKQV 288
              +V
Sbjct: 288 AYSKV 292


>gi|325280261|ref|YP_004252803.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Odoribacter
           splanchnicus DSM 20712]
 gi|324312070|gb|ADY32623.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Odoribacter
           splanchnicus DSM 20712]
          Length = 286

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 81/273 (29%), Positives = 150/273 (54%), Gaps = 20/273 (7%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K  ++  +EE  LA+R R+ GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGKEDLITVEEEVELAQRIRK-GDQKALEKLTRANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     +V++    NQ   
Sbjct: 77  PDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL--PLNQVGS 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
              + +     +   +    PE+   +A  L++  +E ++   R++G   S++A     +
Sbjct: 135 LNKINKAFSRFEQENERRPSPEE---LADSLDLP-AEKVADTLRVSGRHISVDAPFVEGE 190

Query: 195 KNSSQWQDWLVYDHDG-QEQVLIEKEERKNRRNMLTRSMSVLNPRER---RIFEARRLQE 250
            NS    D LV D     ++ LI     ++    + R++S L  RER   ++F     QE
Sbjct: 191 DNS--LLDVLVNDDSPIADRTLI----NESLSTEVERALSTLTERERDIIKLFFGINTQE 244

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +TLE +  +F ++RERVRQI+ +A ++++ S
Sbjct: 245 --MTLEEIGEKFGLTRERVRQIKEKAIRRLRHS 275


>gi|33867026|ref|NP_898585.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. WH 8102]
 gi|33639627|emb|CAE09011.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 8102]
          Length = 328

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 84/276 (30%), Positives = 145/276 (52%), Gaps = 22/276 (7%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRG 70
           EI L+ ++ E++++  L ++E   L  R+R    +   A  R++ ++LRLVV +A  Y+ 
Sbjct: 59  EIELAHHVQEMKQLQELPEEE---LTSRHRHKIRMGKRARDRMMAANLRLVVSVAKKYQN 115

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+  M   I  S   +++    
Sbjct: 116 QGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIRLPIHI 175

Query: 131 NQKRLFFNLRRLK---GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
           ++K     +RR+     H      N L+      +A  + +   E+  +  + A   SL+
Sbjct: 176 SEK--LSKMRRISRELSHRFGRQPNRLE------LASAMGIEPRELEDLISQSAPCASLD 227

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR- 246
           A     +  S+  +  L+ D +G+E   +E  +R  ++  L   +S LN RE++I   R 
Sbjct: 228 AHARGEEDRSTLGE--LIPDPNGEEP--MEGMDRSIQKEHLGGWLSQLNEREQKILRLRF 283

Query: 247 -RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
               E P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 284 GLGGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 319


>gi|307718430|ref|YP_003873962.1| RNA polymerase sigma factor [Spirochaeta thermophila DSM 6192]
 gi|306532155|gb|ADN01689.1| RNA polymerase sigma factor [Spirochaeta thermophila DSM 6192]
          Length = 281

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 85/268 (31%), Positives = 135/268 (50%), Gaps = 20/268 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI++  +L  +EE  L KR R  GD  A  RL+T++LRLVVKIA+ +    +P+ ++
Sbjct: 18  YLREIKRYKLLSPEEERELGKRIR-RGDPEARERLITANLRLVVKIALQFSVPDIPLLDL 76

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGL++A +KFD  R  R +TY+ WWI+ A+   ++     +++    N+K     
Sbjct: 77  IQEGNIGLIRAAEKFDYRRNIRFSTYAAWWIRQAIHRALMNKRRPIRL---PNRKEDV-- 131

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV---ISMNCRLAGDESLNALINSSDK 195
           LR+++   Q +    ++      IA+ L +   EV   I++   +    SL   IN    
Sbjct: 132 LRKIEKAKQLLEQRLMREPSTEEIAELLGMETEEVEELINLGQEVV---SLETQIND--- 185

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP-VT 254
            S    D        +E+V      +  R + LT     L+ RE  +   R     P  T
Sbjct: 186 GSMDLHDVCPGGASPEEEVC----RKACREDTLTLIQRTLDSRESEVVLHRYALTGPRYT 241

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQE 282
           L+ LS    +S E VRQIE RA +K++E
Sbjct: 242 LKTLSEHLGISPETVRQIEIRALRKLRE 269


>gi|57234646|ref|YP_181295.1| RNA polymerase sigma factor RpoD [Dehalococcoides ethenogenes 195]
 gi|57225094|gb|AAW40151.1| RNA polymerase sigma factor RpoD [Dehalococcoides ethenogenes 195]
          Length = 520

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 80/243 (32%), Positives = 127/243 (52%), Gaps = 30/243 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV +A  + G G+P+ +++ EGNIGL++AV+KFD  RGF+ +TY+ WW
Sbjct: 283 AERHLIQANLRLVVSVAKKHIGRGMPLLDLIQEGNIGLIRAVEKFDFHRGFKFSTYATWW 342

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     ++L   L R     +   + +L PE+V
Sbjct: 343 IRQAITRAIADQARTIRIPVHMVETINKLLSISRQLSQKLGREPTPDEIAVEMDLPPEKV 402

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IAK   VS+  V S+   +  +E  +      D+N+    D          Q+L E+ 
Sbjct: 403 REIAK---VSQLPV-SLESPIGEEEDSHLGDFIEDQNALAPPDA------ASRQLLKEQ- 451

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
                   +   +  L PRERR+ + R   E+    TLE +  EF V+RER+RQIEA+A 
Sbjct: 452 --------IDTVLGSLTPRERRVLQLRFGLEDGRSRTLEEVGKEFNVTRERIRQIEAKAL 503

Query: 278 KKV 280
           +K+
Sbjct: 504 RKL 506


>gi|18202317|sp|P58290|RPOD_LACLC RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-42
          Length = 364

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 85/271 (31%), Positives = 141/271 (52%), Gaps = 22/271 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
           Y+ EI + P++   EE  LA+     G+ +  A   L  ++LRLVV IA  Y G G+   
Sbjct: 96  YLKEIGRYPLISLDEETKLAEAIIAGGEGAEFAKQMLAEANLRLVVSIAKRYSGRGMQFL 155

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +     
Sbjct: 156 DLIQEGNMGLMKAVDKFDQTKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETI 213

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDK 195
             L R++ +L      +  PE+   I K+L+++  +V  +  ++A +  SL   I   D 
Sbjct: 214 NKLIRVQRNLLQELGRDPSPEE---IGKELHMAPDKVREV-LKIAQEPVSLETPIGEED- 268

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNR---RNMLTRSMSVLNPRERRIFEAR-RLQEN 251
             S   D++      ++ V+    +  NR   R  L   M  L  RE  +   R  L + 
Sbjct: 269 -DSHLGDFI------EDDVIESPVDYTNRILLREQLDEVMDTLTDREENVLRMRFGLDDG 321

Query: 252 PV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            + TLE++  +F+V+RER+RQIEA+A KK++
Sbjct: 322 RMHTLEDVGKQFKVTRERIRQIEAKAIKKLR 352


>gi|149921032|ref|ZP_01909492.1| RNA polymerase sigma factor RpoD [Plesiocystis pacifica SIR-1]
 gi|149818164|gb|EDM77620.1| RNA polymerase sigma factor RpoD [Plesiocystis pacifica SIR-1]
          Length = 547

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 84/259 (32%), Positives = 130/259 (50%), Gaps = 38/259 (14%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A+R RE    +A   LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +R
Sbjct: 302 ARRERE----AAKAELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQR 357

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQA 148
           G++ +TY+ WWI+ A+   I      +++               ++L     R   H + 
Sbjct: 358 GYKFSTYATWWIRQAITRAISDQARTIRVPVHMIESINKLIRTTRQLVQEFGREPTHQEI 417

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVY 206
               N+  E+V +I   L +++ E IS+   L   GD SL  LI   DKN+      +V 
Sbjct: 418 AEKMNMPVEKVRSI---LRIAK-EPISLETPLGEDGDSSLGDLIE--DKNALDPGSGVVE 471

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEV 264
            H G E                 R+++ L PRE +I   R    + +  TLE +  +F V
Sbjct: 472 RHLGDET---------------RRALASLTPREEKILRLRFGIGEASDHTLEEVGRDFSV 516

Query: 265 SRERVRQIEARAFKKVQES 283
           +RER+RQIEA+A  K++++
Sbjct: 517 TRERIRQIEAKALSKLRKA 535


>gi|168036108|ref|XP_001770550.1| plastid sigma factor SIG1 [Physcomitrella patens subsp. patens]
 gi|14669828|dbj|BAB62006.1| PpSIG1 [Physcomitrella patens]
 gi|14669830|dbj|BAB62007.1| PpSIG1 [Physcomitrella patens]
 gi|162678258|gb|EDQ64719.1| plastid sigma factor SIG1 [Physcomitrella patens subsp. patens]
          Length = 677

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 95/323 (29%), Positives = 154/323 (47%), Gaps = 75/323 (23%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYR--------------------------EHGDLS- 48
           L+ Y+ EI KI +L KQEE  L+K+ R                           H +LS 
Sbjct: 357 LTTYLREITKINLLTKQEEVFLSKKLRIGLNLLEERKKLAAELGYVPSNEEWAPHMNLSV 416

Query: 49  ------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                       A  ++V ++LRLVV +A  Y  +GL +++++ EG+IGL++ V+KFD  
Sbjct: 417 GDLVRKLGEAEWARDKMVMANLRLVVSVAKQYHSFGLEMADLIQEGSIGLLRGVEKFDHT 476

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL---------- 146
           RG++L+TY  WWI+  +   I      V++    +       +R+ K  L          
Sbjct: 477 RGYKLSTYVHWWIRQGVTRAIADHSRTVRLPVHVHDT--LGRIRKAKSTLLSEGCTASVQ 534

Query: 147 ---QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD-ESLNALINSSDKNSSQWQD 202
              +A      K +  + + KKL VS  + I  N   +GD E+L++L+   D  +   Q 
Sbjct: 535 EISEATNLTGTKIKNTLQVTKKL-VSLDKEIGRNTLQSGDGETLHSLVADRDIEN---QP 590

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI----FEARRLQENPVTLENL 258
           W +      E++L++ +  K    +LT   S L PRER I    +   R   + ++LE++
Sbjct: 591 WTIV-----ERMLMKDDVDK----LLT---SQLGPRERDIVRLHYGVGREDGSVMSLESI 638

Query: 259 SSEFEVSRERVRQIEARAFKKVQ 281
           S  + VSRERVRQ+E  A +K+Q
Sbjct: 639 SYRYGVSRERVRQLETAAMRKLQ 661


>gi|19862496|sp|Q04506|RPOD_LACLA RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-42
          Length = 386

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 85/271 (31%), Positives = 141/271 (52%), Gaps = 22/271 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
           Y+ EI + P++   EE  LA+     G+ +  A   L  ++LRLVV IA  Y G G+   
Sbjct: 118 YLKEIGRYPLISLDEETKLAEAIIAGGEGAEFAKQMLAEANLRLVVSIAKRYSGRGMQFL 177

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +     
Sbjct: 178 DLIQEGNMGLMKAVDKFDHTKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETI 235

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDK 195
             L R++ +L      +  PE+   I K+L+++  +V  +  ++A +  SL   I   D 
Sbjct: 236 NKLIRVQRNLLQELGRDPSPEE---IGKELHMAPDKVREV-LKIAQEPVSLETPIGEED- 290

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNR---RNMLTRSMSVLNPRERRIFEAR-RLQEN 251
             S   D++      ++ V+    +  NR   R  L   M  L  RE  +   R  L + 
Sbjct: 291 -DSHLGDFI------EDDVIESPVDYTNRILLREQLDEVMDTLTDREENVLRMRFGLDDG 343

Query: 252 PV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            + TLE++  +F+V+RER+RQIEA+A KK++
Sbjct: 344 RMHTLEDVGKQFKVTRERIRQIEAKAIKKLR 374


>gi|15672535|ref|NP_266709.1| RNA polymerase sigma factor RpoD [Lactococcus lactis subsp. lactis
           Il1403]
 gi|281491019|ref|YP_003352999.1| RNA polymerase sigma factor RpoD [Lactococcus lactis subsp. lactis
           KF147]
 gi|12723439|gb|AAK04651.1|AE006289_2 major RNA polymerase sigma factor [Lactococcus lactis subsp. lactis
           Il1403]
 gi|281374777|gb|ADA64297.1| RNA polymerase sigma factor RpoD (Sigma-42) [Lactococcus lactis
           subsp. lactis KF147]
 gi|326406054|gb|ADZ63125.1| RNA polymerase sigma factor RpoD [Lactococcus lactis subsp. lactis
           CV56]
          Length = 447

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 85/271 (31%), Positives = 141/271 (52%), Gaps = 22/271 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
           Y+ EI + P++   EE  LA+     G+ +  A   L  ++LRLVV IA  Y G G+   
Sbjct: 179 YLKEIGRYPLISLDEETKLAEAIIAGGEGAEFAKQMLAEANLRLVVSIAKRYSGRGMQFL 238

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +     
Sbjct: 239 DLIQEGNMGLMKAVDKFDHTKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETI 296

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDK 195
             L R++ +L      +  PE+   I K+L+++  +V  +  ++A +  SL   I   D 
Sbjct: 297 NKLIRVQRNLLQELGRDPSPEE---IGKELHMAPDKVREV-LKIAQEPVSLETPIGEED- 351

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNR---RNMLTRSMSVLNPRERRIFEAR-RLQEN 251
             S   D++      ++ V+    +  NR   R  L   M  L  RE  +   R  L + 
Sbjct: 352 -DSHLGDFI------EDDVIESPVDYTNRILLREQLDEVMDTLTDREENVLRMRFGLDDG 404

Query: 252 PV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            + TLE++  +F+V+RER+RQIEA+A KK++
Sbjct: 405 RMHTLEDVGKQFKVTRERIRQIEAKAIKKLR 435


>gi|281420436|ref|ZP_06251435.1| RNA polymerase sigma-70 factor [Prevotella copri DSM 18205]
 gi|281405493|gb|EFB36173.1| RNA polymerase sigma-70 factor [Prevotella copri DSM 18205]
          Length = 291

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 80/283 (28%), Positives = 143/283 (50%), Gaps = 33/283 (11%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYG 72
            L +Y+ EI + PM+   EE  LA++ R+ G     A  +LV ++LR VV +A  Y+  G
Sbjct: 17  ALDKYLVEIGREPMVSIDEEIELAQKIRKGGREGERAKEKLVKANLRFVVSVAKQYQHQG 76

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V++    NQ
Sbjct: 77  LSLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRL--PLNQ 134

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRLAG 182
                 L ++   +      N +   V  +A+   + ES++          +S++     
Sbjct: 135 ---VGALSKISAEISKFEQENQRKPSVAELAQITKMEESKIDQTIKADNHHMSIDAPFGS 191

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM-SVLNPRERR 241
           D+  NA++           D +    D +    ++ E   +    L R + SVL  RER+
Sbjct: 192 DDDDNAMV-----------DVMASGDDSRTDKGVDFESMASE---LDRVLNSVLKDRERK 237

Query: 242 IF-EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           I      +  +   LE + SEF ++RERVRQI  ++  K+++S
Sbjct: 238 ILCYCYGIGCHEKGLEEIGSEFNLTRERVRQIREKSIIKLRDS 280


>gi|254481825|ref|ZP_05095068.1| RNA polymerase sigma factor RpoS [marine gamma proteobacterium
           HTCC2148]
 gi|214037954|gb|EEB78618.1| RNA polymerase sigma factor RpoS [marine gamma proteobacterium
           HTCC2148]
          Length = 353

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 82/278 (29%), Positives = 142/278 (51%), Gaps = 27/278 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L   EE   A R    GD S   R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 85  YLNEIGYSPLLTADEEKYYA-RLAIKGDESGRKRMIESNLRLVVKISRRYINRGLTLLDL 143

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 144 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERGIMNQTRTIRLPIHV-VKELNVY 202

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA------GDESLNALINS 192
           LR  +   Q + D+    E++  +  +       ++ +N R+       G +S  A++++
Sbjct: 203 LRAARELTQKL-DHEPTAEEIADMLDRPAADVKRMLGLNERVTSMDTPVGPDSDKAVVDT 261

Query: 193 SDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
                      L+ D D ++ +   L E  E++  R ++ R   +      R +E+    
Sbjct: 262 IADTHESDPSQLLQDSDIKDSIGSWLDELSEKQ--REVVARRFGL------RGYESS--- 310

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
               TLE +  E  ++RERVRQI+  A K+++  ++ Q
Sbjct: 311 ----TLEEVGREIGLTRERVRQIQVEALKRLRGIMETQ 344


>gi|198282770|ref|YP_002219091.1| RpoD family RNA polymerase sigma-70 subunit [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218666687|ref|YP_002424966.1| RNA polymerase sigma-38 factor [Acidithiobacillus ferrooxidans ATCC
           23270]
 gi|198247291|gb|ACH82884.1| RNA polymerase, sigma 70 subunit, RpoD family [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218518900|gb|ACK79486.1| RNA polymerase sigma-38 factor [Acidithiobacillus ferrooxidans ATCC
           23270]
          Length = 317

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 86/273 (31%), Positives = 143/273 (52%), Gaps = 17/273 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  ++E  L  R  + GD +A   ++ S+LRLVVK+A  Y   GLP+ ++
Sbjct: 49  YLREIGHRPLLTAEQEVTLG-RMVQTGDQAARCTMIESNLRLVVKVARHYLNRGLPLLDL 107

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 108 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQNIERALMNQTRTIRLPIHV-MKELSAV 166

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +   Q +   +  PE+V   A+ L+ S   V   +C L  D  + +L     K S 
Sbjct: 167 LRATRCLAQTLQ-RDPTPEEV---AEALDRSVDAV--RDC-LEMDGRVTSLDMPYGKGSD 219

Query: 199 QWQDWLVYDHD--GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVT 254
           +    LV D +  G EQ L    E +N    + + ++ +  + R +   R   +  +  T
Sbjct: 220 RSLADLVADTNAPGVEQRL----ENQNLSRQVHQWIATMTEKHRLVLLWRFGLDGTDGAT 275

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           LE + S   ++RERVRQI+  A   ++  I+ +
Sbjct: 276 LEEVGSRLGITRERVRQIQVEALLVLRHRIEAE 308


>gi|253576089|ref|ZP_04853421.1| RNA polymerase sigma-subunit [Paenibacillus sp. oral taxon 786 str.
           D14]
 gi|251844432|gb|EES72448.1| RNA polymerase sigma-subunit [Paenibacillus sp. oral taxon 786 str.
           D14]
          Length = 374

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 82/265 (30%), Positives = 133/265 (50%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   +E  LAKR  E+GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 108 YLKEIGRVPLLSADDEMELAKRI-ENGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 166

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD ++GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 167 IQEGNMGLIKAVEKFDHKKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 224

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L         PE+   IA ++++S  +V  +        SL   I   D   S
Sbjct: 225 LIRVSRQLLQELGREPAPEE---IAAEMDLSVEKVREIMKIAQEPVSLETPIGEED--DS 279

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++    D +     +    +  +  L   +  L  RE  +   R   ++    TLE
Sbjct: 280 HLGDFI---EDQEALAPADAAAYELLKEQLEDVLDTLTEREENVLRLRFGLDDGRTRTLE 336

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +   F V+RER+RQIEA+A +K++
Sbjct: 337 EVGKVFGVTRERIRQIEAKALRKLR 361


>gi|317473637|ref|ZP_07932926.1| RNA polymerase sigma factor RpoD [Anaerostipes sp. 3_2_56FAA]
 gi|316898927|gb|EFV20952.1| RNA polymerase sigma factor RpoD [Anaerostipes sp. 3_2_56FAA]
          Length = 364

 Score =  107 bits (267), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 84/269 (31%), Positives = 139/269 (51%), Gaps = 21/269 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L   EE  LA+R  E GD  A  +L  ++LRLVV IA  Y G G+   ++
Sbjct: 98  YLKEIGKVPLLSADEEIRLAQRM-EEGDEEAKKKLAEANLRLVVSIAKRYVGRGMLFLDL 156

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 157 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKL- 215

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               +R  +  LQ +    L PE+   IA+++++    V  +        SL   I   +
Sbjct: 216 ----IRVSRQLLQELGREPL-PEE---IAEEMDIPVDRVREILKISQEPVSLETPIG--E 265

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
           +  S   D++    D    V  +       +  L+  +  L  RE+++   R   ++   
Sbjct: 266 EEDSHLGDFI---QDDNVPVPADAAAFTLLKEQLSEVLGTLTEREQKVLRLRFGLDDSRA 322

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 323 RTLEEVGKEFNVTRERIRQIEAKALRKLR 351


>gi|216733|dbj|BAA01038.1| RNA polymerase sigma factor [Lactococcus lactis]
          Length = 340

 Score =  107 bits (266), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 85/271 (31%), Positives = 141/271 (52%), Gaps = 22/271 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
           Y+ EI + P++   EE  LA+     G+ +  A   L  ++LRLVV IA  Y G G+   
Sbjct: 72  YLKEIGRYPLISLDEETKLAEAIIAGGEGAEFAKQMLAEANLRLVVSIAKRYSGRGMQFL 131

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +     
Sbjct: 132 DLIQEGNMGLMKAVDKFDHTKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETI 189

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDK 195
             L R++ +L      +  PE+   I K+L+++  +V  +  ++A +  SL   I   D 
Sbjct: 190 NKLIRVQRNLLQELGRDPSPEE---IGKELHMAPDKVREV-LKIAQEPVSLETPIGEED- 244

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNR---RNMLTRSMSVLNPRERRIFEAR-RLQEN 251
             S   D++      ++ V+    +  NR   R  L   M  L  RE  +   R  L + 
Sbjct: 245 -DSHLGDFI------EDDVIESPVDYTNRILLREQLDEVMDTLTDREENVLRMRFGLDDG 297

Query: 252 PV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            + TLE++  +F+V+RER+RQIEA+A KK++
Sbjct: 298 RMHTLEDVGKQFKVTRERIRQIEAKAIKKLR 328


>gi|160915039|ref|ZP_02077252.1| hypothetical protein EUBDOL_01047 [Eubacterium dolichum DSM 3991]
 gi|158432838|gb|EDP11127.1| hypothetical protein EUBDOL_01047 [Eubacterium dolichum DSM 3991]
          Length = 398

 Score =  107 bits (266), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 80/268 (29%), Positives = 137/268 (51%), Gaps = 18/268 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L+ +EE  +A+R  + GD  A  +L++++LRLVV IA  Y G G+   ++
Sbjct: 129 YLKEIGRVELLDPKEEPEIARRI-QAGDEEAKKKLISANLRLVVSIAKKYVGRGMLFLDL 187

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 188 IQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 245

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R++  L  + D    P      AK  N+S  +V  +        SL   I   D   S
Sbjct: 246 LTRIQRQL--VQDLGRDPTAEEIAAKMENISPEKVREIQKIALEPVSLETPIGEED--DS 301

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNR---RNMLTRSMSVLNPRERRIFEAR--RLQENPV 253
              D++      +++  +  +E  N    ++ +   +  L  RE ++   R         
Sbjct: 302 HLGDFI------EDKEALSPDEYANNQLLKDEINTVLQGLTEREEKVLRLRFGLYDGRTR 355

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 356 TLEEVGKEFNVTRERIRQIEAKALRKLK 383


>gi|194337394|ref|YP_002019188.1| RNA polymerase, sigma 32 subunit, RpoH [Pelodictyon
           phaeoclathratiforme BU-1]
 gi|194309871|gb|ACF44571.1| RNA polymerase, sigma 32 subunit, RpoH [Pelodictyon
           phaeoclathratiforme BU-1]
          Length = 299

 Score =  107 bits (266), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 88/304 (28%), Positives = 158/304 (51%), Gaps = 45/304 (14%)

Query: 9   IVNGE-IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS-----------AAHRLVTS 56
           I N E + L RY+ EI K  +L  ++E  L K  +E  D+            A  +L+  
Sbjct: 10  ITNRESLSLDRYLQEIGKYDLLTAEDEVKLTKAIKEGFDMPVDTTEYKRAKRALDKLIKG 69

Query: 57  HLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM--- 113
           +LR VV +A  Y+  GL + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++   
Sbjct: 70  NLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQA 129

Query: 114 ---QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
              Q  I+R   L ++GT     + +  L +     +   D N +      +A  L + +
Sbjct: 130 LAEQSRIVR-LPLNRVGTLNKISKAYSQLEQ-----EFERDPNTRE-----LATLLEM-D 177

Query: 171 SEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-- 227
           S+ ++   ++AG   S++A     D N  +  D L  D    +  L       NR ++  
Sbjct: 178 SQDVADTLKIAGRHVSVDAPFAQGDDN--RLLDVLQNDGHLPDYGL-------NRDSLTL 228

Query: 228 -LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + RS+SVL PRE  + ++      +NP+TLE +  +F ++RERVRQI+ +A +++++S 
Sbjct: 229 EVERSLSVLAPREADVIKSYFGIGMDNPLTLEEIGEKFRLTRERVRQIKEKAIRRLRQSA 288

Query: 285 QKQV 288
             ++
Sbjct: 289 YSKI 292


>gi|258648463|ref|ZP_05735932.1| RNA polymerase sigma factor [Prevotella tannerae ATCC 51259]
 gi|260851219|gb|EEX71088.1| RNA polymerase sigma factor [Prevotella tannerae ATCC 51259]
          Length = 283

 Score =  107 bits (266), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 86/279 (30%), Positives = 149/279 (53%), Gaps = 44/279 (15%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L RY+ EI + P +  +EE  L +R + +GD +A  RLV ++LR VV +A  Y+G G+ +
Sbjct: 19  LERYLSEISREPRITVEEEVELGRRAK-NGDEAAVERLVRANLRFVVSVAKQYQGQGISL 77

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG---TTANQ 132
            ++++EGN+GL+QA  +FD  RGF+  +Y++WWI+ ++   I     L+++     ++ Q
Sbjct: 78  IDLINEGNLGLIQAAHRFDDTRGFKFISYAVWWIRQSILLAITEKSRLIRLPQNQMSSIQ 137

Query: 133 KRL-FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRLA 181
           K L F+N        Q + D   +P  +  I +++ V+E  V          +S++  L 
Sbjct: 138 KILRFYN--------QYMQDYE-RPPSIEEICEQMQVTEERVRLALQLQNKPLSIDAPLT 188

Query: 182 GDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            DE  +L+  +  SDK SS          DG    L+++ ER      + R +++L P E
Sbjct: 189 EDEARTLSERLR-SDKGSS---------ADGP---LLKEAERWK----VERMLNLLPPLE 231

Query: 240 RRIFEAR-RLQENPVTLENLSSEFEVSRERVRQIEARAF 277
           R + E     +   ++LE + +   +SRERVRQI+ +A 
Sbjct: 232 RSVIEYYLGFKGQGISLEEIGNRIGLSRERVRQIKVKAI 270


>gi|254439671|ref|ZP_05053165.1| RNA polymerase sigma factor, sigma-70 family [Octadecabacter
           antarcticus 307]
 gi|198255117|gb|EDY79431.1| RNA polymerase sigma factor, sigma-70 family [Octadecabacter
           antarcticus 307]
          Length = 235

 Score =  107 bits (266), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 70/218 (32%), Positives = 122/218 (55%), Gaps = 9/218 (4%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           ++V + NIGLM+A  +FDPERG+R +TYS+WWI+A +Q Y L S S+V+   +A+ +   
Sbjct: 19  DLVQQANIGLMKAADRFDPERGYRFSTYSVWWIRAEIQSYKLASMSIVRRPNSADFRNAV 78

Query: 137 FNLRRLKGHLQAITDNNL--KPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSS 193
             L RL    +A++++    + +    +AK L V+   +  +  +++G D SLN  + S 
Sbjct: 79  GKLGRLD---EAVSNDPTINRTDADALVAKALGVNLQRLNDLRQQVSGTDYSLN--LPSF 133

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
             +  +    LV     ++   + + + K  R +L   +  L  RER+I  A +LQ+ P 
Sbjct: 134 GDDGEERMARLVDPASTEDADTMHRLDIKKLRGLLVEIIGSLPDRERKIIMATQLQDPPA 193

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESI-QKQVEL 290
           TL  L   F +S ERVRQ+    F++++ ++ Q+ +EL
Sbjct: 194 TLTALGIHFGISTERVRQLREMGFERLRTTMTQRDLEL 231


>gi|197301814|ref|ZP_03166884.1| hypothetical protein RUMLAC_00540 [Ruminococcus lactaris ATCC
           29176]
 gi|197299254|gb|EDY33784.1| hypothetical protein RUMLAC_00540 [Ruminococcus lactaris ATCC
           29176]
          Length = 372

 Score =  107 bits (266), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 85/269 (31%), Positives = 138/269 (51%), Gaps = 21/269 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  + E  LA+R  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 106 YLKEIGKVPLLSAEREIELAQRM-EEGDEEAKKELAEANLRLVVSIAKRYVGRGMLFLDL 164

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 165 IQEGNLGLIKAVEKFDYHKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKL- 223

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               +R  +  LQ +    L PE+   IAK++++    V  +        SL   I   +
Sbjct: 224 ----IRVSRQLLQELGREPL-PEE---IAKEMDMPVERVREILKISQEPVSLETPI--GE 273

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
           +  S   D++    D    V  E   +   +  L   +  L  RE+++   R    +   
Sbjct: 274 EEDSHLGDFI---QDDNVPVPAEAAAQTLLKEQLDEVLDTLTEREQKVLRLRFGMNDGRA 330

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE +  EF+V+RER+RQIEA+A +K++
Sbjct: 331 RTLEEVGREFDVTRERIRQIEAKALRKLR 359


>gi|78185860|ref|YP_378294.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CC9902]
 gi|78170154|gb|ABB27251.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. CC9902]
          Length = 328

 Score =  107 bits (266), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 82/274 (29%), Positives = 144/274 (52%), Gaps = 18/274 (6%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           EI L+ ++ +++++  L  QEE    ++++      A  R++ ++LRLVV +A  Y+  G
Sbjct: 59  EIELAHHVQDMKQLKEL-PQEELTSRQKHKIRMGKRARDRMMAANLRLVVSVAKKYQNQG 117

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L + ++V EG IGL +AV KFDP  G++ +TY+ WWI+  M   I  S   +++    ++
Sbjct: 118 LELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIRLPIHISE 177

Query: 133 KRLFFNLRRLK---GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
           K     +RR+     H      N L+      +A  + +   E+  +  + A   SL+A 
Sbjct: 178 K--LSKMRRISRELSHRFGRQPNRLE------LASAMGIEPRELEDLITQSAPCASLDAH 229

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--R 247
               +  S+  +  L+ D +G+E   +E  +R  ++  L   +S LN RE++I   R   
Sbjct: 230 ARGEEDRSTLGE--LIPDPNGEEP--MEGMDRSIQKEHLGGWLSQLNEREQKILRLRFGL 285

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             E P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 286 GGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 319


>gi|116071837|ref|ZP_01469105.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. BL107]
 gi|116065460|gb|EAU71218.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. BL107]
          Length = 284

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 82/274 (29%), Positives = 144/274 (52%), Gaps = 18/274 (6%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           EI L+ ++ +++++  L  QEE    ++++      A  R++ ++LRLVV +A  Y+  G
Sbjct: 15  EIELAHHVQDMKQLKEL-PQEELTSRQKHKIRMGKRARDRMMAANLRLVVSVAKKYQNQG 73

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L + ++V EG IGL +AV KFDP  G++ +TY+ WWI+  M   I  S   +++    ++
Sbjct: 74  LELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIRLPIHISE 133

Query: 133 KRLFFNLRRLK---GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
           K     +RR+     H      N L+      +A  + +   E+  +  + A   SL+A 
Sbjct: 134 K--LSKMRRISRELSHRFGRQPNRLE------LASAMGIEPRELEDLITQSAPCASLDAH 185

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--R 247
               +  S+  +  L+ D +G+E   +E  +R  ++  L   +S LN RE++I   R   
Sbjct: 186 ARGEEDRSTLGE--LIPDPNGEEP--MEGMDRSIQKEHLGGWLSQLNEREQKILRLRFGL 241

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             E P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 242 GGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 275


>gi|332980900|ref|YP_004462341.1| RNA polymerase sigma-70 subunit RpoD [Mahella australiensis 50-1
           BON]
 gi|332698578|gb|AEE95519.1| RNA polymerase, sigma 70 subunit, RpoD [Mahella australiensis 50-1
           BON]
          Length = 356

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 88/285 (30%), Positives = 140/285 (49%), Gaps = 35/285 (12%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           VN +  +  Y+ EI KIP+L   EE  LAKR  E GD  A  RL  ++LRLVV IA  Y 
Sbjct: 81  VNIDDPVRMYLKEIGKIPLLSSDEEIELAKRI-EQGDEEAKKRLAEANLRLVVSIAKRYV 139

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT- 128
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 140 GRGMLFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 199

Query: 129 ---TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              T N+     ++L   L R     +   +  +  ++V  I K       E +S+   +
Sbjct: 200 MVETINKLVRVSRQLMQELGREPAPEEVAEEMGISVDKVRDIMK----IAQEPVSLETPI 255

Query: 181 AGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
             +E   L   I   D  +                  + KE+  +  + LT       PR
Sbjct: 256 GEEEDSHLGDFIPDDDAPAPAEAAAFT----------LLKEQLMDVLDTLT-------PR 298

Query: 239 ERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           E ++   R   ++    TLE +  EF+V+RER+RQIEA+A +K++
Sbjct: 299 EEKVLRLRFGLDDGRARTLEEVGKEFDVTRERIRQIEAKALRKLR 343


>gi|168335371|ref|ZP_02693465.1| RNA polymerase, sigma 70 subunit, RpoD family protein [Epulopiscium
           sp. 'N.t. morphotype B']
          Length = 364

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 83/268 (30%), Positives = 139/268 (51%), Gaps = 21/268 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L   +E  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 98  YLKEIGKVPLLSADDEIKLAKRM-ESGDEEARKRLAEANLRLVVSIAKRYVGRGMLFLDL 156

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 157 IQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINK-- 214

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               L R++  L      + +PE+   IA+++ +S ++V  +        +L   I   +
Sbjct: 215 ----LMRIQRQLLQELGRDPQPEE---IAREMELSVNKVREIMKISQEPVALETPI--GE 265

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
           +  +   D+L  +              K +   L   +  L  RE+++ + R   ++   
Sbjct: 266 EEDTNLGDFLADEDAPAPAEAAAFTLLKEQ---LIEVLDTLTDREQKVLKLRFGLDDGRA 322

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKV 280
            TLE +  EF V+RER+RQIEA+A +K+
Sbjct: 323 RTLEEVGREFNVTRERIRQIEAKALRKL 350


>gi|298245985|ref|ZP_06969791.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297553466|gb|EFH87331.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 417

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 84/296 (28%), Positives = 142/296 (47%), Gaps = 45/296 (15%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++PM+  + E  LA+R  E GD  A  + + ++LRLVV IA  Y G GL + ++
Sbjct: 153 YLREIGRVPMITHEREIELAQRI-ESGDRDAMKQFILANLRLVVSIAKRYVGRGLTLLDL 211

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN------- 131
           + EGNIGL++AV+++D  RG R +T++ WWI+ A+   +      +++    N       
Sbjct: 212 IQEGNIGLIRAVQRYDWRRGHRFSTHATWWIRQAISRAVADKGRTIRLPVYVNTALNRIR 271

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             ++RL   L R     +      L P +++    +L  +    +S+   +  D+     
Sbjct: 272 RERQRLLQELGREPSEQELAEATGLDPVRMI----ELQAAPGAPVSLELPVGEDDDQELG 327

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--- 246
               D  S+  +D          Q L ++ +R           SVL PRE+ + + R   
Sbjct: 328 DVLPDTESASPEDLATT------QTLKDEVQRVLE--------SVLTPREQLVLQLRFGL 373

Query: 247 -RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQKPR 301
              Q +P  LE +  E  ++RERVRQIEA A  K+++           PP+L++ R
Sbjct: 374 GNGQAHP--LEQVGRELGITRERVRQIEAGALAKLRQ-----------PPVLERLR 416


>gi|150020921|ref|YP_001306275.1| RpoD family RNA polymerase sigma factor [Thermosipho melanesiensis
           BI429]
 gi|149793442|gb|ABR30890.1| RNA polymerase, sigma 70 subunit, RpoD family [Thermosipho
           melanesiensis BI429]
          Length = 370

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 84/278 (30%), Positives = 137/278 (49%), Gaps = 41/278 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ +I KIP+L +  E  LA+R  + GD  A  +LV S+LRLVV IA  Y G GL   ++
Sbjct: 99  YLKDIGKIPLLSQSMERELARR-AQQGDERAKQKLVESNLRLVVSIAKRYVGKGLSFLDL 157

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-- 132
           + EGN+GL++AV+KFD ++G++ +TY+ WWI+ A+   I      +++      T N+  
Sbjct: 158 IQEGNVGLLKAVEKFDWKKGYKFSTYATWWIRQAITRAIADQARTIRVPVHMVETINKVQ 217

Query: 133 --KRLFFNLRRLKGHLQAITDNNLKP----EQVVAIAKKLNVSESEVISMNCRLAGDESL 186
              R ++     +  ++ +     KP    E+++  AK       E  S+   +  DE  
Sbjct: 218 KIMRDYYQQHGTEIPIEELAKIIGKPVEKVEEILQAAK-------ETTSLEAPVGEDE-- 268

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE--RKNRRNMLTRSMSVLNPRERRIFE 244
                          D  V D    E +   K+E  R   R  + + +  LN RE+ + +
Sbjct: 269 ---------------DSTVGDFVADESIASPKKEAMRMLIREEVEKVLETLNDREKLVLK 313

Query: 245 ARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            R   +     TLE +   F V+RER+RQIE +A +K+
Sbjct: 314 MRYGLIDGKSKTLEEVGQYFNVTRERIRQIEVKALRKL 351


>gi|238854653|ref|ZP_04644983.1| RNA polymerase sigma factor RpoD [Lactobacillus jensenii 269-3]
 gi|260664404|ref|ZP_05865256.1| RNA polymerase sigma factor RpoS [Lactobacillus jensenii SJ-7A-US]
 gi|282932956|ref|ZP_06338353.1| RNA polymerase sigma factor RpoD [Lactobacillus jensenii 208-1]
 gi|238832443|gb|EEQ24750.1| RNA polymerase sigma factor RpoD [Lactobacillus jensenii 269-3]
 gi|260561469|gb|EEX27441.1| RNA polymerase sigma factor RpoS [Lactobacillus jensenii SJ-7A-US]
 gi|281302991|gb|EFA95196.1| RNA polymerase sigma factor RpoD [Lactobacillus jensenii 208-1]
          Length = 364

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 84/273 (30%), Positives = 136/273 (49%), Gaps = 31/273 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   EE  LAKR ++ GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 98  YLKEIGRVPLLNADEEITLAKRIQD-GDEEAKQELAEANLRLVVSIAKRYVGRGMQFLDL 156

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV KF+ + GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 157 IQEGNMGLMKAVDKFNYKLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 216

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + ++  ++V  I   L +++ E +S+   +    D  L 
Sbjct: 217 RIQRQLLQDLGREPTPEEIGAEMDMGTDKVRDI---LKIAQ-EPVSLETPIGEEDDSHLG 272

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S +         +  E+VL    +R+   N+L     + + R R       
Sbjct: 273 DFIEDKDATSPEQHASYEMLKEQLEEVLDTLTDREE--NVLRLRFGLDDGRTR------- 323

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                 TLE +   F V+RER+RQIEA+A +K+
Sbjct: 324 ------TLEEVGKVFGVTRERIRQIEAKALRKL 350


>gi|291550178|emb|CBL26440.1| RNA polymerase, sigma 70 subunit, RpoD [Ruminococcus torques L2-14]
          Length = 373

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 85/269 (31%), Positives = 138/269 (51%), Gaps = 21/269 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  + E  LA+R  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 107 YLKEIGKVPLLSAEREIELAQRM-EEGDEEAKKELAEANLRLVVSIAKRYVGRGMLFLDL 165

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 166 IQEGNLGLIKAVEKFDYHKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKL- 224

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               +R  +  LQ +    L PE+   IAK++++    V  +        SL   I   +
Sbjct: 225 ----IRVSRQLLQELGREPL-PEE---IAKEMDMPVERVREILKISQEPVSLETPI--GE 274

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
           +  S   D++    D    V  E   +   +  L   +  L  RE+++   R    +   
Sbjct: 275 EEDSHLGDFI---QDDNVPVPAEAAAQTLLKEQLDEVLDTLTEREQKVLRLRFGMNDGRA 331

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE +  EF+V+RER+RQIEA+A +K++
Sbjct: 332 RTLEEVGREFDVTRERIRQIEAKALRKLR 360


>gi|283780188|ref|YP_003370943.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pirellula staleyi
           DSM 6068]
 gi|283438641|gb|ADB17083.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pirellula staleyi
           DSM 6068]
          Length = 320

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 82/279 (29%), Positives = 135/279 (48%), Gaps = 27/279 (9%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ EI +  +L  ++E  LA    + GD+ A  R+V ++LRLVV IA GY G GL +
Sbjct: 43  LESYLREINETALLSARDERELAAAIAD-GDVRARDRMVRANLRLVVNIARGYTGKGLSL 101

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GL++AV+ FDP  G R +TY+ +WIK +++  ++ S   ++I   A    L
Sbjct: 102 QDLIEEGNLGLLRAVEGFDPAVGTRFSTYASYWIKQSIKRALINSAKTIRI--PAYMVEL 159

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAI----AKKLNVSESEVISMNCRLAGDESLNALIN 191
               RR    L         PE+V  +     KKL + +  +   N              
Sbjct: 160 LSKWRRATARLTEELGRGPTPEEVARVLGLAKKKLPIIKKAIRIYNS-----------TP 208

Query: 192 SSDKNSSQWQ-DWLVYDH--DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-- 246
            +D++ + W    +V D      E  L+E++  K+   ML      ++ RE  +   R  
Sbjct: 209 QTDQSEAGWSLGEIVMDERLKNPEDELVEQDVLKHVMEML----HTMDSREATVLRMRFG 264

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
                P TL+ +     ++RERVRQIE  A  K+ + ++
Sbjct: 265 LGDTTPHTLKEIGESLGLTRERVRQIETEALGKLADGLK 303


>gi|167747159|ref|ZP_02419286.1| hypothetical protein ANACAC_01873 [Anaerostipes caccae DSM 14662]
 gi|167654119|gb|EDR98248.1| hypothetical protein ANACAC_01873 [Anaerostipes caccae DSM 14662]
          Length = 370

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 84/269 (31%), Positives = 139/269 (51%), Gaps = 21/269 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L   EE  LA+R  E GD  A  +L  ++LRLVV IA  Y G G+   ++
Sbjct: 104 YLKEIGKVPLLSADEEIRLAQRM-EEGDEEAKKKLAEANLRLVVSIAKRYVGRGMLFLDL 162

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 163 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKL- 221

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               +R  +  LQ +    L PE+   IA+++++    V  +        SL   I   +
Sbjct: 222 ----IRVSRQLLQELGREPL-PEE---IAEEMDIPVDRVREILKISQEPVSLETPIG--E 271

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
           +  S   D++    D    V  +       +  L+  +  L  RE+++   R   ++   
Sbjct: 272 EEDSHLGDFI---QDDNVPVPADAAAFTLLKEQLSEVLGTLTEREQKVLRLRFGLDDSRA 328

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 329 RTLEEVGKEFNVTRERIRQIEAKALRKLR 357


>gi|158340411|ref|YP_001521767.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158310652|gb|ABW32266.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 268

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 82/280 (29%), Positives = 148/280 (52%), Gaps = 37/280 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI + P+L  +EE  LA++ +  G+L A  R++  +LRLVV IA  ++  GLP+ ++
Sbjct: 11  YLQEIGRYPLLSPEEEINLARQVKA-GNLRAKQRMIECNLRLVVSIAKKHQNRGLPLLDL 69

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ-----K 133
           + EGNIGL +AV+KFD  +G R +TY+ WWI   +   +     ++++    NQ     K
Sbjct: 70  IQEGNIGLSRAVEKFDLNQGCRFSTYAYWWIWQGITRALHNKTKMIRLPIHLNQLHSKIK 129

Query: 134 RLFFNLRRLKGHLQAITD----NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
           R +F L +  G   ++ +     ++ P     I ++L +S+ EVIS++  +         
Sbjct: 130 RTYFQLNQEYGRQPSLDEVAYAMDIDP---THIQEQLQLSQ-EVISLDKFV--------- 176

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQV--LIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
              S+       + +  DH  Q+    L+ K+E       L++ M  L+ R++ I   R 
Sbjct: 177 ---SENQGDTLGELVAKDHSSQKYFENLMNKDE-------LSKLMGHLSERQQFIIGQRF 226

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             E+  P TL  ++   ++SRE +R+IE +AF+++++  Q
Sbjct: 227 GLEDGQPKTLVEIAKLLDMSREGIRRIEKKAFQQLKKYAQ 266


>gi|206889845|ref|YP_002248858.1| RNA polymerase sigma 70 factor [Thermodesulfovibrio yellowstonii
           DSM 11347]
 gi|206741783|gb|ACI20840.1| RNA polymerase sigma 70 factor [Thermodesulfovibrio yellowstonii
           DSM 11347]
          Length = 427

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 72/247 (29%), Positives = 130/247 (52%), Gaps = 37/247 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A ++++ S+L+LVV IA  Y G GL + +++ EGNIGLM+AV+KF+ ++GF+ +TYS WW
Sbjct: 189 AKNKMIESNLKLVVSIAKKYTGRGLNLEDLIQEGNIGLMKAVEKFEYKKGFKFSTYSTWW 248

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ ++   I      ++I        +  N+ ++    + +  N+     +  I+  LN+
Sbjct: 249 IRQSINRAIAEHSKTIRIPV-----HVIDNICKINKIYRELYQNSENEPDIEEISLNLNI 303

Query: 169 SESEV----------ISMNCRLAGDES-LNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
              ++          +S++  L  D+S L   I   D NS    +  ++D          
Sbjct: 304 PSDKIADFLAISKEPVSIDMSLRDDDSLLKEFI--EDMNSPNPYEEALHD---------- 351

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEA 274
                + ++++ +  S+L+ RE+ I   RR    +E P +L+ +  EF VSRER+RQIE 
Sbjct: 352 -----DLKHLIEKVFSLLSKREKEIL-MRRYGINEEKPKSLDEVGKEFSVSRERIRQIEL 405

Query: 275 RAFKKVQ 281
           RA +K++
Sbjct: 406 RAMRKLK 412


>gi|187251192|ref|YP_001875674.1| DNA-directed RNA polymerase sigma subunit RpoH [Elusimicrobium
           minutum Pei191]
 gi|186971352|gb|ACC98337.1| DNA-directed RNA polymerase, sigma subunit RpoH [Elusimicrobium
           minutum Pei191]
          Length = 380

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 76/275 (27%), Positives = 152/275 (55%), Gaps = 13/275 (4%)

Query: 16  LSRYIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           +++Y  +I ++   L ++E   L KR ++ GD +A  R++  +LRLV+  A  +    + 
Sbjct: 8   INQYFKKISEVSEDLSREEMEKLWKRIKK-GDTAAKQRMMELNLRLVIPAAKRFMRKDID 66

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++ EGN+GL+QA++KFDP +GFR +TY+++WI  A+++YI      +KI + A    
Sbjct: 67  LLDLIEEGNLGLLQAIEKFDPSKGFRFSTYAIYWIDQAIRKYIDEQSGAIKIPSHA---- 122

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSS 193
            + ++++      A+ D+  +   +  ++++L+ S  ++ S+   +   + +++L +   
Sbjct: 123 -WGDIKKWTRTWNALKDSLEREPSLTEMSRELDWSARKIKSILETINAAKGIDSLALAIG 181

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQEN- 251
           +++    +D L  D  G    +     R +  + L  ++  LNPR++ I   R  L+ N 
Sbjct: 182 EEDEVTLEDTLTDDGKGNPDDVF---SRSSSNSALLAALEELNPRDKEILMMRNGLKTNE 238

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           P+TL  +S    +SRERVRQIE RA   +++   K
Sbjct: 239 PMTLSEVSKIMGLSRERVRQIEERAISHIRKKAHK 273


>gi|256851182|ref|ZP_05556571.1| RNA polymerase sigma factor RpoS [Lactobacillus jensenii 27-2-CHN]
 gi|260660606|ref|ZP_05861521.1| RNA polymerase sigma factor RpoS [Lactobacillus jensenii 115-3-CHN]
 gi|282934648|ref|ZP_06339891.1| RNA polymerase sigma factor RpoD [Lactobacillus jensenii 208-1]
 gi|297206047|ref|ZP_06923442.1| RNA polymerase sigma factor rpoD [Lactobacillus jensenii JV-V16]
 gi|256616244|gb|EEU21432.1| RNA polymerase sigma factor RpoS [Lactobacillus jensenii 27-2-CHN]
 gi|260548328|gb|EEX24303.1| RNA polymerase sigma factor RpoS [Lactobacillus jensenii 115-3-CHN]
 gi|281301223|gb|EFA93524.1| RNA polymerase sigma factor RpoD [Lactobacillus jensenii 208-1]
 gi|297149173|gb|EFH29471.1| RNA polymerase sigma factor rpoD [Lactobacillus jensenii JV-V16]
          Length = 364

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 84/273 (30%), Positives = 136/273 (49%), Gaps = 31/273 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   EE  LAKR ++ GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 98  YLKEIGRVPLLNADEEIALAKRIQD-GDEEAKQELAEANLRLVVSIAKRYVGRGMQFLDL 156

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV KF+ + GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 157 IQEGNMGLMKAVDKFNYKLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 216

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + ++  ++V  I   L +++ E +S+   +    D  L 
Sbjct: 217 RIQRQLLQDLGREPTPEEIGAEMDMGTDKVRDI---LKIAQ-EPVSLETPIGEEDDSHLG 272

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S +         +  E+VL    +R+   N+L     + + R R       
Sbjct: 273 DFIEDKDATSPEQHASYEMLKEQLEEVLDTLTDREE--NVLRLRFGLDDGRTR------- 323

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                 TLE +   F V+RER+RQIEA+A +K+
Sbjct: 324 ------TLEEVGKVFGVTRERIRQIEAKALRKL 350


>gi|168187756|ref|ZP_02622391.1| RNA polymerase sigma factor RpoD [Clostridium botulinum C str.
           Eklund]
 gi|169294399|gb|EDS76532.1| RNA polymerase sigma factor RpoD [Clostridium botulinum C str.
           Eklund]
          Length = 368

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 78/265 (29%), Positives = 132/265 (49%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L   EE  LA+R  E G++ A  +L  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGKVPLLTPDEEVDLAQRI-EAGEMYAKKKLAEANLRLVVSIAKRYVGRGMLFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 161 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 218

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L        +PE++  I +       E++ +       E ++      ++  S
Sbjct: 219 LIRVSRQLLQELGREPQPEEIAKIMEMPVDKVREIMKI-----AQEPVSLETPIGEEEDS 273

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++  D              K +   L   +  L PRE ++   R   ++    TLE
Sbjct: 274 HLGDFIPDDEAPAPAEAAAFTMLKEQ---LINVLDTLTPREEKVLRLRFGLDDGRARTLE 330

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF V+RER+RQIEA+A +K++
Sbjct: 331 EVGKEFNVTRERIRQIEAKALRKLR 355


>gi|172056869|ref|YP_001813329.1| RpoD family RNA polymerase sigma factor [Exiguobacterium sibiricum
           255-15]
 gi|171989390|gb|ACB60312.1| RNA polymerase, sigma 70 subunit, RpoD family [Exiguobacterium
           sibiricum 255-15]
          Length = 361

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 85/276 (30%), Positives = 141/276 (51%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  ++E  LAKR  E  D  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 95  YLKEIGRVDLLNAEDEVELAKRI-EQNDEEAKKRLAEANLRLVVSIAKRYVGRGMLFLDL 153

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 154 IQEGNMGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 213

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   +  + PE+V  I   L +++ E +S+   +    D  L 
Sbjct: 214 RVQRQLLQDLGREPTPEEISKEMEITPEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 269

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D++++  QD   Y      ++L E+         L   +  L  RE  +   R 
Sbjct: 270 DFI--EDQDATAPQDAAAY------ELLKEQ---------LEDVLDTLTDREENVLRLRF 312

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 313 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 348


>gi|315185550|gb|EFU19319.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           thermophila DSM 6578]
          Length = 281

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 85/268 (31%), Positives = 136/268 (50%), Gaps = 20/268 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI++  +L  +EE  L KR R  GD  A  RL+T++LRLVVKIA+ +    +P+ ++
Sbjct: 18  YLREIKRYKLLSPEEERELGKRIR-RGDPVARERLITANLRLVVKIALQFSVPDIPLLDL 76

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGL++AV+KFD  R  R +TY+ WWI+ A+   ++     +++    N+K     
Sbjct: 77  IQEGNIGLIRAVEKFDYRRNIRFSTYAAWWIRQAIHRALMNKRRPIRL---PNRKEDV-- 131

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV---ISMNCRLAGDESLNALINSSDK 195
           LR+++   + +    ++      IA  L +   EV   I++   +    SL   IN    
Sbjct: 132 LRKIEKARRLLEQRLMREPSTEEIADLLGMESEEVEELINLGQEVV---SLETQIND--- 185

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP-VT 254
            S    D        +E+V      +  R + LT     L+ RE  +   R     P  T
Sbjct: 186 GSMDLHDVCPGGASPEEEVC----RKACREDTLTLIQRTLDSRESEVVLHRYALTGPRYT 241

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQE 282
           L+ LS +  +S E VRQIE RA +K++E
Sbjct: 242 LKTLSEQMGISPETVRQIEIRALRKLRE 269


>gi|315029422|gb|EFT41354.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX4000]
          Length = 368

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 86/275 (31%), Positives = 133/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGRVQLLTAAEEVELALKI-EEGDQEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 161 IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 220

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 221 RIQRQLLQDLGREPTPEEIGAEMDLPTEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 276

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S         +H   E +          +  L   +  L  RE  +   R 
Sbjct: 277 DFIEDQDATSP-------AEHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 319

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             +N    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 320 GLDNGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 354


>gi|86739990|ref|YP_480390.1| sigma 38 [Frankia sp. CcI3]
 gi|86566852|gb|ABD10661.1| RNA polymerase, sigma 70 subunit, RpoD [Frankia sp. CcI3]
          Length = 409

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 92/310 (29%), Positives = 148/310 (47%), Gaps = 63/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHG--------------------DLSAAHR------ 52
           Y+ EI K+P+L  +EE  LAKR  E G                    DL A  R      
Sbjct: 115 YLKEIGKVPLLTAEEEVDLAKRI-EAGLFASEKLAVATKKTSPQMRRDLEAIERDGQIAK 173

Query: 53  --LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
             LV ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+
Sbjct: 174 RKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIR 233

Query: 111 AAMQEYILRSWSLVKIGT----TAN-----QKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
            A+   I      ++I      T N     Q++L  +L R     +   + +L P++V  
Sbjct: 234 QAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPSPEEIAKEMDLTPDKVRE 293

Query: 162 IAKKLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           I   L VS+ E +S+   +  +E   L   I   D          V   D    +L++++
Sbjct: 294 I---LKVSQ-EPVSLETPIGEEEDSHLGDFIEDCDA---------VVPVDAASFILLQEQ 340

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAF 277
                   L   +  L+ RE+++ + R      +P TLE +  EF V+RER+RQIE++  
Sbjct: 341 --------LDSVLHTLSDREKKVIQLRFGLTDGHPRTLEEVGREFGVTRERIRQIESKTL 392

Query: 278 KKVQESIQKQ 287
            K++   + Q
Sbjct: 393 SKLRHPSRSQ 402


>gi|111221463|ref|YP_712257.1| RNA polymerase essential primary sigma 70 factor [Frankia alni
           ACN14a]
 gi|111148995|emb|CAJ60675.1| RNA polymerase essential primary sigma 70 factor [Frankia alni
           ACN14a]
          Length = 409

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 92/310 (29%), Positives = 148/310 (47%), Gaps = 63/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHG--------------------DLSAAHR------ 52
           Y+ EI K+P+L  +EE  LAKR  E G                    DL A  R      
Sbjct: 115 YLKEIGKVPLLTAEEEVDLAKRI-EAGLFASEKLAVATKKTSPQMRRDLEAIERDGQIAK 173

Query: 53  --LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
             LV ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+
Sbjct: 174 RKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIR 233

Query: 111 AAMQEYILRSWSLVKIGT----TAN-----QKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
            A+   I      ++I      T N     Q++L  +L R     +   + +L P++V  
Sbjct: 234 QAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPSPEEIAKEMDLTPDKVRE 293

Query: 162 IAKKLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           I   L VS+ E +S+   +  +E   L   I   D          V   D    +L++++
Sbjct: 294 I---LKVSQ-EPVSLETPIGEEEDSHLGDFIEDCDA---------VVPVDAASFILLQEQ 340

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAF 277
                   L   +  L+ RE+++ + R      +P TLE +  EF V+RER+RQIE++  
Sbjct: 341 --------LDSVLHTLSDREKKVIQLRFGLTDGHPRTLEEVGREFGVTRERIRQIESKTL 392

Query: 278 KKVQESIQKQ 287
            K++   + Q
Sbjct: 393 SKLRHPSRSQ 402


>gi|331701385|ref|YP_004398344.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Lactobacillus
           buchneri NRRL B-30929]
 gi|329128728|gb|AEB73281.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Lactobacillus
           buchneri NRRL B-30929]
          Length = 414

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 86/276 (31%), Positives = 134/276 (48%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   +E  LAKR  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 148 YLKEIGRVSLLSADQEISLAKRI-EAGDEEAKQELAEANLRLVVSIAKRYVGRGMQFLDL 206

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 207 IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 266

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + ++  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 267 RIQRQLLQDLGREPLPEEIGAEMDMPTEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 322

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR- 246
             I   D  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 323 DFIEDQDATSPA-------DHAAYELL----------KEQLESVLDTLTDREENVLRLRF 365

Query: 247 RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L +    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 366 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 401


>gi|270307915|ref|YP_003329973.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Dehalococcoides sp. VS]
 gi|270153807|gb|ACZ61645.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Dehalococcoides sp. VS]
          Length = 520

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 80/243 (32%), Positives = 127/243 (52%), Gaps = 30/243 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV +A  + G G+P+ +++ EGNIGL++AV+KFD  RGF+ +TY+ WW
Sbjct: 283 AERHLIQANLRLVVSVAKKHIGRGMPLLDLIQEGNIGLIRAVEKFDFHRGFKFSTYATWW 342

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     ++L   L R     +   + +L PE+V
Sbjct: 343 IRQAITRAIADQARTIRIPVHMVETINKLLSISRQLSQKLGREPTPDEIALEMDLPPEKV 402

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IAK   VS+  V S+   +  +E  +      D+N+    D          Q+L E+ 
Sbjct: 403 REIAK---VSQLPV-SLESPIGEEEDSHLGDFIEDQNALAPPDA------ASRQLLKEQ- 451

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
                   +   +  L PRERR+ + R   E+    TLE +  EF V+RER+RQIEA+A 
Sbjct: 452 --------IDTVLGSLTPRERRVLQLRFGLEDGRSRTLEEVGKEFNVTRERIRQIEAKAL 503

Query: 278 KKV 280
           +K+
Sbjct: 504 RKL 506


>gi|158313963|ref|YP_001506471.1| RpoD family RNA polymerase sigma factor [Frankia sp. EAN1pec]
 gi|158109368|gb|ABW11565.1| RNA polymerase, sigma 70 subunit, RpoD family [Frankia sp. EAN1pec]
          Length = 409

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 92/310 (29%), Positives = 148/310 (47%), Gaps = 63/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHG--------------------DLSAAHR------ 52
           Y+ EI K+P+L  +EE  LAKR  E G                    DL A  R      
Sbjct: 115 YLKEIGKVPLLTAEEEVDLAKRI-EAGLFASEKLAVATKKTSPQMRRDLEAIERDGQIAK 173

Query: 53  --LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
             LV ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+
Sbjct: 174 RKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIR 233

Query: 111 AAMQEYILRSWSLVKIGT----TAN-----QKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
            A+   I      ++I      T N     Q++L  +L R     +   + +L P++V  
Sbjct: 234 QAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPSPEEIAKEMDLTPDKVRE 293

Query: 162 IAKKLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           I   L VS+ E +S+   +  +E   L   I   D          V   D    +L++++
Sbjct: 294 I---LKVSQ-EPVSLETPIGEEEDSHLGDFIEDCDA---------VVPVDAASFILLQEQ 340

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAF 277
                   L   +  L+ RE+++ + R      +P TLE +  EF V+RER+RQIE++  
Sbjct: 341 --------LDSVLHTLSDREKKVIQLRFGLTDGHPRTLEEVGREFGVTRERIRQIESKTL 392

Query: 278 KKVQESIQKQ 287
            K++   + Q
Sbjct: 393 SKLRHPSRSQ 402


>gi|220934609|ref|YP_002513508.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thioalkalivibrio
           sp. HL-EbGR7]
 gi|219995919|gb|ACL72521.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thioalkalivibrio
           sp. HL-EbGR7]
          Length = 344

 Score =  106 bits (265), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 87/288 (30%), Positives = 148/288 (51%), Gaps = 30/288 (10%)

Query: 9   IVNGEIGLSR-YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           +  GE+  +R Y+ EI   P+L  +EE   A R  + GD +   +++  +LRLVVKIA  
Sbjct: 64  VPKGELDATRLYLSEIEFSPLLTPEEEVHYA-RLAQKGDEAGRRKMIECNLRLVVKIARR 122

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++ 
Sbjct: 123 YMNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLP 182

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQV-------VAIAKKLNVSESEVISMNCRL 180
                K L   LR  +   Q + D+    E+V       V   K++      V S++  +
Sbjct: 183 IHVI-KELNVYLRTARKLAQEL-DHEPTAEEVARHLDRPVGDVKRILALSERVTSVDLPI 240

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNP 237
            G +   AL++      +     L+ D D  + V   L E +E++  R ++ R    L+ 
Sbjct: 241 -GKDGERALLDVIPDEQTPEPSILIQDEDVVQFVDEWLQELDEKQ--REVIVRRFG-LHG 296

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            ER             TLE + +E  V+RERVRQI+  A K++++ ++
Sbjct: 297 YERS------------TLEQVGAELGVTRERVRQIQMDALKRLRKILE 332


>gi|224533396|ref|ZP_03673990.1| RNA polymerase sigma factor [Borrelia burgdorferi CA-11.2a]
 gi|224513561|gb|EEF83918.1| RNA polymerase sigma factor [Borrelia burgdorferi CA-11.2a]
          Length = 266

 Score =  106 bits (265), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 82/282 (29%), Positives = 149/282 (52%), Gaps = 20/282 (7%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M+I  N ++ +  Y+  +R+  ++  +EE  LA +  + G+  A ++++ ++LRLV+KI 
Sbjct: 1   MNIFSNEDLNI--YLKSVREHKLITHEEEIKLAGQI-QRGNAKAKNKMINANLRLVLKII 57

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y G GL I +++ EGN+GL++A +K+DP +  + +TY+ +WIK ++Q  +     LVK
Sbjct: 58  KRYAGKGLKIEDLIQEGNLGLIRAAEKYDPNKNTKFSTYASFWIKQSLQRALNTKTRLVK 117

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           +          +    L   +        K  +   I K+ N+S ++ I +   L  + S
Sbjct: 118 VP---------YRKENLILQINKYLTEEEKSPKKEEIMKRFNLSPAQYIKIIPYLEKEYS 168

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L+  I  S+ NS+     L  D+    ++ +E++      N +  + S  N +ER I + 
Sbjct: 169 LDKEIEGSE-NSTLLN--LYEDNSFNPEITLEQDSTLKHLNYILETKS--NEKERYIIKK 223

Query: 246 R-RLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L  +P   TL+++S+E  +S E VRQIE R  KK++E I
Sbjct: 224 RYNLDNSPKKSTLKDISTELGISSETVRQIEKRVLKKLKEEI 265


>gi|313674339|ref|YP_004052335.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Marivirga
           tractuosa DSM 4126]
 gi|312941037|gb|ADR20227.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Marivirga
           tractuosa DSM 4126]
          Length = 287

 Score =  106 bits (265), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 77/271 (28%), Positives = 149/271 (54%), Gaps = 15/271 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ +L   EE  LA R ++ GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGKVDLLTPDEEVDLAVRIKQ-GDQLALEKLTKANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     +V++    N+   
Sbjct: 77  GDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL--PLNRVGS 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
              + +    L+   +    P++   +A+ L V+ +EV+    +++G   S++A     +
Sbjct: 135 LNKISKTFSTLEQKFEREPSPDE---LAEVLEVTSNEVVD-TMKISGRHVSMDAPFVQGE 190

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENP 252
           +NS       V ++DG+E    E      RR +  R++S L  RE  +         E+ 
Sbjct: 191 ENSL----LDVLENDGEESPDDELMNDSLRREV-QRALSTLTQREADVITLYFGLNGEHS 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +TLE +  +F ++RERVRQI+ +A ++++ +
Sbjct: 246 MTLEEIGEKFNLTRERVRQIKEKAIRRLRHT 276


>gi|256532386|gb|ACU81351.1| RpoH [Rhizobium leguminosarum bv. trifolii]
 gi|256532388|gb|ACU81352.1| RpoH [Rhizobium leguminosarum bv. trifolii]
 gi|256532392|gb|ACU81354.1| RpoH [Rhizobium leguminosarum bv. trifolii]
 gi|256532394|gb|ACU81355.1| RpoH [Rhizobium leguminosarum bv. trifolii]
 gi|256532398|gb|ACU81357.1| RpoH [Rhizobium leguminosarum bv. trifolii]
 gi|256532400|gb|ACU81358.1| RpoH [Rhizobium leguminosarum bv. trifolii]
 gi|256532402|gb|ACU81359.1| RpoH [Rhizobium leguminosarum bv. trifolii]
 gi|256532404|gb|ACU81360.1| RpoH [Rhizobium leguminosarum bv. trifolii]
 gi|256532406|gb|ACU81361.1| RpoH [Rhizobium leguminosarum bv. trifolii]
          Length = 148

 Score =  106 bits (265), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 67/152 (44%), Positives = 94/152 (61%), Gaps = 9/152 (5%)

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFFNLRRL+  L A  D 
Sbjct: 1   FEPERDVRFSTYASWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRAKL-AKGDT 59

Query: 153 NLKPEQV-VAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDH-- 208
            L  + +   IA  L VS ++V +M+ RL+G D SL A   S D  S++  D+LV D   
Sbjct: 60  QLTLQSIHQEIAAALGVSLADVQTMDARLSGNDASLQAPSVSGDAESAEKMDFLVSDDPL 119

Query: 209 -DGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            D Q   +I+ E    RR  L  ++  LN RE
Sbjct: 120 PDEQVSNMIDGER---RRVWLASALKHLNERE 148


>gi|295695448|ref|YP_003588686.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacillus tusciae
           DSM 2912]
 gi|295411050|gb|ADG05542.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacillus tusciae
           DSM 2912]
          Length = 379

 Score =  106 bits (265), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 84/264 (31%), Positives = 132/264 (50%), Gaps = 13/264 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LAKR  E GD  A   L+ ++LRLVV IA  Y G G+   ++
Sbjct: 113 YLKEIGRVPLLSAEEEIELAKRI-EQGDEEAKAALIKANLRLVVSIAKRYVGRGMLFLDL 171

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 172 IQEGNLGLIKAVEKFDFRKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 229

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L      +  PE+   IA+++++S  +V  +        SL   I   D   S
Sbjct: 230 LIRVSRQLLQELGRDPTPEE---IAEEMDMSPDKVREIMKIAQEPVSLETPIGEED--DS 284

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++  D           E  K +   L   +  L  RE  +   R   ++    TLE
Sbjct: 285 HLGDFIPDDDALAPADAAAYELLKEQ---LEDVLDTLTEREENVLRLRFGLDDGRTRTLE 341

Query: 257 NLSSEFEVSRERVRQIEARAFKKV 280
            +   F V+RER+RQIEA+A +K+
Sbjct: 342 EVGKVFGVTRERIRQIEAKALRKL 365


>gi|260583936|ref|ZP_05851684.1| RNA polymerase sigma-43 factor [Granulicatella elegans ATCC 700633]
 gi|260158562|gb|EEW93630.1| RNA polymerase sigma-43 factor [Granulicatella elegans ATCC 700633]
          Length = 374

 Score =  106 bits (265), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 87/276 (31%), Positives = 138/276 (50%), Gaps = 36/276 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   EE  LA R  + GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 107 YLKEIGRVPLLSADEEVNLALRI-QQGDQEAKQELAEANLRLVVSIAKRYVGRGMQFLDL 165

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 166 IQEGNMGLMKAVEKFDHTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLV 225

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 226 RIQRQLLQDLGREPTPEEIGAEMDLPTEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 281

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR- 246
             I   D N++   +   Y        L++++        L   +  L  RE  +   R 
Sbjct: 282 DFI--EDDNATSPAEHTAY-------ALLKEQ--------LDEVLEQLTDREENVLRLRF 324

Query: 247 RLQENPV--TLENLSSEFEVSRERVRQIEARAFKKV 280
            L +N    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 325 GLDKNGEIRTLEQVGQVFGVTRERIRQIEAKALRKL 360


>gi|6175930|gb|AAF05342.1|AF182106_2 truncated RNA polymerase sigma subunit [Escherichia coli]
          Length = 303

 Score =  106 bits (265), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 80/260 (30%), Positives = 129/260 (49%), Gaps = 25/260 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 179

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 180 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 236

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 237 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 285

Query: 251 NPVTLENLSSEFEVSRERVR 270
              TLE++  E  ++RERVR
Sbjct: 286 --ATLEDVGREIGLTRERVR 303


>gi|15595116|ref|NP_212905.1| RNA polymerase sigma factor (rpoS) [Borrelia burgdorferi B31]
 gi|195941591|ref|ZP_03086973.1| RNA polymerase sigma factor (rpoS) [Borrelia burgdorferi 80a]
 gi|216264706|ref|ZP_03436698.1| RNA polymerase sigma factor (rpoS) [Borrelia burgdorferi 156a]
 gi|218249170|ref|YP_002375269.1| RNA polymerase sigma factor (rpoS) [Borrelia burgdorferi ZS7]
 gi|221217974|ref|ZP_03589441.1| RNA polymerase sigma factor [Borrelia burgdorferi 72a]
 gi|223889406|ref|ZP_03623992.1| RNA polymerase sigma factor [Borrelia burgdorferi 64b]
 gi|224532620|ref|ZP_03673242.1| RNA polymerase sigma factor [Borrelia burgdorferi WI91-23]
 gi|225548870|ref|ZP_03769847.1| RNA polymerase sigma factor [Borrelia burgdorferi 94a]
 gi|225550031|ref|ZP_03770992.1| RNA polymerase sigma factor [Borrelia burgdorferi 118a]
 gi|225551867|ref|ZP_03772810.1| RNA polymerase sigma factor [Borrelia sp. SV1]
 gi|226320640|ref|ZP_03796199.1| RNA polymerase sigma factor [Borrelia burgdorferi 29805]
 gi|226321470|ref|ZP_03796997.1| RNA polymerase sigma factor [Borrelia burgdorferi Bol26]
 gi|2688700|gb|AAC67109.1| RNA polymerase sigma factor (rpoS) [Borrelia burgdorferi B31]
 gi|215981179|gb|EEC21986.1| RNA polymerase sigma factor (rpoS) [Borrelia burgdorferi 156a]
 gi|218164358|gb|ACK74419.1| RNA polymerase sigma factor (rpoS) [Borrelia burgdorferi ZS7]
 gi|221192280|gb|EEE18500.1| RNA polymerase sigma factor [Borrelia burgdorferi 72a]
 gi|223885092|gb|EEF56196.1| RNA polymerase sigma factor [Borrelia burgdorferi 64b]
 gi|224512476|gb|EEF82855.1| RNA polymerase sigma factor [Borrelia burgdorferi WI91-23]
 gi|225369490|gb|EEG98942.1| RNA polymerase sigma factor [Borrelia burgdorferi 118a]
 gi|225370473|gb|EEG99909.1| RNA polymerase sigma factor [Borrelia burgdorferi 94a]
 gi|225371662|gb|EEH01089.1| RNA polymerase sigma factor [Borrelia sp. SV1]
 gi|226233266|gb|EEH32018.1| RNA polymerase sigma factor [Borrelia burgdorferi Bol26]
 gi|226233963|gb|EEH32685.1| RNA polymerase sigma factor [Borrelia burgdorferi 29805]
 gi|312148432|gb|ADQ31091.1| RNA polymerase sigma factor [Borrelia burgdorferi JD1]
 gi|312149704|gb|ADQ29775.1| RNA polymerase sigma factor [Borrelia burgdorferi N40]
          Length = 266

 Score =  106 bits (265), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 82/282 (29%), Positives = 149/282 (52%), Gaps = 20/282 (7%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M+I  N ++ +  Y+  +R+  ++  +EE  LA +  + G+  A ++++ ++LRLV+KI 
Sbjct: 1   MNIFSNEDLNI--YLKSVREHKLITHEEEIKLAGQI-QRGNAKAKNKMINANLRLVLKII 57

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y G GL I +++ EGN+GL++A +K+DP +  + +TY+ +WIK ++Q  +     LVK
Sbjct: 58  KRYAGKGLKIEDLIQEGNLGLIRAAEKYDPNKNTKFSTYASFWIKQSLQRALNTKTRLVK 117

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           +          +    L   +        K  +   I K+ N+S ++ I +   L  + S
Sbjct: 118 VP---------YRKENLILQINKYLTEEEKSPKKEEIMKRFNLSPAQYIKIIPYLEKEYS 168

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L+  I  S+ NS+     L  D+    ++ +E++      N +  +   LN +ER I + 
Sbjct: 169 LDKEIEGSE-NSTLLN--LYEDNSFNPEITLEQDSTLKHLNYILETK--LNEKERYIIKK 223

Query: 246 R-RLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L  +P   TL+++S+E  +S E VRQIE R  KK++E I
Sbjct: 224 RYNLDNSPKKSTLKDISTELGISSETVRQIEKRVLKKLKEEI 265


>gi|332638574|ref|ZP_08417437.1| RNA polymerase sigma factor [Weissella cibaria KACC 11862]
          Length = 377

 Score =  106 bits (265), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 88/281 (31%), Positives = 134/281 (47%), Gaps = 47/281 (16%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LA+R  E GD +A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 111 YLKEIGRVSLLTGDEEVALAERI-EQGDDTAKQELAEANLRLVVSIAKRYVGRGMQFLDL 169

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 170 IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 229

Query: 132 --QKRLFFNLRR------LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-- 181
             Q+ L  +L R      +   +  +TD   K   ++ IA+       E +S+   +   
Sbjct: 230 RIQRNLLQDLGREPTPEEIGAEMDIVTD---KVRDILKIAQ-------EPVSLETPIGEE 279

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
            D  L   I   D  +    D   Y      Q+L E+         L   +  L  RE  
Sbjct: 280 DDSHLGDFI--EDNEAISPADSAAY------QMLKEQ---------LESVLDTLTDREEN 322

Query: 242 IFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
           +   R   E+    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 323 VLRLRFGLEDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 363


>gi|187934045|ref|YP_001885115.1| RNA polymerase sigma factor RpoD [Clostridium botulinum B str.
           Eklund 17B]
 gi|187722198|gb|ACD23419.1| RNA polymerase sigma factor RpoD [Clostridium botulinum B str.
           Eklund 17B]
          Length = 374

 Score =  106 bits (265), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 82/265 (30%), Positives = 133/265 (50%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  ++E   AKR  E GD  A  +L  ++LRLVV IA  Y G G+   ++
Sbjct: 108 YLKEIGKVPLLSSEQEIDYAKRI-EEGDPVAKKKLAEANLRLVVSIAKRYVGRGMLFLDL 166

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 167 IQEGNLGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 224

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R++  L      +  PE+   I+K + +   +V  +        SL   I   ++  S
Sbjct: 225 LIRVQRQLLQELGRDPFPEE---ISKVMELPVDKVREIQKIAQEPVSLETPIG--EEEDS 279

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++  D              K +   L   +  L PRE ++   R   ++    TLE
Sbjct: 280 HLGDFIPDDEAPAPAEAAAFTMLKEQ---LINVLDTLTPREEKVLRLRFGLDDGRARTLE 336

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF V+RER+RQIEA+A +K++
Sbjct: 337 EVGKEFNVTRERIRQIEAKALRKLR 361


>gi|295839080|ref|ZP_06826013.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. SPB74]
 gi|295827312|gb|EDY44634.2| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. SPB74]
          Length = 360

 Score =  106 bits (265), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 92/306 (30%), Positives = 146/306 (47%), Gaps = 62/306 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHG-------------------DL--------SAAH 51
           Y+ EI +IP+L   +E  LA+R  E G                   DL        +A  
Sbjct: 67  YLREIGRIPLLNAADEVELARRV-EAGLFAEEKLAGPGPLDTRLALDLDRLVVLGRAAKR 125

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RL+ S+LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RGF+ +TY+ WWI+ 
Sbjct: 126 RLIESNLRLVVSVAKRYAGRGLTMLDLVQEGNLGLIRAVEKFDYTRGFKFSTYATWWIRQ 185

Query: 112 AMQEYILRSWSLVKIGTTANQ--KRLFFNLRRL---KGHLQAITDN----NLKPEQVVAI 162
           AM   +      +++     +   R+    R L   +GH     +      L PE+V   
Sbjct: 186 AMSRALADQARTIRVPVHVVELINRVVRARRTLLQERGHEPCDAEVAAVLGLTPERV--- 242

Query: 163 AKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + L +++ E +S++  + G++  +L  LI   D  S      L+      E VL     
Sbjct: 243 GEVLRLAQ-EPVSLHTPVGGEDEVALGDLIEDGDAPSPPESAALLLLRRHLEDVL----- 296

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFK 278
                       S L  RER++ + R   ++  P TLE + + F V+RER+RQIEA+   
Sbjct: 297 ------------STLGERERQVVQLRYGLDDGRPRTLEEIGTLFGVTRERIRQIEAKTLA 344

Query: 279 KVQESI 284
           K++  +
Sbjct: 345 KLRSHV 350


>gi|320355021|ref|YP_004196360.1| RpoD subfamily RNA polymerase sigma-70 factor [Desulfobulbus
           propionicus DSM 2032]
 gi|320123523|gb|ADW19069.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfobulbus
           propionicus DSM 2032]
          Length = 533

 Score =  106 bits (265), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 77/245 (31%), Positives = 129/245 (52%), Gaps = 20/245 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   LV ++LRLV+ ++  +   G+ + +++ EGNIGLM+AV+K+D +RG++ +TY+ WW
Sbjct: 295 AKETLVRANLRLVISVSKKFMNRGMQLPDLIQEGNIGLMKAVEKYDYKRGYKFSTYATWW 354

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      +++    +       + R     Q I      PE+   +AK+L  
Sbjct: 355 IRQAVTRGIADQGRTIRL--PVHMIETINRMLRFSKDFQRIESREPTPEE---MAKQLG- 408

Query: 169 SESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDH---DGQEQVLIEKEERKNR 224
           ++ E + +  + A D  SL+A +N  D+  +   D+ + DH   D QE  + E  +R   
Sbjct: 409 TDVEKVQVALKTAKDAISLDAPVN--DEEDTLLSDF-IEDHAHPDPQEHSITESLKR--- 462

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQE 282
              L + M  L PRE ++   R   E     TLE +   F V+RER+RQIEA+A KK++ 
Sbjct: 463 --CLCKVMGSLTPREEKVLRMRYGIEIGCDHTLEEVGQCFAVTRERIRQIEAQALKKLRH 520

Query: 283 SIQKQ 287
             + Q
Sbjct: 521 PARSQ 525


>gi|259503187|ref|ZP_05746089.1| RNA polymerase sigma factor [Lactobacillus antri DSM 16041]
 gi|259168844|gb|EEW53339.1| RNA polymerase sigma factor [Lactobacillus antri DSM 16041]
          Length = 380

 Score =  106 bits (265), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 86/275 (31%), Positives = 133/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LA R  E GD  A  +L  ++LRLVV IA  Y G G+   ++
Sbjct: 114 YLKEIGRVNLLTADEEVKLALRI-EQGDEVAKQQLAEANLRLVVSIAKRYVGRGMQFLDL 172

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  RGF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 173 IQEGNMGLMKAVEKFDYRRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 232

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + ++  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 233 RIQRQLLQDLGREPLPEEIGAEMDMPTEKVRNI---LKIAQ-EPVSLETPIGEEDDSHLG 288

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 289 DFIEDQDATSPA-------DHAAYEMM----------KKQLENVLDTLTDREENVLRLRF 331

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 332 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 366


>gi|73748391|ref|YP_307630.1| RNA polymerase, sigma factor [Dehalococcoides sp. CBDB1]
 gi|147669171|ref|YP_001213989.1| RpoD family RNA polymerase sigma factor [Dehalococcoides sp. BAV1]
 gi|289432439|ref|YP_003462312.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dehalococcoides
           sp. GT]
 gi|73660107|emb|CAI82714.1| RNA polymerase, sigma factor [Dehalococcoides sp. CBDB1]
 gi|146270119|gb|ABQ17111.1| RNA polymerase, sigma 70 subunit, RpoD family [Dehalococcoides sp.
           BAV1]
 gi|288946159|gb|ADC73856.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dehalococcoides
           sp. GT]
          Length = 520

 Score =  106 bits (265), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 80/243 (32%), Positives = 128/243 (52%), Gaps = 30/243 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV +A  + G G+P+ +++ EGNIGL++AV+KFD  RGF+ +TY+ WW
Sbjct: 283 AERHLIQANLRLVVSVAKKHIGRGMPLLDLIQEGNIGLIRAVEKFDFHRGFKFSTYATWW 342

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     ++L   L R     +   + +L PE+V
Sbjct: 343 IRQAITRAIADQARTIRIPVHMVETINKLLSISRQLSQKLGREPTPDEIALEMDLPPEKV 402

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IAK   VS+  V S+   +  +E      +S   +  + Q+ L        Q+L E+ 
Sbjct: 403 REIAK---VSQLPV-SLESPIGEEE------DSHLGDFIEDQNALAPPDAASRQLLKEQ- 451

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
                   +   +  L PRERR+ + R   E+    TLE +  EF V+RER+RQIEA+A 
Sbjct: 452 --------IDTVLGSLTPRERRVLQLRFGLEDGRSRTLEEVGKEFNVTRERIRQIEAKAL 503

Query: 278 KKV 280
           +K+
Sbjct: 504 RKL 506


>gi|217077377|ref|YP_002335095.1| RNA polymerase sigma factor RpoD [Thermosipho africanus TCF52B]
 gi|217037232|gb|ACJ75754.1| RNA polymerase sigma factor RpoD [Thermosipho africanus TCF52B]
          Length = 371

 Score =  106 bits (265), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 82/277 (29%), Positives = 140/277 (50%), Gaps = 37/277 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ +I KIP+L +  E  LA+R  + GD  A  +LV S+LRLVV IA  Y G GL   ++
Sbjct: 100 YLKDIGKIPLLSQSMERELARR-AQLGDERAKQKLVESNLRLVVSIAKRYVGKGLSFLDL 158

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-- 132
           + EGN+GL++AV+KFD ++G++ +TY+ WWI+ A+   I      +++      T N+  
Sbjct: 159 IQEGNVGLLKAVEKFDWKKGYKFSTYATWWIRQAITRAIADQARTIRVPVHMVETINKVQ 218

Query: 133 --KRLFFNLRRLKGHLQAITDNNLKP----EQVVAIAKKLNVSESEVISMNCRLAGDESL 186
              R ++     +  ++ +     KP    E+++  AK+    E+ V   +    GD   
Sbjct: 219 KIMREYYQEHGTEIPIEELAKLIGKPVEKVEEILQAAKETTSLEAPVGEDDDSTVGDFIA 278

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           +  I S  K +               ++LI +E        + + +  LN RE+ + + R
Sbjct: 279 DETIASPKKEAM--------------RMLIREE--------VDKVLETLNDREKLVLKMR 316

Query: 247 R--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +     TLE +   F V+RER+RQIE +A +K++
Sbjct: 317 YGLIDGKAKTLEEVGQYFNVTRERIRQIEVKALRKLR 353


>gi|318040855|ref|ZP_07972811.1| RNA polymerase sigma factor, sigma-70 family protein [Synechococcus
           sp. CB0101]
          Length = 321

 Score =  106 bits (265), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 85/287 (29%), Positives = 139/287 (48%), Gaps = 37/287 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLA--------------------KRYREHGDLSAAHRLVTSHL 58
           Y+  I ++P+L   EE  LA                    ++++      A  R++ ++L
Sbjct: 37  YLSNIGRVPLLTAAEEIELAHHVQLMKQLQELPSDQLTPRQKHQIRMGCRARDRMMAANL 96

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+  M   I 
Sbjct: 97  RLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTRAID 156

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLK---GHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
            S   +++    ++K     +RR+     H      N L+      +A  + +   E+  
Sbjct: 157 NSARTIRLPIHVSEK--LSKMRRITRELSHRFGRQPNRLE------LAHAMGMQPEELED 208

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
           +  + A   SL+A     D  S+  +  L+ D +  E   ++  +R  ++  L   +S L
Sbjct: 209 LISQSAPCASLDAHARGDDDRSTLGE--LIADPNSNES--MDSMDRNLQKEHLGTWLSQL 264

Query: 236 NPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N RERRI E R   E   P+TL  +  +  VSRERVRQ+EA+A  K+
Sbjct: 265 NERERRIIELRFGLEGQEPLTLAEIGRQINVSRERVRQLEAKAILKL 311


>gi|288916958|ref|ZP_06411330.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EUN1f]
 gi|288351667|gb|EFC85872.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EUN1f]
          Length = 392

 Score =  106 bits (265), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 92/310 (29%), Positives = 148/310 (47%), Gaps = 63/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHG--------------------DLSAAHR------ 52
           Y+ EI K+P+L  +EE  LAKR  E G                    DL A  R      
Sbjct: 98  YLKEIGKVPLLTAEEEVDLAKRI-EAGLFASEKLAVATKKTSPQMRRDLEAIERDGQIAK 156

Query: 53  --LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
             LV ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+
Sbjct: 157 RKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIR 216

Query: 111 AAMQEYILRSWSLVKIGT----TAN-----QKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
            A+   I      ++I      T N     Q++L  +L R     +   + +L P++V  
Sbjct: 217 QAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPSPEEIAKEMDLTPDKVRE 276

Query: 162 IAKKLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           I   L VS+ E +S+   +  +E   L   I   D          V   D    +L++++
Sbjct: 277 I---LKVSQ-EPVSLETPIGEEEDSHLGDFIEDCDA---------VVPVDAASFILLQEQ 323

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAF 277
                   L   +  L+ RE+++ + R      +P TLE +  EF V+RER+RQIE++  
Sbjct: 324 --------LDSVLHTLSDREKKVIQLRFGLTDGHPRTLEEVGREFGVTRERIRQIESKTL 375

Query: 278 KKVQESIQKQ 287
            K++   + Q
Sbjct: 376 SKLRHPSRSQ 385


>gi|222097738|ref|YP_002531795.1| RNA polymerase sigma factor rpod [Bacillus cereus Q1]
 gi|221241796|gb|ACM14506.1| RNA polymerase sigma-43 factor [Bacillus cereus Q1]
          Length = 375

 Score =  106 bits (265), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 85/276 (30%), Positives = 135/276 (48%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 109 YLKEIGRVDLLSAEEEIRLATRI-EEGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 167

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++A +KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 168 IQEGNMGLIKAGEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 227

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L PE+V  I   L +++ E +S+   +    D  L 
Sbjct: 228 RVQRQLLQDLGREPSPEEIGEEMDLAPEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 283

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 284 DFIEDQEATSPA-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 326

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 327 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 362


>gi|184155321|ref|YP_001843661.1| RNA polymerase sigma factor RpoD [Lactobacillus fermentum IFO 3956]
 gi|227514580|ref|ZP_03944629.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           fermentum ATCC 14931]
 gi|260662165|ref|ZP_05863061.1| RNA polymerase sigma factor RpoD [Lactobacillus fermentum 28-3-CHN]
 gi|183226665|dbj|BAG27181.1| RNA polymerase sigma factor RpoD [Lactobacillus fermentum IFO 3956]
 gi|227086991|gb|EEI22303.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           fermentum ATCC 14931]
 gi|260553548|gb|EEX26440.1| RNA polymerase sigma factor RpoD [Lactobacillus fermentum 28-3-CHN]
          Length = 380

 Score =  106 bits (265), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 88/288 (30%), Positives = 140/288 (48%), Gaps = 37/288 (12%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           SI +N  + +  Y+ EI ++ +L   EE  LA R  E GD +A   L  ++LRLVV IA 
Sbjct: 104 SIKINDPVRM--YLKEIGRVNLLTADEEVALALRI-EKGDETAKQELAEANLRLVVSIAK 160

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y G G+   +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I
Sbjct: 161 RYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRI 220

Query: 127 GT----TAN-----QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
                 T N     Q++L  +L R     +   + ++  ++V  I   L +S+ E +S+ 
Sbjct: 221 PVHMVETINKLIRIQRQLLQDLGREPLPEEIGAEMDMDTQKVRDI---LKISQ-EPVSLE 276

Query: 178 CRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
             +    D  L   I   D  S         DH   E +          +  L   +  L
Sbjct: 277 TPIGEEDDSHLGDFIEDHDATSPA-------DHAAYEMM----------KKQLENVLDTL 319

Query: 236 NPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             RE  +   R   ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 320 TDREENVLRLRFGLDDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLR 367


>gi|251796255|ref|YP_003010986.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Paenibacillus sp.
           JDR-2]
 gi|247543881|gb|ACT00900.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Paenibacillus sp.
           JDR-2]
          Length = 376

 Score =  106 bits (264), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 81/265 (30%), Positives = 132/265 (49%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   +E  LA+R  E+GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 110 YLKEIGRVPLLSADDEIELARRI-ENGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 168

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD ++GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 169 IQEGNMGLIKAVEKFDHQKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 226

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L         PE+   IA ++ +S  +V  +        SL   I   D   S
Sbjct: 227 LIRVSRQLLQELGREPTPEE---IAAEMELSTDKVREIMKIAQEPVSLETPIGEED--DS 281

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++    D +     +    +  +  L   +  L  RE  +   R   ++    TLE
Sbjct: 282 HLGDFI---EDQEALAPADAAAYELLKEQLEDVLDTLTEREENVLRLRFGLDDGRTRTLE 338

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +   F V+RER+RQIEA+A +K++
Sbjct: 339 EVGKVFGVTRERIRQIEAKALRKLR 363


>gi|148380889|ref|YP_001255430.1| RNA polymerase sigma factor RpoD [Clostridium botulinum A str. ATCC
           3502]
 gi|153931224|ref|YP_001385198.1| RNA polymerase sigma factor RpoD [Clostridium botulinum A str. ATCC
           19397]
 gi|153937635|ref|YP_001388667.1| RNA polymerase sigma factor RpoD [Clostridium botulinum A str.
           Hall]
 gi|153940633|ref|YP_001392215.1| RNA polymerase sigma factor RpoD [Clostridium botulinum F str.
           Langeland]
 gi|168179368|ref|ZP_02614032.1| RNA polymerase sigma factor RpoD [Clostridium botulinum NCTC 2916]
 gi|168181623|ref|ZP_02616287.1| RNA polymerase sigma factor RpoD [Clostridium botulinum Bf]
 gi|170757237|ref|YP_001782571.1| RNA polymerase sigma factor RpoD [Clostridium botulinum B1 str.
           Okra]
 gi|170761654|ref|YP_001788251.1| RNA polymerase sigma factor RpoD [Clostridium botulinum A3 str.
           Loch Maree]
 gi|187778482|ref|ZP_02994955.1| hypothetical protein CLOSPO_02076 [Clostridium sporogenes ATCC
           15579]
 gi|226950364|ref|YP_002805455.1| RNA polymerase sigma factor RpoD [Clostridium botulinum A2 str.
           Kyoto]
 gi|237796391|ref|YP_002863943.1| RNA polymerase sigma factor RpoD [Clostridium botulinum Ba4 str.
           657]
 gi|148290373|emb|CAL84500.1| RNA polymerase sigma factor (sigma-43) [Clostridium botulinum A
           str. ATCC 3502]
 gi|152927268|gb|ABS32768.1| RNA polymerase sigma factor RpoD [Clostridium botulinum A str. ATCC
           19397]
 gi|152933549|gb|ABS39048.1| RNA polymerase sigma factor RpoD [Clostridium botulinum A str.
           Hall]
 gi|152936529|gb|ABS42027.1| RNA polymerase sigma factor RpoD [Clostridium botulinum F str.
           Langeland]
 gi|169122449|gb|ACA46285.1| RNA polymerase sigma factor RpoD [Clostridium botulinum B1 str.
           Okra]
 gi|169408643|gb|ACA57054.1| RNA polymerase sigma factor RpoD [Clostridium botulinum A3 str.
           Loch Maree]
 gi|182669799|gb|EDT81775.1| RNA polymerase sigma factor RpoD [Clostridium botulinum NCTC 2916]
 gi|182675034|gb|EDT86995.1| RNA polymerase sigma factor RpoD [Clostridium botulinum Bf]
 gi|187772107|gb|EDU35909.1| hypothetical protein CLOSPO_02076 [Clostridium sporogenes ATCC
           15579]
 gi|226843729|gb|ACO86395.1| RNA polymerase sigma factor RpoD [Clostridium botulinum A2 str.
           Kyoto]
 gi|229260977|gb|ACQ52010.1| RNA polymerase sigma factor RpoD [Clostridium botulinum Ba4 str.
           657]
 gi|295320212|gb|ADG00590.1| RNA polymerase sigma factor RpoD [Clostridium botulinum F str.
           230613]
 gi|322807253|emb|CBZ04827.1| RNA polymerase sigma factor RpoD [Clostridium botulinum H04402 065]
          Length = 361

 Score =  106 bits (264), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 79/265 (29%), Positives = 132/265 (49%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+ +L  +EE  LA+R  E GD+ A  +L  ++LRLVV IA  Y G G+   ++
Sbjct: 95  YLKEIGKVALLTSEEEIELAQRI-EAGDMVAKKKLAEANLRLVVSIAKRYVGRGMLFLDL 153

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 154 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 211

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L        +PE+V  I +       E++ +       E ++      ++  S
Sbjct: 212 LIRVSRQLLQELGREPQPEEVAKIMEMPVDKVREIMKI-----AQEPVSLETPIGEEEDS 266

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++  D              K +   L   +  L PRE ++   R   ++    TLE
Sbjct: 267 HLGDFIPDDEAPAPAEAAAFTMLKEQ---LINVLDTLTPREEKVLRLRFGLDDGRARTLE 323

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF V+RER+RQIEA+A +K++
Sbjct: 324 EVGKEFNVTRERIRQIEAKALRKLR 348


>gi|325280730|ref|YP_004253272.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Odoribacter
           splanchnicus DSM 20712]
 gi|324312539|gb|ADY33092.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Odoribacter
           splanchnicus DSM 20712]
          Length = 289

 Score =  106 bits (264), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 79/278 (28%), Positives = 155/278 (55%), Gaps = 26/278 (9%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            + +Y+ EI KI +L  +EE  LAK+ R  GD +A  +LV S+LR VV +A  Y+ +GL 
Sbjct: 17  SIEKYLQEIGKIHVLSPEEEADLAKKIR-SGDRAAREKLVLSNLRFVVSVAKQYQNHGLT 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG----TTA 130
           + ++++EGN+GL++A + FD  +GF+  +Y++WWI+ ++ + I  +  L+++     +T 
Sbjct: 76  LGDLINEGNVGLIKAAECFDETKGFKFISYAVWWIRQSILQAIAENARLIRLPLNKISTI 135

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNAL 189
           N+    + L  L+   Q       +P +   IA+K++++  EV   N ++A    S++A 
Sbjct: 136 NKVNRCYTL--LEQEFQR------EPTE-EEIAEKMDMTPEEV-KENMKIATKPVSMDAP 185

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT---RSMSVLNPRERRIFEAR 246
           + + +++ S +  ++  D   Q       E   N+ ++ T   RS + L+ RE  I    
Sbjct: 186 LTTDEESISLYDVYIAPDPSIQ-----APESSLNQDSLKTDIERSFAALSVREATILSMY 240

Query: 247 RLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
                 + ++LE + ++  ++ ERVRQ++ +A +K++E
Sbjct: 241 YGLNGYSSMSLEEIGTKLGLTSERVRQVKTKAIRKLKE 278


>gi|289642669|ref|ZP_06474809.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia symbiont
           of Datisca glomerata]
 gi|289507499|gb|EFD28458.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia symbiont
           of Datisca glomerata]
          Length = 392

 Score =  106 bits (264), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 92/310 (29%), Positives = 148/310 (47%), Gaps = 63/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHG--------------------DLSAAHR------ 52
           Y+ EI K+P+L  +EE  LAKR  E G                    DL A  R      
Sbjct: 98  YLKEIGKVPLLTAEEEVDLAKRI-EAGLFASEKLAAATRKTSPQMRRDLEAIERDGQIAK 156

Query: 53  --LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
             LV ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+
Sbjct: 157 RKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIR 216

Query: 111 AAMQEYILRSWSLVKIGT----TAN-----QKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
            A+   I      ++I      T N     Q++L  +L R     +   + +L P++V  
Sbjct: 217 QAVTRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPSPEEIAKEMDLTPDKVRE 276

Query: 162 IAKKLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           I   L VS+ E +S+   +  +E   L   I   D          V   D    +L++++
Sbjct: 277 I---LKVSQ-EPVSLETPIGEEEDSHLGDFIEDCDA---------VVPVDAASFILLQEQ 323

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAF 277
                   L   +  L+ RE+++ + R      +P TLE +  EF V+RER+RQIE++  
Sbjct: 324 --------LDSVLHTLSDREKKVIQLRFGLTDGHPRTLEEVGREFGVTRERIRQIESKTL 375

Query: 278 KKVQESIQKQ 287
            K++   + Q
Sbjct: 376 SKLRHPSRSQ 385


>gi|163849112|ref|YP_001637156.1| RNA polymerase sigma factor RpoD [Chloroflexus aurantiacus J-10-fl]
 gi|222527085|ref|YP_002571556.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus sp.
           Y-400-fl]
 gi|163670401|gb|ABY36767.1| RNA polymerase sigma factor RpoD [Chloroflexus aurantiacus J-10-fl]
 gi|222450964|gb|ACM55230.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus sp.
           Y-400-fl]
          Length = 398

 Score =  106 bits (264), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 78/290 (26%), Positives = 139/290 (47%), Gaps = 39/290 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLA--------------------------KRYREHGDLSAAHR 52
           Y+ EI ++P+L  ++E  LA                          K+ +  G+  A  +
Sbjct: 104 YLREIGQVPLLTAEQEKRLAQLIEQGQEAERKLATLPPDSPEAARLKQLKAKGE-EARQQ 162

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           +  ++LRLVV IA  YR  GLP+ +++ EG++GL++A++KFD  +G++ +TY+ WWIK A
Sbjct: 163 MAAANLRLVVSIAKRYRDRGLPLLDLIQEGSLGLLRAIEKFDYTKGYKFSTYATWWIKQA 222

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +     LV++        L   L R++   + +T +  +      +A  L +SE +
Sbjct: 223 LSRALADQSRLVRLPV-----HLGETLNRIQSARRQLTQSLGREPTDTELANHLGMSEEK 277

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           +     R    + ++      ++  S   D++   H        +       R  +T ++
Sbjct: 278 L--RELRRTAQDPVSLATPVGEEADSTLADFIPDPH---ALDADDAAASGMLRQQITAAL 332

Query: 233 SVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             L+ RERR+ E R   +   P TLE +   F V+RERVRQIE +A +K+
Sbjct: 333 DQLSERERRVLELRYGLVDGQPRTLEEVGKAFGVTRERVRQIEVKALRKL 382


>gi|156740438|ref|YP_001430567.1| RpoD family RNA polymerase sigma factor [Roseiflexus castenholzii
           DSM 13941]
 gi|156231766|gb|ABU56549.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus
           castenholzii DSM 13941]
          Length = 405

 Score =  106 bits (264), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 88/303 (29%), Positives = 144/303 (47%), Gaps = 63/303 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR---------EHGDLS----------------AAHRL 53
           Y+ EI ++ +L  QEE +LA++           ++GD +                A  RL
Sbjct: 113 YLREIGRVNLLTAQEEIMLAQQVERGEQANERLQNGDYTPVERLQLHRWVQEGQAARERL 172

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           + ++LRLVV IA  Y G G+ + +++ EGNIGLM+A +KFD  +G++ +TY+ WWI+ A+
Sbjct: 173 IQANLRLVVSIAKKYLGRGMSLLDLIQEGNIGLMRATEKFDYRKGYKFSTYATWWIRQAI 232

Query: 114 QEYIL---RSWSL-VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV-----VAIAK 164
              I    R+  L V +G T N+      + R    +Q  T  +  P+++     + + K
Sbjct: 233 TRVIADQSRTIRLPVHVGETINR------VMRTSNRIQQTTGRDPTPDEIALELGIPVEK 286

Query: 165 KLNVSES--EVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
              V E+  + IS+   +   GD  L   I                  DG+    +E   
Sbjct: 287 VRRVLEAARQTISLETPIGPEGDSVLADFIE-----------------DGKGATPMESAS 329

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFK 278
               R  +  ++  L  RERRI + R      +  TLE +  EF ++RER+RQIEAR  +
Sbjct: 330 SHILREQIDSALEKLPERERRIIQLRYGLYDGHYRTLEEVGREFGITRERIRQIEARVLR 389

Query: 279 KVQ 281
           K++
Sbjct: 390 KLR 392


>gi|319935434|ref|ZP_08009871.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
 gi|319809650|gb|EFW06063.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
          Length = 422

 Score =  106 bits (264), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 88/278 (31%), Positives = 142/278 (51%), Gaps = 38/278 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LAKR  E GD  A  +L  ++LRLVV IA  Y G G+   ++
Sbjct: 154 YLKEIGRVELLSHDEEIDLAKRILE-GDEEAKKKLAAANLRLVVSIAKRYVGRGMLFLDL 212

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT---------T 129
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I           T
Sbjct: 213 IQEGNMGLIKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLT 272

Query: 130 ANQKRLFFNLRR--LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDES 185
             Q++L   L R  L   +    D  + PE+V  I +K+++   E +S+   +    D  
Sbjct: 273 RVQRQLIQELGREPLAEEIAEKMD-GMTPEKVREI-QKISL---EPVSLETPIGEEDDSH 327

Query: 186 LNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           L   I   D+ +    D+   +   D   +VL+E  +R+ +  +L     + + R R   
Sbjct: 328 LGDFI--EDEGAMSPDDYAANELLKDELNEVLLELTDREEK--VLRLRFGLDDGRTR--- 380

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                     TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 381 ----------TLEEVGKEFNVTRERIRQIEAKALRKLK 408


>gi|291286384|ref|YP_003503200.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Denitrovibrio
           acetiphilus DSM 12809]
 gi|290883544|gb|ADD67244.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Denitrovibrio
           acetiphilus DSM 12809]
          Length = 322

 Score =  106 bits (264), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 76/270 (28%), Positives = 143/270 (52%), Gaps = 22/270 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI K P+L +++E  L++   E G   +   ++  +LRLVV IA  Y   G+ + ++
Sbjct: 54  YLNEISKYPVLTREQEGELSQGI-EKGCNDSKETMIKCNLRLVVSIAKKYINRGMNLVDL 112

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT--TANQKRLF 136
           V EGNIGL++AV+KFD  +GF+ +TY+ WWI+ A++  I+    +V+I    + N  ++ 
Sbjct: 113 VEEGNIGLLKAVEKFDYTKGFKFSTYATWWIRQAIERAIINQCRMVRIPVHMSENISKVM 172

Query: 137 FNLRRLK---GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L+   G    I + +   +  ++  KK+  +  +  S++  + GDE         
Sbjct: 173 KTQNELQQKLGREPTIHELSTACKMPLSTLKKVFDAIKQDTSLDMPVGGDE--------- 223

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQEN 251
              SS   +++  D    +  L  K E  +++ ++ + ++ L+  E+ I   R      +
Sbjct: 224 ---SSTLHEFIADDEKYLDPYL--KIENTSKKEIIFKWLTFLSDNEKTIIIRRYGLTGND 278

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           P TLE++ ++  ++RERVRQIE R   K++
Sbjct: 279 PETLESIGNDLGITRERVRQIEKRVLSKMR 308


>gi|225011624|ref|ZP_03702062.1| RNA polymerase, sigma 70 subunit, RpoD family [Flavobacteria
           bacterium MS024-2A]
 gi|225004127|gb|EEG42099.1| RNA polymerase, sigma 70 subunit, RpoD family [Flavobacteria
           bacterium MS024-2A]
          Length = 287

 Score =  106 bits (264), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 81/296 (27%), Positives = 157/296 (53%), Gaps = 55/296 (18%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ ++  +EE  LA+R +  GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGKVDLITAEEEVELAQRIKA-GDQIALEKLTKANLRFVVSVAKQYQNQGLTL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
            ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++      Q  I+R   L KIG+ 
Sbjct: 77  PDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVR-LPLNKIGSI 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCR 179
               + +  L   + H +A +           IAK+L+++ ++V          +SM+  
Sbjct: 136 NKINKTYAFLE--QAHERAPSAEE--------IAKELDMTINDVKESLKNSGRHVSMDAP 185

Query: 180 L--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
           L    D +L  ++NS +  +              ++VL+     ++ R  + R++  L P
Sbjct: 186 LVEGEDSNLYDVLNSGESPNP-------------DRVLL----HESLRTEIERALETLTP 228

Query: 238 RERRIFEARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RE  +    RL      ++ +TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 229 READVV---RLYFGLGDQHAMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|188587782|ref|YP_001920276.1| RNA polymerase sigma factor RpoD [Clostridium botulinum E3 str.
           Alaska E43]
 gi|251778486|ref|ZP_04821406.1| RNA polymerase sigma factor RpoD [Clostridium botulinum E1 str.
           'BoNT E Beluga']
 gi|188498063|gb|ACD51199.1| RNA polymerase sigma factor RpoD [Clostridium botulinum E3 str.
           Alaska E43]
 gi|243082801|gb|EES48691.1| RNA polymerase sigma factor RpoD [Clostridium botulinum E1 str.
           'BoNT E Beluga']
          Length = 374

 Score =  106 bits (264), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 82/265 (30%), Positives = 133/265 (50%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  ++E   AKR  E GD  A  +L  ++LRLVV IA  Y G G+   ++
Sbjct: 108 YLKEIGKVPLLSSEQEIDYAKRI-EEGDPVAKKKLAEANLRLVVSIAKRYVGRGMLFLDL 166

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 167 IQEGNLGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 224

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R++  L      +  PE+   I+K + +   +V  +        SL   I   ++  S
Sbjct: 225 LIRVQRQLLQELGRDPFPEE---ISKVMELPVDKVREIQKIAQEPVSLETPIG--EEEDS 279

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++  D              K +   L   +  L PRE ++   R   ++    TLE
Sbjct: 280 HLGDFIPDDEAPAPAEAAAFTMLKEQ---LINVLDTLTPREEKVLRLRFGLDDGRARTLE 336

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF V+RER+RQIEA+A +K++
Sbjct: 337 EVGKEFNVTRERIRQIEAKALRKLR 361


>gi|312880428|ref|ZP_07740228.1| RNA polymerase, sigma 70 subunit, RpoD [Aminomonas paucivorans DSM
           12260]
 gi|310783719|gb|EFQ24117.1| RNA polymerase, sigma 70 subunit, RpoD [Aminomonas paucivorans DSM
           12260]
          Length = 387

 Score =  106 bits (264), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 86/268 (32%), Positives = 137/268 (51%), Gaps = 19/268 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L  +EE  LAK   E G   +  +LV ++LRLVV IA  Y G G+   ++
Sbjct: 121 YLREIGKIPLLTPEEEVELAKGV-EAGHAPSKAKLVEANLRLVVSIAKKYIGRGMLFLDL 179

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 180 IQEGNLGLIRAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 237

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L          E+   IA ++ +  +E +    R+A  E ++      ++  S
Sbjct: 238 LIRVSRQLVQRLGREPTAEE---IAGEMEIP-AERVEEIQRIA-QEPVSLETPIGEEEDS 292

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNR---RNMLTRSMSVLNPRERRIFEARRLQEN--PV 253
           Q  D+L      +++ L   EE       R  L   +  L  RER +   R   E+  P 
Sbjct: 293 QLGDFL------EDKDLPSPEEAAASQILREQLEEMLEDLTDREREVLRLRFGLEDGHPH 346

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TLE +   F V+RER+RQIEA+A +K++
Sbjct: 347 TLEEVGRRFGVTRERIRQIEAKALRKLR 374


>gi|149908225|ref|ZP_01896889.1| hypothetical DNA-directed RNA polymerase, sigma subunit [Moritella
           sp. PE36]
 gi|149808767|gb|EDM68700.1| hypothetical DNA-directed RNA polymerase, sigma subunit [Moritella
           sp. PE36]
          Length = 284

 Score =  106 bits (264), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 77/261 (29%), Positives = 136/261 (52%), Gaps = 12/261 (4%)

Query: 15  GLSRYIHEI-RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
            L  Y+ ++ +K  +L K+EEY +A     +GDL A +R++ ++LRLV+ +A  Y+   +
Sbjct: 9   ALDAYLQQVNKKSKLLTKEEEYDIAVAV-ANGDLRAKNRMIEANLRLVISVAKRYQYSVI 67

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGN GL++AV+KFDP +GFR +TY++WWIK  ++  I+ S   ++I     + 
Sbjct: 68  PLVDIIQEGNTGLIRAVEKFDPNKGFRFSTYAVWWIKNNIERSIMNSDRTIRIPIHVGKM 127

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                    +  L   +DN+L     V IAK L     EV+ +      + SL+  I + 
Sbjct: 128 HKSIAKVAKELGLDVGSDNDL-----VVIAKVLETDVDEVMDVLSYYFSELSLDKGIVTD 182

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQEN 251
           +++ +   D +    D   +    + E  + R+ L   +  L   ER++ E R     E 
Sbjct: 183 NESVTTLVDII---EDQSIRTPSAEIEGGSTRDYLLALLENLPAYERQVVELRFGLTGEE 239

Query: 252 PVTLENLSSEFEVSRERVRQI 272
           P++L  +     +SRE+VR I
Sbjct: 240 PLSLSRIGERLSMSREKVRII 260


>gi|329902595|ref|ZP_08273157.1| RNA polymerase sigma factor RpoS [Oxalobacteraceae bacterium
           IMCC9480]
 gi|327548742|gb|EGF33384.1| RNA polymerase sigma factor RpoS [Oxalobacteraceae bacterium
           IMCC9480]
          Length = 334

 Score =  106 bits (264), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 86/270 (31%), Positives = 141/270 (52%), Gaps = 15/270 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+++I    +L   +E   A   +  GD  A   ++  +LRLVV IA  Y   G+ + ++
Sbjct: 65  YLNQIGARALLTVAQEVHYATLAKA-GDFPARQVMIEHNLRLVVSIAKHYINRGVVLLDL 123

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+A+ KF+PERGFR +TY+ WWI+ +++  I+     V++    +  R    
Sbjct: 124 IEEGNLGLMRAIDKFEPERGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRELNQ 181

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           + R K HL+A+  +  K   +  IA     S  +V  +        SL+A ++ +D  SS
Sbjct: 182 VLRAKYHLEALHHDG-KDASIDDIAHLTGRSAEDVQDILALSDHPASLDAPLD-ADPGSS 239

Query: 199 QWQDWLVYD-HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVT 254
              D L  D  DG E    + E     R+ L R    L+ ++R I   RR     ++P T
Sbjct: 240 -LMDLLPGDPGDGPEARAEQHETALLVRDWLAR----LSDKQRLII-TRRFGLEDDDPAT 293

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESI 284
           LE L++E  V+RERVRQ++  A  K++ ++
Sbjct: 294 LEALAAEIGVTRERVRQVQQEALIKLKRAL 323


>gi|269837239|ref|YP_003319467.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphaerobacter
           thermophilus DSM 20745]
 gi|269786502|gb|ACZ38645.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphaerobacter
           thermophilus DSM 20745]
          Length = 390

 Score =  106 bits (264), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 95/315 (30%), Positives = 157/315 (49%), Gaps = 52/315 (16%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------------- 41
            R++++  V+    +  Y+ EI +  +L  +EE  LAKR                     
Sbjct: 80  TRQDVADAVSVSDSVRLYLQEIGETSLLTMEEEVWLAKRMERGKIAEERLANGDYASEAE 139

Query: 42  -------REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                  +E G+ + AH L+ ++LRLVV +A  Y G GL   +++ EGNIGLM+A  KFD
Sbjct: 140 RAELLADKEDGEKARAH-LIQANLRLVVSVAKKYVGRGLSFLDLIQEGNIGLMKATDKFD 198

Query: 95  PERGFRLATYSMWWIKAAMQEYI---LRSWSL-VKIGTTANQKRLFFNLRRLKGHLQAIT 150
            +RGF+ +TY+ WWI+ A+   I    R+  L V +G T N+      +++    LQ I 
Sbjct: 199 YKRGFKFSTYATWWIRQAITRAISDQSRTIRLPVHVGETINR------VKKTSQRLQQIF 252

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD--H 208
           +     E+V   A+ +++ E +V     R   D S + +  S +    Q  D  + D   
Sbjct: 253 EREPTFEEV---ARAMDIPEEKV-----RQVLDASRHPV--SLEAPVGQEGDAFLGDFIE 302

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSR 266
           D      +E   ++  ++ ++ ++S L  RERRI   R   E+    TLE +  EF ++R
Sbjct: 303 DDTMPPPLELASQELLKHQISDALSKLTERERRIIILRFGLEDGQFRTLEEVGREFGITR 362

Query: 267 ERVRQIEARAFKKVQ 281
           ER+RQIEA+A +K++
Sbjct: 363 ERIRQIEAKALRKLR 377


>gi|295424882|ref|ZP_06817597.1| RNA polymerase sigma factor rpoD [Lactobacillus amylolyticus DSM
           11664]
 gi|295065448|gb|EFG56341.1| RNA polymerase sigma factor rpoD [Lactobacillus amylolyticus DSM
           11664]
          Length = 368

 Score =  106 bits (264), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 83/275 (30%), Positives = 130/275 (47%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   +E  LAKR  E+GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGRVPLLNADKEIALAKRI-ENGDEEAKQELAEANLRLVVSIAKRYVGRGMSFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 161 IQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 220

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + ++   +V  I K       E +S+   +    D  L 
Sbjct: 221 RIQRQLLQDLGREPTPEEIGAEMDMPTNKVRDILK----IAQEPVSLETPIGEEDDSHLG 276

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S +        H   E +          +  L  ++  L  RE  +   R 
Sbjct: 277 DFIEDKEATSPEQ-------HASYEML----------KEQLEETLDTLTDREENVLRLRF 319

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 320 GLDDGRTRTLEEVGRVFGVTRERIRQIEAKALRKL 354


>gi|257066626|ref|YP_003152882.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Anaerococcus
           prevotii DSM 20548]
 gi|256798506|gb|ACV29161.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Anaerococcus
           prevotii DSM 20548]
          Length = 602

 Score =  106 bits (264), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 80/247 (32%), Positives = 124/247 (50%), Gaps = 36/247 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  ++LRLVV IA  Y G G+   +++ EGN+GLM+AV K+D  RGF+ +TY+ WW
Sbjct: 366 AKKKLAETNLRLVVSIAKKYVGRGMSFLDLIQEGNMGLMKAVDKYDYNRGFKFSTYATWW 425

Query: 109 IKAAMQEYILRSWSLVKIGT----TAN-----QKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N     Q++L  +L R   + +      L+ E+V
Sbjct: 426 IRQAITRAIADQARTIRIPVHMVETINKLVRIQRQLVQDLGRDPSNEEIAEQMGLEVEKV 485

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K   +S+  V           SL   I   D   S   D++      ++   I+  
Sbjct: 486 QEIRK---ISQEPV-----------SLETPIGEED--DSHLGDFI------EDDSAIDPG 523

Query: 220 ERKNR---RNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEA 274
           E  N    R  L   +S L  RE+R+ + R   +   P TLE +  EF+V+RER+RQIEA
Sbjct: 524 EAANYTMLREQLNDVLSCLGAREKRVLQLRFGLIDGTPRTLEEVGKEFDVTRERIRQIEA 583

Query: 275 RAFKKVQ 281
           +A +K++
Sbjct: 584 KALRKLK 590


>gi|308069922|ref|YP_003871527.1| RNA polymerase sigma factor rpoD (Sigma-A) [Paenibacillus polymyxa
           E681]
 gi|310643031|ref|YP_003947789.1| RNA polymerase sigma factor rpod [Paenibacillus polymyxa SC2]
 gi|305859201|gb|ADM70989.1| RNA polymerase sigma factor rpoD (Sigma-A) [Paenibacillus polymyxa
           E681]
 gi|309247981|gb|ADO57548.1| RNA polymerase sigma factor rpoD [Paenibacillus polymyxa SC2]
          Length = 377

 Score =  106 bits (264), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 82/265 (30%), Positives = 131/265 (49%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   +E  LAKR   +GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 111 YLKEIGRVPLLSADDEVELAKRIN-NGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 169

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD E+GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 170 IQEGNMGLIKAVEKFDYEKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 227

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L         PE+V A   ++ +S  +V  +        SL   I   D   S
Sbjct: 228 LIRVSRQLLQELGREPTPEEVAA---EMELSVEKVREIMKIAQEPVSLETPIGEED--DS 282

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++    D +     +    +  +  L   +  L  RE  +   R   ++    TLE
Sbjct: 283 HLGDFI---EDQEALAPADAAAYELLKEQLEDVLDTLTEREENVLRLRFGLDDGRTRTLE 339

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +   F V+RER+RQIEA+A +K++
Sbjct: 340 EVGKVFGVTRERIRQIEAKALRKLR 364


>gi|288926163|ref|ZP_06420090.1| RNA polymerase sigma-70 factor [Prevotella buccae D17]
 gi|315608876|ref|ZP_07883849.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella buccae
           ATCC 33574]
 gi|288337055|gb|EFC75414.1| RNA polymerase sigma-70 factor [Prevotella buccae D17]
 gi|315249403|gb|EFU29419.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella buccae
           ATCC 33574]
          Length = 286

 Score =  106 bits (264), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 81/283 (28%), Positives = 149/283 (52%), Gaps = 30/283 (10%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI    ++  +EE  LA+R R+ GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGHEELVTVEEEVELAQRIRK-GDRHALEKLTKANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK-----IGTTA 130
            ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V+     +G+  
Sbjct: 77  PDLINEGNMGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQVGSVN 136

Query: 131 NQKRL---FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESL 186
              R+   F      +  +  I D+   PE  +  A K+N      +S++     GD+  
Sbjct: 137 KINRMLNKFEQENERRPSIDEIADSVDLPEDKIEDALKVNTRH---VSVDAPFVDGDD-- 191

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           N+LI+    + +   D  +     +E++              +R++  LN RER I E  
Sbjct: 192 NSLIDILPNSDAPMADKALVMESLREEI--------------SRALRTLNERERNIIECF 237

Query: 247 RLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
               NP +TLE +  +F ++RERVRQI+ +A ++++ + + +V
Sbjct: 238 FGINNPEMTLEEIGDKFGLTRERVRQIKEKAIRRLRHNTKNRV 280


>gi|168700059|ref|ZP_02732336.1| RNA polymerase sigma factor rpoS [Gemmata obscuriglobus UQM 2246]
          Length = 272

 Score =  106 bits (264), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 86/275 (31%), Positives = 137/275 (49%), Gaps = 21/275 (7%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
            S Y+ EI   P+L   EE  L  R    GD  A  R+V ++LRLVV IA GY G GL +
Sbjct: 11  FSTYLSEIDHTPLLSAAEERDLGARVLT-GDPQARDRMVRANLRLVVNIARGYTGKGLAL 69

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++VSEGN+GL++AV+ F+P    R +TY+ +WIK +++  I+ +   ++I   A    L
Sbjct: 70  DDLVSEGNMGLLRAVEGFEPSMNTRFSTYASYWIKQSIKRAIVNTAKTIRI--PAYMAEL 127

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL----AGDESLNALIN 191
               RR    L   +D   +P     IAK L +S+ ++  +   +    AG +S     +
Sbjct: 128 LTKWRRATNQL---SDELGRPPTHDEIAKFLGLSKKKLAIIKKAIRVANAGTQS-----D 179

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--Q 249
            SD   S  +  +    D  +  L + ++ K   ++L R    ++ RE  +   R     
Sbjct: 180 QSDAGWSIEETLMDSRGDAPDTELGKSDDLKQVLHLLDR----MDQREATVLRMRFGLND 235

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           E P TL+ +     ++RERVRQIE  A  K+ + +
Sbjct: 236 EEPRTLKEIGECLGLTRERVRQIENEALAKLGDGM 270


>gi|153953576|ref|YP_001394341.1| hypothetical protein CKL_0942 [Clostridium kluyveri DSM 555]
 gi|219854198|ref|YP_002471320.1| hypothetical protein CKR_0855 [Clostridium kluyveri NBRC 12016]
 gi|146346457|gb|EDK32993.1| RpoD2 [Clostridium kluyveri DSM 555]
 gi|219567922|dbj|BAH05906.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 354

 Score =  106 bits (264), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 86/291 (29%), Positives = 141/291 (48%), Gaps = 25/291 (8%)

Query: 1   MNRKNMSIIVNGEIGLSR----YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTS 56
           +N KN+ + V   I +      Y+ EI K+P+L  +EE  LAK+  E GD  A  +L  +
Sbjct: 66  LNEKNLDLSVPEGIAIDDPVRMYLKEIGKVPLLLPEEEMSLAKKI-EEGDQIAKKKLAEA 124

Query: 57  HLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           +LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   
Sbjct: 125 NLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGFKFSTYATWWIRQAITRA 184

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
           I      ++I    +       L R+   L          E+V  I +       E++ +
Sbjct: 185 IADQARTIRI--PVHMVETINKLIRVSRQLLQELGREPHAEEVAKIMEMPVDKVREIMKI 242

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWL----VYDHDGQEQVLIEKEERKNRRNMLTRSM 232
                  E ++      ++  S   D++               + KE+  N  + LT   
Sbjct: 243 -----AQEPVSLETPIGEEEDSHLGDFIPDDEAPAPAEAAAFTMLKEQLINVLDTLT--- 294

Query: 233 SVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
               PRE ++   R   ++    TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 295 ----PREEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLR 341


>gi|260886856|ref|ZP_05898119.1| RNA polymerase sigma factor RpoD [Selenomonas sputigena ATCC 35185]
 gi|330839344|ref|YP_004413924.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Selenomonas
           sputigena ATCC 35185]
 gi|260863455|gb|EEX77955.1| RNA polymerase sigma factor RpoD [Selenomonas sputigena ATCC 35185]
 gi|329747108|gb|AEC00465.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Selenomonas
           sputigena ATCC 35185]
          Length = 375

 Score =  106 bits (264), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 83/265 (31%), Positives = 129/265 (48%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   EE  LAKR  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 109 YLKEIGRVPLLSADEEIALAKRM-EAGDEEAQKELAEANLRLVVSIAKRYVGRGMLFLDL 167

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 168 IQEGNLGLIKAVEKFDYNKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 225

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L         PE+   IA+ + +S   V  +        SL   I   ++  S
Sbjct: 226 LIRVSRQLLQQLGREPSPEE---IAEAMEISVERVREIMKIAQEPVSLETPIG--EEEDS 280

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D+ + D D       E       +  L   +  L  RE R+   R   ++    TLE
Sbjct: 281 HLGDF-IEDQDAPAPA--EAASFMLLKEQLEEVLDTLTEREERVLRLRFGLDDGRARTLE 337

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +   F V+RER+RQIEA+A +K++
Sbjct: 338 EVGQNFGVTRERIRQIEAKALRKLR 362


>gi|312869100|ref|ZP_07729274.1| RNA polymerase sigma factor RpoD [Lactobacillus oris PB013-T2-3]
 gi|311095346|gb|EFQ53616.1| RNA polymerase sigma factor RpoD [Lactobacillus oris PB013-T2-3]
          Length = 380

 Score =  106 bits (264), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 85/275 (30%), Positives = 133/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LA R  E GD  A  +L  ++LRLVV IA  Y G G+   ++
Sbjct: 114 YLKEIGRVNLLTADEEVKLALRI-EQGDEVAKQQLAEANLRLVVSIAKRYVGRGMQFLDL 172

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  RGF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 173 IQEGNMGLMKAVEKFDYRRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 232

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + ++  E++  I   L +++ E +S+   +    D  L 
Sbjct: 233 RIQRQLLQDLGREPLPEEIGAEMDMPTEKIRNI---LKIAQ-EPVSLETPIGEEDDSHLG 288

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 289 DFIEDQDATSPA-------DHAAYEMM----------KKQLENVLDTLTDREENVLRLRF 331

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 332 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 366


>gi|260911780|ref|ZP_05918352.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella sp. oral
           taxon 472 str. F0295]
 gi|260634106|gb|EEX52224.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella sp. oral
           taxon 472 str. F0295]
          Length = 287

 Score =  106 bits (264), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 77/279 (27%), Positives = 144/279 (51%), Gaps = 38/279 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI    ++  +EE  LA+R R+ GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGHEELISVEEEVELAQRIRK-GDRKALEKLTKANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V++    NQ   
Sbjct: 77  QDLINEGNVGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRL--PVNQ--- 131

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRLAGDES 185
             ++ ++   L      N +   +  IA+K ++ E ++          IS++      E 
Sbjct: 132 VGSVNKINKILNKFEQENERRPSINEIAEKTDLPEDKIEDAIKVTGRHISVDAPFVDGED 191

Query: 186 ---LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
              L+ L NS         D    D++  ++ L         R  +  ++  LN RER +
Sbjct: 192 NSLLDLLTNS---------DMPTVDNELVKESL---------RAEIAEALQFLNERERNV 233

Query: 243 FEA-RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            EA   + +  +TLE +  ++ ++RERVRQI+ +A +++
Sbjct: 234 IEAFFGINQMEMTLEEIGDKYGLTRERVRQIKEKAIRRL 272


>gi|298241844|ref|ZP_06965651.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297554898|gb|EFH88762.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 366

 Score =  106 bits (264), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 87/285 (30%), Positives = 132/285 (46%), Gaps = 14/285 (4%)

Query: 7   SIIVNG-EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           S   NG E     Y+ +IR   +L   EE  LA+R    GD  A  +LV S+LRLV+ IA
Sbjct: 88  STKANGSEDAFQSYLRDIRGYGLLTHAEEIDLAQRAAA-GDTIARRKLVESNLRLVISIA 146

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y   G+P+ +++ EGN+GLM+A +KFD +RG    TY+ WWI+ A+         ++ 
Sbjct: 147 RRYTSTGVPLIDLIQEGNLGLMRAAEKFDHQRGCHFGTYATWWIRQAVSRAAGEQSRMIH 206

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           +    + +     +RR+   L      +  PEQ   IA+  +    EV ++   +    S
Sbjct: 207 LPEHVSTR--LRKVRRISAQLSQENGLDPMPEQ---IAEACHFEVDEVKNLLGVIEQPVS 261

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L+  ++  D+      D L    D       E   R      L R+++VL PRER +   
Sbjct: 262 LDTPVD--DETRYSLGDTL---EDDTTPAPAETASRHLLGEELHRALAVLTPRERSVVML 316

Query: 246 RR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           R         TL  +  E  +SRERVRQ+E  A  K++     Q 
Sbjct: 317 RYGIGDGRSRTLLEVGKELGISRERVRQLEVVALMKLRSVTNAQA 361


>gi|288800917|ref|ZP_06406374.1| RNA polymerase sigma-70 factor [Prevotella sp. oral taxon 299 str.
           F0039]
 gi|288332378|gb|EFC70859.1| RNA polymerase sigma-70 factor [Prevotella sp. oral taxon 299 str.
           F0039]
          Length = 287

 Score =  105 bits (263), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 84/285 (29%), Positives = 153/285 (53%), Gaps = 34/285 (11%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI +  +L  +EE  LA++ +E GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEITQEKLLTTEEEITLARKIKE-GDKDALQKLTRANLRFVVSVAKQYQHQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + +            A+Q RL
Sbjct: 77  PDLINEGNIGLIKAAEKFDDTRGFKFISYAVWWIRQSIMQAL------------ADQSRL 124

Query: 136 FFNLRRLKGHLQAITDNNLKPEQ-------VVAIAKKLNVSE---SEVISMNCRLAGDES 185
                   G +  I   + K EQ       +  IA+++N+ +   S+ I  N R     S
Sbjct: 125 VRLPLNQVGSVNKINKISHKFEQEFERKPSIAEIAEEINLPQERVSDAIKGNNRHV---S 181

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE-ERKNRRNMLTRSMSVLNPRERRIFE 244
           ++A +  +D N +   D L     G E   I+     ++ R  L  ++++L+ RER + E
Sbjct: 182 MDAPL--TDGNDNGLADLL----QGNEGPDIDTHLLLESLREELKLALNILDERERFVIE 235

Query: 245 ARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           A      P +TL+ + ++  ++RER RQI  +A +K++++ Q ++
Sbjct: 236 AFYGINQPEMTLQEIGAKKGLTRERARQIREKAIRKLRKNTQNKL 280


>gi|118581147|ref|YP_902397.1| RpoD family RNA polymerase sigma factor [Pelobacter propionicus DSM
           2379]
 gi|118503857|gb|ABL00340.1| RNA polymerase, sigma 70 subunit, RpoD family [Pelobacter
           propionicus DSM 2379]
          Length = 323

 Score =  105 bits (263), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 78/280 (27%), Positives = 146/280 (52%), Gaps = 35/280 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ +I++ P+L  ++E  +A++  E GD++A ++++ S+LRLVVKIA  Y   GLP  ++
Sbjct: 64  YLRDIQRTPLLTAEQEKEVARQI-EKGDMAARNKMIESNLRLVVKIAKRYINRGLPFLDL 122

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK--IGTTANQKRLF 136
           + EGN+GL++AV++F+  +  R +TY+ WWI+ A+   ++     ++  +  + +  R+ 
Sbjct: 123 IEEGNLGLIKAVERFNLAKECRFSTYATWWIRQAIDRALVNQSRTIRLPVHVSDDINRMA 182

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV------ISMNCRLA---GDESLN 187
              RRL   LQ       +      IA+++NV  + V      +   C +    GD S  
Sbjct: 183 KVTRRLSQTLQ-------REPHAHEIAEEMNVKLAYVRRLMTLLRRTCSMETPIGDGSDY 235

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
            LI++ +  S      L+ + D  EQ+              +     L+  E++I   R 
Sbjct: 236 FLIDTIEDTSMVAPSDLLENIDRYEQI--------------SEHFKELSESEQKILALRF 281

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             ++  P TL+ +   F V+RER+RQIEA++ +K+   ++
Sbjct: 282 GLDDKEPQTLDTIGRSFGVTRERIRQIEAKSLEKLYACVK 321


>gi|241896072|ref|ZP_04783368.1| DNA-directed RNA polymerase sigma subunit RpoD [Weissella
           paramesenteroides ATCC 33313]
 gi|241870672|gb|EER74423.1| DNA-directed RNA polymerase sigma subunit RpoD [Weissella
           paramesenteroides ATCC 33313]
          Length = 378

 Score =  105 bits (263), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 82/265 (30%), Positives = 135/265 (50%), Gaps = 15/265 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LA+R  E GD +A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 112 YLKEIGRVSLLTGDEEVSLAERI-EAGDETAKQELAEANLRLVVSIAKRYVGRGMQFLDL 170

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 171 IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 228

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R++ +L         PE++ A   +++V+  +V  +  ++A +  SL   I   D   
Sbjct: 229 LIRIQRNLLQDLGREPTPEEIGA---EMDVATEKVRDI-LKIAQEPVSLETPIGEED--D 282

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTL 255
           S   D++    D +     +    +  +  L   +  L  RE  +   R   E+    TL
Sbjct: 283 SHLGDFI---EDNEAVSPADSAAYQMLKEQLESVLDTLTDREENVLRLRFGLEDGRTRTL 339

Query: 256 ENLSSEFEVSRERVRQIEARAFKKV 280
           E +   F V+RER+RQIEA+A +K+
Sbjct: 340 EEVGKVFGVTRERIRQIEAKALRKL 364


>gi|313159603|gb|EFR58965.1| putative RNA polymerase sigma factor RpoD [Alistipes sp. HGB5]
          Length = 286

 Score =  105 bits (263), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 78/271 (28%), Positives = 149/271 (54%), Gaps = 16/271 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K  ++  +EE  LA+R ++ GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGKEELITVEEEVELAQRIKK-GDQEALEKLTKANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     +V++    NQ   
Sbjct: 77  PDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL--PLNQVGS 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
              + +     +   +    PE+   +A +L + + E ++   R+AG   S++A     +
Sbjct: 135 LNKINKAFARFEQEHERTPSPEE---LATELELPK-EKVTDTLRVAGRHVSVDAPFADGE 190

Query: 195 KNSSQWQDWLVY-DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE-ARRLQENP 252
            NS    D LV  D    ++ LI     ++    + R++  L  RER I +    +  + 
Sbjct: 191 DNS--LLDVLVNPDSPNADRGLI----NESLSTEVDRALETLTDRERDIIKYFFGIGTSE 244

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +TLE +  +F+++RERVRQI+ +A ++++ S
Sbjct: 245 MTLEEIGEKFDLTRERVRQIKEKAIRRLRHS 275


>gi|256370771|ref|YP_003108596.1| RNA polymerase sigma factor rpoD [Candidatus Sulcia muelleri
           SMDSEM]
 gi|256009563|gb|ACU52923.1| RNA polymerase sigma factor rpoD [Candidatus Sulcia muelleri
           SMDSEM]
          Length = 334

 Score =  105 bits (263), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 81/276 (29%), Positives = 146/276 (52%), Gaps = 16/276 (5%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREH---GDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           +Y+ EI KIP+L +++E  LAK  R+    G  +A  +L+ S+LR VV +A  Y+  GL 
Sbjct: 63  KYLEEIGKIPLLSQKKELELAKLARKELNAGCSTALEQLIKSNLRFVVSVAKQYQNQGLS 122

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           +S++++EGN+GL++ + +FD ++GF+  +Y +WWI+ A+ + I      ++  T    K 
Sbjct: 123 LSDLINEGNLGLIKGISRFDEKKGFKCISYCVWWIRQAILQAIADQARCIRCPTN---KL 179

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA-LINSS 193
            F+N + +K + +      ++P  V  I   LN SE EV           SL+A ++   
Sbjct: 180 AFYN-KVVKTYSKLEQKLKMQP-TVNDIVVYLNSSEKEVEEALKNSIQPTSLDAPILEGE 237

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENP 252
           D N     D L  +   +    +EKE   +    + R +  L+ +E ++          P
Sbjct: 238 DTN---LYDVLKSETSPEPDFKLEKE---SFFKDIKRLLETLSEKESQVISLHYGFGCKP 291

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TLE ++   +++RER RQIE    K+++ S +K++
Sbjct: 292 MTLEKVAFLLKLTRERCRQIEINGIKRLRISYRKKL 327


>gi|297194519|ref|ZP_06911917.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
 gi|297152294|gb|EFH31643.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
          Length = 366

 Score =  105 bits (263), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 91/294 (30%), Positives = 144/294 (48%), Gaps = 42/294 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHG-------------------DLS--------AAH 51
           Y+ EI +IP+L   EE  LA+R  E G                   DL         A  
Sbjct: 73  YLREIGRIPLLTAAEEVELARRV-EAGLFAEEKLANTPDPDSQLAVDLDRLVVMGRMAKR 131

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY+ WWI+ 
Sbjct: 132 RLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIRQ 191

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           AM   +      +++     +  L   + R++  +         PE+V   A  L ++ S
Sbjct: 192 AMSRALADQARTIRVPVHVVE--LINRVVRVQRRMLQERGYEPTPEEV---ATHLELT-S 245

Query: 172 EVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           E +S   RLA +  SL+A +   D  +    D +    DG     +E       R  L  
Sbjct: 246 ERVSEVLRLAQEPVSLHAPVGEEDDVA--LGDLI---EDGDAASPVESAAFLLLREHLDA 300

Query: 231 SMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            +S L  RER++ + R   ++  P TLE +   F V+RER+RQIE++   K+++
Sbjct: 301 VLSTLGERERKVVQLRYGLDDGRPRTLEEIGRLFGVTRERIRQIESKTLNKLRD 354


>gi|294102609|ref|YP_003554467.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Aminobacterium
           colombiense DSM 12261]
 gi|293617589|gb|ADE57743.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Aminobacterium
           colombiense DSM 12261]
          Length = 377

 Score =  105 bits (263), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 86/294 (29%), Positives = 142/294 (48%), Gaps = 45/294 (15%)

Query: 10  VNGEIG----------LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLR 59
            +GEIG          +  Y+ EI K+P+LE  +E  LAKR  E G+  A  +++ ++LR
Sbjct: 92  ADGEIGKLDDIPLTDPVRMYLREIGKVPLLEPAQEVELAKRV-EAGEEEAKQQIIDANLR 150

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           LVV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I  
Sbjct: 151 LVVSIAKKYIGRGMLFLDLIQEGNLGLIRAVEKFDYRKGFKFSTYATWWIRQAITRAIAD 210

Query: 120 SWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
               +++      T N+     ++L   L R     +   +  ++P +V  I +   +  
Sbjct: 211 QARTIRVPVHMVETINKMVRVSRQLVQKLGREPTDEEIAAEMEIEPSKVEEIRRIAQLP- 269

Query: 171 SEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +S+   +  +E   L   I   D  S +        H   EQ+              
Sbjct: 270 ---VSLETPIGEEEDSQLGDFIEDRDLPSPEEA---AASHLLHEQI-------------- 309

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L+ RER + + R   E+    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 310 DEMLEALSEREREVLQYRFGLEDGRSYTLEEVGKRFGVTRERIRQIEAKALRKL 363


>gi|310777992|ref|YP_003966325.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ilyobacter
           polytropus DSM 2926]
 gi|309747315|gb|ADO81977.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ilyobacter
           polytropus DSM 2926]
          Length = 408

 Score =  105 bits (263), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 84/273 (30%), Positives = 146/273 (53%), Gaps = 29/273 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  ++E   AK   E GD  A  +LV ++LRLVV IA  +   GL + ++
Sbjct: 142 YLREIGQVPLLTHKQEIEHAKNSAE-GDEWATQQLVEANLRLVVSIAKKHTNRGLKLLDL 200

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM+AV+KF+  +G++ +TY+ WWI+ A+   I      ++I        +   
Sbjct: 201 IQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPV-----HMIET 255

Query: 139 LRRLKG----HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSS 193
           + ++K     +LQ  T  +  PE    +A++L + ESE I     +  D  SL   + S 
Sbjct: 256 INKIKKESRIYLQE-TGKDATPE---VLAERLGM-ESEKIKAILEMNQDPISLETPVGSE 310

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNR---RNMLTRSMSVLNPRERRIFEARRLQE 250
           +   S+  D++      ++  ++   E+ NR   +  L   +  L+ RE ++   R   +
Sbjct: 311 E--DSELGDFV------EDNKMLSPYEQTNRNLLKEQLDDVLQSLSEREEKVLRFRYGLD 362

Query: 251 N--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +  P TLE +   F+V+RER+RQIE +A +K++
Sbjct: 363 DGCPRTLEEVGKIFKVTRERIRQIEVKALRKLR 395


>gi|294629207|ref|ZP_06707767.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. e14]
 gi|292832540|gb|EFF90889.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. e14]
          Length = 386

 Score =  105 bits (263), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 87/293 (29%), Positives = 143/293 (48%), Gaps = 40/293 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRY------------------REHGDLS--------AAHR 52
           Y+ EI +IP+L   EE  LA+R                   R  GDL         A  R
Sbjct: 93  YLREIGRIPLLTAAEEVELARRVEAGLFAEEKLSSTPDLDSRLAGDLDRLVVSGRMAKRR 152

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY+ WWI+ A
Sbjct: 153 LIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIRQA 212

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           M   +      +++     +     N R ++   + + +   +P     +A +L+++   
Sbjct: 213 MSRALADQARTIRVPVHVVE---LIN-RVVRVQRRMLQERGYEPTP-AEVAAQLDLTPDR 267

Query: 173 VISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           V  +  RLA +  SL+A +   D  +    D +    DG     +E       R  L   
Sbjct: 268 VGEV-LRLAQEPVSLHAPVGEEDDVA--LGDLI---EDGDAASPVESAAFLLLREHLEAV 321

Query: 232 MSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +S L  RER++ + R   +   P TLE +   F V+RER+RQIE++   K+++
Sbjct: 322 LSTLGERERKVVQLRYGLMDGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRD 374


>gi|294622679|ref|ZP_06701641.1| RNA polymerase sigma factor RpoD [Enterococcus faecium U0317]
 gi|291597877|gb|EFF29007.1| RNA polymerase sigma factor RpoD [Enterococcus faecium U0317]
          Length = 369

 Score =  105 bits (263), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 85/273 (31%), Positives = 133/273 (48%), Gaps = 31/273 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 103 YLKEIGRVSLLTAEEEVALALKI-EEGDQEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 161

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 162 IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 221

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             Q++L  +L R     +   + +L  E+V  I   L +++  V           SL   
Sbjct: 222 RIQRQLLQDLGREPTPEEIGAEMDLPTEKVREI---LKIAQEPV-----------SLETP 267

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   D   S   D++    D +     E    +  +  L   +  L  RE  +   R   
Sbjct: 268 IGEED--DSHLGDFI---EDQEATSPAEHAAYELLKEQLEDVLDTLTDREENVLRLRFGL 322

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
           ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 323 DDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 355


>gi|253701007|ref|YP_003022196.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           M21]
 gi|251775857|gb|ACT18438.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           M21]
          Length = 325

 Score =  105 bits (263), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 82/282 (29%), Positives = 146/282 (51%), Gaps = 21/282 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EIRK  +L+  +E  LA +  + GD  A  R++ S+LRLVVKIA  YR  G+P+ ++
Sbjct: 54  YLIEIRKHALLDAVQEKELALKISQ-GDGDARKRMILSNLRLVVKIAKRYRNRGMPLLDI 112

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK--RLF 136
           + EGNIGL++AV++F   +  R +TY+ WWI+ +++  ++     +++    + +  R+F
Sbjct: 113 IEEGNIGLIKAVERFKLSKECRFSTYATWWIRQSIERALINQVRTIRLPVHVSDEINRMF 172

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
              R L+  L      N +P     +A  L ++   +  +   L    S+       ++ 
Sbjct: 173 RENRVLELKL------NREP-TAKEVADNLGITVQRLRELMVVLKKTFSI-------EQP 218

Query: 197 SSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
             +  D+ + D   D    +  E  E +NR  +++  +  L+  ER+I   R   E+  P
Sbjct: 219 MGERGDFCLTDTIQDTSTVLPTELLENQNRYELISNLLEFLSETERKILTLRFGLEDKAP 278

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSP 294
            TL+ +   F V+RER+RQIE +A +K++  I    +L   P
Sbjct: 279 QTLDTIGQGFGVTRERIRQIEVKALEKLRLMIASFEDLERLP 320


>gi|227551146|ref|ZP_03981195.1| DNA-directed RNA polymerase sigma subunit RpoD [Enterococcus
           faecium TX1330]
 gi|257887737|ref|ZP_05667390.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,141,733]
 gi|257896230|ref|ZP_05675883.1| RNA polymerase sigma-43 factor [Enterococcus faecium Com12]
 gi|257898868|ref|ZP_05678521.1| RNA polymerase sigma-43 factor [Enterococcus faecium Com15]
 gi|293379528|ref|ZP_06625670.1| RNA polymerase sigma factor RpoD [Enterococcus faecium PC4.1]
 gi|293570226|ref|ZP_06681295.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E980]
 gi|227179708|gb|EEI60680.1| DNA-directed RNA polymerase sigma subunit RpoD [Enterococcus
           faecium TX1330]
 gi|257823791|gb|EEV50723.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,141,733]
 gi|257832795|gb|EEV59216.1| RNA polymerase sigma-43 factor [Enterococcus faecium Com12]
 gi|257836780|gb|EEV61854.1| RNA polymerase sigma-43 factor [Enterococcus faecium Com15]
 gi|291609633|gb|EFF38894.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E980]
 gi|292641837|gb|EFF60005.1| RNA polymerase sigma factor RpoD [Enterococcus faecium PC4.1]
          Length = 369

 Score =  105 bits (263), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 85/273 (31%), Positives = 133/273 (48%), Gaps = 31/273 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 103 YLKEIGRVSLLTAEEEVALALKI-EEGDQEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 161

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 162 IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 221

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             Q++L  +L R     +   + +L  E+V  I   L +++  V           SL   
Sbjct: 222 RIQRQLLQDLGREPTPEEIGAEMDLPTEKVREI---LKIAQEPV-----------SLETP 267

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   D   S   D++    D +     E    +  +  L   +  L  RE  +   R   
Sbjct: 268 IGEED--DSHLGDFI---EDQEATSPAEHAAYELLKEQLEDVLDTLTDREENVLRLRFGL 322

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
           ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 323 DDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 355


>gi|77165179|ref|YP_343704.1| RpoS [Nitrosococcus oceani ATCC 19707]
 gi|254434741|ref|ZP_05048249.1| RNA polymerase sigma factor, sigma-70 family [Nitrosococcus oceani
           AFC27]
 gi|76883493|gb|ABA58174.1| RNA polymerase, sigma 38 subunit, RpoS [Nitrosococcus oceani ATCC
           19707]
 gi|207091074|gb|EDZ68345.1| RNA polymerase sigma factor, sigma-70 family [Nitrosococcus oceani
           AFC27]
          Length = 303

 Score =  105 bits (263), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 79/282 (28%), Positives = 143/282 (50%), Gaps = 34/282 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ E  K+P+L  +EE   A R  + GD  A + ++ S+LR+V+++A  +   GLP+ ++
Sbjct: 42  YMREAGKVPLLSAEEERHYA-RLAQQGDREARNHIIESNLRIVIRMATRHINRGLPLMDL 100

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV--------KIGTTA 130
           + EGN+GL+ AV+KF+PE GFR +TY+ WWI+ A++  ++     +        KI    
Sbjct: 101 IEEGNLGLIDAVEKFNPELGFRFSTYASWWIRQAIERALMNQTRTIRVPIHVFKKIRCYQ 160

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNA 188
            + R F     ++ HL  I    L  E +  I + L++   E IS++  L+   D+ L  
Sbjct: 161 KEARYFRQRYNIEPHLGEIA--KLLHEPLERIQRYLSLQAPE-ISLDDPLSEDTDDCLVD 217

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
           L+     N +    W ++D                ++  +   +S L  R++ I + R  
Sbjct: 218 LLPDERNNPAIL--WEIFD----------------KKASIHNQLSQLPERQQEIIKCRYG 259

Query: 249 QEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +     TLE +  +  ++RERVRQI+  A K++++ I+ + 
Sbjct: 260 LDGYEVTTLEEIGQKLGITRERVRQIQQTAIKRLRKIIESET 301


>gi|309792450|ref|ZP_07686915.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Oscillochloris
           trichoides DG6]
 gi|308225522|gb|EFO79285.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Oscillochloris
           trichoides DG6]
          Length = 311

 Score =  105 bits (263), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 73/241 (30%), Positives = 122/241 (50%), Gaps = 12/241 (4%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           H   +A  +L+ S+LRLVV IA  Y+G+GL + +++ EG++GLM+AV KFDP RG + +T
Sbjct: 69  HAGANARAQLINSNLRLVVSIARRYQGHGLSLLDLIQEGSLGLMRAVDKFDPSRGLKFST 128

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ +WI+ ++   I      V++     ++     L R +  L    D +  PE+V   A
Sbjct: 129 YATYWIRQSVGRAIADHGRTVRLPVHLGER--LSRLARARQRLTQRLDRDPTPEEV---A 183

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
            +L ++  +V           SL+     SD  +    + +    D  E   ++      
Sbjct: 184 DELGITTDQVTRAEQAALTPASLDE--THSDDGTGALAEVIS---DPLEPTPLDHVAHGL 238

Query: 224 RRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R+ L  +MS L  RER I   R     E  +TLE +     ++RERVRQ+E+ A +K++
Sbjct: 239 LRDDLCEAMSHLTQRERSILNLRYGLEGETALTLEQIGQRLSLTRERVRQLESEALRKLR 298

Query: 282 E 282
           +
Sbjct: 299 D 299


>gi|269127406|ref|YP_003300776.1| RpoD subfamily RNA polymerase sigma-70 subunit [Thermomonospora
           curvata DSM 43183]
 gi|268312364|gb|ACY98738.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermomonospora
           curvata DSM 43183]
          Length = 385

 Score =  105 bits (263), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 88/306 (28%), Positives = 140/306 (45%), Gaps = 55/306 (17%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRY------------------REHGDLS--------AAHR 52
           Y+ EI ++P+L  +EE  LAK                    RE  DL         A  R
Sbjct: 93  YLREIGRVPLLTAEEEVELAKTIEAGLFAEEKLARAAFISPRERLDLELIAREGARAKQR 152

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 153 LIEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQA 212

Query: 113 MQEYILRSWSLVKIGT----TAN-----QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           +   I      ++I      T N     Q++L  +L R     +   +  L  E+VV I 
Sbjct: 213 ITRAIADQARTIRIPVHMVETINKLVRVQRQLHQDLGREPTPAEIGAEMGLPAERVVEIQ 272

Query: 164 KKLNVSESEVISMNCRLAGDES-LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           +       E +S+   +  ++S L   I  +D          +   D  E +L    ER+
Sbjct: 273 RIAQ----EPVSLQSPIGEEDSDLGDFIEDADAVVPLEAAAFILLQDQLEDILCTLSERE 328

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            R   L   ++  +PR               TLE +  EF V+RER+RQIE++   K++ 
Sbjct: 329 QRIIQLRFGLTDGHPR---------------TLEEVGREFGVTRERIRQIESKTLAKLRH 373

Query: 283 SIQKQV 288
             + Q+
Sbjct: 374 PSRAQM 379


>gi|271963879|ref|YP_003338075.1| RNA polymerase sigma factor RpoD [Streptosporangium roseum DSM
           43021]
 gi|270507054|gb|ACZ85332.1| RNA polymerase sigma factor RpoD [Streptosporangium roseum DSM
           43021]
          Length = 392

 Score =  105 bits (263), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 87/297 (29%), Positives = 146/297 (49%), Gaps = 39/297 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-------------------YREHGDL-----SAAHRLV 54
           Y+ EI ++P+L  +EE  LAK                    + E  +L      A  RL+
Sbjct: 102 YLREIGRVPLLTAEEEVELAKSIEAGLFAEDKLTSVVSRLAFPEFKELVWQGTRAKQRLI 161

Query: 55  TSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114
            ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+ 
Sbjct: 162 EANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAIT 221

Query: 115 EYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVI 174
             I      ++I    +       L R++  L         PE+   IA ++++    VI
Sbjct: 222 RAIADQARTIRI--PVHMVETINKLVRVQRQLHQDLGREPAPEE---IALEMDLPIDRVI 276

Query: 175 SMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
            +  R+A +  SL + I   D   S   D++    D    V +E       ++ L   ++
Sbjct: 277 EIQ-RIAQEPVSLQSPIGEED---SDLGDFI---EDADAVVPMEAAAFIMLQDQLDDILA 329

Query: 234 VLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            L+ RE+RI + R      +P TLE +  EF V+RER+RQIE++   K++   + Q+
Sbjct: 330 TLSDREQRIIQLRFGLADGHPRTLEEVGREFGVTRERIRQIESKTLAKLRHPTRAQM 386


>gi|294674467|ref|YP_003575083.1| RNA polymerase sigma-70 factor [Prevotella ruminicola 23]
 gi|294473044|gb|ADE82433.1| RNA polymerase sigma-70 factor [Prevotella ruminicola 23]
          Length = 290

 Score =  105 bits (263), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 79/272 (29%), Positives = 138/272 (50%), Gaps = 12/272 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKIAMGYRGYG 72
            L +Y+ EI + P++   EE  LA+  R  G     A  RLVT++LR VV +A  Y+  G
Sbjct: 17  ALDKYLVEIGRQPLVTIDEEIELAQAIRRGGPEGEKAKERLVTANLRFVVSVAKQYQHQG 76

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V++    NQ
Sbjct: 77  LTLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRL--PLNQ 134

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 L ++   +      + +   V  +A+   + ES++       +   S++A    
Sbjct: 135 S---GALSKINQEINKFEQQHQRRPSVTELAELTQIEESKIEQTAKADSHHMSIDAPFGE 191

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF-EARRLQEN 251
            D NS    D L    D +   L++ E   +  + + R  +VL  RE +I  E   +   
Sbjct: 192 DDDNS--MADMLSSGEDTRTDKLVDYESLTSDLDNVLR--NVLKDRELKIVKECFGIGCQ 247

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
              LE + +E  ++RERVRQI  ++  K+ +S
Sbjct: 248 ERGLEEIGAEMGLTRERVRQIREKSITKLHDS 279


>gi|78214165|ref|YP_382944.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CC9605]
 gi|78198624|gb|ABB36389.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. CC9605]
          Length = 328

 Score =  105 bits (263), Expect = 6e-21,   Method: Compositional matrix adjust.
 Identities = 83/276 (30%), Positives = 145/276 (52%), Gaps = 22/276 (7%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRG 70
           EI L+ ++  ++++  L ++E   L  R+R    +   A  R++ ++LRLVV +A  Y+ 
Sbjct: 59  EIELAHHVQAMKQLQELPEEE---LTSRHRHKIRMGKRARDRMMAANLRLVVSVAKKYQN 115

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+  M   I  S   +++    
Sbjct: 116 QGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIRLPIHI 175

Query: 131 NQKRLFFNLRRLK---GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
           ++K     +RR+     H      N L+      +A  + +   E+  +  + A   SL+
Sbjct: 176 SEK--LSKMRRISRELSHRFGRQPNRLE------LASAMGIEPRELEDLISQSAPCASLD 227

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR- 246
           A     +  S+  +  L+ D +G+E   +E  +R  ++  L   +S LN RE++I + R 
Sbjct: 228 AHARGEEDRSTLGE--LIPDPNGEEP--MEGMDRSIQKEHLGGWLSQLNEREQKILKLRF 283

Query: 247 -RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
               E P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 284 GLGGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 319


>gi|116618341|ref|YP_818712.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Leuconostoc mesenteroides subsp. mesenteroides ATCC
           8293]
 gi|116097188|gb|ABJ62339.1| RNA polymerase, sigma 70 subunit, RpoD [Leuconostoc mesenteroides
           subsp. mesenteroides ATCC 8293]
          Length = 432

 Score =  105 bits (263), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 82/265 (30%), Positives = 135/265 (50%), Gaps = 15/265 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L+  EE  +AKR  E+GD+ A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 162 YLKEIGRVNLLKGNEEIDIAKRI-ENGDVEAKQELAEANLRLVVSIAKRYVGRGMQFLDL 220

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 221 IQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 278

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R++  L         PE++ A   +++++  +V  +  ++A +  SL   I   D   
Sbjct: 279 LIRIQRQLLQDLGREPLPEEIGA---EMDLTADKVREI-LKIAQEPVSLETPIGEED--D 332

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTL 255
           S   D++    D +     +    +  R  L   +  L  RE  +   R   E+    TL
Sbjct: 333 SHLGDFI---EDNEAVSPADSAAYEMLREQLESVLDTLTDREENVLRLRFGLEDGRTRTL 389

Query: 256 ENLSSEFEVSRERVRQIEARAFKKV 280
           E +   F V+RER+RQIEA+A +K+
Sbjct: 390 EEVGRVFGVTRERIRQIEAKALRKL 414


>gi|34499137|ref|NP_903352.1| RNA polymerase sigma factor RpoS [Chromobacterium violaceum ATCC
           12472]
 gi|34104988|gb|AAQ61344.1| RNA sigma factor RpoS [Chromobacterium violaceum ATCC 12472]
          Length = 316

 Score =  105 bits (263), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 82/279 (29%), Positives = 146/279 (52%), Gaps = 29/279 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+++I    +L  QEE  LA+R    G+  A  +++  +LRLVV IA  Y   GL + ++
Sbjct: 49  YLNDIGNNALLTPQEELALARRVVA-GEFEARQKMIEHNLRLVVNIAKHYINRGLALLDL 107

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM A++KFDPERGFR +TY+ WWI+ +++  I+     +++      K L   
Sbjct: 108 IEEGNIGLMHALEKFDPERGFRFSTYATWWIRQSIERAIMNQSRTIRLPVHV-IKELNVY 166

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS- 197
           LR  + HL++        E++  +  K      +V+++N R+A   SL+A ++     S 
Sbjct: 167 LRASR-HLESQIGREPSVEEIAHLVGKPVEDVRKVLNLNERMA---SLDAPLDIDPMLSI 222

Query: 198 ------SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
                  Q ++  +  H+ Q ++ +               +S LN ++R + E RR   N
Sbjct: 223 GESIPDEQHEEPELQLHNSQLEMFVHD------------WLSQLNEKQRLVIE-RRYGLN 269

Query: 252 P---VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
                TLE L++   ++RERVRQI+    ++++  ++++
Sbjct: 270 GYEICTLEELAASLNLTRERVRQIQIEGLEQLRRILRRK 308


>gi|148543974|ref|YP_001271344.1| RNA polymerase sigma factor RpoD [Lactobacillus reuteri DSM 20016]
 gi|184153369|ref|YP_001841710.1| RNA polymerase sigma factor RpoD [Lactobacillus reuteri JCM 1112]
 gi|227364887|ref|ZP_03848933.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           reuteri MM2-3]
 gi|325682488|ref|ZP_08162005.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           reuteri MM4-1A]
 gi|148531008|gb|ABQ83007.1| RNA polymerase, sigma 70 subunit, RpoD [Lactobacillus reuteri DSM
           20016]
 gi|183224713|dbj|BAG25230.1| RNA polymerase sigma-43 factor RpoD [Lactobacillus reuteri JCM
           1112]
 gi|227070091|gb|EEI08468.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           reuteri MM2-3]
 gi|324978327|gb|EGC15277.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           reuteri MM4-1A]
          Length = 380

 Score =  105 bits (263), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 86/275 (31%), Positives = 132/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LA R  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 114 YLKEIGRVNLLTADEEVQLALRI-EKGDEVAKQELAEANLRLVVSIAKRYVGRGMQFLDL 172

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  RGF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 173 IQEGNMGLMKAVEKFDYRRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 232

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + ++  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 233 RIQRQLLQDLGREPLPEEIGAEMDMPTEKVRNI---LKIAQ-EPVSLETPIGEEDDSHLG 288

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 289 DFIEDQDATSPA-------DHAAYEMM----------KKQLENVLDTLTDREENVLRLRF 331

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 332 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 366


>gi|227431669|ref|ZP_03913702.1| DNA-directed RNA polymerase sigma subunit RpoD [Leuconostoc
           mesenteroides subsp. cremoris ATCC 19254]
 gi|227352572|gb|EEJ42765.1| DNA-directed RNA polymerase sigma subunit RpoD [Leuconostoc
           mesenteroides subsp. cremoris ATCC 19254]
          Length = 432

 Score =  105 bits (263), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 82/265 (30%), Positives = 135/265 (50%), Gaps = 15/265 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L+  EE  +AKR  E+GD+ A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 162 YLKEIGRVNLLKGNEEIDIAKRI-ENGDVEAKQELAEANLRLVVSIAKRYVGRGMQFLDL 220

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 221 IQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 278

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNS 197
           L R++  L         PE++ A   +++++  +V  +  ++A +  SL   I   D   
Sbjct: 279 LIRIQRQLLQDLGREPLPEEIGA---EIDLTADKVREI-LKIAQEPVSLETPIGEED--D 332

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTL 255
           S   D++    D +     +    +  R  L   +  L  RE  +   R   E+    TL
Sbjct: 333 SHLGDFI---EDNEAVSPADSAAYEMLREQLESVLDTLTDREENVLRLRFGLEDGRTRTL 389

Query: 256 ENLSSEFEVSRERVRQIEARAFKKV 280
           E +   F V+RER+RQIEA+A +K+
Sbjct: 390 EEVGRVFGVTRERIRQIEAKALRKL 414


>gi|149190801|ref|ZP_01869066.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Vibrio shilonii AK1]
 gi|148835363|gb|EDL52335.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Vibrio shilonii AK1]
          Length = 289

 Score =  105 bits (263), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 77/275 (28%), Positives = 145/275 (52%), Gaps = 18/275 (6%)

Query: 17  SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL--- 73
           S+YIH++  I +L  ++EY  A   R  GD +A   L+ S+LRLVVKIA  Y   GL   
Sbjct: 21  SKYIHDVVGIDLLSPEQEYHYATLAR-RGDKAARDVLIESNLRLVVKIARNYTKRGLSNH 79

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            I +++ EGN+GL++A+ KF+PE+GFR +TY++WWI+ +++  ++ +   V++       
Sbjct: 80  TILDLIEEGNLGLIKAIDKFEPEKGFRFSTYAVWWIRESIESSLMNTGRTVRLPV----- 134

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            +   + RL      I  +  +P  V  IA+K   S++++  +   ++G    ++ +++ 
Sbjct: 135 HVIKEINRLSKQTNEIIADLQRPPSVKEIAEKTAKSQAQISDL-IHMSGFIESSSSVDTI 193

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR---LQE 250
           DK   ++Q       +   +        K  +++ +  +S+  P + R     R     +
Sbjct: 194 DK---EFQSLETCKSEAIPEPYDICHNEKLSQSLESVVLSL--PEKYRDIVIHRFGLFGK 248

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             +TL+NL   F +S+ERVRQ++     K+Q  ++
Sbjct: 249 EVLTLDNLGEMFGLSKERVRQLQQEGISKLQNKLK 283


>gi|69249285|ref|ZP_00604924.1| Sigma-70 region 1.1:Sigma-70 region 3:Sigma-70 region 2:Sigma-70
           region 4:Sigma-70 region 1.2 [Enterococcus faecium DO]
 gi|257877975|ref|ZP_05657628.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,230,933]
 gi|257881238|ref|ZP_05660891.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,231,502]
 gi|257884904|ref|ZP_05664557.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,231,501]
 gi|257889826|ref|ZP_05669479.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,231,410]
 gi|258616539|ref|ZP_05714309.1| RNA polymerase sigma factor RpoD [Enterococcus faecium DO]
 gi|260559026|ref|ZP_05831212.1| RNA polymerase sigma-43 factor [Enterococcus faecium C68]
 gi|261207559|ref|ZP_05922244.1| RNA polymerase sigma-43 factor [Enterococcus faecium TC 6]
 gi|289565071|ref|ZP_06445524.1| RNA polymerase sigma factor rpoD [Enterococcus faecium D344SRF]
 gi|293556716|ref|ZP_06675279.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1039]
 gi|293563374|ref|ZP_06677823.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1162]
 gi|293568034|ref|ZP_06679372.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1071]
 gi|294614871|ref|ZP_06694766.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1636]
 gi|294618226|ref|ZP_06697809.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1679]
 gi|314939477|ref|ZP_07846711.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133a04]
 gi|314941108|ref|ZP_07848006.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133C]
 gi|314949892|ref|ZP_07853194.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0082]
 gi|314951693|ref|ZP_07854736.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133A]
 gi|314993960|ref|ZP_07859287.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133B]
 gi|314996911|ref|ZP_07861912.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133a01]
 gi|68194219|gb|EAN08744.1| Sigma-70 region 1.1:Sigma-70 region 3:Sigma-70 region 2:Sigma-70
           region 4:Sigma-70 region 1.2 [Enterococcus faecium DO]
 gi|257812203|gb|EEV40961.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,230,933]
 gi|257816896|gb|EEV44224.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,231,502]
 gi|257820742|gb|EEV47890.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,231,501]
 gi|257826186|gb|EEV52812.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,231,410]
 gi|260074783|gb|EEW63099.1| RNA polymerase sigma-43 factor [Enterococcus faecium C68]
 gi|260077942|gb|EEW65648.1| RNA polymerase sigma-43 factor [Enterococcus faecium TC 6]
 gi|289163078|gb|EFD10925.1| RNA polymerase sigma factor rpoD [Enterococcus faecium D344SRF]
 gi|291589255|gb|EFF21065.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1071]
 gi|291592333|gb|EFF23947.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1636]
 gi|291595506|gb|EFF26816.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1679]
 gi|291601048|gb|EFF31337.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1039]
 gi|291604635|gb|EFF34120.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1162]
 gi|313588970|gb|EFR67815.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133a01]
 gi|313591562|gb|EFR70407.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133B]
 gi|313596157|gb|EFR75002.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133A]
 gi|313600109|gb|EFR78952.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133C]
 gi|313641279|gb|EFS05859.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133a04]
 gi|313643734|gb|EFS08314.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0082]
          Length = 369

 Score =  105 bits (263), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 85/273 (31%), Positives = 133/273 (48%), Gaps = 31/273 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 103 YLKEIGRVSLLTAEEEVALALKI-EEGDQEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 161

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 162 IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 221

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             Q++L  +L R     +   + +L  E+V  I   L +++  V           SL   
Sbjct: 222 RIQRQLLQDLGREPTPEEIGAEMDLPTEKVREI---LKIAQEPV-----------SLETP 267

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   D   S   D++    D +     E    +  +  L   +  L  RE  +   R   
Sbjct: 268 IGEED--DSHLGDFI---EDQEATSPAEHAAYELLKEQLEDVLDTLTDREENVLRLRFGL 322

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
           ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 323 DDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 355


>gi|269792833|ref|YP_003317737.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermanaerovibrio
           acidaminovorans DSM 6589]
 gi|269100468|gb|ACZ19455.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermanaerovibrio
           acidaminovorans DSM 6589]
          Length = 387

 Score =  105 bits (263), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 87/282 (30%), Positives = 137/282 (48%), Gaps = 47/282 (16%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI +IP+L  +EE  LAK   E GD  A  +LV ++LRLVV IA  Y G G+   ++
Sbjct: 121 YLREIGRIPLLSPEEEVELAKGV-EAGDKRAKEKLVEANLRLVVSIAKKYIGRGMLFLDL 179

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I            A+Q R    
Sbjct: 180 IQEGNLGLIRAVEKFDYRKGYKFSTYATWWIRQAITRAI------------ADQARTI-- 225

Query: 139 LRRLKGHLQAITDNNLKPEQVVA-----------IAKKLNVSESEVISMNCRLAGDESLN 187
             R+  H+    +  ++  +V+            IA+++ V+   V  +        SL 
Sbjct: 226 --RIPVHMVETINKLIRISRVLVQRLGREPSAEEIAQEMGVTVDRVEEIQKIAQEPVSLE 283

Query: 188 ALINSSDKNSSQWQDWL------VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
             I   ++  SQ  D+L        D     Q+L         R  L   +  L  RE+ 
Sbjct: 284 TPI--GEEEDSQLGDFLEDKDLPSPDEAAANQIL---------REQLEEMLEDLTDREKE 332

Query: 242 IFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   R   E+    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 333 VLRLRFGLEDGHSHTLEEVGRRFGVTRERIRQIEAKALRKLR 374


>gi|291515538|emb|CBK64748.1| RNA polymerase sigma factor, sigma-70 family [Alistipes shahii WAL
           8301]
          Length = 286

 Score =  105 bits (263), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 78/271 (28%), Positives = 149/271 (54%), Gaps = 16/271 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K  ++  +EE  LA+R ++ GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGKEELITVEEEVELAQRIKK-GDQEALEKLTKANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     +V++    NQ   
Sbjct: 77  PDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL--PLNQVGS 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
              + +     +   +    PE+   +A +L + + E ++   R+AG   S++A     +
Sbjct: 135 LNKINKAFARFEQEHERTPSPEE---LATELELPK-EKVTDTLRVAGRHVSVDAPFADGE 190

Query: 195 KNSSQWQDWLVY-DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE-ARRLQENP 252
            NS    D LV  D    ++ LI     ++    + R++  L  RER I +    +  + 
Sbjct: 191 DNS--LLDVLVNPDSPNADRGLI----NESLSTEVDRALETLTERERDIIKYFFGIGTSE 244

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +TLE +  +F+++RERVRQI+ +A ++++ S
Sbjct: 245 MTLEEIGEKFDLTRERVRQIKEKAIRRLRHS 275


>gi|302554830|ref|ZP_07307172.1| RNA polymerase sigma factor rpoD [Streptomyces viridochromogenes
           DSM 40736]
 gi|302472448|gb|EFL35541.1| RNA polymerase sigma factor rpoD [Streptomyces viridochromogenes
           DSM 40736]
          Length = 481

 Score =  105 bits (263), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 93/301 (30%), Positives = 148/301 (49%), Gaps = 37/301 (12%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++  GE GL R     R +P  E       ++R+R      A   LV  + RLV KIA+G
Sbjct: 211 LLRGGEDGLGRSDRLGRDVPAEEIAALPRGSERWR------AYECLVLHNQRLVWKIALG 264

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y+G GL   ++V  G IGLM+AV+KFD  +GF+ +TY+ WWIK A+   I    +L+++ 
Sbjct: 265 YQGRGLDTEDLVQHGTIGLMRAVRKFDATKGFKFSTYATWWIKQAITRAIADEGTLIRLP 324

Query: 128 TTANQK--RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
              ++K  ++    R+L    +  T +N      VA    L  +E E +    R    +S
Sbjct: 325 AHVHEKVSKVAVAERKLLNEGRPRTVDN------VAYVSGLTFAEVEKVRRISR--STDS 376

Query: 186 LNALINSSDKNSSQWQDWLVYDH--DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           L+ +I     + +   D ++      G + VLI KE +   R+++      L+ RER + 
Sbjct: 377 LDRIIG----DDTALGDLIIGPSRLPGPDVVLIRKEFQARLRHVVEH----LSERERHVL 428

Query: 244 EARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQKP 300
             RR     + P TLE++   F V+RER+RQIE +A  K +  + +         LL +P
Sbjct: 429 -VRRTGLDGDEPDTLEDIGVVFGVTRERIRQIEPKAKAKFEGQLLRH-------GLLPRP 480

Query: 301 R 301
           R
Sbjct: 481 R 481


>gi|194467797|ref|ZP_03073783.1| RNA polymerase, sigma 70 subunit, RpoD family [Lactobacillus
           reuteri 100-23]
 gi|194452650|gb|EDX41548.1| RNA polymerase, sigma 70 subunit, RpoD family [Lactobacillus
           reuteri 100-23]
          Length = 380

 Score =  105 bits (263), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 86/275 (31%), Positives = 132/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LA R  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 114 YLKEIGRVNLLTADEEVQLALRI-EKGDEVAKQELAEANLRLVVSIAKRYVGRGMQFLDL 172

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  RGF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 173 IQEGNMGLMKAVEKFDYRRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 232

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + ++  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 233 RIQRQLLQDLGREPLPEEIGAEMDMPTEKVRNI---LKIAQ-EPVSLETPIGEEDDSHLG 288

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 289 DFIEDQDATSP-------ADHAAYEMM----------KKQLENVLDTLTDREENVLRLRF 331

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 332 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 366


>gi|160902123|ref|YP_001567704.1| RpoD family RNA polymerase sigma factor [Petrotoga mobilis SJ95]
 gi|160359767|gb|ABX31381.1| RNA polymerase, sigma 70 subunit, RpoD family [Petrotoga mobilis
           SJ95]
          Length = 418

 Score =  105 bits (263), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 82/270 (30%), Positives = 133/270 (49%), Gaps = 20/270 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+ +L    E  LA+R  + GD  A   L+ ++LRLV+ IA  Y G GL   ++
Sbjct: 148 YLKEISKVELLSPSRERQLARRA-QKGDQKARDELIKANLRLVISIAKRYTGRGLTFLDL 206

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGL++AV KFD  +GF+ +TY+ WWI+ A+   I      ++I        L   
Sbjct: 207 IQEGNIGLIKAVDKFDWRKGFKFSTYATWWIRQAITRAIADQARTIRIPV-----HLVET 261

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS--SDKN 196
           + R+   ++     N        +A+ L+  E ++  +        SLN+ I+S   D  
Sbjct: 262 INRMNKVIREYLQENGDYPSAQELAEILDKPEDKINEILMSAKDVLSLNSPISSGNGDDE 321

Query: 197 SSQWQDWL---VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQEN 251
            S+  D++       + + Q +I KE        L   +  LN +E  + + R   L   
Sbjct: 322 ESETGDFISTEETTPEEEAQKMIMKER-------LEEVLDTLNSKEALVLKMRYGFLDGK 374

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             TLE +   F V+RER+RQIE +A +K++
Sbjct: 375 QKTLEEVGQFFNVTRERIRQIETKALRKLR 404


>gi|227544906|ref|ZP_03974955.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           reuteri CF48-3A]
 gi|300910067|ref|ZP_07127527.1| RNA polymerase sigma factor rpoD [Lactobacillus reuteri SD2112]
 gi|227185118|gb|EEI65189.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           reuteri CF48-3A]
 gi|300892715|gb|EFK86075.1| RNA polymerase sigma factor rpoD [Lactobacillus reuteri SD2112]
          Length = 380

 Score =  105 bits (262), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 86/275 (31%), Positives = 132/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LA R  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 114 YLKEIGRVNLLTADEEVQLALRI-EKGDEVAKQELAEANLRLVVSIAKRYVGRGMQFLDL 172

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  RGF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 173 IQEGNMGLMKAVEKFDYRRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 232

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + ++  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 233 RIQRQLLQDLGREPLPEEIGAEMDMPTEKVRNI---LKIAQ-EPVSLETPIGEEDDSHLG 288

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 289 DFIEDQDATSPA-------DHAAYEMM----------KKQLENVLDTLTDREENVLRLRF 331

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 332 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 366


>gi|256545301|ref|ZP_05472665.1| RNA polymerase sigma factor RpoD [Anaerococcus vaginalis ATCC
           51170]
 gi|256398982|gb|EEU12595.1| RNA polymerase sigma factor RpoD [Anaerococcus vaginalis ATCC
           51170]
          Length = 614

 Score =  105 bits (262), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 75/247 (30%), Positives = 124/247 (50%), Gaps = 36/247 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  ++LRLVV IA  Y G G+   +++ EGN+GLM+AV K+D  RGF+ +TY+ WW
Sbjct: 378 AKQKLAETNLRLVVSIAKKYVGRGMSFLDLIQEGNMGLMKAVDKYDYNRGFKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGT----TAN-----QKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N     Q++L  +L R   + +      ++ E+V
Sbjct: 438 IRQAITRAIADQARTIRIPVHMVETINKLVRIQRQLVQDLGRDPSNEEIAEQMGIEVEKV 497

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K       E +S+   +  +E             S   D++      ++   I  +
Sbjct: 498 QEIRK----IAQEPVSLETPIGEEE------------DSHLGDFI------EDDTAINPD 535

Query: 220 ERKNR---RNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEA 274
           +  N    R+ L   +S L  RE+R+ + R   +   P TLE +  EF+V+RER+RQIEA
Sbjct: 536 DAANYSMLRDQLNDVLSCLGAREKRVLQLRFGLIDGTPRTLEEVGKEFDVTRERIRQIEA 595

Query: 275 RAFKKVQ 281
           +A +K++
Sbjct: 596 KALRKLK 602


>gi|33864510|ref|NP_896070.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9313]
 gi|33641290|emb|CAE22420.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9313]
          Length = 344

 Score =  105 bits (262), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 85/294 (28%), Positives = 142/294 (48%), Gaps = 37/294 (12%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLA--------------------KRYREHGDLSAAH 51
           G   +  Y+  I ++P+L   EE  LA                    +R++      A  
Sbjct: 53  GTDAIGFYLSSIGRVPLLTAAEEIELAHHVQAMKELLELPEQDQTPRQRHKIRMGKRARD 112

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R+++++LRLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+ 
Sbjct: 113 RMMSANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQ 172

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLK---GHLQAITDNNLKPEQVVAIAKKLNV 168
            M   I  S   +++    ++K     +RR+     H      N L+      +A  + +
Sbjct: 173 GMTRAIDNSARTIRLPIHISEK--LSKMRRISRELSHRFGRQPNRLE------LAHAMGI 224

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              ++  +  + A   SL+A     +  S+  +  L+ D DG E   +E  +R  ++  L
Sbjct: 225 QPQDLEDLIAQSAPCASLDAHARGEEDRSTLGE--LIPDPDGAEP--MEGLDRSIQKEHL 280

Query: 229 TRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
              +S LN RE++I   R     E P+TL  +  +  VSRERVRQ+EA+A  K+
Sbjct: 281 GGWLSQLNEREQKILRLRFGLDGEEPLTLAEIGRQISVSRERVRQLEAKAILKL 334


>gi|325849230|ref|ZP_08170681.1| RNA polymerase sigma factor RpoD [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
 gi|325480230|gb|EGC83297.1| RNA polymerase sigma factor RpoD [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
          Length = 612

 Score =  105 bits (262), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 75/247 (30%), Positives = 124/247 (50%), Gaps = 36/247 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  ++LRLVV IA  Y G G+   +++ EGN+GLM+AV K+D  RGF+ +TY+ WW
Sbjct: 376 AKQKLAETNLRLVVSIAKKYVGRGMSFLDLIQEGNMGLMKAVDKYDYNRGFKFSTYATWW 435

Query: 109 IKAAMQEYILRSWSLVKIGT----TAN-----QKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N     Q++L  +L R   + +      ++ E+V
Sbjct: 436 IRQAITRAIADQARTIRIPVHMVETINKLVRIQRQLVQDLGRDPSNEEIAEQMGIEVEKV 495

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K       E +S+   +  +E             S   D++      ++   I  +
Sbjct: 496 QEIRK----IAQEPVSLETPIGEEE------------DSHLGDFI------EDDTAINPD 533

Query: 220 ERKNR---RNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEA 274
           +  N    R+ L   +S L  RE+R+ + R   +   P TLE +  EF+V+RER+RQIEA
Sbjct: 534 DAANYSMLRDQLNDVLSCLGAREKRVLQLRFGLIDGTPRTLEEVGKEFDVTRERIRQIEA 593

Query: 275 RAFKKVQ 281
           +A +K++
Sbjct: 594 KALRKLK 600


>gi|295110289|emb|CBL24242.1| RNA polymerase, sigma 70 subunit, RpoD [Ruminococcus obeum A2-162]
          Length = 376

 Score =  105 bits (262), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 84/274 (30%), Positives = 136/274 (49%), Gaps = 31/274 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+ +L   EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 110 YLKEIGKVSLLTADEEIELAKRM-EQGDEEAKKRLAEANLRLVVSIAKRYVGRGMLFLDL 168

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-- 132
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 169 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 228

Query: 133 ---KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
              ++L   L R     +   +  +  E+V  I   L +S+ E +S+   +  +E  +  
Sbjct: 229 RVSRQLLQELGREPTPEEIAEEMKMPVERVREI---LKISQ-EPVSLETPIGEEEDSHLG 284

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
               D N     D   +        L+        +  L   +  L  RE+++   R   
Sbjct: 285 DFIQDDNVPVPADAAAF-------TLL--------KEQLIEVLGTLTEREQKVLRLRFGL 329

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 330 DDGRARTLEEVGKEFNVTRERIRQIEAKALRKLR 363


>gi|225018167|ref|ZP_03707359.1| hypothetical protein CLOSTMETH_02104 [Clostridium methylpentosum
           DSM 5476]
 gi|224949164|gb|EEG30373.1| hypothetical protein CLOSTMETH_02104 [Clostridium methylpentosum
           DSM 5476]
          Length = 372

 Score =  105 bits (262), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 81/270 (30%), Positives = 132/270 (48%), Gaps = 23/270 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  +EE  LA++    GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 106 YLKEIGKVPLLTAEEEIDLAQKM-SAGDPYARKRLSEANLRLVVSIAKRYVGRGMQFLDL 164

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-K 133
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N+ K
Sbjct: 165 IQEGNLGLIKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKVK 224

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
           ++   L    GH  +  +   + +  V   +++     E +S+   +  +E         
Sbjct: 225 KVSSQLLHKNGHEASAEEIAEELDMPVDKVREIMRVSQEPVSLETPIGEEE--------- 275

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-- 251
               S   D++            E       R  L   +  L  RE ++   R   E+  
Sbjct: 276 ---DSHLSDFIPD---DDAPAPAEAASHTLLREQLGDVLGTLTEREEKVLRLRFGLEDGR 329

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 330 SRTLEEVGKEFNVTRERIRQIEAKALRKLR 359


>gi|260436326|ref|ZP_05790296.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 8109]
 gi|260414200|gb|EEX07496.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 8109]
          Length = 308

 Score =  105 bits (262), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 84/282 (29%), Positives = 146/282 (51%), Gaps = 22/282 (7%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRG 70
           EI L+ ++  ++++  L ++E   L  R+R    +   A  R++ ++LRLVV +A  Y+ 
Sbjct: 39  EIELAHHVQAMKQLQELPEEE---LTSRHRHKIRMGKRARDRMMAANLRLVVSVAKKYQN 95

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+  M   I  S   +++    
Sbjct: 96  QGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIRLPIHI 155

Query: 131 NQKRLFFNLRRLK---GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
           ++K     +RR+     H      N L+      +A  + +   E+  +  + A   SL+
Sbjct: 156 SEK--LSKMRRISRELSHRFGRQPNRLE------LASAMGIEPRELEDLISQSAPCASLD 207

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR- 246
           A     +  S+  +  L+ D +G+E   +E  +R  ++  L   +S LN RE++I + R 
Sbjct: 208 AHARGEEDRSTLGE--LIPDPNGEEP--MEGMDRSIQKEHLGGWLSQLNEREQKILKLRF 263

Query: 247 -RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
               E P+TL  +  +  VSRERVRQ+EA+A  K++     Q
Sbjct: 264 GLGGEEPLTLAEIGRQINVSRERVRQLEAKAILKLRAMTNHQ 305


>gi|284042443|ref|YP_003392783.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Conexibacter
           woesei DSM 14684]
 gi|283946664|gb|ADB49408.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Conexibacter
           woesei DSM 14684]
          Length = 285

 Score =  105 bits (262), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 86/278 (30%), Positives = 134/278 (48%), Gaps = 36/278 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L   + E R  P+L   EE  LA+R  E GDLSA  R+V S+LRLV+ IA  Y+G GL +
Sbjct: 18  LQLLMREARNWPLLTPAEEIELARRI-ERGDLSAKERMVNSNLRLVMSIARHYQGQGLGM 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK-R 134
            ++V EG +GL++AV+KFD  +GFR +TY+  WI+ ++Q  +  +   +++     Q+ R
Sbjct: 77  GDLVQEGTLGLIRAVEKFDWRKGFRFSTYATLWIRQSIQRGLENTGRTIRLPVHVGQRAR 136

Query: 135 LFFNLRR--LKGHLQAITDNN------LKPEQVVAIAKKLNVSESEVISMNCRLA--GDE 184
               +RR     H +  TD        L  EQV+   +    ++ E  S++  +   GD 
Sbjct: 137 KVARIRRELTAKHGRDATDEEIAEAARLPVEQVIEAGR----ADREPTSLDAPVGEDGDT 192

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           +L ALI    K  +   D  V D                R   + R++  L   E+ +  
Sbjct: 193 ALGALI----KTDTPEPDEEVAD--------------TLRHETVQRAIDDLPDNEKTVIH 234

Query: 245 AR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            R     E P TL  +     VS  R R+IE +A +++
Sbjct: 235 LRFGTAGEPPQTLTQIGRRLGVSSSRAREIEEQALRRL 272


>gi|255972833|ref|ZP_05423419.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis T1]
 gi|255963851|gb|EET96327.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis T1]
          Length = 368

 Score =  105 bits (262), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 85/275 (30%), Positives = 133/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGRVQLLTAAEEVELALKI-EEGDQEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 161 IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 220

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 221 RIQRQLLQDLGREPTPEEIGAEMDLPTEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 276

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S         +H   E +          +  L   +  L  RE  +   R 
Sbjct: 277 DFIEDQDATSPA-------EHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 319

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 320 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 354


>gi|149377551|ref|ZP_01895291.1| group 2 sigma 70-type sigma factor F [Marinobacter algicola DG893]
 gi|149358164|gb|EDM46646.1| group 2 sigma 70-type sigma factor F [Marinobacter algicola DG893]
          Length = 332

 Score =  105 bits (262), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 78/246 (31%), Positives = 126/246 (51%), Gaps = 24/246 (9%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           H   S+  RL+ S+LRL V IA  Y   G+P+S+V+ + N+GL++AV++FDP +GFR +T
Sbjct: 91  HLATSSRQRLIRSNLRLAVHIARRYANRGIPMSDVIQDANVGLIKAVERFDPTKGFRFST 150

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI   ++  + R   LV        + +   +R L+    A+     +      +A
Sbjct: 151 YAYWWISEEVKRCMKRGTRLVH-----TPENVVDEIRLLQRTSLALYQTLGRTPSQTELA 205

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKN-----SSQWQDWLVYDHDGQEQVLIEK 218
           +++ VS S +  +   LA  E    L  S++ N     S    D    DHD  +      
Sbjct: 206 REIEVSPSRIGELRA-LASMEVSVDLPVSTEGNITLGESLSADDQSAPDHDMAQ------ 258

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQEN---PVTLENLSSEFEVSRERVRQIEAR 275
              ++R+  L   ++ L+ RE+ +  ARR   +   P TL+ +S +  +SRERVRQIE  
Sbjct: 259 ---RDRKRTLATLLAELSSREKDVL-ARRYGLDLPEPETLQVISDDLGISRERVRQIEKS 314

Query: 276 AFKKVQ 281
           A KK+Q
Sbjct: 315 ALKKLQ 320


>gi|29376087|ref|NP_815241.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis V583]
 gi|227518714|ref|ZP_03948763.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0104]
 gi|227553323|ref|ZP_03983372.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis HH22]
 gi|229545861|ref|ZP_04434586.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX1322]
 gi|229550053|ref|ZP_04438778.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis ATCC 29200]
 gi|255975889|ref|ZP_05426475.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis T2]
 gi|256619027|ref|ZP_05475873.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis ATCC 4200]
 gi|256762453|ref|ZP_05503033.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis T3]
 gi|256853088|ref|ZP_05558458.1| RNA polymerase sigma-43 factor [Enterococcus faecalis T8]
 gi|256958944|ref|ZP_05563115.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis DS5]
 gi|256961963|ref|ZP_05566134.1| sigma 42 [Enterococcus faecalis Merz96]
 gi|256965161|ref|ZP_05569332.1| sigma 42 [Enterococcus faecalis HIP11704]
 gi|257078975|ref|ZP_05573336.1| sigma 42 [Enterococcus faecalis JH1]
 gi|257082587|ref|ZP_05576948.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis E1Sol]
 gi|257085220|ref|ZP_05579581.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis Fly1]
 gi|257086781|ref|ZP_05581142.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis D6]
 gi|257089848|ref|ZP_05584209.1| RNA polymerase sigma factor rpoD [Enterococcus faecalis CH188]
 gi|257416057|ref|ZP_05593051.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis AR01/DG]
 gi|257419260|ref|ZP_05596254.1| RNA polymerase sigma factor rpoD [Enterococcus faecalis T11]
 gi|257422656|ref|ZP_05599646.1| RNA polymerase sigma-43 factor [Enterococcus faecalis X98]
 gi|293383032|ref|ZP_06628950.1| RNA polymerase sigma-43 factor [Enterococcus faecalis R712]
 gi|293389479|ref|ZP_06633936.1| RNA polymerase sigma-43 factor [Enterococcus faecalis S613]
 gi|294779115|ref|ZP_06744526.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis PC1.1]
 gi|300860473|ref|ZP_07106560.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TUSoD Ef11]
 gi|307271055|ref|ZP_07552338.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX4248]
 gi|307273262|ref|ZP_07554508.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0855]
 gi|307274998|ref|ZP_07556161.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX2134]
 gi|307278111|ref|ZP_07559195.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0860]
 gi|307289068|ref|ZP_07569024.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0109]
 gi|307292033|ref|ZP_07571902.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0411]
 gi|312900723|ref|ZP_07760020.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0470]
 gi|312903270|ref|ZP_07762450.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0635]
 gi|312907497|ref|ZP_07766488.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis DAPTO 512]
 gi|312910115|ref|ZP_07768962.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis DAPTO 516]
 gi|312951455|ref|ZP_07770352.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0102]
 gi|30179886|sp|P52329|RPOD_ENTFA RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-42
 gi|29343549|gb|AAO81311.1| RNA polymerase sigma-43 factor [Enterococcus faecalis V583]
 gi|227073834|gb|EEI11797.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0104]
 gi|227177552|gb|EEI58524.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis HH22]
 gi|229304757|gb|EEN70753.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis ATCC 29200]
 gi|229309016|gb|EEN75003.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX1322]
 gi|255968761|gb|EET99383.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis T2]
 gi|256598554|gb|EEU17730.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis ATCC 4200]
 gi|256683704|gb|EEU23399.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis T3]
 gi|256711547|gb|EEU26585.1| RNA polymerase sigma-43 factor [Enterococcus faecalis T8]
 gi|256949440|gb|EEU66072.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis DS5]
 gi|256952459|gb|EEU69091.1| sigma 42 [Enterococcus faecalis Merz96]
 gi|256955657|gb|EEU72289.1| sigma 42 [Enterococcus faecalis HIP11704]
 gi|256987005|gb|EEU74307.1| sigma 42 [Enterococcus faecalis JH1]
 gi|256990617|gb|EEU77919.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis E1Sol]
 gi|256993250|gb|EEU80552.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis Fly1]
 gi|256994811|gb|EEU82113.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis D6]
 gi|256998660|gb|EEU85180.1| RNA polymerase sigma factor rpoD [Enterococcus faecalis CH188]
 gi|257157885|gb|EEU87845.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis ARO1/DG]
 gi|257161088|gb|EEU91048.1| RNA polymerase sigma factor rpoD [Enterococcus faecalis T11]
 gi|257164480|gb|EEU94440.1| RNA polymerase sigma-43 factor [Enterococcus faecalis X98]
 gi|291079697|gb|EFE17061.1| RNA polymerase sigma-43 factor [Enterococcus faecalis R712]
 gi|291081096|gb|EFE18059.1| RNA polymerase sigma-43 factor [Enterococcus faecalis S613]
 gi|294453840|gb|EFG22231.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis PC1.1]
 gi|295112959|emb|CBL31596.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Enterococcus sp. 7L76]
 gi|300849512|gb|EFK77262.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TUSoD Ef11]
 gi|306497031|gb|EFM66579.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0411]
 gi|306499777|gb|EFM69138.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0109]
 gi|306505508|gb|EFM74694.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0860]
 gi|306508446|gb|EFM77553.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX2134]
 gi|306510247|gb|EFM79271.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0855]
 gi|306512553|gb|EFM81202.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX4248]
 gi|310626525|gb|EFQ09808.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis DAPTO 512]
 gi|310630611|gb|EFQ13894.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0102]
 gi|310633146|gb|EFQ16429.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0635]
 gi|311289388|gb|EFQ67944.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis DAPTO 516]
 gi|311292204|gb|EFQ70760.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0470]
 gi|315027303|gb|EFT39235.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX2137]
 gi|315033932|gb|EFT45864.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0017]
 gi|315036941|gb|EFT48873.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0027]
 gi|315144454|gb|EFT88470.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX2141]
 gi|315147227|gb|EFT91243.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX4244]
 gi|315150574|gb|EFT94590.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0012]
 gi|315152521|gb|EFT96537.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0031]
 gi|315155799|gb|EFT99815.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0043]
 gi|315158034|gb|EFU02051.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0312]
 gi|315160483|gb|EFU04500.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0645]
 gi|315163977|gb|EFU07994.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX1302]
 gi|315169073|gb|EFU13090.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX1341]
 gi|315169690|gb|EFU13707.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX1342]
 gi|315172348|gb|EFU16365.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX1346]
 gi|315575904|gb|EFU88095.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0309B]
 gi|315577570|gb|EFU89761.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0630]
 gi|315580556|gb|EFU92747.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0309A]
 gi|327535095|gb|AEA93929.1| RNA polymerase sigma factor rpoD [Enterococcus faecalis OG1RF]
 gi|329571347|gb|EGG53034.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX1467]
          Length = 368

 Score =  105 bits (262), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 85/275 (30%), Positives = 133/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGRVQLLTAAEEVELALKI-EEGDQEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 161 IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 220

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 221 RIQRQLLQDLGREPTPEEIGAEMDLPTEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 276

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S         +H   E +          +  L   +  L  RE  +   R 
Sbjct: 277 DFIEDQDATSP-------AEHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 319

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 320 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 354


>gi|312874241|ref|ZP_07734275.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LEAF 2052A-d]
 gi|311090311|gb|EFQ48721.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LEAF 2052A-d]
          Length = 382

 Score =  105 bits (262), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 86/279 (30%), Positives = 133/279 (47%), Gaps = 43/279 (15%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   +E  LAKR  E+ D  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 116 YLKEIGRVPLLNADQEIDLAKRI-ENNDDDAKQELAEANLRLVVSIAKRYVGRGMSFLDL 174

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 175 IQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 234

Query: 132 --QKRLFFNLRR------LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-- 181
             Q++L  +L R      +   +   TD   K  +++ IA+       E +S+   +   
Sbjct: 235 RIQRQLLQDLGREPTPEEIGAEMDMSTD---KVREILKIAQ-------EPVSLETPIGEE 284

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
            D  L   I   D  S +         +  E+VL    +R+   N+L     + + R R 
Sbjct: 285 DDSHLGDFIEDKDATSPEQHASYELLKEQLEEVLDTLTDREE--NVLRLRFGLNDGRTR- 341

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                       TLE +   F V+RER+RQIEA+A +K+
Sbjct: 342 ------------TLEEVGRVFGVTRERIRQIEAKALRKL 368


>gi|323480687|gb|ADX80126.1| RNA polymerase sigma factor rpoD (Sigma-42) [Enterococcus faecalis
           62]
          Length = 356

 Score =  105 bits (262), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 85/275 (30%), Positives = 133/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 90  YLKEIGRVQLLTAAEEVELALKI-EEGDQEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 148

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 149 IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 208

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 209 RIQRQLLQDLGREPTPEEIGAEMDLPTEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 264

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S         +H   E +          +  L   +  L  RE  +   R 
Sbjct: 265 DFIEDQDATSP-------AEHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 307

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 308 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 342


>gi|281420881|ref|ZP_06251880.1| RNA polymerase sigma-70 factor [Prevotella copri DSM 18205]
 gi|281405173|gb|EFB35853.1| RNA polymerase sigma-70 factor [Prevotella copri DSM 18205]
          Length = 287

 Score =  105 bits (262), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 78/286 (27%), Positives = 139/286 (48%), Gaps = 33/286 (11%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           SI       L +Y+ +I    +L   EE  LA+R R+ GD  A  RL  ++LR VV +A 
Sbjct: 9   SITNRASASLEKYLQDIAHEELLSTDEEVELAQRIRK-GDRRALERLTKANLRFVVSVAK 67

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK- 125
            Y+  G+ + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + I     LV+ 
Sbjct: 68  QYQNQGISLPDLINEGNVGLIKAAQKFDETRGFKFISYAVWWIRQSILQAIAEQSRLVRL 127

Query: 126 ----IGTTANQKRLFFNLRR---LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
               +G+     R      +    K  +  I D    PE  +  A K   S S  +S++ 
Sbjct: 128 PLNQVGSVNKINREMSKFEQEFERKPSVDEIADRIDLPEDKIEDAMKA-TSTSRHLSVDA 186

Query: 179 RLAGDES---LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
             + DE    L+ + NS D    + Q                    ++ R  + R +  L
Sbjct: 187 PFSDDEDGSMLDLMANSDDPTDKELQ-------------------TESLRAEIERLLKTL 227

Query: 236 NPRERRIFEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++++I  A      P +TLE + +++ ++RERVRQI+ +  +++
Sbjct: 228 PDKDQKIIAAFYGIGTPELTLEEIGTKYHLTRERVRQIKEKTIRRL 273


>gi|212697198|ref|ZP_03305326.1| hypothetical protein ANHYDRO_01765 [Anaerococcus hydrogenalis DSM
           7454]
 gi|212675973|gb|EEB35580.1| hypothetical protein ANHYDRO_01765 [Anaerococcus hydrogenalis DSM
           7454]
          Length = 617

 Score =  105 bits (262), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 75/247 (30%), Positives = 124/247 (50%), Gaps = 36/247 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  ++LRLVV IA  Y G G+   +++ EGN+GLM+AV K+D  RGF+ +TY+ WW
Sbjct: 381 AKQKLAETNLRLVVSIAKKYVGRGMSFLDLIQEGNMGLMKAVDKYDYNRGFKFSTYATWW 440

Query: 109 IKAAMQEYILRSWSLVKIGT----TAN-----QKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N     Q++L  +L R   + +      ++ E+V
Sbjct: 441 IRQAITRAIADQARTIRIPVHMVETINKLVRIQRQLVQDLGRDPSNEEIAEQMGIEVEKV 500

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K       E +S+   +  +E             S   D++      ++   I  +
Sbjct: 501 QEIRK----IAQEPVSLETPIGEEE------------DSHLGDFI------EDDTAINPD 538

Query: 220 ERKNR---RNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEA 274
           +  N    R+ L   +S L  RE+R+ + R   +   P TLE +  EF+V+RER+RQIEA
Sbjct: 539 DAANYSMLRDQLNDVLSCLGAREKRVLQLRFGLIDGTPRTLEEVGKEFDVTRERIRQIEA 598

Query: 275 RAFKKVQ 281
           +A +K++
Sbjct: 599 KALRKLK 605


>gi|153813734|ref|ZP_01966402.1| hypothetical protein RUMOBE_04167 [Ruminococcus obeum ATCC 29174]
 gi|149830174|gb|EDM85267.1| hypothetical protein RUMOBE_04167 [Ruminococcus obeum ATCC 29174]
          Length = 330

 Score =  105 bits (262), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 80/270 (29%), Positives = 132/270 (48%), Gaps = 23/270 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+ +L   EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 64  YLKEIGKVSLLTADEEIELAKRM-EQGDEEAKKRLAEANLRLVVSIAKRYVGRGMLFLDL 122

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 123 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 180

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L         PE++    K       E++ ++      E ++      ++  S
Sbjct: 181 LIRVSRQLLQELGREPTPEEIAEEMKMPVDRVREILKIS-----QEPVSLETPIGEEEDS 235

Query: 199 QWQDWLVYDH-----DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-- 251
              D++  D+     D     L+        +  L   +  L  RE+++   R   ++  
Sbjct: 236 HLGDFIQDDNVPVPADAAAFTLL--------KEQLIEVLGTLTEREQKVLRLRFGLDDGR 287

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 288 ARTLEEVGKEFNVTRERIRQIEAKALRKLR 317


>gi|300087894|ref|YP_003758416.1| RNA polymerase sigma 70 subunit RpoD subfamily [Dehalogenimonas
           lykanthroporepellens BL-DC-9]
 gi|299527627|gb|ADJ26095.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dehalogenimonas
           lykanthroporepellens BL-DC-9]
          Length = 502

 Score =  105 bits (262), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 79/243 (32%), Positives = 125/243 (51%), Gaps = 30/243 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV +A  + G G+P+ +++ EGNIGL++AV+KFD  RGF+ +TY+ WW
Sbjct: 265 AERHLIQANLRLVVSVAKKHIGRGMPLLDLIQEGNIGLIRAVEKFDFHRGFKFSTYATWW 324

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     + +   L R     +   +  L PE+V
Sbjct: 325 IRQAITRAIADQARTIRIPVHMVETINKLLSISRSMSQKLGREPTPDEIAAEMELPPEKV 384

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IAK   VS+  V S+   +  +E  +      D+N+    D          Q+L E+ 
Sbjct: 385 REIAK---VSQLPV-SLESPIGEEEDSHLGDFIEDQNALPPPDA------ASRQLLKEQ- 433

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
                   +   +  L PRERR+ + R   E+    TLE +  EF V+RER+RQIEA+A 
Sbjct: 434 --------IDNVLDSLTPRERRVLQLRFGLEDGRSRTLEEVGKEFNVTRERIRQIEAKAL 485

Query: 278 KKV 280
           +K+
Sbjct: 486 RKL 488


>gi|164688461|ref|ZP_02212489.1| hypothetical protein CLOBAR_02106 [Clostridium bartlettii DSM
           16795]
 gi|164602874|gb|EDQ96339.1| hypothetical protein CLOBAR_02106 [Clostridium bartlettii DSM
           16795]
          Length = 306

 Score =  105 bits (262), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 88/287 (30%), Positives = 143/287 (49%), Gaps = 31/287 (10%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           N + +VN +  +  Y+ EI KIP+L +QEE  +AKR  E GD  A   LV S+LRLVV I
Sbjct: 23  NSNNLVNLDDSMKIYLKEIGKIPLLSRQEELDIAKRICE-GDEVAKKILVESNLRLVVSI 81

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y    + + +++ EG +GL++A +KFD  +GF+ +TY+ WWIK  +   I      +
Sbjct: 82  ARKYARKEMAMLDLIQEGTLGLIRAAEKFDYTKGFKFSTYATWWIKQGITRAIADQSRTI 141

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           ++     +K     +  +   L        KPE+   IAK+++V   +V+ +       +
Sbjct: 142 RVPVHMVEK--INKVSTISSQLAKELGREPKPEE---IAKRMHVPVEKVVQVIRISQRPQ 196

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS---------MSVL 235
           S+ + I   D                 EQV+ +KE   +   ++TRS         +  L
Sbjct: 197 SIESTIGQEDDTE-------------LEQVIPDKEAH-SPEEIVTRSLLKDQIEYVLDTL 242

Query: 236 NPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + RE+ + + R  L +    TLE +   F V+RER RQIE +A +K+
Sbjct: 243 SEREKGVIKLRFGLGDGEKKTLEEVGRAFNVTRERARQIEKKALRKL 289


>gi|40353297|gb|AAR84412.1| essential primary sigma 70 factor [Frankia sp. EaI-12]
          Length = 409

 Score =  105 bits (262), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 91/310 (29%), Positives = 148/310 (47%), Gaps = 63/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHG--------------------DLSAAHR------ 52
           Y+ EI K+P+L  +E+  LAKR  E G                    DL A  R      
Sbjct: 115 YLKEIGKVPLLTAEEQVDLAKRI-EAGLFASDKLAVATKKTSPQMRRDLEAIERDGQIAK 173

Query: 53  --LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
             LV ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+
Sbjct: 174 RKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIR 233

Query: 111 AAMQEYILRSWSLVKIGT----TAN-----QKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
            A+   I      ++I      T N     Q++L  +L R     +   + +L P++V  
Sbjct: 234 QAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPSPEEIAKEMDLTPDKVRE 293

Query: 162 IAKKLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           I   L VS+ E +S+   +  +E   L   I   D          V   D    +L++++
Sbjct: 294 I---LKVSQ-EPVSLETPIGEEEDSHLGDFIEDCDA---------VVPVDAASFILLQEQ 340

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAF 277
                   L   +  L+ RE+++ + R      +P TLE +  EF V+RER+RQIE++  
Sbjct: 341 --------LDSVLHTLSDREKKVIQLRFGLTDGHPRTLEEVGREFGVTRERIRQIESKTL 392

Query: 278 KKVQESIQKQ 287
            K++   + Q
Sbjct: 393 SKLRHPSRSQ 402


>gi|86130344|ref|ZP_01048944.1| RNA polymerase sigma factor RpoD [Dokdonia donghaensis MED134]
 gi|332293359|ref|YP_004431968.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Krokinobacter
           diaphorus 4H-3-7-5]
 gi|85819019|gb|EAQ40178.1| RNA polymerase sigma factor RpoD [Dokdonia donghaensis MED134]
 gi|332171445|gb|AEE20700.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Krokinobacter
           diaphorus 4H-3-7-5]
          Length = 288

 Score =  105 bits (261), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 81/285 (28%), Positives = 148/285 (51%), Gaps = 32/285 (11%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+ ++ KI ++  +EE  LA+R  + GD  A   L  ++LR V+ +A  Y+  GL +
Sbjct: 18  LNNYLQDVSKIDLITAEEEVELAQRI-QKGDERALDALTRANLRFVISVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           S++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + I      V++    N+   
Sbjct: 77  SDLINEGNVGLVKAAKRFDETRGFKFISYAVWWIRQSILQAIAEHARTVRL--PLNKIGE 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRLAGDES 185
              + +   +LQ + +   KP     IAK L++SE +V          +SM+   A  E+
Sbjct: 135 ISKINKAMVYLQQVHER--KPTS-GEIAKYLDISEEKVKISLKNVSRSLSMDAPFAEGEN 191

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
            N L +    + S   D  +     QE + IE          + R++  L  +E  +   
Sbjct: 192 DNNLYDVLSSSESPRPDRELM----QESLSIE----------INRALDTLTEKEAEVVRL 237

Query: 246 RR-LQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
              L   P +TL+ +   F++SRERVRQI  +A K+++ + + ++
Sbjct: 238 NYGLGNQPAMTLQEIGDIFDLSRERVRQIREKAIKRLRHTSKSKI 282


>gi|269925873|ref|YP_003322496.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
 gi|269789533|gb|ACZ41674.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
          Length = 326

 Score =  105 bits (261), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 87/306 (28%), Positives = 140/306 (45%), Gaps = 54/306 (17%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE--------HGDLS-------------- 48
             E  +S Y+ +I  IP+L   EE  LAK   +        H DLS              
Sbjct: 29  GSEDSVSVYLRDIGAIPLLTPMEEIALAKAIEKGRQATRKLHQDLSPEEREAALRDKERG 88

Query: 49  --AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  R++  +LRLVV IA  Y G GLP+S+++ EGN+GLM+A  KFD  RG+R +TY+ 
Sbjct: 89  EMARRRMIECNLRLVVSIARRYAGRGLPLSDLIEEGNLGLMRAADKFDYRRGYRFSTYAT 148

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +     +V++     +  L  N+ ++   L          E+   IA +L
Sbjct: 149 WWIRQAVTRALASQSRVVRLPVHVTE--LMHNITKVSHRLSQELGREPTSEE---IAAEL 203

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           N++              E +  ++ +S    S  Q +   D DG  + +IE    ++  +
Sbjct: 204 NITP-------------ERVREVVKASQYPMSLEQPY-GEDGDGTVEEIIEDPNIESPAD 249

Query: 227 MLTRS---------MSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
            ++R          +  L  RER++ + R      +  TLE +     V+RER+RQIE  
Sbjct: 250 QVSRDILREQILALLDDLTDRERQVLDLRYGLTGNHSYTLEEVGKVLGVTRERIRQIEKE 309

Query: 276 AFKKVQ 281
           A  K++
Sbjct: 310 ALSKLR 315


>gi|33866957|ref|NP_898516.1| type II alternative RNA polymerase sigma factor [Synechococcus sp.
           WH 8102]
 gi|33639558|emb|CAE08942.1| Possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 8102]
          Length = 467

 Score =  105 bits (261), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 74/238 (31%), Positives = 117/238 (49%), Gaps = 17/238 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLVV +A  Y+  G+ + ++V EG +GL +AV+KFDP RGFR +TY+ WW
Sbjct: 227 AKDHMIQANLRLVVAVAKKYQQRGMELLDLVQEGTLGLERAVEKFDPTRGFRFSTYAYWW 286

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  M   I      +++     +K     L R+K   Q I  N  +   +  +A+ L +
Sbjct: 287 IRQGMTRAIATQSRTIRLPVHVTEK-----LNRIKRAQQEIATNEGRIASIADLARALKL 341

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SE  V     R+    SL+  +       +Q  D +       EQ L   E   +  ++L
Sbjct: 342 SEDTVRQTLARVPRSVSLDTRVGRD--QDTQLGDLIEDGKATPEQTLTHDELHNDLEHLL 399

Query: 229 ----TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
               +R  +VL    RR F      + P TL  +    ++SRERVRQIE RA  K+++
Sbjct: 400 DELTSREAAVL----RRRFGLE--DDTPQTLAQIGEALKLSRERVRQIETRALLKLRQ 451


>gi|292491540|ref|YP_003526979.1| RNA polymerase sigma factor, sigma-70 family [Nitrosococcus
           halophilus Nc4]
 gi|291580135|gb|ADE14592.1| RNA polymerase sigma factor, sigma-70 family [Nitrosococcus
           halophilus Nc4]
          Length = 311

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 77/271 (28%), Positives = 138/271 (50%), Gaps = 14/271 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ +  K P+L  +EE   A R  + GD  A  R++ S+LR+V+K+A  +   GLP+ ++
Sbjct: 42  YMRDAGKAPLLSAEEEKHYA-RLAQQGDRKARDRMIESNLRMVIKMATRHVNRGLPLMDL 100

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL+ AV+KFDPE GFR +TY+ WWI+ A++  ++     V+I        +   
Sbjct: 101 IEEGNLGLIHAVEKFDPELGFRFSTYASWWIEQAIERALMNQVRTVRIPV-----HVLKT 155

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           +RR +   + +   +    ++  IAK LN    ++         + SLN  +  S+ N  
Sbjct: 156 IRRYQREAKRLGQTHNTEPRLEEIAKALNEPLEKIQRYLSFQIPETSLNDPL--SEDNED 213

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D L+ D      +L E     ++   +   +S L  R++ + + R   +     TLE
Sbjct: 214 CLAD-LLPDERNNPAILWEI---FDKNITINHQLSQLTDRQQEVLKRRYGLDGYEATTLE 269

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +     ++RERVRQI+  A K+++  ++ +
Sbjct: 270 EVGQTIGITRERVRQIQQTAIKRLRAIVESE 300


>gi|116074180|ref|ZP_01471442.1| Possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9916]
 gi|116069485|gb|EAU75237.1| Possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9916]
          Length = 364

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 79/248 (31%), Positives = 120/248 (48%), Gaps = 15/248 (6%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L KR RE     A  R++ ++LRLVV +A  Y+  GL + ++V EG +GL +AV+KFDP 
Sbjct: 114 LQKRLRE--GRRARDRMIQANLRLVVTVAKKYQQRGLELLDLVQEGTLGLERAVEKFDPT 171

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RGFR +TY+ WWI+  +   I      +++     +K     L R+K   Q I  N  + 
Sbjct: 172 RGFRFSTYAYWWIRQGITRAIATQSRTIRLPVHVTEK-----LNRIKKVQQEIATNEGRI 226

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
             +  +++ L +SE  V     R+    SL   +       +Q  D L   H   EQ L 
Sbjct: 227 ASISDLSRALGISEETVRLTLMRVPRSVSLETRVGKD--QDTQLGDLLEDCHATPEQTLT 284

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEA 274
           +     +   +L      L  RE  +   R   E+  P+TL  +     +SRERVRQIE 
Sbjct: 285 KNSLHSDLEELL----GELTAREAEVIRRRFGLEDDTPLTLAEIGETMGLSRERVRQIET 340

Query: 275 RAFKKVQE 282
           RA  K+++
Sbjct: 341 RALLKLRQ 348


>gi|108805110|ref|YP_645047.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108766353|gb|ABG05235.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 366

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 86/281 (30%), Positives = 137/281 (48%), Gaps = 33/281 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   +E  LAK     G   +  +LV ++LRLVV IA  YR  G+   ++
Sbjct: 100 YLAEIGRVPLLTHADEIRLAKAI-SRGCKRSKDKLVEANLRLVVSIAKKYRNRGVSFLDL 158

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK--RLF 136
           + EGNIGL++A +KFD  +GF+ +TY+ WWI+ A+   I      ++I     +K  +  
Sbjct: 159 IQEGNIGLIRAAEKFDYRKGFKFSTYATWWIRQAITRAIADKGRTIRIPVHMVEKVNKYH 218

Query: 137 FNLRRLKGHL-QAITDNNLKPEQVVAIAKKLNVSE--SEVISMNCRLAGDESLNALINSS 193
              RR+   L +  TD  +  E  V + + L + E     IS+   +  DE         
Sbjct: 219 RTQRRMTQALGREPTDEEVAEELGVPVEEVLRLQEISQRSISLETPVGDDE--------- 269

Query: 194 DKNSSQWQDWL-----VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-- 246
              SS   D+L     V   D   + L+        +  L  ++  L  RER+I E R  
Sbjct: 270 ---SSSLGDFLEDASAVTPTDAVSESLL--------KLHLREALDELPERERQIIEMRFG 318

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              + P TLE +  EF+++RERVRQI+ +    ++E  + Q
Sbjct: 319 MKDDRPRTLEEVGREFDITRERVRQIQMKTLNLLREQRRTQ 359


>gi|218282286|ref|ZP_03488585.1| hypothetical protein EUBIFOR_01167 [Eubacterium biforme DSM 3989]
 gi|218216721|gb|EEC90259.1| hypothetical protein EUBIFOR_01167 [Eubacterium biforme DSM 3989]
          Length = 409

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 88/299 (29%), Positives = 146/299 (48%), Gaps = 54/299 (18%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYRE---------HGDLS----------------AAHRL 53
           Y+ EI +IP+L+ +EE ++A++ +E         + DLS                A   L
Sbjct: 116 YLKEIGQIPLLDPKEEPIIARQIQEGEQAKEDIKNPDLSEEEKKKLAKIIADGEEAKQTL 175

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           ++S+LRLVV IA  Y G G+   +++ EGN GL++AV+KFD  +GF+ +TY+ WWI+ ++
Sbjct: 176 ISSNLRLVVSIAKKYVGRGMLFLDLIQEGNCGLIKAVEKFDYTKGFKFSTYATWWIRQSI 235

Query: 114 QEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              I      ++I      T N+      L R++  L      +  PE+   IA+K+   
Sbjct: 236 TRAIADQARTIRIPVHMVETINK------LTRIQRQLVQDLGRDPMPEE---IAEKMENI 286

Query: 170 ESEVISMNCRLAGDE-SLNALINSSDK----NSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            +E +    ++A D  SL   I   D     +  + +D L  D     Q+L         
Sbjct: 287 SAEKVREIQKIALDPVSLETPIGEEDDSHLGDFIEDKDTLSPDDYTNNQLL--------- 337

Query: 225 RNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++ +   +  L  RE ++   R   L     TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 338 KDEINAVLQGLTEREEKVLRLRFGLLDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLK 396


>gi|154249128|ref|YP_001409953.1| RpoD family RNA polymerase sigma factor [Fervidobacterium nodosum
           Rt17-B1]
 gi|154153064|gb|ABS60296.1| RNA polymerase, sigma 70 subunit, RpoD family [Fervidobacterium
           nodosum Rt17-B1]
          Length = 372

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 84/275 (30%), Positives = 139/275 (50%), Gaps = 33/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ +I KI +L   EE  LA+R  + GD  A   L+ S+LRLVV +A  Y G GL   ++
Sbjct: 101 YLRDIGKIRLLTPSEEKRLAQRA-QMGDQRAKEELIISNLRLVVSMAKRYLGKGLSFLDL 159

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-- 132
           + EG++GL++AV+KFD  +G++ +TY+ WWI+ A+   I      +++      T N+  
Sbjct: 160 IQEGSLGLIKAVEKFDWSKGYKFSTYATWWIRQAITRAIADQARTIRVPVHMVETINKIQ 219

Query: 133 --KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
             KR +      +  ++ I +   KP  V  I + L  +   +           SL   +
Sbjct: 220 KIKREYVQEHGEEPSIEYIAEQVGKP--VDKIEEILQAAPETL-----------SLETPV 266

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEE--RKNRRNMLTRSMSVLNPRERRIFEARRL 248
           N  D +S       + D    E +   K+E  R   R  + + +  LN RE+++ + R  
Sbjct: 267 NEEDDSS-------MGDFIADESIGSPKKEAIRTLMREEIDKLLETLNDREKKVLKMRYG 319

Query: 249 QEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             N  P+TLE +   F V+RER+RQIE +A +K++
Sbjct: 320 LYNGKPMTLEEVGQFFGVTRERIRQIEVKALRKLR 354


>gi|227486750|ref|ZP_03917066.1| DNA-directed RNA polymerase sigma subunit RpoD [Anaerococcus
           lactolyticus ATCC 51172]
 gi|227235220|gb|EEI85235.1| DNA-directed RNA polymerase sigma subunit RpoD [Anaerococcus
           lactolyticus ATCC 51172]
          Length = 601

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 78/247 (31%), Positives = 124/247 (50%), Gaps = 36/247 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  ++LRLVV IA  Y G G+   +++ EGN+GLM+AV K+D  RGF+ +TY+ WW
Sbjct: 365 AKEKLAETNLRLVVSIAKKYVGRGMSFLDLIQEGNMGLMKAVDKYDYNRGFKFSTYATWW 424

Query: 109 IKAAMQEYILRSWSLVKIGT----TAN-----QKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N     Q++L  +L R   + +      ++ E+V
Sbjct: 425 IRQAITRAIADQARTIRIPVHMVETINKLVRIQRQLVQDLGRDPSNEEIADIMGIEVEKV 484

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K   +++  V           SL   I   D   S   D++      ++   I+  
Sbjct: 485 SEIRK---IAQEPV-----------SLETPIGEED--DSHLGDFI------EDDTAIDPG 522

Query: 220 ERKNR---RNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEA 274
           E  N    R  L   +S L  RE+R+ + R   +   P TLE +  EF+V+RER+RQIEA
Sbjct: 523 EAANYTMLREQLNDVLSCLGAREKRVLQLRFGLIDGTPRTLEEVGKEFDVTRERIRQIEA 582

Query: 275 RAFKKVQ 281
           +A +K++
Sbjct: 583 KALRKLK 589


>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 =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 72/237 (30%), Positives = 124/237 (52%), Gaps = 14/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 496 DAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 555

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL-KGHLQAITDNNLKPEQVVAIAKKL 166
           WI+ A+   I      ++I    +       + RL + HLQ       +P+  + +A+K+
Sbjct: 556 WIRQAITRSIADQARTIRI--PVHMIETINKMNRLSRQHLQEF---GFEPDASI-LAEKM 609

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E E I    ++A  E ++      D + S   D++    DG     +E   +   R+
Sbjct: 610 EIPE-EKIRKIMKIA-KEPISMETPIGDDDDSHLGDFI---EDGANTAPLEAAMQAGLRD 664

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 665 VVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLK 721


>gi|57505389|ref|ZP_00371317.1| RNA polymerase sigma factor RpoD [Campylobacter upsaliensis RM3195]
 gi|57016214|gb|EAL53000.1| RNA polymerase sigma factor RpoD [Campylobacter upsaliensis RM3195]
          Length = 619

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 84/250 (33%), Positives = 123/250 (49%), Gaps = 41/250 (16%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ +RG++ +TY+ WW
Sbjct: 378 AKGRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T NQ     N + ++ HLQ     N K   V  IAK
Sbjct: 438 IRQAISRAIADQARTIRIPIHMIETINQ----IN-KIIREHLQ----KNGKEPDVNDIAK 488

Query: 165 KLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           ++ +S  +V          IS+   +  +E         DKNS    D ++ D D +EQ+
Sbjct: 489 EVGLSVDKVKQVIKITKEPISLEAPIGSEEDGKFGDFVEDKNSLSPMDNILKD-DLKEQI 547

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQ 271
                            +  LN RE+ +   R      E+  TLE +  E  V+RERVRQ
Sbjct: 548 --------------DEVLDQLNDREKAVIRMRFGLLEDESDRTLEEIGKELNVTRERVRQ 593

Query: 272 IEARAFKKVQ 281
           IE+ A KK++
Sbjct: 594 IESSAIKKLK 603


>gi|268319377|ref|YP_003293033.1| DNA-directed RNA polymerase sigma factor RpoD (Sigma-70)
           [Lactobacillus johnsonii FI9785]
 gi|262397752|emb|CAX66766.1| DNA-directed RNA polymerase sigma factor RpoD (Sigma-70)
           [Lactobacillus johnsonii FI9785]
          Length = 372

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 84/273 (30%), Positives = 133/273 (48%), Gaps = 31/273 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   +E  LAKR  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 106 YLKEIGRVSLLNADQEIALAKRI-ESGDEEAKQELAEANLRLVVSIAKRYVGRGMSFLDL 164

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 165 IQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 224

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + ++  ++V  I   L +++ E +S+   +    D  L 
Sbjct: 225 RIQRQLLQDLGREPTPEEIGAEMDMPTDKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 280

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S +         +  E+VL    +R+   N+L     + + R R       
Sbjct: 281 DFIEDKDATSPEQHASYELLKEQLEEVLDTLTDREE--NVLRLRFGLDDGRTR------- 331

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                 TLE +   F V+RER+RQIEA+A +K+
Sbjct: 332 ------TLEEVGKVFGVTRERIRQIEAKALRKL 358


>gi|259500591|ref|ZP_05743493.1| RNA polymerase sigma factor rpoD [Lactobacillus iners DSM 13335]
 gi|302191282|ref|ZP_07267536.1| RNA polymerase sigma factor RpoD [Lactobacillus iners AB-1]
 gi|309805231|ref|ZP_07699283.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LactinV
           09V1-c]
 gi|309807583|ref|ZP_07701535.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LactinV
           01V1-a]
 gi|312871770|ref|ZP_07731858.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LEAF 3008A-a]
 gi|312875648|ref|ZP_07735649.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LEAF 2053A-b]
 gi|325912054|ref|ZP_08174452.1| RNA polymerase sigma factor RpoD [Lactobacillus iners UPII 143-D]
 gi|259167975|gb|EEW52470.1| RNA polymerase sigma factor rpoD [Lactobacillus iners DSM 13335]
 gi|308165465|gb|EFO67696.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LactinV
           09V1-c]
 gi|308169189|gb|EFO71255.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LactinV
           01V1-a]
 gi|311088902|gb|EFQ47345.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LEAF 2053A-b]
 gi|311092712|gb|EFQ51068.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LEAF 3008A-a]
 gi|325476004|gb|EGC79172.1| RNA polymerase sigma factor RpoD [Lactobacillus iners UPII 143-D]
          Length = 382

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 86/279 (30%), Positives = 133/279 (47%), Gaps = 43/279 (15%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   +E  LAKR  E+ D  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 116 YLKEIGRVPLLNADQEIDLAKRI-ENNDDEAKQELAEANLRLVVSIAKRYVGRGMSFLDL 174

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 175 IQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 234

Query: 132 --QKRLFFNLRR------LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-- 181
             Q++L  +L R      +   +   TD   K  +++ IA+       E +S+   +   
Sbjct: 235 RIQRQLLQDLGREPTPEEIGAEMDMSTD---KVREILKIAQ-------EPVSLETPIGEE 284

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
            D  L   I   D  S +         +  E+VL    +R+   N+L     + + R R 
Sbjct: 285 DDSHLGDFIEDKDATSPEQHASYELLKEQLEEVLDTLTDREE--NVLRLRFGLNDGRTR- 341

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                       TLE +   F V+RER+RQIEA+A +K+
Sbjct: 342 ------------TLEEVGRVFGVTRERIRQIEAKALRKL 368


>gi|42519241|ref|NP_965171.1| RNA polymerase sigma factor RpoD [Lactobacillus johnsonii NCC 533]
 gi|41583529|gb|AAS09137.1| RNA polymerase sigma factor RpoD [Lactobacillus johnsonii NCC 533]
 gi|329667249|gb|AEB93197.1| RNA polymerase sigma factor RpoD [Lactobacillus johnsonii DPC 6026]
          Length = 372

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 84/273 (30%), Positives = 133/273 (48%), Gaps = 31/273 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   +E  LAKR  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 106 YLKEIGRVSLLNADQEIALAKRI-ESGDEEAKQELAEANLRLVVSIAKRYVGRGMSFLDL 164

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 165 IQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 224

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + ++  ++V  I   L +++ E +S+   +    D  L 
Sbjct: 225 RIQRQLLQDLGREPTPEEIGAEMDMPTDKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 280

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S +         +  E+VL    +R+   N+L     + + R R       
Sbjct: 281 DFIEDKDATSPEQHASYELLKEQLEEVLDTLTDREE--NVLRLRFGLDDGRTR------- 331

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                 TLE +   F V+RER+RQIEA+A +K+
Sbjct: 332 ------TLEEVGKVFGVTRERIRQIEAKALRKL 358


>gi|108762696|ref|YP_629049.1| RNA polymerase sigma-32 factor family protein [Myxococcus xanthus
           DK 1622]
 gi|108466576|gb|ABF91761.1| RNA polymerase sigma-32 factor family protein [Myxococcus xanthus
           DK 1622]
          Length = 273

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 76/220 (34%), Positives = 118/220 (53%), Gaps = 8/220 (3%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V  HL+LV ++A  YR  GL + E+V+EGN+GLM+A  +F+ ERG   A Y+  WI+A +
Sbjct: 35  VREHLKLVRRLAWKYRWTGLSMEELVAEGNVGLMEAAGRFE-ERGVPFAAYASQWIRARI 93

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
           + Y+ R+WS+           + F LRR +  L+A       PE    +A+ L   E EV
Sbjct: 94  RAYVGRNWSM----AGGRAPWVVFQLRRERSRLEARWGEG-HPEVEKRLAEALGKREDEV 148

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
                 L+ D SL+A + S D  +++ +  L+ D D QE  +   +  +  R  +  +  
Sbjct: 149 ALAMEALSRDVSLDAPV-SPDSEATRLEG-LMADADSQEDQVDRAKWARRLRASVDAAWP 206

Query: 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
            L+ RER + E R L E+ V+ E L+  F V+  R+RQIE
Sbjct: 207 ELDARERALVEERMLAEDGVSAELLARRFGVTAVRIRQIE 246


>gi|227890104|ref|ZP_04007909.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           johnsonii ATCC 33200]
 gi|227849548|gb|EEJ59634.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           johnsonii ATCC 33200]
          Length = 372

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 84/273 (30%), Positives = 133/273 (48%), Gaps = 31/273 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   +E  LAKR  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 106 YLKEIGRVSLLNADQEIALAKRI-ESGDEEAKQELAEANLRLVVSIAKRYVGRGMSFLDL 164

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 165 IQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 224

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + ++  ++V  I   L +++ E +S+   +    D  L 
Sbjct: 225 RIQRQLLQDLGREPTPEEIGAEMDMPTDKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 280

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S +         +  E+VL    +R+   N+L     + + R R       
Sbjct: 281 DFIEDKDATSPEQHASYELLKEQLEEVLDTLTDREE--NVLRLRFGLDDGRTR------- 331

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                 TLE +   F V+RER+RQIEA+A +K+
Sbjct: 332 ------TLEEVGKVFGVTRERIRQIEAKALRKL 358


>gi|88809396|ref|ZP_01124904.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 7805]
 gi|88786615|gb|EAR17774.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 7805]
          Length = 339

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 87/294 (29%), Positives = 142/294 (48%), Gaps = 37/294 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLA--------------------KRYREHGDLSAAHRLVTSHL 58
           Y+  I ++P+L   EE  LA                    +R+R      A  R++ ++L
Sbjct: 55  YLSTIGRVPLLTAAEEIELAHHVQAMKELLDVPEDERTPRQRHRIRMGKRARDRMMAANL 114

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+  M   I 
Sbjct: 115 RLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTRAID 174

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLK---GHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
            S   +++    ++K     +RR+     H      N L+    + IA + ++ E    S
Sbjct: 175 NSARTIRLPIHISEK--LSKMRRITRELSHRFGRQPNRLELSNAMGIAPR-DLEELIAQS 231

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
             C      SL+A     +  S+  +  L+ D +G E   +E  +R  ++  L   +S L
Sbjct: 232 APC-----ASLDAHARGEEDRSTLGE--LIPDPNGDEP--MEGMDRSIQKEHLGGWLSQL 282

Query: 236 NPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           N RE++I   R   +   P+TL  +  +  VSRERVRQ+EA+A  K++    +Q
Sbjct: 283 NEREQKILRLRFGLDGAEPLTLAEIGRQINVSRERVRQLEAKAILKLRTMTDQQ 336


>gi|444799|prf||1908232B RNA polymerase:SUBUNIT=sigma factor
          Length = 340

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 85/271 (31%), Positives = 140/271 (51%), Gaps = 22/271 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
           Y+ EI + P++   EE  LA+     G+ +  A   L  ++LRLVV IA  Y G G    
Sbjct: 72  YLKEIGRYPLISLDEETKLAEAIIAGGEGAEFAKQMLAEANLRLVVSIAKRYSGRGNQFL 131

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    +     
Sbjct: 132 DLIQEGNMGLMKAVDKFDHTKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETI 189

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDK 195
             L R++ +L      +  PE+   I K+L+++  +V  +  ++A +  SL   I   D 
Sbjct: 190 NKLIRVQRNLLQELGRDPSPEE---IGKELHMAPDKVREV-LKIAQEPVSLETPIGEED- 244

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNR---RNMLTRSMSVLNPRERRIFEAR-RLQEN 251
             S   D++      ++ V+    +  NR   R  L   M  L  RE  +   R  L + 
Sbjct: 245 -DSHLGDFI------EDDVIESPVDYTNRILLREQLDEVMDTLTDREENVLRMRFGLDDG 297

Query: 252 PV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            + TLE++  +F+V+RER+RQIEA+A KK++
Sbjct: 298 RMHTLEDVGKQFKVTRERIRQIEAKAIKKLR 328


>gi|309803186|ref|ZP_07697283.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LactinV
           11V1-d]
 gi|309806578|ref|ZP_07700575.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LactinV
           03V1-b]
 gi|312872984|ref|ZP_07733044.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LEAF
           2062A-h1]
 gi|315653573|ref|ZP_07906493.1| RNA polymerase sigma factor rpoD [Lactobacillus iners ATCC 55195]
 gi|325912624|ref|ZP_08175007.1| RNA polymerase sigma factor RpoD [Lactobacillus iners UPII 60-B]
 gi|329920166|ref|ZP_08276997.1| RNA polymerase sigma factor RpoD [Lactobacillus iners SPIN 1401G]
 gi|308164694|gb|EFO66944.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LactinV
           11V1-d]
 gi|308166998|gb|EFO69180.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LactinV
           03V1-b]
 gi|311091506|gb|EFQ49890.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LEAF
           2062A-h1]
 gi|315488935|gb|EFU78577.1| RNA polymerase sigma factor rpoD [Lactobacillus iners ATCC 55195]
 gi|325478045|gb|EGC81174.1| RNA polymerase sigma factor RpoD [Lactobacillus iners UPII 60-B]
 gi|328936620|gb|EGG33064.1| RNA polymerase sigma factor RpoD [Lactobacillus iners SPIN 1401G]
          Length = 382

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 86/279 (30%), Positives = 133/279 (47%), Gaps = 43/279 (15%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   +E  LAKR  E+ D  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 116 YLKEIGRVPLLNADQEIDLAKRI-ENNDDEAKQELAEANLRLVVSIAKRYVGRGMSFLDL 174

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 175 IQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 234

Query: 132 --QKRLFFNLRR------LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-- 181
             Q++L  +L R      +   +   TD   K  +++ IA+       E +S+   +   
Sbjct: 235 RIQRQLLQDLGREPTPEEIGAEMDMSTD---KVREILKIAQ-------EPVSLETPIGEE 284

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
            D  L   I   D  S +         +  E+VL    +R+   N+L     + + R R 
Sbjct: 285 DDSHLGDFIEDKDATSPEQHASYELLKEQLEEVLDTLTDREE--NVLRLRFGLNDGRTR- 341

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                       TLE +   F V+RER+RQIEA+A +K+
Sbjct: 342 ------------TLEEVGRVFGVTRERIRQIEAKALRKL 368


>gi|126699102|ref|YP_001087999.1| RNA polymerase sigma factor rpoD [Clostridium difficile 630]
 gi|115250539|emb|CAJ68363.1| RNA polymerase sigma factor SigA2 (sigma-43) [Clostridium
           difficile]
          Length = 296

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 77/269 (28%), Positives = 145/269 (53%), Gaps = 11/269 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            +  Y+ EI +  ML   EE  LAK       + A  + + S+ RLVV IA  Y+   + 
Sbjct: 25  AMKMYLKEIEEYKMLSAGEEVELAKEIINSSSV-AKEKFINSNYRLVVSIAKRYKRDSID 83

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  GNIGL++AV+K+D ++G++ +TY+ WWIK ++  YI    + ++I    +Q+ 
Sbjct: 84  MLDLIQAGNIGLIKAVEKYDYKKGYKFSTYATWWIKQSITRYIDDCENTIRIPIHLHQRI 143

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
            F     +K   Q + +  L+   +  IA    +   +V+ +  R     SL+  +   D
Sbjct: 144 NF-----VKKKKQELLNVLLREPTIDEIADACGLEVDKVLELLRRDKNVVSLDTPL-KED 197

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENP 252
           ++SS   +++  D D ++ V+I + E+ N +  +   ++ L  +E+++   R     ++P
Sbjct: 198 EDSS-LVEFIPSDADFKD-VVIHEVEQHNLKEKIEELLTGLGEQEQQVLRMRFGIDDDDP 255

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE +   F V+RER+RQIEA+A +K++
Sbjct: 256 KTLEQIGKVFGVTRERIRQIEAKAIRKLR 284


>gi|309810147|ref|ZP_07703992.1| RNA polymerase sigma factor RpoD [Lactobacillus iners SPIN
           2503V10-D]
 gi|308169419|gb|EFO71467.1| RNA polymerase sigma factor RpoD [Lactobacillus iners SPIN
           2503V10-D]
          Length = 382

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 86/279 (30%), Positives = 133/279 (47%), Gaps = 43/279 (15%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   +E  LAKR  E+ D  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 116 YLKEIGRVPLLNADQEIDLAKRI-ENNDDEAKQELAEANLRLVVSIAKRYVGRGMSFLDL 174

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 175 IQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 234

Query: 132 --QKRLFFNLRR------LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-- 181
             Q++L  +L R      +   +   TD   K  +++ IA+       E +S+   +   
Sbjct: 235 RIQRQLLQDLGREPTPEEIGAEMDMSTD---KVREILKIAQ-------EPVSLETPIGEE 284

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
            D  L   I   D  S +         +  E+VL    +R+   N+L     + + R R 
Sbjct: 285 DDSHLGDFIEDKDATSPEQHASYELLKEQLEEVLDTLTDREE--NVLRLRFGLNDGRTR- 341

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                       TLE +   F V+RER+RQIEA+A +K+
Sbjct: 342 ------------TLEEVGRVFGVTRERIRQIEAKALRKL 368


>gi|227499774|ref|ZP_03929874.1| DNA-directed RNA polymerase sigma subunit RpoD [Anaerococcus
           tetradius ATCC 35098]
 gi|227218160|gb|EEI83426.1| DNA-directed RNA polymerase sigma subunit RpoD [Anaerococcus
           tetradius ATCC 35098]
          Length = 606

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 77/247 (31%), Positives = 124/247 (50%), Gaps = 36/247 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  ++LRLVV IA  Y G G+   +++ EGN+GLM+AV K+D  RGF+ +TY+ WW
Sbjct: 370 AKQKLAETNLRLVVSIAKKYVGRGMSFLDLIQEGNMGLMKAVDKYDYNRGFKFSTYATWW 429

Query: 109 IKAAMQEYILRSWSLVKIGT----TAN-----QKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N     Q++L  +L R   + +      ++ ++V
Sbjct: 430 IRQAITRAIADQARTIRIPVHMVETINKLVRIQRQLVQDLGRDPSNEEIAEQMGIEVDKV 489

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K   +S+  V           SL   I   D   S   D++      ++   ++  
Sbjct: 490 QEIRK---ISQEPV-----------SLETPIGEED--DSHLGDFI------EDDTAVDPG 527

Query: 220 ERKNR---RNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEA 274
           E  N    R  L   +S L  RE+R+ + R   +   P TLE +  EF+V+RER+RQIEA
Sbjct: 528 EAANYTMLREQLNDVLSCLGAREKRVLQLRFGLIDGTPRTLEEVGKEFDVTRERIRQIEA 587

Query: 275 RAFKKVQ 281
           +A +K++
Sbjct: 588 KALRKLK 594


>gi|327538655|gb|EGF25307.1| RNA polymerase sigma factor rpoS [Rhodopirellula baltica WH47]
          Length = 330

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 84/277 (30%), Positives = 142/277 (51%), Gaps = 25/277 (9%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ EI + P+L  +EE  LA R    GD+ A  ++V ++LRLVV I+ GY G GL +
Sbjct: 63  LETYLREINETPLLSAEEELELAARI-AQGDVMARDQMVRANLRLVVNISRGYTGKGLGL 121

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GL++AV+ FDP  G R +TY+ +WIK +++  ++ S   ++I   A    L
Sbjct: 122 QDLIEEGNLGLLRAVEGFDPIHGTRFSTYASYWIKQSIKRALINSAKTIRI--PAYMVEL 179

Query: 136 FFNLRRLKGHLQ---AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
               RR    L      T  N +  +V+ + KK      + I +N             NS
Sbjct: 180 LSKWRRATARLNEELGRTPTNEEVARVLGLPKKKLPIIRKAIKIN-------------NS 226

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN- 251
           + ++      W + D    E++    EE  +  ++L  +MS+L   E R     +L+   
Sbjct: 227 TPQSDQTEAGWSLGDMVQDERLKAPDEEMLD-HDILKHAMSLLGDLEERESTVLKLRFGL 285

Query: 252 ----PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
               P+TL+ + +E  ++RERVRQIE  A +++ + +
Sbjct: 286 GGVEPMTLKEIGAELGLTRERVRQIETEALRRLADGL 322


>gi|261416342|ref|YP_003250025.1| RNA polymerase, sigma 32 subunit, RpoH [Fibrobacter succinogenes
           subsp. succinogenes S85]
 gi|261372798|gb|ACX75543.1| RNA polymerase, sigma 32 subunit, RpoH [Fibrobacter succinogenes
           subsp. succinogenes S85]
 gi|302326200|gb|ADL25401.1| RNA polymerase sigma-70 factor [Fibrobacter succinogenes subsp.
           succinogenes S85]
          Length = 282

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 81/283 (28%), Positives = 147/283 (51%), Gaps = 22/283 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR----EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           Y  ++ + P L  QEE  L K  +    E    SA  RL+  +LR VV +A  Y+G GL 
Sbjct: 9   YFRDLNRYPTLTPQEESALLKIIKNGETEEIRKSALQRLIRGNLRFVVSVARKYQGRGLS 68

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL +A K+FD ++  +  +Y++WWI+ ++Q+ +      V+I    N+  
Sbjct: 69  LLDLINEGNLGLFKAAKRFDMDKDVKFISYAVWWIRQSIQKALFEQVGAVRI--PPNKLA 126

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL-NVSESEV-ISMNCRLAGDESLNALINS 192
           L    +R         D  +  E+     + +  V E  V IS++  +  D    A ++S
Sbjct: 127 LVNRFKRALMQNGGDYDKTISMEEFAPYERDIVEVMEKIVDISLDAPIGDD----AGVSS 182

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER---RIFEARRLQ 249
           +D  S+      V   DG +   +E+EERK    ++  ++S L  RE    R+F      
Sbjct: 183 ADSVSTLMD---VLGSDGNQDEDMEREERK---KLIQETLSSLPQREEEILRMFYGLDTV 236

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
           E+  TL+++  + ++SRERVRQI+ +  +++Q+S + + +L+ 
Sbjct: 237 ED-TTLKDIGEDLKLSRERVRQIKNKTLRRLQKSKEHKEKLAD 278


>gi|167754493|ref|ZP_02426620.1| hypothetical protein ALIPUT_02789 [Alistipes putredinis DSM 17216]
 gi|167659118|gb|EDS03248.1| hypothetical protein ALIPUT_02789 [Alistipes putredinis DSM 17216]
          Length = 286

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 78/271 (28%), Positives = 149/271 (54%), Gaps = 16/271 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K  ++  +EE  LA+R ++ GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGKEELITVEEEVELAQRIKK-GDQEALEKLTKANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     +V++    NQ   
Sbjct: 77  PDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL--PLNQVGS 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
              + +     +   +    PE+   +A +L + + E ++   R+AG   S++A     +
Sbjct: 135 LNKINKAFARFEQEHERTPSPEE---LANELELPK-EKVTDTLRVAGRHVSVDAPFADGE 190

Query: 195 KNSSQWQDWLVY-DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE-ARRLQENP 252
            NS    D LV  D    ++ LI     ++    + R++  L  RER I +    +  + 
Sbjct: 191 DNS--LLDVLVNPDSPNADRGLI----NESLSTEVDRALETLTERERDIIKYFFGIGCSE 244

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +TLE +  +F+++RERVRQI+ +A ++++ S
Sbjct: 245 MTLEEIGEKFDLTRERVRQIKEKAIRRLRHS 275


>gi|167755652|ref|ZP_02427779.1| hypothetical protein CLORAM_01167 [Clostridium ramosum DSM 1402]
 gi|237734400|ref|ZP_04564881.1| RNA polymerase sigma factor rpoD [Mollicutes bacterium D7]
 gi|167704591|gb|EDS19170.1| hypothetical protein CLORAM_01167 [Clostridium ramosum DSM 1402]
 gi|229382630|gb|EEO32721.1| RNA polymerase sigma factor rpoD [Coprobacillus sp. D7]
          Length = 417

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 86/278 (30%), Positives = 143/278 (51%), Gaps = 38/278 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LAK+  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 149 YLKEIGRVELLTHDEEIDLAKKILE-GDEDAKKELAAANLRLVVSIAKRYVGRGMLFLDL 207

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT---------T 129
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I           T
Sbjct: 208 IQEGNMGLIKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLT 267

Query: 130 ANQKRLFFNLRRLKGHLQAITD--NNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDES 185
             Q++L   L R +   + I +  + + PE+V  I +K+++   E +S+   +    D  
Sbjct: 268 RIQRQLIQELGR-EPSAEEIAEKMDGMTPEKVREI-QKISL---EPVSLETPIGEEDDSH 322

Query: 186 LNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           L   I   D+ +    D+   +   D   +VL+E  +R+ +  +L     + + R R   
Sbjct: 323 LGDFI--EDEGAMSPDDYAANELLKDELNEVLLELTDREEK--VLRLRFGLDDGRTR--- 375

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                     TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 376 ----------TLEEVGKEFSVTRERIRQIEAKALRKLK 403


>gi|769798|emb|CAA60113.1| sigma 42 [Enterococcus faecalis]
          Length = 368

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 85/275 (30%), Positives = 132/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGRVQLLTAAEEVELALKI-EEGDQEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 161 IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 220

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q+ L  +L R     +   + +L  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 221 RMQRNLLQDLGREPTPEEIGAEMDLPTEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 276

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S         +H   E +          +  L   +  L  RE  +   R 
Sbjct: 277 DFIEDQDATSPA-------EHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 319

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 320 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 354


>gi|300312263|ref|YP_003776355.1| RNA polymerase sigma S (sigma38) factor protein [Herbaspirillum
           seropedicae SmR1]
 gi|300075048|gb|ADJ64447.1| RNA polymerase sigma S (sigma38) factor protein [Herbaspirillum
           seropedicae SmR1]
          Length = 337

 Score =  105 bits (261), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 77/268 (28%), Positives = 140/268 (52%), Gaps = 17/268 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+++I   P+L   EE   A + +  G+  A  +++  +LRLVV IA  Y   G+ + ++
Sbjct: 68  YLNKIGAKPLLTAAEELHFATQAKA-GEFVARQKMIEHNLRLVVSIAKHYINRGVALLDL 126

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+A+ KF+PERGFR +TY+ WWI+ +++  I+     V++    +  R    
Sbjct: 127 IEEGNLGLMRAIDKFEPERGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHMVRELNQ 184

Query: 139 LRRLKGHLQAITDN--NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
           + R K HL+A   +  +   E +  +  +      +V++++   A   SL+  +++  + 
Sbjct: 185 ILRAKYHLEAQQRDGRDASAEDIAHLVDRPVEEVQDVLALSEHAA---SLDTPLDNDPQA 241

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPV 253
           S    D L    +       E +E         +S+S     ++R+  ARR     ++P 
Sbjct: 242 S--LMDLLPSAVEEHPDTRAESQEMAVLIREWLKSLS----EKQRVVVARRFGLDNDDPS 295

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TLE L+SE  ++RERVRQ++  A  K++
Sbjct: 296 TLEQLASEMGITRERVRQVQQEALIKLK 323


>gi|32472693|ref|NP_865687.1| RNA polymerase sigma factor rpoS [Rhodopirellula baltica SH 1]
 gi|32443930|emb|CAD73372.1| RNA polymerase sigma factor rpoS [Rhodopirellula baltica SH 1]
          Length = 355

 Score =  104 bits (260), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 84/277 (30%), Positives = 143/277 (51%), Gaps = 25/277 (9%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ EI + P+L  +EE  LA R  + GD+ A  ++V ++LRLVV I+ GY G GL +
Sbjct: 88  LETYLREINETPLLSAEEELELAARIAQ-GDVMARDQMVRANLRLVVNISRGYTGKGLGL 146

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GL++AV+ FDP  G R +TY+ +WIK +++  ++ S   ++I   A    L
Sbjct: 147 QDLIEEGNLGLLRAVEGFDPIHGTRFSTYASYWIKQSIKRALINSAKTIRI--PAYMVEL 204

Query: 136 FFNLRRLKGHLQ---AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
               RR    L      T  N +  +V+ + KK      + I +N             NS
Sbjct: 205 LSKWRRATARLNEELGRTPTNEEVARVLGLPKKKLPIIRKAIKIN-------------NS 251

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN- 251
           + ++      W + D    E++    EE  +  ++L  +MS+L   E R     +L+   
Sbjct: 252 TPQSDQTEAGWSLGDMVQDERLKAPDEEMLD-HDILKHAMSLLGDLEERESTVLKLRFGL 310

Query: 252 ----PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
               P+TL+ + +E  ++RERVRQIE  A +++ + +
Sbjct: 311 GGVEPMTLKEIGAELGLTRERVRQIETEALRRLADGL 347


>gi|229824058|ref|ZP_04450127.1| hypothetical protein GCWU000282_01362 [Catonella morbi ATCC 51271]
 gi|229786412|gb|EEP22526.1| hypothetical protein GCWU000282_01362 [Catonella morbi ATCC 51271]
          Length = 379

 Score =  104 bits (260), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 86/273 (31%), Positives = 132/273 (48%), Gaps = 31/273 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA R  + GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 113 YLKEIGNVPLLSAEEEINLAVRI-QGGDDIAKQELAEANLRLVVSIAKRYVGRGMQFLDL 171

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 172 IQEGNMGLMKAVEKFDHTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLV 231

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             Q++L  +L R     +   + +L  E+V  I   L +++  V           SL   
Sbjct: 232 RVQRQLLQDLGREPTPEEIGAEMDLPTEKVREI---LKIAQEPV-----------SLETP 277

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RL 248
           I   D   S   D++  +     +V          R  L   +  L  RE  +   R  L
Sbjct: 278 IGEED--DSHLGDFIEDEGAMSPEVFTSS---ALLREQLEDVLDTLTDREENVLRLRFGL 332

Query: 249 QENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
            +  + TLE +   F V+RER+RQIEA+A +K+
Sbjct: 333 DDGNIRTLEQVGKVFGVTRERIRQIEAKALRKL 365


>gi|320010942|gb|ADW05792.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 358

 Score =  104 bits (260), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 89/293 (30%), Positives = 145/293 (49%), Gaps = 42/293 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHG-------------------DLS--------AAH 51
           Y+ EI +IP+L   +E  LA+R  E G                   DL         A  
Sbjct: 65  YLREIGRIPLLSAADEVELARRV-EAGLFAEERLAGTPDPDSGLAVDLDRLVVMGRMAKR 123

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY+ WWI+ 
Sbjct: 124 RLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIRQ 183

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           AM   +      +++     +  L   + R++  +         PE+V A   +L+++  
Sbjct: 184 AMSRALADQARTIRVPVHVVE--LINRVVRVQRRMLQERGYEPAPEEVAA---QLDLT-P 237

Query: 172 EVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           E +S   RLA +  SL+A +   D  +  + D +    DG     +E       R  L  
Sbjct: 238 ERVSEVLRLAQEPVSLHAPVGEEDDVA--FGDLI---EDGDAASPVETAAFLLLREHLEV 292

Query: 231 SMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +S L  RER++ + R   ++  P TLE +   F V+RER+RQIE++   K++
Sbjct: 293 VLSTLGERERKVVQLRYGLDDGRPRTLEEIGRIFGVTRERIRQIESKTLDKLR 345


>gi|307824679|ref|ZP_07654903.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Methylobacter
           tundripaludum SV96]
 gi|307734333|gb|EFO05186.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Methylobacter
           tundripaludum SV96]
          Length = 342

 Score =  104 bits (260), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 79/273 (28%), Positives = 141/273 (51%), Gaps = 21/273 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++E+ +  +L   +E +   R    GD +A   ++ S+LRLVVKI+  Y   GLP+ ++
Sbjct: 74  YLNELSRSQLLTADQEKIYGSRAL-LGDEAARKIMIESNLRLVVKISRRYLNRGLPLLDL 132

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GLM AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +   + 
Sbjct: 133 IEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKEMNTYL 192

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
             +R   HL  + ++    E    IA+ L++  ++V  M         LN  + S D   
Sbjct: 193 KAQR---HLSQLLEHEPNAED---IAEHLDIPVNKVEKML-------KLNERVTSIDMPG 239

Query: 198 SQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR---LQENP 252
            +  D  + +   DG+     EK +    ++ + + +  L+ ++R +   RR        
Sbjct: 240 GKDFDKPLVESISDGESLSPAEKIQEDGIKHNIAKWVFQLSEKQREVI-CRRYGLCGYEG 298

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            TLE ++ E  V+RERVRQI+    K+++E ++
Sbjct: 299 STLEQVAQELGVTRERVRQIQMDGLKRMKEILE 331


>gi|260683114|ref|YP_003214399.1| RNA polymerase sigma factor rpoD [Clostridium difficile CD196]
 gi|260686712|ref|YP_003217845.1| RNA polymerase sigma factor rpoD [Clostridium difficile R20291]
 gi|260209277|emb|CBA62619.1| RNA polymerase sigma factor rpoD [Clostridium difficile CD196]
 gi|260212728|emb|CBE03837.1| RNA polymerase sigma factor rpoD [Clostridium difficile R20291]
          Length = 301

 Score =  104 bits (260), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 77/269 (28%), Positives = 145/269 (53%), Gaps = 11/269 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            +  Y+ EI +  ML   EE  LAK       + A  + + S+ RLVV IA  Y+   + 
Sbjct: 30  AMKMYLKEIEEYKMLSAGEEVELAKEIINSSSV-AKEKFINSNYRLVVSIAKRYKRDSID 88

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  GNIGL++AV+K+D ++G++ +TY+ WWIK ++  YI    + ++I    +Q+ 
Sbjct: 89  MLDLIQAGNIGLIKAVEKYDYKKGYKFSTYATWWIKQSITRYIDDCENTIRIPIHLHQRI 148

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
            F     +K   Q + +  L+   +  IA    +   +V+ +  R     SL+  +   D
Sbjct: 149 NF-----VKKKKQELLNVLLREPTIDEIADACGLEVDKVLELLRRDKNVVSLDTPL-KED 202

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENP 252
           ++SS   +++  D D ++ V+I + E+ N +  +   ++ L  +E+++   R     ++P
Sbjct: 203 EDSS-LVEFIPSDADFKD-VVIHEVEQHNLKEKIEELLTGLGEQEQQVLRMRFGIDDDDP 260

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE +   F V+RER+RQIEA+A +K++
Sbjct: 261 KTLEQIGKVFGVTRERIRQIEAKAIRKLR 289


>gi|116629751|ref|YP_814923.1| RNA polymerase sigma factor RpoD [Lactobacillus gasseri ATCC 33323]
 gi|238853400|ref|ZP_04643779.1| RNA polymerase sigma factor RpoD [Lactobacillus gasseri 202-4]
 gi|282851794|ref|ZP_06261157.1| RNA polymerase sigma factor RpoD [Lactobacillus gasseri 224-1]
 gi|300361838|ref|ZP_07058015.1| RNA polymerase sigma factor rpoD [Lactobacillus gasseri JV-V03]
 gi|311110607|ref|ZP_07712004.1| RNA polymerase sigma-43 factor [Lactobacillus gasseri MV-22]
 gi|116095333|gb|ABJ60485.1| RNA polymerase, sigma 70 subunit, RpoD [Lactobacillus gasseri ATCC
           33323]
 gi|238833972|gb|EEQ26230.1| RNA polymerase sigma factor RpoD [Lactobacillus gasseri 202-4]
 gi|282557036|gb|EFB62635.1| RNA polymerase sigma factor RpoD [Lactobacillus gasseri 224-1]
 gi|300354457|gb|EFJ70328.1| RNA polymerase sigma factor rpoD [Lactobacillus gasseri JV-V03]
 gi|311065761|gb|EFQ46101.1| RNA polymerase sigma-43 factor [Lactobacillus gasseri MV-22]
          Length = 373

 Score =  104 bits (260), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 84/273 (30%), Positives = 133/273 (48%), Gaps = 31/273 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   +E  LAKR  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 107 YLKEIGRVSLLNADQEIALAKRI-EAGDEEAKQELAEANLRLVVSIAKRYVGRGMSFLDL 165

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 166 IQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 225

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + ++  ++V  I   L +++ E +S+   +    D  L 
Sbjct: 226 RIQRQLLQDLGREPTPEEIGAEMDMPTDKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 281

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S +         +  E+VL    +R+   N+L     + + R R       
Sbjct: 282 DFIEDKDATSPEQHASYELLKEQLEEVLDTLTDREE--NVLRLRFGLDDGRTR------- 332

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                 TLE +   F V+RER+RQIEA+A +K+
Sbjct: 333 ------TLEEVGKVFGVTRERIRQIEAKALRKL 359


>gi|254975054|ref|ZP_05271526.1| RNA polymerase sigma factor rpoD [Clostridium difficile QCD-66c26]
 gi|255092443|ref|ZP_05321921.1| RNA polymerase sigma factor rpoD [Clostridium difficile CIP 107932]
 gi|255100524|ref|ZP_05329501.1| RNA polymerase sigma factor rpoD [Clostridium difficile QCD-63q42]
 gi|255308764|ref|ZP_05352935.1| RNA polymerase sigma factor rpoD [Clostridium difficile ATCC 43255]
 gi|255314181|ref|ZP_05355764.1| RNA polymerase sigma factor rpoD [Clostridium difficile QCD-76w55]
 gi|255516860|ref|ZP_05384536.1| RNA polymerase sigma factor rpoD [Clostridium difficile QCD-97b34]
 gi|255649961|ref|ZP_05396863.1| RNA polymerase sigma factor rpoD [Clostridium difficile QCD-37x79]
 gi|306520043|ref|ZP_07406390.1| RNA polymerase sigma factor rpoD [Clostridium difficile QCD-32g58]
          Length = 294

 Score =  104 bits (260), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 77/269 (28%), Positives = 145/269 (53%), Gaps = 11/269 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            +  Y+ EI +  ML   EE  LAK       + A  + + S+ RLVV IA  Y+   + 
Sbjct: 23  AMKMYLKEIEEYKMLSAGEEVELAKEIINSSSV-AKEKFINSNYRLVVSIAKRYKRDSID 81

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  GNIGL++AV+K+D ++G++ +TY+ WWIK ++  YI    + ++I    +Q+ 
Sbjct: 82  MLDLIQAGNIGLIKAVEKYDYKKGYKFSTYATWWIKQSITRYIDDCENTIRIPIHLHQRI 141

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
            F     +K   Q + +  L+   +  IA    +   +V+ +  R     SL+  +   D
Sbjct: 142 NF-----VKKKKQELLNVLLREPTIDEIADACGLEVDKVLELLRRDKNVVSLDTPL-KED 195

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENP 252
           ++SS   +++  D D ++ V+I + E+ N +  +   ++ L  +E+++   R     ++P
Sbjct: 196 EDSS-LVEFIPSDADFKD-VVIHEVEQHNLKEKIEELLTGLGEQEQQVLRMRFGIDDDDP 253

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE +   F V+RER+RQIEA+A +K++
Sbjct: 254 KTLEQIGKVFGVTRERIRQIEAKAIRKLR 282


>gi|237653675|ref|YP_002889989.1| RNA polymerase sigma factor RpoS [Thauera sp. MZ1T]
 gi|237624922|gb|ACR01612.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thauera sp. MZ1T]
          Length = 312

 Score =  104 bits (260), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 61/173 (35%), Positives = 99/173 (57%), Gaps = 6/173 (3%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE V+A+R R  GD  A   ++  +LRLVV IA  Y   G+P+ ++
Sbjct: 45  YLNEIGANPLLTAEEELVIARRVR-MGDFDARQTMIERNLRLVVNIAKHYLNRGIPLLDL 103

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GLM A++KFDPERGFR +TY+ WWI+  ++  I+     +++     ++     
Sbjct: 104 VEEGNLGLMHALEKFDPERGFRFSTYATWWIRQNIERAIMNQSRTIRLPVHVVKE--LNQ 161

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
           + R + H++A  +     EQ   IA +L  +  EV S+        SL+A ++
Sbjct: 162 VLRAQRHIEADCNGESSLEQ---IANRLGKTIEEVRSILALGEHTASLDAPLD 211


>gi|90961886|ref|YP_535802.1| RNA polymerase sigma factor RpoD [Lactobacillus salivarius UCC118]
 gi|90821080|gb|ABD99719.1| RNA polymerase sigma factor [Lactobacillus salivarius UCC118]
          Length = 372

 Score =  104 bits (260), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 83/276 (30%), Positives = 131/276 (47%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 106 YLKEIGRVNLLTADEEVALALKI-EEGDQEAKQRLAEANLRLVVSIAKRYVGRGMSFLDL 164

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 165 IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 224

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q+++  +L R     +   + ++  E+V  I K       E +S+   +    D  L 
Sbjct: 225 RIQRQMLQDLGREPMPEEIGAEMDMPTEKVREILK----IAQEPVSLETPIGEEDDSHLG 280

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S         +H   E +          +  L   +  L  RE  +   R 
Sbjct: 281 DFIEDQDATSPA-------EHAAYELL----------KEQLESVLDTLTDREENVLRLRF 323

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 324 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 359


>gi|304403970|ref|ZP_07385632.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Paenibacillus
           curdlanolyticus YK9]
 gi|304346948|gb|EFM12780.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Paenibacillus
           curdlanolyticus YK9]
          Length = 377

 Score =  104 bits (260), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 81/264 (30%), Positives = 129/264 (48%), Gaps = 13/264 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   +E  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 111 YLKEIGRVPLLSADDEVELAKRI-EKGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 169

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 170 IQEGNMGLIKAVEKFDHTKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 227

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L         PE+   IA ++ +S  +V  +        SL   I   D   S
Sbjct: 228 LIRVSRQLLQELGREPAPEE---IAAEMELSTDKVREIMKIAQEPVSLETPIGEED--DS 282

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++    D +     +    +  +  L   +  L  RE  +   R   ++    TLE
Sbjct: 283 HLGDFI---EDQEALAPADAAAYELLKEQLEDVLDTLTEREENVLRLRFGLDDGRTRTLE 339

Query: 257 NLSSEFEVSRERVRQIEARAFKKV 280
            +   F V+RER+RQIEA+A +K+
Sbjct: 340 EVGKVFGVTRERIRQIEAKALRKL 363


>gi|300214611|gb|ADJ79027.1| RNA polymerase sigma factor [Lactobacillus salivarius CECT 5713]
          Length = 372

 Score =  104 bits (260), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 83/276 (30%), Positives = 134/276 (48%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 106 YLKEIGRVNLLTADEEVALALKI-EEGDQEAKQRLAEANLRLVVSIAKRYVGRGMSFLDL 164

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 165 IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 224

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q+++  +L R     +   + ++  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 225 RIQRQMLQDLGREPMPEEIGAEMDMPTEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 280

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S         +H   E +          +  L   +  L  RE  +   R 
Sbjct: 281 DFIEDQDATSPA-------EHAAYELL----------KEQLESVLDTLTDREENVLRLRF 323

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 324 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 359


>gi|323340800|ref|ZP_08081052.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           ruminis ATCC 25644]
 gi|323091923|gb|EFZ34543.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           ruminis ATCC 25644]
          Length = 373

 Score =  104 bits (260), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 88/276 (31%), Positives = 139/276 (50%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 107 YLKEIGRVNLLTAEEEKKLALRI-EEGDEEAKQRLAEANLRLVVSIAKRYVGRGMSFLDL 165

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 166 IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 225

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q+++  +L R     +   + NL  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 226 RIQRQMLQDLGREPIPEEIGAEMNLPTEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 281

Query: 188 ALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
             I   D  ++   D   Y+   +  E VL    +R+   N+L     + + R R     
Sbjct: 282 DFI--EDHAATSPADHAAYELLKEQIESVLDTLTDREE--NVLRLRFGLDDGRTR----- 332

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                   TLE +   F V+RER+RQIEA+A +K++
Sbjct: 333 --------TLEEVGKVFGVTRERIRQIEAKALRKLR 360


>gi|258648419|ref|ZP_05735888.1| RNA polymerase sigma factor [Prevotella tannerae ATCC 51259]
 gi|260851166|gb|EEX71035.1| RNA polymerase sigma factor [Prevotella tannerae ATCC 51259]
          Length = 286

 Score =  104 bits (260), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 76/289 (26%), Positives = 150/289 (51%), Gaps = 30/289 (10%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           N SI       L +Y+ EI +  ++   EE  LA+R  + GD  A  +L  ++LR VV +
Sbjct: 7   NKSITNRSSAALDKYLVEIGREGLISTDEEVELAQRIHK-GDAEALEKLTKANLRFVVSV 65

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y+  GL +++++ EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V
Sbjct: 66  AKQYQNQGLALNDLIDEGNLGLIRAAQKFDETRGFKFISYAVWWIRQSILQAISEQSRIV 125

Query: 125 K-----IGTTANQKRLFFNLRR---LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
           +     +G  +   +   N  +    +  +Q + D  +    V  + + +  +  +V S+
Sbjct: 126 RMPLNQVGFQSKLTKAIVNFEQEFERRPSVQELAD--ILDTDVAKVQEAMGTNGKKV-SV 182

Query: 177 NCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
           +     D+S N+LI+  +D+N+    D +               E+++  + L  ++  L
Sbjct: 183 DAPFQDDDS-NSLIDIMTDENAPGTDDQM---------------EKESLSSDLDAALGTL 226

Query: 236 NPRERRIFEAR-RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             RER + +    +  N +T E +++   ++RERVRQI+ RA ++++E+
Sbjct: 227 TERERLVLKMLFGIGRNEMTAEEVANSLSLTRERVRQIKERALRRLREA 275


>gi|229815176|ref|ZP_04445512.1| hypothetical protein COLINT_02221 [Collinsella intestinalis DSM
           13280]
 gi|229809186|gb|EEP44952.1| hypothetical protein COLINT_02221 [Collinsella intestinalis DSM
           13280]
          Length = 448

 Score =  104 bits (260), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 84/262 (32%), Positives = 132/262 (50%), Gaps = 20/262 (7%)

Query: 29  LEKQE----EYVLAKRYR----EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           LEKQE    E   A+  R    E   L A   L++++LRLVV IA  Y G G+   +++ 
Sbjct: 181 LEKQEAGEIELTRAEMRRLMRVEQVGLDAKQALISANLRLVVSIAKRYVGRGMLFLDLIQ 240

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           EGN+GL++AV+KFD E+GF+ +TY+ WWI+ A+   I      ++I    +       L 
Sbjct: 241 EGNLGLIRAVEKFDYEKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINKLV 298

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
           R++  L      +  PE+   I  ++++S   V  +        SL   I   ++  SQ 
Sbjct: 299 RVQRQLLQDLGRDPTPEE---IGAEMDMSADRVREIQKISQEPVSLETPIG--EEEDSQL 353

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENL 258
            D++    D Q  V  +       +  LT+ +  L  RER++ E R   E+  P TLE +
Sbjct: 354 GDFI---EDAQAVVPADAASFSMLQEQLTQVLDGLAERERKVIELRFGLEDGHPRTLEEV 410

Query: 259 SSEFEVSRERVRQIEARAFKKV 280
             EF V+RER+RQIE++   K+
Sbjct: 411 GREFGVTRERIRQIESKTLAKL 432


>gi|301301338|ref|ZP_07207482.1| RNA polymerase sigma factor RpoD [Lactobacillus salivarius
           ACS-116-V-Col5a]
 gi|300851066|gb|EFK78806.1| RNA polymerase sigma factor RpoD [Lactobacillus salivarius
           ACS-116-V-Col5a]
          Length = 372

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 83/276 (30%), Positives = 134/276 (48%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 106 YLKEIGRVNLLTADEEVALALKI-EEGDQEAKQRLAEANLRLVVSIAKRYVGRGMSFLDL 164

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 165 IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 224

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q+++  +L R     +   + ++  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 225 RIQRQMLQDLGREPMPEEIGAEMDMPTEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 280

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S         +H   E +          +  L   +  L  RE  +   R 
Sbjct: 281 DFIEDQDATSPA-------EHAAYELL----------KEQLESVLDTLTDREENVLRLRF 323

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 324 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 359


>gi|282899714|ref|ZP_06307678.1| sigA (Sigma 28 (Flagella/Sporulation)) [Cylindrospermopsis
           raciborskii CS-505]
 gi|281195593|gb|EFA70526.1| sigA (Sigma 28 (Flagella/Sporulation)) [Cylindrospermopsis
           raciborskii CS-505]
          Length = 390

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 75/246 (30%), Positives = 131/246 (53%), Gaps = 17/246 (6%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           RYR H    A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G+
Sbjct: 145 RYRLHVGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGY 204

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT-DNNLKP-E 157
           + +TY+ WWI+ A+   I      +++        L+  + R+K   + ++ +   KP E
Sbjct: 205 KFSTYATWWIRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKLLSQEMGRKPTE 259

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           + +A   ++ + +   I+ + +L    SL   I   +   S+  D++  D +  E  + +
Sbjct: 260 EEIATRMEMTIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIESDGETPEDQVSK 315

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEAR 275
              R++    L R +  L PRER +   R   +N    TLE +   F V+RER+RQIEA+
Sbjct: 316 SLLRED----LERVLDSLGPRERDVLRLRYGLDNGRMKTLEEIGQIFNVTRERIRQIEAK 371

Query: 276 AFKKVQ 281
           A +K++
Sbjct: 372 ALRKLR 377


>gi|158340427|ref|YP_001521783.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158310668|gb|ABW32282.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 273

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 85/290 (29%), Positives = 151/290 (52%), Gaps = 41/290 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI + P+L  +EE  LA++ +  G+L A  R++  +LRLVV IA  ++  GLP  ++
Sbjct: 10  YLKEIGRYPLLSHEEEIQLARQAKA-GNLRAKQRMIECNLRLVVSIAKKHQNRGLPFMDL 68

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EG+IGL +AV+KF+PE+G+R +TY+ WWI+  +   I  +  ++++            
Sbjct: 69  IQEGSIGLSRAVEKFEPEQGYRFSTYAYWWIRQGITRSIQNNSRVIRLPV---------- 118

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
                 H Q  T N +K  Q     ++L+       ++   LA  E++   ++   +N  
Sbjct: 119 -----WHWQ--TGNQIKQTQ-----RQLSQEFGREPTL-AELA--EAMEIDLDKLKQNMH 163

Query: 199 QWQDWLVYDHD-GQEQ-----VLIEKEERK-------NRRNMLTRSMSVLNPRERRIFEA 245
             QD L  D   G+EQ      LIE E+         N+   ++  +S+L+ R+R +   
Sbjct: 164 HLQDVLSLDMQVGKEQDTTLGELIEAEQSTPTHLELLNQSEEVSSYLSLLDERQRYVIVQ 223

Query: 246 RRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           R   E+    T++++  +  VSRER+RQI  +A KK+Q++     E+ ++
Sbjct: 224 RYGLEDGEAKTMQDIGQQLGVSRERIRQIINKAMKKLQKNSDLATEIKTA 273


>gi|254389040|ref|ZP_05004270.1| RNA polymerase principal sigma factor hrdA [Streptomyces
           clavuligerus ATCC 27064]
 gi|326441042|ref|ZP_08215776.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|197702757|gb|EDY48569.1| RNA polymerase principal sigma factor hrdA [Streptomyces
           clavuligerus ATCC 27064]
          Length = 385

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 89/296 (30%), Positives = 143/296 (48%), Gaps = 45/296 (15%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRY-------------------REHGDLS--------AAH 51
           Y+ EI +IP+L   EE  LA+R                    R   DL         A  
Sbjct: 91  YLREIGRIPLLTAAEEVELARRVEAGLFAEEKLAATPDLNSSRLAADLDRLVVMGRMAKR 150

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY+ WWI+ 
Sbjct: 151 RLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYTRGYKFSTYATWWIRQ 210

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           AM   +      +++     +  L   + R++  +     +   PE+V A   +L++   
Sbjct: 211 AMSRALADQARTIRVPVHVVE--LINRVVRVQRRMLQEQGSEPTPEEVAA---QLDLP-P 264

Query: 172 EVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNML 228
           E +S   RLA +  SL+A +        + +D  + D   DG     +E       R  L
Sbjct: 265 ERVSEVLRLAQEPVSLHAPVG-------EEEDVALGDLIEDGDAASPVESAAFLLLREHL 317

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              +S L  RER++ + R       P TLE +   F V+RER+RQIE++   K+++
Sbjct: 318 EAVLSTLGERERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRD 373


>gi|160331013|ref|XP_001712214.1| rpoD [Hemiselmis andersenii]
 gi|159765661|gb|ABW97889.1| rpoD [Hemiselmis andersenii]
          Length = 485

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 79/265 (29%), Positives = 141/265 (53%), Gaps = 18/265 (6%)

Query: 39  KRYRE--HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           K++R   H    A  R+V ++LRLVV IA  Y   G+ + +++ EG++GL++A +KFD E
Sbjct: 193 KKFRAILHNARRAKERMVAANLRLVVSIAKRYVNRGMSLQDLIQEGSLGLIRAAEKFDSE 252

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +GF+ +TY+ WW+K A+   I      +++        L+  +  ++   + +     + 
Sbjct: 253 KGFKFSTYATWWVKQAVTRAIADHSRTIRLPV-----HLYDTISAIRKTTRTLNIEIGRS 307

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
                IA+K+++S  ++ S+        SL   + + D ++SQ  D++  D +  E    
Sbjct: 308 PTEEEIAEKMDMSVEKLRSVLQSAQPTLSLERPLKNDD-DASQLSDFIEADQESPE---- 362

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPV-TLENLSSEFEVSRERVRQIEA 274
           E  E+   R+ L   ++ L+PRER +   R  L +  + TLE +   F V+RERVRQIEA
Sbjct: 363 EHVEKSMLRDDLENVINSLSPRERDVVRMRYGLDDGRIKTLEEIGQIFSVTRERVRQIEA 422

Query: 275 RAFKKVQE----SIQKQVELSSSPP 295
           +A +K+++    SI +   L+S  P
Sbjct: 423 KAIRKLRQPYRSSILRDYVLASLSP 447


>gi|53714034|ref|YP_100026.1| RNA polymerase sigma factor RpoD [Bacteroides fragilis YCH46]
 gi|60682231|ref|YP_212375.1| putative sigma factor A [Bacteroides fragilis NCTC 9343]
 gi|253564677|ref|ZP_04842133.1| RpoD [Bacteroides sp. 3_2_5]
 gi|255010339|ref|ZP_05282465.1| putative sigma factor A [Bacteroides fragilis 3_1_12]
 gi|265766346|ref|ZP_06094387.1| RNA polymerase sigma factor RpoS [Bacteroides sp. 2_1_16]
 gi|313148138|ref|ZP_07810331.1| RNA polymerase sigma factor rpoD [Bacteroides fragilis 3_1_12]
 gi|52216899|dbj|BAD49492.1| RNA polymerase sigma factor RpoD [Bacteroides fragilis YCH46]
 gi|57471281|gb|AAW50926.1| RpoD [Bacteroides fragilis]
 gi|60493665|emb|CAH08454.1| putative sigma factor A [Bacteroides fragilis NCTC 9343]
 gi|251946142|gb|EES86519.1| RpoD [Bacteroides sp. 3_2_5]
 gi|263254014|gb|EEZ25479.1| RNA polymerase sigma factor RpoS [Bacteroides sp. 2_1_16]
 gi|301163709|emb|CBW23263.1| putative sigma factor A [Bacteroides fragilis 638R]
 gi|313136905|gb|EFR54265.1| RNA polymerase sigma factor rpoD [Bacteroides fragilis 3_1_12]
          Length = 286

 Score =  104 bits (260), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 77/272 (28%), Positives = 149/272 (54%), Gaps = 18/272 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI +  ++  +EE  LA+R R+ GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGREDLITVEEEVELAQRIRK-GDRVALEKLTRANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     +V++    NQ   
Sbjct: 77  PDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL--PLNQVGS 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
              + +     +   +    PE+   +A +L++   + IS   +++G   S++A     +
Sbjct: 135 LNKISKAFSKFEQENERRPSPEE---LAGELDIP-VDKISDTLKVSGRHISVDAPFVEGE 190

Query: 195 KNSSQWQDWLVYDHD--GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA-RRLQEN 251
            NS    D LV D        ++ E   R+     + R++S L  RE+ I +    + + 
Sbjct: 191 DNS--LLDVLVNDDSPMADRSLVNESLARE-----IDRALSTLTDREKEIIQMFFGIGQQ 243

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +TLE +  +F ++RERVRQI+ +A +++++S
Sbjct: 244 EMTLEEIGDKFGLTRERVRQIKEKAIRRLRQS 275


>gi|123967121|ref|YP_001012202.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9515]
 gi|123201487|gb|ABM73095.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9515]
          Length = 339

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 81/278 (29%), Positives = 148/278 (53%), Gaps = 26/278 (9%)

Query: 13  EIGLSRYIHEIRK---IPMLEKQEE----YVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           EI L+ ++  ++K   IP +E+         + KR R+        R+++++LRLVV +A
Sbjct: 70  EIELAHHVQNMKKMLKIPEIERSSRNRHLIKVGKRARD--------RMMSANLRLVVSVA 121

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+  M   I  S   ++
Sbjct: 122 KKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIR 181

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           +    ++K     +RR+   L     +  +P + + +A  + + + ++  +  + A   S
Sbjct: 182 LPIHISEK--LSKMRRVSRELS--QKSGRQPTR-LEMATAMGIDQKDLEDLISQSAPCAS 236

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L+A     +  S+  +  L+ D +G+E   +E  +R  ++  L   ++ LN RE++I + 
Sbjct: 237 LDAHARGEEDRSTLGE--LIPDPNGEEP--MEGMDRTIQKEHLGTWLTQLNEREQKIMKL 292

Query: 246 R--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R     E P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 293 RFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 330


>gi|332686632|ref|YP_004456406.1| RNA polymerase sigma factor RpoD [Melissococcus plutonius ATCC
           35311]
 gi|332370641|dbj|BAK21597.1| RNA polymerase sigma factor RpoD [Melissococcus plutonius ATCC
           35311]
          Length = 369

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 84/275 (30%), Positives = 134/275 (48%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 103 YLKEIGRVQLLTAEEEVELALKI-EEGDQEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 161

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 162 IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 221

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + +L  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 222 RIQRQLLQDLGREPTPEEIGAEMDLPTEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 277

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         +H   E +          +  L   +  L  RE  +   R 
Sbjct: 278 DFIEDQEATSP-------AEHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 320

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 321 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 355


>gi|227890913|ref|ZP_04008718.1| RNA polymerase sigma factor RpoD [Lactobacillus salivarius ATCC
           11741]
 gi|227867322|gb|EEJ74743.1| RNA polymerase sigma factor RpoD [Lactobacillus salivarius ATCC
           11741]
          Length = 372

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 83/276 (30%), Positives = 134/276 (48%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 106 YLKEIGRVNLLTADEEVALALKI-EEGDQEAKQRLAEANLRLVVSIAKRYVGRGMSFLDL 164

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 165 IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 224

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q+++  +L R     +   + ++  E+V  I   L +++ E +S+   +    D  L 
Sbjct: 225 RIQRQMLQDLGREPMPEEIGAEMDMPTEKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 280

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   D  S         +H   E +          +  L   +  L  RE  +   R 
Sbjct: 281 DFIEDQDATSPA-------EHAAYELL----------KEQLESVLDTLTDREENVLRLRF 323

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 324 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 359


>gi|224534531|ref|ZP_03675107.1| RNA polymerase sigma factor [Borrelia spielmanii A14S]
 gi|224514208|gb|EEF84526.1| RNA polymerase sigma factor [Borrelia spielmanii A14S]
          Length = 266

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 81/282 (28%), Positives = 148/282 (52%), Gaps = 20/282 (7%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M+I  N ++ +  Y+  +R+  ++  +EE  LA +  + G+  A ++++ ++LRLV+KI 
Sbjct: 1   MNIFSNEDLNI--YLKSVREHKLITHEEEIQLAGQI-QRGNAQAKNKMINANLRLVLKII 57

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y G GL I +++ EGN+GL++A +K+DP +  + +TY+ +WIK ++Q  +     LVK
Sbjct: 58  KRYAGKGLKIEDLIQEGNLGLIRAAEKYDPNKNTKFSTYASFWIKQSLQRALNTKTRLVK 117

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           +          +    L   +        K  +   I K+ N+S ++ I +   L  + S
Sbjct: 118 VP---------YRKENLILQINKYLTEEEKSPKKEEIMKRFNLSPAQYIKIIPYLEKEYS 168

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L+  I  S+ NS+     L  D+    ++ +E++      N +  +   L  +ER I + 
Sbjct: 169 LDKEIEGSE-NSTLLN--LYEDNSFNPEITLEQDSTIKHLNYILETK--LTEKERYIIKK 223

Query: 246 R-RLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L  +P   TL+++S+E  +S E VRQIE R  KK++E I
Sbjct: 224 RYNLDNSPKKSTLKDISTELGISSETVRQIEKRVLKKLKEEI 265


>gi|222056415|ref|YP_002538777.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           FRC-32]
 gi|221565704|gb|ACM21676.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           FRC-32]
          Length = 358

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 80/278 (28%), Positives = 147/278 (52%), Gaps = 18/278 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI+K  +L   EE  LA R  + GD +A  +++ S+LRLVVKIA  Y   GLP  ++
Sbjct: 88  YLREIQKTKLLTADEEKELAARI-DRGDKAARDKMIESNLRLVVKIAKRYINRGLPFLDL 146

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV++F   +  R +TY+ WWI+ +++  ++     +++    +   +   
Sbjct: 147 IEEGNMGLIKAVERFKLSKECRFSTYATWWIRQSIERALVNQSRTIRLPVHVSDD-INKM 205

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +  LQ I   N +P  +  +A  + V+ + +  +   L    S+       ++   
Sbjct: 206 LRITRELLQKI---NREP-SIKEVATAMEVNSAYIRRLMVLLKKTYSI-------ERPMG 254

Query: 199 QWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVT 254
           +  D+ + D   D       E  E  NR  M+++    L+  E++I   R     ++P T
Sbjct: 255 ENNDYFLIDTIEDTSTVSPAELLEDVNRYEMVSKWFDTLSDNEKKILTLRFGLDDKDPQT 314

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
           L+ +   F V+RER+RQIEA++ +K+++ I +  EL++
Sbjct: 315 LDTIGRSFGVTRERIRQIEAKSLEKLRK-IMEATELAA 351


>gi|149188695|ref|ZP_01866986.1| RNA polymerase sigma factor RpoS [Vibrio shilonii AK1]
 gi|148837356|gb|EDL54302.1| RNA polymerase sigma factor RpoS [Vibrio shilonii AK1]
          Length = 296

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 78/280 (27%), Positives = 136/280 (48%), Gaps = 29/280 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y  E+    +L  ++E  +A++ R  GD  A   L+ S+LRLV++ A  Y   GL   ++
Sbjct: 27  YFKEVAGHDLLSAEDERHIARKARA-GDTLARQHLINSNLRLVIRTAKRYSNRGLDFYDL 85

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK----- 133
           ++EGNIGL+QAV KFDPE G+R +TY++WWI+ A+   I+     +++     ++     
Sbjct: 86  INEGNIGLIQAVDKFDPELGYRFSTYAVWWIQQAIDRAIMNQGRTIRVPVHVTKQIRECS 145

Query: 134 RLFFNLRRLKGHLQAITD----NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
           +    LR+   H    ++        PE+V   +K L +SE  +              +L
Sbjct: 146 KAAHELRKEGNHEPTSSEIAERTGRAPEEV---SKLLKLSEQSL--------------SL 188

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--R 247
            N  D+   +       D D   ++  +    +N    L   +  L  ++R I   R   
Sbjct: 189 DNGWDEEGDKKDHLQTIDDDDVFELPEQDIVTQNLNKALIDLVDSLPDKQRVILHHRFGL 248

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L ++P TLE +     V+RERVRQI+  A + +++ +++Q
Sbjct: 249 LDDDPKTLEQVGEIVGVTRERVRQIQKSAMETLRDKLKRQ 288


>gi|312196071|ref|YP_004016132.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EuI1c]
 gi|311227407|gb|ADP80262.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EuI1c]
          Length = 393

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 92/309 (29%), Positives = 148/309 (47%), Gaps = 62/309 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHG-------------------DLSAAHR------- 52
           Y+ EI K+P+L   EE  LAKR  E G                   DL A  R       
Sbjct: 100 YLKEIGKVPLLTAAEEVDLAKRI-EAGLFAAEKLGGGRRLTVALRVDLEAVARDGDVAKR 158

Query: 53  -LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            LV ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 159 KLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 218

Query: 112 AMQEYILRSWSLVKIGT----TAN-----QKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   I      ++I      T N     Q++L  +L R     +   + +L P++V  I
Sbjct: 219 AITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPLPEEIAKEMDLTPDKVREI 278

Query: 163 AKKLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
              L V++ E +S+   +  +E   L   I  SD          V   D    +L++++ 
Sbjct: 279 ---LKVAQ-EPVSLETPIGEEEDSHLGDFIEDSDA---------VVPVDAASFLLLQEQ- 324

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE+++ + R      +P TLE +  EF V+RER+RQIE++   
Sbjct: 325 -------LDSVLHTLSDREKKVIQLRFGLTDGHPRTLEEVGREFGVTRERIRQIESKTLS 377

Query: 279 KVQESIQKQ 287
           K++   + Q
Sbjct: 378 KLRHPSRSQ 386


>gi|305664513|ref|YP_003860800.1| putative sigma factor A [Maribacter sp. HTCC2170]
 gi|88708530|gb|EAR00766.1| putative sigma factor A [Maribacter sp. HTCC2170]
          Length = 287

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 81/288 (28%), Positives = 153/288 (53%), Gaps = 39/288 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ ++   EE  LA+R +  GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGKVDLITADEEVELAQRIKA-GDQIALEKLTKANLRFVVSVAKQYQNQGLTL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
            ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++      Q  I+R   L KIG+ 
Sbjct: 77  PDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVR-LPLNKIGSI 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNA 188
               + F  L +    + +  +          IAK+L+++  E +  + + +G   S++A
Sbjct: 136 NKINKTFAFLEQAHERMPSAEE----------IAKELDMT-VEDVKQSLKNSGRHVSMDA 184

Query: 189 -LINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
            LI   D N        +YD    G+      +   ++ R  + R++  L PRE  +   
Sbjct: 185 PLIAGEDSN--------LYDVLRSGESPNPDRELLHESLRTEIERALETLTPREADVI-- 234

Query: 246 RRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            RL      ++ +TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 235 -RLYFGLAGQHSMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|148658692|ref|YP_001278897.1| RpoD family RNA polymerase sigma factor [Roseiflexus sp. RS-1]
 gi|148570802|gb|ABQ92947.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus sp.
           RS-1]
          Length = 401

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 87/303 (28%), Positives = 143/303 (47%), Gaps = 63/303 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR---------EHGDLS----------------AAHRL 53
           Y+ EI ++ +L  QEE +LA++           + GD +                A  RL
Sbjct: 109 YLREIGRVNLLTAQEEIMLAQQVERGEQASERLQKGDYAPSERLQLHRWVQEGQAARERL 168

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           + ++LRLVV IA  Y G G+ + +++ EGNIGLM+A +KFD  +G++ +TY+ WWI+ A+
Sbjct: 169 IQANLRLVVSIAKKYLGRGMSLLDLIQEGNIGLMRATEKFDYRKGYKFSTYATWWIRQAI 228

Query: 114 QEYIL---RSWSL-VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV-----VAIAK 164
              I    R+  L V +G T N+      + R    +Q  T  +  P+++     + + K
Sbjct: 229 TRVIADQSRTIRLPVHVGETINR------VMRASNRIQQTTGRDPTPDEIALELGIPVEK 282

Query: 165 KLNVSES--EVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
              V E+  + IS+   +   GD  L   I                  DG+    ++   
Sbjct: 283 VRRVLEAARQTISLETPIGTEGDTVLADFIE-----------------DGKGVTPMDSAS 325

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFK 278
               R  +  ++  L  RERRI + R      +  TLE +  EF ++RER+RQIEAR  +
Sbjct: 326 HHILREQIDSALEKLPERERRIIQLRYGLYDGHYRTLEEVGREFGITRERIRQIEARVLR 385

Query: 279 KVQ 281
           K++
Sbjct: 386 KLR 388


>gi|270291312|ref|ZP_06197534.1| RNA polymerase primary sigma factor [Pediococcus acidilactici 7_4]
 gi|304385062|ref|ZP_07367408.1| RNA polymerase sigma factor rpoD [Pediococcus acidilactici DSM
           20284]
 gi|270280158|gb|EFA25994.1| RNA polymerase primary sigma factor [Pediococcus acidilactici 7_4]
 gi|304329256|gb|EFL96476.1| RNA polymerase sigma factor rpoD [Pediococcus acidilactici DSM
           20284]
          Length = 379

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 85/278 (30%), Positives = 138/278 (49%), Gaps = 41/278 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LA R  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 113 YLKEIGRVSLLTADEEVALALRI-EKGDERAKQELAEANLRLVVSIAKRYVGRGMQFLDL 171

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD ++GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 172 IQEGNMGLMKAVEKFDYQKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 231

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + ++  ++V  I   L +++ E +S+   +    D  L 
Sbjct: 232 RIQRQLLQDLGREPMPEEIGAEMDMPSDKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 287

Query: 188 ALINSSDKNSSQWQDWLVYD-----HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             I   D+ ++   D   Y+      +G    L ++EE     N+L     + + R R  
Sbjct: 288 DFIE--DQEATSPADHAAYELLKEQLEGVLDTLTDREE-----NVLRLRFGLDDGRTR-- 338

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                      TLE +   F V+RER+RQIEA+A +K+
Sbjct: 339 -----------TLEEVGKVFGVTRERIRQIEAKALRKL 365


>gi|210633964|ref|ZP_03297935.1| hypothetical protein COLSTE_01853 [Collinsella stercoris DSM 13279]
 gi|210159008|gb|EEA89979.1| hypothetical protein COLSTE_01853 [Collinsella stercoris DSM 13279]
          Length = 445

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 74/236 (31%), Positives = 122/236 (51%), Gaps = 12/236 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L A   L++++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD E+GF+ +TY+ 
Sbjct: 204 LDAKQALISANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYEKGFKFSTYAT 263

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I    +       L R++  L      +  PE+   I  ++
Sbjct: 264 WWIRQAITRAIADQARTIRI--PVHMVETINKLVRVQRQLLQDLGRDPTPEE---IGAEM 318

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++S   V  +        SL   I   ++  SQ  D++    D Q  V  +       + 
Sbjct: 319 DMSADRVREIQKISQEPVSLETPIG--EEEDSQLGDFI---EDAQAVVPADAASFSMLQE 373

Query: 227 MLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            LT+ +  L  RER++ E R   +  +P TLE +  EF V+RER+RQIE++   K+
Sbjct: 374 QLTQVLDGLAERERKVIELRFGLVDGHPRTLEEVGREFGVTRERIRQIESKTLAKL 429


>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 =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 71/236 (30%), Positives = 124/236 (52%), Gaps = 12/236 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 548 DAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 607

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I     +     N R  + HLQ       +P+  + +A K+ 
Sbjct: 608 WIRQAITRSIADQARTIRIPVHMIETINKMN-RISRQHLQEF---GFEPDASI-LAAKME 662

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + E ++  +  ++A  E ++      D + S   D++    DG     IE   +   R++
Sbjct: 663 IPEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDGANTAPIEAAMQAGLRDV 717

Query: 228 LTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  L PRE ++   R   E  +  TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 718 VKDILDGLTPREAKVLRMRFGIEMTSDHTLEEVGKQFDVTRERIRQIEAKALRKLK 773


>gi|317968274|ref|ZP_07969664.1| putative type II alternative RNA polymerase sigma factor
           [Synechococcus sp. CB0205]
          Length = 382

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 75/237 (31%), Positives = 122/237 (51%), Gaps = 15/237 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R++ ++LRLVV +A  Y+  G+ + ++V EG +GL +AV+K+DP RGFR +TY+ WW
Sbjct: 136 ARDRMIQANLRLVVAVAKKYQQRGMELLDLVQEGTLGLERAVEKYDPTRGFRFSTYAYWW 195

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   I      +++     +K     L R+K   + I   + +   V  +AK+L +
Sbjct: 196 IRQGITRAIATQSRTIRLPVHVTEK-----LNRIKKAQRQIASEHGRLASVADLAKELGL 250

Query: 169 SESEVISMNC-RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           SE EVI +   R+    SL+  +       ++  D L   H   EQ L + +   +   +
Sbjct: 251 SE-EVIRLTLMRVPRSVSLDTRVGRD--QDTELGDLLEDGHATPEQALTKTQLHDDLEAL 307

Query: 228 LTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           L      L+ RE  +   R   EN  P TL  +  +  +SRERVRQIE RA  K+++
Sbjct: 308 LEE----LSGREAEVIRLRFGLENDTPQTLSQIGEDLHLSRERVRQIETRALLKLRQ 360


>gi|95930284|ref|ZP_01313022.1| RNA polymerase, sigma 28 subunit [Desulfuromonas acetoxidans DSM
           684]
 gi|95133747|gb|EAT15408.1| RNA polymerase, sigma 28 subunit [Desulfuromonas acetoxidans DSM
           684]
          Length = 296

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 77/285 (27%), Positives = 148/285 (51%), Gaps = 19/285 (6%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
            +G+  +  Y+H+I+K  +L  +EE  LA +  E GD  A  +++ S+LRLVVKIA  Y 
Sbjct: 23  TSGDDAIKYYLHDIQKSKLLTAEEERALATKV-EAGDEQARAKMIESNLRLVVKIAKRYM 81

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
             GLP  +++ EGN+GL++AV++F   +  R +TY+ WWI+ +++  ++     +++   
Sbjct: 82  NRGLPFLDLIEEGNMGLIKAVERFQVAKECRFSTYATWWIRQSIERALVNQSRTIRLPVH 141

Query: 130 ANQKRLFFNLRR-LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
            +      N+ R LK   + +   N +P +   IA+ +     EV  +   +    S+  
Sbjct: 142 VSD-----NVNRMLKATKEVLKKLNHEPSE-AQIAEAMGAPVEEVRRLQQLVKKTYSIEH 195

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKE--ERKNRRNMLTRSMSVLNPRERRIFEAR 246
            +  +D       ++ + D      V+   E  E +++ + + + +S L   ER I   R
Sbjct: 196 PLGDND-------NYSLMDTLEDSSVINPAELLENQDQYDFVNKWLSSLKENERDILMLR 248

Query: 247 RLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
               +  P TL+ +   + V+RER+RQIEA++  K++  ++++ E
Sbjct: 249 FGLNDCEPETLDTIGKRYGVTRERIRQIEAKSLDKLRRMMREEAE 293


>gi|37523928|ref|NP_927305.1| group2 RNA polymerase sigma factor [Gloeobacter violaceus PCC 7421]
 gi|35214934|dbj|BAC92300.1| group2 RNA polymerase sigma factor [Gloeobacter violaceus PCC 7421]
          Length = 344

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 75/256 (29%), Positives = 130/256 (50%), Gaps = 36/256 (14%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L A  +L+ ++LRLVV IA  Y G  +P  +++ EGNIGLM+A +KFDPE+G+R +TY+ 
Sbjct: 104 LWAQRKLINANLRLVVSIAKKYIGRNVPFLDLIQEGNIGLMRATEKFDPEKGYRFSTYAT 163

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT--------DNNLKPEQ 158
           WWI+ ++   I      +++     +K     +R+++  ++  T        ++ L    
Sbjct: 164 WWIRQSITRAIANQARTIRLPIHMVEK-----VRKVRREMRMATLELGRRPSEDELASRL 218

Query: 159 VVAIAKKLNVSE--SEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            + + K   + E   + +S++  +   GD SL  +I   D  + +  D LV      E  
Sbjct: 219 AIKVKKLRTIQEVSRQPVSLDMPVGSEGDISLGEMIE--DGTAERPFDELVQKALASE-- 274

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQI 272
                        L  +M+VL P ER +   R     E  +TL  +   F+++RER+RQI
Sbjct: 275 -------------LYAAMNVLKPVEREVLALRFGLKGEEGLTLREVGERFDLTRERIRQI 321

Query: 273 EARAFKKVQESIQKQV 288
           E+ A +K++ S +KQ+
Sbjct: 322 ESEALRKLRRSKRKQI 337


>gi|187918623|ref|YP_001884188.1| RNA polymerase sigma factor RpoS [Borrelia hermsii DAH]
 gi|119861471|gb|AAX17266.1| RNA polymerase sigma factor RpoS [Borrelia hermsii DAH]
          Length = 267

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 87/287 (30%), Positives = 149/287 (51%), Gaps = 30/287 (10%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M+I  N ++ +  Y+  +R+  ++  +EE  LAK+ +  GDL A ++++ ++LRLV+KI 
Sbjct: 1   MNIFSNEDLNI--YLKSVREHRLITHEEEIELAKQIK-LGDLKAKNKMINANLRLVLKII 57

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y G GL + +++ EGN+GL++A +K+DP +  + +TY+ +WIK ++Q  +     LVK
Sbjct: 58  KRYAGKGLKVEDLIQEGNLGLIRAAEKYDPSKNTKFSTYASFWIKQSLQRALNTKTRLVK 117

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDN-----NLKPEQVVAIAKKLNVSESEVISMNCRL 180
           +        L  N   ++       ++     NL   Q V I   L   E E  S++ +L
Sbjct: 118 VPYRKENLILQINKYLMEEEKSPKKEDIMERFNLTTAQYVKIIPYL---EKEY-SLDKKL 173

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            G E+ + L+N  + NS              E  L +    K+  ++L    + LN +ER
Sbjct: 174 EGSEN-STLLNLYEDNSF-----------NPESTLEQNSTLKHLNHILE---TKLNDKER 218

Query: 241 RIFEARRLQEN---PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            I   R   +N     TL+++SSE  +S E VRQIE R  KK++E +
Sbjct: 219 YIIRKRYNLDNNDKKSTLKDISSELGISSETVRQIEKRVLKKLREEL 265


>gi|315651467|ref|ZP_07904490.1| DNA-directed RNA polymerase sigma subunit RpoD [Eubacterium
           saburreum DSM 3986]
 gi|315486287|gb|EFU76646.1| DNA-directed RNA polymerase sigma subunit RpoD [Eubacterium
           saburreum DSM 3986]
          Length = 389

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 82/278 (29%), Positives = 141/278 (50%), Gaps = 23/278 (8%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL---SAAHRLVTSHLRLVVKIAMGYR 69
           E  +  Y+ EI KIP+L   EE  LAK+  +  +     A  ++  S+LRLVV IA  Y 
Sbjct: 113 EDSIKMYLKEIGKIPLLSVDEEMNLAKKICDPDEAVRKEARKQMAESNLRLVVSIAKRYM 172

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT- 128
           G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ WWI+ A+   I      ++I   
Sbjct: 173 GRGMQFLDLIQEGNLGLLRAVEKFDYQKGFKFSTYATWWIRQAITRSIADQARTIRIPVH 232

Query: 129 ---TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
              T N+      L +++  L        +P++V   AK + +  S+V  +        S
Sbjct: 233 MVETINR------LIKIQRKLVQEFGREPRPDEV---AKVMGIPVSKVREIMSFALEPVS 283

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           +   I   D++ S   D+L    D   ++ +         + L   +  L  RE+++   
Sbjct: 284 METPI--GDEDDSHLGDFL---QDSNAKIPVNFAMDVLLHDQLMEVIKSLTEREQKVILL 338

Query: 246 RRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   E+  P TLE +   F ++RER+RQIEA++ +K++
Sbjct: 339 RFGLEDGKPRTLEEVGKVFGITRERIRQIEAKSLRKLR 376


>gi|298247391|ref|ZP_06971196.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297550050|gb|EFH83916.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 385

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 93/314 (29%), Positives = 143/314 (45%), Gaps = 62/314 (19%)

Query: 8   IIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYR----------------EHGDLSA 49
           I   GE G  L  Y+ E+ ++P+L  ++E  LA++                  EH  + +
Sbjct: 85  IEAAGEPGDTLETYLREMGRVPLLTSEQEVQLAQQIERGKLEQERARLLKVPPEHAIMDS 144

Query: 50  AH----RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           A     RL  ++LRLVV IA  Y G G+ +++++ EGN GLM AV+KFD  RGF+ +TY+
Sbjct: 145 AQNARDRLTEANLRLVVSIARKYMGRGMALADLIQEGNAGLMLAVEKFDYTRGFKFSTYA 204

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI------TDNNLKPE-- 157
            WWI+ A+   I            ANQ R      RL  H          T + L  E  
Sbjct: 205 TWWIRQAINRAI------------ANQARTI----RLPVHFHEAVNRLHRTSSQLFQELG 248

Query: 158 ---QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
                  IA+++++S   V   +   AG + ++      D   S   D++      ++QV
Sbjct: 249 REPSAEEIAERMHISVDTV--YDILEAGKQPISLESPVGDDGDSSLGDFV------EDQV 300

Query: 215 LIEKEERKNR---RNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERV 269
                +   R   R  +   +  LN RER I +     L     TL  +     +SRERV
Sbjct: 301 TASPADITTRNILREQIAHVLDELNERERHIIQYHFGFLDGKEHTLAEIGENLHLSRERV 360

Query: 270 RQIEARAFKKVQES 283
           RQIEA+A +K+++S
Sbjct: 361 RQIEAKALRKLRQS 374


>gi|294812504|ref|ZP_06771147.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|294325103|gb|EFG06746.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 436

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 89/296 (30%), Positives = 143/296 (48%), Gaps = 45/296 (15%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRY-------------------REHGDLS--------AAH 51
           Y+ EI +IP+L   EE  LA+R                    R   DL         A  
Sbjct: 142 YLREIGRIPLLTAAEEVELARRVEAGLFAEEKLAATPDLNSSRLAADLDRLVVMGRMAKR 201

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY+ WWI+ 
Sbjct: 202 RLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYTRGYKFSTYATWWIRQ 261

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           AM   +      +++    +   L   + R++  +     +   PE+V A   +L++   
Sbjct: 262 AMSRALADQARTIRV--PVHVVELINRVVRVQRRMLQEQGSEPTPEEVAA---QLDLP-P 315

Query: 172 EVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNML 228
           E +S   RLA +  SL+A +        + +D  + D   DG     +E       R  L
Sbjct: 316 ERVSEVLRLAQEPVSLHAPVG-------EEEDVALGDLIEDGDAASPVESAAFLLLREHL 368

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              +S L  RER++ + R       P TLE +   F V+RER+RQIE++   K+++
Sbjct: 369 EAVLSTLGERERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRD 424


>gi|224531828|ref|ZP_03672460.1| RNA polymerase sigma factor [Borrelia valaisiana VS116]
 gi|224511293|gb|EEF81699.1| RNA polymerase sigma factor [Borrelia valaisiana VS116]
          Length = 266

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 82/282 (29%), Positives = 147/282 (52%), Gaps = 20/282 (7%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M+I  N ++ +  Y+  +R+  ++  +EE  LA +  + G   A ++++ ++LRLV+KI 
Sbjct: 1   MNIFSNEDLNI--YLKSVREHKLITHEEEIKLAGQI-QRGSAQAKNKMINANLRLVLKII 57

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y G GL I +++ EGN+GL++A +K+DP +  + +TY+ +WIK ++Q  +     LVK
Sbjct: 58  KRYAGKGLKIEDLIQEGNLGLIRAAEKYDPNKNTKFSTYASFWIKQSLQRALNTKTRLVK 117

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           +          +    L   +        K  +   I K+ N+S ++ I +   L  + S
Sbjct: 118 VP---------YRKENLILQINKYLTEEEKSPKKEEIMKRFNLSPAQYIKIIPYLEKEYS 168

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L+  I  S+ NS+     L  D+    ++ +E++      N +  +   LN +ER I + 
Sbjct: 169 LDKEIEGSE-NSTLLN--LYEDNSFNPEITLEQDSTLKHLNYVLETK--LNEKERYIIKK 223

Query: 246 R-RLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L  +P   TL+++S E  +S E VRQIE R  KK++E I
Sbjct: 224 RYNLDNSPKKSTLKDISMELGISSETVRQIEKRVLKKLKEEI 265


>gi|78779769|ref|YP_397881.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9312]
 gi|78713268|gb|ABB50445.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9312]
          Length = 313

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 86/304 (28%), Positives = 152/304 (50%), Gaps = 40/304 (13%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------EHGDLS----------------- 48
           G   +S Y+  I ++P+L   EE  L  + +      E G L+                 
Sbjct: 16  GNDPISWYLQNIGRVPLLTPAEEIELGNQVQKMMILTEDGQLNEKIKEFTTQQKRIIKIG 75

Query: 49  --AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  R++ ++LRLVV +A  Y+G GL + ++V EG++GL +AV+KFDP RG++ +TY+ 
Sbjct: 76  RRAKERMMKANLRLVVSVAKKYQGKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAF 135

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFN--LRRLKGHLQAITDNNLKPEQVVAIAK 164
           WWI+ +M   I      +++    +++        R L   L A+          + IA+
Sbjct: 136 WWIRQSMTRAIACQSRTIRLPVHLSERLAAIRKVSRELAHKLGAMPSR-------IEIAE 188

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            +++   E+ S+  +     SL+A +N  D  S  +   L+ D + +E   ++K E+K  
Sbjct: 189 AMDIDVEELDSVLRQALSTSSLDAPVNGDDGRS--FLGDLIADSNTEEP--LDKVEQKMH 244

Query: 225 RNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +  L + +S L+ +E+ + + R  L  N   TL  +    EVSRERVRQ+E +A +K++ 
Sbjct: 245 QEQLGKWLSHLSEQEQHVLKLRFGLDGNERHTLAEIGRLLEVSRERVRQVELKALRKLRN 304

Query: 283 SIQK 286
             +K
Sbjct: 305 LTRK 308


>gi|167462413|ref|ZP_02327502.1| RNA polymerase sigma factor RpoD [Paenibacillus larvae subsp.
           larvae BRL-230010]
          Length = 367

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 84/265 (31%), Positives = 132/265 (49%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   +E  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 101 YLKEIGRVHLLTADDEIELAKRIME-GDEEAKQRLAEANLRLVVSIARRYVGRGMLFLDL 159

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 160 IQEGNMGLMKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 217

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L         PE+   IAK++ +S  +V  +        SL   I   ++N S
Sbjct: 218 LIRVSRQLLLELGREPTPEE---IAKEMELSTDKVREIMKISQEPVSLETPI--GEENDS 272

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D+ + D D       +    +  +  L   +  L  RE  +   R   E+    TLE
Sbjct: 273 NLGDF-IEDQDALAPA--DAASYELLKEQLEHVLDTLTEREENVLRLRFGLEDGRSRTLE 329

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +   F V+RER+RQIEA+A +K++
Sbjct: 330 EVGKVFGVTRERIRQIEAKALRKLR 354


>gi|239931428|ref|ZP_04688381.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 430

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 89/293 (30%), Positives = 142/293 (48%), Gaps = 40/293 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR----------YREHGDLSA--AH--------------R 52
           Y+ EI +IP+L   EE  LA+R           R   DL +  AH              R
Sbjct: 137 YLREIGRIPLLTAAEEVELARRVEAGLFAEEKLRLTPDLDSRLAHDLDRLVVMGRMAKRR 196

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY+ WWI+ A
Sbjct: 197 LIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIRQA 256

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           M   +      +++    +   L   + R++  +         PE+V A    L++   E
Sbjct: 257 MSRALADQARTIRV--PVHVVELINRVVRVQRRMLQERGREPTPEEVAA---HLDLP-PE 310

Query: 173 VISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
            +    RLA +  SL+A +   D  +    D +    DG     +E       R  L   
Sbjct: 311 RVGEVLRLAQEPVSLHAPVGEEDDVA--LGDLI---EDGDAASPVESAAFLLLREHLEAV 365

Query: 232 MSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +S L  RER++ + R   +   P TLE +   F V+RER+RQIE++   K+++
Sbjct: 366 LSTLGERERKVVQLRYGLVDGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRD 418


>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 =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 71/241 (29%), Positives = 124/241 (51%), Gaps = 12/241 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 570 ERASRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 629

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I     +     N R  + HLQ       +P+  + +
Sbjct: 630 TYATWWIRQAITRSIADQARTIRIPVHMIETINKMN-RISRQHLQEF---GFEPDASI-L 684

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A K+ + E ++  +  ++A  E ++      D + S   D++    DG     I+   + 
Sbjct: 685 AAKMEIPEDKIRKI-MKIAK-EPISMETPIGDDDDSHLGDFI---EDGNNTAPIDAAMQA 739

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKV 280
             R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 740 GLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKL 799

Query: 281 Q 281
           +
Sbjct: 800 K 800


>gi|325297456|ref|YP_004257373.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacteroides
           salanitronis DSM 18170]
 gi|324317009|gb|ADY34900.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacteroides
           salanitronis DSM 18170]
          Length = 286

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 79/274 (28%), Positives = 150/274 (54%), Gaps = 22/274 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI +  ++  +EE  LA+R R+ GD +A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGREDLITVEEEVELAQRIRK-GDRAALEKLTRANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     +V++    NQ   
Sbjct: 77  PDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQARIVRL--PLNQVGS 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
              + +     +   +    PE+   +A +L++   + IS   +++G   S++A     +
Sbjct: 135 LNKISKAFSKFEQENERRPSPEE---LADELDIP-VDKISDTLKVSGRHISVDAPFVEGE 190

Query: 195 KNSSQWQDWLVYDHD--GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI---FEARRLQ 249
            NS    D LV D        ++ E   R+     + R++S L  RE+ I   F     Q
Sbjct: 191 DNS--LLDVLVNDDSPMADRSLVNESLSRE-----IDRALSTLTDREKEIIQMFFGIGTQ 243

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           E  +TLE +  +F ++RERVRQI+ +A ++++++
Sbjct: 244 E--MTLEEIGDKFGLTRERVRQIKEKAIRRLRQN 275


>gi|148240837|ref|YP_001226224.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp. WH
           7803]
 gi|147849376|emb|CAK24927.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 7803]
          Length = 339

 Score =  104 bits (259), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 87/294 (29%), Positives = 142/294 (48%), Gaps = 37/294 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLA--------------------KRYREHGDLSAAHRLVTSHL 58
           Y+  I ++P+L   EE  LA                    +R+R      A  R++ ++L
Sbjct: 55  YLSSIGRVPLLTAAEEIELAHHVQAMKELLDVPEGERTPRQRHRIRMGKRARDRMMAANL 114

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+  M   I 
Sbjct: 115 RLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTRAID 174

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLK---GHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
            S   +++    ++K     +RR+     H      N L+    + I  +      E+IS
Sbjct: 175 NSARTIRLPIHISEK--LSKMRRITRELSHRFGRQPNRLELANAMGIEPR---DLEELIS 229

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
            +   A   SL+A     +  S+  +  L+ D +G E   +E  +R  ++  L   +S L
Sbjct: 230 QSAPCA---SLDAHARGEEDRSTLGE--LIPDPNGDEP--MEGMDRSIQKEHLGGWLSQL 282

Query: 236 NPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           N RE++I   R   +   P+TL  +  +  VSRERVRQ+EA+A  K++    +Q
Sbjct: 283 NDREQKILRLRFGLDGAEPLTLAEIGRQINVSRERVRQLEAKAILKLRSMTDQQ 336


>gi|322384625|ref|ZP_08058303.1| RNA polymerase sigma factor RpoD-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321150510|gb|EFX43991.1| RNA polymerase sigma factor RpoD-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 371

 Score =  103 bits (258), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 84/265 (31%), Positives = 132/265 (49%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   +E  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 105 YLKEIGRVHLLTADDEIELAKRIME-GDEEAKQRLAEANLRLVVSIARRYVGRGMLFLDL 163

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 164 IQEGNMGLMKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 221

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L         PE+   IAK++ +S  +V  +        SL   I   ++N S
Sbjct: 222 LIRVSRQLLLELGREPTPEE---IAKEMELSTDKVREIMKISQEPVSLETPI--GEENDS 276

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D+ + D D       +    +  +  L   +  L  RE  +   R   E+    TLE
Sbjct: 277 NLGDF-IEDQDALAPA--DAASYELLKEQLEHVLDTLTEREENVLRLRFGLEDGRSRTLE 333

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +   F V+RER+RQIEA+A +K++
Sbjct: 334 EVGKVFGVTRERIRQIEAKALRKLR 358


>gi|116491026|ref|YP_810570.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Oenococcus oeni PSU-1]
 gi|290890507|ref|ZP_06553582.1| hypothetical protein AWRIB429_0972 [Oenococcus oeni AWRIB429]
 gi|116091751|gb|ABJ56905.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Oenococcus oeni PSU-1]
 gi|290479903|gb|EFD88552.1| hypothetical protein AWRIB429_0972 [Oenococcus oeni AWRIB429]
          Length = 458

 Score =  103 bits (258), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 80/267 (29%), Positives = 137/267 (51%), Gaps = 14/267 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
           Y+ EI ++ +L   +E  +AKR  + G     A   L  ++LRLVV IA  Y G G+   
Sbjct: 188 YLKEIGRVSLLNADQEVAIAKRIEKGGSDGERARQELAEANLRLVVSIAKRYVGRGMHFL 247

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I    +     
Sbjct: 248 DLIQEGNMGLMKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETI 305

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
             L R++  L      +  PE++ A   ++ ++  +V  +        SL   I   ++N
Sbjct: 306 NKLIRIQRTLIQDLGRDPMPEEIGA---EMELTADKVREIQKIAQEPVSLETPI--GEEN 360

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-T 254
            S   D+ + D++G+    IE    +  ++ L   +  L  RE  +   R  L++    T
Sbjct: 361 DSHLGDF-IEDNEGESP--IESTSDQMLKDQLEEVLGTLTEREENVLRLRFGLEDGKTRT 417

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQ 281
           LE +   F V+RER+RQIEA+A +K++
Sbjct: 418 LEEVGRVFGVTRERIRQIEAKALRKLR 444


>gi|281420133|ref|ZP_06251132.1| RNA polymerase sigma-70 factor [Prevotella copri DSM 18205]
 gi|281405933|gb|EFB36613.1| RNA polymerase sigma-70 factor [Prevotella copri DSM 18205]
          Length = 290

 Score =  103 bits (258), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 79/273 (28%), Positives = 142/273 (52%), Gaps = 16/273 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGL 73
           L +Y+ EI + PM+   EE  LA+  R+ G     A ++L+ ++LR VV +A  Y+  GL
Sbjct: 18  LDKYLVEIGRAPMVSIDEEIELAQAIRKGGRAGERAKNKLIEANLRFVVSVAKQYQHQGL 77

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            +++++ EGNIGL++A ++FD  RGF+  +Y++WWI+ ++ + I     +V++    NQ 
Sbjct: 78  TLTDLIDEGNIGLIKAAERFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRL--PLNQ- 134

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINS 192
               +L ++   +      N +   V  +A +  V E + IS +   +G   S++A  + 
Sbjct: 135 --VGSLNKVNQEINKFEQENQRRPSVEELAARTGVDEDK-ISQSMAASGHHVSIDAPFSD 191

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERRIFEA-RRLQE 250
            D NS    D +    D +    ++ E   ++ R +L      L  RE +I  A   + E
Sbjct: 192 DDDNS--MADVMASGDDARTDKQVDHESMAQDLRQVLK---VCLKDRELKIICACYGIGE 246

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               LE +  +  ++RERVRQI  ++  K++ES
Sbjct: 247 TEKGLEEIGDKMGLTRERVRQIREKSITKLRES 279


>gi|300871837|ref|YP_003786710.1| RNA polymerase sigma factor RpoD [Brachyspira pilosicoli 95/1000]
 gi|300689538|gb|ADK32209.1| RNA polymerase sigma factor, RpoD [Brachyspira pilosicoli 95/1000]
          Length = 314

 Score =  103 bits (258), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 71/239 (29%), Positives = 124/239 (51%), Gaps = 20/239 (8%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           S  H+LV S+LRLV+ IA  Y   G+P  +++ EGNIGL++AVK+F+  +GF+ +TY +W
Sbjct: 75  SIQHKLVKSNLRLVISIAKRYYNSGVPFIDIIDEGNIGLIEAVKRFEYRKGFKFSTYGVW 134

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL-KGHLQA---ITDNNLKPEQVVAIA 163
           WIK ++         + +I +  +  R   ++ RL K  +Q    +T    +   +  IA
Sbjct: 135 WIKQSI---------VKEISSKRHIIRFPMHIARLIKKSIQISKNLTQQLGREPSIDEIA 185

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           K++ +    + S+        S+++   +SD N     D   +  D       +    ++
Sbjct: 186 KEMKIDRKTLSSIIVFTQETASVDSFFKNSDNN-----DMTSFIEDKNFPSPHQDAFMES 240

Query: 224 RRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            R+ LT ++  L+ +ER +   R     + P TLE+   E  ++RERVRQI+ +A KK+
Sbjct: 241 LRDTLTEALKALDEKERTVIIERFGLYGKEPKTLEDTGKELNITRERVRQIQIKALKKL 299


>gi|291439801|ref|ZP_06579191.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291342696|gb|EFE69652.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 390

 Score =  103 bits (258), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 89/293 (30%), Positives = 142/293 (48%), Gaps = 40/293 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR----------YREHGDLSA--AH--------------R 52
           Y+ EI +IP+L   EE  LA+R           R   DL +  AH              R
Sbjct: 97  YLREIGRIPLLTAAEEVELARRVEAGLFAEEKLRLTPDLDSRLAHDLDRLVVMGRMAKRR 156

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY+ WWI+ A
Sbjct: 157 LIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIRQA 216

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           M   +      +++     +  L   + R++  +         PE+V A    L++   E
Sbjct: 217 MSRALADQARTIRVPVHVVE--LINRVVRVQRRMLQERGREPTPEEVAA---HLDLP-PE 270

Query: 173 VISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
            +    RLA +  SL+A +   D  +    D +    DG     +E       R  L   
Sbjct: 271 RVGEVLRLAQEPVSLHAPVGEEDDVA--LGDLI---EDGDAASPVESAAFLLLREHLEAV 325

Query: 232 MSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +S L  RER++ + R   +   P TLE +   F V+RER+RQIE++   K+++
Sbjct: 326 LSTLGERERKVVQLRYGLVDGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRD 378


>gi|313884259|ref|ZP_07818025.1| RNA polymerase sigma factor RpoD [Eremococcus coleocola
           ACS-139-V-Col8]
 gi|312620706|gb|EFR32129.1| RNA polymerase sigma factor RpoD [Eremococcus coleocola
           ACS-139-V-Col8]
          Length = 376

 Score =  103 bits (258), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 87/276 (31%), Positives = 133/276 (48%), Gaps = 37/276 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L    E  LAKR  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 110 YLKEIGRVDLLSADAEISLAKRI-EDGDELAKQELAEANLRLVVSIAKRYVGRGMSFLDL 168

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 169 IQEGNMGLMKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLV 228

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             Q+ L  +L R     +   + +L  E+V  I   L +S+  V           SL   
Sbjct: 229 RVQRNLLQDLGREPTPEEIGAEMDLPTEKVREI---LKISQEPV-----------SLETP 274

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR---RNMLTRSMSVLNPRERRIFEAR 246
           I   D   S   D++      +++  +  E   +    R  L   +  L  RE  +   R
Sbjct: 275 IGEED--DSHLGDFI------EDEGAMSPESFTSSSLLREQLEDVLDTLTDREENVLRLR 326

Query: 247 -RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
             L +  + TLE +   F V+RER+RQIEA+A +K+
Sbjct: 327 FGLDDGNIRTLEQVGKVFGVTRERIRQIEAKALRKL 362


>gi|47679387|gb|AAT36674.1| DNA-directed RNA polymerase sigma A subunit [Oenococcus oeni PSU-1]
          Length = 465

 Score =  103 bits (258), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 80/266 (30%), Positives = 136/266 (51%), Gaps = 14/266 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
           Y+ EI ++ +L   +E  +AKR  + G     A   L  ++LRLVV IA  Y G G+   
Sbjct: 195 YLKEIGRVSLLNADQEVAIAKRIEKGGSDGERARQELAEANLRLVVSIAKRYVGRGMHFL 254

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I    +     
Sbjct: 255 DLIQEGNMGLMKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETI 312

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
             L R++  L      +  PE++ A   ++ ++  +V  +        SL   I   ++N
Sbjct: 313 NKLIRIQRTLIQDLGRDPMPEEIGA---EMELTADKVREIQKIAQEPVSLETPI--GEEN 367

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-T 254
            S   D+ + D++G+    IE    +  ++ L   +  L  RE  +   R  L++    T
Sbjct: 368 DSHLGDF-IEDNEGESP--IESTSDQMLKDQLEEVLGTLTEREENVLRLRFGLEDGKTRT 424

Query: 255 LENLSSEFEVSRERVRQIEARAFKKV 280
           LE +   F V+RER+RQIEA+A +K+
Sbjct: 425 LEEVGRVFGVTRERIRQIEAKALRKL 450


>gi|291277050|ref|YP_003516822.1| RNA polymerase sigma-70 factor [Helicobacter mustelae 12198]
 gi|290964244|emb|CBG40093.1| RNA polymerase sigma factor (sigma-70) [Helicobacter mustelae
           12198]
          Length = 614

 Score =  103 bits (258), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 74/246 (30%), Positives = 118/246 (47%), Gaps = 33/246 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KFD +R F+ +TY+ WW
Sbjct: 375 AKNKMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFDYKRNFKFSTYATWW 434

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + R+   ++       K   V  IA+K+ +
Sbjct: 435 IRQAISRAIADQARTIRIPI-----HMIETINRIHKIMRKYIQETGKEPDVEIIAEKVGL 489

Query: 169 SESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           S  +V          +S+   +  DE         DKNS+   D ++             
Sbjct: 490 SVDKVKHVIKITKEPVSLEAPIGSDEDGKFGDFVEDKNSTNTMDQIM------------- 536

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEAR 275
             +++ R  +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ 
Sbjct: 537 --KEDLRAQIFEVLDQLNEREQAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESS 594

Query: 276 AFKKVQ 281
           A KK++
Sbjct: 595 AIKKLK 600


>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 =  103 bits (258), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 71/241 (29%), Positives = 124/241 (51%), Gaps = 12/241 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 570 ERASRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 629

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I     +     N R  + HLQ       +P+  + +
Sbjct: 630 TYATWWIRQAITRSIADQARTIRIPVHMIETINKMN-RISRQHLQEF---GFEPDASI-L 684

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A K+ + E ++  +  ++A  E ++      D + S   D++    DG     I+   + 
Sbjct: 685 AAKMEIPEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDGNNTAPIDAAMQA 739

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKV 280
             R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 740 GLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKL 799

Query: 281 Q 281
           +
Sbjct: 800 K 800


>gi|264677331|ref|YP_003277237.1| RNA polymerase, sigma 70 subunit, RpoD [Comamonas testosteroni
           CNB-2]
 gi|262207843|gb|ACY31941.1| RNA polymerase, sigma 70 subunit, RpoD [Comamonas testosteroni
           CNB-2]
          Length = 815

 Score =  103 bits (258), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 71/241 (29%), Positives = 124/241 (51%), Gaps = 12/241 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 570 ERASRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 629

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I     +     N R  + HLQ       +P+  + +
Sbjct: 630 TYATWWIRQAITRSIADQARTIRIPVHMIETINKMN-RISRQHLQEF---GFEPDASI-L 684

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A K+ + E ++  +  ++A  E ++      D + S   D++    DG     I+   + 
Sbjct: 685 AAKMEIPEDKIRKI-MKIAK-EPISMETPIGDDDDSHLGDFI---EDGNNTAPIDAAMQA 739

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKV 280
             R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 740 GLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKL 799

Query: 281 Q 281
           +
Sbjct: 800 K 800


>gi|159026614|emb|CAO86546.1| rpoD1 [Microcystis aeruginosa PCC 7806]
          Length = 416

 Score =  103 bits (258), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 78/263 (29%), Positives = 141/263 (53%), Gaps = 21/263 (7%)

Query: 27  PMLE----KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           P+LE    K +EY+ A + R +    A  ++V S+LRLVV IA  Y   GL   +++ EG
Sbjct: 154 PLLEEWLAKSKEYLSAFKRRLYHGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEG 213

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
           ++GL++A +KFD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+
Sbjct: 214 SLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV-----HLYETISRI 268

Query: 143 KGHLQAIT-DNNLKP-EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
           K   + ++ +   KP E+ +A   ++ + +   I+ + +L    SL   I   +   S+ 
Sbjct: 269 KKTTKILSQEMRRKPTEEEIATKMEMTIEKLRFIAKSAQLPI--SLETPIGKEE--DSRL 324

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENL 258
            D++  D +  E  + +   R++  N+L      L+PRER +   R   ++    TLE +
Sbjct: 325 GDFIEADGETPEDEVSKNLLREDLENVL----DTLSPRERDVLRLRYGLDDGRMKTLEEI 380

Query: 259 SSEFEVSRERVRQIEARAFKKVQ 281
              F V+RER+RQIEA+A +K++
Sbjct: 381 GQIFNVTRERIRQIEAKALRKLR 403


>gi|315638945|ref|ZP_07894116.1| DNA-directed RNA polymerase sigma subunit RpoD [Campylobacter
           upsaliensis JV21]
 gi|315480974|gb|EFU71607.1| DNA-directed RNA polymerase sigma subunit RpoD [Campylobacter
           upsaliensis JV21]
          Length = 657

 Score =  103 bits (258), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 83/250 (33%), Positives = 123/250 (49%), Gaps = 41/250 (16%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ +RG++ +TY+ WW
Sbjct: 416 AKGRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWW 475

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T NQ     N + ++ HLQ     N K   V  IAK
Sbjct: 476 IRQAISRAIADQARTIRIPIHMIETINQ----IN-KIIREHLQ----KNGKEPDVNDIAK 526

Query: 165 KLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           ++ +S  +V          IS+   +  ++         DKNS    D ++ D D +EQ+
Sbjct: 527 EVGLSVDKVKQVIKITKEPISLEAPIGSEDDGKFGDFVEDKNSLSPMDNILKD-DLKEQI 585

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQ 271
                            +  LN RE+ +   R      E+  TLE +  E  V+RERVRQ
Sbjct: 586 --------------DEVLDQLNDREKAVIRMRFGLLEDESDRTLEEIGKELNVTRERVRQ 631

Query: 272 IEARAFKKVQ 281
           IE+ A KK++
Sbjct: 632 IESSAIKKLK 641


>gi|1710683|sp|P52328|RPSD2_BACSP RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A
 gi|149623|gb|AAA25264.1| RNA polymerase sigma-subunit [Leptospira borgpetersenii]
          Length = 377

 Score =  103 bits (258), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 87/276 (31%), Positives = 135/276 (48%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   +E  LAKR   +GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 111 YLKEIGRVPLLSADDEVELAKRIM-NGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 169

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-- 132
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 170 IQEGNMGLIKAVEKFDHNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 229

Query: 133 ---KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
              ++L   L R     +   +  L  E+V  I K       E +S+   +    D  L 
Sbjct: 230 RVSRQLLQELGREPTPEEIAAEMELSVEKVREIMK----IAQEPVSLETPIGEEDDSHLG 285

Query: 188 ALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
             I   D+ +    D   Y+   +  E VL    ER+   N+L     + + R R     
Sbjct: 286 DFI--EDQEALTPADAAAYELLKEQLEDVLDTLTEREE--NVLRLRFGLDDGRTR----- 336

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                   TLE +   F V+RER+RQIEA+A +K++
Sbjct: 337 --------TLEEVGKVFGVTRERIRQIEAKALRKLR 364


>gi|320160330|ref|YP_004173554.1| RNA polymerase sigma factor [Anaerolinea thermophila UNI-1]
 gi|319994183|dbj|BAJ62954.1| RNA polymerase sigma factor [Anaerolinea thermophila UNI-1]
          Length = 543

 Score =  103 bits (258), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 88/300 (29%), Positives = 147/300 (49%), Gaps = 40/300 (13%)

Query: 16  LSRYIHEIRKIPMLE-----KQEEYVLAKRY---REHGDLSAAHRLVTSHLRLVVKIAMG 67
           L  Y+ E+  +P +E       +E +LA+     R   +  A   L+ ++LRLVV IA  
Sbjct: 238 LMNYLREVHALPRVEFFVEHMPDEDILAEEVEGVRRRAE-DANQTLIRANLRLVVSIAKR 296

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y G G+   +++ EGN+GL++AV KFDP RG++ +TY+ WWI+ ++  YI      ++I 
Sbjct: 297 YLGRGVSFLDLIQEGNLGLLRAVNKFDPTRGYKFSTYATWWIRQSISRYIAEQARTIRIP 356

Query: 128 TTANQK--RLFFNLRRLKGHLQ--------AITDNNLKPEQVVAIAK------------- 164
               +   RL    R L   L         A+    L  E   AI K             
Sbjct: 357 VHLFESITRLLRVQRTLIQQLGREPTAEELALEAGFLSDEDAQAIRKARAEGKSIDPELM 416

Query: 165 -KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
            + N + S+V       + +E ++      D++SSQ  D++    D +    ++   R+ 
Sbjct: 417 RRWNFATSKV--QRVLQSAEEPVSLERPVGDEDSSQLGDFI---EDDEALEPMDAAAREM 471

Query: 224 RRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R  +  ++S+L+ RER++ E R   +     TLE +S  F V+RER+RQIEA+A +K++
Sbjct: 472 LREQVQNALSILSERERQVLELRFGLIDGKDHTLEEVSRYFNVTRERIRQIEAKALRKLR 531


>gi|288574317|ref|ZP_06392674.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dethiosulfovibrio
           peptidovorans DSM 11002]
 gi|288570058|gb|EFC91615.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dethiosulfovibrio
           peptidovorans DSM 11002]
          Length = 381

 Score =  103 bits (258), Expect = 2e-20,   Method: Compositional matrix adjust.
 Identities = 87/277 (31%), Positives = 133/277 (48%), Gaps = 37/277 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+ +L+  EE  LAKR  E GD  A  +++ ++LRLVV IA  Y G G+   ++
Sbjct: 115 YLREIGKVDLLDASEEVELAKRV-EDGDQVAKQKIIDANLRLVVSIAKKYIGRGMLFLDL 173

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG-----TTANQK 133
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T     
Sbjct: 174 IQEGNLGLIRAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKMV 233

Query: 134 RLFFNLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
           R+   L +  G         +A+   + K E++  IA +L VS    I        D  L
Sbjct: 234 RVSRQLVQRMGREPTDEEISEAMEIESTKVEEIRRIA-QLPVSLETPIGEE----EDSQL 288

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              I   D  S +        H+  E +L                   L+ RER +   R
Sbjct: 289 GDFIEDRDMPSPEDAASCNLLHEQIEDML-----------------DALSDREREVLRYR 331

Query: 247 RLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              E+    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 332 FGLEDGRSYTLEEVGRRFGVTRERIRQIEAKALRKLR 368


>gi|309791990|ref|ZP_07686468.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Oscillochloris
           trichoides DG6]
 gi|308225984|gb|EFO79734.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Oscillochloris
           trichoides DG6]
          Length = 396

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 80/311 (25%), Positives = 147/311 (47%), Gaps = 48/311 (15%)

Query: 7   SIIVNGEIGLSR---------YIHEIRKIPMLEKQEEYVLA------------------- 38
           +++++ + GLS          Y+ EI ++P+L  ++E  LA                   
Sbjct: 81  TVVIDLDEGLSDALLGDSVRLYLREIGQVPLLTAEQEKRLAQTIERGQKAQVKIKDLDPT 140

Query: 39  -------KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                  +R  E G+  A  ++  ++LRLVV IA  YR  GLP+ +++ EG++GL++A++
Sbjct: 141 SAEAVELRRQIEKGN-DARQQMAAANLRLVVSIAKRYRDRGLPLLDLIQEGSLGLLRAIE 199

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD ++GF+ +TY+ WWIK A+   +     LV++        L   L R++   + +T 
Sbjct: 200 KFDHDKGFKFSTYATWWIKQALSRALADQSRLVRLPV-----HLGETLNRIQAARRQLTQ 254

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +      +A +L++S+ ++     R    + ++      ++  S   D++   H   
Sbjct: 255 RLGREPYDSELADELSMSQEKL--RELRRTAQDPVSLATPVGEEADSTLADFIPDPH--- 309

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERV 269
                +       R  +  ++  L  RER++ E R       P TLE +   F V+RERV
Sbjct: 310 ALDADDAAASGMLRQQIATALDQLTERERKVLELRYGLTDGQPRTLEEVGKAFGVTRERV 369

Query: 270 RQIEARAFKKV 280
           RQIE +A +K+
Sbjct: 370 RQIEVKALRKL 380


>gi|189501483|ref|YP_001957200.1| RNA polymerase sigma factor [Candidatus Amoebophilus asiaticus 5a2]
 gi|189496924|gb|ACE05471.1| RNA polymerase sigma factor, sigma-70 family [Candidatus
           Amoebophilus asiaticus 5a2]
          Length = 287

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 79/274 (28%), Positives = 141/274 (51%), Gaps = 27/274 (9%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI ++ +L  +EE  LAKR +  GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGRVDLLTPEEEVELAKRIK-SGDKIALEQLTKANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
           S++++EGN+GL+++ ++FD  RGF+  +Y++WWI+ ++      Q  I+R   L ++GT 
Sbjct: 77  SDLINEGNLGLIKSAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVR-LPLNRVGTL 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNA 188
               R F  L           +   K E       +        IS   +++G   S++A
Sbjct: 136 NKLSRTFSQL-----------EQKYKREPTAEELAEELEVTPGEISDTMKISGRHVSMDA 184

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI--FEAR 246
                +++S         +    +  LI++   K+    + R++S+L  RE  +  +   
Sbjct: 185 PFVQGEEHSLLDVLEDDDEDK-PDDTLIDESLCKD----IERALSLLTEREAGVISYYFG 239

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
               NP+TLE + + F ++RERVRQI+ +A KK+
Sbjct: 240 LKGTNPMTLEEIGTRFNLTRERVRQIKEKAIKKL 273


>gi|169883526|gb|ACA97858.1| RNA polymerase sigma factor [Microcystis aeruginosa PCC 7820]
          Length = 416

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 78/263 (29%), Positives = 141/263 (53%), Gaps = 21/263 (7%)

Query: 27  PMLE----KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           P+LE    K +EY+ A + R +    A  ++V S+LRLVV IA  Y   GL   +++ EG
Sbjct: 154 PLLEEWLAKSKEYLSAFKRRLYHGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEG 213

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
           ++GL++A +KFD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+
Sbjct: 214 SLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV-----HLYETISRI 268

Query: 143 KGHLQAIT-DNNLKP-EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
           K   + ++ +   KP E+ +A   ++ + +   I+ + +L    SL   I   +   S+ 
Sbjct: 269 KKTTKILSQEMRRKPTEEEIATKMEMTIEKLRFIAKSAQLPI--SLETPIGKEE--DSRL 324

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENL 258
            D++  D +  E  + +   R++  N+L      L+PRER +   R   ++    TLE +
Sbjct: 325 GDFIEADGETPEDEVSKNLLREDLENVL----DTLSPRERDVLRLRYGLDDGRMKTLEEI 380

Query: 259 SSEFEVSRERVRQIEARAFKKVQ 281
              F V+RER+RQIEA+A +K++
Sbjct: 381 GQIFNVTRERIRQIEAKALRKLR 403


>gi|1710685|sp|P52322|RPOD_MICAE RecName: Full=RNA polymerase sigma factor rpoD1
 gi|786173|dbj|BAA08853.1| sigma factor [Microcystis aeruginosa]
 gi|1783286|dbj|BAA12850.1| principal sigma factor [Microcystis aeruginosa]
          Length = 416

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 78/263 (29%), Positives = 141/263 (53%), Gaps = 21/263 (7%)

Query: 27  PMLE----KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           P+LE    K +EY+ A + R +    A  ++V S+LRLVV IA  Y   GL   +++ EG
Sbjct: 154 PLLEEWLAKSKEYLSAFKRRLYHGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEG 213

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
           ++GL++A +KFD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+
Sbjct: 214 SLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV-----HLYETISRI 268

Query: 143 KGHLQAIT-DNNLKP-EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
           K   + ++ +   KP E+ +A   ++ + +   I+ + +L    SL   I   +   S+ 
Sbjct: 269 KKTTKILSQEMRRKPTEEEIATKMEMTIEKLRFIAKSAQLPI--SLETPIGKEE--DSRL 324

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENL 258
            D++  D +  E  + +   R++  N+L      L+PRER +   R   ++    TLE +
Sbjct: 325 GDFIEADGETPEDEVSKNLLREDLENVL----DTLSPRERDVLRLRYGLDDGRMKTLEEI 380

Query: 259 SSEFEVSRERVRQIEARAFKKVQ 281
              F V+RER+RQIEA+A +K++
Sbjct: 381 GQIFNVTRERIRQIEAKALRKLR 403


>gi|216263458|ref|ZP_03435453.1| RNA polymerase sigma factor (rpoS) [Borrelia afzelii ACA-1]
 gi|215980302|gb|EEC21123.1| RNA polymerase sigma factor (rpoS) [Borrelia afzelii ACA-1]
          Length = 266

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 81/282 (28%), Positives = 147/282 (52%), Gaps = 20/282 (7%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M+I  N ++ +  Y+  +R+  ++  +EE  LA +  + G   A ++++ ++LRLV+KI 
Sbjct: 1   MNIFSNEDLNI--YLKSVREHKLITHEEEIQLAGQI-QRGSAKAKNKMINANLRLVLKII 57

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y G GL I +++ EGN+GL++A +K+DP +  + +TY+ +WIK ++Q  +     LVK
Sbjct: 58  KRYAGKGLKIEDLIQEGNLGLIRAAEKYDPNKNTKFSTYASFWIKQSLQRALNTKTRLVK 117

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           +          +    L   +        K  +   I K+ N+S ++ I +   L  + S
Sbjct: 118 VP---------YRKENLILQINKYLTEEEKAPKKEEIMKRFNLSPAQYIKIIPYLEKEYS 168

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L+  I  S+ NS+     L  D+    ++ +E++      N +  +   L  +ER I + 
Sbjct: 169 LDKEIEGSE-NSTLLN--LYEDNSFNPEITLEQDSTLQHLNYILETK--LTEKERYIIKK 223

Query: 246 R-RLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L  +P   TL+++S+E  +S E VRQIE R  KK++E I
Sbjct: 224 RYNLDNSPKKSTLKDISTELGISSETVRQIEKRVLKKLKEEI 265


>gi|295087657|emb|CBK69180.1| RNA polymerase sigma factor, sigma-70 family [Bacteroides
           xylanisolvens XB1A]
          Length = 286

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 77/272 (28%), Positives = 148/272 (54%), Gaps = 18/272 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI +  ++  +EE  LA+R R  GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGREDLITVEEEVELAQRIR-KGDRVALEKLTRANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     +V++    NQ   
Sbjct: 77  PDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL--PLNQVGS 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
              + +     +   +    PE+ +A+  ++ V +   IS   +++G   S++A     +
Sbjct: 135 LNKISKAFSKFEQENERRPSPEE-LAVELEIPVDK---ISDTLKVSGRHISVDAPFVEGE 190

Query: 195 KNSSQWQDWLVYDHD--GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA-RRLQEN 251
            NS    D LV D        ++ E   R+     + R++S L  RE+ I +    + + 
Sbjct: 191 DNS--LLDVLVNDDSPMADRSLVNESLARE-----IDRALSTLTDREKEIIQMFFGIGQQ 243

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +TLE +  +F ++RERVRQI+ +A +++++S
Sbjct: 244 EMTLEEIGDKFGLTRERVRQIKEKAIRRLRQS 275


>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 =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 71/241 (29%), Positives = 124/241 (51%), Gaps = 12/241 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 535 ESASRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 594

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I     +     N R  + HLQ       +P+  + +
Sbjct: 595 TYATWWIRQAITRSIADQARTIRIPVHMIETINKMN-RISRQHLQEF---GFEPDASI-L 649

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A K+ + E ++  +  ++A  E ++      D + S   D++    DG     I+   + 
Sbjct: 650 AAKMEIPEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDGANTAPIDAAMQA 704

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKV 280
             R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 705 GLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKL 764

Query: 281 Q 281
           +
Sbjct: 765 K 765


>gi|261405623|ref|YP_003241864.1| RpoD subfamily RNA polymerase sigma-70 factor [Paenibacillus sp.
           Y412MC10]
 gi|329925852|ref|ZP_08280581.1| RNA polymerase sigma factor RpoD [Paenibacillus sp. HGF5]
 gi|261282086|gb|ACX64057.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Paenibacillus sp.
           Y412MC10]
 gi|328939598|gb|EGG35946.1| RNA polymerase sigma factor RpoD [Paenibacillus sp. HGF5]
          Length = 377

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 81/264 (30%), Positives = 129/264 (48%), Gaps = 13/264 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   +E  LA R  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 111 YLKEIGRVPLLSADDEIELANRI-EQGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 169

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD ++GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 170 IQEGNMGLIKAVEKFDYKKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 227

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L         PE+   IA ++ +S  +V  +        SL   I   D   S
Sbjct: 228 LIRVSRQLLQELGREPSPEE---IAAEMELSVEKVREIMKIAQEPVSLETPIGEED--DS 282

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++    D +     +    +  +  L   +  L  RE  +   R   ++    TLE
Sbjct: 283 HLGDFI---EDQEALAPADAAAYELLKEQLEDVLDTLTEREENVLRLRFGLDDGRTRTLE 339

Query: 257 NLSSEFEVSRERVRQIEARAFKKV 280
            +   F V+RER+RQIEA+A +K+
Sbjct: 340 EVGKVFGVTRERIRQIEAKALRKL 363


>gi|29346721|ref|NP_810224.1| RNA polymerase sigma factor rpoD (sigma-A) [Bacteroides
           thetaiotaomicron VPI-5482]
 gi|153808302|ref|ZP_01960970.1| hypothetical protein BACCAC_02591 [Bacteroides caccae ATCC 43185]
 gi|160882661|ref|ZP_02063664.1| hypothetical protein BACOVA_00615 [Bacteroides ovatus ATCC 8483]
 gi|160891864|ref|ZP_02072867.1| hypothetical protein BACUNI_04321 [Bacteroides uniformis ATCC 8492]
 gi|167762326|ref|ZP_02434453.1| hypothetical protein BACSTE_00679 [Bacteroides stercoris ATCC
           43183]
 gi|218130148|ref|ZP_03458952.1| hypothetical protein BACEGG_01736 [Bacteroides eggerthii DSM 20697]
 gi|237712837|ref|ZP_04543318.1| conserved hypothetical protein [Bacteroides sp. D1]
 gi|237718434|ref|ZP_04548915.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 2_2_4]
 gi|255693898|ref|ZP_05417573.1| RNA polymerase sigma-70 factor [Bacteroides finegoldii DSM 17565]
 gi|260173882|ref|ZP_05760294.1| RNA polymerase sigma factor rpoD (sigma-A) [Bacteroides sp. D2]
 gi|262408807|ref|ZP_06085352.1| RNA polymerase sigma factor RpoS [Bacteroides sp. 2_1_22]
 gi|270296469|ref|ZP_06202669.1| conserved hypothetical protein [Bacteroides sp. D20]
 gi|293371428|ref|ZP_06617859.1| putative RNA polymerase sigma factor RpoD [Bacteroides ovatus SD
           CMC 3f]
 gi|294648199|ref|ZP_06725739.1| putative RNA polymerase sigma factor RpoD [Bacteroides ovatus SD CC
           2a]
 gi|294810777|ref|ZP_06769425.1| putative RNA polymerase sigma factor RpoD [Bacteroides
           xylanisolvens SD CC 1b]
 gi|298484065|ref|ZP_07002233.1| RNA polymerase sigma-70 factor [Bacteroides sp. D22]
 gi|299149080|ref|ZP_07042142.1| RNA polymerase sigma-70 factor [Bacteroides sp. 3_1_23]
 gi|315922146|ref|ZP_07918386.1| RNA polymerase sigma factor rpoD [Bacteroides sp. D2]
 gi|317476641|ref|ZP_07935886.1| sigma-70 family RNA polymerase sigma factor [Bacteroides eggerthii
           1_2_48FAA]
 gi|317480344|ref|ZP_07939445.1| sigma-70 family RNA polymerase sigma factor [Bacteroides sp.
           4_1_36]
 gi|329955895|ref|ZP_08296698.1| putative RNA polymerase sigma factor RpoD [Bacteroides clarus YIT
           12056]
 gi|29338618|gb|AAO76418.1| RNA polymerase sigma factor rpoD (Sigma-A) [Bacteroides
           thetaiotaomicron VPI-5482]
 gi|149129205|gb|EDM20421.1| hypothetical protein BACCAC_02591 [Bacteroides caccae ATCC 43185]
 gi|156111976|gb|EDO13721.1| hypothetical protein BACOVA_00615 [Bacteroides ovatus ATCC 8483]
 gi|156858342|gb|EDO51773.1| hypothetical protein BACUNI_04321 [Bacteroides uniformis ATCC 8492]
 gi|167699969|gb|EDS16548.1| hypothetical protein BACSTE_00679 [Bacteroides stercoris ATCC
           43183]
 gi|217987652|gb|EEC53980.1| hypothetical protein BACEGG_01736 [Bacteroides eggerthii DSM 20697]
 gi|229447165|gb|EEO52956.1| conserved hypothetical protein [Bacteroides sp. D1]
 gi|229452367|gb|EEO58158.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 2_2_4]
 gi|260620263|gb|EEX43134.1| RNA polymerase sigma-70 factor [Bacteroides finegoldii DSM 17565]
 gi|262353018|gb|EEZ02113.1| RNA polymerase sigma factor RpoS [Bacteroides sp. 2_1_22]
 gi|270273873|gb|EFA19735.1| conserved hypothetical protein [Bacteroides sp. D20]
 gi|292633625|gb|EFF52183.1| putative RNA polymerase sigma factor RpoD [Bacteroides ovatus SD
           CMC 3f]
 gi|292636474|gb|EFF54952.1| putative RNA polymerase sigma factor RpoD [Bacteroides ovatus SD CC
           2a]
 gi|294442110|gb|EFG10929.1| putative RNA polymerase sigma factor RpoD [Bacteroides
           xylanisolvens SD CC 1b]
 gi|298269746|gb|EFI11339.1| RNA polymerase sigma-70 factor [Bacteroides sp. D22]
 gi|298513841|gb|EFI37728.1| RNA polymerase sigma-70 factor [Bacteroides sp. 3_1_23]
 gi|313696021|gb|EFS32856.1| RNA polymerase sigma factor rpoD [Bacteroides sp. D2]
 gi|316903519|gb|EFV25372.1| sigma-70 family RNA polymerase sigma factor [Bacteroides sp.
           4_1_36]
 gi|316907237|gb|EFV28946.1| sigma-70 family RNA polymerase sigma factor [Bacteroides eggerthii
           1_2_48FAA]
 gi|328525275|gb|EGF52325.1| putative RNA polymerase sigma factor RpoD [Bacteroides clarus YIT
           12056]
          Length = 286

 Score =  103 bits (258), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 77/272 (28%), Positives = 148/272 (54%), Gaps = 18/272 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI +  ++  +EE  LA+R R+ GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGREDLITVEEEVELAQRIRK-GDRVALEKLTRANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     +V++    NQ   
Sbjct: 77  PDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL--PLNQVGS 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
              + +     +   +    PE+   +A +L +   + IS   +++G   S++A     +
Sbjct: 135 LNKISKAFSKFEQENERRPSPEE---LADELEIP-VDKISDTLKVSGRHISVDAPFVEGE 190

Query: 195 KNSSQWQDWLVYDHD--GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA-RRLQEN 251
            NS    D LV D        ++ E   R+     + R++S L  RE+ I +    + + 
Sbjct: 191 DNS--LLDVLVNDDSPMADRSLVNESLARE-----IDRALSTLTDREKEIIQMFFGIGQQ 243

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +TLE +  +F ++RERVRQI+ +A +++++S
Sbjct: 244 EMTLEEIGDKFGLTRERVRQIKEKAIRRLRQS 275


>gi|124024683|ref|YP_001018990.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Prochlorococcus marinus str. MIT 9303]
 gi|123964969|gb|ABM79725.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Prochlorococcus marinus str. MIT 9303]
          Length = 344

 Score =  103 bits (257), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 80/273 (29%), Positives = 143/273 (52%), Gaps = 18/273 (6%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           EI L+ ++  ++++  L +Q+ +   +R++      A  R+++++LRLVV +A  Y+  G
Sbjct: 75  EIELAHHVQAMKELLELPEQD-HTPRQRHKIRMGKRARDRMMSANLRLVVSVAKKYQNQG 133

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L + ++V EG IGL +AV KFDP  G++ +TY+ WWI+  M   I  S   +++    ++
Sbjct: 134 LELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIRLPIHISE 193

Query: 133 KRLFFNLRRLK---GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
           K     +RR+     H      N L+      +A  + +   ++  +  + A   SL+A 
Sbjct: 194 K--LSKMRRISRELSHRFGRQPNRLE------LAHAMGIQPQDLEDLIAQSAPCASLDAH 245

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL- 248
               +  S+  +  L+ D +G E   +E  +R  ++  L   +S LN RE++I   R   
Sbjct: 246 ARGEEDRSTLGE--LIPDPNGAEP--MEGLDRSIQKEHLGGWLSQLNEREQKILRLRFGL 301

Query: 249 -QENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             E P+TL  +  +  VSRERVRQ+EA+A  K+
Sbjct: 302 DGEEPLTLAEIGRQISVSRERVRQLEAKAILKL 334


>gi|29832222|ref|NP_826856.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29609340|dbj|BAC73391.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 389

 Score =  103 bits (257), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 90/295 (30%), Positives = 142/295 (48%), Gaps = 42/295 (14%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHG-------------------DLS--------AA 50
           +Y+ EI +IP+L   EE  LA+R  E G                   DL         A 
Sbjct: 95  QYLREIGRIPLLTAAEEVELARRV-EAGLFAEEKLSSTPDLDSQLGLDLDKLVVMGRMAK 153

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY+ WWI+
Sbjct: 154 RRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIR 213

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            AM   +      +++     +  L   + R++  +         PE+V A    L++  
Sbjct: 214 QAMSRALADQARTIRVPVHVVE--LINRVVRVQRRMLQERGYEPTPEEVAA---HLDLP- 267

Query: 171 SEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
            E +S   RLA +  SL+A +   D  +    D +    DG     +E       R  L 
Sbjct: 268 GERVSEVLRLAQEPVSLHAPVGEEDDVA--LGDLI---EDGDATSPVESAAFLLLREHLD 322

Query: 230 RSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             +S L  RER++ + R       P TLE +   F V+RER+RQIE++   K+++
Sbjct: 323 AVLSTLGERERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRD 377


>gi|325954752|ref|YP_004238412.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Weeksella virosa
           DSM 16922]
 gi|323437370|gb|ADX67834.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Weeksella virosa
           DSM 16922]
          Length = 288

 Score =  103 bits (257), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 82/296 (27%), Positives = 153/296 (51%), Gaps = 55/296 (18%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ ++  +EE  LA+R +  GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGKVDLITAEEEVELAQRIK-AGDRVALEKLTKANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
            ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++      Q  I+R   L KIG+ 
Sbjct: 77  PDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVR-LPLNKIGSI 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCR 179
               + +  L   + H +A +           I++ L++SE +V          +SM+  
Sbjct: 136 NKINKAYALLE--QEHERAPSAEE--------ISEVLDMSEGDVKESLKNSGRHVSMDAP 185

Query: 180 L--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
           L    D +L  ++N  +  S                ++IE     + R  + R++  L P
Sbjct: 186 LVEGEDSNLYDVLNIGESPSP------------DNTLMIE-----SLRVEIERALQTLTP 228

Query: 238 RERRIFEARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RE  +    RL       +P+TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 229 READLI---RLYFGLNGAHPMTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|18310989|ref|NP_562923.1| RNA polymerase sigma factor RpoD [Clostridium perfringens str. 13]
 gi|18145671|dbj|BAB81713.1| transcription initiation factor sigma A [Clostridium perfringens
           str. 13]
          Length = 373

 Score =  103 bits (257), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 78/265 (29%), Positives = 138/265 (52%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  ++E  LAK+  E G   A  +L  ++LRLVV IA  Y G G+   ++
Sbjct: 107 YLKEIGKVPLLSSEDEIELAKKI-EEGSNYAKKKLAEANLRLVVSIAKRYVGRGMLFLDL 165

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 166 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 223

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R++  L      +  PE+   ++K++++   +V  +  ++A  E ++      ++  S
Sbjct: 224 LIRIQRQLVQELGRDPLPEE---LSKQMDMPVDKVREI-LKIA-QEPVSLETPIGEEEDS 278

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++  D              K +   L   +  L PRE ++   R   ++    TLE
Sbjct: 279 HLGDFIPDDDAPAPAEAAAFTMLKEQ---LINVLDTLTPREEKVLRLRFGLDDGRARTLE 335

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF V+RER+RQIEA+A +K++
Sbjct: 336 EVGKEFNVTRERIRQIEAKALRKLR 360


>gi|315645989|ref|ZP_07899110.1| RNA polymerase, sigma 70 subunit, RpoD subfamily protein
           [Paenibacillus vortex V453]
 gi|315278750|gb|EFU42064.1| RNA polymerase, sigma 70 subunit, RpoD subfamily protein
           [Paenibacillus vortex V453]
          Length = 376

 Score =  103 bits (257), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 81/264 (30%), Positives = 129/264 (48%), Gaps = 13/264 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L   +E  LA R  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 110 YLKEIGRVPLLSADDEIELANRI-EQGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 168

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD ++GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 169 IQEGNMGLIKAVEKFDYKKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 226

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L         PE+   IA ++ +S  +V  +        SL   I   D   S
Sbjct: 227 LIRVSRQLLQELGREPSPEE---IAAEMELSVEKVREIMKIAQEPVSLETPIGEED--DS 281

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++    D +     +    +  +  L   +  L  RE  +   R   ++    TLE
Sbjct: 282 HLGDFI---EDQEALAPADAAAYELLKEQLEDVLDTLTEREENVLRLRFGLDDGRTRTLE 338

Query: 257 NLSSEFEVSRERVRQIEARAFKKV 280
            +   F V+RER+RQIEA+A +K+
Sbjct: 339 EVGKVFGVTRERIRQIEAKALRKL 362


>gi|118586868|ref|ZP_01544302.1| DNA-directed RNA polymerase RpoD, sigma subunit, Sigma-42
           [Oenococcus oeni ATCC BAA-1163]
 gi|71466858|emb|CAH41003.1| rpoD protein [Oenococcus oeni]
 gi|118432700|gb|EAV39432.1| DNA-directed RNA polymerase RpoD, sigma subunit, Sigma-42
           [Oenococcus oeni ATCC BAA-1163]
          Length = 458

 Score =  103 bits (257), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 80/267 (29%), Positives = 135/267 (50%), Gaps = 14/267 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
           Y+ EI ++ +L   +E  +AKR  + G     A   L  ++LRLVV IA  Y G G+   
Sbjct: 188 YLKEIGRVSLLNADQEVAIAKRIEKGGSDGERARQELAEANLRLVVSIAKRYVGRGMHFL 247

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I    +     
Sbjct: 248 DLIQEGNMGLMKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETI 305

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
             L R++  L      +  PE++ A   ++ ++  +V  +        SL   I   D  
Sbjct: 306 NKLIRIQRTLIQDLGRDPMPEEIGA---EMELTADKVREIQKIAQEPVSLETPIGEED-- 360

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-T 254
            S   D+ + D++G+    IE    +  ++ L   +  L  RE  +   R  L++    T
Sbjct: 361 DSHLGDF-IEDNEGESP--IESTSDQMLKDQLEEVLGTLTEREENVLRLRFGLEDGKTRT 417

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQ 281
           LE +   F V+RER+RQIEA+A +K++
Sbjct: 418 LEEVGRVFGVTRERIRQIEAKALRKLR 444


>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 =  103 bits (257), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 71/241 (29%), Positives = 124/241 (51%), Gaps = 12/241 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 536 ESASRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 595

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I     +     N R  + HLQ       +P+  + +
Sbjct: 596 TYATWWIRQAITRSIADQARTIRIPVHMIETINKMN-RISRQHLQEF---GFEPDASI-L 650

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A K+ + E ++  +  ++A  E ++      D + S   D++    DG     I+   + 
Sbjct: 651 AAKMEIPEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDGANTAPIDAAMQA 705

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKV 280
             R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 706 GLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKL 765

Query: 281 Q 281
           +
Sbjct: 766 K 766


>gi|187923827|ref|YP_001895469.1| RNA polymerase sigma factor RpoS [Burkholderia phytofirmans PsJN]
 gi|187715021|gb|ACD16245.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia phytofirmans
           PsJN]
          Length = 360

 Score =  103 bits (257), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 81/279 (29%), Positives = 140/279 (50%), Gaps = 27/279 (9%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+P+
Sbjct: 82  IQHYLNRISVKPLLTVEEEQKYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGVPL 140

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++    +  R 
Sbjct: 141 LDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRE 198

Query: 136 FFNLRRLKGHLQAITDN--------NLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESL 186
              + R K HL+  + N        +   + +  +  K     ++++++N   A  D  L
Sbjct: 199 LNQVLRAKRHLEKNSMNSGEAAERRDASIDDIAYLTGKTTDEVTDILALNEHTASLDAPL 258

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS-MSVLNPRERRIFEA 245
           +    SS  +          D + Q + L            LTR+ ++ L+ + R + E 
Sbjct: 259 DLDPASSLLDLLSDDQSQSPDAEVQHREL----------ETLTRAWLARLSDKHRHVIE- 307

Query: 246 RRLQEN---PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           RR   N   P TLE L+ E  ++RERVRQI+  A  +++
Sbjct: 308 RRFGLNHIEPATLEELADEMGLTRERVRQIQQEALVRLK 346


>gi|253573078|ref|ZP_04850470.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 1_1_6]
 gi|251837335|gb|EES65434.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 1_1_6]
          Length = 286

 Score =  103 bits (257), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 77/272 (28%), Positives = 147/272 (54%), Gaps = 18/272 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI +  ++  +EE  LA+R R  GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGREDLITVEEEVELAQRIR-KGDRVALEKLTRANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     +V++    NQ   
Sbjct: 77  PDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL--PLNQVGS 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
              + +     +   +    PE+   +A +L +   + IS   +++G   S++A     +
Sbjct: 135 LNKISKAFSKFEQENERRPSPEE---LADELEIP-VDKISDTLKVSGRHISVDAPFVEGE 190

Query: 195 KNSSQWQDWLVYDHD--GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA-RRLQEN 251
            NS    D LV D        ++ E   R+     + R++S L  RE+ I +    + + 
Sbjct: 191 DNS--LLDVLVNDDSPMADRSLVNESLARE-----IDRALSTLTEREKEIIQMFFGIGQQ 243

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +TLE +  +F ++RERVRQI+ +A +++++S
Sbjct: 244 EMTLEEIGDKFGLTRERVRQIKEKAIRRLRQS 275


>gi|159899067|ref|YP_001545314.1| RpoD family RNA polymerase sigma factor [Herpetosiphon aurantiacus
           ATCC 23779]
 gi|159892106|gb|ABX05186.1| RNA polymerase, sigma 70 subunit, RpoD family [Herpetosiphon
           aurantiacus ATCC 23779]
          Length = 386

 Score =  103 bits (257), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 84/294 (28%), Positives = 139/294 (47%), Gaps = 45/294 (15%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR----------------EHGDL-----------SAAH 51
           Y+ EI ++P+L   EE  LAK+                  EH D            +A  
Sbjct: 92  YLQEIGQVPLLTAAEEVDLAKKMEVAHAANDTLLQDDGMLEHSDRISLKRHIDTGRAARQ 151

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV IA  Y  YGL + ++V EGNIGLM+AV+KFD  +G + +TY+ WWI+ 
Sbjct: 152 HLIQANLRLVVSIAKKYTSYGLTMMDLVQEGNIGLMRAVEKFDYTKGHKFSTYATWWIRQ 211

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           A+   I      +++     +      ++R    LQ        PE+   IA+ + ++ S
Sbjct: 212 AITRAIADQSRTIRLPVHMGEA--ISQVKRTSHKLQQTMQREPTPEE---IAEAMGITAS 266

Query: 172 EVISMNCRLAGDESLNAL---INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +V     R   + S++ L   +    +   +  D++    D +    ++       R  +
Sbjct: 267 KV-----RRTLEASMHPLSLEMPVGQEGEGRMGDFI---EDDRVSTPVDAAAMTMLREQI 318

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L  RER+I + R  L++    TLE +  EF ++RER+RQIEA A +K+
Sbjct: 319 EEVLQKLPERERKIIQLRYGLKDGRYRTLEEVGLEFGITRERIRQIEAVALRKL 372


>gi|189467039|ref|ZP_03015824.1| hypothetical protein BACINT_03421 [Bacteroides intestinalis DSM
           17393]
 gi|224535443|ref|ZP_03675982.1| hypothetical protein BACCELL_00305 [Bacteroides cellulosilyticus
           DSM 14838]
 gi|319901765|ref|YP_004161493.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacteroides
           helcogenes P 36-108]
 gi|189435303|gb|EDV04288.1| hypothetical protein BACINT_03421 [Bacteroides intestinalis DSM
           17393]
 gi|224522909|gb|EEF92014.1| hypothetical protein BACCELL_00305 [Bacteroides cellulosilyticus
           DSM 14838]
 gi|319416796|gb|ADV43907.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacteroides
           helcogenes P 36-108]
          Length = 286

 Score =  103 bits (257), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 77/272 (28%), Positives = 148/272 (54%), Gaps = 18/272 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI +  ++  +EE  LA+R R+ GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGREDLITVEEEVELAQRIRK-GDRIALEKLTRANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     +V++    NQ   
Sbjct: 77  PDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL--PLNQVGS 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
              + +     +   +    PE+   +A +L +   + IS   +++G   S++A     +
Sbjct: 135 LNKISKAFSKFEQENERRPSPEE---LADELEIP-VDKISDTLKVSGRHISVDAPFVEGE 190

Query: 195 KNSSQWQDWLVYDHD--GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA-RRLQEN 251
            NS    D LV D        ++ E   R+     + R++S L  RE+ I +    + + 
Sbjct: 191 DNS--LLDVLVNDDSPMADRSLVNESLARE-----IDRALSTLTDREKEIIQMFFGIGQQ 243

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +TLE +  +F ++RERVRQI+ +A +++++S
Sbjct: 244 EMTLEEIGDKFGLTRERVRQIKEKAIRRLRQS 275


>gi|152995337|ref|YP_001340172.1| RpoD family RNA polymerase sigma factor [Marinomonas sp. MWYL1]
 gi|150836261|gb|ABR70237.1| RNA polymerase, sigma 70 subunit, RpoD family [Marinomonas sp.
           MWYL1]
          Length = 338

 Score =  103 bits (257), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 84/278 (30%), Positives = 142/278 (51%), Gaps = 26/278 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE V   R    GD  A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 66  YLSEIGFSPLLTAEEE-VYFSRLSLKGDQKARTRMIESNLRLVVKISRRYLNRGLSLLDL 124

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 125 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 183

Query: 139 LRRLKGHLQAITDNNLKPEQVV--------AIAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +   Q + D+    E++          + K L ++E +V S++    GD +  +L+
Sbjct: 184 LRAARELTQKL-DHEPSAEEIAEMLDCPVEDVQKMLGLNE-KVSSIDATFGGDNNDKSLV 241

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR-NMLTRSMSVLNPRERRIFEARRLQ 249
                   Q  +    D D    + +  +E   ++  ++TR   +      R  EA    
Sbjct: 242 EILADTLHQGPEADRQDGDVLNSIELWLDELSEKQCEVITRRFGL------RGHEAS--- 292

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
               TLE++ +E  ++RERVRQI+  A +K++  + K+
Sbjct: 293 ----TLEHVGAEIGLTRERVRQIQVEALRKLRLIMDKE 326


>gi|296451502|ref|ZP_06893237.1| RNA polymerase sigma factor rpoD [Clostridium difficile NAP08]
 gi|296880149|ref|ZP_06904116.1| RNA polymerase sigma factor rpoD [Clostridium difficile NAP07]
 gi|296259567|gb|EFH06427.1| RNA polymerase sigma factor rpoD [Clostridium difficile NAP08]
 gi|296428874|gb|EFH14754.1| RNA polymerase sigma factor rpoD [Clostridium difficile NAP07]
          Length = 301

 Score =  103 bits (257), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 77/269 (28%), Positives = 144/269 (53%), Gaps = 11/269 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            +  Y+ EI +  ML   EE  LAK       + A  + + S+ RLVV IA  Y+   + 
Sbjct: 30  AMKMYLKEIEEYKMLSAGEEVELAKEIINSSSV-AKEKFINSNYRLVVSIAKRYKRDSID 88

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  GNIGL++AV+K+D ++G++ +TY+ WWIK ++  YI    + ++I    +Q+ 
Sbjct: 89  MLDLIQAGNIGLIKAVEKYDYKKGYKFSTYATWWIKQSITRYIDDCENTIRIPIHLHQRI 148

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
            F     +K   Q + +  L+   +  IA    +   +V+ +  R     SL+  +   D
Sbjct: 149 NF-----VKKKKQELLNVLLREPTIDEIADACGLEVDKVLELLRRDKNVVSLDTPL-KED 202

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENP 252
           ++SS   +++  D D ++ V+ E E+  N +  +   ++ L  +E+++   R     ++P
Sbjct: 203 EDSS-LVEFIPSDADFKDVVMHEVEQH-NLKEKIEELLTGLGEQEQQVLRMRFGIDDDDP 260

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE +   F V+RER+RQIEA+A +K++
Sbjct: 261 KTLEQIGRVFGVTRERIRQIEAKAIRKLR 289


>gi|295098975|emb|CBK88064.1| RNA polymerase, sigma 70 subunit, RpoD [Eubacterium cylindroides
           T2-87]
          Length = 368

 Score =  103 bits (257), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 85/295 (28%), Positives = 147/295 (49%), Gaps = 46/295 (15%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR---------EHGDLSAAHR----------------L 53
           Y+ EI +IP+L+ +EE ++AKR +         E  DL    R                L
Sbjct: 74  YLKEIGQIPLLDPKEEPIIAKRIQDGEAAKKKLEEPDLDIEERKKLASVVADGEEAKQVL 133

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           ++S+LRLVV IA  Y G G+   +++ EGN GL++AV+KFD  +GF+ +TY+ WWI+ ++
Sbjct: 134 ISSNLRLVVSIAKKYVGRGMLFLDLIQEGNCGLIKAVEKFDYTKGFKFSTYATWWIRQSI 193

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL-NVSESE 172
              I      ++I    +       L R++  L      +  PE+   IA+K+ N++  +
Sbjct: 194 TRAIADQARTIRI--PVHMVETINKLTRIQRQLVQDLGRDPLPEE---IAEKMENITADK 248

Query: 173 VISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR---RNML 228
           V  +  ++A D  SL   I   D   S   D++      +++  +  ++  N    ++ +
Sbjct: 249 VREIQ-KIALDPVSLETPIGEED--DSHLGDFI------EDKETLSPDDYTNNQLLKDEI 299

Query: 229 TRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L  RE ++   R   +     TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 300 NNVLQGLTEREEKVLRLRFGLMDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLK 354


>gi|323526138|ref|YP_004228291.1| RNA polymerase sigma-70 subunit RpoD subfamily [Burkholderia sp.
           CCGE1001]
 gi|323383140|gb|ADX55231.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Burkholderia sp.
           CCGE1001]
          Length = 358

 Score =  103 bits (257), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 79/278 (28%), Positives = 140/278 (50%), Gaps = 25/278 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+P+
Sbjct: 80  IQHYLNRISVKPLLTVEEEQKYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGVPL 138

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++    +  R 
Sbjct: 139 LDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRE 196

Query: 136 FFNLRRLKGHLQAITDN--------NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              + R K HL+  + N        +   + +  +  K     ++++++N   A   SL+
Sbjct: 197 LNQVLRAKRHLEKNSMNSGEAAERRDASIDDIAYLTGKTTDEVTDILALNEHTA---SLD 253

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS-MSVLNPRERRIFEAR 246
           A ++    +S               +V      +      LTR+ ++ L+ + R + E R
Sbjct: 254 APLDLDPASSLLDLLSDDQSQSPDAEV------QHRELETLTRAWLARLSDKHRHVIE-R 306

Query: 247 RLQEN---PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   N   P TLE L+ E  ++RERVRQI+  A  +++
Sbjct: 307 RFGLNHIEPATLEELADEMGLTRERVRQIQQEALVRLK 344


>gi|119953545|ref|YP_945755.1| RNA polymerase sigma factor RpoS [Borrelia turicatae 91E135]
 gi|119862316|gb|AAX18084.1| RNA polymerase sigma factor RpoS [Borrelia turicatae 91E135]
          Length = 267

 Score =  103 bits (257), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 81/282 (28%), Positives = 150/282 (53%), Gaps = 20/282 (7%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M+I  N ++ +  Y+  +R+  ++  +EE  LAK+ +  GDL A ++++ ++LRLV+KI 
Sbjct: 1   MNIFSNEDLNI--YLKSVREHRLITHEEEIELAKQIK-LGDLKAKNKMINANLRLVLKII 57

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y G GL + +++ EGN+GL++A +K+DP +  + +TY+ +WIK ++Q  +     LVK
Sbjct: 58  KRYAGKGLKVEDLIQEGNLGLIRAAEKYDPSKNTKFSTYASFWIKQSLQRALNTKTRLVK 117

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           +        L  N        + + +    P++   I ++ N++ ++ I +   L  + S
Sbjct: 118 VPYRKENLILQIN--------KYLMEEEKSPKK-EDIMERFNLTTAQYIKIIPYLEKEYS 168

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L+  I  S+ NS+     L  D+    +  +E+       N +  +   LN +ER I   
Sbjct: 169 LDKKIEGSE-NSTLLN--LYEDNSFNPESTLEQNSTLKHLNHILETK--LNEKERYIIIK 223

Query: 246 RRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R   +N     TL+++S+E  +S E VRQIE R  KK++E +
Sbjct: 224 RYNLDNSDKKSTLKDISNELGISSETVRQIEKRVLKKLKEEL 265


>gi|110803528|ref|YP_699284.1| RNA polymerase sigma factor RpoD [Clostridium perfringens SM101]
 gi|169343561|ref|ZP_02864560.1| RNA polymerase sigma factor RpoD [Clostridium perfringens C str.
           JGS1495]
 gi|170763881|ref|ZP_02634334.2| RNA polymerase sigma factor RpoD [Clostridium perfringens B str.
           ATCC 3626]
 gi|170764050|ref|ZP_02630759.2| RNA polymerase sigma factor RpoD [Clostridium perfringens E str.
           JGS1987]
 gi|170764227|ref|ZP_02638581.2| RNA polymerase sigma factor RpoD [Clostridium perfringens CPE str.
           F4969]
 gi|182420445|ref|ZP_02641259.2| RNA polymerase sigma factor RpoD [Clostridium perfringens NCTC
           8239]
 gi|182624422|ref|ZP_02952206.1| RNA polymerase sigma factor RpoD [Clostridium perfringens D str.
           JGS1721]
 gi|110684029|gb|ABG87399.1| RNA polymerase sigma factor RpoD [Clostridium perfringens SM101]
 gi|169298121|gb|EDS80211.1| RNA polymerase sigma factor RpoD [Clostridium perfringens C str.
           JGS1495]
 gi|170663661|gb|EDT16344.1| RNA polymerase sigma factor RpoD [Clostridium perfringens E str.
           JGS1987]
 gi|170713105|gb|EDT25287.1| RNA polymerase sigma factor RpoD [Clostridium perfringens B str.
           ATCC 3626]
 gi|170715649|gb|EDT27831.1| RNA polymerase sigma factor RpoD [Clostridium perfringens CPE str.
           F4969]
 gi|177910425|gb|EDT72802.1| RNA polymerase sigma factor RpoD [Clostridium perfringens D str.
           JGS1721]
 gi|182382279|gb|EDT79758.1| RNA polymerase sigma factor RpoD [Clostridium perfringens NCTC
           8239]
          Length = 366

 Score =  103 bits (257), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 78/265 (29%), Positives = 138/265 (52%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  ++E  LAK+  E G   A  +L  ++LRLVV IA  Y G G+   ++
Sbjct: 100 YLKEIGKVPLLSSEDEIELAKKI-EEGSNYAKKKLAEANLRLVVSIAKRYVGRGMLFLDL 158

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 159 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 216

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R++  L      +  PE+   ++K++++   +V  +  ++A  E ++      ++  S
Sbjct: 217 LIRIQRQLVQELGRDPLPEE---LSKQMDMPVDKVREI-LKIA-QEPVSLETPIGEEEDS 271

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++  D              K +   L   +  L PRE ++   R   ++    TLE
Sbjct: 272 HLGDFIPDDDAPAPAEAAAFTMLKEQ---LINVLDTLTPREEKVLRLRFGLDDGRARTLE 328

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF V+RER+RQIEA+A +K++
Sbjct: 329 EVGKEFNVTRERIRQIEAKALRKLR 353


>gi|19910022|dbj|BAB87262.1| RNA polymerase sigma factor [Guillardia theta]
          Length = 490

 Score =  103 bits (257), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 74/248 (29%), Positives = 134/248 (54%), Gaps = 14/248 (5%)

Query: 39  KRYRE--HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           K++R   H    A  R+V ++LRLVV IA  Y   G+ + +++ EG++GL++A +KFD E
Sbjct: 193 KKFRSILHNARRAKERMVAANLRLVVSIAKRYVNRGMSLQDLIQEGSLGLIRAAEKFDSE 252

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +GF+ +TY+ WW+K A+   I      +++        L+  +  ++   + +     + 
Sbjct: 253 KGFKFSTYATWWVKQAVTRAIADHSRTIRLPV-----HLYDTISAIRKTTRTLNIEIGRS 307

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
                IA+K+++S  ++ S+        SL   + + D ++SQ  D++  D +  E    
Sbjct: 308 PTEEEIAEKMDMSVEKLRSVLQSAQPTLSLERPLKNDD-DASQLSDFIEADQESPE---- 362

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPV-TLENLSSEFEVSRERVRQIEA 274
           E  E+   R+ L   ++ L+PRER +   R  L +  + TLE +   F V+RERVRQIEA
Sbjct: 363 EHVEKSMLRDDLENVINSLSPRERDVVRMRYGLDDGRIKTLEEIGQIFSVTRERVRQIEA 422

Query: 275 RAFKKVQE 282
           +A +K+++
Sbjct: 423 KAIRKLRQ 430


>gi|269960386|ref|ZP_06174759.1| RNA polymerase sigma-38 factor [Vibrio harveyi 1DA3]
 gi|269834813|gb|EEZ88899.1| RNA polymerase sigma-38 factor [Vibrio harveyi 1DA3]
          Length = 255

 Score =  103 bits (257), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 77/247 (31%), Positives = 129/247 (52%), Gaps = 30/247 (12%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ S+LRLVVKI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+ 
Sbjct: 15  RMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQ 74

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA--------IA 163
            ++  ++     +++      K L   LR  +  L    D+    E++ A        ++
Sbjct: 75  TIERALMNQTRTIRLPIHV-VKELNIYLRTAR-ELSQKLDHEPTAEEIAAQLDIPVEDVS 132

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           K L ++E  + S++  + GD     L    D N+S   D  V   D             +
Sbjct: 133 KMLRLNE-RISSVDTPIGGDGEKALLDIIPDANNS---DPEVSTQD------------DD 176

Query: 224 RRNMLTRSMSVLNPRERRIFEARR---LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            ++ L   +  LNP+++ +  ARR   L   P TLE +  E  ++RERVRQI+    +++
Sbjct: 177 IKSSLIHWLEELNPKQKEVL-ARRFGLLGYEPSTLEEVGREIGLTRERVRQIQVEGLRRL 235

Query: 281 QESIQKQ 287
           +E + KQ
Sbjct: 236 REILIKQ 242


>gi|170692344|ref|ZP_02883507.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia graminis
           C4D1M]
 gi|170142774|gb|EDT10939.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia graminis
           C4D1M]
          Length = 359

 Score =  103 bits (257), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 81/279 (29%), Positives = 140/279 (50%), Gaps = 27/279 (9%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+P+
Sbjct: 81  IQHYLNRISVKPLLTVEEEQKYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGVPL 139

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++    +  R 
Sbjct: 140 LDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRE 197

Query: 136 FFNLRRLKGHLQAITDN--------NLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESL 186
              + R K HL+  + N        +   + +  +  K     ++++++N   A  D  L
Sbjct: 198 LNQVLRAKRHLEKNSMNSGEAAERRDASIDDIAYLTGKTTDEVTDILALNEHTASLDAPL 257

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS-MSVLNPRERRIFEA 245
           +    SS  +          D + Q + L            LTR+ ++ L+ + R + E 
Sbjct: 258 DLDPASSLLDLLSDDQSQSPDAEVQHREL----------ETLTRAWLARLSDKHRHVIE- 306

Query: 246 RRLQEN---PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           RR   N   P TLE L+ E  ++RERVRQI+  A  +++
Sbjct: 307 RRFGLNHIEPATLEELADEMGLTRERVRQIQQEALVRLK 345


>gi|295676469|ref|YP_003604993.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Burkholderia sp.
           CCGE1002]
 gi|295436312|gb|ADG15482.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Burkholderia sp.
           CCGE1002]
          Length = 362

 Score =  103 bits (256), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 80/278 (28%), Positives = 141/278 (50%), Gaps = 25/278 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+P+
Sbjct: 84  IQHYLNRISVKPLLTVEEEQKYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGVPL 142

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++    +  R 
Sbjct: 143 LDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRE 200

Query: 136 FFNLRRLKGHLQAITDN--------NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              + R K HL+  + N        +   + +  +  K     ++++++N   A   SL+
Sbjct: 201 LNQVLRAKRHLEKNSMNSGEAAERRDASIDDIAYLTGKTTDEVTDILALNEHTA---SLD 257

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS-MSVLNPRERRIFEAR 246
           A ++    +S               +V   + E       LTR+ ++ L+ + R + E R
Sbjct: 258 APLDLDPASSLLDLLSDDQSQSPDAEVQHRELE------TLTRAWLARLSDKHRHVIE-R 310

Query: 247 RLQEN---PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   N   P TLE L+ E  ++RERVRQI+  A  +++
Sbjct: 311 RFGLNHIEPATLEELADEMGLTRERVRQIQQEALVRLK 348


>gi|307324812|ref|ZP_07604018.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306889694|gb|EFN20674.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 414

 Score =  103 bits (256), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 91/295 (30%), Positives = 141/295 (47%), Gaps = 42/295 (14%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHG-------------------DLS--------AA 50
           +Y+ EI +IP+L   EE  LA+R  E G                   DL         A 
Sbjct: 120 QYLREIGRIPLLSAVEEVELARRV-EAGLFAEEKLGNTPDLDSQLAVDLDRLVVLGRVAK 178

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY+ WWI+
Sbjct: 179 RRLIEANLRLVVSVAKRYIGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIR 238

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            AM   +      +++     +  L   + R++  +         PE+V A    L    
Sbjct: 239 QAMSRALADQARTIRVPVHVVE--LINRVVRVQRRMLQERGYEPTPEEVAAHLDLLPERV 296

Query: 171 SEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           SEV+    RLA +  SL+A +   D  +    D +    DG     +E       R  L 
Sbjct: 297 SEVL----RLAQEPVSLHAPVGEEDDVA--LGDLI---EDGDAASPVESAAFLLLREHLE 347

Query: 230 RSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             +S L  RER++ + R       P TLE +   F V+RER+RQIE++   K+++
Sbjct: 348 AVLSTLGERERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRD 402


>gi|288927719|ref|ZP_06421566.1| RNA polymerase sigma-70 factor [Prevotella sp. oral taxon 317 str.
           F0108]
 gi|288330553|gb|EFC69137.1| RNA polymerase sigma-70 factor [Prevotella sp. oral taxon 317 str.
           F0108]
          Length = 287

 Score =  103 bits (256), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 76/268 (28%), Positives = 146/268 (54%), Gaps = 16/268 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI    ++  +EE  LA+R ++ GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGHEELISVEEEVELAQRIKK-GDRKALEKLTKANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V++    NQ   
Sbjct: 77  QDLINEGNVGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRL--PLNQ--- 131

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
             ++ ++   L      N +   +  IA+K ++ E + I    ++ G   S++A     +
Sbjct: 132 VGSVNKINKILSKFEQENERRPSINEIAEKTDLPEDK-IEDAIKVTGRHISVDAPFVDGE 190

Query: 195 KNSSQWQDWLV-YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA-RRLQENP 252
            NS    D L   D    +  L+    +++ R  +  ++  LN RER + EA   + +  
Sbjct: 191 DNS--LLDLLANTDTPTVDNELV----KESLRAEIADALQYLNERERNVIEAFFGINQME 244

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKV 280
           +TLE +  ++ ++RERVRQI+ +A +++
Sbjct: 245 MTLEEIGDKYGLTRERVRQIKEKAIRRL 272


>gi|209522220|ref|ZP_03270857.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia sp. H160]
 gi|209497349|gb|EDZ97567.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia sp. H160]
          Length = 363

 Score =  103 bits (256), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 80/278 (28%), Positives = 141/278 (50%), Gaps = 25/278 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+P+
Sbjct: 85  IQHYLNRISVKPLLTVEEEQKYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGVPL 143

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++    +  R 
Sbjct: 144 LDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRE 201

Query: 136 FFNLRRLKGHLQAITDN--------NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              + R K HL+  + N        +   + +  +  K     ++++++N   A   SL+
Sbjct: 202 LNQVLRAKRHLEKNSMNSGEAAERRDASIDDIAYLTGKTTDEVTDILALNEHTA---SLD 258

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS-MSVLNPRERRIFEAR 246
           A ++    +S               +V   + E       LTR+ ++ L+ + R + E R
Sbjct: 259 APLDLDPASSLLDLLSDDQSQSPDAEVQHRELE------TLTRAWLARLSDKHRHVIE-R 311

Query: 247 RLQEN---PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   N   P TLE L+ E  ++RERVRQI+  A  +++
Sbjct: 312 RFGLNHIEPATLEELADEMGLTRERVRQIQQEALVRLK 349


>gi|329960773|ref|ZP_08299079.1| putative RNA polymerase sigma factor RpoD [Bacteroides fluxus YIT
           12057]
 gi|328532374|gb|EGF59175.1| putative RNA polymerase sigma factor RpoD [Bacteroides fluxus YIT
           12057]
          Length = 286

 Score =  103 bits (256), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 77/272 (28%), Positives = 147/272 (54%), Gaps = 18/272 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI +  ++  +EE  LA+R R  GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGREDLITVEEEVELAQRIR-KGDRIALEKLTRANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     +V++    NQ   
Sbjct: 77  PDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL--PLNQVGS 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
              + +     +   +    PE+   +A +L +   + IS   +++G   S++A     +
Sbjct: 135 LNKISKAFSKFEQENERRPSPEE---LADELEIP-VDKISDTLKVSGRHISVDAPFVEGE 190

Query: 195 KNSSQWQDWLVYDHD--GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA-RRLQEN 251
            NS    D LV D        ++ E   R+     + R++S L  RE+ I +    + + 
Sbjct: 191 DNS--LLDVLVNDDSPMADRSLVNESLARE-----IDRALSTLTEREKEIIQMFFGIGQQ 243

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +TLE +  +F ++RERVRQI+ +A +++++S
Sbjct: 244 EMTLEEIGDKFGLTRERVRQIKEKAIRRLRQS 275


>gi|332880149|ref|ZP_08447831.1| putative RNA polymerase sigma factor RpoD [Capnocytophaga sp. oral
           taxon 329 str. F0087]
 gi|332681908|gb|EGJ54823.1| putative RNA polymerase sigma factor RpoD [Capnocytophaga sp. oral
           taxon 329 str. F0087]
          Length = 286

 Score =  103 bits (256), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 75/277 (27%), Positives = 152/277 (54%), Gaps = 16/277 (5%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI +  ++  +EE  LA+R R+ GD  A  +L  ++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQEIGREDLITVEEEVELAQRIRK-GDRVALEKLTRANLRFVVSVAKQYQNQGLS 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     +V++    NQ  
Sbjct: 76  LPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL--PLNQVG 133

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSS 193
               + +     +   +    PE+   +A +L +   + IS   +++G   S++A     
Sbjct: 134 SLNKISKAFSKFEQENERRPSPEE---LADELEIP-VDKISDTLKVSGRHISVDAPFVEG 189

Query: 194 DKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA-RRLQEN 251
           + NS    D LV D     ++ L+ +   +     + R++S L+ RE+ I +    +   
Sbjct: 190 EDNS--LLDVLVNDDSPMADRTLVNESLSRE----IDRALSTLSEREKEIIQMFFGINHQ 243

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +TLE +  +F ++RERVRQI+ +A ++++++ + ++
Sbjct: 244 EMTLEEIGDKFNLTRERVRQIKEKAIRRLRQNTKSKL 280


>gi|186475727|ref|YP_001857197.1| RNA polymerase sigma factor RpoS [Burkholderia phymatum STM815]
 gi|184192186|gb|ACC70151.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia phymatum
           STM815]
          Length = 364

 Score =  103 bits (256), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 80/278 (28%), Positives = 141/278 (50%), Gaps = 25/278 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+P+
Sbjct: 86  IQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGVPL 144

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++    +  R 
Sbjct: 145 LDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRE 202

Query: 136 FFNLRRLKGHLQAITDN--------NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              + R K HL+  + N        +   + +  +  K     ++++++N   A   SL+
Sbjct: 203 LNQVLRAKRHLEKNSMNSGEAAERRDASIDDIAYLTGKTTDEVTDILALNEHTA---SLD 259

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS-MSVLNPRERRIFEAR 246
           A ++    +S               +V   + E       LTR+ ++ L+ + R + E R
Sbjct: 260 APLDLDPASSLLDLLSDDQSQSPDAEVQHRELE------TLTRAWLARLSDKHRHVIE-R 312

Query: 247 RLQEN---PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   N   P TLE L+ E  ++RERVRQI+  A  +++
Sbjct: 313 RFGLNHIEPATLEELADEMGLTRERVRQIQQEALVRLK 350


>gi|318040801|ref|ZP_07972757.1| type II alternative RNA polymerase sigma factor [Synechococcus sp.
           CB0101]
          Length = 381

 Score =  103 bits (256), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 74/241 (30%), Positives = 122/241 (50%), Gaps = 13/241 (5%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           H    A  R++ ++LRLVV +A  Y+  G+ + ++V EG +GL +AV+K+DP RGFR +T
Sbjct: 131 HHGRRARDRMIQANLRLVVAVAKKYQQRGMELLDLVQEGTLGLERAVEKYDPTRGFRFST 190

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI+  +   I      +++     +K     L R+K   + I   + +   V  +A
Sbjct: 191 YAYWWIRQGITRAIATQSRTIRLPVHVTEK-----LNRIKKAQRQIATEHGRLASVSDLA 245

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           ++L +SE  V     R+    SL+  +    +  +Q  D L   H   EQ L     R++
Sbjct: 246 RELGLSEEVVRLTLMRVPRSVSLDTRVGR--EQDTQLGDLLEDSHATPEQELT----RES 299

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             + L   +  L  RE  +   R   E+  P TL  +  +  +SRERVRQIE+RA  K++
Sbjct: 300 LHDDLESLLEELTAREAAVIRLRYGLEDDTPQTLSQIGEDLHLSRERVRQIESRALLKLR 359

Query: 282 E 282
           +
Sbjct: 360 Q 360


>gi|256827331|ref|YP_003151290.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Cryptobacterium curtum
           DSM 15641]
 gi|256583474|gb|ACU94608.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Cryptobacterium curtum
           DSM 15641]
          Length = 422

 Score =  103 bits (256), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 89/304 (29%), Positives = 141/304 (46%), Gaps = 61/304 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRY-----------------------REHG--------DL 47
           Y+ EI K+P+L   EE  LA +                        REH          L
Sbjct: 123 YLKEIGKVPLLTAAEEIDLAMKIEAGVEAGEQLEAAEADNAEELSRREHRRLTRIEAVGL 182

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A  +L+ ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ W
Sbjct: 183 DAKQQLIEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATW 242

Query: 108 WIKAAMQEYILRSWSLVKIGT----TAN-----QKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           WI+ A+   I      ++I      T N     Q++L   L R     +   + +L P++
Sbjct: 243 WIRQAITRAIADQARTIRIPVHMVETINKLVRIQRQLLQELGREPTPEEIAEEMDLTPDR 302

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           V  I K   +S+ E +S+   +  +E             SQ  D++    D    V  + 
Sbjct: 303 VREIQK---ISQ-EPVSLETPIGEEE------------DSQLGDFI---EDDAAVVPPDA 343

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARA 276
                 +  LT+ +  L  RER++   R   E+  P TLE +  EF V+RER+RQIE++ 
Sbjct: 344 ASFSMLQEQLTKVLDGLAERERKVISLRFGLEDGHPRTLEEVGREFGVTRERIRQIESKT 403

Query: 277 FKKV 280
             K+
Sbjct: 404 LAKL 407


>gi|255655509|ref|ZP_05400918.1| RNA polymerase sigma factor rpoD [Clostridium difficile QCD-23m63]
          Length = 294

 Score =  103 bits (256), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 77/269 (28%), Positives = 144/269 (53%), Gaps = 11/269 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            +  Y+ EI +  ML   EE  LAK       + A  + + S+ RLVV IA  Y+   + 
Sbjct: 23  AMKMYLKEIEEYKMLSAGEEVELAKEIINSSSV-AKEKFINSNYRLVVSIAKRYKRDSID 81

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  GNIGL++AV+K+D ++G++ +TY+ WWIK ++  YI    + ++I    +Q+ 
Sbjct: 82  MLDLIQAGNIGLIKAVEKYDYKKGYKFSTYATWWIKQSITRYIDDCENTIRIPIHLHQRI 141

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
            F     +K   Q + +  L+   +  IA    +   +V+ +  R     SL+  +   D
Sbjct: 142 NF-----VKKKKQELLNVLLREPTIDEIADACGLEVDKVLELLRRDKNVVSLDTPL-KED 195

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENP 252
           ++SS   +++  D D ++ V+ E E+  N +  +   ++ L  +E+++   R     ++P
Sbjct: 196 EDSS-LVEFIPSDADFKDVVMHEVEQH-NLKEKIEELLTGLGEQEQQVLRMRFGIDDDDP 253

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TLE +   F V+RER+RQIEA+A +K++
Sbjct: 254 KTLEQIGRVFGVTRERIRQIEAKAIRKLR 282


>gi|282861771|ref|ZP_06270835.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces sp.
           ACTE]
 gi|282563587|gb|EFB69125.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces sp.
           ACTE]
          Length = 355

 Score =  103 bits (256), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 87/298 (29%), Positives = 146/298 (48%), Gaps = 50/298 (16%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRY------------------REHGDLS--------AAHR 52
           Y+ EI +IP+L   +E  LA+R                   R   DL         A  R
Sbjct: 62  YLREIGRIPLLGAADEVELARRVEAGLFAEERLAATPGPDTRLAQDLGRLVVQGRMAERR 121

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY+ WWI+ A
Sbjct: 122 LIEANLRLVVSVAKRYAGRGLTMLDLVQEGNLGLIRAVEKFDYTRGYKFSTYATWWIRQA 181

Query: 113 MQEYILRSWSLVKIGTTANQ--KRLFFNLRRL---KGHLQAITDNNLKPEQVVAIAKKLN 167
           M   +      +++     +   R+    RRL   +GH  +  +          +A +L+
Sbjct: 182 MSRALADQARTIRVPVHVVELINRVVRVQRRLLQERGHEPSAEE----------VAAQLD 231

Query: 168 VSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   V ++  RLA +  SL+A +   D  +  + D +    DG     +E       R 
Sbjct: 232 LTPERVETI-LRLAQEPVSLHAPVGEEDDVA--FGDLI---EDGDAPSPVESAAFLLLRE 285

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            L   +S L  RER++ + R   ++  P TLE +   F V+RER+RQIE++   ++++
Sbjct: 286 HLEAVLSTLGERERKVVQLRYGLDDGRPRTLEEIGRLFGVTRERIRQIESKTLARLRD 343


>gi|260222953|emb|CBA33035.1| RNA polymerase sigma factor rpoD [Curvibacter putative symbiont of
           Hydra magnipapillata]
          Length = 519

 Score =  103 bits (256), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 71/241 (29%), Positives = 127/241 (52%), Gaps = 12/241 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E+   +A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 274 EYASRAAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 333

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I     +     N R  + HLQ       +P+  V +
Sbjct: 334 TYATWWIRQAITRSIADQARTIRIPVHMIETINKMN-RISRQHLQEF---GFEPDASV-L 388

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+ + E ++  +  ++A  E ++      D + S   D++    D      +E   + 
Sbjct: 389 AEKMEIPEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDSANTAPMEAAMQA 443

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             R+++   +  L PRE ++   R   E  +  TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 444 GLRDVVKDILDSLTPREAKVLRMRFGIEMTSDHTLEEVGKQFDVTRERIRQIEAKALRKL 503

Query: 281 Q 281
           +
Sbjct: 504 K 504


>gi|116074244|ref|ZP_01471506.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9916]
 gi|116069549|gb|EAU75301.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9916]
          Length = 341

 Score =  103 bits (256), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 83/288 (28%), Positives = 142/288 (49%), Gaps = 37/288 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLA--------------------KRYREHGDLSAAHRLVTSHL 58
           Y+  I +IP+L   EE  LA                    +R++      A  R++ ++L
Sbjct: 57  YLSSIGRIPLLTPAEEIELAHHVQAMKQLLETPEDERTPRERHKIRMGKRARDRMMAANL 116

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+  M   I 
Sbjct: 117 RLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTRAID 176

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLK---GHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
            S   +++    ++K     +RR+     H      N L+      +A  + +   ++  
Sbjct: 177 NSARTIRLPIHISEK--LSKMRRISRELSHRFGRQPNRLE------LAHAMGIEPRDLED 228

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
           +  + A   SL+A     +  S+  +  L+ D +G++   +E  +R  ++  L   +S L
Sbjct: 229 LISQSAPCASLDAHARGEEDRSTLGE--LIPDPNGEDS--MEGMDRSIQKEHLGGWLSQL 284

Query: 236 NPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           N RE++I + R     E P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 285 NEREQKILKLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 332


>gi|330995823|ref|ZP_08319720.1| putative RNA polymerase sigma factor RpoD [Paraprevotella
           xylaniphila YIT 11841]
 gi|329574553|gb|EGG56118.1| putative RNA polymerase sigma factor RpoD [Paraprevotella
           xylaniphila YIT 11841]
          Length = 286

 Score =  103 bits (256), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 75/277 (27%), Positives = 152/277 (54%), Gaps = 16/277 (5%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI +  ++  +EE  LA+R R+ GD  A  +L  ++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQEIGREDLITVEEEVELAQRIRK-GDRVALEKLTRANLRFVVSVAKQYQNQGLS 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     +V++    NQ  
Sbjct: 76  LPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL--PLNQVG 133

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSS 193
               + +     +   +    PE+   +A +L +   + IS   +++G   S++A     
Sbjct: 134 SLNKISKAFSKFEQENERRPSPEE---LADELEIP-VDKISDTLKVSGRHISVDAPFVEG 189

Query: 194 DKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA-RRLQEN 251
           + NS    D LV D     ++ L+ +   +     + R++S L+ RE+ I +    +   
Sbjct: 190 EDNS--LLDVLVNDDSPMADRTLVNESLARE----IDRALSTLSEREKEIIQMFFGINHQ 243

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +TLE +  +F ++RERVRQI+ +A ++++++ + ++
Sbjct: 244 EMTLEEIGDKFNLTRERVRQIKEKAIRRLRQNTKSKL 280


>gi|283954552|ref|ZP_06372071.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 414]
 gi|283793956|gb|EFC32706.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 414]
          Length = 622

 Score =  103 bits (256), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 81/250 (32%), Positives = 125/250 (50%), Gaps = 41/250 (16%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ +RG++ +TY+ WW
Sbjct: 381 AKGRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWW 440

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T NQ     N + ++ HLQ     + K   V  IAK
Sbjct: 441 IRQAISRAIADQARTIRIPIHMIETINQ----IN-KIIREHLQ----KDGKEPDVSVIAK 491

Query: 165 KLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           ++++S  +V          IS+   +  ++         D+NS    D ++ D D +EQ+
Sbjct: 492 EVSLSMDKVKQVIKITKEPISLEAPIGNEDDGKFGDFVEDRNSLSPMDHILKD-DLKEQI 550

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQ 271
                            ++ LN RE+ +   R      E+  TLE +  E  V+RERVRQ
Sbjct: 551 --------------DEVLNQLNDREKAVIRMRFGLMDDESDRTLEEIGKELNVTRERVRQ 596

Query: 272 IEARAFKKVQ 281
           IE+ A KK++
Sbjct: 597 IESSAIKKLK 606


>gi|57168867|ref|ZP_00367997.1| RNA polymerase sigma factor RpoD [Campylobacter coli RM2228]
 gi|305431982|ref|ZP_07401149.1| DNA-directed RNA polymerase sigma subunit RpoD [Campylobacter coli
           JV20]
 gi|57019703|gb|EAL56389.1| RNA polymerase sigma factor RpoD [Campylobacter coli RM2228]
 gi|304445066|gb|EFM37712.1| DNA-directed RNA polymerase sigma subunit RpoD [Campylobacter coli
           JV20]
          Length = 621

 Score =  103 bits (256), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 81/250 (32%), Positives = 123/250 (49%), Gaps = 41/250 (16%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ +RG++ +TY+ WW
Sbjct: 380 AKTRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWW 439

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T NQ     N + ++ HLQ     + K   V  IAK
Sbjct: 440 IRQAISRAIADQARTIRIPIHMIETINQ----IN-KIIREHLQ----KDGKEPDVSVIAK 490

Query: 165 KLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           ++ +S  +V          IS+   +  ++         D+NS    D ++ D D +EQ+
Sbjct: 491 EVGLSVDKVKQVIKITKEPISLEAPIGSEDDGKFGDFVEDRNSLSPMDHILKD-DLKEQI 549

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQ 271
                            +  LN RE+ +   R      E+  TLE +  E  V+RERVRQ
Sbjct: 550 --------------DEVLDQLNDREKAVIRMRFGLMDDESDRTLEEIGKELNVTRERVRQ 595

Query: 272 IEARAFKKVQ 281
           IE+ A KK++
Sbjct: 596 IESSAIKKLK 605


>gi|91783466|ref|YP_558672.1| RNA polymerase sigma factor RpoS [Burkholderia xenovorans LB400]
 gi|296157776|ref|ZP_06840610.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Burkholderia sp.
           Ch1-1]
 gi|91687420|gb|ABE30620.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia xenovorans
           LB400]
 gi|295892022|gb|EFG71806.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Burkholderia sp.
           Ch1-1]
          Length = 360

 Score =  103 bits (256), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 79/278 (28%), Positives = 140/278 (50%), Gaps = 25/278 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+P+
Sbjct: 82  IQHYLNRISVKPLLTVEEEQKYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGVPL 140

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++    +  R 
Sbjct: 141 LDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRE 198

Query: 136 FFNLRRLKGHLQAITDN--------NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              + R K HL+  + N        +   + +  +  K     ++++++N   A   SL+
Sbjct: 199 LNQVLRAKRHLEKNSMNSGEAAERRDASIDDIAYLTGKTTDEVTDILALNEHTA---SLD 255

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS-MSVLNPRERRIFEAR 246
           A ++    +S               +V      +      LTR+ ++ L+ + R + E R
Sbjct: 256 APLDLDPASSLLDLLSDDQSQSPDAEV------QHRELETLTRAWLARLSDKHRHVIE-R 308

Query: 247 RLQEN---PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   N   P TLE L+ E  ++RERVRQI+  A  +++
Sbjct: 309 RFGLNHIEPATLEELADEMGLTRERVRQIQQEALVRLK 346


>gi|166368188|ref|YP_001660461.1| RNA polymerase sigma factor RpoD [Microcystis aeruginosa NIES-843]
 gi|166090561|dbj|BAG05269.1| principal RNA polymerase sigma factor [Microcystis aeruginosa
           NIES-843]
          Length = 416

 Score =  103 bits (256), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 76/257 (29%), Positives = 138/257 (53%), Gaps = 17/257 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K +EY+ A + R +    A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++
Sbjct: 160 LAKSKEYLSAFKRRLYHGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIR 219

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A +KFD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + 
Sbjct: 220 AAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKI 274

Query: 149 IT-DNNLKP-EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           ++ +   KP E+ +A   ++ + +   I+ + +L    SL   I   +   S+  D++  
Sbjct: 275 LSQEMRRKPTEEEIATKMEMTIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIEA 330

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEV 264
           D +  E  + +   R++  N+L      L+PRER +   R   ++    TLE +   F V
Sbjct: 331 DGETPEDEVSKNLLREDLENVL----DTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNV 386

Query: 265 SRERVRQIEARAFKKVQ 281
           +RER+RQIEA+A +K++
Sbjct: 387 TRERIRQIEAKALRKLR 403


>gi|239979292|ref|ZP_04701816.1| RNA polymerase sigma factor [Streptomyces albus J1074]
          Length = 357

 Score =  103 bits (256), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 88/293 (30%), Positives = 142/293 (48%), Gaps = 41/293 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAH--------------------------R 52
           Y+ EI +IP+L   +E  LA+R  E G  +AA                           R
Sbjct: 65  YLREIGRIPLLSAADEVELARRV-EAGVFAAAKLAGGCADAGLARDLRRLVVLGERAKGR 123

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RGF+ +TY+ WWI+ A
Sbjct: 124 LIEANLRLVVSVAKRYTGRGLTMLDLVQEGNLGLIRAVEKFDYTRGFKFSTYATWWIRQA 183

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           M   +      +++    +   L   + R +  L          E+V    ++L +S +E
Sbjct: 184 MSRALADQARTIRV--PVHVVELINRVVRTQRALLQEAGREPAAEEV---GERLGLS-AE 237

Query: 173 VISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
            +    RLA +  SL+A +   D     +   L+ D D       E       R  L   
Sbjct: 238 KVEEVLRLAHEPISLHAPVGGED---DVFLGDLIEDADAASPA--ESAALLLLRQHLDAV 292

Query: 232 MSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           ++ L  RER++ + R   ++  P TLE +   F V+RERVRQIE++  ++++E
Sbjct: 293 LATLGDRERQVVQLRYGFDDGRPRTLEEIGRLFGVTRERVRQIESKTLRRLRE 345


>gi|159896548|ref|YP_001542795.1| RpoD family RNA polymerase sigma factor [Herpetosiphon aurantiacus
           ATCC 23779]
 gi|159889587|gb|ABX02667.1| RNA polymerase, sigma 70 subunit, RpoD family [Herpetosiphon
           aurantiacus ATCC 23779]
          Length = 400

 Score =  103 bits (256), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 92/310 (29%), Positives = 149/310 (48%), Gaps = 51/310 (16%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD------------LSAAHR 52
           N  I VN  + L  Y+ EI  +P+L+ ++E  LA R  E GD            LS   R
Sbjct: 94  NEGISVNDTVRL--YLREIGLVPLLKGEQEVELA-RAMEDGDKAQQELIENDHTLSDVER 150

Query: 53  L----------------VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L                 T++LRLVV +A  Y G GL + +++ EGN+GL++AV+KF+  
Sbjct: 151 LALRRRIDRGEQAREHLTTANLRLVVSVAKKYIGRGLSLLDLIQEGNVGLIRAVEKFNYT 210

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDN 152
           +GF+ +TY+ WWI+ A+   I      ++I      T N  R+    RRL       T  
Sbjct: 211 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETIN--RMMRTARRL-------TQE 261

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           N +      +A+ L+++  +V S+  R    E ++       +  SQ  D+L    D + 
Sbjct: 262 NGREPSDEELAQALDLTVEKVRSI--RKTSMEPVSLETPVGQEEDSQLGDFL---PDEKL 316

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
           +   +    +  R  + + +  L  RE+R+ + R   E+    TLE +  EF V+RER+R
Sbjct: 317 EAPSDAASHQMLREQVAQVLDQLTEREKRVLKLRFGLEDGTQRTLEEVGKEFGVTRERIR 376

Query: 271 QIEARAFKKV 280
           QIE +A +K+
Sbjct: 377 QIEVKALRKL 386


>gi|297160766|gb|ADI10478.1| RNA polymerase sigma factor [Streptomyces bingchenggensis BCW-1]
          Length = 453

 Score =  103 bits (256), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 90/295 (30%), Positives = 142/295 (48%), Gaps = 42/295 (14%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHG-------------DLSAAH------------- 51
           +Y+ EI +IP+L   EE  LA+R  E G             D   AH             
Sbjct: 159 QYLREIGRIPLLSAAEEVELARRV-EAGLFAEEKLSNTPDLDTQLAHDFDQLVVLGRMAK 217

Query: 52  -RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY+ WWI+
Sbjct: 218 RRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIR 277

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            AM   +      +++     +  L   + R++  +         PE+V   A  L++  
Sbjct: 278 QAMSRALADQARTIRVPVHVVE--LINRVVRVQRRMLQERGYEPTPEEV---AHHLDLL- 331

Query: 171 SEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
            E +S   RLA +  SL+A +   D  +    D +    DG     +E       R  L 
Sbjct: 332 PERVSEVLRLAQEPVSLHAPVGEEDDVA--LGDLI---EDGDAASPVESAAFLLLREHLE 386

Query: 230 RSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             +S L  RER++ + R       P TLE +   F V+RER+RQIE++   K+++
Sbjct: 387 AVLSTLGERERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRD 441


>gi|282896628|ref|ZP_06304643.1| sigA (Sigma 28 (Flagella/Sporulation)) [Raphidiopsis brookii D9]
 gi|281198498|gb|EFA73384.1| sigA (Sigma 28 (Flagella/Sporulation)) [Raphidiopsis brookii D9]
          Length = 390

 Score =  103 bits (256), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 74/246 (30%), Positives = 131/246 (53%), Gaps = 17/246 (6%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           RYR H    A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G+
Sbjct: 145 RYRLHVGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGY 204

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT-DNNLKP-E 157
           + +TY+ WWI+ A+   I      +++        L+  + R+K   + ++ +   KP E
Sbjct: 205 KFSTYATWWIRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKLLSQEMGRKPTE 259

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           + +A   ++ + +   I+ + +L    SL   I   +   S+  D++  D +  E  + +
Sbjct: 260 EEIATRMEMTIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIESDGETPEDQVSK 315

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEAR 275
              R++    L R +  L PRER +   R   ++    TLE +   F V+RER+RQIEA+
Sbjct: 316 SLLRED----LERVLDSLGPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAK 371

Query: 276 AFKKVQ 281
           A +K++
Sbjct: 372 ALRKLR 377


>gi|2764713|emb|CAA05353.1| sigma 70 [Campylobacter jejuni]
          Length = 622

 Score =  103 bits (256), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 81/250 (32%), Positives = 123/250 (49%), Gaps = 41/250 (16%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ +RG++ +TY+ WW
Sbjct: 381 AKGRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWW 440

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T NQ     N + ++ HLQ     + K   V  IAK
Sbjct: 441 IRQAISRAIADQARTIRIPIHMIETINQ----IN-KIIREHLQ----KDGKEPDVSVIAK 491

Query: 165 KLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           ++ +S  +V          IS+   +  ++         D+NS    D ++ D D +EQ+
Sbjct: 492 EVGLSVDKVKQVIKITKEPISLEAPIGNEDDGKFGDFVEDRNSLSPMDHILKD-DLKEQI 550

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQ 271
                            +  LN RE+ +   R      E+  TLE +  E  V+RERVRQ
Sbjct: 551 --------------DEVLDQLNDREKAVIRMRFGLMDDESDRTLEEIGKELNVTRERVRQ 596

Query: 272 IEARAFKKVQ 281
           IE+ A KK++
Sbjct: 597 IESSAIKKLK 606


>gi|46445811|ref|YP_007176.1| RNA polymerase sigma factor [Candidatus Protochlamydia amoebophila
           UWE25]
 gi|46399452|emb|CAF22901.1| probable transcription initiation factor sigma 70 [Candidatus
           Protochlamydia amoebophila UWE25]
          Length = 554

 Score =  103 bits (256), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 78/243 (32%), Positives = 122/243 (50%), Gaps = 20/243 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+  RG++ +TY+ WW
Sbjct: 312 AKREMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWW 371

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+      + R    L   T     PE+   +AK
Sbjct: 372 IRQAVTRAIADQARTIRIPVHMIETINK------VLRGAKKLMMETGREPSPEE---LAK 422

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L ++   V  +        SL A +   D   SQ+ D+L    D       E       
Sbjct: 423 ELGITAERVREIYKIAQHPISLQAEV--GDGGESQFGDFL---EDTGADSPAEATGYSIL 477

Query: 225 RNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           ++ +   +S L+ RER++   R   L   P TLE +  EF V+RER+RQIEA+A +K++ 
Sbjct: 478 KDKMGEVLSTLSDRERKVLIQRFGLLDGKPKTLEEVGVEFNVTRERIRQIEAKALRKMRH 537

Query: 283 SIQ 285
            I+
Sbjct: 538 PIR 540


>gi|307747900|gb|ADN91170.1| RNA polymerase sigma factor rpoD [Campylobacter jejuni subsp.
           jejuni M1]
          Length = 622

 Score =  103 bits (256), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 81/250 (32%), Positives = 123/250 (49%), Gaps = 41/250 (16%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ +RG++ +TY+ WW
Sbjct: 381 AKGRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWW 440

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T NQ     N + ++ HLQ     + K   V  IAK
Sbjct: 441 IRQAISRAIADQARTIRIPIHMIETINQ----IN-KIIREHLQ----KDGKEPDVSVIAK 491

Query: 165 KLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           ++ +S  +V          IS+   +  ++         D+NS    D ++ D D +EQ+
Sbjct: 492 EVGLSVDKVKQVIKITKEPISLEAPIGNEDDGKFGDFVEDRNSLSPMDHILKD-DLKEQI 550

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQ 271
                            +  LN RE+ +   R      E+  TLE +  E  V+RERVRQ
Sbjct: 551 --------------DEVLDQLNDREKAVIRMRFGLMDDESDRTLEEIGKELNVTRERVRQ 596

Query: 272 IEARAFKKVQ 281
           IE+ A KK++
Sbjct: 597 IESSAIKKLK 606


>gi|1519644|gb|AAB07555.1| SigA [Chlorobaculum tepidum]
          Length = 299

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 87/304 (28%), Positives = 157/304 (51%), Gaps = 45/304 (14%)

Query: 9   IVNGE-IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS-----------AAHRLVTS 56
           I N E + L RY+ EI K  +L  +      + ++E  D+            A  +L+  
Sbjct: 10  ITNRESLSLDRYLQEIGKYDLLTARRRGEAHEGHKEGYDMPVDTVEYKRAKRALDKLIKG 69

Query: 57  HLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM--- 113
           +LR VV +A  Y+  GL + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++   
Sbjct: 70  NLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQA 129

Query: 114 ---QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
              Q  I+R   L ++GT     + +  L +     +   D N K      +A  L++ +
Sbjct: 130 LAEQSRIVR-LPLNRVGTLNKISKAYSQLEQ-----EYERDPNTKE-----LADLLDM-D 177

Query: 171 SEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-- 227
           S+ ++   ++AG   S++A     D N  +  D L  D    +  L       NR ++  
Sbjct: 178 SQDVADTLKIAGRHVSVDAPFAQGDDN--RLLDVLQNDGHMPDYTL-------NRDSLSL 228

Query: 228 -LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + RS+SVL PRE  +  +      +NP+TLE +  +F+++RERVRQI+ +A +++++S 
Sbjct: 229 EVERSLSVLAPREADVIRSYFGIGMDNPLTLEEIGEKFKLTRERVRQIKEKAIRRLRQSA 288

Query: 285 QKQV 288
             +V
Sbjct: 289 YNKV 292


>gi|256847131|ref|ZP_05552577.1| RNA polymerase sigma factor RpoS [Lactobacillus coleohominis
           101-4-CHN]
 gi|256715795|gb|EEU30770.1| RNA polymerase sigma factor RpoS [Lactobacillus coleohominis
           101-4-CHN]
          Length = 381

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 86/278 (30%), Positives = 131/278 (47%), Gaps = 41/278 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   +E  LA R  E GD +A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 115 YLKEIGRVNLLTADQEVELALRI-EKGDETAKQELAEANLRLVVSIAKRYVGRGMQFLDL 173

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 174 IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 233

Query: 132 --QKRLFFNLRR--LKGHLQAITDNNLKP-EQVVAIAKKLNVSESEVISMNCRLA--GDE 184
             Q++L  +L R  L   + A  D   K    ++ IA+       E +S+   +    D 
Sbjct: 234 RIQRQLLQDLGREPLPEEIGAEMDMPTKKVRDILKIAQ-------EPVSLETPIGEEDDS 286

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
            L   I   D  S         DH   E +          +  L   +  L  RE  +  
Sbjct: 287 HLGDFIEDHDATSP-------ADHAAYEMM----------KKQLENVLDTLTDREENVLR 329

Query: 245 ARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
            R   ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 330 LRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 367


>gi|57237826|ref|YP_179074.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni RM1221]
 gi|86150708|ref|ZP_01068924.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 260.94]
 gi|86152585|ref|ZP_01070790.1| RNA polymerase sigma factor rpoD [Campylobacter jejuni subsp.
           jejuni HB93-13]
 gi|121612947|ref|YP_001000680.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 81-176]
 gi|157415258|ref|YP_001482514.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 81116]
 gi|167005602|ref|ZP_02271360.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 81-176]
 gi|205356712|ref|ZP_03223473.1| RNA polymerase sigma factor (sigma 70) [Campylobacter jejuni subsp.
           jejuni CG8421]
 gi|315124489|ref|YP_004066493.1| RNA polymerase sigma factor [Campylobacter jejuni subsp. jejuni
           ICDCCJ07001]
 gi|57166630|gb|AAW35409.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni RM1221]
 gi|85841878|gb|EAQ59124.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 260.94]
 gi|85843470|gb|EAQ60680.1| RNA polymerase sigma factor rpoD [Campylobacter jejuni subsp.
           jejuni HB93-13]
 gi|87249244|gb|EAQ72205.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 81-176]
 gi|157386222|gb|ABV52537.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 81116]
 gi|205345450|gb|EDZ32092.1| RNA polymerase sigma factor (sigma 70) [Campylobacter jejuni subsp.
           jejuni CG8421]
 gi|315018211|gb|ADT66304.1| RNA polymerase sigma factor [Campylobacter jejuni subsp. jejuni
           ICDCCJ07001]
 gi|315932129|gb|EFV11072.1| Phosphatidylserine decarboxylase [Campylobacter jejuni subsp.
           jejuni 327]
          Length = 622

 Score =  103 bits (256), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 81/250 (32%), Positives = 123/250 (49%), Gaps = 41/250 (16%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ +RG++ +TY+ WW
Sbjct: 381 AKGRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWW 440

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T NQ     N + ++ HLQ     + K   V  IAK
Sbjct: 441 IRQAISRAIADQARTIRIPIHMIETINQ----IN-KIIREHLQ----KDGKEPDVSVIAK 491

Query: 165 KLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           ++ +S  +V          IS+   +  ++         D+NS    D ++ D D +EQ+
Sbjct: 492 EVGLSVDKVKQVIKITKEPISLEAPIGNEDDGKFGDFVEDRNSLSPMDHILKD-DLKEQI 550

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQ 271
                            +  LN RE+ +   R      E+  TLE +  E  V+RERVRQ
Sbjct: 551 --------------DEVLDQLNDREKAVIRMRFGLMDDESDRTLEEIGKELNVTRERVRQ 596

Query: 272 IEARAFKKVQ 281
           IE+ A KK++
Sbjct: 597 IESSAIKKLK 606


>gi|212550562|ref|YP_002308879.1| RNA polymerase primary sigma factor [Candidatus Azobacteroides
           pseudotrichonymphae genomovar. CFP2]
 gi|212548800|dbj|BAG83468.1| putative RNA polymerase primary sigma factor [Candidatus
           Azobacteroides pseudotrichonymphae genomovar. CFP2]
          Length = 286

 Score =  102 bits (255), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 74/281 (26%), Positives = 148/281 (52%), Gaps = 36/281 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +++ EI    +L  ++E  LA+R R  GD SA  +LV ++LR VV +A  Y+  GL +
Sbjct: 18  LDKFLQEISHEELLSIEKEIELARRSR-LGDRSALDKLVRANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     +V++         
Sbjct: 77  PDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNR----- 131

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRLAGDES 185
             +L ++   L      + +      +A++L + E +V          IS++   A  E 
Sbjct: 132 VGSLNKISKALSKFEQKHERKPSSEELAQELELPEDKVSETLRISNRHISIDAPFADGEE 191

Query: 186 LNALIN--SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            N+L++  ++D   + +   L+++   QE               +  ++ +LN RE+ I 
Sbjct: 192 -NSLLDVLTNDDTPAAYH-GLIHESLSQE---------------INNALLILNDREKEII 234

Query: 244 E-ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           + +  + +  + LE +   F ++RERVRQI+ +A KK++++
Sbjct: 235 KMSFGIGQQEMNLEEIGDAFNLTRERVRQIKEKAIKKLKQN 275


>gi|94266972|ref|ZP_01290621.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
 gi|93452327|gb|EAT02958.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
          Length = 353

 Score =  102 bits (255), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 84/253 (33%), Positives = 136/253 (53%), Gaps = 27/253 (10%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +RLV ++LRLVV +A  Y G GL + +++ EGNIGLM+AV+KF+  RG++ +TY+ WW
Sbjct: 115 AKNRLVQANLRLVVSVAKKYAGRGLQLLDLIQEGNIGLMKAVEKFEYRRGYKFSTYATWW 174

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKG--HLQAITDNNLKPEQVVAI 162
           I+ A+   I      ++I      T N        R LKG    Q        P++   +
Sbjct: 175 IRQAVTRAIADQGRTIRIPVHMIDTIN--------RMLKGAKEFQRQHGREPTPDE---M 223

Query: 163 AKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           A+ L V  ++V S+  ++A +  SL+  + +S  N S   D++    D +     E    
Sbjct: 224 AQHLGVEVAKVKSV-LKIAKEPLSLDTPVGNS--NDSFLADFI---EDTEAASPDEATIY 277

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKK 279
           +N ++ L R +  L+PRE  +   R   +    +TLE +   F V+RER+RQIEA+A KK
Sbjct: 278 ENLQSNLRRVLKTLSPREEMVLRLRFGLDTAMDLTLEEVGENFAVTRERIRQIEAKALKK 337

Query: 280 VQESIQKQVELSS 292
           ++   ++  +LSS
Sbjct: 338 LKHPARRN-QLSS 349


>gi|86150479|ref|ZP_01068704.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni CF93-6]
 gi|88596833|ref|ZP_01100070.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 84-25]
 gi|148926089|ref|ZP_01809775.1| RNA polymerase sigma factor (sigma-70) [Campylobacter jejuni subsp.
           jejuni CG8486]
 gi|218562617|ref|YP_002344396.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni NCTC 11168]
 gi|85839074|gb|EAQ56338.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni CF93-6]
 gi|88191674|gb|EAQ95646.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 84-25]
 gi|112360323|emb|CAL35119.1| RNA polymerase sigma factor (sigma-70) [Campylobacter jejuni subsp.
           jejuni NCTC 11168]
 gi|145845568|gb|EDK22660.1| RNA polymerase sigma factor (sigma-70) [Campylobacter jejuni subsp.
           jejuni CG8486]
 gi|284926231|gb|ADC28583.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni IA3902]
 gi|315058444|gb|ADT72773.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni S3]
 gi|315928360|gb|EFV07675.1| RNA polymerase sigma factor rpoD [Campylobacter jejuni subsp.
           jejuni DFVF1099]
          Length = 622

 Score =  102 bits (255), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 81/250 (32%), Positives = 123/250 (49%), Gaps = 41/250 (16%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ +RG++ +TY+ WW
Sbjct: 381 AKGRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWW 440

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T NQ     N + ++ HLQ     + K   V  IAK
Sbjct: 441 IRQAISRAIADQARTIRIPIHMIETINQ----IN-KIIREHLQ----KDGKEPDVSVIAK 491

Query: 165 KLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           ++ +S  +V          IS+   +  ++         D+NS    D ++ D D +EQ+
Sbjct: 492 EVGLSVDKVKQVIKITKEPISLEAPIGNEDDGKFGDFVEDRNSLSPMDHILKD-DLKEQI 550

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQ 271
                            +  LN RE+ +   R      E+  TLE +  E  V+RERVRQ
Sbjct: 551 --------------DEVLDQLNDREKAVIRMRFGLMDDESDRTLEEIGKELNVTRERVRQ 596

Query: 272 IEARAFKKVQ 281
           IE+ A KK++
Sbjct: 597 IESSAIKKLK 606


>gi|317051905|ref|YP_004113021.1| sigma-70 family RNA polymerase sigma factor [Desulfurispirillum
           indicum S5]
 gi|316946989|gb|ADU66465.1| RNA polymerase sigma factor, sigma-70 family [Desulfurispirillum
           indicum S5]
          Length = 305

 Score =  102 bits (255), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 91/271 (33%), Positives = 140/271 (51%), Gaps = 18/271 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+  I +I +L  +EE  LA+R    GD  A   LV S+LR VVKIAM YR  G+ +
Sbjct: 35  LRDYLRRISRITLLTAEEEKELARRI-SAGDEQAFRVLVESNLRFVVKIAMKYRDIGINL 93

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGNIGL++A ++FDPERG R  TY++WWIK ++ + I+ S + V++     Q R 
Sbjct: 94  LDLINEGNIGLLEAARRFDPERGNRFITYAVWWIKQSIIQAIISSSNTVRL--PGKQARF 151

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              L   +       D     EQ +     L++S  E I    R     SL+  I   D+
Sbjct: 152 ASKLNSARREFARDHDGREPTEQELRDEYGLDISNIEDILRATRSYI--SLDTPIGEDDE 209

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV---LNPRERRIFEAR-RLQEN 251
            +   +D L      +       EE+  R+ + T   S+   L  R+  + + R  + E 
Sbjct: 210 RT--LKDVL------ESPEESSTEEQYVRQKISTEIRSIIAELESRDALVVDLRFGISEG 261

Query: 252 -PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            P TL+ + +   +S+ERVRQIE RA K++Q
Sbjct: 262 IPQTLDEVGTRLGLSKERVRQIEERALKRLQ 292


>gi|188994502|ref|YP_001928754.1| RNA polymerase sigma factor RpoD [Porphyromonas gingivalis ATCC
           33277]
 gi|188594182|dbj|BAG33157.1| RNA polymerase sigma factor RpoD [Porphyromonas gingivalis ATCC
           33277]
          Length = 287

 Score =  102 bits (255), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 80/274 (29%), Positives = 149/274 (54%), Gaps = 21/274 (7%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI +  ++  +EE  LA+  +  GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGREDLISVEEEVELAQAIK-RGDRKALEKLTRANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     +V++    NQ   
Sbjct: 77  PDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL--PLNQ--- 131

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
              L ++    Q     N +      +AK+L+++E + I+   +++G   S++A     +
Sbjct: 132 VGTLNKIIKAQQKFEQENERRPSSAELAKELDIAEDK-IADTMKVSGRHISVDAPFVEGE 190

Query: 195 KNSSQWQDWLV-YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI----FEARRLQ 249
            NS    D LV  D    ++ LI     ++    + R++S L  RE  I    F     Q
Sbjct: 191 DNS--LLDVLVNEDTPNTDKSLI----NESLAVEIERALSTLTEREAEIVKLFFGIAGCQ 244

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           E  +TLE +  +F ++RERVRQI+ +A +++++S
Sbjct: 245 E--MTLEEIGDKFGLTRERVRQIKEKAIRRLRQS 276


>gi|291451171|ref|ZP_06590561.1| RNA polymerase sigma factor [Streptomyces albus J1074]
 gi|291354120|gb|EFE81022.1| RNA polymerase sigma factor [Streptomyces albus J1074]
          Length = 397

 Score =  102 bits (255), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 88/293 (30%), Positives = 142/293 (48%), Gaps = 41/293 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAH--------------------------R 52
           Y+ EI +IP+L   +E  LA+R  E G  +AA                           R
Sbjct: 105 YLREIGRIPLLSAADEVELARRV-EAGVFAAAKLAGGCADAGLARDLRRLVVLGERAKGR 163

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RGF+ +TY+ WWI+ A
Sbjct: 164 LIEANLRLVVSVAKRYTGRGLTMLDLVQEGNLGLIRAVEKFDYTRGFKFSTYATWWIRQA 223

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           M   +      +++    +   L   + R +  L          E+V    ++L +S +E
Sbjct: 224 MSRALADQARTIRV--PVHVVELINRVVRTQRALLQEAGREPAAEEV---GERLGLS-AE 277

Query: 173 VISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
            +    RLA +  SL+A +   D     +   L+ D D       E       R  L   
Sbjct: 278 KVEEVLRLAHEPISLHAPVGGED---DVFLGDLIEDADAASPA--ESAALLLLRQHLDAV 332

Query: 232 MSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           ++ L  RER++ + R   ++  P TLE +   F V+RERVRQIE++  ++++E
Sbjct: 333 LATLGDRERQVVQLRYGFDDGRPRTLEEIGRLFGVTRERVRQIESKTLRRLRE 385


>gi|78222633|ref|YP_384380.1| sigma 28 (flagella/sporulation) [Geobacter metallireducens GS-15]
 gi|78193888|gb|ABB31655.1| RNA polymerase, sigma 38 subunit, RpoS [Geobacter metallireducens
           GS-15]
          Length = 326

 Score =  102 bits (255), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 79/278 (28%), Positives = 146/278 (52%), Gaps = 31/278 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI++  +L   EE VLA R  + GD +A  +++ S+LRLVVKIA  Y   GLP  ++
Sbjct: 61  YLREIQRTTLLTADEEKVLASRIAK-GDKAARDKMIESNLRLVVKIAKRYINRGLPFLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV++F   +  R +TY+ WWI+ +++  ++     +++    +      N
Sbjct: 120 IEEGNMGLIKAVERFKLSKECRFSTYATWWIRQSIERALVNQSRTIRLPVHVSDD---IN 176

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC---------RLAGDESLNAL 189
            + LK   + +   N +P  V  +A ++NV+ + +  +           R  G+ S   L
Sbjct: 177 -KMLKITRELVNRFNREP-TVKEVATEMNVNSAYIRRLMVLLKKTYSIERPMGENSDYFL 234

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I++ +  SS     L+ D               N+  ++++  + L+  E++I   R   
Sbjct: 235 IDTIEDTSSVSPAVLLEDL--------------NKYEIVSKWFASLSENEQKILTLRFGL 280

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           E+  P TL+ +   F V+RER+RQIEA++ +K+++ I 
Sbjct: 281 EDKEPQTLDTIGRSFGVTRERIRQIEAKSLEKLRKYID 318


>gi|34540402|ref|NP_904881.1| RNA polymerase sigma-70 factor [Porphyromonas gingivalis W83]
 gi|34396715|gb|AAQ65780.1| RNA polymerase sigma-70 factor [Porphyromonas gingivalis W83]
          Length = 287

 Score =  102 bits (255), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 80/274 (29%), Positives = 149/274 (54%), Gaps = 21/274 (7%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI +  ++  +EE  LA+  +  GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGREDLISVEEEVELAQAIK-RGDRKALEKLTRANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     +V++    NQ   
Sbjct: 77  PDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL--PLNQ--- 131

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
              L ++    Q     N +      +AK+L+++E + I+   +++G   S++A     +
Sbjct: 132 VGTLNKIIKAQQKFEQENERRPSSAELAKELDIAEDK-IADTMKVSGRHISVDAPFVEGE 190

Query: 195 KNSSQWQDWLV-YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI----FEARRLQ 249
            NS    D LV  D    ++ LI     ++    + R++S L  RE  I    F     Q
Sbjct: 191 DNS--LLDVLVNEDTPNTDKSLI----NESLAVEIERALSTLTEREAEIVKLFFGIAGCQ 244

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           E  +TLE +  +F ++RERVRQI+ +A +++++S
Sbjct: 245 E--MTLEEIGDKFGLTRERVRQIKEKAIRRLRQS 276


>gi|226226008|ref|YP_002760114.1| RNA polymerase sigma factor [Gemmatimonas aurantiaca T-27]
 gi|226089199|dbj|BAH37644.1| RNA polymerase sigma factor [Gemmatimonas aurantiaca T-27]
          Length = 302

 Score =  102 bits (255), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 88/275 (32%), Positives = 147/275 (53%), Gaps = 16/275 (5%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
              +Y+H+I+K+P++    E     R  + GD +AA RLVT++LR V+     Y+G+GL 
Sbjct: 25  AFDQYLHDIQKLPLITDAAEERRLARLAQKGDEAAAERLVTANLRFVISYVKKYQGHGLD 84

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           +SE+V+ GN GL++AV+KFDP++G +  +Y++WW++ A+ + +      V+I    N + 
Sbjct: 85  LSELVAIGNEGLLKAVRKFDPDQGVKFISYAVWWVRQAVLKALAEQTRSVRIPLNQNSQL 144

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSS 193
               +R  +G +  I    L  E   A   KL     E +    +++  E SL+A I+  
Sbjct: 145 ----IRMARGEM--ILSQVLNREPTDAELSKLLEEPVEQVRNARQISSTEVSLDAPIDRQ 198

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEK-EERKNRRNMLTRSM-SVLNPRERRI-FEARRLQE 250
           D+ +S   +       G+    IE   + +  R  + R     L PRER+I +    L E
Sbjct: 199 DREASTLGERFA----GETHADIEDGTDFRLMREFIDRVFRKYLTPRERKILYLYYGLDE 254

Query: 251 N--PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               +TLE + +   V+RER+RQI  RAF+K++ES
Sbjct: 255 GAEAMTLERIGALMGVTRERIRQIRERAFEKLRES 289


>gi|315929035|gb|EFV08275.1| RNA polymerase sigma factor [Campylobacter jejuni subsp. jejuni
           305]
          Length = 622

 Score =  102 bits (255), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 81/250 (32%), Positives = 123/250 (49%), Gaps = 41/250 (16%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ +RG++ +TY+ WW
Sbjct: 381 AKGRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWW 440

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T NQ     N + ++ HLQ     + K   V  IAK
Sbjct: 441 IRQAISRAIADQARTIRIPIHMIETINQ----IN-KIIREHLQ----KDGKEPDVSVIAK 491

Query: 165 KLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           ++ +S  +V          IS+   +  ++         D+NS    D ++ D D +EQ+
Sbjct: 492 EVGLSVDKVKQVIKITKEPISLEAPIGNEDDGKFGDFVEDRNSLSPMDHILKD-DLKEQI 550

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQ 271
                            +  LN RE+ +   R      E+  TLE +  E  V+RERVRQ
Sbjct: 551 --------------DEVLDQLNDREKAVIRMRFGLMDDESDRTLEEIGKELNVTRERVRQ 596

Query: 272 IEARAFKKVQ 281
           IE+ A KK++
Sbjct: 597 IESSAIKKLK 606


>gi|72383143|ref|YP_292498.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. NATL2A]
 gi|72002993|gb|AAZ58795.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. NATL2A]
          Length = 340

 Score =  102 bits (255), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 83/288 (28%), Positives = 139/288 (48%), Gaps = 37/288 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDL--------------------SAAHRLVTSHL 58
           Y+  I ++P+L   EE  LA   ++  DL                     A  R++ ++L
Sbjct: 56  YLTSIGRVPLLTPAEEIELAHHVQQMKDLLNLPLEERSTRQKHKIKMGKRARDRMMAANL 115

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+  M   I 
Sbjct: 116 RLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTRAID 175

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLK---GHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
            S   +++    ++K     +RR+     H      N L+      +A  + +   ++  
Sbjct: 176 NSARTIRLPIHISEK--LSKMRRISRELSHRFGRQPNRLE------LANAMGIEPQDLED 227

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
           +  + A   SL+A     +  S+  +  L+ D +  E   +E  +R  ++  L   +S L
Sbjct: 228 LVSQSAPCASLDAHARGEEDRSTLGE--LIPDPNSDEP--MEGMDRSIQKEHLGGWLSQL 283

Query: 236 NPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           N RE++I   R     E P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 284 NEREQKIMRLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 331


>gi|283956399|ref|ZP_06373879.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 1336]
 gi|283792119|gb|EFC30908.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 1336]
          Length = 622

 Score =  102 bits (255), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 81/250 (32%), Positives = 123/250 (49%), Gaps = 41/250 (16%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ +RG++ +TY+ WW
Sbjct: 381 AKGRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWW 440

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T NQ     N + ++ HLQ     + K   V  IAK
Sbjct: 441 IRQAISRAIADQARTIRIPIHMIETINQ----IN-KIIREHLQ----KDGKEPDVSVIAK 491

Query: 165 KLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           ++ +S  +V          IS+   +  ++         D+NS    D ++ D D +EQ+
Sbjct: 492 EVGLSVDKVKQVIKITKEPISLEAPIGNEDDGKFGDFVEDRNSLSPMDHILKD-DLKEQI 550

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQ 271
                            +  LN RE+ +   R      E+  TLE +  E  V+RERVRQ
Sbjct: 551 --------------DEVLDQLNDREKAVIRMRFGLMDDESDRTLEEIGKELNVTRERVRQ 596

Query: 272 IEARAFKKVQ 281
           IE+ A KK++
Sbjct: 597 IESSAIKKLK 606


>gi|269925235|ref|YP_003321858.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
 gi|269788895|gb|ACZ41036.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
          Length = 344

 Score =  102 bits (255), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 76/256 (29%), Positives = 118/256 (46%), Gaps = 40/256 (15%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A H+L+  +LRLVV IA  Y G+G+P+++++ EGN+GLM+A +KFD  RGFR +TY+ W
Sbjct: 106 AARHKLIEHNLRLVVSIARRYVGHGMPLADLIEEGNLGLMRAAEKFDWRRGFRFSTYATW 165

Query: 108 WIKAAMQEYILRSW-----------SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           WI+ A+   +               +L KIG     +RL   L R   + +      L P
Sbjct: 166 WIRQAVTRGLAEGGRTIRLPVHVGEALTKIGR--ETQRLSLELGREPTNQELAEATGLSP 223

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLN---ALINSSDKNSSQWQDWLVYDHDGQEQ 213
           E++        +     +S+   L  D   N    L ++   N     D  +   D    
Sbjct: 224 ERIDEYKNASRLP----LSLEAPLGEDGETNLGEVLEDTEAANPEHIADHTMLGED---- 275

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQ 271
                         + R++  LN R+R I   R       P+TLE    +  V+RER RQ
Sbjct: 276 --------------IKRALERLNERQRAIIIMRYGLYGGQPMTLEAAGRKLGVTRERARQ 321

Query: 272 IEARAFKKVQESIQKQ 287
           IE  A  ++++S  KQ
Sbjct: 322 IEQEALNRLRQSDAKQ 337


>gi|56475838|ref|YP_157427.1| RNA polymerase sigma factor RpoS [Aromatoleum aromaticum EbN1]
 gi|56311881|emb|CAI06526.1| RNA sigma factor RpoS [Aromatoleum aromaticum EbN1]
          Length = 311

 Score =  102 bits (255), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 87/281 (30%), Positives = 148/281 (52%), Gaps = 33/281 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L   EE  LA+R R  GD  A   ++  +LRLVV IA  Y   G+P+ ++
Sbjct: 44  YLNEIGANPLLTAAEEAALARRVRT-GDFPARQIMIERNLRLVVNIAKHYLNRGIPLLDL 102

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GLM A++KFDPERGFR +TY+ WWI+  ++  I+     +++     ++     
Sbjct: 103 VEEGNLGLMHALEKFDPERGFRFSTYATWWIRQNIERAIMNQSRTIRLPVHVVKE--LNQ 160

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRLAGDESLNA 188
           + R +  L+A  +     EQV   A +L+ S  EV           S++  L  D +L +
Sbjct: 161 VLRAQRTLEASGNGEFTLEQV---AHRLDKSVDEVRAILALSEHTASLDAPLEIDPTL-S 216

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR- 247
           +  S   + ++  D  + D +      +EK        ++   + +LN ++R +   R  
Sbjct: 217 IGESLADDQAEPPDTHIQDAE------VEK--------LIQEWIGMLNEKQRLVIRHRYG 262

Query: 248 LQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L E  V TLE L+S   ++RERVRQI+  A  +++ +++++
Sbjct: 263 LDECEVMTLEELASRLCLTRERVRQIQLEALGQLRRTVKRR 303


>gi|309786170|ref|ZP_07680798.1| RNA polymerase sigma factor RpoS [Shigella dysenteriae 1617]
 gi|308925915|gb|EFP71394.1| RNA polymerase sigma factor RpoS [Shigella dysenteriae 1617]
          Length = 237

 Score =  102 bits (255), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 73/243 (30%), Positives = 122/243 (50%), Gaps = 24/243 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 113 MQEYILRSWSLVKIGT-TANQKRLFFNLRRLKGH-------LQAITDNNLKPEQVVAIAK 164
           ++  I+     +++      +  ++    R   H        + I +   KP   V+   
Sbjct: 61  IERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRML 120

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +LN     + S++  L GD     L   +D+  +  +D    D   Q  V    E    +
Sbjct: 121 RLN---ERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQ 177

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R +L R   +L       +EA        TLE++  E +++RERVRQI+    ++++E +
Sbjct: 178 REVLARRFGLLG------YEA-------ATLEDVGREIDLTRERVRQIQVEGLRRLREIL 224

Query: 285 QKQ 287
           Q Q
Sbjct: 225 QTQ 227


>gi|124026883|ref|YP_001015998.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. NATL1A]
 gi|123961951|gb|ABM76734.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. NATL1A]
          Length = 340

 Score =  102 bits (255), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 83/288 (28%), Positives = 139/288 (48%), Gaps = 37/288 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDL--------------------SAAHRLVTSHL 58
           Y+  I ++P+L   EE  LA   ++  DL                     A  R++ ++L
Sbjct: 56  YLTSIGRVPLLTPAEEIELAHHVQQMKDLLNLPLEERSTRQKHKIKMGKRARDRMMAANL 115

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+  M   I 
Sbjct: 116 RLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTRAID 175

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLK---GHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
            S   +++    ++K     +RR+     H      N L+      +A  + +   ++  
Sbjct: 176 NSARTIRLPIHISEK--LSKMRRISRELSHRFGRQPNRLE------LANAMGIEPQDLED 227

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
           +  + A   SL+A     +  S+  +  L+ D +  E   +E  +R  ++  L   +S L
Sbjct: 228 LVSQSAPCASLDAHARGEEDRSTLGE--LIPDPNSDEP--MEGMDRSIQKEHLGGWLSQL 283

Query: 236 NPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           N RE++I   R     E P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 284 NEREQKIMRLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 331


>gi|318058872|ref|ZP_07977595.1| RNA polymerase principal sigma factor [Streptomyces sp. SA3_actG]
 gi|333027299|ref|ZP_08455363.1| putative RNA polymerase sigma (70) factor RpoD [Streptomyces sp.
           Tu6071]
 gi|332747151|gb|EGJ77592.1| putative RNA polymerase sigma (70) factor RpoD [Streptomyces sp.
           Tu6071]
          Length = 338

 Score =  102 bits (255), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 92/305 (30%), Positives = 141/305 (46%), Gaps = 66/305 (21%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHG-------------------DL--------SAAH 51
           Y+ EI +IP+L   +E  LA+R  E G                   DL        +A  
Sbjct: 45  YLREIGRIPLLTAADEVDLARRV-EAGLFAEAKLAGPGPLDTRLALDLDRLVVLGRAAKR 103

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RL+ S+LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RGF+ +TY+ WWI+ 
Sbjct: 104 RLIESNLRLVVSVAKRYAGRGLTMLDLVQEGNLGLIRAVEKFDYTRGFKFSTYATWWIRQ 163

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFN--LRRLKGHLQAITDNNLKPEQVVAIA----KK 165
           AM   +      +++     +     N  +R  +G LQ   +   +P      A     K
Sbjct: 164 AMSRALADQARTIRVPVHVVE---LINRVVRVQRGLLQ---ERGHEPSHAEVAALLGLTK 217

Query: 166 LNVSE-----SEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
             V E      E +S++  + G++  +L  LI   D  S      L+      E VL   
Sbjct: 218 ERVGEVLRLAQEPVSLHTPVGGEDEVALGDLIEDGDAPSPPESAALLLLRRHLEDVL--- 274

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARA 276
                         S L  RER++ + R   ++  P TLE + + F V+RER+RQIEA+ 
Sbjct: 275 --------------STLGERERQVVQLRYGLDDGRPRTLEEIGTLFGVTRERIRQIEAKT 320

Query: 277 FKKVQ 281
             K++
Sbjct: 321 LAKLR 325


>gi|206889536|ref|YP_002248786.1| RNA polymerase sigma factor RpoD [Thermodesulfovibrio yellowstonii
           DSM 11347]
 gi|206741474|gb|ACI20531.1| RNA polymerase sigma factor RpoD [Thermodesulfovibrio yellowstonii
           DSM 11347]
          Length = 479

 Score =  102 bits (255), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 69/236 (29%), Positives = 120/236 (50%), Gaps = 13/236 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              + L+T +LRLVV IA  Y G GLP+ +++ EGNIGLM+AV KF  E+GF+ +TY+ W
Sbjct: 235 DTKNELITRNLRLVVNIAKNYVGRGLPLLDLIEEGNIGLMKAVDKFKYEKGFKFSTYATW 294

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   ++     +++     +   F+N  R+    + +T    +      IA+KL 
Sbjct: 295 WIRQAITRALIDQTKTIRVPVHMME---FYN--RVTKASRELTQQLGREPNNEEIAEKLG 349

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           V   +V  +   +     L   I   D   ++ +D++    D      + + ER      
Sbjct: 350 VPVRKVEEVFRAIQDPIGLQTPIGDED---TELEDFI---GDKTSPSPVSEAERTELSEH 403

Query: 228 LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           + R +  L P+E ++ + R    ++   TLE +     ++RERVRQIE +A +K++
Sbjct: 404 IQRILKTLTPKEEKVIKMRFGIGEDRDHTLEEVGRYLSITRERVRQIETKALRKLK 459


>gi|302545597|ref|ZP_07297939.1| RNA polymerase sigma (70) factor RpoD [Streptomyces hygroscopicus
           ATCC 53653]
 gi|302463215|gb|EFL26308.1| RNA polymerase sigma (70) factor RpoD [Streptomyces himastatinicus
           ATCC 53653]
          Length = 443

 Score =  102 bits (255), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 90/295 (30%), Positives = 143/295 (48%), Gaps = 42/295 (14%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHG-------------------DLS--------AA 50
           +Y+ EI +IP+L   EE  LA+R  E G                   DL         A 
Sbjct: 149 QYLREIGRIPLLSAAEEVELARRV-EAGLFAEEKLASAPDLDSQLALDLDRLVVLGRMAK 207

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY+ WWI+
Sbjct: 208 RRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIR 267

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            AM   +      +++    +   L   + R++  +         PE+V   A  L+++ 
Sbjct: 268 QAMSRALADQARTIRV--PVHVVELINRVVRVQRRMLQERGYEPTPEEV---AIHLDLT- 321

Query: 171 SEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
            E +S   RLA +  SL+A +   D  +    D +    DG     +E       R  L 
Sbjct: 322 PERVSEVLRLAQEPVSLHAPVGEEDDVA--LGDLI---EDGDAASPVESAAFLLLREHLE 376

Query: 230 RSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             +S L  RER++ + R       P TLE +   F V+RER+RQIE++   K+++
Sbjct: 377 AVLSTLGERERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRD 431


>gi|307729587|ref|YP_003906811.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Burkholderia sp.
           CCGE1003]
 gi|307584122|gb|ADN57520.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Burkholderia sp.
           CCGE1003]
          Length = 362

 Score =  102 bits (255), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 80/278 (28%), Positives = 141/278 (50%), Gaps = 25/278 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+P+
Sbjct: 84  IQHYLNRISVKPLLTVEEEQKYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGVPL 142

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++    +  R 
Sbjct: 143 LDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRE 200

Query: 136 FFNLRRLKGHLQAITDN--------NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              + R K HL+  + N        +   + +  +  K     ++++++N   A   SL+
Sbjct: 201 LNQVLRAKRHLEKNSMNSGDAAERRDASIDDIAYLTGKTADEVTDILALNEHTA---SLD 257

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS-MSVLNPRERRIFEAR 246
           A ++    +S               +V   + E       LTR+ ++ L+ + R + E R
Sbjct: 258 APLDLDPASSLLDLLSDDQSQSPDAEVQHRELE------TLTRAWLARLSDKHRHVIE-R 310

Query: 247 RLQEN---PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   N   P TLE L+ E  ++RERVRQI+  A  +++
Sbjct: 311 RFGLNHIEPATLEELADEMGLTRERVRQIQQEALVRLK 348


>gi|289523410|ref|ZP_06440264.1| RNA polymerase sigma factor RpoD [Anaerobaculum hydrogeniformans
           ATCC BAA-1850]
 gi|289503102|gb|EFD24266.1| RNA polymerase sigma factor RpoD [Anaerobaculum hydrogeniformans
           ATCC BAA-1850]
          Length = 412

 Score =  102 bits (254), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 88/273 (32%), Positives = 132/273 (48%), Gaps = 31/273 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KI +L  +EE  LAKR  E  +  A  +L+ ++LRLVV IA  Y G GL   ++
Sbjct: 146 YLREIGKISLLTPEEEVELAKRVEEG-EEEAKKKLIEANLRLVVSIAKKYIGRGLSFLDL 204

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-- 132
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 205 IQEGNLGLIRAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 264

Query: 133 ---KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
              ++L   L R     +      L PE+V  I +       E +S+   +  +E     
Sbjct: 265 RVSRQLVQQLGREPTIEEIAQSLGLPPEKVEDIQR----IAQEPVSLETPIGEEEDSQLG 320

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
               DK S   +D          Q+L         R  L   +  L  RER +   R   
Sbjct: 321 DFLEDKESPNPEDATAG------QLL---------REQLEEMLGELTEREREVLRLRFGL 365

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
           E+    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 366 EDGHAHTLEEVGKRFNVTRERIRQIEAKALRKL 398


>gi|149916265|ref|ZP_01904786.1| RNA polymerase sigma factor [Roseobacter sp. AzwK-3b]
 gi|149809925|gb|EDM69776.1| RNA polymerase sigma factor [Roseobacter sp. AzwK-3b]
          Length = 80

 Score =  102 bits (254), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 50/79 (63%), Positives = 61/79 (77%), Gaps = 1/79 (1%)

Query: 2  NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
          N KN+    + E GL+RY+ EIRK P+LE +EEY+LAKR+ E  D  AAHR+VTSHLRL 
Sbjct: 3  NYKNLPA-PSPEGGLNRYLQEIRKFPLLEPEEEYMLAKRWVEKQDTEAAHRMVTSHLRLA 61

Query: 62 VKIAMGYRGYGLPISEVVS 80
           KIAMGYRGYGLP +EV+S
Sbjct: 62 AKIAMGYRGYGLPTAEVIS 80


>gi|269929031|ref|YP_003321352.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphaerobacter
           thermophilus DSM 20745]
 gi|269788388|gb|ACZ40530.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphaerobacter
           thermophilus DSM 20745]
          Length = 359

 Score =  102 bits (254), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 70/238 (29%), Positives = 122/238 (51%), Gaps = 12/238 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  +L+  +LRLVV IA  YR  GLP+ +++ EGNIGLM AV+++DPE G+R +TY+ +
Sbjct: 123 AAREKLIRHNLRLVVSIAKKYRTSGLPLIDLIQEGNIGLMTAVERYDPELGYRFSTYATF 182

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   +      +++    +   L   +RR +  L+ +   + +P     +A+ L+
Sbjct: 183 WIRQAIGRAVANQSRTIRV--PVHMHDLISKVRRTEAQLEQL---HGRPATDQELAQALD 237

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +    +      +    SL+  I   +   S   D L    D     ++++      R+ 
Sbjct: 238 LDVERIEQARSAIPRTSSLDKPIG--EDGESTIGDLL---PDPASDEVVDQAVTSAIRDQ 292

Query: 228 LTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           + RS+  L+ RER +   R     + P TL  ++  + +SRERVRQIE  A  K++ S
Sbjct: 293 IRRSLESLSERERGVLTLRFGLGGQQPQTLAEIAEYYGISRERVRQIEKEALAKLRNS 350


>gi|311696748|gb|ADP99621.1| RNA polymerase, sigma 70 subunit, RpoD family [marine bacterium
           HP15]
          Length = 332

 Score =  102 bits (254), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 84/262 (32%), Positives = 131/262 (50%), Gaps = 38/262 (14%)

Query: 36  VLAKRYREHGDLSAAHR--LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
             + R R    L+ A R  L+ S+LRL V IA  Y  +G+P+S+++ + N+GL++AV++F
Sbjct: 81  AFSSRCRRAFHLATACRRKLIQSNLRLAVHIARRYGQHGIPMSDLIQDANVGLIKAVERF 140

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL-KGHLQAITDN 152
           DP +GFR +TY+ WWI   ++  + R   LV        + +   +R+L K  L+     
Sbjct: 141 DPTKGFRFSTYAYWWISEEVKRCLQRGTRLVH-----TPENVVDEIRQLHKVSLRMHQSL 195

Query: 153 NLKPEQVVAIAKKLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQD 202
              P Q   +A+++  S S +          IS +  L  D S+  L +S D       D
Sbjct: 196 GRTPSQ-SELAREMEASPSRIGELRALATREISTDVPLVEDGSVT-LGDSLDAG-----D 248

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLS 259
            +  DH   +         ++R+  L   +S LN RE+ I   R    L E P TL+ +S
Sbjct: 249 QMAPDHPMSD---------RDRQRTLKSMLSELNDREKDILSRRYGLGLPE-PETLQVIS 298

Query: 260 SEFEVSRERVRQIEARAFKKVQ 281
            +  +SRERVRQIE  A KK+Q
Sbjct: 299 DDLGISRERVRQIEKTALKKLQ 320


>gi|33241312|ref|NP_876254.1| DNA-directed RNA polymerase sigma subunit [Prochlorococcus marinus
           subsp. marinus str. CCMP1375]
 gi|33238842|gb|AAQ00907.1| DNA-directed RNA polymerase sigma subunit [Prochlorococcus marinus
           subsp. marinus str. CCMP1375]
          Length = 339

 Score =  102 bits (254), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 82/292 (28%), Positives = 144/292 (49%), Gaps = 31/292 (10%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL--------------------SAAH 51
           G   +  Y+  I ++P+L   EE  LA   ++   L                     A  
Sbjct: 48  GTDSIGFYLSSIGRVPLLTPAEEIELAHHVQKMKGLLDIPKENINTRQRHQIRMGKRARD 107

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ ++LRLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+ 
Sbjct: 108 RMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQ 167

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            M   I  S   +++    ++K     +RR+    + ++ N  +    V +A +L +   
Sbjct: 168 GMTRAIDNSARTIRLPIHISEK--LSKMRRIS---RELSHNLGRQPNRVELANELGMEPK 222

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           ++  +  + A   SL++     +  S+  +  L+ D +  E   +E  +R  ++  L+  
Sbjct: 223 DLEDLMAQSAPCASLDSHARGEEDRSTLGE--LIPDPNYDEP--MECMDRNMQKEHLSGW 278

Query: 232 MSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +S LN RE++I   R     E P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 279 LSQLNEREQKIMRLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 330


>gi|224542125|ref|ZP_03682664.1| hypothetical protein CATMIT_01300 [Catenibacterium mitsuokai DSM
           15897]
 gi|224524962|gb|EEF94067.1| hypothetical protein CATMIT_01300 [Catenibacterium mitsuokai DSM
           15897]
          Length = 418

 Score =  102 bits (254), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 88/296 (29%), Positives = 152/296 (51%), Gaps = 40/296 (13%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           MN+   ++ +N  + +  Y+ EI ++ +L  ++E  LAKR  E GD  A   L  ++LRL
Sbjct: 134 MNQLGSNVKINDPVKM--YLKEIGRVDLLTHEQEIELAKRILE-GDEQAKKELAAANLRL 190

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 191 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQ 250

Query: 121 WSLVKIGT---------TANQKRLFFNLRRLKGHLQAITD--NNLKPEQVVAIAKKLNVS 169
              ++I           T  Q++L   L R +   + I +  + + P +V  I +K+++ 
Sbjct: 251 ARTIRIPVHMVETINKLTRIQRQLVQELGR-EPTAEEIAEKMDGMTPAKVREI-QKISL- 307

Query: 170 ESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRR 225
             E +S+   +    D  L   I   D+ +    D+   +   D   +VL+E  +R+ + 
Sbjct: 308 --EPVSLETPIGEEDDSHLGDFI--EDEGAMSPDDYASNELLKDELNEVLLELTDREEK- 362

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +L     + + R R             TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 363 -VLRLRFGLDDGRTR-------------TLEEVGKEFNVTRERIRQIEAKALRKLK 404


>gi|317969130|ref|ZP_07970520.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CB0205]
          Length = 309

 Score =  102 bits (254), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 84/296 (28%), Positives = 144/296 (48%), Gaps = 46/296 (15%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYR--------EHGDLSAAH-------------RLV 54
           +S Y+  I ++P+L   EE  L  + +        + G+    H             R++
Sbjct: 20  ISWYLSTIGRVPLLTPAEEIELGNQVQAMMRLAEEDKGEAYTTHEKKIMRVGKRSKERMM 79

Query: 55  TSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114
            ++LRLVV +A  Y+G GL + +++ EG++GL +AV+KFDP RG++ +TY+ WWI+ +M 
Sbjct: 80  KANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWWIRQSMT 139

Query: 115 EYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA-------IAKKLN 167
             I            A Q R       L   L AI   +L+    +        IA++++
Sbjct: 140 RAI------------ACQSRTIRLPVHLSERLTAIRKVSLELAHKLGAMPSRKEIAEEMD 187

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +   E+ S+  +     SL+A +N  +  S  +   L+ D    E   +++ ER   +  
Sbjct: 188 MPLDELDSLLRQALTTSSLDAPVNGEEGRS--FLGDLIADQSNSEP--LDQVERGIHQEQ 243

Query: 228 LTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           L R ++ L  +ER++ E R   E     TL  +    EVSRERVRQ+E +A +K++
Sbjct: 244 LGRWLTHLTDQERQVLELRFGLEGEERHTLAEIGRMLEVSRERVRQVELKALRKLR 299


>gi|94263094|ref|ZP_01286913.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
 gi|93456637|gb|EAT06745.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
          Length = 540

 Score =  102 bits (254), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 83/251 (33%), Positives = 136/251 (54%), Gaps = 23/251 (9%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +RLV ++LRLVV +A  Y G GL + +++ EGNIGLM+AV+KF+  RG++ +TY+ WW
Sbjct: 302 AKNRLVQANLRLVVSVAKKYAGRGLQLLDLIQEGNIGLMKAVEKFEYRRGYKFSTYATWW 361

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N        R LKG  +    +  +P     +A+
Sbjct: 362 IRQAVTRAIADQGRTIRIPVHMIDTIN--------RMLKGAKEFQRQHGREP-TPDEMAQ 412

Query: 165 KLNVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
            L V  ++V S+  ++A +  SL+  + +S  N S   D++    D +     E    +N
Sbjct: 413 HLGVEVAKVKSV-LKIAKEPLSLDTPVGNS--NDSFLADFI---EDTEAASPDEATIYEN 466

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            ++ L R +  L+PRE  +   R   +    +TLE +   F V+RER+RQIEA+A KK++
Sbjct: 467 LQSNLRRVLKTLSPREEMVLRLRFGLDTAMDLTLEEVGENFAVTRERIRQIEAKALKKLK 526

Query: 282 ESIQKQVELSS 292
              ++  +LSS
Sbjct: 527 HPARRN-QLSS 536


>gi|332829288|gb|EGK01942.1| hypothetical protein HMPREF9455_00064 [Dysgonomonas gadei ATCC
           BAA-286]
          Length = 286

 Score =  102 bits (254), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 77/273 (28%), Positives = 151/273 (55%), Gaps = 20/273 (7%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI +  ++  +EE  LA+  +  GD +A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGREDLITVEEEVELAQAIK-KGDRAALEKLTRANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     +V++    NQ   
Sbjct: 77  PDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL--PLNQ--- 131

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
             +L ++          N +      +A++L++   + I+ + +++G   S++A     +
Sbjct: 132 VGSLNKISKAFSKFEQENERKPSAEELAEQLDIP-VDKIADSLKVSGRHISMDAPFVEGE 190

Query: 195 KNSSQWQDWLVYDHDG-QEQVLIEKEERKNRRNMLTRSMSVLNPRERRI---FEARRLQE 250
            NS    D LV D     ++ LI     ++ +  + R++S L  RE  I   F     QE
Sbjct: 191 DNS--LLDVLVNDDAPIADRTLI----NESLQQEIERALSTLTERESEIIKMFFGIGYQE 244

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +TLE +  +F+++RERVRQI+ +A K+++++
Sbjct: 245 --MTLEEIGDKFQLTRERVRQIKEKAIKRLRQN 275


>gi|67459749|ref|YP_247373.1| RNA polymerase sigma factor RpoD [Rickettsia felis URRWXCal2]
 gi|75535861|sp|Q4UJT1|RPOD_RICFE RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|67005282|gb|AAY62208.1| RNA polymerase sigma factor [Rickettsia felis URRWXCal2]
          Length = 635

 Score =  102 bits (254), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 76/252 (30%), Positives = 128/252 (50%), Gaps = 21/252 (8%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E   L A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 376 ERQTLQAKKDMIEANLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 435

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           TY+ WWI+ A+   I      ++I      T N        + L+   Q + +   +P  
Sbjct: 436 TYATWWIRQAITRAIADQARTIRIPVHMIETIN--------KILRTSRQMLNELGYEP-T 486

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
              IA +L++   +V  +  ++A +  SL   +   D +  Q  D++    D      I+
Sbjct: 487 ATEIANRLSMPLDKVRKV-MKIAKEPISLENPV-GDDSDGGQLGDFI---EDKNAVAPID 541

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              + N R + TR ++ L PRE R+   R         TLE +  +F+V+RER+RQIE++
Sbjct: 542 AAIQSNLREVTTRVLATLTPREERVLRMRFGIGMNTDHTLEEVGQQFKVTRERIRQIESK 601

Query: 276 AFKKVQESIQKQ 287
           A +K+Q  I+ +
Sbjct: 602 ALRKLQHPIRSK 613


>gi|34581080|ref|ZP_00142560.1| RNA polymerase sigma factor [Rickettsia sibirica 246]
 gi|229587226|ref|YP_002845727.1| RNA polymerase sigma factor RpoD [Rickettsia africae ESF-5]
 gi|28262465|gb|EAA25969.1| RNA polymerase sigma factor [Rickettsia sibirica 246]
 gi|228022276|gb|ACP53984.1| RNA polymerase sigma factor [Rickettsia africae ESF-5]
          Length = 634

 Score =  102 bits (254), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 76/252 (30%), Positives = 128/252 (50%), Gaps = 21/252 (8%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E   L A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 375 ERQTLQAKKDMIEANLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 434

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           TY+ WWI+ A+   I      ++I      T N        + L+   Q + +   +P  
Sbjct: 435 TYATWWIRQAITRAIADQARTIRIPVHMIETIN--------KILRTSRQMLNELGYEP-T 485

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
              IA +L++   +V  +  ++A +  SL   +   D +  Q  D++    D      I+
Sbjct: 486 ATEIANRLSMPLDKVRKV-MKIAKEPISLENPV-GDDSDGGQLGDFI---EDKNAVAPID 540

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              + N R + TR ++ L PRE R+   R         TLE +  +F+V+RER+RQIE++
Sbjct: 541 AAIQSNLREVTTRVLATLTPREERVLRMRFGIGMNTDHTLEEVGQQFKVTRERIRQIESK 600

Query: 276 AFKKVQESIQKQ 287
           A +K+Q  I+ +
Sbjct: 601 ALRKLQHPIRSK 612


>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 =  102 bits (254), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 70/241 (29%), Positives = 127/241 (52%), Gaps = 12/241 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E+   +A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 538 EYSSRAAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 597

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I     +     N R  + HLQ       +P+  V +
Sbjct: 598 TYATWWIRQAITRSIADQARTIRIPVHMIETINKMN-RISRQHLQEF---GFEPDASV-L 652

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+++ + E ++  +  ++A  E ++      D + S   D++    D      +E   + 
Sbjct: 653 AERMEIPEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDAANTAPMEAAMQA 707

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             R+++   +  L PRE ++   R   E  +  TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 708 GLRDVVKDILDSLTPREAKVLRMRFGIEMTSDHTLEEVGKQFDVTRERIRQIEAKALRKL 767

Query: 281 Q 281
           +
Sbjct: 768 K 768


>gi|157829159|ref|YP_001495401.1| RNA polymerase sigma factor RpoD [Rickettsia rickettsii str.
           'Sheila Smith']
 gi|165933888|ref|YP_001650677.1| RNA polymerase sigma factor RpoD [Rickettsia rickettsii str. Iowa]
 gi|157801640|gb|ABV76893.1| RNA polymerase sigma factor RpoD [Rickettsia rickettsii str.
           'Sheila Smith']
 gi|165908975|gb|ABY73271.1| RNA polymerase sigma factor [Rickettsia rickettsii str. Iowa]
          Length = 634

 Score =  102 bits (254), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 76/252 (30%), Positives = 128/252 (50%), Gaps = 21/252 (8%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E   L A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 375 ERQTLQAKKDMIEANLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 434

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           TY+ WWI+ A+   I      ++I      T N        + L+   Q + +   +P  
Sbjct: 435 TYATWWIRQAITRAIADQARTIRIPVHMIETIN--------KILRTSRQMLNELGYEP-T 485

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
              IA +L++   +V  +  ++A +  SL   +   D +  Q  D++    D      I+
Sbjct: 486 ATEIANRLSMPLDKVRKV-MKIAKEPISLENPV-GDDSDGGQLGDFI---EDKNAVAPID 540

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              + N R + TR ++ L PRE R+   R         TLE +  +F+V+RER+RQIE++
Sbjct: 541 AAIQSNLREVTTRVLATLTPREERVLRMRFGIGMNTDHTLEEVGQQFKVTRERIRQIESK 600

Query: 276 AFKKVQESIQKQ 287
           A +K+Q  I+ +
Sbjct: 601 ALRKLQHPIRSK 612


>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 =  102 bits (253), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 122/236 (51%), Gaps = 12/236 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 514 DAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 573

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I     +     N R  + HLQ       +P+  + +A K+ 
Sbjct: 574 WIRQAITRSIADQARTIRIPVHMIETINKMN-RISRQHLQEF---GFEPDAGI-LAAKME 628

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + E ++  +  ++A  E ++      D + S   D++    D      IE   +   R++
Sbjct: 629 IPEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDSSNTAPIEAAMQAGLRDV 683

Query: 228 LTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 684 VKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLK 739


>gi|124022438|ref|YP_001016745.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str. MIT
           9303]
 gi|123962724|gb|ABM77480.1| Putative principal RNA polymerase sigma factor [Prochlorococcus
           marinus str. MIT 9303]
          Length = 444

 Score =  102 bits (253), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 71/237 (29%), Positives = 130/237 (54%), Gaps = 17/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 208 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 267

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++     KP E+ +A + ++
Sbjct: 268 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEM 322

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  D +  EQ + +   R++   
Sbjct: 323 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIESDTENPEQDVAKNLLREDLEG 378

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +L    + L+PRER +   R   ++    TLE +   FEV+RER+RQIEA+A +K++
Sbjct: 379 VL----ATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFEVTRERIRQIEAKALRKLR 431


>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 =  102 bits (253), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 122/236 (51%), Gaps = 12/236 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 538 DAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 597

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I     +     N R  + HLQ       +P+  + +A K+ 
Sbjct: 598 WIRQAITRSIADQARTIRIPVHMIETINKMN-RISRQHLQEF---GFEPDAGI-LAAKME 652

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + E ++  +  ++A  E ++      D + S   D++    D      IE   +   R++
Sbjct: 653 IPEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDSSNTAPIEAAMQAGLRDV 707

Query: 228 LTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 708 VKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLK 763


>gi|15893252|ref|NP_360966.1| RNA polymerase sigma factor RpoD [Rickettsia conorii str. Malish 7]
 gi|47606046|sp|Q92FZ8|RPOD_RICCN RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|15620471|gb|AAL03867.1| RNA polymerase sigma factor [Rickettsia conorii str. Malish 7]
          Length = 634

 Score =  102 bits (253), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 76/252 (30%), Positives = 128/252 (50%), Gaps = 21/252 (8%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E   L A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 375 ERQTLQAKKDMIEANLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 434

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           TY+ WWI+ A+   I      ++I      T N        + L+   Q + +   +P  
Sbjct: 435 TYATWWIRQAITRAIADQARTIRIPVHMIETIN--------KILRTSRQMLNELGYEP-T 485

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
              IA +L++   +V  +  ++A +  SL   +   D +  Q  D++    D      I+
Sbjct: 486 ATEIANRLSMPLDKVRKV-MKIAKEPISLENPV-GDDSDGGQLGDFI---EDKNAVAPID 540

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              + N R + TR ++ L PRE R+   R         TLE +  +F+V+RER+RQIE++
Sbjct: 541 AAIQSNLREVTTRVLATLTPREERVLRMRFGIGMNTDHTLEEVGQQFKVTRERIRQIESK 600

Query: 276 AFKKVQESIQKQ 287
           A +K+Q  I+ +
Sbjct: 601 ALRKLQHPIRSK 612


>gi|186686393|ref|YP_001869589.1| RNA polymerase sigma factor RpoD [Nostoc punctiforme PCC 73102]
 gi|8118663|gb|AAF73062.1|AF265349_1 primary vegetative sigma factor [Nostoc punctiforme]
 gi|186468845|gb|ACC84646.1| RNA polymerase, sigma 70 subunit, RpoD family [Nostoc punctiforme
           PCC 73102]
          Length = 389

 Score =  102 bits (253), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 74/248 (29%), Positives = 133/248 (53%), Gaps = 17/248 (6%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A RYR H    A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+
Sbjct: 142 AFRYRLHVGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEK 201

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT-DNNLKP 156
           G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++ +   KP
Sbjct: 202 GYKFSTYATWWIRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKLLSQEMGRKP 256

Query: 157 -EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
            E+ +A   ++ + +   I+ + +L    SL   I   +   S+  D++  D +  E  +
Sbjct: 257 TEEEIATRMEMTIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIESDGETPEDQV 312

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIE 273
            +   R++    L + +  L+PRER +   R   ++    TLE +   F V+RER+RQIE
Sbjct: 313 SKNLLRED----LEKVLDSLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIE 368

Query: 274 ARAFKKVQ 281
           A+A +K++
Sbjct: 369 AKALRKLR 376


>gi|157965030|ref|YP_001499854.1| RNA polymerase sigma factor RpoD [Rickettsia massiliae MTU5]
 gi|157844806|gb|ABV85307.1| RNA polymerase sigma factor [Rickettsia massiliae MTU5]
          Length = 633

 Score =  102 bits (253), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 75/248 (30%), Positives = 127/248 (51%), Gaps = 21/248 (8%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 378 LQAKKDMIEANLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 437

Query: 107 WWIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           WWI+ A+   I      ++I      T N        + L+   Q + +   +P     I
Sbjct: 438 WWIRQAITRAIADQARTIRIPVHMIETIN--------KILRTSRQMLNELGYEP-TATEI 488

Query: 163 AKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           A +L++   +V  +  ++A +  SL   +   D +  Q  D++    D      I+   +
Sbjct: 489 ANRLSMPLDKVRKV-MKIAKEPISLENPV-GDDSDGGQLGDFI---EDKNAVAPIDAAIQ 543

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
            N R + TR ++ L PRE R+   R         TLE +  +F+V+RER+RQIE++A +K
Sbjct: 544 SNLREVTTRVLATLTPREERVLRMRFGIGMNTDHTLEEVGQQFKVTRERIRQIESKALRK 603

Query: 280 VQESIQKQ 287
           +Q  I+ +
Sbjct: 604 LQHPIRSK 611


>gi|119512308|ref|ZP_01631394.1| RNA polymerase sigma factor [Nodularia spumigena CCY9414]
 gi|119463021|gb|EAW43972.1| RNA polymerase sigma factor [Nodularia spumigena CCY9414]
          Length = 391

 Score =  102 bits (253), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 74/248 (29%), Positives = 133/248 (53%), Gaps = 17/248 (6%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A RYR H    A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+
Sbjct: 144 AFRYRLHIGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEK 203

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT-DNNLKP 156
           G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++ +   KP
Sbjct: 204 GYKFSTYATWWIRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKLLSQEMGRKP 258

Query: 157 -EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
            E+ +A   ++ + +   I+ + +L    SL   I   +   S+  D++  D +  E  +
Sbjct: 259 TEEEIATRMEMTIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIESDGETPEDQV 314

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIE 273
            +   R++    L + +  L+PRER +   R   ++    TLE +   F V+RER+RQIE
Sbjct: 315 SKNLLRED----LEKVLDSLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIE 370

Query: 274 ARAFKKVQ 281
           A+A +K++
Sbjct: 371 AKALRKLR 378


>gi|51474026|ref|YP_067783.1| RNA polymerase sigma factor RpoD [Rickettsia typhi str. Wilmington]
 gi|81389911|sp|Q68VQ5|RPOD_RICTY RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|51460338|gb|AAU04301.1| RNA polymerase sigma factor RpoD [Rickettsia typhi str. Wilmington]
          Length = 635

 Score =  102 bits (253), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 76/252 (30%), Positives = 128/252 (50%), Gaps = 21/252 (8%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E   L A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 376 ERQTLQAKKDMIEANLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 435

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           TY+ WWI+ A+   I      ++I      T N        + L+   Q + +   +P  
Sbjct: 436 TYATWWIRQAITRAIADQARTIRIPVHMIETIN--------KILRTSRQMLNELGYEP-T 486

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
              IA +L++   +V  +  ++A +  SL   +   D +  Q  D++    D      I+
Sbjct: 487 ATEIANRLSMPLDKVRKV-MKIAKEPISLENPV-GDDSDGGQLGDFI---EDKNAVAPID 541

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              + N R + TR ++ L PRE R+   R         TLE +  +F+V+RER+RQIE++
Sbjct: 542 AAIQSNLREVTTRVLATLTPREERVLRMRFGIGMNTDHTLEEVGQQFKVTRERIRQIESK 601

Query: 276 AFKKVQESIQKQ 287
           A +K+Q  I+ +
Sbjct: 602 ALRKLQHPIRSK 613


>gi|150015739|ref|YP_001307993.1| RNA polymerase sigma factor RpoD [Clostridium beijerinckii NCIMB
           8052]
 gi|149902204|gb|ABR33037.1| RNA polymerase, sigma 70 subunit, RpoD family [Clostridium
           beijerinckii NCIMB 8052]
          Length = 376

 Score =  102 bits (253), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 79/265 (29%), Positives = 132/265 (49%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  ++E   AK   E G+  A  +L  ++LRLVV IA  Y G G+   ++
Sbjct: 110 YLKEIGKVPLLSSEQEITYAKEI-EEGNQKAKKKLAEANLRLVVSIAKRYVGRGMLFLDL 168

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 169 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 226

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R++  L      +  PE+   I+K + +   +V  +        SL   I   ++  S
Sbjct: 227 LIRVQRQLLQELGRDPFPEE---ISKVMELPVDKVREIQKIAQEPVSLETPI--GEEEDS 281

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++  D              K +   L   +  L PRE ++   R   ++    TLE
Sbjct: 282 HLGDFIPDDEAPAPAEAAAFTMLKEQ---LINVLDTLTPREEKVLRLRFGLDDGRARTLE 338

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF V+RER+RQIEA+A +K++
Sbjct: 339 EVGKEFNVTRERIRQIEAKALRKLR 363


>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 =  102 bits (253), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 69/237 (29%), Positives = 123/237 (51%), Gaps = 14/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 544 DAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 603

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL-KGHLQAITDNNLKPEQVVAIAKKL 166
           WI+ A+   I      ++I    +       + RL + HLQ       +P+  + +A K+
Sbjct: 604 WIRQAITRSIADQARTIRI--PVHMIETINKMNRLSRQHLQEF---GFEPDASI-LAAKM 657

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +  ++A  E ++      D + S   D++    D      +E   +   R+
Sbjct: 658 EIPEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDSANTAPLEAAMQAGLRD 712

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 713 VVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLK 769


>gi|298491609|ref|YP_003721786.1| RpoD subfamily RNA polymerase sigma 70 subunit ['Nostoc azollae'
           0708]
 gi|298233527|gb|ADI64663.1| RNA polymerase, sigma 70 subunit, RpoD subfamily ['Nostoc azollae'
           0708]
          Length = 390

 Score =  102 bits (253), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 73/246 (29%), Positives = 132/246 (53%), Gaps = 17/246 (6%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           RYR H    A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G+
Sbjct: 145 RYRLHVGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGY 204

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT-DNNLKP-E 157
           + +TY+ WWI+ A+   I      +++        L+  + R+K   + ++ +   KP E
Sbjct: 205 KFSTYATWWIRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKLLSQEMGRKPTE 259

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           + +A   ++ + +   I+ + +L    SL   I   +   S+  D++  D +  E  + +
Sbjct: 260 EEIATRMEMTIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIESDGETPEDQVSK 315

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEAR 275
              R++    L + +  L+PRER +   R   ++    TLE +   F V+RER+RQIEA+
Sbjct: 316 NLLRED----LEKVLDSLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAK 371

Query: 276 AFKKVQ 281
           A +K++
Sbjct: 372 ALRKLR 377


>gi|254382896|ref|ZP_04998252.1| RNA polymerase sigma factor rpoD [Streptomyces sp. Mg1]
 gi|194341797|gb|EDX22763.1| RNA polymerase sigma factor rpoD [Streptomyces sp. Mg1]
          Length = 362

 Score =  102 bits (253), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 88/294 (29%), Positives = 142/294 (48%), Gaps = 42/294 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS----AAH----------------------- 51
           Y+ EI +IP+L   EE  LA+R  E G  +    A H                       
Sbjct: 69  YLREIGRIPLLTAAEEVELARRV-EAGLFAEEKLAGHTDLDLQLTLDLDKLVVMGRMAKR 127

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RL+ S+LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY+ WWI+ 
Sbjct: 128 RLIESNLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIRQ 187

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           AM   +      +++     +     N R ++   + + +   +P  V  +A  L ++  
Sbjct: 188 AMSRALADQARTIRVPVHVVE---LIN-RVVRVQRRMLQERGYEP-TVEEVAVHLELTPE 242

Query: 172 EVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            V+ +  RLA +  SL+A +   D  +    D +    DG     +E       R  L  
Sbjct: 243 RVLEV-LRLAQEPVSLHAPVGEEDDVA--LGDLI---EDGDAASPVESAAFFLLREHLEA 296

Query: 231 SMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            +S L  RER++ + R       P TLE +   F V+RER+RQIE++   K+++
Sbjct: 297 VLSTLGERERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRD 350


>gi|72161271|ref|YP_288928.1| sigma-70 factor [Thermobifida fusca YX]
 gi|71915003|gb|AAZ54905.1| sigma-70 factor [Thermobifida fusca YX]
          Length = 388

 Score =  102 bits (253), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 87/306 (28%), Positives = 148/306 (48%), Gaps = 49/306 (16%)

Query: 19  YIHEIRKIPMLEKQEEYVLAK------------RYREHGDLSAAH--------------- 51
           Y+ EI ++P+L  +EE  LAK            R    G + A +               
Sbjct: 90  YLREIGRVPLLTAEEEVELAKAIEIGLYAEQKLRAARTGPVPAQYSPEWFEDLNELVREG 149

Query: 52  -----RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                RL+ S+LRLVV +A  Y G GL + +++ EGN+GL++AV+KFD  RG++ +TY+ 
Sbjct: 150 KLAKRRLIESNLRLVVSVAKRYLGRGLALLDLIQEGNLGLIRAVEKFDYTRGYKFSTYAT 209

Query: 107 WWIKAAMQEYILRSWSLVKIGT--TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           WWI+ A+   I      +++      +  RL    RRL  H +   +  L       +++
Sbjct: 210 WWIRQAITRAIADQARTIRVPVHMVESINRLARTRRRL--HQELGREPTLH-----ELSR 262

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +LNV    V+ ++       SL+  I   D   S + D+ + D D    V  E       
Sbjct: 263 ELNVDHDRVVEIHRVSQEPISLHTPIGEED---SAFGDF-IEDTDAVPPV--EAAAFVML 316

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           ++ L + +  L+ RE+R+   R   E+  P TLE +  +F V+RER+RQIE++   K+++
Sbjct: 317 QDQLAQVLGGLSEREQRVITLRFGLEDGKPHTLEEVGRKFGVTRERIRQIESKTLAKLRQ 376

Query: 283 SIQKQV 288
             + ++
Sbjct: 377 PSRARI 382


>gi|15604688|ref|NP_221206.1| RNA polymerase sigma factor RpoD [Rickettsia prowazekii str. Madrid
           E]
 gi|464670|sp|P33451|RPOD_RICPR RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|434681|gb|AAB81404.1| major sigma factor of RNA polymerase [Rickettsia prowazekii]
 gi|3861383|emb|CAA15282.1| RNA POLYMERASE SIGMA FACTOR RPOD (rpoD) [Rickettsia prowazekii]
 gi|292572521|gb|ADE30436.1| RNA polymerase sigma factor [Rickettsia prowazekii Rp22]
          Length = 635

 Score =  102 bits (253), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 76/252 (30%), Positives = 128/252 (50%), Gaps = 21/252 (8%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E   L A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 376 ERQTLQAKKDMIEANLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 435

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           TY+ WWI+ A+   I      ++I      T N        + L+   Q + +   +P  
Sbjct: 436 TYATWWIRQAITRAIADQARTIRIPVHMIETIN--------KILRTSRQMLNELGYEP-T 486

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
              IA +L++   +V  +  ++A +  SL   +   D +  Q  D++    D      I+
Sbjct: 487 ATEIANRLSMPLDKVRKV-MKIAKEPISLENPV-GDDSDGGQLGDFI---EDKNAVAPID 541

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              + N R + TR ++ L PRE R+   R         TLE +  +F+V+RER+RQIE++
Sbjct: 542 AAIQSNLREVTTRVLATLTPREERVLRMRFGIGMNTDHTLEEVGQQFKVTRERIRQIESK 601

Query: 276 AFKKVQESIQKQ 287
           A +K+Q  I+ +
Sbjct: 602 ALRKLQHPIRSK 613


>gi|111115602|ref|YP_710220.1| RNA polymerase sigma factor [Borrelia afzelii PKo]
 gi|110890876|gb|ABH02044.1| RNA polymerase sigma factor [Borrelia afzelii PKo]
          Length = 266

 Score =  102 bits (253), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 80/282 (28%), Positives = 146/282 (51%), Gaps = 20/282 (7%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M+I  N ++ +  Y+  +R+  ++  +EE  L  +  + G   A ++++ ++LRLV+KI 
Sbjct: 1   MNIFSNEDLNI--YLKSVREHKLITHEEEIQLVGQI-QRGSAKAKNKMINANLRLVLKII 57

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y G GL I +++ EGN+GL++A +K+DP +  + +TY+ +WIK ++Q  +     LVK
Sbjct: 58  KRYAGKGLKIEDLIQEGNLGLIRAAEKYDPNKNTKFSTYASFWIKQSLQRALNTKTRLVK 117

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           +          +    L   +        K  +   I K+ N+S ++ I +   L  + S
Sbjct: 118 VP---------YRKENLILQINKYLTEEEKAPKKEEIMKRFNLSPAQYIKIIPYLEKEYS 168

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L+  I  S+ NS+     L  D+    ++ +E++      N +  +   L  +ER I + 
Sbjct: 169 LDKEIEGSE-NSTLLN--LYEDNSFNPEITLEQDSTLQHLNYILETK--LTEKERYIIKK 223

Query: 246 R-RLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L  +P   TL+++S+E  +S E VRQIE R  KK++E I
Sbjct: 224 RYNLDNSPKKSTLKDISTELGISSETVRQIEKRVLKKLKEEI 265


>gi|298246437|ref|ZP_06970243.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297553918|gb|EFH87783.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 422

 Score =  102 bits (253), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 88/290 (30%), Positives = 145/290 (50%), Gaps = 47/290 (16%)

Query: 19  YIHEIRKIPMLEKQEEYVLAK----------------RYREHGDLSAAHRLVTSHLRLVV 62
           Y+ EI ++P+L   EE  LA+                RY   G+  A  RL  ++LRLVV
Sbjct: 140 YLREIGRVPLLTAHEEIRLAQLMERGKAERLKPAPNYRYISEGE-EAQKRLTEANLRLVV 198

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y G G+ + +++ EGNIGL++AV+KFD  +GF+ +TY+ WWI+ A+   I     
Sbjct: 199 SVAKKYIGRGMNLLDLIQEGNIGLIRAVEKFDYNKGFKFSTYATWWIRQAITRAIADQAR 258

Query: 123 LVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
            ++I      T N+     +RL  +L R     +      +  E+V  I K   VS+ E 
Sbjct: 259 TIRIPVHMVETINRLIRISRRLLQDLGREPTSEEIAAQMEISAEKVREIIK---VSQ-EP 314

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
           +S+   + G+E  + L +  + +++     L        Q+L E+ E           + 
Sbjct: 315 VSLETPI-GEEDDSHLGDFIEDHTA-----LAPADAASHQLLKEQVE---------DVLD 359

Query: 234 VLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L  RER++ + R   ++    TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 360 SLTERERKVLQLRFGLDDGRSRTLEEVGKEFHVTRERIRQIEAKALRKLR 409


>gi|123969020|ref|YP_001009878.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. AS9601]
 gi|123199130|gb|ABM70771.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. AS9601]
          Length = 313

 Score =  102 bits (253), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 84/302 (27%), Positives = 153/302 (50%), Gaps = 44/302 (14%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYR------EHGDLS-------------------AA 50
           +S Y+  I ++P+L   EE  L  + +      E G L+                   A 
Sbjct: 20  ISWYLQNIGRVPLLTPAEEIELGNQVQKMMILTEDGQLNEKVNEFTTQQKRTIKIGRRAK 79

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            R++ ++LRLVV +A  Y+G GL + ++V EG++GL +AV+KFDP RG++ +TY+ WWI+
Sbjct: 80  ERMMKANLRLVVSVAKKYQGKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAFWWIR 139

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRR----LKGHLQAITDNNLKPEQVVAIAKKL 166
            +M   I      +++    +++    ++R+    L   L A+          + IA+ +
Sbjct: 140 QSMTRAIACQSRTIRLPVHLSER--LASIRKVSRDLAHKLGAMPSR-------IEIAEAM 190

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   E+ S+  +     SL+A +N  D  S  +   L+ D + +E   +++ E+K  + 
Sbjct: 191 EIDVEELDSVLRQALSTSSLDAPVNGDDGRS--FLGDLIADSNNEEP--LDQVEQKMHQE 246

Query: 227 MLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L + +S L+ +E+ + + R  L  N   TL  +    EVSRERVRQ+E +A +K++   
Sbjct: 247 QLGKWLSHLSEQEQHVLKLRFGLDANERHTLAEIGRLLEVSRERVRQVELKALRKLRNLT 306

Query: 285 QK 286
           +K
Sbjct: 307 RK 308


>gi|318080032|ref|ZP_07987364.1| RNA polymerase sigma factor [Streptomyces sp. SA3_actF]
          Length = 340

 Score =  102 bits (253), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 92/305 (30%), Positives = 141/305 (46%), Gaps = 66/305 (21%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHG-------------------DL--------SAAH 51
           Y+ EI +IP+L   +E  LA+R  E G                   DL        +A  
Sbjct: 47  YLREIGRIPLLTAADEVDLARRV-EAGLFAEAKLAGPGPLDTRLALDLDRLVVLGRAAKR 105

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RL+ S+LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RGF+ +TY+ WWI+ 
Sbjct: 106 RLIESNLRLVVSVAKRYAGRGLTMLDLVQEGNLGLIRAVEKFDYTRGFKFSTYATWWIRQ 165

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFN--LRRLKGHLQAITDNNLKPEQVVAIA----KK 165
           AM   +      +++     +     N  +R  +G LQ   +   +P      A     K
Sbjct: 166 AMSRALADQARTIRVPVHVVE---LINRVVRVQRGLLQ---ERGHEPSHAEVAALLGLTK 219

Query: 166 LNVSE-----SEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
             V E      E +S++  + G++  +L  LI   D  S      L+      E VL   
Sbjct: 220 ERVGEVLRLAQEPVSLHTPVGGEDEVALGDLIEDGDAPSPPESAALLLLRRHLEDVL--- 276

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARA 276
                         S L  RER++ + R   ++  P TLE + + F V+RER+RQIEA+ 
Sbjct: 277 --------------STLGERERQVVQLRYGLDDGRPRTLEEIGTLFGVTRERIRQIEAKT 322

Query: 277 FKKVQ 281
             K++
Sbjct: 323 LAKLR 327


>gi|297539657|ref|YP_003675426.1| RNA polymerase sigma-70 subunit RpoD [Methylotenera sp. 301]
 gi|297259004|gb|ADI30849.1| RNA polymerase, sigma 70 subunit, RpoD [Methylotenera sp. 301]
          Length = 645

 Score =  102 bits (253), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 70/245 (28%), Positives = 122/245 (49%), Gaps = 32/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RGF+ +TY+ WW
Sbjct: 404 AKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGFKFSTYATWW 463

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +  ++P+  + +A+K+ +
Sbjct: 464 IRQAITRSIADQARTIRI--PVHMIETINKMNRISR--QILQETGVEPDPAL-LAEKMEM 518

Query: 169 SESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            E ++          ISM   +  DE             S   D++    DGQ    ++ 
Sbjct: 519 PEDKIRKILKISKEPISMETPIGDDE------------DSHLGDFI---EDGQTLAPVDA 563

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARA 276
               + R+  +  +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A
Sbjct: 564 AIYASLRDATSEVLESLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKA 623

Query: 277 FKKVQ 281
            +K++
Sbjct: 624 LRKLR 628


>gi|239948365|ref|ZP_04700118.1| RNA polymerase sigma factor, sigma-70 family [Rickettsia
           endosymbiont of Ixodes scapularis]
 gi|239922641|gb|EER22665.1| RNA polymerase sigma factor, sigma-70 family [Rickettsia
           endosymbiont of Ixodes scapularis]
          Length = 635

 Score =  102 bits (253), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 76/252 (30%), Positives = 128/252 (50%), Gaps = 21/252 (8%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E   L A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 376 ERQTLQAKKDMIEANLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 435

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           TY+ WWI+ A+   I      ++I      T N        + L+   Q + +   +P  
Sbjct: 436 TYATWWIRQAITRAIADQARTIRIPVHMIETIN--------KILRISRQMLNELGYEP-T 486

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
              IA +L++   +V  +  ++A +  SL   +   D +  Q  D++    D      I+
Sbjct: 487 ATEIANRLSMPLDKVCKV-MKIAKEPISLENPV-GDDIDGGQLGDFI---EDKNAVAPID 541

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              + N R + TR ++ L PRE R+   R         TLE +  +F+V+RER+RQIE++
Sbjct: 542 AAIQSNLREVTTRVLATLTPREERVLRMRFGIGMNTDHTLEEVGQQFKVTRERIRQIESK 601

Query: 276 AFKKVQESIQKQ 287
           A +K+Q  I+ +
Sbjct: 602 ALRKLQHPIRSK 613


>gi|139436983|ref|ZP_01771143.1| Hypothetical protein COLAER_00117 [Collinsella aerofaciens ATCC
           25986]
 gi|133776630|gb|EBA40450.1| Hypothetical protein COLAER_00117 [Collinsella aerofaciens ATCC
           25986]
          Length = 454

 Score =  102 bits (253), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 73/236 (30%), Positives = 123/236 (52%), Gaps = 12/236 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L A   L++++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ 
Sbjct: 214 LEAKQALISANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYQKGFKFSTYAT 273

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I    +       L R++  L      +  PE++ A   ++
Sbjct: 274 WWIRQAITRAIADQARTIRI--PVHMVETINKLVRVQRQLLQDLGRDPTPEEIGA---EM 328

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++S   V  +        SL   I   ++  SQ  D++    D Q  V  +       + 
Sbjct: 329 DMSADRVREIQKISQEPVSLETPIG--EEEDSQLGDFI---EDSQAIVPPDAASFSMLQE 383

Query: 227 MLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            LT+ +  L  RER++ E R   +  +P TLE +  EF V+RER+RQIE++   K+
Sbjct: 384 QLTQVLDSLADRERKVIELRFGLVDGHPRTLEEVGREFGVTRERIRQIESKTLAKL 439


>gi|162605994|ref|XP_001713512.1| RNA-polymerase sigma factor [Guillardia theta]
 gi|13794432|gb|AAK39807.1|AF165818_15 RNA-polymerase sigma factor [Guillardia theta]
          Length = 460

 Score =  102 bits (253), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 82/252 (32%), Positives = 132/252 (52%), Gaps = 34/252 (13%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           H    A  R+V ++LRLVV IA  Y   G+ + +++ EG++GL++A +KFD E+GF+ +T
Sbjct: 183 HNARRAKERMVAANLRLVVSIAKRYVNRGMSLQDLIQEGSLGLIRAAEKFDSEKGFKFST 242

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL----QAI--TDNNLKPE 157
           Y+ WW+K A+   I            A+  R      RL  HL     AI  T  NL  E
Sbjct: 243 YATWWVKQAVTRAI------------ADHSRTI----RLPVHLYDTISAIRKTTRNLNIE 286

Query: 158 -----QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
                    IAK++++S  ++ ++        SL   + + D ++SQ  D++  D +  E
Sbjct: 287 IGRSPTEEEIAKRMDMSVEKLRNVLQSAQPTLSLERPLKNDD-DTSQLSDFIEADQESPE 345

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPV-TLENLSSEFEVSRERVR 270
               E  E+   R+ L   ++ L+PRER +   R  L +  + TLE +   F V+RERVR
Sbjct: 346 ----EHVEKSMLRDDLENVINSLSPRERDVVRMRYGLDDGRIKTLEEIGQIFSVTRERVR 401

Query: 271 QIEARAFKKVQE 282
           QIEA+A +K+++
Sbjct: 402 QIEAKAIRKLRQ 413


>gi|261880495|ref|ZP_06006922.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           bergensis DSM 17361]
 gi|270332834|gb|EFA43620.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           bergensis DSM 17361]
          Length = 290

 Score =  102 bits (253), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 79/273 (28%), Positives = 139/273 (50%), Gaps = 14/273 (5%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKIAMGYRGYG 72
            L RY+ EI + P++   EE  L+++ R+ G     A  +L+TS+LR VV +A  Y+  G
Sbjct: 17  ALDRYLVEIGRAPLISIDEEIELSQKIRKGGREGQRAKDKLITSNLRFVVSVAKQYQHQG 76

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L ++++++EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V++    NQ
Sbjct: 77  LSLTDLINEGNIGLIKATEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRL--PLNQ 134

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALIN 191
                 L ++   +      + +      IA+ ++V E+  I M+    G   S++A   
Sbjct: 135 ---VGTLSKINKEINNFEQRHERRPSTQEIAEAIDV-EAGKIRMSMMADGHHVSIDAPFQ 190

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF-EARRLQE 250
             + NS    D +    D +     + E      N +    SVL  RE  I  E   +  
Sbjct: 191 EDESNS--MADIMASGDDTRTDKRADHESMAQELNTVLE--SVLKEREITIIRECFGIGC 246

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           + + LE +     ++RERVRQI  ++  K++ES
Sbjct: 247 HELGLEEIGDRLGLTRERVRQIREKSIAKLRES 279


>gi|223998999|ref|XP_002289172.1| RNA polymerase [Thalassiosira pseudonana CCMP1335]
 gi|220974380|gb|EED92709.1| RNA polymerase [Thalassiosira pseudonana CCMP1335]
          Length = 318

 Score =  102 bits (253), Expect = 9e-20,   Method: Compositional matrix adjust.
 Identities = 72/239 (30%), Positives = 123/239 (51%), Gaps = 12/239 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L A   L  S+LRLV+ IA  Y+G GL + ++  EG +GL +A +KFDPERGFR +TY+ 
Sbjct: 75  LRAKAALTESNLRLVISIAKRYQGRGLNMQDLCQEGTLGLTRACEKFDPERGFRFSTYAT 134

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWIK  +   I      +++    + +     +R+ +  LQ     +   E+V A   K+
Sbjct: 135 WWIKQGIMRAIADQARTIRLPVHIHDQ--LSIVRKAERDLQNELGRDATKEEVAA---KV 189

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRR 225
            +   ++  +     G  S+   + +S    S    + + D  G  +Q  ++  + +  +
Sbjct: 190 GMKPDKIEFLKRASVGSISMEQELGTSGSERS----FTIQDTLGDPDQKPVDMAQYRMLQ 245

Query: 226 NMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQE 282
           + + R +  LN RE+ +   R  L +    TLE +  +F V+RER+RQIEARA  K+++
Sbjct: 246 DDVGRLICTLNAREQAVIRMRFGLDDGKAKTLEEIGKKFSVTRERIRQIEARALHKLRQ 304


>gi|203284664|ref|YP_002222404.1| RNA polymerase sigma factor [Borrelia duttonii Ly]
 gi|201084107|gb|ACH93698.1| RNA polymerase sigma factor [Borrelia duttonii Ly]
          Length = 267

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 80/282 (28%), Positives = 150/282 (53%), Gaps = 20/282 (7%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M+I  N ++ +  Y+  +R+  ++  +EE  LAK+ +  G L A ++++ ++LRLV+KI 
Sbjct: 1   MNIFSNEDLNI--YLKSVREHRLITHEEEIELAKQIK-LGSLKAKNQMINANLRLVLKII 57

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y G GL I +++ EGN+GL++A +K+DP +  + +TY+ +WIK ++Q  +     LVK
Sbjct: 58  KRYAGKGLKIEDLIQEGNLGLIRAAEKYDPSKNTKFSTYASFWIKQSLQRALNTKTRLVK 117

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           +        L  N        + + +    P++   I ++ N++ ++ + +   L  + S
Sbjct: 118 VPYRKENLILQIN--------KYLMEEEKSPKK-EDIMERFNLTTAQYVKIIPYLEKEYS 168

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L+  I  S+ NS+     L  D+    +  +E+       N +  +   LN +ER I + 
Sbjct: 169 LDKKIEGSE-NSTLLN--LYEDNSFNPESTLEQNSTLKHLNYILETK--LNEKERYIIKK 223

Query: 246 RRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R   +N     TL+++S+E  +S E VRQIE R  KK++E +
Sbjct: 224 RYNLDNSDKKSTLKDISTELGISSETVRQIEKRVLKKLREEL 265


>gi|17232755|ref|NP_489303.1| RNA polymerase sigma factor RpoD [Nostoc sp. PCC 7120]
 gi|75907632|ref|YP_321928.1| RNA polymerase sigma factor RpoD [Anabaena variabilis ATCC 29413]
 gi|133465|sp|P26683|RPOD_ANASP RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A
 gi|142108|gb|AAA22043.1| RNA polymerase sigma-subunit [Nostoc sp. PCC 7120]
 gi|17134402|dbj|BAB76962.1| transcription initiation factor sigma [Nostoc sp. PCC 7120]
 gi|75701357|gb|ABA21033.1| Sigma 28 (Flagella/Sporulation) [Anabaena variabilis ATCC 29413]
          Length = 390

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 74/248 (29%), Positives = 133/248 (53%), Gaps = 17/248 (6%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A RYR H    A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+
Sbjct: 143 AFRYRLHIGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEK 202

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT-DNNLKP 156
           G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++ +   KP
Sbjct: 203 GYKFSTYATWWIRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKLLSQEMGRKP 257

Query: 157 -EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
            E+ +A   ++ + +   I+ + +L    SL   I   +   S+  D++  D +  E  +
Sbjct: 258 TEEEIATRMEMTIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIESDGETPEDQV 313

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIE 273
            +   R++    L + +  L+PRER +   R   ++    TLE +   F V+RER+RQIE
Sbjct: 314 SKNLLRED----LEKVLDSLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIE 369

Query: 274 ARAFKKVQ 281
           A+A +K++
Sbjct: 370 AKALRKLR 377


>gi|303235908|ref|ZP_07322511.1| putative RNA polymerase sigma factor RpoD [Prevotella disiens
           FB035-09AN]
 gi|302483781|gb|EFL46773.1| putative RNA polymerase sigma factor RpoD [Prevotella disiens
           FB035-09AN]
          Length = 293

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 80/289 (27%), Positives = 146/289 (50%), Gaps = 42/289 (14%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ +  +  M+   EE  LAKR RE GD  A  RL  ++LR VV +A  Y+  GL 
Sbjct: 23  ALEKYLQDTSREAMVGLDEEIELAKRIRE-GDEKALERLTKANLRFVVSVAKQYQNQGLA 81

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TA 130
           + ++++EGN GL++A +K+D  RGF+  +Y++WWI+ ++ + I     +V++      +A
Sbjct: 82  LPDLINEGNFGLIKAAQKYDETRGFKFISYAVWWIRQSIMQAISEQSRMVRVPINQMGSA 141

Query: 131 NQKRLFFN-----------LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
           N+ R F N           L  L  H+      +L  E++V   + L ++ ++V SM+  
Sbjct: 142 NRIRKFINQFEQEHERYPSLSELTEHI------DLLEEKIV---EALAMATTQV-SMDAP 191

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
              +E  + L    +KN+    D LV +    E               +  +++ L+ RE
Sbjct: 192 FTSNEEGSLLDVLPNKNAPSADDLLVAESLSTE---------------VANALASLSERE 236

Query: 240 RRIFEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           + I +       P ++LE +     ++RERVRQI+ +A  +++++ Q +
Sbjct: 237 QIIIKCFFGINQPEMSLEEIGERTGLTRERVRQIKEKAIIRLRKNSQSE 285


>gi|157804249|ref|YP_001492798.1| RNA polymerase sigma factor RpoD [Rickettsia canadensis str.
           McKiel]
 gi|157785512|gb|ABV74013.1| RNA polymerase sigma factor RpoD [Rickettsia canadensis str.
           McKiel]
          Length = 635

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 75/248 (30%), Positives = 127/248 (51%), Gaps = 21/248 (8%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 380 LQAKKDMIEANLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 439

Query: 107 WWIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           WWI+ A+   I      ++I      T N        + L+   Q + +   +P     I
Sbjct: 440 WWIRQAITRAIADQARTIRIPVHMIETIN--------KILRTSRQMLNELGYEP-TATEI 490

Query: 163 AKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           A +L++   +V  +  ++A +  SL   +   D +  Q  D++    D      I+   +
Sbjct: 491 ANRLSMPLDKVRKV-MKIAKEPISLENPV-GDDSDGGQLGDFI---EDKNAVAPIDAAIQ 545

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
            N R + TR ++ L PRE R+   R         TLE +  +F+V+RER+RQIE++A +K
Sbjct: 546 SNLREVTTRVLATLTPREERVLRMRFGIGMNTDHTLEEVGQQFKVTRERIRQIESKALRK 605

Query: 280 VQESIQKQ 287
           +Q  I+ +
Sbjct: 606 LQHPIRSK 613


>gi|290960625|ref|YP_003491807.1| Principal sigma factor HrdA [Streptomyces scabiei 87.22]
 gi|260650151|emb|CBG73267.1| Principal sigma factor HrdA [Streptomyces scabiei 87.22]
          Length = 387

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 89/294 (30%), Positives = 142/294 (48%), Gaps = 42/294 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHG-------------------DLS--------AAH 51
           Y+ EI +IP+L   EE  LA+R  E G                   DL         A  
Sbjct: 94  YLREIGRIPLLTAVEEVELARRV-EAGLFAEERLGTASGLDTRLALDLDRLVVMGRMAKR 152

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY+ WWI+ 
Sbjct: 153 RLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIRQ 212

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           AM   +      +++    +   L   + R++  +         P++V A    L+++  
Sbjct: 213 AMSRALADQARTIRV--PVHVVELINRVVRVQRRMLQERGYEPTPDEVAA---HLDLA-P 266

Query: 172 EVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           E +S   RLA +  SL+A +   D  +    D +    DG     +E       R  L  
Sbjct: 267 ERVSEVLRLAQEPVSLHAPVGEEDDVA--LGDLI---EDGDAASPVESAAFLLLREHLEA 321

Query: 231 SMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            +S L  RER++ + R       P TLE +   F V+RER+RQIE++   K+++
Sbjct: 322 VLSTLGERERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRD 375


>gi|257063660|ref|YP_003143332.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Slackia
           heliotrinireducens DSM 20476]
 gi|256791313|gb|ACV21983.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Slackia
           heliotrinireducens DSM 20476]
          Length = 394

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 84/294 (28%), Positives = 136/294 (46%), Gaps = 42/294 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLA-------------KRYREHG-----------------DLS 48
           Y+ EI K+P+L   EE  LA             ++  E G                  L 
Sbjct: 96  YLKEIGKVPLLTPSEEVDLAMKIEAGVAATAELEKAEEEGVELDRRERRRLTRVEQVGLD 155

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L+ ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WW
Sbjct: 156 AKDQLIEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 215

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R++  L      +  PE+   I +K+ +
Sbjct: 216 IRQAITRAIADQARTIRI--PVHMVETINKLVRIQRQLLQELGRDPSPEE---IGEKMGL 270

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S   V  +        SL   I   ++  SQ  D++    D    V ++       +  L
Sbjct: 271 SAERVREIQKLSQEPVSLETPIG--EEEDSQLGDFI---EDDSAIVPVDAASFAMMQEQL 325

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
           ++ +  L  RER +   R   E+  P TLE +  EF V+RER+RQIE++   K+
Sbjct: 326 SKVLDTLGERERNVVIKRFGLEDGQPHTLEEVGREFGVTRERIRQIESKTLAKL 379


>gi|113954631|ref|YP_732094.1| RNA polymerase sigma factor [Synechococcus sp. CC9311]
 gi|113881982|gb|ABI46940.1| RNA polymerase sigma factor [Synechococcus sp. CC9311]
          Length = 340

 Score =  102 bits (253), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 80/294 (27%), Positives = 143/294 (48%), Gaps = 31/294 (10%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLA--------------------KRYREHGDLSAAHRLVT 55
           +  Y+  I ++P+L   EE  LA                    +R+R      A  R++ 
Sbjct: 53  IGHYLSSIGRVPLLTAAEEIELAHHVQAMKELLDIQEEERTPKQRHRIRMGKRARDRMMA 112

Query: 56  SHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQE 115
           ++LRLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+  M  
Sbjct: 113 ANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTR 172

Query: 116 YILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
            I  S   +++    ++K     L +++   + ++    +    + +A  + +   ++  
Sbjct: 173 AIDNSARTIRLPIHISEK-----LSKMRKITRELSHRFGRQPNRLELAHAMGIEPRDLEE 227

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
           +  + A   SL+A     +  S+  +  L+ D +G E   +E  +R  ++  L   +S L
Sbjct: 228 LIAQSAPCASLDAHARGEEDRSTLGE--LIPDPNGDEP--MEGMDRSIQKEHLGGWLSQL 283

Query: 236 NPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           N RE++I   R     E P+TL  +  +  VSRERVRQ+E++A  K++     Q
Sbjct: 284 NEREQKILRLRFGLGGEEPLTLAEIGRQINVSRERVRQLESKAILKLRTMTNHQ 337


>gi|288926192|ref|ZP_06420119.1| RNA polymerase sigma-70 factor [Prevotella buccae D17]
 gi|315608841|ref|ZP_07883815.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella buccae
           ATCC 33574]
 gi|288337084|gb|EFC75443.1| RNA polymerase sigma-70 factor [Prevotella buccae D17]
 gi|315249448|gb|EFU29463.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella buccae
           ATCC 33574]
          Length = 290

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 80/273 (29%), Positives = 142/273 (52%), Gaps = 14/273 (5%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYG 72
            L +Y+ EI   PM+   EE  LA+  R+ G     A  +LV ++LR VV +A  Y+  G
Sbjct: 17  ALDKYLAEISHEPMVSIDEETELAQAIRKGGREGERAKEKLVRANLRFVVSVAKQYQHQG 76

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V++    NQ
Sbjct: 77  LGLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSIMQAIAEQSRIVRL--PLNQ 134

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV-ISMNCRLAGDESLNALIN 191
                 + ++      + ++N +P  +  +A+   + E ++  S+N   +   S++A   
Sbjct: 135 VGAVSKINQVTSKF--VQEHNRRP-SIQELAQITGIDEQKIEQSLNAD-SHHMSIDAPFA 190

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF-EARRLQE 250
             D NS    D L    D +    ++ E   +  N + +  +VL  RE RI  E   +  
Sbjct: 191 EDDDNS--MADVLASGDDSRTDKQVDFESMASELNNVLK--NVLKEREIRIVKECFGIGC 246

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +   LE +  E  ++RERVRQI  ++  K++ES
Sbjct: 247 HEKGLEEIGEEMGLTRERVRQIREKSILKIRES 279


>gi|126696812|ref|YP_001091698.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9301]
 gi|126543855|gb|ABO18097.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9301]
          Length = 313

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 84/302 (27%), Positives = 153/302 (50%), Gaps = 44/302 (14%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYR------EHGDLS-------------------AA 50
           +S Y+  I ++P+L   EE  L  + +      E G L+                   A 
Sbjct: 20  ISWYLQNIGRVPLLTPAEEIELGNQVQKMMILTEDGQLNEKTNEFTTQQKRTIKIGRRAK 79

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            R++ ++LRLVV +A  Y+G GL + ++V EG++GL +AV+KFDP RG++ +TY+ WWI+
Sbjct: 80  ERMMKANLRLVVSVAKKYQGKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAFWWIR 139

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRR----LKGHLQAITDNNLKPEQVVAIAKKL 166
            +M   I      +++    +++    ++R+    L   L A+          + IA+ +
Sbjct: 140 QSMTRAIACQSRTIRLPVHLSER--LASIRKVSRDLAHKLGAMPSR-------IEIAEAM 190

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   E+ S+  +     SL+A +N  D  S  +   L+ D + +E   +++ E+K  + 
Sbjct: 191 EIDVEELDSVLRQALSTSSLDAPVNGDDGRS--FLGDLIADSNNEEP--LDQVEQKMHQE 246

Query: 227 MLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L + +S L+ +E+ + + R  L  N   TL  +    EVSRERVRQ+E +A +K++   
Sbjct: 247 QLGKWLSHLSEQEQHVLKLRFGLDANERHTLAEIGRLLEVSRERVRQVELKALRKLRNLT 306

Query: 285 QK 286
           +K
Sbjct: 307 RK 308


>gi|148264661|ref|YP_001231367.1| RpoD family RNA polymerase sigma factor [Geobacter uraniireducens
           Rf4]
 gi|146398161|gb|ABQ26794.1| RNA polymerase, sigma 38 subunit, RpoS [Geobacter uraniireducens
           Rf4]
          Length = 336

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 81/276 (29%), Positives = 143/276 (51%), Gaps = 27/276 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI+K  +L   EE  LA R  + G+ +A  +++ S+LRLVVKIA  Y   GLP  ++
Sbjct: 66  YLREIQKTKLLTADEEKELAARI-DKGEKAARDKMIESNLRLVVKIAKRYINRGLPFLDL 124

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV++F   +  R +TY+ WWI+ +++  ++            NQ R    
Sbjct: 125 IEEGNMGLIKAVERFKLSKECRFSTYATWWIRQSIERALV------------NQSRTI-- 170

Query: 139 LRRLKGHLQAITDNNLKP--EQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN---SS 193
             RL  H+    +  L+   E V  + ++ ++ E    +M+   A    L  L+    S 
Sbjct: 171 --RLPVHVSDDINKMLRITRELVQKVNREPSIKEV-ATAMDVNSAYIRRLMVLLKKTYSI 227

Query: 194 DKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQ 249
           ++   +  D+ + D   D       E  E  NR  M+++    L+  E+RI   R     
Sbjct: 228 ERPMGENNDYFLIDTIEDTSTVSPAELLEDVNRYEMVSKWFETLSDSEKRILTLRFGLDD 287

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           ++P TL+ +   F V+RER+RQIEA++ +K+++ ++
Sbjct: 288 KDPQTLDTIGRSFGVTRERIRQIEAKSLEKLRKILE 323


>gi|317968319|ref|ZP_07969709.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CB0205]
          Length = 260

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 74/238 (31%), Positives = 124/238 (52%), Gaps = 17/238 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R++ ++LRLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WW
Sbjct: 26  ARDRMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWW 85

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK---GHLQAITDNNLKPEQVVAIAKK 165
           I+  M   I  S   +++    ++K     +RR+     H      N L+      +A  
Sbjct: 86  IRQGMTRAIDNSARTIRLPIHVSEK--LSKMRRITRELSHRFGRQPNRLE------LAHA 137

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           + +   E+  +  + A   SL+A     D  S+  +  L+ D +  E   ++  +R  ++
Sbjct: 138 MGMQPEELEELITQSAPCASLDAHARGDDDRSTLGE--LIADPNSNES--MDSMDRNLQK 193

Query: 226 NMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             L   +S LN RER+I E R     + P+TL  +  +  VSRERVRQ+E++A  K++
Sbjct: 194 EHLGTWLSQLNERERKIIELRFGLAGQEPLTLAEIGRQINVSRERVRQLESKAILKLR 251


>gi|209525810|ref|ZP_03274346.1| RNA polymerase, sigma 70 subunit, RpoD family [Arthrospira maxima
           CS-328]
 gi|209493783|gb|EDZ94102.1| RNA polymerase, sigma 70 subunit, RpoD family [Arthrospira maxima
           CS-328]
          Length = 407

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 67/238 (28%), Positives = 129/238 (54%), Gaps = 13/238 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L A   ++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV+KFDP RG+R +TYS 
Sbjct: 166 LQAKDHMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTRGYRFSTYSY 225

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   I      +++     +K     L ++K   + I+    +   +  IA +L
Sbjct: 226 WWIRQGITRAIATQSRTIRLPVHITEK-----LNKIKKAQRKISQEKSRTATIDDIATEL 280

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++  ++  +  R+    SL   +  +DK+ ++  D L  +    E++L+ +   +  +N
Sbjct: 281 KMTPDQIREVLLRVPRSVSLETKVG-TDKD-TELGDLLETEESTPEELLMRESLYRELQN 338

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +L    + L+ +ER + + R      +P +L  +    ++SRERVRQIEA+A +K+++
Sbjct: 339 LL----ADLSGKERAVIQMRYGLGDGHPYSLAEIGRALDLSRERVRQIEAKALQKLRQ 392


>gi|116492861|ref|YP_804596.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Pediococcus pentosaceus ATCC 25745]
 gi|116103011|gb|ABJ68154.1| RNA polymerase, sigma 70 subunit, RpoD [Pediococcus pentosaceus
           ATCC 25745]
          Length = 379

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 84/278 (30%), Positives = 138/278 (49%), Gaps = 41/278 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   +E  LA R  E GD  A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 113 YLKEIGRVSLLTADQEVELALRI-EKGDPRARQELAEANLRLVVSIAKRYVGRGMQFLDL 171

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GLM+AV+KFD ++GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 172 IQEGNMGLMKAVEKFDYQKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 231

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q++L  +L R     +   + ++  ++V  I   L +++ E +S+   +    D  L 
Sbjct: 232 RIQRQLLQDLGREPMPEEIGAEMDMPSDKVREI---LKIAQ-EPVSLETPIGEEDDSHLG 287

Query: 188 ALINSSDKNSSQWQDWLVYD-----HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             I   D+ ++   D   Y+      +G    L ++EE     N+L     + + R R  
Sbjct: 288 DFIE--DQEATSPADHAAYELLKEQLEGVLDTLTDREE-----NVLRLRFGLDDGRTR-- 338

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                      TLE +   F V+RER+RQIEA+A +K+
Sbjct: 339 -----------TLEEVGKVFGVTRERIRQIEAKALRKL 365


>gi|219847900|ref|YP_002462333.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus
           aggregans DSM 9485]
 gi|219542159|gb|ACL23897.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus
           aggregans DSM 9485]
          Length = 381

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 89/304 (29%), Positives = 141/304 (46%), Gaps = 48/304 (15%)

Query: 12  GEIGLSR----YIHEIRKIPMLEKQEEYVLAKRY------------------REHGDL-- 47
           GEI        Y+ EI ++P+L  ++E  LAK                    RE  +L  
Sbjct: 77  GEIAFDDPVRMYLQEIGQVPLLTAEQEVELAKAMEAGAIARQRLDREEYASARERFELER 136

Query: 48  ------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
                  A H L+ ++LRLVV IA  Y  YGL + ++V EGNIGLM+AV+KFD ++G + 
Sbjct: 137 AVQQGQDARHHLIQANLRLVVSIAKKYTSYGLTMMDLVQEGNIGLMRAVEKFDYKKGHKF 196

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY+ WWI+ A+   I      +++     +      ++R    LQ        PE+   
Sbjct: 197 STYATWWIRQAITRAIADQSRTIRLPVHMGEA--ISQVKRTSHRLQQTMQREPTPEE--- 251

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNAL---INSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           IA  + +S  +V     R   + S++ L   +    +   +  D++    D +     E 
Sbjct: 252 IADAMGISAGKV-----RRTLEASMHPLSLEMPVGQEGEGRMGDFI---EDDRISTPAEA 303

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARA 276
                 R  L   +  L  RER+I + R  L++    TLE +  EF ++RER+RQIEA A
Sbjct: 304 AAASLLREQLEEVLMKLPERERKIIQLRYGLKDGRYRTLEEVGIEFGITRERIRQIEAVA 363

Query: 277 FKKV 280
            +K+
Sbjct: 364 LRKL 367


>gi|33863540|ref|NP_895100.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str. MIT
           9313]
 gi|33640989|emb|CAE21447.1| Putative principal RNA polymerase sigma factor [Prochlorococcus
           marinus str. MIT 9313]
          Length = 461

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 71/237 (29%), Positives = 130/237 (54%), Gaps = 17/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 225 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 284

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++     KP E+ +A + ++
Sbjct: 285 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEM 339

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  D +  EQ + +   R++   
Sbjct: 340 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIESDTENPEQDVAKNLLREDLEG 395

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +L    + L+PRER +   R   ++    TLE +   FEV+RER+RQIEA+A +K++
Sbjct: 396 VL----ATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFEVTRERIRQIEAKALRKLR 448


>gi|157826344|ref|YP_001494064.1| RNA polymerase sigma factor RpoD [Rickettsia akari str. Hartford]
 gi|157800302|gb|ABV75556.1| RNA polymerase sigma factor RpoD [Rickettsia akari str. Hartford]
          Length = 635

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 76/252 (30%), Positives = 128/252 (50%), Gaps = 21/252 (8%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E   L A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 376 ERQTLQAKKDMIEANLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 435

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           TY+ WWI+ A+   I      ++I      T N        + L+   Q + +   +P  
Sbjct: 436 TYATWWIRQAITRAIADQARTIRIPVHMIETIN--------KILRTSRQMLNELGYEP-T 486

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
              IA +L++   +V  +  ++A +  SL   +   D +  Q  D++    D      I+
Sbjct: 487 ATEIANRLSMPLDKVRKV-MKIAKEPISLENPV-GDDSDGGQLGDFI---EDKNAIAPID 541

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              + N R + TR ++ L PRE R+   R         TLE +  +F+V+RER+RQIE++
Sbjct: 542 AAIQSNLREVTTRVLATLTPREERVLRMRFGIGMNTDHTLEEVGQQFKVTRERIRQIESK 601

Query: 276 AFKKVQESIQKQ 287
           A +K+Q  I+ +
Sbjct: 602 ALRKLQHPIRSK 613


>gi|254527154|ref|ZP_05139206.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9202]
 gi|221538578|gb|EEE41031.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9202]
          Length = 313

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 84/302 (27%), Positives = 153/302 (50%), Gaps = 44/302 (14%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYR------EHGDLS-------------------AA 50
           +S Y+  I ++P+L   EE  L  + +      E G L+                   A 
Sbjct: 20  ISWYLQNIGRVPLLTPAEEIELGNQVQKMMILTEDGQLNEKINEFTTQQKRTIKIGRRAK 79

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            R++ ++LRLVV +A  Y+G GL + ++V EG++GL +AV+KFDP RG++ +TY+ WWI+
Sbjct: 80  ERMMKANLRLVVSVAKKYQGKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAFWWIR 139

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRR----LKGHLQAITDNNLKPEQVVAIAKKL 166
            +M   I      +++    +++    ++R+    L   L A+          + IA+ +
Sbjct: 140 QSMTRAIACQSRTIRLPVHLSER--LASIRKVSRDLAHKLGAMPSR-------IEIAEAM 190

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   E+ S+  +     SL+A +N  D  S  +   L+ D + +E   +++ E+K  + 
Sbjct: 191 EIDVEELDSVLRQALSTSSLDAPVNGDDGRS--FLGDLIADSNNEEP--LDQVEQKMHQE 246

Query: 227 MLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L + +S L+ +E+ + + R  L  N   TL  +    EVSRERVRQ+E +A +K++   
Sbjct: 247 QLGKWLSHLSEQEQHVLKLRFGLDANERHTLAEIGRLLEVSRERVRQVELKALRKLRNLT 306

Query: 285 QK 286
           +K
Sbjct: 307 RK 308


>gi|157413850|ref|YP_001484716.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9215]
 gi|157388425|gb|ABV51130.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9215]
          Length = 313

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 84/302 (27%), Positives = 153/302 (50%), Gaps = 44/302 (14%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYR------EHGDLS-------------------AA 50
           +S Y+  I ++P+L   EE  L  + +      E G L+                   A 
Sbjct: 20  ISWYLQNIGRVPLLTPAEEIELGNQVQKMMILTEDGQLNEKIKEFTTQQKRTIKIGRRAK 79

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            R++ ++LRLVV +A  Y+G GL + ++V EG++GL +AV+KFDP RG++ +TY+ WWI+
Sbjct: 80  ERMMKANLRLVVSVAKKYQGKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAFWWIR 139

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRR----LKGHLQAITDNNLKPEQVVAIAKKL 166
            +M   I      +++    +++    ++R+    L   L A+          + IA+ +
Sbjct: 140 QSMTRAIACQSRTIRLPVHLSER--LASIRKVSRDLAHKLGAMPSR-------IEIAEAM 190

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   E+ S+  +     SL+A +N  D  S  +   L+ D + +E   +++ E+K  + 
Sbjct: 191 EIDVEELDSVLRQALSTSSLDAPVNGDDGRS--FLGDLIADSNNEEP--LDQVEQKMHQE 246

Query: 227 MLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L + +S L+ +E+ + + R  L  N   TL  +    EVSRERVRQ+E +A +K++   
Sbjct: 247 QLGKWLSHLSEQEQHVLKLRFGLDANERHTLAEIGRLLEVSRERVRQVELKALRKLRNLT 306

Query: 285 QK 286
           +K
Sbjct: 307 RK 308


>gi|124267677|ref|YP_001021681.1| putative 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 =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 71/242 (29%), Positives = 124/242 (51%), Gaps = 14/242 (5%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 501 EKASRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 560

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL-KGHLQAITDNNLKPEQVVA 161
           TY+ WWI+ A+   I      ++I    +       + RL + HLQ       +P+    
Sbjct: 561 TYATWWIRQAITRSIADQARTIRI--PVHMIETINKMNRLSRQHLQEF---GFEPD-APT 614

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           +A+K+ + E ++  +  ++A  E ++      D + S   D++    D      IE   +
Sbjct: 615 LAEKMEMPEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDTNNTAPIEAAMQ 669

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKK 279
              R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K
Sbjct: 670 AGLRDVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKAIRK 729

Query: 280 VQ 281
           ++
Sbjct: 730 LK 731


>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 =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 124/235 (52%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGN+GLM+AV KF+  RG++ +TY+ WW
Sbjct: 539 AKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNVGLMKAVDKFEYRRGYKFSTYATWW 598

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I     +     N R  + HLQ   +   +P+  V +A+K+ +
Sbjct: 599 IRQAITRSIADQARTIRIPVHMIETINKVN-RISRQHLQ---ETGTEPDAAV-LAEKMEM 653

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E +V  +  ++A  E ++      D + S   D++    D       E   +   R+++
Sbjct: 654 PEDKVRKI-LKIAR-EPISMETPIGDDDDSHLGDFI---EDSGTLAPTEAAMQAGLRDVV 708

Query: 229 TRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E  N  TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 709 KEILDSLTPREAKVLRMRFGIEMANDHTLEEVGKQFDVTRERIRQIEAKALRKLK 763


>gi|203288197|ref|YP_002223212.1| RNA polymerase sigma factor [Borrelia recurrentis A1]
 gi|201085417|gb|ACH94991.1| RNA polymerase sigma factor [Borrelia recurrentis A1]
          Length = 267

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 80/282 (28%), Positives = 150/282 (53%), Gaps = 20/282 (7%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M+I  N ++ +  Y+  +R+  ++  +EE  LAK+ +  G L A ++++ ++LRLV+KI 
Sbjct: 1   MNIFSNEDLNI--YLKSVREHRLITHEEEIELAKQIK-LGSLKAKNQMINANLRLVLKII 57

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y G GL I +++ EGN+GL++A +K+DP +  + +TY+ +WIK ++Q  +     LVK
Sbjct: 58  KRYAGKGLKIEDLIQEGNLGLIRAAEKYDPSKNTKFSTYASFWIKQSLQRALNTKTRLVK 117

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           +        L  N        + + +    P++   I ++ N++ ++ + +   L  + S
Sbjct: 118 VPYRKENLILQIN--------KYLMEEEKSPKK-EDIMERFNLTTAQYVKIIPYLEKEYS 168

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L+  I  S+ NS+     L  D+    +  +E+       N +  +   LN +ER I + 
Sbjct: 169 LDKKIEGSE-NSTLLN--LYEDNSLNPESTLEQNSTLKHLNYILETK--LNEKERYIIKK 223

Query: 246 RRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R   +N     TL+++S+E  +S E VRQIE R  KK++E +
Sbjct: 224 RYNLDNSDKKSTLKDISTELGISSETVRQIEKRVLKKLREEL 265


>gi|292492664|ref|YP_003528103.1| RNA polymerase sigma factor RpoS [Nitrosococcus halophilus Nc4]
 gi|291581259|gb|ADE15716.1| RNA polymerase sigma factor RpoS [Nitrosococcus halophilus Nc4]
          Length = 325

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 80/271 (29%), Positives = 142/271 (52%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE V   R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 57  YLSEIGFAPLLTAEEE-VYHARLAQRGDPAGRKRMIESNLRLVVKIARRYMNRGLALLDL 115

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL+ AV+KFDPE GFR +TY+ WWI+  ++  ++     V++     ++    +
Sbjct: 116 IEEGNLGLIHAVEKFDPEMGFRFSTYATWWIRQTIERALMNQTRTVRLPVHVVKE--IKS 173

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
            +R+   L    +++   E+   +A++L+ S  E+  M        S++    S  + + 
Sbjct: 174 YQRVASKLAQELEHDPTFEE---LAQQLDKSVEEIKRMWSLKDNIASMDTGYRSDQEKT- 229

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQE-NPVTLE 256
              D L  +       L++ ++ ++R  +    +S LN ++R +   R  LQ     TLE
Sbjct: 230 -LLDTLPDEGTPDPTTLLQNDDMQSRLELW---LSQLNNKQREVVIRRFGLQGYESQTLE 285

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +     V+RERVRQI+  A K+++  + K+
Sbjct: 286 QVGQAIGVTRERVRQIQLEALKRLRRIMAKE 316


>gi|294340365|emb|CAZ88746.1| RNA polymerase sigma factor rpoD (Sigma-70) [Thiomonas sp. 3As]
          Length = 778

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 124/235 (52%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGN+GLM+AV KF+  RG++ +TY+ WW
Sbjct: 539 AKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNVGLMKAVDKFEYRRGYKFSTYATWW 598

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I     +     N R  + HLQ   +   +P+  V +A+K+ +
Sbjct: 599 IRQAITRSIADQARTIRIPVHMIETINKVN-RISRQHLQ---ETGTEPDAAV-LAEKMEM 653

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E +V  +  ++A  E ++      D + S   D++    D       E   +   R+++
Sbjct: 654 PEDKVRKI-LKIAR-EPISMETPIGDDDDSHLGDFI---EDSGTLAPTEAAMQAGLRDVV 708

Query: 229 TRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E  N  TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 709 KEILDSLTPREAKVLRMRFGIEMANDHTLEEVGKQFDVTRERIRQIEAKALRKLK 763


>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 =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 77/260 (29%), Positives = 134/260 (51%), Gaps = 17/260 (6%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           +P+ E +   V+ KR  E    S  A   ++ ++LRLV+ IA  Y   GL   +++ EGN
Sbjct: 374 VPLTELK---VINKRMNEGEATSRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGN 430

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I     +     N R  +
Sbjct: 431 IGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMN-RISR 489

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
            HLQ       +P+  + +A K+ + E ++  +  ++A  E ++      D + S   D+
Sbjct: 490 QHLQEF---GFEPDASL-LAAKMEIPEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDF 543

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSE 261
           +    D      IE   +   R+++   +  L PRE ++   R   E  +  TLE +  +
Sbjct: 544 I---EDASNTAPIEAAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMTSDHTLEEVGKQ 600

Query: 262 FEVSRERVRQIEARAFKKVQ 281
           F+V+RER+RQIEA+A +K++
Sbjct: 601 FDVTRERIRQIEAKALRKLK 620


>gi|219847826|ref|YP_002462259.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus
           aggregans DSM 9485]
 gi|219542085|gb|ACL23823.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus
           aggregans DSM 9485]
          Length = 361

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 83/297 (27%), Positives = 143/297 (48%), Gaps = 52/297 (17%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR---------EHGDLS-----------------AAHR 52
           Y+ EI ++P+L  +EE  LA++YR         ++ D +                 A  R
Sbjct: 68  YLQEIGQVPLLTAEEEVELARQYRRGKEARQRLQNEDYANDRERMRLEIEQARGEEARRR 127

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G  +   ++V EGNIGLM+AV+KFD  +G R +TY+ WWI+ A
Sbjct: 128 LIQANLRLVVSVAKKYIGSPMAFMDLVQEGNIGLMRAVEKFDYTKGNRFSTYATWWIRQA 187

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI-------AKK 165
           +   I     L+++    ++     +LRR    L+   +    PE++           K+
Sbjct: 188 VTRAIAEQSRLIRLPVHLSES--IVHLRRAIYRLEQELEREPTPEELAHALNMSLRKVKR 245

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           L  + ++ IS+   L  D+        +D+ ++   +         EQ +++ E      
Sbjct: 246 LLRASTQPISLEQPLNADQEGRVSETLADETAASPMEI-------AEQNMLQAE------ 292

Query: 226 NMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             L  +++ L  RER+I + R   L     TLE + + F ++RER RQIEA A +++
Sbjct: 293 --LNAALNELPERERKILQLRYGLLDGQRRTLEEVGATFGITRERTRQIEAEALRRL 347


>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 =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 85/280 (30%), Positives = 138/280 (49%), Gaps = 44/280 (15%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAH--------RLVTSHLRLVVKIAMGYRGYGLPI 75
           +++ M+EK E+  + +    + DLS A          ++ ++LRLV+ IA  Y   GL  
Sbjct: 324 KRLAMIEKAEKMPINQYKTIYKDLSKAESIARIAKREMIEANLRLVISIAKKYTNRGLQF 383

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AV+KF+  RG++ +TY+ WWI+ A+   I      ++I    +    
Sbjct: 384 LDLIQEGNIGLMKAVEKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI--PVHMIET 441

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRLAGDE- 184
              L R++  L         PE+   +A+++ + E +V          ISM   +  DE 
Sbjct: 442 INKLNRIQRQLLQKMGREPTPEE---LAEEMEMPEDKVRKVMKIAKEPISMETPVGDDED 498

Query: 185 -SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SL   I  S+  S Q       D +G  + +         R ML    S L PRE ++ 
Sbjct: 499 SSLGDFIEDSNILSPQDS----ADLEGMGETV---------REML----STLTPREAKVL 541

Query: 244 EAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
             R  L  N   TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 542 RMRFGLGMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 581


>gi|33861845|ref|NP_893406.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus subsp. pastoris str. CCMP1986]
 gi|33640213|emb|CAE19748.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus subsp. pastoris str. CCMP1986]
          Length = 313

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 85/304 (27%), Positives = 151/304 (49%), Gaps = 40/304 (13%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------EHGDLS----------------- 48
           G   +S Y+  I ++P+L   EE  L  + +      E G L+                 
Sbjct: 16  GNDPISWYLSNIGRVPLLTPAEEIELGNQVQKMMVLTEDGQLNEKTKEFTPQDKRTIKIG 75

Query: 49  --AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  R++ ++LRLVV +A  Y+G GL + ++V EG++GL +AV+KFDP RG++ +TY+ 
Sbjct: 76  RRAKERMMKANLRLVVSVAKKYQGKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAF 135

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFN--LRRLKGHLQAITDNNLKPEQVVAIAK 164
           WWI+ +M   I      +++    +++        R L   L A+          + IA+
Sbjct: 136 WWIRQSMTRAIACQSRTIRLPVHLSERLATIRKISRELAHKLGAMPSR-------IEIAE 188

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            + +   E+ S+  +     SL+A +N  D  S  +   L+ D + +E   +++ E+K  
Sbjct: 189 AMEIDVEELDSVLRQALSTSSLDAPVNGDDGRS--FLGDLIADSNNEEP--LDQVEQKMH 244

Query: 225 RNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +  L + +S L+ +E+ + + R  L  N   TL  +    EVSRERVRQ+E +A +K++ 
Sbjct: 245 QEQLGKWLSHLSEQEQHVLKLRFGLDGNERHTLAEIGRLLEVSRERVRQVELKALRKLRN 304

Query: 283 SIQK 286
             +K
Sbjct: 305 LTRK 308


>gi|150005266|ref|YP_001300010.1| RNA polymerase sigma factor rpoD [Bacteroides vulgatus ATCC 8482]
 gi|212694793|ref|ZP_03302921.1| hypothetical protein BACDOR_04327 [Bacteroides dorei DSM 17855]
 gi|237710938|ref|ZP_04541419.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 9_1_42FAA]
 gi|237727237|ref|ZP_04557718.1| RNA polymerase sigma factor rpoD [Bacteroides sp. D4]
 gi|254883735|ref|ZP_05256445.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 4_3_47FAA]
 gi|265750524|ref|ZP_06086587.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 3_1_33FAA]
 gi|294777100|ref|ZP_06742557.1| putative RNA polymerase sigma factor RpoD [Bacteroides vulgatus
           PC510]
 gi|319643459|ref|ZP_07998082.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 3_1_40A]
 gi|149933690|gb|ABR40388.1| RNA polymerase sigma factor rpoD [Bacteroides vulgatus ATCC 8482]
 gi|212662647|gb|EEB23221.1| hypothetical protein BACDOR_04327 [Bacteroides dorei DSM 17855]
 gi|229434093|gb|EEO44170.1| RNA polymerase sigma factor rpoD [Bacteroides dorei 5_1_36/D4]
 gi|229454782|gb|EEO60503.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 9_1_42FAA]
 gi|254836528|gb|EET16837.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 4_3_47FAA]
 gi|263237420|gb|EEZ22870.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 3_1_33FAA]
 gi|294448969|gb|EFG17512.1| putative RNA polymerase sigma factor RpoD [Bacteroides vulgatus
           PC510]
 gi|317384864|gb|EFV65820.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 3_1_40A]
          Length = 286

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 79/274 (28%), Positives = 148/274 (54%), Gaps = 22/274 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI +  ++  +EE  LA+R R+ GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGREDLITVEEEVELAQRIRK-GDRVALEKLTRANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     +V++    NQ   
Sbjct: 77  PDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL--PLNQVGS 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
              + +     +   +    PE+   +A +L +   + IS   +++G   S++A     +
Sbjct: 135 LNKISKAFSKFEQENERRPSPEE---LADELEIP-VDKISDTLKVSGRHISVDAPFVEGE 190

Query: 195 KNSSQWQDWLVYDHD--GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI---FEARRLQ 249
            NS    D LV D        ++ E   R+     + R++S L  RE+ I   F     Q
Sbjct: 191 DNS--LLDVLVNDDSPMADRSLVNESLARE-----IDRALSTLTEREKDIIQMFFGINTQ 243

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           E  +TLE +  +F ++RERVRQI+ +A ++++++
Sbjct: 244 E--MTLEEIGDKFGLTRERVRQIKEKAIRRLRQN 275


>gi|238060708|ref|ZP_04605417.1| RNA polymerase sigma factor rpoD [Micromonospora sp. ATCC 39149]
 gi|237882519|gb|EEP71347.1| RNA polymerase sigma factor rpoD [Micromonospora sp. ATCC 39149]
          Length = 331

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 87/307 (28%), Positives = 145/307 (47%), Gaps = 68/307 (22%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH-------------GDLS--------AAHR 52
           Y+HEI + P+L+   E  L+K      Y EH              DL         A   
Sbjct: 40  YLHEISRTPLLDAATEVDLSKSIEAGLYAEHLLETDRVPAGVDRDDLERVAAEGERAKDL 99

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            + ++LRLVV IA  Y   G+P+ +++ EGN GL++AV+KFD ERGF+ +TY+ WWI+ A
Sbjct: 100 FIRANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQA 159

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT---DNNLKPEQVVAIAKKLNVS 169
           +   I +    V++        L  ++ R++   + +T    ++ +PEQ   IA  L V+
Sbjct: 160 ISRAIAQQERTVRLPV-----HLVEDVNRMRNAARQLTRELGSDPEPEQ---IAAALGVT 211

Query: 170 ----------ESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
                       + +S++  +   GD +L  L+  SD  S              E +++ 
Sbjct: 212 VERVNELVRWSQDTVSLDTPVGDDGDTNLGDLVADSDAPSP-------------EDIVLT 258

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEAR 275
             ER+    +L      L+ R   I  AR   E+    +L  ++S F +SRER+RQ+E +
Sbjct: 259 GLERQRIEGLLNH----LDDRSAGIMRARYGLEDGREHSLTEVASRFSLSRERIRQLEIQ 314

Query: 276 AFKKVQE 282
           A  +++E
Sbjct: 315 ALGRLRE 321


>gi|291287615|ref|YP_003504431.1| RNA polymerase, sigma 32 subunit, RpoH [Denitrovibrio acetiphilus
           DSM 12809]
 gi|290884775|gb|ADD68475.1| RNA polymerase, sigma 32 subunit, RpoH [Denitrovibrio acetiphilus
           DSM 12809]
          Length = 301

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 76/277 (27%), Positives = 144/277 (51%), Gaps = 16/277 (5%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E  L  Y++ I     + K +E+ + +R  + GD  A + L+  +L+ VV IA  YR  G
Sbjct: 30  ETSLKHYLNSISAYKPMTKAQEFAIGERI-QAGDEDALNTLILCNLKFVVSIANRYRNTG 88

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LPI++++++GN+GL++A K+FD  +  +  +Y++WWI+ ++ + +      VK+     Q
Sbjct: 89  LPIADIINQGNLGLVEAAKRFDHTKDVKFISYAVWWIRQSIIQALAEQSGTVKLPI--KQ 146

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALIN 191
             + +   ++ G  + +     +      +A++L + E+++ ++  R++ +  SL A I 
Sbjct: 147 AGILY---KINGATEKLNKKLNREPTASELAEQLEMDEADIENV-LRVSRNYLSLEAPIK 202

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--Q 249
             +  S  + D L       E+ +I     K  +  L   +  L+ RE +I E R    +
Sbjct: 203 DGEDRS--FIDLLESGTKDIEEDIIS----KTLKTALDDIVDELDERESQIIEWRFGLNE 256

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E P TLE +    ++SRERVRQ+E RA  K+++   K
Sbjct: 257 EAPKTLEEIGELMDISRERVRQLETRALSKLRKKAMK 293


>gi|313892356|ref|ZP_07825948.1| RNA polymerase sigma factor RpoD [Dialister microaerophilus UPII
           345-E]
 gi|313119215|gb|EFR42415.1| RNA polymerase sigma factor RpoD [Dialister microaerophilus UPII
           345-E]
          Length = 393

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 77/275 (28%), Positives = 132/275 (48%), Gaps = 23/275 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHR-----------LVTSHLRLVVKIAMG 67
           Y+ E    P+L  +EE  LAK+  +   L A              +  ++LRLVV IA  
Sbjct: 119 YLRECGATPLLSAEEEMTLAKQIEKGKMLDATEEDKLRAEDAKKEMANANLRLVVSIAKK 178

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y G G+P  +++ EGNIGL++AV KFD ++G++ +TY+ WWI+ A+   I      +++ 
Sbjct: 179 YPGRGMPFLDLIQEGNIGLLKAVDKFDYKKGYKFSTYATWWIRQAITRSIADQARTIRVP 238

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
               +     N R  +  LQ         E    +AK++ +S  ++     + A  + ++
Sbjct: 239 VHMVETINKMN-RIGRKFLQEFGREASNEE----LAKEMGISVEKI--REAKKAAQDPIS 291

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
                 +K  S   D++    D +     E+     RR  + + ++ L  RE+ +   R 
Sbjct: 292 LETPIGEKEDSHLGDFI---EDQKTSSPEEEAAATMRREQIYKLLNELTEREKGVLALRF 348

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++  P TLE +   F V+RER+RQIE +A KK+
Sbjct: 349 GMDDGTPRTLEEVGKYFGVTRERIRQIEGKALKKL 383


>gi|294673146|ref|YP_003573762.1| RNA polymerase sigma-70 factor [Prevotella ruminicola 23]
 gi|294474130|gb|ADE83519.1| RNA polymerase sigma-70 factor [Prevotella ruminicola 23]
          Length = 290

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 79/292 (27%), Positives = 146/292 (50%), Gaps = 36/292 (12%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKI 64
           SI    E  L++Y+ +I +IPM+  ++E  LA+  R+ G     A  +LV ++LR VV +
Sbjct: 9   SITTRTEESLNKYLTDISRIPMITPEQEVELAQTIRKGGRTGAKAKEKLVNANLRFVVSV 68

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y+  G+P+ +++SEGN+GL+ A  KFD  RGF+  +Y++WWI+ ++ + I     +V
Sbjct: 69  AKQYQHQGIPLIDLISEGNVGLITAADKFDETRGFKFISYAIWWIRQSILQAIADYSGMV 128

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI-------AKKLNVSESEVISMN 177
           +     +Q  +   ++            N   E++  I        +K   SE+ V S++
Sbjct: 129 R--RPQSQIAISNKIKNATNAFMLKNQRNPSAEELSEIISLEIEKIEKAIQSEAHVASID 186

Query: 178 CRLAGDESL---NALINSSDKNSSQWQDWLVYDHDGQ---EQVLIEKEERKNRRNMLTRS 231
             ++ D++    +++ ++++  S +  D+     D       VL E+E     R ++ +S
Sbjct: 187 APISDDDTTTMADSIASTAEYASDRKVDYESMCSDVMLVLGAVLSERE-----RAIVVQS 241

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +  P ER              L+++ S   +SRERVRQI  R   K+++S
Sbjct: 242 FGIGCP-ER-------------GLDDIGSSMGLSRERVRQIRERGLDKIRKS 279


>gi|153952229|ref|YP_001397920.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           doylei 269.97]
 gi|152939675|gb|ABS44416.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           doylei 269.97]
          Length = 622

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 81/250 (32%), Positives = 123/250 (49%), Gaps = 41/250 (16%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ +RG++ +TY+ WW
Sbjct: 381 AKGRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWW 440

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T NQ     N + ++ HLQ     + K   V  IAK
Sbjct: 441 IRQAISRAIADQARTIRIPIHMIETINQ----IN-KIIREHLQ----KDGKEPNVSVIAK 491

Query: 165 KLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           ++ +S  +V          IS+   +  ++         D+NS    D ++ D D +EQ+
Sbjct: 492 EVGLSIDKVKQVIKITKEPISLEAPIGNEDDGKFGDFVEDRNSLSPIDHILKD-DLKEQI 550

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQ 271
                            +  LN RE+ +   R      E+  TLE +  E  V+RERVRQ
Sbjct: 551 --------------DEVLDQLNDREKAVIRMRFGLMDDESDRTLEEIGKELNVTRERVRQ 596

Query: 272 IEARAFKKVQ 281
           IE+ A KK++
Sbjct: 597 IESSAIKKLK 606


>gi|87123382|ref|ZP_01079233.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9917]
 gi|86169102|gb|EAQ70358.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9917]
          Length = 293

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 85/288 (29%), Positives = 140/288 (48%), Gaps = 37/288 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLA--------------------KRYREHGDLSAAHRLVTSHL 58
           Y+  I ++P+L   EE  LA                    +R++      A  R++ ++L
Sbjct: 9   YLSSIGRVPLLTAAEEIELAHHVQAMKQLLELPEAERTPRQRHQIRMGKRARDRMMAANL 68

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+  M   I 
Sbjct: 69  RLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTRAID 128

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLK---GHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
            S   +++    ++K     +RR+     H      N L+    + I  K      ++IS
Sbjct: 129 NSARTIRLPIHISEK--LSKMRRISRELSHRFGRQPNRLELAHAMGIEPK---DLEDLIS 183

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
            +   A   SL+A     +  S+  +  L+ D +G E   +E  +R  ++  L   ++ L
Sbjct: 184 QSAPCA---SLDAHARGEEDRSTLGE--LIPDPNGAEP--MEGMDRSIQKEHLGGWLAQL 236

Query: 236 NPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           N RE++I   R     E P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 237 NDREQKILRLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 284


>gi|329121328|ref|ZP_08249954.1| DNA-directed RNA polymerase sigma subunit RpoD [Dialister
           micraerophilus DSM 19965]
 gi|327469737|gb|EGF15203.1| DNA-directed RNA polymerase sigma subunit RpoD [Dialister
           micraerophilus DSM 19965]
          Length = 396

 Score =  101 bits (252), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 77/275 (28%), Positives = 132/275 (48%), Gaps = 23/275 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHR-----------LVTSHLRLVVKIAMG 67
           Y+ E    P+L  +EE  LAK+  +   L A              +  ++LRLVV IA  
Sbjct: 122 YLRECGATPLLSAEEEMTLAKQIEKGKMLDATEEDKLRAEDAKKEMANANLRLVVSIAKK 181

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y G G+P  +++ EGNIGL++AV KFD ++G++ +TY+ WWI+ A+   I      +++ 
Sbjct: 182 YPGRGMPFLDLIQEGNIGLLKAVDKFDYKKGYKFSTYATWWIRQAITRSIADQARTIRVP 241

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
               +     N R  +  LQ         E    +AK++ +S  ++     + A  + ++
Sbjct: 242 VHMVETINKMN-RIGRKFLQEFGREASNEE----LAKEMGISVEKI--REAKKAAQDPIS 294

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
                 +K  S   D++    D +     E+     RR  + + ++ L  RE+ +   R 
Sbjct: 295 LETPIGEKEDSHLGDFI---EDQKTSSPEEEAAATMRREQIYKLLNELTEREKGVLALRF 351

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++  P TLE +   F V+RER+RQIE +A KK+
Sbjct: 352 GMDDGTPRTLEEVGKYFGVTRERIRQIEGKALKKL 386


>gi|189461487|ref|ZP_03010272.1| hypothetical protein BACCOP_02146 [Bacteroides coprocola DSM 17136]
 gi|198275894|ref|ZP_03208425.1| hypothetical protein BACPLE_02077 [Bacteroides plebeius DSM 17135]
 gi|189431821|gb|EDV00806.1| hypothetical protein BACCOP_02146 [Bacteroides coprocola DSM 17136]
 gi|198271523|gb|EDY95793.1| hypothetical protein BACPLE_02077 [Bacteroides plebeius DSM 17135]
          Length = 286

 Score =  101 bits (251), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 79/274 (28%), Positives = 148/274 (54%), Gaps = 22/274 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI +  ++  +EE  LA+R R+ GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGREDLITVEEEVELAQRIRK-GDRIALEKLTRANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     +V++    NQ   
Sbjct: 77  PDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL--PLNQVGS 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
              + +     +   +    PE+   +A +L +   + IS   +++G   S++A     +
Sbjct: 135 LNKISKAFSKFEQENERRPSPEE---LADELEIP-VDKISDTLKVSGRHISVDAPFVEGE 190

Query: 195 KNSSQWQDWLVYDHD--GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI---FEARRLQ 249
            NS    D LV D        ++ E   R+     + R++S L  RE+ I   F     Q
Sbjct: 191 DNS--LLDVLVNDDSPMADRSLVNESLSRE-----IDRALSTLTEREKDIIQMFFGINTQ 243

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           E  +TLE +  +F ++RERVRQI+ +A ++++++
Sbjct: 244 E--MTLEEIGDKFGLTRERVRQIKEKAIRRLRQN 275


>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 =  101 bits (251), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 124/236 (52%), Gaps = 14/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 515 AKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 574

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL-KGHLQAITDNNLKPEQVVAIAKKLN 167
           I+ A+   I      ++I    +       + RL + HLQ       +P+   ++A+K+ 
Sbjct: 575 IRQAITRSIADQARTIRI--PVHMIETINKMNRLSRQHLQEF---GFEPD-APSLAEKME 628

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + E ++  +  ++A  E ++      D + S   D++    D      IE   +   R++
Sbjct: 629 MPEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDTNNTAPIEAAMQSGLRDV 683

Query: 228 LTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 684 VRDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKAIRKLK 739


>gi|158833963|gb|ABW81787.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
          Length = 225

 Score =  101 bits (251), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 59/149 (39%), Positives = 91/149 (61%), Gaps = 6/149 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD S+  R++ S+LRLVVKI+  Y   GLP+ ++
Sbjct: 8   YLGEIGYSPLLTAEEEIYFARRVL-CGDESSRRRMIESNLRLVVKISRRYINRGLPLLDL 66

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 67  IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI-VKELNVY 125

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           LR  +  L    D++  PE+   IA++LN
Sbjct: 126 LRAAR-ELSHKLDHDPSPEE---IAEQLN 150


>gi|303229406|ref|ZP_07316196.1| RNA polymerase sigma factor RpoD [Veillonella atypica
           ACS-134-V-Col7a]
 gi|303230872|ref|ZP_07317619.1| RNA polymerase sigma factor RpoD [Veillonella atypica
           ACS-049-V-Sch6]
 gi|302514632|gb|EFL56627.1| RNA polymerase sigma factor RpoD [Veillonella atypica
           ACS-049-V-Sch6]
 gi|302515942|gb|EFL57894.1| RNA polymerase sigma factor RpoD [Veillonella atypica
           ACS-134-V-Col7a]
          Length = 388

 Score =  101 bits (251), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 85/303 (28%), Positives = 144/303 (47%), Gaps = 39/303 (12%)

Query: 2   NRKNMSI------IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHR--- 52
           + KN+SI       VN +  +  Y+ EI ++P+L   EE VLAK+     +  A ++   
Sbjct: 88  SEKNISIDLSVDASVNIDDPVRMYLKEIGRVPLLSADEEIVLAKQIEAGAEEDATYKEIQ 147

Query: 53  --------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
                   LV ++LRLVV IA  Y G G+   +++ EGN+GL++AV KFD  +G++ +TY
Sbjct: 148 LSKKAKKKLVDANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVDKFDYTKGYKFSTY 207

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + WWI+ A+   I      ++I    +       L R+   L         PE+   IA+
Sbjct: 208 ATWWIRQAITRAIADQARTIRI--PVHMVETINKLIRISRQLLQDKGREPTPEE---IAE 262

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL-----VYDHDGQEQVLIEKE 219
            + ++   V  +        SL   I   ++  S   D++     V   D    +L++++
Sbjct: 263 GMGITAERVREIQKIAQEPVSLETPIG--EEEDSHLGDFIEDQDAVAPDDAASYILLQEQ 320

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAF 277
                   +    + L  RE+++   R  L++  P TLE +   F V+RER+RQIE +A 
Sbjct: 321 --------IEDVFTCLTDREQQVLILRFGLKDGKPRTLEEVGQHFNVTRERIRQIEGKAL 372

Query: 278 KKV 280
            K+
Sbjct: 373 TKL 375


>gi|197247378|ref|YP_002147821.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
 gi|197211081|gb|ACH48478.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
          Length = 269

 Score =  101 bits (251), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 46/108 (42%), Positives = 73/108 (67%), Gaps = 1/108 (0%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRL 167


>gi|160937287|ref|ZP_02084649.1| hypothetical protein CLOBOL_02177 [Clostridium bolteae ATCC
           BAA-613]
 gi|158439851|gb|EDP17600.1| hypothetical protein CLOBOL_02177 [Clostridium bolteae ATCC
           BAA-613]
          Length = 298

 Score =  101 bits (251), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 81/269 (30%), Positives = 141/269 (52%), Gaps = 40/269 (14%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY--GLPISEVVSEGNI 84
           P+L K+EE  LA   +E  D  A  ++++S+LRLV+  A  Y  Y   L + +++ EGN+
Sbjct: 40  PLLTKEEEIELAYLIQEGSD-EARQKMISSNLRLVINQAKKYVTYTQSLTLLDLIQEGNL 98

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF--NLRRL 142
           GL++AV+K++PE GFR +TY+ WWIK A    I R+ S++     A +  + F  +++++
Sbjct: 99  GLIKAVEKYNPELGFRFSTYASWWIKQA----ITRAISVLD---KAIRLPVHFCEDIQKV 151

Query: 143 KGHLQAITDNN--LKPEQVVAIA-------KKLNVSESEVISMNCRLAGDESLNALINSS 193
           K     I   N  + PE++  I        +K+ ++ +  IS+   +  + +L   +  +
Sbjct: 152 KRATHEIMQQNDIVTPEKLKDITGFSEGKIEKILMNMNHTISLETPVGEEATLGDFVEDT 211

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QEN 251
              S             +EQ +    +R+     ++R M  L PRE+ I   R     +N
Sbjct: 212 LTPSI------------EEQAMENAMQRE-----ISRQMECLRPREQTILALRFGLNGQN 254

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKV 280
           P TLE +  +  V+RER+RQIE +A +K+
Sbjct: 255 PHTLEEVGKQMGVTRERIRQIEMKALRKL 283


>gi|332885662|gb|EGK05908.1| hypothetical protein HMPREF9456_02172 [Dysgonomonas mossii DSM
           22836]
          Length = 286

 Score =  101 bits (251), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 76/272 (27%), Positives = 149/272 (54%), Gaps = 18/272 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI +  ++  +EE  LA+  +  GD +A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGREDLITVEEEVELAQAIK-KGDRAALEKLTRANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     +V++    NQ   
Sbjct: 77  PDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL--PLNQ--- 131

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
             +L ++          N +      +A++L++   + I+ + +++G   S++A     +
Sbjct: 132 VGSLNKISKAFSKFEQENERKPSAEELAEQLDIP-VDKIADSLKVSGRHISMDAPFVEGE 190

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI---FEARRLQEN 251
            NS    D LV D      +   K   ++ +  + R++S L  RE  I   F     QE 
Sbjct: 191 DNS--LLDVLVNDD---APIADRKLINESLQQEIERALSTLTERESEIIKMFFGIGYQE- 244

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +TLE +  +F+++RERVRQI+ +A K+++++
Sbjct: 245 -MTLEEIGDKFQLTRERVRQIKEKAIKRLRQN 275


>gi|21220928|ref|NP_626707.1| RNA polymerase principal sigma factor [Streptomyces coelicolor
           A3(2)]
 gi|289771799|ref|ZP_06531177.1| RNA polymerase principal sigma factor hrdA [Streptomyces lividans
           TK24]
 gi|19856645|sp|P18182|HRDA_STRCO RecName: Full=RNA polymerase principal sigma factor hrdA
 gi|6759560|emb|CAB69753.1| RNA polymerase principal sigma factor [Streptomyces coelicolor
           A3(2)]
 gi|289701998|gb|EFD69427.1| RNA polymerase principal sigma factor hrdA [Streptomyces lividans
           TK24]
          Length = 396

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 86/294 (29%), Positives = 140/294 (47%), Gaps = 42/294 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ EI +IP+L   EE  LA+R  E G  +                           A  
Sbjct: 103 YLREIGRIPLLSAAEEVDLARRV-EAGLFAEEKLRCSPGLDDRLALDLDRLVVLGRLAKR 161

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY+ WWI+ 
Sbjct: 162 RLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIRQ 221

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           AM   +      +++     +  L   + R++  +         P++V A    L+++  
Sbjct: 222 AMSRALADQARTIRVPVHVVE--LINRVVRVQRRMLQERGCEPTPQEVAA---HLDLA-P 275

Query: 172 EVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           E +    RLA +  SL+A +   D  +    D +    DG     +E       R  L  
Sbjct: 276 ERVGEVLRLAQEPVSLHAPVGEEDDVA--LGDLI---EDGDAASPVESAAFLLLRQHLEA 330

Query: 231 SMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            +S L  RER++ + R       P TLE +   F V+RER+RQIE++   K+++
Sbjct: 331 VLSTLGERERKVVQLRYGLADGRPRTLEEIGRLFGVTRERIRQIESKTLSKLRD 384


>gi|158833975|gb|ABW81793.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833979|gb|ABW81795.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
          Length = 225

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 59/149 (39%), Positives = 89/149 (59%), Gaps = 6/149 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L   EE   A+R    GD S+  R++ S+LRLVVKI+  Y   GLP+ ++
Sbjct: 8   YLSEIGYSPLLTAAEEIYFARRVL-CGDESSRRRMIESNLRLVVKISRRYINRGLPLLDL 66

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY  WWI+  ++  I+     +++      K L   
Sbjct: 67  IEEGNLGLIRAVEKFDPERGFRFSTYDTWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 125

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           LR  +  L    D++  PE+   IA++LN
Sbjct: 126 LRAAR-ELSHKLDHDPSPEE---IAEQLN 150


>gi|256396128|ref|YP_003117692.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Catenulispora
           acidiphila DSM 44928]
 gi|256362354|gb|ACU75851.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Catenulispora
           acidiphila DSM 44928]
          Length = 390

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 79/237 (33%), Positives = 126/237 (53%), Gaps = 14/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  RL+ ++LRLVV IA  Y G G+ I ++V EGN+GL++AV+KFD  RG++ +TY+ W
Sbjct: 152 AAKRRLIEANLRLVVSIAKRYLGRGMSILDLVQEGNLGLIRAVEKFDYTRGYKFSTYATW 211

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ AM   +      +++    +   L   + RL+  L  + +N ++P     IA+ L 
Sbjct: 212 WIRQAMSRALADQARTIRV--PVHVVELMNRVVRLQRRL--LQENGVEPTP-DDIAEVLG 266

Query: 168 VSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           V+   V+ +  RLA +  SL+A +   D  +    D L+ D D       +       R 
Sbjct: 267 VAVERVVEV-LRLAQEPVSLHAPVGEEDDVA--LGD-LIEDADAVSPA--DSVAVVMLRE 320

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L   +S L  RE+R+ + R       P TLE +   F V+RER+RQIEA+   K++
Sbjct: 321 HLDALLSTLGEREKRVVQLRYGLTDGQPHTLEEIGRTFGVTRERIRQIEAKTLAKLR 377


>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 =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 69/236 (29%), Positives = 122/236 (51%), Gaps = 12/236 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 562 DAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 621

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I     +     N R  + HLQ       +P+  + +A K+ 
Sbjct: 622 WIRQAITRSIADQARTIRIPVHMIETINKMN-RISRQHLQEF---GFEPDASI-LAAKME 676

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + E ++  +  ++A  E ++      D + S   D++    D      I+   +   R++
Sbjct: 677 IPEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDSNNTAPIDAAMQAGLRDV 731

Query: 228 LTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 732 VKDILDGLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLK 787


>gi|229496411|ref|ZP_04390127.1| RNA polymerase sigma-70 factor [Porphyromonas endodontalis ATCC
           35406]
 gi|229316639|gb|EEN82556.1| RNA polymerase sigma-70 factor [Porphyromonas endodontalis ATCC
           35406]
          Length = 287

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 80/274 (29%), Positives = 142/274 (51%), Gaps = 27/274 (9%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI +  +++  EE  LA+  R  G+  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGREELIDVDEEVRLAQEIR-RGNRRAQDKLTRANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
            +++ EGN+GL++A +KFD  RGF+  +Y++WWI+ ++      Q  I+R   L ++G  
Sbjct: 77  PDLIDEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVR-LPLNQVGAQ 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
           A          ++K  ++     N +   +  +A  L+ SE +V       +   S++A 
Sbjct: 136 A----------KIKKAIEQFEQENERRPSIAELAIILDQSEEKVAVTLKSFSKHVSIDAP 185

Query: 190 INSSDKNSSQWQDWLV-YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA-RR 247
               + NS    D LV  D    ++ L+    R +    + R +S L+ RE  I +    
Sbjct: 186 FVDGEDNS--LLDVLVNEDAPSTDRSLM----RDSLNTEIDRVLSTLSEREAEIIKLFFG 239

Query: 248 LQENP-VTLENLSSEFEVSRERVRQIEARAFKKV 280
           +  NP +TLE +  +F ++RERVRQI+ +A +K+
Sbjct: 240 IGPNPEMTLEEIGDKFGLTRERVRQIKEKAIRKL 273


>gi|213417289|ref|ZP_03350433.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
          Length = 277

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 46/108 (42%), Positives = 73/108 (67%), Gaps = 1/108 (0%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRL 167


>gi|302392313|ref|YP_003828133.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acetohalobium
           arabaticum DSM 5501]
 gi|302204390|gb|ADL13068.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acetohalobium
           arabaticum DSM 5501]
          Length = 275

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 85/272 (31%), Positives = 148/272 (54%), Gaps = 20/272 (7%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +++Y  +I    +L K+EE  LA++  + GD  A  +L+  +LRLVV IA  ++G GL +
Sbjct: 5   INQYYQDISH-DLLTKEEEISLARKA-QAGDSEAKDKLIRHNLRLVVSIANKHQGKGLDL 62

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK-- 133
            ++V EGNIGL+ AV+KFDP++G+R +TY+ WWIK  +   I      ++I     QK  
Sbjct: 63  QDLVQEGNIGLITAVEKFDPDKGYRFSTYASWWIKQRVTRAIANQGKTIRIPVHVWQKTN 122

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL--IN 191
           ++F    ++K  LQ         E+   IA++ ++S  E I    R+  D++L +L    
Sbjct: 123 KIF----KVKDDLQTELGREPTAEE---IAEETDIS-LEKIKEVMRVITDQNLASLNQFV 174

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQE 250
             D+++   Q  LV    G     +E   ++  +  L   ++ L+ RE  +   R  L++
Sbjct: 175 GDDRDTELGQ--LV--PSGSADDPVEGTSQQLLKEDLEELLTELSDREAEVIRLRFGLRD 230

Query: 251 N-PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           + P TL+ +  E  V+RER+RQI+ +A  +++
Sbjct: 231 SRPRTLKEVGEELGVTRERIRQIQLKALNRLK 262


>gi|168009564|ref|XP_001757475.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162691169|gb|EDQ77532.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 591

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 73/245 (29%), Positives = 131/245 (53%), Gaps = 36/245 (14%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           ++V S+LRLVV I   Y+G G+ + +++ EG++GL++  +KFDP++GF+ +TY+ WWI+ 
Sbjct: 353 KMVNSNLRLVVSIVKNYQGRGMTLPDLIQEGSMGLIRGAEKFDPDKGFKFSTYAHWWIRQ 412

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRL-KGHLQAITDNNLKP--EQVVAIAK---- 164
           A+   I     ++++        L+  + R+ K     I ++  +P  E+V  +      
Sbjct: 413 AVTRAIADQSRIIRLPI-----HLYEVISRINKAKKMLIQEHGRQPRDEEVAELVGMSVE 467

Query: 165 --KLNVSESEVISMNCRLAG---DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             K  V  ++  S   RL G   D+S+  +I  +DK+    +D L+       QVL    
Sbjct: 468 KLKFIVKSAKTPSSMDRLIGKEKDQSIGEMI--ADKDVESPEDDLI------RQVL---- 515

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
                +  +   +  LNPRER +   R   ++    TLE + + F+V+RER+RQIEA+A 
Sbjct: 516 -----KQDVDGVLCTLNPREREVLRLRFGLDDGQSRTLEEIGTLFKVTRERIRQIEAKAM 570

Query: 278 KKVQE 282
           +K+++
Sbjct: 571 RKLRQ 575


>gi|149916815|ref|ZP_01905317.1| RNA polymerase sigma factor RpoD [Plesiocystis pacifica SIR-1]
 gi|149822532|gb|EDM81921.1| RNA polymerase sigma factor RpoD [Plesiocystis pacifica SIR-1]
          Length = 421

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 78/264 (29%), Positives = 131/264 (49%), Gaps = 22/264 (8%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           YV   R   H    + ++ V ++LRLVV IA  +    +P+ ++V EGN+GLM+AV +FD
Sbjct: 166 YVQKVRSSGHALRWSKNKFVKANLRLVVTIARRFDHGLMPLQDLVQEGNLGLMKAVDRFD 225

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT--TANQKRLFFNLRRLKGHLQAITDN 152
           P RG+R +TY+ WWI+ A+   +      V++    +A+ +R    LRR+   L+A T  
Sbjct: 226 PTRGYRFSTYATWWIRHAINRALANKGRTVRLPAHVSADLQR----LRRVTRELEAKTGE 281

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PEQ   +A+   +S++ V  ++ +L  D +++    S D ++    D L    D   
Sbjct: 282 TPTPEQ---LAQAAGLSKTRVRKLS-KLTLDPTVSLDAPSHDDDARGLLDRL---EDASV 334

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIF---------EARRLQENPVTLENLSSEFE 263
            V  +  E +     L  ++  L P E  I          EA  +   P+TL  L     
Sbjct: 335 PVAADILEHQALNEHLRDALYNLQPIELDILKRRYGIATSEAESVDFEPMTLRQLGERHS 394

Query: 264 VSRERVRQIEARAFKKVQESIQKQ 287
           +SRER+RQ++ RA  K++    ++
Sbjct: 395 LSRERIRQLQERALTKLRREFARR 418


>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 =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 76/250 (30%), Positives = 117/250 (46%), Gaps = 27/250 (10%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           KR RE     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG
Sbjct: 434 KRARE-----AKREMTVANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 488

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIG-----TTANQKRLFFNLRRLKGHLQAITDNN 153
           ++ +TY+ WWI+ A+   I      ++I      T     R+   + +  GH        
Sbjct: 489 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGHEPDAATLA 548

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
           LK E      +K+     E ISM   +  DE             S   D++    DG   
Sbjct: 549 LKMEIPEDKIRKIMKIAKEPISMETPIGDDE------------DSHLGDFI---EDGNTL 593

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQ 271
              E     + R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQ
Sbjct: 594 APAEAALHDSMRDVVKDVLDSLTPREAKVLRMRFGVEMSTDHTLEEVGKQFDVTRERIRQ 653

Query: 272 IEARAFKKVQ 281
           IEA+A +K++
Sbjct: 654 IEAKALRKMR 663


>gi|72382695|ref|YP_292050.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Prochlorococcus marinus str. NATL2A]
 gi|124026414|ref|YP_001015529.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. NATL1A]
 gi|72002545|gb|AAZ58347.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Prochlorococcus marinus str. NATL2A]
 gi|123961482|gb|ABM76265.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. NATL1A]
          Length = 313

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 86/298 (28%), Positives = 150/298 (50%), Gaps = 36/298 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYR------EHGDLSAAHRLVTSH------------ 57
           +S Y+  I ++P+L   EE  L  + +      E G +    +  TSH            
Sbjct: 20  ISWYLSSIGRVPLLTPAEEIELGNQVQTLMSLTEDGQIKEQSKEFTSHQRRLIRIGRRAK 79

Query: 58  -------LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
                  LRLVV +A  Y+G GL + ++V EG++GL +AV+KFDP RG++ +TY+ WWI+
Sbjct: 80  ERMMKANLRLVVSVAKKYQGKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAFWWIR 139

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            +M   I      +++    +++     +R++   L         P + + IA+ + +  
Sbjct: 140 QSMTRAIACQSRTIRLPVHLSER--LATIRKVS--LDLAHKLGAMPSR-IEIAEAMEIEL 194

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            E+ S+  +     SL+A +N  D+  S   D L+ D  G+E   ++K E+K  +  L R
Sbjct: 195 EELDSILRQALTTSSLDAPVN-GDEGRSFLGD-LIADGSGEEP--LDKVEQKIHQEQLGR 250

Query: 231 SMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +S L+ +E+ +   R  L+ N   TL  +    +VSRERVRQ+E +A +K++   +K
Sbjct: 251 WLSHLSEQEQHVIRLRFGLEGNERHTLAEIGRLLQVSRERVRQVELKALRKLRNLTRK 308


>gi|156744261|ref|YP_001434390.1| RpoD family RNA polymerase sigma factor [Roseiflexus castenholzii
           DSM 13941]
 gi|156235589|gb|ABU60372.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus
           castenholzii DSM 13941]
          Length = 399

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 84/299 (28%), Positives = 138/299 (46%), Gaps = 56/299 (18%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHR-------------------------- 52
           Y+ EI ++P+L  ++E +LAK       + A HR                          
Sbjct: 106 YLQEIGQVPLLSAEQEVMLAKA------MEAGHRARRALECEEYSSWQERMMYEQQVAQG 159

Query: 53  ------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                 L+ ++LRLVV IA  Y  YGL + ++V EGNIGLM+AV+KFD  +G + +TY+ 
Sbjct: 160 NEARQHLIQANLRLVVSIAKKYTSYGLTMMDLVQEGNIGLMRAVEKFDYTKGHKFSTYAT 219

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      +++     +      ++R    LQ +      PE+   IA  +
Sbjct: 220 WWIRQAITRAIADQSRTIRLPVHMGEA--ISQVKRASHKLQQMMQREPTPEE---IADAM 274

Query: 167 NVSESEVISMNCRLAGDESLNAL---INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
            +S ++V     R   + S++ L   +    +   +  D++    D +     E      
Sbjct: 275 GISSTKV-----RRTLEASMHPLSLEMPVGQEGEGRMGDFI---EDDRISTPAEAAAASM 326

Query: 224 RRNMLTRSMSVLNPRERRIFEARR-LQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
            R  L   +  L  RER+I + R  L++    TLE +  EF ++RER+RQIEA A +K+
Sbjct: 327 LREQLEEVLQKLPERERKIIQLRYGLKDGRYRTLEEVGMEFGITRERIRQIEAVALRKL 385


>gi|302560773|ref|ZP_07313115.1| RNA polymerase sigma (70) factor RpoD [Streptomyces griseoflavus
           Tu4000]
 gi|302478391|gb|EFL41484.1| RNA polymerase sigma (70) factor RpoD [Streptomyces griseoflavus
           Tu4000]
          Length = 404

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 89/306 (29%), Positives = 142/306 (46%), Gaps = 64/306 (20%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKR----------YREHGDLS----------------AAH 51
           +Y+ EI +IP+L   EE  LA+R           R   DL                 A  
Sbjct: 110 QYLREIGRIPLLTAAEEVELARRVEAGLFAEEKLRLTPDLDSGLALDLDRLVVMGRMAKR 169

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY+ WWI+ 
Sbjct: 170 RLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIRQ 229

Query: 112 AMQEYILRSWSLVKIGTTANQ--KRLFFNLRRL---------KGHLQAITDNNLKPEQVV 160
           AM   +      +++     +   R+    RR+          G + A  D  L PE+V 
Sbjct: 230 AMSRALADQARTIRVPVHVVELINRVVRVQRRMLQERGYEPTPGEVAAHLD--LPPERV- 286

Query: 161 AIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              + L +++ E +S++  +    D +L  LI   D  S                  +E 
Sbjct: 287 --GEVLRLAQ-EPVSLHAPVGEEDDVALGDLIEDGDAASP-----------------VES 326

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARA 276
                 R  L   +S L  RER++ + R   +   P TLE +   F V+RER+RQIE++ 
Sbjct: 327 AAFLLLREHLEAVLSTLGERERKVVQLRYGLVDGRPRTLEEIGRLFGVTRERIRQIESKT 386

Query: 277 FKKVQE 282
             K+++
Sbjct: 387 LNKLRD 392


>gi|255020521|ref|ZP_05292585.1| RNA polymerase sigma factor RpoS [Acidithiobacillus caldus ATCC
           51756]
 gi|254970041|gb|EET27539.1| RNA polymerase sigma factor RpoS [Acidithiobacillus caldus ATCC
           51756]
          Length = 316

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 76/272 (27%), Positives = 141/272 (51%), Gaps = 15/272 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE +   R  + GD+ A  R++  +LRLVV++A  Y   G+P+ ++
Sbjct: 48  YLQEIGHNPLLTAEEE-IYYGRLVQQGDVRARTRMIECNLRLVVRVARRYLHRGMPLLDL 106

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 107 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQNIERALMNQTRTIRLPVHV-MKELAVV 165

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +   Q +     +   V  +A  L+    +V    C L  D  + +L NS  ++  
Sbjct: 166 LRAARCLEQELR----REPSVDEVAAALDRPVDQV--RGC-LEMDGRVTSLDNSGQRDQG 218

Query: 199 QWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           +  + ++ D + Q  + ++  +    R   L   ++ L+ + R +   R   +  +  TL
Sbjct: 219 RDLNEVLSDAEAQGPEAMVAAQNLAVR---LQSWLAGLSEKHRLVLSWRFGLDGGDGATL 275

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E + +   ++RERVRQI+  A   ++  I+ +
Sbjct: 276 EEVGTRLGITRERVRQIQVEALLILRRRIEAE 307


>gi|332707223|ref|ZP_08427276.1| RNA polymerase sigma factor RpoD-like protein [Lyngbya majuscula
           3L]
 gi|332353957|gb|EGJ33444.1| RNA polymerase sigma factor RpoD-like protein [Lyngbya majuscula
           3L]
          Length = 373

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 74/248 (29%), Positives = 132/248 (53%), Gaps = 17/248 (6%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A RYR H    A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+
Sbjct: 126 AFRYRLHVGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEK 185

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT-DNNLKP 156
           G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++ +   KP
Sbjct: 186 GYKFSTYATWWIRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKLLSQEMGRKP 240

Query: 157 -EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
            E+ +A   ++ + +   I+ + +L    SL   I   +   S+  D++  D +  E  +
Sbjct: 241 TEEEIADRMEMTIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIEADGETPEDQV 296

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIE 273
            +   R++    L   +  L+PRER +   R   ++    TLE +   F V+RER+RQIE
Sbjct: 297 SKNLLRED----LESVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIE 352

Query: 274 ARAFKKVQ 281
           A+A +K++
Sbjct: 353 AKALRKLR 360


>gi|162447798|ref|YP_001620930.1| DNA-directed RNA polymerase subunit D [Acholeplasma laidlawii
           PG-8A]
 gi|161985905|gb|ABX81554.1| DNA-directed RNA polymerase subunit D [Acholeplasma laidlawii
           PG-8A]
          Length = 419

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 84/256 (32%), Positives = 129/256 (50%), Gaps = 37/256 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +LV ++ RLVV IA  Y   GL   +++ EGN+GLM+AV KFD E+GF+ +TY+ WW
Sbjct: 179 AKEKLVEANYRLVVSIAKKYTQRGLLFLDLIQEGNMGLMRAVDKFDYEKGFKFSTYATWW 238

Query: 109 IKAAMQEYILRSWSLVKIGT----TAN-----QKRLFFNLRRLKGHLQAITDN-NLKPEQ 158
           I+ A+   +      ++I      T N     Q++L   L R    ++ I +  ++ PE+
Sbjct: 239 IRQAITRAVADQARTIRIPVHMVETINKMIRIQRQLVQELGR-DATIEEIAEKMDITPEK 297

Query: 159 VVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           V  I +       E IS+   +    D SL   I  SD N+    D+++     QE V  
Sbjct: 298 VQNIQR----IAKEPISLEAPVGEEEDSSLGDFI--SDPNALNPHDYMM-----QEMV-- 344

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEA 274
                   +  L   +  L  RE ++   R   L     TLE +  EF V+RER+RQIEA
Sbjct: 345 --------KKTLDEVLETLTDREEKVLRLRYGLLDGKTHTLEEVGREFGVTRERIRQIEA 396

Query: 275 RAFKKVQESIQKQVEL 290
           +A +K++ S Q+Q +L
Sbjct: 397 KALRKLR-SPQRQNKL 411


>gi|312195623|ref|YP_004015684.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EuI1c]
 gi|311226959|gb|ADP79814.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EuI1c]
          Length = 418

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 88/309 (28%), Positives = 145/309 (46%), Gaps = 60/309 (19%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREH--------------GDLS------------AAH 51
           +Y+ +I ++ +L  +EE  LAKR                  GDL             A  
Sbjct: 124 QYLSQIGRVRLLTAEEEVDLAKRVEAGLFAAEKLAAENGLVGDLRRELVWVERDGEIAKS 183

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RLV ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 184 RLVEANLRLVVSIARRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 243

Query: 112 AMQEYILRSWSLVKIGT----TAN-----QKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   I      ++I      T N     Q++L  +L R     +   + +L P++V  I
Sbjct: 244 AITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPTPEEIAKEMDLTPDKVREI 303

Query: 163 AKKLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS+   +  +E   L   I  SD          V   D    +L++++ 
Sbjct: 304 QKVAQ----EPISLETPIGEEEDSHLGDFIEDSDA---------VVPVDAASFLLLQEQ- 349

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE+++ + R      +P TLE +  EF V+RER+RQIE++   
Sbjct: 350 -------LDSVLHTLSDREKKVIQLRFGLTDGHPRTLEEVGREFGVTRERIRQIESKTLS 402

Query: 279 KVQESIQKQ 287
           K++   + Q
Sbjct: 403 KLRHPSRSQ 411


>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 =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 380 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 439

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +   T     PE+   +A+K+ +
Sbjct: 440 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQILQETGREATPEE---LAEKMEL 494

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SE ++  +  ++A  E ++      D + S   D++    D   +  I+    +  R   
Sbjct: 495 SEDKIRKV-LKIAK-EPISMETPVGDDDDSHLGDFI---EDNNIESPIDMATAEGLREAT 549

Query: 229 TRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 550 LEILETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 604


>gi|157414303|ref|YP_001485169.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9215]
 gi|157388878|gb|ABV51583.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9215]
          Length = 339

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 80/278 (28%), Positives = 146/278 (52%), Gaps = 26/278 (9%)

Query: 13  EIGLSRYIHEIRK---IPMLEKQEEYV----LAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           EI L+ ++  ++K   IP  E+ +  +    + KR R+        R++ ++LRLVV +A
Sbjct: 70  EIELAHHVQNMKKLLQIPETERTQRNLYQIKIGKRARD--------RMMAANLRLVVSVA 121

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+  M   I  S   ++
Sbjct: 122 KKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIR 181

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           +    ++K     +RR+   L   +    +    + +A ++ + + ++  +  + A   S
Sbjct: 182 LPIHISEK--LSKMRRVSREL---SHKFGRQPTRLEMATEMGIDQKDLEDLISQSAPCAS 236

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L+A     +  S+  +  L+ D + +E   +E  +R  ++  L   +S LN RE++I + 
Sbjct: 237 LDAHARGEEDRSTLGE--LIPDPNCEEP--MEGMDRTIQKEHLGTWLSQLNEREQKIMKL 292

Query: 246 R--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R     E P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 293 RFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 330


>gi|254526617|ref|ZP_05138669.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9202]
 gi|221538041|gb|EEE40494.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9202]
          Length = 339

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 80/278 (28%), Positives = 146/278 (52%), Gaps = 26/278 (9%)

Query: 13  EIGLSRYIHEIRK---IPMLEKQEEYV----LAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           EI L+ ++  ++K   IP  E+ +  +    + KR R+        R++ ++LRLVV +A
Sbjct: 70  EIELAHHVQNMKKLLQIPETERTQRNLYQIKIGKRARD--------RMMAANLRLVVSVA 121

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+  M   I  S   ++
Sbjct: 122 KKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIR 181

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           +    ++K     +RR+   L   +    +    + +A ++ + + ++  +  + A   S
Sbjct: 182 LPIHISEK--LSKMRRVSREL---SHKFGRQPTRLEMATEMGIDQKDLEDLISQSAPCAS 236

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L+A     +  S+  +  L+ D + +E   +E  +R  ++  L   +S LN RE++I + 
Sbjct: 237 LDAHARGEEDRSTLGE--LIPDPNCEEP--MEGMDRTIQKEHLGTWLSQLNEREQKIMKL 292

Query: 246 R--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R     E P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 293 RFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 330


>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 =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 69/236 (29%), Positives = 122/236 (51%), Gaps = 12/236 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 562 DAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 621

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I     +     N R  + HLQ       +P+  + +A K+ 
Sbjct: 622 WIRQAITRSIADQARTIRIPVHMIETINKMN-RISRQHLQEF---GFEPDASI-LAAKME 676

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + E ++  +  ++A  E ++      D + S   D++    D      I+   +   R++
Sbjct: 677 IPEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDSNNTAPIDAAMQAGLRDV 731

Query: 228 LTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 732 VKDILDGLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLK 787


>gi|158334991|ref|YP_001516163.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158305232|gb|ABW26849.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 371

 Score =  101 bits (251), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 72/246 (29%), Positives = 132/246 (53%), Gaps = 17/246 (6%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R+R H    A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G+
Sbjct: 126 RHRLHAGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGY 185

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT-DNNLKP-E 157
           + +TY+ WWI+ A+   I      +++        L+  + R+K   + ++ +   KP E
Sbjct: 186 KFSTYATWWIRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKLLSQEMGRKPTE 240

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           + +A   ++ + +   I+ + +L    SL   I   +   S+  D++  D +  E  + +
Sbjct: 241 EEIATRMEMTIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIESDGETPEDQVSK 296

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEAR 275
              R++    L   +  L+PRER + + R   ++    TLE +   F V+RER+RQIEA+
Sbjct: 297 SLLRED----LETVLDTLSPRERDVLKLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAK 352

Query: 276 AFKKVQ 281
           A +K++
Sbjct: 353 ALRKLR 358


>gi|330040254|ref|XP_003239821.1| RNA-polymerase sigma factor [Cryptomonas paramecium]
 gi|327206746|gb|AEA38923.1| RNA-polymerase sigma factor [Cryptomonas paramecium]
          Length = 414

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 72/236 (30%), Positives = 128/236 (54%), Gaps = 12/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R++ ++LRLVV IA  Y   G+ + ++V EG++GL++A +KFD E+GF+ +TY+ WW
Sbjct: 159 AKERMIAANLRLVVSIAKRYSNRGMSLQDLVQEGSLGLIRATEKFDSEKGFKFSTYATWW 218

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           IK ++   I      +++        L+  L  +K   + +T    +      IA K++V
Sbjct: 219 IKQSVSRAIADHSRTIRLPV-----HLYDTLSAIKKTTRILTIELGRSPTEEEIACKMDV 273

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +  ++ S+        SL   I  +D +++Q  D++  D +  +    E  E+   R+ L
Sbjct: 274 TVDKLRSVLQSAQPTLSLEKPIK-NDGDTAQLSDFIEADQESPD----EHVEKSMLRDDL 328

Query: 229 TRSMSVLNPRERRIFEARR-LQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQE 282
              ++ L+ RER +   R  L +  + TLE +   F V+RERVRQIEA+A +K+++
Sbjct: 329 RDVINSLSLRERDVIRMRYGLDDGKIRTLEEIGQIFSVTRERVRQIEAKAIRKLRQ 384


>gi|256787912|ref|ZP_05526343.1| RNA polymerase principal sigma factor [Streptomyces lividans TK24]
          Length = 365

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 86/294 (29%), Positives = 140/294 (47%), Gaps = 42/294 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ EI +IP+L   EE  LA+R  E G  +                           A  
Sbjct: 72  YLREIGRIPLLSAAEEVDLARRV-EAGLFAEEKLRCSPGLDDRLALDLDRLVVLGRLAKR 130

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY+ WWI+ 
Sbjct: 131 RLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIRQ 190

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           AM   +      +++    +   L   + R++  +         P++V A    L+++  
Sbjct: 191 AMSRALADQARTIRV--PVHVVELINRVVRVQRRMLQERGCEPTPQEVAA---HLDLA-P 244

Query: 172 EVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           E +    RLA +  SL+A +   D  +    D +    DG     +E       R  L  
Sbjct: 245 ERVGEVLRLAQEPVSLHAPVGEEDDVA--LGDLI---EDGDAASPVESAAFLLLRQHLEA 299

Query: 231 SMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            +S L  RER++ + R       P TLE +   F V+RER+RQIE++   K+++
Sbjct: 300 VLSTLGERERKVVQLRYGLADGRPRTLEEIGRLFGVTRERIRQIESKTLSKLRD 353


>gi|254416308|ref|ZP_05030062.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
 gi|196176990|gb|EDX72000.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
          Length = 416

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 68/238 (28%), Positives = 124/238 (52%), Gaps = 13/238 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L A   ++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV+KFDP +G+R +TY+ 
Sbjct: 175 LQAKEHMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTKGYRFSTYAY 234

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   I      +++     +K     L ++K   + I+    +   +  IAK+L
Sbjct: 235 WWIRQGITRAIATQSRTIRLPVHITEK-----LNKIKKAQRKISQEQGRTATIEDIAKEL 289

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +  R+    SL   I    +  ++  D L  +    E VL+ +  +++ + 
Sbjct: 290 EMDAPQVREVLMRVPRSVSLE--IKVGKEKDTELGDLLETEETSPEDVLMREALQRDLQQ 347

Query: 227 MLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +L    + L  RER +   R      +P +L  +    E+SRERVRQIEA+A +K+++
Sbjct: 348 LL----ADLTSRERDVICMRFGLGDGHPYSLAEIGRALELSRERVRQIEAKALQKLRQ 401


>gi|157737257|ref|YP_001489940.1| RNA polymerase sigma factor RpoD [Arcobacter butzleri RM4018]
 gi|157699111|gb|ABV67271.1| RNA polymerase sigma 70 factor [Arcobacter butzleri RM4018]
          Length = 626

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 76/246 (30%), Positives = 128/246 (52%), Gaps = 14/246 (5%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           KR ++  D S   R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ ++G
Sbjct: 378 KRGKQITDTSKT-RMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKKG 436

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           ++ +TY+ WWI+ A+   I      ++I        +   + R+   ++     N K   
Sbjct: 437 YKFSTYATWWIRQAISRAIADQARTIRIPI-----HMIETINRINKIIRKGVQENGKEPD 491

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           +  IAK++ +   +V  +        SL A I S +    ++ D++    D +    I+ 
Sbjct: 492 IEEIAKEVGLPVDKVKQVIKITKEPVSLEAPIGSDE--DGKFGDFV---PDEKAPTPIDN 546

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV--TLENLSSEFEVSRERVRQIEAR 275
             +++ +  + + +S LN RE+ +   R  L E+    TLE +  E  V+RERVRQIE+ 
Sbjct: 547 IMKEDLQGQIDQILSQLNEREQAVIRMRFGLMEDASDRTLEEIGKELNVTRERVRQIESS 606

Query: 276 AFKKVQ 281
           A KK++
Sbjct: 607 AIKKLK 612


>gi|312964996|ref|ZP_07779236.1| RNA polymerase sigma factor RpoS [Escherichia coli 2362-75]
 gi|312290552|gb|EFR18432.1| RNA polymerase sigma factor RpoS [Escherichia coli 2362-75]
          Length = 237

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 73/243 (30%), Positives = 121/243 (49%), Gaps = 24/243 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 113 MQEYILRSWSLVKIGT-TANQKRLFFNLRRLKGH-------LQAITDNNLKPEQVVAIAK 164
           ++  I+     +++      +  ++    R   H        + I +   KP   V+   
Sbjct: 61  IERAIMNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRML 120

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +LN     + S++  L GD     L   +D+  +  +D    D   Q  V    E    +
Sbjct: 121 RLN---ERITSVDTPLGGDSEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQ 177

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R +L R   +L       +EA        TLE++  E  ++RERVRQI+    ++++E +
Sbjct: 178 REVLARRFGLLG------YEA-------ATLEDVGREIGLTRERVRQIQVEGLRRLREIL 224

Query: 285 QKQ 287
           Q Q
Sbjct: 225 QTQ 227


>gi|52842571|ref|YP_096370.1| RNA polymerase sigma 70 factor (RpoD) [Legionella pneumophila
           subsp. pneumophila str. Philadelphia 1]
 gi|52629682|gb|AAU28423.1| RNA polymerase sigma 70 factor (RpoD) [Legionella pneumophila
           subsp. pneumophila str. Philadelphia 1]
          Length = 623

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 382 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 441

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +   T     PE+   +A+K+ +
Sbjct: 442 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQILQETGREATPEE---LAEKMEL 496

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SE ++  +  ++A  E ++      D + S   D++    D   +  I+    +  R   
Sbjct: 497 SEDKIRKV-LKIAK-EPISMETPVGDDDDSHLGDFI---EDNNIESPIDMATAEGLREAT 551

Query: 229 TRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 552 LEILETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 606


>gi|159039487|ref|YP_001538740.1| RpoD family RNA polymerase sigma factor [Salinispora arenicola
           CNS-205]
 gi|157918322|gb|ABV99749.1| RNA polymerase, sigma 70 subunit, RpoD family [Salinispora
           arenicola CNS-205]
          Length = 329

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 89/307 (28%), Positives = 148/307 (48%), Gaps = 68/307 (22%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH----------GDLSAAHRLVT-------- 55
           Y+HEI + P+L+   E  L+K      Y EH           + +   RLV         
Sbjct: 38  YLHEISRTPLLDAATEVDLSKAIEAGLYAEHLLDEDRVPAGVERAELQRLVAEGERAKDL 97

Query: 56  ---SHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
              ++LRLVV IA  Y   G+P+ +++ EGN GL++AV+KFD ERGF+ +TY+ WWI+ A
Sbjct: 98  FIRANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQA 157

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT---DNNLKPEQVVAIAKKLNVS 169
           +   I +    V++        L  ++ R++   + +T    ++ +PEQ   IA  L VS
Sbjct: 158 ISRAIAQQERTVRLPV-----HLVEDVNRMRNVARQLTRELGSDPEPEQ---IATALGVS 209

Query: 170 ----------ESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
                       + +S++  +   GD +L  L+  SD  S              E++++ 
Sbjct: 210 VERVNELVRWSQDTVSLDTPVGDDGDTNLGDLVADSDAPSP-------------EEIVLT 256

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEAR 275
             ER+    +L    S L+ R   I  AR   E+    +L  ++S F +SRER+RQ+E +
Sbjct: 257 GLERQRIEGLL----SHLDDRSAGIMRARYGLEDGREHSLTEVASRFSLSRERIRQLEIQ 312

Query: 276 AFKKVQE 282
           A  +++E
Sbjct: 313 ALGRLRE 319


>gi|77163721|ref|YP_342246.1| RpoS [Nitrosococcus oceani ATCC 19707]
 gi|254436220|ref|ZP_05049727.1| RNA polymerase sigma factor RpoS [Nitrosococcus oceani AFC27]
 gi|76882035|gb|ABA56716.1| RNA polymerase, sigma 38 subunit, RpoS [Nitrosococcus oceani ATCC
           19707]
 gi|207089331|gb|EDZ66603.1| RNA polymerase sigma factor RpoS [Nitrosococcus oceani AFC27]
          Length = 321

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 80/273 (29%), Positives = 146/273 (53%), Gaps = 17/273 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE V   R  + G+ +   R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 53  YLSEIGCAPLLTAEEE-VYHARLAKKGNPAGRKRMIESNLRLVVKISRRYMNRGLALLDL 111

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL+ AV+KFDPE GFR +TY+ WWI+  ++  ++     V++     ++    +
Sbjct: 112 IEEGNLGLIHAVEKFDPEMGFRFSTYATWWIRQTIERALMNQTRTVRLPVHVVKE--IKS 169

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
            +R+   L    +++   E+   +A++LN    E+     R+   +   A +++  +N+ 
Sbjct: 170 YQRVANKLAQELEHDPSFEE---LAQQLNKPVEEI----KRVWSLKDNTASMDTGYRNNQ 222

Query: 199 QWQ--DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQE-NPVT 254
           +    D L  +      VL++ ++ ++R   L   +S LN ++R +   R  LQ   P T
Sbjct: 223 EKTLLDALPDEDAPDPTVLLQNDDMQSR---LKLWLSQLNDKQREVVIRRFGLQGYEPQT 279

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           LE +     V+RERVRQI+    K+++  + K+
Sbjct: 280 LEQVGQAIGVTRERVRQIQLETLKRLRRILTKE 312


>gi|158833993|gb|ABW81802.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
          Length = 225

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 59/149 (39%), Positives = 90/149 (60%), Gaps = 6/149 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L   EE   A+R    GD S+  R++ S+LRLVVKI+  Y   GLP+ ++
Sbjct: 8   YLGEIGYSPLLTAAEEIYFARRVL-CGDESSRRRMIESNLRLVVKISRRYINRGLPLLDL 66

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 67  IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 125

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           LR  +  L    D++  PE+   IA++LN
Sbjct: 126 LRAAR-ELSHKLDHDPSPEE---IAEQLN 150


>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 =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 380 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 439

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +   T     PE+   +A+K+ +
Sbjct: 440 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQILQETGREATPEE---LAEKMEL 494

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SE ++  +  ++A  E ++      D + S   D++    D   +  I+    +  R   
Sbjct: 495 SEDKIRKV-LKIAK-EPISMETPVGDDDDSHLGDFI---EDNNIESPIDMATAEGLREAT 549

Query: 229 TRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 550 LEILETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 604


>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 =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 381 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 440

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +   T     PE+   +A+K+ +
Sbjct: 441 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQILQETGREATPEE---LAEKMEL 495

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SE ++  +  ++A  E ++      D + S   D++    D   +  I+    +  R   
Sbjct: 496 SEDKIRKV-LKIAK-EPISMETPVGDDDDSHLGDFI---EDNNIESPIDMATAEGLREAT 550

Query: 229 TRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 551 LEILETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 605


>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 =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +   T     PE+   +A+K+ +
Sbjct: 438 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQILQETGREATPEE---LAEKMEL 492

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SE ++  +  ++A  E ++      D + S   D++    D   +  I+    +  R   
Sbjct: 493 SEDKIRKV-LKIAK-EPISMETPVGDDDDSHLGDFI---EDNNIESPIDMATAEGLREAT 547

Query: 229 TRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 548 LEILETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|254497834|ref|ZP_05110600.1| RNA polymerase sigma 70 factor (RpoD) [Legionella drancourtii
           LLAP12]
 gi|254352912|gb|EET11681.1| RNA polymerase sigma 70 factor (RpoD) [Legionella drancourtii
           LLAP12]
          Length = 628

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 387 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 446

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +   T     PE+   +A+K+ +
Sbjct: 447 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQILQETGREATPEE---LAEKMEL 501

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SE ++  +  ++A  E ++      D + S   D++    D   +  I+    +  R   
Sbjct: 502 SEDKIRKV-LKIAK-EPISMETPVGDDDDSHLGDFI---EDNNIESPIDMATAEGLREAT 556

Query: 229 TRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 557 LEILETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 611


>gi|158833967|gb|ABW81789.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833969|gb|ABW81790.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833971|gb|ABW81791.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833973|gb|ABW81792.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833977|gb|ABW81794.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833987|gb|ABW81799.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
          Length = 225

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 59/149 (39%), Positives = 89/149 (59%), Gaps = 6/149 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L   EE   A+R    GD S+  R++ S+LRLVVKI+  Y   GLP+ ++
Sbjct: 8   YLSEIGYSPLLTAAEEIYFARRVL-CGDESSRRRVIESNLRLVVKISRRYINRGLPLLDL 66

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY  WWI+  ++  I+     +++      K L   
Sbjct: 67  IEEGNLGLIRAVEKFDPERGFRFSTYDTWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 125

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           LR  +  L    D++  PE+   IA++LN
Sbjct: 126 LRAAR-ELSHKLDHDPSPEE---IAEQLN 150


>gi|88807657|ref|ZP_01123169.1| RNA polymerase sigma factor [Synechococcus sp. WH 7805]
 gi|88788871|gb|EAR20026.1| RNA polymerase sigma factor [Synechococcus sp. WH 7805]
          Length = 447

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 75/275 (27%), Positives = 148/275 (53%), Gaps = 25/275 (9%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           NG++  ++    + ++P++  +   +L +R +E        ++V S+LRLVV IA  Y  
Sbjct: 181 NGKLPDTKEWAALVEMPVIRFRRRLMLGRRAKE--------KMVQSNLRLVVSIAKKYMN 232

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+   I      +++    
Sbjct: 233 RGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV-- 290

Query: 131 NQKRLFFNLRRLKGHLQAITDN-NLKP-EQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
               L+  + R+K   + ++     KP E+ +A + ++ + +   I+ + +L    SL  
Sbjct: 291 ---HLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPI--SLET 345

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            I   +   S+  D++  D +  EQ + +   R++   +L    + L+PRER +   R  
Sbjct: 346 PIGKEE--DSRLGDFIEADIENPEQDVAKNLLREDLEGVL----ATLSPRERDVLRLRYG 399

Query: 249 QENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            ++    TLE +   F+V+RER+RQIEA+A +K++
Sbjct: 400 LDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLR 434


>gi|158833951|gb|ABW81781.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833953|gb|ABW81782.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833955|gb|ABW81783.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833957|gb|ABW81784.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833961|gb|ABW81786.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833965|gb|ABW81788.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833981|gb|ABW81796.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833983|gb|ABW81797.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833985|gb|ABW81798.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833989|gb|ABW81800.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
          Length = 225

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 59/149 (39%), Positives = 90/149 (60%), Gaps = 6/149 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L   EE   A+R    GD S+  R++ S+LRLVVKI+  Y   GLP+ ++
Sbjct: 8   YLGEIGYSPLLTAAEEIYFARRVL-CGDESSRRRMIESNLRLVVKISRRYINRGLPLLDL 66

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 67  IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 125

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           LR  +  L    D++  PE+   IA++LN
Sbjct: 126 LRAAR-ELSHKLDHDPSPEE---IAEQLN 150


>gi|54298252|ref|YP_124621.1| RNA polymerase sigma factor rpoD (sigma-70) [Legionella pneumophila
           str. Paris]
 gi|53752037|emb|CAH13463.1| RNA polymerase sigma factor rpoD (Sigma-70) [Legionella pneumophila
           str. Paris]
          Length = 621

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 380 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 439

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +   T     PE+   +A+K+ +
Sbjct: 440 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQILQETGREATPEE---LAEKMEL 494

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SE ++  +  ++A  E ++      D + S   D++    D   +  I+    +  R   
Sbjct: 495 SEDKIRKV-LKIAK-EPISMETPVGDDDDSHLGDFI---EDNNIESPIDMATAEGLREAT 549

Query: 229 TRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 550 LEILETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 604


>gi|315636974|ref|ZP_07892198.1| DNA-directed RNA polymerase sigma subunit RpoD [Arcobacter butzleri
           JV22]
 gi|315478804|gb|EFU69513.1| DNA-directed RNA polymerase sigma subunit RpoD [Arcobacter butzleri
           JV22]
          Length = 626

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 76/246 (30%), Positives = 128/246 (52%), Gaps = 14/246 (5%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           KR ++  D S   R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ ++G
Sbjct: 378 KRGKQITDTSKT-RMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKKG 436

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           ++ +TY+ WWI+ A+   I      ++I        +   + R+   ++     N K   
Sbjct: 437 YKFSTYATWWIRQAISRAIADQARTIRIPI-----HMIETINRINKIIRKGVQENGKEPD 491

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           +  IAK++ +   +V  +        SL A I S +    ++ D++    D +    I+ 
Sbjct: 492 IEEIAKEVGLPVDKVKQVIKITKEPVSLEAPIGSDE--DGKFGDFV---PDEKAPTPIDN 546

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV--TLENLSSEFEVSRERVRQIEAR 275
             +++ +  + + +S LN RE+ +   R  L E+    TLE +  E  V+RERVRQIE+ 
Sbjct: 547 IMKEDLQGQIDQILSQLNEREQAVIRMRFGLMEDASDRTLEEIGKELNVTRERVRQIESS 606

Query: 276 AFKKVQ 281
           A KK++
Sbjct: 607 AIKKLK 612


>gi|1575485|gb|AAB09543.1| LprpoD [Legionella pneumophila]
          Length = 620

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 379 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 438

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +   T     PE+   +A+K+ +
Sbjct: 439 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQILQETGREATPEE---LAEKMEL 493

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SE ++  +  ++A  E ++      D + S   D++    D   +  I+    +  R   
Sbjct: 494 SEDKIRKV-LKIAK-EPISMETPVGDDDDSHLGDFI---EDNNIESPIDMATAEGLREAT 548

Query: 229 TRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 549 LEILETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 603


>gi|318041167|ref|ZP_07973123.1| RNA polymerase sigma factor RpoD [Synechococcus sp. CB0101]
          Length = 464

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 73/260 (28%), Positives = 141/260 (54%), Gaps = 25/260 (9%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+++ +   +L +R +E        ++V S+LRLVV IA  Y   GL   +++ EG++G
Sbjct: 213 MPLIKFRRRLMLGRRAKE--------KMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLG 264

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A +KFD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K  
Sbjct: 265 LIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV-----HLYETISRIKKT 319

Query: 146 LQAITDN-NLKP-EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
            + ++     KP E+ +A + ++ + +   I+ + +L    SL   I   +   S+  D+
Sbjct: 320 TKTLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDF 375

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSE 261
           +  D +  EQ + +   R++   +L    + L+PRER +   R   ++    TLE +   
Sbjct: 376 IEADIENPEQDVAKNLLREDLEGVL----ATLSPRERDVLRLRYGLDDGRMKTLEEIGQI 431

Query: 262 FEVSRERVRQIEARAFKKVQ 281
           F+V+RER+RQIEA+A +K++
Sbjct: 432 FDVTRERIRQIEAKALRKLR 451


>gi|296127362|ref|YP_003634614.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Brachyspira
           murdochii DSM 12563]
 gi|296019178|gb|ADG72415.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Brachyspira
           murdochii DSM 12563]
          Length = 309

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 69/246 (28%), Positives = 123/246 (50%), Gaps = 34/246 (13%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           S  H+LV S+LRLV+ IA  Y   G+P  +++ EGNIGL++AVK+F+ ++GF+ +TY +W
Sbjct: 70  SIQHKLVKSNLRLVISIAKRYYNSGVPFIDIIDEGNIGLIEAVKRFEYKKGFKFSTYGVW 129

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA------ 161
           WIK ++ + I             + KR   ++ R   H+  +   +++  +V+       
Sbjct: 130 WIKQSIVKEI-------------SSKR---HIIRFPMHIARLIKKSIQTSKVLTQKLGRE 173

Query: 162 -----IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
                IAK++ +    +  +        S+++   +SD N     D      D       
Sbjct: 174 PTTDEIAKEMKIDRKTLSYIMIFTQDTASVDSFFKNSDNN-----DMTSIIEDKNFPSPH 228

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEA 274
           +K    + R+ LT ++  L+ +ER +  +R     +   TLE+   E  ++RERVRQI+ 
Sbjct: 229 QKAFMDSLRDTLTEALKCLDEKERTVIISRFGLYGKEAKTLEDTGKELNITRERVRQIQI 288

Query: 275 RAFKKV 280
           +A KK+
Sbjct: 289 KAIKKL 294


>gi|158833991|gb|ABW81801.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
          Length = 225

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 59/149 (39%), Positives = 90/149 (60%), Gaps = 6/149 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L   EE   A+R    GD S+  R++ S+LRLVVKI+  Y   GLP+ ++
Sbjct: 8   YLGEICYSPLLTAAEEIYFARRVL-CGDGSSRRRMIESNLRLVVKISRRYINRGLPLLDL 66

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 67  IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 125

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           LR  +  L    D++  PE+   IA++LN
Sbjct: 126 LRAAR-ELSHKLDHDPSPEE---IAEQLN 150


>gi|158833949|gb|ABW81780.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
          Length = 225

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 59/149 (39%), Positives = 90/149 (60%), Gaps = 6/149 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L   EE   A+R    GD S+  R++ S+LRLVVKI+  Y   GLP+ ++
Sbjct: 8   YLGEIGYSPLLTAAEEIYFARRVL-CGDESSRRRMIESNLRLVVKISRRYINRGLPLLDL 66

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 67  IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 125

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           LR  +  L    D++  PE+   IA++LN
Sbjct: 126 LRAAR-ELSHKLDHDPSPEE---IAEQLN 150


>gi|133468|sp|P27785|RPOD_STRAU RecName: Full=RNA polymerase sigma factor rpoD
          Length = 317

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 88/294 (29%), Positives = 141/294 (47%), Gaps = 42/294 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHG-------------------DLS--------AAH 51
           Y+ EI +IP+L   EE  LA+R  E G                   DL         A  
Sbjct: 24  YLREIGRIPLLTAAEEVDLARRV-EAGLFAEEKLGGAADLDSQLAVDLDRLVVMGRMAKR 82

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RL+ S+LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY+ WWI+ 
Sbjct: 83  RLIESNLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIRQ 142

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           AM   +      +++     +     N R ++   + + +   +P     +A  L ++  
Sbjct: 143 AMSRALADQARTIRVPVHVVE---LIN-RVVRVQRRMLQERGYEP-TAEEVAVHLELTPE 197

Query: 172 EVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            V+ +  RLA +  SL+A +   D  +    D +    DG     +E      R   L  
Sbjct: 198 RVLEV-LRLAQEPVSLHAPVGEEDDVA--LGDLI---EDGDAASPVESAAFFLRCEHLEA 251

Query: 231 SMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            +S L  RER++ + R       P TLE +   F V+RER+RQIE++   K+++
Sbjct: 252 VLSTLGERERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRD 305


>gi|307611207|emb|CBX00855.1| RNA polymerase sigma factor rpoD [Legionella pneumophila 130b]
          Length = 619

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +   T     PE+   +A+K+ +
Sbjct: 438 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQILQETGREATPEE---LAEKMEL 492

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SE ++  +  ++A  E ++      D + S   D++    D   +  I+    +  R   
Sbjct: 493 SEDKIRKV-LKIAK-EPISMETPVGDDDDSHLGDFI---EDNNIESPIDMATAEGLREAT 547

Query: 229 TRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 548 LEILETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 602


>gi|302534283|ref|ZP_07286625.1| RNA polymerase sigma factor RpoS [Streptomyces sp. C]
 gi|302443178|gb|EFL14994.1| RNA polymerase sigma factor RpoS [Streptomyces sp. C]
          Length = 361

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 88/295 (29%), Positives = 142/295 (48%), Gaps = 42/295 (14%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHG-------------------DLS--------AA 50
           +Y+ EI +IP+L   EE  LA+R  E G                   DL         A 
Sbjct: 67  QYLREIGRIPLLTAAEEVELARRV-EAGLFAEEKLAGATDLDSQLAVDLDKLVVMGRMAK 125

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            RL+ S+LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY+ WWI+
Sbjct: 126 RRLIESNLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIR 185

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            AM   +      +++     +     N R ++   + + +   +P     +A  L ++ 
Sbjct: 186 QAMSRALADQARTIRVPVHVVE---LIN-RVVRVQRRMLQERGYEP-TAEEVAAHLELTP 240

Query: 171 SEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             V+ +  RLA +  SL+A +   D  +    D +    DG     +E       R  L 
Sbjct: 241 ERVLEV-LRLAQEPVSLHAPVGEEDDVA--LGDLI---EDGDAASPMESAAFFLLREHLE 294

Query: 230 RSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             +S L  RER++ + R       P TLE +   F V+RER+RQIE++   K+++
Sbjct: 295 AVLSTLGERERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRD 349


>gi|153304|gb|AAA26762.1| principal sigma-like factor [Streptomyces aureofaciens]
 gi|450077|prf||1920369A RNA polymerase:SUBUNIT=sigma
          Length = 393

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 88/295 (29%), Positives = 142/295 (48%), Gaps = 42/295 (14%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHG-------------------DLS--------AA 50
           +Y+ EI +IP+L   EE  LA+R  E G                   DL         A 
Sbjct: 99  QYLREIGRIPLLTAAEEVDLARRV-EAGLFAEEKLGGAADLDSQLAVDLDRLVVMGRMAK 157

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            RL+ S+LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY+ WWI+
Sbjct: 158 RRLIESNLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIR 217

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            AM   +      +++     +     N R ++   + + +   +P     +A  L ++ 
Sbjct: 218 QAMSRALADQARTIRVPVHVVE---LIN-RVVRVQRRMLQERGYEP-TAEEVAVHLELTP 272

Query: 171 SEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             V+ +  RLA +  SL+A +   D  +    D +    DG     +E      R   L 
Sbjct: 273 ERVLEV-LRLAQEPVSLHAPVGEEDDVA--LGDLI---EDGDAASPVESAAFFLRCEHLE 326

Query: 230 RSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             +S L  RER++ + R       P TLE +   F V+RER+RQIE++   K+++
Sbjct: 327 AVLSTLGERERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRD 381


>gi|296272949|ref|YP_003655580.1| RpoD subfamily RNA polymerase sigma-70 factor subunit [Arcobacter
           nitrofigilis DSM 7299]
 gi|296097123|gb|ADG93073.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Arcobacter
           nitrofigilis DSM 7299]
          Length = 626

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 72/236 (30%), Positives = 124/236 (52%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ ++G++ +TY+ WW
Sbjct: 387 AKTRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKKGYKFSTYATWW 446

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + R+   ++     N K   V  IAK++ +
Sbjct: 447 IRQAISRAIADQARTIRIPI-----HMIETINRINKIIRKGIQENGKEPNVDEIAKEVGL 501

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL A I S +    ++ D++    D +    ++   +++ +N +
Sbjct: 502 PVDKVKQVIKITKEPVSLEAPIGSDE--DGKFGDFV---PDDKAPTPVDNIMKEDLQNQI 556

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            + ++ LN RE+ +   R  L ++    TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 557 DQILAQLNEREQAVVRMRFGLMDDASDRTLEEIGKELSVTRERVRQIESSAIKKLK 612


>gi|148238947|ref|YP_001224334.1| RNA polymerase sigma factor RpoD [Synechococcus sp. WH 7803]
 gi|147847486|emb|CAK23037.1| RNA polymerase sigma factor RpoD, sigma-70 family [Synechococcus
           sp. WH 7803]
          Length = 450

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 75/275 (27%), Positives = 148/275 (53%), Gaps = 25/275 (9%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           NG++  ++    + ++P++  +   +L +R +E        ++V S+LRLVV IA  Y  
Sbjct: 184 NGKLPDTKEWAALVEMPVIRFRRRLMLGRRAKE--------KMVQSNLRLVVSIAKKYMN 235

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+   I      +++    
Sbjct: 236 RGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV-- 293

Query: 131 NQKRLFFNLRRLKGHLQAITDN-NLKP-EQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
               L+  + R+K   + ++     KP E+ +A + ++ + +   I+ + +L    SL  
Sbjct: 294 ---HLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPI--SLET 348

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            I   +   S+  D++  D +  EQ + +   R++   +L    + L+PRER +   R  
Sbjct: 349 PIGKEE--DSRLGDFIEADIENPEQDVAKNLLREDLEGVL----ATLSPRERDVLRLRYG 402

Query: 249 QENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            ++    TLE +   F+V+RER+RQIEA+A +K++
Sbjct: 403 LDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLR 437


>gi|54401868|gb|AAV34620.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|54401871|gb|AAV34621.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|54401874|gb|AAV34622.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 299

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 46/108 (42%), Positives = 73/108 (67%), Gaps = 1/108 (0%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRL 167


>gi|320161271|ref|YP_004174495.1| RNA polymerase sigma factor [Anaerolinea thermophila UNI-1]
 gi|319995124|dbj|BAJ63895.1| RNA polymerase sigma factor [Anaerolinea thermophila UNI-1]
          Length = 409

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 87/302 (28%), Positives = 143/302 (47%), Gaps = 39/302 (12%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY------REH---GDLSAAHR----- 52
           +I  +  IGL  Y+ E+ ++P+L  +EE  LA+R       RE    G++S   R     
Sbjct: 106 NIDTDDTIGL--YLKEVSRVPLLTAEEEVELAQRIERGRMAREELARGNVSPKRRQELRR 163

Query: 53  -----------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
                      L+T++ RLV+ +A  Y G G+P  +++ EGNIGL++A KKFD  RG + 
Sbjct: 164 LIEDGWAAREHLITANSRLVISVAKKYMGRGVPFLDLIQEGNIGLIRATKKFDYRRGHKF 223

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY+ WWI+ A+   I      +++      +     L R++  L   T    +   V  
Sbjct: 224 STYATWWIRQAVTRAIADQGRTIRVPVHMGDQ--INKLLRVQHQL---TQRLGREPSVEE 278

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           +A+ L+V   +V +M         L+    + D+  S   D++    D +     +    
Sbjct: 279 LAEALDVPPRKVENMIQ--VARRPLSLETPTDDEEDSVLGDFI---EDEEAPPPDDTATY 333

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
              R  L   ++ L PRE RI + R   L     TLE +  +  V+RERVRQIEA+A  +
Sbjct: 334 NLLRQHLEEVLNTLPPREVRILQLRYGLLDGQAYTLEEVGRKMGVTRERVRQIEAQALSR 393

Query: 280 VQ 281
           ++
Sbjct: 394 LR 395


>gi|254430902|ref|ZP_05044605.1| DNA-directed RNA polymerase sigma subunit [Cyanobium sp. PCC 7001]
 gi|197625355|gb|EDY37914.1| DNA-directed RNA polymerase sigma subunit [Cyanobium sp. PCC 7001]
          Length = 503

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 73/260 (28%), Positives = 141/260 (54%), Gaps = 25/260 (9%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+++ +   +L +R +E        ++V S+LRLVV IA  Y   GL   +++ EG++G
Sbjct: 252 MPLIKFRRRLMLGRRAKE--------KMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLG 303

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A +KFD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K  
Sbjct: 304 LIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV-----HLYETISRIKKT 358

Query: 146 LQAITDN-NLKP-EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
            + ++     KP E+ +A + ++ + +   I+ + +L    SL   I   +   S+  D+
Sbjct: 359 TKTLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLP--ISLETPIGKEE--DSRLGDF 414

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSE 261
           +  D +  EQ + +   R++   +L    + L+PRER +   R   ++    TLE +   
Sbjct: 415 IEADIENPEQDVAKNLLREDLEGVL----ATLSPRERDVLRLRYGLDDGRMKTLEEIGQI 470

Query: 262 FEVSRERVRQIEARAFKKVQ 281
           F+V+RER+RQIEA+A +K++
Sbjct: 471 FDVTRERIRQIEAKALRKLR 490


>gi|6010732|gb|AAF01232.1|AF184101_1 mutant RpoS [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
          Length = 242

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 46/108 (42%), Positives = 73/108 (67%), Gaps = 1/108 (0%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRL 167


>gi|123966683|ref|YP_001011764.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9515]
 gi|123201049|gb|ABM72657.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9515]
          Length = 313

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 84/304 (27%), Positives = 151/304 (49%), Gaps = 40/304 (13%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------EHGDLS----------------- 48
           G   +S Y+  I ++P+L   EE  L  + +      E G L+                 
Sbjct: 16  GNDPISWYLSNIGRVPLLTPAEEIELGNQVQKMMTLTEDGQLNEKTKEFTPQQKRTIKIG 75

Query: 49  --AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  R++ ++LRLVV +A  Y+G GL + ++V EG++GL +AV+KFDP RG++ +TY+ 
Sbjct: 76  RRAKERMMKANLRLVVSVAKKYQGKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAF 135

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFN--LRRLKGHLQAITDNNLKPEQVVAIAK 164
           WWI+ +M   I      +++    +++        R L   L A+          + IA+
Sbjct: 136 WWIRQSMTRAIACQSRTIRLPVHLSERLATIRKVSRELAHKLGAMPSR-------IEIAE 188

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            + +   E+ S+  +     SL+A +N  D  S  +   L+ D + +E   +++ E+K  
Sbjct: 189 AMEIDVEELDSVLRQALSTSSLDAPVNGDDGRS--FLGDLIADSNNEEP--LDQVEQKMH 244

Query: 225 RNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +  L + ++ L+ +E+ + + R  L  N   TL  +    EVSRERVRQ+E +A +K++ 
Sbjct: 245 QEQLGKWLTHLSEQEQHVLKLRFGLDGNERHTLAEIGRLLEVSRERVRQVELKALRKLRN 304

Query: 283 SIQK 286
             +K
Sbjct: 305 LTRK 308


>gi|269215371|ref|ZP_06159225.1| RNA polymerase sigma factor RpoD [Slackia exigua ATCC 700122]
 gi|269131227|gb|EEZ62301.1| RNA polymerase sigma factor RpoD [Slackia exigua ATCC 700122]
          Length = 383

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 84/295 (28%), Positives = 138/295 (46%), Gaps = 42/295 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLA-------------KRYREHG-----------------DLS 48
           Y+ EI K+P+L   EE  LA             +R  + G                  L 
Sbjct: 85  YLKEIGKVPLLTAAEEIDLAMKIEAGVAATAELERAEDEGIELNRRDKRRLTRVEAVGLD 144

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L+ ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WW
Sbjct: 145 AKQQLIEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 204

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R++  L    + +  PE+   I +K+ +
Sbjct: 205 IRQAITRAIADQARTIRI--PVHMVETINKLVRIQRQLLQDLNRDPTPEE---IGEKMGL 259

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S   V  +        SL   I   ++  SQ  D++    D    V  +       +  L
Sbjct: 260 SAERVREIQKISQEPVSLETPIG--EEEDSQLGDFI---EDDSAVVPPDAASFSMLQEQL 314

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++ +  L  RER++   R   E+  P TLE +  EF V+RER+RQIE++   K++
Sbjct: 315 SKVLDGLAERERKVISLRFGLEDGHPHTLEEVGREFGVTRERIRQIESKTLAKLR 369


>gi|224024118|ref|ZP_03642484.1| hypothetical protein BACCOPRO_00840 [Bacteroides coprophilus DSM
           18228]
 gi|224017340|gb|EEF75352.1| hypothetical protein BACCOPRO_00840 [Bacteroides coprophilus DSM
           18228]
          Length = 317

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 79/275 (28%), Positives = 148/275 (53%), Gaps = 22/275 (8%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI +  ++  +EE  LA+R R+ GD  A  +L  ++LR VV +A  Y+  GL 
Sbjct: 48  SLDKYLQEIGREDLITVEEEVELAQRIRK-GDRVALEKLTRANLRFVVSVAKQYQNQGLS 106

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     +V++    NQ  
Sbjct: 107 LPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL--PLNQVG 164

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSS 193
               + +     +   +    PE+   +A +L +   + IS   +++G   S++A     
Sbjct: 165 SLNKISKAFSKFEQENERRPSPEE---LADELEIP-VDKISDTLKVSGRHISVDAPFVEG 220

Query: 194 DKNSSQWQDWLVYDHD--GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI---FEARRL 248
           + NS    D LV D        ++ E   R+     + R++S L  RE+ I   F     
Sbjct: 221 EDNS--LLDVLVNDDSPMADRSLVNESLSRE-----IDRALSTLTEREKDIIQMFFGINT 273

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           QE  +TLE +  +F ++RERVRQI+ +A ++++++
Sbjct: 274 QE--MTLEEIGDKFGLTRERVRQIKEKAIRRLRQN 306


>gi|312898762|ref|ZP_07758151.1| RNA polymerase sigma factor RpoD [Megasphaera micronuciformis
           F0359]
 gi|310620193|gb|EFQ03764.1| RNA polymerase sigma factor RpoD [Megasphaera micronuciformis
           F0359]
          Length = 437

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 84/291 (28%), Positives = 142/291 (48%), Gaps = 35/291 (12%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAA------------HRLVTSH 57
           VN +  +  Y+ EI ++P+L  +EE  LAKR  E G    A             +L  ++
Sbjct: 151 VNIDDPVRMYLKEIGRVPLLSAEEEITLAKRI-EAGSAEGATPEEVSAGNIAKKKLTDAN 209

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I
Sbjct: 210 LRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDYSKGYKFSTYATWWIRQAITRAI 269

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
                 ++I    +       L R+   L         PE+   IA+K+ V    V  + 
Sbjct: 270 ADQARTIRI--PVHMVETINKLIRISRQLLQDKGREPLPEE---IAEKMGVPVERVREI- 323

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWL-----VYDHDGQEQVLIEKEERKNRRNMLTRSM 232
            ++A  E ++      ++  S   D++     +   D    +L++++        +    
Sbjct: 324 MKIA-QEPVSLETPIGEEEDSHLGDFIEDQEAIAPDDAASFILLKEQ--------IEDVF 374

Query: 233 SVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           S L  RER++   R  L++  P TLE +   F V+RER+RQIE +A  K++
Sbjct: 375 SCLTDRERKVLYLRFGLKDGRPRTLEEVGQHFNVTRERIRQIEGKALSKLR 425


>gi|290967746|ref|ZP_06559301.1| RNA polymerase sigma factor RpoD [Megasphaera genomosp. type_1 str.
           28L]
 gi|290782262|gb|EFD94835.1| RNA polymerase sigma factor RpoD [Megasphaera genomosp. type_1 str.
           28L]
          Length = 423

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 80/281 (28%), Positives = 137/281 (48%), Gaps = 33/281 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGD-----------LSAAHRLVTSHLRLVVKIAMG 67
           Y+ EI ++P+L   EE  LAK   +  D           + A  +L  ++LRLVV IA  
Sbjct: 146 YLKEIGRVPLLSADEEITLAKAIEKGNDENATVADKKNGIDAKKKLTDANLRLVVSIAKR 205

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y G G+   +++ EGN+GL++AV KFD  +G++ +TY+ WWI+ A+   I      ++I 
Sbjct: 206 YVGRGMLFLDLIQEGNLGLLKAVDKFDYSKGYKFSTYATWWIRQAITRAIADQARTIRI- 264

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              +       L R+   L      +  PE+   IA+K+ +    V  +  ++A  E ++
Sbjct: 265 -PVHMVETINKLIRISRQLIQEKGRDPLPEE---IAEKMEIPVERVREI-MKIA-QEPVS 318

Query: 188 ALINSSDKNSSQWQDWL-----VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
                 ++  S   D++     V   D    +L++++        +    S L  RER++
Sbjct: 319 LETPIGEEEDSHLGDFIEDQEAVAPDDAASFILLKEQ--------IEEVFSCLTDRERKV 370

Query: 243 FEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              R  L++  P TLE +   F V+RER+RQIE +A  K++
Sbjct: 371 LYLRFGLKDGRPRTLEEVGQYFNVTRERIRQIEGKALGKLR 411


>gi|330982601|gb|EGH80704.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. aptata
           str. DSM 50252]
          Length = 459

 Score =  100 bits (250), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 83/270 (30%), Positives = 139/270 (51%), Gaps = 21/270 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 20  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 78

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 79  IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 137

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + +K       ++ +N R++  D SL      SDK  
Sbjct: 138 LRAARELTQKL-DHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSLGP---DSDKT- 192

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVT 254
               D L  D       L++ ++       + + +S L  ++R +   R   R  E+  T
Sbjct: 193 --LLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTEKQREVVIRRFGLRGHESS-T 246

Query: 255 LENLSSEFEVSRER----VRQIEARAFKKV 280
           LE++  E  ++RER    VR +    + +V
Sbjct: 247 LEDVGLEIGLTRERAGFEVRDVHPTHYGRV 276


>gi|148243603|ref|YP_001228760.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp.
           RCC307]
 gi|147851913|emb|CAK29407.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. RCC307]
          Length = 323

 Score =  100 bits (249), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 81/284 (28%), Positives = 139/284 (48%), Gaps = 31/284 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS--------------------AAHRLVTSHL 58
           Y+  I ++P+L   EE  LA + ++   LS                    A  R++ ++L
Sbjct: 39  YLSNIGRVPLLTAAEEIELAHQVQQMKQLSEIPAEERTPKQRQQVRMGCRARDRMMAANL 98

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+  M   I 
Sbjct: 99  RLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTRAID 158

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
            S   +++    ++K     +RR+   L   T    +    + +A  + +   E+  +  
Sbjct: 159 NSARTIRLPIHISEK--LSKMRRITREL---THRFGRQPNRLELAHAMGMEPDELEELLS 213

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           + A   SL+A     +  S+  +  L+ D    +   +E  +R+ ++  L   ++ LN R
Sbjct: 214 QSAPCASLDAHARGEEDRSTLGE--LIPDPSCNDS--MESMDRRIQKEHLGTWITQLNER 269

Query: 239 ERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
           E++I + R   E   P TL  +  +  VSRERVRQ+EA+A  K+
Sbjct: 270 EQKILKLRFGLEGAEPQTLAEIGRQINVSRERVRQLEAKAILKL 313


>gi|328882302|emb|CCA55541.1| RNA polymerase principal sigma factor HrdA [Streptomyces venezuelae
           ATCC 10712]
          Length = 336

 Score =  100 bits (249), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 85/295 (28%), Positives = 145/295 (49%), Gaps = 44/295 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRY------------------REHGDLS--------AAHR 52
           Y+ EI +IP+L  +EE  LA+R                   R   DL         A  +
Sbjct: 43  YLREIGRIPLLTAEEEVDLARRVEAGLFAEEKLANTPDLDSRLASDLDRLVVLGRIAKRK 102

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY+ WWI+ A
Sbjct: 103 LIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIRQA 162

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           M   +      +++     +     N R ++   + + +   +P     +A +L+++  E
Sbjct: 163 MSRALADQARTIRVPVHVVE---LIN-RVIRVQRRMLQERGYEP-TAEEVAAQLDLA-PE 216

Query: 173 VISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLT 229
            +    RLA +  SL+A +        + +D  + D   DG     +E       R  L 
Sbjct: 217 RVGEVLRLAQEPVSLHAPVG-------EEEDVALGDLIEDGDAASPVESAAFLLLRRHLE 269

Query: 230 RSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             +S L  RER++ + R   ++  P TLE +   F V+RER+RQIE++   K+++
Sbjct: 270 DVLSTLGERERKVVQLRYGLDDGRPRTLEEIGRIFGVTRERIRQIESKTLGKLRD 324


>gi|116075287|ref|ZP_01472547.1| RNA polymerase sigma factor [Synechococcus sp. RS9916]
 gi|116067484|gb|EAU73238.1| RNA polymerase sigma factor [Synechococcus sp. RS9916]
          Length = 479

 Score =  100 bits (249), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 73/261 (27%), Positives = 142/261 (54%), Gaps = 25/261 (9%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           ++P+++ +   +L +R +E        ++V S+LRLVV IA  Y   GL   +++ EG++
Sbjct: 227 EMPLIKFRRRLMLGRRAKE--------KMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSL 278

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A +KFD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K 
Sbjct: 279 GLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV-----HLYETISRIKK 333

Query: 145 HLQAITDN-NLKP-EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
             + ++     KP E+ +A + ++ + +   I+ + +L    SL   I   +   S+  D
Sbjct: 334 TTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGD 389

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSS 260
           ++  D +  EQ + +   R++   +L    + L+PRER +   R   ++    TLE +  
Sbjct: 390 FIEADIENPEQDVAKNLLREDLEGVL----ATLSPRERDVLRLRYGLDDGRMKTLEEIGQ 445

Query: 261 EFEVSRERVRQIEARAFKKVQ 281
            F+V+RER+RQIEA+A +K++
Sbjct: 446 IFDVTRERIRQIEAKALRKLR 466


>gi|1526450|dbj|BAA13238.1| RNA polymerase sigma subunit, truncated form of sigma-38
           [Escherichia coli W3110]
 gi|23306704|gb|AAN15271.1| C-terminal truncated RNA polymerase sigma factor S [Escherichia
           coli]
          Length = 269

 Score =  100 bits (249), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 46/108 (42%), Positives = 73/108 (67%), Gaps = 1/108 (0%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRL 167


>gi|78780175|ref|YP_398287.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9312]
 gi|123969439|ref|YP_001010297.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. AS9601]
 gi|126697226|ref|YP_001092112.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9301]
 gi|78713674|gb|ABB50851.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9312]
 gi|123199549|gb|ABM71190.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. AS9601]
 gi|126544269|gb|ABO18511.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9301]
          Length = 339

 Score =  100 bits (249), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 80/285 (28%), Positives = 141/285 (49%), Gaps = 31/285 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDL--------------------SAAHRLVTSHL 58
           Y+  I ++P+L   EE  LA   +    L                     A  R++ ++L
Sbjct: 55  YLSSIGRVPLLTPAEEIELAHHVQNMKKLLQIPETDRTQRNLYQIKIGKRARDRMMAANL 114

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+  M   I 
Sbjct: 115 RLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTRAID 174

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
            S   +++    ++K     +RR+   L   +    +    + +A ++ + + ++  +  
Sbjct: 175 NSARTIRLPIHISEK--LSKMRRVSREL---SHKFGRQPTRLEMATEMGIDQKDLEDLIS 229

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           + A   SL+A     +  S+  +  L+ D + +E   +E  +R  ++  L   +S LN R
Sbjct: 230 QSAPCASLDAHARGEEDRSTLGE--LIPDPNCEEP--MEGMDRTIQKEHLGTWLSQLNER 285

Query: 239 ERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           E++I + R     E P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 286 EQKIMKLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 330


>gi|134036998|gb|ABO47837.1| truncated sigma 38 factor [Escherichia coli]
 gi|134037001|gb|ABO47839.1| truncated sigma 38 factor [Escherichia coli]
          Length = 240

 Score =  100 bits (249), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 46/108 (42%), Positives = 73/108 (67%), Gaps = 1/108 (0%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRL 167


>gi|4100832|gb|AAD00998.1| RpoS [Escherichia coli]
          Length = 269

 Score =  100 bits (249), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 46/108 (42%), Positives = 73/108 (67%), Gaps = 1/108 (0%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 48  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 106

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++
Sbjct: 107 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRL 154


>gi|329934715|ref|ZP_08284756.1| RNA polymerase principal sigma factor HrdA [Streptomyces
           griseoaurantiacus M045]
 gi|329305537|gb|EGG49393.1| RNA polymerase principal sigma factor HrdA [Streptomyces
           griseoaurantiacus M045]
          Length = 363

 Score =  100 bits (249), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 88/297 (29%), Positives = 144/297 (48%), Gaps = 46/297 (15%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHG-------------------DLS--------AA 50
           +Y+ EI +IP+L   EE  LA+R  E G                   DL         A 
Sbjct: 69  QYLREIGRIPLLTAAEEVELARRV-EAGLFAEEKLGSTPDLDSRLALDLDTLVVRGRMAK 127

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY+ WWI+
Sbjct: 128 RRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIR 187

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            AM   +      +++     +     N R ++   + + +   +P     +A +L++S 
Sbjct: 188 QAMSRALADQARTIRVPVHVVE---LIN-RVVRVQRRMLQERGYEP-SAEEVAAQLDLS- 241

Query: 171 SEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNM 227
            E +    RLA +  SL+A +        + +D  + D   DG     +E       R  
Sbjct: 242 PERVGEVLRLAQEPVSLHAPVG-------EEEDVALGDLIEDGDATSPVESAAFLLLREH 294

Query: 228 LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           L   +S L  RER++ + R       P TLE +   F V+RER+RQIE++   K+++
Sbjct: 295 LDAVLSTLGERERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRD 351


>gi|3451022|gb|AAC32644.1| RNA polymerase sigma factor [Escherichia coli RS218]
          Length = 220

 Score =  100 bits (249), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 46/108 (42%), Positives = 73/108 (67%), Gaps = 1/108 (0%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRL 167


>gi|6010722|gb|AAF01227.1|AF184096_1 mutant RpoS [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
          Length = 228

 Score =  100 bits (249), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 46/108 (42%), Positives = 73/108 (67%), Gaps = 1/108 (0%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRL 167


>gi|317060654|ref|ZP_07925139.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. D12]
 gi|313686330|gb|EFS23165.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. D12]
          Length = 276

 Score =  100 bits (249), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 76/252 (30%), Positives = 133/252 (52%), Gaps = 23/252 (9%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A ++L+  +LRLVV +A GYR  G+ + +++SEGN+GL++A++KFD E+GFR +
Sbjct: 37  QSGDEEAKNQLILCNLRLVVNVAKGYRSKGMNLIDLISEGNLGLIRAIEKFDVEKGFRFS 96

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITDNNLKPEQVVA 161
           TY++WWIK ++ + I+     ++I +       +  L ++  ++ + I    + P  V  
Sbjct: 97  TYAVWWIKQSISKAIIFKGREIRIPSYR-----YDILNKINRYVTEEIKLYGVYP-SVEE 150

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD---GQEQVLIEK 218
           +A+ LN+  ++V  +        SL+  I              +Y  D   G E+   EK
Sbjct: 151 VAEYLNMPVNKVEEIMIEFQEPMSLSTEIGED-----------IYLEDTLSGTEEHFEEK 199

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARA 276
              K  +  L   ++ L+ RE+ I + R  L    + TLE +   F ++RERVRQIE   
Sbjct: 200 VYYKMMQQRLKDILNRLDTREQEILKLRFGLDGYEIHTLEEIGKNFNITRERVRQIEKNT 259

Query: 277 FKKVQESIQKQV 288
            KK++    K++
Sbjct: 260 LKKLKRKYTKEL 271


>gi|23099399|ref|NP_692865.1| RNA polymerase sigma factor RpoD [Oceanobacillus iheyensis HTE831]
 gi|22777628|dbj|BAC13900.1| RNA polymerase sigma-43(-A) factor [Oceanobacillus iheyensis
           HTE831]
          Length = 380

 Score =  100 bits (249), Expect = 2e-19,   Method: Compositional matrix adjust.
 Identities = 84/276 (30%), Positives = 129/276 (46%), Gaps = 35/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LA    E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 114 YLKEIGRVNLLSAAEEIDLASSI-EEGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 172

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 173 IQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 232

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
             Q+ L  +L R     +   +  L P++V  I K       E +S+   +    D  L 
Sbjct: 233 RVQRSLLQDLGREPTPEEIGEEMELGPDKVRDILK----IAQEPVSLETPIGEEDDSHLG 288

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +  S         DH   E +          +  L   +  L  RE  +   R 
Sbjct: 289 DFIEDQEAISPS-------DHAAYELL----------KEQLEDVLDTLTDREENVLRLRF 331

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 332 GLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLR 367


>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 =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 68/236 (28%), Positives = 122/236 (51%), Gaps = 12/236 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 557 DAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 616

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I     +     N R  + HLQ       +P+  + +A K+ 
Sbjct: 617 WIRQAITRSIADQARTIRIPVHMIETINKMN-RISRQHLQEF---GFEPDASI-LAAKME 671

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + E ++  +  ++A  E ++      D + S   D++    D      ++   +   R++
Sbjct: 672 IPEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDSNNTAPVDAAMQAGLRDV 726

Query: 228 LTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 727 VKDILDGLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLK 782


>gi|332709863|ref|ZP_08429819.1| RNA polymerase, sigma subunit, RpsC/SigC [Lyngbya majuscula 3L]
 gi|332351234|gb|EGJ30818.1| RNA polymerase, sigma subunit, RpsC/SigC [Lyngbya majuscula 3L]
          Length = 417

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 68/238 (28%), Positives = 128/238 (53%), Gaps = 13/238 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L A   ++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV+KFDP +G+R +TY+ 
Sbjct: 176 LQAKEHMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTKGYRFSTYAY 235

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   I      +++     +K     L ++K   + I+    +   +  IA +L
Sbjct: 236 WWIRQGITRAIATQSRTIRLPVHITEK-----LNKIKKAQRKISQERGRTATIDDIAVEL 290

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++ ++V  +  R+    SL   I    +  ++  D L  +    E+VL+ +  +++ + 
Sbjct: 291 EMTAAQVREVLLRVPRSVSLE--IKVGKERDTELGDLLETEETSPEEVLMREALQRDLQQ 348

Query: 227 MLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +L    + L  RER +   R  L +N P +L  +    ++SRERVRQIEA+A +K+++
Sbjct: 349 LL----ADLTNRERDVIRMRFGLGDNQPYSLAEIGRALDLSRERVRQIEAKALQKLRQ 402


>gi|302551232|ref|ZP_07303574.1| RNA polymerase sigma factor RpoS [Streptomyces viridochromogenes
           DSM 40736]
 gi|302468850|gb|EFL31943.1| RNA polymerase sigma factor RpoS [Streptomyces viridochromogenes
           DSM 40736]
          Length = 438

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 87/294 (29%), Positives = 139/294 (47%), Gaps = 40/294 (13%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRY----------REHGDLS----------------AAH 51
           +Y+ EI ++P+L   EE  LA+R           R   DL                 A  
Sbjct: 144 QYLREIGRVPLLTAAEEVELARRVEAGLFAEEKLRLAPDLDSQLAVDLDRLVVMGRMAKR 203

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY+ WWI+ 
Sbjct: 204 RLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIRQ 263

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           AM   +      +++    +   L   + R++  +         PE+V A    L +   
Sbjct: 264 AMSRALADQARTIRV--PVHVVELINRVVRVQRRMLQERGYEPTPEEVAA---HLELP-P 317

Query: 172 EVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           E +    RLA +  SL+A +   D  +    D +    DG     +E       R  L  
Sbjct: 318 ERVGEVLRLAQEPVSLHAPVGEEDDVA--LGDLI---EDGDAASPVESAAFLLLREHLEA 372

Query: 231 SMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            +S L  RER++ + R       P TLE +   F V+RER+RQIE++   K+++
Sbjct: 373 VLSTLGERERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRD 426


>gi|328947378|ref|YP_004364715.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           succinifaciens DSM 2489]
 gi|328447702|gb|AEB13418.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           succinifaciens DSM 2489]
          Length = 283

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 78/276 (28%), Positives = 141/276 (51%), Gaps = 34/276 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           +++EI+KIP+L   EE  LA R    GD +A  +L+TS++R V+KIA  Y   GL   ++
Sbjct: 15  HLNEIKKIPLLTNDEEIQLATRAAA-GDKAARDKLLTSNMRFVIKIASQYLNKGLEYEDL 73

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           +SEG +GLM+A+  FD  +G+   +Y++WWI+ ++ + I+     +++    + +     
Sbjct: 74  ISEGYLGLMKALDHFDVSKGYHFISYAVWWIRQSIMKAIVDFGRPIRLPVNKDAE----- 128

Query: 139 LRRLKGHLQAITDNNLKPEQVVA-------------IAKKLNVSESEVISMNCRLAGDES 185
           L  +K    ++  +  K E+                I + LN+S+ E+IS++  ++GD S
Sbjct: 129 LTEIKRACHSVNPHGKKSEEEELEEVALKLGMTKHHIREMLNISQ-EMISLDSPISGD-S 186

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
             AL+++    +   +D  +          ++ E  K    +  +S+ VLN R     + 
Sbjct: 187 DTALVDTVSAGTFTPEDAAI-------DASLKTEIDKAFVGLDKKSVEVLNMRYGLNGQG 239

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R      TL+ +  +  +SRERVRQIE  A  K++
Sbjct: 240 ER------TLKEVGEKMNLSRERVRQIEKHAIAKIR 269


>gi|113954073|ref|YP_731235.1| RNA polymerase sigma factor RpoD [Synechococcus sp. CC9311]
 gi|113881424|gb|ABI46382.1| RNA polymerase sigma factor RpoD [Synechococcus sp. CC9311]
          Length = 440

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 75/275 (27%), Positives = 148/275 (53%), Gaps = 25/275 (9%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           NG++  ++    + ++P++  +   +L +R +E        ++V S+LRLVV IA  Y  
Sbjct: 174 NGKLPETKEWAALVEMPVIRFRRRLMLGRRAKE--------KMVQSNLRLVVSIAKKYMN 225

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+   I      +++    
Sbjct: 226 RGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV-- 283

Query: 131 NQKRLFFNLRRLKGHLQAITDN-NLKP-EQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
               L+  + R+K   + ++     KP E+ +A + ++ + +   I+ + +L    SL  
Sbjct: 284 ---HLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEMTIEKLRFIAKSAQLPI--SLET 338

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            I   +   S+  D++  D +  EQ + +   R++   +L    + L+PRER +   R  
Sbjct: 339 PIGKEE--DSRLGDFIEADIENPEQDVAKNLLREDLEGVL----ATLSPRERDVLRLRYG 392

Query: 249 QENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            ++    TLE +   F+V+RER+RQIEA+A +K++
Sbjct: 393 LDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLR 427


>gi|257463050|ref|ZP_05627452.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. D12]
          Length = 272

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 76/252 (30%), Positives = 133/252 (52%), Gaps = 23/252 (9%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A ++L+  +LRLVV +A GYR  G+ + +++SEGN+GL++A++KFD E+GFR +
Sbjct: 33  QSGDEEAKNQLILCNLRLVVNVAKGYRSKGMNLIDLISEGNLGLIRAIEKFDVEKGFRFS 92

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITDNNLKPEQVVA 161
           TY++WWIK ++ + I+     ++I +       +  L ++  ++ + I    + P  V  
Sbjct: 93  TYAVWWIKQSISKAIIFKGREIRIPSYR-----YDILNKINRYVTEEIKLYGVYP-SVEE 146

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD---GQEQVLIEK 218
           +A+ LN+  ++V  +        SL+  I              +Y  D   G E+   EK
Sbjct: 147 VAEYLNMPVNKVEEIMIEFQEPMSLSTEIGED-----------IYLEDTLSGTEEHFEEK 195

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARA 276
              K  +  L   ++ L+ RE+ I + R  L    + TLE +   F ++RERVRQIE   
Sbjct: 196 VYYKMMQQRLKDILNRLDTREQEILKLRFGLDGYEIHTLEEIGKNFNITRERVRQIEKNT 255

Query: 277 FKKVQESIQKQV 288
            KK++    K++
Sbjct: 256 LKKLKRKYTKEL 267


>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 =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 68/236 (28%), Positives = 122/236 (51%), Gaps = 12/236 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 561 DAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 620

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I     +     N R  + HLQ       +P+  + +A K+ 
Sbjct: 621 WIRQAITRSIADQARTIRIPVHMIETINKMN-RISRQHLQEF---GFEPDASI-LAAKME 675

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + E ++  +  ++A  E ++      D + S   D++    D      ++   +   R++
Sbjct: 676 IPEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDSSNTAPVDAAMQAGLRDV 730

Query: 228 LTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 731 VKDILDGLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLK 786


>gi|295102137|emb|CBK99682.1| RNA polymerase sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii L2-6]
          Length = 461

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 80/262 (30%), Positives = 134/262 (51%), Gaps = 25/262 (9%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ E++ + +L  + R  G L+A   L  ++LRLVV IA  + G+ L   +++ EGNIGL
Sbjct: 205 PLTEERRQELL--KTRRDG-LNARRSLSEANLRLVVSIAKKHVGHNLAFLDLIQEGNIGL 261

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKRLFFN-LRR 141
           ++A +KFD +RGFR +TY+ WWI+ A+   I      ++I      T N+ R   N L  
Sbjct: 262 IKAAEKFDCDRGFRFSTYATWWIRQAITRAIADQARTIRIPVHMVETINRMRQATNQLVY 321

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
             GH          PE+   +AK +++S   V  +        SL + +   ++  S   
Sbjct: 322 QNGH-------EPTPEE---LAKAMDMSVERVREIQRMAQEPASLESPV--GEEEDSSLG 369

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLS 259
           D++    D   +   +  +R      + +++  L PRE ++   R   ++  P TLE + 
Sbjct: 370 DFVA---DENAEAPGKAADRAMVAQQINQALKSLTPREEKVIRLRFGLDDGRPRTLEEVG 426

Query: 260 SEFEVSRERVRQIEARAFKKVQ 281
            +F V+RERVRQIEA+A +K+ 
Sbjct: 427 RDFGVTRERVRQIEAKAIRKLH 448


>gi|302869477|ref|YP_003838114.1| sigma-70 family RNA polymerase [Micromonospora aurantiaca ATCC
           27029]
 gi|315504060|ref|YP_004082947.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Micromonospora
           sp. L5]
 gi|302572336|gb|ADL48538.1| RNA polymerase sigma factor, sigma-70 family [Micromonospora
           aurantiaca ATCC 27029]
 gi|315410679|gb|ADU08796.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Micromonospora
           sp. L5]
          Length = 333

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 88/307 (28%), Positives = 146/307 (47%), Gaps = 68/307 (22%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH----------GDLSAAHRLVT-------- 55
           Y+HEI + P+L+   E  L+K      Y EH           D     RLV         
Sbjct: 42  YLHEISRTPLLDAAREVDLSKAIEAGLYAEHLLDEDRIPDGVDREDLERLVAEGERAKDL 101

Query: 56  ---SHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
              ++LRLVV IA  Y   G+P+ +++ EGN GL++AV+KFD ERGF+ +TY+ WWI+ A
Sbjct: 102 FIRANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQA 161

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT---DNNLKPEQVVAIAKKLNVS 169
           +   I +    V++        L  ++ R++   + +T    ++ +PEQ   IA  L V+
Sbjct: 162 ISRAIAQQERTVRLPV-----HLVEDVNRMRNVARQLTRELGSDPEPEQ---IATALGVT 213

Query: 170 ----------ESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
                       + +S++  +   GD +L  L+  SD  S              E++++ 
Sbjct: 214 VERVNELVRWSQDTVSLDTPVGDDGDTNLGDLVADSDAPSP-------------EEIVLT 260

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEAR 275
             ER+    +L      L+ R   I  AR   E+    +L  ++S F +SRER+RQ+E +
Sbjct: 261 GLERQRIEGLLNH----LDDRSAGIMRARYGLEDGREHSLTEVASRFSLSRERIRQLEIQ 316

Query: 276 AFKKVQE 282
           A  +++E
Sbjct: 317 ALGRLRE 323


>gi|4100834|gb|AAD00999.1| RpoS [Escherichia coli]
          Length = 258

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 46/108 (42%), Positives = 73/108 (67%), Gaps = 1/108 (0%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 37  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 95

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++
Sbjct: 96  IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRL 143


>gi|328955627|ref|YP_004372960.1| RNA polymerase, sigma 70 subunit, RpoD [Coriobacterium glomerans
           PW2]
 gi|328455951|gb|AEB07145.1| RNA polymerase, sigma 70 subunit, RpoD [Coriobacterium glomerans
           PW2]
          Length = 442

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 74/236 (31%), Positives = 122/236 (51%), Gaps = 12/236 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L A   L++++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD E+GF+ +TY+ 
Sbjct: 202 LEAKQALISANLRLVVSIAKRYVGRGMHFLDLIQEGNLGLIRAVEKFDYEKGFKFSTYAT 261

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I    +       L R++  L      +  PE++ A   ++
Sbjct: 262 WWIRQAITRAIADQARTIRI--PVHMVETINKLVRVQRQLLQELGRDPTPEEIGA---EM 316

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +S   V  +        SL   I   ++  SQ  D++    D Q  V  +       R 
Sbjct: 317 EMSADRVREIQKISQEPVSLETPIG--EEEDSQLGDFI---EDAQAVVPPDAASFSMLRE 371

Query: 227 MLTRSMSVLNPRERRIFEAR-RLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            L + +  L  RER++ E R  L + +P TLE +  +F V+RER+RQIE++   K+
Sbjct: 372 QLVQVLDSLADRERKVIELRFGLNDGHPRTLEEVGRDFGVTRERIRQIESKTLAKL 427


>gi|124025264|ref|YP_001014380.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str.
           NATL1A]
 gi|123960332|gb|ABM75115.1| Putative principal RNA polymerase sigma factor [Prochlorococcus
           marinus str. NATL1A]
          Length = 420

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 130/237 (54%), Gaps = 17/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 182 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 241

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++     KP E+ +A + ++
Sbjct: 242 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEM 296

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  D +  EQ + +   R++   
Sbjct: 297 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIEADIENPEQDVAKTLLREDLEG 352

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +L    + L+PRER +   R   ++    TLE +   F+V+RER+RQIEA+A +K++
Sbjct: 353 VL----ATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLR 405


>gi|87123878|ref|ZP_01079728.1| Sigma-70 factor [Synechococcus sp. RS9917]
 gi|86168447|gb|EAQ69704.1| Sigma-70 factor [Synechococcus sp. RS9917]
          Length = 456

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 130/237 (54%), Gaps = 17/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 220 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 279

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++     KP E+ +A + ++
Sbjct: 280 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEM 334

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  D +  EQ + +   R++   
Sbjct: 335 TIEKLRFIAKSAQLP--ISLETPIGKEE--DSRLGDFIEADIENPEQDVAKNLLREDLEG 390

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +L    + L+PRER +   R   ++    TLE +   F+V+RER+RQIEA+A +K++
Sbjct: 391 VL----ATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLR 443


>gi|114771658|ref|ZP_01449062.1| RNA polymerase sigma factor [alpha proteobacterium HTCC2255]
 gi|114547730|gb|EAU50620.1| RNA polymerase sigma factor [alpha proteobacterium HTCC2255]
          Length = 656

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 78/251 (31%), Positives = 122/251 (48%), Gaps = 42/251 (16%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           SA   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 417 SAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 476

Query: 108 WIKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRR------LKGHLQAITDN 152
           WI+ A+   I      ++I      T N+     +++   + R      L   LQ   D 
Sbjct: 477 WIRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEIGREPTPEELASKLQMPLD- 535

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             K  +V+ IAK       E IS+   +             D+  SQ  D++    D   
Sbjct: 536 --KVRKVMKIAK-------EPISLETPIG------------DEEDSQLGDFI---EDKNA 571

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVR 270
            + +E   + N +   TR ++ L PRE R+   R         TLE +  +F V+RER+R
Sbjct: 572 ILPLESAIQGNLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIR 631

Query: 271 QIEARAFKKVQ 281
           QIEA+A +K++
Sbjct: 632 QIEAKALRKLK 642


>gi|148654372|ref|YP_001274577.1| RpoD family RNA polymerase sigma factor [Roseiflexus sp. RS-1]
 gi|148566482|gb|ABQ88627.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus sp.
           RS-1]
          Length = 402

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 85/293 (29%), Positives = 138/293 (47%), Gaps = 44/293 (15%)

Query: 19  YIHEIRKIPMLEKQEEYVLAK---------RYREHGDLS-----------------AAHR 52
           Y+ EI ++P+L  ++E +LAK         R  E  + S                 A   
Sbjct: 109 YLQEIGQVPLLSAEQEVMLAKAMEAGHRARRALEREEYSSWQERVMYEQQVAQGNEARQH 168

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV IA  Y  YGL + ++V EGNIGLM+AV+KFD  +G + +TY+ WWI+ A
Sbjct: 169 LIQANLRLVVSIAKKYTSYGLTMMDLVQEGNIGLMRAVEKFDYTKGHKFSTYATWWIRQA 228

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   I      +++     +      ++R    LQ        PE+   IA  + +S ++
Sbjct: 229 ITRAIADQSRTIRLPVHMGEA--ISQVKRTSHKLQQTMQREPTPEE---IADAMGISSTK 283

Query: 173 VISMNCRLAGDESLNAL---INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           V     R   + S++ L   +    +   +  D++    D +     E       R  L 
Sbjct: 284 V-----RRTLEASMHPLSLEMPVGQEGEGRMGDFI---EDDRISTPAEAAAASMLREQLE 335

Query: 230 RSMSVLNPRERRIFEARR-LQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
             +  L  RER+I + R  L++    TLE +  EF ++RER+RQIEA A +K+
Sbjct: 336 EVLQKLPERERKIIQLRYGLKDGRYRTLEEVGMEFGITRERIRQIEAVALRKL 388


>gi|158833959|gb|ABW81785.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
          Length = 225

 Score =  100 bits (249), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 47/100 (47%), Positives = 69/100 (69%), Gaps = 1/100 (1%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L   EE   A+R    GD S+  R++ S+LRLVVKI+  Y   GLP+ ++
Sbjct: 8   YLSEIGYSPLLTAAEEIYFARRVL-CGDESSRRRMIESNLRLVVKISRRYINRGLPLLDL 66

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+
Sbjct: 67  IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIM 106


>gi|317969651|ref|ZP_07971041.1| RNA polymerase sigma factor RpoD [Synechococcus sp. CB0205]
          Length = 470

 Score =  100 bits (248), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 130/237 (54%), Gaps = 17/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 234 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 293

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++     KP E+ +A + ++
Sbjct: 294 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKTLSQEFGRKPTEEEIAESMEM 348

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  D +  EQ + +   R++   
Sbjct: 349 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIEADIENPEQDVAKNLLREDLEG 404

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +L    + L+PRER +   R   ++    TLE +   F+V+RER+RQIEA+A +K++
Sbjct: 405 VL----ATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLR 457


>gi|163781693|ref|ZP_02176693.1| RNA polymerase sigma factor RpoD [Hydrogenivirga sp. 128-5-R1-1]
 gi|159882913|gb|EDP76417.1| RNA polymerase sigma factor RpoD [Hydrogenivirga sp. 128-5-R1-1]
          Length = 571

 Score =  100 bits (248), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 75/246 (30%), Positives = 119/246 (48%), Gaps = 30/246 (12%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           + A   ++ S+LRLVV IA  Y   GL   +++ EGNIGLM+AV K+D  +G++ +TY+ 
Sbjct: 332 VKAKQVMIQSNLRLVVSIAKKYVNRGLHFLDLIQEGNIGLMKAVDKYDYRKGYKFSTYAT 391

Query: 107 WWIKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPE 157
           WWI+ A+   I      ++I      T N+     KRLF  L R     +      + P+
Sbjct: 392 WWIRQAITRAIADQARTIRIPVHMIETINRIIKASKRLFQELGREPTPEEIAKHLGMTPD 451

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           +V    +K+  S  E IS+   +  DE         DK+    ++++             
Sbjct: 452 KV----RKVLRSAQEPISLETPIGDDEDTFLKDFIEDKSVPNPEEYV------------- 494

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              RK  R  L R +  L+ +ER I   R   +     TLE +   F V+RER+RQIE++
Sbjct: 495 --SRKLLREQLERVLETLSDKEREILRYRYGLVDGTEYTLEQVGKMFNVTRERIRQIESK 552

Query: 276 AFKKVQ 281
           A +K++
Sbjct: 553 AIRKLR 558


>gi|78185245|ref|YP_377680.1| RNA polymerase sigma factor RpoD [Synechococcus sp. CC9902]
 gi|78169539|gb|ABB26636.1| Sigma-70 factor [Synechococcus sp. CC9902]
          Length = 451

 Score =  100 bits (248), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 130/237 (54%), Gaps = 17/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 215 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 274

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++     KP E+ +A + ++
Sbjct: 275 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEM 329

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  D +  EQ + +   R++   
Sbjct: 330 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIEADIENPEQDVAKNLLREDLEG 385

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +L    + L+PRER +   R   ++    TLE +   F+V+RER+RQIEA+A +K++
Sbjct: 386 VL----ATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLR 438


>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 =  100 bits (248), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 69/241 (28%), Positives = 123/241 (51%), Gaps = 12/241 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 563 ERASRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 622

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I     +     N R  + HLQ       +P+  + +
Sbjct: 623 TYATWWIRQAITRSIADQARTIRIPVHMIETINKMN-RISRQHLQEF---GFEPDASI-L 677

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A K+ + E ++  +  ++A  E ++      D + S   D++    D      ++   + 
Sbjct: 678 AAKMEIPEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDTNNTAPVDAAMQA 732

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKV 280
             R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 733 GLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKL 792

Query: 281 Q 281
           +
Sbjct: 793 K 793


>gi|72383665|ref|YP_293020.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str.
           NATL2A]
 gi|72003515|gb|AAZ59317.1| sigma-70 factor [Prochlorococcus marinus str. NATL2A]
          Length = 420

 Score =  100 bits (248), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 130/237 (54%), Gaps = 17/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 182 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 241

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++     KP E+ +A + ++
Sbjct: 242 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEM 296

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  D +  EQ + +   R++   
Sbjct: 297 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIEADIENPEQDVAKTLLREDLEG 352

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +L    + L+PRER +   R   ++    TLE +   F+V+RER+RQIEA+A +K++
Sbjct: 353 VL----ATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLR 405


>gi|158339245|ref|YP_001520422.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158309486|gb|ABW31103.1| RNA polymerase sigma-70 factor, putative [Acaryochloris marina
           MBIC11017]
          Length = 268

 Score =  100 bits (248), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 78/279 (27%), Positives = 133/279 (47%), Gaps = 37/279 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ E+ + P+L  +EE  LA++ +  GDL A  R++  +LRLVV IA  ++  GLP+ ++
Sbjct: 11  YLKEMGRYPLLSHEEEIRLARQVKA-GDLKAKQRMIECNLRLVVSIAKKHQHLGLPLMDL 69

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF- 137
           + EG+IGL  AV KFD  +G + +TY+ WWI  A++  +             +Q R  + 
Sbjct: 70  IQEGSIGLNTAVDKFDLAQGCKFSTYAYWWISEAIKRAL------------KSQSRTIYI 117

Query: 138 ------NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
                    R+K  ++ +T    +   +  ++    +  S + +         SL+  + 
Sbjct: 118 PIHQWERAHRIKKAVRQLTQEKGRTPTLKELSAATGIKSSLIRNTLQSFQAVSSLDQPVG 177

Query: 192 SSDKNS----SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
              K++     Q +D  +   DG E   IE        + LTR M+ L  RER I + R 
Sbjct: 178 PEQKDALIDLIQTEDAPLSIMDGLE---IE--------DALTRCMAYLTERERFIVDQRY 226

Query: 248 --LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                 P ++  +  + ++SRERVRQI   A KK+   +
Sbjct: 227 GLTDGQPKSMGAIGKQIDISRERVRQILNIAMKKMTRQV 265


>gi|313203522|ref|YP_004042179.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Paludibacter
           propionicigenes WB4]
 gi|312442838|gb|ADQ79194.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Paludibacter
           propionicigenes WB4]
          Length = 287

 Score =  100 bits (248), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 79/271 (29%), Positives = 146/271 (53%), Gaps = 19/271 (7%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI +  ++  +EE  LA+R R  GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGREDLITVEEEVELAQRIR-AGDRIALEKLTRANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     +V++    NQ   
Sbjct: 77  PDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL--PLNQVGS 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
              + +     +   +    PE+   +A  L++   + I+   +++G   S++A     +
Sbjct: 135 LNKINKAFSKFEQENERKPSPEE---LADVLDIP-VDKIADTMKVSGRHISVDAPFVEGE 190

Query: 195 KNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI---FEARRLQE 250
            NS    D ++ D     ++VLI +   K    +L  ++S    RER I   F    + E
Sbjct: 191 DNS--LLDVMINDDSPNADRVLINESLSKEIERVLAFTLS---DRERDIVKKFFGIGVAE 245

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             +TLE +  EF ++RERVRQI+ +A +K++
Sbjct: 246 --MTLEEIGDEFGLTRERVRQIKEKAIRKLR 274


>gi|182418305|ref|ZP_02949600.1| RNA polymerase sigma factor RpoD [Clostridium butyricum 5521]
 gi|237666788|ref|ZP_04526773.1| RNA polymerase sigma factor RpoD [Clostridium butyricum E4 str.
           BoNT E BL5262]
 gi|182377687|gb|EDT75231.1| RNA polymerase sigma factor RpoD [Clostridium butyricum 5521]
 gi|237657987|gb|EEP55542.1| RNA polymerase sigma factor RpoD [Clostridium butyricum E4 str.
           BoNT E BL5262]
          Length = 369

 Score =  100 bits (248), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 78/264 (29%), Positives = 133/264 (50%), Gaps = 13/264 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  ++E   A++  E G+  A  +L  ++LRLVV IA  Y G G+   ++
Sbjct: 103 YLKEIGKVPLLSSEQEIEYAQQI-EEGNQRAKKKLAEANLRLVVSIAKRYVGRGMLFLDL 161

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 162 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 219

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R++  L      +  PE+   I+K +++   +V  +        SL   I   ++  S
Sbjct: 220 LIRVQRQLLQELGRDPFPEE---ISKVMDLPVDKVREIQKIAQEPVSLETPI--GEEEDS 274

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++  D              K +   L   +  L PRE ++   R   ++    TLE
Sbjct: 275 HLGDFIPDDEAPAPAEAAAFTMLKEQ---LINVLDTLTPREEKVLRLRFGLDDGRARTLE 331

Query: 257 NLSSEFEVSRERVRQIEARAFKKV 280
            +  EF V+RER+RQIEA+A +K+
Sbjct: 332 EVGKEFNVTRERIRQIEAKALRKL 355


>gi|209809124|ref|YP_002264662.1| RNA polymerase sigma factor [Aliivibrio salmonicida LFI1238]
 gi|208010686|emb|CAQ81073.1| RNA polymerase sigma factor [Aliivibrio salmonicida LFI1238]
          Length = 293

 Score =  100 bits (248), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 87/286 (30%), Positives = 141/286 (49%), Gaps = 38/286 (13%)

Query: 17  SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG---L 73
           S Y+ EI K  +L   EE   ++ Y   GDL + + L+ S+LRLVVKIA  YR      L
Sbjct: 20  SLYLKEINKYKLLTASEELEHSRNYLS-GDLKSRNVLIESNLRLVVKIANKYRHRNQREL 78

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFDPE G+R +TY++WWIK +++  +      V++       
Sbjct: 79  APLDIIEEGNLGLMKAVNKFDPELGYRFSTYAVWWIKESIESALFNHSRTVRLPVHIT-- 136

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN-- 191
                 + L  +L+A  D          + K+ ++SE   IS++C     + +N ++   
Sbjct: 137 ------KELNVYLRAARD------LSRTLKKEPSISE---ISVHCN-KDYKKVNKILGLV 180

Query: 192 ---------SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
                    SSD  SS   +    DH   EQ   +   + N  + L+  +++L  RE++I
Sbjct: 181 PSSSTCHSASSDDMSSNLIELCADDH---EQEPAQSLSKSNLESNLSSWLNLLQCREKQI 237

Query: 243 FEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              R      +  TLE L  + ++S+ERVRQI+     K+    +K
Sbjct: 238 IINRYGLFGTDVKTLEELGQDLQLSKERVRQIQTETLTKLNTIFKK 283


>gi|33866315|ref|NP_897874.1| RNA polymerase sigma factor RpoD [Synechococcus sp. WH 8102]
 gi|33639290|emb|CAE08298.1| Putative principal RNA polymerase sigma factor [Synechococcus sp.
           WH 8102]
          Length = 471

 Score =  100 bits (248), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 130/237 (54%), Gaps = 17/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 235 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 294

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++     KP E+ +A + ++
Sbjct: 295 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEM 349

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  D +  EQ + +   R++   
Sbjct: 350 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIEADIENPEQDVAKNLLREDLEG 405

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +L    + L+PRER +   R   ++    TLE +   F+V+RER+RQIEA+A +K++
Sbjct: 406 VL----ATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLR 458


>gi|33240812|ref|NP_875754.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Prochlorococcus marinus subsp. marinus str. CCMP1375]
 gi|33238341|gb|AAQ00407.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Prochlorococcus marinus subsp. marinus str. CCMP1375]
          Length = 313

 Score =  100 bits (248), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 83/301 (27%), Positives = 152/301 (50%), Gaps = 42/301 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLA-------------------KRYREHGDLS------AA 50
           +S Y+  I ++P+L   EE  L                    K++  H   S      A 
Sbjct: 20  ISWYLATIGRVPLLTPAEEIELGNQVQVMMNLTEDGMVNEKTKKFTSHERRSIRIGRRAK 79

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            R++ ++LRLVV +A  Y+G GL + ++V EG++GL +AV+KFDP RG++ +TY+ WWI+
Sbjct: 80  ERMMKANLRLVVSVAKKYQGKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAFWWIR 139

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK---GHLQAITDNNLKPEQVVAIAKKLN 167
            +M   I      +++    +++     +R++     H      N L+      IA++++
Sbjct: 140 QSMTRAIACQSRTIRLPVHLSER--LATIRKVSLDLAHKLGAMPNRLE------IAEEMD 191

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +   E+ S+  +     SL+A +N  D  S  +   L+ D   +E   ++K E+   +  
Sbjct: 192 IEVEELDSILRQALTTSSLDAPVNGDDGRS--FLGDLIADSSVEEP--LDKVEQSIHQEQ 247

Query: 228 LTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L R ++ L+ +E+ + + R  L+ N   TL  +    EVSRERVRQ+E ++ +K++   +
Sbjct: 248 LGRWLTHLSEQEQHVLKLRFGLEGNDRHTLAEIGRLLEVSRERVRQVELKSLRKLRNLTR 307

Query: 286 K 286
           K
Sbjct: 308 K 308


>gi|87123422|ref|ZP_01079273.1| Putative type II alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9917]
 gi|86169142|gb|EAQ70398.1| Putative type II alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9917]
          Length = 376

 Score =  100 bits (248), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 75/236 (31%), Positives = 114/236 (48%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R++ ++LRLVV +A  Y+  GL + ++V EG +GL +AV+KFDP RGFR +TY+ WW
Sbjct: 136 ARDRMIAANLRLVVTVAKKYQQRGLELLDLVQEGTLGLERAVEKFDPTRGFRFSTYAYWW 195

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   I      +++     +K     L R+K   Q I     +   +  +A+KL +
Sbjct: 196 IRQGITRAIATQSRTIRLPVHVTEK-----LNRIKRVQQEIASQEGRIATLTDLAQKLGL 250

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SE  V     R+    SL   +    +  +Q  D L       EQ L     R    + L
Sbjct: 251 SEETVRLTLMRVPRSVSLE--LRVGKEQDTQLGDLLEDGKATPEQELT----RDALHHDL 304

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              +  L  RE  +   R   +N  P TL  +     +SRERVRQIE RA  K+++
Sbjct: 305 EHLLDELTDREAAVIRLRFGLDNDTPCTLAQIGETMALSRERVRQIETRALLKLRQ 360


>gi|260435157|ref|ZP_05789127.1| RNA polymerase sigma factor RpoD [Synechococcus sp. WH 8109]
 gi|260413031|gb|EEX06327.1| RNA polymerase sigma factor RpoD [Synechococcus sp. WH 8109]
          Length = 458

 Score =  100 bits (248), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 130/237 (54%), Gaps = 17/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 222 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 281

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++     KP E+ +A + ++
Sbjct: 282 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEM 336

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  D +  EQ + +   R++   
Sbjct: 337 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIEADIENPEQDVAKNLLREDLEG 392

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +L    + L+PRER +   R   ++    TLE +   F+V+RER+RQIEA+A +K++
Sbjct: 393 VL----ATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLR 445


>gi|254430889|ref|ZP_05044592.1| possible type II alternative RNA polymerase sigma factor [Cyanobium
           sp. PCC 7001]
 gi|197625342|gb|EDY37901.1| possible type II alternative RNA polymerase sigma factor [Cyanobium
           sp. PCC 7001]
          Length = 327

 Score =  100 bits (248), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 75/297 (25%), Positives = 141/297 (47%), Gaps = 44/297 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAK---------RYREHGDLSA-------------------- 49
           Y+ EI ++ +L ++EE +LA+         R R  G+L+A                    
Sbjct: 25  YLREIGRVDLLRQEEEILLARLVQEREELLRQRGDGELTAWAGRCGVPPADLRQALHRGR 84

Query: 50  --AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
               R++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV+++DP RGFR +TY+ W
Sbjct: 85  RAKERMLQANLRLVVAVAKKYQRRGLDLLDLIQEGTLGLERAVERYDPRRGFRFSTYAYW 144

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+  +   +      +++     +      L R++     +T  + +   +  +A+ + 
Sbjct: 145 WIRQGITRALASQSRTIRLPVHVTE-----TLNRIRTCQGELTREHGRQPTLAELARAVG 199

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + E+ + S    +    SL   + ++    +   D L  DH   EQ L  ++   +   +
Sbjct: 200 LDEARLRSTLAHIPRPVSLEGRVGAN--ADTPLVDLLEDDHATPEQTLTRQQLHADLEAL 257

Query: 228 LTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           L      L+ RE  +   R     + P TL  +  + ++SRERVRQIE+RA  K+++
Sbjct: 258 L----DELSAREATVIRQRFGLDDDTPRTLAEIGEQLQLSRERVRQIESRALLKLRQ 310


>gi|83648911|ref|YP_437346.1| RNA polymerase sigma-70 factor RpoD [Hahella chejuensis KCTC 2396]
 gi|83636954|gb|ABC32921.1| RNA polymerase sigma-70 factor RpoD [Hahella chejuensis KCTC 2396]
          Length = 639

 Score =  100 bits (248), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 401 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 460

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+  H+         PE+   +AKK+++
Sbjct: 461 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRHMLQEMGREATPEE---LAKKMDM 515

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E +V  +  ++A  E ++      D   S   D++    D   +  I+    +  +   
Sbjct: 516 PEDKVRKV-LKIA-KEPISMETPIGDDEDSHLGDFI---EDSHAESPIDSATTEGLKEST 570

Query: 229 TRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R ++ L  RE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 571 RRVLAGLTAREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 625


>gi|6010720|gb|AAF01226.1|AF184095_1 mutant RpoS [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
          Length = 254

 Score =  100 bits (248), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 46/100 (46%), Positives = 70/100 (70%), Gaps = 1/100 (1%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIM 159


>gi|167932999|ref|ZP_02520086.1| RNA polymerase sigma factor RpoD [candidate division TM7
           single-cell isolate TM7b]
          Length = 211

 Score =  100 bits (248), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 46/108 (42%), Positives = 71/108 (65%), Gaps = 1/108 (0%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L  +EE  LA R  + GD  A  ++  +++RLVV IA  Y G GL   ++
Sbjct: 54  YLREIGKIPLLSAEEEMELAHRVVQ-GDKKAKDKMAEANMRLVVSIAKRYSGRGLDFLDL 112

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           + EGN GL++AV+KFDP++GF+ +TY+ WWI+ A+   I     +++I
Sbjct: 113 IQEGNTGLLRAVEKFDPDKGFKFSTYATWWIRQAITRAIADQARVIRI 160


>gi|300726043|ref|ZP_07059501.1| RNA polymerase sigma-70 factor [Prevotella bryantii B14]
 gi|299776650|gb|EFI73202.1| RNA polymerase sigma-70 factor [Prevotella bryantii B14]
          Length = 290

 Score =  100 bits (248), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 76/272 (27%), Positives = 140/272 (51%), Gaps = 14/272 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGL 73
           L +Y+ EI + PM+  +EE  LA++ +  G     A  +LVT++LR VV +A  Y+  GL
Sbjct: 18  LDKYLGEISRAPMISIEEEIDLAQQIKRGGREGERAKSKLVTANLRFVVSVAKQYQHQGL 77

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ A+ + I     +V++    NQ 
Sbjct: 78  TLTDLIDEGNIGLIKAAEKFDETRGFKFISYAVWWIRQAILQAIAEQSRIVRL--PLNQ- 134

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINS 192
               +L ++   +        +   +  ++++ ++ E E I+ +   +G   S++A    
Sbjct: 135 --VGSLSKVNQEINKFEQKYQRVPTIQELSQRTDIDE-EKIAQSMMASGKHVSIDAPFQE 191

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF-EARRLQEN 251
            + NS    D +    D +    ++ E      N +    +VLN RE  I  +   +   
Sbjct: 192 GEDNS--MVDIMASGEDSRTDKEVDHESMSYDLNQVLE--TVLNEREITIIRDCFGIGCP 247

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
              LE +     ++RERVRQI  ++  K++ES
Sbjct: 248 EKGLEEIGDLLGLTRERVRQIREKSITKLRES 279


>gi|116072877|ref|ZP_01470142.1| RNA polymerase sigma factor [Synechococcus sp. BL107]
 gi|116064403|gb|EAU70164.1| RNA polymerase sigma factor [Synechococcus sp. BL107]
          Length = 451

 Score =  100 bits (248), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 130/237 (54%), Gaps = 17/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 215 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 274

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++     KP E+ +A + ++
Sbjct: 275 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEM 329

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  D +  EQ + +   R++   
Sbjct: 330 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIEADIENPEQDVAKNLLREDLEG 385

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +L    + L+PRER +   R   ++    TLE +   F+V+RER+RQIEA+A +K++
Sbjct: 386 VL----ATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLR 438


>gi|317176909|dbj|BAJ54698.1| RNA polymerase sigma factor RpoD [Helicobacter pylori F16]
          Length = 671

 Score =  100 bits (248), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 69/236 (29%), Positives = 121/236 (51%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ WW
Sbjct: 432 AKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWW 491

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           IK A+   I      ++I        +   + R+   ++     N K   +  +A+++ +
Sbjct: 492 IKQAISRAIADQARTIRIPI-----HMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGL 546

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  +V   N      E ++      + +  ++ D++    D      I++  R++ +  +
Sbjct: 547 SLDKV--KNVIKVAKEPISLETPVGNDDDGKFGDFV---EDKNIVSSIDRIMREDLKAQI 601

Query: 229 TRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 602 ESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 657


>gi|238651104|ref|YP_002916962.1| RNA polymerase sigma factor RpoD [Rickettsia peacockii str. Rustic]
 gi|238625202|gb|ACR47908.1| RNA polymerase sigma factor RpoD [Rickettsia peacockii str. Rustic]
          Length = 634

 Score =  100 bits (248), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 75/252 (29%), Positives = 127/252 (50%), Gaps = 21/252 (8%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E   L A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 375 ERQTLQAKKDMIEANLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 434

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           TY+ WWI+ A+   I      ++I      T N        + L+   Q + +   +P  
Sbjct: 435 TYATWWIRQAITRAIADQARTIRIPVHMIETIN--------KILRTSRQMLNELGYEP-T 485

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
              IA +L++   +V  +  ++A +  SL   +   D +  Q  D++    D      I+
Sbjct: 486 ATEIANRLSMPLDKVRKV-MKIAKEPISLENPV-GDDSDGGQLGDFI---EDKNAVAPID 540

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              + N R +  R ++ L PRE R+   R         TLE +  +F+V+RER+RQIE++
Sbjct: 541 AAIQSNLREVTIRVLATLTPREERVLRMRFGIGMNTDHTLEEVGQQFKVTRERIRQIESK 600

Query: 276 AFKKVQESIQKQ 287
           A +K+Q  I+ +
Sbjct: 601 ALRKLQHPIRSK 612


>gi|146739110|gb|ABQ42602.1| chloroplast RNA-polymerase sigma factor precursor [Heterosigma
           akashiwo]
          Length = 404

 Score =  100 bits (248), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 67/238 (28%), Positives = 123/238 (51%), Gaps = 17/238 (7%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ ++LRLVV  A  Y+  G+   ++V EG  GL +A +KFDP +GFR +TY+ WWIK  
Sbjct: 152 IINANLRLVVSTAKAYQYRGVSFQDLVQEGTCGLHKATEKFDPRKGFRFSTYATWWIKQG 211

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +     +V++    +     F++RR K +       +L+   +  +A+   ++  +
Sbjct: 212 IMRAVTDQSRVVRLPVHVHDA--LFHIRRAKANFWT---EHLREPTLAELAEATGLTPQK 266

Query: 173 VISMNCRLAGDESLNALI------NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++  +       S++  +      NS +K+     D      +  E    E  + ++ R 
Sbjct: 267 IVFYDTVKDKVSSIDKTVGIGTKTNSMEKSQIAISDMCKDSRNKPE----ETAQVESLRQ 322

Query: 227 MLTRSMSVLNPRERRIFEARR-LQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQE 282
            ++R ++ L+PRE+ +   R  L +  + TLE + S F V+RERVRQIEARA  K+++
Sbjct: 323 DISRLINTLSPREQDVVRMRYGLDDGEIRTLEEIGSIFSVTRERVRQIEARALHKLRQ 380


>gi|78212231|ref|YP_381010.1| RNA polymerase sigma factor RpoD [Synechococcus sp. CC9605]
 gi|78196690|gb|ABB34455.1| Sigma-70 factor [Synechococcus sp. CC9605]
          Length = 435

 Score =  100 bits (248), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 130/237 (54%), Gaps = 17/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 199 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 258

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++     KP E+ +A + ++
Sbjct: 259 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEM 313

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  D +  EQ + +   R++   
Sbjct: 314 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIEADIENPEQDVAKNLLREDLEG 369

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +L    + L+PRER +   R   ++    TLE +   F+V+RER+RQIEA+A +K++
Sbjct: 370 VL----ATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLR 422


>gi|194477302|ref|YP_002049481.1| RNA polymerase sigma factor [Paulinella chromatophora]
 gi|171192309|gb|ACB43271.1| RNA polymerase sigma factor [Paulinella chromatophora]
          Length = 460

 Score =  100 bits (248), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 130/237 (54%), Gaps = 17/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 224 AKAKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 283

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++     KP E+ +A + ++
Sbjct: 284 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEM 338

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  D +  EQ + +   R++   
Sbjct: 339 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIEADIENPEQDVAKNLLREDLEG 394

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +L    + L+PRER +   R   ++    TLE +   F+V+RER+RQIEA+A +K++
Sbjct: 395 VL----ATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLR 447


>gi|300113721|ref|YP_003760296.1| RNA polymerase sigma 70 subunit RpoD [Nitrosococcus watsonii C-113]
 gi|299539658|gb|ADJ27975.1| RNA polymerase, sigma 70 subunit, RpoD [Nitrosococcus watsonii
           C-113]
          Length = 578

 Score =  100 bits (248), Expect = 3e-19,   Method: Compositional matrix adjust.
 Identities = 76/248 (30%), Positives = 124/248 (50%), Gaps = 40/248 (16%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V ++LRLVV +A  YR  GL   +++ EGNIGLM+AV KFD  RG++ +TY+ WW
Sbjct: 340 AKAQMVEANLRLVVSVAKKYRNRGLTFLDLIQEGNIGLMKAVDKFDYHRGYKFSTYAHWW 399

Query: 109 IKAAMQEYILRSWSLVKIGTTANQK-----RLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           I+ A+   I      ++I     +K     R  + LR+ KG          +PE+   +A
Sbjct: 400 IRQAITRAIDDQSRTIRIPVHVMEKLSKLNRASYQLRQEKG-------REGRPEE---LA 449

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           ++L++SE ++  M              +   K     +  L  D D Q   L+E E+  N
Sbjct: 450 ERLDLSEQQIHRM--------------HEIAKQPISLETPLGKDEDSQLGELMEDEQVPN 495

Query: 224 RRNMLT---------RSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQI 272
              +           R ++ L+PRE ++   R     +   TL  ++ +F++SRER+RQI
Sbjct: 496 PMEVAITAGLQTGAQRLLAALSPREAQVVAMRFGIGMDTDHTLGEVARQFDLSRERIRQI 555

Query: 273 EARAFKKV 280
           EA+A  K+
Sbjct: 556 EAQALGKL 563


>gi|312885799|ref|ZP_07745431.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Mucilaginibacter
           paludis DSM 18603]
 gi|311301606|gb|EFQ78643.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Mucilaginibacter
           paludis DSM 18603]
          Length = 285

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 74/270 (27%), Positives = 135/270 (50%), Gaps = 14/270 (5%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y++E+ +  +L  +EE VLA++ R  GD +A  RL  ++LR VV +A  Y+  GLP
Sbjct: 17  SLETYLNELGRTDLLSAEEEVVLAQKIR-LGDQAALDRLTKTNLRFVVSVAKKYQHQGLP 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           +S+++SEGN+GLM+A KKFD  +GF+  +Y++WWI+  +   I     ++++    NQ  
Sbjct: 76  LSDLISEGNVGLMKAAKKFDETKGFKFISYAVWWIRQCILSAIAEHSRMIRL--PMNQ-- 131

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
              ++ ++   L  +     +      +A+ L  SE +V           S +A   + D
Sbjct: 132 -VGDITKMNKALALLEQQMERQPTTNELAEYLETSEDKVSDALYFATRTASYDAPFRTED 190

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
           +N+    D L  +    +  L+    ++  R +L    S L  R++ +       +    
Sbjct: 191 ENN--LLDVLPGNEQATDHELMVLSNQQEVRQLL----STLTSRDQEVIRWTFGLDGKTA 244

Query: 255 LE--NLSSEFEVSRERVRQIEARAFKKVQE 282
           L   +++    +S ERVRQI  +A + ++E
Sbjct: 245 LPPIDIAPLLGISAERVRQIRNQALQTLRE 274


>gi|291298947|ref|YP_003510225.1| RpoD subfamily RNA polymerase sigma-70 subunit [Stackebrandtia
           nassauensis DSM 44728]
 gi|290568167|gb|ADD41132.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Stackebrandtia
           nassauensis DSM 44728]
          Length = 330

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 89/306 (29%), Positives = 143/306 (46%), Gaps = 66/306 (21%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR---------------------EHGDL-----SAAHR 52
           Y+HEI K P+L+   E  LAK                        E G L      A  +
Sbjct: 24  YLHEISKTPLLDAAAEVDLAKAVEAGLYAQRLIGDDQQPEGVTEAELGRLVLDGQKAKEQ 83

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            + ++LRLVV IA  Y   G+P+ +++ EGN GL++AV+KFD +RGF+ +TY+ WWI+ A
Sbjct: 84  FIKANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYQRGFKFSTYATWWIRQA 143

Query: 113 MQEYILRSWSLVKIGT--TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS- 169
           +   I +    V++      +  R+    R+L   L A    + +PEQ   IA  L V+ 
Sbjct: 144 ISRAIAQQERTVRLPVHLVEDVNRMRNTARQLTRELGA----DPEPEQ---IANALGVTV 196

Query: 170 ---------ESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
                      + +S++  +   GD +L  L+  SD+ +              E V+I  
Sbjct: 197 ERVNELIRWSQDTVSLDTPIGDDGDTNLGDLVADSDEPTP-------------EDVVIAG 243

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARA 276
            ER+    ML      L+ R   I +AR   E+    +L  ++  F +SRER+RQ+E +A
Sbjct: 244 MERERIDMMLGH----LDERSAGIVKARYGLEDGREHSLTEVAHRFALSRERIRQLEIQA 299

Query: 277 FKKVQE 282
             +++E
Sbjct: 300 LARLKE 305


>gi|56750024|ref|YP_170725.1| group2 RNA polymerase sigma factor RpoD6 [Synechococcus elongatus
           PCC 6301]
 gi|56684983|dbj|BAD78205.1| group2 RNA polymerase sigma factor RpoD6 [Synechococcus elongatus
           PCC 6301]
          Length = 316

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 83/289 (28%), Positives = 142/289 (49%), Gaps = 33/289 (11%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL----------------------SAAHRL 53
           +S Y+  I +IP+L   +E  L ++ +   +L                       A  R+
Sbjct: 26  VSWYLSSIGRIPLLTADQEIELGQKVQVMMNLLEETSSDRTFTEAETAAIQLGQRAKERM 85

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           + ++LRLVV +A  Y+G GL   +++ EG +GL +AV+KFDP +G++ +TY+ WWI+ +M
Sbjct: 86  IKANLRLVVSVAKKYQGKGLEFLDLIQEGALGLERAVEKFDPSKGYKFSTYAFWWIRQSM 145

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
              I      +++     ++     +R++   L A     L   Q +A A +L +++ E 
Sbjct: 146 TRAIACQSRTIRLPVHLTER--LSQIRKVTREL-AHELGRLPSRQEIAEAVQLPLNDLET 202

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
           I    R     SL+A ++  D  S  +   L+ D +G E + I   E   +R  L   + 
Sbjct: 203 ILRQSRQC--TSLDAPVSGEDGKS--FLGELIADPNGNEPMDI--MENAMQREQLDAWLE 256

Query: 234 VLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
            L P+ER++   R  L +    TL  +    EVSRERVRQ+E +A +K+
Sbjct: 257 HLTPQERQVLYLRFGLGDGERHTLAEIGRMMEVSRERVRQVEVKALRKL 305


>gi|310822395|ref|YP_003954753.1| RNA polymerase sigma factor [Stigmatella aurantiaca DW4/3-1]
 gi|309395467|gb|ADO72926.1| RNA polymerase sigma factor [Stigmatella aurantiaca DW4/3-1]
          Length = 245

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 76/259 (29%), Positives = 120/259 (46%), Gaps = 50/259 (19%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           GLS Y+  +     L +++EY LA+  R+ GD SA   L TS+L  VV +A  +   G  
Sbjct: 11  GLSHYLRHLGGHHQLTREQEYELARAARK-GDESARQTLATSNLAFVVAVAKKFANRGAR 69

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++ EGN+GLM+A++ FDP++  R ATY++WWI+A +  Y+  + S V+ G       
Sbjct: 70  LDDLIQEGNVGLMKAIEHFDPKKNVRFATYAVWWIRAYITRYLKDNRSQVRGG------- 122

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
                                              ESE  SM      D SL+A I+  +
Sbjct: 123 -----------------------------------ESERGSMV-----DFSLDATID--E 140

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
           +  + + D L         V + +E+ +     L +    +      I + R  Q+ P+T
Sbjct: 141 EGETTFMDRLEDGGPSPSDVYLSREQDQEVHEALVKVRKRIGDLGWDILQERLTQDKPLT 200

Query: 255 LENLSSEFEVSRERVRQIE 273
           LE L   + VSRERVRQ+E
Sbjct: 201 LEELGQRWGVSRERVRQVE 219


>gi|257438148|ref|ZP_05613903.1| RNA polymerase sigma factor RpoD [Faecalibacterium prausnitzii
           A2-165]
 gi|257199479|gb|EEU97763.1| RNA polymerase sigma factor RpoD [Faecalibacterium prausnitzii
           A2-165]
          Length = 461

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 80/262 (30%), Positives = 134/262 (51%), Gaps = 25/262 (9%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ E++ + +L  + R  G L+A   L  ++LRLVV IA  + G+ L   +++ EGNIGL
Sbjct: 205 PLTEERRQELL--KIRRDG-LNARRSLSEANLRLVVSIAKKHVGHNLAFLDLIQEGNIGL 261

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKRLFFN-LRR 141
           ++A +KFD +RGFR +TY+ WWI+ A+   I      ++I      T N+ R   N L  
Sbjct: 262 IKAAEKFDCDRGFRFSTYATWWIRQAITRAIADQARTIRIPVHMVETINRMRQATNQLVY 321

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
             GH          PE+   +AK +++S   V  +        SL + +   ++  S   
Sbjct: 322 QNGH-------EPTPEE---LAKAMDMSVERVREIQRMAQEPASLESPV--GEEEDSSLG 369

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLS 259
           D++    D   +   +  +R      + +++  L PRE ++   R   ++  P TLE + 
Sbjct: 370 DFVA---DENAEAPGKAADRAMVAQQINQALKSLTPREEKVIRLRFGLDDGRPRTLEEVG 426

Query: 260 SEFEVSRERVRQIEARAFKKVQ 281
            +F V+RERVRQIEA+A +K+ 
Sbjct: 427 RDFGVTRERVRQIEAKAIRKLH 448


>gi|300114080|ref|YP_003760655.1| RpoD subfamily RNA polymerase sigma 70 subunit [Nitrosococcus
           watsonii C-113]
 gi|299540017|gb|ADJ28334.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nitrosococcus
           watsonii C-113]
          Length = 303

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 73/282 (25%), Positives = 138/282 (48%), Gaps = 36/282 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ E  K+P+L  +EE   A R    GD  A +R++ S+LR+V+K+A  +   GLP+ ++
Sbjct: 42  YMREAGKVPLLNAEEERYYA-RLALQGDREARNRIIESNLRIVIKVASRHVNRGLPLMDL 100

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK----- 133
           + EGN+GL+ AV+KF+PE GFR +TY+ WWI+ A++  ++     +++     +K     
Sbjct: 101 IEEGNLGLINAVEKFNPELGFRFSTYASWWIRQAIERALMNQTRTIRLPVHVFKKIRSYQ 160

Query: 134 ------RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
                 R  +N+    G +  +    L+  Q     + L  S  + ++ +     ++ L 
Sbjct: 161 KEVILFRQRYNIEPRSGEIAKLLHEPLERVQRYLSLQALETSLDDPLNEDT----EDCLA 216

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
            L+     N +    W ++D                ++  +   +S L  R++ I + R 
Sbjct: 217 DLLPDERNNPALL--WEIFD----------------KKASIYNQLSQLPERQQEILKRRY 258

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             +     TLE +     ++RERVRQI+  A K++++ I+ +
Sbjct: 259 GLDGYEVTTLEEIGHNLGITRERVRQIQQAAIKRLRKIIESE 300


>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 =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 76/253 (30%), Positives = 119/253 (47%), Gaps = 33/253 (13%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           KR RE     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG
Sbjct: 656 KRARE-----AKREMTVANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 710

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIG-----TTANQKRLFFNLRRLKGHLQAITDNN 153
           ++ +TY+ WWI+ A+   I      ++I      T     R+   + +  GH        
Sbjct: 711 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGHEPDAATLA 770

Query: 154 LK---PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
           LK   PE  +   +K+     E +SM   +  DE             S   D++    DG
Sbjct: 771 LKMEIPEDKI---RKIMKIAKEPVSMETPIGDDE------------DSHLGDFI---EDG 812

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRER 268
                 E     + R+++   +  L PRE ++   R   E     TLE +  +F+V+RER
Sbjct: 813 NTLAPAEAALHNSMRDVVKDVLDSLTPREAKVLRMRFGVEMSTDHTLEEVGKQFDVTRER 872

Query: 269 VRQIEARAFKKVQ 281
           +RQIEA+A +K++
Sbjct: 873 IRQIEAKALRKMR 885


>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 =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 69/236 (29%), Positives = 124/236 (52%), Gaps = 12/236 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 544 AAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 603

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I     +     N R  + HLQ       +P+  + +A+K+ 
Sbjct: 604 WIRQAITRSIADQARTIRIPVHMIETINKMN-RISRQHLQEF---GFEPDASL-LAQKME 658

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + E ++  +  ++A  E ++      D + S   D++    D      +E   +   R +
Sbjct: 659 IPEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDTANTAPVEAAMQAGLREV 713

Query: 228 LTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  L PRE ++   R   E  +  TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 714 VKEILDGLTPREAKVLRMRFGIEMTSDHTLEEVGKQFDVTRERIRQIEAKALRKLK 769


>gi|144900406|emb|CAM77270.1| RNA polymerase sigma factor rpod [Magnetospirillum gryphiswaldense
           MSR-1]
          Length = 664

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 81/275 (29%), Positives = 137/275 (49%), Gaps = 23/275 (8%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +V+GE GL   I E R+I    ++ E   +K  +E         ++ ++LRLV+ IA  Y
Sbjct: 397 VVSGEAGLP--ITEFRRIIQTVQRGEREASKAKKE---------MIEANLRLVISIAKKY 445

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
              GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I  
Sbjct: 446 TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI-- 503

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
             +       L R    +         PE+   +A+KL++   +V  +  ++A  E ++ 
Sbjct: 504 PVHMIETINKLVRTSRQMLHEIGREPTPEE---LAEKLSMPLEKVRKV-LKIA-KEPISL 558

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR- 247
                D+  S   D++    D    + ++   + N R   TR ++ L PRE R+   R  
Sbjct: 559 ETPIGDEEDSHLGDFI---EDKNAVLPLDAAIQANLRETTTRVLASLTPREERVLRMRFG 615

Query: 248 -LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                  TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 616 IGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 650


>gi|81300366|ref|YP_400574.1| principal RNA polymerase sigma factor SigA [Synechococcus elongatus
           PCC 7942]
 gi|81169247|gb|ABB57587.1| principal RNA polymerase sigma factor SigA [Synechococcus elongatus
           PCC 7942]
          Length = 310

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 83/289 (28%), Positives = 142/289 (49%), Gaps = 33/289 (11%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL----------------------SAAHRL 53
           +S Y+  I +IP+L   +E  L ++ +   +L                       A  R+
Sbjct: 20  VSWYLSSIGRIPLLTADQEIELGQKVQVMMNLLEETSSDRTFTEAETAAIQLGQRAKERM 79

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           + ++LRLVV +A  Y+G GL   +++ EG +GL +AV+KFDP +G++ +TY+ WWI+ +M
Sbjct: 80  IKANLRLVVSVAKKYQGKGLEFLDLIQEGALGLERAVEKFDPSKGYKFSTYAFWWIRQSM 139

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
              I      +++     ++     +R++   L A     L   Q +A A +L +++ E 
Sbjct: 140 TRAIACQSRTIRLPVHLTER--LSQIRKVTREL-AHELGRLPSRQEIAEAVQLPLNDLET 196

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
           I    R     SL+A ++  D  S  +   L+ D +G E + I   E   +R  L   + 
Sbjct: 197 ILRQSRQC--TSLDAPVSGEDGKS--FLGELIADPNGNEPMDI--MENAMQREQLDAWLE 250

Query: 234 VLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
            L P+ER++   R  L +    TL  +    EVSRERVRQ+E +A +K+
Sbjct: 251 HLTPQERQVLYLRFGLGDGERHTLAEIGRMMEVSRERVRQVEVKALRKL 299


>gi|262273681|ref|ZP_06051494.1| RNA polymerase sigma factor RpoS [Grimontia hollisae CIP 101886]
 gi|262222096|gb|EEY73408.1| RNA polymerase sigma factor RpoS [Grimontia hollisae CIP 101886]
          Length = 246

 Score =  100 bits (248), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 47/108 (43%), Positives = 73/108 (67%), Gaps = 1/108 (0%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 54  YLSEIGYSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 112

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++
Sbjct: 113 VEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRL 160


>gi|145596092|ref|YP_001160389.1| RpoD family RNA polymerase sigma factor [Salinispora tropica
           CNB-440]
 gi|145305429|gb|ABP56011.1| RNA polymerase, sigma 70 subunit, RpoD family [Salinispora tropica
           CNB-440]
          Length = 332

 Score = 99.8 bits (247), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 88/307 (28%), Positives = 147/307 (47%), Gaps = 68/307 (22%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH----------GDLSAAHRLVT-------- 55
           Y+HEI + P+L+   E  L+K      Y EH           + +   RLV         
Sbjct: 40  YLHEISRTPLLDAATEVDLSKAIEAGLYAEHLLDEDRVPAGVEKAELQRLVAEGARAKDL 99

Query: 56  ---SHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
              ++LRLVV IA  Y   G+P+ +++ EGN GL++AV+KFD ERGF+ +TY+ WWI+ A
Sbjct: 100 FIRANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQA 159

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT---DNNLKPEQVVAIAKKLNVS 169
           +   I +    V++        L  ++ R++   + +T    ++ +PEQ   IA  L V+
Sbjct: 160 ISRAIAQQERTVRLPV-----HLVEDVNRMRNVARQLTRELGSDPEPEQ---IATALGVT 211

Query: 170 ----------ESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
                       + +S++  +   GD +L  L+  SD  S              E +++ 
Sbjct: 212 VERVNELVRWSQDTVSLDTPVGDDGDTNLGDLVADSDAPSP-------------EDIVLT 258

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEAR 275
             ER+    +L    S L+ R   I  AR   E+    +L  ++S F +SRER+RQ+E +
Sbjct: 259 GLERQRIEGLL----SHLDDRSAGIMRARYGLEDGREHSLTEVASRFSLSRERIRQLEIQ 314

Query: 276 AFKKVQE 282
           A  +++E
Sbjct: 315 ALGRLRE 321


>gi|293392779|ref|ZP_06637097.1| DNA-directed RNA polymerase sigma subunit RpoS [Serratia odorifera
           DSM 4582]
 gi|291424638|gb|EFE97849.1| DNA-directed RNA polymerase sigma subunit RpoS [Serratia odorifera
           DSM 4582]
          Length = 202

 Score = 99.8 bits (247), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 46/108 (42%), Positives = 72/108 (66%), Gaps = 1/108 (0%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 63  YLGEIGYSPLLTAEEEVYFARRAL-RGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRL 169


>gi|91204871|ref|YP_537226.1| RNA polymerase sigma factor RpoD [Rickettsia bellii RML369-C]
 gi|122426123|sp|Q1RKH7|RPOD_RICBR RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|91068415|gb|ABE04137.1| RNA polymerase sigma factor [Rickettsia bellii RML369-C]
          Length = 641

 Score = 99.8 bits (247), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 75/248 (30%), Positives = 127/248 (51%), Gaps = 21/248 (8%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 386 LQAKKDMIEANLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 445

Query: 107 WWIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           WWI+ A+   I      ++I      T N        + ++   Q + +   +P     I
Sbjct: 446 WWIRQAITRAIADQARTIRIPVHMIETIN--------KIIRTSRQMLNELGYEPTP-AEI 496

Query: 163 AKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           A +L++   +V  +  ++A +  SL   +   D N S   D++    D      I+   +
Sbjct: 497 AARLSMPIDKVRKV-MKIAKEPISLENPVGDGDDN-SYLGDFI---EDKNAVAPIDAAIQ 551

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
            N R + TR ++ L PRE R+   R         TLE +  +F+V+RER+RQIE++A +K
Sbjct: 552 SNLREVTTRVLATLTPREERVLRMRFGIGMNTDHTLEEVGQQFKVTRERIRQIESKALRK 611

Query: 280 VQESIQKQ 287
           +Q  I+ +
Sbjct: 612 LQHPIRSK 619


>gi|313647807|gb|EFS12253.1| RNA polymerase sigma factor rpoS [Shigella flexneri 2a str. 2457T]
          Length = 254

 Score = 99.8 bits (247), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 46/100 (46%), Positives = 70/100 (70%), Gaps = 1/100 (1%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIM 159


>gi|258645217|ref|ZP_05732686.1| RNA polymerase sigma factor RpoD [Dialister invisus DSM 15470]
 gi|260402567|gb|EEW96114.1| RNA polymerase sigma factor RpoD [Dialister invisus DSM 15470]
          Length = 388

 Score = 99.8 bits (247), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 93/304 (30%), Positives = 145/304 (47%), Gaps = 47/304 (15%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHR-----------L 53
           N S  +N +  +  Y+ EI  I +L   +E  LAK   +     A  R           L
Sbjct: 100 NTSDSINIDDPVKMYLKEIGAIKLLTGSQEIELAKLVEKGSFDDATGRDKMAADEAKKAL 159

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
             ++LRLVV IA  Y G GL   +++ EGN+GL++AV KFD  +GF+ +TY+ WWI+ A+
Sbjct: 160 SDANLRLVVSIAKKYLGRGLQFLDLIQEGNLGLLKAVDKFDYTKGFKFSTYATWWIRQAI 219

Query: 114 QEYILRSWSLVKIGT----TANQ-KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
              I      +++      T N+  R+   L + KG  +  T+  L     V++AK   V
Sbjct: 220 TRAIADQARTIRVPVHMVETINKLNRISRQLLQEKG--REATNEELAKAMGVSVAKIREV 277

Query: 169 SESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDH------DGQEQVLIEKEER 221
                     ++A D  SL   I   +K  S   D+ + DH      D    +L+     
Sbjct: 278 K---------KIAQDPISLETPI--GEKEDSHLGDF-IEDHEAIAPDDAAGSILL----- 320

Query: 222 KNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAFKK 279
              R  +   +  L  RER++ E R  L++  P TLE +   F+V+RER+RQIE +A  K
Sbjct: 321 ---REQIDELLRELTDRERQVLELRFGLKDGRPRTLEEVGKYFDVTRERIRQIEGKALTK 377

Query: 280 VQES 283
           +++S
Sbjct: 378 LKKS 381


>gi|168703618|ref|ZP_02735895.1| transcription initiation factor sigma 70 [Gemmata obscuriglobus UQM
           2246]
          Length = 521

 Score = 99.8 bits (247), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 72/237 (30%), Positives = 124/237 (52%), Gaps = 16/237 (6%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L  ++LRLVV IA  YR  GLP S+++ EGN GLM+AV K++    F+  TY+ WW++  
Sbjct: 284 LAEANLRLVVSIAKNYRNRGLPFSDLIQEGNRGLMRAVDKYEWRLEFKFGTYATWWVRQG 343

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +  +   V++    +Q  L   + +L+G L   T      E+   +A+ L V   E
Sbjct: 344 ITRALHDNARTVRV--PCHQISLLSRMEKLRGELTVATGREPTSEE---LAEALGVKPEE 398

Query: 173 VISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
             S+  R+ G    SLN  +    + +   +D+L   H       ++    K R   + +
Sbjct: 399 ARSL--RIVGRHPVSLNDSVGGDGERA--LEDFLSDTHISPPGEHVDANLLKERIGEVLK 454

Query: 231 SMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           S++   PRER + E R  L++  P TL+ ++ ++ ++RER+RQIEAR   K+++  +
Sbjct: 455 SLA---PREREVIELRFGLKDGTPKTLDEVAKQYGITRERIRQIEARGLLKLRQPTR 508


>gi|254780289|ref|YP_003064702.1| RNA polymerase sigma factor RpoD [Candidatus Liberibacter asiaticus
           str. psy62]
 gi|254039966|gb|ACT56762.1| RNA polymerase sigma factor RpoD [Candidatus Liberibacter asiaticus
           str. psy62]
          Length = 682

 Score = 99.8 bits (247), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 85/289 (29%), Positives = 138/289 (47%), Gaps = 49/289 (16%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQE-EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           SI V   I +S + H    + M+ K E E  +AK+            +V ++LRLV+ +A
Sbjct: 415 SISVETGISISEFRH---IVSMVRKGECEASIAKK-----------EMVEANLRLVISVA 460

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y   GL   +++ EGNIGLM+A +KFD   G++ +TY+MWW+K A+   I      ++
Sbjct: 461 KKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAITRSIADQSCTIR 520

Query: 126 IGTTANQK--RLFFNLRRLKGHLQAITDNNLKPEQVV--------AIAKKLNVSESEVIS 175
           I      K  ++    RR+   ++        PE++          + K L +++ E IS
Sbjct: 521 IPVHMRDKIHKVVRTARRMSNKIK----REPTPEEIAKKLAMPVEGVRKVLKITK-EPIS 575

Query: 176 MNCRLAGDESLNALINS-SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV 234
           +   + GDE  + L +   DKN+    D  +               + N R   TR ++ 
Sbjct: 576 LETPI-GDEDTSHLGDFIEDKNAVSPLDSAI---------------QANLRETTTRVLAS 619

Query: 235 LNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 620 LTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 668


>gi|22298042|ref|NP_681289.1| group 2 RNA polymerase sigma factor [Thermosynechococcus elongatus
           BP-1]
 gi|22294220|dbj|BAC08051.1| group 2 RNA polymerase sigma factor [Thermosynechococcus elongatus
           BP-1]
          Length = 375

 Score = 99.8 bits (247), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 71/241 (29%), Positives = 136/241 (56%), Gaps = 23/241 (9%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A ++L+ ++LRLVV IA  Y+ +G+   +++ EG++GL +AV+KFDP +GFR +TY+ WW
Sbjct: 136 AKNQLLQANLRLVVNIAKKYQHHGVEFLDLIQEGSLGLERAVEKFDPTKGFRFSTYAYWW 195

Query: 109 IKAAMQEYILRSWSLVKIGTTANQK--RLFFNLRRL---KGHLQAITDNNLKPEQVVAIA 163
           I+ ++   +      +++     +K  ++    RRL   +G + ++ D          IA
Sbjct: 196 IRQSITRAVASQSRTIRLPIHMVEKLNKIKRAQRRLAAQRGAMPSLAD----------IA 245

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           ++LN+  S+V  +   +    +L   + S  +  ++ Q+ +       ++V++    R++
Sbjct: 246 QELNLEVSQVRQVLMAVPKSVALEQRVGSDQE--TELQELIESPAPTPDEVIM----RES 299

Query: 224 RRNMLTRSMSVLNPRERRIFEARR-LQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R  L + +S L+PRER++ E R  L E P + L  ++    +SRER+RQIE RA +K++
Sbjct: 300 LRTTLKQLLSDLSPRERQVMELRYGLGEQPALELAEVAVLLGLSRERIRQIEHRALQKLR 359

Query: 282 E 282
           +
Sbjct: 360 Q 360


>gi|33861053|ref|NP_892614.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus subsp.
           pastoris str. CCMP1986]
 gi|33639785|emb|CAE18955.1| Putative principal RNA polymerase sigma factor [Prochlorococcus
           marinus subsp. pastoris str. CCMP1986]
          Length = 396

 Score = 99.8 bits (247), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 130/237 (54%), Gaps = 17/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 160 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 219

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++     KP E+ +A + ++
Sbjct: 220 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKVLSQEFGRKPSEEEIAESMEM 274

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  D +  EQ + +   R++   
Sbjct: 275 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIEADIENPEQDVSKTLLREDLEG 330

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +L    + L+PRER +   R   ++    TLE +   F+V+RER+RQIEA+A +K++
Sbjct: 331 VL----ATLSPRERDVLRLRYGIDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLR 383


>gi|225621460|ref|YP_002722719.1| R polymerase sigma factor RpoD [Brachyspira hyodysenteriae WA1]
 gi|225216281|gb|ACN85015.1| R polymerase sigma factor RpoD [Brachyspira hyodysenteriae WA1]
          Length = 309

 Score = 99.8 bits (247), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 72/240 (30%), Positives = 123/240 (51%), Gaps = 22/240 (9%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           S  H+LV S+LRLV+ IA  Y   G+P  +++ EGNIGL++AVK+F+ ++GF+ +TY +W
Sbjct: 70  SIQHKLVKSNLRLVISIAKRYYNSGVPFIDIIDEGNIGLIEAVKRFEYKKGFKFSTYGVW 129

Query: 108 WIKAAMQEYILRSWSLVK-IGTTANQKRLFFNLRRL-KGHLQ---AITDNNLKPEQVVAI 162
           WIK           S+VK I +  +  R   ++ RL K  +Q    +T    +   +  I
Sbjct: 130 WIKQ----------SIVKEISSKRHIIRFPMHIARLIKKSIQTSKTLTQKLGRDPTIDEI 179

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           +K++ +    +  +        S+++   +SD N     D      D       +K    
Sbjct: 180 SKEMKIDRKTLSYIMIFTQDTASVDSFFRNSDNN-----DMTSIIEDKNFPSPHQKAFMD 234

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R+ LT ++  L+ +ER +  +R     +   TLE+   E  ++RERVRQI+ +A KK+
Sbjct: 235 SLRDTLTEALKCLDEKERTVIISRYGLYGKEAKTLEDTGKELNITRERVRQIQIKAIKKL 294


>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 = 99.8 bits (247), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 85/282 (30%), Positives = 136/282 (48%), Gaps = 37/282 (13%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +++ + GL+  I E R+I          + K  RE G   A   +V ++LRLV+ IA  Y
Sbjct: 372 MISADAGLT--IGEFRRIVQ-------TVQKGEREAG--RAKKEMVEANLRLVISIAKKY 420

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
              GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I  
Sbjct: 421 TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPV 480

Query: 129 ----TANQKRLFFNLRRLKGHL-QAITDNNLKPEQVVAIAKKLNVSE--SEVISMNCRLA 181
               T N  +L    R++   + +  T   L  + V+ + K   V +   E IS+   + 
Sbjct: 481 HMIETIN--KLVRTSRQMLHEIGREPTPEELAEKLVMPLEKVRKVLKIAKEPISLETPIG 538

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
            +E  +      DKN+ Q  D  ++                N R   TR ++ L PRE R
Sbjct: 539 DEEDSHLGDFIEDKNAVQPLDAAIH---------------ANLRETTTRVLASLTPREER 583

Query: 242 IFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 584 VLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 625


>gi|123965795|ref|YP_001010876.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str. MIT
           9515]
 gi|123200161|gb|ABM71769.1| Putative principal RNA polymerase sigma factor [Prochlorococcus
           marinus str. MIT 9515]
          Length = 397

 Score = 99.8 bits (247), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 130/237 (54%), Gaps = 17/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 161 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 220

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++     KP E+ +A + ++
Sbjct: 221 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKVLSQEFGRKPSEEEIAESMEM 275

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  D +  EQ + +   R++   
Sbjct: 276 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIEADIENPEQDVSKTLLREDLEG 331

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +L    + L+PRER +   R   ++    TLE +   F+V+RER+RQIEA+A +K++
Sbjct: 332 VL----ATLSPRERDVLRLRYGIDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLR 384


>gi|91070600|gb|ABE11500.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [uncultured Prochlorococcus marinus clone HOT0M-8F9]
          Length = 340

 Score = 99.8 bits (247), Expect = 4e-19,   Method: Compositional matrix adjust.
 Identities = 78/284 (27%), Positives = 141/284 (49%), Gaps = 31/284 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDL--------------------SAAHRLVTSHL 58
           Y+  I ++P+L   EE  LA   +    L                     +  R++ ++L
Sbjct: 56  YLSSIGRVPLLTPAEEIELAHHVQNMKKLLQIPETDRTQRNLYQIKIGKKSRDRMMAANL 115

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+  M   I 
Sbjct: 116 RLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTRAID 175

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
            S   +++    ++K     +RR+    + ++    +    + +A ++ + + ++  +  
Sbjct: 176 NSARTIRLPIHISEK--LSKMRRVS---RELSHKFGRQPTRLEMATEMGIDQKDLEDLIS 230

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           + A   SL+A     +  S+  +  L+ D + +E   +E  +R  ++  L   +S LN R
Sbjct: 231 QSAPCASLDAHARGEEDRSTLGE--LIPDPNCEEP--MEGMDRTIQKEHLGTWLSQLNER 286

Query: 239 ERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           E++I + R     E P+TL  +  +  VSRERVRQ+EA+A  K+
Sbjct: 287 EQKIMKLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKL 330


>gi|87302644|ref|ZP_01085461.1| RNA polymerase sigma factor [Synechococcus sp. WH 5701]
 gi|87282988|gb|EAQ74945.1| RNA polymerase sigma factor [Synechococcus sp. WH 5701]
          Length = 469

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 130/237 (54%), Gaps = 17/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 233 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 292

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++     KP E+ +A + ++
Sbjct: 293 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEM 347

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  D +  EQ + +   R++   
Sbjct: 348 TIEKLRFIAKSAQLP--ISLETPIGKEE--DSRLGDFIEADIENPEQDVAKNLLREDLEG 403

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +L    + L+PRER +   R   ++    TLE +   F+V+RER+RQIEA+A +K++
Sbjct: 404 VL----ATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLR 456


>gi|297199501|ref|ZP_06916898.1| RNA polymerase sigma factor RpoS [Streptomyces sviceus ATCC 29083]
 gi|297147415|gb|EDY56986.2| RNA polymerase sigma factor RpoS [Streptomyces sviceus ATCC 29083]
          Length = 428

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 90/295 (30%), Positives = 144/295 (48%), Gaps = 42/295 (14%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHG-------------------DLS--------AA 50
           +Y+ EI +IP+L   EE  LA+R  E G                   DL         A 
Sbjct: 134 QYLREIGRIPLLTAVEEVELARRV-EAGLFAEEKLSSTPDLDSQLALDLDRLVVLGRMAK 192

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY+ WWI+
Sbjct: 193 RRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIR 252

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            AM   +      +++     +  L   + R++  +         PE+V A    L+++ 
Sbjct: 253 QAMSRALADQARTIRVPVHVVE--LINRVVRVQRRMLQERGYEPTPEEVAA---HLDLA- 306

Query: 171 SEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
            E +S   RLA +  SL+A +   D  +    D +    DG     +E       R  L 
Sbjct: 307 PERVSEVLRLAQEPVSLHAPVGEEDDVA--LGDLI---EDGDAASPVESAAFLLLREHLE 361

Query: 230 RSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQE 282
             +S L  RER++ + R  L +    TLE +   F V+RER+RQIE++   K+++
Sbjct: 362 AVLSTLGERERKVVQLRYGLADGRARTLEEIGRIFGVTRERIRQIESKTLNKLRD 416


>gi|255994475|ref|ZP_05427610.1| RNA polymerase sigma factor RpoD [Eubacterium saphenum ATCC 49989]
 gi|255993188|gb|EEU03277.1| RNA polymerase sigma factor RpoD [Eubacterium saphenum ATCC 49989]
          Length = 447

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 85/313 (27%), Positives = 151/313 (48%), Gaps = 51/313 (16%)

Query: 9   IVNGEIGLSR----YIHEIRKIPMLEKQEEYVLAKR------------------------ 40
           IV   IG+      Y+ EI ++P+L ++EE +LA +                        
Sbjct: 133 IVRTSIGIDDPVKMYLKEIGQVPLLTREEEKILATQVKHALAKQNEIRERLERLKEGSAT 192

Query: 41  YREHGDL---------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           Y++   L          A H+L  ++LRLVV IA  ++  G+   +++ EGN+GLM+AV 
Sbjct: 193 YKKEMKLLDEYKQDYNKAMHQLCEANLRLVVSIAKNHKDRGMHFLDLIQEGNLGLMKAVD 252

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD +R F+ +TY+ WWI+ A+   I      ++I    +       L R+   L     
Sbjct: 253 KFDVDRNFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETIHKLTRISRTLLQELG 310

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDG 210
              KPE+   IAK+++++  +V  +  R++ +  SL   I   ++  S   D++    D 
Sbjct: 311 REPKPEE---IAKEMDITTEKVRDI-LRISQEPVSLEKPI--GEEEDSHLGDFI---PDT 361

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRER 268
           +    ++       R+ L   ++ L  RER + + R   +     TLE +  +F+V+RER
Sbjct: 362 EVPSPLDVAFSSMLRDELLEVLNTLGERERNVLKLRFGLVDGKQRTLEEVGKQFDVTRER 421

Query: 269 VRQIEARAFKKVQ 281
           +RQIE++A +K++
Sbjct: 422 IRQIESKAIRKLK 434


>gi|113477826|ref|YP_723887.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
 gi|110168874|gb|ABG53414.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
          Length = 384

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 71/253 (28%), Positives = 129/253 (50%), Gaps = 33/253 (13%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           +R H   +A  R+++S+LRLVV IA  Y   G+P  +++ EG +GL +A +KFDP++G++
Sbjct: 136 HRLHQCRTAKRRMISSNLRLVVSIAKRYLNRGVPFLDLIQEGALGLNRAAEKFDPDKGYK 195

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQ-----KRLFFNLRRLKGHLQAITDNNLK 155
            +TY+ WWI+  +   I      +++     +     +R++ +LRR    +    D  + 
Sbjct: 196 FSTYAYWWIRQGITRTIANQGRTIRLPVHVVEQINKLRRVYRDLRRSLNRIP--NDTEIA 253

Query: 156 PEQVVAIAKKLNVSE--SEVISMNCRLAGDESLNALINSSDKNSS----QWQDWLVYDHD 209
            E  +++ +  N+ +   + +S+N RL  DE+   L    D  +S    Q  D ++    
Sbjct: 254 QELEISLPQLRNLQQIRRKTLSLNHRLGTDENTELLDFLEDNENSTPEAQMNDMMM---- 309

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRE 267
                         R+++L     VL+ RE+ +   R   +   P TL+ +S    +SRE
Sbjct: 310 --------------RQDILEVLNHVLSNREQDVISLRYGLITGEPHTLDEVSRMINLSRE 355

Query: 268 RVRQIEARAFKKV 280
           RVRQI+A+A +K+
Sbjct: 356 RVRQIQAKAMRKL 368


>gi|126695861|ref|YP_001090747.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str. MIT
           9301]
 gi|126542904|gb|ABO17146.1| Putative principal RNA polymerase sigma factor [Prochlorococcus
           marinus str. MIT 9301]
          Length = 394

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 130/237 (54%), Gaps = 17/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 158 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 217

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++     KP E+ +A + ++
Sbjct: 218 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKVLSQEFGRKPSEEEIAESMEM 272

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  D +  EQ + +   R++   
Sbjct: 273 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIEADIENPEQDVSKTLLREDLEG 328

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +L    + L+PRER +   R   ++    TLE +   F+V+RER+RQIEA+A +K++
Sbjct: 329 VL----ATLSPRERDVLRLRYGIDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLR 381


>gi|300867798|ref|ZP_07112441.1| RNA polymerase sigma factor RpoD [Oscillatoria sp. PCC 6506]
 gi|300334215|emb|CBN57613.1| RNA polymerase sigma factor RpoD [Oscillatoria sp. PCC 6506]
          Length = 391

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 73/248 (29%), Positives = 132/248 (53%), Gaps = 17/248 (6%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A R+R H    A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+
Sbjct: 144 AFRHRLHLGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEK 203

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT-DNNLKP 156
           G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++ +   KP
Sbjct: 204 GYKFSTYATWWIRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKLLSQEMGRKP 258

Query: 157 -EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
            E+ +A   ++ + +   I+ + +L    SL   I   +   S+  D++  D +  E  +
Sbjct: 259 TEEEIATRMEMTIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIESDGETPEDQV 314

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIE 273
            +   R++    L   +  L+PRER +   R   ++    TLE +   F V+RER+RQIE
Sbjct: 315 SKNLLRED----LESVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIE 370

Query: 274 ARAFKKVQ 281
           A+A +K++
Sbjct: 371 AKALRKLR 378


>gi|33946401|gb|AAQ55816.1| truncated stationary phase specific sigma factor [Pseudomonas
           syringae]
          Length = 252

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 57/163 (34%), Positives = 94/163 (57%), Gaps = 3/163 (1%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L   EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 66  YLNEIGFSPLLSPAEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 124

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 125 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVY 183

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
           LR  +   Q + D+   PE++  + +K       ++ +N R++
Sbjct: 184 LRAARELTQKL-DHEPSPEEIANLLEKPVAEVKRMLGLNERVS 225


>gi|1621026|gb|AAB17121.1| RpoS [Yersinia enterocolitica]
          Length = 277

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 65/205 (31%), Positives = 108/205 (52%), Gaps = 13/205 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 62  YLGEIGYSPLLTAEEEVYFARRAL-RGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 120

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+ L++AV+KFDPE GFR +TYS WWI+  ++  I+     +++      +  ++F
Sbjct: 121 IEEGNLCLIRAVEKFDPEPGFRFSTYSHWWIRQTIERAIMNQTRTIRLPIHIVKELNVYF 180

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD   + L 
Sbjct: 181 GTARELSHKLDHEPSAEEIAEQLNKPVDDVSRMLRLN---ERITSVDTPLGGDSEKSLLD 237

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVL 215
             SD+N +  +D    D D ++ ++
Sbjct: 238 ILSDENENGPED-TTQDDDMKQSIV 261


>gi|254525463|ref|ZP_05137515.1| sigma-70 factor [Prochlorococcus marinus str. MIT 9202]
 gi|221536887|gb|EEE39340.1| sigma-70 factor [Prochlorococcus marinus str. MIT 9202]
          Length = 393

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 130/237 (54%), Gaps = 17/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 157 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 216

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++     KP E+ +A + ++
Sbjct: 217 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKVLSQEFGRKPSEEEIAESMEM 271

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  D +  EQ + +   R++   
Sbjct: 272 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIEADIENPEQDVSKTLLREDLEG 327

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +L    + L+PRER +   R   ++    TLE +   F+V+RER+RQIEA+A +K++
Sbjct: 328 VL----ATLSPRERDVLRLRYGIDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLR 380


>gi|158340954|ref|YP_001522121.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158311195|gb|ABW32807.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 268

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 79/279 (28%), Positives = 132/279 (47%), Gaps = 37/279 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ E+ + P+L  +EE  LA++ +  GDL A  R++  +LRLVV IA  ++  GLP+ ++
Sbjct: 11  YLKEMGRYPLLSHEEEIRLARQVKA-GDLKAKQRMIECNLRLVVSIAKKHQHLGLPLMDL 69

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF- 137
           + EG+IGL  AV KFD  +G + +TY+ WWI  A++  +             +Q R  + 
Sbjct: 70  IQEGSIGLNTAVDKFDLAQGCKFSTYAYWWISEAIKRAL------------KSQSRTIYI 117

Query: 138 ------NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
                    R+K  ++ +T    +   +  ++    +  S + +         SL+  + 
Sbjct: 118 PIHQWERAHRIKKAVRQLTQEKGRTPTLKELSAATGIKSSLIRNTLQSFQAVSSLDQPVG 177

Query: 192 SSDKNS----SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
              K++     Q +D  +   DG E   IE        + LTR M+ L  RER I + R 
Sbjct: 178 PEQKDALIDLIQTEDAALSIMDGLE---IE--------DALTRCMAYLTERERFIVDQRY 226

Query: 248 --LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                 P ++  +  +  VSRERVRQI   A KK+   +
Sbjct: 227 GLTDGQPKSMGVIGKQIGVSRERVRQILNIAMKKMTRQV 265


>gi|217034615|ref|ZP_03440022.1| hypothetical protein HP9810_881g8 [Helicobacter pylori 98-10]
 gi|216942910|gb|EEC22397.1| hypothetical protein HP9810_881g8 [Helicobacter pylori 98-10]
          Length = 671

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 73/246 (29%), Positives = 121/246 (49%), Gaps = 33/246 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ WW
Sbjct: 432 AKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWW 491

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA-ITDNNLKPEQVVAIAKKLN 167
           IK A+   I      ++I        +   + R+   ++  I +N  +P+          
Sbjct: 492 IKQAISRAIADQARTIRIPI-----HMIDTINRINKVMRKHIQENGKEPDL--------- 537

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE------- 220
               EV++   RL+ D+  N +     K     +  +  D DG+    +E +        
Sbjct: 538 ----EVVAEEVRLSLDKVKNVI--KVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDH 591

Query: 221 --RKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEAR 275
             R++ +  +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ 
Sbjct: 592 IMREDLKAQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESS 651

Query: 276 AFKKVQ 281
           A KK++
Sbjct: 652 AIKKLR 657


>gi|220906934|ref|YP_002482245.1| RNA polymerase sigma-70 subunit RpoD subfamily [Cyanothece sp. PCC
           7425]
 gi|219863545|gb|ACL43884.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7425]
          Length = 378

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 72/246 (29%), Positives = 132/246 (53%), Gaps = 17/246 (6%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R+R H    A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G+
Sbjct: 133 RHRLHIGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGY 192

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT-DNNLKP-E 157
           + +TY+ WWI+ A+   I      +++        L+  + R+K   + ++ +   KP E
Sbjct: 193 KFSTYATWWIRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKLLSQEMGRKPTE 247

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           + +A   ++ + +   I+ + +L    SL   I   +   S+  D++  D +  E  + +
Sbjct: 248 EEIATRMEMTIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIESDGETPEDQVSK 303

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEAR 275
              R++    L   +  L+PRER + + R   ++    TLE +   F V+RER+RQIEA+
Sbjct: 304 NLLRED----LETVLCTLSPRERDVLKLRYGLDDGRMKTLEEIGQLFNVTRERIRQIEAK 359

Query: 276 AFKKVQ 281
           A +K++
Sbjct: 360 ALRKLR 365


>gi|1405331|dbj|BAA11832.1| chloroplast RNA polymerase sigma subunit [Cyanidium caldarium]
          Length = 591

 Score = 99.8 bits (247), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 68/236 (28%), Positives = 118/236 (50%), Gaps = 14/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+VT++LRLVV IA  Y   G+ + +++ EG+IGL++ V+KFD ERGFR +TY+ WW
Sbjct: 352 AKERMVTANLRLVVSIAKRYSNRGVALQDLIQEGSIGLIRGVEKFDAERGFRFSTYATWW 411

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ ++   I  S   +++    +       +  ++   +A+     +P     I + + +
Sbjct: 412 IRQSITRAISDSSRSIRLPVHVHD-----TISLIRKQTKALQVELGRPPSEEEICESVGI 466

Query: 169 SESEV-ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
             ++  + M C      SL   + S D      +  +  +   +E        R   R  
Sbjct: 467 DRAKYRLVMECS-RNIVSLETPLRSGDDVHFLGESLIAPEERAEENC-----SRDTLRES 520

Query: 228 LTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           + + +  L+ RER +   R       P TLE + S F V+RER+RQIE++A KK++
Sbjct: 521 IEKVLHCLSTREREVIRMRFGLTDGRPRTLEEVGSRFNVTRERIRQIESKALKKLR 576


>gi|304383076|ref|ZP_07365551.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella marshii
           DSM 16973]
 gi|304335762|gb|EFM02017.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella marshii
           DSM 16973]
          Length = 290

 Score = 99.4 bits (246), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 76/272 (27%), Positives = 137/272 (50%), Gaps = 14/272 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGL 73
           L +Y+ EI + P++   EE  LA++ ++ G     A  +LVT++LR VV +A  Y+  GL
Sbjct: 18  LDKYLVEIGRAPLISIDEEIELAQKIKKGGPEGERAKDKLVTANLRFVVSVAKQYQHQGL 77

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V++    NQ 
Sbjct: 78  TLTDLIDEGNIGLIKAAQKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRL--PLNQ- 134

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINS 192
               +L ++   +      N +   V  ++   ++ E E I  +    G   S++A    
Sbjct: 135 --VGSLNKINHEINKFEQENQRHPSVSELSDVTHIDE-EKIGQSLMADGHHVSIDAPFQE 191

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF-EARRLQEN 251
            ++N     D +    D +   L++ E      N  T    VL  RE  I  E   +  +
Sbjct: 192 GEENC--MLDVMAGGEDSRTDRLVDHESMAQELN--TVLCKVLKDREITIIRECFGIGCH 247

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
              LE +     ++RERVRQI  ++  K+++S
Sbjct: 248 EKGLEEIGDRLGLTRERVRQIREKSIAKLRDS 279


>gi|91216377|ref|ZP_01253344.1| RNA polymerase sigma factor rpoD (Sigma-A) [Psychroflexus torquis
           ATCC 700755]
 gi|91185515|gb|EAS71891.1| RNA polymerase sigma factor rpoD (Sigma-A) [Psychroflexus torquis
           ATCC 700755]
          Length = 287

 Score = 99.4 bits (246), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 77/280 (27%), Positives = 142/280 (50%), Gaps = 33/280 (11%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI K+ ++  +EE  LA++ +   DL A  +L  ++LR VV ++  Y+  GL +
Sbjct: 18  LDKYLQEIGKVDLITAEEEVELAQKIKAGDDL-ALEKLTKANLRFVVSVSKQYQNQGLTL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
            ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++      Q  ++R   L KIG+ 
Sbjct: 77  PDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILSALAEQSRVVR-LPLNKIGSI 135

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA- 188
               + F  L +           + +P     IAK+L ++ ++V           S++A 
Sbjct: 136 NKINKTFAILEQ----------RHQRPPSPDEIAKELEMTVNDVKESLKNSGRHLSMDAP 185

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
           LI   D N     D L +      +  +  E  +     + R++  L  RE  +    RL
Sbjct: 186 LIEGEDSN---LYDVLKFGESPNPENDLLHESLQTE---IERALETLTTREADVI---RL 236

Query: 249 -----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
                 + P+TLE +   F ++RERVRQI+ +  ++++ +
Sbjct: 237 YFGLGNQQPMTLEEIGETFGLTRERVRQIKEKGVRRLKHT 276


>gi|5921146|dbj|BAA84590.1| RNA polymerase sigma 70 [Helicobacter pylori]
          Length = 675

 Score = 99.4 bits (246), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 71/246 (28%), Positives = 119/246 (48%), Gaps = 33/246 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ WW
Sbjct: 436 AKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWW 495

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           IK A+   I      ++I        +   + R+   ++     N K   +  +A+++ +
Sbjct: 496 IKQAISRAIADQARTIRIPI-----HMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGL 550

Query: 169 SESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           S  +V          IS+   +  D+         DKN +   D ++             
Sbjct: 551 SLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIASSIDHIM------------- 597

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEAR 275
             R++ +  +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ 
Sbjct: 598 --REDLKAQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESS 655

Query: 276 AFKKVQ 281
           A KK++
Sbjct: 656 AIKKLR 661


>gi|300870272|ref|YP_003785143.1| DNA directed RNA polymerase sigma subunit [Brachyspira pilosicoli
           95/1000]
 gi|300687971|gb|ADK30642.1| DNA directed RNA polymerase sigma subunit [Brachyspira pilosicoli
           95/1000]
          Length = 284

 Score = 99.4 bits (246), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 77/276 (27%), Positives = 139/276 (50%), Gaps = 27/276 (9%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            +S Y  + ++  +L ++EE  L +R ++ GD  A  +L+ S+LR V+ IA  Y+  GL 
Sbjct: 15  NISLYFADAKREKLLTREEEIELTQRLKK-GDSQARAKLIRSNLRFVISIAKQYKNSGLL 73

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++ EGN+GL+ A  +FDP++G+   +Y+++WI+ ++   I     L+++    N+  
Sbjct: 74  LEDLIGEGNLGLIIATDRFDPDKGYHFISYAVYWIRQSILRAINEKSRLIRL--PLNKAM 131

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN---CRLAGDESLNALIN 191
              +L R        T +    E + AI KK       ++SMN     L  D +++ + +
Sbjct: 132 DLVDLERAVHQCYYKTGHMPDVEDLAAILKKEPREIRNIMSMNNEYVSLEKDFNMDGVKD 191

Query: 192 S-----SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
                  DKNS   +D L  D +  E++ I  EE              L+  E+ I  AR
Sbjct: 192 RLADVVEDKNSKTVEDILS-DKELTEELKIAMEE--------------LSDIEKEIINAR 236

Query: 247 R-LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             L +   TL+ +  ++  ++ER+RQIE +A KK+ 
Sbjct: 237 YGLDQEKKTLKEVGEKYSFTKERIRQIEKKALKKMH 272


>gi|123968088|ref|YP_001008946.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str.
           AS9601]
 gi|123198198|gb|ABM69839.1| Putative principal RNA polymerase sigma factor [Prochlorococcus
           marinus str. AS9601]
          Length = 394

 Score = 99.4 bits (246), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 130/237 (54%), Gaps = 17/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 158 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 217

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++     KP E+ +A + ++
Sbjct: 218 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKVLSQEFGRKPSEEEIAESMEM 272

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  D +  EQ + +   R++   
Sbjct: 273 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIEADIENPEQDVSKTLLREDLEG 328

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +L    + L+PRER +   R   ++    TLE +   F+V+RER+RQIEA+A +K++
Sbjct: 329 VL----ATLSPRERDVLRLRYGIDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLR 381


>gi|1542976|gb|AAB08043.1| sigma factor [Thermoanaerobacterium thermosulfurigenes]
          Length = 261

 Score = 99.4 bits (246), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 79/260 (30%), Positives = 138/260 (53%), Gaps = 22/260 (8%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           +L K+EE +L +R R +GD SA   LV  ++RLV K+A G+   G+   ++V EG IGL+
Sbjct: 4   LLTKEEEKILFERLR-NGDESAKDVLVECNIRLVDKVAAGFLKSGVEFDDLVQEGLIGLL 62

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK--RLF---FNLRRL 142
            A+ KFD  +G++ +TY+ W+I+ +M+ YI     ++++    N+K  R+    + + + 
Sbjct: 63  TAIDKFDHTKGYKFSTYATWYIQQSMRRYIGNYGKIIRLPIHINEKINRILKARYLIEQK 122

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
           KG L A T+          I++    +E E+           SLN  +N  ++  ++  +
Sbjct: 123 KGSL-ATTEE---------ISRLTGYTEEEIEGYLSYATDVISLNQYVN-DERVDAELIN 171

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPVTLENLSSE 261
           ++  D    E++ IEKE +K  R +L      L  RER I + R     N  TL  + + 
Sbjct: 172 FIQDDTIDVEEMAIEKEIKKEIRKIL----DSLPERERMILKMRFGFGCNLKTLTEIGNI 227

Query: 262 FEVSRERVRQIEARAFKKVQ 281
           F ++RER+RQI+    K+++
Sbjct: 228 FGLTRERIRQIQNNTIKELR 247


>gi|333030005|ref|ZP_08458066.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacteroides
           coprosuis DSM 18011]
 gi|332740602|gb|EGJ71084.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacteroides
           coprosuis DSM 18011]
          Length = 286

 Score = 99.4 bits (246), Expect = 5e-19,   Method: Compositional matrix adjust.
 Identities = 79/280 (28%), Positives = 145/280 (51%), Gaps = 34/280 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI +  ++  +EE  LA+R ++ GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGREDLITVEEEVELAQRIKK-GDRVALEKLTKANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTT 129
            ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++      Q  I+R   L ++G+ 
Sbjct: 77  PDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVR-LPLNQVGSL 135

Query: 130 ANQKRLFFNLRR---LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
               + F    +    +   Q + D    P  V  +   L VS    IS++      E  
Sbjct: 136 NKISKAFAKFEQEYERRPSPQELADELEMP--VDKVTDTLKVS-GRHISVDAPFVEGED- 191

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI---F 243
           N+L++    + S   D  + +    E++               R++S L  RE++I   F
Sbjct: 192 NSLLDVLVNDDSPMADRSLVNESLSEEI--------------DRALSTLEDREKQIIKMF 237

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
                QE  +TLE +  +F ++RERVRQI+ +A ++++++
Sbjct: 238 FGIGCQE--MTLEEIGDKFGLTRERVRQIKEKAIRRLRQN 275


>gi|307721137|ref|YP_003892277.1| RNA polymerase, sigma 70 subunit, RpoD [Sulfurimonas autotrophica
           DSM 16294]
 gi|306979230|gb|ADN09265.1| RNA polymerase, sigma 70 subunit, RpoD [Sulfurimonas autotrophica
           DSM 16294]
          Length = 615

 Score = 99.4 bits (246), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 76/233 (32%), Positives = 125/233 (53%), Gaps = 13/233 (5%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           ++  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ ++G++ +TY+ WWI+ 
Sbjct: 379 KMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYQKGYKFSTYATWWIRQ 438

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           A+   I      ++I     +     N + ++ HLQ   +N  +P+ V  IAK++ +S  
Sbjct: 439 AISRAIADQARTIRIPIHMIETINRIN-KIMRKHLQ---ENGKEPD-VDTIAKEVGLSVE 493

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           +V ++        SL A I S D    ++ D++           I K+   + R  + + 
Sbjct: 494 KVKNVIKITKEPISLEAPIGSED--DGRFGDFIEDKTSLSPSDAILKD---DLRIQIEQV 548

Query: 232 MSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +  LN RE+ + + R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 549 LEQLNEREKAVIKLRFGIMDDESDRTLEEIGKELSVTRERVRQIESSAIKKLK 601


>gi|86608944|ref|YP_477706.1| sigma-70 family RNA polymerase sigma factor [Synechococcus sp.
           JA-2-3B'a(2-13)]
 gi|86557486|gb|ABD02443.1| RNA polymerase sigma-70 factor family [Synechococcus sp.
           JA-2-3B'a(2-13)]
          Length = 320

 Score = 99.4 bits (246), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 84/295 (28%), Positives = 153/295 (51%), Gaps = 21/295 (7%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLR 59
           NR   + +    +G+  ++ E+ + P+L  ++E  L +   E G     A   LV ++LR
Sbjct: 31  NRATQASLSEDSVGV--FLREMARYPLLNAEQEVKLGRLIAEGGAAGERAKRELVRANLR 88

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           LVV IA  Y   G+P  +++ EG IGL++A +KF+ ERG++ +TY+ WWI+  +   +  
Sbjct: 89  LVVSIAKKYLNRGVPFLDLIQEGTIGLIRAAEKFEYERGYKFSTYAYWWIRQGITRAVAN 148

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
              LV+I     +K     ++R++  L      N +P Q   IA+ L +S  ++ ++   
Sbjct: 149 QGRLVRIPVHMVEK--LNQVKRIRRELTETL--NRRPTQ-AEIAEALEISPDKLDALLTL 203

Query: 180 L-AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM---LTRSMSVL 235
           L AG ++L +L     K   +    L+ D +      +  E + +   +   L   +  L
Sbjct: 204 LEAGRQTL-SLHTPVGKEEDRELMQLIEDANS-----LTPESQMDLHLLSAQLEEMLEQL 257

Query: 236 NPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +PRE+ I + R  L++  + TL  +   F +SRERVRQI+ARA +K++   ++++
Sbjct: 258 SPREQEILKLRYGLKDGHLHTLSEIGQLFGLSRERVRQIQARAMRKLRHPRRQEI 312


>gi|110798581|ref|YP_696687.1| RNA polymerase sigma factor RpoD [Clostridium perfringens ATCC
           13124]
 gi|15186722|dbj|BAB62883.1| RNA polymerase major sigma factor [Clostridium perfringens]
 gi|110673228|gb|ABG82215.1| RNA polymerase sigma factor RpoD [Clostridium perfringens ATCC
           13124]
          Length = 366

 Score = 99.4 bits (246), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 77/265 (29%), Positives = 137/265 (51%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+ +L  ++E  LAK+  E G   A  +L  ++LRLVV IA  Y G G+   ++
Sbjct: 100 YLKEIGKVQLLSSEDEIELAKKI-EEGSNYAKKKLAEANLRLVVSIAKRYVGRGMLFLDL 158

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 159 IQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 216

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R++  L      +  PE+   ++K++++   +V  +  ++A  E ++      ++  S
Sbjct: 217 LIRIQRQLVQELGRDPLPEE---LSKQMDMPVDKVREI-LKIA-QEPVSLETPIGEEEDS 271

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++  D              K +   L   +  L PRE ++   R   ++    TLE
Sbjct: 272 HLGDFIPDDDAPAPAEAAAFTMLKEQ---LINVLDTLTPREEKVLRLRFGLDDGRARTLE 328

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF V+RER+RQIEA+A +K++
Sbjct: 329 EVGKEFNVTRERIRQIEAKALRKLR 353


>gi|159904372|ref|YP_001551716.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9211]
 gi|159889548|gb|ABX09762.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9211]
          Length = 338

 Score = 99.4 bits (246), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 78/273 (28%), Positives = 145/273 (53%), Gaps = 16/273 (5%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRG 70
           EI L+ ++ +++++  +EK++   L+ R R    +   A  R++ ++LRLVV +A  Y+ 
Sbjct: 69  EIELAHHVQKMKELLDIEKEK---LSARQRHQIRMGKRARDRMMAANLRLVVSVAKKYQN 125

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+  M   I  S   +++    
Sbjct: 126 QGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTRAIDNSARTIRLPIHI 185

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
           ++K     +RR+    + ++    +    V +A  + +   ++  +  + A   SL++  
Sbjct: 186 SEK--LSKMRRIS---RELSHRFGRQPNRVELANAMGIEPQDLEDLVAQSAPCASLDSHA 240

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RL 248
              +  S+  +  L+ D +  E   +   +RK ++  L   +S LN RE++I   R    
Sbjct: 241 RGEEDRSTLGE--LIPDPNYDEP--MAGMDRKMQKEHLGGWLSQLNEREQKIMRLRFGLD 296

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            E P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 297 GEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 329


>gi|113475621|ref|YP_721682.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
 gi|110166669|gb|ABG51209.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
          Length = 410

 Score = 99.4 bits (246), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 67/238 (28%), Positives = 126/238 (52%), Gaps = 13/238 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           + A H++++++LRLVV IA  Y+  G+ + +++ EG +GL +AV+KFDP+RG+R +TY+ 
Sbjct: 169 IEARHQMISTNLRLVVSIAKKYQNRGVELLDLIQEGTLGLERAVEKFDPQRGYRFSTYAY 228

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   I      +++    ++K     L ++K   Q I        +V  IA++L
Sbjct: 229 WWIRQGITRAIATQSRTIRLPIHVSEK-----LNKIKKVQQKIFQEKGYTAKVEEIAREL 283

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++ ++V  +  ++    SL   +       ++  + L       E++LI    R++   
Sbjct: 284 KITAAQVREVLVKIPHSVSLETKVGRD--RDTELGELLETKDASPEEMLI----RESLVQ 337

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            L   +  L  RER +   R   E+    +L  ++S  ++SRERVRQIE +A  K+++
Sbjct: 338 ALKELLLDLTQRERYVITMRYGLEDGRACSLSEIASALKLSRERVRQIEVKALHKLRQ 395


>gi|107103136|ref|ZP_01367054.1| hypothetical protein PaerPA_01004205 [Pseudomonas aeruginosa PACS2]
          Length = 236

 Score = 99.4 bits (246), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 72/243 (29%), Positives = 125/243 (51%), Gaps = 26/243 (10%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  
Sbjct: 1   MIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           ++  I+     +++      K L   LR  +  L    D+   PE++  + +K       
Sbjct: 61  IERAIMNQTRTIRLPIHV-VKELNVYLRAAR-ELTHKLDHEPSPEEIANLLEKPVAEVKR 118

Query: 173 VISMNCRLA------GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++ +N R+       G +S   L+++   +       L+ D D  E +            
Sbjct: 119 MLGLNERVTSVDVSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLSESI------------ 166

Query: 227 MLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
              + ++ L  ++R +   R   R  E+  TLE +  E  ++RERVRQI+  A K+++E 
Sbjct: 167 --DQWLTELTDKQREVVIRRFGLRGHESS-TLEEVGQEIGLTRERVRQIQVEALKRLREI 223

Query: 284 IQK 286
           ++K
Sbjct: 224 LEK 226


>gi|162458769|ref|NP_001105507.1| sigma-like factor6 [Zea mays]
 gi|4336610|gb|AAD17856.1| sigma factor SIG6 [Zea mays]
          Length = 541

 Score = 99.4 bits (246), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 72/247 (29%), Positives = 126/247 (51%), Gaps = 30/247 (12%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           ++  S+ RLV+ +A  Y G GL I ++V +G  GLM+  +KF+P +G R  TY+ WWI+ 
Sbjct: 304 KMARSNFRLVIHVARKYEGCGLDIQDLVQDGCCGLMKTFEKFNPSKGCRFPTYAYWWIRQ 363

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRL-KGHLQAITDNNLKPEQVVA------IAK 164
           ++++ I ++  L+++  +     ++  LR++ K  ++ I D      +VVA      I K
Sbjct: 364 SIKKSIFKNSRLIRLPES-----VYALLRKVGKARMECIMDGEQPTNEVVARRAGITIEK 418

Query: 165 --KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
             KL     +V SM  R+  D+ +     + D N            +G E  +     R+
Sbjct: 419 LAKLRAKTRKVRSMQDRVWSDDGVTYQEITEDPNI-----------EGPEVSVDRLMMRQ 467

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             R+ LT    +L+PRE+ I E R    +  P TL  +   + +S+ER+RQ++ +A  K+
Sbjct: 468 QVRSFLT---GILSPREKEIIEHRFGIHDGQPKTLHVIGDMYGLSKERIRQVQNKALDKL 524

Query: 281 QESIQKQ 287
           + SI  Q
Sbjct: 525 RNSISAQ 531


>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 = 99.4 bits (246), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 68/241 (28%), Positives = 119/241 (49%), Gaps = 12/241 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 489 EKASRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 548

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I     +     N R  + HLQ       +P+    +
Sbjct: 549 TYATWWIRQAITRSIADQARTIRIPVHMIETINKMN-RISRQHLQEF---GFEPD-APTL 603

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+ + E ++      +   E ++      D + S   D++    D      ++   + 
Sbjct: 604 AEKMEIPEDKI--RKIMMIAKEPISMETPIGDDDDSHLGDFI---EDTNNVAPVDAAMQA 658

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKV 280
             R ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 659 GLREVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKAIRKL 718

Query: 281 Q 281
           +
Sbjct: 719 K 719


>gi|299131999|ref|ZP_07025194.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Afipia sp. 1NLS2]
 gi|298592136|gb|EFI52336.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Afipia sp. 1NLS2]
          Length = 709

 Score = 99.4 bits (246), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 80/268 (29%), Positives = 131/268 (48%), Gaps = 17/268 (6%)

Query: 21  HEIRKIPMLEKQE-----EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           HEI+++  L   E     + VL  +  E     A   +V ++LRLV+ IA  Y   GL  
Sbjct: 438 HEIQQLAALTGLEIGEFRKIVLGVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQF 497

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I    +    
Sbjct: 498 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI--PVHMIET 555

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + R    +         PE+   +A+KL +   +V  +  ++A  E L+      D+
Sbjct: 556 INKIVRTSRQMLNEIGREPTPEE---LAEKLGMPLEKVRKV-LKIA-KEPLSLETPVGDE 610

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPV 253
             S   D++    D    + I+   + N R   TR ++ L PRE R+   R         
Sbjct: 611 EDSHLGDFI---EDKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDH 667

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 668 TLEEVGQQFSVTRERIRQIEAKALRKLK 695


>gi|78778882|ref|YP_396994.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str. MIT
           9312]
 gi|78712381|gb|ABB49558.1| Sigma-70 factor [Prochlorococcus marinus str. MIT 9312]
          Length = 393

 Score = 99.4 bits (246), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 130/237 (54%), Gaps = 17/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 157 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 216

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++     KP E+ +A + ++
Sbjct: 217 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKVLSQEFGRKPSEEEIAESMEM 271

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  D +  EQ + +   R++   
Sbjct: 272 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIEADIENPEQDVSKTLLREDLEG 327

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +L    + L+PRER +   R   ++    TLE +   F+V+RER+RQIEA+A +K++
Sbjct: 328 VL----ATLSPRERDVLRLRYGIDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLR 380


>gi|282891123|ref|ZP_06299627.1| hypothetical protein pah_c047o017 [Parachlamydia acanthamoebae str.
           Hall's coccus]
 gi|281498940|gb|EFB41255.1| hypothetical protein pah_c047o017 [Parachlamydia acanthamoebae str.
           Hall's coccus]
          Length = 546

 Score = 99.4 bits (246), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 75/239 (31%), Positives = 118/239 (49%), Gaps = 20/239 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+  RG++ +TY+ WW
Sbjct: 304 AKREMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWW 363

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+      + R    L   T     PE+   +A 
Sbjct: 364 IRQAVTRAIADQARTIRIPVHMIETINK------VLRGAKKLMMETGREPSPEE---LAN 414

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L ++   V  +        SL A +   D   SQ+ D+L    D       E       
Sbjct: 415 ELGITAERVREIYKIAQHPISLQAEVG--DGGESQFGDFL---EDTGADSPAEATGYSIL 469

Query: 225 RNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++ +   ++ L  RER++   R   L   P TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 470 KDKMNEVLATLTDRERKVLIQRFGLLDGKPKTLEEVGVEFNVTRERIRQIEAKALRKMR 528


>gi|166363676|ref|YP_001655949.1| group 2 RNA polymerase sigma factor [Microcystis aeruginosa
           NIES-843]
 gi|166086049|dbj|BAG00757.1| group 2 RNA polymerase sigma factor [Microcystis aeruginosa
           NIES-843]
          Length = 414

 Score = 99.4 bits (246), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 69/237 (29%), Positives = 123/237 (51%), Gaps = 13/237 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +++ ++LRLVV +A  Y+  GL + +++ EG +GL +AVKKFDP +G+R +TY+ WW
Sbjct: 175 AKEQMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVKKFDPTKGYRFSTYAYWW 234

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  M   I     ++++     +K     L R+K   + I+    +   V  IA++L +
Sbjct: 235 IRQGMTRAIATKSQIIRLPVHITEK-----LNRIKKAQRKISQMRGRTATVEEIAQELAL 289

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +   V  +   +    SL   I    +  ++  D L  +    E   + +  +++ R +L
Sbjct: 290 TPEAVRELLMTVPRSVSLE--IKVGKEKDTELLDLLEIEAVSSENHFVYESLQRDIRELL 347

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               + L  RER + E R   L     +L ++    E+SRERVRQIE +A +K+++S
Sbjct: 348 ----ADLTAREREVIELRYGFLDGKSHSLADIGRTLELSRERVRQIELKALQKLRQS 400


>gi|126727888|ref|ZP_01743716.1| RNA polymerase sigma factor [Rhodobacterales bacterium HTCC2150]
 gi|126702829|gb|EBA01934.1| RNA polymerase sigma factor [Rhodobacterales bacterium HTCC2150]
          Length = 661

 Score = 99.4 bits (246), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 72/236 (30%), Positives = 121/236 (51%), Gaps = 12/236 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 422 AAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 481

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I    +       L R    +         PE+   +AKKL 
Sbjct: 482 WIRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAKKLQ 536

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +   +V  +  ++A  E ++      D+  SQ  D++    D    + ++   ++N +  
Sbjct: 537 MPLEKVRKV-MKIA-KEPISLETPIGDEEDSQLGDFI---EDKNAVLPLDSAIQENLKET 591

Query: 228 LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 592 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 647


>gi|157412913|ref|YP_001483779.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str. MIT
           9215]
 gi|157387488|gb|ABV50193.1| Putative principal RNA polymerase sigma factor [Prochlorococcus
           marinus str. MIT 9215]
          Length = 393

 Score = 99.4 bits (246), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 130/237 (54%), Gaps = 17/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 157 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 216

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++     KP E+ +A + ++
Sbjct: 217 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKVLSQEFGRKPSEEEIAESMEM 271

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  D +  EQ + +   R++   
Sbjct: 272 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIEADIENPEQDVSKTLLREDLEG 327

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +L    + L+PRER +   R   ++    TLE +   F+V+RER+RQIEA+A +K++
Sbjct: 328 VL----ATLSPRERDVLRLRYGIDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLR 380


>gi|194696078|gb|ACF82123.1| unknown [Zea mays]
 gi|323388703|gb|ADX60156.1| SIGMA70-like transcription factor [Zea mays]
          Length = 541

 Score = 99.0 bits (245), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 72/247 (29%), Positives = 126/247 (51%), Gaps = 30/247 (12%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           ++  S+ RLV+ +A  Y G GL I ++V +G  GLM+  +KF+P +G R  TY+ WWI+ 
Sbjct: 304 KMARSNFRLVIHVARKYEGCGLDIQDLVQDGCCGLMKTFEKFNPSKGCRFPTYAYWWIRQ 363

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRL-KGHLQAITDNNLKPEQVVA------IAK 164
           ++++ I ++  L+++  +     ++  LR++ K  ++ I D      +VVA      I K
Sbjct: 364 SIKKSIFKNSRLIRLPES-----VYALLRKVGKARMECIMDGEQPTNEVVARRAGITIEK 418

Query: 165 --KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
             KL     +V SM  R+  D+ +     + D N            +G E  +     R+
Sbjct: 419 LAKLRAKTRKVRSMQDRVWSDDGVTYQEITEDPNI-----------EGPEVSVDRLMMRQ 467

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             R+ LT    +L+PRE+ I E R    +  P TL  +   + +S+ER+RQ++ +A  K+
Sbjct: 468 QVRSFLT---GILSPREKEIIEHRFGIHDGQPKTLHVIGDMYGLSKERIRQVQNKALDKL 524

Query: 281 QESIQKQ 287
           + SI  Q
Sbjct: 525 RNSISAQ 531


>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 = 99.0 bits (245), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 71/236 (30%), Positives = 121/236 (51%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 402 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 461

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +   T     PE    ++KK+ +
Sbjct: 462 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQILQATGKEPSPED---LSKKMGL 516

Query: 169 SESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
            E ++  +  ++A +  S+   I   D + S   D++    D      I+    +  R  
Sbjct: 517 PEDKIRKI-LKIAKEPISMETPIGDEDGD-SHLGDFI---EDAAALSPIDAATIEGLRET 571

Query: 228 LTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
             R ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 572 AQRVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 627


>gi|323345236|ref|ZP_08085459.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella oralis
           ATCC 33269]
 gi|323093350|gb|EFZ35928.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella oralis
           ATCC 33269]
          Length = 290

 Score = 99.0 bits (245), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 73/280 (26%), Positives = 140/280 (50%), Gaps = 30/280 (10%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGL 73
           L +Y+ EI + P++  ++E  LA++ ++ G     A  RLVT++LR VV +A  Y+  GL
Sbjct: 18  LDKYLVEIGRAPLISIEDEIELAQKIKKGGPEGERAKERLVTANLRFVVSVAKQYQHQGL 77

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V++    NQ 
Sbjct: 78  TLTDLIDEGNIGLIKAAQKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRL--PLNQ- 134

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
               +L ++   +      N +   +  ++   N+ E ++           S++A     
Sbjct: 135 --VGSLNKINHEINKFEQENQRRPSISELSDATNIDEEKIGQSMMADGHHVSIDAPFQDG 192

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS---------VLNPRERRIF- 243
           + N+       + D      V+   ++ +  RN+   SM+         VL  RE  I  
Sbjct: 193 EDNT-------MLD------VMPGGDDSRTDRNVDHESMAMELNSVLSRVLKDREITIIK 239

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           E   +  +   LE +  +  ++RERVRQI  ++  K+++S
Sbjct: 240 ECFGIGCHEKGLEEIGDQLGLTRERVRQIREKSIAKLRDS 279


>gi|154498377|ref|ZP_02036755.1| hypothetical protein BACCAP_02366 [Bacteroides capillosus ATCC
           29799]
 gi|150272688|gb|EDM99866.1| hypothetical protein BACCAP_02366 [Bacteroides capillosus ATCC
           29799]
          Length = 441

 Score = 99.0 bits (245), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 82/261 (31%), Positives = 137/261 (52%), Gaps = 24/261 (9%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           +L  +EE  L K  R  G+ +A  RL  ++LRLVV IA  Y G G+   +++ EGN+GL+
Sbjct: 185 VLTPEEEKALKKDIR-RGE-AAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLI 242

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQK-RLFFNLRRL 142
           +AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N+  R+   L + 
Sbjct: 243 KAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKVIRVSRQLLQE 302

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
            GH       +  PE+   IA+++N+   +V  +  ++A  E ++      ++  S   D
Sbjct: 303 LGH-------DPSPEE---IAEEMNMPVDKVREI-LKIA-QEPVSLETPIGEEEDSHLGD 350

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSS 260
           + + D D  E    E       +  L   +  L PRE ++ + R   E+    TLE +  
Sbjct: 351 F-IPDEDASEPS--EAASFTLLKEQLVDVLGTLTPREEKVLKLRFGIEDGRTRTLEEVGK 407

Query: 261 EFEVSRERVRQIEARAFKKVQ 281
           EF V+RER+RQIEA+A +K++
Sbjct: 408 EFNVTRERIRQIEAKALRKLR 428


>gi|291566491|dbj|BAI88763.1| group 2 RNA polymerase sigma factor SigC [Arthrospira platensis
           NIES-39]
          Length = 385

 Score = 99.0 bits (245), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 66/238 (27%), Positives = 128/238 (53%), Gaps = 13/238 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           + A   ++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV+KFDP RG+R +TYS 
Sbjct: 144 IQAKDHMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTRGYRFSTYSY 203

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   I      +++     +K     L ++K   + I+    +   +  IA +L
Sbjct: 204 WWIRQGITRAIATQSRTIRLPVHITEK-----LNKIKKAQRKISQEKSRTATIDDIATEL 258

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++  ++  +  R+    SL   +  +DK+ ++  D L  +    E++L+    R++   
Sbjct: 259 KMTPDQIREVLLRVPRSVSLETKVG-TDKD-TELGDLLETEESTPEELLM----RESLYR 312

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            L   ++ L+ +ER + + R      +P +L  +    ++SRERVRQIEA+A +K+++
Sbjct: 313 ELQHILADLSGKERAVIQMRYGLGDGHPYSLAEIGRALDLSRERVRQIEAKALQKLRQ 370


>gi|295133351|ref|YP_003584027.1| RNA polymerase sigma-70 factor [Zunongwangia profunda SM-A87]
 gi|294981366|gb|ADF51831.1| RNA polymerase sigma-70 factor [Zunongwangia profunda SM-A87]
          Length = 284

 Score = 99.0 bits (245), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 81/293 (27%), Positives = 147/293 (50%), Gaps = 37/293 (12%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  L  Y+ +I  I  +  +EE  L ++ +  GD  A H LVTS+LR VV +A  Y+  G
Sbjct: 15  DASLDFYLKDIGPIARISSEEEVELTRKIK-AGDKKALHTLVTSNLRFVVSVAKQYQFKG 73

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L +S++++EGN+GL++A  +FD  RGF+  +Y++WWI+ AM + I  +  +V++    N+
Sbjct: 74  LSLSDLIAEGNLGLIKAANRFDETRGFKFISYAVWWIRQAMVQSISENARVVRL--PLNK 131

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRLAG 182
             L   +R+    LQ +       E+V   +  LN+  +E+          +S++  L+ 
Sbjct: 132 LTLINKIRKANSALQQLLQREASLEEV---SNFLNLPLTEIEEAGKSNATYLSLDKPLSN 188

Query: 183 DE---SLNALINSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           D    +LN LI S  ++  Q    +   H+  Q   ++EK E++     +   +  LN  
Sbjct: 189 DNDDFTLNQLITSKIEDPDQGLLNVSTSHEINQLMTILEKREKE-----VIILLFGLNGG 243

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +            +L ++S+   ++ ERVRQI+     K++ S +  +  S
Sbjct: 244 EAK------------SLRDISTLLGLTSERVRQIKEMGLIKLRRSPKAAILFS 284


>gi|158341079|ref|YP_001522246.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158311320|gb|ABW32932.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 268

 Score = 99.0 bits (245), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 82/284 (28%), Positives = 133/284 (46%), Gaps = 47/284 (16%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ E+ + P+L  +EE  LA++ +  GDL A  R++  +LRLVV IA  ++  GLP+ ++
Sbjct: 11  YLKEMGRYPLLSHEEEIRLARQVKA-GDLKAKQRMIECNLRLVVSIAKKHQHLGLPLMDL 69

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF- 137
           + EG+IGL  AV KFD  +G + +TY+ WWI  A++  +             +Q R  + 
Sbjct: 70  IQEGSIGLNTAVDKFDLAQGCKFSTYAYWWISEAIKRAL------------KSQSRTIYI 117

Query: 138 ------NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES---------EVISMNCRLAG 182
                    R+K  ++ +T    +   +  ++    +  S         + IS   +  G
Sbjct: 118 PIHQWERAHRIKKAVRQLTQEKGRTPTLKELSAATGIKSSLIRNTLQSFQAISSLDQPVG 177

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
            E  +ALI     +  Q +D  +   DG E   IE        + LTR M+ L  RER I
Sbjct: 178 PEQKDALI-----DLIQTEDAALSIMDGLE---IE--------DALTRCMAYLTERERFI 221

Query: 243 FEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + R       P ++  +     +SRERVRQI   A KK+   +
Sbjct: 222 VDQRYGLTDGQPKSMGAIGKPIGISRERVRQILNIAMKKMTRQV 265


>gi|257458803|ref|ZP_05623926.1| RNA polymerase sigma factor RpoD [Campylobacter gracilis RM3268]
 gi|257443791|gb|EEV18911.1| RNA polymerase sigma factor RpoD [Campylobacter gracilis RM3268]
          Length = 626

 Score = 99.0 bits (245), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 72/237 (30%), Positives = 119/237 (50%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ +RG++ +TY+ W
Sbjct: 386 NAKARMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATW 445

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I        +   + R+    +       K   +  IA+++ 
Sbjct: 446 WIRQAISRAIADQARTIRIPI-----HMIETINRINKITRKYMQEGGKEPDINVIAQEVG 500

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V  +        SL A I + D    ++ D++    D      IE+  + + +  
Sbjct: 501 LSVDKVKQVIKITKEPISLEAPIGNED--DGKFGDFV---EDKSSVSPIEQILKSDLKEQ 555

Query: 228 LTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  LN RER +   R      E+  TLE +  E  ++RERVRQIE+ A KK++
Sbjct: 556 IDDILEQLNDRERTVIRMRFGLLDDESDRTLEEIGKELNITRERVRQIESSAIKKLK 612


>gi|260434805|ref|ZP_05788775.1| RNA polymerase sigma factor RpoD [Synechococcus sp. WH 8109]
 gi|260412679|gb|EEX05975.1| RNA polymerase sigma factor RpoD [Synechococcus sp. WH 8109]
          Length = 312

 Score = 99.0 bits (245), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 84/293 (28%), Positives = 147/293 (50%), Gaps = 36/293 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLA-------------KRYREHGDLSAAHR---------- 52
           +S Y+  I +IP+L   EE  L               R  E G+L+ A R          
Sbjct: 19  VSWYLATIGRIPLLTPAEEIELGNQVQAMMSLTEDGSREFEDGELTTAQRRLLRIGRRAK 78

Query: 53  --LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
             ++ ++LRLVV +A  Y+G GL + +++ EG++GL +AV+KFDP RG++ +TY+ WWI+
Sbjct: 79  ERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWWIR 138

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            +M   I      +++    +++     +R++   L         P + V IA+ +++  
Sbjct: 139 QSMTRAIACQSRTIRLPVHLSER--LTTIRKVS--LDLAHKLGAMPSR-VEIAEAMDIPL 193

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            E+ S+  +     SL+A +N  +  S  +   L+ D    E   +E  E++     L R
Sbjct: 194 DELDSLLRQALTTSSLDAPVNGEEGRS--FLGDLIADSSLDEP--LEIVEQRIHHEQLGR 249

Query: 231 SMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +S L+ +E+ +   R  L+ N   TL  +    EVSRERVRQ+E +A +K++
Sbjct: 250 WLSHLSEQEQHVLRMRFGLEGNERHTLAEIGRLMEVSRERVRQVELKALRKLR 302


>gi|217967697|ref|YP_002353203.1| putative RNA polymerase, sigma 70 family subunit [Dictyoglomus
           turgidum DSM 6724]
 gi|217336796|gb|ACK42589.1| putative RNA polymerase, sigma 70 family subunit [Dictyoglomus
           turgidum DSM 6724]
          Length = 413

 Score = 99.0 bits (245), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 48/108 (44%), Positives = 71/108 (65%), Gaps = 1/108 (0%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L  +EE  LAKR  E GD  A  RL+ ++LRLVV +A  Y G GL   ++
Sbjct: 75  YLKEIGKIPLLTPEEEIELAKRV-EQGDEDAKKRLIEANLRLVVSVAKRYIGRGLSFLDL 133

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I
Sbjct: 134 IQEGNLGLIKAVEKFDWRKGYKFSTYATWWIRQAITRAIADQARTIRI 181



 Score = 41.2 bits (95), Expect = 0.18,   Method: Compositional matrix adjust.
 Identities = 40/144 (27%), Positives = 72/144 (50%), Gaps = 12/144 (8%)

Query: 145 HLQAITDNNLKPEQVVAIAKKL-NVSESEVISMNCR-----LAGDESLNALINSSDKNSS 198
           HL+      L  E++   AK+L +V E E+     +     + G E L+  +   +   +
Sbjct: 259 HLKTKGKKELTKEKINEEAKELRHVLEEEIKQQTEKVREISMMGQEPLSLEMPVGEDEDN 318

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLE 256
           +  D++         + ++K  +K+   +L      L+ RER I + R  L++N P TLE
Sbjct: 319 RLADFVENKDLSPADIAVQKSLKKDIEELLNE----LSEREREILKLRFGLEDNQPRTLE 374

Query: 257 NLSSEFEVSRERVRQIEARAFKKV 280
            +   F V+RER+RQIEA+A +++
Sbjct: 375 EVGKLFNVTRERIRQIEAKALRRL 398


>gi|296171852|ref|ZP_06852951.1| RNA polymerase sigma factor rpoD [Mycobacterium parascrofulaceum
           ATCC BAA-614]
 gi|295893936|gb|EFG73705.1| RNA polymerase sigma factor rpoD [Mycobacterium parascrofulaceum
           ATCC BAA-614]
          Length = 503

 Score = 99.0 bits (245), Expect = 7e-19,   Method: Compositional matrix adjust.
 Identities = 83/318 (26%), Positives = 151/318 (47%), Gaps = 43/318 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGD-LS 48
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E GD L 
Sbjct: 191 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMAEMAERGDKLP 249

Query: 49  AAHR----------------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           AA R                L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 250 AAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 309

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L      
Sbjct: 310 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGR 367

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D + 
Sbjct: 368 EPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEA 419

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVR 270
            V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 420 VVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIR 479

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 480 QIESKTMSKLRHPSRSQV 497


>gi|1519636|gb|AAB07551.1| SigA [Chloroflexus aurantiacus J-10-fl]
          Length = 343

 Score = 99.0 bits (245), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 84/293 (28%), Positives = 137/293 (46%), Gaps = 44/293 (15%)

Query: 19  YIHEIRKIPMLEKQEEYVL------------------AKRYREHGDL--------SAAHR 52
           Y+ EI ++P+L  ++E  L                    R R   +L         A H 
Sbjct: 50  YLQEIGQVPLLTAEQEVELAKAMEAGAAARQRLDREDTPRPRARFELERAVQQGQDARHH 109

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV IA  Y  YGL + ++V EGNIGLM+AV+KFD ++G + +TY+ WWI+ A
Sbjct: 110 LIQANLRLVVSIAKKYTSYGLTMMDLVQEGNIGLMRAVEKFDYKKGHKFSTYATWWIRQA 169

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   I      +++     +      ++R    LQ     +  PE+   IA  + +S  +
Sbjct: 170 ITRAIADQSRTIRLPVHMGEA--ISQVKRTSHRLQQTMQRDATPEE---IADAMGISAGK 224

Query: 173 VISMNCRLAGDESLNAL---INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           V     R   + S++ L   +    +   +  D++    D +     E       R  L 
Sbjct: 225 V-----RRTLEASMHPLSLEMPVGQEGEGRMGDFI---EDDRISTPAEAPAASLLREQLE 276

Query: 230 RSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
             +  L  RER+I + R  L++    TLE +  EF ++RER+RQIEA A +K+
Sbjct: 277 EVLMKLPERERKIIQLRYGLKDGRYRTLEEVGIEFGITRERIRQIEAVALRKL 329


>gi|91779694|ref|YP_554902.1| sigma 70 (RpoD) [Burkholderia xenovorans LB400]
 gi|91692354|gb|ABE35552.1| Sigma 70 (RpoD) [Burkholderia xenovorans LB400]
          Length = 628

 Score = 99.0 bits (245), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 68/247 (27%), Positives = 128/247 (51%), Gaps = 40/247 (16%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ ++LRLVV +A  Y   G+P+ ++V EGNIGLM+AV +F+  RGF+ +TY+ WWI+ +
Sbjct: 394 MIEANLRLVVSVAKKYVQSGMPLLDLVQEGNIGLMKAVDRFEYRRGFKFSTYATWWIRQS 453

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   I      +++    +       ++R+ G ++  T    +P +   +A +L +SE +
Sbjct: 454 VSRAIADYGRTIRV--PVHMADAMHRVKRVAGEMRQETG---RPARSSELAARLGMSEEK 508

Query: 173 V----------ISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
           V          +S++  +    D +L  ++   D ++    D L+               
Sbjct: 509 VRSVQRVTRQPVSLDVPIGEEADTTLGEMVE--DSSTLAPLDALL--------------- 551

Query: 221 RKNRRNMLTRSMSVLNPRERRI----FEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           + + R  +  ++ VL PRE ++    F    + E+  TLE L  +F+V+RERVRQI+ +A
Sbjct: 552 QADLRVAIDAALGVLTPREAKVIKLRFGVDAVSEH--TLEELGDQFDVTRERVRQIQNKA 609

Query: 277 FKKVQES 283
            +K++ S
Sbjct: 610 LQKLRHS 616


>gi|197336747|ref|YP_002158681.1| RNA polymerase sigma factor RpoS (Sigma-38) [Vibrio fischeri MJ11]
 gi|197313999|gb|ACH63448.1| RNA polymerase sigma factor RpoS (Sigma-38) [Vibrio fischeri MJ11]
          Length = 294

 Score = 99.0 bits (245), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 80/286 (27%), Positives = 139/286 (48%), Gaps = 38/286 (13%)

Query: 17  SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG---YGL 73
           S Y+ EI +  +L  +EE V ++ Y++ GDLSA + L+ S+LRLVVK+A  YR      L
Sbjct: 21  SLYLKEINRYQLLTAEEELVYSRLYKK-GDLSARNTLIESNLRLVVKVANKYRKRNQTDL 79

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            I +++ EGN+GL++A+ KF+PE G+R +TY++WWI+ +++  +      V++       
Sbjct: 80  AILDIIEEGNLGLIKAIDKFNPELGYRFSTYAVWWIRESIESALFNHSRTVRLPVHIT-- 137

Query: 134 RLFFNLRRLKGHLQAITD--NNLKPE----QVVAIAKKLNVSESEVIS-----MNCRLAG 182
                 + L  +L+A  +   +LK E     +    ++  +  S++IS     + C  A 
Sbjct: 138 ------KELNTYLRAARELSKSLKREPSIRDISTYCEEEQIKVSKIISLIPNQLTCHSAC 191

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
            + L+        N+   +       D  E               L+  +  LN RE+ I
Sbjct: 192 SDELSPKFFELSSNNKALEPDNSLSQDNLEM-------------NLSSWIDSLNYREKEI 238

Query: 243 FEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              R         TLE+L  + ++S+ERVRQI++    K+    +K
Sbjct: 239 IINRYGLFGCKVKTLEDLGKDLDLSKERVRQIQSETLIKLNTIFKK 284


>gi|198283622|ref|YP_002219943.1| RpoD family RNA polymerase sigma-70 subunit [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218667581|ref|YP_002426250.1| RNA polymerase sigm-70 factor family [Acidithiobacillus
           ferrooxidans ATCC 23270]
 gi|198248143|gb|ACH83736.1| RNA polymerase, sigma 70 subunit, RpoD family [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218519794|gb|ACK80380.1| RNA polymerase sigm-70 factor family [Acidithiobacillus
           ferrooxidans ATCC 23270]
          Length = 316

 Score = 99.0 bits (245), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 79/280 (28%), Positives = 139/280 (49%), Gaps = 30/280 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISE 77
           Y+ EI   P+L  +EE  L    ++ GD++A +RLV  +LRLVV+IA  Y R + LP+ +
Sbjct: 56  YLQEIGHNPLLTAEEEVSLGLSAQQ-GDITARNRLVECNLRLVVRIARRYQRQHTLPLLD 114

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT--TANQKRL 135
           ++ EGN+GL++A + FDP RGFR +TY+ WWI+  +   I++   +V++ T    N   +
Sbjct: 115 LIEEGNLGLIRAAELFDPTRGFRFSTYATWWIRQNIDRGIMQQSRVVRLPTHIIKNLSAV 174

Query: 136 FFNLRRLKGHLQA---ITDNNLKPEQVVAIAKKLNVSESEVISMNC--RLAGDESLNALI 190
             + R++   +Q    + D      + VA  +     +  V+S++   R  G  SL   +
Sbjct: 175 LRSSRQIAQTMQGDPRVEDVAQVMGKSVAYVEDCLQQDRRVVSLDAPSRWEGSPSLAQTL 234

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-- 248
             +D+                   L    E ++ +  + R++  L+ R R I   RR   
Sbjct: 235 VDADQAD-----------------LGASLEEQDLQRQIHRALLGLDVRHRTIL-IRRFGI 276

Query: 249 -QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             ++  +L  +  E  VS ERVRQ++  A   +++  + Q
Sbjct: 277 DGQDGASLSAIGKELGVSHERVRQLQEEALDLLRQHTELQ 316


>gi|152993293|ref|YP_001359014.1| RNA polymerase sigma factor RpoD [Sulfurovum sp. NBC37-1]
 gi|151425154|dbj|BAF72657.1| RNA polymerase sigma 70 factor [Sulfurovum sp. NBC37-1]
          Length = 612

 Score = 99.0 bits (245), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 72/236 (30%), Positives = 119/236 (50%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ E+G++ +TY+ WW
Sbjct: 373 AKTRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYEKGYKFSTYATWW 432

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I     +     N + ++ HLQ       K   +  IAK++ +
Sbjct: 433 IRQAISRAIADQARTIRIPIHMIETINRIN-KIIRKHLQETG----KEPDLETIAKEVGL 487

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +  +V   N      E ++      D++  ++ D++    D       +   + +  N +
Sbjct: 488 TVDKV--KNVIKITKEPVSLETPVGDEDDGRFGDFI---EDKTTLSPTDAVLKDDLNNQI 542

Query: 229 TRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 543 DEVLDQLNEREKAVIRMRFGLLEDESDRTLEEIGKELNVTRERVRQIESSAIKKLK 598


>gi|160902263|ref|YP_001567844.1| RpoD family RNA polymerase sigma factor [Petrotoga mobilis SJ95]
 gi|160359907|gb|ABX31521.1| RNA polymerase, sigma 70 subunit, RpoD family [Petrotoga mobilis
           SJ95]
          Length = 414

 Score = 99.0 bits (245), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 83/276 (30%), Positives = 139/276 (50%), Gaps = 33/276 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  I +L    E  LA R ++     A   LV ++LRLV+ IA  Y G GL   ++
Sbjct: 139 YLREIGGIKLLTPSRERQLAIRAKKGD-KKAKDELVKANLRLVISIAKRYTGRGLTFLDL 197

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT--TANQKRLF 136
           + EGNIGL++AV+KFD +RGF+ +TY+ WW++ A+   I      ++I      +  R+ 
Sbjct: 198 IQEGNIGLIRAVEKFDWKRGFKFSTYATWWVRQAITRAIADQARTIRIPVHLVESINRMN 257

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKK-------LNVSESEVISMNCRLAGDESLNAL 189
             +R+   HLQ  T      E++  +  K       + ++  E+IS++  ++G +   A 
Sbjct: 258 IVIRK---HLQE-TGEYPSTEKLAELLDKPLEKMDEILLATKEIISVDAPISGSDDEEAY 313

Query: 190 INS--SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           I     D  + Q ++  V         +I KEE       + + +  L P+E  + + R 
Sbjct: 314 IGDFLEDSEADQPEEIAVR--------MILKEE-------IEKVLESLRPKEATVLKMRY 358

Query: 248 --LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             L     TLE + + F V+RER+RQIE +A +K++
Sbjct: 359 GLLDGKMKTLEEVGNFFNVTRERIRQIEVKALRKLR 394


>gi|163848612|ref|YP_001636656.1| sigma-70 family RNA polymerase sigma factor [Chloroflexus
           aurantiacus J-10-fl]
 gi|222526547|ref|YP_002571018.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus sp.
           Y-400-fl]
 gi|163669901|gb|ABY36267.1| RNA polymerase sigma factor, sigma-70 family [Chloroflexus
           aurantiacus J-10-fl]
 gi|222450426|gb|ACM54692.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus sp.
           Y-400-fl]
          Length = 381

 Score = 99.0 bits (245), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 74/238 (31%), Positives = 119/238 (50%), Gaps = 18/238 (7%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A H L+ ++LRLVV IA  Y  YGL + ++V EGNIGLM+AV+KFD ++G + +TY+ W
Sbjct: 143 DARHHLIQANLRLVVSIAKKYTSYGLTMMDLVQEGNIGLMRAVEKFDYKKGHKFSTYATW 202

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++     +      ++R    LQ        PE+   IA  + 
Sbjct: 203 WIRQAITRAIADQSRTIRLPVHMGEA--ISQVKRTSHRLQQTMQREPTPEE---IADAMG 257

Query: 168 VSESEVISMNCRLAGDESLNAL---INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +S  +V     R   + S++ L   +    +   +  D++    D +     E       
Sbjct: 258 ISAGKV-----RRTLEASMHPLSLEMPVGQEGEGRMGDFI---EDDRISTPAEAAAASLL 309

Query: 225 RNMLTRSMSVLNPRERRIFEARR-LQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
           R  L   +  L  RER+I + R  L++    TLE +  EF ++RER+RQIEA A +K+
Sbjct: 310 REQLEEVLMKLPERERKIIQLRYGLKDGRYRTLEEVGIEFGITRERIRQIEAVALRKL 367


>gi|239931595|ref|ZP_04688548.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291439967|ref|ZP_06579357.1| transcription initiation factor sigma [Streptomyces ghanaensis ATCC
           14672]
 gi|291342862|gb|EFE69818.1| transcription initiation factor sigma [Streptomyces ghanaensis ATCC
           14672]
          Length = 335

 Score = 99.0 bits (245), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 80/259 (30%), Positives = 135/259 (52%), Gaps = 22/259 (8%)

Query: 33  EEYVLAKRYR-EHGDLS-----AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           EE VL  RYR E G L+     A + L  ++LRLVV +A  Y G GL   +++ EGN GL
Sbjct: 74  EEPVLEPRYRRELGLLAEDGRRAKNHLTEANLRLVVSVAKRYTGRGLQFMDLIQEGNAGL 133

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV+KFD  +GF+ +TY+ WWIK  +   +      ++I   A +  +   + R++  L
Sbjct: 134 IRAVEKFDYTKGFKFSTYATWWIKQGITRAMADQSRTIRIPVHAVE--VINRVARVRREL 191

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
              T     PE V   A++ ++S  ++  ++       SL+  +  S++   ++ D L+ 
Sbjct: 192 IRATGTEPTPEDV---AERASISVEKLAELDAYAREPVSLD--LPLSEEGGGEFGD-LIV 245

Query: 207 DHDGQE--QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEF 262
           D D     +V+     ++  R++L    + L+PRE  I   R     E P TLE +   +
Sbjct: 246 DSDSPSPWEVVAFGHLQRAVRSVL----ADLSPREAGIISLRYGLFGERPRTLEEIGQVY 301

Query: 263 EVSRERVRQIEARAFKKVQ 281
            V+RER+RQIE++   K++
Sbjct: 302 GVTRERIRQIESKTMSKLR 320


>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 = 99.0 bits (245), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 67/235 (28%), Positives = 121/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  +HLRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 566 AKREMTEAHLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 625

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +  L+P+    +A+K+ +
Sbjct: 626 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGLEPDPAT-LAEKMEM 680

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + R+++
Sbjct: 681 PEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDTNTVAPADAALHASMRDVV 735

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 736 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 790


>gi|87310114|ref|ZP_01092246.1| transcription initiation factor sigma 70 [Blastopirellula marina
           DSM 3645]
 gi|87287104|gb|EAQ79006.1| transcription initiation factor sigma 70 [Blastopirellula marina
           DSM 3645]
          Length = 516

 Score = 99.0 bits (245), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 83/253 (32%), Positives = 134/253 (52%), Gaps = 39/253 (15%)

Query: 44  HGDLSAAHRLVTS-HLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           H  L  A R +TS +LRLVV IA  +RG GL   +++ EGN+GLM+AV+KFDP  G++ A
Sbjct: 265 HEGLCRAQRAITSANLRLVVSIAKSFRGRGLSYLDLIQEGNLGLMRAVEKFDPSLGYKFA 324

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ------AITDNNLKP 156
           TY+ WWI+ A+ + +            A+Q R      R++  +Q      AI     + 
Sbjct: 325 TYATWWIRQAVMKGL------------ADQGRTIRLPARMQDRIQKINVAKAILSQEHRS 372

Query: 157 EQVVAI-AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
           E  + + AK+  ++E EV++ + RL G   ++  ++++D +S  + D L       EQ  
Sbjct: 373 EPPIELTAKQAELTEREVVAAD-RL-GRTIMSLDVSNNDDDS--FGDTLA--SGDAEQSS 426

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEAR------RLQENPVTLENLSSEFEVSRERV 269
            +++      N L   +  L  RE+ I   R      R+Q    TLE +S  F V+RER+
Sbjct: 427 ADEQRLPLAINQL---LQELTSREQEIVRRRFGMFDGRVQ----TLEEVSQAFSVTRERI 479

Query: 270 RQIEARAFKKVQE 282
           RQIE+ A +K+++
Sbjct: 480 RQIESAAIRKLRQ 492


>gi|77919031|ref|YP_356846.1| DNA-directed RNA polymerase, sigma 70/sigma 32 subunit [Pelobacter
           carbinolicus DSM 2380]
 gi|77545114|gb|ABA88676.1| RNA polymerase, sigma 38 subunit, RpoS [Pelobacter carbinolicus DSM
           2380]
          Length = 347

 Score = 99.0 bits (245), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 75/281 (26%), Positives = 141/281 (50%), Gaps = 33/281 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI+K  +L  ++E +LA+R    GD++A  R++ S+LRLVVKIA  Y   GLP  ++
Sbjct: 72  YLKEIQKTKLLTAEDERMLARRI-SQGDMAARDRMIESNLRLVVKIAKRYMNRGLPFLDL 130

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV++F   +  R +TY+ WWI+ +++  ++     +++    ++    F 
Sbjct: 131 IEEGNMGLIKAVERFKLSKECRFSTYATWWIRQSIERALVNQSRTIRLPVHVSDDINKFI 190

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA---------GDESLNA 188
            + R     + +   N +P +V  IA+ + V  + +  +   +          G+    +
Sbjct: 191 KISR-----ELVHQYNREP-KVEEIAEYMGVEPAYIRRLMVLVKKTYSIEHPMGENRDYS 244

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
           LI++ +   +      V D D    V                    L+  ER I   R  
Sbjct: 245 LIDTIEDPKADNPSTFVDDIDKYAHV--------------CNWFETLSENEREILMLRFG 290

Query: 249 QEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            ++  P TL+ +   F V+RER+RQIEA++ +K++  +++Q
Sbjct: 291 LDDQEPQTLDTIGRRFGVTRERIRQIEAKSLQKLRNLMEEQ 331


>gi|145347899|ref|XP_001418397.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144578626|gb|ABO96690.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 344

 Score = 99.0 bits (245), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 72/259 (27%), Positives = 131/259 (50%), Gaps = 15/259 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           SA + ++ ++LRLVV IA  Y    +   +++ EG +GL++  +KFD +RG++ +TY+ W
Sbjct: 90  SAKNEMIQANLRLVVSIAKKYANSNMSFQDLIQEGCVGLIRGAEKFDFQRGYKFSTYAHW 149

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++        LF  + R+    Q    +N +      IA +++
Sbjct: 150 WIRQAVTRSISDQSRTIRLPV-----HLFEIISRISKMEQKFALHNGRNPTTEEIAAEMD 204

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  ++  +        SL   +   +K  +     +    +G E+V  +   +++  N+
Sbjct: 205 MSAEKITQIKKAAQAPVSLAQTMGGDNKGRTVEDTLVDVTAEGPEKVSGKSLLKEDLENV 264

Query: 228 LTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQE--- 282
           L    + LNPRER +   R  L +  V TLE + + F V+RER+RQIEA+A +K+++   
Sbjct: 265 L----NTLNPRERDVLRLRYGLDDGRVKTLEEIGTVFSVTRERIRQIEAKALRKLKQPSR 320

Query: 283 -SIQKQVELSSSPPLLQKP 300
            SI ++    S    L KP
Sbjct: 321 NSILQEYFADSDASSLPKP 339


>gi|113954655|ref|YP_729975.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CC9311]
 gi|113882006|gb|ABI46964.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CC9311]
          Length = 313

 Score = 99.0 bits (245), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 85/300 (28%), Positives = 146/300 (48%), Gaps = 50/300 (16%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS-------------------------AA 50
           +S Y+  I +IP+L   EE  L  + ++  +L+                         A 
Sbjct: 20  ISWYLATIGRIPLLTAAEEIELGNQVQKFMELTQDGSVSPDSEEFSSKDRRMIRVGQRAK 79

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            R++ ++LRLVV +A  Y+G GL + +++ EG++GL +AV+KFDP RG++ +TY+ WWI+
Sbjct: 80  QRMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWWIR 139

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK-PEQVVAIAKKLNVS 169
            +M   I            A Q R       L   L  I   +L    ++ A+  +L +S
Sbjct: 140 QSMTRAI------------ACQSRTIRLPVHLSERLTTIRKVSLDLAHKLGAMPSRLEIS 187

Query: 170 ES------EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           E+      E+ S+  +     SL+A +N  D  S  +   L+ D   +E   ++K E++ 
Sbjct: 188 EALDMPVEELDSLLRQALTTSSLDAPVNGEDGRS--FLGDLIADSSAEEP--LDKVEQRI 243

Query: 224 RRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
               L R +S L+ +E+ +   R  L  N   TL  +    +VSRERVRQ+E ++ +K++
Sbjct: 244 HHEQLGRWLSHLSEQEQHVLTLRFGLNGNERHTLAQIGRLLDVSRERVRQVELKSLRKLR 303


>gi|124024644|ref|YP_001018951.1| type II alternative RNA polymerase sigma factor [Prochlorococcus
           marinus str. MIT 9303]
 gi|123964930|gb|ABM79686.1| Putative type II alternative RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9303]
          Length = 376

 Score = 99.0 bits (245), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 76/236 (32%), Positives = 118/236 (50%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +++ ++LRLVV +A  Y+  G+ + ++V EG +GL +AV+KFDP RGFR +TY+ WW
Sbjct: 136 AKDQMIQANLRLVVAVAKKYQQRGIELLDLVQEGTLGLERAVEKFDPARGFRFSTYAYWW 195

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   I      +++     +K     L R+K   Q I  N  +   +  +AK L +
Sbjct: 196 IRQGITRAIATQSRTIRLPMHITEK-----LNRIKRVQQEIASNQGRLASIADLAKALGL 250

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SE  V     R+    SL   I    +  SQ  D L+ D +   +   EK  R    N L
Sbjct: 251 SEETVRLTLMRVPRSISLETRIGQ--EQDSQLGD-LLEDSNATPE---EKLTRDQLHNDL 304

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              +  L+ RE  +   R   E+  P TL  +     +SRERVRQIE+ A  K+++
Sbjct: 305 EILLDELSNREATVIRRRFGLEDDTPQTLTQIGEAMHLSRERVRQIESHALLKLRQ 360


>gi|168012500|ref|XP_001758940.1| plastid sigma facor SIG2 [Physcomitrella patens subsp. patens]
 gi|12697780|dbj|BAB21618.1| PpSIG2 [Physcomitrella patens]
 gi|14669832|dbj|BAB62008.1| PpSIG2 [Physcomitrella patens]
 gi|162690077|gb|EDQ76446.1| plastid sigma facor SIG2 [Physcomitrella patens subsp. patens]
          Length = 579

 Score = 99.0 bits (245), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 73/258 (28%), Positives = 129/258 (50%), Gaps = 56/258 (21%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y+G G+ + +++ EG++GL++  +KFDP +GF+ +TY+ WW
Sbjct: 336 AKDKMVNSNLRLVVSIAKNYQGRGMTLQDLIQEGSMGLVRGAEKFDPTKGFKFSTYAHWW 395

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I            A+Q R      RL  HL  +          +  AK++ V
Sbjct: 396 IRQAVTRSI------------ADQSRTI----RLPIHLYEVISR-------INKAKRMLV 432

Query: 169 SE----------SEVISMNCRLAGDESLNALINSS------------DKNSSQWQDWLVY 206
            E          +E++ +       E L +++ S+            D +++  +     
Sbjct: 433 QEHGREARNEEVAELVGLTV-----EKLKSVVKSAKAPGSMERPIGKDGDTTLGELVADT 487

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEV 264
           D D  E  ++++  R++   +L      LNPRER +   R   ++    TLE +   F+V
Sbjct: 488 DVDSPEDAIVKQLMRQDIEGVL----RTLNPREREVLRLRFGLDDGRSKTLEEIGQIFKV 543

Query: 265 SRERVRQIEARAFKKVQE 282
           +RER+RQIEA+A +K+++
Sbjct: 544 TRERIRQIEAKAMRKLRQ 561


>gi|315586085|gb|ADU40466.1| DNA-directed RNA polymerase sigma subunit RpoD [Helicobacter pylori
           35A]
          Length = 680

 Score = 98.6 bits (244), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 121/236 (51%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ WW
Sbjct: 441 AKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWW 500

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           IK A+   I      ++I        +   + R+   ++     N K   +  +A+++ +
Sbjct: 501 IKQAISRAIADQARTIRIPI-----HMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGL 555

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  +
Sbjct: 556 SLDKVKNVIKVTKEPISLETPVGNDD--DGKFGDFV---EDKNIVSSIDHIMREDLKAQI 610

Query: 229 TRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 611 ESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 666


>gi|119487601|ref|ZP_01621211.1| RNA polymerase sigma-like factor [Lyngbya sp. PCC 8106]
 gi|119455770|gb|EAW36906.1| RNA polymerase sigma-like factor [Lyngbya sp. PCC 8106]
          Length = 404

 Score = 98.6 bits (244), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 69/238 (28%), Positives = 127/238 (53%), Gaps = 13/238 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           + A   ++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV+KFDP RG+R +TYS 
Sbjct: 163 IKAKDHMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTRGYRFSTYSY 222

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   I      +++     +K     L ++K   + I+    +   +  IA +L
Sbjct: 223 WWIRQGITRAIATQSRTIRLPVHITEK-----LNKIKKAQRKISQEKGRIATIDDIAAEL 277

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++ ++V  +  ++    SL   +  SDK++   +     +   ++Q++ E   R     
Sbjct: 278 EMTPAQVREVLLKVPRSVSLETKVG-SDKDTELGELLETEEASPEDQLMRESLHRD---- 332

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVT--LENLSSEFEVSRERVRQIEARAFKKVQE 282
            L + ++ L+ RER + + R    N  T  L  +  E E+SRERVRQIEA+A +K+++
Sbjct: 333 -LQQLLADLSDRERDVIQMRYGLGNGHTYSLAEIGRELELSRERVRQIEAKALQKLRQ 389


>gi|332672929|gb|AEE69746.1| DNA-directed RNA polymerase sigma subunit RpoD [Helicobacter pylori
           83]
          Length = 674

 Score = 98.6 bits (244), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 121/236 (51%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ WW
Sbjct: 435 AKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWW 494

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           IK A+   I      ++I        +   + R+   ++     N K   +  +A+++ +
Sbjct: 495 IKQAISRAIADQARTIRIPI-----HMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGL 549

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  +
Sbjct: 550 SLDKVKNVIKVTKEPISLETPVGNDD--DGKFGDFV---EDKNIVSSIDHIMREDLKAQI 604

Query: 229 TRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 605 ESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 660


>gi|240142271|ref|YP_002966781.1| putative RNA polymerase sigma factor protein (Sigma-70)
           [Methylobacterium extorquens AM1]
 gi|240012215|gb|ACS43440.1| putative RNA polymerase sigma factor protein (Sigma-70)
           [Methylobacterium extorquens AM1]
          Length = 253

 Score = 98.6 bits (244), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 75/258 (29%), Positives = 117/258 (45%), Gaps = 31/258 (12%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           +L   EE  L   YR  G   +  RLV +H R+   +A  +      + ++  EG IG+M
Sbjct: 13  LLSPDEESGLVDAYRNDGCRKSLDRLVRTHARMAFSVARRWSNNEAHMQDLAQEGMIGIM 72

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +A  KF+P  G R A Y  WWI +++     R+  +V +    ++  +    +RL+G   
Sbjct: 73  RAADKFNPSFGKRFAQYCRWWILSSISS---RASEVVCVVDMPDRVFVAHRRKRLEGADA 129

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
           A+         V A    +++SE         L GDE             +   D LV D
Sbjct: 130 AL---------VGAAVTAVSISEP--------LGGDE-----------GGATVGDMLVSD 161

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
               E   ++ E     R  +  +M  L  RER I   RRL E P TLE ++  F+++RE
Sbjct: 162 ETSPESAAVQSEMNWYYRTAVQTAMQGLTEREREILSRRRLAETPETLEVVADFFDLTRE 221

Query: 268 RVRQIEARAFKKVQESIQ 285
           R+RQIE  A  KV+ +++
Sbjct: 222 RIRQIENAAMAKVERNLR 239


>gi|78185087|ref|YP_377522.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CC9902]
 gi|116072338|ref|ZP_01469605.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. BL107]
 gi|78169381|gb|ABB26478.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. CC9902]
 gi|116064860|gb|EAU70619.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. BL107]
          Length = 313

 Score = 98.6 bits (244), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 84/296 (28%), Positives = 148/296 (50%), Gaps = 42/296 (14%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKR------YREHG-------DLS------------AA 50
           +S Y+  I +IP+L   EE  L  +      + E G       DL+            A 
Sbjct: 20  VSWYLSTIGRIPLLTAAEEIELGNQVQAMMAFTEDGSKDFKVEDLTTKQRRMLRIGRRAK 79

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            R++ ++LRLVV +A  Y+G GL + +++ EG++GL +AV+KFDP RG++ +TY+ WWI+
Sbjct: 80  ERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWWIR 139

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK---GHLQAITDNNLKPEQVVAIAKKLN 167
            +M   I      +++    +++     +R++     H      N L+      IA+ ++
Sbjct: 140 QSMTRAIACQSRTIRLPVHLSER--LTTIRKVSLDLAHKLGAMPNRLE------IAEAMD 191

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +   E+ S+  +     SL+A +N  +  S  +   L+ D    E + I   E++     
Sbjct: 192 IPVEELDSLLRQALTTSSLDAPVNGEEGRS--FLGDLIADSSADEPLDI--VEQRIHHEQ 247

Query: 228 LTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           L R +S L+ +E+ +   R  L+ N   TL  +    EVSRERVRQ+E +A +K++
Sbjct: 248 LGRWLSHLSEQEQNVLRLRFGLEGNERHTLAEIGRMMEVSRERVRQVELKALRKLR 303


>gi|308061382|gb|ADO03270.1| RNA polymerase sigma factor RpoD [Helicobacter pylori Cuz20]
          Length = 672

 Score = 98.6 bits (244), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 69/236 (29%), Positives = 120/236 (50%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ WW
Sbjct: 433 AKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWW 492

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           IK A+   I      ++I        +   + R+   ++     N K   +  +A+++ +
Sbjct: 493 IKQAISRAIADQARTIRIPI-----HMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGL 547

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  +V   N      E ++      + +  ++ D++    D      I+   R++ +  +
Sbjct: 548 SLDKV--KNVIKVTKEPISLETPVGNDDDGKFGDFV---EDKNIVSSIDHIMREDLKAQI 602

Query: 229 TRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 603 ESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 658


>gi|254430144|ref|ZP_05043847.1| RNA polymerase sigma factor [Cyanobium sp. PCC 7001]
 gi|197624597|gb|EDY37156.1| RNA polymerase sigma factor [Cyanobium sp. PCC 7001]
          Length = 318

 Score = 98.6 bits (244), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 82/294 (27%), Positives = 134/294 (45%), Gaps = 49/294 (16%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS--------------------AAHRLVTSHL 58
           Y+  I ++P+L   EE  LA   +    L                     A  R++ ++L
Sbjct: 34  YLSNIGRVPLLTPAEEIELAHHVQAGKRLQEVPLEELTPKQKRQIRMAQRARDRMMAANL 93

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+  M   I 
Sbjct: 94  RLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTRAID 153

Query: 119 RSWSLVKIGTTANQK---------RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
            S   +++    ++K          L   L R    L+     +++PE++    ++L   
Sbjct: 154 NSARTIRLPIHISEKLSKMRRITRELSHRLGRQPNRLELSHAMDMRPEEL----EELMAQ 209

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
            +   S++    GDE  + L              L+ D    E    +  +R  ++  L 
Sbjct: 210 SAPCASLDAHARGDEDRSTLGE------------LIADPASNEH--FDSMDRHIQKEHLG 255

Query: 230 RSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             +S LN RE++I + R   E   P+TL  +     VSRERVRQ+EA+A  K++
Sbjct: 256 AWLSQLNEREQKIIKLRFGLEGSEPLTLAEIGRLINVSRERVRQLEAKAIMKLR 309


>gi|78221616|ref|YP_383363.1| RNA polymerase sigma factor RpoD-like [Geobacter metallireducens
           GS-15]
 gi|78192871|gb|ABB30638.1| RNA polymerase, sigma 70 subunit, RpoD [Geobacter metallireducens
           GS-15]
          Length = 579

 Score = 98.6 bits (244), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 77/239 (32%), Positives = 128/239 (53%), Gaps = 20/239 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ WW
Sbjct: 342 AKSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWW 401

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N  +L    R+L   +Q I      PE+   IA+
Sbjct: 402 IRQAITRAIADQARTIRIPVHMIETIN--KLIRTSRQL---VQEIG-REPSPEE---IAE 452

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           ++N+   +V  +  ++A  E ++      ++  S   D++    D      +E   + N 
Sbjct: 453 RMNLPLDKVRKV-LKIA-KEPISLETPIGEEEDSHLGDFI---EDKGVVSPLEAVIKANL 507

Query: 225 RNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
               +R +S L PRE ++   R    +++  TLE +  +FEV+RER+RQIEA+A +K++
Sbjct: 508 SEQTSRVLSTLTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLR 566


>gi|297379310|gb|ADI34197.1| RNA polymerase sigma factor RpoD [Helicobacter pylori v225d]
          Length = 677

 Score = 98.6 bits (244), Expect = 9e-19,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 121/236 (51%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ WW
Sbjct: 438 AKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWW 497

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           IK A+   I      ++I        +   + R+   ++     N K   +  +A+++ +
Sbjct: 498 IKQAISRAIADQARTIRIPI-----HMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGL 552

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  +
Sbjct: 553 SLDKVKNVIKVTKEPISLETPVGNDD--DGKFGDFV---EDKNIVSSIDHIMREDLKAQI 607

Query: 229 TRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 608 ESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 663


>gi|260773542|ref|ZP_05882458.1| RNA polymerase sigma factor RpoS [Vibrio metschnikovii CIP 69.14]
 gi|260612681|gb|EEX37884.1| RNA polymerase sigma factor RpoS [Vibrio metschnikovii CIP 69.14]
          Length = 297

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 45/100 (45%), Positives = 70/100 (70%), Gaps = 1/100 (1%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 52  YLSEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 110

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++
Sbjct: 111 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALM 150


>gi|209884282|ref|YP_002288139.1| RNA polymerase sigma factor RpoD [Oligotropha carboxidovorans OM5]
 gi|209872478|gb|ACI92274.1| RNA polymerase sigma factor RpoD [Oligotropha carboxidovorans OM5]
          Length = 708

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 79/268 (29%), Positives = 131/268 (48%), Gaps = 17/268 (6%)

Query: 21  HEIRKIPMLEKQE-----EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           HE++++  L   E     + VL  +  E     A   +V ++LRLV+ IA  Y   GL  
Sbjct: 437 HEVQQLAALTGLEIGEFRKIVLGVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQF 496

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I    +    
Sbjct: 497 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI--PVHMIET 554

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + R    +         PE+   +A+KL +   +V  +  ++A  E L+      D+
Sbjct: 555 INKIVRTSRQMLNEIGREPTPEE---LAEKLGMPLEKVRKV-LKIA-KEPLSLETPVGDE 609

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPV 253
             S   D++    D    + I+   + N R   TR ++ L PRE R+   R         
Sbjct: 610 EDSHLGDFI---EDKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDH 666

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 667 TLEEVGQQFSVTRERIRQIEAKALRKLK 694


>gi|195953901|ref|YP_002122191.1| RNA polymerase, sigma 70 subunit, RpoD family [Hydrogenobaculum sp.
           Y04AAS1]
 gi|195933513|gb|ACG58213.1| RNA polymerase, sigma 70 subunit, RpoD family [Hydrogenobaculum sp.
           Y04AAS1]
          Length = 578

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 77/256 (30%), Positives = 126/256 (49%), Gaps = 39/256 (15%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           KR +E  D+     +V S+LRLVV IA  Y   GL   +++ EGN+GLM+AV K+D ++G
Sbjct: 335 KRVKESKDM-----MVKSNLRLVVSIAKKYINRGLHFLDLIQEGNMGLMKAVDKYDYKKG 389

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAI 149
           F+ +TY+ WWIK A+   I      ++I      T N+     K+LF    R     +  
Sbjct: 390 FKFSTYATWWIKQAITRAIADQAKTIRIPVHMIETINKISKVSKKLFQEYGREPSPEEIA 449

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYD 207
              N+ PE+V  I K +     E IS+   +  DE   L   I  S  ++ +        
Sbjct: 450 KALNMSPEKVRKILKSIQ----EPISLETPIGDDEDTHLKDFIEDSSISNPE-------- 497

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVS 265
                    E   R+  R  + + ++ L+ +ER +   R    + +  TLE + + F ++
Sbjct: 498 ---------EATARRLLREQIEKIINTLSDKEREVIMYRFGLVDGIEHTLEQVGTMFNLT 548

Query: 266 RERVRQIEARAFKKVQ 281
           RER+RQIE++A +K++
Sbjct: 549 RERIRQIESKAIRKIR 564


>gi|228949811|ref|ZP_04112021.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228809869|gb|EEM56280.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
          Length = 295

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 84/289 (29%), Positives = 142/289 (49%), Gaps = 43/289 (14%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG-LP 74
           + +Y++EI    +L  ++      +Y+E GD+ +   L+ S+LRLVV +A  +  YG   
Sbjct: 11  MGKYLNEICNYDILTDEQSMEHIIKYKEKGDIDSRDLLICSNLRLVVSVAKSFPCYGNCD 70

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ-- 132
           + E++ EG IGLM+ ++ +D  +G +L+TY  WWI+  + +Y+  + S V++ TT  +  
Sbjct: 71  LMEMIQEGTIGLMKGLEDYDYTKGNKLSTYITWWIRQRISKYLSINRSDVRVATTMQKKI 130

Query: 133 ---KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
              K  ++     KG        NL  ++V   A+KL   ES VI     L  D   N +
Sbjct: 131 TEVKNCYYENMGEKG-------TNLTTKEV---AEKLGYKESIVIDA---LVTDRITNTI 177

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVL--------------IEKEERKNRRNMLTRSMSVL 235
              S ++  Q +  L+   D Q+  L              I  EE K   + L      L
Sbjct: 178 ---SIEDDVQNEKTLL---DKQQSTLAILANKNAPNPSEVIATEEEKFEFDELM--FVTL 229

Query: 236 NPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQE 282
           NPRE  +   R   ++ +  TLE+ +    V+RERV+QIE +A +K+++
Sbjct: 230 NPREESVLRYRFGFDDGIELTLEDTARILGVTRERVQQIEKKAIEKMKQ 278


>gi|261837545|gb|ACX97311.1| transcription initiation factor sigma-80 [Helicobacter pylori 51]
          Length = 684

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 121/236 (51%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ WW
Sbjct: 445 AKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWW 504

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           IK A+   I      ++I        +   + R+   ++     N K   +  +A+++ +
Sbjct: 505 IKQAISRAIADQARTIRIPI-----HMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGL 559

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  +
Sbjct: 560 SLDKVKNVIKVTKEPISLETPVGNDD--DGKFGDFV---EDKNIVSSIDHIMREDLKAQI 614

Query: 229 TRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 615 ESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 670


>gi|73666941|ref|YP_302957.1| RNA polymerase sigma factor rpoD [Ehrlichia canis str. Jake]
 gi|72394082|gb|AAZ68359.1| RNA polymerase, sigma 70 subunit, RpoD [Ehrlichia canis str. Jake]
          Length = 622

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 69/238 (28%), Positives = 123/238 (51%), Gaps = 19/238 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLVV IA  Y   GL   ++V EGNIGLM+AV KFD +RG++ +TY+ WW
Sbjct: 385 AKQEMIKANLRLVVSIAKKYSNRGLQFLDLVQEGNIGLMKAVDKFDYKRGYKFSTYATWW 444

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           ++ A+   I      ++I        +   + ++   L+ +     +   +  ++ KLN+
Sbjct: 445 VRQAITRAIADQARTIRIPV-----HMIETVNKINRTLRQMLHEMGREPTLEELSAKLNI 499

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER---KNRR 225
           +  ++  +   +    SL + I   D +SS + D +      +++  ++ E+     + R
Sbjct: 500 NVDKIRKVMKIVKDPVSLESPI--GDDDSSTFGDCI------EDKRAVKPEDAAVLADLR 551

Query: 226 NMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            + T+ +S L P+E RI   R          TLE +   F V+RER+RQIEA+A +K+
Sbjct: 552 EITTKVLSTLTPKEERILRMRFGIGKGGKDHTLEEVGKLFNVTRERIRQIEAKALRKL 609


>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 = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 69/245 (28%), Positives = 119/245 (48%), Gaps = 32/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RGF+ +TY+ WW
Sbjct: 405 AKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGFKFSTYATWW 464

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +  ++P+  + +A+K+ +
Sbjct: 465 IRQAITRSIADQARTIRI--PVHMIETINKMNRISR--QILQETGIEPDPAL-LAEKMEM 519

Query: 169 SESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            E ++          ISM   +  DE  +      D  +    D  VY            
Sbjct: 520 PEDKIRKILKISKEPISMETPIGDDEDSHLGDFIEDSTTLAPVDAAVY------------ 567

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARA 276
               + R+  +  +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A
Sbjct: 568 ---ASLRDATSEVLESLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKA 624

Query: 277 FKKVQ 281
            +K++
Sbjct: 625 LRKLR 629


>gi|308062951|gb|ADO04838.1| RNA polymerase sigma factor RpoD [Helicobacter pylori Sat464]
          Length = 666

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 69/236 (29%), Positives = 120/236 (50%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ WW
Sbjct: 427 AKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWW 486

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           IK A+   I      ++I        +   + R+   ++     N K   +  +A+++ +
Sbjct: 487 IKQAISRAIADQARTIRIPI-----HMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGL 541

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  +V   N      E ++      + +  ++ D++    D      I+   R++ +  +
Sbjct: 542 SLDKV--KNVIKVTKEPISLETPVGNDDDGKFGDFV---EDKNIVSSIDHIMREDLKAQI 596

Query: 229 TRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 597 ESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 652


>gi|208434051|ref|YP_002265717.1| RNA polymerase sigma-80 factor [Helicobacter pylori G27]
 gi|208431980|gb|ACI26851.1| RNA polymerase sigma-80 factor [Helicobacter pylori G27]
          Length = 682

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 121/236 (51%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ WW
Sbjct: 443 AKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWW 502

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           IK A+   I      ++I        +   + R+   ++     N K   +  +A+++ +
Sbjct: 503 IKQAISRAIADQARTIRIPI-----HMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGL 557

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  +
Sbjct: 558 SLDKVKNVIKVTKEPISLETPVGNDD--DGKFGDFV---EDKNIVSSIDHIMREDLKAQI 612

Query: 229 TRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 613 ESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 668


>gi|283779933|ref|YP_003370688.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pirellula staleyi
           DSM 6068]
 gi|283438386|gb|ADB16828.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pirellula staleyi
           DSM 6068]
          Length = 545

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 76/247 (30%), Positives = 128/247 (51%), Gaps = 19/247 (7%)

Query: 41  YREHGDLSAAHRLVTS-HLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           YRE+ D  AA R++++ +LRLVV IA  YR  GL   +++ EGN GLM+AV KF+  RG+
Sbjct: 285 YRENYD--AAKRVLSAGNLRLVVSIAKKYRNRGLSFLDLIQEGNTGLMRAVDKFEYARGY 342

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWI+ A+   I      +++    +       +R +   L         PE+V
Sbjct: 343 KFSTYATWWIRQAITRAIADQSRTIRV--PVHMIDTMSKVRAVTRQLVQELGREPTPEEV 400

Query: 160 VAIAKKLNVSESEVISMNCR--LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
             +A  L + ++  +    R  L+ D+ +       D + S + ++L    D +E+  + 
Sbjct: 401 ARVA-GLTLDDARCVLKMARQPLSLDQPVG------DHDDSYFGEFLA---DHREEDPLY 450

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
              ++  ++ +  +M  LN RER I   R    +    TLE +   F V+RERVRQIE +
Sbjct: 451 DTHQQALKHQIEEAMQGLNYREREILRLRYGLTDGYAYTLEEVGKIFSVTRERVRQIETK 510

Query: 276 AFKKVQE 282
           A +K+Q+
Sbjct: 511 AVRKLQQ 517


>gi|309791233|ref|ZP_07685765.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Oscillochloris
           trichoides DG6]
 gi|308226795|gb|EFO80491.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Oscillochloris
           trichoides DG6]
          Length = 391

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 83/294 (28%), Positives = 138/294 (46%), Gaps = 46/294 (15%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ EI ++P+L  ++E  LAK   E GD++                           +  
Sbjct: 98  YLQEIGQVPLLTAEKEVELAKSM-EAGDIARQRIDREEYTSGRERMELERAYALGCESRQ 156

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV IA  Y  YGL + ++V EGNIGLM+AV+KFD  +G + +TY+ WWI+ 
Sbjct: 157 HLIQANLRLVVSIAKKYTSYGLTMMDLVQEGNIGLMRAVEKFDYTKGHKFSTYATWWIRQ 216

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           A+   I      +++     +      ++R    LQ        PE+   IA+ + +S  
Sbjct: 217 AITRAIADQSRTIRLPVHMGEA--ISQVKRTSHKLQQSMQREPTPEE---IAEAMGISAG 271

Query: 172 EVISMNCRLAGDESLNAL---INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +V     R   + S++ L   +    +   +  D++    D +     E       R  +
Sbjct: 272 KV-----RRTLEASMHPLSLEMPVGQEGEGRMGDFI---EDDRISTPSEAAAAAMLREQI 323

Query: 229 TRSMSVLNPRERRIFEARR-LQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L  RER+I + R  L++    TLE +  EF ++RER+RQIEA A +K+
Sbjct: 324 EEVLQKLPERERKIIQLRYGLKDGRYRTLEEVGVEFGITRERIRQIEAVALRKL 377


>gi|282877365|ref|ZP_06286188.1| putative RNA polymerase sigma factor RpoD [Prevotella buccalis ATCC
           35310]
 gi|281300417|gb|EFA92763.1| putative RNA polymerase sigma factor RpoD [Prevotella buccalis ATCC
           35310]
          Length = 290

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 77/282 (27%), Positives = 144/282 (51%), Gaps = 32/282 (11%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYG 72
            L +Y+ EI + P++   EE  LA++ ++ G     A  +LVT++LR VV +A  Y+  G
Sbjct: 17  ALDKYLVEIGRAPLISIDEEIELAQKIKKGGPEGERAKDKLVTANLRFVVSVAKQYQHQG 76

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V++    NQ
Sbjct: 77  LSLTDLIDEGNIGLIKAAQKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRL--PLNQ 134

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALIN 191
                +L ++   +      N +   +  ++   N+ E + IS +    G   S++A   
Sbjct: 135 ---VGSLNKINHEINRFEQENHRRPSISELSDATNIDEDK-ISQSMMADGHHVSIDAPFQ 190

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM-----SVLNP--RERRIF- 243
             + N+       + D      V+   E+ +  R++   SM     +VLN   +ER I  
Sbjct: 191 DGEDNT-------MLD------VMPSGEDSRTDRHVDHESMAQELDAVLNKVLKEREIII 237

Query: 244 --EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             E   +  +   LE +  +  ++RERVRQI  ++  K+++S
Sbjct: 238 IKECFGIGRHEKGLEEIGDQLGLTRERVRQIREKSIAKLRDS 279


>gi|261838959|gb|ACX98724.1| sigma 70 (RpoD) [Helicobacter pylori 52]
          Length = 685

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 121/236 (51%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ WW
Sbjct: 446 AKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWW 505

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           IK A+   I      ++I        +   + R+   ++     N K   +  +A+++ +
Sbjct: 506 IKQAISRAIADQARTIRIPI-----HMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGL 560

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  +
Sbjct: 561 SLDKVKNVIKVTKEPISLETPVGNDD--DGKFGDFV---EDKNIVSSIDHIMREDLKAQI 615

Query: 229 TRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 616 ESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 671


>gi|322420057|ref|YP_004199280.1| RpoD subfamily RNA polymerase sigma-70 factor [Geobacter sp. M18]
 gi|320126444|gb|ADW14004.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           M18]
          Length = 330

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 77/286 (26%), Positives = 150/286 (52%), Gaps = 23/286 (8%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           +++ + +  +  Y+ EI+K  +L   EE  LA R  + GD +A  R++ S+LRLVVKIA 
Sbjct: 48  AVVEHFDDAIKLYLREIQKTKLLTADEEKELAARI-DLGDKAARDRMIVSNLRLVVKIAK 106

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y   GLP  +++ EGN+GL++AV++F   +  R +TY+ WWI+ +++  ++     +++
Sbjct: 107 RYINRGLPFLDLIEEGNMGLIKAVERFKLSKECRFSTYATWWIRQSIERALVNQSRTIRL 166

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
               +      N + L+   + +   N +P  +  +A  L V+ + V  +   L    S+
Sbjct: 167 PVHVSDD---IN-KMLRVTRELVQKMNREP-TIKEVADTLEVNVTYVRRLMVLLKKTYSI 221

Query: 187 NALINSSDKNSSQWQDWLVYD--HDGQE---QVLIEKEERKNRRNMLTRSMSVLNPRERR 241
                  ++   +  D+ + D   D       VL+E     N+  ++++    L+  E++
Sbjct: 222 -------ERPMGENNDYFLIDTIEDTSTISPAVLLED---LNKYELVSKWFETLSDAEKK 271

Query: 242 IFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           I   R   E  +P TL+ +   F V+RER+RQIEA++ +K+++ ++
Sbjct: 272 ILTLRFGLEDKDPQTLDTIGRSFGVTRERIRQIEAKSLEKLRKILE 317


>gi|15644718|ref|NP_206888.1| RNA polymerase sigma factor RpoD [Helicobacter pylori 26695]
 gi|2500785|sp|P55993|RPOD_HELPY RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|2313167|gb|AAD07156.1| RNA polymerase sigma-70 factor (rpoD) [Helicobacter pylori 26695]
          Length = 671

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 121/236 (51%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ WW
Sbjct: 432 AKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWW 491

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           IK A+   I      ++I        +   + R+   ++     N K   +  +A+++ +
Sbjct: 492 IKQAISRAIADQARTIRIPI-----HMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGL 546

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  +
Sbjct: 547 SLDKVKNVIKVTKEPISLETPVGNDD--DGKFGDFV---EDKNIVSSIDHIMREDLKAQI 601

Query: 229 TRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 602 ESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 657


>gi|330469769|ref|YP_004407512.1| RNA polymerase, sigma 70 subunit, rpod subfamily protein
           [Verrucosispora maris AB-18-032]
 gi|328812740|gb|AEB46912.1| RNA polymerase, sigma 70 subunit, rpod subfamily protein
           [Verrucosispora maris AB-18-032]
          Length = 333

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 85/307 (27%), Positives = 148/307 (48%), Gaps = 68/307 (22%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH-------------GDLS--------AAHR 52
           Y+HEI + P+L+  +E  L+K      Y EH              +L+        A   
Sbjct: 42  YLHEISRTPLLDAAKEVDLSKAIEAGLYAEHLLGEDRVPEGVTRDELTRLVAEGERAKDL 101

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            + ++LRLVV IA  Y   G+P+ +++ EGN GL++AV+KFD ERG++ +TY+ WWI+ A
Sbjct: 102 FIRANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYERGYKFSTYATWWIRQA 161

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT---DNNLKPEQVVAIAKKLNVS 169
           +   I +    V++        L  ++ R++   + +T    ++ +PEQ   IA  L V+
Sbjct: 162 ISRAIAQQERTVRLPV-----HLVEDVNRMRNVARQLTRELGSDPEPEQ---IAAALGVT 213

Query: 170 ----------ESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
                       + +S++  +   GD +L  L+  SD  S              E++++ 
Sbjct: 214 VERVNELVRWSQDTVSLDTPVGDDGDTNLGDLVADSDAPSP-------------EEIVLT 260

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEAR 275
             ER+    +L      L+ R   I  AR   E+    +L  ++S F +SRER+RQ+E +
Sbjct: 261 GLERQRIEGLLNH----LDDRSAGIMRARYGLEDGREHSLTEVASRFSLSRERIRQLEIQ 316

Query: 276 AFKKVQE 282
           A  +++E
Sbjct: 317 ALGRLRE 323


>gi|217032875|ref|ZP_03438353.1| hypothetical protein HPB128_1g12 [Helicobacter pylori B128]
 gi|298736968|ref|YP_003729498.1| RNA polymerase primary sigma factor [Helicobacter pylori B8]
 gi|216945415|gb|EEC24081.1| hypothetical protein HPB128_1g12 [Helicobacter pylori B128]
 gi|298356162|emb|CBI67034.1| RNA polymerase primary sigma factor [Helicobacter pylori B8]
          Length = 679

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 121/236 (51%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ WW
Sbjct: 440 AKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWW 499

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           IK A+   I      ++I        +   + R+   ++     N K   +  +A+++ +
Sbjct: 500 IKQAISRAIADQARTIRIPI-----HMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGL 554

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  +
Sbjct: 555 SLDKVKNVIKVTKEPISLETPVGNDD--DGKFGDFV---EDKNIVSSIDHIMREDLKAQI 609

Query: 229 TRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 610 ESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 665


>gi|317011933|gb|ADU82541.1| RNA polymerase sigma factor RpoD [Helicobacter pylori Lithuania75]
          Length = 680

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 121/236 (51%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ WW
Sbjct: 441 AKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWW 500

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           IK A+   I      ++I        +   + R+   ++     N K   +  +A+++ +
Sbjct: 501 IKQAISRAIADQARTIRIPI-----HMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGL 555

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  +
Sbjct: 556 SLDKVKNVIKVTKEPISLETPVGNDD--DGKFGDFV---EDKNIVSSIDHIMREDLKAQI 610

Query: 229 TRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 611 ESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 666


>gi|297180571|gb|ADI16783.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [uncultured gamma proteobacterium HF0010_11B23]
          Length = 605

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 78/266 (29%), Positives = 124/266 (46%), Gaps = 42/266 (15%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           K YR  G L A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG
Sbjct: 359 KAYR--GLLRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 416

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNL 154
           ++ +TY+ WWI+ A+   I      ++I      T N+      L RL   +        
Sbjct: 417 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK------LNRLSRQMMQEIGREP 470

Query: 155 KPEQVVAIAKKLNVSES----------EVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            PE+   ++K+L++ E           E ISM   +  DE             S   D+L
Sbjct: 471 TPEE---MSKRLDIPEDKMRKVMKIAKEPISMETPIGDDE------------DSNLGDFL 515

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEF 262
               D      I+    +  ++     ++ L  RE ++   R      N  TLE +  +F
Sbjct: 516 ---EDTSINSPIDDASIRGLKDATDEILASLTAREAKVLRMRFGIGMNNDHTLEEVGKQF 572

Query: 263 EVSRERVRQIEARAFKKVQESIQKQV 288
           +V+RER+RQIEA+A +K++   +  V
Sbjct: 573 DVTRERIRQIEAKALRKLRHPTRSDV 598


>gi|317179521|dbj|BAJ57309.1| RNA polymerase sigma factor RpoD [Helicobacter pylori F30]
          Length = 666

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 121/236 (51%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ WW
Sbjct: 427 AKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWW 486

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           IK A+   I      ++I        +   + R+   ++     N K   +  +A+++ +
Sbjct: 487 IKQAISRAIADQARTIRIPI-----HMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGL 541

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  +
Sbjct: 542 SLDKVKNVIKVTKEPISLETPVGNDD--DGKFGDFV---EDKNIVSSIDHIMREDLKAQI 596

Query: 229 TRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 597 ESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 652


>gi|317179895|dbj|BAJ57681.1| RNA polymerase sigma factor RpoD [Helicobacter pylori F32]
          Length = 671

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 121/236 (51%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ WW
Sbjct: 432 AKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWW 491

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           IK A+   I      ++I        +   + R+   ++     N K   +  +A+++ +
Sbjct: 492 IKQAISRAIADQARTIRIPI-----HMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGL 546

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  +
Sbjct: 547 SLDKVKNVIKVTKEPISLETPVGNDD--DGKFGDFV---EDKNIVSSIDHIMREDLKAQI 601

Query: 229 TRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 602 ESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 657


>gi|210134292|ref|YP_002300731.1| RNA polymerase sigma factor RpoD [Helicobacter pylori P12]
 gi|210132260|gb|ACJ07251.1| RNA polymerase sigma-80 factor [Helicobacter pylori P12]
          Length = 680

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 121/236 (51%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ WW
Sbjct: 441 AKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWW 500

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           IK A+   I      ++I        +   + R+   ++     N K   +  +A+++ +
Sbjct: 501 IKQAISRAIADQARTIRIPI-----HMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGL 555

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  +
Sbjct: 556 SLDKVKNVIKVTKEPISLETPVGNDD--DGKFGDFV---EDKNIVSSIDHIMREDLKAQI 610

Query: 229 TRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 611 ESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 666


>gi|197119058|ref|YP_002139485.1| RNA polymerase sigma-38 factor, stationary phase [Geobacter
           bemidjiensis Bem]
 gi|197088418|gb|ACH39689.1| RNA polymerase sigma-38 factor, stationary phase [Geobacter
           bemidjiensis Bem]
          Length = 333

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 76/286 (26%), Positives = 150/286 (52%), Gaps = 23/286 (8%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           +++ + +  +  Y+ EI+K  +L   EE  LA R  + GD +A  R++ S+LRLVVKIA 
Sbjct: 47  AVVEHFDDAIKLYLREIQKTKLLTADEEKELAARI-DLGDKAARDRMIVSNLRLVVKIAK 105

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y   GLP  +++ EGN+GL++AV++F   +  R +TY+ WWI+ +++  ++     +++
Sbjct: 106 RYINRGLPFLDLIEEGNMGLIKAVERFKLSKECRFSTYATWWIRQSIERALVNQSRTIRL 165

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
               +      N + L+   + +   N +P  +  +A  L V+ + V  +   L    S+
Sbjct: 166 PVHVSDD---IN-KMLRVTRELVQKMNREP-SIKEVADTLEVNVTYVRRLMVLLKKTYSI 220

Query: 187 NALINSSDKNSSQWQDWLVYD--HDGQE---QVLIEKEERKNRRNMLTRSMSVLNPRERR 241
                  ++   +  D+ + D   D       VL+E     N+  ++++    L+  E++
Sbjct: 221 -------ERPMGENNDYFLIDTIEDTSTISPAVLLED---LNKYELVSKWFETLSDAEKK 270

Query: 242 IFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           I   R     ++P TL+ +   F V+RER+RQIEA++ +K+++ ++
Sbjct: 271 ILTLRFGLDDKDPQTLDTIGRSFGVTRERIRQIEAKSLEKLRKIVE 316


>gi|159901184|ref|YP_001547431.1| RpoD family RNA polymerase sigma factor [Herpetosiphon aurantiacus
           ATCC 23779]
 gi|159894223|gb|ABX07303.1| RNA polymerase, sigma 70 subunit, RpoD family [Herpetosiphon
           aurantiacus ATCC 23779]
          Length = 375

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 92/306 (30%), Positives = 139/306 (45%), Gaps = 69/306 (22%)

Query: 19  YIHEIRKIPMLEKQEEYVLAK----------RYREHGDL---------------SAAHRL 53
           Y+ EI ++ +L   EE +LAK          R   H  L               +A   L
Sbjct: 82  YLREIGQVHLLTAHEETMLAKQLERGERAMIRLARHEYLLEEKARLQQQVLESEAARQHL 141

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           + ++LRLVV IA  Y G G+   +++ EGNIGLM+A +KFD  +GF+ +TY+ WWI+ A+
Sbjct: 142 IQANLRLVVSIAKKYVGRGMSFLDLIQEGNIGLMRATEKFDYHKGFKFSTYATWWIRQAI 201

Query: 114 QEYI---LRSWSL-VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              I    R+  L V +G T N+      ++R    LQ   +     E+   I + L + 
Sbjct: 202 TRSISDHSRTIRLPVHVGETINR------VKRTAHKLQQALEREPSAEE---IGEALGLP 252

Query: 170 ESEV----------ISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
             +V          +S+   +   GD  L   I   D  SS+  D         E +L  
Sbjct: 253 ADKVRRVLEVARQPVSLETPVGNEGDSVLGDFIE--DDRSSEPLDH------ATEHLL-- 302

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
                  R  L   +  L+ RERRI E R   +     TLE +  EF ++RER+RQIEA+
Sbjct: 303 -------REQLDEVLCKLDERERRIIELRYGLVDGKYRTLEEVGREFGITRERIRQIEAK 355

Query: 276 AFKKVQ 281
             +K++
Sbjct: 356 VLRKLR 361


>gi|217140|dbj|BAA01749.1| principal sigma factor [Synechococcus elongatus PCC 7942]
          Length = 384

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 75/238 (31%), Positives = 130/238 (54%), Gaps = 19/238 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 148 AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 207

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT-DNNLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++ +   KP E+ +A   ++
Sbjct: 208 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEM 262

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RR 225
            + +   I+ + +L    SL   I    +  S+  D++  + DG+     E E  KN  R
Sbjct: 263 TIEKLRFIAKSAQLPI--SLETPIGK--EEDSRLGDFI--EADGETP---EDEVAKNLLR 313

Query: 226 NMLTRSMSVLNPRERRIFEARR-LQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
             L   +S L+PRER +   R  L +  + TLE +   F V+RER+RQIEA+A +K++
Sbjct: 314 EDLEGVLSTLSPRERDVLRLRYGLDDGRMKTLEEIGQLFNVTRERIRQIEAKALRKLR 371


>gi|308182264|ref|YP_003926391.1| RNA polymerase sigma factor RpoD [Helicobacter pylori PeCan4]
 gi|308064449|gb|ADO06341.1| RNA polymerase sigma factor RpoD [Helicobacter pylori PeCan4]
          Length = 682

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 121/236 (51%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ WW
Sbjct: 443 AKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWW 502

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           IK A+   I      ++I        +   + R+   ++     N K   +  +A+++ +
Sbjct: 503 IKQAISRAIADQARTIRIPI-----HMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGL 557

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  +
Sbjct: 558 SLDKVKNVIKVTKEPISLETPVGNDD--DGKFGDFV---EDKNIVSSIDHIMREDLKAQI 612

Query: 229 TRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 613 ESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 668


>gi|297181479|gb|ADI17666.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [uncultured gamma proteobacterium HF0130_23I23]
          Length = 602

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 77/259 (29%), Positives = 123/259 (47%), Gaps = 42/259 (16%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           K YR  G L A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG
Sbjct: 356 KAYR--GLLRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 413

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNL 154
           ++ +TY+ WWI+ A+   I      ++I      T N+      L RL   +        
Sbjct: 414 YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK------LNRLSRQMMQEIGREP 467

Query: 155 KPEQVVAIAKKLNVSES----------EVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            PE+   ++K+L++ E           E ISM   +  DE             S   D+L
Sbjct: 468 TPEE---MSKRLDIPEDKMRKVMKIAKEPISMETPIGDDE------------DSNLGDFL 512

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEF 262
               D      I+    ++ ++     ++ L  RE ++   R      N  TLE +  +F
Sbjct: 513 ---EDSSINSPIDDASIRSLKDSTDEILASLTAREAKVLRMRFGIGMNNDHTLEEVGKQF 569

Query: 263 EVSRERVRQIEARAFKKVQ 281
           +V+RER+RQIEA+A +K++
Sbjct: 570 DVTRERIRQIEAKALRKLR 588


>gi|295103972|emb|CBL01516.1| RNA polymerase sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii SL3/3]
          Length = 457

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 80/262 (30%), Positives = 133/262 (50%), Gaps = 25/262 (9%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ E++ + +L  + R  G L+A   L  ++LRLVV IA  + G+ L   +++ EGNIGL
Sbjct: 201 PLSEERRQELL--KTRRDG-LNARRSLSEANLRLVVSIAKKHVGHNLAFLDLIQEGNIGL 257

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKRLFFN-LRR 141
           ++A +KFD +RGFR +TY+ WWI+ A+   I      ++I      T N+ R   N L  
Sbjct: 258 IKAAEKFDCDRGFRFSTYATWWIRQAITRAIADQARTIRIPVHMVETINRMRQATNQLVY 317

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
             GH          PE+   +AK +++S   V  +        SL + +   ++  S   
Sbjct: 318 QNGH-------EPTPEE---LAKAMDMSVERVREIQRMAQEPASLESPV--GEEEDSSLG 365

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLS 259
           D++    D   +   +  +R      +  ++  L PRE ++   R   ++  P TLE + 
Sbjct: 366 DFVA---DENAEAPGKAADRAMVAQQINLALKSLTPREEKVIRLRFGLDDGRPRTLEEVG 422

Query: 260 SEFEVSRERVRQIEARAFKKVQ 281
            +F V+RERVRQIEA+A +K+ 
Sbjct: 423 RDFGVTRERVRQIEAKAIRKLH 444


>gi|156742920|ref|YP_001433049.1| RpoD family RNA polymerase sigma factor [Roseiflexus castenholzii
           DSM 13941]
 gi|156234248|gb|ABU59031.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus
           castenholzii DSM 13941]
          Length = 348

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 82/294 (27%), Positives = 136/294 (46%), Gaps = 40/294 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHG-----------------------DLSAAH- 51
           +  Y+ EI ++P+L   EE  LA+R  E G                       D++AA  
Sbjct: 52  IQHYLQEIGRVPLLTAAEEIELAERM-ERGAAAERRLASGEDLSPQLRQALLADVAAAQE 110

Query: 52  ---RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
               L+ ++LRLVV IA  Y G GL + +++ EGNIGLM+AV+KFD  +G R +TY+ WW
Sbjct: 111 ARRHLIQANLRLVVSIAKKYVGRGLSLLDLIQEGNIGLMRAVEKFDYHKGNRFSTYATWW 170

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      +++    ++      ++R    L    +    PE++     +   
Sbjct: 171 IRQAVTRAIAEQGRTIRLPVHMSES--VGQVKRTADRLAQALERQPTPEEIATALGQPTE 228

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
               V+  + R     SL   +    +++    D+L    D +    +E   ++  R  L
Sbjct: 229 RIERVLEASRRPV---SLETPVGEDGEHT--LGDFL---QDSELPTPVEAASQQLLRRDL 280

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++  LN RERRI + R   +     TLE +     ++RER RQIEA A +++
Sbjct: 281 AAALDRLNERERRIIDLRYGLVDGQRRTLEEVGRVLGMTRERARQIEAEALRRL 334


>gi|317010368|gb|ADU84115.1| RNA polymerase sigma factor RpoD [Helicobacter pylori SouthAfrica7]
          Length = 685

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 121/236 (51%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ WW
Sbjct: 446 AKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWW 505

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           IK A+   I      ++I        +   + R+   ++     N K   +  +A+++ +
Sbjct: 506 IKQAISRAIADQARTIRIPI-----HMIDTINRINKVMRKYMQENGKEPDLELVAEEVGL 560

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  +
Sbjct: 561 SLDKVKNVIKVTKEPISLETPVGNDD--DGKFGDFV---EDKNIVSSIDHIMREDLKAQI 615

Query: 229 TRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 616 DGVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 671


>gi|168000881|ref|XP_001753144.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162695843|gb|EDQ82185.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 581

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 66/245 (26%), Positives = 130/245 (53%), Gaps = 16/245 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A  +LV S+LRLVV I   Y+G G+ + +++  G++GL++  +KFDPE GF+ +TY+ W
Sbjct: 340 CAKDKLVNSNLRLVVSIVKNYQGRGMTLPDLIQRGSLGLIRGAEKFDPEMGFKFSTYATW 399

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP--EQVVAIAKK 165
           WI+ A+   I     ++++        ++  + R+      I ++  +   ++ VA A  
Sbjct: 400 WIRQAVTRSITDQSRIIRLPV-----HIYEVISRINKSRMMIAEDQGRQARDEEVATAVG 454

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           ++V + + I  + RL    S++ LI   DK+   W+       +  +  L  +  +++  
Sbjct: 455 ISVEKLDFILKSARLPA--SMDQLIG-RDKDLPLWEMVADKGFNSADDFLTNEVLKQDID 511

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +L      L+P ER +   R   ++   +TL+++   F+V+RER+RQIE RA +K++  
Sbjct: 512 GVL----QTLSPTEREVLRLRFGLDDAQSMTLKDIGIFFKVTRERIRQIEVRALRKLRHP 567

Query: 284 IQKQV 288
            ++ +
Sbjct: 568 TRRNI 572


>gi|160942567|ref|ZP_02089814.1| hypothetical protein FAEPRAM212_00042 [Faecalibacterium prausnitzii
           M21/2]
 gi|158446151|gb|EDP23154.1| hypothetical protein FAEPRAM212_00042 [Faecalibacterium prausnitzii
           M21/2]
          Length = 457

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 80/262 (30%), Positives = 133/262 (50%), Gaps = 25/262 (9%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ E++ + +L  + R  G L+A   L  ++LRLVV IA  + G+ L   +++ EGNIGL
Sbjct: 201 PLSEERRQELL--KTRRDG-LNARRSLSEANLRLVVSIAKKHVGHNLAFLDLIQEGNIGL 257

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKRLFFN-LRR 141
           ++A +KFD +RGFR +TY+ WWI+ A+   I      ++I      T N+ R   N L  
Sbjct: 258 IKAAEKFDCDRGFRFSTYATWWIRQAITRAIADQARTIRIPVHMVETINRMRQATNQLVY 317

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
             GH          PE+   +AK +++S   V  +        SL + +   ++  S   
Sbjct: 318 QNGH-------EPTPEE---LAKAMDMSVERVREIQRMAQEPASLESPV--GEEEDSSLG 365

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLS 259
           D++    D   +   +  +R      +  ++  L PRE ++   R   ++  P TLE + 
Sbjct: 366 DFVA---DENAEAPGKAADRAMVAQQINLALKSLTPREEKVIRLRFGLDDGRPRTLEEVG 422

Query: 260 SEFEVSRERVRQIEARAFKKVQ 281
            +F V+RERVRQIEA+A +K+ 
Sbjct: 423 RDFGVTRERVRQIEAKAIRKLH 444


>gi|288927698|ref|ZP_06421545.1| RNA polymerase sigma-70 factor [Prevotella sp. oral taxon 317 str.
           F0108]
 gi|288330532|gb|EFC69116.1| RNA polymerase sigma-70 factor [Prevotella sp. oral taxon 317 str.
           F0108]
          Length = 290

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 76/272 (27%), Positives = 135/272 (49%), Gaps = 14/272 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           L +Y+ EI + P++   EE  LA++ R+ G     A  +LVT++LR VV +A  Y+  GL
Sbjct: 18  LDKYLVEIGRAPLISIDEEIELAQKIRKGGPEGEKAKDKLVTANLRFVVSVAKQYQHQGL 77

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V++    NQ 
Sbjct: 78  TLTDLIDEGNIGLIKAAQKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRL--PLNQ- 134

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINS 192
               +L ++   +      N +   V  ++   N+ E E I  +    G   S++A    
Sbjct: 135 --VGSLNKINHEINKFEQENQRHPSVSELSDATNIDE-EKIGQSLMADGHHVSIDAPFQD 191

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF-EARRLQEN 251
            + N     D +    D +     + E      N +     VL  RE  I  E   +  +
Sbjct: 192 GEDNC--MLDVMASGDDSRTDKQADHESMALELNSVL--AKVLKDREITIIRECFGIGCH 247

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
              LE +  +  ++RERVRQI  ++  K+++S
Sbjct: 248 EKGLEEIGDQLGLTRERVRQIREKSIAKLRDS 279


>gi|213964575|ref|ZP_03392775.1| RNA polymerase sigma factor A [Corynebacterium amycolatum SK46]
 gi|213952768|gb|EEB64150.1| RNA polymerase sigma factor A [Corynebacterium amycolatum SK46]
          Length = 520

 Score = 98.6 bits (244), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 81/318 (25%), Positives = 154/318 (48%), Gaps = 43/318 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR---------------------- 40
           RK+ ++  + +  +  Y+ +I K+ +L  +EE  LAKR                      
Sbjct: 208 RKDAALTASAD-SVRAYLKQIGKVALLTAEEEVSLAKRIEAGLYAQYKIDEAKQAGERIA 266

Query: 41  YREHGDLS--------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           Y +  DL         A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 267 YAQKRDLREISRDGQRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 326

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L      
Sbjct: 327 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGR 384

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE+   +AK+++++E +V+ +        SL+  I   D+  SQ  D++    D + 
Sbjct: 385 EPTPEE---LAKEMDITEEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEA 436

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVR 270
            + ++       ++ L   +  L+ RE  +   R  L +  P TL+ +   + V+RER+R
Sbjct: 437 VIAVDAVSFTLLQDQLGDVLETLSEREAGVVRLRFGLTDGMPRTLDEIGQVYGVTRERIR 496

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 497 QIESKTMSKLRHPSRSQV 514


>gi|77165531|ref|YP_344056.1| hypothetical protein Noc_2066 [Nitrosococcus oceani ATCC 19707]
 gi|76883845|gb|ABA58526.1| RNA polymerase, sigma 70 subunit, RpoD [Nitrosococcus oceani ATCC
           19707]
          Length = 579

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 75/248 (30%), Positives = 123/248 (49%), Gaps = 40/248 (16%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V ++LRLVV +A  YR  GL   +++ EGNIGLM+AV KFD  RG++ +TY+ WW
Sbjct: 341 AKAQMVEANLRLVVSVAKKYRNRGLTFLDLIQEGNIGLMKAVDKFDYHRGYKFSTYAHWW 400

Query: 109 IKAAMQEYILRSWSLVKIGTTANQK-----RLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           I+ A+   I      ++I     +K     R  + LR+ KG          +PE+   +A
Sbjct: 401 IRQAITRAIDDQSRTIRIPVHVMEKLSKLNRASYQLRQEKG-------REGRPEE---LA 450

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           ++L +SE ++  M              +   K     +  L  D D Q   L+E E+  N
Sbjct: 451 ERLALSEQQIHRM--------------HEIAKQPISLETPLGKDEDSQLGELMEDEQVPN 496

Query: 224 RRNMLTRS---------MSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQI 272
              +   +         ++ L+PRE ++   R     +   TL  ++ +F++SRER+RQI
Sbjct: 497 PMEVAITAGLQTGAQQLLAALSPREAQVVAMRFGIGMDTDHTLGEVAQQFDLSRERIRQI 556

Query: 273 EARAFKKV 280
           EA+A  K+
Sbjct: 557 EAQALGKL 564


>gi|254434698|ref|ZP_05048206.1| RNA polymerase sigma factor, sigma-70 family [Nitrosococcus oceani
           AFC27]
 gi|207091031|gb|EDZ68302.1| RNA polymerase sigma factor, sigma-70 family [Nitrosococcus oceani
           AFC27]
          Length = 595

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 75/248 (30%), Positives = 123/248 (49%), Gaps = 40/248 (16%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V ++LRLVV +A  YR  GL   +++ EGNIGLM+AV KFD  RG++ +TY+ WW
Sbjct: 357 AKAQMVEANLRLVVSVAKKYRNRGLTFLDLIQEGNIGLMKAVDKFDYHRGYKFSTYAHWW 416

Query: 109 IKAAMQEYILRSWSLVKIGTTANQK-----RLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           I+ A+   I      ++I     +K     R  + LR+ KG          +PE+   +A
Sbjct: 417 IRQAITRAIDDQSRTIRIPVHVMEKLSKLNRASYQLRQEKG-------REGRPEE---LA 466

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           ++L +SE ++  M              +   K     +  L  D D Q   L+E E+  N
Sbjct: 467 ERLALSEQQIHRM--------------HEIAKQPISLETPLGKDEDSQLGELMEDEQVPN 512

Query: 224 RRNMLTRS---------MSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQI 272
              +   +         ++ L+PRE ++   R     +   TL  ++ +F++SRER+RQI
Sbjct: 513 PMEVAITAGLQTGAQQLLAALSPREAQVVAMRFGIGMDTDHTLGEVAQQFDLSRERIRQI 572

Query: 273 EARAFKKV 280
           EA+A  K+
Sbjct: 573 EAQALGKL 580


>gi|81299460|ref|YP_399668.1| RNA polymerase sigma factor RpoD [Synechococcus elongatus PCC 7942]
 gi|93141306|sp|P38023|RPOD1_SYNE7 RecName: Full=RNA polymerase sigma factor rpoD1
 gi|81168341|gb|ABB56681.1| Sigma-70 factor [Synechococcus elongatus PCC 7942]
          Length = 399

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 74/238 (31%), Positives = 129/238 (54%), Gaps = 19/238 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 163 AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 222

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT-DNNLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++ +   KP E+ +A   ++
Sbjct: 223 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEM 277

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RR 225
            + +   I+ + +L    SL   I    +  S+  D++  + DG+     E E  KN  R
Sbjct: 278 TIEKLRFIAKSAQLPI--SLETPIGK--EEDSRLGDFI--EADGETP---EDEVAKNLLR 328

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             L   +S L+PRER +   R   ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 329 EDLEGVLSTLSPRERDVLRLRYGLDDGRMKTLEEIGQLFNVTRERIRQIEAKALRKLR 386


>gi|56750888|ref|YP_171589.1| RNA polymerase sigma factor RpoD [Synechococcus elongatus PCC 6301]
 gi|56685847|dbj|BAD79069.1| principal RNA polymerase sigma factor RpoD1 [Synechococcus
           elongatus PCC 6301]
          Length = 399

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 74/238 (31%), Positives = 129/238 (54%), Gaps = 19/238 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 163 AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 222

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT-DNNLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++ +   KP E+ +A   ++
Sbjct: 223 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEM 277

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RR 225
            + +   I+ + +L    SL   I    +  S+  D++  + DG+     E E  KN  R
Sbjct: 278 TIEKLRFIAKSAQLPI--SLETPIGK--EEDSRLGDFI--EADGETP---EDEVAKNLLR 328

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             L   +S L+PRER +   R   ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 329 EDLEGVLSTLSPRERDVLRLRYGLDDGRMKTLEEIGQLFNVTRERIRQIEAKALRKLR 386


>gi|190575994|ref|YP_001973839.1| RNA polymerase sigma factor RpoD [Stenotrophomonas maltophilia
           K279a]
 gi|190013916|emb|CAQ47556.1| putative RNA polymerase sigma factor RpoD [Stenotrophomonas
           maltophilia K279a]
          Length = 617

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 77/265 (29%), Positives = 126/265 (47%), Gaps = 32/265 (12%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           LE+ +E   A  Y E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+
Sbjct: 358 LEELKEISRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 417

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           AV KF+  RG++ +TY+ WWI+ A+   I      ++I    +       L R+   +  
Sbjct: 418 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQ 475

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSS 198
                  PE+   +AK++++ E ++          ISM   +  DE             S
Sbjct: 476 QYGREATPEE---LAKEMDMPEDKIRKVMKIAKEPISMETPIGDDE------------DS 520

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLE 256
              D++    D   +  IE     N    +   ++ L PRE ++   R  +  N   TLE
Sbjct: 521 HLGDFI---EDTNVESPIENTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLE 577

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  +F+V+RER+RQIEA+A +K++
Sbjct: 578 EVGKQFDVTRERIRQIEAKALRKLR 602


>gi|269798255|ref|YP_003312155.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Veillonella
           parvula DSM 2008]
 gi|282850493|ref|ZP_06259872.1| RNA polymerase sigma factor RpoD [Veillonella parvula ATCC 17745]
 gi|294792116|ref|ZP_06757264.1| RNA polymerase sigma factor RpoD [Veillonella sp. 6_1_27]
 gi|294793987|ref|ZP_06759124.1| RNA polymerase sigma factor RpoD [Veillonella sp. 3_1_44]
 gi|269094884|gb|ACZ24875.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Veillonella
           parvula DSM 2008]
 gi|282579986|gb|EFB85390.1| RNA polymerase sigma factor RpoD [Veillonella parvula ATCC 17745]
 gi|294455557|gb|EFG23929.1| RNA polymerase sigma factor RpoD [Veillonella sp. 3_1_44]
 gi|294457346|gb|EFG25708.1| RNA polymerase sigma factor RpoD [Veillonella sp. 6_1_27]
          Length = 386

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 80/291 (27%), Positives = 139/291 (47%), Gaps = 37/291 (12%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHR-----------LVTSHL 58
           VN +  +  Y+ EI ++P+L   EE VLAK+        A ++           LV ++L
Sbjct: 100 VNIDDPVRMYLKEIGRVPLLSADEEIVLAKQIEAGAQEDATYKDIQLSKKAKKKLVDANL 159

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV IA  Y G G+   +++ EGN+GL++AV KFD  +G++ +TY+ WWI+ A+   I 
Sbjct: 160 RLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVDKFDYTKGYKFSTYATWWIRQAITRAIA 219

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV-------VAIAKKLNVSES 171
                ++I    +       L R+   L         PE++       V   +++     
Sbjct: 220 DQARTIRI--PVHMVETINKLIRISRQLLQDKGREPLPEEIAEGMGITVERVREIQKIAQ 277

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           E +S+   +  +E      +S   +  + QD +  D D    +L++++        +   
Sbjct: 278 EPVSLETPIGEEE------DSHLGDFIEDQDAIAPD-DAASYILLQEQ--------IEDV 322

Query: 232 MSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKV 280
            + L  RE+++   R  L++  P TLE +   F V+RER+RQIE +A  K+
Sbjct: 323 FTCLTDREQQVLILRFGLKDGKPRTLEEVGQHFNVTRERIRQIEGKALTKL 373


>gi|269126637|ref|YP_003300007.1| RpoD subfamily RNA polymerase sigma-70 subunit [Thermomonospora
           curvata DSM 43183]
 gi|268311595|gb|ACY97969.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermomonospora
           curvata DSM 43183]
          Length = 444

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 77/251 (30%), Positives = 131/251 (52%), Gaps = 19/251 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLVV +A  Y   GL + +VV EGN+GL++AV+KFD  +GF+ +TY+MWW
Sbjct: 207 AKSHMLEANLRLVVSVAKKYSDRGLSLLDVVQEGNLGLIRAVEKFDYTKGFKFSTYAMWW 266

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+Q     S   +++    +   +   L R++  +         PE++ A   +L+ 
Sbjct: 267 IRQAIQRGFADSARTIRL--PVHVLEMLSKLSRVERDMHQRLGREPTPEELAA---ELDK 321

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S ++V  +        SL++ I   +   ++  D L+ D D  E    E  +R+   + L
Sbjct: 322 SPAQVRELLRTSRQPISLDSTIG--EDGETRIGD-LIEDIDSPEAS--EMVDRQLMADQL 376

Query: 229 TRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            RS+S+L+PRE  I   R       P TL+ +     ++RER+RQ+E       +ES+ K
Sbjct: 377 RRSLSILSPREEMIMSMRFGLYDGTPRTLDEIGKHLGLTRERIRQLE-------KESLSK 429

Query: 287 QVELSSSPPLL 297
               S++ PLL
Sbjct: 430 LRHPSNATPLL 440


>gi|78212423|ref|YP_381202.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CC9605]
 gi|78196882|gb|ABB34647.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. CC9605]
          Length = 312

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 83/293 (28%), Positives = 148/293 (50%), Gaps = 36/293 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGDLSAAHR---------- 52
           +S Y+  I +IP+L   EE  L  + +             E G+L+ A R          
Sbjct: 19  VSWYLATIGRIPLLTPAEEIELGNQVQAMMAFTEDGSREIEDGELTTAQRRLLRIGRRAK 78

Query: 53  --LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
             ++ ++LRLVV +A  Y+G GL + +++ EG++GL +AV+KFDP RG++ +TY+ WWI+
Sbjct: 79  ERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWWIR 138

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            +M   I      +++    +++     +R++   L         P + V IA+ +++  
Sbjct: 139 QSMTRAIACQSRTIRLPVHLSER--LTTIRKVS--LDLAHKLGAMPSR-VEIAEAMDIPL 193

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            E+ S+  +     SL+A +N  +  S  +   L+ D    E + I   E++     L R
Sbjct: 194 DELDSLLRQALTTSSLDAPVNGEEGRS--FLGDLIADSSLDEPLDI--VEQRIHHEQLGR 249

Query: 231 SMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +S L+ +E+ +   R  L+ N   TL  +    EVSRERVRQ+E +A +K++
Sbjct: 250 WLSHLSEQEQHVLRMRFGLEGNERHTLAEIGRLMEVSRERVRQVELKALRKLR 302


>gi|328954372|ref|YP_004371706.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfobacca
           acetoxidans DSM 11109]
 gi|328454696|gb|AEB10525.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfobacca
           acetoxidans DSM 11109]
          Length = 436

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 79/262 (30%), Positives = 130/262 (49%), Gaps = 31/262 (11%)

Query: 37  LAKRYREHGD--LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           LAK+ RE  +  + A   ++ ++LRLVV IA  Y   GL  S+++ EGN+GLM+AV ++D
Sbjct: 186 LAKKIREKENEVVRARDEMIKANLRLVVSIAKKYLHRGLSFSDLIQEGNLGLMKAVTRYD 245

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ-----KRLFFNLRRLKGH---L 146
              G+RL+T++ WWI+  +   I      ++I     +      R F++L +  G    L
Sbjct: 246 YTTGYRLSTFASWWIRQTITRAIYDKTRTIRIPVHLQEIRNRCYRAFYDLLKELGREPLL 305

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           + I + +  PE  + +   L+    E IS+   + GDE              +  D++  
Sbjct: 306 KEIAERSGVPEDKILVVTNLS---DEPISLETPV-GDE------------GDRLGDFIRN 349

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEV 264
           D        I   E   + + +   +S L PRE +I + R     E   TLE +  EF+V
Sbjct: 350 DQAISPFDSIISSELSEKTDAI---LSTLTPREEKIMKMRFGIGAEVEHTLEEIGREFKV 406

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           SRER+RQIE +A K+++   +K
Sbjct: 407 SRERIRQIEKKALKRLKHPTRK 428


>gi|113478384|ref|YP_724445.1| RNA polymerase sigma factor RpoD [Trichodesmium erythraeum IMS101]
 gi|110169432|gb|ABG53972.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
          Length = 386

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 73/238 (30%), Positives = 130/238 (54%), Gaps = 19/238 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 150 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 209

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT-DNNLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++ +   KP E+ +A + ++
Sbjct: 210 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKLLSQEMGRKPTEEEIATSMEM 264

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RR 225
            + +   I+ + +L    SL   I   +   S+  D++  + DG+     E E  KN  R
Sbjct: 265 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFI--ESDGETP---EDEVSKNLLR 315

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             L   ++ L+PRER +   R   ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 316 EDLESVLNSLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLR 373


>gi|284928680|ref|YP_003421202.1| hypothetical protein UCYN_00890 [cyanobacterium UCYN-A]
 gi|284809139|gb|ADB94844.1| hypothetical protein UCYN_00890 [cyanobacterium UCYN-A]
          Length = 420

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 78/268 (29%), Positives = 142/268 (52%), Gaps = 18/268 (6%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + I  + KI  LE Q+ Y+   + R +    A  ++V S+LRLVV IA  Y   GL   +
Sbjct: 154 KTISNLEKIWELE-QKSYLPKFKRRLYLGRKAKDKMVHSNLRLVVSIAKKYMNRGLSFQD 212

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+   I      +++        L+ 
Sbjct: 213 LIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV-----HLYE 267

Query: 138 NLRRLKGHLQAIT-DNNLKP-EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
            + R+K   + ++ +   KP E+ +A   ++ + +   I+ + +L    SL   I   + 
Sbjct: 268 TISRIKKTTKLLSQEMRRKPTEEEIATRMEMTIEKLRFIAKSAQLPI--SLETPIGKEE- 324

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--V 253
             S+  D++  D +  E  + +   R++  N+L      L+PRER +   R   ++    
Sbjct: 325 -DSRLGDFIEADGETPEDEVAKNLLREDLENVL----DTLSPRERDVLRLRYGLDDGRMK 379

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TLE +   F V+RER+RQIEA+A +K++
Sbjct: 380 TLEEIGQIFNVTRERIRQIEAKALRKLR 407


>gi|225620189|ref|YP_002721446.1| DNA-directed RNA polymerase sigma-70/sigma-32 subunit RpoD
           [Brachyspira hyodysenteriae WA1]
 gi|225215008|gb|ACN83742.1| RpoD, DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Brachyspira hyodysenteriae WA1]
          Length = 287

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 76/280 (27%), Positives = 143/280 (51%), Gaps = 35/280 (12%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            +S Y  + +K  +L ++EE  L KR +E GD  A  +L+ S+LR V+ IA  Y+  GL 
Sbjct: 18  NISLYFADAKKEKLLTREEEIELTKRLKE-GDAEARSKLIRSNLRFVITIAKQYKNSGLL 76

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++SEGN+GL+ A  +FDP++G+   +Y+++WI+ ++   I     L+++    N+  
Sbjct: 77  LEDLISEGNLGLIIAADRFDPDKGYHFISYAVYWIRQSILRAINEKSRLIRL--PLNKAM 134

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
              +L R     Q    +   P+ V  +A  LN   +++            L+ +  S++
Sbjct: 135 DLVDLER--AVHQYYYKSGYTPD-VNELATILNKDPNDI------------LHIMSMSTE 179

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM------------LTRSMSVLNPRERRI 242
             S + +    Y++DG +  LI+  E K  +N+            L  ++  L+  E++I
Sbjct: 180 HISLEGE----YNYDGMKDRLIDTIEDKTSKNVEETAINKELMEELKTAIESLSDIEKQI 235

Query: 243 FEARR-LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             AR  + +   TL+ +   F  ++ER+RQIE +A +K+ 
Sbjct: 236 INARYGIDQERKTLKEVGEMFSFTKERIRQIEKKALRKMH 275


>gi|207093142|ref|ZP_03240929.1| RNA polymerase sigma factor RpoD [Helicobacter pylori
           HPKX_438_AG0C1]
          Length = 319

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 69/236 (29%), Positives = 120/236 (50%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ WW
Sbjct: 80  AKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWW 139

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           IK A+   I      ++I        +   + R+   ++     N K   +  +A+++ +
Sbjct: 140 IKQAISRAIADQARTIRIPI-----HMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGL 194

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  +V   N      E ++      + +  ++ D++    D      I+   R++ +  +
Sbjct: 195 SLDKV--KNVIKVTKEPISLETPVGNDDDGKFGDFV---EDKNIVSSIDHIMREDLKVQI 249

Query: 229 TRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 250 ESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 305


>gi|292491943|ref|YP_003527382.1| RNA polymerase sigma factor, sigma-70 family [Nitrosococcus
           halophilus Nc4]
 gi|291580538|gb|ADE14995.1| RNA polymerase sigma factor, sigma-70 family [Nitrosococcus
           halophilus Nc4]
          Length = 578

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 75/248 (30%), Positives = 122/248 (49%), Gaps = 40/248 (16%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V ++LRLVV +A  YR  GL   +++ EGNIGLM+AV KFD  RG++ +TY+ WW
Sbjct: 340 AKAQMVEANLRLVVSVAKKYRNRGLTFLDLIQEGNIGLMRAVDKFDYRRGYKFSTYAHWW 399

Query: 109 IKAAMQEYILRSWSLVKIGTTANQK-----RLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           I+ A+   I      ++I     +K     R  + LR+ KG          +PE+   +A
Sbjct: 400 IRQAITRAIDDQSRTIRIPVHVMEKLSKLNRASYQLRQEKG-------REGRPEE---LA 449

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           ++L +SE ++  M              +   K     +  L  D D Q   L+E E+  N
Sbjct: 450 ERLALSEQQIHHM--------------HEIAKQPISLETPLGKDEDSQLGELMEDEQVPN 495

Query: 224 RRNMLTRS---------MSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQI 272
              +   +         ++ L PRE ++   R     +   TL  ++ +F++SRER+RQI
Sbjct: 496 PMEVAISAGLQAGTQQLLATLTPREAQVVAMRFGIGMDTDHTLGEVAQQFDLSRERIRQI 555

Query: 273 EARAFKKV 280
           EA+A  K+
Sbjct: 556 EAQALSKL 563


>gi|158335266|ref|YP_001516438.1| RNA polymerase sigma factor SigC [Acaryochloris marina MBIC11017]
 gi|158305507|gb|ABW27124.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 423

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 62/238 (26%), Positives = 128/238 (53%), Gaps = 13/238 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           + A   ++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV+KFDP +G+R +TY+ 
Sbjct: 182 IKAKEHMIQANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTKGYRFSTYAY 241

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   I      +++     +K     L ++K   + ++ +  +   +  IA+++
Sbjct: 242 WWIRQGITRAIATQSRTIRLPVHITEK-----LNKIKKAQRKLSQSKGRTASIEDIAQEM 296

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  ++  +  R+    SL   I       ++  D L  D    E++++    R++ + 
Sbjct: 297 DMTPEQIRELLVRVPRSVSLE--IKVGKDKDTELGDLLETDDISPEELIM----RESLQQ 350

Query: 227 MLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQE 282
            L + ++ L PRER +   R  L +    +L  +    ++SRERVRQIE++A +K+++
Sbjct: 351 ELKQLLADLTPRERDVITMRFGLNDGKTHSLAQIGKSLDLSRERVRQIESKALQKLRQ 408


>gi|62550939|emb|CAI79314.1| putative RNA polymerase sigma-32 [Aeromonas caviae]
          Length = 100

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 48/96 (50%), Positives = 66/96 (68%), Gaps = 2/96 (2%)

Query: 3  RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
          ++ M++I  G   L  YI  +  IP+L  +E+  LA+R ++ GDL AA +LV SHLR VV
Sbjct: 6  QRTMALIPQGS--LEGYIQAVNSIPVLSAEEKRELAERLQQDGDLEAARQLVMSHLRFVV 63

Query: 63 KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           +A  Y GYGLP +++V EGNIGLM+AVK+FDP  G
Sbjct: 64 HVAKSYSGYGLPQADLVQEGNIGLMKAVKRFDPSVG 99


>gi|313673328|ref|YP_004051439.1| RNA polymerase, sigma 70 subunit, rpod [Calditerrivibrio
           nitroreducens DSM 19672]
 gi|312940084|gb|ADR19276.1| RNA polymerase, sigma 70 subunit, RpoD [Calditerrivibrio
           nitroreducens DSM 19672]
          Length = 601

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 78/252 (30%), Positives = 123/252 (48%), Gaps = 52/252 (20%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +L+ S+LRLVV IA  Y   GL   +++ EGNIGLM+AV+KF+ +RG++ +TY+ WWI+ 
Sbjct: 367 KLIQSNLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVEKFEYQRGYKFSTYATWWIRQ 426

Query: 112 AMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           A+   I      ++I      T N+      + ++   LQ        PE+   IA+K++
Sbjct: 427 AITRAIADQARTIRIPVHMIETINK------MMKISRQLQVDLGREPTPEE---IAEKMD 477

Query: 168 VSESEV----------ISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVY----DHDGQ 211
           V   +V          +S+   +  DE  SL   I   DK S    D +VY    +H  Q
Sbjct: 478 VPVEKVKKVLRIAKEPVSLETPIGEDEDSSLGDFI--EDKKSKNPLDEVVYLKLSEHTKQ 535

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERV 269
                               +  L+PRE  +   R   +  +  TLE +  +F V+RER+
Sbjct: 536 -------------------ILDTLSPREASVLRLRFGIDCSSDHTLEEVGKKFNVTRERI 576

Query: 270 RQIEARAFKKVQ 281
           RQIEA+A +K++
Sbjct: 577 RQIEAKALRKLR 588


>gi|284990384|ref|YP_003408938.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geodermatophilus
           obscurus DSM 43160]
 gi|284063629|gb|ADB74567.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geodermatophilus
           obscurus DSM 43160]
          Length = 429

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 82/318 (25%), Positives = 152/318 (47%), Gaps = 43/318 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHG---- 45
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G    
Sbjct: 117 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVDLAKRIEAGLYGAERLRQAEEEGQKLS 175

Query: 46  -----DLS--------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                DL+        A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 176 PQMRRDLNWIVRDGERAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 235

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L      
Sbjct: 236 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGR 293

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D + 
Sbjct: 294 EPTPEE---LAKEMDITPDKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEA 345

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVR 270
            V ++       ++ LT  +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 346 VVAVDAVSFTLMQDQLTSVLQTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIR 405

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 406 QIESKTMSKLRHPSRSQV 423


>gi|159903037|ref|YP_001550381.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str. MIT
           9211]
 gi|159888213|gb|ABX08427.1| Putative principal RNA polymerase sigma factor [Prochlorococcus
           marinus str. MIT 9211]
          Length = 425

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 69/237 (29%), Positives = 129/237 (54%), Gaps = 17/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 189 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 248

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++     KP E+ +A + ++
Sbjct: 249 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKVLSQEFGRKPSEEEIAESMEM 303

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  D +  E  + +   R++   
Sbjct: 304 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIESDSENPELDVAKTLLREDLEG 359

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +L    + L+PRER +   R   ++    TLE +   F+V+RER+RQIEA+A +K++
Sbjct: 360 VL----ATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLR 412


>gi|221195781|ref|ZP_03568834.1| RNA polymerase sigma factor RpoD [Atopobium rimae ATCC 49626]
 gi|221184255|gb|EEE16649.1| RNA polymerase sigma factor RpoD [Atopobium rimae ATCC 49626]
          Length = 455

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 75/249 (30%), Positives = 125/249 (50%), Gaps = 30/249 (12%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E   L A  +L++++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +
Sbjct: 211 EQVGLDAKQQLISANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFS 270

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGT----TAN-----QKRLFFNLRRLKGHLQAITDNN 153
           TY+ WWI+ A+   I      ++I      T N     Q++L  +L R     +   +  
Sbjct: 271 TYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGRDPTPEEIGAEMG 330

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
           + P++V  I K   +S+ E +S+   +  +E             SQ  D++    D    
Sbjct: 331 MSPDRVREIQK---ISQ-EPVSLETPIGEEE------------DSQLGDFI---EDSTAI 371

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQ 271
              +       R  L + +  L  RER++ + R   E+  P TLE +  EF V+RER+RQ
Sbjct: 372 APPDAASDSMLREQLEQVLDGLADRERKVIKFRFGLEDGRPRTLEEVGREFGVTRERIRQ 431

Query: 272 IEARAFKKV 280
           IE++   K+
Sbjct: 432 IESKTLAKL 440


>gi|282856776|ref|ZP_06266037.1| RNA polymerase sigma factor RpoD [Pyramidobacter piscolens W5455]
 gi|282585399|gb|EFB90706.1| RNA polymerase sigma factor RpoD [Pyramidobacter piscolens W5455]
          Length = 642

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 81/278 (29%), Positives = 138/278 (49%), Gaps = 39/278 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  ++E  LA +  E GD  A  +++ ++LRLVV IA  Y G G+   ++
Sbjct: 376 YLREIGKVPLLSGEKERELAIKV-EAGDAEAKQQIIDANLRLVVSIAKKYIGRGMLFLDL 434

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-- 132
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 435 IQEGNLGLIRAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKMV 494

Query: 133 ---KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES--LN 187
              ++L   L R     +   +  ++  +V  I +   +     +S+   +  +E   L 
Sbjct: 495 RISRQLVQKLGREPSDEEIAHEMEIESGRVEEIRRIAQLP----VSLETPIGEEEDSQLG 550

Query: 188 ALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
             I   D+N    +D    +  H+  E++L                   L+ RER +   
Sbjct: 551 DFIE--DRNMPSPEDAAAGNLLHEQIEEML-----------------DALSDREREVLRY 591

Query: 246 RRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   E+    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 592 RFGLEDGRSYTLEEVGRRFGVTRERIRQIEAKALRKLR 629


>gi|149914287|ref|ZP_01902818.1| RNA polymerase sigma factor RpoD [Roseobacter sp. AzwK-3b]
 gi|149811806|gb|EDM71639.1| RNA polymerase sigma factor RpoD [Roseobacter sp. AzwK-3b]
          Length = 662

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 73/235 (31%), Positives = 119/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 424 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 483

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 484 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 538

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   + N R   
Sbjct: 539 PLEKVRKV-MKIA-KEPISLETPIGDEEDSQLGDFI---EDKNVVLPLDSAIQDNLRETT 593

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR +S L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 594 TRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 648


>gi|54401876|gb|AAV34623.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|54401880|gb|AAV34625.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|54401882|gb|AAV34626.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|54401884|gb|AAV34627.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|54401886|gb|AAV34628.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|54401888|gb|AAV34629.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 238

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 78/263 (29%), Positives = 126/263 (47%), Gaps = 34/263 (12%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           GEIG S         P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   
Sbjct: 2   GEIGYS---------PLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNR 51

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TA 130
           GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++     
Sbjct: 52  GLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV 111

Query: 131 NQKRLFFNLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
            +  ++    R   H        + I +   KP   V+   +LN     + S++  L GD
Sbjct: 112 KELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGD 168

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
                L   +D+  +  +D    D   Q  V    E    +R +L R   +L       +
Sbjct: 169 SEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------Y 222

Query: 244 EARRLQENPVTLENLSSEFEVSR 266
           EA        TLE++  E  ++R
Sbjct: 223 EA-------ATLEDVGREIGLTR 238


>gi|193884351|dbj|BAG54997.1| Sigma70 [Ralstonia solanacearum]
          Length = 758

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 67/234 (28%), Positives = 113/234 (48%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 516 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 575

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+   +   T N   P     +A+K+ +
Sbjct: 576 IRQAITRSIADQARTIRI--PVHMIETINKMNRISRQILQETGNEPDP---ATLAEKMEM 630

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++     R    E ++      D + S   D++    D       E     + R ++
Sbjct: 631 PEDKI--RKIRKIAKEPISMETPIGDDDDSHLGDFI---EDTNTLAPAEAALHGSMRGVV 685

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 686 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKL 739


>gi|86134980|ref|ZP_01053562.1| RNA polymerase sigma-70 factor [Polaribacter sp. MED152]
 gi|85821843|gb|EAQ42990.1| RNA polymerase sigma-70 factor [Polaribacter sp. MED152]
          Length = 287

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 76/288 (26%), Positives = 147/288 (51%), Gaps = 39/288 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y  EI KI ++   EE  LA + +  GD  A  +LV ++LR VV +A  Y+  GL +
Sbjct: 18  LEKYFQEIGKIDLITADEEVELALKIK-AGDQRALDKLVKANLRFVVSVAKQYQNQGLKL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV-----KIGTTA 130
           S++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + +     +V     KIG+ +
Sbjct: 77  SDLINEGNLGLVKAAKRFDETRGFKFISYAVWWIRQSIMQSLAEQSRIVRLPLNKIGSIS 136

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              +++  L +           N +    V IA +L+ +   V + + + +G        
Sbjct: 137 KINKVYSKLEQ----------RNERIPTYVEIANELDTTVRNV-AQSMKNSGRHV----- 180

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV--------LNPRERRI 242
            S D    + +D  +Y+      VL   E  +  +N++ +S+ +        L+ +E ++
Sbjct: 181 -SMDAPFREGEDSNLYN------VLKSDESPRPDKNLMKQSLDIEIDRALETLSHKEAKV 233

Query: 243 FEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +      N    +L  +   F+++RERVRQ++ RA +++Q   + +V
Sbjct: 234 IKMFFGLGNHTASSLSEIGETFDLTRERVRQVKQRAIRRLQNKSRTEV 281


>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 = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 77/265 (29%), Positives = 126/265 (47%), Gaps = 32/265 (12%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           LE+ +E   A  Y E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+
Sbjct: 358 LEELKEISRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 417

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           AV KF+  RG++ +TY+ WWI+ A+   I      ++I    +       L R+   +  
Sbjct: 418 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQ 475

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSS 198
                  PE+   +AK++++ E ++          ISM   +  DE             S
Sbjct: 476 QYGREATPEE---LAKEMDMPEDKIRKVMKIAKEPISMETPIGDDE------------DS 520

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLE 256
              D++    D   +  IE     N    +   ++ L PRE ++   R  +  N   TLE
Sbjct: 521 HLGDFI---EDTNVESPIENTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLE 577

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  +F+V+RER+RQIEA+A +K++
Sbjct: 578 EVGKQFDVTRERIRQIEAKALRKLR 602


>gi|73540591|ref|YP_295111.1| RNA polymerase sigma factor RpoD [Ralstonia eutropha JMP134]
 gi|72118004|gb|AAZ60267.1| Sigma-70 region 1.2 [Ralstonia eutropha JMP134]
          Length = 783

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 71/245 (28%), Positives = 122/245 (49%), Gaps = 17/245 (6%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           KR RE     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG
Sbjct: 539 KRARE-----AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 593

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           ++ +TY+ WWI+ A+   I      ++I    +       + R+   +   T N   P  
Sbjct: 594 YKFSTYATWWIRQAITRSIADQARTIRI--PVHMIETINKMNRISRQILQETGNEPDP-- 649

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              +A+K+ + E ++  +  ++A  E ++      D + S   D++    D       E 
Sbjct: 650 -ATLAEKMEMPEDKIRKI-MKIAK-EPISMETPIGDDDDSHLGDFI---EDTNTLAPAEA 703

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARA 276
               + R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A
Sbjct: 704 ALHGSMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKA 763

Query: 277 FKKVQ 281
            +K++
Sbjct: 764 LRKLR 768


>gi|253700182|ref|YP_003021371.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           M21]
 gi|251775032|gb|ACT17613.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           M21]
          Length = 333

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 76/286 (26%), Positives = 150/286 (52%), Gaps = 23/286 (8%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           +++ + +  +  Y+ EI+K  +L   EE  LA R  + GD +A  R++ S+LRLVVKIA 
Sbjct: 47  AVVEHFDDAIKLYLREIQKTKLLTADEEKELAARI-DLGDKAARDRMIVSNLRLVVKIAK 105

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y   GLP  +++ EGN+GL++AV++F   +  R +TY+ WWI+ +++  ++     +++
Sbjct: 106 RYINRGLPFLDLIEEGNMGLIKAVERFKLSKECRFSTYATWWIRQSIERALVNQSRTIRL 165

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
               +      N + L+   + +   N +P  +  +A  L V+ + V  +   L    S+
Sbjct: 166 PVHVSDD---IN-KMLRVTRELVQKMNREP-TIKEVADTLEVNITYVRRLMVLLKKTYSI 220

Query: 187 NALINSSDKNSSQWQDWLVYD--HDGQE---QVLIEKEERKNRRNMLTRSMSVLNPRERR 241
                  ++   +  D+ + D   D       VL+E     N+  ++++    L+  E++
Sbjct: 221 -------ERPMGENNDYFLIDTIEDTSTISPAVLLED---LNKYELVSKWFETLSDAEKK 270

Query: 242 IFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           I   R     ++P TL+ +   F V+RER+RQIEA++ +K+++ ++
Sbjct: 271 ILTLRFGLDDKDPQTLDTIGRSFGVTRERIRQIEAKSLEKLRKIVE 316


>gi|158833997|gb|ABW81804.1| RNA polymerase sigma 38 [Candidatus Regiella insecticola]
          Length = 268

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 46/108 (42%), Positives = 71/108 (65%), Gaps = 1/108 (0%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD  +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 51  YLGEIGYSPLLTAEEEVYFARRAL-CGDQQSRRRMIESNLRLVVKIARRYGNRGLALLDL 109

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++
Sbjct: 110 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRL 157


>gi|298490007|ref|YP_003720184.1| RpoD subfamily RNA polymerase sigma 70 subunit ['Nostoc azollae'
           0708]
 gi|298231925|gb|ADI63061.1| RNA polymerase, sigma 70 subunit, RpoD subfamily ['Nostoc azollae'
           0708]
          Length = 417

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 68/238 (28%), Positives = 132/238 (55%), Gaps = 13/238 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L A   ++ ++LRLVV +A  Y+  GL + ++V EG +GL +AV+KFDP +G+R +TY+ 
Sbjct: 176 LQAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAY 235

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   I  S   +++     +K     L ++K   + I+    +   +  +A +L
Sbjct: 236 WWIRQGITRAIATSSRTIRLPVHITEK-----LNKIKKAQRKISQEKGRTPTLEDLAIEL 290

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++ ++V  +  R+    SL   +   DK+ ++  + L  D    E++L+ +  +K+  +
Sbjct: 291 DMTPTQVREVLLRVPRSVSLETKVG-KDKD-TELGELLETDSITPEEMLMRESLQKDLHH 348

Query: 227 MLTRSMSVLNPRERRIFEAR-RLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +L    + L  RER +   R  L + +P +L  +    ++SRERVRQIE++A +K+++
Sbjct: 349 LL----ADLTSRERDVILMRFGLSDGHPYSLAEIGRALDLSRERVRQIESKALQKLRQ 402


>gi|327539483|gb|EGF26098.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhodopirellula
           baltica WH47]
          Length = 562

 Score = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 79/274 (28%), Positives = 142/274 (51%), Gaps = 29/274 (10%)

Query: 22  EIRKIPMLEKQEEYVLAKR------YREHGDLSAAHRLVTS-HLRLVVKIAMGYRGYGLP 74
           E+R +  L  +    L++R      YR+  D  AA R++++ +LRLVV IA  YR  GL 
Sbjct: 280 ELRSLMRLTYETPRTLSRRVDRCDTYRD--DYDAAKRVLSAGNLRLVVSIAKKYRNRGLS 337

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
             +++ EGN GLM+AV KF+  RG++ +TY+ WWI+ A+   I      +++        
Sbjct: 338 FLDLIQEGNTGLMRAVDKFEHARGYKFSTYATWWIRQAITRAIADQSRTIRVPV-----H 392

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKK--LNVSESEVISMNCR--LAGDESLNALI 190
           +   + +++   + +   + +      ++K+  L++ ++ VI    R  L+ D+ +    
Sbjct: 393 MIDTMNKIRQITRDLVQEHGREPTAEEVSKRSGLSLDDTRVILKMSRQPLSLDQPVG--- 449

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
              D + S + ++L    D    V   +E  K++ ++   +M  LN RER I   R    
Sbjct: 450 ---DHDDSVFGEFLQDHRDDDPLVETNREALKHQIDL---AMETLNYREREILRLRYGLA 503

Query: 251 N--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +    TLE +   F+V+RERVRQIE++A +K+Q+
Sbjct: 504 DGYTYTLEEVGRIFQVTRERVRQIESKAVRKLQQ 537


>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 = 98.2 bits (243), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 70/245 (28%), Positives = 118/245 (48%), Gaps = 32/245 (13%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           SA   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 507 SAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 566

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I    +       + R+    Q + +   +PE  V +A+K+ 
Sbjct: 567 WIRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGQEPEPAV-LAEKME 621

Query: 168 VSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           ++E ++          ISM   +  DE  +      D ++ +  D  +Y           
Sbjct: 622 MTEEKIRKILKISKEPISMETPIGDDEDSHLGDFIEDVSTMEPADAAIY----------- 670

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEAR 275
                  R +    +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+
Sbjct: 671 ----AGLRTVTKDVLDSLTPREAKVLRMRFGIEMNTDHTLEEVGRQFDVTRERIRQIEAK 726

Query: 276 AFKKV 280
           A +K+
Sbjct: 727 ALRKL 731


>gi|317181391|dbj|BAJ59175.1| RNA polymerase sigma factor RpoD [Helicobacter pylori F57]
          Length = 665

 Score = 97.8 bits (242), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 69/236 (29%), Positives = 120/236 (50%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ WW
Sbjct: 426 AKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWW 485

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           IK A+   I      ++I        +   + R+   ++     N K   +  +A+++ +
Sbjct: 486 IKQAISRAIADQARTIRIPI-----HMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGL 540

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  +V   N      E ++      + +  ++ D++    D      I+   R++ +  +
Sbjct: 541 SLDKV--KNVIKVTKEPISLETPVGNDDDGKFGDFV---EDKNIVSSIDHIMREDLKVQI 595

Query: 229 TRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 596 ESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 651


>gi|218245044|ref|YP_002370415.1| RNA polymerase sigma-70 subunit RpoD subfamily [Cyanothece sp. PCC
           8801]
 gi|257058068|ref|YP_003135956.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8802]
 gi|218165522|gb|ACK64259.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8801]
 gi|256588234|gb|ACU99120.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8802]
          Length = 379

 Score = 97.8 bits (242), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 128/237 (54%), Gaps = 17/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 143 AKDKMVHSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 202

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT-DNNLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++ +   KP E+ +A   ++
Sbjct: 203 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKILSQEMRRKPTEEEIATRMEM 257

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  D +  E  + +   R++  N
Sbjct: 258 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIEADGENPEDEVSKNLLREDLEN 313

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +L      L+PRER +   R   ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 314 VL----DTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLR 366


>gi|158833999|gb|ABW81805.1| RNA polymerase sigma 38 [Candidatus Regiella insecticola]
          Length = 268

 Score = 97.8 bits (242), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 46/100 (46%), Positives = 68/100 (68%), Gaps = 1/100 (1%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD  +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 51  YLGEIGYSPLLTAEEEVYFARRAL-CGDQQSRRRMIESNLRLVVKIARRYGNRGLALLDL 109

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+
Sbjct: 110 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIM 149


>gi|163868737|ref|YP_001609951.1| RNA polymerase sigma factor RpoD [Bartonella tribocorum CIP 105476]
 gi|161018398|emb|CAK01956.1| RNA polymerase sigma factor [Bartonella tribocorum CIP 105476]
          Length = 671

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V S+LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 433 AKKEMVESNLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 492

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   ++ KL++
Sbjct: 493 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQILHEIGREPTPEE---LSSKLSM 547

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D++ S   D++    D    + I+   + N R+  
Sbjct: 548 PLEKVRKV-LKIA-KEPISLETPVGDEDDSHLGDFI---EDRNALLPIDAAIQANLRDTT 602

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 603 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 657


>gi|163848723|ref|YP_001636767.1| sigma-70 family RNA polymerase sigma factor [Chloroflexus
           aurantiacus J-10-fl]
 gi|222526666|ref|YP_002571137.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus sp.
           Y-400-fl]
 gi|163670012|gb|ABY36378.1| RNA polymerase sigma factor, sigma-70 family [Chloroflexus
           aurantiacus J-10-fl]
 gi|222450545|gb|ACM54811.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus sp.
           Y-400-fl]
          Length = 360

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 88/292 (30%), Positives = 141/292 (48%), Gaps = 42/292 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRY------------------REHGDLS--------AAHR 52
           Y+ EI ++P+L  +EE  LA++Y                  RE   L         A  R
Sbjct: 67  YLQEIGQVPLLTAEEEVELARQYSRGKEARQRLRNEDFANDRERMRLEMEMARGEEARRR 126

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G  +   ++V EGNIGLM+AV+KFD  +G R +TY+ WWI+ A
Sbjct: 127 LIQANLRLVVSVAKKYIGSPMAFMDLVQEGNIGLMRAVEKFDYTKGNRFSTYATWWIRQA 186

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   I     L+++    ++     +LRR    L+   +     E+   +A  LN+S  +
Sbjct: 187 VTRAIAEQSRLIRLPVHLSES--IVHLRRAIYRLEQELEREPTAEE---LAHALNMSVRK 241

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL--IEKEERKNRRNMLTR 230
           V  +        SL   +N+        Q+  V +    E V   +E  E+K     LT 
Sbjct: 242 VKRLIRASTQPISLEQPLNNE-------QEGRVSETLADETVASPMEIAEQKMLHAELTA 294

Query: 231 SMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           +++ L  RER+I + R   +     TLE + + F ++RER RQIEA A +++
Sbjct: 295 ALNELPERERKILQLRYGLIDGQRRTLEEVGATFGITRERTRQIEAEALRRL 346


>gi|188526895|ref|YP_001909582.1| RNA polymerase sigma factor RpoD [Helicobacter pylori Shi470]
 gi|188143135|gb|ACD47552.1| RNA polymerase sigma factor RpoD [Helicobacter pylori Shi470]
          Length = 661

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 69/236 (29%), Positives = 120/236 (50%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ WW
Sbjct: 422 AKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWW 481

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           IK A+   I      ++I        +   + R+   ++     N K   +  +A+++ +
Sbjct: 482 IKQAISRAIADQARTIRIPI-----HMIDTINRINKVMRKHIQENGKEPDLEVVAEEVGL 536

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  +V   N      E ++      + +  ++ D++    D      I+   R++ +  +
Sbjct: 537 SLDKV--KNVIKVTKEPISLETPVGNDDDGKFGDFV---EDKNIVSSIDHIMREDLKVQI 591

Query: 229 TRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 592 ESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 647


>gi|218438948|ref|YP_002377277.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
 gi|218171676|gb|ACK70409.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
          Length = 376

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 128/237 (54%), Gaps = 17/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 140 AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 199

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT-DNNLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++ +   KP E+ +A   ++
Sbjct: 200 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKILSQEMRRKPTEEEIATRMEM 254

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  D +  E  + +   R++  N
Sbjct: 255 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIEADGETPEDEVSKNLLREDLEN 310

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +L      L+PRER +   R   ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 311 VL----DTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLR 363


>gi|192289891|ref|YP_001990496.1| RNA polymerase sigma factor RpoD [Rhodopseudomonas palustris TIE-1]
 gi|192283640|gb|ACF00021.1| RNA polymerase, sigma 70 subunit, RpoD family [Rhodopseudomonas
           palustris TIE-1]
          Length = 698

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 72/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 460 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 519

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 520 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLNEIGREPTPEE---LAEKLGM 574

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E L+      D+  S   D++    D    + I+   + N R   
Sbjct: 575 PLEKVRKV-LKIA-KEPLSLETPVGDEEDSHLGDFI---EDKNAVLPIDAAIQSNLRETT 629

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 630 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 684


>gi|114764808|ref|ZP_01443990.1| RNA polymerase sigma factor [Pelagibaca bermudensis HTCC2601]
 gi|114542694|gb|EAU45717.1| RNA polymerase sigma factor [Roseovarius sp. HTCC2601]
          Length = 661

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 72/235 (30%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 423 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 482

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 483 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 537

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   ++N +   
Sbjct: 538 PLEKVRKV-MKIA-KEPISLETPIGDEEDSQLGDFI---EDKNAILPLDSAIQENLKETT 592

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR +S L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 593 TRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 647


>gi|318042101|ref|ZP_07974057.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CB0101]
          Length = 309

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 84/300 (28%), Positives = 142/300 (47%), Gaps = 46/300 (15%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------AA 50
           G   +S Y+  I ++P+L   EE  L  + +    L+                     + 
Sbjct: 16  GSDPISWYLSTIGRVPLLTPAEEIELGNQVQAMMRLTEEEPENGYTDQQKKTIRVGRRSK 75

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            R++ ++LRLVV +A  Y+G GL + +++ EG++GL +AV+KFDP RG++ +TY+ WWI+
Sbjct: 76  ERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWWIR 135

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA-------IA 163
            +M   I            A Q R       L   L AI   +L     +        IA
Sbjct: 136 QSMTRAI------------ACQSRTIRLPVHLSERLTAIRKVSLDLAHKLGAMPSRKEIA 183

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + +++   E+ S+  +     SL+A +N  +  S  +   L+ D+   E   +++ ER  
Sbjct: 184 EAMDMPIDELDSLLRQALTTSSLDAPVNGEEGRS--FLGDLIADNSHVEP--LDQVERGM 239

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
               L R +S L  +ER++ E R   E     TL  +    +VSRERVRQ+E +A +K++
Sbjct: 240 HHEQLGRWLSHLTEQERQVLELRFGLEGEERHTLAEIGRMLDVSRERVRQVELKALRKLR 299


>gi|313112817|ref|ZP_07798464.1| putative RNA polymerase sigma factor RpoD [Faecalibacterium cf.
           prausnitzii KLE1255]
 gi|310624887|gb|EFQ08195.1| putative RNA polymerase sigma factor RpoD [Faecalibacterium cf.
           prausnitzii KLE1255]
          Length = 458

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 75/242 (30%), Positives = 122/242 (50%), Gaps = 22/242 (9%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L+A   L  ++LRLVV IA  + G+ L   +++ EGNIGL++A +KFD +RGFR +TY+ 
Sbjct: 219 LNARRSLSEANLRLVVSIAKKHVGHNLAFLDLIQEGNIGLIKAAEKFDCDRGFRFSTYAT 278

Query: 107 WWIKAAMQEYILRSWSLVKIGT----TANQKRLFFN-LRRLKGHLQAITDNNLKPEQVVA 161
           WWI+ A+   I      ++I      T N+ R   N L    GH          PE+   
Sbjct: 279 WWIRQAITRAIADQARTIRIPVHMVETINRMRQATNQLVYQNGH-------EPTPEE--- 328

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           +AK +++S   V  +        SL + +   ++  S   D++    D   +   +  +R
Sbjct: 329 LAKAMDMSVERVREIQRMAQEPASLESPV--GEEEDSSLGDFVA---DENAEAPGKAADR 383

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKK 279
                 +  ++  L PRE ++   R   ++  P TLE +  +F V+RERVRQIEA+A +K
Sbjct: 384 AMVAQQINLALKSLTPREEKVIRLRFGLDDGRPRTLEEVGRDFGVTRERVRQIEAKAIRK 443

Query: 280 VQ 281
           + 
Sbjct: 444 LH 445


>gi|296161690|ref|ZP_06844493.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. Ch1-1]
 gi|295888004|gb|EFG67819.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. Ch1-1]
          Length = 628

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 68/235 (28%), Positives = 127/235 (54%), Gaps = 16/235 (6%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ ++LRLVV +A  Y   G+P+ ++V EGNIGLM+AV +F+  RGF+ +TY+ WWI+ +
Sbjct: 394 MIEANLRLVVSVAKKYVQSGMPLLDLVQEGNIGLMKAVDRFEYRRGFKFSTYATWWIRQS 453

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   I      +++    +       ++R+ G ++  T    +  +   +A +L +SE +
Sbjct: 454 VSRAIADYGRTIRV--PVHMADAMHRVKRVAGEMRQETGRQARSSE---LAARLGMSEEK 508

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           V S+        SL+  I   D +++  +  +V D        ++   + + R  +  ++
Sbjct: 509 VRSVQRVTRQPVSLDVPIG-EDADTTLGE--MVEDPSALAP--LDALLQADLRVAIDAAL 563

Query: 233 SVLNPRERRI----FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            VL PRE ++    F    + E+  TLE L  +F+V+RERVRQI+ +A +K++ S
Sbjct: 564 GVLTPREAKVIKLRFGVDAVSEH--TLEELGDQFDVTRERVRQIQNKALQKLRHS 616


>gi|254821650|ref|ZP_05226651.1| RNA polymerase sigma factor [Mycobacterium intracellulare ATCC
           13950]
          Length = 488

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 83/318 (26%), Positives = 151/318 (47%), Gaps = 43/318 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGD-LS 48
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E GD L 
Sbjct: 176 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTEMTERGDKLP 234

Query: 49  AAHR----------------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           AA R                L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 235 AAQRRDMQWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 294

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L      
Sbjct: 295 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGR 352

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D + 
Sbjct: 353 EPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEA 404

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVR 270
            V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 405 VVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIR 464

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 465 QIESKTMSKLRHPSRSQV 482


>gi|32474487|ref|NP_867481.1| transcription initiation factor sigma 70 [Rhodopirellula baltica SH
           1]
 gi|32445025|emb|CAD75027.1| transcription initiation factor sigma 70 [Rhodopirellula baltica SH
           1]
          Length = 568

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 79/274 (28%), Positives = 142/274 (51%), Gaps = 29/274 (10%)

Query: 22  EIRKIPMLEKQEEYVLAKR------YREHGDLSAAHRLVTS-HLRLVVKIAMGYRGYGLP 74
           E+R +  L  +    L++R      YR+  D  AA R++++ +LRLVV IA  YR  GL 
Sbjct: 286 ELRSLMRLTYETPRTLSRRVDRCDTYRD--DYDAAKRVLSAGNLRLVVSIAKKYRNRGLS 343

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
             +++ EGN GLM+AV KF+  RG++ +TY+ WWI+ A+   I      +++        
Sbjct: 344 FLDLIQEGNTGLMRAVDKFEHARGYKFSTYATWWIRQAITRAIADQSRTIRVPV-----H 398

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKK--LNVSESEVISMNCR--LAGDESLNALI 190
           +   + +++   + +   + +      ++K+  L++ ++ VI    R  L+ D+ +    
Sbjct: 399 MIDTMNKIRQITRDLVQEHGREPTAEEVSKRSGLSLDDTRVILKMSRQPLSLDQPVG--- 455

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
              D + S + ++L    D    V   +E  K++ ++   +M  LN RER I   R    
Sbjct: 456 ---DHDDSVFGEFLQDHRDDDPLVETNREALKHQIDL---AMETLNYREREILRLRYGLA 509

Query: 251 N--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +    TLE +   F+V+RERVRQIE++A +K+Q+
Sbjct: 510 DGYTYTLEEVGRIFQVTRERVRQIESKAVRKLQQ 543


>gi|37519772|ref|NP_923149.1| group 2 sigma 70-type sigma factor [Gloeobacter violaceus PCC 7421]
 gi|35210763|dbj|BAC88144.1| group 2 sigma 70-type sigma factor [Gloeobacter violaceus PCC 7421]
          Length = 356

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 83/278 (29%), Positives = 140/278 (50%), Gaps = 35/278 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGY 71
           +GL  Y+ EI +IP+L+ +EE +LA+   + G     A  +LV ++LRLVV IA  Y   
Sbjct: 82  VGL--YLQEIGRIPLLKPEEEVMLARAIAQGGPKGEWAKRKLVQANLRLVVSIAKKYLNR 139

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           G+P  +++ EG++GL++A +KF+ ERG++ +TY+ WWI+ A+   +      V++     
Sbjct: 140 GVPFLDLIQEGSMGLIRAAEKFEHERGYKFSTYAYWWIRQAITRAVASQARTVRLPVHLV 199

Query: 132 Q-----KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES- 185
           +     K++   L +  G   +  +     E      + +  +    +S+N  +  +E  
Sbjct: 200 EKINRVKKVRRTLAQELGRTPSQGELAEALELAEEDLEHILRAARRTVSLNITVGKEEDT 259

Query: 186 -LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERRI- 242
            L  LI  S  +              Q  V I++E  R    ++L R    L PRER I 
Sbjct: 260 ELIHLIEDSQTD--------------QPDVHIDRESMRVEVSDLLDRH---LTPRERDIL 302

Query: 243 ---FEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
              F  R  Q+   TL+ +   F++SRER+RQI+A+AF
Sbjct: 303 QLRFGLRDGQQR--TLDQVGRMFDLSRERIRQIQAKAF 338


>gi|296125976|ref|YP_003633228.1| RNA polymerase, sigma 32 subunit, RpoH [Brachyspira murdochii DSM
           12563]
 gi|296017792|gb|ADG71029.1| RNA polymerase, sigma 32 subunit, RpoH [Brachyspira murdochii DSM
           12563]
          Length = 285

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 76/279 (27%), Positives = 143/279 (51%), Gaps = 35/279 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +S Y  + +K  +L ++EE  L KR +E GD  A  +L+ S+LR V+ IA  Y+  GL +
Sbjct: 17  ISLYFADAKKEKLLTREEEIELTKRLKE-GDAEARSKLIRSNLRFVITIAKQYKNSGLLL 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++SEGN+GL+ A  +FDP++G+   +Y+++WI+ ++   I     L+++    N+   
Sbjct: 76  EDLISEGNMGLIIAADRFDPDKGYHFISYAVYWIRQSILRAINEKSRLIRL--PLNKAMD 133

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
             +L R     Q    +   P+ V  +A  LN   +++            L+ +  S++ 
Sbjct: 134 LVDLERTVH--QYYYKSGYTPD-VNELAAILNKDPNDI------------LHIMSMSTEH 178

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM------------LTRSMSVLNPRERRIF 243
            S + +    Y++DG +  LI+  E K  +N+            L  ++  L+  E++I 
Sbjct: 179 ISLEGE----YNYDGMKDRLIDTIEDKTSKNVEETAINKELMEELKTAIESLSDIEKQII 234

Query: 244 EARR-LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            AR  + +   TL+ +   F  ++ER+RQIE +A +K+ 
Sbjct: 235 NARYGIDQERKTLKEVGEMFSFTKERIRQIEKKALRKMH 273


>gi|4100836|gb|AAD01000.1| RpoS [Escherichia coli]
          Length = 259

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 45/108 (41%), Positives = 72/108 (66%), Gaps = 2/108 (1%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +E Y   +  R  GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 39  YLGEIGYSPLLTAEEVYFARRALR--GDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 96

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++
Sbjct: 97  IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRL 144


>gi|254469018|ref|ZP_05082424.1| sigma 70 [beta proteobacterium KB13]
 gi|207087828|gb|EDZ65111.1| sigma 70 [beta proteobacterium KB13]
          Length = 658

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 69/245 (28%), Positives = 115/245 (46%), Gaps = 32/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 418 AKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 477

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+   +   T    +P     +A+K+ +
Sbjct: 478 IRQAITRSIADQARTIRI--PVHMIETINKMNRISRQILQATGQEPEP---AVLAEKMEM 532

Query: 169 SESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            E ++          ISM   +  DE  +      D  +    D  VY            
Sbjct: 533 PEDKIRKILKISKEPISMETPIGDDEDSHLGDFIEDLGTLTPDDAAVY------------ 580

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARA 276
               + RN+    +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A
Sbjct: 581 ---SSLRNVTNEILEGLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKA 637

Query: 277 FKKVQ 281
            +K++
Sbjct: 638 LRKLR 642


>gi|39934363|ref|NP_946639.1| RNA polymerase sigma factor RpoD [Rhodopseudomonas palustris
           CGA009]
 gi|39648212|emb|CAE26731.1| RNA polymerase sigma 70 subunit, RpoD [Rhodopseudomonas palustris
           CGA009]
          Length = 698

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 72/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 460 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 519

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 520 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLNEIGREPTPEE---LAEKLGM 574

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E L+      D+  S   D++    D    + I+   + N R   
Sbjct: 575 PLEKVRKV-LKIA-KEPLSLETPVGDEEDSHLGDFI---EDKNAVLPIDAAIQSNLRETT 629

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 630 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 684


>gi|91978433|ref|YP_571092.1| RNA polymerase sigma factor RpoD [Rhodopseudomonas palustris BisB5]
 gi|91684889|gb|ABE41191.1| RNA polymerase sigma factor RpoD-like [Rhodopseudomonas palustris
           BisB5]
          Length = 711

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 72/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 473 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 532

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 533 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLNEIGREPTPEE---LAEKLGM 587

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E L+      D+  S   D++    D    + I+   + N R   
Sbjct: 588 PLEKVRKV-LKIA-KEPLSLETPVGDEEDSHLGDFI---EDKNAVLPIDAAIQSNLRETT 642

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 643 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 697


>gi|158833995|gb|ABW81803.1| RNA polymerase sigma 38 [Candidatus Regiella insecticola]
          Length = 268

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 46/108 (42%), Positives = 71/108 (65%), Gaps = 1/108 (0%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD  +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 51  YLGEIGYSPLLTAEEEVYFARRAL-CGDQQSRRRMIESNLRLVVKIARRYGNRGLALLDL 109

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++
Sbjct: 110 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRL 157


>gi|257784627|ref|YP_003179844.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Atopobium
           parvulum DSM 20469]
 gi|257473134|gb|ACV51253.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Atopobium
           parvulum DSM 20469]
          Length = 455

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 73/246 (29%), Positives = 125/246 (50%), Gaps = 30/246 (12%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L A  +L++++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ 
Sbjct: 215 LDAKQQLISANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYAT 274

Query: 107 WWIKAAMQEYILRSWSLVKIGT----TAN-----QKRLFFNLRRLKGHLQAITDNNLKPE 157
           WWI+ A+   I      ++I      T N     Q++L  +  R     +  ++  + P+
Sbjct: 275 WWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDFGRDPTPEEIGSEMGMSPD 334

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           +V  I K   +S+ E +S+   +  +E             SQ  D++    D       +
Sbjct: 335 RVREIQK---ISQ-EPVSLETPIGEEE------------DSQLGDFI---EDSTAVAPPD 375

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
                  R  L + +  L  RER++ + R   E+  P TLE +  EF V+RER+RQIE++
Sbjct: 376 AASDSMLREQLEQVLDSLADRERKVIKFRFGLEDGHPRTLEEVGKEFGVTRERIRQIESK 435

Query: 276 AFKKVQ 281
              K++
Sbjct: 436 TLAKLR 441


>gi|163747450|ref|ZP_02154802.1| RNA polymerase sigma factor RpoD [Oceanibulbus indolifex HEL-45]
 gi|161379303|gb|EDQ03720.1| RNA polymerase sigma factor RpoD [Oceanibulbus indolifex HEL-45]
          Length = 671

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 72/235 (30%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 433 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 492

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 493 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 547

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   ++N +   
Sbjct: 548 PLEKVRKV-MKIAK-EPISLETPIGDEEDSQLGDFI---EDKNAVLPLDSAIQENLKETT 602

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR +S L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 603 TRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 657


>gi|221636011|ref|YP_002523887.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Thermomicrobium roseum DSM 5159]
 gi|221157983|gb|ACM07101.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Thermomicrobium roseum DSM 5159]
          Length = 334

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 118/237 (49%), Gaps = 12/237 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L+  +LRLVV IA  YR   LP+ +++ EGNIGLM AV+++DPE G+R +TY+ +W
Sbjct: 99  AREKLIRHNLRLVVSIAKRYRSSELPLIDLIQEGNIGLMTAVERYDPELGYRFSTYATFW 158

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   +      +++    +   L   +RR +     I     +P     +A+ L +
Sbjct: 159 IRQAIGRAVANLSRTIRV--PVHMHDLIAKIRRAEAQ---IEQQKGRPATNEELAELLGI 213

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
             + +     ++    SL+  I   +   S   D L    D +   ++E+      R  +
Sbjct: 214 DVARIEQARTQIPRTSSLDKPIG--EDGESSIGDLL---PDPRSDDVVEEALTNAIREQI 268

Query: 229 TRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            RS+  L  RER +   R     E P TL  ++   ++SRERVRQ+E  A +K++ S
Sbjct: 269 RRSLEQLTERERTVLVMRFGLDGEQPRTLAEIADALKISRERVRQVEKEALQKLRNS 325


>gi|189424079|ref|YP_001951256.1| RNA polymerase, sigma 70 subunit, RpoD family [Geobacter lovleyi
           SZ]
 gi|189420338|gb|ACD94736.1| RNA polymerase, sigma 70 subunit, RpoD family [Geobacter lovleyi
           SZ]
          Length = 586

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 74/247 (29%), Positives = 128/247 (51%), Gaps = 14/247 (5%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A R  EH    A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +R
Sbjct: 338 AIREGEHKARIAKSELIEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQR 397

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL-KGHLQAITDNNLKP 156
           G++ +TY+ WWI+ A+   I      ++I        +   + +L +   Q + +N  +P
Sbjct: 398 GYKFSTYATWWIRQAITRAIADQARTIRIPV-----HMIETINKLIRTSRQLVQENGREP 452

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
                IA ++ +   +V  +  ++A  E ++      ++  S   D++    D      +
Sbjct: 453 SP-EEIADRMQLPLDKVRKV-LKIAK-EPISLETPIGEEEDSHLGDFI---EDKGVVNPL 506

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEA 274
           E   + N     +R +S L PRE ++   R    +++  TLE +  +FEV+RER+RQIEA
Sbjct: 507 EAVIKANLSEQTSRVLSTLTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEA 566

Query: 275 RAFKKVQ 281
           +A +K++
Sbjct: 567 KALRKLR 573


>gi|28899327|ref|NP_798932.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus RIMD
           2210633]
 gi|28807551|dbj|BAC60816.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus RIMD
           2210633]
          Length = 319

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 78/251 (31%), Positives = 129/251 (51%), Gaps = 31/251 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 57  YLGEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 115

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 116 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-VKELNIY 174

Query: 139 LRRLKGHLQAITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALI 190
           LR  +   Q + D+    E++ A        ++K L ++E  + S++  + GD     L 
Sbjct: 175 LRTARELSQKL-DHEPTAEEIAAQLDIPVEDVSKMLRLNE-RISSVDTPIGGDGEKALLD 232

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--- 247
              D N+S   D  V   D             + ++ L   +  LNP+++ +  ARR   
Sbjct: 233 IIPDANNS---DPEVSTQD------------DDIKSSLIHWLEELNPKQKEVL-ARRFGL 276

Query: 248 LQENPVTLENL 258
           L   P TLE +
Sbjct: 277 LGYEPSTLEEV 287


>gi|316935466|ref|YP_004110448.1| RpoD subfamily RNA polymerase sigma 70 subunit [Rhodopseudomonas
           palustris DX-1]
 gi|315603180|gb|ADU45715.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhodopseudomonas
           palustris DX-1]
          Length = 698

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 72/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 460 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 519

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 520 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLNEIGREPTPEE---LAEKLGM 574

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E L+      D+  S   D++    D    + I+   + N R   
Sbjct: 575 PLEKVRKV-LKIAK-EPLSLETPVGDEEDSHLGDFI---EDKNAVLPIDAAIQSNLRETT 629

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 630 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 684


>gi|322421611|ref|YP_004200834.1| RpoD subfamily RNA polymerase sigma-70 factor [Geobacter sp. M18]
 gi|320127998|gb|ADW15558.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           M18]
          Length = 583

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 81/259 (31%), Positives = 128/259 (49%), Gaps = 36/259 (13%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           +LA    EH    A   LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ 
Sbjct: 333 LLAIEEGEHKAKLAKSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 392

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITD 151
           +RG++ +TY+ WWI+ A+   I      ++I      T N  +L    R+L   +Q I  
Sbjct: 393 QRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETIN--KLIRTSRQL---VQEIG- 446

Query: 152 NNLKPEQVV--------AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
               PE++          + K L +++ E IS+   +  +E             S   D+
Sbjct: 447 REPSPEEIAERMALPLDKVRKVLKIAK-EPISLETPIGEEE------------DSHLGDF 493

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSE 261
           +    D      +E   + N     +R +S L PRE ++   R    +++  TLE +  +
Sbjct: 494 I---EDKGVVSPLEAVIKANLSEQTSRVLSTLTPREEKVLRMRFGIGEKSDHTLEEVGQD 550

Query: 262 FEVSRERVRQIEARAFKKV 280
           FEV+RER+RQIEA+A +K+
Sbjct: 551 FEVTRERIRQIEAKALRKL 569


>gi|240850913|ref|YP_002972313.1| RNA polymerase sigma factor RpoD [Bartonella grahamii as4aup]
 gi|240268036|gb|ACS51624.1| RNA polymerase sigma factor RpoD [Bartonella grahamii as4aup]
          Length = 671

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V S+LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 433 AKKEMVESNLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 492

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   ++ KL++
Sbjct: 493 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQILHEIGREPTPEE---LSSKLSM 547

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D++ S   D++    D    + I+   + N R+  
Sbjct: 548 PLEKVRKV-LKIA-KEPISLETPVGDEDDSHLGDFI---EDRNALLPIDAAIQANLRDTT 602

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 603 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 657


>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 = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 119/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 434 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 493

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 494 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLTM 548

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R+  
Sbjct: 549 PLEKVRKV-LKIAK-EPISLETPVGDEEDSHLGDFI---EDKNALLPIDAAIQANLRDTT 603

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 604 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 658


>gi|145224520|ref|YP_001135198.1| RNA polymerase sigma factor [Mycobacterium gilvum PYR-GCK]
 gi|315444851|ref|YP_004077730.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Mycobacterium sp. Spyr1]
 gi|145217006|gb|ABP46410.1| RNA polymerase, sigma 70 subunit, RpoD family [Mycobacterium gilvum
           PYR-GCK]
 gi|315263154|gb|ADT99895.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Mycobacterium sp. Spyr1]
          Length = 488

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 81/318 (25%), Positives = 152/318 (47%), Gaps = 43/318 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-------------YREHGD-LS 48
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR             + E G+ L+
Sbjct: 176 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYCTQLMAEFAEKGEKLT 234

Query: 49  AAHR----------------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
            A R                L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 235 TAQRRDYMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 294

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L      
Sbjct: 295 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGR 352

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D + 
Sbjct: 353 EPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEA 404

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVR 270
            V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 405 VVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIR 464

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 465 QIESKTMSKLRHPSRSQV 482


>gi|49475878|ref|YP_033919.1| RNA polymerase sigma factor RpoD [Bartonella henselae str.
           Houston-1]
 gi|49238686|emb|CAF27936.1| RNA polymerase sigma factor rpod [Bartonella henselae str.
           Houston-1]
          Length = 667

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 121/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 429 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 488

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +      +  PE+   ++ KL++
Sbjct: 489 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQILHEIGRDPTPEE---LSSKLSM 543

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D++ S   D++    D    + I+   + N R+  
Sbjct: 544 PLEKVRKV-LKIA-KEPISLETPVGDEDDSHLGDFI---EDRNALLPIDAAIQANLRDTT 598

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 599 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 653


>gi|86751238|ref|YP_487734.1| RNA polymerase sigma factor RpoD [Rhodopseudomonas palustris HaA2]
 gi|86574266|gb|ABD08823.1| sigma 70 (RpoD) [Rhodopseudomonas palustris HaA2]
          Length = 714

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 72/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 476 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 535

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 536 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLNEIGREPTPEE---LAEKLGM 590

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E L+      D+  S   D++    D    + I+   + N R   
Sbjct: 591 PLEKVRKV-LKIA-KEPLSLETPVGDEEDSHLGDFI---EDKNAVLPIDAAIQSNLRETT 645

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 646 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 700


>gi|115523078|ref|YP_779989.1| RNA polymerase sigma factor RpoD [Rhodopseudomonas palustris
           BisA53]
 gi|115517025|gb|ABJ05009.1| RNA polymerase, sigma 70 subunit, RpoD [Rhodopseudomonas palustris
           BisA53]
          Length = 704

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 72/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 466 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 525

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 526 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLNEIGREPTPEE---LAEKLGM 580

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E L+      D+  S   D++    D    + I+   + N R   
Sbjct: 581 PLEKVRKV-LKIAK-EPLSLETPVGDEEDSHLGDFI---EDKNAVLPIDAAIQSNLRETT 635

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 636 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 690


>gi|222053802|ref|YP_002536164.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           FRC-32]
 gi|221563091|gb|ACM19063.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           FRC-32]
          Length = 586

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 80/246 (32%), Positives = 131/246 (53%), Gaps = 22/246 (8%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           EH    A   LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +
Sbjct: 343 EHKAKLAKSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFS 402

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           TY+ WWI+ A+   I      ++I      T N  +L    R+L   +Q I      PE+
Sbjct: 403 TYATWWIRQAITRAIADQARTIRIPVHMIETIN--KLIRTSRQL---VQEIG-REPSPEE 456

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
              IA+++++   +V  +  ++A +  SL   I   ++  S   D++    D      +E
Sbjct: 457 ---IAERMSLPLDKVRKV-LKIAKEPISLETPIG--EEEDSHLGDFI---EDKGVVSPLE 507

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              + N     +R +S L PRE ++   R    +++  TLE +  +FEV+RER+RQIEA+
Sbjct: 508 AVIKANLSEQTSRVLSTLTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAK 567

Query: 276 AFKKVQ 281
           A +K++
Sbjct: 568 ALRKLR 573


>gi|87125501|ref|ZP_01081346.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9917]
 gi|86166801|gb|EAQ68063.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9917]
          Length = 312

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 83/293 (28%), Positives = 145/293 (49%), Gaps = 36/293 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAK------RYREHGDLSAAH------------------ 51
           +S Y+  I +IP+L   EE  L        R  E G L+  H                  
Sbjct: 20  ISWYLATIGRIPLLTPAEEIELGNQVQEMMRLTEDGTLAPDHDGFSSHDRRMIRVGKRAK 79

Query: 52  -RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            R++ ++LRLVV +A  Y+G GL + +++ EG++GL +AV+KFDP RG++ +TY+ WWI+
Sbjct: 80  ERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWWIR 139

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            +M   I      +++    +++     +R++   L         P + V IA+ +++  
Sbjct: 140 QSMTRAIACQSRTIRLPVHLSER--LTTIRKVS--LDLAHKLGAMPSR-VEIAEAMDMPL 194

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            E+ ++  +     SL+A +N  +  S  +   L+ D    E   ++K E+      L R
Sbjct: 195 DELDALLRQALTTSSLDAPVNGEEGRS--FLGDLIADTSHDEP--LDKVEQSIHHEQLGR 250

Query: 231 SMSVLNPRERRIFEAR-RLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +S L+ +E+ +   R  L  N   TL  +    EVSRERVRQ+E +A +K++
Sbjct: 251 WLSHLSEQEQYVLGLRFGLNGNERHTLAEIGRLMEVSRERVRQVELKALRKLR 303


>gi|254424926|ref|ZP_05038644.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
 gi|196192415|gb|EDX87379.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
          Length = 404

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 128/237 (54%), Gaps = 17/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 168 AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 227

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++     KP E+ +A   ++
Sbjct: 228 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKLLSQELGRKPTEEEIATRMEM 282

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  D +  E  + +   R++  +
Sbjct: 283 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIESDGETPEDEVSKSLLREDLES 338

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +L    S L+PRER +   R   ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 339 VL----STLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLR 391


>gi|197120055|ref|YP_002140482.1| RNA polymerase sigma-70 factor RpoD [Geobacter bemidjiensis Bem]
 gi|197089415|gb|ACH40686.1| RNA polymerase sigma-70 factor RpoD [Geobacter bemidjiensis Bem]
          Length = 584

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 81/260 (31%), Positives = 129/260 (49%), Gaps = 36/260 (13%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           +LA    EH    A   LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ 
Sbjct: 334 LLAIEEGEHKAKLAKSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 393

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITD 151
           +RG++ +TY+ WWI+ A+   I      ++I      T N  +L    R+L   +Q I  
Sbjct: 394 QRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETIN--KLIRTSRQL---VQEIG- 447

Query: 152 NNLKPEQVV--------AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
               PE++          + K L +++ E IS+   +  +E             S   D+
Sbjct: 448 REPSPEEIAERMALPLDKVRKVLKIAK-EPISLETPIGEEE------------DSHLGDF 494

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSE 261
           +    D      +E   + N     +R +S L PRE ++   R    +++  TLE +  +
Sbjct: 495 I---EDKGVVSPLEAVIKANLSEQTSRVLSTLTPREEKVLRMRFGIGEKSDHTLEEVGQD 551

Query: 262 FEVSRERVRQIEARAFKKVQ 281
           FEV+RER+RQIEA+A +K++
Sbjct: 552 FEVTRERIRQIEAKALRKLR 571


>gi|253702377|ref|YP_003023566.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           M21]
 gi|251777227|gb|ACT19808.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           M21]
          Length = 584

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 81/259 (31%), Positives = 128/259 (49%), Gaps = 36/259 (13%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           +LA    EH    A   LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ 
Sbjct: 334 LLAIEEGEHKAKLAKSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEY 393

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITD 151
           +RG++ +TY+ WWI+ A+   I      ++I      T N  +L    R+L   +Q I  
Sbjct: 394 QRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETIN--KLIRTSRQL---VQEI-G 447

Query: 152 NNLKPEQVV--------AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
               PE++          + K L +++ E IS+   +  +E             S   D+
Sbjct: 448 REPSPEEIAERMALPLDKVRKVLKIAK-EPISLETPIGEEE------------DSHLGDF 494

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSE 261
           +    D      +E   + N     +R +S L PRE ++   R    +++  TLE +  +
Sbjct: 495 I---EDKGVVSPLEAVIKANLSEQTSRVLSTLTPREEKVLRMRFGIGEKSDHTLEEVGQD 551

Query: 262 FEVSRERVRQIEARAFKKV 280
           FEV+RER+RQIEA+A +K+
Sbjct: 552 FEVTRERIRQIEAKALRKL 570


>gi|260911629|ref|ZP_05918210.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella sp. oral
           taxon 472 str. F0295]
 gi|260634235|gb|EEX52344.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella sp. oral
           taxon 472 str. F0295]
          Length = 290

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 76/272 (27%), Positives = 135/272 (49%), Gaps = 14/272 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           L +Y+ EI + P++   EE  LA++ R+ G     A  +LVT++LR VV +A  Y+  GL
Sbjct: 18  LDKYLVEIGRAPLISIDEEIELAQKIRKGGPEGEKAKDKLVTANLRFVVSVAKQYQHQGL 77

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V++    NQ 
Sbjct: 78  TLTDLIDEGNIGLIKAAQKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRL--PLNQ- 134

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINS 192
               +L ++   +      N +   V  ++   N+ E E I  +    G   S++A    
Sbjct: 135 --VGSLNKINHEINKFEQENQRHPSVSELSDATNLDE-EKIGQSLMADGHHVSIDAPFQD 191

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF-EARRLQEN 251
            + N     D +    D +     + E      N +     VL  RE  I  E   +  +
Sbjct: 192 GEDNC--MLDVMASGDDSRTDKQADHESMALELNSVL--AKVLKDREITIIRECFGIGCH 247

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
              LE +  +  ++RERVRQI  ++  K+++S
Sbjct: 248 EKGLEEIGDQLGLTRERVRQIREKSIAKLRDS 279


>gi|300023333|ref|YP_003755944.1| RNA polymerase, sigma 70 subunit, RpoD [Hyphomicrobium
           denitrificans ATCC 51888]
 gi|299525154|gb|ADJ23623.1| RNA polymerase, sigma 70 subunit, RpoD [Hyphomicrobium
           denitrificans ATCC 51888]
          Length = 666

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 72/235 (30%), Positives = 119/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 428 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 487

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 488 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 542

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + IE   + N R+  
Sbjct: 543 PLEKVRKV-LKIA-KEPISLETPIGDEEDSHLGDFI---EDRNAVLPIEAAIQSNLRDTT 597

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 598 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 652


>gi|254461643|ref|ZP_05075059.1| RNA polymerase sigma-70 factor RpoD [Rhodobacterales bacterium
           HTCC2083]
 gi|206678232|gb|EDZ42719.1| RNA polymerase sigma-70 factor RpoD [Rhodobacteraceae bacterium
           HTCC2083]
          Length = 660

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 76/250 (30%), Positives = 122/250 (48%), Gaps = 42/250 (16%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 422 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 481

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRR------LKGHLQAITDNN 153
           I+ A+   I      ++I      T N+     +++   + R      L   LQ   +  
Sbjct: 482 IRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEIGREPTPEELAAKLQMPLE-- 539

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            K  +V+ IAK       E IS+   +             D+  SQ  D++    D    
Sbjct: 540 -KVRKVMKIAK-------EPISLETPIG------------DEEDSQLGDFI---EDKNAV 576

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQ 271
           + ++   ++N +   TR +S L PRE R+   R         TLE +  +F V+RER+RQ
Sbjct: 577 LPLDSAIQENLKETTTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQ 636

Query: 272 IEARAFKKVQ 281
           IEA+A +K++
Sbjct: 637 IEAKALRKLK 646


>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 = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 73/246 (29%), Positives = 119/246 (48%), Gaps = 36/246 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A H +  ++LRLV+ IA  Y   G+   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 416 AKHEMTQANLRLVISIAKKYTNRGMQFLDLIQEGNIGLMKAVDKFEYRRGWKFSTYATWW 475

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           ++ A+   I      +++     ++     L RL   +   T     P     +A++L++
Sbjct: 476 VRQAVTRAIADQARTIRVPVHMIEQ--INKLNRLSREIMQQTGKEPDP---AVLAERLDM 530

Query: 169 SESEV----------ISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           +E +V          +SM   +   GD SL  +I  SD  +           D   Q  +
Sbjct: 531 TEDKVRSIMKIAKEPVSMETPVGEDGDTSLGDMIADSDTATP---------ADAALQAGL 581

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEA 274
               R   R ML      L+PRE ++   R         TLE +  +F+V+RER+RQIE+
Sbjct: 582 ----RAVVREMLDE----LSPREAKVLRMRFGIDMSTDYTLEEVGKQFDVTRERIRQIES 633

Query: 275 RAFKKV 280
           +A KK+
Sbjct: 634 KAMKKL 639


>gi|146338438|ref|YP_001203486.1| RNA polymerase sigma factor RpoD [Bradyrhizobium sp. ORS278]
 gi|146191244|emb|CAL75249.1| sigma D (sigma 70) factor of RNA polymerase [Bradyrhizobium sp.
           ORS278]
          Length = 703

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 72/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 465 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 524

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 525 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLNEIGREPTPEE---LAEKLGM 579

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E L+      D+  S   D++    D    + I+   + N R   
Sbjct: 580 PLEKVRKV-LKIA-KEPLSLETPVGDEEDSHLGDFI---EDKNAILPIDAAIQSNLRETT 634

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 635 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 689


>gi|296161119|ref|ZP_06843929.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. Ch1-1]
 gi|295888642|gb|EFG68450.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. Ch1-1]
          Length = 705

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 77/279 (27%), Positives = 141/279 (50%), Gaps = 32/279 (11%)

Query: 24  RKIPMLEKQEEYVLAKRYR------------------EHGDLSAAHRLVTSHLRLVVKIA 65
           R +P ++ ++E +LA + R                  E   L A   ++ ++LRLV+ IA
Sbjct: 423 RNLPAIDLEQEKLLALQQRVVLPLDEFREVCRALSASEAKTLRAKGEMIEANLRLVISIA 482

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++
Sbjct: 483 KRYTNRGLLFLDLIQEGNIGLMRAVDKFEYRRGYKFSTYATWWIRQAVSRSIADQARTIR 542

Query: 126 IGTTANQKRLFFNLRRLKG-HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +        +  +L +LK    Q + +   +P+  + +A+++ + E +V +M   +    
Sbjct: 543 VPV-----HMIESLNKLKRISRQILQETGSEPDAAL-LAQRMEMQEQKVRAMLRIVREPV 596

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL+A +  +D  S    D +    D    +  +     + R+ ++ ++  L PRE +I  
Sbjct: 597 SLDASVGENDDTS--IGDLI---EDSTAILPDDAALHASMRDAISEALMTLTPREAKILR 651

Query: 245 ARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R   E+    TLE L  +FE++RER+RQIE +A +K++
Sbjct: 652 LRFGIESGRDHTLEELGEQFELTRERIRQIEVKALRKLR 690


>gi|126730240|ref|ZP_01746051.1| RNA polymerase sigma factor RpoD [Sagittula stellata E-37]
 gi|126708973|gb|EBA08028.1| RNA polymerase sigma factor RpoD [Sagittula stellata E-37]
          Length = 667

 Score = 97.8 bits (242), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 72/235 (30%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 429 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 488

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 489 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 543

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   ++N +   
Sbjct: 544 PLEKVRKV-MKIA-KEPISLETPIGDEEDSQLGDFI---EDKNAILPLDSAIQENLKETT 598

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR +S L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 599 TRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 653


>gi|307152414|ref|YP_003887798.1| RpoD subfamily RNA polymerase sigma-70 factor [Cyanothece sp. PCC
           7822]
 gi|306982642|gb|ADN14523.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7822]
          Length = 377

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 128/237 (54%), Gaps = 17/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 141 AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 200

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT-DNNLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++ +   KP E+ +A   ++
Sbjct: 201 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKILSQEMRRKPTEEEIATRMEM 255

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  D +  E  + +   R++  N
Sbjct: 256 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIEADGETPEDEVSKNLLREDLEN 311

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +L      L+PRER +   R   ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 312 VL----DTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLR 364


>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 = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 71/244 (29%), Positives = 118/244 (48%), Gaps = 32/244 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +   T     PE+   +A+++ +
Sbjct: 438 IRQAITRSIADQARTIRI--PVHMIETINKLNRVSRQILQETGCEPTPEE---LAERMFM 492

Query: 169 SESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           SE ++          +SM   +  DE             S   D++    D    + ++ 
Sbjct: 493 SEDKIRKVLKIAKEPVSMETPIGDDE------------DSHLGDFI---EDTNLDLPLDS 537

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARA 276
               N R      +S L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A
Sbjct: 538 ATSDNLRAATNDVLSGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 597

Query: 277 FKKV 280
            +K+
Sbjct: 598 LRKL 601


>gi|90422490|ref|YP_530860.1| RNA polymerase sigma factor RpoD [Rhodopseudomonas palustris
           BisB18]
 gi|90104504|gb|ABD86541.1| sigma 70 (RpoD) [Rhodopseudomonas palustris BisB18]
          Length = 702

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 72/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 464 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 523

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 524 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLNEIGREPTPEE---LAEKLGM 578

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E L+      D+  S   D++    D    + I+   + N R   
Sbjct: 579 PLEKVRKV-LKIAK-EPLSLETPVGDEEDSHLGDFI---EDKNAILPIDAAIQSNLRETT 633

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 634 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 688


>gi|32266044|ref|NP_860076.1| RNA polymerase sigma factor RpoD [Helicobacter hepaticus ATCC
           51449]
 gi|32262093|gb|AAP77142.1| RNA polymerase sigma 70 factor [Helicobacter hepaticus ATCC 51449]
          Length = 623

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 73/236 (30%), Positives = 119/236 (50%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ ++GF+ +TY+ WW
Sbjct: 384 AKAKMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKKGFKFSTYATWW 443

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + R+   ++       K   +  IAK++ +
Sbjct: 444 IRQAISRAIADQARTIRIPI-----HMIETINRIHKIMRKHVQETGKEPDIDFIAKEVGL 498

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V ++        SL+A I S D    ++ D++           I KE+ K +   +
Sbjct: 499 PIDKVKNVIKITKEPVSLDAPIGSDD--DGKFGDFVEDKSSVGPMDYILKEDLKVQ---I 553

Query: 229 TRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 554 DEVLEQLNDREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLK 609


>gi|148257986|ref|YP_001242571.1| RNA polymerase sigma factor RpoD [Bradyrhizobium sp. BTAi1]
 gi|146410159|gb|ABQ38665.1| RNA polymerase, sigma 70 subunit, RpoD [Bradyrhizobium sp. BTAi1]
          Length = 702

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 72/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 464 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 523

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 524 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLNEIGREPTPEE---LAEKLGM 578

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E L+      D+  S   D++    D    + I+   + N R   
Sbjct: 579 PLEKVRKV-LKIA-KEPLSLETPVGDEEDSHLGDFI---EDKNAILPIDAAIQSNLRETT 633

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 634 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 688


>gi|256371989|ref|YP_003109813.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidimicrobium
           ferrooxidans DSM 10331]
 gi|256008573|gb|ACU54140.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidimicrobium
           ferrooxidans DSM 10331]
          Length = 302

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 77/268 (28%), Positives = 137/268 (51%), Gaps = 18/268 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           ++ ++ K P+    E+  LAKR RE GD  A   +V ++LRLVV  A  Y+  G+ ++++
Sbjct: 40  FLDDLAKHPLPSAAEQVELAKRVRE-GDEDAKAEMVAANLRLVVHWARRYQDRGVELADL 98

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK-RLFF 137
           + EG  GL++AV+KFD  RGF+ +TY+ WW++ ++Q  +      +++   A ++ R   
Sbjct: 99  IQEGTFGLIRAVEKFDWRRGFKFSTYATWWVRQSLQRAVHNHGQAIRLPMEAAERSRRVD 158

Query: 138 NLRRLKGHLQAITDNNLKP-EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
           N+ R     +   D    P E+ +A+A  L+ S+   +    R+    SL+  +    + 
Sbjct: 159 NVTR-----ELAADLGRAPTEEEIAMAANLSASQLADVRHAARVVA--SLDQAVGPEGET 211

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQ-ENPVT 254
           S    D +V     Q+    E+ +    R ML R++  L+  ER++   R  LQ + P +
Sbjct: 212 S--LGDLVV----AQDTSFEEEVDESISREMLRRAVEELDELERQVVTLRFGLQGDRPAS 265

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQE 282
           LE  +    +   R R++EA A  K+ E
Sbjct: 266 LEATARILGIGPRRARRLEASALAKLAE 293


>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 = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 119/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 416 AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 475

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +        +PE+   +A+KL +
Sbjct: 476 IRQAITRSIADQARTIRI--PVHMIETINKLVRTSRQMLHEIGREPQPEE---LAEKLGM 530

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + ++   + N R   
Sbjct: 531 PLEKVRKV-LKIA-KEPISLETPIGDEEDSHLGDFI---EDKAAIIPLDAAIQANLREAT 585

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR +S L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 586 TRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTRERIRQIEAKALRKLK 640


>gi|300112902|ref|YP_003759477.1| RpoD subfamily RNA polymerase sigma 70 subunit [Nitrosococcus
           watsonii C-113]
 gi|299538839|gb|ADJ27156.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nitrosococcus
           watsonii C-113]
          Length = 310

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 79/273 (28%), Positives = 145/273 (53%), Gaps = 17/273 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A R  + G+ +   R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 42  YLSEIGFAPLLTAEEEVYYA-RLAKKGNSAGRKRMIESNLRLVVKISRRYMNRGLALLDL 100

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL+ AV+KFDPE GFR +TY+ WWI+  ++  ++     V++     ++    +
Sbjct: 101 IEEGNLGLIHAVEKFDPEMGFRFSTYATWWIRQTIERALMNQTRTVRLPVHVVKE--IKS 158

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
            +R+   L    +++   E+   +A++L+    E+     R+   +   A +++  +N+ 
Sbjct: 159 YQRVANKLAQELEHDPSFEE---LAQQLDKPVEEI----KRVWSLKDNTASMDTGYRNNQ 211

Query: 199 QWQ--DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQE-NPVT 254
           +    D L  +      VL++ ++ + R   L   +S LN ++R +   R  LQ   P T
Sbjct: 212 EKTLLDALPDEGAPDPTVLLQNDDMQAR---LELWLSQLNDKQREVVIRRFGLQGYEPQT 268

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           LE +     V+RERVRQI+    K+++  + K+
Sbjct: 269 LEQVGQAIGVTRERVRQIQLETLKRLRRILAKE 301


>gi|315453594|ref|YP_004073864.1| RNA polymerase sigma factor (sigma-70) [Helicobacter felis ATCC
           49179]
 gi|315132646|emb|CBY83274.1| RNA polymerase sigma factor (sigma-70) [Helicobacter felis ATCC
           49179]
          Length = 621

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 69/238 (28%), Positives = 121/238 (50%), Gaps = 17/238 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ E+ +R +TY+ WW
Sbjct: 382 AKNKMARSNLRLVVSIAKRYTSRGLPFLDLIQEGNIGLMKAVDKFEHEKNYRFSTYATWW 441

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           IK A+   I      ++I        +   + R+   ++     N K   +  +AK++ +
Sbjct: 442 IKQAISRAIADQARTIRIPI-----HMIDTINRINKVMRKYMQENGKEPDLDLVAKEVGL 496

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH--DGQEQVLIEKEERKNRRN 226
              +V ++        SL + + + D    ++ D++  D      + ++     R++ + 
Sbjct: 497 PLDKVKNVIKITKEPISLESPVGNDD--DGKFGDFVENDKVVGSMDHIM-----REDLKT 549

Query: 227 MLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 550 QIDGVLDQLNEREKSVIRMRFGLLEDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 607


>gi|260425299|ref|ZP_05779279.1| RNA polymerase sigma factor RpoD [Citreicella sp. SE45]
 gi|260423239|gb|EEX16489.1| RNA polymerase sigma factor RpoD [Citreicella sp. SE45]
          Length = 665

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 72/235 (30%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 427 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 486

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 487 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 541

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   ++N +   
Sbjct: 542 PLEKVRKV-MKIA-KEPISLETPIGDEEDSQLGDFI---EDKNAILPLDSAIQENLKETT 596

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR +S L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 597 TRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 651


>gi|187736115|ref|YP_001878227.1| RNA polymerase, sigma 70 subunit, RpoD family [Akkermansia
           muciniphila ATCC BAA-835]
 gi|187426167|gb|ACD05446.1| RNA polymerase, sigma 70 subunit, RpoD family [Akkermansia
           muciniphila ATCC BAA-835]
          Length = 688

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 74/239 (30%), Positives = 125/239 (52%), Gaps = 20/239 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+  RG++ +TY+ WW
Sbjct: 447 AKDEMVEANLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWW 506

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+      L R++  L         PE+   IA+
Sbjct: 507 IRQAITRSIADQARTIRIPVHMIETINK------LMRVQKQLVQEYGREPTPEE---IAE 557

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           ++++    V S+        SL A +  SD  S  + D++    D   +  +E+      
Sbjct: 558 EIHLPVERVRSVLKMAQQPISLQAPVGDSDDTS--FGDFI---EDKAAENPMEEASFSFL 612

Query: 225 RNMLTRSMSVLNPRERRIFEAR-RLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +  +   +  L  RER + E R  L++ +P TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 613 KEKIKDVLDTLTDREREVIEQRFGLRDGSPRTLEEVGRQFSVTRERIRQIEAKALRKLR 671


>gi|33862619|ref|NP_894179.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9313]
 gi|33634535|emb|CAE20521.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9313]
          Length = 313

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 81/297 (27%), Positives = 147/297 (49%), Gaps = 44/297 (14%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS-------------------------AA 50
           +S Y+  I +IP+L   EE  L  + +    L+                         A 
Sbjct: 20  VSWYLTTIGRIPLLTPAEEIELGNQVQTMMSLTQDGSVAPDDKEFTTHQRRMIRIGRRAK 79

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            R++ ++LRLVV +A  Y+G GL + +++ EG++GL +AV+KFDP RG++ +TY+ WWI+
Sbjct: 80  ERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWWIR 139

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRR----LKGHLQAITDNNLKPEQVVAIAKKL 166
            +M   I      +++    +++     +R+    L   L AI   +        IA+ +
Sbjct: 140 QSMTRAIACQSRTIRLPVHLSER--LTTIRKVSLDLAHKLGAIPSRS-------EIAEAM 190

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   E+ S+  +     SL+A +N  ++ S  +   L+ D    E   ++K E++    
Sbjct: 191 DIPVDELDSLLRQALTTSSLDAPVNGEERRS--FLGDLIADSSLGEP--LDKVEQRIHHE 246

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L R +S L+ +E+ + + R   E  +  TL  +    EVSRERVRQ+E +A +K++
Sbjct: 247 QLGRWLSHLSEQEQHVLKLRFGLETHDRHTLAEIGRLMEVSRERVRQVELKALRKLR 303


>gi|68171251|ref|ZP_00544654.1| 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 [Ehrlichia chaffeensis str. Sapulpa]
 gi|88657966|ref|YP_507558.1| RNA polymerase sigma factor RpoD [Ehrlichia chaffeensis str.
           Arkansas]
 gi|67999333|gb|EAM85979.1| 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 [Ehrlichia chaffeensis str. Sapulpa]
 gi|88599423|gb|ABD44892.1| RNA polymerase sigma factor RpoD [Ehrlichia chaffeensis str.
           Arkansas]
          Length = 622

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 68/239 (28%), Positives = 124/239 (51%), Gaps = 19/239 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLVV IA  Y   GL   ++V EGNIGLM+AV KFD +RG++ +TY+ WW
Sbjct: 385 AKQEMIKANLRLVVSIAKKYSNRGLQFLDLVQEGNIGLMKAVDKFDYKRGYKFSTYATWW 444

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           ++ A+   I      ++I        +   + ++   L+ +     +   +  ++ +LN+
Sbjct: 445 VRQAITRAIADQARTIRIPV-----HMIETVNKINRTLRQMLHEMGREPTLEELSARLNI 499

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER---KNRR 225
           +  ++  +   +    SL + I   D +SS + D +      +++  ++ E+     + R
Sbjct: 500 NVDKIRKVMKIVKDPVSLESPI--GDDDSSTFGDCI------EDKRAVKPEDAAVLADLR 551

Query: 226 NMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            + T+ +S L P+E RI   R          TLE +   F V+RER+RQIEA+A +K++
Sbjct: 552 EITTKVLSTLTPKEERILRMRFGIGKGGKDHTLEEVGKLFNVTRERIRQIEAKALRKLR 610


>gi|254704732|ref|ZP_05166560.1| RNA polymerase sigma factor RpoD [Brucella suis bv. 3 str. 686]
          Length = 257

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 75/239 (31%), Positives = 123/239 (51%), Gaps = 20/239 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 19  AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 78

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+      +R  +  L  I      PE+   +A+
Sbjct: 79  IRQAITRSIADQARTIRIPVHMIETINK-----IVRTSRQMLHEI-GREPTPEE---LAE 129

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           KL +   +V  +  ++A  E ++      D+  S   D++    D    + I+   + N 
Sbjct: 130 KLAMPLEKVRKV-LKIA-KEPISLETPVGDEEDSHLGDFI---EDKNALLPIDAAIQANL 184

Query: 225 RNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R+  TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 185 RDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 243


>gi|118475308|ref|YP_891711.1| RNA polymerase sigma factor RpoD [Campylobacter fetus subsp. fetus
           82-40]
 gi|118414534|gb|ABK82954.1| RNA polymerase sigma factor [Campylobacter fetus subsp. fetus
           82-40]
          Length = 623

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 76/241 (31%), Positives = 125/241 (51%), Gaps = 21/241 (8%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ ++G++ +TY+ W
Sbjct: 382 DAKARMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKKGYKFSTYATW 441

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL-KGHLQAITDNNLKPEQVVAIAKKL 166
           WI+ A+   I      ++I        +   + R+ K + + + +   +P+ V  IA+++
Sbjct: 442 WIRQAISRAIADQARTIRIPI-----HMIETINRINKINRKYLQEEGKEPD-VSIIAREV 495

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG---QEQVLIEKEERKN 223
            +S  +V  +        SL A I S D    ++ D+ V D       EQ+L     + +
Sbjct: 496 GLSIDKVKQVIKITKEPISLEAPIGSED--DGKYGDF-VEDKTTLSPMEQIL-----KGD 547

Query: 224 RRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            +  +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK+
Sbjct: 548 LKEQIDEVLDQLNDREKAVIRMRFGLLEDESDRTLEEIGKELNVTRERVRQIESSAIKKL 607

Query: 281 Q 281
           +
Sbjct: 608 K 608


>gi|87307232|ref|ZP_01089377.1| transcription initiation factor sigma 70 [Blastopirellula marina
           DSM 3645]
 gi|87289972|gb|EAQ81861.1| transcription initiation factor sigma 70 [Blastopirellula marina
           DSM 3645]
          Length = 507

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 79/263 (30%), Positives = 132/263 (50%), Gaps = 39/263 (14%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           E QEEY  AKR            L   +LRLVV IA  YR  GL   +++ EGN GLM+A
Sbjct: 249 EFQEEYDAAKRL-----------LSAGNLRLVVSIAKKYRNRGLSFLDLIQEGNTGLMRA 297

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V KF+ +RG++ +TY+ WWI+ A+   I      +++           ++    G ++A+
Sbjct: 298 VDKFEYQRGYKFSTYATWWIRQAITRAIADQSRTIRVPV---------HMIDTMGKVRAV 348

Query: 150 TDNNLK------PEQVVAIAKKLNVSESEVISMNCR--LAGDESLNALINSSDKNSSQWQ 201
           T + L+        + VA    L++ ++ VI    R  L+ D+ +       D + S + 
Sbjct: 349 TRDLLQELGRDPTAEEVAERAGLSIDDARVILKMNRNPLSLDQPVG------DHDDSFFG 402

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLS 259
           ++L    D +++  + +  ++  ++ L   +  LN RER I   R    +    TLE + 
Sbjct: 403 EFL---EDHRDEDPLYETHQQALKDRLCEVLEALNHREREIIRLRYGLTDGYSYTLEEVG 459

Query: 260 SEFEVSRERVRQIEARAFKKVQE 282
             F V+RERVRQIE++A +K+Q+
Sbjct: 460 KIFSVTRERVRQIESKAVRKLQQ 482


>gi|238018971|ref|ZP_04599397.1| hypothetical protein VEIDISOL_00831 [Veillonella dispar ATCC 17748]
 gi|237864455|gb|EEP65745.1| hypothetical protein VEIDISOL_00831 [Veillonella dispar ATCC 17748]
          Length = 387

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 83/303 (27%), Positives = 146/303 (48%), Gaps = 43/303 (14%)

Query: 4   KNMSIIVNGEIGLS------RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHR----- 52
           KN+SI ++ + G++       Y+ EI ++P+L   EE VLAK+        A ++     
Sbjct: 89  KNISIDLSVDSGVNIDDPVRMYLKEIGRVPLLSADEEIVLAKQIEAGAAEDATYKDVQLA 148

Query: 53  ------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                 LV ++LRLVV IA  Y G G+   +++ EGN+GL++AV KFD  +G++ +TY+ 
Sbjct: 149 KKAKKKLVDANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVDKFDYTKGYKFSTYAT 208

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV------- 159
           WWI+ A+   I      ++I    +       L R+   L         PE++       
Sbjct: 209 WWIRQAITRAIADQARTIRI--PVHMVETINKLIRISRQLLQDKGREPLPEEIAEGMGIT 266

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           V   +++     E +S+   +  +E      +S   +  + QD +  D D    +L++++
Sbjct: 267 VERVREIQKIAQEPVSLETPIGEEE------DSHLGDFIEDQDAIAPD-DAASYILLQEQ 319

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAF 277
                   +    + L  RE+++   R  L++  P TLE +   F V+RER+RQIE +A 
Sbjct: 320 --------IEDVFTCLTDREQQVLILRFGLKDGKPRTLEEVGQHFNVTRERIRQIEGKAL 371

Query: 278 KKV 280
            K+
Sbjct: 372 TKL 374


>gi|149184445|ref|ZP_01862763.1| RNA polymerase sigma factor RpoD [Erythrobacter sp. SD-21]
 gi|148831765|gb|EDL50198.1| RNA polymerase sigma factor RpoD [Erythrobacter sp. SD-21]
          Length = 668

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 123/236 (52%), Gaps = 14/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 430 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 489

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL-KGHLQAITDNNLKPEQVVAIAKKLN 167
           I+ A+   I      ++I        +   + +L +   Q + D   +P     +A+KL+
Sbjct: 490 IRQAITRSIADQARTIRIPV-----HMIETINKLVRCSRQFLHDQGREP-TPEEMAEKLS 543

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +   +V  +  ++A  E ++      D+  S   D++    D    + ++   + N +  
Sbjct: 544 MPLEKVRKV-MKIAK-EPISLETPIGDEEDSHLGDFI---EDKNAIIPVDAAIQANLKET 598

Query: 228 LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 599 VTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 654


>gi|2338708|gb|AAC46374.1| sigma factor RpoS [Vibrio cholerae]
          Length = 168

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 45/100 (45%), Positives = 70/100 (70%), Gaps = 1/100 (1%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 6   YLSEIGFSPLLTAEEEVLYARRAL-RGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 64

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++
Sbjct: 65  IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALM 104


>gi|57239060|ref|YP_180196.1| RNA polymerase sigma factor rpoD [Ehrlichia ruminantium str.
           Welgevonden]
 gi|58579003|ref|YP_197215.1| RNA polymerase sigma factor rpoD [Ehrlichia ruminantium str.
           Welgevonden]
 gi|58617062|ref|YP_196261.1| RNA polymerase sigma factor rpoD [Ehrlichia ruminantium str.
           Gardel]
 gi|57161139|emb|CAH58052.1| RNA polymerase sigma-70 factor [Ehrlichia ruminantium str.
           Welgevonden]
 gi|58416674|emb|CAI27787.1| RNA polymerase sigma factor rpoD [Ehrlichia ruminantium str.
           Gardel]
 gi|58417629|emb|CAI26833.1| RNA polymerase sigma factor rpoD [Ehrlichia ruminantium str.
           Welgevonden]
          Length = 622

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 73/245 (29%), Positives = 124/245 (50%), Gaps = 19/245 (7%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLVV IA  Y   GL   ++V EGNIGLM+AV KFD +RG++ +
Sbjct: 379 ERAATQAKQEMIKANLRLVVSIAKKYSNRGLQFLDLVQEGNIGLMKAVDKFDYKRGYKFS 438

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WW++ A+   I      ++I     +     N R L+  L  I     +   +  +
Sbjct: 439 TYATWWVRQAITRAIADQARTIRIPVHMIETVNKIN-RTLRQMLHEIG----REPTLEEL 493

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER- 221
           + +LN++  ++  +   +    SL + I   D +SS + D +      +++  +  E+  
Sbjct: 494 SARLNINVDKIRKVMKIVKDPVSLESPI--GDDDSSTFGDCI------EDKRAVRPEDAA 545

Query: 222 --KNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARA 276
              + R + T+ +S L P+E RI   R          TLE +   F V+RER+RQIEA+A
Sbjct: 546 VLADLREITTKVLSTLTPKEERILRMRFGIGKGGKDHTLEEVGKLFNVTRERIRQIEAKA 605

Query: 277 FKKVQ 281
            +K++
Sbjct: 606 LRKLR 610


>gi|83951483|ref|ZP_00960215.1| RNA polymerase sigma factor [Roseovarius nubinhibens ISM]
 gi|83836489|gb|EAP75786.1| RNA polymerase sigma factor [Roseovarius nubinhibens ISM]
          Length = 660

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 72/235 (30%), Positives = 119/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 422 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 481

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 482 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 536

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   + N +   
Sbjct: 537 PLEKVRKV-MKIA-KEPISLETPIGDEEDSQLGDFI---EDKNAVLPLDSAIQDNLKETT 591

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR +S L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 592 TRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 646


>gi|238024932|ref|YP_002909164.1| RNA polymerase, sigma 70 subunit, RpoD family protein [Burkholderia
           glumae BGR1]
 gi|237879597|gb|ACR31929.1| RNA polymerase, sigma 70 subunit, RpoD family protein [Burkholderia
           glumae BGR1]
          Length = 805

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 77/279 (27%), Positives = 139/279 (49%), Gaps = 30/279 (10%)

Query: 23  IRKIPMLEKQEEYVL---------------AKRYREHGDLSA--AHRLVT-SHLRLVVKI 64
           +R IP + +Q++ +L                 R    G+L A  A R +T ++LRLV+ I
Sbjct: 522 VRNIPAIHEQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISI 581

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      +
Sbjct: 582 AKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTI 641

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I    +       + R+    Q + +  L+P+    +A+K+ + E ++  +  ++A  E
Sbjct: 642 RI--PVHMIETINKMNRI--SRQILQETGLEPDPAT-LAEKMEMPEDKIRKI-MKIA-KE 694

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
            ++      D + S   D++    D       +     + R+++   +  L PRE ++  
Sbjct: 695 PISMETPIGDDDDSHLGDFI---EDSNTVAPADAALHASMRDVVKDVLDSLTPREAKVLR 751

Query: 245 ARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 752 MRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 790


>gi|288799880|ref|ZP_06405339.1| RNA polymerase sigma-70 factor [Prevotella sp. oral taxon 299 str.
           F0039]
 gi|288333128|gb|EFC71607.1| RNA polymerase sigma-70 factor [Prevotella sp. oral taxon 299 str.
           F0039]
          Length = 290

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 77/285 (27%), Positives = 142/285 (49%), Gaps = 38/285 (13%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYG 72
            L +Y+ EI + P++   +E  LA++ ++ G     A  +LVT++LR VV +A  Y+  G
Sbjct: 17  ALDKYLVEIGRAPLISIDDEIELAQKIKKGGPEGERAKDKLVTANLRFVVSVAKQYQHQG 76

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V++    NQ
Sbjct: 77  LTLTDLIDEGNIGLIKAAQKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRL--PLNQ 134

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRLAG 182
                +L ++   +      N +   V  ++   N+ E ++          +S++     
Sbjct: 135 ---VGSLNKINHEINKFEQENQRHPSVSELSDATNIDEEKIGQSLMADGHHVSIDAPFQD 191

Query: 183 DESLNALIN---SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            E  N +++   SSD + +  Q     DH+   Q   E E   N+         VL  RE
Sbjct: 192 GED-NCMLDVMPSSDDSRTDRQ----VDHESMAQ---ELEAVLNK---------VLKDRE 234

Query: 240 RRIF-EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             I  E   +  +   LE +  +  ++RERVRQI  ++  K+++S
Sbjct: 235 ITIIRECFGIGCHEKGLEEIGDQLGLTRERVRQIREKSIAKLRDS 279


>gi|581612|emb|CAA37172.1| unnamed protein product [Streptomyces coelicolor A3(2)]
          Length = 396

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 85/294 (28%), Positives = 139/294 (47%), Gaps = 42/294 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ EI +IP+L   EE  LA+R  E G  +                           A  
Sbjct: 103 YLREIGRIPLLSAAEEVDLARRV-EAGLFAEEKLRCSPGLDDRLALDLDRLVVLGRLAKR 161

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY+ WWI+ 
Sbjct: 162 RLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWIRQ 221

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           AM   +      +++    +   L   + R++  +         P++V A    L+++  
Sbjct: 222 AMSRALADQARTIRV--PVHVVELINRVVRVQRRMLQERGCEPTPQEVAA---HLDLA-P 275

Query: 172 EVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           E +    RLA +  SL+A +   D  +    D +    DG     +E       R  L  
Sbjct: 276 ERVGEVLRLAQEPVSLHAPVGEEDDVA--LGDLI---EDGDAASPVESAAFLLLRQHLEA 330

Query: 231 SMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            +S L  RER++ + R       P TLE +     V+RER+RQIE++   K+++
Sbjct: 331 VLSTLGERERKVVQLRYGLADGRPRTLEEIGRLGGVTRERIRQIESKTLSKLRD 384


>gi|206901861|ref|YP_002251028.1| RNA polymerase sigma factor RpoD [Dictyoglomus thermophilum H-6-12]
 gi|206740964|gb|ACI20022.1| RNA polymerase sigma factor RpoD [Dictyoglomus thermophilum H-6-12]
          Length = 413

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 47/108 (43%), Positives = 71/108 (65%), Gaps = 1/108 (0%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI KIP+L  +EE  LAKR  E GD  A  +L+ ++LRLVV +A  Y G GL   ++
Sbjct: 75  YLKEIGKIPLLTPEEEIELAKRV-EQGDEEAKKKLIEANLRLVVSVAKRYIGRGLSFLDL 133

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I
Sbjct: 134 IQEGNLGLIKAVEKFDWRKGYKFSTYATWWIRQAITRAIADQARTIRI 181



 Score = 40.0 bits (92), Expect = 0.40,   Method: Compositional matrix adjust.
 Identities = 40/144 (27%), Positives = 73/144 (50%), Gaps = 12/144 (8%)

Query: 145 HLQAITDNNLKPEQVVAIAKKL-NVSESEVISMNCR-----LAGDESLNALINSSDKNSS 198
           HL+A  +     E++   AK+L +V E E+     +     + G E L+  +   +   +
Sbjct: 259 HLKAKNNKVPTKEEINEKAKELKHVLEEEIRQQTEKVREISMMGQEPLSLEMPVGEDEDN 318

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLE 256
           +  D++         + ++K  +K+   +L      L+ RER I + R  L++N P TLE
Sbjct: 319 RLADFVENKDLSPADIAVQKSLKKDIEELLNE----LSEREREILKLRFGLEDNQPRTLE 374

Query: 257 NLSSEFEVSRERVRQIEARAFKKV 280
            +   F V+RER+RQIEA+A +++
Sbjct: 375 EVGKLFNVTRERIRQIEAKALRRL 398


>gi|296532787|ref|ZP_06895466.1| RNA polymerase sigma factor RpoD [Roseomonas cervicalis ATCC 49957]
 gi|296266895|gb|EFH12841.1| RNA polymerase sigma factor RpoD [Roseomonas cervicalis ATCC 49957]
          Length = 639

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 74/249 (29%), Positives = 126/249 (50%), Gaps = 13/249 (5%)

Query: 36  VLAKRYREHGDLSAAHR-LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           V A   R   D++ A + ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+
Sbjct: 387 VYATVSRGERDMTQAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 446

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             RG++ +TY+ WWI+ A+   I      ++I    +       L R    +        
Sbjct: 447 YRRGYKFSTYATWWIRQAITRSIADQARTIRI--PVHMIETINKLVRTSRQMLHEIGREP 504

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +PE+   +A+KL +   +V  +  ++A  E ++      D+  S   D++    D    +
Sbjct: 505 QPEE---LAEKLGMPLEKVRKV-LKIA-KEPISLETPIGDEEDSHLGDFI---EDKAAII 556

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQI 272
            ++   + N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQI
Sbjct: 557 PLDAAIQSNLREATTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTRERIRQI 616

Query: 273 EARAFKKVQ 281
           EA+A +K++
Sbjct: 617 EAKALRKLK 625


>gi|312113102|ref|YP_004010698.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhodomicrobium
           vannielii ATCC 17100]
 gi|311218231|gb|ADP69599.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhodomicrobium
           vannielii ATCC 17100]
          Length = 697

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 119/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 459 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 518

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL++
Sbjct: 519 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMMHEIGREPTPEE---LAEKLSM 573

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 574 PLEKVRKV-LKIA-KEPISLETPIGDEEDSHLGDFI---EDKNAILPIDAAIQSNLRETT 628

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 629 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 683


>gi|85715949|ref|ZP_01046926.1| RNA polymerase sigma factor [Nitrobacter sp. Nb-311A]
 gi|85697147|gb|EAQ35028.1| RNA polymerase sigma factor [Nitrobacter sp. Nb-311A]
          Length = 716

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 72/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 478 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 537

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 538 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLNEIGREPTPEE---LAEKLGM 592

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E L+      D+  S   D++    D    + I+   + N R   
Sbjct: 593 PLEKVRKV-LKIAK-EPLSLETPVGDEEDSHLGDFI---EDKNAVLPIDAAIQSNLRETT 647

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 648 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 702


>gi|261755428|ref|ZP_05999137.1| RNA polymerase sigma factor RpoD [Brucella suis bv. 3 str. 686]
 gi|261745181|gb|EEY33107.1| RNA polymerase sigma factor RpoD [Brucella suis bv. 3 str. 686]
          Length = 235

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 74/235 (31%), Positives = 122/235 (51%), Gaps = 20/235 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A
Sbjct: 1   MVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 60

Query: 113 MQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           +   I      ++I      T N+      +R  +  L  I      PE+   +A+KL +
Sbjct: 61  ITRSIADQARTIRIPVHMIETINKI-----VRTSRQMLHEI-GREPTPEE---LAEKLAM 111

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R+  
Sbjct: 112 PLEKVRKV-LKIA-KEPISLETPVGDEEDSHLGDFI---EDKNALLPIDAAIQANLRDTT 166

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 167 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 221


>gi|109948008|ref|YP_665236.1| RNA polymerase sigma factor RpoD [Helicobacter acinonychis str.
           Sheeba]
 gi|109715229|emb|CAK00237.1| RNA polymerase sigma-70 factor [Helicobacter acinonychis str.
           Sheeba]
          Length = 659

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 69/236 (29%), Positives = 120/236 (50%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ WW
Sbjct: 420 AKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEYEKGFKFSTYATWW 479

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           IK A+   I      ++I        +   + R+   ++     N K   +  +A+++ +
Sbjct: 480 IKQAISRAIADQARTIRIPI-----HMIDTINRINKVMRKHMQENGKEPDLEVVAEEVGL 534

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  +V   N      E ++      + +  ++ D++    D      I+   R++ +  +
Sbjct: 535 SLDKV--KNVIKVTKEPISLETPVGNDDDGKFGDFV---EDKNIVSSIDHIMREDLKVQI 589

Query: 229 TRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 590 EGVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 645


>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 = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 84/273 (30%), Positives = 135/273 (49%), Gaps = 27/273 (9%)

Query: 13  EIGLSRYIHEIRKI-PMLEKQE-EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           E GL   I E RKI  M++K E E  +AK+            +V ++LRLV+ IA  Y  
Sbjct: 403 ETGLE--ITEFRKIVAMVQKGEREARIAKK-----------EMVEANLRLVISIAKKYTN 449

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I    
Sbjct: 450 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI--PV 507

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
           +       + R    +         PE+   +A+KL +   +V  +  ++A  E ++   
Sbjct: 508 HMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLQMPLEKVRKV-LKIA-KEPISLET 562

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--L 248
              D+  S   D++    D    + I+   + N R   TR ++ L PRE R+   R    
Sbjct: 563 PIGDEEDSHLGDFI---EDKNAVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIG 619

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 620 MNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 652


>gi|4103484|gb|AAD01787.1| sigma-D factor [Myxococcus xanthus]
          Length = 297

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 74/259 (28%), Positives = 119/259 (45%), Gaps = 50/259 (19%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           GLS Y+  +     L +++EY LA+R R+ GD SA     +S+L  VV +A  +   G  
Sbjct: 11  GLSHYLRNLGGHQQLTREQEYELARRARK-GDESARQTTASSNLAFVVAVAKKFANRGAR 69

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++ EGN+GLM+A++ FDP++  R ATY++WWI+A +  Y+  + S V+ G       
Sbjct: 70  LDDLIQEGNVGLMKAIEHFDPKKNVRFATYAVWWIRAYITRYLKDNRSQVRGG------- 122

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
                                              E+E  SM      D SL+A I+  +
Sbjct: 123 -----------------------------------EAERGSMV-----DFSLDATID--E 140

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
              + + D L  +    +QV +  E+    +  L +    +      I   R  Q+ P+T
Sbjct: 141 DGETTFLDRLEDNSPSPQQVFLAHEQDTEIQEALAKVRKRIGDLGWDILTERLTQDKPLT 200

Query: 255 LENLSSEFEVSRERVRQIE 273
           LE L   + VSRE VRQ+E
Sbjct: 201 LEELGQRWGVSREPVRQVE 219


>gi|148241988|ref|YP_001227145.1| RNA polymerase sigma factor RpoD [Synechococcus sp. RCC307]
 gi|147850298|emb|CAK27792.1| RNA polymerase sigma factor RpoD, sigma-70 family [Synechococcus
           sp. RCC307]
          Length = 401

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 69/237 (29%), Positives = 129/237 (54%), Gaps = 17/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 165 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 224

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++     KP E+ +A + ++
Sbjct: 225 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKVLSQEFGRKPTEEEIAESMEM 279

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  D +  +Q + +   R++   
Sbjct: 280 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIEADIENPDQDVAKNLLREDLEG 335

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +L    + L+PRER +   R   ++    TLE +   F+V+RER+RQIEA+A  K++
Sbjct: 336 VL----ATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALLKLR 388


>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 = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 68/235 (28%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 373 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 432

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +     +   PE+   +A+++ +
Sbjct: 433 IRQAITRSIADQARTIRI--PVHMIETINKLNRVSRQMLQEIGHEPTPEE---LAERMLM 487

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SE ++  +  ++A  E ++      D   S   D++    D    + ++     N R   
Sbjct: 488 SEDKIRKV-LKIAK-EPISMETPVGDDEDSHLGDFI---EDTNHDLPLDSATSDNLRTAT 542

Query: 229 TRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +S L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 543 HDILSGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 597


>gi|282881579|ref|ZP_06290248.1| sigma-70 region 2 [Prevotella timonensis CRIS 5C-B1]
 gi|281304565|gb|EFA96656.1| sigma-70 region 2 [Prevotella timonensis CRIS 5C-B1]
          Length = 290

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 70/271 (25%), Positives = 135/271 (49%), Gaps = 12/271 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGL 73
           L +Y+ EI + P++   EE  LA++ ++ G     A  +LVT++LR VV +A  Y+  GL
Sbjct: 18  LDKYLVEIGRAPLISIDEEIELAQKIKKGGPEGERAKDKLVTANLRFVVSVAKQYQHQGL 77

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V++    NQ 
Sbjct: 78  TLTDLIDEGNIGLIKAAQKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRL--PLNQ- 134

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
               +L ++   +      + +   +  ++   N+ E ++           S++A     
Sbjct: 135 --VGSLNKINHEINRFEQEHHRRPSITELSDATNIDEEKIGQSMMADGHHVSIDAPFQDG 192

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF-EARRLQENP 252
           + N+    D +    D +    ++ E      N +     VL  RE  I  E   +  + 
Sbjct: 193 EDNT--MLDVMPSGDDSRTDRQVDHESMAQELNTVLN--KVLKDREITIIKECFGIGCHE 248

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             LE +  +  ++RERVRQI  ++  K+++S
Sbjct: 249 KGLEEIGDQLGLTRERVRQIREKSIAKLRDS 279


>gi|186681474|ref|YP_001864670.1| RNA polymerase sigma factor SigC [Nostoc punctiforme PCC 73102]
 gi|186463926|gb|ACC79727.1| RNA polymerase, sigma 70 subunit, RpoD family [Nostoc punctiforme
           PCC 73102]
          Length = 416

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 67/238 (28%), Positives = 128/238 (53%), Gaps = 13/238 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L A   ++ ++LRLVV +A  Y+  GL + ++V EG +GL +AV+KFDP +G+R +TY+ 
Sbjct: 175 LQAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAY 234

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   I  S   +++     +K     L ++K   + I     +   +  +A +L
Sbjct: 235 WWIRQGITRAIATSSRTIRLPVHITEK-----LNKIKKAQRKIAQEKGRTPTLEDLATEL 289

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++ ++V  +  R+    SL   +   DK+ ++  + L  D    E++L+ +  +++  +
Sbjct: 290 EMTPTQVREVLLRVPRSVSLETKVG-KDKD-TELGELLETDCVTPEEMLMRESLQRDLHH 347

Query: 227 MLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +L    S L  RER +   R      +P +L  +    ++SRERVRQIE++A +K+++
Sbjct: 348 LL----SDLTSRERDVILMRFGLADGHPYSLAEIGRALDLSRERVRQIESKALQKLRQ 401


>gi|298373668|ref|ZP_06983657.1| RNA polymerase sigma-70 factor [Bacteroidetes oral taxon 274 str.
           F0058]
 gi|298274720|gb|EFI16272.1| RNA polymerase sigma-70 factor [Bacteroidetes oral taxon 274 str.
           F0058]
          Length = 287

 Score = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 77/276 (27%), Positives = 141/276 (51%), Gaps = 31/276 (11%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI +  ++  ++E  LA+R R+ GD +A  +LV ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGREELITIEQEVELAQRIRK-GDHAALDKLVRANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     +V++    NQ   
Sbjct: 77  PDLIDEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL--PLNQ--- 131

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRLAGDES 185
              L ++    Q     + +   V  IA  L +S  ++          IS++      E 
Sbjct: 132 VGALNKINKAFQRFEQEHERLPSVEEIATDLEISLDKITDTMKVSGRHISVDAPFVDGED 191

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
            N L++    +SS   D  +      E +L E E   +         ++L  RER I + 
Sbjct: 192 -NTLLDVLMNDSSPATDQKLM----SESLLTEIERALD---------ALLQERERDIVKM 237

Query: 246 -RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
              +    +TLE +  +F ++RERVRQI+ +A +++
Sbjct: 238 FFGIGCAEMTLEEIGDQFGLTRERVRQIKEKAIRRL 273


>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 = 97.4 bits (241), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 67/235 (28%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 444 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 503

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+   +   T N   P     +A+K+ +
Sbjct: 504 IRQAITRSIADQARTIRI--PVHMIETINKMNRISRQILQETGNEPDP---ATLAEKMEM 558

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       E     + R+++
Sbjct: 559 PEDKIRKI-MKIAK-EPISMETPIGDDDDSHLGDFI---EDTNTLAPAEAALHGSMRDVV 613

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 614 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 668


>gi|228988887|ref|ZP_04148936.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228770801|gb|EEM19317.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
          Length = 295

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 83/289 (28%), Positives = 142/289 (49%), Gaps = 43/289 (14%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG-LP 74
           + +Y++EI    +L  ++      +Y+E GD+ +   L+ S+LRLVV +A  +  YG   
Sbjct: 11  MGKYLNEICNYDILTDEQSMEHIIKYKEKGDIDSRDLLICSNLRLVVSVAKSFPCYGNCD 70

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ-- 132
           + E++ EG IGLM+ ++ +D  +G +L+TY  WWI+  + +Y+  + S V++ TT  +  
Sbjct: 71  LMEMIQEGTIGLMKGLEDYDYTKGNKLSTYITWWIRQRISKYLSINRSDVRVATTMQKKI 130

Query: 133 ---KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
              K  ++     KG        NL  ++V   A++L   ES VI     L  D   N +
Sbjct: 131 TEVKNCYYENMGEKG-------TNLTTKEV---AERLGYKESIVIDA---LVTDRITNTI 177

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVL--------------IEKEERKNRRNMLTRSMSVL 235
              S ++  Q +  L+   D Q+  L              I  EE K   + L      L
Sbjct: 178 ---SIEDDVQNEKTLL---DKQQSTLAILANKNAPNPSEVIATEEEKFEFDELM--FVTL 229

Query: 236 NPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQE 282
           NPRE  +   R   ++ +  TLE+ +    V+RERV+QIE +A +K+++
Sbjct: 230 NPREESVLRYRFGFDDGIELTLEDTARILGVTRERVQQIEKKAIEKMKQ 278


>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 = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 72/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 418 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 477

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 478 IRQAITRSIADQARTIRI--PVHMIETINKLVRTSRQMLHEIGREPTPEE---LAEKLGM 532

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 533 PLEKVRKV-LKIA-KEPISLETPIGDEEDSHLGDFI---EDKNAILPIDAAIQSNLRETT 587

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 588 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 642


>gi|75676624|ref|YP_319045.1| RNA polymerase sigma factor RpoD [Nitrobacter winogradskyi Nb-255]
 gi|74421494|gb|ABA05693.1| RNA polymerase, sigma 70 subunit, RpoD [Nitrobacter winogradskyi
           Nb-255]
          Length = 717

 Score = 97.4 bits (241), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 72/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 479 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 538

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 539 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLNEIGREPTPEE---LAEKLGM 593

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E L+      D+  S   D++    D    + I+   + N R   
Sbjct: 594 PLEKVRKV-LKIA-KEPLSLETPVGDEEDSHLGDFI---EDKNAVLPIDAAIQSNLRETT 648

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 649 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 703


>gi|330936784|gb|EGH40944.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. pisi
           str. 1704B]
          Length = 176

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 46/100 (46%), Positives = 69/100 (69%), Gaps = 1/100 (1%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIM 165


>gi|302036356|ref|YP_003796678.1| RNA polymerase sigma factor RpoD (Sigma-70) [Candidatus Nitrospira
           defluvii]
 gi|300604420|emb|CBK40752.1| RNA polymerase sigma factor RpoD (Sigma-70) [Candidatus Nitrospira
           defluvii]
          Length = 601

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 70/231 (30%), Positives = 121/231 (52%), Gaps = 12/231 (5%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ WWI+ A
Sbjct: 366 LVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWWIRQA 425

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   I      ++I    +       L R   HL         PE+   IA+++++   +
Sbjct: 426 ITRAIADQARTIRI--PVHMIETINKLIRTSRHLVQKLGREPTPEE---IAERMDLPLDK 480

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           V  +  ++A  E ++      ++  S   D++    D +    +E   R + +  +  ++
Sbjct: 481 VRKI-LKIA-REPISLETPIGEEEDSHLGDFI---EDKKAVSPLEAAIRYDLQRQINGAL 535

Query: 233 SVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             L PRE ++   R    +    TLE +  +FEV+RER+RQIEA+A +K++
Sbjct: 536 ETLTPREEKVLRKRFGIGEATDHTLEEVGQDFEVTRERIRQIEAKALRKLR 586


>gi|154148465|ref|YP_001406295.1| RNA polymerase sigma factor RpoD [Campylobacter hominis ATCC
           BAA-381]
 gi|153804474|gb|ABS51481.1| RNA polymerase sigma factor RpoD (Sigma-A) (Major vegetative
           sigmafactor) [Campylobacter hominis ATCC BAA-381]
          Length = 624

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 118/236 (50%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+  +G++ +TY+ WW
Sbjct: 385 AKSLMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYRKGYKFSTYATWW 444

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + R+    +     N K   +  +AK++ +
Sbjct: 445 IRQAISRAIADQARTIRIPI-----HMIETINRINKINRKYVQENGKEPDITILAKEVGL 499

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  ++  +        SL A + + D    ++ D++    D      I++  + + +  +
Sbjct: 500 SIDKIKQVIKITKEPISLEAPVGNED--DGKFGDFV---EDKGTISPIDQILKNDLKEQI 554

Query: 229 TRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            + +  LN RER +   R      E+  TLE +  E  V+RERVRQIEA A KK++
Sbjct: 555 DKVLDQLNERERAVIRMRFGLLDDESDRTLEEIGKELSVTRERVRQIEASAIKKLK 610


>gi|222824021|ref|YP_002575595.1| RNA polymerase sigma 70 factor [Campylobacter lari RM2100]
 gi|222539243|gb|ACM64344.1| RNA polymerase sigma 70 factor [Campylobacter lari RM2100]
          Length = 625

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 73/246 (29%), Positives = 118/246 (47%), Gaps = 33/246 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ +RG++ +TY+ WW
Sbjct: 384 AKTRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWW 443

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++   ++       K   V  IAK++ +
Sbjct: 444 IRQAISRAIADQARTIRIPI-----HMIETINQINKIIREYLQKEGKEPDVSIIAKEVGL 498

Query: 169 SESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           S  +V          IS+   ++ ++         D+ S    D ++ D D +EQ+    
Sbjct: 499 SVDKVKQVIKITKEPISLEAPISNEDDGKFGDFVEDRTSISPMDHILKD-DLKEQI---- 553

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEAR 275
                        +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ 
Sbjct: 554 ----------DEVLDQLNDREKAVIRMRFGLMDDESDRTLEEIGKELNVTRERVRQIESS 603

Query: 276 AFKKVQ 281
           A KK++
Sbjct: 604 AIKKLK 609


>gi|158334481|ref|YP_001515653.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158304722|gb|ABW26339.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 318

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 73/255 (28%), Positives = 126/255 (49%), Gaps = 21/255 (8%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           IP+ + Q+E  L +        +A  ++V S+LRLVV IA  Y    L   +++ EG IG
Sbjct: 68  IPVSQLQKELKLGQ--------TANRKMVESNLRLVVSIAKKYNKAKLEFLDLIQEGTIG 119

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L + V+KFDP +G+R +TY+ WWI+ AM   I      +++    N+K     LR++K  
Sbjct: 120 LQRGVEKFDPTKGYRFSTYAYWWIRQAMTRAIAEQERTIRLPIHINEK--LNKLRKVKRQ 177

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           L      +     V  +A ++ +S  +V +         SL+  +   D+ +++  + L 
Sbjct: 178 LSLKLHRD---PTVAELATEMELSPKKVEAFLSYARHSISLD--VQVGDQQNTELWELLE 232

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFE 263
             H   E        + +    L + ++VLNP++R +   R   + +NP+TL  +     
Sbjct: 233 DPHASPEDYATASYLQSD----LAKLLNVLNPQQREVITLRYGLIDQNPLTLAKVGERLN 288

Query: 264 VSRERVRQIEARAFK 278
           VSRE VR++E  AF+
Sbjct: 289 VSREWVRRVEREAFQ 303


>gi|92118365|ref|YP_578094.1| RNA polymerase sigma factor RpoD [Nitrobacter hamburgensis X14]
 gi|91801259|gb|ABE63634.1| RNA polymerase, sigma 70 subunit, RpoD [Nitrobacter hamburgensis
           X14]
          Length = 717

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 72/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 479 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 538

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 539 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLNEIGREPTPEE---LAEKLGM 593

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E L+      D+  S   D++    D    + I+   + N R   
Sbjct: 594 PLEKVRKV-LKIA-KEPLSLETPVGDEEDSHLGDFI---EDKNAVLPIDAAIQSNLRETT 648

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 649 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 703


>gi|306844486|ref|ZP_07477075.1| RNA polymerase sigma factor RpoD [Brucella sp. BO1]
 gi|306275097|gb|EFM56853.1| RNA polymerase sigma factor RpoD [Brucella sp. BO1]
          Length = 672

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 119/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 434 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 493

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 494 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 548

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R+  
Sbjct: 549 PLEKVRKV-LKIAK-EPISLETPVGDEEDSHLGDFI---EDKNALLPIDAAIQANLRDTT 603

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 604 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 658


>gi|59714198|ref|YP_206973.1| sigma-Q factor RpoQ, quorum-sensing regulated RpoS-like sigma
           subunit [Vibrio fischeri ES114]
 gi|59482446|gb|AAW88085.1| sigma-Q factor RpoQ, quorum-sensing regulated RpoS-like sigma
           subunit [Vibrio fischeri ES114]
          Length = 294

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 86/296 (29%), Positives = 140/296 (47%), Gaps = 58/296 (19%)

Query: 17  SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG---YGL 73
           S Y+ EI +  +L  +EE   ++ Y++ GD+SA + L+ S+LRLVVK+A  YR      L
Sbjct: 21  SLYLKEINRYQLLTAEEELAYSRLYKK-GDVSARNTLIESNLRLVVKVANKYRKRNQTDL 79

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK--IGTTAN 131
            I +++ EGN+GL++A+ KF+PE G+R +TY++WWI+ +++  +      V+  +  T  
Sbjct: 80  AILDIIEEGNLGLIKAIDKFNPELGYRFSTYAVWWIRESIESALFNHSRTVRLPVHITKE 139

Query: 132 QKRLFFNLRRLKGHLQ---AITD---------------NNLKPEQVV---AIAKKLNVSE 170
                   R L   L+   +I D                +L P Q+    A + +L+   
Sbjct: 140 LNTYLRAARELSKSLKREPSIRDISTYCEEEQIKVSKIISLIPNQLTCHSACSDELSPKF 199

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            E+ S N  L  D SL+   N+ + N S W D L Y          EKE   NR  +   
Sbjct: 200 FELSSNNKALEPDSSLSQ--NNLEMNLSSWIDSLNYR---------EKEIIINRYGLFGC 248

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +                     TLE+L  + ++S+ERVRQI++    K+    +K
Sbjct: 249 KVK--------------------TLEDLGKDLDLSKERVRQIQSETLIKLNTIFKK 284


>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 = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 73/246 (29%), Positives = 118/246 (47%), Gaps = 36/246 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A H +  ++LRLV+ IA  Y   G+   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 417 AKHEMTQANLRLVISIAKKYTNRGMLFLDLIQEGNIGLMKAVDKFEYRRGWKFSTYATWW 476

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           ++ A+   I      +++     ++     L RL   +   T     P     +A++L++
Sbjct: 477 VRQAVTRAIADQARTIRVPVHMIEQ--INKLNRLSREIMQQTGKEPDP---AVLAERLDM 531

Query: 169 SESEV----------ISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           +E +V          +SM   +   GD SL  +I  SD  +           D   Q  +
Sbjct: 532 TEDKVRSIMKIAKEPVSMETPVGEDGDTSLGDMIADSDTATP---------ADAALQAGL 582

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEA 274
               R   R ML      L PRE ++   R         TLE +  +F+V+RER+RQIE+
Sbjct: 583 ----RAVVREMLDE----LTPREAKVLRMRFGIDMSTDYTLEEVGKQFDVTRERIRQIES 634

Query: 275 RAFKKV 280
           +A KK+
Sbjct: 635 KAMKKL 640


>gi|225627926|ref|ZP_03785962.1| RNA polymerase sigma factor RpoD [Brucella ceti str. Cudo]
 gi|256160209|ref|ZP_05457903.1| RNA polymerase sigma factor RpoD [Brucella ceti M490/95/1]
 gi|256255415|ref|ZP_05460951.1| RNA polymerase sigma factor RpoD [Brucella ceti B1/94]
 gi|260169148|ref|ZP_05755959.1| RNA polymerase sigma factor RpoD [Brucella sp. F5/99]
 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 = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 119/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 434 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 493

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 494 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 548

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R+  
Sbjct: 549 PLEKVRKV-LKIAK-EPISLETPVGDEEDSHLGDFI---EDKNALLPIDAAIQANLRDTT 603

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 604 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 658


>gi|256061534|ref|ZP_05451676.1| RNA polymerase sigma factor RpoD [Brucella neotomae 5K33]
 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 = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 119/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 434 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 493

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 494 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 548

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R+  
Sbjct: 549 PLEKVRKV-LKIAK-EPISLETPVGDEEDSHLGDFI---EDKNALLPIDAAIQANLRDTT 603

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 604 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 658


>gi|154245186|ref|YP_001416144.1| RNA polymerase sigma factor RpoD [Xanthobacter autotrophicus Py2]
 gi|154159271|gb|ABS66487.1| RNA polymerase, sigma 70 subunit, RpoD [Xanthobacter autotrophicus
           Py2]
          Length = 666

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 84/272 (30%), Positives = 134/272 (49%), Gaps = 25/272 (9%)

Query: 13  EIGLSRYIHEIRKI-PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           E GL   I E RKI  M++K E     K  R+     A   +V ++LRLV+ IA  Y   
Sbjct: 403 ETGLE--IAEFRKIVQMVQKGE-----KEARQ-----AKKEMVEANLRLVISIAKKYTNR 450

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I    +
Sbjct: 451 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI--PVH 508

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
                  + R    +         PE+   +A+KL +   +V  +  ++A  E ++    
Sbjct: 509 MIETINKIVRTSRQMLHEIGREPTPEE---LAEKLGMPLEKVRKV-LKIA-KEPISLETP 563

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQ 249
             D+  S   D++    D    + I+   + N R   TR ++ L PRE R+   R     
Sbjct: 564 IGDEEDSHLGDFI---EDKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGM 620

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
               TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 621 NTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 652


>gi|148259873|ref|YP_001234000.1| RNA polymerase sigma factor RpoD [Acidiphilium cryptum JF-5]
 gi|326403199|ref|YP_004283280.1| RNA polymerase sigma factor RpoD [Acidiphilium multivorum AIU301]
 gi|146401554|gb|ABQ30081.1| RNA polymerase, sigma 70 subunit, RpoD [Acidiphilium cryptum JF-5]
 gi|325050060|dbj|BAJ80398.1| RNA polymerase sigma factor RpoD [Acidiphilium multivorum AIU301]
          Length = 638

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 76/259 (29%), Positives = 126/259 (48%), Gaps = 13/259 (5%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           ++P+ E +  Y    R  E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNI
Sbjct: 377 QLPIEEFRRVYSTVSRG-ERDSTRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNI 435

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I    +       L R   
Sbjct: 436 GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI--PVHMIETINKLVRTSR 493

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            +         PE+   +A+KL +   +V  +  ++A  E ++      D+  S   D++
Sbjct: 494 QMLHEIGREPTPEE---LAEKLGMPLEKVRKV-LKIA-KEPISLETPIGDEEDSHLGDFI 548

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEF 262
               D    + ++     N R   TR +S L PRE R+   R         TLE +  +F
Sbjct: 549 ---EDKNAIIPLDAAVHANLREAATRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQF 605

Query: 263 EVSRERVRQIEARAFKKVQ 281
            V+RER+RQIEA+A +K++
Sbjct: 606 NVTRERIRQIEAKALRKLK 624


>gi|293375429|ref|ZP_06621710.1| RNA polymerase sigma factor RpoD [Turicibacter sanguinis PC909]
 gi|325844412|ref|ZP_08168139.1| RNA polymerase sigma factor RpoD [Turicibacter sp. HGF1]
 gi|292645982|gb|EFF64011.1| RNA polymerase sigma factor RpoD [Turicibacter sanguinis PC909]
 gi|325489086|gb|EGC91470.1| RNA polymerase sigma factor RpoD [Turicibacter sp. HGF1]
          Length = 464

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 80/246 (32%), Positives = 121/246 (49%), Gaps = 34/246 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  RLV S+LRLVV IA  + G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WW
Sbjct: 226 AKKRLVESNLRLVVSIARRHIGRGMLFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWW 285

Query: 109 IKAAMQEYILRSWSLVKIGT----TAN-----QKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N     Q++L   L R     +      + PE+ 
Sbjct: 286 IRQAITRAIADQARTIRIPVHMIETINKLVRIQRQLVQELGREPLPEEIAEKMEITPEKA 345

Query: 160 VAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
             I   L +S+ E IS+   +    D SL   I  +D  S           D     +++
Sbjct: 346 REI---LKISQ-EPISLESPVGDEADSSLGDFIPDADALSPS---------DFTSNEMLK 392

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
           KE        L   +  L  RE R+   R   E+    TLE +  EF V+RER+RQIEA+
Sbjct: 393 KE--------LAEVLETLTDREERVLRLRFGLEDGHTRTLEEVGKEFGVTRERIRQIEAK 444

Query: 276 AFKKVQ 281
           A +K++
Sbjct: 445 ALRKLR 450


>gi|239832356|ref|ZP_04680685.1| RNA polymerase sigma factor RpoD [Ochrobactrum intermedium LMG
           3301]
 gi|239824623|gb|EEQ96191.1| RNA polymerase sigma factor RpoD [Ochrobactrum intermedium LMG
           3301]
          Length = 672

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 75/239 (31%), Positives = 123/239 (51%), Gaps = 20/239 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 434 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 493

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+      +R  +  L  I      PE+   +A+
Sbjct: 494 IRQAITRSIADQARTIRIPVHMIETINKI-----VRTSRQMLHEIG-REPTPEE---LAE 544

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           KL +   +V  +  ++A  E ++      D+  S   D++    D    + I+   + N 
Sbjct: 545 KLAMPLEKVRKV-LKIAK-EPISLETPVGDEEDSHLGDFI---EDKNALLPIDAAIQANL 599

Query: 225 RNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R+  TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 600 RDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 658


>gi|27382460|ref|NP_773989.1| RNA polymerase sigma factor RpoD [Bradyrhizobium japonicum USDA
           110]
 gi|1742976|emb|CAA67902.1| primary sigma factor [Bradyrhizobium japonicum]
 gi|27355631|dbj|BAC52614.1| primary sigma factor [Bradyrhizobium japonicum USDA 110]
          Length = 719

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 72/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 481 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 540

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 541 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLNEIGREPTPEE---LAEKLGM 595

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E L+      D+  S   D++    D    + I+   + N R   
Sbjct: 596 PLEKVRKV-LKIA-KEPLSLETPVGDEEDSHLGDFI---EDKNAILPIDAAIQSNLRETT 650

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 651 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 705


>gi|224438138|ref|ZP_03659073.1| RNA polymerase sigma factor RpoD [Helicobacter cinaedi CCUG 18818]
 gi|313144578|ref|ZP_07806771.1| RNA polymerase sigma factor RpoD [Helicobacter cinaedi CCUG 18818]
 gi|313129609|gb|EFR47226.1| RNA polymerase sigma factor RpoD [Helicobacter cinaedi CCUG 18818]
          Length = 623

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 73/236 (30%), Positives = 119/236 (50%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ ++GF+ +TY+ WW
Sbjct: 384 AKAKMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKKGFKFSTYATWW 443

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + R+   ++       K   +  IAK++ +
Sbjct: 444 IRQAISRAIADQARTIRIPI-----HMIETINRIHKIMRKHIQETGKEPDIEYIAKEVGL 498

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V ++        SL+A I S D    ++ D++           I KE+ K +   +
Sbjct: 499 PIDKVKNVIKITKEPVSLDAPIGSDD--DGKFGDFVEDKSSVGPMDYILKEDLKVQ---I 553

Query: 229 TRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 554 DDVLEQLNDREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLK 609


>gi|119386779|ref|YP_917834.1| RNA polymerase sigma factor RpoD [Paracoccus denitrificans PD1222]
 gi|119377374|gb|ABL72138.1| RNA polymerase, sigma 70 subunit, RpoD [Paracoccus denitrificans
           PD1222]
          Length = 664

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 426 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 485

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 486 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 540

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   ++N +   
Sbjct: 541 PLEKVRKV-MKIA-KEPISLETPIGDEEDSQLGDFI---EDKNAVLPLDSAIQENLKETT 595

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 596 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 650


>gi|319406862|emb|CBI80497.1| RNA polymerase sigma factor [Bartonella sp. 1-1C]
          Length = 669

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 121/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 431 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 490

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   ++ KL++
Sbjct: 491 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQILHEIGREPTPEE---LSSKLSM 545

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+++S   D++    D    + I+   + N R+  
Sbjct: 546 PLEKVRKV-LKIAK-EPISLETPVGDEDASHLGDFI---EDRNALLPIDAAIQANLRDTT 600

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 601 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 655


>gi|89055941|ref|YP_511392.1| RNA polymerase sigma factor RpoD [Jannaschia sp. CCS1]
 gi|88865490|gb|ABD56367.1| RNA polymerase, sigma 70 subunit, RpoD [Jannaschia sp. CCS1]
          Length = 668

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 430 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 489

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 490 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 544

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   ++N +   
Sbjct: 545 PLEKVRKV-MKIA-KEPISLETPIGDEEDSQLGDFI---EDKNAVLPLDSAIQENLKETT 599

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 600 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 654


>gi|62290370|ref|YP_222163.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 1 str.
           9-941]
 gi|254708148|ref|ZP_05169976.1| RNA polymerase sigma factor RpoD [Brucella pinnipedialis
           M163/99/10]
 gi|261315652|ref|ZP_05954849.1| RNA polymerase sigma factor RpoD [Brucella pinnipedialis
           M163/99/10]
 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]
          Length = 672

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 119/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 434 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 493

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 494 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 548

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R+  
Sbjct: 549 PLEKVRKV-LKIAK-EPISLETPVGDEEDSHLGDFI---EDKNALLPIDAAIQANLRDTT 603

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 604 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 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|254689668|ref|ZP_05152922.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 6 str. 870]
 gi|254694158|ref|ZP_05155986.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 3 str.
           Tulya]
 gi|254697811|ref|ZP_05159639.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 2 str.
           86/8/59]
 gi|254702196|ref|ZP_05164024.1| RNA polymerase sigma factor RpoD [Brucella suis bv. 5 str. 513]
 gi|254714701|ref|ZP_05176512.1| RNA polymerase sigma factor RpoD [Brucella ceti M644/93/1]
 gi|254717762|ref|ZP_05179573.1| RNA polymerase sigma factor RpoD [Brucella ceti M13/05/1]
 gi|254730700|ref|ZP_05189278.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 4 str. 292]
 gi|256045103|ref|ZP_05448004.1| RNA polymerase sigma factor RpoD [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|256114033|ref|ZP_05454810.1| RNA polymerase sigma factor RpoD [Brucella melitensis bv. 3 str.
           Ether]
 gi|256257919|ref|ZP_05463455.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 9 str. C68]
 gi|256369896|ref|YP_003107407.1| RNA polymerase sigma factor [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|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]
          Length = 672

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 119/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 434 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 493

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 494 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 548

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R+  
Sbjct: 549 PLEKVRKV-LKIAK-EPISLETPVGDEEDSHLGDFI---EDKNALLPIDAAIQANLRDTT 603

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 604 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 658


>gi|229526927|ref|ZP_04416329.1| RNA polymerase sigma factor RpoD [Vibrio cholerae bv. albensis
           VL426]
 gi|229336054|gb|EEO01074.1| RNA polymerase sigma factor RpoD [Vibrio cholerae bv. albensis
           VL426]
          Length = 547

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 119/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 309 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 368

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 369 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 423

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R+  
Sbjct: 424 PLEKVRKV-LKIA-KEPISLETPVGDEEDSHLGDFI---EDKNALLPIDAAIQANLRDTT 478

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 479 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 533


>gi|254719520|ref|ZP_05181331.1| RNA polymerase sigma factor RpoD [Brucella sp. 83/13]
 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 = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 119/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 434 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 493

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 494 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 548

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R+  
Sbjct: 549 PLEKVRKV-LKIAK-EPISLETPVGDEEDSHLGDFI---EDKNALLPIDAAIQANLRDTT 603

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 604 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 658


>gi|16332132|ref|NP_442860.1| RNA polymerase sigma factor RpoD [Synechocystis sp. PCC 6803]
 gi|47717353|sp|P74565|RPOD_SYNY3 RecName: Full=RNA polymerase sigma factor rpoD
 gi|1653761|dbj|BAA18672.1| RNA polymerase sigma factor [Synechocystis sp. PCC 6803]
          Length = 425

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 127/236 (53%), Gaps = 17/236 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 189 AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 248

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT-DNNLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++ +   KP E+ +A   ++
Sbjct: 249 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKLLSQEMRRKPTEEEIAEKMEM 303

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  D +  E  + +   R++  N
Sbjct: 304 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIEADGETPEDEVSKNLLREDLEN 359

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKV 280
           +L      L+PRER +   R   ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 360 VL----DTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKL 411


>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|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]
          Length = 672

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 119/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 434 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 493

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 494 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 548

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R+  
Sbjct: 549 PLEKVRKV-LKIAK-EPISLETPVGDEEDSHLGDFI---EDKNALLPIDAAIQANLRDTT 603

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 604 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 658


>gi|89070863|ref|ZP_01158102.1| RNA polymerase sigma factor [Oceanicola granulosus HTCC2516]
 gi|89043551|gb|EAR49761.1| RNA polymerase sigma factor [Oceanicola granulosus HTCC2516]
          Length = 657

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 419 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 478

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 479 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 533

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   ++N +   
Sbjct: 534 PLEKVRKV-MKIA-KEPISLETPIGDEEDSQLGDFI---EDKNAVLPLDSAIQENLKETT 588

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 589 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 643


>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 = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 76/265 (28%), Positives = 125/265 (47%), Gaps = 32/265 (12%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L+  +E   A  Y E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+
Sbjct: 359 LDDLKELSRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 418

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           AV KF+  RG++ +TY+ WWI+ A+   I      ++I    +       L R+   +  
Sbjct: 419 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQ 476

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSS 198
                  PE+   +AK++++ E ++          ISM   +  DE             S
Sbjct: 477 QYGREATPEE---LAKEMDMPEDKIRKVMKIAKEPISMETPIGDDE------------DS 521

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLE 256
              D++    D   +  IE     N    +   ++ L PRE ++   R  +  N   TLE
Sbjct: 522 HLGDFI---EDTNVESPIENTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLE 578

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  +F+V+RER+RQIEA+A +K++
Sbjct: 579 EVGKQFDVTRERIRQIEAKALRKLR 603


>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 = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 75/239 (31%), Positives = 123/239 (51%), Gaps = 20/239 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 428 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 487

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+      +R  +  L  I      PE+   +A+
Sbjct: 488 IRQAITRSIADQARTIRIPVHMIETINKI-----VRTSRQMLHEIG-REPTPEE---LAE 538

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           KL +   +V  +  ++A  E ++      D+  S   D++    D    + I+   + N 
Sbjct: 539 KLAMPLEKVRKV-LKIAK-EPISLETPVGDEEDSHLGDFI---EDKNALLPIDAAIQANL 593

Query: 225 RNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R+  TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 594 RDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 652


>gi|163742972|ref|ZP_02150355.1| RNA polymerase sigma factor [Phaeobacter gallaeciensis 2.10]
 gi|161383655|gb|EDQ08041.1| RNA polymerase sigma factor [Phaeobacter gallaeciensis 2.10]
          Length = 662

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 424 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 483

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 484 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 538

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   ++N +   
Sbjct: 539 PLEKVRKV-MKIAK-EPISLETPIGDEEDSQLGDFI---EDKNAVLPLDSAIQENLKETT 593

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 594 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 648


>gi|110679091|ref|YP_682098.1| RNA polymerase sigma factor RpoD [Roseobacter denitrificans OCh
           114]
 gi|109455207|gb|ABG31412.1| RNA polymerase sigma-70 factor RpoD [Roseobacter denitrificans OCh
           114]
          Length = 661

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 423 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 482

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 483 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 537

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   ++N +   
Sbjct: 538 PLEKVRKV-MKIA-KEPISLETPIGDEEDSQLGDFI---EDKNAVLPLDSAIQENLKETT 592

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 593 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 647


>gi|296535367|ref|ZP_06897567.1| possible DNA-directed RNA polymerase sigma subunit SigA [Roseomonas
            cervicalis ATCC 49957]
 gi|296264309|gb|EFH10734.1| possible DNA-directed RNA polymerase sigma subunit SigA [Roseomonas
            cervicalis ATCC 49957]
          Length = 1063

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 70/236 (29%), Positives = 119/236 (50%), Gaps = 13/236 (5%)

Query: 47   LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + A   +V  +L+ VV +A  Y    +P  ++V EG IGL++A+ +FDP+RGFR  TY+ 
Sbjct: 825  IDARQEIVEGNLKRVVWLARRYARAAVPFLDLVQEGQIGLLRAIDRFDPDRGFRFGTYAT 884

Query: 107  WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            WWI+ +M  Y+      V++     ++      +R    L+A T     P+++ A     
Sbjct: 885  WWIRQSMSRYVQDQGRTVRVPVHMLER--IAKAKRASEALRAKTGVVPTPQELAA----- 937

Query: 167  NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
               E++V+S+   LA D      I+  D  S   +D  +      E   +      + R 
Sbjct: 938  -ALEADVVSVERALAADLE---GISFDDMGSLPDEDAALVAPLVDEATPLTALLHHDLRR 993

Query: 227  MLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            +L  S+  L+ R+ RI + R      NP+TLE +   + V+RER+RQIEA++ K++
Sbjct: 994  LLAASLRRLDARQARIIDLRFGLTDGNPLTLEEVGQFYGVTRERIRQIEAKSLKRL 1049


>gi|148657222|ref|YP_001277427.1| RpoD family RNA polymerase sigma factor [Roseiflexus sp. RS-1]
 gi|148569332|gb|ABQ91477.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus sp.
           RS-1]
          Length = 349

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 83/303 (27%), Positives = 133/303 (43%), Gaps = 56/303 (18%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHG----------DLS----------------A 49
           +  Y+ EI ++P+L   EE  LA+R               DLS                A
Sbjct: 53  IQHYLQEIGRVPLLTAAEEVELAERMERGAAAARRLASAEDLSPQLRQALLDDVAAGQEA 112

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+ ++LRLVV IA  Y G GL + +++ EGNIGLM+AV+KFD  +G R +TY+ WWI
Sbjct: 113 RRHLIQANLRLVVSIAKKYVGRGLSLLDLIQEGNIGLMRAVEKFDHRKGNRFSTYATWWI 172

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA-------- 161
           + A+   I      +++    ++      ++R    L  + +    PE++          
Sbjct: 173 RQAVTRAIAEQGRTIRLPVHMSES--VGQVKRAADRLAQVLERQPTPEEIATALGQPTER 230

Query: 162 IAKKLNVSESEV-ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
           I + L  S   V + M     G+ +L   +  SD  +                  +E   
Sbjct: 231 IERVLEASRRPVSLEMPVGEDGEHTLGDFLQDSDLPTP-----------------VEAAS 273

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFK 278
            +  R  L  ++  LN RERRI + R   +     TLE +     ++RER RQIEA A +
Sbjct: 274 HQLLRRDLAAALDRLNERERRIIDLRYGLVDGQRRTLEEVGRVLGMTRERARQIEAEALR 333

Query: 279 KVQ 281
           +++
Sbjct: 334 RLR 336


>gi|126659035|ref|ZP_01730176.1| RNA polymerase sigma factor RpoD [Cyanothece sp. CCY0110]
 gi|126619692|gb|EAZ90420.1| RNA polymerase sigma factor RpoD [Cyanothece sp. CCY0110]
          Length = 416

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 128/237 (54%), Gaps = 17/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 180 AKDKMVHSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 239

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT-DNNLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++ +   KP E+ +A   ++
Sbjct: 240 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKLLSQEMRRKPTEEEIATRMEM 294

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  D +  E  + +   R++  N
Sbjct: 295 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIEADGETPEDEVSKNLLREDLEN 350

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +L      L+PRER +   R   ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 351 VL----DTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLR 403


>gi|121601699|ref|YP_989245.1| RNA polymerase sigma factor RpoD [Bartonella bacilliformis KC583]
 gi|120613876|gb|ABM44477.1| RNA polymerase sigma factor RpoD [Bartonella bacilliformis KC583]
          Length = 666

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 428 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 487

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   ++ KL++
Sbjct: 488 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQILHEIGREPTPEE---LSSKLSM 542

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D++ S   D++    D    + I+   + N R+  
Sbjct: 543 PLEKVQKV-LKIAK-EPISLETPVGDEDDSHLGDFI---EDRNALLPIDAAIQANLRDTT 597

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 598 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 652


>gi|169630092|ref|YP_001703741.1| RNA polymerase sigma factor [Mycobacterium abscessus ATCC 19977]
 gi|169242059|emb|CAM63087.1| Probable RNA polymerase sigma factor RpoD (Sigma-A) [Mycobacterium
           abscessus]
          Length = 467

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 82/318 (25%), Positives = 151/318 (47%), Gaps = 43/318 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGD-LS 48
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+ L 
Sbjct: 155 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQIVTELTEKGEKLP 213

Query: 49  AAHR----------------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           AA R                L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 214 AAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 273

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L      
Sbjct: 274 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGR 331

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D + 
Sbjct: 332 EPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEA 383

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVR 270
            V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 384 VVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIR 443

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 444 QIESKTMSKLRHPSRSQV 461


>gi|163738642|ref|ZP_02146056.1| RNA polymerase, sigma 38 subunit, RpoS [Phaeobacter gallaeciensis
           BS107]
 gi|161387970|gb|EDQ12325.1| RNA polymerase, sigma 38 subunit, RpoS [Phaeobacter gallaeciensis
           BS107]
          Length = 662

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 424 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 483

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 484 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 538

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   ++N +   
Sbjct: 539 PLEKVRKV-MKIAK-EPISLETPIGDEEDSQLGDFI---EDKNAVLPLDSAIQENLKETT 593

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 594 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 648


>gi|153009018|ref|YP_001370233.1| RNA polymerase sigma factor RpoD [Ochrobactrum anthropi ATCC 49188]
 gi|151560906|gb|ABS14404.1| RNA polymerase, sigma 70 subunit, RpoD [Ochrobactrum anthropi ATCC
           49188]
          Length = 671

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 75/239 (31%), Positives = 123/239 (51%), Gaps = 20/239 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 433 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 492

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+      +R  +  L  I      PE+   +A+
Sbjct: 493 IRQAITRSIADQARTIRIPVHMIETINKI-----VRTSRQMLHEIG-REPTPEE---LAE 543

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           KL +   +V  +  ++A  E ++      D+  S   D++    D    + I+   + N 
Sbjct: 544 KLAMPLEKVRKV-LKIAK-EPISLETPVGDEEDSHLGDFI---EDKNALLPIDAAIQANL 598

Query: 225 RNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R+  TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 599 RDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 657


>gi|310816221|ref|YP_003964185.1| RNA polymerase sigma factor [Ketogulonicigenium vulgare Y25]
 gi|308754956|gb|ADO42885.1| RNA polymerase sigma factor [Ketogulonicigenium vulgare Y25]
          Length = 658

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 420 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 479

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 480 IRQAITRSIADQARTIRI--PVHMIETINKLVRTSRQMLHEIGREPTPEE---LAEKLQM 534

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   ++N +   
Sbjct: 535 PLEKVRKV-MKIA-KEPISLETPIGDEEDSQLGDFI---EDKNAILPLDSAIQENLKETT 589

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 590 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 644


>gi|332653408|ref|ZP_08419153.1| RNA polymerase sigma factor RpoD [Ruminococcaceae bacterium D16]
 gi|332518554|gb|EGJ48157.1| RNA polymerase sigma factor RpoD [Ruminococcaceae bacterium D16]
          Length = 446

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 75/239 (31%), Positives = 125/239 (52%), Gaps = 22/239 (9%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  RL  ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WW
Sbjct: 209 AKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWW 268

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQK-RLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           I+ A+   I      ++I      T N+  R+   L +  GH       +  PE+   IA
Sbjct: 269 IRQAITRAIADQARTIRIPVHMVETINKVIRVSRQLLQELGH-------DPSPEE---IA 318

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           +++++    V  +  ++A  E ++      ++  S   D+ + D D  E    E      
Sbjct: 319 EEMSMPVERVREI-LKIA-QEPVSLETPIGEEEDSHLGDF-IPDEDASEPA--EAASFTL 373

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
            +  L   +S L PRE ++ + R   E+    TLE +  EF V+RER+RQIEA+A +K+
Sbjct: 374 LKEQLVEVLSTLTPREEKVLKLRFGIEDGRTRTLEEVGKEFNVTRERIRQIEAKALRKL 432


>gi|56696627|ref|YP_166988.1| RNA polymerase sigma factor RpoD [Ruegeria pomeroyi DSS-3]
 gi|56678364|gb|AAV95030.1| RNA polymerase sigma-70 factor RpoD [Ruegeria pomeroyi DSS-3]
          Length = 660

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 422 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 481

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 482 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 536

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   ++N +   
Sbjct: 537 PLEKVRKV-MKIAK-EPISLETPIGDEEDSQLGDFI---EDKNAVLPLDSAIQENLKETT 591

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 592 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 646


>gi|83941156|ref|ZP_00953618.1| RNA polymerase sigma factor [Sulfitobacter sp. EE-36]
 gi|83955715|ref|ZP_00964295.1| RNA polymerase sigma factor [Sulfitobacter sp. NAS-14.1]
 gi|83840009|gb|EAP79185.1| RNA polymerase sigma factor [Sulfitobacter sp. NAS-14.1]
 gi|83846976|gb|EAP84851.1| RNA polymerase sigma factor [Sulfitobacter sp. EE-36]
          Length = 660

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 422 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 481

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 482 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 536

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   ++N +   
Sbjct: 537 PLEKVRKV-MKIA-KEPISLETPIGDEEDSQLGDFI---EDKNAVLPLDSAIQENLKETT 591

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 592 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 646


>gi|254511749|ref|ZP_05123816.1| Sigma-70, region 3 family [Rhodobacteraceae bacterium KLH11]
 gi|221535460|gb|EEE38448.1| Sigma-70, region 3 family [Rhodobacteraceae bacterium KLH11]
          Length = 662

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 424 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 483

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 484 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 538

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   ++N +   
Sbjct: 539 PLEKVRKV-MKIAK-EPISLETPIGDEEDSQLGDFI---EDKNAVLPLDSAIQENLKETT 593

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 594 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 648


>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 = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 76/258 (29%), Positives = 126/258 (48%), Gaps = 13/258 (5%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+ E +  Y    R  E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIG
Sbjct: 398 LPVGEFRRVYATVSRG-ERDSARAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 456

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           LM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I    +       L R    
Sbjct: 457 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI--PVHMIETINKLVRTSRQ 514

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           +         PE+   +A+KL +   +V  +  ++A  E ++      D+  S   D++ 
Sbjct: 515 MLHEIGREPAPEE---LAEKLGMPLEKVRKV-LKIA-KEPISLETPIGDEEDSHLGDFI- 568

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFE 263
              D    + ++   + N R   TR +S L PRE R+   R         TLE +  +F 
Sbjct: 569 --EDKAAVIPLDAAIQTNLREATTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFN 626

Query: 264 VSRERVRQIEARAFKKVQ 281
           V+RER+RQIEA+A +K++
Sbjct: 627 VTRERIRQIEAKALRKLK 644


>gi|269926188|ref|YP_003322811.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
 gi|269789848|gb|ACZ41989.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
          Length = 463

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 81/286 (28%), Positives = 138/286 (48%), Gaps = 36/286 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKR---------YREHGDLSAAHRLVTSHLRLVVKIAM 66
           ++ YI    K P ++   + +LA +          R+ G+  A  +L+ ++ RLVV IA 
Sbjct: 184 ITEYIERSNKCPDVKTVSQVLLANKSIVINHWNKVRKEGE-GAKCKLIEANTRLVVSIAK 242

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y G GL + +++ EGNIGLM+A  KFD  RG++ +TY+ WWI+ A+   I      +++
Sbjct: 243 KYLGRGLSLLDLIQEGNIGLMRAADKFDYTRGYKFSTYATWWIRQAVTRAIADQSRTIRL 302

Query: 127 G-----TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
                 T +   +    L++  GH   I    L  E  + + K + + ++    +     
Sbjct: 303 PVHVCETVSKIHKTSQKLQQELGHEPTI--EQLSSELGMPMKKVVQIQQASKFPV----- 355

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL--IEKEERKNRRNMLTRSMSVLNPRE 239
              SL A I   +   S   D+L   H     VL  ++K      R  +   +  L P+E
Sbjct: 356 ---SLEAPIG--EDGDSMLGDFLEDVH-----VLNPVQKAANDILREQINSVLQNLPPKE 405

Query: 240 RRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           R++ E R   +     TLE + +EF ++RERVRQIE  A ++++E+
Sbjct: 406 RKVLELRFGLVDGKCRTLEEVGNEFAITRERVRQIECTALRRLREN 451


>gi|117928920|ref|YP_873471.1| RNA polymerase, sigma 28 subunit [Acidothermus cellulolyticus 11B]
 gi|117649383|gb|ABK53485.1| RNA polymerase, sigma 28 subunit [Acidothermus cellulolyticus 11B]
          Length = 413

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 80/305 (26%), Positives = 143/305 (46%), Gaps = 63/305 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR----------------------------YREHGDLSAA 50
           Y++EI + P+L+  +E  LAKR                             R+ G  + A
Sbjct: 119 YLNEIGRTPLLDAAQEVELAKRIEAGVYADVKLNDPTLQLTEEERRDLEAIRDDGARAKA 178

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           H ++ ++LRLVV +A  Y   G+   +V+ EGN+GL++AV+KFD  +G++ +TY+MWWI+
Sbjct: 179 H-MLEANLRLVVSVAKRYSNRGMAFLDVIQEGNLGLIRAVEKFDYTKGYKFSTYAMWWIR 237

Query: 111 AAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
            A+   +      +++           T  Q+ L     R     +   + +  PEQ+  
Sbjct: 238 QAITRALADQARTIRLPVHVVEQLNKLTRLQRELHQQFGREPTAEELAAELDRTPEQI-- 295

Query: 162 IAKKLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +++  +  + +S++  +  DE   L  LI   D  +    D L Y      Q +I   
Sbjct: 296 --EEMLRNARQPVSLDNPVGDDEDTLLGDLIE--DMEAPAASDALEY------QAMI--- 342

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAF 277
                 + + R+++ L+PRE R+   R   +   P TL+ +  +  ++RERVRQIE  A 
Sbjct: 343 ------DTVHRALAGLDPREARVIALRFGLVGGRPHTLDEIGRDVGLTRERVRQIEREAL 396

Query: 278 KKVQE 282
            K+++
Sbjct: 397 AKLRD 401


>gi|319898528|ref|YP_004158621.1| RNA polymerase sigma factor [Bartonella clarridgeiae 73]
 gi|319402492|emb|CBI76035.1| RNA polymerase sigma factor [Bartonella clarridgeiae 73]
          Length = 669

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 121/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 431 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 490

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   ++ KL++
Sbjct: 491 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQILHEIGREPTPEE---LSSKLSM 545

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+++S   D++    D    + I+   + N R+  
Sbjct: 546 PLEKVRKV-LKIA-KEPISLETPVGDEDASHLGDFI---EDRNALLPIDAAIQANLRDTT 600

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 601 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 655


>gi|269836760|ref|YP_003318988.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphaerobacter
           thermophilus DSM 20745]
 gi|269786023|gb|ACZ38166.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphaerobacter
           thermophilus DSM 20745]
          Length = 538

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 81/267 (30%), Positives = 135/267 (50%), Gaps = 34/267 (12%)

Query: 29  LEKQEEYVLAKRYRE---HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           L +++E  L  R+ E    GD+ A  +L  ++LRLVV +A  Y G G+ + ++V EGN+G
Sbjct: 279 LLRRDEAALQARWEEFVVRGDI-ARKKLTEANLRLVVSVAKKYGGRGMSMLDLVQEGNLG 337

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK--RLFFNLRRLK 143
           L++AV+KF   +GF+ +TY+ WWI+ A+   I      ++I     ++  RL    RRL+
Sbjct: 338 LIRAVEKFQHHKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVEQINRLIRTSRRLQ 397

Query: 144 GHL-------QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
             L       +   +  L P++V  I   L +S+ E +S+   +  +E  N         
Sbjct: 398 QELGREPTSEEIAAEMGLPPDKVREI---LKISQ-EPVSLEMPIGEEEDSN--------- 444

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-T 254
                D++    D +     +    K  +  +   +  L  RERR+ E R  L +    T
Sbjct: 445 ---LGDFI---EDSKALAPSDAASLKLLKEQVDDVLGSLGDRERRVLELRFGLDDGRTRT 498

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQ 281
           LE +  EF V+RER+RQIEA+A +K++
Sbjct: 499 LEEVGREFGVTRERIRQIEAKALRKLR 525


>gi|254432880|ref|ZP_05046583.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Cyanobium sp. PCC 7001]
 gi|197627333|gb|EDY39892.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Cyanobium sp. PCC 7001]
          Length = 331

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 72/239 (30%), Positives = 123/239 (51%), Gaps = 25/239 (10%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ ++LRLVV +A  Y+G GL + +++ EG++GL +AV+KFDP RG++ +TY+ WWI+ 
Sbjct: 99  RMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWWIRQ 158

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA-------IAK 164
           +M   I            A Q R       L   L AI   +L     +        IA+
Sbjct: 159 SMTRAI------------ACQSRTIRLPVHLSERLSAIRKVSLDLAHKLGAMPSRHEIAE 206

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            +++   E+  +  +     SL+A +N  D+  S   D +    D  E+  +++ ER   
Sbjct: 207 AMDMPLDELDGLLRQALTTSSLDAPVN-GDEGRSFLGDLIA---DSSEEEPLDRVERGLN 262

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              L   M+ L+ +ER + + R   E  +  TL  +  + +VSRERVRQ+E +A +K++
Sbjct: 263 HEQLDHWMNHLSEQERHVLQLRFGLEGRDRHTLAEIGRQLDVSRERVRQVELKALRKLR 321


>gi|149197872|ref|ZP_01874921.1| RNA polymerase sigma factor RpoD [Lentisphaera araneosa HTCC2155]
 gi|149139093|gb|EDM27497.1| RNA polymerase sigma factor RpoD [Lentisphaera araneosa HTCC2155]
          Length = 274

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 75/270 (27%), Positives = 140/270 (51%), Gaps = 23/270 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+  I ++P++ + +E  LA+    +G  SA  +L+  +LRLVVKIA  ++  G+P++++
Sbjct: 11  YMKNIAELPLISRDDEVELAELIN-NGSESAREQLIVGNLRLVVKIAHDFKSLGVPLADL 69

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           +SEGNIGLM+AV+KF P  G + ++Y  WWIK A++  +     +++I   +  K   + 
Sbjct: 70  ISEGNIGLMKAVEKFKPGMGAKFSSYGAWWIKQAIRRCVAEQSRVIRIPVQSAVK--MYK 127

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM----NCRLAGDESLNALINS-S 193
           ++R+  HL          E++  +  +  ++E+  +S     N ++A      +L  S  
Sbjct: 128 IQRVAMHL---------AEELGRVPSEKEIAEAADMSQRSVHNLKVAATSPTISLSTSLK 178

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV-LNPRERRIFEARRLQENP 252
           D      +D L    D   ++   + + ++ +++L   +   L  RE+ I   R      
Sbjct: 179 DGEDGVLEDML---PDLMAKMPGGEMDDRDVKSLLQDCVDQHLTEREKLIINMRYGLNGG 235

Query: 253 V--TLENLSSEFEVSRERVRQIEARAFKKV 280
              TL+ +S     +RERVRQI+ +A KK+
Sbjct: 236 EQHTLDEISELIGRTRERVRQIQHKALKKL 265


>gi|99081981|ref|YP_614135.1| RNA polymerase sigma factor RpoD [Ruegeria sp. TM1040]
 gi|99038261|gb|ABF64873.1| RNA polymerase, sigma 38 subunit, RpoS [Ruegeria sp. TM1040]
          Length = 664

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 426 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 485

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 486 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 540

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   ++N +   
Sbjct: 541 PLEKVRKV-MKIAK-EPISLETPIGDEEDSQLGDFI---EDKNAVLPLDSAIQENLKETT 595

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 596 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 650


>gi|326384438|ref|ZP_08206118.1| RNA polymerase sigma factor [Gordonia neofelifaecis NRRL B-59395]
 gi|326196783|gb|EGD53977.1| RNA polymerase sigma factor [Gordonia neofelifaecis NRRL B-59395]
          Length = 466

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 82/318 (25%), Positives = 151/318 (47%), Gaps = 43/318 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGD-LS 48
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+ LS
Sbjct: 154 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLFATERLRRVMESGEKLS 212

Query: 49  AAHR----------------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
            A R                L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 213 VAQRRDLSWISRDGNRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 272

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L      
Sbjct: 273 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGR 330

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D + 
Sbjct: 331 EPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEA 382

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVR 270
            V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 383 VVAVDAVSFTLLQDQLQDVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIR 442

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 443 QIESKTMSKLRHPSRSQV 460


>gi|33239946|ref|NP_874888.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus subsp.
           marinus str. CCMP1375]
 gi|33237472|gb|AAP99540.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Prochlorococcus marinus subsp. marinus str. CCMP1375]
          Length = 438

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 68/234 (29%), Positives = 128/234 (54%), Gaps = 17/234 (7%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ 
Sbjct: 205 KMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQ 264

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKP-EQVVAIAKKLNVS 169
           A+   I      +++        L+  + R+K   + ++     KP E+ +A + ++ + 
Sbjct: 265 AITRAIADQSRTIRLPV-----HLYETISRIKKTTKVLSQEFGRKPSEEEIAESMEMTIE 319

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           +   I+ + +L    SL   I   +   S+  D++  D +  E  + +   R++   +L 
Sbjct: 320 KLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIESDSENPELDVAKTLLREDLEGVL- 374

Query: 230 RSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              + L+PRER +   R   ++    TLE +   F+V+RER+RQIEA+A +K++
Sbjct: 375 ---ATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIRQIEAKALRKLR 425


>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 = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 76/258 (29%), Positives = 126/258 (48%), Gaps = 13/258 (5%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+ E +  Y    R  E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIG
Sbjct: 398 LPVGEFRRVYATVSRG-ERDSARAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 456

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           LM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I    +       L R    
Sbjct: 457 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI--PVHMIETINKLVRTSRQ 514

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           +         PE+   +A+KL +   +V  +  ++A  E ++      D+  S   D++ 
Sbjct: 515 MLHEIGREPAPEE---LAEKLGMPLEKVRKV-LKIA-KEPISLETPIGDEEDSHLGDFI- 568

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFE 263
              D    + ++   + N R   TR +S L PRE R+   R         TLE +  +F 
Sbjct: 569 --EDKTAVIPLDAAIQTNLREATTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFN 626

Query: 264 VSRERVRQIEARAFKKVQ 281
           V+RER+RQIEA+A +K++
Sbjct: 627 VTRERIRQIEAKALRKLK 644


>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 = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 66/245 (26%), Positives = 120/245 (48%), Gaps = 32/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 510 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 569

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+  + Q + +   +P+    +A+K+++
Sbjct: 570 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--NRQILQETGAEPDPAT-LAQKMDM 624

Query: 169 SESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            E +V          ISM   +  D+  +      D  +    +W ++            
Sbjct: 625 PEDKVRKILKIAKEPISMETPIGDDDDSHLGDFIEDTGTLSPSEWALH------------ 672

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARA 276
               + R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A
Sbjct: 673 ---GSMRDVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKA 729

Query: 277 FKKVQ 281
            +K++
Sbjct: 730 LRKLR 734


>gi|218674803|ref|ZP_03524472.1| RNA polymerase sigma factor RpoD [Rhizobium etli GR56]
          Length = 254

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 75/239 (31%), Positives = 122/239 (51%), Gaps = 20/239 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 16  AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 75

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+      +R  +  L  I      PE+   +A+
Sbjct: 76  IRQAITRSIADQARTIRIPVHMIETINK-----IVRTSRQMLHEI-GREPTPEE---LAE 126

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           KL +   +V  +  ++A  E ++      D+  S   D++    D    + I+   + N 
Sbjct: 127 KLAMPLEKVRKV-LKIA-KEPISLETPVGDEEDSHLGDFI---EDKNALLPIDAAIQANL 181

Query: 225 RNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 182 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 240


>gi|159044804|ref|YP_001533598.1| RNA polymerase sigma factor RpoD [Dinoroseobacter shibae DFL 12]
 gi|157912564|gb|ABV93997.1| RNA polymerase sigma factor [Dinoroseobacter shibae DFL 12]
          Length = 664

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 73/236 (30%), Positives = 121/236 (51%), Gaps = 14/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 426 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 485

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 486 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 540

Query: 169 SESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
              +V  +  ++A +  SL   I   D+  SQ  D++    D    + ++   ++N +  
Sbjct: 541 PLEKVRKV-MKIAKEPISLETPIG--DEEDSQLGDFI---EDKNAVLPLDSAIQENLKET 594

Query: 228 LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 595 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 650


>gi|259416365|ref|ZP_05740285.1| RNA polymerase sigma factor RpoD [Silicibacter sp. TrichCH4B]
 gi|259347804|gb|EEW59581.1| RNA polymerase sigma factor RpoD [Silicibacter sp. TrichCH4B]
          Length = 664

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 426 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 485

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 486 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 540

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   ++N +   
Sbjct: 541 PLEKVRKV-MKIA-KEPISLETPIGDEEDSQLGDFI---EDKNAVLPLDSAIQENLKETT 595

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 596 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 650


>gi|163733984|ref|ZP_02141425.1| RNA polymerase sigma-70 factor RpoD [Roseobacter litoralis Och 149]
 gi|161392520|gb|EDQ16848.1| RNA polymerase sigma-70 factor RpoD [Roseobacter litoralis Och 149]
          Length = 660

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 422 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 481

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 482 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 536

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   ++N +   
Sbjct: 537 PLEKVRKV-MKIA-KEPISLETPIGDEEDSQLGDFI---EDKNAVLPLDSAIQENLKETT 591

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 592 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 646


>gi|308232215|ref|ZP_07415319.2| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu001]
 gi|308373480|ref|ZP_07667590.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu005]
 gi|308214639|gb|EFO74038.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu001]
 gi|308337452|gb|EFP26303.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu005]
          Length = 413

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 82/318 (25%), Positives = 151/318 (47%), Gaps = 43/318 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGD-LS 48
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+ L 
Sbjct: 101 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSERGEKLP 159

Query: 49  AAHR----------------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           AA R                L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 160 AAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 219

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L      
Sbjct: 220 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGR 277

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D + 
Sbjct: 278 EPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEA 329

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVR 270
            V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 330 VVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIR 389

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 390 QIESKTMSKLRHPSRSQV 407


>gi|303233350|ref|ZP_07320019.1| RNA polymerase sigma factor RpoD [Atopobium vaginae PB189-T1-4]
 gi|302480479|gb|EFL43570.1| RNA polymerase sigma factor RpoD [Atopobium vaginae PB189-T1-4]
          Length = 441

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 86/282 (30%), Positives = 136/282 (48%), Gaps = 49/282 (17%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           GEI LSR   E+R++     +EE V          L A   L +++LRL V IA  Y G 
Sbjct: 181 GEIELSR--SEMRRL----MREEQV---------GLDAKQALTSANLRLTVSIAKRYVGR 225

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT--- 128
           G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     
Sbjct: 226 GMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMV 285

Query: 129 -TAN-----QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA- 181
            T N     Q++L   L R     +   + N+ P+++  I K   +S+ E +S+   +  
Sbjct: 286 ETINKLVRIQRQLLQELGRDPSPEEIGKEMNMSPDKIREIQK---ISQ-EPVSLETPIGE 341

Query: 182 -GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
             D SL   I  S           V   D     ++        R  L + +  L  RER
Sbjct: 342 EEDSSLGDFIEDS---------TAVAPPDAASDSML--------REQLNQVLDSLADRER 384

Query: 241 RIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
           ++ + R   E+  P TLE +  EF V+RER+RQIE++   K+
Sbjct: 385 KVIKFRFGLEDGHPRTLEEVGREFGVTRERIRQIESKTLAKL 426


>gi|255261823|ref|ZP_05341165.1| RNA polymerase sigma factor RpoD (Sigma-A) [Thalassiobium sp.
           R2A62]
 gi|255104158|gb|EET46832.1| RNA polymerase sigma factor RpoD (Sigma-A) [Thalassiobium sp.
           R2A62]
          Length = 658

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 420 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 479

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 480 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 534

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   ++N +   
Sbjct: 535 PLEKVRKV-MKIAK-EPISLETPIGDEEDSQLGDFI---EDKNAVLPLDSAIQENLKETT 589

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 590 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 644


>gi|221639823|ref|YP_002526085.1| RNA polymerase sigma factor RpoD [Rhodobacter sphaeroides KD131]
 gi|332558839|ref|ZP_08413161.1| RNA polymerase sigma factor RpoD [Rhodobacter sphaeroides WS8N]
 gi|221160604|gb|ACM01584.1| RNA polymerase sigma factor [Rhodobacter sphaeroides KD131]
 gi|332276551|gb|EGJ21866.1| RNA polymerase sigma factor RpoD [Rhodobacter sphaeroides WS8N]
          Length = 668

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 430 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 489

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 490 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 544

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   ++N +   
Sbjct: 545 PLEKVRKV-MKIA-KEPISLETPIGDEEDSQLGDFI---EDKNAILPLDSAIQENLKETT 599

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 600 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 654


>gi|172035791|ref|YP_001802292.1| RNA polymerase sigma factor RpoD [Cyanothece sp. ATCC 51142]
 gi|171697245|gb|ACB50226.1| group 1 sigma-70 RNA polymerase sigma factor A [Cyanothece sp. ATCC
           51142]
          Length = 416

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 128/237 (54%), Gaps = 17/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 180 AKDKMVHSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 239

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT-DNNLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++ +   KP E+ +A   ++
Sbjct: 240 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKLLSQEMRRKPTEEEIATRMEM 294

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  D +  E  + +   R++  N
Sbjct: 295 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIEADGETPEDEVSKNLLREDLEN 350

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +L      L+PRER +   R   ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 351 VL----DTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLR 403


>gi|49474476|ref|YP_032518.1| RNA polymerase sigma factor RpoD [Bartonella quintana str.
           Toulouse]
 gi|49239980|emb|CAF26393.1| RNA polymerase sigma factor rpod [Bartonella quintana str.
           Toulouse]
          Length = 670

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 432 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 491

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   ++ KL++
Sbjct: 492 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQILHEIGREPTPEE---LSSKLSM 546

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D++ S   D++    D    + I+   + N R+  
Sbjct: 547 PLEKVRKV-LKIA-KEPISLETPVGDEDDSHLGDFI---EDRNALLPIDAAIQANLRDTT 601

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 602 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 656


>gi|299472559|emb|CBN79861.1| chloroplast RNA-polymerase sigma factor precursor [Ectocarpus
           siliculosus]
          Length = 694

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 70/234 (29%), Positives = 119/234 (50%), Gaps = 9/234 (3%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ ++LRLVV +A  YR   L   +++ EG  GL++A +KFDPERGF+ +TY+ WWIK +
Sbjct: 127 MLAANLRLVVSVAKRYRFQKLSFQDLIQEGTFGLVKAAEKFDPERGFKFSTYATWWIKQS 186

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   I     ++++    +    F N  R++     +TD N K      +A+ L VS   
Sbjct: 187 IMRGIADQSRIIRLPVHVHD---FLN--RVRKATLEMTDKNGKLPTDDELAEHLEVSAVR 241

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH--DGQEQVLIEKEERKNRRNMLTR 230
           +           S+ A  N + K S+     +       G E+   ++ +    +  +T 
Sbjct: 242 IQYYRDAAQATLSMEAPRNIASKTSTSPGKKVEMGQGVSGPEKTPDKQAQSDVMKQKVTE 301

Query: 231 SMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            +  L+ RE+ + +AR       P TLE +  +F ++RERVRQIEARA  K+++
Sbjct: 302 LLMTLSIREQEVVKARFGLGGALPRTLEEVGRDFRLTRERVRQIEARALHKLRQ 355


>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 = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 417 AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 476

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 477 IRQAITRSIADQARTIRI--PVHMIETINKLVRTSRQMLHEIGREPAPEE---LAEKLGM 531

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + ++   + N R   
Sbjct: 532 PLEKVRKV-LKIA-KEPISLETPIGDEEDSHLGDFI---EDKTAVIPLDAAIQTNLREAT 586

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR +S L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 587 TRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTRERIRQIEAKALRKLK 641


>gi|148242910|ref|YP_001228067.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp.
           RCC307]
 gi|147851220|emb|CAK28714.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. RCC307]
          Length = 293

 Score = 97.1 bits (240), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 79/283 (27%), Positives = 136/283 (48%), Gaps = 26/283 (9%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E+ L R +   +  P    Q    + KR      L A  RLV ++LRLVV +A      G
Sbjct: 27  EVSLGRQVRAWQDHPGGPGQAPAAVQKR-----GLRARGRLVQANLRLVVHLAKKQHLRG 81

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L + ++V EG+IGL +A +K+DP  G+R +TY+ WWIK A+   I      +++    ++
Sbjct: 82  LAMEDLVQEGSIGLQRAAEKYDPSTGYRFSTYAYWWIKQALHRAIQLQTPALRLPCRVSE 141

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVV-AIAKKLN----VSESEVISMNCRLAGDESLN 187
           +     LR  +  L        +PE++  A+ ++++    +  ++VIS  C L  D  + 
Sbjct: 142 R--LGRLRSTRQRLSQELGRQPRPEELAEAMGERIDQLQELERAQVISRGCSL--DTPMG 197

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV--LNPRERRIFEA 245
                SD +     D L  D        +++ E+  R   L   +S   L+ RE  + +A
Sbjct: 198 -----SDPDHGSLVDLLEDDRTSP----MDQLEQALRSEQLAELLSSAGLSEREATVVQA 248

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           R  +E+ +  + L+  F +SRER RQ+E  A +K++   + Q 
Sbjct: 249 RHSEEH-IPYQQLADRFGISRERTRQLEHNALRKLRHCAEAQT 290


>gi|254488657|ref|ZP_05101862.1| Sigma-70, region 3 family [Roseobacter sp. GAI101]
 gi|214045526|gb|EEB86164.1| Sigma-70, region 3 family [Roseobacter sp. GAI101]
          Length = 671

 Score = 96.7 bits (239), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 433 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 492

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 493 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 547

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   ++N +   
Sbjct: 548 PLEKVRKV-MKIAK-EPISLETPIGDEEDSQLGDFI---EDKNAVLPLDSAIQENLKETT 602

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 603 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 657


>gi|158425267|ref|YP_001526559.1| RNA polymerase sigma factor RpoD [Azorhizobium caulinodans ORS 571]
 gi|158332156|dbj|BAF89641.1| sigma-70 [Azorhizobium caulinodans ORS 571]
          Length = 690

 Score = 96.7 bits (239), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 452 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 511

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 512 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLGM 566

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 567 PLEKVRKV-LKIA-KEPISLETPIGDEEDSHLGDFI---EDKNAVLPIDAAIQSNLRETT 621

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 622 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 676


>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 = 96.7 bits (239), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 121/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 566 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 625

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +  L+P+    +A+K+ +
Sbjct: 626 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGLEPDPAT-LAEKMEM 680

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + R+++
Sbjct: 681 PEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDTNTVAPADAAPHASMRDVV 735

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 736 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 790


>gi|146276891|ref|YP_001167050.1| RNA polymerase sigma factor RpoD [Rhodobacter sphaeroides ATCC
           17025]
 gi|145555132|gb|ABP69745.1| RNA polymerase, sigma 70 subunit, RpoD [Rhodobacter sphaeroides
           ATCC 17025]
          Length = 667

 Score = 96.7 bits (239), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 429 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 488

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 489 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 543

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   ++N +   
Sbjct: 544 PLEKVRKV-MKIA-KEPISLETPIGDEEDSQLGDFI---EDKNAILPLDSAIQENLKETT 598

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 599 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 653


>gi|254476970|ref|ZP_05090356.1| Sigma-70, region 3 family [Ruegeria sp. R11]
 gi|214031213|gb|EEB72048.1| Sigma-70, region 3 family [Ruegeria sp. R11]
          Length = 661

 Score = 96.7 bits (239), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 423 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 482

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 483 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 537

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   ++N +   
Sbjct: 538 PLEKVRKV-MKIAK-EPISLETPIGDEEDSQLGDFI---EDKNAVLPLDSAIQENLKETT 592

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 593 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 647


>gi|149183340|ref|ZP_01861778.1| RNA polymerase sigma factor RpoD [Bacillus sp. SG-1]
 gi|148848937|gb|EDL63149.1| RNA polymerase sigma factor RpoD [Bacillus sp. SG-1]
          Length = 330

 Score = 96.7 bits (239), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 58/155 (37%), Positives = 87/155 (56%), Gaps = 10/155 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  QEE  LA R  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 116 YLKEIGRVDLLSAQEEISLANRI-EEGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLDL 174

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN--- 131
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N   
Sbjct: 175 IQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLI 234

Query: 132 --QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
             Q++L  +L R     +   + +L PE+V  I K
Sbjct: 235 RVQRQLLQDLGREPSPEEIAEEMDLTPEKVREILK 269


>gi|126738765|ref|ZP_01754461.1| RNA polymerase sigma factor RpoD [Roseobacter sp. SK209-2-6]
 gi|126719946|gb|EBA16653.1| RNA polymerase sigma factor RpoD [Roseobacter sp. SK209-2-6]
          Length = 663

 Score = 96.7 bits (239), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 425 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 484

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 485 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 539

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   ++N +   
Sbjct: 540 PLEKVRKV-MKIA-KEPISLETPIGDEEDSQLGDFI---EDKNAVLPLDSAIQENLKETT 594

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 595 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 649


>gi|126733203|ref|ZP_01748950.1| RNA polymerase sigma-70 factor RpoD [Roseobacter sp. CCS2]
 gi|126716069|gb|EBA12933.1| RNA polymerase sigma-70 factor RpoD [Roseobacter sp. CCS2]
          Length = 660

 Score = 96.7 bits (239), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 422 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 481

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 482 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 536

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   ++N +   
Sbjct: 537 PLEKVRKV-MKIA-KEPISLETPIGDEEDSQLGDFI---EDKNAILPLDSAIQENLKETT 591

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 592 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 646


>gi|73541439|ref|YP_295959.1| sigma-70 region 1.2 [Ralstonia eutropha JMP134]
 gi|72118852|gb|AAZ61115.1| Sigma-70 region 1.2 [Ralstonia eutropha JMP134]
          Length = 653

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 71/247 (28%), Positives = 119/247 (48%), Gaps = 36/247 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A H +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 414 AKHEMTQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGWKFSTYATWW 473

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           ++ A+   I      +++     ++     L RL   L   T     P     +A+++++
Sbjct: 474 VRQAVTRAIADQARTIRVPVHMIEQ--INKLNRLSRELMQQTGKEPDP---AVLAERMDM 528

Query: 169 SESEV----------ISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
            E +V          +SM   +   GD SL  +I  SD  +                  +
Sbjct: 529 PEEKVRAIMKIAREPVSMETPVGEDGDTSLGDMIADSDTATPA-------------DAAL 575

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEA 274
           +   R+  R ML      L PRE ++   R   +     TLE +  +F+V+RER+RQIE+
Sbjct: 576 QASLREVVREMLDE----LTPREAKVLRMRFGIDMATDYTLEEVGKQFDVTRERIRQIES 631

Query: 275 RAFKKVQ 281
           +A +K++
Sbjct: 632 KAMRKLR 638


>gi|319405291|emb|CBI78905.1| RNA polymerase sigma factor [Bartonella sp. AR 15-3]
          Length = 669

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 121/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 431 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 490

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   ++ KL++
Sbjct: 491 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQILHEIGREPTPEE---LSSKLSM 545

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+++S   D++    D    + I+   + N R+  
Sbjct: 546 PLEKVRKV-LKIA-KEPISLETPVGDEDASHLGDFI---EDRNALLPIDAAIQANLRDTT 600

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 601 TRILASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 655


>gi|254464472|ref|ZP_05077883.1| Sigma-70 region 3 family [Rhodobacterales bacterium Y4I]
 gi|206685380|gb|EDZ45862.1| Sigma-70 region 3 family [Rhodobacterales bacterium Y4I]
          Length = 662

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 119/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 424 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 483

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A KL +
Sbjct: 484 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LADKLQM 538

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   ++N +   
Sbjct: 539 PLEKVRKV-MKIAK-EPISLETPIGDEEDSQLGDFI---EDKNAVLPLDSAIQENLKETT 593

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 594 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 648


>gi|86137897|ref|ZP_01056473.1| RNA polymerase sigma-70 factor RpoD [Roseobacter sp. MED193]
 gi|85825489|gb|EAQ45688.1| RNA polymerase sigma-70 factor RpoD [Roseobacter sp. MED193]
          Length = 663

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 425 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 484

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 485 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 539

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   ++N +   
Sbjct: 540 PLEKVRKV-MKIAK-EPISLETPIGDEEDSQLGDFI---EDKNAVLPLDSAIQENLKETT 594

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 595 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 649


>gi|294678570|ref|YP_003579185.1| RNA polymerase sigma factor RpoD [Rhodobacter capsulatus SB 1003]
 gi|1173126|sp|P46400|RPOD_RHOCA RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|881516|gb|AAA70413.1| RpoD [Rhodobacter capsulatus SB 1003]
 gi|294477390|gb|ADE86778.1| RNA polymerase sigma factor RpoD [Rhodobacter capsulatus SB 1003]
          Length = 674

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 436 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 495

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 496 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 550

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   ++N +   
Sbjct: 551 PLEKVRKV-MKIA-KEPISLETPIGDEEDSQLGDFI---EDKNAILPLDSAIQENLKETT 605

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 606 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 660


>gi|297180868|gb|ADI17073.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [uncultured alpha proteobacterium HF0010_30A23]
          Length = 668

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 115/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 430 AKAEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 489

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA------- 161
           I+ A+   I      ++I    +       L R    +         PE++ A       
Sbjct: 490 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREATPEELAARLGMPLE 547

Query: 162 -IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + K + +++ E IS+   +             D+  S   D++    D    + +E   
Sbjct: 548 KVRKVMKIAK-EPISLETPIG------------DEEDSHLGDFI---KDENAIIPVEAAI 591

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFK 278
             N R   TR +S L PRE R+   R         TLE +  +F V+RER+RQIEA+A +
Sbjct: 592 NNNLRESTTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALR 651

Query: 279 KVQ 281
           K++
Sbjct: 652 KLK 654


>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 = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 411 AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 470

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 471 IRQAITRSIADQARTIRI--PVHMIETINKLVRTSRQMLHEIGREPAPEE---LAEKLGM 525

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + ++   + N R   
Sbjct: 526 PLEKVRKV-LKIA-KEPISLETPIGDEEDSHLGDFI---EDKTAVIPLDAAIQTNLREAT 580

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR +S L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 581 TRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTRERIRQIEAKALRKLK 635


>gi|319403851|emb|CBI77437.1| RNA polymerase sigma factor [Bartonella rochalimae ATCC BAA-1498]
          Length = 669

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 121/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 431 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 490

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   ++ KL++
Sbjct: 491 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQILHEIGREPTPEE---LSSKLSM 545

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+++S   D++    D    + I+   + N R+  
Sbjct: 546 PLEKVRKV-LKIA-KEPISLETPVGDEDASHLGDFI---EDRNALLPIDAAIQANLRDTT 600

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 601 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 655


>gi|297163178|gb|ADI12890.1| RNA polymerase sigma factor [Streptomyces bingchenggensis BCW-1]
          Length = 336

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 88/305 (28%), Positives = 141/305 (46%), Gaps = 52/305 (17%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH-------------GDLSA----AHR---- 52
           Y+  I ++ +L  ++E  LAKR     Y E              G+L A     HR    
Sbjct: 42  YLKLIARVRLLTAEQEVDLAKRIEAGLYAERLLRERPGLDRHSRGELGALAEDGHRAKTH 101

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV ++LRLVV +A  Y G GL   +++ EGN GL++A +KFD  +GF+ +TY+ WWIK A
Sbjct: 102 LVEANLRLVVSVAKRYTGRGLAFLDLIQEGNTGLIRAAEKFDYAKGFKFSTYATWWIKQA 161

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK-------K 165
           +   +      +++    +   L   + R++  L   T     PEQV   A+       +
Sbjct: 162 VSRALADQSRTIRV--PVHTVELINRIARVRRELILDTGAEPTPEQVAEKAEVPVGRLAE 219

Query: 166 LNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           L+    E +S++  L+  GD     LI  SD   S W D + +        L+++  R  
Sbjct: 220 LDGYTKEPVSLHVALSDEGDSEFGDLIVDSD-TPSPW-DMVTFS-------LLQQALRTL 270

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
              M  R   +++ R   +F  R       TLE +   + V+RER+RQIE+R   K++  
Sbjct: 271 LAEMTPREAGIISLR-YGLFGGR-----ARTLEEIGQVYGVTRERIRQIESRTMSKLRHP 324

Query: 284 IQKQV 288
            + Q 
Sbjct: 325 SRSQA 329


>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 = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 71/245 (28%), Positives = 122/245 (49%), Gaps = 17/245 (6%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           KR RE     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG
Sbjct: 611 KRARE-----AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG 665

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           ++ +TY+ WWI+ A+   I      ++I    +       + R+   +   T N   P  
Sbjct: 666 YKFSTYATWWIRQAITRSIADQARTIRI--PVHMIETINKMNRISRQILQETGNEPDP-- 721

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              +A+K+ + E ++  +  ++A  E ++      D + S   D++    D       E 
Sbjct: 722 -ATLAEKMEMPEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDTNTLAPAEA 775

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARA 276
               + R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A
Sbjct: 776 ALDGSMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKA 835

Query: 277 FKKVQ 281
            +K++
Sbjct: 836 LRKLR 840


>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 = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 67/235 (28%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 588 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 647

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+   +   T N   P     +A+K+ +
Sbjct: 648 IRQAITRSIADQARTIRI--PVHMIETINKMNRISRQILQETGNEPDP---ATLAEKMEM 702

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       E     + R+++
Sbjct: 703 PEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDTNTLAPAEAALHGSMRDVV 757

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 758 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 812


>gi|84687692|ref|ZP_01015565.1| RNA polymerase sigma factor [Maritimibacter alkaliphilus HTCC2654]
 gi|84664275|gb|EAQ10766.1| RNA polymerase sigma factor [Rhodobacterales bacterium HTCC2654]
          Length = 670

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 432 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 491

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 492 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 546

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   ++N +   
Sbjct: 547 PLEKVRKV-MKIA-KEPISLETPIGDEEDSQLGDFI---EDKNAVLPLDSAIQENLKETT 601

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 602 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 656


>gi|120553093|ref|YP_957444.1| RNA polymerase, sigma 32 subunit, RpoH [Marinobacter aquaeolei VT8]
 gi|120322942|gb|ABM17257.1| RNA polymerase, sigma 32 subunit, RpoH [Marinobacter aquaeolei VT8]
          Length = 330

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 75/242 (30%), Positives = 124/242 (51%), Gaps = 16/242 (6%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           H  L+  HRL+ S+LRL V IA  Y  +G+ +S+++ + N+GL++AV+++DP +GFR +T
Sbjct: 91  HLALACRHRLIQSNLRLAVHIARRYGHHGIAMSDLIQDANVGLIKAVERYDPGKGFRFST 150

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITDNNLKPEQVVAI 162
           Y+ WWI   ++  + R   +V   T  N       L+++   L Q++     + E    +
Sbjct: 151 YAYWWISEEVRRCLQRGVRVVH--TPENVVEEIRQLQKVSMRLHQSLGREPTQSE----L 204

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+++  + S +  +    A + S +  +   +  S    D L    D +        +R 
Sbjct: 205 AREMEATPSRIGELRALAAREVSTD--VPLVEDGSVTLADSLDAGADTRPDQPFRARDRM 262

Query: 223 NRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
            R   L R M  L+ RER I   R    L E P TL+ +S +  +SRERVRQIE  A +K
Sbjct: 263 IR---LERMMGALSDRERDILTRRYGLGLIE-PETLQTISEQLGLSRERVRQIEKGALRK 318

Query: 280 VQ 281
           +Q
Sbjct: 319 LQ 320


>gi|67921267|ref|ZP_00514786.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
 gi|67857384|gb|EAM52624.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
          Length = 414

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 128/237 (54%), Gaps = 17/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 178 AKDKMVHSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 237

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT-DNNLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++ +   KP E+ +A   ++
Sbjct: 238 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKLLSQEMRRKPTEEEIATRMEM 292

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  D +  E  + +   R++  N
Sbjct: 293 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIEADGETPEDEVSKNLLREDLEN 348

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +L      L+PRER +   R   ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 349 VL----DTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLR 401


>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 = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 70/244 (28%), Positives = 118/244 (48%), Gaps = 32/244 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 381 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 440

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +   T     PE+   ++K++ +
Sbjct: 441 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQILQETGCEPTPEE---LSKRMLI 495

Query: 169 SESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           SE ++          +SM   +  DE             S   D++    D    + ++ 
Sbjct: 496 SEDKIRKVLKIAKEPVSMETPIGDDE------------DSHLGDFI---EDTNLDLPLDS 540

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARA 276
               N +      +S L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A
Sbjct: 541 ATSDNLKAATNDVLSGLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKA 600

Query: 277 FKKV 280
            +K+
Sbjct: 601 LRKL 604


>gi|77463967|ref|YP_353471.1| RNA polymerase sigma factor RpoD [Rhodobacter sphaeroides 2.4.1]
 gi|126462810|ref|YP_001043924.1| RNA polymerase sigma factor RpoD [Rhodobacter sphaeroides ATCC
           17029]
 gi|77388385|gb|ABA79570.1| RNA polymerase sigma factor RpoD [Rhodobacter sphaeroides 2.4.1]
 gi|126104474|gb|ABN77152.1| RNA polymerase, sigma 70 subunit, RpoD family [Rhodobacter
           sphaeroides ATCC 17029]
          Length = 668

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 430 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 489

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 490 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 544

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   ++N +   
Sbjct: 545 PLEKVRKV-MKIA-KEPISLETPIGDEEDSQLGDFI---EDKNAILPLDSAIQENLKETT 599

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 600 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 654


>gi|254293486|ref|YP_003059509.1| RNA polymerase sigma factor RpoD [Hirschia baltica ATCC 49814]
 gi|254042017|gb|ACT58812.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Hirschia baltica
           ATCC 49814]
          Length = 683

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 74/244 (30%), Positives = 119/244 (48%), Gaps = 30/244 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 445 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 504

Query: 109 IKAAMQEYILRSWSLVKIGT----TAN-----QKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N     Q+++   + R     +      L  E+ 
Sbjct: 505 IRQAITRSIADQARTIRIPVHMIETINKIVRTQRQMLHEIGREPTPEELAEKLGLPLEK- 563

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E IS+   +  DE             S   D++    D    + ++  
Sbjct: 564 --IRKVLKIAK-EPISLETPIGDDE------------DSNLGDFI---EDKMALLPVDAA 605

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAF 277
            + N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A 
Sbjct: 606 IQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKAL 665

Query: 278 KKVQ 281
           +K++
Sbjct: 666 RKLK 669


>gi|83594214|ref|YP_427966.1| RNA polymerase sigma factor RpoD [Rhodospirillum rubrum ATCC 11170]
 gi|83577128|gb|ABC23679.1| Sigma 70 (RpoD) [Rhodospirillum rubrum ATCC 11170]
          Length = 696

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 76/250 (30%), Positives = 119/250 (47%), Gaps = 42/250 (16%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 458 AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 517

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRR------LKGHLQAITDNN 153
           I+ A+   I      ++I      T N+     +++   + R      L   LQ   +  
Sbjct: 518 IRQAITRSIADQARTIRIPVHMIETINKLVRTSRQMLHEIGREPTPEELAEKLQMPLE-- 575

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            K  +V+ IAK       E IS+   +  +E  +      DKN+ Q  D  +        
Sbjct: 576 -KVRKVLKIAK-------EPISLETPIGDEEDSHLGDFIEDKNAVQPLDAAI-------- 619

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQ 271
                    N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQ
Sbjct: 620 -------NSNLRETCTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQ 672

Query: 272 IEARAFKKVQ 281
           IEA+A +K++
Sbjct: 673 IEAKALRKLK 682


>gi|37522141|ref|NP_925518.1| RNA polymerase sigma factor RpoD [Gloeobacter violaceus PCC 7421]
 gi|35213141|dbj|BAC90513.1| principal RNA polymerase sigma factor [Gloeobacter violaceus PCC
           7421]
          Length = 400

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 126/237 (53%), Gaps = 17/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 164 AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 223

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++     KP E+ +A   ++
Sbjct: 224 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKLLSQELGRKPTEEEIATRMEM 278

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  D +  E    +K  +   R 
Sbjct: 279 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIEADGETPE----DKVAKNLLRE 330

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L   ++ L+PRER +   R   ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 331 DLEAVLNTLSPRERDVLRLRYGLDDGRMKTLEEIGQLFNVTRERIRQIEAKALRKLR 387


>gi|255532556|ref|YP_003092928.1| sigma-70 family RNA polymerase sigma factor [Pedobacter heparinus
           DSM 2366]
 gi|255345540|gb|ACU04866.1| RNA polymerase sigma factor, sigma-70 family [Pedobacter heparinus
           DSM 2366]
          Length = 289

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 75/276 (27%), Positives = 145/276 (52%), Gaps = 37/276 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI +I + + +EE+ L    R +GD  A HRL+  +LR VV +A  Y+  GL + ++
Sbjct: 21  YLSEIGRISLTDPEEEFRLVSAIR-NGDQEALHRLIKGNLRFVVSVAKKYQDKGLKLGDL 79

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           ++EGNIGL++A  +FD  RGF+  T+++WW++ A+ + I            A Q+RL   
Sbjct: 80  INEGNIGLIKAAHRFDATRGFKFITFAVWWVRQAILQAI------------AEQRRLI-- 125

Query: 139 LRRLKGH-LQAITDNNLKPEQVVAIAKKLN-VSESEVISMNCRLAGDESLNALINSSDKN 196
             RL G+ L  I+  N   + V+ + ++L  +   E +++      D+ ++   N++   
Sbjct: 126 --RLPGNQLLGISRLN---QAVLKLEQQLERMPTVEELAVYTGFTVDKVMDYTANAAFTY 180

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT----------RSMSVLNPRERR-IFEA 245
           S    D ++ +  G   + +  +E  ++ +  T          R++ +L+ RE++ I   
Sbjct: 181 S---LDDVIKEESGSTLMEVIADEATHQTDHFTLAASLSTDLNRALDILSKREQKIIILF 237

Query: 246 RRLQENPVT-LENLSSEFEVSRERVRQIEARAFKKV 280
             L   P T +E++    ++S+ER+RQ++ +A K +
Sbjct: 238 YGLNGYPQTAIEDMQKILKLSKERIRQLKDKAHKTL 273


>gi|298292324|ref|YP_003694263.1| RNA polymerase, sigma 70 subunit, RpoD [Starkeya novella DSM 506]
 gi|296928835|gb|ADH89644.1| RNA polymerase, sigma 70 subunit, RpoD [Starkeya novella DSM 506]
          Length = 666

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 428 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 487

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 488 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLGM 542

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 543 PLEKVRKV-LKIA-KEPISLETPIGDEEDSHLGDFI---EDKNAILPIDAAIQSNLRETT 597

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 598 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 652


>gi|39998179|ref|NP_954130.1| RNA polymerase sigma factor RpoD [Geobacter sulfurreducens PCA]
 gi|39985125|gb|AAR36480.1| RNA polymerase sigma factor RpoD [Geobacter sulfurreducens PCA]
 gi|298507117|gb|ADI85840.1| RNA polymerase sigma-70 factor RpoD [Geobacter sulfurreducens
           KN400]
          Length = 577

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 78/240 (32%), Positives = 128/240 (53%), Gaps = 22/240 (9%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ WW
Sbjct: 340 AKSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWW 399

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N  +L    R+L   +Q I      PE+   IA+
Sbjct: 400 IRQAITRAIADQARTIRIPVHMIETIN--KLIRTSRQL---VQEIG-REPSPEE---IAE 450

Query: 165 KLNVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           ++N+   +V  +  ++A +  SL   I   ++  S   D++    D      +E   + N
Sbjct: 451 RMNLPLDKVRKV-LKIAKEPISLETPIG--EEEDSHLGDFI---EDKGVVSPLEAVIKAN 504

Query: 224 RRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                 R ++ L PRE ++   R    +++  TLE +  +FEV+RER+RQIEA+A +K++
Sbjct: 505 LSEQTARVLATLTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLR 564


>gi|85705219|ref|ZP_01036318.1| RNA polymerase sigma factor [Roseovarius sp. 217]
 gi|85670092|gb|EAQ24954.1| RNA polymerase sigma factor [Roseovarius sp. 217]
          Length = 661

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 72/235 (30%), Positives = 119/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 423 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 482

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 483 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 537

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   + N +   
Sbjct: 538 PLEKVRKV-MKIA-KEPISLETPIGDEEDSQLGDFI---EDKNVILPLDSAIQDNLKETT 592

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR +S L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 593 TRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 647


>gi|284052417|ref|ZP_06382627.1| RNA polymerase sigma factor RpoD [Arthrospira platensis str.
           Paraca]
 gi|291570496|dbj|BAI92768.1| principal RNA polymerase sigma factor SigA [Arthrospira platensis
           NIES-39]
          Length = 387

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 69/237 (29%), Positives = 128/237 (54%), Gaps = 17/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 151 AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 210

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT-DNNLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++ +   KP E+ +A   ++
Sbjct: 211 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEM 265

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  D +  E  + +   R++  +
Sbjct: 266 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIESDGETPEDQVSKNLLREDLES 321

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +L      L+PRER +   R   ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 322 VL----DTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLR 374


>gi|260434101|ref|ZP_05788072.1| RNA polymerase sigma factor RpoD [Silicibacter lacuscaerulensis
           ITI-1157]
 gi|260417929|gb|EEX11188.1| RNA polymerase sigma factor RpoD [Silicibacter lacuscaerulensis
           ITI-1157]
          Length = 662

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 424 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 483

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 484 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 538

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   ++N +   
Sbjct: 539 PLEKVRKV-MKIAK-EPISLETPIGDEEDSQLGDFI---EDKNAVLPLDSAIQENLKETT 593

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 594 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 648


>gi|225851205|ref|YP_002731439.1| RNA polymerase sigma factor RpoD (Sigma-70) [Persephonella marina
           EX-H1]
 gi|225645895|gb|ACO04081.1| RNA polymerase sigma factor RpoD (Sigma-70) [Persephonella marina
           EX-H1]
          Length = 577

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 73/240 (30%), Positives = 122/240 (50%), Gaps = 26/240 (10%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            ++V S+LRLVV IA  Y   GL   +++ EGNIGLM+AV KFD ++G++ +TY+ WWI+
Sbjct: 341 QKIVQSNLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFDYKKGYKFSTYATWWIR 400

Query: 111 AAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            A+   I      ++I      T N+      L R+   +         PE+   IAKK+
Sbjct: 401 QAITRAIADQARTIRIPVHMIETINK------LVRVARSMVQELGREPTPEE---IAKKV 451

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKN 223
            +   +V          E ++      D + S   D++      +++ ++  E+   R+ 
Sbjct: 452 GMPPEKV--RKILRTSQEPISLETPIGDDDESHLGDFI------EDKTVMSPEQHVLRQA 503

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R  L   +S L+ RE ++   R   E+    TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 504 LRQQLEEVLSTLSEREEQVLRYRFGLEDDTEYTLEQVGKKFGVTRERIRQIEAKALRKLR 563


>gi|228471226|ref|ZP_04056039.1| RNA polymerase sigma-70 factor [Porphyromonas uenonis 60-3]
 gi|228307041|gb|EEK16123.1| RNA polymerase sigma-70 factor [Porphyromonas uenonis 60-3]
          Length = 286

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 79/291 (27%), Positives = 137/291 (47%), Gaps = 34/291 (11%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           N SI       L RY+ EI +  ++  +EE  LA+     G+  A ++LV ++LR VV +
Sbjct: 7   NQSITNRESASLDRYLQEIGRTSLISPEEEVELAREIH-RGNRRALNKLVEANLRFVVSV 65

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYIL 118
           A  Y+  GL + ++++EGNIG+++A +KFD  RGF+  +Y++WWI+ ++      Q  I+
Sbjct: 66  AKQYQNQGLSLPDLINEGNIGMIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIV 125

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGH---LQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
           R   L ++G      +      +L G     Q I D    PE  +  A K+      + +
Sbjct: 126 R-LPLNQVGLQQKMNKAIVKFEQLNGRRPSPQEIADELELPEDKIREALKVQGKHQSLDA 184

Query: 176 MNCRLAGDESLNALIN--SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
                  +  L+ L+N  +   +SS   + L  + D                    R + 
Sbjct: 185 PFVEGEDNNMLDVLVNEDTPSTDSSLINESLSAEID--------------------RILE 224

Query: 234 VLNPRERRIFEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            L  RE  +         P +TLE +    ++SRERVRQI+ +A +++++S
Sbjct: 225 QLGDREAEVLRCFFGIGCPEMTLEEIGERTKLSRERVRQIKEKAIRRLKQS 275


>gi|254441274|ref|ZP_05054767.1| Sigma-70 region 3 family [Octadecabacter antarcticus 307]
 gi|198251352|gb|EDY75667.1| Sigma-70 region 3 family [Octadecabacter antarcticus 307]
          Length = 655

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 75/250 (30%), Positives = 122/250 (48%), Gaps = 42/250 (16%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 417 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 476

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRR------LKGHLQAITDNN 153
           I+ A+   I      ++I      T N+     +++   + R      L   LQ   +  
Sbjct: 477 IRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEIGREPTPEELAAKLQMPLE-- 534

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            K  +V+ IAK       E IS+   +             D+  SQ  D++    D    
Sbjct: 535 -KVRKVMKIAK-------EPISLETPIG------------DEEDSQLGDFI---EDKNAV 571

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQ 271
           + ++   ++N +   TR ++ L PRE R+   R         TLE +  +F V+RER+RQ
Sbjct: 572 LPLDSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQ 631

Query: 272 IEARAFKKVQ 281
           IEA+A +K++
Sbjct: 632 IEAKALRKLK 641


>gi|158316157|ref|YP_001508665.1| RpoD family RNA polymerase sigma factor [Frankia sp. EAN1pec]
 gi|158111562|gb|ABW13759.1| RNA polymerase, sigma 70 subunit, RpoD family [Frankia sp. EAN1pec]
          Length = 400

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 86/306 (28%), Positives = 139/306 (45%), Gaps = 56/306 (18%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRY------------------REHGDLSAAH--------R 52
           Y+  I ++ +L  +EE  LAKR                   R   DL A          +
Sbjct: 107 YLKAIGRVRLLTAEEEVDLAKRIEAGLFASEKLAAIRRTSPRLRRDLEAIEQDGQIAKRK 166

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV ++LRLVV IA  Y G G+ + +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A
Sbjct: 167 LVEANLRLVVSIAKRYVGRGMLLLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQA 226

Query: 113 MQEYILRSWSLVKIG---------TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           +   I      ++I           T  Q++L  +L R     +  T  +L P +V  I 
Sbjct: 227 VTRAIADQGRTIRIPVHMVETINKVTRIQRQLLQDLGREPSPEEIATQVDLAPHRVEEI- 285

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
             L V ++ V           +L   I   ++  SQ  D++    D    V  E      
Sbjct: 286 --LKVGQTPV-----------ALETPIG--EEQDSQLGDFI---EDNDAIVPFEAASFVL 327

Query: 224 RRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +  +   +  L+ RE+++ + R       P TLE +  EF V+RER+RQIE+R   K+ 
Sbjct: 328 LQEQIDSVLHTLSEREKKVIQLRFGLTDGQPRTLEQVGREFGVTRERIRQIESRTLAKLS 387

Query: 282 ESIQKQ 287
              + Q
Sbjct: 388 HPARSQ 393


>gi|169351085|ref|ZP_02868023.1| hypothetical protein CLOSPI_01864 [Clostridium spiroforme DSM 1552]
 gi|169292147|gb|EDS74280.1| hypothetical protein CLOSPI_01864 [Clostridium spiroforme DSM 1552]
          Length = 415

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 85/277 (30%), Positives = 137/277 (49%), Gaps = 36/277 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   +E  LAK+  E GD +A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 147 YLKEIGRVELLSHDDEIKLAKKILE-GDEAAKKELAAANLRLVVSIAKRYVGRGMLFLDL 205

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-- 132
           + EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I      T N+  
Sbjct: 206 IQEGNMGLIKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLT 265

Query: 133 --KRLFFNLRRLKGHLQAITD--NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
             +RL       +   + I +  + + PE+V  I K         IS+        SL  
Sbjct: 266 RIQRLLIQELGREPTAEEIAERIDGMTPEKVREIQK---------ISLEPV-----SLET 311

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR--RNMLTRSMSVLNPRERRIFEAR 246
            I   D   S   D++       E V+   +   N   ++ L   +  L  RE ++   R
Sbjct: 312 PIGEED--DSHLGDFI-----EDEGVMSPDDYAANELLKDELNEVLLELTDREEKVLRLR 364

Query: 247 RLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              ++    TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 365 FGLDDGRTRTLEEVGKEFSVTRERIRQIEAKALRKLK 401


>gi|313886597|ref|ZP_07820310.1| putative RNA polymerase sigma factor RpoD [Porphyromonas
           asaccharolytica PR426713P-I]
 gi|332300881|ref|YP_004442802.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Porphyromonas
           asaccharolytica DSM 20707]
 gi|312923953|gb|EFR34749.1| putative RNA polymerase sigma factor RpoD [Porphyromonas
           asaccharolytica PR426713P-I]
 gi|332177944|gb|AEE13634.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Porphyromonas
           asaccharolytica DSM 20707]
          Length = 286

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 78/282 (27%), Positives = 141/282 (50%), Gaps = 16/282 (5%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           N SI       L RY+ EI +  ++  +EE  LA+     G+  A ++LV ++LR VV +
Sbjct: 7   NQSITNRESASLDRYLQEIGRTSLISPEEEVELAREIH-RGNRRALNKLVEANLRFVVSV 65

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y+  GL + ++++EGNIG+++A +KFD  RGF+  +Y++WWI+ ++ + +     +V
Sbjct: 66  AKQYQNQGLSLPDLINEGNIGMIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIV 125

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           ++    NQ  L   + +     + +      P++   IA +L + E ++          +
Sbjct: 126 RL--PLNQVGLQQKMNKAIVKFEQLNGRRPSPQE---IAAELELPEDKIREALKVQGKHQ 180

Query: 185 SLNA-LINSSDKNSSQWQDWLVY-DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
           SL+A  +   D N     D LV  D    +  LI +         + R +  L  RE  +
Sbjct: 181 SLDAPFVEGEDNN---MLDVLVNEDTPSTDSSLINESLSAE----IDRILDQLGDREAEV 233

Query: 243 FEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
                    P +TLE +    ++SRERVRQI+ +A +++++S
Sbjct: 234 LRCFFGIGCPEMTLEEIGERTKLSRERVRQIKEKAIRRLKQS 275


>gi|260576520|ref|ZP_05844509.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhodobacter sp.
           SW2]
 gi|259021243|gb|EEW24550.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhodobacter sp.
           SW2]
          Length = 668

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 430 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 489

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 490 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 544

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   ++N +   
Sbjct: 545 PLEKVRKV-MKIA-KEPISLETPIGDEEDSQLGDFI---EDKNAILPLDSAIQENLKETT 599

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 600 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 654


>gi|84502758|ref|ZP_01000877.1| RNA polymerase sigma factor [Oceanicola batsensis HTCC2597]
 gi|84389153|gb|EAQ01951.1| RNA polymerase sigma factor [Oceanicola batsensis HTCC2597]
          Length = 663

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 425 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 484

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 485 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 539

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   ++N +   
Sbjct: 540 PLEKVRKV-MKIAK-EPISLETPIGDEEDSQLGDFI---EDKNAILPLDSAIQENLKETT 594

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 595 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 649


>gi|149202116|ref|ZP_01879089.1| RNA polymerase sigma factor RpoD [Roseovarius sp. TM1035]
 gi|149144214|gb|EDM32245.1| RNA polymerase sigma factor RpoD [Roseovarius sp. TM1035]
          Length = 661

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 72/235 (30%), Positives = 119/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 423 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 482

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 483 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 537

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   + N +   
Sbjct: 538 PLEKVRKV-MKIA-KEPISLETPIGDEEDSQLGDFI---EDKNVILPLDSAIQDNLKETT 592

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR +S L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 593 TRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 647


>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 = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 413 AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 472

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 473 IRQAITRSIADQAKTIRI--PVHMIETINKLVRTSRQMLHEIGREPAPEE---LAEKLGM 527

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + ++   + N R   
Sbjct: 528 PLEKVRKV-LKIA-KEPISLETPIGDEEDSHLGDFI---EDKTAVIPLDAAIQTNLREAT 582

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 583 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTRERIRQIEAKALRKLK 637


>gi|22298160|ref|NP_681407.1| RNA polymerase sigma factor RpoD [Thermosynechococcus elongatus
           BP-1]
 gi|22294339|dbj|BAC08169.1| principal RNA polymerase sigma factor [Thermosynechococcus
           elongatus BP-1]
          Length = 418

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 73/250 (29%), Positives = 133/250 (53%), Gaps = 17/250 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           V A R+R      A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD 
Sbjct: 169 VPAFRHRLFVGRKAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDH 228

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT-DNNL 154
           E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++ +   
Sbjct: 229 EKGYKFSTYATWWIRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKLLSQEMGR 283

Query: 155 KP-EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
           KP E+ +A   ++ + +   I+ + +L    SL   I   +   S+  D++  D +  E 
Sbjct: 284 KPTEEEIADRMEMTIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIESDGETPED 339

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQ 271
            + +   R++    L   +  L+PRER + + R   ++    TLE +   F V+RER+RQ
Sbjct: 340 QVSKHLLRED----LETVLCTLSPRERDVLKLRYGLDDGRMKTLEEIGQLFNVTRERIRQ 395

Query: 272 IEARAFKKVQ 281
           IEA+A +K++
Sbjct: 396 IEAKALRKLR 405


>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 = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 66/245 (26%), Positives = 119/245 (48%), Gaps = 32/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGN+GLM+AV KF+  RGF+ +TY+ WW
Sbjct: 546 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNVGLMKAVDKFEFRRGFKFSTYATWW 605

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +  ++P+    +A+K+++
Sbjct: 606 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGVEPDPAT-LAEKMDM 660

Query: 169 SESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            E ++          ISM   +  D+  +      D  +    D  ++D           
Sbjct: 661 PEDKIRKILKIAKEPISMETPIGDDDDSHLGDFIEDTTTLAPSDAALHD----------- 709

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARA 276
               + R ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A
Sbjct: 710 ----SMREVVKEVLDSLTPREAKVLRMRFGVEMSTDHTLEEVGKQFDVTRERIRQIEAKA 765

Query: 277 FKKVQ 281
            +K++
Sbjct: 766 LRKLR 770


>gi|114797662|ref|YP_761566.1| RNA polymerase sigma factor RpoD [Hyphomonas neptunium ATCC 15444]
 gi|114737836|gb|ABI75961.1| RNA polymerase sigma factor RpoD [Hyphomonas neptunium ATCC 15444]
          Length = 666

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 74/244 (30%), Positives = 119/244 (48%), Gaps = 30/244 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 428 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 487

Query: 109 IKAAMQEYILRSWSLVKIGT----TAN-----QKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N     Q+++   + R     +      L  E+ 
Sbjct: 488 IRQAITRSIADQARTIRIPVHMIETINKIIRTQRQMLHEIGREPTPEELAEKLGLPLEK- 546

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E IS+   +  DE             S   D++    D    + ++  
Sbjct: 547 --IRKVLKIAK-EPISLETPIGDDE------------DSNLGDFI---EDKMALLPVDAA 588

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAF 277
            + N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A 
Sbjct: 589 IQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKAL 648

Query: 278 KKVQ 281
           +K++
Sbjct: 649 RKLK 652


>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 = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 115/234 (49%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 414 AKRDMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 473

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + I            +A K+ +
Sbjct: 474 IRQAITRSIADQARTIRIPV-----HMIETINKMNRISRQILQETGMEADAATLAIKMEM 528

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D      IE     + RN+ 
Sbjct: 529 PEDKIRKI-LKIAK-EPISMETPVGDDDDSHLGDFI---EDANSLAPIEAAVYDSLRNVT 583

Query: 229 TRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 584 KDILDSLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 637


>gi|258406014|ref|YP_003198756.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfohalobium
           retbaense DSM 5692]
 gi|257798241|gb|ACV69178.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfohalobium
           retbaense DSM 5692]
          Length = 587

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 73/245 (29%), Positives = 127/245 (51%), Gaps = 16/245 (6%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L A   L+ S+LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ 
Sbjct: 347 LRAKQELIRSNLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYAT 406

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I    +       L R   +L      + +PE+   IA+++
Sbjct: 407 WWIRQAITRAIADQARTIRI--PVHMIETINKLIRTSRYLVQELGRDPQPEE---IAERM 461

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR- 225
           +    E +    ++A  E ++      D+  S   D++       ++ +   EE  N + 
Sbjct: 462 DYP-VEKVKKVLKIA-KEPISLETPIGDEEDSSLGDFI-----EDKKAVAPAEEAVNSKL 514

Query: 226 -NMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              ++  +S L PRE ++   R    +++  TLE +   F V+RER+RQIEA+A +K++ 
Sbjct: 515 AEQISTVLSELTPREEQVLRKRFGIGEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRH 574

Query: 283 SIQKQ 287
            ++ Q
Sbjct: 575 PVRSQ 579


>gi|111225055|ref|YP_715849.1| alternative primary sigma 70 transcriptional factor [Frankia alni
           ACN14a]
 gi|111152587|emb|CAJ64329.1| Alternative primary sigma 70 transcriptional factor [Frankia alni
           ACN14a]
          Length = 373

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 88/294 (29%), Positives = 137/294 (46%), Gaps = 60/294 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH---------GDL------------SAAHR 52
           Y+ EI K+P+L   +E  L+KR     + EH          DL            +A  +
Sbjct: 80  YLREIGKVPLLNAAQEVELSKRVEAGLFAEHKLESDPDLPADLRRDLGLLVKDGHAAKQQ 139

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV+++LRLVV +A  Y G G+ + ++V EGN+GL++AV+KFD  +G++ +TY+ WWI+ A
Sbjct: 140 LVSANLRLVVSVAKKYSGRGMTLLDLVQEGNLGLIRAVEKFDYAKGYKFSTYATWWIRQA 199

Query: 113 MQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           +   +      ++I           T  Q++L   L R     +   + ++  EQVV   
Sbjct: 200 IGRALADQARTIRIPVHVVEQINKITRLQRQLVSTLGREPTDEELALELDMPIEQVV--- 256

Query: 164 KKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
            +L     + +S+   +   GD  L   I  SD  S    D   Y   G  Q  IE    
Sbjct: 257 -ELRRYAQDTVSLETSVGDDGDSVLGDFIEDSDATSP--ADAASY---GAMQDEIE---- 306

Query: 222 KNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIE 273
               N+L      LNPRER +   R  L +    TL  + +   ++RER+RQIE
Sbjct: 307 ----NVL----GGLNPREREVMRLRFGLADGKQHTLAEVGNRLGLTRERIRQIE 352


>gi|83309796|ref|YP_420060.1| RNA polymerase sigma factor RpoD [Magnetospirillum magneticum
           AMB-1]
 gi|82944637|dbj|BAE49501.1| DNA-directed RNA polymerase [Magnetospirillum magneticum AMB-1]
          Length = 679

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 119/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 441 AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 500

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL++
Sbjct: 501 IRQAITRSIADQARTIRI--PVHMIETINKLVRTSRQMLHEIGREPTPEE---LAEKLSM 555

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + ++   + N R   
Sbjct: 556 PLEKVRKV-LKIA-KEPISLETPIGDEEDSHLGDFI---EDKNAVLPLDAAIQANLRETT 610

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 611 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 665


>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 = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 69/235 (29%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 431 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 490

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R        +     PE+   +A++L++
Sbjct: 491 IRQAITRSIADQARTIRI--PVHMIETINKLVRCSRQFLHESGREPTPEE---MAERLSM 545

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + ++   + N +  +
Sbjct: 546 PLEKVRKV-MKIAK-EPISLETPIGDEEDSHLGDFI---EDKNAVIPVDAAVQSNLKETV 600

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 601 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 655


>gi|317013514|gb|ADU80950.1| RNA polymerase sigma factor RpoD [Helicobacter pylori Gambia94/24]
          Length = 681

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 75/242 (30%), Positives = 120/242 (49%), Gaps = 25/242 (10%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ WW
Sbjct: 442 AKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWW 501

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI---TDNNLKPEQV-VAIAK 164
           IK A+   I      ++I           N + ++ H+Q      D  +  E+V +++ K
Sbjct: 502 IKQAISRAIADQARTIRIPIHMIDTINRIN-KVMRKHIQETGKEPDLEVVAEEVGLSLDK 560

Query: 165 KLNVSE--SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
             NV +   E IS+   +  D+         DKN     D ++               R+
Sbjct: 561 VKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIM---------------RE 605

Query: 223 NRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           + +  +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK
Sbjct: 606 DLKAQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKK 665

Query: 280 VQ 281
           ++
Sbjct: 666 LR 667


>gi|240169695|ref|ZP_04748354.1| RNA polymerase sigma factor [Mycobacterium kansasii ATCC 12478]
          Length = 518

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 82/318 (25%), Positives = 151/318 (47%), Gaps = 43/318 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGD-LS 48
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+ L 
Sbjct: 206 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMAEMAERGEKLP 264

Query: 49  AAHR----------------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           AA R                L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 265 AAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 324

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L      
Sbjct: 325 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGR 382

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D + 
Sbjct: 383 EPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEA 434

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVR 270
            V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 435 VVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIR 494

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 495 QIESKTMSKLRHPSRSQV 512


>gi|148266058|ref|YP_001232764.1| RpoD family RNA polymerase sigma factor [Geobacter uraniireducens
           Rf4]
 gi|146399558|gb|ABQ28191.1| RNA polymerase, sigma 70 subunit, RpoD [Geobacter uraniireducens
           Rf4]
          Length = 586

 Score = 96.7 bits (239), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 76/238 (31%), Positives = 127/238 (53%), Gaps = 20/238 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ WW
Sbjct: 349 AKSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWW 408

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N  +L    R+L   +Q I      PE+   IA+
Sbjct: 409 IRQAITRAIADQARTIRIPVHMIETIN--KLIRTSRQL---VQEIG-REPSPEE---IAE 459

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           ++++   +V  +  ++A  E ++      ++  S   D++    D      +E   + N 
Sbjct: 460 RMSLPLDKVRKV-LKIA-KEPISLETPIGEEEDSHLGDFI---EDKGVVSPLEAVIKANL 514

Query: 225 RNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
               +R +S L PRE ++   R    +++  TLE +  +FEV+RER+RQIEA+A +K+
Sbjct: 515 SEQTSRVLSTLTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKL 572


>gi|308371101|ref|ZP_07423832.2| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu003]
 gi|308379284|ref|ZP_07485758.2| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu010]
 gi|308405944|ref|ZP_07494511.2| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu012]
 gi|308329814|gb|EFP18665.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu003]
 gi|308357496|gb|EFP46347.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu010]
 gi|308365045|gb|EFP53896.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu012]
 gi|323718698|gb|EGB27860.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           CDC1551A]
          Length = 530

 Score = 96.3 bits (238), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 82/318 (25%), Positives = 151/318 (47%), Gaps = 43/318 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGD-LS 48
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+ L 
Sbjct: 218 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSERGEKLP 276

Query: 49  AAHR----------------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           AA R                L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 277 AAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 336

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L      
Sbjct: 337 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGR 394

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D + 
Sbjct: 395 EPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEA 446

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVR 270
            V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 447 VVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIR 506

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 507 QIESKTMSKLRHPSRSQV 524


>gi|91070519|gb|ABE11426.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [uncultured Prochlorococcus marinus clone HOT0M-3E5]
          Length = 231

 Score = 96.3 bits (238), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 70/231 (30%), Positives = 125/231 (54%), Gaps = 11/231 (4%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ ++LRLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+  
Sbjct: 1   MMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQG 60

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           M   I  S   +++    ++K     +RR+   L        +P + + +A ++ + + +
Sbjct: 61  MTRAIDNSARTIRLPIHISEK--LSKMRRVSRELS--HKFGRQPTR-LEMATEMGIDQKD 115

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           +  +  + A   SL+A     +  S+  +  L+ D + +E   +E  +R  ++  L   +
Sbjct: 116 LEDLISQSAPCASLDAHARGEEDRSTLGE--LIPDPNCEEP--MEGMDRTIQKEHLGTWL 171

Query: 233 SVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           S LN RE++I   R     E P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 172 SQLNEREQKIMRLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 222


>gi|313891780|ref|ZP_07825385.1| RNA polymerase sigma factor RpoD [Dialister microaerophilus UPII
           345-E]
 gi|329121139|ref|ZP_08249770.1| DNA-directed RNA polymerase sigma subunit RpoD [Dialister
           micraerophilus DSM 19965]
 gi|313119774|gb|EFR42961.1| RNA polymerase sigma factor RpoD [Dialister microaerophilus UPII
           345-E]
 gi|327471301|gb|EGF16755.1| DNA-directed RNA polymerase sigma subunit RpoD [Dialister
           micraerophilus DSM 19965]
          Length = 374

 Score = 96.3 bits (238), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 80/275 (29%), Positives = 138/275 (50%), Gaps = 35/275 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHR-----------LVTSHLRLVVKIAMG 67
           Y+ EI  + +L  +EE  LAK   +   L A              L  ++LRLVV IA  
Sbjct: 102 YLKEIGTVDLLTAEEEVTLAKAVEKGLLLGATEEEKINADKAKKALSDANLRLVVSIAKK 161

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y G GL   +++ EGN+GL++AV KFD  +G++ +TY+ WWI+ ++   I      +++ 
Sbjct: 162 YLGRGLQFLDLIQEGNLGLLKAVDKFDYTKGYKFSTYATWWIRQSITRAIADQARTIRV- 220

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SL 186
              +       L R+   L  + +   +P +   IAK ++VS  +V  +  ++A D  SL
Sbjct: 221 -PVHMVETINKLNRISRQL--LQEKGREPTE-YEIAKAMDVSVGKVREVK-KIAQDPISL 275

Query: 187 NALINSSDKNSSQWQDWL-----VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              I   +K  S   D++     +   D  + +L++++        +   ++ L  RER+
Sbjct: 276 ETPI--GEKEDSHLGDFIEDQDAIAPDDATDSILLKEQ--------IEELLTNLTDRERQ 325

Query: 242 IFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEA 274
           + E R  L++  P TLE + + F+V+RER+RQIE 
Sbjct: 326 VLELRFGLKDGRPRTLEEVGNNFDVTRERIRQIEG 360


>gi|254452739|ref|ZP_05066176.1| RNA polymerase sigma-70 factor RpoD [Octadecabacter antarcticus
           238]
 gi|198267145|gb|EDY91415.1| RNA polymerase sigma-70 factor RpoD [Octadecabacter antarcticus
           238]
          Length = 637

 Score = 96.3 bits (238), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 75/250 (30%), Positives = 122/250 (48%), Gaps = 42/250 (16%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 399 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 458

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRR------LKGHLQAITDNN 153
           I+ A+   I      ++I      T N+     +++   + R      L   LQ   +  
Sbjct: 459 IRQAITRSIADQARTIRIPVHMIETINKLVRTGRQMLHEIGREPTPEELAAKLQMPLE-- 516

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            K  +V+ IAK       E IS+   +             D+  SQ  D++    D    
Sbjct: 517 -KVRKVMKIAK-------EPISLETPIG------------DEEDSQLGDFI---EDKNAV 553

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQ 271
           + ++   ++N +   TR ++ L PRE R+   R         TLE +  +F V+RER+RQ
Sbjct: 554 LPLDSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQ 613

Query: 272 IEARAFKKVQ 281
           IEA+A +K++
Sbjct: 614 IEAKALRKLK 623


>gi|50955189|ref|YP_062477.1| ECF subfamily RNA polymerase sigma-70 factor [Leifsonia xyli subsp.
           xyli str. CTCB07]
 gi|50951671|gb|AAT89372.1| RNA polymerase, sigma-70 family factor [Leifsonia xyli subsp. xyli
           str. CTCB07]
          Length = 308

 Score = 96.3 bits (238), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 79/263 (30%), Positives = 135/263 (51%), Gaps = 35/263 (13%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           EK+E +VL+   +      A  R + ++LRLVV IA  Y G GL + +++ EGN+GL++A
Sbjct: 61  EKRELHVLSDDGKR-----AFERFIEANLRLVVSIAKRYAGRGLAVMDLIQEGNLGLVRA 115

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK--RLFFNLRRLKGH-- 145
           V+KFD   G + +TY+ WWI+ ++   I  +  +++I     +K  +L    R L G   
Sbjct: 116 VEKFDYRTGNKFSTYATWWIRQSILRGIADTARVIRIPVHTVEKIDKLDRIRRDLGGELG 175

Query: 146 ----LQAITD-NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES--LNALINSSDKNSS 198
               L+ I D  +L P +V     KL +S+SE +S+   +  +E   L  LI   D    
Sbjct: 176 RTPTLEEIADAASLTPAEV----HKLQMSDSETVSLAVPVGENEGAELGDLIEDGDAPGP 231

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
             +  + + H   E+ L         R +  R   V+  R R   + R+    P+TL+ +
Sbjct: 232 SERVEVEFRHRDLEERL---------RELPLRDAKVV--RMRFGLDGRK----PMTLDEV 276

Query: 259 SSEFEVSRERVRQIEARAFKKVQ 281
            + + ++RERVRQ+E R+ K+++
Sbjct: 277 GAVYGITRERVRQLETRSLKRLR 299


>gi|15611152|ref|NP_222803.1| RNA polymerase sigma factor RpoD [Helicobacter pylori J99]
 gi|11387124|sp|Q9ZMY3|RPOD_HELPJ RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|4154591|gb|AAD05665.1| RNA POLYMERASE SIGMA FACTOR (SIGMA-70) [Helicobacter pylori J99]
          Length = 681

 Score = 96.3 bits (238), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 75/246 (30%), Positives = 121/246 (49%), Gaps = 33/246 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ WW
Sbjct: 442 AKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWW 501

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR----LKGHLQAI---TDNNLKPEQV-V 160
           IK A+   I      ++I        +   + R    ++ H+Q      D  +  E+V +
Sbjct: 502 IKQAISRAIADQARTIRIPI-----HMIDTINRINKVMRKHIQETGKEPDLEVVAEEVGL 556

Query: 161 AIAKKLNVSE--SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           ++ K  NV +   E IS+   +  D+         DKN     D ++             
Sbjct: 557 SLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIM------------- 603

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEAR 275
             R++ +  +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ 
Sbjct: 604 --REDLKAQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESS 661

Query: 276 AFKKVQ 281
           A KK++
Sbjct: 662 AIKKLR 667


>gi|261415107|ref|YP_003248790.1| RNA polymerase, sigma 32 subunit, RpoH [Fibrobacter succinogenes
           subsp. succinogenes S85]
 gi|261371563|gb|ACX74308.1| RNA polymerase, sigma 32 subunit, RpoH [Fibrobacter succinogenes
           subsp. succinogenes S85]
 gi|302326239|gb|ADL25440.1| RNA polymerase sigma-70 factor [Fibrobacter succinogenes subsp.
           succinogenes S85]
          Length = 270

 Score = 96.3 bits (238), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 74/274 (27%), Positives = 140/274 (51%), Gaps = 26/274 (9%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           I + +  L RY+ +IR+   L ++EE +L ++ +E GD  A  +L+++++R V+K+A+ Y
Sbjct: 3   IDSTDTTLKRYLEDIRRTAPLSREEEQILFQKAKE-GDKIARKKLISANMRFVLKVAIQY 61

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           RG  +P+ ++VSEG +GL++A++ F+  RG +  +Y +WWIKA +   I    +L+++  
Sbjct: 62  RGCPIPLPDLVSEGAMGLVRAIESFEHTRGLKFISYGVWWIKAYITRAINEQGNLIRL-- 119

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
            ANQ      +R+         + N +  +++ I ++  VS    +  + +    E L  
Sbjct: 120 PANQ---HLRVRKALHEQSRGKEINEEIRELIQIGQR-GVSFDSPLKADSKATYAEVLPD 175

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
              S+ +  S+ Q       D  EQ L E+E R      +   +  +N            
Sbjct: 176 SGASNPEADSEIQSVEALARDLMEQ-LPEREAR------VITGIFGIN------------ 216

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           QE P TL  +     +S ERVRQ+  +A +++++
Sbjct: 217 QEAPQTLREVGESMNISHERVRQLRDQALRRIRK 250


>gi|119489756|ref|ZP_01622514.1| RNA polymerase sigma factor [Lyngbya sp. PCC 8106]
 gi|119454330|gb|EAW35480.1| RNA polymerase sigma factor [Lyngbya sp. PCC 8106]
          Length = 391

 Score = 96.3 bits (238), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 69/237 (29%), Positives = 127/237 (53%), Gaps = 17/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 155 AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 214

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT-DNNLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++ +   KP E+ +A   ++
Sbjct: 215 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEM 269

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  D +  E  + +   R++   
Sbjct: 270 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIESDGETPEDQVSKNLLRED--- 322

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L   +  L+PRER +   R   ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 323 -LESVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLR 378


>gi|88607510|ref|YP_505167.1| RNA polymerase sigma factor RpoD [Anaplasma phagocytophilum HZ]
 gi|88598573|gb|ABD44043.1| RNA polymerase sigma factor RpoD [Anaplasma phagocytophilum HZ]
          Length = 627

 Score = 96.3 bits (238), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 72/239 (30%), Positives = 123/239 (51%), Gaps = 19/239 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLVV IA  Y   GL   ++V EGNIGLM+AV KFD +RG++ +TY+ WW
Sbjct: 390 AKQEMIKANLRLVVSIAKKYSNRGLQFLDLVQEGNIGLMKAVDKFDYKRGYKFSTYATWW 449

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           ++ A+   I      ++I     +     N R L+  L  I     +   +  ++ +LN+
Sbjct: 450 VRQAITRAIADQARTIRIPVHMIETVNKIN-RTLRQMLHEIG----REPTLEELSARLNI 504

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER---KNRR 225
           +  ++  +   +    SL + I   D +SS + D +      +++  ++ E      + R
Sbjct: 505 NVEKIRKVMKIVKDPVSLESPIG--DDDSSTFGDCI------EDKRAVKPENAAVLADLR 556

Query: 226 NMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            + T+ +S L P+E RI   R          TLE +   F V+RER+RQIEA+A +K++
Sbjct: 557 EITTKVLSTLTPKEERILRMRFGIGKSGKDHTLEEVGRLFNVTRERIRQIEAKALRKLR 615


>gi|317008763|gb|ADU79343.1| RNA polymerase sigma factor RpoD [Helicobacter pylori India7]
          Length = 676

 Score = 96.3 bits (238), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 75/246 (30%), Positives = 121/246 (49%), Gaps = 33/246 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ WW
Sbjct: 437 AKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWW 496

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR----LKGHLQAI---TDNNLKPEQV-V 160
           IK A+   I      ++I        +   + R    ++ H+Q      D  +  E+V +
Sbjct: 497 IKQAISRAIADQARTIRIPI-----HMIDTINRINKVMRKHIQETGKEPDLEVVAEEVGL 551

Query: 161 AIAKKLNVSE--SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           ++ K  NV +   E IS+   +  D+         DKN     D ++             
Sbjct: 552 SLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIM------------- 598

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEAR 275
             R++ +  +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ 
Sbjct: 599 --REDLKAQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESS 656

Query: 276 AFKKVQ 281
           A KK++
Sbjct: 657 AIKKLR 662


>gi|209523577|ref|ZP_03272131.1| RNA polymerase, sigma 70 subunit, RpoD family [Arthrospira maxima
           CS-328]
 gi|209495982|gb|EDZ96283.1| RNA polymerase, sigma 70 subunit, RpoD family [Arthrospira maxima
           CS-328]
          Length = 387

 Score = 96.3 bits (238), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 69/237 (29%), Positives = 128/237 (54%), Gaps = 17/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 151 AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 210

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT-DNNLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++ +   KP E+ +A   ++
Sbjct: 211 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEM 265

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  D +  E  + +   R++  +
Sbjct: 266 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIESDGETPEDQVSKNLLREDLES 321

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +L      L+PRER +   R   ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 322 VL----DTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLR 374


>gi|288926119|ref|ZP_06420047.1| RNA polymerase sigma-70 factor [Prevotella buccae D17]
 gi|315608396|ref|ZP_07883384.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella buccae
           ATCC 33574]
 gi|288337159|gb|EFC75517.1| RNA polymerase sigma-70 factor [Prevotella buccae D17]
 gi|315249856|gb|EFU29857.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella buccae
           ATCC 33574]
          Length = 290

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 74/285 (25%), Positives = 141/285 (49%), Gaps = 38/285 (13%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYG 72
            L +Y+ EI + PM+  +EE  LA+  +  G  +  A  +LVT++LR VV +A  Y+  G
Sbjct: 17  ALDKYLVEIGRAPMVTIEEEIELAQAIKRGGRDAERAKEKLVTANLRFVVSVAKQYQHQG 76

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V++    NQ
Sbjct: 77  LTLTDLIDEGNIGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRL--PLNQ 134

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRL-- 180
                +L ++   +      + +   V  ++ + ++ E ++          +S++     
Sbjct: 135 ---VGSLNKVNHEINRFEQEHHRRPSVQELSDRTHIDEEKIQQSMMADGHHVSIDAPFQE 191

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER--KNRRNMLTRSMSVLNPR 238
             D S+  ++  SD + +  Q     DHD     L    +R  K R  ++ R    +  +
Sbjct: 192 GEDNSMVDVMAGSDDSRTDRQ----VDHDSMAMELNSVLDRVLKEREQIIIRECFGIGCQ 247

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           E+              LE +  +  ++RERVRQI  ++  K++ES
Sbjct: 248 EK-------------GLEEIGDQLGLTRERVRQIREKSITKLRES 279


>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 = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 424 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 483

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 484 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLQM 538

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 539 PLEKVRKV-LKIA-KEPISLETPIGDEEDSHLGDFI---EDKNAVLPIDAAIQSNLRETT 593

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 594 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 648


>gi|87300555|ref|ZP_01083397.1| Putative type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 5701]
 gi|87284426|gb|EAQ76378.1| Putative type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 5701]
          Length = 398

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 70/240 (29%), Positives = 117/240 (48%), Gaps = 13/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R++ ++LRLVV +A  Y+  G+ + ++V EG +GL +AV+K+DP RGFR +TY+ WW
Sbjct: 158 ARDRMIQANLRLVVAVAKKYQKRGVELLDLVQEGTLGLERAVEKYDPTRGFRFSTYAYWW 217

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   I      +++     +K     L R+K   +    ++ +   +  +A+ L  
Sbjct: 218 IRQGVTRAIATQSRTIRLPVHVTEK-----LNRIKKAQRQFASDHGRTASLAELAEALQW 272

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SE  V     R+    SL A +       +   D L    D  EQ L     R+   + L
Sbjct: 273 SEEAVRLTLLRVPRSISLEAKVGRD--QDTPLGDLLEATSDTPEQSLT----RQQLHSDL 326

Query: 229 TRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +  L+ RE  +   R     + P TL  +    ++SRERVRQIE RA  K+++  ++
Sbjct: 327 DALLDELSEREAEVIRLRFGLADDTPRTLAQIGEGMQLSRERVRQIETRALHKLRQPARR 386


>gi|307636779|gb|ADN79229.1| RNA polymerase sigma factor [Helicobacter pylori 908]
 gi|325995367|gb|ADZ50772.1| RNA polymerase sigma factor [Helicobacter pylori 2018]
 gi|325996964|gb|ADZ49172.1| RNA polymerase sigma factor [Helicobacter pylori 2017]
          Length = 681

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 75/242 (30%), Positives = 120/242 (49%), Gaps = 25/242 (10%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ WW
Sbjct: 442 AKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWW 501

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI---TDNNLKPEQV-VAIAK 164
           IK A+   I      ++I           N + ++ H+Q      D  +  E+V +++ K
Sbjct: 502 IKQAISRAIADQARTIRIPIHMIDTINRIN-KVMRKHIQETGKEPDLEVVAEEVGLSLDK 560

Query: 165 KLNVSE--SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
             NV +   E IS+   +  D+         DKN     D ++               R+
Sbjct: 561 VKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIM---------------RE 605

Query: 223 NRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           + +  +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK
Sbjct: 606 DLKAQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKK 665

Query: 280 VQ 281
           ++
Sbjct: 666 LR 667


>gi|315499353|ref|YP_004088157.1| RNA polymerase, sigma 70 subunit, rpod [Asticcacaulis excentricus
           CB 48]
 gi|315417365|gb|ADU14006.1| RNA polymerase, sigma 70 subunit, RpoD [Asticcacaulis excentricus
           CB 48]
          Length = 696

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 458 AKTEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 517

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 518 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 572

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 573 PLEKVRKV-LKIA-KEPISLETPIGDEEDSHLGDFI---EDKNAVLPIDAAIQSNLRETT 627

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 628 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 682


>gi|148242803|ref|YP_001227960.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp.
           RCC307]
 gi|147851113|emb|CAK28607.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. RCC307]
          Length = 309

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 85/297 (28%), Positives = 145/297 (48%), Gaps = 40/297 (13%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------EHGDLS---------------AA 50
           G   +S Y+  I ++P+L   EE  L  + +      E G+ +               + 
Sbjct: 16  GNDPVSWYLSSIGRVPLLTPAEEIELGNQVQTMMTLVEQGEEATYTAREKKLIRVGRRSK 75

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            R++ ++LRLVV +A  Y+G GL + +++ EG++GL +AV+KFDP RG++ +TY+ WWI+
Sbjct: 76  ERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWWIR 135

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNL-RRLKGHLQAITDNNLKPEQVVA---IAKKL 166
            +M            I   +   RL  +L  RL    +A  D   K   + +   IA +L
Sbjct: 136 QSMTR---------AIACQSRTIRLPVHLSERLATVRKATMDLAHKLGAMPSRREIATEL 186

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   E+  +  +     SL+A I+  +  S  +   L+ D   +E   ++  ER+    
Sbjct: 187 GMGLEELDGLLRQALTTSSLDAPISGEEGRS--FLGELIADPRNEEP--LDAVERRMHHE 242

Query: 227 MLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L R +S L  +E+++ E R     E   TL  +    EVSRERVRQ+E +A +K++
Sbjct: 243 QLGRWLSYLTAQEKQVLEMRFGLGGEQRHTLAEIGRLMEVSRERVRQVELKALRKLR 299


>gi|84515379|ref|ZP_01002741.1| RNA polymerase sigma factor [Loktanella vestfoldensis SKA53]
 gi|84510662|gb|EAQ07117.1| RNA polymerase sigma factor [Loktanella vestfoldensis SKA53]
          Length = 659

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 421 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 480

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 481 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 535

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   ++N +   
Sbjct: 536 PLEKVRKV-MKIA-KEPISLETPIGDEEDSQLGDFI---EDKNAILPLDSAIQENLKETT 590

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 591 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 645


>gi|25991936|gb|AAN76995.1|AF481769_1 primary sigma 70 transcriptional factor [Frankia sp. ACN14a]
          Length = 385

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 88/294 (29%), Positives = 137/294 (46%), Gaps = 60/294 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH---------GDL------------SAAHR 52
           Y+ EI K+P+L   +E  L+KR     + EH          DL            +A  +
Sbjct: 92  YLREIGKVPLLNAAQEVELSKRVEAGLFAEHKLESDPDLPADLRRDLGLLVKDGHAAKQQ 151

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV+++LRLVV +A  Y G G+ + ++V EGN+GL++AV+KFD  +G++ +TY+ WWI+ A
Sbjct: 152 LVSANLRLVVSVAKKYSGRGMTLLDLVQEGNLGLIRAVEKFDYAKGYKFSTYATWWIRQA 211

Query: 113 MQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           +   +      ++I           T  Q++L   L R     +   + ++  EQVV   
Sbjct: 212 IGRALADQARTIRIPVHVVEQINKITRLQRQLVSTLGREPTDEELALELDMPIEQVV--- 268

Query: 164 KKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
            +L     + +S+   +   GD  L   I  SD  S    D   Y   G  Q  IE    
Sbjct: 269 -ELRRYAQDTVSLETSVGDDGDSVLGDFIEDSDATSP--ADAASY---GAMQDEIE---- 318

Query: 222 KNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIE 273
               N+L      LNPRER +   R  L +    TL  + +   ++RER+RQIE
Sbjct: 319 ----NVL----GGLNPREREVMRLRFGLADGKQHTLAEVGNRLGLTRERIRQIE 364


>gi|2267165|gb|AAC64856.1| sigma 80 [Helicobacter pylori]
          Length = 685

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 75/246 (30%), Positives = 121/246 (49%), Gaps = 33/246 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ WW
Sbjct: 446 AKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWW 505

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR----LKGHLQAI---TDNNLKPEQV-V 160
           IK A+   I      ++I        +   + R    ++ H+Q      D  +  E+V +
Sbjct: 506 IKQAISRAIADQARTIRIPI-----HMIDTINRINKVMRKHIQETGKEPDLEVVAEEVGL 560

Query: 161 AIAKKLNVSE--SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           ++ K  NV +   E IS+   +  D+         DKN     D ++             
Sbjct: 561 SLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIM------------- 607

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEAR 275
             R++ +  +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ 
Sbjct: 608 --REDLKAQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESS 665

Query: 276 AFKKVQ 281
           A KK++
Sbjct: 666 AIKKLR 671


>gi|150397423|ref|YP_001327890.1| RNA polymerase sigma factor RpoD [Sinorhizobium medicae WSM419]
 gi|150028938|gb|ABR61055.1| RNA polymerase, sigma 70 subunit, RpoD [Sinorhizobium medicae
           WSM419]
          Length = 684

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 83/273 (30%), Positives = 136/273 (49%), Gaps = 27/273 (9%)

Query: 13  EIGLSRYIHEIRKI-PMLEKQE-EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           E G+S  I E R+I  M++K E E  +AK+            +V ++LRLV+ IA  Y  
Sbjct: 421 ETGIS--IAEFRRIVSMVQKGEREARIAKK-----------EMVEANLRLVISIAKKYTN 467

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I    
Sbjct: 468 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI--PV 525

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
           +       + R    +         PE+   +A+KL +   +V  +  ++A  E ++   
Sbjct: 526 HMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAMPLEKVRKV-LKIA-KEPISLET 580

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--L 248
              D+  S   D++    D    + I+   + N R   TR ++ L PRE R+   R    
Sbjct: 581 PVGDEEDSHLGDFI---EDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIG 637

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 638 MNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 670


>gi|15966067|ref|NP_386420.1| RNA polymerase sigma factor RpoD [Sinorhizobium meliloti 1021]
 gi|307305622|ref|ZP_07585369.1| RNA polymerase, sigma 70 subunit, RpoD [Sinorhizobium meliloti
           BL225C]
 gi|307317625|ref|ZP_07597064.1| RNA polymerase, sigma 70 subunit, RpoD [Sinorhizobium meliloti
           AK83]
 gi|7388096|sp|Q59753|RPOD_RHIME RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A;
           AltName: Full=Major vegetative sigma factor
 gi|1050336|gb|AAA88524.1| sigma factor [Sinorhizobium meliloti]
 gi|15075337|emb|CAC46893.1| RNA polymerase sigma factor transcription regulation protein
           [Sinorhizobium meliloti 1021]
 gi|306896783|gb|EFN27530.1| RNA polymerase, sigma 70 subunit, RpoD [Sinorhizobium meliloti
           AK83]
 gi|306902325|gb|EFN32921.1| RNA polymerase, sigma 70 subunit, RpoD [Sinorhizobium meliloti
           BL225C]
          Length = 684

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 83/273 (30%), Positives = 136/273 (49%), Gaps = 27/273 (9%)

Query: 13  EIGLSRYIHEIRKI-PMLEKQE-EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           E G+S  I E R+I  M++K E E  +AK+            +V ++LRLV+ IA  Y  
Sbjct: 421 ETGIS--IAEFRRIVSMVQKGEREARIAKK-----------EMVEANLRLVISIAKKYTN 467

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I    
Sbjct: 468 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI--PV 525

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
           +       + R    +         PE+   +A+KL +   +V  +  ++A  E ++   
Sbjct: 526 HMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAMPLEKVRKV-LKIA-KEPISLET 580

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--L 248
              D+  S   D++    D    + I+   + N R   TR ++ L PRE R+   R    
Sbjct: 581 PVGDEEDSHLGDFI---EDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIG 637

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 638 MNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 670


>gi|2522316|gb|AAB81010.1| RNA polymerase principal sigma factor RpoD [Helicobacter pylori]
          Length = 680

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 75/246 (30%), Positives = 121/246 (49%), Gaps = 33/246 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ WW
Sbjct: 441 AKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWW 500

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR----LKGHLQAI---TDNNLKPEQV-V 160
           IK A+   I      ++I        +   + R    ++ H+Q      D  +  E+V +
Sbjct: 501 IKQAISRAIADQARTIRIPI-----HMIDTINRINKVMRKHIQETGKEPDLEVVAEEVGL 555

Query: 161 AIAKKLNVSE--SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           ++ K  NV +   E IS+   +  D+         DKN     D ++             
Sbjct: 556 SLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIM------------- 602

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEAR 275
             R++ +  +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ 
Sbjct: 603 --REDLKAQIESVLDQLNEREKAVIRMRFGLLDDESERTLEEIGKELNVTRERVRQIESS 660

Query: 276 AFKKVQ 281
           A KK++
Sbjct: 661 AIKKLR 666


>gi|83746506|ref|ZP_00943557.1| RpoD [Ralstonia solanacearum UW551]
 gi|83726837|gb|EAP73964.1| RpoD [Ralstonia solanacearum UW551]
          Length = 391

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 67/235 (28%), Positives = 117/235 (49%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 152 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 211

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+   +   T N   P     +A+K+ +
Sbjct: 212 IRQAITRSIADQARTIRI--PVHMIETINKMNRISRQILQETGNEPDP---ATLAEKMEM 266

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       E     + R ++
Sbjct: 267 PEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDTNTLAPAEAALHGSMRGVV 321

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 322 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 376


>gi|227822807|ref|YP_002826779.1| RNA polymerase sigma factor RpoD [Sinorhizobium fredii NGR234]
 gi|227341808|gb|ACP26026.1| RNA polymerase sigma factor RpoD [Sinorhizobium fredii NGR234]
          Length = 684

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 83/273 (30%), Positives = 136/273 (49%), Gaps = 27/273 (9%)

Query: 13  EIGLSRYIHEIRKI-PMLEKQE-EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           E G+S  I E R+I  M++K E E  +AK+            +V ++LRLV+ IA  Y  
Sbjct: 421 ETGIS--IAEFRRIVSMVQKGEREARIAKK-----------EMVEANLRLVISIAKKYTN 467

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I    
Sbjct: 468 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI--PV 525

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
           +       + R    +         PE+   +A+KL +   +V  +  ++A  E ++   
Sbjct: 526 HMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAMPLEKVRKV-LKIA-KEPISLET 580

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--L 248
              D+  S   D++    D    + I+   + N R   TR ++ L PRE R+   R    
Sbjct: 581 PVGDEEDSHLGDFI---EDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIG 637

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 638 MNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 670


>gi|254504180|ref|ZP_05116331.1| Sigma-70 region 3 family [Labrenzia alexandrii DFL-11]
 gi|222440251|gb|EEE46930.1| Sigma-70 region 3 family [Labrenzia alexandrii DFL-11]
          Length = 671

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 77/240 (32%), Positives = 123/240 (51%), Gaps = 22/240 (9%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 433 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 492

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+      +R  +  L  I      PE+   +A+
Sbjct: 493 IRQAITRSIADQARTIRIPVHMIETINKI-----VRTSRQMLHEIG-REPTPEE---LAE 543

Query: 165 KLNVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           KL +   +V  +  ++A +  SL   I   D+  S   D++    D    + I+   + N
Sbjct: 544 KLQMPLEKVRKV-LKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAVLPIDAAIQSN 597

Query: 224 RRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 598 LRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 657


>gi|15889446|ref|NP_355127.1| RNA polymerase sigma factor RpoD [Agrobacterium tumefaciens str.
           C58]
 gi|20141718|sp|P33452|RPOD_AGRT5 RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A;
           AltName: Full=Major vegetative sigma factor
 gi|15157308|gb|AAK87912.1| RNA polymerase sigma factor RpoD [Agrobacterium tumefaciens str.
           C58]
          Length = 684

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 83/276 (30%), Positives = 138/276 (50%), Gaps = 27/276 (9%)

Query: 10  VNGEIGLSRYIHEIRKI-PMLEKQE-EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++ E G+S  I E R+I  M++K E E  +AK+            +V ++LRLV+ IA  
Sbjct: 418 LSTETGIS--IAEFRRIVSMVQKGEREARIAKK-----------EMVEANLRLVISIAKK 464

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I 
Sbjct: 465 YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI- 523

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              +       + R    +         PE+   +A+KL +   +V  +  ++A  E ++
Sbjct: 524 -PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAMPLEKVRKV-LKIA-KEPIS 577

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
                 D+  S   D++    D    + I+   + N R   TR ++ L PRE R+   R 
Sbjct: 578 LETPVGDEEDSHLGDFI---EDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRF 634

Query: 248 --LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                   TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 635 GIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 670


>gi|268680166|ref|YP_003304597.1| RNA polymerase sigma factor RpoD [Sulfurospirillum deleyianum DSM
           6946]
 gi|268618197|gb|ACZ12562.1| RNA polymerase sigma factor RpoD [Sulfurospirillum deleyianum DSM
           6946]
          Length = 617

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 76/246 (30%), Positives = 125/246 (50%), Gaps = 14/246 (5%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           KR ++  D S   R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ ++G
Sbjct: 369 KRGKKIADESKT-RMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKKG 427

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           ++ +TY+ WWI+ A+   I      ++I     +     N + ++ HLQ       K   
Sbjct: 428 YKFSTYATWWIRQAISRAIADQARTIRIPIHMIETINRIN-KIIRKHLQ----EEGKEPD 482

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           +  IA ++ +S  +V ++        SL A I + D    ++ D++    D      +E 
Sbjct: 483 IETIALEVGLSADKVKNVIKITKEPISLEAPIGNED--DGKFGDFV---EDKTSIAPLEH 537

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEAR 275
             + + +  +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ 
Sbjct: 538 ILKSDLKEQIDDVLDQLNDREKAVIRMRFGLMHDESDRTLEEIGKELNVTRERVRQIESS 597

Query: 276 AFKKVQ 281
           A KK++
Sbjct: 598 AIKKLK 603


>gi|72161811|ref|YP_289468.1| RNA polymerase sigma factor [Thermobifida fusca YX]
 gi|71915543|gb|AAZ55445.1| RNA polymerase sigma factor [Thermobifida fusca YX]
          Length = 438

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 70/241 (29%), Positives = 124/241 (51%), Gaps = 13/241 (5%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E G  + AH ++ ++LRLVV +A  Y   G+P+ +VV EGN+GL++AV+KFD  +G++ +
Sbjct: 196 EDGRRAKAH-MLEANLRLVVSVAKKYSDRGMPLLDVVQEGNLGLIRAVEKFDYAKGYKFS 254

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+MWWI+ A+Q     S   +++    +   L   L RL+  +         P+++   
Sbjct: 255 TYAMWWIRQAIQRGFADSARTIRL--PVHVLELLSKLSRLERDMHQTLGREPTPDELAQE 312

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
             K      E++ +  +     SL++ I   +   ++  D L+ D D  E    E  +R+
Sbjct: 313 LGKTPAQIEELLRITRQPI---SLDSTIG--EDGETRIGD-LIEDVDASEAS--EVVDRQ 364

Query: 223 NRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
              + L R++  L PRE  I   R       P TL+ +     ++RER+RQ+E ++  K+
Sbjct: 365 LMADQLRRALDDLEPREATIMSLRFGLFDGRPRTLDEIGKHLGLTRERIRQLEKQSLSKL 424

Query: 281 Q 281
           +
Sbjct: 425 R 425


>gi|258542087|ref|YP_003187520.1| RNA polymerase sigma factor RpoD [Acetobacter pasteurianus IFO
           3283-01]
 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 = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 78/277 (28%), Positives = 134/277 (48%), Gaps = 16/277 (5%)

Query: 10  VNGEIGLSRYIHEIRK---IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
            N  +GL   + ++ +   +P+ E +  Y    R  E     A   ++ ++LRLV+ IA 
Sbjct: 392 ANTVVGLRDQVAQLAQETGLPIGEFRRVYATVARG-ERDSARAKKEMIEANLRLVISIAK 450

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I
Sbjct: 451 KYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 510

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
               +       L R    +         PE+   +A+KL +   +V  +  ++A  E +
Sbjct: 511 --PVHMIETINKLVRTSRQMLHEIGREPAPEE---LAEKLGMPLEKVRKV-LKIA-KEPI 563

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           +      D+  S   D++    D    + ++   + N R   TR ++ L PRE R+   R
Sbjct: 564 SLETPIGDEEDSHLGDFI---EDKTAIIPLDAAIQTNLREATTRVLASLTPREERVLRMR 620

Query: 247 R--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                    TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 621 FGIGMNTDHTLEEVGQQFNVTRERIRQIEAKALRKLK 657


>gi|317132028|ref|YP_004091342.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ethanoligenens
           harbinense YUAN-3]
 gi|315470007|gb|ADU26611.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ethanoligenens
           harbinense YUAN-3]
          Length = 372

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 46/108 (42%), Positives = 72/108 (66%), Gaps = 1/108 (0%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++P+L  +EE  LAKR  E GD++A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 106 YLKEIGRVPLLSGEEEIELAKRMGE-GDVAARKRLSEANLRLVVSIAKRYVGRGMQFLDL 164

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           + EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I
Sbjct: 165 IQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRI 212



 Score = 40.0 bits (92), Expect = 0.38,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 35/59 (59%), Gaps = 2/59 (3%)

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +  L   +  L  RE ++   R   ++  P TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 301 KEQLGDVLKTLTQREAKVLRLRFGLDDGRPRTLEEVGREFNVTRERIRQIEAKALRKLR 359


>gi|148240072|ref|YP_001225459.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp. WH
           7803]
 gi|147848611|emb|CAK24162.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 7803]
          Length = 313

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 80/293 (27%), Positives = 148/293 (50%), Gaps = 36/293 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYR------EHGDLSA-------------------A 50
           +S Y+  I +IP+L   EE  L  + +      E G ++A                    
Sbjct: 20  ISWYLATIGRIPLLTPAEEIELGNQVQQLMQLTEDGSIAADSDQFDGKQRRLIRVGQRAK 79

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            R++ ++LRLVV +A  Y+G GL + +++ EG++GL +AV+KFDP RG++ +TY+ WWI+
Sbjct: 80  QRMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWWIR 139

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            +M   I      +++    +++     +R++   L         P + + IA+ +++  
Sbjct: 140 QSMTRAIACQSRTIRLPVHLSER--LTTIRKVS--LDLAHKLGAMPSR-LEIAEAMDMPV 194

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            E+ S+  +     SL+A +N  +  S  +   L+ D   +E   +++ E++     L R
Sbjct: 195 EELDSLLRQALTTSSLDAPVNGEEGRS--FLGDLIADSSLEEP--LDRVEQRMHHEQLGR 250

Query: 231 SMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            MS L+ +E+ +   R  L  N   TL  +    +VSRERVRQ+E +A +K++
Sbjct: 251 WMSHLSDQEQHVLTLRFGLNGNERHTLAEIGRLLDVSRERVRQVELKALRKLR 303


>gi|110633818|ref|YP_674026.1| RNA polymerase sigma factor RpoD [Mesorhizobium sp. BNC1]
 gi|110284802|gb|ABG62861.1| RNA polymerase, sigma 38 subunit, RpoS [Chelativorans sp. BNC1]
          Length = 668

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 430 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 489

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 490 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 544

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 545 PLEKVRKV-LKIA-KEPISLETPVGDEEDSHLGDFI---EDKSAILPIDAAIQANLRETT 599

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 600 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 654


>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 = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 72/243 (29%), Positives = 118/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 381 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 440

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 441 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 498

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   Q+ ++   
Sbjct: 499 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLQLPMDAAT 542

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
           + N R      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 543 QTNLRAATNEVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 602

Query: 279 KVQ 281
           K++
Sbjct: 603 KLR 605


>gi|308183886|ref|YP_003928019.1| RNA polymerase sigma factor RpoD [Helicobacter pylori SJM180]
 gi|308059806|gb|ADO01702.1| RNA polymerase sigma factor RpoD [Helicobacter pylori SJM180]
          Length = 679

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 75/246 (30%), Positives = 121/246 (49%), Gaps = 33/246 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ WW
Sbjct: 440 AKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWW 499

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR----LKGHLQAI---TDNNLKPEQV-V 160
           IK A+   I      ++I        +   + R    ++ H+Q      D  +  E+V +
Sbjct: 500 IKQAISRAIADQARTIRIPI-----HMIDTINRINKVMRKHIQETGKEPDLEVVAEEVGL 554

Query: 161 AIAKKLNVSE--SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           ++ K  NV +   E IS+   +  D+         DKN     D ++             
Sbjct: 555 SLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIM------------- 601

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEAR 275
             R++ +  +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ 
Sbjct: 602 --REDLKAQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESS 659

Query: 276 AFKKVQ 281
           A KK++
Sbjct: 660 AIKKLR 665


>gi|307944279|ref|ZP_07659620.1| RNA polymerase sigma factor RpoD [Roseibium sp. TrichSKD4]
 gi|307772625|gb|EFO31845.1| RNA polymerase sigma factor RpoD [Roseibium sp. TrichSKD4]
          Length = 669

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 75/239 (31%), Positives = 122/239 (51%), Gaps = 20/239 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 431 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 490

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+      +R  +  L  I      PE+   +A+
Sbjct: 491 IRQAITRSIADQARTIRIPVHMIETINKI-----VRTSRQMLHEIG-REPTPEE---LAE 541

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           KL +   +V  +  ++A  E ++      D+  S   D++    D    + I+   + N 
Sbjct: 542 KLQMPLEKVRKV-LKIA-KEPISLETPIGDEEDSHLGDFI---EDKNAVLPIDAAIQSNL 596

Query: 225 RNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 597 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 655


>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 = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 121/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 99  AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 158

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +  L+P+    +A+K+ +
Sbjct: 159 IRQAITRSIADQARTIRI--PVHMIETINKMNRISR--QILQETGLEPDPAT-LAEKMEM 213

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + R+++
Sbjct: 214 PEDKIRKI-MKIAK-EPISMETPIGDDDDSHLGDFI---EDNNTVAPADAALHASMRDVV 268

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 269 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 323


>gi|329848685|ref|ZP_08263713.1| RNA polymerase sigma factor rpoD [Asticcacaulis biprosthecum C19]
 gi|328843748|gb|EGF93317.1| RNA polymerase sigma factor rpoD [Asticcacaulis biprosthecum C19]
          Length = 699

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 461 AKTEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 520

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 521 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 575

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 576 PLEKVRKV-LKIA-KEPISLETPIGDEEDSHLGDFI---EDKNAVLPIDAAIQSNLRETT 630

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 631 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 685


>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 = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 75/241 (31%), Positives = 115/241 (47%), Gaps = 26/241 (10%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RGF+ +TY+ WW
Sbjct: 385 AKEEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGFKFSTYATWW 444

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV-VAIA---- 163
           I+ A+   I      ++I    +       L R+   LQ     +  PE++ VA+     
Sbjct: 445 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRMLQQKNGRDPTPEELSVAMDMPED 502

Query: 164 --KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
             +K+     E ISM   +  DE             S   D+L    D      +E    
Sbjct: 503 KIRKVWKIAKEPISMETPIGDDE------------DSHLGDFL---EDSNVISPLEAATT 547

Query: 222 KNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKK 279
           +         ++ L PRE R+   R  +  N   TLE +  +F+V+RER+RQIEA+A +K
Sbjct: 548 RGLSEATNEVLASLTPREERVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKALRK 607

Query: 280 V 280
           +
Sbjct: 608 L 608


>gi|15609840|ref|NP_217219.1| RNA polymerase sigma factor [Mycobacterium tuberculosis H37Rv]
 gi|15842241|ref|NP_337278.1| RNA polymerase sigma factor [Mycobacterium tuberculosis CDC1551]
 gi|31793875|ref|NP_856368.1| RNA polymerase sigma factor [Mycobacterium bovis AF2122/97]
 gi|121638578|ref|YP_978802.1| RNA polymerase sigma factor [Mycobacterium bovis BCG str. Pasteur
           1173P2]
 gi|148662544|ref|YP_001284067.1| RNA polymerase sigma factor [Mycobacterium tuberculosis H37Ra]
 gi|148823893|ref|YP_001288647.1| RNA polymerase sigma factor [Mycobacterium tuberculosis F11]
 gi|167970074|ref|ZP_02552351.1| RNA polymerase sigma factor RpoD [Mycobacterium tuberculosis H37Ra]
 gi|218754439|ref|ZP_03533235.1| RNA polymerase sigma factor [Mycobacterium tuberculosis GM 1503]
 gi|224991070|ref|YP_002645759.1| RNA polymerase sigma factor [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|253798215|ref|YP_003031216.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis KZN
           1435]
 gi|254551759|ref|ZP_05142206.1| RNA polymerase sigma factor [Mycobacterium tuberculosis '98-R604
           INH-RIF-EM']
 gi|260187720|ref|ZP_05765194.1| RNA polymerase sigma factor [Mycobacterium tuberculosis CPHL_A]
 gi|289448358|ref|ZP_06438102.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           CPHL_A]
 gi|289553511|ref|ZP_06442721.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis KZN
           605]
 gi|289762874|ref|ZP_06522252.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis GM
           1503]
 gi|294994205|ref|ZP_06799896.1| RNA polymerase sigma factor [Mycobacterium tuberculosis 210]
 gi|297635311|ref|ZP_06953091.1| RNA polymerase sigma factor [Mycobacterium tuberculosis KZN 4207]
 gi|297732307|ref|ZP_06961425.1| RNA polymerase sigma factor [Mycobacterium tuberculosis KZN R506]
 gi|306780885|ref|ZP_07419222.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu002]
 gi|306790106|ref|ZP_07428428.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu004]
 gi|306798608|ref|ZP_07436910.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu006]
 gi|306804467|ref|ZP_07441135.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu008]
 gi|306807495|ref|ZP_07444163.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu007]
 gi|306968762|ref|ZP_07481423.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu009]
 gi|307080806|ref|ZP_07489976.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu011]
 gi|313659640|ref|ZP_07816520.1| RNA polymerase sigma factor [Mycobacterium tuberculosis KZN V2475]
 gi|61234251|sp|P0A602|RPOD_MYCTU RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A
 gi|61234258|sp|P0A603|RPOD_MYCBO RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A
 gi|1072023|gb|AAA81643.1| sigma factor [Mycobacterium bovis]
 gi|1072025|gb|AAA81644.1| sigma factor [Mycobacterium tuberculosis str. Erdman]
 gi|1171102|gb|AAA86043.1| sigma factor MysA [Mycobacterium tuberculosis H37Rv]
 gi|2181994|emb|CAB09463.1| RNA POLYMERASE SIGMA FACTOR SIGA (SIGMA-A) [Mycobacterium
           tuberculosis H37Rv]
 gi|13882532|gb|AAK47092.1| RNA polymerase principal sigma factor SigA [Mycobacterium
           tuberculosis CDC1551]
 gi|31619469|emb|CAD94907.1| RNA POLYMERASE SIGMA FACTOR SIGA (SIGMA-A) [Mycobacterium bovis
           AF2122/97]
 gi|121494226|emb|CAL72704.1| RNA polymerase sigma factor sigA [Mycobacterium bovis BCG str.
           Pasteur 1173P2]
 gi|148506696|gb|ABQ74505.1| RNA polymerase sigma factor [Mycobacterium tuberculosis H37Ra]
 gi|148722420|gb|ABR07045.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis F11]
 gi|224774185|dbj|BAH26991.1| RNA polymerase sigma factor [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|253319718|gb|ACT24321.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis KZN
           1435]
 gi|289421316|gb|EFD18517.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           CPHL_A]
 gi|289438143|gb|EFD20636.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis KZN
           605]
 gi|289710380|gb|EFD74396.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis GM
           1503]
 gi|308326286|gb|EFP15137.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu002]
 gi|308333457|gb|EFP22308.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu004]
 gi|308341125|gb|EFP29976.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu006]
 gi|308346090|gb|EFP34941.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu007]
 gi|308348951|gb|EFP37802.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu008]
 gi|308353649|gb|EFP42500.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu009]
 gi|308361450|gb|EFP50301.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu011]
 gi|326904319|gb|EGE51252.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis W-148]
 gi|328457987|gb|AEB03410.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis KZN
           4207]
          Length = 528

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 82/318 (25%), Positives = 151/318 (47%), Gaps = 43/318 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGD-LS 48
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+ L 
Sbjct: 216 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSERGEKLP 274

Query: 49  AAHR----------------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           AA R                L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 275 AAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 334

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L      
Sbjct: 335 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGR 392

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D + 
Sbjct: 393 EPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEA 444

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVR 270
            V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 445 VVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIR 504

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 505 QIESKTMSKLRHPSRSQV 522


>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]
          Length = 620

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 72/246 (29%), Positives = 123/246 (50%), Gaps = 12/246 (4%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A  Y E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 370 AMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 429

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I    +       L R+   +         PE
Sbjct: 430 GYKFSTYATWWIRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQQYGREATPE 487

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           +   +AK++++ E ++  +  ++A  E ++      D   S   D++    D   +  IE
Sbjct: 488 E---LAKEMDMPEDKIRKV-MKIA-KEPISMETPIGDDEDSHLGDFI---EDTNVESPIE 539

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEAR 275
                N    +   ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+
Sbjct: 540 NTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 599

Query: 276 AFKKVQ 281
           A +K++
Sbjct: 600 ALRKLR 605


>gi|54401878|gb|AAV34624.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 238

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 77/263 (29%), Positives = 126/263 (47%), Gaps = 34/263 (12%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           GEIG S         P+L  +E+   A+R    GD+++  R++ S+LRLVVKIA  Y   
Sbjct: 2   GEIGYS---------PLLTAEEKVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNR 51

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TA 130
           GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++     
Sbjct: 52  GLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV 111

Query: 131 NQKRLFFNLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
            +  ++    R   H        + I +   KP   V+   +LN     + S++  L GD
Sbjct: 112 KELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGD 168

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
                L   +D+  +  +D    D   Q  V    E    +R +L R   +L       +
Sbjct: 169 SEKALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------Y 222

Query: 244 EARRLQENPVTLENLSSEFEVSR 266
           EA        TLE++  E  ++R
Sbjct: 223 EA-------ATLEDVGREIGLTR 238


>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 = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 65/235 (27%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 415 AKRDMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 474

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + I     +      +A+K+ +
Sbjct: 475 IRQAITRSIADQARTIRIPV-----HMIETINKMNRISRQILQETGQEADAATLAEKMEM 529

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +E ++  +  ++A  E ++      D + S   D++    D    V IE    ++ R+  
Sbjct: 530 TEDKIHKI-LKIAK-EPISMETPVGDDDDSHLGDFI---EDSNTTVPIEAAVYESLRSAT 584

Query: 229 TRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +  +  L  RE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 585 SDILDSLTQREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 639


>gi|240142885|ref|YP_002967398.1| putative RNA polymerase, sigma 70 (sigma D) factor
           [Methylobacterium extorquens AM1]
 gi|240012832|gb|ACS44057.1| putative RNA polymerase, sigma 70 (sigma D) factor
           [Methylobacterium extorquens AM1]
          Length = 531

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 73/241 (30%), Positives = 128/241 (53%), Gaps = 13/241 (5%)

Query: 44  HGDLSAA-HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           HGDL  A   LVTS+LRLV  +A  Y    LPI ++V EGNIGLM+A++KFD  RG++ +
Sbjct: 285 HGDLRKARDTLVTSNLRLVFSVAKKYTNRPLPILDLVQEGNIGLMRAIEKFDYRRGWKFS 344

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++WWIK ++   I      +++    ++K     + R    L+A       P + +A 
Sbjct: 345 TYAIWWIKQSISRSIADHGRTIRLPVHLHEKAA--KIDRTAARLRAELGRPPSPPE-LAQ 401

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A  ++V + E +    R    E+++  +   +    ++ D LV D    + V +   +  
Sbjct: 402 ALDIDVRQVERLMNMSR----ETVSLDLPVGEDGDVRFGD-LVEDEKAPDPVGL--ADLA 454

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++ ++ ++  L  RE+ I   R      + +TLE +   F +SRERVRQ+E++A +++
Sbjct: 455 KLKDAVSDAVGDLPEREQTIIRMRFGIGYADQMTLEEIGQHFRISRERVRQVESKAIQRL 514

Query: 281 Q 281
           +
Sbjct: 515 R 515


>gi|1072017|gb|AAA81640.1| sigma factor [Mycobacterium bovis]
 gi|1072019|gb|AAA81641.1| sigma factor [Mycobacterium bovis]
          Length = 528

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 82/318 (25%), Positives = 151/318 (47%), Gaps = 43/318 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGD-LS 48
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+ L 
Sbjct: 216 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSERGEKLP 274

Query: 49  AAHR----------------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           AA R                L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 275 AAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 334

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L      
Sbjct: 335 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGR 392

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D + 
Sbjct: 393 EPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEA 444

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVR 270
            V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 445 VVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIR 504

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 505 QIESKTMSKLRHPSRSQV 522


>gi|258653895|ref|YP_003203051.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nakamurella
           multipartita DSM 44233]
 gi|258557120|gb|ACV80062.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nakamurella
           multipartita DSM 44233]
          Length = 448

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 81/318 (25%), Positives = 151/318 (47%), Gaps = 43/318 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-------------YREHG---- 45
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR             + E G    
Sbjct: 136 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVDLAKRIEAGLYSSERMRQFEEAGERLP 194

Query: 46  -----DLS--------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                DL         A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 195 NQMRRDLRWIKRDGERAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 254

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L      
Sbjct: 255 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGR 312

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D + 
Sbjct: 313 EPTPEE---LAKEMDITPDKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEA 364

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVR 270
            V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 365 VVAVDAVSFTLLQDQLQAVLQTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIR 424

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 425 QIESKTMSKLRHPSRSQV 442


>gi|190892699|ref|YP_001979241.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CIAT
           652]
 gi|190697978|gb|ACE92063.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CIAT
           652]
 gi|327189666|gb|EGE56814.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli
           CNPAF512]
          Length = 685

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 447 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 506

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 507 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 561

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 562 PLEKVRKV-LKIA-KEPISLETPVGDEEDSHLGDFI---EDKNALLPIDAAIQANLRETT 616

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 617 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 671


>gi|108562514|ref|YP_626830.1| RNA polymerase sigma factor RpoD [Helicobacter pylori HPAG1]
 gi|107836287|gb|ABF84156.1| RNA polymerase sigma-80 factor [Helicobacter pylori HPAG1]
          Length = 692

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 75/246 (30%), Positives = 121/246 (49%), Gaps = 33/246 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ WW
Sbjct: 453 AKNKMAQSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWW 512

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR----LKGHLQAI---TDNNLKPEQV-V 160
           IK A+   I      ++I        +   + R    ++ H+Q      D  +  E+V +
Sbjct: 513 IKQAISRAIADQARTIRIPI-----HMIDTINRINKVMRKHIQETGKEPDLEVVAEEVGL 567

Query: 161 AIAKKLNVSE--SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           ++ K  NV +   E IS+   +  D+         DKN     D ++             
Sbjct: 568 SLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIM------------- 614

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEAR 275
             R++ +  +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ 
Sbjct: 615 --REDLKAQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESS 672

Query: 276 AFKKVQ 281
           A KK++
Sbjct: 673 AIKKLR 678


>gi|1072021|gb|AAA81642.1| sigma factor [Mycobacterium bovis]
          Length = 528

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 82/318 (25%), Positives = 150/318 (47%), Gaps = 43/318 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGD-LS 48
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+ L 
Sbjct: 216 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSERGEKLP 274

Query: 49  AAHR----------------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           AA R                L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 275 AAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 334

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L      
Sbjct: 335 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGR 392

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D + 
Sbjct: 393 EPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEA 444

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVR 270
            V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 445 VVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIR 504

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K+    + QV
Sbjct: 505 QIESKTMSKLHHPSRSQV 522


>gi|86358552|ref|YP_470444.1| RNA polymerase sigma factor RpoD [Rhizobium etli CFN 42]
 gi|86282654|gb|ABC91717.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CFN
           42]
          Length = 685

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 447 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 506

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 507 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 561

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 562 PLEKVRKV-LKIA-KEPISLETPVGDEEDSHLGDFI---EDKNALLPIDAAIQANLRETT 616

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 617 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 671


>gi|87301519|ref|ZP_01084359.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
 gi|87283736|gb|EAQ75690.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
          Length = 322

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 87/289 (30%), Positives = 141/289 (48%), Gaps = 39/289 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLA------KRYREHGDLS--------------AAHRLVTSHL 58
           Y+  I ++P+L   EE  LA      K   E  D S              A  R++ ++L
Sbjct: 38  YLSNIGRVPLLTAAEEIELAHHVQAMKLLLELPDASLTPRQRHQIRMGGRARDRMMAANL 97

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+  M   I 
Sbjct: 98  RLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTRAID 157

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLK---GHLQAITDNNLKPEQVVAIAKKLNVSESE-VI 174
            S   +++    ++K     +RR+     H      N L+    ++ A  +++ + E +I
Sbjct: 158 NSARTIRLPIHVSEK--LSKMRRITRELSHRFGRQPNRLE----LSHAMGMDIKDLEDLI 211

Query: 175 SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV 234
           S +   A   SL+A     +  S+  +  L+ D    E   ++  +R  ++  L   +S 
Sbjct: 212 SQSAPCA---SLDAHARGEEDRSTLGE--LIADPASTEP--MDHMDRSIQKEHLGTWLSQ 264

Query: 235 LNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           LN RE+ I   R   E   P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 265 LNEREQEILRLRFGLEGKEPLTLAEIGRKINVSRERVRQLEAKAIMKLR 313


>gi|320103437|ref|YP_004179028.1| RpoD subfamily RNA polymerase sigma-70 factor [Isosphaera pallida
           ATCC 43644]
 gi|319750719|gb|ADV62479.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Isosphaera
           pallida ATCC 43644]
          Length = 286

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 81/269 (30%), Positives = 135/269 (50%), Gaps = 23/269 (8%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           +L  +EE  LA+R    GD SA  R++ ++LRLV  +A  YRG GL   ++V EGN+GL+
Sbjct: 32  LLTAEEERELARRVL-RGDASARRRMIEANLRLVAMVAARYRGLGLDWEDLVGEGNLGLI 90

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL-------R 140
           +AV  +DP+RG R +TY+  WI+  ++         V + TTA   RL  ++       R
Sbjct: 91  RAVSSYDPDRGVRFSTYAAHWIRQTIR---------VALTTTAATIRLPAHMVTKLALWR 141

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
           R +  L   T N  +      +A +L  S S  +SM   +      +    +++   S+ 
Sbjct: 142 RAEARL---TRNLGRSPTFEEVADELGWSSSTRLSMKRAMESGRVHHEEPGATEGRGSES 198

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENL 258
           +  +    D + +   E  ER++    L RS+  L  RER +   R    +  P  L  +
Sbjct: 199 RRPIDQAVDPRPEPAWEI-ERRDELLELRRSLQRLGERERLVLALRYGLGDIAPKPLREV 257

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++   V+RE VR+IEARA +++ E ++ +
Sbjct: 258 ATTLGVTREWVRRIEARALRQLHEEVEPE 286


>gi|167829080|ref|ZP_02460551.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia pseudomallei
           9]
          Length = 285

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 121/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 46  AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 105

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +  L+P+    +A+K+ +
Sbjct: 106 IRQAITRSIADQARTIRI--PVHMIETINKMNRISR--QILQETGLEPDPAT-LAEKMEM 160

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + R+++
Sbjct: 161 PEDKIRKI-MKIAK-EPISMETPIGDDDDSHLGDFI---EDTNTVAPADAALHASMRDVV 215

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 216 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 270


>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 = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 70/243 (28%), Positives = 116/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 414 AKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 473

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       + R+   +   T    +P ++         
Sbjct: 474 IRQAITRSIADQARTIRI--PVHMIETINKMNRISRQILQSTGQEPEPSELAEKMEMPEE 531

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +S+ E ISM   +  DE  +      D  +    D  VY              
Sbjct: 532 KIRKILKISK-EPISMETPIGDDEDSHLGDFIEDVGTLTPDDAAVYG------------- 577

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
             + R++ +  +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 578 --SLRSVTSEILEGLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALR 635

Query: 279 KVQ 281
           K++
Sbjct: 636 KLR 638


>gi|91779751|ref|YP_554959.1| sigma 70 (RpoD) [Burkholderia xenovorans LB400]
 gi|91692411|gb|ABE35609.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia xenovorans
           LB400]
          Length = 647

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 73/255 (28%), Positives = 126/255 (49%), Gaps = 12/255 (4%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L++  E   A    E   L A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+
Sbjct: 388 LDEFREVCRALSASEAKTLRAKGEMIEANLRLVISIAKRYTNRGLLFLDLIQEGNIGLMR 447

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           AV KF+  RG++ +TY+ WWI+ A+   I      +++        +  +L +LK   + 
Sbjct: 448 AVDKFEYRRGYKFSTYATWWIRQAVSRSIADQARTIRVPV-----HMIESLNKLKRISRK 502

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           I            +A+ + + E +V +M   +    SL+A +  +D  S    D +    
Sbjct: 503 ILQETGNEPDAALLAQLMEMQEQKVRAMLRIVKEPVSLDASVGENDDTS--IGDLI---E 557

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSR 266
           D    +  +       R+ ++ ++  L PRE +I   R   E+    TLE L  +FE++R
Sbjct: 558 DSAAILPDDAALHAGMRDAISEALMTLTPREAKILRLRFGIESSRDHTLEELGEQFELTR 617

Query: 267 ERVRQIEARAFKKVQ 281
           ER+RQIE +A +K++
Sbjct: 618 ERIRQIEVKALRKLR 632


>gi|257056422|ref|YP_003134254.1| RNA polymerase, sigma 70 subunit, RpoD [Saccharomonospora viridis
           DSM 43017]
 gi|256586294|gb|ACU97427.1| RNA polymerase, sigma 70 subunit, RpoD [Saccharomonospora viridis
           DSM 43017]
          Length = 439

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 84/320 (26%), Positives = 150/320 (46%), Gaps = 47/320 (14%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRL--------- 53
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR  E G L AA RL         
Sbjct: 127 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRI-EAG-LYAAERLRIAEEEGEK 183

Query: 54  -----------------------VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
                                  + ++LRLVV +A  Y G G+   +++ EGN+GL++AV
Sbjct: 184 LSTQMRRDLKWIVRDGERAKSHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAV 243

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +KFD  +GF+ +TY+ WWI+ A+   +      ++I    +   +   L R++  L    
Sbjct: 244 EKFDYTKGFKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDL 301

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
                PE+   +AK++++S  +V+ +        SL+  I   D+  SQ  D++    D 
Sbjct: 302 GREPTPEE---LAKEMDISPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDS 353

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRER 268
           +  V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER
Sbjct: 354 EAVVAVDAVSFTLLQDQLQSVLQTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRER 413

Query: 269 VRQIEARAFKKVQESIQKQV 288
           +RQIE++   K++   + QV
Sbjct: 414 IRQIESKTMSKLRHPSRSQV 433


>gi|217977790|ref|YP_002361937.1| RNA polymerase sigma factor RpoD [Methylocella silvestris BL2]
 gi|217503166|gb|ACK50575.1| RNA polymerase, sigma 70 subunit, RpoD [Methylocella silvestris
           BL2]
          Length = 683

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 75/239 (31%), Positives = 122/239 (51%), Gaps = 20/239 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 445 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 504

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+      +R  +  L  I      PE+   +A+
Sbjct: 505 IRQAITRSIADQARTIRIPVHMIETINKI-----VRTSRQMLHEIG-REPTPEE---LAE 555

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           KL +   +V  +  ++A  E ++      D+  S   D++    D    + I+   + N 
Sbjct: 556 KLAMPLEKVRKV-LKIAK-EPISLETPIGDEEDSHLGDFI---EDKNAILPIDAAIQSNL 610

Query: 225 RNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 611 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 669


>gi|111018672|ref|YP_701644.1| sigma factor, sigma 70 type, group 2 [Rhodococcus jostii RHA1]
 gi|110818202|gb|ABG93486.1| sigma factor, sigma 70 type, probable group 2 [Rhodococcus jostii
           RHA1]
          Length = 520

 Score = 96.3 bits (238), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 68/239 (28%), Positives = 121/239 (50%), Gaps = 20/239 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R + ++LRLVV IA  Y+G GL + ++V EGN+GL++AV+KFD + GF+ +TY+ WW
Sbjct: 283 AKRRFLEANLRLVVSIARRYQGRGLDLLDLVQEGNLGLIRAVEKFDYKTGFKFSTYATWW 342

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   +     +++I     ++     L + +  L   T     P +   +A  L+ 
Sbjct: 343 IRQAITRALADQSRVIRIPVHMVEQ--IDQLGKERARLTKETGREPTPSE---LATALDT 397

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +   +  +        SL+ L ++++ +   ++D L           +  EE   RR   
Sbjct: 398 TIEHIGDLEKYDQRVLSLDVLTDNAEHDGLDFEDDLA----------VVAEEVAERRRFY 447

Query: 229 TRSMSVLNPRERRIFEARRLQ-----ENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
               SVL+P   R  +  RL+      +P TL+ +   + V+RER+RQIE++  K ++E
Sbjct: 448 ETLESVLSPLSERDAQVIRLRYGLTGSDPYTLDEIGKIYGVTRERIRQIESKLLKAMKE 506


>gi|144616|gb|AAA23168.1| sigma-A protein (sigA) [Chlamydia muridarum]
          Length = 571

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 77/246 (31%), Positives = 116/246 (47%), Gaps = 28/246 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+  RG++ +TY+ WW
Sbjct: 317 AKQEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWW 376

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+      + R    L   T     PE+   + +
Sbjct: 377 IRQAVTRAIADQARTIRIPVHMIETINK------VLRGAKKLMMETGKEPTPEE---LGE 427

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L  +   V  +        SL A +   D   S + D+L       E   +E       
Sbjct: 428 ELGFTPDRVREIYKIAQHPISLQAEVG--DSGESSFGDFL-------EDTAVESPAEATG 478

Query: 225 RNMLTRSM----SVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
            +ML   M      L  RER +   R   L   P TLE + S F V+RER+RQIEA+A +
Sbjct: 479 YSMLKDKMKKVLKTLTDRERFVLIHRFGLLDGRPKTLEEVGSAFNVTRERIRQIEAKALR 538

Query: 279 KVQESI 284
           K++  I
Sbjct: 539 KMRHPI 544


>gi|325293528|ref|YP_004279392.1| RNA polymerase sigma factor RpoD [Agrobacterium sp. H13-3]
 gi|325061381|gb|ADY65072.1| RNA polymerase sigma factor RpoD [Agrobacterium sp. H13-3]
          Length = 684

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 83/276 (30%), Positives = 138/276 (50%), Gaps = 27/276 (9%)

Query: 10  VNGEIGLSRYIHEIRKI-PMLEKQE-EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++ E G+S  I E R+I  M++K E E  +AK+            +V ++LRLV+ IA  
Sbjct: 418 LSTETGIS--IAEFRRIVSMVQKGEREARIAKK-----------EMVEANLRLVISIAKK 464

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I 
Sbjct: 465 YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI- 523

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              +       + R    +         PE+   +A+KL +   +V  +  ++A  E ++
Sbjct: 524 -PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAMPLEKVRKV-LKIA-KEPIS 577

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
                 D+  S   D++    D    + I+   + N R   TR ++ L PRE R+   R 
Sbjct: 578 LETPVGDEEDSHLGDFI---EDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRF 634

Query: 248 --LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                   TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 635 GIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 670


>gi|254710518|ref|ZP_05172329.1| RNA polymerase sigma factor RpoD [Brucella pinnipedialis B2/94]
 gi|256032011|ref|ZP_05445625.1| RNA polymerase sigma factor RpoD [Brucella pinnipedialis M292/94/1]
 gi|261318089|ref|ZP_05957286.1| RNA polymerase sigma factor RpoD [Brucella pinnipedialis B2/94]
 gi|265989123|ref|ZP_06101680.1| RNA polymerase sigma factor RpoD [Brucella pinnipedialis M292/94/1]
 gi|261297312|gb|EEY00809.1| RNA polymerase sigma factor RpoD [Brucella pinnipedialis B2/94]
 gi|264661320|gb|EEZ31581.1| RNA polymerase sigma factor RpoD [Brucella pinnipedialis M292/94/1]
          Length = 672

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 75/239 (31%), Positives = 123/239 (51%), Gaps = 20/239 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 434 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 493

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+      +R  +  L  I      PE+   +A+
Sbjct: 494 IRQAITRSIADQARTIRIPVHMIETINKI-----VRTSRQMLHEIG-REPTPEE---LAE 544

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           KL +   +V  +  ++A  E ++      D+  S   D++    D    + I+   + N 
Sbjct: 545 KLAMPLEKVRKV-LKIAK-EPISLETPVGDEEDSLLGDFI---EDKNALLPIDAAIQANL 599

Query: 225 RNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R+  TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 600 RDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 658


>gi|167842198|ref|ZP_02468882.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis
           MSMB43]
          Length = 680

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 121/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 441 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 500

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +  L+P+    +A+K+ +
Sbjct: 501 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGLEPDPAT-LAEKMEM 555

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + R+++
Sbjct: 556 PEDKIRKI-MKIAK-EPISMETPIGDDDDSHLGDFI---EDSNTVAPADAALHASMRDVV 610

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 611 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 665


>gi|329890710|ref|ZP_08269053.1| RNA polymerase sigma factor rpoD [Brevundimonas diminuta ATCC
           11568]
 gi|328846011|gb|EGF95575.1| RNA polymerase sigma factor rpoD [Brevundimonas diminuta ATCC
           11568]
          Length = 640

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 119/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 402 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 461

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R +  +         PE+   +A++L +
Sbjct: 462 IRQAITRSIADQARTIRI--PVHMIETINKIVRTQRQMLHEIGREATPEE---LAERLAM 516

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 517 PLEKVRKV-LKIA-KEPISLETPIGDEEDSHLGDFI---EDKNAVLPIDAAIQSNLRETT 571

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 572 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 626


>gi|296159636|ref|ZP_06842459.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. Ch1-1]
 gi|295890080|gb|EFG69875.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. Ch1-1]
          Length = 680

 Score = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 121/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 441 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 500

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +  L+P+    +A+K+ +
Sbjct: 501 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGLEPDPAT-LAEKMEM 555

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + R+++
Sbjct: 556 PEDKIRKI-MKIAK-EPISMETPIGDDDDSHLGDFI---EDNNTVAPADAALHASMRDVV 610

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 611 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 665


>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 = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 121/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 441 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 500

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +  L+P+    +A+K+ +
Sbjct: 501 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGLEPDPAT-LAEKMEM 555

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + R+++
Sbjct: 556 PEDKIRKI-MKIAK-EPISMETPIGDDDDSHLGDFI---EDNNTVAPADAALHASMRDVV 610

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 611 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 665


>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 = 96.3 bits (238), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 82/280 (29%), Positives = 141/280 (50%), Gaps = 24/280 (8%)

Query: 16  LSRYIHEIRKIP--MLEKQEEYVL-------AKRYREHGDLSA--AHRLVT-SHLRLVVK 63
           LSR I  IR+    +L+ Q   VL         R    G+L A  A R +T ++LRLV+ 
Sbjct: 525 LSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVIS 584

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      
Sbjct: 585 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 644

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           ++I    +       + R+    Q + +  L+P+    +A+K+ + E ++  +  ++A  
Sbjct: 645 IRI--PVHMIETINKMNRI--SRQILQETGLEPDPAT-LAEKMEMPEDKIRKI-MKIA-K 697

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           E ++      D + S   D++    D       +     + R+++   +  L PRE ++ 
Sbjct: 698 EPISMETPIGDDDDSHLGDFI---EDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVL 754

Query: 244 EARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
             R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 755 RMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 794


>gi|116253144|ref|YP_768982.1| RNA polymerase sigma factor RpoD [Rhizobium leguminosarum bv.
           viciae 3841]
 gi|115257792|emb|CAK08890.1| putative RNA polymerase sigma factor RpoD [Rhizobium leguminosarum
           bv. viciae 3841]
          Length = 685

 Score = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 447 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 506

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 507 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 561

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 562 PLEKVRKV-LKIA-KEPISLETPVGDEEDSHLGDFI---EDKNALLPIDAAIQANLRETT 616

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 617 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 671


>gi|90418027|ref|ZP_01225939.1| DNA-directed RNA polymerase major sigma factor [Aurantimonas
           manganoxydans SI85-9A1]
 gi|90337699|gb|EAS51350.1| DNA-directed RNA polymerase major sigma factor [Aurantimonas
           manganoxydans SI85-9A1]
          Length = 668

 Score = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 430 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 489

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 490 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 544

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 545 PLEKVRKV-LKIA-KEPISLETPVGDEEDSHLGDFI---EDKNAILPIDAAIQGNLRETT 599

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 600 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 654


>gi|172062815|ref|YP_001810466.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia ambifaria
           MC40-6]
 gi|171995332|gb|ACB66250.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia ambifaria
           MC40-6]
          Length = 805

 Score = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 82/280 (29%), Positives = 141/280 (50%), Gaps = 24/280 (8%)

Query: 16  LSRYIHEIRKIP--MLEKQEEYVL-------AKRYREHGDLSA--AHRLVT-SHLRLVVK 63
           LSR I  IR+    +L+ Q   VL         R    G+L A  A R +T ++LRLV+ 
Sbjct: 521 LSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVIS 580

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      
Sbjct: 581 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 640

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           ++I    +       + R+    Q + +  L+P+    +A+K+ + E ++  +  ++A  
Sbjct: 641 IRI--PVHMIETINKMNRI--SRQILQETGLEPDPAT-LAEKMEMPEDKIRKI-MKIA-K 693

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           E ++      D + S   D++    D       +     + R+++   +  L PRE ++ 
Sbjct: 694 EPISMETPIGDDDDSHLGDFI---EDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVL 750

Query: 244 EARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
             R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 751 RMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 790


>gi|159903877|ref|YP_001551221.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9211]
 gi|159889053|gb|ABX09267.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9211]
          Length = 313

 Score = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 79/298 (26%), Positives = 150/298 (50%), Gaps = 36/298 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYR------EHGDLS-------------------AA 50
           +S Y+  I ++P+L   EE  L  + +      E G +                    A 
Sbjct: 20  ISWYLSTIGRVPLLTPAEEIELGNQVQVMMNLTEDGSIDVKSEEFTSHQRRLIRIGRRAK 79

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            R++ ++LRLVV +A  Y+G GL + ++V EG++GL +AV+KFDP RG++ +TY+ WWI+
Sbjct: 80  ERMMKANLRLVVSVAKKYQGKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAFWWIR 139

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            +M   I      +++    +++     +R++   L         P +   +A+ + +  
Sbjct: 140 QSMTRAIACQSRTIRLPVHLSER--LATIRKISSDLAH--KLGAMPSR-AELAEAMEIDA 194

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            E+ S+  +     SL+A +N  D  S  +   L+ D   +E   ++K E++  +  L R
Sbjct: 195 EELDSILRQALTTSSLDAPVNGDDGRS--FLGDLIADSSLEEP--LDKVEQRIHQEQLGR 250

Query: 231 SMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            ++ L+ +E+ + + R  L+ N   TL  +    +VSRERVRQ+E ++ +K++   +K
Sbjct: 251 WLTHLSEQEQHVLKLRFGLEGNERHTLAEIGRLLQVSRERVRQVELKSLRKLRNLTRK 308


>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 = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 432 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 491

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +++KL +
Sbjct: 492 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LSEKLAM 546

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + IE   + N R   
Sbjct: 547 PLEKVRKV-LKIA-KEPISLETPIGDEEDSHLGDFI---EDKNAVLPIEAAIQSNLRETT 601

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 602 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 656


>gi|319441597|ref|ZP_07990753.1| RNA polymerase sigma factor [Corynebacterium variabile DSM 44702]
          Length = 536

 Score = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 81/318 (25%), Positives = 155/318 (48%), Gaps = 43/318 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------REHG---- 45
           RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR              +E G    
Sbjct: 224 RKDAELTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYATYKMEQIKESGEKVS 282

Query: 46  -----DL--------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                DL         A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 283 PMQKRDLREIDRDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 342

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L      
Sbjct: 343 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGR 400

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE+   +AK+++++E +V+ +        SL+  I   D+  SQ  D++    D + 
Sbjct: 401 EPTPEE---LAKEMDITEDKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEA 452

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVR 270
            + ++       ++ L   +  L+ RE  + + R  L +  P TL+ +   + V+RER+R
Sbjct: 453 VIAVDAVSFTLLQDQLQDVLHTLSEREAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERIR 512

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 513 QIESKTMSKLRHPSRSQV 530


>gi|330836587|ref|YP_004411228.1| RNA polymerase, sigma 70 subunit, RpoD [Spirochaeta coccoides DSM
           17374]
 gi|329748490|gb|AEC01846.1| RNA polymerase, sigma 70 subunit, RpoD [Spirochaeta coccoides DSM
           17374]
          Length = 685

 Score = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 71/248 (28%), Positives = 125/248 (50%), Gaps = 38/248 (15%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  RL  ++LRLVV IA  Y   GLP +++V EGNIGL++AV+KF+  + F+ +TY+ W
Sbjct: 448 AAKDRLTQANLRLVVSIAKKYTNRGLPFNDLVQEGNIGLIKAVEKFEFRKNFKFSTYATW 507

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++        +   + ++K    A+  +  +      IAKKL 
Sbjct: 508 WIRQAITRAISDQGRTIRVPV-----HMIEQINKVKKEENALIQSLGRNPTDEEIAKKLG 562

Query: 168 VSESEV----------ISMNCRLAGDES--LNALINSSD-KNSSQWQDWLVYDHDGQEQV 214
             E +V          IS+   +  +E   L+  I   D +N +    +++     QEQ 
Sbjct: 563 WPEEKVKGVKNVAREPISLETPVGEEEDSLLSDFIEDKDAENPASQTSYMLL----QEQ- 617

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
                        L + ++ L PRE+ + + R   ++   +TLE +   F+V+RER+RQI
Sbjct: 618 -------------LQKELATLPPREKDVLKMRFGLDDGFALTLEEVGLSFKVTRERIRQI 664

Query: 273 EARAFKKV 280
           EA++ +++
Sbjct: 665 EAKSLRRM 672


>gi|320531403|ref|ZP_08032370.1| RNA polymerase sigma factor RpoD [Actinomyces sp. oral taxon 171
           str. F0337]
 gi|320136375|gb|EFW28356.1| RNA polymerase sigma factor RpoD [Actinomyces sp. oral taxon 171
           str. F0337]
          Length = 537

 Score = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 84/310 (27%), Positives = 141/310 (45%), Gaps = 61/310 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH------GDLSAAHR--------------- 52
           Y+ +I K+ +L  ++E  LAKR     Y EH       DL A  R               
Sbjct: 243 YLKQIGKVALLNAEQEVELAKRIEAGLYAEHRLAEKGNDLPAKLRRELHWVAQDGQRAKN 302

Query: 53  -LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ 
Sbjct: 303 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQ 362

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+VV +
Sbjct: 363 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAVELDMTPEKVVEV 422

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 423 QK----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 468

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 469 -------LHAVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 521

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 522 KLRHPSRSQV 531


>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 = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 67/235 (28%), Positives = 117/235 (49%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 516 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 575

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+   +   T N   P     +A+K+ +
Sbjct: 576 IRQAITRSIADQARTIRI--PVHMIETINKMNRISRQILQETGNEPDP---ATLAEKMEM 630

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       E     + R ++
Sbjct: 631 PEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDTNTLAPAEAALHGSMRGVV 685

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 686 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 740


>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 = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 121/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 566 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 625

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +  L+P+    +A+K+ +
Sbjct: 626 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGLEPDPAT-LAEKMEM 680

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + R+++
Sbjct: 681 PEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDNNTVAPADAALHASMRDVV 735

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 736 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 790


>gi|256830224|ref|YP_003158952.1| RpoD subfamily RNA polymerase sigma-70 subunit [Desulfomicrobium
           baculatum DSM 4028]
 gi|256579400|gb|ACU90536.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfomicrobium
           baculatum DSM 4028]
          Length = 588

 Score = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 74/252 (29%), Positives = 126/252 (50%), Gaps = 30/252 (11%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ 
Sbjct: 348 LDAKQELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYAT 407

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV------ 160
           WWI+ A+   I      ++I    +       L R   +L      +  PE++       
Sbjct: 408 WWIRQAITRAIADQARTIRI--PVHMIETINKLVRTSRYLVQELGRDPSPEEIAERMDYP 465

Query: 161 --AIAKKLNVSESEVISMNCRLAGDESLNALINS-SDKNSSQWQDWLVYDHDGQEQVLIE 217
              + K L +++ E IS+   + GDE  ++L +   DK +    D +V     ++     
Sbjct: 466 LEKVKKVLKIAK-EPISLETPI-GDEEDSSLGDFIEDKKAVAPADEVVNTKLAEQ----- 518

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
                     + + +S L PRE ++   R    +++  TLE +   F V+RER+RQIEA+
Sbjct: 519 ----------IAQVLSDLTPREEQVLRKRFGIGEKSDHTLEEVGKLFNVTRERIRQIEAK 568

Query: 276 AFKKVQESIQKQ 287
           A +K++  ++ Q
Sbjct: 569 ALRKLRHPVRSQ 580


>gi|254419911|ref|ZP_05033635.1| Sigma-70 region 3 family [Brevundimonas sp. BAL3]
 gi|196186088|gb|EDX81064.1| Sigma-70 region 3 family [Brevundimonas sp. BAL3]
          Length = 648

 Score = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 75/239 (31%), Positives = 122/239 (51%), Gaps = 20/239 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 410 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 469

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+      +R  +  L  I      PE+   +A+
Sbjct: 470 IRQAITRSIADQARTIRIPVHMIETINKI-----VRTSRQMLHEI-GREPTPEE---LAE 520

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           KL +   +V  +  ++A  E ++      D+  S   D++    D    + I+   + N 
Sbjct: 521 KLAMPLEKVRKV-LKIA-KEPISLETPIGDEEDSHLGDFI---EDKNAVLPIDAAIQSNL 575

Query: 225 RNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 576 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 634


>gi|87307035|ref|ZP_01089181.1| RNA polymerase sigma factor rpoD [Blastopirellula marina DSM 3645]
 gi|87290408|gb|EAQ82296.1| RNA polymerase sigma factor rpoD [Blastopirellula marina DSM 3645]
          Length = 519

 Score = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 77/246 (31%), Positives = 122/246 (49%), Gaps = 22/246 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L   +LRLVV IA  YR  GL   +++ EGN GLM+AV KF+  RGF+  TY+ WW
Sbjct: 282 AKRELSEGNLRLVVSIAKKYRNRGLSFLDLIQEGNAGLMRAVDKFEYRRGFKFCTYATWW 341

Query: 109 IKAAMQEYILRSWSLVKIG-----TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           I+ A+   +      ++I      T +  + +   L + KG    + +   +    V  A
Sbjct: 342 IRQAITRAVADQSRTIRIPVHMVETMSRVRNVARQLLQEKGREPTLEETARRAGTTVEEA 401

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           +++       IS++ R  G        NS D   SQ+ D L    DG+ +       ++ 
Sbjct: 402 RRVLAMSRYPISLD-RPVG--------NSED---SQFGDLL---PDGEAESPAIGAAQEM 446

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R  ++R +  L+ RER I + R    +    TLE +   F+V+RER+RQIEA+A +K+Q
Sbjct: 447 LRTRISRVLKTLSYREREIIKLRYGLGDGYSYTLEEVGHIFKVTRERIRQIEAKAVRKLQ 506

Query: 282 ESIQKQ 287
           +  + Q
Sbjct: 507 QPSRSQ 512


>gi|330821204|ref|YP_004350066.1| RNA polymerase, sigma 70 subunit, RpoD family protein [Burkholderia
           gladioli BSR3]
 gi|327373199|gb|AEA64554.1| RNA polymerase, sigma 70 subunit, RpoD family protein [Burkholderia
           gladioli BSR3]
          Length = 805

 Score = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 121/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 566 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 625

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +  L+P+    +A+K+ +
Sbjct: 626 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGLEPDPAT-LAEKMEM 680

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + R+++
Sbjct: 681 PEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDSNTVAPADAALHASMRDVV 735

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 736 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 790


>gi|149200222|ref|ZP_01877244.1| RNA polymerase sigma factor RpoD [Lentisphaera araneosa HTCC2155]
 gi|149136664|gb|EDM25095.1| RNA polymerase sigma factor RpoD [Lentisphaera araneosa HTCC2155]
          Length = 279

 Score = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 76/273 (27%), Positives = 137/273 (50%), Gaps = 29/273 (10%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+  I  +P++  ++E  LAK   E G   A  +L+ ++L+LVVKIA  Y+  G+P++++
Sbjct: 11  YMQSIATLPLVSVEDEIELAKLI-EAGSEDAREKLIIANLKLVVKIAHDYKSLGVPLADL 69

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           +SEGNIGLM+AV+KF P  G + ++Y  WWIK A++  +     +++I   +  K     
Sbjct: 70  ISEGNIGLMKAVEKFRPGHGAKFSSYGAWWIKQAIRRAVAEQGRVIRIPVQSAVK----- 124

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN-CRLAGDESLNALINSSDKNS 197
           +R++      + +   +   +  +A+    S   V  M+    A   SLN  + + ++  
Sbjct: 125 IRKIHHEAMLLAEKLGRVPSMEEVAEATGFSVRSVRGMSVASTAPAVSLNTTLKTGEEGV 184

Query: 198 SQ--WQDWLV------YDHDGQEQVLIEKEERK--NRRNMLTRSMSVLNPRERRIFEARR 247
            +    D L+       +    +QVL+E  + K   R  M+ +    L+  +++      
Sbjct: 185 LEDVIPDTLLKLPGDNMNETDVKQVLLEVIDSKLTEREQMIIKMRYGLDGHQQK------ 238

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                 TLE LS     +RERVRQI+ +A +K+
Sbjct: 239 ------TLEELSDMVGRTRERVRQIQYQALRKL 265


>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|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]
          Length = 623

 Score = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 72/253 (28%), Positives = 120/253 (47%), Gaps = 32/253 (12%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RGF+
Sbjct: 376 YGEAKASKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVCKFEHRRGFK 435

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I    +       L R+   +         PE+  
Sbjct: 436 FSTYATWWIRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQQFGREATPEE-- 491

Query: 161 AIAKKLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
            +AK++++ E ++          ISM   +  DE             S   D++    D 
Sbjct: 492 -LAKEMDMPEDKIRKVMKIAKEPISMETPIGDDE------------DSHLGDFI---EDP 535

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRER 268
             +  ++     N    +   ++ L PRE ++   R  +  N   TLE +  +F+V+RER
Sbjct: 536 NVESPVDTTTNVNLSETVREVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRER 595

Query: 269 VRQIEARAFKKVQ 281
           +RQIEA+A +K++
Sbjct: 596 IRQIEAKALRKLR 608


>gi|222086540|ref|YP_002545074.1| RNA polymerase sigma factor protein (sigma-70) [Agrobacterium
           radiobacter K84]
 gi|221723988|gb|ACM27144.1| RNA polymerase sigma factor protein (sigma-70) [Agrobacterium
           radiobacter K84]
          Length = 687

 Score = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 449 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 508

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 509 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 563

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 564 PLEKVRKV-LKIA-KEPISLETPVGDEEDSHLGDFI---EDKNALLPIDAAIQANLRETT 618

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 619 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 673


>gi|187929499|ref|YP_001899986.1| RNA polymerase sigma factor RpoD [Ralstonia pickettii 12J]
 gi|187726389|gb|ACD27554.1| RNA polymerase, sigma 70 subunit, RpoD [Ralstonia pickettii 12J]
          Length = 829

 Score = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 67/235 (28%), Positives = 117/235 (49%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 590 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 649

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+   +   T N   P     +A+K+ +
Sbjct: 650 IRQAITRSIADQARTIRI--PVHMIETINKMNRISRQILQETGNEPDP---ATLAEKMEM 704

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       E     + R ++
Sbjct: 705 PEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDTNTLAPAEAALHGSMRGVV 759

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 760 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 814


>gi|1765926|emb|CAA70052.1| RNA polymerase sigma-70 subunit [Rhizobium etli]
          Length = 685

 Score = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 447 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 506

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 507 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 561

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 562 PLEKVRKV-LKIA-KEPISLETPVGDEEDSHLGDFI---EDKNALLPIDAAIQANLRETT 616

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 617 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 671


>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|71902125|ref|ZP_00684157.1| 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|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 = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 72/253 (28%), Positives = 120/253 (47%), Gaps = 32/253 (12%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RGF+
Sbjct: 376 YGEAKASKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVCKFEHRRGFK 435

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I    +       L R+   +         PE+  
Sbjct: 436 FSTYATWWIRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQQFGREATPEE-- 491

Query: 161 AIAKKLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
            +AK++++ E ++          ISM   +  DE             S   D++    D 
Sbjct: 492 -LAKEMDMPEDKIRKVMKIAKEPISMETPIGDDE------------DSHLGDFI---EDP 535

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRER 268
             +  ++     N    +   ++ L PRE ++   R  +  N   TLE +  +F+V+RER
Sbjct: 536 NVESPVDTTTNVNLSETVREVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRER 595

Query: 269 VRQIEARAFKKVQ 281
           +RQIEA+A +K++
Sbjct: 596 IRQIEAKALRKLR 608


>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 = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 67/235 (28%), Positives = 117/235 (49%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 582 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 641

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+   +   T N   P     +A+K+ +
Sbjct: 642 IRQAITRSIADQARTIRI--PVHMIETINKMNRISRQILQETGNEPDP---ATLAEKMEM 696

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       E     + R ++
Sbjct: 697 PEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDTNTLAPAEAALHGSMRGVV 751

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 752 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 806


>gi|294055048|ref|YP_003548706.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Coraliomargarita
           akajimensis DSM 45221]
 gi|293614381|gb|ADE54536.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Coraliomargarita
           akajimensis DSM 45221]
          Length = 639

 Score = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 75/244 (30%), Positives = 118/244 (48%), Gaps = 30/244 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+  RG++ +TY+ WW
Sbjct: 381 AKTEMVEANLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWW 440

Query: 109 IKAAMQEYILRSWSLVKIGT----TAN-----QKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N     QK+L   L       +   + NL  E+V
Sbjct: 441 IRQAITRSIADQARTIRIPVHMIETLNKVMQVQKQLLQELGHEPTAEEVADEMNLPIERV 500

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
            +I K       + IS+   +   +  N      DK +    D   Y       +L EK 
Sbjct: 501 QSIMKMAQ----QPISLQSPVGDSDDTNFGDFIEDKGAENPYDMTAY------SLLREK- 549

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAF 277
                   +T  +  L  RERR+   R    +    TLE +  +F+V+RER+RQIEA+A 
Sbjct: 550 --------ITDVLDSLTERERRVLSLRFGLADGYSRTLEEVGRQFKVTRERIRQIEAKAL 601

Query: 278 KKVQ 281
           +K++
Sbjct: 602 RKMR 605


>gi|209550278|ref|YP_002282195.1| RNA polymerase sigma factor RpoD [Rhizobium leguminosarum bv.
           trifolii WSM2304]
 gi|209536034|gb|ACI55969.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhizobium
           leguminosarum bv. trifolii WSM2304]
          Length = 685

 Score = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 447 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 506

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 507 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 561

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 562 PLEKVRKV-LKIA-KEPISLETPVGDEEDSHLGDFI---EDKNALLPIDAAIQANLRETT 616

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 617 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 671


>gi|150007022|ref|YP_001301765.1| RNA polymerase sigma factor rpoD [Parabacteroides distasonis ATCC
           8503]
 gi|154495210|ref|ZP_02034215.1| hypothetical protein PARMER_04266 [Parabacteroides merdae ATCC
           43184]
 gi|218256952|ref|ZP_03474423.1| hypothetical protein PRABACTJOHN_00076 [Parabacteroides johnsonii
           DSM 18315]
 gi|255015941|ref|ZP_05288067.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 2_1_7]
 gi|256841904|ref|ZP_05547409.1| RNA polymerase sigma factor RpoS [Parabacteroides sp. D13]
 gi|262384222|ref|ZP_06077357.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 2_1_33B]
 gi|298377447|ref|ZP_06987400.1| RNA polymerase sigma-70 factor [Bacteroides sp. 3_1_19]
 gi|301308863|ref|ZP_07214815.1| RNA polymerase sigma-70 factor [Bacteroides sp. 20_3]
 gi|149935446|gb|ABR42143.1| RNA polymerase sigma factor rpoD [Parabacteroides distasonis ATCC
           8503]
 gi|154085357|gb|EDN84402.1| hypothetical protein PARMER_04266 [Parabacteroides merdae ATCC
           43184]
 gi|218225859|gb|EEC98509.1| hypothetical protein PRABACTJOHN_00076 [Parabacteroides johnsonii
           DSM 18315]
 gi|256736220|gb|EEU49549.1| RNA polymerase sigma factor RpoS [Parabacteroides sp. D13]
 gi|262293925|gb|EEY81858.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 2_1_33B]
 gi|298265861|gb|EFI07521.1| RNA polymerase sigma-70 factor [Bacteroides sp. 3_1_19]
 gi|300833387|gb|EFK64005.1| RNA polymerase sigma-70 factor [Bacteroides sp. 20_3]
          Length = 286

 Score = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 76/278 (27%), Positives = 149/278 (53%), Gaps = 20/278 (7%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI +  ++  +EE  LA+  +  GD  A  +L  ++LR VV +A  Y+  GL +
Sbjct: 18  LDKYLQEIGREDLITVEEEVELAQAIK-RGDRRALEKLTRANLRFVVSVAKQYQNQGLSL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     +V++    NQ   
Sbjct: 77  PDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL--PLNQVGS 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
              + +     +   +    PE+   +A +L++   + IS   +++G   S++A     +
Sbjct: 135 LNKISKAFSKFEQENERRPSPEE---LADELDIP-VDKISDTLKVSGRHISVDAPFVEGE 190

Query: 195 KNSSQWQDWLVYDHDG-QEQVLIEKEERKNRRNMLTRSMSVLNPRERRI---FEARRLQE 250
            NS    D LV D     ++ L+ +   K     + R+++ L  RE  I   F     QE
Sbjct: 191 DNS--LLDVLVNDDAPIADRSLMNESLAKE----IDRALATLTERECEIIKMFFGIGCQE 244

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
             +TLE +  +F ++RERVRQI+ +A +++++  + ++
Sbjct: 245 --MTLEEIGDKFGLTRERVRQIKEKAIRRLRQGTRSKL 280


>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 = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 75/258 (29%), Positives = 126/258 (48%), Gaps = 13/258 (5%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+ E +  Y    R  E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIG
Sbjct: 411 LPIGEFRRVYATVARG-ERDSARAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIG 469

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           LM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I    +       L R    
Sbjct: 470 LMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI--PVHMIETINKLVRTSRQ 527

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           +         PE+   +A+KL +   +V  +  ++A  E ++      D+  S   D++ 
Sbjct: 528 MLHEIGREPAPEE---LAEKLGMPLEKVRKV-LKIA-KEPISLETPIGDEEDSHLGDFI- 581

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFE 263
              D    + ++   + N R   TR ++ L PRE R+   R         TLE +  +F 
Sbjct: 582 --EDKTAIIPLDAAIQTNLREATTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFN 639

Query: 264 VSRERVRQIEARAFKKVQ 281
           V+RER+RQIEA+A +K++
Sbjct: 640 VTRERIRQIEAKALRKLK 657


>gi|325518128|gb|EGC97914.1| RNA polymerase sigma factor RpoD [Burkholderia sp. TJI49]
          Length = 682

 Score = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 82/280 (29%), Positives = 141/280 (50%), Gaps = 24/280 (8%)

Query: 16  LSRYIHEIRKIP--MLEKQEEYVL-------AKRYREHGDLSA--AHRLVT-SHLRLVVK 63
           LSR I  IR+    +L+ Q   VL         R    G+L A  A R +T ++LRLV+ 
Sbjct: 398 LSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVIS 457

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      
Sbjct: 458 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 517

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           ++I    +       + R+    Q + +  L+P+    +A+K+ + E ++  +  ++A  
Sbjct: 518 IRI--PVHMIETINKMNRI--SRQILQETGLEPDPAT-LAEKMEMPEDKIRKI-MKIAK- 570

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           E ++      D + S   D++    D       +     + R+++   +  L PRE ++ 
Sbjct: 571 EPISMETPIGDDDDSHLGDFI---EDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVL 627

Query: 244 EARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
             R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 628 RMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 667


>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 = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 67/235 (28%), Positives = 117/235 (49%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 582 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 641

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+   +   T N   P     +A+K+ +
Sbjct: 642 IRQAITRSIADQARTIRI--PVHMIETINKMNRISRQILQETGNEPDP---ATLAEKMEM 696

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       E     + R ++
Sbjct: 697 PEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDTNTLAPAEAALHGSMRGVV 751

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 752 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 806


>gi|319408880|emb|CBI82537.1| RNA polymerase sigma factor [Bartonella schoenbuchensis R1]
          Length = 667

 Score = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 429 AKKEMVEANLRLVISIAKRYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 488

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   ++ KL++
Sbjct: 489 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQILHEIGREPTPEE---LSSKLSM 543

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D++ S   D++    D    + I+   + N R+  
Sbjct: 544 PLEKVRKV-LKIAK-EPISLETPVGDEDDSHLGDFI---EDRNALLPIDAAIQANLRDTT 598

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 599 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 653


>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 = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 82/280 (29%), Positives = 141/280 (50%), Gaps = 24/280 (8%)

Query: 16  LSRYIHEIRKIP--MLEKQEEYVL-------AKRYREHGDLSA--AHRLVT-SHLRLVVK 63
           LSR I  IR+    +L+ Q   VL         R    G+L A  A R +T ++LRLV+ 
Sbjct: 520 LSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVIS 579

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      
Sbjct: 580 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 639

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           ++I    +       + R+    Q + +  L+P+    +A+K+ + E ++  +  ++A  
Sbjct: 640 IRI--PVHMIETINKMNRI--SRQILQETGLEPDPAT-LAEKMEMPEDKIRKI-MKIA-K 692

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           E ++      D + S   D++    D       +     + R+++   +  L PRE ++ 
Sbjct: 693 EPISMETPIGDDDDSHLGDFI---EDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVL 749

Query: 244 EARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
             R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 750 RMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 789


>gi|33240031|ref|NP_874973.1| putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus subsp. marinus str. CCMP1375]
 gi|33237557|gb|AAP99625.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Prochlorococcus marinus subsp. marinus str. CCMP1375]
          Length = 310

 Score = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 81/307 (26%), Positives = 138/307 (44%), Gaps = 53/307 (17%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAK----------RYREHGDLSA---------------- 49
           LS ++ EI + P+L  +EE  + +          R    GD  A                
Sbjct: 4   LSDFLGEIGRHPLLTPEEELTMGRKVQAMVGLIERCHRAGDQGADCVYTEAERRTIKIGE 63

Query: 50  --AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              + ++T++LRLVV +A  Y+G GL + +++ EG IGL +AV+K+DP+RG R +TY+ W
Sbjct: 64  KAKNHMITANLRLVVNLAKKYQGKGLDLLDLIQEGTIGLTRAVEKYDPKRGHRFSTYAYW 123

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+  +   +      ++I    N+K     L +L+     +      P     +AKKL+
Sbjct: 124 WIRQGLNRALSTQSRTIRIPVNINEK-----LTKLRAAKSELMQEYGTPPSAEQLAKKLS 178

Query: 168 VS--------ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           VS        E E+ S+   L G       +  S  + S+  D L  D     ++    E
Sbjct: 179 VSKQIIGDLLECEMRSITVSLQG-------VIQSKTDPSELGDVLPSDEIPPMELAELAE 231

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARA 276
              +  ++L ++   L P+ER I   R   +      TL  ++     SRE  RQ+  RA
Sbjct: 232 RNDSAWSLLNKAN--LTPKERTIVSLRFGLDGTNEWRTLAEVAKHMNCSREYCRQVVQRA 289

Query: 277 FKKVQES 283
            +K++++
Sbjct: 290 LRKLRKT 296


>gi|328474970|gb|EGF45764.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes 220]
          Length = 346

 Score = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 47/108 (43%), Positives = 69/108 (63%), Gaps = 1/108 (0%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LAKR  E GD+ A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 108 YLKEIGRVDLLTADEEIALAKRI-EAGDIEAKGRLAEANLRLVVSIAKRYVGRGMLFLDL 166

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I
Sbjct: 167 IQEGNMGLMKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRI 214


>gi|315122849|ref|YP_004063338.1| RNA polymerase sigma factor RpoD [Candidatus Liberibacter
           solanacearum CLso-ZC1]
 gi|313496251|gb|ADR52850.1| RNA polymerase sigma factor RpoD [Candidatus Liberibacter
           solanacearum CLso-ZC1]
          Length = 683

 Score = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 77/240 (32%), Positives = 119/240 (49%), Gaps = 22/240 (9%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ +A  Y   GL   +++ EGNIGLM+AV+KFD   G++ +TY MWW
Sbjct: 445 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAVEKFDWCLGYKFSTYGMWW 504

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-AIA 163
           +K A+   I      ++I      T N  ++    RR+         N +K E     IA
Sbjct: 505 VKQAVTRSIADQSRTIRIPVHMIETIN--KVVRTARRMS--------NTIKREPTPDEIA 554

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           KKL +    V  +        SL   I   D+++S   D++    D      ++   + N
Sbjct: 555 KKLAMPLERVQKVLKITKEPISLETPIG--DEDTSHLGDFI---EDKNAVSPVDSAIQAN 609

Query: 224 RRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 610 LRENTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLK 669


>gi|4128212|gb|AAD03549.1| principal sigma factor [Burkholderia cepacia]
          Length = 621

 Score = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 121/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 382 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 441

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +  L+P+    +A+K+ +
Sbjct: 442 IRQAITRSIADQARTIRI--PVHMIETINKMNRISR--QILQETGLEPDPAT-LAEKMEM 496

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + R+++
Sbjct: 497 PEDKIRKI-MKIAK-EPISMETPIGDDDDSHLGDFI---EDNNTVAPADAALHASMRDVV 551

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 552 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 606


>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 = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 70/245 (28%), Positives = 117/245 (47%), Gaps = 32/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 510 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 569

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +   +PE  V +A+K+ +
Sbjct: 570 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGQEPEPAV-LAEKMEM 624

Query: 169 SESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            E ++          ISM   +  DE  +      D ++ +  D  VY            
Sbjct: 625 PEEKIRKILKISKEPISMETPIGDDEDSHLGDFIEDASTMEPADAAVY------------ 672

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARA 276
                 R +    +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A
Sbjct: 673 ---AGLRTVTKDVLDSLTPREAKVLRMRFGIEMNTDHTLEEVGRQFDVTRERIRQIEAKA 729

Query: 277 FKKVQ 281
            +K++
Sbjct: 730 LRKLR 734


>gi|71899844|ref|ZP_00681993.1| 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|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 = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 72/253 (28%), Positives = 120/253 (47%), Gaps = 32/253 (12%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RGF+
Sbjct: 376 YGEAKASKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVCKFEHRRGFK 435

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I    +       L R+   +         PE+  
Sbjct: 436 FSTYATWWIRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQQFGREATPEE-- 491

Query: 161 AIAKKLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
            +AK++++ E ++          ISM   +  DE             S   D++    D 
Sbjct: 492 -LAKEMDMPEDKIRKVMKIAKEPISMETPIGDDE------------DSHLGDFI---EDP 535

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRER 268
             +  ++     N    +   ++ L PRE ++   R  +  N   TLE +  +F+V+RER
Sbjct: 536 NVESPVDTTTNVNLSETVREVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRER 595

Query: 269 VRQIEARAFKKVQ 281
           +RQIEA+A +K++
Sbjct: 596 IRQIEAKALRKLR 608


>gi|23013315|ref|ZP_00053224.1| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Magnetospirillum magnetotacticum
           MS-1]
          Length = 333

 Score = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 81/274 (29%), Positives = 135/274 (49%), Gaps = 23/274 (8%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++GE GL   I E R+I    ++ E       RE     A   ++ ++LRLV+ IA  Y 
Sbjct: 67  ISGEAGLP--ISEYRRIVQTVQRGE-------RESS--RAKKEMIEANLRLVISIAKKYT 115

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
             GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I   
Sbjct: 116 NRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI--P 173

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
            +       L R    +         PE+   +A+KL++   +V  +  ++A  E ++  
Sbjct: 174 VHMIETINKLVRTSRQMLHEIGREPTPEE---LAEKLSMPLEKVRKV-LKIA-KEPISLE 228

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-- 247
               D+  S   D++    D    + ++   + N R   TR ++ L PRE R+   R   
Sbjct: 229 TPIGDEEDSHLGDFI---EDKNAVLPLDAAIQANLRETTTRVLASLTPREERVLRMRFGI 285

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                 TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 286 GMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 319


>gi|162450883|ref|YP_001613250.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
 gi|161161465|emb|CAN92770.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
          Length = 463

 Score = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 69/238 (28%), Positives = 119/238 (50%), Gaps = 15/238 (6%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V ++LRLV   A   R  G+P+ +++ EGN+GL++A +KFD  RG+R +TY+MWWIK A+
Sbjct: 231 VRANLRLVAAAARQLRHRGVPLLDLIQEGNLGLIRAAEKFDYRRGYRFSTYAMWWIKQAL 290

Query: 114 QEYILRSWSLVKIGT-TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
              +L    ++++    A  +R     RR    L+        PE+V   A++  +S  +
Sbjct: 291 SRALLYQGQVIRVPVHIAETRRRALQARR---ELEQEHAREAAPEEV---AERSGLSMEK 344

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           + ++         L+A +   D + ++  D+   +    +++L+ +        +L    
Sbjct: 345 LQALREMALPPVYLDAPVG--DDDGARQGDFFASEGAAPDELLVHRRLHAQVSALL---- 398

Query: 233 SVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
             L PRER +   R   +   P TL  +   F VSRERVRQIE  A  K++   ++Q 
Sbjct: 399 ESLTPRERDVLRLRFGLDGGQPHTLAEIGGMFSVSRERVRQIEESALSKLRTLSRRQA 456


>gi|319782038|ref|YP_004141514.1| RNA polymerase sigma factor RpoD [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
 gi|317167926|gb|ADV11464.1| RNA polymerase sigma factor RpoD [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
          Length = 673

 Score = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 435 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 494

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 495 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 549

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 550 PLEKVRKV-LKIAK-EPISLETPVGDEEDSHLGDFI---EDKMAILPIDAAIQANLRETT 604

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 605 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 659


>gi|182680201|ref|YP_001834347.1| RNA polymerase sigma factor RpoD [Beijerinckia indica subsp. indica
           ATCC 9039]
 gi|182636084|gb|ACB96858.1| RNA polymerase, sigma 70 subunit, RpoD family [Beijerinckia indica
           subsp. indica ATCC 9039]
          Length = 685

 Score = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 447 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 506

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 507 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 561

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 562 PLEKVRKV-LKIAK-EPISLETPIGDEEDSHLGDFI---EDKNAILPIDAAIQSNLRETT 616

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 617 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 671


>gi|167583913|ref|ZP_02376301.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia ubonensis Bu]
          Length = 681

 Score = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 82/280 (29%), Positives = 141/280 (50%), Gaps = 24/280 (8%)

Query: 16  LSRYIHEIRKIP--MLEKQEEYVL-------AKRYREHGDLSA--AHRLVT-SHLRLVVK 63
           LSR I  IR+    +L+ Q   VL         R    G+L A  A R +T ++LRLV+ 
Sbjct: 397 LSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVIS 456

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      
Sbjct: 457 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 516

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           ++I    +       + R+    Q + +  L+P+    +A+K+ + E ++  +  ++A  
Sbjct: 517 IRI--PVHMIETINKMNRI--SRQILQETGLEPDPAT-LAEKMEMPEDKIRKI-MKIAK- 569

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           E ++      D + S   D++    D       +     + R+++   +  L PRE ++ 
Sbjct: 570 EPISMETPIGDDDDSHLGDFI---EDNNTVAPADAALHASMRDVVKDVLDSLTPREAKVL 626

Query: 244 EARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
             R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 627 RMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 666


>gi|15618665|ref|NP_224951.1| RNA polymerase sigma factor [Chlamydophila pneumoniae CWL029]
 gi|15836289|ref|NP_300813.1| RNA polymerase sigma factor [Chlamydophila pneumoniae J138]
 gi|33242115|ref|NP_877056.1| RNA polymerase sigma factor [Chlamydophila pneumoniae TW-183]
 gi|6831651|sp|Q9Z7F0|RPOD_CHLPN RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A;
           AltName: Full=Sigma-66; AltName: Full=Sigma-70
 gi|4377063|gb|AAD18894.1| RNA Polymerase Sigma-66 [Chlamydophila pneumoniae CWL029]
 gi|8979129|dbj|BAA98964.1| RNA polymerase sigma-66 [Chlamydophila pneumoniae J138]
 gi|33236625|gb|AAP98713.1| sigma factor 70 [Chlamydophila pneumoniae TW-183]
          Length = 572

 Score = 95.9 bits (237), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 77/247 (31%), Positives = 120/247 (48%), Gaps = 28/247 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+  RG++ +TY+ WW
Sbjct: 317 AKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWW 376

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+      + R    L   T     PE+   +A+
Sbjct: 377 IRQAVTRAIADQARTIRIPVHMIETINK------VLRGAKKLMMETGKEPTPEE---LAE 427

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L ++   V  +        SL A +    ++S  + D+L       E   +E       
Sbjct: 428 ELGLTPDRVREIYKIAQHPISLQAEVGEGSESS--FGDFL-------EDTAVESPAEATG 478

Query: 225 RNMLTRSM----SVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
            +ML   M      L  RER +   R   L   P TLE + S F V+RER+RQIEA+A +
Sbjct: 479 YSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGKPKTLEEVGSAFNVTRERIRQIEAKALR 538

Query: 279 KVQESIQ 285
           K++  I+
Sbjct: 539 KMRHPIR 545


>gi|222149282|ref|YP_002550239.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis S4]
 gi|221736266|gb|ACM37229.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis S4]
          Length = 681

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 83/273 (30%), Positives = 136/273 (49%), Gaps = 27/273 (9%)

Query: 13  EIGLSRYIHEIRKI-PMLEKQE-EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           E G+S  I E R+I  M++K E E  +AK+            +V ++LRLV+ IA  Y  
Sbjct: 418 ETGIS--IAEFRRIVSMVQKGEREARIAKK-----------EMVEANLRLVISIAKKYTN 464

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I    
Sbjct: 465 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI--PV 522

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
           +       + R    +         PE+   +A+KL +   +V  +  ++A  E ++   
Sbjct: 523 HMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAMPLEKVRKV-LKIA-KEPISLET 577

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--L 248
              D+  S   D++    D    + I+   + N R   TR ++ L PRE R+   R    
Sbjct: 578 PVGDEEDSHLGDFI---EDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIG 634

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 635 MNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 667


>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 = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 411 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 470

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 471 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 525

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 526 PLEKVRKV-LKIA-KEPISLETPIGDEEDSHLGDFI---EDKNAILPIDAAIQSNLRETT 580

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 581 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 635


>gi|16752284|ref|NP_445653.1| RNA polymerase sigma factor [Chlamydophila pneumoniae AR39]
 gi|7190028|gb|AAF38883.1| RNA polymerase sigma factor, sigma-70 family [Chlamydophila
           pneumoniae AR39]
          Length = 591

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 77/247 (31%), Positives = 120/247 (48%), Gaps = 28/247 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+  RG++ +TY+ WW
Sbjct: 336 AKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWW 395

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+      + R    L   T     PE+   +A+
Sbjct: 396 IRQAVTRAIADQARTIRIPVHMIETINK------VLRGAKKLMMETGKEPTPEE---LAE 446

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L ++   V  +        SL A +    ++S  + D+L       E   +E       
Sbjct: 447 ELGLTPDRVREIYKIAQHPISLQAEVGEGSESS--FGDFL-------EDTAVESPAEATG 497

Query: 225 RNMLTRSM----SVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
            +ML   M      L  RER +   R   L   P TLE + S F V+RER+RQIEA+A +
Sbjct: 498 YSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGKPKTLEEVGSAFNVTRERIRQIEAKALR 557

Query: 279 KVQESIQ 285
           K++  I+
Sbjct: 558 KMRHPIR 564


>gi|158313089|ref|YP_001505597.1| RpoD family RNA polymerase sigma factor [Frankia sp. EAN1pec]
 gi|158108494|gb|ABW10691.1| RNA polymerase, sigma 70 subunit, RpoD family [Frankia sp. EAN1pec]
          Length = 423

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 87/294 (29%), Positives = 137/294 (46%), Gaps = 60/294 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH---------GDL------------SAAHR 52
           Y+ EI K+P+L   +E  L+KR     + EH          DL            +A  +
Sbjct: 130 YLREIGKVPLLNAAQEVELSKRVEAGLFAEHKLDTDQDLADDLRRDLGVLVTDGQAAKQQ 189

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV+++LRLVV +A  Y G G+ + ++V EGN+GL++AV+KFD  +G++ +TY+ WWI+ A
Sbjct: 190 LVSANLRLVVSVAKKYSGRGMTLLDLVQEGNLGLIRAVEKFDYAKGYKFSTYATWWIRQA 249

Query: 113 MQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           +   +      ++I           T  Q++L   L R     +   + ++  EQVV   
Sbjct: 250 IGRALADQARTIRIPVHVVEQINKITRLQRQLVSTLGREPTDEELALELDMPIEQVV--- 306

Query: 164 KKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
            +L     + +S+   +   GD  L   I  SD  S    D   Y   G  Q  I+    
Sbjct: 307 -ELRRYAQDTVSLETSVGDDGDSVLGDFIEDSDATSP--ADAASY---GAMQDEID---- 356

Query: 222 KNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIE 273
               N+L      LNPRER +   R  L +    TL  + +   ++RER+RQIE
Sbjct: 357 ----NVL----GALNPREREVMRLRFGLADGKQHTLAEVGNRLGLTRERIRQIE 402


>gi|313893234|ref|ZP_07826811.1| RNA polymerase sigma factor RpoD [Veillonella sp. oral taxon 158
           str. F0412]
 gi|313442587|gb|EFR61002.1| RNA polymerase sigma factor RpoD [Veillonella sp. oral taxon 158
           str. F0412]
          Length = 386

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 80/291 (27%), Positives = 139/291 (47%), Gaps = 37/291 (12%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHR-----------LVTSHL 58
           VN +  +  Y+ EI ++P+L   EE VLAK+        A ++           LV ++L
Sbjct: 100 VNIDDPVRMYLKEIGRVPLLSADEEIVLAKQIEAGAAEDATYKDIQLAKKAKKKLVDANL 159

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV IA  Y G G+   +++ EGN+GL++AV KFD  +G++ +TY+ WWI+ A+   I 
Sbjct: 160 RLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVDKFDYTKGYKFSTYATWWIRQAITRAIA 219

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV-------VAIAKKLNVSES 171
                ++I    +       L R+   L         PE++       V   +++     
Sbjct: 220 DQARTIRI--PVHMVETINKLIRISRQLLQDKGREPLPEEIAEGMGITVERVREIQKIAQ 277

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           E +S+   +  +E      +S   +  + QD +  D D    +L++++        +   
Sbjct: 278 EPVSLETPIGEEE------DSHLGDFIEDQDAIAPD-DAASYILLQEQ--------IEDV 322

Query: 232 MSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKV 280
            + L  RE+++   R  L++  P TLE +   F V+RER+RQIE +A  K+
Sbjct: 323 FTCLTDREQQVLILRFGLKDGKPRTLEEVGQHFNVTRERIRQIEGKALTKL 373


>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 = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 414 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 473

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 474 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 528

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 529 PLEKVRKV-LKIA-KEPISLETPIGDEEDSHLGDFI---EDKNAVLPIDAAIQSNLRETT 583

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 584 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 638


>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 = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 121/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 444 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 503

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +  L+P+    +A+K+ +
Sbjct: 504 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGLEPDPAT-LAEKMEM 558

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + R+++
Sbjct: 559 PEDKIRKI-MKIAK-EPISMETPIGDDDDSHLGDFI---EDNNTVAPADAALHASMRDVV 613

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 614 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 668


>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 = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 121/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 539 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 598

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +  L+P+    +A+K+ +
Sbjct: 599 IRQAITRSIADQARTIRI--PVHMIETINKMNRIS--RQILQETGLEPDPAT-LAEKMEM 653

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + R+++
Sbjct: 654 PEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDNNTVAPADAALHASMRDVV 708

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 709 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 763


>gi|186472768|ref|YP_001860110.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia phymatum
           STM815]
 gi|184195100|gb|ACC73064.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia phymatum
           STM815]
          Length = 685

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 67/245 (27%), Positives = 119/245 (48%), Gaps = 32/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 446 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 505

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +  L+P+    +A+K+ +
Sbjct: 506 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGLEPDPAT-LAEKMEM 560

Query: 169 SESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            E ++          ISM   +  D+  +      D N+    D  ++            
Sbjct: 561 PEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPSDAALH------------ 608

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARA 276
               + R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A
Sbjct: 609 ---ASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKA 665

Query: 277 FKKVQ 281
            +K++
Sbjct: 666 LRKLR 670


>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 = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 121/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 442 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 501

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +  L+P+    +A+K+ +
Sbjct: 502 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGLEPDPAT-LAEKMEM 556

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + R+++
Sbjct: 557 PEDKIRKI-MKIAK-EPISMETPIGDDDDSHLGDFI---EDNNTVAPADAALHASMRDVV 611

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 612 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 666


>gi|41408918|ref|NP_961754.1| RNA polymerase sigma factor [Mycobacterium avium subsp.
           paratuberculosis K-10]
 gi|41397277|gb|AAS05137.1| SigA [Mycobacterium avium subsp. paratuberculosis K-10]
          Length = 509

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 80/302 (26%), Positives = 144/302 (47%), Gaps = 42/302 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR-------------EHGD-LSAAHR------------ 52
           Y+ +I K+ +L  +EE  LAKR               E G+ L AA R            
Sbjct: 212 YLKQIGKVALLNAEEEVELAKRIEAGLYATQLMSEMAERGEKLPAAQRRDMMWICRDGDR 271

Query: 53  ----LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
               L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WW
Sbjct: 272 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 331

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   +      ++I    +   +   L R++  L         PE+   +AK++++
Sbjct: 332 IRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDPGREPTPEE---LAKEMDI 386

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +  +V+ +        SL+  I   D+  SQ  D++    D +  V ++       ++ L
Sbjct: 387 TPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEAVVAVDAVSFTLLQDQL 441

Query: 229 TRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   + 
Sbjct: 442 QSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRS 501

Query: 287 QV 288
           QV
Sbjct: 502 QV 503


>gi|254416030|ref|ZP_05029786.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
 gi|196177205|gb|EDX72213.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
          Length = 380

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 69/237 (29%), Positives = 126/237 (53%), Gaps = 17/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 144 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 203

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++     KP E+ +A   ++
Sbjct: 204 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKILSQELGRKPTEEEIADRMEM 258

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  D +  E  + +   R++   
Sbjct: 259 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIEADGETPEDQVSKNLLRED--- 311

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L   +  L+PRER +   R   ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 312 -LESVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLR 367


>gi|32130003|sp|Q87DT7|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 = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 72/253 (28%), Positives = 120/253 (47%), Gaps = 32/253 (12%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RGF+
Sbjct: 371 YGEAKASKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVCKFEHRRGFK 430

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I    +       L R+   +         PE+  
Sbjct: 431 FSTYATWWIRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQQFGREATPEE-- 486

Query: 161 AIAKKLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
            +AK++++ E ++          ISM   +  DE             S   D++    D 
Sbjct: 487 -LAKEMDMPEDKIRKVMKIAKEPISMETPIGDDE------------DSHLGDFI---EDP 530

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRER 268
             +  ++     N    +   ++ L PRE ++   R  +  N   TLE +  +F+V+RER
Sbjct: 531 NVESPVDTTTNVNLSETVREVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRER 590

Query: 269 VRQIEARAFKKVQ 281
           +RQIEA+A +K++
Sbjct: 591 IRQIEAKALRKLR 603


>gi|15837951|ref|NP_298639.1| RNA polymerase sigma factor RpoD [Xylella fastidiosa 9a5c]
 gi|20140311|sp|Q9PDM9|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 = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 72/253 (28%), Positives = 120/253 (47%), Gaps = 32/253 (12%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RGF+
Sbjct: 371 YGEAKASKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVCKFEHRRGFK 430

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I    +       L R+   +         PE+  
Sbjct: 431 FSTYATWWIRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQQFGREATPEE-- 486

Query: 161 AIAKKLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
            +AK++++ E ++          ISM   +  DE             S   D++    D 
Sbjct: 487 -LAKEMDMPEDKIRKVMKIAKEPISMETPIGDDE------------DSHLGDFI---EDP 530

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRER 268
             +  ++     N    +   ++ L PRE ++   R  +  N   TLE +  +F+V+RER
Sbjct: 531 NVESPVDTTTNVNLSETVREVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRER 590

Query: 269 VRQIEARAFKKVQ 281
           +RQIEA+A +K++
Sbjct: 591 IRQIEAKALRKLR 603


>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 = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 82/280 (29%), Positives = 141/280 (50%), Gaps = 24/280 (8%)

Query: 16  LSRYIHEIRKIP--MLEKQEEYVL-------AKRYREHGDLSA--AHRLVT-SHLRLVVK 63
           LSR I  IR+    +L+ Q   VL         R    G+L A  A R +T ++LRLV+ 
Sbjct: 516 LSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVIS 575

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      
Sbjct: 576 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 635

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           ++I    +       + R+    Q + +  L+P+    +A+K+ + E ++  +  ++A  
Sbjct: 636 IRI--PVHMIETINKMNRI--SRQILQETGLEPDPAT-LAEKMEMPEDKIRKI-MKIA-K 688

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           E ++      D + S   D++    D       +     + R+++   +  L PRE ++ 
Sbjct: 689 EPISMETPIGDDDDSHLGDFI---EDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVL 745

Query: 244 EARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
             R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 746 RMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 785


>gi|298492420|ref|YP_003722597.1| RpoD subfamily RNA polymerase sigma 70 subunit ['Nostoc azollae'
           0708]
 gi|298234338|gb|ADI65474.1| RNA polymerase, sigma 70 subunit, RpoD subfamily ['Nostoc azollae'
           0708]
          Length = 389

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 87/317 (27%), Positives = 143/317 (45%), Gaps = 76/317 (23%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR---EHGDLSAA------------------------- 50
           +  E+ + P+L+  EE  LA+R R   E  DL AA                         
Sbjct: 82  FFKEMARYPLLKPDEEVELARRVRFLEEVKDLQAALEEELGQQPSRSEVAAKFEMTEKQL 141

Query: 51  -----------HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                       +++ S+LRLVV IA  Y   G+P  +++ EG +GL +A +KFDP++G+
Sbjct: 142 ESRLYQGRVAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAMGLNRATEKFDPDKGY 201

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK--RLFFNLRRLKGHLQAITDNNLKPE 157
           + +TY+ WWI+ A+   I      +++     +K  +L    R LK   Q +  N  + E
Sbjct: 202 KFSTYAYWWIRQAITRAIANDARTIRLPIHIVEKLNKLKKAQRELK---QKLARNPSEAE 258

Query: 158 QVVAI------AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              A+       ++L     + +S+N R+ G E    L++            L+ D D Q
Sbjct: 259 MATALEISIQQLRQLQQLRRQALSLNHRV-GKEEDTELMD------------LLEDEDNQ 305

Query: 212 EQVLIEKEERKNRRNMLTRSM-----SVLNPRERRIFEARR--LQENPVTLENLSSEFEV 264
                   E K   NM+ + +      VL PRE+ +   R       P TLE + + F +
Sbjct: 306 ------SPEAKMNENMMRQEIWEVLGDVLTPREKDVISLRYGLTTSEPCTLEEVGNMFNL 359

Query: 265 SRERVRQIEARAFKKVQ 281
           SRERVRQI+++A +K++
Sbjct: 360 SRERVRQIQSKAMRKLR 376


>gi|1519634|gb|AAC44891.1| sigma 70-type sigma factor SigA [Rhodobacter sphaeroides]
          Length = 666

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 428 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 487

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 488 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 542

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  SQ  D++    D    + ++   ++N +   
Sbjct: 543 PLEKVRKV-MKIA-KEPISLETPIGDEEDSQLGDFI---EDKNAILPLDSAIQENLKETT 597

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 598 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERLRQIEAKALRKLK 652


>gi|71065817|ref|YP_264544.1| putative sigma-70 factor (RpoD) [Psychrobacter arcticus 273-4]
 gi|71038802|gb|AAZ19110.1| putative sigma-70 factor (RpoD) [Psychrobacter arcticus 273-4]
          Length = 647

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 115/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 408 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 467

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV--------V 160
           I+ A+   I      ++I    +       + R+   L         PE++        V
Sbjct: 468 IRQAITRSIADQARTIRI--PVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEV 525

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + K L +++ E ISM   +  DE             S   D++    DG     ++   
Sbjct: 526 KVRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDGTISSPVDDAT 569

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFK 278
               R      +  L  RE R+ + R   + P   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 570 AAGLREATRDVLGNLTEREARVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALR 629

Query: 279 KVQ 281
           K++
Sbjct: 630 KLR 632


>gi|269302545|gb|ACZ32645.1| RNA polymerase sigma factor RpoD [Chlamydophila pneumoniae LPCoLN]
          Length = 570

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 77/247 (31%), Positives = 120/247 (48%), Gaps = 28/247 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+  RG++ +TY+ WW
Sbjct: 315 AKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWW 374

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+      + R    L   T     PE+   +A+
Sbjct: 375 IRQAVTRAIADQARTIRIPVHMIETINK------VLRGAKKLMMETGKEPTPEE---LAE 425

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L ++   V  +        SL A +    ++S  + D+L       E   +E       
Sbjct: 426 ELGLTPDRVREIYKIAQHPISLQAEVGEGGESS--FGDFL-------EDTAVESPAEATG 476

Query: 225 RNMLTRSM----SVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
            +ML   M      L  RER +   R   L   P TLE + S F V+RER+RQIEA+A +
Sbjct: 477 YSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGKPKTLEEVGSAFNVTRERIRQIEAKALR 536

Query: 279 KVQESIQ 285
           K++  I+
Sbjct: 537 KMRHPIR 543


>gi|300781032|ref|ZP_07090886.1| RNA polymerase sigma factor rpoD [Corynebacterium genitalium ATCC
           33030]
 gi|300532739|gb|EFK53800.1| RNA polymerase sigma factor rpoD [Corynebacterium genitalium ATCC
           33030]
          Length = 536

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 82/324 (25%), Positives = 155/324 (47%), Gaps = 49/324 (15%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREHG------------ 45
           RK+  +  + +  +  Y+ +I K+ +L+ ++E  LAKR     Y +H             
Sbjct: 218 RKDAQLTASAD-SVRAYLKQIGKVALLDAEQEVSLAKRIEAGLYAQHRLDEMQRAADEGD 276

Query: 46  -----------DLSAAHR--------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
                      DL A  R        L+ ++LRLVV +A  Y G G+   +++ EGN+GL
Sbjct: 277 KDAKLTPAVKRDLRAVARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGL 336

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L
Sbjct: 337 IRAVEKFDYSKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQREL 394

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    P++   +AK+++++E +V+ +        SL+  I   D+  SQ  D++  
Sbjct: 395 LQDLGREPTPQE---LAKEMDITEEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI-- 447

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEV 264
             D +  V ++       ++ L   +  L+ RE  +   R  L +  P TL+ +   + V
Sbjct: 448 -EDSEAVVAVDAVSFTLLQDQLQDVLHTLSEREAGVVRLRFGLTDGMPRTLDEIGQVYGV 506

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           +RER+RQIE++   K++   + QV
Sbjct: 507 TRERIRQIESKTMSKLRHPSRSQV 530


>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 = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 400 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 459

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 460 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 514

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 515 PLEKVRKV-LKIA-KEPISLETPIGDEEDSHLGDFI---EDKNAVLPIDAAIQSNLRETT 569

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 570 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 624


>gi|218848158|ref|YP_002454701.1| RNA polymerase sigma factor, sigma-70 family [Bacillus cereus
           G9842]
 gi|218546289|gb|ACK98682.1| RNA polymerase sigma factor, sigma-70 family [Bacillus cereus
           G9842]
          Length = 295

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 85/299 (28%), Positives = 143/299 (47%), Gaps = 40/299 (13%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
            N++N S     EIG  +Y++EI    +L  ++      +Y+E GD+ +   L+ S+LRL
Sbjct: 3   FNKRNSS-----EIG--KYLNEICNYDILTDEQSMEHIIKYKEKGDIDSRELLICSNLRL 55

Query: 61  VVKIAMGYRGYG-LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           VV +A  +  YG   + E++ EG IGLM+ ++ +D  +G +L+TY  WWI+  + +Y+  
Sbjct: 56  VVSVAKSFPCYGNCDLMEMIQEGTIGLMKGLEDYDYTKGNKLSTYITWWIRQRISKYLSI 115

Query: 120 SWSLVKIGTTANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVI 174
           + S V++ TT  +     K  ++     KG        NL   +V   A++L   ES VI
Sbjct: 116 NRSDVRVATTMQKKITEVKNCYYENMGEKG-------TNLTTMEV---AERLGYKESIVI 165

Query: 175 SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS--- 231
                L  D   N +   S ++  Q +  L+        +L  K        M T     
Sbjct: 166 DA---LVTDRITNTI---SIEDDVQNEKTLLDRQQSTLAILANKNAPNPSEVMATEEEKF 219

Query: 232 ------MSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQE 282
                    LNPRE  +   R   ++ +  TLE+ +    V+RERV+QIE +A +K+++
Sbjct: 220 EFDELMFVTLNPREESVLRYRFGFDDGIELTLEDTARILGVTRERVQQIEKKAIEKMKQ 278


>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 = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 431 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 490

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +++KL +
Sbjct: 491 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LSEKLAM 545

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + IE   + N R   
Sbjct: 546 PLEKVRKV-LKIA-KEPISLETPIGDEEDSHLGDFI---EDKNAILPIEAAIQSNLRETT 600

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 601 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 655


>gi|257791063|ref|YP_003181669.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Eggerthella lenta
           DSM 2243]
 gi|317488219|ref|ZP_07946788.1| RNA polymerase sigma factor RpoD [Eggerthella sp. 1_3_56FAA]
 gi|325830757|ref|ZP_08164141.1| RNA polymerase sigma factor RpoD [Eggerthella sp. HGA1]
 gi|257474960|gb|ACV55280.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Eggerthella lenta
           DSM 2243]
 gi|316912661|gb|EFV34201.1| RNA polymerase sigma factor RpoD [Eggerthella sp. 1_3_56FAA]
 gi|325487164|gb|EGC89607.1| RNA polymerase sigma factor RpoD [Eggerthella sp. HGA1]
          Length = 409

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 85/303 (28%), Positives = 137/303 (45%), Gaps = 60/303 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR------------------------------EHGDLS 48
           Y+ EI K+P+L   EE  LA +                                E   + 
Sbjct: 111 YLKEIGKVPLLTAAEEIDLAMKIEAGVAAMEELEKAEDEGIELERREKRRLGRIEQVGID 170

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L+ ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WW
Sbjct: 171 AKQQLIEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 230

Query: 109 IKAAMQEYILRSWSLVKIGT----TAN-----QKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N     Q++L   L R     +   +  L  E+V
Sbjct: 231 IRQAITRAIADQARTIRIPVHMVETINKLVRIQRQLLQELGREPSPEEIGKEMGLPAERV 290

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K   +S+ E +S+   +  +E             SQ  D++    D    V  +  
Sbjct: 291 REIQK---ISQ-EPVSLETPIGEEE------------DSQLGDFI---EDDAAVVPPDAA 331

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
                +  L++ +  L  RER++   R   E+  P TLE +  EF V+RER+RQIE++  
Sbjct: 332 SFSMLQEQLSKVLDGLAERERKVISLRFGLEDGHPRTLEEVGREFGVTRERIRQIESKTL 391

Query: 278 KKV 280
            K+
Sbjct: 392 AKL 394


>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|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]
          Length = 682

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 82/280 (29%), Positives = 141/280 (50%), Gaps = 24/280 (8%)

Query: 16  LSRYIHEIRKIP--MLEKQEEYVL-------AKRYREHGDLSA--AHRLVT-SHLRLVVK 63
           LSR I  IR+    +L+ Q   VL         R    G+L A  A R +T ++LRLV+ 
Sbjct: 398 LSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVIS 457

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      
Sbjct: 458 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 517

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           ++I    +       + R+    Q + +  L+P+    +A+K+ + E ++  +  ++A  
Sbjct: 518 IRI--PVHMIETINKMNRI--SRQILQETGLEPDPAT-LAEKMEMPEDKIRKI-MKIAK- 570

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           E ++      D + S   D++    D       +     + R+++   +  L PRE ++ 
Sbjct: 571 EPISMETPIGDDDDSHLGDFI---EDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVL 627

Query: 244 EARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
             R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 628 RMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 667


>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 = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 415 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 474

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 475 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 529

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 530 PLEKVRKV-LKIA-KEPISLETPIGDEEDSHLGDFI---EDKNAILPIDAAIQSNLRETT 584

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 585 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 639


>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 = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 70/245 (28%), Positives = 117/245 (47%), Gaps = 32/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 467 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 526

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +   +PE  V +A+K+ +
Sbjct: 527 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGQEPEPAV-LAQKMEM 581

Query: 169 SESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            E ++          ISM   +  DE  +      D  +    D  VY            
Sbjct: 582 PEEKIRKILKISKEPISMETPIGDDEDSHLGDFIEDSATMAPADAAVY------------ 629

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARA 276
               + R++    +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A
Sbjct: 630 ---ASLRDVTKDILDSLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKA 686

Query: 277 FKKVQ 281
            +K++
Sbjct: 687 LRKLR 691


>gi|51244645|ref|YP_064529.1| RNA polymerase sigma factor (RpoD) [Desulfotalea psychrophila
           LSv54]
 gi|50875682|emb|CAG35522.1| probable RNA polymerase sigma factor (RpoD) [Desulfotalea
           psychrophila LSv54]
          Length = 534

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 77/251 (30%), Positives = 127/251 (50%), Gaps = 44/251 (17%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   LV ++LRLV+ ++  +   GL  S+++ EGNIGLM+AV+KFD  RGF+ +TY+ WW
Sbjct: 296 AKEALVRANLRLVISVSKRFVNRGLQFSDLIQEGNIGLMKAVEKFDYRRGFKFSTYATWW 355

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ---------- 158
           I+ ++   I            A+Q R      RL  H+    +  L+  +          
Sbjct: 356 IRQSITRGI------------ADQGRTI----RLPVHMIETINRMLRVSKDFYLEEHREP 399

Query: 159 -VVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDH----DGQE 212
            V  +A +L  +E + +    ++A D  SL+  +   D   +   D++V  +    DG  
Sbjct: 400 SVEEVAGQLG-TEVDKVKSALKIAKDAISLDTPVG--DDGETYLGDFIVDKNCLGPDGFA 456

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVR 270
            V   KE        L++ +S L+PRE ++ + R   L++   TLE +   F V+RER+R
Sbjct: 457 MVASLKE-------CLSQVLSSLSPREEKVLKMRYGILEKREYTLEEVGRCFNVTRERIR 509

Query: 271 QIEARAFKKVQ 281
           QIEA+A  K++
Sbjct: 510 QIEAQAISKLK 520


>gi|170736023|ref|YP_001777283.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia cenocepacia
           MC0-3]
 gi|169818211|gb|ACA92793.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia cenocepacia
           MC0-3]
          Length = 683

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 121/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 444 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 503

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +  L+P+    +A+K+ +
Sbjct: 504 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGLEPDPAT-LAEKMEM 558

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + R+++
Sbjct: 559 PEDKIRKI-MKIAK-EPISMETPIGDDDDSHLGDFI---EDTNTVAPADAALHASMRDVV 613

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 614 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 668


>gi|241205658|ref|YP_002976754.1| RNA polymerase sigma factor RpoD [Rhizobium leguminosarum bv.
           trifolii WSM1325]
 gi|240859548|gb|ACS57215.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhizobium
           leguminosarum bv. trifolii WSM1325]
          Length = 685

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 447 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 506

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 507 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 561

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 562 PLEKVRKV-LKIA-KEPISLETPVGDEEDSHLGDFI---EDKNALLPIDAAIQANLRETT 616

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 617 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 671


>gi|163761137|ref|ZP_02168214.1| RNA polymerase sigma factor protein (sigma-70) [Hoeflea
           phototrophica DFL-43]
 gi|162281688|gb|EDQ31982.1| RNA polymerase sigma factor protein (sigma-70) [Hoeflea
           phototrophica DFL-43]
          Length = 680

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 83/273 (30%), Positives = 136/273 (49%), Gaps = 27/273 (9%)

Query: 13  EIGLSRYIHEIRKI-PMLEKQE-EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           E G+S  I E R+I  M++K E E  +AK+            +V ++LRLV+ IA  Y  
Sbjct: 417 ETGIS--ISEFRRIVQMVQKGEREARIAKK-----------EMVEANLRLVISIAKKYTN 463

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I    
Sbjct: 464 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI--PV 521

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
           +       + R    +         PE+   +A+KL +   +V  +  ++A  E ++   
Sbjct: 522 HMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAMPLEKVRKV-LKIA-KEPISLET 576

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--L 248
              D+  S   D++    D    + I+   + N R   TR ++ L PRE R+   R    
Sbjct: 577 PVGDEEDSHLGDFI---EDKNAILPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIG 633

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 634 MNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 666


>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 = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 70/243 (28%), Positives = 122/243 (50%), Gaps = 12/243 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 371 YGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 430

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I    +       L R+   +         PE+  
Sbjct: 431 FSTYATWWIRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQQYGREATPEE-- 486

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +AK++++ E ++  +  ++A  E ++      D   S   D++    D   +  I+   
Sbjct: 487 -LAKEMDMPEDKIRKV-MKIAK-EPISMETPIGDDEDSHLGDFI---EDTNVESPIDSTT 540

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             N    +   ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 541 NTNLMETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 600

Query: 279 KVQ 281
           K++
Sbjct: 601 KLR 603


>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 = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 67/245 (27%), Positives = 119/245 (48%), Gaps = 32/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 441 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 500

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +  L+P+    +A+K+ +
Sbjct: 501 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGLEPDPAT-LAEKMEM 555

Query: 169 SESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            E ++          ISM   +  D+  +      D N+    D  ++            
Sbjct: 556 PEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDTNTVAPADAALH------------ 603

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARA 276
               + R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A
Sbjct: 604 ---ASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKA 660

Query: 277 FKKVQ 281
            +K++
Sbjct: 661 LRKLR 665


>gi|221212356|ref|ZP_03585333.1| RNA polymerase sigma factor RpoD [Burkholderia multivorans CGD1]
 gi|221167455|gb|EED99924.1| RNA polymerase sigma factor RpoD [Burkholderia multivorans CGD1]
          Length = 682

 Score = 95.9 bits (237), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 82/280 (29%), Positives = 141/280 (50%), Gaps = 24/280 (8%)

Query: 16  LSRYIHEIRKIP--MLEKQEEYVL-------AKRYREHGDLSA--AHRLVT-SHLRLVVK 63
           LSR I  IR+    +L+ Q   VL         R    G+L A  A R +T ++LRLV+ 
Sbjct: 398 LSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVIS 457

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      
Sbjct: 458 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 517

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           ++I    +       + R+    Q + +  L+P+    +A+K+ + E ++  +  ++A  
Sbjct: 518 IRI--PVHMIETINKMNRI--SRQILQETGLEPDPAT-LAEKMEMPEDKIRKI-MKIAK- 570

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           E ++      D + S   D++    D       +     + R+++   +  L PRE ++ 
Sbjct: 571 EPISMETPIGDDDDSHLGDFI---EDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVL 627

Query: 244 EARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
             R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 628 RMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 667


>gi|327485473|gb|AEA79879.1| RNA polymerase sigma factor RpoH [Vibrio cholerae LMA3894-4]
          Length = 185

 Score = 95.5 bits (236), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 62/187 (33%), Positives = 105/187 (56%), Gaps = 11/187 (5%)

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           ++++ WIKA + EY+LR+W +VKI TT  Q++LFFNLR+ K  L    +      +V  +
Sbjct: 2   SFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKLFFNLRKSKKRLGWFNNG-----EVETV 56

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A++L V  +EV  M  RLA  ++   +    D+N   +   ++Y  D     L +  E +
Sbjct: 57  ARELGVEPAEVREMESRLAAQDAAFEMSAEDDENGMAYTAPVLYLEDKHSD-LADNLEAE 115

Query: 223 NRRNMLTRSMSV----LNPRERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAF 277
           N     T+ +S+    L+ R + I  AR L  +N  TL++L+  + VS ER+RQ+E  A 
Sbjct: 116 NWEAHTTQRLSMALASLDERSQHIVRARWLDDDNKTTLQDLAEMYGVSAERIRQLEKNAM 175

Query: 278 KKVQESI 284
           +K++E++
Sbjct: 176 RKLKEAV 182


>gi|254778811|ref|YP_003056916.1| RNA polymerase sigma factor RpoD [Helicobacter pylori B38]
 gi|254000722|emb|CAX28640.1| RNA polymerase sigma factor rpoD (Sigma-70) [Helicobacter pylori
           B38]
          Length = 679

 Score = 95.5 bits (236), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 75/246 (30%), Positives = 121/246 (49%), Gaps = 33/246 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ WW
Sbjct: 440 AKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATWW 499

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR----LKGHLQAI---TDNNLKPEQV-V 160
           IK A+   I      ++I        +   + R    ++ H+Q      D  +  E+V +
Sbjct: 500 IKQAISRAIADQARTIRIPI-----HMIDTINRINKVMRKHIQETGKEPDLEVVAEEVGL 554

Query: 161 AIAKKLNVSE--SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           ++ K  NV +   E IS+   +  D+         DKN     D ++             
Sbjct: 555 SLDKVKNVIKVTKEPISLETPVGNDDDGKFGDFVEDKNIVSSIDHIM------------- 601

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEAR 275
             R++ +  +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ 
Sbjct: 602 --REDLKVQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESS 659

Query: 276 AFKKVQ 281
           A KK++
Sbjct: 660 AIKKLR 665


>gi|16127277|ref|NP_421841.1| RNA polymerase sigma factor RpoD [Caulobacter crescentus CB15]
 gi|1710678|sp|P52324|RPOD_CAUCR RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|1079588|gb|AAA82054.1| RNA polymerase principal sigma factor [Caulobacter crescentus CB15]
 gi|13424691|gb|AAK25009.1| RNA polymerase sigma factor RpoD [Caulobacter crescentus CB15]
 gi|1585612|prf||2201399A sigma73 factor
          Length = 652

 Score = 95.5 bits (236), Expect = 7e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 414 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 473

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 474 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 528

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 529 PLEKVRKV-LKIA-KEPISLETPIGDEEDSHLGDFI---EDKNAILPIDAAIQSNLRETT 583

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 584 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 638


>gi|302382122|ref|YP_003817945.1| RNA polymerase, sigma 70 subunit, RpoD [Brevundimonas subvibrioides
           ATCC 15264]
 gi|302192750|gb|ADL00322.1| RNA polymerase, sigma 70 subunit, RpoD [Brevundimonas subvibrioides
           ATCC 15264]
          Length = 652

 Score = 95.5 bits (236), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 414 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 473

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 474 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 528

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 529 PLEKVRKV-LKIA-KEPISLETPIGDEEDSHLGDFI---EDKNAILPIDAAIQSNLRETT 583

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 584 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 638


>gi|269102892|ref|ZP_06155589.1| RNA polymerase sigma factor RpoS [Photobacterium damselae subsp.
           damselae CIP 102761]
 gi|268162790|gb|EEZ41286.1| RNA polymerase sigma factor RpoS [Photobacterium damselae subsp.
           damselae CIP 102761]
          Length = 282

 Score = 95.5 bits (236), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 75/263 (28%), Positives = 137/263 (52%), Gaps = 22/263 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ ++R   +L K+EE  L+ +  + GD  A  +L+ S+LRLVV IA   +  GL + ++
Sbjct: 10  YLKQLRSRALLTKEEEIELSIKV-QAGDQKARAKLIESNLRLVVSIAKKMQHRGLDLDDL 68

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK--RLF 136
           ++EGNIGL+ AV+KF+P+ G+R +TY+ WWIK AM   I      V++    +++   ++
Sbjct: 69  INEGNIGLITAVEKFNPDYGYRFSTYATWWIKQAMDRAIHNHSREVRLPVHISKELCTIY 128

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
              + +    + +T      +QV A+         +++    R +   SL+   +   K 
Sbjct: 129 SAFKEMSTKSEQVT-----IDQVSALTGSPKEEIEKILKYERRYS---SLDDQFDEGAKF 180

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR---LQENPV 253
           S      ++ DH   +   +  EE  ++  +L   ++ L PR++ I  ARR       P 
Sbjct: 181 SE-----IIPDHSKLDHTELLNEE--DQTEVLAMLLAELKPRDQEII-ARRFGLFGYEPH 232

Query: 254 TLENLSSEFEVSRERVRQIEARA 276
           TL+ +++   ++RERVRQ++  A
Sbjct: 233 TLQEVATAVNLTRERVRQLQILA 255


>gi|157273328|gb|ABV27227.1| sigma 38 RpoS [Candidatus Chloracidobacterium thermophilum]
          Length = 549

 Score = 95.5 bits (236), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 79/249 (31%), Positives = 120/249 (48%), Gaps = 37/249 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGY--RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           A   ++ ++LRLVV IA  Y  R  GL  S+++ EGNIGLM+AV+KFD  RG++ +TY+ 
Sbjct: 306 ARREMIEANLRLVVSIAKNYINRSRGLQFSDLIQEGNIGLMRAVEKFDYRRGYKFSTYAT 365

Query: 107 WWIKAAMQEYILRSWSLVKIGT----TANQ----KRLFFN-LRRLKGHLQAITDNNLKPE 157
           WWI+ A+   I      +++      T N+     RL    L R   H +     +L   
Sbjct: 366 WWIRQAVTRAIADQGRTIRVPVHMVETINKIVRTARLMVQELGREPTHEELAQRTDLP-- 423

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
            V  + + L +++ E IS+   +  D   N      D+NS    + +V            
Sbjct: 424 -VAKVRQALKIAQ-EPISLETPIGDDGESNLGSFIEDRNSLNPAEMIVG----------- 470

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEAR-----RLQENPVTLENLSSEFEVSRERVRQI 272
               K  R      +S L PRE +I + R       QE   TLE +   F V+RER+RQI
Sbjct: 471 ----KGLREATLEVLSTLTPREEQILKMRFGLDGDGQER--TLEEVGRYFHVTRERIRQI 524

Query: 273 EARAFKKVQ 281
           EA+A +K++
Sbjct: 525 EAKALRKLR 533


>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 = 95.5 bits (236), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 121/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 566 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 625

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +  L+P+    +A+K+ +
Sbjct: 626 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGLEPDPAT-LAEKMEM 680

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + R+++
Sbjct: 681 PEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDTNTVAPADAALHASMRDVV 735

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 736 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 790


>gi|299066184|emb|CBJ37368.1| RNA polymerase sigma70 factor [Ralstonia solanacearum CMR15]
          Length = 777

 Score = 95.5 bits (236), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 67/235 (28%), Positives = 117/235 (49%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 538 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 597

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+   +   T N   P     +A+K+ +
Sbjct: 598 IRQAITRSIADQARTIRI--PVHMIETINKMNRISRQILQETGNEPDP---ATLAEKMEM 652

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       E     + R ++
Sbjct: 653 PEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDTNTLAPAEAALHGSMRGVV 707

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 708 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 762


>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 = 95.5 bits (236), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 588 AKKEMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 647

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +   +P+    +A K+++
Sbjct: 648 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGAEPDPAT-LAVKMDM 702

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + RN++
Sbjct: 703 PEDKIRKI-MKIAK-EPISMETPIGDDDDSHLGDFI---EDNNTLAPADAALHASMRNVV 757

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 758 KDVLDSLTPREAKVLRMRFGVEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 812


>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 = 95.5 bits (236), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 82/280 (29%), Positives = 141/280 (50%), Gaps = 24/280 (8%)

Query: 16  LSRYIHEIRKIP--MLEKQEEYVL-------AKRYREHGDLSA--AHRLVT-SHLRLVVK 63
           LSR I  IR+    +L+ Q   VL         R    G+L A  A R +T ++LRLV+ 
Sbjct: 516 LSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVIS 575

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      
Sbjct: 576 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 635

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           ++I    +       + R+    Q + +  L+P+    +A+K+ + E ++  +  ++A  
Sbjct: 636 IRI--PVHMIETINKMNRI--SRQILQETGLEPDPAT-LAEKMEMPEDKIRKI-MKIA-K 688

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           E ++      D + S   D++    D       +     + R+++   +  L PRE ++ 
Sbjct: 689 EPISMETPIGDDDDSHLGDFI---EDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVL 745

Query: 244 EARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
             R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 746 RMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 785


>gi|260464077|ref|ZP_05812272.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Mesorhizobium
           opportunistum WSM2075]
 gi|259030248|gb|EEW31529.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Mesorhizobium
           opportunistum WSM2075]
          Length = 674

 Score = 95.5 bits (236), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 436 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 495

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 496 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 550

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 551 PLEKVRKV-LKIA-KEPISLETPVGDEEDSHLGDFI---EDKMAILPIDAAIQANLRETT 605

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 606 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 660


>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 = 95.5 bits (236), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 121/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 382 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 441

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +  L+P+    +A+K+ +
Sbjct: 442 IRQAITRSIADQARTIRI--PVHMIETINKMNRISR--QILQETGLEPDPAT-LAEKMEM 496

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + R+++
Sbjct: 497 PEDKIRKI-MKIAK-EPISMETPIGDDDDSHLGDFI---EDTNTVAPADAALHASMRDVV 551

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 552 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 606


>gi|88809137|ref|ZP_01124646.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 7805]
 gi|88787079|gb|EAR18237.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 7805]
          Length = 313

 Score = 95.5 bits (236), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 80/293 (27%), Positives = 149/293 (50%), Gaps = 36/293 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYR------EHGDLSA-------------------A 50
           +S Y+  I +IP+L   EE  L  + +      E G ++A                    
Sbjct: 20  ISWYLATIGRIPLLTPAEEIELGNQVQKLMQLTEDGSIAADSELFDSKQRRLIRVGQRAK 79

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            R++ ++LRLVV +A  Y+G GL + +++ EG++GL +AV+KFDP RG++ +TY+ WWI+
Sbjct: 80  QRMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWWIR 139

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            +M   I      +++    +++    ++R++   L         P + + IA+ +++  
Sbjct: 140 QSMTRAIACQSRTIRLPVHLSER--LTSIRKVS--LDLAHKLGAMPSR-LEIAEAMDMPV 194

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            E+ S+  +     SL+A +N  +  S  +   L+ D   +E   +++ E++     L R
Sbjct: 195 EELDSLLRQALTTSSLDAPVNGEEGRS--FLGDLIADSSLEEP--LDRVEQRIHHEQLGR 250

Query: 231 SMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            MS L+ +E+ +   R  L  N   TL  +    +VSRERVRQ+E +A +K++
Sbjct: 251 WMSHLSDQEQHVLTLRFGLNGNERHTLAEIGRLLDVSRERVRQVELKALRKLR 303


>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|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]
          Length = 680

 Score = 95.5 bits (236), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 121/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 441 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 500

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +  L+P+    +A+K+ +
Sbjct: 501 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGLEPDPAT-LAEKMEM 555

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + R+++
Sbjct: 556 PEDKIRKI-MKIAK-EPISMETPIGDDDDSHLGDFI---EDTNTVAPADAALHASMRDVV 610

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 611 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 665


>gi|330813718|ref|YP_004357957.1| RNA polymerase sigma factor RpoD [Candidatus Pelagibacter sp.
           IMCC9063]
 gi|327486813|gb|AEA81218.1| RNA polymerase sigma factor RpoD [Candidatus Pelagibacter sp.
           IMCC9063]
          Length = 621

 Score = 95.5 bits (236), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 69/239 (28%), Positives = 122/239 (51%), Gaps = 20/239 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 383 AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 442

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+      + R    + +       PE+   ++K
Sbjct: 443 IRQAITRSIADQARTIRIPVHMIETINK------IVRTSRQMMSEYGREPTPEE---LSK 493

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           KL +   +V  +  ++A  E ++      D++ S   D++    D    + ++   +   
Sbjct: 494 KLAMPLEKVRKV-LKIAK-EPISLETPVGDEDDSSLGDFI---EDTNALIPVDAAIQTGL 548

Query: 225 RNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +N  T+ ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 549 KNSTTKVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 607


>gi|283457795|ref|YP_003362387.1| DNA-directed RNA polymerase, sigma subunit [Rothia mucilaginosa
           DY-18]
 gi|283133802|dbj|BAI64567.1| DNA-directed RNA polymerase, sigma subunit [Rothia mucilaginosa
           DY-18]
          Length = 460

 Score = 95.5 bits (236), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 84/309 (27%), Positives = 141/309 (45%), Gaps = 60/309 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREHG---------DLSAAHR------------ 52
           Y+ +I K+ +L  Q+E  LAKR     Y EH          DL  A R            
Sbjct: 167 YLKQIGKVSLLNAQQEVDLAKRIEAGLYAEHKLAENPDMDKDLKKALRWVVHDGKRAKNH 226

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 227 LLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYSKGFKFSTYATWWIRQA 286

Query: 113 MQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           +   +      ++I              Q+++  +L R     +   + ++ PE+V+ + 
Sbjct: 287 ITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELGKELDMTPEKVIEVQ 346

Query: 164 KKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           K       E IS++  L   GD     LI  S+          V   D     L++++  
Sbjct: 347 K----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ-- 391

Query: 222 KNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
                 L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K
Sbjct: 392 ------LHSVLDTLSEREAGVVAMRFGMTDGQPKTLDEIGKVYGVTRERIRQIESKTMSK 445

Query: 280 VQESIQKQV 288
           ++   + QV
Sbjct: 446 LRHPSRSQV 454


>gi|152990473|ref|YP_001356195.1| RNA polymerase sigma factor RpoD [Nitratiruptor sp. SB155-2]
 gi|151422334|dbj|BAF69838.1| RNA polymerase sigma 70 factor [Nitratiruptor sp. SB155-2]
          Length = 608

 Score = 95.5 bits (236), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 74/236 (31%), Positives = 123/236 (52%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ ++G++ +TY+ WW
Sbjct: 369 AKTRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKKGYKFSTYATWW 428

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I     +     N + ++ HLQ       K   V  IA+++ +
Sbjct: 429 IRQAISRAIADQARTIRIPIHMIETINRIN-KIVRKHLQETG----KEPDVETIAEEVGM 483

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V ++        SL A I + +    ++ D++   +      +I KE+ K++   +
Sbjct: 484 PVEKVKNVIKITKEPVSLEAPIGNEE--DGKFGDFIEDKNAPNPLEVIMKEDMKSK---I 538

Query: 229 TRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 539 EEILENLNEREKAVVRMRFGLMPDESDRTLEEIGKELNVTRERVRQIESSAIKKLK 594


>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 = 95.5 bits (236), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 121/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 441 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 500

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +  L+P+    +A+K+ +
Sbjct: 501 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGLEPDPAT-LAEKMEM 555

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + R+++
Sbjct: 556 PEDKIRKI-MKIAK-EPISMETPIGDDDDSHLGDFI---EDTNTVAPADAALHASMRDVV 610

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 611 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 665


>gi|54025729|ref|YP_119971.1| RNA polymerase sigma factor [Nocardia farcinica IFM 10152]
 gi|54017237|dbj|BAD58607.1| putative principal sigma factor [Nocardia farcinica IFM 10152]
          Length = 454

 Score = 95.5 bits (236), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 81/318 (25%), Positives = 151/318 (47%), Gaps = 43/318 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-------------YREHGD-LS 48
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR             + E G+ L 
Sbjct: 142 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYAAEKMREFAESGEKLP 200

Query: 49  AAHR----------------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
            A R                L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 201 VAMRRDYNWIVRDGNRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 260

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L      
Sbjct: 261 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGR 318

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D + 
Sbjct: 319 EPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEA 370

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVR 270
            V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 371 VVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIR 430

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 431 QIESKTMSKLRHPSRSQV 448


>gi|329946883|ref|ZP_08294295.1| RNA polymerase sigma factor RpoD [Actinomyces sp. oral taxon 170
           str. F0386]
 gi|328526694|gb|EGF53707.1| RNA polymerase sigma factor RpoD [Actinomyces sp. oral taxon 170
           str. F0386]
          Length = 543

 Score = 95.5 bits (236), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 84/310 (27%), Positives = 141/310 (45%), Gaps = 61/310 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH------GDLSAAHR--------------- 52
           Y+ +I K+ +L  ++E  LAKR     Y EH       DL A  R               
Sbjct: 249 YLKQIGKVALLNAEQEVELAKRIEAGLYAEHRLAEEGNDLPAKLRRELHWVAQDGQRAKN 308

Query: 53  -LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ 
Sbjct: 309 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQ 368

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+VV +
Sbjct: 369 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAVELDMTPEKVVEV 428

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 429 QK----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 474

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 475 -------LHAVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 527

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 528 KLRHPSRSQV 537


>gi|218248849|ref|YP_002374220.1| RNA polymerase sigma-70 subunit RpoD subfamily [Cyanothece sp. PCC
           8801]
 gi|257061911|ref|YP_003139799.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8802]
 gi|218169327|gb|ACK68064.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8801]
 gi|256592077|gb|ACV02964.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8802]
          Length = 417

 Score = 95.5 bits (236), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 64/238 (26%), Positives = 129/238 (54%), Gaps = 13/238 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           + A  +++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV+KFDP +G+R +TY+ 
Sbjct: 176 IRAKEQMIKANLRLVVSVAKKYQHRGLELLDLIQEGTLGLERAVEKFDPTKGYRFSTYAY 235

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   I     ++++     +K     L ++K   + ++    +   +  ++K+L
Sbjct: 236 WWIRQGITRAISTQSRIIRLPVHITEK-----LNKIKRAQRKLSQEKGRKATIEEMSKEL 290

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++S  ++  +  R+    SL   +    +  ++  D L  +    E+ LI +  RK+ + 
Sbjct: 291 DMSAEQIREVLLRIPRSVSLE--VKVGKEKDTELVDLLETECQSPEESLISESLRKDLQV 348

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +L      L  RE+ + + R   E+    +L ++    E+SRERVRQIEA+A +K+++
Sbjct: 349 LLED----LTEREQDVIKLRYGFEDGTCYSLADIGRVLELSRERVRQIEAKALQKLRQ 402


>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 = 95.5 bits (236), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 82/280 (29%), Positives = 141/280 (50%), Gaps = 24/280 (8%)

Query: 16  LSRYIHEIRKIP--MLEKQEEYVL-------AKRYREHGDLSA--AHRLVT-SHLRLVVK 63
           LSR I  IR+    +L+ Q   VL         R    G+L A  A R +T ++LRLV+ 
Sbjct: 452 LSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVIS 511

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      
Sbjct: 512 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 571

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           ++I    +       + R+    Q + +  L+P+    +A+K+ + E ++  +  ++A  
Sbjct: 572 IRI--PVHMIETINKMNRI--SRQILQETGLEPDPAT-LAEKMEMPEDKIRKI-MKIAK- 624

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           E ++      D + S   D++    D       +     + R+++   +  L PRE ++ 
Sbjct: 625 EPISMETPIGDDDDSHLGDFI---EDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVL 681

Query: 244 EARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
             R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 682 RMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 721


>gi|118465794|ref|YP_882772.1| RNA polymerase sigma factor [Mycobacterium avium 104]
 gi|254776035|ref|ZP_05217551.1| RNA polymerase sigma factor [Mycobacterium avium subsp. avium ATCC
           25291]
 gi|118167081|gb|ABK67978.1| sigma factor MysA [Mycobacterium avium 104]
          Length = 496

 Score = 95.5 bits (236), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 82/318 (25%), Positives = 151/318 (47%), Gaps = 43/318 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGD-LS 48
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+ L 
Sbjct: 184 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMSEMAERGEKLP 242

Query: 49  AAHR----------------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           AA R                L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 243 AAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 302

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L      
Sbjct: 303 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGR 360

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D + 
Sbjct: 361 EPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEA 412

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVR 270
            V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 413 VVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIR 472

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 473 QIESKTMSKLRHPSRSQV 490


>gi|325068636|ref|ZP_08127309.1| RNA polymerase, sigma 70 subunit, RpoD [Actinomyces oris K20]
          Length = 542

 Score = 95.5 bits (236), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 84/310 (27%), Positives = 141/310 (45%), Gaps = 61/310 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH------GDLSAAHR--------------- 52
           Y+ +I K+ +L  ++E  LAKR     Y EH       DL A  R               
Sbjct: 248 YLKQIGKVALLNAEQEVELAKRIEAGLYAEHRLAEEGNDLPAKLRRELHWVAQDGQRAKN 307

Query: 53  -LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ 
Sbjct: 308 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQ 367

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+VV +
Sbjct: 368 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAVELDMTPEKVVEV 427

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 428 QK----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 473

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 474 -------LHAVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 526

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 527 KLRHPSRSQV 536


>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 = 95.5 bits (236), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 121/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 441 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 500

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +  L+P+    +A+K+ +
Sbjct: 501 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGLEPDPAT-LAEKMEM 555

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + R+++
Sbjct: 556 PEDKIRKI-MKIAK-EPISMETPIGDDDDSHLGDFI---EDTNTVAPADAALHASMRDVV 610

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 611 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 665


>gi|114704974|ref|ZP_01437882.1| RNA polymerase sigma factor protein (sigma-70) [Fulvimarina pelagi
           HTCC2506]
 gi|114539759|gb|EAU42879.1| RNA polymerase sigma factor protein (sigma-70) [Fulvimarina pelagi
           HTCC2506]
          Length = 682

 Score = 95.5 bits (236), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 444 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 503

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 504 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 558

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 559 PLEKVRKV-LKIA-KEPISLETPVGDEEDSHLGDFI---EDKNAVLPIDAAIQGNLRETT 613

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 668


>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 = 95.5 bits (236), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 72/243 (29%), Positives = 117/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 374 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 433

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 434 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPIPEELAERMQMPED 491

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   Q+ ++   
Sbjct: 492 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDNTLQLPMDAAT 535

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             N R      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 536 ATNLRAATNDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 595

Query: 279 KVQ 281
           K++
Sbjct: 596 KLR 598


>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 = 95.5 bits (236), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 82/280 (29%), Positives = 141/280 (50%), Gaps = 24/280 (8%)

Query: 16  LSRYIHEIRKIP--MLEKQEEYVL-------AKRYREHGDLSA--AHRLVT-SHLRLVVK 63
           LSR I  IR+    +L+ Q   VL         R    G+L A  A R +T ++LRLV+ 
Sbjct: 452 LSRNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVIS 511

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      
Sbjct: 512 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 571

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           ++I    +       + R+    Q + +  L+P+    +A+K+ + E ++  +  ++A  
Sbjct: 572 IRI--PVHMIETINKMNRI--SRQILQETGLEPDPAT-LAEKMEMPEDKIRKI-MKIAK- 624

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           E ++      D + S   D++    D       +     + R+++   +  L PRE ++ 
Sbjct: 625 EPISMETPIGDDDDSHLGDFI---EDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVL 681

Query: 244 EARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
             R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 682 RMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 721


>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 = 95.5 bits (236), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 121/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 569 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 628

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +  L+P+    +A+K+ +
Sbjct: 629 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGLEPDPAT-LAEKMEM 683

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + R+++
Sbjct: 684 PEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDTNTVAPADAALHASMRDVV 738

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 739 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 793


>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 = 95.5 bits (236), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 77/278 (27%), Positives = 138/278 (49%), Gaps = 30/278 (10%)

Query: 24  RKIPMLEKQEEYVL---------------AKRYREHGDLSA--AHRLVT-SHLRLVVKIA 65
           R IP + +Q++ +L                 R    G+L A  A R +T ++LRLV+ IA
Sbjct: 521 RNIPAIREQQQRLLDLQARVVLPLKDLKETNRQMAAGELKARQAKREMTEANLRLVISIA 580

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++
Sbjct: 581 KKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIR 640

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           I    +       + R+    Q + +  L+P+    +A+K+ + E ++  +  ++A  E 
Sbjct: 641 I--PVHMIETINKMNRI--SRQILQETGLEPDPAT-LAEKMEMPEDKIRKI-MKIA-KEP 693

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           ++      D + S   D++    D       +     + R+++   +  L PRE ++   
Sbjct: 694 ISMETPIGDDDDSHLGDFI---EDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRM 750

Query: 246 RRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 751 RFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 788


>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 = 95.5 bits (236), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 73/256 (28%), Positives = 121/256 (47%), Gaps = 32/256 (12%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A  Y E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 375 AMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 434

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I    +       L R+   +         PE
Sbjct: 435 GYKFSTYATWWIRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQQFGREATPE 492

Query: 158 QVVAIAKKLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
           +   +AK++++ E ++          ISM   +  DE             S   D++   
Sbjct: 493 E---LAKEMDMPEDKIRKVMKIAKEPISMETPIGDDE------------DSHLGDFI--- 534

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVS 265
            D   +  I+     N    +   ++ L PRE ++   R  +  N   TLE +  +F+V+
Sbjct: 535 EDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVT 594

Query: 266 RERVRQIEARAFKKVQ 281
           RER+RQIEA+A +K++
Sbjct: 595 RERIRQIEAKALRKLR 610


>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 = 95.5 bits (236), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 72/243 (29%), Positives = 117/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 374 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 433

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 434 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPIPEELAERMQMPED 491

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   Q+ ++   
Sbjct: 492 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDNTLQLPMDAAT 535

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             N R      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 536 ATNLRAATNDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 595

Query: 279 KVQ 281
           K++
Sbjct: 596 KLR 598


>gi|71082746|ref|YP_265465.1| RNA polymerase sigma factor RpoD [Candidatus Pelagibacter ubique
           HTCC1062]
 gi|71061859|gb|AAZ20862.1| RNA polymerase sigma factor [Candidatus Pelagibacter ubique
           HTCC1062]
          Length = 595

 Score = 95.5 bits (236), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 73/245 (29%), Positives = 119/245 (48%), Gaps = 32/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 357 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 416

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I            A+Q R      R+  H+   T N +   Q + +++    
Sbjct: 417 IRQAITRSI------------ADQARTI----RIPVHMIE-TINKIVRTQRLILSEFGRE 459

Query: 169 SESEVISMNCRLAGDESLNALINS----------SDKNSSQWQDWLVYDHDGQEQVLIEK 218
           +  E ++   R+  D+    L  S           D+  S   D++    D +    +E+
Sbjct: 460 ATPEELAQKLRMPLDKVRKVLKISKEPVSLEKPVGDEEDSSLGDFI---EDTKALAPLEQ 516

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARA 276
             + N     T+ +S L PRE R+   R         TLE +  +F V+RER+RQIEA+A
Sbjct: 517 AIKSNLSEATTKILSTLTPREERVLRMRFGVGMNTDHTLEEVGLQFSVTRERIRQIEAKA 576

Query: 277 FKKVQ 281
            +K++
Sbjct: 577 LRKLK 581


>gi|296437079|gb|ADH19249.1| RNA polymerase sigma factor [Chlamydia trachomatis G/11222]
          Length = 571

 Score = 95.5 bits (236), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 77/247 (31%), Positives = 117/247 (47%), Gaps = 28/247 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+  RG++ +TY+ WW
Sbjct: 317 AKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWW 376

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+      + R    L   T     PE+   + +
Sbjct: 377 IRQAVTRAIADQARTIRIPVHMIETINK------VLRGAKKLMMETGKEPTPEE---LGE 427

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L  +   V  +        SL A +   D   S + D+L       E   +E       
Sbjct: 428 ELGFTPDRVREIYKIAQHPISLQAEVG--DGGESSFGDFL-------EDTAVESPAEATG 478

Query: 225 RNMLTRSM----SVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
            +ML   M      L  RER +   R   L   P TLE + S F V+RER+RQIEA+A +
Sbjct: 479 YSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGRPKTLEEVGSAFNVTRERIRQIEAKALR 538

Query: 279 KVQESIQ 285
           K++  I+
Sbjct: 539 KMRHPIR 545


>gi|91762832|ref|ZP_01264797.1| RNA polymerase sigma factor [Candidatus Pelagibacter ubique
           HTCC1002]
 gi|91718634|gb|EAS85284.1| RNA polymerase sigma factor [Candidatus Pelagibacter ubique
           HTCC1002]
          Length = 607

 Score = 95.5 bits (236), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 73/245 (29%), Positives = 119/245 (48%), Gaps = 32/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 369 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 428

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I            A+Q R      R+  H+   T N +   Q + +++    
Sbjct: 429 IRQAITRSI------------ADQARTI----RIPVHMIE-TINKIVRTQRLILSEFGRE 471

Query: 169 SESEVISMNCRLAGDESLNALINS----------SDKNSSQWQDWLVYDHDGQEQVLIEK 218
           +  E ++   R+  D+    L  S           D+  S   D++    D +    +E+
Sbjct: 472 ATPEELAQKLRMPLDKVRKVLKISKEPVSLEKPVGDEEDSSLGDFI---EDTKALAPLEQ 528

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARA 276
             + N     T+ +S L PRE R+   R         TLE +  +F V+RER+RQIEA+A
Sbjct: 529 AIKSNLSEATTKILSTLTPREERVLRMRFGVGMNTDHTLEEVGLQFSVTRERIRQIEAKA 588

Query: 277 FKKVQ 281
            +K++
Sbjct: 589 LRKLK 593


>gi|315185771|gb|EFU19537.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           thermophila DSM 6578]
          Length = 338

 Score = 95.5 bits (236), Expect = 8e-18,   Method: Compositional matrix adjust.
 Identities = 78/262 (29%), Positives = 131/262 (50%), Gaps = 35/262 (13%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           +EE  L +R RE       +R++T++LRLVV IA  Y+  GL + +++ EGNIGL++AV+
Sbjct: 90  EEERRLDQRLRE-----LKNRMITANLRLVVSIAKKYQHRGLSLLDLIDEGNIGLIEAVE 144

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           +FD  +G R +TY  WWI+ A+            + + A++ R+     R+  H+     
Sbjct: 145 RFDYTKGCRFSTYGTWWIRQAI------------VKSLADKSRVI----RIPIHMLNTIK 188

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNC----RLA-----GDESLNALINSSDKNSSQWQD 202
           N     + +A     + +E E+         R+A       E+ +  I   ++N +   D
Sbjct: 189 NVFMLSKELAQELGRDPTEEELSRYTGLPDRRVAEIMQVSQETASLDITVDEENMTTLGD 248

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSS 260
            +  D D   Q   EK   +  R++L  ++S L+ RER +   R     E P+TLE    
Sbjct: 249 LVSDDED---QGPFEKVFHRYLRDVLLEALSDLSERERNVISLRFGLNGEGPLTLEETGK 305

Query: 261 EFEVSRERVRQIEARAFKKVQE 282
              ++RERVRQI+ +A  K++E
Sbjct: 306 LLGITRERVRQIQEKALAKLRE 327


>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|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]
          Length = 625

 Score = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 73/256 (28%), Positives = 121/256 (47%), Gaps = 32/256 (12%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A  Y E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 375 AMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 434

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I    +       L R+   +         PE
Sbjct: 435 GYKFSTYATWWIRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQQFGREATPE 492

Query: 158 QVVAIAKKLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
           +   +AK++++ E ++          ISM   +  DE             S   D++   
Sbjct: 493 E---LAKEMDMPEDKIRKVMKIAKEPISMETPIGDDE------------DSHLGDFI--- 534

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVS 265
            D   +  I+     N    +   ++ L PRE ++   R  +  N   TLE +  +F+V+
Sbjct: 535 EDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVT 594

Query: 266 RERVRQIEARAFKKVQ 281
           RER+RQIEA+A +K++
Sbjct: 595 RERIRQIEAKALRKLR 610


>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 = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 68/235 (28%), Positives = 119/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 411 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 470

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   +A+K+ +
Sbjct: 471 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEKGREPTPEE---LAEKMGL 525

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D    V  E    ++ +N +
Sbjct: 526 PEDKIRKV-MKIAK-EPISLETPVGDDDDSHLGDFI---EDSSIVVPAEAATSESLKNAI 580

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  + PRE ++   R     P   TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 581 NNVLDEMPPREAQVLRMRFGIGMPSDHTLEEVGRQFGVTRERIRQIEAKALRKLR 635


>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 = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 73/256 (28%), Positives = 121/256 (47%), Gaps = 32/256 (12%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A  Y E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 375 AMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 434

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I    +       L R+   +         PE
Sbjct: 435 GYKFSTYATWWIRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQQFGREATPE 492

Query: 158 QVVAIAKKLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
           +   +AK++++ E ++          ISM   +  DE             S   D++   
Sbjct: 493 E---LAKEMDMPEDKIRKVMKIAKEPISMETPIGDDE------------DSHLGDFI--- 534

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVS 265
            D   +  I+     N    +   ++ L PRE ++   R  +  N   TLE +  +F+V+
Sbjct: 535 EDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVT 594

Query: 266 RERVRQIEARAFKKVQ 281
           RER+RQIEA+A +K++
Sbjct: 595 RERIRQIEAKALRKLR 610


>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 = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 73/256 (28%), Positives = 121/256 (47%), Gaps = 32/256 (12%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A  Y E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 371 AMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 430

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I    +       L R+   +         PE
Sbjct: 431 GYKFSTYATWWIRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQQFGREATPE 488

Query: 158 QVVAIAKKLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
           +   +AK++++ E ++          ISM   +  DE             S   D++   
Sbjct: 489 E---LAKEMDMPEDKIRKVMKIAKEPISMETPIGDDE------------DSHLGDFI--- 530

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVS 265
            D   +  I+     N    +   ++ L PRE ++   R  +  N   TLE +  +F+V+
Sbjct: 531 EDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVT 590

Query: 266 RERVRQIEARAFKKVQ 281
           RER+RQIEA+A +K++
Sbjct: 591 RERIRQIEAKALRKLR 606


>gi|75907387|ref|YP_321683.1| RNA polymerase sigma factor SigC [Anabaena variabilis ATCC 29413]
 gi|75701112|gb|ABA20788.1| RNA polymerase, sigma subunit, RpsC/SigC [Anabaena variabilis ATCC
           29413]
          Length = 416

 Score = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 65/238 (27%), Positives = 130/238 (54%), Gaps = 13/238 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L +   ++ ++LRLVV +A  Y+  GL + ++V EG +GL +AV+KFDP +G+R +TY+ 
Sbjct: 175 LQSKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAY 234

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   I  S   +++     +K     L ++K   + I     +   +  +A +L
Sbjct: 235 WWIRQGITRAIATSSRTIRLPVHITEK-----LNKIKKAQRKIAQEKGRTPTLEDLAIEL 289

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++ ++V  +  R+    SL   +   DK+ ++  + L  D    E++L+ +  +++ ++
Sbjct: 290 DMTPTQVREVLLRVPRSVSLETKVG-KDKD-TELGELLETDGVTPEEMLMRESLQRDLQH 347

Query: 227 MLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +L    + L  RER +   R      +P +L  +    ++SRERVRQIE++A +K+++
Sbjct: 348 LL----ADLTSRERDVILMRFGLADGHPYSLAEIGRALDLSRERVRQIESKALQKLRQ 401


>gi|21244512|ref|NP_644094.1| RNA polymerase sigma factor RpoD [Xanthomonas axonopodis pv. citri
           str. 306]
 gi|32130007|sp|Q8PG33|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]
          Length = 625

 Score = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 73/256 (28%), Positives = 121/256 (47%), Gaps = 32/256 (12%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A  Y E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 375 AMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 434

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I    +       L R+   +         PE
Sbjct: 435 GYKFSTYATWWIRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQQFGREATPE 492

Query: 158 QVVAIAKKLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
           +   +AK++++ E ++          ISM   +  DE             S   D++   
Sbjct: 493 E---LAKEMDMPEDKIRKVMKIAKEPISMETPIGDDE------------DSHLGDFI--- 534

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVS 265
            D   +  I+     N    +   ++ L PRE ++   R  +  N   TLE +  +F+V+
Sbjct: 535 EDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVT 594

Query: 266 RERVRQIEARAFKKVQ 281
           RER+RQIEA+A +K++
Sbjct: 595 RERIRQIEAKALRKLR 610


>gi|254470295|ref|ZP_05083699.1| sigma 70 [Pseudovibrio sp. JE062]
 gi|211960606|gb|EEA95802.1| sigma 70 [Pseudovibrio sp. JE062]
          Length = 701

 Score = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 76/250 (30%), Positives = 120/250 (48%), Gaps = 42/250 (16%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 463 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 522

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRR------LKGHLQAITDNN 153
           I+ A+   I      ++I      T N+     +++   + R      L   LQ   +  
Sbjct: 523 IRQAITRSIADQARTIRIPVHMIETINKIVRTSRQMLHEIGREPTPEELSEKLQMPLE-- 580

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            K  +V+ IAK       E IS+   +             D+  S   D++    D    
Sbjct: 581 -KVRKVLKIAK-------EPISLETPIG------------DEEDSHLGDFI---EDKNAI 617

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQ 271
           + I+   + N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQ
Sbjct: 618 LPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQ 677

Query: 272 IEARAFKKVQ 281
           IEA+A +K++
Sbjct: 678 IEAKALRKLK 687


>gi|226306303|ref|YP_002766263.1| RNA polymerase sigma factor SigA [Rhodococcus erythropolis PR4]
 gi|226185420|dbj|BAH33524.1| RNA polymerase sigma factor SigA [Rhodococcus erythropolis PR4]
          Length = 452

 Score = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 81/318 (25%), Positives = 151/318 (47%), Gaps = 43/318 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGD-LS 48
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               + G+ L 
Sbjct: 140 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYAVQIMQDLADKGEKLP 198

Query: 49  AAHR----------------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           AA R                L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 199 AAQRRDMSWICRDGNRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 258

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L      
Sbjct: 259 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGR 316

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D + 
Sbjct: 317 EPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEA 368

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVR 270
            V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 369 VVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIR 428

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 429 QIESKTMSKLRHPSRSQV 446


>gi|111023781|ref|YP_706753.1| RNA polymerase sigma factor [Rhodococcus jostii RHA1]
 gi|110823311|gb|ABG98595.1| sigma factor, sigma 70 type, probable group 1 (principle sigma
           factor) [Rhodococcus jostii RHA1]
          Length = 457

 Score = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 82/318 (25%), Positives = 151/318 (47%), Gaps = 43/318 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR----------YREHGD----LS 48
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR           +E  D    L 
Sbjct: 145 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQIMQELSDSGEKLP 203

Query: 49  AAHR----------------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           AA R                L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 204 AAQRRDMSWICRDGNRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 263

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L      
Sbjct: 264 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGR 321

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D + 
Sbjct: 322 EPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEA 373

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVR 270
            V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 374 VVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIR 433

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 434 QIESKTMSKLRHPSRSQV 451


>gi|86610159|ref|YP_478921.1| RNA polymerase sigma factor SigC [Synechococcus sp.
           JA-2-3B'a(2-13)]
 gi|86558701|gb|ABD03658.1| RNA polymerase sigma-70 factor family [Synechococcus sp.
           JA-2-3B'a(2-13)]
          Length = 366

 Score = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 68/248 (27%), Positives = 129/248 (52%), Gaps = 21/248 (8%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           + KR +EH        ++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV+KFDP+
Sbjct: 123 IGKRAKEH--------MIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPK 174

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +G+R +TY+ WWI+  +   I      +++     +K     L ++K   + ++    + 
Sbjct: 175 KGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEK-----LNKIKKAQRKLSQEKGRT 229

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
             +  IA +L ++  +V  +  R+    SL   +   DK+ ++  D L  D    E+ ++
Sbjct: 230 PTIEDIASELEMTPPQVRELLVRVPRSVSLETKVG-KDKD-TELGDLLETDDISPEETMM 287

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT--LENLSSEFEVSRERVRQIEA 274
            +   ++ + +L    S L  RER +   R    +  T  L  +    ++SRERVRQIEA
Sbjct: 288 REALHRDLQQLL----SDLTSRERDVIRMRFGLGDGRTYSLAEIGRALDLSRERVRQIEA 343

Query: 275 RAFKKVQE 282
           +A +K+++
Sbjct: 344 KALQKLRQ 351


>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 = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 67/235 (28%), Positives = 117/235 (49%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 637 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 696

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+   +   T N   P     +A+K+ +
Sbjct: 697 IRQAITRSIADQARTIRI--PVHMIETINKMNRISRQILQETGNEPDP---ATLAEKMEM 751

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       E     + R ++
Sbjct: 752 PEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDTNTLAPAEAALHGSMRGVV 806

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 807 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 861


>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 = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 67/235 (28%), Positives = 117/235 (49%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 634 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 693

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+   +   T N   P     +A+K+ +
Sbjct: 694 IRQAITRSIADQARTIRI--PVHMIETINKMNRISRQILQETGNEPDP---ATLAEKMEM 748

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       E     + R ++
Sbjct: 749 PEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDTNTLAPAEAALHGSMRGVV 803

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 804 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 858


>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 = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 121/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 441 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 500

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +  L+P+    +A+K+ +
Sbjct: 501 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGLEPDPAT-LAEKMEM 555

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + R+++
Sbjct: 556 PEDKIRKI-MKIAK-EPISMETPIGDDDDSHLGDFI---EDTNTVAPADAALHASMRDVV 610

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 611 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 665


>gi|237804965|ref|YP_002889119.1| RNA polymerase sigma factor [Chlamydia trachomatis B/TZ1A828/OT]
 gi|231273265|emb|CAX10180.1| RNA polymerase sigma factor [Chlamydia trachomatis B/TZ1A828/OT]
          Length = 571

 Score = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 77/247 (31%), Positives = 117/247 (47%), Gaps = 28/247 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+  RG++ +TY+ WW
Sbjct: 317 AKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWW 376

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+      + R    L   T     PE+   + +
Sbjct: 377 IRQAVTRAIADQARTIRIPVHMIETINK------VLRGAKKLMMETGKEPTPEE---LGE 427

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L  +   V  +        SL A +   D   S + D+L       E   +E       
Sbjct: 428 ELGFTPDRVREIYKIAQHPISLQAEVG--DGGESSFGDFL-------EDTAVESPAEATG 478

Query: 225 RNMLTRSM----SVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
            +ML   M      L  RER +   R   L   P TLE + S F V+RER+RQIEA+A +
Sbjct: 479 YSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGRPKTLEEVGSAFNVTRERIRQIEAKALR 538

Query: 279 KVQESIQ 285
           K++  I+
Sbjct: 539 KMRHPIR 545


>gi|15605346|ref|NP_220132.1| RNA polymerase sigma factor [Chlamydia trachomatis D/UW-3/CX]
 gi|76789354|ref|YP_328440.1| RNA polymerase sigma factor [Chlamydia trachomatis A/HAR-13]
 gi|166154830|ref|YP_001654948.1| RNA polymerase sigma factor [Chlamydia trachomatis 434/Bu]
 gi|166155705|ref|YP_001653960.1| RNA polymerase sigma factor [Chlamydia trachomatis
           L2b/UCH-1/proctitis]
 gi|255311437|ref|ZP_05354007.1| RNA polymerase sigma factor [Chlamydia trachomatis 6276]
 gi|255317738|ref|ZP_05358984.1| RNA polymerase sigma factor [Chlamydia trachomatis 6276s]
 gi|255348997|ref|ZP_05381004.1| RNA polymerase sigma factor [Chlamydia trachomatis 70]
 gi|255503536|ref|ZP_05381926.1| RNA polymerase sigma factor [Chlamydia trachomatis 70s]
 gi|255507214|ref|ZP_05382853.1| RNA polymerase sigma factor [Chlamydia trachomatis D(s)2923]
 gi|301336109|ref|ZP_07224353.1| RNA polymerase sigma factor [Chlamydia trachomatis L2tet1]
 gi|1710679|sp|P18333|RPOD_CHLTR RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A;
           AltName: Full=Sigma-66; AltName: Full=Sigma-70
 gi|144609|gb|AAA23165.1| RNA polymerase sigma-subunit [Chlamydia trachomatis]
 gi|3329060|gb|AAC68218.1| RNA Polymerase Sigma-66 [Chlamydia trachomatis D/UW-3/CX]
 gi|76167884|gb|AAX50892.1| RpoD [Chlamydia trachomatis A/HAR-13]
 gi|165930818|emb|CAP04316.1| RNA polymerase sigma factor [Chlamydia trachomatis 434/Bu]
 gi|165931693|emb|CAP07270.1| RNA polymerase sigma factor [Chlamydia trachomatis
           L2b/UCH-1/proctitis]
 gi|289525658|emb|CBJ15139.1| RNA polymerase sigma factor [Chlamydia trachomatis Sweden2]
 gi|296435222|gb|ADH17400.1| RNA polymerase sigma factor [Chlamydia trachomatis E/150]
 gi|296436151|gb|ADH18325.1| RNA polymerase sigma factor [Chlamydia trachomatis G/9768]
 gi|296438011|gb|ADH20172.1| RNA polymerase sigma factor [Chlamydia trachomatis G/11074]
 gi|296438941|gb|ADH21094.1| RNA polymerase sigma factor [Chlamydia trachomatis E/11023]
 gi|297140513|gb|ADH97271.1| RNA polymerase sigma factor [Chlamydia trachomatis G/9301]
 gi|297748745|gb|ADI51291.1| RpoD [Chlamydia trachomatis D-EC]
 gi|297749625|gb|ADI52303.1| RpoD [Chlamydia trachomatis D-LC]
          Length = 571

 Score = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 77/247 (31%), Positives = 117/247 (47%), Gaps = 28/247 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+  RG++ +TY+ WW
Sbjct: 317 AKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWW 376

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+      + R    L   T     PE+   + +
Sbjct: 377 IRQAVTRAIADQARTIRIPVHMIETINK------VLRGAKKLMMETGKEPTPEE---LGE 427

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L  +   V  +        SL A +   D   S + D+L       E   +E       
Sbjct: 428 ELGFTPDRVREIYKIAQHPISLQAEVG--DGGESSFGDFL-------EDTAVESPAEATG 478

Query: 225 RNMLTRSM----SVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
            +ML   M      L  RER +   R   L   P TLE + S F V+RER+RQIEA+A +
Sbjct: 479 YSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGRPKTLEEVGSAFNVTRERIRQIEAKALR 538

Query: 279 KVQESIQ 285
           K++  I+
Sbjct: 539 KMRHPIR 545


>gi|15835519|ref|NP_297278.1| RNA polymerase sigma factor [Chlamydia muridarum Nigg]
 gi|270285702|ref|ZP_06195096.1| RNA polymerase sigma factor [Chlamydia muridarum Nigg]
 gi|270289710|ref|ZP_06196012.1| RNA polymerase sigma factor [Chlamydia muridarum Weiss]
 gi|301337097|ref|ZP_07225299.1| RNA polymerase sigma factor [Chlamydia muridarum MopnTet14]
 gi|7388084|sp|P56835|RPOD_CHLMU RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A;
           AltName: Full=Sigma-66; AltName: Full=Sigma-70
 gi|7190932|gb|AAF39698.1| RNA polymerase sigma factor RpoD [Chlamydia muridarum Nigg]
          Length = 571

 Score = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 77/246 (31%), Positives = 116/246 (47%), Gaps = 28/246 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+  RG++ +TY+ WW
Sbjct: 317 AKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWW 376

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+      + R    L   T     PE+   + +
Sbjct: 377 IRQAVTRAIADQARTIRIPVHMIETINK------VLRGAKKLMMETGKEPTPEE---LGE 427

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L  +   V  +        SL A +   D   S + D+L       E   +E       
Sbjct: 428 ELGFTPDRVREIYKIAQHPISLQAEVG--DSGESSFGDFL-------EDTAVESPAEATG 478

Query: 225 RNMLTRSM----SVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
            +ML   M      L  RER +   R   L   P TLE + S F V+RER+RQIEA+A +
Sbjct: 479 YSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGRPKTLEEVGSAFNVTRERIRQIEAKALR 538

Query: 279 KVQESI 284
           K++  I
Sbjct: 539 KMRHPI 544


>gi|226366217|ref|YP_002784000.1| RNA polymerase sigma factor [Rhodococcus opacus B4]
 gi|226244707|dbj|BAH55055.1| RNA polymerase sigma factor SigA [Rhodococcus opacus B4]
 gi|254553058|dbj|BAH85841.1| RNA polymerase sigma A factor [Rhodococcus opacus]
          Length = 457

 Score = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 82/318 (25%), Positives = 151/318 (47%), Gaps = 43/318 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR----------YREHGD----LS 48
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR           +E  D    L 
Sbjct: 145 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQIMQELSDSGEKLP 203

Query: 49  AAHR----------------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           AA R                L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 204 AAQRRDMSWICRDGNRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 263

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L      
Sbjct: 264 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGR 321

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D + 
Sbjct: 322 EPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEA 373

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVR 270
            V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 374 VVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIR 433

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 434 QIESKTMSKLRHPSRSQV 451


>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 = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 73/256 (28%), Positives = 121/256 (47%), Gaps = 32/256 (12%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A  Y E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 374 AMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 433

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I    +       L R+   +         PE
Sbjct: 434 GYKFSTYATWWIRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQQFGREATPE 491

Query: 158 QVVAIAKKLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
           +   +AK++++ E ++          ISM   +  DE             S   D++   
Sbjct: 492 E---LAKEMDMPEDKIRKVMKIAKEPISMETPIGDDE------------DSHLGDFI--- 533

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVS 265
            D   +  I+     N    +   ++ L PRE ++   R  +  N   TLE +  +F+V+
Sbjct: 534 EDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVT 593

Query: 266 RERVRQIEARAFKKVQ 281
           RER+RQIEA+A +K++
Sbjct: 594 RERIRQIEAKALRKLR 609


>gi|13472238|ref|NP_103805.1| RNA polymerase sigma factor RpoD [Mesorhizobium loti MAFF303099]
 gi|14022983|dbj|BAB49591.1| RNA polymerase sigma subunit [Mesorhizobium loti MAFF303099]
          Length = 674

 Score = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 436 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 495

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 496 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 550

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 551 PLEKVRKV-LKIA-KEPISLETPVGDEEDSHLGDFI---EDKMAILPIDAAIQANLRETT 605

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 606 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 660


>gi|255017998|ref|ZP_05290124.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           F2-515]
          Length = 209

 Score = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 46/99 (46%), Positives = 66/99 (66%), Gaps = 1/99 (1%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LAKR  E GD+ A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 108 YLKEIGRVDLLTADEEIALAKRI-EAGDIEAKGRLAEANLRLVVSIAKRYVGRGMLFLDL 166

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I
Sbjct: 167 IQEGNMGLMKAVEKFDFNKGFKFSTYATWWIRQAITRAI 205


>gi|158338579|ref|YP_001519756.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158308820|gb|ABW30437.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 268

 Score = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 77/278 (27%), Positives = 136/278 (48%), Gaps = 31/278 (11%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ EI + P+L  +EE  LA++  + G+  A  +++ ++LRLVV IA  ++  GLP+
Sbjct: 8   LHYYLKEIGRFPLLTHEEEITLARQV-QAGNPRAKRKMIEANLRLVVSIAKKHQNRGLPL 66

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN 131
            +++ EGN+GL  AV KF+PE+G R +TY+ WWI   +   +     +V++        N
Sbjct: 67  LDLIQEGNLGLSIAVDKFEPEQGNRFSTYAYWWILQGVTRSLQNKGRVVRLPVKHWQVGN 126

Query: 132 Q-KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG---DESLN 187
           Q KR    L +  G    + +     E  +   KK   S  E +S++ +  G   D +L 
Sbjct: 127 QIKRTRHQLSQELGREPTVVEIADAMEMDLTRLKKYLHSLQETVSLD-KFVGSEQDTTLG 185

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
            LI  +D   S                     +   +   L+  +++L+ R+R +   R 
Sbjct: 186 DLIEGNDSTQSY-------------------LDLLLQDEELSGYLALLDDRQRFVISERY 226

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             E+  P ++E +  +  +SRERVRQI  +A + +++ 
Sbjct: 227 GLEDGKPKSMEKIGQKLGISRERVRQIIKKAMQTLEKC 264


>gi|322379076|ref|ZP_08053479.1| RNA polymerase sigma factor RpoD [Helicobacter suis HS1]
 gi|322379940|ref|ZP_08054217.1| RNA polymerase sigma factor RpoD [Helicobacter suis HS5]
 gi|321147638|gb|EFX42261.1| RNA polymerase sigma factor RpoD [Helicobacter suis HS5]
 gi|321148568|gb|EFX43065.1| RNA polymerase sigma factor RpoD [Helicobacter suis HS1]
          Length = 634

 Score = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 69/236 (29%), Positives = 120/236 (50%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ E+ ++ +TY+ WW
Sbjct: 395 AKNKMARSNLRLVVSIAKRYTSRGLPFLDLIQEGNIGLMKAVDKFEHEKNYKFSTYATWW 454

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           IK A+   I      ++I        +   + R+   ++     N K   +  +AK++ +
Sbjct: 455 IKQAISRAIADQARTIRIPI-----HMIDTINRINKVMRKYMQENGKEPDLDLVAKEVGL 509

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V ++        SL + + + D    ++ D++    D      +E   R++ +  +
Sbjct: 510 PLDKVRNVIKITKEPISLESPVGNDD--DGKFGDFV---EDKNVVGSMEHIMREDLKAQI 564

Query: 229 TRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 565 DGVLDQLNEREKSVIRMRFGLLEDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 620


>gi|317403353|gb|EFV83866.1| RNA polymerase sigma-70 factor [Achromobacter xylosoxidans C54]
          Length = 813

 Score = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 65/235 (27%), Positives = 121/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 574 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 633

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +   +P+    +A+K+++
Sbjct: 634 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGAEPDPAT-LAQKMDM 688

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + R+++
Sbjct: 689 PEDKIRKI-LKIA-KEPISMETPIGDDDDSHLGDFI---EDTSTLAPSDAALHGSMRDVV 743

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 744 KEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLR 798


>gi|300728464|ref|ZP_07061824.1| RNA polymerase sigma-43 factor [Prevotella bryantii B14]
 gi|299774265|gb|EFI70897.1| RNA polymerase sigma-43 factor [Prevotella bryantii B14]
          Length = 251

 Score = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 76/270 (28%), Positives = 130/270 (48%), Gaps = 51/270 (18%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ EI K  +L +QEE  L+ +  ++GD SA  +L T++LR VV IA  Y+  GL I
Sbjct: 18  LQTYLSEIGKENLLSEQEEQELSAKI-QNGDESAIEKLTTANLRFVVSIAKRYQDRGLGI 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++SEGN GL++A +KFD  +G R   Y++ +I+ A++  I     +  +  + +    
Sbjct: 77  NDLISEGNFGLIKAARKFDAAKGQRFVQYAVHFIRQAIENAIQEQSGIYTLPHSMDD--- 133

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
                                         + + +S+  S++  L   ++ + L   SD 
Sbjct: 134 -----------------------------PVELKQSKAFSVDAPLVQGKTASLLHVLSDP 164

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI---FEARRLQENP 252
           N+      ++ D    + VL         R  L RS+SVLN RERR+   F     Q   
Sbjct: 165 NA------VIPDKPYLDDVL---------RQGLIRSLSVLNDRERRVVSMFYGLNDQNAG 209

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +T E + ++  + RERVR I  +A +K+++
Sbjct: 210 LTYEEIGTQLGLKRERVRDIRKKAERKMKK 239


>gi|156563504|dbj|BAF76047.1| Sigma70 [Ralstonia solanacearum]
          Length = 755

 Score = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 67/235 (28%), Positives = 117/235 (49%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 516 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 575

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+   +   T N   P     +A+K+ +
Sbjct: 576 IRQAITRSIADQARTIRI--PVHMIETINKMNRISRQILQETGNEPDP---ATLAEKMEM 630

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       E     + R ++
Sbjct: 631 PEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDTNTLAPAEAALHGSMRGVV 685

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 686 KDVLDSLAPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 740


>gi|39996625|ref|NP_952576.1| RNA polymerase sigma-70 factor family [Geobacter sulfurreducens
           PCA]
 gi|39983506|gb|AAR34899.1| RNA polymerase sigma-70 factor family [Geobacter sulfurreducens
           PCA]
 gi|298505638|gb|ADI84361.1| RNA polymerase sigma-38 factor, stationary phase [Geobacter
           sulfurreducens KN400]
          Length = 328

 Score = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 77/279 (27%), Positives = 144/279 (51%), Gaps = 31/279 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI++  +L   EE  LA R    GD +A  +++ S+LRLVVKIA  Y   GLP  ++
Sbjct: 63  YLREIQRTRLLTADEEKELAGRI-AKGDKAARDKMIESNLRLVVKIAKRYINRGLPFLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV++F   +  R +TY+ WWI+ +++  ++     +++    +      N
Sbjct: 122 IEEGNMGLIKAVERFKLSKECRFSTYATWWIRQSIERALVNQSRTIRLPVHVSDD---IN 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC---------RLAGDESLNAL 189
            + LK   + +   N +P  V  +A ++ V+ + V  +           R  G+ S   L
Sbjct: 179 -KMLKITRELVQRLNREP-SVKEVATEMKVNSAYVRRLMVLLKKTYSIERPMGENSDYFL 236

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I++ +  S+     L+ D               N+  ++++  + L+  E+ I   R   
Sbjct: 237 IDTIEDTSTVSPAVLLEDL--------------NKYEIVSKWFASLSENEQTILTLRFGL 282

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E+  P TL+ +   F V+RER+RQIEA++ +K+++ I++
Sbjct: 283 EDKEPQTLDTIGRSFGVTRERIRQIEAKSLEKLRKYIEE 321


>gi|16331621|ref|NP_442349.1| RNA polymerase sigma factor SigC [Synechocystis sp. PCC 6803]
 gi|2500787|sp|Q59996|RPSC_SYNY3 RecName: Full=Probable RNA polymerase sigma-C factor
 gi|1001684|dbj|BAA10419.1| RNA polymerase sigma factor [Synechocystis sp. PCC 6803]
          Length = 404

 Score = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 67/240 (27%), Positives = 126/240 (52%), Gaps = 13/240 (5%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E   ++A   ++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV+KFDP +G+R +
Sbjct: 159 EKQGITAKAHMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTKGYRFS 218

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TYS WWI+  +   I     ++++     +K     L ++K   + I+       ++  +
Sbjct: 219 TYSYWWIRQGITRAIATQSRMIRLPVHITEK-----LNKIKRAQRKISQEKGHTPKIDEV 273

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A++L ++  +V  +  ++    SL   +   DK+ ++  D L  D    E  L+    R+
Sbjct: 274 AEELGMTPEQVREVLTQVPRSVSLELKVG-QDKD-TELMDLLETDTQSPEDELM----RE 327

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKV 280
             +N +   +  L PRE+ +   R   ++ V  +L  +     +SRERVRQIEA+A +K+
Sbjct: 328 ALQNDMQEILLDLTPREQEVIALRFGFQDGVAHSLSEIGRILNLSRERVRQIEAKALQKL 387


>gi|319949012|ref|ZP_08023109.1| RNA polymerase sigma factor [Dietzia cinnamea P4]
 gi|319437300|gb|EFV92323.1| RNA polymerase sigma factor [Dietzia cinnamea P4]
          Length = 460

 Score = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 82/318 (25%), Positives = 153/318 (48%), Gaps = 43/318 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGD-LS 48
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+ L+
Sbjct: 148 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATWYMAQVTERGEKLT 206

Query: 49  AAHR----------------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
            A R                L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 207 TAQRRDFKWIERDGVRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 266

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L      
Sbjct: 267 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGR 324

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D + 
Sbjct: 325 EPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEA 376

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVR 270
            V ++       ++ L   +  L+ RE  +   R  L +  P TL+ +   + V+RER+R
Sbjct: 377 VVAVDAVSFTLLQDQLRSVLDTLSEREAGVVRLRFGLTDGLPRTLDEIGQVYGVTRERIR 436

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 437 QIESKTMSKLRHPSRSQV 454


>gi|282900303|ref|ZP_06308254.1| Sigma 28 (Flagella/Sporulation) [Cylindrospermopsis raciborskii
           CS-505]
 gi|281194808|gb|EFA69754.1| Sigma 28 (Flagella/Sporulation) [Cylindrospermopsis raciborskii
           CS-505]
          Length = 399

 Score = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 82/309 (26%), Positives = 141/309 (45%), Gaps = 60/309 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR---EHGDLSAA------------------------- 50
           +  E+ + P+L+  EE  LA+R R   E  DL AA                         
Sbjct: 92  FFKEMARYPLLKPDEEVELARRVRFLEEVKDLQAALEEQLGHSVSKSEVASKFDLNEKQL 151

Query: 51  -----------HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                       +++ S+LRLVV IA  Y   G+P  +++ EG +GL +A +KFDP++G+
Sbjct: 152 ESRLYQGRVAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAMGLNRATEKFDPDKGY 211

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWI+ A+   I      +++     +K     L +LK   + +     +    
Sbjct: 212 KFSTYAYWWIRQAITRAIANDARTIRLPIHIVEK-----LNKLKKAQRELKQKFARNPTE 266

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           V +A+ L ++  ++  +        SLN  +   +   ++  D L+ D D Q        
Sbjct: 267 VEMAEFLEMTVQQLRQLQQLRRQALSLNHRVGKEE--DTELMD-LLEDEDNQ------SP 317

Query: 220 ERKNRRNMLTRSM-----SVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQI 272
           E K   NM+ + +      VL PRE+ +   R       P TLE + + F +SRERVRQI
Sbjct: 318 EAKMNENMMRQEIWEVLGDVLTPREKDVISLRYGLTTSEPCTLEEVGNMFNLSRERVRQI 377

Query: 273 EARAFKKVQ 281
           +++A +K++
Sbjct: 378 QSKAMRKLR 386


>gi|153005080|ref|YP_001379405.1| RNA polymerase sigma-32 subunit RpoH [Anaeromyxobacter sp. Fw109-5]
 gi|152028653|gb|ABS26421.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter sp.
           Fw109-5]
          Length = 241

 Score = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 55/149 (36%), Positives = 85/149 (57%), Gaps = 6/149 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+  +R  P L + EE+ LA R R+ GD+ A  +LV  +L  VV IA   R   + +
Sbjct: 16  LAPYLKAVRDFPPLSRDEEHALALRARK-GDVRAKQKLVRHNLAFVVAIARKQRRGTVRL 74

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI--GTTANQK 133
            +++ EGN+GLM+AV+KFDP  G R +TY++WWI+A + +Y+  + S V+   GT A   
Sbjct: 75  DDLIQEGNVGLMRAVEKFDPHAGTRFSTYAVWWIRAYIGKYLKEARSTVRPQSGTVAQPD 134

Query: 134 RLFFNLRRLKG---HLQAITDNNLKPEQV 159
               +    +G   HL+ I D+   PE  
Sbjct: 135 LSLDSAIDEEGDATHLERIEDDGPGPEDT 163


>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 = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 121/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 442 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 501

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +  L+P+    +A+K+ +
Sbjct: 502 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGLEPDPAT-LAEKMEM 556

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + R+++
Sbjct: 557 PEDKIRKI-MKIAK-EPISMETPIGDDDDSHLGDFI---EDTNTVAPADAALHASMRDVV 611

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 612 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 666


>gi|4105839|gb|AAD02575.1| RNA polymerase sigma factor [Cyanidium caldarium]
          Length = 589

 Score = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 78/262 (29%), Positives = 136/262 (51%), Gaps = 18/262 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +R+V ++LRLV+  A  +R  G+   ++V EG+IGL++ V+K+D  RGFR +TY+ WW
Sbjct: 331 AKNRMVAANLRLVICFAKRFRNRGVAFQDLVQEGSIGLIRGVEKYDANRGFRFSTYASWW 390

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  + + +L    + ++    N+  +   +RR    L  I     +P ++  IA K+ +
Sbjct: 391 IRQGIHKALLECSKMFRLPVHVNE--MIKEIRRCSYELMNILGR--EPTKL-EIAMKVGM 445

Query: 169 SESEVISMNCRLAGDESLNALINSSDKN--SSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            E +VI +  R     SL   +  SD +  S    D +        +   +     + R 
Sbjct: 446 PEEKVIFLLQRAQTALSLEMPLRGSDSSLESRTLGDVVSSTASPSPE---DSAFGTSLRY 502

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVT--LENLSSEFEVSRERVRQIEARAFKKVQES- 283
            L R++S L+ RER +   R   ++  T  L  + S F V+RERVRQIE RA +K+++  
Sbjct: 503 DLERALSQLDFREREVIRMRFGLDDGRTKSLGEVGSLFCVTRERVRQIETRALRKLRDPR 562

Query: 284 ----IQKQVE-LSSSPPLLQKP 300
               +++ +E +S   P ++KP
Sbjct: 563 CNIFLKEYMEWISDERPGMKKP 584


>gi|142114|gb|AAA22047.1| RNA polymerase sigma-subunit [Nostoc sp. PCC 7120]
          Length = 416

 Score = 95.5 bits (236), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 65/238 (27%), Positives = 130/238 (54%), Gaps = 13/238 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L +   ++ ++LRLVV +A  Y+  GL + ++V EG +GL +AV+KFDP +G+R +TY+ 
Sbjct: 175 LQSKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAY 234

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   I  S   +++     +K     L ++K   + I     +   +  +A +L
Sbjct: 235 WWIRQGITRAIATSSRTIRLPVHITEK-----LNKIKKAQRKIAQEKGRTPTLEDLAIEL 289

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++ ++V  +  R+    SL   +   DK+ ++  + L  D    E++L+ +  +++ ++
Sbjct: 290 DMTPTQVREVLLRVPRSVSLETKVG-KDKD-TELGELLETDGVTPEEMLMRESLQRDLQH 347

Query: 227 MLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +L    + L  RER +   R      +P +L  +    ++SRERVRQIE++A +K+++
Sbjct: 348 LL----ADLTSRERDVILMRFGLADGHPYSLAEIGRALDLSRERVRQIESKALQKLRQ 401


>gi|302525743|ref|ZP_07278085.1| RNA polymerase sigma factor RpoS [Streptomyces sp. AA4]
 gi|302434638|gb|EFL06454.1| RNA polymerase sigma factor RpoS [Streptomyces sp. AA4]
          Length = 476

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 82/318 (25%), Positives = 150/318 (47%), Gaps = 43/318 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHG---- 45
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G    
Sbjct: 164 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYAAERVRTAEEEGEKLV 222

Query: 46  -----DLS--------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                DL         A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 223 TQMRRDLKWIVRDGERAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 282

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L      
Sbjct: 283 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGR 340

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE+   +AK++++S  +V+ +        SL+  I   D+  SQ  D++    D + 
Sbjct: 341 EPTPEE---LAKEMDISPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEA 392

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVR 270
            V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 393 VVAVDAVSFTLLQDQLQSVLQTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIR 452

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 453 QIESKTMSKLRHPSRSQV 470


>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 = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 73/256 (28%), Positives = 121/256 (47%), Gaps = 32/256 (12%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A  Y E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 374 AMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 433

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I    +       L R+   +         PE
Sbjct: 434 GYKFSTYATWWIRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQQFGREATPE 491

Query: 158 QVVAIAKKLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
           +   +AK++++ E ++          ISM   +  DE             S   D++   
Sbjct: 492 E---LAKEMDMPEDKIRKVMKIAKEPISMETPIGDDE------------DSHLGDFI--- 533

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVS 265
            D   +  I+     N    +   ++ L PRE ++   R  +  N   TLE +  +F+V+
Sbjct: 534 EDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVT 593

Query: 266 RERVRQIEARAFKKVQ 281
           RER+RQIEA+A +K++
Sbjct: 594 RERIRQIEAKALRKLR 609


>gi|120403451|ref|YP_953280.1| RNA polymerase sigma factor [Mycobacterium vanbaalenii PYR-1]
 gi|119956269|gb|ABM13274.1| RNA polymerase, sigma 70 subunit, RpoD family [Mycobacterium
           vanbaalenii PYR-1]
          Length = 478

 Score = 95.5 bits (236), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 81/318 (25%), Positives = 151/318 (47%), Gaps = 43/318 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGD-LS 48
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               + G+ L 
Sbjct: 166 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMAELADKGEKLP 224

Query: 49  AAHR----------------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           AA R                L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 225 AAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 284

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L      
Sbjct: 285 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGR 342

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D + 
Sbjct: 343 EPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEA 394

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVR 270
            V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 395 VVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIR 454

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 455 QIESKTMSKLRHPSRSQV 472


>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 = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 74/243 (30%), Positives = 118/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 376 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 435

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA------- 161
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 436 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREATPEELAVRMDMPED 493

Query: 162 -IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++  + DG E   I+   
Sbjct: 494 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI--EDDGAESP-IDTAT 537

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            +  R   T  +S L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 538 IEGLREATTSVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 597

Query: 279 KVQ 281
           K++
Sbjct: 598 KLR 600


>gi|85373960|ref|YP_458022.1| RNA polymerase sigma factor RpoD [Erythrobacter litoralis HTCC2594]
 gi|84787043|gb|ABC63225.1| RNA polymerase sigma-70 factor [Erythrobacter litoralis HTCC2594]
          Length = 675

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 72/239 (30%), Positives = 122/239 (51%), Gaps = 20/239 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 437 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 496

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+        R   H Q        PE+   +A+
Sbjct: 497 IRQAITRSIADQARTIRIPVHMIETINK---LVRTSRQFLHEQG---REPTPEE---MAE 547

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L++   +V  +  ++A  E ++      D+  S   D++    D    + ++   + N 
Sbjct: 548 RLSMPLEKVRKV-MKIA-KEPISLETPIGDEEDSHLGDFI---EDKNAIIPVDAAIQANL 602

Query: 225 RNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +  +TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 603 KETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 661


>gi|33864481|ref|NP_896041.1| putative type II alternative RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9313]
 gi|33641261|emb|CAE22391.1| Putative type II alternative RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9313]
          Length = 376

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 74/236 (31%), Positives = 117/236 (49%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +++ ++LRLVV +A  Y+  G+ + ++V EG +GL +AV+KFDP RGFR +TY+ WW
Sbjct: 136 AKDQMIQANLRLVVAVAKKYQQRGIELLDLVQEGTLGLERAVEKFDPTRGFRFSTYAYWW 195

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   I      +++     +K     L R+K   Q I  +  +   +  +AK L +
Sbjct: 196 IRQGITRAIATQSRTIRLPMHITEK-----LNRIKRVQQEIASSQGRLASIADLAKALGL 250

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SE  V     R+    SL   I    +  +Q  D L+ D +   +   EK  R    N L
Sbjct: 251 SEETVRLTLMRVPRSISLETRIGQ--EQDTQLGD-LLEDSNATPE---EKLTRNQLHNDL 304

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              +  L+ RE  +   R   E+  P TL  +     +SRERVRQIE  A  K+++
Sbjct: 305 EILLDELSNREATVIRRRFGLEDDTPQTLTQIGEAMHLSRERVRQIETHALLKLRQ 360


>gi|262276866|ref|ZP_06054659.1| RNA polymerase sigma factor RpoD [alpha proteobacterium HIMB114]
 gi|262223969|gb|EEY74428.1| RNA polymerase sigma factor RpoD [alpha proteobacterium HIMB114]
          Length = 613

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 69/239 (28%), Positives = 122/239 (51%), Gaps = 20/239 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 375 AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+      + R +  + +       PE+   ++K
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINK------IVRTQRQMMSEFGREPTPEE---LSK 485

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           KL +   +V  +  ++A  E ++      D+  S   D++    D    + ++   +   
Sbjct: 486 KLAMPLEKVRKV-LKIAK-EPVSLETPVGDEEDSTLGDFI---EDSNALIPVDAAVQTAL 540

Query: 225 RNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +N  T+ ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 541 KNTTTKVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 599


>gi|254455607|ref|ZP_05069036.1| RNA polymerase sigma factor [Candidatus Pelagibacter sp. HTCC7211]
 gi|207082609|gb|EDZ60035.1| RNA polymerase sigma factor [Candidatus Pelagibacter sp. HTCC7211]
          Length = 608

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 73/245 (29%), Positives = 119/245 (48%), Gaps = 32/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 370 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 429

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I            A+Q R      R+  H+   T N +   Q + +++    
Sbjct: 430 IRQAITRSI------------ADQARTI----RIPVHMIE-TINKIVRTQRLILSEFGRE 472

Query: 169 SESEVISMNCRLAGDESLNALINS----------SDKNSSQWQDWLVYDHDGQEQVLIEK 218
           +  E ++   R+  D+    L  S           D+  S   D++    D +    +E+
Sbjct: 473 ATPEELAQKLRMPLDKVRKVLKISKEPVSLEKPVGDEEDSSLGDFI---EDTKALAPLEQ 529

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARA 276
             + N     T+ +S L PRE R+   R         TLE +  +F V+RER+RQIEA+A
Sbjct: 530 AIKSNLGEATTKILSTLTPREERVLRMRFGVGMNTDHTLEEVGLQFSVTRERIRQIEAKA 589

Query: 277 FKKVQ 281
            +K++
Sbjct: 590 LRKLK 594


>gi|220907205|ref|YP_002482516.1| RNA polymerase sigma-70 subunit RpoD subfamily [Cyanothece sp. PCC
           7425]
 gi|219863816|gb|ACL44155.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7425]
          Length = 455

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 64/241 (26%), Positives = 121/241 (50%), Gaps = 23/241 (9%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV+KFDP +G+R +TY+ WW
Sbjct: 216 AKEHMIQANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTKGYRFSTYAYWW 275

Query: 109 IKAAMQEYILRSWSLVKIGTTANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           I+  +   I      +++     +     K+    + + KGH  +I D   + E  V   
Sbjct: 276 IRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGHTPSIEDIATELEMTVPQV 335

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           ++L V     +S+  ++  D              ++  D L  D    E++++    R++
Sbjct: 336 RELLVRVPRSVSLETKVGKD------------KDTELGDLLETDDLSPEEMMM----RES 379

Query: 224 RRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
               L + ++ L  RER +   R      +  +L ++    ++SRERVRQIEA+A +K++
Sbjct: 380 LHRELEKLLADLTSRERDVISMRFGLGDGHAYSLADIGRALDLSRERVRQIEAKALQKLR 439

Query: 282 E 282
           +
Sbjct: 440 Q 440


>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 = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 65/235 (27%), Positives = 121/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 567 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 626

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +   +P+    +A+K+++
Sbjct: 627 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGAEPDPAT-LAQKMDM 681

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + R+++
Sbjct: 682 PEDKIRKI-LKIA-KEPISMETPIGDDDDSHLGDFI---EDTSTLAPSDAALHGSMRDVV 736

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 737 KEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLR 791


>gi|68536164|ref|YP_250869.1| RNA polymerase sigma factor [Corynebacterium jeikeium K411]
 gi|68263763|emb|CAI37251.1| RNA polymerase sigma factor A [Corynebacterium jeikeium K411]
          Length = 544

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 83/318 (26%), Positives = 156/318 (49%), Gaps = 43/318 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR--------YR-----EHGD-LS 48
           RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR        YR     E G+ LS
Sbjct: 232 RKDAELTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYAAYRLQEIKESGEKLS 290

Query: 49  AAHR----------------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
             HR                L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 291 PMHRRDLREIDRDGRRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 350

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L      
Sbjct: 351 FDYVKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGR 408

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE+   +A++++++  +V+ +        SL+  I   D+  SQ  D++    D + 
Sbjct: 409 EPTPEE---LAREMDITVDKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEA 460

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVR 270
            V ++       ++ L   +  L+ RE  + + R  L +  P TL+ +   + V+RER+R
Sbjct: 461 VVAVDAVSFTLLQDQLQDVLHTLSEREAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERIR 520

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 521 QIESKTMSKLRHPSRSQV 538


>gi|17229184|ref|NP_485732.1| RNA polymerase sigma factor SigC [Nostoc sp. PCC 7120]
 gi|20141790|sp|Q03066|RPSC_ANASP RecName: Full=RNA polymerase sigma-C factor
 gi|17135512|dbj|BAB78058.1| RNA polymerase sigma-subunit [Nostoc sp. PCC 7120]
          Length = 416

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 65/238 (27%), Positives = 130/238 (54%), Gaps = 13/238 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L +   ++ ++LRLVV +A  Y+  GL + ++V EG +GL +AV+KFDP +G+R +TY+ 
Sbjct: 175 LQSKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAY 234

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   I  S   +++     +K     L ++K   + I     +   +  +A +L
Sbjct: 235 WWIRQGITRAIATSSRTIRLPVHITEK-----LNKIKKAQRKIAQEKGRTPTLEDLAIEL 289

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++ ++V  +  R+    SL   +   DK+ ++  + L  D    E++L+ +  +++ ++
Sbjct: 290 DMTPTQVREVLLRVPRSVSLETKVG-KDKD-TELGELLETDGVTPEEMLMRESLQRDLQH 347

Query: 227 MLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +L    + L  RER +   R      +P +L  +    ++SRERVRQIE++A +K+++
Sbjct: 348 LL----ADLTSRERDVILMRFGLADGHPYSLAEIGRALDLSRERVRQIESKALQKLRQ 401


>gi|260578861|ref|ZP_05846767.1| RNA polymerase principal sigma factor SigA [Corynebacterium
           jeikeium ATCC 43734]
 gi|258603008|gb|EEW16279.1| RNA polymerase principal sigma factor SigA [Corynebacterium
           jeikeium ATCC 43734]
          Length = 552

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 83/318 (26%), Positives = 156/318 (49%), Gaps = 43/318 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR--------YR-----EHGD-LS 48
           RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR        YR     E G+ LS
Sbjct: 240 RKDAELTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYAAYRLQEIKESGEKLS 298

Query: 49  AAHR----------------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
             HR                L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 299 PMHRRDLREIDRDGRRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 358

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L      
Sbjct: 359 FDYVKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGR 416

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE+   +A++++++  +V+ +        SL+  I   D+  SQ  D++    D + 
Sbjct: 417 EPTPEE---LAREMDITVDKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEA 468

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVR 270
            V ++       ++ L   +  L+ RE  + + R  L +  P TL+ +   + V+RER+R
Sbjct: 469 VVAVDAVSFTLLQDQLQDVLHTLSEREAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERIR 528

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 529 QIESKTMSKLRHPSRSQV 546


>gi|229491308|ref|ZP_04385134.1| RNA polymerase sigma factor RpoD [Rhodococcus erythropolis SK121]
 gi|229321847|gb|EEN87642.1| RNA polymerase sigma factor RpoD [Rhodococcus erythropolis SK121]
          Length = 430

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 81/318 (25%), Positives = 151/318 (47%), Gaps = 43/318 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGD-LS 48
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               + G+ L 
Sbjct: 118 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYAVQIMQDLADKGEKLP 176

Query: 49  AAHR----------------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           AA R                L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 177 AAQRRDMSWICRDGNRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 236

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L      
Sbjct: 237 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGR 294

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D + 
Sbjct: 295 EPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEA 346

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVR 270
            V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 347 VVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIR 406

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 407 QIESKTMSKLRHPSRSQV 424


>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|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 = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 73/256 (28%), Positives = 121/256 (47%), Gaps = 32/256 (12%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A  Y E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 374 AMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 433

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I    +       L R+   +         PE
Sbjct: 434 GYKFSTYATWWIRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQQFGREATPE 491

Query: 158 QVVAIAKKLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
           +   +AK++++ E ++          ISM   +  DE             S   D++   
Sbjct: 492 E---LAKEMDMPEDKIRKVMKIAKEPISMETPIGDDE------------DSHLGDFI--- 533

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVS 265
            D   +  I+     N    +   ++ L PRE ++   R  +  N   TLE +  +F+V+
Sbjct: 534 EDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVT 593

Query: 266 RERVRQIEARAFKKVQ 281
           RER+RQIEA+A +K++
Sbjct: 594 RERIRQIEAKALRKLR 609


>gi|330444010|ref|YP_004376996.1| RNA polymerase sigma factor, sigma-70 family [Chlamydophila pecorum
           E58]
 gi|328807120|gb|AEB41293.1| RNA polymerase sigma factor, sigma-70 family [Chlamydophila pecorum
           E58]
          Length = 562

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 77/247 (31%), Positives = 118/247 (47%), Gaps = 28/247 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+  RG++ +TY+ WW
Sbjct: 307 AKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWW 366

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+      + R    L   T     PE+   +A+
Sbjct: 367 IRQAVTRAIADQARTIRIPVHMIETINK------VLRGAKKLMMETGKEPSPEE---LAE 417

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L ++   V  +        SL A +       S + D+L       E   +E       
Sbjct: 418 ELGLTPDRVREIYKIAQHPISLQAEVGEG--GESAFGDFL-------EDTAVESPAEATG 468

Query: 225 RNMLTRSM----SVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
            +ML   M      L  RER +   R   L   P TLE + S F V+RER+RQIEA+A +
Sbjct: 469 YSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGKPKTLEEVGSAFNVTRERIRQIEAKALR 528

Query: 279 KVQESIQ 285
           K++  I+
Sbjct: 529 KMRHPIR 535


>gi|148553355|ref|YP_001260937.1| RNA polymerase sigma factor RpoD [Sphingomonas wittichii RW1]
 gi|148498545|gb|ABQ66799.1| RNA polymerase, sigma 70 subunit, RpoD [Sphingomonas wittichii RW1]
          Length = 674

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 69/235 (29%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 436 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 495

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A++L++
Sbjct: 496 IRQAITRSIADQARTIRI--PVHMIETINKLVRTSRQILHEIGREPTPEE---LAERLSM 550

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + ++   + N +  +
Sbjct: 551 PLEKVRKV-MKIA-KEPISLETPIGDEEDSHLGDFI---EDKNAIIPVDAAIQSNLKETV 605

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 606 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 660


>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 = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 73/256 (28%), Positives = 121/256 (47%), Gaps = 32/256 (12%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A  Y E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 374 AMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 433

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I    +       L R+   +         PE
Sbjct: 434 GYKFSTYATWWIRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQQFGREATPE 491

Query: 158 QVVAIAKKLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
           +   +AK++++ E ++          ISM   +  DE             S   D++   
Sbjct: 492 E---LAKEMDMPEDKIRKVMKIAKEPISMETPIGDDE------------DSHLGDFI--- 533

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVS 265
            D   +  I+     N    +   ++ L PRE ++   R  +  N   TLE +  +F+V+
Sbjct: 534 EDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVT 593

Query: 266 RERVRQIEARAFKKVQ 281
           RER+RQIEA+A +K++
Sbjct: 594 RERIRQIEAKALRKLR 609


>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 = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 65/235 (27%), Positives = 121/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 487 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 546

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +   +P+    +A+K+++
Sbjct: 547 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGAEPDPAT-LAQKMDM 601

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + R+++
Sbjct: 602 PEDKIRKI-LKIA-KEPISMETPIGDDDDSHLGDFI---EDTSTLAPSDAALHGSMRDVV 656

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 657 KEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLR 711


>gi|300784507|ref|YP_003764798.1| RNA polymerase primary sigma factor [Amycolatopsis mediterranei
           U32]
 gi|299794021|gb|ADJ44396.1| RNA polymerase primary sigma factor [Amycolatopsis mediterranei
           U32]
          Length = 467

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 82/318 (25%), Positives = 150/318 (47%), Gaps = 43/318 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHG---- 45
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G    
Sbjct: 155 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYAAERVRTAEEEGEKLV 213

Query: 46  -----DLS--------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                DL         A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 214 TQMRRDLKWIVRDGERAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 273

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L      
Sbjct: 274 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGR 331

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE+   +AK++++S  +V+ +        SL+  I   D+  SQ  D++    D + 
Sbjct: 332 EPTPEE---LAKEMDISPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEA 383

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVR 270
            V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 384 VVAVDAVSFTLLQDQLQSVLQTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIR 443

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 444 QIESKTMSKLRHPSRSQV 461


>gi|209965297|ref|YP_002298212.1| RNA polymerase sigma factor RpoD [Rhodospirillum centenum SW]
 gi|209958763|gb|ACI99399.1| DNA-directed RNA polymerase, sigma subunit RpoD [Rhodospirillum
           centenum SW]
          Length = 648

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 114/243 (46%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 410 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 469

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R    +         PE++         
Sbjct: 470 IRQAITRSIADQARTIRI--PVHMIETINKLVRTSRQMLHEIGREPTPEELAERLMMPLE 527

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + K L +++ E IS+   +  +E  +      DKN+    D  +               
Sbjct: 528 KVRKVLKIAK-EPISLETPIGDEEDSHLGDFIEDKNAVLPLDAAI--------------- 571

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           + N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +
Sbjct: 572 QANLRETTTRILATLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALR 631

Query: 279 KVQ 281
           K++
Sbjct: 632 KLK 634


>gi|183982025|ref|YP_001850316.1| RNA polymerase sigma factor SigA [Mycobacterium marinum M]
 gi|183175351|gb|ACC40461.1| RNA polymerase sigma factor SigA [Mycobacterium marinum M]
          Length = 501

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 81/318 (25%), Positives = 151/318 (47%), Gaps = 43/318 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGD-LS 48
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               + G+ L 
Sbjct: 189 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMAELTDRGEKLP 247

Query: 49  AAHR----------------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           AA R                L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 248 AAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 307

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L      
Sbjct: 308 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGR 365

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D + 
Sbjct: 366 EPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEA 417

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVR 270
            V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 418 VVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIR 477

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 478 QIESKTMSKLRHPSRSQV 495


>gi|85708548|ref|ZP_01039614.1| RNA polymerase sigma factor [Erythrobacter sp. NAP1]
 gi|85690082|gb|EAQ30085.1| RNA polymerase sigma factor [Erythrobacter sp. NAP1]
          Length = 674

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 116/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 436 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 495

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA------- 161
           I+ A+   I      ++I    +       L R              PE++ A       
Sbjct: 496 IRQAITRSIADQARTIRI--PVHMIETINKLVRTSRQFLHEEGREPTPEEMAARLSMPLE 553

Query: 162 -IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + K + +++ E IS+   +             D+  S   D++    D    + ++   
Sbjct: 554 KVRKVMKIAK-EPISLETPIG------------DEEDSHLGDFI---EDKNAVIPVDAAI 597

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           + N +  +TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +
Sbjct: 598 QANLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALR 657

Query: 279 KVQ 281
           K++
Sbjct: 658 KLK 660


>gi|297559739|ref|YP_003678713.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
 gi|296844187|gb|ADH66207.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
          Length = 364

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 86/297 (28%), Positives = 136/297 (45%), Gaps = 54/297 (18%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREHG----------DLS--------AAHRLVT 55
           Y+ EI ++P+L  ++E  LAK      Y +H           +L+        A   L+ 
Sbjct: 73  YLREIGRVPLLSAEQEVELAKAVEVGLYAQHCAPVEGVRTAEELACLVEEGRRAKRSLIE 132

Query: 56  SHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQE 115
           ++LRLVV IA  Y G GL + ++V EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+  
Sbjct: 133 ANLRLVVSIAKRYMGRGLLLLDLVQEGNLGLIRAVEKFDYGKGFKFSTYATWWIRQAITR 192

Query: 116 YILRSWSLVKIGT----TAN-----QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            I      ++I      T N     Q +L   L R     +  +      ++VV I +  
Sbjct: 193 AIADQARTIRIPVHMVETINKVVRVQHQLHQQLGREPSVEEISSAAGFVGQRVVEIQRIA 252

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
                E +S+   +  +ES                D+  +  D      +E       + 
Sbjct: 253 R----EPVSLQSPIGEEES----------------DFGDFIEDSDAVAPVEAAAFTVLQE 292

Query: 227 MLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L   +  L+ RERRI   R      +P TLE +  EF V+RER+RQIEA+   K++
Sbjct: 293 QLGAILGGLSDRERRIIRLRFGMADGHPHTLEEVGREFGVTRERIRQIEAKTLAKLR 349


>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 = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 72/243 (29%), Positives = 117/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 438 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 495

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   Q+ ++   
Sbjct: 496 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLQLPMDAAT 539

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             N R      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 540 ATNLRAATNDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 279 KVQ 281
           K++
Sbjct: 600 KLR 602


>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 = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 65/235 (27%), Positives = 121/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 531 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 590

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +   +P+    +A+K+++
Sbjct: 591 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGAEPDPAT-LAQKMDM 645

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + R+++
Sbjct: 646 PEDKIRKI-LKIA-KEPISMETPIGDDDDSHLGDFI---EDTSTLAPSDAALHGSMRDVV 700

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 701 KEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLR 755


>gi|157164653|ref|YP_001467098.1| RNA polymerase sigma factor RpoD [Campylobacter concisus 13826]
 gi|112799942|gb|EAT97286.1| RNA polymerase sigma factor RpoD (Sigma-A) (Major vegetative
           sigmafactor) [Campylobacter concisus 13826]
          Length = 617

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 73/237 (30%), Positives = 124/237 (52%), Gaps = 15/237 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+  +G++ +TY+ WW
Sbjct: 378 AKARMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYRKGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL-KGHLQAITDNNLKPEQVVAIAKKLN 167
           I+ A+   I      ++I        +   + R+ K + + + +   +P+ V  IAK++ 
Sbjct: 438 IRQAISRAIADQARTIRIPI-----HMIETINRINKINRKYLQEEGKEPD-VSVIAKEVG 491

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V  +        SL A I  +++   ++ D++    D      I++  + + R  
Sbjct: 492 LSVDKVKQVIKITKEPISLEAPI--ANEEDGKFGDFV---EDKTSLSPIDQILKSDLREQ 546

Query: 228 LTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +S LN RE+ +   R      E+  TLE +     V+RERVRQIE+ A KK++
Sbjct: 547 IDDVLSQLNEREKAVISMRFGLLEDESDRTLEEIGKALNVTRERVRQIESSAIKKLK 603


>gi|90580773|ref|ZP_01236576.1| RNA polymerase sigma factor [Vibrio angustum S14]
 gi|90438041|gb|EAS63229.1| RNA polymerase sigma factor [Vibrio angustum S14]
          Length = 616

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 72/243 (29%), Positives = 117/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 438 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 495

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   Q+ ++   
Sbjct: 496 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLQLPMDAAT 539

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             N R      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 540 ATNLRAATNDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 279 KVQ 281
           K++
Sbjct: 600 KLR 602


>gi|114570679|ref|YP_757359.1| RNA polymerase sigma factor RpoD [Maricaulis maris MCS10]
 gi|114341141|gb|ABI66421.1| RNA polymerase, sigma 70 subunit, RpoD [Maricaulis maris MCS10]
          Length = 710

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 71/235 (30%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 472 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 531

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 532 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 586

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 587 PLEKVRKV-MKIA-KEPISLETPIGDEEDSHLGDFI---EDKNAVLPIDAAIQANLRETT 641

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 642 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 696


>gi|154173683|ref|YP_001408074.1| RNA polymerase sigma factor RpoD [Campylobacter curvus 525.92]
 gi|112802903|gb|EAU00247.1| RNA polymerase sigma factor RpoD (Sigma-A) (Major vegetative
           sigmafactor) [Campylobacter curvus 525.92]
          Length = 614

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 74/237 (31%), Positives = 124/237 (52%), Gaps = 15/237 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+  +G++ +TY+ WW
Sbjct: 375 AKARMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYRKGYKFSTYATWW 434

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL-KGHLQAITDNNLKPEQVVAIAKKLN 167
           I+ A+   I      ++I        +   + R+ K + + + +   +P+ V  IAK++ 
Sbjct: 435 IRQAISRAIADQARTIRIPI-----HMIETINRINKINRKYLQEEGKEPD-VSVIAKEVG 488

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V  +        SL A I  +++   ++ D++    D      IE+  + + R  
Sbjct: 489 LSVDKVKQVIKITKEPISLEAPI--ANEEDGKFGDFV---EDKSSLSPIEQILKGDLREQ 543

Query: 228 LTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +S LN RE+ +   R      E+  TLE +     V+RERVRQIE+ A KK++
Sbjct: 544 IDDVLSQLNDREKAVICMRFGLLEDESDRTLEEIGKALNVTRERVRQIESSAIKKLK 600


>gi|58580221|ref|YP_199237.1| RNA polymerase sigma factor RpoD [Xanthomonas oryzae pv. oryzae
           KACC10331]
 gi|58424815|gb|AAW73852.1| RNA polymerase sigma-70 factor [Xanthomonas oryzae pv. oryzae
           KACC10331]
          Length = 629

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 73/256 (28%), Positives = 121/256 (47%), Gaps = 32/256 (12%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A  Y E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 379 AMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 438

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I    +       L R+   +         PE
Sbjct: 439 GYKFSTYATWWIRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQQFGREATPE 496

Query: 158 QVVAIAKKLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
           +   +AK++++ E ++          ISM   +  DE             S   D++   
Sbjct: 497 E---LAKEMDMPEDKIRKVMKIAKEPISMETPIGDDE------------DSHLGDFI--- 538

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVS 265
            D   +  I+     N    +   ++ L PRE ++   R  +  N   TLE +  +F+V+
Sbjct: 539 EDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVT 598

Query: 266 RERVRQIEARAFKKVQ 281
           RER+RQIEA+A +K++
Sbjct: 599 RERIRQIEAKALRKLR 614


>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 = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 65/235 (27%), Positives = 121/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 511 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 570

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +   +P+    +A+K+++
Sbjct: 571 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGAEPDPAT-LAQKMDM 625

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + R+++
Sbjct: 626 PEDKIRKI-LKIA-KEPISMETPIGDDDDSHLGDFI---EDTSTLAPSDAALHGSMRDVV 680

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 681 KEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLR 735


>gi|304391338|ref|ZP_07373282.1| RNA polymerase sigma factor RpoD [Ahrensia sp. R2A130]
 gi|303296694|gb|EFL91050.1| RNA polymerase sigma factor RpoD [Ahrensia sp. R2A130]
          Length = 692

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 73/239 (30%), Positives = 116/239 (48%), Gaps = 20/239 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 454 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 513

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+      +R  +  L  I       E    +A 
Sbjct: 514 IRQAITRSIADQARTIRIPVHMIETINKI-----VRTSRQMLHEIGREPTPEELSTKLAM 568

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            L     E +    ++A  E ++      D+  S   D++    D    + I+   + N 
Sbjct: 569 PL-----EKVRKVLKIA-KEPISLETPIGDEEDSHLGDFI---EDKNAILPIDAAIQSNL 619

Query: 225 RNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 620 RETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 678


>gi|297622151|ref|YP_003710288.1| RNA polymerase sigma factor rpoD [Waddlia chondrophila WSU 86-1044]
 gi|297377452|gb|ADI39282.1| RNA polymerase sigma factor rpoD [Waddlia chondrophila WSU 86-1044]
          Length = 555

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 73/236 (30%), Positives = 116/236 (49%), Gaps = 14/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+  RG++ +TY+ WW
Sbjct: 313 AKREMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWW 372

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    L   T     PE+   +A +L +
Sbjct: 373 IRQAVTRAIADQARTIRI--PVHMIETINKVLRGAKKLMMETGREPTPEE---LANELGL 427

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S   +  +        SL A +   D   SQ+ D+L    D       E       ++ +
Sbjct: 428 SAERIREIYKIAQHPISLQAEV--GDGGESQFGDFL---EDTGADSPAEATGYSILKDKM 482

Query: 229 TRSMSVLNPRERRIFEARRLQEN---PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L  RER++   +R   N   P TLE +  EF V+RER+RQIEA+A +K++
Sbjct: 483 NEVLLTLTDRERKVL-IQRFGLNDGKPKTLEEVGVEFNVTRERIRQIEAKALRKMR 537


>gi|255325126|ref|ZP_05366232.1| RNA polymerase major sigma subunit [Corynebacterium
           tuberculostearicum SK141]
 gi|311739588|ref|ZP_07713423.1| RNA polymerase sigma factor rpoD [Corynebacterium pseudogenitalium
           ATCC 33035]
 gi|255297691|gb|EET77002.1| RNA polymerase major sigma subunit [Corynebacterium
           tuberculostearicum SK141]
 gi|311305404|gb|EFQ81472.1| RNA polymerase sigma factor rpoD [Corynebacterium pseudogenitalium
           ATCC 33035]
          Length = 490

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 80/324 (24%), Positives = 156/324 (48%), Gaps = 49/324 (15%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREH-----------GD 46
           RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR     Y +H           GD
Sbjct: 172 RKDAQLTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYAQHRMDEMEKARAEGD 230

Query: 47  LSAA--------------------HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
            +A                     + L+ ++LRLVV +A  Y G G+   +++ EGN+GL
Sbjct: 231 KAAKLSPMEKRDLRSIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGL 290

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L
Sbjct: 291 IRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQREL 348

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    P++   +AK+++++E +V+ +        SL+  I   D+  SQ  D++  
Sbjct: 349 LQDLGREPTPQE---LAKEMDITEEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI-- 401

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEV 264
             D +  + ++       ++ L   ++ L+ RE  +   R  L +  P TL+ +   + V
Sbjct: 402 -EDSEAVIAVDAVSFTLLQDQLQDVLTTLSEREAGVVRLRFGLTDGMPRTLDEIGQVYGV 460

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           +RER+RQIE++   K++   + QV
Sbjct: 461 TRERIRQIESKTMSKLRHPSRSQV 484


>gi|93005952|ref|YP_580389.1| sigma 70 (RpoD) [Psychrobacter cryohalolentis K5]
 gi|92393630|gb|ABE74905.1| sigma 70 (RpoD) [Psychrobacter cryohalolentis K5]
          Length = 648

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 68/235 (28%), Positives = 117/235 (49%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 409 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 468

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+   L         PE+   + ++L +
Sbjct: 469 IRQAITRSIADQARTIRI--PVHMIETINKINRVSRQLLQEMGREPTPEE---LGERLEM 523

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E++V  +  ++A  E ++      D   S   D++    DG     ++       R   
Sbjct: 524 DEAKVRKV-LKIAK-EPISMETPIGDDEDSHLGDFI---EDGTISSPVDDATAAGLREAT 578

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L  RE R+ + R   + P   TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 579 RDVLGNLTEREARVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 633


>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 = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 80/285 (28%), Positives = 142/285 (49%), Gaps = 26/285 (9%)

Query: 11  NGEIGLSRYIHEIR----KIPMLEKQEEYVLAKRYRE------HGDLSA---AHRLVTSH 57
            G   L+ Y+ +IR     +  LE+Q    +A+  RE      +G+L A      +V ++
Sbjct: 333 GGAPKLANYVEKIRINIVNLQNLEQQSGLTIAQ-IREIGGRIANGELKARRAKKEMVEAN 391

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I
Sbjct: 392 LRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSI 451

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
                 ++I    +       L R+             PE+   +A+++N+ E ++  + 
Sbjct: 452 ADQARTIRI--PVHMIETINKLNRISRQCLQEMGREATPEE---LAERMNMPEDKIRKV- 505

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
            ++A  E ++      D + S   D++    D   ++ ++    ++ R      +  L P
Sbjct: 506 LKIAK-EPISMETPIGDDDDSHLGDFI---QDESLELPLDSATAESLRIATNEVLEGLTP 561

Query: 238 RERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
           RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 562 REAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 606


>gi|118618666|ref|YP_906998.1| RNA polymerase sigma factor [Mycobacterium ulcerans Agy99]
 gi|118570776|gb|ABL05527.1| RNA polymerase sigma factor SigA [Mycobacterium ulcerans Agy99]
          Length = 501

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 81/318 (25%), Positives = 151/318 (47%), Gaps = 43/318 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGD-LS 48
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               + G+ L 
Sbjct: 189 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMAELTDRGEKLP 247

Query: 49  AAHR----------------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           AA R                L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 248 AAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 307

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L      
Sbjct: 308 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGR 365

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D + 
Sbjct: 366 EPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEA 417

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVR 270
            V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 418 VVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIR 477

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 478 QIESKTMSKLRHPSRSQV 495


>gi|289667862|ref|ZP_06488937.1| RNA polymerase sigma factor RpoD [Xanthomonas campestris pv.
           musacearum NCPPB4381]
          Length = 624

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 73/256 (28%), Positives = 121/256 (47%), Gaps = 32/256 (12%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A  Y E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 374 AMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 433

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I    +       L R+   +         PE
Sbjct: 434 GYKFSTYATWWIRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQQFGREATPE 491

Query: 158 QVVAIAKKLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
           +   +AK++++ E ++          ISM   +  DE             S   D++   
Sbjct: 492 E---LAKEMDMPEDKIRKVMKIAKEPISMETPIGDDE------------DSHLGDFI--- 533

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVS 265
            D   +  I+     N    +   ++ L PRE ++   R  +  N   TLE +  +F+V+
Sbjct: 534 EDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVT 593

Query: 266 RERVRQIEARAFKKVQ 281
           RER+RQIEA+A +K++
Sbjct: 594 RERIRQIEAKALRKLR 609


>gi|289664793|ref|ZP_06486374.1| RNA polymerase sigma factor RpoD [Xanthomonas campestris pv.
           vasculorum NCPPB702]
          Length = 624

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 73/256 (28%), Positives = 121/256 (47%), Gaps = 32/256 (12%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A  Y E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 374 AMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 433

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I    +       L R+   +         PE
Sbjct: 434 GYKFSTYATWWIRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQQFGREATPE 491

Query: 158 QVVAIAKKLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
           +   +AK++++ E ++          ISM   +  DE             S   D++   
Sbjct: 492 E---LAKEMDMPEDKIRKVMKIAKEPISMETPIGDDE------------DSHLGDFI--- 533

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVS 265
            D   +  I+     N    +   ++ L PRE ++   R  +  N   TLE +  +F+V+
Sbjct: 534 EDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVT 593

Query: 266 RERVRQIEARAFKKVQ 281
           RER+RQIEA+A +K++
Sbjct: 594 RERIRQIEAKALRKLR 609


>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 = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 71/236 (30%), Positives = 121/236 (51%), Gaps = 14/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 433 AKTEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 492

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A++L++
Sbjct: 493 IRQAITRSIADQARTIRI--PVHMIETINKLVRTSRQILHEIGREPTPEE---LAERLSM 547

Query: 169 SESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
              +V  +  ++A +  SL   I   D+  S   D++    D    + ++   + N +  
Sbjct: 548 PLEKVRKV-MKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAIIPVDAAIQANLKET 601

Query: 228 LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 602 VTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 657


>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 = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 72/243 (29%), Positives = 117/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 438 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 495

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   Q+ ++   
Sbjct: 496 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLQLPMDAAT 539

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             N R      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 540 ATNLRAATNDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 279 KVQ 281
           K++
Sbjct: 600 KLR 602


>gi|166713725|ref|ZP_02244932.1| RNA polymerase sigma factor RpoD [Xanthomonas oryzae pv. oryzicola
           BLS256]
          Length = 624

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 73/256 (28%), Positives = 121/256 (47%), Gaps = 32/256 (12%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A  Y E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 374 AMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 433

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I    +       L R+   +         PE
Sbjct: 434 GYKFSTYATWWIRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQQFGREATPE 491

Query: 158 QVVAIAKKLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
           +   +AK++++ E ++          ISM   +  DE             S   D++   
Sbjct: 492 E---LAKEMDMPEDKIRKVMKIAKEPISMETPIGDDE------------DSHLGDFI--- 533

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVS 265
            D   +  I+     N    +   ++ L PRE ++   R  +  N   TLE +  +F+V+
Sbjct: 534 EDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVT 593

Query: 266 RERVRQIEARAFKKVQ 281
           RER+RQIEA+A +K++
Sbjct: 594 RERIRQIEAKALRKLR 609


>gi|257469126|ref|ZP_05633220.1| RpoD family RNA polymerase sigma factor [Fusobacterium ulcerans
           ATCC 49185]
          Length = 116

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 45/103 (43%), Positives = 72/103 (69%), Gaps = 1/103 (0%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +S Y+ +IRK  +L+K EE  L  + +  GD  A ++L+ S+LRLVV IA GY   GL  
Sbjct: 7   ISLYLADIRKYKILDKDEELNLLIKAK-AGDEEAKNQLILSNLRLVVNIAKGYINKGLSF 65

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
            +++SEGN+GL+ A++KFD  +GFR +TY++WWIK ++ + ++
Sbjct: 66  IDLISEGNLGLIYAIEKFDITKGFRFSTYAVWWIKQSISKAVI 108


>gi|324997280|ref|ZP_08118392.1| RNA polymerase sigma factor [Pseudonocardia sp. P1]
          Length = 469

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 79/318 (24%), Positives = 151/318 (47%), Gaps = 43/318 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR--------------YREHGDLS 48
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR              +  +  LS
Sbjct: 157 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYGAERIRKLFESNDKLS 215

Query: 49  ----------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 216 PQMRRDLRWIVRDGERAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 275

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L      
Sbjct: 276 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGR 333

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D + 
Sbjct: 334 EPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEA 385

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVR 270
            V ++       ++ L   ++ L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 386 VVAVDAVSFTLLQDQLQSVLATLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIR 445

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 446 QIESKTMSKLRHPSRSQV 463


>gi|218528655|ref|YP_002419471.1| RNA polymerase sigma factor RpoD [Methylobacterium chloromethanicum
           CM4]
 gi|240137186|ref|YP_002961655.1| sigma D (sigma 70) factor of RNA polymerase [Methylobacterium
           extorquens AM1]
 gi|218520958|gb|ACK81543.1| RNA polymerase, sigma 70 subunit, RpoD [Methylobacterium
           chloromethanicum CM4]
 gi|240007152|gb|ACS38378.1| sigma D (sigma 70) factor of RNA polymerase [Methylobacterium
           extorquens AM1]
          Length = 666

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 428 AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 487

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 488 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 542

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 543 PLEKVRKV-LKIA-KEPISLETPIGDEEDSHLGDFI---EDKNVVLPIDAAIQSNLRETT 597

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 598 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 652


>gi|317063372|ref|ZP_07927857.1| RNA polymerase [Fusobacterium ulcerans ATCC 49185]
 gi|313689048|gb|EFS25883.1| RNA polymerase [Fusobacterium ulcerans ATCC 49185]
          Length = 118

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 45/103 (43%), Positives = 72/103 (69%), Gaps = 1/103 (0%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +S Y+ +IRK  +L+K EE  L  + +  GD  A ++L+ S+LRLVV IA GY   GL  
Sbjct: 9   ISLYLADIRKYKILDKDEELNLLIKAK-AGDEEAKNQLILSNLRLVVNIAKGYINKGLSF 67

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
            +++SEGN+GL+ A++KFD  +GFR +TY++WWIK ++ + ++
Sbjct: 68  IDLISEGNLGLIYAIEKFDITKGFRFSTYAVWWIKQSISKAVI 110


>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 = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 73/242 (30%), Positives = 112/242 (46%), Gaps = 28/242 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RGF+ +TY+ WW
Sbjct: 379 AKEEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGFKFSTYATWW 438

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   L         PE++         
Sbjct: 439 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRTLVQKNGREPTPEELAEAMDMPEE 496

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L ++  E ISM   +  DE             S   D++    D      +E   
Sbjct: 497 KIRKVLKIA-KEPISMETPIGDDE------------DSHLGDFI---EDSNVMSPLEAAT 540

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            +         ++ L PRE R+   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 541 TRGLSEATNEVLASLTPREERVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKALR 600

Query: 279 KV 280
           K+
Sbjct: 601 KL 602


>gi|56552519|ref|YP_163358.1| RNA polymerase sigma factor RpoD [Zymomonas mobilis subsp. mobilis
           ZM4]
 gi|241762241|ref|ZP_04760323.1| 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|241373288|gb|EER62907.1| RNA polymerase, sigma 70 subunit, RpoD [Zymomonas mobilis subsp.
           mobilis ATCC 10988]
          Length = 671

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 69/235 (29%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 433 AKTEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 492

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A++L++
Sbjct: 493 IRQAITRSIADQARTIRI--PVHMIETINKLVRTSRQILHEIGREPTPEE---LAERLSM 547

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + ++   + N +  +
Sbjct: 548 PLEKVRKV-MKIA-KEPISLETPIGDEEDSHLGDFI---EDKNAIIPVDAAIQANLKETV 602

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 603 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 657


>gi|288920765|ref|ZP_06415065.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EUN1f]
 gi|288347841|gb|EFC82118.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EUN1f]
          Length = 425

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 87/294 (29%), Positives = 137/294 (46%), Gaps = 60/294 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREHG-------------DL--------SAAHR 52
           Y+ EI K+P+L   +E  L+KR     + EH              DL        +A  +
Sbjct: 132 YLREIGKVPLLNAAQEVELSKRVEAGLFAEHKLETDEGLAEDLRRDLGLLVTDGQAAKQQ 191

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV+++LRLVV +A  Y G G+ + ++V EGN+GL++AV+KFD  +G++ +TY+ WWI+ A
Sbjct: 192 LVSANLRLVVSVAKKYSGRGMTLLDLVQEGNLGLIRAVEKFDYAKGYKFSTYATWWIRQA 251

Query: 113 MQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           +   +      ++I           T  Q++L   L R     +   + ++  EQVV   
Sbjct: 252 IGRALADQARTIRIPVHVVEQINKITRLQRQLVSTLGREPTDEELAFELDMPIEQVV--- 308

Query: 164 KKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
            +L     + +S+   +   GD  L   I  SD  S    D   Y   G  Q  I+    
Sbjct: 309 -ELRRYAQDTVSLETSVGDDGDSVLGDFIEDSDATSP--ADAASY---GAMQDEID---- 358

Query: 222 KNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIE 273
               N+L      LNPRER +   R  L +    TL  + +   ++RER+RQIE
Sbjct: 359 ----NVL----GALNPREREVMRLRFGLADGKQHTLAEVGNRLGLTRERIRQIE 404


>gi|254559198|ref|YP_003066293.1| sigma D factor of RNA polymerase [Methylobacterium extorquens DM4]
 gi|254266476|emb|CAX22240.1| sigma D (sigma 70) factor of RNA polymerase [Methylobacterium
           extorquens DM4]
          Length = 666

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 428 AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 487

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 488 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 542

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 543 PLEKVRKV-LKIA-KEPISLETPIGDEEDSHLGDFI---EDKNVVLPIDAAIQSNLRETT 597

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 598 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 652


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

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 65/235 (27%), Positives = 121/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 494 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 553

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +   +P+    +A+K+++
Sbjct: 554 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGAEPDPAT-LAQKMDM 608

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + R+++
Sbjct: 609 PEDKIRKI-LKIAK-EPISMETPIGDDDDSHLGDFI---EDTATLAPSDAALHGSMRDVV 663

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 664 KEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLR 718


>gi|118581452|ref|YP_902702.1| RpoD family RNA polymerase sigma factor [Pelobacter propionicus DSM
           2379]
 gi|118504162|gb|ABL00645.1| RNA polymerase, sigma 70 subunit, RpoD [Pelobacter propionicus DSM
           2379]
          Length = 582

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 71/239 (29%), Positives = 124/239 (51%), Gaps = 20/239 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ WW
Sbjct: 345 AKSELIEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWW 404

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N        + ++   Q + +N  +P     IA+
Sbjct: 405 IRQAITRAIADQARTIRIPVHMIETIN--------KLIRTSRQLVQENGREPAP-EEIAE 455

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           ++ +   +V  +  ++A  E ++      ++  S   D++    D      IE   + N 
Sbjct: 456 RMQLPLDKVRKV-LKIA-KEPISLETPIGEEEDSHLGDFI---EDKAVISPIEAVIKANL 510

Query: 225 RNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
               +R +S L PRE ++   R    +++  TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 511 SEQTSRVLSTLTPREEKVLRMRFGIGEKSDHTLEEVGQDFAVTRERIRQIEAKALRKLR 569


>gi|188579854|ref|YP_001923299.1| RNA polymerase sigma factor RpoD [Methylobacterium populi BJ001]
 gi|179343352|gb|ACB78764.1| RNA polymerase, sigma 70 subunit, RpoD [Methylobacterium populi
           BJ001]
          Length = 667

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 429 AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 488

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 489 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 543

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 544 PLEKVRKV-LKIA-KEPISLETPIGDEEDSHLGDFI---EDKNVVLPIDAAIQSNLRETT 598

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 599 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 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 = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 427 AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 486

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 487 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 541

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 542 PLEKVRKV-LKIA-KEPISLETPIGDEEDSHLGDFI---EDKNVVLPIDAAIQSNLRETT 596

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 597 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 651


>gi|227504950|ref|ZP_03934999.1| RNA polymerase major sigma subunit [Corynebacterium striatum ATCC
           6940]
 gi|227198459|gb|EEI78507.1| RNA polymerase major sigma subunit [Corynebacterium striatum ATCC
           6940]
          Length = 465

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 80/324 (24%), Positives = 156/324 (48%), Gaps = 49/324 (15%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY----------------REHGD 46
           RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR                 R  GD
Sbjct: 147 RKDAQLTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYAQYRMDEMEKARAEGD 205

Query: 47  LSAA--------------------HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
            +A                     + L+ ++LRLVV +A  Y G G+   +++ EGN+GL
Sbjct: 206 KAAKLSPMEKRDLRSIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGL 265

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L
Sbjct: 266 IRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQREL 323

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
             + D   +P   + +AK+++++E +V+ +        SL+  I   D+  SQ  D++  
Sbjct: 324 --LQDLGREPTP-IELAKEMDITEEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI-- 376

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEV 264
             D +  + ++       ++ L   ++ L+ RE  +   R  L +  P TL+ +   + V
Sbjct: 377 -EDSEAVIAVDAVSFTLLQDQLQDVLTTLSEREAGVVRLRFGLTDGMPRTLDEIGQVYGV 435

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           +RER+RQIE++   K++   + QV
Sbjct: 436 TRERIRQIESKTMSKLRHPSRSQV 459


>gi|124023660|ref|YP_001017967.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Prochlorococcus marinus str. MIT 9303]
 gi|123963946|gb|ABM78702.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Prochlorococcus marinus str. MIT 9303]
          Length = 313

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 80/297 (26%), Positives = 146/297 (49%), Gaps = 44/297 (14%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS-------------------------AA 50
           +S Y+  I +IP+L   EE  L  + +    L+                         A 
Sbjct: 20  VSWYLTTIGRIPLLTPAEEIELGNQVQTMMSLTQDGSVAPDDKEFTTHQRRMIRIGRRAK 79

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            R++ ++LRLVV +A  Y+G GL + +++ EG++GL +AV+KFDP RG++ +TY+ WWI+
Sbjct: 80  ERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWWIR 139

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRR----LKGHLQAITDNNLKPEQVVAIAKKL 166
            +M   I      +++    +++     +R+    L   L A+   +        IA+ +
Sbjct: 140 QSMTRAIACQSRTIRLPVHLSER--LTTIRKVSLDLAHKLGAMPSRS-------EIAEAM 190

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   E+ S+  +     SL+A +N  +  S  +   L+ D    E   ++K E++    
Sbjct: 191 DIPVDELDSLLRQALTTSSLDAPVNGEEGRS--FLGDLIADSSLGEP--LDKVEQRIHHE 246

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L R +S L+ +E+ + + R   E  +  TL  +    EVSRERVRQ+E +A +K++
Sbjct: 247 QLGRWLSHLSEQEQHVLKLRFGLETHDRHTLAEIGRLMEVSRERVRQVELKALRKLR 303


>gi|258592807|emb|CBE69116.1| RNA polymerase sigma factor RpoS [NC10 bacterium 'Dutch sediment']
          Length = 286

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 87/282 (30%), Positives = 146/282 (51%), Gaps = 42/282 (14%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+  I ++P+L+K+EE  L K   + GD  A  +LV ++LR VVK+A+ YRG GL 
Sbjct: 17  ALGAYLKRIAQVPLLKKEEELKLGK-ATQRGDEKALKQLVEANLRFVVKVALRYRGCGLS 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGNIGL++A +++ P+   +  TY++WWI+ A+ + +  S   V++     + R
Sbjct: 76  LPDLINEGNIGLLEAARRYSPDYNVKFITYAVWWIRQAIMQALAISGGAVRL--PLRKAR 133

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVA-IAKKLNVSESEVISMNCRLAGDESLNALINSS 193
           L   L  ++  L       L+ E   + + ++L++S S++     R AG           
Sbjct: 134 LASQLDDVRADLS----QQLQAEPTDSEVTEELDLSASDLEGALHR-AG----------- 177

Query: 194 DKNSSQWQDWLVYDHDGQEQ----VLIEKEE---------RKNRRNMLTRSMSVLNPRER 240
                  Q   + D  G EQ     L E ++         R++ R  + R +  LN RER
Sbjct: 178 -------QLAFLSDEIGLEQRIGMELYESKQLPPADYELIRRSLREEVERMLRSLNDRER 230

Query: 241 RIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            I E R    +E  +TL+ +    ++SRERVRQIE RA +K+
Sbjct: 231 LIVELRFGLGKEEAMTLKEVGKRLKLSRERVRQIEERAKQKL 272


>gi|148657263|ref|YP_001277468.1| RpoD family RNA polymerase sigma factor [Roseiflexus sp. RS-1]
 gi|148569373|gb|ABQ91518.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus sp.
           RS-1]
          Length = 345

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 88/291 (30%), Positives = 139/291 (47%), Gaps = 40/291 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLA----------KRYREHGDLSAAHRL--------------- 53
           Y+ EI ++ +L  +EE  LA          +R + H   S A RL               
Sbjct: 52  YLREIGQVSLLSAEEEITLANDIRAGREAQERLKSHRFESLAERLLLERRVMQAEEARRR 111

Query: 54  -VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            + ++LRLVV IA  Y G  L   ++V EGNIGLM+AV+KFD  +G R +TY+ WWI+ A
Sbjct: 112 LIQANLRLVVSIAKKYIGGPLSFMDLVQEGNIGLMRAVEKFDAGKGNRFSTYATWWIRQA 171

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-AIAKKLNVSES 171
           +   I     L+++    +   +   LRR+   L+     +L+ E  V  IA  +++ E 
Sbjct: 172 ITRAIAEQSRLIRLPVHLSD--VIAQLRRVARRLE----QSLEREPTVEEIAAAIDMPEH 225

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           +V  +    A   SL   I S  +        L+ D D      +E   R+  ++ L ++
Sbjct: 226 KVKLLLQASAQPISLEQPITSDGEGQIS---ELLADDDA--DAPMEIATRRMLQHDLAQA 280

Query: 232 MSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKV 280
           +  L  RER + + R    +    TLE + S F ++RER RQIEA A +++
Sbjct: 281 LMELPDRERAVLQLRYGLTDGRRRTLEEVGSAFGITRERTRQIEADALRQL 331


>gi|87301096|ref|ZP_01083937.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
 gi|87284064|gb|EAQ76017.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
          Length = 308

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 83/301 (27%), Positives = 143/301 (47%), Gaps = 48/301 (15%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL---------------------SAA 50
           G   +S Y+  I ++P+L   EE  L  + +    L                      A 
Sbjct: 15  GSDPISWYLGTIGRVPLLTPAEEIELGNQVQAMMQLIDSGVEDPPSLRQKQLLRLGRRAK 74

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            R++ ++LRLVV +A  Y+G GL + +++ EG++GL +AV+KFDP RG++ +TY+ WWI+
Sbjct: 75  ERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWWIR 134

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK-PEQVVAIAKKLNVS 169
            +M   I            A Q R       L   L A+   +L+   ++ A+  +  ++
Sbjct: 135 QSMTRAI------------ACQSRTIRLPVHLSERLSAVRRVSLELAHKLGAMPSRSEIA 182

Query: 170 ESEVISMNCRLAG-------DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           E+  I +   L G         SL+A +N  +  S  +   L+ D    E   +++ ER 
Sbjct: 183 EAMAIPIQ-ELDGLLRQSLTTSSLDAPVNGEEGRS--FLGDLIADSSHDEP--LDQVERG 237

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKV 280
                L R +S L+ +ER++ + R   +     TL  +    +VSRERVRQ+E +A +K+
Sbjct: 238 MHHEQLERWLSYLSEQERQVLDLRFGLDGHERHTLAEIGRLLDVSRERVRQVELKALRKL 297

Query: 281 Q 281
           +
Sbjct: 298 R 298


>gi|304322159|ref|YP_003855802.1| RNA polymerase sigma factor [Parvularcula bermudensis HTCC2503]
 gi|303301061|gb|ADM10660.1| RNA polymerase sigma factor [Parvularcula bermudensis HTCC2503]
          Length = 650

 Score = 95.1 bits (235), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 412 AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 471

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE++ A   KL++
Sbjct: 472 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQILNEIGREPTPEELAA---KLSM 526

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 527 PLEKVRKV-MKIAK-EPISLETPIGDEEDSHLGDFI---EDKNAILPIDAAIQSNLRETT 581

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 582 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 636


>gi|219558712|ref|ZP_03537788.1| RNA polymerase sigma factor [Mycobacterium tuberculosis T17]
          Length = 530

 Score = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 80/319 (25%), Positives = 151/319 (47%), Gaps = 45/319 (14%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR---------------------- 40
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR                      
Sbjct: 218 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSERGEKLP 276

Query: 41  ---YRE------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
              +R+       GD +  H L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 277 GIHHRDMMWICRDGDRAKNH-LLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 335

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L     
Sbjct: 336 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLG 393

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 394 REPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSE 445

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 446 AVVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 505

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 506 RQIESKTMSKLRHPSRSQV 524


>gi|300933014|ref|ZP_07148270.1| RNA polymerase sigma factor [Corynebacterium resistens DSM 45100]
          Length = 571

 Score = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 81/302 (26%), Positives = 149/302 (49%), Gaps = 42/302 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR--------YR-----EHGD-LSAAHR------------ 52
           Y+ +I K+ +L  ++E  LAKR        YR     E G+ LS  HR            
Sbjct: 274 YLKQIGKVALLNAEQEVSLAKRIEAGLYAAYRLQEIKESGEKLSPMHRRDLREIERDGRR 333

Query: 53  ----LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
               L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WW
Sbjct: 334 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYVKGYKFSTYATWW 393

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   +      ++I    +   +   L R++  L         PE+   +A+++++
Sbjct: 394 IRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGREPSPEE---LAREMDI 448

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +  +V+ +        SL+  I   D+  SQ  D++    D +  V ++       ++ L
Sbjct: 449 TVDKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEAVVAVDAVSFTLLQDQL 503

Query: 229 TRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +  L+ RE  + + R  L +  P TL+ +   + V+RER+RQIE++   K++   + 
Sbjct: 504 QDVLHTLSDREAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRS 563

Query: 287 QV 288
           QV
Sbjct: 564 QV 565


>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 = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 117/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 377 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 436

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 437 IRQAITRSIADQARTIRI--PVHMIETINKLNRVSRQMLQEMGREPTPEELAERMVMPED 494

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    DG  ++ ++   
Sbjct: 495 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDGSGELPVDSAT 538

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            +N +      ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 539 SENLKGATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 598

Query: 279 KVQ 281
           K++
Sbjct: 599 KLR 601


>gi|296284010|ref|ZP_06862008.1| RNA polymerase sigma factor RpoD [Citromicrobium bathyomarinum
           JL354]
          Length = 667

 Score = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 72/247 (29%), Positives = 120/247 (48%), Gaps = 36/247 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 429 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 488

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ----KRLFFNLRRLKGHLQAITDNNLKP---- 156
           I+ A+   I      ++I      T N+     R F + +  +   + + +    P    
Sbjct: 489 IRQAITRSIADQARTIRIPVHMIETINKLVRTSRQFLHEQGREPTPEEMAERLSMPLEKV 548

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
            +V+ IAK       E IS+   +             D+  S   D++    D    + +
Sbjct: 549 RKVMKIAK-------EPISLETPIG------------DEEDSHLGDFI---EDKNAIIPV 586

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEA 274
           +   + N +  +TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA
Sbjct: 587 DAAIQSNLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEA 646

Query: 275 RAFKKVQ 281
           +A +K++
Sbjct: 647 KALRKLK 653


>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 = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 65/235 (27%), Positives = 121/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 521 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 580

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +   +P+    +A+K+++
Sbjct: 581 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGAEPDPAT-LAQKMDM 635

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + R+++
Sbjct: 636 PEDKIRKI-LKIA-KEPISMETPIGDDDDSHLGDFI---EDTATLAPSDAALHGSMRDVV 690

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 691 KEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLR 745


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

 Score = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 65/235 (27%), Positives = 121/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 483 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 542

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +   +P+    +A+K+++
Sbjct: 543 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGAEPDPAT-LAQKMDM 597

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + R+++
Sbjct: 598 PEDKIRKI-LKIAK-EPISMETPIGDDDDSHLGDFI---EDTATLAPSDAALHGSMRDVV 652

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 653 KEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLR 707


>gi|332185826|ref|ZP_08387573.1| RNA polymerase sigma factor RpoD [Sphingomonas sp. S17]
 gi|332014184|gb|EGI56242.1| RNA polymerase sigma factor RpoD [Sphingomonas sp. S17]
          Length = 671

 Score = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 72/247 (29%), Positives = 120/247 (48%), Gaps = 36/247 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 433 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 492

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ----KRLFFNLRRLKGHLQAITDNNLKP---- 156
           I+ A+   I      ++I      T N+     R F + +  +   + + +    P    
Sbjct: 493 IRQAITRSIADQARTIRIPVHMIETINKLVRTSRQFLHEQGREPTPEEMAERLSMPLEKV 552

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
            +V+ IAK       E IS+   +             D+  S   D++    D    + +
Sbjct: 553 RKVMKIAK-------EPISLETPIG------------DEEDSHLGDFI---EDKNAVIPV 590

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEA 274
           +   + N +  +TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA
Sbjct: 591 DAAIQANLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEA 650

Query: 275 RAFKKVQ 281
           +A +K++
Sbjct: 651 KALRKLK 657


>gi|289570879|ref|ZP_06451106.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis T17]
 gi|289544633|gb|EFD48281.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis T17]
          Length = 528

 Score = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 80/319 (25%), Positives = 151/319 (47%), Gaps = 45/319 (14%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR---------------------- 40
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR                      
Sbjct: 216 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSERGEKLP 274

Query: 41  ---YRE------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
              +R+       GD +  H L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 275 GIHHRDMMWICRDGDRAKNH-LLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 333

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L     
Sbjct: 334 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLG 391

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 392 REPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSE 443

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 444 AVVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 503

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 504 RQIESKTMSKLRHPSRSQV 522


>gi|520418|gb|AAA50747.1| major sigma factor [Chlamydophila psittaci]
          Length = 571

 Score = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 77/247 (31%), Positives = 120/247 (48%), Gaps = 28/247 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+  RG++ +TY+ WW
Sbjct: 317 AKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWW 376

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+      + R    L   T     PE+   +A+
Sbjct: 377 IRQAVTRAIADQARTIRIPVHMIETINK------VLRGAKKLMMETGKEPTPEE---LAE 427

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L ++   V  +        SL A +    ++S  + D+L       E   +E       
Sbjct: 428 ELGLTPDRVREIYKIAQHPISLQAEVGEGGESS--FGDFL-------EDTGVESPAEATG 478

Query: 225 RNMLTRSM----SVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
            +ML   M      L  RER +   R   L   P TLE + S F V+RER+RQIEA+A +
Sbjct: 479 YSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGKPKTLEEVGSAFNVTRERIRQIEAKALR 538

Query: 279 KVQESIQ 285
           K++  I+
Sbjct: 539 KMRHPIR 545


>gi|326387391|ref|ZP_08209000.1| RNA polymerase sigma factor RpoD [Novosphingobium nitrogenifigens
           DSM 19370]
 gi|326208047|gb|EGD58855.1| RNA polymerase sigma factor RpoD [Novosphingobium nitrogenifigens
           DSM 19370]
          Length = 667

 Score = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 72/247 (29%), Positives = 120/247 (48%), Gaps = 36/247 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 429 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 488

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ----KRLFFNLRRLKGHLQAITDNNLKP---- 156
           I+ A+   I      ++I      T N+     R F + +  +   + + +    P    
Sbjct: 489 IRQAITRSIADQARTIRIPVHMIETINKLVRTSRQFLHEQGREPTPEEMAERLSMPLEKV 548

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
            +V+ IAK       E IS+   +             D+  S   D++    D    + +
Sbjct: 549 RKVMKIAK-------EPISLETPIG------------DEEDSHLGDFI---EDKNAIIPV 586

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEA 274
           +   + N +  +TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA
Sbjct: 587 DAAIQSNLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEA 646

Query: 275 RAFKKVQ 281
           +A +K++
Sbjct: 647 KALRKLK 653


>gi|237803044|ref|YP_002888238.1| RNA polymerase sigma factor [Chlamydia trachomatis B/Jali20/OT]
 gi|231274278|emb|CAX11073.1| RNA polymerase sigma factor [Chlamydia trachomatis B/Jali20/OT]
          Length = 571

 Score = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 77/247 (31%), Positives = 117/247 (47%), Gaps = 28/247 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+  RG++ +TY+ WW
Sbjct: 317 AKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWW 376

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+      + R    L   T     PE+   + +
Sbjct: 377 IRQAVTRAIADQARTIRIPVHMIETINK------VLRGAKKLMMETGKEPTPEE---LGE 427

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L  +   V  +        SL A +   D   S + D+L       E   +E       
Sbjct: 428 ELGFTPDRVREIYKIAQHPISLQAEVG--DGGESSFGDFL-------EDTAVESPAEVTG 478

Query: 225 RNMLTRSM----SVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
            +ML   M      L  RER +   R   L   P TLE + S F V+RER+RQIEA+A +
Sbjct: 479 YSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGRPKTLEEVGSAFNVTRERIRQIEAKALR 538

Query: 279 KVQESIQ 285
           K++  I+
Sbjct: 539 KMRHPIR 545


>gi|226355184|ref|YP_002784924.1| RNA polymerase sigma factor, sigma-70 family [Deinococcus deserti
           VCD115]
 gi|226317174|gb|ACO45170.1| putative RNA polymerase sigma factor, sigma-70 family [Deinococcus
           deserti VCD115]
          Length = 399

 Score = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 81/295 (27%), Positives = 137/295 (46%), Gaps = 38/295 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYRE----------HGDLSAAHR------------- 52
           L +Y+HEI +I +L   EE  LA+RY E          + DL   HR             
Sbjct: 100 LRQYLHEIGQIELLSAVEEMDLARRYEEGEAARNELESNPDLDDRHRRHLQRLVEDGEAA 159

Query: 53  ---LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L  ++LRLVV IA  Y   GL + +++ EGN GL++AV+KF+  RG++ +TY+ WWI
Sbjct: 160 KKSLTEANLRLVVSIAKKYANRGLNLLDLIQEGNQGLIRAVEKFEYRRGYKFSTYATWWI 219

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ-AITDNNLKPEQVVAIAKKLNV 168
           + A+   I      +++    +       L R+   L+  ++   L  E   A+    + 
Sbjct: 220 RQALTRAIADKSRTIRV--PVHMVETINKLSRISRQLEMELSREPLAEEMAEAMGPGWDA 277

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            +      + +  G E ++      D+  S + D+L  +  G     ++   +      L
Sbjct: 278 EK----VTDTQKVGHEPISLETPIGDEGDSFYGDFLPDERFGSP---VQNASQTLLSEAL 330

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R++S L  RE  + + R   +     TLE +     V+RERVRQIE++A +K++
Sbjct: 331 ERALSSLGEREALVLKLRNGFVDGREHTLEEVGQLLSVTRERVRQIESKALRKLK 385


>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 = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 421 AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 480

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 481 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 535

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 536 PLEKVRKV-LKIA-KEPISLETPIGDEEDSHLGDFI---EDKNVVLPIDAAIQSNLRETT 590

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 591 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 645


>gi|152656|gb|AAA26473.1| sigma factor [Stigmatella aurantiaca]
          Length = 706

 Score = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 73/242 (30%), Positives = 127/242 (52%), Gaps = 26/242 (10%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ WW
Sbjct: 468 AKSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWW 527

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+      L R   +L         PE+   IA+
Sbjct: 528 IRQAITRAIADQARTIRIPVHMIETINK------LIRTSRYLVQEIGREPTPEE---IAE 578

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           K+ +   +V  +  ++A  E ++      ++  S   D++      +++ L+   +    
Sbjct: 579 KMELPLDKVRKV-LKIAK-EPISLETPIGEEEDSHLGDFI------EDKSLVSPADAVIN 630

Query: 225 RNMLTRS---MSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
            N+  R+   ++ L PRE ++   R    +++  TLE +  +FEV+RER+RQIEA+A +K
Sbjct: 631 MNLAARTRKVLATLTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRK 690

Query: 280 VQ 281
           ++
Sbjct: 691 LR 692


>gi|33593188|ref|NP_880832.1| RNA polymerase sigma factor RpoD [Bordetella pertussis Tohama I]
 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]
          Length = 760

 Score = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 65/235 (27%), Positives = 121/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 521 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 580

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +   +P+    +A+K+++
Sbjct: 581 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGAEPDPAT-LAQKMDM 635

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + R+++
Sbjct: 636 PEDKIRKI-LKIA-KEPISMETPIGDDDDSHLGDFI---EDTATLAPSDAALHGSMRDVV 690

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 691 KEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKLR 745


>gi|29840756|ref|NP_829862.1| RNA polymerase sigma factor [Chlamydophila caviae GPIC]
 gi|29835106|gb|AAP05740.1| RNA polymerase sigma factor, sigma-70 family [Chlamydophila caviae
           GPIC]
          Length = 572

 Score = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 77/247 (31%), Positives = 120/247 (48%), Gaps = 28/247 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+  RG++ +TY+ WW
Sbjct: 317 AKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWW 376

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+      + R    L   T     PE+   +A+
Sbjct: 377 IRQAVTRAIADQARTIRIPVHMIETINK------VLRGAKKLMMETGKEPTPEE---LAE 427

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L ++   V  +        SL A +    ++S  + D+L       E   +E       
Sbjct: 428 ELGLTPDRVREIYKIAQHPISLQAEVGEGGESS--FGDFL-------EDTGVESPAEATG 478

Query: 225 RNMLTRSM----SVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
            +ML   M      L  RER +   R   L   P TLE + S F V+RER+RQIEA+A +
Sbjct: 479 YSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGKPKTLEEVGSAFNVTRERIRQIEAKALR 538

Query: 279 KVQESIQ 285
           K++  I+
Sbjct: 539 KMRHPIR 545


>gi|294011419|ref|YP_003544879.1| RNA polymerase primary sigma factor [Sphingobium japonicum UT26S]
 gi|292674749|dbj|BAI96267.1| RNA polymerase primary sigma factor [Sphingobium japonicum UT26S]
          Length = 681

 Score = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 72/247 (29%), Positives = 120/247 (48%), Gaps = 36/247 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 443 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 502

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ----KRLFFNLRRLKGHLQAITDNNLKP---- 156
           I+ A+   I      ++I      T N+     R F + +  +   + + +    P    
Sbjct: 503 IRQAITRSIADQARTIRIPVHMIETINKLVRTSRQFLHEQGREPTPEEMAERLSMPLEKV 562

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
            +V+ IAK       E IS+   +             D+  S   D++    D    + +
Sbjct: 563 RKVMKIAK-------EPISLETPIG------------DEEDSHLGDFI---EDKNAIIPV 600

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEA 274
           +   + N +  +TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA
Sbjct: 601 DAAIQANLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEA 660

Query: 275 RAFKKVQ 281
           +A +K++
Sbjct: 661 KALRKLK 667


>gi|163850052|ref|YP_001638095.1| RNA polymerase sigma factor RpoD [Methylobacterium extorquens PA1]
 gi|163661657|gb|ABY29024.1| RNA polymerase sigma factor RpoD [Methylobacterium extorquens PA1]
          Length = 718

 Score = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 480 AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 539

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 540 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 594

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 595 PLEKVRKV-LKIA-KEPISLETPIGDEEDSHLGDFI---EDKNVVLPIDAAIQSNLRETT 649

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 650 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 704


>gi|255531277|ref|YP_003091649.1| sigma-70 family RNA polymerase sigma factor [Pedobacter heparinus
           DSM 2366]
 gi|255344261|gb|ACU03587.1| RNA polymerase sigma factor, sigma-70 family [Pedobacter heparinus
           DSM 2366]
          Length = 286

 Score = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 74/277 (26%), Positives = 142/277 (51%), Gaps = 33/277 (11%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           + +Y+++I +I +L  +EE VLA++ R+ GD SA  RLV ++LR VV +A  Y+  G+ +
Sbjct: 18  IEKYLYDIARIDLLSVEEEIVLAQKIRK-GDQSALDRLVKANLRFVVSVAKKYQNQGIRL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           S++++EGN+GL++A ++FD  +GF+  ++++WWI+ ++   I     +V++   ANQ   
Sbjct: 77  SDLIAEGNLGLIKAAQRFDETKGFKFISFAVWWIRQSIMIAIAEQKRIVRL--PANQIGG 134

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVI----------SMNCRLAGDES 185
              + +    L+   +     E+V      + + E +V+          S++  +A +ES
Sbjct: 135 IMKINKAMADLEQQLERVPSLEEVCEF---IELPEEKVVDYLHHAPMTTSLDTVIA-EES 190

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
              L  + +  + +  D  V  H     V ++          + R M  L  RE+ I   
Sbjct: 191 GFTLAETIEDTNVEKTDTTVLQH----SVTVD----------VKRLMRGLPEREKEILSM 236

Query: 246 -RRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKV 280
              L   P + L+ +  +  + +ERVRQI+ +A K +
Sbjct: 237 FYGLGGYPAIGLDEIGGKMNLGKERVRQIKDKALKTL 273


>gi|254423226|ref|ZP_05036944.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
 gi|196190715|gb|EDX85679.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
          Length = 431

 Score = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 62/236 (26%), Positives = 124/236 (52%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV+KFDP +G+R +TY+ WW
Sbjct: 192 AKEHMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTKGYRFSTYAYWW 251

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   I      +++     +K     L ++K   + I+    +  +   IAK+L++
Sbjct: 252 IRQGITRAIATQSRTIRLPVHITEK-----LNKIKKAQRKISQTQGRTAKAEDIAKELDM 306

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           + +++  +  ++    SL+  +       ++  D L  +    E  L+ +  ++    +L
Sbjct: 307 TVAQIREVLLKVPRSVSLDTKVGKD--RDTELGDLLETEDISPEDRLMRESLKRELHQLL 364

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           T     L  RE+ +   R   ++  P +L  +    E+SRERVRQIE++A +K+++
Sbjct: 365 TD----LTTREQEVITLRFGLDDGVPYSLAEIGRTLELSRERVRQIESKALQKLRQ 416


>gi|256375646|ref|YP_003099306.1| RNA polymerase sigma factor [Actinosynnema mirum DSM 43827]
 gi|255919949|gb|ACU35460.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Actinosynnema
           mirum DSM 43827]
          Length = 435

 Score = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 82/320 (25%), Positives = 151/320 (47%), Gaps = 47/320 (14%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRL--------- 53
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR  E G L AA RL         
Sbjct: 123 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRI-EAG-LYAAERLRRAEDESEK 179

Query: 54  -----------------------VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
                                  + ++LRLVV +A  Y G G+   +++ EGN+GL++AV
Sbjct: 180 LTPQMRRDLRWIVRDGERAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAV 239

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +KFD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L    
Sbjct: 240 EKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDL 297

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
                PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D 
Sbjct: 298 GREPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDS 349

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRER 268
           +  V ++       ++ L   ++ L+ RE  +   R       P TL+ +   + V+RER
Sbjct: 350 EAVVAVDAVSFTLLQDQLQSVLATLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRER 409

Query: 269 VRQIEARAFKKVQESIQKQV 288
           +RQIE++   K++   + QV
Sbjct: 410 IRQIESKTMSKLRHPSRSQV 429


>gi|307155201|ref|YP_003890585.1| RpoD subfamily RNA polymerase sigma-70 factor [Cyanothece sp. PCC
           7822]
 gi|306985429|gb|ADN17310.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7822]
          Length = 295

 Score = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 80/287 (27%), Positives = 142/287 (49%), Gaps = 38/287 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLA-------------------KRYREHGDLSAAHRLVTSHLR 59
           Y+ EI + P+L  Q+E  LA                   KR  + G   A  +++ ++LR
Sbjct: 12  YLQEIGRTPLLNAQQEIELATQVQKMMALIDKENPTPEEKRIIQQGK-RAKRKMINANLR 70

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           LVV IA  Y+  GL   +++ EG+IGL++ V+KFDP +G++ +TY+ WWI+ AM   I  
Sbjct: 71  LVVSIAKKYQRRGLSFLDLIQEGSIGLIRGVEKFDPSKGYKFSTYAYWWIRQAMTRAIAD 130

Query: 120 SWSLVKIGT--TANQKRLFFNLRRLKGHLQAITDNNLKP-EQVVAIAKKLNVSESEVISM 176
               +++ +  T +  +L    R+L G L        +P EQ +A A +L++ E   I  
Sbjct: 131 QSRTIRLPSHLTESLNKLKRVTRQLTGEL------GRRPTEQELANALELSLHELHAIRQ 184

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
                   SLN  +   +   ++ ++ L  + +     + + E     R+M+   +  L 
Sbjct: 185 ADHRTRSYSLNMKM---EDEQTELEELLADNSETPNDFVAQIE----LRSMVDELLESLP 237

Query: 237 PRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           PR++ I   R   +N   ++LE + +   +SRERVRQ++ RA + ++
Sbjct: 238 PRQQEIIALRYGLKNGRQMSLEEVGNYCNLSRERVRQLQNRAMRTLK 284


>gi|89897819|ref|YP_514929.1| RNA polymerase sigma factor [Chlamydophila felis Fe/C-56]
 gi|89331191|dbj|BAE80784.1| DNA-directed RNA polymerase sigma 70 [Chlamydophila felis Fe/C-56]
          Length = 570

 Score = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 77/247 (31%), Positives = 120/247 (48%), Gaps = 28/247 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+  RG++ +TY+ WW
Sbjct: 315 AKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWW 374

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+      + R    L   T     PE+   +A+
Sbjct: 375 IRQAVTRAIADQARTIRIPVHMIETINK------VLRGAKKLMMETGKEPTPEE---LAE 425

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L ++   V  +        SL A +    ++S  + D+L       E   +E       
Sbjct: 426 ELGLTPDRVREIYKIAQHPISLQAEVGEGGESS--FGDFL-------EDTGVESPAEATG 476

Query: 225 RNMLTRSM----SVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
            +ML   M      L  RER +   R   L   P TLE + S F V+RER+RQIEA+A +
Sbjct: 477 YSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGKPKTLEEVGSAFNVTRERIRQIEAKALR 536

Query: 279 KVQESIQ 285
           K++  I+
Sbjct: 537 KMRHPIR 543


>gi|293977922|ref|YP_003543352.1| sigma-70 family RNA polymerase sigma factor [Candidatus Sulcia
           muelleri DMIN]
 gi|292667853|gb|ADE35488.1| RNA polymerase sigma factor, sigma-70 family [Candidatus Sulcia
           muelleri DMIN]
          Length = 342

 Score = 94.7 bits (234), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 70/244 (28%), Positives = 123/244 (50%), Gaps = 11/244 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   LV ++LR V+ IA  Y+  GL +S++++EGN GL++ + +FD  +GF+  +Y +WW
Sbjct: 105 ALDNLVKANLRFVISIAKQYQNQGLSLSDLINEGNFGLIKGINRFDERKGFKCISYCVWW 164

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ ++ + I      V+  T    K  F+N  ++      +      P  +  I+  LNV
Sbjct: 165 IRQSILQAISDKARCVRYPTN---KLAFYN--KVNKTYSKLEQKLKMPPSIKYISDYLNV 219

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SE +V           SL+A +   D  +S   D +  D   +    +EKE  +    +L
Sbjct: 220 SEKDVEEALINSIKHTSLDAPLGEGD--NSNLYDVIKIDESPKTDHSLEKESLQQDIKIL 277

Query: 229 TRSMSVLNPRERRIFEARR-LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             ++S    RE +I      L    + LE ++   +++RER RQIE  A K++++S +K+
Sbjct: 278 LETLS---ERESQIITLHYGLGCFSMNLEKIAYLLKLTRERCRQIEMHAIKRLKKSSRKE 334

Query: 288 VELS 291
           + LS
Sbjct: 335 ILLS 338


>gi|23008120|ref|ZP_00049697.1| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Magnetospirillum magnetotacticum
           MS-1]
          Length = 307

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 69  AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 128

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 129 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 183

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 184 PLEKVRKV-LKIA-KEPISLETPIGDEEDSHLGDFI---EDKNVVLPIDAAIQSNLRETT 238

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 239 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 293


>gi|328915181|gb|AEB56014.1| transcription initiation factor sigma 70 [Chlamydophila psittaci
           6BC]
          Length = 561

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 77/247 (31%), Positives = 120/247 (48%), Gaps = 28/247 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+  RG++ +TY+ WW
Sbjct: 307 AKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWW 366

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+      + R    L   T     PE+   +A+
Sbjct: 367 IRQAVTRAIADQARTIRIPVHMIETINK------VLRGAKKLMMETGKEPTPEE---LAE 417

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L ++   V  +        SL A +    ++S  + D+L       E   +E       
Sbjct: 418 ELGLTPDRVREIYKIAQHPISLQAEVGEGGESS--FGDFL-------EDTGVESPAEATG 468

Query: 225 RNMLTRSM----SVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
            +ML   M      L  RER +   R   L   P TLE + S F V+RER+RQIEA+A +
Sbjct: 469 YSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGKPKTLEEVGSAFNVTRERIRQIEAKALR 528

Query: 279 KVQESIQ 285
           K++  I+
Sbjct: 529 KMRHPIR 535


>gi|288818771|ref|YP_003433119.1| RNA polymerase sigma factor RpoD [Hydrogenobacter thermophilus
           TK-6]
 gi|288788171|dbj|BAI69918.1| RNA polymerase sigma factor RpoD [Hydrogenobacter thermophilus
           TK-6]
 gi|308752357|gb|ADO45840.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Hydrogenobacter
           thermophilus TK-6]
          Length = 570

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 76/251 (30%), Positives = 115/251 (45%), Gaps = 44/251 (17%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V  +LRLVV IA  Y   GL   +++ EGNIGLM+AV K+D  +G++ +TY+ WW
Sbjct: 333 AKQVMVKCNLRLVVSIAKKYVNRGLHFLDLIQEGNIGLMKAVDKYDYRKGYKFSTYATWW 392

Query: 109 IKAAMQEYILRSWSLVKI---------GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I           T   K+LF  L R              PE++
Sbjct: 393 IRQAITRAIADQARTIRIPVHMIETINDITKAHKKLFQELGR-----------EPFPEEI 441

Query: 160 -------VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
                  V  A+K+  +  E IS+   +  DE  +      DK+              +E
Sbjct: 442 AKYLGISVEKARKVMRTSQEPISLETPIGDDEETHLKDFIEDKSVLS----------PEE 491

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVR 270
           QV      RK  R  L + +S L  +E+ I   R   +     TLE +   F V+RER+R
Sbjct: 492 QV-----SRKLLREQLIKVLSTLGEKEKEILMYRYGLVDGTEYTLEQIGKMFNVTRERIR 546

Query: 271 QIEARAFKKVQ 281
           QIE +A +K++
Sbjct: 547 QIETKAIRKLR 557


>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 = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 79/280 (28%), Positives = 141/280 (50%), Gaps = 26/280 (9%)

Query: 16  LSRYIHEIR----KIPMLEKQEEYVLAKRYRE------HGDLSA---AHRLVTSHLRLVV 62
           L+ Y+ +IR     +  LE+Q    +A+  RE      +G+L A      +V ++LRLV+
Sbjct: 338 LANYVEKIRINIVNLQNLEQQSGLTIAQ-IREIGGRIANGELKARRAKKEMVEANLRLVI 396

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I     
Sbjct: 397 SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 456

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            ++I    +       L R+             PE+   +A+++N+ E ++  +  ++A 
Sbjct: 457 TIRI--PVHMIETINKLNRISRQCLQEMGREATPEE---LAERMNMPEDKIRKV-LKIAK 510

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
            E ++      D + S   D++    D   ++ ++    ++ R      +  L PRE ++
Sbjct: 511 -EPISMETPIGDDDDSHLGDFI---QDESLELPLDSATAESLRIATNEVLEGLTPREAKV 566

Query: 243 FEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 567 LRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 606


>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 = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 74/243 (30%), Positives = 119/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 374 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 433

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA------- 161
           I+ A+   I      ++I    +       L R+   +         PE++ A       
Sbjct: 434 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREATPEELAARMDMPED 491

Query: 162 -IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++  + DG E   I+   
Sbjct: 492 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI--EDDGAESP-IDIAT 535

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            +  R   T  ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 536 IEGLRESTTMVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 595

Query: 279 KVQ 281
           K++
Sbjct: 596 KLR 598


>gi|87200249|ref|YP_497506.1| RNA polymerase sigma factor RpoD [Novosphingobium aromaticivorans
           DSM 12444]
 gi|87135930|gb|ABD26672.1| RNA polymerase, sigma 70 subunit, RpoD [Novosphingobium
           aromaticivorans DSM 12444]
          Length = 667

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 69/235 (29%), Positives = 119/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 429 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 488

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R              PE+   +A++L++
Sbjct: 489 IRQAITRSIADQARTIRI--PVHMIETINKLVRTSRQFLHEQGREPTPEE---MAERLSM 543

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + ++   + N +  +
Sbjct: 544 PLEKVRKV-MKIA-KEPISLETPIGDEEDSHLGDFI---EDKNAIIPVDAAIQANLKETV 598

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 599 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 653


>gi|62185569|ref|YP_220354.1| RNA polymerase sigma factor [Chlamydophila abortus S26/3]
 gi|62148636|emb|CAH64409.1| major sigma factor [Chlamydophila abortus S26/3]
          Length = 571

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 77/247 (31%), Positives = 120/247 (48%), Gaps = 28/247 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+  RG++ +TY+ WW
Sbjct: 317 AKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWW 376

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+      + R    L   T     PE+   +A+
Sbjct: 377 IRQAVTRAIADQARTIRIPVHMIETINK------VLRGAKKLMMETGKEPTPEE---LAE 427

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L ++   V  +        SL A +    ++S  + D+L       E   +E       
Sbjct: 428 ELGLTPDRVREIYKIAQHPISLQAEVGEGGESS--FGDFL-------EDTGVESPAEATG 478

Query: 225 RNMLTRSM----SVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
            +ML   M      L  RER +   R   L   P TLE + S F V+RER+RQIEA+A +
Sbjct: 479 YSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGKPKTLEEVGSAFNVTRERIRQIEAKALR 538

Query: 279 KVQESIQ 285
           K++  I+
Sbjct: 539 KMRHPIR 545


>gi|307295455|ref|ZP_07575291.1| RNA polymerase, sigma 70 subunit, RpoD [Sphingobium
           chlorophenolicum L-1]
 gi|306878494|gb|EFN09714.1| RNA polymerase, sigma 70 subunit, RpoD [Sphingobium
           chlorophenolicum L-1]
          Length = 681

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 72/247 (29%), Positives = 120/247 (48%), Gaps = 36/247 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 443 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 502

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ----KRLFFNLRRLKGHLQAITDNNLKP---- 156
           I+ A+   I      ++I      T N+     R F + +  +   + + +    P    
Sbjct: 503 IRQAITRSIADQARTIRIPVHMIETINKLVRTSRQFLHEQGREPTPEEMAERLSMPLEKV 562

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
            +V+ IAK       E IS+   +             D+  S   D++    D    + +
Sbjct: 563 RKVMKIAK-------EPISLETPIG------------DEEDSHLGDFI---EDKNAIIPV 600

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEA 274
           +   + N +  +TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA
Sbjct: 601 DAAIQANLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEA 660

Query: 275 RAFKKVQ 281
           +A +K++
Sbjct: 661 KALRKLK 667


>gi|299472557|emb|CBN79859.1| chloroplast RNA-polymerase sigma factor precursor [Ectocarpus
           siliculosus]
          Length = 835

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 71/260 (27%), Positives = 130/260 (50%), Gaps = 33/260 (12%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           E  +A   +EH        +++++LRLVV +A GYRG GL   +++ EG +GL++A +KF
Sbjct: 293 ELAVADEAKEH--------MISANLRLVVSMARGYRGRGLAFPDLIQEGTMGLVKACEKF 344

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL----QAI 149
           +PE GF+  TY+ WWIK ++   I     ++++ T  +      ++R+    L    +  
Sbjct: 345 NPEMGFQFYTYARWWIKKSILTGIANQSRVIRLPTQVHA--FLSSIRKYTYELTVDGKVP 402

Query: 150 TDNNLKPEQVVAIAKKLN-----VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
           TD  L  +++ A  +K+         ++ IS++ R +   S  A    +D   +Q  +  
Sbjct: 403 TDEELG-DKLGATVEKIQHYRQAALRTDSISLDIRASNKVSDGA----ADDLGTQIGEKS 457

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEF 262
             D +   Q    K         +T  ++ L  RE+++  AR   +     TLE +  + 
Sbjct: 458 TPDPEDATQAFYMK-------GKVTALLATLKDREQKVVRARYGLDGATSKTLEEIGRDL 510

Query: 263 EVSRERVRQIEARAFKKVQE 282
            ++RERVRQIE++A  K+++
Sbjct: 511 GLTRERVRQIESKALSKLRQ 530


>gi|19910024|dbj|BAB87263.1| RNA polymerase sigma factor [Cyanophora paradoxa]
          Length = 431

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 87/313 (27%), Positives = 149/313 (47%), Gaps = 60/313 (19%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKR---------YREH------------------------ 44
           RY+ EI +I +L+ ++E  LAKR          +EH                        
Sbjct: 116 RYLQEIGEISLLKAEDEIELAKRIETFRKLEKVKEHMKWKTGVEPTDEEWARAAALSDAE 175

Query: 45  --------GDLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLMQAVKKF 93
                   G L A  RLV ++LR VV +A  Y   RG  + + +++ EGNIGL++AV+KF
Sbjct: 176 ELRHMVRVGTL-ARDRLVRANLRWVVAVAKKYHKQRGT-MSMQDLIQEGNIGLIRAVEKF 233

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           DP  G+R  TY+ WWI+ A+   I  S   +++    ++K     + R+K    A++ + 
Sbjct: 234 DPRMGYRFTTYATWWIRQAITRSIQNSSREIRLPAHRHEK-----INRIKRATVALSRSL 288

Query: 154 LKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
            +      IA+ + +  S +     +       SL+  IN SD  S+   D++  +++G 
Sbjct: 289 GRQPTEAEIAEHVGLDPSRMRKFVESAAAVATVSLDVPINESDNQSATIGDFIRSENEGP 348

Query: 212 EQVLIEKEERKNRRNMLTRSMS-VLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRER 268
                ++ ER+  R  + R+++  L+ RE  +   R   ++  P TL  +     V+RER
Sbjct: 349 ----ADRAERELMRESVARTLAKALSEREYMVLRMRFGLDDGEPKTLNQVGETLGVTRER 404

Query: 269 VRQIEARAFKKVQ 281
           VRQIE +A +K++
Sbjct: 405 VRQIEMKALRKLR 417


>gi|283851053|ref|ZP_06368337.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio sp.
           FW1012B]
 gi|283573449|gb|EFC21425.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio sp.
           FW1012B]
          Length = 588

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 72/243 (29%), Positives = 125/243 (51%), Gaps = 16/243 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ WW
Sbjct: 350 AKQELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWW 409

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R   +L      +  PE+   IA++++ 
Sbjct: 410 IRQAITRAIADQARTIRI--PVHMIETINKLIRTSRYLVQELGRDPTPEE---IAERMDY 464

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR--N 226
              E +    ++A  E ++      D+  S   D++       ++ L   EE  N +   
Sbjct: 465 P-LEKVKKVLKIAK-EPISLETPIGDEEDSSLGDFI-----EDKKALAPAEEVVNTKLGE 517

Query: 227 MLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + + +S L PRE ++   R    +++  TLE +   F V+RER+RQIEA+A +K++  +
Sbjct: 518 QIGKVLSDLTPREEQVLRKRFGLGEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPV 577

Query: 285 QKQ 287
           + Q
Sbjct: 578 RSQ 580


>gi|260906542|ref|ZP_05914864.1| RNA polymerase principal sigma factor [Brevibacterium linens BL2]
          Length = 473

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 84/309 (27%), Positives = 143/309 (46%), Gaps = 60/309 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH----GDLS-----------------AAHR 52
           Y+ +I K+ +L   EE  LAKR     Y EH    G ++                 A + 
Sbjct: 180 YLKQIGKVALLNAAEEVDLAKRIEAGMYAEHLLDAGGITEPRESMDYKWIIHDGRIAKNH 239

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 240 LLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQA 299

Query: 113 MQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           +   +      ++I              Q+++  +L R     +   + ++ PE+VV + 
Sbjct: 300 ITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPSPEELAKELDMTPERVVEVQ 359

Query: 164 KKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           K       E IS++  L   GD     LI  S+          V   D     L++++  
Sbjct: 360 KYGR----EPISLHTPLGEDGDSEFGDLIEDSEA---------VVPSDSVSFTLLQEQ-- 404

Query: 222 KNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAFKK 279
                 L   +  L+ RE  +   R  L +  P TL+ +   + V+RER+RQIE++   K
Sbjct: 405 ------LHSVLDTLSEREAGVVSMRFGLNDGQPKTLDEIGKVYGVTRERIRQIESKTMAK 458

Query: 280 VQESIQKQV 288
           ++   + QV
Sbjct: 459 LRHPSRSQV 467


>gi|323450165|gb|EGB06048.1| hypothetical protein AURANDRAFT_11909 [Aureococcus anophagefferens]
          Length = 325

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 71/254 (27%), Positives = 123/254 (48%), Gaps = 38/254 (14%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +LRLV+ +A  Y   GL  +++  EGN GL +A  +FDP +GFR +TY++WWI+ A
Sbjct: 82  LIQRNLRLVLSVAKRYGDCGLAFTDLCQEGNFGLAKACDRFDPSKGFRFSTYAVWWIRQA 141

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +      +++ T  ++K     LRR+K H  A+     +      IA+++++   +
Sbjct: 142 VAHAVAHQSRTIRLPTHVHEK-----LRRMKKHKVALEKQTGRDATDDEIAREMSLDADK 196

Query: 173 VISMNCRLAGDESL----------------NALINSSDKNSSQWQDWLVYD------HDG 210
           +  +     G  S                 N    +S  + +Q  D L++D       D 
Sbjct: 197 LRRLRRAARGTVSTDVDAENLGSRRGAAPGNGRRGASYASGAQLAD-LLHDATQHPERDA 255

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF--EARRLQENPVTLENLSSEFEVSRER 268
            E +L ++  R    ++  R   VLN    R F  + RR    P TL  ++  F+++RER
Sbjct: 256 AESLLKDEVRRMLDDDLEDREEDVLN----RHFGLDGRR----PETLAEIAVRFDLTRER 307

Query: 269 VRQIEARAFKKVQE 282
           +RQIE  AF K+++
Sbjct: 308 IRQIEKSAFAKLRQ 321


>gi|329943340|ref|ZP_08292114.1| RNA polymerase sigma factor rpoD [Chlamydophila psittaci Cal10]
 gi|332287916|ref|YP_004422817.1| RNA polymerase sigma factor [Chlamydophila psittaci 6BC]
 gi|313848489|emb|CBY17493.1| major sigma factor [Chlamydophila psittaci RD1]
 gi|325507028|gb|ADZ18666.1| RNA polymerase sigma factor [Chlamydophila psittaci 6BC]
 gi|328814887|gb|EGF84877.1| RNA polymerase sigma factor rpoD [Chlamydophila psittaci Cal10]
          Length = 571

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 77/247 (31%), Positives = 120/247 (48%), Gaps = 28/247 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+  RG++ +TY+ WW
Sbjct: 317 AKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWW 376

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+      + R    L   T     PE+   +A+
Sbjct: 377 IRQAVTRAIADQARTIRIPVHMIETINK------VLRGAKKLMMETGKEPTPEE---LAE 427

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L ++   V  +        SL A +    ++S  + D+L       E   +E       
Sbjct: 428 ELGLTPDRVREIYKIAQHPISLQAEVGEGGESS--FGDFL-------EDTGVESPAEATG 478

Query: 225 RNMLTRSM----SVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
            +ML   M      L  RER +   R   L   P TLE + S F V+RER+RQIEA+A +
Sbjct: 479 YSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGKPKTLEEVGSAFNVTRERIRQIEAKALR 538

Query: 279 KVQESIQ 285
           K++  I+
Sbjct: 539 KMRHPIR 545


>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 = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 78/264 (29%), Positives = 127/264 (48%), Gaps = 44/264 (16%)

Query: 36  VLAKRYREHGD---LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
            L K YR  GD     A  +++ ++LRLV+ IA  Y   GL   +++ EGN+GLM+AV K
Sbjct: 348 TLNKMYR-RGDRRAKKAKSQMIEANLRLVISIAKKYANRGLQFLDLIQEGNVGLMKAVDK 406

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQA 148
           F+  RG++ +TY+ WWI+ A+   I      ++I      T N+      L R++  L  
Sbjct: 407 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK------LNRVRRQLLQ 460

Query: 149 ITDNNLKPEQVVAIAKKLNVSE----------SEVISMNCRLAGDESLNALINSSDKNSS 198
                  PE+   +A ++ + E           E +SM   +  DE  N      D N S
Sbjct: 461 KFGREASPEE---LATEMELPEYKIIKILKISKEPLSMETPVGDDEDSNIGDFIEDTNLS 517

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLE 256
                            +E   +++ R   +  +S L+PRE ++ + R  +  N   TLE
Sbjct: 518 SP---------------VEITTKESLRETTSELLSNLSPREAKVLKMRFGIDMNTDHTLE 562

Query: 257 NLSSEFEVSRERVRQIEARAFKKV 280
            +  +F+V+RER+RQIEA+A +K+
Sbjct: 563 EVGRQFDVTRERIRQIEAKALRKL 586


>gi|116073370|ref|ZP_01470632.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9916]
 gi|116068675|gb|EAU74427.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9916]
          Length = 313

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 80/293 (27%), Positives = 145/293 (49%), Gaps = 36/293 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS-------------------------AA 50
           +S Y+  I +IP+L   EE  L  + ++   L+                         A 
Sbjct: 20  ISWYLATIGRIPLLTPAEEIELGNQVQQLMALTQDGTIPIDSDQFSSKDRRIIRVGRRAK 79

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            R++ ++LRLVV +A  Y+G GL + ++V EG++GL +AV+KFDP RG++ +TY+ WWI+
Sbjct: 80  ERMMKANLRLVVSVAKKYQGKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAFWWIR 139

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            +M   I      +++    +++     +R++   L         P + + IA+ +++  
Sbjct: 140 QSMTRAIACQSRTIRLPVHLSER--LTTIRKVS--LDLAHKLGAMPSR-LEIAEAMDMPL 194

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            E+ S+  +     SL+A +N  +  S  +   L+ D+   E   + K E+      L R
Sbjct: 195 EELDSLLRQALTTSSLDAPVNGEEGRS--FLGDLIADNSSDEP--LAKVEQSIHHEQLGR 250

Query: 231 SMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +S L+ +E+ +   R  L  N   TL  +    EVSRER+RQ+E +A +K++
Sbjct: 251 WLSHLSDQEQHVLNLRFGLNGNERHTLAEIGRLLEVSRERIRQVELKALRKLR 303


>gi|94498543|ref|ZP_01305098.1| sigma 70 (RpoD) [Sphingomonas sp. SKA58]
 gi|94421986|gb|EAT07032.1| sigma 70 (RpoD) [Sphingomonas sp. SKA58]
          Length = 682

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 72/247 (29%), Positives = 120/247 (48%), Gaps = 36/247 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 444 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 503

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ----KRLFFNLRRLKGHLQAITDNNLKP---- 156
           I+ A+   I      ++I      T N+     R F + +  +   + + +    P    
Sbjct: 504 IRQAITRSIADQARTIRIPVHMIETINKLVRTSRQFLHEQGREPTPEEMAERLSMPLEKV 563

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
            +V+ IAK       E IS+   +             D+  S   D++    D    + +
Sbjct: 564 RKVMKIAK-------EPISLETPIG------------DEEDSHLGDFI---EDKNAIIPV 601

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEA 274
           +   + N +  +TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA
Sbjct: 602 DAAIQANLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEA 661

Query: 275 RAFKKVQ 281
           +A +K++
Sbjct: 662 KALRKLK 668


>gi|294085800|ref|YP_003552560.1| sigma-70 factor RpoD [Candidatus Puniceispirillum marinum IMCC1322]
 gi|292665375|gb|ADE40476.1| Sigma 70 (RpoD) [Candidatus Puniceispirillum marinum IMCC1322]
          Length = 674

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 76/250 (30%), Positives = 118/250 (47%), Gaps = 42/250 (16%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 436 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 495

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRR------LKGHLQAITDNN 153
           I+ A+   I      ++I      T N+     +++   + R      L   L    D  
Sbjct: 496 IRQAITRSIADQARTIRIPVHMIETINKLVRTSRQMLHEIGREPTPEELAEKLSMPID-- 553

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            K  +V+ IAK       E IS+   +  +E  +      DKN+ Q  D  ++       
Sbjct: 554 -KVRKVLKIAK-------EPISLETPIGDEEDSHLGDFIEDKNAVQPLDAAIH------- 598

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQ 271
                    N R   TR ++ L  RE R+   R         TLE +  +F V+RER+RQ
Sbjct: 599 --------ANLRETTTRVLASLTAREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQ 650

Query: 272 IEARAFKKVQ 281
           IEA+A +K++
Sbjct: 651 IEAKALRKLK 660


>gi|269125851|ref|YP_003299221.1| RpoD subfamily RNA polymerase sigma-70 subunit [Thermomonospora
           curvata DSM 43183]
 gi|268310809|gb|ACY97183.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermomonospora
           curvata DSM 43183]
          Length = 559

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 80/311 (25%), Positives = 140/311 (45%), Gaps = 63/311 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR----------------------------EHGDLSAA 50
           Y+ +I K+P+L  ++E  LAKR                              E G  + A
Sbjct: 265 YLKQIGKVPLLNAEQEVELAKRIEAGLFAEERLATMGDQLSEEDKADLEWIAEDGRRAKA 324

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           H L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+
Sbjct: 325 H-LLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIR 383

Query: 111 AAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
            A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ 
Sbjct: 384 QAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIE 443

Query: 162 IAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           + K       E IS++  L   GD     LI  S+          +   D     L++++
Sbjct: 444 VQKYGR----EPISLHTPLGEDGDSEFGDLIEDSEA---------IVPADAVSFTLLQEQ 490

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAF 277
                   L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++  
Sbjct: 491 --------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTM 542

Query: 278 KKVQESIQKQV 288
            K++   + QV
Sbjct: 543 SKLRHPSRSQV 553


>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 = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 428 AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 487

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL +
Sbjct: 488 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAM 542

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+   + N R   
Sbjct: 543 PLEKVRKV-LKIA-KEPISLETPIGDEEDSHLGDFI---EDKNVVLPIDAAIQSNLRETT 597

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 598 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 652


>gi|161833810|ref|YP_001598006.1| RNA polymerase sigma factor rpoD [Candidatus Sulcia muelleri GWSS]
 gi|152206300|gb|ABS30610.1| RNA polymerase sigma factor rpoD [Candidatus Sulcia muelleri GWSS]
          Length = 351

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 70/244 (28%), Positives = 123/244 (50%), Gaps = 11/244 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   LV ++LR V+ IA  Y+  GL +S++++EGN GL++ + +FD  +GF+  +Y +WW
Sbjct: 114 ALDNLVKANLRFVISIAKQYQNQGLSLSDLINEGNFGLIKGINRFDERKGFKCISYCVWW 173

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ ++ + I      V+  T    K  F+N  ++      +      P  +  I+  LNV
Sbjct: 174 IRQSILQAISDKARCVRYPTN---KLAFYN--KVNKTYSKLEQKLKMPPSIKYISDYLNV 228

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SE +V           SL+A +   D  +S   D +  D   +    +EKE  +    +L
Sbjct: 229 SEKDVEEALINSIKHTSLDAPLGEGD--NSNLYDVIKIDESPKTDHSLEKESLQQDIKIL 286

Query: 229 TRSMSVLNPRERRIFEARR-LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             ++S    RE +I      L    + LE ++   +++RER RQIE  A K++++S +K+
Sbjct: 287 LETLS---ERESQIITLHYGLGCFSMNLEKIAYLLKLTRERCRQIEMHAIKRLKKSSRKE 343

Query: 288 VELS 291
           + LS
Sbjct: 344 ILLS 347


>gi|118469122|ref|YP_887090.1| RNA polymerase sigma factor [Mycobacterium smegmatis str. MC2 155]
 gi|555680|gb|AAA85642.1| sigma factor MysA [Mycobacterium smegmatis]
 gi|118170409|gb|ABK71305.1| sigma factor MysA [Mycobacterium smegmatis str. MC2 155]
          Length = 466

 Score = 94.7 bits (234), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 79/319 (24%), Positives = 148/319 (46%), Gaps = 45/319 (14%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------- 43
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR                      
Sbjct: 154 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQKLAELAEKGEKLP 212

Query: 44  ------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                        GD +  H L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 213 VQQRRDMQWICRDGDRAKNH-LLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 271

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L     
Sbjct: 272 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLG 329

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 330 REPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSE 381

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 382 AVVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 441

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 442 RQIESKTMSKLRHPSRSQV 460


>gi|91203809|emb|CAJ71462.1| strongly similar to transcription initiation factor sigma RpoD
           [Candidatus Kuenenia stuttgartiensis]
          Length = 551

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 70/247 (28%), Positives = 128/247 (51%), Gaps = 14/247 (5%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y+EH   SA  +L  ++LRLVV IA  YR  GL   +++ EGN GLM+AV K++  RG++
Sbjct: 302 YKEHE--SAKRKLSGANLRLVVSIAKKYRNRGLSFLDLIQEGNTGLMRAVDKYEYRRGYK 359

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I        +   + +++   + +  +  +   + 
Sbjct: 360 FSTYATWWIRQAITRSIADQARTIRIPV-----HMIETMSKIRNISKKLLQDKGREPTIE 414

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            IA+++ +S  E   +        SL+  +  S+ +S  + D++    D + +  +    
Sbjct: 415 EIAREVKISVPEARRVLKISRHQISLDRPVGESEDSS--FGDFI---EDEKAESPVAAAT 469

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFK 278
           ++  ++ +   +  L  RER I + R    +    TLE +   F+V+RERVRQIEA+A +
Sbjct: 470 QEMLKDKIESVLETLTYREREIIKLRYGIGDGYTYTLEEVGKIFKVTRERVRQIEAKAVR 529

Query: 279 KVQESIQ 285
           K+Q  I+
Sbjct: 530 KLQHPIR 536


>gi|262202178|ref|YP_003273386.1| RNA polymerase sigma factor RpoD [Gordonia bronchialis DSM 43247]
 gi|262085525|gb|ACY21493.1| RNA polymerase sigma factor RpoD [Gordonia bronchialis DSM 43247]
          Length = 489

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 81/318 (25%), Positives = 151/318 (47%), Gaps = 43/318 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHG---- 45
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G    
Sbjct: 177 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLFATERLRRIMESGEKIT 235

Query: 46  -----DLS--------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                DL+        A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 236 TAQKRDLNWISRDGNRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 295

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L      
Sbjct: 296 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGR 353

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D + 
Sbjct: 354 EPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEA 405

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVR 270
            V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 406 VVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIR 465

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 466 QIESKTMSKLRHPSRSQV 483


>gi|227503480|ref|ZP_03933529.1| RNA polymerase major sigma subunit [Corynebacterium accolens ATCC
           49725]
 gi|227075983|gb|EEI13946.1| RNA polymerase major sigma subunit [Corynebacterium accolens ATCC
           49725]
          Length = 493

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 80/324 (24%), Positives = 156/324 (48%), Gaps = 49/324 (15%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREH-----------GD 46
           RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR     Y +H           GD
Sbjct: 175 RKDAQLTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYAQHRMDEMEKARAEGD 233

Query: 47  LSAA--------------------HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
            +A                     + L+ ++LRLVV +A  Y G G+   +++ EGN+GL
Sbjct: 234 KAAKLSPMEKRDLRSIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGL 293

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L
Sbjct: 294 IRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQREL 351

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    P++   +AK+++++E +V+ +        SL+  I   D+  SQ  D++  
Sbjct: 352 LQDLGREPTPQE---LAKEMDITEEKVMEIQQYAREPISLDQTIG--DEGDSQLGDFI-- 404

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEV 264
             D +  + ++       ++ L   ++ L+ RE  +   R  L +  P TL+ +   + V
Sbjct: 405 -EDSEAVIAVDAVSFTLLQDQLQDVLTTLSEREAGVVRLRFGLTDGMPRTLDEIGQVYGV 463

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           +RER+RQIE++   K++   + QV
Sbjct: 464 TRERIRQIESKTMSKLRHPSRSQV 487


>gi|94502401|ref|ZP_01308854.1| RNA polymerase sigma factor rpoD [Candidatus Sulcia muelleri str.
           Hc (Homalodisca coagulata)]
 gi|94451042|gb|EAT14014.1| RNA polymerase sigma factor rpoD [Candidatus Sulcia muelleri str.
           Hc (Homalodisca coagulata)]
          Length = 341

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 70/244 (28%), Positives = 123/244 (50%), Gaps = 11/244 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   LV ++LR V+ IA  Y+  GL +S++++EGN GL++ + +FD  +GF+  +Y +WW
Sbjct: 104 ALDNLVKANLRFVISIAKQYQNQGLSLSDLINEGNFGLIKGINRFDERKGFKCISYCVWW 163

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ ++ + I      V+  T    K  F+N  ++      +      P  +  I+  LNV
Sbjct: 164 IRQSILQAISDKARCVRYPTN---KLAFYN--KVNKTYSKLEQKLKMPPSIKYISDYLNV 218

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SE +V           SL+A +   D  +S   D +  D   +    +EKE  +    +L
Sbjct: 219 SEKDVEEALINSIKHTSLDAPLGEGD--NSNLYDVIKIDESPKTDHSLEKESLQQDIKIL 276

Query: 229 TRSMSVLNPRERRIFEARR-LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             ++S    RE +I      L    + LE ++   +++RER RQIE  A K++++S +K+
Sbjct: 277 LETLS---ERESQIITLHYGLGCFSMNLEKIAYLLKLTRERCRQIEMHAIKRLKKSSRKE 333

Query: 288 VELS 291
           + LS
Sbjct: 334 ILLS 337


>gi|303245332|ref|ZP_07331616.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           fructosovorans JJ]
 gi|302493181|gb|EFL53043.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           fructosovorans JJ]
          Length = 588

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 72/243 (29%), Positives = 125/243 (51%), Gaps = 16/243 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ WW
Sbjct: 350 AKQELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWW 409

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R   +L      +  PE+   IA++++ 
Sbjct: 410 IRQAITRAIADQARTIRI--PVHMIETINKLIRTSRYLVQELGRDPTPEE---IAERMDY 464

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR--N 226
              E +    ++A  E ++      D+  S   D++       ++ L   EE  N +   
Sbjct: 465 P-LEKVKKVLKIAK-EPISLETPIGDEEDSSLGDFI-----EDKKALAPAEEVVNTKLGE 517

Query: 227 MLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + + +S L PRE ++   R    +++  TLE +   F V+RER+RQIEA+A +K++  +
Sbjct: 518 QIGKVLSDLTPREEQVLRKRFGLGEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPV 577

Query: 285 QKQ 287
           + Q
Sbjct: 578 RSQ 580


>gi|33866155|ref|NP_897714.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. WH 8102]
 gi|33639130|emb|CAE08136.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 8102]
          Length = 313

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 82/294 (27%), Positives = 150/294 (51%), Gaps = 38/294 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVL--------------AKRYREHGDLS------------A 49
           +S Y+  I +IP+L   EE  L              +K + +H +L+            A
Sbjct: 20  VSWYLATIGRIPLLTPAEEIELGNQVQAMMTLTEDGSKTFEDH-ELTGKQRRMLRIGRRA 78

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             R++ ++LRLVV +A  Y+G GL + +++ EG++GL +AV+KFDP RG++ +TY+ WWI
Sbjct: 79  KERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWWI 138

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + +M   I      +++    +++     +R++   L         P + V IA+ +++ 
Sbjct: 139 RQSMTRAIACQSRTIRLPVHLSER--LTTIRKVS--LDLAHKLGAMPSR-VEIAEAMDIP 193

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             E+ S+  +     SL+A +N  +  S  +   L+ D    E + I   E++     L 
Sbjct: 194 LDELDSLLRQALTTSSLDAPVNGEEGRS--FLGDLIADSSLDEPLDI--VEQRIHHEQLG 249

Query: 230 RSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R +S L+ +E+ + + R  L+ N   TL  +    +VSRERVRQ+E +A +K++
Sbjct: 250 RWLSHLSEQEQHVLKLRFGLEGNERHTLAEIGRLMDVSRERVRQVELKALRKLR 303


>gi|116620135|ref|YP_822291.1| RpoD family RNA polymerase sigma factor [Candidatus Solibacter
           usitatus Ellin6076]
 gi|116223297|gb|ABJ82006.1| RNA polymerase, sigma 70 subunit, RpoD family [Candidatus
           Solibacter usitatus Ellin6076]
          Length = 563

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 76/243 (31%), Positives = 124/243 (51%), Gaps = 26/243 (10%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 319 TAKKELIEANLRLVVSIAKRYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 378

Query: 108 WIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           W++ A+   I      ++I      T N  +L    R++   L     N         +A
Sbjct: 379 WVRQAITRAIADQARTIRIPVHMIETIN--KLIRTSRQMVQELGREPSNE-------ELA 429

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG---QEQVLIEKEE 220
           K+L +  S+V  +  R+A  E ++      ++  S   D++V D +G    + V+     
Sbjct: 430 KRLQLPVSKVRKV-LRVA-QEPISLETPIGEEEESHLGDFIV-DQNGISPSDAVI----- 481

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFK 278
             N R    + +  L PRE +I + R   E+    TLE +   F V+RER+RQIEA+A +
Sbjct: 482 NLNLREQTAQVLKTLTPREEKIIKMRFGLEDGSEHTLEEVGQNFAVTRERIRQIEAKALR 541

Query: 279 KVQ 281
           K++
Sbjct: 542 KLR 544


>gi|317484461|ref|ZP_07943373.1| RNA polymerase sigma factor RpoD [Bilophila wadsworthia 3_1_6]
 gi|316924285|gb|EFV45459.1| RNA polymerase sigma factor RpoD [Bilophila wadsworthia 3_1_6]
          Length = 590

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 76/255 (29%), Positives = 124/255 (48%), Gaps = 34/255 (13%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           + A   L+ S+LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ 
Sbjct: 350 MRAKQELIRSNLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYAT 409

Query: 107 WWIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQV--- 159
           WWI+ A+   I      ++I      T N+      L R   +L      +  PE++   
Sbjct: 410 WWIRQAITRAIADQARTIRIPVHMIETINK------LIRTSRYLVQELGRDPTPEEIADR 463

Query: 160 ----VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
               V   KK+     E IS+   + GDE  ++L +  +   +      V +    EQ+ 
Sbjct: 464 MEYPVDKVKKVLKIAKEPISLETPI-GDEEDSSLGDFIEDKKAVAPAEEVVNTKLSEQI- 521

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIE 273
                           ++ L PRE ++   R    +++  TLE +   F V+RER+RQIE
Sbjct: 522 -------------ASVLADLTPREEQVLRKRFGIGEKSDHTLEEVGKLFNVTRERIRQIE 568

Query: 274 ARAFKKVQESIQKQV 288
           A+A +K++  ++ QV
Sbjct: 569 AKALRKLRHPVRSQV 583


>gi|18477828|emb|CAC83737.1| RNA polymerase sigma 70 [Rhodococcus fascians]
          Length = 474

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 81/318 (25%), Positives = 150/318 (47%), Gaps = 43/318 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGD-LS 48
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+ L 
Sbjct: 162 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLFAVEKMRESAEKGEKLP 220

Query: 49  AAHR----------------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
            A R                L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 221 VAQRRDMTWICRDGNRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 280

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L      
Sbjct: 281 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGR 338

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D + 
Sbjct: 339 EPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEA 390

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVR 270
            V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 391 VVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIR 450

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 451 QIESKTMSKLRHPSRSQV 468


>gi|331696864|ref|YP_004333103.1| RpoD subfamily RNA polymerase sigma-70 subunit [Pseudonocardia
           dioxanivorans CB1190]
 gi|326951553|gb|AEA25250.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pseudonocardia
           dioxanivorans CB1190]
          Length = 461

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 82/320 (25%), Positives = 151/320 (47%), Gaps = 47/320 (14%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRL--------- 53
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR  E G L AA RL         
Sbjct: 149 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRI-EAG-LYAAERLRRAIESGEK 205

Query: 54  -----------------------VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
                                  + ++LRLVV +A  Y G G+   +++ EGN+GL++AV
Sbjct: 206 VSPQLRRDLRWIVRDGERAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAV 265

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +KFD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L    
Sbjct: 266 EKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDL 323

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
                PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D 
Sbjct: 324 GREPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDS 375

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRER 268
           +  V ++       ++ L   ++ L+ RE  +   R       P TL+ +   + V+RER
Sbjct: 376 EAVVAVDAVSFTLLQDQLQSVLATLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRER 435

Query: 269 VRQIEARAFKKVQESIQKQV 288
           +RQIE++   K++   + QV
Sbjct: 436 IRQIESKTMSKLRHPSRSQV 455


>gi|306836272|ref|ZP_07469254.1| RNA polymerase sigma factor rpoD [Corynebacterium accolens ATCC
           49726]
 gi|304567864|gb|EFM43447.1| RNA polymerase sigma factor rpoD [Corynebacterium accolens ATCC
           49726]
          Length = 492

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 80/324 (24%), Positives = 156/324 (48%), Gaps = 49/324 (15%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREH-----------GD 46
           RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR     Y +H           GD
Sbjct: 174 RKDAQLTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYAQHRMDEMEKARAEGD 232

Query: 47  LSAA--------------------HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
            +A                     + L+ ++LRLVV +A  Y G G+   +++ EGN+GL
Sbjct: 233 KAAKLSPMEKRDLRSIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGL 292

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L
Sbjct: 293 IRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQREL 350

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    P++   +AK+++++E +V+ +        SL+  I   D+  SQ  D++  
Sbjct: 351 LQDLGREPTPQE---LAKEMDITEEKVMEIQQYAREPISLDQTIG--DEGDSQLGDFI-- 403

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEV 264
             D +  + ++       ++ L   ++ L+ RE  +   R  L +  P TL+ +   + V
Sbjct: 404 -EDSEAVIAVDAVSFTLLQDQLQDVLTTLSEREAGVVRLRFGLTDGMPRTLDEIGQVYGV 462

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           +RER+RQIE++   K++   + QV
Sbjct: 463 TRERIRQIESKTMSKLRHPSRSQV 486


>gi|312139434|ref|YP_004006770.1| sigma-70 factor siga [Rhodococcus equi 103S]
 gi|325672677|ref|ZP_08152373.1| RNA polymerase principal sigma factor SigA [Rhodococcus equi ATCC
           33707]
 gi|311888773|emb|CBH48085.1| sigma-70 factor SigA [Rhodococcus equi 103S]
 gi|325556554|gb|EGD26220.1| RNA polymerase principal sigma factor SigA [Rhodococcus equi ATCC
           33707]
          Length = 459

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 79/304 (25%), Positives = 143/304 (47%), Gaps = 46/304 (15%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHR-------------------------- 52
           Y+ +I K+ +L  +EE  LAKR  E G L A H+                          
Sbjct: 162 YLKQIGKVALLNAEEEVELAKRI-EAG-LFATHKMNEMAEKGEKPSPTDRRNLNWITRDG 219

Query: 53  ------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                 L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 220 NRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 279

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I    +   +   L R++  L         PE+   +AK++
Sbjct: 280 WWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGREPTPEE---LAKEM 334

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +V+ +        SL+  I   D+  SQ  D++    D +  V ++       ++
Sbjct: 335 DITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEAVVAVDAVSFTLLQD 389

Query: 227 MLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 390 QLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPS 449

Query: 285 QKQV 288
           + QV
Sbjct: 450 RSQV 453


>gi|325283594|ref|YP_004256135.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Deinococcus
           proteolyticus MRP]
 gi|324315403|gb|ADY26518.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Deinococcus
           proteolyticus MRP]
          Length = 487

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 81/299 (27%), Positives = 140/299 (46%), Gaps = 51/299 (17%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS--------------------------AAHR 52
           Y+HEI ++P+L  +EE  LA+R  E G+ +                          AA R
Sbjct: 190 YLHEIGRVPLLTLEEEIALARRI-EDGEFARVELEEKGEELDDRGRRALQRRMEDGAAAR 248

Query: 53  --LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
             L+ ++LRLVV IA  Y G GL   +++ EGN GL++AV+KF+  R ++ +TY+ WWI+
Sbjct: 249 QGLIEANLRLVVSIAKKYTGRGLNFLDLIQEGNQGLIRAVEKFEYRRRYKFSTYATWWIR 308

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-AIAKKLNVS 169
            A+   I      ++I    +       L R    LQ        PE++  A+    + +
Sbjct: 309 QAINRAIADQARTIRI--PVHMVETINKLTRTARQLQQELSREALPEEIAEAMGPGWDAN 366

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH-----DGQEQVLIEKEERKNR 224
           + E +    +    E ++      D+  S + D++  D+     D   + L+ +E     
Sbjct: 367 KVEEVQKVSQ----EPVSLETPIGDEKDSFYGDFIPDDNLDSPVDNAAKTLLSEE----- 417

Query: 225 RNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              L +++  L  RE  + + R+  +     TLE +   F V+RER+RQIE +A +K++
Sbjct: 418 ---LEKALGKLTEREAMVLKFRKGLVDGREHTLEEVGQRFNVTRERIRQIENKALRKLK 473


>gi|239906706|ref|YP_002953447.1| RNA polymerase sigma factor SigA [Desulfovibrio magneticus RS-1]
 gi|239796572|dbj|BAH75561.1| RNA polymerase sigma factor SigA [Desulfovibrio magneticus RS-1]
          Length = 588

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 72/243 (29%), Positives = 126/243 (51%), Gaps = 16/243 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ WW
Sbjct: 350 AKQELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWW 409

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R   +L      +  PE+   IA++++ 
Sbjct: 410 IRQAITRAIADQARTIRI--PVHMIETINKLIRTSRYLVQELGRDPTPEE---IAERMDY 464

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR--N 226
              +V  +  ++A  E ++      D+  S   D++       ++ L   EE  N +   
Sbjct: 465 PLEKVKKV-LKIAK-EPISLETPIGDEEDSSLGDFI-----EDKKALAPAEEVVNTKLGE 517

Query: 227 MLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + + +S L PRE ++   R    +++  TLE +   F V+RER+RQIEA+A +K++  +
Sbjct: 518 QIGKVLSDLTPREEQVLRKRFGLGEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPV 577

Query: 285 QKQ 287
           + Q
Sbjct: 578 RSQ 580


>gi|86158019|ref|YP_464804.1| sigma 32 (RpoH) [Anaeromyxobacter dehalogenans 2CP-C]
 gi|197122674|ref|YP_002134625.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter sp. K]
 gi|220917457|ref|YP_002492761.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter
           dehalogenans 2CP-1]
 gi|85774530|gb|ABC81367.1| sigma 32 (RpoH) [Anaeromyxobacter dehalogenans 2CP-C]
 gi|196172523|gb|ACG73496.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter sp. K]
 gi|219955311|gb|ACL65695.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter
           dehalogenans 2CP-1]
          Length = 241

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 54/149 (36%), Positives = 87/149 (58%), Gaps = 6/149 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+  +R  P L +++E+ LA R R+ G++SA  +LV  +L  VV IA   R   + +
Sbjct: 16  LAPYLKAVRDFPPLTREDEHALAIRARK-GEVSAKQKLVRHNLAFVVAIARKQRRGTVRL 74

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI--GTTANQK 133
            +++ EGN+GLM+AV+KFDP  G R +TY++WWI+A + +Y+  + S V+   GT A   
Sbjct: 75  DDLIQEGNVGLMRAVEKFDPHAGTRFSTYAVWWIRAYIGKYLKEARSTVRPQSGTVAQPD 134

Query: 134 RLFFNLRRLKG---HLQAITDNNLKPEQV 159
               +    +G   HL+ I D+   PE  
Sbjct: 135 LSLDSAIDEEGDATHLERIEDDGPGPEDT 163


>gi|94985446|ref|YP_604810.1| RNA polymerase, sigma 28 subunit [Deinococcus geothermalis DSM
           11300]
 gi|94555727|gb|ABF45641.1| RNA polymerase, sigma 28 subunit [Deinococcus geothermalis DSM
           11300]
          Length = 403

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 80/295 (27%), Positives = 138/295 (46%), Gaps = 38/295 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYRE----------HGDL----------------SA 49
           L +Y+HEI ++P+L   EE  LA+RY E          + DL                +A
Sbjct: 104 LRQYLHEIGRVPLLTVAEEMDLARRYEEGEAARQALDSNPDLDDRTRRQLQRQVEDGAAA 163

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+ ++LRLVV IA  Y   GL + +++ EGN GL++AV+KF+  RG++ +TY+ WWI
Sbjct: 164 KQALIEANLRLVVSIAKRYTNRGLGLLDLIQEGNQGLIRAVEKFEYRRGYKFSTYATWWI 223

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ-AITDNNLKPEQVVAIAKKLNV 168
           + ++   I      +++    +       L R+   L+  ++   L  E   A+    + 
Sbjct: 224 RQSLTRAIADKSRTIRV--PVHMVETINRLSRMTRQLEMELSREPLPAEIAEAMGPGWDA 281

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           ++ E      +  G E ++  +   ++  S + D+L  D        I+   +      L
Sbjct: 282 AKVE----ETQKVGWEPMSLEMPIGEEGDSTYGDFLPDDRFASP---IQNASQALLSEAL 334

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R+   LN RE  +   R   +  +  TLE +     V+RERVRQIE +A +K++
Sbjct: 335 ERAFGTLNEREALVLRLRHGFVDGHEHTLEEVGQLLSVTRERVRQIENKALRKLK 389


>gi|282900041|ref|ZP_06308000.1| sigC (Sigma 28 (Flagella/Sporulation)) [Cylindrospermopsis
           raciborskii CS-505]
 gi|281195073|gb|EFA70011.1| sigC (Sigma 28 (Flagella/Sporulation)) [Cylindrospermopsis
           raciborskii CS-505]
          Length = 432

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 67/238 (28%), Positives = 127/238 (53%), Gaps = 13/238 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           + A   ++ ++LRLVV +A  Y+  GL + ++V EG +GL +AV+KFDP +G+R +TY+ 
Sbjct: 191 IQAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAY 250

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   I  S   +++     +K     L ++K   + I     +   +  +A +L
Sbjct: 251 WWIRQGITRAIATSSRTIRLPVHITEK-----LNKIKKAQRKIAQEKGRTPTLEDLALEL 305

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++ ++V  +  R+    SL   +   DK+ ++  + L  D    E+ L+ +  +K+  +
Sbjct: 306 DMTPNQVREVLLRVPRSVSLETKVG-KDKD-TELGELLETDTITPEETLMRESLQKDIHH 363

Query: 227 MLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +L    S L  RER +   R      +  +L  +    E+SRERVRQIE++A +K+++
Sbjct: 364 LL----SDLTTREREVILMRFGLADGHSYSLAEIGRALELSRERVRQIESKALQKLRQ 417


>gi|87311289|ref|ZP_01093411.1| transcription initiation factor sigma 70 [Blastopirellula marina
           DSM 3645]
 gi|87286029|gb|EAQ77941.1| transcription initiation factor sigma 70 [Blastopirellula marina
           DSM 3645]
          Length = 567

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 81/263 (30%), Positives = 122/263 (46%), Gaps = 32/263 (12%)

Query: 38  AKRYREHGDL--SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            +RYR   D        L + +LRLVV IA  YR  GL   +++ EGN GLM+AV K++ 
Sbjct: 312 CERYRRQFDEYEKVKRELSSGNLRLVVSIAKKYRNRGLSFLDLIQEGNTGLMRAVDKYEY 371

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA---------NQKRLFFNLRRLKGHL 146
            RGF+ +TY+ WWI+ A+   I      ++I              QKRL   LRR     
Sbjct: 372 RRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMIDVLSKLRNVQKRLLQELRR----- 426

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +   D          IA++  +   EV  +        SL+  I  S+ +S     +  +
Sbjct: 427 EPTMDE---------IARRAEIDLEEVRRVMDIGRQPVSLDRPIGESEDSS-----FGEF 472

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEV 264
             D  E+  I     +  R+ +   +  L  RER I + R    +    TLE +   F+V
Sbjct: 473 IEDSHEETPIRSASNQILRDRIQGLLKTLTYREREIIKLRYGLGDGYTYTLEEVGRIFKV 532

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RERVRQIEA+A +K+Q  ++ Q
Sbjct: 533 TRERVRQIEAKAVRKLQHPVRSQ 555


>gi|291566702|dbj|BAI88974.1| group 2 RNA polymerase sigma factor SigB [Arthrospira platensis
           NIES-39]
          Length = 334

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 70/300 (23%), Positives = 142/300 (47%), Gaps = 52/300 (17%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDL------------------------------- 47
           Y+HEI ++P+L ++EE +  K+ ++  +L                               
Sbjct: 30  YLHEIGRVPLLTREEEIIYGKKVQQMMNLLEVRDELTKELDRDPTPEEWSAKAGLSESEM 89

Query: 48  --------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                    A  +++ ++LRLVV IA  Y+   +   +++ EG +GL + V+KFDP RG+
Sbjct: 90  TDIINRGRRAKQKMIEANLRLVVSIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPMRGY 149

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWI+ A+   I ++   +++     +K     ++R++  L      N  P + 
Sbjct: 150 KFSTYAYWWIRQAITRAIAQNSRTIRLPIHITEK--LNKIKRVQRELFQQYGRNATPTE- 206

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IAK L++  S++   +  LA    ++  +   D   ++ QD L  +    +  + ++ 
Sbjct: 207 --IAKALDLEPSQI--RDYLLASRHPVSLDLRVGDNQDTELQDLLEDESASADSYVTQQL 262

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
            R++ ++M    M+ L P++R +   R    +   ++L  +  +  +SRERVRQ+E +A 
Sbjct: 263 LRQDLKDM----MADLTPQQREVLTLRYGLNDGKEMSLSKVGVQMNISRERVRQLENQAL 318


>gi|78777303|ref|YP_393618.1| RNA polymerase sigma factor RpoD [Sulfurimonas denitrificans DSM
           1251]
 gi|78497843|gb|ABB44383.1| sigma 28 (Flagella/Sporulation) [Sulfurimonas denitrificans DSM
           1251]
          Length = 623

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 72/242 (29%), Positives = 121/242 (50%), Gaps = 31/242 (12%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           ++  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ ++G++ +TY+ WWI+ 
Sbjct: 387 KMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYQKGYKFSTYATWWIRQ 446

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE-QVVAIAKKLNVSE 170
           A+   I      ++I     +     N + ++ HLQ   ++  +P+ +V+A+   L+V +
Sbjct: 447 AISRAIADQARTIRIPIHMIETINRIN-KIMRKHLQ---EHGKEPDVEVIALEVGLSVEK 502

Query: 171 --------SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
                    E IS+   +  ++         DK S    D ++ D               
Sbjct: 503 VKNVIKITKEPISLEAPIGSEDDGRFGDFIEDKTSLSPSDAILKD--------------- 547

Query: 223 NRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           + R  +   +  LN RE+ + + R      E+  TLE +  E  V+RERVRQIE+ A KK
Sbjct: 548 DLRVQIESVLEQLNEREKAVIKLRFGIMDDESDRTLEEIGKELNVTRERVRQIESSAIKK 607

Query: 280 VQ 281
           ++
Sbjct: 608 LK 609


>gi|34558185|ref|NP_908000.1| RNA polymerase sigma factor RpoD [Wolinella succinogenes DSM 1740]
 gi|34483904|emb|CAE10900.1| RNA POLYMERASE SIGMA FACTOR [Wolinella succinogenes]
          Length = 620

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 71/256 (27%), Positives = 121/256 (47%), Gaps = 34/256 (13%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           KR ++  D  A  ++  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ ++G
Sbjct: 372 KRGKDIAD-KAKTKMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKKG 430

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           ++ +TY+ WWI+ A+   I      ++I        +   + R+   ++       K   
Sbjct: 431 YKFSTYATWWIRQAISRAIADQARTIRIPI-----HMIETINRINKIIRKYLQEEGKEPD 485

Query: 159 VVAIAKKLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           V  I++++ +   +V          IS+   +  DE         DK+S    D ++   
Sbjct: 486 VETISEEVGLPVDKVKNVIKITKEPISLEAPIGSDEDGKFGDFVEDKSSVGPMDHIL--- 542

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVS 265
                       +++ +  +   +  LN RE+ +   R      E+  TLE +  E  V+
Sbjct: 543 ------------KEDLKTQIDEVLDQLNEREKAVIRMRFGLLEDESDRTLEEIGKELNVT 590

Query: 266 RERVRQIEARAFKKVQ 281
           RERVRQIE+ A KK++
Sbjct: 591 RERVRQIESSAIKKLK 606


>gi|168704590|ref|ZP_02736867.1| RNA polymerase sigma factor rpoS [Gemmata obscuriglobus UQM 2246]
          Length = 278

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 79/278 (28%), Positives = 127/278 (45%), Gaps = 27/278 (9%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ EI +  +L   +E  LA R    GD  A  ++V ++LRLVV IA GY G GL +
Sbjct: 16  LETYLREINETALLTADQEKSLA-RAIAQGDTEARDQMVRANLRLVVNIARGYTGKGLAL 74

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GL++AV+ FDP    R +TY+ +WIK +++  ++ +   ++I   A    L
Sbjct: 75  QDLIEEGNLGLLRAVEGFDPTMNTRFSTYASYWIKQSIKRALVNTAKTIRI--PAYMVEL 132

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM----NCRLAGDE-----SL 186
               RR    L          E+V  +        + +       N     D+     S+
Sbjct: 133 LAKWRRATNKLSDELGRPPTHEEVGKLLGLPKKKLAIIKKAIRVYNAAPQADQGDQGWSI 192

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
             ++     N ++  D  + + D  +QVLI  E+   R   + R    LN          
Sbjct: 193 EEMLMD---NRAKTPDTEMVETDDLKQVLILLEKMDQREATVLRMRFGLN---------- 239

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              E P TL+ +     ++RERVRQIE  A  K+ E +
Sbjct: 240 --DEEPKTLKEIGECLGLTRERVRQIEGEALAKLGEDL 275


>gi|14581457|gb|AAK29754.1| stationary phase sigma factor RpoS [Azotobacter vinelandii]
          Length = 238

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 45/99 (45%), Positives = 67/99 (67%), Gaps = 1/99 (1%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           ++EI   P+L   EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + +++
Sbjct: 1   LNEIGFSPLLTPAEEVHFA-RLAQRGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDLI 59

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
            EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+
Sbjct: 60  EEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIM 98


>gi|282897491|ref|ZP_06305492.1| sigC (Sigma 28 (Flagella/Sporulation)) [Raphidiopsis brookii D9]
 gi|281197586|gb|EFA72481.1| sigC (Sigma 28 (Flagella/Sporulation)) [Raphidiopsis brookii D9]
          Length = 429

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 67/238 (28%), Positives = 127/238 (53%), Gaps = 13/238 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           + A   ++ ++LRLVV +A  Y+  GL + ++V EG +GL +AV+KFDP +G+R +TY+ 
Sbjct: 188 IQAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAY 247

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   I  S   +++     +K     L ++K   + I     +   +  +A +L
Sbjct: 248 WWIRQGITRAIATSSRTIRLPVHITEK-----LNKIKKAQRKIAQEKGRTPTLEDLALEL 302

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++ ++V  +  R+    SL   +   DK+ ++  + L  D    E+ L+ +  +K+  +
Sbjct: 303 DMTPNQVREVLLRVPRSVSLETKVG-KDKD-TELGELLETDTITPEETLMRESLQKDIHH 360

Query: 227 MLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +L    S L  RER +   R      +  +L  +    E+SRERVRQIE++A +K+++
Sbjct: 361 LL----SDLTTREREVILMRFGLADGHSYSLAEIGRALELSRERVRQIESKALQKLRQ 414


>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 = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 119/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 580 AKKEMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 639

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +   +P+    +A K+ +
Sbjct: 640 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGAEPDPAT-LAVKMEM 694

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + RN++
Sbjct: 695 PEDKIRKI-MKIAK-EPISMETPIGDDDDSHLGDFI---EDNNTLAPSDAALHASMRNVV 749

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 750 KDVLDSLTPREAKVLRMRFGVEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 804


>gi|242279084|ref|YP_002991213.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           salexigens DSM 2638]
 gi|242121978|gb|ACS79674.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           salexigens DSM 2638]
          Length = 585

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 75/256 (29%), Positives = 125/256 (48%), Gaps = 35/256 (13%)

Query: 44  HGDLSA---AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           HG+ SA      L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++
Sbjct: 339 HGNRSAMRAKQELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYK 398

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I    +       L R   +L      +  PE++ 
Sbjct: 399 FSTYATWWIRQAITRAIADQARTIRI--PVHMIETINKLIRTSRYLVQELGRDPSPEEIA 456

Query: 161 --------AIAKKLNVSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDG 210
                    + K L +++ E IS+   +    D SL   I   DK ++   + +V    G
Sbjct: 457 ERMDYPLEKVKKVLKIAK-EPISLETPIGDEEDSSLGDFI--EDKKAAAPAEEVVSTKLG 513

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRER 268
           ++               +   +S L PRE ++   R    +++  TLE +   F V+RER
Sbjct: 514 EQ---------------IATVLSDLTPREEQVLRKRFGIGEKSDHTLEEVGKLFNVTRER 558

Query: 269 VRQIEARAFKKVQESI 284
           +RQIEA+A +K++  +
Sbjct: 559 IRQIEAKALRKLRHPV 574


>gi|148284623|ref|YP_001248713.1| RNA polymerase sigma factor [Orientia tsutsugamushi str. Boryong]
 gi|146740062|emb|CAM80186.1| RNA polymerase sigma factor [Orientia tsutsugamushi str. Boryong]
          Length = 614

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 74/243 (30%), Positives = 126/243 (51%), Gaps = 16/243 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+ RLVV +A  Y   GLP  +++ EGNIGLM+AV K++   G++ +T + WW
Sbjct: 365 AKKKMVESNTRLVVHVAKPYVNRGLPFLDLIQEGNIGLMKAVDKYNYLLGYKFSTCATWW 424

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA-IAKKLN 167
           ++ ++   +      ++I    +       + R+   +     N L  E   + IA+KL+
Sbjct: 425 VRQSISRAVADQARTIRI--PVHMADTISKIVRVSKQMH----NELGYEPTASEIAEKLS 478

Query: 168 VSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +   +V  +  R+A +  SL   I   D   S   D++    D    + IE+  + + R 
Sbjct: 479 MPIDKVKKV-MRIAKEPVSLENPIGEED--GSCLSDFI---EDKNAVLPIEEAIKFSLRE 532

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR++S L  RE R+   R     P   TLE +  EF+V+RERVRQIEA+A +K++  +
Sbjct: 533 TTTRALSTLTAREERVLRLRFGIGLPTDYTLEEVGGEFKVTRERVRQIEAKALRKLKHPV 592

Query: 285 QKQ 287
           + +
Sbjct: 593 RSK 595


>gi|225874024|ref|YP_002755483.1| RNA polymerase sigma factor rpoD [Acidobacterium capsulatum ATCC
           51196]
 gi|83356350|gb|ABC16653.1| major sigma factor RpoD [Acidobacterium capsulatum]
 gi|225793569|gb|ACO33659.1| RNA polymerase sigma factor rpoD [Acidobacterium capsulatum ATCC
           51196]
          Length = 597

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 75/247 (30%), Positives = 127/247 (51%), Gaps = 23/247 (9%)

Query: 44  HGDLSAAH---RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
            GD+ A      L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 347 QGDMDAEQAKRELIEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 406

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKP 156
            +TY+ WWI+ A+   I      ++I      T N  +L    R+L   +Q +       
Sbjct: 407 FSTYATWWIRQAITRAIADQARTIRIPVHMIETIN--KLIRTSRQL---VQELGREPTSE 461

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           E    IA+++++  ++V  +  ++A  E ++      ++  S   D++    D Q     
Sbjct: 462 E----IARRMDIPVAKVRKV-LKIA-QEPISLETPIGEEEDSHLGDFI---EDSQAVSPS 512

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEA 274
           E     N +   ++ +  L PRE R+ + R   E+    TLE +   F+V+RER+RQIEA
Sbjct: 513 EAVISVNLKEYTSQVLRTLTPREERVIKMRFGLEDGSEHTLEEVGQSFQVTRERIRQIEA 572

Query: 275 RAFKKVQ 281
           +A +K++
Sbjct: 573 KALRKLR 579


>gi|242078297|ref|XP_002443917.1| hypothetical protein SORBIDRAFT_07g004340 [Sorghum bicolor]
 gi|241940267|gb|EES13412.1| hypothetical protein SORBIDRAFT_07g004340 [Sorghum bicolor]
          Length = 500

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 78/247 (31%), Positives = 131/247 (53%), Gaps = 28/247 (11%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L  S++RLV+ IA  Y   G+ +++++  G IGL++ ++KFD  RGFR++TY  WWI+  
Sbjct: 261 LTMSNIRLVISIAQKYDNLGVELADLIQGGLIGLLRGIEKFDASRGFRISTYVYWWIRQG 320

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +  +    ++ T  +++     L  ++G   A+ D  + P  V  IA+ LN+SE +
Sbjct: 321 VSRALADNSKAFRLPTYLHER-----LIAIRGAKYALEDQGIAP-TVENIAESLNISEKK 374

Query: 173 VI----SMNCRLAGDE----SLNALINSSDKNSSQWQDWLVYD---HDGQEQVLIEKEER 221
           V     ++N  L+ D+    SLN L    D   S  +D  V +   H  +E+ L  KEE 
Sbjct: 375 VHNATEAVNKVLSLDQQAFPSLNGL--PGDTLHSYIEDQNVANDPWHGFEERYL--KEEV 430

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARR-LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            N  N      S LN RER I      + +   T E++S +F +SRERVRQ+   A +K+
Sbjct: 431 NNLIN------STLNERERDIIRLYHGIGKQCHTWEDISRQFGLSRERVRQVGLVAMEKL 484

Query: 281 QESIQKQ 287
           + + +++
Sbjct: 485 KHAARRK 491


>gi|42521867|ref|NP_967247.1| RNA polymerase sigma factor RpoD [Bdellovibrio bacteriovorus HD100]
 gi|39574397|emb|CAE77901.1| RNA polymerase sigma factor RpoD [Bdellovibrio bacteriovorus HD100]
          Length = 609

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 75/243 (30%), Positives = 125/243 (51%), Gaps = 26/243 (10%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 370 AAKSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 429

Query: 108 WIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           WI+ A+   I      ++I      T N+      L R   +L         PE+   IA
Sbjct: 430 WIRQAITRAIADQARTIRIPVHMIETINK------LVRTSRYLIQELGREPTPEE---IA 480

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
            K+++   +V  +  ++A  E ++      ++  S   D++      +++ +I   E   
Sbjct: 481 DKMDMPVDKVRKV-LKIA-KEPISLETPVGEEEDSHLGDFI------EDKKVINPAEAIV 532

Query: 224 RRNMLT---RSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFK 278
             N+     R +S L PRE ++   R    +E+  TLE +  +F V+RER+RQIEA+A +
Sbjct: 533 NLNLAEQTRRVLSTLTPREEKVLRMRFGIGEESDHTLEEVGQDFNVTRERIRQIEAKALR 592

Query: 279 KVQ 281
           K++
Sbjct: 593 KLR 595


>gi|4587113|dbj|BAA76622.1| RpoT [Mycobacterium leprae]
          Length = 576

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 79/319 (24%), Positives = 148/319 (46%), Gaps = 45/319 (14%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------- 43
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR                      
Sbjct: 264 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSERGTKLP 322

Query: 44  ------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                        GD +  H L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 323 TAQRRDMMWICRDGDRAKNH-LLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 381

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L     
Sbjct: 382 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLG 439

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 440 REPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSE 491

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 492 AVVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 551

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 552 RQIESKTMSKLRHPSRSQV 570


>gi|307700837|ref|ZP_07637862.1| RNA polymerase sigma factor RpoD [Mobiluncus mulieris FB024-16]
 gi|307613832|gb|EFN93076.1| RNA polymerase sigma factor RpoD [Mobiluncus mulieris FB024-16]
          Length = 614

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 80/309 (25%), Positives = 145/309 (46%), Gaps = 61/309 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH----------------------GDLSAAH 51
           Y+ +I K+ +L  ++E  LAKR     Y EH                        ++A +
Sbjct: 320 YLKQIGKVALLNAEQEVNLAKRIEAGLYAEHLLKTEQDSMTPKHARELHWVVQDGVNAKN 379

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 380 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYSKGYKFSTYATWWIRQ 439

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      +++              Q+++  +L R     +   + ++ PE+VV +
Sbjct: 440 AITRAMADQARTIRVPVHMVEVINKLARVQRQMLQDLGREPTPDELARELDMTPEKVVEV 499

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D    V+++++ 
Sbjct: 500 QKYGR----EPISLHTPLGEDGDSEFGDLIEDSE---------AVVPADAVSFVMLQEQ- 545

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAFK 278
                  L R +  L+ RE  +   R  L +  P TL+++   + V+RER+RQIE++   
Sbjct: 546 -------LQRVLDTLSEREAGVIAMRYGLNDGVPKTLDDIGHRYGVTRERIRQIESKTMS 598

Query: 279 KVQESIQKQ 287
           K++   + Q
Sbjct: 599 KLRHPARSQ 607


>gi|288957899|ref|YP_003448240.1| RNA polymerase primary sigma factor [Azospirillum sp. B510]
 gi|288910207|dbj|BAI71696.1| RNA polymerase primary sigma factor [Azospirillum sp. B510]
          Length = 670

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 114/243 (46%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 432 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 491

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R    +         PE++         
Sbjct: 492 IRQAITRSIADQARTIRI--PVHMIETINKLVRTSRQMLHEIGREPTPEELAERLMMPLE 549

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + K L +++ E IS+   +  +E  +      DKN+    D  +               
Sbjct: 550 KVRKVLKIAK-EPISLETPIGDEEDSHLGDFIEDKNAVLPLDAAI--------------- 593

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           + N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +
Sbjct: 594 QANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTRERIRQIEAKALR 653

Query: 279 KVQ 281
           K++
Sbjct: 654 KLK 656


>gi|262199546|ref|YP_003270755.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Haliangium
           ochraceum DSM 14365]
 gi|262082893|gb|ACY18862.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Haliangium
           ochraceum DSM 14365]
          Length = 697

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 82/278 (29%), Positives = 138/278 (49%), Gaps = 40/278 (14%)

Query: 24  RKIPMLEKQ-----EEYVLAKRYREHGDLS-----AAHRLVTSHLRLVVKIAMGYRGYGL 73
           +KI +LE++     EE  L + +RE  D       A   LV ++LRLVV IA  Y   GL
Sbjct: 426 KKIKVLEEECRSSVEE--LRQTFREMSDGERMAERAKSELVEANLRLVVSIAKKYTNRGL 483

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGNIGLM+AV KF+ +RG++ +TY+ WWI+ A+   I      ++I    +  
Sbjct: 484 QFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMI 541

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVV--------AIAKKLNVSESEVISMNCRLAGDES 185
                L R   +L         PE++          + K L +++ E IS+   +  +E 
Sbjct: 542 ETINKLVRTSRYLVQELGREPTPEEIAERMELPLDKVRKVLKIAK-EPISLETPIGEEED 600

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
            +      DK+ +   D ++        V + ++ RK         ++ L PRE ++   
Sbjct: 601 SHLGDFIEDKSVTSPSDAVI-------SVNLAEQTRK--------VLATLTPREEKVLRM 645

Query: 246 RR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R    +++  TLE +  +FEV+RER+RQIEA+A +K++
Sbjct: 646 RFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLR 683


>gi|56752254|ref|YP_172955.1| RNA polymerase sigma factor SigC [Synechococcus elongatus PCC 6301]
 gi|81300658|ref|YP_400866.1| RNA polymerase sigma factor SigC [Synechococcus elongatus PCC 7942]
 gi|56687213|dbj|BAD80435.1| group2 RNA polymerase sigma factor RpoD5 [Synechococcus elongatus
           PCC 6301]
 gi|81169539|gb|ABB57879.1| group2 RNA polymerase sigma factor SigC [Synechococcus elongatus
           PCC 7942]
          Length = 398

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 75/271 (27%), Positives = 140/271 (51%), Gaps = 24/271 (8%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           ++GL R+  E+ ++ + E ++     +R ++H        ++ ++LRLVV +A  Y+  G
Sbjct: 132 QLGLHRWA-EVCQLDLEELKQVCKEGQRAKDH--------MIKANLRLVVSVAKKYQNRG 182

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L + ++V EG +GL +AV+KFDP +G+R +TY+ WWI+  +   I      +++     +
Sbjct: 183 LELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHVTE 242

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
           K     L R+K   + I     +   +  IA++L ++  +V  +  R+    SL   +  
Sbjct: 243 K-----LNRIKKAQRKIAQTKGRTANLEEIAQELEMTPDQVREVLLRVPKSISLETRVGK 297

Query: 193 SDKNSSQWQDWL-VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQE 250
             +  ++  D L   D   +E++  E     +  N L R +  LN RER +   R  L++
Sbjct: 298 --EKDTELGDLLETTDFTPEERLTQE-----SLSNDLQRLLLELNHRERDVIRMRFGLRD 350

Query: 251 NPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
             + +L  +    ++SRERVRQIEA+A +K+
Sbjct: 351 GQIYSLAEIGQVLDLSRERVRQIEAKALQKL 381


>gi|224823888|ref|ZP_03696997.1| RNA polymerase, sigma 70 subunit, RpoD [Lutiella nitroferrum 2002]
 gi|224604343|gb|EEG10517.1| RNA polymerase, sigma 70 subunit, RpoD [Lutiella nitroferrum 2002]
          Length = 640

 Score = 94.4 bits (233), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 73/245 (29%), Positives = 119/245 (48%), Gaps = 32/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 397 AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 456

Query: 109 IKAAMQEYILRSWSLVKIG-----TTANQKRLFFNLRRLKGH---LQAITDNNLKPEQVV 160
           I+ A+   I      ++I      T     R+   + +  GH      + +    PE   
Sbjct: 457 IRQAITRSIADQARTIRIPVHMIETINKMNRISRQILQETGHEPDPAELAERMEMPED-- 514

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEK 218
            I K + +S+ E ISM   +  D+  +      D+N+    D  +Y    D  ++VL   
Sbjct: 515 KIRKIMKISK-EPISMETPIGDDDDSHLGDFIEDQNNLAPSDAAMYSSLKDATKEVL--- 570

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARA 276
                           L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A
Sbjct: 571 --------------ETLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 616

Query: 277 FKKVQ 281
            +K++
Sbjct: 617 LRKLR 621


>gi|212702263|ref|ZP_03310391.1| hypothetical protein DESPIG_00274 [Desulfovibrio piger ATCC 29098]
 gi|212674326|gb|EEB34809.1| hypothetical protein DESPIG_00274 [Desulfovibrio piger ATCC 29098]
          Length = 589

 Score = 94.0 bits (232), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 75/252 (29%), Positives = 122/252 (48%), Gaps = 30/252 (11%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           + A   L+ S+LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ 
Sbjct: 349 MRAKQELIRSNLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYAT 408

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV------- 159
           WWI+ A+   I      ++I    +       L R   +L      +  PE++       
Sbjct: 409 WWIRQAITRAIADQARTIRI--PVHMIETINKLIRTSRYLVQELGRDPTPEEIAERMEYP 466

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           V   KK+     E IS+   + GDE                +D  + D    ++ +   E
Sbjct: 467 VEKVKKVLKIAKEPISLETPI-GDE----------------EDSSLGDFIEDKKAVAPAE 509

Query: 220 ERKNRR--NMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
           E  N +    L   ++ L PRE ++   R    +++  TLE +   F V+RER+RQIEA+
Sbjct: 510 EVINTKLSEQLAAVLADLTPREEQVLRKRFGIAEKSDHTLEEVGKLFNVTRERIRQIEAK 569

Query: 276 AFKKVQESIQKQ 287
           A +K++  ++ Q
Sbjct: 570 ALRKLRHPVRSQ 581


>gi|153003633|ref|YP_001377958.1| RNA polymerase sigma-70 subunit RpoD [Anaeromyxobacter sp. Fw109-5]
 gi|152027206|gb|ABS24974.1| RNA polymerase, sigma 70 subunit, RpoD [Anaeromyxobacter sp.
           Fw109-5]
          Length = 819

 Score = 94.0 bits (232), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 72/249 (28%), Positives = 118/249 (47%), Gaps = 28/249 (11%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           EH    A   LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +
Sbjct: 575 EHKAERAKTELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYKRGYKFS 634

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-- 160
           TY+ WWI+ A+   I      ++I    +       L R   +L         PE++   
Sbjct: 635 TYATWWIRQAITRAIADQARTIRI--PVHMIETINKLIRTSRYLVQELGREPTPEEIAEK 692

Query: 161 ------AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
                  + K L ++  E IS+   +  +E  +      DK+     D ++         
Sbjct: 693 MELPLDKVRKVLKIA-KEPISLETPIGEEEDSHLGDFIEDKSLVSPSDAVIN-------- 743

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQI 272
                   N      + ++ L PRE ++   R    +++  TLE +  +FEV+RER+RQI
Sbjct: 744 -------MNLAEQTRKVLATLTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQI 796

Query: 273 EARAFKKVQ 281
           EA+A +K++
Sbjct: 797 EAKALRKLR 805


>gi|113953662|ref|YP_731106.1| type II alternative RNA polymerase sigma factor [Synechococcus sp.
           CC9311]
 gi|113881013|gb|ABI45971.1| Possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. CC9311]
          Length = 307

 Score = 94.0 bits (232), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 80/247 (32%), Positives = 128/247 (51%), Gaps = 22/247 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A ++++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG R +TY+ WW
Sbjct: 65  AKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSTYAYWW 124

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE-QVVAIAKKLN 167
           I+  +   +      ++I    N+K     LR  K  L  +  N L P  + +A   KL 
Sbjct: 125 IRQGLNRALSTQSRTIRIPVNVNEK--LTRLRAAKARL--MQSNGLAPSAEQLAECMKLP 180

Query: 168 VSESEVISMNCRL-AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR- 225
           +SE E + + C L +   SL  ++ S   + S+  D L  D    E   +E+ E   R  
Sbjct: 181 ISEVEDL-LGCELRSVTVSLQGVVKSKS-DPSELVDVLPSD----EIPPMERAEIAERTD 234

Query: 226 ---NMLTRSMSVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKK 279
              N+L  S   L P+ER I   R   +      TL  ++ +   SRE  RQ+  RA +K
Sbjct: 235 SAWNLLDNSN--LTPKERTIVMLRFGLDGSHEWRTLAEVARQMNCSREYCRQVVQRALRK 292

Query: 280 VQE-SIQ 285
           +++ SIQ
Sbjct: 293 LRKTSIQ 299


>gi|20808499|ref|NP_623670.1| DNA-directed RNA polymerase sigma subunits (sigma70/sigma32)
           [Thermoanaerobacter tengcongensis MB4]
 gi|20517120|gb|AAM25274.1| DNA-directed RNA polymerase sigma subunits (sigma70/sigma32)
           [Thermoanaerobacter tengcongensis MB4]
          Length = 265

 Score = 94.0 bits (232), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 77/267 (28%), Positives = 133/267 (49%), Gaps = 35/267 (13%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQ 88
           EK +E+ L +R R +GD  A   +V  ++ LVV IA  + + YG+ + +++ EG IGL+ 
Sbjct: 8   EKTDEFELFERLR-NGDKKARDEIVEKNIGLVVSIAANFSKAYGVELDDLIQEGFIGLLA 66

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++ FD  +G+R +TY++++IK  +Q YI      + +     QK            L  
Sbjct: 67  AIEGFDHTKGYRFSTYAVFYIKQKIQRYIWGRSRTIHLPVKTYQK------------LNQ 114

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           +    LK EQV   A    ++E   I        +E +N L   S KN +   +  +Y++
Sbjct: 115 VLSAQLKLEQVKGEAFPEEIAEETGIKT------EEVVNLL---SLKNPTVSLNQQLYEN 165

Query: 209 DGQEQV-LIEKEERKNR----------RNMLTRSMSVLNPRERRIFEARR-LQENPVTLE 256
           D  E + +I  E+ +N           R +L   + VL  +ER + E R  L   P+TL+
Sbjct: 166 DNTELIDVILDEQSENEIDRNYSLEELRKILKECLEVLPEKERSVLEMRYGLNGTPMTLK 225

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQES 283
            ++    +S++R  QIE RA ++++ S
Sbjct: 226 QIAEILNISKQRAGQIEKRALQRLRNS 252


>gi|189183187|ref|YP_001936972.1| RNA polymerase sigma factor RpoD [Orientia tsutsugamushi str.
           Ikeda]
 gi|189179958|dbj|BAG39738.1| RNA polymerase sigma factor RpoD [Orientia tsutsugamushi str.
           Ikeda]
          Length = 615

 Score = 94.0 bits (232), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 74/243 (30%), Positives = 126/243 (51%), Gaps = 16/243 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+ RLVV +A  Y   GLP  +++ EGNIGLM+AV K++   G++ +T + WW
Sbjct: 366 AKKKMVESNTRLVVHVAKPYVNRGLPFLDLIQEGNIGLMKAVDKYNYLLGYKFSTCATWW 425

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA-IAKKLN 167
           ++ ++   +      ++I    +       + R+   +     N L  E   + IA+KL+
Sbjct: 426 VRQSISRAVADQARTIRI--PVHMADTISKIVRVSKQMH----NELGYEPTASEIAEKLS 479

Query: 168 VSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +   +V  +  R+A +  SL   I   D   S   D++    D    + IE+  + + R 
Sbjct: 480 MPIDKVKKV-MRIAKEPVSLENPIGEED--GSCLSDFI---EDKNAILPIEEAIKFSLRE 533

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR++S L  RE R+   R     P   TLE +  EF+V+RERVRQIEA+A +K++  +
Sbjct: 534 TTTRALSTLTAREERVLRLRFGIGLPTDYTLEEVGGEFKVTRERVRQIEAKALRKLKHPV 593

Query: 285 QKQ 287
           + +
Sbjct: 594 RSK 596


>gi|219130701|ref|XP_002185497.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217403028|gb|EEC42984.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 329

 Score = 94.0 bits (232), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 72/245 (29%), Positives = 123/245 (50%), Gaps = 14/245 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L A   L  S++RLVV IA  Y+  GL   ++  EG +GL +A +KFDPERGFR +TY+ 
Sbjct: 75  LRAKAALTESNIRLVVSIAKRYQHRGLSFQDLAQEGILGLTRACEKFDPERGFRFSTYAS 134

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA----I 162
           WWIK ++   I      +++    + +     LR+++  L+A    + + E++       
Sbjct: 135 WWIKQSIMRAIADQGRTIRLPVHIHDQ--INALRKVERELKAELGRDARLEEITEKSTLT 192

Query: 163 AKK---LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           A+K   LN    + +SM   L   +S  +       +       ++ D + Q     E+ 
Sbjct: 193 AEKIEFLNRVSQQDVSMEQELRTSKSKGSSAGLGGPDGGLTLGDVMGDPEAQP---AEEA 249

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             +  ++ ++R +  LN RE+ +   R  L +    TLE +   F V+RER+RQIE+RA 
Sbjct: 250 SYQMLKDDISRLICTLNSREQAVIRMRFGLDDGKAKTLEEIGRRFSVTRERIRQIESRAL 309

Query: 278 KKVQE 282
            K+++
Sbjct: 310 HKLRQ 314


>gi|220906009|ref|YP_002481320.1| RNA polymerase sigma-70 subunit RpoD subfamily [Cyanothece sp. PCC
           7425]
 gi|219862620|gb|ACL42959.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7425]
          Length = 372

 Score = 94.0 bits (232), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 75/245 (30%), Positives = 126/245 (51%), Gaps = 27/245 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +++ S+LRLVV IA  Y   G+P  ++V EG +GL +A +KFDPE+GF+ +TY+ WW
Sbjct: 134 AKSKMIRSNLRLVVSIAKRYLNRGVPFLDLVQEGALGLNRATEKFDPEKGFKFSTYAYWW 193

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   I      +++     +K     L++L+ HL+     N   EQ +A A ++ +
Sbjct: 194 IRQGITRAIANDSRTIRLPIHIVEK--LNKLKKLQRHLKKELQRN-PTEQELADALEITL 250

Query: 169 SE--------SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +         + +S+N R+ G E    L++  + +S+Q            E+ + E   
Sbjct: 251 EQLQMLQRARQQALSLNRRV-GREEDTELLDLLEADSTQ----------SPEKQMGEVMM 299

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           R+    +L     VL  +ER +   R   +   P TLE +S  F +SRERVRQI+ +A  
Sbjct: 300 RQEISQLLD---LVLTKQERDVIILRYGLVSGEPNTLEEVSGLFNLSRERVRQIQNKAIG 356

Query: 279 KVQES 283
           K++ S
Sbjct: 357 KLRRS 361


>gi|227875511|ref|ZP_03993651.1| RNA polymerase sigma factor SigA [Mobiluncus mulieris ATCC 35243]
 gi|269977243|ref|ZP_06184216.1| RNA polymerase principal sigma factor HrdB [Mobiluncus mulieris
           28-1]
 gi|306818820|ref|ZP_07452542.1| DNA-directed RNA polymerase sigma subunit RpoD [Mobiluncus mulieris
           ATCC 35239]
 gi|227843847|gb|EEJ54016.1| RNA polymerase sigma factor SigA [Mobiluncus mulieris ATCC 35243]
 gi|269934546|gb|EEZ91107.1| RNA polymerase principal sigma factor HrdB [Mobiluncus mulieris
           28-1]
 gi|304648506|gb|EFM45809.1| DNA-directed RNA polymerase sigma subunit RpoD [Mobiluncus mulieris
           ATCC 35239]
          Length = 614

 Score = 94.0 bits (232), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 80/309 (25%), Positives = 145/309 (46%), Gaps = 61/309 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH----------------------GDLSAAH 51
           Y+ +I K+ +L  ++E  LAKR     Y EH                        ++A +
Sbjct: 320 YLKQIGKVALLNAEQEVNLAKRIEAGLYAEHLLKTEQDSMTPKHARELHWVVQDGVNAKN 379

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 380 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYSKGYKFSTYATWWIRQ 439

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      +++              Q+++  +L R     +   + ++ PE+VV +
Sbjct: 440 AITRAMADQARTIRVPVHMVEVINKLARVQRQMLQDLGREPTPDELARELDMTPEKVVEV 499

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D    V+++++ 
Sbjct: 500 QKYGR----EPISLHTPLGEDGDSEFGDLIEDSE---------AVVPADAVSFVMLQEQ- 545

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAFK 278
                  L R +  L+ RE  +   R  L +  P TL+++   + V+RER+RQIE++   
Sbjct: 546 -------LQRVLDTLSEREAGVIAMRYGLNDGVPKTLDDIGHRYGVTRERIRQIESKTMS 598

Query: 279 KVQESIQKQ 287
           K++   + Q
Sbjct: 599 KLRHPARSQ 607


>gi|188996275|ref|YP_001930526.1| RNA polymerase, sigma 70 subunit, RpoD family [Sulfurihydrogenibium
           sp. YO3AOP1]
 gi|188931342|gb|ACD65972.1| RNA polymerase, sigma 70 subunit, RpoD family [Sulfurihydrogenibium
           sp. YO3AOP1]
          Length = 590

 Score = 94.0 bits (232), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 77/239 (32%), Positives = 124/239 (51%), Gaps = 28/239 (11%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV K+D ++GF+ +TY+ WWI+ A
Sbjct: 355 LVKANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKYDYKKGFKFSTYATWWIRQA 414

Query: 113 MQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           +   I      ++I      T N+      L R+   L         PE+   IAKK  +
Sbjct: 415 ITRAIADQARTIRIPVHMIETINK------LLRISRTLVQELGREPTPEE---IAKKAGM 465

Query: 169 SESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNR 224
              +V  +  R + D  SL   I S ++  S   D++      +++ ++  E+   ++  
Sbjct: 466 PADKVRKI-LRTSQDPVSLETPIGSDEE--SHLGDFI------EDKTVLSPEQHMLKQAL 516

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R  L   +S L+ RE ++   R   E+    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 517 RLQLDEVLSTLSEREEQVLRYRFGLEDDTEHTLEQVGKRFGVTRERIRQIEAKALRKLR 575


>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 = 94.0 bits (232), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 122/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGN+GLM+AV KF+  RG++ +TY+ WW
Sbjct: 639 AKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNVGLMKAVDKFEYRRGYKFSTYATWW 698

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +  ++P+    +A+++ +
Sbjct: 699 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGIEPDPAT-LAERMEM 753

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E E I    ++A  E ++      D + S   D++  +H    Q   +  +  + R + 
Sbjct: 754 PE-EKIRKILKIA-KEPISMETPIGDDDDSHLGDFIEDNHTLAPQ---DAAQYSSLRFVT 808

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 809 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 863


>gi|119512139|ref|ZP_01631231.1| RNA polymerase sigma-like factor [Nodularia spumigena CCY9414]
 gi|119463229|gb|EAW44174.1| RNA polymerase sigma-like factor [Nodularia spumigena CCY9414]
          Length = 442

 Score = 94.0 bits (232), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 67/238 (28%), Positives = 130/238 (54%), Gaps = 13/238 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L A   ++ ++LRLVV +A  Y+  GL + ++V EG +GL +AV+KFDP +G+R +TY+ 
Sbjct: 201 LQAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAY 260

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   I  S   +++     +K     L ++K   + I     +   +  +A +L
Sbjct: 261 WWIRQGITRAIATSSRTIRLPVHITEK-----LNKIKKAQRKIAQEKGRTPTLEDLAIEL 315

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++ ++V  +  ++    SL   +   DK+ ++  + L  D    E++L+ +  +K+  +
Sbjct: 316 EMTPTQVREVLLKVPRSVSLETKVG-KDKD-TELGELLETDCVTPEEMLMRESLQKDLHS 373

Query: 227 MLTRSMSVLNPRERRIFEAR-RLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +L    + L  RER +   R  L + +P +L  +    ++SRERVRQIE++A +K+++
Sbjct: 374 LL----ADLTSRERDVILMRFGLSDGHPYSLAEIGRALDLSRERVRQIESKALQKLRQ 427


>gi|311895920|dbj|BAJ28328.1| putative RNA polymerase sigma factor [Kitasatospora setae KM-6054]
          Length = 389

 Score = 94.0 bits (232), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 75/252 (29%), Positives = 122/252 (48%), Gaps = 44/252 (17%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  RL+ ++LRLVV +A  Y G GL + +++ EGN+GL++AV+KFD  RG++ +TY+ WW
Sbjct: 152 AKRRLIEANLRLVVSVAKRYVGRGLTLLDLIQEGNVGLIRAVEKFDYARGYKFSTYATWW 211

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFN--LRRLKGHLQ------------AITDNNL 154
           I+ AM   +      +++     +     N  LR  +G LQ            A+    L
Sbjct: 212 IRQAMSRALADQARTIRVPVHVVE---LINRVLRVQRGLLQERGVEPTAAEVGAVL--QL 266

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
            PE+V  + K       E +S++  +    D +L  LI  +D  S       +   +  E
Sbjct: 267 PPERVREVLKLAQ----EPVSLHTPVGEEDDVALGDLIEDADAASPPESAAFLLLREHLE 322

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVR 270
            VL                 + L  RER++ + R   ++  P TLE +   F V+RER+R
Sbjct: 323 AVL-----------------ATLGERERQVVQLRYGLDDGRPRTLEEIGHLFGVTRERIR 365

Query: 271 QIEARAFKKVQE 282
           QIEA+   K+++
Sbjct: 366 QIEAKTLGKLRD 377


>gi|291301996|ref|YP_003513274.1| RpoD subfamily RNA polymerase sigma-70 subunit [Stackebrandtia
           nassauensis DSM 44728]
 gi|290571216|gb|ADD44181.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Stackebrandtia
           nassauensis DSM 44728]
          Length = 559

 Score = 94.0 bits (232), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 81/302 (26%), Positives = 144/302 (47%), Gaps = 42/302 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-------------YREHG---------DLS-------- 48
           Y+ +I K+P+L   +E  LAKR              +E G         DL         
Sbjct: 262 YLKQIGKVPLLNAAQEVELAKRIEAGLYAVERLRQLKEAGEEIPTQVRRDLEWVTRDGDR 321

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WW
Sbjct: 322 AKNHLLAANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 381

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   +      ++I    +   +   L R++  L         PE+   +AK++++
Sbjct: 382 IRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGREPAPEE---LAKEMDI 436

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  +V+ +        SL+  I   D+  SQ  D++    D +  V ++       +  L
Sbjct: 437 SPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEAVVAVDAVSFSLLQGQL 491

Query: 229 TRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   + 
Sbjct: 492 QQVLQTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRS 551

Query: 287 QV 288
           QV
Sbjct: 552 QV 553


>gi|15894582|ref|NP_347931.1| RNA polymerase sigma factor RpoD [Clostridium acetobutylicum ATCC
           824]
 gi|464686|sp|P33656|RPOD_CLOAB RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A;
           AltName: Full=Major vegetative sigma factor
 gi|15024230|gb|AAK79271.1|AE007642_3 RNA polymerase sigma factor RPOD [Clostridium acetobutylicum ATCC
           824]
 gi|312373|emb|CAA80625.1| major vegetative sigma factor [Clostridium acetobutylicum ATCC 824]
 gi|325508714|gb|ADZ20350.1| major vegetative sigma factor [Clostridium acetobutylicum EA 2018]
          Length = 378

 Score = 94.0 bits (232), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 82/265 (30%), Positives = 144/265 (54%), Gaps = 13/265 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI K+P+L  +EE  LA+R + +GD SA  +L  ++LRLVV IA  Y G G+   ++
Sbjct: 112 YLKEIGKVPLLSPEEEIDLAQRIK-NGDRSARKKLAEANLRLVVSIAKRYVGRGMLFLDL 170

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFD ++GF+ +TY+ WWI+ A+   I      ++I    +       
Sbjct: 171 IQEGNLGLIKAVEKFDFKKGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMVETINK 228

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R+   L        +PE+   IAK +++   +V  +  ++A  E ++      ++  S
Sbjct: 229 LIRVSRQLLQELGREPQPEE---IAKIMDMPVDKVREI-MKIA-QEPVSLETPIGEEEDS 283

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
              D++  D   +     +    +  +  L + ++ L PRE ++   R   ++    TLE
Sbjct: 284 HLGDFIPDD---EAPAPADAAAFRMLKEQLLKILNTLTPREEKVLRLRFGLDDGRARTLE 340

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF V+RER+RQIEA+A +K++
Sbjct: 341 EVGKEFNVTRERIRQIEAKALRKLR 365


>gi|94986960|ref|YP_594893.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Lawsonia intracellularis PHE/MN1-00]
 gi|94731209|emb|CAJ54571.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Lawsonia intracellularis PHE/MN1-00]
          Length = 590

 Score = 94.0 bits (232), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 74/250 (29%), Positives = 129/250 (51%), Gaps = 24/250 (9%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           + A   L+ S+LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ 
Sbjct: 350 MRAKQELIRSNLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYAT 409

Query: 107 WWIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           WWI+ A+   I      ++I      T N+      L R   +L      +  PE+   I
Sbjct: 410 WWIRQAITRAIADQARTIRIPVHMIETINK------LIRTSRYLVQEFGRDPTPEE---I 460

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A++++    +V  +  ++A  E ++      D+  S   D++       ++ +   EE  
Sbjct: 461 AERMDYPLDKVKKV-LKIAK-EPISLETPIGDEEDSSLGDFI-----EDKKAVAPSEEVV 513

Query: 223 NRR--NMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           N +    +   ++ L PRE ++   R    +++  TLE +   F V+RER+RQIEA+A +
Sbjct: 514 NTKLSEQIASVLADLTPREEQVLRKRFGIGEKSDHTLEEVGKLFNVTRERIRQIEAKALR 573

Query: 279 KVQESIQKQV 288
           K++  ++ QV
Sbjct: 574 KLRHPVRSQV 583


>gi|126434760|ref|YP_001070451.1| RNA polymerase sigma factor [Mycobacterium sp. JLS]
 gi|126234560|gb|ABN97960.1| RNA polymerase, sigma 70 subunit, RpoD family [Mycobacterium sp.
           JLS]
          Length = 480

 Score = 94.0 bits (232), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 79/319 (24%), Positives = 148/319 (46%), Gaps = 45/319 (14%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------- 43
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR                      
Sbjct: 168 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLFATQKLAELAEKGEKLP 226

Query: 44  ------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                        GD +  H L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 227 VQQRRDMQWICRDGDRAKNH-LLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 285

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L     
Sbjct: 286 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLG 343

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 344 REPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSE 395

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 396 AVVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 455

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 456 RQIESKTMSKLRHPSRSQV 474


>gi|15827492|ref|NP_301755.1| RNA polymerase sigma factor [Mycobacterium leprae TN]
 gi|221229969|ref|YP_002503385.1| RNA polymerase sigma factor [Mycobacterium leprae Br4923]
 gi|699190|gb|AAA62955.1| rpoT [Mycobacterium leprae]
 gi|4587111|dbj|BAA76621.1| RpoT [Mycobacterium leprae]
 gi|13093042|emb|CAC31403.1| RNA polymerase sigma factor [Mycobacterium leprae]
 gi|219933076|emb|CAR71117.1| RNA polymerase sigma factor [Mycobacterium leprae Br4923]
          Length = 574

 Score = 94.0 bits (232), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 79/319 (24%), Positives = 148/319 (46%), Gaps = 45/319 (14%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------- 43
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR                      
Sbjct: 262 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSERGTKLP 320

Query: 44  ------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                        GD +  H L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 321 TAQRRDMMWICRDGDRAKNH-LLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 379

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L     
Sbjct: 380 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLG 437

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 438 REPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSE 489

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 490 AVVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 549

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 550 RQIESKTMSKLRHPSRSQV 568


>gi|227833276|ref|YP_002834983.1| RNA polymerase sigma factor A [Corynebacterium aurimucosum ATCC
           700975]
 gi|262184260|ref|ZP_06043681.1| RNA polymerase sigma factor [Corynebacterium aurimucosum ATCC
           700975]
 gi|227454292|gb|ACP33045.1| RNA polymerase sigma factor A [Corynebacterium aurimucosum ATCC
           700975]
          Length = 485

 Score = 94.0 bits (232), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 80/324 (24%), Positives = 156/324 (48%), Gaps = 49/324 (15%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY----------------REHGD 46
           RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR                 R  GD
Sbjct: 167 RKDAELTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYAQYRMDEMEKARAEGD 225

Query: 47  LSAA--------------------HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
            +A                     + L+ ++LRLVV +A  Y G G+   +++ EGN+GL
Sbjct: 226 KAAKLSPMEKRDMRAIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGL 285

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L
Sbjct: 286 IRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQREL 343

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
             + D   +P   + +AK+++++E +V+ +        SL+  I   D+  SQ  D++  
Sbjct: 344 --LQDLGREP-TPLELAKEMDITEEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI-- 396

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEV 264
             D +  + ++       ++ L   ++ L+ RE  +   R  L +  P TL+ +   + V
Sbjct: 397 -EDSEAVIAVDAVSFTLLQDQLQDVLTTLSEREAGVVRLRFGLTDGMPRTLDEIGQVYGV 455

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           +RER+RQIE++   K++   + QV
Sbjct: 456 TRERIRQIESKTMSKLRHPSRSQV 479


>gi|9837536|gb|AAG00589.1|AF288784_1 SigC [Synechococcus elongatus PCC 7942]
          Length = 398

 Score = 94.0 bits (232), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 75/271 (27%), Positives = 140/271 (51%), Gaps = 24/271 (8%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           ++GL R+  E+ ++ + E ++     +R ++H        ++ ++LRLVV +A  Y+  G
Sbjct: 132 QLGLHRWA-EVCQLDLEELKQVCKEGQRAKDH--------MIKANLRLVVSVAKKYQNRG 182

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L + ++V EG +GL +AV+KFDP +G+R +TY+ WWI+  +   I      +++     +
Sbjct: 183 LELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHVTE 242

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
           K     L R+K   + I     +   +  IA++L ++  +V  +  R+    SL   +  
Sbjct: 243 K-----LTRIKKAQRKIAQTKGRTANLEEIAQELEMTPDQVREVLLRVPKSISLETRVGK 297

Query: 193 SDKNSSQWQDWL-VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQE 250
             +  ++  D L   D   +E++  E     +  N L R +  LN RER +   R  L++
Sbjct: 298 --EKDTELGDLLETTDFTPEERLTQE-----SLSNDLQRLLLELNHRERDVIRMRFGLRD 350

Query: 251 NPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
             + +L  +    ++SRERVRQIEA+A +K+
Sbjct: 351 GQIYSLAEIGQVLDLSRERVRQIEAKALQKL 381


>gi|227549126|ref|ZP_03979175.1| RNA polymerase major sigma subunit [Corynebacterium lipophiloflavum
           DSM 44291]
 gi|227078794|gb|EEI16757.1| RNA polymerase major sigma subunit [Corynebacterium lipophiloflavum
           DSM 44291]
          Length = 520

 Score = 94.0 bits (232), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 82/324 (25%), Positives = 154/324 (47%), Gaps = 49/324 (15%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREHG------------ 45
           RK+  +  + +  +  Y+ +I K+ +L+ + E  LAKR     Y +H             
Sbjct: 202 RKDAQLTASAD-SVRAYLKQIGKVALLDAELEVSLAKRIEAGLYAQHRLDEMERAAAEGD 260

Query: 46  -----------DLSAAHR--------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
                      DL A  R        L+ ++LRLVV +A  Y G G+   +++ EGN+GL
Sbjct: 261 KEAKLTPAVKRDLRAVARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGL 320

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L
Sbjct: 321 IRAVEKFDYSKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQREL 378

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    P++   +AK+++++E +V+ +        SL+  I   D+  SQ  D++  
Sbjct: 379 LQDLGREPTPQE---LAKEMDITEEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI-- 431

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEV 264
             D +  V ++       ++ L   +  L+ RE  +   R  L +  P TL+ +   + V
Sbjct: 432 -EDSEAVVAVDAVSFTLLQDQLQDVLHTLSEREAGVVRLRFGLTDGMPRTLDEIGQVYGV 490

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           +RER+RQIE++   K++   + QV
Sbjct: 491 TRERIRQIESKTMSKLRHPSRSQV 514


>gi|254457867|ref|ZP_05071294.1| sigma 28 [Campylobacterales bacterium GD 1]
 gi|207085260|gb|EDZ62545.1| sigma 28 [Campylobacterales bacterium GD 1]
          Length = 623

 Score = 94.0 bits (232), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 72/242 (29%), Positives = 122/242 (50%), Gaps = 31/242 (12%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           ++  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ ++G++ +TY+ WWI+ 
Sbjct: 387 KMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYQKGYKFSTYATWWIRQ 446

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE-QVVAIAKKLNVSE 170
           A+   I      ++I     +     N + ++ HLQ   ++  +P+ +V+A+   L+V +
Sbjct: 447 AISRAIADQARTIRIPIHMIETINRIN-KIMRKHLQ---EHGKEPDVEVIALEVGLSVEK 502

Query: 171 --------SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
                    E IS+   +  ++         DK+S    D ++ D               
Sbjct: 503 VKNVIKITKEPISLEAPIGNEDDGRFGDFIEDKSSISPSDAILKD--------------- 547

Query: 223 NRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           + R  +   +  LN RE+ + + R      E+  TLE +  E  V+RERVRQIE+ A KK
Sbjct: 548 DLRVQIEGVLEQLNEREKAVIKLRFGIMDDESDRTLEEIGRELNVTRERVRQIESSAIKK 607

Query: 280 VQ 281
           ++
Sbjct: 608 LK 609


>gi|76799605|ref|ZP_00781725.1| RNA polymerase major sigma factor RpoD [Streptococcus agalactiae
           18RS21]
 gi|76585040|gb|EAO61678.1| RNA polymerase major sigma factor RpoD [Streptococcus agalactiae
           18RS21]
          Length = 278

 Score = 94.0 bits (232), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 47/108 (43%), Positives = 67/108 (62%), Gaps = 1/108 (0%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI  +P+L  +EE  LA    E GDL A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 102 YLKEIGVVPLLTNEEEKELAVAVAE-GDLMAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 160

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           + EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I
Sbjct: 161 IQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI 208


>gi|301165749|emb|CBW25321.1| RNA polymerase sigma-70 factor [Bacteriovorax marinus SJ]
          Length = 582

 Score = 94.0 bits (232), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 78/249 (31%), Positives = 121/249 (48%), Gaps = 40/249 (16%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 343 AKSQLVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 402

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQV----- 159
           I+ A+   I      ++I      T N  ++    R+L   L         PE++     
Sbjct: 403 IRQAITRAIADQARTIRIPVHMIETIN--KMVRTSRQLIQELG----REPTPEEIAERME 456

Query: 160 --VAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
             V   KK+     E IS+   +    D SL   I           D ++   D    V 
Sbjct: 457 LPVDKVKKVQKISKEPISLETPIGEEEDSSLGDFIED---------DKIISPADAVMSVT 507

Query: 216 IEKEERKNRRNMLTRS-MSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQI 272
           + ++         TRS +S L PRE ++   R    +++  TLE +  +F V+RER+RQI
Sbjct: 508 LSEQ---------TRSVLSTLTPREEKVLRMRFGIGEKSDHTLEEVGQDFFVTRERIRQI 558

Query: 273 EARAFKKVQ 281
           EA+A +K++
Sbjct: 559 EAKALRKLR 567


>gi|251771800|gb|EES52375.1| RNA polymerase, sigma 70 subunit, RpoD [Leptospirillum
           ferrodiazotrophum]
          Length = 590

 Score = 94.0 bits (232), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 73/237 (30%), Positives = 123/237 (51%), Gaps = 16/237 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RGF+ +TY+ WW
Sbjct: 352 AKSELIKANLRLVVSIAKRYTNRGLQFLDLIQEGNIGLMKAVDKFEYKRGFKFSTYATWW 411

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R   HL         PE+   +AK++ +
Sbjct: 412 IRQAITRAIADQARTIRI--PVHMIETINKLIRTSRHLVQELGREPLPEE---LAKEMQM 466

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      ++  S   D++    D +    IE   R +    +
Sbjct: 467 PVDKVRRV-LKIAR-EPISLETPIGEEEDSHLGDFI---EDKKTISPIEAAVRYDLVRKI 521

Query: 229 TRSMSVLNPRERRIFEAR----RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +S+S L  RE ++   R     L ++  TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 522 GQSLSTLTDREEKVIRLRFGIGELTDH--TLEEVGQDFDVTRERIRQIEAKALRKLR 576


>gi|171914125|ref|ZP_02929595.1| RNA polymerase sigma factor RpoD [Verrucomicrobium spinosum DSM
           4136]
          Length = 576

 Score = 94.0 bits (232), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 75/243 (30%), Positives = 123/243 (50%), Gaps = 29/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+ +RG++ +TY+ WW
Sbjct: 336 AKTEMVEANLRLVISIAKKYTNRGLSFLDLIQEGNMGLMRAVEKFEYKRGYKFSTYATWW 395

Query: 109 IKAAMQEYILRSWSLVKIGT----TAN-----QKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N     QK+L   L R     +   + +L  E+V
Sbjct: 396 IRQAITRSIADQARTIRIPVHMIDTINKLLRVQKQLVQELGRDPTPDEIAEEIHLPVERV 455

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
            A+   L +S+  V           SL   +  SD + +++ D++    D      +E  
Sbjct: 456 NAV---LRMSQQPV-----------SLQTKVGDSDGD-TEFGDFI---EDNTSVSPMELT 497

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAF 277
                R+ L   +  L  RER + E R   +  +  TLE +  +F V+RER+RQIEA+A 
Sbjct: 498 AMNLLRDKLKDVLDSLTDRERAVLEQRFGLVDGSGRTLEEVGRQFHVTRERIRQIEAKAL 557

Query: 278 KKV 280
           +K+
Sbjct: 558 RKL 560


>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 = 94.0 bits (232), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 68/235 (28%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 360 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 419

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         P++   +A+++ +
Sbjct: 420 IRQAITRSIADQARTIRI--PVHMIETINKLNRVSRQMLQEMGREPSPDE---LAERMEM 474

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E +V  +  ++A  E ++      D   S   D++    D      ++   R+  R  +
Sbjct: 475 PEDKVRKV-LKIA-KEPISMETPIGDDEDSHLGDFI---EDINAMSPVDSATREGLRESV 529

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +S L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 530 KGVLSGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 584


>gi|13195265|gb|AAK15630.1|AF326348_2 RNA polymerase major sigma subunit [Corynebacterium ammoniagenes]
          Length = 467

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 81/324 (25%), Positives = 157/324 (48%), Gaps = 49/324 (15%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREH-----------GD 46
           RK+  +  + +  +  Y+ +I K+ +L  ++E  LA+R     Y +H           GD
Sbjct: 149 RKDAQLTASAD-SVRAYLKQIGKVALLNAEQEVSLAERIEAGLYAQHRLDEMERLIAEGD 207

Query: 47  ----LSAAHR----------------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
               LS A +                L+ ++LRLVV +A  Y G G+   +++ EGN+GL
Sbjct: 208 AAAKLSPAQKRDLRWIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGL 267

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L
Sbjct: 268 IRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQREL 325

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    P++   +AK+++++E +V+ +        SL+  I   D+  SQ  D++  
Sbjct: 326 LQDLGREPTPQE---LAKEMDITEEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI-- 378

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEV 264
             D +  + ++       ++ L   ++ L+ RE  +   R  L +  P TL+ +   + V
Sbjct: 379 -EDSEAVIAVDAVSFTLLQDQLQDVLTTLSEREAGVVRLRFGLTDGMPRTLDEIGQVYGV 437

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           +RER+RQIE++   K++   + QV
Sbjct: 438 TRERIRQIESKTMSKLRHPSRSQV 461


>gi|303327390|ref|ZP_07357831.1| RNA polymerase sigma-70 factor [Desulfovibrio sp. 3_1_syn3]
 gi|302862330|gb|EFL85263.1| RNA polymerase sigma-70 factor [Desulfovibrio sp. 3_1_syn3]
          Length = 589

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 75/252 (29%), Positives = 122/252 (48%), Gaps = 30/252 (11%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           + A   L+ S+LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ 
Sbjct: 349 MRAKQELIRSNLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYAT 408

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV------- 159
           WWI+ A+   I      ++I    +       L R   +L      +  PE++       
Sbjct: 409 WWIRQAITRAIADQARTIRI--PVHMIETINKLIRTSRYLVQELGRDPTPEEIAERMEYP 466

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           V   KK+     E IS+   + GDE                +D  + D    ++ +   E
Sbjct: 467 VEKVKKVLKIAKEPISLETPI-GDE----------------EDSSLGDFIEDKKAVAPAE 509

Query: 220 ERKNRR--NMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
           E  N +    L   ++ L PRE ++   R    +++  TLE +   F V+RER+RQIEA+
Sbjct: 510 EVINTKLSEQLAAVLADLTPREEQVLRKRFGIAEKSDHTLEEVGKLFNVTRERIRQIEAK 569

Query: 276 AFKKVQESIQKQ 287
           A +K++  ++ Q
Sbjct: 570 ALRKLRHPVRSQ 581


>gi|78357095|ref|YP_388544.1| sigma-70 factor [Desulfovibrio desulfuricans subsp. desulfuricans
           str. G20]
 gi|78219500|gb|ABB38849.1| RNA polymerase, sigma 70 subunit, RpoD [Desulfovibrio desulfuricans
           subsp. desulfuricans str. G20]
          Length = 589

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 74/254 (29%), Positives = 129/254 (50%), Gaps = 17/254 (6%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           KR   H  + A   L+ S+LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG
Sbjct: 342 KRGNSHA-MRAKQELIRSNLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRG 400

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           ++ +TY+ WWI+ A+   I      ++I    +       L R   +L      +  PE+
Sbjct: 401 YKFSTYATWWIRQAITRAIADQARTIRI--PVHMIETINKLIRTSRYLVQELGRDPTPEE 458

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              IA++++    +V  +  ++A  E ++      D+  S   D++       ++ +   
Sbjct: 459 ---IAERMDYPIDKVKKV-LKIAK-EPISLETPIGDEEDSSLGDFI-----EDKKAVAPA 508

Query: 219 EERKNRR--NMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEA 274
           EE  N +    +   ++ L PRE ++   R    +++  TLE +   F V+RER+RQIEA
Sbjct: 509 EEVVNTKLSEQIAAVLADLTPREEQVLRKRFGINEKSDHTLEEVGKLFNVTRERIRQIEA 568

Query: 275 RAFKKVQESIQKQV 288
           +A +K++  ++ Q 
Sbjct: 569 KALRKLRHPVRSQT 582


>gi|325106737|ref|YP_004267805.1| RNA polymerase, sigma 70 subunit, RpoD [Planctomyces brasiliensis
           DSM 5305]
 gi|324967005|gb|ADY57783.1| RNA polymerase, sigma 70 subunit, RpoD [Planctomyces brasiliensis
           DSM 5305]
          Length = 575

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 67/235 (28%), Positives = 117/235 (49%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L   +LRLVV IA  YR  GL   +++ EGN GLM+ V+K++  RG++ +TY+ WW
Sbjct: 316 AKQKLSGGNLRLVVSIAKKYRNRGLSFLDLIQEGNAGLMRGVEKYEYRRGYKFSTYATWW 375

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   +      ++I        +F ++  LK   + I     +   +  +A  +++
Sbjct: 376 IRQAITRAVADHARTIRIPV-----HMFQSISTLKAKAEQIRQETGREPTMEELAAAIDM 430

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  E   +        SL+  +  S+ +S  + D+L    D  E    +   ++  R+ +
Sbjct: 431 SVEETERIMKTWKHPVSLDTPVGESEDSS--FGDFL---QDDSENTPADTAMQQMLRDKI 485

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L  RER I + R    +    TLE     F+V+RER+RQIE++A +K+Q
Sbjct: 486 NHVLKSLTYREREIIKLRYGLGDGYSYTLEETGRIFKVTRERIRQIESKALRKLQ 540


>gi|220904357|ref|YP_002479669.1| RpoD subfamily RNA polymerase sigma-70 subunit [Desulfovibrio
           desulfuricans subsp. desulfuricans str. ATCC 27774]
 gi|219868656|gb|ACL48991.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           desulfuricans subsp. desulfuricans str. ATCC 27774]
          Length = 589

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 75/252 (29%), Positives = 122/252 (48%), Gaps = 30/252 (11%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           + A   L+ S+LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ 
Sbjct: 349 MRAKQELIRSNLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYAT 408

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV------- 159
           WWI+ A+   I      ++I    +       L R   +L      +  PE++       
Sbjct: 409 WWIRQAITRAIADQARTIRI--PVHMIETINKLIRTSRYLVQELGRDPTPEEIAERMEYP 466

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           V   KK+     E IS+   + GDE                +D  + D    ++ +   E
Sbjct: 467 VEKVKKVLKIAKEPISLETPI-GDE----------------EDSSLGDFIEDKKAVAPAE 509

Query: 220 ERKNRR--NMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
           E  N +    L   ++ L PRE ++   R    +++  TLE +   F V+RER+RQIEA+
Sbjct: 510 EVINTKLSEQLAAVLADLTPREEQVLRKRFGIAEKSDHTLEEVGKLFNVTRERIRQIEAK 569

Query: 276 AFKKVQESIQKQ 287
           A +K++  ++ Q
Sbjct: 570 ALRKLRHPVRSQ 581


>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 = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 65/235 (27%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 441 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 500

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +  L+P+    +A+K+ +
Sbjct: 501 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGLEPDPAT-LAEKMEM 555

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + R+++
Sbjct: 556 PEDKIRKI-MKIAK-EPISMETPIGDDDDSHLGDFI---EDTNTVAPADAALHASMRDVV 610

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+  +K++
Sbjct: 611 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKTLRKLR 665


>gi|134098380|ref|YP_001104041.1| RNA polymerase sigma factor [Saccharopolyspora erythraea NRRL 2338]
 gi|291006918|ref|ZP_06564891.1| RNA polymerase sigma factor [Saccharopolyspora erythraea NRRL 2338]
 gi|133911003|emb|CAM01116.1| RNA polymerase major sigma factor [Saccharopolyspora erythraea NRRL
           2338]
          Length = 467

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 82/320 (25%), Positives = 151/320 (47%), Gaps = 47/320 (14%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRL--------- 53
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR  E G L AA RL         
Sbjct: 155 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRI-EAG-LYAAERLRQAEEAEER 211

Query: 54  -----------------------VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
                                  + ++LRLVV +A  Y G G+   +++ EGN+GL++AV
Sbjct: 212 LAMQMRRDLRWIVRDGERAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAV 271

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +KFD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L    
Sbjct: 272 EKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDL 329

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
                PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D 
Sbjct: 330 GREPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDS 381

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRER 268
           +  V ++       ++ L   ++ L+ RE  +   R       P TL+ +   + V+RER
Sbjct: 382 EAVVAVDAVSFTLLQDQLQSVLATLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRER 441

Query: 269 VRQIEARAFKKVQESIQKQV 288
           +RQIE++   K++   + QV
Sbjct: 442 IRQIESKTMSKLRHPSRSQV 461


>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 = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 72/243 (29%), Positives = 119/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 390 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 449

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ----KRLFFNLRRLKGHLQAITDNNLKPEQVV 160
           I+ A+   I      ++I      T N+     R        +   + +++  L PE+  
Sbjct: 450 IRQAITRSIADQARTIRIPVHMIETINKLNHISRQILQETGREPSPEELSERMLIPEE-- 507

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L ++  E ISM   +  DE             S   D++    D   ++ +E   
Sbjct: 508 KIRKVLKIAR-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLESAT 551

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFK 278
            ++ R+     +S L  RE ++   R         TLE +  +F+V+RER+RQIEA+A +
Sbjct: 552 SESLRSATNEVLSGLTTREAKVLRMRFGIDMHTDHTLEEVGKQFDVTRERIRQIEAKALR 611

Query: 279 KVQ 281
           K++
Sbjct: 612 KLR 614


>gi|46580198|ref|YP_011006.1| RNA polymerase sigma-70 factor [Desulfovibrio vulgaris str.
           Hildenborough]
 gi|120602415|ref|YP_966815.1| RpoD family RNA polymerase sigma factor [Desulfovibrio vulgaris
           DP4]
 gi|46449615|gb|AAS96265.1| RNA polymerase sigma-70 factor [Desulfovibrio vulgaris str.
           Hildenborough]
 gi|120562644|gb|ABM28388.1| RNA polymerase, sigma 70 subunit, RpoD [Desulfovibrio vulgaris DP4]
 gi|311233814|gb|ADP86668.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           vulgaris RCH1]
          Length = 590

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 73/254 (28%), Positives = 123/254 (48%), Gaps = 32/254 (12%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           + A   L+ S+LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ 
Sbjct: 350 MRAKQELIRSNLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYAT 409

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV------ 160
           WWI+ A+   I      ++I    +       L R   +L      +  PE++       
Sbjct: 410 WWIRQAITRAIADQARTIRI--PVHMIETINKLIRTSRYLVQELGRDPTPEEIAERMDYP 467

Query: 161 --AIAKKLNVSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
              + K L +++ E IS+   +    D SL   I   DK +    + +V    G++    
Sbjct: 468 IDKVKKVLKIAK-EPISLETPIGDEEDSSLGDFIE--DKKAVAPAEEVVNTKLGEQ---- 520

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEA 274
                      +   ++ L PRE ++   R    +++  TLE +   F V+RER+RQIEA
Sbjct: 521 -----------IASVLADLTPREEQVLRKRFGIGEKSDHTLEEVGKLFNVTRERIRQIEA 569

Query: 275 RAFKKVQESIQKQV 288
           +A +K++  ++ Q 
Sbjct: 570 KALRKLRHPVRSQT 583


>gi|1588486|prf||2208419B RNA polymerase sigma factor
          Length = 391

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 69/237 (29%), Positives = 126/237 (53%), Gaps = 17/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 155 AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 214

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++     KP E+ +A   ++
Sbjct: 215 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKILSQELGRKPTEEEIAERMEM 269

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  D +  E  + +   R++  N
Sbjct: 270 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIEADGETPEDQVSKSLLREDLEN 325

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +L      L+ RER +   R   ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 326 VL----DTLSARERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLR 378


>gi|108799152|ref|YP_639349.1| RNA polymerase sigma factor [Mycobacterium sp. MCS]
 gi|119868267|ref|YP_938219.1| RNA polymerase sigma factor [Mycobacterium sp. KMS]
 gi|108769571|gb|ABG08293.1| RNA polymerase, sigma 28 subunit [Mycobacterium sp. MCS]
 gi|119694356|gb|ABL91429.1| RNA polymerase, sigma 70 subunit, RpoD family [Mycobacterium sp.
           KMS]
          Length = 480

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 79/319 (24%), Positives = 148/319 (46%), Gaps = 45/319 (14%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------- 43
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR                      
Sbjct: 168 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLFATQKLAELAEKGEKLP 226

Query: 44  ------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                        GD +  H L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 227 VQQRRDMQWICRDGDRAKNH-LLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 285

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L     
Sbjct: 286 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLG 343

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 344 REPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSE 395

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 396 AVVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 455

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 456 RQIESKTMSKLRHPSRSQV 474


>gi|317153216|ref|YP_004121264.1| RNA polymerase sigma factor RpoD [Desulfovibrio aespoeensis Aspo-2]
 gi|316943467|gb|ADU62518.1| RNA polymerase sigma factor RpoD [Desulfovibrio aespoeensis Aspo-2]
          Length = 581

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 75/255 (29%), Positives = 129/255 (50%), Gaps = 33/255 (12%)

Query: 45  GDLSA---AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
           G+LSA      L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ 
Sbjct: 336 GNLSAMRAKQELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKF 395

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV- 160
           +TY+ WWI+ A+   I      ++I    +       L R   +L      +  PE++  
Sbjct: 396 STYATWWIRQAITRAIADQARTIRI--PVHMIETINKLIRTSRYLVQELGRDPSPEEIAE 453

Query: 161 -------AIAKKLNVSESEVISMNCRLAGDESLNALINS-SDKNSSQWQDWLVYDHDGQE 212
                   + K L +++ E IS+   + GDE  ++L +   DK ++   + +V    G++
Sbjct: 454 RMDYPLEKVKKVLKIAK-EPISLETPI-GDEEDSSLGDFIEDKKATAPAEEVVSTKLGEQ 511

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVR 270
                          +   +S L PRE ++   R    +++  TLE +   F V+RER+R
Sbjct: 512 ---------------IASVLSDLTPREEQVLRKRFGIGEKSDHTLEEVGKLFNVTRERIR 556

Query: 271 QIEARAFKKVQESIQ 285
           QIEA+A +K++  ++
Sbjct: 557 QIEAKALRKLRHPVR 571


>gi|218885598|ref|YP_002434919.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           vulgaris str. 'Miyazaki F']
 gi|218756552|gb|ACL07451.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           vulgaris str. 'Miyazaki F']
          Length = 590

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 74/254 (29%), Positives = 130/254 (51%), Gaps = 17/254 (6%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           KR   H  + A   L+ S+LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG
Sbjct: 343 KRGNTHA-MRAKQELIRSNLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRG 401

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           ++ +TY+ WWI+ A+   I      ++I    +       L R   +L      +  PE+
Sbjct: 402 YKFSTYATWWIRQAITRAIADQARTIRI--PVHMIETINKLIRTSRYLVQELGRDPTPEE 459

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              IA++++    +V  +  ++A  E ++      D+  S   D++       ++ +   
Sbjct: 460 ---IAERMDYPIDKVKKV-LKIAK-EPISLETPIGDEEDSSLGDFI-----EDKKAVAPA 509

Query: 219 EERKNRR--NMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEA 274
           EE  N +    +   ++ L PRE ++   R    +++  TLE +   F V+RER+RQIEA
Sbjct: 510 EEVVNTKLSEQIASVLADLTPREEQVLRKRFGIGEKSDHTLEEVGKLFNVTRERIRQIEA 569

Query: 275 RAFKKVQESIQKQV 288
           +A +K++  ++ Q+
Sbjct: 570 KALRKLRHPVRSQM 583


>gi|256371066|ref|YP_003108890.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidimicrobium
           ferrooxidans DSM 10331]
 gi|256007650|gb|ACU53217.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidimicrobium
           ferrooxidans DSM 10331]
          Length = 337

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 71/240 (29%), Positives = 117/240 (48%), Gaps = 30/240 (12%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            + ++LRLVV IA  Y+  GLP+ +++ EGN+GL+ AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 103 FIQANLRLVVSIAKRYQASGLPLLDLIQEGNMGLIHAVEKFDWRKGFKFSTYATWWIRQA 162

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ-----AITDNNLKPEQVVAIAKKLN 167
           +   I  +   +++   A        ++R +  L+     A T   L  E  +   K + 
Sbjct: 163 ITRGIANTGRTIRLPVHAGDS--LSRVQRAQVQLEVRLGRAPTVRELAAEVDLPYDKLVE 220

Query: 168 V----SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
                +E   +S   R  GD  L  ++  S   +           D   + L+  E    
Sbjct: 221 ALRFRAEPVSLSEPLRDDGDAELGDVVEDSQSATP---------FDVAAEHLLPSE---- 267

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
               ++R ++ L+ RER I   R   +   P TLE +   F ++RER+RQIEARA  K++
Sbjct: 268 ----VSRLLAPLDGREREILRLRYGLDRGEPRTLEEVGEYFHLTRERIRQIEARAMSKLR 323


>gi|12958492|gb|AAK09321.1|AF320817_2 sigma factor SigA [[Brevibacterium] flavum]
          Length = 498

 Score = 94.0 bits (232), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 83/324 (25%), Positives = 156/324 (48%), Gaps = 49/324 (15%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREH-----------GD 46
           RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR     Y  H           GD
Sbjct: 180 RKDAELTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYATHRMEEMEEAFAAGD 238

Query: 47  ----LSAAHR----------------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
               L+ A R                L+ ++LRLVV +A  Y G G+   +++ EGN+GL
Sbjct: 239 KDAKLTPAVRRDLRAIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGL 298

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L
Sbjct: 299 IRAVEKFDYSKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQREL 356

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    P++   ++K++++SE +V+ +        SL+  I   D+  SQ  D++  
Sbjct: 357 LQELGREPTPQE---LSKEMDISEEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI-- 409

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEV 264
             D +  V ++       ++ L   +  L+ RE  + + R  L +  P TL+ +   + V
Sbjct: 410 -EDSEAVVAVDAVSFTLLQDQLQDVLETLSEREAGVVKLRFGLTDGMPRTLDEIGQVYGV 468

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           +RER+RQIE++   K++   + QV
Sbjct: 469 TRERIRQIESKTMSKLRHPSRSQV 492


>gi|119509984|ref|ZP_01629125.1| group 2 sigma 70-type sigma factor F [Nodularia spumigena CCY9414]
 gi|119512944|ref|ZP_01632006.1| group 2 sigma 70-type sigma factor F [Nodularia spumigena CCY9414]
 gi|119462397|gb|EAW43372.1| group 2 sigma 70-type sigma factor F [Nodularia spumigena CCY9414]
 gi|119465308|gb|EAW46204.1| group 2 sigma 70-type sigma factor F [Nodularia spumigena CCY9414]
          Length = 389

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 68/240 (28%), Positives = 120/240 (50%), Gaps = 21/240 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +++ S+LRLVV IA  Y   G+P  +++ EG +GL +A +KFDP++G++ +TY+ WW
Sbjct: 151 AKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAMGLNRATEKFDPDKGYKFSTYAYWW 210

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      +++     +K     L +LK   + +     +      +A+ L +
Sbjct: 211 IRQAITRAIANDARTIRLPIHIVEK-----LNKLKKAQRELKQKLCRNPNEAEMAEALEI 265

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  ++  +        SLN  +   +   ++  D L+ D D          E K   NM+
Sbjct: 266 SVQQLRQLQQLRRQALSLNHRVGKEE--DTELMD-LLEDEDNL------SPEAKMNENMM 316

Query: 229 TRSM-----SVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            + +      VL PRE+ +   R       P TLE + + F +SRERVRQI+++A +K++
Sbjct: 317 RQEIWEVLGDVLTPREKDVISLRYGLTTSEPCTLEEVGNMFNLSRERVRQIQSKAMRKLR 376


>gi|225377779|ref|ZP_03755000.1| hypothetical protein ROSEINA2194_03430 [Roseburia inulinivorans DSM
           16841]
 gi|225210363|gb|EEG92717.1| hypothetical protein ROSEINA2194_03430 [Roseburia inulinivorans DSM
           16841]
          Length = 426

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 88/315 (27%), Positives = 141/315 (44%), Gaps = 77/315 (24%)

Query: 19  YIHEIRKIPMLEKQEEYVLAK---------------RYRE------------------HG 45
           Y+ EI K+P+L  +EE  LAK               + RE                    
Sbjct: 122 YLKEIGKVPLLSAEEEIELAKNMEAGAVAKEKIAILKSREEKATEEELAEIKEEIKNLQK 181

Query: 46  DLSAAH----RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
           DL A      RL  ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ 
Sbjct: 182 DLDAGDEAKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKF 241

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDN 152
           +TY+ WWI+ A+   I      ++I      T N+     ++L   L R     +   + 
Sbjct: 242 STYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPSPEEIAAEM 301

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH---- 208
           N+  E+V  I   L +S+ E +S+   +  +E             S   D++  D+    
Sbjct: 302 NMPVERVREI---LKISQ-EPVSLETPIGEEE------------DSHLGDFIQDDNVPVP 345

Query: 209 -DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVS 265
            D     L+        +  L   +  L  RE+++   R   E+    TLE +  EF V+
Sbjct: 346 ADAAAFTLL--------KEQLEEVLGTLTEREQKVLTLRFGLEDGRARTLEEVGKEFNVT 397

Query: 266 RERVRQIEARAFKKV 280
           RER+RQIEA+A +K+
Sbjct: 398 RERIRQIEAKALRKL 412


>gi|296117756|ref|ZP_06836340.1| RNA polymerase sigma factor [Corynebacterium ammoniagenes DSM
           20306]
 gi|295969487|gb|EFG82728.1| RNA polymerase sigma factor [Corynebacterium ammoniagenes DSM
           20306]
          Length = 471

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 81/324 (25%), Positives = 157/324 (48%), Gaps = 49/324 (15%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREH-----------GD 46
           RK+  +  + +  +  Y+ +I K+ +L  ++E  LA+R     Y +H           GD
Sbjct: 153 RKDAQLTASAD-SVRAYLKQIGKVALLNAEQEVSLAERIEAGLYAQHRMDEMERLTAEGD 211

Query: 47  ----LSAAHR----------------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
               LS A +                L+ ++LRLVV +A  Y G G+   +++ EGN+GL
Sbjct: 212 AAAKLSPAQKRDLRWIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGL 271

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L
Sbjct: 272 IRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQREL 329

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    P++   +AK+++++E +V+ +        SL+  I   D+  SQ  D++  
Sbjct: 330 LQDLGREPTPQE---LAKEMDITEEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI-- 382

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEV 264
             D +  + ++       ++ L   ++ L+ RE  +   R  L +  P TL+ +   + V
Sbjct: 383 -EDSEAVIAVDAVSFTLLQDQLQDVLTTLSEREAGVVRLRFGLTDGMPRTLDEIGQVYGV 441

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           +RER+RQIE++   K++   + QV
Sbjct: 442 TRERIRQIESKTMSKLRHPSRSQV 465


>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 = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 119/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 611 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 670

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +   +P+    +A K+ +
Sbjct: 671 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGAEPDPAT-LAIKMEM 725

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + RN++
Sbjct: 726 PEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDNNTLAPADAALHASMRNVV 780

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 781 KDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 835


>gi|126659335|ref|ZP_01730471.1| RNA polymerase sigma factor SigD [Cyanothece sp. CCY0110]
 gi|126619417|gb|EAZ90150.1| RNA polymerase sigma factor SigD [Cyanothece sp. CCY0110]
          Length = 318

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 78/306 (25%), Positives = 138/306 (45%), Gaps = 58/306 (18%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDL------------------------------- 47
           Y+ EI ++P+L  +EE + AKR +   +L                               
Sbjct: 14  YLKEIGRVPLLTHEEEILYAKRVQRLVNLEKLRDDIIEETGQEPTEIQWAKTAKISRKEL 73

Query: 48  --------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                   +A  ++V ++LRLVV +A  Y    L + +++ EG IG+ + V+KFDP +G+
Sbjct: 74  QSIIEIGEAAKRKMVEANLRLVVSVAKKYLKRNLDLLDLIQEGTIGMQRGVEKFDPTKGY 133

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           R +TY+ WWI+ A+   I      +++     +K     L ++K   + ++    +   V
Sbjct: 134 RFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEK-----LNKIKKAQRELSQQKGRAATV 188

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           V +A++L+++  +V     R     SL+  +   D   ++  D L  + DGQ       E
Sbjct: 189 VELAEELDLTPKQVREYLERARQPLSLD--LRVGDNQDTELGDLL--EDDGQ-----SPE 239

Query: 220 ERKNRRNM---LTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEA 274
           +     ++   L R M  L  +++ +   R   L   P+TL  + S   +SRERVRQIE 
Sbjct: 240 DFATHSSLQFDLERLMEDLTSQQKEVIALRFGLLDGQPLTLAKIGSRLNISRERVRQIER 299

Query: 275 RAFKKV 280
            A  K+
Sbjct: 300 EALSKL 305


>gi|170078618|ref|YP_001735256.1| RNA polymerase sigma factor [Synechococcus sp. PCC 7002]
 gi|558881|gb|AAB41506.1| SigA [Synechococcus sp. PCC 7002]
 gi|169886287|gb|ACB00001.1| RNA polymerase sigma factor [Synechococcus sp. PCC 7002]
          Length = 375

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 69/237 (29%), Positives = 126/237 (53%), Gaps = 17/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 139 AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 198

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++     KP E+ +A   ++
Sbjct: 199 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKTTKILSQELGRKPTEEEIAERMEM 253

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  D +  E  + +   R++  N
Sbjct: 254 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIEADGETPEDQVSKSLLREDLEN 309

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +L      L+ RER +   R   ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 310 VL----DTLSARERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLR 362


>gi|1938356|gb|AAC45155.1| RpoD [Xanthomonas campestris pv. campestris]
          Length = 622

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 71/246 (28%), Positives = 123/246 (50%), Gaps = 12/246 (4%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A  Y E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 372 AMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 431

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I    +       L R+   +         PE
Sbjct: 432 GYKFSTYATWWIRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQQFGREPTPE 489

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           +   +AK++++ E ++  +  ++A  E ++      D   S   D++    D   +  I+
Sbjct: 490 E---LAKEMDMPEDKIRKV-MKIA-KEPISMETPIGDDEDSHLGDFI---EDTNVESPID 541

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEAR 275
                N    +   ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+
Sbjct: 542 NTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 601

Query: 276 AFKKVQ 281
           A +K++
Sbjct: 602 ALRKLR 607


>gi|259507416|ref|ZP_05750316.1| RNA polymerase principal sigma factor SigA [Corynebacterium
           efficiens YS-314]
 gi|259164981|gb|EEW49535.1| RNA polymerase principal sigma factor SigA [Corynebacterium
           efficiens YS-314]
          Length = 381

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 82/324 (25%), Positives = 154/324 (47%), Gaps = 49/324 (15%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREHG------------ 45
           RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR     Y  H             
Sbjct: 63  RKDAELTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYATHKMEEMEAAYAAGD 121

Query: 46  -----------DLSAAHR--------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
                      DL A  R        L+ ++LRLVV +A  Y G G+   +++ EGN+GL
Sbjct: 122 KDAKLTPAVKRDLRAIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGL 181

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L
Sbjct: 182 IRAVEKFDYSKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQREL 239

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    P++   ++K++++SE +V+ +        SL+  I   D+  SQ  D++  
Sbjct: 240 LQELGREPTPQE---LSKEMDISEEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI-- 292

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEV 264
             D +  V ++       ++ L   +  L+ RE  + + R  L +  P TL+ +   + V
Sbjct: 293 -EDSEAVVAVDAVSFTLLQDQLQDVLETLSEREAGVVKLRFGLTDGMPRTLDEIGQVYGV 351

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           +RER+RQIE++   K++   + QV
Sbjct: 352 TRERIRQIESKTMSKLRHPSRSQV 375


>gi|218438398|ref|YP_002376727.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
 gi|218171126|gb|ACK69859.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
          Length = 295

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 76/286 (26%), Positives = 140/286 (48%), Gaps = 36/286 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDL------------------SAAHRLVTSHLRL 60
           Y+ EI + P+L  Q+E  LA + +    L                   A  ++++++LRL
Sbjct: 12  YLQEIGRTPLLSSQQEVELATQVQNMMALLDKENLTPEEIKIIQQGKRAKRKMISANLRL 71

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y+  GL   +++ EG+IGL++ V+KFDP +G++ +TY+ WWI+ AM   I   
Sbjct: 72  VVSIAKKYQRRGLSFLDLIQEGSIGLIRGVEKFDPSKGYKFSTYAYWWIRQAMTRAIADQ 131

Query: 121 WSLVKIGT--TANQKRLFFNLRRLKGHLQAITDNNLKP-EQVVAIAKKLNVSESEVISMN 177
              +++ +  T +  +L    R+L G L        +P E+ +A   +++++E   I   
Sbjct: 132 SRTIRLPSHLTESLNKLKRITRQLTGEL------GRRPTEEEIATELEISMNELRTIRQA 185

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                  SLN  +   D   ++  + L  D     + + + E      +M+ + +  L P
Sbjct: 186 DHRTRSYSLNMKM---DDEQTELAELLADDSANPNEFVAQIE----LSSMVEQLLETLPP 238

Query: 238 RERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R++ I   R   +N   ++LE +     +SRERVRQ++ RA + ++
Sbjct: 239 RQQEIIALRYGLKNGKQMSLEEVGHHCNLSRERVRQLQNRAMRTLK 284


>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 = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RGF+ +TY+ WW
Sbjct: 587 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGFKFSTYATWW 646

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +   +P+    +A K+ +
Sbjct: 647 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGAEPDPAT-LAIKMEM 701

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + R ++
Sbjct: 702 PEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDNNTLAPADAALHASMRGVV 756

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 757 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 811


>gi|156740279|ref|YP_001430408.1| RpoD family RNA polymerase sigma factor [Roseiflexus castenholzii
           DSM 13941]
 gi|156231607|gb|ABU56390.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus
           castenholzii DSM 13941]
          Length = 541

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 73/242 (30%), Positives = 123/242 (50%), Gaps = 26/242 (10%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   L  ++LRLVV +A  Y G GL + +++ EGN+GL++AV+KFD  +GF+ +TY+ W
Sbjct: 303 TAREDLTQANLRLVVSVAKKYIGRGLQLLDLIQEGNVGLIRAVEKFDYRKGFKFSTYATW 362

Query: 108 WIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHL-QAITDNNLKPEQVVAI 162
           WI+ A+   I      ++I      T N  RL    RR+   L +  TD  L     + +
Sbjct: 363 WIRQAITRAIADQARTIRIPVHMVETIN--RLMRESRRMLQELGREPTDEELSRALGIPV 420

Query: 163 AKKLNVSES--EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K  ++ ++  E +S+   +  +E             SQ  D++    D +     +   
Sbjct: 421 DKVRSIRKTSLEPVSLETPVGQEE------------DSQLGDFI---EDSKVLAPSDAAS 465

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFK 278
            +  R  + + ++ L  RERR+ + R   E+    TLE +  EF V+RER+RQIE +A +
Sbjct: 466 HQMLREQVEQVLNQLTERERRVLQLRFGLEDGHSRTLEEVGKEFGVTRERIRQIEVKALR 525

Query: 279 KV 280
           K+
Sbjct: 526 KL 527


>gi|326801849|ref|YP_004319668.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphingobacterium
           sp. 21]
 gi|326552613|gb|ADZ80998.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphingobacterium
           sp. 21]
          Length = 285

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 74/280 (26%), Positives = 132/280 (47%), Gaps = 32/280 (11%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            LS Y++E+ K  ++   EE  LA++ RE GD  A  RL  ++LR V+ +A  Y+  GL 
Sbjct: 17  SLSLYLNEVSKFELISADEEVSLAEKIRE-GDQLALERLTKANLRFVISVAKQYQHQGLV 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN GL++A ++FD  +GF+  +Y++WWI+ ++   I      V++    NQ  
Sbjct: 76  LEDLINEGNAGLVKAARRFDETKGFKFISYAVWWIRQSIMSAISIQSRAVRL--PGNQIS 133

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVA---------IAKKLNVSESEVISMNCRLAGDES 185
               LRR +  ++   +     E++           IA   N      I      + +E 
Sbjct: 134 NLIKLRRSQAEMEQRLEREPSVEELAVELGTTTDRIIASFTNAERQLSIDAPSVFSEEER 193

Query: 186 LNALINSSDKNSSQW--QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           L   + SSD  + Q   QD L    D     L+ K+     R +LT    + N       
Sbjct: 194 LLDSLASSDPATDQQLIQDSLFLRID-----LVLKKLSSRERQILTMFYGLSNS------ 242

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
                   P TL+ ++ + +++ ER+RQ++ +A   ++ S
Sbjct: 243 -------EPQTLDEIAYQLKLTPERIRQLKTKALLHIKNS 275


>gi|23308878|ref|NP_601117.2| RNA polymerase sigma factor [Corynebacterium glutamicum ATCC 13032]
 gi|21324681|dbj|BAB99304.1| DNA-directed RNA polymerase sigma subunits (sigma70/sigma32) (SigA)
           [Corynebacterium glutamicum ATCC 13032]
          Length = 498

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 81/324 (25%), Positives = 154/324 (47%), Gaps = 49/324 (15%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREH-----------GD 46
           RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR     Y  H           GD
Sbjct: 180 RKDAELTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYATHRMEEMEEAFAAGD 238

Query: 47  LSAA--------------------HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
             A                     + L+ ++LRLVV +A  Y G G+   +++ EGN+GL
Sbjct: 239 KDAKLTPAVKRDLRAIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGL 298

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L
Sbjct: 299 IRAVEKFDYSKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQREL 356

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    P++   ++K++++SE +V+ +        SL+  I   D+  SQ  D++  
Sbjct: 357 LQELGREPTPQE---LSKEMDISEEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI-- 409

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEV 264
             D +  V ++       ++ L   +  L+ RE  + + R  L +  P TL+ +   + V
Sbjct: 410 -EDSEAVVAVDAVSFTLLQDQLQDVLETLSEREAGVVKLRFGLTDGMPRTLDEIGQVYGV 468

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           +RER+RQIE++   K++   + QV
Sbjct: 469 TRERIRQIESKTMSKLRHPSRSQV 492


>gi|328954514|ref|YP_004371848.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfobacca
           acetoxidans DSM 11109]
 gi|328454838|gb|AEB10667.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfobacca
           acetoxidans DSM 11109]
          Length = 577

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 72/237 (30%), Positives = 121/237 (51%), Gaps = 12/237 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV+KF+ ERG++ +TY+ WW
Sbjct: 339 AKSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVEKFEYERGYKFSTYATWW 398

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R   +L         PE+   +A+K+  
Sbjct: 399 IRQAITRAIADQARTIRI--PVHMIETINKLLRTSRYLVQEIGREPTPEE---LAEKMEY 453

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      ++  S   D++    D +     E  E  N   + 
Sbjct: 454 PLEKVRKV-LKIA-KEPISLETPIGEEEDSYLADFI---EDKKISSPTEAVENLNLAEIT 508

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            + +S L PRE ++   R    ++   TLE +  +F V+RER+RQIEA+A +K++ +
Sbjct: 509 RKVLSTLTPREEKVIRLRFGIGEKTDHTLEEVGKKFMVTRERIRQIEAKALRKLRHA 565


>gi|300868700|ref|ZP_07113311.1| RNA polymerase, sigma 28 subunit [Oscillatoria sp. PCC 6506]
 gi|300333261|emb|CBN58503.1| RNA polymerase, sigma 28 subunit [Oscillatoria sp. PCC 6506]
          Length = 462

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 66/240 (27%), Positives = 127/240 (52%), Gaps = 16/240 (6%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           + A   ++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV+KFDP RG+R +TY+ 
Sbjct: 220 IQAKDHMIQANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTRGYRFSTYAY 279

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   I      +++     +K     L ++K   + I+    +   +  IA +L
Sbjct: 280 WWIRQGITRAIATQSRTIRLPVHITEK-----LNKIKKAQRKISQEKGRTASIEDIAAEL 334

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD--GQEQVLIEKEERKNR 224
            ++  +V  +  R+    SL   +   ++  ++  D L+ D D    E++L+ +   ++ 
Sbjct: 335 GMTAPQVREVLLRVPRSVSLETKVG--NEKDTELGD-LLDDADSVSPEELLMREALHRDL 391

Query: 225 RNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           + +L    + L  RER +   R      +P +L  +    ++SRERVRQIEA+A +K+++
Sbjct: 392 QQLL----ADLTSRERDVILMRFGLGDGHPYSLAEIGRALDLSRERVRQIEAKALQKLRQ 447


>gi|296139587|ref|YP_003646830.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Tsukamurella
           paurometabola DSM 20162]
 gi|296027721|gb|ADG78491.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Tsukamurella
           paurometabola DSM 20162]
          Length = 483

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 80/318 (25%), Positives = 152/318 (47%), Gaps = 43/318 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-------------YREHG---- 45
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR             + E G    
Sbjct: 171 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLFAEQMINRWVERGEKPA 229

Query: 46  -----DLS--------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                D++        A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 230 IGIRRDMNWIARDGNRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 289

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L      
Sbjct: 290 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGR 347

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D + 
Sbjct: 348 EPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEA 399

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVR 270
            V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 400 VVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIR 459

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 460 QIESKTMSKLRHPSRSQV 477


>gi|87302558|ref|ZP_01085375.1| Sigma-70 factor family protein [Synechococcus sp. WH 5701]
 gi|87282902|gb|EAQ74859.1| Sigma-70 factor family protein [Synechococcus sp. WH 5701]
          Length = 307

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 71/241 (29%), Positives = 123/241 (51%), Gaps = 15/241 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +++T++LRLVV +A  Y+G GL + +++ EG +GL++AV+K+DP RG R +TY+ WW
Sbjct: 66  AKDQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLVRAVEKYDPTRGHRFSTYAYWW 125

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   +      ++I    N+K     LR  K  L         P+++ A    L +
Sbjct: 126 IRQGLNRALSTQSRTIRIPVNVNEK--LTKLRAAKARLLQANGLTASPQELAA-TMHLPL 182

Query: 169 SESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +E E + ++C L     SL  ++ S   + ++  D L  D    E   +E+ E   R   
Sbjct: 183 AEVEDL-LSCELRSITVSLQGVVKSKS-DPTELVDVLASD----EMPPMERAELSERSAS 236

Query: 228 LTRSMSV--LNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           + R + V  L PRER +   R   +      TL  ++ +   SRE  RQ+  RA +K+++
Sbjct: 237 VWRLLDVSNLTPRERTVVMLRFGLDGGHEWRTLAEVARQLGCSREYCRQVVQRALRKLRK 296

Query: 283 S 283
           +
Sbjct: 297 A 297


>gi|319941926|ref|ZP_08016247.1| hypothetical protein HMPREF9464_01466 [Sutterella wadsworthensis
           3_1_45B]
 gi|319804579|gb|EFW01449.1| hypothetical protein HMPREF9464_01466 [Sutterella wadsworthensis
           3_1_45B]
          Length = 779

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 71/258 (27%), Positives = 138/258 (53%), Gaps = 18/258 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L +Q E   A +  +   + A  +++ ++LRLV+ IA GY   GL +++++ EGN+GLM+
Sbjct: 521 LSEQRELGRAMKLAQTNLMQAKAKMIEANLRLVISIAKGYVNRGLAMTDLIQEGNLGLMK 580

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           AV KF+  RG++ +TY+ WW++ ++   +    + ++I     +   +  LRR K     
Sbjct: 581 AVDKFEYRRGYKFSTYATWWVRQSVTRAVADFGNTIRIPVHMTES--YNKLRRQKQKF-- 636

Query: 149 ITDNNLKP-EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
           +  +  +P EQ +A    L + +  +++   R  G ES++A I   D+  +   D++  +
Sbjct: 637 LQQHGRQPTEQELAELADLPLQKVNLLTQAMR--GVESIDAPIG--DEEDATKLDFVRGN 692

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR----RLQENPVTLENLSSEFE 263
                 V  +    ++  + + +S++ LNPRE ++   R      Q++  TLE +     
Sbjct: 693 ERDDPGVAFQD---RSMIDCIQKSLNELNPREAQVLRLRYGIGTNQDH--TLEEVGRTLG 747

Query: 264 VSRERVRQIEARAFKKVQ 281
           ++RERVRQIE+ A +K++
Sbjct: 748 LTRERVRQIESAAIRKLR 765


>gi|269468904|gb|EEZ80491.1| DNA-directed RNA polymerase, sigma subunit [uncultured SUP05
           cluster bacterium]
          Length = 603

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 77/262 (29%), Positives = 126/262 (48%), Gaps = 40/262 (15%)

Query: 36  VLAKRYREHGD---LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
            L K YR  GD     A  +++ ++LRLV+ IA  Y   GL   +++ EGN+GLM+AV K
Sbjct: 351 ALNKLYR-RGDRRAKKAKSQMIEANLRLVISIAKKYANRGLQFLDLIQEGNVGLMKAVDK 409

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQA 148
           F+  RG++ +TY+ WWI+ A+   I      ++I      T N+      L R++  L  
Sbjct: 410 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK------LNRVRRQLLQ 463

Query: 149 ITDNNLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
                  PE++          I K L +++ E +SM   +  DE  N      D N S  
Sbjct: 464 KFGREATPEELAVEMELPEYKINKILKIAK-EPLSMETPVGDDEDSNIGDFIEDTNLSSP 522

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENL 258
                          +E   R++ +      ++ L+PRE ++ + R   +     TLE +
Sbjct: 523 ---------------VEITTRESLKETTGELLANLSPREAKVLKMRFGIDMNTDHTLEEV 567

Query: 259 SSEFEVSRERVRQIEARAFKKV 280
             +F+V+RER+RQIEA+A +K+
Sbjct: 568 GRQFDVTRERIRQIEAKALRKL 589


>gi|148654464|ref|YP_001274669.1| RpoD family RNA polymerase sigma factor [Roseiflexus sp. RS-1]
 gi|148566574|gb|ABQ88719.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus sp.
           RS-1]
          Length = 541

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 73/242 (30%), Positives = 123/242 (50%), Gaps = 26/242 (10%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   L  ++LRLVV +A  Y G GL + +++ EGN+GL++AV+KFD  +GF+ +TY+ W
Sbjct: 303 TAREDLTQANLRLVVSVAKKYIGRGLQLLDLIQEGNVGLIRAVEKFDYRKGFKFSTYATW 362

Query: 108 WIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHL-QAITDNNLKPEQVVAI 162
           WI+ A+   I      ++I      T N  RL    RR+   L +  TD  L     + +
Sbjct: 363 WIRQAITRAIADQARTIRIPVHMVETIN--RLMRESRRMLQELGREPTDEELSRALGIPV 420

Query: 163 AKKLNVSES--EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K  ++ ++  E +S+   +  +E             SQ  D++    D +     +   
Sbjct: 421 DKVRSIRKTSLEPVSLETPVGQEE------------DSQLGDFI---EDSKVLAPSDAAS 465

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFK 278
            +  R  + + ++ L  RERR+ + R   E+    TLE +  EF V+RER+RQIE +A +
Sbjct: 466 HQMLREQVEQVLNQLTERERRVLQLRFGLEDGHSRTLEEVGKEFGVTRERIRQIEVKALR 525

Query: 279 KV 280
           K+
Sbjct: 526 KL 527


>gi|25028360|ref|NP_738414.1| RNA polymerase sigma factor [Corynebacterium efficiens YS-314]
 gi|23493645|dbj|BAC18614.1| sigma factor SigA [Corynebacterium efficiens YS-314]
          Length = 506

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 81/324 (25%), Positives = 154/324 (47%), Gaps = 49/324 (15%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREH-----------GD 46
           RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR     Y  H           GD
Sbjct: 188 RKDAELTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYATHKMEEMEAAYAAGD 246

Query: 47  LSAA--------------------HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
             A                     + L+ ++LRLVV +A  Y G G+   +++ EGN+GL
Sbjct: 247 KDAKLTPAVKRDLRAIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGL 306

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L
Sbjct: 307 IRAVEKFDYSKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQREL 364

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    P++   ++K++++SE +V+ +        SL+  I   D+  SQ  D++  
Sbjct: 365 LQELGREPTPQE---LSKEMDISEEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI-- 417

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEV 264
             D +  V ++       ++ L   +  L+ RE  + + R  L +  P TL+ +   + V
Sbjct: 418 -EDSEAVVAVDAVSFTLLQDQLQDVLETLSEREAGVVKLRFGLTDGMPRTLDEIGQVYGV 476

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           +RER+RQIE++   K++   + QV
Sbjct: 477 TRERIRQIESKTMSKLRHPSRSQV 500


>gi|145295815|ref|YP_001138636.1| RNA polymerase sigma factor [Corynebacterium glutamicum R]
 gi|140845735|dbj|BAF54734.1| hypothetical protein [Corynebacterium glutamicum R]
          Length = 494

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 81/324 (25%), Positives = 154/324 (47%), Gaps = 49/324 (15%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREH-----------GD 46
           RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR     Y  H           GD
Sbjct: 176 RKDAELTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYATHRMEEMEEAFAAGD 234

Query: 47  LSAA--------------------HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
             A                     + L+ ++LRLVV +A  Y G G+   +++ EGN+GL
Sbjct: 235 KDAKLTPAVKRDLRAIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGL 294

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L
Sbjct: 295 IRAVEKFDYSKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQREL 352

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    P++   ++K++++SE +V+ +        SL+  I   D+  SQ  D++  
Sbjct: 353 LQELGREPTPQE---LSKEMDISEEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI-- 405

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEV 264
             D +  V ++       ++ L   +  L+ RE  + + R  L +  P TL+ +   + V
Sbjct: 406 -EDSEAVVAVDAVSFTLLQDQLQDVLETLSEREAGVVKLRFGLTDGMPRTLDEIGQVYGV 464

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           +RER+RQIE++   K++   + QV
Sbjct: 465 TRERIRQIESKTMSKLRHPSRSQV 488


>gi|86606677|ref|YP_475440.1| RNA polymerase sigma factor SigC [Synechococcus sp. JA-3-3Ab]
 gi|86555219|gb|ABD00177.1| RNA polymerase sigma-70 factor family [Synechococcus sp. JA-3-3Ab]
          Length = 364

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 67/248 (27%), Positives = 129/248 (52%), Gaps = 21/248 (8%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           + KR +EH        ++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV+KFDP+
Sbjct: 121 IGKRAKEH--------MIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPK 172

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +G+R +TY+ WWI+  +   I      +++     +K     L ++K   + ++    + 
Sbjct: 173 KGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEK-----LNKIKKAQRKLSQEKGRT 227

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
             +  IA +L ++  +V  +  R+    SL   +   DK+ ++  D L  D    E+ ++
Sbjct: 228 PTIEDIASELEMTVPQVRELLVRVPRSVSLETKVG-KDKD-TELGDLLETDDISPEETMM 285

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT--LENLSSEFEVSRERVRQIEA 274
            +   ++ + +L    + L  RER +   R    +  T  L  +    ++SRERVRQIEA
Sbjct: 286 REALHRDLQQLL----ADLTSRERDVIRMRFGLGDGRTYSLAEIGRALDLSRERVRQIEA 341

Query: 275 RAFKKVQE 282
           +A +K+++
Sbjct: 342 KALQKLRQ 349


>gi|326518320|dbj|BAJ88189.1| predicted protein [Hordeum vulgare subsp. vulgare]
 gi|326533296|dbj|BAJ93620.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 552

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 75/255 (29%), Positives = 134/255 (52%), Gaps = 23/255 (9%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E  L KR  +HG +   +R+VTS++RLV+ IA  + G GL + +++ EG  GL++  +K
Sbjct: 297 DENTLRKRL-DHG-IHCKNRMVTSNVRLVISIAREFEGPGLELYDLIQEGMQGLIRGAEK 354

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +GFR +TYS WWIK AM++ +     + ++   A+     + ++     L+     
Sbjct: 355 FDASKGFRFSTYSHWWIKQAMRKSVSEQTQIFRL--PAHMVEASYRVKECTKRLRRKLKR 412

Query: 153 NLKPEQV-VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               E++ V I   +   E+ V      +    SL++ I S+D         + Y     
Sbjct: 413 RPSNEEIAVDIGMPVKRVEAAVSLPKYSV----SLDSKIGSTD---------MTYQEVTA 459

Query: 212 EQVLIEKEERKNRRNM---LTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSR 266
           +      EE  NR +M   + +++  L+PRER++ + R  + +  + TL+ + +   VSR
Sbjct: 460 DPSAETAEEMLNRMSMKKDVHQALDTLSPRERQVVKLRFGINDGRIRTLQEIGNIMGVSR 519

Query: 267 ERVRQIEARAFKKVQ 281
           ER+RQIE+ AF+K++
Sbjct: 520 ERIRQIESGAFRKLR 534


>gi|186680839|ref|YP_001864035.1| RpoD family RNA polymerase sigma factor [Nostoc punctiforme PCC
           73102]
 gi|186463291|gb|ACC79092.1| RNA polymerase, sigma 70 subunit, RpoD family [Nostoc punctiforme
           PCC 73102]
          Length = 378

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 68/240 (28%), Positives = 121/240 (50%), Gaps = 21/240 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +++ S+LRLVV IA  Y   G+P  +++ EG +GL +A +KFDP++G++ +TY+ WW
Sbjct: 140 AKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAMGLNRATEKFDPDKGYKFSTYAYWW 199

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      +++     +K     L +LK   + +     +      +A+ L++
Sbjct: 200 IRQAITRAIANDARTIRLPIHIVEK-----LNKLKKAQRELKQKLCRNPTEGEMAEALDI 254

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  ++  +        SLN  +   +   ++  D L+ D D          E K   NM+
Sbjct: 255 SVQQLRQLQQLRRQALSLNHRVGKEE--DTELMD-LLEDEDNL------SPEAKMNENMM 305

Query: 229 TRSM-----SVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            + +      VL PRE+ +   R       P TLE + + F +SRERVRQI+++A +K++
Sbjct: 306 RQEIWEVLGDVLTPREKDVISLRYGLTTSEPCTLEEVGNMFNLSRERVRQIQSKAMRKLR 365


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

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RGF+ +TY+ WW
Sbjct: 561 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGFKFSTYATWW 620

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +   +P+    +A K+ +
Sbjct: 621 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGAEPDPAT-LAIKMEM 675

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + R ++
Sbjct: 676 PEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDNNTLAPADAALHASMRGVV 730

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 731 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 785


>gi|218200736|gb|EEC83163.1| hypothetical protein OsI_28384 [Oryza sativa Indica Group]
          Length = 537

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 63/243 (25%), Positives = 125/243 (51%), Gaps = 23/243 (9%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           ++  S+ RLV+ +A  Y GYGL I ++V +G  GLM+  +KF+P +G R  TY+ WWI+ 
Sbjct: 301 KMARSNFRLVIHVARKYEGYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQ 360

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRL-KGHLQAITDNNLKPEQVVAIAKKLNVSE 170
           ++++ I ++  L+++  +     ++  LR++ K  ++ I +   +P     +A++  ++ 
Sbjct: 361 SIKKSIFKNSRLIRLPES-----VYALLRKVGKARMECIMEGE-QPTN-ANVARRAGITI 413

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            ++  +  +     S+   +         W D  V   +  E   +E  +    R M+ +
Sbjct: 414 EKLAKLRAKTRKPRSMQDHV---------WSDEGVTFQEITEDPNVEPPDLSVDRMMMRQ 464

Query: 231 S----MSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                + +L+PRE+ I E R    +  P TL  +   F +S+ER+RQ++ RA +K++ S 
Sbjct: 465 QVRDFLGILSPREKEIIEHRFGIHDGEPKTLHVIGDMFGLSKERIRQLQNRALEKLKRSA 524

Query: 285 QKQ 287
             Q
Sbjct: 525 SLQ 527


>gi|196229539|ref|ZP_03128404.1| RNA polymerase, sigma 70 subunit, RpoD family [Chthoniobacter
           flavus Ellin428]
 gi|196226771|gb|EDY21276.1| RNA polymerase, sigma 70 subunit, RpoD family [Chthoniobacter
           flavus Ellin428]
          Length = 671

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 81/264 (30%), Positives = 130/264 (49%), Gaps = 35/264 (13%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           E QEEY   K + +   L A   +V ++LRLV+ IA  Y   GL   +++ EGN+GLM+A
Sbjct: 412 EFQEEYKELKVWLKKA-LKAKTEMVEANLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKA 470

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN-----QKRLFFNLR 140
           V+KF+  RG++ +TY+ WWI+ A+   I      ++I      T N     QK+L  +  
Sbjct: 471 VEKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLMRVQKQLVQDYG 530

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL--AGDESLNALINSSDKNSS 198
           R     +   +  L  E+V A+ K       + IS+   +  + D S    I   DK + 
Sbjct: 531 REPTPEEVADEIQLPVERVRAVLKMAQ----QPISLQSPVGESDDTSFGDFIE--DKGAE 584

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLE 256
              D           +++ KE+ K+        +  L  RER++ E R   +     TLE
Sbjct: 585 NLSDMTA--------IVLLKEKIKD-------VLETLTERERQVLEQRFGLVDGYSRTLE 629

Query: 257 NLSSEFEVSRERVRQIEARAFKKV 280
            +  +F+V+RER+RQIEA+A +K+
Sbjct: 630 EVGRQFKVTRERIRQIEAKALRKM 653


>gi|115475493|ref|NP_001061343.1| Os08g0242800 [Oryza sativa Japonica Group]
 gi|30698490|dbj|BAC76602.1| Sig6 [Oryza sativa Japonica Group]
 gi|40253642|dbj|BAD05586.1| Sig6, plastid RNA polymerase sigma factor [Oryza sativa Japonica
           Group]
 gi|40253689|dbj|BAD05631.1| Sig6, plastid RNA polymerase sigma factor [Oryza sativa Japonica
           Group]
 gi|113623312|dbj|BAF23257.1| Os08g0242800 [Oryza sativa Japonica Group]
 gi|215712228|dbj|BAG94355.1| unnamed protein product [Oryza sativa Japonica Group]
          Length = 572

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 63/243 (25%), Positives = 125/243 (51%), Gaps = 23/243 (9%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           ++  S+ RLV+ +A  Y GYGL I ++V +G  GLM+  +KF+P +G R  TY+ WWI+ 
Sbjct: 336 KMARSNFRLVIHVARKYEGYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQ 395

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRL-KGHLQAITDNNLKPEQVVAIAKKLNVSE 170
           ++++ I ++  L+++  +     ++  LR++ K  ++ I +   +P     +A++  ++ 
Sbjct: 396 SIKKSIFKNSRLIRLPES-----VYALLRKVGKARMECIMEGE-QPTN-ANVARRAGITI 448

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            ++  +  +     S+   +         W D  V   +  E   +E  +    R M+ +
Sbjct: 449 EKLAKLRAKTRKPRSMQDHV---------WSDEGVTFQEITEDPNVEPPDLSVDRMMMRQ 499

Query: 231 S----MSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                + +L+PRE+ I E R    +  P TL  +   F +S+ER+RQ++ RA +K++ S 
Sbjct: 500 QVRDFLGILSPREKEIIEHRFGIHDGEPKTLHVIGDMFGLSKERIRQLQNRALEKLKRSA 559

Query: 285 QKQ 287
             Q
Sbjct: 560 SLQ 562


>gi|254424042|ref|ZP_05037760.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
 gi|196191531|gb|EDX86495.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
          Length = 319

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 65/249 (26%), Positives = 134/249 (53%), Gaps = 37/249 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +++ S+LRLVV IA  YRG  L + +++ EG++GL + V+KFDP +G+R +TY+ WW
Sbjct: 83  AKDKMMRSNLRLVVSIAKKYRGSKLDMMDLIQEGSLGLCRGVEKFDPLKGYRFSTYAYWW 142

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I  +   +++    N+K     L +++   + ++    +P  V  +A+K+++
Sbjct: 143 IRQAITRAIADTGRTIRLPIHINEK-----LSKIRKAQREVSLELGRPATVSEVAEKVSL 197

Query: 169 SESEV----------ISMNCRLAGDES--LNALINSSDKNSSQW--QDWLVYDHDGQEQV 214
              +V          +S+N R+  +++  L AL+ S  ++  ++  Q+ L  D     Q+
Sbjct: 198 PAEKVRELQRQSRLPLSLNMRIGSEQNTELGALLESDSQSPEEYATQNLLKRDIG---QL 254

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
           L    ER+  +++++    + + +++             TL  +  + ++SRERVRQIE 
Sbjct: 255 LARLTERQ--KDVISMRFGLDDGKKK-------------TLAQIGHDLDISRERVRQIER 299

Query: 275 RAFKKVQES 283
           +A + ++ +
Sbjct: 300 KALRTLRHT 308


>gi|62390750|ref|YP_226152.1| RNA polymerase sigma factor [Corynebacterium glutamicum ATCC 13032]
 gi|41326088|emb|CAF20251.1| RNA POLYMERASE SIGMA 70 FACTOR [Corynebacterium glutamicum ATCC
           13032]
          Length = 494

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 81/324 (25%), Positives = 154/324 (47%), Gaps = 49/324 (15%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREH-----------GD 46
           RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR     Y  H           GD
Sbjct: 176 RKDAELTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYATHRMEEMEEAFAAGD 234

Query: 47  LSAA--------------------HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
             A                     + L+ ++LRLVV +A  Y G G+   +++ EGN+GL
Sbjct: 235 KDAKLTPAVKRDLRAIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGL 294

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L
Sbjct: 295 IRAVEKFDYSKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQREL 352

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    P++   ++K++++SE +V+ +        SL+  I   D+  SQ  D++  
Sbjct: 353 LQELGREPTPQE---LSKEMDISEEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI-- 405

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEV 264
             D +  V ++       ++ L   +  L+ RE  + + R  L +  P TL+ +   + V
Sbjct: 406 -EDSEAVVAVDAVSFTLLQDQLQDVLETLSEREAGVVKLRFGLTDGMPRTLDEIGQVYGV 464

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           +RER+RQIE++   K++   + QV
Sbjct: 465 TRERIRQIESKTMSKLRHPSRSQV 488


>gi|332704204|ref|ZP_08424292.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           africanus str. Walvis Bay]
 gi|332554353|gb|EGJ51397.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           africanus str. Walvis Bay]
          Length = 594

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 73/248 (29%), Positives = 128/248 (51%), Gaps = 24/248 (9%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ WW
Sbjct: 356 AKRELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWW 415

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+      L R   +L      +  PE+   IA+
Sbjct: 416 IRQAITRAIADQARTIRIPVHMIETINK------LIRTSRYLVQELGRDPTPEE---IAE 466

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +++    E +    ++A  E ++      D+  S   D++       ++ +   EE  N 
Sbjct: 467 RMDYP-IEKVKKVLKIAK-EPISLETPIGDEEDSSLGDFI-----EDKKAVAPAEEVVNT 519

Query: 225 R--NMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           +    + + +S L PRE ++   R    +++  TLE +   F V+RER+RQIEA+A +K+
Sbjct: 520 KLSEQIGKVLSDLTPREEQVLRKRFGIGEKSDHTLEEVGKLFNVTRERIRQIEAKALRKL 579

Query: 281 QESIQKQV 288
           +  ++ Q+
Sbjct: 580 RHPVRSQI 587


>gi|298529696|ref|ZP_07017099.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Desulfonatronospira thiodismutans ASO3-1]
 gi|298511132|gb|EFI35035.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Desulfonatronospira thiodismutans ASO3-1]
          Length = 588

 Score = 93.6 bits (231), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 72/250 (28%), Positives = 126/250 (50%), Gaps = 30/250 (12%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ 
Sbjct: 348 LRAKQELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYAT 407

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV------ 160
           WWI+ A+   I      ++I    +       L R   +L      +  PE++       
Sbjct: 408 WWIRQAITRAIADQARTIRI--PVHMIETINKLVRTSRYLVQELGRDPSPEEIAERMDYP 465

Query: 161 --AIAKKLNVSESEVISMNCRLAGDESLNALINS-SDKNSSQWQDWLVYDHDGQEQVLIE 217
              + K L +++ E IS+   + GDE  ++L +   DK +    D +V     ++     
Sbjct: 466 LEKVKKVLKIAK-EPISLETPI-GDEEDSSLGDFIEDKKAVAPADEVVNSKLSEQ----- 518

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
                     +++ ++ L PRE ++   R    +++  TLE +   F V+RER+RQIEA+
Sbjct: 519 ----------ISKVLAELTPREEQVLRKRFGIGEKSDHTLEEVGKLFNVTRERIRQIEAK 568

Query: 276 AFKKVQESIQ 285
           A +K++  ++
Sbjct: 569 ALRKLRHPVR 578


>gi|299135760|ref|ZP_07028944.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidobacterium
           sp. MP5ACTX8]
 gi|298601884|gb|EFI58038.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidobacterium
           sp. MP5ACTX8]
          Length = 573

 Score = 93.6 bits (231), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 77/250 (30%), Positives = 125/250 (50%), Gaps = 29/250 (11%)

Query: 44  HGDLSA--AHR-LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
            GD+ A  A R L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 323 QGDMDAEKAKRELIEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 382

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHL--QAITDNNL 154
            +TY+ WWI+ A+   I      ++I      T N  +L    R+L   L  +A ++   
Sbjct: 383 FSTYATWWIRQAITRAIADQARTIRIPVHMIETIN--KLIRTSRQLVQELGREASSEEIA 440

Query: 155 KPEQV-VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
           K   + VA  +K+     E IS+   +  +E  +      D+ +    D ++        
Sbjct: 441 KRMDIPVAKVRKVLKIAQEPISLETPIGEEEDSHLGDFIEDRMAVSPSDAVIS------- 493

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQ 271
                    N +   ++ +  L PRE R+ + R   E+    TLE +   F+V+RER+RQ
Sbjct: 494 --------VNLKEYTSQVLRTLTPREERVIKMRFGLEDGSEHTLEEVGQSFQVTRERIRQ 545

Query: 272 IEARAFKKVQ 281
           IEA+A +K++
Sbjct: 546 IEAKALRKLR 555


>gi|237785650|ref|YP_002906355.1| RNA polymerase sigma factor [Corynebacterium kroppenstedtii DSM
           44385]
 gi|237758562|gb|ACR17812.1| RNA polymerase sigma factor A [Corynebacterium kroppenstedtii DSM
           44385]
          Length = 621

 Score = 93.2 bits (230), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 82/318 (25%), Positives = 153/318 (48%), Gaps = 43/318 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREHG------------ 45
           RK+  +  + +  +  Y+ +I K+ +L  ++E  LA+R     Y  H             
Sbjct: 309 RKDAELTASAD-SVRAYLKQIGKVALLNAEQEVSLAQRIEAGLYANHKLEELKASNTKLS 367

Query: 46  -----DL-SAAH-------RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                DL S AH        L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 368 PAQSRDLRSIAHDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 427

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L      
Sbjct: 428 FDYTKGYKFSTYATWWIRQAITRSMADQARTIRI--PVHMVEVINKLGRIQRELLQDLSR 485

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE+   +A++++++E +V+ +        SL+  I   D+  SQ  D++    D + 
Sbjct: 486 EPTPEE---LAREMDITEDKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEA 537

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVR 270
            V ++       ++ L   +  L  RE  +   R  L +  P TL+ +   + V+RER+R
Sbjct: 538 VVAVDAVSFTLLQDQLQDVLKTLTEREAGVVRLRFGLTDGMPRTLDEIGQVYGVTRERIR 597

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 598 QIESKTMSKLRHPSRSQV 615


>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 = 93.2 bits (230), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 73/246 (29%), Positives = 118/246 (47%), Gaps = 34/246 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 458 AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 517

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +   T     PE+   + +++++
Sbjct: 518 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQILQETGIEATPEE---LGRRMDM 572

Query: 169 SESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            E +V          ISM   +  DE  N      D N     D+           L+E 
Sbjct: 573 PEEKVRKVLKIAKEPISMETPIGEDEDSNLGDFIEDINMESPVDF------ATSAGLMEA 626

Query: 219 EERKNRRNMLTRS-MSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEAR 275
                     TR  +S L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+
Sbjct: 627 ----------TREILSTLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 676

Query: 276 AFKKVQ 281
           A +K++
Sbjct: 677 ALRKLR 682


>gi|167724581|ref|ZP_02407817.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei DM98]
          Length = 680

 Score = 93.2 bits (230), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 65/235 (27%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 441 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 500

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +  L+P+    +A+K+ +
Sbjct: 501 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGLEPDPAT-LAEKMEM 555

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + R+++
Sbjct: 556 PEDKIRKI-MKIAK-EPISMETPIGDDDDSHLGDFI---EDTNTVAPADAALHASMRDVV 610

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L P E ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 611 KDVLDSLTPSEAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 665


>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 = 93.2 bits (230), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 68/235 (28%), Positives = 119/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 364 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 423

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   +A+++ +
Sbjct: 424 IRQAITRSIADQARTIRI--PVHMIETINKLNRVSRQMLQEMGREATPEE---LAERMEM 478

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E +V  +  ++A  E ++      D   S   D++    D      ++    +  R  +
Sbjct: 479 PEDKVRKV-LKIAK-EPISMETPIGDDEDSHLGDFI---EDTSVTSPVDSATSEGLRESV 533

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +S L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 534 REVLSGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 588


>gi|302867958|ref|YP_003836595.1| sigma-70 family RNA polymerase [Micromonospora aurantiaca ATCC
           27029]
 gi|302570817|gb|ADL47019.1| RNA polymerase sigma factor, sigma-70 family [Micromonospora
           aurantiaca ATCC 27029]
          Length = 314

 Score = 93.2 bits (230), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 143/310 (46%), Gaps = 54/310 (17%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLA----------KRYREHGDLSAA--------------- 50
           ++ Y+  I + P+L  ++E  L           +R  + GD   A               
Sbjct: 16  VAAYLRTIGRTPLLTAEQETRLGARIEAGALAQRRLDDDGDRVGAAEQDRLRRLVADGRR 75

Query: 51  --HRLVTSHLRLVVKIAMGYRGYG-LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
             H ++ ++LRLVV +A  Y   G LP+ +++ EG IGLM+AV+KFD  RG + +TY+ W
Sbjct: 76  ARHHMIEANLRLVVSVAKRYALAGRLPLLDLIQEGTIGLMRAVEKFDHRRGLKFSTYATW 135

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA----IA 163
           WIK A+   +      +++   A+   +   + R +  L    D    P +V A     A
Sbjct: 136 WIKQAIGRALTDQSRTIRL--PAHLVEVLNRVNRTRRTLAGELDREPTPAEVAARVEVPA 193

Query: 164 KKLNV---SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
           +K+ +    + E +S++  +AG              +++  D L  +  G   V++    
Sbjct: 194 EKVELLLRHDREPVSLHTPVAG-----------AAGTTELGDLLPDEAPGPAGVVVSSW- 241

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFK 278
              RR  L   +  L+ RE  +   R   ++  P TL+ + +   ++RERVRQIE++A +
Sbjct: 242 ---RRRYLDEVLGTLSEREAAVICQRYGLDDDRPSTLDEIGTRIGLTRERVRQIESQALR 298

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 299 KLRHPTRARV 308


>gi|298346920|ref|YP_003719607.1| RNA polymerase sigma factor SigA [Mobiluncus curtisii ATCC 43063]
 gi|298236981|gb|ADI68113.1| RNA polymerase sigma factor SigA [Mobiluncus curtisii ATCC 43063]
          Length = 563

 Score = 93.2 bits (230), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 81/310 (26%), Positives = 144/310 (46%), Gaps = 63/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH-----------------------GDLSAA 50
           Y+ +I K+ +L  ++E  L+KR     Y EH                       G ++  
Sbjct: 269 YLKQIGKVALLNAEQEVDLSKRIEAGLYAEHLLKTKQETMTPKQIRELHYVVQDGQMAKN 328

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           H L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+
Sbjct: 329 H-LLEANLRLVVALAKKYTGRGMLFLDLIQEGNLGLIRAVEKFDYSKGYKFSTYATWWIR 387

Query: 111 AAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
            A+   +      ++I              Q+++  +L R     +   +  + PE+VV 
Sbjct: 388 QAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPDELAQELEMTPEKVVE 447

Query: 162 IAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           + K       E IS++  L   GD     LI  S+          V   D    ++++++
Sbjct: 448 VQKYGR----EPISLHTPLGEDGDSEFGDLIEDSE---------AVVPADAVSFMMLQEQ 494

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAF 277
                   L R +  L+ RE  +   R  L++  P TL+ +   + V+RER+RQIEA+  
Sbjct: 495 --------LQRVLDTLSERESGVIAMRFGLKDGQPKTLDEIGRRYGVTRERIRQIEAKTM 546

Query: 278 KKVQESIQKQ 287
            K++   + Q
Sbjct: 547 SKLRHPARSQ 556


>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 = 93.2 bits (230), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 68/238 (28%), Positives = 127/238 (53%), Gaps = 20/238 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A H ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 601 AKHEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 660

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I     +++I    +       + R+    Q + +  ++P+  + +A+K+++
Sbjct: 661 IRQAITRSIADQARIIRI--PVHMIETINKINRI--TRQILQETGVEPDSAM-LAEKMDM 715

Query: 169 SESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
              E I    +++ D  S+   I   D + S   D++      ++   +  EE   +R+M
Sbjct: 716 P-IEKIRKILKISKDPISMETPIG--DDDDSHLGDFI------EDTSTLSPEEAALQRSM 766

Query: 228 LTRSMSVLNPRERRIFEARRLQ-----ENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                 V+N   +R  +  R++      +  TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 767 SEVFDEVINSLTQREGKVLRMRFGIGMSSDQTLEEVGKQFDVTRERIRQIEAKALRKL 824


>gi|1237088|emb|CAA92648.1| major sigma factor [Rhodobacter capsulatus]
          Length = 674

 Score = 93.2 bits (230), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 72/236 (30%), Positives = 119/236 (50%), Gaps = 14/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 436 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 495

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   +A+KL +
Sbjct: 496 IRQAITRSIADQARTIRI--PVHMIETINKLVRTGRQMLHEIGREPTPEE---LAEKLQM 550

Query: 169 SESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
              +V  +  ++A +  SL   I   +   SQ  D++    D    + ++   ++N +  
Sbjct: 551 PLEKVRKV-MKIAKEPISLETPIGHEE--DSQLGDFI---EDKNAILPLDSAIQENLKET 604

Query: 228 LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TR +  L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 605 TTRVLPSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 660


>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 = 93.2 bits (230), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 71/250 (28%), Positives = 121/250 (48%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 377 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 436

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 437 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 494

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 495 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPMDSAT 538

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             N +   +  ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 539 MNNLKMATSEVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 598

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 599 KLRHPSRSEV 608


>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 = 93.2 bits (230), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 73/246 (29%), Positives = 118/246 (47%), Gaps = 34/246 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 458 AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 517

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +   T     PE+   + +++++
Sbjct: 518 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQILQETGIEATPEE---LGRRMDM 572

Query: 169 SESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            E +V          ISM   +  DE  N      D N     D+           L+E 
Sbjct: 573 PEEKVRKVLKIAKEPISMETPIGEDEDSNLGDFIEDINMESPVDF------ATSAGLMEA 626

Query: 219 EERKNRRNMLTRS-MSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEAR 275
                     TR  +S L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+
Sbjct: 627 ----------TREILSTLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 676

Query: 276 AFKKVQ 281
           A +K++
Sbjct: 677 ALRKLR 682


>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 = 93.2 bits (230), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 64/237 (27%), Positives = 125/237 (52%), Gaps = 16/237 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGN+GLM+AV KF+  RG++ +TY+ WW
Sbjct: 676 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNVGLMKAVDKFEYRRGYKFSTYATWW 735

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL-KGHLQAITDNNLKPEQVVAIAKKLN 167
           I+ A+   I      ++I        +   + R+ +   Q + +  ++P+    +A+ + 
Sbjct: 736 IRQAITRSIADQARTIRIPV-----HMIETINRMNRITRQELQETGVEPDS-RRLAELME 789

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + E +++ +  ++A  E ++      D + S   D+L    D Q     E  +  +  + 
Sbjct: 790 MPEDKILKI-MKIAK-EPISMETPIGDDDDSHLGDFL---EDTQTVAPAEAVQNASLSDT 844

Query: 228 LTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           + + +  L+PRE ++   R    +Q +  TLE +  +F+V+RER+RQIE +A +K++
Sbjct: 845 VKQVLDSLSPREAKVLRMRFGIEMQSDH-TLEEVGKQFDVTRERIRQIETKALRKLR 900


>gi|257892237|ref|ZP_05671890.1| LOW QUALITY PROTEIN: RNA polymerase sigma factor RpoD [Enterococcus
           faecium 1,231,408]
 gi|257828616|gb|EEV55223.1| LOW QUALITY PROTEIN: RNA polymerase sigma factor RpoD [Enterococcus
           faecium 1,231,408]
          Length = 332

 Score = 93.2 bits (230), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 45/108 (41%), Positives = 68/108 (62%), Gaps = 1/108 (0%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L  +EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 103 YLKEIGRVSLLTAEEEVALALKI-EEGDQEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 161

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I
Sbjct: 162 IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRI 209


>gi|125602683|gb|EAZ42008.1| hypothetical protein OsJ_26557 [Oryza sativa Japonica Group]
          Length = 497

 Score = 93.2 bits (230), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 63/243 (25%), Positives = 125/243 (51%), Gaps = 23/243 (9%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           ++  S+ RLV+ +A  Y GYGL I ++V +G  GLM+  +KF+P +G R  TY+ WWI+ 
Sbjct: 261 KMARSNFRLVIHVARKYEGYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAYWWIRQ 320

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRL-KGHLQAITDNNLKPEQVVAIAKKLNVSE 170
           ++++ I ++  L+++  +     ++  LR++ K  ++ I +   +P     +A++  ++ 
Sbjct: 321 SIKKSIFKNSRLIRLPES-----VYALLRKVGKARMECIMEGE-QPTN-ANVARRAGITI 373

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            ++  +  +     S+   +         W D  V   +  E   +E  +    R M+ +
Sbjct: 374 EKLAKLRAKTRKPRSMQDHV---------WSDEGVTFQEITEDPNVEPPDLSVDRMMMRQ 424

Query: 231 S----MSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                + +L+PRE+ I E R    +  P TL  +   F +S+ER+RQ++ RA +K++ S 
Sbjct: 425 QVRDFLGILSPREKEIIEHRFGIHDGEPKTLHVIGDMFGLSKERIRQLQNRALEKLKRSA 484

Query: 285 QKQ 287
             Q
Sbjct: 485 SLQ 487


>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|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 = 93.2 bits (230), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 73/246 (29%), Positives = 118/246 (47%), Gaps = 34/246 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 458 AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 517

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +   T     PE+   + +++++
Sbjct: 518 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQILQETGIEATPEE---LGRRMDM 572

Query: 169 SESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            E +V          ISM   +  DE  N      D N     D+           L+E 
Sbjct: 573 PEEKVRKVLKIAKEPISMETPIGEDEDSNLGDFIEDINMESPVDF------ATSAGLMEA 626

Query: 219 EERKNRRNMLTRS-MSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEAR 275
                     TR  +S L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+
Sbjct: 627 ----------TREILSTLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 676

Query: 276 AFKKVQ 281
           A +K++
Sbjct: 677 ALRKLR 682


>gi|312200424|ref|YP_004020485.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EuI1c]
 gi|311231760|gb|ADP84615.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EuI1c]
          Length = 403

 Score = 93.2 bits (230), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 87/292 (29%), Positives = 134/292 (45%), Gaps = 39/292 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR---------------------------EHGDLSAAH 51
           Y+  I K P+L  + E  LAKR                             E     AA 
Sbjct: 109 YLASIGKTPLLTAEGEVDLAKRIEAGLFAGHKLETAVEEMSPGQRLDLIAVERDGQVAAR 168

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +LV ++LRLVV IA  Y G G+   +VV EGN+GL++AV+KFD  +G++ +TY+ WW++ 
Sbjct: 169 QLVEANLRLVVSIAKRYAGRGMLFLDVVQEGNLGLIRAVEKFDYTKGYKFSTYATWWVRQ 228

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           A+   +      V++    +   L   L RL+  L          E+   +A  L V+ +
Sbjct: 229 AITRALADQSRTVRL--PVHLVELLNQLVRLRRELLMELGREATREE---LATALGVTAN 283

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
            V  +        SL++ +   D   ++  D L+ D    E V  E      R   L+  
Sbjct: 284 RVDELQRISREPVSLDSPVG--DDADTELGD-LIEDTAAIEPV--EAAMVSVRAAQLSAV 338

Query: 232 MSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +  L  RERR+ + R  L +  V TLE +  EF ++RER+RQIE R   K++
Sbjct: 339 LRALPDRERRVIQLRFGLADGQVHTLEEIGREFGLTRERIRQIEQRTLAKLR 390


>gi|296121158|ref|YP_003628936.1| RNA polymerase sigma factor, sigma-70 family [Planctomyces
           limnophilus DSM 3776]
 gi|296013498|gb|ADG66737.1| RNA polymerase sigma factor, sigma-70 family [Planctomyces
           limnophilus DSM 3776]
          Length = 577

 Score = 93.2 bits (230), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 123/235 (52%), Gaps = 16/235 (6%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            +L   +LRLVV IA  YR  GL   +++ EGN GLM+ V+K++  RG++ +TY+ WWI+
Sbjct: 300 QQLSGGNLRLVVSIAKKYRNRGLSFLDLIQEGNAGLMRGVEKYEFRRGYKFSTYATWWIR 359

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV--VAIAKKLNV 168
            A+   +      ++I        +F ++  LK   + I     +   +  +A+A  ++V
Sbjct: 360 QAITRAVADHARTIRIPV-----HMFQSISTLKNKSEQIRQETGREPTIEELALAVDMSV 414

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            ++E I    +     SL+  I  S+ +S  + D+L   H+        +E  +++ +++
Sbjct: 415 EDTERIMKTWK--HPMSLDTPIGESEDSS--FGDFLEDSHESTPADNALREMLRDKIDIV 470

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            RS++    RER I   R    +    TLE     F+V+RER+RQIE++A KK+Q
Sbjct: 471 LRSLTY---REREIIRLRYGLGDGYSYTLEETGRIFKVTRERIRQIESKALKKLQ 522


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

 Score = 93.2 bits (230), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RGF+ +TY+ WW
Sbjct: 619 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGFKFSTYATWW 678

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +   +P+    +A K+ +
Sbjct: 679 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGAEPDPAT-LAIKMEM 733

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       +     + R ++
Sbjct: 734 PEDKIRKI-MKIA-KEPISMETPIGDDDDSHLGDFI---EDNNTLAPADAALHASMRGVV 788

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 789 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 843


>gi|313682108|ref|YP_004059846.1| RNA polymerase, sigma 70 subunit, rpod [Sulfuricurvum kujiense DSM
           16994]
 gi|313154968|gb|ADR33646.1| RNA polymerase, sigma 70 subunit, RpoD [Sulfuricurvum kujiense DSM
           16994]
          Length = 620

 Score = 93.2 bits (230), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 73/243 (30%), Positives = 121/243 (49%), Gaps = 33/243 (13%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ ++G++ +TY+ WWI+ 
Sbjct: 384 RMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYQKGYKFSTYATWWIRQ 443

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           A+   I      ++I     +     N + ++ HLQ   ++  +P+ V  IA+++ +S  
Sbjct: 444 AISRAIADQARTIRIPIHMIETINRIN-KIMRKHLQ---EHGKEPD-VETIAEEVGLSVE 498

Query: 172 EV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           +V          IS+   +  +E         DK S    D ++ D              
Sbjct: 499 KVKNVIKITKEPISLEAPIGNEEDGRFGDFIEDKMSLSPSDAILKD-------------- 544

Query: 222 KNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
            + +  +   +  LN RE+ + + R      E+  TLE +  E  V+RERVRQIE+ A K
Sbjct: 545 -DLKVQIESVLEQLNEREKAVIKMRFGIMDDESDRTLEEIGKELNVTRERVRQIESSAIK 603

Query: 279 KVQ 281
           K++
Sbjct: 604 KLK 606


>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 = 93.2 bits (230), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 72/243 (29%), Positives = 116/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 390 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 449

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 450 IRQAITRSIADQARTIRI--PVHMIETINKLNRVSRQMLQEMGREATPEELAERMEMPED 507

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +S+ E ISM   +  DE             S   D++    D +     +   
Sbjct: 508 KIRKVLKISK-EPISMETPIGDDE------------DSHLGDFI---EDEKVASPSDSAA 551

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
           R++        +S L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 552 RESLSEATREILSTLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 611

Query: 279 KVQ 281
           K++
Sbjct: 612 KLR 614


>gi|17231741|ref|NP_488289.1| group 2 sigma 70-type sigma factor F [Nostoc sp. PCC 7120]
 gi|8489803|gb|AAF75759.1|AF262218_1 group 2 sigma 70-type sigma factor F [Nostoc sp. PCC 7120]
 gi|17133384|dbj|BAB75948.1| group 2 sigma 70-type sigma factor F [Nostoc sp. PCC 7120]
          Length = 390

 Score = 93.2 bits (230), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 68/240 (28%), Positives = 120/240 (50%), Gaps = 21/240 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +++ S+LRLVV IA  Y   G+P  +++ EG +GL +A +KFDP++G++ +TY+ WW
Sbjct: 152 AKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAMGLNRATEKFDPDKGYKFSTYAYWW 211

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      +++     +K     L +LK   + +     +      +A+ L +
Sbjct: 212 IRQAITRAIANDARTIRLPIHIVEK-----LNKLKKAQRELKQKFSRNPSEAEMAEALEI 266

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  ++  +        SLN  +   +   ++  D L+ D D          E K   NM+
Sbjct: 267 SVPQLRQLQQLRRQALSLNHRVGKEE--DTELMD-LLEDEDNL------SPEAKMNENMM 317

Query: 229 TRSM-----SVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            + +      VL PRE+ +   R       P TLE + + F +SRERVRQI+++A +K++
Sbjct: 318 RQEIWEVLGDVLTPREKDVISLRYGLTTSEPCTLEEVGNMFNLSRERVRQIQSKAMRKLR 377


>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 = 93.2 bits (230), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 73/246 (29%), Positives = 118/246 (47%), Gaps = 34/246 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 458 AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 517

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +   T     PE+   + +++++
Sbjct: 518 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQILQETGIEATPEE---LGRRIDM 572

Query: 169 SESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            E +V          ISM   +  DE  N      D N     D+           L+E 
Sbjct: 573 PEEKVRKVLKIAKEPISMETPIGEDEDSNLGDFIEDINMESPVDF------ATSAGLMEA 626

Query: 219 EERKNRRNMLTRS-MSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEAR 275
                     TR  +S L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+
Sbjct: 627 ----------TREILSTLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 676

Query: 276 AFKKVQ 281
           A +K++
Sbjct: 677 ALRKLR 682


>gi|86608620|ref|YP_477382.1| RNA polymerase sigma factor [Synechococcus sp. JA-2-3B'a(2-13)]
 gi|86557162|gb|ABD02119.1| RNA polymerase sigma factor [Synechococcus sp. JA-2-3B'a(2-13)]
          Length = 319

 Score = 93.2 bits (230), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 67/228 (29%), Positives = 120/228 (52%), Gaps = 13/228 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  R+V  +LRLVV IA  YR  GLP  +++ EG IGL +AV+KFDP RG++ +TY+ W
Sbjct: 75  AAKKRMVECNLRLVVSIAKRYRNRGLPFLDLIQEGTIGLTRAVEKFDPTRGYKFSTYATW 134

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ ++   I     ++++     +K     ++R    L A   +  + E+V      L+
Sbjct: 135 WIRQSVNRGIQNKGRMIRLPAHMYEK--VSQVKRRYRELSAERGSRPQAEEVF---DSLD 189

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + ++    +   +A   SLN  +   D++ ++ Q ++  + +   + L +   R+  R +
Sbjct: 190 IGDNYRELITRHMAEMRSLN--VGVGDEDGTELQHFIPDEDNDPVEHLTQLARREEVRAL 247

Query: 228 LTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIE 273
           + +    L+ RER++  AR   +    +TL  +     +SRERVRQIE
Sbjct: 248 VGQ----LSERERQVIVARYGLDGSRGLTLREIGEHIGLSRERVRQIE 291


>gi|302335781|ref|YP_003800988.1| RNA polymerase, sigma 70 subunit, RpoD [Olsenella uli DSM 7084]
 gi|301319621|gb|ADK68108.1| RNA polymerase, sigma 70 subunit, RpoD [Olsenella uli DSM 7084]
          Length = 453

 Score = 93.2 bits (230), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 70/237 (29%), Positives = 117/237 (49%), Gaps = 12/237 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L A   L++++LRL V IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ 
Sbjct: 213 LEAKQALISANLRLTVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYAT 272

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I    +       L R++  L      +  PE++ A   ++
Sbjct: 273 WWIRQAITRAIADQARTIRI--PVHMVETINKLVRVQRQLLQDLGRDPTPEEIGA---EM 327

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +S   V  +        SL   I   ++  S   D++    D       E       R 
Sbjct: 328 GISADRVREIQKISQEPVSLETPIG--EEEDSSLGDFI---EDSSAVAPPEAASDSMLRE 382

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L + +  L  RER++ + R   E+  P TLE +  EF V+RER+RQIE++   K++
Sbjct: 383 QLEQVLDSLADRERKVIKFRFGLEDGHPRTLEEVGREFGVTRERIRQIESKTLAKLR 439


>gi|255327076|ref|ZP_05368152.1| RNA polymerase sigma factor SigA [Rothia mucilaginosa ATCC 25296]
 gi|255296293|gb|EET75634.1| RNA polymerase sigma factor SigA [Rothia mucilaginosa ATCC 25296]
          Length = 457

 Score = 93.2 bits (230), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 83/309 (26%), Positives = 140/309 (45%), Gaps = 60/309 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREHG---------DLSAAHR------------ 52
           Y+ +I K+ +L  Q+E  LA R     Y EH          DL  A R            
Sbjct: 164 YLKQIGKVSLLNAQQEVDLAMRIEAGLYAEHKLAENPDMDKDLKKALRWVIHDGKRAKNH 223

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 224 LLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYSKGFKFSTYATWWIRQA 283

Query: 113 MQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           +   +      ++I              Q+++  +L R     +   + ++ PE+V+ + 
Sbjct: 284 ITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELGKELDMTPEKVIEVQ 343

Query: 164 KKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           K       E IS++  L   GD     LI  S+          V   D     L++++  
Sbjct: 344 K----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ-- 388

Query: 222 KNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
                 L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K
Sbjct: 389 ------LHSVLDTLSEREAGVVAMRFGMTDGQPKTLDEIGKVYGVTRERIRQIESKTMSK 442

Query: 280 VQESIQKQV 288
           ++   + QV
Sbjct: 443 LRHPSRSQV 451


>gi|67925817|ref|ZP_00519113.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4 [Crocosphaera
           watsonii WH 8501]
 gi|67852341|gb|EAM47804.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4 [Crocosphaera
           watsonii WH 8501]
          Length = 386

 Score = 93.2 bits (230), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 61/245 (24%), Positives = 130/245 (53%), Gaps = 28/245 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +++ ++LRLVV ++  Y+G GL   ++VSEGN+GL++AV+KF+ ++G++ +TY+  W
Sbjct: 23  AKEKMIQANLRLVVAVSKKYQGKGLEFMDLVSEGNLGLIRAVEKFEYDKGYKFSTYAYHW 82

Query: 109 IKAAMQEYILRSWSLVKIGTTANQ-----KRLFFNLRRLKGHLQAITDNN----LKPEQV 159
           I+ A+   I      +++    N+     K++   +R+  G    + + +    + PE++
Sbjct: 83  IRQALVRAICDKGRTIRVPVHINEEISKLKKVQLEIRQKYGRSATVRELSERLEISPEKI 142

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
               + L    + ++S++ ++ GDE  + L++     +   Q +L  D+ G ++      
Sbjct: 143 ----RVLRSVNNPMLSLDQKVLGDEDNSTLLSFLADPNGDLQKFL--DNLGNKE------ 190

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
                  ++ + +  L P+E+R+     L+   +TL  +  +  +SRERVR I+  A  K
Sbjct: 191 -------LVEQCLCGLKPQEQRVLREYYLETPSLTLNEIGKKMNLSRERVRHIKNNALDK 243

Query: 280 VQESI 284
           +++ I
Sbjct: 244 LKQVI 248


>gi|296112900|ref|YP_003626838.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis RH4]
 gi|295920594|gb|ADG60945.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis RH4]
 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 = 93.2 bits (230), Expect = 4e-17,   Method: Compositional matrix adjust.
 Identities = 70/245 (28%), Positives = 116/245 (47%), Gaps = 32/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 387 AKKDMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 446

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+   L         PE+   + ++L++
Sbjct: 447 IRQAITRSIADQARTIRI--PVHMIETINKINRVSRQLLQEMGREPTPEE---LGERLDM 501

Query: 169 SESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            E++V          ISM   +  DE             S   D++    D      IE 
Sbjct: 502 DEAKVRKVLKIAKEPISMETPIGDDE------------DSHLGDFI---EDNTISSPIEN 546

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARA 276
              +  R      +  L  RE ++ + R   + P   TLE +  +F+V+RER+RQIEA+A
Sbjct: 547 ATAEGLREATREVLDNLTEREAKVLKMRFGIDMPSDHTLEEVGKQFDVTRERIRQIEAKA 606

Query: 277 FKKVQ 281
            +K++
Sbjct: 607 LRKLR 611


>gi|222475070|ref|YP_002563485.1| RNA polymerase sigma factor (rpoD) [Anaplasma marginale str.
           Florida]
 gi|255003048|ref|ZP_05278012.1| RNA polymerase sigma factor (rpoD) [Anaplasma marginale str. Puerto
           Rico]
 gi|255004170|ref|ZP_05278971.1| RNA polymerase sigma factor (rpoD) [Anaplasma marginale str.
           Virginia]
 gi|222419206|gb|ACM49229.1| RNA polymerase sigma factor (rpoD) [Anaplasma marginale str.
           Florida]
          Length = 646

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 71/239 (29%), Positives = 122/239 (51%), Gaps = 19/239 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLVV IA  Y   GL   ++V EGNIGLM+AV KFD +RG++ +TY+ WW
Sbjct: 409 AKQEMIKANLRLVVSIAKKYSNRGLQFLDLVQEGNIGLMKAVDKFDYKRGYKFSTYATWW 468

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           ++ A+   I      ++I     +     N R L+  L  I     +   +  ++ +L +
Sbjct: 469 VRQAITRAIADQARTIRIPVHMIETVNKIN-RTLRQMLHEIG----REPTLEELSTRLGM 523

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER---KNRR 225
           +  ++  +   +    SL + I   D +SS + D +      +++  ++ E      + R
Sbjct: 524 NVEKIRKVMKIVKDPVSLESPIG--DDDSSTFGDCI------EDKRAVKPENAAVLADLR 575

Query: 226 NMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            + T+ +S L P+E RI   R          TLE +   F V+RER+RQIEA+A +K++
Sbjct: 576 EITTKVLSTLTPKEERILRMRFGIGKGGKDHTLEEVGKLFNVTRERIRQIEAKALRKLR 634


>gi|87124019|ref|ZP_01079869.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9917]
 gi|86168588|gb|EAQ69845.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9917]
          Length = 308

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 80/263 (30%), Positives = 135/263 (51%), Gaps = 20/263 (7%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           KR  + G+  A ++++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG
Sbjct: 57  KRVIKRGE-KAKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRG 115

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
            R +TY+ WWI+  +   +      ++I    N+K     LR  K  L         PEQ
Sbjct: 116 HRFSTYAYWWIRQGLNRALSTQSRTIRIPVNVNEK--LTKLRAAKARLMQQHGQPANPEQ 173

Query: 159 VVAIAKKLNVSESEVISMNCRL-AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
            +A A K+ +SE E + + C L +   SL  ++ S   + S+  D L  D    E   +E
Sbjct: 174 -LAEAMKIPLSEVEDL-LACELRSVTVSLQGIVKSK-ADPSELVDVLPSD----ELPPME 226

Query: 218 KEERKNRR----NMLTRSMSVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVR 270
           + E   R      +L ++   L P+ER +   R   +      TL  ++     SRE  R
Sbjct: 227 RAEIAERTASAWTLLEKAN--LTPKERTVVMLRFGLDGSHEWRTLAEVARHMSCSREYCR 284

Query: 271 QIEARAFKKVQESIQKQVELSSS 293
           Q+  RA +K++++  +Q  +SS+
Sbjct: 285 QVVQRALRKLRKTGIQQGLVSSA 307


>gi|223936990|ref|ZP_03628898.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [bacterium
           Ellin514]
 gi|223894271|gb|EEF60724.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [bacterium
           Ellin514]
          Length = 614

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 70/243 (28%), Positives = 118/243 (48%), Gaps = 30/243 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ I   Y   GL   +++ EGN+GLM+ V+KF+  RG++ +TY+ WW
Sbjct: 372 AKTEMAEANLRLVISIGKKYTNRGLAFLDIIQEGNMGLMKGVEKFEYRRGYKFSTYATWW 431

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +   +   L R +  L         PE+   IA ++ +
Sbjct: 432 IRQAITRAIADQARTIRI--PVHMIEIIGKLMRAQKQLLQEFGREATPEE---IADEMQI 486

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S   V S+        S+ A +  SD   + + D+            IE +  +N  +M 
Sbjct: 487 SVERVKSILKMAQQPISMQASVGDSD--DATFGDF------------IEDKSAENPSDMT 532

Query: 229 TRS---------MSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAF 277
           + S         ++ L  RERRI E R   +     TLE +  +++V+RER+RQIEA+A 
Sbjct: 533 SYSLLKDKLNDVLATLTERERRIVELRFGLVDGYARTLEEVGKQYKVTRERIRQIEAKAL 592

Query: 278 KKV 280
           +K+
Sbjct: 593 RKL 595


>gi|145594022|ref|YP_001158319.1| RNA polymerase sigma factor [Salinispora tropica CNB-440]
 gi|145303359|gb|ABP53941.1| RNA polymerase sigma factor RpoD [Salinispora tropica CNB-440]
          Length = 542

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 78/302 (25%), Positives = 144/302 (47%), Gaps = 42/302 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR------------EHGDLS------------------ 48
           Y+ +I K+P+L  ++E  LAKR              E GD                    
Sbjct: 245 YLKQIGKVPLLNAEQEVELAKRIEAGLYATEQLRAAEEGDEKFNRDMQRDMMWISRDGER 304

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WW
Sbjct: 305 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 364

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   +      ++I    +   +   L R++  L         PE+   +AK++++
Sbjct: 365 IRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGREPTPEE---LAKEMDI 419

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +  +V+ +        SL+  I   D+  SQ  D++    D +  V ++       ++ L
Sbjct: 420 TPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEAVVAVDAVSFSLLQDQL 474

Query: 229 TRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   + 
Sbjct: 475 QQVLQTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRS 534

Query: 287 QV 288
           QV
Sbjct: 535 QV 536


>gi|75907421|ref|YP_321717.1| sigma 28 (flagella/sporulation) [Anabaena variabilis ATCC 29413]
 gi|75701146|gb|ABA20822.1| Sigma 28 (Flagella/Sporulation) [Anabaena variabilis ATCC 29413]
          Length = 378

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 68/240 (28%), Positives = 120/240 (50%), Gaps = 21/240 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +++ S+LRLVV IA  Y   G+P  +++ EG +GL +A +KFDP++G++ +TY+ WW
Sbjct: 140 AKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAMGLNRATEKFDPDKGYKFSTYAYWW 199

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      +++     +K     L +LK   + +     +      +A+ L +
Sbjct: 200 IRQAITRAIANDARTIRLPIHIVEK-----LNKLKKAQRELKQKFSRNPSEAEMAEALEI 254

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  ++  +        SLN  +   +   ++  D L+ D D          E K   NM+
Sbjct: 255 SVPQLRQLQQLRRQALSLNHRVGKEE--DTELMD-LLEDEDNL------SPEAKMNENMM 305

Query: 229 TRSM-----SVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            + +      VL PRE+ +   R       P TLE + + F +SRERVRQI+++A +K++
Sbjct: 306 RQEIWEVLGDVLTPREKDVISLRYGLTTSEPCTLEEVGNMFNLSRERVRQIQSKAMRKLR 365


>gi|56416704|ref|YP_153778.1| RNA polymerase sigma factor [Anaplasma marginale str. St. Maries]
 gi|56387936|gb|AAV86523.1| RNA polymerase sigma factor [Anaplasma marginale str. St. Maries]
          Length = 632

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 71/239 (29%), Positives = 122/239 (51%), Gaps = 19/239 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLVV IA  Y   GL   ++V EGNIGLM+AV KFD +RG++ +TY+ WW
Sbjct: 395 AKQEMIKANLRLVVSIAKKYSNRGLQFLDLVQEGNIGLMKAVDKFDYKRGYKFSTYATWW 454

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           ++ A+   I      ++I     +     N R L+  L  I     +   +  ++ +L +
Sbjct: 455 VRQAITRAIADQARTIRIPVHMIETVNKIN-RTLRQMLHEIG----REPTLEELSTRLGM 509

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER---KNRR 225
           +  ++  +   +    SL + I   D +SS + D +      +++  ++ E      + R
Sbjct: 510 NVEKIRKVMKIVKDPVSLESPI--GDDDSSTFGDCI------EDKRAVKPENAAVLADLR 561

Query: 226 NMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            + T+ +S L P+E RI   R          TLE +   F V+RER+RQIEA+A +K++
Sbjct: 562 EITTKVLSTLTPKEERILRMRFGIGKGGKDHTLEEVGKLFNVTRERIRQIEAKALRKLR 620


>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|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 = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 120/234 (51%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 391 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 450

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   L         PE+   +A+++ +
Sbjct: 451 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQLLQEMGREATPEE---LAERMGM 505

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ +   
Sbjct: 506 PEDKIRKV-LKIAK-EPISMETPIGDDDDSHLGDFI---EDSTLELPLDSATAQSLKVAT 560

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 561 HEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 614


>gi|300727091|ref|ZP_07060510.1| RNA polymerase sigma-70 factor [Prevotella bryantii B14]
 gi|299775635|gb|EFI72226.1| RNA polymerase sigma-70 factor [Prevotella bryantii B14]
          Length = 290

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 82/291 (28%), Positives = 136/291 (46%), Gaps = 50/291 (17%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYG 72
            L +Y+ EI + PM+   EE  LA++ R+ G     A  +LV ++LR VV +A  Y+  G
Sbjct: 17  ALDKYLAEISREPMVSIDEETELAQQIRKGGRAGDRAKEKLVKANLRFVVSVAKQYQHQG 76

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V        
Sbjct: 77  LTLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSIMQAIAEQSRIV-------- 128

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNAL- 189
            RL  N                   QV A++K   V+   V   N R + DE  +L  + 
Sbjct: 129 -RLPLN-------------------QVGAVSKINQVTAKFVQEHNRRPSADELATLTGID 168

Query: 190 -------INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM---------S 233
                  +N+     S    +   D +    +L   ++ +  R +   SM         S
Sbjct: 169 ADKIQKSLNADSHQMSIDAPFSDDDDNSMSDMLSSGDDSRTDRQVDYESMQNDMEGVLKS 228

Query: 234 VLNPRERRIFEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           VL  RE +I +       P   LE +  E  ++RERVRQI  ++  K+++S
Sbjct: 229 VLKDRELKIVKDCFGIGGPEKGLEEIGEEMGLTRERVRQIREKSIMKIRQS 279


>gi|227495998|ref|ZP_03926309.1| RNA polymerase sigma factor [Actinomyces urogenitalis DSM 15434]
 gi|226834486|gb|EEH66869.1| RNA polymerase sigma factor [Actinomyces urogenitalis DSM 15434]
          Length = 541

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 82/310 (26%), Positives = 141/310 (45%), Gaps = 61/310 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH------GDLSAAHR--------------- 52
           Y+ +I K+ +L   EE  LAKR     Y E+       +L A +R               
Sbjct: 247 YLKQIGKVALLNAAEEVELAKRIEAGMYAEYLLGTEGNELDAKYRRELHWISNDGQRAKN 306

Query: 53  -LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ 
Sbjct: 307 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQ 366

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ +
Sbjct: 367 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAVELDMTPEKVIEV 426

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 427 QKY----GREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 472

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 473 -------LHAVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 525

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 526 KLRHPSRSQV 535


>gi|309702135|emb|CBJ01450.1| putative RNA polymerase sigma factor [Escherichia coli ETEC H10407]
          Length = 697

 Score = 93.2 bits (230), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 70/238 (29%), Positives = 126/238 (52%), Gaps = 26/238 (10%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            + ++LRLVV IA  + G GL I +++ EGN+GL++AV+KFD  RGF+ +TY+ WWI+  
Sbjct: 448 FIHANLRLVVAIAKKHCGRGLDIEDLIQEGNLGLIKAVEKFDFRRGFKFSTYASWWIRQK 507

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKG------HLQAITDNNLKPEQVVAIAKK- 165
           +   I     L+++         + + RR +       H Q IT    + +++  + ++ 
Sbjct: 508 ISRAIADQAQLIRLPV-----HFYEHFRRWRSSRDQLLHRQGITPTLRRLQEMTDLPERQ 562

Query: 166 -LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            L +++ E  ++   L GD   +A     D+ ++   D L+   D     +   E R++ 
Sbjct: 563 LLQMAKYEEQTV---LIGDFHEDA----QDREAALSGDALLTRRDFTSAPVQSLELREH- 614

Query: 225 RNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
              ++  ++ L PRE +I + R         TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 615 ---ISSVLNTLLPRETQIIKMRFGIGMTQDFTLEEVGKQFDVTRERIRQIEAKALRKL 669


>gi|291287657|ref|YP_003504473.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Denitrovibrio
           acetiphilus DSM 12809]
 gi|290884817|gb|ADD68517.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Denitrovibrio
           acetiphilus DSM 12809]
          Length = 626

 Score = 92.8 bits (229), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 74/246 (30%), Positives = 121/246 (49%), Gaps = 34/246 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV+KF+ +RG++ +TY+ WW
Sbjct: 389 AKSKLIEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVEKFEYKRGYKFSTYATWW 448

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV-------VA 161
           I+ A+   I      ++I    +       + ++   LQ        PE++       V 
Sbjct: 449 IRQAITRAIADQARTIRI--PVHMIETINKMMKITRQLQQDMGREPTPEEISSKMDIPVE 506

Query: 162 IAKKLNVSESEVISMNCRLAGDE--SLNALI-NSSDKNSSQWQDWL-VYDHDGQEQVLIE 217
             KK+     E +S+   +  DE  SL   I + S KN S+   +L + +H  Q      
Sbjct: 507 KIKKVMKIAKEPVSLETPIGEDEDSSLGDFIEDKSAKNPSEEVTYLKLKEHTKQ------ 560

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEAR 275
                         +  L+ RE  + + R   E  +  TLE +  +F V+RER+RQIEA+
Sbjct: 561 -------------ILETLSHREASVLKLRFGIECDSDHTLEEVGKQFNVTRERIRQIEAK 607

Query: 276 AFKKVQ 281
           A +K++
Sbjct: 608 ALRKLR 613


>gi|119493081|ref|ZP_01624006.1| Sigma 28 (Flagella/Sporulation) [Lyngbya sp. PCC 8106]
 gi|119452826|gb|EAW34001.1| Sigma 28 (Flagella/Sporulation) [Lyngbya sp. PCC 8106]
          Length = 331

 Score = 92.8 bits (229), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 71/238 (29%), Positives = 126/238 (52%), Gaps = 19/238 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++++S+LRLVV IA  Y   G+P  +++ EG +GL +A +KFDP++G++ +TY+ WW
Sbjct: 93  AKQKMISSNLRLVVSIAKRYLNRGVPFLDLIQEGALGLNRATEKFDPDKGYKFSTYAYWW 152

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   I      V++     ++     L +L+G  Q +  +  +      +A+ L++
Sbjct: 153 IRQGITRTIANQGRTVRLPVHVVEQ-----LNKLQGIHQDLRRSLRRKPTEDELAEALSI 207

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN----R 224
           S  ++  +        SLN  + S +  +S+  D L+ D++      +  E + N    R
Sbjct: 208 SPQQLRLLEQVRRKSLSLNHRVGSEE--NSELMD-LLEDYES-----LSPESQINELMMR 259

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + +L    SVLN RE+ I   R       P TL+ +S    +SRERVRQI+A+A +K+
Sbjct: 260 QELLEVLRSVLNEREQDILSLRYGLTTGVPYTLDEVSGMCSLSRERVRQIQAKAMRKL 317


>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 = 92.8 bits (229), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 120/234 (51%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 391 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 450

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   L         PE+   +A+++ +
Sbjct: 451 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQLLQEMGREATPEE---LAERMGM 505

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ +   
Sbjct: 506 PEDKIRKV-LKIAK-EPISMETPIGDDDDSHLGDFI---EDSTLELPLDSATAQSLKVAT 560

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 561 HEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 614


>gi|325295045|ref|YP_004281559.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Desulfurobacterium thermolithotrophum DSM 11699]
 gi|325065493|gb|ADY73500.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Desulfurobacterium thermolithotrophum DSM 11699]
          Length = 563

 Score = 92.8 bits (229), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 83/265 (31%), Positives = 132/265 (49%), Gaps = 42/265 (15%)

Query: 35  YVLAKR--YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           Y LA+R  + +     A   LV S+LRLVV IA  Y   GL   +++ EGNIGLM+AV K
Sbjct: 309 YKLAERIYFYKKDSQEAKQILVRSNLRLVVSIAKKYINRGLHFLDLIQEGNIGLMKAVDK 368

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQA 148
           F+  RG++ +TY+ WWI+ A+   I      ++I      T N        + +K   Q 
Sbjct: 369 FEYRRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIETIN--------KVIKASRQM 420

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA----------GDESLNALINSSDKNSS 198
             +   +P +   IA++L +  S+V S+  +LA          GD+  + L N  + + S
Sbjct: 421 FLEKGREP-RPEEIAERLRMPASKVRSI-IQLAQEPVSLETPIGDDEDSTLGNFIEDSKS 478

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLE 256
              +  V   D QE+V              ++ +S L+ RE  + + R  L   P  TLE
Sbjct: 479 PIPEHEVIKKDLQEKV--------------SQLLSTLSEREALVLKLRFGLDGYPEHTLE 524

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  E +V+RER+RQIE++A +K++
Sbjct: 525 QVGRELKVTRERIRQIESKALRKLK 549


>gi|269958878|ref|YP_003328667.1| RNA polymerase sigma factor [Anaplasma centrale str. Israel]
 gi|269848709|gb|ACZ49353.1| RNA polymerase sigma factor [Anaplasma centrale str. Israel]
          Length = 649

 Score = 92.8 bits (229), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 71/239 (29%), Positives = 122/239 (51%), Gaps = 19/239 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLVV IA  Y   GL   ++V EGNIGLM+AV KFD +RG++ +TY+ WW
Sbjct: 412 AKQEMIKANLRLVVSIAKKYSNRGLQFLDLVQEGNIGLMKAVDKFDYKRGYKFSTYATWW 471

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           ++ A+   I      ++I     +     N R L+  L  I     +   +  ++ +L +
Sbjct: 472 VRQAITRAIADQARTIRIPVHMIETVNKIN-RTLRQMLHEIG----REPTLEELSARLGM 526

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER---KNRR 225
           +  ++  +   +    SL + I   D +SS + D +      +++  ++ E      + R
Sbjct: 527 NVEKIRKVMKIVKDPVSLESPIG--DDDSSTFGDCI------EDKRAVKPENAAVLADLR 578

Query: 226 NMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            + T+ +S L P+E RI   R          TLE +   F V+RER+RQIEA+A +K++
Sbjct: 579 EITTKVLSTLTPKEERILRMRFGIGKGGKDHTLEEVGKLFNVTRERIRQIEAKALRKLR 637


>gi|315656627|ref|ZP_07909514.1| DNA-directed RNA polymerase sigma subunit RpoD [Mobiluncus curtisii
           subsp. holmesii ATCC 35242]
 gi|315492582|gb|EFU82186.1| DNA-directed RNA polymerase sigma subunit RpoD [Mobiluncus curtisii
           subsp. holmesii ATCC 35242]
          Length = 564

 Score = 92.8 bits (229), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 81/310 (26%), Positives = 144/310 (46%), Gaps = 63/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH-----------------------GDLSAA 50
           Y+ +I K+ +L  ++E  L+KR     Y EH                       G ++  
Sbjct: 270 YLKQIGKVALLNAEQEVDLSKRIEAGLYAEHLLKTKQETMTPKQIRELHYVVQDGQMAKN 329

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           H L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+
Sbjct: 330 H-LLEANLRLVVALAKKYTGRGMLFLDLIQEGNLGLIRAVEKFDYSKGYKFSTYATWWIR 388

Query: 111 AAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
            A+   +      ++I              Q+++  +L R     +   +  + PE+VV 
Sbjct: 389 QAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPDELAQELEMTPEKVVE 448

Query: 162 IAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           + K       E IS++  L   GD     LI  S+          V   D    ++++++
Sbjct: 449 VQKYGR----EPISLHTPLGEDGDSEFGDLIEDSE---------AVVPADAVSFMMLQEQ 495

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAF 277
                   L R +  L+ RE  +   R  L++  P TL+ +   + V+RER+RQIEA+  
Sbjct: 496 --------LQRVLDTLSERESGVIAMRFGLKDGQPKTLDEIGRRYGVTRERIRQIEAKTM 547

Query: 278 KKVQESIQKQ 287
            K++   + Q
Sbjct: 548 SKLRHPARSQ 557


>gi|315655467|ref|ZP_07908366.1| DNA-directed RNA polymerase sigma subunit RpoD [Mobiluncus curtisii
           ATCC 51333]
 gi|315490122|gb|EFU79748.1| DNA-directed RNA polymerase sigma subunit RpoD [Mobiluncus curtisii
           ATCC 51333]
          Length = 553

 Score = 92.8 bits (229), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 81/310 (26%), Positives = 144/310 (46%), Gaps = 63/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH-----------------------GDLSAA 50
           Y+ +I K+ +L  ++E  L+KR     Y EH                       G ++  
Sbjct: 259 YLKQIGKVALLNAEQEVDLSKRIEAGLYAEHLLKTKQETMTPKQIRELHYVVQDGQMAKN 318

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           H L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+
Sbjct: 319 H-LLEANLRLVVALAKKYTGRGMLFLDLIQEGNLGLIRAVEKFDYSKGYKFSTYATWWIR 377

Query: 111 AAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
            A+   +      ++I              Q+++  +L R     +   +  + PE+VV 
Sbjct: 378 QAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPDELAQELEMTPEKVVE 437

Query: 162 IAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           + K       E IS++  L   GD     LI  S+          V   D    ++++++
Sbjct: 438 VQKYGR----EPISLHTPLGEDGDSEFGDLIEDSE---------AVVPADAVSFMMLQEQ 484

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAF 277
                   L R +  L+ RE  +   R  L++  P TL+ +   + V+RER+RQIEA+  
Sbjct: 485 --------LQRVLDTLSERESGVIAMRFGLKDGQPKTLDEIGRRYGVTRERIRQIEAKTM 536

Query: 278 KKVQESIQKQ 287
            K++   + Q
Sbjct: 537 SKLRHPARSQ 546


>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 = 92.8 bits (229), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 120/234 (51%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 407 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 466

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   L         PE+   +A+++ +
Sbjct: 467 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQLLQEMGREATPEE---LAERMGM 521

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ +   
Sbjct: 522 PEDKIRKV-LKIAK-EPISMETPIGDDDDSHLGDFI---EDSTLELPLDSATAQSLKVAT 576

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 577 HEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 630


>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 = 92.8 bits (229), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 67/245 (27%), Positives = 116/245 (47%), Gaps = 32/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 415 AKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 474

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +  ++P+    +A K+ +
Sbjct: 475 IRQAITRSIADQARTIRI--PVHMIETINKMNRIS--RQILQETGIEPDPAT-LAIKMEM 529

Query: 169 SESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            E ++          ISM   +  DE  +      D ++    D  +Y            
Sbjct: 530 PEDKIRKIMKIAKEPISMETPIGDDEDSHLGDFIEDASTLSPDDSAIY------------ 577

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARA 276
               N R+     +  L  RE ++   R   E     TLE +  +F+V+RER+RQIEA+A
Sbjct: 578 ---ANLRDATREVLDSLTSREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKA 634

Query: 277 FKKVQ 281
            +K++
Sbjct: 635 LRKLR 639


>gi|148827724|ref|YP_001292477.1| DNA primase [Haemophilus influenzae PittGG]
 gi|148718966|gb|ABR00094.1| DNA primase [Haemophilus influenzae PittGG]
          Length = 629

 Score = 92.8 bits (229), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 120/234 (51%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 391 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 450

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   L         PE+   +A+++ +
Sbjct: 451 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQLLQEMGREATPEE---LAERMGM 505

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ +   
Sbjct: 506 PEDKIRKV-LKIAK-EPISMETPIGDDDDSHLGDFI---EDSTLELPLDSATAQSLKVAT 560

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 561 HEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 614


>gi|189219555|ref|YP_001940196.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Methylacidiphilum infernorum V4]
 gi|189186413|gb|ACD83598.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Methylacidiphilum infernorum V4]
          Length = 623

 Score = 92.8 bits (229), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 72/240 (30%), Positives = 118/240 (49%), Gaps = 20/240 (8%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           + A   +V ++LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+  RG++ +TY+ 
Sbjct: 379 IKAKSEMVEANLRLVISIAKKYSNRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYAT 438

Query: 107 WWIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           WWI+ A+   I      ++I      T N+      L R++  L         PE+   I
Sbjct: 439 WWIRQAITRSIADQARTIRIPVHMIETINK------LMRVQKQLIQELGREPTPEE---I 489

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A +  +S   + ++        SL A +  S+  +  + D++    D   +   E     
Sbjct: 490 ADETQMSVDRIRTIIKMAQHPISLQAQVGESEDTT--FGDFI---EDKAAENPSEMTGYS 544

Query: 223 NRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             R  +   +  L  RER + E R   L   P TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 545 LLREKIKDVLGTLTERERTVIEQRFGLLDGYPRTLEEVGKQFRVTRERIRQIEAKALRKM 604


>gi|89901840|ref|YP_524311.1| sigma 28 [Rhodoferax ferrireducens T118]
 gi|89346577|gb|ABD70780.1| sigma 28 [Rhodoferax ferrireducens T118]
          Length = 726

 Score = 92.8 bits (229), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 77/297 (25%), Positives = 147/297 (49%), Gaps = 37/297 (12%)

Query: 14  IGLSR-YIHEIRKIPMLEKQEEYV----LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +GLSR ++ E+     LE QE  +      + YR+  D     ++V ++L+LV+ IA  Y
Sbjct: 336 LGLSRGFLLELADFEQLEVQESAIEFSQAMQAYRQARD-----QMVIANLKLVLFIAKKY 390

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
              G P+ +++ EGNIGL++AV ++D  RGF+L+TY+ WWI+  +  Y+      +++  
Sbjct: 391 LYSGQPLDDLLQEGNIGLIKAVDRYDWRRGFKLSTYATWWIRQQVGRYVADKSKTIRLPV 450

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-----GD 183
                 ++   +++     AI     +   +  IAKK+ +  S+V  +   +       D
Sbjct: 451 -----HVYVKTQQIAHAAHAIELATGRMPTIEEIAKKMEMPASKVAPLALAIPEPLPIHD 505

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
             +++LI    +++   +D +    D Q   LI           + R ++ L P++ ++ 
Sbjct: 506 VDVDSLIAIDAQDNYVARDPMDIVSDSQ---LI---------GSIDRFLATLKPKDEQVL 553

Query: 244 EARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ---VELSSSPP 295
             R        +TLE + +  EV+RER+RQIEA+A   ++   + +    +L+ +PP
Sbjct: 554 RLRFGIGAHEAMTLEEIGTRLEVTRERIRQIEAKAICHLKHPARLERLLRDLNGTPP 610


>gi|320105405|ref|YP_004180995.1| RpoD subfamily RNA polymerase sigma-70 factor [Terriglobus
           saanensis SP1PR4]
 gi|319923926|gb|ADV81001.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Terriglobus
           saanensis SP1PR4]
          Length = 567

 Score = 92.8 bits (229), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 76/250 (30%), Positives = 125/250 (50%), Gaps = 29/250 (11%)

Query: 44  HGDLSA--AHR-LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
            GD+ A  A R L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 317 QGDMDAEKAKRELIEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 376

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHL--QAITDNNL 154
            +TY+ WWI+ A+   I      ++I      T N  +L    R+L   L  +A ++   
Sbjct: 377 FSTYATWWIRQAITRAIADQARTIRIPVHMIETIN--KLIRTSRQLVQELGREASSEEIA 434

Query: 155 KPEQV-VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
           +   + VA  +K+     E IS+   +  +E  +      D+ +    D ++        
Sbjct: 435 RRMDIPVAKVRKVLKIAQEPISLETPIGEEEDSHLGDFIEDRMAVSPSDAVIS------- 487

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQ 271
                    N +   ++ +  L PRE R+ + R   E+    TLE +   F+V+RER+RQ
Sbjct: 488 --------VNLKEYTSQVLRTLTPREERVIKMRFGLEDGSEHTLEEVGQSFQVTRERIRQ 539

Query: 272 IEARAFKKVQ 281
           IEA+A +K++
Sbjct: 540 IEAKALRKLR 549


>gi|322433717|ref|YP_004215929.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidobacterium
           sp. MP5ACTX9]
 gi|321161444|gb|ADW67149.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidobacterium
           sp. MP5ACTX9]
          Length = 566

 Score = 92.8 bits (229), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 76/250 (30%), Positives = 125/250 (50%), Gaps = 29/250 (11%)

Query: 44  HGDLSA--AHR-LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
            GD+ A  A R L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 316 QGDMDAEKAKRELIEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 375

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHL--QAITDNNL 154
            +TY+ WWI+ A+   I      ++I      T N  +L    R+L   L  +A ++   
Sbjct: 376 FSTYATWWIRQAITRAIADQARTIRIPVHMIETIN--KLIRTSRQLVQELGREASSEEIA 433

Query: 155 KPEQV-VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
           +   + VA  +K+     E IS+   +  +E  +      D+ +    D ++        
Sbjct: 434 RRMDIPVAKVRKVLKIAQEPISLETPIGEEEDSHLGDFIEDRMAVSPADAVIS------- 486

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQ 271
                    N +   ++ +  L PRE R+ + R   E+    TLE +   F+V+RER+RQ
Sbjct: 487 --------VNLKEYTSQVLRTLTPREERVIKMRFGLEDGSEHTLEEVGQSFQVTRERIRQ 538

Query: 272 IEARAFKKVQ 281
           IEA+A +K++
Sbjct: 539 IEAKALRKLR 548


>gi|168009782|ref|XP_001757584.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162691278|gb|EDQ77641.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 583

 Score = 92.8 bits (229), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 86/300 (28%), Positives = 145/300 (48%), Gaps = 52/300 (17%)

Query: 13  EIGLSRYIHEIRKI--------------PMLEKQEEYV------LAKRYREHGDLSAAHR 52
           E+ LSR I +I K+              P L +  + V      L  R +E    SA  +
Sbjct: 289 EVALSRKIQDILKLEKIRAELQRDIGREPTLSEWSQAVSLDQTSLELRVKEG--RSAKDK 346

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV S+LRLVV I   Y+G G+ + +++ EG++GL++  +KFDPE G++ +TY+ WWI+ A
Sbjct: 347 LVNSNLRLVVSIVKNYQGRGMTLPDLIQEGSLGLIRGAEKFDPEMGYKFSTYATWWIRQA 406

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA-----IAKKLN 167
           +   I     ++++     +  +   + + K  +        + E+V A     + K L 
Sbjct: 407 VTRAIADQSRIIRLPVHIYE--VISRINKAKMTISQELGRQPRDEEVAAMVGMSVEKLLF 464

Query: 168 VSES--EVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + +S     SM+  +   G++SL  ++  +DK     +D      D   QVL +  E   
Sbjct: 465 IVKSARPPTSMDRPIGKDGEQSLGEMV--ADKGVGSPED------DIMTQVLKQDIEDVL 516

Query: 224 RRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R          LNP ER +   R        +TL++L   F+V+RER+RQIEA+A +K++
Sbjct: 517 RS---------LNPMEREVLRLRFGLSGAQSMTLKDLGIIFKVTRERIRQIEAKALRKLR 567


>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|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 = 92.8 bits (229), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 120/234 (51%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 391 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 450

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   L         PE+   +A+++ +
Sbjct: 451 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQLLQEMGREATPEE---LAERMGM 505

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ +   
Sbjct: 506 PEDKIRKV-LKIAK-EPISMETPIGDDDDSHLGDFI---EDSTLELPLDSATAQSLKVAT 560

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 561 HEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 614


>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 = 92.8 bits (229), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 120/234 (51%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 391 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 450

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   L         PE+   +A+++ +
Sbjct: 451 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQLLQEMGREATPEE---LAERMGM 505

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ +   
Sbjct: 506 PEDKIRKV-LKIAK-EPISMETPIGDDDDSHLGDFI---EDSTLELPLDSATAQSLKVAT 560

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 561 HEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 614


>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 = 92.8 bits (229), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 120/234 (51%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 391 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 450

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   L         PE+   +A+++ +
Sbjct: 451 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQLLQEMGREATPEE---LAERMGM 505

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ +   
Sbjct: 506 PEDKIRKV-LKIAK-EPISMETPIGDDDDSHLGDFI---EDSTLELPLDSATAQSLKVAT 560

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 561 HEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 614


>gi|149178485|ref|ZP_01857074.1| transcription initiation factor sigma 70 [Planctomyces maris DSM
           8797]
 gi|148842698|gb|EDL57072.1| transcription initiation factor sigma 70 [Planctomyces maris DSM
           8797]
          Length = 588

 Score = 92.8 bits (229), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 71/237 (29%), Positives = 118/237 (49%), Gaps = 16/237 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L   +LRLVV IA  YR  GL   +++ EGN GLM+ V+K++  RG++ +TY+ WW
Sbjct: 320 AKQQLSGGNLRLVVSIAKKYRNRGLSFLDLIQEGNAGLMRGVEKYEYRRGYKFSTYATWW 379

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK--L 166
           I+ A+   +      ++I        +F ++  LK   + I     +   +  +A    L
Sbjct: 380 IRQAITRAVADHARTIRIPV-----HMFQSISTLKARSEQIRQETGREPTMEELADSVGL 434

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            V E+E I    +     SL+  +  S+ +S  + D+L    DG E    +   R+  ++
Sbjct: 435 GVEETERIMKTWKHPI--SLDTPVGESEDSS--FGDFL---EDGHESSPADAAMREMLKD 487

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +   +  L  RER I   R    +    TLE     F+V+RER+RQIE++A +K+Q
Sbjct: 488 KIEHVLKSLTYREREIIRLRYGLGDGYSYTLEETGRIFKVTRERIRQIESKALRKLQ 544


>gi|301169248|emb|CBW28845.1| RNA polymerase, sigma 70 (sigma D) factor [Haemophilus influenzae
           10810]
          Length = 629

 Score = 92.8 bits (229), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 120/234 (51%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 391 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 450

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   L         PE+   +A+++ +
Sbjct: 451 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQLLQEMGREATPEE---LAERMGM 505

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ +   
Sbjct: 506 PEDKIRKV-LKIAK-EPISMETPIGDDDDSHLGDFI---EDSTLELPLDSATAQSLKVAT 560

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 561 HEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 614


>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 = 92.8 bits (229), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 120/234 (51%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 385 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 444

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   L         PE+   +A+++ +
Sbjct: 445 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQLLQEMGREATPEE---LAERMGM 499

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ +   
Sbjct: 500 PEDKIRKV-LKIAK-EPISMETPIGDDDDSHLGDFI---EDSTLELPLDSATAQSLKVAT 554

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 555 HEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 608


>gi|197121174|ref|YP_002133125.1| RNA polymerase, sigma 70 subunit, RpoD family [Anaeromyxobacter sp.
           K]
 gi|196171023|gb|ACG71996.1| RNA polymerase, sigma 70 subunit, RpoD family [Anaeromyxobacter sp.
           K]
          Length = 805

 Score = 92.8 bits (229), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 75/260 (28%), Positives = 122/260 (46%), Gaps = 33/260 (12%)

Query: 37  LAKRYREHGDLS-----AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           L + YR  GD       A   LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV 
Sbjct: 550 LRRTYRMIGDGERKAERAKTELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVD 609

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KF+ +RG++ +TY+ WWI+ A+   I      ++I    +       L R   +L     
Sbjct: 610 KFEYKRGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMIETINKLIRTSRYLVQELG 667

Query: 152 NNLKPEQVV--------AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
               PE++          + K L ++  E IS+   +  +E  +      DK+     D 
Sbjct: 668 REPTPEEIAEKMELPLDKVRKVLKIA-KEPISLETPIGEEEDSHLGDFIEDKSLVSPSDA 726

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSE 261
           ++                 N      + ++ L PRE ++   R    +++  TLE +  +
Sbjct: 727 VIN---------------MNLAEQTRKVLATLTPREEKVLRMRFGIGEKSDHTLEEVGQD 771

Query: 262 FEVSRERVRQIEARAFKKVQ 281
           FEV+RER+RQIEA+A +K++
Sbjct: 772 FEVTRERIRQIEAKALRKLR 791


>gi|125602291|gb|EAZ41616.1| hypothetical protein OsJ_26150 [Oryza sativa Japonica Group]
          Length = 420

 Score = 92.8 bits (229), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 79/263 (30%), Positives = 132/263 (50%), Gaps = 34/263 (12%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R R H    A   L  S+LRLV+ IA  Y   G+ +++++  G IGL++ ++KFD  RGF
Sbjct: 168 RSRMHESFLAREMLTMSNLRLVISIAQKYDNLGVELADLIQGGLIGLLRGIEKFDASRGF 227

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           R++TY  WWI+  +   +  +    ++ T  +++     L  ++G    + D  + P  +
Sbjct: 228 RISTYVYWWIRQGVSRALAENSKTFRLPTYLHER-----LIAIRGAKYELEDQGIAP-TI 281

Query: 160 VAIAKKLNVSESEVI----SMNCRLAGDE----SLNALINSS------DKNSSQWQDWLV 205
             IA  LN+SE +V+    ++N  L+ D+    SLN L   +      D+N +    W  
Sbjct: 282 ENIAGSLNISEKKVLNATEAVNKVLSLDQQAFPSLNGLPGETLHSYIEDQNVAN-DPW-- 338

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPVTLENLSSEFEV 264
             H  +E  L  KEE     N      S LN RER I      + +   T E++S +F +
Sbjct: 339 --HGFEEWYL--KEEVNKLLN------STLNERERDIIRLYHGIGKQCHTWEDISRQFGL 388

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           SRERVRQ+   A +K++ + +++
Sbjct: 389 SRERVRQVGLIAMEKLKHAARRK 411


>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 = 92.8 bits (229), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 73/249 (29%), Positives = 122/249 (48%), Gaps = 40/249 (16%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 363 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 422

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHL----------QAITDNNL 154
           I+ A+   I      ++I      T N+      L R+   +          + +++  L
Sbjct: 423 IRQAITRSIADQARTIRIPVHMIETINK------LNRISRQMLQEIGREPTPEELSEKML 476

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            PE    I K L +++ E ISM   +  DE             S   D+L    D    +
Sbjct: 477 IPED--KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFL---EDTSLDL 518

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQI 272
            ++    ++ R+     +S L  RE ++ + R   +     TLE +  +F+V+RER+RQI
Sbjct: 519 PLDSATSESLRSATHDVLSGLTAREAKVLKMRFGIDMSTDHTLEEVGKQFDVTRERIRQI 578

Query: 273 EARAFKKVQ 281
           EA+A +K++
Sbjct: 579 EAKALRKLR 587


>gi|300858628|ref|YP_003783611.1| RNA polymerase sigma factor A [Corynebacterium pseudotuberculosis
           FRC41]
 gi|300686082|gb|ADK29004.1| RNA polymerase sigma factor A [Corynebacterium pseudotuberculosis
           FRC41]
 gi|302206337|gb|ADL10679.1| RNA polymerase sigma factor rpoD (Sigma-A) [Corynebacterium
           pseudotuberculosis C231]
 gi|302330894|gb|ADL21088.1| RNA polymerase sigma factor rpoD (Sigma-A) [Corynebacterium
           pseudotuberculosis 1002]
 gi|308276579|gb|ADO26478.1| RNA polymerase sigma factor rpoD (Sigma-A) [Corynebacterium
           pseudotuberculosis I19]
          Length = 517

 Score = 92.8 bits (229), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 80/324 (24%), Positives = 155/324 (47%), Gaps = 49/324 (15%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR--------YR--------EHGD 46
           RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR        YR         +GD
Sbjct: 199 RKDAELTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYATYRMEQMEEAFNNGD 257

Query: 47  LSAA--------------------HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
             A                     + L+ ++LRLVV +A  Y G G+   +++ EGN+GL
Sbjct: 258 KEAKLTPAVKRDLRAIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGL 317

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L
Sbjct: 318 IRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQREL 375

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    P++   +AK+++++E +V+ +        SL+  I   D+  SQ  D++  
Sbjct: 376 LQDLGREPTPQE---LAKEMDITEEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI-- 428

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEV 264
             D +  + ++       ++ L   +  L+ RE  + + R  L +  P TL+ +   + V
Sbjct: 429 -EDSEAVIAVDAVSFTLLQDQLQDVLHTLSEREAGVVKLRFGLTDGMPRTLDEIGQVYGV 487

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           +RER+RQIE++   K++   + QV
Sbjct: 488 TRERIRQIESKTMSKLRHPSRSQV 511


>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 = 92.8 bits (229), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 120/234 (51%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 391 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 450

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   L         PE+   +A+++ +
Sbjct: 451 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQLLQEMGREATPEE---LAERMGM 505

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ +   
Sbjct: 506 PEDKIRKV-LKIAK-EPISMETPIGDDDDSHLGDFI---EDSTLELPLDSATAQSLKVAT 560

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 561 HEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 614


>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 = 92.8 bits (229), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 120/234 (51%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 390 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 449

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   L         PE+   +A+++ +
Sbjct: 450 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQLLQEMGREATPEE---LAERMGM 504

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ +   
Sbjct: 505 PEDKIRKV-LKIAK-EPISMETPIGDDDDSHLGDFI---EDSTLELPLDSATAQSLKVAT 559

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 560 HEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 613


>gi|2624403|emb|CAA74653.1| plastid RNA polymerase sigma factor [Sorghum bicolor]
          Length = 500

 Score = 92.8 bits (229), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 78/247 (31%), Positives = 131/247 (53%), Gaps = 28/247 (11%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L  S++RLV+ IA  Y   G+ +++++  G IGL++ ++KFD  RGFR++TY  WWI+  
Sbjct: 261 LTMSNIRLVISIAQKYDNLGVELADLIQGGLIGLLRGIEKFDASRGFRISTYVYWWIRQG 320

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +  +    ++ T  +++     L  ++G   A+ D  + P  V  IA+ LN+SE +
Sbjct: 321 VSRALADNSKAFRLPTYLHER-----LIAIRGAKYALEDQGIAP-TVENIAESLNISEKK 374

Query: 173 VI----SMNCRLAGDE----SLNALINSSDKNSSQWQDWLVYD---HDGQEQVLIEKEER 221
           V     ++N  L+ D+    SLN L    D   S  +D  V +   H  +E+ L  KEE 
Sbjct: 375 VHNATEAVNKVLSLDQQAFPSLNGL--PGDTLHSYIEDQNVANDPWHGFEERYL--KEEV 430

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARR-LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            N  N      S LN RER I      + +   T E++S +F +SRERVRQ+   A +K+
Sbjct: 431 NNLIN------SNLNERERDIIRLYHGIGKQCHTWEDISRQFGLSRERVRQVGLVAMEKL 484

Query: 281 QESIQKQ 287
           + + +++
Sbjct: 485 KHAARRK 491


>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 = 92.8 bits (229), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 67/246 (27%), Positives = 117/246 (47%), Gaps = 36/246 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 400 AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 459

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + I   + +      +A+K+ +
Sbjct: 460 IRQAITRSIADQARTIRIPV-----HMIETINKMNRISRQILQESGREPDPAELAEKMEM 514

Query: 169 SESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLI 216
            E ++          ISM   +  D+  +      D+N+    D  +Y    D  ++VL 
Sbjct: 515 PEEKIRKIMKISKEPISMETPIGDDDDSHLGDFIEDQNNLAPSDAAMYSSLKDATKEVL- 573

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEA 274
                             L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA
Sbjct: 574 ----------------DTLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEA 617

Query: 275 RAFKKV 280
           +A +K+
Sbjct: 618 KALRKL 623


>gi|125560253|gb|EAZ05701.1| hypothetical protein OsI_27933 [Oryza sativa Indica Group]
          Length = 372

 Score = 92.8 bits (229), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 79/263 (30%), Positives = 132/263 (50%), Gaps = 34/263 (12%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R R H    A   L  S+LRLV+ IA  Y   G+ +++++  G IGL++ ++KFD  RGF
Sbjct: 120 RSRMHESFLAREMLTMSNLRLVISIAQKYDNLGVELADLIQGGLIGLLRGIEKFDASRGF 179

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           R++TY  WWI+  +   +  +    ++ T  +++     L  ++G    + D  + P  +
Sbjct: 180 RISTYVYWWIRQGVSRALAENSKTFRLPTYLHER-----LIAIRGAKYELEDQGIAP-TI 233

Query: 160 VAIAKKLNVSESEVI----SMNCRLAGDE----SLNALINSS------DKNSSQWQDWLV 205
             IA  LN+SE +V+    ++N  L+ D+    SLN L   +      D+N +    W  
Sbjct: 234 ENIAGSLNISEKKVLNATEAVNKVLSLDQQAFPSLNGLPGETLHSYIEDQNVAN-DPW-- 290

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPVTLENLSSEFEV 264
             H  +E  L  KEE     N      S LN RER I      + +   T E++S +F +
Sbjct: 291 --HGFEEWYL--KEEVNKLLN------STLNERERDIIRLYHGIGKQCHTWEDISRQFGL 340

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           SRERVRQ+   A +K++ + +++
Sbjct: 341 SRERVRQVGLIAMEKLKHAARRK 363


>gi|37806470|dbj|BAC99905.1| putative plastid RNA polymerase sigma factor [Oryza sativa Japonica
           Group]
          Length = 388

 Score = 92.8 bits (229), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 79/263 (30%), Positives = 132/263 (50%), Gaps = 34/263 (12%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R R H    A   L  S+LRLV+ IA  Y   G+ +++++  G IGL++ ++KFD  RGF
Sbjct: 136 RSRMHESFLAREMLTMSNLRLVISIAQKYDNLGVELADLIQGGLIGLLRGIEKFDASRGF 195

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           R++TY  WWI+  +   +  +    ++ T  +++     L  ++G    + D  + P  +
Sbjct: 196 RISTYVYWWIRQGVSRALAENSKTFRLPTYLHER-----LIAIRGAKYELEDQGIAP-TI 249

Query: 160 VAIAKKLNVSESEVI----SMNCRLAGDE----SLNALINSS------DKNSSQWQDWLV 205
             IA  LN+SE +V+    ++N  L+ D+    SLN L   +      D+N +    W  
Sbjct: 250 ENIAGSLNISEKKVLNATEAVNKVLSLDQQAFPSLNGLPGETLHSYIEDQNVAN-DPW-- 306

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPVTLENLSSEFEV 264
             H  +E  L  KEE     N      S LN RER I      + +   T E++S +F +
Sbjct: 307 --HGFEEWYL--KEEVNKLLN------STLNERERDIIRLYHGIGKQCHTWEDISRQFGL 356

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           SRERVRQ+   A +K++ + +++
Sbjct: 357 SRERVRQVGLIAMEKLKHAARRK 379


>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 = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 120/234 (51%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 385 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 444

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   L         PE+   +A+++ +
Sbjct: 445 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQLLQEMGREATPEE---LAERMGM 499

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ +   
Sbjct: 500 PEDKIRKV-LKIAK-EPISMETPIGDDDDSHLGDFI---EDSTLELPLDSATAQSLKVAT 554

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 555 HEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 608


>gi|85057387|ref|YP_456303.1| RNA polymerase sigma factor RpoD [Aster yellows witches'-broom
           phytoplasma AYWB]
 gi|84789492|gb|ABC65224.1| RNA polymerase sigma factor RpoD [Aster yellows witches'-broom
           phytoplasma AYWB]
          Length = 465

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 80/273 (29%), Positives = 138/273 (50%), Gaps = 34/273 (12%)

Query: 21  HEIRKIPMLEKQ--EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           H+ ++I + E Q  E +   K+ R   D+     LV S+ RLVV IA  Y G G+   ++
Sbjct: 197 HKTKEIELSEDQLQEAHDQIKQARRAKDI-----LVESNYRLVVSIAKRYIGRGILFLDL 251

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKR 134
           + EGN+GLM+AV KFD ++GF+ +TY+ WWI+ A+   I      ++I      T N  +
Sbjct: 252 IQEGNMGLMRAVDKFDYQKGFKFSTYATWWIRQAITRAIADQARTIRIPVHIVETIN--K 309

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +    R+L   L+       KP  V  +A K+N+S  ++ S+        SL A    ++
Sbjct: 310 MALCTRKLTQKLKK------KP-TVEELADKMNISAEKIRSIQYIEKKPISLEAPARENE 362

Query: 195 KNSSQWQDW-----LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-- 247
           ++ +   D+     ++  H+   + + +K   +   N LT        RE ++ + R   
Sbjct: 363 EDETSLGDFISDPNILSPHEYMMKEVTQKLLDEVLENTLTE-------REEKVLKMRYGL 415

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           L     TLE + + F V+RER+RQIE++A +++
Sbjct: 416 LDGKTHTLEEVGTLFGVTRERIRQIESKALRRL 448


>gi|148271746|ref|YP_001221307.1| putative RNA polymerase sigma 70 factor [Clavibacter michiganensis
           subsp. michiganensis NCPPB 382]
 gi|147829676|emb|CAN00592.1| putative RNA polymerase sigma 70 factor [Clavibacter michiganensis
           subsp. michiganensis NCPPB 382]
          Length = 347

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 79/303 (26%), Positives = 138/303 (45%), Gaps = 59/303 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR----------EHGDLSAAHR---------------- 52
           Y+ +I ++P+L  ++E  +A+R               DL+ A R                
Sbjct: 54  YLRQIGRVPLLTAEQEVTVARRIEVGVLSQEVLDTRTDLTPAERREYQTLAQDGMRAKQH 113

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV ++LRLVV IA  Y G GLP  +++ EGN+GL++AV+KFD + GF+ +TY+ WWIK +
Sbjct: 114 LVNANLRLVVSIAKRYTGRGLPFLDLIQEGNMGLVRAVEKFDYQAGFKFSTYASWWIKQS 173

Query: 113 MQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           +   +  +   ++I            A Q+ L   L R         D +++      IA
Sbjct: 174 ITRGMADTSRTIRIPVHTVEHINRINAVQRELAVELGR---------DPSME-----EIA 219

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           ++ +   ++V  +  R     SL  L+  S  +       L+ D D  + + +  ++   
Sbjct: 220 RESDTPVTKVRYLLDRAQEPMSLQVLVGGSGGDGDTEMADLIEDADVTQPIDVVTQQL-- 277

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQEN-----PVTLENLSSEFEVSRERVRQIEARAFK 278
              M    M +++    R  E  R++       P +L  +S +  V+RERVRQIE +   
Sbjct: 278 ---MAAHVMRLIDGLAERDAEVVRMRFGLAGLEPRSLAFVSQQLGVTRERVRQIEKKVLA 334

Query: 279 KVQ 281
           K++
Sbjct: 335 KLR 337


>gi|159896899|ref|YP_001543146.1| RpoD family RNA polymerase sigma factor [Herpetosiphon aurantiacus
           ATCC 23779]
 gi|159889938|gb|ABX03018.1| RNA polymerase, sigma 70 subunit, RpoD family [Herpetosiphon
           aurantiacus ATCC 23779]
          Length = 391

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 84/292 (28%), Positives = 138/292 (47%), Gaps = 38/292 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAK-----RYREH----------GDLSAAHR----------- 52
           Y+ EI ++ +L  +EE  LAK     R  EH           + +A  R           
Sbjct: 98  YLREIGEVELLTAEEEITLAKQIETGRKAEHQLQTEQYATWDERTALERRVDFGNEGRRK 157

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L  ++LRLVV +A  Y G  +   +++ EGNIGLM+AV+KFD  +G R +TY+ WWI+ A
Sbjct: 158 LTQANLRLVVSVAKKYIGNHMSFMDLIQEGNIGLMRAVEKFDYRKGNRFSTYATWWIRQA 217

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   I      +++    ++      +RR+   L+        P++   +A  L VS  +
Sbjct: 218 VTRAIAEQSRTIRLPVHLSES--IAQMRRVAYQLEQALQREATPDE---LADALGVSLRK 272

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           V  M        SL   I    +   +  ++L  D D   +  +E+  R   ++ L  ++
Sbjct: 273 VKRMLNASVQPVSLEQPIGK--EGQGRVGEFLADDTD---EAPLEQATRMMLQDELADAL 327

Query: 233 SVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQE 282
           S L  RER+I   R    +    TLE + +EF ++RER RQIEA A + +++
Sbjct: 328 SQLPDRERQILLLRYGLADGKRRTLEEVGAEFGITRERTRQIEAEAMRHLRQ 379


>gi|1519638|gb|AAB07552.1| SigB [Chloroflexus aurantiacus J-10-fl]
          Length = 346

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 84/292 (28%), Positives = 140/292 (47%), Gaps = 41/292 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRY----------REHGDLSAAHRL--------------- 53
           Y+ EI ++P+L  +EE  LA++Y          R     + A+                 
Sbjct: 54  YLQEIGQVPLLTAEEEVELARQYSRGKEARQRLRNEDSPTTANGCGWRWKWLAVKRRGGR 113

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           + ++LRLVV +A  Y G  +   ++V EGNIGLM+AV+KFD  +G R +TY+ WWI+ A+
Sbjct: 114 IQANLRLVVSVAKKYIGSPMAFMDLVQEGNIGLMRAVEKFDYTKGNRFSTYATWWIRQAV 173

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
              I     L+++    ++     +LRR    L+   +     E+   +A  LN+S  +V
Sbjct: 174 TRAIAEQSRLIRLPVHLSES--IVHLRRAIYRLEQELEREPTAEE---LAHALNMSVRKV 228

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL--IEKEERKNRRNMLTRS 231
             +        SL   +N+        Q+  V +    E V   +E  E+K     LT +
Sbjct: 229 KRLIRASTQPISLEQPLNNE-------QEGRVSETLADETVASPMEIAEQKMLHAELTAA 281

Query: 232 MSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++ L  RER+I + R   +     TLE + + F ++RER RQIEA A ++++
Sbjct: 282 LNELPERERKILQLRYGLIDGQRRTLEEVGATFGITRERTRQIEAEALRRLR 333


>gi|304389369|ref|ZP_07371334.1| DNA-directed RNA polymerase sigma subunit RpoD [Mobiluncus curtisii
           subsp. curtisii ATCC 35241]
 gi|304327487|gb|EFL94720.1| DNA-directed RNA polymerase sigma subunit RpoD [Mobiluncus curtisii
           subsp. curtisii ATCC 35241]
          Length = 564

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 81/310 (26%), Positives = 144/310 (46%), Gaps = 63/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH-----------------------GDLSAA 50
           Y+ +I K+ +L  ++E  L+KR     Y EH                       G ++  
Sbjct: 270 YLKQIGKVALLNAEQEVDLSKRIEAGLYAEHLLKTKQETMTPKQIRELHYVVQDGQMAKN 329

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           H L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+
Sbjct: 330 H-LLEANLRLVVALAKKYTGRGMLFLDLIQEGNLGLIRAVEKFDYSKGYKFSTYATWWIR 388

Query: 111 AAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
            A+   +      ++I              Q+++  +L R     +   +  + PE+VV 
Sbjct: 389 QAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPDELAQELEMTPEKVVE 448

Query: 162 IAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           + K       E IS++  L   GD     LI  S+          V   D    ++++++
Sbjct: 449 VQKYGR----EPISLHTPLGEDGDSEFGDLIEDSE---------AVVPADAVSFMMLQEQ 495

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAF 277
                   L R +  L+ RE  +   R  L++  P TL+ +   + V+RER+RQIEA+  
Sbjct: 496 --------LQRVLDTLSERESGVIAMRFGLKDGQPKTLDEIGRRYGVTRERIRQIEAKTM 547

Query: 278 KKVQESIQKQ 287
            K++   + Q
Sbjct: 548 SKLRHPARSQ 557


>gi|300725901|ref|ZP_07059364.1| RNA polymerase sigma-70 factor [Prevotella bryantii B14]
 gi|299776838|gb|EFI73385.1| RNA polymerase sigma-70 factor [Prevotella bryantii B14]
          Length = 290

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 73/281 (25%), Positives = 138/281 (49%), Gaps = 30/281 (10%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYG 72
            L +Y+ EI   PM+   +E  LA+  R+ G     A  +LV ++LR VV +A  Y+  G
Sbjct: 17  ALDKYLAEISHEPMINIDQEIELAQAIRKGGRAGERAKDKLVKANLRFVVSVAKQYQHQG 76

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V++    NQ
Sbjct: 77  LSLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRL--PLNQ 134

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 L ++   +     +N +   +  I++   + E ++         ++S+ A  N 
Sbjct: 135 ---VGALSKINATISKFEQDNQRRPSIQEISRLTGIEEEKI---------EQSIKA-DNH 181

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS---------VLNPRERRIF 243
                + +QD    + +    ++   E+ +  R +   SM+         VL  RE +I 
Sbjct: 182 HTSIDAPFQDG---EENSMVDIMASGEDTRTDRQVDHDSMAQELHSVLKNVLKDREIKIL 238

Query: 244 -EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            E   +  +   LE +     ++RERVRQI  ++  K++E+
Sbjct: 239 CECYGIGCHEKGLEEIGDRMGLTRERVRQIREKSILKLREA 279


>gi|295394756|ref|ZP_06804971.1| DNA-directed RNA polymerase sigma subunit RpoD [Brevibacterium
           mcbrellneri ATCC 49030]
 gi|294972352|gb|EFG48212.1| DNA-directed RNA polymerase sigma subunit RpoD [Brevibacterium
           mcbrellneri ATCC 49030]
          Length = 473

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 84/309 (27%), Positives = 143/309 (46%), Gaps = 60/309 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH----GDLS-----------------AAHR 52
           Y+ +I K+ +L   EE  LAKR     Y EH    G ++                 A + 
Sbjct: 180 YLKQIGKVALLNAAEEVDLAKRIEAGMYAEHLVDEGKVTDARDLRDYKWIIHDGRIAKNH 239

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 240 LLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQA 299

Query: 113 MQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           +   +      ++I              Q+++  +L R     +   + ++ PE+VV + 
Sbjct: 300 ITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPERVVEVQ 359

Query: 164 KKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           K       E IS++  L   GD     LI  S+          V   D     L++++  
Sbjct: 360 KYGR----EPISLHTPLGEDGDSEFGDLIEDSE---------AVVPADSVSFTLLQEQ-- 404

Query: 222 KNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAFKK 279
                 L   +  L+ RE  +   R  L +  P TL+ +   + V+RER+RQIE++   K
Sbjct: 405 ------LHSVLDTLSEREAGVVSMRFGLNDGQPKTLDEIGKVYGVTRERIRQIESKTMAK 458

Query: 280 VQESIQKQV 288
           ++   + QV
Sbjct: 459 LRHPSRSQV 467


>gi|116619924|ref|YP_822080.1| RpoD family RNA polymerase sigma factor [Candidatus Solibacter
           usitatus Ellin6076]
 gi|116223086|gb|ABJ81795.1| RNA polymerase, sigma 70 subunit, RpoD family [Candidatus
           Solibacter usitatus Ellin6076]
          Length = 518

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 73/250 (29%), Positives = 123/250 (49%), Gaps = 29/250 (11%)

Query: 44  HGDLSAAH---RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           HG+  A      LV ++LRLVV +A  Y   GL + +++ EGNIGLM+A  KF+  RG++
Sbjct: 271 HGEAEAERAKKDLVEANLRLVVSVAKKYVNRGLHLLDLIQEGNIGLMRAADKFEYRRGYK 330

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQK--RLFFNLRRLKGHL-QAITDNNLKPE 157
            +TY+ WWI+ A+   I      ++I    N+   +     R L+  L +  T++ +   
Sbjct: 331 FSTYATWWIRQAITRAIADQSRTIRIPVHMNESMNKFLRATRELEKELGRTPTNDEIGRR 390

Query: 158 QVVAIAK--KLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
             + + K  KL     + +S+   +   G+ +L  LI            W+    D    
Sbjct: 391 MDIPVEKVQKLKTISRDPVSLETPVGRDGESALGDLIEDR---------WVGSPVDA--- 438

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQ 271
            +IE     N R+     +  L+P+E ++   R     E   TLE +  EF+V+RER+RQ
Sbjct: 439 -VIE----SNVRDETAGILKTLSPKEEKVIRMRFGIGCEREHTLEEIGQEFDVTRERIRQ 493

Query: 272 IEARAFKKVQ 281
           IEA+A ++++
Sbjct: 494 IEAKALRQLR 503


>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 = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 67/245 (27%), Positives = 118/245 (48%), Gaps = 32/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGN+GLM+AV KF+  RG++ +TY+ WW
Sbjct: 572 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNVGLMKAVDKFEYRRGYKFSTYATWW 631

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +  ++P+    +A+K+++
Sbjct: 632 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGVEPDP-AELAEKMDM 686

Query: 169 SESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            E ++          ISM   +  DE             S   D+L    D       E 
Sbjct: 687 PEDKIRKILKIAKEPISMETPIGDDE------------DSHLGDFL---EDFGTVAPAEA 731

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARA 276
            ++ +   +    +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A
Sbjct: 732 AQQSSLTEITKEVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGRQFDVTRERIRQIEAKA 791

Query: 277 FKKVQ 281
            +K++
Sbjct: 792 LRKLR 796


>gi|239917829|ref|YP_002957387.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Micrococcus luteus NCTC
           2665]
 gi|281413678|ref|ZP_06245420.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family protein [Micrococcus
           luteus NCTC 2665]
 gi|239839036|gb|ACS30833.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Micrococcus luteus NCTC
           2665]
          Length = 497

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 83/322 (25%), Positives = 145/322 (45%), Gaps = 62/322 (19%)

Query: 8   IIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKR------------------YREHGDL 47
           ++V G     +  Y+ +I K+ +L  ++E  LA R                  YRE  D+
Sbjct: 191 VVVAGATADPVKDYLKQIGKVALLNAEQEVDLAMRIEAGLYAEHVVQHEASDDYRERRDI 250

Query: 48  S--------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                    A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF
Sbjct: 251 QLIIADGRKAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGF 310

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAIT 150
           + +TY+ WWI+ A+   +      ++I              Q+++  +L R     +   
Sbjct: 311 KFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAK 370

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDH 208
           + ++ PE+VV + K       E IS++  L   GD     LI  S+          V   
Sbjct: 371 ELDMTPEKVVEVQKYGR----EPISLHTPLGEDGDSEFGDLIEDSEA---------VVPA 417

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSR 266
           D     L++++        L   +  L+ RE  +   R       P TL+ +   + V+R
Sbjct: 418 DAVSFTLLQEQ--------LHSVLDTLSEREAGVVAMRFGLTDGQPKTLDEIGKVYGVTR 469

Query: 267 ERVRQIEARAFKKVQESIQKQV 288
           ER+RQIE++   K++   + QV
Sbjct: 470 ERIRQIESKTMSKLRHPSRSQV 491


>gi|256390959|ref|YP_003112523.1| RNA polymerase sigma factor [Catenulispora acidiphila DSM 44928]
 gi|256357185|gb|ACU70682.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Catenulispora
           acidiphila DSM 44928]
          Length = 559

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 80/309 (25%), Positives = 141/309 (45%), Gaps = 60/309 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR--------------------YREHGDL------SAAHR 52
           Y+ +I K+P+L  ++E  LAKR                    +R   D+       A + 
Sbjct: 266 YLKQIGKVPLLNAEQEVELAKRIEAGLFAEEKLNDGEPLTPEFRRELDIIAEDGRRAKNH 325

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A
Sbjct: 326 LLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQA 385

Query: 113 MQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           +   +      ++I              Q+++  +L R     +   + ++ PE+VV + 
Sbjct: 386 ITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQ 445

Query: 164 KKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           K       E IS++  L   GD     LI  S+          V   D     L++++  
Sbjct: 446 KYGR----EPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ-- 490

Query: 222 KNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
                 L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K
Sbjct: 491 ------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSK 544

Query: 280 VQESIQKQV 288
           ++   + QV
Sbjct: 545 LRHPSRSQV 553


>gi|37806471|dbj|BAC99906.1| putative plastid RNA polymerase sigma factor [Oryza sativa Japonica
           Group]
          Length = 342

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 79/263 (30%), Positives = 132/263 (50%), Gaps = 34/263 (12%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R R H    A   L  S+LRLV+ IA  Y   G+ +++++  G IGL++ ++KFD  RGF
Sbjct: 90  RSRMHESFLAREMLTMSNLRLVISIAQKYDNLGVELADLIQGGLIGLLRGIEKFDASRGF 149

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           R++TY  WWI+  +   +  +    ++ T  +++     L  ++G    + D  + P  +
Sbjct: 150 RISTYVYWWIRQGVSRALAENSKTFRLPTYLHER-----LIAIRGAKYELEDQGIAP-TI 203

Query: 160 VAIAKKLNVSESEVI----SMNCRLAGDE----SLNALINSS------DKNSSQWQDWLV 205
             IA  LN+SE +V+    ++N  L+ D+    SLN L   +      D+N +    W  
Sbjct: 204 ENIAGSLNISEKKVLNATEAVNKVLSLDQQAFPSLNGLPGETLHSYIEDQNVAN-DPW-- 260

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPVTLENLSSEFEV 264
             H  +E  L  KEE     N      S LN RER I      + +   T E++S +F +
Sbjct: 261 --HGFEEWYL--KEEVNKLLN------STLNERERDIIRLYHGIGKQCHTWEDISRQFGL 310

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           SRERVRQ+   A +K++ + +++
Sbjct: 311 SRERVRQVGLIAMEKLKHAARRK 333


>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 = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 67/245 (27%), Positives = 118/245 (48%), Gaps = 32/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGN+GLM+AV KF+  RG++ +TY+ WW
Sbjct: 572 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNVGLMKAVDKFEYRRGYKFSTYATWW 631

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +  ++P+    +A+K+++
Sbjct: 632 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGVEPDP-AELAEKMDM 686

Query: 169 SESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            E ++          ISM   +  DE             S   D+L    D       E 
Sbjct: 687 PEDKIRKILKIAKEPISMETPIGDDE------------DSHLGDFL---EDFGTVAPAEA 731

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARA 276
            ++ +   +    +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A
Sbjct: 732 AQQSSLTEITKEVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGRQFDVTRERIRQIEAKA 791

Query: 277 FKKVQ 281
            +K++
Sbjct: 792 LRKLR 796


>gi|325673633|ref|ZP_08153324.1| RNA polymerase principal sigma factor SigA [Rhodococcus equi ATCC
           33707]
 gi|325555654|gb|EGD25325.1| RNA polymerase principal sigma factor SigA [Rhodococcus equi ATCC
           33707]
          Length = 448

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 66/240 (27%), Positives = 116/240 (48%), Gaps = 20/240 (8%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           SA  R++ ++LRLVV  A  Y G GL + ++V EGN GL++AV+KFD   G + +TY+ W
Sbjct: 212 SARTRMIEANLRLVVSTAQNYEGRGLDMLDLVQEGNTGLIRAVEKFDYRLGNKFSTYATW 271

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ---AITDNNLKPEQVVAIAK 164
           WI+ A+   I      +++     +        R++G ++   A+TD  +     + + K
Sbjct: 272 WIRQAITRGIADKSRTIRLPVHVVEDLSRMTTVRVEGEIELGRALTDAEVAQRADLTLEK 331

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
              + + +   +        S+ AL +S D      +D   +D         E   R + 
Sbjct: 332 VRELDDCDRTVL--------SIEALTDSDDGAGLDIEDDCAHDP-------YEALHRADV 376

Query: 225 RNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           R  +   +  L  RE  + + R   +   P TLE +   ++V+RER+RQIEA+  + ++E
Sbjct: 377 RERIDIVLETLTEREAGVMKLRHGLVDGVPRTLEEIGKVYKVTRERIRQIEAKTLQLLRE 436


>gi|283781338|ref|YP_003372093.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pirellula staleyi
           DSM 6068]
 gi|283439791|gb|ADB18233.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pirellula staleyi
           DSM 6068]
          Length = 524

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 83/282 (29%), Positives = 136/282 (48%), Gaps = 27/282 (9%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRY----REHGDLSAAHR-LVTSHLRLVVKIAMGYRGYG 72
           +++ E+R I +  ++    + KR     R + D   A R L   +LRLVV IA  YR  G
Sbjct: 251 QWLSELRSILVATQETPASMQKRVDMLKRVYTDYQQAKRELSEGNLRLVVSIAKKYRNRG 310

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG----- 127
           L   +++ EGN GLM+AV KF+  RGF+  TY+ WWI+ A+   +      ++I      
Sbjct: 311 LSFLDLIQEGNAGLMRAVDKFEYRRGFKFCTYATWWIRQAITRAVADQSRTIRIPVHMVE 370

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
           T +  + +   L +  G    + +   K +  V  A+++       IS++ R  G     
Sbjct: 371 TMSRVRNVSRQLLQELGREPTLEETARKAKTTVDEARRVLAMSRYPISLD-RPVG----- 424

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
              NS D   S + D L    DG  +       ++  R  + + +  L+ RER I + R 
Sbjct: 425 ---NSED---SHFGDLL---PDGTAESPATGASQEMLRTRINKVLKTLSYREREIIKLRY 475

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              +    TLE +   F+V+RER+RQIEA+A +K+Q+  + Q
Sbjct: 476 GLGDGYSYTLEEVGHIFKVTRERIRQIEAKAVRKLQQPSRSQ 517


>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 = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 120/234 (51%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 391 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 450

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   L         PE+   +A+++ +
Sbjct: 451 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQLLQEMGREATPEE---LAERMGM 505

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ +   
Sbjct: 506 PEDKIRKV-LKIAK-EPISMETPIGDDDDSHLGDFI---EDSTLELPLDSATAQSLKVAT 560

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 561 HEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 614


>gi|196234461|ref|ZP_03133287.1| RNA polymerase, sigma 32 subunit, RpoH [Chthoniobacter flavus
           Ellin428]
 gi|196221517|gb|EDY16061.1| RNA polymerase, sigma 32 subunit, RpoH [Chthoniobacter flavus
           Ellin428]
          Length = 479

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 73/241 (30%), Positives = 126/241 (52%), Gaps = 20/241 (8%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L A   +V  +LRLVV IA  Y+  G P  +++ EGNIGLM+AV++F+  RG++ AT + 
Sbjct: 240 LEARTEMVECNLRLVVSIAREYQNRGQPFLDLIQEGNIGLMRAVERFEYRRGYKFATCAT 299

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I T  +   L   L R++   + +T  + +      +A +L
Sbjct: 300 WWIRQAISRSIANQARTIRIPT--HMIDLLAKLIRVQ---RQMTQESGRDPTAEDLAGEL 354

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL----VYDHDGQEQVLIEKEERK 222
           ++    V ++  ++A +E ++      ++  S+  D++    V D   Q  V + +E+  
Sbjct: 355 HLPLRRVRAL-LKMA-EEPISIHTPVGEEGGSRLGDFIEDHSVEDPSKQAAVAMLREK-- 410

Query: 223 NRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                +   +  L  RER I E R   +     TLE +   F+V+RERVRQIEA+A +K+
Sbjct: 411 -----INAVLHTLTEREREILEQRFGLIDGRERTLEEIGRHFKVTRERVRQIEAKALRKM 465

Query: 281 Q 281
           +
Sbjct: 466 R 466


>gi|38233991|ref|NP_939758.1| RNA polymerase sigma factor [Corynebacterium diphtheriae NCTC
           13129]
 gi|38200253|emb|CAE49937.1| RNA polymerase sigma factor [Corynebacterium diphtheriae]
          Length = 502

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 65/242 (26%), Positives = 128/242 (52%), Gaps = 12/242 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WW
Sbjct: 265 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 324

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   +      ++I    +   +   L R++  L         P++   +AK++++
Sbjct: 325 IRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGREPTPQE---LAKEMDI 379

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +E +V+ +        SL+  I   D+  SQ  D++    D +  + ++       ++ L
Sbjct: 380 TEEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEAVIAVDAVSFTLLQDQL 434

Query: 229 TRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +  L+ RE  + + R  L +  P TL+ +   + V+RER+RQIE++   K++   + 
Sbjct: 435 QDVLHTLSEREAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRS 494

Query: 287 QV 288
           QV
Sbjct: 495 QV 496


>gi|302670285|ref|YP_003830245.1| RNA polymerase sigma factor RpoD [Butyrivibrio proteoclasticus
           B316]
 gi|302394758|gb|ADL33663.1| RNA polymerase sigma factor RpoD [Butyrivibrio proteoclasticus
           B316]
          Length = 521

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 83/308 (26%), Positives = 137/308 (44%), Gaps = 69/308 (22%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS-----------------------------A 49
           Y+ EI K+P+L   +E  LA+      D                               A
Sbjct: 225 YLKEIGKVPLLTADQEIDLAQAMEAGADAEKELADDKDVNKLSDARKKELNAIIYEGEEA 284

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             RL  ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI
Sbjct: 285 KKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDFRKGFKFSTYATWWI 344

Query: 110 KAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQVV 160
           + A+   I      ++I      T N+     ++L   L R     +   + N+  E+V 
Sbjct: 345 RQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPLPEEVAKEMNMPVERVR 404

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH-----DGQEQVL 215
            I   L +S+ E +S+   +  +E             S   D++  D+     D     L
Sbjct: 405 EI---LKISQ-EPVSLETPIGEEE------------DSHLGDFIQDDNVPVPADAAAFTL 448

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIE 273
           +        +  L   +  L  RE+++   R   ++    TLE +  EF V+RER+RQIE
Sbjct: 449 L--------KEQLVEVLGTLTEREQKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIE 500

Query: 274 ARAFKKVQ 281
           A+A +K++
Sbjct: 501 AKALRKLR 508


>gi|289706929|ref|ZP_06503266.1| RNA polymerase sigma factor RpoD [Micrococcus luteus SK58]
 gi|289556364|gb|EFD49718.1| RNA polymerase sigma factor RpoD [Micrococcus luteus SK58]
          Length = 509

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 83/322 (25%), Positives = 145/322 (45%), Gaps = 62/322 (19%)

Query: 8   IIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKR------------------YREHGDL 47
           ++V G     +  Y+ +I K+ +L  ++E  LA R                  YRE  D+
Sbjct: 203 VVVAGATADPVKDYLKQIGKVALLNAEQEVDLAMRIEAGLYAEHVVQHEASDDYRERRDI 262

Query: 48  S--------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                    A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF
Sbjct: 263 QLIIADGRKAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGF 322

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAIT 150
           + +TY+ WWI+ A+   +      ++I              Q+++  +L R     +   
Sbjct: 323 KFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAK 382

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDH 208
           + ++ PE+VV + K       E IS++  L   GD     LI  S+          V   
Sbjct: 383 ELDMTPEKVVEVQKYGR----EPISLHTPLGEDGDSEFGDLIEDSEA---------VVPA 429

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSR 266
           D     L++++        L   +  L+ RE  +   R       P TL+ +   + V+R
Sbjct: 430 DAVSFTLLQEQ--------LHSVLDTLSEREAGVVAMRFGLTDGQPKTLDEIGKVYGVTR 481

Query: 267 ERVRQIEARAFKKVQESIQKQV 288
           ER+RQIE++   K++   + QV
Sbjct: 482 ERIRQIESKTMSKLRHPSRSQV 503


>gi|115375627|ref|ZP_01462884.1| sigma factor [Stigmatella aurantiaca DW4/3-1]
 gi|310823184|ref|YP_003955542.1| RNA polymerase sigma factor rpod [Stigmatella aurantiaca DW4/3-1]
 gi|115367403|gb|EAU66381.1| sigma factor [Stigmatella aurantiaca DW4/3-1]
 gi|309396256|gb|ADO73715.1| RNA polymerase sigma factor RpoD [Stigmatella aurantiaca DW4/3-1]
          Length = 706

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 75/247 (30%), Positives = 123/247 (49%), Gaps = 36/247 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ WW
Sbjct: 468 AKSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWW 527

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVV---- 160
           I+ A+   I      ++I      T N+      L R   +L         PE++     
Sbjct: 528 IRQAITRAIADQARTIRIPVHMIETINK------LIRTSRYLVQEIGREPTPEEIAEKME 581

Query: 161 ----AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
                + K L +++ E IS+   +  +E  +      DK+       LV   D    + +
Sbjct: 582 LPLDKVRKVLKIAK-EPISLETPIGEEEDSHLGDFIEDKS-------LVSPADAVINMNL 633

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEA 274
            ++ RK         ++ L PRE ++   R    +++  TLE +  +FEV+RER+RQIEA
Sbjct: 634 AEQTRK--------VLATLTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEA 685

Query: 275 RAFKKVQ 281
           +A +K++
Sbjct: 686 KALRKLR 692


>gi|220915874|ref|YP_002491178.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Anaeromyxobacter
           dehalogenans 2CP-1]
 gi|219953728|gb|ACL64112.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Anaeromyxobacter
           dehalogenans 2CP-1]
          Length = 802

 Score = 92.8 bits (229), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 75/260 (28%), Positives = 122/260 (46%), Gaps = 33/260 (12%)

Query: 37  LAKRYREHGDLS-----AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           L + YR  GD       A   LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV 
Sbjct: 547 LRRTYRMIGDGERKAERAKTELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVD 606

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KF+ +RG++ +TY+ WWI+ A+   I      ++I    +       L R   +L     
Sbjct: 607 KFEYKRGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMIETINKLIRTSRYLVQELG 664

Query: 152 NNLKPEQVV--------AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
               PE++          + K L ++  E IS+   +  +E  +      DK+     D 
Sbjct: 665 REPTPEEIAEKMELPLDKVRKVLKIA-KEPISLETPIGEEEDSHLGDFIEDKSLVSPSDA 723

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSE 261
           ++                 N      + ++ L PRE ++   R    +++  TLE +  +
Sbjct: 724 VIN---------------MNLAEQTRKVLATLTPREEKVLRMRFGIGEKSDHTLEEVGQD 768

Query: 262 FEVSRERVRQIEARAFKKVQ 281
           FEV+RER+RQIEA+A +K++
Sbjct: 769 FEVTRERIRQIEAKALRKLR 788


>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 = 92.4 bits (228), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 70/242 (28%), Positives = 117/242 (48%), Gaps = 28/242 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 385 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 444

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 445 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 502

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 503 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 546

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + R     +++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 547 ATSLRAATRDALAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 606

Query: 279 KV 280
           K+
Sbjct: 607 KL 608


>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 = 92.4 bits (228), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 70/243 (28%), Positives = 117/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 376 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 435

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 436 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 493

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 494 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 537

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + R      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 538 ATSLRGATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 597

Query: 279 KVQ 281
           K++
Sbjct: 598 KLR 600


>gi|83859451|ref|ZP_00952972.1| RNA polymerase sigma factor [Oceanicaulis alexandrii HTCC2633]
 gi|83852898|gb|EAP90751.1| RNA polymerase sigma factor [Oceanicaulis alexandrii HTCC2633]
          Length = 678

 Score = 92.4 bits (228), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 117/235 (49%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 440 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 499

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R    +         PE+   +A+KL++
Sbjct: 500 IRQAITRSIADQARTIRI--PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLSM 554

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      D+  S   D++    D    + I+     N R   
Sbjct: 555 PLEKVRKV-MKIA-KEPISLETPIGDEEDSHLGDFI---EDKNAVLPIDAAIHSNLRETT 609

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           T  ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 610 TLVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLK 664


>gi|86607034|ref|YP_475797.1| RNA polymerase sigma factor RpoD [Synechococcus sp. JA-3-3Ab]
 gi|86555576|gb|ABD00534.1| RNA polymerase sigma factor RpoD [Synechococcus sp. JA-3-3Ab]
          Length = 404

 Score = 92.4 bits (228), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 68/237 (28%), Positives = 125/237 (52%), Gaps = 17/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 168 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 227

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++     +P E+ +A   ++
Sbjct: 228 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKVTKQLSQELGRRPTEEEIATRMEI 282

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +   I+ + +L    SL   I   +   S+  D++  + +  E    E+  +   R 
Sbjct: 283 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIESEGETPE----ERVAKVLLRE 334

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L   +  L PRER + + R   ++    TLE +   F V+RER+RQIEA+A +K++
Sbjct: 335 DLESVLETLTPRERDVLKLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLR 391


>gi|2780746|dbj|BAA24364.1| plastid RNA polymerase sigma factor [Oryza sativa Japonica Group]
          Length = 519

 Score = 92.4 bits (228), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 79/263 (30%), Positives = 132/263 (50%), Gaps = 34/263 (12%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R R H    A   L  S+LRLV+ IA  Y   G+ +++++  G IGL++ ++KFD  RGF
Sbjct: 267 RSRMHESFLAREMLTMSNLRLVISIAQKYDNLGVELADLIQGGLIGLLRGIEKFDASRGF 326

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           R++TY  WWI+  +   +  +    ++ T  +++     L  ++G    + D  + P  +
Sbjct: 327 RISTYVYWWIRQGVSRALAENSKTFRLPTYLHER-----LIAIRGAKYELEDQGIAP-TI 380

Query: 160 VAIAKKLNVSESEVI----SMNCRLAGDE----SLNALINSS------DKNSSQWQDWLV 205
             IA  LN+SE +V+    ++N  L+ D+    SLN L   +      D+N +    W  
Sbjct: 381 ENIAGSLNISEKKVLNATEAVNKVLSLDQQAFPSLNGLPGETLHSYIEDQNVAN-DPW-- 437

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPVTLENLSSEFEV 264
             H  +E  L  KEE     N      S LN RER I      + +   T E++S +F +
Sbjct: 438 --HGFEEWYL--KEEVNKLLN------STLNERERDIIRLYHGIGKQCHTWEDISRQFGL 487

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           SRERVRQ+   A +K++ + +++
Sbjct: 488 SRERVRQVGLIAMEKLKHAARRK 510


>gi|320103352|ref|YP_004178943.1| RNA polymerase sigma-38 subunit RpoS [Isosphaera pallida ATCC
           43644]
 gi|319750634|gb|ADV62394.1| RNA polymerase, sigma 38 subunit, RpoS [Isosphaera pallida ATCC
           43644]
          Length = 287

 Score = 92.4 bits (228), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 80/276 (28%), Positives = 132/276 (47%), Gaps = 28/276 (10%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ +I + P+L   EE  L +R  E GD  A   LV ++LRLVV IA GY G GL +
Sbjct: 16  LEVYLKQINETPLLSAAEERELGRRVSE-GDYFARDHLVKANLRLVVSIARGYNGKGLGL 74

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ E N+GL++AV+ FD  +  R +TY+ +WIK +++  ++ +   +++   A    L
Sbjct: 75  DDLIEERNLGLIRAVETFDYSQNIRFSTYASYWIKQSIRRAVMNNGKPIRL--PAYMVTL 132

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES---------EVISMNCRLAGDESL 186
               R+    L A       PE+V    K+L +S           EV  +     GDE  
Sbjct: 133 LAKWRQATTKLTARLGRPPTPEEV---GKELRLSPRKIPIVSKAMEVSKLQPYSEGDEDT 189

Query: 187 NALINSS--DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
              ++    D N+    + + +D D Q ++ I  +E   R + + R    L+     + E
Sbjct: 190 GVPLDDVLIDGNNRSPDELMAHDDD-QARMKILLDELDERESAVIRLRFGLD---ESVPE 245

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           A       +TL  +     ++RERVRQ+E  A  K+
Sbjct: 246 A-------MTLRQIGERLGLTRERVRQLEQAALTKL 274


>gi|257056437|ref|YP_003134269.1| RNA polymerase sigma factor SigB [Saccharomonospora viridis DSM
           43017]
 gi|256586309|gb|ACU97442.1| RNA polymerase sigma factor, sigma-70 family [Saccharomonospora
           viridis DSM 43017]
          Length = 342

 Score = 92.4 bits (228), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 81/300 (27%), Positives = 135/300 (45%), Gaps = 56/300 (18%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH-----GDLS----------------AAHR 52
           Y++ I K  +L  +EE  LAKR     + +H      DLS                A + 
Sbjct: 49  YLNGIGKTALLTAEEEVDLAKRIEAGVFAQHVLDTSDDLSEERKAELSEVVRDGEEAKNH 108

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 109 LLQANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQA 168

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +      +++     ++     L R+K  L          E+   +A +  ++E +
Sbjct: 169 ITRGMADQGRTIRLPVHLVEQ--VNKLARIKRDLHQRLGREATHEE---LAAESGIAEKK 223

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM----- 227
           V  +        SL+  + +              D D      IE  E  N  N      
Sbjct: 224 VADLLDHARDPVSLDMPVGA--------------DEDAPLGDFIEDSEAANAENSVISTL 269

Query: 228 ----LTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
               L R ++ L+ RE  +   R   ++  P TL+ +   F +SRERVRQIE     K++
Sbjct: 270 LQDDLRRVLATLDDREEHVIRLRYGLDDGQPRTLDQIGKHFSLSRERVRQIEREVMAKLR 329


>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 = 92.4 bits (228), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 70/243 (28%), Positives = 117/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 376 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 435

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 436 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 493

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 494 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 537

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + R      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 538 ATSLRGATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 597

Query: 279 KVQ 281
           K++
Sbjct: 598 KLR 600


>gi|108763751|ref|YP_633357.1| RNA polymerase sigma factor RpoD [Myxococcus xanthus DK 1622]
 gi|133312|sp|P17531|RPOD_MYXXA RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-80
 gi|150118|gb|AAA25404.1| sigma factor (rpoD) [Myxococcus xanthus]
 gi|710343|gb|AAB60208.1| major sigma factor [Myxococcus xanthus]
 gi|108467631|gb|ABF92816.1| RNA polymerase sigma factor RpoD [Myxococcus xanthus DK 1622]
 gi|1586812|prf||2204381D sigma factor
          Length = 708

 Score = 92.4 bits (228), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 70/238 (29%), Positives = 125/238 (52%), Gaps = 18/238 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ WW
Sbjct: 470 AKSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWW 529

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R   +L         PE+   IA+K+ +
Sbjct: 530 IRQAITRAIADQARTIRI--PVHMIETINKLIRTSRYLVQEIGREPTPEE---IAEKMEL 584

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      ++  S   D++      +++ L+   +     N+ 
Sbjct: 585 PLDKVRKV-LKIAK-EPISLETPIGEEEDSHLGDFI------EDKSLVSPADAVINMNLA 636

Query: 229 TRS---MSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            ++   ++ L PRE ++   R    +++  TLE +  +FEV+RER+RQIEA+A +K++
Sbjct: 637 EQTRKVLATLTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLR 694


>gi|218439766|ref|YP_002378095.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
 gi|218172494|gb|ACK71227.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
          Length = 418

 Score = 92.4 bits (228), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 61/242 (25%), Positives = 129/242 (53%), Gaps = 13/242 (5%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           +   + A + ++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV+KFDP +G+R +
Sbjct: 173 QKAGIEAKNHMIKANLRLVVSVAKRYQNRGLELLDLIQEGTLGLERAVEKFDPTKGYRFS 232

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+  +   I     ++++     +K     L ++K   + +     +   +  +
Sbjct: 233 TYAYWWIRQGITRAIATQSRIIRLPVHITEK-----LNKIKKAQRKMAQIKGRTPTMEEL 287

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A +++++  ++  +  R+    SL   I    +  ++  D L       E+ L+ +  R+
Sbjct: 288 AVEVDMTAPQIREVLMRVPRSVSLE--IKVGKEKDTELVDLLETTEASPEESLVNETLRQ 345

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + +N+L    + L  RER + + R   ++    +L ++    ++SRERVRQIEA+A +K+
Sbjct: 346 DLQNLL----ADLTTREREVIQMRYGFKDGKCYSLADIGRALQLSRERVRQIEAKAIQKL 401

Query: 281 QE 282
           ++
Sbjct: 402 RQ 403


>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 = 92.4 bits (228), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 120/234 (51%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 385 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 444

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   +A+++ +
Sbjct: 445 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREASPEE---LAERMGM 499

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ +   
Sbjct: 500 PEDKIRKV-LKIAK-EPISMETPIGDDDDSHLGDFI---EDSTLELPLDSATAQSLKAAT 554

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 555 HEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 608


>gi|297608012|ref|NP_001061065.2| Os08g0163400 [Oryza sativa Japonica Group]
 gi|255678168|dbj|BAF22979.2| Os08g0163400 [Oryza sativa Japonica Group]
          Length = 520

 Score = 92.4 bits (228), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 79/263 (30%), Positives = 132/263 (50%), Gaps = 34/263 (12%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R R H    A   L  S+LRLV+ IA  Y   G+ +++++  G IGL++ ++KFD  RGF
Sbjct: 268 RSRMHESFLAREMLTMSNLRLVISIAQKYDNLGVELADLIQGGLIGLLRGIEKFDASRGF 327

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           R++TY  WWI+  +   +  +    ++ T  +++     L  ++G    + D  + P  +
Sbjct: 328 RISTYVYWWIRQGVSRALAENSKTFRLPTYLHER-----LIAIRGAKYELEDQGIAP-TI 381

Query: 160 VAIAKKLNVSESEVI----SMNCRLAGDE----SLNALINSS------DKNSSQWQDWLV 205
             IA  LN+SE +V+    ++N  L+ D+    SLN L   +      D+N +    W  
Sbjct: 382 ENIAGSLNISEKKVLNATEAVNKVLSLDQQAFPSLNGLPGETLHSYIEDQNVAN-DPW-- 438

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPVTLENLSSEFEV 264
             H  +E  L  KEE     N      S LN RER I      + +   T E++S +F +
Sbjct: 439 --HGFEEWYL--KEEVNKLLN------STLNERERDIIRLYHGIGKQCHTWEDISRQFGL 488

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           SRERVRQ+   A +K++ + +++
Sbjct: 489 SRERVRQVGLIAMEKLKHAARRK 511


>gi|170076898|ref|YP_001733536.1| group 2 sigma factor [Synechococcus sp. PCC 7002]
 gi|169884567|gb|ACA98280.1| Group 2 sigma factor [Synechococcus sp. PCC 7002]
          Length = 398

 Score = 92.4 bits (228), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 68/247 (27%), Positives = 123/247 (49%), Gaps = 35/247 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV KFDP +G+R +TY+ WW
Sbjct: 159 AKEHMIQANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVDKFDPTKGYRFSTYAYWW 218

Query: 109 IKAAMQEYILRSWSLVKIGTTANQ-----KRLFFNLRRLKGHLQAITDN----NLKPEQV 159
           I+  +   I      +++     +     K+    + + +G   ++ D      + PEQV
Sbjct: 219 IRQGITRAIATQSRTIRLPVHVTEKLNKIKKAQRQISQTQGCTPSLDDVAQALEMTPEQV 278

Query: 160 VAIAKKLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
             + +K+  S    +S+  R+  D    L  L+ + D +               E+ L+ 
Sbjct: 279 REVLQKVPRS----VSLEIRVGKDRDTELGDLLETQDASP--------------EENLVR 320

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT--LENLSSEFEVSRERVRQIEAR 275
           +  +++  N+LT     L  RER + + R    +  T  L  +    E+SRERVRQIEA+
Sbjct: 321 ESLQRDLHNLLTE----LTDREREVIQLRYGLGDGKTYSLAEIGRMLELSRERVRQIEAK 376

Query: 276 AFKKVQE 282
           A +K+++
Sbjct: 377 ALQKLRQ 383


>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 = 92.4 bits (228), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 120/234 (51%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 383 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 442

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   +A+++ +
Sbjct: 443 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREATPEE---LAERMGM 497

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ +   
Sbjct: 498 PEDKIRKV-LKIAK-EPISMETPIGDDDDSHLGDFI---EDSTLELPLDSATAQSLKAAT 552

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 553 HEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 606


>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 = 92.4 bits (228), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 70/245 (28%), Positives = 116/245 (47%), Gaps = 32/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 499 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 558

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +   +PE  V +A+K+ +
Sbjct: 559 IRQAITRSIADQARTIRI--PVHMIETINKMNRIS--RQILQETGQEPEPAV-LAQKMEM 613

Query: 169 SESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            E ++          ISM   +  DE  +      D  +    D  VY            
Sbjct: 614 PEEKIRKILKISKEPISMETPIGDDEDSHLGDFIEDAATMAPADAAVY------------ 661

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARA 276
               + R +    +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A
Sbjct: 662 ---ASLRGVTKDILDSLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKA 718

Query: 277 FKKVQ 281
            +K++
Sbjct: 719 LRKLR 723


>gi|320181954|gb|EFW56860.1| RNA polymerase sigma factor RpoH [Shigella boydii ATCC 9905]
          Length = 186

 Score = 92.4 bits (228), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 67/202 (33%), Positives = 106/202 (52%), Gaps = 32/202 (15%)

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
            RL ++++ WIKA + EY+LR+W +VK+ TT  Q++LFFNLR+ K  L          ++
Sbjct: 1   MRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRL-----GWFNQDE 55

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDE--------------SLNALINSSDKNSSQWQDWL 204
           V  +A++L V+  +V  M  R+A  +               +  ++   DK SS + D  
Sbjct: 56  VEMVARELGVTSKDVREMESRMAAQDMTFDLSSDDDSDSQPMAPVLYLQDK-SSNFAD-G 113

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE-NPVTLENLSSEFE 263
           + D + +EQ            N LT +M  L+ R + I  AR L E N  TL+ L+  + 
Sbjct: 114 IEDDNWEEQAA----------NRLTDAMQGLDERSQDIIRARWLDEDNKSTLQELADRYG 163

Query: 264 VSRERVRQIEARAFKKVQESIQ 285
           VS ERVRQ+E  A KK++ +I+
Sbjct: 164 VSAERVRQLEKNAMKKLRAAIE 185


>gi|227488750|ref|ZP_03919066.1| RNA polymerase sigma factor A [Corynebacterium glucuronolyticum
           ATCC 51867]
 gi|227091172|gb|EEI26484.1| RNA polymerase sigma factor A [Corynebacterium glucuronolyticum
           ATCC 51867]
          Length = 599

 Score = 92.4 bits (228), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 81/323 (25%), Positives = 154/323 (47%), Gaps = 48/323 (14%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREH------------- 44
           RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR     Y  H             
Sbjct: 282 RKDAELTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYATHLLNQFKDPEWLES 340

Query: 45  ---------GDL--------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
                     DL         A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL+
Sbjct: 341 HEKPANSQKKDLRTVARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLI 400

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV+KFD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L 
Sbjct: 401 RAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELL 458

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                   P++   +AK+++++E +V+ +        SL+  I   D+  SQ  D++   
Sbjct: 459 QDLGREPTPQE---LAKEMDITEEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI--- 510

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVS 265
            D +  V ++       ++ L   +  L+ RE  + + R  L +  P TL+ +   + V+
Sbjct: 511 EDSEAVVAVDAVSFTLLQDQLQDVLKTLSEREAGVVKLRFGLTDGMPRTLDEIGQVYGVT 570

Query: 266 RERVRQIEARAFKKVQESIQKQV 288
           RER+RQIE++   K++   + QV
Sbjct: 571 RERIRQIESKTMSKLRHPSRSQV 593


>gi|319789700|ref|YP_004151333.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermovibrio
           ammonificans HB-1]
 gi|317114202|gb|ADU96692.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermovibrio
           ammonificans HB-1]
          Length = 563

 Score = 92.4 bits (228), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 82/256 (32%), Positives = 128/256 (50%), Gaps = 50/256 (19%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   LV S+LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 325 AKQILVRSNLRLVVSIAKKYINRGLHFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 384

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++F  + R             KPE+ 
Sbjct: 385 IRQAITRAIADQARTIRIPVHMIETINKVIKISRQMFQEMGR-----------EPKPEE- 432

Query: 160 VAIAKKLNVSESEVISMNCRLA----------GDESLNALINSSDKNSSQWQDWLVYDHD 209
             IA++L +  S+V S+  +LA          GD+  + L N  +   S   +  V   D
Sbjct: 433 --IAERLKMPASKVRSI-LQLAQEPVSLETPIGDDEDSTLGNFIEDTKSPIPEQEVIKKD 489

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRE 267
            QE+V              ++ +S L+ RE  + + R  L   P  TLE +  E +V+RE
Sbjct: 490 LQEKV--------------SQLLSQLSEREALVLKLRFGLDGYPEHTLEQVGKELKVTRE 535

Query: 268 RVRQIEARAFKKVQES 283
           R+RQIE++A +K++ S
Sbjct: 536 RIRQIESKALRKLRNS 551


>gi|172038507|ref|YP_001805008.1| RNA polymerase sigma factor SigD [Cyanothece sp. ATCC 51142]
 gi|171699961|gb|ACB52942.1| group 2 sigma-70 RNA polymerase sigma factor D [Cyanothece sp. ATCC
           51142]
          Length = 318

 Score = 92.4 bits (228), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 78/307 (25%), Positives = 138/307 (44%), Gaps = 60/307 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR------------------------------------ 42
           Y+ EI ++P+L  +EE + AKR +                                    
Sbjct: 14  YLKEIGRVPLLTHEEEILYAKRVQRLVNLEKLREEIIEETGQEPTESQWAKAAKLSKREF 73

Query: 43  ----EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
               E G+ +A  ++V ++LRLVV +A  Y    L + +++ EG IG+ + V+KFDP +G
Sbjct: 74  RSIVESGE-AAKRKMVEANLRLVVSVAKKYLKRNLDLLDLIQEGTIGMQRGVEKFDPTKG 132

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           +R +TY+ WWI+ A+   I      +++     +K     L ++K   + ++    +   
Sbjct: 133 YRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEK-----LNKIKKAQRELSQQKGRAAT 187

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           V  +A++L+++  +V     R     SL+  +   D   ++  D L  + DGQ       
Sbjct: 188 VTELAEELDLTPKQVREYLERARQPLSLD--LRVGDNQDTELGDLL--EDDGQ-----SP 238

Query: 219 EERKNRRNM---LTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIE 273
           E+     ++   L R M  L  +++ +   R   L   P+TL  + S   +SRERVRQIE
Sbjct: 239 EDFATHSSLQFDLERLMEDLTSQQKEVIALRFGLLDGQPLTLAKIGSRLNISRERVRQIE 298

Query: 274 ARAFKKV 280
             A  K+
Sbjct: 299 REALSKL 305


>gi|254362696|ref|ZP_04978782.1| DNA-directed RNA polymerase sigma subunit RpoD [Mannheimia
           haemolytica PHL213]
 gi|153094317|gb|EDN75178.1| DNA-directed RNA polymerase sigma subunit RpoD [Mannheimia
           haemolytica PHL213]
          Length = 623

 Score = 92.4 bits (228), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 119/234 (50%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 385 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 444

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+             PE+   +A+++ +
Sbjct: 445 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQCLQEMGREATPEE---LAERMGM 499

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ R   
Sbjct: 500 PEDKIRKV-LKIAK-EPISMETPIGDDDDSHLGDFI---QDESLELPLDSATAESLRMAT 554

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 555 NEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 608


>gi|39939114|ref|NP_950880.1| DNA-directed RNA polymerase sigma subunit [Onion yellows
           phytoplasma OY-M]
 gi|39722223|dbj|BAD04713.1| DNA-directed RNA polymerase sigma subunit [Onion yellows
           phytoplasma OY-M]
          Length = 460

 Score = 92.4 bits (228), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 84/303 (27%), Positives = 142/303 (46%), Gaps = 57/303 (18%)

Query: 19  YIHEIRKIPMLEKQEE------YVLAKRYRE--------------------HGDLSAAHR 52
           Y+ EI +IP+L   EE        L K+ ++                    H  +  A R
Sbjct: 157 YLKEIGQIPLLSLAEEQKKSILVFLGKQAKQKLAKHKTKEIELSEEQLQEAHDQIEQARR 216

Query: 53  ----LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
               LV S+ RLVV IA  Y G G+   +++ EGN+GLM+AV KFD ++GF+ +TY+ WW
Sbjct: 217 AKDILVESNYRLVVSIAKRYIGRGILFLDLIQEGNMGLMRAVDKFDYQKGFKFSTYATWW 276

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N  ++    R+L   L+       K   V  +A 
Sbjct: 277 IRQAITRAIADQARTIRIPVHIVETIN--KMALCTRKLTQKLK-------KKPTVEELAD 327

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW-----LVYDHDGQEQVLIEKE 219
           K+N+S  ++ S+        SL A    ++++ +   D+     ++  H+   + + +K 
Sbjct: 328 KMNISAEKIRSIQYIEKKPISLEAPARENEEDETSLGDFISDPNILSPHEYMMKEVTQKL 387

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAF 277
             +   N LT        RE ++ + R   L     TLE + + F V+RER+RQIE++A 
Sbjct: 388 LDEVLENTLT-------DREEKVLKMRYGLLDGKTHTLEEVGTLFGVTRERIRQIESKAL 440

Query: 278 KKV 280
           +++
Sbjct: 441 RRL 443


>gi|84394590|ref|ZP_00993293.1| RNA polymerase sigma factor [Vibrio splendidus 12B01]
 gi|84374781|gb|EAP91725.1| RNA polymerase sigma factor [Vibrio splendidus 12B01]
          Length = 573

 Score = 92.4 bits (228), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 70/243 (28%), Positives = 117/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 335 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 394

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 395 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 452

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 453 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 496

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + R      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 497 ATSLRGATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 556

Query: 279 KVQ 281
           K++
Sbjct: 557 KLR 559


>gi|227542254|ref|ZP_03972303.1| RNA polymerase sigma factor A [Corynebacterium glucuronolyticum
           ATCC 51866]
 gi|227182083|gb|EEI63055.1| RNA polymerase sigma factor A [Corynebacterium glucuronolyticum
           ATCC 51866]
          Length = 603

 Score = 92.4 bits (228), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 81/323 (25%), Positives = 154/323 (47%), Gaps = 48/323 (14%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREH------------- 44
           RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR     Y  H             
Sbjct: 286 RKDAELTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYATHLLNQFKDPEWLES 344

Query: 45  ---------GDL--------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
                     DL         A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL+
Sbjct: 345 HEKPANSQKKDLRTVARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLI 404

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV+KFD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L 
Sbjct: 405 RAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELL 462

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                   P++   +AK+++++E +V+ +        SL+  I   D+  SQ  D++   
Sbjct: 463 QDLGREPTPQE---LAKEMDITEEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI--- 514

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVS 265
            D +  V ++       ++ L   +  L+ RE  + + R  L +  P TL+ +   + V+
Sbjct: 515 EDSEAVVAVDAVSFTLLQDQLQDVLKTLSEREAGVVKLRFGLTDGMPRTLDEIGQVYGVT 574

Query: 266 RERVRQIEARAFKKVQESIQKQV 288
           RER+RQIE++   K++   + QV
Sbjct: 575 RERIRQIESKTMSKLRHPSRSQV 597


>gi|296393381|ref|YP_003658265.1| RpoD subfamily RNA polymerase sigma-70 factor [Segniliparus
           rotundus DSM 44985]
 gi|296180528|gb|ADG97434.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Segniliparus
           rotundus DSM 44985]
          Length = 441

 Score = 92.4 bits (228), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 78/318 (24%), Positives = 147/318 (46%), Gaps = 43/318 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGDL-- 47
           RKN  +  + +  +  Y+ +I K+ +L  ++E  LAKR               E GD   
Sbjct: 129 RKNAELTASAD-SVRAYLKQIGKVALLNAEQEVELAKRIEAGLYAQERLRIAAEEGDRLP 187

Query: 48  ---------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 188 TTSRRDLNWVVRDGNRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 247

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L      
Sbjct: 248 FDYSKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGR 305

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE+   + +++++   +V+ +        SL+  I   D+  SQ  D++    D + 
Sbjct: 306 EPTPEE---LGREMDIPPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEA 357

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVR 270
            V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 358 VVAVDAVSFTLLQDQLQAVLETLSEREAGVVRMRFGLTDGQPRTLDEIGQVYGVTRERIR 417

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 418 QIESKTMSKLRHPSRSQV 435


>gi|320159820|ref|YP_004173044.1| RNA polymerase sigma factor [Anaerolinea thermophila UNI-1]
 gi|319993673|dbj|BAJ62444.1| RNA polymerase sigma factor [Anaerolinea thermophila UNI-1]
          Length = 396

 Score = 92.4 bits (228), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 82/297 (27%), Positives = 134/297 (45%), Gaps = 44/297 (14%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------------REHGDL- 47
           I  +  +GL  Y+ E+ ++P+L  +EE  LAKR                    +  G+L 
Sbjct: 93  ISSDDTVGL--YLKEMSRVPLLSSEEEVELAKRIERGRAAKKELTRNSARLSPQRRGELE 150

Query: 48  -------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
                  SA   L+ ++ RLVV IA  Y G G+P  +++ EGN+GLM+AV+K++ +RGFR
Sbjct: 151 AQIQDGESAREHLIKANTRLVVSIAKRYIGRGVPFLDLIQEGNLGLMKAVEKYEYQRGFR 210

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGT--TANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
            +TY+ WWI+  +   I      +++        +RL+     ++  L     N      
Sbjct: 211 FSTYATWWIRQTITRSIADQGRTIRVPVHMVDRIRRLYRTTHEMEQKLGRTPTNE----- 265

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              +A  + +  S+V  M        SL + IN  +++S   Q    +  D      ++ 
Sbjct: 266 --ELADAIGIKASKVDWMMRVSWLPLSLESPINEDEEDSELGQ----FIEDQVTPSPMQT 319

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIE 273
                 R  +   +  L  RE RI   R   EN    TLE +  +F ++RER+RQIE
Sbjct: 320 TYSNLLREKIQEVLDTLPAREARILRLRFGLENGRTYTLEEVGQKFGLTRERIRQIE 376


>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 = 92.4 bits (228), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 64/236 (27%), Positives = 117/236 (49%), Gaps = 12/236 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L A   ++ ++LRLV+ IA  Y   G+   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 423 LQAKREMIEANLRLVISIAKKYVNRGMHFLDLIQEGNIGLMKAVDKFEYRRGWKFSTYAT 482

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WW++ A+   +      ++I    +       L R+   +   T     P     +A+++
Sbjct: 483 WWVRQAVTRSLADQARTIRI--PVHMMESINKLNRISREILQQTGREAHP---AVLAQRM 537

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            V E +V +M     G + L+      D+  +   D +    D       +   + N R 
Sbjct: 538 EVPEEKVRAM--LKIGRQPLSLETPVGDEADTTLSDVI---EDPMATSPADAAVQANLRA 592

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKV 280
            +  ++  L+PRE ++   R   +     TLE L  +F+++RER+RQIE++A +K+
Sbjct: 593 AINTALDALSPREAKVLRMRFGIDTASDCTLEELGKQFDLTRERIRQIESKAMRKL 648


>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 = 92.4 bits (228), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 73/251 (29%), Positives = 127/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 374 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 433

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 434 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 491

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 492 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 534

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             +N R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 535 TSENLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 594

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 595 RKLRHPSRSEV 605


>gi|86157148|ref|YP_463933.1| sigma 70 (RpoD) [Anaeromyxobacter dehalogenans 2CP-C]
 gi|85773659|gb|ABC80496.1| RNA polymerase, sigma 70 subunit, RpoD [Anaeromyxobacter
           dehalogenans 2CP-C]
          Length = 805

 Score = 92.4 bits (228), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 75/260 (28%), Positives = 122/260 (46%), Gaps = 33/260 (12%)

Query: 37  LAKRYREHGDLS-----AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           L + YR  GD       A   LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV 
Sbjct: 550 LRRTYRMIGDGERKAERAKTELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVD 609

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KF+ +RG++ +TY+ WWI+ A+   I      ++I    +       L R   +L     
Sbjct: 610 KFEYKRGYKFSTYATWWIRQAITRAIADQARTIRI--PVHMIETINKLIRTSRYLVQELG 667

Query: 152 NNLKPEQVV--------AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
               PE++          + K L ++  E IS+   +  +E  +      DK+     D 
Sbjct: 668 REPTPEEIAEKMELPLDKVRKVLKIA-KEPISLETPIGEEEDSHLGDFIEDKSLVSPSDA 726

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSE 261
           ++                 N      + ++ L PRE ++   R    +++  TLE +  +
Sbjct: 727 VIN---------------MNLAEQTRKVLATLTPREEKVLRMRFGIGEKSDHTLEEVGQD 771

Query: 262 FEVSRERVRQIEARAFKKVQ 281
           FEV+RER+RQIEA+A +K++
Sbjct: 772 FEVTRERIRQIEAKALRKLR 791


>gi|58584650|ref|YP_198223.1| DNA-directed RNA polymerase sigma 70 subunit, RpoD [Wolbachia
           endosymbiont strain TRS of Brugia malayi]
 gi|58418966|gb|AAW70981.1| DNA-directed RNA polymerase sigma 70 subunit, RpoD [Wolbachia
           endosymbiont strain TRS of Brugia malayi]
          Length = 649

 Score = 92.4 bits (228), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 78/262 (29%), Positives = 137/262 (52%), Gaps = 29/262 (11%)

Query: 32  QEEYVLAKRYREHG-DLSAAHR-LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           QE   L KR ++H  ++S A + ++ ++LRLVV IA  Y   GL + +++ EGNIGLM+A
Sbjct: 393 QEFKELIKRTQKHEREVSEAKQGMIKANLRLVVSIAKKYSNRGLALLDLIQEGNIGLMKA 452

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V KFD +RG++ +TY  WW++ ++   I     +V+I        +   + ++   L+ +
Sbjct: 453 VDKFDYKRGYKFSTYGTWWVRQSITRAIPEQSKVVRIPV-----HMVEIISKINRALRKL 507

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDH 208
           T    +   +  ++ +L +   E I    ++A D  SL+A     D  SS + D +    
Sbjct: 508 THEMGREPTLEELSMELGMP-LERIRKVMKIARDPVSLDAPTGKDD--SSTFGDCI---- 560

Query: 209 DGQEQVLIEKEER----KNRRNMLTRSMSVLNPRERRIFEAR-----RLQENPVTLENLS 259
              E   + K E      + R + T  ++ L P+E RI   R       +E+  TLE + 
Sbjct: 561 ---EDKRVSKPEDAAILTDLRCITTNLLATLTPKEERIIRMRFGLGKDCKEH--TLEEIG 615

Query: 260 SEFEVSRERVRQIEARAFKKVQ 281
             F+V+RER+RQ+E++A +K++
Sbjct: 616 CIFKVTRERIRQVESKALRKLK 637


>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 = 92.4 bits (228), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 119/234 (50%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 385 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 444

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+             PE+   +A+++ +
Sbjct: 445 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQCLQEMGREATPEE---LAERMGM 499

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ R   
Sbjct: 500 PEDKIRKV-LKIA-KEPISMETPIGDDDDSHLGDFI---QDESLELPLDSATAESLRMAT 554

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 555 NEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 608


>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 = 92.0 bits (227), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 370 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 429

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +        +P++   +A+++ +
Sbjct: 430 IRQAITRSIADQARTIRI--PVHMIETINKLNRTSRQMLQEMGREPQPDE---LAERMEM 484

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E +V  +  ++A  E ++      D   S   D++    D      ++   R+  +  +
Sbjct: 485 PEDKVRKV-LKIA-KEPISMETPIGDDEDSHLGDFI---EDAAVMSPVDSATREGLKESV 539

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 540 REVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 594


>gi|58698250|ref|ZP_00373169.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of
           Drosophila ananassae]
 gi|58535222|gb|EAL59302.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of
           Drosophila ananassae]
          Length = 270

 Score = 92.0 bits (227), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 75/260 (28%), Positives = 128/260 (49%), Gaps = 25/260 (9%)

Query: 32  QEEYVLAKRYREHG-DLS-AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           QE   L KR ++H  ++S A   ++ ++LRLVV IA  Y   GL + +++ EGNIGLM+A
Sbjct: 14  QEFKELIKRIQKHEREVSEAKQEMIKANLRLVVSIAKKYSKRGLDLLDLIQEGNIGLMKA 73

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ--KRLFFNLRRLKGHL- 146
           V KFD +RG++ +TY  WW++ ++   I     +V+I     +   ++   LR++   + 
Sbjct: 74  VDKFDYKRGYKFSTYGTWWVRQSITRAIPEQSKVVRIPVHMVEIISKINRALRKMTHEMG 133

Query: 147 QAITDNNLKPEQVVAIAK--KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
           +  T   L  E  + + +  K+     + +S+      D+S        DK  S+ +D  
Sbjct: 134 REPTLEELSVELTMPLERIRKVMKIARDPVSLEAPTGKDDSSTFGDCIEDKRVSRPEDAA 193

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSE 261
           +                 + R + T  ++ L P+E RI   R          TLE +   
Sbjct: 194 IL---------------ADLRGITTNVLATLTPKEERILRMRFGLGKDGKEHTLEEVGKI 238

Query: 262 FEVSRERVRQIEARAFKKVQ 281
           F V+RER+RQIEA+A +K++
Sbjct: 239 FNVTRERIRQIEAKALRKLK 258


>gi|254232809|ref|ZP_04926136.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis C]
 gi|124601868|gb|EAY60878.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis C]
          Length = 528

 Score = 92.0 bits (227), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 81/318 (25%), Positives = 150/318 (47%), Gaps = 43/318 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGD-LS 48
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+ L 
Sbjct: 216 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSERGEKLP 274

Query: 49  AAHR----------------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           AA R                L+ ++LRLVV +A  Y G G+   +++ EGN+ L++AV+K
Sbjct: 275 AAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLRLIRAVEK 334

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L      
Sbjct: 335 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGR 392

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D + 
Sbjct: 393 EPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEA 444

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVR 270
            V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 445 VVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIR 504

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 505 QIESKTMSKLRHPSRSQV 522


>gi|116075407|ref|ZP_01472667.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9916]
 gi|116067604|gb|EAU73358.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9916]
          Length = 310

 Score = 92.0 bits (227), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 76/251 (30%), Positives = 127/251 (50%), Gaps = 16/251 (6%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           KR  + G+  A ++++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG
Sbjct: 57  KRTIKKGE-KAKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRG 115

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
            R +TY+ WWI+  +   +      ++I    N+K     LR  K  L         P Q
Sbjct: 116 HRFSTYAYWWIRQGLNRALSTQSRTIRIPVNVNEK--LTKLRAAKARLMQRNGQAATPAQ 173

Query: 159 VVAIAKKLNVSESEVIS-MNCRL-AGDESLNALINSSDKNSSQWQDWLVYDH-DGQEQVL 215
              +A+ + +S +EV   + C L +   SL  ++ S   + S+  D L  +     EQ  
Sbjct: 174 ---LAEAMQISRAEVDDLLGCELRSVTVSLQGIVKSKS-DPSELVDVLPSEELPPMEQAE 229

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQI 272
           I+ E   +   +L RS   L P+ER +   R   +      TL  ++     SRE  RQ+
Sbjct: 230 ID-ERTASAWTLLDRSN--LTPKERTVVMLRFGLDGSNEWRTLAEVARHMGCSREYCRQV 286

Query: 273 EARAFKKVQES 283
             RA +K+++S
Sbjct: 287 VQRALRKLRKS 297


>gi|15240693|ref|NP_196877.1| SIG4 (SIGMA FACTOR 4); DNA binding / DNA-directed RNA polymerase/
           sigma factor/ transcription factor [Arabidopsis
           thaliana]
 gi|3983260|gb|AAC97954.1| sigma-like factor [Arabidopsis thaliana]
 gi|4972296|dbj|BAA78110.1| RNA polymerase sigma subunit SigD [Arabidopsis thaliana]
 gi|9758039|dbj|BAB08700.1| sigma-like factor [Arabidopsis thaliana]
 gi|332004550|gb|AED91933.1| sigma factor 4 [Arabidopsis thaliana]
          Length = 419

 Score = 92.0 bits (227), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 74/249 (29%), Positives = 128/249 (51%), Gaps = 40/249 (16%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++   + RLVV IA GY+G GL + +++ EG+IGL++  ++FDP+RG++L+TY  WW
Sbjct: 179 AREKITRCYRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWW 238

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA------- 161
           IK A    ILR+         A++ RL     +L G +  +T    +   V+        
Sbjct: 239 IKQA----ILRA--------IAHKSRLV----KLPGSMWELTAKVAEASNVLTRKLRRQP 282

Query: 162 ----IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ-----WQDWLVYDHDGQE 212
               IA+ LN++ S V     RLA + S + +  S D+ +SQ      Q+ +    + + 
Sbjct: 283 SCEEIAEHLNLNVSAV-----RLAVERSRSPV--SLDRVASQNGRMTLQEIVRGPDETRP 335

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           + ++++E  K+    L  S++    R   ++      E P++ E +    ++SRERVRQI
Sbjct: 336 EEMVKREHMKHEIEQLLGSLTARESRVLGLYFGLN-GETPMSFEEIGKSLKLSRERVRQI 394

Query: 273 EARAFKKVQ 281
              A KK++
Sbjct: 395 NGIALKKLR 403


>gi|95928999|ref|ZP_01311744.1| RNA polymerase, sigma 38 subunit, RpoS [Desulfuromonas acetoxidans
           DSM 684]
 gi|95134900|gb|EAT16554.1| RNA polymerase, sigma 38 subunit, RpoS [Desulfuromonas acetoxidans
           DSM 684]
          Length = 583

 Score = 92.0 bits (227), Expect = 8e-17,   Method: Compositional matrix adjust.
 Identities = 77/251 (30%), Positives = 122/251 (48%), Gaps = 44/251 (17%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ W
Sbjct: 343 AAKTELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATW 402

Query: 108 WIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHL------QAITDNNLKP- 156
           WI+ A+   I      ++I      T N  +L    R+L   L      + I +    P 
Sbjct: 403 WIRQAITRAIADQARTIRIPVHMIETIN--KLIRTSRQLVQELGREPIPEEIAERMDLPL 460

Query: 157 ---EQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQ 211
               +V+ IAK       E IS+   +  +E  SL   I   DK +    + ++      
Sbjct: 461 EKVRRVLKIAK-------EPISLETPIGEEEDSSLGDFIE--DKGAVSPLEAVI------ 505

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERV 269
                    + N  +     +S L+PRE ++   R    + +  TLE +  +F V+RER+
Sbjct: 506 ---------KGNLSDQTAEVLSTLSPREEKVLRMRFGIGERSDHTLEEVGQDFNVTRERI 556

Query: 270 RQIEARAFKKV 280
           RQIEA+A +K+
Sbjct: 557 RQIEAKALRKL 567


>gi|260762514|ref|ZP_05874851.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 2 str.
           86/8/59]
 gi|260672940|gb|EEX59761.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 2 str.
           86/8/59]
          Length = 131

 Score = 92.0 bits (227), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 36/82 (43%), Positives = 59/82 (71%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE++EE  LA R++E  D  A HR+ ++H+RLV+ +A  +R + LP+S+++ EG +GL
Sbjct: 50  PYLEREEERALAIRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGL 109

Query: 87  MQAVKKFDPERGFRLATYSMWW 108
           ++A  +FDP+R  R +TY+ WW
Sbjct: 110 LEAAARFDPDRDVRFSTYASWW 131


>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]
          Length = 628

 Score = 92.0 bits (227), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 70/245 (28%), Positives = 115/245 (46%), Gaps = 32/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 389 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 448

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV--------V 160
           I+ A+   I      ++I    +       + R+   L         PE++        V
Sbjct: 449 IRQAITRSIADQARTIRI--PVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEV 506

Query: 161 AIAKKLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            + K L +++ E ISM   +  DE   L   I  S+  S                  I+ 
Sbjct: 507 KVRKVLKIAK-EPISMETPIGDDEDSHLGDFIEDSNITSP-----------------IDA 548

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARA 276
              +  +      +  L  RE ++ + R   + P   TLE +  +F+V+RER+RQIEA+A
Sbjct: 549 ATSEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKA 608

Query: 277 FKKVQ 281
            +K++
Sbjct: 609 LRKLR 613


>gi|86742187|ref|YP_482587.1| sigma 38 [Frankia sp. CcI3]
 gi|86569049|gb|ABD12858.1| sigma 38 [Frankia sp. CcI3]
          Length = 422

 Score = 92.0 bits (227), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 86/302 (28%), Positives = 140/302 (46%), Gaps = 60/302 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRY---------------------REHGDL-----SAAHR 52
           Y+ EI K+P+L   +E  L+KR                      R+ G L     +A  +
Sbjct: 129 YLREIGKVPLLNAAQEVELSKRVEAGLFAEYKLESVPDLPADLRRDLGLLVKDGHAAKQQ 188

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV+++LRLVV +A  Y G G+ + ++V EGN+GL++AV+KFD  +G++ +TY+ WWI+ A
Sbjct: 189 LVSANLRLVVSVAKKYSGRGMTLLDLVQEGNLGLIRAVEKFDYAKGYKFSTYATWWIRQA 248

Query: 113 MQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           +   +      ++I           T  Q++L   L R     +   + ++  EQVV   
Sbjct: 249 IGRALADQARTIRIPVHVVEQINKITRLQRQLVSTLGREPTDEELALELDMPIEQVV--- 305

Query: 164 KKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
            +L     + +S+   +   GD  L   I  SD  S    D   Y   G  Q  IE    
Sbjct: 306 -ELRRYAQDTVSLETSVGDDGDSVLGDFIEDSDATSP--ADAASY---GAMQDEIE---- 355

Query: 222 KNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKK 279
               N+L      L+PRER +   R  L +    TL  + +   ++RER+RQIE    ++
Sbjct: 356 ----NVL----GGLSPREREVMRLRFGLADGKQHTLAEVGNRLGLTRERIRQIERDTLRE 407

Query: 280 VQ 281
           ++
Sbjct: 408 LR 409


>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 = 92.0 bits (227), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 118/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 372 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 431

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA------- 161
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 432 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREATPEELAVRMDMPED 489

Query: 162 -IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++  + DG E   ++   
Sbjct: 490 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI--EDDGAESP-VDTAT 533

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            +  +   T  ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 534 IEGLKESTTTVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 593

Query: 279 KVQ 281
           K++
Sbjct: 594 KLR 596


>gi|317506483|ref|ZP_07964284.1| RNA polymerase sigma factor RpoD [Segniliparus rugosus ATCC
           BAA-974]
 gi|316255244|gb|EFV14513.1| RNA polymerase sigma factor RpoD [Segniliparus rugosus ATCC
           BAA-974]
          Length = 452

 Score = 92.0 bits (227), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 78/318 (24%), Positives = 147/318 (46%), Gaps = 43/318 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGDL-- 47
           RKN  +  + +  +  Y+ +I K+ +L  ++E  LAKR               E GD   
Sbjct: 140 RKNAELTASAD-SVRAYLKQIGKVALLNAEQEVELAKRIEAGLYAQERLRIATEEGDRLP 198

Query: 48  ---------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 199 TTSRRDMNWVVRDGNRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 258

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L      
Sbjct: 259 FDYSKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGR 316

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE+   + +++++   +V+ +        SL+  I   D+  SQ  D++    D + 
Sbjct: 317 EPTPEE---LGREMDIPPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEA 368

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVR 270
            V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 369 VVAVDAVSFTLLQDQLQAVLETLSEREAGVVRMRFGLTDGQPRTLDEIGQVYGVTRERIR 428

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 429 QIESKTMSKLRHPSRSQV 446


>gi|254698074|ref|ZP_05159902.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 2 str.
           86/8/59]
          Length = 118

 Score = 92.0 bits (227), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 36/82 (43%), Positives = 59/82 (71%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE++EE  LA R++E  D  A HR+ ++H+RLV+ +A  +R + LP+S+++ EG +GL
Sbjct: 37  PYLEREEERALAIRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLIQEGYVGL 96

Query: 87  MQAVKKFDPERGFRLATYSMWW 108
           ++A  +FDP+R  R +TY+ WW
Sbjct: 97  LEAAARFDPDRDVRFSTYASWW 118


>gi|149923522|ref|ZP_01911923.1| RNA polymerase sigma factor RpoD [Plesiocystis pacifica SIR-1]
 gi|149815591|gb|EDM75122.1| RNA polymerase sigma factor RpoD [Plesiocystis pacifica SIR-1]
          Length = 589

 Score = 92.0 bits (227), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 75/256 (29%), Positives = 123/256 (48%), Gaps = 37/256 (14%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           + R   D + A  LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG+
Sbjct: 342 KARRQADRAKAE-LVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYKRGY 400

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLK 155
           + +TY+ WWI+ A+   I      ++I      T N  +L    R L   L         
Sbjct: 401 KFSTYATWWIRQAITRAIADQARTIRIPVHMIETIN--KLIRTSRSLVQEL----GREPT 454

Query: 156 PEQVV--------AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
           PE++          + K L +++ E IS+   +  +E  +      DKN+    + ++  
Sbjct: 455 PEEIAEKMELPLDKVRKVLKIAK-EPISLETPIGEEEDSHLGDFIEDKNAVSPAEVVI-- 511

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVS 265
                          N  +   R ++ L PRE ++   R    + +  TLE +  +F V+
Sbjct: 512 -------------NINLADQTRRVLATLTPREEKVLRMRFGIGETSDHTLEEVGQDFSVT 558

Query: 266 RERVRQIEARAFKKVQ 281
           RER+RQIEA+A +K++
Sbjct: 559 RERIRQIEAKALRKLR 574


>gi|148243538|ref|YP_001228695.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp.
           RCC307]
 gi|147851848|emb|CAK29342.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. RCC307]
          Length = 370

 Score = 92.0 bits (227), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 69/238 (28%), Positives = 118/238 (49%), Gaps = 19/238 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R++ ++LRLVV +A  Y+  G+ + ++V EG +GL + V+K+DP RGFR +TY+ WW
Sbjct: 131 AKERMIQANLRLVVAVAKKYQHRGMELLDLVQEGTLGLERGVEKYDPTRGFRFSTYAYWW 190

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   I      +++     +K     L R+K   + I     +   +  ++++L +
Sbjct: 191 IRQGITRAIATQSRTIRLPVHITEK-----LNRIKKAQRDIASRLGRTATLKDLSQELQL 245

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SE  V     R+    SL+  +       ++  D L    DG    +   E+R  R  + 
Sbjct: 246 SEEVVRQTLMRVPRSVSLDTRVGRD--MDTELGDLL---EDG----MPTPEQRLTREKLH 296

Query: 229 TRSMSVLNP---RERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              + +LN    RE R+   R     + P TL  +    ++SRERVRQIE+RA  K++
Sbjct: 297 DDLLVLLNELSGREARVIRLRFGLDDDTPQTLAEIGKTLDLSRERVRQIESRALHKLR 354


>gi|303235620|ref|ZP_07322227.1| RNA polymerase sigma factor RpoD family protein [Prevotella disiens
           FB035-09AN]
 gi|302484067|gb|EFL47055.1| RNA polymerase sigma factor RpoD family protein [Prevotella disiens
           FB035-09AN]
          Length = 290

 Score = 92.0 bits (227), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 76/272 (27%), Positives = 136/272 (50%), Gaps = 12/272 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYG 72
            L +Y+ EI + PM+   EE  LA+   + G     A  +L+ ++LR VV +A  Y+  G
Sbjct: 17  ALDKYLVEIGREPMITVDEEIELAQEIHKGGRKGERAKEKLIKANLRFVVSVAKQYQHQG 76

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V++    NQ
Sbjct: 77  LSLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRL--PLNQ 134

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 + ++      I  +N +P  +  +A    + E+ +           S++A  + 
Sbjct: 135 VGAISKINQVSNEF--IQKHNRRP-SIHELADLTGIDEARIRQSQSADNHHMSIDAPFSD 191

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI-FEARRLQEN 251
            D NS      L    D +    ++ E   +  N + +  + L  RERRI  E   +   
Sbjct: 192 DDDNSMSDM--LASGDDSRTDKAVDFESMSDDLNAVLQ--NTLKDRERRIVIECFGIGCP 247

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
              LE + +E  ++RERVRQI  +A +K++ S
Sbjct: 248 EKGLEEIGTEMALTRERVRQIREKAIEKIRLS 279


>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 = 92.0 bits (227), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 70/243 (28%), Positives = 115/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 391 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 450

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV--------V 160
           I+ A+   I      ++I    +       + R+   L         PE++        V
Sbjct: 451 IRQAITRSIADQARTIRI--PVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEV 508

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + K L +++ E ISM   +  DE             S   D++    D      I+   
Sbjct: 509 KVRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDQNITSPIDAAT 552

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFK 278
            K  +      +  L  RE ++ + R   + P   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 553 SKGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALR 612

Query: 279 KVQ 281
           K++
Sbjct: 613 KLR 615


>gi|307151291|ref|YP_003886675.1| RpoD subfamily RNA polymerase sigma-70 factor [Cyanothece sp. PCC
           7822]
 gi|306981519|gb|ADN13400.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7822]
          Length = 318

 Score = 92.0 bits (227), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 77/314 (24%), Positives = 138/314 (43%), Gaps = 72/314 (22%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR---------------------EH------------- 44
           Y+ EI ++P+L  +EE VLAKR +                     EH             
Sbjct: 14  YLREIGRVPLLTHEEEIVLAKRVQRSMALQEIKDTLTKNLSREPLEHEWAEAAKISEEEL 73

Query: 45  -----GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                   +A  ++V ++LRLVV +A  Y    L + +++ EG IG+ + V+KFDP +G+
Sbjct: 74  RRTMAAGKAAKEKMVEANLRLVVSVAKKYLKRNLDLLDLIQEGTIGMQRGVEKFDPTKGY 133

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           R +TY+ WWI+ A+   I      +++     +K     L ++K   + +     +   +
Sbjct: 134 RFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEK-----LNKIKKAQRQLAQKQGRAATI 188

Query: 160 VAIAKKLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
             +A++L ++  +V          +S++ R+ GD     L    +   +  +D+  +   
Sbjct: 189 SELAQELELTPRQVREYLERARQPLSLDLRV-GDNQDTELGELLEDTGTSPEDYATH--- 244

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRE 267
              Q+ +EK             MS L P++R +   R   +   P+TL  +     +SRE
Sbjct: 245 SSLQLDLEK------------LMSDLTPQQREVLALRFGLVDGQPLTLAKIGVRLNISRE 292

Query: 268 RVRQIEARAFKKVQ 281
           RVRQIE  A  K++
Sbjct: 293 RVRQIEREALSKLR 306


>gi|212633971|ref|YP_002310496.1| RNA polymerase sigma factor [Shewanella piezotolerans WP3]
 gi|212555455|gb|ACJ27909.1| RNA polymerase sigma factor [Shewanella piezotolerans WP3]
          Length = 612

 Score = 92.0 bits (227), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 72/244 (29%), Positives = 124/244 (50%), Gaps = 30/244 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 374 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 433

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 434 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPSPEELAERMLMPED- 491

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 492 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 534

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ RN     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 535 TGESLRNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 594

Query: 278 KKVQ 281
           +K++
Sbjct: 595 RKLR 598


>gi|307718699|ref|YP_003874231.1| RNA polymerase sigma factor RpoD [Spirochaeta thermophila DSM 6192]
 gi|306532424|gb|ADN01958.1| RNA polymerase sigma factor RpoD [Spirochaeta thermophila DSM 6192]
          Length = 338

 Score = 92.0 bits (227), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 76/262 (29%), Positives = 129/262 (49%), Gaps = 35/262 (13%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           +EE  L +R RE       +R++T++LRLVV IA  Y+  GL + +++ EGNIGL++AV+
Sbjct: 90  EEERRLDQRLRE-----LKNRMITANLRLVVSIAKKYQHRGLSLLDLIDEGNIGLIEAVE 144

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           +FD  +G R +TY  WWI+ A+            + + A++ R+     R+  H+     
Sbjct: 145 RFDYTKGCRFSTYGTWWIRQAI------------VKSLADKSRVI----RIPIHMLNTIK 188

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNC----RLA-----GDESLNALINSSDKNSSQWQD 202
           N     + +A     + +E E+         R+A       E+ +  I   ++N +   D
Sbjct: 189 NVFMLSKELAQELGRDPTEEELSRYTGLPDRRVAEIMQVSQETASLDITVDEENMTTLGD 248

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSS 260
            +  D D   Q   EK   +   ++L  ++  L+ RER +   R     E P+TLE    
Sbjct: 249 LVSDDED---QGPFEKVFHRYLHDVLLEALGDLSERERNVISLRFGLNGEGPLTLEETGK 305

Query: 261 EFEVSRERVRQIEARAFKKVQE 282
              ++RERVRQI+ +A  K++E
Sbjct: 306 LLGITRERVRQIQEKALAKLRE 327


>gi|293376344|ref|ZP_06622581.1| RNA polymerase sigma factor RpoD [Turicibacter sanguinis PC909]
 gi|325843397|ref|ZP_08167955.1| RNA polymerase sigma factor RpoD [Turicibacter sp. HGF1]
 gi|292645033|gb|EFF63106.1| RNA polymerase sigma factor RpoD [Turicibacter sanguinis PC909]
 gi|325489319|gb|EGC91693.1| RNA polymerase sigma factor RpoD [Turicibacter sp. HGF1]
          Length = 456

 Score = 92.0 bits (227), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 82/257 (31%), Positives = 126/257 (49%), Gaps = 35/257 (13%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A+R  + G+  A  RLV ++LRLVV IA  + G G+   +++ EGN+GL++AV+KFD  +
Sbjct: 208 ARRVIQEGEY-AKKRLVEANLRLVVSIAKRHVGRGMLFLDLIQEGNMGLIKAVEKFDYRK 266

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN-----QKRLFFNLRRLKGHLQA 148
           GF+ +TY+ WWI+ A+   I      ++I      T N     Q++L   L R     + 
Sbjct: 267 GFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVRIQRQLVQELGREPLPEEI 326

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                + PE+V  I   L +S+  V           SL + +   D   S   D+ + D 
Sbjct: 327 SEKMGIAPEKVREI---LKISQEPV-----------SLESPVGEED--DSHLGDF-IPDA 369

Query: 209 DGQEQVLIEKEERKNR--RNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEV 264
           D     L   E   N   +  L   +  L  RE R+   R   E+    TLE +  EF V
Sbjct: 370 DA----LSPSEFASNEMLKKELDDVLETLTDREERVLRLRFGLEDGRTRTLEEVGKEFGV 425

Query: 265 SRERVRQIEARAFKKVQ 281
           +RER+RQIEA+A +K++
Sbjct: 426 TRERIRQIEAKALRKLR 442


>gi|293391709|ref|ZP_06636043.1| DNA-directed RNA polymerase sigma subunit RpoD [Aggregatibacter
           actinomycetemcomitans D7S-1]
 gi|290952243|gb|EFE02362.1| DNA-directed RNA polymerase sigma subunit RpoD [Aggregatibacter
           actinomycetemcomitans D7S-1]
          Length = 616

 Score = 92.0 bits (227), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 120/234 (51%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   +A+++ +
Sbjct: 438 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREASPEE---LAERMGM 492

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ +   
Sbjct: 493 PEDKIRKV-LKIA-KEPISMETPIGDDDDSHLGDFI---EDSTLELPLDSATVQSLKAAT 547

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 548 HEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 601


>gi|126660028|ref|ZP_01731150.1| RNA polymerase sigma-C factor [Cyanothece sp. CCY0110]
 gi|126618706|gb|EAZ89453.1| RNA polymerase sigma-C factor [Cyanothece sp. CCY0110]
          Length = 418

 Score = 92.0 bits (227), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 68/243 (27%), Positives = 127/243 (52%), Gaps = 23/243 (9%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           + A   ++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV+KFDP +G+R +TY+ 
Sbjct: 177 IRAKDEMIKANLRLVVSVAKKYQHRGLELLDLIQEGTLGLEKAVEKFDPIKGYRFSTYAY 236

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   I     ++++     +K     L ++K   + I+    +   +  I K+L
Sbjct: 237 WWIRQGITRAIATQSRIIRLPVHITEK-----LNKIKQVQRKISQAKGRSATLEEIGKEL 291

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL-VYDHDGQEQVLIEKEERKNRR 225
           N+S ++V  +  ++    SL   I    +  ++  D L   D   +E + IE        
Sbjct: 292 NMSSTQVRDVLMKIPRSVSLE--IKVGKEKDTELVDLLESEDISPEENLAIES------- 342

Query: 226 NMLTRSMSV----LNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKK 279
             L R + +    L  RE+ + + R   E+ V  +L ++    ++SRERVRQIEA+A +K
Sbjct: 343 --LRRDIGILLEDLTEREQEVIKLRYGFEDGVSYSLADIGRTLDLSRERVRQIEAKALQK 400

Query: 280 VQE 282
           +++
Sbjct: 401 LRQ 403


>gi|294139649|ref|YP_003555627.1| RNA polymerase sigma-70 factor [Shewanella violacea DSS12]
 gi|7388082|sp|O24744|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 = 92.0 bits (227), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 71/244 (29%), Positives = 123/244 (50%), Gaps = 30/244 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 376 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 435

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 436 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 493

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 494 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 536

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAF 277
             ++ RN     ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A 
Sbjct: 537 TGESLRNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 596

Query: 278 KKVQ 281
           +K++
Sbjct: 597 RKLR 600


>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 = 92.0 bits (227), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 67/235 (28%), Positives = 117/235 (49%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 588 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 647

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +   +P+    +A K+ +
Sbjct: 648 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGAEPDPAT-LAIKMEM 702

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E E I    ++A  E ++      D + S   D++    D       +     + R ++
Sbjct: 703 PE-EKIRKIMKIA-KEPISMETPIGDDDDSHLGDFI---EDNNTLAPADAALHASMRGVV 757

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 758 KDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 812


>gi|261868195|ref|YP_003256117.1| RNA polymerase sigma factor RpoD [Aggregatibacter
           actinomycetemcomitans D11S-1]
 gi|261413527|gb|ACX82898.1| RNA polymerase sigma factor RpoD (Sigma-70) [Aggregatibacter
           actinomycetemcomitans D11S-1]
          Length = 616

 Score = 92.0 bits (227), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 120/234 (51%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   +A+++ +
Sbjct: 438 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREASPEE---LAERMGM 492

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ +   
Sbjct: 493 PEDKIRKV-LKIA-KEPISMETPIGDDDDSHLGDFI---EDSTLELPLDSATVQSLKAAT 547

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 548 HEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 601


>gi|220936192|ref|YP_002515091.1| RNA polymerase, sigma 70 subunit, RpoD [Thioalkalivibrio sp.
           HL-EbGR7]
 gi|219997502|gb|ACL74104.1| RNA polymerase, sigma 70 subunit, RpoD [Thioalkalivibrio sp.
           HL-EbGR7]
          Length = 619

 Score = 92.0 bits (227), Expect = 9e-17,   Method: Compositional matrix adjust.
 Identities = 70/245 (28%), Positives = 116/245 (47%), Gaps = 32/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 380 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 439

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   +++++ +
Sbjct: 440 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREATPEE---LSERMEM 494

Query: 169 SESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            E +V          ISM   +  DE             S   D++    D      IE 
Sbjct: 495 PEDKVRKVLKIAKEPISMETPIGDDE------------DSHLGDFI---EDVNVMSPIEA 539

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARA 276
             R+         ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A
Sbjct: 540 ATREGLSEATRDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 599

Query: 277 FKKVQ 281
            +K++
Sbjct: 600 LRKLR 604


>gi|237751866|ref|ZP_04582346.1| LOW QUALITY PROTEIN: RNA polymerase sigma factor RpoD [Helicobacter
           winghamensis ATCC BAA-430]
 gi|229376742|gb|EEO26833.1| LOW QUALITY PROTEIN: RNA polymerase sigma factor RpoD [Helicobacter
           winghamensis ATCC BAA-430]
          Length = 615

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 72/249 (28%), Positives = 126/249 (50%), Gaps = 20/249 (8%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           KR ++  D  A  ++  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ ++G
Sbjct: 370 KRGKDIAD-KAKTKMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKKG 428

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           +R +TY+ WWI+ A+   I      ++I        +   + R+   ++       K   
Sbjct: 429 YRFSTYATWWIRQAISRAIADQARTIRIPI-----HMIETINRINKIMRKCLQEEGKEPD 483

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG---QEQVL 215
           +  IA+++ +   +V ++        SL A I + +    ++ D+ V D       + +L
Sbjct: 484 LEKIAEEVGLPLDKVKNVIKITKEPISLEAPIGNGE--DGKFGDF-VEDKSAVGPMDHIL 540

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQI 272
                +++ ++ +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQI
Sbjct: 541 -----KEDLKSQIDDVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQI 595

Query: 273 EARAFKKVQ 281
           E+ A KK++
Sbjct: 596 ESSAIKKLK 604


>gi|238063497|ref|ZP_04608206.1| rpoD family RNA polymerase, sigma-70 subunit [Micromonospora sp.
           ATCC 39149]
 gi|237885308|gb|EEP74136.1| rpoD family RNA polymerase, sigma-70 subunit [Micromonospora sp.
           ATCC 39149]
          Length = 534

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 79/302 (26%), Positives = 145/302 (48%), Gaps = 42/302 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR------------EHG----------DLS-------- 48
           Y+ +I K+P+L  ++E  LAKR              E G          DL         
Sbjct: 237 YLKQIGKVPLLNAEQEVELAKRIEAGLYAAERLRAAEEGEEKLVREMVRDLGWISRDGER 296

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WW
Sbjct: 297 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 356

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   +      ++I    +   +   L R++  L         PE+   +AK++++
Sbjct: 357 IRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGREPTPEE---LAKEMDI 411

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +  +V+ +        SL+  I   D+  SQ  D++    D +  V ++       ++ L
Sbjct: 412 TPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEAVVAVDAVSFSLLQDQL 466

Query: 229 TRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   + 
Sbjct: 467 QQVLQTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRS 526

Query: 287 QV 288
           QV
Sbjct: 527 QV 528


>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 = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 119/234 (50%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 381 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 440

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+             PE+   +A+++ +
Sbjct: 441 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQCLQEMGREATPEE---LAERMGM 495

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ R   
Sbjct: 496 PEDKIRKV-LKIAK-EPISMETPIGDDDDSHLGDFI---QDESLELPLDSATAESLRLAT 550

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 551 NEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 604


>gi|301155442|emb|CBW14908.1| RNA polymerase, sigma 70 (sigma D) factor [Haemophilus
           parainfluenzae T3T1]
          Length = 629

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 120/234 (51%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 391 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 450

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   +A+++ +
Sbjct: 451 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREATPEE---LAERMGM 505

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ +   
Sbjct: 506 PEDKIRKV-LKIAK-EPISMETPIGDDDDSHLGDFI---EDSTLELPLDSATAQSLKVAT 560

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 561 HEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 614


>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 = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 78/279 (27%), Positives = 140/279 (50%), Gaps = 24/279 (8%)

Query: 16  LSRYIHEIR-KIPMLEKQEEY--VLAKRYRE------HGDLSA---AHRLVTSHLRLVVK 63
           L+ YI +IR  I  L++ E+   +   + RE      +G+L A      +V ++LRLV+ 
Sbjct: 336 LTNYIDQIRVNIDNLQRMEQTTGLTIAQIREIGGRIANGELKARRAKKEMVEANLRLVIS 395

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      
Sbjct: 396 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 455

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           ++I    +       L R+             PE+   +A+++ + E ++  +  ++A  
Sbjct: 456 IRI--PVHMIETINKLNRISRQCLQEMGREATPEE---LAERMGMPEDKIRKV-LKIA-K 508

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           E ++      D + S   D++    D   ++ ++    ++ R      +  L PRE ++ 
Sbjct: 509 EPISMETPIGDDDDSHLGDFI---QDESLELPLDSATAESLRLATNEVLEGLTPREAKVL 565

Query: 244 EAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
             R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 566 RMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 604


>gi|302342714|ref|YP_003807243.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfarculus
           baarsii DSM 2075]
 gi|301639327|gb|ADK84649.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfarculus
           baarsii DSM 2075]
          Length = 590

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 70/239 (29%), Positives = 125/239 (52%), Gaps = 18/239 (7%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ W
Sbjct: 351 DAKQELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATW 410

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I    +       L R   +L         PE+   IA+K++
Sbjct: 411 WIRQAITRAIADQARTIRI--PVHMIETINKLIRTSRYLVQEFGREPTPEE---IAEKMD 465

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
               +V  +  ++A  E ++      ++  S   D++      +++ +I   +     N+
Sbjct: 466 FPLEKVRKV-LKIAK-EPISLETPIGEEEDSHLGDFI------EDKKVINPADAVISLNL 517

Query: 228 LTRS---MSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++   ++ L PRE ++   R    Q++  TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 518 CEQTRKVLATLTPREEKVLRMRFGIGQKSDHTLEEVGRDFDVTRERIRQIEAKALRKLR 576


>gi|312195044|ref|YP_004015105.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EuI1c]
 gi|311226380|gb|ADP79235.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EuI1c]
          Length = 424

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 83/294 (28%), Positives = 135/294 (45%), Gaps = 60/294 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREHGDLSAA------HR--------------- 52
           Y+ EI ++P+L   +E  L+KR     + EH   +AA      HR               
Sbjct: 131 YLREIGRVPLLNAAQEVELSKRVEAGLFAEHKLATAADLEPELHRDLKLLVRDGEAAKQQ 190

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV+++LRLVV +A  Y G G+ + ++V EGN+GL++AV+KFD  +G++ +TY+ WWI+ A
Sbjct: 191 LVSANLRLVVSVAKKYSGRGMTLLDLVQEGNLGLIRAVEKFDYAKGYKFSTYATWWIRQA 250

Query: 113 MQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           +   +      ++I           T  Q++L   L R     +   + ++  EQVV   
Sbjct: 251 IGRALADQARTIRIPVHVVEQINKITRLQRQLVSTLGREPTDEELALELDMPLEQVV--- 307

Query: 164 KKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
            +L     + +S+   +   GD  L   I  SD  S    D   Y   G  Q        
Sbjct: 308 -ELRRYAQDTVSLETTVGDDGDSVLGDFIEDSDATSP--ADAASY---GAMQ-------- 353

Query: 222 KNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIE 273
               + +   +  L+PRER +   R  L +    TL  + +   ++RER+RQIE
Sbjct: 354 ----DEIDHVLGNLSPREREVMRLRFGLADGKQHTLAEVGNRLGLTRERIRQIE 403


>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
           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 = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 119/234 (50%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 381 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 440

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+             PE+   +A+++ +
Sbjct: 441 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQCLQEMGREATPEE---LAERMGM 495

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ R   
Sbjct: 496 PEDKIRKV-LKIAK-EPISMETPIGDDDDSHLGDFI---QDESLELPLDSATAESLRLAT 550

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 551 NEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 604


>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 = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 120/234 (51%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 390 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 449

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   +A+++ +
Sbjct: 450 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREASPEE---LAERMGM 504

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ +   
Sbjct: 505 PEDKIRKV-LKIAK-EPISMETPIGDDDDSHLGDFI---EDSTLELPLDSATAQSLKVAT 559

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 560 HEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 613


>gi|28572422|ref|NP_789202.1| RNA polymerase sigma factor [Tropheryma whipplei TW08/27]
 gi|28410553|emb|CAD66939.1| RNA polymerase principal sigma factor hrdb [Tropheryma whipplei
           TW08/27]
          Length = 387

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 83/307 (27%), Positives = 140/307 (45%), Gaps = 56/307 (18%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR----------EHGDLS----------------AAHR 52
           Y+ +I K+ +L   EE  LAKR            E GDL+                A   
Sbjct: 94  YLKQIGKVSLLTADEEVSLAKRIEAGLFAEEKLSESGDLAPKLKRELRWVVRDGQRAKDH 153

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 154 LLAANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEKFDYVKGFKFSTYATWWIRQA 213

Query: 113 MQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           +   +      ++I           +  Q++L  +L R     +   + ++ PE+VV + 
Sbjct: 214 ITRAMADQARTIRIPVHMVEVINKLSRVQRQLLQDLGREPTPDELGRELDMPPERVVEVQ 273

Query: 164 KKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           K       E IS++  L   GD     LI   D          V   D     +++++ R
Sbjct: 274 KYGR----EPISLHTPLGDEGDSEFGDLIEDVDA---------VAPDDAVGFSMLQQQLR 320

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
               ++  R   V+  R    ++       P TL+ +   F+V+RER+RQIEA+   K++
Sbjct: 321 LLLDSLSEREAGVIRMRFGLDYDM------PKTLDYVGEYFDVTRERIRQIEAKTMAKLR 374

Query: 282 ESIQKQV 288
              + Q 
Sbjct: 375 HPSRSQC 381


>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 = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 119/234 (50%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 381 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 440

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+             PE+   +A+++ +
Sbjct: 441 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQCLQEMGREATPEE---LAERMGM 495

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ R   
Sbjct: 496 PEDKIRKV-LKIAK-EPISMETPIGDDDDSHLGDFI---QDESLELPLDSATAESLRLAT 550

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 551 NEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 604


>gi|299783172|gb|ADJ41170.1| RNA polymerase sigma factor [Lactobacillus fermentum CECT 5716]
          Length = 287

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 48/120 (40%), Positives = 73/120 (60%), Gaps = 3/120 (2%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           SI +N  + +  Y+ EI ++ +L   EE  LA R  E GD +A   L  ++LRLVV IA 
Sbjct: 104 SIKINDPVRM--YLKEIGRVNLLTADEEVALALRI-EKGDETAKQELAEANLRLVVSIAK 160

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y G G+   +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I
Sbjct: 161 RYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRI 220


>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 = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 119/234 (50%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 381 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 440

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+             PE+   +A+++ +
Sbjct: 441 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQCLQEMGREATPEE---LAERMGM 495

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ R   
Sbjct: 496 PEDKIRKV-LKIA-KEPISMETPIGDDDDSHLGDFI---QDESLELPLDSATAESLRLAT 550

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 551 NEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 604


>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 = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 70/243 (28%), Positives = 118/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 371 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 430

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 431 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELAERMMMPED 488

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 489 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 532

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ RN     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 533 GESLRNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 592

Query: 279 KVQ 281
           K++
Sbjct: 593 KLR 595


>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 = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 120/234 (51%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 391 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 450

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   +A+++ +
Sbjct: 451 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREATPEE---LAERMGM 505

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ +   
Sbjct: 506 PEDKIRKV-LKIAK-EPISMETPIGDDDDSHLGDFI---EDSTLELPLDSATAQSLKVAT 560

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 561 HEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 614


>gi|256372040|ref|YP_003109864.1| RNA polymerase, sigma 32 subunit, RpoH [Acidimicrobium ferrooxidans
           DSM 10331]
 gi|256008624|gb|ACU54191.1| RNA polymerase, sigma 32 subunit, RpoH [Acidimicrobium ferrooxidans
           DSM 10331]
          Length = 294

 Score = 92.0 bits (227), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 72/241 (29%), Positives = 123/241 (51%), Gaps = 22/241 (9%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  R V  ++ LVV IA  Y   G+ + ++V EG IGL++A+  +D  RGFR +TY+ W
Sbjct: 55  AARERFVEGNMGLVVSIARRYVQPGISLDDLVQEGTIGLLRAIDLYDGRRGFRFSTYATW 114

Query: 108 WIKAAMQEYILRSWSLVKI--GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA-K 164
           WI+ A+ + + R+   V +  G  A   R+    R L+   QA+       E   A    
Sbjct: 115 WIRQAIAQALTRTRRDVVLPRGIAAELARVEVQRRELE---QALGRQPSMAELAAASGID 171

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERK 222
           +L V E +  + +            + S D+   + +D  + D   D   + + E  E  
Sbjct: 172 ELRVRELQGYARS------------VLSLDQAVGEERDVTLADIVPDRDAEPIEETIEHA 219

Query: 223 NRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R ++  +++ L PRER +   R  L+ N P +LE+ ++ F ++RER+RQIEARA  ++
Sbjct: 220 DLRTVIAGALAHLEPREREVLAFRFGLEGNEPHSLEDAAAYFGIARERIRQIEARAIARL 279

Query: 281 Q 281
           +
Sbjct: 280 R 280


>gi|255322395|ref|ZP_05363541.1| RNA polymerase sigma factor RpoD [Campylobacter showae RM3277]
 gi|255300768|gb|EET80039.1| RNA polymerase sigma factor RpoD [Campylobacter showae RM3277]
          Length = 627

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 70/239 (29%), Positives = 117/239 (48%), Gaps = 19/239 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ ++G++ +TY+ WW
Sbjct: 388 AKARMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKKGYKFSTYATWW 447

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + R+    +       K   +  IA ++ +
Sbjct: 448 IRQAISRAIADQARTIRIPI-----HMIETINRINKINRKYLQEEGKEPDINVIAAEVGL 502

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG---QEQVLIEKEERKNRR 225
           S  ++  +        SL A I + D    ++ D+ V D       + +L     + + +
Sbjct: 503 SADKIKQVIKITKEPISLEAPIGNED--DGKFGDF-VEDRSSLSPMDHIL-----KNDLK 554

Query: 226 NMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 555 EQIDEVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLK 613


>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 = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 120/234 (51%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 386 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 445

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   +A+++ +
Sbjct: 446 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREASPEE---LAERMGM 500

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ +   
Sbjct: 501 PEDKIRKV-LKIAK-EPISMETPIGDDDDSHLGDFI---EDNTLELPLDSATAQSLKVAT 555

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 556 HEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 609


>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 = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 119/234 (50%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 380 AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 439

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+             PE+   +A+++ +
Sbjct: 440 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQCLQEMGREATPEE---LAERMGM 494

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ R   
Sbjct: 495 PEDKIRKV-LKIAK-EPISMETPIGDDDDSHLGDFI---QDESLELPLDSATAESLRIAT 549

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 550 NEVLEGLTPREEKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 603


>gi|295836123|ref|ZP_06823056.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. SPB74]
 gi|295825874|gb|EDY42152.2| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. SPB74]
          Length = 493

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 139/310 (44%), Gaps = 62/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR---------------------------EHGDLSAAH 51
           Y+ +I K+P+L  ++E  LAKR                             E G  +  H
Sbjct: 200 YLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANSDKLAPKLQRELEIIAEDGGRAKNH 259

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 260 -LLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 318

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ +
Sbjct: 319 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEV 378

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 379 QK----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 424

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 425 -------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 477

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 478 KLRHPSRSQV 487


>gi|37523331|ref|NP_926708.1| RNA polymerase sigma factor SigC [Gloeobacter violaceus PCC 7421]
 gi|35214335|dbj|BAC91703.1| group2 RNA polymerase sigma factor [Gloeobacter violaceus PCC 7421]
          Length = 362

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 64/236 (27%), Positives = 123/236 (52%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +++ ++LRLVV +A  Y+  GL + ++V EG +GL +AV+KFDP +G+R +TY+ WW
Sbjct: 123 AKKKMIEANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAYWW 182

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   I      +++     +K     L R+K   + ++ N  +   +  IA++L +
Sbjct: 183 IRQGITRAIATQSRTIRLPVHITEK-----LNRIKKTQRKLSQNLGRTPTISEIAEELEM 237

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
             + V  +  R+    SL   +   DK++   +     +   +E   +++  R++ + +L
Sbjct: 238 EPAHVRELMSRVPRSVSLETRVG-KDKDTELGELLEAEEVSPEESA-VQESLRRDVKELL 295

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
                 L  RER +   R   L     +L  +    ++SRERVRQIE++A +K+++
Sbjct: 296 ----DDLTLRERDVITMRYGLLDGRTYSLSEIGRALDLSRERVRQIESKALQKLRQ 347


>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 = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 120/234 (51%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 384 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 443

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   +A+++ +
Sbjct: 444 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREASPEE---LAERMGM 498

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ +   
Sbjct: 499 PEDKIRKV-LKIAK-EPISMETPIGDDDDSHLGDFI---EDSTLELPLDSATAQSLKVAT 553

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 554 HEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 607


>gi|91202979|emb|CAJ72618.1| similar to DNA-directed RNA polymerase sigma subunit [Candidatus
           Kuenenia stuttgartiensis]
          Length = 256

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 73/265 (27%), Positives = 132/265 (49%), Gaps = 17/265 (6%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           ML  +EE  +A++  + GD  A  +L+ ++LRLVV IA  +   G    +++ EGN+GL+
Sbjct: 1   MLTFEEELEIARKVAK-GDAEAREKLIKANLRLVVSIAKEFVNRGFSFLDLIEEGNLGLI 59

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV+ FD   G R +TY+ WWIK A++  I     +++I +   Q+     + ++K    
Sbjct: 60  RAVEDFDITTGNRFSTYATWWIKQAIRRAIANKARIIRIPSYMLQR-----ISQMKHASS 114

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA-LINSSDKNSSQWQDWLVY 206
            +   + +      IA +++++   V ++   L    SL+A L++ +D        W + 
Sbjct: 115 GLLKKHERSPSEQEIAAEIDITAQNVKNIELSLQSMTSLDAPLVSGADII------WALS 168

Query: 207 DHDGQEQVLIEKE--ERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEF 262
           D     + L  +E  E    +  L + +  L+ R   +   R   +     TLE++S   
Sbjct: 169 DITPNGKTLPPEEGLEETYEKETLKKLLDTLDKRAATVITMRYGLVDGESRTLEDISKIL 228

Query: 263 EVSRERVRQIEARAFKKVQESIQKQ 287
           ++SRERVRQIE    +K+   I K+
Sbjct: 229 KISRERVRQIEKETIQKLHYLITKE 253


>gi|172040581|ref|YP_001800295.1| RNA polymerase sigma factor [Corynebacterium urealyticum DSM 7109]
 gi|171851885|emb|CAQ04861.1| RNA polymerase sigma factor A [Corynebacterium urealyticum DSM
           7109]
          Length = 545

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 79/302 (26%), Positives = 148/302 (49%), Gaps = 42/302 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR--------YR-----EHG---------DL--------S 48
           Y+ +I K+ +L  ++E  LAKR        YR     E G         DL         
Sbjct: 248 YLKQIGKVALLNAEQEVSLAKRIEAGLYANYRLKQIKESGERLSPMNRRDLREIDRDGRK 307

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WW
Sbjct: 308 AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYSKGYKFSTYATWW 367

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   +      ++I    +   +   L R++  L         PE+   +A+++++
Sbjct: 368 IRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGREPTPEE---LAREMDI 422

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +  +V+ +        SL+  I   D+  SQ  D++    D +  + ++       ++ L
Sbjct: 423 TVDKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEAVIAVDAVSFTLLQDQL 477

Query: 229 TRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +  L+ RE  + + R  L +  P TL+ +   + V+RER+RQIE++   K++   + 
Sbjct: 478 QDVLHTLSEREAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRS 537

Query: 287 QV 288
           QV
Sbjct: 538 QV 539


>gi|227495524|ref|ZP_03925840.1| sigma factor [Actinomyces coleocanis DSM 15436]
 gi|226831071|gb|EEH63454.1| sigma factor [Actinomyces coleocanis DSM 15436]
          Length = 505

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 82/311 (26%), Positives = 143/311 (45%), Gaps = 63/311 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH-----------------------GDLSAA 50
           Y+ +I K+ +L   +E  LA+R     Y EH                       G LS  
Sbjct: 211 YLKQIGKVSLLTAADEVDLARRIEAGLYAEHKIKTEGDELPSKLRRELQILVHDGQLSKN 270

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           H L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+
Sbjct: 271 H-LLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIR 329

Query: 111 AAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
            A+   +      ++I              Q+++  +L R     +   + ++ PE+VV 
Sbjct: 330 QAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVE 389

Query: 162 IAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           + K       E IS++  L   GD     LI  S+          +   D     L++++
Sbjct: 390 VQKYGR----EPISLHTPLGEDGDSEFGDLIEDSEA---------IVPTDAVSFTLLQEQ 436

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAF 277
                   L + +  L+ RE  +   R  L +  P TL+ +   + V+RER+RQIE++  
Sbjct: 437 --------LHKVLDTLSEREAGVVSMRFGLGDGQPKTLDEIGKVYGVTRERIRQIESKTM 488

Query: 278 KKVQESIQKQV 288
            K++   + QV
Sbjct: 489 SKLRHPSRSQV 499


>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 = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 65/235 (27%), Positives = 113/235 (48%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 422 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 481

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +   +P+    +A+K+ +
Sbjct: 482 IRQAITRSIADQARTIRI--PVHMIETINKMNRIS--RQILQETGAEPDPAT-LAEKMEM 536

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++          E ++      D + S   D++    D       E       R+  
Sbjct: 537 PEEKI--RKIMKISKEPISMETPIGDDDDSHLGDFI---EDTATLAPAEAAMYSGLRDAT 591

Query: 229 TRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 592 AEVLDSLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 646


>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 = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 70/242 (28%), Positives = 116/242 (47%), Gaps = 28/242 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 438 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 495

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 496 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPVDSAT 539

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + R      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 540 MTSLRVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 279 KV 280
           K+
Sbjct: 600 KL 601


>gi|86609652|ref|YP_478414.1| RNA polymerase sigma factor RpoD [Synechococcus sp.
           JA-2-3B'a(2-13)]
 gi|86558194|gb|ABD03151.1| RNA polymerase sigma factor RpoD [Synechococcus sp.
           JA-2-3B'a(2-13)]
          Length = 403

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 70/241 (29%), Positives = 125/241 (51%), Gaps = 25/241 (10%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 167 AKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 226

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKP-EQVVAIAKKL 166
           I+ A+   I      +++        L+  + R+K   + ++     KP E+ +A   ++
Sbjct: 227 IRQAITRAIADQSRTIRLPV-----HLYETISRIKKVTKLLSQELGRKPTEEEIATRMEI 281

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE----QVLIEKEERK 222
            + +   I+ + +L    SL   I   +   S+  D++  D +  E    +VL+      
Sbjct: 282 TIEKLRFIAKSAQLPI--SLETPIGKEE--DSRLGDFIESDGETPEDRVAKVLL------ 331

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKV 280
             R  L   +  L  RER + + R   ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 332 --REDLESVLETLTARERDVLKLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKL 389

Query: 281 Q 281
           +
Sbjct: 390 R 390


>gi|225436223|ref|XP_002273602.1| PREDICTED: similar to SIGB (SIGMA FACTOR B); DNA binding /
           DNA-directed RNA polymerase/ transcription factor [Vitis
           vinifera]
          Length = 578

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 72/250 (28%), Positives = 129/250 (51%), Gaps = 24/250 (9%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R R +  +    +++ S++RLV+ IA  Y+G G+ I ++V EG  GL++  +KFD  +GF
Sbjct: 331 RRRTNYGIRCKDKMIKSNIRLVISIAKNYQGAGMNIQDLVQEGCRGLVRGAEKFDASKGF 390

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL-----RRLKGHLQAITDNNL 154
           + +TY+ WWIK A+++          +   +   RL F++     R  +   Q  ++N  
Sbjct: 391 KFSTYAHWWIKQAVRK---------SLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGR 441

Query: 155 KP-EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            P  + VA A  L++     + +  +          IN + K S    D    D +  E+
Sbjct: 442 HPNNEEVAEATGLSMKRLNAVLLTPKAPRSLDQKIGINQNLKPSEVIAD---PDAETAEE 498

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQ 271
           +LI++  R++    L + ++ LNPRE+++   R   E+    TL+ +     VSRER+RQ
Sbjct: 499 LLIKQFMRED----LEKVLNSLNPREKQVIRWRYGLEDGRTKTLQEIGELMGVSRERIRQ 554

Query: 272 IEARAFKKVQ 281
           IE+ AF+K++
Sbjct: 555 IESCAFRKLK 564


>gi|311111671|ref|YP_003982893.1| DNA-directed RNA polymerase sigma subunit RpoD [Rothia dentocariosa
           ATCC 17931]
 gi|310943165|gb|ADP39459.1| DNA-directed RNA polymerase sigma subunit RpoD [Rothia dentocariosa
           ATCC 17931]
          Length = 468

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 81/309 (26%), Positives = 140/309 (45%), Gaps = 60/309 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH-----GDLS----------------AAHR 52
           Y+ +I K+ +L  Q+E  LA R     Y EH      D+                 A + 
Sbjct: 175 YLKQIGKVSLLNAQQEVDLAMRIEAGLYAEHKLADNPDMDPKLKKELRWVIHDGKRAKNH 234

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 235 LLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYSKGFKFSTYATWWIRQA 294

Query: 113 MQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           +   +      ++I              Q+++  +L R     +   + ++ PE+V+ + 
Sbjct: 295 ITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELGKELDMAPEKVIEVQ 354

Query: 164 KKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           K       E IS++  L   GD     LI  S+          V   D     L++++  
Sbjct: 355 K----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ-- 399

Query: 222 KNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
                 L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K
Sbjct: 400 ------LHSVLDTLSEREAGVVAMRFGMTDGQPKTLDEIGKVYGVTRERIRQIESKTMSK 453

Query: 280 VQESIQKQV 288
           ++   + QV
Sbjct: 454 LRHPSRSQV 462


>gi|300741779|ref|ZP_07071800.1| RNA polymerase sigma (70) factor RpoD [Rothia dentocariosa M567]
 gi|300380964|gb|EFJ77526.1| RNA polymerase sigma (70) factor RpoD [Rothia dentocariosa M567]
          Length = 468

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 81/309 (26%), Positives = 140/309 (45%), Gaps = 60/309 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH-----GDLS----------------AAHR 52
           Y+ +I K+ +L  Q+E  LA R     Y EH      D+                 A + 
Sbjct: 175 YLKQIGKVSLLNAQQEVDLAMRIEAGLYAEHKLADNPDMDPKLKKELRWVIHDGKRAKNH 234

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 235 LLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYSKGFKFSTYATWWIRQA 294

Query: 113 MQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           +   +      ++I              Q+++  +L R     +   + ++ PE+V+ + 
Sbjct: 295 ITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELGKELDMAPEKVIEVQ 354

Query: 164 KKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           K       E IS++  L   GD     LI  S+          V   D     L++++  
Sbjct: 355 K----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ-- 399

Query: 222 KNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
                 L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K
Sbjct: 400 ------LHSVLDTLSEREAGVVAMRFGMTDGQPKTLDEIGKVYGVTRERIRQIESKTMSK 453

Query: 280 VQESIQKQV 288
           ++   + QV
Sbjct: 454 LRHPSRSQV 462


>gi|1149588|emb|CAA89984.1| SigA sigma factor [Corynebacterium glutamicum]
          Length = 497

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 81/324 (25%), Positives = 153/324 (47%), Gaps = 49/324 (15%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREH-----------GD 46
           RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR     Y  H           GD
Sbjct: 179 RKDAELTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYATHRMEEMEEAFAAGD 237

Query: 47  LSAA--------------------HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
             A                     + L+ ++LRLVV +A  Y G G+   +++ EGN+GL
Sbjct: 238 KDAKLTPAVKRDLRAIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGL 297

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L
Sbjct: 298 IRAVEKFDYSKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQREL 355

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    P++   ++K++++SE +V+ +        SL+  I   D+  SQ  D++  
Sbjct: 356 LQELGREPTPQE---LSKEMDISEEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI-- 408

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEV 264
             D +  V ++       ++ L   +  L+ RE  + + R  L +  P TL+ +   + V
Sbjct: 409 -EDSEAVVAVDAVSFTLLQDQLQDVLETLSEREAGVVKLRFGLTDGMPRTLDEIGQVYGV 467

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           +RER+RQIE++   K +   + QV
Sbjct: 468 TRERIRQIESKTMSKRRHPSRSQV 491


>gi|296270363|ref|YP_003652995.1| RpoD subfamily RNA polymerase sigma-70 [Thermobispora bispora DSM
           43833]
 gi|296093150|gb|ADG89102.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobispora
           bispora DSM 43833]
          Length = 555

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 140/310 (45%), Gaps = 61/310 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR----------EHGD-----------------LSAAH 51
           Y+ +I K+P+L  ++E  LAKR            + GD                   A +
Sbjct: 261 YLKQIGKVPLLNAEQEVELAKRIEAGLFAEEQLAKEGDKLPPDVKAELEWIAEDGKRAKN 320

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 321 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 380

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ +
Sbjct: 381 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELARELDMTPEKVIEV 440

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 441 QKYGR----EPISLHTPLGEEGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 486

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 487 -------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 539

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 540 KLRHPSRSQV 549


>gi|319957164|ref|YP_004168427.1| RNA polymerase, sigma 70 subunit, rpod [Nitratifractor salsuginis
           DSM 16511]
 gi|319419568|gb|ADV46678.1| RNA polymerase, sigma 70 subunit, RpoD [Nitratifractor salsuginis
           DSM 16511]
          Length = 618

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 78/243 (32%), Positives = 122/243 (50%), Gaps = 27/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ ++G++ +TY+ WW
Sbjct: 379 AKTRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYQKGYKFSTYATWW 438

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI---TDNNLKPEQV-VAIAK 164
           I+ A+   I      ++I     +     N + ++ HLQ      D     E+V +++ K
Sbjct: 439 IRQAISRAIADQARTIRIPIHMIETINRIN-KIIRKHLQETGKEPDLETIAEEVGLSVDK 497

Query: 165 KLNVSE--SEVISMNCRLAGDESLNALINS-SDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
             NV +   E +S+   + GDE      +   DKNS    + ++ D   Q+         
Sbjct: 498 VKNVIKITKEPVSLETPV-GDEDDGRFGDFIEDKNSISPTEAVLNDDLNQQ--------- 547

Query: 222 KNRRNMLTRSMSVLNPRERRIFEAR-RLQEN--PVTLENLSSEFEVSRERVRQIEARAFK 278
                 +   +  LN RE+ +   R  L E+    TLE +  E  V+RERVRQIE+ A K
Sbjct: 548 ------IDEVLGQLNEREQAVIRMRFGLLEDMSDRTLEEIGKELNVTRERVRQIESSAIK 601

Query: 279 KVQ 281
           K++
Sbjct: 602 KLK 604


>gi|237751154|ref|ZP_04581634.1| RNA polymerase sigma factor RpoD [Helicobacter bilis ATCC 43879]
 gi|229373599|gb|EEO23990.1| RNA polymerase sigma factor RpoD [Helicobacter bilis ATCC 43879]
          Length = 632

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 71/237 (29%), Positives = 120/237 (50%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  ++  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+  + ++ +TY+ W
Sbjct: 392 TAKTKMSRSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYRKQYKFSTYATW 451

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WIK A+   I      ++I        +   + ++K  ++       +   V +IA ++ 
Sbjct: 452 WIKQAISRAIADQARTIRIPI-----HMIDTINKIKNLMRKHAQEKGEELDVESIANQVG 506

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V ++        SL A I + D    ++ D+ V D      + I  +E  + R  
Sbjct: 507 LSVDKVKNVIKITKEPISLEAPIGNDD--DGKFGDF-VEDKSTMSSMDIMLKE--DLREQ 561

Query: 228 LTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  LN RE+ + + R      E+  TLE +     V+RERVRQIE+ A KK++
Sbjct: 562 IDNVLDQLNEREKAVIKMRFGLLEDESDRTLEEIGKALNVTRERVRQIESSAIKKLK 618


>gi|258653916|ref|YP_003203072.1| RNA polymerase sigma factor SigB [Nakamurella multipartita DSM
           44233]
 gi|258557141|gb|ACV80083.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nakamurella
           multipartita DSM 44233]
          Length = 334

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 71/254 (27%), Positives = 123/254 (48%), Gaps = 36/254 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A + L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++AV+KFD  +GF+ +TY+ WW
Sbjct: 97  ARNHLLVANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 156

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG--HLQAITDNNLK--------PEQ 158
           I+ A+   +      +++     ++     L RLK   H Q   D  L         PE+
Sbjct: 157 IRQAISRGMADQGRTIRLPVHLVEQ--VNKLSRLKRELHQQLGRDATLAELAHESGIPEE 214

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
            +A    L     + +S++  +  DE   L   I  S+  S++      + HD       
Sbjct: 215 KIA---DLLDHARDPVSLDMPVGSDEEAPLGDFIEDSESTSAEAAVVAGFMHDD------ 265

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEA 274
                      + R +  L+ RE+ +   R   ++  P TL+ +   F +SRERVRQIE 
Sbjct: 266 -----------INRVLRTLDDREQTVVRLRYGLDDGRPRTLDEIGRHFGISRERVRQIER 314

Query: 275 RAFKKVQESIQKQV 288
            +  K++   + +V
Sbjct: 315 DSMAKLRVGDRSEV 328


>gi|28493466|ref|NP_787627.1| RNA polymerase sigma factor [Tropheryma whipplei str. Twist]
 gi|28476507|gb|AAO44596.1| RNA polymerase sigma factor [Tropheryma whipplei str. Twist]
          Length = 387

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 84/307 (27%), Positives = 141/307 (45%), Gaps = 56/307 (18%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR----------EHGDLS----------------AAHR 52
           Y+ +I K+ +L   EE  LAKR            E GDL+                A   
Sbjct: 94  YLKQIGKVSLLTADEEVSLAKRIEAGLFAEEKLSESGDLAPKLKRELRWVVRDGQRAKDH 153

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 154 LLAANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEKFDYVKGFKFSTYATWWIRQA 213

Query: 113 MQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           +   +      ++I           +  Q++L  +L R     +   + ++ PE+VV + 
Sbjct: 214 ITRAMADQARTIRIPVHMVEVINKLSRVQRQLLQDLGREPTPDELGRELDMPPERVVEVQ 273

Query: 164 KKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           K       E IS++  L   GD     LI   D          V   D     +++++ R
Sbjct: 274 KYGR----EPISLHTPLGDEGDSEFGDLIEDVDA---------VAPDDAVGFSMLQQQLR 320

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
               ++  R   V+  R R   +     + P TL+ +   F+V+RER+RQIEA+   K++
Sbjct: 321 LLLDSLSEREAGVI--RMRFGLD----DDMPKTLDYVGEYFDVTRERIRQIEAKTMAKLR 374

Query: 282 ESIQKQV 288
              + Q 
Sbjct: 375 HPSRSQC 381


>gi|328480117|gb|EGF49090.1| RNA polymerase sigma factor RpoD [Lactobacillus rhamnosus MTCC
           5462]
          Length = 206

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 45/108 (41%), Positives = 67/108 (62%), Gaps = 1/108 (0%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+   ++
Sbjct: 19  YLKEIGRVSLLTADEEVALALKI-EQGDQEAKQRLAEANLRLVVSIAKRYVGRGMQFLDL 77

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I
Sbjct: 78  IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRI 125


>gi|149916650|ref|ZP_01905152.1| RNA polymerase sigma factor rpoD [Plesiocystis pacifica SIR-1]
 gi|149822367|gb|EDM81756.1| RNA polymerase sigma factor rpoD [Plesiocystis pacifica SIR-1]
          Length = 398

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 71/246 (28%), Positives = 124/246 (50%), Gaps = 17/246 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +  V ++LRLVV IA  Y    +P+S+++ EGNIGLM+AV +FD +RG+R +TY+ WW
Sbjct: 160 AKNEFVQANLRLVVTIARRYDQRLMPLSDLIQEGNIGLMKAVDRFDGKRGYRFSTYATWW 219

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ ++   +      V++    +      +++R++   + +     +   V  +AK+  +
Sbjct: 220 IRHSINRALANKGRTVRLPAHVSA-----DIQRIQRATRELETRTGESPSVDELAKETGL 274

Query: 169 SESEVISMN-CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           S++ V  ++   L    SL+A   SSD +S    D L    D     L +  E ++    
Sbjct: 275 SKTRVRKLSKLSLHNPVSLDA--PSSDDDSRGLLDRL---EDSSAPRLADMVELEDMSEH 329

Query: 228 LTRSMSVLNPRERRIFEARRL------QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           L  +MS L P E  I   R        +   +TL  L    ++SRER+RQ++ RA  K++
Sbjct: 330 LREAMSALEPIEADILRRRYGLGVAGEEFEAMTLRELGEMHQLSRERIRQLQQRALNKLR 389

Query: 282 ESIQKQ 287
               ++
Sbjct: 390 REFARR 395


>gi|196047982|ref|ZP_03115160.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43) [Bacillus
           cereus 03BB108]
 gi|196021238|gb|EDX59967.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43) [Bacillus
           cereus 03BB108]
          Length = 289

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 73/279 (26%), Positives = 139/279 (49%), Gaps = 10/279 (3%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           N  +  + Y++EI +  +L ++EE +  ++Y+E+GD+ A   L+  +LRLVV +   Y  
Sbjct: 5   NDSVEYNLYLNEIGQHSLLTEEEEKMYLRKYKENGDMEARRILIECNLRLVVSVVNSYPR 64

Query: 71  YG-LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
            G     +++  GN+GL++ ++ F+  +  +LATY  WWI+  +  +I  + + ++   T
Sbjct: 65  VGNCEKMDMIQVGNVGLIRGIEAFEISKNCKLATYVTWWIRHEISRFITFNKNDIRCSVT 124

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
              K     + +LK +         +   +  IA++L  S   V+ +   L   ES++  
Sbjct: 125 IQNK-----MDKLKKYFSNENGKAKRKLNIEQIAEELGYSVETVLQIMDTLMLKESVSLD 179

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--R 247
             SSD++S    + +          LI  EE+  +   L    +VLN +E  +   R   
Sbjct: 180 APSSDEDSRPVMNSVKNAKAPNPVELITSEEQLYQIEELL--FTVLNEKEESVIRYRFGF 237

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             E  +TLE ++  F ++RER++QIE +A  K++  + K
Sbjct: 238 DTEKDLTLEEVARIFGITRERIQQIEKKAIGKLKNRMDK 276


>gi|162452723|ref|YP_001615090.1| RNA polymerase sigma factor RpoD [Sorangium cellulosum 'So ce 56']
 gi|161163305|emb|CAN94610.1| RNA polymerase sigma factor RpoD [Sorangium cellulosum 'So ce 56']
          Length = 639

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 71/238 (29%), Positives = 124/238 (52%), Gaps = 18/238 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ WW
Sbjct: 401 AKAELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWW 460

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R   +L         PE+   IA+K+ +
Sbjct: 461 IRQAITRAIADQARTIRI--PVHMIETINKLIRTSRYLVQEYGREPTPEE---IAEKMEL 515

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      ++  S   D++      +++ +I   E     N+ 
Sbjct: 516 PLDKVRKV-LKIA-KEPISLETPIGEEEDSHLGDFI------EDKSVISPAEAVINMNLA 567

Query: 229 TRS---MSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            ++   +  L PRE ++   R    +++  TLE +  +FEV+RER+RQIEA+A +K++
Sbjct: 568 EQTRKVLKTLTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLR 625


>gi|323342093|ref|ZP_08082326.1| DNA-directed RNA polymerase sigma subunit RpoD [Erysipelothrix
           rhusiopathiae ATCC 19414]
 gi|322464518|gb|EFY09711.1| DNA-directed RNA polymerase sigma subunit RpoD [Erysipelothrix
           rhusiopathiae ATCC 19414]
          Length = 459

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 79/252 (31%), Positives = 120/252 (47%), Gaps = 35/252 (13%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           +  L A   L++++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +T
Sbjct: 214 YDGLEARRILISANLRLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKGFKFST 273

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGT---------TANQKRLFFNL-RRLKGHLQAITDNN 153
           Y+ WWI+ A+   I      ++I           T  Q+ L   L R       A    N
Sbjct: 274 YATWWIRQAITRAIADQARTIRIPVHMVETINKLTRIQRSLVQTLGREPTAEEIAAEMEN 333

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
           + PE+V  I K       + +S+   +    D  L   I          +D L  D    
Sbjct: 334 ITPEKVREIQK----IALDPVSLETPIGEEDDSHLGDFIED--------KDALSPDEYAN 381

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERV 269
            Q+L  KEE K         +  L  RE ++   R   E+    TLE +  EF V+RER+
Sbjct: 382 NQLL--KEEIK-------MVLEGLTEREEKVLRLRFGLEDGRTRTLEEVGKEFNVTRERI 432

Query: 270 RQIEARAFKKVQ 281
           RQIEA+A +K++
Sbjct: 433 RQIEAKALRKLK 444


>gi|170782897|ref|YP_001711231.1| RNA polymerase principal sigma factor HrdD [Clavibacter
           michiganensis subsp. sepedonicus]
 gi|169157467|emb|CAQ02657.1| RNA polymerase principal sigma factor HrdD [Clavibacter
           michiganensis subsp. sepedonicus]
          Length = 347

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 75/291 (25%), Positives = 136/291 (46%), Gaps = 35/291 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR----------EHGDLSAAHR---------------- 52
           Y+ +I ++P+L  + E  +A+R               DL+ A R                
Sbjct: 54  YLRQIGRVPLLTAELEVSVARRIEVGVLSQEVLDTRTDLTPAERREYQTLAQDGMRAKQH 113

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV ++LRLVV IA  Y G GLP  +++ EGN+GL++AV+KFD + GF+ +TY+ WWIK +
Sbjct: 114 LVNANLRLVVSIAKRYTGRGLPFLDLIQEGNMGLVRAVEKFDYQAGFKFSTYASWWIKQS 173

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +  +   ++I     +     ++ R+    + + D   +   +  IA++ +   ++
Sbjct: 174 ITRGMADTSRTIRIPVHTVE-----HINRINAVQRELGDELGRDPSMEEIARESDTPVTK 228

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           V  +  R     SL  L+  S  +       L+ D D  + + +  ++       +TR +
Sbjct: 229 VRYLLDRAQEPMSLQVLVGGSGGDGDTEMADLIEDADVTQPIDVVTQQLMAAH--VTRLI 286

Query: 233 SVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             L  R+  +   R       P +L  +S +  V+RERVRQIE +   K++
Sbjct: 287 DGLAERDAEVVRMRFGLAGLEPRSLAFVSQQLGVTRERVRQIEKKVLAKLR 337


>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 = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 70/250 (28%), Positives = 120/250 (48%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 435 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 492

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 493 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDNTLELPVDSAT 536

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 537 STSLKFATNDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 596

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 597 KLRHPSRSEV 606


>gi|296090195|emb|CBI40014.3| unnamed protein product [Vitis vinifera]
          Length = 575

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 72/250 (28%), Positives = 129/250 (51%), Gaps = 24/250 (9%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R R +  +    +++ S++RLV+ IA  Y+G G+ I ++V EG  GL++  +KFD  +GF
Sbjct: 328 RRRTNYGIRCKDKMIKSNIRLVISIAKNYQGAGMNIQDLVQEGCRGLVRGAEKFDASKGF 387

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL-----RRLKGHLQAITDNNL 154
           + +TY+ WWIK A+++          +   +   RL F++     R  +   Q  ++N  
Sbjct: 388 KFSTYAHWWIKQAVRK---------SLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGR 438

Query: 155 KP-EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            P  + VA A  L++     + +  +          IN + K S    D    D +  E+
Sbjct: 439 HPNNEEVAEATGLSMKRLNAVLLTPKAPRSLDQKIGINQNLKPSEVIAD---PDAETAEE 495

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQ 271
           +LI++  R++    L + ++ LNPRE+++   R   E+    TL+ +     VSRER+RQ
Sbjct: 496 LLIKQFMRED----LEKVLNSLNPREKQVIRWRYGLEDGRTKTLQEIGELMGVSRERIRQ 551

Query: 272 IEARAFKKVQ 281
           IE+ AF+K++
Sbjct: 552 IESCAFRKLK 561


>gi|323697926|ref|ZP_08109838.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio sp.
           ND132]
 gi|323457858|gb|EGB13723.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           desulfuricans ND132]
          Length = 583

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 69/240 (28%), Positives = 120/240 (50%), Gaps = 12/240 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           + A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ 
Sbjct: 343 MQAKQELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYAT 402

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I    +       L R   +L      +  PE+   IA+++
Sbjct: 403 WWIRQAITRAIADQARTIRI--PVHMIETINKLIRTSRYLVQELGRDPSPEE---IAERM 457

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +    E +    ++A  E ++      D+  S   D++    D +     E+        
Sbjct: 458 DYP-LEKVKKVLKIAK-EPISLETPIGDEEDSSLGDFI---EDKKATAPAEEVVSTKLSE 512

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +   +S L PRE ++   R    +++  TLE +   F V+RER+RQIEA+A +K++  +
Sbjct: 513 QIASVLSDLTPREEQVLRKRFGIGEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPV 572


>gi|282862331|ref|ZP_06271393.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces sp.
           ACTE]
 gi|282562670|gb|EFB68210.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces sp.
           ACTE]
          Length = 515

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 140/310 (45%), Gaps = 62/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ +I K+P+L  ++E  LAKR  E G  +                           A +
Sbjct: 222 YLKQIGKVPLLNAEQEVELAKRI-EAGLFAEDKLANSDKLAPKLKRELEIIAEDGRRAKN 280

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 281 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 340

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ +
Sbjct: 341 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEV 400

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 401 QK----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 446

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 447 -------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 499

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 500 KLRHPSRSQV 509


>gi|290956933|ref|YP_003488115.1| major vegetative sigma factor HrdB [Streptomyces scabiei 87.22]
 gi|260646459|emb|CBG69556.1| major vegetative sigma factor HrdB [Streptomyces scabiei 87.22]
          Length = 516

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 140/310 (45%), Gaps = 62/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ +I K+P+L  ++E  LAKR  E G  +                           A +
Sbjct: 223 YLKQIGKVPLLNAEQEVELAKRI-EAGLFAEDKLANADKLAPKLKRELEIIAEDGRRAKN 281

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 282 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 341

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ +
Sbjct: 342 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEV 401

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 402 QK----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 447

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 448 -------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 500

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 501 KLRHPSRSQV 510


>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 = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 73/243 (30%), Positives = 122/243 (50%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 371 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 430

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-KRLFFNLRRLKGH---LQAITDNNLKPEQVV 160
           I+ A+   I      ++I      T N+  R+   + +  G     + + +  + PE   
Sbjct: 431 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPLPEELAERMMMPED-- 488

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D    + I+   
Sbjct: 489 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDNTLDLPIDSAT 532

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ RN +   +  L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 533 SESLRNSVRDVLGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 592

Query: 279 KVQ 281
           K++
Sbjct: 593 KLR 595


>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 = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 76/279 (27%), Positives = 138/279 (49%), Gaps = 24/279 (8%)

Query: 16  LSRYIHEIR-KIPMLE--KQEEYVLAKRYREHGDL---------SAAHRLVTSHLRLVVK 63
           L++Y   IR  I  L+  +QE ++  ++ R  GD           A   +V ++LRLV+ 
Sbjct: 340 LAKYADNIRASIARLQNLEQEAHLTIEQIRNIGDRISQGELKARRAKKEMVEANLRLVIS 399

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      
Sbjct: 400 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 459

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           ++I    +       L R+             PE+   +A+++ + E ++  +  ++A  
Sbjct: 460 IRI--PVHMIETINKLNRISRQCLQEMGREATPEE---LAERMGMPEDKIRKV-LKIAK- 512

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           E ++      D + S   D++    D   ++ ++    ++ +      +  L PRE ++ 
Sbjct: 513 EPISMETPIGDDDDSHLGDFI---EDSTLELPLDSATAQSLKVATHEVLEGLTPREAKVL 569

Query: 244 EAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
             R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 570 RMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 608


>gi|239991260|ref|ZP_04711924.1| RNA polymerase sigma factor [Streptomyces roseosporus NRRL 11379]
          Length = 515

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 140/310 (45%), Gaps = 62/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ +I K+P+L  ++E  LAKR  E G  +                           A +
Sbjct: 222 YLKQIGKVPLLNAEQEVELAKRI-EAGLFAEDKLANADKLAPKLKRELEIIAEDGRRAKN 280

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 281 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 340

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ +
Sbjct: 341 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEV 400

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 401 QK----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 446

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 447 -------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 499

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 500 KLRHPSRSQV 509


>gi|158341157|ref|YP_001522480.1| RNA polymerase sigma-70 factor, putative [Acaryochloris marina
           MBIC11017]
 gi|158311398|gb|ABW33009.1| RNA polymerase sigma-70 factor, putative [Acaryochloris marina
           MBIC11017]
          Length = 274

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 76/277 (27%), Positives = 137/277 (49%), Gaps = 29/277 (10%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ EI + P+L  +EE +LA++    G+L A  RL+  +LRLVV IA  ++  GLP+
Sbjct: 8   LHFYLKEIARYPILSHEEEILLARQVNA-GNLRAKQRLIECNLRLVVSIAKKHQNRGLPL 66

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EG+IGL  AV KFD  +G R +TY+ WWI+             V     A  + +
Sbjct: 67  QDLIQEGSIGLSNAVDKFDLAQGCRFSTYAYWWIRQG-----------VTAALRAKSRPI 115

Query: 136 FFN------LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
           +        + ++K H + +     +   +  +AK  N+ + + IS    L         
Sbjct: 116 YLPQYQWEMISKIKKHFRELNQQLGREPSLSELAKATNL-KPKTISRTLHLFQK------ 168

Query: 190 INSSDKN-SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
           ++S D+    Q +D L+    G++Q  +  E  +     L++ M+ L+ RE+ +   R  
Sbjct: 169 VSSLDQPVGHQQKDTLLDLMAGEDQPTLYLESLQ-LDEQLSQVMAHLDKREQFVLSQRFG 227

Query: 249 QEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            E+  P ++  +  +  +SRE +R I  +  KK+Q++
Sbjct: 228 LEDDQPKSMREIGEQIGLSREGIRLILNKIMKKLQKN 264


>gi|297202863|ref|ZP_06920260.1| RNA polymerase sigma factor RpoS [Streptomyces sviceus ATCC 29083]
 gi|297148238|gb|EDY59236.2| RNA polymerase sigma factor RpoS [Streptomyces sviceus ATCC 29083]
          Length = 512

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 140/310 (45%), Gaps = 62/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ +I K+P+L  ++E  LAKR  E G  +                           A +
Sbjct: 219 YLKQIGKVPLLNAEQEVELAKRI-EAGLFAEDKLANADKLAPKLKRELEIIAEDGRRAKN 277

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 278 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 337

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ +
Sbjct: 338 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEV 397

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 398 QK----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 443

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 444 -------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 496

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 497 KLRHPSRSQV 506


>gi|320008126|gb|ADW02976.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 515

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 140/310 (45%), Gaps = 62/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ +I K+P+L  ++E  LAKR  E G  +                           A +
Sbjct: 222 YLKQIGKVPLLNAEQEVELAKRI-EAGLFAEDKLANSDKLAPKLKRELEIIAEDGRRAKN 280

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 281 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 340

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ +
Sbjct: 341 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEV 400

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 401 QK----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 446

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 447 -------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 499

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 500 KLRHPSRSQV 509


>gi|311086952|gb|ADP67032.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. JF99
           (Acyrthosiphon pisum)]
          Length = 612

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 66/242 (27%), Positives = 124/242 (51%), Gaps = 12/242 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 374 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 433

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   +++K+ +
Sbjct: 434 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEIGREPTPEE---LSEKMLI 488

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ R+  
Sbjct: 489 PEDKIRKV-LKIAK-EPISMETPIGDDDDSHLGDFI---EDTTLELPLDSATSESLRSAT 543

Query: 229 TRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +S L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   + 
Sbjct: 544 HDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 603

Query: 287 QV 288
           +V
Sbjct: 604 EV 605


>gi|302537370|ref|ZP_07289712.1| RNA polymerase, subunit sigma [Streptomyces sp. C]
 gi|302446265|gb|EFL18081.1| RNA polymerase, subunit sigma [Streptomyces sp. C]
          Length = 526

 Score = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 81/323 (25%), Positives = 145/323 (44%), Gaps = 64/323 (19%)

Query: 8   IIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS----------------- 48
           ++V G     +  Y+ +I K+P+L  ++E  LAKR  E G  +                 
Sbjct: 220 VVVAGATADPVKDYLKQIGKVPLLNAEQEVELAKRI-EAGLFAEDKLANSDKLAPKLKRE 278

Query: 49  ----------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
                     A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G
Sbjct: 279 LEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKG 338

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAI 149
           ++ +TY+ WWI+ A+   +      ++I              Q+++  +L R     +  
Sbjct: 339 YKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELA 398

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYD 207
            + ++ PE+V+ + K       E IS++  L   GD     LI  S+          V  
Sbjct: 399 KELDMTPEKVIEVQK----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVP 445

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVS 265
            D     L++++        L   +  L+ RE  +   R       P TL+ +   + V+
Sbjct: 446 ADAVSFTLLQEQ--------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVT 497

Query: 266 RERVRQIEARAFKKVQESIQKQV 288
           RER+RQIE++   K++   + QV
Sbjct: 498 RERIRQIESKTMSKLRHPSRSQV 520


>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 [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|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 = 91.7 bits (226), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 66/242 (27%), Positives = 124/242 (51%), Gaps = 12/242 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 374 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 433

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   +++K+ +
Sbjct: 434 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEIGREPTPEE---LSEKMLI 488

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ R+  
Sbjct: 489 PEDKIRKV-LKIAK-EPISMETPIGDDDDSHLGDFI---EDTTLELPLDSATSESLRSAT 543

Query: 229 TRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +S L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   + 
Sbjct: 544 HDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 603

Query: 287 QV 288
           +V
Sbjct: 604 EV 605


>gi|328885546|emb|CCA58785.1| RNA polymerase sigma factor RpoD [Streptomyces venezuelae ATCC
           10712]
          Length = 567

 Score = 91.3 bits (225), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 140/310 (45%), Gaps = 62/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ +I K+P+L  ++E  LAKR  E G  +                           A +
Sbjct: 274 YLKQIGKVPLLNAEQEVELAKRI-EAGLFAEDKLANSDKLAPKLKRELEIIAEDGRRAKN 332

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 333 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 392

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ +
Sbjct: 393 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEV 452

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 453 QKYGR----EPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 498

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 499 -------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 551

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 552 KLRHPSRSQV 561


>gi|224418172|ref|ZP_03656178.1| RNA polymerase sigma factor RpoD [Helicobacter canadensis MIT
           98-5491]
 gi|253827499|ref|ZP_04870384.1| RNA polymerase sigma factor RpoD [Helicobacter canadensis MIT
           98-5491]
 gi|313141707|ref|ZP_07803900.1| RNA polymerase sigma factor RpoD [Helicobacter canadensis MIT
           98-5491]
 gi|253510905|gb|EES89564.1| RNA polymerase sigma factor RpoD [Helicobacter canadensis MIT
           98-5491]
 gi|313130738|gb|EFR48355.1| RNA polymerase sigma factor RpoD [Helicobacter canadensis MIT
           98-5491]
          Length = 616

 Score = 91.3 bits (225), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 70/246 (28%), Positives = 124/246 (50%), Gaps = 14/246 (5%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           KR ++  D  A  ++  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ ++G
Sbjct: 368 KRGKDIAD-RAKTKMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKKG 426

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           ++ +TY+ WWI+ A+   I      ++I        +   + R+   ++       K   
Sbjct: 427 YKFSTYATWWIRQAISRAIADQARTIRIPI-----HMIETINRINKIMRKYLQEEGKEPD 481

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           +  IA+++ +   +V ++        SL A I + +    ++ D++    D      +E 
Sbjct: 482 IDKIAEEVGLPVDKVKNVIKITKEPISLEAPIGNGE--DGKFGDFV---EDKGSVGPMES 536

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEAR 275
             +++ +  +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ 
Sbjct: 537 ILKEDLKEQIDDVLDQLNEREKAVIRMRFGLLEDESDRTLEEIGKELNVTRERVRQIESS 596

Query: 276 AFKKVQ 281
           A KK++
Sbjct: 597 AIKKLK 602


>gi|302522320|ref|ZP_07274662.1| RNA polymerase sigma factor RpoS [Streptomyces sp. SPB78]
 gi|302431215|gb|EFL03031.1| RNA polymerase sigma factor RpoS [Streptomyces sp. SPB78]
          Length = 514

 Score = 91.3 bits (225), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 140/310 (45%), Gaps = 62/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ +I K+P+L  ++E  LAKR  E G  +                           A +
Sbjct: 221 YLKQIGKVPLLNAEQEVELAKRI-EAGLFAEDKLANSDKLAPKLQRELEIIAEDGRRAKN 279

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 280 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 339

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ +
Sbjct: 340 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEV 399

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 400 QKYGR----EPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 445

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 446 -------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 498

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 499 KLRHPSRSQV 508


>gi|298500963|ref|ZP_07010764.1| RNA polymerase sigma factor RpoS [Vibrio cholerae MAK 757]
 gi|297540211|gb|EFH76271.1| RNA polymerase sigma factor RpoS [Vibrio cholerae MAK 757]
          Length = 233

 Score = 91.3 bits (225), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 69/238 (28%), Positives = 122/238 (51%), Gaps = 30/238 (12%)

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           +VKI+  Y    L + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++  
Sbjct: 1   MVKISRRYSNRRLTLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQ 60

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV--------AIAKKLNVSESE 172
              +++      K L   LR  +  L    D+   PE++          + K L ++E  
Sbjct: 61  TRTIRLPIHV-VKELNIYLRTAR-ELSQRLDHEPTPEEIALELDRPVDDVTKMLRLNER- 117

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           + S++  + GD    AL++    + +   ++   D D +E +L   +E            
Sbjct: 118 ISSVDTPIGGDGD-KALLDILPDSHNADPEFSTQDDDIRESLLNWLDE------------ 164

Query: 233 SVLNPRERRIFEARR---LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             LNP+++ +  ARR   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 165 --LNPKQKEVL-ARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVKQ 219


>gi|297156708|gb|ADI06420.1| RNA polymerase sigma factor [Streptomyces bingchenggensis BCW-1]
          Length = 515

 Score = 91.3 bits (225), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 140/310 (45%), Gaps = 62/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ +I K+P+L  ++E  LAKR  E G  +                           A +
Sbjct: 222 YLKQIGKVPLLNAEQEVELAKRI-EAGLFAEDKLANSDKLAPKLKRELEIIAEDGRRAKN 280

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 281 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 340

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ +
Sbjct: 341 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEV 400

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 401 QK----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 446

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 447 -------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 499

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 500 KLRHPSRSQV 509


>gi|323154963|gb|EFZ41155.1| RNA polymerase sigma factor rpoS domain protein [Escherichia coli
           EPECa14]
          Length = 148

 Score = 91.3 bits (225), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 43/89 (48%), Positives = 63/89 (70%), Gaps = 1/89 (1%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           + EGN+GL++AV+KFDPERGFR +TY+ W
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATW 148


>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 = 91.3 bits (225), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 72/243 (29%), Positives = 121/243 (49%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 372 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 431

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-KRLFFNLRRLKG---HLQAITDNNLKPEQVV 160
           I+ A+   I      ++I      T N+  R+   + +  G   H   + +  + PE   
Sbjct: 432 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGRDPHPDELAERMMMPED-- 489

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D    + ++   
Sbjct: 490 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTIALPVDCAT 533

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ +N     +  L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 534 SESLKNATNEVLEGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 593

Query: 279 KVQ 281
           K++
Sbjct: 594 KLR 596


>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 = 91.3 bits (225), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 69/245 (28%), Positives = 115/245 (46%), Gaps = 32/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 389 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 448

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV--------V 160
           I+ A+   I      ++I    +       + R+   L         PE++        V
Sbjct: 449 IRQAITRSIADQARTIRI--PVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEV 506

Query: 161 AIAKKLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            + K L +++ E ISM   +  DE   L   I  S+  S                  ++ 
Sbjct: 507 KVRKVLKIAK-EPISMETPIGDDEDSHLGDFIEDSNITSP-----------------VDA 548

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARA 276
              +  +      +  L  RE ++ + R   + P   TLE +  +F+V+RER+RQIEA+A
Sbjct: 549 ATSEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKA 608

Query: 277 FKKVQ 281
            +K++
Sbjct: 609 LRKLR 613


>gi|206603677|gb|EDZ40157.1| RNA polymerase, sigma 38 subunit, RpoS [Leptospirillum sp. Group II
           '5-way CG']
          Length = 598

 Score = 91.3 bits (225), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RGF+ +TY+ WW
Sbjct: 360 AKAELIKANLRLVVSIAKRYTNRGLQFLDLIQEGNIGLMKAVDKFEYKRGFKFSTYATWW 419

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R   HL         PE+   +AK++ +
Sbjct: 420 IRQAITRAIADQARTIRI--PVHMIETINKLIRTTRHLVQELGREPLPEE---LAKEMQM 474

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              E +    ++A  E ++      ++  S   D++    D +    I+   R +    +
Sbjct: 475 P-VEKVRRVLKIA-REPISLETPIGEEEDSHLGDFI---EDKKSISPIDSAVRYDLVRKI 529

Query: 229 TRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +++S L  RE ++   R    +    TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 530 GKALSSLTEREEKVIRLRFGVGESTDHTLEEVGQDFDVTRERIRQIEAKALRKLR 584


>gi|332974186|gb|EGK11120.1| DNA-directed RNA polymerase sigma subunit RpoD [Psychrobacter sp.
           1501(2011)]
          Length = 624

 Score = 91.3 bits (225), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 70/243 (28%), Positives = 114/243 (46%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 385 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 444

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV--------V 160
           I+ A+   I      ++I    +       + R+   L         PE++        V
Sbjct: 445 IRQAITRSIADQARTIRI--PVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEV 502

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + K L +++ E ISM   +  DE             S   D++    D      +E   
Sbjct: 503 KVRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDQTISSPVEDAT 546

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFK 278
               +      +S L  RE ++   R   + P   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 547 SAGLQEATRDVLSNLTEREAKVLRMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALR 606

Query: 279 KVQ 281
           K++
Sbjct: 607 KLR 609


>gi|238924709|ref|YP_002938225.1| RNA polymerase sigma factor RpoD [Eubacterium rectale ATCC 33656]
 gi|238876384|gb|ACR76091.1| RNA polymerase sigma factor RpoD [Eubacterium rectale ATCC 33656]
          Length = 434

 Score = 91.3 bits (225), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 72/244 (29%), Positives = 122/244 (50%), Gaps = 30/244 (12%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A  RL  ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD ++G++ +TY+ W
Sbjct: 196 DAKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYKKGYKFSTYATW 255

Query: 108 WIKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQ 158
           WI+ A+   I      ++I      T N+     ++L   L R     +   + N+  E+
Sbjct: 256 WIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPSPEEIAKEMNMPVER 315

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           V  I   L +S+ E +S+   +  +E  +      D N     D   +        L+++
Sbjct: 316 VREI---LKISQ-EPVSLETPIGEEEDSHLGDFIKDDNVPVPADAAAF-------TLLKE 364

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARA 276
           +        L   +  L  RE+++   R   E+    TLE +  EF V+RER+RQIEA+A
Sbjct: 365 Q--------LEEVLGTLTEREQKVLTLRFGLEDGRARTLEEVGKEFNVTRERIRQIEAKA 416

Query: 277 FKKV 280
            +K+
Sbjct: 417 LRKL 420


>gi|219681993|ref|YP_002468377.1| RNA polymerase sigma factor [Buchnera aphidicola str. Tuc7
           (Acyrthosiphon pisum)]
 gi|219621726|gb|ACL29882.1| RNA polymerase sigma factor [Buchnera aphidicola str. Tuc7
           (Acyrthosiphon pisum)]
          Length = 612

 Score = 91.3 bits (225), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 66/242 (27%), Positives = 124/242 (51%), Gaps = 12/242 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 374 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 433

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   +++K+ +
Sbjct: 434 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEIGREPTPEE---LSEKMLI 488

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ R+  
Sbjct: 489 PEDKIRKV-LKIAK-EPISMETPIGDDDDSHLGDFI---EDTTLELPLDSATSESLRSAT 543

Query: 229 TRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +S L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   + 
Sbjct: 544 HDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 603

Query: 287 QV 288
           +V
Sbjct: 604 EV 605


>gi|153306|gb|AAA26763.1| principal sigma-like factor [Streptomyces aureofaciens]
 gi|450078|prf||1920369B RNA polymerase:SUBUNIT=sigma
          Length = 525

 Score = 91.3 bits (225), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 81/323 (25%), Positives = 145/323 (44%), Gaps = 64/323 (19%)

Query: 8   IIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS----------------- 48
           ++V G     +  Y+ +I K+P+L  ++E  LAKR  E G  +                 
Sbjct: 219 VVVAGATADPVKDYLKQIGKVPLLNAEQEVELAKRI-EAGLFAEDKLANSDKLAPKLKRE 277

Query: 49  ----------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
                     A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G
Sbjct: 278 LEIIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKG 337

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAI 149
           ++ +TY+ WWI+ A+   +      ++I              Q+++  +L R     +  
Sbjct: 338 YKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELA 397

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYD 207
            + ++ PE+V+ + K       E IS++  L   GD     LI  S+          V  
Sbjct: 398 KELDMTPEKVIEVQKYGR----EPISLHTPLGEDGDSEFGDLIEDSEA---------VVP 444

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVS 265
            D     L++++        L   +  L+ RE  +   R       P TL+ +   + V+
Sbjct: 445 ADAVSFTLLQEQ--------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVT 496

Query: 266 RERVRQIEARAFKKVQESIQKQV 288
           RER+RQIE++   K++   + QV
Sbjct: 497 RERIRQIESKTMSKLRHPSRSQV 519


>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 = 91.3 bits (225), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 66/242 (27%), Positives = 124/242 (51%), Gaps = 12/242 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 374 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 433

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   +++K+ +
Sbjct: 434 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEIGREPTPEE---LSEKMLI 488

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ R+  
Sbjct: 489 PEDKIRKV-LKIAK-EPISMETPIGDDDDSHLGDFI---EDTTLELPLDSATSESLRSAT 543

Query: 229 TRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +S L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   + 
Sbjct: 544 HDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 603

Query: 287 QV 288
           +V
Sbjct: 604 EV 605


>gi|297562250|ref|YP_003681224.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
 gi|296846698|gb|ADH68718.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
          Length = 571

 Score = 91.3 bits (225), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 80/311 (25%), Positives = 141/311 (45%), Gaps = 63/311 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR----------------------------EHGDLSAA 50
           Y+ +I K+P+L  ++E  LAKR                              E G  +  
Sbjct: 277 YLKQIGKVPLLNAEQEVELAKRIEAGLFAEEKLAEEAELLTVELRDELEWIAEDGGRAKK 336

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           H L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+
Sbjct: 337 H-LLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIR 395

Query: 111 AAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
            A+   +      ++I              Q+++  +L R     +   + ++ PE+VV 
Sbjct: 396 QAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELARELDMTPEKVVE 455

Query: 162 IAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           + K       E IS++  L   GD     LI   D  + Q  + + +        L++++
Sbjct: 456 VQKYGR----EPISLHTPLGEDGDSEFGDLIE--DSEAIQPGEAVSF-------TLLQEQ 502

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAF 277
                   L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++  
Sbjct: 503 --------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTM 554

Query: 278 KKVQESIQKQV 288
            K++   + QV
Sbjct: 555 SKLRHPSRSQV 565


>gi|315502644|ref|YP_004081531.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Micromonospora
           sp. L5]
 gi|315409263|gb|ADU07380.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Micromonospora
           sp. L5]
          Length = 551

 Score = 91.3 bits (225), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 80/304 (26%), Positives = 145/304 (47%), Gaps = 46/304 (15%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRL------------------------- 53
           Y+ +I K+P+L  ++E  LAKR  E G L AA RL                         
Sbjct: 254 YLKQIGKVPLLNAEQEVELAKRI-EAG-LYAAERLRAADEGEEKLVRDLQRDLMWISRDG 311

Query: 54  -------VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                  + ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 312 ERAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 371

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I    +   +   L R++  L         PE+   +AK++
Sbjct: 372 WWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGREPTPEE---LAKEM 426

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +V+ +        SL+  I   D+  SQ  D++    D +  V ++       ++
Sbjct: 427 DITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEAVVAVDAVSFSLLQD 481

Query: 227 MLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L + +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 482 QLQQVLQTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPS 541

Query: 285 QKQV 288
           + QV
Sbjct: 542 RSQV 545


>gi|209527735|ref|ZP_03276230.1| RNA polymerase, sigma 70 subunit, RpoD family [Arthrospira maxima
           CS-328]
 gi|209491813|gb|EDZ92173.1| RNA polymerase, sigma 70 subunit, RpoD family [Arthrospira maxima
           CS-328]
          Length = 332

 Score = 91.3 bits (225), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 70/300 (23%), Positives = 141/300 (47%), Gaps = 52/300 (17%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDL------------------------------- 47
           Y+HEI ++P+L ++EE +  K+ ++   L                               
Sbjct: 28  YLHEIGRVPLLTREEEIIYGKKVQQMMSLLEMRDELTKELDHDPTAAEWSAKAGLSESEM 87

Query: 48  --------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                    A  +++ ++LRLVV IA  Y+   +   +++ EG +GL + V+KFDP RG+
Sbjct: 88  TEIMNRGRRAKQKMIEANLRLVVSIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPMRGY 147

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWI+ A+   I ++   +++     +K     ++R++  L      N  P + 
Sbjct: 148 KFSTYAYWWIRQAITRAIAQNSRTIRLPIHITEK--LNKIKRVQRELFQQYGRNATPTE- 204

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IAK L++  S++   +  LA    ++  +   D   ++ QD L  +    +  + ++ 
Sbjct: 205 --IAKALDLEPSQI--RDYLLASRHPVSLDLRVGDNQDTELQDLLEDESASADNYVTQQL 260

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARR-LQENP-VTLENLSSEFEVSRERVRQIEARAF 277
            R++ +++    M+ L P++R +   R  L +   ++L  +     +SRERVRQ+E +A 
Sbjct: 261 LRQDLKDL----MADLTPQQREVLTLRYGLNDGKEMSLSKVGVHMNISRERVRQLENQAL 316


>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 = 91.3 bits (225), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 69/234 (29%), Positives = 117/234 (50%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 364 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 423

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   +A+++ +
Sbjct: 424 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREATPEE---LAERMEM 478

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E +V  +  ++A  E ++      D   S   D+L    D   +  IE    +      
Sbjct: 479 PEDKVRKV-LKIAK-EPISMETPVGDDEDSSLGDFL---QDVNAESPIEAAVGEGLSEST 533

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 534 RDILAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 587


>gi|197335189|ref|YP_002157048.1| RNA polymerase sigma factor RpoD (Sigma-70) [Vibrio fischeri MJ11]
 gi|197316679|gb|ACH66126.1| RNA polymerase sigma factor RpoD (Sigma-70) [Vibrio fischeri MJ11]
          Length = 613

 Score = 91.3 bits (225), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 70/250 (28%), Positives = 120/250 (48%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 435 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 492

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 493 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDNTLELPVDSAT 536

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 537 STSLKFATNDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 596

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 597 KLRHPSRSEV 606


>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 = 91.3 bits (225), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 70/243 (28%), Positives = 114/243 (46%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 384 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 443

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV--------V 160
           I+ A+   I      ++I    +       + R+   L         PE++        V
Sbjct: 444 IRQAITRSIADQARTIRI--PVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEV 501

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + K L +++ E ISM   +  DE             S   D++    D      +E   
Sbjct: 502 KVRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDQTISSPVEDAT 545

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFK 278
               +      +S L  RE ++   R   + P   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 546 SAGLQEATRDVLSNLTEREAKVLRMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALR 605

Query: 279 KVQ 281
           K++
Sbjct: 606 KLR 608


>gi|291279867|ref|YP_003496702.1| DNA-directed RNA polymerase sigma 70 factor [Deferribacter
           desulfuricans SSM1]
 gi|290754569|dbj|BAI80946.1| DNA-directed RNA polymerase sigma 70 factor [Deferribacter
           desulfuricans SSM1]
          Length = 598

 Score = 91.3 bits (225), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 75/249 (30%), Positives = 122/249 (48%), Gaps = 40/249 (16%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV+KF+  RG++ +TY+ WW
Sbjct: 361 AKSELIEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVEKFEYRRGYKFSTYATWW 420

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQV----- 159
           I+ ++   I      ++I      T N  ++   +R+L+  L         PE++     
Sbjct: 421 IRQSITRAIADQARTIRIPVHMIETIN--KMIRTIRQLQIELG----KEPTPEEIAERMD 474

Query: 160 --VAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
             V   KK+     E +S+   +  DE  SL   I   D+++    D +VY+   +    
Sbjct: 475 IPVEKVKKVLKIAKEPVSLETPIGEDEDSSLGDFI--EDQSAKNPLDEVVYEKLKEH--- 529

Query: 216 IEKEERKNRRNMLTRS-MSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQI 272
                        TR+ +  L PRE  +   R     ++  TLE +   F V+RER+RQI
Sbjct: 530 -------------TRAILDTLTPREASVLRLRFGIDCDSDHTLEEVGRRFNVTRERIRQI 576

Query: 273 EARAFKKVQ 281
           EA+A +K++
Sbjct: 577 EAKALRKLR 585


>gi|302866088|ref|YP_003834725.1| RNA polymerase sigma factor RpoD [Micromonospora aurantiaca ATCC
           27029]
 gi|302568947|gb|ADL45149.1| RNA polymerase sigma factor RpoD [Micromonospora aurantiaca ATCC
           27029]
          Length = 551

 Score = 91.3 bits (225), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 80/304 (26%), Positives = 145/304 (47%), Gaps = 46/304 (15%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRL------------------------- 53
           Y+ +I K+P+L  ++E  LAKR  E G L AA RL                         
Sbjct: 254 YLKQIGKVPLLNAEQEVELAKRI-EAG-LYAAERLRAADEGEEKLVRDLQRDLMWISRDG 311

Query: 54  -------VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                  + ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 312 ERAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 371

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I    +   +   L R++  L         PE+   +AK++
Sbjct: 372 WWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGREPTPEE---LAKEM 426

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +V+ +        SL+  I   D+  SQ  D++    D +  V ++       ++
Sbjct: 427 DITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEAVVAVDAVSFSLLQD 481

Query: 227 MLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L + +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 482 QLQQVLQTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPS 541

Query: 285 QKQV 288
           + QV
Sbjct: 542 RSQV 545


>gi|281423630|ref|ZP_06254543.1| RNA polymerase sigma-70 factor [Prevotella oris F0302]
 gi|299141293|ref|ZP_07034430.1| RNA polymerase sigma-70 factor [Prevotella oris C735]
 gi|281402182|gb|EFB33013.1| RNA polymerase sigma-70 factor [Prevotella oris F0302]
 gi|298577253|gb|EFI49122.1| RNA polymerase sigma-70 factor [Prevotella oris C735]
          Length = 290

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 72/275 (26%), Positives = 136/275 (49%), Gaps = 18/275 (6%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYG 72
            L +Y+ EI + P++   EE  LA++ ++ G     A  +LVT++LR VV +A  Y+  G
Sbjct: 17  ALDKYLVEIGRAPLISIDEEIELAQKIKKGGRDGERAKEKLVTANLRFVVSVAKQYQHQG 76

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V++    NQ
Sbjct: 77  LSLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRL--PLNQ 134

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE---SLNAL 189
                +L ++   +        +   +  ++    + E ++   +  L  D    S++A 
Sbjct: 135 ---VGSLNKINREINKFEQEFQRKPSLAELSSATKIEEEKI---DQSLMADSHHVSIDAP 188

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF-EARRL 248
               + NS    D +    D +    ++ E        + R   VL  RE  I  E   +
Sbjct: 189 FQEGEDNS--MVDVMAGGEDSRTDKQVDHESMALELESVLR--KVLKDREITIIRECFGI 244

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +   LE +  +  ++RERVRQI  ++  K+++S
Sbjct: 245 GCHEKGLEEIGDQLGLTRERVRQIREKSIAKLRDS 279


>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 = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/245 (28%), Positives = 115/245 (46%), Gaps = 32/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 387 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 446

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV--------V 160
           I+ A+   I      ++I    +       + R+   L         PE++        V
Sbjct: 447 IRQAITRSIADQARTIRI--PVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEV 504

Query: 161 AIAKKLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            + K L +++ E ISM   +  DE   L   I  S+  S                  ++ 
Sbjct: 505 KVRKVLKIAK-EPISMETPIGDDEDSHLGDFIEDSNITSP-----------------VDA 546

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARA 276
              +  +      +  L  RE ++ + R   + P   TLE +  +F+V+RER+RQIEA+A
Sbjct: 547 ATSEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKA 606

Query: 277 FKKVQ 281
            +K++
Sbjct: 607 LRKLR 611


>gi|254391058|ref|ZP_05006266.1| RNA polymerase principal sigma factor hrdB [Streptomyces
           clavuligerus ATCC 27064]
 gi|197704753|gb|EDY50565.1| RNA polymerase principal sigma factor hrdB [Streptomyces
           clavuligerus ATCC 27064]
          Length = 514

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 140/310 (45%), Gaps = 62/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ +I K+P+L  ++E  LAKR  E G  +                           A +
Sbjct: 221 YLKQIGKVPLLNAEQEVELAKRI-EAGLFAEDKLANADKLAPKLKRELEIIAEDGRRAKN 279

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 280 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 339

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ +
Sbjct: 340 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEV 399

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 400 QK----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 445

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 446 -------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 498

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 499 KLRHPSRSQV 508


>gi|116670178|ref|YP_831111.1| RNA polymerase, sigma 28 subunit [Arthrobacter sp. FB24]
 gi|116610287|gb|ABK03011.1| RNA polymerase, sigma 70 subunit, RpoD [Arthrobacter sp. FB24]
          Length = 441

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 74/275 (26%), Positives = 131/275 (47%), Gaps = 40/275 (14%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L+++ E+V+      H    A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL
Sbjct: 188 PKLKRELEFVI------HDGKRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGL 241

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT---------TANQKRLFF 137
           ++AV+KFD  +GF+ +TY+ WWI+ A+   +      ++I              Q+++  
Sbjct: 242 IRAVEKFDYTKGFKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQ 301

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDK 195
           +L R     +   + ++ PE+VV + K       E IS++  L   GD     LI  S+ 
Sbjct: 302 DLGREPTPEELALELDMTPEKVVEVQKYGR----EPISLHTPLGEDGDSEFGDLIEDSEA 357

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPV 253
                    V   D     L++++        L   +  L+ RE  +   R       P 
Sbjct: 358 ---------VVPADAVSFTLLQEQ--------LHSVLDTLSEREAGVVAMRFGLTDGQPK 400

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           TL+ +   + V+RER+RQIE++   K++   + QV
Sbjct: 401 TLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQV 435


>gi|119717187|ref|YP_924152.1| RNA polymerase sigma factor [Nocardioides sp. JS614]
 gi|119537848|gb|ABL82465.1| RNA polymerase, sigma 70 subunit, RpoD [Nocardioides sp. JS614]
          Length = 495

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 79/309 (25%), Positives = 140/309 (45%), Gaps = 60/309 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR----------EHGDLSAA----------------HR 52
           Y+ +I K+P+L  + E  LAKR            + G LSA                 + 
Sbjct: 202 YLKQIGKVPLLNAEMEVELAKRIEAGLFSEEKLGKGGKLSAKVSEELEWIAEDGRRAKNH 261

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A
Sbjct: 262 LLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQA 321

Query: 113 MQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           +   +      ++I              Q+++  +L R     +   + ++ PE+V+ + 
Sbjct: 322 ITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEVQ 381

Query: 164 KKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           K       E IS++  L   GD     LI  S+          +   D     L++++  
Sbjct: 382 K----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------IVPADAVSFTLLQEQ-- 426

Query: 222 KNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
                 L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K
Sbjct: 427 ------LHAVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSK 480

Query: 280 VQESIQKQV 288
           ++   + QV
Sbjct: 481 LRHPSRSQV 489


>gi|330466485|ref|YP_004404228.1| RNA polymerase sigma factor [Verrucosispora maris AB-18-032]
 gi|328809456|gb|AEB43628.1| RNA polymerase sigma factor [Verrucosispora maris AB-18-032]
          Length = 535

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 80/304 (26%), Positives = 145/304 (47%), Gaps = 46/304 (15%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRL------------------------- 53
           Y+ +I K+P+L  ++E  LAKR  E G L AA RL                         
Sbjct: 238 YLKQIGKVPLLNAEQEVELAKRI-EAG-LYAAERLRAAEEGEEKLARDMQRDLLWISRDG 295

Query: 54  -------VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                  + ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 296 ERAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 355

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I    +   +   L R++  L         PE+   +AK++
Sbjct: 356 WWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGREPTPEE---LAKEM 410

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +V+ +        SL+  I   D+  SQ  D++    D +  V ++       ++
Sbjct: 411 DITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEAVVAVDAVSFSLLQD 465

Query: 227 MLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L + +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 466 QLQQVLQTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPS 525

Query: 285 QKQV 288
           + QV
Sbjct: 526 RSQV 529


>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 = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 68/235 (28%), Positives = 114/235 (48%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 407 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 466

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+   +   T     P     +AKK+ +
Sbjct: 467 IRQAITRSIADQARTIRI--PVHMIETINKMNRISRQILQETGLEADP---ATLAKKMEM 521

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E E I    +++  E ++      D + S   D++    D       E     + R + 
Sbjct: 522 PE-EKIRKILKISK-EPISMETPIGDDDDSHLGDFI---EDHATLAPTEAALYSSLRFIT 576

Query: 229 TRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 577 KDVLDTLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 631


>gi|329940007|ref|ZP_08289289.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
 gi|329300833|gb|EGG44729.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
          Length = 512

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 140/310 (45%), Gaps = 62/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ +I K+P+L  ++E  LAKR  E G  +                           A +
Sbjct: 219 YLKQIGKVPLLNAEQEVELAKRI-EAGLFAEDKLASADKLAPKLKRELEIIAEDGRRAKN 277

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 278 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 337

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ +
Sbjct: 338 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEV 397

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 398 QK----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 443

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 444 -------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 496

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 497 KLRHPSRSQV 506


>gi|302542036|ref|ZP_07294378.1| RNA polymerase sigma (70) factor RpoD [Streptomyces hygroscopicus
           ATCC 53653]
 gi|302459654|gb|EFL22747.1| RNA polymerase sigma (70) factor RpoD [Streptomyces himastatinicus
           ATCC 53653]
          Length = 502

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 140/310 (45%), Gaps = 62/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ +I K+P+L  ++E  LAKR  E G  +                           A +
Sbjct: 209 YLKQIGKVPLLNAEQEVELAKRI-EAGLFAEDKLANSDKLAPKLKRELEIIAEDGRRAKN 267

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 268 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 327

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ +
Sbjct: 328 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEV 387

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 388 QK----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 433

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 434 -------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 486

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 487 KLRHPSRSQV 496


>gi|226357433|ref|YP_002787172.1| RNA polymerase sigma factor, sigma-70 family [Deinococcus deserti
           VCD115]
 gi|226319423|gb|ACO47418.1| putative RNA polymerase sigma factor, sigma-70 family [Deinococcus
           deserti VCD115]
          Length = 363

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 81/303 (26%), Positives = 136/303 (44%), Gaps = 58/303 (19%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYR---------------------------EHGDLSAA 50
           +Y+HEI ++P+L   EE  LA+R                             E G+  A 
Sbjct: 65  QYLHEIGRVPLLTVTEEIDLARRMEAGQEARTQLETEHELGERERRRLQRTVEDGE-HAK 123

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            +L+ ++LRLVV IA  Y   G+ + +++ EGN GL++  +KF+  RGF+ +TY+ WWI+
Sbjct: 124 QQLIEANLRLVVSIAKKYANRGMGLLDLIQEGNQGLIRGAEKFEYRRGFKFSTYATWWIR 183

Query: 111 AAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
            A+   I      ++I      T N+     ++L   L R   H +              
Sbjct: 184 QAVNRAIADQARNIRIPVHMVETINKLNRTTRQLQMELSREPSHAET------------- 230

Query: 162 IAKKLNVSESEV-ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            A+ +     EV +    RL  D +++      D+  S   D+L    D + +  + +  
Sbjct: 231 -AEAMGPGWDEVKVEETLRLTRD-TISLATPVGDEGDSSIADFLP---DDRRESPLSRVS 285

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFK 278
                  L R+++ L PRE  +   R   E+    TLE +   F V+RER+RQIE +A +
Sbjct: 286 SVLMSEALDRTLATLEPREALVIRLRNGLEDGREHTLEEVGKHFGVTRERIRQIENKALR 345

Query: 279 KVQ 281
           K++
Sbjct: 346 KIK 348


>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 = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/250 (28%), Positives = 120/250 (48%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 372 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 431

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 432 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 489

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 490 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDNTLELPVDSAT 533

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 534 STSLKFATNDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 593

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 594 KLRHPSRSEV 603


>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|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 = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/245 (28%), Positives = 115/245 (46%), Gaps = 32/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 387 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 446

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV--------V 160
           I+ A+   I      ++I    +       + R+   L         PE++        V
Sbjct: 447 IRQAITRSIADQARTIRI--PVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEV 504

Query: 161 AIAKKLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            + K L +++ E ISM   +  DE   L   I  S+  S                  ++ 
Sbjct: 505 KVRKVLKIAK-EPISMETPIGDDEDSHLGDFIEDSNITSP-----------------VDA 546

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARA 276
              +  +      +  L  RE ++ + R   + P   TLE +  +F+V+RER+RQIEA+A
Sbjct: 547 ATSEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKA 606

Query: 277 FKKVQ 281
            +K++
Sbjct: 607 LRKLR 611


>gi|77920269|ref|YP_358084.1| RNA polymerase, sigma(70) factor [Pelobacter carbinolicus DSM 2380]
 gi|77546352|gb|ABA89914.1| RNA polymerase, sigma 70 subunit, RpoD [Pelobacter carbinolicus DSM
           2380]
          Length = 588

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 76/251 (30%), Positives = 123/251 (49%), Gaps = 44/251 (17%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ W
Sbjct: 348 AAKSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATW 407

Query: 108 WIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHL------QAITDNNLKP- 156
           WI+ A+   I      ++I      T N  +L    R+L   +      + I +    P 
Sbjct: 408 WIRQAITRAIADQARTIRIPVHMIETIN--KLIRTSRQLVQEMGREPVPEEIAERMELPL 465

Query: 157 ---EQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQ 211
               +V+ IAK       E IS+   +  +E  SL   I   DK      + ++      
Sbjct: 466 EKVRRVLKIAK-------EPISLETPIGEEEDSSLGDFIE--DKGVVSPLEAVI------ 510

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERV 269
                    + N  +  +R ++ L PRE ++   R    +++  TLE +  +F V+RER+
Sbjct: 511 ---------KGNLSDQTSRVLASLTPREEKVLRMRFGIGEKSDHTLEEVGQDFAVTRERI 561

Query: 270 RQIEARAFKKV 280
           RQIEA+A +K+
Sbjct: 562 RQIEAKALRKL 572


>gi|32476381|ref|NP_869375.1| RNA polymerase sigma factor rpoD [Rhodopirellula baltica SH 1]
 gi|32446926|emb|CAD78832.1| RNA polymerase sigma factor rpoD [Rhodopirellula baltica SH 1]
 gi|327539012|gb|EGF25646.1| RNA polymerase sigma factor rpoD [Rhodopirellula baltica WH47]
          Length = 519

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 83/280 (29%), Positives = 134/280 (47%), Gaps = 27/280 (9%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDL-----SAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           +HE R+I    ++    L  R +  G +      A   L   +LRLVV IA  YR  GL 
Sbjct: 248 LHERRQILTACQETPTSLRNRVKMLGSVYSDYQQAKRELSEGNLRLVVSIAKKYRNRGLS 307

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG-----TT 129
             +++ EGN GLM+AV KF+  RGF+  TY+ WWI+ A+   +      ++I      T 
Sbjct: 308 FLDLIQEGNAGLMRAVDKFEYRRGFKFCTYATWWIRQAITRAVADQSRTIRIPVHMVETM 367

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
           +  + +   L +  G   +I +   + +  +  A+++       IS++ R  G       
Sbjct: 368 SRVRNVARQLLQELGREPSIEETARRADVTIEEARRVLTMSRFPISLD-RPVG------- 419

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
            NS D   SQ+ D L        Q+   +E  + R   +T  +  L+ RER I + R   
Sbjct: 420 -NSED---SQFGDLLPDGTAESPQIGATQEMLRQR---ITGVLKSLSYREREIIKLRYGL 472

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +    TLE +   F+V+RER+RQIEA+A +K+Q+  + Q
Sbjct: 473 GDGYSYTLEEVGHIFKVTRERIRQIEAKAVRKLQQPSRSQ 512


>gi|302554625|ref|ZP_07306967.1| RNA polymerase sigma factor RpoS [Streptomyces viridochromogenes
           DSM 40736]
 gi|302472243|gb|EFL35336.1| RNA polymerase sigma factor RpoS [Streptomyces viridochromogenes
           DSM 40736]
          Length = 513

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 140/310 (45%), Gaps = 62/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ +I K+P+L  ++E  LAKR  E G  +                           A +
Sbjct: 220 YLKQIGKVPLLNAEQEVELAKRI-EAGLFAEDKLANSDKLAPKLKRELEIIAEDGRRAKN 278

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 279 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 338

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ +
Sbjct: 339 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEV 398

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 399 QK----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 444

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 445 -------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 497

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 498 KLRHPSRSQV 507


>gi|159037077|ref|YP_001536330.1| RNA polymerase sigma factor [Salinispora arenicola CNS-205]
 gi|157915912|gb|ABV97339.1| RNA polymerase, sigma 70 subunit, RpoD family [Salinispora
           arenicola CNS-205]
          Length = 532

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 80/304 (26%), Positives = 145/304 (47%), Gaps = 46/304 (15%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRL------------------------- 53
           Y+ +I K+P+L  ++E  LAKR  E G L AA RL                         
Sbjct: 235 YLKQIGKVPLLNAEQEVELAKRI-EAG-LYAAERLRATEEGEEKLNRDMQRDLMWISRDG 292

Query: 54  -------VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                  + ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 293 ERAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 352

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I    +   +   L R++  L         PE+   +AK++
Sbjct: 353 WWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQDLGREPTPEE---LAKEM 407

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +V+ +        SL+  I   D+  SQ  D++    D +  V ++       ++
Sbjct: 408 DITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEAVVAVDAVSFSLLQD 462

Query: 227 MLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L + +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 463 QLQQVLQTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPS 522

Query: 285 QKQV 288
           + QV
Sbjct: 523 RSQV 526


>gi|238786819|ref|ZP_04630620.1| RNA polymerase sigma factor rpoS [Yersinia frederiksenii ATCC
           33641]
 gi|238725187|gb|EEQ16826.1| RNA polymerase sigma factor rpoS [Yersinia frederiksenii ATCC
           33641]
          Length = 306

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 75/277 (27%), Positives = 123/277 (44%), Gaps = 51/277 (18%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+RY                              GL + ++
Sbjct: 63  YLGEIGYSPLLTAEEEVYFARRYSNR---------------------------GLALLDL 95

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 96  IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 155

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 156 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 212

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             SD+N +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 213 ILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 261

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 262 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQGQ 296


>gi|318059566|ref|ZP_07978289.1| RNA polymerase sigma factor [Streptomyces sp. SA3_actG]
 gi|318075441|ref|ZP_07982773.1| RNA polymerase sigma factor [Streptomyces sp. SA3_actF]
          Length = 446

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 140/310 (45%), Gaps = 62/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ +I K+P+L  ++E  LAKR  E G  +                           A +
Sbjct: 153 YLKQIGKVPLLNAEQEVELAKRI-EAGLFAEDKLANSDKLAPKLQRELEIIAEDGRRAKN 211

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 212 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 271

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ +
Sbjct: 272 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEV 331

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 332 QKYGR----EPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 377

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 378 -------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 430

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 431 KLRHPSRSQV 440


>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 = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/244 (28%), Positives = 121/244 (49%), Gaps = 28/244 (11%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 398 AAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 457

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD--NNLKPEQVVAIA-- 163
           WI+ A+   I      ++I     +     N R  + HLQ   +  ++ K  +++ +   
Sbjct: 458 WIRQAITRSIADQARTIRIPVHMIETINKMN-RISRQHLQETGEEPDSAKLAELMQMPED 516

Query: 164 --KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKE 219
             +K+     E ISM   +  D+  +      D N+    D  +Y   H+  +++L    
Sbjct: 517 KIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDSNNIAPADAAMYTSLHEVTKEIL---- 572

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
                          L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 573 -------------ESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 619

Query: 278 KKVQ 281
           +K++
Sbjct: 620 RKLR 623


>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 = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 118/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 376 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 435

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 436 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPED 493

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 494 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 537

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ +N     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 538 SESLKNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 597

Query: 279 KVQ 281
           K++
Sbjct: 598 KLR 600


>gi|159897807|ref|YP_001544054.1| RNA polymerase, sigma 32 subunit, RpoH [Herpetosiphon aurantiacus
           ATCC 23779]
 gi|159890846|gb|ABX03926.1| RNA polymerase, sigma 32 subunit, RpoH [Herpetosiphon aurantiacus
           ATCC 23779]
          Length = 303

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 81/301 (26%), Positives = 142/301 (47%), Gaps = 56/301 (18%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVL--------------AKRYREHGDLS------------ 48
           GL RY++EI + P+L  +EE  L              A R       +            
Sbjct: 14  GLQRYLNEIAETPLLAAEEEQKLTQIVHVARQAQPTPACRIERCPSCALFEQCVTKLKEP 73

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +LV ++LRLVV IA  YRG+GLP  +++ EGNIGLM A+++FD  +G R +TY+ WW
Sbjct: 74  AHEQLVRANLRLVVSIAKRYRGFGLPFQDLIQEGNIGLMNAIERFDATKGVRFSTYATWW 133

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH-LQAITDNNLKPEQVVAIAKKLN 167
           I+ A+   +     L+++    ++  L   +RR++   LQA+       E    I+  L 
Sbjct: 134 IRQAITRSLANQGRLIRL--PVHRWELLIKVRRIETKLLQALGREPSANE----ISTALG 187

Query: 168 VSESEV--------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           V E ++        + ++     +E  + L+  S  +   W+D L        + L+   
Sbjct: 188 VPEEKICDLLSIAQVPISLATPKNEETDMLLGDSLPDED-WEDEL--------ECLLTSI 238

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPV-TLENLSSEFEVSRERVRQIEARAF 277
           + +  R ML +    L+ +E+ +   R  L++    +L  + +    +R+R++QIEA A 
Sbjct: 239 DAQYTRAMLNQ----LSEQEQEVLTLRYGLKDGKSRSLSEVGAVVGRTRQRIQQIEAGAL 294

Query: 278 K 278
           +
Sbjct: 295 Q 295


>gi|294631847|ref|ZP_06710407.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. e14]
 gi|292835180|gb|EFF93529.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. e14]
          Length = 515

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 140/310 (45%), Gaps = 62/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ +I K+P+L  ++E  LAKR  E G  +                           A +
Sbjct: 222 YLKQIGKVPLLNAEQEVELAKRI-EAGLFAEDKLANSDKLAPKLKRELEIIAEDGRRAKN 280

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 281 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 340

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ +
Sbjct: 341 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEV 400

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 401 QK----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 446

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 447 -------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 499

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 500 KLRHPSRSQV 509


>gi|291526136|emb|CBK91723.1| RNA polymerase, sigma 70 subunit, RpoD [Eubacterium rectale DSM
           17629]
 gi|291527130|emb|CBK92716.1| RNA polymerase, sigma 70 subunit, RpoD [Eubacterium rectale M104/1]
          Length = 418

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 72/244 (29%), Positives = 122/244 (50%), Gaps = 30/244 (12%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A  RL  ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD ++G++ +TY+ W
Sbjct: 180 DAKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYKKGYKFSTYATW 239

Query: 108 WIKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQ 158
           WI+ A+   I      ++I      T N+     ++L   L R     +   + N+  E+
Sbjct: 240 WIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPSPEEIAKEMNMPVER 299

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           V  I   L +S+ E +S+   +  +E  +      D N     D   +        L+++
Sbjct: 300 VREI---LKISQ-EPVSLETPIGEEEDSHLGDFIKDDNVPVPADAAAF-------TLLKE 348

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARA 276
           +        L   +  L  RE+++   R   E+    TLE +  EF V+RER+RQIEA+A
Sbjct: 349 Q--------LEEVLGTLTEREQKVLTLRFGLEDGRARTLEEVGKEFNVTRERIRQIEAKA 400

Query: 277 FKKV 280
            +K+
Sbjct: 401 LRKL 404


>gi|239928504|ref|ZP_04685457.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 490

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 140/310 (45%), Gaps = 62/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ +I K+P+L  ++E  LAKR  E G  +                           A +
Sbjct: 197 YLKQIGKVPLLNAEQEVELAKRI-EAGLFAEDKLANSDKLAPKLKRELEIIAEDGRRAKN 255

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 256 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 315

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ +
Sbjct: 316 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEV 375

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 376 QK----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 421

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 422 -------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 474

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 475 KLRHPSRSQV 484


>gi|29828986|ref|NP_823620.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29606091|dbj|BAC70155.1| RNA polymerase major sigma factor, sigma-70 family [Streptomyces
           avermitilis MA-4680]
          Length = 512

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 140/310 (45%), Gaps = 62/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ +I K+P+L  ++E  LAKR  E G  +                           A +
Sbjct: 219 YLKQIGKVPLLNAEQEVELAKRI-EAGLFAEDKLANADKLAPKLKRELEIIAEDGRRAKN 277

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 278 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 337

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ +
Sbjct: 338 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEV 397

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 398 QK----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 443

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 444 -------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 496

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 497 KLRHPSRSQV 506


>gi|294815528|ref|ZP_06774171.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|294328127|gb|EFG09770.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 529

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 140/310 (45%), Gaps = 62/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ +I K+P+L  ++E  LAKR  E G  +                           A +
Sbjct: 236 YLKQIGKVPLLNAEQEVELAKRI-EAGLFAEDKLANADKLAPKLKRELEIIAEDGRRAKN 294

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 295 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 354

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ +
Sbjct: 355 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEV 414

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 415 QK----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 460

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 461 -------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 513

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 514 KLRHPSRSQV 523


>gi|124515193|gb|EAY56704.1| RNA polymerase, sigma 70 subunit, RpoD [Leptospirillum rubarum]
          Length = 598

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RGF+ +TY+ WW
Sbjct: 360 AKAELIKANLRLVVSIAKRYTNRGLQFLDLIQEGNIGLMKAVDKFEYKRGFKFSTYATWW 419

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R   HL         PE+   +AK++ +
Sbjct: 420 IRQAITRAIADQARTIRI--PVHMIETINKLIRTTRHLVQELGREPLPEE---LAKEMQM 474

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              E +    ++A  E ++      ++  S   D++    D +    I+   R +    +
Sbjct: 475 P-VEKVRRVLKIA-REPISLETPIGEEEDSHLGDFI---EDKKSISPIDSAVRYDLVRKI 529

Query: 229 TRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +++S L  RE ++   R    +    TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 530 GKALSSLTEREEKVIRLRFGVGESTDHTLEEVGQDFDVTRERIRQIEAKALRKLR 584


>gi|116514979|ref|YP_802608.1| RNA polymerase major s factor [Buchnera aphidicola str. Cc (Cinara
           cedri)]
 gi|116256833|gb|ABJ90515.1| RNA polymerase major s factor [Buchnera aphidicola str. Cc (Cinara
           cedri)]
          Length = 613

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/236 (29%), Positives = 122/236 (51%), Gaps = 14/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 374 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 433

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   +++K+ +
Sbjct: 434 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEIGREPTPEE---LSEKMLI 488

Query: 169 SESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           SE E I    ++A +  S+   I   D   +   D++    D   ++ +E    ++ + +
Sbjct: 489 SE-EKIRKVLKIAKEPISMETPIGEDD--DTHLGDFI---EDTNLELPLESATSESLKTI 542

Query: 228 LTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
               +S L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 543 TNDVLSGLTDREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKALRKLR 598


>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 = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/245 (28%), Positives = 115/245 (46%), Gaps = 32/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 390 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 449

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV--------V 160
           I+ A+   I      ++I    +       + R+   L         PE++        V
Sbjct: 450 IRQAITRSIADQARTIRI--PVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEV 507

Query: 161 AIAKKLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            + K L +++ E ISM   +  DE   L   I  S+  S                  ++ 
Sbjct: 508 KVRKVLKIAK-EPISMETPIGDDEDSHLGDFIEDSNITSP-----------------VDA 549

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARA 276
              +  +      +  L  RE ++ + R   + P   TLE +  +F+V+RER+RQIEA+A
Sbjct: 550 ATSEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKA 609

Query: 277 FKKVQ 281
            +K++
Sbjct: 610 LRKLR 614


>gi|182435494|ref|YP_001823213.1| RNA polymerase sigma factor [Streptomyces griseus subsp. griseus
           NBRC 13350]
 gi|326776131|ref|ZP_08235396.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces cf.
           griseus XylebKG-1]
 gi|11132962|sp|P77951|HRDB_STRGR RecName: Full=RNA polymerase principal sigma factor hrdB
 gi|1617256|gb|AAB16905.1| principal sigma factor [Streptomyces griseus]
 gi|178464010|dbj|BAG18530.1| RNA polymerase principal sigma factor hrdB [Streptomyces griseus
           subsp. griseus NBRC 13350]
 gi|326656464|gb|EGE41310.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces cf.
           griseus XylebKG-1]
          Length = 514

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 140/310 (45%), Gaps = 62/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ +I K+P+L  ++E  LAKR  E G  +                           A +
Sbjct: 221 YLKQIGKVPLLNAEQEVELAKRI-EAGLFAEDKLANADKLAPKLKRELEIIAEDGRRAKN 279

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 280 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 339

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ +
Sbjct: 340 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEV 399

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 400 QK----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 445

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 446 -------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 498

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 499 KLRHPSRSQV 508


>gi|291436829|ref|ZP_06576219.1| RNA polymerase sigma factor RpoD [Streptomyces ghanaensis ATCC
           14672]
 gi|291339724|gb|EFE66680.1| RNA polymerase sigma factor RpoD [Streptomyces ghanaensis ATCC
           14672]
          Length = 509

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 140/310 (45%), Gaps = 62/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ +I K+P+L  ++E  LAKR  E G  +                           A +
Sbjct: 216 YLKQIGKVPLLNAEQEVELAKRI-EAGLFAEDKLANSDKLAPKLKRELEIIAEDGRRAKN 274

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 275 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 334

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ +
Sbjct: 335 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEV 394

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 395 QK----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 440

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 441 -------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 493

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 494 KLRHPSRSQV 503


>gi|269219424|ref|ZP_06163278.1| carbamoyl-phosphate synthase L chain, ATP-binding [Actinomyces sp.
           oral taxon 848 str. F0332]
 gi|269211120|gb|EEZ77460.1| carbamoyl-phosphate synthase L chain, ATP-binding [Actinomyces sp.
           oral taxon 848 str. F0332]
          Length = 592

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 84/313 (26%), Positives = 147/313 (46%), Gaps = 65/313 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH----GDLSAA------------------- 50
           Y+ +I K+P+L  +EE  LA+R     Y +H    G L  A                   
Sbjct: 296 YLKQIGKVPLLNAEEEVELARRIEAGLYAQHILESGSLDKAKDRMYMRELKLISRDGQQA 355

Query: 51  -HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI
Sbjct: 356 KNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLVRAVEKFDFTKGFKFSTYATWWI 415

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + A+   +      ++I    +   +   L R+    Q + D   +P   + +AK+L+++
Sbjct: 416 RQAITRAMADQARTIRI--PVHMVEVINKLARV--QRQMLQDLGREP-TTIELAKELDMT 470

Query: 170 ESEV----------ISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           E +V          IS++  L   GD     LI  S+          V   D     L++
Sbjct: 471 EEKVIEVQKYGREPISLHTPLGEDGDSEFGDLIEDSE---------AVVPADAVGFTLLQ 521

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEAR 275
           ++        L + +  L+ RE  +   R  L +    TL+ +   + V+RER+RQIE++
Sbjct: 522 EQ--------LRQVLDTLSEREAGVVAMRFGLTDGQTKTLDEIGKVYGVTRERIRQIESK 573

Query: 276 AFKKVQESIQKQV 288
              K++   + QV
Sbjct: 574 TMSKLRHPSRSQV 586


>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 = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/245 (28%), Positives = 115/245 (46%), Gaps = 32/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 388 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 447

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV--------V 160
           I+ A+   I      ++I    +       + R+   L         PE++        V
Sbjct: 448 IRQAITRSIADQARTIRI--PVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEV 505

Query: 161 AIAKKLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            + K L +++ E ISM   +  DE   L   I  S+  S                  ++ 
Sbjct: 506 KVRKVLKIAK-EPISMETPIGDDEDSHLGDFIEDSNITSP-----------------VDA 547

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARA 276
              +  +      +  L  RE ++ + R   + P   TLE +  +F+V+RER+RQIEA+A
Sbjct: 548 ATSEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKA 607

Query: 277 FKKVQ 281
            +K++
Sbjct: 608 LRKLR 612


>gi|254672481|emb|CBA05947.1| RNA polymerase sigma factor 70 [Neisseria meningitidis alpha275]
          Length = 642

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/244 (28%), Positives = 121/244 (49%), Gaps = 28/244 (11%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 398 AAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 457

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD--NNLKPEQVVAIA-- 163
           WI+ A+   I      ++I     +     N R  + HLQ   +  ++ K  +++ +   
Sbjct: 458 WIRQAITRSIADQARTIRIPVHMIETINKMN-RISRQHLQETGEEPDSAKLAELMQMPED 516

Query: 164 --KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKE 219
             +K+     E ISM   +  D+  +      D N+    D  +Y   H+  +++L    
Sbjct: 517 KIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPADAAMYTSLHEVTKEIL---- 572

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
                          L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 573 -------------ESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKAL 619

Query: 278 KKVQ 281
           +K++
Sbjct: 620 RKLR 623


>gi|221633686|ref|YP_002522912.1| RNA polymerase sigma 70 subunit, RpoD [Thermomicrobium roseum DSM
           5159]
 gi|221156620|gb|ACM05747.1| RNA polymerase sigma 70 subunit, RpoD [Thermomicrobium roseum DSM
           5159]
          Length = 509

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 71/245 (28%), Positives = 120/245 (48%), Gaps = 13/245 (5%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           +R R  G+ +A  +L  ++LRLVV IA  Y G GL + +++ EGN+GLM+AV KF   +G
Sbjct: 263 QRLRRDGE-AARRKLTEANLRLVVSIAKRYTGRGLTLLDLIQEGNLGLMRAVDKFQTHKG 321

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           F+ +TY+ WWI+ A+   +      +++        L   L R+    + +T    +   
Sbjct: 322 FKFSTYATWWIRQAITRALADHARTIRLPV-----HLVETLNRVSRVARQLTQELGREPT 376

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              +A  +N+    +  +        SL A +   ++  S   D+L    D +    ++ 
Sbjct: 377 TSELAAAVNMPLDRLRELLQAAQDPVSLEAPVGQEEE--STLGDFL---EDERAVAPLDA 431

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARA 276
                 R  +   ++ L  RERR+   R   E+    TLE +   F V+RERVRQIEA+A
Sbjct: 432 AALSLLREQVQSLLATLTERERRVLAMRFGLEDGQTYTLEEVGRAFGVTRERVRQIEAKA 491

Query: 277 FKKVQ 281
            +K++
Sbjct: 492 LRKLR 496


>gi|326443878|ref|ZP_08218612.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 537

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 140/310 (45%), Gaps = 62/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ +I K+P+L  ++E  LAKR  E G  +                           A +
Sbjct: 244 YLKQIGKVPLLNAEQEVELAKRI-EAGLFAEDKLANADKLAPKLKRELEIIAEDGRRAKN 302

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 303 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 362

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ +
Sbjct: 363 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEV 422

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 423 QK----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 468

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 469 -------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 521

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 522 KLRHPSRSQV 531


>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 = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 118/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 379 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 438

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 439 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPED 496

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 497 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 540

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ +N     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 541 SESLKNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 600

Query: 279 KVQ 281
           K++
Sbjct: 601 KLR 603


>gi|21224164|ref|NP_629943.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
 gi|289768642|ref|ZP_06528020.1| transcription initiation factor sigma [Streptomyces lividans TK24]
 gi|12644145|sp|P18183|HRDB_STRCO RecName: Full=RNA polymerase principal sigma factor hrdB
 gi|3036885|emb|CAA18518.1| major vegetative sigma factor [Streptomyces coelicolor A3(2)]
 gi|289698841|gb|EFD66270.1| transcription initiation factor sigma [Streptomyces lividans TK24]
          Length = 511

 Score = 91.3 bits (225), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 140/310 (45%), Gaps = 62/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ +I K+P+L  ++E  LAKR  E G  +                           A +
Sbjct: 218 YLKQIGKVPLLNAEQEVELAKRI-EAGLFAEDKLANSDKLAPKLKRELEIIAEDGRRAKN 276

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 277 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 336

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ +
Sbjct: 337 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEV 396

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 397 QKYGR----EPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 442

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 443 -------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 495

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 496 KLRHPSRSQV 505


>gi|333024008|ref|ZP_08452072.1| putative RNA polymerase sigma factor RpoS [Streptomyces sp. Tu6071]
 gi|332743860|gb|EGJ74301.1| putative RNA polymerase sigma factor RpoS [Streptomyces sp. Tu6071]
          Length = 493

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 140/310 (45%), Gaps = 62/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ +I K+P+L  ++E  LAKR  E G  +                           A +
Sbjct: 200 YLKQIGKVPLLNAEQEVELAKRI-EAGLFAEDKLANSDKLAPKLQRELEIIAEDGRRAKN 258

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 259 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 318

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ +
Sbjct: 319 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEV 378

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 379 QK----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 424

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 425 -------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 477

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 478 KLRHPSRSQV 487


>gi|225848841|ref|YP_002729005.1| RNA polymerase sigma factor RpoD (Sigma-A) (Major vegetative
           sigmafactor) [Sulfurihydrogenibium azorense Az-Fu1]
 gi|225644391|gb|ACN99441.1| RNA polymerase sigma factor RpoD (Sigma-A) (Major vegetative
           sigmafactor) [Sulfurihydrogenibium azorense Az-Fu1]
          Length = 586

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 72/242 (29%), Positives = 114/242 (47%), Gaps = 34/242 (14%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV K+D +RGF+ +TY+ WWI+ A
Sbjct: 351 LVKANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKYDYKRGFKFSTYATWWIRQA 410

Query: 113 MQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA------- 161
           +   I      ++I      T N+      L R+   +         PE++         
Sbjct: 411 ITRAIADQARTIRIPVHMIETINK------LIRVARSMVQELGREPTPEEIAKKVGMPAE 464

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
             KK+  +  E IS+   +  DE  +      DK+    +  ++               +
Sbjct: 465 KVKKILRTSQEPISLETPIGTDEETHLGDFIEDKSVLSPEAHML---------------K 509

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKK 279
              R  L   +S L+ RE ++   R   E+    TLE +   F V+RER+RQIEA+A +K
Sbjct: 510 NALRMQLDEVLSTLSEREEQVLRYRFGLEDDTEHTLEQVGKRFGVTRERIRQIEAKALRK 569

Query: 280 VQ 281
           ++
Sbjct: 570 LR 571


>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 = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/244 (28%), Positives = 121/244 (49%), Gaps = 28/244 (11%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 414 AAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 473

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD--NNLKPEQVVAIA-- 163
           WI+ A+   I      ++I     +     N R  + HLQ   +  ++ K  +++ +   
Sbjct: 474 WIRQAITRSIADQARTIRIPVHMIETINKMN-RISRQHLQETGEEPDSAKLAELMQMPED 532

Query: 164 --KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKE 219
             +K+     E ISM   +  D+  +      D N+    D  +Y   H+  +++L    
Sbjct: 533 KIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPADAAMYTSLHEVTKEIL---- 588

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
                          L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 589 -------------ESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKAL 635

Query: 278 KKVQ 281
           +K++
Sbjct: 636 RKLR 639


>gi|15677390|ref|NP_274545.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis MC58]
 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]
          Length = 642

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/244 (28%), Positives = 121/244 (49%), Gaps = 28/244 (11%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 398 AAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 457

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD--NNLKPEQVVAIA-- 163
           WI+ A+   I      ++I     +     N R  + HLQ   +  ++ K  +++ +   
Sbjct: 458 WIRQAITRSIADQARTIRIPVHMIETINKMN-RISRQHLQETGEEPDSAKLAELMQMPED 516

Query: 164 --KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKE 219
             +K+     E ISM   +  D+  +      D N+    D  +Y   H+  +++L    
Sbjct: 517 KIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPADAAMYTSLHEVTKEIL---- 572

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
                          L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 573 -------------ESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKAL 619

Query: 278 KKVQ 281
           +K++
Sbjct: 620 RKLR 623


>gi|187250727|ref|YP_001875209.1| RNA polymerase, sigma 70 subunit, RpoD family [Elusimicrobium
           minutum Pei191]
 gi|186970887|gb|ACC97872.1| RNA polymerase, sigma 70 subunit, RpoD family [Elusimicrobium
           minutum Pei191]
          Length = 571

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 82/279 (29%), Positives = 140/279 (50%), Gaps = 27/279 (9%)

Query: 14  IGLSRYIHE--IRKIPMLEKQEEYVLAKR--YREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           I + R  HE  I  +PM EK E      R  + E   L    +L+ ++LRLVV IA  + 
Sbjct: 295 IDMIRSRHEKLINTLPMSEK-EFLAFNDRIVFFEDMILQDKLKLIKANLRLVVSIAKKHV 353

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
              L +S+++ EG +GLM+AV+KF+ +RGF+ +TY+ WWI+ ++            I   
Sbjct: 354 NSNLELSDLIQEGGLGLMKAVEKFEYKRGFKFSTYATWWIRQSINRA---------IADQ 404

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQ-----VVAIAKKLNVSESEVISMNCRLAGDE 184
           AN  R+  +++ L   L  +T N  + E      +   +K L +S  +V  +   +    
Sbjct: 405 ANTIRIPVHMKELVSKLTKVT-NKFRQEHGREPSLEDYSKSLRLSMEKVKGVLKIMQDPI 463

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL+  +   +   S  +D+ + D  G    +   +    R+  ++  ++ L+ RE +I  
Sbjct: 464 SLSTPVGEDE--DSNLEDF-IEDKAGANPTVTASDFL--RKQEVSEVLNTLSEREAKIIR 518

Query: 245 ARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R   ++  P TLE +   F V+RERVRQIEA+A +K++
Sbjct: 519 LRFGIDSGYPRTLEEVGKMFNVTRERVRQIEAKAIRKLR 557


>gi|91200070|emb|CAJ73113.1| similar to transcription initiation factor sigma 70 [Candidatus
           Kuenenia stuttgartiensis]
          Length = 491

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 74/271 (27%), Positives = 126/271 (46%), Gaps = 57/271 (21%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           EYV+A++           R    +LRLVV IA  YR  G+   +++ EGN GLM+AV K+
Sbjct: 246 EYVMARK-----------RFSEGNLRLVVSIAKKYRKRGMAFHDLIQEGNTGLMRAVDKY 294

Query: 94  DPERGFRLATYSMWWIKAA-----------------MQEYILRSWSLVKIGTTANQKRLF 136
           D   GF+ +TY+ WWIK A                 M + I +S  + K G  ++ +++ 
Sbjct: 295 DYRMGFKFSTYATWWIKQAIIRATEEKVRTIRIPVHMMDVINKSTYVAKAGQGSSAEKI- 353

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
                    L+AI  +   P  +  I + L ++ S+ IS+   +  D             
Sbjct: 354 --------QLEAIARDTNTP--LPEIYRLLQIT-SQPISLETPIGSD------------G 390

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT-- 254
            + ++D++    D +    I   +R   +  + + +  L+ RER I + R    +  T  
Sbjct: 391 ETMFEDFI---QDKKIDAPIFLAQRSLLKEQIQKVLDTLSYREREIIKLRFGISDGYTHS 447

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           LE +   F ++RER+RQIEA A +K+Q  ++
Sbjct: 448 LEEIGKRFNITRERIRQIEAIALRKLQHPVR 478


>gi|317493716|ref|ZP_07952133.1| RNA polymerase sigma factor RpoD [Enterobacteriaceae bacterium
           9_2_54FAA]
 gi|316918043|gb|EFV39385.1| RNA polymerase sigma factor RpoD [Enterobacteriaceae bacterium
           9_2_54FAA]
          Length = 610

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 71/250 (28%), Positives = 121/250 (48%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 372 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 431

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 432 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELAERMMMPED 489

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 490 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 533

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ R+     +S L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 534 SESLRSATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 593

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 594 KLRHPSRSEV 603


>gi|311898773|dbj|BAJ31181.1| putative RNA polymerase major sigma factor [Kitasatospora setae
           KM-6054]
          Length = 541

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 81/310 (26%), Positives = 140/310 (45%), Gaps = 62/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHG-----DLSAAHRLVT------------------ 55
           Y+ +I K+P+L  ++E  LAKR  E G      LS A +L                    
Sbjct: 248 YLKQIGKVPLLNAEQEVELAKRI-EAGLFAEDKLSQADKLAPKLKRELEIIAEDGRRAKN 306

Query: 56  ----SHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
               ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 307 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 366

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ +
Sbjct: 367 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEV 426

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 427 QKYGR----EPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 472

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 473 -------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 525

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 526 KLRHPSRSQV 535


>gi|297191610|ref|ZP_06909008.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
 gi|297151002|gb|EFH30922.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
          Length = 516

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 139/310 (44%), Gaps = 62/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR---------------------------EHGDLSAAH 51
           Y+ +I K+P+L  ++E  LAKR                             E G  +  H
Sbjct: 223 YLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANSDKLAPKLKRELEIIAEDGRRAKNH 282

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 283 -LLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 341

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ +
Sbjct: 342 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEV 401

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 402 QKYGR----EPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 447

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 448 -------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 500

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 501 KLRHPSRSQV 510


>gi|254386999|ref|ZP_05002279.1| RNA polymerase sigma factor [Streptomyces sp. Mg1]
 gi|194345824|gb|EDX26790.1| RNA polymerase sigma factor [Streptomyces sp. Mg1]
          Length = 520

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 140/310 (45%), Gaps = 62/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ +I K+P+L  ++E  LAKR  E G  +                           A +
Sbjct: 227 YLKQIGKVPLLNAEQEVELAKRI-EAGLFAEDKLANSDKLAPKLKRELEIIAEDGRRAKN 285

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 286 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 345

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ +
Sbjct: 346 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEV 405

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 406 QKYGR----EPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 451

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 452 -------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 504

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 505 KLRHPSRSQV 514


>gi|291454591|ref|ZP_06593981.1| RNA polymerase sigma factor RpoD [Streptomyces albus J1074]
 gi|581664|emb|CAA53564.1| sigma factor (RNA polymerase subunit) [Streptomyces griseus]
 gi|291357540|gb|EFE84442.1| RNA polymerase sigma factor RpoD [Streptomyces albus J1074]
          Length = 510

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 140/310 (45%), Gaps = 62/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ +I K+P+L  ++E  LAKR  E G  +                           A +
Sbjct: 217 YLKQIGKVPLLNAEQEVELAKRI-EAGLFAEDKLANADKIAPKLKRELEIIAEDGRRAKN 275

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 276 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 335

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ +
Sbjct: 336 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEV 395

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 396 QKYGR----EPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 441

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 442 -------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 494

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 495 KLRHPSRSQV 504


>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 [Neisseria meningitidis alpha14]
 gi|304387052|ref|ZP_07369304.1| DNA-directed RNA polymerase sigma subunit RpoD [Neisseria
           meningitidis ATCC 13091]
 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]
          Length = 642

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/244 (28%), Positives = 121/244 (49%), Gaps = 28/244 (11%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 398 AAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 457

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD--NNLKPEQVVAIA-- 163
           WI+ A+   I      ++I     +     N R  + HLQ   +  ++ K  +++ +   
Sbjct: 458 WIRQAITRSIADQARTIRIPVHMIETINKMN-RISRQHLQETGEEPDSAKLAELMQMPED 516

Query: 164 --KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKE 219
             +K+     E ISM   +  D+  +      D N+    D  +Y   H+  +++L    
Sbjct: 517 KIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPADAAMYTSLHEVTKEIL---- 572

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
                          L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 573 -------------ESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKAL 619

Query: 278 KKVQ 281
           +K++
Sbjct: 620 RKLR 623


>gi|308233952|ref|ZP_07664689.1| RNA polymerase, sigma 70 subunit, RpoD [Atopobium vaginae DSM
           15829]
 gi|328943964|ref|ZP_08241429.1| putative DNA-directed RNA polymerase sigma subunit RpoD [Atopobium
           vaginae DSM 15829]
 gi|327491933|gb|EGF23707.1| putative DNA-directed RNA polymerase sigma subunit RpoD [Atopobium
           vaginae DSM 15829]
          Length = 441

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 85/305 (27%), Positives = 133/305 (43%), Gaps = 64/305 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGD------------------------------LS 48
           Y+ EI K+ +L   EE  LA + +   D                              L 
Sbjct: 143 YLKEIGKVDLLNASEEVHLAMKIQAGTDASKKLEAAENGEIELTRAEQRRLMRIEQVGLD 202

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L +++LRL V IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WW
Sbjct: 203 AKQALTSANLRLTVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 262

Query: 109 IKAAMQEYILRSWSLVKIGT----TAN-----QKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N     QK L  +L R     +      +  ++V
Sbjct: 263 IRQAITRAIADQARTIRIPVHMVETINKLVRVQKELLQDLGREPTPEEIGEQMKMSADRV 322

Query: 160 VAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
             I K   +S+ E +S+   +    D SL   I  S           V   D     ++ 
Sbjct: 323 REIQK---ISQ-EPVSLETPIGEEEDSSLGDFIEDS---------TAVAPPDAASDSML- 368

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
                  R  L + +  L  RER++ + R   E+  P TLE +  EF V+RER+RQIE++
Sbjct: 369 -------REQLNQVLDGLADRERKVIKFRFGLEDGHPRTLEEVGREFGVTRERIRQIESK 421

Query: 276 AFKKV 280
              K+
Sbjct: 422 TLAKL 426


>gi|307325028|ref|ZP_07604232.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306889174|gb|EFN20156.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 502

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 140/310 (45%), Gaps = 62/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ +I K+P+L  ++E  LAKR  E G  +                           A +
Sbjct: 209 YLKQIGKVPLLNAEQEVELAKRI-EAGLFAEDKLANSDKLAPKLKRELEIIAEDGRRAKN 267

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 268 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 327

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ +
Sbjct: 328 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEV 387

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 388 QK----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 433

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 434 -------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 486

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 487 KLRHPSRSQV 496


>gi|240115443|ref|ZP_04729505.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae PID18]
 gi|260440745|ref|ZP_05794561.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae DGI2]
 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 = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/244 (28%), Positives = 121/244 (49%), Gaps = 28/244 (11%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 398 AAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 457

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD--NNLKPEQVVAIA-- 163
           WI+ A+   I      ++I     +     N R  + HLQ   +  ++ K  +++ +   
Sbjct: 458 WIRQAITRSIADQARTIRIPVHMIETINKMN-RISRQHLQETGEEPDSAKLAELMQMPED 516

Query: 164 --KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKE 219
             +K+     E ISM   +  D+  +      D N+    D  +Y   H+  +++L    
Sbjct: 517 KIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPADAAMYTSLHEVTKEIL---- 572

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
                          L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 573 -------------ESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKAL 619

Query: 278 KKVQ 281
           +K++
Sbjct: 620 RKLR 623


>gi|213018850|ref|ZP_03334658.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of Culex
           quinquefasciatus JHB]
 gi|212995801|gb|EEB56441.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of Culex
           quinquefasciatus JHB]
          Length = 632

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 68/241 (28%), Positives = 120/241 (49%), Gaps = 23/241 (9%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLVV IA  Y   GL + +++ EGNIGLM+AV KFD +RG++ +TY  WW
Sbjct: 395 AKQEMIKANLRLVVSIAKKYSKRGLDLLDLIQEGNIGLMKAVDKFDYKRGYKFSTYGTWW 454

Query: 109 IKAAMQEYILRSWSLVKIGTTANQ--KRLFFNLRRLK---GHLQAITDNNLKPEQVVAIA 163
           +K ++   I     +V+I     +   ++   LR++    G    + + +++    +   
Sbjct: 455 VKQSITRAIPEQSKVVRIPVHMVEIISKINKALRKMTHEMGREPTLEELSIELAMPLERI 514

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           +K+     + +S+      D+S        DK  S+ +D  +                 +
Sbjct: 515 RKVMKIARDPVSLEAPTGKDDSSTFGDCIEDKRVSKPEDAAIL---------------AD 559

Query: 224 RRNMLTRSMSVLNPRERRIFEAR-RLQENPV--TLENLSSEFEVSRERVRQIEARAFKKV 280
            R + T  ++ L P+E RI   R  L ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 560 LRGITTNVLATLTPKEERILRMRFGLGKDGKEHTLEEVGKIFNVTRERIRQIEAKALRKL 619

Query: 281 Q 281
           +
Sbjct: 620 K 620


>gi|119961685|ref|YP_947521.1| RNA polymerase sigma (70) factor RpoD [Arthrobacter aurescens TC1]
 gi|119948544|gb|ABM07455.1| RNA polymerase sigma (70) factor RpoD [Arthrobacter aurescens TC1]
          Length = 437

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 75/277 (27%), Positives = 132/277 (47%), Gaps = 44/277 (15%)

Query: 27  PMLEKQEEYVL--AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           P L+++ E+V+   KR + H        L+ ++LRLVV +A  Y G G+   +++ EGN+
Sbjct: 184 PKLKRELEFVIHDGKRAKNH--------LLEANLRLVVSLAKRYTGRGMLFLDLIQEGNL 235

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT---------TANQKRL 135
           GL++AV+KFD  +GF+ +TY+ WWI+ A+   +      ++I              Q+++
Sbjct: 236 GLIRAVEKFDYTKGFKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQM 295

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSS 193
             +L R     +   + ++ PE+VV + K       E IS++  L   GD     LI  S
Sbjct: 296 LQDLGREPTPEELALELDMTPEKVVEVQKYGR----EPISLHTPLGEDGDSEFGDLIEDS 351

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQEN 251
           +          V   D     L++++        L   +  L+ RE  +   R       
Sbjct: 352 EA---------VVPADAVSFTLLQEQ--------LHSVLDTLSEREAGVVAMRFGLTDGQ 394

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           P TL+ +   + V+RER+RQIE++   K++   + QV
Sbjct: 395 PKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQV 431


>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 = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/244 (28%), Positives = 121/244 (49%), Gaps = 28/244 (11%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 398 AAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 457

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD--NNLKPEQVVAIA-- 163
           WI+ A+   I      ++I     +     N R  + HLQ   +  ++ K  +++ +   
Sbjct: 458 WIRQAITRSIADQARTIRIPVHMIETINKMN-RISRQHLQETGEEPDSAKLAELMQMPED 516

Query: 164 --KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKE 219
             +K+     E ISM   +  D+  +      D N+    D  +Y   H+  +++L    
Sbjct: 517 KIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPADAAMYTSLHEVTKEIL---- 572

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
                          L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 573 -------------ESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKAL 619

Query: 278 KKVQ 281
           +K++
Sbjct: 620 RKLR 623


>gi|220907004|ref|YP_002482315.1| RNA polymerase sigma factor [Cyanothece sp. PCC 7425]
 gi|219863615|gb|ACL43954.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7425]
          Length = 327

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 73/300 (24%), Positives = 137/300 (45%), Gaps = 52/300 (17%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR--------------------------YREHGDLSAA-- 50
           Y+HEI ++P+L  ++E VL K+                          + E  +LS A  
Sbjct: 23  YLHEIGRVPLLTHEQEIVLGKQVQQLMELLEAREKLTTSLDRSPTAEEWAEQANLSVADL 82

Query: 51  -----------HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                       +++ ++LRLVV +A  Y+   L + +++ EG +GL + V+KFDP RG+
Sbjct: 83  NTAVRRGQRAKQKMIEANLRLVVSVAKKYQKRNLELLDLIQEGTLGLERGVEKFDPTRGY 142

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWI+ A+   I +    V++     +K     L ++K   + ++    +    
Sbjct: 143 KFSTYAYWWIRQAITRAIAQQARTVRLPIHITEK-----LNKIKKAQRVLSQRLGRSATP 197

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IA++L +  S++           SL+  +   D   ++ +D L  D    EQ    + 
Sbjct: 198 AEIAQELELEPSQIREYLTLARQPVSLD--LRVGDNQDTELRDLLEDDSPSPEQYTTGEA 255

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
            R +  ++L      L P++R +   R   E+   ++L  +  +  +SRERVRQ+E +A 
Sbjct: 256 LRDDVNHLLAE----LTPQQREVLTLRFGLEDGKELSLAKVGEQLSLSRERVRQLERQAL 311


>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]
          Length = 642

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/244 (28%), Positives = 121/244 (49%), Gaps = 28/244 (11%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 398 AAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 457

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD--NNLKPEQVVAIA-- 163
           WI+ A+   I      ++I     +     N R  + HLQ   +  ++ K  +++ +   
Sbjct: 458 WIRQAITRSIADQARTIRIPVHMIETINKMN-RISRQHLQETGEEPDSAKLAELMQMPED 516

Query: 164 --KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKE 219
             +K+     E ISM   +  D+  +      D N+    D  +Y   H+  +++L    
Sbjct: 517 KIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPADAAMYTSLHEVTKEIL---- 572

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
                          L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 573 -------------ESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKAL 619

Query: 278 KKVQ 281
           +K++
Sbjct: 620 RKLR 623


>gi|62734062|gb|AAX96171.1| Sigma-70 region 3, putative [Oryza sativa Japonica Group]
 gi|125589330|gb|EAZ29680.1| hypothetical protein OsJ_13741 [Oryza sativa Japonica Group]
          Length = 563

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 73/262 (27%), Positives = 132/262 (50%), Gaps = 37/262 (14%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E  L KR  +HG +   +R+VTS++RLV+ IA  + G G+ + +++ EG  GL++  +K
Sbjct: 309 DERTLRKRL-DHG-IYCKNRMVTSNVRLVISIAREFEGPGMELYDLIQEGMQGLIRGAEK 366

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +GFR +TYS WWIK AM++ +     + ++   A+     + ++     L+     
Sbjct: 367 FDASKGFRFSTYSHWWIKQAMRKSVSEQSQIFRL--PAHMVEASYRVKECIKRLRRKLKR 424

Query: 153 NLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
               E++ A        +   +N+ +  V           SL++ I S+D         +
Sbjct: 425 RPTNEEIAADTGMPIKRVEAAVNLPKYSV-----------SLDSKIGSTD---------M 464

Query: 205 VYDHDGQEQVLIEKEERKNRRNM---LTRSMSVLNPRERRIFEAR-RLQENPV-TLENLS 259
            Y     +      EE  NR +M   + +++  L  RER++   R  L++  + TL+ + 
Sbjct: 465 TYQEVTADPTAETAEEMLNRLSMKRDVHKALDTLTTRERQVVTLRFGLEDGRIRTLQEIG 524

Query: 260 SEFEVSRERVRQIEARAFKKVQ 281
           +   VSRER+RQIE+ AF+K++
Sbjct: 525 NTMGVSRERIRQIESAAFRKLR 546


>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 = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 71/242 (29%), Positives = 116/242 (47%), Gaps = 28/242 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 373 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 432

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 433 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMAMPED 490

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D    + I+   
Sbjct: 491 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDNTLDLPIDSAT 534

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ RN +   +  L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 535 SESLRNSVRDVLGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 594

Query: 279 KV 280
           K+
Sbjct: 595 KL 596


>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 = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 71/244 (29%), Positives = 124/244 (50%), Gaps = 30/244 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 438 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPSPEELAERMLMPED- 495

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 496 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 538

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ +N     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 539 TGESLKNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 598

Query: 278 KKVQ 281
           +K++
Sbjct: 599 RKLR 602


>gi|313668077|ref|YP_004048361.1| RNA polymerase sigma factor [Neisseria lactamica ST-640]
 gi|313005539|emb|CBN86975.1| RNA polymerase sigma factor [Neisseria lactamica 020-06]
          Length = 642

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/244 (28%), Positives = 121/244 (49%), Gaps = 28/244 (11%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 398 AAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 457

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD--NNLKPEQVVAIA-- 163
           WI+ A+   I      ++I     +     N R  + HLQ   +  ++ K  +++ +   
Sbjct: 458 WIRQAITRSIADQARTIRIPVHMIETINKMN-RISRQHLQETGEEPDSAKLAELMQMPED 516

Query: 164 --KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKE 219
             +K+     E ISM   +  D+  +      D N+    D  +Y   H+  +++L    
Sbjct: 517 KIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPADAAMYTSLHEVTKEIL---- 572

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
                          L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 573 -------------ESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKAL 619

Query: 278 KKVQ 281
           +K++
Sbjct: 620 RKLR 623


>gi|256784755|ref|ZP_05523186.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
          Length = 492

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 140/310 (45%), Gaps = 62/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ +I K+P+L  ++E  LAKR  E G  +                           A +
Sbjct: 199 YLKQIGKVPLLNAEQEVELAKRI-EAGLFAEDKLANSDKLAPKLKRELEIIAEDGRRAKN 257

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 258 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 317

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ +
Sbjct: 318 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEV 377

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 378 QK----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 423

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 424 -------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 476

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 477 KLRHPSRSQV 486


>gi|225677095|ref|ZP_03788097.1| RNA polymerase sigma 70 subunit, RpoD [Wolbachia endosymbiont of
           Muscidifurax uniraptor]
 gi|225590854|gb|EEH12079.1| RNA polymerase sigma 70 subunit, RpoD [Wolbachia endosymbiont of
           Muscidifurax uniraptor]
          Length = 669

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 77/261 (29%), Positives = 128/261 (49%), Gaps = 27/261 (10%)

Query: 32  QEEYVLAKRYREHG-DLS-AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           QE   L KR ++H  ++S A   ++ ++LRLVV IA  Y   GL + +++ EGNIGLM+A
Sbjct: 413 QEFKELIKRIQKHEREVSEAKQEMIKANLRLVVSIAKKYSKRGLDLLDLIQEGNIGLMKA 472

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ--KRLFFNLRRLKGHL- 146
           V KFD +RG++ +TY  WW++ ++   I     +V+I     +   ++   LR++   + 
Sbjct: 473 VDKFDYKRGYKFSTYGTWWVRQSITRAIPEQSKVVRIPVHMVEIISKINRALRKMTHEMG 532

Query: 147 QAITDNNLKPEQVVA---IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
           +  T   L  E  +    I K + ++   V S+      D+S        DK  S+ +D 
Sbjct: 533 REPTLEELSVELTMPLERIRKVMKIARDPV-SLEAPTGKDDSSTFGDCIEDKRVSRPEDA 591

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSS 260
            +                 + R + T  ++ L P+E RI   R          TLE +  
Sbjct: 592 AIL---------------ADLRGITTNVLATLTPKEERILRMRFGLGKDGKEHTLEEVGK 636

Query: 261 EFEVSRERVRQIEARAFKKVQ 281
            F V+RER+RQIEA+A +K++
Sbjct: 637 IFNVTRERIRQIEAKALRKLK 657


>gi|190571452|ref|YP_001975810.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of Culex
           quinquefasciatus Pel]
 gi|190357724|emb|CAQ55173.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of Culex
           quinquefasciatus Pel]
          Length = 633

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 67/241 (27%), Positives = 117/241 (48%), Gaps = 23/241 (9%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLVV IA  Y   GL + +++ EGNIGLM+AV KFD +RG++ +TY  WW
Sbjct: 396 AKQEMIKANLRLVVSIAKKYSKRGLDLLDLIQEGNIGLMKAVDKFDYKRGYKFSTYGTWW 455

Query: 109 IKAAMQEYILRSWSLVKIGTTANQ--KRLFFNLRRLK---GHLQAITDNNLKPEQVVAIA 163
           +K ++   I     +V+I     +   ++   LR++    G    + + +++    +   
Sbjct: 456 VKQSITRAIPEQSKVVRIPVHMVEIISKINKALRKMTHEMGREPTLEELSIELAMPLERI 515

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           +K+     + +S+      D+S        DK  S+ +D  +                 +
Sbjct: 516 RKVMKIARDPVSLEAPTGKDDSSTFGDCIEDKRVSKPEDAAIL---------------AD 560

Query: 224 RRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            R + T  ++ L P+E RI   R          TLE +   F V+RER+RQIEA+A +K+
Sbjct: 561 LRGITTNVLATLTPKEERILRMRFGLGKDGKEHTLEEVGKIFNVTRERIRQIEAKALRKL 620

Query: 281 Q 281
           +
Sbjct: 621 K 621


>gi|271968332|ref|YP_003342528.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)-like
           protein [Streptosporangium roseum DSM 43021]
 gi|270511507|gb|ACZ89785.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)-like
           protein [Streptosporangium roseum DSM 43021]
          Length = 561

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 139/310 (44%), Gaps = 61/310 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR----------EHGDL-----------------SAAH 51
           Y+ +I K+P+L  ++E  LAKR              GD                   A +
Sbjct: 267 YLKQIGKVPLLNAEQEVELAKRIEAGLFAEEQLGTDGDKLPVDVRAELEWIAEDGRRAKN 326

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 327 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 386

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+VV +
Sbjct: 387 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELARELDMTPEKVVEV 446

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          +   D     L++++ 
Sbjct: 447 QKYGR----EPISLHTPLGEEGDSEFGDLIEDSEA---------IVPADAVSFTLLQEQ- 492

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 493 -------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 545

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 546 KLRHPSRSQV 555


>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 = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 71/244 (29%), Positives = 124/244 (50%), Gaps = 30/244 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 373 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 432

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 433 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPSPEELAERMLMPED- 490

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 491 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 533

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ +N     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 534 TGESLKNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 593

Query: 278 KKVQ 281
           +K++
Sbjct: 594 RKLR 597


>gi|1582791|prf||2119302A sigma factor
          Length = 445

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 140/310 (45%), Gaps = 62/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ +I K+P+L  ++E  LAKR  E G  +                           A +
Sbjct: 152 YLKQIGKVPLLNAEQEVELAKRI-EAGLFAEDKLANADKLAPKLKRELEIIAEDGRRAKN 210

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 211 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 270

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ +
Sbjct: 271 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEV 330

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 331 QK----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 376

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 377 -------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 429

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 430 KLRHPSRSQV 439


>gi|240127996|ref|ZP_04740657.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae SK-93-1035]
 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 = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/244 (28%), Positives = 121/244 (49%), Gaps = 28/244 (11%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 398 AAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 457

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD--NNLKPEQVVAIA-- 163
           WI+ A+   I      ++I     +     N R  + HLQ   +  ++ K  +++ +   
Sbjct: 458 WIRQAITRSIADQARTIRIPVHMIETINKMN-RISRQHLQETGEEPDSAKLAELMQMPED 516

Query: 164 --KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKE 219
             +K+     E ISM   +  D+  +      D N+    D  +Y   H+  +++L    
Sbjct: 517 KIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPADAAMYTSLHEVTKEIL---- 572

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
                          L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 573 -------------ESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKAL 619

Query: 278 KKVQ 281
           +K++
Sbjct: 620 RKLR 623


>gi|33862729|ref|NP_894289.1| RNA polymerase sigma-70 factor family protein [Prochlorococcus
           marinus str. MIT 9313]
 gi|33634645|emb|CAE20631.1| Sigma-70 factor family [Prochlorococcus marinus str. MIT 9313]
          Length = 308

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/244 (28%), Positives = 123/244 (50%), Gaps = 21/244 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A ++++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG R +TY+ WW
Sbjct: 66  AKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSTYAYWW 125

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   +      ++I    N+K     L +L+     +  NN  P     +AK + +
Sbjct: 126 IRQGLNRALSTQSRTIRIPVNVNEK-----LTKLRAAKSRLMQNNGLPPTAEQLAKTMRL 180

Query: 169 SESEVIS-MNCRL-AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR- 225
             +EV   + C L +   SL  ++ S   + S+  D L      +E   +E+ E   R  
Sbjct: 181 PMAEVEDLLACELRSVTVSLQGVVKSKS-DPSELADVL----PSEEIPPMERAEMSERTA 235

Query: 226 ---NMLTRSMSVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKK 279
               +L R+   L P+ER +   R   +      TL  ++     SRE  RQ+  RA +K
Sbjct: 236 SVWTLLNRAN--LTPKERMVVTLRFGLDGSHEWRTLAEVARHMSCSREYCRQVLQRALRK 293

Query: 280 VQES 283
           ++++
Sbjct: 294 LRKA 297


>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 = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 72/243 (29%), Positives = 119/243 (48%), Gaps = 27/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 380 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 439

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA------- 161
           I+ A+   I      ++I    +       L R+   +         PE++ A       
Sbjct: 440 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELAARMEMPED 497

Query: 162 -IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE  +      D+N +   D  V   +   + ++E+  
Sbjct: 498 KIRKVLKIAK-EPISMETPIGDDEDSHLGDFIEDRNVAAPTDAAV---NAAIREVVEE-- 551

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                 +L    + L PRE ++   R         TLE +  +F+V+RER+RQIEA+A +
Sbjct: 552 ------LLD---TGLTPREAKVLRMRFGIGMNTDHTLEEVGKQFDVTRERIRQIEAKALR 602

Query: 279 KVQ 281
           K++
Sbjct: 603 KLR 605


>gi|297580668|ref|ZP_06942594.1| LOW QUALITY PROTEIN: RNA polymerase sigma factor RpoS [Vibrio
           cholerae RC385]
 gi|297535084|gb|EFH73919.1| LOW QUALITY PROTEIN: RNA polymerase sigma factor RpoS [Vibrio
           cholerae RC385]
          Length = 236

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 67/231 (29%), Positives = 118/231 (51%), Gaps = 30/231 (12%)

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++ 
Sbjct: 11  YSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLP 70

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV--------AIAKKLNVSESEVISMNCR 179
                K L   LR  +  L    D+   PE++          + K L ++E  + S++  
Sbjct: 71  IHV-VKELNIYLRTAR-ELSQRLDHEPTPEEIALELDRPVDDVTKMLRLNE-RISSVDTP 127

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           + GD    AL++    + +   ++   D D +E +L   +E              LNP++
Sbjct: 128 IGGDGD-KALLDILPDSHNADPEFSTQDDDIRESLLNWLDE--------------LNPKQ 172

Query: 240 RRIFEARR---LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           + +  ARR   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 173 KEVL-ARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVKQ 222


>gi|239982743|ref|ZP_04705267.1| RNA polymerase sigma factor [Streptomyces albus J1074]
          Length = 491

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 140/310 (45%), Gaps = 62/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ +I K+P+L  ++E  LAKR  E G  +                           A +
Sbjct: 198 YLKQIGKVPLLNAEQEVELAKRI-EAGLFAEDKLANADKIAPKLKRELEIIAEDGRRAKN 256

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 257 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 316

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ +
Sbjct: 317 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEV 376

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 377 QK----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 422

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 423 -------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 475

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 476 KLRHPSRSQV 485


>gi|218194307|gb|EEC76734.1| hypothetical protein OsI_14770 [Oryza sativa Indica Group]
          Length = 563

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 73/262 (27%), Positives = 132/262 (50%), Gaps = 37/262 (14%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E  L KR  +HG +   +R+VTS++RLV+ IA  + G G+ + +++ EG  GL++  +K
Sbjct: 308 DERTLRKRL-DHG-IYCKNRMVTSNVRLVISIAREFEGPGMELYDLIQEGMQGLIRGAEK 365

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +GFR +TYS WWIK AM++ +     + ++   A+     + ++     L+     
Sbjct: 366 FDASKGFRFSTYSHWWIKQAMRKSVSEQSQIFRL--PAHMVEASYRVKECIKRLRRKLKR 423

Query: 153 NLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
               E++ A        +   +N+ +  V           SL++ I S+D         +
Sbjct: 424 RPTNEEIAADTGMPIKRVEAAVNLPKYSV-----------SLDSKIGSTD---------M 463

Query: 205 VYDHDGQEQVLIEKEERKNRRNM---LTRSMSVLNPRERRIFEAR-RLQENPV-TLENLS 259
            Y     +      EE  NR +M   + +++  L  RER++   R  L++  + TL+ + 
Sbjct: 464 TYQEVTADPTAETAEEMLNRLSMKRDVHKALDTLTTRERQVVTLRFGLEDGRIRTLQEIG 523

Query: 260 SEFEVSRERVRQIEARAFKKVQ 281
           +   VSRER+RQIE+ AF+K++
Sbjct: 524 NTMGVSRERIRQIESAAFRKLR 545


>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|240123293|ref|ZP_04736249.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae PID332]
 gi|240125543|ref|ZP_04738429.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae SK-92-679]
 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 = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/244 (28%), Positives = 121/244 (49%), Gaps = 28/244 (11%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 398 AAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 457

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD--NNLKPEQVVAIA-- 163
           WI+ A+   I      ++I     +     N R  + HLQ   +  ++ K  +++ +   
Sbjct: 458 WIRQAITRSIADQARTIRIPVHMIETINKMN-RISRQHLQETGEEPDSAKLAELMQMPED 516

Query: 164 --KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKE 219
             +K+     E ISM   +  D+  +      D N+    D  +Y   H+  +++L    
Sbjct: 517 KIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPADAAMYTSLHEVTKEIL---- 572

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
                          L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 573 -------------ESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKAL 619

Query: 278 KKVQ 281
           +K++
Sbjct: 620 RKLR 623


>gi|48745|emb|CAA37175.1| unnamed protein product [Streptomyces coelicolor A3(2)]
          Length = 442

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 140/310 (45%), Gaps = 62/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ +I K+P+L  ++E  LAKR  E G  +                           A +
Sbjct: 149 YLKQIGKVPLLNAEQEVELAKRI-EAGLFAEDKLANSDKLAPKLKRELEIIAEDGRRAKN 207

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 208 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 267

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ +
Sbjct: 268 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEV 327

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 328 QK----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 373

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 374 -------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 426

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 427 KLRHPSRSQV 436


>gi|194098357|ref|YP_002001415.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae NCCP11945]
 gi|239998768|ref|ZP_04718692.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae 35/02]
 gi|240112698|ref|ZP_04727188.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae MS11]
 gi|240117739|ref|ZP_04731801.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae PID1]
 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|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 = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/244 (28%), Positives = 121/244 (49%), Gaps = 28/244 (11%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 398 AAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 457

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD--NNLKPEQVVAIA-- 163
           WI+ A+   I      ++I     +     N R  + HLQ   +  ++ K  +++ +   
Sbjct: 458 WIRQAITRSIADQARTIRIPVHMIETINKMN-RISRQHLQETGEEPDSAKLAELMQMPED 516

Query: 164 --KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKE 219
             +K+     E ISM   +  D+  +      D N+    D  +Y   H+  +++L    
Sbjct: 517 KIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPADAAMYTSLHEVTKEIL---- 572

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
                          L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 573 -------------ESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKAL 619

Query: 278 KKVQ 281
           +K++
Sbjct: 620 RKLR 623


>gi|271962349|ref|YP_003336545.1| RNA polymerase sigma factor RpoD [Streptosporangium roseum DSM
           43021]
 gi|270505524|gb|ACZ83802.1| RNA polymerase sigma factor RpoD [Streptosporangium roseum DSM
           43021]
          Length = 324

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 82/308 (26%), Positives = 137/308 (44%), Gaps = 61/308 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS--------------------------AAHR 52
           Y+ +I +IP+L   +E  LA+R  E G  +                          A  R
Sbjct: 32  YLRQIARIPLLTAGQEVELARRV-EAGLFARERLGAEGLPAALRAELECVADDGRRAKDR 90

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            V ++LRLVV IA  + G G+P+ +++ EGN+GL++AV+KFD   GF+ +TY+ WWIK A
Sbjct: 91  FVEANLRLVVSIAKRHAGRGVPLLDLIQEGNLGLIRAVEKFDHRLGFKFSTYATWWIKQA 150

Query: 113 MQEYILRSWSLVKIG---------TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           +   +      V++              +++L  +L R     +   + +L PE+V  I 
Sbjct: 151 ITRAMADQARTVRVPVHMVEMINKVARVERQLLCDLGREPTPEEIAAELDLTPEKVTEIK 210

Query: 164 KKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
                   E IS++  L   GD  L  LI  ++  + +           QEQV       
Sbjct: 211 GH----GREPISLHTPLGDEGDSELGDLIEDAEAVTPEAAVAFTLL---QEQV------- 256

Query: 222 KNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
              R +L    + L  RE  +   R       P TL+ +   + ++RER+RQIE++   +
Sbjct: 257 ---RALL----ATLTGREAGVISMRFGFADGRPWTLDEIGRVYGLTRERIRQIESKTMSR 309

Query: 280 VQESIQKQ 287
           ++   + Q
Sbjct: 310 LRHPSRSQ 317


>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 = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 71/244 (29%), Positives = 124/244 (50%), Gaps = 30/244 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 377 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 436

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 437 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPSPEELAERMLMPED- 494

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 495 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 537

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ +N     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 538 TGESLKNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 597

Query: 278 KKVQ 281
           +K++
Sbjct: 598 RKLR 601


>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 = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 118/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 389 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 448

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 449 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPED 506

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 507 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 550

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ +N     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 551 SESLKNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 610

Query: 279 KVQ 281
           K++
Sbjct: 611 KLR 613


>gi|32351878|dbj|BAC78528.1| plastid sigma factor 2A [Oryza sativa Japonica Group]
          Length = 564

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 73/262 (27%), Positives = 132/262 (50%), Gaps = 37/262 (14%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E  L KR  +HG +   +R+VTS++RLV+ IA  + G G+ + +++ EG  GL++  +K
Sbjct: 309 DERTLRKRL-DHG-IYCKNRMVTSNVRLVISIAREFEGPGMELYDLIQEGMQGLIRGAEK 366

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +GFR +TYS WWIK AM++ +     + ++   A+     + ++     L+     
Sbjct: 367 FDASKGFRFSTYSHWWIKQAMRKSVSEQSQIFRL--PAHMVEASYRVKECIKRLRRKLKR 424

Query: 153 NLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
               E++ A        +   +N+ +  V           SL++ I S+D         +
Sbjct: 425 RPTNEEIAADTGMPIKRVEAAVNLPKYSV-----------SLDSKIGSTD---------M 464

Query: 205 VYDHDGQEQVLIEKEERKNRRNM---LTRSMSVLNPRERRIFEAR-RLQENPV-TLENLS 259
            Y     +      EE  NR +M   + +++  L  RER++   R  L++  + TL+ + 
Sbjct: 465 TYQEVTADPTAETAEEMLNRLSMKRDVHKALDTLTTRERQVVTLRFGLEDGRIRTLQEIG 524

Query: 260 SEFEVSRERVRQIEARAFKKVQ 281
           +   VSRER+RQIE+ AF+K++
Sbjct: 525 NTMGVSRERIRQIESAAFRKLR 546


>gi|297611772|ref|NP_001067832.2| Os11g0448400 [Oryza sativa Japonica Group]
 gi|62701714|gb|AAX92787.1| Sigma-70 region 3, putative [Oryza sativa Japonica Group]
 gi|108864350|gb|ABA93405.2| Sigma-70 region 3 family protein, expressed [Oryza sativa Japonica
           Group]
 gi|255680064|dbj|BAF28195.2| Os11g0448400 [Oryza sativa Japonica Group]
          Length = 564

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 73/262 (27%), Positives = 132/262 (50%), Gaps = 37/262 (14%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E  L KR  +HG +   +R+VTS++RLV+ IA  + G G+ + +++ EG  GL++  +K
Sbjct: 309 DERTLRKRL-DHG-IYCKNRMVTSNVRLVISIAREFEGPGMELYDLIQEGMQGLIRGAEK 366

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +GFR +TYS WWIK AM++ +     + ++   A+     + ++     L+     
Sbjct: 367 FDASKGFRFSTYSHWWIKQAMRKSVSEQSQIFRL--PAHMVEASYRVKECIKRLRRKLKR 424

Query: 153 NLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
               E++ A        +   +N+ +  V           SL++ I S+D         +
Sbjct: 425 RPTNEEIAADTGMPIKRVEAAVNLPKYSV-----------SLDSKIGSTD---------M 464

Query: 205 VYDHDGQEQVLIEKEERKNRRNM---LTRSMSVLNPRERRIFEAR-RLQENPV-TLENLS 259
            Y     +      EE  NR +M   + +++  L  RER++   R  L++  + TL+ + 
Sbjct: 465 TYQEVTADPTAETAEEMLNRLSMKRDVHKALDTLTTRERQVVTLRFGLEDGRIRTLQEIG 524

Query: 260 SEFEVSRERVRQIEARAFKKVQ 281
           +   VSRER+RQIE+ AF+K++
Sbjct: 525 NTMGVSRERIRQIESAAFRKLR 546


>gi|309378741|emb|CBX22691.1| unnamed protein product [Neisseria lactamica Y92-1009]
          Length = 642

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/244 (28%), Positives = 121/244 (49%), Gaps = 28/244 (11%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 398 AAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 457

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD--NNLKPEQVVAIA-- 163
           WI+ A+   I      ++I     +     N R  + HLQ   +  ++ K  +++ +   
Sbjct: 458 WIRQAITRSIADQARTIRIPVHMIETINKMN-RISRQHLQETGEEPDSAKLAELMQMPED 516

Query: 164 --KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKE 219
             +K+     E ISM   +  D+  +      D N+    D  +Y   H+  +++L    
Sbjct: 517 KIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPADAAMYTSLHEVTKEIL---- 572

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
                          L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 573 -------------ESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKAL 619

Query: 278 KKVQ 281
           +K++
Sbjct: 620 RKLR 623


>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 = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 71/244 (29%), Positives = 124/244 (50%), Gaps = 30/244 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 438 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPSPEELAERMLMPED- 495

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 496 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 538

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ +N     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 539 TGESLKNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 598

Query: 278 KKVQ 281
           +K++
Sbjct: 599 RKLR 602


>gi|21672345|ref|NP_660412.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. Sg
           (Schizaphis graminum)]
 gi|401010|sp|P32001|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 = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 67/242 (27%), Positives = 125/242 (51%), Gaps = 12/242 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 379 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 438

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   +++K+ +
Sbjct: 439 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEIGREPTPEE---LSEKMLI 493

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ R+  
Sbjct: 494 PEDKIRKV-LKIAK-EPISMETPIGDDDDSHLGDFI---EDTTLELPLDSATSESLRSAT 548

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +S L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K++   + 
Sbjct: 549 HDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 608

Query: 287 QV 288
           +V
Sbjct: 609 EV 610


>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 = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 71/244 (29%), Positives = 124/244 (50%), Gaps = 30/244 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 374 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 433

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 434 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPSPEELAERMLMPED- 491

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 492 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 534

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ +N     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 535 TGESLKNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 594

Query: 278 KKVQ 281
           +K++
Sbjct: 595 RKLR 598


>gi|42521092|ref|NP_967007.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of
           Drosophila melanogaster]
 gi|42410833|gb|AAS14941.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of
           Drosophila melanogaster]
          Length = 642

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 77/261 (29%), Positives = 128/261 (49%), Gaps = 27/261 (10%)

Query: 32  QEEYVLAKRYREHG-DLS-AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           QE   L KR ++H  ++S A   ++ ++LRLVV IA  Y   GL + +++ EGNIGLM+A
Sbjct: 386 QEFKELIKRIQKHEREVSEAKQEMIKANLRLVVSIAKKYSKRGLDLLDLIQEGNIGLMKA 445

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ--KRLFFNLRRLKGHL- 146
           V KFD +RG++ +TY  WW++ ++   I     +V+I     +   ++   LR++   + 
Sbjct: 446 VDKFDYKRGYKFSTYGTWWVRQSITRAIPEQSKVVRIPVHMVEIISKINRALRKMTHEMG 505

Query: 147 QAITDNNLKPEQVVA---IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
           +  T   L  E  +    I K + ++   V S+      D+S        DK  S+ +D 
Sbjct: 506 REPTLEELSVELTMPLERIRKVMKIARDPV-SLEAPTGKDDSSTFGDCIEDKRVSRPEDA 564

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSS 260
            +                 + R + T  ++ L P+E RI   R          TLE +  
Sbjct: 565 AIL---------------ADLRGITTNVLATLTPKEERILRMRFGLGKDGKEHTLEEVGK 609

Query: 261 EFEVSRERVRQIEARAFKKVQ 281
            F V+RER+RQIEA+A +K++
Sbjct: 610 IFNVTRERIRQIEAKALRKLK 630


>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 = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 115/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 397 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 456

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV--------V 160
           I+ A+   I      ++I    +       + R+   L         PE++        V
Sbjct: 457 IRQAITRSIADQARTIRI--PVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEV 514

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + K L +++ E ISM   +  DE             S   D++    D      I+   
Sbjct: 515 KVRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDQNITSPIDAAT 558

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFK 278
            +  +      +  L  RE ++ + R   + P   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 559 SEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALR 618

Query: 279 KVQ 281
           K++
Sbjct: 619 KLR 621


>gi|304409306|ref|ZP_07390926.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica OS183]
 gi|307303664|ref|ZP_07583417.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica BA175]
 gi|304351824|gb|EFM16222.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica OS183]
 gi|306912562|gb|EFN42985.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica BA175]
 gi|315266575|gb|ADT93428.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica OS678]
          Length = 611

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 118/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 373 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 432

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 433 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPED 490

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 491 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 534

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ +N     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 535 SESLKNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 594

Query: 279 KVQ 281
           K++
Sbjct: 595 KLR 597


>gi|225630998|ref|YP_002727789.1| RNA polymerase sigma 70 subunit, RpoD [Wolbachia sp. wRi]
 gi|225592979|gb|ACN95998.1| RNA polymerase sigma 70 subunit, RpoD [Wolbachia sp. wRi]
          Length = 650

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 77/261 (29%), Positives = 128/261 (49%), Gaps = 27/261 (10%)

Query: 32  QEEYVLAKRYREHG-DLS-AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           QE   L KR ++H  ++S A   ++ ++LRLVV IA  Y   GL + +++ EGNIGLM+A
Sbjct: 394 QEFKELIKRIQKHEREVSEAKQEMIKANLRLVVSIAKKYSKRGLDLLDLIQEGNIGLMKA 453

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ--KRLFFNLRRLKGHL- 146
           V KFD +RG++ +TY  WW++ ++   I     +V+I     +   ++   LR++   + 
Sbjct: 454 VDKFDYKRGYKFSTYGTWWVRQSITRAIPEQSKVVRIPVHMVEIISKINRALRKMTHEMG 513

Query: 147 QAITDNNLKPEQVVA---IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
           +  T   L  E  +    I K + ++   V S+      D+S        DK  S+ +D 
Sbjct: 514 REPTLEELSVELTMPLERIRKVMKIARDPV-SLEAPTGKDDSSTFGDCIEDKRVSRPEDA 572

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSS 260
            +                 + R + T  ++ L P+E RI   R          TLE +  
Sbjct: 573 AIL---------------ADLRGITTNVLATLTPKEERILRMRFGLGKDGKEHTLEEVGK 617

Query: 261 EFEVSRERVRQIEARAFKKVQ 281
            F V+RER+RQIEA+A +K++
Sbjct: 618 IFNVTRERIRQIEAKALRKLK 638


>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 = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 118/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 389 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 448

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 449 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPED 506

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 507 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 550

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ +N     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 551 SESLKNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 610

Query: 279 KVQ 281
           K++
Sbjct: 611 KLR 613


>gi|117928637|ref|YP_873188.1| RNA polymerase, sigma 28 subunit [Acidothermus cellulolyticus 11B]
 gi|117649100|gb|ABK53202.1| RNA polymerase, sigma 70 subunit, RpoD [Acidothermus cellulolyticus
           11B]
          Length = 495

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 80/310 (25%), Positives = 141/310 (45%), Gaps = 62/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHG-------------------DLS--------AAH 51
           Y+ +I K+P+L  ++E  LAKR  E G                   DL         A +
Sbjct: 202 YLKQIGKVPLLNAEQEVELAKRI-EAGLFAEEKLNSGEELSPELRKDLEWIAEDGRRAKN 260

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 261 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 320

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ +
Sbjct: 321 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGRDPTPEELAVELDMTPEKVMEV 380

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          +   D     L++++ 
Sbjct: 381 QKY----GREPISLHTPLGEDGDSEFGDLIEDSEA---------IVPSDAVSFTLLQEQ- 426

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 427 -------LHSVLETLSEREAGVVSMRFGLTDGQPKTLDEIGRVYGVTRERIRQIESKTMS 479

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 480 KLRHPSRSQV 489


>gi|294787697|ref|ZP_06752941.1| 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 = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/250 (28%), Positives = 118/250 (47%), Gaps = 40/250 (16%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 409 AAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 468

Query: 108 WIKAAMQEYILRSWSLVKIG-----TTANQKRLFFNLRRLKG---------HLQAITDNN 153
           WI+ A+   I      ++I      T     R+     +  G          L  + ++ 
Sbjct: 469 WIRQAITRSIADQARTIRIPVHMIETINKMNRISRQYLQETGEEPDSAKLAELMEMPEDK 528

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
           ++  +++ IAK       E ISM   +  DE  +      D N+    D  +Y       
Sbjct: 529 IR--KIMKIAK-------EPISMETPIGDDEDSHLGDFIEDANNVAPSDAAMY------- 572

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQ 271
                    + R +    +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQ
Sbjct: 573 --------SSLREVTKDVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 624

Query: 272 IEARAFKKVQ 281
           IEA+A +K++
Sbjct: 625 IEAKALRKLR 634


>gi|240080942|ref|ZP_04725485.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae FA19]
 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 = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/244 (28%), Positives = 121/244 (49%), Gaps = 28/244 (11%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 398 AAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 457

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD--NNLKPEQVVAIA-- 163
           WI+ A+   I      ++I     +     N R  + HLQ   +  ++ K  +++ +   
Sbjct: 458 WIRQAITRSIADQARTIRIPVHMIETINKMN-RISRQHLQETGEEPDSAKLAELMQMPED 516

Query: 164 --KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKE 219
             +K+     E ISM   +  D+  +      D N+    D  +Y   H+  +++L    
Sbjct: 517 KIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPADVAMYTSLHEVTKEIL---- 572

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
                          L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 573 -------------ESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKAL 619

Query: 278 KKVQ 281
           +K++
Sbjct: 620 RKLR 623


>gi|86605925|ref|YP_474688.1| RNA polymerase sigma factor [Synechococcus sp. JA-3-3Ab]
 gi|86554467|gb|ABC99425.1| RNA polymerase sigma factor [Synechococcus sp. JA-3-3Ab]
          Length = 318

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/228 (30%), Positives = 116/228 (50%), Gaps = 13/228 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  R+V  +LRLVV IA  YR  GLP  +++ EG IGL +AV+KFDP RG++ +TY+ W
Sbjct: 75  AAKKRMVECNLRLVVSIAKRYRNRGLPFLDLIQEGTIGLTRAVEKFDPTRGYKFSTYATW 134

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ ++   I     L+++     +K     ++R    L A   +    E+V      L+
Sbjct: 135 WIRQSVNRGIQNKGRLIRLPAHMYEK--VSQVKRRYRELSAEKGSRPAAEEVF---DSLD 189

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + ++    +   +A   SLN  +   D++ ++ Q + + D D      IE   R      
Sbjct: 190 IGDNYRELITRHMAEIRSLN--VGVGDEDGTELQHF-IPDEDNDP---IEHLNRVAHCEE 243

Query: 228 LTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIE 273
           +   +S L+ RE+++  AR   +    +TL  +     +SRERVRQIE
Sbjct: 244 VRALVSQLSEREQQVIVARYGLDGSKGLTLREIGEHIGLSRERVRQIE 291


>gi|1710686|sp|P52325|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 = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 70/244 (28%), Positives = 121/244 (49%), Gaps = 28/244 (11%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 398 AAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 457

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD--NNLKPEQVVAIA-- 163
           WI+ A+   I      ++I     +     N R  + HLQ   +  ++ K  +++ +   
Sbjct: 458 WIRQAITRSIADQARTIRIPVHMIETINKMN-RISRQHLQETGEEPDSAKLAELMQMPED 516

Query: 164 --KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKE 219
             +K+     E ISM   +  D+  +      D N+    D  +Y   H+  +++L    
Sbjct: 517 KIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNVAPADAAMYTSLHEVTKEIL---- 572

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
                          L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 573 -------------ESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKAL 619

Query: 278 KKVQ 281
           +K++
Sbjct: 620 RKLR 623


>gi|225021265|ref|ZP_03710457.1| hypothetical protein CORMATOL_01277 [Corynebacterium matruchotii
           ATCC 33806]
 gi|224945998|gb|EEG27207.1| hypothetical protein CORMATOL_01277 [Corynebacterium matruchotii
           ATCC 33806]
          Length = 617

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 80/324 (24%), Positives = 156/324 (48%), Gaps = 49/324 (15%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR--------YR--------EHGD 46
           RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR        YR         +GD
Sbjct: 299 RKDAELTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYADYRMKQMEKAYSNGD 357

Query: 47  LSAA--------------------HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
             A                     + L+ ++LRLVV +A  Y G G+   +++ EGN+GL
Sbjct: 358 KEAKLTPAVKRDLRAIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGL 417

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L
Sbjct: 418 IRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQREL 475

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
             + D   +P     ++K+++++E +V+ +        SL+  I   D+  SQ  D++  
Sbjct: 476 --LQDLGREPTP-YELSKEMDITEDKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI-- 528

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEV 264
             D +  + ++       ++ L   +  L+ RE  + + R  L +  P TL+ +   + V
Sbjct: 529 -EDSEAVIAVDAVSFTLLQDQLQDVLHTLSEREAGVVKLRFGLTDGMPRTLDEIGQVYGV 587

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           +RER+RQIE++   K++   + QV
Sbjct: 588 TRERIRQIESKTMSKLRHPSRSQV 611


>gi|212711167|ref|ZP_03319295.1| hypothetical protein PROVALCAL_02239 [Providencia alcalifaciens DSM
           30120]
 gi|212686335|gb|EEB45863.1| hypothetical protein PROVALCAL_02239 [Providencia alcalifaciens DSM
           30120]
          Length = 615

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 127/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 377 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 436

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 437 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPSPEELAERMLMPED- 494

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 495 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 537

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 538 TSESLRSATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 597

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 598 RKLRHPSRSEV 608


>gi|254421657|ref|ZP_05035375.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family,
           putative [Synechococcus sp. PCC 7335]
 gi|196189146|gb|EDX84110.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family,
           putative [Synechococcus sp. PCC 7335]
          Length = 467

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/244 (28%), Positives = 116/244 (47%), Gaps = 29/244 (11%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  R++ S+LRLVV IA  Y   G+P  +++ EG +GL +A +KFDP++G++ +TY+ W
Sbjct: 228 AAKRRMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGALGLNRAAEKFDPDKGYKFSTYAYW 287

Query: 108 WIKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           WI+  +   I      +++              Q+ L   L+R    ++      + PEQ
Sbjct: 288 WIRQGITRTIANDARTIRLPIHIVEKLNKLKKAQRELRKELQRTPTEVEVAAALEMTPEQ 347

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           +    + L   + + +S+N R+   E    +    D NS              E  + E 
Sbjct: 348 L----RTLQQVQRKSLSLNHRVGKGEDTELMELLEDGNSL-----------SPESQISES 392

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARA 276
             R+   ++LT    VL  RE+ I   R         TLE +   F++SRERVRQI+ +A
Sbjct: 393 MMRQEISDVLT---EVLTEREKEIIALRYGLTTGETHTLEEVGGIFQLSRERVRQIQTKA 449

Query: 277 FKKV 280
            +K+
Sbjct: 450 MRKL 453


>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 = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 66/245 (26%), Positives = 115/245 (46%), Gaps = 32/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 416 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 475

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +   +P+    +AKK+++
Sbjct: 476 IRQAITRSIADQARTIRI--PVHMIETINKMNRI--SRQILQETGAEPDPAT-LAKKMDM 530

Query: 169 SESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            E ++          ISM   +  D+  +      D  +    D  +Y            
Sbjct: 531 PEDKIRKIMKISKEPISMETPIGDDDDSHLGDFIEDSGTLAPADAAMY------------ 578

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARA 276
               + R +    +  L  RE ++   R   E     TLE +  +F+V+RER+RQIEA+A
Sbjct: 579 ---SSLRGVTKEILDTLTTREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKA 635

Query: 277 FKKVQ 281
            +K++
Sbjct: 636 LRKLR 640


>gi|303279757|ref|XP_003059171.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226459007|gb|EEH56303.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 587

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 73/255 (28%), Positives = 127/255 (49%), Gaps = 50/255 (19%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A ++++ ++LRLVV IA  Y    +   +++ EG +GL++  +KFD +RG++ +TY+ WW
Sbjct: 333 AKNQMIQANLRLVVSIAKRYANKSMSFQDLIQEGCVGLIRGAEKFDFKRGYKFSTYAHWW 392

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ--VVAIAKKL 166
           I+ A+   I            ++Q R      RL  HL  I     K E+  V+   +  
Sbjct: 393 IRQAVTRSI------------SDQSRTI----RLPVHLFEIISRMSKVERQLVMKYGRDP 436

Query: 167 NVSE-SEVISMNCRLAGDESLNALINSS-----------DKNSSQWQDWLVYDH-----D 209
              E +EV+ M       E +N +  +S           D +S   ++ LV DH     D
Sbjct: 437 TTEEIAEVMDMTV-----EKINQIQKASLVPISLSQSVNDDDSRTVEETLVDDHAEHPDD 491

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRE 267
              +VL++++        L   ++ L+PRER +   R   ++    TLE + + F V+RE
Sbjct: 492 ATGKVLLKED--------LENVLNTLSPRERDVLRLRYGMDDGRVKTLEEIGNVFSVTRE 543

Query: 268 RVRQIEARAFKKVQE 282
           R+RQIEA+A +K+++
Sbjct: 544 RIRQIEAKALRKLRQ 558


>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 = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 118/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 373 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 432

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 433 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPED 490

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 491 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 534

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ +N     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 535 SESLKNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 594

Query: 279 KVQ 281
           K++
Sbjct: 595 KLR 597


>gi|99035119|ref|ZP_01314904.1| hypothetical protein Wendoof_01000264 [Wolbachia endosymbiont of
           Drosophila willistoni TSC#14030-0811.24]
          Length = 502

 Score = 90.9 bits (224), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 77/261 (29%), Positives = 128/261 (49%), Gaps = 27/261 (10%)

Query: 32  QEEYVLAKRYREHG-DLS-AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           QE   L KR ++H  ++S A   ++ ++LRLVV IA  Y   GL + +++ EGNIGLM+A
Sbjct: 246 QEFKELIKRIQKHEREVSEAKQEMIKANLRLVVSIAKKYSKRGLDLLDLIQEGNIGLMKA 305

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ--KRLFFNLRRLKGHL- 146
           V KFD +RG++ +TY  WW++ ++   I     +V+I     +   ++   LR++   + 
Sbjct: 306 VDKFDYKRGYKFSTYGTWWVRQSITRAIPEQSKVVRIPVHMVEIISKINRALRKMTHEMG 365

Query: 147 QAITDNNLKPEQVVA---IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
           +  T   L  E  +    I K + ++   V S+      D+S        DK  S+ +D 
Sbjct: 366 REPTLEELSVELTMPLERIRKVMKIARDPV-SLEAPTGKDDSSTFGDCIEDKRVSRPEDA 424

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSS 260
            +                 + R + T  ++ L P+E RI   R          TLE +  
Sbjct: 425 AIL---------------ADLRGITTNVLATLTPKEERILRMRFGLGKDGKEHTLEEVGK 469

Query: 261 EFEVSRERVRQIEARAFKKVQ 281
            F V+RER+RQIEA+A +K++
Sbjct: 470 IFNVTRERIRQIEAKALRKLK 490


>gi|299768976|ref|YP_003731002.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter sp. DR1]
 gi|298699064|gb|ADI89629.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter sp. DR1]
          Length = 627

 Score = 90.5 bits (223), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 115/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 388 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 447

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV--------V 160
           I+ A+   I      ++I    +       + R+   L         PE++        V
Sbjct: 448 IRQAITRSIADQARTIRI--PVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEV 505

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + K L +++ E ISM   +  DE             S   D++    D      I+   
Sbjct: 506 KVRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDQNITSPIDAAT 549

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFK 278
            +  +      +  L  RE ++ + R   + P   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 550 SEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALR 609

Query: 279 KVQ 281
           K++
Sbjct: 610 KLR 612


>gi|320104559|ref|YP_004180150.1| RNA polymerase sigma-70 subunit RpoD [Isosphaera pallida ATCC
           43644]
 gi|319751841|gb|ADV63601.1| RNA polymerase, sigma 70 subunit, RpoD [Isosphaera pallida ATCC
           43644]
          Length = 592

 Score = 90.5 bits (223), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 82/290 (28%), Positives = 140/290 (48%), Gaps = 29/290 (10%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           R  M + +    GL+R + E     M E+ +EY  AKR           +L   +LRLVV
Sbjct: 321 RDLMLMTLETPAGLARRVRE-----MNERFKEYEKAKR-----------KLSGGNLRLVV 364

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA  YR  GL   +++ EGN GLM+AV K++  RGF+ +TY+ WWI+ A+   I     
Sbjct: 365 SIAKKYRNRGLSFLDLIQEGNTGLMRAVDKYEWRRGFKFSTYATWWIRQAITRAIADQAR 424

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            ++I        +   + +L+   + +     +   +   A+  N+S  E   +      
Sbjct: 425 TIRIPV-----HMIETMSKLRNVNKKLLQEKGREPTIEETARAANISIEETRRVMKISRH 479

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             SL+  +  S+   S + D++    D   +  I    ++  ++ + + +  L  RER I
Sbjct: 480 PISLDRPVGESE--DSYFGDFI---EDTTAENPINSATQEMLKDKIDQVLKTLTYREREI 534

Query: 243 FEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ-KQVE 289
            + R    +    TLE +   F+V+RERVRQIEA+A +K+Q  ++ +Q+E
Sbjct: 535 IKLRYGLGDGYTYTLEEVGRIFKVTRERVRQIEAKAVRKLQHPVRSRQLE 584


>gi|134098366|ref|YP_001104027.1| RNA polymerase sigma factor SigB [Saccharopolyspora erythraea NRRL
           2338]
 gi|291006932|ref|ZP_06564905.1| RNA polymerase sigma factor SigB [Saccharopolyspora erythraea NRRL
           2338]
 gi|133910989|emb|CAM01102.1| RNA polymerase sigma factor [Saccharopolyspora erythraea NRRL 2338]
          Length = 324

 Score = 90.5 bits (223), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 89/315 (28%), Positives = 138/315 (43%), Gaps = 82/315 (26%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH-----GDLS----------------AAHR 52
           Y++ I +  +L  QEE  LAKR     +  H     G LS                A + 
Sbjct: 31  YLNGIGRTALLTAQEEVDLAKRIEAGVFANHVLETSGKLSPERRSDLKAVVRDGVLAKNH 90

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 91  LMEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQA 150

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +            A+Q R      RL  HL          EQV  IA+        
Sbjct: 151 ITRGM------------ADQSRTI----RLPVHL---------VEQVNKIARIKR----- 180

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD--------GQEQ-----VLIEKE 219
              ++ +L  + +   L N +     +  D L +  D        G E+       IE  
Sbjct: 181 --DLHQKLGREATDEELANEAGLTVEKVADLLDHSRDPVSLDMPVGAEEDAPLGDFIEDA 238

Query: 220 ERKNRRNM---------LTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRER 268
           E  +  N          L R +S L  RE+ +   R   ++  P TL+ +   F +SRER
Sbjct: 239 ESADAENAVISGFLQDDLRRVLSTLEEREQAVIRMRYGLDDGQPRTLDQIGKAFGLSRER 298

Query: 269 VRQIEARAFKKVQES 283
           VRQIE     K+++ 
Sbjct: 299 VRQIEREVMSKLRQG 313


>gi|293610908|ref|ZP_06693207.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|292826560|gb|EFF84926.1| conserved hypothetical protein [Acinetobacter sp. SH024]
          Length = 628

 Score = 90.5 bits (223), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 115/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 389 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 448

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV--------V 160
           I+ A+   I      ++I    +       + R+   L         PE++        V
Sbjct: 449 IRQAITRSIADQARTIRI--PVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEV 506

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + K L +++ E ISM   +  DE             S   D++    D      I+   
Sbjct: 507 KVRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDQNITSPIDAAT 550

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFK 278
            +  +      +  L  RE ++ + R   + P   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 551 SEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALR 610

Query: 279 KVQ 281
           K++
Sbjct: 611 KLR 613


>gi|254409611|ref|ZP_05023392.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
 gi|196183608|gb|EDX78591.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
          Length = 374

 Score = 90.5 bits (223), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 72/235 (30%), Positives = 122/235 (51%), Gaps = 19/235 (8%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +++ S+LRLVV IA  Y   G+P  +++ EG +GL +A +KFDP +G++ +TY+ WWI+ 
Sbjct: 139 KMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGALGLNRAAEKFDPAKGYKFSTYAYWWIRQ 198

Query: 112 AMQEYILRSWSLVKIGTTANQK--RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           A+   I      +++     +K  +L    R LK  LQ   D          +A+ L++S
Sbjct: 199 AITRTIANDARTIRLPIHIVEKLNKLKKVQRELKQKLQRTPDE-------TELAEALDIS 251

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ--EQVLIEKEERKNRRNM 227
            + +  +        SLN  +   +   ++  D L+ D+D    EQ + E   R+   ++
Sbjct: 252 RTNLRQLLQLRRRSLSLNHRVGKGE--DTELVD-LLEDNDLHLPEQQMSESMMRQEISDV 308

Query: 228 LTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKV 280
           L+    VL  RE+ +   R     P   TLE + S F +SRERVRQI+++A +K+
Sbjct: 309 LS---DVLTEREKDVISLRYGLATPESYTLEEVGSMFNLSRERVRQIQSKAMRKL 360


>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 = 90.5 bits (223), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 115/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 388 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 447

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV--------V 160
           I+ A+   I      ++I    +       + R+   L         PE++        V
Sbjct: 448 IRQAITRSIADQARTIRI--PVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEV 505

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + K L +++ E ISM   +  DE             S   D++    D      I+   
Sbjct: 506 KVRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDQNITSPIDAAT 549

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFK 278
            +  +      +  L  RE ++ + R   + P   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 550 SEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALR 609

Query: 279 KVQ 281
           K++
Sbjct: 610 KLR 612


>gi|254000081|ref|YP_003052144.1| RNA polymerase sigma-70 subunit RpoD [Methylovorus sp. 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 sp. SIP3-4]
 gi|312441356|gb|ADQ85462.1| RNA polymerase, sigma 70 subunit, RpoD [Methylovorus sp. MP688]
          Length = 638

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 67/244 (27%), Positives = 114/244 (46%), Gaps = 32/244 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 397 AKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 456

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +  L+P+    +A+K+ +
Sbjct: 457 IRQAITRSIADQARTIRI--PVHMIETINKMNRISR--QILQETGLEPDP-ATLAEKMEM 511

Query: 169 SESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            E ++          ISM   +  D+  +      D  +    D  VY            
Sbjct: 512 PEDKIRKILKISKEPISMETPIGDDDDSHLGDFIEDMTTLAPVDAAVY------------ 559

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARA 276
               + R      +  L  RE ++   R   E     TLE +  +F+V+RER+RQIEA+A
Sbjct: 560 ---ASLREATKEVLESLTAREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKA 616

Query: 277 FKKV 280
            +K+
Sbjct: 617 LRKL 620


>gi|305681425|ref|ZP_07404232.1| RNA polymerase sigma factor RpoD [Corynebacterium matruchotii ATCC
           14266]
 gi|305659630|gb|EFM49130.1| RNA polymerase sigma factor RpoD [Corynebacterium matruchotii ATCC
           14266]
          Length = 608

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 80/324 (24%), Positives = 156/324 (48%), Gaps = 49/324 (15%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR--------YR--------EHGD 46
           RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR        YR         +GD
Sbjct: 290 RKDAELTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYADYRMKQMEKAYSNGD 348

Query: 47  LSAA--------------------HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
             A                     + L+ ++LRLVV +A  Y G G+   +++ EGN+GL
Sbjct: 349 KEAKLTPAVKRDLRAIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGL 408

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L
Sbjct: 409 IRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQREL 466

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
             + D   +P     ++K+++++E +V+ +        SL+  I   D+  SQ  D++  
Sbjct: 467 --LQDLGREPTP-YELSKEMDITEDKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI-- 519

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEV 264
             D +  + ++       ++ L   +  L+ RE  + + R  L +  P TL+ +   + V
Sbjct: 520 -EDSEAVIAVDAVSFTLLQDQLQDVLHTLSEREAGVVKLRFGLTDGMPRTLDEIGQVYGV 578

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           +RER+RQIE++   K++   + QV
Sbjct: 579 TRERIRQIESKTMSKLRHPSRSQV 602


>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 = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 65/236 (27%), Positives = 122/236 (51%), Gaps = 12/236 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  +++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 428 AAKQKMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 487

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I    +       + R+    Q + +   +P+    +A+ ++
Sbjct: 488 WIRQAITRSIADQARTIRI--PVHMIETINKMNRISR--QYLQETGEEPDS-AKLAELMD 542

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + E ++  +  ++A  E ++      D + S   D++    D       E     + R +
Sbjct: 543 MPEDKIRKI-MKIAK-EPISMETPIGDDDDSHLGDFI---EDVNNVAPAEAAMYSSLREV 597

Query: 228 LTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
               +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 598 TADVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 653


>gi|289548873|ref|YP_003473861.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermocrinis
           albus DSM 14484]
 gi|289182490|gb|ADC89734.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermocrinis
           albus DSM 14484]
          Length = 568

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 76/244 (31%), Positives = 113/244 (46%), Gaps = 30/244 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V  +LRLVV IA  Y   GL   +++ EGNIGLM+AV K+D  +G++ +TY+ WW
Sbjct: 331 AKQVMVKCNLRLVVSIAKKYVNRGLHFLDLIQEGNIGLMKAVDKYDYRKGYKFSTYATWW 390

Query: 109 IKAAMQEYILRSWSLVKI---------GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I           T   K+L   L R +   + I      P   
Sbjct: 391 IRQAITRAIADQARTIRIPVHMIETINDITKAHKKLTQELGR-EPTAEEIAKYLGIP--- 446

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           V  A+K+     E IS+   +  DE  +      DK+              +EQV     
Sbjct: 447 VDKARKVMRMAQEPISLETPIGDDEDAHLKDFIEDKSVPS----------PEEQVT---- 492

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAF 277
            RK  R  L + +S L  +ER I   R   +     TLE +   F V+RER+RQIE +A 
Sbjct: 493 -RKLLREQLIKVLSTLGEKEREILMYRYGLVDGTEYTLEQIGRMFNVTRERIRQIETKAI 551

Query: 278 KKVQ 281
           +K++
Sbjct: 552 RKLR 555


>gi|225440035|ref|XP_002276710.1| PREDICTED: hypothetical protein [Vitis vinifera]
 gi|297741628|emb|CBI32760.3| unnamed protein product [Vitis vinifera]
          Length = 561

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 73/253 (28%), Positives = 124/253 (49%), Gaps = 32/253 (12%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           H    +  +L+ ++LR+VV IA  Y+G GL + +++ EG++GLM +V+KF P  G R A+
Sbjct: 316 HSGNRSRQKLIYANLRMVVHIAKQYQGRGLNLQDLLQEGSMGLMNSVEKFKPNAGCRFAS 375

Query: 104 YSMWWIKAAMQEYILRSWSLVKI--------GTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           Y+ WWI+ A+++ I +    +++        G     KRLF      +GH    T   + 
Sbjct: 376 YAYWWIRQAVRKAIFQHSRTIRLPENMYSLLGKVKEAKRLFIQ----EGH-HDPTKEEIA 430

Query: 156 PEQVVAIAK--KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
               + I K  +L +     +SM   +  D+       ++D          + D    +Q
Sbjct: 431 ERVGITIEKLQRLLLHTRMPLSMQQPVWADQDTTFQEVTADTGIE------IPDVSVAKQ 484

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQ 271
           ++     R++ RN+L     VL P+ERRI   R    +  P TL  +   F  S+ERVRQ
Sbjct: 485 LM-----RQHVRNLL----HVLTPKERRIIRLRFGIGDGIPRTLSEIGLVFGFSKERVRQ 535

Query: 272 IEARAFKKVQESI 284
           +E RA  K+++ +
Sbjct: 536 LEQRALHKLKQCL 548


>gi|67920853|ref|ZP_00514372.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
 gi|67856970|gb|EAM52210.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
          Length = 297

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 77/275 (28%), Positives = 141/275 (51%), Gaps = 28/275 (10%)

Query: 13  EIGLSRYIHEIRKIPMLEKQ-----EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           EI L+  I  +  +P+LEK+     EE ++AK  +      A  R++ ++LRLVV IA  
Sbjct: 28  EIKLAEEIQAM--LPLLEKEQLSREEEKIVAKGQK------ARERMIEANLRLVVSIAKK 79

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y   GL + +++ EG++GL++ V+KFDP RG++ +TY+ WWI+  +   I      +++ 
Sbjct: 80  YLNSGLSLLDLIQEGSLGLIRGVEKFDPARGYKFSTYAYWWIRQGITRAIAEQSRTIRLP 139

Query: 128 TTANQKRLFFNLRRLKGHLQAITDN-NLKPEQ-VVAIAKKLNVSESEVISMNCRLAGDES 185
              N+     NL + +  ++ +T     KP Q  +A   +++V   + +          S
Sbjct: 140 IHINE-----NLNKYRKSIRELTLKLGRKPTQREIAENMEISVDRLQFLQQAAFKTKSRS 194

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           LN +I   D+N ++    L  +        +++EE+ ++ N L  S   L PR++ +   
Sbjct: 195 LNVVI---DENQTELGQLLPDEESISPSDFVKQEEKISQINNLLES---LTPRQKEVIIL 248

Query: 246 R-RLQENP-VTLENLSSEFEVSRERVRQIEARAFK 278
           R  L++   ++ + +  +  VS ER RQI +RA K
Sbjct: 249 RFGLRDGKQMSYKAIGEKCGVSHERARQIYSRALK 283


>gi|237755496|ref|ZP_04584118.1| RNA polymerase sigma factor RpoD [Sulfurihydrogenibium
           yellowstonense SS-5]
 gi|237692360|gb|EEP61346.1| RNA polymerase sigma factor RpoD [Sulfurihydrogenibium
           yellowstonense SS-5]
          Length = 570

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 76/234 (32%), Positives = 120/234 (51%), Gaps = 28/234 (11%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV K+D ++GF+ +TY+ WWI+ A
Sbjct: 355 LVKANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKYDYKKGFKFSTYATWWIRQA 414

Query: 113 MQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           +   I      ++I      T N+      L R+   L         PE+   IAKK  +
Sbjct: 415 ITRAIADQARTIRIPVHMIETINK------LLRISRTLVQELGREPTPEE---IAKKAGM 465

Query: 169 SESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNR 224
              +V  +  R + D  SL   I S ++  S   D++      +++ ++  E+   ++  
Sbjct: 466 PADKVRKI-LRTSQDPVSLETPIGSDEE--SHLGDFI------EDKSVLSPEQHMLKQAL 516

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARA 276
           R  L   +S L+ RE ++   R   E+    TLE +   F V+RER+RQIEA+A
Sbjct: 517 RLQLDEVLSTLSEREEQVLRYRFGLEDDTEHTLEQVGKRFGVTRERIRQIEAKA 570


>gi|260548994|ref|ZP_05823216.1| RNA polymerase sigma factor sigma-70 [Acinetobacter sp. RUH2624]
 gi|260408162|gb|EEX01633.1| RNA polymerase sigma factor sigma-70 [Acinetobacter sp. RUH2624]
          Length = 628

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 115/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 389 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 448

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV--------V 160
           I+ A+   I      ++I    +       + R+   L         PE++        V
Sbjct: 449 IRQAITRSIADQARTIRI--PVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEV 506

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + K L +++ E ISM   +  DE             S   D++    D      I+   
Sbjct: 507 KVRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDQNITSPIDAAT 550

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFK 278
            +  +      +  L  RE ++ + R   + P   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 551 SEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALR 610

Query: 279 KVQ 281
           K++
Sbjct: 611 KLR 613


>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 = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 64/235 (27%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 403 AKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 462

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + +  L+P+    +A+K+ +
Sbjct: 463 IRQAITRSIADQARTIRI--PVHMIETINKMNRIS--RQILQETGLEPDPAT-LAEKMEM 517

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  +++  E ++      D + S   D++    D      ++     + R+  
Sbjct: 518 PEDKIRKI-LKISK-EPISMETPIGDDDDSHLGDFI---EDVATLAPVDAAVYASLRDAT 572

Query: 229 TRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L  RE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 573 KEVLESLTAREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 627


>gi|284008589|emb|CBA75169.1| RNA polymerase sigma-70 factor [Arsenophonus nasoniae]
          Length = 622

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 127/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 384 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 443

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 444 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPSPEELAERMLMPED- 501

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 502 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 544

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 545 TSESLRSATHEVLAGLTTREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 604

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 605 RKLRHPSRSEV 615


>gi|332975259|gb|EGK12159.1| DNA-directed RNA polymerase sigma subunit RpoD [Kingella kingae
           ATCC 23330]
          Length = 654

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 69/249 (27%), Positives = 119/249 (47%), Gaps = 40/249 (16%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  +++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 411 AAKQKMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 470

Query: 108 WIKAAMQEYILRSWSLVKIG-----TTANQKRLFFNLRRLKG---------HLQAITDNN 153
           WI+ A+   I      ++I      T     R+     +  G          L  + ++ 
Sbjct: 471 WIRQAITRSIADQARTIRIPVHMIETINKMNRISRQYLQETGEEPDSAKLAELMEMPEDK 530

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
           ++  +++ IAK       E ISM   +  D+  +      D N+    D  +Y       
Sbjct: 531 IR--KIMKIAK-------EPISMETPIGDDDDSHLGDFIEDVNNVAPADAAMY------- 574

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQ 271
                    + R + +  +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQ
Sbjct: 575 --------SSLREVTSDILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQ 626

Query: 272 IEARAFKKV 280
           IEA+A +K+
Sbjct: 627 IEAKALRKL 635


>gi|116749951|ref|YP_846638.1| RpoD family RNA polymerase sigma factor [Syntrophobacter
           fumaroxidans MPOB]
 gi|116699015|gb|ABK18203.1| RNA polymerase, sigma 70 subunit, RpoD family [Syntrophobacter
           fumaroxidans MPOB]
          Length = 433

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 75/241 (31%), Positives = 123/241 (51%), Gaps = 23/241 (9%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           SA   +V ++LRLV+ IA  YRG G+   +++ EGN+GL++AV +FD  +G R +TY+ W
Sbjct: 196 SAKQEMVKANLRLVLSIAKRYRGRGMSFDDLIQEGNLGLLKAVGRFDHTKGNRFSTYATW 255

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQ-KRLFFNLRRLKGHLQAITDNNLKPE-QVVAIAKK 165
           W++ ++   I      +++     + K LFF     K   + + +   +P  Q +A   K
Sbjct: 256 WVRQSIIRGIYDKTRTIRLPVHFIELKNLFF-----KVFYELLKELGREPSPQEIAERAK 310

Query: 166 LNVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           L + +   + M   LA    SL   I   ++         + D    E+     EE  +R
Sbjct: 311 LPLDK---VQMVLTLAAQPISLETPIGEDEQR--------LGDFIEDERAASPMEECSDR 359

Query: 225 R-NMLTRS-MSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
               +TRS +S L PRE +I   R  +   P  TLE +   F+VS+ER+RQIE +A +K+
Sbjct: 360 ELAEITRSLLSSLQPREEKILRLRFGIDGQPAETLEKIGKTFKVSKERIRQIEKKALRKL 419

Query: 281 Q 281
           +
Sbjct: 420 R 420


>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 = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 69/242 (28%), Positives = 116/242 (47%), Gaps = 28/242 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 386 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 445

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 446 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 503

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 504 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 547

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 548 ATSLKAATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 607

Query: 279 KV 280
           K+
Sbjct: 608 KL 609


>gi|78778962|ref|YP_397074.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9312]
 gi|78712461|gb|ABB49638.1| putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus str. MIT 9312]
          Length = 307

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 84/299 (28%), Positives = 144/299 (48%), Gaps = 38/299 (12%)

Query: 12  GEIGLSRYIHEIRKIPMLEK-QEEYVLAKRYREHG------DLSAAHR------------ 52
           GEIG  + +   R++ M  K QE  VL  R +E G      + S A R            
Sbjct: 9   GEIGRHQLLTPERELTMGRKVQEMVVLVNRCQEAGGKGPACEYSEAERKKIKIGEKAKNE 68

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG R +TY+ WWI+  
Sbjct: 69  MITANLRLVVNLAKRYQGKGLELLDLIQEGTLGLTRAVEKYDPSRGHRFSTYAYWWIRQG 128

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKG---HLQAITDNNLKPEQVVAIAKKLNVS 169
           +   +      ++I    N+K     LR  K     L+ IT N+ +      +A++L ++
Sbjct: 129 LNRALSTQSRTIRIPVNINEK--LTKLRSAKSKLMQLKGITPNSDE------LAEELKIT 180

Query: 170 ESEVIS-MNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + E+   ++C L     SL   + S   + S+  D L  D     ++    E   +   +
Sbjct: 181 KEEIDELLSCELRSITVSLQGTVKSKS-DPSELVDILPSDQTPPMELAELAERTASAWKL 239

Query: 228 LTRSMSVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           L ++   L  +ER+I   R   +      TL  ++     SRE  RQ+  RA +K++++
Sbjct: 240 LDKAN--LTEKERKIVSLRFGLDGSNEWRTLAEVARHMSCSREYCRQVVQRALRKLRKA 296


>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 = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 117/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 405 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 464

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 465 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 522

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 523 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 566

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 567 ATSLKAATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 626

Query: 279 KVQ 281
           K++
Sbjct: 627 KLR 629


>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 = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 127/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 438 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPSPEELAERMLMPED- 495

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 496 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 538

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 539 TSESLRSATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 598

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 599 RKLRHPSRSEV 609


>gi|297561520|ref|YP_003680494.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
 gi|296845968|gb|ADH67988.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
          Length = 468

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 70/247 (28%), Positives = 126/247 (51%), Gaps = 13/247 (5%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E G  + +H ++ ++LRLVV +A  Y   G+ + +VV EGN+GL++AV+KFD  +GF+ +
Sbjct: 226 EDGRKAKSH-MLEANLRLVVSVAKKYSDRGMSLLDVVQEGNLGLIRAVEKFDYTKGFKFS 284

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+MWWI+ A+Q     S   +++    +   L   + RL+  +         PE++   
Sbjct: 285 TYAMWWIRQAIQRGFADSARTIRL--PVHVLELLSKVSRLERDMHQALGREPTPEELGLE 342

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
             K      E++ +  +     SL++ I   +   ++  D L+ D D  E    E  +R+
Sbjct: 343 LDKTPAQIEELLRVTRQPI---SLDSTIG--EDGETRIGD-LIEDVDASEAS--EVVDRQ 394

Query: 223 NRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
              + L  ++S L PRE  I   R   +   P TL+ +     ++RER+RQ+E ++  K+
Sbjct: 395 LMADQLRNALSDLEPREATIMSLRFGLMDGRPRTLDEIGKHLGLTRERIRQLEKQSLSKL 454

Query: 281 QESIQKQ 287
           +   + Q
Sbjct: 455 RHPSRAQ 461


>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]
 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|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]
 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]
          Length = 628

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 115/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 389 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 448

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV--------V 160
           I+ A+   I      ++I    +       + R+   L         PE++        V
Sbjct: 449 IRQAITRSIADQARTIRI--PVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEV 506

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + K L +++ E ISM   +  DE             S   D++    D      I+   
Sbjct: 507 KVRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDQNITSPIDAAT 550

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFK 278
            +  +      +  L  RE ++ + R   + P   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 551 SEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALR 610

Query: 279 KVQ 281
           K++
Sbjct: 611 KLR 613


>gi|84502385|ref|ZP_01000521.1| RNA polymerase sigma-70 factor family protein [Oceanicola batsensis
           HTCC2597]
 gi|84389197|gb|EAQ01994.1| RNA polymerase sigma-70 factor family protein [Oceanicola batsensis
           HTCC2597]
          Length = 249

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 72/265 (27%), Positives = 127/265 (47%), Gaps = 38/265 (14%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           I    KIP+L+  EE    +R+++HGD  A   L+ SH R    +A  +    + + ++ 
Sbjct: 6   IQAAAKIPLLDIDEERNAIRRWQDHGDREALTLLLRSHARQAWSMAARWTDNPVHLEDLA 65

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
           +EG IGL++A   FD  +  R +TY+ WW+   +     R  S++ +       R    +
Sbjct: 66  AEGVIGLIRAADNFDLGQDVRFSTYAAWWVMNGVSAAAARIRSVIDV-----PPRAVTEM 120

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES---LNALINSSDKN 196
           R   G L A  DN +           + ++   +++++  + GD +   L+AL++S    
Sbjct: 121 R--SGRL-ADEDNTV-----------ITMAMQGIVALDAPV-GDGTHSLLDALVSS---- 161

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
                     D   +E    E      RR ++ ++MS LN +E  I   RRLQ  P TLE
Sbjct: 162 ----------DLTPEETAAAESLHDVQRR-LIAKAMSGLNAQEAEIIRRRRLQAVPETLE 210

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
           +L+    ++R+R+RQ+E RA  +++
Sbjct: 211 DLADAMNMTRDRLRQVERRAMTRLR 235


>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 = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 127/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 379 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 438

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 439 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPSPEELAERMLMPED- 496

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 497 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 539

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 540 TSESLRSATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 599

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 600 RKLRHPSRSEV 610


>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|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]
          Length = 620

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 69/242 (28%), Positives = 116/242 (47%), Gaps = 28/242 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 382 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 441

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 442 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 499

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 500 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 543

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 544 ATSLKMATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 603

Query: 279 KV 280
           K+
Sbjct: 604 KL 605


>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 = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 69/242 (28%), Positives = 116/242 (47%), Gaps = 28/242 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 382 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 441

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 442 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 499

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 500 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 543

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 544 ATSLKMATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 603

Query: 279 KV 280
           K+
Sbjct: 604 KL 605


>gi|94499953|ref|ZP_01306488.1| RNA polymerase sigma factor [Oceanobacter sp. RED65]
 gi|94427811|gb|EAT12786.1| RNA polymerase sigma factor [Oceanobacter sp. RED65]
          Length = 606

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 121/236 (51%), Gaps = 14/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 368 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 427

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   +A+++++
Sbjct: 428 IRQAITRSIADQARTIRI--PVHMIETINKLNRVSRQMLQEMGREATPEE---LAERMDM 482

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D   S   D+ + D +G   +    E         
Sbjct: 483 PEDKIRKV-LKIAK-EPISMETPIGDDEDSHLGDF-IEDVNGHSPIDTATE---TGLTDA 536

Query: 229 TRS-MSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TRS +S L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 537 TRSVLSGLTARESKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 592


>gi|94984583|ref|YP_603947.1| RNA polymerase, sigma 28 subunit [Deinococcus geothermalis DSM
           11300]
 gi|94554864|gb|ABF44778.1| RNA polymerase, sigma 28 subunit [Deinococcus geothermalis DSM
           11300]
          Length = 532

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 79/299 (26%), Positives = 139/299 (46%), Gaps = 49/299 (16%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKR----------YREHGD-----------------LSAA 50
           +Y+HEI ++P+L  +EE  LA+R            E GD                  +A 
Sbjct: 234 QYLHEIGRVPLLTLEEEIALARRIEEGEEARKMLEEAGDELDDRARRRLMRQMEDGAAAR 293

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
             L+ ++LRLVV IA  Y G GL   +++ EGN GL++AV+KF+  R ++ +TY+ WWI+
Sbjct: 294 QGLIEANLRLVVSIAKKYTGRGLGFLDLIQEGNQGLIRAVEKFEYRRRYKFSTYATWWIR 353

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-AIAKKLNVS 169
            A+   I      ++I    +       L R    LQ         E++  A+    + +
Sbjct: 354 QAINRAIADQARTIRI--PVHMVETINKLTRTARQLQQELSREPTYEEIAEAMGPGWDAA 411

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH-----DGQEQVLIEKEERKNR 224
           + E +    +    E ++      D+  S + D++  ++     D   + L+ +E     
Sbjct: 412 KVEEVQKVSQ----EPVSLETPIGDEKDSFYGDFIPDENLDSPVDNAAKTLLSEE----- 462

Query: 225 RNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              L +++S L  RE  + + R+  +     TLE +   F V+RER+RQIE +A +K++
Sbjct: 463 ---LEKALSKLTEREALVLKFRKGLVDGREHTLEEVGQRFNVTRERIRQIENKALRKLK 518


>gi|218441429|ref|YP_002379758.1| RNA polymerase sigma factor SigD [Cyanothece sp. PCC 7424]
 gi|218174157|gb|ACK72890.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
          Length = 318

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 81/315 (25%), Positives = 142/315 (45%), Gaps = 72/315 (22%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRY------------------REHGD---LSAA------- 50
           Y+ EI ++P+L  +EE VLAKR                   RE  D    SAA       
Sbjct: 14  YLREIGRVPLLTHEEEIVLAKRVQRFMALQDIKDALTQTLKREPQDSEWASAAKITEEEL 73

Query: 51  HR-----------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           HR           +V ++LRLVV +A  Y    L + +++ EG IG+ + V+KFDP +G+
Sbjct: 74  HRAIAAGKAAKEKMVEANLRLVVSVAKKYLKRNLDLLDLIQEGTIGMQRGVEKFDPTKGY 133

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           R +TY+ WWI+ A+   I      +++     +K     L ++K   + ++    +   +
Sbjct: 134 RFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEK-----LNKIKKAQRQLSQAKGRAATI 188

Query: 160 VAIAKKLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
             +A++L ++  +V          +S++ ++ GD     L    +   +  +D+  +   
Sbjct: 189 SELAEELELTPRQVRDYLERARQPLSLDLKV-GDNQDTELGELLEDTGTSPEDYATH--- 244

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRE 267
              QV +EK             MS L P+++ +   R   +   P+TL  +     +SRE
Sbjct: 245 SSLQVDLEK------------LMSDLTPQQKEVLALRFGLVDGQPLTLAKIGVRLNISRE 292

Query: 268 RVRQIEARAFKKVQE 282
           RVRQIE  A  K+++
Sbjct: 293 RVRQIEREALSKLRK 307


>gi|291618943|ref|YP_003521685.1| RpoD [Pantoea ananatis LMG 20103]
 gi|291153973|gb|ADD78557.1| RpoD [Pantoea ananatis LMG 20103]
 gi|327395293|dbj|BAK12715.1| RNA polymerase sigma factor RpoD [Pantoea ananatis AJ13355]
          Length = 614

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 73/250 (29%), Positives = 126/250 (50%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 376 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 435

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-KRLFFNLRRLKGH---LQAITDNNLKPEQVV 160
           I+ A+   I      ++I      T N+  R+   + +  G     + + +  L PE   
Sbjct: 436 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPED-- 493

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 494 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 537

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 538 SESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 597

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 598 KLRHPSRSEV 607


>gi|158337702|ref|YP_001518878.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158307943|gb|ABW29560.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 318

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 81/316 (25%), Positives = 142/316 (44%), Gaps = 74/316 (23%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKR-------------YREHGD--------------- 46
            ++ Y+ EI + P+L  +EE +  K+              +EH D               
Sbjct: 10  SITTYLREIGRFPLLNHEEEIIFGKQVQRFVALQDLKQDLQEHLDREPTQAEWADKAEIS 69

Query: 47  -------LSAAHR----LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
                  L   H+    +V S+LRLVV IA  Y    +   +++ EG IGL + V+KFDP
Sbjct: 70  VSQLQKELKLGHKANRKMVESNLRLVVSIAKKYNKAKVEFLDLIQEGTIGLQRGVEKFDP 129

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL--------- 146
            +G+R +TY+ WWI+ AM   I      +++    N+K     LR+++  L         
Sbjct: 130 MKGYRFSTYAYWWIRQAMTRAIAEQERTIRLPIHINEK--LSKLRKVRRQLSQKLHRDPT 187

Query: 147 --QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             +   + +L P++   I   LN +    IS++ ++ GD+          +N+  W+  L
Sbjct: 188 VQELAVEMDLAPKK---IEDYLNYARRS-ISLDIQI-GDQ----------QNTELWE--L 230

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEF 262
           + D +      +      + R+ L + +  L+P++R +   R   + +NP+TL  +    
Sbjct: 231 LEDPNESPDTYVTA---SSLRSDLAKLLQDLSPQQREVITLRYGLIDQNPLTLAKVGERL 287

Query: 263 EVSRERVRQIEARAFK 278
            VSRE VR++E  AFK
Sbjct: 288 NVSREWVRRVEREAFK 303


>gi|289642419|ref|ZP_06474565.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia symbiont
           of Datisca glomerata]
 gi|289507764|gb|EFD28717.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia symbiont
           of Datisca glomerata]
          Length = 425

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 82/302 (27%), Positives = 137/302 (45%), Gaps = 60/302 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR--------YREHGDL------------------SAAHR 52
           Y+ EI K+P+L   +E  L+KR        Y+   D                   +A  +
Sbjct: 132 YLREIGKVPLLNAAQEVELSKRVEAGLFAEYKLDTDTDLAPELRRDLQTLVRDGHAAKQQ 191

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV+++LRLVV +A  Y G G+ + ++V EGN+GL++AV+KFD  +G++ +TY+ WWI+ A
Sbjct: 192 LVSANLRLVVSVAKKYSGRGMTLLDLVQEGNLGLIRAVEKFDYAKGYKFSTYATWWIRQA 251

Query: 113 MQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           +   +      ++I           T  Q++L   L R     +   + ++  EQVV   
Sbjct: 252 IGRALADQARTIRIPVHVVEQINKITRLQRQLVSTLGREPTDEELALELDMPIEQVV--- 308

Query: 164 KKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
            +L     + +S+   +   GD  L   I  +D  S    D   Y   G  Q  IE    
Sbjct: 309 -ELRRYAQDTVSLETAVGDDGDSVLGDFIEDADATSP--ADAASY---GAMQDEIEG--- 359

Query: 222 KNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKK 279
                     ++ L PRER +   R  L +    TL  + +   ++RER+RQIE    ++
Sbjct: 360 ---------VLNSLTPREREVMRLRFGLADGKQHTLAEVGNRLGLTRERIRQIERDTLRE 410

Query: 280 VQ 281
           ++
Sbjct: 411 LR 412


>gi|22127411|ref|NP_670834.1| RNA polymerase sigma factor RpoD [Yersinia pestis KIM 10]
 gi|21960500|gb|AAM87085.1|AE013956_10 RNA polymerase, sigma(70) factor [Yersinia pestis KIM 10]
          Length = 632

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 127/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 394 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 453

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 454 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 511

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 512 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 554

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 555 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 614

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 615 RKLRHPSRSEV 625


>gi|262378901|ref|ZP_06072058.1| RNA polymerase sigma factor sigma-70 [Acinetobacter radioresistens
           SH164]
 gi|262300186|gb|EEY88098.1| RNA polymerase sigma factor sigma-70 [Acinetobacter radioresistens
           SH164]
          Length = 629

 Score = 90.5 bits (223), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 70/243 (28%), Positives = 117/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 390 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 449

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV--------V 160
           I+ A+   I      ++I    +       + R+   L         PE++        V
Sbjct: 450 IRQAITRSIADQARTIRI--PVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEV 507

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + K L +++ E ISM   +  DE  +      D+N +   D      +G ++   E   
Sbjct: 508 KVRKVLKIAK-EPISMETPIGDDEDSHLGDFIEDQNITSPVDAAT--SEGLKEATRE--- 561

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFK 278
                      +  L  RE ++ + R   + P   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 562 ----------VLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALR 611

Query: 279 KVQ 281
           K++
Sbjct: 612 KLR 614


>gi|317503800|ref|ZP_07961812.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella salivae
           DSM 15606]
 gi|315665097|gb|EFV04752.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella salivae
           DSM 15606]
          Length = 290

 Score = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 72/275 (26%), Positives = 136/275 (49%), Gaps = 18/275 (6%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYG 72
            L +Y+ EI + P++   EE  LA++ ++ G     A  +LVT++LR VV +A  Y+  G
Sbjct: 17  ALDKYLVEIGRAPLISIDEEIELAQKIKKGGRDGERAKEKLVTANLRFVVSVAKQYQHQG 76

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V++    NQ
Sbjct: 77  LSLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRL--PLNQ 134

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE---SLNAL 189
                +L ++   +        +   +  ++    + E ++   +  L  D    S++A 
Sbjct: 135 ---VGSLNKINREINKFEQEYQRKPSLSELSHATKIEEEKI---DQSLMADSHHVSIDAP 188

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF-EARRL 248
               + NS    D +    D +    ++ E        + R   VL  RE  I  E   +
Sbjct: 189 FQEGEDNS--MVDVMAGGDDSRTDKQVDHESMALELESVLR--KVLKEREITIIRECFGI 244

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +   LE +  +  ++RERVRQI  ++  K+++S
Sbjct: 245 GCHEKGLEEIGDQLGLTRERVRQIREKSIAKLRDS 279


>gi|15606649|ref|NP_214029.1| RNA polymerase sigma factor RpoD [Aquifex aeolicus VF5]
 gi|2983864|gb|AAC07417.1| RNA polymerase sigma factor RpoD [Aquifex aeolicus VF5]
          Length = 575

 Score = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 74/250 (29%), Positives = 118/250 (47%), Gaps = 38/250 (15%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           + A   ++ S+LRLVV IA  Y   GL   +++ EGNIGLM+AV K+D  +G++ +TY+ 
Sbjct: 336 VQAKQVMIQSNLRLVVSIAKKYVNRGLHFLDLIQEGNIGLMKAVDKYDYRKGYKFSTYAT 395

Query: 107 WWIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLK--PEQV- 159
           WWI+ A+   I      ++I      T N        + +K   +   +N  +  PE++ 
Sbjct: 396 WWIRQAITRAIADQARTIRIPVHMIETIN--------KIIKASKKLFQENGREPTPEEIA 447

Query: 160 ------VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
                 V   KK+     E IS+   +  D+         DK+            + +EQ
Sbjct: 448 EYLDIPVEKVKKVMKFSQEPISLETPIGDDDDTFLKDFIEDKSIP----------NPEEQ 497

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQ 271
           V      RK  R  L + +S L+ +ER I   R   +     TLE +   F V+RER+RQ
Sbjct: 498 VT-----RKLLREQLQKVLSTLSEKEREILMYRYGLVDGTEYTLEQVGKMFNVTRERIRQ 552

Query: 272 IEARAFKKVQ 281
           IE +A +K++
Sbjct: 553 IENKALRKLR 562


>gi|297250830|ref|ZP_06934304.1| RNA polymerase sigma factor RpoD [Neisseria polysaccharea ATCC
           43768]
 gi|296837936|gb|EFH21874.1| RNA polymerase sigma factor RpoD [Neisseria polysaccharea ATCC
           43768]
          Length = 322

 Score = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 69/244 (28%), Positives = 120/244 (49%), Gaps = 28/244 (11%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 78  AAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 137

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD--NNLKPEQVVAIA-- 163
           WI+ A+   I      ++I     +     N R  + HLQ   +  ++ K  +++ +   
Sbjct: 138 WIRQAITRSIADQARTIRIPVHMIETINKMN-RISRQHLQETGEEPDSAKLAELMQMPED 196

Query: 164 --KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKE 219
             +K+     E ISM   +  D+  +      D N+    D  +Y   H+  +++L    
Sbjct: 197 KIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDANNIAPADAAMYTSLHEVTKEIL---- 252

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAF 277
                          L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A 
Sbjct: 253 -------------ESLTPREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKAL 299

Query: 278 KKVQ 281
           +K++
Sbjct: 300 RKLR 303


>gi|183597880|ref|ZP_02959373.1| hypothetical protein PROSTU_01215 [Providencia stuartii ATCC 25827]
 gi|188022641|gb|EDU60681.1| hypothetical protein PROSTU_01215 [Providencia stuartii ATCC 25827]
          Length = 617

 Score = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 70/250 (28%), Positives = 121/250 (48%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 379 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 438

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 439 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPED 496

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 497 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDNTLELPLDSAT 540

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 541 SESLRSATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 600

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 601 KLRHPSRSEV 610


>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 = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 114/243 (46%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 374 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 433

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 434 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPED 491

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D Q    ++   
Sbjct: 492 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDIQALSPVDSAT 535

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            +  R      +S L  RE ++   R   E     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 536 AEGLREATRSVLSGLTARESKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALR 595

Query: 279 KVQ 281
           K++
Sbjct: 596 KLR 598


>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 = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 71/255 (27%), Positives = 123/255 (48%), Gaps = 38/255 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 393 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 452

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG-------------HLQAITDNNLK 155
           I+ A+   I      ++I        +   + +L G               + + +  L 
Sbjct: 453 IRQAITRSIADQARTIRIPV-----HMIETINKLNGISRQMLQEMGREPTPEELAERMLM 507

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
           PE    I K L +++ E ISM   +  DE             S   D++    D   ++ 
Sbjct: 508 PED--KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELP 549

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIE 273
           ++    ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIE
Sbjct: 550 LDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 609

Query: 274 ARAFKKVQESIQKQV 288
           A+A +K++   + +V
Sbjct: 610 AKALRKLRHPSRSEV 624


>gi|311742667|ref|ZP_07716476.1| DNA-directed RNA polymerase sigma subunit RpoD [Aeromicrobium
           marinum DSM 15272]
 gi|311314295|gb|EFQ84203.1| DNA-directed RNA polymerase sigma subunit RpoD [Aeromicrobium
           marinum DSM 15272]
          Length = 464

 Score = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 80/309 (25%), Positives = 139/309 (44%), Gaps = 60/309 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR----------EHGDLS----------------AAHR 52
           Y+ +I K+ +L   EE  LAKR            + G +S                A + 
Sbjct: 171 YLKQIGKVSLLTAGEEVELAKRIEAGLFAEEKLAKGGRISPKMREELDWIVVDGRRAKNH 230

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 231 LLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQA 290

Query: 113 MQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           +   +      ++I              Q+++  +L R     +   + ++ PE+VV + 
Sbjct: 291 ITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPDELAKELDMTPEKVVEVQ 350

Query: 164 KKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           K       E IS++  L   GD     LI  S+          +   D     L++++  
Sbjct: 351 K----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------IVPADAVSFTLLQEQ-- 395

Query: 222 KNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
                 L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K
Sbjct: 396 ------LHAVLDTLSERESGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSK 449

Query: 280 VQESIQKQV 288
           ++   + QV
Sbjct: 450 LRHPSRSQV 458


>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|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]
          Length = 625

 Score = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 70/250 (28%), Positives = 120/250 (48%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 387 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 446

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 447 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 504

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 505 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 548

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 549 ATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 608

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 609 KLRHPSRSEV 618


>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 = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 70/250 (28%), Positives = 120/250 (48%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 357 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 416

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 417 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 474

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 475 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 518

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 519 ATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 578

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 579 KLRHPSRSEV 588


>gi|156973168|ref|YP_001444075.1| RNA polymerase sigma factor RpoD [Vibrio harveyi ATCC BAA-1116]
 gi|156524762|gb|ABU69848.1| hypothetical protein VIBHAR_00848 [Vibrio harveyi ATCC BAA-1116]
          Length = 620

 Score = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 69/242 (28%), Positives = 116/242 (47%), Gaps = 28/242 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 382 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 441

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 442 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 499

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 500 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 543

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 544 ATSLKMATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 603

Query: 279 KV 280
           K+
Sbjct: 604 KL 605


>gi|254422659|ref|ZP_05036377.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
 gi|196190148|gb|EDX85112.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
          Length = 298

 Score = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 66/236 (27%), Positives = 119/236 (50%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A HR+V ++LRLVV +A  Y    + + +++ EG IG+ + V+KFDP +G+R +TY+ WW
Sbjct: 63  AKHRMVEANLRLVVSVAKKYIKRNVDLLDLIQEGTIGMQRGVEKFDPSKGYRFSTYAYWW 122

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      +++     +K     L ++K   +  T  + +      IA+    
Sbjct: 123 IRQAITRAIAEKSRTIRLPIHITEK-----LNKIKKAQRQFTQQHGRTPTASEIAQATGF 177

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +  +V     R     SL+  +   D   +Q  D L  + DG  Q   +     + ++ L
Sbjct: 178 TIKQVREYLDRSRQPLSLD--LKVGDNQDTQLGDLL--EDDG--QTPDDYATASSLKSDL 231

Query: 229 TRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            R M+ L P+++++   R   E+   +TL  + +  ++SRERVRQIE  A  K+++
Sbjct: 232 KRIMADLTPQQQQVIALRFGLEDGKNMTLAKIGAMLDISRERVRQIEREALTKLRK 287


>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 = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 127/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 396 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 455

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 456 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 513

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 514 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 556

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 557 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 616

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 617 RKLRHPSRSEV 627


>gi|116748652|ref|YP_845339.1| RpoD family RNA polymerase sigma factor [Syntrophobacter
           fumaroxidans MPOB]
 gi|116697716|gb|ABK16904.1| RNA polymerase, sigma 70 subunit, RpoD family [Syntrophobacter
           fumaroxidans MPOB]
          Length = 599

 Score = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 68/242 (28%), Positives = 114/242 (47%), Gaps = 28/242 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ WW
Sbjct: 361 AKSELIEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWW 420

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R   +L         PE++         
Sbjct: 421 IRQAITRAIADQARTIRI--PVHMIETINKLIRTSRYLVQELGREPTPEEIAEKMEFPVE 478

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + K L ++  E IS+   +  +E  +      DK  +   D ++               
Sbjct: 479 KVRKVLKIA-KEPISLETPIGEEEDSHLGDFIEDKRVASPVDAVI--------------- 522

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFK 278
             N      ++++ L PRE ++   R    ++   TLE +  +F V+RER+RQIEA+A +
Sbjct: 523 NLNLSEQTRKALATLTPREEKVLRMRFGIGEKADHTLEEVGQDFAVTRERIRQIEAKALR 582

Query: 279 KV 280
           K+
Sbjct: 583 KL 584


>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 = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 115/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 341 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 400

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV--------V 160
           I+ A+   I      ++I    +       + R+   L         PE++        V
Sbjct: 401 IRQAITRSIADQARTIRI--PVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEV 458

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + K L +++ E ISM   +  DE             S   D++    D      I+   
Sbjct: 459 KVRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDQNITSPIDAAT 502

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFK 278
            +  +      +  L  RE ++ + R   + P   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 503 SEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALR 562

Query: 279 KVQ 281
           K++
Sbjct: 563 KLR 565


>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 = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 127/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 492

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 493 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 535

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 536 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 595

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 596 RKLRHPSRSEV 606


>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 = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 127/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 409 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 468

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 469 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 526

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 527 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 569

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 570 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 629

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 630 RKLRHPSRSEV 640


>gi|304396867|ref|ZP_07378747.1| RNA polymerase, sigma 70 subunit, RpoD [Pantoea sp. aB]
 gi|304355663|gb|EFM20030.1| RNA polymerase, sigma 70 subunit, RpoD [Pantoea sp. aB]
          Length = 613

 Score = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 127/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 492

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 493 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 535

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 536 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 595

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 596 RKLRHPSRSEV 606


>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 = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 73/250 (29%), Positives = 126/250 (50%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 374 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 433

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-KRLFFNLRRLKGH---LQAITDNNLKPEQVV 160
           I+ A+   I      ++I      T N+  R+   + +  G     + + +  L PE   
Sbjct: 434 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPED-- 491

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 492 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 535

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 536 SESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 595

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 596 KLRHPSRSEV 605


>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 = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 127/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 492

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 493 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 535

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 536 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 595

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 596 RKLRHPSRSEV 606


>gi|270263179|ref|ZP_06191449.1| RNA polymerase sigma factor RpoD [Serratia odorifera 4Rx13]
 gi|270042867|gb|EFA15961.1| RNA polymerase sigma factor RpoD [Serratia odorifera 4Rx13]
          Length = 648

 Score = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 127/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 410 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 469

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 470 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 527

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 528 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 570

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 571 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 630

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 631 RKLRHPSRSEV 641


>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 = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 127/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 377 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 436

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 437 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 494

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 495 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 537

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 538 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 597

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 598 RKLRHPSRSEV 608


>gi|186683480|ref|YP_001866676.1| RpoD family RNA polymerase sigma factor [Nostoc punctiforme PCC
           73102]
 gi|186465932|gb|ACC81733.1| RNA polymerase, sigma 70 subunit, RpoD family [Nostoc punctiforme
           PCC 73102]
          Length = 332

 Score = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 65/246 (26%), Positives = 121/246 (49%), Gaps = 33/246 (13%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           H    A  +++ ++LRLVV IA  Y+ + L   +++ EG++GL + V+KFDP +G++ +T
Sbjct: 92  HQGQKAKQKMIQANLRLVVSIAKKYQRHNLDFLDLIQEGSLGLERGVEKFDPTKGYKFST 151

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y  WWI+ A+   I      +++     +K     L ++K   + +T    +    V IA
Sbjct: 152 YGYWWIRQAITRAIAEQGRTIRLPIHITEK-----LNKIKRIQRELTQKLGRTPTAVDIA 206

Query: 164 KKLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
           ++L++   ++          +S+  R+  D+ +            + QD L  +    E 
Sbjct: 207 EELSLDPKQIRDYLLLARQPVSLELRVGSDKDI------------ELQDMLEDNGLSPEL 254

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQ 271
               K  ++N +N+L++    LNP++R+I   R      N ++L  +     +SRERVRQ
Sbjct: 255 YADHKFLQQNIQNLLSK----LNPQQRQILTFRFGLTDGNELSLAEIGQRMGISRERVRQ 310

Query: 272 IEARAF 277
           IE +A 
Sbjct: 311 IEQQAL 316


>gi|332163001|ref|YP_004299578.1| RNA polymerase sigma factor RpoD [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 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)]
          Length = 612

 Score = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 127/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 374 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 433

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 434 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 491

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 492 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 534

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 535 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 594

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 595 RKLRHPSRSEV 605


>gi|123443868|ref|YP_001007839.1| RNA polymerase sigma factor RpoD [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|122090829|emb|CAL13711.1| RNA polymerase sigma factor RpoD [Yersinia enterocolitica subsp.
           enterocolitica 8081]
          Length = 612

 Score = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 127/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 374 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 433

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 434 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 491

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 492 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 534

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 535 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 594

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 595 RKLRHPSRSEV 605


>gi|56750962|ref|YP_171663.1| group2 RNA polymerase sigma factor RpoD4 [Synechococcus elongatus
           PCC 6301]
 gi|81299380|ref|YP_399588.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)-like
           [Synechococcus elongatus PCC 7942]
 gi|123769297|sp|Q31QR8|RPOD4_SYNE7 RecName: Full=RNA polymerase sigma factor rpoD4
 gi|56685921|dbj|BAD79143.1| group2 RNA polymerase sigma factor RpoD4 [Synechococcus elongatus
           PCC 6301]
 gi|81168261|gb|ABB56601.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)-like
           [Synechococcus elongatus PCC 7942]
          Length = 311

 Score = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 84/307 (27%), Positives = 152/307 (49%), Gaps = 43/307 (14%)

Query: 3   RKNMSIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYR------EHGD-------- 46
           R+N++  V       +S Y+  I +IP+L  +EE  L+++ +      E+ D        
Sbjct: 6   RRNLNAAVERHTSDHVSWYLSSIGRIPLLTAEEEVELSRKVQLMMALLENPDAESNSENQ 65

Query: 47  --LSAAHR----LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             L A  R    ++ ++LRLVV +A  Y+  GL + +++ EG++GL +AV+KFDP  G++
Sbjct: 66  AVLQAGQRAKTKMLKANLRLVVSVAKKYQNQGLELLDLIQEGSLGLERAVEKFDPALGYK 125

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN--NLKPEQ 158
            +TY+ WWI+ +M   I      +++    ++K     + R+K   + +T     L    
Sbjct: 126 FSTYAYWWIRQSMTRAIDNHARTIRLPIHVSEK-----ISRIKKMTRELTHQLKRLPSRA 180

Query: 159 VVAIAKKLNVSESEVI---SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
            +A A KL + + E++   S  C      SL+A     D  S  +   L+ D    E   
Sbjct: 181 EIAEALKLPLQDVEMLLSQSTPC-----TSLDAQARGDDGRS--FLGDLIPDPKSLEP-- 231

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIE 273
           ++  +R  +   ++  ++ L  RE+++ + R  L +    TL  +     VSRER+RQ+E
Sbjct: 232 MDAMDRHIQHEQISTWLAHLTEREQQVLQLRFGLHDGEQHTLAEIGRRLNVSRERIRQVE 291

Query: 274 ARAFKKV 280
           ARA +K+
Sbjct: 292 ARALQKL 298


>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 = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 70/243 (28%), Positives = 117/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 387 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 446

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV--------V 160
           I+ A+   I      ++I    +       + R+   L         PE++        V
Sbjct: 447 IRQAITRSIADQARTIRI--PVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEV 504

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + K L +++ E ISM   +  DE  +      D+N +   D      +G ++   E   
Sbjct: 505 KVRKVLKIAK-EPISMETPIGDDEDSHLGDFIEDQNITSPVDAAT--SEGLKEATRE--- 558

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFK 278
                      +  L  RE ++ + R   + P   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 559 ----------VLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALR 608

Query: 279 KVQ 281
           K++
Sbjct: 609 KLR 611


>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 = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 127/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 373 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 432

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 433 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 490

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 491 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 533

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 534 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 593

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 594 RKLRHPSRSEV 604


>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 = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 127/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 492

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 493 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 535

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 536 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 595

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 596 RKLRHPSRSEV 606


>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|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]
          Length = 595

 Score = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 70/250 (28%), Positives = 120/250 (48%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 357 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 416

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 417 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 474

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 475 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 518

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 519 ATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 578

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 579 KLRHPSRSEV 588


>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|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]
          Length = 612

 Score = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 127/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 374 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 433

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 434 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 491

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 492 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 534

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 535 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 594

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 595 RKLRHPSRSEV 605


>gi|329298675|ref|ZP_08256011.1| RNA polymerase sigma factor RpoD [Plautia stali symbiont]
          Length = 610

 Score = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 127/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 372 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 431

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 432 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 489

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 490 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 532

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 533 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 592

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 593 RKLRHPSRSEV 603


>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 = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 127/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 373 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 432

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 433 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 490

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 491 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 533

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 534 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 593

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 594 RKLRHPSRSEV 604


>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 = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 127/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 409 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 468

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 469 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 526

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 527 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 569

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 570 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 629

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 630 RKLRHPSRSEV 640


>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 = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 70/250 (28%), Positives = 120/250 (48%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 390 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 449

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 450 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 507

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 508 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 551

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 552 ATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 611

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 612 KLRHPSRSEV 621


>gi|260767412|ref|ZP_05876349.1| RNA polymerase sigma factor RpoD [Vibrio furnissii CIP 102972]
 gi|260617524|gb|EEX42706.1| RNA polymerase sigma factor RpoD [Vibrio furnissii CIP 102972]
 gi|315181195|gb|ADT88109.1| RNA polymerase sigma factor RpoD [Vibrio furnissii NCTC 11218]
          Length = 628

 Score = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 69/242 (28%), Positives = 116/242 (47%), Gaps = 28/242 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 390 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 449

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 450 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 507

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 508 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 551

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 552 ATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 611

Query: 279 KV 280
           K+
Sbjct: 612 KL 613


>gi|147674012|ref|YP_001216017.1| 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 = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 70/250 (28%), Positives = 120/250 (48%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 383 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 442

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 443 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 500

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 501 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 544

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 545 ATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 604

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 605 KLRHPSRSEV 614


>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 = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 127/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 374 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 433

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 434 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 491

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 492 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 534

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 535 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 594

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 595 RKLRHPSRSEV 605


>gi|153309|gb|AAA26764.1| principal sigma-like factor [Streptomyces aureofaciens]
          Length = 528

 Score = 90.1 bits (222), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 77/299 (25%), Positives = 141/299 (47%), Gaps = 40/299 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+  I K+P+L  ++E  LAKR  E G  S                           A +
Sbjct: 235 YLKLIGKVPLLNAEQEVELAKRI-EAGLFSEYKLEEEEDHKPAFKRELEILVEDGRRAKN 293

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ 
Sbjct: 294 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNVGLIRAVEKFDYTKGFKFSTYATWWIRQ 353

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           A+   +      ++I    +   +   L R++  +         PE+   + K+L+++  
Sbjct: 354 AITRAMADQSRTIRI--PVHMVEIINKLARVQRQMLQDLGREPTPEE---LGKELDMTPE 408

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           +VI +     G E ++      ++  S++ D +    D +  V  +       +  L   
Sbjct: 409 KVIEVQKY--GREPISLHTPLGEEGDSEFGDLI---EDSEAVVPADAVSFTFLQEQLQSI 463

Query: 232 MSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +  L+ RE  +   R  L +  P TL+ +   + V+RER+RQIE++   K++   + QV
Sbjct: 464 LGTLSEREAGVVSMRYGLNDGQPKTLDEIGRVYGVTRERIRQIESKTMSKLRHPSRSQV 522


>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 = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 127/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 374 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 433

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 434 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 491

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 492 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 534

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 535 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 594

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 595 RKLRHPSRSEV 605


>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 = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 71/250 (28%), Positives = 119/250 (47%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 438 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPNPEELAMRMGMPED 495

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D    +  +   
Sbjct: 496 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLALPADAAT 539

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ RN     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 540 SESLRNATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 600 KLRHPSRSEV 609


>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 = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 117/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 401 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 460

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 461 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 518

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 519 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 562

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 563 ATSLKMATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 622

Query: 279 KVQ 281
           K++
Sbjct: 623 KLR 625


>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 = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 127/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 373 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 432

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 433 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 490

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 491 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 533

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 534 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 593

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 594 RKLRHPSRSEV 604


>gi|253991033|ref|YP_003042389.1| RNA polymerase sigma factor RpoD [Photorhabdus asymbiotica subsp.
           asymbiotica ATCC 43949]
 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 = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 127/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 413 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 472

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 473 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 530

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 531 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 573

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 574 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 633

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 634 RKLRHPSRSEV 644


>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 = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 73/250 (29%), Positives = 126/250 (50%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-KRLFFNLRRLKGH---LQAITDNNLKPEQVV 160
           I+ A+   I      ++I      T N+  R+   + +  G     + + +  L PE   
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPED-- 492

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 493 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 536

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 537 SESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 596

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 597 KLRHPSRSEV 606


>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 = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 73/250 (29%), Positives = 126/250 (50%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 369 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 428

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-KRLFFNLRRLKGH---LQAITDNNLKPEQVV 160
           I+ A+   I      ++I      T N+  R+   + +  G     + + +  L PE   
Sbjct: 429 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPMPEELAERMLMPED-- 486

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 487 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTFELPLDSAT 530

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 531 SESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 590

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 591 KLRHPSRSEV 600


>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 = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 127/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 374 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 433

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 434 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 491

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 492 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 534

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 535 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 594

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 595 RKLRHPSRSEV 605


>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 = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 75/245 (30%), Positives = 118/245 (48%), Gaps = 32/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 384 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 443

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA------- 161
           I+ A+   I      ++I    +       L R+   +         PE++ A       
Sbjct: 444 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMIQEMGREATPEELAARMDMPED 501

Query: 162 -IAKKLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            + K L +++ E ISM   +  DE   L   I  S   S         D    E +    
Sbjct: 502 KVRKVLKIAK-EPISMETPIGDDEDSHLGDFIEDSGVISP-------LDSATAEGL---- 549

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARA 276
             R+  +NML    + L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A
Sbjct: 550 --REATQNML----ASLTSREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 603

Query: 277 FKKVQ 281
            +K++
Sbjct: 604 LRKLR 608


>gi|284031355|ref|YP_003381286.1| RpoD subfamily RNA polymerase sigma-70 subunit [Kribbella flavida
           DSM 17836]
 gi|283810648|gb|ADB32487.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Kribbella flavida
           DSM 17836]
          Length = 442

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 76/300 (25%), Positives = 140/300 (46%), Gaps = 41/300 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS----------------------------AA 50
           Y+ +I K+P+L  ++E  LAKR  E G  +                            A 
Sbjct: 148 YLKQIGKVPLLNAEQEVELAKRI-EAGLFAEEQLSDESAKLKDKVRDEYDWISEDGRRAK 206

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+
Sbjct: 207 NHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIR 266

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            A+   +      ++I    +   +   L R++  +         PE+   +AK+L+++ 
Sbjct: 267 QAITRAMADQARTIRI--PVHMVEVINKLARVQRQMLQDLGREPTPEE---LAKELDMTP 321

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            +VI +     G E ++      +   S++ D +    D +  V  E       +  L  
Sbjct: 322 EKVIEVQKY--GREPISLHTPLGEDGDSEFGDLI---EDSEAIVPAEAVSFTLLQEQLHA 376

Query: 231 SMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   + QV
Sbjct: 377 VLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQV 436


>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 = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 73/250 (29%), Positives = 126/250 (50%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 374 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 433

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-KRLFFNLRRLKGH---LQAITDNNLKPEQVV 160
           I+ A+   I      ++I      T N+  R+   + +  G     + + +  L PE   
Sbjct: 434 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPED-- 491

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 492 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 535

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 536 SESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 595

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 596 KLRHPSRSEV 605


>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 = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 127/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 373 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 432

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 433 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 490

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 491 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 533

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 534 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 593

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 594 RKLRHPSRSEV 604


>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 = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 70/250 (28%), Positives = 120/250 (48%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 387 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 446

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 447 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 504

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 505 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 548

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 549 ATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 608

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 609 KLRHPSRSEV 618


>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 = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 70/250 (28%), Positives = 120/250 (48%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 383 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 442

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 443 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 500

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 501 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 544

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 545 ATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 604

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 605 KLRHPSRSEV 614


>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 = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 70/250 (28%), Positives = 120/250 (48%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 404 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 463

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 464 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 521

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 522 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 565

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 566 ATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 625

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 626 KLRHPSRSEV 635


>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|133310|sp|P26480|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]
          Length = 617

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 119/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 379 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 438

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   + +++++
Sbjct: 439 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEE---LGERMDM 493

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D   S   D++    D   Q  IE    ++ +   
Sbjct: 494 PEDKIRKV-LKIA-KEPISMETPIGDDEDSHLGDFI---EDSTMQSPIEMATSESLKEST 548

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 549 REVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 603


>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|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]
          Length = 625

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 70/250 (28%), Positives = 120/250 (48%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 387 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 446

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 447 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 504

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 505 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 548

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 549 ATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 608

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 609 KLRHPSRSEV 618


>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 = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 70/250 (28%), Positives = 120/250 (48%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 389 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 448

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 449 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 506

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 507 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 550

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 551 ATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 610

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 611 KLRHPSRSEV 620


>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 = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 117/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 379 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 438

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 439 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 496

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 497 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 540

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 541 STSLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 600

Query: 279 KVQ 281
           K++
Sbjct: 601 KLR 603


>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 = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 127/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 376 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 435

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 436 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 493

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 494 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 536

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 537 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 596

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 597 RKLRHPSRSEV 607


>gi|254445278|ref|ZP_05058754.1| Sigma-70 region 3 family [Verrucomicrobiae bacterium DG1235]
 gi|198259586|gb|EDY83894.1| Sigma-70 region 3 family [Verrucomicrobiae bacterium DG1235]
          Length = 576

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 79/267 (29%), Positives = 125/267 (46%), Gaps = 36/267 (13%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHR----LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           LE ++   L    R H  L AAH+    +V ++LRLV+ IA  Y   GL   +++ EGN+
Sbjct: 294 LEPEKLLSLIAEVRRH--LKAAHKAKTEMVEANLRLVISIAKKYTNRGLSFLDLIQEGNM 351

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN-----QKRL 135
           GLM+AV+KF+  RG++ +TY+ WWI+ A+   I      ++I      T N     QK+L
Sbjct: 352 GLMKAVEKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETLNKVMQVQKQL 411

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
                      +   +  L  E+V  I K       + IS+   +   +  N      DK
Sbjct: 412 LQEYGHEPTPEEVAEEMALPVERVQTIMK----MAQQPISLQSPVGDGDDTNFGDFIEDK 467

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPV 253
           ++    D   +       +L EK         +   +  L  RERR+   R   +     
Sbjct: 468 SAENPYDQTAF------SLLREK---------IIDVLDSLTERERRVLSLRFGLVDGYSR 512

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKV 280
           TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 513 TLEEVGKQFKVTRERIRQIEAKALRKM 539


>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 = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 70/250 (28%), Positives = 120/250 (48%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 387 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 446

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 447 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 504

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 505 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 548

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 549 ATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 608

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 609 KLRHPSRSEV 618


>gi|88798840|ref|ZP_01114422.1| RNA polymerase sigma factor [Reinekea sp. MED297]
 gi|88778320|gb|EAR09513.1| RNA polymerase sigma factor [Reinekea sp. MED297]
          Length = 614

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 113/243 (46%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 376 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 435

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 436 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELAERMDMPED 493

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +S+ E IS+   +  DE             S   D++    D    + +    
Sbjct: 494 KIRKVLKISK-EPISLETPIGDDE------------DSSLGDFI---EDNTMILPVNSAT 537

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFK 278
               R+  T  ++ L  RE ++   R         TLE +  +F+V+RER+RQIEA+A +
Sbjct: 538 STGLRDATTEVLAGLTAREAKVLRMRFGINMNTDHTLEEVGKQFDVTRERIRQIEAKALR 597

Query: 279 KVQ 281
           K++
Sbjct: 598 KLR 600


>gi|298250072|ref|ZP_06973876.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297548076|gb|EFH81943.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 319

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 84/293 (28%), Positives = 148/293 (50%), Gaps = 50/293 (17%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRY-------REHGDLS------------AAHRLVTSHLR 59
           Y +EI ++ +L K E   LA+R        R+   LS            A  +L+ ++LR
Sbjct: 32  YRYEIGQVELLSKDEVTDLAQRIEKAQANIRKQRGLSRSARLDDNEAQEAKRQLIEANLR 91

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           LV+ IA  YRG+G+ + +++ EGN+GLM AV KFD ++G+R +TY+ WWI+    +YI R
Sbjct: 92  LVMHIARKYRGFGVDLMDLIQEGNLGLMHAVDKFDYKKGYRFSTYATWWIR----QYITR 147

Query: 120 SWS------LVKIGTTANQKRLFFNLRRL-KGHLQAITDNNLKPEQVVAIAKKLNV--SE 170
           + S       V +      KRL    R++ +G     T   L  +  +++ + + +  + 
Sbjct: 148 ALSEQAHMIRVPLYKIEEIKRLGRVKRKMQQGETGEPTLEELAVQMEISVPEVIALLSTN 207

Query: 171 SEVISMNC-RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
            E IS++  R  GD+ ++         S   +D  +Y     E+V++ +  ++  +++L 
Sbjct: 208 QETISLDMPRKGGDDEISL--------SEVLEDDPIY---SPERVVLTQTLQEQVQDIL- 255

Query: 230 RSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              + L PRE+++ + R  L  N   +L     +  +S E VRQ+E RA KK+
Sbjct: 256 ---NCLTPREKKVLQLRFGLNGNGEHSLTETGKKMGLSHEAVRQMEFRALKKL 305


>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 = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 73/250 (29%), Positives = 126/250 (50%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 373 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 432

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-KRLFFNLRRLKGH---LQAITDNNLKPEQVV 160
           I+ A+   I      ++I      T N+  R+   + +  G     + + +  L PE   
Sbjct: 433 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPED-- 490

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 491 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 534

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 535 SESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 594

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 595 KLRHPSRSEV 604


>gi|153828433|ref|ZP_01981100.1| RNA polymerase sigma factor RpoD [Vibrio cholerae 623-39]
 gi|148876142|gb|EDL74277.1| RNA polymerase sigma factor RpoD [Vibrio cholerae 623-39]
          Length = 572

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 70/250 (28%), Positives = 120/250 (48%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 334 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 393

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 394 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 451

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 452 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 495

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 496 ATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 555

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 556 KLRHPSRSEV 565


>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 = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 70/250 (28%), Positives = 120/250 (48%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 365 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 424

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 425 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 482

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 483 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 526

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 527 ATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 586

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 587 KLRHPSRSEV 596


>gi|323359909|ref|YP_004226305.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Microbacterium testaceum StLB037]
 gi|323276280|dbj|BAJ76425.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Microbacterium testaceum StLB037]
          Length = 436

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 81/311 (26%), Positives = 142/311 (45%), Gaps = 64/311 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHG--------DLSAAHR------------------ 52
           Y+ +I K+P+L   EE  LA R  E G        ++SAA +                  
Sbjct: 141 YLKQIGKVPLLNAAEEVELAMRI-EAGLFAEEKLSNMSAAEKTSQLGLDLQWVARDGQRA 199

Query: 53  ---LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI
Sbjct: 200 KSHLLGANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWI 259

Query: 110 KAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
           + A+   +      ++I              Q+++  +L R     +   + ++ PE+V+
Sbjct: 260 RQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELSRELDMTPEKVI 319

Query: 161 AIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            + K       E IS++  L   GD     LI  ++          V   D     ++++
Sbjct: 320 EVQK----YGREPISLHTPLGEDGDSEFGDLIEDTEA---------VVPADAVGFTMLQR 366

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARA 276
           +        L   +  L+ RE  +   R  L +  P TL+ +   F V+RER+RQIE++ 
Sbjct: 367 Q--------LESLLDSLSEREAGVIRMRFGLGDGQPKTLDQIGDTFGVTRERIRQIESKT 418

Query: 277 FKKVQESIQKQ 287
             K++   + Q
Sbjct: 419 MAKLRHPSRSQ 429


>gi|261820103|ref|YP_003258209.1| RNA polymerase sigma factor RpoD [Pectobacterium wasabiae WPP163]
 gi|261604116|gb|ACX86602.1| RNA polymerase, sigma 70 subunit, RpoD [Pectobacterium wasabiae
           WPP163]
          Length = 611

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 127/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 373 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 432

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 433 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 490

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 491 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 533

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 534 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 593

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 594 RKLRHPSRSEV 604


>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 = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 70/250 (28%), Positives = 120/250 (48%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 404 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 463

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 464 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 521

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 522 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 565

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 566 ATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 625

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 626 KLRHPSRSEV 635


>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 = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 119/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 379 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 438

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   + +++++
Sbjct: 439 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEE---LGERMDM 493

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D   S   D++    D   Q  IE    ++ +   
Sbjct: 494 PEDKIRKV-LKIA-KEPISMETPIGDDEDSHLGDFI---EDSTMQSPIEMATSESLKEST 548

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 549 REVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 603


>gi|115378523|ref|ZP_01465679.1| sigma-D factor [Stigmatella aurantiaca DW4/3-1]
 gi|115364445|gb|EAU63524.1| sigma-D factor [Stigmatella aurantiaca DW4/3-1]
          Length = 171

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 46/125 (36%), Positives = 76/125 (60%), Gaps = 1/125 (0%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           GLS Y+  +     L +++EY LA+  R+ GD SA   L TS+L  VV +A  +   G  
Sbjct: 11  GLSHYLRHLGGHHQLTREQEYELARAARK-GDESARQTLATSNLAFVVAVAKKFANRGAR 69

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++ EGN+GLM+A++ FDP++  R ATY++WWI+A +  Y+  + S V+ G +     
Sbjct: 70  LDDLIQEGNVGLMKAIEHFDPKKNVRFATYAVWWIRAYITRYLKDNRSQVRGGESERGSM 129

Query: 135 LFFNL 139
           + F+L
Sbjct: 130 VDFSL 134


>gi|107099562|ref|ZP_01363480.1| hypothetical protein PaerPA_01000575 [Pseudomonas aeruginosa PACS2]
          Length = 604

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 119/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 366 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 425

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   + +++++
Sbjct: 426 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEE---LGERMDM 480

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D   S   D++    D   Q  IE    ++ +   
Sbjct: 481 PEDKIRKV-LKIA-KEPISMETPIGDDEDSHLGDFI---EDSTMQSPIEMATSESLKEST 535

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 536 REVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 590


>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 = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 119/234 (50%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 383 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 442

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +          E+   +A+++ +
Sbjct: 443 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQKMGREATSEE---LAERMGM 497

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ R   
Sbjct: 498 PEDKIRKV-LKIAK-EPISMETPIGDDDDSHLGDFI---EDNTLELPLDSATAQSLRAAT 552

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 553 HEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 606


>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 = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 127/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 374 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 433

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 434 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 491

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 492 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 534

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 535 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 594

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 595 RKLRHPSRSEV 605


>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 = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 127/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 374 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 433

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 434 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 491

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 492 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 534

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 535 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 594

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 595 RKLRHPSRSEV 605


>gi|292486903|ref|YP_003529773.1| RNA polymerase sigma factor rpoD (Sigma-70) [Erwinia amylovora
           CFBP1430]
 gi|292900702|ref|YP_003540071.1| RNA polymerase sigma-70 factor [Erwinia amylovora ATCC 49946]
 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]
          Length = 614

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 73/250 (29%), Positives = 126/250 (50%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 376 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 435

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-KRLFFNLRRLKGH---LQAITDNNLKPEQVV 160
           I+ A+   I      ++I      T N+  R+   + +  G     + + +  L PE   
Sbjct: 436 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPED-- 493

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 494 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 537

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 538 SESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 597

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 598 KLRHPSRSEV 607


>gi|269956779|ref|YP_003326568.1| RpoD subfamily RNA polymerase sigma-70 subunit [Xylanimonas
           cellulosilytica DSM 15894]
 gi|269305460|gb|ACZ31010.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Xylanimonas
           cellulosilytica DSM 15894]
          Length = 549

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 71/258 (27%), Positives = 126/258 (48%), Gaps = 34/258 (13%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           H    A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +T
Sbjct: 307 HDGKRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFST 366

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNL 154
           Y+ WWI+ A+   +      ++I              Q+++  +L R     +   + ++
Sbjct: 367 YATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDM 426

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
            PE+VV + K       E IS++  L   GD     LI  S+          V   D   
Sbjct: 427 TPEKVVEVQK----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVS 473

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVR 270
             L++++        L + +  L+ RE  +   R  LQ+  P TL+ +   + V+RER+R
Sbjct: 474 FTLLQEQ--------LHQVLDTLSEREAGVVSMRFGLQDGQPKTLDEIGKVYGVTRERIR 525

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 526 QIESKTMSKLRHPSRSQV 543


>gi|238918478|ref|YP_002931992.1| RNA polymerase sigma factor RpoD [Edwardsiella ictaluri 93-146]
 gi|238868046|gb|ACR67757.1| RNA polymerase sigma factor RpoD, putative [Edwardsiella ictaluri
           93-146]
          Length = 611

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 70/250 (28%), Positives = 121/250 (48%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 373 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 432

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 433 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELAERMMMPED 490

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 491 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 534

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 535 SESLRSATRDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 594

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 595 KLRHPSRSEV 604


>gi|149194280|ref|ZP_01871377.1| RNA polymerase sigma factor RpoD [Caminibacter mediatlanticus TB-2]
 gi|149135455|gb|EDM23934.1| RNA polymerase sigma factor RpoD [Caminibacter mediatlanticus TB-2]
          Length = 604

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 68/240 (28%), Positives = 122/240 (50%), Gaps = 21/240 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++  ++LRLVV IA  Y   GLP  +++ EGNIGLM+A+ KF+ E+G++ +TY+ WW
Sbjct: 365 AKEKMARANLRLVVSIAKKYTNRGLPFLDLIQEGNIGLMKAIDKFEFEKGYKFSTYATWW 424

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      V+I        +  N+ ++   ++       K   +  IAK++ +
Sbjct: 425 IRQAISRAIADQARTVRIPI-----HMIENINQINKIIRKYVQEEGKEPSLEVIAKEMKM 479

Query: 169 SESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWL---VYDHDGQEQVLIEKEERKNR 224
              E I    +++ +  SL A +   +    ++ D++    + +   E VL      ++ 
Sbjct: 480 P-VEKIKQILKISKEPISLEAPVGEEE--DGKFGDFIEDKSFSNPYDEVVL------EDL 530

Query: 225 RNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R  +   +  LN RE+ + + R      ++  TLE +     V+RERVRQIE+ A KK++
Sbjct: 531 RKHIDEILENLNEREKAVIKMRFGLMPDKSERTLEEIGKALNVTRERVRQIESSAIKKLR 590


>gi|94263318|ref|ZP_01287133.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
 gi|93456273|gb|EAT06403.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
          Length = 442

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 70/244 (28%), Positives = 124/244 (50%), Gaps = 19/244 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLVV IA  Y   GL +++++ EGN+GLM+AV +FD  +G + +TY+ WW
Sbjct: 206 AKDAMIKANLRLVVSIAKRYMHQGLTLADLIQEGNLGLMRAVFRFDYTKGNKFSTYASWW 265

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR--LKGHLQAITDNNLKPEQVVAIAKKL 166
           I+ A+   IL     +++         F  LR    K     + +   +P   V I++K 
Sbjct: 266 IRQAITRAILDKTRTIRLPVH------FLELRSQFFKAFYSLLKELGREP-TPVEISEKT 318

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-R 225
            +   +++++        SL   +   D   S   D+L    + QE +   +  + N+  
Sbjct: 319 GLPMEKILAIFEASREPISLETPVGDDD---STLGDFL----ENQESISPYEAVKGNQLA 371

Query: 226 NMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +T  +S L+PRE +I   R    ++   TLE +   F VSRER+RQIE +A  +++ S
Sbjct: 372 ERVTTILSTLSPREEKIIRLRFGIGEDAEYTLEEIGKRFNVSRERIRQIEKKALNRLRHS 431

Query: 284 IQKQ 287
            +++
Sbjct: 432 SRRE 435


>gi|269137812|ref|YP_003294512.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Edwardsiella tarda EIB202]
 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 = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 70/250 (28%), Positives = 121/250 (48%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 373 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 432

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 433 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELAERMMMPED 490

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 491 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 534

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 535 SESLRSATRDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 594

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 595 KLRHPSRSEV 604


>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 = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 119/234 (50%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 357 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 416

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +          E+   +A+++ +
Sbjct: 417 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQKMGREATSEE---LAERMGM 471

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ R   
Sbjct: 472 PEDKIRKV-LKIAK-EPISMETPIGDDDDSHLGDFI---EDNTLELPLDSATAQSLRAAT 526

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 527 HEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 580


>gi|322831339|ref|YP_004211366.1| RNA polymerase, sigma 70 subunit, RpoD [Rahnella sp. Y9602]
 gi|321166540|gb|ADW72239.1| RNA polymerase, sigma 70 subunit, RpoD [Rahnella sp. Y9602]
          Length = 612

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 127/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 374 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 433

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 434 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 491

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 492 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 534

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 535 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 594

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 595 RKLRHPSRSEV 605


>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 = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 119/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 379 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 438

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   + +++++
Sbjct: 439 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPNPEE---LGERMDM 493

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D   S   D++    D   Q  IE    ++ +   
Sbjct: 494 PEDKIRKV-LKIA-KEPISMETPIGDDEDSHLGDFI---EDSTMQSPIEMATSESLKEST 548

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 549 REVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 603


>gi|147756|gb|AAA24601.1| RNA polymerase sigma-subunit [Escherichia coli]
          Length = 613

 Score = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 71/251 (28%), Positives = 125/251 (49%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 492

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 493 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 535

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A 
Sbjct: 536 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKAL 595

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 596 RKLRHPSRSEV 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 = 90.1 bits (222), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 127/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 376 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 435

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 436 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 493

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 494 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 536

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 537 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 596

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 597 RKLRHPSRSEV 607


>gi|242310656|ref|ZP_04809811.1| RNA polymerase sigma factor [Helicobacter pullorum MIT 98-5489]
 gi|239523054|gb|EEQ62920.1| RNA polymerase sigma factor [Helicobacter pullorum MIT 98-5489]
          Length = 615

 Score = 89.7 bits (221), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 69/246 (28%), Positives = 124/246 (50%), Gaps = 14/246 (5%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           KR ++  D  A  ++  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ ++G
Sbjct: 367 KRGKDIAD-RAKTKMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKKG 425

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           ++ +TY+ WWI+ A+   I      ++I        +   + R+   ++       K   
Sbjct: 426 YKFSTYATWWIRQAISRAIADQARTIRIPI-----HMIETINRINKIMRKYLQEEGKEPD 480

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           +  IA+++ +   +V ++        SL A I + +    ++ D++    D      ++ 
Sbjct: 481 IEKIAEEVGLPVDKVKNVIKITKEPISLEAPIGNGE--DGKFGDFV---EDKASLGPMDS 535

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEAR 275
             +++ +  +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ 
Sbjct: 536 ILKEDLKAQIDDVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESS 595

Query: 276 AFKKVQ 281
           A KK++
Sbjct: 596 AIKKLK 601


>gi|262392398|ref|YP_003284252.1| RNA polymerase sigma factor RpoD [Vibrio sp. Ex25]
 gi|262335992|gb|ACY49787.1| RNA polymerase sigma factor RpoD [Vibrio sp. Ex25]
          Length = 620

 Score = 89.7 bits (221), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 117/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 382 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 441

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 442 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 499

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 500 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 543

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 544 ATSLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 603

Query: 279 KVQ 281
           K++
Sbjct: 604 KLR 606


>gi|294634612|ref|ZP_06713146.1| RNA polymerase sigma factor RpoD [Edwardsiella tarda ATCC 23685]
 gi|291091942|gb|EFE24503.1| RNA polymerase sigma factor RpoD [Edwardsiella tarda ATCC 23685]
          Length = 613

 Score = 89.7 bits (221), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 70/250 (28%), Positives = 121/250 (48%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 435 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELAERMMMPED 492

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 493 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 536

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 537 SESLRSATRDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 596

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 597 KLRHPSRSEV 606


>gi|259907100|ref|YP_002647456.1| RNA polymerase sigma factor RpoD [Erwinia pyrifoliae Ep1/96]
 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 = 89.7 bits (221), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 73/250 (29%), Positives = 126/250 (50%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-KRLFFNLRRLKGH---LQAITDNNLKPEQVV 160
           I+ A+   I      ++I      T N+  R+   + +  G     + + +  L PE   
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPED-- 492

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 493 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 536

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 537 SESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 596

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 597 KLRHPSRSEV 606


>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 = 89.7 bits (221), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 68/243 (27%), Positives = 116/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 371 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 430

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA------- 161
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 431 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREATPEELAERMMMPED 488

Query: 162 -IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D    + ++   
Sbjct: 489 RIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLSLPVDAAT 532

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
           + + +      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 533 KDSLKGATDDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 592

Query: 279 KVQ 281
           K++
Sbjct: 593 KLR 595


>gi|330831100|ref|YP_004394052.1| RNA polymerase sigma factor [Aeromonas veronii B565]
 gi|328806236|gb|AEB51435.1| RNA polymerase sigma factor [Aeromonas veronii B565]
          Length = 618

 Score = 89.7 bits (221), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 71/250 (28%), Positives = 119/250 (47%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 380 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 439

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 440 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPNPEELAMRMGMPED 497

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D    +  +   
Sbjct: 498 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLALPADAAT 541

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ RN     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 542 SESLRNATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 601

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 602 KLRHPSRSEV 611


>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 = 89.7 bits (221), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 127/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 370 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 429

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 430 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 487

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 488 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLKLPLDSA 530

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 531 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 590

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 591 RKLRHPSRSEV 601


>gi|72162538|ref|YP_290195.1| RNA polymerase sigma factor [Thermobifida fusca YX]
 gi|71916270|gb|AAZ56172.1| carbamoyl-phosphate synthase L chain, ATP-binding [Thermobifida
           fusca YX]
          Length = 616

 Score = 89.7 bits (221), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 79/311 (25%), Positives = 141/311 (45%), Gaps = 63/311 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR----------------------------EHGDLSAA 50
           Y+ +I K+P+L  ++E  LAKR                              E G  +  
Sbjct: 322 YLKQIGKVPLLNAEQEVELAKRIEAGLFAEEKLSKKGHELTPEEREELEWIAEDGKRAKK 381

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           H L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+
Sbjct: 382 H-LLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIR 440

Query: 111 AAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
            A+   +      ++I              Q+++  +L R     +   + ++ PE+VV 
Sbjct: 441 QAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVE 500

Query: 162 IAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           + K       E IS++  L   GD     LI   D  + Q  + + +        L++++
Sbjct: 501 VQKYGR----EPISLHTPLGEDGDSEFGDLIE--DSEAIQPGEAVSF-------TLLQEQ 547

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAF 277
                   L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++  
Sbjct: 548 --------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTM 599

Query: 278 KKVQESIQKQV 288
            K++   + QV
Sbjct: 600 SKLRHPSRSQV 610


>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 = 89.7 bits (221), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 117/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 382 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 441

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 442 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 499

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 500 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 543

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 544 ATSLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 603

Query: 279 KVQ 281
           K++
Sbjct: 604 KLR 606


>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 = 89.7 bits (221), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 70/250 (28%), Positives = 120/250 (48%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 284 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 343

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 344 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 401

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 402 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 445

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 446 ATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 505

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 506 KLRHPSRSEV 515


>gi|227329605|ref|ZP_03833629.1| RNA polymerase sigma factor RpoD [Pectobacterium carotovorum subsp.
           carotovorum WPP14]
          Length = 611

 Score = 89.7 bits (221), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 127/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 373 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 432

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 433 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 490

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 491 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 533

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 534 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 593

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 594 RKLRHPSRSEV 604


>gi|50726933|gb|AAT81163.1| principal sigma factor [Streptomyces ansochromogenes]
          Length = 440

 Score = 89.7 bits (221), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 79/308 (25%), Positives = 140/308 (45%), Gaps = 58/308 (18%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ +I K+P+L  ++E  LAKR  E G  +                           A +
Sbjct: 147 YLKQIGKVPLLNAEQEVELAKRI-EAGLFAEDKLANSDKLAPKLKRELEIIAEDGRRAKN 205

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 206 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 265

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ +
Sbjct: 266 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEV 325

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 326 QK----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQP 372

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                 +  R   V++ R    F     Q  P TL+ +   + V+RER+RQIE++   K+
Sbjct: 373 DSVLDTLSEREAGVVSMR----FGLTDGQ--PKTLDEIGKVYGVTRERIRQIESKTMSKL 426

Query: 281 QESIQKQV 288
           +   + QV
Sbjct: 427 RHPSRSQV 434


>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 = 89.7 bits (221), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 117/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 379 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 438

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 439 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 496

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 497 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 540

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 541 ATSLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 600

Query: 279 KVQ 281
           K++
Sbjct: 601 KLR 603


>gi|256832655|ref|YP_003161382.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Jonesia
           denitrificans DSM 20603]
 gi|256686186|gb|ACV09079.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Jonesia
           denitrificans DSM 20603]
          Length = 504

 Score = 89.7 bits (221), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 81/310 (26%), Positives = 141/310 (45%), Gaps = 61/310 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH--------GDLS--------------AAH 51
           Y+ +I K+ +L  ++E  LAKR     Y E         GD                A +
Sbjct: 210 YLKQIGKVALLNAEQEVELAKRIEAGLYAEERLAAGVAEGDRKLEREYRWIIQDGKRAKN 269

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 270 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 329

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+VV +
Sbjct: 330 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEV 389

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 390 QKYGR----EPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 435

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L + +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 436 -------LHQVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 488

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 489 KLRHPSRSQV 498


>gi|172036788|ref|YP_001803289.1| group 2 sigma-70 RNA polymerase sigma factor C [Cyanothece sp. ATCC
           51142]
 gi|171698242|gb|ACB51223.1| group 2 sigma-70 RNA polymerase sigma factor C [Cyanothece sp. ATCC
           51142]
          Length = 420

 Score = 89.7 bits (221), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 64/232 (27%), Positives = 125/232 (53%), Gaps = 13/232 (5%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV+KFDP +G+R +TY+ WWI+  
Sbjct: 185 MIKANLRLVVSVAKKYQHRGLELLDLIQEGTLGLEKAVEKFDPIKGYRFSTYAYWWIRQG 244

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   I     ++++     +K     L ++K   + I+    +   +  I K+LN++ ++
Sbjct: 245 ITRAIATQSRIIRLPVHVTEK-----LNKIKQVQRQISQAKGRNATLEEIGKELNMTPTQ 299

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           V  +  ++    SL   I    +  ++  D L  +    E+ L  +  R++   +L    
Sbjct: 300 VREVFMKIPRSVSLE--IKVGKEKDTELVDLLESEDISPEENLAIESLRRDIGILLED-- 355

Query: 233 SVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQE 282
             L  RE+ + + R   E+ V  +L ++    ++SRERVRQIEA+A +K+++
Sbjct: 356 --LTEREQEVIKLRYGFEDGVSYSLADIGRTLDLSRERVRQIEAKALQKLRQ 405


>gi|16130963|ref|NP_417539.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli str.
           K-12 substr. MG1655]
 gi|89109837|ref|AP_003617.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli str.
           K-12 substr. W3110]
 gi|170082610|ref|YP_001731930.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli str.
           K-12 substr. DH10B]
 gi|238902178|ref|YP_002927974.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli BW2952]
 gi|1710680|sp|P00579|RPOD_ECOLI RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 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]
          Length = 613

 Score = 89.7 bits (221), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 71/251 (28%), Positives = 125/251 (49%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 492

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 493 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 535

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A 
Sbjct: 536 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKAL 595

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 596 RKLRHPSRSEV 606


>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 = 89.7 bits (221), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 68/245 (27%), Positives = 117/245 (47%), Gaps = 32/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 385 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 444

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   + +++++
Sbjct: 445 IRQAITRSIADQARTIRI--PVHMIETINKLNRVSRQMLQEMGREPTPEE---LGERMDM 499

Query: 169 SESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            E +V          ISM   +  DE             S   D++    D   Q  ++ 
Sbjct: 500 PEDKVRKVLKIAKEPISMETPIGDDE------------DSHLGDFI---EDTTMQSPVDA 544

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARA 276
              ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A
Sbjct: 545 ATAESLREATRDVLASLTAREAKVLAMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 604

Query: 277 FKKVQ 281
            +K++
Sbjct: 605 LRKLR 609


>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 = 89.7 bits (221), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 117/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 401 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 460

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 461 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 518

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 519 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 562

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 563 ATSLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 622

Query: 279 KVQ 281
           K++
Sbjct: 623 KLR 625


>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 = 89.7 bits (221), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 117/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 336 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 395

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 396 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 453

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 454 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 497

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 498 ATSLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 557

Query: 279 KVQ 281
           K++
Sbjct: 558 KLR 560


>gi|224372659|ref|YP_002607031.1| RNA polymerase sigma factor RpoD [Nautilia profundicola AmH]
 gi|223588464|gb|ACM92200.1| rna polymerase sigma factor [Nautilia profundicola AmH]
          Length = 604

 Score = 89.7 bits (221), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 67/239 (28%), Positives = 119/239 (49%), Gaps = 19/239 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++  ++LRLVV IA  Y   GLP  +++ EGNIGLM+A+ KF+ E+G++ +TY+ WW
Sbjct: 365 AKEKMARANLRLVVSIAKKYTNRGLPFLDLIQEGNIGLMKAIDKFEFEKGYKFSTYATWW 424

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      V+I        +  N+ ++   ++       K   +  IAK++ +
Sbjct: 425 IRQAISRAIADQARTVRIPI-----HMIENINQINKIVRKYVQEEGKEPSLEVIAKEMKM 479

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL---VYDHDGQEQVLIEKEERKNRR 225
              +V  +        SL A +   +    ++ D++    + +  +E V       ++ R
Sbjct: 480 PIEKVKQILKISKEPVSLEAPVGEEE--DGKFGDFIEDKTFTNPYEEVV------NEDLR 531

Query: 226 NMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             +   +  LN RER + + R      ++  TLE +     V+RERVRQIE+ A KK++
Sbjct: 532 KHIEEILEQLNERERAVIKMRFGLMPDKSERTLEEIGKALNVTRERVRQIESSAIKKLR 590


>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 = 89.7 bits (221), Expect = 4e-16,   Method: Compositional matrix adjust.
 Identities = 71/250 (28%), Positives = 119/250 (47%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 380 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 439

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 440 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPNPEELAMRMGMPED 497

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D    +  +   
Sbjct: 498 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLALPADAAT 541

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ RN     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 542 SESLRNATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 601

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 602 KLRHPSRSEV 611


>gi|227113748|ref|ZP_03827404.1| RNA polymerase sigma factor RpoD [Pectobacterium carotovorum subsp.
           brasiliensis PBR1692]
          Length = 611

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 127/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 373 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 432

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 433 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 490

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 491 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 533

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 534 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 593

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 594 RKLRHPSRSEV 604


>gi|27904560|ref|NP_777686.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. Bp
           (Baizongia pistaciae)]
 gi|31340403|sp|Q89B10|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 = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 72/248 (29%), Positives = 119/248 (47%), Gaps = 40/248 (16%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 371 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 430

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL----------QAITDNNLKPE- 157
           I+ A+   I      ++I    +       L R+   +          + +++  L PE 
Sbjct: 431 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQILQEIGREPTPEELSERMLIPED 488

Query: 158 ---QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
              +V+ IAK       E ISM   +  D+             S   D+L    D   ++
Sbjct: 489 KIRKVLKIAK-------EPISMETPIGEDD------------DSHLGDFL---EDTNIEL 526

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQI 272
            ++     + R+     +S L  RE ++   R  +  N   TLE +  +F+V+RER+RQI
Sbjct: 527 PLDSATSASLRSATKNVLSGLTTREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQI 586

Query: 273 EARAFKKV 280
           EA+A +K+
Sbjct: 587 EAKALRKL 594


>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 = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 66/242 (27%), Positives = 125/242 (51%), Gaps = 12/242 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   +A+++ +
Sbjct: 438 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPSPEE---LAERMLM 492

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ R+  
Sbjct: 493 PEDKIRKV-LKIAK-EPISMETPVGDDDDSHLGDFI---EDTTLELPLDSATSESLRSAT 547

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K++   + 
Sbjct: 548 HDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 607

Query: 287 QV 288
           +V
Sbjct: 608 EV 609


>gi|225163701|ref|ZP_03726004.1| RNA polymerase, sigma 70 subunit, RpoD family [Opitutaceae
           bacterium TAV2]
 gi|224801692|gb|EEG19985.1| RNA polymerase, sigma 70 subunit, RpoD family [Opitutaceae
           bacterium TAV2]
          Length = 631

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 74/245 (30%), Positives = 116/245 (47%), Gaps = 34/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+  RG++ +TY+ WW
Sbjct: 332 AKTEMVEANLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWW 391

Query: 109 IKAAMQEYILRSWSLVKIGT----TAN-----QKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N     QK+L           +   + NL  E+V
Sbjct: 392 IRQAITRSIADQARTIRIPVHMIETLNKVMQVQKQLLQEFGHEPTPEEVADEMNLPVERV 451

Query: 160 VAIAKKLNVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
             I K       + IS+   +    D S    I   DK++    D   Y       +L E
Sbjct: 452 QQIMKMAQ----QPISLQSPVGDGDDTSFGDFIE--DKSAENPYDMTAYS------LLRE 499

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEAR 275
           K         +   +  L  RER++   R   +     TLE +  +F+V+RER+RQIEA+
Sbjct: 500 K---------IIDVLDSLTERERKVLSLRFGLVDGYSRTLEEVGKQFKVTRERIRQIEAK 550

Query: 276 AFKKV 280
           A +K+
Sbjct: 551 ALRKM 555


>gi|302537866|ref|ZP_07290208.1| RNA polymerase sigma factor RpoS [Streptomyces sp. C]
 gi|302446761|gb|EFL18577.1| RNA polymerase sigma factor RpoS [Streptomyces sp. C]
          Length = 481

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 79/313 (25%), Positives = 147/313 (46%), Gaps = 42/313 (13%)

Query: 7   SIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------- 48
           +++V G     +  Y+  I K+P+L  ++E  LAKR  E G  S                
Sbjct: 174 TVMVAGATADPVKDYLKLIGKVPLLNAEQEVELAKRI-EAGLFSEYKLEEEEDHKPAFKR 232

Query: 49  -----------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
                      A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +
Sbjct: 233 ELEILVEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNVGLIRAVEKFDYTK 292

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           GF+ +TY+ WWI+ A+   +      ++I    +   +   L R++  +         PE
Sbjct: 293 GFKFSTYATWWIRQAITRAMADQSRTIRI--PVHMVEIINKLARVQRQMLQDLGREPTPE 350

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           +   + K+L+++  +VI +     G E ++      ++  S++ D +    D +  V  +
Sbjct: 351 E---LGKELDMTPEKVIEVQKY--GREPISLHTPLGEEGDSEFGDLI---EDSEAVVPAD 402

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEAR 275
                  +  L   +  L+ RE  +   R  L +  P TL+ +   + V+RER+RQIE++
Sbjct: 403 AVSFTFLQEQLQSILGTLSEREAGVVSMRYGLNDGQPKTLDEIGRVYGVTRERIRQIESK 462

Query: 276 AFKKVQESIQKQV 288
              K++   + QV
Sbjct: 463 TMSKLRHPSRSQV 475


>gi|297827203|ref|XP_002881484.1| RNA polymerase sigma-70 factor [Arabidopsis lyrata subsp. lyrata]
 gi|297327323|gb|EFH57743.1| RNA polymerase sigma-70 factor [Arabidopsis lyrata subsp. lyrata]
          Length = 546

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 75/256 (29%), Positives = 128/256 (50%), Gaps = 38/256 (14%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           H   S+  +L+T++LRLVV IA  Y+  GL   +++ EG++GLM++V+KF P+ G R AT
Sbjct: 301 HRGRSSREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFAT 360

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI+ ++++ I ++   +         RL  N+  L G               V+ A
Sbjct: 361 YAYWWIRQSIRKSIFQNSRTI---------RLPENVYMLLGK--------------VSEA 397

Query: 164 KKLNVSESEVISMNCRLAG-----DESLNALI-NSSDKNSSQWQDWLVYDHDGQE----- 212
           +K  V E        +LAG      E L+ L+ N+    S Q   W   D   QE     
Sbjct: 398 RKTCVQEGNYRPSKEQLAGHVGVSTEKLDKLLYNTRTPLSMQQPIWSDQDTTFQEITPDS 457

Query: 213 --QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRER 268
             +       ++  RN +   ++VL+P+ERRI + R   +     +L  +   + +S+ER
Sbjct: 458 GIETPTMSVGKQMMRNHVRNLLNVLSPKERRIIKLRFGIDGGKQRSLSEIGEIYGLSKER 517

Query: 269 VRQIEARAFKKVQESI 284
           VRQ+E+RA  ++++ +
Sbjct: 518 VRQLESRALYRLKQHM 533


>gi|218442621|ref|YP_002380941.1| RNA polymerase, sigma 32 subunit, RpoH [Cyanothece sp. PCC 7424]
 gi|218174979|gb|ACK73711.1| RNA polymerase, sigma 32 subunit, RpoH [Cyanothece sp. PCC 7424]
          Length = 308

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 68/238 (28%), Positives = 117/238 (49%), Gaps = 14/238 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A ++LV  +LRLV+ +A  Y G GL   +++ EGNIGL++A + F+P +G++ +TY+ WW
Sbjct: 83  AKNQLVQGNLRLVINLAKKYLGRGLSFEDLLQEGNIGLIRAAELFEPSKGYKFSTYAYWW 142

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   I  S   +++        +   L R+K     +     +   V  IA  L +
Sbjct: 143 IRQQIIRAINNSARTIRLPV-----HIIARLNRIKKTQHKLAAQLGRTPTVQEIATSLQM 197

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  E+           SL+ +++   + +   QD L+ D + Q   L    ER      +
Sbjct: 198 SAQEIEKYREVAQKTISLSTIVDEQGRET--LQD-LIADPNPQPDFL----ERVFSYEQI 250

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              M  L PR + I + R  +E   TLE + +  ++S+ERVRQI  +A  +++E   K
Sbjct: 251 LEKMETLPPRYQDILKKRIYEEQ--TLEAIGTSTKLSKERVRQIFQKALSRLREEFLK 306


>gi|254382161|ref|ZP_04997522.1| sigma factor [Streptomyces sp. Mg1]
 gi|194341067|gb|EDX22033.1| sigma factor [Streptomyces sp. Mg1]
          Length = 416

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 79/313 (25%), Positives = 147/313 (46%), Gaps = 42/313 (13%)

Query: 7   SIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------- 48
           +++V G     +  Y+  I K+P+L  ++E  LAKR  E G  S                
Sbjct: 109 TVMVAGATADPVKDYLKLIGKVPLLNAEQEVELAKRI-EAGLFSEYKLEEEEDHKATFKR 167

Query: 49  -----------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
                      A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +
Sbjct: 168 ELEILVEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNVGLIRAVEKFDYTK 227

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           GF+ +TY+ WWI+ A+   +      ++I    +   +   L R++  +         PE
Sbjct: 228 GFKFSTYATWWIRQAITRAMADQSRTIRI--PVHMVEIINKLARVQRQMLQDLGREPTPE 285

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           +   + K+L+++  +VI +     G E ++      ++  S++ D +    D +  V  +
Sbjct: 286 E---LGKELDMTPEKVIEVQK--YGREPISLHTPLGEEGDSEFGDLI---EDSEAVVPAD 337

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEAR 275
                  +  L   +  L+ RE  +   R  L +  P TL+ +   + V+RER+RQIE++
Sbjct: 338 AVSFTFLQEQLQSILGTLSEREAGVVSMRYGLNDGQPKTLDEIGRVYGVTRERIRQIESK 397

Query: 276 AFKKVQESIQKQV 288
              K++   + QV
Sbjct: 398 TMSKLRHPSRSQV 410


>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 = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 81/281 (28%), Positives = 141/281 (50%), Gaps = 27/281 (9%)

Query: 16  LSRYIHEIR-KIPMLEKQEEY--VLAKRYRE------HGDLSA---AHRLVTSHLRLVVK 63
           L+ Y+  IR  I  L+K EE   +   + RE       G+L A      +V ++LRLV+ 
Sbjct: 337 LANYVDNIRVNIANLQKLEETTGLTITQIREIGGRIADGELKARKAKKEMVEANLRLVIS 396

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      
Sbjct: 397 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 456

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           ++I    +       L R+             PE+   +A+K+ + E ++  +  ++A  
Sbjct: 457 IRI--PVHMIETINKLNRISRQCLQEMGREATPEE---LAEKMGMPEDKIRKV-LKIAK- 509

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM--SVLNPRERR 241
           E ++      D + S   D++    D   ++ ++    ++ R + T ++    L PRE +
Sbjct: 510 EPISMETPVGDDDDSHLGDFI---EDSSLELPLDSATAESLR-IATNAVLEEGLTPREAK 565

Query: 242 IFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
           +   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 566 VLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 606


>gi|326332703|ref|ZP_08198965.1| RNA polymerase sigma (70) factor RpoD [Nocardioidaceae bacterium
           Broad-1]
 gi|325949484|gb|EGD41562.1| RNA polymerase sigma (70) factor RpoD [Nocardioidaceae bacterium
           Broad-1]
          Length = 530

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 79/328 (24%), Positives = 147/328 (44%), Gaps = 62/328 (18%)

Query: 2   NRKNMSIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYR----------EHGDLS- 48
           +    +++V G     +  Y+ +I K+P+L  + E  LAKR            + G ++ 
Sbjct: 218 DEPEQTVMVAGATADPVKDYLKQIGKVPLLNAEMEVELAKRIEAGLFAEEKLGKGGKITP 277

Query: 49  ---------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
                          A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KF
Sbjct: 278 KMLDELEWIAEDGKRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 337

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKG 144
           D  +G++ +TY+ WWI+ A+   +      ++I              Q+++  +L R   
Sbjct: 338 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPT 397

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQD 202
             +   + ++ PE+V+ + K       E IS++  L   GD     LI  S+        
Sbjct: 398 PEELAKELDMTPEKVIEVQK----YGREPISLHTPLGEDGDSEFGDLIEDSEA------- 446

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSS 260
             +   D     L++++        L   +  L+ RE  +   R       P TL+ +  
Sbjct: 447 --IVPADAVSFTLLQEQ--------LHAVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGK 496

Query: 261 EFEVSRERVRQIEARAFKKVQESIQKQV 288
            + V+RER+RQIE++   K++   + QV
Sbjct: 497 VYGVTRERIRQIESKTMSKLRHPSRSQV 524


>gi|312282671|dbj|BAJ34201.1| unnamed protein product [Thellungiella halophila]
          Length = 547

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 73/255 (28%), Positives = 130/255 (50%), Gaps = 36/255 (14%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           H   S+  +L+T++LRLVV IA  Y+  GL   +++ EG++GLM++V+KF P+ G R AT
Sbjct: 302 HRGRSSREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFAT 361

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ-----AITDNNLKPEQ 158
           Y+ WWI+ ++++ I ++   +         RL  N+  L G +       I D N +P +
Sbjct: 362 YAYWWIRQSIRKSIFQNSRTI---------RLPENVYMLLGKVSEARKTCIQDGNYRPSK 412

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL--- 215
              +A  + VS  ++  +            L N+    S Q   W   D   QE      
Sbjct: 413 -EQLASHVGVSTEKLDKL------------LYNTRTPLSMQQPIWSDQDTTFQEVTPDSG 459

Query: 216 IEKEE----RKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERV 269
           IE       ++  RN +   ++VL+P+E+RI + R   +     +L  +   + +S+ERV
Sbjct: 460 IETPSMSVGKQLMRNHVRNLLNVLSPKEKRIIKLRFGIDGGKQRSLSEIGEIYGLSKERV 519

Query: 270 RQIEARAFKKVQESI 284
           RQ+E+RA  ++++++
Sbjct: 520 RQLESRALYRLKQNM 534


>gi|302557983|ref|ZP_07310325.1| RNA polymerase sigma (70) factor RpoD [Streptomyces griseoflavus
           Tu4000]
 gi|302475601|gb|EFL38694.1| RNA polymerase sigma (70) factor RpoD [Streptomyces griseoflavus
           Tu4000]
          Length = 509

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 139/310 (44%), Gaps = 62/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ +I K+P+L  ++E  LAKR  E G  +                           A +
Sbjct: 216 YLKQIGKVPLLNAEQEVELAKRI-EAGLFAEDKLANSDKLAPKLKRELEIIAEDGRRAKN 274

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI  
Sbjct: 275 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWICQ 334

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+V+ +
Sbjct: 335 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEV 394

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 395 QKYGR----EPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 440

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 441 -------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 493

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 494 KLRHPSRSQV 503


>gi|184201082|ref|YP_001855289.1| RNA polymerase sigma factor SigA [Kocuria rhizophila DC2201]
 gi|183581312|dbj|BAG29783.1| RNA polymerase sigma factor SigA [Kocuria rhizophila DC2201]
          Length = 572

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 83/323 (25%), Positives = 145/323 (44%), Gaps = 63/323 (19%)

Query: 8   IIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKR-----YREH--GDLS---------- 48
           ++V G     +  Y+ +I K+ +L  ++E  LA R     Y EH   D +          
Sbjct: 265 VVVAGATADPVKDYLKQIGKVALLNAEQEVDLALRIEAGLYAEHKFADEADSMDANTRRA 324

Query: 49  ----------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
                     A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G
Sbjct: 325 YRWVIHDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKG 384

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAI 149
           F+ +TY+ WWI+ A+   +      ++I              Q+++  +L R     +  
Sbjct: 385 FKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELA 444

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYD 207
            + ++ PE+VV + K       E IS++  L   GD     LI  S+          V  
Sbjct: 445 NELDMTPEKVVEVQKYGR----EPISLHTPLGEDGDSEFGDLIEDSE---------AVVP 491

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVS 265
            D     L++++        L   +  L+ RE  +   R       P TL+ +   + V+
Sbjct: 492 ADAVSFTLLQEQ--------LHSVLDTLSEREAGVVAMRFGLTDGQPKTLDEIGKVYGVT 543

Query: 266 RERVRQIEARAFKKVQESIQKQV 288
           RER+RQIE++   K++   + QV
Sbjct: 544 RERIRQIESKTMSKLRHPSRSQV 566


>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 = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 78/250 (31%), Positives = 119/250 (47%), Gaps = 42/250 (16%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 393 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 452

Query: 109 IKAAMQEYILRSWSLVKIGT----TAN-----QKRLFFNLRR------LKGHLQAITDNN 153
           I+ A+   I      ++I      T N     Q+++   + R      L   L+   D  
Sbjct: 453 IRQAITRSIADQARTIRIPVHMIETINKINRVQRQMLQEMGREPTPEELGVRLEMPED-- 510

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQ 211
            K  +V+ IAK       E ISM   +  DE  SL   I   +  S           D  
Sbjct: 511 -KVRKVLKIAK-------EPISMETPIGDDEDSSLGDFIEDGNMESPV---------DSA 553

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
             + +E+  R    N+  R   VL  R    F      ++  TLE +  +F+V+RER+RQ
Sbjct: 554 TSLGLEEATRDVLANLTAREAKVLRMR----FGIDMNTDH--TLEEVGKQFDVTRERIRQ 607

Query: 272 IEARAFKKVQ 281
           IEA+A +K++
Sbjct: 608 IEAKALRKLR 617


>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 = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 116/234 (49%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   G+   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 439 AKREMIEANLRLVISIAKKYVNRGMQFLDLIQEGNIGLMKAVDKFEYRRGWKFSTYATWW 498

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           ++ A+   +      +++    +       L R+   +   T     P     +AK++ +
Sbjct: 499 VRQAVTRALADQARTIRV--PVHMIETINKLNRISREILQQTGQEAHP---AVLAKRMEM 553

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SE +V S+        SL   +   D   +   D +    D       E     N R  +
Sbjct: 554 SEEKVRSILKIAKQPVSLETPVG--DDADATLGDMI---EDVSASSPAEAAIHANMRAAI 608

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
             +++ L+PRE ++   R  L  N   TLE +  +F+V+RER+RQIE++A +K+
Sbjct: 609 DEALNGLSPREAKVLRMRFGLDTNSDHTLEEVGKQFDVTRERIRQIESKAMRKL 662


>gi|307152083|ref|YP_003887467.1| RpoD subfamily RNA polymerase sigma-70 factor [Cyanothece sp. PCC
           7822]
 gi|306982311|gb|ADN14192.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7822]
          Length = 418

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 62/236 (26%), Positives = 122/236 (51%), Gaps = 13/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV KFDP +G+R +TY+ WW
Sbjct: 179 AKEQMIKANLRLVVSVAKRYQNRGLELLDLIQEGTLGLERAVDKFDPTKGYRFSTYAYWW 238

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   I     ++++     +K     L ++K   + I         +  ++++L +
Sbjct: 239 IRQGITRAIATQSRIIRLPVHITEK-----LNKIKKAQRKIAQLKGATPSIEELSQELEM 293

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  ++  +  R+    SL   I    +  ++  D L       E  +  +  R++  N+L
Sbjct: 294 SPPQIREVLMRVPRSVSLE--IKVGKEKDTELIDLLETTEASPEDNIANEALRQDLHNLL 351

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
               + L  RER + + R   ++    +L ++    ++SRERVRQIEA+A +K+++
Sbjct: 352 ----ADLTTREREVIQLRYGFKDGKSYSLADIGRTLQLSRERVRQIEAKAIQKLRQ 403


>gi|198284078|ref|YP_002220399.1| RNA polymerase sigma-32 subunit RpoH [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218665176|ref|YP_002426733.1| RNA polymerase sigm-70 factor family [Acidithiobacillus
           ferrooxidans ATCC 23270]
 gi|198248599|gb|ACH84192.1| RNA polymerase, sigma 32 subunit, RpoH [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218517389|gb|ACK77975.1| RNA polymerase sigm-70 factor family [Acidithiobacillus
           ferrooxidans ATCC 23270]
          Length = 285

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 72/282 (25%), Positives = 132/282 (46%), Gaps = 37/282 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           LS ++ +    P L +++E  L +R R  GD  A   L+++H+ LV  +A GYR  GL  
Sbjct: 25  LSDFVDDENGGPFLSQKQELQLIRRLR-RGDECARATLISAHMPLVRAVARGYRNKGLSQ 83

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EG +GL++AV +F    G R ++Y+ WWI+ AMQ  ++RS  +      A     
Sbjct: 84  EDLLQEGYMGLLRAVDRFQEGLGTRFSSYATWWIREAMQRALIRSRFIRLPDYLAKSLHA 143

Query: 136 FFNLRRLKGHLQAITDNNLKPEQ-------VVAIAKKLNVSESEVISMNCRLAGD----E 184
           +     ++   +  +D  ++ EQ         +  + L+ ++  V S++  ++      E
Sbjct: 144 Y-----MQSGAEEDSDAGVRREQRREALGVRESTMRALDFADIRVFSLDEEISDGPGRIE 198

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
            +   + S D +         YD D   + L E     N +            RE  +F 
Sbjct: 199 QVTGDVASPDSD---------YDRDAICKALREHLTELNEKQ-----------REVMVFR 238

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                + P+TLE ++    VSRE VRQ++ RA  ++++S+ +
Sbjct: 239 YGMHGDAPMTLEAVAERMGVSREAVRQLQVRALTRLRQSLSE 280


>gi|323453176|gb|EGB09048.1| hypothetical protein AURANDRAFT_53467 [Aureococcus anophagefferens]
          Length = 468

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 72/245 (29%), Positives = 122/245 (49%), Gaps = 14/245 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L A   ++ ++LRLVV I+  Y+  GL   +V+ EG  GL +AV+KFDPE+GF+ +TY+ 
Sbjct: 211 LKAKAAMINANLRLVVSISKRYQHRGLHFQDVIQEGTFGLTRAVEKFDPEKGFKFSTYAT 270

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA-----ITDNNLKPEQVVA 161
           WWIK A+   I      +++    + +    +++++   L A      TD  L  +  +A
Sbjct: 271 WWIKQAVMRAIADQSRTIRLPVHVHDQ--LQSMKKVTRDLGAELGRECTDEELAGKLDLA 328

Query: 162 IAKK--LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             K   L   E + +SM+  +      ++       N ++  D L  D         E +
Sbjct: 329 TTKMDWLRSCERQTMSMDATVRVSGKGSSAGTGGAGNEAKLSDNLA-DAAALPDERAETK 387

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++  + L R  + L+ RE  +   R  L +    TLE + + F ++RERVRQIEARA 
Sbjct: 388 SLQSDIHGLLR--TALSDRECDVVRLRFGLDDGKARTLEEIGTVFSITRERVRQIEARAL 445

Query: 278 KKVQE 282
            K+++
Sbjct: 446 HKLRQ 450


>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 = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 70/250 (28%), Positives = 121/250 (48%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 438 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPED 495

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 496 KIRKVLKIAK-EPISMETPVGDDE------------DSHLGDFI---EDTTLELPLDSAT 539

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 540 SESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 600 KLRHPSRSEV 609


>gi|261250212|ref|ZP_05942788.1| RNA polymerase sigma factor RpoD [Vibrio orientalis CIP 102891]
 gi|260939328|gb|EEX95314.1| RNA polymerase sigma factor RpoD [Vibrio orientalis CIP 102891]
          Length = 618

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 117/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 380 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 439

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 440 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 497

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 498 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 541

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 542 AGSLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 601

Query: 279 KVQ 281
           K++
Sbjct: 602 KLR 604


>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 = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 117/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 382 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 441

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 442 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 499

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 500 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 543

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 544 AGSLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 603

Query: 279 KVQ 281
           K++
Sbjct: 604 KLR 606


>gi|282895663|ref|ZP_06303788.1| sigF (Sigma 28 (Flagella/Sporulation)) [Raphidiopsis brookii D9]
 gi|281199357|gb|EFA74222.1| sigF (Sigma 28 (Flagella/Sporulation)) [Raphidiopsis brookii D9]
          Length = 396

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 72/248 (29%), Positives = 121/248 (48%), Gaps = 37/248 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +++ S+LRLVV IA  Y   G+P  +++ EG +GL +A +KFDP++G++ +TY+ WW
Sbjct: 158 AKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAMGLNRATEKFDPDKGYKFSTYAYWW 217

Query: 109 IKAAMQEYILRSWSLVKIGTTANQK--RLFFNLRRLKGHLQAITDNNLKP------EQVV 160
           I+ A+   I      +++     +K  +L    R LK   Q    N  +       E  V
Sbjct: 218 IRQAITRAIANDARTIRLPIHIVEKLNKLKKAQRELK---QKFARNPTEAEMAEFLEMTV 274

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
              ++L     + +S+N R+  +E             ++  D L+ D D Q        E
Sbjct: 275 QQLRQLQQLRRQALSLNHRVGKEE------------DTELMD-LLEDEDNQ------SPE 315

Query: 221 RKNRRNMLTRSM-----SVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIE 273
            K   NM+ + +      VL  RE+ +   R       P TLE + + F +SRERVRQI+
Sbjct: 316 AKMNENMMRQEIWEVLGDVLTSREKDVISLRYGLTTSEPCTLEEVGNIFNLSRERVRQIQ 375

Query: 274 ARAFKKVQ 281
           ++A +K++
Sbjct: 376 SKAMRKLR 383


>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 = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 62/236 (26%), Positives = 119/236 (50%), Gaps = 16/236 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   G+   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 425 AKREMIEANLRLVISIAKKYVNRGMHFLDLIQEGNIGLMKAVDKFEYRRGWKFSTYATWW 484

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           ++ A+   I      +++     +      L R++  +   T     P     +A+++++
Sbjct: 485 VRQAITRAIADQARTIRVPVHMIES--INKLNRIQREIVQQTGQEPHPS---VLAERMDM 539

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRN 226
            E+++ S+  ++A + +      S D    +  D  + D   D       +     N R 
Sbjct: 540 PEAKIRSI-LKIAKNPA------SLDSPVGEDADTTLGDMIEDTSATSPADAAVHANMRR 592

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKV 280
            +  ++  L PRE ++   R   +    +TLE +  +F+V+RER+RQIE +A +K+
Sbjct: 593 AIDEALDALTPREAKVLRMRYGIDTASELTLEEVGRQFDVTRERIRQIEGKAIRKL 648


>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 = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 117/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 380 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 439

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 440 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 497

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 498 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 541

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 542 AGSLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 601

Query: 279 KVQ 281
           K++
Sbjct: 602 KLR 604


>gi|126695941|ref|YP_001090827.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9301]
 gi|126542984|gb|ABO17226.1| Putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus str. MIT 9301]
          Length = 307

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 81/296 (27%), Positives = 140/296 (47%), Gaps = 32/296 (10%)

Query: 12  GEIGLSRYIHEIRKIPMLEK-QEEYVLAKRYREHG------DLSAAHR------------ 52
           GEIG  + +   R++ M  K QE  VL  R +E G      + S A R            
Sbjct: 9   GEIGRHQLLTPERELTMGRKVQEMVVLVNRCQEAGGKGPACEYSEAERKKIKIGEKAKNE 68

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG R +TY+ WWI+  
Sbjct: 69  MITANLRLVVNLAKRYQGKGLELLDLIQEGTLGLTRAVEKYDPSRGHRFSTYAYWWIRQG 128

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +      ++I    N+K     LR  K  L  +      P     +A+++ +++ E
Sbjct: 129 LNRALSTQSRTIRIPVNINEK--LTKLRSAKSKLMQLKG---IPPSTDELAEEMKITKEE 183

Query: 173 VIS-MNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           +   ++C L     SL   + S   + S+  D L  D     ++    E   +   +L +
Sbjct: 184 IDELLSCELRSITVSLQGTVKSKS-DPSELVDILPSDQTPPMELAELAERTASAWKLLDK 242

Query: 231 SMSVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +   L  +ER+I   R   +      TL  ++     SRE  RQ+  RA +K++++
Sbjct: 243 AN--LTEKERKIVSLRFGLDGSNEWRTLAEVARHMSCSREYCRQVVQRALRKLRKA 296


>gi|323142246|ref|ZP_08077080.1| RNA polymerase sigma factor RpoD [Phascolarctobacterium sp. YIT
           12067]
 gi|322413309|gb|EFY04194.1| RNA polymerase sigma factor RpoD [Phascolarctobacterium sp. YIT
           12067]
          Length = 546

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 80/251 (31%), Positives = 125/251 (49%), Gaps = 21/251 (8%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L K     GD  A   L  ++LRLVV IA  Y G G+   +++ EGN+GL++AV KFD  
Sbjct: 298 LLKAVAHQGD-EAKQCLSEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVDKFDYN 356

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDN 152
           +GF+ +TY+ WWI+ A+   I      ++I      T N  +L    R+L   LQ +   
Sbjct: 357 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETIN--KLIRVSRQL---LQELGRE 411

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
            L PE+   IAK+++ S   V  +  ++A  E ++      ++  S   D++    D   
Sbjct: 412 PL-PEE---IAKEMDTSVDRVREI-MKIA-QEPVSLETPIGEEEDSHLGDFI---EDHDA 462

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVR 270
               +       R  L   +  L  RE+R+ E R   E+    TLE +   F V+RER+R
Sbjct: 463 PAPADAASFTLLREQLEEVLETLTIREKRVLELRFGLEDGRSRTLEEVGQHFGVTRERIR 522

Query: 271 QIEARAFKKVQ 281
           QIEA+A +K++
Sbjct: 523 QIEAKALRKLR 533


>gi|117924113|ref|YP_864730.1| RpoD family RNA polymerase sigma factor [Magnetococcus sp. MC-1]
 gi|117607869|gb|ABK43324.1| RNA polymerase, sigma 70 subunit, RpoD [Magnetococcus sp. MC-1]
          Length = 683

 Score = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 69/238 (28%), Positives = 119/238 (50%), Gaps = 18/238 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 445 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEWRRGYKFSTYATWW 504

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R    +         PE+   IA+++++
Sbjct: 505 IRQAITRSIADQARTIRI--PVHMIETINKLVRTSRQMVQEMGREPTPEE---IAERMSM 559

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER---KNRR 225
           S  +V  +  ++A  E ++      D+  S   D++      +++ ++   E     N R
Sbjct: 560 SLEKVRKV-LKIA-KEPISLETPVGDEEDSHLGDFI------EDKSMLSPSEHAIMSNLR 611

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   R +  L  RE  +   R     P   TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 612 DTTGRVLQTLTSREEHVLRMRFGIGLPTDHTLEEVGKQFNVTRERIRQIEAKALRKLR 669


>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 = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 77/258 (29%), Positives = 122/258 (47%), Gaps = 34/258 (13%)

Query: 37  LAKRYREHGD---LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           L K YR  GD     A  +++ ++LRLV+ IA  Y   GL   +++ EGN+GLM+AV KF
Sbjct: 352 LNKMYR-RGDRRAKKAKSQMIEANLRLVISIAKKYANRGLQFLDLIQEGNVGLMKAVDKF 410

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKG 144
           +  RG++ +TY+ WWI+ A+   I      ++I      T N+     ++L     R   
Sbjct: 411 EYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRVRRQLLQKFGREAS 470

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             +  T+  L PE  +    K      E +SM   +  DE  N      D N S      
Sbjct: 471 SEELATEMEL-PEYKIIKILK---IAKEPLSMETPVGDDEDSNIGDFIEDTNLSSP---- 522

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEF 262
                      +E   +++ R      +S L+PRE ++ + R         TLE +  +F
Sbjct: 523 -----------VEITTKESLRETTGDLLSNLSPREAKVLKMRFGINMNTDHTLEEVGRQF 571

Query: 263 EVSRERVRQIEARAFKKV 280
           +V+RER+RQIEA+A +K+
Sbjct: 572 DVTRERIRQIEAKALRKL 589


>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 = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 78/250 (31%), Positives = 119/250 (47%), Gaps = 42/250 (16%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 393 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 452

Query: 109 IKAAMQEYILRSWSLVKIGT----TAN-----QKRLFFNLRR------LKGHLQAITDNN 153
           I+ A+   I      ++I      T N     Q+++   + R      L   L+   D  
Sbjct: 453 IRQAITRSIADQARTIRIPVHMIETINKINRVQRQMLQEMGREPTPEELGVRLEMPED-- 510

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQ 211
            K  +V+ IAK       E ISM   +  DE  SL   I   +  S           D  
Sbjct: 511 -KVRKVLKIAK-------EPISMETPIGDDEDSSLGDFIEDGNMESPV---------DSA 553

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
             + +E+  R    N+  R   VL  R    F      ++  TLE +  +F+V+RER+RQ
Sbjct: 554 TSLGLEEATRDVLANLTAREAKVLRMR----FGIDMNTDH--TLEEVGKQFDVTRERIRQ 607

Query: 272 IEARAFKKVQ 281
           IEA+A +K++
Sbjct: 608 IEAKALRKLR 617


>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 = 89.7 bits (221), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 119/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 382 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 441

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   + +++++
Sbjct: 442 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEE---LGERMDM 496

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D   S   D++    D   Q  IE    ++ +   
Sbjct: 497 PEDKIRKV-LKIA-KEPISMETPIGDDEDSHLGDFI---EDSTMQSPIEVATVESLKEAT 551

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 552 REVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 606


>gi|330970856|gb|EGH70922.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. aceris
           str. M302273PT]
          Length = 616

 Score = 89.4 bits (220), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 71/244 (29%), Positives = 116/244 (47%), Gaps = 30/244 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 438 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPED 495

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   Q  I+   
Sbjct: 496 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDSTMQSPIDVAT 539

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAF 277
            ++ +      +S L  RE ++   R    +  N  TLE +  +F+V+RER+RQIEA+A 
Sbjct: 540 VESLKEATREVLSGLTAREAKVLRMRFGIDMNTNH-TLEEVGKQFDVTRERIRQIEAKAL 598

Query: 278 KKVQ 281
           +K++
Sbjct: 599 RKLR 602


>gi|220912379|ref|YP_002487688.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Arthrobacter
           chlorophenolicus A6]
 gi|219859257|gb|ACL39599.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Arthrobacter
           chlorophenolicus A6]
          Length = 433

 Score = 89.4 bits (220), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 72/275 (26%), Positives = 130/275 (47%), Gaps = 40/275 (14%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P  +++ E+++      H    A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL
Sbjct: 180 PKYKRELEFII------HDGKRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGL 233

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT---------TANQKRLFF 137
           ++AV+KFD  +GF+ +TY+ WWI+ A+   +      ++I              Q+++  
Sbjct: 234 IRAVEKFDYTKGFKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQ 293

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDK 195
           +L R     +   + ++ PE+VV + K       E IS++  L   GD     LI  S+ 
Sbjct: 294 DLGREPTPEELALELDMTPEKVVEVQK----YGREPISLHTPLGEDGDSEFGDLIEDSEA 349

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPV 253
                    V   D     L++++        L   +  L+ RE  +   R       P 
Sbjct: 350 ---------VVPADAVSFTLLQEQ--------LHSVLDTLSEREAGVVAMRFGLTDGQPK 392

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           TL+ +   + V+RER+RQIE++   K++   + QV
Sbjct: 393 TLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQV 427


>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 = 89.4 bits (220), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 65/235 (27%), Positives = 117/235 (49%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 376 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 435

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   + +++++
Sbjct: 436 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEE---LGERMDM 490

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D   S   D++    D Q    ++    +  R   
Sbjct: 491 PEDKIRKV-LKIA-KEPISMETPIGDDEDSHLGDFI---EDIQALSPVDSATAEGLREAT 545

Query: 229 TRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              ++ L  RE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 546 RSVLAGLTARESKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|297569039|ref|YP_003690383.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfurivibrio
           alkaliphilus AHT2]
 gi|296924954|gb|ADH85764.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfurivibrio
           alkaliphilus AHT2]
          Length = 445

 Score = 89.4 bits (220), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 33/251 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLVV IA  Y   GL +++++ EGN+GLM+AV +FD  +G + +TY+ WW
Sbjct: 209 AKDAMIKANLRLVVSIAKRYMHQGLTLADLIQEGNLGLMRAVFRFDYTKGNKFSTYASWW 268

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKR-----LFFNLRRLKGHLQAITD----NNLKPEQV 159
           I+ A+   IL     +++     + R      F++L +  G      +      L  E++
Sbjct: 269 IRQAITRAILDKTRTIRLPVHFLELRSQFFKAFYSLLKELGREPTPAEISEKTGLPMEKI 328

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           +AI +    +  E IS+   +  D+             S   D+L    + QE V   + 
Sbjct: 329 LAIFE----ASREPISLETPVGDDD-------------STLGDFL----ENQESVSPYEA 367

Query: 220 ERKNR-RNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARA 276
            + N+    +T  +S L+PRE +I   R    ++   TLE +   F VSRER+RQIE +A
Sbjct: 368 VKGNQLAERVTTILSTLSPREEKIIRLRFGIGEDAEYTLEEIGKRFNVSRERIRQIEKKA 427

Query: 277 FKKVQESIQKQ 287
             +++ S +++
Sbjct: 428 LNRLRHSSRRE 438


>gi|229828460|ref|ZP_04454529.1| hypothetical protein GCWU000342_00522 [Shuttleworthia satelles DSM
           14600]
 gi|229793054|gb|EEP29168.1| hypothetical protein GCWU000342_00522 [Shuttleworthia satelles DSM
           14600]
          Length = 614

 Score = 89.4 bits (220), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 87/314 (27%), Positives = 142/314 (45%), Gaps = 73/314 (23%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRY-------------REH---GDLS-------------- 48
           Y+ EI K+ +L  +EE  LA++              RE    GDLS              
Sbjct: 308 YLKEIGKVHLLTAEEEVDLAQKMEKGLKADEQIEILREEIRSGDLSEEDMMNLEAQIKIL 367

Query: 49  ---------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                    A  +L  ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G+
Sbjct: 368 KNDSAVGERAKQKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYTKGY 427

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAIT 150
           + +TY+ WWI+ A+   I      ++I      T N+     ++L   L R     +   
Sbjct: 428 KFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVSRQLLQELGREPSPEEIAR 487

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDH 208
           +    P++V  I   L +S+ E +S+   +  +E   L   I   D+N+    +   +  
Sbjct: 488 EMETTPDRVREI---LKISQ-EPVSLETPIGEEEDSHLGDFIQ--DENAPVPAEAATF-- 539

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSR 266
                 L+        +  L   +  L  RER++   R   E+    TLE +  EF V+R
Sbjct: 540 -----TLL--------KEQLNEVLDTLTERERKVLILRFGLEDGRGRTLEEVGKEFNVTR 586

Query: 267 ERVRQIEARAFKKV 280
           ER+RQIEA+A +K+
Sbjct: 587 ERIRQIEAKALRKL 600


>gi|262364690|gb|ACY61247.1| RNA polymerase sigma factor RpoD [Yersinia pestis D182038]
          Length = 352

 Score = 89.4 bits (220), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 73/250 (29%), Positives = 126/250 (50%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 114 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 173

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-KRLFFNLRRLKGH---LQAITDNNLKPEQVV 160
           I+ A+   I      ++I      T N+  R+   + +  G     + + +  L PE   
Sbjct: 174 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPED-- 231

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 232 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 275

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 276 SESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 335

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 336 KLRHPSRSEV 345


>gi|119473196|ref|ZP_01614893.1| RNA polymerase sigma factor rpoD (Sigma-70) [Alteromonadales
           bacterium TW-7]
 gi|119444560|gb|EAW25875.1| RNA polymerase sigma factor rpoD (Sigma-70) [Alteromonadales
           bacterium TW-7]
          Length = 614

 Score = 89.4 bits (220), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 71/244 (29%), Positives = 122/244 (50%), Gaps = 30/244 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R + + + + +  + PE  
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPNPEELAERMMMPED- 492

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D      I+  
Sbjct: 493 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTIDSPIDSA 535

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 536 TMESLRGATNDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 595

Query: 278 KKVQ 281
           +K++
Sbjct: 596 RKLR 599


>gi|91227014|ref|ZP_01261551.1| RpoS-like sigma factor [Vibrio alginolyticus 12G01]
 gi|91188816|gb|EAS75102.1| RpoS-like sigma factor [Vibrio alginolyticus 12G01]
 gi|210148643|gb|ACJ09227.1| RpoS-like sigma factor [Vibrio alginolyticus]
          Length = 279

 Score = 89.4 bits (220), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 47/118 (39%), Positives = 74/118 (62%), Gaps = 4/118 (3%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY--- 68
           G+   + Y+ +I  I +L ++EE   AK  R  GD  A   L+ S+LRLVVKIA GY   
Sbjct: 8   GKDPYAHYLKDIVGIDLLSREEELHYAKLNRA-GDEEAREMLIESNLRLVVKIAKGYLKR 66

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            G    + +++ EGNIGL++AV KFDPE G+R +TY++WWI+  ++  ++ +   V++
Sbjct: 67  PGNNFTLLDLIEEGNIGLIKAVDKFDPEPGYRFSTYAVWWIRENIEAALMNNGRTVRL 124


>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 = 89.4 bits (220), Expect = 5e-16,   Method: Compositional matrix adjust.
 Identities = 67/235 (28%), Positives = 119/235 (50%), Gaps = 15/235 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 376 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 435

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+             PE+   +A+++ +
Sbjct: 436 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQCLQEMGREATPEE---LAERMGM 490

Query: 169 SESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
            E ++  +  ++A +  S+   I   D   S   D++    D   ++ ++    ++ R  
Sbjct: 491 PEDKIRKV-LKIAKEPISMETPIGDDD---SHLGDFI---QDENLELPLDSATAESLRLA 543

Query: 228 LTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
               +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 544 TNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 598


>gi|72383848|ref|YP_293202.1| sigma-70 region 1.2 [Ralstonia eutropha JMP134]
 gi|72123191|gb|AAZ65345.1| Sigma-70 region 1.2 [Ralstonia eutropha JMP134]
          Length = 624

 Score = 89.4 bits (220), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 64/234 (27%), Positives = 116/234 (49%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLV+ IA  Y   G+   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 386 AKRELIEANLRLVISIAKKYVNRGMHFLDLIQEGNIGLMKAVDKFEYRRGWKFSTYATWW 445

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           ++ A+   +      +++    +   +   L R+    +  T     P     +A+++ +
Sbjct: 446 VRQAVTRALADQARTIRV--PVHMVEMINKLNRISRDFRQQTGREAHP---AVLAERMEM 500

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SE +V S+        SL   +   D   +   D +    D       E     + R  +
Sbjct: 501 SEEKVRSILRSARQPVSLETPVG--DDADATLGDMI---EDVSASSPAEAAIHADMRAAI 555

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKV 280
             ++  L+PRE ++   R   +     TLE +S +F+V+RER+RQIE++A +K+
Sbjct: 556 DEALDGLSPREAKVLRMRFGLDTTSDRTLEEVSKQFDVTRERIRQIESQAMRKL 609


>gi|162455526|ref|YP_001617893.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
 gi|161166108|emb|CAN97413.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
          Length = 715

 Score = 89.4 bits (220), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 69/242 (28%), Positives = 124/242 (51%), Gaps = 17/242 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +R V ++LRLVV IA  Y    LP+ +++ EGNIGLM+AV++FD  RG+R +TY+ WW
Sbjct: 484 AKNRFVKANLRLVVSIARRYNRGRLPLIDLIQEGNIGLMKAVERFDHSRGYRFSTYASWW 543

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   +      V+I        +     R+    QAI         +  + K+  V
Sbjct: 544 IRHAISRALADKGRAVRIPV-----HMLDTYNRVARATQAIIARTGHEPTIEELEKETGV 598

Query: 169 SESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR-- 225
              ++  +    A    SL+  +   D++  ++ D+L      +E  L   +   NR+  
Sbjct: 599 PREKLDKVKDFYAETPFSLDRPVG--DEDGRKFIDFLQ-----EENALSPFDHLANRKWS 651

Query: 226 NMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           + + R ++ L P E RI   R     E+ +TL+ +  ++ +SRER+RQ++ +A  K+++ 
Sbjct: 652 DEVRRLLTTLTPIESRIIRWRFGLDDEDELTLKEIGDKYNLSRERIRQLQEQALGKIRKQ 711

Query: 284 IQ 285
           ++
Sbjct: 712 MR 713


>gi|302338308|ref|YP_003803514.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           smaragdinae DSM 11293]
 gi|301635493|gb|ADK80920.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           smaragdinae DSM 11293]
          Length = 281

 Score = 89.4 bits (220), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 69/247 (27%), Positives = 125/247 (50%), Gaps = 28/247 (11%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD +A HRL+ ++LRLVVKIA  Y   G  + +++ EGN+GL++A +K+D  +  R +TY
Sbjct: 42  GDEAARHRLIEANLRLVVKIAKSYVTPGFGLLDLIQEGNMGLIRAAEKYDHRKQVRFSTY 101

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + WWI+ ++   I +    +++    N      +R ++ L +   H  +  +  ++    
Sbjct: 102 AAWWIRQSIVRAIAKKQKAIRLPHRKNNLLKKIQRTYYQLSQELEHEPSAEEIAVEIGIE 161

Query: 160 VAIAKKLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
            +I  ++    + V+S++C +  D S  L+ L +S+            Y+    E+V I 
Sbjct: 162 PSIVDQMLQVGNPVVSLDCEIGDDASTLLDMLEDST------------YE---PERVCIN 206

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEAR 275
           K  +++  + L      L  RER+I   R         TL+ +  E  +S E VRQIE R
Sbjct: 207 KSMQEDTMHFLDH----LKERERQILLYRFAFFGGKKYTLKKIGMEMGISPETVRQIEMR 262

Query: 276 AFKKVQE 282
           A +K+++
Sbjct: 263 AIRKLRD 269


>gi|327398426|ref|YP_004339295.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Hippea maritima
           DSM 10411]
 gi|327181055|gb|AEA33236.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Hippea maritima
           DSM 10411]
          Length = 491

 Score = 89.4 bits (220), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 65/233 (27%), Positives = 118/233 (50%), Gaps = 12/233 (5%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            R++ ++LRLVV IA  +   GL   +++ EGNIGLM++V KFD ++GF+ +TY+ WWI+
Sbjct: 256 QRMIKANLRLVVSIAKKHLNRGLSFLDLIQEGNIGLMKSVDKFDYKKGFKFSTYATWWIR 315

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            ++   I      ++I        +   + ++    + +   N K      +A+ L + E
Sbjct: 316 QSISRAIADQARTIRIPV-----HMIETINKIVRASKLLIQENGKEPTAQELAEYLGMDE 370

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            ++ S+        SL   I   D N +  +D++    D + +  ++   + N +  +  
Sbjct: 371 EKIKSIIKIAKEPISLETPI--GDDNDTHLEDFI---EDTKSESPLDYVIKSNLKEKVEE 425

Query: 231 SMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +S L  RER++   R    +    TLE +     V+RERVRQIEA+A +K++
Sbjct: 426 VLSTLTDRERKVLMMRYGIGDGFDHTLEEVGKVLGVTRERVRQIEAKALRKLR 478


>gi|288919497|ref|ZP_06413828.1| RNA polymerase, sigma 32 subunit, RpoH [Frankia sp. EUN1f]
 gi|288349100|gb|EFC83346.1| RNA polymerase, sigma 32 subunit, RpoH [Frankia sp. EUN1f]
          Length = 936

 Score = 89.4 bits (220), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 66/236 (27%), Positives = 118/236 (50%), Gaps = 10/236 (4%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  + RLV  IA+ Y G GL + ++   G IGL++AV+KFD  +G++ +TYS WWI+ A
Sbjct: 478 LVLHNQRLVHSIALKYEGQGLELEDLSQHGMIGLLRAVQKFDATKGYKFSTYSTWWIRQA 537

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +     L+++     +K     +RR+ G L    D         A        E  
Sbjct: 538 ITRALADEGRLIRLPAHFVEK--VNKVRRVLGQLGMSVDGADVVTVAAAAGLSEQEVERC 595

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           +++++ R+ G ++   + +  D    +            + VL    +RK  R  + RS+
Sbjct: 596 LLALHQRVVGLDT--PVGDGGDTVLGELVGLPAPPDTDPDTVL----DRKWLRMAVARSL 649

Query: 233 SVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           + L+PR   +   R   ++  P TLE +   F V+RER+RQIE +A ++++E +++
Sbjct: 650 AELSPRNAEVVRLRFGFDDGEPRTLEQIGQVFGVTRERIRQIEKKALEQLREPLRQ 705


>gi|256375630|ref|YP_003099290.1| RNA polymerase sigma factor SigB [Actinosynnema mirum DSM 43827]
 gi|255919933|gb|ACU35444.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Actinosynnema
           mirum DSM 43827]
          Length = 330

 Score = 89.4 bits (220), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 71/249 (28%), Positives = 120/249 (48%), Gaps = 32/249 (12%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L A + L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++AV+KFD  +GF+ +TY+ 
Sbjct: 91  LRAKNHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAVEKFDYTKGFKFSTYAT 150

Query: 107 WWIKAAMQEYILRSWSLVK--------IGTTANQKR-LFFNLRRLKGHLQAITDNNLKPE 157
           WWI+ A+   +      ++        +   A  KR L   L R   + +   ++ L P 
Sbjct: 151 WWIRQAITRGMADQGRTIRLPVHLVEQVNKLARIKRDLHQQLGREATNEELAAESGLSPT 210

Query: 158 QVVAIAKKLNVSESEV-ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           +V  +   L+ +   V + M      D  L   I  SD   +             E  +I
Sbjct: 211 KVSDL---LDHARDPVSLDMPVGAEEDAPLGDFIEDSDATDA-------------ESAVI 254

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEA 274
               + + R    R ++ L  RE+ +   R   E+  P TL+ +  +F +SRERVRQIE 
Sbjct: 255 SGLLQDDLR----RVLATLEQREQAVIRLRYGLEDGQPRTLDQIGKQFGLSRERVRQIER 310

Query: 275 RAFKKVQES 283
               K+++ 
Sbjct: 311 EVMSKLRQG 319


>gi|218661227|ref|ZP_03517157.1| RNA polymerase factor sigma-32 [Rhizobium etli IE4771]
          Length = 62

 Score = 89.4 bits (220), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 42/62 (67%), Positives = 48/62 (77%)

Query: 1  MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
          M R  +  I  GE GL+RY+ EIRK PMLE Q+EY+LAKRY EHGD  AAH+LVTSHLRL
Sbjct: 1  MARNTLPSITAGEAGLNRYLDEIRKFPMLEPQQEYMLAKRYAEHGDRDAAHKLVTSHLRL 60

Query: 61 VV 62
          VV
Sbjct: 61 VV 62


>gi|170076992|ref|YP_001733630.1| group II sigma-70 type sigma factor [Synechococcus sp. PCC 7002]
 gi|1769590|gb|AAB95227.1| sigma factor [Synechococcus sp. PCC 7002]
 gi|169884661|gb|ACA98374.1| Group II sigma-70 type sigma factor (RpoD family) [Synechococcus
           sp. PCC 7002]
          Length = 365

 Score = 89.4 bits (220), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 66/234 (28%), Positives = 117/234 (50%), Gaps = 11/234 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +++ S+LRLVV IA  Y   G+P  +++ EG IGL +A +KFDP +G++ +TY+ WW
Sbjct: 127 AKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPNKGYKFSTYAYWW 186

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      +++     +K     L +LK   + +     +      +A++L++
Sbjct: 187 IRQAITRTIANDARTIRLPIHIVEK-----LNKLKKAQRTLKQTLQRNPTEAELAQELDI 241

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +  ++  +        SLN  +   +   ++  D L  + DG +       E   R+ + 
Sbjct: 242 TADQLHQLLQLRRQSLSLNHRVGKGE--DTELVDLL--EDDGLQLPEERMSEAMMRQELW 297

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                VL  RE+ +   R     E P TLE +   F +SRERVRQI+++A +K+
Sbjct: 298 DVLGDVLTDREKEVIALRYGLSSEQPHTLEEVGGMFNLSRERVRQIQSKAMRKL 351


>gi|153826548|ref|ZP_01979215.1| RNA polymerase sigma factor RpoD [Vibrio cholerae MZO-2]
 gi|149739640|gb|EDM53854.1| RNA polymerase sigma factor RpoD [Vibrio cholerae MZO-2]
          Length = 302

 Score = 89.4 bits (220), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 70/250 (28%), Positives = 120/250 (48%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 64  AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 123

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 124 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPLPEELAERMQMPED 181

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 182 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 225

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 226 ATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 285

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 286 KLRHPSRSEV 295


>gi|62181728|ref|YP_218145.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 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. A50]
          Length = 658

 Score = 89.4 bits (220), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 420 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 479

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 480 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 537

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 538 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 580

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 581 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 640

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 641 RKLRHPSRSEV 651


>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 = 89.4 bits (220), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 393 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 452

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 453 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 510

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 511 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 553

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 554 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 613

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 614 RKLRHPSRSEV 624


>gi|326629245|gb|EGE35588.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 9]
          Length = 660

 Score = 89.4 bits (220), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 422 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 481

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 482 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 539

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 540 -KIRKVLKIAK-EPISMEAPIGDDE------------DSHLGDFI---EDTTLELPLDSA 582

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 583 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 642

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 643 RKLRHPSRSEV 653


>gi|16761985|ref|NP_457602.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. CT18]
 gi|29143472|ref|NP_806814.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
 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 = 89.4 bits (220), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 422 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 481

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 482 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 539

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 540 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 582

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 583 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 642

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 643 RKLRHPSRSEV 653


>gi|6273430|emb|CAB60192.1| putative sigma-like transcription factor [Arabidopsis thaliana]
          Length = 487

 Score = 89.4 bits (220), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 76/256 (29%), Positives = 128/256 (50%), Gaps = 38/256 (14%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           H   S+  +L+T++LRLVV IA  Y+  GL   +++ EG++GLM++V+KF P+ G R AT
Sbjct: 242 HRGRSSREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFAT 301

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI+ ++++ I ++   +         RL  N+  L G               V+ A
Sbjct: 302 YAYWWIRQSIRKSIFQNSRTI---------RLPENVYMLLGK--------------VSEA 338

Query: 164 KKLNVSESEVISMNCRLAG-----DESLNALI-NSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           +K  V E         LAG      E L+ L+ N+    S Q   W   D   QE     
Sbjct: 339 RKTCVQEGNYRPSKEELAGHVGVSTEKLDKLLYNTRTPLSMQQPIWSDQDTTFQEITPDS 398

Query: 218 KEE-------RKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRER 268
             E       ++  RN +   ++VL+P+ERRI + R   +     +L  +   + +S+ER
Sbjct: 399 GIETPTMSVGKQLMRNHVRNLLNVLSPKERRIIKLRFGIDGGKQRSLSEIGEIYGLSKER 458

Query: 269 VRQIEARAFKKVQESI 284
           VRQ+E+RA  ++++++
Sbjct: 459 VRQLESRALYRLKQNM 474


>gi|51246355|ref|YP_066239.1| RNA polymerase sigma factor (RpoD) [Desulfotalea psychrophila
           LSv54]
 gi|50877392|emb|CAG37232.1| probable RNA polymerase sigma factor (RpoD) [Desulfotalea
           psychrophila LSv54]
          Length = 447

 Score = 89.4 bits (220), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 70/246 (28%), Positives = 120/246 (48%), Gaps = 31/246 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLVV IA  Y   GL +++++ EGN+GLM+AV +FD  +G + +TY+ WW
Sbjct: 211 AKDTMIRANLRLVVSIAKRYMHQGLTLADLIQEGNLGLMRAVFRFDYTKGNKFSTYASWW 270

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKR---------LFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   IL     +++     + R         LF  L R    L+     NL  +++
Sbjct: 271 IRQAITRAILDKTRTIRLPVHFLELRSQFFKAFYALFKELGREPTPLEISKTTNLPMDKI 330

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           ++I +    +  E IS+   +  D+             S   D+L    + + Q   E  
Sbjct: 331 LSILE----ASREPISLETPVGDDD-------------STLGDFL---ENQESQSPYEAV 370

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAF 277
           + +     +T  +S L+ RE +I   R    ++   TLE +   F VSRER+RQIE +A 
Sbjct: 371 QNRELSGRVTEILSTLSDREEKIIRLRFGIGEKAEYTLEEIGKRFNVSRERIRQIEKKAL 430

Query: 278 KKVQES 283
            +++ S
Sbjct: 431 NRLRHS 436


>gi|89094383|ref|ZP_01167323.1| RNA polymerase sigma factor [Oceanospirillum sp. MED92]
 gi|89081275|gb|EAR60507.1| RNA polymerase sigma factor [Oceanospirillum sp. MED92]
          Length = 616

 Score = 89.4 bits (220), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 69/247 (27%), Positives = 115/247 (46%), Gaps = 36/247 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 377 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 436

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   +A+++ +
Sbjct: 437 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREATPEE---LAERMEM 491

Query: 169 SESEV----------ISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
            E +V          ISM   +  DE  SL   I  +  +S                  +
Sbjct: 492 PEDKVRKVLKIAKEPISMETPIGDDEDSSLGDFIEDTTISSP-----------------V 534

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEA 274
           +    +  R      ++ L  RE ++   R   E     TLE +  +F+V+RER+RQIEA
Sbjct: 535 DSATGEGLREATREVLAGLTVRESKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEA 594

Query: 275 RAFKKVQ 281
           +A +K++
Sbjct: 595 KALRKLR 601


>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 = 89.4 bits (220), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 71/244 (29%), Positives = 122/244 (50%), Gaps = 30/244 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R + + + + +  + PE  
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPNPEELAERMMMPED- 492

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D      I+  
Sbjct: 493 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTIDSPIDSA 535

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 536 TMESLRGATNDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 595

Query: 278 KKVQ 281
           +K++
Sbjct: 596 RKLR 599


>gi|260592476|ref|ZP_05857934.1| RNA polymerase sigma-43 factor [Prevotella veroralis F0319]
 gi|260535522|gb|EEX18139.1| RNA polymerase sigma-43 factor [Prevotella veroralis F0319]
          Length = 228

 Score = 89.4 bits (220), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 72/269 (26%), Positives = 122/269 (45%), Gaps = 47/269 (17%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +YI EI +  +L  +EE  LA + +  GD  A  +L  ++L+ VV +A  Y+  GL   +
Sbjct: 6   KYIEEIVQEQLLSSEEEQTLAAKIK-LGDAKALEKLTKANLKFVVSLAHHYKNQGLGEDD 64

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +VSEGNIG+M A +KFD  +G R  +Y+  +I+ AM+E I    +L K+      K    
Sbjct: 65  LVSEGNIGMMHAAQKFDGTKGIRFVSYAAPYIRKAMEEAIKEQTALYKLPKDEKSK---- 120

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
              R + H  +I       +Q + +    N +   V+        DE LN          
Sbjct: 121 -FERKRTHAISI-------DQPIPVGSSNNFTLQHVLENEDAPQADEHLN---------- 162

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA-RRLQENPVTLE 256
              ++ L ++                    + + ++ LN RE+RI  A   L     T+ 
Sbjct: 163 ---KELLNFE--------------------IQKGLNELNEREKRIIIAIYGLNGTHYTMA 199

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            ++    + RERVRQI  +A +K+ + ++
Sbjct: 200 EIAENMGLKRERVRQIRNKALRKLHKKMK 228


>gi|167584375|ref|ZP_02376763.1| sigma 70 (RpoD) [Burkholderia ubonensis Bu]
          Length = 611

 Score = 89.4 bits (220), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 64/234 (27%), Positives = 115/234 (49%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +++ ++LRLV+ IA  Y   G+   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 373 AKRQMIEANLRLVISIAKKYVNRGMQFLDLIQEGNIGLMKAVDKFEYRRGWKFSTYATWW 432

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           ++ A+   +      +++    +       L R+   +   T     P     +AK++ +
Sbjct: 433 VRQAVTRALADQARTIRV--PVHMIETINKLNRISREILQQTGQEAHP---AVLAKRMEM 487

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SE +V S+        SL   +   D   +   D +    D       E     N R  +
Sbjct: 488 SEEKVRSILKIAKQPVSLETPVG--DDADATLGDMI---EDVSASSPAEAAIHANMRAAI 542

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKV 280
             ++  L+PRE ++   R   +     TLE +  +F+V+RER+RQIE++A +K+
Sbjct: 543 DEALDGLSPREAKVLRMRFGLDTTSDHTLEEVGKQFDVTRERIRQIESKAMRKL 596


>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 = 89.4 bits (220), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 492

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 493 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 535

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 536 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 595

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 596 RKLRHPSRSEV 606


>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 = 89.4 bits (220), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 492

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 493 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 535

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 536 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 595

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 596 RKLRHPSRSEV 606


>gi|161506225|ref|YP_001573337.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:-- str. RSK2980]
 gi|160867572|gb|ABX24195.1| hypothetical protein SARI_04418 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 660

 Score = 89.4 bits (220), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 422 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 481

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 482 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 539

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 540 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 582

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 583 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 642

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 643 RKLRHPSRSEV 653


>gi|156932573|ref|YP_001436489.1| RNA polymerase sigma factor RpoD [Cronobacter sakazakii ATCC
           BAA-894]
 gi|156530827|gb|ABU75653.1| hypothetical protein ESA_00355 [Cronobacter sakazakii ATCC BAA-894]
          Length = 614

 Score = 89.4 bits (220), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 376 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 435

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 436 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 493

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 494 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 536

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 537 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 596

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 597 RKLRHPSRSEV 607


>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|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]
          Length = 613

 Score = 89.4 bits (220), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 492

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 493 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 535

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 536 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 595

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 596 RKLRHPSRSEV 606


>gi|123968168|ref|YP_001009026.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. AS9601]
 gi|123198278|gb|ABM69919.1| Putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus str. AS9601]
          Length = 307

 Score = 89.4 bits (220), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 82/296 (27%), Positives = 140/296 (47%), Gaps = 32/296 (10%)

Query: 12  GEIGLSRYIHEIRKIPMLEK-QEEYVLAKRYREHG------DLSAAHR------------ 52
           GEIG  + +   R++ M  K QE  VL  R +E G      + S A R            
Sbjct: 9   GEIGRHQLLTPERELTMGRKVQEMVVLVNRCQEAGGKGPACEYSEAERKKIKIGEKAKNE 68

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG R +TY+ WWI+  
Sbjct: 69  MITANLRLVVNLAKRYQGKGLELLDLIQEGTLGLTRAVEKYDPSRGHRFSTYAYWWIRQG 128

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +      ++I    N+K     LR  K  L  +      P     +A+++ +++ E
Sbjct: 129 LNRALSTQSRTIRIPVNINEK--LTKLRSAKSKLMQLKG---IPPTSDELAEEMKITKEE 183

Query: 173 VIS-MNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           V   ++C L     SL   + S   + S+  D L  D     ++    E   +   +L +
Sbjct: 184 VDELLSCELRSITVSLQGTVKSKS-DPSELVDILPSDQTPPMELAELAERTASAWKLLDK 242

Query: 231 SMSVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +   L  +ER+I   R   +      TL  ++     SRE  RQ+  RA +K++++
Sbjct: 243 AN--LTEKERKIVSLRFGLDGSNEWRTLAEVARHMSCSREYCRQVVQRALRKLRKA 296


>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 = 89.4 bits (220), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 420 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 479

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 480 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 537

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 538 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 580

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 581 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 640

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 641 RKLRHPSRSEV 651


>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|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. 4/74]
 gi|326624968|gb|EGE31313.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Dublin str. 3246]
 gi|332990077|gb|AEF09060.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhimurium str. UK-1]
          Length = 660

 Score = 89.4 bits (220), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 422 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 481

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 482 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 539

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 540 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 582

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 583 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 642

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 643 RKLRHPSRSEV 653


>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 = 89.4 bits (220), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 70/243 (28%), Positives = 115/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 377 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 436

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 437 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPNPEELAERMMMPED 494

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D      I+   
Sbjct: 495 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTIDSPIDSAT 538

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 539 MESLRGATNDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 598

Query: 279 KVQ 281
           K++
Sbjct: 599 KLR 601


>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 = 89.4 bits (220), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 72/242 (29%), Positives = 122/242 (50%), Gaps = 28/242 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 372 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 431

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-KRLFFNLRRLKGHLQA---ITDNNLKPEQVV 160
           I+ A+   I      ++I      T N+  R+   + +  G   A   + +  L PE+  
Sbjct: 432 IRQAITRSIADQARTIRIPVHMIETINKLNRVSRQMLQEMGREPAPEELAERMLMPEE-- 489

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +             D + S   D++    D   ++ ++   
Sbjct: 490 KIRKVLKIAK-EPISMETPIG------------DDDDSHLGDFI---EDTTLELPLDSAT 533

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 534 SESLRLATNDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 593

Query: 279 KV 280
           K+
Sbjct: 594 KL 595


>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 = 89.4 bits (220), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 376 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 435

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 436 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 493

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 494 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 536

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 537 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 596

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 597 RKLRHPSRSEV 607


>gi|289827081|ref|ZP_06545870.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-3139]
          Length = 615

 Score = 89.4 bits (220), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 377 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 436

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 437 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 494

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 495 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 537

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 538 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 597

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 598 RKLRHPSRSEV 608


>gi|116333403|ref|YP_794930.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Lactobacillus brevis ATCC 367]
 gi|116098750|gb|ABJ63899.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Lactobacillus brevis ATCC 367]
          Length = 368

 Score = 89.4 bits (220), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 44/108 (40%), Positives = 68/108 (62%), Gaps = 1/108 (0%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI ++ +L   EE  LA R  E+G+ +A   L  ++LRLVV IA  Y G G+   ++
Sbjct: 108 YLKEIGRVNLLTADEEVALALRI-ENGEEAAKQELAEANLRLVVSIAKRYVGRGMQFLDL 166

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           + EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I
Sbjct: 167 IQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRI 214


>gi|301064644|ref|ZP_07205038.1| RNA polymerase sigma factor RpoD [delta proteobacterium NaphS2]
 gi|300441264|gb|EFK05635.1| RNA polymerase sigma factor RpoD [delta proteobacterium NaphS2]
          Length = 590

 Score = 89.4 bits (220), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 79/249 (31%), Positives = 121/249 (48%), Gaps = 40/249 (16%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ WW
Sbjct: 351 AKSELIQANLRLVVSIAKKYTNRGLMFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWW 410

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRL-KGHLQAITDNNL--------- 154
           I+ A+   I      ++I      T N  +L    R L + H +  T   +         
Sbjct: 411 IRQAITRAIADQARTIRIPVHMIETIN--KLMRTSRYLVQEHGREPTSEEIAEKMEFPLD 468

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           K  +V+ IAK       E IS+   +  +E  +      DKN     D +V +    EQ 
Sbjct: 469 KVRKVLKIAK-------EPISLETPIGEEEDSHLGDFIEDKNILSPGDAVV-NFGLAEQT 520

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQI 272
                     R +LT     L PRE ++   R    ++   TLE +  +F V+RER+RQI
Sbjct: 521 ----------RKVLT----TLTPREEKVLRMRFGIGEKADHTLEEVGRDFSVTRERIRQI 566

Query: 273 EARAFKKVQ 281
           EA+A +K++
Sbjct: 567 EAKALRKLR 575


>gi|170731361|ref|YP_001763308.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia cenocepacia
           MC0-3]
 gi|169814603|gb|ACA89186.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia cenocepacia
           MC0-3]
          Length = 857

 Score = 89.4 bits (220), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 71/247 (28%), Positives = 122/247 (49%), Gaps = 38/247 (15%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+  ++L+LV  +A  YR  G P+ ++  EGNIGL++AV++FD  RGF+ +TY+ WW
Sbjct: 515 ARERMAVANLKLVFHLAKKYRYSGEPLDDLAQEGNIGLLKAVERFDWRRGFKFSTYATWW 574

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +  ++      V++    ++K      +RL    QA+     +  ++  IA +LN+
Sbjct: 575 IRQQIGRHLADKCRTVRVPVHVHEK-----AQRLSRETQALESETGRAPELHEIAARLNM 629

Query: 169 SESEVISMNCRLAGD---------ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           +  +V  +  RLA +         + L A+   SD  S    D            ++ K 
Sbjct: 630 AVQKVAELQ-RLAPEPLPIHELPIDELIAVEVRSDFVSPDPMD------------IVSKS 676

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQ-----ENPVTLENLSSEFEVSRERVRQIEA 274
           E     + L   +S L P+E +     RL+     E  +TLE +  ++ V+RERVRQIE 
Sbjct: 677 ELLETIDKL---LSTLKPKEEQTL---RLRFGIGVEEALTLEEIGCQYGVTRERVRQIEV 730

Query: 275 RAFKKVQ 281
            A + ++
Sbjct: 731 AALRNLK 737


>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 = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 74/251 (29%), Positives = 120/251 (47%), Gaps = 34/251 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK-----PE----QV 159
           I+ A+   I      ++I     +     N R  +  LQ             PE    +V
Sbjct: 438 IRQAITRSIADQARTIRIPVHMIETINKLN-RVARQMLQEXXXXXXXXXXXMPEDKIRKV 496

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           + IAK       E ISM   +  DE             S   D++    D   ++ +   
Sbjct: 497 LKIAK-------EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLGSA 534

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 535 TSESLRSATHEVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 594

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 595 RKLRHPSRSEV 605


>gi|302344687|ref|YP_003809216.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfarculus baarsii DSM
           2075]
 gi|301641300|gb|ADK86622.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfarculus baarsii DSM
           2075]
          Length = 363

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 68/241 (28%), Positives = 120/241 (49%), Gaps = 23/241 (9%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   +V ++LRL V IA  Y   GL  ++++ EGNIGLM+AV ++D   G+R +T++ W
Sbjct: 125 AAVSEMVEANLRLAVSIAKKYTFRGLSFADLIQEGNIGLMKAVNRYDYRTGYRFSTFASW 184

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+  +   I      ++I     + R  +  R   G L+ +       E    +A+K+ 
Sbjct: 185 WIRQTISRAIYDQARTIRIPIHLLELRSKY-FRVYYGLLKELGREPTPKE----VAEKVG 239

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW-----LVYDHDGQEQVLIEKEERK 222
           ++E +V          E +N  ++S+   +   +D       + + D ++   +  E   
Sbjct: 240 ITEDKV---------KEIINLTLDSTSLETPVGEDGDELGDFIENKDAEDPFSMVGETEM 290

Query: 223 NRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           +    L  ++  L+ RERRI E R     E+  TLE +   F +SRERVRQIE +A +++
Sbjct: 291 H--GHLEAALDSLDGRERRILEMRFGLGDEDEHTLEEVGQVFGLSRERVRQIEKKALQRL 348

Query: 281 Q 281
           +
Sbjct: 349 R 349


>gi|238896571|ref|YP_002921314.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae NTUH-K2044]
 gi|238548896|dbj|BAH65247.1| RNA polymerase sigma factor [Klebsiella pneumoniae subsp.
           pneumoniae NTUH-K2044]
          Length = 632

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 394 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 453

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 454 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 511

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 512 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 554

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 555 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 614

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 615 RKLRHPSRSEV 625


>gi|218550316|ref|YP_002384107.1| RNA polymerase sigma factor RpoD [Escherichia fergusonii ATCC
           35469]
 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 = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 492

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 493 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 535

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 536 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 595

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 596 RKLRHPSRSEV 606


>gi|18404292|ref|NP_565856.1| SIGF (RNA POLYMERASE SIGMA-SUBUNIT F); DNA binding / DNA-directed
           RNA polymerase/ sigma factor/ transcription factor
           [Arabidopsis thaliana]
 gi|7209640|dbj|BAA92288.1| SigF [Arabidopsis thaliana]
 gi|7688083|emb|CAB89775.1| sigma factor-like protein [Arabidopsis thaliana]
 gi|16604647|gb|AAL24116.1| putative RNA polymerase sigma-70 factor [Arabidopsis thaliana]
 gi|20197948|gb|AAD31584.2| putative RNA polymerase sigma-70 factor [Arabidopsis thaliana]
 gi|20259557|gb|AAM14121.1| putative RNA polymerase sigma-70 factor protein [Arabidopsis
           thaliana]
 gi|330254238|gb|AEC09332.1| RNApolymerase sigma-subunit F [Arabidopsis thaliana]
          Length = 547

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 76/256 (29%), Positives = 128/256 (50%), Gaps = 38/256 (14%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           H   S+  +L+T++LRLVV IA  Y+  GL   +++ EG++GLM++V+KF P+ G R AT
Sbjct: 302 HRGRSSREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFAT 361

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI+ ++++ I ++   +         RL  N+  L G               V+ A
Sbjct: 362 YAYWWIRQSIRKSIFQNSRTI---------RLPENVYMLLGK--------------VSEA 398

Query: 164 KKLNVSESEVISMNCRLAG-----DESLNALI-NSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           +K  V E         LAG      E L+ L+ N+    S Q   W   D   QE     
Sbjct: 399 RKTCVQEGNYRPSKEELAGHVGVSTEKLDKLLYNTRTPLSMQQPIWSDQDTTFQEITPDS 458

Query: 218 KEE-------RKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRER 268
             E       ++  RN +   ++VL+P+ERRI + R   +     +L  +   + +S+ER
Sbjct: 459 GIETPTMSVGKQLMRNHVRNLLNVLSPKERRIIKLRFGIDGGKQRSLSEIGEIYGLSKER 518

Query: 269 VRQIEARAFKKVQESI 284
           VRQ+E+RA  ++++++
Sbjct: 519 VRQLESRALYRLKQNM 534


>gi|269968333|ref|ZP_06182353.1| conserved hypothetical protein [Vibrio alginolyticus 40B]
 gi|269827051|gb|EEZ81365.1| conserved hypothetical protein [Vibrio alginolyticus 40B]
          Length = 296

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 47/118 (39%), Positives = 74/118 (62%), Gaps = 4/118 (3%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY--- 68
           G+   + Y+ +I  I +L ++EE   AK  R  GD  A   L+ S+LRLVVKIA GY   
Sbjct: 25  GKDPYAHYLKDIVGIDLLSREEELHYAKLNR-VGDEEAREMLIESNLRLVVKIAKGYLKR 83

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            G    + +++ EGNIGL++AV KFDPE G+R +TY++WWI+  ++  ++ +   V++
Sbjct: 84  PGNNFTLLDLIEEGNIGLIKAVDKFDPEPGYRFSTYAVWWIRENIEAALMNNGRTVRL 141


>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 = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 422 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 481

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 482 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 539

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 540 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 582

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 583 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 642

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 643 RKLRHPSRSEV 653


>gi|288923254|ref|ZP_06417393.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EUN1f]
 gi|288345398|gb|EFC79788.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EUN1f]
          Length = 400

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 70/253 (27%), Positives = 120/253 (47%), Gaps = 36/253 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +LV ++LRLVV IA  Y G G+ + +++ EGN+GL++AV+KFD  +G++ +TY+ WW
Sbjct: 163 AKRKLVEANLRLVVSIAKRYVGRGMLLLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 222

Query: 109 IKAAMQEYILRSWSLVKI----GTTAN-----QKRLFFNLRRLKGHLQAITDNNL---KP 156
           I+ A+   +      ++I      T N     Q++L   L R     +  T  +L   K 
Sbjct: 223 IRQAVTRALADQGRTIRIPVHMAETVNKVTRIQRQLLQELGREPSPEEIGTQIDLTAHKV 282

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           E+++ IA+     E+ + +       D  L   I   D          +   +    VL+
Sbjct: 283 EEILKIAQTPVALETPIGAEQ-----DSQLGDFIEDDDA---------IAPFEAASSVLL 328

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEA 274
           +K         +   +  L  RE+++ + R       P TLE +  EF + +ER+RQIE+
Sbjct: 329 QKH--------IESVLHTLPAREKKVIQLRFGLTDGQPRTLEQIGREFGIPQERIRQIES 380

Query: 275 RAFKKVQESIQKQ 287
           R   K+    + Q
Sbjct: 381 RTLAKLSHPARSQ 393


>gi|266618720|pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact Activator-
           Dependent Transcription Initiation Complex
          Length = 613

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 492

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 493 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 535

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 536 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 595

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 596 RKLRHPSRSEV 606


>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|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]
          Length = 613

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 492

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 493 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 535

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 536 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 595

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 596 RKLRHPSRSEV 606


>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 = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 492

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 493 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 535

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 536 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 595

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 596 RKLRHPSRSEV 606


>gi|15803609|ref|NP_289642.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 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|256019017|ref|ZP_05432882.1| RNA polymerase sigma factor RpoD [Shigella sp. D9]
 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 70 factor [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|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 1180]
 gi|323183651|gb|EFZ69048.1| RNA polymerase sigma factor rpoD [Escherichia coli 1357]
 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 KO11]
 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]
          Length = 613

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 492

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 493 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 535

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 536 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 595

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 596 RKLRHPSRSEV 606


>gi|90416498|ref|ZP_01224429.1| RNA polymerase sigma factor RpoD [marine gamma proteobacterium
           HTCC2207]
 gi|90331697|gb|EAS46925.1| RNA polymerase sigma factor RpoD [marine gamma proteobacterium
           HTCC2207]
          Length = 612

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 76/246 (30%), Positives = 118/246 (47%), Gaps = 34/246 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 374 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 433

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 434 IRQAITRSIADQARTIRI--PVHMIETINKLNRVSRQMLQEMGREPSPEELAERMEMPED 491

Query: 161 AIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            I K L +++ E ISM   +  DE  S+  LI          +D  +         L   
Sbjct: 492 KIRKVLKIAK-EPISMETPIGEDEDASIGDLI----------EDTTI--------ALPLD 532

Query: 219 EERKNRRNMLTRS-MSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEAR 275
           E  KN     TR  +S L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+
Sbjct: 533 EATKNNLTESTRGVLSSLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 592

Query: 276 AFKKVQ 281
           A +K++
Sbjct: 593 ALRKLR 598


>gi|18477825|emb|CAC83730.1| sigma factor [Rhodococcus fascians]
          Length = 323

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 82/303 (27%), Positives = 142/303 (46%), Gaps = 58/303 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHG--------------------------DLSAAH- 51
           Y++ I +  +L  +EE  LAKR  E G                          D SAA  
Sbjct: 30  YLNGIGRTALLTAEEEVDLAKRI-EAGLYAKQVLENTKRLSAVKKRNLAIIVRDGSAARS 88

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ 
Sbjct: 89  HLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTYATWWIRQ 148

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-----QAITDNNLKPEQVVAIAKKL 166
           A+   +      +++     ++     L R+K  L     +  TD  L  E  +A+ K  
Sbjct: 149 AITRGMADQSRTIRLPVHLVEQ--VNKLARIKRELHQQLGREATDEELSSESGIAVEKIA 206

Query: 167 NVSES--EVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           ++ +   + +S++  +  DE   L   I  S+  S+             E  +I      
Sbjct: 207 DLLDHSRDPVSLDMPVGSDEEAPLGDFIEDSEATSA-------------ENAVIAGLLHS 253

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R +L      L+ RE+++   R   ++  P TL+ +   F +SRERVRQIE     K+
Sbjct: 254 DVRVVL----GTLDEREQQVIRLRYGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMVKL 309

Query: 281 QES 283
           ++ 
Sbjct: 310 RQG 312


>gi|3893860|gb|AAC78467.1| RNA polymerase sigma factor 1 [Zea mays]
          Length = 398

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 74/253 (29%), Positives = 128/253 (50%), Gaps = 40/253 (15%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L  S+ RLV+ IA  Y   G+ + +++  G IGL++ ++KFD  RGFR++TY  WWI+  
Sbjct: 159 LAMSNTRLVISIAQKYDNLGVELPDLIQGGLIGLLRGIEKFDASRGFRISTYVYWWIRQG 218

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES- 171
           +   +  +    ++ T  +++     L  ++G   A+ D  + P  V  IA+ LN+SE  
Sbjct: 219 VSRALADNSRSFRLPTYLHER-----LVAIRGAKYALEDQGIAP-TVENIAESLNISEKK 272

Query: 172 ---------EVISMNCR-------LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
                    +VIS++ +       L GD +L++ I   +  +  W       H  +E+ L
Sbjct: 273 VHNATEAVHKVISLDQQAFPSLNGLPGD-TLHSYIEDQNVANDPW-------HGFEERYL 324

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPVTLENLSSEFEVSRERVRQIEA 274
             KEE  +  N      S LN RER I      + +   T E++S +F +SRERVRQ+  
Sbjct: 325 --KEEVNSLIN------STLNERERDIIRLYHGIGKQCHTWEDISRQFGLSRERVRQVGL 376

Query: 275 RAFKKVQESIQKQ 287
            A +K++ + +++
Sbjct: 377 VAMEKLKHAARRE 389


>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 = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 72/248 (29%), Positives = 122/248 (49%), Gaps = 38/248 (15%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 376 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 435

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPE-- 157
           I+ A+   I      ++I      T N+     +++   + R + + + + +  + PE  
Sbjct: 436 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPNPEELAERMMMPEDK 494

Query: 158 --QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
             +V+ IAK       E ISM   +  DE             S   D++    D      
Sbjct: 495 VRKVLKIAK-------EPISMETPIGDDE------------DSHLGDFI---EDTTIDSP 532

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIE 273
           I+    ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIE
Sbjct: 533 IDSATMESLRGATNDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 592

Query: 274 ARAFKKVQ 281
           A+A +K++
Sbjct: 593 AKALRKLR 600


>gi|262042263|ref|ZP_06015428.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|259040327|gb|EEW41433.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
          Length = 611

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 373 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 432

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 433 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 490

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 491 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 533

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 534 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 593

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 594 RKLRHPSRSEV 604


>gi|1072030|gb|AAB60181.1| RNA polymerase sigma-subunit [Escherichia coli]
          Length = 603

 Score = 89.4 bits (220), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 365 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 424

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 425 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 482

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 483 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 525

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 526 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 585

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 586 RKLRHPSRSEV 596


>gi|324115354|gb|EGC09318.1| RNA polymerase sigma proteinRpoD [Escherichia fergusonii B253]
          Length = 613

 Score = 89.0 bits (219), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 492

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 493 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 535

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 536 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 595

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 596 RKLRHPSRSEV 606


>gi|302336705|ref|YP_003801911.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           smaragdinae DSM 11293]
 gi|301633890|gb|ADK79317.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           smaragdinae DSM 11293]
          Length = 322

 Score = 89.0 bits (219), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 83/299 (27%), Positives = 139/299 (46%), Gaps = 44/299 (14%)

Query: 16  LSRYIHEIRKIPMLEKQEE------------------------------YVLAKRYREHG 45
           LS Y+ +I   P+L K+EE                              Y+  KR  E  
Sbjct: 23  LSLYLKQISAYPLLTKEEELMIGREIQERKQELLELEELLGKEEIERSAYLFRKRTIEAV 82

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
              +  R++TS+LRLVV IA  Y+  GL   +++ EGNIGL++AV++FD  +  + +TY 
Sbjct: 83  LRKSRDRMITSNLRLVVSIAKKYQHRGLSFLDLIDEGNIGLIEAVERFDYTKRCKFSTYG 142

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN-LRRLKGHLQAITDNNLKPEQVVAIAK 164
            WWI    Q+ +++  +L   G T        N +R+L    + +T    +      IA 
Sbjct: 143 TWWI----QQSVIK--ALADKGRTIRIPIHVLNIIRKLFSVTKHLTQELGRDPSSAEIAA 196

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            +++    V S+        SL+  ++  D+N +   D LV+  D  E    E       
Sbjct: 197 YMDLPVERVESILQYSGETASLDVTVD--DENITSLSD-LVFSDDYIEP--FESVFHVTL 251

Query: 225 RNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +++L   +  L+ RE+ I + R       P+TLE + S   ++RERVRQI+ +A +K++
Sbjct: 252 KDLLDTILGQLSEREQTIIKLRFGLADRTPLTLEEIGSILGITRERVRQIQNKAIEKLR 310


>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 = 89.0 bits (219), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 377 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 436

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 437 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 494

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 495 -KIRKVLKIAK-EPISMEAPIGDDE------------DSHLGDFI---EDTTLELPLDSA 537

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 538 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 597

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 598 RKLRHPSRSEV 608


>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 = 89.0 bits (219), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 492

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 493 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 535

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 536 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 595

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 596 RKLRHPSRSEV 606


>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|61234163|sp|P0A2E3|RPOD_SALTY RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|61234169|sp|P0A2E4|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]
          Length = 615

 Score = 89.0 bits (219), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 377 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 436

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 437 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 494

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 495 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 537

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 538 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 597

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 598 RKLRHPSRSEV 608


>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|253772097|ref|YP_003034928.1| RNA polymerase sigma factor RpoD [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254038237|ref|ZP_04872295.1| RNA polymerase sigma factor RpoD [Escherichia sp. 1_1_43]
 gi|254163014|ref|YP_003046122.1| RNA polymerase sigma factor RpoD [Escherichia coli B str. REL606]
 gi|256024353|ref|ZP_05438218.1| RNA polymerase sigma factor RpoD [Escherichia sp. 4_1_40B]
 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|307139755|ref|ZP_07499111.1| RNA polymerase sigma factor RpoD [Escherichia coli H736]
 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|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]
          Length = 613

 Score = 89.0 bits (219), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 492

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 493 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 535

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 536 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 595

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 596 RKLRHPSRSEV 606


>gi|331017645|gb|EGH97701.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv.
           lachrymans str. M302278PT]
          Length = 616

 Score = 89.0 bits (219), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 116/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 438 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPED 495

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   Q  I+   
Sbjct: 496 KIRKVLKITK-EPISMETPIGDDE------------DSHLGDFI---EDSTMQSPIDVAT 539

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ +      +S L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 540 VESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 279 KVQ 281
           K++
Sbjct: 600 KLR 602


>gi|309790481|ref|ZP_07685041.1| sigma-70 family RNA polymerase sigma factor [Oscillochloris
           trichoides DG6]
 gi|308227468|gb|EFO81136.1| sigma-70 family RNA polymerase sigma factor [Oscillochloris
           trichoides DG6]
          Length = 346

 Score = 89.0 bits (219), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 88/305 (28%), Positives = 138/305 (45%), Gaps = 66/305 (21%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGD-----------LSAAHR--------------- 52
           Y+ EI ++ +L   EE  L++R  E GD           LS   R               
Sbjct: 53  YLQEIGRVSLLTANEEVELSERI-ERGDEAEERLATEDQLSGTQRRNLEHEVERGNDARR 111

Query: 53  -LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV IA  Y G GL + +++ EGNIGLM+AV+KFD  +G R +TY+ WWI+ 
Sbjct: 112 HLIQANLRLVVSIAKKYVGRGLSLLDLIQEGNIGLMRAVEKFDHRKGNRFSTYATWWIRQ 171

Query: 112 AMQEYILRSWSLVKIGTTANQ---------KRLFFNLRRLKGHLQ---AITDNNLKPEQV 159
           A+   I      +++    ++         +RL  +L R     +   A+     + E+V
Sbjct: 172 AVTRSIAEQGRTIRLPVHMSESVSQVKRTSERLSQSLERQPSAEEIAIALGQPTERIERV 231

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINS-SDKNSSQWQDWLVYDHDGQEQVLIEK 218
           +  A++    E+ V        GDE  + L +   D +     D+         Q+L   
Sbjct: 232 LEAARRPVSLETPV--------GDEGEHTLGDFLPDDDLPTPGDF------ASAQLL--- 274

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARA 276
                 R  L  ++  LN RERRI + R   L     TLE +     ++RER RQIEA A
Sbjct: 275 ------RQDLCAALDHLNERERRIIDLRYGLLDGRRRTLEEVGRTLGMTRERARQIEAEA 328

Query: 277 FKKVQ 281
            ++++
Sbjct: 329 LRRLR 333


>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 = 89.0 bits (219), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 376 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 435

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 436 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 493

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 494 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 536

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 537 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 596

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 597 RKLRHPSRSEV 607


>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 = 89.0 bits (219), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 377 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 436

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 437 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 494

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 495 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 537

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 538 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 597

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 598 RKLRHPSRSEV 608


>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 = 89.0 bits (219), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 70/243 (28%), Positives = 114/243 (46%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 374 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 433

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 434 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPED 491

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D Q    ++   
Sbjct: 492 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDIQALSPVDSAT 535

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            +  R      ++ L  RE ++   R   E     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 536 AEGLREATRSVLAGLTARESKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALR 595

Query: 279 KVQ 281
           K++
Sbjct: 596 KLR 598


>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 = 89.0 bits (219), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 492

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 493 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 535

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 536 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 595

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 596 RKLRHPSRSEV 606


>gi|54025745|ref|YP_119987.1| RNA polymerase sigma factor SigB [Nocardia farcinica IFM 10152]
 gi|54017253|dbj|BAD58623.1| putative principal sigma factor [Nocardia farcinica IFM 10152]
          Length = 322

 Score = 89.0 bits (219), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 80/302 (26%), Positives = 143/302 (47%), Gaps = 56/302 (18%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH-----GDLSAAHR---------------- 52
           Y++ I +  +L   +E  LAKR     Y +H       LSAA +                
Sbjct: 29  YLNGIGRTALLTAADEVELAKRIEAGLYAQHLLETSKRLSAAKKKDLAMIVRDGQAARSH 88

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A
Sbjct: 89  LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQA 148

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA-----ITDNNLKPEQVVAIAKKLN 167
           +   +      +++     ++     L R+K  L        TD  L  E  + + K  +
Sbjct: 149 ITRGMADQSRTIRLPVHLVEQ--VNKLARIKRELHQQLGREATDEELAAESGIPVEKIAD 206

Query: 168 VSES--EVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + +   + +S++  +  DE   L   I  S+  S+             E  +I      +
Sbjct: 207 LLDHSRDPVSLDMPVGNDEEAPLGDFIEDSEATSA-------------ESAVIAGLLHHD 253

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R++L    + L+ RE+++   R   ++  P TL+ +   F +SRERVRQIE     K++
Sbjct: 254 VRSVL----ATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMAKLR 309

Query: 282 ES 283
           + 
Sbjct: 310 KG 311


>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 = 89.0 bits (219), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 376 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 435

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 436 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 493

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 494 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 536

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 537 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 596

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 597 RKLRHPSRSEV 607


>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 = 89.0 bits (219), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 376 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 435

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 436 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 493

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 494 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 536

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 537 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 596

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 597 RKLRHPSRSEV 607


>gi|297626466|ref|YP_003688229.1| RNA polymerase principal sigma factor HrdB [Propionibacterium
           freudenreichii subsp. shermanii CIRM-BIA1]
 gi|296922231|emb|CBL56801.1| RNA polymerase principal sigma factor HrdB [Propionibacterium
           freudenreichii subsp. shermanii CIRM-BIA1]
          Length = 509

 Score = 89.0 bits (219), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 82/310 (26%), Positives = 140/310 (45%), Gaps = 61/310 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR----------EHGDLSA-------------AHR--- 52
           Y+ +I K+ +L   +E  LAKR            ++GD  A              HR   
Sbjct: 215 YLKQIGKVALLNAAQEVDLAKRIEAGLFAGEQLTKNGDKIARADRGDYEWITEDGHRAKN 274

Query: 53  -LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWIK 
Sbjct: 275 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIKQ 334

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+VV +
Sbjct: 335 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEV 394

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 395 QKYGR----EPISLHTPLGEDGDSEFGDLIEDSE---------AVVPADAVNFTLLQEQ- 440

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 441 -------LHDVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 493

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 494 KLRHPSRSQV 503


>gi|158339615|ref|YP_001521004.1| RNA polymerase sigma-70 factor, putative [Acaryochloris marina
           MBIC11017]
 gi|158309856|gb|ABW31472.1| RNA polymerase sigma-70 factor, putative [Acaryochloris marina
           MBIC11017]
          Length = 268

 Score = 89.0 bits (219), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 71/279 (25%), Positives = 130/279 (46%), Gaps = 29/279 (10%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  +  EI + P+L  +EE  LA R  + G L A  R++  +LR VV IA  Y+  GLP+
Sbjct: 8   LHFFFKEIARYPLLSHEEEIQLA-RQAQAGSLRAKQRMIECNLRFVVSIAKKYQNRGLPL 66

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EG+IGL  AV KFD  +G R +TY+ WWI+             +     A  + +
Sbjct: 67  LDLIQEGSIGLSTAVDKFDLAQGCRFSTYAYWWIRQG-----------ITAAVRAKSRPI 115

Query: 136 FF------NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD-ESLNA 188
           +        + ++K H + +T    +   +  +++  N+ + + IS   +L     SL+ 
Sbjct: 116 YLPHYHWDTVGKIKKHFRVLTQQLGREPSLSELSEATNI-KPKTISRTLQLFQQISSLDQ 174

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
           L+    K++       + D    E       E     + L++ M+ L+ RER +   R  
Sbjct: 175 LVGPQQKDT-------LLDMLAGEDQPTHYLESLQLDDELSQVMASLDERERFVLSQRYG 227

Query: 249 QEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            E+  P +++ +  +  +S E +R I  +  +K++   Q
Sbjct: 228 LEDDHPKSMKEIGQQIGLSHEGIRLILKKIMQKLERYAQ 266


>gi|219849486|ref|YP_002463919.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus
           aggregans DSM 9485]
 gi|219543745|gb|ACL25483.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus
           aggregans DSM 9485]
          Length = 345

 Score = 89.0 bits (219), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 79/292 (27%), Positives = 137/292 (46%), Gaps = 40/292 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRY------------------REHGDL--------SAAHR 52
           Y+ EI ++ +L   EE  LA+R                   RE  +L         A   
Sbjct: 52  YLQEIGRVALLTAVEEVELAERIERGNAAEQRLATATDLTPRERCELLKAVQEGEEARRH 111

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV IA  Y G GL + +++ EGNIGLM+AV+KFD  +G R +TY+ WWI+ A
Sbjct: 112 LIQANLRLVVSIAKKYVGRGLSLLDLIQEGNIGLMRAVEKFDHHKGNRFSTYATWWIRQA 171

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV-VAIAKKLNVSES 171
           +   +      +++    ++      ++R+   L    +    PE++ +A+ + +   + 
Sbjct: 172 VTRALAEQGRTIRLPVHMSES--VAQVKRIADRLAQSLERQPTPEEIAMALGQPVERIQR 229

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
            + +  C +    SL   +   D+      D++    D +     E   +K     L  +
Sbjct: 230 ILEAARCPV----SLETPVG--DEGEHTLGDFIT---DEELPAPGEIAAQKLLHRDLCAA 280

Query: 232 MSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++ L+ RERRI + R   L     TLE +     ++RER RQIEA A ++++
Sbjct: 281 LNQLSDRERRIIDLRYGLLDGRRRTLEEVGRVLGMTRERARQIEAEALRRLR 332


>gi|311693206|gb|ADP96079.1| RNA polymerase, sigma 70 subunit, RpoD [marine bacterium HP15]
          Length = 615

 Score = 89.0 bits (219), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 70/243 (28%), Positives = 114/243 (46%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 372 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 431

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV--------V 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 432 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPED 489

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D Q    ++   
Sbjct: 490 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDIQALSPVDSAT 533

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            +  R      ++ L  RE ++   R   E     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 534 AEGLREATRSVLAGLTARESKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALR 593

Query: 279 KVQ 281
           K++
Sbjct: 594 KLR 596


>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 = 89.0 bits (219), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 376 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 435

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 436 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 493

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 494 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 536

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 537 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 596

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 597 RKLRHPSRSEV 607


>gi|124023525|ref|YP_001017832.1| type II alternative sigma factor, sigma70 family [Prochlorococcus
           marinus str. MIT 9303]
 gi|123963811|gb|ABM78567.1| Putative type II alternative sigma factor, sigma70 family protein
           [Prochlorococcus marinus str. MIT 9303]
          Length = 308

 Score = 89.0 bits (219), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 74/245 (30%), Positives = 124/245 (50%), Gaps = 23/245 (9%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A ++++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG R +TY+ WW
Sbjct: 66  AKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSTYAYWW 125

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP--EQVVAIAKKL 166
           I+  +   +      ++I    N+K     LR  K  L  +  N L P  EQ+V    +L
Sbjct: 126 IRQGLNRALSTQSRTIRIPVNVNEK--LTKLRAAKSRL--MQSNGLPPTAEQLVK-TMRL 180

Query: 167 NVSESEVISMNCRL-AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
            ++E E + + C L +   SL  ++ S    S      LV     +E   +E+ E   R 
Sbjct: 181 PMAEVEDL-LACELRSVTVSLQGVVKSKSDPSE-----LVDVLPSEEIPPMERAEMAERT 234

Query: 226 ----NMLTRSMSVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFK 278
                +L R+   L P+ER +   R   +      TL  ++     SRE  RQ+  RA +
Sbjct: 235 ASVWTLLNRAN--LTPKERMVVTLRFGLDGSHEWRTLAEVARHMSCSREYCRQVVQRALR 292

Query: 279 KVQES 283
           K++++
Sbjct: 293 KLRKT 297


>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|323208002|gb|EFZ92948.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 507440-20]
 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]
          Length = 615

 Score = 89.0 bits (219), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 377 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 436

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 437 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 494

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 495 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 537

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 538 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 597

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 598 RKLRHPSRSEV 608


>gi|1769598|gb|AAB39998.1| sigma factor [Synechococcus sp. PCC 7002]
          Length = 398

 Score = 89.0 bits (219), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 67/247 (27%), Positives = 122/247 (49%), Gaps = 35/247 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV KFDP +G+R +TY+ WW
Sbjct: 159 AKEHMIQANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVDKFDPTKGYRFSTYAYWW 218

Query: 109 IKAAMQEYILRSWSLVKIGTTANQ-----KRLFFNLRRLKGHLQAITDN----NLKPEQV 159
           I+  +          +++     +     K+    + + +G   ++ D      + PEQV
Sbjct: 219 IRQGITRGDRTQSRTIRLPVHVTEKLNKIKKAQRQISQTQGCTPSLDDVAQALEMTPEQV 278

Query: 160 VAIAKKLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
             + +K+  S    +S+  R+  D    L  L+ + D +               E+ L+ 
Sbjct: 279 REVLQKVPRS----VSLEIRVGKDRDTELGDLLETQDASP--------------EENLVR 320

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT--LENLSSEFEVSRERVRQIEAR 275
           +  +++  N+LT     L  RER + + R    +  T  L  +    +VSRERVRQIEA+
Sbjct: 321 ESLQRDLHNLLTE----LTDREREVIQLRYGLGDGKTYSLAEIGRMLDVSRERVRQIEAK 376

Query: 276 AFKKVQE 282
           A +K+++
Sbjct: 377 ALQKLRQ 383


>gi|269925486|ref|YP_003322109.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
 gi|269789146|gb|ACZ41287.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
          Length = 338

 Score = 89.0 bits (219), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 80/302 (26%), Positives = 139/302 (46%), Gaps = 61/302 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR--------------------------EHGDLSAAHR 52
           Y+ EI  +P+L  ++E  LAK+                            + G+ +  H 
Sbjct: 46  YLREIGLVPLLTAEQEVELAKKMERGKKAQSVLDSGKYEPEQRDKLLAEVDEGERARRH- 104

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  +   GL + +++ EGNIGLM+A  KFD  +GF+ +TY+ WWI+ A
Sbjct: 105 LIEANLRLVVSVAKKHMNRGLSLLDLIEEGNIGLMRATDKFDYRKGFKFSTYATWWIRQA 164

Query: 113 MQEYILRSWSLVK--IGTTANQKRLFFNLRRLKGHL-------QAITDNNLKPEQVVAIA 163
           +   I      ++  +  T     L+   R+L   L       +      + PE+V  I 
Sbjct: 165 VTRAIADQARTIRLPVHITETMNHLYKASRKLSQELGREPTCEELAEYMGMNPEKVRLIM 224

Query: 164 KKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           +    +    +S+   +   GD SL   I   D  +    D  + +       ++++E  
Sbjct: 225 R----ASRHPLSLEGPVGTDGDSSLGQFI--PDSTTETPVDLAIGE-------VLKRE-- 269

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKK 279
                 L++ ++ L  +ER++   R   E  +P TLE +     V+RERVRQIEA+A +K
Sbjct: 270 ------LSKVLNSLTEKERKVMVLRYGLEGSSPHTLEEVGHRLGVTRERVRQIEAKALEK 323

Query: 280 VQ 281
           ++
Sbjct: 324 LR 325


>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 = 89.0 bits (219), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 492

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 493 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDPTLELPLDSA 535

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 536 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 595

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 596 RKLRHPSRSEV 606


>gi|26249652|ref|NP_755692.1| RpoD protein [Escherichia coli CFT073]
 gi|26110080|gb|AAN82266.1|AE016767_26 RpoD protein [Escherichia coli CFT073]
          Length = 246

 Score = 89.0 bits (219), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 72/250 (28%), Positives = 124/250 (49%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 8   AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 67

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-KRLFFNLRRLKGH---LQAITDNNLKPEQVV 160
           I+ A+   I      ++I      T N+  R+   + +  G     + + +  L PE   
Sbjct: 68  IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPED-- 125

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 126 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 169

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            ++ R      ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 170 TESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 229

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 230 KLRHPSRSEV 239


>gi|257483092|ref|ZP_05637133.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. tabaci
           ATCC 11528]
 gi|289627702|ref|ZP_06460656.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. aesculi
           str. NCPPB3681]
 gi|289649021|ref|ZP_06480364.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. aesculi
           str. 2250]
 gi|298485287|ref|ZP_07003379.1| RNA polymerase sigma factor RpoD [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
 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
           ATCC 11528]
          Length = 616

 Score = 89.0 bits (219), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 116/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 438 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPED 495

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   Q  I+   
Sbjct: 496 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDSTMQSPIDVAT 539

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ +      +S L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 540 VESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 279 KVQ 281
           K++
Sbjct: 600 KLR 602


>gi|24372864|ref|NP_716906.1| RNA polymerase sigma-70 factor [Shewanella oneidensis MR-1]
 gi|24346976|gb|AAN54351.1|AE015572_6 RNA polymerase sigma-70 factor [Shewanella oneidensis MR-1]
          Length = 616

 Score = 89.0 bits (219), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 68/243 (27%), Positives = 118/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 438 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPED 495

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 496 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 539

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ ++     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 540 SESLKSATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 279 KVQ 281
           K++
Sbjct: 600 KLR 602


>gi|330963831|gb|EGH64091.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv.
           actinidiae str. M302091]
          Length = 616

 Score = 89.0 bits (219), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 116/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 438 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPED 495

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   Q  I+   
Sbjct: 496 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDSTMQSPIDVAT 539

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ +      +S L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 540 VESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 279 KVQ 281
           K++
Sbjct: 600 KLR 602


>gi|296932701|gb|ADH93504.1| RNA polymerase sigma factor RpoD [Pseudomonas sp. In5]
          Length = 616

 Score = 89.0 bits (219), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 116/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 438 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPED 495

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   Q  I+   
Sbjct: 496 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDSTMQSPIDVAT 539

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ +      +S L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 540 VESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 279 KVQ 281
           K++
Sbjct: 600 KLR 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|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. M302280PT]
          Length = 616

 Score = 89.0 bits (219), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 116/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 438 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPED 495

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   Q  I+   
Sbjct: 496 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDSTMQSPIDVAT 539

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ +      +S L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 540 VESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 279 KVQ 281
           K++
Sbjct: 600 KLR 602


>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 = 89.0 bits (219), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 70/249 (28%), Positives = 120/249 (48%), Gaps = 42/249 (16%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLVV IA  Y   G+   +++ EGNIGL++AV KF+  RG++ +TY+ WW
Sbjct: 213 AKRDMTEANLRLVVSIAKKYINRGMQFLDLIQEGNIGLLKAVDKFEYRRGYKFSTYATWW 272

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLF------FNLRRLKGHLQAITDNN 153
           I+ A+   I      +++      T N+     +R+        +L  L  H++ +T+  
Sbjct: 273 IRQAVSRAIADQARTIRVPVHMLETVNKLNRIARRILQETGVEADLPTLALHME-LTEQK 331

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
           ++  +++ IA+       E ISM   +             D   SQ  D++    D    
Sbjct: 332 VR--EIMKIAR-------EPISMESPVG------------DDGDSQLGDFI---QDSTTT 367

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQ 271
             +E     + R  +   +  L PRE +I   R     ++  TLE +  +FEV+RER+RQ
Sbjct: 368 APLEAAVDASMRTAIKEVLDALPPREAKILRMRYGLDTQSDHTLEEVGKQFEVTRERIRQ 427

Query: 272 IEARAFKKV 280
           IE++A  K+
Sbjct: 428 IESKALVKL 436


>gi|326384463|ref|ZP_08206143.1| RNA polymerase sigma factor SigB [Gordonia neofelifaecis NRRL
           B-59395]
 gi|326196808|gb|EGD54002.1| RNA polymerase sigma factor SigB [Gordonia neofelifaecis NRRL
           B-59395]
          Length = 332

 Score = 89.0 bits (219), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 74/262 (28%), Positives = 132/262 (50%), Gaps = 30/262 (11%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K+ +Y +  R    G+ + AH L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++AV
Sbjct: 81  KKRDYAILVR---EGEQARAH-LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAV 136

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFFNLRR-LKGHL-Q 147
           +KFD  +G++ +TY+ WWI+ A+   +      +++      Q      +RR L   L +
Sbjct: 137 EKFDYAKGYKFSTYATWWIRQAISRGMADQSRTIRLPVHLVEQVNKLARIRRELHQQLGR 196

Query: 148 AITDNNLKPEQVVAIAKKLNVSES--EVISMNCRLAGDE--SLNALINSSDKNSSQWQDW 203
             TD  L  E  +   K  ++ +   + +S++  +  DE   L   I  ++  S+     
Sbjct: 197 EATDEELALESGIPAEKIADLMDHSRDPVSLDMPVGNDEEAPLGDFIEDAEATSA----- 251

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSE 261
                   E V+I      + R++L    S L+ RE ++   R   ++  P TL+ +   
Sbjct: 252 --------ETVVIANLLHSDIRSVL----STLDEREMQVITMRYGLDDGQPRTLDQIGRA 299

Query: 262 FEVSRERVRQIEARAFKKVQES 283
           F +SRERVRQIE     K+++ 
Sbjct: 300 FGLSRERVRQIEREVMGKLRQG 321


>gi|302185957|ref|ZP_07262630.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. syringae
           642]
          Length = 616

 Score = 89.0 bits (219), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 116/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 438 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPED 495

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   Q  I+   
Sbjct: 496 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDSTMQSPIDVAT 539

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ +      +S L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 540 VESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 279 KVQ 281
           K++
Sbjct: 600 KLR 602


>gi|302338588|ref|YP_003803794.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           smaragdinae DSM 11293]
 gi|301635773|gb|ADK81200.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           smaragdinae DSM 11293]
          Length = 612

 Score = 89.0 bits (219), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 74/251 (29%), Positives = 117/251 (46%), Gaps = 33/251 (13%)

Query: 44  HGDL---SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           HG +   +A  RL+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+KF+  +GF+
Sbjct: 366 HGQVMMKNAKDRLIQANLRLVVSIAKKYTNRGLHFFDLVQEGNIGLIKAVEKFEYSKGFK 425

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV- 159
            +TY+ WWI+ A+   I      +++     ++     + R    L  I   +   E+V 
Sbjct: 426 FSTYATWWIRQAITRSISDQARTIRVPVHMIEQ--INKVVRESRQLMQILGRDPTDEEVA 483

Query: 160 ------VAIAKKLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQ 211
                 V   K +     E IS+   +  +E   L   I   D  +   Q         Q
Sbjct: 484 ERLGWTVLRVKSVKNVAREPISLETPIGEEEDSLLGDFIEDKDIENPANQTAFTL---LQ 540

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERV 269
           EQ              L   M  L PRE+ + + R   ++   +TLE +   F V+RER+
Sbjct: 541 EQ--------------LQEVMKTLPPREQEVLKMRFGLDDGYSLTLEEVGLYFNVTRERI 586

Query: 270 RQIEARAFKKV 280
           RQIEA+A +++
Sbjct: 587 RQIEAKALRRL 597


>gi|295097580|emb|CBK86670.1| RNA polymerase, sigma 70 subunit, RpoD [Enterobacter cloacae subsp.
           cloacae NCTC 9394]
          Length = 614

 Score = 89.0 bits (219), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 376 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 435

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 436 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 493

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 494 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 536

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 537 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 596

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 597 RKLRHPSRSEV 607


>gi|296104731|ref|YP_003614877.1| RNA polymerase sigma-70 factor [Enterobacter cloacae subsp. cloacae
           ATCC 13047]
 gi|295059190|gb|ADF63928.1| RNA polymerase sigma-70 factor [Enterobacter cloacae subsp. cloacae
           ATCC 13047]
          Length = 615

 Score = 89.0 bits (219), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 377 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 436

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 437 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 494

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 495 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 537

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 538 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 597

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 598 RKLRHPSRSEV 608


>gi|66047868|ref|YP_237709.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. syringae
           B728a]
 gi|63258575|gb|AAY39671.1| 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 [Pseudomonas syringae pv. syringae B728a]
          Length = 616

 Score = 89.0 bits (219), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 116/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 438 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPED 495

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   Q  I+   
Sbjct: 496 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDSTMQSPIDVAT 539

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ +      +S L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 540 VESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 279 KVQ 281
           K++
Sbjct: 600 KLR 602


>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 = 89.0 bits (219), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 68/243 (27%), Positives = 118/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 381 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 440

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 441 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPED 498

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 499 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 542

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ ++     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 543 SESLKSATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 602

Query: 279 KVQ 281
           K++
Sbjct: 603 KLR 605


>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 = 89.0 bits (219), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 116/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 377 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 436

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 437 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPED 494

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   Q  I+   
Sbjct: 495 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDSTMQSPIDVAT 538

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ +      +S L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 539 VESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 598

Query: 279 KVQ 281
           K++
Sbjct: 599 KLR 601


>gi|172035517|ref|YP_001802018.1| group 2 sigma-70 RNA polymerase sigma factor E [Cyanothece sp. ATCC
           51142]
 gi|171696971|gb|ACB49952.1| group 2 sigma-70 RNA polymerase sigma factor E [Cyanothece sp. ATCC
           51142]
          Length = 374

 Score = 89.0 bits (219), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 73/244 (29%), Positives = 124/244 (50%), Gaps = 15/244 (6%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           +R H   +A  +++ S+LRLVV IA  Y   G+P  +++ EG IGL +A +KFDP +G++
Sbjct: 128 HRLHRGRTAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPNKGYK 187

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      +++     +K     L +LK   + +     +     
Sbjct: 188 FSTYAYWWIRQAITRTIANDARTIRLPIHVVEK-----LNKLKKAQRVLKQKLQRNPNEK 242

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ--EQVLIEK 218
            +A +L VS S++  +        SLN  +   +   ++  D L+ D D Q  E+++ E 
Sbjct: 243 ELADELEVSPSQLRQLLQLRRQSLSLNHRVGKGE--DTELVD-LLEDQDLQLPEELMNEG 299

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARA 276
             R     +L+    VL  RE+ +   R       P TLE +   F +SRERVRQI+++A
Sbjct: 300 MLRYEVSAVLS---DVLTQREKDVISLRYGLCTSQPHTLEEVGGIFNLSRERVRQIQSKA 356

Query: 277 FKKV 280
            +K+
Sbjct: 357 MRKL 360


>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 = 89.0 bits (219), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 116/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 377 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 436

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 437 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPED 494

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   Q  I+   
Sbjct: 495 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDSTMQSPIDVAT 538

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ +      +S L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 539 VESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 598

Query: 279 KVQ 281
           K++
Sbjct: 599 KLR 601


>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 = 89.0 bits (219), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 68/243 (27%), Positives = 118/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 381 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 440

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 441 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPED 498

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 499 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 542

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ ++     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 543 SESLKSATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 602

Query: 279 KVQ 281
           K++
Sbjct: 603 KLR 605


>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 = 89.0 bits (219), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 64/245 (26%), Positives = 114/245 (46%), Gaps = 32/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 406 AKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 465

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+   +   T     P +   +A+++++
Sbjct: 466 IRQAITRSIADQARTIRI--PVHMIETINKMNRISRQILQETGAEPDPAE---LARRMDM 520

Query: 169 SESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            E ++          ISM   +  D+  +      D  +    D  +Y            
Sbjct: 521 PEDKIRKIMKISKEPISMETPIGDDDDSHLGDFIEDLATMAPSDAAMY------------ 568

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARA 276
               + +      +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A
Sbjct: 569 ---ASLKEATKEVLDSLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKA 625

Query: 277 FKKVQ 281
            +K++
Sbjct: 626 LRKLR 630


>gi|194699556|gb|ACF83862.1| unknown [Zea mays]
 gi|223944677|gb|ACN26422.1| unknown [Zea mays]
          Length = 496

 Score = 89.0 bits (219), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 74/253 (29%), Positives = 128/253 (50%), Gaps = 40/253 (15%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L  S+ RLV+ IA  Y   G+ + +++  G IGL++ ++KFD  RGFR++TY  WWI+  
Sbjct: 257 LAMSNTRLVISIAQKYDNLGVELPDLIQGGLIGLLRGIEKFDASRGFRISTYVYWWIRQG 316

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES- 171
           +   +  +    ++ T  +++     L  ++G   A+ D  + P  V  IA+ LN+SE  
Sbjct: 317 VSRALADNSRSFRLPTYLHER-----LVAIRGAKYALEDQGIAP-TVENIAESLNISEKK 370

Query: 172 ---------EVISMNCR-------LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
                    +VIS++ +       L GD +L++ I   +  +  W       H  +E+ L
Sbjct: 371 VHNATEAVHKVISLDQQAFPSLNGLPGD-TLHSYIEDQNVANDPW-------HGFEERYL 422

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPVTLENLSSEFEVSRERVRQIEA 274
             KEE  +  N      S LN RER I      + +   T E++S +F +SRERVRQ+  
Sbjct: 423 --KEEVNSLIN------STLNERERDIIRLYHGIGKQCHTWEDISRQFGLSRERVRQVGL 474

Query: 275 RAFKKVQESIQKQ 287
            A +K++ + +++
Sbjct: 475 VAMEKLKHAARRE 487


>gi|182416400|ref|YP_001821466.1| RpoD family RNA polymerase sigma factor [Opitutus terrae PB90-1]
 gi|177843614|gb|ACB77866.1| RNA polymerase, sigma 70 subunit, RpoD family [Opitutus terrae
           PB90-1]
          Length = 640

 Score = 89.0 bits (219), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 74/245 (30%), Positives = 116/245 (47%), Gaps = 34/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+  RG++ +TY+ WW
Sbjct: 337 AKTEMVEANLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWW 396

Query: 109 IKAAMQEYILRSWSLVKIGT----TAN-----QKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N     QK+L           +   + NL  E+V
Sbjct: 397 IRQAITRSIADQARTIRIPVHMIETLNKVMQVQKQLLQEYGHEPTPEEVADEMNLPVERV 456

Query: 160 VAIAKKLNVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
             I K       + IS+   +    D S    I   DK++    D   +       +L E
Sbjct: 457 QQIMKMAQ----QPISLQSPVGDGDDTSFGDFIE--DKSAENPYDMTAF------SLLRE 504

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEAR 275
           K         +   +  L  RERR+   R   +     TLE +  +F+V+RER+RQIEA+
Sbjct: 505 K---------IIDVLDSLTERERRVLSLRFGLIDGYSRTLEEVGKQFKVTRERIRQIEAK 555

Query: 276 AFKKV 280
           A +K+
Sbjct: 556 ALRKM 560


>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 = 89.0 bits (219), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 116/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 438 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPED 495

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   Q  I+   
Sbjct: 496 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDSTMQSPIDVAT 539

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ +      +S L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 540 VESLKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 279 KVQ 281
           K++
Sbjct: 600 KLR 602


>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 = 89.0 bits (219), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 64/234 (27%), Positives = 119/234 (50%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 385 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 444

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   +A+++ +
Sbjct: 445 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREASPEE---LAERMGM 499

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ +   
Sbjct: 500 PEDKIRKV-LKIAK-EPISMETPIGDDDDSHLGDFI---EDSTLELPLDSATAQSLKAAT 554

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 555 HEVLEGLTSREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 608


>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 = 89.0 bits (219), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 68/243 (27%), Positives = 118/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 381 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 440

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 441 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPED 498

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 499 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 542

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ ++     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 543 SESLKSATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 602

Query: 279 KVQ 281
           K++
Sbjct: 603 KLR 605


>gi|330812146|ref|YP_004356608.1| RNA polymerase sigma factor (sigma-70) [Pseudomonas brassicacearum
           subsp. brassicacearum NFM421]
 gi|327380254|gb|AEA71604.1| RNA polymerase sigma factor (sigma-70) [Pseudomonas brassicacearum
           subsp. brassicacearum NFM421]
          Length = 615

 Score = 89.0 bits (219), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 116/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 377 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 436

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 437 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPED 494

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   Q  I+   
Sbjct: 495 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDSTMQSPIDVAT 538

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ +      +S L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 539 VESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 598

Query: 279 KVQ 281
           K++
Sbjct: 599 KLR 601


>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|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]
          Length = 618

 Score = 89.0 bits (219), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 380 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 439

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 440 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPSPEELAERMLMPED- 497

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 498 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 540

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     +  L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 541 TSESLRSATHEVLGGLTLREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 600

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 601 RKLRHPSRSEV 611


>gi|312963434|ref|ZP_07777916.1| sigma-70 [Pseudomonas fluorescens WH6]
 gi|311282240|gb|EFQ60839.1| sigma-70 [Pseudomonas fluorescens WH6]
          Length = 616

 Score = 89.0 bits (219), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 116/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 438 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPED 495

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   Q  I+   
Sbjct: 496 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDSTMQSPIDVAT 539

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ +      +S L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 540 VESLKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 279 KVQ 281
           K++
Sbjct: 600 KLR 602


>gi|255066480|ref|ZP_05318335.1| RNA polymerase sigma factor RpoD [Neisseria sicca ATCC 29256]
 gi|255049360|gb|EET44824.1| RNA polymerase sigma factor RpoD [Neisseria sicca ATCC 29256]
          Length = 649

 Score = 89.0 bits (219), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 70/252 (27%), Positives = 120/252 (47%), Gaps = 44/252 (17%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 405 AAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 464

Query: 108 WIKAAMQEYILRSWSLVKIG-----TTANQKRLFFNLRRLKG---------HLQAITDNN 153
           WI+ A+   I      ++I      T     R+     +  G          L  + ++ 
Sbjct: 465 WIRQAITRSIADQARTIRIPVHMIETINKMNRISRQYLQETGEEPDSAKLAELMEMPEDK 524

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQ 211
           ++  +++ IAK       E ISM   +  D+  +      D N+    D  +Y   H+  
Sbjct: 525 IR--KIMKIAK-------EPISMETPIGDDDDSHLGDFIEDANNVAPADAAMYTSLHEVT 575

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERV 269
           +++L                   L PRE ++   R  +  N   TLE +  +F+V+RER+
Sbjct: 576 KEIL-----------------ESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 618

Query: 270 RQIEARAFKKVQ 281
           RQIEA+A +K++
Sbjct: 619 RQIEAKALRKLR 630


>gi|111023771|ref|YP_706743.1| RNA polymerase sigma factor SigB [Rhodococcus jostii RHA1]
 gi|110823301|gb|ABG98585.1| sigma factor, sigma 70 type, group 2 (proven non-essential)
           [Rhodococcus jostii RHA1]
          Length = 323

 Score = 89.0 bits (219), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 72/248 (29%), Positives = 124/248 (50%), Gaps = 32/248 (12%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           SA   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ W
Sbjct: 85  SARAHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTYATW 144

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA-----ITDNNLKPEQVVA- 161
           WI+ A+   +      +++     ++     L R+K  L        TD+ L  E  +  
Sbjct: 145 WIRQAITRGMADQSRTIRLPVHLVEQ--VNKLARIKRELHQQLGREATDDELAEESGIPA 202

Query: 162 --IAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
             IA  L+ S   V S++  +  DE   L   I  S+  S+             E  +I 
Sbjct: 203 HKIADLLDHSRDPV-SLDMPVGNDEEAPLGDFIEDSEATSA-------------ENAVIA 248

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
                + R++L    + L+ RE+++   R   ++  P TL+ +   F +SRERVRQIE  
Sbjct: 249 GLLHSDVRSVL----ATLDEREQQVIRLRYGLDDGQPRTLDQIGKLFGLSRERVRQIERE 304

Query: 276 AFKKVQES 283
              K+++ 
Sbjct: 305 VMGKLRQG 312


>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 = 89.0 bits (219), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 116/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 438 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPED 495

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   Q  I+   
Sbjct: 496 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDSTMQSPIDVAT 539

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ +      +S L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 540 VESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 279 KVQ 281
           K++
Sbjct: 600 KLR 602


>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 = 89.0 bits (219), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 64/235 (27%), Positives = 119/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 360 AKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 419

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         P+++ A   ++++
Sbjct: 420 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPDELAA---RMDM 474

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E +V  +  ++A  E ++      D + S   D++    D +    +E     + R   
Sbjct: 475 PEDKVRKV-MKIAK-EPISMETPIGDDDDSHLGDFI---EDSRVLSPVEHATVASLRETT 529

Query: 229 TRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            + ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 530 QQVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 584


>gi|70732951|ref|YP_262722.1| RNA polymerase sigma factor RpoD [Pseudomonas fluorescens Pf-5]
 gi|1710687|sp|P52326|RPOD_PSEFL RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|929808|emb|CAA59134.1| sigma 70 [Pseudomonas fluorescens]
 gi|68347250|gb|AAY94856.1| RNA polymerase sigma factor RpoD [Pseudomonas fluorescens Pf-5]
          Length = 615

 Score = 89.0 bits (219), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 116/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 377 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 436

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 437 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPED 494

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   Q  I+   
Sbjct: 495 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDSTMQSPIDVAT 538

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ +      +S L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 539 VESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 598

Query: 279 KVQ 281
           K++
Sbjct: 599 KLR 601


>gi|330898880|gb|EGH30299.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. japonica
           str. M301072PT]
 gi|330980978|gb|EGH79081.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. aptata
           str. DSM 50252]
          Length = 616

 Score = 89.0 bits (219), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 116/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 438 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPED 495

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   Q  I+   
Sbjct: 496 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDSTMQSPIDVAT 539

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ +      +S L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 540 VESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 279 KVQ 281
           K++
Sbjct: 600 KLR 602


>gi|124025343|ref|YP_001014459.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. NATL1A]
 gi|123960411|gb|ABM75194.1| Putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus str. NATL1A]
          Length = 307

 Score = 89.0 bits (219), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 73/255 (28%), Positives = 129/255 (50%), Gaps = 13/255 (5%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           EY  A++ R      A ++++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+
Sbjct: 50  EYSSAEKKRFKAGERAKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKY 109

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           DP+RG R +TY+ WWI+  +   +      ++I    N+K     LR  K  L  + +  
Sbjct: 110 DPKRGHRFSTYAYWWIRQGLNRALSTQSRTIRIPVNINEK--LTKLRAAKSRL--MQELG 165

Query: 154 LKPE-QVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQ 211
           + P    +AI  K+ + E E + + C L     SL   +  S  + S+  D L  +    
Sbjct: 166 VHPSTNQIAIQMKIPLEEVEEL-LACELRSITVSLQGAVK-SKADPSELVDILPSEEVPP 223

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRER 268
            ++    E   +  ++L +S   L P+ER I   R   +      TL  ++ +   SRE 
Sbjct: 224 MELAELAERSASAWSLLDKSN--LTPKERTILSLRFGLDGSNEWRTLAEVARQMNCSREY 281

Query: 269 VRQIEARAFKKVQES 283
            RQ+  RA +K++++
Sbjct: 282 CRQVVQRALRKLRKT 296


>gi|226366207|ref|YP_002783990.1| RNA polymerase sigma factor SigB [Rhodococcus opacus B4]
 gi|226244697|dbj|BAH55045.1| RNA polymerase sigma factor SigB [Rhodococcus opacus B4]
 gi|254553060|dbj|BAH85842.1| RNA polymerase sigma B factor [Rhodococcus opacus]
          Length = 323

 Score = 89.0 bits (219), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 72/248 (29%), Positives = 123/248 (49%), Gaps = 32/248 (12%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           SA   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ W
Sbjct: 85  SARAHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTYATW 144

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA-----ITDNNLKPEQVVA- 161
           WI+ A+   +      +++     ++     L R+K  L        TD+ L  E  +  
Sbjct: 145 WIRQAITRGMADQSRTIRLPVHLVEQ--VNKLARIKRELHQQLGREATDDELAEESGIPA 202

Query: 162 --IAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
             IA  L+ S   V S++  +  DE   L   I  S+  S+             E  +I 
Sbjct: 203 HKIADLLDHSRDPV-SLDMPVGNDEEAPLGDFIEDSEATSA-------------ENAVIA 248

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
                + R +L    + L+ RE+++   R   ++  P TL+ +   F +SRERVRQIE  
Sbjct: 249 GLLHSDVRTVL----ATLDEREQQVIRLRYGLDDGQPRTLDQIGKLFGLSRERVRQIERE 304

Query: 276 AFKKVQES 283
              K+++ 
Sbjct: 305 VMGKLRQG 312


>gi|325264732|ref|ZP_08131461.1| RNA polymerase sigma factor RpoD [Clostridium sp. D5]
 gi|324030024|gb|EGB91310.1| RNA polymerase sigma factor RpoD [Clostridium sp. D5]
          Length = 292

 Score = 88.6 bits (218), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 85/282 (30%), Positives = 138/282 (48%), Gaps = 28/282 (9%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ EI +I  L   EE  L K+  E GD  A  +L  S L LVV IA  Y G GL  
Sbjct: 29  LKIYLKEIGQISPLSSGEELELGKKIAE-GDEGAKLKLEESALCLVVSIAGQYSGRGLLF 87

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLMQA +K+D  +    + Y+  WI+ A++  +      +++     +   
Sbjct: 88  MDLIQEGNIGLMQAAEKYDYTKDGGFSGYARRWIEDAIKHAVDEQSREIRVPAYVAE--- 144

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKL-NVSESEVISMNCRLAGDESLNALINSSD 194
             N+++++     +     +      IA KL + SE E+ S+   L    SL+A +   D
Sbjct: 145 --NMKKVQKAAYELQQELGREATAGEIAGKLGDKSEEEIESILTFLKNPVSLDAPVEDGD 202

Query: 195 KNSSQWQDWLVYDHDGQEQV-------LIEKEERKNRRNMLTRSMSVLNPRERRIFEAR- 246
             +   +D +    D +E+        LI+KEE       +   +  L+ +ER++   R 
Sbjct: 203 DEN--LEDTIA---DREEKTPEDAVNSLIQKEE-------VLHLLESLSEKERQVISKRF 250

Query: 247 RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            L++  V TLE +  E  VSRER+ QIE  A KK++++  K+
Sbjct: 251 GLEDGRVHTLEEVGQELNVSRERISQIEEHAMKKLRQAAGKE 292


>gi|325962990|ref|YP_004240896.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Arthrobacter
           phenanthrenivorans Sphe3]
 gi|323469077|gb|ADX72762.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Arthrobacter
           phenanthrenivorans Sphe3]
          Length = 437

 Score = 88.6 bits (218), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 72/275 (26%), Positives = 130/275 (47%), Gaps = 40/275 (14%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P  +++ E+++      H    A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL
Sbjct: 184 PKYKRELEFII------HDGKRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGL 237

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT---------TANQKRLFF 137
           ++AV+KFD  +GF+ +TY+ WWI+ A+   +      ++I              Q+++  
Sbjct: 238 IRAVEKFDYTKGFKFSTYATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQ 297

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDK 195
           +L R     +   + ++ PE+VV + K       E IS++  L   GD     LI  S+ 
Sbjct: 298 DLGREPTPEELALELDMTPEKVVEVQK----YGREPISLHTPLGEDGDSEFGDLIEDSEA 353

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPV 253
                    V   D     L++++        L   +  L+ RE  +   R       P 
Sbjct: 354 ---------VVPADAVSFTLLQEQ--------LHSVLDTLSEREAGVVAMRFGLTDGQPK 396

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           TL+ +   + V+RER+RQIE++   K++   + QV
Sbjct: 397 TLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQV 431


>gi|57864855|gb|AAW57030.1| putative group 2 RNA polymerase sigma factor [Cyanothece sp. ATCC
           51142]
          Length = 368

 Score = 88.6 bits (218), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 73/244 (29%), Positives = 124/244 (50%), Gaps = 15/244 (6%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           +R H   +A  +++ S+LRLVV IA  Y   G+P  +++ EG IGL +A +KFDP +G++
Sbjct: 122 HRLHRGRTAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPNKGYK 181

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      +++     +K     L +LK   + +     +     
Sbjct: 182 FSTYAYWWIRQAITRTIANDARTIRLPIHVVEK-----LNKLKKAQRVLKQKLQRNPNEK 236

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ--EQVLIEK 218
            +A +L VS S++  +        SLN  +   +   ++  D L+ D D Q  E+++ E 
Sbjct: 237 ELADELEVSPSQLRQLLQLRRQSLSLNHRVGKGE--DTELVD-LLEDQDLQLPEELMNEG 293

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARA 276
             R     +L+    VL  RE+ +   R       P TLE +   F +SRERVRQI+++A
Sbjct: 294 MLRYEVSAVLS---DVLTQREKDVISLRYGLCTSQPHTLEEVGGIFNLSRERVRQIQSKA 350

Query: 277 FKKV 280
            +K+
Sbjct: 351 MRKL 354


>gi|256825489|ref|YP_003149449.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Kytococcus sedentarius
           DSM 20547]
 gi|256688882|gb|ACV06684.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Kytococcus sedentarius
           DSM 20547]
          Length = 594

 Score = 88.6 bits (218), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 80/309 (25%), Positives = 141/309 (45%), Gaps = 60/309 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH----GDL-----------------SAAHR 52
           Y+ +I K+ +L  ++E  LAKR     + E     GD                  +A + 
Sbjct: 301 YLKQIGKVALLNAEQEVDLAKRIEAGLFAEQRLNSGDKIDAKLKRELWWVASDGKNAKNH 360

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A
Sbjct: 361 LLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQA 420

Query: 113 MQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           +   +      ++I              Q+++  +L R     +   + ++ PE+VV + 
Sbjct: 421 ITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQ 480

Query: 164 KKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           K       E IS++  L   GD     LI  S+          V   D     L++++  
Sbjct: 481 K----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPSDAVSFTLLQEQ-- 525

Query: 222 KNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
                 L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K
Sbjct: 526 ------LHSVLDTLSEREAGVVSMRFGLADGQPKTLDEIGRVYGVTRERIRQIESKTMSK 579

Query: 280 VQESIQKQV 288
           ++   + QV
Sbjct: 580 LRHPSRSQV 588


>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 = 88.6 bits (218), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 70/252 (27%), Positives = 120/252 (47%), Gaps = 44/252 (17%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 405 AAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 464

Query: 108 WIKAAMQEYILRSWSLVKIG-----TTANQKRLFFNLRRLKG---------HLQAITDNN 153
           WI+ A+   I      ++I      T     R+     +  G          L  + ++ 
Sbjct: 465 WIRQAITRSIADQARTIRIPVHMIETINKMNRISRQYLQETGEEPDSAKLAELMEMPEDK 524

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQ 211
           ++  +++ IAK       E ISM   +  D+  +      D N+    D  +Y   H+  
Sbjct: 525 IR--KIMKIAK-------EPISMETPIGDDDDSHLGDFIEDANNVAPADAAMYTSLHEVT 575

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERV 269
           +++L                   L PRE ++   R  +  N   TLE +  +F+V+RER+
Sbjct: 576 KEIL-----------------ESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERI 618

Query: 270 RQIEARAFKKVQ 281
           RQIEA+A +K++
Sbjct: 619 RQIEAKALRKLR 630


>gi|327479259|gb|AEA82569.1| RNA polymerase sigma factor RpoD [Pseudomonas stutzeri DSM 4166]
          Length = 617

 Score = 88.6 bits (218), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 71/242 (29%), Positives = 115/242 (47%), Gaps = 28/242 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 379 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 438

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 439 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPED 496

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   Q  I+   
Sbjct: 497 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDSAMQSPIDVAT 540

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ +      +S L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 541 VESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 600

Query: 279 KV 280
           K+
Sbjct: 601 KL 602


>gi|319425507|gb|ADV53581.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella putrefaciens
           200]
          Length = 613

 Score = 88.6 bits (218), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 68/243 (27%), Positives = 118/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 435 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPED 492

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 493 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 536

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ ++     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 537 SESLKSATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 596

Query: 279 KVQ 281
           K++
Sbjct: 597 KLR 599


>gi|308177806|ref|YP_003917212.1| RNA polymerase sigma factor RpoD [Arthrobacter arilaitensis Re117]
 gi|307745269|emb|CBT76241.1| RNA polymerase sigma factor RpoD [Arthrobacter arilaitensis Re117]
          Length = 403

 Score = 88.6 bits (218), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 69/253 (27%), Positives = 121/253 (47%), Gaps = 34/253 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WW
Sbjct: 166 AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 225

Query: 109 IKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   +      ++I              Q+++  +L R     +   + ++ PE+V
Sbjct: 226 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 285

Query: 160 VAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           V + K       E IS++  L   GD     LI  S+          V   D     L++
Sbjct: 286 VEVQK----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQ 332

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEAR 275
           ++        L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++
Sbjct: 333 EQ--------LHSVLDTLSEREAGVVAMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESK 384

Query: 276 AFKKVQESIQKQV 288
              K++   + QV
Sbjct: 385 TMSKLRHPSRSQV 397


>gi|307153454|ref|YP_003888838.1| RpoD subfamily RNA polymerase sigma-70 factor [Cyanothece sp. PCC
           7822]
 gi|306983682|gb|ADN15563.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7822]
          Length = 372

 Score = 88.6 bits (218), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 71/242 (29%), Positives = 120/242 (49%), Gaps = 25/242 (10%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  +++ S+LRLVV IA  Y   G+P  +++ EG IGL +A +KFDP +G++ +TY+ W
Sbjct: 133 AAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPNKGYKFSTYAYW 192

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+              T AN  R      RL  H+    +   K ++V+      N
Sbjct: 193 WIRQAITR------------TIANDARTI----RLPIHIVEKLNKLKKAQRVLKQQLHRN 236

Query: 168 VSESEV---ISMNC-RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE---E 220
            +E E+   + ++C  L     L     S +    + +D  + D    E++ + +E   E
Sbjct: 237 PTEQELAQALEIDCEHLRQLLQLRRQSLSLNHRVGKGEDTELVDLLEDEELQLPEEKMNE 296

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFK 278
              R+++      VL  RE+ +   R   +   P TLE +   F +SRERVRQI+++A +
Sbjct: 297 AMMRQDIAAVLTDVLTEREKDVIALRYGLITSQPYTLEEVGGIFNLSRERVRQIQSKAMR 356

Query: 279 KV 280
           K+
Sbjct: 357 KL 358


>gi|222034799|emb|CAP77541.1| RNA polymerase sigma factor rpoD [Escherichia coli LF82]
          Length = 613

 Score = 88.6 bits (218), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 435 IRQAITRSIAVQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 492

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 493 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 535

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A 
Sbjct: 536 TTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKAL 595

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 596 RKLRHPSRSEV 606


>gi|33340521|gb|AAQ14856.1| RpoD [Pseudomonas fluorescens]
          Length = 616

 Score = 88.6 bits (218), Expect = 9e-16,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 116/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 438 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPED 495

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   Q  I+   
Sbjct: 496 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDSTMQSPIDVAT 539

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ +      +S L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 540 VESLKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 279 KVQ 281
           K++
Sbjct: 600 KLR 602


>gi|227499199|ref|ZP_03929334.1| RNA polymerase [Acidaminococcus sp. D21]
 gi|226904646|gb|EEH90564.1| RNA polymerase [Acidaminococcus sp. D21]
          Length = 582

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 73/235 (31%), Positives = 115/235 (48%), Gaps = 13/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L  ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WW
Sbjct: 344 AKKALSEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYNKGFKFSTYATWW 403

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   L         PE+   IA++++V
Sbjct: 404 IRQAITRAIADQARTIRI--PVHMVETINKLVRVSRQLLQELGREPTPEE---IAQEMDV 458

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
               V  +        SL   I   ++  S   D++    D +     E       +  L
Sbjct: 459 PVERVREIQKIAQEPVSLETPIG--EEEDSHLGDFI---EDQEAPSPAEAASYTLLQEQL 513

Query: 229 TRSMSV-LNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            + +   L+PRERR+ E R   L     TLE +   F V+RER+RQIEA+A +K+
Sbjct: 514 GKVLQEHLSPRERRVLELRFGLLDGRTRTLEEVGQYFGVTRERIRQIEAKALRKL 568


>gi|13357909|ref|NP_078183.1| RNA polymerase sigma factor [Ureaplasma parvum serovar 3 str. ATCC
           700970]
 gi|170762330|ref|YP_001752432.1| RNA polymerase sigma factor [Ureaplasma parvum serovar 3 str. ATCC
           27815]
 gi|11357048|pir||E82901 RNA polymerase sigma factor UU349 [imported] - Ureaplasma
           urealyticum
 gi|6899329|gb|AAF30758.1|AE002132_2 RNA polymerase sigma factor [Ureaplasma parvum serovar 3 str. ATCC
           700970]
 gi|168827907|gb|ACA33169.1| RNA polymerase sigma factor [Ureaplasma parvum serovar 3 str. ATCC
           27815]
          Length = 448

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 70/254 (27%), Positives = 124/254 (48%), Gaps = 40/254 (15%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           ++L TS++RLV  IA  Y   GL + +++ EG+ GL++A+ KFD E+G + +TY+ WWI+
Sbjct: 195 NQLYTSNMRLVTSIAKKYLNRGLDLEDLIQEGSSGLLKAIDKFDHEKGHKFSTYATWWIR 254

Query: 111 AAMQEYILRSWSLVKIGT---------TANQKRLFFNLRR------LKGHLQAITDNNLK 155
            ++   I      ++I           T  ++ L   L R      +   +  ++    +
Sbjct: 255 QSITRAIADQARQIRIPVHMVETINKLTKAERNLIQELGRDPTAEEIAQAMNKVSQAKNQ 314

Query: 156 PEQVVAIA-----KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
            EQ++        KKLNV   + +S++ ++  DE             SQ+ D++  D   
Sbjct: 315 KEQLITAQKVVEIKKLNV---DPVSLDKQIGHDE------------ESQFSDFISDDEII 359

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ---ENPVTLENLSSEFEVSRE 267
             +   EK+   ++ N +     VLN  E+R+ + R      E P TLE +     V+RE
Sbjct: 360 SPEKYTEKKALNDQINEMFE--KVLNDNEQRVIKMRYGLLPFERPYTLEEVGEYLGVTRE 417

Query: 268 RVRQIEARAFKKVQ 281
           R RQIE++A +K++
Sbjct: 418 RARQIESKAIRKLK 431


>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 = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 69/244 (28%), Positives = 116/244 (47%), Gaps = 32/244 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +        +PE++         
Sbjct: 438 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPQPEELAERMEMPED 495

Query: 161 AIAKKLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            I K L +++ E ISM   +  DE   L   I  S  +S                  ++ 
Sbjct: 496 KIRKVLKIAK-EPISMETPIGDDEDSHLGDFIEDSTIDSP-----------------VDA 537

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARA 276
              ++ + +    ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A
Sbjct: 538 ATGESLKEVTDEILAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 597

Query: 277 FKKV 280
            +K+
Sbjct: 598 LRKL 601


>gi|3769432|gb|AAC78468.1| RNA polymerase sigma factor 2 [Zea mays]
          Length = 349

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 72/253 (28%), Positives = 128/253 (50%), Gaps = 40/253 (15%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L  S++RLV+ IA  Y   G+ +++++  G IGL++ ++KFD  RGFR++TY  WWI+  
Sbjct: 110 LTMSNIRLVISIAHKYDNLGVDLADLIQGGLIGLLRGIEKFDASRGFRISTYVYWWIRQG 169

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES- 171
           +   +  +    ++ T  +++     L  ++G   A+ D  + P  +  IA+ LN+S   
Sbjct: 170 VSRALADNSKTFRLPTYLHER-----LLAIRGAKYALEDQGIAP-TIENIAESLNISVKK 223

Query: 172 ---------EVISMNCR-------LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
                    +V+S++ +       L GD +L++ I   +  +  W       H  +E  L
Sbjct: 224 VHNATEAVHKVLSLDQQAFPSLNGLPGD-TLHSYIEDQNVANDPW-------HGFEEMYL 275

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPVTLENLSSEFEVSRERVRQIEA 274
             KEE  N  N      S LN RER I      + +   T E++S +F +SRERVRQ+  
Sbjct: 276 --KEEVNNLIN------SNLNERERDIIRLYHGIGKQCHTWEDISRQFGLSRERVRQVRL 327

Query: 275 RAFKKVQESIQKQ 287
            A +K++ + +++
Sbjct: 328 VAMEKLKHAARRK 340


>gi|159903122|ref|YP_001550466.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9211]
 gi|159888298|gb|ABX08512.1| Putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus str. MIT 9211]
          Length = 312

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 72/246 (29%), Positives = 124/246 (50%), Gaps = 25/246 (10%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A ++++TS+LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP+RG R +TY+ WW
Sbjct: 65  AKNQMITSNLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPKRGHRFSTYAYWW 124

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   +      ++I    N+K     LR  K  L  +  N L P   + +AKK+++
Sbjct: 125 IRQGLNRALSTQSRTIRIPVNINEK--LTKLRAAKSQL--MQANGLTPSSEM-LAKKMHL 179

Query: 169 SESEVI--------SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
           S+ EV         S+   L G       +  S  + S+  D L  +     +V    E 
Sbjct: 180 SKEEVEELLECELRSITVSLQG-------VVQSKSDPSELGDVLPSEEIPPMEVAELAER 232

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAF 277
             +  ++L ++   L P+ER I   R   +      TL  ++     SRE  RQ+  RA 
Sbjct: 233 NDSAWSLLNKAN--LTPKERTIVSLRFGLDGSNEWRTLAEVAKHMNCSREYCRQVVQRAL 290

Query: 278 KKVQES 283
           +K++++
Sbjct: 291 RKLRKT 296


>gi|269794902|ref|YP_003314357.1| RNA polymerase sigma-70 subunit RpoD [Sanguibacter keddieii DSM
           10542]
 gi|269097087|gb|ACZ21523.1| RNA polymerase, sigma 70 subunit, RpoD [Sanguibacter keddieii DSM
           10542]
          Length = 516

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 81/311 (26%), Positives = 141/311 (45%), Gaps = 63/311 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHG----------DLS------------------AA 50
           Y+ +I K+ +L  ++E  LAKR  E G          D S                  A 
Sbjct: 222 YLKQIGKVALLNAEQEVDLAKRI-EAGLFAEERLSAPDASFAPKARRELEWIAGDGRRAK 280

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+
Sbjct: 281 NHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIR 340

Query: 111 AAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
            A+   +      ++I              Q+++  +L R     +   + ++ PE+VV 
Sbjct: 341 QAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVE 400

Query: 162 IAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           + K       E IS++  L   GD     LI  S+          V   D     L++++
Sbjct: 401 VQK----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ 447

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAF 277
                   L + +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++  
Sbjct: 448 --------LHQVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTM 499

Query: 278 KKVQESIQKQV 288
            K++   + QV
Sbjct: 500 SKLRHPSRSQV 510


>gi|3646419|emb|CAA07705.1| sigma-70 factor [Pseudomonas tolaasii]
          Length = 616

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 116/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 438 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPED 495

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   Q  I+   
Sbjct: 496 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDSTMQSPIDVAT 539

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ +      +S L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 540 VESLKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 279 KVQ 281
           K++
Sbjct: 600 KLR 602


>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 = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 68/243 (27%), Positives = 117/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 382 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 441

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 442 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPSPEELAERMAMPED 499

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 500 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 543

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ +      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 544 SESLKQATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 603

Query: 279 KVQ 281
           K++
Sbjct: 604 KLR 606


>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 = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 67/235 (28%), Positives = 117/235 (49%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 376 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 435

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   + ++L +
Sbjct: 436 IRQAITRSIADQARTIRI--PVHMIETINKLNRVSRQMLQEMGREPTPEE---LGERLEM 490

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E +V  +  ++A  E ++      D + S   D++    DG   + I+    +      
Sbjct: 491 PEDKVRKV-LKIA-KEPISMETPIGDDDDSHLGDFI---EDGTMLLPIDSATGEGLIEAT 545

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 546 RNVLGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>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 = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 68/236 (28%), Positives = 123/236 (52%), Gaps = 14/236 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  +++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 411 AAKQKMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 470

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I     +     N R  + +LQ   ++   P+    +A+ + 
Sbjct: 471 WIRQAITRSIADQARTIRIPVHMIETINKMN-RISRQYLQETGED---PDS-AKLAELME 525

Query: 168 VSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           + E ++  +  ++A +  S+ + I   D + S   D++    D       E     + R 
Sbjct: 526 MPEDKIRKI-MKIAKEPISMESPI--GDDDDSHLGDFI---EDVNNVAPAEAAMYSSLRE 579

Query: 227 MLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
           +    +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 580 VTAGVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 635


>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 = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 116/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 438 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPED 495

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   Q  I+   
Sbjct: 496 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDSTMQSPIDVAT 539

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ +      +S L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 540 VESLKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 279 KVQ 281
           K++
Sbjct: 600 KLR 602


>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 = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 68/243 (27%), Positives = 118/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 438 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPSPEELAERMMMPED 495

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 496 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 539

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ ++     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 540 SESLKSATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 279 KVQ 281
           K++
Sbjct: 600 KLR 602


>gi|171920395|ref|ZP_02931720.1| RNA polymerase sigma factor [Ureaplasma parvum serovar 1 str. ATCC
           27813]
 gi|183508771|ref|ZP_02958238.1| RNA polymerase sigma factor [Ureaplasma parvum serovar 14 str. ATCC
           33697]
 gi|186701631|ref|ZP_02971335.1| RNA polymerase sigma factor [Ureaplasma parvum serovar 6 str. ATCC
           27818]
 gi|171902833|gb|EDT49122.1| RNA polymerase sigma factor [Ureaplasma parvum serovar 1 str. ATCC
           27813]
 gi|182675710|gb|EDT87615.1| RNA polymerase sigma factor [Ureaplasma parvum serovar 14 str. ATCC
           33697]
 gi|186700864|gb|EDU19146.1| RNA polymerase sigma factor [Ureaplasma parvum serovar 6 str. ATCC
           27818]
          Length = 448

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 70/254 (27%), Positives = 124/254 (48%), Gaps = 40/254 (15%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           ++L TS++RLV  IA  Y   GL + +++ EG+ GL++A+ KFD E+G + +TY+ WWI+
Sbjct: 195 NQLYTSNMRLVTSIAKKYLNRGLDLEDLIQEGSSGLLKAIDKFDHEKGHKFSTYATWWIR 254

Query: 111 AAMQEYILRSWSLVKIGT---------TANQKRLFFNLRR------LKGHLQAITDNNLK 155
            ++   I      ++I           T  ++ L   L R      +   +  ++    +
Sbjct: 255 QSITRAIADQARQIRIPVHMVETINKLTKAERNLIQELGRDPTAEEIAQAMNKVSQAKNQ 314

Query: 156 PEQVVAIA-----KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
            EQ++        KKLNV   + +S++ ++  DE             SQ+ D++  D   
Sbjct: 315 KEQLITAQKVVEIKKLNV---DPVSLDKQIGHDE------------ESQFSDFISDDEII 359

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ---ENPVTLENLSSEFEVSRE 267
             +   EK+   ++ N +     VLN  E+R+ + R      E P TLE +     V+RE
Sbjct: 360 SPEKYTEKKALNDQINEMFE--KVLNDNEQRVIKMRYGLLPFERPYTLEEVGEYLGVTRE 417

Query: 268 RVRQIEARAFKKVQ 281
           R RQIE++A +K++
Sbjct: 418 RARQIESKAIRKLK 431


>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 = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 68/245 (27%), Positives = 118/245 (48%), Gaps = 32/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 254 AKEEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 313

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I     +     N R  + +LQ   ++   P+    +A+ + +
Sbjct: 314 IRQAITRSIADQARTIRIPVHMIETINKMN-RISRQYLQETGED---PDS-AKLAELMEM 368

Query: 169 SESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            E ++          ISM   +  D+  +      D N+    D  +Y            
Sbjct: 369 PEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDVNNVAPADAAMY------------ 416

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARA 276
               + R +    +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A
Sbjct: 417 ---SSLREVTADVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 473

Query: 277 FKKVQ 281
            +K++
Sbjct: 474 LRKLR 478


>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 = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 116/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 438 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPED 495

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   Q  I+   
Sbjct: 496 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDSTMQSPIDVAT 539

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ +      +S L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 540 VESLKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 279 KVQ 281
           K++
Sbjct: 600 KLR 602


>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 = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 67/235 (28%), Positives = 117/235 (49%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 377 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 436

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   + ++L +
Sbjct: 437 IRQAITRSIADQARTIRI--PVHMIETINKLNRVSRQMLQEMGREPTPEE---LGERLEM 491

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E +V  +  ++A  E ++      D + S   D++    DG   + I+    +      
Sbjct: 492 PEDKVRKV-LKIA-KEPISMETPIGDDDDSHLGDFI---EDGTMVLPIDSATGEGLIEAT 546

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 547 RNVLGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 601


>gi|297520936|ref|ZP_06939322.1| RNA polymerase sigma factor RpoD [Escherichia coli OP50]
          Length = 436

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 72/250 (28%), Positives = 124/250 (49%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 198 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 257

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-KRLFFNLRRLKGH---LQAITDNNLKPEQVV 160
           I+ A+   I      ++I      T N+  R+   + +  G     + + +  L PE   
Sbjct: 258 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPED-- 315

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   ++ ++   
Sbjct: 316 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSAT 359

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            ++ R      ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 360 TESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 419

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 420 KLRHPSRSEV 429


>gi|50954703|ref|YP_061991.1| RNA polymerase sigma factor [Leifsonia xyli subsp. xyli str.
           CTCB07]
 gi|50951185|gb|AAT88886.1| RNA polymerase, sigma-70 family factor [Leifsonia xyli subsp. xyli
           str. CTCB07]
          Length = 440

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 82/309 (26%), Positives = 139/309 (44%), Gaps = 62/309 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRY---------------------RE------HGDLSAAH 51
           Y+ +I K+P+L   EE  LA R                      RE       G  + +H
Sbjct: 147 YLKQIGKVPLLNAAEEVELAMRIEAGLFAEDRLANTPNMPRELERELRWVARDGQRAKSH 206

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ 
Sbjct: 207 -LLGANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQ 265

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+VV +
Sbjct: 266 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELSKELDMTPEKVVEV 325

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI   +          V   D     +++K+ 
Sbjct: 326 QK----YGREPISLHTPLGEDGDSEFGDLIEDIEA---------VVPADAVGFTMLQKQ- 371

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R  L +  P TL+ +   F V+RER+RQIE++   
Sbjct: 372 -------LESLLDSLSEREAGVIRMRFGLGDGMPKTLDQIGDTFGVTRERIRQIESKTMA 424

Query: 279 KVQESIQKQ 287
           K++   + Q
Sbjct: 425 KLRHPSRSQ 433


>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 = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 69/242 (28%), Positives = 115/242 (47%), Gaps = 28/242 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 376 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 435

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 436 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPNPEELAERMMMPED 493

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   +  I+   
Sbjct: 494 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDSTIESPIDSAT 537

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ +      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 538 MESLKGATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 597

Query: 279 KV 280
           K+
Sbjct: 598 KL 599


>gi|224370025|ref|YP_002604189.1| RpoD [Desulfobacterium autotrophicum HRM2]
 gi|223692742|gb|ACN16025.1| RpoD [Desulfobacterium autotrophicum HRM2]
          Length = 618

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 380 AKSELVRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 439

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R   +L         PE+   IA+K+ +
Sbjct: 440 IRQAITRAIADQARTIRI--PVHMIETINKLIRTSRYLVQEMGKEPSPEE---IAEKMEI 494

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      ++  S   D++    D +  +  E     N     
Sbjct: 495 PLDKVRRV-LKIAR-EPISLETPIGEEEDSHLGDFI---EDKKFSLPSEAAINLNLAEQT 549

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            + ++ L PRE ++   R    ++   TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 550 RKVLATLTPREEKVLRMRFGIGEKADHTLEEVGRDFTVTRERIRQIEAKALRKLR 604


>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 = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 116/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 438 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPED 495

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   Q  I+   
Sbjct: 496 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDSTMQSPIDVAT 539

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ +      +S L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 540 VESLKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 279 KVQ 281
           K++
Sbjct: 600 KLR 602


>gi|158335492|ref|YP_001516664.1| RNA polymerase sigma factor [Acaryochloris marina MBIC11017]
 gi|158305733|gb|ABW27350.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 327

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 77/326 (23%), Positives = 142/326 (43%), Gaps = 73/326 (22%)

Query: 4   KNMSIIVNGEIGLSR-YIHEIRKIPMLEKQEEYVLAKR---------------------- 40
           K  +I V+    + R Y+HEI ++P+L  +EE V  K+                      
Sbjct: 7   KQQAISVSPTTDMVRTYLHEIGRVPLLTHEEEIVFGKQVQAMMALLDLQKTVMDELGREP 66

Query: 41  ----YREHGDLS-------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
               + E  +LS             A  +++ ++LRLVV +A  Y+   L + +++ EG 
Sbjct: 67  SLEEWAEKANLSPSQLELSLHQGQQAKQKMIEANLRLVVSVAKKYQKRNLELLDLIQEGT 126

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           +GL + V+KFDP RG++ +TY+ WWI+ A+   I +    +++     +K     L ++K
Sbjct: 127 LGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEK-----LNKIK 181

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRLAGDESLNALINSS 193
              + ++    +      IA+ L +  S++          IS++ R+             
Sbjct: 182 KAQRELSQKLGRSATPAEIAEALELEPSQIRDYLTIARQPISLDLRVG------------ 229

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-- 251
           D   ++ +D L  D    EQ    +  R +   +L      L P++R +   R    N  
Sbjct: 230 DNQDTELRDLLEDDGQSPEQFTTTEALRDDVNQLLKE----LTPQQRDVLMLRFGLNNGK 285

Query: 252 PVTLENLSSEFEVSRERVRQIEARAF 277
            ++L  +  +  +SRERVRQ+E +A 
Sbjct: 286 ELSLAKVGQQLSLSRERVRQLERQAL 311


>gi|81299483|ref|YP_399691.1| RNA polymerase sigma factor SigD [Synechococcus elongatus PCC 7942]
 gi|123557285|sp|Q31QG5|RPOD3_SYNE7 RecName: Full=RNA polymerase sigma factor rpoD3
 gi|81168364|gb|ABB56704.1| group2 RNA polymerase sigma factor SigD [Synechococcus elongatus
           PCC 7942]
          Length = 320

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 74/308 (24%), Positives = 143/308 (46%), Gaps = 55/308 (17%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR--------------EHGD-------------LS--- 48
           Y+ EI ++P+L  +EE VL KR +              E GD             LS   
Sbjct: 15  YLREIGRVPLLTHEEEVVLGKRVQQWMKLQELRQTLQSEEGDRDPSDLEWAAAAGLSIEE 74

Query: 49  ----------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
                     A  +++ ++LRLVV +A  Y    + + +++ EG IG+ + V+KFDP +G
Sbjct: 75  LRQQQHLGEQAKRKMIEANLRLVVSVAKKYLKRNMDLLDLIQEGTIGMQRGVEKFDPTKG 134

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITDNNLKPE 157
           +R +TY+ WWI+ A+   I      +++     +K     +++++  L Q +      PE
Sbjct: 135 YRFSTYAYWWIRQAITRAIAEKARTIRLPIHITEK--LNKIKKMQRQLSQQLGRTATLPE 192

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A  L+++ ++V     +     SL+  +   D   ++  D L  D    E+  ++
Sbjct: 193 ----LAAALDLTPAQVRDYLEKARHPLSLD--LRVGDNQDTELGDLLETDCTTPEEFTLQ 246

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEAR 275
              R++    + R +  L  ++R++   R   E+   +TL ++    ++SRERVRQ+E  
Sbjct: 247 ASMRRD----IDRLLDQLTEQQRQVIALRYGLEDGQVMTLASIGDRLQISRERVRQLERE 302

Query: 276 AFKKVQES 283
           A   ++++
Sbjct: 303 ALHTLRQA 310


>gi|56750866|ref|YP_171567.1| RNA polymerase sigma factor SigD [Synechococcus elongatus PCC 6301]
 gi|56685825|dbj|BAD79047.1| group2 RNA polymerase sigma factor RpoD3 [Synechococcus elongatus
           PCC 6301]
          Length = 326

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 74/308 (24%), Positives = 143/308 (46%), Gaps = 55/308 (17%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR--------------EHGD-------------LS--- 48
           Y+ EI ++P+L  +EE VL KR +              E GD             LS   
Sbjct: 21  YLREIGRVPLLTHEEEVVLGKRVQQWMKLQELRQTLQSEEGDRDPSDLEWAAAAGLSIEE 80

Query: 49  ----------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
                     A  +++ ++LRLVV +A  Y    + + +++ EG IG+ + V+KFDP +G
Sbjct: 81  LRQQQHLGEQAKRKMIEANLRLVVSVAKKYLKRNMDLLDLIQEGTIGMQRGVEKFDPTKG 140

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITDNNLKPE 157
           +R +TY+ WWI+ A+   I      +++     +K     +++++  L Q +      PE
Sbjct: 141 YRFSTYAYWWIRQAITRAIAEKARTIRLPIHITEK--LNKIKKMQRQLSQQLGRTATLPE 198

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A  L+++ ++V     +     SL+  +   D   ++  D L  D    E+  ++
Sbjct: 199 ----LAAALDLTPAQVRDYLEKARHPLSLD--LRVGDNQDTELGDLLETDCTTPEEFTLQ 252

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEAR 275
              R++    + R +  L  ++R++   R   E+   +TL ++    ++SRERVRQ+E  
Sbjct: 253 ASMRRD----IDRLLDQLTEQQRQVIALRYGLEDGQVMTLASIGDRLQISRERVRQLERE 308

Query: 276 AFKKVQES 283
           A   ++++
Sbjct: 309 ALHTLRQA 316


>gi|16330303|ref|NP_441031.1| RNA polymerase sigma factor SigD [Synechocystis sp. PCC 6803]
 gi|1652792|dbj|BAA17711.1| RNA polymerase sigma factor [Synechocystis sp. PCC 6803]
          Length = 318

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 76/315 (24%), Positives = 140/315 (44%), Gaps = 73/315 (23%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYRE---------------------------HGDLS--- 48
           Y+ EI ++P+L  +EE V AK+ ++                             DLS   
Sbjct: 13  YLREIGRVPLLTHEEEIVYAKQIQQVVSLNEIKKSLAEGKDGEPVSPSEWAKAADLSIRE 72

Query: 49  ----------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
                     A  ++V ++LRLVV +A  Y    L + +++ EG IG+ + V+KFDP +G
Sbjct: 73  LEKAIKEGERAKRKMVEANLRLVVSVAKKYLKRNLDLLDLIQEGTIGMQRGVEKFDPTKG 132

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           +R +TY+ WWI+ A+   I      +++     +K     L ++K   + ++    +   
Sbjct: 133 YRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEK-----LNKIKKAQRQLSQEKGRAAS 187

Query: 159 VVAIAKKLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           +  +A+ L ++  +V          +S++ R+ GD     L +  + +    +D+  Y  
Sbjct: 188 IAELAEHLELTPKQVREYLERSRHPLSLDLRV-GDNQDTELGDLLEDDGPLPEDFATY-- 244

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSR 266
                         + +  L   M+ L P++R +   R  L +  P+TL ++ S   +SR
Sbjct: 245 -------------ASLQLDLDSLMAELTPQQREVLILRFGLNDGQPLTLASIGSMLSISR 291

Query: 267 ERVRQIEARAFKKVQ 281
           ERVRQIE  A  K++
Sbjct: 292 ERVRQIEREALNKLR 306


>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 = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 67/243 (27%), Positives = 113/243 (46%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 361 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 420

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         P+++         
Sbjct: 421 IRQAITRSIADQARTIRI--PVHMIETINKLNRVSRQMLQEMGREPTPDELAERVDMPKD 478

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + K L +++ E ISM   +  DE  +      D       D  ++              
Sbjct: 479 KVRKVLKIAK-EPISMETPIGDDEDSHLGDFVEDAEVVSPPDAAIF-------------- 523

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
               R    + ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 524 -SGLRETTQQILAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 582

Query: 279 KVQ 281
           K++
Sbjct: 583 KLR 585


>gi|295698783|ref|YP_003603438.1| RNA polymerase sigma factor RpoD [Candidatus Riesia pediculicola
           USDA]
 gi|291157386|gb|ADD79831.1| RNA polymerase sigma factor RpoD [Candidatus Riesia pediculicola
           USDA]
          Length = 607

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 113/236 (47%), Gaps = 28/236 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 390 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 449

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ----KRLFFNLRRLKGHLQAITDNNLKPEQVV 160
           I+ A+   I      ++I      T N+     R        +   + +++  L PE+  
Sbjct: 450 IRQAITRSIADQARTIRIPVHMIETINKLNHISRQILQETGREPSPEELSERMLIPEE-- 507

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L ++  E ISM   +  DE             S   D++    D   ++ +E   
Sbjct: 508 KIRKVLKIAR-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLESAT 551

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEA 274
            ++ R+     +S L  RE ++   R         TLE +  +F+V+RER+RQIEA
Sbjct: 552 SESLRSATNEVLSGLTTREAKVLRMRFGIDMHTDHTLEEVGKQFDVTRERIRQIEA 607


>gi|112702894|emb|CAL34114.1| RNA polymerase sigma factor rpoD [Cronobacter sakazakii]
          Length = 359

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 71/254 (27%), Positives = 121/254 (47%), Gaps = 36/254 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 121 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 180

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVV---- 160
           I+ A+   I      ++I      T N+      L R+   +         PE++     
Sbjct: 181 IRQAITRSIADQARTIRIPVHMIETINK------LNRISRQMLQEMGREPTPEELAERML 234

Query: 161 ----AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
                I K L +++ E ISM   +  DE             S   D++    D   ++ +
Sbjct: 235 MPEDKIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPL 278

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEA 274
           +    ++ R      ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA
Sbjct: 279 DSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEA 338

Query: 275 RAFKKVQESIQKQV 288
           +A +K++   + +V
Sbjct: 339 KALRKLRHPSRSEV 352


>gi|120403441|ref|YP_953270.1| RNA polymerase sigma factor SigB [Mycobacterium vanbaalenii PYR-1]
 gi|119956259|gb|ABM13264.1| RNA polymerase, sigma 70 subunit, RpoD family [Mycobacterium
           vanbaalenii PYR-1]
          Length = 329

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 80/300 (26%), Positives = 142/300 (47%), Gaps = 56/300 (18%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH-------------GDLSAAHR-------- 52
           Y++ I K  +L   +E  LAKR     Y +H              DL+A  R        
Sbjct: 36  YLNGIGKTALLNAADEVELAKRIEAGLYAQHLLDTRKRLGENRKRDLAAVVRDGEAARRH 95

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A
Sbjct: 96  LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTYATWWIRQA 155

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA-----ITDNNLKPEQVVAIAKKLN 167
           +   +      +++     ++     L R+K  +        TD  L  E  + + K  +
Sbjct: 156 ITRGMADQSRTIRLPVHLVEQ--VNKLARIKREMHQNLGREATDEELAAESGIPVEKITD 213

Query: 168 VSES--EVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + E   + +S++  +  DE   L   I  ++  S+             E  +I +    +
Sbjct: 214 LLEHSRDPVSLDMPVGSDEEAPLGDFIEDAEAMSA-------------ENAVISELLHTD 260

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R +L    + L+ RE+++   R   ++  P TL+ +   F +SRERVRQIE     K++
Sbjct: 261 IRYVL----ATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMAKLR 316


>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 = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 116/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 331 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 390

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 391 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPED 448

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   Q  I+   
Sbjct: 449 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDSAMQSPIDVAT 492

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ +      +S L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 493 VESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 552

Query: 279 KVQ 281
           K++
Sbjct: 553 KLR 555


>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|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]
          Length = 616

 Score = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 116/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 438 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPED 495

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   Q  I+   
Sbjct: 496 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDSTMQSPIDVAT 539

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ +      +S L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 540 VESLKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 279 KVQ 281
           K++
Sbjct: 600 KLR 602


>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 = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 68/248 (27%), Positives = 120/248 (48%), Gaps = 36/248 (14%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 404 AAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 463

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I    +       + R+    Q + +   +P+    +A+ + 
Sbjct: 464 WIRQAITRSIADQARTIRI--PVHMIETINKMNRISR--QYLQETGEEPDS-AKLAELME 518

Query: 168 VSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVL 215
           + E ++          ISM   +  D+  +      D N+    D  +Y   H+  ++VL
Sbjct: 519 MPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDINNVAPADAAMYSSLHEVTKEVL 578

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIE 273
                              L PRE ++   R  +  N   TLE +  +F+V+RER+RQIE
Sbjct: 579 -----------------ESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 621

Query: 274 ARAFKKVQ 281
           A+A +K++
Sbjct: 622 AKALRKLR 629


>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 = 88.6 bits (218), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 67/242 (27%), Positives = 123/242 (50%), Gaps = 12/242 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 374 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 433

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   +A+++ +
Sbjct: 434 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEIGREPTPEE---LAERMFM 488

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E L+      D   +   D++    D   ++ +E    ++ R+  
Sbjct: 489 PEDKIRKV-LKIAK-EPLSMETPIGDDEDTHLGDFI---EDTTLELPLESATSESLRSAT 543

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              ++ L  RE ++   R  +  N   TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 544 HEILAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFAVTRERIRQIEAKALRKLRHPSRS 603

Query: 287 QV 288
           +V
Sbjct: 604 EV 605


>gi|255076341|ref|XP_002501845.1| predicted protein [Micromonas sp. RCC299]
 gi|226517109|gb|ACO63103.1| predicted protein [Micromonas sp. RCC299]
          Length = 595

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 68/249 (27%), Positives = 130/249 (52%), Gaps = 35/249 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A + ++ ++LRLVV IA  Y    +   +++ EG +GL++  +KFD +RG++ +TY+ WW
Sbjct: 345 AKNAMIQANLRLVVSIAKRYANKSMSFQDLIQEGCVGLIRGAEKFDFKRGYKFSTYAHWW 404

Query: 109 IKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      +++           +  ++++   L R   H +      +  E++
Sbjct: 405 IRQAVTRSISDQSRTIRLPVHLFEIISRMSKVERQMVLKLGRDPTHEELADAMEMTVEKI 464

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH----DGQEQVL 215
             I K   V     IS++      +++N   NS+ ++    +D L+ D+    +G+   +
Sbjct: 465 KQIKKASLVP----ISLS------QTVN---NSNGEDKRTVEDTLIDDYTEHPEGETGKV 511

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIE 273
           + KE+ +N        ++ LNPRER +   R  L +  V TLE + + F V+RER+RQIE
Sbjct: 512 LLKEDLEN-------VLNTLNPRERDVLRLRYGLDDGRVKTLEEIGNVFSVTRERIRQIE 564

Query: 274 ARAFKKVQE 282
           A+A +K+++
Sbjct: 565 AKALRKLRQ 573


>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 = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 116/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 378 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 438 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPED 495

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   Q  I+   
Sbjct: 496 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDSTMQSPIDVAT 539

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ +      +S L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 540 VESLKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 279 KVQ 281
           K++
Sbjct: 600 KLR 602


>gi|254526924|ref|ZP_05138976.1| sigma-70 factor family protein [Prochlorococcus marinus str. MIT
           9202]
 gi|221538348|gb|EEE40801.1| sigma-70 factor family protein [Prochlorococcus marinus str. MIT
           9202]
          Length = 307

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 81/296 (27%), Positives = 140/296 (47%), Gaps = 32/296 (10%)

Query: 12  GEIGLSRYIHEIRKIPMLEK-QEEYVLAKRYREHG------DLSAAHR------------ 52
           GEIG  + +   R++ M  K QE  VL  R +E G      + S A R            
Sbjct: 9   GEIGRHQLLTPERELTMGRKVQEMVVLVNRCQEAGGKGPACEYSEAERKKIKIGEKAKNE 68

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG R +TY+ WWI+  
Sbjct: 69  MITANLRLVVNLAKRYQGKGLELLDLIQEGTLGLTRAVEKYDPSRGHRFSTYAYWWIRQG 128

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +      ++I    N+K     LR  K  L  +      P     +A+++ +++ E
Sbjct: 129 LNRALSTQSRTIRIPVNINEK--LTKLRSAKSKLMQLKG---IPPTSDELAEEMKITKEE 183

Query: 173 VIS-MNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           +   ++C L     SL   + S   + S+  D L  D     ++    E   +   +L +
Sbjct: 184 IDELLSCELRSITVSLQGTVKSKS-DPSELVDILPSDQAPPMELAELAERTASAWKLLDK 242

Query: 231 SMSVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +   L  +ER+I   R   +      TL  ++     SRE  RQ+  RA +K++++
Sbjct: 243 AN--LTEKERKIVSLRFGLDGSNEWRTLAEVARHMSCSREYCRQVVQRALRKLRKA 296


>gi|167627930|ref|YP_001678430.1| RNA polymerase sigma-70 factor [Francisella philomiragia subsp.
           philomiragia ATCC 25017]
 gi|167597931|gb|ABZ87929.1| RNA polymerase sigma-70 factor [Francisella philomiragia subsp.
           philomiragia ATCC 25017]
          Length = 578

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 74/248 (29%), Positives = 115/248 (46%), Gaps = 36/248 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLVV  A  Y   GL   +++ EGNIGLM+AV KFD  +GF+ +TY+ WW
Sbjct: 340 AKKEMIEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKGFKFSTYATWW 399

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITDNNLKPEQVVAIAKKLN 167
           I+ A+   I            A+Q R      R+  H+ + I   N    Q++   K   
Sbjct: 400 IRQAITRSI------------ADQARTI----RVPVHMIETINKVNRIKRQILQ-EKGRE 442

Query: 168 VSESEVISMNCRLAGDESLNALINSS-----------DKNSSQWQDWLVYDHDGQEQVLI 216
            +E E+I     +  D+ L  ++N S           D   S   D++    D      I
Sbjct: 443 ATEEEIIEYTPNMTKDK-LKKILNISHTPISMESPIGDDEDSTVGDFI---EDKNNYSPI 498

Query: 217 EKEERKNRRNMLTRSMSV-LNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIE 273
           E    +N R  +   +   L  RE ++   R         TLE +  +F V+RER+RQIE
Sbjct: 499 EAANLENLREAIKELIDTGLTEREAKVLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIE 558

Query: 274 ARAFKKVQ 281
           A+A +K++
Sbjct: 559 AKALRKLK 566


>gi|94971322|ref|YP_593370.1| sigma 38, RpoS [Candidatus Koribacter versatilis Ellin345]
 gi|94553372|gb|ABF43296.1| RNA polymerase, sigma 70 subunit, RpoD [Candidatus Koribacter
           versatilis Ellin345]
          Length = 574

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 68/247 (27%), Positives = 127/247 (51%), Gaps = 23/247 (9%)

Query: 44  HGDLSAAH---RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
            GD+ A      L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 325 QGDMDAEQAKKELIEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 384

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL-KGHLQAITDNNLKPEQV 159
            +TY+ WWI+ A+   I      ++I        +   + +L +   Q + +   +P   
Sbjct: 385 FSTYATWWIRQAITRAIADQARTIRIPV-----HMIETINKLIRTSRQLVQELGREPSS- 438

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IAK++++  ++V  +  ++A  E ++      ++  S   D++      +++ ++   
Sbjct: 439 EEIAKRMDIPVAKVRKV-LKIA-QEPISLETPIGEEEDSHLGDFI------EDRSMVSPA 490

Query: 220 E---RKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEA 274
           E     N ++   + +  L  RE ++ + R   E+    TLE +   F V+RER+RQIEA
Sbjct: 491 EAVINVNLKDQTAQVLRTLTAREEKVIKMRFGLEDGSEHTLEEVGQSFAVTRERIRQIEA 550

Query: 275 RAFKKVQ 281
           +A +K++
Sbjct: 551 KALRKLR 557


>gi|159904297|ref|YP_001551641.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9211]
 gi|159889473|gb|ABX09687.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9211]
          Length = 335

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 67/243 (27%), Positives = 119/243 (48%), Gaps = 12/243 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+V ++LRLVV IA  Y    + + +++ EG IGL++ V+KFDP RG++ +TY+ WW
Sbjct: 100 AKERMVAANLRLVVSIAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPARGYKFSTYAYWW 159

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   I      +++     +      L +LK   + ++    +   V  +A+ ++V
Sbjct: 160 IRQGITRAIAEKSRAIRLPIHITEM-----LNKLKKGQRDLSQQLSRTPSVAELAEYIDV 214

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SE EV  +  + +   SL   +   DK+ +   D L  D+D  +Q  IE +  K    +L
Sbjct: 215 SEEEVKDLMLKASQPVSLE--MKVGDKDDTVLLDLLSTDNDSPQQQ-IELDCMKGDLEIL 271

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE---ARAFKKVQESIQ 285
              +  L  R  R+       E P++L  +     +SR+RVR +E    R  +   E+++
Sbjct: 272 LEKLPELQYRVLRMRYGID-GEEPMSLTGIGRVLGISRDRVRNLERSGLRGLRSKGEAVE 330

Query: 286 KQV 288
             V
Sbjct: 331 AYV 333


>gi|152965499|ref|YP_001361283.1| RNA polymerase sigma factor [Kineococcus radiotolerans SRS30216]
 gi|151360016|gb|ABS03019.1| RNA polymerase, sigma 70 subunit, RpoD family [Kineococcus
           radiotolerans SRS30216]
          Length = 502

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 139/310 (44%), Gaps = 62/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ +I K+ +L  ++E  LAKR  E G  +                           A +
Sbjct: 209 YLKQIGKVALLNAEQEVELAKRI-EAGLFAEEKLHSGEDIDSIFKRELWWISEDGRRAKN 267

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 268 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 327

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+VV +
Sbjct: 328 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEV 387

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 388 QK----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 433

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 434 -------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 486

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 487 KLRHPSRSQV 496


>gi|241668482|ref|ZP_04756060.1| RNA polymerase sigma-70 factor [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
 gi|254877016|ref|ZP_05249726.1| RNA polymerase sigma-70 factor [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
 gi|254843037|gb|EET21451.1| RNA polymerase sigma-70 factor [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
          Length = 578

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 74/248 (29%), Positives = 115/248 (46%), Gaps = 36/248 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLVV  A  Y   GL   +++ EGNIGLM+AV KFD  +GF+ +TY+ WW
Sbjct: 340 AKKEMIEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKGFKFSTYATWW 399

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITDNNLKPEQVVAIAKKLN 167
           I+ A+   I            A+Q R      R+  H+ + I   N    Q++   K   
Sbjct: 400 IRQAITRSI------------ADQARTI----RVPVHMIETINKVNRIKRQILQ-EKGRE 442

Query: 168 VSESEVISMNCRLAGDESLNALINSS-----------DKNSSQWQDWLVYDHDGQEQVLI 216
            +E E+I     +  D+ L  ++N S           D   S   D++    D      I
Sbjct: 443 ATEEEIIEYTPNMTKDK-LKKILNISHTPISMESPIGDDEDSTVGDFI---EDKNNYSPI 498

Query: 217 EKEERKNRRNMLTRSMSV-LNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIE 273
           E    +N R  +   +   L  RE ++   R         TLE +  +F V+RER+RQIE
Sbjct: 499 EAANLENLREAIKELIDTGLTEREAKVLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIE 558

Query: 274 ARAFKKVQ 281
           A+A +K++
Sbjct: 559 AKALRKLK 566


>gi|163841160|ref|YP_001625565.1| RNA polymerase principal sigma factor [Renibacterium salmoninarum
           ATCC 33209]
 gi|1808669|emb|CAA71796.1| RNA polymerase [Renibacterium salmoninarum]
 gi|162954636|gb|ABY24151.1| RNA polymerase principal sigma factor [Renibacterium salmoninarum
           ATCC 33209]
          Length = 462

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 70/258 (27%), Positives = 122/258 (47%), Gaps = 34/258 (13%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           H    A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +T
Sbjct: 220 HDGKRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNMGLIRAVEKFDYTKGFKFST 279

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNL 154
           Y+ WWI+ A+   +      ++I              Q+++  +L R     +   + ++
Sbjct: 280 YATWWIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELALELDM 339

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
            PE+VV + K       E IS++  L   GD     LI  S+          V   D   
Sbjct: 340 TPEKVVEVQKYGR----EPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVS 386

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVR 270
             L++++        L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 387 FTLLQEQ--------LHSVLDTLSEREAGVVAMRFGLTDGQPKTLDEIGKVYGVTRERIR 438

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 439 QIESKTMSKLRHPSRSQV 456


>gi|148823899|ref|YP_001288653.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis F11]
 gi|253798208|ref|YP_003031209.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis KZN
           1435]
 gi|308232219|ref|ZP_07415326.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu001]
 gi|308369834|ref|ZP_07419229.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu002]
 gi|308371106|ref|ZP_07423839.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu003]
 gi|308372374|ref|ZP_07428435.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu004]
 gi|308373485|ref|ZP_07432499.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu005]
 gi|308374669|ref|ZP_07436917.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu006]
 gi|308375503|ref|ZP_07444157.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu007]
 gi|308377104|ref|ZP_07441142.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu008]
 gi|308378072|ref|ZP_07481430.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu009]
 gi|308379289|ref|ZP_07485765.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu010]
 gi|308380449|ref|ZP_07489983.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu011]
 gi|148722426|gb|ABR07051.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis F11]
 gi|253319711|gb|ACT24314.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis KZN
           1435]
 gi|308214646|gb|EFO74045.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu001]
 gi|308326293|gb|EFP15144.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu002]
 gi|308329821|gb|EFP18672.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu003]
 gi|308333464|gb|EFP22315.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu004]
 gi|308337459|gb|EFP26310.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu005]
 gi|308341132|gb|EFP29983.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu006]
 gi|308346083|gb|EFP34934.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu007]
 gi|308348958|gb|EFP37809.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu008]
 gi|308353656|gb|EFP42507.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu009]
 gi|308357503|gb|EFP46354.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu010]
 gi|308361457|gb|EFP50308.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu011]
          Length = 345

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 82/298 (27%), Positives = 143/298 (47%), Gaps = 52/298 (17%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH-------------GDLSAAHR-------- 52
           Y++ I K  +L    E  LAKR     Y EH              DL+A  R        
Sbjct: 52  YLNGIGKTALLNAAGEVELAKRIEAGLYAEHLLETRKRLGENRKRDLAAVVRDGEAARRH 111

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A
Sbjct: 112 LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQA 171

Query: 113 MQEYILRSWSLVKIGTTANQK--RLFFNLRRLKGHL-QAITDNNLKPEQVVAIAKKLNVS 169
           +   +      +++     ++  +L    R +  HL +  TD  L  E  + I K  ++ 
Sbjct: 172 ITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQHLGREATDEELAAESGIPIDKINDLL 231

Query: 170 ES--EVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           E   + +S++  +  +E   L   I  ++  S+             E  +I +    + R
Sbjct: 232 EHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSA-------------ENAVIAELLHTDIR 278

Query: 226 NMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++L    + L+ RE ++   R   ++  P TL+ +   F +SRERVRQIE     K++
Sbjct: 279 SVL----ATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMSKLR 332


>gi|166367266|ref|YP_001659539.1| RNA polymerase sigma factor SigD [Microcystis aeruginosa NIES-843]
 gi|166089639|dbj|BAG04347.1| group 2 RNA polymerase sigma factor [Microcystis aeruginosa
           NIES-843]
          Length = 318

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 65/250 (26%), Positives = 122/250 (48%), Gaps = 34/250 (13%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A  ++V ++LRLVV +A  Y    L + +++ EG IG+ + V+KFDP +G+R +TY
Sbjct: 80  GDF-AKRKMVEANLRLVVSVAKKYLKRNLDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTY 138

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + WWI+ A+   I      +++     +K     L ++K   + +  +  +   +  +A+
Sbjct: 139 AYWWIRQAITRAIAEKSRTIRLPIHITEK-----LNKIKKAQRQLAQDKGRAATIAELAE 193

Query: 165 KLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +L+++  +V          +S++ ++ GD     L    +      +D+  Y      QV
Sbjct: 194 ELDLTPKQVRDYLERSRQPLSLDLKV-GDNQDTELGELLEDTGLSPEDYTAY---SSLQV 249

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
            +EK             M+ L P+++ +   R   +N  P+TL  +     +SRERVRQI
Sbjct: 250 DLEK------------LMADLTPQQKEVICLRFGLDNGQPLTLAKIGVRLNISRERVRQI 297

Query: 273 EARAFKKVQE 282
           E  A  K+++
Sbjct: 298 EREAIAKLRK 307


>gi|257068601|ref|YP_003154856.1| RNA polymerase, sigma 70 subunit, RpoD [Brachybacterium faecium DSM
           4810]
 gi|256559419|gb|ACU85266.1| RNA polymerase, sigma 70 subunit, RpoD [Brachybacterium faecium DSM
           4810]
          Length = 433

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 69/254 (27%), Positives = 123/254 (48%), Gaps = 34/254 (13%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ W
Sbjct: 195 AAKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYAKGYKFSTYATW 254

Query: 108 WIKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           WI+ A+   +      ++I              Q+++  +L R     +   + ++ PE+
Sbjct: 255 WIRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEK 314

Query: 159 VVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           VV + K       E IS++  L   GD     LI  S+          V   D     L+
Sbjct: 315 VVEVQKYGR----EPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLL 361

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEA 274
           +++        L   +  L+ RE  +   R   E+  P TL+ +   + V+RER+RQIE+
Sbjct: 362 QEQ--------LHSVLDTLSEREAGVVSMRFGLEDGQPKTLDEIGKVYGVTRERIRQIES 413

Query: 275 RAFKKVQESIQKQV 288
           +   K++   + QV
Sbjct: 414 KTMSKLRHPSRSQV 427


>gi|163847594|ref|YP_001635638.1| sigma-70 family RNA polymerase sigma factor [Chloroflexus
           aurantiacus J-10-fl]
 gi|222525449|ref|YP_002569920.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus sp.
           Y-400-fl]
 gi|163668883|gb|ABY35249.1| RNA polymerase sigma factor, sigma-70 family [Chloroflexus
           aurantiacus J-10-fl]
 gi|222449328|gb|ACM53594.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus sp.
           Y-400-fl]
          Length = 345

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 83/294 (28%), Positives = 139/294 (47%), Gaps = 44/294 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHG-----------DLSAAHR--------------- 52
           Y+ EI ++ +L   EE  LA+R  E G           DL+   R               
Sbjct: 52  YLQEIGRVSLLTAAEEIELAERI-ERGNEAEAQLATATDLTPRERYELLQAVQQGEEARR 110

Query: 53  -LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV IA  Y G GL + +++ EGNIGLM+AV+KFD  +G R +TY+ WWI+ 
Sbjct: 111 HLIQANLRLVVSIAKKYVGRGLALLDLIQEGNIGLMRAVEKFDYHKGNRFSTYATWWIRQ 170

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           A+      + ++ + G T    RL  ++    G ++ I +   +  +    A+++ ++  
Sbjct: 171 AV------TRAIAEQGRTI---RLPVHMSESVGQVKRIAERLAQSLERQPTAEEIAMALG 221

Query: 172 EVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           + +    R+  A    ++      D+      D+L    D +     E   +K  R  L 
Sbjct: 222 QPVERIQRILEAARRPVSLETPVGDEGEHTLGDFLT---DEELPTPGEMAAQKLLRRDLC 278

Query: 230 RSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            ++  LN RERRI + R   +     TLE +     ++RER RQIEA A ++++
Sbjct: 279 AALDRLNDRERRIIDLRYGLVDGRRRTLEEVGRVLGMTRERARQIEAEALRRLR 332


>gi|317050370|ref|YP_004111486.1| RNA polymerase sigma factor RpoD [Desulfurispirillum indicum S5]
 gi|316945454|gb|ADU64930.1| RNA polymerase sigma factor RpoD [Desulfurispirillum indicum S5]
          Length = 627

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 79/255 (30%), Positives = 129/255 (50%), Gaps = 36/255 (14%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  +L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 388 AAKMQLIEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 447

Query: 108 WIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHL------QAITDNNLKPE 157
           WI+ A+   I      ++I      T N  +L    R L   L      + I D    P 
Sbjct: 448 WIRQAITRAIADQARTIRIPVHMIETIN--KLVRTSRNLVQELGREPTPEEIADKMDLP- 504

Query: 158 QVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
            V  + K L +++ E IS+   +    D SL   I   DKN+    + ++   + +EQV 
Sbjct: 505 -VEKVRKVLKIAK-EPISLETPIGEEEDSSLGDFIE--DKNTVSPAEAVI-SFNLKEQV- 558

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIE 273
                    R++L      L+ RE  + + R     ++  TLE +  +F V+RER+RQIE
Sbjct: 559 ---------RSVL----HTLSAREAEVLKLRFGIDTDSDHTLEEVGKKFNVTRERIRQIE 605

Query: 274 ARAFKKVQESIQKQV 288
           A+A +K++   + ++
Sbjct: 606 AKALRKLRHPTRSKI 620


>gi|37520903|ref|NP_924280.1| RNA polymerase sigma factor RpoD [Gloeobacter violaceus PCC 7421]
 gi|35211898|dbj|BAC89275.1| group2 RNA polymerase sigma factor [Gloeobacter violaceus PCC 7421]
          Length = 350

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 69/248 (27%), Positives = 118/248 (47%), Gaps = 32/248 (12%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            G+ + AH LV ++LRLVV +A  Y+G GL + +++ EG +GL++A +KFD  RGF+ +T
Sbjct: 105 EGERAKAH-LVKANLRLVVSVAKKYQGRGLHLLDLIQEGTLGLIRAAEKFDYTRGFKFST 163

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQK--RLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           Y+ WWI+  +   I      +++     +K  R+    R+L   L          E  +A
Sbjct: 164 YATWWIRQGITRAIAMQARTIRLPVHIVEKVNRIKKATRQLSQQL-----GRSPSEDEIA 218

Query: 162 IAKKLNVSESEVISMNCRL-------AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            A +++  +   +    +L        G E   AL +      ++ +  +V D   Q+  
Sbjct: 219 QAVEMDADQLRFVRKAIQLPVSLETPVGREEDTALGDLIQAKGNEPEHGVVRDLMNQD-- 276

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQI 272
                        L   +  L PRER +   R   +     TL+ +  +F ++RER+RQI
Sbjct: 277 -------------LESLLQTLTPRERDVLRLRYGLIDGRSRTLDEVGQQFGLTRERIRQI 323

Query: 273 EARAFKKV 280
           EARA +K+
Sbjct: 324 EARALRKL 331


>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 = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 64/236 (27%), Positives = 119/236 (50%), Gaps = 14/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 367 AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 426

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   +A+++++
Sbjct: 427 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREATPEE---LAERMDL 481

Query: 169 SESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
            E ++  +  ++A +  S+   I   D   S   D++    D      ++     +   +
Sbjct: 482 PEDKIRKV-LKIAKEPISMETPIGEDD--DSNLGDFI---EDQSAISPMDSATNASLSEI 535

Query: 228 LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   ++ L PRE ++   R         TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 536 VREILASLTPREAKVLMMRFGIGMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 591


>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 = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 67/243 (27%), Positives = 116/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 395 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 454

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV--------V 160
           I+ A+   I      ++I    +       + R+   L         PE++        V
Sbjct: 455 IRQAITRSIADQARTIRI--PVHMIETINKINRVSRQLLQEMGREPTPEELGERLEMDEV 512

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + K L +++ E ISM   +  DE             S   D++    D      +++  
Sbjct: 513 KVRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDSSISSPVDEAT 556

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFK 278
            +  +      ++ L  RE ++ + R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 557 AQGLKEATREVLANLTEREAKVLKMRFGIDMSTDHTLEEVGKQFDVTRERIRQIEAKALR 616

Query: 279 KVQ 281
           K++
Sbjct: 617 KLR 619


>gi|169837518|ref|ZP_02870706.1| RNA polymerase sigma factor rpoD [candidate division TM7
           single-cell isolate TM7a]
          Length = 149

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 44/108 (40%), Positives = 71/108 (65%), Gaps = 1/108 (0%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI +IP+L  +EE   A+R   +G+  A  +L+ S+LRLVV IA  +   GL + ++
Sbjct: 2   YLREIGQIPLLSYEEEIDYAQRVL-NGEEEAKQKLIESNLRLVVSIAKKHTNRGLKMLDL 60

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           + EGN+GLM+AV+KF+ E+GF+ +TY+ WWI+ A+   I      ++I
Sbjct: 61  IQEGNMGLMKAVEKFEYEKGFKFSTYATWWIRQAITRAIADQGRTIRI 108


>gi|226306291|ref|YP_002766251.1| RNA polymerase sigma factor SigB [Rhodococcus erythropolis PR4]
 gi|229491301|ref|ZP_04385127.1| RNA polymerase sigma factor RpoD [Rhodococcus erythropolis SK121]
 gi|226185408|dbj|BAH33512.1| RNA polymerase sigma factor SigB [Rhodococcus erythropolis PR4]
 gi|229321840|gb|EEN87635.1| RNA polymerase sigma factor RpoD [Rhodococcus erythropolis SK121]
          Length = 323

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 72/246 (29%), Positives = 122/246 (49%), Gaps = 32/246 (13%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           SA   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ W
Sbjct: 85  SARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTYATW 144

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA-----ITDNNLKPEQVVA- 161
           WI+ A+   +      +++     ++     L R+K  L        TD+ L  E  +  
Sbjct: 145 WIRQAITRGMADQSRTIRLPVHLVEQ--VNKLARIKRELHQQLGREATDDELAEESGIPA 202

Query: 162 --IAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
             IA  L+ S   V S++  +  DE   L   I  S+  S+             E  +I 
Sbjct: 203 HKIADLLDHSRDPV-SLDMPVGNDEEAPLGDFIEDSEATSA-------------ENAVIA 248

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
                + R++L      L+ RE+++   R   ++  P TL+ +   F +SRERVRQIE  
Sbjct: 249 GLLHSDVRSVL----GTLDEREQQVIRLRYGLDDGQPRTLDQIGKLFGLSRERVRQIERE 304

Query: 276 AFKKVQ 281
              K++
Sbjct: 305 VMGKLR 310


>gi|320353903|ref|YP_004195242.1| RpoD subfamily RNA polymerase sigma-70 factor [Desulfobulbus
           propionicus DSM 2032]
 gi|320122405|gb|ADW17951.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfobulbus
           propionicus DSM 2032]
          Length = 439

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 72/253 (28%), Positives = 129/253 (50%), Gaps = 37/253 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLVV IA  Y   GL +++++ EGN+GLM+AV +FD ++G + +TY+ WW
Sbjct: 203 AKDSMIRANLRLVVSIAKRYMHQGLTLADLIQEGNLGLMRAVFRFDYKKGNKFSTYASWW 262

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKR-----LFFNLRRLKG------HLQAITDNNLKPE 157
           I+ A+   IL     +++     + R      F++L +  G       +  +TD  L  +
Sbjct: 263 IRQAITRAILDKTRTIRLPVHFLELRSQFFKAFYSLLKELGREPTPVEISKMTD--LPMD 320

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDES-LNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           +++AI +    +  E IS+   +  D+S L   + + +  S        YD        +
Sbjct: 321 KILAILE----ASREPISLETPVGDDDSTLGDFLENQESESP-------YDA-------V 362

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEA 274
           +  E  +R   +T  +S L  RE +I   R    ++   TLE +   F VSRER+RQIE 
Sbjct: 363 QNRELAHR---VTEVLSTLTDREEKIIRLRFGIGEKAEYTLEEIGKRFNVSRERIRQIEK 419

Query: 275 RAFKKVQESIQKQ 287
           +A  +++ S +++
Sbjct: 420 KALNRLRHSSRRE 432


>gi|218247827|ref|YP_002373198.1| RNA polymerase sigma factor SigD [Cyanothece sp. PCC 8801]
 gi|257060853|ref|YP_003138741.1| RNA polymerase sigma factor SigD [Cyanothece sp. PCC 8802]
 gi|218168305|gb|ACK67042.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8801]
 gi|256591019|gb|ACV01906.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8802]
          Length = 318

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 77/308 (25%), Positives = 139/308 (45%), Gaps = 60/308 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR------------------------------------ 42
           Y+ EI ++P+L  +EE + AKR +                                    
Sbjct: 14  YLREIGRVPLLTHEEEILYAKRVQRFVALETLKESLTEELGQEPTIAQWAKAAKMTQKEL 73

Query: 43  ----EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
               E G+ +A  ++V ++LRLVV +A  Y    L + +++ EG IG+ + V+KFDP +G
Sbjct: 74  RSAIEAGE-AAKRKMVEANLRLVVSVAKKYLKRNLDLLDLIQEGTIGMQRGVEKFDPTKG 132

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           +R +TY+ WWI+ A+   I      +++     +K     L ++K   + ++    +   
Sbjct: 133 YRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEK-----LNKIKKAQRQLSQEKGRAAT 187

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           +  +A++L ++  +V     R     SL+  +   D   ++  D L  +  GQ       
Sbjct: 188 IAELAEELELTPRQVREYLERARQPLSLD--LRVGDNQDTELGDLL--EDTGQ-----SP 238

Query: 219 EERKNRRNM---LTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIE 273
           E+     ++   L R M  L P+++ +   R  L +  P+TL  + S   +SRERVRQIE
Sbjct: 239 EDYATHSSLQLDLDRLMEELTPQQKEVLALRFGLSDGKPLTLAKIGSILNISRERVRQIE 298

Query: 274 ARAFKKVQ 281
             A  K++
Sbjct: 299 REALAKLR 306


>gi|149175263|ref|ZP_01853885.1| transcription initiation factor sigma 70 [Planctomyces maris DSM
           8797]
 gi|148845872|gb|EDL60213.1| transcription initiation factor sigma 70 [Planctomyces maris DSM
           8797]
          Length = 561

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 74/242 (30%), Positives = 124/242 (51%), Gaps = 16/242 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   L   +LRLVV IA  YR  GL   +++ EGN GLM+AV K++  RG++ +TY+ W
Sbjct: 299 TAMRELSGGNLRLVVSIAKKYRNRGLSFLDLIQEGNTGLMRAVDKYEYRRGYKFSTYATW 358

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP--EQVVAIAKK 165
           WI+ A+   I      ++I    +       LR++   L  + +N  +P  E+   +A  
Sbjct: 359 WIRQAITRAIADQARTIRI--PVHMIETMSKLRKVSKQL--LQENGREPTLEETAEVA-G 413

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           +++ E+  +    R     SL+  +  S+   S + D+ + D D    V    +E    +
Sbjct: 414 ISLEETRRVLKISRHPI--SLDRPVGESE--DSYFGDF-IEDSDSDSPVNTASQE--MLK 466

Query: 226 NMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           + +   +  L  RER I + R  L +    TLE +   F+V+RERVRQIEA+A +K+Q  
Sbjct: 467 DKIDHVLKTLTYREREIIKLRFGLGDGYTYTLEEVGRIFKVTRERVRQIEAKAVRKLQHP 526

Query: 284 IQ 285
           ++
Sbjct: 527 VR 528


>gi|119511025|ref|ZP_01630145.1| RNA polymerase sigma factor [Nodularia spumigena CCY9414]
 gi|119464276|gb|EAW45193.1| RNA polymerase sigma factor [Nodularia spumigena CCY9414]
          Length = 332

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 75/299 (25%), Positives = 138/299 (46%), Gaps = 53/299 (17%)

Query: 13  EIGLSRYIHEIR-----KIPMLEKQEEYVLAKRYR--EHGDL-----SAAHRLVTSHLRL 60
           ++  SR +HE+R     +I      EE+ LA      E  D      +A  ++V ++LRL
Sbjct: 49  QVQFSRILHEVRDSLINQIGREPSLEEWALAANLEVAELNDAIADGETAKRKMVEANLRL 108

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y    + + +++ EG+IG+ + V+KFDP +G+R +TY+ WWI+ A+   I   
Sbjct: 109 VVSVAKKYIKRNVDLLDLIQEGSIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEK 168

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV------- 173
              +++     +K     L ++K   + ++    +      +A++L+++  +V       
Sbjct: 169 ARTIRLPIHITEK-----LNKIKKAQRQLSQQLGRAPSAAELAQELDLTPKQVREYLERA 223

Query: 174 ---ISMNCRLAG--DESLNALINSSDKNSSQW--QDWLVYDHDGQEQVLIEKEERKNRRN 226
              +S++ RL    D  L  ++     +  ++  Q  L YD                   
Sbjct: 224 RLPLSLDLRLGDNYDTELGEMLEDPGASPEEFVMQSSLSYD------------------- 264

Query: 227 MLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            L R M  L P+++ + + R   L    +TL  +     +SRERVRQIE  A  K+++S
Sbjct: 265 -LERLMEELTPQQKEVIKLRFGLLDGQALTLAKIGDILNISRERVRQIEREALTKLRKS 322


>gi|1657704|gb|AAC44535.1| sigma factor MytB [Mycobacterium tuberculosis]
          Length = 345

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 82/298 (27%), Positives = 143/298 (47%), Gaps = 52/298 (17%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH-------------GDLSAAHR-------- 52
           Y++ I K  +L    E  LAKR     Y EH              DL+A  R        
Sbjct: 52  YLNGIGKTALLNPAGEVELAKRIEAGLYAEHLLETRKRLGENRKRDLAAVVRDGEAARRH 111

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A
Sbjct: 112 LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQA 171

Query: 113 MQEYILRSWSLVKIGTTANQK--RLFFNLRRLKGHL-QAITDNNLKPEQVVAIAKKLNVS 169
           +   +      +++     ++  +L    R +  HL +  TD  L  E  + I K  ++ 
Sbjct: 172 ITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQHLGREATDEELAAESGIPIDKINDLL 231

Query: 170 ES--EVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           E   + +S++  +  +E   L   I  ++  S+             E  +I +    + R
Sbjct: 232 EHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSA-------------ENAVIAELLHTDIR 278

Query: 226 NMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++L    + L+ RE ++   R   ++  P TL+ +   F +SRERVRQIE     K++
Sbjct: 279 SVL----ATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMSKLR 332


>gi|296129901|ref|YP_003637151.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cellulomonas
           flavigena DSM 20109]
 gi|296021716|gb|ADG74952.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cellulomonas
           flavigena DSM 20109]
          Length = 495

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 79/311 (25%), Positives = 140/311 (45%), Gaps = 63/311 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS----------------------------AA 50
           Y+ +I K+ +L  ++E  LAKR  E G  +                            A 
Sbjct: 201 YLKQIGKVALLNAEQEVELAKRI-EAGLFAEEKLAETRDSLEPKLRRELEWIAQDGRRAK 259

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+
Sbjct: 260 NHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIR 319

Query: 111 AAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
            A+   +      ++I              Q+++  +L R     +   + ++ PE+VV 
Sbjct: 320 QAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVE 379

Query: 162 IAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           + K       E IS++  L   GD     LI  S+          V   D     L++++
Sbjct: 380 VQKYGR----EPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ 426

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAF 277
                   L + +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++  
Sbjct: 427 --------LHQVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTM 478

Query: 278 KKVQESIQKQV 288
            K++   + QV
Sbjct: 479 SKLRHPSRSQV 489


>gi|300784474|ref|YP_003764765.1| RNA polymerase primary-like sigma factor [Amycolatopsis
           mediterranei U32]
 gi|299793988|gb|ADJ44363.1| RNA polymerase primary-like sigma factor [Amycolatopsis
           mediterranei U32]
          Length = 343

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 67/246 (27%), Positives = 118/246 (47%), Gaps = 30/246 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A + L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++AV+KFD  +GF+ +TY+ WW
Sbjct: 106 AKNHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAVEKFDYSKGFKFSTYATWW 165

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA------- 161
           I+ A+   +      +++     ++     L R+K  L      +   E++ A       
Sbjct: 166 IRQAITRGMADQGRTIRLPVHLVEQ--VNKLARIKRDLHQQLGRDATHEELAAESGIPAH 223

Query: 162 -IAKKLNVSESEV-ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
            I+  L+ S   V + M      D  L   I  S+   +             E  +I   
Sbjct: 224 KISDLLDHSRDPVSLDMPVGTEEDAPLGDFIEDSEATDA-------------ESAVISGL 270

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
            + +    L R ++ L+ RE+ +   R   ++  P TL+ +   F +SRERVRQIE    
Sbjct: 271 LQDD----LRRVLATLDDREQHVIRLRYGLDDGQPRTLDQIGKHFGLSRERVRQIEREVM 326

Query: 278 KKVQES 283
            K+++ 
Sbjct: 327 SKLRQG 332


>gi|320334918|ref|YP_004171629.1| RpoD subfamily RNA polymerase sigma-70 factor [Deinococcus
           maricopensis DSM 21211]
 gi|319756207|gb|ADV67964.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Deinococcus
           maricopensis DSM 21211]
          Length = 525

 Score = 88.2 bits (217), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 78/293 (26%), Positives = 136/293 (46%), Gaps = 38/293 (12%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHG-------------------------DLSAAHR 52
           +Y+HEI ++P+L  +EE  LA+R  E                           D +AA +
Sbjct: 228 QYLHEIGRVPLLTLEEEISLARRIEEGEEARKVLDEQPELEDRQRRRLQRQVEDGAAARQ 287

Query: 53  -LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV IA  Y G GL   +++ EGN GL++AV+KF+  R ++ +TY+ WWI+ 
Sbjct: 288 GLIEANLRLVVSIAKKYTGRGLGFLDLIQEGNQGLIRAVEKFEYRRRYKFSTYATWWIRQ 347

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-AIAKKLNVSE 170
           A+   I      ++I    +       L R    LQ         E++  A+    + ++
Sbjct: 348 AINRAIADQARTIRI--PVHMVETINKLTRTARQLQQELSREPTYEEIAEAMGPGWDAAK 405

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            E +    +    E ++      D+  S + D++    D      +E   +      L +
Sbjct: 406 VEEVQKVSQ----EPVSLETPIGDEKDSFYGDFI---PDENLDSPVENAAKTLLSEELEK 458

Query: 231 SMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++S L  RE  + + R+  +     TLE +   F V+RER+RQIE +A +K++
Sbjct: 459 ALSKLTEREAMVLKFRKGLVDGREHTLEEVGQRFNVTRERIRQIENKALRKLK 511


>gi|22297808|ref|NP_681055.1| RNA polymerase sigma factor SigD [Thermosynechococcus elongatus
           BP-1]
 gi|22293985|dbj|BAC07817.1| group2 RNA polymerase sigma factor [Thermosynechococcus elongatus
           BP-1]
          Length = 315

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 67/253 (26%), Positives = 124/253 (49%), Gaps = 38/253 (15%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E+G+  A  ++V ++LRLVV +A  Y    + + +++ EG IG+ + V+KFDP +G+R +
Sbjct: 75  ENGE-RAKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFS 133

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      +++     +K     L ++K   + ++    +   +  +
Sbjct: 134 TYAYWWIRQAITRAIAEKGRTIRLPIHITEK-----LNKIKKAQRQLSQRLGRAATINEL 188

Query: 163 AKKLNVSESEV----------ISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDG 210
           A +L ++ ++V          +S++ R+    D  L  L+  S  +  ++          
Sbjct: 189 AAELELTPAQVREYLERARQPLSLDVRVGDNQDTELGELLEDSSISPEEFAT-------- 240

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRER 268
             Q L+        R+ L R M+ L P++R +   R   EN  P+TL  +     +SRER
Sbjct: 241 --QSLL--------RSDLERLMAELTPQQRHVLSLRFGLENGQPLTLAKVGELLNISRER 290

Query: 269 VRQIEARAFKKVQ 281
           VRQIE  A  K++
Sbjct: 291 VRQIEREALSKLR 303


>gi|256377300|ref|YP_003100960.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Actinosynnema
           mirum DSM 43827]
 gi|255921603|gb|ACU37114.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Actinosynnema
           mirum DSM 43827]
          Length = 349

 Score = 88.2 bits (217), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 81/294 (27%), Positives = 133/294 (45%), Gaps = 43/294 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREHG-DLSAAHR-------------------- 52
           Y+  I ++ +L   +E  LA+R     Y EH  DL  A R                    
Sbjct: 55  YLKAIGRVRLLTADQEVELARRVEAGLYAEHLLDLPPAARGSRRPIELRRVVRDGQRAKD 114

Query: 53  -LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV IA  Y G G+ + +V+ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ 
Sbjct: 115 HLLEANLRLVVSIAKRYTGKGMALLDVIQEGNLGLVRAVEKFDYAKGFKFSTYATWWIRQ 174

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           A+   +      +++    +   +   L R++  L          E+V   A +L+V+  
Sbjct: 175 AITRALADQSRTIRL--PVHMVEVVTKLARVERDLLHRNGREATAEEV---AVELDVTPE 229

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR--RNMLT 229
           +V+ +        SL+  I +    S       + D    E  +   E   +      L 
Sbjct: 230 KVVELRQHARTPVSLDQTIGAEADTS-------IGDLIADENAVAPLEAVSSALLSADLR 282

Query: 230 RSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
             +  L PRE  +   R    + V  TLE +   + V+RER+RQIE+R   K+Q
Sbjct: 283 AVLDTLTPREAGVVRMRYGFPDGVLHTLEEVGRVYGVTRERIRQIESRTMAKLQ 336


>gi|289676145|ref|ZP_06497035.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. syringae
           FF5]
          Length = 438

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 116/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 200 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 259

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV--------V 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 260 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPED 317

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   Q  I+   
Sbjct: 318 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDSTMQSPIDVAT 361

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ +      +S L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 362 VESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 421

Query: 279 KVQ 281
           K++
Sbjct: 422 KLR 424


>gi|167970067|ref|ZP_02552344.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis H37Ra]
 gi|215404675|ref|ZP_03416856.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis
           02_1987]
 gi|215428138|ref|ZP_03426057.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis T92]
 gi|215431649|ref|ZP_03429568.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis
           EAS054]
 gi|218754446|ref|ZP_03533242.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis GM
           1503]
 gi|219558719|ref|ZP_03537795.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis T17]
 gi|254551766|ref|ZP_05142213.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis
           '98-R604 INH-RIF-EM']
 gi|260187727|ref|ZP_05765201.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis
           CPHL_A]
 gi|260201835|ref|ZP_05769326.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis T46]
 gi|260206019|ref|ZP_05773510.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis K85]
 gi|289746512|ref|ZP_06505890.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           02_1987]
 gi|294994199|ref|ZP_06799890.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis 210]
 gi|297635318|ref|ZP_06953098.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis KZN
           4207]
 gi|297732314|ref|ZP_06961432.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis KZN
           R506]
 gi|289687040|gb|EFD54528.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           02_1987]
 gi|323718704|gb|EGB27866.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           CDC1551A]
 gi|328457981|gb|AEB03404.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis KZN
           4207]
          Length = 333

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 82/298 (27%), Positives = 143/298 (47%), Gaps = 52/298 (17%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH-------------GDLSAAHR-------- 52
           Y++ I K  +L    E  LAKR     Y EH              DL+A  R        
Sbjct: 40  YLNGIGKTALLNAAGEVELAKRIEAGLYAEHLLETRKRLGENRKRDLAAVVRDGEAARRH 99

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A
Sbjct: 100 LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQA 159

Query: 113 MQEYILRSWSLVKIGTTANQK--RLFFNLRRLKGHL-QAITDNNLKPEQVVAIAKKLNVS 169
           +   +      +++     ++  +L    R +  HL +  TD  L  E  + I K  ++ 
Sbjct: 160 ITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQHLGREATDEELAAESGIPIDKINDLL 219

Query: 170 ES--EVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           E   + +S++  +  +E   L   I  ++  S+             E  +I +    + R
Sbjct: 220 EHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSA-------------ENAVIAELLHTDIR 266

Query: 226 NMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++L    + L+ RE ++   R   ++  P TL+ +   F +SRERVRQIE     K++
Sbjct: 267 SVL----ATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMSKLR 320


>gi|171920947|ref|ZP_02932089.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 13 str.
           ATCC 33698]
 gi|185178923|ref|ZP_02964687.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 5 str.
           ATCC 27817]
 gi|188024158|ref|ZP_02996885.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 7 str.
           ATCC 27819]
 gi|188518597|ref|ZP_03004049.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 11 str.
           ATCC 33695]
 gi|188524519|ref|ZP_03004514.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 12 str.
           ATCC 33696]
 gi|195868018|ref|ZP_03080013.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 9 str.
           ATCC 33175]
 gi|198273631|ref|ZP_03206166.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 4 str.
           ATCC 27816]
 gi|209554143|ref|YP_002284749.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 10 str.
           ATCC 33699]
 gi|225550349|ref|ZP_03771298.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 2 str.
           ATCC 27814]
 gi|225551084|ref|ZP_03772030.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 8 str.
           ATCC 27618]
 gi|171903184|gb|EDT49473.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 13 str.
           ATCC 33698]
 gi|184209186|gb|EDU06229.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 5 str.
           ATCC 27817]
 gi|188018789|gb|EDU56829.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 7 str.
           ATCC 27819]
 gi|188997798|gb|EDU66895.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 11 str.
           ATCC 33695]
 gi|195659715|gb|EDX53095.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 12 str.
           ATCC 33696]
 gi|195660310|gb|EDX53572.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 9 str.
           ATCC 33175]
 gi|198249659|gb|EDY74440.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 4 str.
           ATCC 27816]
 gi|209541644|gb|ACI59873.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 10 str.
           ATCC 33699]
 gi|225378899|gb|EEH01264.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 8 str.
           ATCC 27618]
 gi|225379503|gb|EEH01865.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 2 str.
           ATCC 27814]
          Length = 448

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 73/254 (28%), Positives = 123/254 (48%), Gaps = 40/254 (15%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           ++L TS++RLV  IA  Y   GL + +++ EG+ GL++A+ KFD E+G + +TY+ WWI+
Sbjct: 195 NQLYTSNMRLVTSIAKKYLNRGLDLEDLIQEGSSGLLKAIDKFDHEKGHKFSTYATWWIR 254

Query: 111 AAMQEYILRSWSLVKIGT---------TANQKRLFFNLRR-------LKGHLQAITDNNL 154
            ++   I      ++I           T  ++ L   L R        +   +A    N 
Sbjct: 255 QSITRAIADQARQIRIPVHMVETINKLTKAERSLIQELGRDPTAEEIAQAMNKASQAKNQ 314

Query: 155 KPE----QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
           K +    Q V   KKLNV   + +S++ ++  DE             SQ+ D++  D   
Sbjct: 315 KEQLITAQKVVEIKKLNV---DPVSLDKQIGHDE------------ESQFSDFISDDEII 359

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ---ENPVTLENLSSEFEVSRE 267
             +   EK+   ++ N +     VLN  E+R+ + R      E P TLE +     V+RE
Sbjct: 360 SPEKYTEKKALNDQINEMFE--KVLNDNEQRVIKMRYGLLPFERPYTLEEVGEHLGVTRE 417

Query: 268 RVRQIEARAFKKVQ 281
           R RQIE++A +K++
Sbjct: 418 RARQIESKAIRKLK 431


>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 = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 68/245 (27%), Positives = 117/245 (47%), Gaps = 32/245 (13%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 404 AAKREMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 463

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I     +     N R  + +LQ   ++   P+    +A+ + 
Sbjct: 464 WIRQAITRSIADQARTIRIPVHMIETINKMN-RISRQYLQETGED---PD-AAKLAELME 518

Query: 168 VSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           + E ++          ISM   +  D+  +      D N+    D  +Y           
Sbjct: 519 MPEDKIRKIMKIAKEPISMETPIGDDDDSHLGDFIEDVNNIAPADAAMY----------- 567

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEAR 275
                + R      +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+
Sbjct: 568 ----SSLREATKDVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 623

Query: 276 AFKKV 280
           A +K+
Sbjct: 624 ALRKL 628


>gi|332670669|ref|YP_004453677.1| RpoD subfamily RNA polymerase sigma-70 subunit [Cellulomonas fimi
           ATCC 484]
 gi|332339707|gb|AEE46290.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cellulomonas fimi
           ATCC 484]
          Length = 538

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 81/309 (26%), Positives = 141/309 (45%), Gaps = 60/309 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRY---------------------RE----HGD-LSAAHR 52
           Y+ +I K+ +L  ++E  LAKR                      RE     GD   A + 
Sbjct: 245 YLKQIGKVALLNAEQEVELAKRIEAGLFAEERLNAGVAMEPKLRRELEWIAGDGRRAKNH 304

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A
Sbjct: 305 LLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQA 364

Query: 113 MQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           +   +      ++I              Q+++  +L R     +   + ++ PE+VV + 
Sbjct: 365 ITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQ 424

Query: 164 KKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           K       E IS++  L   GD     LI  S+          V   D     L++++  
Sbjct: 425 KYGR----EPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ-- 469

Query: 222 KNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
                 L + +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K
Sbjct: 470 ------LHQVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSK 523

Query: 280 VQESIQKQV 288
           ++   + QV
Sbjct: 524 LRHPSRSQV 532


>gi|320536473|ref|ZP_08036507.1| RNA polymerase sigma factor RpoD family protein [Treponema
           phagedenis F0421]
 gi|320146682|gb|EFW38264.1| RNA polymerase sigma factor RpoD family protein [Treponema
           phagedenis F0421]
          Length = 282

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 43/111 (38%), Positives = 74/111 (66%), Gaps = 1/111 (0%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+ +I KIP+L  +EE  LA R  E GD +A  +L+ ++LR VV +A  Y+  GLP+
Sbjct: 12  LAGYLRDINKIPLLTLEEEVELATRAAE-GDKAAKDKLIQANLRFVVNVAKKYQNQGLPL 70

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            +++SEGNIGLM A  +FD  +G++  +Y++WWI+ ++ + I     ++++
Sbjct: 71  MDLISEGNIGLMNAADRFDVTKGYKFISYAVWWIRQSILKAICEKSRMIRL 121


>gi|323388685|gb|ADX60147.1| SIGMA70-like transcription factor [Zea mays]
          Length = 428

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 67/256 (26%), Positives = 121/256 (47%), Gaps = 36/256 (14%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           +R   HG +   +R+V S++RLV+ IA  + G G+  S+++ +G  GL++  +KFD  +G
Sbjct: 178 RRRLNHG-VYCKNRMVKSNVRLVISIAKEHEGPGMEFSDLIQDGMQGLIRGAEKFDASKG 236

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ---------KRLFFNLRRLKGHLQAI 149
           FR +TYS WWIK A+++ +L    ++++     +         +RL   L+RL  + +  
Sbjct: 237 FRFSTYSHWWIKQAIRKSVLEQTQIIRLPAHMAEASSRVKECCRRLGRELKRLPSNEEIA 296

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI--NSSDKNSSQWQDWLVYD 207
            D  +   +V A       S S    + C    D +   ++   S++        WL+  
Sbjct: 297 VDTGMTIRRVEAAMSLPKYSVSFTSKVGCT---DVTYQEIMPDTSAETAEETLHRWLM-- 351

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVS 265
                            +  +  ++  L+PRE+++   R   E     TL ++     VS
Sbjct: 352 -----------------KKDVNTALDSLSPREKQVMRYRFGIEGGRARTLHDIGQLMGVS 394

Query: 266 RERVRQIEARAFKKVQ 281
           RER+RQIE  AF+K++
Sbjct: 395 RERIRQIELGAFRKLR 410


>gi|307824736|ref|ZP_07654959.1| RNA polymerase, sigma 70 subunit, RpoD [Methylobacter tundripaludum
           SV96]
 gi|307734094|gb|EFO04948.1| RNA polymerase, sigma 70 subunit, RpoD [Methylobacter tundripaludum
           SV96]
          Length = 602

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 67/245 (27%), Positives = 113/245 (46%), Gaps = 32/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 363 AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 422

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   +A+++ +
Sbjct: 423 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQILQELGREATPEE---LAERMEM 477

Query: 169 SESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            E +V          ISM   +  DE             S   D++    D +    +E 
Sbjct: 478 PEDKVRKVLKIAKEPISMETPIGDDE------------DSHLGDFI---EDAKVLSPVEA 522

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARA 276
                 R      ++ L  RE ++   R         TLE +  +F+V+RER+RQIEA+A
Sbjct: 523 ATIAGLRESTQNVLAGLTAREAKVLRMRFGINMNTDHTLEEVGKQFDVTRERIRQIEAKA 582

Query: 277 FKKVQ 281
            +K++
Sbjct: 583 LRKLR 587


>gi|289553505|ref|ZP_06442715.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis KZN
           605]
 gi|289438137|gb|EFD20630.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis KZN
           605]
          Length = 338

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 82/298 (27%), Positives = 143/298 (47%), Gaps = 52/298 (17%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH-------------GDLSAAHR-------- 52
           Y++ I K  +L    E  LAKR     Y EH              DL+A  R        
Sbjct: 45  YLNGIGKTALLNAAGEVELAKRIEAGLYAEHLLETRKRLGENRKRDLAAVVRDGEAARRH 104

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A
Sbjct: 105 LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQA 164

Query: 113 MQEYILRSWSLVKIGTTANQK--RLFFNLRRLKGHL-QAITDNNLKPEQVVAIAKKLNVS 169
           +   +      +++     ++  +L    R +  HL +  TD  L  E  + I K  ++ 
Sbjct: 165 ITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQHLGREATDEELAAESGIPIDKINDLL 224

Query: 170 ES--EVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           E   + +S++  +  +E   L   I  ++  S+             E  +I +    + R
Sbjct: 225 EHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSA-------------ENAVIAELLHTDIR 271

Query: 226 NMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++L    + L+ RE ++   R   ++  P TL+ +   F +SRERVRQIE     K++
Sbjct: 272 SVL----ATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMSKLR 325


>gi|332711345|ref|ZP_08431277.1| RNA polymerase sigma factor, sigma-70 family//RpoD-like family
           [Lyngbya majuscula 3L]
 gi|332349894|gb|EGJ29502.1| RNA polymerase sigma factor, sigma-70 family//RpoD-like family
           [Lyngbya majuscula 3L]
          Length = 319

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 66/245 (26%), Positives = 120/245 (48%), Gaps = 33/245 (13%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           SA  ++V ++LRLVV +A  Y    L + +++ EG IGL + V+KFDP +G+R +TY+ W
Sbjct: 82  SAKRKMVEANLRLVVAVAKKYIKRNLELLDLIQEGTIGLQRGVEKFDPTKGYRFSTYAYW 141

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++     +K     L ++K   + ++    +   +  +A +LN
Sbjct: 142 WIRQAITRAIAEKGRTIRLPIHITEK-----LNKIKKAQRQLSQKLGRTATISELAIELN 196

Query: 168 VSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           ++  ++          +S+  R+ GD     L+   +      +D++        Q L++
Sbjct: 197 LTPDQLREYFEQARQPLSLELRV-GDNKDTELVELLEDTGPGPEDFV-------NQSLMQ 248

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR-LQE-NPVTLENLSSEFEVSRERVRQIEAR 275
            +        L + M  L P++R++   R  L E  P+TL  +     +SRERVRQIE  
Sbjct: 249 LD--------LEKFMDDLTPQQRQVLRLRYGLAEVEPMTLAKIGQHLNISRERVRQIERE 300

Query: 276 AFKKV 280
           A  K+
Sbjct: 301 AIAKL 305


>gi|312139424|ref|YP_004006760.1| sigma-70 factor sigb [Rhodococcus equi 103S]
 gi|325672687|ref|ZP_08152383.1| RNA polymerase principal sigma factor SigB [Rhodococcus equi ATCC
           33707]
 gi|311888763|emb|CBH48075.1| sigma-70 factor SigB [Rhodococcus equi 103S]
 gi|325556564|gb|EGD26230.1| RNA polymerase principal sigma factor SigB [Rhodococcus equi ATCC
           33707]
          Length = 322

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 74/251 (29%), Positives = 125/251 (49%), Gaps = 33/251 (13%)

Query: 46  DLSAAHR-LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           D  AA R L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY
Sbjct: 81  DGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTY 140

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA-----ITDNNLKPEQV 159
           + WWI+ A+   +      +++     ++     L R+K  L        TD  L  E  
Sbjct: 141 ATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLARIKRELHQQLGREATDEELSQESG 198

Query: 160 VA---IAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +    IA  L+ S   V S++  +  DE   L   I  S+  S+             E  
Sbjct: 199 IPEHKIADLLDHSRDPV-SLDMPVGNDEEAPLGDFIEDSEATSA-------------ENA 244

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
           +I      + R++L    + L+ RE+++   R   ++  P TL+ +   F +SRERVRQI
Sbjct: 245 VIAGLLHSDVRSVL----ATLDEREQQVIRLRYGLDDGQPRTLDQIGKLFGLSRERVRQI 300

Query: 273 EARAFKKVQES 283
           E     K+++ 
Sbjct: 301 EREVMGKLRQG 311


>gi|269793869|ref|YP_003313324.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Sanguibacter keddieii DSM
           10542]
 gi|269096054|gb|ACZ20490.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Sanguibacter keddieii DSM
           10542]
          Length = 342

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 76/307 (24%), Positives = 139/307 (45%), Gaps = 56/307 (18%)

Query: 19  YIHEIRKIPMLEKQEEY---------VLAKRYREHGD-----------------LSAAHR 52
           Y+  I ++P+L  ++E          +LA  Y E G+                 + A   
Sbjct: 49  YLKIIGRVPLLNAEQEIEIAMRIEAGMLAAHYLESGEYPKGATKRELEVITADGVRAKSH 108

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV ++LRLVV IA  Y G GL   +++ EGN GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 109 LVEANLRLVVSIAKKYTGRGLLFLDLIQEGNTGLIRAVEKFDYAKGFKFSTYATWWIRQA 168

Query: 113 MQEYILRSWSLVKIG---------TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           +   +      ++I           +  Q+++  +L R     +   + ++ PE+V+ + 
Sbjct: 169 ITRGMADQARTIRIPVHMVEVINKVSRAQRQMLQDLGREPTPEELALELDMTPEKVLEVQ 228

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           K       E IS++  L             ++  S++ D +    D +  V  +      
Sbjct: 229 KH----GREPISLHTPLG------------EEGGSEFGDLI---EDTEAVVPADAVNFSF 269

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +  +   +  L+ RE  +   R    +  P TL+ +   + V+RER+RQIE++   K++
Sbjct: 270 LQQQIHGILDTLSEREAGVITMRYGLTDGLPKTLDQIGHVYGVTRERIRQIESKTMSKLR 329

Query: 282 ESIQKQV 288
              + QV
Sbjct: 330 HPSRSQV 336


>gi|72381853|ref|YP_291208.1| putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus str. NATL2A]
 gi|72001703|gb|AAZ57505.1| possible type II alternative RNA polymerase sigma factor
           [Prochlorococcus marinus str. NATL2A]
          Length = 307

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 72/255 (28%), Positives = 129/255 (50%), Gaps = 13/255 (5%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           EY  A++ +      A ++++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+
Sbjct: 50  EYSSAEKKKFKAGERAKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKY 109

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           DP+RG R +TY+ WWI+  +   +      ++I    N+K     LR  K  L  + +  
Sbjct: 110 DPKRGHRFSTYAYWWIRQGLNRALSTQSRTIRIPVNINEK--LTKLRAAKSRL--MQELG 165

Query: 154 LKPE-QVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQ 211
           + P    +AI  K+ + E E + + C L     SL   +  S  + S+  D L  +    
Sbjct: 166 VHPSTNQIAIQMKIPLEEVEEL-LACELRSITVSLQGAVK-SKADPSELVDILPSEEVPP 223

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRER 268
            ++    E   +  ++L +S   L P+ER I   R   +      TL  ++ +   SRE 
Sbjct: 224 MELAELAERSASAWSLLDKSN--LTPKERTILSLRFGLDGSNEWRTLAEVARQMNCSREY 281

Query: 269 VRQIEARAFKKVQES 283
            RQ+  RA +K++++
Sbjct: 282 CRQVVQRALRKLRKT 296


>gi|15609847|ref|NP_217226.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis H37Rv]
 gi|15842248|ref|NP_337285.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis
           CDC1551]
 gi|31793882|ref|NP_856375.1| RNA polymerase sigma factor SigB [Mycobacterium bovis AF2122/97]
 gi|121638585|ref|YP_978809.1| RNA polymerase sigma factor SigB [Mycobacterium bovis BCG str.
           Pasteur 1173P2]
 gi|148662551|ref|YP_001284074.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis H37Ra]
 gi|215412516|ref|ZP_03421250.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis
           94_M4241A]
 gi|215446963|ref|ZP_03433715.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis T85]
 gi|224991077|ref|YP_002645766.1| RNA polymerase sigma factor [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|254365367|ref|ZP_04981412.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis str.
           Haarlem]
 gi|289444252|ref|ZP_06433996.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis T46]
 gi|289448365|ref|ZP_06438109.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           CPHL_A]
 gi|289570886|ref|ZP_06451113.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis T17]
 gi|289575408|ref|ZP_06455635.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis K85]
 gi|289751363|ref|ZP_06510741.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis T92]
 gi|289754812|ref|ZP_06514190.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           EAS054]
 gi|289758838|ref|ZP_06518216.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis T85]
 gi|289762881|ref|ZP_06522259.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis GM
           1503]
 gi|298526180|ref|ZP_07013589.1| RNA polymerase principal sigma factor SigB [Mycobacterium
           tuberculosis 94_M4241A]
 gi|307085405|ref|ZP_07494518.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu012]
 gi|313659647|ref|ZP_07816527.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis KZN
           V2475]
 gi|1171103|gb|AAA86044.1| sigma factor MysB [Mycobacterium tuberculosis H37Rv]
 gi|2182001|emb|CAB09470.1| RNA POLYMERASE SIGMA FACTOR SIGB [Mycobacterium tuberculosis H37Rv]
 gi|13882539|gb|AAK47099.1| RNA polymerase principal sigma factor SigB [Mycobacterium
           tuberculosis CDC1551]
 gi|31619476|emb|CAD94914.1| RNA POLYMERASE SIGMA FACTOR SIGB [Mycobacterium bovis AF2122/97]
 gi|121494233|emb|CAL72711.1| RNA polymerase sigma factor sigB [Mycobacterium bovis BCG str.
           Pasteur 1173P2]
 gi|134150880|gb|EBA42925.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis str.
           Haarlem]
 gi|148506703|gb|ABQ74512.1| RNA polymerase sigma factor [Mycobacterium tuberculosis H37Ra]
 gi|224774192|dbj|BAH26998.1| RNA polymerase sigma factor [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|289417171|gb|EFD14411.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis T46]
 gi|289421323|gb|EFD18524.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           CPHL_A]
 gi|289539839|gb|EFD44417.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis K85]
 gi|289544640|gb|EFD48288.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis T17]
 gi|289691950|gb|EFD59379.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis T92]
 gi|289695399|gb|EFD62828.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           EAS054]
 gi|289710387|gb|EFD74403.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis GM
           1503]
 gi|289714402|gb|EFD78414.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis T85]
 gi|298495974|gb|EFI31268.1| RNA polymerase principal sigma factor SigB [Mycobacterium
           tuberculosis 94_M4241A]
 gi|308365051|gb|EFP53902.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu012]
 gi|326904326|gb|EGE51259.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis W-148]
          Length = 323

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 82/298 (27%), Positives = 143/298 (47%), Gaps = 52/298 (17%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH-------------GDLSAAHR-------- 52
           Y++ I K  +L    E  LAKR     Y EH              DL+A  R        
Sbjct: 30  YLNGIGKTALLNAAGEVELAKRIEAGLYAEHLLETRKRLGENRKRDLAAVVRDGEAARRH 89

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A
Sbjct: 90  LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQA 149

Query: 113 MQEYILRSWSLVKIGTTANQK--RLFFNLRRLKGHL-QAITDNNLKPEQVVAIAKKLNVS 169
           +   +      +++     ++  +L    R +  HL +  TD  L  E  + I K  ++ 
Sbjct: 150 ITRGMADQSRTIRLPVHLVEQVNKLARIKREMHQHLGREATDEELAAESGIPIDKINDLL 209

Query: 170 ES--EVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           E   + +S++  +  +E   L   I  ++  S+             E  +I +    + R
Sbjct: 210 EHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSA-------------ENAVIAELLHTDIR 256

Query: 226 NMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++L    + L+ RE ++   R   ++  P TL+ +   F +SRERVRQIE     K++
Sbjct: 257 SVL----ATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMSKLR 310


>gi|288801981|ref|ZP_06407422.1| RNA polymerase sigma-70 factor [Prevotella melaninogenica D18]
 gi|302347072|ref|YP_003815370.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           melaninogenica ATCC 25845]
 gi|288335416|gb|EFC73850.1| RNA polymerase sigma-70 factor [Prevotella melaninogenica D18]
 gi|302150546|gb|ADK96807.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           melaninogenica ATCC 25845]
          Length = 290

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 82/292 (28%), Positives = 135/292 (46%), Gaps = 52/292 (17%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYG 72
            L +Y+ EI + PM+   EE  LA+   + G     A  +L+ ++LR VV +A  Y+  G
Sbjct: 17  ALDKYLVEIGREPMITVDEEIELAQEIHKGGRKGERAKEKLIKANLRFVVSVAKQYQHQG 76

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I            A Q
Sbjct: 77  LSLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAI------------AEQ 124

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL--I 190
            R+                  L   QV AI+ K+N   +E +  + R      L  L  I
Sbjct: 125 SRIV----------------RLPLNQVGAIS-KINQVTNEFVQQHNRRPSIHELAELTGI 167

Query: 191 NSSDKNSSQWQD---------WLVYDHDGQEQVLIEKEERKNRRNMLTRSMS-------- 233
           + +    SQ  D         +   D +    +L   ++ +  R +   SMS        
Sbjct: 168 DEARIRQSQSADNHHMSIDAPFSDDDDNSMSDMLSSGDDSRTDRGVDFESMSDDLRAVLQ 227

Query: 234 -VLNPRERRIF-EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             L  RE +I  E   +      LE + +E  ++RERVRQI  +A +K++ES
Sbjct: 228 NTLKDREIKIVTECFGIGCQEKGLEEIGTEMGLTRERVRQIREKAIEKIRES 279


>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 = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 72/243 (29%), Positives = 121/243 (49%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-KRLFFNLRRLKGH---LQAITDNNLKPEQVV 160
           I+ A+   I      ++I      T N+  R+   + +  G     + +++  L PE   
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELSERMLMPED-- 492

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D      ++   
Sbjct: 493 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDSTIVQPLDSAT 536

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + +N     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 537 GGSLKNATQEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 596

Query: 279 KVQ 281
           K++
Sbjct: 597 KLR 599


>gi|330466466|ref|YP_004404209.1| RNA polymerase sigma factor SigB [Verrucosispora maris AB-18-032]
 gi|328809437|gb|AEB43609.1| RNA polymerase sigma factor SigB [Verrucosispora maris AB-18-032]
          Length = 335

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 65/230 (28%), Positives = 118/230 (51%), Gaps = 16/230 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A + L+ ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ W
Sbjct: 97  AAKNHLLEANLRLVVSIAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATW 156

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQK--RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
           WI+ A+   +      ++I     ++  R+    R L   L        +   V  IA+ 
Sbjct: 157 WIRQAITRAMADQARTIRIPVHMVEQVNRMVRARRELSVSLG-------REPSVAEIARA 209

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           L+V E +VI +        SL+  +   +   S   D++          +++  +R   R
Sbjct: 210 LDVPEFQVIELISYDREPVSLDQTVG--EDGESALGDFVAAVDPSS---MVDDADRGELR 264

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIE 273
           N ++  ++ L+ RE+ +   R   ++    TL+ +  EF +SRER+RQIE
Sbjct: 265 NEVSIVLATLSQREQAVIRLRFGLDDGRQRTLDEVGREFGLSRERIRQIE 314


>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 = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 64/235 (27%), Positives = 109/235 (46%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 426 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 485

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+   +   T     P     +A+K+ +
Sbjct: 486 IRQAITRSIADQARTIRI--PVHMIETINKMNRISRQILQETGQEPDP---ATLAEKMEM 540

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++          E ++      D + S   D++    D       E       R+  
Sbjct: 541 PEEKI--RKIMKISKEPISMETPIGDDDDSHLGDFI---EDTATLAPAEAAMYSGLRDAT 595

Query: 229 TRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L  RE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 596 CEVLDSLTQREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 650


>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 = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 65/245 (26%), Positives = 112/245 (45%), Gaps = 32/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 423 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 482

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+   +   T     P     +A+K+ +
Sbjct: 483 IRQAITRSIADQARTIRI--PVHMIETINKMNRISRQILQETGQEPDP---ATLAEKMEM 537

Query: 169 SESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            E ++          ISM   +  D+  +      D+ +    D  +Y            
Sbjct: 538 PEEKIRKIMKISKEPISMETPIGDDDDSHLGDFIEDQATLAPADAAMY------------ 585

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARA 276
               + R+     +  L  RE ++   R   E     TLE +  +F+V+RER+RQIEA+A
Sbjct: 586 ---SSLRDATGEVLDSLTAREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKA 642

Query: 277 FKKVQ 281
            +K++
Sbjct: 643 LRKLR 647


>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 = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 118/234 (50%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 407 AKEEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 466

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       + R+    Q + ++   P+    +A+ + +
Sbjct: 467 IRQAITRSIADQARTIRI--PVHMIETINKMNRIS--RQYLQEHGEDPDS-AKLAELMEM 521

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D       E     + R + 
Sbjct: 522 PEDKIRKI-MKIAK-EPISMETPIGDDDDSHLGDFI---EDVNNVAPAEAAMYSSLREVT 576

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 577 ADVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 630


>gi|332307721|ref|YP_004435572.1| RNA polymerase, sigma 70 subunit, RpoD [Glaciecola agarilytica
           4H-3-7+YE-5]
 gi|332175050|gb|AEE24304.1| RNA polymerase, sigma 70 subunit, RpoD [Glaciecola agarilytica
           4H-3-7+YE-5]
          Length = 613

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 72/243 (29%), Positives = 121/243 (49%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-KRLFFNLRRLKGH---LQAITDNNLKPEQVV 160
           I+ A+   I      ++I      T N+  R+   + +  G     + +++  L PE   
Sbjct: 435 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELSERMLMPED-- 492

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D      ++   
Sbjct: 493 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDSTIVQPLDSAT 536

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
             + +N     ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 537 GGSLKNATQEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 596

Query: 279 KVQ 281
           K++
Sbjct: 597 KLR 599


>gi|86607249|ref|YP_476012.1| RNA polymerase sigma factor, group 1 [Synechococcus sp. JA-3-3Ab]
 gi|86555791|gb|ABD00749.1| RNA polymerase sigma factor, group 1 [Synechococcus sp. JA-3-3Ab]
          Length = 361

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 65/239 (27%), Positives = 119/239 (49%), Gaps = 22/239 (9%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L+ ++LRLVV +A  Y   G+P  +++ EGN+GL++A +KF+ ERGFR +TY+ WW
Sbjct: 124 AQRKLINANLRLVVSVAKKYLNRGVPFLDLIQEGNMGLIRATEKFNAERGFRFSTYAHWW 183

Query: 109 IKAAMQEYILRSWSLVKIGT-TANQKRLFFNLRR--LKGHLQAITDNNLKPEQVVAIAKK 165
           I+  +   I      +++     ++ RL     R  +K   +  T+  L     + + K 
Sbjct: 184 IRQGITRCIANQARTIRLPVHMVDKVRLLKRTNRELMKARGRRPTEAELAEALGIKVKKL 243

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ--EQVLIEKEERKN 223
             + ++  + +        SL+  +    +  S+  D L  +   Q  E++L++     +
Sbjct: 244 RMIQQAAALPL--------SLDVPVGQ--EGESRLGDLLPDERQEQPFEEILVQ-----S 288

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
            R  +  +M  L P ER++ E R   +     TL  +   F ++RER+RQIE  A +K+
Sbjct: 289 LRQDVRSAMQALKPIERQVLELRYGLDGQRARTLREVGDHFNLTRERIRQIERDALRKL 347


>gi|239927194|ref|ZP_04684147.1| RNA polymerase principal sigma factor HrdC [Streptomyces ghanaensis
           ATCC 14672]
 gi|291435537|ref|ZP_06574927.1| RNA polymerase principal sigma factor HrdC [Streptomyces ghanaensis
           ATCC 14672]
 gi|291338432|gb|EFE65388.1| RNA polymerase principal sigma factor HrdC [Streptomyces ghanaensis
           ATCC 14672]
          Length = 339

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 81/306 (26%), Positives = 147/306 (48%), Gaps = 46/306 (15%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKR-------------------------YRE-----HG 45
           L +Y+ +I   P+L+ ++E  LA+R                         +RE     H 
Sbjct: 39  LGQYLRQIGATPLLDAEDEVRLAQRIAAGLRAKEEYERAESGGHHLTRERWRELEAAVHD 98

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
             +A  R++ ++LRLVV +A  +   GLP+ +V+ EGN+GL++AV+KFD  +GF+ +TY+
Sbjct: 99  GQAAKDRMIRANLRLVVSMAKRHAHRGLPLLDVIQEGNLGLIRAVEKFDHTKGFKFSTYA 158

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
            WWI+ A++  +      V++     ++     L +++  L    D     E+V   A++
Sbjct: 159 TWWIRQAIERGVATHARTVRLPVHVVEQ--LQKLGKVERRLHLSLDREPTVEEV---ARE 213

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE--ERKN 223
             ++E +V+ +  R  G +     + S D       D +V D     +VL   E  E + 
Sbjct: 214 SGLAEKKVVWL--RRVGRQ-----VVSLDTPVDDTGDTVVGDLIPDTEVLQAPEVAEFQA 266

Query: 224 RRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
               L  ++  L PRE  I   R  L +    TL+ ++    ++RERVRQ+E ++  +++
Sbjct: 267 LAEELRGAVDTLAPREALILSLRYGLHDGQTRTLQEVADHVGLTRERVRQLEKQSLAQLR 326

Query: 282 ESIQKQ 287
           E  Q +
Sbjct: 327 EREQGE 332


>gi|84495969|ref|ZP_00994823.1| RNA polymerase sigma factor [Janibacter sp. HTCC2649]
 gi|84382737|gb|EAP98618.1| RNA polymerase sigma factor [Janibacter sp. HTCC2649]
          Length = 546

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 78/309 (25%), Positives = 138/309 (44%), Gaps = 60/309 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYRE---------HGDL-----------------SAAHR 52
           Y+ +I K+ +L  ++E  LAKR             GD                  +A + 
Sbjct: 253 YLKQIGKVALLNAEQEVELAKRIEAGLFGEERLNSGDKIDMKLKRELWWIAQDGKNAKNH 312

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A
Sbjct: 313 LLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQA 372

Query: 113 MQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           +   +      ++I              Q+++  +L R     +   + ++ PE+VV + 
Sbjct: 373 ITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAIELDMTPEKVVEVQ 432

Query: 164 KKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           K       E IS++  L   GD     LI  S+          V   D     L++++  
Sbjct: 433 K----YGREPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ-- 477

Query: 222 KNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
                 L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K
Sbjct: 478 ------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSK 531

Query: 280 VQESIQKQV 288
           ++   + Q 
Sbjct: 532 LRHPSRSQA 540


>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 = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 70/243 (28%), Positives = 116/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 377 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 436

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 437 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPED 494

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   Q  I+   
Sbjct: 495 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDSTMQSPIDVAT 538

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ +      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 539 VESLKEATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 598

Query: 279 KVQ 281
           K++
Sbjct: 599 KLR 601


>gi|39132|emb|CAA49185.1| vegetative sigma factor [Agrobacterium tumefaciens str. C58]
          Length = 684

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 81/279 (29%), Positives = 136/279 (48%), Gaps = 33/279 (11%)

Query: 10  VNGEIGLSRYIHEIRKI-PMLEKQE-EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++ E G+S  I E R+I  M++K E E  +AK+            +V ++LRLV+ IA  
Sbjct: 418 LSTETGIS--IAEFRRIVSMVQKGEREARIAKK-----------EMVEANLRLVISIAKK 464

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I 
Sbjct: 465 YTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI- 523

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              +       + R    +         PE+   +A+KL +   +V  +  ++A  E ++
Sbjct: 524 -PVHMIETINKIVRTSRQMLHEIGREPTPEE---LAEKLAMPLEKVRKV-LKIA-KEPIS 577

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
                 D+  S   D++    D    + I+   +   R   TR ++ L P E R+    R
Sbjct: 578 LETPVGDEEDSHLGDFI---EDKNALLPIDAAIQGFLRETTTRVLASLTPSEERVL---R 631

Query: 248 L-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +          TLE +  +F V+RER+RQIEA+A + V+
Sbjct: 632 MPFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRNVK 670


>gi|172037252|ref|YP_001803753.1| group 2 sigma-70 RNA polymerase sigma factor [Cyanothece sp. ATCC
           51142]
 gi|171698706|gb|ACB51687.1| group 2 sigma-70 RNA polymerase sigma factor [Cyanothece sp. ATCC
           51142]
          Length = 297

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 73/275 (26%), Positives = 142/275 (51%), Gaps = 28/275 (10%)

Query: 13  EIGLSRYIHEIRKIPMLEKQ-----EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           EI L+  I  +  +P+LEK+     EE ++AK  R      A  +++ ++LRLVV IA  
Sbjct: 28  EIKLAEEIQAM--LPLLEKEALSKEEEKIVAKGQR------ARDKMIQANLRLVVSIAKK 79

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y   GL + +++ EG++GL++ V+KFDP RG++ +TY+ WWI+  +   I      +++ 
Sbjct: 80  YLNSGLSLLDLIQEGSLGLIRGVEKFDPSRGYKFSTYAYWWIRQGITRAIAEQSRTIRLP 139

Query: 128 TTANQKRLFFNLRRLKGHLQAITDN-NLKP-EQVVAIAKKLNVSESEVISMNCRLAGDES 185
              N+     NL + +  ++ +T     KP +Q +A    ++V +   +          S
Sbjct: 140 IHINE-----NLNKYRKSIRELTLKLGRKPTQQEIAENMDISVDKLRFLQQAAFKTKSRS 194

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           LN +I   D+N ++    L  +        ++++E+ ++ N   R +  L+PR++ +   
Sbjct: 195 LNIVI---DENHTELGQLLPDEDSVSPSDFVKQQEKISQIN---RMLENLSPRQKEVIIL 248

Query: 246 R-RLQENP-VTLENLSSEFEVSRERVRQIEARAFK 278
           R  L++   ++ + +  +  +S ER RQI +RA +
Sbjct: 249 RFGLRDGKQLSYKAIGEQCGISHERARQIYSRALR 283


>gi|218440090|ref|YP_002378419.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
 gi|218172818|gb|ACK71551.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
          Length = 295

 Score = 87.8 bits (216), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 81/287 (28%), Positives = 142/287 (49%), Gaps = 36/287 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR------EHGDLSAAHR------------LVTSHLRL 60
           Y+ EI +IP+L  +EE  LA + +      E  +L+AA +            ++ ++LRL
Sbjct: 12  YLQEIGRIPLLNSEEEVQLATKVQNMLPLLEKENLTAAEKKIVEQGQIAKRKMIQANLRL 71

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y+  GL + +++ EG++GL++AV+KFDP +G++ +TY+ WW++ A+   +   
Sbjct: 72  VVSIAKRYQRRGLSLLDLIQEGSLGLIRAVEKFDPSKGYKFSTYAYWWVRQAITRALAEK 131

Query: 121 WSLVK--IGTTANQKRLFFNLRRLKGHLQAITDNNLKP-EQVVAIAKKLNVSESEVISMN 177
              ++  I  T N  +L  ++R L G L        KP EQ VA   ++ V +   I   
Sbjct: 132 SRTIRLPIHMTENLNQLKKSVRELTGEL------GRKPNEQEVAQRMEIPVEKLREIRHA 185

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                 +SLN  +   D N ++  + L  D        + + E   + N L   +  L P
Sbjct: 186 VYRTDAKSLNITL---DDNQTELGEVLP-DETSLPIEFVSQWELVTKINDL---LEDLPP 238

Query: 238 RERRIFEAR-RLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           R+R I   R  LQ    ++ + +  +  +S ER RQ+  RA + +++
Sbjct: 239 RQREIITLRFGLQTGKRMSYKEIGRQCGISHERARQLLNRAMRTLKQ 285


>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 = 87.4 bits (215), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 65/238 (27%), Positives = 118/238 (49%), Gaps = 18/238 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 381 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 440

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   + +++ +
Sbjct: 441 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEE---LGERMEM 495

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E +V  +  ++A  E ++      D   S   D++      ++  +    E    + ++
Sbjct: 496 PEDKVRKV-LKIAK-EPISMETPIGDDEDSHLGDFI------EDTTITSPVESATSQGLM 547

Query: 229 TRSMSV---LNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             + +V   L  RE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 548 EATKAVLAGLTAREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 605


>gi|309812669|ref|ZP_07706413.1| RNA polymerase sigma factor RpoD [Dermacoccus sp. Ellin185]
 gi|308433364|gb|EFP57252.1| RNA polymerase sigma factor RpoD [Dermacoccus sp. Ellin185]
          Length = 550

 Score = 87.4 bits (215), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 79/309 (25%), Positives = 141/309 (45%), Gaps = 60/309 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR---------EHG---DL--------------SAAHR 52
           Y+ +I K+ +L  ++E  LAKR           E G   D+              +A + 
Sbjct: 257 YLKQIGKVALLNAEQEVELAKRIEAGLFAEQKLESGVKMDMKLKRELWWIASDGKNAKNH 316

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A
Sbjct: 317 LLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQA 376

Query: 113 MQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           +   +      ++I              Q+++  +L R     +   + ++ PE+V+ + 
Sbjct: 377 ITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVIEVQ 436

Query: 164 KKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           K       E IS++  L   GD     LI  S+          V   D     L++++  
Sbjct: 437 KYGR----EPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ-- 481

Query: 222 KNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
                 L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K
Sbjct: 482 ------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSK 535

Query: 280 VQESIQKQV 288
           ++   + QV
Sbjct: 536 LRHPSRSQV 544


>gi|1710688|sp|P52327|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 = 87.4 bits (215), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 72/245 (29%), Positives = 119/245 (48%), Gaps = 32/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 376 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 435

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 436 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPED 493

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D+ + D   Q  + +   E
Sbjct: 494 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDF-IEDSTMQSPIYVATVE 539

Query: 221 --RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARA 276
             ++  R++L    S L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A
Sbjct: 540 SLKEATRDVL----SGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 595

Query: 277 FKKVQ 281
           ++K++
Sbjct: 596 WRKLR 600


>gi|284049111|ref|YP_003399450.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidaminococcus
           fermentans DSM 20731]
 gi|283953332|gb|ADB48135.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidaminococcus
           fermentans DSM 20731]
          Length = 589

 Score = 87.4 bits (215), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 75/248 (30%), Positives = 121/248 (48%), Gaps = 32/248 (12%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD +A   L  ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY
Sbjct: 348 GD-NAKKCLSEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYNKGFKFSTY 406

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + WWI+ A+   I      ++I    +       L R+   L         PE+   IAK
Sbjct: 407 ATWWIRQAITRAIADQARTIRI--PVHMVETINKLVRVSRQLLQELGREPTPEE---IAK 461

Query: 165 KLNVS----------ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +++VS            E +S+   +  +E  +      D+ +    D   Y        
Sbjct: 462 EMDVSVERVREIQKIAQEPVSLETPIGEEEDSHLGDFIEDQEAPSPADAASY-------T 514

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQI 272
           L++++  K    +L   +S    RERR+ E R   +     TLE +   F V+RER+RQI
Sbjct: 515 LLQEQLGK----VLQEHLSA---RERRVLELRFGLMDGRTRTLEEVGQYFGVTRERIRQI 567

Query: 273 EARAFKKV 280
           EA+A +K+
Sbjct: 568 EAKALRKL 575


>gi|157412994|ref|YP_001483860.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9215]
 gi|157387569|gb|ABV50274.1| Putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus str. MIT 9215]
          Length = 307

 Score = 87.4 bits (215), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 80/296 (27%), Positives = 141/296 (47%), Gaps = 32/296 (10%)

Query: 12  GEIGLSRYIHEIRKIPMLEK-QEEYVLAKRYREHG------DLSAAHR------------ 52
           GEIG  + +   R++ M  K QE  VL  R +E G      + S A R            
Sbjct: 9   GEIGRHQLLTPERELTMGRKVQEMVVLVNRCQEAGGKGPACEYSEAERKKIKIGEKAKNE 68

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG R +TY+ WWI+  
Sbjct: 69  MITANLRLVVNLAKRYQGKGLELLDLIQEGTLGLTRAVEKYDPSRGHRFSTYAYWWIRQG 128

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           + + +      ++I    N+K     LR  K  L  +      P     +++++ +++ E
Sbjct: 129 LNKALSTQSRTIRIPVNINEK--LTKLRSAKSKLMQLKGI---PPTSDELSEEMKITKEE 183

Query: 173 VIS-MNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           +   ++C L     SL   + S   + S+  D L  D     ++    E   +   +L +
Sbjct: 184 IEELLSCELRSITVSLQGTVKSKS-DPSELVDILPSDQTPPMELAELAERTASAWKLLDK 242

Query: 231 SMSVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +   L  +ER+I   R   +      TL  ++     SRE  RQ+  RA +K++++
Sbjct: 243 AN--LTEKERKIVSLRFGLDGSNEWRTLAEVARHMSCSREYCRQVVQRALRKLRKA 296


>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 = 87.4 bits (215), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 70/243 (28%), Positives = 116/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 377 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 436

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 437 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELGERMEMPED 494

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D   Q  I+   
Sbjct: 495 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDSTMQSPIDVAT 538

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ +      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 539 VESLKEATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 598

Query: 279 KVQ 281
           K++
Sbjct: 599 KLR 601


>gi|320537570|ref|ZP_08037508.1| RNA polymerase sigma factor RpoD family protein [Treponema
           phagedenis F0421]
 gi|320145572|gb|EFW37250.1| RNA polymerase sigma factor RpoD family protein [Treponema
           phagedenis F0421]
          Length = 274

 Score = 87.4 bits (215), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 74/277 (26%), Positives = 134/277 (48%), Gaps = 23/277 (8%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           GE   S+Y+ +I++ P+L  QEE  LA +  ++GD  A  +L+ S+LRLVVK+A      
Sbjct: 2   GENIFSQYLKDIKRYPLLTAQEELCLADKI-QNGDRGALQQLINSNLRLVVKMAKDRTPS 60

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
              + +++ EGN+GLM A +KF      R ++Y+ WWI+ ++  Y+      +++     
Sbjct: 61  ENLLMDLIQEGNMGLMIAAEKFSSSFNARFSSYACWWIRQSLNRYLNGKHETIRLPFRKA 120

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC-----RLAGDESL 186
                  LR+++  +    +   +      IA+ + V    VI + C      ++ D  L
Sbjct: 121 DL-----LRKIEKTIDLFKEKYRRTPSYEEIAEIIQVPLKSVIQI-CVFTEKPISFDSPL 174

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
               +++  + ++  D+        E+    K + +  R  L    + L  RE+ I E R
Sbjct: 175 QIHFSANLYDLTENNDY------NPEKEYFRKVQIEAFRKFL---QNTLKSREKDIIEER 225

Query: 247 R--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                +NP +L +L  ++ +S E VRQ E RA KK++
Sbjct: 226 LPITDKNPKSLRSLGIKYGISAESVRQTEIRALKKLR 262


>gi|229820409|ref|YP_002881935.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Beutenbergia
           cavernae DSM 12333]
 gi|229566322|gb|ACQ80173.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Beutenbergia
           cavernae DSM 12333]
          Length = 499

 Score = 87.4 bits (215), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 79/310 (25%), Positives = 139/310 (44%), Gaps = 62/310 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ +I K+ +L  ++E  LAKR  E G  +                           A +
Sbjct: 206 YLKQIGKVALLNAEQEVELAKRI-EAGLFAEETLAAGGSMEFKLRRELEWIAADGRRAKN 264

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 265 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 324

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++I              Q+++  +L R     +   + ++ PE+VV +
Sbjct: 325 AITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEV 384

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  S+          V   D     L++++ 
Sbjct: 385 QKYGR----EPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ- 430

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   
Sbjct: 431 -------LHAVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMS 483

Query: 279 KVQESIQKQV 288
           K++   + QV
Sbjct: 484 KLRHPSRSQV 493


>gi|284931435|gb|ADC31373.1| RNA polymerase sigma factor RpoD (Sigma-A) [Mycoplasma
           gallisepticum str. F]
          Length = 646

 Score = 87.4 bits (215), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 77/255 (30%), Positives = 126/255 (49%), Gaps = 45/255 (17%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A ++LVTS+LRLV  IA  Y   GL   +++ EG+IGLM+A+ KF+ + G + +TY+ WW
Sbjct: 397 AINQLVTSNLRLVTSIAKKYLNRGLDFVDLIQEGSIGLMKAISKFNYKLGNKFSTYATWW 456

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ----KRLFFNLRRLKGHLQAITD------NNL 154
           I+ A+   I      V+I      T N+    +R+          L+ +T+      N  
Sbjct: 457 IRQAITRAIADQARTVRIPVHMVETINKLIKTERMLTQQLGRDPTLEELTEAMGGQVNGF 516

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            P++V  I KKLN    E +S++  +  DE             SQ+ D+ V D D     
Sbjct: 517 TPKKVADI-KKLN---QEPVSLDKPIGHDE------------ESQFVDF-VKDRD----- 554

Query: 215 LIEKEERKNRRNMLTRSM-----SVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSR 266
            I K +    + ++T  +     + L  +E +I   R         +TLE +  +F V+R
Sbjct: 555 -ILKPDEYTEKLIVTEHINELFVNTLTKKEEQIIRMRYGLHPWHQQMTLEEVGQKFNVTR 613

Query: 267 ERVRQIEARAFKKVQ 281
           ER+RQIE++A +K++
Sbjct: 614 ERIRQIESKALRKLK 628


>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 = 87.4 bits (215), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 65/238 (27%), Positives = 118/238 (49%), Gaps = 18/238 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 395 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 454

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   + +++++
Sbjct: 455 IRQAITRSIADQARTIRI--PVHMIETINKLNRVSRQMLQEMGREPTPEE---LGERMDM 509

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E +V  +  ++A  E ++      D   S   D++      ++  +I   E      ++
Sbjct: 510 PEDKVRKV-LKIA-KEPISMETPIGDDEDSHLGDFI------EDTTIISPVESATMEGLM 561

Query: 229 TRSMSV---LNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             +  V   L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 562 EATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 619


>gi|218440063|ref|YP_002378392.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
 gi|218172791|gb|ACK71524.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
          Length = 372

 Score = 87.4 bits (215), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 71/237 (29%), Positives = 119/237 (50%), Gaps = 15/237 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           SA  +++ S+LRLVV IA  Y   G+P  +++ EG IGL +A +KFDP +G++ +TY+ W
Sbjct: 133 SAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPNKGYKFSTYAYW 192

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++     +K     L +LK   + +     +      +A+ L 
Sbjct: 193 WIRQAITRTIANDARTIRLPIHIVEK-----LNKLKKAQRVLKQQLHRNPTEKELAQALE 247

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ--EQVLIEKEERKNRR 225
           V    +  +        SLN  +   +   ++  D L+ D D Q  E+ + E   R++  
Sbjct: 248 VDAENLRQLLQLRRQSLSLNHRVGKGE--DTELVD-LLEDEDLQLPEEKMNEAMMRQDIS 304

Query: 226 NMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            +LT    VL  RE+ +   R       P TLE +   F +SRERVRQI+++A +K+
Sbjct: 305 AVLT---DVLTEREKDVIALRYGLSTSQPYTLEEVGGIFNLSRERVRQIQSKAMRKL 358


>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 = 87.4 bits (215), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 65/235 (27%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 362 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 421

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   + +++++
Sbjct: 422 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEE---LGERMDM 476

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E +V  +  ++A  E ++      D   S   D++    D      ++    +  +   
Sbjct: 477 PEDKVRKV-LKIAK-EPISMETPIGDDEDSHLGDFI---EDVTIASPVDSATGQGLQEAT 531

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           T  ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 532 TEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 586


>gi|148239078|ref|YP_001224465.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp. WH
           7803]
 gi|147847617|emb|CAK23168.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 7803]
          Length = 308

 Score = 87.4 bits (215), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 78/252 (30%), Positives = 126/252 (50%), Gaps = 19/252 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A ++++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG R + Y+ WW
Sbjct: 66  AKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSNYAYWW 125

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   +      ++I    N+K     LR  K  L  +  N L P     +A  LN+
Sbjct: 126 IRQGLNRALSTQSRTIRIPVNVNEK--LTKLRASKARL--MQRNGLSP-STEQLADDLNL 180

Query: 169 SESEVIS-MNCRL-AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             SEV   + C L +   SL  ++ S    S      LV     +E   +E+ E   R  
Sbjct: 181 PISEVEDLLGCELRSVTVSLQGVVKSKSDPSE-----LVDVLPSEEVPPMERAEIAERTA 235

Query: 227 MLTRSM--SVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              + +  S L P+ER +   R   +      TL  ++ +   SRE  RQ+  RA +K++
Sbjct: 236 SAWKLLDKSNLTPKERTVVMLRFGLDGSNEWRTLAEVARQMNCSREYCRQVVQRALRKLR 295

Query: 282 ES-IQKQ-VELS 291
           ++ IQ   VELS
Sbjct: 296 KTGIQHGLVELS 307


>gi|317124635|ref|YP_004098747.1| RNA polymerase, sigma 70 subunit, RpoD [Intrasporangium calvum DSM
           43043]
 gi|315588723|gb|ADU48020.1| RNA polymerase, sigma 70 subunit, RpoD [Intrasporangium calvum DSM
           43043]
          Length = 587

 Score = 87.4 bits (215), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 79/309 (25%), Positives = 139/309 (44%), Gaps = 60/309 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR------------EHGDLS--------------AAHR 52
           Y+ +I K+ +L  ++E  LAKR              E  D+               A + 
Sbjct: 294 YLKQIGKVALLNAEQEVELAKRIEAGLFAEEKLNSGEKIDMKLKRELWWIAQDGKKAKNH 353

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A
Sbjct: 354 LLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQA 413

Query: 113 MQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           +   +      ++I              Q+++  +L R     +   + ++ PE+VV + 
Sbjct: 414 ITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKVVEVQ 473

Query: 164 KKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           K       E IS++  L   GD     LI  S+          V   D     L++++  
Sbjct: 474 KYGR----EPISLHTPLGEDGDSEFGDLIEDSEA---------VVPADAVSFTLLQEQ-- 518

Query: 222 KNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
                 L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K
Sbjct: 519 ------LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSK 572

Query: 280 VQESIQKQV 288
           ++   + QV
Sbjct: 573 LRHPSRSQV 581


>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 = 87.4 bits (215), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 68/242 (28%), Positives = 113/242 (46%), Gaps = 28/242 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 372 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 431

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 432 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEELAERMMMPED 489

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D      ++   
Sbjct: 490 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLAQPVDSAT 533

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            ++ +      ++ L  RE ++   R   E     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 534 AESLKAATAEVLAGLTAREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALR 593

Query: 279 KV 280
           K+
Sbjct: 594 KL 595


>gi|297571337|ref|YP_003697111.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Arcanobacterium
           haemolyticum DSM 20595]
 gi|296931684|gb|ADH92492.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Arcanobacterium
           haemolyticum DSM 20595]
          Length = 510

 Score = 87.4 bits (215), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 76/298 (25%), Positives = 142/298 (47%), Gaps = 38/298 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH---------------------GDLSAAHR 52
           Y+ +I K+ +L  +EE  LAKR     + +H                         A + 
Sbjct: 217 YLKQIGKVALLNAEEEVELAKRIEAGLFAQHILETTTIDDPRKRRELEIISRDGHKAKNH 276

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A
Sbjct: 277 LLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLVRAVEKFDYAKGYKFSTYATWWIRQA 336

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +      ++I    +   +   L R++   Q + D   +P  V  +A +L+++E +
Sbjct: 337 ITRAMADQARTIRI--PVHMVEVINKLARVQ--RQMLQDLGREP-TVEELAHELDMTEEK 391

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           VI +     G E ++      +   S++ D +    D +  V  +       +  L + +
Sbjct: 392 VIEVQKY--GREPISLHTPLGEDGDSEFGDLI---EDSEAVVPADAVGFTLLQEQLHQVL 446

Query: 233 SVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
             L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   + QV
Sbjct: 447 DTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQV 504


>gi|158336372|ref|YP_001517546.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158306613|gb|ABW28230.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 318

 Score = 87.4 bits (215), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 120/243 (49%), Gaps = 35/243 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y    +   +++ EG IGL + V+KFDP +G+R +TY+ WW
Sbjct: 83  ANRKMVESNLRLVVSIAKKYNKAKVEFLDLIQEGTIGLQRGVEKFDPMKGYRFSTYAYWW 142

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-----------QAITDNNLKPE 157
           I+ AM   I      +++    N+K     LR+++  L           +   + +L P+
Sbjct: 143 IRQAMTRAIAEQERTIRLPIHINEK--LSKLRKVRRQLSQKLHRDPTVQELAVEMDLAPK 200

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           +   I   LN +    IS++ ++ GD+          +N+  W+  L+ D +        
Sbjct: 201 K---IEDYLNYARRS-ISLDIQI-GDQ----------QNTELWE--LLEDPNESPDTYAT 243

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
                + R+ L + +  L+P++R +   R   + +NP+TL  +     VSRE VR++E  
Sbjct: 244 A---SSLRSDLAKLLQDLSPQQREVITLRYGLIDQNPLTLAKVGERLNVSREWVRRVERE 300

Query: 276 AFK 278
           AFK
Sbjct: 301 AFK 303


>gi|148239880|ref|YP_001225267.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. WH 7803]
 gi|147848419|emb|CAK23970.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 7803]
          Length = 322

 Score = 87.4 bits (215), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 72/306 (23%), Positives = 135/306 (44%), Gaps = 51/306 (16%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAH--------------------------- 51
           Y+ +I ++P+L  Q+E  L ++ +E  DL A                             
Sbjct: 16  YLRDIGRVPLLSHQQEITLGRQVQELMDLEATEAELQEKRGGEAVPAAELAKAAGLSAVQ 75

Query: 52  -------------RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
                        R+V ++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP RG
Sbjct: 76  LKRKLQAGRRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRG 135

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           ++ +TY+ WWI+  +   I      +++     +      L +LK   + ++ +  +   
Sbjct: 136 YKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITE-----MLNKLKKGQRELSQDLGRTPS 190

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD-GQEQVLIE 217
           V  +A  + + E EV  + CR     SL   +   D + ++  D L  D +   EQV  E
Sbjct: 191 VTELAAFVELPEDEVKELMCRARQPVSLE--MKVGDGDDTELLDLLAGDGELPSEQV--E 246

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
            E  K     L   +  L  R  R+       E+P++L  ++   ++SR+R R++E    
Sbjct: 247 GECLKGDLRDLLGQLPELQERVLRMRYGMD-GEDPMSLTGIAKTLKMSRDRTRRLEREGL 305

Query: 278 KKVQES 283
           + ++++
Sbjct: 306 ESLRQA 311


>gi|108799144|ref|YP_639341.1| RNA polymerase sigma factor SigB [Mycobacterium sp. MCS]
 gi|119868259|ref|YP_938211.1| RNA polymerase sigma factor SigB [Mycobacterium sp. KMS]
 gi|126434752|ref|YP_001070443.1| RNA polymerase sigma factor SigB [Mycobacterium sp. JLS]
 gi|108769563|gb|ABG08285.1| RNA polymerase, sigma 28 subunit [Mycobacterium sp. MCS]
 gi|119694348|gb|ABL91421.1| RNA polymerase, sigma 70 subunit, RpoD family [Mycobacterium sp.
           KMS]
 gi|126234552|gb|ABN97952.1| RNA polymerase, sigma 70 subunit, RpoD family [Mycobacterium sp.
           JLS]
          Length = 319

 Score = 87.4 bits (215), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 80/300 (26%), Positives = 142/300 (47%), Gaps = 56/300 (18%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH-------------GDLSAAHR-------- 52
           Y++ I K  +L   +E  LAKR     Y +H              DL+A  R        
Sbjct: 26  YLNGIGKTALLNAADEVELAKRIEAGLYAQHLLNTKKRLGESRKRDLAAVVRDGEAARRH 85

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A
Sbjct: 86  LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQA 145

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ-----AITDNNLKPEQVVAIAKKLN 167
           +   +      +++     ++     L R+K  +        TD  L  E  +   K  +
Sbjct: 146 ITRGMADQSRTIRLPVHLVEQ--VNKLARIKREMHQNLGREATDEELAEESGIPAEKIAD 203

Query: 168 VSES--EVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + E   + +S++  +  DE   L   I  ++  S+             E  +I +    +
Sbjct: 204 LLEHSRDPVSLDMPVGSDEEAPLGDFIEDAEAMSA-------------ENAVISELLHTD 250

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R++L    + L+ RE+++   R   ++  P TL+ +   F +SRERVRQIE     K++
Sbjct: 251 IRHVL----ATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMAKLR 306


>gi|4218586|emb|CAA10725.1| chloroplast sigma factor [Triticum aestivum]
          Length = 461

 Score = 87.4 bits (215), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 77/242 (31%), Positives = 125/242 (51%), Gaps = 28/242 (11%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L  S++RLV+ IA  Y   G+ +S+++  G IGL++ ++KFD  RGFR++TY  WWI+  
Sbjct: 222 LTMSNIRLVISIAQKYDKLGVELSDLIQGGLIGLLRGIEKFDASRGFRISTYVYWWIRQG 281

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +  +    ++ T  +++     L  ++G   A+ D  + P     IAK LN+SE +
Sbjct: 282 VSRALADNSKTFRLPTYLHER-----LIAIRGAKYALEDQGVSPT-TQNIAKLLNISEKK 335

Query: 173 VI----SMNCRLAGDE----SLNALINSSDKNSSQWQDWLVYD---HDGQEQVLIEKEER 221
           V     ++N  L+ D+    SLN L    D   S  +D  V +   H  +E  L  KEE 
Sbjct: 336 VHNATEAVNKALSLDQQAFPSLNGL--PGDTLHSYIEDQNVANDPWHGFEEWYL--KEEV 391

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARR-LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
               N      S L  RER I +    + +   T E++S +F +SRERVRQ+   A +K+
Sbjct: 392 NKLLN------SNLTERERDIIQLYHGIGKQCHTWEDISRQFGLSRERVRQVGLIAMEKL 445

Query: 281 QE 282
           ++
Sbjct: 446 KQ 447


>gi|308270755|emb|CBX27365.1| RNA polymerase sigma factor rpoD [uncultured Desulfobacterium sp.]
          Length = 568

 Score = 87.4 bits (215), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 70/239 (29%), Positives = 120/239 (50%), Gaps = 20/239 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L  ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 330 AKSELTRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 389

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+      L R   +L         PE+   IA+
Sbjct: 390 IRQAITRAIADQARTIRIPVHMIETINK------LIRTSRYLVQEQGREPSPEE---IAE 440

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           K+ +   +V  +  ++A  E ++      ++  S   D++    D +  +  +    +N 
Sbjct: 441 KMEIPLEKVRKV-LKIAR-EPISLETPIGEEEDSHLGDFI---EDKKFMLPSDAAINQNL 495

Query: 225 RNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                + ++ L PRE ++   R    +    TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 496 AEQTRKVLATLTPREEKVLRMRFGIGERADHTLEEVGQDFQVTRERIRQIEAKALRKLR 554


>gi|158340842|ref|YP_001522010.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158311083|gb|ABW32696.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 299

 Score = 87.4 bits (215), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 70/246 (28%), Positives = 119/246 (48%), Gaps = 28/246 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A HR++  +LRLVV IA  Y+  G+ + +++ EG++GL +AV+KFDP +G+R +TY+ WW
Sbjct: 62  AKHRMICGNLRLVVTIAKKYQKRGMDLIDLIQEGSLGLERAVEKFDPAKGYRFSTYAYWW 121

Query: 109 IKAAMQEYILRSWSLVKIGTTANQK---------RLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ ++   I      ++I     +K          L   L R   H + + +  +  EQ+
Sbjct: 122 IRQSITRAIAMQSHTIRIPVHMTEKLNRIKRVRRELSQTLGRTPTHQEMVAELGITLEQL 181

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
               +   +S  E  S+N R+  D+ +            +  D L    D Q     E  
Sbjct: 182 QKTLQAAQISNPE--SLNIRVGKDQEM------------ELGDLL---EDLQMPSPNEVV 224

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAF 277
           E+   RN L  +++ LN  ER +   R   E+    +L  +S +  +SRE VR++E  A 
Sbjct: 225 EQDFLRNALWSALAQLNDNERTVLILRYGLEDGRERSLYRVSQQMGISREWVRKLEQTAK 284

Query: 278 KKVQES 283
            K+ +S
Sbjct: 285 SKLLQS 290


>gi|294660419|ref|NP_853171.2| RNA polymerase sigma factor RpoD [Mycoplasma gallisepticum str.
           R(low)]
 gi|284812078|gb|AAP56739.2| RNA polymerase sigma factor RpoD (Sigma-A) [Mycoplasma
           gallisepticum str. R(low)]
 gi|284930653|gb|ADC30592.1| RNA polymerase sigma factor RpoD (Sigma-A) [Mycoplasma
           gallisepticum str. R(high)]
          Length = 643

 Score = 87.4 bits (215), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 77/255 (30%), Positives = 126/255 (49%), Gaps = 45/255 (17%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A ++LVTS+LRLV  IA  Y   GL   +++ EG+IGLM+A+ KF+ + G + +TY+ WW
Sbjct: 394 AINQLVTSNLRLVTSIAKKYLNRGLDFVDLIQEGSIGLMKAISKFNYKLGNKFSTYATWW 453

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ----KRLFFNLRRLKGHLQAITD------NNL 154
           I+ A+   I      V+I      T N+    +R+          L+ +T+      N  
Sbjct: 454 IRQAITRAIADQARTVRIPVHMVETINKLIKTERMLTQQLGRDPTLEELTEAMGGQVNGF 513

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            P++V  I KKLN    E +S++  +  DE             SQ+ D+ V D D     
Sbjct: 514 TPKKVADI-KKLN---QEPVSLDKPIGHDE------------ESQFVDF-VKDRD----- 551

Query: 215 LIEKEERKNRRNMLTRS-----MSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSR 266
            I K +    + ++T       ++ L  +E +I   R         +TLE +  +F V+R
Sbjct: 552 -ILKPDEYTEKLIVTEHINELFINTLTKKEEQIIRMRYGLHPWHQQMTLEEVGQKFNVTR 610

Query: 267 ERVRQIEARAFKKVQ 281
           ER+RQIE++A +K++
Sbjct: 611 ERIRQIESKALRKLK 625


>gi|302035824|ref|YP_003796146.1| RNA polymerase sigma-70 factor [Candidatus Nitrospira defluvii]
 gi|300603888|emb|CBK40220.1| RNA polymerase sigma-70 factor [Candidatus Nitrospira defluvii]
          Length = 419

 Score = 87.4 bits (215), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 67/256 (26%), Positives = 119/256 (46%), Gaps = 39/256 (15%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   LV  +LRLVV +A  Y G GL + ++V EGNIGLM+A +++   +GF+ +TY+ W
Sbjct: 183 TAKDELVRCNLRLVVNVAKHYTGRGLTLLDLVQEGNIGLMKAAERYQHRKGFKFSTYATW 242

Query: 108 WIKAAMQEYILRSWSLVKIGT--TANQKRLFFNLRRLKGHL-------QAITDNNLKPEQ 158
           WI+  +   +      ++I    T    R+    RRL   L       +  +   ++P++
Sbjct: 243 WIRQGITRSLADQSRTIRIPVHQTEASNRILRASRRLVQQLGRQPRLEEVASTMRMRPDR 302

Query: 159 VVAIAKKLNVSESEVISMNCRLA-GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           +    +       E +++  R+  G   L  L+                     +Q  + 
Sbjct: 303 LHETIQAFQ----EPVALEHRVGDGGTELGELLP--------------------DQQAVP 338

Query: 218 KEERKNRRNM---LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQI 272
            +   NR  +   + R +  L PRE+ +   R    ++   TLE +     V+RER+RQI
Sbjct: 339 PDAHVNRTELTREMDRILGTLTPREQTVIRLRFGIGEDQARTLEQVGQHLSVTRERIRQI 398

Query: 273 EARAFKKVQESIQKQV 288
           EA+A KK++  + K++
Sbjct: 399 EAKALKKLKTPMVKEM 414


>gi|225619915|ref|YP_002721172.1| RNA polymerase sigma factor RpoD [Brachyspira hyodysenteriae WA1]
 gi|225214734|gb|ACN83468.1| RNA polymerase sigma factor RpoD [Brachyspira hyodysenteriae WA1]
          Length = 587

 Score = 87.4 bits (215), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 72/250 (28%), Positives = 130/250 (52%), Gaps = 30/250 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   ++V EGNIGL++AV KF+ ++G++ +TY+ WW
Sbjct: 349 AKDHIVKANLRLVIAIAKKYVNRGLHFFDLVQEGNIGLIKAVDKFEYKKGYKFSTYATWW 408

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      +++        +   + +++  L+     + +   +  IAK L+ 
Sbjct: 409 IRQAITRSISDQARTIRVPV-----HMIEQINKVQRVLRQYMQQHGREPSIQEIAKALSW 463

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            ES V S+        SLNA I          +D ++    G+   LIE +E ++ +N+ 
Sbjct: 464 PESRVKSVRNVAKDPVSLNAPIGDE-------EDTIL----GE---LIEDKEFESPQNIT 509

Query: 229 TRSM------SVLN---PRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAF 277
           T  +      S+L+    RE+++   R   +     TLE +   F+V+RER+RQIEA+A 
Sbjct: 510 TFKILRKQIDSILDSLPDREQKVIRMRFGLVDGYSHTLEEVGYVFKVTRERIRQIEAKAI 569

Query: 278 KKVQESIQKQ 287
           ++++   +K+
Sbjct: 570 RRLRAQSKKK 579


>gi|158340730|ref|YP_001521898.1| RNA polymerase sigma-70 factor, putative [Acaryochloris marina
           MBIC11017]
 gi|158310971|gb|ABW32584.1| RNA polymerase sigma-70 factor, putative [Acaryochloris marina
           MBIC11017]
          Length = 269

 Score = 87.4 bits (215), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 77/279 (27%), Positives = 146/279 (52%), Gaps = 37/279 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ E+ + P+L  +EE  LA++ +  G L A  R++  +LRLVV IA  ++  GLP+
Sbjct: 9   LHFYLKEMARYPLLSHEEEIELARQAKA-GSLRAKQRMIECNLRLVVSIAKKHQNRGLPL 67

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK----AAMQEYILRSWSLVKIGTTAN 131
            +++ EG+IGL  AV KFD  +G R +TY+ WWI+    AA++E     +        AN
Sbjct: 68  LDLIQEGSIGLSTAVDKFDLAQGCRFSTYAYWWIRQGITAALREKSRPIYLPHNHWDKAN 127

Query: 132 Q-KRLFFNLRRLKGHLQAITD----NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
           + K+ +  L +  G   ++++     ++KP+    I + L + + +V S++ +  G E  
Sbjct: 128 KIKKHYRELNQTLGRKPSLSELSEATDIKPK---TINRTLQLFQ-KVSSLD-QPVGPEQK 182

Query: 187 NALIN--SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           ++L++  + D   +Q+ + L  D +                  L++ M+ L+ RER +  
Sbjct: 183 DSLLDLLAGDDQPTQYMESLQLDEE------------------LSQVMANLDERERFVLS 224

Query: 245 ARR-LQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R  L++N P +++ +  +  +S E +R I  +  KK++
Sbjct: 225 QRYGLEDNQPKSMKAIGQQIGLSHEAIRLILNKIMKKLE 263


>gi|144227447|gb|AAZ44150.2| DNA-directed RNA polymerase sigma factor [Mycoplasma hyopneumoniae
           J]
          Length = 676

 Score = 87.4 bits (215), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 33/271 (12%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHR--LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +L  +EE  LAK+ +  G +    R  L+  +LRLVV  A  Y+  GL   +++SEGN+G
Sbjct: 408 LLTAEEERELAKKMKIKGRIGKKARDTLIKRNLRLVVNSAKRYKNRGLGFIDLISEGNLG 467

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-KRLFFNLR 140
           +++AV K+D  RGF+ +TY+ WWI+ A+   +     L++I      T N+  ++   L+
Sbjct: 468 IIKAVAKYDYTRGFKFSTYATWWIRQAITRAVADQARLIRIPVHMVETINKINKVERELQ 527

Query: 141 RLKG------HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG--DESLNALINS 192
           + KG       +    D    P+++  I KK+N+   + IS++  +    D S +  I  
Sbjct: 528 QEKGLNPTAEEISERLDGEFSPDKIRYI-KKINI---DPISLDKAIGKEEDSSFSDFI-- 581

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERK---NRRNMLTRSMSVLNPRERRIFEARRLQ 249
            D+N     D+ +   + + +VL+E  +     + R+ + R   V    E   ++A    
Sbjct: 582 KDENMISPVDYAI--REEKAKVLLEMIDSTLDYDERDFIKRRYGVGTNDEGIPYQAH--- 636

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
               + E L++   V++ERVRQIEA+  KK+
Sbjct: 637 ----SFEELAAMRRVTKERVRQIEAKILKKL 663


>gi|163846411|ref|YP_001634455.1| sigma-70 family RNA polymerase sigma factor [Chloroflexus
           aurantiacus J-10-fl]
 gi|222524178|ref|YP_002568649.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus sp.
           Y-400-fl]
 gi|163667700|gb|ABY34066.1| RNA polymerase sigma factor, sigma-70 family [Chloroflexus
           aurantiacus J-10-fl]
 gi|222448057|gb|ACM52323.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus sp.
           Y-400-fl]
          Length = 313

 Score = 87.4 bits (215), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 70/244 (28%), Positives = 122/244 (50%), Gaps = 13/244 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L+ S+LRLVV IA  Y+G+GL + +++ EG++GLM+AV KFD  RG + +TY+ +W
Sbjct: 74  ARAQLINSNLRLVVSIARRYQGHGLSLLDLIQEGSVGLMRAVDKFDASRGLKFSTYATYW 133

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ ++   I      V++     ++     L RL+  L    D     E+ +A A  L+V
Sbjct: 134 IRQSIGRAIADHSRTVRLPVHLGER--LSRLSRLRQELSQQLDREPTLEE-LAQAAGLSV 190

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            + E        AG    +     ++       + L    D  +    ++      +  +
Sbjct: 191 EQVE----RAEQAGLAPTSLDEPHTEDGGGALAEILT---DPLQPTPFDEVSESMLQADV 243

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQE-SIQ 285
             ++  L+PRER I   R  L   P+ TLE +     ++RERVRQ+E  A +K+++ S+ 
Sbjct: 244 QHALQQLSPRERSILRLRYGLDGEPMHTLEQIGQRLRLTRERVRQLEHEALRKLRDPSLH 303

Query: 286 KQVE 289
            Q++
Sbjct: 304 PQLQ 307


>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 = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 67/235 (28%), Positives = 115/235 (48%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 363 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 422

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   + +++ +
Sbjct: 423 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEE---LGERMEM 477

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E +V  +  ++A  E ++      D   S   D++    DG     +E           
Sbjct: 478 PEEKVRKV-LKIA-KEPISMETPIGDDEDSHLGDFI---EDGTITSPVESATDVGLTEST 532

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +S L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 533 RDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 587


>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 = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 118/234 (50%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 381 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 440

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+             PE+   +A+++ +
Sbjct: 441 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQCLQEMGREATPEE---LAERMGM 495

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +  ++A  E ++      D + S   D++    D   ++ ++    ++ R   
Sbjct: 496 PEDKIRKV-LKIA-KEPISMETPIGDDDDSHLGDFI---QDESLELPLDSATAESLRLAT 550

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 551 NEVLEGLTLREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 604


>gi|118618673|ref|YP_907005.1| RNA polymerase sigma factor SigB [Mycobacterium ulcerans Agy99]
 gi|118570783|gb|ABL05534.1| RNA polymerase sigma factor SigB [Mycobacterium ulcerans Agy99]
          Length = 323

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 81/292 (27%), Positives = 140/292 (47%), Gaps = 56/292 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH--------GD-----LSAAHR-------- 52
           Y++ I K  +L  + E  LAKR     Y EH        GD     L+A  R        
Sbjct: 30  YLNGIGKTALLNAEGEVELAKRIEAGLYAEHLLATRKRLGDNRKRELAAVVRDGAEARRH 89

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A
Sbjct: 90  LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQA 149

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ-----AITDNNLKPEQVVAIAKKLN 167
           +   +      +++     ++     L R+K  +        TD  L  E  + + K  +
Sbjct: 150 ITRGMADQSRTIRLPVHLVEQ--VNKLARIKREIHQNLGREATDEELAAESGIPVEKIND 207

Query: 168 VSES--EVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + E   + +S++  +  DE   L   I  ++  S+             E  +I +    +
Sbjct: 208 LLEHSRDPVSLDMPVGSDEEAPLGDFIEDAEAMSA-------------ENAVIAELLHTD 254

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIE 273
            R++L    + L+ RE ++   R   ++  P TL+ +   F +SRERVRQIE
Sbjct: 255 IRSVL----ATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIE 302


>gi|237785656|ref|YP_002906361.1| RNA polymerase sigma factor SigB [Corynebacterium kroppenstedtii
           DSM 44385]
 gi|237758568|gb|ACR17818.1| RNA polymerase sigma factor B [Corynebacterium kroppenstedtii DSM
           44385]
          Length = 326

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 75/270 (27%), Positives = 137/270 (50%), Gaps = 32/270 (11%)

Query: 28  MLEKQEEYVLAKR-----YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           +LE  E++  +K+       + G  + AH L+ ++LRLVV +A  Y G G+P+ +++ EG
Sbjct: 65  LLESDEQFTPSKKRDLKAVAKDGRAARAH-LLEANLRLVVSLAKRYTGRGMPLLDLIQEG 123

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK--RLFFNLR 140
           N+GL++AV+KFD  +GF+ +TY+ WWI+ A+   +      +++     ++  +L    R
Sbjct: 124 NLGLIRAVEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKR 183

Query: 141 RLKGHL-QAITDNNLKPEQVVAIAK-KLNVSES-EVISMNCRLAGDES--LNALINSSDK 195
            +  HL +  T+  L  E  +  +K  L + +S + +S++  +  DE   L   I  S+ 
Sbjct: 184 EMYQHLGREATNEELAEESGIDESKIDLLLKQSRDPVSLDMPVGTDEEAPLGDFIEDSEA 243

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PV 253
                        D +E V+        R + +   ++ L  RE+ +   R   ++  P 
Sbjct: 244 T------------DAEEAVVASL-----RHSDIRTVLATLEKREQDVIRLRFGLDDGVPR 286

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQES 283
           TL+ +  EF +SRERVRQIE     K+++ 
Sbjct: 287 TLDQIGREFGLSRERVRQIEREVMAKLRKG 316


>gi|328676046|gb|AEB28721.1| RNA polymerase sigma factor RpoD [Francisella cf. novicida 3523]
          Length = 577

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 73/246 (29%), Positives = 116/246 (47%), Gaps = 32/246 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLVV  A  Y   GL   +++ EGNIGLM+AV KFD  +GF+ +TY+ WW
Sbjct: 339 AKKEMIEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKGFKFSTYATWW 398

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ----KRLFFNLRRLKGHLQAITDN--NLKPEQ 158
           I+ A+   I      +++      T N+    KR     +  +   + I ++  N+  E+
Sbjct: 399 IRQAITRSIADQARTIRVPVHMIETINKVNRIKRQILQEKGREATEEEIIEHTPNMTKEK 458

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           +  I   LN+S +  ISM   +  DE         DKN+                  IE 
Sbjct: 459 LKKI---LNISHTP-ISMESPIGDDEDSTVGDFIEDKNNYSP---------------IEA 499

Query: 219 EERKNRRNMLTRSMSV-LNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              +N R  +   +   L  RE ++   R         TLE +  +F V+RER+RQIEA+
Sbjct: 500 ANLENLREAIKELIETGLTEREAKVLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIEAK 559

Query: 276 AFKKVQ 281
           A +K++
Sbjct: 560 ALRKLK 565


>gi|255556952|ref|XP_002519509.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
 gi|223541372|gb|EEF42923.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
          Length = 548

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 64/247 (25%), Positives = 124/247 (50%), Gaps = 36/247 (14%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +L+ ++LR+VV IA  Y+G GL + +++ EG++GLM++++KF P+ G R ATY+ WWI+ 
Sbjct: 311 KLINANLRMVVHIAKQYQGRGLSLQDLLQEGSMGLMKSIEKFKPQVGCRFATYAYWWIRQ 370

Query: 112 AMQEYILRSWSLVK--------IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
            +++ I +    ++        +G  +  KR +            I + N  P +   +A
Sbjct: 371 TVRKAIFQHSRTIRLPENVYHTLGKVSEAKRSY------------IMEGNHNPTK-EELA 417

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE--- 220
           K++ ++   +  +        S+   +         W D      +    + +E  E   
Sbjct: 418 KRIGITTVRLERLLYMARMPLSMQQTV---------WADQETTFQEITADIEVEIPELCV 468

Query: 221 -RKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
            ++  R  +   +++LNPRER+I   R   E+    +L  + S F +S+ERVRQ+E+RA 
Sbjct: 469 AKQLMRKHVLSLLNILNPRERKIIRLRYGIEDGKKKSLSEIGSVFGLSKERVRQLESRAL 528

Query: 278 KKVQESI 284
            K+++ +
Sbjct: 529 YKLKQCL 535


>gi|219849586|ref|YP_002464019.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus
           aggregans DSM 9485]
 gi|219543845|gb|ACL25583.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus
           aggregans DSM 9485]
          Length = 314

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 70/236 (29%), Positives = 118/236 (50%), Gaps = 12/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L+ S+LRLVV IA  Y+G+GL + +++ EG+IGLM+AV KFD  RG + +TY+ +W
Sbjct: 74  ARAQLINSNLRLVVSIARRYQGHGLTLLDLIQEGSIGLMRAVDKFDAGRGLKFSTYATYW 133

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ ++   I      V++     ++     L RL+  L    D     E+ +A A  L+V
Sbjct: 134 IRQSIGRAIADHSRTVRLPVHLGER--LSRLARLRQELAQQLDREPTLEE-LANAAGLSV 190

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            + E        AG    +     ++       + L    D  +    ++      +  +
Sbjct: 191 EQVE----RAEQAGLAPTSLDEAHTEDGGGALSEILT---DPLQPTPFDEVSEGMLQADV 243

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQE 282
             ++S L+PRER I   R  L   P+ TLE +     ++RERVRQ+E  A +K+++
Sbjct: 244 QAALSQLSPRERNILRLRYGLDGEPMHTLEQIGQRLRLTRERVRQLEYEALRKLRD 299


>gi|225351336|ref|ZP_03742359.1| hypothetical protein BIFPSEUDO_02929 [Bifidobacterium
           pseudocatenulatum DSM 20438]
 gi|225157680|gb|EEG70963.1| hypothetical protein BIFPSEUDO_02929 [Bifidobacterium
           pseudocatenulatum DSM 20438]
          Length = 472

 Score = 87.4 bits (215), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 66/253 (26%), Positives = 125/253 (49%), Gaps = 34/253 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ WW
Sbjct: 234 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 293

Query: 109 IKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   +      +++           +  Q+++  +L R     +   + ++  E+V
Sbjct: 294 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 353

Query: 160 VAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
             + K       E IS++  L   GD     LI  +D          +   D     L++
Sbjct: 354 QEVQK----YGREPISLHTPLGEDGDSEFGDLIEDTDA---------IAPSDAVAFSLLQ 400

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
           ++ R+         +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++
Sbjct: 401 EQFRQ--------VLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESK 452

Query: 276 AFKKVQESIQKQV 288
              K++   + Q 
Sbjct: 453 TMSKLRHPSRSQT 465


>gi|257061333|ref|YP_003139221.1| RNA polymerase sigma factor [Cyanothece sp. PCC 8802]
 gi|256591499|gb|ACV02386.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8802]
          Length = 328

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 67/305 (21%), Positives = 143/305 (46%), Gaps = 56/305 (18%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR------------------------------------ 42
           Y+HEI ++P+L  ++E V  K+ +                                    
Sbjct: 23  YLHEIGRVPLLTHEQEIVYGKQVQRMMSLFEMKDQLTQAQGTEPSDKEWAKAVNLKEPEL 82

Query: 43  ----EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
               E G+  A  +++ ++LRLVV IA  Y+   +   +++ EG++GL + V+KFDP +G
Sbjct: 83  QKTIEQGN-RAKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGSLGLERGVEKFDPTKG 141

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           ++ +TY+ WWI+ A+   I +    +++     +K     +++ +  L      +  P +
Sbjct: 142 YKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEK--LNKIKKTQRELSQKLGRSATPAE 199

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIE 217
           + A+   L +  S++    C     + ++  +   D   ++  + L+ DH+   +Q + +
Sbjct: 200 IAAV---LEIEPSQI--RECLSMARQPISLDVRVGDNQDTELSE-LLEDHEASPDQYITQ 253

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
           +  R++ +N+    M  L P++R +   R   E+   ++L  +  +  +SRERVRQ+E +
Sbjct: 254 ELLRQDLKNL----MEELTPQQRSVLILRFGLEDGKELSLAKIGKKLNISRERVRQLEHQ 309

Query: 276 AFKKV 280
           A  ++
Sbjct: 310 ALAQL 314


>gi|37362432|gb|AAO23112.1| sigma factor S [Vibrio vulnificus]
          Length = 167

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 36/74 (48%), Positives = 56/74 (75%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD +A  R++ S+LRLVVKI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY
Sbjct: 9   GDEAARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTY 68

Query: 105 SMWWIKAAMQEYIL 118
           + WWI+  ++  ++
Sbjct: 69  ATWWIRQTIERALM 82


>gi|170782020|ref|YP_001710352.1| putative RNA polymerase sigma factor [Clavibacter michiganensis
           subsp. sepedonicus]
 gi|169156588|emb|CAQ01739.1| putative RNA polymerase sigma factor [Clavibacter michiganensis
           subsp. sepedonicus]
          Length = 355

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 68/252 (26%), Positives = 121/252 (48%), Gaps = 34/252 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WW
Sbjct: 118 AKSHLLGANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 177

Query: 109 IKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   +      ++I              Q+++  +L R     +   + ++ PE+V
Sbjct: 178 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELSRELDMTPEKV 237

Query: 160 VAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           + + K       E IS++  L   GD     LI  ++          V   D     +++
Sbjct: 238 IEVQK----YGREPISLHTPLGEDGDSEFGDLIEDTEA---------VVPADAVGFTMLQ 284

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEAR 275
           K+        L   +  L+ RE  +   R  L +  P TL+ +   F V+RER+RQIE++
Sbjct: 285 KQ--------LESLLDSLSEREAGVIRMRFGLGDGMPKTLDQIGDTFGVTRERIRQIESK 336

Query: 276 AFKKVQESIQKQ 287
              K++   + Q
Sbjct: 337 TMAKLRHPSRSQ 348


>gi|26554290|ref|NP_758224.1| RNA polymerase sigma factor [Mycoplasma penetrans HF-2]
 gi|26454299|dbj|BAC44628.1| RNA polymerase sigma factor [Mycoplasma penetrans HF-2]
          Length = 427

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 79/293 (26%), Positives = 140/293 (47%), Gaps = 50/293 (17%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAK-------RYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           G+  +++ +    ML  QEE  + K         RE+    A ++L+TS+LRLV  IA  
Sbjct: 142 GIKSFLNVLGSSKMLTSQEEQEIGKMLDSEDKTIREY----AINQLMTSNLRLVTSIAKK 197

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y   GL + +++ EG++GLM+A+ KFD + G + +TY+ WWI+ A+   I      ++I 
Sbjct: 198 YLNRGLDLEDLLQEGSLGLMKAITKFDYKLGNKFSTYATWWIRQAITRAIADQARTIRIP 257

Query: 128 T----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA---------IAKK-LNVSESEV 173
                T N+      L + +  L      +  PE++            AKK LN+ +  +
Sbjct: 258 VHMVETINK------LSKAERQLMQEYGRDPTPEELADAMDGTAAGFTAKKILNIKKLNI 311

Query: 174 --ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
             +S++  +  DE             S++ D++  D +   +   EKE      + + + 
Sbjct: 312 DPVSLDKPVGKDE------------ESKFVDFVKDDDNLNPEQFTEKELMGEHIDDILKK 359

Query: 232 MSVLNPRERRIFEARR---LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              L  +E  I   R       +P+TLE +  ++ ++RERVRQIEA+A +K++
Sbjct: 360 F--LQEKEEDIIRMRYGLPPYSHPMTLEEVGEKYGITRERVRQIEAKALRKIK 410


>gi|308234847|ref|ZP_07665584.1| RNA polymerase sigma factor [Gardnerella vaginalis ATCC 14018]
 gi|311114490|ref|YP_003985711.1| DNA-directed RNA polymerase sigma subunit RpoD [Gardnerella
           vaginalis ATCC 14019]
 gi|310945984|gb|ADP38688.1| DNA-directed RNA polymerase sigma subunit RpoD [Gardnerella
           vaginalis ATCC 14019]
          Length = 434

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 66/253 (26%), Positives = 125/253 (49%), Gaps = 34/253 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ WW
Sbjct: 196 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 255

Query: 109 IKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   +      +++           +  Q+++  +L R     +   + ++  E+V
Sbjct: 256 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 315

Query: 160 VAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
             + K       E IS++  L   GD     LI  +D          +   D     L++
Sbjct: 316 QEVQK----YGREPISLHTPLGEDGDSEFGDLIEDTDA---------IAPSDAVAFSLLQ 362

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
           ++ R+         +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++
Sbjct: 363 EQFRQ--------VLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESK 414

Query: 276 AFKKVQESIQKQV 288
              K++   + Q 
Sbjct: 415 TMSKLRHPSRSQT 427


>gi|218780916|ref|YP_002432234.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfatibacillum
           alkenivorans AK-01]
 gi|218762300|gb|ACL04766.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfatibacillum
           alkenivorans AK-01]
          Length = 595

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 69/235 (29%), Positives = 115/235 (48%), Gaps = 12/235 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 356 DAKAELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 415

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I    +       L R   +L         PE+   IA+K+ 
Sbjct: 416 WIRQAITRAIADQARTIRI--PVHMIETINKLIRTSRYLVQELGREPTPEE---IAQKME 470

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
               E +    ++A  E ++      ++  S   D++    D +  +  E     N    
Sbjct: 471 FP-LEKVRRVLKIA-KEPISLETPIGEEEDSHLGDFI---EDKKFMLPSEAAISLNLAEQ 525

Query: 228 LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             + ++ L PRE ++   R    ++   TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 526 TRKVLATLTPREEKVLRMRFGIGEKADHTLEEVGKDFSVTRERIRQIEAKALRKL 580


>gi|300933022|ref|ZP_07148278.1| RNA polymerase sigma factor SigB [Corynebacterium resistens DSM
           45100]
          Length = 337

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 80/300 (26%), Positives = 141/300 (47%), Gaps = 52/300 (17%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH-----GDLSAAHR---------------- 52
           Y++ I K  +L  ++E  L++R     Y EH      DL+ A +                
Sbjct: 44  YLNGIGKTALLTAEDEVELSQRIEVGLYAEHLLKNSTDLTRARKRDLKILAREGKAARSH 103

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A
Sbjct: 104 LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQA 163

Query: 113 MQEYILRSWSLVKIGTTANQK--RLFFNLRRLKGHL-QAITDNNLKPEQVVAIAK-KLNV 168
           +   +      +++     ++  +L    R +  HL +  T+  L  E  +  +K +L +
Sbjct: 164 ITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQHLGREATNEELAEESGIEESKIELLL 223

Query: 169 SES-EVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
            +S + +S++  +  DE   L   I  SD   ++        H     VL          
Sbjct: 224 KQSRDPVSLDMPVGSDEEAPLGDFIEDSDATDAEAAVVASLRHSDVRAVL---------- 273

Query: 226 NMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
                    L  RE+ + + R   ++  P TL+ +   F +SRERVRQIE     K++E 
Sbjct: 274 -------GTLEEREQDVIKLRYGLDDGMPRTLDQIGRRFGLSRERVRQIEREVMAKLREG 326


>gi|220907092|ref|YP_002482403.1| RNA polymerase sigma factor SigD [Cyanothece sp. PCC 7425]
 gi|219863703|gb|ACL44042.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7425]
          Length = 318

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 64/248 (25%), Positives = 122/248 (49%), Gaps = 34/248 (13%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           G+L A  ++V ++LRLVV +A  Y    + + +++ EG IG+ + V+KFDP +G+R +TY
Sbjct: 80  GEL-AKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTY 138

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + WWI+ A+   I      +++     +K     L ++K   + ++    +   +  +A+
Sbjct: 139 AYWWIRQAITRAIAEKGRTIRLPIHITEK-----LNKIKKAQRQLSQQLGRAATIGELAQ 193

Query: 165 KLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +L ++  +V          +S++ R+ GD     L    +  ++  +D+           
Sbjct: 194 ELELTPKQVREYLERSRQPLSLDVRV-GDNQDTELGELLEDTAASPEDFT---------- 242

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
                 + + R  L R M+ L P++R++   R   E+  P+TL  +     +SRERVRQI
Sbjct: 243 -----SQASLRADLDRLMADLTPQQRQVLSLRFGLEDGQPLTLAKVGDMLNISRERVRQI 297

Query: 273 EARAFKKV 280
           E  A  K+
Sbjct: 298 EREALSKL 305


>gi|213964561|ref|ZP_03392761.1| RNA polymerase sigma factor RpoD [Corynebacterium amycolatum SK46]
 gi|213952754|gb|EEB64136.1| RNA polymerase sigma factor RpoD [Corynebacterium amycolatum SK46]
          Length = 329

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 81/303 (26%), Positives = 140/303 (46%), Gaps = 58/303 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH----------------------GDLSAAH 51
           Y++ I K  +L  +EE  L+KR     Y EH                      G  + AH
Sbjct: 36  YLNGIGKTALLSAEEEVELSKRIEAGVYAEHLLQTGAKMTRAKKRDVKILAKEGKAARAH 95

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y   G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ 
Sbjct: 96  -LLEANLRLVVSLAKRYTNRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQ 154

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-----QAITDNNLKPEQVVAIAK-- 164
           A+   +      +++     ++     + R+K  L     +  T+  L  E  +  AK  
Sbjct: 155 AITRGMADQSRTIRLPVHLVEQ--VNKISRIKRELYQQLGREATNEELAEESGIPEAKIE 212

Query: 165 KLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
            L     + +S++  +  DE   L   I  S+              D +E V+       
Sbjct: 213 MLLRQSRDPVSLDMPVGTDEEAPLGDFIEDSEAT------------DAEEAVVASL---- 256

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
            R + + + +S L  RE+ + + R   ++  P TL+ +   F +SRERVRQIE     K+
Sbjct: 257 -RHHDVRKVLSTLEIREQEVIKLRYGLDDGLPRTLDQIGRHFGLSRERVRQIEREVMSKL 315

Query: 281 QES 283
           +E 
Sbjct: 316 REG 318


>gi|261342189|ref|ZP_05970047.1| RNA polymerase sigma factor [Enterobacter cancerogenus ATCC 35316]
 gi|288315522|gb|EFC54460.1| RNA polymerase sigma factor [Enterobacter cancerogenus ATCC 35316]
          Length = 147

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 42/87 (48%), Positives = 62/87 (71%), Gaps = 1/87 (1%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYS 105
           + EGN+GL++AV+KFDPERGFR +TY+
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYA 146


>gi|332678201|gb|AEE87330.1| RNA polymerase sigma factor RpoD [Francisella cf. novicida Fx1]
          Length = 577

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 73/246 (29%), Positives = 116/246 (47%), Gaps = 32/246 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLVV  A  Y   GL   +++ EGNIGLM+AV KFD  +GF+ +TY+ WW
Sbjct: 339 AKKEMIEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKGFKFSTYATWW 398

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ----KRLFFNLRRLKGHLQAITDN--NLKPEQ 158
           I+ A+   I      +++      T N+    KR     +  +   + I ++  N+  E+
Sbjct: 399 IRQAITRSIADQARTIRVPVHMIETINKVNRIKRQILQEKGREATEEEIIEHTPNMTKEK 458

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           +  I   LN+S +  ISM   +  DE         DKN+                  IE 
Sbjct: 459 LKKI---LNISHTP-ISMESPIGDDEDSTVGDFIEDKNNYSP---------------IEA 499

Query: 219 EERKNRRNMLTRSMSV-LNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              +N R  +   +   L  RE ++   R         TLE +  +F V+RER+RQIEA+
Sbjct: 500 ANLENLREAIKELIETGLTEREAKVLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIEAK 559

Query: 276 AFKKVQ 281
           A +K++
Sbjct: 560 ALRKLK 565


>gi|218247332|ref|YP_002372703.1| RNA polymerase sigma factor [Cyanothece sp. PCC 8801]
 gi|218167810|gb|ACK66547.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8801]
          Length = 328

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 67/305 (21%), Positives = 143/305 (46%), Gaps = 56/305 (18%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR------------------------------------ 42
           Y+HEI ++P+L  ++E V  K+ +                                    
Sbjct: 23  YLHEIGRVPLLTHEQEIVYGKQVQRMMSLFEMKDQLTQAQGTEPSDKEWAKAVNLKEPEL 82

Query: 43  ----EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
               E G+  A  +++ ++LRLVV IA  Y+   +   +++ EG++GL + V+KFDP +G
Sbjct: 83  KKTIEQGN-RAKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGSLGLERGVEKFDPTKG 141

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           ++ +TY+ WWI+ A+   I +    +++     +K     +++ +  L      +  P +
Sbjct: 142 YKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEK--LNKIKKTQRELSQKLGRSATPAE 199

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIE 217
           + A+   L +  S++    C     + ++  +   D   ++  + L+ DH+   +Q + +
Sbjct: 200 IAAV---LEIEPSQI--RECLSMARQPISLDVRVGDNQDTELSE-LLEDHEASPDQYITQ 253

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
           +  R++ +N+    M  L P++R +   R   E+   ++L  +  +  +SRERVRQ+E +
Sbjct: 254 ELLRQDLKNL----MEELTPQQRSVLILRFGLEDGKELSLAKIGKKLNISRERVRQLEHQ 309

Query: 276 AFKKV 280
           A  ++
Sbjct: 310 ALAQL 314


>gi|89256388|ref|YP_513750.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica LVS]
 gi|115314834|ref|YP_763557.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica OSU18]
 gi|156502477|ref|YP_001428542.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica FTNF002-00]
 gi|167010407|ref|ZP_02275338.1| RNA polymerase sigma factor RpoD [Francisella tularensis subsp.
           holarctica FSC200]
 gi|254367725|ref|ZP_04983746.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica 257]
 gi|290953811|ref|ZP_06558432.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica URFT1]
 gi|295312822|ref|ZP_06803554.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica URFT1]
 gi|89144219|emb|CAJ79489.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica LVS]
 gi|115129733|gb|ABI82920.1| DNA-directed RNA polymerase sigma subunit RpoD [Francisella
           tularensis subsp. holarctica OSU18]
 gi|134253536|gb|EBA52630.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica 257]
 gi|156253080|gb|ABU61586.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica FTNF002-00]
          Length = 577

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 73/246 (29%), Positives = 116/246 (47%), Gaps = 32/246 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLVV  A  Y   GL   +++ EGNIGLM+AV KFD  +GF+ +TY+ WW
Sbjct: 339 AKKEMIEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKGFKFSTYATWW 398

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ----KRLFFNLRRLKGHLQAITDN--NLKPEQ 158
           I+ A+   I      +++      T N+    KR     +  +   + I ++  N+  E+
Sbjct: 399 IRQAITRSIADQARTIRVPVHMIETINKVNRIKRQILQEKGREATEEEIIEHTPNMSKEK 458

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           +  I   LN+S +  ISM   +  DE         DKN+                  IE 
Sbjct: 459 LKKI---LNISHTP-ISMESPIGDDEDSTVGDFIEDKNNYSP---------------IEA 499

Query: 219 EERKNRRNMLTRSMSV-LNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              +N R  +   +   L  RE ++   R         TLE +  +F V+RER+RQIEA+
Sbjct: 500 ANLENLREAIKELIETGLTEREAKVLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIEAK 559

Query: 276 AFKKVQ 281
           A +K++
Sbjct: 560 ALRKLK 565


>gi|134301933|ref|YP_001121902.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis WY96-3418]
 gi|254369360|ref|ZP_04985372.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica FSC022]
 gi|254372870|ref|ZP_04988359.1| DNA-directed RNA polymerase sigma subunit RpoD [Francisella
           tularensis subsp. novicida GA99-3549]
 gi|134049710|gb|ABO46781.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis WY96-3418]
 gi|151570597|gb|EDN36251.1| DNA-directed RNA polymerase sigma subunit RpoD [Francisella
           novicida GA99-3549]
 gi|157122310|gb|EDO66450.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica FSC022]
          Length = 577

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 73/246 (29%), Positives = 116/246 (47%), Gaps = 32/246 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLVV  A  Y   GL   +++ EGNIGLM+AV KFD  +GF+ +TY+ WW
Sbjct: 339 AKKEMIEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKGFKFSTYATWW 398

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ----KRLFFNLRRLKGHLQAITDN--NLKPEQ 158
           I+ A+   I      +++      T N+    KR     +  +   + I ++  N+  E+
Sbjct: 399 IRQAITRSIADQARTIRVPVHMIETINKVNRIKRQILQEKGREATEEEIIEHTPNMTKEK 458

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           +  I   LN+S +  ISM   +  DE         DKN+                  IE 
Sbjct: 459 LKKI---LNISHTP-ISMESPIGDDEDSTVGDFIEDKNNYSP---------------IEA 499

Query: 219 EERKNRRNMLTRSMSV-LNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              +N R  +   +   L  RE ++   R         TLE +  +F V+RER+RQIEA+
Sbjct: 500 ANLENLREAIKELIETGLTEREAKVLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIEAK 559

Query: 276 AFKKVQ 281
           A +K++
Sbjct: 560 ALRKLK 565


>gi|325002338|ref|ZP_08123450.1| RpoD family RNA polymerase sigma factor [Pseudonocardia sp. P1]
          Length = 425

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 79/292 (27%), Positives = 132/292 (45%), Gaps = 61/292 (20%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYR---------EHGDLS----------------AAHR 52
           RY  E  +  +++  EE VLA+            E+GD +                A  R
Sbjct: 152 RYRQETGRAGLIDAGEEVVLARAIEVGLLAAERLENGDETTPAALPLRLLIAAGEGAYER 211

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            VT++LRLV+ IA GY   GL   ++V EG +GL++AV+KFD  +G + +TY+ WWI+ A
Sbjct: 212 FVTANLRLVLSIASGYGAPGLDALDLVQEGTLGLIRAVQKFDIAQGTKFSTYATWWIRQA 271

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   I            A+Q R       L   L A +   L P+   A A+ +    + 
Sbjct: 272 ITRAI------------ADQSRTIRYPVHLVERLNAFSRRAL-PDDDSATAELVATLPTT 318

Query: 173 VISMNCR-LAGDESLNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           V   + R + G+E L  + +   D  +   + + V D                    +  
Sbjct: 319 VPFESARDVLGEEVLQDVADRYLDPPAPDLRGFTVED--------------------VAA 358

Query: 231 SMSVLNPRERRIFEAR-RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++S+L+ RER I + R     +  TL+ +  E  V+RER+RQI+++A  +++
Sbjct: 359 ALSILSERERTIVDRRFGFVGDAATLDVIGGELGVTRERIRQIQSKALGRLE 410


>gi|149917806|ref|ZP_01906301.1| sigma 70 (RpoD) [Plesiocystis pacifica SIR-1]
 gi|149821326|gb|EDM80728.1| sigma 70 (RpoD) [Plesiocystis pacifica SIR-1]
          Length = 431

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 71/259 (27%), Positives = 128/259 (49%), Gaps = 12/259 (4%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           EYV   R       SA ++ V ++LRLVV IA  +    +P+ +++ EGNIGLM+AV +F
Sbjct: 182 EYVANVRRSSRKLRSAKNKFVKANLRLVVSIARRFNHGRMPLQDLIQEGNIGLMKAVDRF 241

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D  +GFR +TY  WWI+ A+   I      V++    +    +  + + +  L+A     
Sbjct: 242 DYRKGFRFSTYGSWWIRHAISRAIADKGRQVRL--PVHMIDAYHKVNKARRELEAKLGRE 299

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
              E+   +A+   ++ +++  M   L  D  ++     SD +  +  D+L    D   +
Sbjct: 300 PTREE---LAQHTGIALAKIERMGTMLV-DNPISLDKPVSDADGRKMGDFL---EDENAE 352

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQ 271
              E  E       + R +S L P E  I   R   + +  +TL+ +  ++ +SRER+RQ
Sbjct: 353 DPGEGLEADALNEQVKRLVSKLRPIEADIIRKRFGLIDDEELTLKEIGGQYSLSRERIRQ 412

Query: 272 IEARAFKKVQESIQKQVEL 290
           ++ +A  K++  + K++EL
Sbjct: 413 LQEQALGKIRREL-KRLEL 430


>gi|254374325|ref|ZP_04989807.1| RNA polymerase sigma-70 factor [Francisella novicida GA99-3548]
 gi|151572045|gb|EDN37699.1| RNA polymerase sigma-70 factor [Francisella novicida GA99-3548]
          Length = 577

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 73/246 (29%), Positives = 116/246 (47%), Gaps = 32/246 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLVV  A  Y   GL   +++ EGNIGLM+AV KFD  +GF+ +TY+ WW
Sbjct: 339 AKKEMIEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKGFKFSTYATWW 398

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ----KRLFFNLRRLKGHLQAITDN--NLKPEQ 158
           I+ A+   I      +++      T N+    KR     +  +   + I ++  N+  E+
Sbjct: 399 IRQAITRSIADQARTIRVPVHMIETINKVNRIKRQILQEKGREATEEEIIEHTPNMTKEK 458

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           +  I   LN+S +  ISM   +  DE         DKN+                  IE 
Sbjct: 459 LKKI---LNISHTP-ISMESPIGDDEDSTVGDFIEDKNNYSP---------------IEA 499

Query: 219 EERKNRRNMLTRSMSV-LNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              +N R  +   +   L  RE ++   R         TLE +  +F V+RER+RQIEA+
Sbjct: 500 ANLENLREAIKELIETGLTEREAKVLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIEAK 559

Query: 276 AFKKVQ 281
           A +K++
Sbjct: 560 ALRKLK 565


>gi|118497505|ref|YP_898555.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           novicida U112]
 gi|195536199|ref|ZP_03079206.1| RNA polymerase sigma factor RpoD [Francisella tularensis subsp.
           novicida FTE]
 gi|208779304|ref|ZP_03246650.1| RNA polymerase sigma factor RpoD [Francisella novicida FTG]
 gi|118423411|gb|ABK89801.1| RNA polymerase sigma-70 factor [Francisella novicida U112]
 gi|194372676|gb|EDX27387.1| RNA polymerase sigma factor RpoD [Francisella tularensis subsp.
           novicida FTE]
 gi|208745104|gb|EDZ91402.1| RNA polymerase sigma factor RpoD [Francisella novicida FTG]
          Length = 577

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 73/246 (29%), Positives = 116/246 (47%), Gaps = 32/246 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLVV  A  Y   GL   +++ EGNIGLM+AV KFD  +GF+ +TY+ WW
Sbjct: 339 AKKEMIEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKGFKFSTYATWW 398

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ----KRLFFNLRRLKGHLQAITDN--NLKPEQ 158
           I+ A+   I      +++      T N+    KR     +  +   + I ++  N+  E+
Sbjct: 399 IRQAITRSIADQARTIRVPVHMIETINKVNRIKRQILQEKGREATEEEIIEHTPNMTKEK 458

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           +  I   LN+S +  ISM   +  DE         DKN+                  IE 
Sbjct: 459 LKKI---LNISHTP-ISMESPIGDDEDSTVGDFIEDKNNYSP---------------IEA 499

Query: 219 EERKNRRNMLTRSMSV-LNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              +N R  +   +   L  RE ++   R         TLE +  +F V+RER+RQIEA+
Sbjct: 500 ANLENLREAIKELIETGLTEREAKVLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIEAK 559

Query: 276 AFKKVQ 281
           A +K++
Sbjct: 560 ALRKLK 565


>gi|187931644|ref|YP_001891628.1| RNA polymerase sigma 70 factor RpoD [Francisella tularensis subsp.
           mediasiatica FSC147]
 gi|187712553|gb|ACD30850.1| RNA polymerase sigma 70 factor RpoD [Francisella tularensis subsp.
           mediasiatica FSC147]
          Length = 577

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 73/246 (29%), Positives = 116/246 (47%), Gaps = 32/246 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLVV  A  Y   GL   +++ EGNIGLM+AV KFD  +GF+ +TY+ WW
Sbjct: 339 AKKEMIEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKGFKFSTYATWW 398

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ----KRLFFNLRRLKGHLQAITDN--NLKPEQ 158
           I+ A+   I      +++      T N+    KR     +  +   + I ++  N+  E+
Sbjct: 399 IRQAITRSIADQARTIRVPVHMIETINKVNRIKRQILQEKGREATEEEIIEHTPNMTKEK 458

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           +  I   LN+S +  ISM   +  DE         DKN+                  IE 
Sbjct: 459 LKKI---LNISHTP-ISMESPIGDDEDSTVGDFIEDKNNYSP---------------IEA 499

Query: 219 EERKNRRNMLTRSMSV-LNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              +N R  +   +   L  RE ++   R         TLE +  +F V+RER+RQIEA+
Sbjct: 500 ANLENLREAIKELIETGLTEREAKVLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIEAK 559

Query: 276 AFKKVQ 281
           A +K++
Sbjct: 560 ALRKLK 565


>gi|156742838|ref|YP_001432967.1| RpoD family RNA polymerase sigma factor [Roseiflexus castenholzii
           DSM 13941]
 gi|156234166|gb|ABU58949.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus
           castenholzii DSM 13941]
          Length = 351

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 73/233 (31%), Positives = 118/233 (50%), Gaps = 14/233 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  RL+ ++LRLVV +A  Y G  L   ++V EGNIGLM+AV+KFD  +G R +TY+ WW
Sbjct: 114 ARRRLIQANLRLVVSVAKKYIGGPLSFMDLVQEGNIGLMRAVEKFDASKGNRFSTYATWW 173

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA-IAKKLN 167
           I+ A+   I     L+++    +   +   +RR+   L+     +L+ E  +  IA+ + 
Sbjct: 174 IRQAITRAIAEQSRLIRLPVHLSD--VIAQVRRVARRLE----QSLEREPTIKEIAEAVG 227

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + E +V  +    A   SL   I     N  + Q   +   DG +  +    +   +R+ 
Sbjct: 228 MPERKVKMLLQASAQPISLEQPIT----NDGEGQIGELLADDGADAPMEIATQHMLQRD- 282

Query: 228 LTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFK 278
           L +++  L  RER +   R    +    TLE + S F ++RER RQIEA A +
Sbjct: 283 LEQALMDLPDRERAVLRLRYGLTDGRRRTLEEIGSAFGITRERTRQIEADALR 335


>gi|254421571|ref|ZP_05035289.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
 gi|196189060|gb|EDX84024.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
          Length = 390

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 75/319 (23%), Positives = 140/319 (43%), Gaps = 82/319 (25%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYRE--------------------------HGDLSAA-- 50
           Y+HEI ++P+L  ++E VL K+ ++                          + D +AA  
Sbjct: 79  YLHEIGRVPLLSHEDEIVLGKQVQKMMALLAIKEELAAKLSEAEGEEAEVSNADWAAAAS 138

Query: 51  -----------------HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
                             +++ ++LRLVV +A  Y+   L   +++ EG +GL + V+KF
Sbjct: 139 IPESELDHHMRRGQRSKRKMIEANLRLVVAVAKKYQKRNLEFLDLIQEGTLGLERGVEKF 198

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN---------QKRLFFNLRRLKG 144
           DP +G++ +TY+ WWI+ A+   I +    +++              Q+ L   L R   
Sbjct: 199 DPMKGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEKLNKIKRVQRELSQKLGRSPN 258

Query: 145 HLQAITDNNLKPEQV---VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
             +   +  L+P+QV   ++IA+       + IS++ R+             D   ++ Q
Sbjct: 259 AAEIGQELELEPKQVREYLSIAR-------QPISLDVRIG------------DNQDTELQ 299

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLS 259
           D L  D    E   +++  R +    + R +S L  +++ +   R      NP++L  + 
Sbjct: 300 DLLEDDGASPEDYTVQQSLRSD----IFRMLSELTSQQQEVINLRFGLADGNPLSLAKVG 355

Query: 260 SEFEVSRERVRQIEARAFK 278
               +SRERVRQ+E +A K
Sbjct: 356 QRMGISRERVRQLEQQALK 374


>gi|86608149|ref|YP_476911.1| RNA polymerase sigma factor, group 1 [Synechococcus sp.
           JA-2-3B'a(2-13)]
 gi|86556691|gb|ABD01648.1| RNA polymerase sigma factor, group 1 [Synechococcus sp.
           JA-2-3B'a(2-13)]
          Length = 361

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 69/237 (29%), Positives = 115/237 (48%), Gaps = 18/237 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L+ ++LRLVV +A  Y   G+P  +++ EGNIGL++A +KF+ ERGFR +TY+ WW
Sbjct: 124 AQRKLINANLRLVVSVAKKYLNRGVPFLDLIQEGNIGLIRATEKFNAERGFRFSTYAHWW 183

Query: 109 IKAAMQEYILRSWSLVKIGT-TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           I+  +   I      +++     ++ RL     R    LQ         E  +A A  + 
Sbjct: 184 IRQGITRCIANQARTIRLPVHMVDKVRLLKRTNRELMKLQG----RRPTEAELAEALGIK 239

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ--EQVLIEKEERKNRR 225
           V +  +I     L     L+  +    +  S+  D L  +   Q  + +L++  ++  R 
Sbjct: 240 VKKLRMIQQAAAL----PLSLDVPVGQEGESRLGDLLQDERQEQPFQGILVQSMQQDVRS 295

Query: 226 NMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            M T     L P ER++ E R     +   TL  +   F ++RER+RQIE  A +K+
Sbjct: 296 AMQT-----LKPIERQVLELRYGLDGQQARTLREVGDHFNLTRERIRQIERDALRKL 347


>gi|126659670|ref|ZP_01730799.1| RNA polymerase sigma factor [Cyanothece sp. CCY0110]
 gi|126619015|gb|EAZ89755.1| RNA polymerase sigma factor [Cyanothece sp. CCY0110]
          Length = 369

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 74/247 (29%), Positives = 122/247 (49%), Gaps = 21/247 (8%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           +R H   +A  +++ S+LRLVV IA  Y   G+P  +++ EG IGL +A +KFDP +G++
Sbjct: 123 HRLHRGRTAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPNKGYK 182

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      +++     +K     L +LK   + +     +     
Sbjct: 183 FSTYAYWWIRQAITRTIANDARTIRLPIHVVEK-----LNKLKKAQRVLKQKLQRNPNEK 237

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A +L VS S++  +        SLN  +   +   ++  D L      ++Q L   EE
Sbjct: 238 ELADELEVSPSQLRQLLQLRRQSLSLNHRVGKGE--DTELVDLL------EDQELQLPEE 289

Query: 221 RKNRRNMLTRSMS-----VLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIE 273
             N   ML   +S     VL  RE+ +   R       P TLE +   F +SRERVRQI+
Sbjct: 290 LMN-EGMLRYEVSAVLSDVLTQREKDVISLRYGLCTAQPHTLEEVGGIFNLSRERVRQIQ 348

Query: 274 ARAFKKV 280
           ++A +K+
Sbjct: 349 SKAMRKL 355


>gi|6175924|gb|AAF05338.1|AF182104_2 truncated RNA polymerase sigma subunit [Escherichia coli]
          Length = 147

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 42/87 (48%), Positives = 62/87 (71%), Gaps = 1/87 (1%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYS 105
           + EGN+GL++AV+KFDPERGFR +TY+
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYA 146


>gi|71893415|ref|YP_278861.1| RNA polymerase sigma factor [Mycoplasma hyopneumoniae J]
          Length = 489

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 76/270 (28%), Positives = 138/270 (51%), Gaps = 29/270 (10%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHR--LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +L  +EE  LAK+ +  G +    R  L+  +LRLVV  A  Y+  GL   +++SEGN+G
Sbjct: 221 LLTAEEERELAKKMKIKGRIGKKARDTLIKRNLRLVVNSAKRYKNRGLGFIDLISEGNLG 280

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-KRLFFNLR 140
           +++AV K+D  RGF+ +TY+ WWI+ A+   +     L++I      T N+  ++   L+
Sbjct: 281 IIKAVAKYDYTRGFKFSTYATWWIRQAITRAVADQARLIRIPVHMVETINKINKVERELQ 340

Query: 141 RLKG------HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           + KG       +    D    P+++  I KK+N+   + IS++  +  +E  +      D
Sbjct: 341 QEKGLNPTAEEISERLDGEFSPDKIRYI-KKINI---DPISLDKAIGKEEDSSFSDFIKD 396

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERK---NRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           +N     D+ +   + + +VL+E  +     + R+ + R   V    E   ++A      
Sbjct: 397 ENMISPVDYAI--REEKAKVLLEMIDSTLDYDERDFIKRRYGVGTNDEGIPYQAH----- 449

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             + E L++   V++ERVRQIEA+  KK++
Sbjct: 450 --SFEELAAMRRVTKERVRQIEAKILKKLR 477


>gi|33866043|ref|NP_897602.1| type II alternative RNA polymerase sigma factor [Synechococcus sp.
           WH 8102]
 gi|33639018|emb|CAE08024.1| Possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 8102]
          Length = 308

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 74/253 (29%), Positives = 123/253 (48%), Gaps = 39/253 (15%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A ++++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG R +TY+ WW
Sbjct: 66  AKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSTYAYWW 125

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP--EQV-----VA 161
           I+  +   +      ++I    N+K     LR  K  L  +  N L P  EQ+     + 
Sbjct: 126 IRQGLNRALSTQSRTIRIPVNVNEK--LTKLRAAKARL--MQRNGLTPTAEQLADFMEIP 181

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           IA+  ++   E+ S+   L G       +  S  + S+  D L  D    E   +E+ E 
Sbjct: 182 IAEVEDLLACELRSVTVSLQG-------VVKSKSDPSELVDVLPSD----ELPPMERAE- 229

Query: 222 KNRRNMLTRSMSV--------LNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVR 270
                +  RS SV        L P+ER +   R   +      TL  ++     SRE  R
Sbjct: 230 -----IAERSASVWTLLGKANLTPKERTVVTLRFGLDGTNEWRTLAEVARHMNCSREYCR 284

Query: 271 QIEARAFKKVQES 283
           Q+  RA +K++++
Sbjct: 285 QVVQRALRKLRKT 297


>gi|282854020|ref|ZP_06263357.1| sigma-70 region 2 [Propionibacterium acnes J139]
 gi|282583473|gb|EFB88853.1| sigma-70 region 2 [Propionibacterium acnes J139]
 gi|314922987|gb|EFS86818.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL001PA1]
 gi|314966764|gb|EFT10863.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL082PA2]
 gi|314981098|gb|EFT25192.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL110PA3]
 gi|315091924|gb|EFT63900.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL110PA4]
 gi|315093320|gb|EFT65296.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL060PA1]
 gi|315103425|gb|EFT75401.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL050PA2]
 gi|327327589|gb|EGE69365.1| RNA polymerase principal sigma factor SigA [Propionibacterium acnes
           HL103PA1]
          Length = 312

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 82/312 (26%), Positives = 142/312 (45%), Gaps = 59/312 (18%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------------- 43
           ++G+  +  Y+  I + P+L   EE  LA+R                             
Sbjct: 13  IDGKDAVGLYLDGIARTPLLNAAEEVALARRIEAGVFARAVLEGHAETTSDATTEELHQI 72

Query: 44  --HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
              GD + AH  V ++LRLVV +A  Y    +P+ ++V EGN GL++AV+KFD  +GF+ 
Sbjct: 73  AADGDEALAH-FVRANLRLVVSVARKYGRSQMPLLDLVQEGNTGLIRAVEKFDYAKGFKF 131

Query: 102 ATYSMWWIKAAMQEYILRSWSLVK----IGTTANQ-KRLFFNLRRLKGHLQAITDNNLKP 156
           +TY+ WW++ A+   I +   +V+    +    NQ      NL R  G          +P
Sbjct: 132 STYATWWVRQAISRGIAQQGRIVRLPVHVAEQVNQVSAARRNLERQLGR---------EP 182

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHD-GQEQV 214
           E    IA +L ++E  VI +  R   D  SL+A +   D   +   D +  +   G + +
Sbjct: 183 E-TFEIADELEITEERVIEL-IRFGRDHVSLDAPVE--DDGDTSLGDLIARETSPGPDDI 238

Query: 215 LIEKEERKNRRNMLT----RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
           +++ E+R     +L     RS  V+  R   + + R+ +     L ++   + ++ ERVR
Sbjct: 239 VLDAEDRSRLEGLLDDLDERSADVVR-RRYGLVDGRQAK-----LADIGKVWGITAERVR 292

Query: 271 QIEARAFKKVQE 282
           QIE  A   +++
Sbjct: 293 QIERAALASMRQ 304


>gi|55980501|ref|YP_143798.1| RNA polymerase pricipal sigma factor RpoD [Thermus thermophilus
           HB8]
 gi|209447478|pdb|3DXJ|F Chain F, Crystal Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme In Complex With The Antibiotic Myxopyronin
 gi|209447484|pdb|3DXJ|P Chain P, Crystal Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme In Complex With The Antibiotic Myxopyronin
 gi|55771914|dbj|BAD70355.1| RNA polymerase pricipal sigma factor (RpoD) [Thermus thermophilus
           HB8]
          Length = 423

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 69/242 (28%), Positives = 123/242 (50%), Gaps = 22/242 (9%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   L+ ++LRLVV IA  Y G GL   +++ EGN GL++AV+KF+ +R F+ +TY+ W
Sbjct: 182 AARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATW 241

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I    +       L R    LQ         E+   IA+ + 
Sbjct: 242 WIRQAINRAIADQARTIRI--PVHMVETINKLSRTARQLQQELGREPTYEE---IAEAMG 296

Query: 168 VS-ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH-----DGQEQVLIEKEER 221
              +++ +    ++A  E ++      D+  S + D++  +H     D   Q L+ +E  
Sbjct: 297 PGWDAKRVEETLKIA-QEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEE-- 353

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
                 L +++S L+ RE  + + R+  +     TLE + + F V+RER+RQIE +A +K
Sbjct: 354 ------LEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRK 407

Query: 280 VQ 281
           ++
Sbjct: 408 LK 409


>gi|6463986|dbj|BAA86958.1| group 2 sigma factor RpoD4 [Synechococcus sp. PCC 7942]
          Length = 311

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 83/307 (27%), Positives = 151/307 (49%), Gaps = 43/307 (14%)

Query: 3   RKNMSIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYR------EHGD-------- 46
           R+N++  V       +S Y+  I +IP+L  +EE  L+++ +      E+ D        
Sbjct: 6   RRNLNAAVERHTSDHVSWYLSSIGRIPLLTAEEEVELSRKVQLMMALLENPDAESNSENQ 65

Query: 47  --LSAAHR----LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             L A  R    ++ ++LRLVV +A   +  GL + +++ EG++GL +AV+KFDP  G++
Sbjct: 66  AVLQAGQRAKTKMLKANLRLVVSVAKKCQNQGLELLDLIQEGSLGLERAVEKFDPALGYK 125

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN--NLKPEQ 158
            +TY+ WWI+ +M   I      +++    ++K     + R+K   + +T     L    
Sbjct: 126 FSTYAYWWIRQSMTRAIDNHARTIRLPIHVSEK-----ISRIKKMTRELTHQLKRLPSRA 180

Query: 159 VVAIAKKLNVSESEVI---SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
            +A A KL + + E++   S  C      SL+A     D  S  +   L+ D    E   
Sbjct: 181 EIAEALKLPLQDVEMLLSQSTPC-----TSLDAQARGDDGRS--FLGDLIPDPKSLEP-- 231

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIE 273
           ++  +R  +   ++  ++ L  RE+++ + R  L +    TL  +     VSRER+RQ+E
Sbjct: 232 MDAMDRHIQHEQISTWLAHLTEREQQVLQLRFGLHDGEQHTLAEIGRRLNVSRERIRQVE 291

Query: 274 ARAFKKV 280
           ARA +K+
Sbjct: 292 ARALQKL 298


>gi|46198472|ref|YP_004139.1| RNA polymerase sigma factor rpoD [Thermus thermophilus HB27]
 gi|21730342|pdb|1IW7|F Chain F, Crystal Structure Of The Rna Polymerase Holoenzyme From
           Thermus Thermophilus At 2.6a Resolution
 gi|21730348|pdb|1IW7|P Chain P, Crystal Structure Of The Rna Polymerase Holoenzyme From
           Thermus Thermophilus At 2.6a Resolution
 gi|49259060|pdb|1SMY|F Chain F, Structural Basis For Transcription Regulation By Alarmone
           Ppgpp
 gi|49259066|pdb|1SMY|P Chain P, Structural Basis For Transcription Regulation By Alarmone
           Ppgpp
 gi|78101162|pdb|1ZYR|F Chain F, Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme In Complex With The Antibiotic Streptolydigin
 gi|78101168|pdb|1ZYR|P Chain P, Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme In Complex With The Antibiotic Streptolydigin
 gi|78101224|pdb|2A68|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Rifabutin
 gi|78101230|pdb|2A68|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Rifabutin
 gi|78101236|pdb|2A69|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Rifapentin
 gi|78101242|pdb|2A69|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Rifapentin
 gi|78101248|pdb|2A6E|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme
 gi|78101254|pdb|2A6E|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme
 gi|78101260|pdb|2A6H|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Sterptolydigin
 gi|78101266|pdb|2A6H|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Sterptolydigin
 gi|78101762|pdb|2CW0|F Chain F, Crystal Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme At 3.3 Angstroms Resolution
 gi|78101768|pdb|2CW0|P Chain P, Crystal Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme At 3.3 Angstroms Resolution
 gi|83754377|pdb|2BE5|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Inhibitor Tagetitoxin
 gi|83754383|pdb|2BE5|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Inhibitor Tagetitoxin
 gi|210061069|pdb|3EQL|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Myxopyronin
 gi|210061075|pdb|3EQL|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Myxopyronin
 gi|4239959|dbj|BAA74758.1| principal sigma factor [Thermus thermophilus]
 gi|46196094|gb|AAS80512.1| RNA polymerase sigma factor rpoD [Thermus thermophilus HB27]
          Length = 423

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 69/242 (28%), Positives = 123/242 (50%), Gaps = 22/242 (9%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   L+ ++LRLVV IA  Y G GL   +++ EGN GL++AV+KF+ +R F+ +TY+ W
Sbjct: 182 AARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATW 241

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I    +       L R    LQ         E+   IA+ + 
Sbjct: 242 WIRQAINRAIADQARTIRI--PVHMVETINKLSRTARQLQQELGREPTYEE---IAEAMG 296

Query: 168 VS-ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH-----DGQEQVLIEKEER 221
              +++ +    ++A  E ++      D+  S + D++  +H     D   Q L+ +E  
Sbjct: 297 PGWDAKRVEETLKIA-QEPVSLETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEE-- 353

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
                 L +++S L+ RE  + + R+  +     TLE + + F V+RER+RQIE +A +K
Sbjct: 354 ------LEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRK 407

Query: 280 VQ 281
           ++
Sbjct: 408 LK 409


>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 = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 70/250 (28%), Positives = 118/250 (47%), Gaps = 28/250 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 379 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 438

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 439 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPNPEELAERMGMPED 496

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++    D    +  +   
Sbjct: 497 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLALPADAAT 540

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            ++ +      +S L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 541 SESLKAATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 600

Query: 279 KVQESIQKQV 288
           K++   + +V
Sbjct: 601 KLRHPSRSEV 610


>gi|327539652|gb|EGF26260.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhodopirellula
           baltica WH47]
          Length = 567

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 82/277 (29%), Positives = 124/277 (44%), Gaps = 35/277 (12%)

Query: 21  HEIRKIPMLEKQEEYVLAKRY---REHGDLSAAHR--LVTSHLRLVVKIAMGYRGYGLPI 75
            E+R++ ++ ++    L  R    R H D   A +  L   +LRLVV IA  YR  GL  
Sbjct: 294 QELRELMLVTQESPTSLHNRMAKVRRHFDQYEATKRELSAGNLRLVVSIAKKYRNRGLSF 353

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT------- 128
            +++ EGN GLM+AV K++  RGF+ +TY+ WWI+ A+   I      ++I         
Sbjct: 354 LDLIQEGNTGLMRAVDKYEYRRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMIDVLS 413

Query: 129 --TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
                QKRL   LRR   +       ++  E+V  +   +++    V           SL
Sbjct: 414 KLRQAQKRLTQTLRREPTYEDIAEATDVPIEEVRRV---MDIGRHPV-----------SL 459

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           +  +   + +S       V D +    V I        RN +   +  L  RER I   R
Sbjct: 460 DRPVGEGEDSSF---GEFVQDSETDNPVRIAAS--GMLRNKIDELLKTLTFREREIIRLR 514

Query: 247 R--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +     TLE     F+V+RERVRQIEA+A  K+Q
Sbjct: 515 YGLVDGYSYTLEECGRIFKVTRERVRQIEAKAVAKMQ 551


>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 = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 64/236 (27%), Positives = 119/236 (50%), Gaps = 12/236 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 406 AAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 465

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I    +       + R+    Q + +   +P+    +A+ + 
Sbjct: 466 WIRQAITRSIADQARTIRI--PVHMIETINKMNRISR--QYLQETGEEPDS-AKLAELME 520

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + E ++  +  ++A  E ++      D + S   D++    D       E     +   +
Sbjct: 521 MPEDKIRKI-MKIAK-EPISMETPIGDDDDSHLGDFI---EDANNVAPAEAAMYTSLHEV 575

Query: 228 LTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
               +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 576 TKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 631


>gi|315444860|ref|YP_004077739.1| RNA polymerase sigma factor, sigma-70 family [Mycobacterium sp.
           Spyr1]
 gi|315263163|gb|ADT99904.1| RNA polymerase sigma factor, sigma-70 family [Mycobacterium sp.
           Spyr1]
          Length = 319

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 80/300 (26%), Positives = 142/300 (47%), Gaps = 56/300 (18%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH-------------GDLSAAHR-------- 52
           Y++ I K  +L   +E  LAKR     Y +H              DL+A  R        
Sbjct: 26  YLNGIGKTALLTAADEVELAKRIEAGLYAQHLLATRKRLGENRKRDLAAVVRDGEAARRH 85

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A
Sbjct: 86  LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTYATWWIRQA 145

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ-----AITDNNLKPEQVVAIAKKLN 167
           +   +      +++     ++     L R+K  +        TD  L  E  + + K  +
Sbjct: 146 ITRGMADQSRTIRLPVHLVEQ--VNKLARIKREMHQNLGREATDEELAEESGIPVEKIND 203

Query: 168 VSES--EVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + E   + +S++  +  DE   L   I  ++  S+             E  +I +    +
Sbjct: 204 LLEHSRDPVSLDMPVGSDEEAPLGDFIEDAEAMSA-------------ENAVISELLHTD 250

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R +L    + L+ RE+++   R   ++  P TL+ +   F +SRERVRQIE     K++
Sbjct: 251 IRYVL----ATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMAKLR 306


>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 = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 64/236 (27%), Positives = 119/236 (50%), Gaps = 12/236 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 406 AAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 465

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I    +       + R+    Q + +   +P+    +A+ + 
Sbjct: 466 WIRQAITRSIADQARTIRI--PVHMIETINKMNRISR--QYLQETGEEPDS-AKLAELME 520

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + E ++  +  ++A  E ++      D + S   D++    D       E     +   +
Sbjct: 521 MPEDKIRKI-MKIAK-EPISMETPIGDDDDSHLGDFI---EDANNVAPAEAAMYTSLHEV 575

Query: 228 LTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
               +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 576 TKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 631


>gi|50842514|ref|YP_055741.1| RNA polymerase principal sigma factor HrdD [Propionibacterium acnes
           KPA171202]
 gi|289425060|ref|ZP_06426837.1| sigma-70 region 2 [Propionibacterium acnes SK187]
 gi|289427240|ref|ZP_06428956.1| sigma-70 region 2 [Propionibacterium acnes J165]
 gi|295130591|ref|YP_003581254.1| RNA polymerase principal sigma factor HrdD [Propionibacterium acnes
           SK137]
 gi|50840116|gb|AAT82783.1| RNA polymerase principal sigma factor HrdD [Propionibacterium acnes
           KPA171202]
 gi|289154038|gb|EFD02726.1| sigma-70 region 2 [Propionibacterium acnes SK187]
 gi|289159709|gb|EFD07897.1| sigma-70 region 2 [Propionibacterium acnes J165]
 gi|291376720|gb|ADE00575.1| RNA polymerase principal sigma factor HrdD [Propionibacterium acnes
           SK137]
 gi|313764457|gb|EFS35821.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL013PA1]
 gi|313772161|gb|EFS38127.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL074PA1]
 gi|313807516|gb|EFS46003.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL087PA2]
 gi|313810025|gb|EFS47746.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL083PA1]
 gi|313815996|gb|EFS53710.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL059PA1]
 gi|313818558|gb|EFS56272.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL046PA2]
 gi|313820325|gb|EFS58039.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL036PA1]
 gi|313822868|gb|EFS60582.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL036PA2]
 gi|313825200|gb|EFS62914.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL063PA1]
 gi|313827776|gb|EFS65490.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL063PA2]
 gi|313830353|gb|EFS68067.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL007PA1]
 gi|313833726|gb|EFS71440.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL056PA1]
 gi|314915450|gb|EFS79281.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL005PA4]
 gi|314918267|gb|EFS82098.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL050PA1]
 gi|314920080|gb|EFS83911.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL050PA3]
 gi|314925213|gb|EFS89044.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL036PA3]
 gi|314931602|gb|EFS95433.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL067PA1]
 gi|314955755|gb|EFT00155.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL027PA1]
 gi|314958169|gb|EFT02272.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL002PA1]
 gi|314960004|gb|EFT04106.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL002PA2]
 gi|314967831|gb|EFT11930.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL037PA1]
 gi|314973357|gb|EFT17453.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL053PA1]
 gi|314976035|gb|EFT20130.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL045PA1]
 gi|314978426|gb|EFT22520.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL072PA2]
 gi|314983943|gb|EFT28035.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL005PA1]
 gi|314988127|gb|EFT32218.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL005PA2]
 gi|314989932|gb|EFT34023.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL005PA3]
 gi|315080642|gb|EFT52618.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL078PA1]
 gi|315084315|gb|EFT56291.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL027PA2]
 gi|315085658|gb|EFT57634.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL002PA3]
 gi|315088920|gb|EFT60896.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL072PA1]
 gi|315095902|gb|EFT67878.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL038PA1]
 gi|315098533|gb|EFT70509.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL059PA2]
 gi|315101109|gb|EFT73085.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL046PA1]
 gi|315105655|gb|EFT77631.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL030PA1]
 gi|315108329|gb|EFT80305.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL030PA2]
 gi|327326184|gb|EGE67974.1| RNA polymerase principal sigma factor SigA [Propionibacterium acnes
           HL096PA2]
 gi|327331941|gb|EGE73678.1| RNA polymerase principal sigma factor SigA [Propionibacterium acnes
           HL096PA3]
 gi|327443142|gb|EGE89796.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL013PA2]
 gi|327445926|gb|EGE92580.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL043PA2]
 gi|327448094|gb|EGE94748.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL043PA1]
 gi|327450785|gb|EGE97439.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL087PA3]
 gi|327453871|gb|EGF00526.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL083PA2]
 gi|328753473|gb|EGF67089.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL020PA1]
 gi|328754203|gb|EGF67819.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL087PA1]
 gi|328754545|gb|EGF68161.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL025PA2]
 gi|328760855|gb|EGF74421.1| RNA polymerase principal sigma factor SigA [Propionibacterium acnes
           HL099PA1]
 gi|332675431|gb|AEE72247.1| RNA polymerase principal sigma factor HrdD [Propionibacterium acnes
           266]
          Length = 312

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 82/312 (26%), Positives = 142/312 (45%), Gaps = 59/312 (18%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------------- 43
           ++G+  +  Y+  I + P+L   EE  LA+R                             
Sbjct: 13  IDGKDAVGLYLDGIARTPLLNAAEEVALARRIEAGVFARAILEGHAETTSDTTTKELHQI 72

Query: 44  --HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
              GD + AH  V ++LRLVV +A  Y    +P+ ++V EGN GL++AV+KFD  +GF+ 
Sbjct: 73  AADGDEALAH-FVRANLRLVVSVARKYGRSQMPLLDLVQEGNTGLIRAVEKFDYAKGFKF 131

Query: 102 ATYSMWWIKAAMQEYILRSWSLVK----IGTTANQ-KRLFFNLRRLKGHLQAITDNNLKP 156
           +TY+ WW++ A+   I +   +V+    +    NQ      NL R  G          +P
Sbjct: 132 STYATWWVRQAISRGIAQQGRIVRLPVHVAEQVNQVSAARRNLERQLGR---------EP 182

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHD-GQEQV 214
           E    IA +L ++E  VI +  R   D  SL+A +   D   +   D +  +   G + +
Sbjct: 183 E-TFEIADELEITEERVIEL-IRFGRDHVSLDAPVE--DDGDTSLGDLIARETSPGPDDI 238

Query: 215 LIEKEERKNRRNMLT----RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
           +++ E+R     +L     RS  V+  R   + + R+ +     L ++   + ++ ERVR
Sbjct: 239 VLDAEDRSRLEGLLDDLDERSADVVR-RRYGLVDGRQAK-----LADIGKVWGITAERVR 292

Query: 271 QIEARAFKKVQE 282
           QIE  A   +++
Sbjct: 293 QIERAALASMRQ 304


>gi|88856913|ref|ZP_01131565.1| RNA polymerase sigma factor [marine actinobacterium PHSC20C1]
 gi|88813881|gb|EAR23751.1| RNA polymerase sigma factor [marine actinobacterium PHSC20C1]
          Length = 454

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 69/252 (27%), Positives = 121/252 (48%), Gaps = 34/252 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WW
Sbjct: 217 AKSHLLGANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 276

Query: 109 IKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   +      ++I              Q+++  +L R     +   + ++ PE+V
Sbjct: 277 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELSRELDMTPEKV 336

Query: 160 VAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           V + K       E IS++  L   GD     LI  ++          V   D     +++
Sbjct: 337 VEVQKYGR----EPISLHTPLGEDGDSEFGDLIEDTEA---------VVPADAVGFTMLQ 383

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEAR 275
           K+        L   +  L+ RE  +   R  L +  P TL+ +   F V+RER+RQIE++
Sbjct: 384 KQ--------LESLLDSLSEREAGVIRMRFGLGDGMPKTLDQIGDTFGVTRERIRQIESK 435

Query: 276 AFKKVQESIQKQ 287
              K++   + Q
Sbjct: 436 TMAKLRHPSRSQ 447


>gi|32474203|ref|NP_867197.1| transcription initiation factor sigma 70 [Rhodopirellula baltica SH
           1]
 gi|32444741|emb|CAD74742.1| transcription initiation factor sigma 70 [Rhodopirellula baltica SH
           1]
          Length = 567

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 82/277 (29%), Positives = 124/277 (44%), Gaps = 35/277 (12%)

Query: 21  HEIRKIPMLEKQEEYVLAKRY---REHGDLSAAHR--LVTSHLRLVVKIAMGYRGYGLPI 75
            E+R++ ++ ++    L  R    R H D   A +  L   +LRLVV IA  YR  GL  
Sbjct: 294 QELRELMLVTQESPTSLHNRMAKVRRHFDQYEATKRELSAGNLRLVVSIAKKYRNRGLSF 353

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT------- 128
            +++ EGN GLM+AV K++  RGF+ +TY+ WWI+ A+   I      ++I         
Sbjct: 354 LDLIQEGNTGLMRAVDKYEYRRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMIDVLS 413

Query: 129 --TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
                QKRL   LRR   +       ++  E+V  +   +++    V           SL
Sbjct: 414 KLRQAQKRLTQTLRREPTYEDIAEATDVPIEEVRRV---MDIGRHPV-----------SL 459

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           +  +   + +S       V D +    V I        RN +   +  L  RER I   R
Sbjct: 460 DRPVGEGEDSSF---GEFVQDSETDNPVRIAAS--GMLRNKIDELLKTLTFREREIIRLR 514

Query: 247 R--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +     TLE     F+V+RERVRQIEA+A  K+Q
Sbjct: 515 YGLVDGYSYTLEECGRIFKVTRERVRQIEAKAVAKMQ 551


>gi|555686|gb|AAA85644.1| sigma factor MysB [Mycobacterium smegmatis str. MC2 155]
          Length = 319

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 81/300 (27%), Positives = 141/300 (47%), Gaps = 56/300 (18%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH-------------GDLSAAHR-------- 52
           Y++ I K  +L   +E  LAKR     Y +H              DL A  R        
Sbjct: 26  YLNGIGKTALLNAADEVELAKRIEAGLYAQHLLDTKKRLGEARKRDLQAVVRDGEAARRH 85

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A
Sbjct: 86  LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQA 145

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ-----AITDNNLKPEQVVAIAKKLN 167
           +   +      +++     ++     L R+K  +        TD  L  E  + + K  +
Sbjct: 146 ITRGMADQSRTIRLPVHLVEQ--VNKLARIKREMHQNLGREATDEELAEESGIPVEKIND 203

Query: 168 VSES--EVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + E   + +S++  +  DE   L   I  S+  S+             E  +I +    +
Sbjct: 204 LLEHSRDPVSLDMPVGTDEEAPLGDFIEDSEAMSA-------------ENAVISELLHTD 250

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R +L    + L+ RE+++   R   ++  P TL+ +   F +SRERVRQIE     K++
Sbjct: 251 IRYVL----ATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMAKLR 306


>gi|145224529|ref|YP_001135207.1| RNA polymerase sigma factor SigB [Mycobacterium gilvum PYR-GCK]
 gi|145217015|gb|ABP46419.1| RNA polymerase, sigma 70 subunit, RpoD family [Mycobacterium gilvum
           PYR-GCK]
          Length = 329

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 80/300 (26%), Positives = 142/300 (47%), Gaps = 56/300 (18%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH-------------GDLSAAHR-------- 52
           Y++ I K  +L   +E  LAKR     Y +H              DL+A  R        
Sbjct: 36  YLNGIGKTALLTAADEVELAKRIEAGLYAQHLLATRKRLGENRKRDLAAVVRDGEAARRH 95

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A
Sbjct: 96  LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTYATWWIRQA 155

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA-----ITDNNLKPEQVVAIAKKLN 167
           +   +      +++     ++     L R+K  +        TD  L  E  + + K  +
Sbjct: 156 ITRGMADQSRTIRLPVHLVEQ--VNKLARIKREMHQNLGREATDEELAEESGIPVEKIND 213

Query: 168 VSES--EVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + E   + +S++  +  DE   L   I  ++  S+             E  +I +    +
Sbjct: 214 LLEHSRDPVSLDMPVGSDEEAPLGDFIEDAEAMSA-------------ENAVISELLHTD 260

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R +L    + L+ RE+++   R   ++  P TL+ +   F +SRERVRQIE     K++
Sbjct: 261 IRYVL----ATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMAKLR 316


>gi|332298226|ref|YP_004440148.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           brennaborense DSM 12168]
 gi|332181329|gb|AEE17017.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           brennaborense DSM 12168]
          Length = 332

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 82/305 (26%), Positives = 143/305 (46%), Gaps = 55/305 (18%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREH---------GDLSAA---------------- 50
           LS Y+ +I +  +L  QEE   A   +EH         G L  A                
Sbjct: 34  LSLYLKQISRYKLLSVQEEQATAAAIQEHKSRIRQLKSGLLEPAENSPAYEEIDRLERDL 93

Query: 51  ----HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
               ++++ ++LRLVV IA  Y+  GL + +++ EGNIGL++AV +F+P R  R +TY +
Sbjct: 94  LVLKNKMIQANLRLVVSIAKRYQHRGLGLLDLIDEGNIGLIEAVDRFEPARNCRFSTYGI 153

Query: 107 WWIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           WWI+ A+ + +     ++++      T N  + FF  + L       T    +      +
Sbjct: 154 WWIRQAIIKSLADKGRVIRVPVHMLNTIN--KCFFMAKLL-------TQEYGREPTTAEL 204

Query: 163 AKKLNVSESEV---ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           A+ L V+  +V   I ++  ++  E+     N  D NS++  D L+ D +G+    IE+ 
Sbjct: 205 ARFLCVTNEKVEDYIRLSQEMSSLET-----NVDDDNSTRLGD-LLTDENGEAP--IERV 256

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
                 + +   ++ L+ RE  I   R   +   P TL    +   ++RERVRQI+ +  
Sbjct: 257 FAAALTDTVNLVLNQLSEREMSIIRLRYGLDGKAPRTLTETGNVLGITRERVRQIQEKTL 316

Query: 278 KKVQE 282
           KK++E
Sbjct: 317 KKLRE 321


>gi|325971191|ref|YP_004247382.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta sp.
           Buddy]
 gi|324026429|gb|ADY13188.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta sp.
           Buddy]
          Length = 685

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 71/244 (29%), Positives = 125/244 (51%), Gaps = 30/244 (12%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A  RL+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+KF+  +GF+ +TY+ W
Sbjct: 448 DAKDRLIRANLRLVVSIAKKYTNRGLHFFDLVQEGNIGLIKAVEKFEYRKGFKFSTYATW 507

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++     ++ +   +R  +  +Q++       E    +A+KL 
Sbjct: 508 WIRQAITRSISDQARTIRVPVHMIEQ-INKVVRESRMLMQSLGREPTDEE----VAEKLG 562

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR--- 224
            +ES+V ++        SL   +        + +D L+ D        IE +E +N    
Sbjct: 563 WTESKVKAVKNVAREPISLETPVG-------EEEDSLLSD-------FIEDKEVENPATQ 608

Query: 225 ------RNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARA 276
                 +  L   ++ L  RE+ + + R   E+   +TLE +   FE++RER+RQIEA+A
Sbjct: 609 TAYSLLQEQLKDVLATLPAREQEVLKMRFGLEDGYSLTLEEVGLYFELTRERIRQIEAKA 668

Query: 277 FKKV 280
            +++
Sbjct: 669 LRRL 672


>gi|296127158|ref|YP_003634410.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Brachyspira
           murdochii DSM 12563]
 gi|296018974|gb|ADG72211.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Brachyspira
           murdochii DSM 12563]
          Length = 587

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 72/250 (28%), Positives = 129/250 (51%), Gaps = 30/250 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   ++V EGNIGL++AV KF+ ++G++ +TY+ WW
Sbjct: 349 AKDHIVKANLRLVIAIAKKYVNRGLHFFDLVQEGNIGLIKAVDKFEYKKGYKFSTYATWW 408

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      +++        +   + +++  L+     + +   +  IAK L  
Sbjct: 409 IRQAITRSISDQARTIRVPV-----HMIEQINKVQRVLRQYMQQHGREPSIQEIAKALGW 463

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            ES V S+        SLNA I          +D ++    G+   LIE +E ++ +N+ 
Sbjct: 464 PESRVKSVRNVAKDPVSLNAPIGDE-------EDTIL----GE---LIEDKEFESPQNIT 509

Query: 229 TRSM------SVLN---PRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAF 277
           T  +      S+L+    RE+++   R   +     TLE +   F+V+RER+RQIEA+A 
Sbjct: 510 TFKILRKQIDSILDSLPDREQKVIRMRFGLVDGYSHTLEEVGYVFKVTRERIRQIEAKAI 569

Query: 278 KKVQESIQKQ 287
           ++++   +K+
Sbjct: 570 RRLRAQSKKK 579


>gi|56708122|ref|YP_170018.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis SCHU S4]
 gi|110670593|ref|YP_667150.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis FSC198]
 gi|224457213|ref|ZP_03665686.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|254370608|ref|ZP_04986613.1| DNA-directed RNA polymerase sigma subunit RpoD [Francisella
           tularensis subsp. tularensis FSC033]
 gi|254874922|ref|ZP_05247632.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|56604614|emb|CAG45668.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis SCHU S4]
 gi|110320926|emb|CAL09051.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis FSC198]
 gi|151568851|gb|EDN34505.1| DNA-directed RNA polymerase sigma subunit RpoD [Francisella
           tularensis subsp. tularensis FSC033]
 gi|254840921|gb|EET19357.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|282159323|gb|ADA78714.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis NE061598]
          Length = 577

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 74/248 (29%), Positives = 114/248 (45%), Gaps = 36/248 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLVV  A  Y   GL   +++ EGNIGLM+AV KFD  +GF+ +TY+ WW
Sbjct: 339 AKKEMIEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKGFKFSTYATWW 398

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITDNNLKPEQVVAIAKKLN 167
           I+ A+   I            A+Q R      R+  H+ + I   N    Q++   K   
Sbjct: 399 IRQAITRSI------------ADQARTI----RVPVHMIETINKVNRIKRQILQ-EKGRE 441

Query: 168 VSESEVISMNCRLAGDESLNALINSS-----------DKNSSQWQDWLVYDHDGQEQVLI 216
            +E E+I     +   E L  ++N S           D   S   D++    D      I
Sbjct: 442 ATEEEIIEHTPNMTK-EKLKKILNISHTPISMESPIGDDEDSTVGDFI---EDKSNYSPI 497

Query: 217 EKEERKNRRNMLTRSMSV-LNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIE 273
           E    +N R  +   +   L  RE ++   R         TLE +  +F V+RER+RQIE
Sbjct: 498 EAANLENLREAIKELIETGLTEREAKVLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIE 557

Query: 274 ARAFKKVQ 281
           A+A +K++
Sbjct: 558 AKALRKLK 565


>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 = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 64/235 (27%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 406 AAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 465

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I    +       + R+    Q + +   +P+    +A+ + 
Sbjct: 466 WIRQAITRSIADQARTIRI--PVHMIETINKMNRISR--QYLQETGEEPDS-AKLAELME 520

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + E ++  +  ++A  E ++      D + S   D++    D       E     +   +
Sbjct: 521 MPEDKIRKI-MKIAK-EPISMETPIGDDDDSHLGDFI---EDANNVAPAEAAMYTSLHEV 575

Query: 228 LTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
               +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 576 TKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 630


>gi|332708973|ref|ZP_08428943.1| RNA polymerase sigma factor, sigma-70 family//RpoD-like family
           [Lyngbya majuscula 3L]
 gi|332352162|gb|EGJ31732.1| RNA polymerase sigma factor, sigma-70 family//RpoD-like family
           [Lyngbya majuscula 3L]
          Length = 373

 Score = 87.0 bits (214), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 71/242 (29%), Positives = 123/242 (50%), Gaps = 25/242 (10%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +++ S+LRLVV IA  Y   G+P  +++ EG +GL +A +KFDP++G++ +TY+ WW
Sbjct: 135 AKRKMIRSNLRLVVSIAKRYINRGVPFLDLIQEGALGLNRAAEKFDPDKGYKFSTYAYWW 194

Query: 109 IKAAMQEYILRSWSLVKIGTTANQK--RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           I+ A+   I      +++     +K  +L    R LK  LQ        P + + +A+ L
Sbjct: 195 IRQAITRTIANDARTIRLPIHIVEKLNKLKKAQRELKQKLQR------NPNE-LELAQAL 247

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +S S +  +        SLN  +   +   ++  D L+ D+D      +   E K   +
Sbjct: 248 EISLSHLRQLLELRRRSLSLNHRVGKGE--DTELMD-LLEDND------LRLPEDKMNES 298

Query: 227 MLTRSM-----SVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           M+ + +      VL  RE+ +   R       P TLE +   F +SRERVRQI+++A +K
Sbjct: 299 MMRQEIWEVLSDVLTEREKDVISLRYGLASSEPYTLEEVGGMFNLSRERVRQIQSKAMRK 358

Query: 280 VQ 281
           ++
Sbjct: 359 LR 360


>gi|283456279|ref|YP_003360843.1| RNA polymerase principal sigma factor hrdB [Bifidobacterium dentium
           Bd1]
 gi|283102913|gb|ADB10019.1| RNA polymerase principal sigma factor hrdB [Bifidobacterium dentium
           Bd1]
          Length = 328

 Score = 86.7 bits (213), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 65/253 (25%), Positives = 124/253 (49%), Gaps = 34/253 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ WW
Sbjct: 90  AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 149

Query: 109 IKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   +      +++           +  Q+++  +L R     +   + ++  E+V
Sbjct: 150 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 209

Query: 160 VAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
             + K       E IS++  L   GD     LI  +D          +   D     L++
Sbjct: 210 QEVQK----YGREPISLHTPLGEDGDSEFGDLIEDTDA---------IAPSDAVAFSLLQ 256

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
           ++          + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++
Sbjct: 257 EQ--------FKQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESK 308

Query: 276 AFKKVQESIQKQV 288
              K++   + Q 
Sbjct: 309 TMSKLRHPSRSQT 321


>gi|313812945|gb|EFS50659.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL025PA1]
          Length = 312

 Score = 86.7 bits (213), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 82/312 (26%), Positives = 142/312 (45%), Gaps = 59/312 (18%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------------- 43
           ++G+  +  Y+  I + P+L   EE  LA+R                             
Sbjct: 13  IDGKDAVGLYLDGIARTPLLNAAEEVALARRIEAGVFARAILEGHAETTSDATTKELHQI 72

Query: 44  --HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
              GD + AH  V ++LRLVV +A  Y    +P+ ++V EGN GL++AV+KFD  +GF+ 
Sbjct: 73  AADGDEALAH-FVRANLRLVVSVARKYGRSQMPLLDLVQEGNTGLIRAVEKFDYAKGFKF 131

Query: 102 ATYSMWWIKAAMQEYILRSWSLVK----IGTTANQ-KRLFFNLRRLKGHLQAITDNNLKP 156
           +TY+ WW++ A+   I +   +V+    +    NQ      NL R  G          +P
Sbjct: 132 STYATWWVRQAISRGIAQQGRIVRLPVHVAEQVNQVSAARRNLERQLGR---------EP 182

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHD-GQEQV 214
           E    IA +L ++E  VI +  R   D  SL+A +   D   +   D +  +   G + +
Sbjct: 183 E-TFEIADELEITEERVIEL-IRFGRDHVSLDAPVE--DDGDTSLGDLIARETSPGPDDI 238

Query: 215 LIEKEERKNRRNMLT----RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
           +++ E+R     +L     RS  V+  R   + + R+ +     L ++   + ++ ERVR
Sbjct: 239 VLDAEDRSRLEGLLDDLDERSADVVR-RRYGLVDGRQAK-----LADIGKVWGITAERVR 292

Query: 271 QIEARAFKKVQE 282
           QIE  A   +++
Sbjct: 293 QIERAALASMRQ 304


>gi|168700394|ref|ZP_02732671.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Gemmata obscuriglobus UQM 2246]
          Length = 335

 Score = 86.7 bits (213), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 67/238 (28%), Positives = 116/238 (48%), Gaps = 15/238 (6%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           HRL ++++RL   +A  +R + L  S+++ E   GLMQA+ +FD   G RLATY+ WWI+
Sbjct: 101 HRLASANIRLAAHVAKRFRHHSLAYSDLLQEAVCGLMQAIDRFDVSHGTRLATYATWWIR 160

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
             +Q  + R   LV +     Q+     L  L+   +A+            +A +   S 
Sbjct: 161 QTLQIAVARQSHLVSLSPHHLQE-----LGLLQQESEALAHGGKHLPSPQELASRTGSSL 215

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
             +  +        SLNA+++  D +  +  + +    D    V+ E  ER+   + L  
Sbjct: 216 EHLTHLQTATRTPVSLNAVLD--DDSDFKLTEAMP---DTGTLVMQENNERQEALSFL-- 268

Query: 231 SMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            M  L PRER++ + R  L  N   +L  +     +S+ERVRQI+ RA +K++ + ++
Sbjct: 269 -MENLRPRERKVLDLRFGLTGNGTHSLRQIGHLLRISKERVRQIQNRALEKLKANAER 325


>gi|158522162|ref|YP_001530032.1| RpoD family RNA polymerase sigma factor [Desulfococcus oleovorans
           Hxd3]
 gi|158510988|gb|ABW67955.1| RNA polymerase, sigma 70 subunit, RpoD family [Desulfococcus
           oleovorans Hxd3]
          Length = 738

 Score = 86.7 bits (213), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 69/232 (29%), Positives = 117/232 (50%), Gaps = 14/232 (6%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV IA  Y   GL   +++ EGN+GLM+AV KF+  RG++ +TY+ WWI+ A
Sbjct: 504 LIRANLRLVVSIAKKYTNRGLQFLDLIQEGNVGLMKAVDKFEYRRGYKFSTYATWWIRQA 563

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   I      ++I    +       L R   +L         PE+   IA+K+ +   E
Sbjct: 564 ITRAIADQARTIRI--PVHMIETINKLIRTSRYLVQERGYEPSPEE---IAEKMEIP-LE 617

Query: 173 VISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
            +    ++A +  SL   I   ++  S   D++    D +  +  E     N      + 
Sbjct: 618 KVRRVLKIAREPISLETPIG--EEEDSHLGDFI---EDKKFMIPSEAAVSMNLSEQTRKV 672

Query: 232 MSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++ L PRE ++   R    ++   TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 673 LATLTPREEKVLRMRFGIGEKADHTLEEVGRDFAVTRERIRQIEAKALRKLR 724


>gi|15807631|ref|NP_294640.1| RNA polymerase sigma-A factor [Deinococcus radiodurans R1]
          Length = 360

 Score = 86.7 bits (213), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 77/298 (25%), Positives = 139/298 (46%), Gaps = 48/298 (16%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKR-------------------------YREHGDLSAAHR 52
           +Y+HEI ++ +L  +EE  LA+R                          R+  D +AA +
Sbjct: 63  QYLHEIGRVSLLTLEEEIALARRIEEGEEARKQLEEDESLDDRSRRRLMRQMEDGAAARQ 122

Query: 53  -LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV IA  Y G GL   +++ EGN GL++AV+KF+  R ++ +TY+ WWI+ 
Sbjct: 123 GLIEANLRLVVSIAKKYTGRGLGFLDLIQEGNQGLIRAVEKFEYRRRYKFSTYATWWIRQ 182

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-AIAKKLNVSE 170
           A+   I      ++I    +       L R    LQ         E++  A+    + ++
Sbjct: 183 AINRAIADQARTIRI--PVHMVETINKLTRTARQLQQELSREATHEEIAEAMGPGWDAAK 240

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH-----DGQEQVLIEKEERKNRR 225
            E +    +    E ++      D+  S + D++  ++     D   + L+ +E      
Sbjct: 241 VEEVQKVSQ----EPVSLETPIGDEKDSFYGDFIPDENLDSPVDNAAKTLLSEE------ 290

Query: 226 NMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             L +++  L  RE  + + R+  +     TLE +   F V+RER+RQIE +A +K++
Sbjct: 291 --LEKALGKLTEREAMVLKFRKGLVDGREHTLEEVGQRFSVTRERIRQIENKALRKLK 346


>gi|21449377|gb|AAM54109.1|AF453501_35 RNA polymerase sigma factor [Actinosynnema pretiosum subsp.
           auranticum]
          Length = 348

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 80/294 (27%), Positives = 133/294 (45%), Gaps = 43/294 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREHG-DLSAAHR-------------------- 52
           Y+  I ++ +L   +E  LA+R     Y EH  DL  A R                    
Sbjct: 54  YLKAIGRVRLLTADQEVELARRVEAGLYAEHLLDLPPAARGSRRPVELRRVVRDGQRAKD 113

Query: 53  -LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV IA  Y G G+ + +V+ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ 
Sbjct: 114 HLLEANLRLVVSIAKRYTGKGMALLDVIQEGNLGLVRAVEKFDYAKGFKFSTYATWWIRQ 173

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           A+   +      +++    +   +   L R++  L          E+V   A +L+V+  
Sbjct: 174 AITRALADQSRTIRL--PVHMVEVVTKLARIERDLLHRNGREATAEEV---AVELDVTPE 228

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR--RNMLT 229
           +V+ +        SL+  I +    S       + D    E  +   E   +      L 
Sbjct: 229 KVVELRQHARTPVSLDQTIGAEADTS-------IGDLIADENAVAPLEAVSSALLSADLR 281

Query: 230 RSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
             +  L PRE  +   R    + V  TL+ +   + V+RER+RQIE+R   K+Q
Sbjct: 282 AVLETLTPREAGVVRMRYGFPDGVLHTLDEVGRVYGVTRERIRQIESRTMAKLQ 335


>gi|313680173|ref|YP_004057912.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Oceanithermus
           profundus DSM 14977]
 gi|313152888|gb|ADR36739.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Oceanithermus
           profundus DSM 14977]
          Length = 484

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 71/246 (28%), Positives = 126/246 (51%), Gaps = 25/246 (10%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           G+++  H L+ ++LRLVV IA  Y G GL   +++ EGN GL++AV+KF+ +R ++ +TY
Sbjct: 241 GEIARQH-LIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRYKFSTY 299

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA-IA 163
           + WWI+ A+   I      ++I    +       L R    LQ      L  E   A IA
Sbjct: 300 ATWWIRQAINRAIADQARTIRI--PVHMVETINKLTRTARQLQ----QELGREATYAEIA 353

Query: 164 KKLNVS-ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH-----DGQEQVLIE 217
             +    +++ +    ++A  E ++      D+  S + D++  +H     D   Q L+ 
Sbjct: 354 DAMGPGWDAKKVEETFKIA-QEPVSLETPIGDEKDSFYGDFIPDEHLASPVDSAAQSLLS 412

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
           +E        L +++S L+ RE  + + R+  +     TLE + + F V+RER+RQIE +
Sbjct: 413 EE--------LEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENK 464

Query: 276 AFKKVQ 281
           A +K++
Sbjct: 465 ALRKLK 470


>gi|168704760|ref|ZP_02737037.1| transcription initiation factor sigma 70 [Gemmata obscuriglobus UQM
           2246]
          Length = 556

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 74/253 (29%), Positives = 125/253 (49%), Gaps = 16/253 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           ++ +R+ E+    A   L   +LRLVV IA  YR  GL   +++ EGN GLM+AV K++ 
Sbjct: 301 IMKQRFAEYE--QAKRDLSGGNLRLVVSIAKKYRNRGLSFLDLIQEGNTGLMRAVDKYEH 358

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            RGF+ +TY+ WWI+ A+   I      ++I    +       LR +   L  + +   +
Sbjct: 359 RRGFKFSTYATWWIRQAITRAIADQARTIRI--PVHMIETMSKLRNVSKQL--LQELGRE 414

Query: 156 PE-QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           P  Q  A A K++  E + +    R     SL+  +  S+   S + D++    D   + 
Sbjct: 415 PTVQETADAAKISYEECKRVLKISRQPI--SLDRPVGESE--DSYFGDFI---EDNSVES 467

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
            +     +  ++ +   +  L  RER I + R    +    TLE +   F+V+RERVRQI
Sbjct: 468 PVNAATNEMLKDKIEGVLKTLTYREREIIKLRYGLGDGYTYTLEEVGRIFKVTRERVRQI 527

Query: 273 EARAFKKVQESIQ 285
           EA+A +K+Q  ++
Sbjct: 528 EAKAVRKLQHPVR 540


>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 = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 64/235 (27%), Positives = 118/235 (50%), Gaps = 12/235 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 406 AAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 465

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I    +       + R+    Q + +   +P+    +A+ + 
Sbjct: 466 WIRQAITRSIADQARTIRI--PVHMIETINKMNRISR--QYLQETGEEPDS-AKLAELME 520

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + E ++  +  ++A  E ++      D + S   D++    D       E     +   +
Sbjct: 521 MPEDKIRKI-MKIAK-EPISMETPIGDDDDSHLGDFI---EDANNVAPAEAAMYTSLHEV 575

Query: 228 LTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
               +  L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 576 TKEILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 630


>gi|118472772|ref|YP_887083.1| RNA polymerase sigma factor SigB [Mycobacterium smegmatis str. MC2
           155]
 gi|118174059|gb|ABK74955.1| sigma factor SigB [Mycobacterium smegmatis str. MC2 155]
          Length = 319

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 81/300 (27%), Positives = 142/300 (47%), Gaps = 56/300 (18%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH-------------GDLSAAHR-------- 52
           Y++ I K  +L   +E  LAKR     Y +H              DL A  R        
Sbjct: 26  YLNGIGKTALLNAADEVELAKRIEAGLYAQHLLDTKKRLGEARKRDLQAVVRDGEAARRH 85

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A
Sbjct: 86  LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQA 145

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-----QAITDNNLKPEQVVAIAKKLN 167
           +   +      +++     ++     L R+K  +     +  TD  L  E  + + K  +
Sbjct: 146 ITRGMADQSRTIRLPVHLVEQ--VNKLARIKREMHQNLGREATDEELAEESGIPVEKIND 203

Query: 168 VSES--EVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + E   + +S++  +  DE   L   I  S+  S+             E  +I +    +
Sbjct: 204 LLEHSRDPVSLDMPVGTDEEAPLGDFIEDSEAMSA-------------ENAVISELLHTD 250

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R +L    + L+ RE+++   R   ++  P TL+ +   F +SRERVRQIE     K++
Sbjct: 251 IRYVL----ATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMAKLR 306


>gi|262202171|ref|YP_003273379.1| sigma-70 family RNA polymerase sigma factor [Gordonia bronchialis
           DSM 43247]
 gi|262085518|gb|ACY21486.1| RNA polymerase sigma factor, sigma-70 family [Gordonia bronchialis
           DSM 43247]
          Length = 337

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 72/251 (28%), Positives = 126/251 (50%), Gaps = 33/251 (13%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           G+ + AH L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY
Sbjct: 97  GEAARAH-LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTY 155

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-----QAITDNNLKPEQV 159
           + WWI+ A+   +      +++     ++     L R+K  L     +  TD  L  E  
Sbjct: 156 ATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLARIKRELHQQLGREATDEELANESG 213

Query: 160 VA---IAKKLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +    IA  L+ S   V S++  +  DE   L   I  ++  S+             E  
Sbjct: 214 IPAEKIADLLDHSRDPV-SLDMPVGSDEEAPLGDFIEDAEATSA-------------ESA 259

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
           +I      + R +L    + L+ RE+++   R   ++  P TL+ +   F +SRERVRQI
Sbjct: 260 VIAGLMHTDVRAVL----ATLDEREQQVIRMRYGLDDGQPRTLDQIGRMFGLSRERVRQI 315

Query: 273 EARAFKKVQES 283
           E     K+++ 
Sbjct: 316 EREVMGKLRQG 326


>gi|320096194|ref|ZP_08027783.1| DNA-directed RNA polymerase sigma subunit RpoD [Actinomyces sp.
           oral taxon 178 str. F0338]
 gi|319976875|gb|EFW08629.1| DNA-directed RNA polymerase sigma subunit RpoD [Actinomyces sp.
           oral taxon 178 str. F0338]
          Length = 543

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 68/253 (26%), Positives = 123/253 (48%), Gaps = 34/253 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WW
Sbjct: 306 AKNHLLEANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 365

Query: 109 IKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   +      ++I              Q+++  +L R     +   + ++ PE+V
Sbjct: 366 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELAKELDMTPEKV 425

Query: 160 VAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           V + K       E IS++  L   GD     LI  S+          +   D     L++
Sbjct: 426 VEVQKYGR----EPISLHTPLGEDGDSEFGDLIEDSEA---------IVPADAVSFTLLQ 472

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEAR 275
           ++        L   +  L+ RE  +   R  L +  P TL+ +   + V+RER+RQIE++
Sbjct: 473 EQ--------LHHVLDTLSEREAGVVSMRFGLGDGQPKTLDEIGKVYGVTRERIRQIESK 524

Query: 276 AFKKVQESIQKQV 288
              K++   + QV
Sbjct: 525 TMSKLRHPSRSQV 537


>gi|302525710|ref|ZP_07278052.1| RNA polymerase sigma factor RpoS [Streptomyces sp. AA4]
 gi|302434605|gb|EFL06421.1| RNA polymerase sigma factor RpoS [Streptomyces sp. AA4]
          Length = 317

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 78/302 (25%), Positives = 137/302 (45%), Gaps = 56/302 (18%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH-----GDLS----------------AAHR 52
           Y++ I K  +L   +E  LAKR     + +H      DL+                A + 
Sbjct: 24  YLNGIGKTALLTAADEVELAKRIEAGVFAQHMLDTAEDLTPQRRKELRALVRDGHVAKNH 83

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 84  LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAVEKFDYSKGFKFSTYATWWIRQA 143

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA--------IAK 164
           +   +      +++     ++     L R++  L      +   E++ A        I+ 
Sbjct: 144 ITRGMADQGRTIRLPVHLVEQ--VNKLARIRRDLHQQLGRDATHEELSAESGIPVHKISD 201

Query: 165 KLNVSESEV-ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
            L+ S   V + M      D  L   I  S+   +             E  +I    + +
Sbjct: 202 LLDQSRDPVSLDMPVGTEEDAPLGDFIEDSEATDA-------------ESAVISGLLQDD 248

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
               L R ++ L+ RE+ +   R   ++  P TL+ +   F +SRERVRQIE     K++
Sbjct: 249 ----LRRVLATLDDREQHVIRLRYGLDDGQPRTLDQIGKHFGLSRERVRQIEREVMAKLR 304

Query: 282 ES 283
           + 
Sbjct: 305 QG 306


>gi|238926534|ref|ZP_04658294.1| DNA-directed RNA polymerase sigma subunit RpoD [Selenomonas
           flueggei ATCC 43531]
 gi|238885480|gb|EEQ49118.1| DNA-directed RNA polymerase sigma subunit RpoD [Selenomonas
           flueggei ATCC 43531]
          Length = 352

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 69/254 (27%), Positives = 124/254 (48%), Gaps = 33/254 (12%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           + G+L A   L   + +LV K A+GY     + L   ++   G IGL+ A KKFD   G+
Sbjct: 104 QQGNLQAEQDLCVKNKKLVDKYALGYEKRYRHRLDFDDIEQAGFIGLITAAKKFDISMGY 163

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGT--------TANQKRLFFNLRRLKGHLQAITD 151
             +TY++WWIK A+   I+    +++I           A  + +F  L R +  ++ + +
Sbjct: 164 SFSTYAVWWIKQAITREIMDHGFVIRIPVHMMEQIIKVAGVENMFSELNREERIVKVMDE 223

Query: 152 NNLKPEQV--VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
              K E+V    + K+  ++ S   S+N  +  DE++      SD  +   ++ +     
Sbjct: 224 TGYKEERVRECMMLKEYVLTYS---SLNVTVGEDETVELGEFLSDDGAISIEEMI----- 275

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRE 267
                     E K  R ML   ++ L  +E+++ + R  L++N   TLE +   F V+RE
Sbjct: 276 ----------ENKELRRMLDDVLNTLTEKEKKVIKLRFGLEDNRQWTLEEVGKLFNVTRE 325

Query: 268 RVRQIEARAFKKVQ 281
           R+RQIE++A +K++
Sbjct: 326 RIRQIESKALRKLR 339


>gi|328950970|ref|YP_004368305.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Marinithermus
           hydrothermalis DSM 14884]
 gi|328451294|gb|AEB12195.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Marinithermus
           hydrothermalis DSM 14884]
          Length = 477

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 70/245 (28%), Positives = 126/245 (51%), Gaps = 23/245 (9%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           G+L+  H L+ ++LRLVV IA  Y G GL   +++ EGN GL++AV+KF+ +R ++ +TY
Sbjct: 234 GELARQH-LIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRYKFSTY 292

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + WWI+ A+   I      ++I    +       L R    LQ         E+   IA+
Sbjct: 293 ATWWIRQAINRAIADQARTIRI--PVHMVETINKLTRTARQLQQEKGREPSYEE---IAE 347

Query: 165 KLNVS-ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH-----DGQEQVLIEK 218
            +    +++ +    ++A  E ++      D+  S + D++  +H     D   Q L+ +
Sbjct: 348 AMGPGWDAKRVEETFKIA-QEPVSLETPIGDEKDSFYGDFIPDEHMASPVDAAAQSLLSE 406

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARA 276
           E        L +++S L+ RE  + + R+  +     TLE + + F V+RER+RQIE +A
Sbjct: 407 E--------LEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKA 458

Query: 277 FKKVQ 281
            +K++
Sbjct: 459 LRKLK 463


>gi|327330254|gb|EGE72003.1| RNA polymerase principal sigma factor SigA [Propionibacterium acnes
           HL097PA1]
          Length = 312

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 82/309 (26%), Positives = 143/309 (46%), Gaps = 53/309 (17%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------------- 43
           ++G+  +  Y+  I + P+L   EE  LA+R                             
Sbjct: 13  IDGKDAVGLYLDGIARTPLLNAAEEVALARRIEAGVFARAILEGHAETTSDATTKELHQI 72

Query: 44  --HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
              GD + AH  V ++LRLVV +A  Y    +P+ ++V EGN GL++AV+KFD  +GF+ 
Sbjct: 73  AADGDEALAH-FVRANLRLVVSVARKYGRSQMPLLDLVQEGNTGLIRAVEKFDYAKGFKF 131

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFFNLRR-LKGHLQAITDNNLKPEQV 159
           +TY+ WW++ A+   I +   +V++    A Q       RR L+  L        +PE  
Sbjct: 132 STYATWWVRQAISRGIAQQGRIVRLPVHVAEQVNQVSAARRSLERQL------GREPE-T 184

Query: 160 VAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHD-GQEQVLIE 217
             IA +L ++E  VI +  R   D  SL+A +   D   +   D +  +   G + ++++
Sbjct: 185 FEIADELEITEERVIEL-IRFGRDHVSLDAPVE--DDGDTSLGDLIARETSPGPDDIVLD 241

Query: 218 KEERKNRRNMLT----RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
            E+R     +L     RS  V+  R   + + R+ +     L ++   + ++ ERVRQIE
Sbjct: 242 AEDRSRLEGLLDDLDERSADVVR-RRYGLVDGRQAK-----LADIGKVWGITAERVRQIE 295

Query: 274 ARAFKKVQE 282
             A   +++
Sbjct: 296 RAALASMRQ 304


>gi|229817449|ref|ZP_04447731.1| hypothetical protein BIFANG_02712 [Bifidobacterium angulatum DSM
           20098]
 gi|229785238|gb|EEP21352.1| hypothetical protein BIFANG_02712 [Bifidobacterium angulatum DSM
           20098]
          Length = 482

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 75/310 (24%), Positives = 143/310 (46%), Gaps = 61/310 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH-----GDL-----------------SAAH 51
           Y+ +I ++ +L  ++E  L++R     Y +H     GD                   A  
Sbjct: 187 YLKQIGRVSLLNAEQEVDLSERIEAGLYAQHLLDTEGDTMDFKRKRELKWAANDGKKAKD 246

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ WWI+ 
Sbjct: 247 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWWIRQ 306

Query: 112 AMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      +++           +  Q+++  +L R     +   + ++  E+V  +
Sbjct: 307 AITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKVQEV 366

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K       E IS++  L   GD     LI  +D          +   D     L++   
Sbjct: 367 QK----YGREPISLHTPLGEDGDSEFGDLIEDTD---------AIAPSDAVAFSLLQ--- 410

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFK 278
                +   + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++   
Sbjct: 411 -----DQFKQVLETLSPRESGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMS 465

Query: 279 KVQESIQKQV 288
           K++   + Q 
Sbjct: 466 KLRHPSRSQT 475


>gi|148242708|ref|YP_001227865.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp.
           RCC307]
 gi|147851018|emb|CAK28512.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. RCC307]
          Length = 301

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 79/279 (28%), Positives = 137/279 (49%), Gaps = 20/279 (7%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLA--KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           E+ L R +  +  +P+ +K  E +    KR    G+  A ++++T++LRLVV +A  Y+G
Sbjct: 24  ELTLGRKVQAM--VPLQDKPVESLSEDEKRALRLGE-RAKNQMITANLRLVVNLAKRYQG 80

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            GL + +++ EG +GL +AV+KFDP RG R +TY+ WWI+  +   +      ++I    
Sbjct: 81  KGLELLDLIQEGTLGLTRAVEKFDPTRGHRFSTYAYWWIRQGLNRALSTQSRTIRIPVNI 140

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNAL 189
           N+K     LR  K  L   T      E+ +A   KL + E E + + C L +   SL  +
Sbjct: 141 NEK--LTKLRAAKARLFQSTGRQPIAEE-LADYLKLPLDEVEDL-LGCELRSVTVSLQGV 196

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM--SVLNPRERRIFEARR 247
           + S    S      LV     +E   +E+ E   R   + + +  + L P+ER +   R 
Sbjct: 197 VKSKSDPSE-----LVDVLPSEEMPPMERAELDERTQTVWKLLDQANLTPKERTVVMLRF 251

Query: 248 LQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +      TL  ++ +   SRE  RQ+  R+ +K++ +
Sbjct: 252 GLDGTNEWRTLAEVARQMSCSREYCRQVVQRSLRKLRRA 290


>gi|17233195|ref|NP_490285.1| group 2 sigma 70-type sigma factor [Nostoc sp. PCC 7120]
 gi|17135717|dbj|BAB78263.1| group 2 sigma 70-type sigma factor [Nostoc sp. PCC 7120]
          Length = 316

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 64/231 (27%), Positives = 115/231 (49%), Gaps = 13/231 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +++T++LRLVV IA  Y+   L   ++V EG IGL + ++KFDP RG++L+TY+ WW
Sbjct: 81  AKQKMITANLRLVVSIAKKYQRRNLEFLDLVQEGAIGLQRGIEKFDPNRGYKLSTYAYWW 140

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           +  A+   I      V++    N+K     L ++K   +       +   V  IA+KL +
Sbjct: 141 VTQAITRAIAEKSRTVRLPIHVNEK-----LNQIKKVQREFFQTLGRRATVAEIAQKLEL 195

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
             S++       +G  SL+  I   D   ++  + L  +    ++ +  +  R++  ++L
Sbjct: 196 EPSQIREYLKVASGTISLDLKIG--DNKETELSELLASEGVSPDENITHEMLRQDLSDLL 253

Query: 229 TRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAF 277
               + L P +R +   R   L     +L  +  +  +SRERVRQI+ +A 
Sbjct: 254 ----ASLKPMQREVLILRFGLLDNQEQSLAQIGEKLNLSRERVRQIQQKAM 300


>gi|291302005|ref|YP_003513283.1| RpoD subfamily RNA polymerase sigma-70 subunit [Stackebrandtia
           nassauensis DSM 44728]
 gi|290571225|gb|ADD44190.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Stackebrandtia
           nassauensis DSM 44728]
          Length = 323

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 69/233 (29%), Positives = 117/233 (50%), Gaps = 14/233 (6%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV IA  Y G G+ + +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 90  LLKANLRLVVSIAKRYVGRGVALLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQA 149

Query: 113 MQEYILRSWSLVKIGT-TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           +   +      +++   TA Q      +RR    L A      + E+   IA+++ +   
Sbjct: 150 ITRAMADQARTIRVPAHTAEQINRIAKIRR---ELTAEQGREPRHEE---IAERMGLEPY 203

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
            V+ +        SL+  +  SD   +   D +    D   +           R  L R+
Sbjct: 204 RVLELLSYDRDPISLDQPV--SDDRQTPLSDLVARPVDPAAE---PNPANAQLRQELERA 258

Query: 232 MSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           ++ L  RER +  AR   ++    TLE +  E  +SRERVRQ+E  +  K++E
Sbjct: 259 LTDLPARERAVLRARFGIDDGRQRTLEEVGEELGLSRERVRQLEKLSLNKLRE 311


>gi|148272828|ref|YP_001222389.1| RNA polymerase sigma factor [Clavibacter michiganensis subsp.
           michiganensis NCPPB 382]
 gi|147830758|emb|CAN01698.1| RNA polymerase principal sigma factor [Clavibacter michiganensis
           subsp. michiganensis NCPPB 382]
          Length = 492

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 68/252 (26%), Positives = 121/252 (48%), Gaps = 34/252 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WW
Sbjct: 255 AKSHLLGANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWW 314

Query: 109 IKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   +      ++I              Q+++  +L R     +   + ++ PE+V
Sbjct: 315 IRQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEELSRELDMTPEKV 374

Query: 160 VAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           + + K       E IS++  L   GD     LI  ++          V   D     +++
Sbjct: 375 IEVQKYGR----EPISLHTPLGEDGDSEFGDLIEDTEA---------VVPADAVGFTMLQ 421

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEAR 275
           K+        L   +  L+ RE  +   R  L +  P TL+ +   F V+RER+RQIE++
Sbjct: 422 KQ--------LESLLDSLSEREAGVIRMRFGLGDGMPKTLDQIGDTFGVTRERIRQIESK 473

Query: 276 AFKKVQESIQKQ 287
              K++   + Q
Sbjct: 474 TMAKLRHPSRSQ 485


>gi|284991968|ref|YP_003410522.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geodermatophilus
           obscurus DSM 43160]
 gi|284065213|gb|ADB76151.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geodermatophilus
           obscurus DSM 43160]
          Length = 327

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 74/269 (27%), Positives = 133/269 (49%), Gaps = 34/269 (12%)

Query: 28  MLEKQEEYVLAKRYRE-HGDLSAAHR-LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           + E+Q    L + Y+    D  AA R L+ ++LRLVV +A  Y G+G+   +++ EGN+G
Sbjct: 67  LTERQLTPALQRDYKALAADGKAAKRHLLEANLRLVVSVAKRYTGHGMTFLDLIQEGNVG 126

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI---------GTTANQKRLF 136
           L++AV+KFD  +GF+ +TY+ WWI+ A+   +  S   +++              ++R+ 
Sbjct: 127 LIRAVEKFDYTKGFKFSTYATWWIRQAITRAMADSGRTIRLPVHLAEQVNKVVRTRRRIH 186

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
             L R     +   + ++ PE++  +   L  S  +++S++  +  DE            
Sbjct: 187 QELEREPTAEELGLELDMTPERITEL---LEYSR-DLVSLDQTVGADE------------ 230

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLNPRERRIFEARRLQEN--PV 253
            S+  D++        +  +  +  K + RN+L    S L  RER +   R   +   P 
Sbjct: 231 ESRLGDFIEDADAAVAEDAVAFQMMKGDVRNVL----STLEERERDVVVLRFGLDGGQPR 286

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQE 282
           TLE +  +F +SRERVRQIE     K+++
Sbjct: 287 TLEQIGKQFGLSRERVRQIERETMAKLRD 315


>gi|159026170|emb|CAO88820.1| unnamed protein product [Microcystis aeruginosa PCC 7806]
          Length = 318

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 64/252 (25%), Positives = 121/252 (48%), Gaps = 38/252 (15%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A  ++V ++LRLVV +A  Y    L + +++ EG IG+ + V+KFDP +G+R +TY
Sbjct: 80  GDF-AKRKMVEANLRLVVSVAKKYLKRNLDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTY 138

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + WWI+ A+   I      +++     +K     L ++K   + +  +  +   +  +A+
Sbjct: 139 AYWWIRQAITRAIAEKSRTIRLPIHITEK-----LNKIKKAQRQLAQDKGRAATIAELAE 193

Query: 165 KLNVSESEV----------ISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +L+++  +V          +S++ ++    D  L  L+  +  +         Y      
Sbjct: 194 ELDLTPKQVRDYLERSRQPLSLDLKVGDNQDTELGELLEDTGLSPED------YTAHSSL 247

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVR 270
           QV +EK             M+ L P+++ +   R   +N  P+TL  +     +SRERVR
Sbjct: 248 QVDLEK------------LMADLTPQQKEVICLRFGLDNGQPLTLAKIGVRLNISRERVR 295

Query: 271 QIEARAFKKVQE 282
           QIE  A  K+++
Sbjct: 296 QIEREAIAKLRK 307


>gi|284122199|ref|ZP_06386842.1| RNA polymerase, sigma 70 subunit, RpoD family [Candidatus
           Poribacteria sp. WGA-A3]
 gi|283829365|gb|EFC33758.1| RNA polymerase, sigma 70 subunit, RpoD family [Candidatus
           Poribacteria sp. WGA-A3]
          Length = 414

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 77/249 (30%), Positives = 115/249 (46%), Gaps = 39/249 (15%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  +LRLVV IA  + G G+   +++ EGNIGLM+A ++F   +GF+ +TY+ WW++  
Sbjct: 183 LVQHNLRLVVDIAKRFTGRGMGFLDLIQEGNIGLMRAAERFQYRKGFKFSTYATWWVRQG 242

Query: 113 MQEYILRSWS------LVKIGTTANQKRLFFNLRRLKGHLQAITDNN-------LKPEQV 159
               ILR+ +       V + TT   +R+     RL   L     N        +KPE+V
Sbjct: 243 ----ILRAVADQSRTIRVPVHTTEAWQRMIKISHRLAQKLGREPSNEEIALALAVKPERV 298

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
               +       E IS +   A  E+                D L  DH       +++E
Sbjct: 299 QHTTQAF----LEPISFDQPNADGETF-------------LGDCLPDDHASPPDEHLQEE 341

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
           +    R+ L R + VL PRE ++   R    N    TLE +     V+RER+RQIE  A 
Sbjct: 342 Q---MRSQLHRLLRVLTPREEQVIRLRFGIGNGQSRTLEEVGKLLNVTRERIRQIEVLAM 398

Query: 278 KKVQESIQK 286
           KK++E   K
Sbjct: 399 KKLREPTVK 407


>gi|271963319|ref|YP_003337515.1| RNA polymerase sigma factor RpoD [Streptosporangium roseum DSM
           43021]
 gi|270506494|gb|ACZ84772.1| RNA polymerase sigma factor RpoD [Streptosporangium roseum DSM
           43021]
          Length = 312

 Score = 86.7 bits (213), Expect = 4e-15,   Method: Compositional matrix adjust.
 Identities = 81/303 (26%), Positives = 135/303 (44%), Gaps = 53/303 (17%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYRE--------HGDLS------------------- 48
           L  Y+ EI ++P+L  +EE  LAKR            G L+                   
Sbjct: 20  LGTYLAEIGRVPLLTAEEEVELAKRIEAGLFAEQLLDGGLAEPRIADAADEELERLAVSG 79

Query: 49  --AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A    + ++LRLVV +A  Y G G+P+ ++V EGN+GL++AV+KFD  RG++ +TY+ 
Sbjct: 80  QRAKDEFIQANLRLVVAVARKYSGRGMPLIDLVQEGNLGLVRAVEKFDYRRGYKFSTYAT 139

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRL-FFNLRR--LKGHLQAITDNNLKP--EQVVA 161
           WWI+ ++   I      V++ T A ++      +RR  L    Q  TD +L    E  + 
Sbjct: 140 WWIRQSVGRAIHEQARPVRLPTHAGEQMTRLMRVRRDMLAEFDQEPTDADLAAVLELPIE 199

Query: 162 IAKKLNVSESEVISMNCRLAGDES---LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
             ++L    S+ +S+   + GDE    L  +I        + Q   + + +  EQ L   
Sbjct: 200 RVRELRRWASDPVSLQLGV-GDEDETELGDMIADETWADPEQQAMDILERERLEQWLTGL 258

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           E     R ML     +++ RE              TL  +   + + R+R R+IE  A  
Sbjct: 259 E--GQTREMLRWRYGLMDGREH-------------TLTEVGERYGIGRDRARRIERDALA 303

Query: 279 KVQ 281
           +++
Sbjct: 304 RLR 306


>gi|297625160|ref|YP_003706594.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Truepera
           radiovictrix DSM 17093]
 gi|297166340|gb|ADI16051.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Truepera
           radiovictrix DSM 17093]
          Length = 446

 Score = 86.3 bits (212), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 79/300 (26%), Positives = 138/300 (46%), Gaps = 51/300 (17%)

Query: 18  RYIHEIRKIPMLEKQEEYVLA----------------------------KRYREHGDLSA 49
           +Y+HEI ++ +L  +EE  LA                            KR  E G+++ 
Sbjct: 148 QYLHEIGRVSLLTLEEEISLARRIEEGEAAQKRLDEEGDSLPEREQRALKRIVEDGEMAR 207

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            H L+ ++LRLVV IA  Y G GL   +++ EGN GL++AV+KF+  R ++ +TY+ WWI
Sbjct: 208 QH-LIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYRRRYKFSTYATWWI 266

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-AIAKKLNV 168
           + A+   I      ++I    +       L R    LQ         E+V  A+    + 
Sbjct: 267 RQAINRAIADQARTIRI--PVHMVETINKLTRTARQLQQELSREPSYEEVAEAMGPGWSA 324

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH-----DGQEQVLIEKEERKN 223
            + E +    +    E ++      D+  S + D++  D+     D   + L+ +E    
Sbjct: 325 EKVEEVFKVSQ----EPVSLETPIGDEKDSFYGDFIPDDNVESPVDQASKTLLSEE---- 376

Query: 224 RRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
               L +++  L  RE  + + R+  +     TLE + + F V+RER+RQIE +A +K++
Sbjct: 377 ----LEKALDKLTERESMVLKFRKGLVDGREHTLEEVGAHFGVTRERIRQIENKALRKLK 432


>gi|300871651|ref|YP_003786524.1| RNA polymerase sigma-70 factor RpoD [Brachyspira pilosicoli
           95/1000]
 gi|300689352|gb|ADK32023.1| RNA polymerase sigma factor rpoD (Sigma-70) [Brachyspira pilosicoli
           95/1000]
          Length = 568

 Score = 86.3 bits (212), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 71/250 (28%), Positives = 130/250 (52%), Gaps = 30/250 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   ++V EGNIGL++AV KF+ ++G++ +TY+ WW
Sbjct: 330 AKDHIVKANLRLVISIAKKYTNRGLHFFDLVQEGNIGLIKAVDKFEYKKGYKFSTYATWW 389

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      +++        +   + ++   L+       +   +  IA+ L+ 
Sbjct: 390 IRQAITRSISDQARTIRVPV-----HMIEQINKVTRVLRQYMQQYGREPSIQEIARALSW 444

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            ES V S+        SLNA I          +D ++    G+   LIE +E ++ +N+ 
Sbjct: 445 PESRVKSVRNVAKDPVSLNAPIGDE-------EDTIL----GE---LIEDKEFESPQNIT 490

Query: 229 TRSM------SVLN---PRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAF 277
           T  +      S+L+    RE+++   R   ++    TLE +   F+V+RER+RQIEA+A 
Sbjct: 491 TFKILRKHIDSLLDNLPEREQKVIRMRYGLDDGYNHTLEEVGYVFKVTRERIRQIEAKAI 550

Query: 278 KKVQESIQKQ 287
           ++++ + +K+
Sbjct: 551 RRLRATSKKK 560


>gi|270283843|ref|ZP_05965086.2| RNA polymerase principal sigma factor; sigma 70 [Bifidobacterium
           gallicum DSM 20093]
 gi|270277549|gb|EFA23403.1| RNA polymerase principal sigma factor; sigma 70 [Bifidobacterium
           gallicum DSM 20093]
          Length = 485

 Score = 86.3 bits (212), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 65/253 (25%), Positives = 124/253 (49%), Gaps = 34/253 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ WW
Sbjct: 247 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 306

Query: 109 IKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   +      +++           +  Q+++  +L R     +   + ++  E+V
Sbjct: 307 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 366

Query: 160 VAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
             + K       E IS++  L   GD     LI  +D          +   D     L++
Sbjct: 367 QEVQK----YGREPISLHTPLGEDGDPEFGDLIEDTDA---------IAPSDAVAFSLLQ 413

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
           ++          + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++
Sbjct: 414 EQ--------FKQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESK 465

Query: 276 AFKKVQESIQKQV 288
              K++   + Q 
Sbjct: 466 TMSKLRHPSRSQT 478


>gi|119026029|ref|YP_909874.1| RNA polymerase sigma factor [Bifidobacterium adolescentis ATCC
           15703]
 gi|118765613|dbj|BAF39792.1| RNA polymerase principal sigma factor; sigma 70 [Bifidobacterium
           adolescentis ATCC 15703]
          Length = 479

 Score = 86.3 bits (212), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 65/253 (25%), Positives = 124/253 (49%), Gaps = 34/253 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ WW
Sbjct: 241 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 300

Query: 109 IKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   +      +++           +  Q+++  +L R     +   + ++  E+V
Sbjct: 301 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 360

Query: 160 VAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
             + K       E IS++  L   GD     LI  +D          +   D     L++
Sbjct: 361 QEVQK----YGREPISLHTPLGEDGDSEFGDLIEDTD---------AIAPSDAVAFSLLQ 407

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
           ++          + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++
Sbjct: 408 EQ--------FKQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESK 459

Query: 276 AFKKVQESIQKQV 288
              K++   + Q 
Sbjct: 460 TMSKLRHPSRSQT 472


>gi|313837136|gb|EFS74850.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL037PA2]
 gi|314927842|gb|EFS91673.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL044PA1]
 gi|314971907|gb|EFT16005.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL037PA3]
          Length = 370

 Score = 86.3 bits (212), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 77/314 (24%), Positives = 143/314 (45%), Gaps = 43/314 (13%)

Query: 7   SIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYR---------------------- 42
           +++V G     +  Y+ +I K+ +L   EE  LAKR                        
Sbjct: 62  TVMVAGATADPVKDYLKQIGKVALLNAVEEVDLAKRIEAGLFAGEQLADPDAKIPEKDRE 121

Query: 43  ------EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                 E G ++  H L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  
Sbjct: 122 DYEWIAEDGKVAKNH-LLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYT 180

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +G++ +TY+ WWIK A+   +      ++I    +   +   L R++  +         P
Sbjct: 181 KGYKFSTYATWWIKQAITRAMADQARTIRI--PVHMVEVINKLARVQRQMLQDLGREPTP 238

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           E+   +A +L+++  +VI +     G E ++      +   S++ D +    D +  V  
Sbjct: 239 EE---LANELDMTAEKVIEVQKY--GREPISLHTPLGEDGDSEFGDLI---EDSEAIVPA 290

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEA 274
           +       +  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE+
Sbjct: 291 DAVNFTLLQEQLHDVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIES 350

Query: 275 RAFKKVQESIQKQV 288
           +   K++   + QV
Sbjct: 351 KTMSKLRHPSRSQV 364


>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 = 86.3 bits (212), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 68/243 (27%), Positives = 113/243 (46%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 360 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 419

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         P+++         
Sbjct: 420 IRQAITRSIADQARTIRI--PVHMIETINKLNRVSRQMLQEMGREPTPDELAERVEMPKD 477

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + K L ++  E ISM   +  DE  +      D       D  ++    +   LI    
Sbjct: 478 KVRKVLKIA-REPISMETPIGDDEDSHLGDFVEDAAVISPPDSAIFSGLRETTQLI---- 532

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
                      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 533 -----------LAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 581

Query: 279 KVQ 281
           K++
Sbjct: 582 KLR 584


>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 = 86.3 bits (212), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 64/235 (27%), Positives = 117/235 (49%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 367 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 426

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   + +++++
Sbjct: 427 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEE---LGERMDM 481

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E +V  +  ++A  E ++      D   S   D++    D      ++    +  +   
Sbjct: 482 PEDKVRKV-LKIA-KEPISMETPIGDDEDSHLGDFI---EDSTISSPVDSATGQGLQEAT 536

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 537 KDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 591


>gi|212715646|ref|ZP_03323774.1| hypothetical protein BIFCAT_00546 [Bifidobacterium catenulatum DSM
           16992]
 gi|212661013|gb|EEB21588.1| hypothetical protein BIFCAT_00546 [Bifidobacterium catenulatum DSM
           16992]
          Length = 448

 Score = 86.3 bits (212), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 66/253 (26%), Positives = 125/253 (49%), Gaps = 34/253 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ WW
Sbjct: 210 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 269

Query: 109 IKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   +      +++           +  Q+++  +L R     +   + ++  E+V
Sbjct: 270 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 329

Query: 160 VAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
             + K       E IS++  L   GD     LI  +D          +   D     L++
Sbjct: 330 QEVQK----YGREPISLHTPLGEDGDSEFGDLIEDTD---------AIAPSDAVAFSLLQ 376

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
           ++ R+         +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++
Sbjct: 377 EQFRQ--------VLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESK 428

Query: 276 AFKKVQESIQKQV 288
              K++   + Q 
Sbjct: 429 TMSKLRHPSRSQT 441


>gi|307150096|ref|YP_003885480.1| RpoD subfamily RNA polymerase sigma-70 factor [Cyanothece sp. PCC
           7822]
 gi|306980324|gb|ADN12205.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7822]
          Length = 298

 Score = 86.3 bits (212), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 77/289 (26%), Positives = 141/289 (48%), Gaps = 38/289 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYRE--------HGDLSAA------------HRLVTSHL 58
           Y+ EI +IP+L  +EE  LA + ++          +L+AA             +++ ++L
Sbjct: 12  YLQEIGRIPLLNSEEEIQLATKVQKMLSLLELKKDNLAAAEQKIIEQGQRAKQQMIQANL 71

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV IA  Y+  GL + +++ EG++GL++AV+KFDP +G++ +TY+ WW++ A+   + 
Sbjct: 72  RLVVSIAKRYQRRGLSLLDLIQEGSLGLIRAVEKFDPSKGYKFSTYAYWWVRQAITRALA 131

Query: 119 RSWSLVK--IGTTANQKRLFFNLRRLKGHLQAITDNNLKP-EQVVAIAKKLNVSESEVIS 175
                ++  I  T N   L  ++R L G L        KP EQ VA   ++ + + + I 
Sbjct: 132 EKSRTIRLPIHMTENLNHLKKSVRELTGEL------GRKPTEQEVAQRMEIPLEKLQEIR 185

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
                   +SLN  +   D N ++  + L  +       + E+E      ++L      L
Sbjct: 186 HAVYRTDAKSLNITL---DDNQTELGEVLPDETSLPIDFVSERELMTKVDDLLED----L 238

Query: 236 NPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            PR+R I   R   L    ++ + +  +  +S ER RQ+  RA + +++
Sbjct: 239 PPRQREIITLRFGLLTGKRMSYKEIGRQCGISHERARQLLNRAMRTLKQ 287


>gi|119489578|ref|ZP_01622338.1| RNA polymerase sigma factor [Lyngbya sp. PCC 8106]
 gi|119454490|gb|EAW35638.1| RNA polymerase sigma factor [Lyngbya sp. PCC 8106]
          Length = 319

 Score = 86.3 bits (212), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 62/240 (25%), Positives = 119/240 (49%), Gaps = 13/240 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  ++V ++LRLVV +A  Y    + + +++ EG IG+ + V+KFDP +G+R +TY+ W
Sbjct: 83  TAKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYW 142

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++     +K     L ++K   +++  +  +   +  +A +L+
Sbjct: 143 WIRQAITRAIAEKGRTIRLPIHITEK-----LNKIKKAQRSLAQDLGRAATIAELADELD 197

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++  ++     R     SL+  +   D   ++  D L  D    E   ++   R +    
Sbjct: 198 LNPKQIREYLERARLPLSLD--LRVGDNQDTELGDLLEDDGASPEDYALQSSMRSD---- 251

Query: 228 LTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L   M+ L  ++R++   R   EN   +TL  +     +SRERVRQIE  A  K+++  Q
Sbjct: 252 LEVLMADLTDQQRQVLALRFGLENGQTMTLAKIGDRLNISRERVRQIEREALTKLRKRKQ 311


>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 = 86.3 bits (212), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 68/243 (27%), Positives = 113/243 (46%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 360 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 419

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         P+++         
Sbjct: 420 IRQAITRSIADQARTIRI--PVHMIETINKLNRVSRQMLQEMGREPTPDELAERVEMPKD 477

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + K L ++  E ISM   +  DE  +      D       D  ++    +   LI    
Sbjct: 478 KVRKVLKIAR-EPISMETPIGDDEDSHLGDFVEDAAVISPPDSAIFSGLRETTQLI---- 532

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
                      ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 533 -----------LAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 581

Query: 279 KVQ 281
           K++
Sbjct: 582 KLR 584


>gi|154488794|ref|ZP_02029643.1| hypothetical protein BIFADO_02101 [Bifidobacterium adolescentis
           L2-32]
 gi|154082931|gb|EDN81976.1| hypothetical protein BIFADO_02101 [Bifidobacterium adolescentis
           L2-32]
          Length = 478

 Score = 86.3 bits (212), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 65/253 (25%), Positives = 124/253 (49%), Gaps = 34/253 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ WW
Sbjct: 240 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 299

Query: 109 IKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   +      +++           +  Q+++  +L R     +   + ++  E+V
Sbjct: 300 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 359

Query: 160 VAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
             + K       E IS++  L   GD     LI  +D          +   D     L++
Sbjct: 360 QEVQK----YGREPISLHTPLGEDGDSEFGDLIEDTD---------AIAPSDAVAFSLLQ 406

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
           ++          + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++
Sbjct: 407 EQ--------FKQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESK 458

Query: 276 AFKKVQESIQKQV 288
              K++   + Q 
Sbjct: 459 TMSKLRHPSRSQT 471


>gi|257055481|ref|YP_003133313.1| RNA polymerase sigma factor, sigma-70 family [Saccharomonospora
           viridis DSM 43017]
 gi|256585353|gb|ACU96486.1| RNA polymerase sigma factor, sigma-70 family [Saccharomonospora
           viridis DSM 43017]
          Length = 315

 Score = 86.3 bits (212), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 79/295 (26%), Positives = 143/295 (48%), Gaps = 41/295 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR------------EHGDLS-----------------A 49
           Y+ E+ + P+L   +E  LAKR              + G+++                 A
Sbjct: 19  YLDEVGETPLLTANQEVELAKRIEAGVYAAELLRRADEGEITLDYDRRDLEIVARDGQRA 78

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              ++ ++LRLVV  A   R   LP+ + + EGN+GL++AV+KFD  +GF+ +TY+MWWI
Sbjct: 79  KDHMIRANLRLVVTAARKNRHTNLPLLDAIQEGNLGLIRAVEKFDYAKGFKFSTYAMWWI 138

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + A+Q       + +++    +++     L RL+  LQ+ +++ L  E++ A A ++ V 
Sbjct: 139 RQAIQRGNAFQSNAIRLPMHVSEQ--VAKLDRLERTLQSRSNHELTVEELAA-AAEMPVE 195

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             E +    R     S  +L  S D++   +   LV   DG    + E  ER+   + + 
Sbjct: 196 RVEALRQAGR-----STVSLDMSLDEDGELYLRDLVA--DGTVPAVGEGIERQAMVDQVR 248

Query: 230 RSMSVLNPRERRIFEAR-RLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            ++  L P E  +   R  L++ +  T+  +S    +SR+RVR +E RA   ++E
Sbjct: 249 ATIDSLPPMEAAVVSLRYGLRDGHQHTIPEISQRLGLSRKRVRTLEQRAMAMLRE 303


>gi|284929771|ref|YP_003422293.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase sigma
           factor, cyanobacterial RpoD-like family [cyanobacterium
           UCYN-A]
 gi|284810215|gb|ADB95912.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase sigma
           factor, cyanobacterial RpoD-like family [cyanobacterium
           UCYN-A]
          Length = 318

 Score = 86.3 bits (212), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 72/304 (23%), Positives = 131/304 (43%), Gaps = 52/304 (17%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDL------------------------------- 47
           Y+ EI ++P+L  +EE + AKR +   DL                               
Sbjct: 14  YLREIGRVPLLTHEEEILYAKRVQRFVDLEKYRELFTKETGKEPTETQWAQAARISRREL 73

Query: 48  --------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                   +A  ++V ++LRLVV +A  Y    L + +++ EG IG+ + V+KFDP +G+
Sbjct: 74  HSAIASGEAAKRKMVEANLRLVVSVAKKYLKRNLDLLDLIQEGTIGMQRGVEKFDPTKGY 133

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           R +TY+ WWI+ A+   I      +++     +K     L ++K   + ++    +   +
Sbjct: 134 RFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEK-----LNKIKKAQRELSQARGRDATI 188

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +A++L+++  +V     R     SL+  +   D   ++  D L  D    E       
Sbjct: 189 AELAEELDLTPKQVREYLERARQPLSLD--LRVGDNQDTELGDLLEDDGPSPEDFATHSS 246

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAF 277
            + +    L   M  L  +++ +   R       P+TL  +     +SRERVRQIE  A 
Sbjct: 247 LQFD----LEILMEDLTTQQKEVIALRFGLTDGQPLTLAKIGCRLNISRERVRQIEREAL 302

Query: 278 KKVQ 281
            K++
Sbjct: 303 SKLR 306


>gi|306822519|ref|ZP_07455897.1| DNA-directed RNA polymerase sigma subunit RpoD [Bifidobacterium
           dentium ATCC 27679]
 gi|304554064|gb|EFM41973.1| DNA-directed RNA polymerase sigma subunit RpoD [Bifidobacterium
           dentium ATCC 27679]
          Length = 472

 Score = 86.3 bits (212), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 65/253 (25%), Positives = 124/253 (49%), Gaps = 34/253 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ WW
Sbjct: 234 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 293

Query: 109 IKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   +      +++           +  Q+++  +L R     +   + ++  E+V
Sbjct: 294 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 353

Query: 160 VAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
             + K       E IS++  L   GD     LI  +D          +   D     L++
Sbjct: 354 QEVQK----YGREPISLHTPLGEDGDSEFGDLIEDTD---------AIAPSDAVAFSLLQ 400

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
           ++          + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++
Sbjct: 401 EQ--------FKQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESK 452

Query: 276 AFKKVQESIQKQV 288
              K++   + Q 
Sbjct: 453 TMSKLRHPSRSQT 465


>gi|119944095|ref|YP_941775.1| RNA polymerase sigma-70 factor RpoD [Psychromonas ingrahamii 37]
 gi|119862699|gb|ABM02176.1| RNA polymerase sigma-70 factor RpoD [Psychromonas ingrahamii 37]
          Length = 617

 Score = 86.3 bits (212), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 70/244 (28%), Positives = 114/244 (46%), Gaps = 32/244 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 379 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 438

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +        +PE+   +A+++ +
Sbjct: 439 IRQAITRSIADQARTIRI--PVHMIETINKLNRVSRQMLQEMGREPQPEE---LAERMMM 493

Query: 169 SESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            E +V          ISM   +  DE             S   D++              
Sbjct: 494 PEDKVRKVLKIAKEPISMETPIGDDE------------DSHLGDFIEDTTIALPANCATS 541

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARA 276
           E  KN  N +   +  L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A
Sbjct: 542 ESLKNATNDV---LEGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKA 598

Query: 277 FKKV 280
            +K+
Sbjct: 599 LRKL 602


>gi|309801431|ref|ZP_07695558.1| RNA polymerase sigma factor RpoD [Bifidobacterium dentium
           JCVIHMP022]
 gi|308221946|gb|EFO78231.1| RNA polymerase sigma factor RpoD [Bifidobacterium dentium
           JCVIHMP022]
          Length = 461

 Score = 86.3 bits (212), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 65/253 (25%), Positives = 124/253 (49%), Gaps = 34/253 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ WW
Sbjct: 223 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 282

Query: 109 IKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   +      +++           +  Q+++  +L R     +   + ++  E+V
Sbjct: 283 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 342

Query: 160 VAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
             + K       E IS++  L   GD     LI  +D          +   D     L++
Sbjct: 343 QEVQK----YGREPISLHTPLGEDGDSEFGDLIEDTD---------AIAPSDAVAFSLLQ 389

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
           ++          + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++
Sbjct: 390 EQ--------FKQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESK 441

Query: 276 AFKKVQESIQKQV 288
              K++   + Q 
Sbjct: 442 TMSKLRHPSRSQT 454


>gi|227547666|ref|ZP_03977715.1| RNA polymerase sigma factor [Bifidobacterium longum subsp. infantis
           ATCC 55813]
 gi|227211921|gb|EEI79817.1| RNA polymerase sigma factor [Bifidobacterium longum subsp. infantis
           ATCC 55813]
          Length = 464

 Score = 86.3 bits (212), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 75/278 (26%), Positives = 137/278 (49%), Gaps = 37/278 (13%)

Query: 28  MLEKQEEYVLAKRYRE------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           +L+ + E +  KR RE       G  +  H L+ ++LRLVV +A  Y G G+   +++ E
Sbjct: 200 LLDTESEGMEFKRKRELKWAAADGKKAKDH-LLEANLRLVVSLAKRYTGRGMLFLDLIQE 258

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           GN+GL++AV+KFD ++GF+ +TY+ WWI+ A+   +      +++    +   +   L R
Sbjct: 259 GNLGLIRAVEKFDWKKGFKFSTYATWWIRQAITRAMADQARTIRV--PVHMVEVINKLSR 316

Query: 142 LKGH-LQAI----TDNNLKPEQVVAIAKKLNVSE--SEVISMNCRLA--GDESLNALINS 192
           ++   LQ +    T + L  E  + + K   V +   E IS++  L   GD     LI  
Sbjct: 317 VQRQMLQDLGREPTPDELARELDMPVEKVQEVQKYGREPISLHTPLGEDGDSEFGDLIED 376

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN- 251
           +D          +   D     L++++          + +  L+PRE  + + R   E+ 
Sbjct: 377 TD---------AIAPSDAVAFSLLQEQ--------FKQVLETLSPREAGVIKMRYGLEDG 419

Query: 252 -PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            P TL+++   + V+RER+RQIE++   K++   + Q 
Sbjct: 420 QPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQT 457


>gi|254413477|ref|ZP_05027247.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
 gi|196179584|gb|EDX74578.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
          Length = 331

 Score = 86.3 bits (212), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 67/246 (27%), Positives = 118/246 (47%), Gaps = 35/246 (14%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  ++V ++LRLVV +A  Y    + + +++ EG IG+ + V+KFDP +G+R +TY+ W
Sbjct: 94  TAKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYW 153

Query: 108 WIKAAMQEYILRSWSLVKIGTTAN---------QKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           WI+ A+   I      +++              Q++L   L R     +  T+ +L P+Q
Sbjct: 154 WIRQAITRAIAEKGRTIRLPIHITEKLNKIKKAQRQLSQTLGRAATISELATELDLTPKQ 213

Query: 159 VVAIAKKLNVSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           V    +K      + +S++ R+    D  L  L+  S  +    +D+  Y      QV +
Sbjct: 214 VREYLEKAR----QPLSLDLRVGDNQDTELGELLEDSGPSP---EDFATYSA---MQVDL 263

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEA 274
           EK             M+ L  ++R +   R   +   P+TL  +  + ++SRERVRQIE 
Sbjct: 264 EK------------LMADLTEQQREVLMLRFGLVDGQPMTLAKIGDQLKISRERVRQIER 311

Query: 275 RAFKKV 280
            A  K+
Sbjct: 312 EALSKL 317


>gi|23465986|ref|NP_696589.1| RNA polymerase sigma factor [Bifidobacterium longum NCC2705]
 gi|46191322|ref|ZP_00206768.1| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Bifidobacterium longum DJO10A]
 gi|189439160|ref|YP_001954241.1| RNA polymerase sigma factor [Bifidobacterium longum DJO10A]
 gi|312132592|ref|YP_003999931.1| rpod [Bifidobacterium longum subsp. longum BBMN68]
 gi|317482450|ref|ZP_07941467.1| RNA polymerase sigma factor RpoD [Bifidobacterium sp. 12_1_47BFAA]
 gi|322689398|ref|YP_004209132.1| RNA polymerase sigma factor RpoD [Bifidobacterium longum subsp.
           infantis 157F]
 gi|322691364|ref|YP_004220934.1| RNA polymerase sigma factor RpoD [Bifidobacterium longum subsp.
           longum JCM 1217]
 gi|23326702|gb|AAN25225.1| RNA polymerase principal sigma factor; sigma 70 [Bifidobacterium
           longum NCC2705]
 gi|189427595|gb|ACD97743.1| DNA-directed RNA polymerase sigma subunit [Bifidobacterium longum
           DJO10A]
 gi|311773536|gb|ADQ03024.1| RpoD [Bifidobacterium longum subsp. longum BBMN68]
 gi|316916110|gb|EFV37515.1| RNA polymerase sigma factor RpoD [Bifidobacterium sp. 12_1_47BFAA]
 gi|320456220|dbj|BAJ66842.1| RNA polymerase sigma factor RpoD [Bifidobacterium longum subsp.
           longum JCM 1217]
 gi|320460734|dbj|BAJ71354.1| RNA polymerase sigma factor RpoD [Bifidobacterium longum subsp.
           infantis 157F]
          Length = 474

 Score = 86.3 bits (212), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 75/278 (26%), Positives = 137/278 (49%), Gaps = 37/278 (13%)

Query: 28  MLEKQEEYVLAKRYRE------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           +L+ + E +  KR RE       G  +  H L+ ++LRLVV +A  Y G G+   +++ E
Sbjct: 210 LLDTESEGMEFKRKRELKWAAADGKKAKDH-LLEANLRLVVSLAKRYTGRGMLFLDLIQE 268

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           GN+GL++AV+KFD ++GF+ +TY+ WWI+ A+   +      +++    +   +   L R
Sbjct: 269 GNLGLIRAVEKFDWKKGFKFSTYATWWIRQAITRAMADQARTIRV--PVHMVEVINKLSR 326

Query: 142 LKGH-LQAI----TDNNLKPEQVVAIAKKLNVSE--SEVISMNCRLA--GDESLNALINS 192
           ++   LQ +    T + L  E  + + K   V +   E IS++  L   GD     LI  
Sbjct: 327 VQRQMLQDLGREPTPDELARELDMPVEKVQEVQKYGREPISLHTPLGEDGDSEFGDLIED 386

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN- 251
           +D          +   D     L++++          + +  L+PRE  + + R   E+ 
Sbjct: 387 TD---------AIAPSDAVAFSLLQEQ--------FKQVLETLSPREAGVIKMRYGLEDG 429

Query: 252 -PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            P TL+++   + V+RER+RQIE++   K++   + Q 
Sbjct: 430 QPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQT 467


>gi|123965877|ref|YP_001010958.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9515]
 gi|123200243|gb|ABM71851.1| Putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus str. MIT 9515]
          Length = 307

 Score = 86.3 bits (212), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 77/296 (26%), Positives = 138/296 (46%), Gaps = 32/296 (10%)

Query: 12  GEIGLSRYIHEIRKIPMLEK-QEEYVLAKRYREHGDLSAA------------------HR 52
           GEIG  + +   +++ M  K QE  VL  R +  G   +A                  + 
Sbjct: 9   GEIGRHQLLTPEKELTMGRKVQEMVVLINRCQTAGGKGSACEYSEVEKKKIKIGEKAKNA 68

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG R +TY+ WWI+  
Sbjct: 69  MITANLRLVVNLAKRYQGKGLELLDLIQEGTLGLTRAVEKYDPSRGHRFSTYAYWWIRQG 128

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +      ++I    N+K     LR  K  L  +      P     +A+++ +++ E
Sbjct: 129 LNRALSTQSRTIRIPVNINEK--LTKLRAAKSKLMQLKGF---PPTSFELAEEMKITKEE 183

Query: 173 VIS-MNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           +   ++C L     SL   + S   + S+  D L  D     ++    E   +   +L +
Sbjct: 184 IDELLSCELRSITVSLQGTVKSKS-DPSELVDILPSDQTPPMELAELAERTASAWTLLDK 242

Query: 231 SMSVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +   L  +ER+I   R   +      TL  ++     SRE  RQ+  RA +K++++
Sbjct: 243 AN--LTEKERKIVSLRFGLDGSNEWKTLAEVARHMSCSREYCRQVVQRALRKLRKA 296


>gi|23428541|gb|AAL11450.1| RNA polymerase sigma-70 subunit [Serratia plymuthica]
          Length = 612

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 71/251 (28%), Positives = 126/251 (50%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ +GNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 374 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIRKGNIGLMKAVDKFEYRRGYKFSTYATWW 433

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-----KRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N+     +++   + R +   + + +  L PE  
Sbjct: 434 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGR-EPTPEELAERMLMPED- 491

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I K L +++ E ISM   +  DE             S   D++    D   ++ ++  
Sbjct: 492 -KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI---EDTTLELPLDSA 534

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAF 277
             ++ R+     ++ L  RE ++   R  +  N   TLE +  +F+V RER+RQIEA+A 
Sbjct: 535 TSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVIRERIRQIEAKAL 594

Query: 278 KKVQESIQKQV 288
           +K++   + +V
Sbjct: 595 RKLRHPSRSEV 605


>gi|283780465|ref|YP_003371220.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pirellula staleyi
           DSM 6068]
 gi|283438918|gb|ADB17360.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pirellula staleyi
           DSM 6068]
          Length = 544

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 76/252 (30%), Positives = 119/252 (47%), Gaps = 14/252 (5%)

Query: 42  REHGDLSAAHR-LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           R++ +  AA R L + +LRLVV IA  YR  GL   +++ EGN GLM+AV K++  RGF+
Sbjct: 295 RQYIEYEAAKRQLSSGNLRLVVSIAKKYRNRGLSFLDLIQEGNTGLMRAVDKYEYRRGFK 354

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I    +   +   LR ++  L          E+V 
Sbjct: 355 FSTYATWWIRQAITRAIADQARTIRI--PVHMIDVLSKLRNVQKKLLQELGREPTTEEVT 412

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
           A+          V+ +     G   ++      D   S + ++ + D      VL     
Sbjct: 413 ALVDLPLEEVKRVLDI-----GRHPVSLDRPVGDSEDSSFGEF-IEDTASDNPVLCATN- 465

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFK 278
               R  +   +  L  RER I   R         TLE +   F+V+RERVRQIEA+A +
Sbjct: 466 -GILRERIDGLLKTLTWREREIIRLRYGLCDGYTYTLEEVGRIFKVTRERVRQIEAKAVR 524

Query: 279 KVQESIQ-KQVE 289
           K+Q  ++ KQ+E
Sbjct: 525 KLQHPVRSKQLE 536


>gi|332994458|gb|AEF04513.1| RNA polymerase sigma factor [Alteromonas sp. SN2]
          Length = 608

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 72/245 (29%), Positives = 122/245 (49%), Gaps = 34/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 370 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 429

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-KRLFFNLRRLKGH---LQAITDNNLKPEQVV 160
           I+ A+   I      ++I      T N+  R+   + +  G     + +++  L PE   
Sbjct: 430 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELSERMLMPED-- 487

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++      ++  +I+  +
Sbjct: 488 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI------EDSTIIQPLD 528

Query: 221 RKNRRNMLTRSMSV---LNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEAR 275
                ++   +  V   L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+
Sbjct: 529 SATGGSLKDATQEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 588

Query: 276 AFKKV 280
           A +K+
Sbjct: 589 ALRKL 593


>gi|331696792|ref|YP_004333031.1| RpoD subfamily RNA polymerase sigma-70 subunit [Pseudonocardia
           dioxanivorans CB1190]
 gi|326951481|gb|AEA25178.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pseudonocardia
           dioxanivorans CB1190]
          Length = 348

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 75/257 (29%), Positives = 118/257 (45%), Gaps = 56/257 (21%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A + L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++AV+KFD  +GF+ +TY+ WW
Sbjct: 111 ARNHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAVEKFDYAKGFKFSTYATWW 170

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   +            A+Q R      RL  HL          EQV  +A+    
Sbjct: 171 IRQAITRGM------------ADQARTI----RLPVHLV---------EQVNKLARIKR- 204

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD--------GQEQ-----VL 215
                  M+ RL  + +   L   S     +  D L +  D        G E+       
Sbjct: 205 ------DMHQRLGREATHAELAEESGLPEEKIADLLDHARDPVSLDMPVGSEEEAPLGDF 258

Query: 216 IEKEERKNRRNM---------LTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEV 264
           IE  E  +  N          L R ++ L+ RE+ +   R   ++  P TL+ +   F +
Sbjct: 259 IEDAEAADAENTVISHLLHDDLRRVLATLDEREQNVIRMRYGLDDGQPCTLDQIGRRFGL 318

Query: 265 SRERVRQIEARAFKKVQ 281
           SRERVRQIE     K++
Sbjct: 319 SRERVRQIEREVMAKLR 335


>gi|260424772|ref|ZP_05733235.2| RNA polymerase sigma-43 factor [Dialister invisus DSM 15470]
 gi|260403136|gb|EEW96683.1| RNA polymerase sigma-43 factor [Dialister invisus DSM 15470]
          Length = 394

 Score = 86.3 bits (212), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 70/270 (25%), Positives = 124/270 (45%), Gaps = 25/270 (9%)

Query: 19  YIHEIRKIPMLEKQEEYVLAK-----RYREHGD------LSAAHRLVTSHLRLVVKIAMG 67
           Y+ E    P+L  ++E  LA+     +  E  D        A   +  ++LRLVV IA  
Sbjct: 120 YLRECGTTPLLTSEQEMKLAQTIEIGKMPEATDEQKRMAAEAKKEMANANLRLVVSIAKK 179

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y G G+P  +++ EGN+GL++AV KFD  +G++ +TY+ WWI+ A+   I      +++ 
Sbjct: 180 YPGRGMPFLDLIQEGNMGLLKAVDKFDYTKGYKFSTYATWWIRQAITRSIADQARTIRV- 238

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              +       + R+  H           E+   +AK++  S  ++     + A  + ++
Sbjct: 239 -PVHMVETINKMNRVGRHFLQEHGREATNEE---LAKEMETSVEKI--REAKKAAQDPIS 292

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFEAR 246
                 +K  S   D++    + Q+    E E     RR  + + +  L  RE+ +   R
Sbjct: 293 LETPIGEKEDSHLGDFI----EDQKTASPEDEAAATMRREQIHQLLETLTEREKGVIALR 348

Query: 247 RLQENPV--TLENLSSEFEVSRERVRQIEA 274
              ++    TLE +   F V+RER+RQIE 
Sbjct: 349 YGIDDGTQRTLEEVGKYFGVTRERIRQIEG 378


>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 = 85.9 bits (211), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 67/239 (28%), Positives = 115/239 (48%), Gaps = 20/239 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 368 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 427

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   + +++ +
Sbjct: 428 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEE---LGERMEM 482

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E +V  +  ++A  E ++      D   S   D++       E V I           L
Sbjct: 483 PEDKVRKV-LKIA-KEPISMETPIGDDEDSHLGDFI-------EDVTISSPVDSATEEGL 533

Query: 229 TRS----MSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           T +    ++ L  RE ++   R         TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 534 TEATQDVLAGLTAREAKVLRMRFGIGMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 592


>gi|261415258|ref|YP_003248941.1| RNA polymerase, sigma 32 subunit, RpoH [Fibrobacter succinogenes
           subsp. succinogenes S85]
 gi|261371714|gb|ACX74459.1| RNA polymerase, sigma 32 subunit, RpoH [Fibrobacter succinogenes
           subsp. succinogenes S85]
 gi|302327293|gb|ADL26494.1| RNA polymerase sigma-70 factor [Fibrobacter succinogenes subsp.
           succinogenes S85]
          Length = 283

 Score = 85.9 bits (211), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 73/276 (26%), Positives = 140/276 (50%), Gaps = 27/276 (9%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +Y+++I + P+L +++E +L ++  E G+ +A   LV S+LR VV IA  Y+G GL I E
Sbjct: 15  QYLNDISRYPLLTREQETILLQKSAE-GNKAALDMLVNSNLRFVVNIANLYKGRGLDIME 73

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +++EGN+GL++A ++FD     +  +Y++WWI+  +   I     +++I     +K L  
Sbjct: 74  LINEGNMGLIEAARRFDRSLKIKFISYAVWWIRQNITRAISEKGRMIRISA---EKELM- 129

Query: 138 NLRRLKGHL----QAITDNNLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLN---- 187
            LRR   H     Q I        Q +    K   SE E I M  N   + D  +N    
Sbjct: 130 -LRRFNRHAKDVQQVIGGTFTINTQSLEGLSKYKASEIEKILMMGNSTSSLDAPVNEDGD 188

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           A +  +  +S    D L  D++ + +V            +L +++S       +++   +
Sbjct: 189 ATLGDTISDSQSRTDELA-DNNNRAEVF---------DKVLDKNLSNQEKEIIKLYYGFK 238

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           + ++ + L+ ++    +S+ERVRQ++  A  K++++
Sbjct: 239 M-DSDLNLKEIAPMVGLSKERVRQLKENALNKLRDA 273


>gi|75812337|ref|YP_319956.1| sigma-28 [Anabaena variabilis ATCC 29413]
 gi|75705093|gb|ABA24767.1| Sigma-28 [Anabaena variabilis ATCC 29413]
          Length = 316

 Score = 85.9 bits (211), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 65/231 (28%), Positives = 112/231 (48%), Gaps = 13/231 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +++T++LRLVV IA  Y+   L   ++V EG IGL + ++KFDP RG++L+TY+ WW
Sbjct: 81  AKQKMITANLRLVVSIAKKYQRRNLEFLDLVQEGAIGLQRGIEKFDPNRGYKLSTYAYWW 140

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           +  A+   I      V++    N+K     L ++K   +       +   V  IA+KL +
Sbjct: 141 VTQAITRAIAEKSRTVRLPIHVNEK-----LNQIKKVQREFFQTLGRRPSVAEIAQKLEL 195

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
             S++       +G  SL+  +   D   ++  + L  +         E    +  R  L
Sbjct: 196 EPSQIREYLKVASGTISLD--LKVGDNQETELSELLASEGVSPN----ENTTHEMLRQDL 249

Query: 229 TRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAF 277
           +  ++ L P +R +   R   L     +L  +S +  +SRERVRQI+ +A 
Sbjct: 250 SDLLASLKPMQREVLILRFGLLDNQEQSLAQISEKLNLSRERVRQIQQKAM 300


>gi|271965471|ref|YP_003339667.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)-like
           protein [Streptosporangium roseum DSM 43021]
 gi|270508646|gb|ACZ86924.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)-like
           protein [Streptosporangium roseum DSM 43021]
          Length = 452

 Score = 85.9 bits (211), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 72/252 (28%), Positives = 126/252 (50%), Gaps = 19/252 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLVV +A  Y   G+ + +VV EGN+GL++AV+KFD  +G++ +TY+MWW
Sbjct: 215 AKDHMLEANLRLVVSVAKKYTDRGMALLDVVQEGNLGLIRAVEKFDYTKGYKFSTYAMWW 274

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+Q     S   +++    +   +   L R++  +         PE+   +A +L+ 
Sbjct: 275 IRQAIQRGFADSARTIRL--PVHVLEMLSKLSRVERDMHQRLGREPTPEE---LAVELDK 329

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +  ++  +        SLNA I   +   +   D L+ D D  E    E  +R+     L
Sbjct: 330 TPDQIEELLRTSRQPISLNATIG--EDGETTIGD-LIEDVDSPEAS--EVVDRQLLGEQL 384

Query: 229 TRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +  L+PRE +I   R   +   P TL+ +     ++RER+RQ+E       +ES+ K
Sbjct: 385 RGVLGNLSPREAKIMALRFGLVDGKPHTLDEIGKHLGLTRERIRQLE-------KESLSK 437

Query: 287 QVELSSSPPLLQ 298
               S++ PLL 
Sbjct: 438 LRHPSNTRPLLD 449


>gi|67922139|ref|ZP_00515654.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
 gi|67856039|gb|EAM51283.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
          Length = 318

 Score = 85.9 bits (211), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 74/307 (24%), Positives = 139/307 (45%), Gaps = 60/307 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR------------------------------------ 42
           Y+ EI ++P+L  +EE + AKR +                                    
Sbjct: 14  YLKEIGRVPLLSHEEEILYAKRVQRLINLEKLREEIIQETGKEPTNSQWAKAAKLSRKEF 73

Query: 43  ----EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
               E G+ +A  ++V ++LRLVV +A  Y    L + +++ EG IG+ + V+KFDP +G
Sbjct: 74  CSVVEAGE-AAKRKMVEANLRLVVSVAKKYLKRNLDLLDLIQEGTIGMQRGVEKFDPTKG 132

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           +R +TY+ WWI+ A+   I      +++     +K     L ++K   + ++    +   
Sbjct: 133 YRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEK-----LNKIKKAQRELSQQKGRAAT 187

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           +  +A++L+++  +V     R     SL+  +   D   ++  D L  + +GQ       
Sbjct: 188 ISELAEELDLTPKQVRDYLERSRQPLSLD--LRVGDNQDTELGDLL--EDEGQ-----SP 238

Query: 219 EERKNRRNM---LTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIE 273
           E+     ++   L + M  L  +++++   R   +   P+TL  + S   +SRERVRQIE
Sbjct: 239 EDFATHSSLQFDLEKLMEDLTIQQKQVIALRFGLMDGQPLTLAKIGSRLNISRERVRQIE 298

Query: 274 ARAFKKV 280
             A  K+
Sbjct: 299 REALSKL 305


>gi|19910026|dbj|BAB87264.1| RNA polymerase sigma factor [Cyanophora paradoxa]
          Length = 427

 Score = 85.9 bits (211), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 69/246 (28%), Positives = 129/246 (52%), Gaps = 15/246 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRG-YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A  RLV S+LR VV IA  Y   + +P+ +++ EG+IGLM+A ++FD ++GF+  TY+ W
Sbjct: 178 ARARLVQSNLRWVVSIAKKYANKHTMPLQDLIQEGSIGLMKAAERFDLDKGFKFLTYATW 237

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   +      +++    +     + +++ +  L +       PE+   +A +LN
Sbjct: 238 WIRQAIFRSLQDQGRTIRLPVHVHDS--LYLIKKTRQQLASRLGRIPTPEE---LADELN 292

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR--- 224
           +  S +  +    +   SL + I SS+ +S++ ++ L    D  E   ++ +E+  R   
Sbjct: 293 IPVSRLAFITQAASLPISLESPI-SSETSSTKARNNL---GDFIESECLQPDEQLERTML 348

Query: 225 RNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           R  L   ++ L  RER I   R   +  +P TL+ +     ++RER+RQIE  A +K++ 
Sbjct: 349 REDLENVLATLKARERDIIRMRYGLVDGSPKTLDEIGEIVGLTRERIRQIEQSAMRKLKA 408

Query: 283 SIQKQV 288
             +K +
Sbjct: 409 PYRKAI 414


>gi|189485247|ref|YP_001956188.1| RNA polymerase sigma factor [uncultured Termite group 1 bacterium
           phylotype Rs-D17]
 gi|170287206|dbj|BAG13727.1| RNA polymerase sigma factor [uncultured Termite group 1 bacterium
           phylotype Rs-D17]
          Length = 573

 Score = 85.9 bits (211), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 69/242 (28%), Positives = 127/242 (52%), Gaps = 31/242 (12%)

Query: 52  RLVTSHLRLVVKIAMGYRGYG-LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           +L+ ++ RLVV IA  + G   L +S+++ EGN+GL +AV+KF+ +RGF+ +TY+ WWI+
Sbjct: 338 KLIEANFRLVVSIAKKHVGISNLELSDLIQEGNLGLSKAVEKFEWKRGFKFSTYATWWIR 397

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            ++   I      ++I    + K L   L + K   Q     N+  E  +          
Sbjct: 398 QSINRAIADQARTIRI--PVHMKELISKLTKSKKECQ----QNMGREPTIQ-------EY 444

Query: 171 SEVISMNC----RLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           S+++ ++C    R+     E ++  +   ++  S+ +D+ + D +    V+  K ++   
Sbjct: 445 SKILKLSCDRIRRILKMMQEPVSLAMPVGEEEDSRLEDF-IEDQNSPNPVV--KTQQYRL 501

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQEN-----PVTLENLSSEFEVSRERVRQIEARAFKK 279
           +  L + ++ L PRE  I    RL+       P TLE +  +F ++RERVRQIEA+A +K
Sbjct: 502 QLELEKVLATLAPREAEII---RLRYGIGIGYPSTLEEVGKKFGITRERVRQIEAKAIRK 558

Query: 280 VQ 281
           ++
Sbjct: 559 LK 560


>gi|194476921|ref|YP_002049100.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Paulinella chromatophora]
 gi|171191928|gb|ACB42890.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Paulinella chromatophora]
          Length = 321

 Score = 85.9 bits (211), Expect = 6e-15,   Method: Compositional matrix adjust.
 Identities = 82/323 (25%), Positives = 144/323 (44%), Gaps = 75/323 (23%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYRE--------------HG------------DLS---- 48
           Y+ EI +IP+L  ++E  L ++ +E              +G            DLS    
Sbjct: 18  YLKEISRIPLLTHEQEITLGRQVQELICIQETEQKLELKNGIKPTQEELANSLDLSINQV 77

Query: 49  ---------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                    A  ++V+S+LRLVV IA  Y    + + ++V EG IGL++ V+KFDP RG+
Sbjct: 78  KRKIIHGKRAKEQMVSSNLRLVVSIAKKYTKRSMELLDLVQEGTIGLIRGVEKFDPTRGY 137

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWI+  +   I      +++     ++     L +LK   + ++ +  +   V
Sbjct: 138 KFSTYAYWWIRQGITRAISEQSRTIRLPIHITEE-----LNKLKKAQRDLSQSLGRTPTV 192

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE-- 217
           + +AK + ++E EV  + C      SL   I                  DG + VL+E  
Sbjct: 193 IELAKMIKLTEKEVKELLCHAKQPVSLEMKIG-----------------DGDDTVLLELL 235

Query: 218 ------KEERKNRRNM---LTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSR 266
                  EE  NR+ +   L   +  L   + RI + R   ++  P+TL  +     +SR
Sbjct: 236 PSEIELPEEYVNRKCLRRDLLALVEQLPEIQVRILKMRYGFDSTEPLTLTGIGRVLGMSR 295

Query: 267 ERVRQIEARAFKKVQESIQKQVE 289
           +RVR +E     ++Q+ + K +E
Sbjct: 296 DRVRNLERDGINRLQK-LSKSIE 317


>gi|330721841|gb|EGG99811.1| RNA polymerase sigma factor RpoD [gamma proteobacterium IMCC2047]
          Length = 614

 Score = 85.9 bits (211), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 68/239 (28%), Positives = 119/239 (49%), Gaps = 20/239 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 376 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 435

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   + +++++
Sbjct: 436 IRQAITRSIADQARTIRI--PVHMIETINKLNRVSRQMLQEMGREPTPEE---LGERMDM 490

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E +V  +  ++A  E ++      D   S   D++       E V I+          L
Sbjct: 491 PEDKVRKV-LKIA-KEPISMETPIGDDEDSHLGDFI-------EDVNIDSPIDSATAEGL 541

Query: 229 TRS----MSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           + +    +S L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 542 SEATRGVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 600


>gi|313792143|gb|EFS40244.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL110PA1]
 gi|313801904|gb|EFS43138.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL110PA2]
 gi|313838730|gb|EFS76444.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL086PA1]
 gi|314962802|gb|EFT06902.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL082PA1]
 gi|315078018|gb|EFT50069.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL053PA2]
 gi|327453138|gb|EGE99792.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL092PA1]
          Length = 312

 Score = 85.9 bits (211), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 81/311 (26%), Positives = 142/311 (45%), Gaps = 57/311 (18%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------HGDLS----------- 48
           ++G+  +  Y+  I + P+L   EE  LA+R             H + +           
Sbjct: 13  IDGKDAVGLYLDGIARTPLLNAAEEVALARRIEAGVFARAILEGHAETTSDTTTKELHQI 72

Query: 49  ------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
                 A  R V ++LRLVV +A  Y    +P+ ++V EGN GL++AV+KFD  +GF+ +
Sbjct: 73  AADGDEALARFVRANLRLVVSVARKYGRSQMPLLDLVQEGNTGLIRAVEKFDYAKGFKFS 132

Query: 103 TYSMWWIKAAMQEYILRSWSLVK----IGTTANQ-KRLFFNLRRLKGHLQAITDNNLKPE 157
           TY+ WW++ A+   I +   +V+    +    NQ      NL R  G          +PE
Sbjct: 133 TYATWWVRQAISRGIAQQGRIVRLPVHVAEQVNQVSAARRNLERQLGR---------EPE 183

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHD-GQEQVL 215
               IA +L ++E  VI +  R   D  SL+A +   D   +   D +  +   G + ++
Sbjct: 184 -TFEIADELEITEERVIEL-IRFGRDHVSLDAPVE--DDGDTSLGDLIARETSPGPDDIV 239

Query: 216 IEKEERKNRRNMLT----RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           ++ E+R     +L     RS  V+  R   + + R+ +     L ++   + ++ ERVRQ
Sbjct: 240 LDAEDRSRLEGLLDDLDERSADVVR-RRYGLVDGRQAK-----LADIGKVWGITAERVRQ 293

Query: 272 IEARAFKKVQE 282
           IE  A   +++
Sbjct: 294 IERAALASMRQ 304


>gi|302851352|ref|XP_002957200.1| hypothetical protein VOLCADRAFT_109400 [Volvox carteri f.
           nagariensis]
 gi|300257450|gb|EFJ41698.1| hypothetical protein VOLCADRAFT_109400 [Volvox carteri f.
           nagariensis]
          Length = 733

 Score = 85.9 bits (211), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 75/258 (29%), Positives = 125/258 (48%), Gaps = 33/258 (12%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           V+A   R    L A   L+ S+ RLV+ +   Y G G+ + ++VSEG  GL++ V+ +D 
Sbjct: 461 VMAYNMRYDAGLKAKELLLKSNYRLVMTVCKRYIGKGMHLQDLVSEGVKGLLRGVEMYDA 520

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT-DNNL 154
            RGFR  TY+ WWI+ A+   +  +   V++        +   L +LK    A+  + N 
Sbjct: 521 SRGFRFGTYAHWWIRQAVSRSMAETGRAVRLPV-----HMIEQLTKLKNATAALAMELNR 575

Query: 155 KPE-QVVAIAKKLNVSESEVI--------SMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           +P  + +A A  L  S  E++        SM   + GD+ L        K++ Q +    
Sbjct: 576 EPSVEEMAEAVGLPPSRVELLLDAARAASSMESAIGGDDGLTI------KDAVQDERMAA 629

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFE 263
            +  G + +      R +  +ML      L+ RE  +   R   E+ V  TLE++ S   
Sbjct: 630 DEAFGSDSM------RADVESML----EGLSDREACVLRLRFGLEDGVEWTLEDIGSRLG 679

Query: 264 VSRERVRQIEARAFKKVQ 281
           V+RER+RQ+EA+A +K+Q
Sbjct: 680 VTRERIRQLEAKALRKLQ 697


>gi|213691851|ref|YP_002322437.1| RNA polymerase, sigma 70 subunit, RpoD family [Bifidobacterium
           longum subsp. infantis ATCC 15697]
 gi|213523312|gb|ACJ52059.1| RNA polymerase, sigma 70 subunit, RpoD family [Bifidobacterium
           longum subsp. infantis ATCC 15697]
 gi|320457946|dbj|BAJ68567.1| RNA polymerase sigma factor RpoD [Bifidobacterium longum subsp.
           infantis ATCC 15697]
          Length = 464

 Score = 85.9 bits (211), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 75/278 (26%), Positives = 137/278 (49%), Gaps = 37/278 (13%)

Query: 28  MLEKQEEYVLAKRYRE------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           +L+ + E +  KR RE       G  +  H L+ ++LRLVV +A  Y G G+   +++ E
Sbjct: 200 LLDTESEGMEFKRKRELKWAAADGKKAKDH-LLEANLRLVVSLAKRYTGRGMLFLDLIQE 258

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           GN+GL++AV+KFD ++GF+ +TY+ WWI+ A+   +      +++    +   +   L R
Sbjct: 259 GNLGLIRAVEKFDWKKGFKFSTYATWWIRQAITRAMADQARTIRV--PVHMVEVINKLSR 316

Query: 142 LKGH-LQAI----TDNNLKPEQVVAIAKKLNVSE--SEVISMNCRLA--GDESLNALINS 192
           ++   LQ +    T + L  E  + + K   V +   E IS++  L   GD     LI  
Sbjct: 317 VQRQMLQDLGREPTPDELARELDMPVEKVQEVQKYGREPISLHTPLGEDGDSEFGDLIED 376

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN- 251
           +D          +   D     L++++          + +  L+PRE  + + R   E+ 
Sbjct: 377 TD---------AIAPSDAVAFSLLQEQ--------FKQVLETLSPREAGVIKMRYGLEDG 419

Query: 252 -PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            P TL+++   + V+RER+RQIE++   K++   + Q 
Sbjct: 420 QPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQT 457


>gi|19553123|ref|NP_601125.1| RNA polymerase sigma factor SigB [Corynebacterium glutamicum ATCC
           13032]
 gi|62390759|ref|YP_226161.1| RNA polymerase sigma factor SigB [Corynebacterium glutamicum ATCC
           13032]
 gi|1149591|emb|CAA89988.1| SigB sigma factor [Corynebacterium glutamicum]
 gi|21324689|dbj|BAB99312.1| DNA-directed RNA polymerase sigma subunits (sigma70/sigma32) (SigB)
           [Corynebacterium glutamicum ATCC 13032]
 gi|41326097|emb|CAF20260.1| RNA POLYMERASE SIGMA FACTOR [Corynebacterium glutamicum ATCC 13032]
          Length = 331

 Score = 85.9 bits (211), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 73/262 (27%), Positives = 130/262 (49%), Gaps = 31/262 (11%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++  VLAK     G  + +H L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A+
Sbjct: 81  KRDLKVLAK----DGKKARSH-LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAM 135

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK--RLFFNLRRLKGHL-Q 147
           +KFD  +GF+ +TY+ WWI+ A+   +      +++     ++  +L    R L  HL +
Sbjct: 136 EKFDYSKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKRELYQHLGR 195

Query: 148 AITDNNLKPEQVVAIAK--KLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDW 203
             T+  L  E  +  +K   L     + +S++  +  DE   L   I  S+   +     
Sbjct: 196 EATNEELAEESGIEESKIEMLLRQSRDPVSLDMPVGADEEAPLGDFIEDSEATDA----- 250

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSE 261
                   E  ++      + R +L    + L PRE+ +   R   ++  P TL+ +   
Sbjct: 251 --------ESAVVASMRHSDIRAVL----NTLEPREQDVIRLRYGLDDGVPRTLDQIGRR 298

Query: 262 FEVSRERVRQIEARAFKKVQES 283
           F +SRERVRQIE     K+++ 
Sbjct: 299 FGLSRERVRQIEREVMSKLRDG 320


>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 = 85.9 bits (211), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 71/241 (29%), Positives = 113/241 (46%), Gaps = 23/241 (9%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 379 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 438

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 439 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPSPEELAERMEMPED 496

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE  +      D+N +   D  V         + E  E
Sbjct: 497 KIRKVLKIAK-EPISMETPIGDDEDSHLGDFIEDRNVTAPADSAV------NAAIREVVE 549

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                 +  R   VL  R    F      ++  TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 550 ELLDNGLTAREAKVLRMR----FGIGMNTDH--TLEEVGKQFDVTRERIRQIEAKALRKL 603

Query: 281 Q 281
           +
Sbjct: 604 R 604


>gi|227488742|ref|ZP_03919058.1| RNA polymerase sigma factor SigB [Corynebacterium glucuronolyticum
           ATCC 51867]
 gi|227542262|ref|ZP_03972311.1| RNA polymerase sigma factor SigB [Corynebacterium glucuronolyticum
           ATCC 51866]
 gi|227091164|gb|EEI26476.1| RNA polymerase sigma factor SigB [Corynebacterium glucuronolyticum
           ATCC 51867]
 gi|227182091|gb|EEI63063.1| RNA polymerase sigma factor SigB [Corynebacterium glucuronolyticum
           ATCC 51866]
          Length = 327

 Score = 85.9 bits (211), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 78/304 (25%), Positives = 138/304 (45%), Gaps = 59/304 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH-----------------------GDLSAA 50
           Y++ I K P+L  +EE  LAK      Y  H                       GD +  
Sbjct: 33  YLNGIGKTPLLSAEEEVELAKTVEVGLYARHLLNDPEYKPTRAMKRDLKELAREGDKARN 92

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           H ++ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+
Sbjct: 93  H-MLEANLRLVVSLAKRYSGRGMPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTYATWWIR 151

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-----QAITDNNLKPEQVVAIAK- 164
            A+   +      +++     ++     L R+K  +     + +T+  L  E  +   K 
Sbjct: 152 QAITRGMADQSRTIRLPVHLVEQ--VNKLSRIKREMYQQFGREVTNEELAEESGIDENKI 209

Query: 165 -KLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
             L     + +S++  +  DE   L   I  S+              D +E V++     
Sbjct: 210 EMLFRQSRDPVSLDMPVGADEEAPLGDFIEDSEAT------------DAEEAVVVSL--- 254

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKK 279
             R + +   +  L  RE+ +   R   ++  P TL+ +   + +SRERVRQIE     K
Sbjct: 255 --RHSDIRAVIDTLEGREQDVIRMRYGLDDGVPRTLDQIGRRYGLSRERVRQIEREVMAK 312

Query: 280 VQES 283
           ++E 
Sbjct: 313 LREG 316


>gi|325475291|gb|EGC78476.1| region 2 family RNA polymerase sigma-70 factor [Treponema denticola
           F0402]
          Length = 275

 Score = 85.9 bits (211), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 71/282 (25%), Positives = 137/282 (48%), Gaps = 30/282 (10%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +YI + +K P+L  ++E  LA   ++ G+  A   LVTS+LRLV+K+A  +      I
Sbjct: 6   LLQYIKDSKKYPLLSAEQEAELADEVKK-GNTEAIEVLVTSNLRLVIKMAKKFSSNENQI 64

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT------- 128
            E++ EGN+GLM+A  KF      R ++Y+ WWIK +   Y+  +  ++K+         
Sbjct: 65  LELIQEGNMGLMKAASKFSKSFKVRFSSYAAWWIKQSFIRYLNSADKVIKLPVRKEALIR 124

Query: 129 TANQKRLFFNLRRLKGHLQAITD-NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
             N++   + ++   G L + +    +  E+V  IA+  + + +++ S++  +  + S N
Sbjct: 125 QVNKEEENYKIKY--GILPSYSQLAEIMKEKVDIIAQVKSFNYTDICSLDDPVDNERSAN 182

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
                         D++  +    E+  I+ E ++     L + + +LN RE+ +   R 
Sbjct: 183 ------------LYDFIPCNTYNPEEEFIDNEFKEK----LNKCLEILNDREKDVLRNRY 226

Query: 248 LQENPV---TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             +  +   T   L  ++ +S E +RQ + RA KK++    K
Sbjct: 227 GLDGTMTSTTFAVLGKKYSISAESIRQTQLRALKKLRADTNK 268


>gi|149197281|ref|ZP_01874333.1| RNA polymerase sigma factor RpoD [Lentisphaera araneosa HTCC2155]
 gi|149139827|gb|EDM28228.1| RNA polymerase sigma factor RpoD [Lentisphaera araneosa HTCC2155]
          Length = 404

 Score = 85.9 bits (211), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 72/245 (29%), Positives = 124/245 (50%), Gaps = 30/245 (12%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           ++ + +V  +LRLV+ IA  Y        +++ EGNIGL+ AV+K+D   G+  +TY+ W
Sbjct: 167 NSVNAMVEGNLRLVISIARKYSNSQEGFLDLIQEGNIGLVSAVEKYDASFGYTFSTYATW 226

Query: 108 WIKAAMQEY---ILRSWSL-----VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           WI+ A+      ++R+  L     VK+      +R  F     K   +A  D        
Sbjct: 227 WIRQAVSRARTELVRTMKLPANIMVKVNKIYRTERELFQ----KFGREATIDE------- 275

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +++ + +S +++ S+        SL   +  S++++ +  D +  D D    VL + E
Sbjct: 276 --VSEAVELSPAKIRSLKRMCQQPISLQTTV--SEEHTGELGDIVSNDDD----VLPDAE 327

Query: 220 -ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARA 276
            E+K     L   + +LN RE+ I   R  L +    TLEN+++EF +SRER+RQIE  A
Sbjct: 328 VEQKQLHESLVAMLDILNEREQEILRMRFGLADGEYHTLENIANEFGISRERIRQIETSA 387

Query: 277 FKKVQ 281
            KK++
Sbjct: 388 LKKLR 392


>gi|325107209|ref|YP_004268277.1| RNA polymerase, sigma 70 subunit, RpoD [Planctomyces brasiliensis
           DSM 5305]
 gi|324967477|gb|ADY58255.1| RNA polymerase, sigma 70 subunit, RpoD [Planctomyces brasiliensis
           DSM 5305]
          Length = 590

 Score = 85.9 bits (211), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 71/250 (28%), Positives = 120/250 (48%), Gaps = 22/250 (8%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
           R H   +A   L   +LRLVV IA  YR  G+   +++ EGN GLM+AV K++  RG++ 
Sbjct: 336 RYHDYETAMRELSGGNLRLVVSIAKKYRNRGMNFLDLIQEGNTGLMRAVDKYEYRRGYKF 395

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIG-----TTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +TY+ WWI+ A+   I      ++I      T +  +++  +L +  G    I +     
Sbjct: 396 STYATWWIRQAITRAIADQARTIRIPVHMIETMSKLRKVGKDLVQELGREPTIEEMAEAA 455

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           E  +  A+++     + IS++  +   E             S + D+ + DH     V  
Sbjct: 456 EVSLEEARRVMKISRQPISLDRPIGEGE------------DSYFGDF-IEDHSTDSPVST 502

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEA 274
             +E    ++ +   +  L  RER I + R    +    TLE +   F+V+RERVRQIEA
Sbjct: 503 ATQE--MLKDKIDHVLKTLTYREREIIKLRYGLGDGYTYTLEEVGRIFKVTRERVRQIEA 560

Query: 275 RAFKKVQESI 284
           +A +K+Q  +
Sbjct: 561 KAVRKLQHPV 570


>gi|239621277|ref|ZP_04664308.1| RNA polymerase principal sigma factor [Bifidobacterium longum
           subsp. infantis CCUG 52486]
 gi|239515738|gb|EEQ55605.1| RNA polymerase principal sigma factor [Bifidobacterium longum
           subsp. infantis CCUG 52486]
          Length = 488

 Score = 85.9 bits (211), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 75/278 (26%), Positives = 137/278 (49%), Gaps = 37/278 (13%)

Query: 28  MLEKQEEYVLAKRYRE------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           +L+ + E +  KR RE       G  +  H L+ ++LRLVV +A  Y G G+   +++ E
Sbjct: 224 LLDTESEGMEFKRKRELKWAAADGKKAKDH-LLEANLRLVVSLAKRYTGRGMLFLDLIQE 282

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           GN+GL++AV+KFD ++GF+ +TY+ WWI+ A+   +      +++    +   +   L R
Sbjct: 283 GNLGLIRAVEKFDWKKGFKFSTYATWWIRQAITRAMADQARTIRV--PVHMVEVINKLSR 340

Query: 142 LKGH-LQAI----TDNNLKPEQVVAIAKKLNVSE--SEVISMNCRLA--GDESLNALINS 192
           ++   LQ +    T + L  E  + + K   V +   E IS++  L   GD     LI  
Sbjct: 341 VQRQMLQDLGREPTPDELARELDMPVEKVQEVQKYGREPISLHTPLGEDGDSEFGDLIED 400

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN- 251
           +D          +   D     L++++          + +  L+PRE  + + R   E+ 
Sbjct: 401 TD---------AIAPSDAVAFSLLQEQ--------FKQVLETLSPREAGVIKMRYGLEDG 443

Query: 252 -PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            P TL+++   + V+RER+RQIE++   K++   + Q 
Sbjct: 444 QPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQT 481


>gi|148238489|ref|YP_001223876.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp. WH
           7803]
 gi|147847028|emb|CAK22579.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 7803]
          Length = 355

 Score = 85.9 bits (211), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 73/296 (24%), Positives = 128/296 (43%), Gaps = 51/296 (17%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAH--------------------------- 51
           Y+ +I ++P+L  Q+E  L ++ +E  DL A                             
Sbjct: 50  YLRDIGRVPLLSHQQEITLGRQVQELMDLEATEAELQEKRGGEAVPAAELAKAAGLSAVQ 109

Query: 52  -------------RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
                        R+V ++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP RG
Sbjct: 110 LKRKLQAGRRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRG 169

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           ++ +TY+ WWI+  +   I      +++     +      L +LK   + ++ +  +   
Sbjct: 170 YKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITEM-----LNKLKKGQRELSQDLGRTPS 224

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD-GQEQVLIE 217
           V  +A  + + E EV  + CR     SL   +   D + ++  D L  D +   EQV  E
Sbjct: 225 VTELAAFVELPEDEVKELMCRARQPVSLE--MKVGDGDDTELLDLLAGDGELPSEQV--E 280

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
            E  K     L   +  L  R  R+       E+P++L  +     +SR+RVR +E
Sbjct: 281 GECLKGDLRDLLGQLPELQERVLRMRYGMD-GEDPMSLTGIGRVIGISRDRVRNLE 335


>gi|262197687|ref|YP_003268896.1| RNA polymerase, sigma 32 subunit, RpoH [Haliangium ochraceum DSM
           14365]
 gi|262081034|gb|ACY17003.1| RNA polymerase, sigma 32 subunit, RpoH [Haliangium ochraceum DSM
           14365]
          Length = 465

 Score = 85.9 bits (211), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 67/257 (26%), Positives = 130/257 (50%), Gaps = 11/257 (4%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           YV   R  EH   +A +  V ++LRLVV IA  +    + +++++ EGN+GL++AV+++D
Sbjct: 215 YVDQVRAAEHAARNARNEFVKANLRLVVSIARRFNHGRMSLADLIQEGNLGLIKAVERYD 274

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             RGFR +TY+ WWI+ A+   +      V++        L  + R LK   Q       
Sbjct: 275 YRRGFRFSTYASWWIRHAIGRALADKGREVRLPV----HMLDAHHRLLKAQHQLTNTLGR 330

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
           +P     +++  N+S  ++  M   L     SL+  +N  D  S      ++ D  G+E 
Sbjct: 331 QPTS-EELSEAANLSVEKIEKMRTHLLDQALSLDRPMNDEDGRSVA---EVLQDPHGEEH 386

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQ 271
             +    ++   + + +++  L P E  I   R   +N   +TL+ +  ++ +SRER+RQ
Sbjct: 387 SALNVLAQRTMSDEVRKTLQTLRPIEADILRRRFGLDNDEELTLKQIGEQYNLSRERIRQ 446

Query: 272 IEARAFKKVQESIQKQV 288
           ++ +A  K++ +++++ 
Sbjct: 447 LQEQALTKMRVALRRKA 463


>gi|291457726|ref|ZP_06597116.1| RNA polymerase sigma factor RpoD [Bifidobacterium breve DSM 20213]
 gi|291380779|gb|EFE88297.1| RNA polymerase sigma factor RpoD [Bifidobacterium breve DSM 20213]
          Length = 472

 Score = 85.9 bits (211), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 72/280 (25%), Positives = 136/280 (48%), Gaps = 41/280 (14%)

Query: 28  MLEKQEEYVLAKRYRE------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           +L+ + E +  KR RE       G  +  H L+ ++LRLVV +A  Y G G+   +++ E
Sbjct: 208 LLDTESEGMEFKRKRELKWAAADGKKAKDH-LLEANLRLVVSLAKRYTGRGMLFLDLIQE 266

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT---------TANQ 132
           GN+GL++AV+KFD ++GF+ +TY+ WWI+ A+   +      +++           +  Q
Sbjct: 267 GNLGLIRAVEKFDWKKGFKFSTYATWWIRQAITRAMADQARTIRVPVHMVEVINKLSRVQ 326

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALI 190
           +++  +L R     +   + ++  E+V  + K       E IS++  L   GD     LI
Sbjct: 327 RQMLQDLGREPTPDELARELDMPVEKVQEVQK----YGREPISLHTPLGEDGDSEFGDLI 382

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D          +   D     L++++          + +  L+PRE  + + R   E
Sbjct: 383 EDTD---------AIAPSDAVAFSLLQEQ--------FKQVLETLSPREAGVIKMRYGLE 425

Query: 251 N--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +  P TL+++   + V+RER+RQIE++   K++   + Q 
Sbjct: 426 DGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQT 465


>gi|257058077|ref|YP_003135965.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8802]
 gi|256588243|gb|ACU99129.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8802]
          Length = 375

 Score = 85.9 bits (211), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 69/239 (28%), Positives = 122/239 (51%), Gaps = 19/239 (7%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  +++ S+LRLVV IA  Y   G+P  +++ EG IGL +A +KFDP +G++ +TY+ W
Sbjct: 136 TAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPNKGYKFSTYAYW 195

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++     +K     L +LK   + +     +      +A++L 
Sbjct: 196 WIRQAITRTIANDARTIRLPIHIVEK-----LNKLKKAQRILKQKLQRNPNEKELAQELE 250

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR--- 224
           ++  ++  +        SLN  +   +   ++  D L      ++Q L   EE+ N    
Sbjct: 251 MTPPQLRQLLQLRRQSLSLNHRVGKGE--DTELVDLL------EDQDLQLPEEQMNEGML 302

Query: 225 RNMLTRSMS-VLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           RN ++  +S VL  RE+ +   R       P TLE +   F +SRERVRQI+++A +K+
Sbjct: 303 RNEISAVLSDVLTEREKDVISLRYGLSTSQPHTLEEVGGMFNLSRERVRQIQSKAMRKL 361


>gi|296454312|ref|YP_003661455.1| RpoD family RNA polymerase sigma-70 factor [Bifidobacterium longum
           subsp. longum JDM301]
 gi|296183743|gb|ADH00625.1| RNA polymerase, sigma 70 subunit, RpoD family [Bifidobacterium
           longum subsp. longum JDM301]
          Length = 474

 Score = 85.9 bits (211), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 72/280 (25%), Positives = 136/280 (48%), Gaps = 41/280 (14%)

Query: 28  MLEKQEEYVLAKRYRE------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           +L+ + E +  KR RE       G  +  H L+ ++LRLVV +A  Y G G+   +++ E
Sbjct: 210 LLDTESEGMEFKRKRELKWAAADGKKAKDH-LLEANLRLVVSLAKRYTGRGMLFLDLIQE 268

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT---------TANQ 132
           GN+GL++AV+KFD ++GF+ +TY+ WWI+ A+   +      +++           +  Q
Sbjct: 269 GNLGLIRAVEKFDWKKGFKFSTYATWWIRQAITRAMADQARTIRVPVHMVEVINKLSRVQ 328

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALI 190
           +++  +L R     +   + ++  E+V  + K       E IS++  L   GD     LI
Sbjct: 329 RQMLQDLGREPTPDELARELDMPVEKVQEVQKYGR----EPISLHTPLGEDGDSEFGDLI 384

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D          +   D     L++++          + +  L+PRE  + + R   E
Sbjct: 385 EDTD---------AIAPSDAVAFSLLQEQ--------FKQVLETLSPREAGVIKMRYGLE 427

Query: 251 N--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +  P TL+++   + V+RER+RQIE++   K++   + Q 
Sbjct: 428 DGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRSQT 467


>gi|171742642|ref|ZP_02918449.1| hypothetical protein BIFDEN_01756 [Bifidobacterium dentium ATCC
           27678]
 gi|171278256|gb|EDT45917.1| hypothetical protein BIFDEN_01756 [Bifidobacterium dentium ATCC
           27678]
          Length = 461

 Score = 85.9 bits (211), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 65/253 (25%), Positives = 124/253 (49%), Gaps = 34/253 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ WW
Sbjct: 223 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 282

Query: 109 IKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   +      +++           +  Q+++  +L R     +   + ++  E+V
Sbjct: 283 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 342

Query: 160 VAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
             + K       E IS++  L   GD     LI  +D          +   D     L++
Sbjct: 343 QEVQK----YGREPISLHTPLGEDGDSEFGDLIEDTD---------AIAPSDAVAFSLLQ 389

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
           ++          + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++
Sbjct: 390 EQ--------FKQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESK 441

Query: 276 AFKKVQESIQKQV 288
              K++   + Q 
Sbjct: 442 TMSKLRHPSRSQT 454


>gi|310777993|ref|YP_003966326.1| RNA polymerase, sigma 32 subunit, RpoH [Ilyobacter polytropus DSM
           2926]
 gi|309747316|gb|ADO81978.1| RNA polymerase, sigma 32 subunit, RpoH [Ilyobacter polytropus DSM
           2926]
          Length = 329

 Score = 85.9 bits (211), Expect = 7e-15,   Method: Compositional matrix adjust.
 Identities = 78/272 (28%), Positives = 137/272 (50%), Gaps = 27/272 (9%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y H+I     + K++E  + K+ ++ GD  A   LVTS+L+LV KIAM Y   G+  
Sbjct: 71  LEQYFHDISLYTPIPKEKEKDIVKKAQD-GDEEAREMLVTSNLKLVAKIAMKYSKSGVNY 129

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA---NQ 132
            +++ +G IGL+ A+ K+D  +G    +YS+WWIK  +   I    + +KI +     N+
Sbjct: 130 IDLIQDGTIGLIAAIDKYDLSKGHSFTSYSVWWIKREIINSIANRINAIKIPSYVYLMNK 189

Query: 133 K-RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
           K R+F +          +  NN KP     I++ LN+S  EV  M  + A +  +     
Sbjct: 190 KIRIFED--------DFMERNNKKP-SYQEISEALNLSLEEVEKM--KEASEIGVGGF-- 236

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQE 250
            +D N     D+   D   +E  L+E+      R+ ++  M  ++P E+++ E    L +
Sbjct: 237 -ADGNEPDLGDFNTVDQIDKELNLLEE------RSKISNLMRKISPEEQKVVEMYYGLDD 289

Query: 251 NP-VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           N  +  + +S    VS E+V+ ++ RA  K++
Sbjct: 290 NKRLGFKEISKIMGVSVEKVKFLKERAILKLK 321


>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 = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 71/248 (28%), Positives = 116/248 (46%), Gaps = 38/248 (15%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 375 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   + +++ +
Sbjct: 435 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEE---LGERMEM 489

Query: 169 SESEV----------ISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
            E +V          ISM   +  DE   L   I  +  +S      +        Q L 
Sbjct: 490 PEDKVRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTIDSPVDSATI--------QGLT 541

Query: 217 EKEERKNRRNMLTRS-MSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIE 273
           E           TRS ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIE
Sbjct: 542 EA----------TRSVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 591

Query: 274 ARAFKKVQ 281
           A+A +K++
Sbjct: 592 AKALRKLR 599


>gi|25028367|ref|NP_738421.1| RNA polymerase sigma factor SigB [Corynebacterium efficiens YS-314]
 gi|259507424|ref|ZP_05750324.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           efficiens YS-314]
 gi|23493652|dbj|BAC18621.1| sigma factor SigB [Corynebacterium efficiens YS-314]
 gi|259164989|gb|EEW49543.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           efficiens YS-314]
          Length = 333

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 74/262 (28%), Positives = 130/262 (49%), Gaps = 31/262 (11%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++  VLAK     G  + AH L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A+
Sbjct: 83  KRDLKVLAK----EGKKARAH-LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAM 137

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK--RLFFNLRRLKGHL-Q 147
           +KFD  +GF+ +TY+ WWI+ A+   +      +++     ++  +L    R +  HL +
Sbjct: 138 EKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQHLGR 197

Query: 148 AITDNNLKPEQVVAIAK--KLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDW 203
             T+  L  E  +  +K   L     + +S++  +  DE   L   I  S+   +     
Sbjct: 198 EATNEELAEESGIEESKIEMLLRQSRDPVSLDMPVGADEEAPLGDFIEDSEATDA----- 252

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSE 261
                   E  ++      + R++L    S L  RE+ +   R   E+  P TL+ +   
Sbjct: 253 --------ETAVVASMRHSDIRSVL----STLEQREQDVIRLRYGLEDGVPRTLDQIGRR 300

Query: 262 FEVSRERVRQIEARAFKKVQES 283
           F +SRERVRQIE     K+++ 
Sbjct: 301 FGLSRERVRQIEREVMSKLRDG 322


>gi|313812944|gb|EFS50658.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL025PA1]
          Length = 511

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 80/325 (24%), Positives = 144/325 (44%), Gaps = 65/325 (20%)

Query: 7   SIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYR---------------------- 42
           +++V G     +  Y+ +I K+ +L   EE  LAKR                        
Sbjct: 203 TVMVAGATADPVKDYLKQIGKVALLNAVEEVDLAKRIEAGLFAGEQLADPDAKIREKDRE 262

Query: 43  ------EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                 E G ++  H L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  
Sbjct: 263 DYEWIAEDGKVAKNH-LLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYT 321

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQ 147
           +G++ +TY+ WWIK A+   +      ++I              Q+++  +L R     +
Sbjct: 322 KGYKFSTYATWWIKQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEE 381

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLV 205
             ++ ++  E+V+ + K       E IS++  L   GD     LI  S+          +
Sbjct: 382 LASELDMTAEKVIEVQKYGR----EPISLHTPLGEDGDSEFGDLIEDSE---------AI 428

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFE 263
              D     L++++        L   +  L+ RE  +   R       P TL+ +   + 
Sbjct: 429 VPADAVNFTLLQEQ--------LHDVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYG 480

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           V+RER+RQIE++   K++   + QV
Sbjct: 481 VTRERIRQIESKTMSKLRHPSRSQV 505


>gi|218245053|ref|YP_002370424.1| RNA polymerase sigma-70 subunit RpoD subfamily [Cyanothece sp. PCC
           8801]
 gi|218165531|gb|ACK64268.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8801]
          Length = 375

 Score = 85.9 bits (211), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 69/239 (28%), Positives = 122/239 (51%), Gaps = 19/239 (7%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  +++ S+LRLVV IA  Y   G+P  +++ EG IGL +A +KFDP +G++ +TY+ W
Sbjct: 136 TAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPNKGYKFSTYAYW 195

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++     +K     L +LK   + +     +      +A++L 
Sbjct: 196 WIRQAITRTIANDARTIRLPIHIVEK-----LNKLKKAQRILKQKLQRNPNEKELAQELE 250

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR--- 224
           ++  ++  +        SLN  +   +   ++  D L      ++Q L   EE+ N    
Sbjct: 251 MTPPQLRQLLQLRRQSLSLNHRVGKGE--DTELVDLL------EDQDLQLPEEQMNEGML 302

Query: 225 RNMLTRSMS-VLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           RN ++  +S VL  RE+ +   R       P TLE +   F +SRERVRQI+++A +K+
Sbjct: 303 RNEISAVLSDVLTEREKDVISLRYGLSTSQPHTLEEVGGMFNLSRERVRQIQSKAMRKL 361


>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 = 85.5 bits (210), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 65/235 (27%), Positives = 116/235 (49%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 365 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 424

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   + +++ +
Sbjct: 425 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEE---LGERMEM 479

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E +V  +  ++A  E ++      D   S   D++    D      ++    +      
Sbjct: 480 PEDKVRKV-LKIAK-EPISMETPIGDDEDSSLGDFI---EDVTIASPVDSATEEGLTEAT 534

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           T  ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 535 TDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 589


>gi|298253932|ref|ZP_06977519.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Gardnerella vaginalis 5-1]
 gi|297532075|gb|EFH71050.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Gardnerella vaginalis 5-1]
          Length = 489

 Score = 85.5 bits (210), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 69/251 (27%), Positives = 125/251 (49%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ WW
Sbjct: 251 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 310

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH-LQAI----TDNNLKPEQVVAIA 163
           I+ A+   +      +++    +   +   L R++   LQ +    T + L  E  + + 
Sbjct: 311 IRQAITRAMADQARTIRV--PVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVE 368

Query: 164 KKLNVSE--SEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           K   V +   E IS++  L   GD     LI  +D          +   D     L++++
Sbjct: 369 KVQEVQKYGREPISLHTPLGEDGDSEFGDLIEDTDA---------IAPSDAVAFSLLQEQ 419

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
            R+         +  L PRE  + + R   E+  P TL+++   + V+RER+RQIE++  
Sbjct: 420 FRQ--------VLETLAPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTM 471

Query: 278 KKVQESIQKQV 288
            K++   + Q 
Sbjct: 472 SKLRHPSRSQT 482


>gi|78212534|ref|YP_381313.1| type II alternative RNA polymerase sigma factor [Synechococcus sp.
           CC9605]
 gi|78196993|gb|ABB34758.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. CC9605]
          Length = 309

 Score = 85.5 bits (210), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 72/249 (28%), Positives = 123/249 (49%), Gaps = 31/249 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A ++++TS+LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG R +TY+ WW
Sbjct: 67  AKNQMITSNLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSTYAYWW 126

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP--EQV-----VA 161
           I+  +   +      ++I    N+K     LR  K  L  +  N L P  EQ+     + 
Sbjct: 127 IRQGLNRALSTQSRTIRIPVNVNEK--LTKLRAAKARL--MQRNGLSPSGEQLAEFMEIP 182

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           IA+  ++   E+ S+   L G       +  S  + S+  D L  D    E   +E+ E 
Sbjct: 183 IAEVEDLLACELRSVTVSLQG-------VVKSKSDPSELVDVLPSD----ELPPMERAEI 231

Query: 222 KNRR----NMLTRSMSVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEA 274
             R     ++L ++   L P+E  +   R   +      TL  ++     SRE  RQ+  
Sbjct: 232 AERTASVWSLLAKAN--LTPKEHTVVTLRFGLDGTNEWRTLAEVARHMNCSREYCRQVVQ 289

Query: 275 RAFKKVQES 283
           RA +K++++
Sbjct: 290 RALRKLRKT 298


>gi|315078017|gb|EFT50068.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL053PA2]
          Length = 511

 Score = 85.5 bits (210), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 80/325 (24%), Positives = 144/325 (44%), Gaps = 65/325 (20%)

Query: 7   SIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYR---------------------- 42
           +++V G     +  Y+ +I K+ +L   EE  LAKR                        
Sbjct: 203 TVMVAGATADPVKDYLKQIGKVALLNAVEEVDLAKRIEAGLFAGEQLADPDAKIREKDRE 262

Query: 43  ------EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                 E G ++  H L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  
Sbjct: 263 DYEWIAEDGKVAKNH-LLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYT 321

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQ 147
           +G++ +TY+ WWIK A+   +      ++I              Q+++  +L R     +
Sbjct: 322 KGYKFSTYATWWIKQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEE 381

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLV 205
             ++ ++  E+V+ + K       E IS++  L   GD     LI  S+          +
Sbjct: 382 LASELDMTAEKVIEVQKYGR----EPISLHTPLGEDGDSEFGDLIEDSE---------AI 428

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFE 263
              D     L++++        L   +  L+ RE  +   R       P TL+ +   + 
Sbjct: 429 VPADAVNFTLLQEQ--------LHDVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYG 480

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           V+RER+RQIE++   K++   + QV
Sbjct: 481 VTRERIRQIESKTMSKLRHPSRSQV 505


>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 = 85.5 bits (210), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 71/241 (29%), Positives = 113/241 (46%), Gaps = 23/241 (9%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 386 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 445

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         PE++         
Sbjct: 446 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPSPEELAERMEMPED 503

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE  +      D+N +   D  V         + E  E
Sbjct: 504 KIRKVLKIAK-EPISMETPIGDDEDSHLGDFIEDRNVTAPADSAV------NAAIREVVE 556

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                 +  R   VL  R    F      ++  TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 557 ELLDNGLTAREAKVLRMR----FGIGMNTDH--TLEEVGKQFDVTRERIRQIEAKALRKL 610

Query: 281 Q 281
           +
Sbjct: 611 R 611


>gi|313838731|gb|EFS76445.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL086PA1]
          Length = 511

 Score = 85.5 bits (210), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 80/325 (24%), Positives = 144/325 (44%), Gaps = 65/325 (20%)

Query: 7   SIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYR---------------------- 42
           +++V G     +  Y+ +I K+ +L   EE  LAKR                        
Sbjct: 203 TVMVAGATADPVKDYLKQIGKVALLNAVEEVDLAKRIEAGLFAGEQLADPDAKIREKDRE 262

Query: 43  ------EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                 E G ++  H L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  
Sbjct: 263 DYEWIAEDGKVAKNH-LLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYT 321

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQ 147
           +G++ +TY+ WWIK A+   +      ++I              Q+++  +L R     +
Sbjct: 322 KGYKFSTYATWWIKQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEE 381

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLV 205
             ++ ++  E+V+ + K       E IS++  L   GD     LI  S+          +
Sbjct: 382 LASELDMTAEKVIEVQKYGR----EPISLHTPLGEDGDSEFGDLIEDSE---------AI 428

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFE 263
              D     L++++        L   +  L+ RE  +   R       P TL+ +   + 
Sbjct: 429 VPADAVNFTLLQEQ--------LHDVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYG 480

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           V+RER+RQIE++   K++   + QV
Sbjct: 481 VTRERIRQIESKTMSKLRHPSRSQV 505


>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 = 85.5 bits (210), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 63/246 (25%), Positives = 119/246 (48%), Gaps = 36/246 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   G+   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 427 AKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEGNIGLMKAVDKFEYRRGWKFSTYATWW 486

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           ++ A+   +      +++    +       L R+   +   T     P     +A+++ +
Sbjct: 487 VRQAVTRSLADQARTIRV--PVHMIETINKLNRISREILQQTGQEAHP---AVLAERMEL 541

Query: 169 SESEV----------ISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           SE +V          +S+   +   GD +L  +I   D   S   D  +           
Sbjct: 542 SEEKVRGILKIAKQPVSLETPVGDDGDATLGDMIE--DAAVSSPADAAM----------- 588

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEA 274
               + + R  +  ++  L+PRE ++   R     ++  TLE +  +F+V+RER+RQIE+
Sbjct: 589 ----QADLRAAIDDALDSLSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIRQIES 644

Query: 275 RAFKKV 280
           +A +K+
Sbjct: 645 KAMRKL 650


>gi|314960003|gb|EFT04105.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL002PA2]
          Length = 511

 Score = 85.5 bits (210), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 80/325 (24%), Positives = 144/325 (44%), Gaps = 65/325 (20%)

Query: 7   SIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYR---------------------- 42
           +++V G     +  Y+ +I K+ +L   EE  LAKR                        
Sbjct: 203 TVMVAGATADPVKDYLKQIGKVALLNAVEEVDLAKRIEAGLFAGEQLADPDAKIREKDRE 262

Query: 43  ------EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                 E G ++  H L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  
Sbjct: 263 DYEWIAEDGKVAKNH-LLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYT 321

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQ 147
           +G++ +TY+ WWIK A+   +      ++I              Q+++  +L R     +
Sbjct: 322 KGYKFSTYATWWIKQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEE 381

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLV 205
             ++ ++  E+V+ + K       E IS++  L   GD     LI  S+          +
Sbjct: 382 LASELDMTAEKVIEVQKYGR----EPISLHTPLGEDGDSEFGDLIEDSE---------AI 428

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFE 263
              D     L++++        L   +  L+ RE  +   R       P TL+ +   + 
Sbjct: 429 VPADAVNFTLLQEQ--------LHDVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYG 480

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           V+RER+RQIE++   K++   + QV
Sbjct: 481 VTRERIRQIESKTMSKLRHPSRSQV 505


>gi|973980|gb|AAB05357.1| RNA polymerase sigma factor [Cyanidium caldarium]
          Length = 609

 Score = 85.5 bits (210), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 72/266 (27%), Positives = 132/266 (49%), Gaps = 36/266 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   LV ++LRLVV +A  +   GL + +++ EG+IGL++  ++FD   GFR +TY+MWW
Sbjct: 333 ARESLVAANLRLVVSVAKQFTNRGLSMQDLIQEGSIGLIKGAERFDYRTGFRFSTYAMWW 392

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI-----TDNNLKPEQVVAIA 163
           I+ AMQ  I  +   ++I +T     L   + R +  L +      TD  L     +++ 
Sbjct: 393 IRQAMQRAIADTSRPIRIPSTITD--LSVQIYRARLELSSTLGRDPTDAELADFLDISVQ 450

Query: 164 K----KLNVSESEVISMNCRLAGDESLNALINS-----SDKNSSQWQDWLVYDHDGQEQV 214
           +    KL  ++S  +S++  ++  +  N  I S     +D  SS+    L  +  G    
Sbjct: 451 RLQDVKLYTNQSATVSLDAPVSR-QVTNTCIKSKGTGDTDVFSSKADGKLSKNGYGSRHK 509

Query: 215 L--------IEKEERKNRRNMLTRS---------MSVLNPRERRIFEAR-RLQENPV-TL 255
           L        ++ +E  +  +M+  S         +S+LNP ER +   R  L +  + ++
Sbjct: 510 LGDFTLGDTVQTDESVSPEHMMADSLMRDDIECALSLLNPYEREVIRMRFGLDDGRMKSV 569

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           + + + + V   R+R+IEARA +K++
Sbjct: 570 DEVCAYYCVQTSRIRRIEARALRKLR 595


>gi|313764456|gb|EFS35820.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL013PA1]
 gi|313772162|gb|EFS38128.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL074PA1]
 gi|313792142|gb|EFS40243.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL110PA1]
 gi|313801905|gb|EFS43139.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL110PA2]
 gi|313807517|gb|EFS46004.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL087PA2]
 gi|313815995|gb|EFS53709.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL059PA1]
 gi|313818559|gb|EFS56273.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL046PA2]
 gi|313820326|gb|EFS58040.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL036PA1]
 gi|313822867|gb|EFS60581.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL036PA2]
 gi|313825201|gb|EFS62915.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL063PA1]
 gi|313827777|gb|EFS65491.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL063PA2]
 gi|313830354|gb|EFS68068.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL007PA1]
 gi|313833727|gb|EFS71441.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL056PA1]
 gi|314915449|gb|EFS79280.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL005PA4]
 gi|314918269|gb|EFS82100.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL050PA1]
 gi|314920081|gb|EFS83912.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL050PA3]
 gi|314925214|gb|EFS89045.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL036PA3]
 gi|314931603|gb|EFS95434.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL067PA1]
 gi|314955756|gb|EFT00156.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL027PA1]
 gi|314958170|gb|EFT02273.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL002PA1]
 gi|314962801|gb|EFT06901.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL082PA1]
 gi|314967832|gb|EFT11931.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL037PA1]
 gi|314973358|gb|EFT17454.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL053PA1]
 gi|314976037|gb|EFT20132.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL045PA1]
 gi|314978425|gb|EFT22519.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL072PA2]
 gi|314983942|gb|EFT28034.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL005PA1]
 gi|314988126|gb|EFT32217.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL005PA2]
 gi|314989931|gb|EFT34022.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL005PA3]
 gi|315080641|gb|EFT52617.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL078PA1]
 gi|315084314|gb|EFT56290.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL027PA2]
 gi|315085657|gb|EFT57633.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL002PA3]
 gi|315088921|gb|EFT60897.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL072PA1]
 gi|315095903|gb|EFT67879.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL038PA1]
 gi|315098534|gb|EFT70510.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL059PA2]
 gi|315101108|gb|EFT73084.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL046PA1]
 gi|315105654|gb|EFT77630.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL030PA1]
 gi|315108328|gb|EFT80304.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL030PA2]
 gi|327326185|gb|EGE67975.1| RNA polymerase principal sigma factor HrdB [Propionibacterium acnes
           HL096PA2]
 gi|327330255|gb|EGE72004.1| RNA polymerase principal sigma factor HrdB [Propionibacterium acnes
           HL097PA1]
 gi|327331940|gb|EGE73677.1| RNA polymerase principal sigma factor HrdB [Propionibacterium acnes
           HL096PA3]
 gi|327443141|gb|EGE89795.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL013PA2]
 gi|327445925|gb|EGE92579.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL043PA2]
 gi|327448095|gb|EGE94749.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL043PA1]
 gi|327450784|gb|EGE97438.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL087PA3]
 gi|327453139|gb|EGE99793.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL092PA1]
 gi|327453872|gb|EGF00527.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL083PA2]
 gi|328753472|gb|EGF67088.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL020PA1]
 gi|328754202|gb|EGF67818.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL087PA1]
 gi|328754546|gb|EGF68162.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL025PA2]
 gi|328760854|gb|EGF74420.1| RNA polymerase principal sigma factor HrdB [Propionibacterium acnes
           HL099PA1]
          Length = 511

 Score = 85.5 bits (210), Expect = 8e-15,   Method: Compositional matrix adjust.
 Identities = 80/325 (24%), Positives = 144/325 (44%), Gaps = 65/325 (20%)

Query: 7   SIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYR---------------------- 42
           +++V G     +  Y+ +I K+ +L   EE  LAKR                        
Sbjct: 203 TVMVAGATADPVKDYLKQIGKVALLNAVEEVDLAKRIEAGLFAGEQLADPDAKIREKDRE 262

Query: 43  ------EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                 E G ++  H L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  
Sbjct: 263 DYEWIAEDGKVAKNH-LLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYT 321

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQ 147
           +G++ +TY+ WWIK A+   +      ++I              Q+++  +L R     +
Sbjct: 322 KGYKFSTYATWWIKQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEE 381

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLV 205
             ++ ++  E+V+ + K       E IS++  L   GD     LI  S+          +
Sbjct: 382 LASELDMTAEKVIEVQKYGR----EPISLHTPLGEDGDSEFGDLIEDSE---------AI 428

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFE 263
              D     L++++        L   +  L+ RE  +   R       P TL+ +   + 
Sbjct: 429 VPADAVNFTLLQEQ--------LHDVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYG 480

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           V+RER+RQIE++   K++   + QV
Sbjct: 481 VTRERIRQIESKTMSKLRHPSRSQV 505


>gi|67925121|ref|ZP_00518496.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
 gi|67853040|gb|EAM48424.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
          Length = 374

 Score = 85.5 bits (210), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 72/247 (29%), Positives = 120/247 (48%), Gaps = 21/247 (8%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           +R H    A  +++ S+LRLVV IA  Y   G+P  +++ EG IGL +A +KFDP +G++
Sbjct: 128 HRLHKGRIAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPNKGYK 187

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      +++     +K     L +LK   + +     +     
Sbjct: 188 FSTYAYWWIRQAITRTIANDARTIRLPIHVVEK-----LNKLKKAQRVLKQKLQRNPNEK 242

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A +L V+  ++  +        SLN  +   +   ++  D L      ++Q L   EE
Sbjct: 243 ELADELEVTPPQLRQLLQLRRQSLSLNHRVGKGE--DTELVDLL------EDQDLQLPEE 294

Query: 221 RKNRRNMLTRSMS-----VLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIE 273
             N   ML   +S     VL  RE+ +   R       P TLE +   F +SRERVRQI+
Sbjct: 295 LMN-EGMLQYEVSAVLSDVLTQREKDVISLRYGLCTSQPHTLEEVGGIFNLSRERVRQIQ 353

Query: 274 ARAFKKV 280
           ++A +K+
Sbjct: 354 SKAMRKL 360


>gi|258593489|emb|CBE69828.1| RNA polymerase sigma factor rpoD (Sigma-80) [NC10 bacterium 'Dutch
           sediment']
          Length = 654

 Score = 85.5 bits (210), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 69/235 (29%), Positives = 120/235 (51%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ WW
Sbjct: 416 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMRAVDKFEYQRGYKFSTYATWW 475

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           ++ A+   I      ++I    +       L R   +L         PE+   IA+K+++
Sbjct: 476 VRQAITRAIADQARTIRI--PVHMIETINKLTRASRYLVQEFGREPTPEE---IAQKIDL 530

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +  ++A  E ++      ++  S   D++    D      IE     N     
Sbjct: 531 PVDKVRKV-LKIA-QEPISLETPIGEEEGSHLGDFI---EDKGVISPIEAVIGMNLSGQT 585

Query: 229 TRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            + +  L  RE++I + R  L +    TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 586 EQVLETLTEREQKILKLRFGLGDGRDHTLEEVGQQFDVTRERIRQIEAKALRKLR 640


>gi|281421843|ref|ZP_06252842.1| RNA polymerase sigma-70 factor [Prevotella copri DSM 18205]
 gi|281404085|gb|EFB34765.1| RNA polymerase sigma-70 factor [Prevotella copri DSM 18205]
          Length = 136

 Score = 85.5 bits (210), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 46/119 (38%), Positives = 76/119 (63%), Gaps = 9/119 (7%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           RY+ +I + P+L   EE  LA++ R+ G     A  +L+ ++LR VV +A  Y+  GL +
Sbjct: 17  RYLMKIGREPLLSHDEELELARKIRKGGSEGERAKEKLIRANLRFVVSVAKRYQHRGLAL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGT 128
           ++++ EGNIGL++AV++FD  RGF+   Y++WWI+ ++      Q +I R  SL KIG+
Sbjct: 77  TDLIDEGNIGLIKAVERFDETRGFKFIQYAIWWIRQSILQAIAEQNHITRI-SLDKIGS 134


>gi|50842515|ref|YP_055742.1| RNA polymerase sigma factor [Propionibacterium acnes KPA171202]
 gi|289425323|ref|ZP_06427100.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes SK187]
 gi|289427207|ref|ZP_06428923.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes J165]
 gi|295130592|ref|YP_003581255.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes SK137]
 gi|50840117|gb|AAT82784.1| RNA polymerase principal sigma factor HrdB [Propionibacterium acnes
           KPA171202]
 gi|289154301|gb|EFD02989.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes SK187]
 gi|289159676|gb|EFD07864.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes J165]
 gi|291377120|gb|ADE00975.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes SK137]
 gi|332675432|gb|AEE72248.1| RNA polymerase principal sigma factor HrdB [Propionibacterium acnes
           266]
          Length = 506

 Score = 85.5 bits (210), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 80/325 (24%), Positives = 144/325 (44%), Gaps = 65/325 (20%)

Query: 7   SIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYR---------------------- 42
           +++V G     +  Y+ +I K+ +L   EE  LAKR                        
Sbjct: 198 TVMVAGATADPVKDYLKQIGKVALLNAVEEVDLAKRIEAGLFAGEQLADPDAKIREKDRE 257

Query: 43  ------EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                 E G ++  H L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  
Sbjct: 258 DYEWIAEDGKVAKNH-LLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYT 316

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQ 147
           +G++ +TY+ WWIK A+   +      ++I              Q+++  +L R     +
Sbjct: 317 KGYKFSTYATWWIKQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEE 376

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLV 205
             ++ ++  E+V+ + K       E IS++  L   GD     LI  S+          +
Sbjct: 377 LASELDMTAEKVIEVQKYGR----EPISLHTPLGEDGDSEFGDLIEDSE---------AI 423

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFE 263
              D     L++++        L   +  L+ RE  +   R       P TL+ +   + 
Sbjct: 424 VPADAVNFTLLQEQ--------LHDVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYG 475

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           V+RER+RQIE++   K++   + QV
Sbjct: 476 VTRERIRQIESKTMSKLRHPSRSQV 500


>gi|260590675|ref|ZP_05856133.1| RNA polymerase sigma-70 factor [Prevotella veroralis F0319]
 gi|260537416|gb|EEX20033.1| RNA polymerase sigma-70 factor [Prevotella veroralis F0319]
          Length = 290

 Score = 85.5 bits (210), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 40/114 (35%), Positives = 71/114 (62%), Gaps = 2/114 (1%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYG 72
            L +Y+ EI + PM+   EE  LA+   + G     A  +L+ ++LR VV +A  Y+  G
Sbjct: 17  ALDKYLVEIGREPMITVDEEIELAQEIHKGGRKGERAKEKLIKANLRFVVSVAKQYQHQG 76

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           L +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V++
Sbjct: 77  LSLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRL 130


>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 = 85.5 bits (210), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 63/246 (25%), Positives = 119/246 (48%), Gaps = 36/246 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   G+   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 427 AKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEGNIGLMKAVDKFEYRRGWKFSTYATWW 486

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           ++ A+   +      +++    +       L R+   +   T     P     +A+++ +
Sbjct: 487 VRQAVTRSLADQARTIRV--PVHMIETINKLNRISREILQQTGQEAHP---AVLAERMEL 541

Query: 169 SESEV----------ISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           SE +V          +S+   +   GD +L  +I  +  +S           D   Q   
Sbjct: 542 SEEKVRGILKIAKQPVSLETPVGDDGDATLGDMIEDAAVSSPA---------DAAMQA-- 590

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEA 274
                 + R  +  ++  L+PRE ++   R     ++  TLE +  +F+V+RER+RQIE+
Sbjct: 591 ------DLRAAIDDALDSLSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIRQIES 644

Query: 275 RAFKKV 280
           +A +K+
Sbjct: 645 KAMRKL 650


>gi|86145220|ref|ZP_01063551.1| RpoS-like sigma factor [Vibrio sp. MED222]
 gi|85836797|gb|EAQ54917.1| RpoS-like sigma factor [Vibrio sp. MED222]
          Length = 298

 Score = 85.5 bits (210), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 73/278 (26%), Positives = 142/278 (51%), Gaps = 23/278 (8%)

Query: 17  SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY---RGYGL 73
           + Y+ +I  I +L +++E   AK  R  GD  A   ++ S+LRLVVKIA  Y   +G   
Sbjct: 30  AHYLKDIVGIDLLSREDELYYAKLNRA-GDKHARDIMIESNLRLVVKIAKSYLKRKGNNF 88

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++ EGNIGL++A+ K+DPE G+R +TY++WWI+  ++  ++     V++     ++
Sbjct: 89  TLLDLIEEGNIGLIKAIDKYDPEPGYRFSTYAVWWIRENIEAALMNKGRTVRLPAHVCKE 148

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS--ESEVISMNCRLAGDESLNALIN 191
                 ++L        D + K  + ++I++  N+S  ++E +     L+G   +   + 
Sbjct: 149 INSLASKKL--------DVSKKMRKEISISELSNISGVKAERVDQLVALSGFIDVTTTVG 200

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQE 250
            S       Q    Y  D Q+       E ++  + L + ++ L P+ +++   R    +
Sbjct: 201 ISHAPLVLEQCESEYIPDPQQDC-----EDQSFTHALEQIINTLPPKLQKVLIHRFGFFD 255

Query: 251 NPV-TLENLSS--EFEVSRERVRQIEARAFKKVQESIQ 285
           N V TL  +    +  VS ERVRQ++  A +++Q+ ++
Sbjct: 256 NKVKTLSEVGQMLDVNVSNERVRQMQKEAVERIQKRLK 293


>gi|282859310|ref|ZP_06268422.1| sigma-70 region 2 [Prevotella bivia JCVIHMP010]
 gi|282587890|gb|EFB93083.1| sigma-70 region 2 [Prevotella bivia JCVIHMP010]
          Length = 290

 Score = 85.5 bits (210), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 40/114 (35%), Positives = 71/114 (62%), Gaps = 2/114 (1%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYG 72
            L +Y+ EI + PM+   EE  LA+   + G     A  +L+ ++LR VV +A  Y+  G
Sbjct: 17  ALDKYLVEIGREPMITVDEEIELAQEIHKGGRKGERAKEKLIKANLRFVVSVAKQYQHQG 76

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           L +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V++
Sbjct: 77  LSLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRL 130


>gi|297243591|ref|ZP_06927522.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Gardnerella vaginalis AMD]
 gi|296888342|gb|EFH27083.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Gardnerella vaginalis AMD]
          Length = 489

 Score = 85.5 bits (210), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 69/251 (27%), Positives = 125/251 (49%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ WW
Sbjct: 251 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 310

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH-LQAI----TDNNLKPEQVVAIA 163
           I+ A+   +      +++    +   +   L R++   LQ +    T + L  E  + + 
Sbjct: 311 IRQAITRAMADQARTIRV--PVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVE 368

Query: 164 KKLNVSE--SEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           K   V +   E IS++  L   GD     LI  +D          +   D     L++++
Sbjct: 369 KVQEVQKYGREPISLHTPLGEDGDSEFGDLIEDTDA---------IAPSDAVAFSLLQEQ 419

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
            R+         +  L PRE  + + R   E+  P TL+++   + V+RER+RQIE++  
Sbjct: 420 FRQ--------VLETLAPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTM 471

Query: 278 KKVQESIQKQV 288
            K++   + Q 
Sbjct: 472 SKLRHPSRSQT 482


>gi|186681941|ref|YP_001865137.1| RpoD family RNA polymerase sigma factor [Nostoc punctiforme PCC
           73102]
 gi|186464393|gb|ACC80194.1| RNA polymerase, sigma 70 subunit, RpoD family [Nostoc punctiforme
           PCC 73102]
          Length = 339

 Score = 85.5 bits (210), Expect = 9e-15,   Method: Compositional matrix adjust.
 Identities = 58/231 (25%), Positives = 114/231 (49%), Gaps = 13/231 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +++ ++LRLVV +A  Y+   L   +++ EG +GL + V KFDP  G++ +TY+ WW
Sbjct: 104 AKQKMIQANLRLVVAVAKKYQHRNLEFMDLIQEGTLGLERGVDKFDPALGYKFSTYAYWW 163

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   I +    +++        +F  L ++K   + ++    +      IA  L++
Sbjct: 164 IRQGITRAIAQQGRTIRLPI-----HVFEKLNKIKRVQRELSQQLGRVPTTAEIANALSL 218

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           + S+V    C     +  +      ++  ++ QD L  D    E   +E+   ++ +++L
Sbjct: 219 TPSQV--RECLYLARQPFSLEARVGEQQDTELQDILEDDGPSPEDYAVEESLHQDLQDLL 276

Query: 229 TRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAF 277
            +    L+P++R I   R  L +   ++L  +     +SRERVRQIE +A 
Sbjct: 277 AK----LSPQQREILTLRFGLTDGYELSLAQIGDRMGISRERVRQIEQKAL 323


>gi|325269444|ref|ZP_08136061.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           multiformis DSM 16608]
 gi|325855020|ref|ZP_08171736.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           denticola CRIS 18C-A]
 gi|327313288|ref|YP_004328725.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           denticola F0289]
 gi|324988365|gb|EGC20331.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           multiformis DSM 16608]
 gi|325483998|gb|EGC86938.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           denticola CRIS 18C-A]
 gi|326946004|gb|AEA21889.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           denticola F0289]
          Length = 290

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 40/114 (35%), Positives = 71/114 (62%), Gaps = 2/114 (1%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYG 72
            L +Y+ EI + PM+   EE  LA+   + G     A  +L+ ++LR VV +A  Y+  G
Sbjct: 17  ALDKYLVEIGREPMITVDEEIELAQEIHKGGRKGERAKEKLIKANLRFVVSVAKQYQHQG 76

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           L +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V++
Sbjct: 77  LSLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRL 130


>gi|68536171|ref|YP_250876.1| RNA polymerase sigma factor SigB [Corynebacterium jeikeium K411]
 gi|260578869|ref|ZP_05846775.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           jeikeium ATCC 43734]
 gi|68263770|emb|CAI37258.1| RNA polymerase sigma factor B [Corynebacterium jeikeium K411]
 gi|258603016|gb|EEW16287.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           jeikeium ATCC 43734]
          Length = 343

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 77/284 (27%), Positives = 139/284 (48%), Gaps = 37/284 (13%)

Query: 13  EIGL-SRYI-HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           E+GL S Y+     K+   +K++  VLA+     G  + +H L+ ++LRLVV +A  Y G
Sbjct: 73  EVGLYSEYLLSNAEKLTRAKKRDLKVLAR----EGKAARSH-LLEANLRLVVSLAKRYTG 127

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A+   +      +++    
Sbjct: 128 RGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHL 187

Query: 131 NQKRLFFNLRRLKGHL-----QAITDNNLKPEQVVAIAK-KLNVSES-EVISMNCRLAGD 183
            ++     L R+K  +     +  T+  L  E  +  +K ++ + +S + +S++  +  D
Sbjct: 188 VEQ--VNKLSRIKREMYQQLGREATNEELSEESGIEESKIEMLLKQSRDPVSLDMPVGSD 245

Query: 184 ES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           E   L   I  SD   ++        H     VL                   L  RE+ 
Sbjct: 246 EEAPLGDFIEDSDATDAETAVVASLRHSDVRAVL-----------------GTLEEREQD 288

Query: 242 IFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           + + R   ++  P TL+ +   F +SRERVRQIE     K++E 
Sbjct: 289 VIKLRYGLDDGMPRTLDQIGRRFGLSRERVRQIEREVMAKLREG 332


>gi|296268951|ref|YP_003651583.1| RpoD subfamily RNA polymerase sigma-70 [Thermobispora bispora DSM
           43833]
 gi|296091738|gb|ADG87690.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobispora
           bispora DSM 43833]
          Length = 311

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 49/147 (33%), Positives = 79/147 (53%), Gaps = 29/147 (19%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKR-----YREH-----------GDLS----------- 48
           L  Y+ EI ++P+L  +EE  LAKR     + E+           GD +           
Sbjct: 18  LGTYLAEIGRVPLLTAEEEVELAKRIEAGLFAEYLLDSALTEPRIGDATDEELERIAISG 77

Query: 49  --AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A    + ++LRLVV +A  Y G G+P+ ++V EGN+GL++AV+KFD  RG++ +TY+ 
Sbjct: 78  RRAKDEFIKANLRLVVAVARKYAGRGMPLIDLVQEGNVGLVRAVEKFDYRRGYKFSTYAT 137

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQK 133
           WWI+ A+   I      V++ T A ++
Sbjct: 138 WWIRQAVGRSIHEQGRPVRLPTHAGEQ 164


>gi|283783165|ref|YP_003373919.1| RNA polymerase sigma factor RpoD [Gardnerella vaginalis 409-05]
 gi|283441732|gb|ADB14198.1| RNA polymerase sigma factor RpoD [Gardnerella vaginalis 409-05]
          Length = 489

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 69/251 (27%), Positives = 125/251 (49%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ WW
Sbjct: 251 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 310

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH-LQAI----TDNNLKPEQVVAIA 163
           I+ A+   +      +++    +   +   L R++   LQ +    T + L  E  + + 
Sbjct: 311 IRQAITRAMADQARTIRV--PVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVE 368

Query: 164 KKLNVSE--SEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           K   V +   E IS++  L   GD     LI  +D          +   D     L++++
Sbjct: 369 KVQEVQKYGREPISLHTPLGEDGDSEFGDLIEDTDA---------IAPSDAVAFSLLQEQ 419

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
            R+         +  L PRE  + + R   E+  P TL+++   + V+RER+RQIE++  
Sbjct: 420 FRQ--------VLETLAPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTM 471

Query: 278 KKVQESIQKQV 288
            K++   + Q 
Sbjct: 472 SKLRHPSRSQT 482


>gi|239996603|ref|ZP_04717127.1| RNA polymerase sigma factor [Alteromonas macleodii ATCC 27126]
          Length = 382

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 72/246 (29%), Positives = 123/246 (50%), Gaps = 34/246 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 144 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 203

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-KRLFFNLRRLKGH---LQAITDNNLKPEQVV 160
           I+ A+   I      ++I      T N+  R+   + +  G     + +++  L PE   
Sbjct: 204 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELSERMLMPED-- 261

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++      ++  +I+  +
Sbjct: 262 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI------EDSTIIQPLD 302

Query: 221 RKNRRNMLTRSMSV---LNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEAR 275
                ++   +  V   L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+
Sbjct: 303 SATGGSLKDATQEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 362

Query: 276 AFKKVQ 281
           A +K++
Sbjct: 363 ALRKLR 368


>gi|317969234|ref|ZP_07970624.1| RNA polymerase sigma factor, sigma-70 family protein [Synechococcus
           sp. CB0205]
          Length = 311

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 70/241 (29%), Positives = 120/241 (49%), Gaps = 17/241 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG R +TY+ WW
Sbjct: 66  AKDQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSTYAYWW 125

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP-EQVVAIAKKLN 167
           I+  +   +      ++I    N+K     LR  K  L  +  N + P  Q +A A  L 
Sbjct: 126 IRQGLNRALSTQSRTIRIPVNVNEK--LTRLRAAKARL--MQRNGMAPNSQQLATALGLP 181

Query: 168 VSESEVISMNCRL-AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           + E E + + C L +   SL  ++ S    +      LV     ++   +E+ E   R  
Sbjct: 182 LDEIEDL-LGCELRSVTVSLQGIVKSKSDPTE-----LVDVLPSEDLPPMERCELAERNA 235

Query: 227 MLTRSM--SVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            + + +  S L P+ER +   R   +      TL  ++     SRE  RQ+  RA +K++
Sbjct: 236 AVWKLLDQSNLTPKERTVVMLRFGLDGSHEWRTLAEVARLLGCSREYCRQVVQRALRKLR 295

Query: 282 E 282
           +
Sbjct: 296 K 296


>gi|221134905|ref|ZP_03561208.1| RNA polymerase, sigma 70 subunit, RpoD [Glaciecola sp. HTCC2999]
          Length = 607

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 69/246 (28%), Positives = 122/246 (49%), Gaps = 34/246 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 369 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 428

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQ-KRLFFNLRRLKGH---LQAITDNNLKPEQVV 160
           I+ A+   I      ++I      T N+  R+   + +  G     + +++  + PE   
Sbjct: 429 IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEMGREPTPEELSERMIMPED-- 486

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I K L +++ E ISM   +  DE             S   D++      ++  +I+  +
Sbjct: 487 KIRKVLKIAK-EPISMETPIGDDE------------DSHLGDFI------EDNTIIQPLD 527

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQ-----ENPVTLENLSSEFEVSRERVRQIEAR 275
                ++   +  VL    +R  +  R++         TLE +  +F+V+RER+RQIEA+
Sbjct: 528 SATGGSLKDATQDVLAGLTQREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAK 587

Query: 276 AFKKVQ 281
           A +K++
Sbjct: 588 ALRKLR 593


>gi|78184480|ref|YP_376915.1| type II alternative RNA polymerase sigma factor [Synechococcus sp.
           CC9902]
 gi|78168774|gb|ABB25871.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. CC9902]
          Length = 309

 Score = 85.5 bits (210), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 72/248 (29%), Positives = 120/248 (48%), Gaps = 29/248 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A ++++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG R +TY+ WW
Sbjct: 67  AKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSTYAYWW 126

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   +      ++I    N+K     LR  K  +          EQ   +A+ +NV
Sbjct: 127 IRQGLNRALSTQSRTIRIPVNVNEK--LTKLRAAKARIMQRNGLTATGEQ---LAEFMNV 181

Query: 169 SESEVIS-MNCRL-AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             +EV   + C L +   SL  ++ S   + S+  D L  D        I   ER     
Sbjct: 182 PLTEVEDLLACELRSVTVSLQGIVKSKS-DPSELVDILPSDE-------IPPMERA---E 230

Query: 227 MLTRSMSV--------LNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEAR 275
           +  RS SV        L P+E ++   R   +      TL  ++     SRE  RQ+  R
Sbjct: 231 IAERSASVWALLSKANLTPKEHKVVTLRFGLDGTNEWRTLAEVARHMNCSREYCRQVVQR 290

Query: 276 AFKKVQES 283
           A +K++++
Sbjct: 291 ALRKLRKT 298


>gi|289178873|gb|ADC86119.1| HrdB [Bifidobacterium animalis subsp. lactis BB-12]
          Length = 522

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 75/302 (24%), Positives = 147/302 (48%), Gaps = 45/302 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH-----GDL-----------------SAAH 51
           Y+ +I ++ +L  ++E  L++R     Y +H     GD                   A  
Sbjct: 227 YLKQIGRVSLLNAEQEVDLSERIEAGLYAQHLLDTEGDTMEFRRKRELKWAAADGKKAKD 286

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ WWI+ 
Sbjct: 287 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWWIRQ 346

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           A+   +      +++    +   +   L R++  +         P++   +A++L++   
Sbjct: 347 AITRAMADQARTIRV--PVHMVEVINKLSRVQRQMLQDLGREPTPDE---LARELDMPVE 401

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG---QEQVLIEKEERKNRRNML 228
           +V     +  G E ++      +   S++ D L+ D D     E V     + + R+ + 
Sbjct: 402 KV--QEVQKYGREPISLHTPLGEDGDSEFGD-LIEDTDAIAPSEAVAFSLLQEQFRQVLE 458

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           T     L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++   K++   + 
Sbjct: 459 T-----LSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRS 513

Query: 287 QV 288
           Q 
Sbjct: 514 QT 515


>gi|218962087|ref|YP_001741862.1| RNA polymerase sigma factor [Candidatus Cloacamonas
           acidaminovorans]
 gi|167730744|emb|CAO81656.1| RNA polymerase sigma factor [Candidatus Cloacamonas
           acidaminovorans]
          Length = 579

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 65/238 (27%), Positives = 119/238 (50%), Gaps = 17/238 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A + ++ +++RLV+ IA  Y   GL   +++ EGN GLM+AV+K+D  +G++ +TY+ WW
Sbjct: 336 AQNEMIEANVRLVISIAKHYNNRGLEFLDLIQEGNTGLMRAVEKYDYRKGYKFSTYATWW 395

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I     +      + R    L         PE+   I++ L++
Sbjct: 396 IRQAITRAIADQARTIRIPVHMIES--INKINRTSRRLMQKLGREPYPEE---ISEVLDI 450

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE---ERKNRR 225
              ++ ++        SL+  I   D   S   D++      +++ +I  E   ER   +
Sbjct: 451 PVEKIKNIMSISKEPVSLDKPI-GHDSEDSILGDFI------EDRTIISPERLAERSLLK 503

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
             +   +  L PRE R+   R   ++    TLE + + F+V+RER+RQIE +A KK++
Sbjct: 504 KQVDEVLKTLTPREERVIRLRFGIDDGYHRTLEEVGNIFQVTRERIRQIEDKALKKLR 561


>gi|67810071|gb|AAY81984.1| RNase polymerase sigma factor [Wolbachia pipientis]
          Length = 571

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 75/254 (29%), Positives = 122/254 (48%), Gaps = 27/254 (10%)

Query: 32  QEEYVLAKRYREHG-DLS-AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           QE   L KR ++H  ++S A   ++ ++LRLVV IA  Y   GL + +++ EGNIGLM+A
Sbjct: 334 QEFKELIKRIQKHEREVSEAKQEMIKANLRLVVSIAKKYSKRGLDLLDLIQEGNIGLMKA 393

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ--KRLFFNLRRLKGHL- 146
           V KFD +RG++ +TY  WW++ ++   I     +V+I     +   ++   LR++   + 
Sbjct: 394 VDKFDYKRGYKFSTYGTWWVRQSITRAIPEQSKVVRIPVHMVEIISKINRALRKMTHEMG 453

Query: 147 QAITDNNLKPEQVVA---IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
           +  T   L  E  +    I K + ++   V S+      D+S        DK  S+ +D 
Sbjct: 454 REPTLEELSVELTMPLERIRKVMKIARDPV-SLEAPTGKDDSSTFGDCIEDKRVSRPEDA 512

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSS 260
            +                 + R + T  ++ L P+E RI   R          TLE +  
Sbjct: 513 AIL---------------ADLRGITTNVLATLTPKEERILRMRFGLGKDGKEHTLEEVGK 557

Query: 261 EFEVSRERVRQIEA 274
            F V+RER+RQIEA
Sbjct: 558 IFNVTRERIRQIEA 571


>gi|297843640|ref|XP_002889701.1| hypothetical protein ARALYDRAFT_470915 [Arabidopsis lyrata subsp.
           lyrata]
 gi|297335543|gb|EFH65960.1| hypothetical protein ARALYDRAFT_470915 [Arabidopsis lyrata subsp.
           lyrata]
          Length = 572

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 66/242 (27%), Positives = 128/242 (52%), Gaps = 17/242 (7%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           HG L    +++ S++RLV+ IA  Y+G G+ + ++V EG  GL++  +KFD  +GF+ +T
Sbjct: 328 HGTL-CKDKMIKSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKGFKFST 386

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWIK A+++ +     ++++    +     + ++  +  L + T  + K E+   IA
Sbjct: 387 YAHWWIKQAVRKSLSDQSRMIRL--PFHMVEATYRVKEARKQLYSETGKHPKNEE---IA 441

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG--QEQVLIEKEER 221
           +   +S   ++++        SL+  I     N +     ++ D +    E +LI++  R
Sbjct: 442 EATGLSMKRLMAVLLSPKPPRSLDQKIG---MNQNLKPSEVIADPEAVTSEDILIKEFMR 498

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKK 279
           ++    L + +  L  RE+++   R   E+    TL+ +     VSRERVRQIE+ AF+K
Sbjct: 499 QD----LDKVLDSLGTREKQVIRWRFGMEDGRMKTLQEIGEMMGVSRERVRQIESSAFRK 554

Query: 280 VQ 281
           ++
Sbjct: 555 LK 556


>gi|257457793|ref|ZP_05622954.1| RNA polymerase sigma factor RpoD [Treponema vincentii ATCC 35580]
 gi|257444843|gb|EEV19925.1| RNA polymerase sigma factor RpoD [Treponema vincentii ATCC 35580]
          Length = 607

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 79/262 (30%), Positives = 125/262 (47%), Gaps = 40/262 (15%)

Query: 36  VLAKRYREHGDL---SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
            LAK  R HG      A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 354 ALAKEIR-HGHAMLKKAKDKLINANLRLVVSIAKKYTNRGLHFFDLVQEGNIGLIKAVEK 412

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI---------GTTANQKRLFFNLRRLK 143
           F+  +G++ +TY+ WWI+ A+   I      +++           T   ++L     R  
Sbjct: 413 FEYRKGYKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINKVTRESRQLMQKFGREP 472

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSD-KNSSQW 200
              +         E+V  +    NV+  E IS+   +  +E  SL   I   D +N S  
Sbjct: 473 TDEEIAVQLGWNVERVKQVK---NVA-REPISLETPIGEEEDSSLGDFIEDKDVENPSNL 528

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENL 258
            ++++     QEQ              L   +S L  RE+ + + R  L E   +TLE +
Sbjct: 529 TEYILL----QEQ--------------LRSVLSCLPLREQEVLKMRFGLDEGYALTLEEV 570

Query: 259 SSEFEVSRERVRQIEARAFKKV 280
              F V+RER+RQIEA+A +++
Sbjct: 571 GLYFNVTRERIRQIEAKALRRL 592


>gi|224068757|ref|XP_002326192.1| predicted protein [Populus trichocarpa]
 gi|222833385|gb|EEE71862.1| predicted protein [Populus trichocarpa]
          Length = 535

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 63/243 (25%), Positives = 128/243 (52%), Gaps = 28/243 (11%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +L+ ++LR+VV IA  Y+  GL + +++ EG +GLM++++KF P+ G R ATY+ WWI+ 
Sbjct: 298 KLINANLRMVVHIAKRYQNRGLGLQDLLQEGTVGLMKSIEKFKPQAGCRFATYAYWWIRQ 357

Query: 112 AMQEYILRSWSLVK--------IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
            + + I +    ++        +G     KR +            I + N +P     IA
Sbjct: 358 TITKAIFQHSRTIRLPENVYGLLGKVMEAKRSY------------IQEGNHQP-TAEEIA 404

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           +++ ++  ++  + C      S+   +  SD+N++  +     + +  +  + ++  RK+
Sbjct: 405 RRVGIAIDKLEKLLCFTRTPLSMQQTV-WSDQNTTFQEITADTEIEIPDMSVAKQLMRKH 463

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R +L    ++L+ +ERRI   R   E+    +L  + + F +S+ERVRQ+E+RA  K++
Sbjct: 464 IRGLL----NILSLKERRIIRLRFGIEDGKQKSLSEIGNVFGLSKERVRQLESRALYKLK 519

Query: 282 ESI 284
           + +
Sbjct: 520 QCV 522


>gi|255565968|ref|XP_002523972.1| RNA polymerase sigma factor rpoD1, putative [Ricinus communis]
 gi|223536699|gb|EEF38340.1| RNA polymerase sigma factor rpoD1, putative [Ricinus communis]
          Length = 569

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 69/249 (27%), Positives = 133/249 (53%), Gaps = 31/249 (12%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           HG +    +++ S++RLV+ IA  Y+G G+ + ++V EG  GL++  +KFD  +GF+ +T
Sbjct: 327 HGTI-CKDKMIKSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDASKGFKFST 385

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL-----RRLKGHLQAITDNNLKP-E 157
           Y+ WWIK A+++          +   +   RL F++     R  +   Q  ++N   P +
Sbjct: 386 YAHWWIKQAVRK---------SLSDQSRTIRLPFHMVEATYRVKEARKQLYSENGRHPDD 436

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQ--EQV 214
           + VA A  L++     + +  +     SL+  I  + D   S+    ++ D + +  E++
Sbjct: 437 EEVAEAAGLSMKRLSAVLLTPK--APRSLDQKIGMNMDLKPSE----VIADPEAETAEEL 490

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQI 272
           L+++  +++    L + ++ LNPRE ++   R   E+    TL+ +     VSRER+RQI
Sbjct: 491 LMKQFMKQD----LEKVLNTLNPRETQVVRWRFGLEDGRMKTLQEIGEIMGVSRERIRQI 546

Query: 273 EARAFKKVQ 281
           E+ AF+K++
Sbjct: 547 ESSAFRKLK 555


>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 = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 65/238 (27%), Positives = 119/238 (50%), Gaps = 18/238 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 367 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 426

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   + +++ +
Sbjct: 427 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEE---LGERMEM 481

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E +V  +  ++A  E ++      D   S   D++      ++Q +    +    + ++
Sbjct: 482 PEDKVRKV-LKIA-KEPISMETPIGDDEDSHLGDFI------EDQTINSPIDAATGQGLM 533

Query: 229 TRSMSV---LNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
             +  V   L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 534 EATKDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 591


>gi|15223259|ref|NP_172330.1| SIG2 (RNA POLYMERASE SIGMA SUBUNIT 2); DNA binding / DNA-directed
           RNA polymerase/ sigma factor/ transcription factor
           [Arabidopsis thaliana]
 gi|6664315|gb|AAF22897.1|AC006932_14 T27G7.22 [Arabidopsis thaliana]
 gi|9802550|gb|AAF99752.1|AC003981_2 F22O13.2 [Arabidopsis thaliana]
 gi|2443357|dbj|BAA22427.1| SigB [Arabidopsis thaliana]
 gi|2597831|emb|CAA75584.1| sigma factor [Arabidopsis thaliana]
 gi|2879922|dbj|BAA24825.1| plastid RNA polymerase sigma-subunit [Arabidopsis thaliana]
 gi|5478446|dbj|BAA82449.1| sigma factor SigB [Arabidopsis thaliana]
 gi|133778838|gb|ABO38759.1| At1g08540 [Arabidopsis thaliana]
 gi|332190182|gb|AEE28303.1| RNApolymerase sigma subunit 2 [Arabidopsis thaliana]
          Length = 572

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 66/242 (27%), Positives = 128/242 (52%), Gaps = 17/242 (7%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           HG L    +++ S++RLV+ IA  Y+G G+ + ++V EG  GL++  +KFD  +GF+ +T
Sbjct: 328 HGTL-CKDKMIKSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKGFKFST 386

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWIK A+++ +     ++++    +     + ++  +  L + T  + K E+   IA
Sbjct: 387 YAHWWIKQAVRKSLSDQSRMIRL--PFHMVEATYRVKEARKQLYSETGKHPKNEE---IA 441

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG--QEQVLIEKEER 221
           +   +S   ++++        SL+  I     N +     ++ D +    E +LI++  R
Sbjct: 442 EATGLSMKRLMAVLLSPKPPRSLDQKIG---MNQNLKPSEVIADPEAVTSEDILIKEFMR 498

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKK 279
           ++    L + +  L  RE+++   R   E+    TL+ +     VSRERVRQIE+ AF+K
Sbjct: 499 QD----LDKVLDSLGTREKQVIRWRFGMEDGRMKTLQEIGEMMGVSRERVRQIESSAFRK 554

Query: 280 VQ 281
           ++
Sbjct: 555 LK 556


>gi|260435993|ref|ZP_05789963.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 8109]
 gi|260413867|gb|EEX07163.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 8109]
          Length = 309

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 73/260 (28%), Positives = 128/260 (49%), Gaps = 31/260 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A ++++TS+LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG R +TY+ WW
Sbjct: 67  AKNQMITSNLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSTYAYWW 126

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP--EQV-----VA 161
           I+  +   +      ++I    N+K     LR  K  L  +  N L P  EQ+     + 
Sbjct: 127 IRQGLNRALSTQSRTIRIPVNVNEK--LTKLRAAKARL--MQRNGLSPSGEQLAEFMEIP 182

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           IA+  ++   E+ S+   L G       +  S  + S+  D L      +E   +E+ E 
Sbjct: 183 IAEVEDLLACELRSVTVSLQG-------VVKSKSDPSELVDVL----PSEELPPLERAEI 231

Query: 222 KNRR----NMLTRSMSVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEA 274
             R     ++L ++   L P+E  +   R   +      TL  ++     SRE  RQ+  
Sbjct: 232 AERTASAWSLLAKAN--LTPKEHTVVTLRFGLDGTNEWRTLAEVARHMNCSREYCRQVVQ 289

Query: 275 RAFKKVQESIQKQVELSSSP 294
           RA +K++++  +   + S+P
Sbjct: 290 RALRKLRKTGIQSGLVESTP 309


>gi|297736323|emb|CBI24961.3| unnamed protein product [Vitis vinifera]
          Length = 319

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 67/249 (26%), Positives = 125/249 (50%), Gaps = 40/249 (16%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            R+  S+ RLVV IA  Y+G GL + +++ EG+IGL++  ++FDP+RG++L+TY  WWI+
Sbjct: 84  ERINQSYRRLVVSIAARYQGKGLSLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIR 143

Query: 111 AAM------QEYILR-SWSLVKIGTTANQKRLFFN--LRRLKGH--LQAITDNNLKPEQV 159
            A+      +  I+R   S+ ++     + R   +  LRRL  +  +    D N+   ++
Sbjct: 144 QAIVRAIANKSRIIRLPGSICEMVAKIAEARTVLSRRLRRLPTYDEIAEFIDVNVSTVRL 203

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           V+   +  +S  + ++      G  +L  +I   D+ + Q                 +  
Sbjct: 204 VSERSRTPISVDQAVTSQ----GCMTLQEIIPGPDETTPQ-----------------KMV 242

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRL-----QENPVTLENLSSEFEVSRERVRQIEA 274
           +R+  +  + R+++ L  RE  I    RL      E P++ E +    ++SRERVRQI +
Sbjct: 243 KRQLMKQEVERALNTLCEREAYIL---RLYFGINGETPLSFEEIGRLMKLSRERVRQINS 299

Query: 275 RAFKKVQES 283
            A  K++++
Sbjct: 300 IALSKLRQT 308


>gi|307565781|ref|ZP_07628247.1| sigma-70 region 2 [Prevotella amnii CRIS 21A-A]
 gi|307345508|gb|EFN90879.1| sigma-70 region 2 [Prevotella amnii CRIS 21A-A]
          Length = 290

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 40/114 (35%), Positives = 71/114 (62%), Gaps = 2/114 (1%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKIAMGYRGYG 72
            L +Y+ EI + PM+   EE  LA+   + G     A  +L+ ++LR VV +A  Y+  G
Sbjct: 17  ALDKYLVEIGREPMITVDEEIELAQEIHKGGLKGERAKEKLIKANLRFVVSVAKQYQHQG 76

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           L +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V++
Sbjct: 77  LSLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRL 130


>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 = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 64/234 (27%), Positives = 115/234 (49%), Gaps = 12/234 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 362 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 421

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   + +++++
Sbjct: 422 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEE---LGERMDM 476

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E +V  +  ++A  E ++      D   S   D++    D      ++    +  +   
Sbjct: 477 PEDKVRKV-LKIAK-EPISMETPIGDDEDSHLGDFI---EDNTIAQPVDSATGQGLQEAT 531

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 532 KDVLGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 585


>gi|88808921|ref|ZP_01124430.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 7805]
 gi|88786863|gb|EAR18021.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 7805]
          Length = 322

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 72/293 (24%), Positives = 134/293 (45%), Gaps = 34/293 (11%)

Query: 13  EIGLSRYIHEIRKIPMLEKQ------EEYVLAKRYREHGDLSAAH-------------RL 53
           EI L R + E+ ++  +E +       E VLA    +   LSA               R+
Sbjct: 31  EITLGRQVQELMELESVEAELQEKRGGEAVLAAELAKAAGLSAVQLKRKLQAGRRAKERM 90

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V ++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP RG++ +TY+ WWI+  +
Sbjct: 91  VAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWWIRQGI 150

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
              I      +++     +      L +LK   + ++    +   V  +A  + + E EV
Sbjct: 151 TRAIAEKSRTIRLPIHITE-----MLNKLKKGQRELSQELGRTPSVTELASFVELPEDEV 205

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSM 232
             + CR     SL   +   D + ++  D L  D +   EQV     E +  +  L   +
Sbjct: 206 KELMCRARQPVSLE--MKVGDGDDTELLDLLAGDGELPSEQV-----EGECLKGDLRDLL 258

Query: 233 SVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             L   + R+   R     E P++L  ++   ++SR+R R++E    + ++++
Sbjct: 259 GQLPELQERVLRMRYGMDGEEPMSLTGIAKTLKMSRDRTRRLEREGLQSLRQA 311


>gi|113474981|ref|YP_721042.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
 gi|110166029|gb|ABG50569.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
          Length = 496

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 60/237 (25%), Positives = 129/237 (54%), Gaps = 16/237 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++VT++LRLV  +A  Y+  GL   +++ EG IGL++A +KFD  +G++ +TY +WW
Sbjct: 261 AKNQMVTANLRLVTSVAKRYQNRGLDFQDLIQEGVIGLLRATEKFDHTKGYKFSTYGIWW 320

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I     +V++        L+  + ++K  ++ I+     P     +A ++ +
Sbjct: 321 IRQAITRAICDYSRIVRLPV-----YLYETISQIKKIVKQISI-ECSPLTAEEVATRMEM 374

Query: 169 SESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + +E +      A +  SL+  IN  +  +  +++ + ++ +   + + E   +++  ++
Sbjct: 375 T-TEKLQFIIECAQETLSLDYPINKGE--NIIYKEMIKFNGETPTKYVFENCLQEDVESV 431

Query: 228 LTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           L      L  RER + + R   ++    TL+ +   F ++RER+RQIEA+A +K+++
Sbjct: 432 L----KTLTERERNVLQMRFGLDDGQEKTLKEIGDTFNLTRERIRQIEAKALRKLED 484


>gi|226356403|ref|YP_002786143.1| RNA polymerase sigma factor, sigma-70 family [Deinococcus deserti
           VCD115]
 gi|226318393|gb|ACO46389.1| putative RNA polymerase sigma factor, sigma-70 family [Deinococcus
           deserti VCD115]
          Length = 547

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 75/293 (25%), Positives = 132/293 (45%), Gaps = 38/293 (12%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYRE--------------------------HGDLSAAH 51
           +Y+HEI ++ +L  +EE  LA+R  E                              +A  
Sbjct: 250 QYLHEIGRVSLLTLEEEIALARRIEEGEEARKLLEEDVELDDRGRRRLMRQMEDGANARQ 309

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV IA  Y G GL   +++ EGN GL++AV+KF+  R ++ +TY+ WWI+ 
Sbjct: 310 GLIEANLRLVVSIAKKYTGRGLGFLDLIQEGNQGLIRAVEKFEYRRRYKFSTYATWWIRQ 369

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-AIAKKLNVSE 170
           A+   I      ++I    +       L R    LQ         E++  A+    + ++
Sbjct: 370 AINRAIADQARTIRI--PVHMVETINKLTRTARQLQQELSREATHEEIAEAMGPGWDAAK 427

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            E +    +    E ++      D+  S + D++    D      +E   +      L +
Sbjct: 428 VEEVQKVSQ----EPVSLETPIGDEKDSFYGDFI---PDENLDSPVENAAKTLLSEELEK 480

Query: 231 SMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++S L  RE  + + R+  +     TLE +   F V+RER+RQIE +A +K++
Sbjct: 481 ALSKLTEREAMVLKFRKGLVDGREHTLEEVGQRFSVTRERIRQIENKALRKLK 533


>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 = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 65/235 (27%), Positives = 115/235 (48%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 367 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 426

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I    +       L R+   +         PE+   + +++ +
Sbjct: 427 IRQAITRSIADQARTIRI--PVHMIETINKLNRISRQMLQEMGREPTPEE---LGERMEM 481

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E +V  +  ++A  E ++      D   S   D++    D      I+    +  +   
Sbjct: 482 PEDKVRKV-LKIA-KEPISMETPIGDDEDSHLGDFI---EDQTIHSPIDSATGQGLQEAT 536

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 537 KDVLGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 591


>gi|293189827|ref|ZP_06608541.1| carbamoyl-phosphate synthase L chain, ATP-binding [Actinomyces
           odontolyticus F0309]
 gi|292821242|gb|EFF80187.1| carbamoyl-phosphate synthase L chain, ATP-binding [Actinomyces
           odontolyticus F0309]
          Length = 561

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 74/299 (24%), Positives = 142/299 (47%), Gaps = 39/299 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRY-------------------REHGDL--------SAAH 51
           Y+ +I K+ +L  ++E  LA+R                    RE  +L         A +
Sbjct: 267 YLKQIGKVSLLNAEQEVDLARRIEAGLYAEYKLKNQADEMTSRERRELHFLAQDGQQAKN 326

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 327 HLLEANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 386

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           A+   +      ++I    +   +   L R++  +         PE+   +AK+L+++  
Sbjct: 387 AITRAMADQARTIRI--PVHMVEVINKLARVQRQMLQDLGREPTPEE---LAKELDMTAE 441

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           +V+ +     G E ++      +   S++ D +    D +  V  +       +  L   
Sbjct: 442 KVVEVQKY--GREPISLHTPLGEDGDSEFGDLI---EDSEAIVPADAVSFTLLQEQLHHV 496

Query: 232 MSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +  L+ RE  +   R  L +  P TL+ +   + V+RER+RQIE++   K++   + QV
Sbjct: 497 LDTLSEREAGVVSMRFGLGDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQV 555


>gi|183982017|ref|YP_001850308.1| RNA polymerase sigma factor SigB [Mycobacterium marinum M]
 gi|183175343|gb|ACC40453.1| RNA polymerase sigma factor SigB [Mycobacterium marinum M]
          Length = 333

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 80/292 (27%), Positives = 140/292 (47%), Gaps = 56/292 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH--------GD-----LSAAHR-------- 52
           Y++ I K  +L  + E  LAKR     Y EH        GD     L+A  R        
Sbjct: 40  YLNGIGKTALLNAEGEVELAKRIEAGLYAEHLLATRKRLGDNRKRELAAVVRDGAEARRH 99

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A
Sbjct: 100 LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQA 159

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ-----AITDNNLKPEQVVAIAKKLN 167
           +   +      +++     ++     L R+K  +        TD  L  E  + + K  +
Sbjct: 160 ITRGMADQSRTIRLPVHLVEQ--VNKLARIKREMHQNLGREATDEELAAESGIPVEKIND 217

Query: 168 VSES--EVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + E   + +S++  +  +E   L   I  ++  S+             E  +I +    +
Sbjct: 218 LLEHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSA-------------ENAVIAELLHTD 264

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIE 273
            R++L    + L+ RE ++   R   ++  P TL+ +   F +SRERVRQIE
Sbjct: 265 IRSVL----ATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIE 312


>gi|225450015|ref|XP_002272444.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 426

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 67/249 (26%), Positives = 125/249 (50%), Gaps = 40/249 (16%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            R+  S+ RLVV IA  Y+G GL + +++ EG+IGL++  ++FDP+RG++L+TY  WWI+
Sbjct: 191 ERINQSYRRLVVSIAARYQGKGLSLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIR 250

Query: 111 AAM------QEYILR-SWSLVKIGTTANQKRLFFN--LRRLKGH--LQAITDNNLKPEQV 159
            A+      +  I+R   S+ ++     + R   +  LRRL  +  +    D N+   ++
Sbjct: 251 QAIVRAIANKSRIIRLPGSICEMVAKIAEARTVLSRRLRRLPTYDEIAEFIDVNVSTVRL 310

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           V+   +  +S  + ++      G  +L  +I   D+ + Q                 +  
Sbjct: 311 VSERSRTPISVDQAVTSQ----GCMTLQEIIPGPDETTPQ-----------------KMV 349

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRL-----QENPVTLENLSSEFEVSRERVRQIEA 274
           +R+  +  + R+++ L  RE  I    RL      E P++ E +    ++SRERVRQI +
Sbjct: 350 KRQLMKQEVERALNTLCEREAYIL---RLYFGINGETPLSFEEIGRLMKLSRERVRQINS 406

Query: 275 RAFKKVQES 283
            A  K++++
Sbjct: 407 IALSKLRQT 415


>gi|26452898|dbj|BAC43527.1| putative plastid RNA polymerase sigma-subunit SIG1 [Arabidopsis
           thaliana]
          Length = 572

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 66/242 (27%), Positives = 128/242 (52%), Gaps = 17/242 (7%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           HG L    +++ S++RLV+ IA  Y+G G+ + ++V EG  GL++  +KFD  +GF+ +T
Sbjct: 328 HGTL-CKDKMIKSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKGFKFST 386

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWIK A+++ +     ++++    +     + ++  +  L + T  + K E+   IA
Sbjct: 387 YAHWWIKQAVRKSLSDQSRMIRL--PFHMVEATYRVKEARKQLYSETGKHPKNEE---IA 441

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG--QEQVLIEKEER 221
           +   +S   ++++        SL+  I     N +     ++ D +    E +LI++  R
Sbjct: 442 EATGLSMKRLMAVLLSPKPPRSLDQKIG---MNQNLKPSEVIADPEAVTPEDILIKEFMR 498

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKK 279
           ++    L + +  L  RE+++   R   E+    TL+ +     VSRERVRQIE+ AF+K
Sbjct: 499 QD----LDKVLDSLGTREKQVIRWRFGMEDGRMKTLQEIGEMMGVSRERVRQIESSAFRK 554

Query: 280 VQ 281
           ++
Sbjct: 555 LK 556


>gi|313140538|ref|ZP_07802731.1| RNA polymerase principal sigma factor [Bifidobacterium bifidum
           NCIMB 41171]
 gi|313133048|gb|EFR50665.1| RNA polymerase principal sigma factor [Bifidobacterium bifidum
           NCIMB 41171]
          Length = 500

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 68/251 (27%), Positives = 125/251 (49%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ WW
Sbjct: 262 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 321

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH-LQAI----TDNNLKPEQVVAIA 163
           I+ A+   +      +++    +   +   L R++   LQ +    T + L  E  + + 
Sbjct: 322 IRQAITRAMADQARTIRV--PVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVE 379

Query: 164 KKLNVSE--SEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           K   V +   E IS++  L   GD     LI  +D          +   D     L++++
Sbjct: 380 KVQEVQKYGREPISLHTPLGEDGDSEFGDLIEDTD---------AIAPSDAVAFSLLQEQ 430

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
                     + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++  
Sbjct: 431 --------FKQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTM 482

Query: 278 KKVQESIQKQV 288
            K++   + Q 
Sbjct: 483 SKLRHPSRSQT 493


>gi|162458864|ref|NP_001104924.1| sigma-like factor2B [Zea mays]
 gi|4336608|gb|AAD17855.1| sigma factor SIG2B [Zea mays]
          Length = 527

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 66/256 (25%), Positives = 121/256 (47%), Gaps = 36/256 (14%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           +R   HG +   +R+V S++RLV+ IA  + G G+  S+++ +G  GL++  +KFD  +G
Sbjct: 277 RRRLNHG-VYCKNRMVKSNVRLVISIAKEHEGPGMEFSDLIQDGMQGLIRGAEKFDASKG 335

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ---------KRLFFNLRRLKGHLQAI 149
           FR +TYS WWIK A+++ +L    ++++     +         +RL   L+RL  + +  
Sbjct: 336 FRFSTYSHWWIKQAIRKSVLEQTQIIRLPAHMAEASSRVKECCRRLGRELKRLPSNEEIA 395

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI--NSSDKNSSQWQDWLVYD 207
            D  +   +V A       S S    + C    D +   ++   S++        WL+  
Sbjct: 396 VDTGMTIRRVEAAMSLPKYSVSFTSKVGCT---DVTYQEIMPDTSAETAEETLHRWLM-- 450

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVS 265
                            +  +  ++  L+PR++++   R   E     TL ++     VS
Sbjct: 451 -----------------KKDVNTALDSLSPRKKQVMRYRFGIEGGRARTLHDIGQLMGVS 493

Query: 266 RERVRQIEARAFKKVQ 281
           RER+RQIE  AF+K++
Sbjct: 494 RERIRQIELGAFRKLR 509


>gi|23295779|gb|AAN12882.1| principal sigma factor RpoD [Bifidobacterium animalis subsp.
           lactis]
          Length = 508

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 75/302 (24%), Positives = 147/302 (48%), Gaps = 45/302 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH-----GDL-----------------SAAH 51
           Y+ +I ++ +L  ++E  L++R     Y +H     GD                   A  
Sbjct: 213 YLKQIGRVSLLNAEQEVDLSERIEAGLYAQHLLDTEGDTMEFRRKRELKWAAADGKKAKD 272

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ WWI+ 
Sbjct: 273 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWWIRQ 332

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           A+   +      +++    +   +   L R++  +         P++   +A++L++   
Sbjct: 333 AITRAMADQARTIRV--PVHMVEVINKLSRVQRQMLQDLGREPTPDE---LARELDMPVE 387

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG---QEQVLIEKEERKNRRNML 228
           +V     +  G E ++      +   S++ D L+ D D     E V     + + R+ + 
Sbjct: 388 KV--QEVQKYGREPISLHTPLGEDGDSEFGD-LIEDTDAIAPSEAVAFSLLQEQFRQVLE 444

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           T     L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++   K++   + 
Sbjct: 445 T-----LSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRS 499

Query: 287 QV 288
           Q 
Sbjct: 500 QT 501


>gi|99034132|ref|ZP_01314232.1| hypothetical protein Wendoof_01000979 [Wolbachia endosymbiont of
           Drosophila willistoni TSC#14030-0811.24]
          Length = 148

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 52/135 (38%), Positives = 82/135 (60%), Gaps = 1/135 (0%)

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           L  E++ AI+ +L+VSE +V+ MN R+A  D+SLN  I   D +  + QD +  +   QE
Sbjct: 6   LNNEEIKAISNELSVSEGDVLQMNYRMACKDQSLNDCIKIGDDSKRELQDMIPCNLVSQE 65

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
                 EE++ +  +L  +++ LN R R IF +R L EN  TL+ LS ++ VSRER+RQ+
Sbjct: 66  VTYQNHEEKELKETILNNALASLNERARDIFISRYLSENIQTLDELSKKYCVSRERIRQL 125

Query: 273 EARAFKKVQESIQKQ 287
             +A  KV++ IQ +
Sbjct: 126 AEQAMAKVKQYIQSE 140


>gi|145295824|ref|YP_001138645.1| RNA polymerase sigma factor SigB [Corynebacterium glutamicum R]
 gi|12958494|gb|AAK09322.1|AF320818_1 sigma factor SigB [[Brevibacterium] flavum]
 gi|140845744|dbj|BAF54743.1| hypothetical protein [Corynebacterium glutamicum R]
          Length = 331

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 72/262 (27%), Positives = 130/262 (49%), Gaps = 31/262 (11%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++  VLAK     G  + +H L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A+
Sbjct: 81  KRDLKVLAK----DGKKARSH-LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAM 135

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK--RLFFNLRRLKGHL-Q 147
           +KFD  +GF+ +TY+ WWI+ A+   +      +++     ++  +L    R +  HL +
Sbjct: 136 EKFDYSKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQHLGR 195

Query: 148 AITDNNLKPEQVVAIAK--KLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDW 203
             T+  L  E  +  +K   L     + +S++  +  DE   L   I  S+   +     
Sbjct: 196 EATNEELAEESGIEESKIEMLLRQSRDPVSLDMPVGADEEAPLGDFIEDSEATDA----- 250

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSE 261
                   E  ++      + R +L    + L PRE+ +   R   ++  P TL+ +   
Sbjct: 251 --------ESAVVASMRHSDIRAVL----NTLEPREQDVIRLRYGLDDGVPRTLDQIGRR 298

Query: 262 FEVSRERVRQIEARAFKKVQES 283
           F +SRERVRQIE     K+++ 
Sbjct: 299 FGLSRERVRQIEREVMSKLRDG 320


>gi|16331222|ref|NP_441950.1| RNA polymerase sigma factor [Synechocystis sp. PCC 6803]
 gi|1001398|dbj|BAA10020.1| RNA polymerase sigma factor [Synechocystis sp. PCC 6803]
          Length = 345

 Score = 85.1 bits (209), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 68/314 (21%), Positives = 142/314 (45%), Gaps = 72/314 (22%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR--------------------------YREHGDLS---- 48
           Y+HEI ++P+L  ++E +L K+                          + E  DLS    
Sbjct: 40  YLHEIGRVPLLTHEQEIILGKQVQQMMALLEHKKALADRLGREPSDPEWAEAADLSVTKL 99

Query: 49  ---------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                    A  +++ ++LRLVV IA  Y+   +   +++ EG++GL + V+KFDP +G+
Sbjct: 100 HRYLGQGERAKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGSLGLERGVEKFDPTKGY 159

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWI+ A+   I +    +++     +K     L ++K   + ++    +    
Sbjct: 160 KFSTYAYWWIRQAITRAIAQQGRTIRLPIHITEK-----LNKIKKTQRELSQQLGRSATP 214

Query: 160 VAIAKKLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
             +AK L +  S++          IS++ R+             D   ++  + L  +  
Sbjct: 215 AEVAKALEIDPSQIREYLSLSRQPISLDVRVG------------DNQDTELSELLEDEGV 262

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRE 267
             +  + ++  R++ +N+L      L P+++ +   R  L +   ++L  +     +SRE
Sbjct: 263 SPDAYITQESMRQDLQNLLAE----LTPQQQAVLTMRFGLNDGQELSLAKIGQHLNISRE 318

Query: 268 RVRQIEARAFKKVQ 281
           RVRQ+E +A  +++
Sbjct: 319 RVRQLENQALAQLK 332


>gi|118463509|ref|YP_882780.1| RNA polymerase sigma factor SigB [Mycobacterium avium 104]
 gi|254776043|ref|ZP_05217559.1| RNA polymerase sigma factor SigB [Mycobacterium avium subsp. avium
           ATCC 25291]
 gi|118164796|gb|ABK65693.1| sigma factor SigB [Mycobacterium avium 104]
          Length = 319

 Score = 84.7 bits (208), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 81/300 (27%), Positives = 140/300 (46%), Gaps = 56/300 (18%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH-------------GDLSAAHR-------- 52
           Y++ I K  +L    E  LAKR     Y EH              DL A  R        
Sbjct: 26  YLNGIGKTALLNAAGEVELAKRIEAGLYAEHLLETRKRLGENRKRDLEAVVRDGQAARRH 85

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A
Sbjct: 86  LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQA 145

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ-----AITDNNLKPEQVVAIAKKLN 167
           +   +      +++     ++     L R+K  +        TD  L  E  + I K  +
Sbjct: 146 ITRGMADQSRTIRLPVHLVEQ--VNKLARIKREMHQNLGREATDEELAAESGIPIDKIND 203

Query: 168 VSES--EVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + E   + +S++  +  +E   L   I  ++  S+             E  +I +    +
Sbjct: 204 LLEHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSA-------------ENAVIAELLHTD 250

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R++L    + L+ RE ++   R   ++  P TL+ +   F +SRERVRQIE     K++
Sbjct: 251 IRSVL----ATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMSKLR 306


>gi|41408924|ref|NP_961760.1| RNA polymerase sigma factor SigB [Mycobacterium avium subsp.
           paratuberculosis K-10]
 gi|41397283|gb|AAS05143.1| SigB [Mycobacterium avium subsp. paratuberculosis K-10]
          Length = 332

 Score = 84.7 bits (208), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 81/300 (27%), Positives = 140/300 (46%), Gaps = 56/300 (18%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH-------------GDLSAAHR-------- 52
           Y++ I K  +L    E  LAKR     Y EH              DL A  R        
Sbjct: 39  YLNGIGKTALLNAAGEVELAKRIEAGLYAEHLLETRKRLGENRKRDLEAVVRDGQAARRH 98

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A
Sbjct: 99  LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQA 158

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ-----AITDNNLKPEQVVAIAKKLN 167
           +   +      +++     ++     L R+K  +        TD  L  E  + I K  +
Sbjct: 159 ITRGMADQSRTIRLPVHLVEQ--VNKLARIKREMHQNLGREATDEELAAESGIPIDKIND 216

Query: 168 VSES--EVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + E   + +S++  +  +E   L   I  ++  S+             E  +I +    +
Sbjct: 217 LLEHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSA-------------ENAVIAELLHTD 263

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R++L    + L+ RE ++   R   ++  P TL+ +   F +SRERVRQIE     K++
Sbjct: 264 IRSVL----ATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMSKLR 319


>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 = 84.7 bits (208), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 63/246 (25%), Positives = 119/246 (48%), Gaps = 36/246 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   G+   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 426 AKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEGNIGLMKAVDKFEYRRGWKFSTYATWW 485

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           ++ A+   +      +++    +       L R+   +   T     P     +A+++++
Sbjct: 486 VRQAVTRSLADQARTIRV--PVHMIETINKLNRISREILQQTGQEAHPS---VLAERMDL 540

Query: 169 SESEV----------ISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           SE +V          +SM   +   GD +L  +I  S  +S                   
Sbjct: 541 SEEKVRGILKIAKQPVSMETPVGDDGDATLGDMIEDSAASSPADAAM------------- 587

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEA 274
               + + R  +  ++  L+PRE ++   R     ++  TLE +  +F+V+RER+RQIE+
Sbjct: 588 ----QADLRAAIDDALDSLSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIRQIES 643

Query: 275 RAFKKV 280
           +A +K+
Sbjct: 644 KAMRKL 649


>gi|282854019|ref|ZP_06263356.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes J139]
 gi|282583472|gb|EFB88852.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes J139]
 gi|314922986|gb|EFS86817.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL001PA1]
 gi|314966763|gb|EFT10862.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL082PA2]
 gi|314981097|gb|EFT25191.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL110PA3]
 gi|315091922|gb|EFT63898.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL110PA4]
 gi|315093321|gb|EFT65297.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL060PA1]
 gi|327327588|gb|EGE69364.1| RNA polymerase principal sigma factor HrdB [Propionibacterium acnes
           HL103PA1]
          Length = 510

 Score = 84.7 bits (208), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 80/325 (24%), Positives = 143/325 (44%), Gaps = 65/325 (20%)

Query: 7   SIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYR---------------------- 42
           +++V G     +  Y+ +I K+ +L   EE  LAKR                        
Sbjct: 202 TVMVAGATADPVKDYLKQIGKVALLNAVEEVDLAKRIEAGLFAGEQLADPDAKIREKDRE 261

Query: 43  ------EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                 E G ++  H L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  
Sbjct: 262 DYEWIAEDGKVAKNH-LLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYT 320

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQ 147
           +G++ +TY+ WWIK A+   +      ++I              Q+++  +L R     +
Sbjct: 321 KGYKFSTYATWWIKQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEE 380

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLV 205
              + ++  E+V+ + K       E IS++  L   GD     LI  S+          +
Sbjct: 381 LANELDMTAEKVIEVQKYGR----EPISLHTPLGEDGDSEFGDLIEDSE---------AI 427

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFE 263
              D     L++++        L   +  L+ RE  +   R       P TL+ +   + 
Sbjct: 428 VPADAVNFTLLQEQ--------LHDVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYG 479

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           V+RER+RQIE++   K++   + QV
Sbjct: 480 VTRERIRQIESKTMSKLRHPSRSQV 504


>gi|2353173|gb|AAB69385.1| sigma factor 2 [Arabidopsis thaliana]
          Length = 574

 Score = 84.7 bits (208), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 66/242 (27%), Positives = 128/242 (52%), Gaps = 17/242 (7%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           HG L    +++ S++RLV+ IA  Y+G G+ + ++V EG  GL++  +KFD  +GF+ +T
Sbjct: 330 HGTL-CKDKMIKSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKGFKFST 388

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWIK A+++ +     ++++    +     + ++  +  L + T  + K E+   IA
Sbjct: 389 YAHWWIKQAVRKSLSDQSRMIRL--PFHMVEATYRVKEARKQLYSETGKHPKNEE---IA 443

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG--QEQVLIEKEER 221
           +   +S   ++++        SL+  I     N +     ++ D +    E +LI++  R
Sbjct: 444 EATGLSMKRLMAVLLSPKPPRSLDRKIG---MNQNLKPSEVIADPEAVTSEDILIKEFMR 500

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKK 279
           ++    L + +  L  RE+++   R   E+    TL+ +     VSRERVRQIE+ AF+K
Sbjct: 501 QD----LDKVLDSLGTREKQVIRWRFGMEDGRMKTLQEIGEMMGVSRERVRQIESSAFRK 556

Query: 280 VQ 281
           ++
Sbjct: 557 LK 558


>gi|328907303|gb|EGG27069.1| RNA polymerase sigma factor RpoD [Propionibacterium sp. P08]
          Length = 506

 Score = 84.7 bits (208), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 80/325 (24%), Positives = 143/325 (44%), Gaps = 65/325 (20%)

Query: 7   SIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYR---------------------- 42
           +++V G     +  Y+ +I K+ +L   EE  LAKR                        
Sbjct: 198 TVMVAGATADPVKDYLKQIGKVALLNAVEEVDLAKRIEAGLFAGEQLADPDAKIPEKDRE 257

Query: 43  ------EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                 E G ++  H L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  
Sbjct: 258 DYEWIAEDGKVAKNH-LLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYT 316

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQ 147
           +G++ +TY+ WWIK A+   +      ++I              Q+++  +L R     +
Sbjct: 317 KGYKFSTYATWWIKQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEE 376

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLV 205
              + ++  E+V+ + K       E IS++  L   GD     LI  S+          +
Sbjct: 377 LANELDMTAEKVIEVQKYGR----EPISLHTPLGEDGDSEFGDLIEDSE---------AI 423

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFE 263
              D     L++++        L   +  L+ RE  +   R       P TL+ +   + 
Sbjct: 424 VPADAVNFTLLQEQ--------LHDVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYG 475

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           V+RER+RQIE++   K++   + QV
Sbjct: 476 VTRERIRQIESKTMSKLRHPSRSQV 500


>gi|294790965|ref|ZP_06756123.1| RNA polymerase sigma (70) factor RpoD [Scardovia inopinata F0304]
 gi|294458862|gb|EFG27215.1| RNA polymerase sigma (70) factor RpoD [Scardovia inopinata F0304]
          Length = 588

 Score = 84.7 bits (208), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 71/252 (28%), Positives = 126/252 (50%), Gaps = 32/252 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ WW
Sbjct: 349 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 408

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH-LQAI----TDNNLKPEQVVAIA 163
           I+ A+   +      +++    +   +   L R++   LQ +    T + L  E  + + 
Sbjct: 409 IRQAITRAMADQARTIRV--PVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVE 466

Query: 164 KKLNVSE--SEVISMNCRLA--GDESLNALINSSDK-NSSQWQDWLVYDHDGQEQVLIEK 218
           K   V +   E IS++  L   GD     LI  +D    S+   + +     QEQ     
Sbjct: 467 KVQEVQKYGREPISLHTPLGEDGDSEFGDLIEDTDAIAPSEAVAFSLL----QEQ----- 517

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARA 276
                     T+ +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++ 
Sbjct: 518 ---------FTQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGHVYGVTRERIRQIESKT 568

Query: 277 FKKVQESIQKQV 288
             K++   + Q 
Sbjct: 569 MSKLRHPSRSQT 580


>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 = 84.7 bits (208), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 63/246 (25%), Positives = 119/246 (48%), Gaps = 36/246 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   G+   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 426 AKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEGNIGLMKAVDKFEYRRGWKFSTYATWW 485

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           ++ A+   +      +++    +       L R+   +   T     P     +A+++++
Sbjct: 486 VRQAVTRSLADQARTIRV--PVHMIETINKLNRISREILQQTGQEAHPS---VLAERMDL 540

Query: 169 SESEV----------ISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           SE +V          +SM   +   GD +L  +I  S  +S                   
Sbjct: 541 SEEKVRGILKIAKQPVSMETPVGDDGDATLGDMIEDSAASSPADAAM------------- 587

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEA 274
               + + R  +  ++  L+PRE ++   R     ++  TLE +  +F+V+RER+RQIE+
Sbjct: 588 ----QADLRAAIDDALDSLSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIRQIES 643

Query: 275 RAFKKV 280
           +A +K+
Sbjct: 644 KAMRKL 649


>gi|311064624|ref|YP_003971349.1| RNA polymerase principal sigma factor HrdB [Bifidobacterium bifidum
           PRL2010]
 gi|310866943|gb|ADP36312.1| RNA polymerase principal sigma factor HrdB [Bifidobacterium bifidum
           PRL2010]
          Length = 506

 Score = 84.7 bits (208), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 65/253 (25%), Positives = 124/253 (49%), Gaps = 34/253 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ WW
Sbjct: 268 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 327

Query: 109 IKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   +      +++           +  Q+++  +L R     +   + ++  E+V
Sbjct: 328 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 387

Query: 160 VAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
             + K       E IS++  L   GD     LI  +D          +   D     L++
Sbjct: 388 QEVQK----YGREPISLHTPLGEDGDSEFGDLIEDTD---------AIAPSDAVAFSLLQ 434

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
           ++          + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++
Sbjct: 435 EQ--------FKQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESK 486

Query: 276 AFKKVQESIQKQV 288
              K++   + Q 
Sbjct: 487 TMSKLRHPSRSQT 499


>gi|224283384|ref|ZP_03646706.1| RNA polymerase sigma factor [Bifidobacterium bifidum NCIMB 41171]
          Length = 506

 Score = 84.7 bits (208), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 65/253 (25%), Positives = 124/253 (49%), Gaps = 34/253 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ WW
Sbjct: 268 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 327

Query: 109 IKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   +      +++           +  Q+++  +L R     +   + ++  E+V
Sbjct: 328 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 387

Query: 160 VAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
             + K       E IS++  L   GD     LI  +D          +   D     L++
Sbjct: 388 QEVQK----YGREPISLHTPLGEDGDSEFGDLIEDTD---------AIAPSDAVAFSLLQ 434

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
           ++          + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++
Sbjct: 435 EQ--------FKQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESK 486

Query: 276 AFKKVQESIQKQV 288
              K++   + Q 
Sbjct: 487 TMSKLRHPSRSQT 499


>gi|296120487|ref|YP_003628265.1| RNA polymerase sigma factor RpoD [Planctomyces limnophilus DSM
           3776]
 gi|296012827|gb|ADG66066.1| RNA polymerase sigma factor RpoD [Planctomyces limnophilus DSM
           3776]
          Length = 550

 Score = 84.7 bits (208), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 71/240 (29%), Positives = 122/240 (50%), Gaps = 14/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L   +LRLVV IA  YR  GL   +++ EGN GLM+AV K++  RG++ +TY+ WW
Sbjct: 305 AMRDLSGGNLRLVVSIAKKYRNRGLSFLDLIQEGNTGLMRAVDKYEYRRGYKFSTYATWW 364

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE-QVVAIAKKLN 167
           I+ A+   I      ++I    +       LR++   L  + +   +P  +  A A  ++
Sbjct: 365 IRQAITRAIADQARTIRI--PVHMIETMSKLRKVAKKL--LQEMGREPTLEETAEAAGVS 420

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + E+  +    R     SL+  +  S+   S + D+ + D + +  V+   +E    ++ 
Sbjct: 421 LEETRRVMKISRHPI--SLDRPVGESE--DSYFGDF-IEDDNTESPVMAATQE--MLKDK 473

Query: 228 LTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           +   +  L  RER I + R    +    TLE +   F+V+RERVRQIEA+A +K+Q  ++
Sbjct: 474 IDNVLKTLTYREREIIKLRYGLGDGYTYTLEEVGRIFKVTRERVRQIEAKAVRKLQHPVR 533


>gi|187918567|ref|YP_001884130.1| RNA polymerase sigma factor RpoD [Borrelia hermsii DAH]
 gi|119861415|gb|AAX17210.1| RNA polymerase sigma factor RpoD [Borrelia hermsii DAH]
          Length = 630

 Score = 84.7 bits (208), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 75/262 (28%), Positives = 134/262 (51%), Gaps = 38/262 (14%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE +  K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 378 EEILKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 433

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RGF+ +TY+ WWI+ A+   I      +++     ++     L R   +L  +   
Sbjct: 434 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQ--INRLNRETRYLIQVLGK 491

Query: 153 NLKPEQVVA--------IAKKLNVSESEVISMNCRLAGDES--LNALI-NSSDKNSSQWQ 201
           +   E++ A        +    NVS  E +S+   +  +E   L+  I + + KN ++  
Sbjct: 492 DPTDEELSARLGWDLKKVKTVKNVSR-EPVSLETPIGEEEDSVLSDFIEDKAIKNPAKHT 550

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLS 259
            ++V     Q+Q+          R++L      L  RE+ + + R   E+   +TLE + 
Sbjct: 551 SFVVL----QDQI----------RSVL----GTLPEREQEVVKMRFGLEDGYSLTLEEVG 592

Query: 260 SEFEVSRERVRQIEARAFKKVQ 281
             F V+RER+RQIE++A ++++
Sbjct: 593 LHFNVTRERIRQIESKALRRLK 614


>gi|186687052|ref|YP_001870195.1| RpoD family RNA polymerase sigma factor [Nostoc punctiforme PCC
           73102]
 gi|186469355|gb|ACC85154.1| RNA polymerase, sigma 70 subunit, RpoD family [Nostoc punctiforme
           PCC 73102]
          Length = 316

 Score = 84.7 bits (208), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 64/235 (27%), Positives = 122/235 (51%), Gaps = 21/235 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++VT++LRLVV +A  Y+ Y L   +++ EG +GL + ++KFDP +G++L+TY  WW
Sbjct: 81  AKQKMVTANLRLVVSVAKKYQNYSLDFLDLLQEGALGLQRGIEKFDPNKGYKLSTYVYWW 140

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I  ++   +      +++    N+K     +RR++   Q ++ +  +P  V  IA+ LN+
Sbjct: 141 ITQSITRAVADKSRTIRLPIHINEK--LNKIRRVQ---QQLSQSLGRPPVVAEIAESLNL 195

Query: 169 SESEV---ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG-QEQVLIEKEERKNR 224
           S +++   + ++  L   E         D+  S+  D L  D     EQ+ +E  ++   
Sbjct: 196 SPNQIREYLQISKPLVSLEK-----RVGDEGESELADILPMDGISLDEQITLESLQQDL- 249

Query: 225 RNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAF 277
                + +++L PR+R +   R  L +N  +TL  ++    +SRE +R+ E  A 
Sbjct: 250 ----AKLLALLKPRQREVLTLRFGLSDNQQLTLSQVAKRLNLSRETIRKTEHLAL 300


>gi|315103424|gb|EFT75400.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL050PA2]
          Length = 510

 Score = 84.7 bits (208), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 80/325 (24%), Positives = 143/325 (44%), Gaps = 65/325 (20%)

Query: 7   SIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYR---------------------- 42
           +++V G     +  Y+ +I K+ +L   EE  LAKR                        
Sbjct: 202 TVMVAGATADPVKDYLKQIGKVALLNAVEEVDLAKRIEAGLFAGEQLADPDAKIREKDRE 261

Query: 43  ------EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                 E G ++  H L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  
Sbjct: 262 DYEWIAEDGKVAKNH-LLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYT 320

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQ 147
           +G++ +TY+ WWIK A+   +      ++I              Q+++  +L R     +
Sbjct: 321 KGYKFSTYATWWIKQAITRAMADQARTIRIPVHMVEVINKLARVQRQMLQDLGREPTPEE 380

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLV 205
              + ++  E+V+ + K       E IS++  L   GD     LI  S+          +
Sbjct: 381 LANELDMTAEKVIEVQKYGR----EPISLHTPLGEDGDSEFGDLIEDSE---------AI 427

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFE 263
              D     L++++        L   +  L+ RE  +   R       P TL+ +   + 
Sbjct: 428 VPADAVNFTLLQEQ--------LHDVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYG 479

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           V+RER+RQIE++   K++   + QV
Sbjct: 480 VTRERIRQIESKTMSKLRHPSRSQV 504


>gi|183601374|ref|ZP_02962744.1| RNA polymerase sigma factor RpoD [Bifidobacterium animalis subsp.
           lactis HN019]
 gi|219683429|ref|YP_002469812.1| RNA polymerase sigma factor [Bifidobacterium animalis subsp. lactis
           AD011]
 gi|241191127|ref|YP_002968521.1| RNA polymerase sigma factor [Bifidobacterium animalis subsp. lactis
           Bl-04]
 gi|241196533|ref|YP_002970088.1| RNA polymerase sigma factor [Bifidobacterium animalis subsp. lactis
           DSM 10140]
 gi|183218980|gb|EDT89621.1| RNA polymerase sigma factor RpoD [Bifidobacterium animalis subsp.
           lactis HN019]
 gi|219621079|gb|ACL29236.1| principal sigma factor RpoD [Bifidobacterium animalis subsp. lactis
           AD011]
 gi|240249519|gb|ACS46459.1| DNA-directed RNA polymerase sigma subunit [Bifidobacterium animalis
           subsp. lactis Bl-04]
 gi|240251087|gb|ACS48026.1| DNA-directed RNA polymerase sigma subunit [Bifidobacterium animalis
           subsp. lactis DSM 10140]
 gi|295794116|gb|ADG33651.1| DNA-directed RNA polymerase sigma subunit [Bifidobacterium animalis
           subsp. lactis V9]
          Length = 488

 Score = 84.7 bits (208), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 75/302 (24%), Positives = 147/302 (48%), Gaps = 45/302 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH-----GDL-----------------SAAH 51
           Y+ +I ++ +L  ++E  L++R     Y +H     GD                   A  
Sbjct: 193 YLKQIGRVSLLNAEQEVDLSERIEAGLYAQHLLDTEGDTMEFRRKRELKWAAADGKKAKD 252

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ WWI+ 
Sbjct: 253 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWWIRQ 312

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           A+   +      +++    +   +   L R++  +         P++   +A++L++   
Sbjct: 313 AITRAMADQARTIRV--PVHMVEVINKLSRVQRQMLQDLGREPTPDE---LARELDMPVE 367

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG---QEQVLIEKEERKNRRNML 228
           +V     +  G E ++      +   S++ D L+ D D     E V     + + R+ + 
Sbjct: 368 KV--QEVQKYGREPISLHTPLGEDGDSEFGD-LIEDTDAIAPSEAVAFSLLQEQFRQVLE 424

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           T     L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++   K++   + 
Sbjct: 425 T-----LSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPSRS 479

Query: 287 QV 288
           Q 
Sbjct: 480 QT 481


>gi|310287737|ref|YP_003938995.1| RNA polymerase sigma factor [Bifidobacterium bifidum S17]
 gi|309251673|gb|ADO53421.1| RNA polymerase sigma factor [Bifidobacterium bifidum S17]
          Length = 506

 Score = 84.7 bits (208), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 68/251 (27%), Positives = 125/251 (49%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ WW
Sbjct: 268 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 327

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH-LQAI----TDNNLKPEQVVAIA 163
           I+ A+   +      +++    +   +   L R++   LQ +    T + L  E  + + 
Sbjct: 328 IRQAITRAMADQARTIRV--PVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVE 385

Query: 164 KKLNVSE--SEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           K   V +   E IS++  L   GD     LI  +D          +   D     L++++
Sbjct: 386 KVQEVQKYGREPISLHTPLGEDGDSEFGDLIEDTD---------AIAPSDAVAFSLLQEQ 436

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
                     + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++  
Sbjct: 437 --------FKQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTM 488

Query: 278 KKVQESIQKQV 288
            K++   + Q 
Sbjct: 489 SKLRHPSRSQT 499


>gi|298490014|ref|YP_003720191.1| RpoD subfamily RNA polymerase sigma 70 subunit ['Nostoc azollae'
           0708]
 gi|298231932|gb|ADI63068.1| RNA polymerase, sigma 70 subunit, RpoD subfamily ['Nostoc azollae'
           0708]
          Length = 332

 Score = 84.7 bits (208), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 63/246 (25%), Positives = 115/246 (46%), Gaps = 31/246 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+V ++LRLVV +A  Y    + + +++ EG+IG+ + V+KFDP +G+R +TY+ WW
Sbjct: 97  AKRRMVEANLRLVVSVAKKYIKRNIDLLDLIQEGSIGMQRGVEKFDPTKGYRFSTYAYWW 156

Query: 109 IKAAMQEYILRSWSLVKIGTTAN---------QKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      +++              Q++L   L R    ++   +  L P QV
Sbjct: 157 IRQAITRAIAEKARTIRLPIHITEKLNKIKKAQRQLSQKLGRAPTAIELADELELTPRQV 216

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
               +K  +     +S++ RL GD     L    +   +  +D+++      +       
Sbjct: 217 RECLEKARLP----LSLDLRL-GDNYDTELGEMLEDTGATPEDFVIQSSLSSD------- 264

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAF 277
                   + R M  L P+++ + + R   +    +TL  +     +SRERVRQIE  A 
Sbjct: 265 --------IERLMKELTPQQKEVIKLRFGLIDGQALTLSKIGEILNISRERVRQIEREAL 316

Query: 278 KKVQES 283
            K+++S
Sbjct: 317 TKLRKS 322


>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 = 84.7 bits (208), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 68/243 (27%), Positives = 113/243 (46%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ WW
Sbjct: 369 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWW 428

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-------- 160
           I+ A+   I      ++I    +       L R+   +         P+++         
Sbjct: 429 IRQAITRSIADQARTIRI--PVHMIETINKLNRVARQMLQEMGREPTPDELAERVEMPED 486

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + K L +S+ E ISM   +  DE  +      D N     D  +               
Sbjct: 487 KVRKVLKISK-EPISMETPIGDDEDSHLGDFVEDVNVISPSDSAII-------------- 531

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
            +  R      ++ L  RE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 532 -EGLREATQGVLNGLTEREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 590

Query: 279 KVQ 281
           K++
Sbjct: 591 KLR 593


>gi|282899735|ref|ZP_06307698.1| sigD (sigma 28 (flagella/spoulation)) [Cylindrospermopsis
           raciborskii CS-505]
 gi|281195350|gb|EFA70284.1| sigD (sigma 28 (flagella/spoulation)) [Cylindrospermopsis
           raciborskii CS-505]
          Length = 332

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 60/244 (24%), Positives = 117/244 (47%), Gaps = 33/244 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V ++LRLVV +A  Y    + + +++ EG+IG+ + V+KFDP +G+R +TY+ WW
Sbjct: 97  AKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGSIGMQRGVEKFDPSKGYRFSTYAYWW 156

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      +++     +K     L ++K   + ++    +   +  +A++L +
Sbjct: 157 IRQAITRAIAEKARTIRLPIHITEK-----LNKIKKAQRYLSQTLGRSPSIAELAQELEI 211

Query: 169 SESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           +  +V          +S++ RL GD     L    +   +  +D+++      E      
Sbjct: 212 TPKQVRDCLEKARLPLSLDLRL-GDNYDTELGEMLEDPGASPEDYVIQSSLSSE------ 264

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARA 276
                    L R M+ L P++R + + R   +    +TL  +     +SRERVRQIE  A
Sbjct: 265 ---------LDRMMTHLTPQQREVIKLRFGLVDGQSMTLARIGEVLNISRERVRQIEREA 315

Query: 277 FKKV 280
             ++
Sbjct: 316 LTRL 319


>gi|33861134|ref|NP_892695.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus subsp. pastoris str. CCMP1986]
 gi|33639866|emb|CAE19036.1| Putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus subsp. pastoris str. CCMP1986]
          Length = 307

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 77/296 (26%), Positives = 137/296 (46%), Gaps = 32/296 (10%)

Query: 12  GEIGLSRYIHEIRKIPMLEK-QEEYVLAKRYREHGD------------------LSAAHR 52
           GEIG  + +   +++ M  K QE  VL  R +  G                     A + 
Sbjct: 9   GEIGRHQLLTPEKELTMGRKVQEMVVLINRCQTAGGKGPDCEYSEEEKKKIKIGEKAKNE 68

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++T++LRLVV ++  Y+G GL + +++ EG +GL +AV+K+DP RG R +TY+ WWI+  
Sbjct: 69  MITANLRLVVNLSKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPSRGHRFSTYAYWWIRQG 128

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +      ++I    N+K     LR  K  L  +      P   + +A +L +++ E
Sbjct: 129 LNRALSTQSRTIRIPVNINEK--LTKLRAAKSKLMQLKGF---PPTSIELANELKITKEE 183

Query: 173 VIS-MNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           +   ++C L     SL   + S   + S+  D L  D     ++    E   +   +L +
Sbjct: 184 IDELLSCELRSITVSLQGTVKSKS-DPSELVDILPSDQTPPMELAELAERTASAWTLLDK 242

Query: 231 SMSVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +   L  +ER+I   R   +      TL  ++     SRE  RQ+  RA +K++++
Sbjct: 243 AN--LTEKERKIVSLRFGLDGSNEWRTLAEVARHMSCSREYCRQVVQRALRKLRKA 296


>gi|55274930|gb|AAV49266.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 198

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 35/67 (52%), Positives = 52/67 (77%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+ 
Sbjct: 2   RMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQ 61

Query: 112 AMQEYIL 118
            ++  I+
Sbjct: 62  TIERAIM 68


>gi|55274989|gb|AAV49292.1| RNA polymerase subunit sigma-38 [Shigella flexneri]
          Length = 199

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 35/67 (52%), Positives = 52/67 (77%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+ 
Sbjct: 1   RMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQ 60

Query: 112 AMQEYIL 118
            ++  I+
Sbjct: 61  TIERAIM 67


>gi|54401890|gb|AAV34630.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274947|gb|AAV49273.1| RNA polymerase subunit sigma-38 [Shigella dysenteriae]
          Length = 203

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 35/67 (52%), Positives = 52/67 (77%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+ 
Sbjct: 2   RMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQ 61

Query: 112 AMQEYIL 118
            ++  I+
Sbjct: 62  TIERAIM 68


>gi|319441590|ref|ZP_07990746.1| RNA polymerase sigma factor SigB [Corynebacterium variabile DSM
           44702]
          Length = 397

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 73/266 (27%), Positives = 125/266 (46%), Gaps = 27/266 (10%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+    K++  +LA+  R     +A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+
Sbjct: 141 KLTRARKRDLKILAREGR-----AARTHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNL 195

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK--RLFFNLRRL 142
           GL++A++KFD  +GF+ +TY+ WWI+ A+   +      +++     ++  +L    R +
Sbjct: 196 GLIRAMEKFDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKREM 255

Query: 143 KGHL-QAITDNNLKPEQVVAIAK--KLNVSESEVISMNCRLAGDES--LNALINSSDKNS 197
             HL +  T+  L  E  +  +K   L     + +S++  +  DE   L   I  SD   
Sbjct: 256 YQHLGREATNEELAEESGIDESKIETLLKQSRDPVSLDMPVGSDEEAPLGDFIEDSDSTD 315

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           ++        H     VL   EER+     L   +    PR               TL+ 
Sbjct: 316 AEAAVVASLRHSDVRAVLDTLEEREQDVIKLRYGLDDGMPR---------------TLDQ 360

Query: 258 LSSEFEVSRERVRQIEARAFKKVQES 283
           +   F +SRERVRQIE     K++E 
Sbjct: 361 IGRSFGLSRERVRQIEREVMAKLREG 386


>gi|294786990|ref|ZP_06752244.1| RNA polymerase sigma (70) factor RpoD [Parascardovia denticolens
           F0305]
 gi|294485823|gb|EFG33457.1| RNA polymerase sigma (70) factor RpoD [Parascardovia denticolens
           F0305]
          Length = 403

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 64/245 (26%), Positives = 127/245 (51%), Gaps = 18/245 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ WW
Sbjct: 164 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 223

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   +      +++    +   +   L R++  +         P++   +A++L++
Sbjct: 224 IRQAITRAMADQARTIRV--PVHMVEVINKLSRVQRQMLQDLGREPTPDE---LARELDM 278

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG---QEQVLIEKEERKNRR 225
              +V     +  G E ++      +   S++ D L+ D D     E V     + + ++
Sbjct: 279 PVEKV--QEVQKYGREPISLHTPLGEDGDSEFGD-LIEDTDAIAPSEAVAFSLLQEQFKQ 335

Query: 226 NMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            + T     L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++   K++  
Sbjct: 336 VLET-----LSPREAGVIKMRYGLEDGQPKTLDDIGHVYGVTRERIRQIESKTMSKLRHP 390

Query: 284 IQKQV 288
            + Q 
Sbjct: 391 SRSQT 395


>gi|218676616|ref|YP_002395435.1| RpoS-like sigma factor [Vibrio splendidus LGP32]
 gi|218324884|emb|CAV26646.1| RpoS-like sigma factor [Vibrio splendidus LGP32]
          Length = 298

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 41/113 (36%), Positives = 71/113 (62%), Gaps = 4/113 (3%)

Query: 17  SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY---RGYGL 73
           + Y+ +I  I +L +++E   AK  R  GD  A   ++ S+LRLVVKIA  Y   +G   
Sbjct: 30  AHYLKDIVGIDLLSREDELYYAKLNRA-GDKQARDIMIESNLRLVVKIAKSYLKRKGNNF 88

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            + +++ EGNIGL++A+ K+DPE G+R +TY++WWI+  ++  ++     V++
Sbjct: 89  TLLDLIEEGNIGLIKAIDKYDPEPGYRFSTYAVWWIRENIEAALMNKGRTVRL 141


>gi|154509177|ref|ZP_02044819.1| hypothetical protein ACTODO_01698 [Actinomyces odontolyticus ATCC
           17982]
 gi|153798811|gb|EDN81231.1| hypothetical protein ACTODO_01698 [Actinomyces odontolyticus ATCC
           17982]
          Length = 561

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 74/299 (24%), Positives = 142/299 (47%), Gaps = 39/299 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRY-------------------REHGDL--------SAAH 51
           Y+ +I K+ +L  ++E  LA+R                    RE  +L         A +
Sbjct: 267 YLKQIGKVSLLNAEQEVDLARRIEAGLYAEYKLKNQADEMTSRERRELHFLAQDGQQAKN 326

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 327 HLLEANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 386

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           A+   +      ++I    +   +   L R++  +         PE+   +AK+L+++  
Sbjct: 387 AITRAMADQARTIRI--PVHMVEVINKLARVQRQMLQDLGREPTPEE---LAKELDMTAE 441

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           +V+ +     G E ++      +   S++ D +    D +  V  +       +  L   
Sbjct: 442 KVVEVQKY--GREPISLHTPLGEDGDSEFGDLI---EDSEAIVPADAVSFTLLQEQLHHV 496

Query: 232 MSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +  L+ RE  +   R  L +  P TL+ +   + V+RER+RQIE++   K++   + QV
Sbjct: 497 LDTLSEREAGVVSMRFGLGDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQV 555


>gi|312601028|gb|ADQ90283.1| RNA polymerase sigma factor [Mycoplasma hyopneumoniae 168]
          Length = 676

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 78/271 (28%), Positives = 140/271 (51%), Gaps = 33/271 (12%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHR--LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +L  +EE  LAK+ +  G +    R  L+  +LRLVV  A  Y+  GL   +++SEGN+G
Sbjct: 408 LLTAEEERELAKKMKIKGRIGKKARDTLIKRNLRLVVNSAKRYKNRGLGFIDLISEGNLG 467

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-KRLFFNLR 140
           +++AV K+D  RGF+ +TY+ WWI+ A+   +     L++I      T N+  ++   L+
Sbjct: 468 IIKAVAKYDYTRGFKFSTYATWWIRQAITRAVADQARLIRIPVHMVETINKINKVERELQ 527

Query: 141 RLKG---HLQAITD---NNLKPEQVVAIAKKLNVSESEVISMNCRLAG--DESLNALINS 192
           + KG     + I++       P+++  I KK+N+   + IS++  +    D S +  I  
Sbjct: 528 QEKGLNPTAEEISERLGGEFSPDKIRYI-KKINI---DPISLDKAIGKEEDSSFSDFI-- 581

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERK---NRRNMLTRSMSVLNPRERRIFEARRLQ 249
            D+N     D+ +   + + +VL+E  +     + R+ + R   V    E   ++A    
Sbjct: 582 KDENMISPVDYAI--REEKAKVLLEMIDSTLDYDERDFIKRRYGVGTNDEGIPYQAH--- 636

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
               + E L++   V++ERVRQIEA+  KK+
Sbjct: 637 ----SFEELAAMRRVTKERVRQIEAKILKKL 663


>gi|302802267|ref|XP_002982889.1| hypothetical protein SELMODRAFT_117159 [Selaginella moellendorffii]
 gi|302818650|ref|XP_002990998.1| hypothetical protein SELMODRAFT_132663 [Selaginella moellendorffii]
 gi|300141329|gb|EFJ08042.1| hypothetical protein SELMODRAFT_132663 [Selaginella moellendorffii]
 gi|300149479|gb|EFJ16134.1| hypothetical protein SELMODRAFT_117159 [Selaginella moellendorffii]
          Length = 292

 Score = 84.7 bits (208), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 70/235 (29%), Positives = 120/235 (51%), Gaps = 18/235 (7%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           +V+S+L LV+K+A  +   G  I +++ EG  GL+  V+KFD  RGFRL+TY +WWI+ +
Sbjct: 51  MVSSNLGLVIKVARKFGLKGTTIEDLIQEGINGLLHGVEKFDTSRGFRLSTYVLWWIELS 110

Query: 113 MQEYILRSWSLVKIGTTANQKRLF-FNLRRLKGHLQAITDNNLKP--EQVVAIAKKLNVS 169
           ++   ++   + ++        LF  + R LK   +   +    P  E+V  I   L  +
Sbjct: 111 VRRASVKRSIMCQV-----PMHLFDTHTRVLKTRARIFEERGTFPTNEEVATI---LGTT 162

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             +V      +   +SL+  +   D N +  +  ++ D + +  +L+   E+   +  L 
Sbjct: 163 AQKVHLAANLMRHPKSLDDNVPGCD-NVTLLE--ILPDPEVESSLLV--AEKALLKEQLD 217

Query: 230 RSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           + +++L PRE+ +   R         TLE LS  F +SRERVRQIE RA  K+ E
Sbjct: 218 KVLNLLKPREKEVLTLRYGIGDGRDRTLEELSHHFNLSRERVRQIEKRALAKIHE 272


>gi|33862185|ref|NP_893746.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus subsp. pastoris str. CCMP1986]
 gi|33634403|emb|CAE20088.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus subsp. pastoris str. CCMP1986]
          Length = 333

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 61/242 (25%), Positives = 114/242 (47%), Gaps = 16/242 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+V ++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP RG++ +TY+ WW
Sbjct: 98  AKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPARGYKFSTYAYWW 157

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   I      +++     +      L +LK   + ++    +   +  +AK + +
Sbjct: 158 IRQGITRAIAEKSRAIRLPIHITEM-----LNKLKKGQRELSQEMSRTPTISELAKYVEL 212

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E +V  + C+     SL   +   D   +   D L     G E +  E+ E    R  L
Sbjct: 213 PEDDVKDLMCKAGQPVSLETKVG--DGEDTVLLDLLA----GGEDLPDEQIEMDCMRGDL 266

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIE---ARAFKKVQES 283
              +  L   + R+   R   +   P++L  +     +SR+RVR +E    R  +++ ES
Sbjct: 267 HSLLHQLPDLQCRVLRMRYGMDGDEPMSLTGIGRVLGISRDRVRNLERDGLRGLRRLSES 326

Query: 284 IQ 285
           ++
Sbjct: 327 VE 328


>gi|55274951|gb|AAV49275.1| RNA polymerase subunit sigma-38 [Shigella flexneri]
          Length = 205

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 35/67 (52%), Positives = 52/67 (77%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+ 
Sbjct: 2   RMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQ 61

Query: 112 AMQEYIL 118
            ++  I+
Sbjct: 62  TIERAIM 68


>gi|55274970|gb|AAV49284.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 196

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 35/67 (52%), Positives = 52/67 (77%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+ 
Sbjct: 1   RMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQ 60

Query: 112 AMQEYIL 118
            ++  I+
Sbjct: 61  TIERAIM 67


>gi|54401892|gb|AAV34631.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 200

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 35/67 (52%), Positives = 52/67 (77%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+ 
Sbjct: 1   RMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQ 60

Query: 112 AMQEYIL 118
            ++  I+
Sbjct: 61  TIERAIM 67


>gi|53987186|gb|AAV27387.1| RNA polymerase sigma factor [Mycoplasma hyopneumoniae 232]
          Length = 676

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 78/271 (28%), Positives = 140/271 (51%), Gaps = 33/271 (12%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHR--LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +L  +EE  LAK+ +  G +    R  L+  +LRLVV  A  Y+  GL   +++SEGN+G
Sbjct: 408 LLTAEEERELAKKMKIKGRIGKKARDTLIKRNLRLVVNSAKRYKNRGLGFIDLISEGNLG 467

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-KRLFFNLR 140
           +++AV K+D  RGF+ +TY+ WWI+ A+   +     L++I      T N+  ++   L+
Sbjct: 468 IIKAVAKYDYTRGFKFSTYATWWIRQAITRAVADQARLIRIPVHMVETINKINKVERELQ 527

Query: 141 RLKG---HLQAITD---NNLKPEQVVAIAKKLNVSESEVISMNCRLAG--DESLNALINS 192
           + KG     + I++       P+++  I KK+N+   + IS++  +    D S +  I  
Sbjct: 528 QEKGLNPTAEEISERLGGEFSPDKIRYI-KKINI---DPISLDKAIGKEEDSSFSDFI-- 581

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERK---NRRNMLTRSMSVLNPRERRIFEARRLQ 249
            D+N     D+ +   + + +VL+E  +     + R+ + R   V    E   ++A    
Sbjct: 582 KDENMISPVDYAI--REEKAKVLLEMIDSTLDYDERDFIKRRYGVGTNDEGIPYQAH--- 636

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
               + E L++   V++ERVRQIEA+  KK+
Sbjct: 637 ----SFEELAAMRRVTKERVRQIEAKILKKL 663


>gi|144575263|gb|AAZ53437.2| DNA-directed RNA polymerase sigma factor [Mycoplasma hyopneumoniae
           7448]
          Length = 676

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 78/271 (28%), Positives = 140/271 (51%), Gaps = 33/271 (12%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHR--LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +L  +EE  LAK+ +  G +    R  L+  +LRLVV  A  Y+  GL   +++SEGN+G
Sbjct: 408 LLTAEEERELAKKMKIKGRIGKKARDTLIKRNLRLVVNSAKRYKNRGLGFIDLISEGNLG 467

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-KRLFFNLR 140
           +++AV K+D  RGF+ +TY+ WWI+ A+   +     L++I      T N+  ++   L+
Sbjct: 468 IIKAVAKYDYTRGFKFSTYATWWIRQAITRAVADQARLIRIPVHMVETINKINKVERELQ 527

Query: 141 RLKG---HLQAITD---NNLKPEQVVAIAKKLNVSESEVISMNCRLAG--DESLNALINS 192
           + KG     + I++       P+++  I KK+N+   + IS++  +    D S +  I  
Sbjct: 528 QEKGLNPTAEEISERLGGEFSPDKIRYI-KKINI---DPISLDKAIGKEEDSSFSDFI-- 581

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERK---NRRNMLTRSMSVLNPRERRIFEARRLQ 249
            D+N     D+ +   + + +VL+E  +     + R+ + R   V    E   ++A    
Sbjct: 582 KDENMISPVDYAI--REEKAKVLLEMIDSTLDYDERDFIKRRYGVGTNDEGIPYQAH--- 636

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
               + E L++   V++ERVRQIEA+  KK+
Sbjct: 637 ----SFEELAAMRRVTKERVRQIEAKILKKL 663


>gi|55274937|gb|AAV49269.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 204

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 35/67 (52%), Positives = 52/67 (77%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+ 
Sbjct: 1   RMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQ 60

Query: 112 AMQEYIL 118
            ++  I+
Sbjct: 61  TIERAIM 67


>gi|213621937|ref|ZP_03374720.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 197

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 35/67 (52%), Positives = 52/67 (77%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+ 
Sbjct: 3   RMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQ 62

Query: 112 AMQEYIL 118
            ++  I+
Sbjct: 63  TIERAIM 69


>gi|55274943|gb|AAV49271.1| RNA polymerase subunit sigma-38 [Shigella dysenteriae]
          Length = 204

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 35/67 (52%), Positives = 52/67 (77%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+ 
Sbjct: 1   RMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQ 60

Query: 112 AMQEYIL 118
            ++  I+
Sbjct: 61  TIERAIM 67


>gi|254821657|ref|ZP_05226658.1| RNA polymerase sigma factor SigB [Mycobacterium intracellulare ATCC
           13950]
          Length = 319

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 80/300 (26%), Positives = 140/300 (46%), Gaps = 56/300 (18%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH-------------GDLSAAHR-------- 52
           Y++ I K  +L    E  LAKR     Y EH              DL A  R        
Sbjct: 26  YLNGIGKTALLNAAGEVELAKRIEAGLYAEHLLETRKRLGENRKRDLEAVVRDGKAARRH 85

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A
Sbjct: 86  LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQA 145

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ-----AITDNNLKPEQVVAIAKKLN 167
           +   +      +++     ++     L R+K  +        TD  L  E  + + K  +
Sbjct: 146 ITRGMADQSRTIRLPVHLVEQ--VNKLARIKREMHQNLGREATDEELAAESGIPVDKIND 203

Query: 168 VSES--EVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + E   + +S++  +  +E   L   I  ++  S+             E  +I +    +
Sbjct: 204 LLEHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSA-------------ENAVIAELLHTD 250

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R++L    + L+ RE ++   R   ++  P TL+ +   F +SRERVRQIE     K++
Sbjct: 251 IRSVL----ATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMSKLR 306


>gi|326523529|dbj|BAJ92935.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 506

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 76/247 (30%), Positives = 129/247 (52%), Gaps = 28/247 (11%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L  S++RLV+ IA  Y   G+ +S+++  G IGL++ ++KFD  RGFR++TY  WWI+  
Sbjct: 267 LTMSNIRLVISIAQKYDKLGVELSDLIQGGLIGLLRGIEKFDASRGFRISTYVYWWIRQG 326

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +  +    ++ T  +++     L  ++    A+ D  + P     IA+ LN+SE +
Sbjct: 327 VSRALADNSKTFRLPTYMHER-----LIAIRAAKYALEDQGVSPT-TQNIAELLNISEKK 380

Query: 173 VI----SMNCRLAGDE----SLNALINSSDKNSSQWQDWLVYD---HDGQEQVLIEKEER 221
           V     ++N  L+ D+    SLN L    D   S  +D  V +   H  +E  L  KEE 
Sbjct: 381 VHNATEAVNKALSLDQQAFPSLNGL--PGDTLHSYIEDQNVANDPWHGFEEWYL--KEEV 436

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARR-LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
               N+L   +S L  RER I      + +   T E++S +F +SRERVRQ+   A +K+
Sbjct: 437 N---NLL---ISNLTERERHIIRLYHGIGKQCHTWEDISRQFGLSRERVRQVGLIAMEKL 490

Query: 281 QESIQKQ 287
           + + +++
Sbjct: 491 KHAARRK 497


>gi|55274915|gb|AAV49259.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274917|gb|AAV49260.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274923|gb|AAV49263.1| RNA polymerase subunit sigma-38 [Shigella flexneri]
 gi|55274925|gb|AAV49264.1| RNA polymerase subunit sigma-38 [Shigella boydii]
 gi|55274928|gb|AAV49265.1| RNA polymerase subunit sigma-38 [Shigella sonnei]
 gi|55274932|gb|AAV49267.1| RNA polymerase subunit sigma-38 [Shigella boydii]
 gi|55274939|gb|AAV49270.1| RNA polymerase subunit sigma-38 [Shigella boydii]
 gi|55274949|gb|AAV49274.1| RNA polymerase subunit sigma-38 [Shigella dysenteriae]
 gi|55274955|gb|AAV49277.1| RNA polymerase subunit sigma-38 [Shigella dysenteriae]
 gi|55274957|gb|AAV49278.1| RNA polymerase subunit sigma-38 [Shigella dysenteriae]
 gi|55274959|gb|AAV49279.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274961|gb|AAV49280.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274974|gb|AAV49286.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274980|gb|AAV49289.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274991|gb|AAV49293.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274993|gb|AAV49294.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 204

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 35/67 (52%), Positives = 52/67 (77%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+ 
Sbjct: 1   RMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQ 60

Query: 112 AMQEYIL 118
            ++  I+
Sbjct: 61  TIERAIM 67


>gi|302346408|ref|YP_003814706.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           melaninogenica ATCC 25845]
 gi|302150820|gb|ADK97081.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           melaninogenica ATCC 25845]
          Length = 228

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 70/269 (26%), Positives = 120/269 (44%), Gaps = 47/269 (17%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +YI +I    +L  +EE  LA++ +  GD  A  +L  ++L+ VV +A  YR  GL   +
Sbjct: 6   KYIEDIANEQLLSDKEEQELAEKIKV-GDARALEKLTKANLKFVVSLAHQYRNRGLGEDD 64

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++SEGNIG+M A +KFD  +G R   ++  +I+ AM+E I    +L K+      +   F
Sbjct: 65  LISEGNIGMMYAAQKFDGSKGVRFVIFAAPYIRKAMEETIKEQATLYKLPKNETSR---F 121

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
             +R   H  +I       +Q V +    N +   ++        DE LN  I S     
Sbjct: 122 EQKR--SHAISI-------DQPVPVGSNNNFTLQHILENENAKHADEHLNQEILS----- 167

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE-ARRLQENPVTLE 256
                                       N + + + VL+ RE+R+      L     T+ 
Sbjct: 168 ----------------------------NEIQKGLDVLDEREKRVITYIYGLTGAHYTMA 199

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            ++ +  + RERVRQI  +A +K+ + ++
Sbjct: 200 EIAEDMGLKRERVRQIRDKALRKLHKKMK 228


>gi|296171822|ref|ZP_06852936.1| RNA polymerase principal sigma factor SigB [Mycobacterium
           parascrofulaceum ATCC BAA-614]
 gi|295893958|gb|EFG73726.1| RNA polymerase principal sigma factor SigB [Mycobacterium
           parascrofulaceum ATCC BAA-614]
          Length = 329

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 80/300 (26%), Positives = 140/300 (46%), Gaps = 56/300 (18%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH-------------GDLSAAHR-------- 52
           Y++ I K  +L    E  LAKR     Y EH              DL A  R        
Sbjct: 36  YLNGIGKTALLNAAGEVELAKRIEAGLYAEHLLETRKRLGENRRRDLEAVVRDGQAARRH 95

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A
Sbjct: 96  LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQA 155

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ-----AITDNNLKPEQVVAIAKKLN 167
           +   +      +++     ++     L R+K  +        TD  L  E  + + K  +
Sbjct: 156 ITRGMADQSRTIRLPVHLVEQ--VNKLARIKREMHQNLGREATDEELAAESGIPVEKIND 213

Query: 168 VSES--EVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + E   + +S++  +  +E   L   I  ++  S+             E  +I +    +
Sbjct: 214 LLEHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSA-------------ENAVIAELLHTD 260

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R++L    + L+ RE ++   R   ++  P TL+ +   F +SRERVRQIE     K++
Sbjct: 261 IRSVL----ATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDVMSKLR 316


>gi|42525589|ref|NP_970687.1| sigma-70 family RNA polymerase sigma factor [Treponema denticola
           ATCC 35405]
 gi|41815600|gb|AAS10568.1| RNA polymerase sigma-70 factor, region 2 family [Treponema
           denticola ATCC 35405]
          Length = 275

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 72/283 (25%), Positives = 135/283 (47%), Gaps = 32/283 (11%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +YI + +K P+L  ++E  LA   ++ G+  A   LVTS+LRLV+K+A  +      I
Sbjct: 6   LLQYIKDSKKYPLLSAEQEAELADEVKK-GNTEAIEVLVTSNLRLVIKMAKKFSSNENQI 64

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            E++ EGN+GLM+A  KF      R ++Y+ WWIK +   Y+  +  ++K+     +K  
Sbjct: 65  LELIQEGNMGLMKAASKFSKSFKVRFSSYAAWWIKQSFIRYLNSADKVIKLPV---RKEA 121

Query: 136 FF--------NLRRLKGHLQAITD-NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
                     N +   G L + +    +  E+V  IA+  + + +++ S++  +  + S 
Sbjct: 122 LIRQVHKEEENYKIKYGILPSYSQLAEIMKEKVDIIAQIKSFNYTDICSLDDPVDNERSA 181

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           N              D++  +    E+  I+ E ++     L + + +LN RE+ +   R
Sbjct: 182 N------------LYDFIPCNTYNPEEEFIDNEFKEK----LNKCLEILNDREKDVLRNR 225

Query: 247 RLQENPV---TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +  +   T   L  ++ +S E +RQ + RA KK++    K
Sbjct: 226 YGLDGTMTSTTFAVLGKKYSISAESIRQTQLRALKKLRADTNK 268


>gi|296269678|ref|YP_003652310.1| RpoD subfamily RNA polymerase sigma-70 [Thermobispora bispora DSM
           43833]
 gi|296092465|gb|ADG88417.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobispora
           bispora DSM 43833]
          Length = 478

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 70/272 (25%), Positives = 131/272 (48%), Gaps = 48/272 (17%)

Query: 27  PMLEKQEEYVL--AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           P   +  E+V+   KR ++H        ++ ++LRLVV +A  Y   G+ + +VV EGN+
Sbjct: 225 PGFREDLEWVIEDGKRAKDH--------MLEANLRLVVSVAKKYTDRGMSLLDVVQEGNL 276

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++AV+KFD  +G++ +TY+MWWI+ A+Q     S   +++    +   +   L R++ 
Sbjct: 277 GLIRAVEKFDYTKGYKFSTYAMWWIRQAIQRGFADSARTIRL--PVHVLEMLSKLSRVER 334

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRLA--GDESLNALINS 192
            +         PE+   +A +L+ +  ++          IS++  +   G+  +  LI  
Sbjct: 335 DMHQRLGREPTPEE---LAVELDKTPDQIEELLRTSRQPISLDSTIGEDGETCIGDLIED 391

Query: 193 SDK-NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQ 249
            D   +S+  D          Q+L E+         L   +  L+PRE +I   R   + 
Sbjct: 392 VDSLEASEIVD---------RQLLAEQ---------LKGMLDNLSPREAKIMSLRFGLVD 433

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             P TL+ +     ++RER+RQ+E  +  K++
Sbjct: 434 GKPHTLDEIGKRLGLTRERIRQLEKESLSKLR 465


>gi|193222342|emb|CAL62001.1| Putative RNA polymerase sigma-70 factor [Herminiimonas
           arsenicoxydans]
          Length = 808

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 73/251 (29%), Positives = 126/251 (50%), Gaps = 39/251 (15%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++  ++L+LV   A  Y   G+   +++ EGNIGL++A++KFD  RGF+ +TY++WW
Sbjct: 436 ARSQMAIANLKLVHSTATKYSWSGMEFLDLIQEGNIGLLRAIEKFDYRRGFKFSTYAIWW 495

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I     L+++      + NQ      + R K  ++ I   +LK +++     
Sbjct: 496 IRQAITRAIADQTRLIRVPVHLVESINQ------VERHKNQVEHILGKSLKAQEI----- 544

Query: 165 KLNVSESEVISMNCR-----LAGDES---LNALINSSDKNSSQ---WQDWLVYDHDGQEQ 213
                 S+ +SM  R     LA + S   ++ LI    +N  +    ++ L+      EQ
Sbjct: 545 ------SDALSMPLRKVEQCLAANVSILNIDDLIERETENQDEALVLEENLIDPSATPEQ 598

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN--PVTLENLSSEFEVSRERVR 270
           + I+    K    +L R +S L  +E  I   R  L +N  P TLE +     ++RERVR
Sbjct: 599 LAIKTSLSK----VLNRILSDLPEKEAHILRLRFGLYKNVEPHTLEEVGQLLGITRERVR 654

Query: 271 QIEARAFKKVQ 281
           QIEA+A  +++
Sbjct: 655 QIEAKALTRIR 665


>gi|72080402|ref|YP_287460.1| RNA polymerase sigma factor [Mycoplasma hyopneumoniae 7448]
          Length = 489

 Score = 84.3 bits (207), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 76/270 (28%), Positives = 140/270 (51%), Gaps = 29/270 (10%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHR--LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +L  +EE  LAK+ +  G +    R  L+  +LRLVV  A  Y+  GL   +++SEGN+G
Sbjct: 221 LLTAEEERELAKKMKIKGRIGKKARDTLIKRNLRLVVNSAKRYKNRGLGFIDLISEGNLG 280

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-KRLFFNLR 140
           +++AV K+D  RGF+ +TY+ WWI+ A+   +     L++I      T N+  ++   L+
Sbjct: 281 IIKAVAKYDYTRGFKFSTYATWWIRQAITRAVADQARLIRIPVHMVETINKINKVERELQ 340

Query: 141 RLKG---HLQAITD---NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           + KG     + I++       P+++  I KK+N+   + IS++  +  +E  +      D
Sbjct: 341 QEKGLNPTAEEISERLGGEFSPDKIRYI-KKINI---DPISLDKAIGKEEDSSFSDFIKD 396

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERK---NRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           +N     D+ +   + + +VL+E  +     + R+ + R   V    E   ++A      
Sbjct: 397 ENMISPVDYAI--REEKAKVLLEMIDSTLDYDERDFIKRRYGVGTNDEGIPYQAH----- 449

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             + E L++   V++ERVRQIEA+  KK++
Sbjct: 450 --SFEELAAMRRVTKERVRQIEAKILKKLR 477


>gi|291059871|gb|ADD72606.1| RNA polymerase sigma factor RpoD [Treponema pallidum subsp.
           pallidum str. Chicago]
          Length = 610

 Score = 84.0 bits (206), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 81/289 (28%), Positives = 135/289 (46%), Gaps = 61/289 (21%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++G + ++R IH  R   ML+K                 A  +L+ ++LRLVV IA  Y 
Sbjct: 352 IDGILSMARAIH--RGHVMLKK-----------------AKDKLINANLRLVVSIAKKYT 392

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI--- 126
             GL   ++V EGNIGL++AV+KF+  +G++ +TY+ WWI+ A+   I      +++   
Sbjct: 393 NRGLLFFDLVQEGNIGLIKAVEKFEYRKGYKFSTYATWWIRQAITRSISDQARTIRVPVH 452

Query: 127 ------GTTANQKRLFFNLRRLKGH---LQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
                   T   ++L     R        Q +     K +QV ++A+       E IS+ 
Sbjct: 453 MIEQINKVTRESRQLLQKFGREPSDEEIAQQLCWTVEKVKQVKSVAR-------EPISLE 505

Query: 178 CRLA--GDESLNALINSSD-KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV 234
             +    D SL   +  +D +N S+            E+VL+++E R          +S 
Sbjct: 506 TPIGEEEDSSLGDFVPDADVENPSRV----------TERVLLKEEVRS--------ILSA 547

Query: 235 LNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           L  RE  +   R   +     TLE +   F+V+RER+RQIEA+A K+++
Sbjct: 548 LPAREHEVLRMRFGLDGDYSQTLEEVGLYFDVTRERIRQIEAKALKRLR 596


>gi|55274872|gb|AAV49239.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 179

 Score = 84.0 bits (206), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 35/67 (52%), Positives = 52/67 (77%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+ 
Sbjct: 1   RMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQ 60

Query: 112 AMQEYIL 118
            ++  I+
Sbjct: 61  TIERAIM 67


>gi|87124760|ref|ZP_01080608.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9917]
 gi|86167639|gb|EAQ68898.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9917]
          Length = 321

 Score = 84.0 bits (206), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 61/228 (26%), Positives = 115/228 (50%), Gaps = 15/228 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+V ++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP RG++ +TY+ WW
Sbjct: 86  AKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWW 145

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   I      +++     +      L +LK   + ++    +   V  +A  + +
Sbjct: 146 IRQGITRAIAEKSRTIRLPIHITEM-----LNKLKKGQRELSQELGRTPTVTELAGFVEL 200

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNM 227
            E EV  + CR     SL   +   D + ++  + L  D +  +EQV +E   + + R++
Sbjct: 201 PEEEVKDLMCRARQPVSLE--MKVGDGDDTELLELLAGDGELPEEQVEVEC-LKGDLRDL 257

Query: 228 LTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIE 273
           L +    L   +RR+   R     E P++L  ++    +SR+R R++E
Sbjct: 258 LEQ----LPDLQRRVLRMRYGMDGEEPMSLTGIAKSLRMSRDRTRRLE 301


>gi|15639484|ref|NP_218934.1| RNA polymerase sigma factor RpoD [Treponema pallidum subsp.
           pallidum str. Nichols]
 gi|189025724|ref|YP_001933496.1| RNA polymerase sigma factor RpoD [Treponema pallidum subsp.
           pallidum SS14]
 gi|6094131|sp|O83506|RPOD_TREPA RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A;
           AltName: Full=Major vegetative sigma factor
 gi|3322782|gb|AAC65480.1| RNA polymerase sigma-70 factor (rpoD) [Treponema pallidum subsp.
           pallidum str. Nichols]
 gi|189018299|gb|ACD70917.1| RNA polymerase sigma-70 factor [Treponema pallidum subsp. pallidum
           SS14]
          Length = 611

 Score = 84.0 bits (206), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 81/289 (28%), Positives = 135/289 (46%), Gaps = 61/289 (21%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++G + ++R IH  R   ML+K                 A  +L+ ++LRLVV IA  Y 
Sbjct: 353 IDGILSMARAIH--RGHVMLKK-----------------AKDKLINANLRLVVSIAKKYT 393

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI--- 126
             GL   ++V EGNIGL++AV+KF+  +G++ +TY+ WWI+ A+   I      +++   
Sbjct: 394 NRGLLFFDLVQEGNIGLIKAVEKFEYRKGYKFSTYATWWIRQAITRSISDQARTIRVPVH 453

Query: 127 ------GTTANQKRLFFNLRRLKGH---LQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
                   T   ++L     R        Q +     K +QV ++A+       E IS+ 
Sbjct: 454 MIEQINKVTRESRQLLQKFGREPSDEEIAQQLCWTVEKVKQVKSVAR-------EPISLE 506

Query: 178 CRLA--GDESLNALINSSD-KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV 234
             +    D SL   +  +D +N S+            E+VL+++E R          +S 
Sbjct: 507 TPIGEEEDSSLGDFVPDADVENPSRV----------TERVLLKEEVRS--------ILSA 548

Query: 235 LNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           L  RE  +   R   +     TLE +   F+V+RER+RQIEA+A K+++
Sbjct: 549 LPAREHEVLRMRFGLDGDYSQTLEEVGLYFDVTRERIRQIEAKALKRLR 597


>gi|116328273|ref|YP_797993.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Leptospira borgpetersenii serovar Hardjo-bovis L550]
 gi|116330997|ref|YP_800715.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Leptospira borgpetersenii serovar Hardjo-bovis JB197]
 gi|116121017|gb|ABJ79060.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Leptospira borgpetersenii serovar Hardjo-bovis L550]
 gi|116124686|gb|ABJ75957.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Leptospira borgpetersenii serovar Hardjo-bovis JB197]
          Length = 585

 Score = 84.0 bits (206), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 66/243 (27%), Positives = 119/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   LV ++LRLVV IA  Y   G+   +++ EGNIGL++AV KF+ ++G++ +TY+ WW
Sbjct: 347 AKKELVKANLRLVVSIAKRYANRGMHFFDLIQEGNIGLIKAVDKFEYKKGYKFSTYATWW 406

Query: 109 IKAAMQEYILRSWSLVK--------IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
           I+ A+   I      ++        +     + RLF        + + I +    P Q V
Sbjct: 407 IRQAITRAISDQARTIRVPVHMIEQVNKVIRETRLFIQEFGRDPNNEEIAERLGWPVQKV 466

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + K  NV+  E IS+   +  +E             S+  D++    D + +  +    
Sbjct: 467 KMVK--NVA-REPISLEIPVGSEE------------DSELGDFI---PDTEVETPVNTAA 508

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFK 278
                  + + +  L  RE+++   R   ++  P TLE +  +F+V+RER+RQIEA+A +
Sbjct: 509 SSILAEQIRQVLHTLPAREQKVIRMRFGLDDGYPQTLEEVGYQFKVTRERIRQIEAKALR 568

Query: 279 KVQ 281
           +++
Sbjct: 569 RLR 571


>gi|203284607|ref|YP_002222347.1| RNA polymerase sigma-70 factor [Borrelia duttonii Ly]
 gi|201084050|gb|ACH93641.1| RNA polymerase sigma-70 factor [Borrelia duttonii Ly]
          Length = 630

 Score = 84.0 bits (206), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 75/261 (28%), Positives = 133/261 (50%), Gaps = 36/261 (13%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE +  K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 378 EEILKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 433

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RGF+ +TY+ WWI+ A+   I      +++     ++    N R  +  +Q +  +
Sbjct: 434 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLN-RETRYLVQVLGKD 492

Query: 153 NLKPEQVVAIAKKL-------NVSESEVISMNCRLAGDES--LNALI-NSSDKNSSQWQD 202
               E  + +   L       NVS  E +S+   +  +E   L+  I + + KN ++   
Sbjct: 493 PTDEELSIRLGWDLKKVKTVKNVS-REPVSLETPIGEEEDSVLSDFIEDKAIKNPAKHTS 551

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSS 260
           ++V     Q+Q+          R +L      L  RE+ + + R   E+   +TLE +  
Sbjct: 552 FVVL----QDQI----------RAVL----GTLPEREQEVVKMRFGLEDGYSLTLEEVGL 593

Query: 261 EFEVSRERVRQIEARAFKKVQ 281
            F V+RER+RQIE++A ++++
Sbjct: 594 HFNVTRERIRQIESKALRRLK 614


>gi|307718768|ref|YP_003874300.1| RNA polymerase sigma factor [Spirochaeta thermophila DSM 6192]
 gi|306532493|gb|ADN02027.1| RNA polymerase sigma factor [Spirochaeta thermophila DSM 6192]
          Length = 580

 Score = 84.0 bits (206), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 67/237 (28%), Positives = 120/237 (50%), Gaps = 16/237 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+KF+  +G++ +TY+ W
Sbjct: 341 TAKDKLIQANLRLVVSIAKKYTNRGLHFFDLVQEGNIGLIKAVEKFEYRKGYKFSTYATW 400

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++     ++     ++R    L  +       E+   IA +L 
Sbjct: 401 WIRQAITRSISDQARTIRVPVHMIEQ--INKVQREARQLMQVLGREPTDEE---IADRLG 455

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNS--SQWQDWLVYDHDGQEQVLIEKEERKNRR 225
              S V S+        SL + I   + +S     +D    +   Q    + +++ K+  
Sbjct: 456 WPLSRVKSVKNVAREPISLESPIGEEEDSSVGDFIEDKTAINPSHQTAYALLQQQIKD-- 513

Query: 226 NMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
                 ++ L PRE+ + + R   E+   +TLE +   F V+RER+RQIEA+A +++
Sbjct: 514 -----VLATLPPREQEVLKMRFGLEDGYSLTLEEVGLYFNVTRERIRQIEAKALRRL 565


>gi|203288141|ref|YP_002223156.1| RNA polymerase sigma-70 factor [Borrelia recurrentis A1]
 gi|201085361|gb|ACH94935.1| RNA polymerase sigma-70 factor [Borrelia recurrentis A1]
          Length = 630

 Score = 84.0 bits (206), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 76/261 (29%), Positives = 127/261 (48%), Gaps = 36/261 (13%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE +  K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 378 EEILKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 433

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITD 151
           F+ +RGF+ +TY+ WWI+ A    I RS S        +Q R      R+  H+ + I  
Sbjct: 434 FEYKRGFKFSTYATWWIRQA----ITRSIS--------DQARTI----RVPVHMIEQINR 477

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
            N +   +V I  K    E     ++ RL  D      + +  +     +  +  + D  
Sbjct: 478 LNRETRYLVQILGKDPTDEE----LSIRLGWDLKKVKTVKNVSREPVSLETPIGEEEDSV 533

Query: 212 EQVLIEKEERKN---------RRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSS 260
               IE +  KN          ++ +   +  L  RE+ + + R   E+   +TLE +  
Sbjct: 534 LSDFIEDKAIKNPAKHTSFVILQDQIRAVLGTLPEREQEVVKMRFGLEDGYSLTLEEVGL 593

Query: 261 EFEVSRERVRQIEARAFKKVQ 281
            F V+RER+RQIE++A ++++
Sbjct: 594 YFNVTRERIRQIESKALRRLK 614


>gi|315604554|ref|ZP_07879617.1| DNA-directed RNA polymerase sigma subunit RpoD [Actinomyces sp.
           oral taxon 180 str. F0310]
 gi|315313566|gb|EFU61620.1| DNA-directed RNA polymerase sigma subunit RpoD [Actinomyces sp.
           oral taxon 180 str. F0310]
          Length = 516

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 74/299 (24%), Positives = 142/299 (47%), Gaps = 39/299 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRY-------------------REHGDL--------SAAH 51
           Y+ +I K+ +L  ++E  LA+R                    RE  +L         A +
Sbjct: 222 YLKQIGKVSLLNAEQEVDLARRIEAGLYAEYKLKNQADEMTSRERRELHFLAQDGQQAKN 281

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 282 HLLEANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 341

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           A+   +      ++I    +   +   L R++  +         PE+   +AK+L+++  
Sbjct: 342 AITRAMADQARTIRI--PVHMVEVINKLARVQRQMLQDLGREPTPEE---LAKELDMTAE 396

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           +V+ +     G E ++      +   S++ D +    D +  V  +       +  L   
Sbjct: 397 KVVEVQKY--GREPISLHTPLGEDGDSEFGDLI---EDSEAIVPADAVSFTLLQEQLHHV 451

Query: 232 MSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +  L+ RE  +   R  L +  P TL+ +   + V+RER+RQIE++   K++   + QV
Sbjct: 452 LDTLSEREAGVVSMRFGLGDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQV 510


>gi|326512474|dbj|BAJ99592.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 506

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 76/247 (30%), Positives = 129/247 (52%), Gaps = 28/247 (11%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L  S++RLV+ IA  Y   G+ +S+++  G IGL++ ++KFD  RGFR++TY  WWI+  
Sbjct: 267 LTMSNIRLVISIAQKYDKLGVELSDLIQGGLIGLLRGIEKFDASRGFRISTYVYWWIRQG 326

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +  +    ++ T  +++     L  ++    A+ D  + P     IA+ LN+SE +
Sbjct: 327 VSRALADNSRTFRLPTYMHER-----LIAIRAAKYALEDQGVSPT-TQNIAELLNISEKK 380

Query: 173 VI----SMNCRLAGDE----SLNALINSSDKNSSQWQDWLVYD---HDGQEQVLIEKEER 221
           V     ++N  L+ D+    SLN L    D   S  +D  V +   H  +E  L  KEE 
Sbjct: 381 VHNATEAVNKALSLDQQAFPSLNGL--PGDTLHSYIEDQNVANDPWHGFEEWYL--KEEV 436

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARR-LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
               N+L   +S L  RER I      + +   T E++S +F +SRERVRQ+   A +K+
Sbjct: 437 N---NLL---ISNLTERERHIIRLYHGIGKQCHTWEDISRQFGLSRERVRQVGLIAMEKL 490

Query: 281 QESIQKQ 287
           + + +++
Sbjct: 491 KHAARRK 497


>gi|315185629|gb|EFU19397.1| RNA polymerase, sigma 70 subunit, RpoD [Spirochaeta thermophila DSM
           6578]
          Length = 568

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 67/238 (28%), Positives = 121/238 (50%), Gaps = 16/238 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+KF+  +G++ +TY+ W
Sbjct: 329 TAKDKLIQANLRLVVSIAKKYTNRGLHFFDLVQEGNIGLIKAVEKFEYRKGYKFSTYATW 388

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++     ++     ++R    L  +       E+   IA +L 
Sbjct: 389 WIRQAITRSISDQARTIRVPVHMIEQ--INKVQREARQLMQVLGREPTDEE---IADRLG 443

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNS--SQWQDWLVYDHDGQEQVLIEKEERKNRR 225
              S V S+        SL + I   + +S     +D    +   Q    + +++ K+  
Sbjct: 444 WPLSRVKSVKNVAREPISLESPIGEEEDSSVGDFIEDKTAVNPSHQTAYALLQQQIKD-- 501

Query: 226 NMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                 ++ L PRE+ + + R   E+   +TLE +   F V+RER+RQIEA+A ++++
Sbjct: 502 -----VLATLPPREQEVLKMRFGLEDGYSLTLEEVGLYFNVTRERIRQIEAKALRRLR 554


>gi|161936260|ref|YP_115577.2| RNA polymerase sigma factor [Mycoplasma hyopneumoniae 232]
          Length = 489

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 76/270 (28%), Positives = 140/270 (51%), Gaps = 29/270 (10%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHR--LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +L  +EE  LAK+ +  G +    R  L+  +LRLVV  A  Y+  GL   +++SEGN+G
Sbjct: 221 LLTAEEERELAKKMKIKGRIGKKARDTLIKRNLRLVVNSAKRYKNRGLGFIDLISEGNLG 280

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-KRLFFNLR 140
           +++AV K+D  RGF+ +TY+ WWI+ A+   +     L++I      T N+  ++   L+
Sbjct: 281 IIKAVAKYDYTRGFKFSTYATWWIRQAITRAVADQARLIRIPVHMVETINKINKVERELQ 340

Query: 141 RLKG---HLQAITD---NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           + KG     + I++       P+++  I KK+N+   + IS++  +  +E  +      D
Sbjct: 341 QEKGLNPTAEEISERLGGEFSPDKIRYI-KKINI---DPISLDKAIGKEEDSSFSDFIKD 396

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERK---NRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           +N     D+ +   + + +VL+E  +     + R+ + R   V    E   ++A      
Sbjct: 397 ENMISPVDYAI--REEKAKVLLEMIDSTLDYDERDFIKRRYGVGTNDEGIPYQAH----- 449

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             + E L++   V++ERVRQIEA+  KK++
Sbjct: 450 --SFEELAAMRRVTKERVRQIEAKILKKLR 477


>gi|87123242|ref|ZP_01079093.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9917]
 gi|86168962|gb|EAQ70218.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9917]
          Length = 309

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 62/228 (27%), Positives = 114/228 (50%), Gaps = 15/228 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+V ++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP RG++ +TY+ WW
Sbjct: 74  AKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWW 133

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   I      +++     +      L +LK   + ++    +   V  +A  + +
Sbjct: 134 IRQGITRAIAEKSRTIRLPIHITEM-----LNKLKKGQRELSQELGRTPTVTELAGFVEL 188

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNM 227
            E EV  + CR     SL   +   D + ++  + L  D +  +EQV +E   + + R++
Sbjct: 189 PEEEVKDLMCRARQPVSLE--MKVGDGDDTELLELLAGDGELPEEQVEVEC-LKGDLRDL 245

Query: 228 LTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIE 273
           L +    L   +RR+   R     E P++L  +     +SR+RVR +E
Sbjct: 246 LEQ----LPDLQRRVLRMRYGMDGEEPMSLTGIGRVIGISRDRVRNLE 289


>gi|24214932|ref|NP_712413.1| RNA polymerase sigma-70 factor [Leptospira interrogans serovar Lai
           str. 56601]
 gi|45657567|ref|YP_001653.1| RNA polymerase sigma-70 factor [Leptospira interrogans serovar
           Copenhageni str. Fiocruz L1-130]
 gi|26399555|sp|P59117|RPOD_LEPIN RecName: Full=RNA polymerase sigma factor rpoD
 gi|47605974|sp|P61540|RPOD_LEPIC RecName: Full=RNA polymerase sigma factor rpoD
 gi|24195965|gb|AAN49431.1|AE011394_5 RNA polymerase sigma-70 factor [Leptospira interrogans serovar Lai
           str. 56601]
 gi|45600806|gb|AAS70290.1| RNA polymerase sigma-70 factor [Leptospira interrogans serovar
           Copenhageni str. Fiocruz L1-130]
          Length = 585

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 66/243 (27%), Positives = 119/243 (48%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   LV ++LRLVV IA  Y   G+   +++ EGNIGL++AV KF+ ++G++ +TY+ WW
Sbjct: 347 AKKELVKANLRLVVSIAKRYANRGMHFFDLIQEGNIGLIKAVDKFEYKKGYKFSTYATWW 406

Query: 109 IKAAMQEYILRSWSLVK--------IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
           I+ A+   I      ++        +     + RLF        + + I +    P Q V
Sbjct: 407 IRQAITRAISDQARTIRVPVHMIEQVNKVIRETRLFIQEFGRDPNNEEIAERLGWPVQKV 466

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + K  NV+  E IS+   +  +E             S+  D++    D + +  +    
Sbjct: 467 KMVK--NVA-REPISLEIPVGSEE------------DSELGDFI---PDTEVETPVNAAA 508

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFK 278
                  + + +  L  RE+++   R   ++  P TLE +  +F+V+RER+RQIEA+A +
Sbjct: 509 SSILAEQIRQVLHTLPAREQKVIRMRFGLDDGYPQTLEEVGYQFKVTRERIRQIEAKALR 568

Query: 279 KVQ 281
           +++
Sbjct: 569 RLR 571


>gi|296159716|ref|ZP_06842538.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. Ch1-1]
 gi|295889930|gb|EFG69726.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. Ch1-1]
          Length = 665

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 63/246 (25%), Positives = 118/246 (47%), Gaps = 36/246 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   G+   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 427 AKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEGNIGLMKAVDKFEYRRGWKFSTYATWW 486

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           ++ A+   +      +++    +       L R+   +   T     P     +A+++ +
Sbjct: 487 VRQAVTRSLADQARTIRV--PVHMIETINKLNRISREILQQTGQEAHPS---VLAERMEL 541

Query: 169 SESEV----------ISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           SE +V          +SM   +   GD +L  +I  S  +S                   
Sbjct: 542 SEEKVRGILKIAKQPVSMETPVGDDGDATLGDMIEDSAASSPADAAM------------- 588

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEA 274
               + + R  +  ++  L+PRE ++   R     ++  TLE +  +F+V+RER+RQIE+
Sbjct: 589 ----QADLRAAIDDALDSLSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIRQIES 644

Query: 275 RAFKKV 280
           +A +K+
Sbjct: 645 KAMRKL 650


>gi|113477482|ref|YP_723543.1| RNA polymerase sigma factor SigD [Trichodesmium erythraeum IMS101]
 gi|110168530|gb|ABG53070.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
          Length = 319

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 61/239 (25%), Positives = 115/239 (48%), Gaps = 13/239 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V ++LRLVV +A  Y    + + +++ EG IG+ + V+KFDP +G+R +TY+ WW
Sbjct: 84  AKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWW 143

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      +++     +K     L ++K   + +T    +      IA++L +
Sbjct: 144 IRQAITRAIAEKGRTIRLPIHITEK-----LNKIKKVQRQLTQQLGRSATTGEIAEELGL 198

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +  ++    C       L+  +   D   ++  D L       E   ++   R +    L
Sbjct: 199 TPKQI--RECLERARLPLSLDLRVGDNQDTELGDLLEDTGASPEDYALQSSMRTD----L 252

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              M  L P+++++   R   E+   +TL  + +   +SRERVRQIE  A  K+++  Q
Sbjct: 253 ESIMVDLTPQQKQVLALRFGLEDGQTMTLSKIGAHLNISRERVRQIEREALSKLRKRKQ 311


>gi|119953489|ref|YP_945698.1| RNA polymerase sigma factor RpoD [Borrelia turicatae 91E135]
 gi|119862260|gb|AAX18028.1| RNA polymerase sigma factor RpoD [Borrelia turicatae 91E135]
          Length = 630

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 75/261 (28%), Positives = 127/261 (48%), Gaps = 36/261 (13%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE +  K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 378 EEILKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 433

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITD 151
           F+ +RGF+ +TY+ WWI+ A    I RS S        +Q R      R+  H+ + I  
Sbjct: 434 FEYKRGFKFSTYATWWIRQA----ITRSIS--------DQARTI----RVPVHMIEQINR 477

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
            N +   +V +  K    E     ++ RL  D      + +  +     +  +  + D  
Sbjct: 478 LNRETRYLVQVLGKDPTDEE----LSSRLGWDLKKVKTVKNVSREPVSLETPIGEEEDSV 533

Query: 212 EQVLIEKEERKNR---------RNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSS 260
               IE +  KN          ++ +   +  L  RE+ + + R   E+   +TLE +  
Sbjct: 534 LSDFIEDKAIKNPAKHTSFVVLQDQIRAVLGTLPEREQEVVKMRFGLEDGYSLTLEEVGL 593

Query: 261 EFEVSRERVRQIEARAFKKVQ 281
            F V+RER+RQIE++A ++++
Sbjct: 594 HFNVTRERIRQIESKALRRLK 614


>gi|113955141|ref|YP_730472.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CC9311]
 gi|113882492|gb|ABI47450.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CC9311]
          Length = 282

 Score = 84.0 bits (206), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 80/293 (27%), Positives = 141/293 (48%), Gaps = 51/293 (17%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-----------EHGDLSAAHRLVTSHLR 59
           NG I   +++ EI + P+L   EE  L    R           +     A  R++ ++LR
Sbjct: 6   NGNI--DQFLDEIGRTPLLTAAEEITLGTSVRMSQSPEATPAQKRAGKRAKDRMIKANLR 63

Query: 60  LVVKIAMGY--RGYG-LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           LVV ++  Y  R  G L   ++V EG+IGL +AV+KFDPE G++ +TY+ WWI+ ++   
Sbjct: 64  LVVTVSRKYLHRQLGQLEFGDLVQEGSIGLNRAVEKFDPELGYKFSTYAYWWIRQSISRA 123

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLK--------GHLQAITDNNLKPEQVVAIAKKLNV 168
           I ++ + +++ T+ N   +   L +L           L  ++D  LK  +   +AK+   
Sbjct: 124 IDQTSATIRVPTSMN--LVLAKLNQLPQGLNDEQICELLEVSDTQLKNLRHAFVAKR--- 178

Query: 169 SESEVISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
               + S++ +L  D   + L     D+ S+     L YD    E V         +R++
Sbjct: 179 ----IASLDMKLGADRDGSTLTELLCDEQST-----LNYDEFQWEAV---------KRSL 220

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++   LN  +  +   RR   +  +L+++++E  +SRERVRQ   RA K +
Sbjct: 221 GDQAKIALNNDQELL---RRNVVDEQSLQSIANEIGISRERVRQKVDRAKKHL 270


>gi|6463980|dbj|BAA86957.1| group 2 sigma factor RpoD3 [Synechococcus sp. PCC 7942]
          Length = 320

 Score = 83.6 bits (205), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 74/307 (24%), Positives = 141/307 (45%), Gaps = 53/307 (17%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR--------------EHGD-------------LS--- 48
           Y+ EI ++P+L  +EE VL KR +              E GD             LS   
Sbjct: 15  YLREIGRVPLLTHEEEVVLGKRVQQWMKLQELRQTLQSEEGDRDPSDLEWAAAAGLSIEE 74

Query: 49  ----------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
                     A  +++ ++LRLVV +A  Y    + + +++ EG IG+ + V+KFDP +G
Sbjct: 75  LRQQQHLGEQAKRKMIEANLRLVVSVAKKYLKRNMDLLDLIQEGTIGMQRGVEKFDPTKG 134

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           +R +TY+ WWI+ A+   I      +++     +K     +++++  L         PE 
Sbjct: 135 YRFSTYAYWWIRQAITRAIAEKARTIRLPIHITEK--LNKIKKMQRQLSQQLSTATLPE- 191

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              +A  L+++ ++V     +     SL+  +   D   ++  D L  D   + +   E 
Sbjct: 192 ---LAAALDLTPAQVRDYLEKARHPLSLD--LRVGDNQDTELGDLLETDMQRRRK---EF 243

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPV-TLENLSSEFEVSRERVRQIEARA 276
             + + R  + R +  L  ++R++   R  L++  V TL ++    ++SRERVRQ+E  A
Sbjct: 244 TLQASMRRDIDRLLDQLTEQQRQVIALRYGLEDGQVMTLASIGDRLQISRERVRQLEREA 303

Query: 277 FKKVQES 283
              ++++
Sbjct: 304 LHTLRQA 310


>gi|186685842|ref|YP_001869038.1| RNA polymerase sigma factor SigD [Nostoc punctiforme PCC 73102]
 gi|186468294|gb|ACC84095.1| RNA polymerase, sigma 70 subunit, RpoD family [Nostoc punctiforme
           PCC 73102]
          Length = 332

 Score = 83.6 bits (205), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 66/250 (26%), Positives = 113/250 (45%), Gaps = 39/250 (15%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V ++LRLVV +A  Y    + + +++ EG+IG+ + V+KFDP +G+R +TY+ WW
Sbjct: 97  AKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGSIGMQRGVEKFDPTKGYRFSTYAYWW 156

Query: 109 IKAAMQEYILRSWSLVKIGTTAN---------QKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      +++              Q++L   L R     +   +  L P+QV
Sbjct: 157 IRQAITRAIAEKARTIRLPIHITEKLNKIKKAQRQLSQKLGRAPTAGELAQELELTPKQV 216

Query: 160 VAIAKKLNVSESEVISMNCRLAG--DESLNALINSSDKNSSQW--QDWLVYDHDGQEQVL 215
               +K  +     +S++ RL    D  L  ++     +  ++  Q  L YD D      
Sbjct: 217 REYLEKARLP----LSLDLRLGDNYDTELGEMLEDPGASPEEFVMQSSLSYDLD------ 266

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIE 273
                         R M  L P++R +   R        +TL  +     +SRERVRQIE
Sbjct: 267 --------------RLMGDLTPQQREVITLRFGLTDGQALTLAKIGEILNISRERVRQIE 312

Query: 274 ARAFKKVQES 283
             A  K+++S
Sbjct: 313 REALTKLRKS 322


>gi|254430393|ref|ZP_05044096.1| possible type II alternative RNA polymerase sigma factor [Cyanobium
           sp. PCC 7001]
 gi|197624846|gb|EDY37405.1| possible type II alternative RNA polymerase sigma factor [Cyanobium
           sp. PCC 7001]
          Length = 302

 Score = 83.6 bits (205), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 79/304 (25%), Positives = 140/304 (46%), Gaps = 47/304 (15%)

Query: 16  LSRYIHEIRKIPMLEKQEEY----------VLAKRYREHGDLSAA--------------- 50
           +S Y+ EI +  +L  ++E           VL +R RE G    A               
Sbjct: 1   MSAYLGEIGRHQLLTPEQELTLGRKVQAMAVLQERCREAGGQGPACEYDDREKRVLRLGE 60

Query: 51  ---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              ++++T++LRLVV +A  Y+  GL + +++ EG +GL +AV+K+DP RG R +TY+ W
Sbjct: 61  RAKNQMITANLRLVVNLAKRYQNKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSTYAYW 120

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQK--RL-FFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           WI+  +   +      ++I    N+K  RL     R L+ H  + +   L  E  + +A+
Sbjct: 121 WIRQGLNRALSTQSRTIRIPVNVNEKLTRLRAAKARYLQSHGVSPSPKALAGEMQLPLAE 180

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
              +   E+ S+   L G       +  S  + S+  D L       E   +E+ E   R
Sbjct: 181 VEELLGCELRSITVSLQG-------VVKSKADPSELVDVL----PSPELAPMERAELAER 229

Query: 225 RNMLTRSM--SVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKK 279
              + + +  S L P+ER +   R   +      TL  ++ + + SRE  RQ+  RA +K
Sbjct: 230 SASVWKLLESSNLTPKERTVVMLRFGLDGSHEWRTLAEVARQLDCSREYCRQVVQRALRK 289

Query: 280 VQES 283
           ++++
Sbjct: 290 LRKT 293


>gi|91777566|ref|YP_552774.1| sigma 70 (RpoD) [Burkholderia xenovorans LB400]
 gi|91690226|gb|ABE33424.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia xenovorans
           LB400]
          Length = 665

 Score = 83.6 bits (205), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 63/246 (25%), Positives = 118/246 (47%), Gaps = 36/246 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   G+   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 427 AKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEGNIGLMKAVDKFEYRRGWKFSTYATWW 486

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           ++ A+   +      +++    +       L R+   +   T     P     +A+++ +
Sbjct: 487 VRQAVTRSLADQARTIRV--PVHMIETINKLNRISREILQQTGQEAHPS---VLAERMEL 541

Query: 169 SESEV----------ISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           SE +V          +SM   +   GD +L  +I  S  +S                   
Sbjct: 542 SEEKVRGILKIAKQPVSMETPVGDDGDATLGDMIEDSAASSPADAAM------------- 588

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEA 274
               + + R  +  ++  L+PRE ++   R     ++  TLE +  +F+V+RER+RQIE+
Sbjct: 589 ----QADLRAAIDDALDSLSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIRQIES 644

Query: 275 RAFKKV 280
           +A +K+
Sbjct: 645 KAMRKL 650


>gi|307592489|ref|YP_003900080.1| RNA polymerase sigma-32 factor RpoH [Cyanothece sp. PCC 7822]
 gi|306986134|gb|ADN18014.1| RNA polymerase, sigma 32 subunit, RpoH [Cyanothece sp. PCC 7822]
          Length = 307

 Score = 83.6 bits (205), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 71/243 (29%), Positives = 116/243 (47%), Gaps = 44/243 (18%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           AA  LV ++L+ V+ IA  Y G GL +S+++ EG++GL++A ++FDP  G++ +TY+ WW
Sbjct: 82  AADTLVRANLKFVIFIANRYVGRGLELSDLIQEGSLGLIRAAERFDPSLGYQFSTYANWW 141

Query: 109 IKAAMQEYILRSWSLVKIGTTANQ-----KRLFFNLRRLKGH-------LQAITDNNLKP 156
           ++A M   +      +++ +  N      K+   NL +L G         QA+  + L+ 
Sbjct: 142 VRAFMTRALANQSRTIRLPSQVNDKLNKIKKTRHNLAQLLGRSPSSSELAQALGISVLQL 201

Query: 157 EQVVAIAKKLNVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
             +  + KK        IS++  +   G E+L  LI SSD+ S           D  EQ+
Sbjct: 202 HSLAQLDKK-------TISLSVWVDEQGRETLQDLIPSSDEPSLDE----TLKPDEIEQL 250

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
           L                   L+PR + I   R L+    TL  +   F +SRERVR+I  
Sbjct: 251 L-----------------QTLSPRNQEIVRLRILEGK--TLSEIGQSFHLSRERVRKICL 291

Query: 275 RAF 277
           R+ 
Sbjct: 292 RSL 294


>gi|254415890|ref|ZP_05029647.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
 gi|196177317|gb|EDX72324.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
          Length = 352

 Score = 83.6 bits (205), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 71/303 (23%), Positives = 136/303 (44%), Gaps = 52/303 (17%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR--------------------------YREHGDLS---- 48
           Y+HEI ++P+L  ++E V  K+                          + +H DL     
Sbjct: 48  YLHEIGRVPLLTHEQEIVYGKQVQQMMPLLEAKDALAETLEREPTMQEWADHVDLEESAL 107

Query: 49  ---------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                    A  +++ ++LRLVV IA  Y+   +   +++ EG +GL + V+KFDP RG+
Sbjct: 108 KKIINQGTRAKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGY 167

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWI+ A+   I +    +++     +K     +++++  L      N  P + 
Sbjct: 168 KFSTYAYWWIRQAITRAIAQQARAIRLPIHITEK--LNKIKKVQRELSQRLGRNATPTE- 224

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I ++L +  +++           SL+  +   D   ++  D L  +  G   V    +
Sbjct: 225 --IGQELELEPAQIREYLSIARQPVSLD--VRVGDNQDTELSDLL--EDSGPTPVHYTTQ 278

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAF 277
           E  + R  L   ++ L P++R +   R   E  N ++L  +     +SRERVRQ+E +A 
Sbjct: 279 E--SLRQDLDNLLAELTPQQREVLALRFGLEDGNELSLAKVGQRLNLSRERVRQLEHQAL 336

Query: 278 KKV 280
            ++
Sbjct: 337 AQL 339


>gi|88809912|ref|ZP_01125417.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 7805]
 gi|88786102|gb|EAR17264.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 7805]
          Length = 355

 Score = 83.6 bits (205), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 75/281 (26%), Positives = 126/281 (44%), Gaps = 30/281 (10%)

Query: 13  EIGLSRYIHEIRKIPMLEKQ------EEYVLAKRYREHGDLSAAH-------------RL 53
           EI L R + E+ ++  +E +       E VLA    +   LSA               R+
Sbjct: 65  EITLGRQVQELMELESVEAELQEKRGGEAVLAAELAKAAGLSAVQLKRKLQAGRRAKERM 124

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V ++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP RG++ +TY+ WWI+  +
Sbjct: 125 VAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWWIRQGI 184

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
              I      +++     +      L +LK   + ++    +   V  +A  + + E EV
Sbjct: 185 TRAIAEKSRTIRLPIHITEM-----LNKLKKGQRELSQELGRTPSVTELASFVELPEDEV 239

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSM 232
             + CR     SL   +   D + ++  D L  D +   EQV  E E  K     L   +
Sbjct: 240 KELMCRARQPVSLE--MKVGDGDDTELLDLLAGDGELPSEQV--EGECLKGDLRDLLGQL 295

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
             L  R  R+       E P++L  +     +SR+RVR +E
Sbjct: 296 PELQERVLRMRYGMD-GEEPMSLTGIGRVIGISRDRVRNLE 335


>gi|51598964|ref|YP_073152.1| RNA polymerase sigma factor RpoD [Borrelia garinii PBi]
 gi|51573535|gb|AAU07560.1| RNA polymerase sigma-70 factor [Borrelia garinii PBi]
          Length = 631

 Score = 83.6 bits (205), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 72/261 (27%), Positives = 130/261 (49%), Gaps = 36/261 (13%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 379 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 434

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RGF+ +TY+ WWI+ A+   I      +++     ++     L R   +L  +   
Sbjct: 435 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQ--INRLNRETRYLVQVLGK 492

Query: 153 NLKPEQV-------VAIAKKLNVSESEVISMNCRLAGDES--LNALI-NSSDKNSSQWQD 202
           +   E++       +   K +     E +S+   +  +E   L+  I + + KN +    
Sbjct: 493 DPTDEELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTS 552

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSS 260
           ++V     Q+Q+          R++L      L  RE+ + + R   E+   +TLE +  
Sbjct: 553 FVVL----QDQI----------RSIL----GTLPEREQEVVKMRFGLEDGYSLTLEEVGL 594

Query: 261 EFEVSRERVRQIEARAFKKVQ 281
            F V+RER+RQIE++A ++++
Sbjct: 595 HFNVTRERIRQIESKALRRLK 615


>gi|39840783|emb|CAD20832.1| sigma factor [Spinacia oleracea]
          Length = 548

 Score = 83.6 bits (205), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 62/234 (26%), Positives = 122/234 (52%), Gaps = 19/234 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ S   LV+ ++  YRG G+   +++  GNIG++Q  ++FD  RG++ +TY  +WI+ A
Sbjct: 315 LLKSGRSLVLYLSRYYRGLGVAHEDLMQAGNIGILQGAERFDHTRGYQFSTYVQYWIRKA 374

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           M + + R    +K+ TT     L   + R++   + +  +  K    V ++K   +S  +
Sbjct: 375 MSQLVSRHGRGIKVPTT-----LSTTINRVQKARKILKRSQGKHPDDVEVSKSTGLSLDK 429

Query: 173 VISM-NC-RLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           + S  NC R+ G  D+ +   IN           +L    D   ++  +   +++ RN +
Sbjct: 430 IKSADNCLRIVGSLDQKVGHFIN---------MKYLECTPDTALEMPEKTVMKQHMRNDV 480

Query: 229 TRSMSVLNPRERRIFEAR-RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            + +  L+P+ERR+   R  L+ + ++L  +   F+VS+E +R++E RA  K++
Sbjct: 481 HKLLQELDPKERRVLIHRYGLEGHCMSLHEVGKVFDVSKEWIRKMEKRALTKLR 534


>gi|324999213|ref|ZP_08120325.1| RNA polymerase sigma factor SigB [Pseudonocardia sp. P1]
          Length = 380

 Score = 83.6 bits (205), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 77/261 (29%), Positives = 119/261 (45%), Gaps = 57/261 (21%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           G L+  H L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++AV+KFD  +GF+ +TY
Sbjct: 140 GALAKNH-LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAVEKFDYTKGFKFSTY 198

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + WWI+ A+   +            A+Q R      RL  HL          EQV  +A+
Sbjct: 199 ATWWIRQAITRGM------------ADQARTI----RLPVHLV---------EQVNKLAR 233

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD--------GQEQ--- 213
                      M+ R   + S   L   S     +  D L +  D        G E+   
Sbjct: 234 IKR-------DMHQRQGREPSEAELAQESGIPEHKISDLLDHARDPVSLDMPVGSEEEAP 286

Query: 214 --VLIEKEERKNRRNM---------LTRSMSVLNPRERRIFEARRLQEN--PVTLENLSS 260
               IE  E  +  N          L R ++ L  RE+++   R   ++  P TL+ +  
Sbjct: 287 LGDFIEDAEATDAENTVISSLLSDDLRRVLATLEDREQKVIRMRFGLDDGQPRTLDQIGR 346

Query: 261 EFEVSRERVRQIEARAFKKVQ 281
            F +SRERVRQIE     K++
Sbjct: 347 AFTLSRERVRQIEREVMAKLR 367


>gi|269963639|ref|ZP_06177962.1| conserved hypothetical protein [Vibrio harveyi 1DA3]
 gi|269831652|gb|EEZ85788.1| conserved hypothetical protein [Vibrio harveyi 1DA3]
          Length = 279

 Score = 83.6 bits (205), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 42/118 (35%), Positives = 73/118 (61%), Gaps = 4/118 (3%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY--- 68
           G+   + Y+ +I  I +L +++E   AK  R  GD  A   ++ S+LRLVVKIA  Y   
Sbjct: 8   GKDPYAHYLKDIVGIDLLSREDELHYAKLNRA-GDKEAREVMIESNLRLVVKIAKSYLKR 66

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            G    + +++ EGNIGL++A+ K+DPE G+R +TY++WWI+  ++  ++ +   V++
Sbjct: 67  TGNNFTLLDLIEEGNIGLIKAIDKYDPEPGYRFSTYAVWWIRENIEAALMNNGRTVRL 124


>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 = 83.6 bits (205), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 63/246 (25%), Positives = 118/246 (47%), Gaps = 36/246 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   G+   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 427 AKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEGNIGLMKAVDKFEYRRGWKFSTYATWW 486

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           ++ A+   +      +++    +       L R+   +   T     P     +A+++ +
Sbjct: 487 VRQAVTRSLADQARTIRV--PVHMIETINKLNRISREILQQTGQEAHPS---VLAERMEL 541

Query: 169 SESEV----------ISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           SE +V          +SM   +   GD +L  +I  S  +S                   
Sbjct: 542 SEEKVRGILKIAKQPVSMETPVGDDGDATLGDMIEDSAASSPADAAM------------- 588

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEA 274
               + + R  +  ++  L+PRE ++   R     ++  TLE +  +F+V+RER+RQIE+
Sbjct: 589 ----QADLRAAIDDALDSLSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIRQIES 644

Query: 275 RAFKKV 280
           +A +K+
Sbjct: 645 KAMRKL 650


>gi|158337052|ref|YP_001518227.1| RNA polymerase sigma factor SigD [Acaryochloris marina MBIC11017]
 gi|158307293|gb|ABW28910.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 318

 Score = 83.6 bits (205), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 59/239 (24%), Positives = 117/239 (48%), Gaps = 13/239 (5%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           H   +A  ++V ++LRLVV +A  Y    + + +++ EG IG+ + V+KFDP +G+R +T
Sbjct: 78  HEGEAAKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFST 137

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI+ A+   I      +++     +K     L ++K   + ++    +   +  +A
Sbjct: 138 YAYWWIRQAITRAIAEKGRTIRLPIHITEK-----LNKIKKTQRQLSQKLGRAATISELA 192

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
             L+++  +V     R     SL+  +   D   ++  + +    +  E   ++   R +
Sbjct: 193 TSLDLTTKQVREYLERARQPLSLD--VRVGDNQDTELGELIEDPSESPENFTLQASLRGD 250

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
               L R M+ L  +++++   R   ++  P+TL  +     +SRERVRQIE  A  K+
Sbjct: 251 ----LERLMADLTDQQQQVLHLRFGLDDGQPLTLAKIGDRLSISRERVRQIEREALSKL 305


>gi|85813983|emb|CAD20831.2| sigma factor [Spinacia oleracea]
          Length = 575

 Score = 83.6 bits (205), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 69/251 (27%), Positives = 126/251 (50%), Gaps = 25/251 (9%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           +R   HG      +++ S++RLV+ IA  Y+G G+ + ++V EG  GL++  +KFD  +G
Sbjct: 328 RRRLNHGTF-CKDKMIKSNVRLVISIAKNYQGSGMNLQDLVQEGCRGLVRGAEKFDASKG 386

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL-----RRLKGHLQAITDNN 153
           F+ +TY+ WWIK A+++          +   +   RL F++     R  +   Q +++N 
Sbjct: 387 FKFSTYAHWWIKQAVRK---------SLSDQSRTIRLPFHMVEATYRVKEARKQLLSENG 437

Query: 154 LKP-EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
            +P  + VA A  L++     + M  +           N + K S    D    + +  E
Sbjct: 438 KQPNNEEVAEATGLSMKRLTAVLMTPKAPRSLDQKIGFNMNLKPSEVIAD---PEAETAE 494

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
            +L ++  R++    L + +  L+ RE+++   R   E+    TL+ +     VSRER+R
Sbjct: 495 DLLTKQFMRQD----LEKVLDTLSSREKQVIRWRFGLEDGRMKTLQEIGELMGVSRERIR 550

Query: 271 QIEARAFKKVQ 281
           QIE+ AF+K+Q
Sbjct: 551 QIESSAFRKLQ 561


>gi|219684458|ref|ZP_03539402.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia garinii PBr]
 gi|219672447|gb|EED29500.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia garinii PBr]
          Length = 631

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 72/261 (27%), Positives = 130/261 (49%), Gaps = 36/261 (13%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 379 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 434

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RGF+ +TY+ WWI+ A+   I      +++     ++     L R   +L  +   
Sbjct: 435 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQ--INRLNRETRYLVQVLGK 492

Query: 153 NLKPEQV-------VAIAKKLNVSESEVISMNCRLAGDES--LNALI-NSSDKNSSQWQD 202
           +   E++       +   K +     E +S+   +  +E   L+  I + + KN +    
Sbjct: 493 DPTDEELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTS 552

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSS 260
           ++V     Q+Q+          R++L      L  RE+ + + R   E+   +TLE +  
Sbjct: 553 FVVL----QDQI----------RSIL----GTLPEREQEVVKMRFGLEDGYSLTLEEVGL 594

Query: 261 EFEVSRERVRQIEARAFKKVQ 281
            F V+RER+RQIE++A ++++
Sbjct: 595 HFNVTRERIRQIESKALRRLK 615


>gi|328948870|ref|YP_004366207.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           succinifaciens DSM 2489]
 gi|328449194|gb|AEB14910.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           succinifaciens DSM 2489]
          Length = 272

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 44/106 (41%), Positives = 66/106 (62%), Gaps = 2/106 (1%)

Query: 13  EIGLSR-YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           EI +++ Y++ ++K P+L   EE  LAKR +  GD  A + LV S+LRLVV +A  +   
Sbjct: 2   EIDVAKGYLNSLKKYPLLSADEEIALAKRIKS-GDKEAFNLLVNSNLRLVVSVAGRFNKG 60

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
              I +++ EGN+GLM A KKFDP  G R +TY+  WI   + ++I
Sbjct: 61  AFCIMDLIQEGNLGLMVAAKKFDPAFGTRFSTYAYRWIVQRIMKFI 106


>gi|219685543|ref|ZP_03540360.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia garinii
           Far04]
 gi|219672942|gb|EED29964.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia garinii
           Far04]
          Length = 631

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 72/261 (27%), Positives = 130/261 (49%), Gaps = 36/261 (13%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 379 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 434

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RGF+ +TY+ WWI+ A+   I      +++     ++     L R   +L  +   
Sbjct: 435 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQ--INRLNRETRYLVQVLGK 492

Query: 153 NLKPEQV-------VAIAKKLNVSESEVISMNCRLAGDES--LNALI-NSSDKNSSQWQD 202
           +   E++       +   K +     E +S+   +  +E   L+  I + + KN +    
Sbjct: 493 DPTDEELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTS 552

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSS 260
           ++V     Q+Q+          R++L      L  RE+ + + R   E+   +TLE +  
Sbjct: 553 FVVL----QDQI----------RSIL----GTLPEREQEVVKMRFGLEDGYSLTLEEVGL 594

Query: 261 EFEVSRERVRQIEARAFKKVQ 281
            F V+RER+RQIE++A ++++
Sbjct: 595 HFNVTRERIRQIESKALRRLK 615


>gi|21219415|ref|NP_625194.1| RNA polymerase principal sigma factor HrdC [Streptomyces coelicolor
           A3(2)]
 gi|256789543|ref|ZP_05527974.1| RNA polymerase principal sigma factor HrdC [Streptomyces lividans
           TK24]
 gi|289773432|ref|ZP_06532810.1| RNA polymerase principal sigma factor hrdC [Streptomyces lividans
           TK24]
 gi|123520|sp|P18184|HRDC_STRCO RecName: Full=RNA polymerase principal sigma factor hrdC
 gi|48741|emb|CAA37173.1| unnamed protein product [Streptomyces coelicolor A3(2)]
 gi|6562877|emb|CAB62686.1| RNA polymerase principal sigma factor HrdC [Streptomyces coelicolor
           A3(2)]
 gi|289703631|gb|EFD71060.1| RNA polymerase principal sigma factor hrdC [Streptomyces lividans
           TK24]
          Length = 339

 Score = 83.6 bits (205), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 80/292 (27%), Positives = 136/292 (46%), Gaps = 46/292 (15%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRY------RE------------------------HG 45
           L +Y+ +I   P+L  ++E  LA R       RE                        H 
Sbjct: 39  LGQYLTQIGATPLLTAEDEVRLATRIEAGVRAREELETADTGEPAPTPRRRRTLEETVHD 98

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
              A   +V ++LRLVV +A  +   GLP+ +V+ EGN+GL++AV+KFD  +GF+ +TY+
Sbjct: 99  GQEAKDHMVRANLRLVVSMAKRHAHRGLPLLDVIQEGNLGLIRAVEKFDHTKGFKFSTYA 158

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
            WWI+ A++  +      V++     ++     L +++  L+A  D     E+V A   +
Sbjct: 159 TWWIRQAIERGLATHARTVRLPVHVVEQ--LQKLAKVERKLRAGLDREPTTEEVAA---E 213

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE--ERKN 223
             +   +V+ +  R  G +++     S D    +  D +V D     +VL   E  E + 
Sbjct: 214 SGIDVDKVVWL--RRVGRDAV-----SLDTPVDETGDTVVGDLIPDTEVLRAPEVAEFQA 266

Query: 224 RRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIE 273
               L  ++  L PRE  I   R  L +  P TL+ ++    ++RERVRQ+E
Sbjct: 267 LAAELREAVGTLAPRESLILSLRYGLHDGRPRTLQQVAQHVGLTRERVRQLE 318


>gi|301320481|gb|ADK69124.1| putative RNA polymerase sigma factor RpoD [Mycoplasma mycoides
           subsp. mycoides SC str. Gladysdale]
          Length = 506

 Score = 83.2 bits (204), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 39/114 (34%), Positives = 71/114 (62%), Gaps = 3/114 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRY--REHGDLSAA-HRLVTSHLRLVVKIAMGYRGYG 72
           +  Y ++I + P+L K++E + AK     +  D+    ++L+ S+L+LV+ +A  +   G
Sbjct: 171 IKTYFYKIGQAPILTKEQEIIYAKMAVSDDPEDVQEGRNKLIESNLKLVISVARKHLNRG 230

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           L  ++++ EGNIGLM+AV KF+ E+GF+ +TY+ WWI+ A+   I      ++I
Sbjct: 231 LDFADLIEEGNIGLMKAVDKFEYEKGFKFSTYATWWIRQAITRAIADQARTIRI 284


>gi|319948428|ref|ZP_08022566.1| RNA polymerase sigma factor SigB [Dietzia cinnamea P4]
 gi|319437910|gb|EFV92892.1| RNA polymerase sigma factor SigB [Dietzia cinnamea P4]
          Length = 322

 Score = 83.2 bits (204), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 77/303 (25%), Positives = 135/303 (44%), Gaps = 58/303 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH----------------------GDLSAAH 51
           Y++ I K  +L  ++E  L+KR     Y +H                      G+ + AH
Sbjct: 29  YLNGIGKTALLNAEDEVELSKRIEAGLYAKHLLETKKRLGPAKKADLKTIVAEGEAARAH 88

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ 
Sbjct: 89  -LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTYATWWIRQ 147

Query: 112 AMQEYILRSWSLVK--------IGTTANQKR-LFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           A+   +      ++        +   A  KR L   L R     +   ++ +   ++   
Sbjct: 148 AITRGMADQSRTIRLPVHLVEQVNKLARIKRELHQQLGREATLEELAEESGIPAHKI--- 204

Query: 163 AKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            ++L     + +S++  +  DE   L   I  ++  S++        H     VL   EE
Sbjct: 205 -EELLDHSRDPVSLDMPVGADEEAPLGDFIEDAEATSAENTVVSNVMHSDVRAVLATLEE 263

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           R+ +   L   +    PR               TL+ +   F +SRERVRQIE     K+
Sbjct: 264 REQQVITLRFGLDDGQPR---------------TLDQIGKRFGLSRERVRQIEREVMAKL 308

Query: 281 QES 283
           +E 
Sbjct: 309 REG 311


>gi|320449783|ref|YP_004201879.1| RNA polymerase sigma factor RpoD [Thermus scotoductus SA-01]
 gi|320149952|gb|ADW21330.1| RNA polymerase sigma factor RpoD [Thermus scotoductus SA-01]
          Length = 494

 Score = 83.2 bits (204), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 64/242 (26%), Positives = 124/242 (51%), Gaps = 22/242 (9%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   L+ ++LRLVV IA  Y G GL   +++ EGN GL++AV+KF+ +R F+ +TY+ W
Sbjct: 253 AARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATW 312

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I        +   + +L    +++     +      IA+ + 
Sbjct: 313 WIRQAINRAIADQARTIRIPV-----HMVETINKLSRTARSLQQELGREPTYEEIAEAMG 367

Query: 168 VS-ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH-----DGQEQVLIEKEER 221
              +++ +    ++A  E ++      D+  S + D++  ++     D   Q L+ +E  
Sbjct: 368 PGWDAKRVEETLKIA-QEPVSLETPIGDEKDSFYGDFIPDENLPSPVDAAAQSLLAEE-- 424

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
                 L +++S L+ RE  + + R+  +     TLE + + F V+RER+RQIE +A +K
Sbjct: 425 ------LEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRK 478

Query: 280 VQ 281
           ++
Sbjct: 479 LK 480


>gi|317505016|ref|ZP_07962964.1| RNA polymerase sigma factor rpoD [Prevotella salivae DSM 15606]
 gi|315663898|gb|EFV03617.1| RNA polymerase sigma factor rpoD [Prevotella salivae DSM 15606]
          Length = 260

 Score = 83.2 bits (204), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 76/268 (28%), Positives = 132/268 (49%), Gaps = 50/268 (18%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGL 73
           L+ Y++EI K  +L   EE  L+++ ++ G  S  A ++L +++LR VV IA  Y   G+
Sbjct: 27  LNLYLNEIGKEELLSDDEENKLSQQIQQGGASSERAINKLTSANLRFVVAIAKQYTDRGV 86

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            I +++SEGNIGLM+A   FD  RG R   Y+  +++ A++  +             N++
Sbjct: 87  AILDLISEGNIGLMKAAMSFDGSRGLRFVGYAEPFVRRAIEAAV-------------NEQ 133

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
              F   RL  H  +       PE+      K N   S   S++  L   ++++ L   S
Sbjct: 134 SGIF---RLPKHENS-------PEE------KAN---SRAFSVDAPLENGKNMSLLSVLS 174

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           D N+++  D  V +   +E+              L ++M++LN RE+ + EA      P 
Sbjct: 175 DPNAARP-DQEVLEASVKEE--------------LMQAMNILNQREKNVVEAFYGIGQPH 219

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKV 280
           +T   ++ +  + RERVRQI  +A +K+
Sbjct: 220 LTFAEIAEKMGLKRERVRQIRNKAVRKL 247


>gi|256383860|gb|ACU78430.1| RNA polymerase sigma-A factor [Mycoplasma mycoides subsp. capri
           str. GM12]
 gi|256384691|gb|ACU79260.1| RNA polymerase sigma-A factor [Mycoplasma mycoides subsp. capri
           str. GM12]
 gi|296455677|gb|ADH21912.1| RNA polymerase sigma-A factor [synthetic Mycoplasma mycoides
           JCVI-syn1.0]
          Length = 506

 Score = 83.2 bits (204), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 39/114 (34%), Positives = 71/114 (62%), Gaps = 3/114 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRY--REHGDLSAA-HRLVTSHLRLVVKIAMGYRGYG 72
           +  Y ++I + P+L K++E + AK     +  D+    ++L+ S+L+LV+ +A  +   G
Sbjct: 171 IKTYFYKIGQAPILTKEQEIIYAKMAVSDDPEDVQEGRNKLIESNLKLVISVARKHLNRG 230

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           L  ++++ EGNIGLM+AV KF+ E+GF+ +TY+ WWI+ A+   I      ++I
Sbjct: 231 LDFADLIEEGNIGLMKAVDKFEYEKGFKFSTYATWWIRQAITRAIADQARTIRI 284


>gi|331703466|ref|YP_004400153.1| RNA polymerase sigma A factor [Mycoplasma mycoides subsp. capri LC
           str. 95010]
 gi|328802021|emb|CBW54175.1| RNA polymerase sigma A factor [Mycoplasma mycoides subsp. capri LC
           str. 95010]
          Length = 506

 Score = 83.2 bits (204), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 39/114 (34%), Positives = 71/114 (62%), Gaps = 3/114 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRY--REHGDLSAA-HRLVTSHLRLVVKIAMGYRGYG 72
           +  Y ++I + P+L K++E + AK     +  D+    ++L+ S+L+LV+ +A  +   G
Sbjct: 171 IKTYFYKIGQAPILTKEQEIIYAKMAVSDDPEDVQEGRNKLIESNLKLVISVARKHLNRG 230

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           L  ++++ EGNIGLM+AV KF+ E+GF+ +TY+ WWI+ A+   I      ++I
Sbjct: 231 LDFADLIEEGNIGLMKAVDKFEYEKGFKFSTYATWWIRQAITRAIADQARTIRI 284


>gi|1553019|gb|AAC45101.1| primary sigma factor [Borrelia garinii]
          Length = 450

 Score = 83.2 bits (204), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 78/260 (30%), Positives = 126/260 (48%), Gaps = 36/260 (13%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 215 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 270

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITD 151
           F+ +RGF+ +TY+ WWI+ A    I RS S        +Q R      R+  H+ + I  
Sbjct: 271 FEYKRGFKFSTYATWWIRQA----ITRSIS--------DQARTI----RVPVHMIEQINR 314

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
            N +   +V +  K    E     ++ RL  +      + S  +     +  +  + D  
Sbjct: 315 LNRETRYLVQVLGKDPTDEE----LSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSV 370

Query: 212 EQVLIEKEERKNRRNMLT--------RS-MSVLNPRERRIFEARRLQEN--PVTLENLSS 260
               IE +  KN  N  +        RS +  L  RE+ + + R   E+   +TLE +  
Sbjct: 371 LSDFIEDKAIKNPANHTSFVVLQDQIRSILGTLPEREQEVVKMRFGLEDGYSLTLEEVGL 430

Query: 261 EFEVSRERVRQIEARAFKKV 280
            F V+RER+RQIE++A +++
Sbjct: 431 HFNVTRERIRQIESKALRRL 450


>gi|169630111|ref|YP_001703760.1| RNA polymerase sigma factor SigB [Mycobacterium abscessus ATCC
           19977]
 gi|169242078|emb|CAM63106.1| RNA polymerase sigma factor [Mycobacterium abscessus]
          Length = 323

 Score = 83.2 bits (204), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 76/301 (25%), Positives = 143/301 (47%), Gaps = 58/301 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH----------------------GDLSAAH 51
           Y++ I K  +L  ++E  LAKR     Y +H                      G+ + +H
Sbjct: 30  YLNGIGKTALLTAEDEVELAKRIEAGLYAQHLLDTKKRLGEARKKDLAVIVREGNAARSH 89

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ 
Sbjct: 90  -LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTYATWWIRQ 148

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ-----AITDNNLKPEQVVAIAKKL 166
           A+   +      +++     ++     L R+K  L        +D  L  E  + + K  
Sbjct: 149 AITRGMADQSRTIRLPVHLVEQ--VNKLARIKRELHQRLGREASDEELAEESGIPVEKIG 206

Query: 167 NVSES--EVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           ++ +   + +S++  +  DE   L   I  ++  S+             E  +I +    
Sbjct: 207 DLLDHSRDPVSLDMPVGTDEEAPLGDFIEDTEAMSA-------------ENAVIAELLHS 253

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R++L    + L+ RE+++   R   ++    TL+ +   F +SRERVRQIE     K+
Sbjct: 254 DVRSVL----ATLDEREQQVIRLRYGLDDGQARTLDQIGKLFGLSRERVRQIEREVMAKL 309

Query: 281 Q 281
           +
Sbjct: 310 R 310


>gi|42561001|ref|NP_975452.1| RNA polymerase sigma-A factor [Mycoplasma mycoides subsp. mycoides
           SC str. PG1]
 gi|42492498|emb|CAE77094.1| RNA polymerase sigma-A factor [Mycoplasma mycoides subsp. mycoides
           SC str. PG1]
          Length = 522

 Score = 83.2 bits (204), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 39/114 (34%), Positives = 71/114 (62%), Gaps = 3/114 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRY--REHGDLSAA-HRLVTSHLRLVVKIAMGYRGYG 72
           +  Y ++I + P+L K++E + AK     +  D+    ++L+ S+L+LV+ +A  +   G
Sbjct: 187 IKTYFYKIGQAPILTKEQEIIYAKMAVSDDPEDVQEGRNKLIESNLKLVISVARKHLNRG 246

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           L  ++++ EGNIGLM+AV KF+ E+GF+ +TY+ WWI+ A+   I      ++I
Sbjct: 247 LDFADLIEEGNIGLMKAVDKFEYEKGFKFSTYATWWIRQAITRAIADQARTIRI 300


>gi|253761922|ref|XP_002489335.1| hypothetical protein SORBIDRAFT_0010s016080 [Sorghum bicolor]
 gi|241946983|gb|EES20128.1| hypothetical protein SORBIDRAFT_0010s016080 [Sorghum bicolor]
          Length = 238

 Score = 83.2 bits (204), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 68/246 (27%), Positives = 122/246 (49%), Gaps = 43/246 (17%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           +VTS++RLV+ IA  + G G+ + +++ EG  GL++  +KFD  +GFR +TYS WWIK A
Sbjct: 1   MVTSNVRLVISIAREFEGPGMDLYDLIQEGMQGLIRGAEKFDASKGFRFSTYSHWWIKQA 60

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           M++ +            + Q ++F    RL  H+   +   +K        K      +E
Sbjct: 61  MRKSV------------SEQSQIF----RLPAHMVEAS-YRVKECTKRLRRKLRRRPTNE 103

Query: 173 VISMNCRLAGDE------------SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I+++  +                SL++ I S+D         + Y     +      EE
Sbjct: 104 EIALDTGMPIKRVEAAVNLPKYSVSLDSKIGSTD---------MTYQEVTADPSAETAEE 154

Query: 221 RKNRRNM---LTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEAR 275
             NR +M   + +++  L  RE+++   R  L+++ + TL+ + +   VSRER+RQIE+ 
Sbjct: 155 MLNRMSMKKDVHKALDTLTTREKQVVVLRFGLEDDRIRTLQEIGNIMGVSRERIRQIESG 214

Query: 276 AFKKVQ 281
           AF+K++
Sbjct: 215 AFRKLR 220


>gi|110626973|gb|ABG79025.1| RpoH [Wolbachia endosymbiont of Armadillidium vulgare]
 gi|110626982|gb|ABG79031.1| RpoH [Wolbachia endosymbiont of Armadillidium nasatum]
 gi|110626985|gb|ABG79033.1| RpoH [Wolbachia endosymbiont of Armadillidium album]
          Length = 78

 Score = 83.2 bits (204), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 37/72 (51%), Positives = 54/72 (75%)

Query: 7  SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
          ++ VN    L +YI E+RK PML ++EE  LAK ++EH D+S+AH+L+TSHL LVVKIAM
Sbjct: 7  NLYVNSSTNLMQYIAEVRKFPMLSQEEEVRLAKNWQEHKDISSAHKLITSHLNLVVKIAM 66

Query: 67 GYRGYGLPISEV 78
           ++ YGL + ++
Sbjct: 67 KFKNYGLLLMDL 78


>gi|313837139|gb|EFS74853.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL037PA2]
 gi|314927839|gb|EFS91670.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL044PA1]
 gi|314971910|gb|EFT16008.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL037PA3]
 gi|328907302|gb|EGG27068.1| sigma-70 region 2 [Propionibacterium sp. P08]
          Length = 312

 Score = 83.2 bits (204), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 81/312 (25%), Positives = 141/312 (45%), Gaps = 59/312 (18%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------------- 43
           ++G+  +  Y+  I +  +L   EE  LA+R                             
Sbjct: 13  IDGKDAVGLYLDGIARTSLLNAAEEVALARRIEAGVFARAVLEGQAETTSDATTEELHQI 72

Query: 44  --HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
              GD + AH  V ++LRLVV +A  Y    +P+ ++V EGN GL++AV+KFD  +GF+ 
Sbjct: 73  AADGDEAMAH-FVRANLRLVVSVARKYGRSQMPLLDLVQEGNTGLIRAVEKFDYAKGFKF 131

Query: 102 ATYSMWWIKAAMQEYILRSWSLVK----IGTTANQ-KRLFFNLRRLKGHLQAITDNNLKP 156
           +TY+ WW++ A+   I +   +V+    +    NQ      NL R  G          +P
Sbjct: 132 STYATWWVRQAISRGIAQQGRIVRLPVHVAEQVNQVSAARRNLERQLGR---------EP 182

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHD-GQEQV 214
           E    IA +L ++E  VI +  R   D  SL+A +   D   +   D +  +   G + +
Sbjct: 183 E-TSEIADELEITEERVIEL-IRFGRDHVSLDAPVE--DDGDTSLGDLIARETSPGPDDI 238

Query: 215 LIEKEERKNRRNMLT----RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
           +++ E+R     +L     RS  V+  R   + + R+ +     L ++   + ++ ERVR
Sbjct: 239 VLDAEDRGRLEGLLDNLDERSADVVR-RRYGLVDGRQAK-----LADIGKVWGITAERVR 292

Query: 271 QIEARAFKKVQE 282
           QIE  A   +++
Sbjct: 293 QIERAALDSMRQ 304


>gi|284044896|ref|YP_003395236.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Conexibacter
           woesei DSM 14684]
 gi|283949117|gb|ADB51861.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Conexibacter
           woesei DSM 14684]
          Length = 300

 Score = 83.2 bits (204), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 45/120 (37%), Positives = 70/120 (58%), Gaps = 2/120 (1%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG-L 73
            L  ++    + P+L   EE  L++R  E GDL+A  RLV  +LRLVV IA  ++G   L
Sbjct: 30  ALQLFLRRASRYPLLTPAEELALSRRI-ERGDLAAKERLVNHNLRLVVSIARRFQGVSEL 88

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + ++V EG +GL++A +KFD  RGFR +TY+  WI+ A+Q  I      +++     Q+
Sbjct: 89  TLLDLVQEGVVGLIRAAEKFDWRRGFRFSTYATLWIRQAIQRGIATHGRTIRLPVNVAQR 148


>gi|1553023|gb|AAC45103.1| primary sigma factor [Borrelia garinii]
          Length = 450

 Score = 83.2 bits (204), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 78/260 (30%), Positives = 126/260 (48%), Gaps = 36/260 (13%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 215 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 270

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITD 151
           F+ +RGF+ +TY+ WWI+ A    I RS S        +Q R      R+  H+ + I  
Sbjct: 271 FEYKRGFKFSTYATWWIRQA----ITRSIS--------DQARTI----RVPVHMIEQINR 314

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
            N +   +V +  K    E     ++ RL  +      + S  +     +  +  + D  
Sbjct: 315 LNRETRYLVQVLGKDPTDEE----LSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSV 370

Query: 212 EQVLIEKEERKNRRNMLT--------RS-MSVLNPRERRIFEARRLQEN--PVTLENLSS 260
               IE +  KN  N  +        RS +  L  RE+ + + R   E+   +TLE +  
Sbjct: 371 LSDFIEDKAIKNPANHTSFVVLQDQIRSILGTLPEREQEVVKMRFGLEDGYSLTLEEVGL 430

Query: 261 EFEVSRERVRQIEARAFKKV 280
            F V+RER+RQIE++A +++
Sbjct: 431 HFNVTRERIRQIESKALRRL 450


>gi|1553029|gb|AAC45106.1| primary sigma factor [Borrelia garinii]
          Length = 450

 Score = 83.2 bits (204), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 78/260 (30%), Positives = 126/260 (48%), Gaps = 36/260 (13%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 215 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 270

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITD 151
           F+ +RGF+ +TY+ WWI+ A    I RS S        +Q R      R+  H+ + I  
Sbjct: 271 FEYKRGFKFSTYATWWIRQA----ITRSIS--------DQARTI----RVPVHMIEQINR 314

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
            N +   +V +  K    E     ++ RL  +      + S  +     +  +  + D  
Sbjct: 315 LNRETRYLVQVLGKDPTDEE----LSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSV 370

Query: 212 EQVLIEKEERKNRRNMLT--------RS-MSVLNPRERRIFEARRLQEN--PVTLENLSS 260
               IE +  KN  N  +        RS +  L  RE+ + + R   E+   +TLE +  
Sbjct: 371 LSDFIEDKAIKNPANHTSFVVLQDQIRSILGTLPEREQEVVKMRFGLEDGYSLTLEEVGL 430

Query: 261 EFEVSRERVRQIEARAFKKV 280
            F V+RER+RQIE++A +++
Sbjct: 431 HFNVTRERIRQIESKALRRL 450


>gi|1553025|gb|AAC45104.1| primary sigma factor [Borrelia garinii]
 gi|1553031|gb|AAC45107.1| primary sigma factor [Borrelia garinii]
          Length = 450

 Score = 83.2 bits (204), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 78/260 (30%), Positives = 126/260 (48%), Gaps = 36/260 (13%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 215 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 270

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITD 151
           F+ +RGF+ +TY+ WWI+ A    I RS S        +Q R      R+  H+ + I  
Sbjct: 271 FEYKRGFKFSTYATWWIRQA----ITRSIS--------DQARTI----RVPVHMIEQINR 314

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
            N +   +V +  K    E     ++ RL  +      + S  +     +  +  + D  
Sbjct: 315 LNRETRYLVQVLGKDPTDEE----LSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSV 370

Query: 212 EQVLIEKEERKNRRNMLT--------RS-MSVLNPRERRIFEARRLQEN--PVTLENLSS 260
               IE +  KN  N  +        RS +  L  RE+ + + R   E+   +TLE +  
Sbjct: 371 LSDFIEDKAIKNPANHTSFVVLQDQIRSILGTLPEREQEVVKMRFGLEDGYSLTLEEVGL 430

Query: 261 EFEVSRERVRQIEARAFKKV 280
            F V+RER+RQIE++A +++
Sbjct: 431 HFNVTRERIRQIESKALRRL 450


>gi|284031338|ref|YP_003381269.1| RpoD subfamily RNA polymerase sigma-70 subunit [Kribbella flavida
           DSM 17836]
 gi|283810631|gb|ADB32470.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Kribbella flavida
           DSM 17836]
          Length = 316

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 77/310 (24%), Positives = 146/310 (47%), Gaps = 51/310 (16%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--------------------- 48
           ++G+  +  Y+ EI + P+L  +EE  LA+   E G L+                     
Sbjct: 11  IDGKDSVGLYLEEIARTPLLTAEEEVELAETV-EAGLLAEQLLAEGRVGRKKGGAPKYAT 69

Query: 49  -------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
                        A  R VT++LRLVV IA  Y    +P+ ++V EGN GL++AV+KFD 
Sbjct: 70  EEELEWLAAEGQRAQQRFVTANLRLVVSIARRYGRSQMPLLDLVQEGNTGLIRAVEKFDY 129

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            +GF+ +TY+ WW++ A+   I +   +V++     ++     L ++    + +     +
Sbjct: 130 RKGFKFSTYATWWVRQAITRGIAQQARVVRLPVHVVEQ-----LNQIGSARRTLERKLGR 184

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYD-HDGQEQ 213
             ++  IA +L++ E  V  +  R+  D  SL+  I+  D+  +   D +  +   G +Q
Sbjct: 185 EPEIDEIAAELDLDEERVTEL-IRIGRDHISLDNPID--DEGETSLGDLIAAETAPGPDQ 241

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQ 271
           ++ +  +R    +++ +    L+PR   +   R  L +     L ++ +   +S ERVRQ
Sbjct: 242 LVADASDRSGLFSLVDQ----LDPRSADVIRRRYGLHDGRQAKLADIGAVHGISAERVRQ 297

Query: 272 IEARAFKKVQ 281
           IE  A  +++
Sbjct: 298 IEREALGRLR 307


>gi|55274945|gb|AAV49272.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 204

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 34/67 (50%), Positives = 52/67 (77%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ S+LRL+VKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+ 
Sbjct: 1   RMIESNLRLMVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQ 60

Query: 112 AMQEYIL 118
            ++  I+
Sbjct: 61  TIERAIM 67


>gi|88854620|ref|ZP_01129287.1| RNA polymerase sigma factor [marine actinobacterium PHSC20C1]
 gi|88816428|gb|EAR26283.1| RNA polymerase sigma factor [marine actinobacterium PHSC20C1]
          Length = 1108

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 74/256 (28%), Positives = 119/256 (46%), Gaps = 40/256 (15%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R   S+ RLV  IA  Y   GL  ++++ EG +GL++A++KFD  +GF+ +TY+ WW
Sbjct: 683 AFARFAASNYRLVFSIARRYVNNGLDYADLIQEGALGLLRAIQKFDYMKGFKFSTYATWW 742

Query: 109 IKAAMQEYILRSWSLVKIGT--TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           ++ A+   +    S ++I       Q +L    R  +  LQ    N+ KP  +  +A   
Sbjct: 743 VRQAITRALADLGSTIRIPVHMVEQQNKLRQAARSFE--LQ----NDRKP-TISELAAGA 795

Query: 167 NVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
            V+E +           +S++  L   E   +L N            LV +      +LI
Sbjct: 796 EVTEQDASRALGYEYSFLSIDKELDPGEGFGSLHN-----------LLVDESVAPVDLLI 844

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEA 274
             E R    N+L    S L  RE    + R     ++P TL+++   F V+RER+RQIE 
Sbjct: 845 HAEFRGAMNNVL----SALPKRESTTIQMRFGIGGQDPATLDHIGDIFGVTRERIRQIE- 899

Query: 275 RAFKKVQESIQKQVEL 290
              KK  ES++   E+
Sbjct: 900 ---KKTMESLRSSAEV 912


>gi|17231292|ref|NP_487840.1| RNA polymerase sigma factor [Nostoc sp. PCC 7120]
 gi|8489801|gb|AAF75758.1|AF262217_2 group 2 sigma 70-type sigma factor E [Nostoc sp. PCC 7120]
 gi|17132934|dbj|BAB75499.1| group 2 sigma 70-type sigma factor E [Nostoc sp. PCC 7120]
          Length = 327

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 59/231 (25%), Positives = 114/231 (49%), Gaps = 13/231 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +++ ++LRLVV IA  Y+   +   +++ EG +GL + V+KFDP RG++ +TY+ WW
Sbjct: 92  AKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPMRGYKFSTYAYWW 151

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I +    +++     +K     +++++  L      +  P +   IAK+L +
Sbjct: 152 IRQAITRAIAQQGRTIRLPIHITEK--LNKIKKVQRELAQTLGRSPSPAE---IAKELEL 206

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
             +++           SL+  +   D   ++ Q+ L  D    E    ++  R++   +L
Sbjct: 207 EPAQIREYLNMARQPVSLD--VKVGDNQDTELQEMLEDDGPSPEYYTTQEFLRQDLNTLL 264

Query: 229 TRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAF 277
                 L P++R +   R   L  N ++L  +     +SRERVRQ+E +A 
Sbjct: 265 AE----LTPQQREVVALRFGLLDGNELSLAKVGERLNLSRERVRQLEHQAL 311


>gi|1553027|gb|AAC45105.1| primary sigma factor [Borrelia garinii]
          Length = 450

 Score = 83.2 bits (204), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 78/260 (30%), Positives = 126/260 (48%), Gaps = 36/260 (13%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 215 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 270

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITD 151
           F+ +RGF+ +TY+ WWI+ A    I RS S        +Q R      R+  H+ + I  
Sbjct: 271 FEYKRGFKFSTYATWWIRQA----ITRSIS--------DQARTI----RVPVHMIEQINR 314

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
            N +   +V +  K    E     ++ RL  +      + S  +     +  +  + D  
Sbjct: 315 LNRETRYLVQVLGKDPTDEE----LSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSV 370

Query: 212 EQVLIEKEERKNRRNMLT--------RS-MSVLNPRERRIFEARRLQEN--PVTLENLSS 260
               IE +  KN  N  +        RS +  L  RE+ + + R   E+   +TLE +  
Sbjct: 371 LSDFIEDKAIKNPANHTSFVVLQDQIRSILGTLPEREQEVVKMRFGLEDGYSLTLEEVGL 430

Query: 261 EFEVSRERVRQIEARAFKKV 280
            F V+RER+RQIE++A +++
Sbjct: 431 HFNVTRERIRQIESKALRRL 450


>gi|596248|gb|AAC44104.1| primary sigma factor [Borrelia burgdorferi]
          Length = 543

 Score = 82.8 bits (203), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 76/261 (29%), Positives = 134/261 (51%), Gaps = 36/261 (13%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 291 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 346

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI--- 149
           F+ +RGF+ +TY+ WWI+ A+   I      +++     ++    N R  +  +Q +   
Sbjct: 347 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLN-RETRYLIQVLGKD 405

Query: 150 -TDNNLKPEQVVAIAKKLNVSES---EVISMNCRLAGDES--LNALI-NSSDKNSSQWQD 202
            TD  L  +++    KK+   +S   E +S+   +  +E   L+  I + + KN +    
Sbjct: 406 PTDEEL-SDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTS 464

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSS 260
           ++V     Q+Q+          R +L      L  RE+ + + R   E+   +TLE +  
Sbjct: 465 FVVL----QDQI----------RAIL----GTLPEREQEVVKMRFGLEDGYSLTLEEVGL 506

Query: 261 EFEVSRERVRQIEARAFKKVQ 281
            F V+RER+RQIE++A ++++
Sbjct: 507 HFNVTRERIRQIESKALRRLK 527


>gi|332708935|ref|ZP_08428906.1| RNA polymerase sigma factor, sigma-70 family//RpoD-like family
           [Lyngbya majuscula 3L]
 gi|332352477|gb|EGJ32046.1| RNA polymerase sigma factor, sigma-70 family//RpoD-like family
           [Lyngbya majuscula 3L]
          Length = 333

 Score = 82.8 bits (203), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 72/313 (23%), Positives = 140/313 (44%), Gaps = 72/313 (23%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR-------EHGDLS----------------------- 48
           Y+HEI ++P+L  ++E V  K+ +       E   L+                       
Sbjct: 29  YLHEIGRVPLLTHEQEIVYGKQVQQMMALLGEKATLAQELEREPTTEEWASYVNKSEAEL 88

Query: 49  ---------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                    A  +++ ++LRLVV IA  Y+   +   +++ EG +GL + V+KFDP RG+
Sbjct: 89  KKAIDQGTRAKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGY 148

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWI+ A+   I +    +++     +K     +++++  L      N  P + 
Sbjct: 149 KFSTYAYWWIRQAITRAIAQQARAIRLPIHITEK--LNKIKKVQRELSQTLGRNATPTE- 205

Query: 160 VAIAKKLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
             IAK+L++  +++          IS++ R+             D   ++  + L  + D
Sbjct: 206 --IAKELDLEPAQIREYLSIARQPISLDVRVG------------DNQDTELSELL--EDD 249

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRE 267
           G   V    +E  + R  L   ++ L P++R +   R   E+   ++L  +     +SRE
Sbjct: 250 GLTPVNYTTQE--SLRQDLNLLLAELTPQQREVLALRFGLEDGKELSLAKVGKRLNLSRE 307

Query: 268 RVRQIEARAFKKV 280
           RVRQ+E +A  ++
Sbjct: 308 RVRQLEHQALAQL 320


>gi|162448460|ref|YP_001610827.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
 gi|161159042|emb|CAN90347.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
          Length = 446

 Score = 82.8 bits (203), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 77/249 (30%), Positives = 128/249 (51%), Gaps = 20/249 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   LV ++LRL V IA  ++ +G+P+ ++V EGN+GL++A  KF+  RG R  TY+ WW
Sbjct: 209 AKSELVQANLRLAVAIAREHQRFGVPLLDLVQEGNLGLIRAADKFEYRRGHRFGTYAAWW 268

Query: 109 IKAAMQEYILRSWSLVKIGT--TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK- 165
           IK A++  IL     V++    TA + ++    R L      + +   +P  V  IA++ 
Sbjct: 269 IKQAIKRTILNQGKPVRMPVHLTAIRSQVVRARRDL------VQERGREP-SVEEIAERS 321

Query: 166 -LNVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
            L V +  VIS    LA +  SL+A +   ++  +++ D L  D      +L  +   + 
Sbjct: 322 GLTVEKVRVIS---ELALEPLSLDAPVG--EEGDTRYGDLLANDEPTPADMLARRRLIEQ 376

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            R +L           RR F     ++   TLE +   F ++RER+RQIEA+  +K++ +
Sbjct: 377 TRELLDSLQPRERELLRRRFGLDGNEDE--TLEEIGQSFSLTRERIRQIEAKLLEKLR-T 433

Query: 284 IQKQVELSS 292
             +Q EL S
Sbjct: 434 RSRQRELGS 442


>gi|1553011|gb|AAC45097.1| primary sigma factor [Borrelia afzelii]
          Length = 450

 Score = 82.8 bits (203), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 78/260 (30%), Positives = 126/260 (48%), Gaps = 36/260 (13%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 215 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 270

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITD 151
           F+ +RGF+ +TY+ WWI+ A    I RS S        +Q R      R+  H+ + I  
Sbjct: 271 FEYKRGFKFSTYATWWIRQA----ITRSIS--------DQARTI----RVPVHMIEQINR 314

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
            N +   +V +  K    E     ++ RL  +      + S  +     +  +  + D  
Sbjct: 315 LNRETRYLVQVLGKDPTDEE----LSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSV 370

Query: 212 EQVLIEKEERKNRRNMLT--------RS-MSVLNPRERRIFEARRLQEN--PVTLENLSS 260
               IE +  KN  N  +        RS +  L  RE+ + + R   E+   +TLE +  
Sbjct: 371 LSDFIEDKAIKNPANHTSFVVLQDQIRSILGTLPEREQEVVKMRFGLEDGYSLTLEEVGL 430

Query: 261 EFEVSRERVRQIEARAFKKV 280
            F V+RER+RQIE++A +++
Sbjct: 431 HFNVTRERIRQIESKALRRL 450


>gi|110626976|gb|ABG79027.1| RpoH [Wolbachia endosymbiont of Armadillidium vulgare]
          Length = 78

 Score = 82.8 bits (203), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 37/67 (55%), Positives = 51/67 (76%)

Query: 7  SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
          ++ VN    L +YI E+RK PML ++EE  LAK ++EH D+S+AH+L+TSHL LVVKIAM
Sbjct: 7  NLYVNSSTNLMQYIAEVRKFPMLSQEEEVRLAKNWQEHKDISSAHKLITSHLNLVVKIAM 66

Query: 67 GYRGYGL 73
           ++ YGL
Sbjct: 67 KFKNYGL 73


>gi|331028036|ref|YP_004421751.1| group 2 RNA polymerase sigma factor [Synechococcus phage S-CBS3]
 gi|294805649|gb|ADF42487.1| group 2 RNA polymerase sigma factor [Synechococcus phage S-CBS3]
          Length = 299

 Score = 82.8 bits (203), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 76/302 (25%), Positives = 142/302 (47%), Gaps = 51/302 (16%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYR-------EHGDLS---------------AAHRL 53
           ++ Y+ +I + P+L   EE   +++ +       EH D S               A  R+
Sbjct: 4   VADYLKQIGRHPLLTATEEIEYSRQIQAMLAVQAEHPDSSTHTHQQRVIIRRGQRAKERM 63

Query: 54  VTSHLRLVVKIAMGY--RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +  +LRLVV IA  Y  R   L + ++V +GN+GL +A + FDP RG++ +TY+ WWI+ 
Sbjct: 64  IVRNLRLVVTIAKKYVKRCTSLEMLDLVQDGNMGLARATELFDPSRGYKFSTYAYWWIRQ 123

Query: 112 AMQEYILRSWSLVKIGTTANQK----RLFFNLR-RLKGHLQAITDN----NLKPEQVVAI 162
           ++   +     ++++    ++K    R + N +  + G +  I +     +  P ++ A 
Sbjct: 124 SISRGLQDRDRMIRLPIHRHEKVIKARAYMNHQLAMTGKMPTIAECAAAVDADPHELQAS 183

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
                V   +V S++ + +G + L+ +++     +S  +D         ++ LIE+E   
Sbjct: 184 L----VMAQDVCSLDAKASGRDDLSPILDLIPDPASLHKD---------DEYLIEREILH 230

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +  NML+     +  R   +  A +     VTL  L  E  VSRE +RQ   +A  KV++
Sbjct: 231 DAINMLSEDEQDIVRRHNGLGGAPK-----VTLGQLGQERGVSREAIRQKHTKAMNKVRQ 285

Query: 283 SI 284
            I
Sbjct: 286 QI 287


>gi|90580452|ref|ZP_01236258.1| hypothetical DNA-directed RNA polymerase, sigma subunit [Vibrio
           angustum S14]
 gi|90438361|gb|EAS63546.1| hypothetical DNA-directed RNA polymerase, sigma subunit [Vibrio
           angustum S14]
          Length = 231

 Score = 82.8 bits (203), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 62/230 (26%), Positives = 118/230 (51%), Gaps = 19/230 (8%)

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           + IA  YR   L + +++ EGN+GL+ AV+KFDPE+GFR +TY+ WWIK  ++  I    
Sbjct: 1   MSIAKKYRAAHLLLGDMIDEGNLGLITAVEKFDPEKGFRFSTYATWWIKQNIERAIHNQN 60

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             +++    +++        L+ H   +   N +P     IA++LN    ++  +     
Sbjct: 61  RTIRLPVHVSKEINGL----LRTHRDLMKKQNHEPTH-EDIAQQLNKETHDISILFSYEQ 115

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN---PR 238
              SL+  I   D+N+      +V +       ++E+       +M+  +  +LN   PR
Sbjct: 116 KIVSLDQTI-GDDENTGTIASLIVDEQIPSPSHIVEE------NSMVNLAEDILNKIKPR 168

Query: 239 ERRIFEARR---LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           ER I   RR   +   P TL+ ++    ++RERVRQ++A++ ++++ +++
Sbjct: 169 EREIL-CRRFGVMGYEPQTLQEVALALGITRERVRQLQAKSLERLKMNLK 217


>gi|123967051|ref|YP_001012132.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9515]
 gi|123201417|gb|ABM73025.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9515]
          Length = 333

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 60/242 (24%), Positives = 114/242 (47%), Gaps = 16/242 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+V ++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP RG++ +TY+ WW
Sbjct: 98  AKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPARGYKFSTYAYWW 157

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   I      +++     +      L +LK   + ++    +   +  +AK + +
Sbjct: 158 IRQGITRAIAEKSRAIRLPIHITEM-----LNKLKKGQRELSQEMSRTPTISELAKYVEL 212

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E +V  + C+     SL   +   D   +   D L     G E +  E+ E    R  L
Sbjct: 213 PEDDVKDLMCKAGQPVSLETKVG--DGEDTVLLDLLA----GGEDLPDEQIEMDCMRGDL 266

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIE---ARAFKKVQES 283
              +  L   + R+   R   +   P++L  +     +SR+RVR +E    R  +++ E+
Sbjct: 267 HSLLHQLPDLQCRVLRMRYGMDGDEPMSLTGIGRVLGISRDRVRNLERDGLRGLRRLSEN 326

Query: 284 IQ 285
           ++
Sbjct: 327 VE 328


>gi|123969371|ref|YP_001010229.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. AS9601]
 gi|123199481|gb|ABM71122.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. AS9601]
          Length = 344

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 71/324 (21%), Positives = 141/324 (43%), Gaps = 56/324 (17%)

Query: 7   SIIVNGEIGLSR-YIHEIRKIPMLEKQEEYVLAKRYREHGDLS----------------- 48
           SI  + ++ L R Y+ +I ++P+L  ++E  L ++ +E+ ++                  
Sbjct: 27  SIKASNDVDLVRSYLRDIGRVPLLSHEQEITLGRQVQEYMEVERIELEIIELTGEKPSID 86

Query: 49  ----------------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
                                 A  R+V ++LRLVV +A  Y    + + +++ EG IGL
Sbjct: 87  ELSAKLNLTTSTIKKRLRAGQRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGL 146

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++ V+KFDP RG++ +TY+ WWI+  +   I      +++     +      L +LK   
Sbjct: 147 VRGVEKFDPARGYKFSTYAYWWIRQGITRAIAEKSRAIRLPIHITEM-----LNKLKKGQ 201

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           + ++    +   V  +AK + + E +V  + C+     SL   +   D   +   D L  
Sbjct: 202 RELSQEMSRTPTVSELAKYVELPEDDVKDLMCKAGQPVSLETKVG--DGEDTVLLDLLA- 258

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEV 264
              G E +  E+ E    R  L   +  L   + R+   R   +   P++L  +     +
Sbjct: 259 ---GGEDLPDEQIEMDCMRGDLHSLLHQLPDLQCRVLRMRYGMDGDEPMSLTGIGRVLGI 315

Query: 265 SRERVRQIE---ARAFKKVQESIQ 285
           SR+RVR +E    R  +++ ++++
Sbjct: 316 SRDRVRNLERDGLRGLRRLSDNVE 339


>gi|223889384|ref|ZP_03623970.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           64b]
 gi|223885070|gb|EEF56174.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           64b]
          Length = 631

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 76/261 (29%), Positives = 134/261 (51%), Gaps = 36/261 (13%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 379 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 434

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI--- 149
           F+ +RGF+ +TY+ WWI+ A+   I      +++     ++    N R  +  +Q +   
Sbjct: 435 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLN-RETRYLIQVLGKD 493

Query: 150 -TDNNLKPEQVVAIAKKLNVSES---EVISMNCRLAGDES--LNALI-NSSDKNSSQWQD 202
            TD  L  +++    KK+   +S   E +S+   +  +E   L+  I + + KN +    
Sbjct: 494 PTDEEL-SDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTS 552

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSS 260
           ++V     Q+Q+          R +L      L  RE+ + + R   E+   +TLE +  
Sbjct: 553 FVVL----QDQI----------RAIL----GTLPEREQEVVKMRFGLEDGYSLTLEEVGL 594

Query: 261 EFEVSRERVRQIEARAFKKVQ 281
            F V+RER+RQIE++A ++++
Sbjct: 595 HFNVTRERIRQIESKALRRLK 615


>gi|225551881|ref|ZP_03772824.1| RNA polymerase sigma factor RpoD [Borrelia sp. SV1]
 gi|225371676|gb|EEH01103.1| RNA polymerase sigma factor RpoD [Borrelia sp. SV1]
          Length = 631

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 76/261 (29%), Positives = 134/261 (51%), Gaps = 36/261 (13%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 379 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 434

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI--- 149
           F+ +RGF+ +TY+ WWI+ A+   I      +++     ++    N R  +  +Q +   
Sbjct: 435 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLN-RETRYLIQVLGKD 493

Query: 150 -TDNNLKPEQVVAIAKKLNVSES---EVISMNCRLAGDES--LNALI-NSSDKNSSQWQD 202
            TD  L  +++    KK+   +S   E +S+   +  +E   L+  I + + KN +    
Sbjct: 494 PTDEEL-SDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTS 552

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSS 260
           ++V     Q+Q+          R +L      L  RE+ + + R   E+   +TLE +  
Sbjct: 553 FVVL----QDQI----------RAIL----GTLPEREQEVVKMRFGLEDGYSLTLEEVGL 594

Query: 261 EFEVSRERVRQIEARAFKKVQ 281
            F V+RER+RQIE++A ++++
Sbjct: 595 HFNVTRERIRQIESKALRRLK 615


>gi|15595057|ref|NP_212846.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi B31]
 gi|216264471|ref|ZP_03436463.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           156a]
 gi|221217929|ref|ZP_03589396.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           72a]
 gi|225548954|ref|ZP_03769931.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi 94a]
 gi|225549892|ref|ZP_03770853.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi 118a]
 gi|226320452|ref|ZP_03796018.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi 29805]
 gi|226321409|ref|ZP_03796936.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi Bol26]
 gi|3915854|sp|P52323|RPOD_BORBU RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|2688647|gb|AAC67061.1| RNA polymerase sigma-70 factor (rpoD) [Borrelia burgdorferi B31]
 gi|215980944|gb|EEC21751.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           156a]
 gi|221192235|gb|EEE18455.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           72a]
 gi|225369351|gb|EEG98803.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi 118a]
 gi|225370557|gb|EEG99993.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi 94a]
 gi|226233205|gb|EEH31957.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi Bol26]
 gi|226234094|gb|EEH32809.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi 29805]
 gi|312148540|gb|ADQ31199.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           JD1]
          Length = 631

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 76/261 (29%), Positives = 134/261 (51%), Gaps = 36/261 (13%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 379 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 434

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI--- 149
           F+ +RGF+ +TY+ WWI+ A+   I      +++     ++    N R  +  +Q +   
Sbjct: 435 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLN-RETRYLIQVLGKD 493

Query: 150 -TDNNLKPEQVVAIAKKLNVSES---EVISMNCRLAGDES--LNALI-NSSDKNSSQWQD 202
            TD  L  +++    KK+   +S   E +S+   +  +E   L+  I + + KN +    
Sbjct: 494 PTDEEL-SDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTS 552

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSS 260
           ++V     Q+Q+          R +L      L  RE+ + + R   E+   +TLE +  
Sbjct: 553 FVVL----QDQI----------RAIL----GTLPEREQEVVKMRFGLEDGYSLTLEEVGL 594

Query: 261 EFEVSRERVRQIEARAFKKVQ 281
            F V+RER+RQIE++A ++++
Sbjct: 595 HFNVTRERIRQIESKALRRLK 615


>gi|38233998|ref|NP_939765.1| RNA polymerase sigma factor SigB [Corynebacterium diphtheriae NCTC
           13129]
 gi|38605711|sp|P33118|RPSB_CORDI RecName: Full=RNA polymerase sigma factor sigB
 gi|38200260|emb|CAE49944.1| RNA polymerase sigma factor [Corynebacterium diphtheriae]
          Length = 329

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 74/288 (25%), Positives = 138/288 (47%), Gaps = 44/288 (15%)

Query: 13  EIGL-SRYIHEIRKIPMLE--KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           E+GL + Y+ E  + P+    K++  VL K  R+     A   L+ ++LRLVV +A  Y 
Sbjct: 58  EVGLYAEYLLENSQEPLTRAMKRDLKVLVKEGRK-----ARSHLLEANLRLVVSLAKRYT 112

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A+   +      +++   
Sbjct: 113 GRGMPLLDLIQEGNLGLIRAMEKFDYSKGFKFSTYATWWIRQAITRGMADQSRTIRLPVH 172

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCR 179
             ++     L R+K  +          E+   +A++  + ES++          +S++  
Sbjct: 173 LVEQ--VNKLSRIKREMYQQLGREATNEE---LAEESGIEESKIEMLLRQSRDPVSLDMP 227

Query: 180 LAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
           +  DE   L   I  S+   +             E  ++      + R +L      L  
Sbjct: 228 VGADEEAPLGDFIEDSEATDA-------------ESAVVASLRHSDIRTVL----DTLEQ 270

Query: 238 RERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           RE+ +   R   ++  P TL+ +  +F +SRERVRQIE     K+++ 
Sbjct: 271 REQDVIRLRYGLDDGVPRTLDQIGRQFGLSRERVRQIEREVMSKLRDG 318


>gi|328948111|ref|YP_004365448.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           succinifaciens DSM 2489]
 gi|328448435|gb|AEB14151.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           succinifaciens DSM 2489]
          Length = 655

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 68/242 (28%), Positives = 125/242 (51%), Gaps = 28/242 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +RL+ ++LRLVV IA  Y   GL + +++ EGNIGL++AV+KF+  +G++ +TY+ WW
Sbjct: 417 AKNRLINANLRLVVSIAKKYTNRGLQLFDLIQEGNIGLIKAVEKFEYRKGYKFSTYATWW 476

Query: 109 IKAAMQEYILRSWSLVKIGTTANQK--RLFFNLRRL-KGHLQAITDNNLKPEQV--VAIA 163
           I+ A+   I      +++     ++  ++    R+L + + +  TD  +  +    +A  
Sbjct: 477 IRQAITRSISDQARTIRVPVHMIEQINKVVRESRQLMQKYGREPTDEEIAAQLSWPLARV 536

Query: 164 KKLNVSESEVISMNCRLAGDE--SLNALINSSD-KNSSQWQDWLVYDHDGQEQVLIEKEE 220
           K++     E IS+   +  +E  SL   I   + +N +    + +     QEQ       
Sbjct: 537 KQVKNVAREPISLETPIGEEEDSSLGDFIEDKEIENPANQTAYTLL----QEQ------- 585

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +S L  RE+ + + R   ++   +TLE +   F V+RER+RQIEA+A +
Sbjct: 586 -------LRSVLSTLPQREQEVLKMRFGLDDGYSLTLEEVGLYFNVTRERIRQIEAKALR 638

Query: 279 KV 280
           ++
Sbjct: 639 RL 640


>gi|195941530|ref|ZP_03086912.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi 80a]
          Length = 631

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 76/261 (29%), Positives = 134/261 (51%), Gaps = 36/261 (13%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 379 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 434

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI--- 149
           F+ +RGF+ +TY+ WWI+ A+   I      +++     ++    N R  +  +Q +   
Sbjct: 435 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLN-RETRYLIQVLGKD 493

Query: 150 -TDNNLKPEQVVAIAKKLNVSES---EVISMNCRLAGDES--LNALI-NSSDKNSSQWQD 202
            TD  L  +++    KK+   +S   E +S+   +  +E   L+  I + + KN +    
Sbjct: 494 PTDEEL-SDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTS 552

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSS 260
           ++V     Q+Q+          R +L      L  RE+ + + R   E+   +TLE +  
Sbjct: 553 FVVL----QDQI----------RAIL----GTLPEREQEVVKMRFGLEDGYSLTLEEVGL 594

Query: 261 EFEVSRERVRQIEARAFKKVQ 281
            F V+RER+RQIE++A ++++
Sbjct: 595 HFNVTRERIRQIESKALRRLK 615


>gi|224532358|ref|ZP_03672988.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi WI91-23]
 gi|224512665|gb|EEF83036.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi WI91-23]
          Length = 631

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 76/261 (29%), Positives = 134/261 (51%), Gaps = 36/261 (13%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 379 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 434

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI--- 149
           F+ +RGF+ +TY+ WWI+ A+   I      +++     ++    N R  +  +Q +   
Sbjct: 435 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLN-RETRYLIQVLGKD 493

Query: 150 -TDNNLKPEQVVAIAKKLNVSES---EVISMNCRLAGDES--LNALI-NSSDKNSSQWQD 202
            TD  L  +++    KK+   +S   E +S+   +  +E   L+  I + + KN +    
Sbjct: 494 PTDEEL-SDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTS 552

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSS 260
           ++V     Q+Q+          R +L      L  RE+ + + R   E+   +TLE +  
Sbjct: 553 FVVL----QDQI----------RAIL----GTLPEREQEVVKMRFGLEDGYSLTLEEVGL 594

Query: 261 EFEVSRERVRQIEARAFKKVQ 281
            F V+RER+RQIE++A ++++
Sbjct: 595 HFNVTRERIRQIESKALRRLK 615


>gi|216263390|ref|ZP_03435385.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia afzelii
           ACA-1]
 gi|215980234|gb|EEC21055.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia afzelii
           ACA-1]
          Length = 631

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 72/261 (27%), Positives = 129/261 (49%), Gaps = 36/261 (13%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 379 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 434

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RGF+ +TY+ WWI+ A+   I      +++     ++     L R   +L  +   
Sbjct: 435 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQ--INRLNRETRYLVQVLGK 492

Query: 153 NLKPEQV-------VAIAKKLNVSESEVISMNCRLAGDES--LNALI-NSSDKNSSQWQD 202
           +   E++       +   K +     E +S+   +  +E   L+  I + + KN +    
Sbjct: 493 DPTDEELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTS 552

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSS 260
           ++V     Q+Q+          R +L      L  RE+ + + R   E+   +TLE +  
Sbjct: 553 FVVL----QDQI----------RAIL----GTLPEREQEVVKMRFGLEDGYSLTLEEVGL 594

Query: 261 EFEVSRERVRQIEARAFKKVQ 281
            F V+RER+RQIE++A ++++
Sbjct: 595 HFNVTRERIRQIESKALRRLK 615


>gi|1519640|gb|AAB07553.1| SigC [Chloroflexus aurantiacus J-10-fl]
          Length = 312

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 69/249 (27%), Positives = 118/249 (47%), Gaps = 29/249 (11%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +L+ S+LRLVV IA  Y+G+ L + +++ EG++GLM AV KFD  RG + +TY+ +WI+ 
Sbjct: 76  QLINSNLRLVVSIARRYQGHALSLLDLIQEGSVGLMGAVDKFDASRGLKFSTYATYWIRQ 135

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++   I      V++     ++     L RL+  L    D     E++ A          
Sbjct: 136 SIGRAIADHSRTVRLPVHLGER--LSRLSRLRQELSQQLDREPTLEELAA---------- 183

Query: 172 EVISMNCRL---AGDESLNALINSSDKNSSQWQDWL-----VYDHDGQEQVLIEKEERKN 223
                 CR    AG  +  A +  +  +    +D       +     Q     E  E   
Sbjct: 184 -----GCRPERRAGRTAEQAGLAPTSLDEPHTEDGGGALAEILTDPLQPTPFDEVSESML 238

Query: 224 RRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           + ++   ++  L+PRER I   R  L   P+ TLE +     ++RERVRQ+E  A +K++
Sbjct: 239 QADV-QHALQQLSPRERSILRLRYGLDGEPMHTLEQIGQRLRLTRERVRQLEHEALRKLR 297

Query: 282 E-SIQKQVE 289
           + S+  Q++
Sbjct: 298 DPSLHPQLQ 306


>gi|291295726|ref|YP_003507124.1| RNA polymerase sigma 70 subunit, RpoD subfamily [Meiothermus ruber
           DSM 1279]
 gi|290470685|gb|ADD28104.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Meiothermus ruber
           DSM 1279]
          Length = 507

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 72/260 (27%), Positives = 127/260 (48%), Gaps = 53/260 (20%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           G++   H L+ ++LRLVV IA  Y G GL   +++ EGN GL++AV+KF+ +R F+ +TY
Sbjct: 264 GEICRQH-LIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEFKRRFKFSTY 322

Query: 105 SMWWIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHL------QAITD--- 151
           + WWI+ A+   I      ++I      T N  +L    R+++  L      + I D   
Sbjct: 323 ATWWIRQAINRAIADQARTIRIPVHMVETIN--KLTRTARQMQQELGREPSYEEIADAMG 380

Query: 152 ---NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              +  K E+   IA+       E +S+   +             D+  S + D++  +H
Sbjct: 381 PGWDAKKVEETFKIAQ-------EPVSLETPIG------------DEKDSFYGDFIPDEH 421

Query: 209 -----DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSE 261
                D   Q ++ +E        L +++  L+ RE  + + R+  +     TLE + + 
Sbjct: 422 MASPVDSAAQSMLSEE--------LEKALGKLSEREAMVLKLRKGLIDGREHTLEEVGAY 473

Query: 262 FEVSRERVRQIEARAFKKVQ 281
           F V+RER+RQIE +A +K++
Sbjct: 474 FGVTRERIRQIENKALRKLK 493


>gi|16330349|ref|NP_441077.1| RNA polymerase sigma factor [Synechocystis sp. PCC 6803]
 gi|1652838|dbj|BAA17757.1| RNA polymerase sigma factor [Synechocystis sp. PCC 6803]
          Length = 369

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 66/237 (27%), Positives = 117/237 (49%), Gaps = 15/237 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  R++ S+LRLVV IA  Y   G+P  +++ EG IGL +A +KFDP++G++ +TY+ W
Sbjct: 131 AAKRRMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPDKGYKFSTYAYW 190

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++     +K     L ++K   +++     +      +A  L+
Sbjct: 191 WIRQAITRTIANDARTIRLPIHVVEK-----LNKIKKAQRSLKQELKRNPNEGELAAALD 245

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK--EERKNRR 225
           ++ +++  +        SLN  +   +         LV   + Q+  L E    E   RR
Sbjct: 246 ITPAQLRQLLQLRRQSLSLNHRVGKGEDTE------LVDLLEDQQLQLPEDLMNESMLRR 299

Query: 226 NMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            ++     VL  RE  +   R         TLE + + F +SRERVRQI+++A +K+
Sbjct: 300 EIVEVLAEVLTEREMEVICLRYGIASHQSYTLEEVGNMFNLSRERVRQIQSKAMRKL 356


>gi|218249968|ref|YP_002375211.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           ZS7]
 gi|218165156|gb|ACK75217.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           ZS7]
          Length = 631

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 76/261 (29%), Positives = 134/261 (51%), Gaps = 36/261 (13%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 379 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 434

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI--- 149
           F+ +RGF+ +TY+ WWI+ A+   I      +++     ++    N R  +  +Q +   
Sbjct: 435 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLN-RETRYLIQVLGKD 493

Query: 150 -TDNNLKPEQVVAIAKKLNVSES---EVISMNCRLAGDES--LNALI-NSSDKNSSQWQD 202
            TD  L  +++    KK+   +S   E +S+   +  +E   L+  I + + KN +    
Sbjct: 494 PTDEEL-SDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTS 552

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSS 260
           ++V     Q+Q+          R +L      L  RE+ + + R   E+   +TLE +  
Sbjct: 553 FVVL----QDQI----------RAIL----GTLPEREQEVVKMRFGLEDGYSLTLEEVGL 594

Query: 261 EFEVSRERVRQIEARAFKKVQ 281
            F V+RER+RQIE++A ++++
Sbjct: 595 HFNVTRERIRQIESKALRRLK 615


>gi|312149387|gb|ADQ29458.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           N40]
          Length = 631

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 76/261 (29%), Positives = 134/261 (51%), Gaps = 36/261 (13%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 379 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 434

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI--- 149
           F+ +RGF+ +TY+ WWI+ A+   I      +++     ++    N R  +  +Q +   
Sbjct: 435 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLN-RETRYLIQVLGKD 493

Query: 150 -TDNNLKPEQVVAIAKKLNVSES---EVISMNCRLAGDES--LNALI-NSSDKNSSQWQD 202
            TD  L  +++    KK+   +S   E +S+   +  +E   L+  I + + KN +    
Sbjct: 494 PTDEEL-SDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTS 552

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSS 260
           ++V     Q+Q+          R +L      L  RE+ + + R   E+   +TLE +  
Sbjct: 553 FVVL----QDQI----------RAIL----GTLPEREQEVVKMRFGLEDGYSLTLEEVGL 594

Query: 261 EFEVSRERVRQIEARAFKKVQ 281
            F V+RER+RQIE++A ++++
Sbjct: 595 HFNVTRERIRQIESKALRRLK 615


>gi|111115542|ref|YP_710160.1| RNA polymerase sigma factor RpoD [Borrelia afzelii PKo]
 gi|110890816|gb|ABH01984.1| RNA polymerase sigma-70 factor [Borrelia afzelii PKo]
          Length = 631

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 72/261 (27%), Positives = 129/261 (49%), Gaps = 36/261 (13%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 379 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 434

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RGF+ +TY+ WWI+ A+   I      +++     ++     L R   +L  +   
Sbjct: 435 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQ--INRLNRETRYLVQVLGK 492

Query: 153 NLKPEQV-------VAIAKKLNVSESEVISMNCRLAGDES--LNALI-NSSDKNSSQWQD 202
           +   E++       +   K +     E +S+   +  +E   L+  I + + KN +    
Sbjct: 493 DPTDEELSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTS 552

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSS 260
           ++V     Q+Q+          R +L      L  RE+ + + R   E+   +TLE +  
Sbjct: 553 FVVL----QDQI----------RAIL----GTLPEREQEVVKMRFGLEDGYSLTLEEVGL 594

Query: 261 EFEVSRERVRQIEARAFKKVQ 281
            F V+RER+RQIE++A ++++
Sbjct: 595 HFNVTRERIRQIESKALRRLK 615


>gi|320105081|ref|YP_004180672.1| RNA polymerase sigma-32 subunit RpoH [Isosphaera pallida ATCC
           43644]
 gi|319752363|gb|ADV64123.1| RNA polymerase, sigma 32 subunit, RpoH [Isosphaera pallida ATCC
           43644]
          Length = 322

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 64/240 (26%), Positives = 122/240 (50%), Gaps = 26/240 (10%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +L  +++RLV  +A  +R  G+  S+++ EG  GL++A+ +FD   G +LATY+ WWI+ 
Sbjct: 94  KLALANMRLVAHVAKRFRDRGVSYSDLLQEGFCGLLEAIDRFDLAHGTKLATYATWWIRQ 153

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA--IAKKLNVS 169
           AMQ  +  +   V++ +  + ++L  N   ++   Q  T      E+ V+  + ++++ +
Sbjct: 154 AMQRAVAATAYPVRL-SPRHLRQLARNQEEIERGGQPRTRKKASDEESVSPEMIQRIHAA 212

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
               +S++  +  D S + L   SD            D  G+    ++ +E       + 
Sbjct: 213 TRPTVSLDATVDSDSSFSLLHTMSDPEG---------DRTGE----VDMDE------TIV 253

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSS---EFEVSRERVRQIEARAFKKVQESIQK 286
           + M  L PRE ++  + R   N  T  +LS      +VS+ERVRQI+ RA +K++  +Q+
Sbjct: 254 KLMENLRPREIQVL-SLRFGLNGATRHSLSQVGKVLDVSKERVRQIQDRALEKLRLCVQE 312


>gi|238063483|ref|ZP_04608192.1| sigma-70 region 2 domain-containing protein [Micromonospora sp.
           ATCC 39149]
 gi|237885294|gb|EEP74122.1| sigma-70 region 2 domain-containing protein [Micromonospora sp.
           ATCC 39149]
          Length = 334

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 70/233 (30%), Positives = 119/233 (51%), Gaps = 21/233 (9%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   L+ ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ W
Sbjct: 95  TAKDHLLEANLRLVVSIAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATW 154

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQK--RLFFNLRRLKGHLQAITDNNLKPEQVVA-IAK 164
           WI+ A+   +      ++I     ++  R+    R L     A+T   L  E  VA +A+
Sbjct: 155 WIRQAITRAMADQARTIRIPVHMVEQVNRMVRARREL-----AVT---LGREPTVAEVAR 206

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE--QVLIEKEERK 222
            ++V E +VI +        SL+  +   +   S   D++       E     ++ E R 
Sbjct: 207 AMDVPEFQVIELISYDREPVSLDQAVG--EDGESALGDFVAAVDPAAEPGATAVDGELRN 264

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIE 273
             R +L    + L+ RE+ +   R   ++    TL+ +  EF +SRER+RQIE
Sbjct: 265 EVRIVL----ATLSQREQAVIRLRFGLDDGRQRTLDEVGREFGLSRERIRQIE 313


>gi|55274998|gb|AAV49296.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 198

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 34/66 (51%), Positives = 51/66 (77%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 113 MQEYIL 118
           ++  I+
Sbjct: 61  IERAIM 66


>gi|224534471|ref|ZP_03675047.1| RNA polymerase sigma factor RpoD [Borrelia spielmanii A14S]
 gi|224514148|gb|EEF84466.1| RNA polymerase sigma factor RpoD [Borrelia spielmanii A14S]
          Length = 631

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 76/261 (29%), Positives = 134/261 (51%), Gaps = 36/261 (13%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 379 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 434

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI--- 149
           F+ +RGF+ +TY+ WWI+ A+   I      +++     ++    N R  +  +Q +   
Sbjct: 435 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLN-RETRYLIQVLGKD 493

Query: 150 -TDNNLKPEQVVAIAKKLNVSES---EVISMNCRLAGDES--LNALI-NSSDKNSSQWQD 202
            TD  L  +++    KK+   +S   E +S+   +  +E   L+  I + + KN +    
Sbjct: 494 PTDEEL-SDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTS 552

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSS 260
           ++V     Q+Q+          R +L      L  RE+ + + R   E+   +TLE +  
Sbjct: 553 FVVL----QDQI----------RAIL----GTLPEREQEVVKMRFGLEDGYSLTLEEVGL 594

Query: 261 EFEVSRERVRQIEARAFKKVQ 281
            F V+RER+RQIE++A ++++
Sbjct: 595 HFNVTRERIRQIESKALRRLK 615


>gi|54401898|gb|AAV34634.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274877|gb|AAV49241.1| RNA polymerase subunit sigma-38 [Escherichia albertii]
 gi|55274996|gb|AAV49295.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 201

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 34/66 (51%), Positives = 51/66 (77%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 113 MQEYIL 118
           ++  I+
Sbjct: 61  IERAIM 66


>gi|224531865|ref|ZP_03672497.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia valaisiana
           VS116]
 gi|224511330|gb|EEF81736.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia valaisiana
           VS116]
          Length = 631

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 76/261 (29%), Positives = 134/261 (51%), Gaps = 36/261 (13%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 379 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 434

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI--- 149
           F+ +RGF+ +TY+ WWI+ A+   I      +++     ++    N R  +  +Q +   
Sbjct: 435 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLN-RETRYLIQVLGKD 493

Query: 150 -TDNNLKPEQVVAIAKKLNVSES---EVISMNCRLAGDES--LNALI-NSSDKNSSQWQD 202
            TD  L  +++    KK+   +S   E +S+   +  +E   L+  I + + KN +    
Sbjct: 494 PTDEEL-SDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTS 552

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSS 260
           ++V     Q+Q+          R +L      L  RE+ + + R   E+   +TLE +  
Sbjct: 553 FVVL----QDQI----------RAIL----GTLPEREQEVVKMRFGLEDGYSLTLEEVGL 594

Query: 261 EFEVSRERVRQIEARAFKKVQ 281
            F V+RER+RQIE++A ++++
Sbjct: 595 HFNVTRERIRQIESKALRRLK 615


>gi|186684216|ref|YP_001867412.1| RNA polymerase sigma factor [Nostoc punctiforme PCC 73102]
 gi|186466668|gb|ACC82469.1| RNA polymerase, sigma 70 subunit, RpoD family [Nostoc punctiforme
           PCC 73102]
          Length = 327

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 71/300 (23%), Positives = 135/300 (45%), Gaps = 52/300 (17%)

Query: 19  YIHEIRKIPMLEKQEEYV-----------------LAKRYREHGDLS------------- 48
           Y+ EI ++P+L +++E V                 LAK+     D+S             
Sbjct: 23  YLREIGRVPLLTREQEIVYGKQVQQMMTLIDAKEVLAKKLHREPDMSEWADVVQQSETEV 82

Query: 49  ---------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                    A  +++ ++LRLVV IA  Y+   +   +++ EG +GL + V+KFDP RG+
Sbjct: 83  QQTVAQGKRAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPMRGY 142

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWI+ A+   I +    +++     +K     +++++  L      +  P + 
Sbjct: 143 KFSTYAYWWIRQAITRAIAQQGRTIRLPIHITEK--LNKIKKVQRELAQTLGRSPTPAE- 199

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IAK+L +  +++           SL+  +   D   ++ Q+ L       E    ++ 
Sbjct: 200 --IAKELELEPAQIREYLNMARQPVSLD--VKVGDNQDTELQEMLEDSGPSPEYYTNQEF 255

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAF 277
            R++  N+L      L P++R +   R   E  N ++L  +     +SRERVRQ+E +A 
Sbjct: 256 LRQDLNNLLAE----LTPQQREVLALRFGLEDGNEMSLAKVGERLNLSRERVRQLEHQAL 311


>gi|332297995|ref|YP_004439917.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           brennaborense DSM 12168]
 gi|332181098|gb|AEE16786.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           brennaborense DSM 12168]
          Length = 599

 Score = 82.8 bits (203), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 66/244 (27%), Positives = 121/244 (49%), Gaps = 30/244 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +RL+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+KF+  +G++ +TY+ WW
Sbjct: 362 AKNRLINANLRLVVSIAKKYTNRGLQFFDLVQEGNIGLIKAVEKFEYRKGYKFSTYATWW 421

Query: 109 IKAAMQEYILRSWSLVKIGTTANQK--RLFFNLRRLKGHL-QAITDNNLKPEQ--VVAIA 163
           I+ A+   I      +++     ++  ++    R+L     +  TD  +  +    V   
Sbjct: 422 IRQAITRSISDQARTIRVPVHMIEQINKVVRESRQLMQRFGREPTDEEIAAQLGWPVNRV 481

Query: 164 KKLNVSESEVISMNCRLAGDES--LNALINSS--DKNSSQWQDWLVYDHDGQEQVLIEKE 219
           K++     E IS+   +  +E   L   I     +  +++    ++ DH           
Sbjct: 482 KQVKSVAREPISLETPIGEEEDSLLGDFIEDKEVENPAAKTAYTMLQDH----------- 530

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
                   L   ++ L PRE+ + + R   ++   +TLE +   F V+RER+RQIEA+A 
Sbjct: 531 --------LRSILATLPPREQEVLKMRFGLDDGFSLTLEEVGLYFNVTRERIRQIEAKAL 582

Query: 278 KKVQ 281
           ++++
Sbjct: 583 RRLR 586


>gi|33864638|ref|NP_896197.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. WH 8102]
 gi|33632161|emb|CAE06617.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 8102]
          Length = 332

 Score = 82.4 bits (202), Expect = 6e-14,   Method: Compositional matrix adjust.
 Identities = 64/253 (25%), Positives = 122/253 (48%), Gaps = 15/253 (5%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           KR  +HG   A  R+V ++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP RG
Sbjct: 88  KRKLQHGR-RAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRG 146

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           ++ +TY+ WWI+  +   I      +++     +      L +LK   + ++    +   
Sbjct: 147 YKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITEM-----LNKLKKGQRELSQELGRTPT 201

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           +  +A+ + + E +V  + CR     SL   +   D + ++  + L  D D     + E 
Sbjct: 202 ITELAQYVELPEDDVKDLMCRARQPVSLE--MKVGDGDDTELLELLAGDADLPSDQVEED 259

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARA 276
             + + R++L +    L   + ++   R     E+P++L  +     +SR+RVR +E   
Sbjct: 260 CMKGDLRSLLGQ----LPHLQEQVLRMRYGMDGEDPMSLTGIGRILGMSRDRVRNLERDG 315

Query: 277 FKKVQESIQKQVE 289
              ++  I  QVE
Sbjct: 316 LAGLRR-ISDQVE 327


>gi|55274913|gb|AAV49258.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274972|gb|AAV49285.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 200

 Score = 82.4 bits (202), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 34/66 (51%), Positives = 51/66 (77%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 113 MQEYIL 118
           ++  I+
Sbjct: 61  IERAIM 66


>gi|197294657|ref|YP_001799198.1| RNA polymerase sigma factor [Candidatus Phytoplasma australiense]
 gi|171853984|emb|CAM11947.1| RNA polymerase sigma factor [Candidatus Phytoplasma australiense]
          Length = 476

 Score = 82.4 bits (202), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 87/315 (27%), Positives = 146/315 (46%), Gaps = 58/315 (18%)

Query: 19  YIHEIRKIPMLEKQEEYV--------------LAKRYREHGDLS---------------- 48
           Y+ EI +IP+L K+EE                L K   +  DLS                
Sbjct: 175 YLKEIGRIPLLSKEEEQKKTFAVFLGKEAKKKLTKFRNQEIDLSDQEVKQLESQIIQANQ 234

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   LV S+ RLVV IA  Y G G+   +++ EGN+GLM+AV KFD ++G RL+TY+ +W
Sbjct: 235 AKDVLVESNYRLVVSIAKRYIGRGVLFLDLIQEGNMGLMRAVDKFDYQKGLRLSTYATYW 294

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +   +   I      ++I      T N+  L    R+L   L+       KP  +  +A+
Sbjct: 295 VIQGVTRAIADQARTIRIPVHIVETINKMSLC--TRKLTQELKK------KP-TIEELAE 345

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL-----VYDHDGQEQVLIEKE 219
           K+N+   ++ S+        SL      + ++ +   D++     +  H+   + + +K 
Sbjct: 346 KMNIPADKLRSIQYIEKKPISLEVPPAENKEDETSLGDFISDPNVLSPHEYMMKEVTQKL 405

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAF 277
             +   N LT        RE ++ + R   L     TLE + + F V+RER+RQIE++A 
Sbjct: 406 LDEVLENTLTE-------REEKVLKMRYGFLDGKVYTLEEIGNLFGVTRERIRQIESKAL 458

Query: 278 KKVQESIQKQVELSS 292
           ++++ +  KQ +L S
Sbjct: 459 RRLR-TPAKQSKLKS 472


>gi|55274911|gb|AAV49257.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274963|gb|AAV49281.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 202

 Score = 82.4 bits (202), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 34/66 (51%), Positives = 51/66 (77%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 113 MQEYIL 118
           ++  I+
Sbjct: 61  IERAIM 66


>gi|157414236|ref|YP_001485102.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9215]
 gi|157388811|gb|ABV51516.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9215]
          Length = 344

 Score = 82.4 bits (202), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 60/242 (24%), Positives = 114/242 (47%), Gaps = 16/242 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+V ++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP RG++ +TY+ WW
Sbjct: 109 AKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPARGYKFSTYAYWW 168

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   I      +++     +      L +LK   + ++    +   V  +AK + +
Sbjct: 169 IRQGITRAIAEKSRAIRLPIHITEM-----LNKLKKGQRELSQEMSRTPTVSELAKYVEL 223

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E +V  + C+     SL   +   D   +   D L     G E +  E+ E    R  L
Sbjct: 224 PEDDVKDLMCKAGQPVSLETKVG--DGEDTVLLDLLA----GGEDLPDEQIEMDCMRGDL 277

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIE---ARAFKKVQES 283
              +  L   + R+   R   +   P++L  +     +SR+RVR +E    R  +++ ++
Sbjct: 278 HSLLHQLPDLQCRVLRMRYGMDGDEPMSLTGIGRVLGISRDRVRNLERDGLRGLRRLSDN 337

Query: 284 IQ 285
           ++
Sbjct: 338 VE 339


>gi|148241197|ref|YP_001226354.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp.
           RCC307]
 gi|147849507|emb|CAK27001.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. RCC307]
          Length = 324

 Score = 82.4 bits (202), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 62/245 (25%), Positives = 120/245 (48%), Gaps = 16/245 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+V ++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP RG++ +TY+ WW
Sbjct: 89  AKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWW 148

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   I      +++     +      L +LK   + ++    +   V  +A+ L +
Sbjct: 149 IRQGITRAIAEKSRTIRLPIHITE-----TLNKLKKGQRELSQELGRTPTVGELAEFLEL 203

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E EV  +  R     SL   +  SD   ++  + L  D     +++     + + R++L
Sbjct: 204 PEPEVKDLLSRARQPVSLEMKVGDSD--DTELCELLQNDAPMPHELVDGDCLKGDMRSLL 261

Query: 229 TRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIE---ARAFKKVQES 283
            +    L P + R+ + R     E P++L  +  E  +SR+RVR +E       +++ E+
Sbjct: 262 EQ----LPPLQGRVLKMRYGIDVEEPMSLTGIGRELGMSRDRVRNLERDGLAGLRRLSEA 317

Query: 284 IQKQV 288
           ++  V
Sbjct: 318 VEAYV 322


>gi|55274875|gb|AAV49240.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 193

 Score = 82.4 bits (202), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 34/66 (51%), Positives = 51/66 (77%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 113 MQEYIL 118
           ++  I+
Sbjct: 61  IERAIM 66


>gi|271966792|ref|YP_003340988.1| RNA polymerase sigma factor RpoD [Streptosporangium roseum DSM
           43021]
 gi|270509967|gb|ACZ88245.1| RNA polymerase sigma factor RpoD [Streptosporangium roseum DSM
           43021]
          Length = 331

 Score = 82.4 bits (202), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 63/248 (25%), Positives = 117/248 (47%), Gaps = 34/248 (13%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L A + L+ ++LRLVV IA  + G G+  ++++ EGN+GL++A +KFD  +GF+ +TY+ 
Sbjct: 92  LRAKNHLLEANLRLVVSIAKRHTGRGMAFADLIQEGNLGLIRAAEKFDYTKGFKFSTYAT 151

Query: 107 WWIKAAMQEYILRSWSLVKI---------GTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           WWIK A+   +      ++I              Q+++   L R     +   + ++  E
Sbjct: 152 WWIKQAVTRALADQGRTIRIPVHMVEVINKVARVQRQMMVTLGREPSPQELAVELDMTVE 211

Query: 158 QVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
           ++  + K       E IS++  L   GD     +I  S+          +   +    +L
Sbjct: 212 KITEVQK----YGREPISLHTPLGAEGDAEFGDVIEDSEA---------ILPEEAVTFIL 258

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIE 273
           ++++        L   +  L+ RE  +   R       P TL+ +   F V+RER+RQIE
Sbjct: 259 LQRQ--------LHAVLEALSEREAGVMRLRFGLADGQPKTLDEIGKVFGVTRERIRQIE 310

Query: 274 ARAFKKVQ 281
           ++   K++
Sbjct: 311 SKTMSKLR 318


>gi|325270141|ref|ZP_08136748.1| RNA polymerase sigma-43 factor [Prevotella multiformis DSM 16608]
 gi|324987442|gb|EGC19418.1| RNA polymerase sigma-43 factor [Prevotella multiformis DSM 16608]
          Length = 228

 Score = 82.4 bits (202), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 71/273 (26%), Positives = 117/273 (42%), Gaps = 47/273 (17%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           I   +Y+ EI     L  +EE  LA R +  GD  A  +L  ++L+ VV +A  YR  GL
Sbjct: 2   IANEKYMEEIAGGQPLSDREERTLAGRIKV-GDAQALEKLTKANLKYVVSLAHQYRNRGL 60

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++SEGNIG+M A ++FD  RG R   ++  +I+ AM+E I    +L ++       
Sbjct: 61  GEDDLISEGNIGMMHAAQRFDGSRGVRFVVFAAPYIRKAMEEAIKEQAALYRLP------ 114

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                 R  K   +    + +  +Q V +    N +   V+  +     DE LN  I SS
Sbjct: 115 ------RNEKNRSEQKRSHAISIDQPVPVGSSNNFTLQNVLENDNAPHADEQLNQEILSS 168

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA-RRLQENP 252
           +                                 + + + VLN RER++      L    
Sbjct: 169 E---------------------------------IQKGLGVLNERERQVIACLYGLSGVH 195

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            T+   +    + RERVRQI  +A +K+ + ++
Sbjct: 196 YTMAEAAEHMGLKRERVRQIRDKALRKLHKRLK 228


>gi|255019642|ref|ZP_05291721.1| RNA polymerase, sigma 70 subunit, RpoD family [Acidithiobacillus
           caldus ATCC 51756]
 gi|254970865|gb|EET28348.1| RNA polymerase, sigma 70 subunit, RpoD family [Acidithiobacillus
           caldus ATCC 51756]
          Length = 285

 Score = 82.4 bits (202), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 74/276 (26%), Positives = 130/276 (47%), Gaps = 51/276 (18%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L  ++E  +  + R  GD +A   LV++H+ LV  IA  YR  GL   ++V EG +GL
Sbjct: 36  PFLSPEQESAVIAQIRS-GDEAARATLVSAHMPLVRAIARSYRNKGLSQEDLVQEGYMGL 94

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW------SLVKIGTTANQKRLFFNLR 140
           M+A+ +F    G R ++Y+ WWI+ AMQ  ++R+        L K      QK    +L 
Sbjct: 95  MRAMDRFQEGLGTRFSSYATWWIREAMQRALIRARFIRLPDYLAKSLHALQQK----SLD 150

Query: 141 RLKGH---------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALI 190
            + GH            + D+ ++          L+ ++  V S++  +A G   +  ++
Sbjct: 151 EVDGHDAQRAQRREALGVRDSTMR---------ALDFADVRVCSLDEEMADGPSRIEQVV 201

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR--IFEARRL 248
            +    +S  QD   YD D   + L E              + +LN ++R   I+     
Sbjct: 202 GNV---ASPAQD---YDRDASVRALREH-------------LKLLNEKQREVMIYRFGLH 242

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + P+TLE ++    VSRE VRQ++ RA  ++++++
Sbjct: 243 GDAPMTLEAIAERLGVSREAVRQLQVRALLRLRQAL 278


>gi|116073053|ref|ZP_01470315.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9916]
 gi|116068358|gb|EAU74110.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9916]
          Length = 321

 Score = 82.4 bits (202), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 57/227 (25%), Positives = 110/227 (48%), Gaps = 13/227 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+V ++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP RG++ +TY+ WW
Sbjct: 86  AKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWW 145

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   I      +++     +      L +LK   + ++    +   V  +A+ + +
Sbjct: 146 IRQGITRAIAEKSRTIRLPIHITEM-----LNKLKKGQRELSQELGRTPTVTELAEFVEL 200

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E EV  + CR     SL   +   D         L+    G  ++  E+ E +  +  L
Sbjct: 201 PEEEVKDLMCRARQPVSLEMKVGDGDDTE------LLELLSGDGELPSEQVESECLKGDL 254

Query: 229 TRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIE 273
              +  L   +R++   R     E+P++L  ++   ++SR+R R++E
Sbjct: 255 RDLLEQLPELQRKVLRMRYGMNGEDPMSLTGIAKTLKMSRDRTRRLE 301


>gi|145594010|ref|YP_001158307.1| RNA polymerase sigma factor SigB [Salinispora tropica CNB-440]
 gi|145303347|gb|ABP53929.1| sigma-70 region 2 domain protein [Salinispora tropica CNB-440]
          Length = 332

 Score = 82.4 bits (202), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 66/240 (27%), Positives = 119/240 (49%), Gaps = 19/240 (7%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   L+ ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ W
Sbjct: 93  AAKDHLLEANLRLVVSIAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATW 152

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQK--RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
           WI+ A+   +      ++I     ++  R+    R L   L        +   V  +A+ 
Sbjct: 153 WIRQAITRAMADQARTIRIPVHMVEQVNRMVRTRRELSVSLG-------REPTVAEVART 205

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL--VYDHDGQEQVLIEKEERKN 223
           L++ E +VI +        SL+  +   +   S   D++  V    G +  +   E R+ 
Sbjct: 206 LDIPEIQVIELISYDREPVSLDQTVG--EDGESPLGDFVAAVDSTAGTDDTVSGGELRQE 263

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +L    + L+ RE+ +   R   ++    TL+ +  EF +SRER+RQIE     K++
Sbjct: 264 MCGVL----ATLSQREQAVIRLRFGLDDGRQRTLDEVGREFGLSRERIRQIEKGTLHKLR 319


>gi|54401894|gb|AAV34632.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|54401896|gb|AAV34633.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274921|gb|AAV49262.1| RNA polymerase subunit sigma-38 [Shigella boydii]
 gi|55274982|gb|AAV49290.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 203

 Score = 82.4 bits (202), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 34/66 (51%), Positives = 51/66 (77%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 113 MQEYIL 118
           ++  I+
Sbjct: 61  IERAIM 66


>gi|55274919|gb|AAV49261.1| RNA polymerase subunit sigma-38 [Shigella flexneri]
          Length = 201

 Score = 82.4 bits (202), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 34/67 (50%), Positives = 52/67 (77%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ S+LRLVVKIA  Y   GL + +++ EG++GL++AV+KFDPERGFR +TY+ WWI+ 
Sbjct: 1   RMIESNLRLVVKIARRYGNRGLALLDLIEEGSLGLIRAVEKFDPERGFRFSTYATWWIRQ 60

Query: 112 AMQEYIL 118
            ++  I+
Sbjct: 61  TIERAIM 67


>gi|323454681|gb|EGB10551.1| hypothetical protein AURANDRAFT_23034 [Aureococcus anophagefferens]
          Length = 388

 Score = 82.4 bits (202), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 67/244 (27%), Positives = 119/244 (48%), Gaps = 18/244 (7%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L +++LRLVV IA  YR  GL   +++ EG  GL +AV++FDPERGFR +TY+ +WI+ A
Sbjct: 137 LTSANLRLVVSIAKRYRFCGLAQEDLLQEGAFGLSRAVERFDPERGFRFSTYATFWIRQA 196

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +         ++++    + +    ++R+    L      +   ++   +A  L + + E
Sbjct: 197 VLRACAEQSRVIRLPAHVHDQ--LASMRKASAELSRRLGRDATDDE---LADHLELEKPE 251

Query: 173 VISMNCRLAGDE--------SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE---ER 221
            ++   R A  +        +++A   SS           + +    + +L+  E   E 
Sbjct: 252 KLAFLRRCAAQDPSSLDEKHAIHAGRGSSVGGGGAAGATTIAESLSDDTILVPDEFVAEA 311

Query: 222 KNRRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAFKK 279
            +R  +     +V N RER +   R  L  N P++   ++    VSRERVRQIE RA  K
Sbjct: 312 ASREYVGDLLATVCNDRERDVLGMRFGLYGNAPISKTKIAERLAVSRERVRQIEVRALTK 371

Query: 280 VQES 283
           ++++
Sbjct: 372 LRQT 375


>gi|288802544|ref|ZP_06407983.1| RNA polymerase sigma-70 factor [Prevotella melaninogenica D18]
 gi|288335072|gb|EFC73508.1| RNA polymerase sigma-70 factor [Prevotella melaninogenica D18]
          Length = 257

 Score = 82.4 bits (202), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 69/269 (25%), Positives = 119/269 (44%), Gaps = 47/269 (17%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +YI +I    +L  +EE  LA++ +  GD  A  +L  ++L+ VV +A  Y   GL   +
Sbjct: 35  KYIEDIANEQLLSDKEEQDLAEKIKV-GDARALEKLTKANLKFVVSLAHQYHNRGLGEDD 93

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++SEGNIG+M A +KFD  +G R   ++  +I+ AM+E I    +L K+      +   F
Sbjct: 94  LISEGNIGMMYAAQKFDGSKGVRFVVFAAPYIRKAMEEAIKEQATLYKLPKNETSR---F 150

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
             +R   H  +I       +Q V +    N +   ++        DE LN  I S     
Sbjct: 151 EQKR--SHAISI-------DQPVPVGSNNNFTLQHILENENAKHADEHLNQEILS----- 196

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE-ARRLQENPVTLE 256
                                       N + + + VL+ RE+R+      L     T+ 
Sbjct: 197 ----------------------------NEIQKGLDVLDEREKRVITYIYGLTGAHYTMA 228

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            ++ +  + RERVRQI  +A +K+ + ++
Sbjct: 229 EIAEDMGLKRERVRQIRDKALRKLHKKMK 257


>gi|240169688|ref|ZP_04748347.1| RNA polymerase sigma factor SigB [Mycobacterium kansasii ATCC
           12478]
          Length = 319

 Score = 82.4 bits (202), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 78/292 (26%), Positives = 138/292 (47%), Gaps = 56/292 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH--------------------GDLSAAHR- 52
           Y++ I K  +L   +E  LAKR     Y E+                     D  AA R 
Sbjct: 26  YLNGIGKTALLNAADEVELAKRIEAGLYAEYLLETRKRLGENRKRELAAVVRDGEAARRH 85

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A
Sbjct: 86  LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQA 145

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ-----AITDNNLKPEQVVAIAKKLN 167
           +   +      +++     ++     L R+K  +        TD  L  E  + + K  +
Sbjct: 146 ITRGMADQSRTIRLPVHLVEQ--VNKLARIKREMHQNLGREATDEELAEESGIPVDKIND 203

Query: 168 VSES--EVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + E   + +S++  +  +E   L   I  ++  S+             E  +I +    +
Sbjct: 204 LLEHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSA-------------ENAVIAELLHTD 250

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIE 273
            R++L    + L+ RE ++   R   ++  P TL+ +   F +SRERVRQIE
Sbjct: 251 IRSVL----ATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIE 298


>gi|55274976|gb|AAV49287.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 204

 Score = 82.4 bits (202), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 34/66 (51%), Positives = 51/66 (77%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 113 MQEYIL 118
           ++  I+
Sbjct: 61  IERAIM 66


>gi|78780107|ref|YP_398219.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9312]
 gi|78713606|gb|ABB50783.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9312]
          Length = 344

 Score = 82.4 bits (202), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 74/324 (22%), Positives = 143/324 (44%), Gaps = 56/324 (17%)

Query: 7   SIIVNGEIGLSR-YIHEIRKIPMLEKQEEYVLAKRYREH--------------GD----- 46
           S+  + ++ L R Y+ +I ++P+L  ++E  L ++ +E+              GD     
Sbjct: 27  SLKASNDVDLVRSYLRDIGRVPLLSHEQEITLGRQVQEYMQVERAELEIIELTGDKPSIE 86

Query: 47  -------LS-------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
                  LS             A  R+V ++LRLVV +A  Y    + + +++ EG IGL
Sbjct: 87  ELSSKLNLSIPIIKKRLRAGQRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGL 146

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++ V+KFDP RG++ +TY+ WWI+  +   I      +++     +      L +LK   
Sbjct: 147 VRGVEKFDPARGYKFSTYAYWWIRQGITRAIAEKSRAIRLPIHITEM-----LNKLKKGQ 201

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           + ++    +   V  +AK + + E +V  + C+     SL   +   D   +   D L  
Sbjct: 202 RELSQEMSRTPTVSELAKYVELPEEDVKDLMCKAGQPVSLETKVG--DGEDTVLLDLLA- 258

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEV 264
              G E +  E+ E    R  L   +  L   + R+   R   +   P++L  +     +
Sbjct: 259 ---GGEDLPDEQIEMDCMRGDLHSLLHQLPDLQCRVLRMRYGMDGDEPMSLTGIGRVLGI 315

Query: 265 SRERVRQIE---ARAFKKVQESIQ 285
           SR+RVR +E    R  +++ ++++
Sbjct: 316 SRDRVRNLERDGLRGLRRLSDNVE 339


>gi|254255220|ref|ZP_04948536.1| DNA-directed RNA polymerase sigma subunit [Burkholderia dolosa
           AUO158]
 gi|124900957|gb|EAY71707.1| DNA-directed RNA polymerase sigma subunit [Burkholderia dolosa
           AUO158]
          Length = 241

 Score = 82.4 bits (202), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 61/240 (25%), Positives = 110/240 (45%), Gaps = 26/240 (10%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L  ++LRLVV IA  YR  GLP ++++ EGNIGL++A++++D  RGFR +TY+ WWI+ +
Sbjct: 8   LFDANLRLVVSIAKRYRDRGLPFADLIQEGNIGLLKAIERYDYRRGFRFSTYATWWIRQS 67

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA-------IAKK 165
           +   +      +++ T  +       L RL    +    +   P Q+ A         + 
Sbjct: 68  VTHALADLGRTIRVPT--HTVDALNKLARLAREHRQRAGSAATPAQLAAHIGEPVDKVRD 125

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           L     E +S +  ++ D  L  +  + D  +   +D                 +    R
Sbjct: 126 LLAIVKEPVSADLPVSPDGDLTFIDVAPDTATPSPED---------------AADATQLR 170

Query: 226 NMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +  ++  L  RE  + + R     +   +L ++  +  +S ERVRQIEA A  +++ S
Sbjct: 171 RTIAAAIERLPQREAMVLKLRYGLHADEGCSLRDIGRQLNLSAERVRQIEASALARLRAS 230


>gi|1553013|gb|AAC45098.1| primary sigma factor [Borrelia afzelii]
 gi|1553015|gb|AAC45099.1| primary sigma factor [Borrelia afzelii]
 gi|1553021|gb|AAC45102.1| primary sigma factor [Borrelia garinii]
          Length = 450

 Score = 82.4 bits (202), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 76/260 (29%), Positives = 124/260 (47%), Gaps = 36/260 (13%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 215 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 270

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITD 151
           F+ +RGF+ +TY+ WWI+ A    I RS S        +Q R      R+  H+ + I  
Sbjct: 271 FEYKRGFKFSTYATWWIRQA----ITRSIS--------DQARTI----RVPVHMIEQINR 314

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
            N +   +V +  K    E     ++ RL  +      + S  +     +  +  + D  
Sbjct: 315 LNRETRYLVQVLGKDPTDEE----LSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSV 370

Query: 212 EQVLIEKEERKNRRN---------MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSS 260
               IE +  KN  N          +   +  L  RE+ + + R   E+   +TLE +  
Sbjct: 371 LSDFIEDKAIKNPANHTSFVVLQDQIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGL 430

Query: 261 EFEVSRERVRQIEARAFKKV 280
            F V+RER+RQIE++A +++
Sbjct: 431 HFNVTRERIRQIESKALRRL 450


>gi|15827487|ref|NP_301750.1| RNA polymerase sigma factor SigB [Mycobacterium leprae TN]
 gi|221229964|ref|YP_002503380.1| RNA polymerase sigma factor SigB [Mycobacterium leprae Br4923]
 gi|699187|gb|AAA62952.1| u1764a [Mycobacterium leprae]
 gi|13093037|emb|CAC31395.1| RNA polymerase sigma factor [Mycobacterium leprae]
 gi|219933071|emb|CAR71109.1| RNA polymerase sigma factor [Mycobacterium leprae Br4923]
          Length = 319

 Score = 82.4 bits (202), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 78/292 (26%), Positives = 138/292 (47%), Gaps = 56/292 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH--------GD-------------LSAAHR 52
           Y++ I K  +L   +E  LAKR     Y EH        G+              +A   
Sbjct: 26  YLNGIGKTALLNAADEVELAKRIEAGLYAEHLLQTRKRFGEGRKRALAAVARDGAAARRH 85

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A
Sbjct: 86  LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQA 145

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ-----AITDNNLKPEQVVAIAKKLN 167
           +   +      +++     ++     L R+K  +        TD  L  E  + I K  +
Sbjct: 146 ITRGMADQSRTIRLPVHLVEQ--VNKLARIKREMHQNLGREATDEELAAESGIPIEKIND 203

Query: 168 VSES--EVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + E   + +S++  +  +E   L   I  ++  S+             E  +I +    +
Sbjct: 204 LLEHSRDPVSLDMPVGSEEEAPLGDFIEDAEAMSA-------------ENAVIAELLHTD 250

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIE 273
            R++L    + L+ RE ++   R   ++  P TL+ +   F +SRERVRQIE
Sbjct: 251 IRSVL----ATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIE 298


>gi|305681000|ref|ZP_07403807.1| RNA polymerase sigma factor SigB [Corynebacterium matruchotii ATCC
           14266]
 gi|305659205|gb|EFM48705.1| RNA polymerase sigma factor SigB [Corynebacterium matruchotii ATCC
           14266]
          Length = 365

 Score = 82.4 bits (202), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 72/288 (25%), Positives = 139/288 (48%), Gaps = 44/288 (15%)

Query: 13  EIGL-SRYIHEIRKIPML--EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           E+GL + Y+      P+   +K++  VL K  R+     A   L+ ++LRLVV +A  Y 
Sbjct: 94  EVGLYAEYLLTDSDEPLTRAKKRDLKVLVKEGRK-----ARSHLLEANLRLVVSLAKRYT 148

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A+   +      +++   
Sbjct: 149 GRGMPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVH 208

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCR 179
             ++     L R+K  +          E+   +A++  + ES++          +S++  
Sbjct: 209 LVEQ--VNKLSRIKREMYQQLGREATNEE---LAEESGIDESKIELLLRQSRDPVSLDMP 263

Query: 180 LAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
           +  DE   L   I  S+   +             E  ++      + R+++      L  
Sbjct: 264 VGADEEAPLGDFIEDSEAADA-------------ESAVVASLRHSDIRDVI----GTLED 306

Query: 238 RERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           RE+ +   R   ++  P TL+ +  +F +SRERVRQIE    +K+++ 
Sbjct: 307 REQDVIRMRYGLDDGVPRTLDQIGRQFGLSRERVRQIEREVMRKLRDG 354


>gi|307822780|ref|ZP_07653011.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacter tundripaludum
           SV96]
 gi|307736384|gb|EFO07230.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacter tundripaludum
           SV96]
          Length = 448

 Score = 82.4 bits (202), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 69/263 (26%), Positives = 135/263 (51%), Gaps = 22/263 (8%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           ++YV    + E   LS+   L  ++  LV+ +A  Y+   L   ++V EG  GL++A+ K
Sbjct: 197 QQYVTDMIFAEQLWLSSRQALAEANSGLVLFLANQYKCGFLDFDDLVQEGQTGLLRAIDK 256

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT--TANQKRLFFNLRRLKGHLQAIT 150
           FD   GF+ +TY+ +WIK A+   + R+  +V++     AN  ++     R K  L + T
Sbjct: 257 FDYHLGFQFSTYAAYWIKQAISRALSRNERVVRVPCEQVANIHKVL----RAKNELLSKT 312

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
                 +++   +K  +   + ++S++      E+L+      D++S    D+L      
Sbjct: 313 GREPSIKELTEYSKIPDDQINVILSISQTAVSLENLD-----DDEDSLAPIDFL------ 361

Query: 211 QEQVL---IEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVS 265
           ++QV     +K E+ + +  L +++ +L+PRE ++          N +TL+ + +E  ++
Sbjct: 362 EQQVFANPFKKIEQSDLKAWLGKAIKILDPRELKVICCHFGINTGNEMTLQEIGAELNLT 421

Query: 266 RERVRQIEARAFKKVQESIQKQV 288
           RERVRQI+ +A  K++ S  KQ+
Sbjct: 422 RERVRQIQVKALNKMKLSYGKQL 444


>gi|254526733|ref|ZP_05138785.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9202]
 gi|221538157|gb|EEE40610.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9202]
          Length = 333

 Score = 82.4 bits (202), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 60/242 (24%), Positives = 114/242 (47%), Gaps = 16/242 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+V ++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP RG++ +TY+ WW
Sbjct: 98  AKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPARGYKFSTYAYWW 157

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   I      +++     +      L +LK   + ++    +   V  +AK + +
Sbjct: 158 IRQGITRAIAEKSRAIRLPIHITEM-----LNKLKKGQRELSQEMSRTPTVSELAKYVEL 212

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E +V  + C+     SL   +   D   +   D L     G E +  E+ E    R  L
Sbjct: 213 PEDDVKDLMCKAGQPVSLETKVG--DGEDTVLLDLLA----GGEDLPDEQIEMDCMRGDL 266

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIE---ARAFKKVQES 283
              +  L   + R+   R   +   P++L  +     +SR+RVR +E    R  +++ ++
Sbjct: 267 HSLLHQLPDLQCRVLRMRYGMDGDEPMSLTGIGRVLGISRDRVRNLERDGLRGLRRLSDN 326

Query: 284 IQ 285
           ++
Sbjct: 327 VE 328


>gi|224533326|ref|ZP_03673920.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi CA-11.2a]
 gi|224513491|gb|EEF83848.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi CA-11.2a]
          Length = 255

 Score = 82.0 bits (201), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 75/261 (28%), Positives = 125/261 (47%), Gaps = 36/261 (13%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 3   EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 58

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITD 151
           F+ +RGF+ +TY+ WWI+ A    I RS S        +Q R      R+  H+ + I  
Sbjct: 59  FEYKRGFKFSTYATWWIRQA----ITRSIS--------DQARTI----RVPVHMIEQINR 102

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
            N +   ++ +  K    E     ++ RL  +      + S  +     +  +  + D  
Sbjct: 103 LNRETRYLIQVLGKDPTDEE----LSDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSV 158

Query: 212 EQVLIEKEERKNRRN---------MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSS 260
               IE +  KN  N          +   +  L  RE+ + + R   E+   +TLE +  
Sbjct: 159 LSDFIEDKAIKNPANHTSFVVLQDQIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGL 218

Query: 261 EFEVSRERVRQIEARAFKKVQ 281
            F V+RER+RQIE++A ++++
Sbjct: 219 HFNVTRERIRQIESKALRRLK 239


>gi|126660003|ref|ZP_01731125.1| RNA polymerase sigma factor [Cyanothece sp. CCY0110]
 gi|126618681|gb|EAZ89428.1| RNA polymerase sigma factor [Cyanothece sp. CCY0110]
          Length = 297

 Score = 82.0 bits (201), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 71/282 (25%), Positives = 134/282 (47%), Gaps = 33/282 (11%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS------------------AAHRLVTSHLRL 60
           Y+  I K P+L   EE  LA+  +    L                   A  +++ ++LRL
Sbjct: 13  YLQSIGKTPLLSGAEEIKLAEEIQAMLPLLEKEELNKEEKKIVVIGQRARDKMIQANLRL 72

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y   GL + +++ EG++GL++ V+KFDP RG++ +TY+ WWI+  +   I   
Sbjct: 73  VVSIAKKYLNSGLSLLDLIQEGSLGLIRGVEKFDPSRGYKFSTYAYWWIRQGITRAIAEQ 132

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKP-EQVVAIAKKLNVSESEVISMNC 178
              +++    N+     NL + +  ++ +T     KP +Q +A    + V +   +    
Sbjct: 133 SRTIRLPIHINE-----NLNKYRKSIRELTLKLGRKPTQQEIAENMDITVDKLRFLQQAA 187

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
                 SLN +I+ ++    Q    L+ D +G       K++ K   + + R +  L+PR
Sbjct: 188 FKTKSRSLNIVIDENNTELGQ----LLPDEEGVSPSDFVKQQEKI--SQINRMLENLSPR 241

Query: 239 ERRIFEAR-RLQENP-VTLENLSSEFEVSRERVRQIEARAFK 278
           ++ +   R  L++   ++ + +  +  +S ER RQI +RA +
Sbjct: 242 QKEVIILRFGLRDGKQLSYKAIGEQCGISHERARQIYSRALR 283


>gi|162458688|ref|NP_001104923.1| sigma factor SIG2A [Zea mays]
 gi|4336606|gb|AAD17854.1| sigma factor SIG2A [Zea mays]
          Length = 539

 Score = 82.0 bits (201), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 67/247 (27%), Positives = 125/247 (50%), Gaps = 19/247 (7%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R R +  +   +R+VTS++RLV+ IA  + G G+   +++ EG  GL++  +KFD  +GF
Sbjct: 289 RKRLNYGIYCKNRMVTSNVRLVISIAREFEGPGMDFYDLIQEGMQGLIRGAEKFDSSKGF 348

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           R +TYS WWIK AM++ +     + ++   A+     + ++     L+         E+ 
Sbjct: 349 RFSTYSHWWIKQAMRKSVSEQSQIFRL--PAHMVEASYRVKECTKRLRRKLRRRPTNEE- 405

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           +A+   + +   E      + +   SL++ I S+D         + Y     +      E
Sbjct: 406 IAVDTGIPIKRVEAAVNLPKYS--VSLDSKIGSTD---------MTYQEVTADPSAETAE 454

Query: 220 ERKNRRNM---LTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEA 274
           E  NR +M   +  ++  L  RE+++   R  L++  + TL+ + +   VSRER+RQIE+
Sbjct: 455 EMLNRMSMKKDVHMALDTLTTREKQVVVLRFGLEDGRIRTLQEIGNIMGVSRERIRQIES 514

Query: 275 RAFKKVQ 281
            AF+K++
Sbjct: 515 GAFRKLR 521


>gi|21466008|pdb|1L9U|H Chain H, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
           Resolution
 gi|21466014|pdb|1L9U|Q Chain Q, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
           Resolution
          Length = 332

 Score = 82.0 bits (201), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 67/242 (27%), Positives = 123/242 (50%), Gaps = 22/242 (9%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   L+ ++LRLVV IA  Y G GL   +++ EGN GL++AV+KF+ +R F+ +TY+ W
Sbjct: 91  AARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATW 150

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I    +       L R    LQ         E+   IA+ + 
Sbjct: 151 WIRQAINRAIADQARTIRI--PVHMVETINKLSRTARQLQQELGREPSYEE---IAEAMG 205

Query: 168 VS-ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH-----DGQEQVLIEKEER 221
              +++ +    ++A  E ++      D+  S + D++  ++     +   Q L+ +E  
Sbjct: 206 PGWDAKRVEETLKIA-QEPVSLETPIGDEKDSFYGDFIPDENLPSPVEAAAQSLLSEE-- 262

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
                 L +++S L+ RE  + + R+  +     TLE + + F V+RER+RQIE +A +K
Sbjct: 263 ------LEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRK 316

Query: 280 VQ 281
           ++
Sbjct: 317 LK 318


>gi|1553017|gb|AAC45100.1| primary sigma factor [Borrelia burgdorferi 297]
          Length = 450

 Score = 82.0 bits (201), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 76/260 (29%), Positives = 133/260 (51%), Gaps = 36/260 (13%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 215 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 270

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI--- 149
           F+ +RGF+ +TY+ WWI+ A+   I      +++     ++    N R  +  +Q +   
Sbjct: 271 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLN-RETRYLIQVLGKD 329

Query: 150 -TDNNLKPEQVVAIAKKLNVSES---EVISMNCRLAGDES--LNALI-NSSDKNSSQWQD 202
            TD  L  +++    KK+   +S   E +S+   +  +E   L+  I + + KN +    
Sbjct: 330 PTDEEL-SDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTS 388

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSS 260
           ++V     Q+Q+          R +L      L  RE+ + + R   E+   +TLE +  
Sbjct: 389 FVVL----QDQI----------RAIL----GTLPEREQEVVKMRFGLEDGYSLTLEEVGL 430

Query: 261 EFEVSRERVRQIEARAFKKV 280
            F V+RER+RQIE++A +++
Sbjct: 431 HFNVTRERIRQIESKALRRL 450


>gi|256376033|ref|YP_003099693.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Actinosynnema
           mirum DSM 43827]
 gi|255920336|gb|ACU35847.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Actinosynnema
           mirum DSM 43827]
          Length = 320

 Score = 82.0 bits (201), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 70/291 (24%), Positives = 137/291 (47%), Gaps = 39/291 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKR-----YREH--GDLS------------------AA 50
             +Y+ ++   P+L   EE VL++R     Y EH   D +                  A 
Sbjct: 25  FGQYLRQVGSTPLLTAAEEVVLSRRIEAGVYAEHLLADTAPTPARRRALNQVVADGRDAK 84

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
             ++ ++LRLVV +A  +   GLP+ +VV EGN+GL++AV+KFD  +G++ +TY++WWI+
Sbjct: 85  DHMIRANLRLVVSVAKKHSFRGLPLLDVVQEGNLGLIRAVEKFDYSKGYKFSTYAIWWIR 144

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            A++  +      V++     ++     +++ +  L+A  D     E+   +A    +  
Sbjct: 145 QAIERGLAEQTRTVRLPVHVVEE--LSKIKKAERKLRAELDREPTVEE---LAGATGLRA 199

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
             V  +  R AG  +++      D+ S+   D +           +E+    +    L  
Sbjct: 200 PRVAEL--RDAGRATISLETPVGDEGSASVADLIEDADAASAYDAVEQAAFSSELRALVE 257

Query: 231 SMSVLNPRERRIFEARR--LQENPV-TLENLSSEFEVSRERVRQIEARAFK 278
           ++    P  + +  +RR  L +  V TL+ ++ E  ++RER+RQ+E  + +
Sbjct: 258 TL----PARQALIVSRRYGLTDGRVHTLQEVAEELGLTRERIRQLEKESLR 304


>gi|40353309|gb|AAR84418.1| essential primary sigma 70 factor [Frankia sp. D11]
 gi|40353317|gb|AAR84422.1| essential primary sigma 70 factor [Frankia sp. HR2714]
 gi|40353319|gb|AAR84423.1| essential primary sigma 70 factor [Frankia sp. Flec]
          Length = 255

 Score = 82.0 bits (201), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 67/231 (29%), Positives = 114/231 (49%), Gaps = 34/231 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +LV ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WW
Sbjct: 46  AKRKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 105

Query: 109 IKAAMQEYILRSWSLVKIGT----TAN-----QKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N     Q++L  +L R     +   + +L P++V
Sbjct: 106 IRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPSPEEIAKEMDLTPDKV 165

Query: 160 VAIAKKLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
             I   L VS+ E +S+   +  +E   L   I   D          V   D    +L++
Sbjct: 166 REI---LKVSQ-EPVSLETPIGEEEDSHLGDFIEDCDA---------VVPVDAASFILLQ 212

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSR 266
           ++        L   +  L+ RE+++ + R      +P TLE +  EF V+R
Sbjct: 213 EQ--------LDSVLHTLSDREKKVIQLRFGLTDGHPRTLEEVGREFGVTR 255


>gi|169883528|gb|ACA97859.1| RNA polymerase sigma factor [Microcystis aeruginosa PCC 7820]
          Length = 377

 Score = 82.0 bits (201), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 61/236 (25%), Positives = 112/236 (47%), Gaps = 11/236 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  +++ S+LRLVV IA  Y   G+P  +++ EG IGL +A +KFDP +G++ +TY+ W
Sbjct: 138 TAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPNKGYKFSTYAYW 197

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++     +K     L +LK   + +  +  +      +A+ L 
Sbjct: 198 WIRQAITRTIANDARTIRLPIHIVEK-----LNKLKKAQRILKQDLQRNPNERELAEALE 252

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++  ++  +        SLN  +   +                ++++     E   R+ +
Sbjct: 253 ITPEQLRQLLQLRRQSLSLNHRVGKGEDTELVDLLEDDDLQLPEDKM----NEMMMRQEI 308

Query: 228 LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                 VL  RE+ +   R       P TLE +   F +SRERVRQI+ +A +K++
Sbjct: 309 FAVLSDVLTEREKDVISLRYGLATSQPYTLEEVGGMFNLSRERVRQIQTKAMRKLR 364


>gi|254432127|ref|ZP_05045830.1| group2 RNA polymerase sigma factor RpoD6 [Cyanobium sp. PCC 7001]
 gi|197626580|gb|EDY39139.1| group2 RNA polymerase sigma factor RpoD6 [Cyanobium sp. PCC 7001]
          Length = 335

 Score = 82.0 bits (201), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 83/292 (28%), Positives = 129/292 (44%), Gaps = 45/292 (15%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---HGD---------LSAAHRLVTSHLR 59
           G  GLS Y+  I ++P+L   EE  LA   +E   H D           A +R+VT++LR
Sbjct: 55  GGDGLSDYLRLIARVPLLTPAEELHLAGTVQEWLQHPDPPLSLRRRGTRARNRMVTANLR 114

Query: 60  LVVKIAMGYRG----YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQE 115
           LVV +   YRG      L + ++   GNIGLM+AV+ FDP RG+RL+TY+  WI  A+Q 
Sbjct: 115 LVVMVCRRYRGRIGNLQLEMLDLYQAGNIGLMRAVELFDPSRGYRLSTYAFSWIHQAVQR 174

Query: 116 YILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
            +           T N  R+   LR +    Q +     +P  + AIA  L   E  +  
Sbjct: 175 CMT---------ATGNGIRIPTALRNIAYRAQLLEACAEQPLSIGAIAALLGEKEQRL-- 223

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE--KEERKNRRN----MLT 229
              + A          S DK S+           G++  LIE   + R N  +     L 
Sbjct: 224 ---QTALTVVRQCSTTSLDKPSASM---------GEDTTLIEVIPDRRGNVPHDDYRWLH 271

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             +  L+ R+R++ + R   +   +    +    VS+  V+ +E R  K ++
Sbjct: 272 EHLDALDLRDRQVLQLRYGDDESRSCSKTARVLGVSKSCVQSVERRTLKNLR 323


>gi|1769413|dbj|BAA13122.1| RpoD2 sigma factor [Microcystis aeruginosa]
          Length = 376

 Score = 82.0 bits (201), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 63/236 (26%), Positives = 112/236 (47%), Gaps = 12/236 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  +++ S+LRLVV IA  Y   G+P  +++ EG IGL +A +KFDP +G++ +TY+ W
Sbjct: 138 TAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPNKGYKFSTYAYW 197

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++     +K     L +LK       D    P +   +A++L 
Sbjct: 198 WIRQAITRTIANDARTIRLPIHIVEK-----LNKLKKAQILKQDLQRNPNE-RELAERLE 251

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++  ++  +        SLN  +   +                ++++     E   R+ +
Sbjct: 252 ITPEQLRQLLQLRRQSLSLNHRVGKGEDTELVDLLEDDDLQLPEDKM----NEMMMRQEI 307

Query: 228 LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                 VL  RE+ +   R       P TLE +   F +SRERVRQI+ +A +K++
Sbjct: 308 FAVLSDVLTEREKDVISLRYGLATSQPYTLEEVGGMFNLSRERVRQIQTKAMRKLR 363


>gi|194246700|ref|YP_002004339.1| probable RNA polymerase sigma factor RpoD [Candidatus Phytoplasma
           mali]
 gi|193807057|emb|CAP18493.1| probable RNA polymerase sigma factor RpoD [Candidatus Phytoplasma
           mali]
          Length = 419

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 93/313 (29%), Positives = 144/313 (46%), Gaps = 77/313 (24%)

Query: 19  YIHEIRKIPML---EKQEEYVLA----------------------KRYREHGDL-----S 48
           Y+ EI +IP+L   E+QE++ L                       K   E  D+      
Sbjct: 116 YLKEIGQIPLLTLEEEQEQFRLVYDGREAEAKLESYRKKEIELSEKEISELNDILKISNK 175

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A HRLV ++ RLVV IA  Y   GL   +++ EGN GLM+A++KF+ ++G +L+TY+ +W
Sbjct: 176 AKHRLVEANYRLVVSIAKRYIRRGLEFLDLIQEGNRGLMRAIEKFNIDKGCKLSTYATFW 235

Query: 109 I------KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           I        A Q  I+R    V I    N   +  +  RLK H         +   +  +
Sbjct: 236 IVQKILRAVADQARIIRLP--VHIVDRINIISMAKSKLRLKLH---------REPTIEEL 284

Query: 163 AKKLNVSE----------SEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDG 210
           ++ +N+SE           + IS+  R+    D SL   I  SD +S    D+++     
Sbjct: 285 SEFINISEKKLRIIEIIKKKPISLEARVGEKDDSSLGEFI--SDPDSLSPHDYML----- 337

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPV-TLENLSSEFEVSRER 268
                  +E  KN  N +      L  RE +I   R  L    V TLE + + F V+RER
Sbjct: 338 -------QEIMKNTLNEILE--DTLTDREEKILRMRYGLSNGKVHTLEEVGNVFGVTRER 388

Query: 269 VRQIEARAFKKVQ 281
           +RQIEA+AF++++
Sbjct: 389 IRQIEAKAFRRLR 401


>gi|67924587|ref|ZP_00518002.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
 gi|67853561|gb|EAM48905.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
          Length = 328

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 73/315 (23%), Positives = 144/315 (45%), Gaps = 76/315 (24%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR------------------------------------ 42
           Y+HEI ++P+L  ++E +  K+ +                                    
Sbjct: 23  YLHEIGRVPLLTHEQEIIYGKQVQKMMNFLEKKEELADKLGKEPTVKEWSKELEIEQKAL 82

Query: 43  ----EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
               E G+  A  +++ ++LRLVV IA  Y+   +   +++ EG++GL + V+KFDP +G
Sbjct: 83  NQALEQGE-RAKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGSLGLERGVEKFDPTKG 141

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           ++ +TY+ WWI+ A+   I +    +++     +K     +++ +  L      +  P +
Sbjct: 142 YKFSTYAYWWIRQAITRAIAQQSRTIRLPIHITEK--LNKIKKTQRELSQTLGRSATPSE 199

Query: 159 VVAIAKKLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              IA++L +  S++          IS++ R+ GD        + D   S+    L+ D 
Sbjct: 200 ---IAQELEIEPSQIREFLSIARQPISLDVRV-GD--------NQDTELSE----LLEDQ 243

Query: 209 DGQEQVLIEKE-ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVS 265
                + I +E  R++ RN+    M+ L P++R +   R   E+   ++L  +     +S
Sbjct: 244 GVSPDLYITQELLRQDLRNL----MAELTPQQRTVLTLRFGLEDGKELSLAKIGKRMNIS 299

Query: 266 RERVRQIEARAFKKV 280
           RERVRQ+E +A  ++
Sbjct: 300 RERVRQLEHQALAQL 314


>gi|159029420|emb|CAO90796.1| unnamed protein product [Microcystis aeruginosa PCC 7806]
          Length = 377

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 61/236 (25%), Positives = 112/236 (47%), Gaps = 11/236 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  +++ S+LRLVV IA  Y   G+P  +++ EG IGL +A +KFDP +G++ +TY+ W
Sbjct: 138 TAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPNKGYKFSTYAYW 197

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++     +K     L +LK   + +  +  +      +A+ L 
Sbjct: 198 WIRQAITRTIANDARTIRLPIHIVEK-----LNKLKKAQRILKQDLQRNPNERELAEALE 252

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++  ++  +        SLN  +   +                ++++     E   R+ +
Sbjct: 253 ITPEQLRQLLQLRRQSLSLNHRVGKGEDTELVDLLEDDDLQLPEDKM----NEMMMRQEI 308

Query: 228 LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                 VL  RE+ +   R       P TLE +   F +SRERVRQI+ +A +K++
Sbjct: 309 FAVLSDVLTEREKDVISLRYGLATSQPYTLEEVGGMFNLSRERVRQIQTKAMRKLR 364


>gi|300858635|ref|YP_003783618.1| RNA polymerase sigma factor B [Corynebacterium pseudotuberculosis
           FRC41]
 gi|300686089|gb|ADK29011.1| RNA polymerase sigma factor B [Corynebacterium pseudotuberculosis
           FRC41]
 gi|302206344|gb|ADL10686.1| RNA polymerase sigma factor sigB [Corynebacterium
           pseudotuberculosis C231]
 gi|302330901|gb|ADL21095.1| RNA polymerase sigma factor sigB [Corynebacterium
           pseudotuberculosis 1002]
 gi|308276586|gb|ADO26485.1| RNA polymerase sigma factor sigB [Corynebacterium
           pseudotuberculosis I19]
          Length = 329

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 64/243 (26%), Positives = 118/243 (48%), Gaps = 27/243 (11%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           AH L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI
Sbjct: 94  AH-LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYSKGFKFSTYATWWI 152

Query: 110 KAAMQEYILRSWSLVKIGTTANQK--RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           + A+   +      +++     ++  +L    R +  HL     N    E+      K+ 
Sbjct: 153 RQAITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQHLGREATNEELAEESGIDESKIE 212

Query: 168 V---SESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           +      + +S++  +  DE   L   I  S+   +             E  ++      
Sbjct: 213 ILLRQSRDPVSLDMPVGADEEAPLGDFIEDSEATDA-------------ESAVVASLRHS 259

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R++L      L  RE+ +   R   ++  P TL+ +  +F +SRERVRQIE     K+
Sbjct: 260 DIRSVL----DTLERREQDVIRMRYGLDDGVPRTLDQIGRQFGLSRERVRQIEREVMTKL 315

Query: 281 QES 283
           ++ 
Sbjct: 316 RDG 318


>gi|170078438|ref|YP_001735076.1| sigma factor [Synechococcus sp. PCC 7002]
 gi|169886107|gb|ACA99820.1| sigma factor [Synechococcus sp. PCC 7002]
          Length = 318

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 60/244 (24%), Positives = 116/244 (47%), Gaps = 29/244 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V ++LRLVV +A  Y    + + +++ EG IG+ + V+KFDP +G+R +TY+ WW
Sbjct: 83  AKQKMVEANLRLVVSVAKKYIKRNMDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWW 142

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      +++     +K     L ++K   + +   N +   +  +A +L +
Sbjct: 143 IRQAITRAIAEKSRTIRLPIHITEK-----LNKIKKAQRQLAQANGRSASIPELADELGL 197

Query: 169 SESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           +  +V          +S++ R+ GD +   LI   + +     D+  +         +++
Sbjct: 198 TTKQVRDYLEKSRQPLSLDLRV-GDNNDTELIELLEDDGLTPDDYATH-------AALKR 249

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           +  +   ++  +   VL  R    F  R     P TL  +     +SRERVRQIE  A  
Sbjct: 250 DLARMLNDLTAQQQEVLTLR----FGLR--DGTPHTLAKIGEHLSISRERVRQIEREALA 303

Query: 279 KVQE 282
           K+++
Sbjct: 304 KLRK 307


>gi|1553033|gb|AAC45108.1| primary sigma factor [Borrelia japonica]
          Length = 450

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 76/260 (29%), Positives = 133/260 (51%), Gaps = 36/260 (13%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 215 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 270

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI--- 149
           F+ +RGF+ +TY+ WWI+ A+   I      +++     ++    N R  +  +Q +   
Sbjct: 271 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINRLN-RETRYLIQVLGKD 329

Query: 150 -TDNNLKPEQVVAIAKKLNVSES---EVISMNCRLAGDES--LNALI-NSSDKNSSQWQD 202
            TD  L  +++    KK+   +S   E +S+   +  +E   L+  I + + KN +    
Sbjct: 330 PTDEEL-SDRLGWELKKVKTVKSVSREPVSLETPIGEEEDSVLSDFIEDKAIKNPANHTS 388

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSS 260
           ++V     Q+Q+          R +L      L  RE+ + + R   E+   +TLE +  
Sbjct: 389 FVVL----QDQI----------RAIL----GTLPEREQEVVKMRFGLEDGYSLTLEEVGL 430

Query: 261 EFEVSRERVRQIEARAFKKV 280
            F V+RER+RQIE++A +++
Sbjct: 431 HFNVTRERIRQIESKALRRL 450


>gi|297566693|ref|YP_003685665.1| RpoD subfamily RNA polymerase sigma-70 subunit [Meiothermus
           silvanus DSM 9946]
 gi|296851142|gb|ADH64157.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Meiothermus
           silvanus DSM 9946]
          Length = 483

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 68/246 (27%), Positives = 126/246 (51%), Gaps = 25/246 (10%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           G+L+  H L+ ++LRLVV IA  Y G GL   +++ EGN GL++AV+KF+ +R ++ +TY
Sbjct: 240 GELARQH-LIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRYKFSTY 298

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + WWI+ A+   I      ++I    +       L R    +Q         E+   I++
Sbjct: 299 ATWWIRQAINRAIADQARTIRI--PVHMVETINKLTRTARQMQQELGREPTYEE---ISE 353

Query: 165 KLNVS-ESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDH-----DGQEQVLIE 217
            +    +++ +    ++A +  SL   I   D+  S + D++  +H     D   Q ++ 
Sbjct: 354 AMGPGWDAKKVEETFKIAQEPVSLETPIG--DEKDSFYGDFIPDEHMASPVDSAAQSMLS 411

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
           +E        L +++  L+ RE  + + R+  +     TLE + + F V+RER+RQIE +
Sbjct: 412 EE--------LEKALGKLSDREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENK 463

Query: 276 AFKKVQ 281
           A +K++
Sbjct: 464 ALRKLK 469


>gi|225021249|ref|ZP_03710441.1| hypothetical protein CORMATOL_01261 [Corynebacterium matruchotii
           ATCC 33806]
 gi|224945982|gb|EEG27191.1| hypothetical protein CORMATOL_01261 [Corynebacterium matruchotii
           ATCC 33806]
          Length = 391

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 72/288 (25%), Positives = 139/288 (48%), Gaps = 44/288 (15%)

Query: 13  EIGL-SRYIHEIRKIPML--EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           E+GL + Y+      P+   +K++  VL K  R+     A   L+ ++LRLVV +A  Y 
Sbjct: 120 EVGLYAEYLLTDSDEPLTRAKKRDLKVLVKEGRK-----ARSHLLEANLRLVVSLAKRYT 174

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A+   +      +++   
Sbjct: 175 GRGMPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVH 234

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCR 179
             ++     L R+K  +          E+   +A++  + ES++          +S++  
Sbjct: 235 LVEQ--VNKLSRIKREMYQQLGREATNEE---LAEESGIDESKIELLLRQSRDPVSLDMP 289

Query: 180 LAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
           +  DE   L   I  S+   +             E  ++      + R+++      L  
Sbjct: 290 VGADEEAPLGDFIEDSEAADA-------------ESAVVASLRHSDIRDVI----GTLED 332

Query: 238 RERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           RE+ +   R   ++  P TL+ +  +F +SRERVRQIE    +K+++ 
Sbjct: 333 REQDVIRMRYGLDDGVPRTLDQIGRQFGLSRERVRQIEREVMRKLRDG 380


>gi|126697159|ref|YP_001092045.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9301]
 gi|126544202|gb|ABO18444.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9301]
          Length = 344

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 73/317 (23%), Positives = 138/317 (43%), Gaps = 53/317 (16%)

Query: 7   SIIVNGEIGLSR-YIHEIRKIPMLEKQEEYVLAKRYREH--------------GD----- 46
           S+  + ++ L R Y+ +I ++P+L  ++E  L ++ +E+              GD     
Sbjct: 27  SLKASNDVDLVRSYLRDIGRVPLLSHEQEITLGRQVQEYMQVERAELEISELTGDKPSID 86

Query: 47  -------LS-------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
                  LS             A  R+V ++LRLVV +A  Y    + + +++ EG IGL
Sbjct: 87  ELSTKLNLSTSVIKKRLRAGQRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGL 146

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++ V+KFDP RG++ +TY+ WWI+  +   I      +++     +      L +LK   
Sbjct: 147 VRGVEKFDPARGYKFSTYAYWWIRQGITRAIAEKSRAIRLPIHITEM-----LNKLKKGQ 201

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           + ++    +   V  +AK + + E +V  + C+     SL   +   D   +   D L  
Sbjct: 202 RELSQEMSRTPTVSELAKYVELPEDDVKDLMCKAGQPVSLETKVG--DGEDTVLLDLLA- 258

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEV 264
              G E +  E+ E    R  L   +  L   + R+   R   +   P++L  +     +
Sbjct: 259 ---GGEDLPDEQIEMDCMRGDLHSLLHQLPDLQCRVLRMRYGMDGDEPMSLTGIGRVLGI 315

Query: 265 SRERVRQIEARAFKKVQ 281
           SR+RVR +E    + ++
Sbjct: 316 SRDRVRNLERDGLRGLR 332


>gi|55274978|gb|AAV49288.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 200

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 34/65 (52%), Positives = 50/65 (76%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           + S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  +
Sbjct: 1   IESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTI 60

Query: 114 QEYIL 118
           +  I+
Sbjct: 61  ERAIM 65


>gi|55274953|gb|AAV49276.1| RNA polymerase subunit sigma-38 [Shigella flexneri 2a]
          Length = 193

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 34/65 (52%), Positives = 50/65 (76%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           + S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  +
Sbjct: 1   IESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTI 60

Query: 114 QEYIL 118
           +  I+
Sbjct: 61  ERAIM 65


>gi|255325135|ref|ZP_05366241.1| RNA polymerase sigma factor RpoD [Corynebacterium
           tuberculostearicum SK141]
 gi|255297700|gb|EET77011.1| RNA polymerase sigma factor RpoD [Corynebacterium
           tuberculostearicum SK141]
          Length = 365

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 78/286 (27%), Positives = 141/286 (49%), Gaps = 41/286 (14%)

Query: 13  EIGL-SRY-IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           E+GL + Y ++   K+   EK++  +LA+     G  + +H L+ ++LRLVV +A  Y G
Sbjct: 95  EVGLYAEYKLNNAEKLTRAEKRDLKILAR----EGKKARSH-LLEANLRLVVSLAKRYTG 149

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A+   +            A
Sbjct: 150 RGMPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTYATWWIRQAITRGM------------A 197

Query: 131 NQKRLFFNLRRLKGHL--QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           +Q R      RL  HL  Q    + +K E   ++ ++   + +E +S    +  DE+   
Sbjct: 198 DQSRTI----RLPVHLVEQVNKLSRIKREMYQSLGRE---ATNEELSEESGI--DENKIE 248

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM------SVLNPRERRI 242
           ++    ++       +  D +      IE  E  +    +  SM       V++  E+R 
Sbjct: 249 MLLRQSRDPVSLDMPVGTDEEAPLGDFIEDAEATDAETAVVASMRHSDIRGVIDTLEKRE 308

Query: 243 FEARRLQEN-----PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +  RL+       P TL+ +   F +SRERVRQIE     K+++ 
Sbjct: 309 QDVIRLRYGLDDGVPRTLDQIGRRFGLSRERVRQIEREVMAKLRDG 354


>gi|227833285|ref|YP_002834992.1| RNA polymerase sigma factor B [Corynebacterium aurimucosum ATCC
           700975]
 gi|262184270|ref|ZP_06043691.1| RNA polymerase sigma factor SigB [Corynebacterium aurimucosum ATCC
           700975]
 gi|227454301|gb|ACP33054.1| RNA polymerase sigma factor B [Corynebacterium aurimucosum ATCC
           700975]
          Length = 331

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 79/285 (27%), Positives = 139/285 (48%), Gaps = 39/285 (13%)

Query: 13  EIGL-SRY-IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           E+GL + Y +    K+   EK++  +LA+     G  + +H L+ ++LRLVV +A  Y G
Sbjct: 61  EVGLYAEYKLANAEKLTRAEKRDLKILAR----EGKKARSH-LLEANLRLVVSLAKRYTG 115

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A+   +      +++    
Sbjct: 116 RGMPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHL 175

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNAL 189
            ++     L R+K  +          E+   +A++  + ES+ I M  R + D  SL+  
Sbjct: 176 VEQ--VNKLSRIKREMYQSLGREATNEE---LAEESGIEESK-IEMLLRQSRDPVSLDMP 229

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM------SVLNPRERRIF 243
           + +              D +      IE  E  +    +  SM      SV+   E R  
Sbjct: 230 VGT--------------DEEAPLGDFIEDAEATDAETAVVASMRHSDIRSVIGSLEEREQ 275

Query: 244 EARRLQEN-----PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +  RL+       P TL+ +  +F +SRERVRQIE     K++E 
Sbjct: 276 DVIRLRYGLDDGVPRTLDQIGRKFGLSRERVRQIEREVMAKLREG 320


>gi|7363218|emb|CAB83106.1| sigma factor 2 [Sinapis alba]
          Length = 575

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 65/240 (27%), Positives = 124/240 (51%), Gaps = 13/240 (5%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           HG      R++ S++RLV+ IA  Y+G G+   ++V EG  GL++  +KFD  +GF+ +T
Sbjct: 328 HG-TQCKDRMIKSNIRLVISIAKNYQGAGMDFQDLVQEGCRGLVRGAEKFDATKGFKFST 386

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWIK A+++ +     ++++    +     + ++  +  L + T    K E+ VA A
Sbjct: 387 YAHWWIKQAVRKSLSDQSRMIRL--PFHMVEATYRVKEARKQLYSETGKQPKNEE-VAEA 443

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
             L++     + ++ +          IN + K S    D    + +  E +L+++  R++
Sbjct: 444 TGLSMKRLMAVLLSPKPPRSLDQKIGINLNLKPSEVIAD---PEAETSEDILMKQFMRQD 500

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
               L + +  L+ RE+++   R   E+    TL+ +     VSRERVRQI+  AF+K++
Sbjct: 501 ----LDKVLDSLSTREKQVIRWRFGMEDGRMKTLQEIGETMGVSRERVRQIDTSAFRKLK 556


>gi|55274967|gb|AAV49283.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 194

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 34/65 (52%), Positives = 50/65 (76%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           + S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  +
Sbjct: 1   IESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTI 60

Query: 114 QEYIL 118
           +  I+
Sbjct: 61  ERAIM 65


>gi|171322946|ref|ZP_02911628.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           MEX-5]
 gi|171091683|gb|EDT37240.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           MEX-5]
          Length = 498

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 64/240 (26%), Positives = 109/240 (45%), Gaps = 30/240 (12%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L  ++LRLVV IA  Y   GLP ++++ EGNIGL++A++++D  RGFR +TY+ WWI+ A
Sbjct: 265 LFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIERYDYRRGFRFSTYATWWIRQA 324

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRL-KGHLQAITDNNLKPEQVVAIAKKLN---- 167
           +   +      +++ T  +       L RL + H Q         E  V + + ++    
Sbjct: 325 ITHALADLGRTIRVPT--HTVDALNKLSRLARAHRQRAGTAATPAELAVHMGEPVDKVRD 382

Query: 168 ----VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
               V E     +     GD +   +   +   S +       D  G  Q+         
Sbjct: 383 LMAIVKEPVSADVPVSPEGDMTFADVAPDTTTPSPE-------DAAGAAQL--------- 426

Query: 224 RRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R  +T  +  L PRE  + + R     +   +L ++  +  +S ERVRQIEA A  +++
Sbjct: 427 -RRTITAVIDRLPPREAMVLKLRYGLHTDEGCSLRDIGRQLNLSAERVRQIEASALARLR 485


>gi|21466021|pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
           Promoter Dna Complex At 6.5 A Resolution
 gi|11527292|gb|AAG36964.1|AF291720_1 sigma factor SigA [Thermus aquaticus]
          Length = 438

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 67/242 (27%), Positives = 123/242 (50%), Gaps = 22/242 (9%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   L+ ++LRLVV IA  Y G GL   +++ EGN GL++AV+KF+ +R F+ +TY+ W
Sbjct: 197 AARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATW 256

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I    +       L R    LQ         E+   IA+ + 
Sbjct: 257 WIRQAINRAIADQARTIRI--PVHMVETINKLSRTARQLQQELGREPSYEE---IAEAMG 311

Query: 168 VS-ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH-----DGQEQVLIEKEER 221
              +++ +    ++A  E ++      D+  S + D++  ++     +   Q L+ +E  
Sbjct: 312 PGWDAKRVEETLKIA-QEPVSLETPIGDEKDSFYGDFIPDENLPSPVEAAAQSLLSEE-- 368

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
                 L +++S L+ RE  + + R+  +     TLE + + F V+RER+RQIE +A +K
Sbjct: 369 ------LEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRK 422

Query: 280 VQ 281
           ++
Sbjct: 423 LK 424


>gi|318041996|ref|ZP_07973952.1| RNA polymerase sigma factor, sigma-70 family protein [Synechococcus
           sp. CB0101]
          Length = 318

 Score = 82.0 bits (201), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 69/242 (28%), Positives = 121/242 (50%), Gaps = 17/242 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG R +TY+ WW
Sbjct: 75  AKDQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSTYAYWW 134

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE-QVVAIAKKLN 167
           I+  +   +      ++I    N+K     LR  K  L  +  +  +P  Q ++ A  L 
Sbjct: 135 IRQGLNRALSTQSRTIRIPVNVNEK--LTRLRAAKARL--LQRHGSQPSAQQLSEAMDLP 190

Query: 168 VSESEVISMNCRL-AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           V E E + + C L +   SL  ++ S    +      LV     ++   +E+ E   R  
Sbjct: 191 VQEVEDL-LGCELRSVTVSLQGVVKSKSDPTE-----LVDVLPSEDLPPMERCELAERNA 244

Query: 227 MLTRSM--SVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            + + +  S L P+ER +   R   +      TL  ++     SRE  RQ+  RA +K++
Sbjct: 245 AVWKLLDQSNLTPKERTVVMLRFGLDGSHEWRTLAEVARLLGCSREYCRQVVQRALRKLR 304

Query: 282 ES 283
           ++
Sbjct: 305 KA 306


>gi|297626467|ref|YP_003688230.1| RNA polymerase principal sigma factor HrdD [Propionibacterium
           freudenreichii subsp. shermanii CIRM-BIA1]
 gi|296922232|emb|CBL56802.1| RNA polymerase principal sigma factor HrdD [Propionibacterium
           freudenreichii subsp. shermanii CIRM-BIA1]
          Length = 309

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 81/310 (26%), Positives = 143/310 (46%), Gaps = 53/310 (17%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAK-----RYR---------------------- 42
           ++G+  +  Y+  I K P+L   EE  LA+     +Y                       
Sbjct: 13  IDGKDSVGLYLESIAKTPLLTAAEEVELARLIEVGQYAQAVLRGEVKTKTKATEEELLGI 72

Query: 43  -EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            E G+ +  H  V ++LRLVV +A  Y    +P+ ++V EGN GL++AV+KFD  +GF+ 
Sbjct: 73  AEEGERAMQH-FVRANLRLVVSVARKYGRSQMPLLDLVQEGNTGLIRAVEKFDYAKGFKF 131

Query: 102 ATYSMWWIKAAMQEYILRSWSLVK----IGTTANQ-KRLFFNLRRLKGHLQAITDNNLKP 156
           +TY+ WW++ A+   I +   +V+    +    NQ   +  NL R  G          +P
Sbjct: 132 STYATWWVRQAISRGIAQQGRIVRLPVHVAEQVNQISAVRRNLERQLGR---------EP 182

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD-HDGQEQVL 215
           E V  IA +L + E++VI +        SL+A +   D   +   D +  +   G ++++
Sbjct: 183 E-VSEIANELGLEENKVIDLIRYSREHVSLDAPVE--DDGDTSLGDLIARETAPGPDELV 239

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIE 273
           ++ E+R     +L      L+ R   +   R   L  +   L ++   + ++ ERVRQIE
Sbjct: 240 LDLEDRSRLEALLAN----LDDRSADVMRRRYGLLDGHQAKLSDIGKVWGITAERVRQIE 295

Query: 274 ARAFKKVQES 283
             A  +++ S
Sbjct: 296 RAALNQLRTS 305


>gi|260436019|ref|ZP_05789989.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 8109]
 gi|260413893|gb|EEX07189.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 8109]
          Length = 335

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 75/298 (25%), Positives = 137/298 (45%), Gaps = 34/298 (11%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEY---------VLAK----------RYREHGDLSAAHRL 53
           EI L R + E+  +  LE + E          VLAK          R  +HG   A  R+
Sbjct: 46  EITLGRQVQELMDLESLEAELESKAGEKPSRDVLAKASGLSSMQLKRKLQHGR-RAKERM 104

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V ++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP RG++ +TY+ WWI+  +
Sbjct: 105 VAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWWIRQGI 164

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
              I      +++     +      L +LK   + ++    +   V  +A+ + + E +V
Sbjct: 165 TRAIAEKSRTIRLPIHITEM-----LNKLKKGQRELSQELGRTPTVTELAEFVELPEDDV 219

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             + CR     SL   +   D + ++  + L  D D     + E   + + R++L +   
Sbjct: 220 KDLMCRARQPVSLE--MKVGDGDDTELLELLSGDGDLPSDQVEEDCLKGDLRSLLGQ--- 274

Query: 234 VLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
            L   + ++   R     E+P++L  +     +SR+RVR +E      ++  +  QVE
Sbjct: 275 -LPHLQEQVLRMRYGMDGEDPMSLTGIGRILGMSRDRVRNLERDGLAGLRR-VSDQVE 330


>gi|110626979|gb|ABG79029.1| RpoH [Wolbachia endosymbiont of Armadillidium vulgare]
          Length = 78

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 36/67 (53%), Positives = 51/67 (76%)

Query: 7  SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
          ++ VN    L +YI E+RK PML ++EE  LAK ++E+ D+S+AH+L+TSHL LVVKIAM
Sbjct: 7  NLCVNSSTNLMQYIAEVRKFPMLSQEEEVRLAKNWQEYKDISSAHKLITSHLNLVVKIAM 66

Query: 67 GYRGYGL 73
           ++ YGL
Sbjct: 67 KFKNYGL 73


>gi|254432638|ref|ZP_05046341.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Cyanobium sp. PCC 7001]
 gi|197627091|gb|EDY39650.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Cyanobium sp. PCC 7001]
          Length = 335

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 60/237 (25%), Positives = 116/237 (48%), Gaps = 12/237 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+V ++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP RG++ +TY+ WW
Sbjct: 95  AKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWW 154

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   I      +++     +      L +LK   + ++    +   V  +A  + +
Sbjct: 155 IRQGITRAIAEKSRTIRLPIHITE-----TLNKLKKGQRELSQELGRTPTVTELAGYVEL 209

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E EV  + CR     SL   +   D   ++  D L  D +  E+ +  +  + + R +L
Sbjct: 210 PEEEVKDLLCRARQPVSLETKVG--DGEDTELLDLLAGDGELPEERVDGECLKGDLRALL 267

Query: 229 TR----SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +       VL  R     E + L E P++L +++    +SR++ R +E +A + ++
Sbjct: 268 EQLPELQGRVLKMRYGLDPEGQGLTE-PMSLSSIAKNLGMSRDKTRNLERKALEGIR 323


>gi|218295160|ref|ZP_03495996.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermus aquaticus
           Y51MC23]
 gi|218244363|gb|EED10888.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermus aquaticus
           Y51MC23]
          Length = 439

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 67/242 (27%), Positives = 123/242 (50%), Gaps = 22/242 (9%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   L+ ++LRLVV IA  Y G GL   +++ EGN GL++AV+KF+ +R F+ +TY+ W
Sbjct: 198 AARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATW 257

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I    +       L R    LQ         E+   IA+ + 
Sbjct: 258 WIRQAINRAIADQARTIRI--PVHMVETINKLSRTARQLQQELGREPSYEE---IAEAMG 312

Query: 168 VS-ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH-----DGQEQVLIEKEER 221
              +++ +    ++A  E ++      D+  S + D++  ++     +   Q L+ +E  
Sbjct: 313 PGWDAKRVEETLKIA-QEPVSLETPIGDEKDSFYGDFIPDENLPSPVEAAAQSLLSEE-- 369

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
                 L +++S L+ RE  + + R+  +     TLE + + F V+RER+RQIE +A +K
Sbjct: 370 ------LEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRK 423

Query: 280 VQ 281
           ++
Sbjct: 424 LK 425


>gi|116070855|ref|ZP_01468124.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. BL107]
 gi|116066260|gb|EAU72017.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. BL107]
          Length = 239

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 67/238 (28%), Positives = 116/238 (48%), Gaps = 17/238 (7%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG R +TY+ WWI+  
Sbjct: 1   MITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSTYAYWWIRQG 60

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +      ++I    N+K     LR  K  +          EQ   +A+ +N+  +E
Sbjct: 61  LNRALSTQSRTIRIPVNVNEK--LTKLRAAKARVMQRNGLTATAEQ---LAEFMNLPLTE 115

Query: 173 VIS-MNCRL-AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML-- 228
           V   + C L +   SL  ++ S    S      LV     +E   +E+ E   R   +  
Sbjct: 116 VEDLLACELRSVTVSLQGIVKSKSDPSE-----LVDILPSEEIPPMERAEIAERSASVWA 170

Query: 229 TRSMSVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             S + L P+E ++   R   +      TL  ++     SRE  RQ+  RA +K++++
Sbjct: 171 LLSKANLTPKEHKVVTLRFGLDGTNEWRTLAEVARHMNCSREYCRQVVQRALRKLRKT 228


>gi|158339957|ref|YP_001521127.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158310198|gb|ABW31813.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 268

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 39/98 (39%), Positives = 63/98 (64%), Gaps = 1/98 (1%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ E+ + P+L  +EE  LA++ +  G L A  R++  +LRLVV IA  ++  GLP+
Sbjct: 8   LHYYLQEMGRYPLLSHEEEIELARQAKA-GSLRAKQRMIECNLRLVVSIAKKHQNRGLPL 66

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
            +++ EG+IGL  AV KF+  +G R +TY+ WWI+  +
Sbjct: 67  LDLIQEGSIGLSTAVDKFEIAQGCRFSTYAYWWIRQGI 104


>gi|94313583|ref|YP_586792.1| RNA polymerase sigma 70 (sigma D) factor [Cupriavidus metallidurans
           CH34]
 gi|93357435|gb|ABF11523.1| RNA polymerase sigma 70 (sigma D) factor [Cupriavidus metallidurans
           CH34]
          Length = 617

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 67/241 (27%), Positives = 111/241 (46%), Gaps = 32/241 (13%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ S+LRLVV  A  Y   G+P+ +++ EGN+GLM+AV +FD  RG++ +TY+ WWI+  
Sbjct: 382 MIRSNLRLVVSNAKKYLHRGMPLLDLIQEGNLGLMRAVDRFDYRRGYKFSTYATWWIRQG 441

Query: 113 MQEYILRSWSLVKI--------GTTANQKR-LFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           +   I      ++I        G      R LF                +L  ++V AI 
Sbjct: 442 ITRAIADKGPTIRIPIHLVEVVGKVNRASRELFHETGEAPAPEALAARLSLSVKKVKAIL 501

Query: 164 KKLNVSESEVISMNCRLAGDESL-NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
               V E   + M+   +GD  L + L +    +                    E   R 
Sbjct: 502 DL--VKEPLSLEMSVGESGDALLWDTLTDECSASPD------------------ESAMRV 541

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R  L  +++ L PRE +I + R   +     TLE +  ++ +SRERVRQ+E +A +K+
Sbjct: 542 SLRKDLDEALATLKPREAKIVKMRYGVDAGTDYTLEEIGQQYGLSRERVRQLERQALRKL 601

Query: 281 Q 281
           +
Sbjct: 602 R 602


>gi|315608976|ref|ZP_07883948.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella buccae
           ATCC 33574]
 gi|315249356|gb|EFU29373.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella buccae
           ATCC 33574]
          Length = 287

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 76/285 (26%), Positives = 130/285 (45%), Gaps = 49/285 (17%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
            +K+  +  N    L+ Y+ EI +   L  ++E  LA    + GD  A  +L  ++L+ V
Sbjct: 41  TKKSKDMDSNERNALNTYLDEIGQESPLTPEKEQDLAACI-QAGDRGALEQLTRANLKFV 99

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V +A  +RG GL  S+++SEGNIGLM+A  KFD  RG R   Y+  +++ AM+  + +  
Sbjct: 100 VAMARRFRGRGLAQSDLISEGNIGLMEAAGKFDGSRGNRFVAYAAPYVRKAMERAVEQQA 159

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            L ++           ++ R K      + + ++P  V A      +SE    ++     
Sbjct: 160 GLYRVPR---------DIMRQK------SRHEVQPASVDA-----PLSEGNKFTL----- 194

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
               L+ L N         +D +  D D   Q +IE          L   ++ L+ RE+R
Sbjct: 195 ----LDILEN---------KDAIHPDDDYNVQAMIE---------ALESLVATLDEREQR 232

Query: 242 IFEA-RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           +      L    ++L  ++ +  + RER RQI  RA +K+  S Q
Sbjct: 233 VVRGFYGLGTGRISLAEIAEQMGIKRERARQIRDRALRKIARSTQ 277


>gi|9082209|gb|AAF82776.1|AF273254_1 RNA polymerase sigma factor [Coxiella burnetii]
          Length = 410

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 70/260 (26%), Positives = 114/260 (43%), Gaps = 62/260 (23%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 170 AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 229

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           I+ A+   I      ++I      T N+      L R+   +   T     PE+   + +
Sbjct: 230 IRQAITRSIADQARTIRIPVHMIETINK------LNRISRQILQETGIEATPEE---LGR 280

Query: 165 KLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDW----------- 203
           ++++ E +V          ISM   +  DE  N      D N     D+           
Sbjct: 281 RMDMPEEKVRKVLKIAKEPISMETPIGEDEDSNLGDFIEDINMESPVDFATSAGLMEATR 340

Query: 204 --LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
              VY +  + QVL         R      M+  +                 TLE + + 
Sbjct: 341 RNFVYAYPARSQVL---------RMRFGIDMNTDH-----------------TLEEVGNN 374

Query: 262 FEVSRERVRQIEARAFKKVQ 281
            +V+RER+RQIEA+A +K++
Sbjct: 375 SDVTRERIRQIEAKALRKLR 394


>gi|296393377|ref|YP_003658261.1| RpoD subfamily RNA polymerase sigma-70 factor [Segniliparus
           rotundus DSM 44985]
 gi|296180524|gb|ADG97430.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Segniliparus
           rotundus DSM 44985]
          Length = 377

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 69/238 (28%), Positives = 118/238 (49%), Gaps = 32/238 (13%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ W
Sbjct: 139 AARTHLLEANLRLVVSLAKRYTGRGIPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTYATW 198

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-----QAITDNNLKPEQVVA- 161
           WI+ A+   +      +++     ++     L R+K  L     +  T   L  E  +  
Sbjct: 199 WIRQAITRGVADQSRTIRLPVHLVEQ--VNKLSRIKRELHQQLGREATSEELSRETGIPE 256

Query: 162 --IAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
             IA  L+ S   V S++  +  DE   L   I  S+  S+             E  +I 
Sbjct: 257 HRIADLLDHSRDPV-SLDMPVGADEEAPLGDFIEDSEGASA-------------ENAVIA 302

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIE 273
               ++ R +L    + LN  E+++   R   ++  P TL+ +   F +SRERVRQIE
Sbjct: 303 GFLHRDVRTVL----ATLNEVEQQVIRLRYGLDDGQPRTLDQIGKVFSLSRERVRQIE 356


>gi|227503471|ref|ZP_03933520.1| RNA polymerase sigma factor SigB [Corynebacterium accolens ATCC
           49725]
 gi|306836281|ref|ZP_07469263.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           accolens ATCC 49726]
 gi|227075974|gb|EEI13937.1| RNA polymerase sigma factor SigB [Corynebacterium accolens ATCC
           49725]
 gi|304567873|gb|EFM43456.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           accolens ATCC 49726]
          Length = 337

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 78/286 (27%), Positives = 141/286 (49%), Gaps = 41/286 (14%)

Query: 13  EIGL-SRY-IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           E+GL + Y ++   K+   EK++  +LA+     G  + +H L+ ++LRLVV +A  Y G
Sbjct: 67  EVGLYAEYKLNNAEKLTRAEKRDLKILAR----EGKKARSH-LLEANLRLVVSLAKRYTG 121

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A+   +            A
Sbjct: 122 RGMPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTYATWWIRQAITRGM------------A 169

Query: 131 NQKRLFFNLRRLKGHL--QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           +Q R      RL  HL  Q    + +K E   ++ ++   + +E +S    +  DE+   
Sbjct: 170 DQSRTI----RLPVHLVEQVNKLSRIKREMYQSLGRE---ATNEELSEESGI--DENKIE 220

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM------SVLNPRERRI 242
           ++    ++       +  D +      IE  E  +    +  SM       V++  E+R 
Sbjct: 221 MLLRQSRDPVSLDMPVGTDEEAPLGDFIEDAEATDAETAVVASMRHSDIRGVIDTLEKRE 280

Query: 243 FEARRLQEN-----PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +  RL+       P TL+ +   F +SRERVRQIE     K+++ 
Sbjct: 281 QDVIRLRYGLDDGVPRTLDQIGRRFGLSRERVRQIEREVMAKLRDG 326


>gi|159037062|ref|YP_001536315.1| RNA polymerase sigma factor SigB [Salinispora arenicola CNS-205]
 gi|157915897|gb|ABV97324.1| RNA polymerase, sigma 70 subunit, RpoD family [Salinispora
           arenicola CNS-205]
          Length = 328

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 67/240 (27%), Positives = 121/240 (50%), Gaps = 19/240 (7%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   L+ ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ W
Sbjct: 89  AAKDHLLEANLRLVVSIAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATW 148

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQK--RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
           WI+ A+   +      ++I     ++  R+    R L   L        +   V  +A+ 
Sbjct: 149 WIRQAITRAMADQSRTIRIPVHMVEQVNRMVRTRRDLSVSLG-------REPTVTEVARA 201

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL-VYDHDGQEQVLIEKEE-RKN 223
           L+V E ++I +        SL+  +   +   S   D++ V +         E+ E R+ 
Sbjct: 202 LDVPEVQIIELISYDREPVSLDQAVG--EDGESPLGDFVAVVNATAAPDNTAERGELRQE 259

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R +L    + L+ RE+ +   R   ++    TL+ +  EF +SRER+RQIE    +K++
Sbjct: 260 VRGVL----ATLSQREQAVIRLRFGLDDGRQRTLDEVGREFGLSRERIRQIEKGTLRKLR 315


>gi|170704115|ref|ZP_02894732.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           ambifaria IOP40-10]
 gi|170130976|gb|EDS99686.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           ambifaria IOP40-10]
          Length = 575

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 62/238 (26%), Positives = 113/238 (47%), Gaps = 22/238 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L  ++LRLVV IA  Y   GLP ++++ EGNIGL++A++++D  RGFR +TY+ WWI+ A
Sbjct: 342 LFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIERYDYRRGFRFSTYATWWIRQA 401

Query: 113 MQEYILRSWSLVKIGT-TANQ----KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +   +      +++ T T +      RL    R+  G      +  +   + V   + L 
Sbjct: 402 ITHALADLGRTIRVPTHTVDALNKLSRLAREHRQRAGTAATPAELAVHMGEPVDKVRDLM 461

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
               E +S +  ++ +  +     ++D ++   +D       G  Q+          R  
Sbjct: 462 AIVKEPVSADVPVSPEGDMTFADVAADTSTPSPEDAA-----GATQL----------RRT 506

Query: 228 LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +   +  L PRE  + + R     +   +L ++  +  +S ERVRQIEA A  +++ S
Sbjct: 507 IAAVIDRLPPREAMVLKLRYGLHADEGCSLRDIGRQLNLSAERVRQIEASALARLRAS 564


>gi|116074383|ref|ZP_01471645.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9916]
 gi|116069688|gb|EAU75440.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9916]
          Length = 341

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 71/283 (25%), Positives = 130/283 (45%), Gaps = 34/283 (12%)

Query: 13  EIGLSRYIHEIRKIPMLEKQ------EEYVLAKRYREHGDLS-------------AAHRL 53
           EI L R + ++ ++  LE +      EE V  +   +   LS             A  R+
Sbjct: 51  EITLGRQVQDLMELEALESELKSESGEEVVAPEALAKKAGLSGVQLKRKLQAGRRAKERM 110

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V ++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP RG++ +TY+ WWI+  +
Sbjct: 111 VAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWWIRQGI 170

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
              I      +++     +      L +LK   + ++    +   V  +A+ + + E EV
Sbjct: 171 TRAIAEKSRTIRLPIHITEM-----LNKLKKGQRELSQELGRTPTVTELAEFVELPEEEV 225

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSM 232
             + CR     SL   +   D + ++  + L  D +   EQV     E +  +  L   +
Sbjct: 226 KDLMCRARQPVSLE--MKVGDGDDTELLELLAGDGELPSEQV-----EGECLKGDLRDLL 278

Query: 233 SVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIE 273
             L   +R++   R     E+P++L  +     +SR+RVR +E
Sbjct: 279 EQLPELQRKVLRMRYGMNGEDPMSLTGIGRIIGISRDRVRNLE 321


>gi|313665390|ref|YP_004047261.1| RNA polymerase sigma factor RpoD [Mycoplasma leachii PG50]
 gi|312949647|gb|ADR24243.1| putative RNA polymerase sigma factor RpoD [Mycoplasma leachii PG50]
          Length = 498

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 39/114 (34%), Positives = 70/114 (61%), Gaps = 3/114 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRY--REHGDLSAA-HRLVTSHLRLVVKIAMGYRGYG 72
           +  Y ++I + P+L K +E + AK     +  D+    ++L+ S+L+LV+ +A  +   G
Sbjct: 163 IKTYFYKIGQAPILTKDQEIMYAKMAVSDDPEDVKEGRNKLIESNLKLVISVARKHLNRG 222

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           L  ++++ EGNIGLM+AV KF+ E+GF+ +TY+ WWI+ A+   I      ++I
Sbjct: 223 LDFADLIEEGNIGLMKAVDKFEYEKGFKFSTYATWWIRQAITRAIADQARTIRI 276


>gi|311739612|ref|ZP_07713447.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           pseudogenitalium ATCC 33035]
 gi|311305428|gb|EFQ81496.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           pseudogenitalium ATCC 33035]
          Length = 337

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 78/286 (27%), Positives = 141/286 (49%), Gaps = 41/286 (14%)

Query: 13  EIGL-SRY-IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           E+GL + Y ++   K+   EK++  +LA+     G  + +H L+ ++LRLVV +A  Y G
Sbjct: 67  EVGLYAEYKLNNAEKLTRAEKRDLKILAR----EGKKARSH-LLEANLRLVVSLAKRYTG 121

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A+   +            A
Sbjct: 122 RGMPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTYATWWIRQAITRGM------------A 169

Query: 131 NQKRLFFNLRRLKGHL--QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           +Q R      RL  HL  Q    + +K E   ++ ++   + +E +S    +  DE+   
Sbjct: 170 DQSRTI----RLPVHLVEQVNKLSRIKREMYQSLGRE---ATNEELSEESGI--DENKIE 220

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM------SVLNPRERRI 242
           ++    ++       +  D +      IE  E  +    +  SM       V++  E+R 
Sbjct: 221 MLLRQSRDPVSLDMPVGTDEEAPLGDFIEDAEATDAETAVVASMRHSDIRGVIDTLEKRE 280

Query: 243 FEARRLQEN-----PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +  RL+       P TL+ +   F +SRERVRQIE     K+++ 
Sbjct: 281 QDVIRLRYGLDDGVPRTLDQIGRRFGLSRERVRQIEREVMAKLRDG 326


>gi|115360900|ref|YP_778037.1| RNA polymerase, sigma 28 subunit [Burkholderia ambifaria AMMD]
 gi|115286228|gb|ABI91703.1| RNA polymerase, sigma 28 subunit [Burkholderia ambifaria AMMD]
          Length = 617

 Score = 81.6 bits (200), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 62/238 (26%), Positives = 112/238 (47%), Gaps = 22/238 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L  ++LRLVV IA  Y   GLP ++++ EGNIGL++A++++D  RGFR +TY+ WWI+ A
Sbjct: 384 LFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIERYDHRRGFRFSTYATWWIRQA 443

Query: 113 MQEYILRSWSLVKIGT-TANQ----KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +   +      +++ T T +      RL    R+  G      +  +   + V   ++L 
Sbjct: 444 ITHALADLGRTIRVPTHTVDALNKLSRLAREHRQRAGTAATPAELAVHMGEPVDKVRELM 503

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
               E +S +  ++ +  +     + D  +   +D       G  Q+          R  
Sbjct: 504 AIVKEPVSADVPVSPEGDMTFADVAPDTTTPSPEDAA-----GATQL----------RRT 548

Query: 228 LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +   +  L PRE  + + R     +   +L ++  +  +S ERVRQIEA A  +++ S
Sbjct: 549 IAAVIDRLPPREAMVLKLRYGLHTDEGCSLRDIGRQLNLSAERVRQIEASALARLRAS 606


>gi|126661338|ref|ZP_01732404.1| RNA polymerase sigma factor [Cyanothece sp. CCY0110]
 gi|126617371|gb|EAZ88174.1| RNA polymerase sigma factor [Cyanothece sp. CCY0110]
          Length = 328

 Score = 81.3 bits (199), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 72/314 (22%), Positives = 142/314 (45%), Gaps = 74/314 (23%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR------------------------------------ 42
           Y+HEI ++P+L  ++E +  K+ +                                    
Sbjct: 23  YLHEIGRVPLLTHEQEIIYGKQVQTMMNLLEKKEELAQRVGKEPSIQEWAKEVNIEEKAL 82

Query: 43  ----EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
               E G+  A  +++ ++LRLVV IA  Y+   +   +++ EG++GL + V+KFDP +G
Sbjct: 83  QKALEQGE-RAKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGSLGLERGVEKFDPTKG 141

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           ++ +TY+ WWI+ A+   I +    +++     +K     L ++K   + ++ +  +   
Sbjct: 142 YKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEK-----LNKIKKTQRELSQSLGRSAT 196

Query: 159 VVAIAKKLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              IA++L +  S++          IS++ R+ GD        + D   S+    L+ D 
Sbjct: 197 PAEIAQELEIEPSQIREFLSIARQPISLDVRV-GD--------NQDTELSE----LLEDQ 243

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSR 266
                + I +E     R  L+  M+ L P++R +   R   E+   ++L  +     +SR
Sbjct: 244 GVSPDIYITQE---LLRQDLSNLMAELTPQQRTVLTLRFGLEDGKELSLAKIGKRLNISR 300

Query: 267 ERVRQIEARAFKKV 280
           ERVRQ+E +A  ++
Sbjct: 301 ERVRQLEHQALAQL 314


>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 = 81.3 bits (199), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 64/248 (25%), Positives = 113/248 (45%), Gaps = 26/248 (10%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV+KF+  RG++ +TY+ WW
Sbjct: 411 AKREMIEANLRLVISIAKKYTNRGLGFLDLIQEGNIGLMKAVEKFEWRRGYKFSTYATWW 470

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV-----VAIA 163
           I+ A+   I      ++I    +       + R+   +         PE++     + + 
Sbjct: 471 IRQAITRSIADQARTIRI--PVHMIETINKMMRVSRQIAQEIGREPTPEELAEHLELPVE 528

Query: 164 KKLNVSE--SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           K L + E   E +S+   +  DE         D N+    D  +     +  + +     
Sbjct: 529 KVLQILEVAKEPVSLETPIGDDEDSQLGDFVEDDNAENPLDSTIGAALAEATLEV----- 583

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
                     +  L  RE+++   R         TLE +  +F V+RER+RQIEA+A +K
Sbjct: 584 ----------LENLTDREQKVLRMRFGIGMNTDHTLEEVGKQFGVTRERIRQIEAKALRK 633

Query: 280 VQESIQKQ 287
           ++   + Q
Sbjct: 634 LRHPSRSQ 641


>gi|113474616|ref|YP_720677.1| RNA polymerase sigma factor [Trichodesmium erythraeum IMS101]
 gi|110165664|gb|ABG50204.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
          Length = 336

 Score = 81.3 bits (199), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 72/300 (24%), Positives = 138/300 (46%), Gaps = 52/300 (17%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR--------------------------YREHGDLS---- 48
           Y+HEI ++P+L ++EE V  K+                          + EH  +S    
Sbjct: 32  YLHEIGRVPLLTREEEIVYGKQVQQMMQFLELKEKLEEKLNRTATLLEWAEHLLVSEKVL 91

Query: 49  ---------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                    A  +++ ++LRLVV IA  Y+   +   +++ EG +GL + V+KFDP RG+
Sbjct: 92  KQAIKQGQRAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGY 151

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWI+ A+   I +    +++     +K     ++R++  L      +  P + 
Sbjct: 152 KFSTYAYWWIRQAITRAIAQQARTIRLPIHITEK--LNKIKRVQRELIQSLGRSPTPSE- 208

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IA+ L +  S++      L     ++  +   D   ++ Q+ L+ D        I  E
Sbjct: 209 --IAQALELEPSQI--REYLLMARHPISLDLRVGDNQDTELQE-LLEDETSSPDDYITGE 263

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
             +   N L   ++ L+ ++RR+   R   E+   ++L  +  + ++SRERVRQ+E +A 
Sbjct: 264 LLRQDINTL---LAELSEQQRRVLVLRFGLEDGKEMSLAKVGDKLQLSRERVRQLEHQAL 320


>gi|172035560|ref|YP_001802061.1| RNA polymerase sigma factor [Cyanothece sp. ATCC 51142]
 gi|171697014|gb|ACB49995.1| group 2 sigma-70 RNA polymerase sigma factor B [Cyanothece sp. ATCC
           51142]
          Length = 328

 Score = 81.3 bits (199), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 72/314 (22%), Positives = 141/314 (44%), Gaps = 74/314 (23%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR------------------------------------ 42
           Y+HEI ++P+L  ++E +  K+ +                                    
Sbjct: 23  YLHEIGRVPLLTHEQEIIYGKQVQKMMSLLETKEELAQSLGKEPSLQEWAKEVNLEEKAL 82

Query: 43  ----EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
               E G+  A  +++ ++LRLVV IA  Y+   +   +++ EG++GL + V+KFDP +G
Sbjct: 83  TKALEQGE-RAKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGSLGLERGVEKFDPTKG 141

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           ++ +TY+ WWI+ A+   I +    +++     +K     +++ +  L      +  P +
Sbjct: 142 YKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEK--LNKIKKTQRELSQTLGRSATPAE 199

Query: 159 VVAIAKKLNVSESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              IA++L +  S++          IS++ R+ GD        + D   S+    L+ D 
Sbjct: 200 ---IAQELEIEPSQIREFLSIARQPISLDVRV-GD--------NQDTELSE----LLEDQ 243

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSR 266
                + I +E     R  L+  M+ L P++R +   R   E+   ++L  +     +SR
Sbjct: 244 GVSPDIYITQE---LLRQDLSNLMAELTPQQRTVLTLRFGLEDGKELSLAKIGKRLNISR 300

Query: 267 ERVRQIEARAFKKV 280
           ERVRQ+E +A  ++
Sbjct: 301 ERVRQLEHQALAQL 314


>gi|170737511|ref|YP_001778771.1| RpoD family RNA polymerase sigma factor [Burkholderia cenocepacia
           MC0-3]
 gi|169819699|gb|ACA94281.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           cenocepacia MC0-3]
          Length = 627

 Score = 81.3 bits (199), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 69/244 (28%), Positives = 115/244 (47%), Gaps = 34/244 (13%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +L  S+LRLVV +A  Y   GLP S+++ EGNIGLM+AV ++D  RGF+ +TY+ WWI+ 
Sbjct: 393 KLFQSNLRLVVSVAKRYADRGLPFSDLIQEGNIGLMKAVDRYDHRRGFKFSTYATWWIRQ 452

Query: 112 AMQEYILRSWSLVKIGT-TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
           A+   +      +++ T T +       L RL  H Q                +  +V++
Sbjct: 453 AITHALADLGRTIRVPTHTVDTLNKLSRLARL--HRQ----------------RTGDVAD 494

Query: 171 SEVISMNCRLAGDE--SLNALIN---SSDKNSSQWQDWLVYDH--DGQEQVLIEKEERKN 223
           +  +S   RL  D+   L +++    S+D   S   D  + D   D       E      
Sbjct: 495 ARALSTQMRLPVDKVRELMSIVREPISADLPVSPDHDLTLCDVTIDPDAPTPEEAASAGQ 554

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQ-----ENPVTLENLSSEFEVSRERVRQIEARAFK 278
            R ++   +  L  RE  I    RL+     +N  +L  +  +  +S ERVRQ+E  A +
Sbjct: 555 LRAVVAELIDSLPVREAWIL---RLRYGIDVDNEYSLREIGRQLNLSAERVRQLEVSALE 611

Query: 279 KVQE 282
           ++++
Sbjct: 612 RIRQ 615


>gi|40353313|gb|AAR84420.1| essential primary sigma 70 factor [Frankia sp. ACN1ag]
          Length = 255

 Score = 81.3 bits (199), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 67/231 (29%), Positives = 113/231 (48%), Gaps = 34/231 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +LV ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WW
Sbjct: 46  AKRKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 105

Query: 109 IKAAMQEYILRSWSLVKIGT----TAN-----QKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N     Q++L  +L R     +   + +L P++V
Sbjct: 106 IRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPSPEEIAKEMDLTPDKV 165

Query: 160 VAIAKKLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
             I   L VS+ E +S+   +  +E   L   I   D          V   D    +L++
Sbjct: 166 REI---LKVSQ-EPVSLETPIGEEEDSHLGDFIEDCDA---------VVPVDAASFILLQ 212

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSR 266
           +         L   +  L+ RE+++ + R      +P TLE +  EF V+R
Sbjct: 213 E--------XLDSVLHTLSDREKKVIQLRFGLTDGHPRTLEEVGREFGVTR 255


>gi|269126860|ref|YP_003300230.1| RpoD subfamily RNA polymerase sigma-70 subunit [Thermomonospora
           curvata DSM 43183]
 gi|268311818|gb|ACY98192.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermomonospora
           curvata DSM 43183]
          Length = 360

 Score = 81.3 bits (199), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 79/295 (26%), Positives = 135/295 (45%), Gaps = 44/295 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH---------------------GDLSAAHR 52
           Y+  I +  +L+ QEE  LAK      Y EH                       + A  R
Sbjct: 22  YLDRIGRTHLLDAQEEVDLAKAIEGGLYAEHLLEEDRVPPGVTRQELEELVAAGVRAKQR 81

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            V ++LRLVV IA  Y    LP+ +++ EGN+GLM+AV+KFD  RGF+ +TY+ WWI+ +
Sbjct: 82  FVEANLRLVVSIARKYPTDALPLIDLIQEGNLGLMRAVEKFDYRRGFKFSTYATWWIRQS 141

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +  +   +++     ++     LRR +  L          E+   +A+ L  +   
Sbjct: 142 IGRGLSHTARTIRLPVHVEEE--LSRLRRAERQLGRELGREPTREE---LAEALGAAVDH 196

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG---QEQVLIEKEERKNRRNMLT 229
           V  +        SL+A ++  D   +   D L+ D +G   + +VL   +        L 
Sbjct: 197 VDELLRWRRDPASLDAAVD--DAGETPMGD-LLEDPEGVSPEAEVLALDDI-----AGLA 248

Query: 230 RSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           R +  L  RE  I  AR   E+  P++   + + + +S  RVRQI  R+ +++++
Sbjct: 249 RLLDRLPERESAILRARFGIEDGQPLSYAQIGARYGLSHNRVRQITDRSLRRLRQ 303


>gi|83944156|ref|ZP_00956612.1| RNA polymerase sigma-32 factor [Sulfitobacter sp. EE-36]
 gi|83955144|ref|ZP_00963800.1| RNA polymerase sigma-32 factor [Sulfitobacter sp. NAS-14.1]
 gi|83840473|gb|EAP79646.1| RNA polymerase sigma-32 factor [Sulfitobacter sp. NAS-14.1]
 gi|83845023|gb|EAP82904.1| RNA polymerase sigma-32 factor [Sulfitobacter sp. EE-36]
          Length = 223

 Score = 81.3 bits (199), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 69/258 (26%), Positives = 111/258 (43%), Gaps = 57/258 (22%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           R  PML  ++E VL K ++   D  A   LV SH R+V   A           +++SEG 
Sbjct: 9   RNAPMLALEDERVLLKDWQVSKDKFALESLVLSHARIVFYWARKLSDDQAEREDLISEGI 68

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           +GL+ A   FD +R  R +TY+ WW+K A                TA            +
Sbjct: 69  LGLIHAADLFDLDRDVRFSTYAKWWVKNA--------------TMTA------------R 102

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
            HL+AI +     ++ V                   +  D+S  AL+ S D N       
Sbjct: 103 NHLRAIVETPAGVQKTV----------------QHSIDDDDSF-ALLASEDPNP------ 139

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
                   E+ +I +  +   R  L  +M  L P +R +  AR LQ+ P ++++L++  E
Sbjct: 140 --------EEAVIAQSSQTLIRARLLEAMERLQPMDREVLRARTLQQPPESIQDLATRME 191

Query: 264 VSRERVRQIEARAFKKVQ 281
           V+  ++RQIE RA  +++
Sbjct: 192 VTPAKLRQIERRAMSRLK 209


>gi|323456432|gb|EGB12299.1| hypothetical protein AURANDRAFT_12561 [Aureococcus anophagefferens]
          Length = 233

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 62/239 (25%), Positives = 113/239 (47%), Gaps = 27/239 (11%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           SA   LV +++RLVV +A  Y G GL +S++V EG++GLM+A  KFDP RG + +TY+ W
Sbjct: 6   SARQALVATNMRLVVSVAKRYTGLGLGLSDLVQEGSLGLMRAATKFDPARGCKFSTYACW 65

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   +     L+++    +Q     +L +LK   +  T  + +      +A+ L 
Sbjct: 66  WIQQAILRAVAFQSRLIRLPMHVHQ-----DLAKLKRGTRDFTAAHGREPSDGELAELLE 120

Query: 168 VSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           ++ +++  +    R      L   + S +       +  +   D                
Sbjct: 121 MTPAKLRKVRAAARQGDTLKLEDTLASKEPTGETAVELALLHED---------------- 164

Query: 226 NMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             L  +M  L+  E+R+   R   E+  P T   +++    S+E VR+ E RA +K+++
Sbjct: 165 --LHAAMDDLDADEKRVISLRYGLEDGVPCTPAQVAASCAESKEWVRRCEMRAIRKLRK 221


>gi|317506478|ref|ZP_07964279.1| sigma-70 protein [Segniliparus rugosus ATCC BAA-974]
 gi|316255239|gb|EFV14508.1| sigma-70 protein [Segniliparus rugosus ATCC BAA-974]
          Length = 348

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 79/294 (26%), Positives = 135/294 (45%), Gaps = 60/294 (20%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH----------------------GDLSAAH 51
           Y++ I +  +L  ++E  LAK      Y EH                      G  +  H
Sbjct: 55  YLNGIGRTALLTAEDEVTLAKSIEAGLYAEHLINTSEGLTPQRRRELKAVVRDGRAARTH 114

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ 
Sbjct: 115 -LLEANLRLVVSLAKRYTGRGIPLLDLIQEGNLGLIRAMEKFDYSKGFKFSTYATWWIRQ 173

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ-----AITDNNLKPEQVVA---IA 163
           A+   +      +++     ++     L R+K  L        T   L  E  +    IA
Sbjct: 174 AITRGVADQSRTIRLPVHLVEQ--VNKLSRIKRELHQQLGREATSEELSRETGIPEHRIA 231

Query: 164 KKLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
             L+ S   V S++  +  DE   L   I  S+  S+             E  +I     
Sbjct: 232 DLLDHSRDPV-SLDMPVGADEEAPLGDFIEDSEGASA-------------ENAVIAGFLH 277

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIE 273
           ++ R++L    + L+  E+++   R   ++  P TL+ +   F +SRERVRQIE
Sbjct: 278 RDVRSVL----ATLSDSEQQVIRLRYGLDDGQPRTLDQIGKIFSLSRERVRQIE 327


>gi|224144900|ref|XP_002325455.1| predicted protein [Populus trichocarpa]
 gi|222862330|gb|EEE99836.1| predicted protein [Populus trichocarpa]
          Length = 564

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 69/238 (28%), Positives = 122/238 (51%), Gaps = 24/238 (10%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +++ S++RLV+ IA  Y+G G+ + ++V EG  GL++ V+KFD  +GF+ +TY+ WWI+ 
Sbjct: 329 KMIKSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGVEKFDASKGFKFSTYAHWWIRQ 388

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNL-----RRLKGHLQAITDNNLKP-EQVVAIAKK 165
           A++    RS S       +   RL F++     R  +   Q  ++N   P ++ VA A  
Sbjct: 389 AVR----RSLS-----DQSRTIRLPFHMVDATYRVKEARKQFYSENGRHPDDKEVAEATG 439

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           L++     + +  +           N   K S    D    + +  E +L+++  +K+  
Sbjct: 440 LSMKRLSAVLLTPKAPRSLDQKMGFNMDLKLSEVTAD---PEAETAEDLLMKEFMKKD-- 494

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             L R +  L+PRE ++   R   E+    TL+ +     VSRER+RQIE  AF+K++
Sbjct: 495 --LERVLESLSPRENQVIRWRFGMEDGRMKTLQEIGELMGVSRERIRQIELSAFRKLK 550


>gi|40353315|gb|AAR84421.1| essential primary sigma 70 factor [Frankia sp. HRX401a]
          Length = 255

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 67/231 (29%), Positives = 113/231 (48%), Gaps = 34/231 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +LV ++LRLVV IA  Y G G+    ++ EGN+GL++AV+KFD  +G++ +TY+ WW
Sbjct: 46  AKRKLVEANLRLVVSIAKRYVGRGMLFLHLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 105

Query: 109 IKAAMQEYILRSWSLVKIGT----TAN-----QKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N     Q++L  +L R     +   + +L P++V
Sbjct: 106 IRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPSPEEIAKEMDLTPDKV 165

Query: 160 VAIAKKLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
             I   L VS+ E +S+   +  +E   L   I   D          V   D    +L++
Sbjct: 166 REI---LKVSQ-EPVSLETPIGEEEDSHLGDFIEDCDA---------VVPVDAASFILLQ 212

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSR 266
           ++        L   +  L+ RE+++ + R      +P TLE +  EF V+R
Sbjct: 213 EQ--------LDSVLHTLSDREKKVIQLRFGLTDGHPRTLEEVGREFGVTR 255


>gi|288927103|ref|ZP_06420991.1| RNA polymerase sigma-70 factor [Prevotella buccae D17]
 gi|288336130|gb|EFC74523.1| RNA polymerase sigma-70 factor [Prevotella buccae D17]
          Length = 287

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 76/285 (26%), Positives = 130/285 (45%), Gaps = 49/285 (17%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
            +K+  +  N    L+ Y+ EI +   L  ++E  LA    + GD  A  +L  ++L+ V
Sbjct: 41  TKKSKDMDSNERNALNTYLDEIGQESPLTPEKEQDLAACI-QAGDRGALEQLTRANLKFV 99

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V +A  +RG GL  S+++SEGNIGLM+A  KFD  RG R   Y+  +++ AM+  + +  
Sbjct: 100 VAMARRFRGRGLAQSDLISEGNIGLMEAAGKFDGSRGNRFVAYAAPYVRKAMERAVEQQA 159

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            L ++           ++ R K      + + ++P  V A      +SE    ++     
Sbjct: 160 GLYRVPR---------DIMRQK------SRHEVQPASVDA-----PLSEGNKFTL----- 194

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
               L+ L N         +D +  D D   Q +IE          L   ++ L+ RE+R
Sbjct: 195 ----LDILEN---------KDAIHPDDDYNVQAMIE---------ALESLVATLDEREQR 232

Query: 242 IFEA-RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           +      L    ++L  ++ +  + RER RQI  RA +K+  S Q
Sbjct: 233 VVRGFYGLGTGRISLAEIAEQMGIKRERARQIRDRALRKIARSTQ 277


>gi|55275000|gb|AAV49297.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 203

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 34/66 (51%), Positives = 50/66 (75%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ S+LRLVVKIA  Y   GL +  ++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 113 MQEYIL 118
           ++  I+
Sbjct: 61  IERAIM 66


>gi|332753462|gb|EGJ83842.1| RNA polymerase sigma factor rpoS domain protein [Shigella flexneri
           4343-70]
          Length = 215

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 61/219 (27%), Positives = 105/219 (47%), Gaps = 24/219 (10%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRL 135
           +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  +
Sbjct: 3   DLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNV 62

Query: 136 FFNLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           +    R   H        + I +   KP   V+   +LN     + S++  L GD     
Sbjct: 63  YLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKAL 119

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
           L   +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA   
Sbjct: 120 LDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA--- 170

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
                TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 171 ----ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 205


>gi|166368031|ref|YP_001660304.1| group 2 RNA polymerase sigma factor [Microcystis aeruginosa
           NIES-843]
 gi|166090404|dbj|BAG05112.1| group 2 RNA polymerase sigma factor [Microcystis aeruginosa
           NIES-843]
          Length = 377

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 61/236 (25%), Positives = 112/236 (47%), Gaps = 11/236 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  +++ S+LRLVV IA  Y   G+P  +++ EG IGL +A +KFDP +G++ +TY+ W
Sbjct: 138 TAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAEKFDPNKGYKFSTYAYW 197

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++     +K     L +LK   + +  +  +      +A+ L 
Sbjct: 198 WIRQAITRTIANDARTIRLPIHIVEK-----LNKLKKAQRILKQDLQRNPNERELAEALE 252

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++  ++  +        SLN  +   +                ++++     E   R+ +
Sbjct: 253 MTPEQLRQLLQLRRQSLSLNHRVGKGEDTELVDLLEDDDLQLPEDKM----NEMMMRQEI 308

Query: 228 LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                 VL  RE+ +   R       P TLE +   F +SRERVRQI+ +A +K++
Sbjct: 309 FAVLSDVLTEREKDVISLRYGLATSQPYTLEEVGGMFNLSRERVRQIQTKAMRKLR 364


>gi|54401900|gb|AAV34635.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 203

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 34/66 (51%), Positives = 50/66 (75%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ S+LRLVVKIA  Y   GL + +++ EGN+GL +AV+KFDPERGFR +TY+ WWI+  
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLNRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 113 MQEYIL 118
           ++  I+
Sbjct: 61  IERAIM 66


>gi|282895449|ref|ZP_06303586.1| sigE (Sigma 28 (Flagella/Sporulation)) [Raphidiopsis brookii D9]
 gi|281199482|gb|EFA74345.1| sigE (Sigma 28 (Flagella/Sporulation)) [Raphidiopsis brookii D9]
          Length = 327

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 63/240 (26%), Positives = 113/240 (47%), Gaps = 31/240 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +++ ++LRLVV IA  Y+   +   +++ EG +GL + V+KFDP  G++ +TY+ WW
Sbjct: 92  AKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTMGYKFSTYAYWW 151

Query: 109 IKAAMQEYILRSWSLVKIGTTAN---------QKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I +    +++              Q+ L   L R     +   +  L+P Q 
Sbjct: 152 IRQAITRAIAQQGRTIRLPIHITEKLNKIKKVQRELAQKLGRSPSPTEIAKELELEPAQ- 210

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I + LN++  + IS++ R+             D   ++ Q+ L  D    E    ++ 
Sbjct: 211 --IREYLNIA-RQPISLDVRVG------------DNQDTELQEMLEDDGLSPEHYTTQEF 255

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAF 277
            R +  N+L      L P++R +   R   E  N ++L  +     +SRERVRQ+E +A 
Sbjct: 256 LRHDLNNLLAE----LTPQQREVVTLRFGLEDGNEMSLAKVGDRLNISRERVRQLEHQAL 311


>gi|224126061|ref|XP_002319746.1| predicted protein [Populus trichocarpa]
 gi|222858122|gb|EEE95669.1| predicted protein [Populus trichocarpa]
          Length = 567

 Score = 81.3 bits (199), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 71/254 (27%), Positives = 128/254 (50%), Gaps = 26/254 (10%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L  R R +  +    +++ S++RLV+ IA  Y+G G+ + ++V EG  GL++  +KFD  
Sbjct: 317 LTLRKRLNYGILCKDKMIKSNVRLVISIAKNYQGTGMNLQDLVQEGCRGLVRGAEKFDAS 376

Query: 97  RGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNL-----RRLKGHLQAIT 150
           +GF+ +TY+ WWIK A+++ +  RS ++          RL F++     R  +   Q  +
Sbjct: 377 KGFKFSTYAHWWIKQAVRKSLSDRSRTI----------RLPFHMVDATYRVKEARKQLYS 426

Query: 151 DNNLKP-EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
           +N   P ++ VA A  L++     + +  +           N   K S    D    + +
Sbjct: 427 ENGRHPDDKEVAEAAGLSMKRLSAVLLTPKAPRSLDQKMGFNMDLKLSEVTAD---PEAE 483

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRE 267
             E +L+++  +K+    L + +  L+PRE ++   R   E+    TL+ +     VSRE
Sbjct: 484 TAEDLLMKEFMKKD----LAKVLGSLSPRENQVVRWRFGMEDGRMKTLQEIGELMGVSRE 539

Query: 268 RVRQIEARAFKKVQ 281
           RVRQIE  AF+K++
Sbjct: 540 RVRQIELSAFRKLK 553


>gi|298490639|ref|YP_003720816.1| RpoD subfamily RNA polymerase sigma 70 subunit ['Nostoc azollae'
           0708]
 gi|298232557|gb|ADI63693.1| RNA polymerase, sigma 70 subunit, RpoD subfamily ['Nostoc azollae'
           0708]
          Length = 327

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 59/231 (25%), Positives = 115/231 (49%), Gaps = 13/231 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +++ ++LRLVV IA  Y+   +   +++ EG +GL + V+KFDP RG++ +TY+ WW
Sbjct: 92  AKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPMRGYKFSTYAYWW 151

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I +    +++     +K     +++++  L      +  P +   IAK+L +
Sbjct: 152 IRQAITRAIAQQGRTIRLPIHITEK--LNKIKKVQRELAQKLGRSPSPTE---IAKELEL 206

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
             +++           SL+  +   D   ++ Q+ L  +    E    ++  R++  N+L
Sbjct: 207 EPAQIREYLNMARQPVSLD--VRVGDNQDTELQEMLEDEGPSPEYYTTQEFLRQDLNNLL 264

Query: 229 TRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAF 277
                 L P++R +   R   E  N ++L  +     +SRERVRQ+E +A 
Sbjct: 265 AE----LTPQQREVLALRFGLEDGNEMSLAKVGERLNLSRERVRQLEHQAL 311


>gi|83319868|ref|YP_424476.1| RNA polymerase sigma factor RpoD [Mycoplasma capricolum subsp.
           capricolum ATCC 27343]
 gi|83283754|gb|ABC01686.1| RNA polymerase sigma factor RpoD [Mycoplasma capricolum subsp.
           capricolum ATCC 27343]
          Length = 505

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 39/114 (34%), Positives = 69/114 (60%), Gaps = 3/114 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRY--REHGDLSAA-HRLVTSHLRLVVKIAMGYRGYG 72
           +  Y ++I + P+L K +E + AK     +  D+    ++L+ S+L+LV+ +A  +   G
Sbjct: 171 IKTYFYKIGQAPILTKDQEIMYAKMAVSDDPEDVKEGRNKLIESNLKLVISVARKHLNRG 230

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           L  ++++ EGNIGLM+AV KF+ E+GF+ +TY+ WWI  A+   I      ++I
Sbjct: 231 LDFADLIEEGNIGLMKAVDKFEYEKGFKFSTYATWWISQAITRAIADQARTIRI 284


>gi|294673921|ref|YP_003574537.1| RNA polymerase sigma-70 factor [Prevotella ruminicola 23]
 gi|294472533|gb|ADE81922.1| RNA polymerase sigma-70 factor [Prevotella ruminicola 23]
          Length = 250

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 40/119 (33%), Positives = 73/119 (61%), Gaps = 1/119 (0%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L+RY+ EI +  +L  +EE  LA+R  + GD  A  +L+ ++L+ VV +A  Y+G G+ 
Sbjct: 21  ALNRYLDEIGREQLLTNEEERELAERIAK-GDERALSKLIEANLKFVVSVARQYKGKGVD 79

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           + ++VSEGN+GLM+A  KFD  +G R   ++  +I+ ++++ I +   L ++     Q+
Sbjct: 80  MEDLVSEGNLGLMKAAAKFDASKGVRFVNFAFVYIRQSIEKAIDQQGGLYQVPKDVKQE 138


>gi|75908126|ref|YP_322422.1| RNA polymerase sigma factor [Anabaena variabilis ATCC 29413]
 gi|75701851|gb|ABA21527.1| Sigma 28 (Flagella/Sporulation) [Anabaena variabilis ATCC 29413]
          Length = 327

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 58/231 (25%), Positives = 114/231 (49%), Gaps = 13/231 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +++ ++LRLVV IA  Y+   +   +++ EG +GL + V+KFDP RG++ +TY+ WW
Sbjct: 92  AKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPMRGYKFSTYAYWW 151

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I +    +++     +K     +++++  L      +  P +   IAK+L +
Sbjct: 152 IRQAITRAIAQQGRTIRLPIHITEK--LNKIKKVQRELAQTLGRSPSPAE---IAKELEL 206

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
             +++           SL+  +   D   ++ Q+ L  +    E    ++  R++   +L
Sbjct: 207 EPAQIREYLNMARQPVSLD--VKVGDNQDTELQEMLEDEGPSPEYYTTQEFLRQDLNTLL 264

Query: 229 TRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAF 277
                 L P++R +   R   L  N ++L  +     +SRERVRQ+E +A 
Sbjct: 265 AE----LTPQQREVVALRFGLLDGNELSLAKVGERLNLSRERVRQLEHQAL 311


>gi|227549119|ref|ZP_03979168.1| RNA polymerase sigma factor SigB [Corynebacterium lipophiloflavum
           DSM 44291]
 gi|227078816|gb|EEI16779.1| RNA polymerase sigma factor SigB [Corynebacterium lipophiloflavum
           DSM 44291]
          Length = 331

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 69/264 (26%), Positives = 126/264 (47%), Gaps = 27/264 (10%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+   +K++  +LAK+ R      A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+
Sbjct: 75  KLTRAKKRDLKILAKQGRR-----ARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNL 129

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFFNLRR-- 141
           GL++A++KFD  +GF+ +TY+ WWI+ A+   +      +++      Q      +RR  
Sbjct: 130 GLIRAMEKFDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIRREM 189

Query: 142 LKGHLQAITDNNLKPEQVVAIAK--KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
            +   +  T+  L  E  +  +K   L     + +S++  +  DE         D  ++ 
Sbjct: 190 YQSLGREPTNEELSDESGIEESKIEMLLRQSRDPVSLDMPVGADEEAPLGDFIEDAEATD 249

Query: 200 WQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
            +D +V    HD  + ++   E+R+     L   +    PR               TL+ 
Sbjct: 250 AEDAVVSSLRHDDIQDIIGGLEQREQDVIRLRYGLDDGVPR---------------TLDQ 294

Query: 258 LSSEFEVSRERVRQIEARAFKKVQ 281
           +  +F +SRERVRQIE     K++
Sbjct: 295 IGRQFGLSRERVRQIEREVMAKLR 318


>gi|119492598|ref|ZP_01623816.1| RNA polymerase sigma factor [Lyngbya sp. PCC 8106]
 gi|119453067|gb|EAW34237.1| RNA polymerase sigma factor [Lyngbya sp. PCC 8106]
          Length = 333

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 72/321 (22%), Positives = 146/321 (45%), Gaps = 57/321 (17%)

Query: 3   RKNMSIIVNGEIGLS-----RYIHEIRKIPMLEKQEEY-------VLAKRYREHGDLS-- 48
           +K+ S   N   G+S      Y+HEI ++P+L ++EE         + K+  E   L+  
Sbjct: 8   KKDQSTKRNTRPGVSVDTVRTYLHEIGRVPLLTQEEEIHYGKQVQQMMKQLEEKDKLTKK 67

Query: 49  ------------------------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
                                         A  +++ ++LRLVV IA  Y+   +   ++
Sbjct: 68  LEHEPSKTEWANEVELTEDELDRILDCGRRAKQKMIEANLRLVVSIAKKYQKRNMEFLDL 127

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EG +GL + V+KFDP RG++ +TY+ WW++ A+   I ++   +++     +K     
Sbjct: 128 IQEGTLGLERGVEKFDPMRGYKFSTYAYWWVRQAITRAIAQNGRTIRLPIHITEK--LNK 185

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           ++R++  L      N  P +   IA+ L +  S++      LA    ++  +   D   +
Sbjct: 186 IKRVQRDLVQKYGRNPTPTE---IAEALELEPSQI--REYLLASRHPISLDLRVGDNQDT 240

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
           + Q+ L  +    +  +  +  R++ ++++      L P++R +   R   E+   ++L 
Sbjct: 241 ELQELLEDETASADNYVTHELLRQDLKSLIDE----LTPQQREVILLRYGLEDGKELSLS 296

Query: 257 NLSSEFEVSRERVRQIEARAF 277
            + +   +SRERVRQ+E +A 
Sbjct: 297 KVGARMSISRERVRQLENQAL 317


>gi|315226631|ref|ZP_07868419.1| DNA-directed RNA polymerase sigma subunit RpoD [Parascardovia
           denticolens DSM 10105]
 gi|315120763|gb|EFT83895.1| DNA-directed RNA polymerase sigma subunit RpoD [Parascardovia
           denticolens DSM 10105]
          Length = 690

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 66/253 (26%), Positives = 121/253 (47%), Gaps = 34/253 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ WW
Sbjct: 451 AKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYATWW 510

Query: 109 IKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   +      +++           +  Q+++  +L R     +   + ++  E+V
Sbjct: 511 IRQAITRAMADQARTIRVPVHMVEVINKLSRVQRQMLQDLGREPTPDELARELDMPVEKV 570

Query: 160 VAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
             + K       E IS++  L   GD     LI  +D  +           +  +QVL  
Sbjct: 571 QEVQKYGR----EPISLHTPLGEDGDSEFGDLIEDTDAIAPSEAVAFSLLQEQFKQVL-- 624

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
                            L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++
Sbjct: 625 ---------------ETLSPREAGVIKMRYGLEDGQPKTLDDIGHVYGVTRERIRQIESK 669

Query: 276 AFKKVQESIQKQV 288
              K++   + Q 
Sbjct: 670 TMSKLRHPSRSQT 682


>gi|210633875|ref|ZP_03297890.1| hypothetical protein COLSTE_01807 [Collinsella stercoris DSM 13279]
 gi|210159044|gb|EEA90015.1| hypothetical protein COLSTE_01807 [Collinsella stercoris DSM 13279]
          Length = 261

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 70/262 (26%), Positives = 127/262 (48%), Gaps = 27/262 (10%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           +K++   L +R++E GD+ A  +LV SHL LV  IA  ++  G PI ++V  G +GL++A
Sbjct: 12  DKEKTRELFRRFKEEGDMDAREKLVMSHLNLVRFIANKFKNRGEPIDDLVQVGYLGLLKA 71

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           + +FDP RG    T++   I   ++ +   + WS+          R+   L+ L   +  
Sbjct: 72  IDRFDPARGLEFTTFATPTIMGEIKRHFRDKGWSV----------RVPRRLQELSAKVNQ 121

Query: 149 ITD---NNLKPEQVVA-IAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQD 202
            TD   + L+    +A IA+ L+ +  EV+    +       SL A     D ++    D
Sbjct: 122 ATDTLTSQLQRSPTIAEIAEYLDATVDEVLEAMESSSAYSSVSLEAPSGMEDDDAPSVID 181

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
              Y  + +E    +       R ++  +++  +PRER + E R LQ   +T   ++ + 
Sbjct: 182 R--YATEDEELAFTDD------RIIIEEALASFSPREREVIEMRFLQ--GMTQIEIAEKL 231

Query: 263 EVSRERVRQIEARAFKKVQESI 284
            +S+ +V ++  R  KK+QE I
Sbjct: 232 GISQVQVSRLLRRTLKKIQEKI 253


>gi|172065170|ref|YP_001815882.1| RpoD family RNA polymerase sigma factor [Burkholderia ambifaria
           MC40-6]
 gi|171997412|gb|ACB68329.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           ambifaria MC40-6]
          Length = 621

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 62/238 (26%), Positives = 111/238 (46%), Gaps = 22/238 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L  ++LRLVV IA  Y   GLP ++++ EGNIGL++A++++D  RGFR +TY+ WWI+ A
Sbjct: 388 LFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIERYDYRRGFRFSTYATWWIRQA 447

Query: 113 MQEYILRSWSLVKIGT-TANQ----KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +   +      +++ T T +      RL    R+  G      +  +   + V   + L 
Sbjct: 448 ITHALADLGRTIRVPTHTVDALNKLSRLAREHRQRAGTAATPAELAVHMGEPVDKVRDLM 507

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
               E +S +  ++ +  +     + D  +   +D       G  Q+          R  
Sbjct: 508 AIVKEPVSADVPVSPEGDMTFADVAPDTTTPSPEDAA-----GATQL----------RRT 552

Query: 228 LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +   +  L PRE  + + R     +   +L ++  +  +S ERVRQIEA A  +++ S
Sbjct: 553 IAAVIDRLPPREAMVLKLRYGLHTDEGCSLRDIGRQLNLSAERVRQIEASALARLRAS 610


>gi|78211648|ref|YP_380427.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CC9605]
 gi|78196107|gb|ABB33872.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. CC9605]
          Length = 335

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 72/322 (22%), Positives = 141/322 (43%), Gaps = 54/322 (16%)

Query: 10  VNGEIGLSR-YIHEIRKIPMLEKQEEYVLAKRYREHGDLS-------------------- 48
           V  ++ L R Y+ +I ++P+L  ++E  L ++ +E  DL                     
Sbjct: 21  VTADVDLVRSYLRDIGRVPLLTHEQEITLGRQVQELMDLESLESELKSKAGEKPSRDQLA 80

Query: 49  -------------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
                              A  R+V ++LRLVV +A  Y    + + +++ EG IGL++ 
Sbjct: 81  KASGLSSIQLKRKLQHGRRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRG 140

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V+KFDP RG++ +TY+ WWI+  +   I      +++     +      L +LK   + +
Sbjct: 141 VEKFDPTRGYKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITEM-----LNKLKKGQREL 195

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
           +    +   V  +A+ + + E +V  + CR     SL   +   D + ++  + L  D D
Sbjct: 196 SQELGRTPTVTELAEFVELPEDDVKDLMCRARQPVSLE--MKVGDGDDTELLELLSGDGD 253

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRE 267
                + E   + + R++L +    L   + ++   R     E+P++L  +     +SR+
Sbjct: 254 LPSDQVEEDCLKGDLRSLLGQ----LPHLQEQVLRMRYGMDGEDPMSLTGIGRILGMSRD 309

Query: 268 RVRQIEARAFKKVQESIQKQVE 289
           RVR +E      ++  +  QVE
Sbjct: 310 RVRNLERDGLAGLRR-VSDQVE 330


>gi|320537364|ref|ZP_08037319.1| RNA polymerase sigma factor RpoD [Treponema phagedenis F0421]
 gi|320145829|gb|EFW37490.1| RNA polymerase sigma factor RpoD [Treponema phagedenis F0421]
          Length = 604

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 72/252 (28%), Positives = 127/252 (50%), Gaps = 29/252 (11%)

Query: 41  YREHGDLSAA-HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           +R H  L  A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+KF+  +G+
Sbjct: 357 HRGHTMLKKAKDKLINANLRLVVSIAKKYTNRGLLFFDLVQEGNIGLIKAVEKFEYRKGY 416

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK--RLFFNLRRLKGHL-QAITDNNLKP 156
           + +TY+ WWI+ A+   I      +++     ++  ++    R+L   L +  TD  +  
Sbjct: 417 KFSTYATWWIRQAITRSISDQARTIRVPVHMIEQINKVARESRQLLQKLGRDPTDEEIAT 476

Query: 157 EQV--VAIAKKLNVSESEVISMNCRLA--GDESLNALINSSD-KNSSQWQDWLVYDHDGQ 211
           +    V   K++     E IS+   +    D SL   I  ++ +N S          +  
Sbjct: 477 QLCWTVEKVKQVKNVAREPISLETPIGEEEDSSLGDFIPDTEIENPS----------NVT 526

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERV 269
           E++L+ +E        +   +S L  RE  + + R   +     TLE +   F+V+RER+
Sbjct: 527 EKILLREE--------VQSVLSTLPSREHEVLKMRFGLDGDYSQTLEEVGLYFDVTRERI 578

Query: 270 RQIEARAFKKVQ 281
           RQIEA+A ++++
Sbjct: 579 RQIEAKALRRLR 590


>gi|325473907|gb|EGC77095.1| RNA polymerase sigma-70 factor family protein [Treponema denticola
           F0402]
          Length = 619

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 67/243 (27%), Positives = 125/243 (51%), Gaps = 26/243 (10%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+KF+  +G++ +TY+ W
Sbjct: 380 NAKDKLINANLRLVVSIAKKYINRGLQFFDLVQEGNIGLIKAVEKFEYRKGYKFSTYATW 439

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQK--RLFFNLRRLKGHLQAITDNNLKPEQV---VAI 162
           WI+ A+   I      +++     ++  ++    R+L   L    +++    Q+   +  
Sbjct: 440 WIRQAITRSISDQARTIRVPVHMIEQINKVNRESRQLMQKLGREPNDDEIALQLGWSIEK 499

Query: 163 AKKLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            K++     E IS+   +  +E   L  LI          +D  V +   + ++ + +E+
Sbjct: 500 VKQVKNVAREPISLETPIGEEEDTLLGDLI----------EDKGVENPSNRTELTLLQEQ 549

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFK 278
                  L   +S L  RE+ + + R   E   P+TLE +   F+V+RER+RQIEA+  +
Sbjct: 550 -------LEMVLSSLPEREQEVLKMRFGIEGGYPLTLEEVGLYFDVTRERIRQIEAKGLR 602

Query: 279 KVQ 281
           +++
Sbjct: 603 RLR 605


>gi|42526854|ref|NP_971952.1| RNA polymerase sigma factor RpoD [Treponema denticola ATCC 35405]
 gi|41817169|gb|AAS11863.1| RNA polymerase sigma-70 factor family protein [Treponema denticola
           ATCC 35405]
          Length = 619

 Score = 80.5 bits (197), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 69/244 (28%), Positives = 122/244 (50%), Gaps = 28/244 (11%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+KF+  +G++ +TY+ W
Sbjct: 380 NAKDKLINANLRLVVSIAKKYINRGLQFFDLVQEGNIGLIKAVEKFEYRKGYKFSTYATW 439

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQK--RLFFNLRRLKGHLQAITDNNLKPEQV---VAI 162
           WI+ A+   I      +++     ++  ++    R+L   L    +++    Q+   +  
Sbjct: 440 WIRQAITRSISDQARTIRVPVHMIEQINKVNRESRQLMQKLGREPNDDEIALQLGWSIEK 499

Query: 163 AKKLNVSESEVISMNCRLAGDES--LNALINSSD-KNSSQWQDWLVYDHDGQEQVLIEKE 219
            K++     E IS+   +  +E   L  LI     +N S   +  +     QEQ      
Sbjct: 500 VKQVKNVAREPISLETPIGEEEDTLLGDLIEDKGVENPSNRTELTLL----QEQ------ 549

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
                   L   +S L  RE+ + + R   E   P+TLE +   F+V+RER+RQIEA+  
Sbjct: 550 --------LEMVLSSLPEREQEVLKMRFGIEGGYPLTLEEVGLYFDVTRERIRQIEAKGL 601

Query: 278 KKVQ 281
           ++++
Sbjct: 602 RRLR 605


>gi|1769596|gb|AAB39997.1| sigma factor [Synechococcus sp. PCC 7002]
          Length = 317

 Score = 80.5 bits (197), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 65/257 (25%), Positives = 122/257 (47%), Gaps = 34/257 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V ++LRLVV +A  Y    + + +++ EG IG+ + V+KFDP +G+R +TY+ WW
Sbjct: 83  AKQKMVEANLRLVVSVAKKYIKRNMDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWW 142

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      +++     +K     L ++K   + +   N +   +  +A +L +
Sbjct: 143 IRQAITRAIAEQSRTIRLPIHITEK-----LNKIKKAQRQLAQANGRSASIPELADELGL 197

Query: 169 SESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           +  +V          +S++ R+ GD +   LI   D       D  + D       L   
Sbjct: 198 TTKQVRDYLEKSRQPLSLDLRV-GDNNDTELIELED-------DGELPDDYATHAAL--- 246

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEAR-RLQE-NPVTLENLSSEFEVSRERVRQIEARA 276
                 +  L R ++ L  +++ +   R  L++  P TL  +     +SRERVRQIE  +
Sbjct: 247 ------KRDLARMLNDLTAQQQEVLTLRFGLRDGTPHTLAKIGEHLNISRERVRQIEHGS 300

Query: 277 FKKVQESIQKQVELSSS 293
             K+++  +K  E  +S
Sbjct: 301 LAKLRKQKRKLGEYLAS 317


>gi|217968787|ref|YP_002354021.1| sigma-70 region 2 domain protein [Thauera sp. MZ1T]
 gi|217506114|gb|ACK53125.1| sigma-70 region 2 domain protein [Thauera sp. MZ1T]
          Length = 590

 Score = 80.1 bits (196), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 34/76 (44%), Positives = 52/76 (68%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           +R++ S+LRLV+ IA  Y   G P  +++ EGN+GLM+AV+KFD  RGF+ +TY+ WWI+
Sbjct: 477 NRMIKSNLRLVISIAKKYTHTGFPFLDLIQEGNLGLMKAVEKFDYRRGFKFSTYATWWIR 536

Query: 111 AAMQEYILRSWSLVKI 126
            A+   I     LV++
Sbjct: 537 QAITRGIADQQRLVRV 552


>gi|108707415|gb|ABF95210.1| Sigma-70 region 3 family protein, expressed [Oryza sativa Japonica
           Group]
 gi|215695353|dbj|BAG90544.1| unnamed protein product [Oryza sativa Japonica Group]
          Length = 343

 Score = 80.1 bits (196), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 67/250 (26%), Positives = 120/250 (48%), Gaps = 25/250 (10%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R R +  +S  + +V S++RLV+ IA  + G G+  S+++ EG  GL++  +KFD  +GF
Sbjct: 93  RKRLNYGISCKNTMVKSNVRLVISIAREFEGPGMEFSDLIQEGIQGLVRGAEKFDASKGF 152

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           R +TYS WWIK A+++ +L    ++                RL  H+ A   + +K  + 
Sbjct: 153 RFSTYSHWWIKQAIRKSVLEQTQII----------------RLPAHM-AEASSRVKECRR 195

Query: 160 VAIAKKLNVSESEVISMNC-----RLAGDESL-NALINSSDKNSSQWQDWLVYDHDGQEQ 213
               +   +  +E I+ +      R+    SL    ++ + K       +     D   +
Sbjct: 196 RLRRQLKRLPTNEEIASDTGMPLRRVEAAMSLPKYTVSLTSKVGCTDMTYQEITPDTSTE 255

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQ 271
              E   R   +  + R++  L+PRER++   R   ++    TL ++     VSRER+RQ
Sbjct: 256 TAEEMLHRWLMKEDVDRALDGLSPRERQVIRYRFGMDDGRLRTLHDIGRLMGVSRERIRQ 315

Query: 272 IEARAFKKVQ 281
           IE  AF+K++
Sbjct: 316 IELVAFRKLR 325


>gi|229082715|ref|ZP_04215161.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock4-2]
 gi|228700606|gb|EEL53146.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock4-2]
          Length = 323

 Score = 80.1 bits (196), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 80/296 (27%), Positives = 132/296 (44%), Gaps = 59/296 (19%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY--GLPISE 77
           I EI    +L KQE   L +RY+ HG+      L   ++ LV+ IA  Y+     +   +
Sbjct: 40  IKEIGNYKVLSKQESLKLFQRYK-HGEKDLRDYLFHVNVGLVLSIARKYKNKHPDIEFDD 98

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS-LVKIGTTANQKRLF 136
           +V EGN G+++A++ F+P  G+  +TY+ WWIK +M   I R  S   KI    NQ    
Sbjct: 99  LVQEGNEGMLRAMEDFNPALGYCFSTYAFWWIKKSMLGIICRKKSGPFKIPNYVNQ---- 154

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC--RLAGDESLN------- 187
           FNLR ++   + +   N  P  V  +AK+LNV+   VI  N   + A   +L+       
Sbjct: 155 FNLRYVELEDKYLQMYNRTP-SVEEVAKELNVTSETVIKYNVYYKRATTMTLDVDTINED 213

Query: 188 -ALINSSDKNSS-------------QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             ++N    +SS              ++ WL++D                          
Sbjct: 214 IGILNPFYDDSSTIPSTNEMVIEDLNYEIWLIFDE------------------------- 248

Query: 234 VLNPRERRIFE-ARRLQENPVTL-ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           VLNP+++ +      L +  V L + ++    ++ ERV QI+  A KK+++   K 
Sbjct: 249 VLNPKQKMVLNLCFGLLDGKVYLHKEIAKALMITTERVSQIKDEAIKKLKKGDYKD 304


>gi|296139548|ref|YP_003646791.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Tsukamurella
           paurometabola DSM 20162]
 gi|296027682|gb|ADG78452.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Tsukamurella
           paurometabola DSM 20162]
          Length = 330

 Score = 80.1 bits (196), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 78/296 (26%), Positives = 134/296 (45%), Gaps = 48/296 (16%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH-------------GDLS--------AAHR 52
           Y++ I +  +L  ++E  LAKR     Y +H              DL+        A   
Sbjct: 37  YLNGIGRTALLTAEDEVELAKRIEAGLYAQHLLDTKKRLSASKKRDLAFIVRDGQAARQH 96

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A
Sbjct: 97  LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTYATWWIRQA 156

Query: 113 MQEYILRSWSLVKIGT-TANQKRLFFNLRR-LKGHL-QAITDNNLKPEQVVAIAKKLNVS 169
           +   +      +++      Q      +RR L   L +  TD  L  E  +   K  ++ 
Sbjct: 157 ITRGMADQSRTIRLPVHLVEQVNKLARIRRELHQQLGREATDAELAAESGIPAEKIADLM 216

Query: 170 ES--EVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           +   + +S++  +  DE   L   I  ++  S++        H     VL   +ER+ + 
Sbjct: 217 DHSRDPVSLDMPVGSDEEAPLGDFIEDAEAASAESAVISTLMHSDVRSVLATLDEREQQV 276

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             L   +    PR               TL+ +   F +SRERVRQIE     K++
Sbjct: 277 IRLRYGLDDGQPR---------------TLDQIGKLFGLSRERVRQIEREVMSKLR 317


>gi|113954287|ref|YP_730230.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CC9311]
 gi|113881638|gb|ABI46596.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CC9311]
          Length = 318

 Score = 80.1 bits (196), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 69/311 (22%), Positives = 138/311 (44%), Gaps = 56/311 (18%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSA---------------- 49
           M+++ + ++ +  Y+ +I ++P+L  Q+E  L ++ +E  DL A                
Sbjct: 1   MALLPDADL-VRSYLRDIGRVPLLSHQQEITLGRQVQELMDLEALEAELKDQRGGEEVAR 59

Query: 50  ------------------------AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
                                     R+V ++LRLVV +A  Y    + + +++ EG IG
Sbjct: 60  DEWAKAAGMSAAQLKRKLQAGRRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIG 119

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++ V+KFDP RG++ +TY+ WWI+  +   I      +++     +      L +LK  
Sbjct: 120 LVRGVEKFDPTRGYKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITE-----MLNKLKKG 174

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            + ++    +   V  +A  + + E EV  + CR     SL   +   D + ++  + L 
Sbjct: 175 QRELSQELGRTPSVTELASFVELPEEEVKDLMCRARQPVSLE--MKVGDGDDTELLELLA 232

Query: 206 YDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEF 262
            D +   +QV     E +  +  L   +S L   + ++   R     E P++L  ++   
Sbjct: 233 GDGELPSDQV-----EGECLKGDLRDLLSQLPELQGKVLRMRYGMDGEEPMSLTGIAKSM 287

Query: 263 EVSRERVRQIE 273
           ++SR+R R++E
Sbjct: 288 KMSRDRTRRLE 298


>gi|84385871|ref|ZP_00988901.1| RNA polymerase sigma factor RpoS [Vibrio splendidus 12B01]
 gi|84379187|gb|EAP96040.1| RNA polymerase sigma factor RpoS [Vibrio splendidus 12B01]
          Length = 262

 Score = 80.1 bits (196), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 77/274 (28%), Positives = 136/274 (49%), Gaps = 33/274 (12%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEG 82
           I +L +++E   AK  R  GD  A   ++ S+LRLVVKIA  Y   +G    + +++ EG
Sbjct: 3   IDLLSREDEVYYAKLNR-AGDKQARDIMIESNLRLVVKIAKSYLKRKGNNFTLLDLIEEG 61

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
           NIGL++A+ K+DPE G+R +TY++WWI+  ++       +L+  G T           RL
Sbjct: 62  NIGLIKAIDKYDPEPGYRFSTYAVWWIRENIEA------ALMNKGRTV----------RL 105

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLN--VSESEVI-SMNCRLAGDESLNALINSSDKNSSQ 199
             H+    + N    + + ++KK++  +S SE+  S   +    + L AL    D  ++ 
Sbjct: 106 PAHV--CKEINSLASKKLDVSKKMSKEISISELSDSSGVKAKRVDQLVALSGFIDVTTTV 163

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM----SVLNPRERRIFEAR-RLQENPV- 253
             +      D  E   I   +R       T+++    S L P+ +++   R    +N V 
Sbjct: 164 GTNHAPMVLDQCESEYIPDPQRDCEDQSFTQALEQIISTLPPKLQKVLIHRFGFFDNKVK 223

Query: 254 TLENLSS--EFEVSRERVRQIEARAFKKVQESIQ 285
           TL  +    +  VS ERVRQ++  A +++Q+ ++
Sbjct: 224 TLSEVGQMLDVNVSSERVRQMQKEAVERIQKRLK 257


>gi|307152078|ref|YP_003887462.1| RpoD subfamily RNA polymerase sigma-70 factor [Cyanothece sp. PCC
           7822]
 gi|306982306|gb|ADN14187.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7822]
          Length = 328

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 69/324 (21%), Positives = 151/324 (46%), Gaps = 59/324 (18%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------------- 43
           +N KN     + ++ +  Y+HEI ++P+L  ++E V  K+ ++                 
Sbjct: 6   VNPKNQKPTFSADM-VRTYLHEIGRVPLLTHEQEIVYGKQVQKMMTLLEKKDELAIQLER 64

Query: 44  ---------HGDLS-------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
                    H  +S             A  +++ ++LRLVV IA  Y+   +   +++ E
Sbjct: 65  EPSLTEWANHVQMSEEELNRAIQQGKRAKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQE 124

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           G++GL + V+KFDP +G++ +TY+ WWI+ A+   I +    +++     +K     L +
Sbjct: 125 GSLGLERGVEKFDPTKGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEK-----LNK 179

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEV---ISMNCRLAGDESLNALINSSDKNSS 198
           +K   + ++    +      IAK L++   ++   +SM+      + ++  +   D   +
Sbjct: 180 IKKTQRELSQQLGRSATPSEIAKALDLEPDQIREFLSMSR-----QPISLDVRVGDNQDT 234

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENP-VTLE 256
           +  + L  +    +  + ++  R++ +++L      L P++R +   R  LQ+   ++L 
Sbjct: 235 ELSELLEDEGISPDNYITQELMRQDLQDLLAE----LTPQQREVLSLRFGLQDGKELSLA 290

Query: 257 NLSSEFEVSRERVRQIEARAFKKV 280
            +     +SRERVRQ+E +A  ++
Sbjct: 291 KIGQRMNISRERVRQLEHQALSQL 314


>gi|296117743|ref|ZP_06836327.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           ammoniagenes DSM 20306]
 gi|295969474|gb|EFG82715.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           ammoniagenes DSM 20306]
          Length = 334

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 71/287 (24%), Positives = 140/287 (48%), Gaps = 43/287 (14%)

Query: 13  EIGL-SRY-IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           EIGL + Y ++   K+   EK++  +L K     G  + +H L+ ++LRLVV +A  Y G
Sbjct: 64  EIGLYAEYKLNTAEKLTRAEKRDMKILVK----EGKKARSH-LLEANLRLVVSLAKRYTG 118

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A+   +      +++    
Sbjct: 119 RGMPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHL 178

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMNCRL 180
            ++     L R+K  +          E+   +A++  + E+++          +S++  +
Sbjct: 179 VEQ--VNKLSRIKREMYQSLGREATNEE---LAEESGIEENKIEMLLRQSRDPVSLDMPV 233

Query: 181 AGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
             DE   L   I  ++   +             E  ++      + R+++      L  R
Sbjct: 234 GADEEAPLGDFIEDAEATDA-------------ETAVVASMRHSDIRDVI----GTLEQR 276

Query: 239 ERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           E+ +   R   ++  P TL+ +  +F +SRERVRQIE     K+++ 
Sbjct: 277 EQDVIRLRYGLDDGVPRTLDQIGRKFGLSRERVRQIEREVMAKLRDG 323


>gi|46201746|ref|ZP_00054445.2| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Magnetospirillum magnetotacticum
           MS-1]
          Length = 756

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 73/256 (28%), Positives = 126/256 (49%), Gaps = 49/256 (19%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A+R RE        R   ++L+LVV  A  + G   P  + + EGN+GL++AV++FD  R
Sbjct: 524 ARRARE--------RFALANLKLVVWGAKKFGGLTWP--DRIQEGNLGLLKAVERFDHRR 573

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G + +TY+ WWIK A+   +      ++I   A +      LRR +  + A+T     PE
Sbjct: 574 GAKFSTYATWWIKQAVTRAVADKGRTIRIPVHAQEA--MRKLRRAQNEVFALTGREALPE 631

Query: 158 QV-----VAIAKK---LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
           +V     + +A+    L V+E E  S++    G       +++++  S +         D
Sbjct: 632 EVGELTEIPLARVRRFLAVAE-EPASLDVEEVG-------LHAAEMASRE--------PD 675

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ-----ENPVTLENLSSEFEV 264
            +E++ +        + M+   + +L PRE  +    RL+     E   TLE +  +F V
Sbjct: 676 PEERLAV-----AEIKAMVRGQLELLPPREATVI---RLRFGIGCEREYTLEEIGQQFGV 727

Query: 265 SRERVRQIEARAFKKV 280
           +RER+RQIEA+A +K+
Sbjct: 728 TRERIRQIEAKALRKL 743


>gi|312282731|dbj|BAJ34231.1| unnamed protein product [Thellungiella halophila]
          Length = 269

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 35/78 (44%), Positives = 53/78 (67%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++   + RLVV IA GY+G GL + +++ EG+IGL++  ++FDPERG++L+TY  WW
Sbjct: 181 AREKITRCYRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPERGYKLSTYVYWW 240

Query: 109 IKAAMQEYILRSWSLVKI 126
           IK A+   I     LVK+
Sbjct: 241 IKQAILRAIAHKSRLVKL 258


>gi|218439771|ref|YP_002378100.1| RNA polymerase sigma factor [Cyanothece sp. PCC 7424]
 gi|218172499|gb|ACK71232.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
          Length = 328

 Score = 80.1 bits (196), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 65/306 (21%), Positives = 141/306 (46%), Gaps = 58/306 (18%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDL------------------------------- 47
           Y+HEI ++P+L  ++E V  K+ ++   L                               
Sbjct: 23  YLHEIGRVPLLTHEQEIVYGKQVQKMMTLLEKKDQLAIELGKEPNLTEWANQVQMSEEEL 82

Query: 48  --------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                    A  +++ ++LRLVV IA  Y+   +   +++ EG++GL + V+KFDP +G+
Sbjct: 83  NRAIQQGKRAKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGSLGLERGVEKFDPTKGY 142

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWI+ A+   I +    +++     +K     L ++K   + ++    +    
Sbjct: 143 KFSTYAYWWIRQAITRAIAQQARTIRLPIHITEK-----LNKIKKTQRELSQQLGRSATP 197

Query: 160 VAIAKKLNVSESEV---ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
             IAK L++  +++   +SM+      + ++  +   D   ++  + L  +    +  + 
Sbjct: 198 AEIAKALDLEPAQIREFLSMS-----RQPISLDVRVGDNQDTELSELLEDEGISPDNYIT 252

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENP-VTLENLSSEFEVSRERVRQIEA 274
           ++  R++  ++L      L P++R +   R  LQ+   ++L  +     +SRERVRQ+E 
Sbjct: 253 QELMRQDLHDLLAE----LTPQQREVLSLRFGLQDGKELSLAKIGQRMNISRERVRQLEH 308

Query: 275 RAFKKV 280
           +A  ++
Sbjct: 309 QALSQL 314


>gi|242041441|ref|XP_002468115.1| hypothetical protein SORBIDRAFT_01g039810 [Sorghum bicolor]
 gi|241921969|gb|EER95113.1| hypothetical protein SORBIDRAFT_01g039810 [Sorghum bicolor]
          Length = 528

 Score = 79.7 bits (195), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 69/251 (27%), Positives = 121/251 (48%), Gaps = 26/251 (10%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           +R   HG +   +R+V S++RLV+ IA  + G G+  S+++ EG  GL++  +KFD  +G
Sbjct: 278 RRRLNHG-VYCKNRMVKSNVRLVISIAKEHEGPGMEFSDLIQEGMQGLIRGAEKFDASKG 336

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           FR +TYS WWIK A+++ +L    ++                RL  H+ A   + +K   
Sbjct: 337 FRFSTYSHWWIKQAIRKSVLEQTQII----------------RLPAHM-AEASSRVKECC 379

Query: 159 VVAIAKKLNVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
                +   +  +E I+++  +     E+  +L   S   +S+     V   +       
Sbjct: 380 RRLRRELKRLPSNEEIAVDTGMTIRRVEAAMSLPKYSVSFTSKVGCTDVTYQEIMPDTSA 439

Query: 217 EKEERKNRRNMLTRSMSV----LNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVR 270
           E  E    R ++ + ++     L+PRE+ +   R   E   P TL ++     VSRER+R
Sbjct: 440 ETAEEVLHRWLMKKDVNTALESLSPREKLVMRYRFGIEGGRPRTLHDIGQIMGVSRERIR 499

Query: 271 QIEARAFKKVQ 281
           QIE  AF+K++
Sbjct: 500 QIELGAFRKLR 510


>gi|57996880|emb|CAI45888.1| negative response regulator [Escherichia coli]
          Length = 158

 Score = 79.7 bits (195), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 33/69 (47%), Positives = 50/69 (72%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 LRSWSLVKI 126
           +     +++
Sbjct: 61  MNQTRTIRL 69


>gi|309790033|ref|ZP_07684607.1| sigma-70 family RNA polymerase sigma factor [Oscillochloris
           trichoides DG6]
 gi|308227888|gb|EFO81542.1| sigma-70 family RNA polymerase sigma factor [Oscillochloris
           trichoides DG6]
          Length = 358

 Score = 79.7 bits (195), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 78/302 (25%), Positives = 131/302 (43%), Gaps = 58/302 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS--------------------------AAHR 52
           Y+HEI ++ +L  +EE  LA + R   +                            A  R
Sbjct: 65  YLHEIGQVALLSAEEERDLAMQIRAGKEAQMQLDTERFANGAARAQLELTVARGHEARRR 124

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y    +   ++V EGNIGLM+AV+KFD  +G R +TY+ WWI+ A
Sbjct: 125 LIQANLRLVVSVAKKYINSPMAFMDLVQEGNIGLMRAVEKFDHTKGNRFSTYATWWIRQA 184

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   I     ++++    ++      +RR    L+   +     ++   IA  + +S  +
Sbjct: 185 VSRSIAEQSRVIRLPVHLSES--LVQMRRAIYKLEQQFEREPTAQE---IAHSMGLSLRK 239

Query: 173 VISMNCRLAGDESLNALINS----------SDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           V  +    A   SL   +N+          +D+N     D        QE          
Sbjct: 240 VKRLLQASAQPVSLEQPLNNEQEGRVGEVLADENVETPMDLATQKMFHQE---------- 289

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                L  +++ L  RER+I + R         TLE +   F ++RER RQIEA A +++
Sbjct: 290 -----LYAALNDLPDRERKILQLRYGLFDGQRRTLEEVGMAFGITRERTRQIEAEAMRRL 344

Query: 281 QE 282
           ++
Sbjct: 345 RQ 346


>gi|311897949|dbj|BAJ30357.1| putative RNA polymerase sigma factor [Kitasatospora setae KM-6054]
          Length = 323

 Score = 79.7 bits (195), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 84/299 (28%), Positives = 137/299 (45%), Gaps = 54/299 (18%)

Query: 19  YIHEIRKIPMLEKQEEY---------VLAKRYREHGD-------------LSAAHR---- 52
           Y+ EI + P+L+  EE          V A+   + G+                A R    
Sbjct: 32  YLDEIARTPLLDAAEEVELSLRIEAGVFAQHLLDEGEGLDGVSTEELRAIAEDAERAKDV 91

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 92  FIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYSKGFKFSTYATWWIRQA 151

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK-----PEQVVAIAKKLN 167
               I RS     I   +   RL  +L    G ++ +     K     P+    IA +L+
Sbjct: 152 ----ITRS-----IADQSRTIRLPVHLVEELGRIRKVQREKAKELGREPDP-AEIAAELD 201

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG---QEQVLIEKEERKNR 224
            +E  V  +        SLN  ++  D+  +Q+ D LV D      ++ V++       R
Sbjct: 202 TTEQRVKDVLDWARDPVSLNMAVD--DEGETQFGD-LVEDTGAVSPEDAVMV-----MLR 253

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R  L   +  L+ R   I  +R   E+    TL  +  +  ++RER+RQIE  A  +++
Sbjct: 254 REELDGLIGRLDDRTASIIRSRYGMEDGRERTLTEVGKQHGLTRERIRQIEKHALAELK 312


>gi|148241530|ref|YP_001226687.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp.
           RCC307]
 gi|147849840|emb|CAK27334.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. RCC307]
          Length = 280

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 62/222 (27%), Positives = 114/222 (51%), Gaps = 15/222 (6%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ ++LRLVV +A  Y+G GL + ++V EG++GL++AV+KFDP  G+R +TY+  WI+ A
Sbjct: 60  MIQANLRLVVTVAKTYQGRGLDLMDLVQEGSLGLIRAVEKFDPTLGYRFSTYAWNWIRQA 119

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +      +++     Q+     LR L+   + +    L  + +VA+A +  V + +
Sbjct: 120 ISRGLETKGRTLRLPIHVTQQ-----LRALRRAHERLWQQGLSTD-LVAVAAEAGV-DLK 172

Query: 173 VISMNCRLA-GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
             S+  R+A G  SL+     S+ +       L+      E   +++ ER +    + R 
Sbjct: 173 AASLALRMAPGTLSLDTPAAGSESD-------LLQLLPSAEPSPLDEAERHDGWERMGRQ 225

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
           +  L  R++++ + R L      L  +  +   SRER RQIE
Sbjct: 226 LRHLPERDQQVLQWRYLTPERQKLSVVGEQLGCSRERARQIE 267


>gi|113954561|ref|YP_729335.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CC9311]
 gi|113881912|gb|ABI46870.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CC9311]
          Length = 335

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 72/306 (23%), Positives = 134/306 (43%), Gaps = 54/306 (17%)

Query: 11  NGEIGLSR-YIHEIRKIPMLEKQEEYVLAKRYREHGDL---------------------- 47
             E+ L R Y+ +I ++P+L  Q+E  L ++ +E  DL                      
Sbjct: 21  GAEVDLVRSYLRDIGRVPLLSHQQEITLGRQVQELMDLEALEAELKDQRGGEEVAREEVA 80

Query: 48  -----SAAH-------------RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
                SAA              R+V ++LRLVV +A  Y    + + +++ EG IGL++ 
Sbjct: 81  KAAGVSAAQLKRKLQAGRRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRG 140

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V+KFDP RG++ +TY+ WWI+  +   I      +++     +      L +LK   + +
Sbjct: 141 VEKFDPTRGYKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITEM-----LNKLKKGQREL 195

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
           +    +   V  +A  + + E EV  + CR     SL   +   D + ++  + L  D  
Sbjct: 196 SQELGRTPSVTELASFVELPEEEVKDLMCRARQPVSLE--MKVGDGDDTELLELLAGDG- 252

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRE 267
              ++  ++ E +  +  L   +S L   + ++   R     E P++L  +     +SR+
Sbjct: 253 ---ELPSDQVEGECLKGDLRDLLSQLPELQGKVLRMRYGMDGEEPMSLTGIGRIIGISRD 309

Query: 268 RVRQIE 273
           RVR +E
Sbjct: 310 RVRNLE 315


>gi|255312689|gb|ACU01754.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 33/69 (47%), Positives = 50/69 (72%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 LRSWSLVKI 126
           +     +++
Sbjct: 61  MNQTRTIRL 69


>gi|327314688|ref|YP_004330125.1| sigma-70, region 4 [Prevotella denticola F0289]
 gi|326944846|gb|AEA20731.1| sigma-70, region 4 [Prevotella denticola F0289]
          Length = 228

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 71/273 (26%), Positives = 116/273 (42%), Gaps = 47/273 (17%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           I   +YI EI     L   EE  LA+R +  GD  A  +L  ++L+ VV +A  YR  GL
Sbjct: 2   IANEKYIEEIAGGQPLSDVEERTLAERIKV-GDAHALEKLTKANLKYVVSLAHQYRNRGL 60

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++SEGNIG+M A ++FD  RG R   ++  +I+ AM+E I    +L ++       
Sbjct: 61  GEDDLISEGNIGMMHAAQRFDGARGVRFVVFAAPYIRKAMEEAIKEQAALYRLP------ 114

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                 R  K   +    + +  +Q V +    N +   V+  +     DE LN  I S+
Sbjct: 115 ------RNEKNRSEQKRSHAISIDQPVPVGSSNNFTLQNVLENDNAPHADEQLNQEILSA 168

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA-RRLQENP 252
           +                                 + + + VLN RER++      L    
Sbjct: 169 E---------------------------------IQKGLGVLNERERQVITCLYGLSGIH 195

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            T+   +    + RERVRQI   A +K+ + ++
Sbjct: 196 YTMAEAAEHMGLKRERVRQIRDGALRKLHKRMK 228


>gi|107025596|ref|YP_623107.1| RNA polymerase, sigma 28 subunit [Burkholderia cenocepacia AU 1054]
 gi|116693222|ref|YP_838755.1| RNA polymerase, sigma 28 subunit [Burkholderia cenocepacia HI2424]
 gi|105894970|gb|ABF78134.1| RNA polymerase, sigma 28 subunit [Burkholderia cenocepacia AU 1054]
 gi|116651222|gb|ABK11862.1| RNA polymerase, sigma 28 subunit [Burkholderia cenocepacia HI2424]
          Length = 628

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 69/240 (28%), Positives = 113/240 (47%), Gaps = 26/240 (10%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +L  S+LRLVV +A  Y   GLP S+++ EGNIGLM+AV ++D  RGF+ +TY+ WWI+ 
Sbjct: 394 KLFQSNLRLVVSVAKRYADRGLPFSDLIQEGNIGLMKAVDRYDHRRGFKFSTYATWWIRQ 453

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           A+      + +L  +G T           R+  H    T N L     +   +  +V+++
Sbjct: 454 AI------THALADLGRTI----------RVPAH-TVDTLNKLSRLARLHRQRTGDVADA 496

Query: 172 EVISMNCRLAGDE--SLNALIN---SSDKNSSQWQDWLVYDH--DGQEQVLIEKEERKNR 224
             +S   RL  D+   L +++    S+D   S   D  + D   D       E       
Sbjct: 497 RALSTQMRLPVDKVRELMSIVREPISADLPVSPDHDLTLCDVTIDPDAPTPEEAASAGQL 556

Query: 225 RNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           R  +   +  L  RE  I   R     +N  +L  +  +  +S ERVRQ+E  A +++++
Sbjct: 557 RAAVAELIDSLPVREAWILRLRYGIDVDNEYSLREIGRQLNLSAERVRQLEVSALERIRQ 616


>gi|54401902|gb|AAV34636.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 194

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 33/62 (53%), Positives = 48/62 (77%)

Query: 57  HLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           +LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  
Sbjct: 1   NLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERA 60

Query: 117 IL 118
           I+
Sbjct: 61  IM 62


>gi|303237309|ref|ZP_07323879.1| sigma-70, region 4 [Prevotella disiens FB035-09AN]
 gi|302482696|gb|EFL45721.1| sigma-70, region 4 [Prevotella disiens FB035-09AN]
          Length = 235

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 68/257 (26%), Positives = 116/257 (45%), Gaps = 48/257 (18%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +YI +I    +L  +EE  LAK+ +  GD  A  +L  S+L+ VV IA  Y+  GL   +
Sbjct: 8   KYIKDIANEQLLSDKEEQELAKQIK-IGDAKALEKLTKSNLKFVVSIAHQYKNRGLGEDD 66

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++SEGNIG+M A +KFD  +G R   ++  +I+ AM+E I       K+     +K    
Sbjct: 67  LISEGNIGMMYAAQKFDGTKGTRFVKFAAPYIRKAMEEAINEQLETFKVQNKDEKKP--- 123

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
             R+   H              V+I + +    +   ++   L      NA    +D+N 
Sbjct: 124 --RKRTAHR-------------VSIDQPIPAGSNGTFTLQTILE-----NANSQHADENL 163

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
           ++             Q++         R  + ++MSVL+ R+R++         E   T+
Sbjct: 164 TK-------------QIV---------REEIKKAMSVLDARQRKVISLLYAIKDEEAYTM 201

Query: 256 ENLSSEFEVSRERVRQI 272
           +  +   ++ RERVRQI
Sbjct: 202 QETADIMDIKRERVRQI 218


>gi|262197834|ref|YP_003269043.1| RNA polymerase, sigma 32 subunit, RpoH [Haliangium ochraceum DSM
           14365]
 gi|262081181|gb|ACY17150.1| RNA polymerase, sigma 32 subunit, RpoH [Haliangium ochraceum DSM
           14365]
          Length = 436

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 63/242 (26%), Positives = 118/242 (48%), Gaps = 17/242 (7%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            V ++LRLVV +A  Y   G+P+++++ EGN+GLM AV +FD  RG R +TY+ WWI+ A
Sbjct: 206 FVHANLRLVVTMARRYDRGGMPLADLIQEGNLGLMHAVSRFDYRRGLRFSTYACWWIRHA 265

Query: 113 MQEYILRSWSLVKIGT---TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           +   +      V+I      A Q+     L +++  L         P +   +AK   V 
Sbjct: 266 IGRALADKSRAVRIPVHMLEAQQQ-----LAKVQAKLIGELGREPTPSE---LAKAAQVP 317

Query: 170 ESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            +++  M+  L G   SL+  +   D  +  + D L  D   ++   ++    +   + +
Sbjct: 318 LAKLNQMHRYLMGQPMSLDRPLYDDDDRA--FGDMLA-DPLSEDSSPVDDLTTQTLTSRV 374

Query: 229 TRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +  L P E  +   R   + +   T   +  ++++SRER+RQI+  A  K++ ++++
Sbjct: 375 ETLLDHLTPIEADVLRQRFGLMDDEERTFREIGDQYDLSRERIRQIQNAALGKLRRALER 434

Query: 287 QV 288
            V
Sbjct: 435 AV 436


>gi|33241240|ref|NP_876182.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Prochlorococcus marinus subsp. marinus str. CCMP1375]
 gi|33238770|gb|AAQ00835.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Prochlorococcus marinus subsp. marinus str. CCMP1375]
          Length = 328

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 64/237 (27%), Positives = 113/237 (47%), Gaps = 15/237 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+V+++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP RG++ +TY+ WW
Sbjct: 93  AKERMVSANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPARGYKFSTYAYWW 152

Query: 109 IKAAMQEYILRSWSLVK--IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           I+  +   I     +++  I  T    +L    R L  HL+       +   +  ++  +
Sbjct: 153 IRQGITRAIAEKSRIIRLPIHITELLNKLKKGQRELSQHLE-------RTPTMQELSAYV 205

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   EV  +  R +   SL + +   D   +   D L  D D  +Q  IE +  K    
Sbjct: 206 EIPVEEVKDLMFRASQPVSLESKVG--DGEDTSLLDLLAIDTDLPDQQ-IELDCMKGDLE 262

Query: 227 MLTRSMSVLNPRERRI-FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +L + +  L  R  R+ F      E P+TL  +     +SR+RVR +     K +++
Sbjct: 263 VLLQKLPELQNRVLRMRFGIN--GEEPMTLTGIGRMLGISRDRVRNLLRDGLKGLRQ 317


>gi|323452445|gb|EGB08319.1| hypothetical protein AURANDRAFT_5759 [Aureococcus anophagefferens]
          Length = 239

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 71/262 (27%), Positives = 120/262 (45%), Gaps = 45/262 (17%)

Query: 49  AAHRLVTSHLRLVVKIAMGYR----GYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           A H LV ++  LVV IA GY+    G G+  + ++V EG +GL++AV+K++PERG R  T
Sbjct: 1   AKHALVRANGGLVVSIARGYQRLRTGAGVEALDDLVQEGTLGLIRAVEKYEPERGIRFGT 60

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+  WIKA++  ++ R  +++K+   +    L     R    LQ     +   E+V   A
Sbjct: 61  YATAWIKASISAWLKRGDAMIKV--PSRVADLGLRAARSSSALQNDLGRDATAEEV---A 115

Query: 164 KKLN------------VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
           + L             +  S V+S +    GD   N +   +D      +D  V D    
Sbjct: 116 RDLGASTAAVEAAASALHGSRVVSYDASAGGDSESNFVACLAD------EDCAVGDL--- 166

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERV 269
                    + +  N L    +VL+ RE R+   R   ++    +    ++   + +E V
Sbjct: 167 ---------KADLTNALA---AVLDDRELRVVRLRYGLDDGTQRSTRECAAALGIGKESV 214

Query: 270 RQIEARAFKKVQESIQKQVELS 291
           RQI  +AF+K++ + Q    LS
Sbjct: 215 RQICLKAFRKLRGTAQGSALLS 236


>gi|282896368|ref|ZP_06304389.1| sigD (sigma 28 (flagella/spoulation)) [Raphidiopsis brookii D9]
 gi|281198656|gb|EFA73536.1| sigD (sigma 28 (flagella/spoulation)) [Raphidiopsis brookii D9]
          Length = 332

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 58/244 (23%), Positives = 116/244 (47%), Gaps = 33/244 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V ++LRL+V +A  Y    + + +++ EG+IG+ + V+KFDP +G+R +TY+ WW
Sbjct: 97  AKRKMVEANLRLLVSVAKKYIKRNVDLLDLIQEGSIGMQRGVEKFDPSKGYRFSTYAYWW 156

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      +++     +K     L ++K   + ++    +   +  +A++L +
Sbjct: 157 IRQAITRAIAEKARTIRLPIHITEK-----LNKIKKAQRDLSQTLGRSPSIAELAQELEI 211

Query: 169 SESEV----------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           +  +V          +S++ RL GD     L    +   +  +D+++      E      
Sbjct: 212 TPKQVRDCLEKARLPLSLDLRL-GDNYDTELGEMLEDPGASPEDYVIQSSLSSE------ 264

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARA 276
                    L R M+ L  ++R + + R   +    +TL  +     +SRERVRQIE  A
Sbjct: 265 ---------LERMMTHLTTQQREVIKLRFGLVDGQSMTLARIGEVLNISRERVRQIEREA 315

Query: 277 FKKV 280
             ++
Sbjct: 316 LTRL 319


>gi|78183723|ref|YP_376157.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CC9902]
 gi|78168017|gb|ABB25114.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. CC9902]
          Length = 332

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 72/296 (24%), Positives = 135/296 (45%), Gaps = 30/296 (10%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEE-------------------YVLAKRYREHGDLSAAHRL 53
           EI L R + ++ +I  LE + E                    V  KR  + G   A  R+
Sbjct: 43  EITLGRQVQQLMEIETLEAELESRDGAKPARDQLAKAAELSTVQLKRKLQQGH-RAKERM 101

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V ++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP RG++ +TY+ WWI+  +
Sbjct: 102 VAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWWIRQGI 161

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
              I      +++     +      L +LK   + ++    +   V  +A+ +++ E EV
Sbjct: 162 TRAIAEKSRTIRLPIHITEM-----LNKLKKGQRELSQELGRTPTVTELAQFVDLPEDEV 216

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             + CR     SL   +   D + ++  + L  D++     + E   + + R++L +   
Sbjct: 217 KDLMCRARQPVSLE--MKVGDGDDTELLELLSGDNELPSDQVEEDCLKGDLRSLLGQLPH 274

Query: 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           +     R  F      E+P++L  +     +SR+RVR +E      ++  +  QVE
Sbjct: 275 LQEQVLRMRFGMD--GEDPMSLTGIGRILGMSRDRVRNLERDGLAGLRR-VSDQVE 327


>gi|116071698|ref|ZP_01468966.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. BL107]
 gi|116065321|gb|EAU71079.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. BL107]
          Length = 332

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 69/280 (24%), Positives = 129/280 (46%), Gaps = 29/280 (10%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEE-------------------YVLAKRYREHGDLSAAHRL 53
           EI L R + ++ +I  LE + E                    V  KR  + G   A  R+
Sbjct: 43  EITLGRQVQQLMEIETLEAELESRDGAKPARDQLAKAAELSTVQLKRKLQQGH-RAKERM 101

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V ++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP RG++ +TY+ WWI+  +
Sbjct: 102 VAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWWIRQGI 161

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
              I      +++     +      L +LK   + ++    +   V  +A+ +++ E EV
Sbjct: 162 TRAIAEKSRTIRLPIHITEM-----LNKLKKGQRELSQELGRTPTVTELAQFVDLPEDEV 216

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             + CR     SL   +   D + ++  + L  D++     + E   + + R++L +   
Sbjct: 217 KDLMCRARQPVSLE--MKVGDGDDTELLELLSGDNELPSDQVEEDCLKGDLRSLLGQLPH 274

Query: 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
           +     R  F      E+P++L  +     +SR+RVR +E
Sbjct: 275 LQEQVLRMRFGMD--GEDPMSLTGIGRILGMSRDRVRNLE 312


>gi|186682180|ref|YP_001865376.1| SigH/RpoD family RNA polymerase sigma factor [Nostoc punctiforme
           PCC 73102]
 gi|186464632|gb|ACC80433.1| RNA polymerase, sigma 70 subunit SigH, RpoD family [Nostoc
           punctiforme PCC 73102]
          Length = 321

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 62/236 (26%), Positives = 114/236 (48%), Gaps = 31/236 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A H+++T++LRLVV IA  Y+   L + +++ EG +GL + V+KF+P  G+R +TY+ WW
Sbjct: 94  AKHKMITANLRLVVSIAKQYQRRNLELMDLIQEGTLGLERGVEKFNPALGYRFSTYAYWW 153

Query: 109 IKAAMQEYILRSWSLVKIGTTAN---------QKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+  +   I +    +++    N         Q+ L   L R+    +     +LKP Q+
Sbjct: 154 IRQGITRAIAQQGRAIRLPIHINEKLNKIKRVQRELSQTLGRIPTSTEIANALSLKPSQI 213

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
               ++  +  +  IS++ R++ ++ L            + QD L+ D+       I +E
Sbjct: 214 ----REFLLLATRTISLDIRVSSEKDL------------RLQD-LIEDYKYSSNSYITEE 256

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIE 273
                 N L   +S L+ +++ I            ++L+ +     +SRERVRQIE
Sbjct: 257 SLNQEVNSL---LSNLSRQQQEILNLHFGLTDGEELSLQQIGQRLGISRERVRQIE 309


>gi|298250481|ref|ZP_06974285.1| RNA polymerase, sigma 32 subunit, RpoH [Ktedonobacter racemifer DSM
           44963]
 gi|297548485|gb|EFH82352.1| RNA polymerase, sigma 32 subunit, RpoH [Ktedonobacter racemifer DSM
           44963]
          Length = 313

 Score = 79.7 bits (195), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 35/74 (47%), Positives = 53/74 (71%), Gaps = 4/74 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +RLV ++LRLV  +A  YRG+G+ I +++ EGNIGL+ AV+KFDP +G+R +TY+  W
Sbjct: 70  AKNRLVEANLRLVRSVAYQYRGFGVDIMDLIQEGNIGLIHAVEKFDPTKGYRFSTYATHW 129

Query: 109 IKAAMQEYILRSWS 122
           I+    +YI R  +
Sbjct: 130 IR----QYICRELA 139


>gi|88809561|ref|ZP_01125068.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 7805]
 gi|88786311|gb|EAR17471.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 7805]
          Length = 211

 Score = 79.3 bits (194), Expect = 5e-13,   Method: Compositional matrix adjust.
 Identities = 51/155 (32%), Positives = 84/155 (54%), Gaps = 10/155 (6%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P  E  E+    KR  + G+  A ++++T++LRLVV +A  Y+G GL + +++ EG +GL
Sbjct: 48  PACEYSED---EKRIIKRGE-KAKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGL 103

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
            +AV+K+DP RG R +TY+ WWI+  +   +      ++I    N+K     LR  K  L
Sbjct: 104 TRAVEKYDPTRGHRFSTYAYWWIRQGLNRALSTQSRTIRIPVNVNEK--LTKLRASKARL 161

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVIS-MNCRL 180
             +  N L P     ++  +N+  SEV   + C L
Sbjct: 162 --MQRNGLSPS-TEQLSDDMNLPISEVEDLLGCEL 193


>gi|58699437|ref|ZP_00374184.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Drosophila
           ananassae]
 gi|58534044|gb|EAL58296.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Drosophila
           ananassae]
          Length = 57

 Score = 79.3 bits (194), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 32/57 (56%), Positives = 48/57 (84%)

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           M AVKKF+P+ GFR +TY++WWI+A+++++IL+SWS VKIG+T  Q+ L F+LR +K
Sbjct: 1   MHAVKKFNPDLGFRFSTYAVWWIEASIKDFILKSWSFVKIGSTQAQRILCFSLREIK 57


>gi|255312633|gb|ACU01726.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score = 79.3 bits (194), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 49/142 (34%), Positives = 78/142 (54%), Gaps = 12/142 (8%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 LRSWSLVKIGT-TANQKRLFFNLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVS 169
           +     +++      +  ++    R   H        + IT+   KP   V+   +LN  
Sbjct: 61  MNQTRTIRLPIHIVKELNVYLRTARELSHKLDHEPSAEEITEQLDKPVDDVSRMLRLN-- 118

Query: 170 ESEVISMNCRLAGDESLNALIN 191
              + S++  L GD S  AL++
Sbjct: 119 -ERITSVDTPLGGD-SEKALLD 138


>gi|55274965|gb|AAV49282.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 193

 Score = 79.3 bits (194), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 33/61 (54%), Positives = 47/61 (77%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 L 118
           +
Sbjct: 61  M 61


>gi|299115565|emb|CBN75768.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ectocarpus
           siliculosus]
          Length = 244

 Score = 79.3 bits (194), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 31/66 (46%), Positives = 54/66 (81%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   +V +++R+V+ IA  Y+  G+P+++++ EG++GL++AV+KFDPERGF+L+TYS W
Sbjct: 81  AAKKTMVEANMRMVISIARKYQHLGVPLTDLIQEGSLGLVRAVEKFDPERGFKLSTYSAW 140

Query: 108 WIKAAM 113
           WI+ A+
Sbjct: 141 WIQQAI 146


>gi|57996884|emb|CAI45890.1| negative response regulator [Escherichia coli]
          Length = 191

 Score = 79.3 bits (194), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 33/61 (54%), Positives = 47/61 (77%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 L 118
           +
Sbjct: 61  M 61


>gi|255312665|gb|ACU01742.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312669|gb|ACU01744.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score = 79.3 bits (194), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 33/61 (54%), Positives = 47/61 (77%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 L 118
           +
Sbjct: 61  M 61


>gi|55274883|gb|AAV49244.1| RNA polymerase subunit sigma-38 [Shigella boydii]
 gi|55274899|gb|AAV49251.1| RNA polymerase subunit sigma-38 [Escherichia albertii]
          Length = 193

 Score = 79.3 bits (194), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 33/61 (54%), Positives = 47/61 (77%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 L 118
           +
Sbjct: 61  M 61


>gi|291060369|gb|ADD73104.1| RNA polymerase sigma-43 factor [Treponema pallidum subsp. pallidum
           str. Chicago]
          Length = 296

 Score = 79.3 bits (194), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 34/98 (34%), Positives = 65/98 (66%), Gaps = 1/98 (1%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y++++++IP++  ++E          GD  A + LV +++R V+ +A  YR  GLP+
Sbjct: 13  LTAYLNDLKRIPLM-NEKEEYACACAAYAGDAQAKNALVRANVRFVISVARHYRTCGLPL 71

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           ++++SEGNIGL+ A ++F+P RG R  +Y+  WI+ ++
Sbjct: 72  ADLISEGNIGLLTAAERFNPARGCRFISYAACWIRQSI 109


>gi|307564926|ref|ZP_07627446.1| sigma-70, region 4 [Prevotella amnii CRIS 21A-A]
 gi|307346366|gb|EFN91683.1| sigma-70, region 4 [Prevotella amnii CRIS 21A-A]
          Length = 228

 Score = 79.3 bits (194), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 65/264 (24%), Positives = 120/264 (45%), Gaps = 47/264 (17%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +YI +I    +L  +EE  L+ R +  GD  A  +L  ++L  VV IA  Y+  GL   +
Sbjct: 6   KYIGDIIGENLLSDEEEVQLSNRIK-IGDAKALEKLTKANLTFVVSIAHQYKEQGLDEDD 64

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++SEGNIG+M A +KFD  +G R   ++  +I+ A+++ I    +L K+    N+    F
Sbjct: 65  LISEGNIGMMYAAQKFDGSKGIRFVKFAAPYIRKAIEKSIKEQTTLYKVPKKENK---LF 121

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
             +R K          +  +Q + +     ++   +I  N     D+S+N+ I ++    
Sbjct: 122 EKKRAKP---------VSLDQPIPVGSNNKLTLQNLIPNNNNKDTDDSVNSNILNT---- 168

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF-EARRLQENPVTLE 256
                                        +L +S++ LN RE+ +  +   +    +T+ 
Sbjct: 169 -----------------------------ILMQSINCLNEREKAVITQLYGINGTSLTMA 199

Query: 257 NLSSEFEVSRERVRQIEARAFKKV 280
            +++   + RERVRQI   A +K+
Sbjct: 200 EVATSLGLKRERVRQIRNTALRKL 223


>gi|255312671|gb|ACU01745.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score = 79.3 bits (194), Expect = 6e-13,   Method: Compositional matrix adjust.
 Identities = 33/61 (54%), Positives = 47/61 (77%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 L 118
           +
Sbjct: 61  M 61


>gi|57996874|emb|CAI45885.1| negative response regulator [Escherichia coli]
 gi|57996882|emb|CAI45889.1| negative response regulator [Escherichia coli]
          Length = 191

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 33/61 (54%), Positives = 47/61 (77%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 L 118
           +
Sbjct: 61  M 61


>gi|117165089|emb|CAJ88642.1| putative RNA polymerase principal sigma factor HrdC [Streptomyces
           ambofaciens ATCC 23877]
          Length = 338

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 68/232 (29%), Positives = 118/232 (50%), Gaps = 20/232 (8%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   +V ++LRLVV +A  +   GLP+ +V+ EGN+GL++AV+KFD  +GF+ +TY+ W
Sbjct: 100 AAKDHMVRANLRLVVSMAKRHAHRGLPLLDVIQEGNLGLIRAVEKFDHTKGFKFSTYATW 159

Query: 108 WIKAAMQEYILRSWSLVK--IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
           WI+ A++  +      V+  +      ++L    R+L+G L    D     ++V A   +
Sbjct: 160 WIRQAIERGLATHARTVRLPVHVVEQLQKLAKVERKLRGRL----DREPTADEVAA---E 212

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE--ERKN 223
             +   +V+ +  R  G +++     S D    +  + +V D     +VL   E  E + 
Sbjct: 213 SGIDGDKVVWL--RRVGRDAV-----SLDTPVDEAGETVVGDLIPDTEVLQAPEVAEFQA 265

Query: 224 RRNMLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIE 273
               L  ++  L PRE  I   R  L +  P TL  ++    ++RERVRQ+E
Sbjct: 266 LAAELREAVGTLAPREAMILSLRYGLHDGRPRTLHQVAQHVGLTRERVRQLE 317


>gi|332297914|ref|YP_004439836.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           brennaborense DSM 12168]
 gi|332181017|gb|AEE16705.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           brennaborense DSM 12168]
          Length = 269

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 79/267 (29%), Positives = 132/267 (49%), Gaps = 19/267 (7%)

Query: 17  SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
           + Y+ +I++ P+L  ++E  L+     +GD SA  +LV S+LRLVV IA  Y    + + 
Sbjct: 7   ASYMAQIQRYPLLTPEQEKKLSADIH-NGDTSAKLKLVQSNLRLVVSIANKYVSDRIGVM 65

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++ EGN+GL+ A  KF      R +TY+  WI     +YILR +   KI       R  
Sbjct: 66  DLIQEGNLGLLTAASKFHYSFNTRFSTYAYSWIT----QYILR-FIQNKIPYITLPHRKE 120

Query: 137 FNLRRLKGHLQAIT-DNNLKPEQVV-AIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
             LR++  H+  I     L+ E  +  IA  ++VSES++           S++A I+ + 
Sbjct: 121 EMLRKI--HMAKIDLMQQLQSEPTLREIASYMDVSESDISGALMHEYVYSSIDAEIDGTS 178

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--- 251
             +    D +       EQ+ ++  E ++ R+++      L  RER++   R   +N   
Sbjct: 179 NLTC--ADMIADPSPSPEQLCLKNLEAEDIRSLV----ETLPDRERQVIYYRFNFDNSRK 232

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFK 278
           P TL  +S    +S E VRQ+E RA +
Sbjct: 233 PWTLRQISEMLGISAETVRQMELRALQ 259


>gi|55274892|gb|AAV49248.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 190

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 33/61 (54%), Positives = 47/61 (77%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 L 118
           +
Sbjct: 61  M 61


>gi|55274885|gb|AAV49245.1| RNA polymerase subunit sigma-38 [Shigella boydii]
 gi|255312609|gb|ACU01714.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312611|gb|ACU01715.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312613|gb|ACU01716.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312615|gb|ACU01717.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312617|gb|ACU01718.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312619|gb|ACU01719.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312621|gb|ACU01720.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312623|gb|ACU01721.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312625|gb|ACU01722.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312627|gb|ACU01723.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312629|gb|ACU01724.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312631|gb|ACU01725.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312635|gb|ACU01727.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312637|gb|ACU01728.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312649|gb|ACU01734.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312651|gb|ACU01735.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312655|gb|ACU01737.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312657|gb|ACU01738.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312667|gb|ACU01743.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312673|gb|ACU01746.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312675|gb|ACU01747.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312677|gb|ACU01748.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312679|gb|ACU01749.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312681|gb|ACU01750.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312683|gb|ACU01751.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312685|gb|ACU01752.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312687|gb|ACU01753.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312691|gb|ACU01755.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312693|gb|ACU01756.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312695|gb|ACU01757.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312699|gb|ACU01759.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312701|gb|ACU01760.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312703|gb|ACU01761.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312705|gb|ACU01762.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 33/61 (54%), Positives = 47/61 (77%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 L 118
           +
Sbjct: 61  M 61


>gi|254249954|ref|ZP_04943274.1| DNA-directed RNA polymerase, sigma subunit [Burkholderia
           cenocepacia PC184]
 gi|124876455|gb|EAY66445.1| DNA-directed RNA polymerase, sigma subunit [Burkholderia
           cenocepacia PC184]
          Length = 662

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 70/243 (28%), Positives = 115/243 (47%), Gaps = 32/243 (13%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +L  S+LRLVV +A  Y   GLP S+++ EGNIGLM+AV ++D  RGF+ +TY+ WWI+ 
Sbjct: 428 KLFQSNLRLVVSVAKRYADRGLPFSDLIQEGNIGLMKAVDRYDHRRGFKFSTYATWWIRQ 487

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           A+      + +L  +G T           R+  H    T N L     +   +  +V+++
Sbjct: 488 AI------THALADLGRTI----------RVPAH-TVDTLNKLSRLARLHRQRTGDVADA 530

Query: 172 EVISMNCRLAGDE--SLNALIN---SSDKNSSQWQDWLVYDH--DGQEQVLIEKEERKNR 224
             +S   RL  D+   L +++    S+D   S   D  + D   D       E       
Sbjct: 531 RALSTQMRLPVDKVRELMSIVREPISADLPVSPDHDLTLCDVTIDPDAPTPEEAASAGQL 590

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQ-----ENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           R  +   +  L  RE  I    RL+     +N  +L  +  +  +S ERVRQ+E  A ++
Sbjct: 591 RAAVAELIDSLPVREAWIL---RLRYGIDVDNEYSLREIGRQLNLSAERVRQLEVSALER 647

Query: 280 VQE 282
           +++
Sbjct: 648 IRQ 650


>gi|110004382|emb|CAK98720.1| probable rna polymerase sigma-a factor protein [Spiroplasma citri]
          Length = 445

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 34/75 (45%), Positives = 51/75 (68%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +L+TS+L+LVV +A  +   GL  S+++ EGNIGLM+AV KFD +RGF+ +TY+ WWI+ 
Sbjct: 150 KLITSNLKLVVSVARKHLNRGLDFSDLIEEGNIGLMKAVDKFDYKRGFKFSTYATWWIRQ 209

Query: 112 AMQEYILRSWSLVKI 126
           A    I      ++I
Sbjct: 210 ATTRAIADQARTIRI 224



 Score = 39.3 bits (90), Expect = 0.77,   Method: Compositional matrix adjust.
 Identities = 16/32 (50%), Positives = 25/32 (78%)

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++P TLE +  EF+V+RER+RQIEA+  +K +
Sbjct: 397 DSPKTLEEVGKEFKVTRERIRQIEAKTIRKFK 428


>gi|209524631|ref|ZP_03273179.1| RNA polymerase, sigma 70 subunit, RpoD family [Arthrospira maxima
           CS-328]
 gi|209495089|gb|EDZ95396.1| RNA polymerase, sigma 70 subunit, RpoD family [Arthrospira maxima
           CS-328]
          Length = 331

 Score = 79.3 bits (194), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 61/248 (24%), Positives = 116/248 (46%), Gaps = 31/248 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V ++LRLVV +A  Y    + + +++ EG IG+ + V+KFDP +G+R +TY+ WW
Sbjct: 96  AKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWW 155

Query: 109 IKAAMQEYILRSWSLVKIGTTAN---------QKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      +++              Q++L   L R     +   + +L P+Q+
Sbjct: 156 IRQAITRAIAEKGRTIRLPIHITEKLNKIKKAQRQLAQQLGRAATMNELAAELDLTPKQI 215

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
               +K  +     +S++ R+             D   ++  D L    +  EQ  +   
Sbjct: 216 REYLEKSRLP----LSLDLRVG------------DNQDTELVDLLEDTSNSPEQFALNSS 259

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
            R +  +++T     L  ++R++   R   ++   +TL  +     +SRERVRQIE  A 
Sbjct: 260 LRSDLESLMTD----LTDQQRQVLALRFGLDDGQTLTLAKIGDRLNISRERVRQIEREAL 315

Query: 278 KKVQESIQ 285
            K+++  Q
Sbjct: 316 TKLRKRKQ 323


>gi|55274887|gb|AAV49246.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 199

 Score = 79.0 bits (193), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 33/61 (54%), Positives = 47/61 (77%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 L 118
           +
Sbjct: 61  M 61


>gi|55274901|gb|AAV49252.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 198

 Score = 79.0 bits (193), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 33/61 (54%), Positives = 47/61 (77%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 L 118
           +
Sbjct: 61  M 61


>gi|213425678|ref|ZP_03358428.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. E02-1180]
          Length = 304

 Score = 79.0 bits (193), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 72/277 (25%), Positives = 122/277 (44%), Gaps = 51/277 (18%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRL+                 
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLI----------------- 102

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT-TANQKRLFF 137
                    +AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      +  ++ 
Sbjct: 103 ---------RAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIVKELNVYL 153

Query: 138 NLRRLKGH-------LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R   H        + I +   KP   V+   +LN     + S++  L GD     L 
Sbjct: 154 RTARELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLN---ERITSVDTPLGGDSEKALLD 210

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D+  +  +D    D   Q  V    E    +R +L R   +L       +EA     
Sbjct: 211 ILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG------YEA----- 259

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 260 --ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 294


>gi|291565943|dbj|BAI88215.1| group 2 RNA polymerase sigma factor SigD [Arthrospira platensis
           NIES-39]
          Length = 331

 Score = 79.0 bits (193), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 61/248 (24%), Positives = 116/248 (46%), Gaps = 31/248 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V ++LRLVV +A  Y    + + +++ EG IG+ + V+KFDP +G+R +TY+ WW
Sbjct: 96  AKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWW 155

Query: 109 IKAAMQEYILRSWSLVKIGTTAN---------QKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      +++              Q++L   L R     +   + +L P+Q+
Sbjct: 156 IRQAITRAIAEKGRTIRLPIHITEKLNKIKKAQRQLAQQLGRAATMNELAAELDLTPKQI 215

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
               +K  +     +S++ R+             D   ++  D L    +  EQ  +   
Sbjct: 216 REYLEKSRLP----LSLDLRVG------------DNQDTELVDLLEDTTNSPEQFALNSS 259

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
            R +  +++T     L  ++R++   R   ++   +TL  +     +SRERVRQIE  A 
Sbjct: 260 LRSDLESLMTD----LTDQQRQVLALRFGLDDGQTLTLAKIGDRLNISRERVRQIEREAL 315

Query: 278 KKVQESIQ 285
            K+++  Q
Sbjct: 316 TKLRKRKQ 323


>gi|227504896|ref|ZP_03934945.1| RNA polymerase sigma factor SigB [Corynebacterium striatum ATCC
           6940]
 gi|227198489|gb|EEI78537.1| RNA polymerase sigma factor SigB [Corynebacterium striatum ATCC
           6940]
          Length = 337

 Score = 79.0 bits (193), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 73/288 (25%), Positives = 133/288 (46%), Gaps = 45/288 (15%)

Query: 13  EIGL-SRY-IHEIRKIPMLEKQEEYVL---AKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           E+GL + Y +    KI   EK++  +L    K+ R H        L+ ++LRLVV +A  
Sbjct: 67  EVGLYAEYKLANAEKITRAEKRDLKILVREGKKARSH--------LLEANLRLVVSLAKR 118

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A+   +      +++ 
Sbjct: 119 YTGRGMPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLP 178

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----------ISMN 177
               ++     L R+K  +          E+   +A++  + ES++          +S++
Sbjct: 179 VHLVEQ--VNKLSRIKREMYQSLGREATNEE---LAEESGIEESKIEMLLRQSRDPVSLD 233

Query: 178 CRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
             +  DE   L   I  ++   ++        H     V+   EER+     L   +   
Sbjct: 234 MPVGTDEEAPLGDFIEDAEATDAETAVVAAMRHSDIRGVIETLEEREQDVIRLRYGLDDG 293

Query: 236 NPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            PR               TL+ +  +F +SRERVRQIE     K+++ 
Sbjct: 294 VPR---------------TLDQIGRKFGLSRERVRQIEREVMAKLRDG 326


>gi|119513754|ref|ZP_01632741.1| Sigma 28 (Flagella/Sporulation) [Nodularia spumigena CCY9414]
 gi|119461595|gb|EAW42645.1| Sigma 28 (Flagella/Sporulation) [Nodularia spumigena CCY9414]
          Length = 327

 Score = 79.0 bits (193), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 58/231 (25%), Positives = 112/231 (48%), Gaps = 13/231 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +++ ++LRLVV IA  Y+   +   +++ EG +GL + V+KFDP RG++ +TY+ WW
Sbjct: 92  AKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGYKFSTYAYWW 151

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I +    +++     +K     L ++K   + +     +      IA +L +
Sbjct: 152 IRQAITRAIAQQGRTIRLPIHITEK-----LNKIKKVQRELAQKFGRSPTPTEIAHELEL 206

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              ++           SL+  +   D   ++ Q+ L  +    E    ++  R++  N+L
Sbjct: 207 EPMQIREYLNMARQPVSLD--VKVGDNQDTELQEMLEDEGPSPEYYTTQEFLRQDLNNLL 264

Query: 229 TRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAF 277
                 L P++R++   R   E  N ++L  +     +SRERVRQ+E +A 
Sbjct: 265 AE----LTPQQRQVLALRFGLEDGNEMSLAKVGERLNLSRERVRQLEHQAL 311


>gi|284051429|ref|ZP_06381639.1| RNA polymerase sigma factor SigD [Arthrospira platensis str.
           Paraca]
          Length = 319

 Score = 79.0 bits (193), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 61/248 (24%), Positives = 116/248 (46%), Gaps = 31/248 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V ++LRLVV +A  Y    + + +++ EG IG+ + V+KFDP +G+R +TY+ WW
Sbjct: 84  AKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWW 143

Query: 109 IKAAMQEYILRSWSLVKIGTTAN---------QKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      +++              Q++L   L R     +   + +L P+Q+
Sbjct: 144 IRQAITRAIAEKGRTIRLPIHITEKLNKIKKAQRQLAQQLGRAATMNELAAELDLTPKQI 203

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
               +K  +     +S++ R+             D   ++  D L    +  EQ  +   
Sbjct: 204 REYLEKSRLP----LSLDLRVG------------DNQDTELVDLLEDTTNSPEQFALNSS 247

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
            R +  +++T     L  ++R++   R   ++   +TL  +     +SRERVRQIE  A 
Sbjct: 248 LRSDLESLMTD----LTDQQRQVLALRFGLDDGQTLTLAKIGDRLNISRERVRQIEREAL 303

Query: 278 KKVQESIQ 285
            K+++  Q
Sbjct: 304 TKLRKRKQ 311


>gi|15639996|ref|NP_219449.1| RNA polymerase sigma-43 factor (sigA) [Treponema pallidum subsp.
           pallidum str. Nichols]
 gi|189026235|ref|YP_001934007.1| RNA polymerase sigma-43 factor [Treponema pallidum subsp. pallidum
           SS14]
 gi|3323340|gb|AAC65963.1| RNA polymerase sigma-43 factor (sigA) [Treponema pallidum subsp.
           pallidum str. Nichols]
 gi|189018810|gb|ACD71428.1| RNA polymerase sigma-43 factor [Treponema pallidum subsp. pallidum
           SS14]
          Length = 311

 Score = 79.0 bits (193), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 34/98 (34%), Positives = 65/98 (66%), Gaps = 1/98 (1%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y++++++IP++  ++E          GD  A + LV +++R V+ +A  YR  GLP+
Sbjct: 28  LTAYLNDLKRIPLM-NEKEEYACACAAYAGDAQAKNALVRANVRFVISVARHYRTCGLPL 86

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           ++++SEGNIGL+ A ++F+P RG R  +Y+  WI+ ++
Sbjct: 87  ADLISEGNIGLLTAAERFNPARGCRFISYAACWIRQSI 124


>gi|281357254|ref|ZP_06243743.1| RNA polymerase, sigma 32 subunit, RpoH [Victivallis vadensis ATCC
           BAA-548]
 gi|281316285|gb|EFB00310.1| RNA polymerase, sigma 32 subunit, RpoH [Victivallis vadensis ATCC
           BAA-548]
          Length = 428

 Score = 79.0 bits (193), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 62/231 (26%), Positives = 117/231 (50%), Gaps = 21/231 (9%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +++ ++LRLV+ IA  YR  GLP ++++ EGN+GL++A++KFD   G + +TY+ WWIK 
Sbjct: 189 KMIEANLRLVISIAQKYRNRGLPFNDLIQEGNLGLLRALEKFDFRLGNKFSTYASWWIKH 248

Query: 112 AMQEYILRSWSLVKIGT---TANQKRLFFNLRRLKGHLQAITDNNLKPE--QVVAIAKKL 166
            +   I     +++I      A     +   R ++ H         +PE  ++ A+ +  
Sbjct: 249 NISRSIAEQSRVIRIPAHMVHAINSMTWAEQRFIQSH-------GREPEIDELAAVLEMP 301

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
               S +  M+C+     SL A ++SS+ + +  +D +  D        +    RK   +
Sbjct: 302 VARISAIRKMSCQTI---SLQAPVSSSE-DGAMLEDLIADDSTANP---VRDFARKILYD 354

Query: 227 MLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEAR 275
            L   +  L  R+++I   R     +  + L ++S  F ++RER+RQ+EA+
Sbjct: 355 KLYEMLRTLPERDQQIIILRFGLFGQPCLPLVDISRRFNLTRERIRQLEAK 405


>gi|219883041|ref|YP_002478205.1| RNA polymerase, sigma 32 subunit, RpoH [Arthrobacter
           chlorophenolicus A6]
 gi|219862047|gb|ACL42388.1| RNA polymerase, sigma 32 subunit, RpoH [Arthrobacter
           chlorophenolicus A6]
          Length = 951

 Score = 79.0 bits (193), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 74/251 (29%), Positives = 118/251 (47%), Gaps = 50/251 (19%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +LV+ +LRLVV IA  + G G+   +++ EGN GL +AV+KFD  +GF+ +TY+ WW
Sbjct: 528 AVLKLVSCNLRLVVSIAKRHTGRGMDFLDLIQEGNAGLYRAVQKFDYTKGFKFSTYATWW 587

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI---AKK 165
           I+ A+   I            A+Q R      RL  H           EQVV++    + 
Sbjct: 588 IRQAITRGI------------ADQSRTI----RLPVHFH---------EQVVSVFIAERN 622

Query: 166 LNVSE-----SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
              SE     +E I+  C    DE +NA+       +S   DW V +  G  ++L E   
Sbjct: 623 FLQSEGRDGTAEEIAEACGKTVDE-INAVRRHRTPPAS--LDWEVPNGKGGVELLGETLY 679

Query: 221 RKNR------------RNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSR 266
             +             ++ +  ++  L+ RE  +   R        +TL+ + + + V+R
Sbjct: 680 DPDEPTAYDAAVLAQLQSAVHGALDRLSEREAGVLAYRFGLATGEQLTLDQIGTIYGVTR 739

Query: 267 ERVRQIEARAF 277
           ER+RQIEA+AF
Sbjct: 740 ERIRQIEAKAF 750


>gi|2706544|emb|CAA75859.1| Sig1 [Sinapis alba]
          Length = 481

 Score = 79.0 bits (193), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 72/254 (28%), Positives = 126/254 (49%), Gaps = 34/254 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  S++RLV+ IA  Y   G  +S++V  G IGL++ ++KFD  +GFR++TY  WW
Sbjct: 238 AREKLAMSNVRLVMSIAQRYDNMGAEMSDLVQGGLIGLLRGIEKFDSSKGFRISTYVYWW 297

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   ++ +   +++ T  +++       +L+   + IT +      +  IA+ LN+
Sbjct: 298 IRQGVSRALVDNSRTLRLPTHLHERLGLIRNAKLRLQEKGITPS------IDRIAESLNM 351

Query: 169 SE------SEVISMNCRLAGDE--SLNALINSSD-----KNSSQWQDWLVYDHDGQEQVL 215
           S+      +E +S    L  D   SLN L   +       N  +   W  YD       L
Sbjct: 352 SQKKVRNATEAVSKIFSLDRDAFPSLNGLPGETHHSYIADNRLENNPWHGYD------AL 405

Query: 216 IEKEERKNRRNMLTRSMSV-LNPRERRIFEARR-LQENPVTLENLSSEFEVSRERVRQIE 273
             K+E       +++ +SV L  RER I      L +  +T E++S    +SRERVRQ+ 
Sbjct: 406 ALKDE-------VSKLISVTLGEREREIIRLYYGLDKECLTWEDISQRIGLSRERVRQVG 458

Query: 274 ARAFKKVQESIQKQ 287
             A +K++ + +K+
Sbjct: 459 LVALEKLKHAARKR 472


>gi|229815207|ref|ZP_04445543.1| hypothetical protein COLINT_02253 [Collinsella intestinalis DSM
           13280]
 gi|229809217|gb|EEP44983.1| hypothetical protein COLINT_02253 [Collinsella intestinalis DSM
           13280]
          Length = 261

 Score = 78.6 bits (192), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 68/269 (25%), Positives = 130/269 (48%), Gaps = 35/269 (13%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           +K++   L +R++E GD+ A  +LV SHL LV  IA  ++  G PI +++  G +GL++A
Sbjct: 12  DKEKTRELFRRFKEEGDMDAREKLVMSHLNLVRFIANKFKNRGEPIDDLIQVGYLGLLKA 71

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           + +FDP RG    T++   I   ++ +   + WS+          R+   L+ L   +  
Sbjct: 72  IDRFDPSRGLEFTTFATPTIMGEIKRHFRDKGWSV----------RVPRRLQELSAKVNQ 121

Query: 149 ITD---NNLKPEQVVA-IAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQD 202
            TD   + L+    +A IA  L+ +  EV+    +       SL A   + D ++    D
Sbjct: 122 ATDTLTSQLQRSPTIAEIADYLDATVDEVLEAMESSSAYSSVSLEAPSGADDDDTPSVID 181

Query: 203 -WLVYDHD---GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
            +   D D     ++++IE+            +++  +PRER + E R L+   +T   +
Sbjct: 182 RYATEDSDLAFTDDRIIIEE------------ALASFSPRERDVIEMRFLK--GMTQIEI 227

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           + +  +S+ +V ++  R  KK+Q+ I  +
Sbjct: 228 AEKLGISQVQVSRLLRRTLKKIQDKIDPE 256


>gi|325860122|ref|ZP_08173248.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           denticola CRIS 18C-A]
 gi|325482407|gb|EGC85414.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           denticola CRIS 18C-A]
          Length = 228

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 71/273 (26%), Positives = 115/273 (42%), Gaps = 47/273 (17%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           I   +YI EI     L   EE  LA+R +  GD  A  +L  ++L+ VV +A  YR  GL
Sbjct: 2   IANEKYIEEIAGGQPLSDVEERTLAERIKV-GDAHALEKLTKANLKYVVSLAHQYRNRGL 60

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++SEGNIG+M A ++FD  RG R   ++  +I+ AM+E I     L ++       
Sbjct: 61  GEDDLISEGNIGMMHAAQRFDGTRGVRFVVFAAPYIRKAMEEAIKEQAVLYRLP------ 114

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                 R  K   +    + +  +Q V +    N +   V+  +     DE LN  I S+
Sbjct: 115 ------RNEKNRSEQKRSHAISIDQPVPVGSSNNFTLQNVLENDNAPHADEQLNQEILSA 168

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA-RRLQENP 252
           +                                 + + + VLN RER++      L    
Sbjct: 169 E---------------------------------IQKGLGVLNERERQVITCLYGLSGIH 195

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            T+   +    + RERVRQI   A +K+ + ++
Sbjct: 196 YTMAEAAEHMGLKRERVRQIRDGALRKLHKRMK 228


>gi|206564209|ref|YP_002234972.1| putative RNA polymerase sigma-subunit [Burkholderia cenocepacia
           J2315]
 gi|198040249|emb|CAR56232.1| putative RNA polymerase sigma-subunit [Burkholderia cenocepacia
           J2315]
          Length = 628

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 68/242 (28%), Positives = 116/242 (47%), Gaps = 30/242 (12%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +L  S+LRLVV +A  Y   GLP ++++ EGNIGLM+AV ++D  RGF+ +TY+ WWI+ 
Sbjct: 394 KLFQSNLRLVVSVAKRYADRGLPFADLIQEGNIGLMKAVDRYDHRRGFKFSTYATWWIRQ 453

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL--NVS 169
           A+      + +L  +G T           R+  H     D+  K  ++  I ++   +V+
Sbjct: 454 AI------THALADLGRTI----------RVPAH---TVDSLNKLSRLARIHRQRTGDVA 494

Query: 170 ESEVISMNCRLAGDE--SLNALIN---SSDKNSSQWQDWLVYDH--DGQEQVLIEKEERK 222
           ++  +S   RL  D+   L +++    S+D   S   D  + D   D       E     
Sbjct: 495 DARALSPQMRLPVDKVRELMSIVREPISADLPVSPDHDLTLCDVTIDADAPTPEEAASAG 554

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             R  +   +  L  RE  I   R     +N  +L  +  +  +S ERVRQ+E  A +++
Sbjct: 555 QLRAAVAELIDSLPVREAWILRLRYGIDVDNEYSLREIGRQLNLSAERVRQLEVSALERI 614

Query: 281 QE 282
           ++
Sbjct: 615 RQ 616


>gi|87303408|ref|ZP_01086196.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
 gi|87282056|gb|EAQ74018.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
          Length = 330

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 57/235 (24%), Positives = 113/235 (48%), Gaps = 13/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+V ++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP RG++ +TY+ WW
Sbjct: 95  AKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWW 154

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   I      +++     +      L +LK   + ++    +   +  +A  + +
Sbjct: 155 IRQGITRAIAEKSRTIRLPIHITE-----TLNKLKKGQRELSQELGRTPTLSELAVCVEL 209

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E EV  + CR     SL   +   D   ++  D L  D     + +  +  R + R +L
Sbjct: 210 PEEEVKDLLCRARQPVSLETKVG--DGEDTELLDLLQGDGTLPAESVDSECLRGDMRALL 267

Query: 229 TRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +    L   +R +   R     + P++L +++    +SR++ R +E RA + ++
Sbjct: 268 EQ----LPELQRSVLSMRYGIDGDEPMSLTSIARTLGMSRDKTRNLERRALEGIR 318


>gi|299141532|ref|ZP_07034668.1| RNA polymerase sigma-70 factor [Prevotella oris C735]
 gi|298576868|gb|EFI48738.1| RNA polymerase sigma-70 factor [Prevotella oris C735]
          Length = 252

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 74/268 (27%), Positives = 126/268 (47%), Gaps = 50/268 (18%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGL 73
           L+ Y++EI K  +L   EE  L+++    G  +  A  +L +++LR VV IA  Y   G+
Sbjct: 18  LNIYLNEIGKETILSDDEEKQLSQQIMAGGAAAERAIGKLTSANLRFVVSIAKQYVDRGV 77

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            I +++SEGNIGLM+A + FD  RG R   Y+  +++ A++  +             N++
Sbjct: 78  AILDLISEGNIGLMKAARSFDGSRGLRFVGYAEPFVRKAVEAAV-------------NEQ 124

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
              F L                P+   +  +K N   S   S++  L   +++N L   S
Sbjct: 125 SGIFRL----------------PKHEHSAEEKAN---SRAFSVDAPLQNGKNVNLLSILS 165

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           D  +++       D +  E  +  KEE       L  +M++L+ RER + EA      P 
Sbjct: 166 DPTAARP------DQEALETSV--KEE-------LLEAMNILDNRERNVVEAFYGIGQPH 210

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKV 280
           +T   +  +  + RERVRQI  +A +K+
Sbjct: 211 LTFAEIGEKMGLKRERVRQIRNKAVRKL 238


>gi|281425346|ref|ZP_06256259.1| RNA polymerase sigma-43 factor [Prevotella oris F0302]
 gi|281400509|gb|EFB31340.1| RNA polymerase sigma-43 factor [Prevotella oris F0302]
          Length = 252

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 74/268 (27%), Positives = 126/268 (47%), Gaps = 50/268 (18%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGL 73
           L+ Y++EI K  +L   EE  L+++    G  +  A  +L +++LR VV IA  Y   G+
Sbjct: 18  LNIYLNEIGKETILSDDEEKQLSQQIMAGGAAAEQAIGKLTSANLRFVVSIAKQYVDRGV 77

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            I +++SEGNIGLM+A + FD  RG R   Y+  +++ A++  +             N++
Sbjct: 78  AILDLISEGNIGLMKAARSFDGSRGLRFVGYAEPFVRKAVEAAV-------------NEQ 124

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
              F L                P+   +  +K N   S   S++  L   +++N L   S
Sbjct: 125 SGIFRL----------------PKHEHSAEEKAN---SRAFSVDAPLQNGKNVNLLSILS 165

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           D  +++       D +  E  +  KEE       L  +M++L+ RER + EA      P 
Sbjct: 166 DPTAARP------DQEALETSV--KEE-------LLEAMNILDNRERNVVEAFYGIGQPH 210

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKV 280
           +T   +  +  + RERVRQI  +A +K+
Sbjct: 211 LTFAEIGEKMGLKRERVRQIRNKAVRKL 238


>gi|167579340|ref|ZP_02372214.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis TXDOH]
          Length = 482

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 64/242 (26%), Positives = 126/242 (52%), Gaps = 24/242 (9%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  R+  ++LRLV+ IA  Y   GL +++++ EGN+GL++A++KF+  RGF+ +TY+ W
Sbjct: 241 AATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEYRRGFKFSTYATW 300

Query: 108 WIKAAMQEYIL-RSWSL---VKIGTTANQKRLFFN-LRRLKGHLQAITDNNLKPEQVVAI 162
           WI+ A+   I  R+ ++   V +G  A + R   + + R  G   ++ +        ++ 
Sbjct: 301 WIRQAISRAIADRARTIRVPVHVGDEARRVRKVADRIERRSGARASLAE--------LSE 352

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A  L+      + M  R     SLNA +   D + +++ D +    D     L +   + 
Sbjct: 353 ATGLSAERLRAVLMLPREP--RSLNAPLG--DDDQAEFGDIV---EDASTPSLFDALAQG 405

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKK 279
              +++T  +  ++ +E  I   RR     + P + E ++++  VSRE++R+IE RA + 
Sbjct: 406 QMCDVVTSLLKTMSAQEADILR-RRFGIGGDEPWSYEQIAAQAGVSREQIRRIEKRALQT 464

Query: 280 VQ 281
           ++
Sbjct: 465 LR 466


>gi|83720670|ref|YP_440648.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis E264]
 gi|167617444|ref|ZP_02386075.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis Bt4]
 gi|83654495|gb|ABC38558.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis E264]
          Length = 483

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 64/242 (26%), Positives = 126/242 (52%), Gaps = 24/242 (9%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  R+  ++LRLV+ IA  Y   GL +++++ EGN+GL++A++KF+  RGF+ +TY+ W
Sbjct: 242 AATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEYRRGFKFSTYATW 301

Query: 108 WIKAAMQEYIL-RSWSL---VKIGTTANQKRLFFN-LRRLKGHLQAITDNNLKPEQVVAI 162
           WI+ A+   I  R+ ++   V +G  A + R   + + R  G   ++ +        ++ 
Sbjct: 302 WIRQAISRAIADRARTIRVPVHVGDEARRVRKVADRIERRSGARASLAE--------LSE 353

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A  L+      + M  R     SLNA +   D + +++ D +    D     L +   + 
Sbjct: 354 ATGLSAERLRAVLMLPREP--RSLNAPLG--DDDQAEFGDIV---EDASTPSLFDALAQG 406

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKK 279
              +++T  +  ++ +E  I   RR     + P + E ++++  VSRE++R+IE RA + 
Sbjct: 407 QMCDVVTSLLKTMSAQEADILR-RRFGIGGDEPWSYEQIAAQAGVSREQIRRIEKRALQT 465

Query: 280 VQ 281
           ++
Sbjct: 466 LR 467


>gi|12045103|ref|NP_072914.1| RNA polymerase sigma factor [Mycoplasma genitalium G37]
 gi|255660251|ref|ZP_05405660.1| RNA polymerase sigma factor [Mycoplasma genitalium G37]
 gi|1350862|sp|P47491|RPOD_MYCGE RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A
 gi|1045940|gb|AAC71469.1| RNA polymerase sigma factor RpoD [Mycoplasma genitalium G37]
 gi|166078711|gb|ABY79329.1| RNA polymerase sigma factor RpoD [synthetic Mycoplasma genitalium
           JCVI-1.0]
          Length = 497

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 78/246 (31%), Positives = 126/246 (51%), Gaps = 19/246 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A ++LVTS+LRLVV IA  +   GL  ++++ EGN+GL++A+ KF+   G + +TY+ WW
Sbjct: 246 AINQLVTSNLRLVVSIAKKHLERGLDFNDLIQEGNLGLLKAISKFNWSLGNKFSTYATWW 305

Query: 109 IKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKGHL-QAITDNNLKPEQVVAIA 163
           IK A+   I      V+I      T N  RL    R L   L +  TD  L  E++   A
Sbjct: 306 IKQAITRAIADQARTVRIPVHMVETIN--RLAKAERALYQELGREPTDEEL-AEKMGGQA 362

Query: 164 KKLNVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           +  NV +   I+   RL+ D  SL+  +   ++  SQ+ D+ V D D Q       E R 
Sbjct: 363 EGFNVKK---IAEIKRLSLDPVSLDKTVGHDEE--SQFGDF-VKDTDAQTPDEF-TESRS 415

Query: 223 NRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           N   +     + L+ +E  I   R        P TL+ +  +  + RE++RQIE +A +K
Sbjct: 416 NSEKIDELLNNNLSEQEELIVRMRIGMPPYNEPKTLDEVGQKILIPREKIRQIENKAIRK 475

Query: 280 VQESIQ 285
           ++ +++
Sbjct: 476 LRHAVR 481


>gi|161899381|ref|XP_001712917.1| sigma 2 transcription factor [Bigelowiella natans]
 gi|75756411|gb|ABA27305.1| sigma 2 transcription factor [Bigelowiella natans]
          Length = 389

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 60/238 (25%), Positives = 118/238 (49%), Gaps = 24/238 (10%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+   L+L++ IA  Y G GL   ++++EG +GLM+ ++K+D  +G + +TY+ WWI+ +
Sbjct: 154 LIKRSLKLIISIAKRYNGCGLSFEDLIAEGILGLMKGIRKYDFSKGHKFSTYAHWWIRQS 213

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI-------AKK 165
           +   I     ++++      K +   + ++K             E++  +        +K
Sbjct: 214 ISRSIDDQSRIIRLPVYV--KEILSKINKIKNKFYEDKKRYPTEEEISLLIGIPLKKLRK 271

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           L +S +++IS++  +  D + + ++N S ++S              E   IEK  +++  
Sbjct: 272 LLLSCNDLISLDSLIENDSNDSNMLNDSIEDSKVI---------NSEVYAIEKSLKQD-- 320

Query: 226 NMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             L +++  L+ RE  +   R   +  N  TLE +     V+RER RQIE +A KK+Q
Sbjct: 321 --LNKALLTLSDRESAVIRLRYGLDDGNERTLEEIGEYLNVTRERARQIEIKALKKLQ 376


>gi|209883307|ref|YP_002287164.1| RNA polymerase sigma factor RpoD [Oligotropha carboxidovorans OM5]
 gi|209871503|gb|ACI91299.1| RNA polymerase sigma factor RpoD [Oligotropha carboxidovorans OM5]
          Length = 387

 Score = 78.6 bits (192), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 69/245 (28%), Positives = 118/245 (48%), Gaps = 32/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYG-LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A  R V S+L  V K+A   R    L   ++  EG +GL++A + FDPE GFR  TY+ W
Sbjct: 146 AKARFVESNLLYVRKLANRKRNLKHLTADDLFQEGLMGLLKATELFDPELGFRFKTYATW 205

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQ---------KRLFFNLRRLKGHLQAITDNNLKPEQ 158
           WI+  M   +      +++    ++          +L F L R     +  T+  L+ E+
Sbjct: 206 WIQQYMSRALDDGDRTIRLPVHRHEYFRKIKRKTAKLTFELGREPTLNELATELGLERER 265

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           +  +  +L+V  +E +  +  +  D ++  L   +D++ S      + D    +Q+    
Sbjct: 266 LAKLLWRLHV--TECVEADAPIGEDTTV--LSYKADESPS------ILDLVALQQL---- 311

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARA 276
                 R M+ R ++ L PRE RI   R   +     TLE + + F V+RER+RQIEA+A
Sbjct: 312 ------RTMVARVLATLVPREERIIRMRFGLDGSGEQTLEAIGNVFGVTRERIRQIEAKA 365

Query: 277 FKKVQ 281
            +K++
Sbjct: 366 LRKLK 370


>gi|297837779|ref|XP_002886771.1| RNA polymerase sigma subunit 1 [Arabidopsis lyrata subsp. lyrata]
 gi|297332612|gb|EFH63030.1| RNA polymerase sigma subunit 1 [Arabidopsis lyrata subsp. lyrata]
          Length = 503

 Score = 78.2 bits (191), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 72/254 (28%), Positives = 125/254 (49%), Gaps = 34/254 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  S++RLV+ IA  Y   G  +S++V  G IGL++ ++KFD  +GFR++TY  WW
Sbjct: 260 AREKLAMSNVRLVMSIAQRYDNLGAEMSDLVQGGLIGLLRGIEKFDSSKGFRISTYVYWW 319

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   ++ +   +++ T  +++       +L+   + IT +      +  IA+ LN+
Sbjct: 320 IRQGVSRALVDNSRTLRLPTHLHERLGLIRNAKLRLQEKGITPS------IDRIAESLNM 373

Query: 169 SE------SEVISMNCRLAGDE--SLNALINSSD-----KNSSQWQDWLVYDHDGQEQVL 215
           S+      +E +S    L  D   SLN L   +       N  +   W  YD       L
Sbjct: 374 SQKKVRNATEAVSKIFSLDRDAFPSLNGLPGETHHSYIADNRVENNPWHGYDD------L 427

Query: 216 IEKEERKNRRNMLTRSMS-VLNPRERRIFEA-RRLQENPVTLENLSSEFEVSRERVRQIE 273
             KEE       +++ +S  L  RER I      L +  +T E++S    +SRERVRQ+ 
Sbjct: 428 ALKEE-------VSKLISATLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVG 480

Query: 274 ARAFKKVQESIQKQ 287
             A +K++ + +K+
Sbjct: 481 LVALEKLKHAARKR 494


>gi|50365086|ref|YP_053511.1| RNA polymerase sigma factor [Mesoplasma florum L1]
 gi|50363642|gb|AAT75627.1| RNA polymerase sigma factor [Mesoplasma florum L1]
          Length = 471

 Score = 78.2 bits (191), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 41/119 (34%), Positives = 67/119 (56%), Gaps = 13/119 (10%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAK--------RYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           +  Y   I +  +L K +E V AK          +E  D+     L+TS+L+LV+ +A  
Sbjct: 137 IKTYFSTIGQTKILTKDQEIVYAKLANSEDPEERKEGRDM-----LITSNLKLVISVARK 191

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           +   GL  ++++ EGNIGL++AV KFD E+GF+ +TY+ WWI+ A+   I      ++I
Sbjct: 192 HLNRGLDFADLIEEGNIGLIKAVDKFDYEKGFKFSTYATWWIRQAITRAIADQARTIRI 250


>gi|213162104|ref|ZP_03347814.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. E00-7866]
          Length = 225

 Score = 78.2 bits (191), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 63/235 (26%), Positives = 109/235 (46%), Gaps = 28/235 (11%)

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      
Sbjct: 2   IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 61

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV--------AIAKKLNVSESEVIS 175
           ++I    +       L R+   +         PE++          I K L +++ E IS
Sbjct: 62  IRI--PVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAK-EPIS 118

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
           M   +  DE             S   D++    D   ++ ++    ++ R      ++ L
Sbjct: 119 METPIGDDE------------DSHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGL 163

Query: 236 NPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
             RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   + +V
Sbjct: 164 TAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 218


>gi|172040574|ref|YP_001800288.1| RNA polymerase sigma factor SigB [Corynebacterium urealyticum DSM
           7109]
 gi|171851878|emb|CAQ04854.1| RNA polymerase sigma factor B [Corynebacterium urealyticum DSM
           7109]
          Length = 340

 Score = 78.2 bits (191), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 62/248 (25%), Positives = 116/248 (46%), Gaps = 32/248 (12%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD ++GF+ +TY+ W
Sbjct: 102 AARTHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYKKGFKFSTYATW 161

Query: 108 WIKAAMQEYILRSWSLVK--------IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           WI+ A+   +      ++        +   +  KR  +     +   + + + +  PE  
Sbjct: 162 WIRQAITRGMADQSRTIRLPVHLVEQVNKLSRIKREMYQHLGREATYEELAEESGIPEDR 221

Query: 160 VAIAKKLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           + +  K      + +S++  +  DE   L   I  S+   ++        H     VL  
Sbjct: 222 IEMLMK---QSRDPVSLDMPVGTDEEAPLGDFIEDSEAEDAEAAVVASLRHSDIRSVL-- 276

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
                          + L  RE+ +   R   ++  P TL+ +  +F +SRERVRQIE  
Sbjct: 277 ---------------ATLEQREQDVITLRYGLDDGLPRTLDQIGRQFGLSRERVRQIERE 321

Query: 276 AFKKVQES 283
              K++E 
Sbjct: 322 VMAKLREG 329


>gi|254432550|ref|ZP_05046253.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Cyanobium sp. PCC 7001]
 gi|197627003|gb|EDY39562.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Cyanobium sp. PCC 7001]
          Length = 319

 Score = 78.2 bits (191), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 59/229 (25%), Positives = 106/229 (46%), Gaps = 12/229 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+V ++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP RG++ +TY+ WW
Sbjct: 79  AKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWW 138

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   I      +++     +      L +LK   + ++    +   V  +A  + +
Sbjct: 139 IRQGITRAIAEKSRTIRLPIHITE-----TLNKLKKGQRELSQELGRTPTVTELAGYVEL 193

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E EV  + CR     SL   +   D   ++  D L  D +  E+  ++ E  K     L
Sbjct: 194 PEEEVKDLLCRARQPVSLETKVG--DGEDTELLDLLAGDGELPEE-RVDGECLKGDLRAL 250

Query: 229 TRSMSVLNPRERRIFEARRLQE----NPVTLENLSSEFEVSRERVRQIE 273
              +  L  R  ++      Q      P++L  +     +SR+RVR +E
Sbjct: 251 LEQLPELQGRVLKMRYGIDPQSAEMAEPMSLTGIGRILGISRDRVRNLE 299


>gi|4972297|dbj|BAA78111.1| RNA polymerase sigma subunit SigD* [Arabidopsis thaliana]
 gi|16649075|gb|AAL24389.1| sigma-like factor [Arabidopsis thaliana]
 gi|21387209|gb|AAM48008.1| sigma-like factor [Arabidopsis thaliana]
          Length = 267

 Score = 78.2 bits (191), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 34/78 (43%), Positives = 53/78 (67%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++   + RLVV IA GY+G GL + +++ EG+IGL++  ++FDP+RG++L+TY  WW
Sbjct: 179 AREKITRCYRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWW 238

Query: 109 IKAAMQEYILRSWSLVKI 126
           IK A+   I     LVK+
Sbjct: 239 IKQAILRAIAHKSRLVKL 256


>gi|255312697|gb|ACU01758.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score = 78.2 bits (191), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 33/61 (54%), Positives = 46/61 (75%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL +  ++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLNLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 L 118
           +
Sbjct: 61  M 61


>gi|57996876|emb|CAI45886.1| negative response regulator [Escherichia coli]
          Length = 191

 Score = 78.2 bits (191), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 33/61 (54%), Positives = 46/61 (75%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL +  ++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLNLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 L 118
           +
Sbjct: 61  M 61


>gi|22298374|ref|NP_681621.1| RNA polymerase sigma factor [Thermosynechococcus elongatus BP-1]
 gi|22294553|dbj|BAC08383.1| group 2 RNA polymerase sigma factor [Thermosynechococcus elongatus
           BP-1]
          Length = 309

 Score = 78.2 bits (191), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 64/247 (25%), Positives = 122/247 (49%), Gaps = 13/247 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +++ ++LRLVV +A  Y+   L + ++V EG +GL + V+KFDP RG++ +TY+ WW
Sbjct: 74  AKQKMIEANLRLVVSVAKKYQKRNLELLDLVQEGTLGLERGVEKFDPTRGYKFSTYAYWW 133

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I +    +++     +K     ++R +  L      +  P +V   AK L +
Sbjct: 134 IRQAITRAIAQQARTIRLPIHITEK--LNKIKRTQRELAQKLGRSATPAEV---AKALEL 188

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E E I     LA  + ++  +   D   ++  + L  D    EQ        ++ R+ +
Sbjct: 189 -EPEQIREYLTLA-RQPVSLDLRVGDNQDTELGELLEDDSLSPEQFTTV----ESLRDDV 242

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              ++ L P++R++   R        ++L  +  +  +SRERVRQ+E +A   ++   Q+
Sbjct: 243 NLWLAELTPQQRQVLTLRYGLGDGQELSLAKVGEQLNLSRERVRQLERQALDHLRRRRQQ 302

Query: 287 QVELSSS 293
             E  +S
Sbjct: 303 MYEYLAS 309


>gi|17231302|ref|NP_487850.1| RNA polymerase sigma factor SigD [Nostoc sp. PCC 7120]
 gi|8489797|gb|AAF75755.1|AF262216_2 group 2 sigma 70-type sigma factor D [Nostoc sp. PCC 7120]
 gi|17132944|dbj|BAB75509.1| group 2 sigma 70-type sigma factor D [Nostoc sp. PCC 7120]
          Length = 332

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 63/246 (25%), Positives = 115/246 (46%), Gaps = 31/246 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V ++LRLVV +A  Y    + + +++ EG+IG+ + V+KFDP +G+R +TY+ WW
Sbjct: 97  AKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGSIGMQRGVEKFDPTKGYRFSTYAYWW 156

Query: 109 IKAAMQEYILRSWSLVKIGTTAN---------QKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      +++              Q++L   L R     +   +  L P+QV
Sbjct: 157 IRQAITRAIAEKARTIRLPIHITEKLNKIKKAQRQLSQRLGRAPTAGELANELELTPKQV 216

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
               +K  +     +S++ RL GD     L    +   +  +D+++              
Sbjct: 217 REYLEKARLP----LSLDLRL-GDNYDTELGEMLEDPGASPEDFVM-------------- 257

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAF 277
            + +  N L   M  L P+++ +   R   +    +TL  +     +SRERVRQIE  A 
Sbjct: 258 -QSSLSNDLEVLMEQLTPQQKEVITLRFGLIDGQALTLARIGEILNISRERVRQIEREAL 316

Query: 278 KKVQES 283
            K+++S
Sbjct: 317 TKLRKS 322


>gi|55274894|gb|AAV49249.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 195

 Score = 78.2 bits (191), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 33/61 (54%), Positives = 46/61 (75%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL +  ++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 L 118
           +
Sbjct: 61  M 61


>gi|55274897|gb|AAV49250.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 198

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 33/61 (54%), Positives = 46/61 (75%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL +  ++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 L 118
           +
Sbjct: 61  M 61


>gi|75908113|ref|YP_322409.1| RNA polymerase sigma factor SigD [Anabaena variabilis ATCC 29413]
 gi|75701838|gb|ABA21514.1| Sigma 28 (Flagella/Sporulation) [Anabaena variabilis ATCC 29413]
          Length = 332

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 63/246 (25%), Positives = 115/246 (46%), Gaps = 31/246 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V ++LRLVV +A  Y    + + +++ EG+IG+ + V+KFDP +G+R +TY+ WW
Sbjct: 97  AKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGSIGMQRGVEKFDPTKGYRFSTYAYWW 156

Query: 109 IKAAMQEYILRSWSLVKIGTTAN---------QKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      +++              Q++L   L R     +   +  L P+QV
Sbjct: 157 IRQAITRAIAEKARTIRLPIHITEKLNKIKKAQRQLSQRLGRAPTAGELANELELTPKQV 216

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
               +K  +     +S++ RL GD     L    +   +  +D+++              
Sbjct: 217 REYLEKARLP----LSLDLRL-GDNYDTELGEMLEDPGASPEDFVM-------------- 257

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAF 277
            + +  N L   M  L P+++ +   R   +    +TL  +     +SRERVRQIE  A 
Sbjct: 258 -QSSLSNDLEVLMEQLTPQQKEVITLRFGLIDGQALTLARIGEILNISRERVRQIEREAL 316

Query: 278 KKVQES 283
            K+++S
Sbjct: 317 TKLRKS 322


>gi|57996878|emb|CAI45887.1| negative response regulator [Escherichia coli]
          Length = 191

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 33/61 (54%), Positives = 46/61 (75%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL + +++ EGN+GL +AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLNRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 L 118
           +
Sbjct: 61  M 61


>gi|85860024|ref|YP_462226.1| RNA polymerase sigma factor [Syntrophus aciditrophicus SB]
 gi|85723115|gb|ABC78058.1| RNA polymerase sigma factor [Syntrophus aciditrophicus SB]
          Length = 580

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 37/87 (42%), Positives = 55/87 (63%), Gaps = 3/87 (3%)

Query: 43  EHGDLSAAH---RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           EHG+  A     +LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG+
Sbjct: 337 EHGEKKAEEAKRKLVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGY 396

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKI 126
           + +TY+ WWI+ A+   I      ++I
Sbjct: 397 KFSTYATWWIRQAITRAIADQARTIRI 423


>gi|298248273|ref|ZP_06972078.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
            racemifer DSM 44963]
 gi|297550932|gb|EFH84798.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
            racemifer DSM 44963]
          Length = 1341

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 74/298 (24%), Positives = 140/298 (46%), Gaps = 49/298 (16%)

Query: 15   GLSRYIHEIRKIPMLEKQEEYVLAKRYR----------EHGDLS------------AAHR 52
             L +Y  EI + P+L  ++E  LA + +          + G+ S            A  +
Sbjct: 1048 SLRQYFREITQFPLLNAEQEKKLAHQIKFGQQAKEELEKRGEASSYIHVRIQQGKIAREK 1107

Query: 53   LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            L+  +LRLV+ +A  Y   G  + +++ EGN+GL++A +KFD ++G+R +TY+ WWI+ A
Sbjct: 1108 LIEHNLRLVISVAKKYARVGRQLEDLIQEGNLGLIRACEKFDTDKGYRFSTYATWWIRQA 1167

Query: 113  MQEYILRSWSLVKIGTTANQK--RLFFNLRRLKGHL-QAITDNNLKPEQVVAIAK--KLN 167
            +   +      +++     +K  +L    R L+  L +  T   L   Q + I K  +  
Sbjct: 1168 ITRSLAEQSRTIRLPVYLVEKLHQLHRGQRDLELQLGREPTLEELAKHQNLDIDKVQEYL 1227

Query: 168  VSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
            V   +++S++  +  ++  +L  +I                  D QE +          +
Sbjct: 1228 VLRQQILSLDAPIGAEQETTLGEMIEQPRS-------------DPQENI-----NNYADK 1269

Query: 226  NMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +++ M  L  R+RR+   R  L++  +  LE + S   V+RERVRQIE +A ++++
Sbjct: 1270 EAVSQLMQNLTERQRRVISLRFGLEDGKIHKLEEIGSMLNVTRERVRQIEEKALRQLK 1327


>gi|282858710|ref|ZP_06267864.1| sigma-70 region 2 [Prevotella bivia JCVIHMP010]
 gi|282588514|gb|EFB93665.1| sigma-70 region 2 [Prevotella bivia JCVIHMP010]
          Length = 228

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 72/269 (26%), Positives = 117/269 (43%), Gaps = 47/269 (17%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +YI  I    +L  +EE  LA R +  GD  A  +L  ++L  VV IA  Y+  GL  ++
Sbjct: 6   KYIENIIGETILTNEEERQLADRIKV-GDAKALEKLTKANLTFVVSIAHQYKEQGLDEND 64

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++SEGNIG+M A +KFD  +G R   ++  +I+ AM++ I    +L K+    N+K   F
Sbjct: 65  LISEGNIGMMYAAQKFDGTKGVRFVNFAASYIRKAMEDAIKEQTALYKV--PKNEKNR-F 121

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
             +R K          +  +Q V +    N +   VI               +N    N+
Sbjct: 122 EQKRAKA---------ISLDQPVPVGSNNNFTLQNVI---------------VNGDTANT 157

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF-EARRLQENPVTLE 256
                    D D    +L            L +SM  LN RE  +  +   L     T+ 
Sbjct: 158 ---------DDDVTTNML---------NTALKQSMKFLNERETAVITQLYGLDGVHFTMA 199

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            ++    + RER+RQI   A +K+  +++
Sbjct: 200 EVAETLGLKRERIRQIRNTALRKLHRNLK 228


>gi|325523156|gb|EGD01548.1| RpoD family RNA polymerase sigma factor [Burkholderia sp. TJI49]
          Length = 206

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 32/66 (48%), Positives = 49/66 (74%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +LV S+LRLVV IA  Y   GLP+ +++ EGNIGL++AV+++D  RGF+ +TY+ WWI+ 
Sbjct: 107 KLVKSNLRLVVSIAKRYPDRGLPLPDLIQEGNIGLLKAVERYDHRRGFKFSTYATWWIRQ 166

Query: 112 AMQEYI 117
           A+   +
Sbjct: 167 AITHAL 172


>gi|87303841|ref|ZP_01086550.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
 gi|87281651|gb|EAQ73647.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
          Length = 215

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 31/69 (44%), Positives = 51/69 (73%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R++ ++LRLVV +A  Y+G GL + +++ EG++GL +AV+KFDP RG++ +TY+ WW
Sbjct: 31  AKERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWW 90

Query: 109 IKAAMQEYI 117
           I+ +M   I
Sbjct: 91  IRQSMTRAI 99


>gi|240047243|ref|YP_002960631.1| RNA polymerase sigma factor [Mycoplasma conjunctivae HRC/581]
 gi|239984815|emb|CAT04802.1| RNA polymerase sigma factor [Mycoplasma conjunctivae]
          Length = 533

 Score = 77.8 bits (190), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 72/275 (26%), Positives = 137/275 (49%), Gaps = 39/275 (14%)

Query: 28  MLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +L  +EE  LA++    G +   A   L+  +LRLV+  A  Y+  GL   +++SEGN+G
Sbjct: 265 LLTYEEEQELARKMEIPGRVGRKARDTLIKRNLRLVINNAKRYKNRGLNFIDLISEGNLG 324

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-KRLFFNLR 140
           +M+A+ K+D  +GF+ +TY+ WWI+ ++   +     L++I      T N+  ++   L+
Sbjct: 325 IMKAISKYDRTKGFKFSTYATWWIRQSITRAVADQARLIRIPVHMVETINKINKIERELQ 384

Query: 141 RLKG------HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG--DESLNALINS 192
           +  G       +  +   +  PE+V  I +K+N+   + IS++  +    D S +  I  
Sbjct: 385 QKNGVTPSAEEIADVMGADFTPEKVRYI-RKINI---DPISLDKAIGKEEDSSFSDFI-- 438

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIE------KEERKNRRNMLTRSMSVLNPRERRIFEAR 246
             K+ S        + + + +VLIE      +EE    +  + R   + N +  R + A 
Sbjct: 439 --KDESVISPSDYAEQEEKSKVLIEMIKNNLEEE---EQEFIMRRYGIGNDKNGRQYRAH 493

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              E       L+++  V++ER+RQIE++  KK++
Sbjct: 494 SYDE-------LAADRGVTKERIRQIESKILKKLR 521


>gi|55274909|gb|AAV49256.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 193

 Score = 77.4 bits (189), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 33/63 (52%), Positives = 48/63 (76%)

Query: 56  SHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQE 115
           S+LRLVVKIA  Y   GL + +++ EGN+ L++AV+KFDPERGFR +TY+ WWI+  ++ 
Sbjct: 2   SNLRLVVKIARRYGNRGLALLDLIEEGNLVLIRAVEKFDPERGFRFSTYATWWIRQTIER 61

Query: 116 YIL 118
            I+
Sbjct: 62  AIM 64


>gi|40353299|gb|AAR84413.1| alternative primary sigma 70 factor [Frankia sp. ORS020607]
          Length = 220

 Score = 77.4 bits (189), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 49/161 (30%), Positives = 84/161 (52%), Gaps = 15/161 (9%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  +LV+++LRLVV +A  Y G G+ + ++V EGN+GL++AV+KFD  +G++ +TY+ W
Sbjct: 22  AAKQQLVSANLRLVVSVAKKYSGRGMTLLDLVQEGNLGLIRAVEKFDYAKGYKFSTYATW 81

Query: 108 WIKAAMQEYILRSWSLVKIGT---------TANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           WI+ A+   +      ++I           T  Q++L   L R     +   + ++  EQ
Sbjct: 82  WIRQAIGRALADQARTIRIPVHVVEQINKITRLQRQLVSTLGREPTDEELALELDMPIEQ 141

Query: 159 VVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNS 197
           VV    +L     + +S+   +   GD  L   I  SD  S
Sbjct: 142 VV----ELRRYAQDTVSLETSVGDDGDSVLGDFIEDSDATS 178


>gi|304373196|ref|YP_003856405.1| RNA polymerase sigma factor [Mycoplasma hyorhinis HUB-1]
 gi|304309387|gb|ADM21867.1| RNA polymerase sigma factor [Mycoplasma hyorhinis HUB-1]
          Length = 524

 Score = 77.4 bits (189), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 68/271 (25%), Positives = 130/271 (47%), Gaps = 31/271 (11%)

Query: 28  MLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +L  +EE  LAK+ +  G     A H L+  +LRLV+  A  Y+  GL   +++SEGN G
Sbjct: 256 LLTPEEENNLAKQIKNGGRAGKRARHTLINRNLRLVINNAKRYKNRGLTFIDLISEGNQG 315

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRR 141
           +++AV K+D  +G++ +TY+ WWI+ A+   +     +++I      T N+      + +
Sbjct: 316 ILKAVDKYDYTKGYKFSTYATWWIRQAITRAVADQARIIRIPVHMVETINK------INK 369

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           ++  LQ         EQ+        V   +  +   R     +++ +  S DK   + +
Sbjct: 370 IERELQQEYGVTPTDEQIAE------VMGGDFTAEKVRYTKKINIDPI--SLDKAIGKEE 421

Query: 202 DWLVYDHDGQEQVL--IEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPV---- 253
           D    D    E V+  I+  ER+ +  +L + +      + ++F  +R     +P     
Sbjct: 422 DSSFSDFIKDESVISPIDYSEREEKTKILKQMIENNLDNDEKVFIMKRYGFGTDPNGEQY 481

Query: 254 ---TLENLSSEFEVSRERVRQIEARAFKKVQ 281
              + + L+ E  V++ER+RQIE++  KK++
Sbjct: 482 RIHSFDELAKERGVTKERIRQIESKILKKLR 512


>gi|269114989|ref|YP_003302752.1| RNA polymerase sigma factor rpoD [Mycoplasma hominis]
 gi|268322614|emb|CAX37349.1| RNA polymerase sigma factor rpoD [Mycoplasma hominis ATCC 23114]
          Length = 538

 Score = 77.4 bits (189), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 74/276 (26%), Positives = 129/276 (46%), Gaps = 36/276 (13%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHR-------LVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           +L   EE  LAK+ +E  + +  ++       LV  +LRLV+  A  Y+  GL   +++S
Sbjct: 257 LLTTNEEQALAKKMQEAKEANNYYKYKKARDMLVKRNLRLVINNAKRYKNRGLNFIDLIS 316

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKRLF 136
           EGN G+M+AV K+D  +GF+ +TY+ WWI+ A+   +      V++      T N+    
Sbjct: 317 EGNAGIMKAVSKYDYTKGFKFSTYATWWIRQAITRAVADQARTVRVPVHMVETINK---- 372

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
             + +++  LQ     N  P     IAKK      +  +   R     +++ +  S DKN
Sbjct: 373 --ILKIERELQQ---ENGYPPTDEEIAKKYG---GDFTAEKVRYIRKINIDPI--SLDKN 422

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRR------NMLTRSMSVLNPRE--RRIFEARRL 248
             + ++    D    E V+       +         M+   +S    R+  R+ F    L
Sbjct: 423 IGKEENSSFSDFVKDESVISPTSYASHEELSVIINEMIEEGLSDQADRDLIRKRFGINDL 482

Query: 249 QEN---PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           + N   P TL+ LS E  +S+E+VRQ+E +  +K++
Sbjct: 483 KGNKYKPHTLDELSKELGISKEKVRQLETKVLRKLK 518


>gi|257067128|ref|YP_003153384.1| RNA polymerase, sigma 32 subunit, RpoH [Anaerococcus prevotii DSM
           20548]
 gi|256799008|gb|ACV29663.1| RNA polymerase, sigma 32 subunit, RpoH [Anaerococcus prevotii DSM
           20548]
          Length = 343

 Score = 77.4 bits (189), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 64/246 (26%), Positives = 123/246 (50%), Gaps = 19/246 (7%)

Query: 45  GDLSAAHRLVTSHLRLV-VKIAMGYRGYG--LPISEVVSEGNIGLMQAVKKFDPERGFRL 101
           G+ +A   LV  +  LV  + +  +R +G  L + ++V  G +G+++A +KFD   G++ 
Sbjct: 103 GNQNALAALVEKNQGLVRSRASYFFRSHGNDLDLEDLVQSGMLGMIRAAEKFDLSLGYKF 162

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
            TY+  WI  A+++ I +    ++I         +  L +LK  L+A  +     E++  
Sbjct: 163 TTYAYKWIDKAIRKAINKEGHTIRIPAGK-----YLKLNKLKQILKA--NPEASDEELYR 215

Query: 162 IAKKLNVSE---SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           I +K  + +    ++  +N       SLN  ++S D    +  D +  +    + +++E 
Sbjct: 216 ILEKEGIDKKQADDLFLINRNQVNSTSLNINLDSEDSTGDELMDMVGDESTPVDMLILE- 274

Query: 219 EERKNRRNMLTRSMSVLNPRERR--IFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
              K+  N L +++  L  RE++  IF      E P TLE +   +++SRER+RQIE +A
Sbjct: 275 ---KDMENFLLKALDQLTDREKQIIIFRYGLDNEKPKTLEEIGKIYDLSRERIRQIENQA 331

Query: 277 FKKVQE 282
             K++E
Sbjct: 332 LGKLKE 337


>gi|81300555|ref|YP_400763.1| group2 RNA polymerase sigma factor SigB [Synechococcus elongatus
           PCC 7942]
 gi|123556657|sp|Q31ME3|RPOD2_SYNE7 RecName: Full=RNA polymerase sigma factor rpoD2
 gi|81169436|gb|ABB57776.1| group2 RNA polymerase sigma factor SigB [Synechococcus elongatus
           PCC 7942]
          Length = 320

 Score = 77.4 bits (189), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 60/235 (25%), Positives = 120/235 (51%), Gaps = 21/235 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +++ ++LRLVV IA  Y+   +   +++ EG +GL + V+KFDP +G++ +TY+ WW
Sbjct: 85  AKRKMIEANLRLVVSIAKKYQKRHMEFLDLIQEGTLGLERGVEKFDPSKGYKFSTYAYWW 144

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I +    +++     +K     L +LK   + ++    +      +A+ L +
Sbjct: 145 IRQAITRAIAQQSRTIRLPIHITEK-----LNKLKKTQRELSQQLGRSATASELAEVLEL 199

Query: 169 SESEV---ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE-RKNR 224
              +V   I MN      + ++  +   D   ++ Q+ L+ D        +E+E  R++ 
Sbjct: 200 PLEQVREYIQMN-----RQPVSLDVKVGDSQDTELQE-LLEDEQSSPSDYVEQESLRRDL 253

Query: 225 RNMLTRSMSVLNPRERRIFEARR-LQE-NPVTLENLSSEFEVSRERVRQIEARAF 277
           RN+    M+ L P+++ +   R  L E + ++L  +     +SRERVR++E +A 
Sbjct: 254 RNL----MAELTPQQQAVIALRYGLDEGDSLSLAKVGERLNISRERVRKLERQAM 304


>gi|257886121|ref|ZP_05665774.1| RNA polymerase sigma-70 factor [Enterococcus faecium 1,231,501]
 gi|257821977|gb|EEV49107.1| RNA polymerase sigma-70 factor [Enterococcus faecium 1,231,501]
          Length = 383

 Score = 77.4 bits (189), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 68/256 (26%), Positives = 128/256 (50%), Gaps = 20/256 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPER 97
           Y+   D S+   LV ++ RLV+KIA  Y  Y    L I ++   G IGL++A  KFD  +
Sbjct: 121 YQRERDNSSLDALVKANRRLVLKIAQRYNKYLTSSLDIDDLEQFGMIGLLKAADKFDLSK 180

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
            +  +TY+ +WI+ ++   I+ +   V++     +K     L RL+  +      N    
Sbjct: 181 EYAFSTYATYWIRQSISRGIMDTSLTVRLPVHIFEK--INKLNRLEARMMT----NSSTT 234

Query: 158 QVVAIAKKLNVSES---EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            + +I K++++SE    +++++        SL+  I       +   D L  ++   E+V
Sbjct: 235 DISSILKEMDISEEQYYDLLAIRSTYLSLPSLDTPIGID--GDATIGDMLPDNNYDIEEV 292

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQI 272
           +    +    R  + +SM+ L  +ER +   R     E   TLE + + F V+RER+RQI
Sbjct: 293 I----DLGFLREDIKKSMTYLKEKEREVLYLRFGFDGEGRKTLEEIGNIFGVTRERIRQI 348

Query: 273 EARAFKKVQESIQKQV 288
           EA+A +K+++ + +++
Sbjct: 349 EAKAIRKMKKKVNREL 364


>gi|297811483|ref|XP_002873625.1| hypothetical protein ARALYDRAFT_909325 [Arabidopsis lyrata subsp.
           lyrata]
 gi|297319462|gb|EFH49884.1| hypothetical protein ARALYDRAFT_909325 [Arabidopsis lyrata subsp.
           lyrata]
          Length = 273

 Score = 77.4 bits (189), Expect = 2e-12,   Method: Compositional matrix adjust.
 Identities = 66/230 (28%), Positives = 115/230 (50%), Gaps = 40/230 (17%)

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y+G GL + +++ EG+IGL++  ++FDP+RG++L+TY  WWIK A    ILR+       
Sbjct: 52  YQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQA----ILRA------- 100

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA-----------IAKKLNVSESEVISM 176
             A++ RL     +L G +  +T    +   V+            IA+ LN+  S V   
Sbjct: 101 -IAHKSRLV----KLPGSMWELTAKVAEASNVLTRKLRRQPSCEEIAEHLNLHVSAV--- 152

Query: 177 NCRLAGDESLNALINSSDKNSSQ-----WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
             RLA + S + +  S D+  SQ      Q+ +    + + + ++++E  K+    L  S
Sbjct: 153 --RLAVERSRSPV--SLDRVVSQNGRMTLQEIVRGPDETRPEEMVKREHMKHEIEQLLGS 208

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    R   ++      E P++ E +    ++SRERVRQI   A KK++
Sbjct: 209 LTARESRVLGLYFGLN-GETPMSFEEIGKSLKLSRERVRQINGIALKKLR 257


>gi|254388870|ref|ZP_05004102.1| RNA polymerase principal sigma factor hrdD [Streptomyces
           clavuligerus ATCC 27064]
 gi|294813166|ref|ZP_06771809.1| RNA polymerase principal sigma factor hrdD [Streptomyces
           clavuligerus ATCC 27064]
 gi|326441537|ref|ZP_08216271.1| RNA polymerase principal sigma factor hrdD [Streptomyces
           clavuligerus ATCC 27064]
 gi|197702589|gb|EDY48401.1| RNA polymerase principal sigma factor hrdD [Streptomyces
           clavuligerus ATCC 27064]
 gi|294325765|gb|EFG07408.1| RNA polymerase principal sigma factor hrdD [Streptomyces
           clavuligerus ATCC 27064]
          Length = 333

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 72/299 (24%), Positives = 132/299 (44%), Gaps = 60/299 (20%)

Query: 19  YIHEIRKIPMLEKQEEY---------VLAKRYREHGDLS----AAHR------------- 52
           Y+ EI + P+L+  +E          V A++  + G  S    A H+             
Sbjct: 39  YLDEIARTPLLDAAKEVELSQIIEAGVYARQILDQGVESDAGGATHKELEALVAEGERAK 98

Query: 53  --LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
              + S+LRLVV +A  Y   GLP+ ++V EGN GL++AV+KFD  +GF+ +TY+ WWI+
Sbjct: 99  DVFIRSNLRLVVAVARRYPRSGLPLLDLVQEGNAGLVRAVEKFDYSKGFKFSTYATWWIR 158

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            A+   I      +++        L   L R++   +       +  +   IA++L  + 
Sbjct: 159 QAITRSIADQSRTIRLPV-----HLVEELGRIRRVQREFNREKGREPEAAEIAQELGSTP 213

Query: 171 SEV----------ISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
             V          +S+N  +  AG+     L+  +   S +     +   +G + ++ + 
Sbjct: 214 ERVTDVLDWARDPVSLNMAVDDAGETQFGDLLEDTSAVSPEQSVLTLLRSEGLDDLIGKL 273

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
           ++R    +++     +++ RER             TL  +  E  ++RER+RQIE  A 
Sbjct: 274 DQRTA--SIIRMRYGIMDGRER-------------TLTEVGKEHGLTRERIRQIEKHAL 317


>gi|2385506|dbj|BAA22190.1| RpoD2 protein [Synechococcus elongatus PCC 7942]
          Length = 320

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 60/235 (25%), Positives = 120/235 (51%), Gaps = 21/235 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +++ ++LRLVV IA  Y+   +   +++ EG +GL + V+KFDP +G++ +TY+ WW
Sbjct: 85  AKRKMIEANLRLVVSIAKKYQKRHMEFLDLIQEGTLGLERGVEKFDPSKGYKFSTYAYWW 144

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I +    +++     +K     L +LK   + ++    +      +A+ L +
Sbjct: 145 IRQAITRAIAQQSRTIRLPIHITEK-----LNKLKKTQRELSQQLGRSATASELAEVLEL 199

Query: 169 SESEV---ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE-RKNR 224
              +V   I MN      + ++  +   D   ++ Q+ L+ D        +E+E  R++ 
Sbjct: 200 PLEQVREYIQMN-----RQPVSLDVKVGDSQDTELQE-LLEDEQSSPSDYVEQESLRRDL 253

Query: 225 RNMLTRSMSVLNPRERRIFEARR-LQE-NPVTLENLSSEFEVSRERVRQIEARAF 277
           RN+    M+ L P+++ +   R  L E + ++L  +     +SRERVR++E +A 
Sbjct: 254 RNL----MAELTPQQQAVIALRYGLDEGDSLSLAKVGERLNISRERVRKLERQAM 304


>gi|307824191|ref|ZP_07654417.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacter tundripaludum
           SV96]
 gi|307734571|gb|EFO05422.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacter tundripaludum
           SV96]
          Length = 391

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 63/247 (25%), Positives = 124/247 (50%), Gaps = 12/247 (4%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            +++  ++RL   +A  ++   L   +++ EG +GL++AV +FDP RG++ +TY++ WIK
Sbjct: 150 QQMIAGNVRLAAFVAHKHKTTVLSFDDLLQEGVVGLIKAVDRFDPYRGYQFSTYAIPWIK 209

Query: 111 AAMQEYILRSWSLVKIGTT-ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
            A+   I++   +V++    A +    F   R   +LQ  T+     EQ+ ++    ++S
Sbjct: 210 QAISRLIVKQEKIVRLPVALAERACAVFEAMR-NAYLQ--TERWPSIEQLKSLC---DLS 263

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E E+ ++        SL+A+    D    + Q  +      Q  + +++   +N    L 
Sbjct: 264 EDEIKTIRNYYQATHSLDAV---GDAEEDEGQALMARMKQRQFALPLDELIDRNLGRYLD 320

Query: 230 RSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           + ++ L  +E  I   R   +N   +TL+ ++ + +VSRERVRQI+  A KK++      
Sbjct: 321 QVVATLPDKEAAILNMRFGLKNHTEMTLQAIADQLQVSRERVRQIQNDALKKLKNQFGYD 380

Query: 288 VELSSSP 294
           + L   P
Sbjct: 381 LMLFLEP 387


>gi|300781025|ref|ZP_07090879.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           genitalium ATCC 33030]
 gi|300532732|gb|EFK53793.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           genitalium ATCC 33030]
          Length = 330

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 66/260 (25%), Positives = 127/260 (48%), Gaps = 41/260 (15%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           +LAK+ R+    + AH L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD 
Sbjct: 85  ILAKQGRK----ARAH-LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDY 139

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            +GF+ +TY+ WWI+ A+   +      +++     ++     L R++  +         
Sbjct: 140 SKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLSRIRREMYQSLGREPS 197

Query: 156 PEQVVAIAKKLNVSESEV----------ISMNCRLAGDES--LNALINSSDKNSSQWQDW 203
            E+   +A++  + ES++          +S++  +  DE   L   I  ++   ++    
Sbjct: 198 NEE---LAEESGIDESKIEMLLRQSRDPVSLDMPVGADEEAPLGDFIEDAEAADAEDAVV 254

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSE 261
            V  HD    ++                 + L  RE+ +   R   ++  P TL+ +  +
Sbjct: 255 SVLRHDDIHDII-----------------NGLEQREQDVIRLRYGLDDGVPRTLDQIGRK 297

Query: 262 FEVSRERVRQIEARAFKKVQ 281
           F +SRERVRQIE     K++
Sbjct: 298 FGLSRERVRQIEREVMSKLR 317


>gi|254282580|ref|ZP_04957548.1| RNA polymerase principal sigma factor SigA [gamma proteobacterium
           NOR51-B]
 gi|219678783|gb|EED35132.1| RNA polymerase principal sigma factor SigA [gamma proteobacterium
           NOR51-B]
          Length = 429

 Score = 77.4 bits (189), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 69/232 (29%), Positives = 116/232 (50%), Gaps = 14/232 (6%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  +LRLV  IA  Y+G G+   ++V EG +GL++A +KF+ E+G+R +TY   WI  +
Sbjct: 192 LVMHNLRLVYSIAARYKGRGVNYLDLVQEGTLGLIRAAEKFEFEKGYRFSTYCFNWITQS 251

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           ++ Y+    SL++  T   ++     L R K    A T   ++P++   +AK L +   +
Sbjct: 252 VRRYVGDVGSLIRFPTHVQEQ--MGRLYREKALETART--GIEPDEET-LAKNLGMDLDK 306

Query: 173 VIS-MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
               +  R  G  SL+A     D +     D +  D  G  +   +  E+ +    LT +
Sbjct: 307 TRELLQLRNLG-VSLDA--PRFDDDEGTMVDSMTGDTFGDTE---DTAEQDSLNRFLTNA 360

Query: 232 MSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +  L P ER +  AR  L    P++   ++ +  VSRE VRQ+E    KK++
Sbjct: 361 IDTLEPAERDVVTARWGLHSGPPLSRAEIADKLGVSREWVRQLERSGLKKLR 412


>gi|256546106|ref|ZP_05473459.1| RNA polymerase sigma factor RpoD (sigma-A) [Anaerococcus vaginalis
           ATCC 51170]
 gi|256398223|gb|EEU11847.1| RNA polymerase sigma factor RpoD (sigma-A) [Anaerococcus vaginalis
           ATCC 51170]
          Length = 333

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 63/249 (25%), Positives = 127/249 (51%), Gaps = 21/249 (8%)

Query: 43  EHGDLSAAHRLVTSHLRLV-VKIAMGYRGYG--LPISEVVSEGNIGLMQAVKKFDPERGF 99
           + G+ +A   LV  +  LV  + +  YR +G  L + ++V  G +G+++A +KFD   G+
Sbjct: 92  QEGNQNALGALVDKNQGLVRSRASYFYRSHGNDLELEDLVQSGMLGMIRAAEKFDLTLGY 151

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           +  TY+  WI  A+++ I +    ++I         +  L +LK  L+A  +     E++
Sbjct: 152 KFTTYAYKWIDKAIRKAINKEGHTIRIPAGK-----YLKLNKLKQILKA--NPEASEEEL 204

Query: 160 VAIAKKLNVSE---SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
             I K+  + +    ++  +N       SLN  ++S D    +  D +     G + + +
Sbjct: 205 YKILKQEGIDKKQADDLFLINRNQVNSTSLNINLDSEDSTGDELMDMV-----GDDSIPV 259

Query: 217 EKE-ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIE 273
           + +  +K+  + L +++  L+ RE++I   R   +N  P TLE + + + +SRER+RQIE
Sbjct: 260 DDQILKKDMEDFLMKALDQLSDREKQIIIYRYGLDNEKPKTLEEIGTIYNLSRERIRQIE 319

Query: 274 ARAFKKVQE 282
            +A  K+++
Sbjct: 320 NQALGKLKQ 328


>gi|147865632|emb|CAN83254.1| hypothetical protein VITISV_036980 [Vitis vinifera]
          Length = 611

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 70/247 (28%), Positives = 123/247 (49%), Gaps = 42/247 (17%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ S   LV+ IA  YRG G+   +++  GN+G++Q  ++FD  +G+R +TY  +WI+ +
Sbjct: 377 LLRSTHSLVLYIARNYRGMGVAFEDILQAGNLGVLQGAERFDHTKGYRFSTYVQYWIRKS 436

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ----AITDNNLKPEQVVAIAKKLNV 168
           M   + R    VKI          F L R  G +Q    A+  ++ +      IAK   +
Sbjct: 437 MSTLVARHARGVKIP---------FTLNRAIGQIQKARKALYKSHGRYPDDNEIAKFTGL 487

Query: 169 SESEVISM-NC-RLAGDESLNALINSSDKNSSQWQD-W----LVYDHD----GQEQVLIE 217
           S +++ S  NC R+ G         S+D++   +QD W    L +  D      E+  ++
Sbjct: 488 SLAKIRSAGNCLRVVG---------STDQS---FQDCWGATILEFTPDTSIKSPEEGFMQ 535

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
           + +RK+  N+L      L+PRER+I   R    ++   +LE +   F VS+E +R++E  
Sbjct: 536 QCKRKDIHNLL----KGLDPRERQILVLRYGFGEQQRKSLEEIGRRFNVSKEWIRKLEKT 591

Query: 276 AFKKVQE 282
           A   +++
Sbjct: 592 ALANLRD 598


>gi|282900289|ref|ZP_06308240.1| sigE (Sigma 28 (Flagella/Sporulation)) [Cylindrospermopsis
           raciborskii CS-505]
 gi|281194794|gb|EFA69740.1| sigE (Sigma 28 (Flagella/Sporulation)) [Cylindrospermopsis
           raciborskii CS-505]
          Length = 327

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 64/241 (26%), Positives = 114/241 (47%), Gaps = 33/241 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +++ ++LRLVV IA  Y+   +   +++ EG +GL + V+KFDP  G++ +TY+ WW
Sbjct: 92  AKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTMGYKFSTYAYWW 151

Query: 109 IKAAMQEYILRSWSLVKIGTTAN---------QKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I +    +++              Q+ L   L R     +   +  L+P Q 
Sbjct: 152 IRQAITRAIAQQGRTIRLPIHITEKLNKIKKVQRELAQKLGRSPSPTEIAKELELEPAQ- 210

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD-GQEQVLIEK 218
             I + LN++  + IS++ R+             D   ++ Q+ L  DH    E    ++
Sbjct: 211 --IREYLNIA-RQPISLDVRVG------------DNQDTELQEML-EDHGLSPEHYTTQE 254

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARA 276
             R +  N+L      L P++R +   R   E  N ++L  +     +SRERVRQ+E +A
Sbjct: 255 FLRHDLNNLLAE----LTPQQREVVILRFGLEDGNEMSLAKVGDRLNISRERVRQLEHQA 310

Query: 277 F 277
            
Sbjct: 311 L 311


>gi|225429414|ref|XP_002275831.1| PREDICTED: hypothetical protein [Vitis vinifera]
 gi|296081598|emb|CBI20603.3| unnamed protein product [Vitis vinifera]
          Length = 561

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 70/247 (28%), Positives = 123/247 (49%), Gaps = 42/247 (17%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ S   LV+ IA  YRG G+   +++  GN+G++Q  ++FD  +G+R +TY  +WI+ +
Sbjct: 327 LLRSTHSLVLYIARNYRGMGVAFEDILQAGNLGVLQGAERFDHTKGYRFSTYVQYWIRKS 386

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ----AITDNNLKPEQVVAIAKKLNV 168
           M   + R    VKI          F L R  G +Q    A+  ++ +      IAK   +
Sbjct: 387 MSTLVARHARGVKIP---------FTLNRAIGQIQKARKALYKSHGRYPDDNEIAKFTGL 437

Query: 169 SESEVISMNCRLAGDESLNAL--INSSDKNSSQWQD-W----LVYDHD----GQEQVLIE 217
           S +++     R AG    N L  + S+D++   +QD W    L +  D      E+  ++
Sbjct: 438 SLAKI-----RSAG----NCLRVVGSTDQS---FQDCWGATILEFTPDTSIKSPEEGFMQ 485

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
           + +RK+  N+L      L+PRER+I   R    ++   +LE +   F VS+E +R++E  
Sbjct: 486 QCKRKDIHNLLKG----LDPRERQILVLRYGFGEQQRKSLEEIGRRFNVSKEWIRKLEKT 541

Query: 276 AFKKVQE 282
           A   +++
Sbjct: 542 ALANLRD 548


>gi|148909485|gb|ABR17840.1| unknown [Picea sitchensis]
          Length = 495

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 59/245 (24%), Positives = 123/245 (50%), Gaps = 26/245 (10%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +++  +LRLV+ +A  Y+  GL + +++  G++GLM++ +KFD  RGF+ +TY+ WWI+ 
Sbjct: 260 KIINCNLRLVISVAKNYQNRGLSLQDLIQAGSMGLMRSAEKFDYSRGFKFSTYAYWWIRQ 319

Query: 112 AMQEYILRSWSLVK--IGTTANQKRLFFNLRRL-KGHLQAITDNNLKPEQVVAIAKKLNV 168
           ++ + +      ++  +    +  R+    R L + H +  T   +     +++ +  +V
Sbjct: 320 SITKALTEQSRTIRLPVHIVESMTRIRTAWRLLYQEHKRDPTKEEVAEVAGISMTRLRHV 379

Query: 169 SE-SEVISMNCRLAG---DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +  S V +   R  G   DE  + ++  ++  S+              + ++ KE  K  
Sbjct: 380 TRCSRVPTSLDRCVGKDMDEKFSEIVADTNSEST--------------ETIVSKELFKKD 425

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              L R +  L  RE+++   R   ++    +L  +   F +SRERVRQIE +A +K+++
Sbjct: 426 ---LDRVLDTLTAREKQVVRLRYGLDDGRMKSLHEVGENFSLSRERVRQIEMKAMRKLRQ 482

Query: 283 SIQKQ 287
           + + Q
Sbjct: 483 NHRTQ 487


>gi|261880927|ref|ZP_06007354.1| RNA polymerase sigma factor rpoD [Prevotella bergensis DSM 17361]
 gi|270332314|gb|EFA43100.1| RNA polymerase sigma factor rpoD [Prevotella bergensis DSM 17361]
          Length = 243

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 69/266 (25%), Positives = 123/266 (46%), Gaps = 48/266 (18%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           ++RY+++I    +L  +EE  LA R  + GD  A   L +++L  V+ +A  Y   GL +
Sbjct: 10  INRYLNDIGHHNLLSNEEELQLADRI-QAGDSQAIEELTSANLTYVITLANQYVKRGLAL 68

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++SEGNIG++QA  KF  + G R   ++  +I+ AM++ I +   L ++   A     
Sbjct: 69  EDLISEGNIGMLQAATKFSRDAGKRFVAFAAPYIRDAMEQAIEQQAGLYRVPRNA----- 123

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
                          DNN           KL    S+ +S++  L G   L+      D+
Sbjct: 124 ---------------DNN-----------KLEKKRSKALSIDEPLCGSHELSLGHVIPDR 157

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA-RRLQENPVT 254
           N++      V D D ++ +L+ +         LT  ++ L+ RE+++  A   +     T
Sbjct: 158 NAT------VPDEDLEKDMLLGE---------LTELIADLDQREQQVIRALYGIGTEAKT 202

Query: 255 LENLSSEFEVSRERVRQIEARAFKKV 280
           +        + RERVRQI  +A +K+
Sbjct: 203 MLETGMAMGLKRERVRQIRNKAIRKI 228


>gi|167843756|ref|ZP_02469264.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei B7210]
 gi|254197157|ref|ZP_04903580.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei S13]
 gi|169653899|gb|EDS86592.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei S13]
          Length = 482

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 63/265 (23%), Positives = 130/265 (49%), Gaps = 18/265 (6%)

Query: 23  IRKIPMLEKQEEYVLAKRYREHGDL---SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           +R++P   K+ +   A+R    G+    +A  R+  ++LRLV+ IA  Y   GL +++++
Sbjct: 214 MRRLPTSPKKSD-AGAQRAFADGEARISAATARMAEANLRLVLSIARKYASRGLDLADLL 272

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EGN+GL++A++KF+  RGF+ +TY+ WWI+ A+   I      +++      +      
Sbjct: 273 QEGNLGLLRAIEKFEHRRGFKFSTYATWWIRQAISRAIADRARTIRVPVHVGDE-----A 327

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
           RR++     I   +     +  +++   +    + ++        SLNA +   D + ++
Sbjct: 328 RRVRKAADRIERRSGVSASLAELSEATGLPAERLRAVLTLPREPRSLNAPLG--DDDQAE 385

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLE 256
           + D +    D     L +        +++T  +  ++ +E  I   RR     + P + E
Sbjct: 386 FGDIV---EDTSTPSLFDALAHGQMCDVVTSLLKTMSAQEADILR-RRFGIGGDEPWSYE 441

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +++   VSRE+VR+IE RA + ++
Sbjct: 442 QIAARAGVSREQVRRIEKRALQTLR 466


>gi|139436946|ref|ZP_01771106.1| Hypothetical protein COLAER_00079 [Collinsella aerofaciens ATCC
           25986]
 gi|133776593|gb|EBA40413.1| Hypothetical protein COLAER_00079 [Collinsella aerofaciens ATCC
           25986]
          Length = 263

 Score = 77.0 bits (188), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 69/267 (25%), Positives = 127/267 (47%), Gaps = 35/267 (13%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           +K++   L +RY+E GD  A  +LV SH+ LV  +A  ++  G P+ +++  G +GL++A
Sbjct: 13  DKEKTRELFRRYKETGDPDAREQLVMSHMNLVRFLANKFKNRGEPLDDLMQVGYLGLLKA 72

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           + +FDPERG    T++   I   ++ +   + WS+          R+   L+ L   +  
Sbjct: 73  IDRFDPERGLEFTTFATPTILGEIKRHFRDKGWSV----------RVPRRLQELSAKVNQ 122

Query: 149 ITD---NNL-KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            TD   N L +  +V  IA+ L+V+  EV            L A+ +SS   S   +   
Sbjct: 123 ATDKLTNELQRSPKVEEIAEYLDVTVDEV------------LEAMESSSAYTSVPIEAPG 170

Query: 205 VYDHDGQEQVLIEKEERKNR------RNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
             D D    +L    +  N       R ++  ++   +PRER + E R ++   +T   +
Sbjct: 171 ASDSDDAPSILDRYADDDNELDFTDDRLVIEEAIRDFSPREREVIELRFVK--GMTQIEI 228

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQ 285
           + +  +S+ +V ++  R  KK+Q+ I 
Sbjct: 229 AKKLGISQVQVSRLLRRTLKKIQDKID 255


>gi|300865041|ref|ZP_07109868.1| RNA polymerase sigma factor [Oscillatoria sp. PCC 6506]
 gi|300336978|emb|CBN55018.1| RNA polymerase sigma factor [Oscillatoria sp. PCC 6506]
          Length = 334

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 56/236 (23%), Positives = 115/236 (48%), Gaps = 13/236 (5%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           H    A  +++ ++LRLVV IA  Y+   +   +++ EG +GL + V+KFDP RG++ +T
Sbjct: 94  HQGRRAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPMRGYKFST 153

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI+ A+   I +    +++     +K     +++++  L      +  P +   I 
Sbjct: 154 YAYWWIRQAITRAIAQHARTIRLPIHITEK--LNKIKKVQRELAQQLGRSPTPAE---IG 208

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
             L +  S++      L     ++  +   D   ++ Q+ L  +    +  +  +  R++
Sbjct: 209 SALELHPSQI--REYLLMARHPVSLDLRVGDNQDTELQELLEDESASPDDYITGELLRQD 266

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
             N+    M+ L P++R +   R   E+   ++L  +    ++SRERVRQ+E +A 
Sbjct: 267 LNNL----MAELTPQQRDVLSLRFGLEDGHEMSLAKVGERLKLSRERVRQLEHQAL 318


>gi|212695902|ref|ZP_03304030.1| hypothetical protein ANHYDRO_00435 [Anaerococcus hydrogenalis DSM
           7454]
 gi|212677025|gb|EEB36632.1| hypothetical protein ANHYDRO_00435 [Anaerococcus hydrogenalis DSM
           7454]
          Length = 333

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 63/249 (25%), Positives = 127/249 (51%), Gaps = 21/249 (8%)

Query: 43  EHGDLSAAHRLVTSHLRLV-VKIAMGYRGYG--LPISEVVSEGNIGLMQAVKKFDPERGF 99
           + G+ +A   LV  +  LV  + +  YR +G  L + ++V  G +G+++A +KFD   G+
Sbjct: 92  QEGNQNALGALVDKNQGLVRSRASYFYRSHGNDLELEDLVQSGMLGMIRAAEKFDLTLGY 151

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           +  TY+  WI  A+++ I +    ++I         +  L +LK  L+A  +     E++
Sbjct: 152 KFTTYAYKWIDKAIRKAINKEGHTIRIPAGK-----YLKLNKLKQILKA--NPEASEEEL 204

Query: 160 VAIAKKLNVSE---SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
             I K+  + +    ++  +N       SLN  ++S D    +  D +     G + + +
Sbjct: 205 YKILKQEGIDKKQADDLFLINRNQVNSTSLNINLDSEDSTGDELMDMV-----GDDSIPV 259

Query: 217 EKE-ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIE 273
           + +  +K+  + L +++  L+ RE++I   R   +N  P TLE + + + +SRER+RQIE
Sbjct: 260 DDQILKKDMEDFLMKALDQLSDREKQIIIYRYGLDNEKPKTLEEIGTIYSLSRERIRQIE 319

Query: 274 ARAFKKVQE 282
            +A  K+++
Sbjct: 320 NQALGKLKQ 328


>gi|325845925|ref|ZP_08169123.1| putative RNA polymerase sigma factor RpoD [Anaerococcus
           hydrogenalis ACS-025-V-Sch4]
 gi|325481831|gb|EGC84863.1| putative RNA polymerase sigma factor RpoD [Anaerococcus
           hydrogenalis ACS-025-V-Sch4]
          Length = 333

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 63/249 (25%), Positives = 127/249 (51%), Gaps = 21/249 (8%)

Query: 43  EHGDLSAAHRLVTSHLRLV-VKIAMGYRGYG--LPISEVVSEGNIGLMQAVKKFDPERGF 99
           + G+ +A   LV  +  LV  + +  YR +G  L + ++V  G +G+++A +KFD   G+
Sbjct: 92  QEGNQNALGALVDKNQGLVRSRASYFYRSHGNDLELEDLVQSGMLGMIRAAEKFDLTLGY 151

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           +  TY+  WI  A+++ I +    ++I         +  L +LK  L+A  +     E++
Sbjct: 152 KFTTYAYKWIDKAIRKAINKEGHTIRIPAGK-----YLKLNKLKQILKA--NPEASEEEL 204

Query: 160 VAIAKKLNVSE---SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
             I K+  + +    ++  +N       SLN  ++S D    +  D +     G + + +
Sbjct: 205 YKILKQEGIDKKQADDLFLINRNQVNSTSLNINLDSEDSTGDELMDMV-----GDDSIPV 259

Query: 217 EKE-ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIE 273
           + +  +K+  + L +++  L+ RE++I   R   +N  P TLE + + + +SRER+RQIE
Sbjct: 260 DDQILKKDMEDFLMKALDQLSDREKQIIIYRYGLDNEKPKTLEEIGTIYSLSRERIRQIE 319

Query: 274 ARAFKKVQE 282
            +A  K+++
Sbjct: 320 NQALGKLKQ 328


>gi|15558898|dbj|BAB64922.1| chloroplast RNA polymerase sigma factor [Chlamydomonas reinhardtii]
          Length = 250

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 71/247 (28%), Positives = 119/247 (48%), Gaps = 21/247 (8%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R R HG   A   L+ S+ +LV+ +   + G G  I ++VSEG  GL++ V+K+D  +GF
Sbjct: 1   RIRVHG---AKELLLKSNYKLVMTVCKSFVGKGPHIQDLVSEGVKGLLKGVEKYDATKGF 57

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           R  TY+ WWI+ A+   +  +   V++        +   L RLK +L A     L  E  
Sbjct: 58  RFGTYAHWWIRQAVSRSLAETGRAVRL-----PMHMIEQLTRLK-NLSAKLQTQLAREPT 111

Query: 160 ---VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
              +A A  L V+  +++    R A   SL+  I  ++   +  +D +  + +  ++   
Sbjct: 112 LPELAKAAGLPVTRVQMLMETARSAA--SLDTPIGGNELGPTV-KDSVEDEREAADEEFG 168

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEA 274
               R +   ML      L  RE R+   R   ++    TLE +     V+RER+RQIEA
Sbjct: 169 SDSLRNDMEAMLLE----LPEREARVVRLRFGLDDGKEWTLEEIGEALNVTRERIRQIEA 224

Query: 275 RAFKKVQ 281
           +A +K++
Sbjct: 225 KALRKLR 231


>gi|149198541|ref|ZP_01875585.1| RNA polymerase sigma factor RpoD [Lentisphaera araneosa HTCC2155]
 gi|149138256|gb|EDM26665.1| RNA polymerase sigma factor RpoD [Lentisphaera araneosa HTCC2155]
          Length = 282

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 67/269 (24%), Positives = 125/269 (46%), Gaps = 12/269 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+  +    +++   E  LA +  + GD SA   L  ++LRLVV IA  +   G+ 
Sbjct: 5   ALDNYLKNLSDYDLIDSDREIALANKIAK-GDESAIQELTLANLRLVVTIAKQFMNRGVA 63

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + E+++EGN GL++A ++F P  G + A+Y+ WWIK  ++  I     +V++   +    
Sbjct: 64  LGELIAEGNHGLVKAAQRFRPGHGAKFASYAAWWIKQNIRRAIRDDKRIVRVPVQS---- 119

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSS 193
               ++++K     I           A+AK++ +S   V + +  +     S+N  I+  
Sbjct: 120 -LLRMQKIKNARLKIQQETGDASNDKAVAKEVGISPRLVRTTSLHVDTSSFSINEQISQD 178

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENP 252
            K + + +  L+ D   Q    +  E     + ++      L  RE +I  AR  L +  
Sbjct: 179 GKATEKGE--LIPDSQAQTPGEV-MEFHDGYKTLMEIVRQELTEREYKILSARFGLDDGE 235

Query: 253 V-TLENLSSEFEVSRERVRQIEARAFKKV 280
             TL   S    ++ ERVRQ++  A +++
Sbjct: 236 AKTLAETSELVGLTSERVRQLQQEALRRL 264


>gi|255550882|ref|XP_002516489.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
 gi|223544309|gb|EEF45830.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
          Length = 560

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 68/241 (28%), Positives = 127/241 (52%), Gaps = 32/241 (13%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ S   LV+  A  YRG G+ + +++  GN+G+++  ++FD  RG+R +TY  +WI+ +
Sbjct: 326 LIKSTRSLVLYFARNYRGTGIALEDLLQAGNLGVLEGAERFDHTRGYRFSTYVQYWIRKS 385

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK--KLNVSE 170
           M + + R    ++I  T +  R  + +++ +   +A+T +N K      IAK   L++++
Sbjct: 386 MSKIVSRLARGIQIPCTLS--RAIYQIQKAR---KALTTSNGKYPDDDEIAKYTGLSLAK 440

Query: 171 SEVISMNCRLAGD------ESLNALINSSDKNSSQWQDWLVYDHDGQ--EQVLIEKEERK 222
            E  S   R+ G       ESLNA          ++ ++L  D   Q  E+V++ +   +
Sbjct: 441 IESASRCLRVVGSIDQKIGESLNA----------KYLEFLP-DTSVQSPEEVVMRQHMIQ 489

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
           +  N+L RS   L+ RER++   R    +  P +LE +   F VS+E VR++E R   ++
Sbjct: 490 DMHNLL-RS---LDSRERQVLILRFGLNDYQPKSLEEIGRHFHVSKEWVRRLEKRVMTRL 545

Query: 281 Q 281
           +
Sbjct: 546 R 546


>gi|2564653|gb|AAC45358.1| group 2 alternative sigma factor [Nostoc punctiforme PCC 73102]
          Length = 321

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 62/236 (26%), Positives = 112/236 (47%), Gaps = 31/236 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A H+++T++LRLVV IA  Y+   L + +++ EG +GL + V+KF+P  G+R  TY+ WW
Sbjct: 94  AKHKMITANLRLVVSIAKQYQRRNLELMDLIQEGTLGLERGVEKFNPALGYRKTTYAYWW 153

Query: 109 IKAAMQEYILRSWSLVKIGTTAN---------QKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+  +   I +    +++    N         Q+ L   L R+    +     +LKP Q+
Sbjct: 154 IRQGITRAIAQQGRAIRLPIHINEKLNKIKRVQRELSQTLGRIPTSTEIANALSLKPSQI 213

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
               ++  +  +  IS++ R++  + L            + QD L+ D+       I +E
Sbjct: 214 ----REFLLLATRTISLDIRVSSAKDL------------RLQD-LIEDYKYSSNSYITEE 256

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIE 273
                 N L   +S L+ +++ I            ++L+ +     +SRERVRQIE
Sbjct: 257 SLNQEVNSL---LSNLSRQQQEILNLHFGLTDGEELSLQQIGQRLGISRERVRQIE 309


>gi|148907004|gb|ABR16646.1| unknown [Picea sitchensis]
          Length = 592

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 57/245 (23%), Positives = 122/245 (49%), Gaps = 26/245 (10%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +++  +LRLV+ +A  Y+  GL + +++  G++GLM++ +KFD  RGF+ +TY+ WWI+ 
Sbjct: 357 KIINCNLRLVISVAKNYQNRGLSLQDLIQAGSMGLMRSAEKFDYSRGFKFSTYAYWWIRQ 416

Query: 112 AMQEYILRSWSLVK--IGTTANQKRLFFNLRRL-KGHLQAITDNNLKPEQVVAIAKKLNV 168
           ++ + +      ++  +    +  R+    R L + H +  T   +     +++ +  +V
Sbjct: 417 SITKALTEQSRTIRLPVHIVESMTRIRTAWRLLYQEHKRDPTKEEVAEVAGISMTRLRHV 476

Query: 169 SESEVISMNC-RLAG---DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +    +  +  R  G   DE  + ++  ++  S+              + ++ KE  K  
Sbjct: 477 TRCSRVPTSLDRCVGKDMDEKFSEIVADTNSEST--------------ETIVSKELFKKD 522

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              L R +  L  RE+++   R   ++    +L  +   F +SRERVRQIE +A +K+++
Sbjct: 523 ---LDRVLDTLTAREKQVVRLRYGLDDGRMKSLHEVGENFSLSRERVRQIEMKAMRKLRQ 579

Query: 283 SIQKQ 287
           + + Q
Sbjct: 580 NHRTQ 584


>gi|108803518|ref|YP_643455.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108764761|gb|ABG03643.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 274

 Score = 76.6 bits (187), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 71/251 (28%), Positives = 114/251 (45%), Gaps = 34/251 (13%)

Query: 45  GDLSAAHRLVTSHL-RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           GD  A  R++ SHL           R + +P  +++ EG + L+ AV  +DP RG R +T
Sbjct: 34  GDREARRRVIESHLGLAAALARRYARRWVVPFEDLLQEGALALVHAVDHYDPSRGMRFST 93

Query: 104 YSMWWIKAAMQEYIL----------RSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITDN 152
           Y+ WW+K A++   +          R+W L         +RL    R L+  L + I D 
Sbjct: 94  YATWWVKQAIRRAAMAYARPMRVPERTWRL--------SERLAEAERELRAELGREIEDR 145

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +L+          L  SE E+  +   +    SL + +   +++     D LV D + ++
Sbjct: 146 DLR--------SGLGWSEEELSEVRRAMGPVVSLESPVGEEEEDV--LGD-LVADENAED 194

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPVTLENLSSEFEVSRERVRQ 271
               E   R + R  L  ++S L  RER +   R  L   P T  +L  E  VSRER RQ
Sbjct: 195 PA--ELAARNDARRRLAHALSALPRRERAVLAGRYGLTGEPRTFVDLGRELGVSRERARQ 252

Query: 272 IEARAFKKVQE 282
           +E  A ++++E
Sbjct: 253 LERAAAERLRE 263


>gi|330723944|gb|AEC46314.1| RNA polymerase sigma factor [Mycoplasma hyorhinis MCLD]
          Length = 524

 Score = 76.3 bits (186), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 70/288 (24%), Positives = 136/288 (47%), Gaps = 55/288 (19%)

Query: 28  MLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +L  +EE  LAK+ +  G     A H L+  +LRLV+  A  Y+  GL   +++SEGN G
Sbjct: 256 LLTPEEENNLAKQIKNGGRAGKRARHTLINRNLRLVINNAKRYKNRGLTFIDLISEGNQG 315

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRR 141
           +++AV K+D  +G++ +TY+ WWI+ A+   +     +++I      T N+      + +
Sbjct: 316 ILKAVDKYDYTKGYKFSTYATWWIRQAITRAVADQARIIRIPVHMVETINK------INK 369

Query: 142 LKGHLQAITDNNLKPEQVVAI------------AKKLNVSESEVISMNCRLAGDESLNAL 189
           ++  LQ         EQ+  +             KK+N+   + IS++  +  +E     
Sbjct: 370 IERELQQEYGVTPTDEQIAEVMGGDFTAEKVRYTKKINI---DPISLDKAIGKEE----- 421

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVL--IEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
                   S + D++       E V+  I+  ER+ +  +L + +      + ++F  +R
Sbjct: 422 -------YSSFSDFI-----KDESVISPIDYSEREEKTKILKQMIENNLDNDEKVFIMKR 469

Query: 248 --LQENPV-------TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                +P        + + L+ E  V++ER+RQIE++  KK++   +K
Sbjct: 470 YGFGTDPNGEQYRIHSFDELAKERGVTKERIRQIESKILKKLRHPQKK 517


>gi|71894468|ref|YP_278576.1| RNA polymerase sigma factor [Mycoplasma synoviae 53]
          Length = 490

 Score = 76.3 bits (186), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 80/287 (27%), Positives = 134/287 (46%), Gaps = 55/287 (19%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHR--LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +L  QEE  LA+   + G      R  ++  +LRLVV  A  Y+  GL   ++VSEGN G
Sbjct: 207 LLTPQEEKDLAEEMDKGGSRGKRARDLIIKRNLRLVVNAAKKYKNRGLSFIDLVSEGNAG 266

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A +KFD ++GF+ +TY+ WWI+ ++   +            A+Q R+     R+  H
Sbjct: 267 LLKAAQKFDIKKGFKFSTYATWWIRQSISRAV------------ADQARII----RVPVH 310

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-----DES-------LNALINSS 193
           +    +   K E+ +       + + E+     RL G     D S       +N    S 
Sbjct: 311 MVETINKIYKIEREIQQENGGEIIDEEIA---ARLGGKSKKYDASYIRYIRKINTSPISL 367

Query: 194 DKNSSQWQDWLVYDHDGQEQVL-----IEKEERKNRRN-----MLTRSMSVLNPRERRI- 242
           DK   +  D    D    E ++      +KEE   + N     +L+ + + L  R   I 
Sbjct: 368 DKQVGKENDSFFGDFVKDESIISPVEFADKEELITKINYYVEKLLSEAEADLIKRYHGIG 427

Query: 243 FEARRLQENPV---TLENLSSEF-----EVSRERVRQIEARAFKKVQ 281
           ++A+    NPV   TL+ +S +F     ++S+ERVRQI  + +KK++
Sbjct: 428 YDAKG---NPVRSATLDEISKDFRGEGKKISKERVRQIITKIYKKLR 471


>gi|302765387|ref|XP_002966114.1| hypothetical protein SELMODRAFT_266972 [Selaginella moellendorffii]
 gi|300165534|gb|EFJ32141.1| hypothetical protein SELMODRAFT_266972 [Selaginella moellendorffii]
          Length = 249

 Score = 76.3 bits (186), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 67/250 (26%), Positives = 110/250 (44%), Gaps = 43/250 (17%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ S+LRLVV IA  Y   G+ I +++ EG +GL+  ++KFD  RGF+ +TY+ WWI  A
Sbjct: 1   MILSNLRLVVAIARRYENMGVEIGDLIQEGTLGLIHGLEKFDVSRGFKFSTYAYWWIFQA 60

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL--QAITDNNLKPEQVVAIAK------ 164
           M        SL K G             R    L  + + D  +  E ++ + K      
Sbjct: 61  MIR------SLDKRGKCVRYPFHLCEAIRKINQLRNRQVDDRPVSVETMMQVLKLPRARI 114

Query: 165 ---------KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
                    +L   +  V +  C   GD   + +++ + +N    Q WL+ + D  ++ L
Sbjct: 115 EIALQASNYRLTSLDRHVANKRCFEEGDPLEDFIVDQNVEN----QPWLMAERDAVKEEL 170

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRL----QENPVTLENLSSEFEVSRERVRQ 271
               E K            L+ RER +   R      Q +P++   +     +SRERVRQ
Sbjct: 171 DRLLESK------------LDAREREVIRKRFGLHPNQTSPLSRHEIGRSCGISRERVRQ 218

Query: 272 IEARAFKKVQ 281
           +E  A  K++
Sbjct: 219 LENDAMAKLR 228


>gi|260589293|ref|ZP_05855206.1| RNA polymerase sigma-F factor [Blautia hansenii DSM 20583]
 gi|331082700|ref|ZP_08331823.1| hypothetical protein HMPREF0992_00747 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|260540374|gb|EEX20943.1| RNA polymerase sigma-F factor [Blautia hansenii DSM 20583]
 gi|330400319|gb|EGG79961.1| hypothetical protein HMPREF0992_00747 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 237

 Score = 76.3 bits (186), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 74/254 (29%), Positives = 122/254 (48%), Gaps = 25/254 (9%)

Query: 36  VLAKRYREH-GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           +LA   R H GD SA   L   ++ LV  IA  ++  G  + ++V  G IGL++A+ KFD
Sbjct: 4   ILALIGRAHQGDKSARDILTEKNMGLVHSIARRFQNRGAELEDLVQIGCIGLLKAIDKFD 63

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
                R +TY++  I   ++ + LR   +VK+  +         L+   G   A+ +  L
Sbjct: 64  LSYEVRFSTYAVPMITGEIKRF-LRDDGMVKVSRS---------LKEAAGKAYAVREELL 113

Query: 155 ----KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
               +   +  IAK+L+VSE E+I      A  ESL   I  SD +    +D L Y+ D 
Sbjct: 114 MKTGQEPSMEEIAKELSVSEEELIMAMESSAQVESLQKTIYQSDGSDIALEDKLPYEKDE 173

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
           QE+VL         + +L   +  LN RER +   R  +E   T  +++    +S+ +V 
Sbjct: 174 QEEVL--------DKLLLEDILGSLNARERELIYLRFFKEKTQT--SIAKMMGMSQVQVS 223

Query: 271 QIEARAFKKVQESI 284
           ++E +  K ++E I
Sbjct: 224 RLEKKILKALRERI 237


>gi|119503379|ref|ZP_01625463.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2080]
 gi|119461025|gb|EAW42116.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2080]
          Length = 430

 Score = 76.3 bits (186), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 69/243 (28%), Positives = 124/243 (51%), Gaps = 18/243 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +LV  +LRLV  IA  Y+G G+   ++V EG +GL++A +KF+ E+GFR +TY   W
Sbjct: 188 ARDKLVMHNLRLVYSIAGRYKGRGVSYLDLVQEGTLGLIRAAEKFEFEKGFRFSTYCFNW 247

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I  A++ Y+    +L+++ T   ++     L + K   Q  T   ++P++   +A KL +
Sbjct: 248 ITQAVRRYVGDVGTLIRLPTHVQEQ--MGRLYKEKAIEQLRT--GVEPDEET-LAAKLGM 302

Query: 169 SESEVISMNCRLAGDESLNALINSS--DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
                I    +L    +L   +++   D +     D L  +  G  +   +  E+ +   
Sbjct: 303 D----IEKTRQLLQMRNLGVSLDAPRFDDDEGTLLDTLSGEPYGGTE---DSAEQASLHK 355

Query: 227 MLTRSMSVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKV--QE 282
            L  ++  L P E+R+  AR  L +  P++   ++    VSRE VRQ+E  A +K+  Q+
Sbjct: 356 FLGGAVDALEPSEQRVVVARWGLHDGPPLSRAEVADSLGVSREWVRQLERSALRKLKAQD 415

Query: 283 SIQ 285
           S++
Sbjct: 416 SVK 418


>gi|255312661|gb|ACU01740.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score = 76.3 bits (186), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 32/61 (52%), Positives = 46/61 (75%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           L LVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LLLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 L 118
           +
Sbjct: 61  M 61


>gi|46241495|gb|AAS82950.1| chloroplast RPOD [Chlamydomonas reinhardtii]
          Length = 311

 Score = 76.3 bits (186), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 69/247 (27%), Positives = 118/247 (47%), Gaps = 18/247 (7%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           + R    L A   L+ S+ +LV+ +   + G G  I ++VSEG  GL++ V+K+D  +GF
Sbjct: 40  KLRYDAGLKAKELLLKSNYKLVMTVCKSFVGKGPHIQDLVSEGVKGLLKGVEKYDATKGF 99

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           R  TY+ WWI+ A+   +  +   V++        +   L RLK +L A     L  E  
Sbjct: 100 RFGTYAHWWIRQAVSRSLAETGRAVRL-----PMHMIEQLTRLK-NLSAKLQTQLAREPT 153

Query: 160 ---VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
              +A A  L V+  +++    R A   SL+  I  ++   +  +D +  + +  ++   
Sbjct: 154 LPELAKAAGLPVTRVQMLMETARSAA--SLDTPIGGNELGPT-VKDSVEDEREAADEEFG 210

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEA 274
               R +   ML      L  RE R+   R   ++    TLE +     V+RER+RQIEA
Sbjct: 211 SDSLRNDMEAMLLE----LPEREARVVRLRFGLDDGKEWTLEEIGEALNVTRERIRQIEA 266

Query: 275 RAFKKVQ 281
           +A +K++
Sbjct: 267 KALRKLR 273


>gi|293363636|ref|ZP_06610388.1| putative RNA polymerase sigma factor RpoD [Mycoplasma alligatoris
           A21JP2]
 gi|292552792|gb|EFF41550.1| putative RNA polymerase sigma factor RpoD [Mycoplasma alligatoris
           A21JP2]
          Length = 492

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 76/287 (26%), Positives = 141/287 (49%), Gaps = 58/287 (20%)

Query: 28  MLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +L+  +E  LAK+  + G     A  +L+  +LRLV+  A  Y+  GL   +++SEGN G
Sbjct: 220 LLKPDQEKQLAKQMEKGGFRGKRARDKLIMRNLRLVINNAKKYKNRGLTFIDLISEGNAG 279

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-KRLFFNLR 140
           +++AV+K++ E+GF+ +TY+ WWI+ A+   +      +++      T N+  ++   L+
Sbjct: 280 ILKAVQKYNVEKGFKFSTYATWWIRQAITRAVADQARTIRVPVHMVETINKITKIERELQ 339

Query: 141 RLKGHLQAITDN-------NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
           +  GH    TD+       N   E+ V   +K+NV   + IS++ ++             
Sbjct: 340 QELGH--EPTDSQIANRFGNDYTEEKVRYIRKINV---DPISLDKQIGK----------- 383

Query: 194 DKNSSQWQDWL-------VYDHDGQEQV------LIEKEERKNRRNMLTRSMSV---LNP 237
            +N S + D++         D+  QEQ+      LI+K   K+ R ++ +   V    N 
Sbjct: 384 -ENDSSFSDFVKDDNILNPVDYASQEQLSELLIDLIDKSLEKDERELICKRYGVGVDSNG 442

Query: 238 RERRIFEARRLQENPVTLENLSSE-FEVSRERVRQIEARAFKKVQES 283
            + R+           +L+ L+ E   VS+ER+RQIE +  +K++ S
Sbjct: 443 EKYRVH----------SLDELARERGGVSKERIRQIENKILRKLKNS 479


>gi|255312639|gb|ACU01729.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312641|gb|ACU01730.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312643|gb|ACU01731.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312645|gb|ACU01732.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 32/61 (52%), Positives = 46/61 (75%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           L LVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LGLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 L 118
           +
Sbjct: 61  M 61


>gi|255312647|gb|ACU01733.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312653|gb|ACU01736.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 32/61 (52%), Positives = 46/61 (75%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           L LVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LLLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 L 118
           +
Sbjct: 61  M 61


>gi|134291946|ref|YP_001115715.1| RpoD family RNA polymerase sigma factor [Burkholderia vietnamiensis
           G4]
 gi|134135135|gb|ABO59460.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           vietnamiensis G4]
          Length = 628

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 61/240 (25%), Positives = 111/240 (46%), Gaps = 26/240 (10%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L  ++LRLVV IA  Y   GLP ++++ EGNIGL++A+ ++D  RGFR +TY+ WWI+ A
Sbjct: 395 LFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWWIRQA 454

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRL-KGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           +   +      +++ T  +       L R+ + H Q         E  V + + L+    
Sbjct: 455 ITHALADLGRTIRVPT--HTVDAINKLTRIAREHRQRSGAAATPHELAVQMGEPLDKVRD 512

Query: 172 ------EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
                 E +S +  ++ +  +  +  + D ++   +D       G  Q+          R
Sbjct: 513 LMSIVKEPMSADAPVSPEGEMTFVDVAPDVSTPSPEDAA-----GAAQL----------R 557

Query: 226 NMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           + +   +  L  RE  +   R     +   +L ++  +  +S ERVRQIEA A  +++ S
Sbjct: 558 DTIAAMIGRLPAREATVLRLRYGLHADEGCSLRDIGRQLNLSAERVRQIEASALARLRAS 617


>gi|159470255|ref|XP_001693275.1| chloroplast RNA polymerase sigma factor, c [Chlamydomonas
           reinhardtii]
 gi|42742499|gb|AAM88387.2|AF525691_1 RNA polymerase sigma factor [Chlamydomonas reinhardtii]
 gi|47076042|emb|CAF25319.1| sigma-like transcription factor [Chlamydomonas reinhardtii]
 gi|158277533|gb|EDP03301.1| chloroplast RNA polymerase sigma factor, c [Chlamydomonas
           reinhardtii]
          Length = 752

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 69/247 (27%), Positives = 118/247 (47%), Gaps = 18/247 (7%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           + R    L A   L+ S+ +LV+ +   + G G  I ++VSEG  GL++ V+K+D  +GF
Sbjct: 481 KLRYDAGLKAKELLLKSNYKLVMTVCKSFVGKGPHIQDLVSEGVKGLLKGVEKYDATKGF 540

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           R  TY+ WWI+ A+   +  +   V++        +   L RLK +L A     L  E  
Sbjct: 541 RFGTYAHWWIRQAVSRSLAETGRAVRL-----PMHMIEQLTRLK-NLSAKLQTQLAREPT 594

Query: 160 ---VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
              +A A  L V+  +++    R A   SL+  I  ++   +  +D +  + +  ++   
Sbjct: 595 LPELAKAAGLPVTRVQMLMETARSAA--SLDTPIGGNELGPT-VKDSVEDEREAADEEFG 651

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEA 274
               R +   ML      L  RE R+   R   ++    TLE +     V+RER+RQIEA
Sbjct: 652 SDSLRNDMEAMLLE----LPEREARVVRLRFGLDDGKEWTLEEIGEALNVTRERIRQIEA 707

Query: 275 RAFKKVQ 281
           +A +K++
Sbjct: 708 KALRKLR 714


>gi|6682869|dbj|BAA88921.1| sigma factor [Nicotiana tabacum]
          Length = 508

 Score = 76.3 bits (186), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 71/258 (27%), Positives = 124/258 (48%), Gaps = 42/258 (16%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  RL  S++RLV+ IA  Y   G  ++++V  G IGL++ ++KFDP +G++++TY  WW
Sbjct: 265 ARERLAMSNVRLVMSIAQRYDNVGAEMADLVQGGLIGLLRGIEKFDPSKGYKISTYVYWW 324

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   ++ +   +++ T  ++ RL   +R  K  L+   +  + P  V  IA  LN+
Sbjct: 325 IRQGVSRALVENSRTLRLPTYLHE-RLSL-IRNAKARLE---EKGITP-SVNNIAASLNM 378

Query: 169 SESEV------------------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
           S+ +V                   S+N  L G E+L++ I  +   ++ W    V+    
Sbjct: 379 SQKKVRNATEASSKMYSLDREAFPSLN-GLPG-ETLHSYIADNHLENNPWHGVDVWALKD 436

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPVTLENLSSEFEVSRERV 269
           +   LI                S L  RER I      L    +T E++S    +SRERV
Sbjct: 437 EVNNLIS---------------STLRDREREIIRLYYGLDNECLTWEDISKRIGLSRERV 481

Query: 270 RQIEARAFKKVQESIQKQ 287
           RQ+   A +K++ + +K+
Sbjct: 482 RQVGLVALEKLKHAARKR 499


>gi|167822153|ref|ZP_02453624.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 9]
          Length = 299

 Score = 75.9 bits (185), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 57/237 (24%), Positives = 117/237 (49%), Gaps = 14/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  R+  ++LRLV+ IA  Y   GL +++++ EGN+GL++A++KF+  RGF+ +TY+ W
Sbjct: 58  AATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKFSTYATW 117

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++      +      RR++     I   +     +  +++   
Sbjct: 118 WIRQAISRAIADRARTIRVPVHVGDE-----ARRVRKAADRIERRSGVSASLAELSEATG 172

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +    + ++        SLNA +   D + +++ D +    D     L +        ++
Sbjct: 173 LPAERLRAVLTLPREPRSLNAPLG--DDDQAEFGDIV---EDTSTPSLFDALAHGQMCDV 227

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +T  +  ++ +E  I   RR     + P + E +++   VSRE+VR+IE RA + ++
Sbjct: 228 VTSLLKTMSAQEADILR-RRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLR 283


>gi|13508091|ref|NP_110040.1| RNA polymerase sigma factor [Mycoplasma pneumoniae M129]
 gi|2500786|sp|P78022|RPOD_MYCPN RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A
 gi|1674175|gb|AAB96132.1| Sigma-70 Factor Family [Mycoplasma pneumoniae M129]
 gi|301633308|gb|ADK86862.1| RNA polymerase sigma factor RpoD [Mycoplasma pneumoniae FH]
          Length = 499

 Score = 75.9 bits (185), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 70/247 (28%), Positives = 127/247 (51%), Gaps = 21/247 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A ++LVTS+LRLVV IA  +   GL  ++++ EGN+GL++A+ KF+   G + +TY+ WW
Sbjct: 248 AINQLVTSNLRLVVSIAKKHLERGLDFNDLIQEGNLGLLKAISKFNWSLGNKFSTYATWW 307

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           IK A+   I      V+I        +   + RL    +A+     +      +A+K+  
Sbjct: 308 IKQAITRAIADQARTVRIPV-----HMVETINRLAKAERALNQELGREPTAEELAEKMG- 361

Query: 169 SESEVISMN-----CRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
            ++E  ++       RL+ D  SL+  +   ++  SQ+ D+ V D D Q       E R 
Sbjct: 362 GQAEGFTVKKIAEIKRLSLDPVSLDKTVGHDEE--SQFGDF-VRDTDAQMPDEF-TESRS 417

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPV----TLENLSSEFEVSRERVRQIEARAFK 278
           N   +     + L+ +E  I    R+   P     TL+ +S + ++ RE++RQIE +A +
Sbjct: 418 NYEKIDELLNNCLSEQEELIVRM-RIGMPPYNETKTLDEVSQKIKIPREKIRQIETKAIR 476

Query: 279 KVQESIQ 285
           K++++++
Sbjct: 477 KLRQAVR 483


>gi|11762220|gb|AAG40388.1|AF325036_1 At1g64860 [Arabidopsis thaliana]
          Length = 502

 Score = 75.9 bits (185), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 72/256 (28%), Positives = 126/256 (49%), Gaps = 38/256 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  S++RLV+ IA  Y   G  +S++V  G IGL++ ++KFD  +GFR++TY  WW
Sbjct: 259 AREKLAMSNVRLVMSIAQRYNNLGAEMSDLVQGGLIGLLRGIEKFDSSKGFRISTYVYWW 318

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   ++ +   +++ T  +++       +L+   + IT +      +  IA+ LN+
Sbjct: 319 IRQGVSRALVDNSRTLRLPTHLHERLGLIRNAKLRLQEKGITPS------IDRIAESLNM 372

Query: 169 SE------SEVISMNCRLAGDE--SLNALINSSDKNSSQWQD-------WLVYDHDGQEQ 213
           S+      +E +S    L  D   SLN L    + + S   D       W  YD      
Sbjct: 373 SQKKVRNATEAVSKVFSLDRDAFPSLNGL--PGETHHSYIADTRLENNPWHGYDD----- 425

Query: 214 VLIEKEERKNRRNMLTRSMS-VLNPRERRIFEA-RRLQENPVTLENLSSEFEVSRERVRQ 271
            L  KEE       +++ +S  L  RE+ I      L +  +T E++S    +SRERVRQ
Sbjct: 426 -LALKEE-------VSKLISATLGEREKEIIRLYYGLDKECLTWEDISKRIGLSRERVRQ 477

Query: 272 IEARAFKKVQESIQKQ 287
           +   A +K++ + +K+
Sbjct: 478 VGLVALEKLKHAARKR 493


>gi|302866072|ref|YP_003834709.1| sigma-70 family RNA polymerase [Micromonospora aurantiaca ATCC
           27029]
 gi|315502628|ref|YP_004081515.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Micromonospora
           sp. L5]
 gi|302568931|gb|ADL45133.1| RNA polymerase sigma factor, sigma-70 family [Micromonospora
           aurantiaca ATCC 27029]
 gi|315409247|gb|ADU07364.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Micromonospora
           sp. L5]
          Length = 328

 Score = 75.9 bits (185), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 67/250 (26%), Positives = 120/250 (48%), Gaps = 21/250 (8%)

Query: 44  HGDLS--------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           H DL+        A   L+ ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD 
Sbjct: 77  HADLALIAAEGRAAKDHLLEANLRLVVSIAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDY 136

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            +G++ +TY+ WWI+ A+   +      ++I     ++     + R++  L       L 
Sbjct: 137 TKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVEQ--VNRMVRVRRELSV----TLG 190

Query: 156 PEQVVA-IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            E  V+ +A  L + E +VI +        SL+  +   +   S   D++       E  
Sbjct: 191 REPTVSEVATALEIPEFQVIELISYDREPVSLDQAVG--EDGESALGDFVAAVDPRTEPG 248

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQI 272
             +       RN +   ++ L+ RE+ +   R   ++    TL+ +  EF +SRER+RQI
Sbjct: 249 --DAATNGELRNEVRIVLATLSQREQAVIRLRFGLDDGRQRTLDEVGREFGLSRERIRQI 306

Query: 273 EARAFKKVQE 282
           E     K+++
Sbjct: 307 EKVTLLKLRD 316


>gi|47565382|ref|ZP_00236424.1| RNA polymerase sigma-43 factor, putative [Bacillus cereus G9241]
 gi|208742286|ref|YP_002267738.1| RNA polymerase sigma factor (sigma-A) (sigma-43) [Bacillus cereus]
 gi|47557736|gb|EAL16062.1| RNA polymerase sigma-43 factor, putative [Bacillus cereus G9241]
          Length = 325

 Score = 75.9 bits (185), Expect = 6e-12,   Method: Compositional matrix adjust.
 Identities = 76/296 (25%), Positives = 133/296 (44%), Gaps = 59/296 (19%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY--GLPISE 77
           I  I    +L KQE   L +RY+ HG+      L   ++ LV+ IA  Y+     +   +
Sbjct: 42  IKGIGNYKVLSKQESLKLFQRYK-HGEKDLRDYLFHVNVGLVLSIARKYKNKHPDIEFDD 100

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS-LVKIGTTANQKRLF 136
           +V EGN G+++A++ F+P  G+  +TY+ WWI+ +M   I +  S   KI  + NQ    
Sbjct: 101 LVQEGNEGMLRAMEDFNPALGYCFSTYAFWWIQKSMLGIICKKKSGPFKIPNSVNQ---- 156

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC--RLAGDESLN------- 187
           FNLR ++   + +   N +P  V  + K+LNV+   VI  N   + A   +L+       
Sbjct: 157 FNLRYVELEDKYLQMYN-RPPSVEEVVKELNVTSETVIKHNVYYKRATTMTLDVDTINED 215

Query: 188 -ALINSSDKNSS-------------QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             ++N    +SS              ++ WL++D                          
Sbjct: 216 IGILNPFYDDSSAIPSTNEMVIEDLNYEIWLIFD-------------------------E 250

Query: 234 VLNPRERRIFE-ARRLQENPVTL-ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           VLNP+++ +      L +  V L + ++    ++ ERV QI+  A KK+++   K+
Sbjct: 251 VLNPKQKMVLNLCFGLLDGKVYLHKEIAKALMITTERVSQIKDEAIKKLKKCDYKE 306


>gi|21221637|ref|NP_627416.1| RNA polymerase principal sigma factor [Streptomyces coelicolor
           A3(2)]
 gi|256787171|ref|ZP_05525602.1| RNA polymerase principal sigma factor [Streptomyces lividans TK24]
 gi|289771070|ref|ZP_06530448.1| RNA polymerase principal sigma factor hrdD [Streptomyces lividans
           TK24]
 gi|19856654|sp|P18249|HRDD_STRCO RecName: Full=RNA polymerase principal sigma factor hrdD
 gi|7799522|emb|CAB90986.1| RNA polymerase principal sigma factor [Streptomyces coelicolor
           A3(2)]
 gi|289701269|gb|EFD68698.1| RNA polymerase principal sigma factor hrdD [Streptomyces lividans
           TK24]
          Length = 332

 Score = 75.9 bits (185), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 75/290 (25%), Positives = 131/290 (45%), Gaps = 43/290 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-------------YREHGDLSAAHRL------------ 53
           Y+ EI + P+L+  +E  L++              Y E G  +    L            
Sbjct: 39  YLDEIARTPLLDAAKEVELSQTIEAGVFARQVLEGYEETGADATREELQALIDESERAKD 98

Query: 54  --VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
             + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ WWI+ 
Sbjct: 99  VFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTYATWWIRQ 158

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           A+   I      +++        L   L R++   +     + +  +   IA +L  +  
Sbjct: 159 AITRSIADQSRTIRLPV-----HLVEELGRIRRVQREFNREHGREPEPAEIAAELGSTPE 213

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG--QEQVLIEKEERKNRRNMLT 229
            V  +        SLN  ++  D+  +Q+ D L+ D      EQ ++     +   +++ 
Sbjct: 214 RVTDVLDWARDPVSLNMSVD--DEGETQFGD-LLEDTSAVSPEQSVLTLLRSEELDDLIG 270

Query: 230 RSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
           R    L+PR   I + R   ++    TL  +  E  ++RER+RQIE  A 
Sbjct: 271 R----LDPRTASIIKMRYGIDDGRERTLTEVGKEHGLTRERIRQIEKHAL 316


>gi|269926941|ref|YP_003323564.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
 gi|269790601|gb|ACZ42742.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
          Length = 596

 Score = 75.9 bits (185), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 34/82 (41%), Positives = 56/82 (68%), Gaps = 1/82 (1%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD+ A  RL+ ++LRLVV IA  Y G G+ + +++ EGNIGL++AV+KF  ++G++ +TY
Sbjct: 252 GDI-ARKRLIEANLRLVVSIAKKYTGRGITLLDLIQEGNIGLIKAVEKFRHQKGYKFSTY 310

Query: 105 SMWWIKAAMQEYILRSWSLVKI 126
           + WWI+ A+   I      ++I
Sbjct: 311 ATWWIRQAITRAIADQARTIRI 332



 Score = 35.8 bits (81), Expect = 7.4,   Method: Compositional matrix adjust.
 Identities = 15/33 (45%), Positives = 24/33 (72%)

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           P TLE +   F V+RER+RQIE++A +K++  +
Sbjct: 554 PRTLEEVGRAFGVTRERIRQIESKALRKLRRDV 586


>gi|144575120|gb|AAZ43865.2| DNA-directed RNA polymerase sigma factor [Mycoplasma synoviae 53]
          Length = 798

 Score = 75.9 bits (185), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 80/287 (27%), Positives = 134/287 (46%), Gaps = 55/287 (19%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHR--LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +L  QEE  LA+   + G      R  ++  +LRLVV  A  Y+  GL   ++VSEGN G
Sbjct: 515 LLTPQEEKDLAEEMDKGGSRGKRARDLIIKRNLRLVVNAAKKYKNRGLSFIDLVSEGNAG 574

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A +KFD ++GF+ +TY+ WWI+ ++   +            A+Q R+     R+  H
Sbjct: 575 LLKAAQKFDIKKGFKFSTYATWWIRQSISRAV------------ADQARII----RVPVH 618

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-----DES-------LNALINSS 193
           +    +   K E+ +       + + E+     RL G     D S       +N    S 
Sbjct: 619 MVETINKIYKIEREIQQENGGEIIDEEIA---ARLGGKSKKYDASYIRYIRKINTSPISL 675

Query: 194 DKNSSQWQDWLVYDHDGQEQVL-----IEKEERKNRRN-----MLTRSMSVLNPRERRI- 242
           DK   +  D    D    E ++      +KEE   + N     +L+ + + L  R   I 
Sbjct: 676 DKQVGKENDSFFGDFVKDESIISPVEFADKEELITKINYYVEKLLSEAEADLIKRYHGIG 735

Query: 243 FEARRLQENPV---TLENLSSEF-----EVSRERVRQIEARAFKKVQ 281
           ++A+    NPV   TL+ +S +F     ++S+ERVRQI  + +KK++
Sbjct: 736 YDAKG---NPVRSATLDEISKDFRGEGKKISKERVRQIITKIYKKLR 779


>gi|2398851|dbj|BAA22214.1| plastid RNA polymerase sigma-subunit [Arabidopsis thaliana]
          Length = 502

 Score = 75.9 bits (185), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 72/256 (28%), Positives = 126/256 (49%), Gaps = 38/256 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  S++RLV+ IA  Y   G  +S++V  G IGL++ ++KFD  +GFR++TY  WW
Sbjct: 259 AREKLAMSNVRLVMSIAQRYDNLGAEMSDLVQGGLIGLLRGIEKFDSSKGFRISTYVYWW 318

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   ++ +   +++ T  +++       +L+   + IT +      +  IA+ LN+
Sbjct: 319 IRQGVSRALVDNSRTLRLPTHLHERLGLIRNAKLRLQEKGITPS------IDRIAESLNM 372

Query: 169 SE------SEVISMNCRLAGDE--SLNALINSSDKNSSQWQD-------WLVYDHDGQEQ 213
           S+      +E +S    L  D   SLN L    + + S   D       W  YD      
Sbjct: 373 SQKKVRNATEAVSKVFSLDRDAFPSLNGL--PGETHHSYIADTRLENNPWHGYDD----- 425

Query: 214 VLIEKEERKNRRNMLTRSMS-VLNPRERRIFEA-RRLQENPVTLENLSSEFEVSRERVRQ 271
            L  KEE       +++ +S  L  RE+ I      L +  +T E++S    +SRERVRQ
Sbjct: 426 -LALKEE-------VSKLISATLGEREKEIIRLYYGLDKECLTWEDISKRIGLSRERVRQ 477

Query: 272 IEARAFKKVQESIQKQ 287
           +   A +K++ + +K+
Sbjct: 478 VGLVALEKLKHAARKR 493


>gi|318041080|ref|ZP_07973036.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)-like
           protein [Synechococcus sp. CB0101]
          Length = 279

 Score = 75.9 bits (185), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 41/115 (35%), Positives = 65/115 (56%), Gaps = 16/115 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLA---KRYREHGDLSAA---------HRLVTSHLRLVVKIAM 66
           Y+  I +IP+L  QEE  L    K + E  D S A          R+VT++LRLVV +A+
Sbjct: 8   YLRTIGRIPLLTAQEEVHLGTIVKDWMESNDPSPALQRRGRRALQRIVTANLRLVVTVAL 67

Query: 67  GY----RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
            Y    +       ++V  GN+GL++A +K+DP RG++ +TY  WWI+ ++  Y+
Sbjct: 68  RYIRRLKHLAHDPMDLVQAGNLGLLRAAEKYDPTRGYKFSTYGYWWIRQSINRYL 122


>gi|167813607|ref|ZP_02445287.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 91]
          Length = 302

 Score = 75.9 bits (185), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 57/237 (24%), Positives = 117/237 (49%), Gaps = 14/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  R+  ++LRLV+ IA  Y   GL +++++ EGN+GL++A++KF+  RGF+ +TY+ W
Sbjct: 61  AATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKFSTYATW 120

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++      +      RR++     I   +     +  +++   
Sbjct: 121 WIRQAISRAIADRARTIRVPVHVGDE-----ARRVRKAADRIERRSGVSASLAELSEATG 175

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +    + ++        SLNA +   D + +++ D +    D     L +        ++
Sbjct: 176 LPAERLRAVLTLPREPRSLNAPLG--DDDQAEFGDIV---EDTSTPSLFDALAHGQMCDV 230

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +T  +  ++ +E  I   RR     + P + E +++   VSRE+VR+IE RA + ++
Sbjct: 231 VTSLLKTMSAQEADILR-RRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLR 286


>gi|183220954|ref|YP_001838950.1| RNA polymerase sigma factor RpoD [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Paris)']
 gi|189911049|ref|YP_001962604.1| DNA-directed RNA polymerase sigma sigma70/sigma32 subunit
           [Leptospira biflexa serovar Patoc strain 'Patoc 1
           (Ames)']
 gi|167775725|gb|ABZ94026.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Leptospira biflexa serovar Patoc strain 'Patoc 1
           (Ames)']
 gi|167779376|gb|ABZ97674.1| RNA polymerase sigma factor rpoD (Sigma-70) [Leptospira biflexa
           serovar Patoc strain 'Patoc 1 (Paris)']
          Length = 590

 Score = 75.9 bits (185), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 67/245 (27%), Positives = 115/245 (46%), Gaps = 32/245 (13%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   LV ++LRLVV IA  Y   G+   +++ EGNIGL++AV KF+ ++G++ +TY+ WW
Sbjct: 353 AKRELVRANLRLVVSIAKRYANRGMHFFDLIQEGNIGLIRAVDKFEYKKGYKFSTYATWW 412

Query: 109 IKAAMQEYILRSWSLVK--------IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
           I+ A+   I      ++        +     + RLF            I +    P Q V
Sbjct: 413 IRQAITRAISDQARTIRVPVHMIEQVNKVIRETRLFVQEFGRDPSNDEIAERLGWPVQKV 472

Query: 161 AIAKKLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              K  NV+  E IS+   +  +E   L   I   +  S          +     +L E+
Sbjct: 473 KAVK--NVA-REPISLEIPVGSEEDSELGDFIEDKEVISPL--------NSAASSILSEQ 521

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARA 276
                    + + +  L  RE+++   R   ++    TLE +  +F+V+RER+RQIEA+A
Sbjct: 522 ---------IRQVLQTLPAREQKVIRMRFGLDDGYAQTLEEVGYQFKVTRERIRQIEAKA 572

Query: 277 FKKVQ 281
            ++++
Sbjct: 573 LRRLR 577


>gi|124386302|ref|YP_001028216.1| putative RNA polymerase sigma factor RpoD [Burkholderia mallei NCTC
           10229]
 gi|126449023|ref|YP_001081831.1| RNA polymerase sigma factor [Burkholderia mallei NCTC 10247]
 gi|126450673|ref|YP_001081854.1| RNA polymerase sigma factor RpoD [Burkholderia mallei NCTC 10247]
 gi|124294322|gb|ABN03591.1| putative RNA polymerase sigma factor RpoD [Burkholderia mallei NCTC
           10229]
 gi|126241893|gb|ABO04986.1| RNA polymerase sigma factor [Burkholderia mallei NCTC 10247]
 gi|126243543|gb|ABO06636.1| RNA polymerase sigma factor RpoD [Burkholderia mallei NCTC 10247]
          Length = 482

 Score = 75.9 bits (185), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 57/237 (24%), Positives = 117/237 (49%), Gaps = 14/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  R+  ++LRLV+ IA  Y   GL +++++ EGN+GL++A++KF+  RGF+ +TY+ W
Sbjct: 241 AATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKFSTYATW 300

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++      +      RR++     I   +     +  +++   
Sbjct: 301 WIRQAISRAIAERARTIRVPVHVGDE-----ARRVRKAADRIERRSGVSASLAELSEATG 355

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +    + ++        SLNA +   D + +++ D +    D     L +        ++
Sbjct: 356 LPAERLRAVLTLPREPRSLNAPLG--DDDQAEFGDIV---EDTSTPSLFDALAHGQMCDV 410

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +T  +  ++ +E  I   RR     + P + E +++   VSRE+VR+IE RA + ++
Sbjct: 411 VTSLLKTMSAQEADILR-RRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLR 466


>gi|329895346|ref|ZP_08270971.1| RNA polymerase sigma factor [gamma proteobacterium IMCC3088]
 gi|328922359|gb|EGG29703.1| RNA polymerase sigma factor [gamma proteobacterium IMCC3088]
          Length = 424

 Score = 75.9 bits (185), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 70/245 (28%), Positives = 121/245 (49%), Gaps = 22/245 (8%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            G L+A  +LV  ++RLV K+A   +  G+ + ++V EG IGL++A +KFD   GFR +T
Sbjct: 181 QGYLAARDKLVMHNVRLVYKLAREKQNRGIAVRDLVQEGIIGLVRAAEKFDYRLGFRFST 240

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQK-RLFFNLRR----LKGHLQAITDNNLKPEQ 158
           Y+  W    +Q     + SLV   T   Q+    + +R      +G   ++ +  L    
Sbjct: 241 YAYNWTNQHIQRVCEGNGSLVTYPTHVTQEVNALYRVRNEWMDRRGEEPSLAE--LAEHS 298

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              + +   +++   ++++ +   DE  NAL  S+          LV   D      +E+
Sbjct: 299 GFTLERVRELTQLTNLTVSIQSDDDEDTNALPESA----------LV---DEAANPALEQ 345

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARA 276
            + ++ + +L + +  L+ RE+ I  AR  L   P  TL  L+ + EVSRE VRQ+E  A
Sbjct: 346 AQSRSLKRLLEQQLKQLDRREQMIVTARWGLDGRPSRTLAQLADQLEVSRELVRQLEKSA 405

Query: 277 FKKVQ 281
            +K+Q
Sbjct: 406 LRKLQ 410


>gi|55274934|gb|AAV49268.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 191

 Score = 75.9 bits (185), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 31/59 (52%), Positives = 45/59 (76%)

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           LVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+
Sbjct: 1   LVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIM 59


>gi|2385344|emb|CAA74896.1| sigma factorB [Arabidopsis thaliana]
          Length = 500

 Score = 75.9 bits (185), Expect = 7e-12,   Method: Compositional matrix adjust.
 Identities = 72/256 (28%), Positives = 126/256 (49%), Gaps = 38/256 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  S++RLV+ IA  Y   G  +S++V  G IGL++ ++KFD  +GFR++TY  WW
Sbjct: 257 AREKLAMSNVRLVMSIAQRYDNLGAEMSDLVQGGLIGLLRGIEKFDSSKGFRISTYVYWW 316

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   ++ +   +++ T  +++       +L+   + IT +      +  IA+ LN+
Sbjct: 317 IRQGVSRALVDNSRTLRLPTHLHERLGLIRNAKLRLQEKGITPS------IDRIAESLNM 370

Query: 169 SE------SEVISMNCRLAGDE--SLNALINSSDKNSSQWQD-------WLVYDHDGQEQ 213
           S+      +E +S    L  D   SLN L    + + S   D       W  YD      
Sbjct: 371 SQKKVRNATEAVSKVFSLDRDAFPSLNGL--PGETHHSYIADTRLENNPWHGYDD----- 423

Query: 214 VLIEKEERKNRRNMLTRSMS-VLNPRERRIFEA-RRLQENPVTLENLSSEFEVSRERVRQ 271
            L  KEE       +++ +S  L  RE+ I      L +  +T E++S    +SRERVRQ
Sbjct: 424 -LALKEE-------VSKLISATLGEREKEIIRLYYGLDKECLTWEDISKRIGLSRERVRQ 475

Query: 272 IEARAFKKVQESIQKQ 287
           +   A +K++ + +K+
Sbjct: 476 VGLVALEKLKHAARKR 491


>gi|54401904|gb|AAV34637.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 183

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 31/59 (52%), Positives = 45/59 (76%)

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           LVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+
Sbjct: 1   LVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIM 59


>gi|126441635|ref|YP_001057174.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 668]
 gi|126221128|gb|ABN84634.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 668]
          Length = 482

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 57/237 (24%), Positives = 117/237 (49%), Gaps = 14/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  R+  ++LRLV+ IA  Y   GL +++++ EGN+GL++A++KF+  RGF+ +TY+ W
Sbjct: 241 AATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKFSTYATW 300

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++      +      RR++     I   +     +  +++   
Sbjct: 301 WIRQAISRAIAERARTIRVPVHVGDE-----ARRVRKAADRIERRSGVSASLAELSEATG 355

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +    + ++        SLNA +   D + +++ D +    D     L +        ++
Sbjct: 356 LPAERLRAVLTLPREPRSLNAPLG--DDDQAEFGDIV---EDTSTPSLFDALAHGQMCDV 410

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +T  +  ++ +E  I   RR     + P + E +++   VSRE+VR+IE RA + ++
Sbjct: 411 VTSLLKTMSAQEADILR-RRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLR 466


>gi|15217767|ref|NP_176666.1| SIGA (SIGMA FACTOR A); DNA binding / DNA-directed RNA polymerase/
           sigma factor/ transcription factor [Arabidopsis
           thaliana]
 gi|5042421|gb|AAD38260.1|AC006193_16 RNA polymerase sigma subunit 1 [Arabidopsis thaliana]
 gi|2353171|gb|AAB69384.1| sigma factor 1 [Arabidopsis thaliana]
 gi|2443408|dbj|BAA22421.1| SigA [Arabidopsis thaliana]
 gi|2558514|emb|CAA74640.1| plastid RNA polymerase sigma factor [Arabidopsis thaliana]
 gi|5478439|dbj|BAA82448.1| sigma factor SigA [Arabidopsis thaliana]
 gi|17064900|gb|AAL32604.1| RNA polymerase sigma subunit 1 [Arabidopsis thaliana]
 gi|20259916|gb|AAM13305.1| RNA polymerase sigma subunit 1 [Arabidopsis thaliana]
 gi|222423019|dbj|BAH19492.1| AT1G64860 [Arabidopsis thaliana]
 gi|332196177|gb|AEE34298.1| sigma factor A [Arabidopsis thaliana]
          Length = 502

 Score = 75.9 bits (185), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 72/256 (28%), Positives = 126/256 (49%), Gaps = 38/256 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  S++RLV+ IA  Y   G  +S++V  G IGL++ ++KFD  +GFR++TY  WW
Sbjct: 259 AREKLAMSNVRLVMSIAQRYDNLGAEMSDLVQGGLIGLLRGIEKFDSSKGFRISTYVYWW 318

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   ++ +   +++ T  +++       +L+   + IT +      +  IA+ LN+
Sbjct: 319 IRQGVSRALVDNSRTLRLPTHLHERLGLIRNAKLRLQEKGITPS------IDRIAESLNM 372

Query: 169 SE------SEVISMNCRLAGDE--SLNALINSSDKNSSQWQD-------WLVYDHDGQEQ 213
           S+      +E +S    L  D   SLN L    + + S   D       W  YD      
Sbjct: 373 SQKKVRNATEAVSKVFSLDRDAFPSLNGL--PGETHHSYIADTRLENNPWHGYDD----- 425

Query: 214 VLIEKEERKNRRNMLTRSMS-VLNPRERRIFEA-RRLQENPVTLENLSSEFEVSRERVRQ 271
            L  KEE       +++ +S  L  RE+ I      L +  +T E++S    +SRERVRQ
Sbjct: 426 -LALKEE-------VSKLISATLGEREKEIIRLYYGLDKECLTWEDISKRIGLSRERVRQ 477

Query: 272 IEARAFKKVQESIQKQ 287
           +   A +K++ + +K+
Sbjct: 478 VGLVALEKLKHAARKR 493


>gi|224007213|ref|XP_002292566.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220971428|gb|EED89762.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 338

 Score = 75.5 bits (184), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 61/252 (24%), Positives = 120/252 (47%), Gaps = 21/252 (8%)

Query: 49  AAHRLVTSHLRLVVKIA-----------MGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A   L+ ++LRLV+ +A             +    +   +   +G IGL +A +KFDPE 
Sbjct: 75  AKAALIEANLRLVITVARQAVKKSPFRSSSHAASSVQFQDACQQGIIGLTRATEKFDPEL 134

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK--RLFFNLRRLKGHLQAITDNNLK 155
           GFR +TY++WWI+  + + +      V++  +A +K   +    R L   L     ++  
Sbjct: 135 GFRFSTYAIWWIQKEVAKNVNEQSRTVRVPGSAIKKINDIRIQERVLMNELGRRPSDDEV 194

Query: 156 PEQVVAIAKKLNV---SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
            E+     +KLN    S  EV S++ ++       +  +  D +    +   ++  D + 
Sbjct: 195 AEKCGLTVEKLNFYRQSAKEVKSLDKKIDSRTGKGSAASGGDDDGKTME---IFVRDTEH 251

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVR 270
               E  +++  +  + R +  L+PRE+ +   R   ++  P TL ++  +F V +ER++
Sbjct: 252 PSPSELIDQQMMQQDIRRLVKTLSPREQAVIRLRFGLDDGKPQTLGDIGEKFGVEKERIK 311

Query: 271 QIEARAFKKVQE 282
           +IEARA  K+++
Sbjct: 312 KIEARALLKLRQ 323


>gi|302535003|ref|ZP_07287345.1| RNA polymerase sigma factor RpoS [Streptomyces sp. C]
 gi|302443898|gb|EFL15714.1| RNA polymerase sigma factor RpoS [Streptomyces sp. C]
          Length = 325

 Score = 75.5 bits (184), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 77/291 (26%), Positives = 131/291 (45%), Gaps = 44/291 (15%)

Query: 19  YIHEIRKIPMLEKQEEY--------------VLAKRYREHGDLSAAHRL----------- 53
           Y+ EI + P+L+   E               +L       G+L A   L           
Sbjct: 31  YLDEIARTPLLDAAREVELSQIIEAGVYARQILDGEIERDGELPAREELEALAAEGERAK 90

Query: 54  ---VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
              + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ WWI+
Sbjct: 91  EVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYAKGFKFSTYATWWIR 150

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            A+   I      +++     ++     +RR++       +N   PE    IA  L+ +E
Sbjct: 151 QAITRSIADQSRTIRLPVHLVEE--LGRIRRIQREFN--RENGRDPEH-AEIAAALDSTE 205

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG--QEQVLIEKEERKNRRNML 228
             V  +        SLN  ++  D+  +Q+ D L+ D      EQ ++     +   ++L
Sbjct: 206 KRVGDVLDWARDPVSLNMSVD--DEGDTQFGD-LLEDTSAISPEQSVLSLLRSEELEDLL 262

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
            +    L+ R   I + R   E+    TL  +  +  ++RER+RQIE  A 
Sbjct: 263 GK----LDQRTASIIKMRYGIEDGRERTLTEVGKQHGLTRERIRQIEKHAL 309


>gi|53724654|ref|YP_101962.1| RNA polymerase sigma factor RpoD [Burkholderia mallei ATCC 23344]
 gi|121599433|ref|YP_994127.1| putative RNA polymerase sigma factor RpoD [Burkholderia mallei
           SAVP1]
 gi|167001162|ref|ZP_02266961.1| RNA polymerase sigma factor [Burkholderia mallei PRL-20]
 gi|238561900|ref|ZP_00441190.2| RNA polymerase sigma factor RpoD [Burkholderia mallei GB8 horse 4]
 gi|254176911|ref|ZP_04883568.1| RNA polymerase sigma factor RpoD [Burkholderia mallei ATCC 10399]
 gi|254203640|ref|ZP_04910000.1| RNA polymerase sigma factor RpoD [Burkholderia mallei FMH]
 gi|254208616|ref|ZP_04914964.1| RNA polymerase sigma factor RpoD [Burkholderia mallei JHU]
 gi|254360328|ref|ZP_04976598.1| RNA polymerase sigma factor RpoD [Burkholderia mallei 2002721280]
 gi|52428077|gb|AAU48670.1| RNA polymerase sigma factor RpoD, putative [Burkholderia mallei
           ATCC 23344]
 gi|121228243|gb|ABM50761.1| putative RNA polymerase sigma factor RpoD [Burkholderia mallei
           SAVP1]
 gi|147745152|gb|EDK52232.1| RNA polymerase sigma factor RpoD [Burkholderia mallei FMH]
 gi|147750492|gb|EDK57561.1| RNA polymerase sigma factor RpoD [Burkholderia mallei JHU]
 gi|148029568|gb|EDK87473.1| RNA polymerase sigma factor RpoD [Burkholderia mallei 2002721280]
 gi|160697952|gb|EDP87922.1| RNA polymerase sigma factor RpoD [Burkholderia mallei ATCC 10399]
 gi|238523583|gb|EEP87020.1| RNA polymerase sigma factor RpoD [Burkholderia mallei GB8 horse 4]
 gi|243062992|gb|EES45178.1| RNA polymerase sigma factor [Burkholderia mallei PRL-20]
          Length = 482

 Score = 75.5 bits (184), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 57/237 (24%), Positives = 117/237 (49%), Gaps = 14/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  R+  ++LRLV+ IA  Y   GL +++++ EGN+GL++A++KF+  RGF+ +TY+ W
Sbjct: 241 AATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKFSTYATW 300

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++      +      RR++     I   +     +  +++   
Sbjct: 301 WIRQAISRAIAERARTIRVPVHVGDE-----ARRVRKAADRIERRSGVSASLAELSEATG 355

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +    + ++        SLNA +   D + +++ D +    D     L +        ++
Sbjct: 356 LPAERLRAVLTLPREPRSLNAPLG--DDDQAEFGDIV---EDTSTPSLFDALAHGQMCDV 410

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +T  +  ++ +E  I   RR     + P + E +++   VSRE+VR+IE RA + ++
Sbjct: 411 VTSLLKTMSAQEADILR-RRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLR 466


>gi|159027100|emb|CAO89285.1| rpoD [Microcystis aeruginosa PCC 7806]
          Length = 328

 Score = 75.5 bits (184), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 65/304 (21%), Positives = 134/304 (44%), Gaps = 60/304 (19%)

Query: 19  YIHEIRKIPMLEKQEEYVLAK--------------------------------------- 39
           Y+HEI ++P+L  ++E +  K                                       
Sbjct: 23  YLHEIGRVPLLTHEQEIIYGKQVQRMMSLLEAKEALSKQLGREPQHLEWADSVNLSENEL 82

Query: 40  -RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
            R  + GD  A  +++ ++LRLVV IA  Y+   +   +++ EG++GL + V+KFDP +G
Sbjct: 83  DRALKTGD-RAKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGSLGLERGVEKFDPTKG 141

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           ++ +TY+ WWI+ A+   I +    +++     +K     ++R +  L      +  P +
Sbjct: 142 YKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEK--LNKIKRTQRELAQKLGRSATPAE 199

Query: 159 VVAIAKKLNVSESEV---ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
              IA +L++  +++   +SM       + ++  +   D   ++  + L       +  +
Sbjct: 200 ---IALELDLEPAQIREYLSM-----ARQPISLDVRVGDNQDTELSELLEDSGVSPDTFI 251

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIE 273
            ++  R++  N+L      L P++R +   R        ++L  +     +SRERVRQ+E
Sbjct: 252 TQELLRQDLANLLAE----LTPQQREVITLRFGLTDGKELSLAKIGQRMNISRERVRQLE 307

Query: 274 ARAF 277
            +A 
Sbjct: 308 HQAL 311


>gi|56752354|ref|YP_173055.1| group2 RNA polymerase sigma factor RpoD2 [Synechococcus elongatus
           PCC 6301]
 gi|56687313|dbj|BAD80535.1| group2 RNA polymerase sigma factor RpoD2 [Synechococcus elongatus
           PCC 6301]
          Length = 320

 Score = 75.5 bits (184), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 59/235 (25%), Positives = 119/235 (50%), Gaps = 21/235 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +++ ++LRLVV IA  Y+   +   +++ EG +GL +  +KFDP +G++ +TY+ WW
Sbjct: 85  AKRKMIEANLRLVVSIAKKYQKRHMEFLDLIQEGTLGLERGFEKFDPSKGYKFSTYAYWW 144

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I +    +++     +K     L +LK   + ++    +      +A+ L +
Sbjct: 145 IRQAITRAIAQQSRTIRLPIHITEK-----LNKLKKTQRELSQQLGRSATASELAEVLEL 199

Query: 169 SESEV---ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE-RKNR 224
              +V   I MN      + ++  +   D   ++ Q+ L+ D        +E+E  R++ 
Sbjct: 200 PLEQVREYIQMN-----RQPVSLDVKVGDSQDTELQE-LLEDEQSSPSDYVEQESLRRDL 253

Query: 225 RNMLTRSMSVLNPRERRIFEARR-LQE-NPVTLENLSSEFEVSRERVRQIEARAF 277
           RN+    M+ L P+++ +   R  L E + ++L  +     +SRERVR++E +A 
Sbjct: 254 RNL----MAELTPQQQAVIALRYGLDEGDSLSLAKVGERLNISRERVRKLERQAM 304


>gi|55274986|gb|AAV49291.1| RNA polymerase subunit sigma-38 [Shigella flexneri]
          Length = 196

 Score = 75.5 bits (184), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 31/59 (52%), Positives = 45/59 (76%)

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           LVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+
Sbjct: 1   LVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIM 59


>gi|2565297|gb|AAB81958.1| RNA polymerase sigma subunit 1 [Arabidopsis thaliana]
          Length = 502

 Score = 75.5 bits (184), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 72/256 (28%), Positives = 126/256 (49%), Gaps = 38/256 (14%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  S++RLV+ IA  Y   G  +S++V  G IGL++ ++KFD  +GFR++TY  WW
Sbjct: 259 AREKLAMSNVRLVMSIAQRYDNLGAEMSDLVQGGLIGLLRGIEKFDSSKGFRISTYVYWW 318

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   ++ +   +++ T  +++       +L+   + IT +      +  IA+ LN+
Sbjct: 319 IRQGVSRALVDNSRTLRLPTHLHERLGLIRNAKLRLQEKGITPS------IDRIAESLNM 372

Query: 169 SE------SEVISMNCRLAGDE--SLNALINSSDKNSSQWQD-------WLVYDHDGQEQ 213
           S+      +E +S    L  D   SLN L    + + S   D       W  YD      
Sbjct: 373 SQKKVRNATEAVSKVFSLDRDAFPSLNGL--PGETHHSYIADTRLENNPWHGYDD----- 425

Query: 214 VLIEKEERKNRRNMLTRSMS-VLNPRERRIFEA-RRLQENPVTLENLSSEFEVSRERVRQ 271
            L  KEE       +++ +S  L  RE+ I      L +  +T E++S    +SRERVRQ
Sbjct: 426 -LALKEE-------VSKLISATLGEREKEIIRLYYGLDKECLTWEDISKRIGLSRERVRQ 477

Query: 272 IEARAFKKVQESIQKQ 287
           +   A +K++ + +K+
Sbjct: 478 VGLVALEKLKHAARKR 493


>gi|300868245|ref|ZP_07112876.1| RNA polymerase sigma factor SigD [Oscillatoria sp. PCC 6506]
 gi|300333769|emb|CBN58060.1| RNA polymerase sigma factor SigD [Oscillatoria sp. PCC 6506]
          Length = 319

 Score = 75.5 bits (184), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 61/244 (25%), Positives = 112/244 (45%), Gaps = 13/244 (5%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           H    A   +V ++LRLVV +A  Y    + + +++ EG IG+ + V+KFDP +G+R +T
Sbjct: 79  HAGERAKRMMVEANLRLVVSVAKKYIKRNVDLLDLIQEGTIGMQRGVEKFDPTKGYRFST 138

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI+ A+   I      +++     +K     L ++K   + +     +      +A
Sbjct: 139 YAYWWIRQAITRAIAEKGRTIRLPIHITEK-----LNKIKKAQRYLAQKLGRAATANELA 193

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
            +L ++  ++     R     SL+  +   D   ++  D L       E   ++   R +
Sbjct: 194 AELELTPKQIREYLERARLPLSLD--LRVGDNQDTELGDLLEDTGASPEDFALQASLRAD 251

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
               L   M+ L  ++R +   R   E+   +TL  +     +SRERVRQIE  A  K++
Sbjct: 252 ----LEMLMADLTQQQREVLALRFGLEDGQTLTLSKIGDRLNISRERVRQIEREALTKLR 307

Query: 282 ESIQ 285
           +  Q
Sbjct: 308 KRKQ 311


>gi|302876248|ref|YP_003844881.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium cellulovorans
           743B]
 gi|307686980|ref|ZP_07629426.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium cellulovorans
           743B]
 gi|302579105|gb|ADL53117.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium cellulovorans
           743B]
          Length = 281

 Score = 75.5 bits (184), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 68/265 (25%), Positives = 125/265 (47%), Gaps = 33/265 (12%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDP 95
           L   Y+ + D++A   L+ ++ RLV K A   +   L    ++V EG IGLM  ++KF+ 
Sbjct: 16  LVTLYQTNKDITARDYLIINNKRLVYKAASLKKDTSLLAYDDLVQEGLIGLMIGIEKFNA 75

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           +   + +TY  +WIK  +   I  + + +++            + ++   +     NN+K
Sbjct: 76  DYNSKFSTYIYYWIKQRIDRAIYNTGTSIRLPIHL--------INKINKVMYVENKNNVK 127

Query: 156 --PEQVVAIAKKLNVSESE-------------VISMNCRLAGD--ESLNALINSSDKNSS 198
                   +   L++++ +             +IS+N  L  D  E    LI+  D+NSS
Sbjct: 128 SLDNDSTDLCTDLDITDKQYDYYKFLVKQFKNIISLNSALLSDNSEGDEELIDFIDENSS 187

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLE 256
            + D    ++     ++  KEE  +    L   +  LN RE+ +   R  L +  + TLE
Sbjct: 188 NFGDPGSKNYSIDSNII--KEELSHD---LNEVLKTLNEREQHVLRMRFGLDDGEMKTLE 242

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            + + F V+RER+RQIE++A KK++
Sbjct: 243 QIGNHFNVTRERIRQIESKALKKLR 267


>gi|255312663|gb|ACU01741.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score = 75.5 bits (184), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 32/61 (52%), Positives = 46/61 (75%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL + +++ EGN+ L++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLVLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 L 118
           +
Sbjct: 61  M 61


>gi|207743452|ref|YP_002259844.1| sigma factor, ecf;peptidase aspartic, active site;;; protein
           [Ralstonia solanacearum IPO1609]
 gi|206594849|emb|CAQ61776.1| sigma factor, ecf;peptidase aspartic, active site;;; protein
           [Ralstonia solanacearum IPO1609]
          Length = 203

 Score = 75.5 bits (184), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 62/208 (29%), Positives = 103/208 (49%), Gaps = 20/208 (9%)

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M A++KFDPERGFR +TY+ WWI+ +++  I+     V++    +  R    + R K HL
Sbjct: 1   MHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRELNQVLRAKRHL 58

Query: 147 Q--AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS-SQWQDW 203
           +   I   +   E +  +  K      +V+S+N      E   +L    D +S +   D+
Sbjct: 59  EKSGIDGRDASIEDIAHLLGKTTEEVQDVLSLN------EHTTSLDTPFDLDSGTSLLDF 112

Query: 204 LVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN---PVTLENLS 259
           L  +H    +Q +  +E  +  ++ L R    L+ + R + E RR   N   P TLE L+
Sbjct: 113 LSDEHGASPDQEVAHRELSQLMKSWLAR----LSDKHRYVVE-RRFGLNHIEPATLEELA 167

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +E  ++RERVRQI+  A  K++     Q
Sbjct: 168 AEMGLTRERVRQIQQEALVKLKRHFASQ 195


>gi|87301677|ref|ZP_01084517.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
 gi|87283894|gb|EAQ75848.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
          Length = 349

 Score = 75.5 bits (184), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 57/227 (25%), Positives = 107/227 (47%), Gaps = 13/227 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+V ++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP RG++ +TY+ WW
Sbjct: 111 AKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWW 170

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   I      +++     +      L +LK   + ++    +   +  +A  + +
Sbjct: 171 IRQGITRAIAEKSRTIRLPIHITE-----TLNKLKKGQRELSQELGRTPTLSELAVCVEL 225

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E EV  + CR     SL   +   D   ++  D L  D     + +  +  R + R +L
Sbjct: 226 PEEEVKDLLCRARQPVSLETKVG--DGEDTELLDLLQGDGTLPAESVDSECLRGDMRALL 283

Query: 229 TRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIE 273
            +    L   +R +   R     E P++L  +     +SR+R+R +E
Sbjct: 284 EQ----LPELQRSVLSMRYGIDVEEPMSLTGIGRILGMSRDRIRNLE 326


>gi|224000633|ref|XP_002289989.1| plastid RNA polymerase sigma factor [Thalassiosira pseudonana
           CCMP1335]
 gi|220975197|gb|EED93526.1| plastid RNA polymerase sigma factor [Thalassiosira pseudonana
           CCMP1335]
          Length = 321

 Score = 75.5 bits (184), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 48/65 (73%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+V  ++RLVV IA  Y G G+ + ++V EG++GL +A +KFDP++GF+ +TY+ WW
Sbjct: 62  AKQRMVQCNMRLVVSIARRYHGVGVNVQDLVQEGSLGLARAAEKFDPKKGFKFSTYASWW 121

Query: 109 IKAAM 113
           I+ A+
Sbjct: 122 IQQAV 126


>gi|167834949|ref|ZP_02461832.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis
           MSMB43]
          Length = 301

 Score = 75.5 bits (184), Expect = 9e-12,   Method: Compositional matrix adjust.
 Identities = 57/237 (24%), Positives = 119/237 (50%), Gaps = 14/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  R+  ++LRLV+ IA  +   GL +++++ EGN+GL++A++KF+  RGF+ +TY+ W
Sbjct: 60  AATARMAEANLRLVLSIARKHASRGLDLADLLQEGNLGLLRAIEKFEYRRGFKFSTYATW 119

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++      +     +RR++     I   +     +  ++    
Sbjct: 120 WIRQAISRAIADRARTIRVPVHVGDE-----VRRVRKVADRIERRSGARASLAELSAATG 174

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +    + +M        SLNA + + D+  +++ D +    D     L +        ++
Sbjct: 175 LPVERLRAMLMLPREPRSLNAPLGNDDQ--AEFGDLV---EDASTPSLFDALAHGQMCDV 229

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +T  +  ++ +E  I   RR     + P + E ++++  VSRE+VR+IE RA + ++
Sbjct: 230 VTSLLKTMSAQEADILR-RRFGIGGDEPWSYEQIAAQTGVSREQVRRIEKRALQTLR 285


>gi|325479184|gb|EGC82281.1| sigma-70, region 4 [Anaerococcus prevotii ACS-065-V-Col13]
          Length = 343

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 63/246 (25%), Positives = 123/246 (50%), Gaps = 19/246 (7%)

Query: 45  GDLSAAHRLVTSHLRLV-VKIAMGYRGYG--LPISEVVSEGNIGLMQAVKKFDPERGFRL 101
           G+ +A   LV  +  LV  + +  +R +G  L + ++V  G +G+++A +KFD   G++ 
Sbjct: 103 GNQNALAALVEKNQGLVRSRASYFFRSHGNDLDLEDLVQSGMLGMIRAAEKFDLSLGYKF 162

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
            TY+  WI  A+++ I +    ++I         +  L +LK  L+A  +     E++  
Sbjct: 163 TTYAYKWIDKAIRKAINKEGHTIRIPAGK-----YLKLNKLKQILKA--NPEASDEELYR 215

Query: 162 IAKKLNVSE---SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           I +   + +    ++  +N       SLN  ++S D    +  D +  +    + +++E 
Sbjct: 216 ILENEGIDKKQADDLFLINRNQVNSTSLNINLDSEDSTGDELMDMVGDESTPVDMLILE- 274

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARA 276
              K+  N L +++  L  RE++I   R   +N  P TLE +   +++SRER+RQIE +A
Sbjct: 275 ---KDMENFLLKALDQLTDREKQIIIYRYGLDNEKPKTLEEIGKIYDLSRERIRQIENQA 331

Query: 277 FKKVQE 282
             K++E
Sbjct: 332 LGKLKE 337


>gi|167916992|ref|ZP_02504083.1| RNA polymerase sigma factor [Burkholderia pseudomallei BCC215]
          Length = 482

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 57/237 (24%), Positives = 117/237 (49%), Gaps = 14/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  R+  ++LRLV+ IA  Y   GL +++++ EGN+GL++A++KF+  RGF+ +TY+ W
Sbjct: 241 AATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKFSTYATW 300

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++      +      RR++     I   +     +  +++   
Sbjct: 301 WIRQAISRAIADRARTIRVPVHVGDE-----ARRVRKAADRIERRSGVSASLAELSEATG 355

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +    + ++        SLNA +   D + +++ D +    D     L +        ++
Sbjct: 356 LPAERLRAVLTLPREPRSLNAPLG--DDDQAEFGDIV---EDTSTPSLFDALAHGQMCDV 410

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +T  +  ++ +E  I   RR     + P + E +++   VSRE+VR+IE RA + ++
Sbjct: 411 VTSLLKTMSAQEADILR-RRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLR 466


>gi|126453822|ref|YP_001064420.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1106a]
 gi|167736534|ref|ZP_02409308.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 14]
 gi|217424965|ref|ZP_03456461.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 576]
 gi|242317344|ref|ZP_04816360.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1106b]
 gi|254188239|ref|ZP_04894751.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei Pasteur
           52237]
 gi|254295684|ref|ZP_04963141.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 406e]
 gi|126227464|gb|ABN91004.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1106a]
 gi|157805995|gb|EDO83165.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 406e]
 gi|157935919|gb|EDO91589.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei Pasteur
           52237]
 gi|217391985|gb|EEC32011.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 576]
 gi|242140583|gb|EES26985.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1106b]
          Length = 482

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 57/237 (24%), Positives = 117/237 (49%), Gaps = 14/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  R+  ++LRLV+ IA  Y   GL +++++ EGN+GL++A++KF+  RGF+ +TY+ W
Sbjct: 241 AATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKFSTYATW 300

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++      +      RR++     I   +     +  +++   
Sbjct: 301 WIRQAISRAIADRARTIRVPVHVGDE-----ARRVRKAADRIERRSGVSASLAELSEATG 355

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +    + ++        SLNA +   D + +++ D +    D     L +        ++
Sbjct: 356 LPAERLRAVLTLPREPRSLNAPLG--DDDQAEFGDIV---EDTSTPSLFDALAHGQMCDV 410

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +T  +  ++ +E  I   RR     + P + E +++   VSRE+VR+IE RA + ++
Sbjct: 411 VTSLLKTMSAQEADILR-RRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLR 466


>gi|134284106|ref|ZP_01770800.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 305]
 gi|167900733|ref|ZP_02487938.1| RNA polymerase sigma factor [Burkholderia pseudomallei NCTC 13177]
 gi|167908960|ref|ZP_02496051.1| RNA polymerase sigma factor [Burkholderia pseudomallei 112]
 gi|226194652|ref|ZP_03790247.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei
           Pakistan 9]
 gi|134244558|gb|EBA44662.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 305]
 gi|225933353|gb|EEH29345.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei
           Pakistan 9]
          Length = 482

 Score = 75.5 bits (184), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 57/237 (24%), Positives = 117/237 (49%), Gaps = 14/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  R+  ++LRLV+ IA  Y   GL +++++ EGN+GL++A++KF+  RGF+ +TY+ W
Sbjct: 241 AATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKFSTYATW 300

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++      +      RR++     I   +     +  +++   
Sbjct: 301 WIRQAISRAIADRARTIRVPVHVGDE-----ARRVRKAADRIERRSGVSASLAELSEATG 355

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +    + ++        SLNA +   D + +++ D +    D     L +        ++
Sbjct: 356 LPAERLRAVLTLPREPRSLNAPLG--DDDQAEFGDIV---EDTSTPSLFDALAHGQMCDV 410

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +T  +  ++ +E  I   RR     + P + E +++   VSRE+VR+IE RA + ++
Sbjct: 411 VTSLLKTMSAQEADILR-RRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLR 466


>gi|167717486|ref|ZP_02400722.1| RNA polymerase sigma factor [Burkholderia pseudomallei DM98]
          Length = 294

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 56/237 (23%), Positives = 117/237 (49%), Gaps = 14/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  R+  ++LRLV+ IA  Y   GL +++++ EGN+GL++A++KF+  RGF+ +TY+ W
Sbjct: 53  AATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKFSTYATW 112

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   +      +++      +      RR++     I   +     +  +++   
Sbjct: 113 WIRQAISRAVADRARTIRVPVHVGDE-----ARRVRKAADRIERRSGVSASLAELSEATG 167

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +    + ++        SLNA +   D + +++ D +    D     L +        ++
Sbjct: 168 LPAERLRAVLTLPREPRSLNAPLG--DDDQAEFGDIV---EDTSTPSLFDALAHGQMCDV 222

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +T  +  ++ +E  I   RR     + P + E +++   VSRE+VR+IE RA + ++
Sbjct: 223 VTSLLKTMSAQEADILR-RRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLR 278


>gi|221212018|ref|ZP_03584996.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           multivorans CGD1]
 gi|221168103|gb|EEE00572.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           multivorans CGD1]
          Length = 625

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 66/241 (27%), Positives = 114/241 (47%), Gaps = 28/241 (11%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L  ++LRLVV IA  Y   GLP ++++ EGNIGL++A+ ++D  RGFR +TY+ WWI+ +
Sbjct: 392 LFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWWIRQS 451

Query: 113 MQEYILRSWSLVKIGT-TANQ----KRLFFNLRRLKGHLQAITDNNLKPE--QVVAIAKK 165
           +   +      +++ T T +      RL    R+  G   A T + L  +  + V   ++
Sbjct: 452 ITHALADLGRTIRVPTHTVDAINKLARLAREHRQRAG--AAATPDELAAQMGEPVDKVRE 509

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           L     E +S++  +A D  +  +    D ++   +               +  +   RR
Sbjct: 510 LMAIVKEPVSVDLPIAPDGDMTFVDVVPDASTPSPE---------------DAADAAQRR 554

Query: 226 NMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             +  ++  L PRE  I   R      E   +L ++     +S ERVRQIEA A  +++ 
Sbjct: 555 AAIAAAIDRLPPREALIVRLRYGLHAGEG-CSLRDIGRRLNLSAERVRQIEASALARLRA 613

Query: 283 S 283
           S
Sbjct: 614 S 614


>gi|229118995|ref|ZP_04248338.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock1-3]
 gi|228664438|gb|EEL19936.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock1-3]
          Length = 294

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 71/273 (26%), Positives = 130/273 (47%), Gaps = 13/273 (4%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY--GLPISE 77
           I EI    +L KQE   L +RY+ HG+      L   ++ LV+ IA  Y+     +   +
Sbjct: 11  IKEIGNYKVLSKQESLKLFQRYK-HGEKDLRDYLFHVNVGLVLSIARKYKNKHPDIEFDD 69

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS-LVKIGTTANQKRLF 136
           +V EGN G+++A++ F+P  G+  +TY+ WWI+ +M   I +  S   KI    NQ    
Sbjct: 70  LVQEGNEGMLRAMEDFNPALGYCFSTYAFWWIQKSMLGIICKKKSGPFKIPNYVNQ---- 125

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
           FNL+ ++   + +   N  P  V  + K+L+V+   VI  N       ++   I++ +++
Sbjct: 126 FNLKYVELEDKYLQMYNRTP-TVEEVVKELDVTSETVIRHNVYYKRATTMTLDIDTINED 184

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE-ARRLQENPVTL 255
               + +  YD +    ++ E         +      VLNP+++ +      L +  V L
Sbjct: 185 IGMSKPF--YDDNSAIPLINEIVIEDLNYEIWLIFDEVLNPKQKMVLNLCFGLLDGKVYL 242

Query: 256 -ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            + ++    ++ ERV QI+  A KK+++   K 
Sbjct: 243 HKEIAKALMITTERVSQIKEEAIKKLKKCDYKD 275


>gi|167950928|ref|ZP_02538002.1| RNA polymerase sigma factor RpoS [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 216

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 64/223 (28%), Positives = 115/223 (51%), Gaps = 24/223 (10%)

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           + + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      
Sbjct: 1   MALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-V 59

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
           K +   LR  +   Q++ D+    E++  +  K        IS   R+ G   LN  + S
Sbjct: 60  KEINVYLRAARQLAQSL-DHEPTSEEIADLLDK-------PISEVKRMLG---LNERVTS 108

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN-----MLTRSMSVLNPRERRIFEAR- 246
            D    +  D  + D    E+V   ++   N +N      L   +  LN ++R + E R 
Sbjct: 109 VDTPFGKDADKPLLDTIPDERV---QDPTVNIQNDGLNTNLDTWLLKLNDKQREVVERRF 165

Query: 247 --RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
                EN  TLE +++E  V+RERVRQI+  A +++++ +++ 
Sbjct: 166 GLHGYENS-TLEQVANELGVTRERVRQIQMDALRRLRDILERD 207


>gi|33862400|ref|NP_893960.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9313]
 gi|33640513|emb|CAE20302.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9313]
          Length = 335

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 56/225 (24%), Positives = 104/225 (46%), Gaps = 9/225 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+V+++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP RG++ +TY+ WW
Sbjct: 100 AKERMVSANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWW 159

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   I      +++     +      L +LK   + ++    +   V  +A+ + +
Sbjct: 160 IRQGITRAIAEKSRTIRLPIHITEM-----LNKLKKGQRELSQEMGRTPTVSELAEFVEL 214

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E EV  + CR     SL   +   D+           +   ++   +E +  K     L
Sbjct: 215 PEEEVKDLMCRARQPMSLEMKVGDGDETELLELLAGEEELPSEK---VEVDCMKGDLRTL 271

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
              +  L  R  R+       E P+ L  +    ++SR+RVR +E
Sbjct: 272 LEKLPELQGRVLRMRYGIDGGE-PMNLTGIGRILDISRDRVRNLE 315


>gi|227485585|ref|ZP_03915901.1| DNA-directed RNA polymerase sigma subunit RpoD [Anaerococcus
           lactolyticus ATCC 51172]
 gi|227236451|gb|EEI86466.1| DNA-directed RNA polymerase sigma subunit RpoD [Anaerococcus
           lactolyticus ATCC 51172]
          Length = 340

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 56/222 (25%), Positives = 114/222 (51%), Gaps = 18/222 (8%)

Query: 68  YRGYG--LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
           +R +G  L + ++V  G +G+++A +KFD   G++  TY+  WI  A+++ I +    ++
Sbjct: 124 FRSHGNDLDLEDLVQSGMLGMIRAAEKFDLTLGYKFTTYAYKWIDKAIRKAINKEGHTIR 183

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE---SEVISMNCRLAG 182
           I         +  L +LK  L+A  +     E++  I +   +++    ++  +N     
Sbjct: 184 IPAGK-----YLKLNKLKQILKA--NPEASDEEIYRILENEGINKKQADDLFLINRNQVN 236

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             SLN  ++S D    +  D +  +    + +++EK+      N L +++  L  RE++I
Sbjct: 237 STSLNINLDSEDSTGDELMDMVGDESTPVDMLILEKD----MENFLMQALDQLTDREKQI 292

Query: 243 FEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              R   +N  P TLE + + +++SRER+RQIE +A  K+++
Sbjct: 293 IIYRYGLDNEKPKTLEQIGAIYDLSRERIRQIENQALGKLKD 334


>gi|291529642|emb|CBK95228.1| RNA polymerase sigma factor, sigma-70 family [Eubacterium rectale
           M104/1]
          Length = 340

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 77/296 (26%), Positives = 141/296 (47%), Gaps = 47/296 (15%)

Query: 16  LSRYIHEIRKI-PMLEKQEEYV---LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG- 70
           LS Y++E+ K  P  E++E+ V   L++   E         + + ++RLVV +A  Y   
Sbjct: 44  LSMYMYEMSKWQPFTEEEEKQVFKELSETESEDKKKQLKDEIFSRNIRLVVYVAKRYYKN 103

Query: 71  --YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
             +  PI +++ E ++GL++A+ ++D   G++ +TY+ WWI  A    I     L++   
Sbjct: 104 LKHMEPI-DLIDEASLGLLKAIDRYDYTTGYKFSTYAYWWINQACTRSIANDNDLIRQPV 162

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV-------------IS 175
             ++      +++ +       DNN     V  IAK+LNVSE +V             IS
Sbjct: 163 HIHE--FIIKVKKAQRKWGQTHDNNAP---VDYIAKELNVSEEKVRNILIIIDCQSNYIS 217

Query: 176 MNCRLA------GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           ++C ++      GD  +  ++     N     D+   + +  +  +IE   + N +    
Sbjct: 218 LDCTMSKGSEEPGDTEVGEIVLDPKGNV----DFEKVEVNQFQNRIIEILSKANNKTSAK 273

Query: 230 RSMSV------LNPRERRI-FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
            + SV      ++  +RR  F+  R++    TLE ++  + VSRER+RQIEA+A K
Sbjct: 274 SNRSVEQTKRMIDVIKRRFGFDNCRIE----TLEEIAQSYGVSRERIRQIEAQALK 325


>gi|40353301|gb|AAR84414.1| essential primary sigma 70 factor [Frankia sp. ORS020607]
 gi|40353303|gb|AAR84415.1| essential primary sigma 70 factor [Frankia sp. CcI3]
 gi|40353305|gb|AAR84416.1| essential primary sigma 70 factor [Frankia sp. CeD]
          Length = 217

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 51/157 (32%), Positives = 84/157 (53%), Gaps = 15/157 (9%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +LV ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WW
Sbjct: 32  AKRKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 91

Query: 109 IKAAMQEYILRSWSLVKIGT----TAN-----QKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N     Q++L  +L R     +   + +L P++V
Sbjct: 92  IRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPSPEEIAKEMDLTPDKV 151

Query: 160 VAIAKKLNVSESEVISMNCRLAGDES--LNALINSSD 194
             I   L VS+ E +S+   +  +E   L   I   D
Sbjct: 152 REI---LKVSQ-EPVSLETPIGEEEDSHLGDFIEDCD 184


>gi|255312659|gb|ACU01739.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 32/61 (52%), Positives = 46/61 (75%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFD ERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDLERGFRFSTYATWWIRQTIERAI 60

Query: 118 L 118
           +
Sbjct: 61  M 61


>gi|33863339|ref|NP_894899.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9313]
 gi|33640788|emb|CAE21243.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9313]
          Length = 320

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 41/146 (28%), Positives = 75/146 (51%), Gaps = 5/146 (3%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+V+++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP RG++ +TY+ WW
Sbjct: 85  AKERMVSANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWW 144

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   I      +++     +      L +LK   + ++    +   V  +A+ + +
Sbjct: 145 IRQGITRAIAEKSRTIRLPIHITE-----MLNKLKKGQRELSQEMGRTPTVSELAEFVEL 199

Query: 169 SESEVISMNCRLAGDESLNALINSSD 194
            E EV  + CR     SL   +   D
Sbjct: 200 PEEEVKDLMCRARQPMSLEMKVGDGD 225


>gi|227501074|ref|ZP_03931123.1| DNA-directed RNA polymerase sigma subunit RpoD [Anaerococcus
           tetradius ATCC 35098]
 gi|227216847|gb|EEI82245.1| DNA-directed RNA polymerase sigma subunit RpoD [Anaerococcus
           tetradius ATCC 35098]
          Length = 344

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 63/246 (25%), Positives = 123/246 (50%), Gaps = 19/246 (7%)

Query: 45  GDLSAAHRLVTSHLRLV-VKIAMGYRGYG--LPISEVVSEGNIGLMQAVKKFDPERGFRL 101
           G+ +A   LV  +  LV  + +  +R +G  L + ++V  G +G+++A +KFD   G++ 
Sbjct: 104 GNQNALAALVEKNQGLVRSRASYFFRSHGNDLDLEDLVQSGMLGMIRAAEKFDLSLGYKF 163

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
            TY+  WI  A+++ I +    ++I         +  L +LK  L+A  +     E++  
Sbjct: 164 TTYAYKWIDKAIRKAINKEGHTIRIPAGK-----YLKLNKLKQILKA--NPEASDEELYR 216

Query: 162 IAKKLNVSE---SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           I +   + +    ++  +N       SLN  ++S D    +  D +  +    + +++E 
Sbjct: 217 ILENEGIDKKQADDLFLINRNQVNSTSLNINLDSEDSTGDELMDMVGDESTPVDMLILE- 275

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARA 276
              K+  N L +++  L  RE++I   R   +N  P TLE +   +++SRER+RQIE +A
Sbjct: 276 ---KDMENFLLKALDQLTDREKQIIIYRYGLDNEKPKTLEEIGKIYDLSRERIRQIENQA 332

Query: 277 FKKVQE 282
             K++E
Sbjct: 333 LGKLKE 338


>gi|40353311|gb|AAR84419.1| essential primary sigma 70 factor [Frankia sp. ACN14a]
          Length = 214

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 51/157 (32%), Positives = 84/157 (53%), Gaps = 15/157 (9%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +LV ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WW
Sbjct: 29  AKRKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 88

Query: 109 IKAAMQEYILRSWSLVKIGT----TAN-----QKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N     Q++L  +L R     +   + +L P++V
Sbjct: 89  IRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPSPEEIAKEMDLTPDKV 148

Query: 160 VAIAKKLNVSESEVISMNCRLAGDES--LNALINSSD 194
             I   L VS+ E +S+   +  +E   L   I   D
Sbjct: 149 REI---LKVSQ-EPVSLETPIGEEEDSHLGDFIEDCD 181


>gi|328883104|emb|CCA56343.1| RNA polymerase principal sigma factor HrdD [Streptomyces venezuelae
           ATCC 10712]
          Length = 333

 Score = 75.1 bits (183), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 69/231 (29%), Positives = 117/231 (50%), Gaps = 20/231 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 101 FIKSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYAKGFKFSTYATWWIRQA 160

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   I      +++     ++     +RR++       ++  +PE    IA +L+     
Sbjct: 161 ITRSIADQSRTIRLPVHLVEE--LGRIRRVQREFN--REHGREPEP-AEIAAELDTKPER 215

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG--QEQ---VLIEKEERKNRRNM 227
           V+ +        SLN  ++  D+  +Q+ D L+ D      EQ    L+  EE  +  + 
Sbjct: 216 VVDVLDWARDPVSLNMSVD--DEGETQFGD-LLEDTSAVSPEQSVLTLLRSEELDDLIDK 272

Query: 228 LT-RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
           L  R+ S++  R R   E  R +    TL  +  E  ++RER+RQIE  A 
Sbjct: 273 LDHRTASII--RMRYGIEDGRER----TLTEVGKEHGLTRERIRQIEKHAL 317


>gi|17158751|ref|NP_478262.1| transcription initiation factor sigma [Nostoc sp. PCC 7120]
 gi|464687|sp|Q03065|RPSB_ANASP RecName: Full=RNA polymerase sigma-B factor
 gi|424021|pir||B47017 probable transcription initiation factor sigma SigB - Anabaena sp
 gi|142112|gb|AAA22046.1| RNA polymerase sigma-subunit [Nostoc sp. PCC 7120]
 gi|17134700|dbj|BAB77258.1| transcription initiation factor sigma [Nostoc sp. PCC 7120]
          Length = 332

 Score = 74.7 bits (182), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 63/235 (26%), Positives = 111/235 (47%), Gaps = 21/235 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +++ ++LRLVV IA  Y+   L   +++ EG +GL + V+KFDP  G++ +TY+ WW
Sbjct: 97  AKQKMIQANLRLVVSIAKKYQKRNLEFLDLIQEGALGLERGVEKFDPTLGYKFSTYAYWW 156

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   I +    +++      K     L ++K   + ++        V  IA+ LN+
Sbjct: 157 IRQGITRAIAQQSRTIRLPIHMADK-----LNKIKCVQRELSQKLGYIAGVTEIAQALNL 211

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
             S++      +    SL+  I    +  +Q QD L    DG         ER   R +L
Sbjct: 212 EPSQIREYLQLVRQPVSLDMRIGF--EQDTQLQDLL--KDDGM------SPERYAERELL 261

Query: 229 TRS----MSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAF 277
            +     ++ L P+++ +   R        +TL  +S    +SRERVRQ+E +A 
Sbjct: 262 YQDIHNLLAKLTPQQKEVLILRFGLAGGCELTLVQISQRMGISRERVRQVEKQAL 316


>gi|229100411|ref|ZP_04231282.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock3-29]
 gi|229107324|ref|ZP_04237193.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock3-28]
 gi|228676119|gb|EEL31095.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock3-28]
 gi|228683031|gb|EEL37038.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock3-29]
          Length = 323

 Score = 74.7 bits (182), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 71/273 (26%), Positives = 130/273 (47%), Gaps = 13/273 (4%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY--GLPISE 77
           I EI    +L KQE   L +RY+ HG+      L   ++ LV+ IA  Y+     +   +
Sbjct: 40  IKEIGNYKVLSKQESLKLFQRYK-HGEKDLRDYLFHVNVGLVLSIARKYKNKHPDIEFDD 98

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS-LVKIGTTANQKRLF 136
           +V EGN G+++A++ F+P  G+  +TY+ WWI+ +M   I +  S   KI    NQ    
Sbjct: 99  LVQEGNEGMLRAMEDFNPALGYCFSTYAFWWIQKSMLGIICKKKSGPFKIPNYVNQ---- 154

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
           FNL+ ++   + +   N  P  V  + K+L+V+   VI  N       ++   I++ +++
Sbjct: 155 FNLKYVELEDKYLQMYNRTP-TVEEVVKELDVTSETVIRHNVYYKRATTMTLDIDTINED 213

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE-ARRLQENPVTL 255
               + +  YD +    ++ E         +      VLNP+++ +      L +  V L
Sbjct: 214 IGMSKPF--YDDNSAIPLINEIVIEDLNYEIWLIFDEVLNPKQKMVLNLCFGLLDGKVYL 271

Query: 256 -ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            + ++    ++ ERV QI+  A KK+++   K 
Sbjct: 272 HKEIAKALMITTERVSQIKEEAIKKLKKCDYKD 304


>gi|166364164|ref|YP_001656437.1| RNA polymerase sigma factor [Microcystis aeruginosa NIES-843]
 gi|166086537|dbj|BAG01245.1| group 2 RNA polymerase sigma factor [Microcystis aeruginosa
           NIES-843]
          Length = 328

 Score = 74.7 bits (182), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 65/302 (21%), Positives = 133/302 (44%), Gaps = 56/302 (18%)

Query: 19  YIHEIRKIPMLEKQEEYVLAK--------------------------------------- 39
           Y+HEI ++P+L  ++E +  K                                       
Sbjct: 23  YLHEIGRVPLLTHEQEIIYGKQVQRMMSLLETKEALSKQLGREPDRLEWADSVNLSENEL 82

Query: 40  -RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
            R  + GD  A  +++ ++LRLVV IA  Y+   +   +++ EG++GL + V+KFDP +G
Sbjct: 83  DRALKTGD-RAKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGSLGLERGVEKFDPTKG 141

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           ++ +TY+ WWI+ A+   I +    +++     +K     ++R +  L      +  P +
Sbjct: 142 YKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEK--LNKIKRTQRELAQKLGRSATPAE 199

Query: 159 VVAIAKKLNVSE-SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
            +A+  +L  ++  E +SM       + ++  +   D   ++  + L       +  + +
Sbjct: 200 -IALELELEPAQIREYLSM-----ARQPISLDVRVGDNQDTELSELLEDSGVSPDTFITQ 253

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEAR 275
           +  R++  N+L      L P++R +   R        ++L  +     +SRERVRQ+E +
Sbjct: 254 ELLRQDLANLLAE----LTPQQREVITLRFGLTDGKELSLAKIGQRMNISRERVRQLEHQ 309

Query: 276 AF 277
           A 
Sbjct: 310 AL 311


>gi|124026787|ref|YP_001015902.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. NATL1A]
 gi|123961855|gb|ABM76638.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. NATL1A]
          Length = 335

 Score = 74.7 bits (182), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 61/241 (25%), Positives = 114/241 (47%), Gaps = 14/241 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+V ++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP RG++ +TY+ WW
Sbjct: 100 AKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWW 159

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   I      +++     +      L +LK   + ++    +   +  +++ + +
Sbjct: 160 IRQGITRAIAEKSRSIRLPIHITEM-----LNKLKKGQRELSQELSRTPTLKELSEYVEL 214

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNM 227
            E++V  +  R     SL   I   D   +   D L  + D   EQ  IE +  K     
Sbjct: 215 PETDVKDLMSRAGQPVSLETKIG--DGEDTILLDLLSNEIDMPSEQ--IESDCMKGDLET 270

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE---ARAFKKVQESI 284
           L   +  L  R  R+       ++P++L  +     +SR+RVR +E    R  +K  +S+
Sbjct: 271 LLEQLPELQNRVLRMRYGMD-GDDPMSLTGIGRVLGISRDRVRNLERDGLRGLRKTGDSV 329

Query: 285 Q 285
           +
Sbjct: 330 E 330


>gi|326773494|ref|ZP_08232777.1| RNA polymerase sigma (70) factor RpoD [Actinomyces viscosus C505]
 gi|326636724|gb|EGE37627.1| RNA polymerase sigma (70) factor RpoD [Actinomyces viscosus C505]
          Length = 164

 Score = 74.7 bits (182), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 44/122 (36%), Positives = 68/122 (55%), Gaps = 27/122 (22%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH------GDLSAAHR--------------- 52
           Y+ +I K+ +L  ++E  LAKR     Y EH       DL A  R               
Sbjct: 27  YLKQIGKVALLNAEQEVELAKRIEAGLYAEHRLAEEGNDLPAKLRRELHWVAQDGQRAKN 86

Query: 53  -LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ 
Sbjct: 87  HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQ 146

Query: 112 AM 113
           A+
Sbjct: 147 AI 148


>gi|326773500|ref|ZP_08232783.1| RNA polymerase sigma (70) factor RpoD [Actinomyces viscosus C505]
 gi|326636730|gb|EGE37633.1| RNA polymerase sigma (70) factor RpoD [Actinomyces viscosus C505]
          Length = 311

 Score = 74.7 bits (182), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 44/122 (36%), Positives = 68/122 (55%), Gaps = 27/122 (22%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH------GDLSAAHR--------------- 52
           Y+ +I K+ +L  ++E  LAKR     Y EH       DL A  R               
Sbjct: 167 YLKQIGKVALLNAEQEVELAKRIEAGLYAEHRLAEEGNDLPAKLRRELHWVAQDGQRAKN 226

Query: 53  -LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ 
Sbjct: 227 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQ 286

Query: 112 AM 113
           A+
Sbjct: 287 AI 288


>gi|48743|emb|CAA37174.1| unnamed protein product [Streptomyces coelicolor A3(2)]
          Length = 332

 Score = 74.7 bits (182), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 76/290 (26%), Positives = 134/290 (46%), Gaps = 43/290 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-------------YREHGDLSAAHRL------------ 53
           Y+ EI + P+L+  +E  L++              Y E G  +    L            
Sbjct: 39  YLDEIARTPLLDAAKEVELSQTIEAGVFARQVLEGYEETGADATREELQALIDESERAKD 98

Query: 54  --VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
             + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ WWI+ 
Sbjct: 99  VFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTYATWWIRQ 158

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           A+   I      +++     ++     +RR++       ++  +PE    IA +L  +  
Sbjct: 159 AITRSIADQSRTIRLPVHLVEE--LGRIRRVQREFN--REHGREPEP-AEIAAELGSTPE 213

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG--QEQVLIEKEERKNRRNMLT 229
            V  +        SLN  ++  D+  +Q+ D L+ D      EQ ++     +   +++ 
Sbjct: 214 RVHDVLDWARDPVSLNMSVD--DEGETQFGD-LLEDTSAVSPEQSVLTLLRSEELDDLIG 270

Query: 230 RSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
           R    L+PR   I + R   ++    TL  +  E  ++RER+RQIE  A 
Sbjct: 271 R----LDPRTASIIKMRYGIDDGRERTLTEVGKEHGLTRERIRQIEKHAL 316


>gi|124022691|ref|YP_001016998.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Prochlorococcus marinus str. MIT 9303]
 gi|123962977|gb|ABM77733.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Prochlorococcus marinus str. MIT 9303]
          Length = 320

 Score = 74.7 bits (182), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 41/146 (28%), Positives = 75/146 (51%), Gaps = 5/146 (3%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+V+++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP RG++ +TY+ WW
Sbjct: 85  AKERMVSANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWW 144

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   I      +++     +      L +LK   + ++    +   V  +A+ + +
Sbjct: 145 IRQGITRAIAEKSRTIRLPIHITE-----MLNKLKKGQRELSQEMGRTPTVSELAEFVEL 199

Query: 169 SESEVISMNCRLAGDESLNALINSSD 194
            E EV  + CR     SL   +   D
Sbjct: 200 PEEEVKDLMCRARQPMSLEMKVGDGD 225


>gi|124021877|ref|YP_001016184.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Prochlorococcus marinus str. MIT 9303]
 gi|123962163|gb|ABM76919.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Prochlorococcus marinus str. MIT 9303]
          Length = 350

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 56/225 (24%), Positives = 104/225 (46%), Gaps = 9/225 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+V+++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP RG++ +TY+ WW
Sbjct: 115 AKERMVSANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWW 174

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   I      +++     +      L +LK   + ++    +   V  +A+ + +
Sbjct: 175 IRQGITRAIAEKSRTIRLPIHITEM-----LNKLKKGQRELSQEMGRTPTVSELAEFVEL 229

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E EV  + CR     SL   +   D+           +   ++   +E +  K     L
Sbjct: 230 PEEEVKDLMCRARQPMSLEMKVGDGDETELLELLAGEEELPSEK---VEVDCMKGDLRTL 286

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
              +  L  R  R+       E P+ L  +    ++SR+RVR +E
Sbjct: 287 LEKLPELQGRVLRMRYGIDGGE-PMNLTGIGRILDISRDRVRNLE 330


>gi|53717743|ref|YP_106729.1| RNA polymerase sigma factor [Burkholderia pseudomallei K96243]
 gi|52208157|emb|CAH34087.1| RNA polymerase sigma factor [Burkholderia pseudomallei K96243]
          Length = 482

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 57/237 (24%), Positives = 117/237 (49%), Gaps = 14/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  R+  ++LRLV+ IA  Y   GL +++++ EGN+GL++A++KF+  RGF+ +TY+ W
Sbjct: 241 AATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKFSTYATW 300

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++      +      RR++     I   +     +  +++   
Sbjct: 301 WIRQAISRAIADRARTIRVPVHVGDE-----ARRVRKAADRIERRSGVNASLAELSEATG 355

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +    + ++        SLNA +   D + +++ D +    D     L +        ++
Sbjct: 356 LPAERLRAVLTLPREPRSLNAPLG--DDDQAEFGDIV---EDTSTPSLFDALAHGQMCDV 410

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +T  +  ++ +E  I   RR     + P + E +++   VSRE+VR+IE RA + ++
Sbjct: 411 VTSLLKTMSAQEADILR-RRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLR 466


>gi|302335912|ref|YP_003801119.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Olsenella uli DSM
           7084]
 gi|301319752|gb|ADK68239.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Olsenella uli DSM
           7084]
          Length = 276

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 69/266 (25%), Positives = 121/266 (45%), Gaps = 29/266 (10%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           +K+    L +RY+  GD  A  +LV SHL LV  +A  ++  G P+ ++V  G IGL++A
Sbjct: 28  DKERTRELFRRYKVEGDEDAREQLVMSHLNLVRFLASKFKNRGEPLDDLVQVGTIGLIKA 87

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           + +FDPERG    T++   I   ++ +   + WS+          R+   L+ L   +  
Sbjct: 88  IDRFDPERGLEFTTFATPTIMGEIKRHFRDKGWSV----------RVPRRLQELSAKVNQ 137

Query: 149 ITDNNLKPEQVVAIAKKLNVSES-EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
           +TD          + K L  S S E I+       DE L A+ +SS  +S   +      
Sbjct: 138 VTDE---------LTKDLQRSPSVEEIAAALDTTVDEVLEAMESSSAYSSVPLEGTGPGA 188

Query: 208 HDGQEQVL------IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
            D    V+       E     + R ++  ++   +PRE+ I   R ++   +T   ++  
Sbjct: 189 DDDAPSVIDHYATVDEDLAASDDRMVIEETVRDFSPREQEIIRMRFIE--GLTQVEIARR 246

Query: 262 FEVSRERVRQIEARAFKKVQESIQKQ 287
             +S+ +V ++  R  +KVQE I  +
Sbjct: 247 LGISQVQVSRLLRRTLQKVQEKIDPE 272


>gi|76812098|ref|YP_331741.1| RNA polymerase sigma factor [Burkholderia pseudomallei 1710b]
 gi|254261622|ref|ZP_04952676.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1710a]
 gi|76581551|gb|ABA51026.1| RNA polymerase sigma factor [Burkholderia pseudomallei 1710b]
 gi|254220311|gb|EET09695.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1710a]
          Length = 482

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 56/237 (23%), Positives = 117/237 (49%), Gaps = 14/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  R+  ++LRLV+ IA  Y   GL +++++ EGN+GL++A++KF+  RGF+ +TY+ W
Sbjct: 241 AATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKFSTYATW 300

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   +      +++      +      RR++     I   +     +  +++   
Sbjct: 301 WIRQAISRAVADRARTIRVPVHVGDE-----ARRVRKAADRIERRSGVSASLAELSEATG 355

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +    + ++        SLNA +   D + +++ D +    D     L +        ++
Sbjct: 356 LPAERLRAVLTLPREPRSLNAPLG--DDDQAEFGDIV---EDTSTPSLFDALAHGQMCDV 410

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +T  +  ++ +E  I   RR     + P + E +++   VSRE+VR+IE RA + ++
Sbjct: 411 VTSLLKTMSAQEADILR-RRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLR 466


>gi|237810316|ref|YP_002894767.1| RNA polymerase sigma factor [Burkholderia pseudomallei MSHR346]
 gi|237504080|gb|ACQ96398.1| RNA polymerase sigma factor [Burkholderia pseudomallei MSHR346]
          Length = 482

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 56/237 (23%), Positives = 117/237 (49%), Gaps = 14/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  R+  ++LRLV+ IA  Y   GL +++++ EGN+GL++A++KF+  RGF+ +TY+ W
Sbjct: 241 AATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKFSTYATW 300

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   +      +++      +      RR++     I   +     +  +++   
Sbjct: 301 WIRQAISRAVADRARTIRVPVHVGDE-----ARRVRKAADRIERRSGVSASLAELSEATG 355

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +    + ++        SLNA +   D + +++ D +    D     L +        ++
Sbjct: 356 LPAERLRAVLTLPREPRSLNAPLG--DDDQAEFGDIV---EDTSTPSLFDALAHGQMCDV 410

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +T  +  ++ +E  I   RR     + P + E +++   VSRE+VR+IE RA + ++
Sbjct: 411 VTSLLKTMSAQEADILR-RRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLR 466


>gi|254182275|ref|ZP_04888872.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1655]
 gi|184212813|gb|EDU09856.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1655]
          Length = 482

 Score = 74.7 bits (182), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 56/237 (23%), Positives = 117/237 (49%), Gaps = 14/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  R+  ++LRLV+ IA  Y   GL +++++ EGN+GL++A++KF+  RGF+ +TY+ W
Sbjct: 241 AATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEHRRGFKFSTYATW 300

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   +      +++      +      RR++     I   +     +  +++   
Sbjct: 301 WIRQAISRAVADRARTIRVPVHVGDE-----ARRVRKAADRIERRSGVSASLAELSEATG 355

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +    + ++        SLNA +   D + +++ D +    D     L +        ++
Sbjct: 356 LPAERLRAVLTLPREPRSLNAPLG--DDDQAEFGDIV---EDTSTPSLFDALAHGQMCDV 410

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +T  +  ++ +E  I   RR     + P + E +++   VSRE+VR+IE RA + ++
Sbjct: 411 VTSLLKTMSAQEADILR-RRFGIGGDEPWSYEQIAARAGVSREQVRRIEKRALQTLR 466


>gi|221195774|ref|ZP_03568827.1| RNA polymerase sigma-F factor [Atopobium rimae ATCC 49626]
 gi|221184248|gb|EEE16642.1| RNA polymerase sigma-F factor [Atopobium rimae ATCC 49626]
          Length = 276

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 72/277 (25%), Positives = 123/277 (44%), Gaps = 38/277 (13%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           R  P  +K     L  +Y+E  D     +L+ SHL LV  +A  ++  G P+ +++  G 
Sbjct: 21  RGTPAWDKDRTRKLFAQYQETHDSEVRDQLIVSHLNLVRFLASKFKNRGEPLDDLIQVGT 80

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRL 142
           IGL++A+ +FDP RG    TY+   I   ++ +   + WS+          R+   L+ L
Sbjct: 81  IGLIKAIDRFDPSRGLEFTTYATPTIMGEIKRHFRDKGWSV----------RVPRRLQEL 130

Query: 143 KGHLQAITDNNLKPEQ----VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
              +  ITD      Q    +  IAKKL VS  EV+               + SS   SS
Sbjct: 131 SAKVNQITDELTTELQRSPSIEEIAKKLGVSVDEVLEA-------------MESSGAYSS 177

Query: 199 QWQDWLVYDHDGQE------QVLIEKE--ERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
              +      DG E      Q + E E     + R +L  +++  +PRE+ I   R ++ 
Sbjct: 178 VPLEGGGSSVDGDEAPSIIDQYITEDEALAGSDDRIVLEDAIADFSPREQEIIRMRFVE- 236

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             +T   ++ +  +S+ +V ++  R  K++QE I  +
Sbjct: 237 -GLTQVEIAEKLGISQVQVSRLLRRTLKRIQEKIDPE 272


>gi|294629875|ref|ZP_06708435.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. e14]
 gi|292833208|gb|EFF91557.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. e14]
          Length = 332

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 65/231 (28%), Positives = 107/231 (46%), Gaps = 20/231 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 100 FIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTYATWWIRQA 159

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   I      +++        L   L R++   +     N +  +   IA +L  +   
Sbjct: 160 ITRSIADQSRTIRLPV-----HLVEELGRIRRVQREFNRENGRDPEPAEIAAELGSTPER 214

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWL----VYDHDGQEQVLIEKEERKNRRNML 228
           V  +        SLN  ++  D+  +Q+ D L        +     L+  EE       L
Sbjct: 215 VADVLDWARDPVSLNMSVD--DEGETQFGDLLEDTSAVSPEQSVMTLLRSEE-------L 265

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
              +  L+ R   I + R   E+    TL  +  E  ++RER+RQIE  A 
Sbjct: 266 DDLIGRLDQRTASIIKMRYGIEDGRERTLTEVGKEHGLTRERIRQIEKHAL 316


>gi|239981636|ref|ZP_04704160.1| RNA polymerase principal sigma factor hrdD [Streptomyces albus
           J1074]
 gi|291453499|ref|ZP_06592889.1| RNA polymerase sigma factor [Streptomyces albus J1074]
 gi|17366575|sp|Q59914|HRDD_STRGR RecName: Full=RNA polymerase principal sigma factor hrdD
 gi|510454|emb|CAA56305.1| sigma factor [Streptomyces griseus]
 gi|291356448|gb|EFE83350.1| RNA polymerase sigma factor [Streptomyces albus J1074]
          Length = 332

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 83/311 (26%), Positives = 137/311 (44%), Gaps = 56/311 (18%)

Query: 7   SIIVNGEIG----LSRYIHEIRKIPMLEKQEEYVLAKRYREHG-------------DLSA 49
           S+   GEI     +  Y+ EI + P+L+  +E  L++   E G             D + 
Sbjct: 22  SVRATGEIADRDLVGMYLDEIARTPLLDAAKEVELSQTI-EAGVYAGKILDGEVDSDSAG 80

Query: 50  AHR----------------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           A R                 + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KF
Sbjct: 81  ASREELEALVAEGERAKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKF 140

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D  +GF+ +TY+ WWI+ A+   I      +++        L   L R++   +     N
Sbjct: 141 DYAKGFKFSTYATWWIRQAITRSIADQSRTIRLPV-----HLVEELGRIRRVQREFNREN 195

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG--Q 211
            +  +   IA +L+ +   V  +        SLN  ++  D+  +Q+ D L+ D      
Sbjct: 196 GRDPEPAEIAAELSSTPERVTDVLDWARDPVSLNMSVD--DEGETQFGD-LLEDTSAVSP 252

Query: 212 EQ---VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSR 266
           EQ    L+  EE       L   +  L+ R   I + R   E+    TL  +  +  ++R
Sbjct: 253 EQSVLTLLRSEE-------LDDLIGQLDDRTASIIKMRYGIEDGRERTLTEVGKQHGLTR 305

Query: 267 ERVRQIEARAF 277
           ER+RQIE  A 
Sbjct: 306 ERIRQIEKHAL 316


>gi|307107488|gb|EFN55731.1| hypothetical protein CHLNCDRAFT_35462 [Chlorella variabilis]
          Length = 267

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 68/247 (27%), Positives = 117/247 (47%), Gaps = 26/247 (10%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA-TYS 105
           L A   +V  ++RLVV IA  Y G GL + ++V+EG +GL +AV KFD     ++   Y+
Sbjct: 24  LQAREHMVNCNMRLVVSIAKKYVGRGLALQDLVAEGMVGLQRAVDKFDASTRLQVTPAYA 83

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
            WWI+ ++   I     +V++    ++      +RR +   QA+ D         A+A +
Sbjct: 84  HWWIRQSVTRAISDQARVVRLPVHLHEA--MGKVRRAE---QALWDETGLLPAPQAVADR 138

Query: 166 LNVSESEVISMNCRL------AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             ++ S+++++           G  +L A    +     QW      +  G+E    +  
Sbjct: 139 CGLTHSKLMALYKSFRAPTSRDGVPTLGAGSVDAKAPGEQW-----VEEVGEE----DPA 189

Query: 220 ERKNRRNM---LTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEA 274
           E  + R M   L   +  L  RE  I + R   ++    TLE +   F V+RER+RQIEA
Sbjct: 190 ELAHHRMMKEDLNHVLLTLTERECGIIKMRYGLDDGEEKTLEEVGRAFNVTRERIRQIEA 249

Query: 275 RAFKKVQ 281
           +A +K++
Sbjct: 250 KAIRKLR 256


>gi|260653773|dbj|BAI44426.1| DNA-directed RNA polymerase sigma 32 subunit, RpoH subfamily
          [Monochamus alternatus]
          Length = 56

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 32/54 (59%), Positives = 43/54 (79%)

Query: 46 DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
          D+S+AH+L+TSHL LV KIAM ++ YGL   ++V EGN+GLM  VKKF+P+ GF
Sbjct: 3  DISSAHKLITSHLNLVXKIAMKFKNYGLLFMDLVMEGNMGLMHPVKKFNPDLGF 56


>gi|219111033|ref|XP_002177268.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217411803|gb|EEC51731.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 324

 Score = 74.3 bits (181), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 64/249 (25%), Positives = 126/249 (50%), Gaps = 28/249 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+V S++RLVV IA  Y   G+ + ++V EG++GL +A +KF+P++GF+ +TY+ WW
Sbjct: 71  AKQRMVQSNMRLVVSIARKYSNVGVSLQDLVQEGSLGLSRAAEKFEPKKGFKFSTYASWW 130

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ-----AITDNNLKPEQVVAIA 163
           I+ A+   I      +++    +   L   +R+++ +LQ       T+  +  E  + + 
Sbjct: 131 IQQAVFRSIAYHSRTIRLPVHVHN--LLNRVRKVRNNLQRELSRTPTNEEMAEELGMTLQ 188

Query: 164 K--------KLNVS-ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           K        K ++S E+     N +  G ES + L ++   +S+      ++D    E+ 
Sbjct: 189 KYNKMLRLTKRSISLETPKYQSNPKDLGHESHDLLGDTISASSA------LFDESTPEK- 241

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQI 272
              + +R      L   + +L+  ERR+  +R    + +  T+  ++S+ + S+  VR  
Sbjct: 242 ---RVDRGIFHEDLHEMLEILDEDERRVICSRYGLSDGLTRTVTAVASQMKQSKAWVRSQ 298

Query: 273 EARAFKKVQ 281
           E RA +K++
Sbjct: 299 ECRALRKLR 307


>gi|23978372|dbj|BAC21150.1| principal sigma factor [Synechococcus sp. PCC 7001]
          Length = 203

 Score = 73.9 bits (180), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 58/216 (26%), Positives = 111/216 (51%), Gaps = 17/216 (7%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V S  RLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+
Sbjct: 1   VQSKFRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT-DNNLKP-EQVVAIAKKLNVSES 171
              I      +++        L+  + R+K   + ++ +   KP E+ +A + ++ + + 
Sbjct: 61  TRAIADQSRTIRLPV-----HLYETISRIKKTTKTLSQEFGRKPTEEEIAESMEMTIEKL 115

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
             I+ + +L    SL   I   +   S+  D++  D +  EQ + +   R++   +L   
Sbjct: 116 RFIAKSAQLPI--SLETPIGKEE--DSRLGDFIEADIENPEQDVAKNLLREDLEGVL--- 168

Query: 232 MSVLNPRERRIFEARRLQENP--VTLENLSSEFEVS 265
            + L+PRER +   R   ++    TLE +   F+V+
Sbjct: 169 -ATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVT 203


>gi|72383045|ref|YP_292400.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. NATL2A]
 gi|72002895|gb|AAZ58697.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. NATL2A]
          Length = 335

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 61/241 (25%), Positives = 114/241 (47%), Gaps = 14/241 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+V ++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP RG++ +TY+ WW
Sbjct: 100 AKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPTRGYKFSTYAYWW 159

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   I      +++     +      L +LK   + ++    +   +  +++ + +
Sbjct: 160 IRQGITRAIAEKSRSIRLPIHITEM-----LNKLKKGQRELSQELSRTPTLKELSEYVEL 214

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNM 227
            E++V  +  R     SL   I   D   +   D L  + D   EQ  IE +  K     
Sbjct: 215 PETDVKDLMSRAGQPVSLETKIG--DGEDTILLDLLSNEIDMPSEQ--IESDCMKGDLET 270

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE---ARAFKKVQESI 284
           L   +  L  R  R+       ++P++L  +     +SR+RVR +E    R  +K  +S+
Sbjct: 271 LLEQLPELQNRVLRMRYGID-GDDPMSLTGIGRVLGISRDRVRNLERDGLRGLRKTGDSV 329

Query: 285 Q 285
           +
Sbjct: 330 E 330


>gi|67078088|ref|YP_245708.1| RNA polymerase sigma factor (sigma-A) (sigma-43) [Bacillus cereus
           E33L]
 gi|66970394|gb|AAY60370.1| RNA polymerase sigma factor (sigma-A) (sigma-43) [Bacillus cereus
           E33L]
          Length = 323

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 75/296 (25%), Positives = 126/296 (42%), Gaps = 59/296 (19%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY--GLPISE 77
           I EI    +L KQE   L +RY+ HG+      L   ++ LV+ IA  Y+     +   +
Sbjct: 40  IKEIGNYQVLSKQESLNLFQRYK-HGEKDLRDYLFHVNVGLVLSIARKYKNKHPDIEFDD 98

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS-LVKIGTTANQKRLF 136
           +V EGN G+++A++ F+P+ G+  +TY+ WWIK  M   I +  S   KI    NQ    
Sbjct: 99  LVQEGNEGMLRAMEDFNPDLGYCFSTYAFWWIKKRMLGIICKKRSGPFKIPNYVNQ---- 154

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC------------------ 178
           FNL+ ++   + +   N +P  V  + K+L+V+   VI  N                   
Sbjct: 155 FNLKYVELEDKYLQMYN-RPPSVEEVVKELDVTSEIVIRHNVYYKRVTTMTLDIDTINED 213

Query: 179 -----RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
                    D+S    IN        ++ WL++D                          
Sbjct: 214 IGISNSFYDDKSAIPSINEMVIEDLNYEIWLIFD-------------------------E 248

Query: 234 VLNPRERRIFE-ARRLQENPVTL-ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           VLNP+++ +      L +  V L + ++    ++ ERV QI+  A KK+++   K 
Sbjct: 249 VLNPKQKMVLNLCFGLLDGKVYLHKEIAKALMITTERVSQIKEEAIKKLKKCDYKD 304


>gi|24215303|ref|NP_712784.1| RNA polymerase sigma factor WhiG [Leptospira interrogans serovar
           Lai str. 56601]
 gi|45657258|ref|YP_001344.1| RNA polymerase sigma factor WhiG [Leptospira interrogans serovar
           Copenhageni str. Fiocruz L1-130]
 gi|24196402|gb|AAN49802.1| RNA polymerase sigma factor WhiG [Leptospira interrogans serovar
           Lai str. 56601]
 gi|45600496|gb|AAS69981.1| RNA polymerase sigma-28 factor [Leptospira interrogans serovar
           Copenhageni str. Fiocruz L1-130]
          Length = 266

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 78/267 (29%), Positives = 131/267 (49%), Gaps = 29/267 (10%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGL 86
           +Q+E  L K YRE  D      LV  +  LV  +A G    G+P      ++VS G  GL
Sbjct: 10  QQDETELWKSYRETKDQDIRSYLVEKYSPLVKHVA-GRIAIGMPQNVEFDDLVSYGVFGL 68

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS--WSLVKIGTTANQKRLFFNLRRLKG 144
           + A++KFDPER  +  TY+M  I+ ++ +  LRS  W    I   A Q      L ++ G
Sbjct: 69  LDAIEKFDPERLIKFKTYAMTRIRGSIFDE-LRSIDWIPRSIRQKAKQ------LEQIIG 121

Query: 145 HLQAITDNNLKPEQV--VAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSS-Q 199
            L+     N + +QV   AIAK+L +S  E  S+  +++G    SLN +    D+N    
Sbjct: 122 MLE-----NKEGQQVDDDAIAKELGISMEEYNSLLTKISGTSLVSLNDIWFLGDENDEVS 176

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
           + + L    +     +IEKEE K   N++  ++  L  +E+++      ++  +TL+ + 
Sbjct: 177 FMETLESPMNMNPDTIIEKEEIK---NVIVEAIKTLPEKEKKVIVLYYYED--LTLKEIG 231

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQK 286
              EV+  R+ Q+  RA  +++  + K
Sbjct: 232 EVLEVTESRISQLHTRAVSRLRSKLGK 258


>gi|157826499|ref|YP_001495563.1| RNA polymerase sigma factor RpoD [Rickettsia bellii OSU 85-389]
 gi|157801803|gb|ABV78526.1| RNA polymerase sigma factor RpoD [Rickettsia bellii OSU 85-389]
          Length = 514

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 32/80 (40%), Positives = 50/80 (62%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 386 LQAKKDMIEANLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 445

Query: 107 WWIKAAMQEYILRSWSLVKI 126
           WWI+ A+   I      ++I
Sbjct: 446 WWIRQAITRAIADQARTIRI 465


>gi|153311|gb|AAA26765.1| principal sigma-like factor [Streptomyces aureofaciens]
 gi|450079|prf||1920369C RNA polymerase:SUBUNIT=sigma
          Length = 325

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 65/229 (28%), Positives = 114/229 (49%), Gaps = 16/229 (6%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            + S+LRLVV +   Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 93  FIRSNLRLVVAVVRRYPRSGLPLLDLIQEGNAGLVRAVEKFDYAKGFKFSTYATWWIRQA 152

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   I      +++     ++     +RR++       +N   PE    IA +L+ +E  
Sbjct: 153 ITRSIADQSRTIRLPVHLVEE--LGRIRRVQREFN--RENGRDPEH-AEIAAELDSTEKR 207

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG--QEQVLIEKEERKNRRNMLTR 230
           V  +        SLN  ++  D+  +Q+ D L+ D      EQ ++     +   ++L +
Sbjct: 208 VGDVLDWARDPVSLNMSVD--DEGDTQFGD-LLEDTSAISPEQSVLSLLRSEELEDLLGK 264

Query: 231 SMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
               L+ R   I + R   E+    TL  +  +  ++RER+RQIE  A 
Sbjct: 265 ----LDQRTASIIKMRYGIEDGRERTLTEVGKQHGLTRERIRQIEKHAL 309


>gi|291448259|ref|ZP_06587649.1| LOW QUALITY PROTEIN: RNA polymerase sigma factor RpoD [Streptomyces
           roseosporus NRRL 15998]
 gi|291351206|gb|EFE78110.1| LOW QUALITY PROTEIN: RNA polymerase sigma factor RpoD [Streptomyces
           roseosporus NRRL 15998]
          Length = 360

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 40/122 (32%), Positives = 67/122 (54%), Gaps = 28/122 (22%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ +I K+P+L  ++E  LAKR  E G  +                           A +
Sbjct: 222 YLKQIGKVPLLNAEQEVELAKRI-EAGLFAEDKLANADKLAPKLKRELEIIAEDGRRAKN 280

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 281 HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 340

Query: 112 AM 113
           A+
Sbjct: 341 AI 342


>gi|260906263|ref|ZP_05914585.1| RNA polymerase, sigma 32 subunit, RpoH [Brevibacterium linens BL2]
          Length = 903

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 82/295 (27%), Positives = 128/295 (43%), Gaps = 64/295 (21%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKR-----YREH--------------------GDLSAA 50
           L  Y+ +I + P+L   EE  +AKR     Y  H                     D +AA
Sbjct: 579 LGVYLKQIGQYPLLSAAEEVAVAKRIEAGMYATHVLSLGQYQTRRERRALEWVKADGAAA 638

Query: 51  HR-LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           +  +VTS+LRLVV IA  +    L + +++ EGN+GL++AV+KFD  +G + +TY+ WWI
Sbjct: 639 YEEMVTSNLRLVVSIAKRFNRSKLDLLDLIQEGNLGLVRAVQKFDYTKGNKFSTYATWWI 698

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRL----------FFNLRRLKGHLQAITDNNLKPEQV 159
           +  +            IG TA   RL          F+N  R      A   ++ K EQ 
Sbjct: 699 RQGIDR---------GIGDTAKTIRLPIHLFEKASEFWNCMRDDESRAACDHDHSKVEQA 749

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           +   +   VS    + +       ESL +          +  D  V+  D  E  +++ E
Sbjct: 750 L---RMQPVSLEGYLELQWDGHYAESLMSF-------DDRIADPDVF-TDNPETKIVDGE 798

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQ 271
             +   +++      L  RE  I   RR     E P TL+ + + F V+RER+RQ
Sbjct: 799 LLETVNSVVDS----LPAREAEIIR-RRFGWNGEPPQTLDAIGNRFAVTRERIRQ 848


>gi|167561013|ref|ZP_02353929.1| RNA polymerase sigma factor [Burkholderia oklahomensis EO147]
          Length = 476

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 61/246 (24%), Positives = 126/246 (51%), Gaps = 32/246 (13%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  ++  ++LRLV+ IA  Y   GL +++++ EGN+GL++A++KF+  RGF+ +TY+ W
Sbjct: 235 AATGKMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIQKFEYRRGFKFSTYATW 294

Query: 108 WIKAAMQEYIL-RSWSL---VKIGTTANQKRLFFN-LRRLKGHLQAITD----NNLKPEQ 158
           WI+ A+   +  R+ ++   V +G  A + R   + +++  G   ++ +      L  E+
Sbjct: 295 WIRQAISRAVADRARTIRLPVHVGDQARRVRKIADRIKQRSGMRASLAELSEATELSTER 354

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           + A+   L +   E  S+N  L             D + +++ D +    D     L + 
Sbjct: 355 LRAV---LELPR-EPRSLNTPLG------------DDDQAEFGDLV---EDASTPSLFDA 395

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEAR 275
                 R+++   +  ++ +E  I   RR     + P + E ++++  VSRE++R+IE R
Sbjct: 396 LAGAQMRDVVASLLKTMSAQEADILR-RRFGIGGDEPWSYEQIAAQSGVSREQIRRIEKR 454

Query: 276 AFKKVQ 281
           A + ++
Sbjct: 455 ALQTLR 460


>gi|167568274|ref|ZP_02361148.1| RNA polymerase sigma factor [Burkholderia oklahomensis C6786]
          Length = 483

 Score = 73.9 bits (180), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 61/246 (24%), Positives = 126/246 (51%), Gaps = 32/246 (13%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  ++  ++LRLV+ IA  Y   GL +++++ EGN+GL++A++KF+  RGF+ +TY+ W
Sbjct: 242 AATGKMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIQKFEYRRGFKFSTYATW 301

Query: 108 WIKAAMQEYIL-RSWSL---VKIGTTANQKRLFFN-LRRLKGHLQAITD----NNLKPEQ 158
           WI+ A+   +  R+ ++   V +G  A + R   + +++  G   ++ +      L  E+
Sbjct: 302 WIRQAISRAVADRARTIRLPVHVGDQARRVRKIADRIKQRSGMRASLAELSEATELSTER 361

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           + A+   L +   E  S+N  L             D + +++ D +    D     L + 
Sbjct: 362 LRAV---LELPR-EPRSLNTPLG------------DDDQAEFGDLV---EDASTPSLFDA 402

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEAR 275
                 R+++   +  ++ +E  I   RR     + P + E ++++  VSRE++R+IE R
Sbjct: 403 LAGAQMRDVVASLLKTMSAQEADILR-RRFGIGGDEPWSYEQIAAQSGVSREQIRRIEKR 461

Query: 276 AFKKVQ 281
           A + ++
Sbjct: 462 ALQTLR 467


>gi|330955107|gb|EGH55367.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae Cit 7]
          Length = 216

 Score = 73.6 bits (179), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 61/220 (27%), Positives = 102/220 (46%), Gaps = 28/220 (12%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I    +
Sbjct: 1   GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI--PVH 58

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQV--------VAIAKKLNVSESEVISMNCRLAGD 183
                  L R+   +         PE++          I K L +++ E ISM   +  D
Sbjct: 59  MIETINKLNRISRQMLQEMGREPTPEELGERMEMPEDKIRKVLKIAK-EPISMETPIGDD 117

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           E             S   D++    D   Q  I+    ++ +      +S L  RE ++ 
Sbjct: 118 E------------DSHLGDFI---EDSTMQSPIDVATVESLKEATREVLSGLTAREAKVL 162

Query: 244 EARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             R   +     TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 163 RMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 202


>gi|189348175|ref|YP_001941371.1| RNA polymerase sigma 28 subunit [Burkholderia multivorans ATCC
           17616]
 gi|189338313|dbj|BAG47381.1| RNA polymerase sigma 28 subunit [Burkholderia multivorans ATCC
           17616]
          Length = 612

 Score = 73.6 bits (179), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 63/239 (26%), Positives = 109/239 (45%), Gaps = 24/239 (10%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L  ++LRLVV IA  Y   GLP ++++ EGNIGL++A+ ++D  RGFR +TY+ WWI+ +
Sbjct: 379 LFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWWIRQS 438

Query: 113 MQEYILRSWSLVKIGT-TANQ----KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +   +      +++ T T +      RL    R+  G      +   +  + V   + L 
Sbjct: 439 ITHALADLGRTIRVPTHTVDAINKLARLAREHRQRAGATATPAELAAQMGEPVDKVRDLM 498

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
               E +S +  +A D  +  +    D ++   +               +  +   RR  
Sbjct: 499 AIVKEPVSADLPIAPDGDMTFVDVVPDASTPSPE---------------DAADAAQRRAA 543

Query: 228 LTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +  ++  L PRE  I   R      E   +L ++     +S ERVRQIEA A  +++ S
Sbjct: 544 IAAAIDRLPPREALIVRLRYGLHAGEG-CSLRDIGRRLNLSAERVRQIEASALARLRAS 601


>gi|11133042|sp|Q60012|HRDD_STRVF RecName: Full=RNA polymerase principal sigma factor hrdD
 gi|1407711|gb|AAB03580.1| sigma factor [Streptomyces viridifaciens]
          Length = 332

 Score = 73.6 bits (179), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 68/231 (29%), Positives = 113/231 (48%), Gaps = 20/231 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 100 FIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTYATWWIRQA 159

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   I      +++     ++     +RR++         + +P +V A   +L  +   
Sbjct: 160 ITRSIADQSRTIRLPVHLVEE--LGRIRRVQREFNREHGRDPEPAEVAA---ELGSTPER 214

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG--QEQ---VLIEKEERKNRRNM 227
           VI +        SLN  ++  D   +Q+ D L+ D      EQ    L+  EE  +    
Sbjct: 215 VIDVLDWARDPVSLNMAVD--DAGETQFGD-LLEDTSAVSPEQSVLTLLRSEELDDLIGR 271

Query: 228 LT-RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
           L  R+ S++  R   I + R       TL  +  E  ++RER+RQIE  A 
Sbjct: 272 LDQRTASIIKMR-YGIDDGRER-----TLTEVGKEHGLTRERIRQIEKHAL 316


>gi|302555769|ref|ZP_07308111.1| RNA polymerase sigma factor RpoS [Streptomyces viridochromogenes
           DSM 40736]
 gi|302473387|gb|EFL36480.1| RNA polymerase sigma factor RpoS [Streptomyces viridochromogenes
           DSM 40736]
          Length = 339

 Score = 73.6 bits (179), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 75/301 (24%), Positives = 140/301 (46%), Gaps = 46/301 (15%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYR----------------------EHGDLSAAHR- 52
           L +Y+ +I   P+L  ++E  LA+R                          G+L    R 
Sbjct: 39  LGQYLAQIGATPLLTAEDEVRLARRMEAGVRALEELDRSDADDDGLAPGRRGELEETARD 98

Query: 53  -------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
                  +V ++LRLVV +A  +   GLP+ +V+ EGN+GL++AV+KFD  +GF+ +TY+
Sbjct: 99  GQRAKDHMVRANLRLVVSMARRHAHRGLPLLDVIQEGNLGLIRAVEKFDHTKGFKFSTYA 158

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
            WWI+ +++  +      V++     ++     + +++  LQ   D   +P  V  +A++
Sbjct: 159 TWWIRQSIERGLAAHARTVRLPMQVVEQ--LQKIAKVERRLQ--LDLGREP-SVAEVARE 213

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE--ERKN 223
             ++E  +  +  R  G ++++      D   +   D L+ D     +VL   E  E   
Sbjct: 214 SGLAEDRIDWL--RRVGRQAVSLDTPVDDTGETVVGD-LIPD----TEVLQAPEVAEYTA 266

Query: 224 RRNMLTRSMSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
               L  ++  L PRE  I   R  L +    T + ++    ++RERVRQ+E  +  +++
Sbjct: 267 LAEELREAVGTLGPREAMILSLRYGLHDGHTRTRDEVARRVGLTRERVRQLEKASLARLR 326

Query: 282 E 282
           E
Sbjct: 327 E 327


>gi|284030454|ref|YP_003380385.1| putative RNA polymerase, sigma 70 family subunit [Kribbella flavida
           DSM 17836]
 gi|283809747|gb|ADB31586.1| putative RNA polymerase, sigma 70 family subunit [Kribbella flavida
           DSM 17836]
          Length = 301

 Score = 73.6 bits (179), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 34/79 (43%), Positives = 53/79 (67%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++  +LRLVV +A  Y G GL + +++ EGNIGLM+AV++FD + G R +TY++WWI+ 
Sbjct: 82  RMIEGNLRLVVSLAKRYTGKGLSLLDLIQEGNIGLMRAVERFDYKLGHRFSTYAIWWIRQ 141

Query: 112 AMQEYILRSWSLVKIGTTA 130
           A+   I     LV++   A
Sbjct: 142 ALGRAISDRSRLVRMPAQA 160


>gi|302543058|ref|ZP_07295400.1| RNA polymerase principal sigma factor HrdD [Streptomyces
           hygroscopicus ATCC 53653]
 gi|302460676|gb|EFL23769.1| RNA polymerase principal sigma factor HrdD [Streptomyces
           himastatinicus ATCC 53653]
          Length = 333

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 68/230 (29%), Positives = 120/230 (52%), Gaps = 18/230 (7%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 101 FIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYTKGFKFSTYATWWIRQA 160

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   I      +++     ++     +RR++       ++  +PE  + IA++L  S  E
Sbjct: 161 ITRSIADQSRTIRLPVHLVEE--LGRIRRVQREFN--REHGREPEH-MEIAEELG-STPE 214

Query: 173 VISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDG--QEQVLIEKEERKNRRNMLT 229
            +S     A D  SLN  ++  D+  +Q+ D L+ D      EQ ++     +   +++ 
Sbjct: 215 RVSDVLDWARDPVSLNMSVD--DEGETQFGD-LLEDTSAVSPEQSVMTLLRSEELEDLIG 271

Query: 230 RSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAF 277
           R    L+ R   I +AR   ++    TL  +  +  ++RER+RQIE  A 
Sbjct: 272 R----LDDRTASIIKARYGIDDGRERTLTEVGKQHGLTRERIRQIEKHAL 317


>gi|297200336|ref|ZP_06917733.1| RNA polymerase sigma factor RpoS [Streptomyces sviceus ATCC 29083]
 gi|197709451|gb|EDY53485.1| RNA polymerase sigma factor RpoS [Streptomyces sviceus ATCC 29083]
          Length = 332

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 64/229 (27%), Positives = 113/229 (49%), Gaps = 16/229 (6%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 100 FIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTYATWWIRQA 159

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   I      +++     ++     +RR++         + +P +   IA +L  +   
Sbjct: 160 ITRSIADQSRTIRLPVHLVEE--LGRIRRVQREFNREHGRDPEPAE---IAAELGSNAER 214

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG--QEQVLIEKEERKNRRNMLTR 230
           V+ +        SLN  ++  D   +Q+ D L+ D      EQ ++     +   +++ R
Sbjct: 215 VVDVLDWARDPVSLNMSVD--DDGDTQFGD-LLEDTSAVSPEQSVLTLLRSEELDDLIGR 271

Query: 231 SMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
               L+ R   I + R   E+    TL  +  E  ++RER+RQIE  A 
Sbjct: 272 ----LDQRTASIIKMRYGIEDGRERTLTEVGKEHGLTRERIRQIEKHAL 316


>gi|125585746|gb|EAZ26410.1| hypothetical protein OsJ_10293 [Oryza sativa Japonica Group]
          Length = 497

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 32/87 (36%), Positives = 57/87 (65%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R R +  +S  + +V S++RLV+ IA  + G G+  S+++ EG  GL++  +KFD  +GF
Sbjct: 247 RKRLNYGISCKNTMVKSNVRLVISIAREFEGPGMEFSDLIQEGIQGLVRGAEKFDASKGF 306

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKI 126
           R +TYS WWIK A+++ +L    ++++
Sbjct: 307 RFSTYSHWWIKQAIRKSVLEQTQIIRL 333


>gi|23978337|dbj|BAC21138.1| principal sigma factor [Pseudanabaena sp. PCC 7367]
          Length = 203

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 58/216 (26%), Positives = 111/216 (51%), Gaps = 17/216 (7%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+
Sbjct: 1   VQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT-DNNLKP-EQVVAIAKKLNVSES 171
              I      +++        L+  + R+K   + ++ +   KP E+ +A   ++ + + 
Sbjct: 61  TRAIADQSRTIRLPV-----HLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKL 115

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
             I+ + +L    SL   I   +   S+  D++  D +  +  + +   R++  N+L   
Sbjct: 116 RFIAKSAQLP--ISLETPIGKEE--DSRLGDFIESDGETPDDQVAKNLLREDLENVL--- 168

Query: 232 MSVLNPRERRIFEARRLQENP--VTLENLSSEFEVS 265
              L+PRER + + R   ++    TLE +   F V+
Sbjct: 169 -GTLSPRERDVLKLRYGLDDGRMKTLEEIGQIFNVT 203


>gi|159137617|gb|ABW88899.1| HrdB [Streptomyces cacaoi subsp. asoensis]
          Length = 133

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 40/122 (32%), Positives = 67/122 (54%), Gaps = 28/122 (22%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ +I K+P+L  ++E  LAKR  E G  +                           A +
Sbjct: 2   YLKQIGKVPLLNAEQEVELAKRI-EAGLFAEDKLANADKLAPKLKRELEIIAEDGRRAKN 60

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 61  HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 120

Query: 112 AM 113
           A+
Sbjct: 121 AI 122


>gi|161522996|ref|YP_001585925.1| RpoD family RNA polymerase sigma factor [Burkholderia multivorans
           ATCC 17616]
 gi|160346549|gb|ABX19633.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           multivorans ATCC 17616]
          Length = 625

 Score = 73.6 bits (179), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 63/239 (26%), Positives = 109/239 (45%), Gaps = 24/239 (10%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L  ++LRLVV IA  Y   GLP ++++ EGNIGL++A+ ++D  RGFR +TY+ WWI+ +
Sbjct: 392 LFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWWIRQS 451

Query: 113 MQEYILRSWSLVKIGT-TANQ----KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +   +      +++ T T +      RL    R+  G      +   +  + V   + L 
Sbjct: 452 ITHALADLGRTIRVPTHTVDAINKLARLAREHRQRAGATATPAELAAQMGEPVDKVRDLM 511

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
               E +S +  +A D  +  +    D ++   +               +  +   RR  
Sbjct: 512 AIVKEPVSADLPIAPDGDMTFVDVVPDASTPSPE---------------DAADAAQRRAA 556

Query: 228 LTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +  ++  L PRE  I   R      E   +L ++     +S ERVRQIEA A  +++ S
Sbjct: 557 IAAAIDRLPPREALIVRLRYGLHAGEG-CSLRDIGRRLNLSAERVRQIEASALARLRAS 614


>gi|297159879|gb|ADI09591.1| RNA polymerase principal sigma factor hrdD [Streptomyces
           bingchenggensis BCW-1]
          Length = 333

 Score = 73.2 bits (178), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 68/230 (29%), Positives = 119/230 (51%), Gaps = 18/230 (7%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 101 FIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYTKGFKFSTYATWWIRQA 160

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   I      +++     ++     +RR++       ++  +PE    IA +L  S +E
Sbjct: 161 ITRSIADQSRTIRLPVHLVEE--LGRIRRVQREFN--REHGREPEH-SEIAAELG-STTE 214

Query: 173 VISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDG--QEQVLIEKEERKNRRNMLT 229
            +S     A D  SLN  ++  D+  +Q+ D L+ D      EQ ++     +   +++ 
Sbjct: 215 RVSDVLDWARDPVSLNMSVD--DEGETQFGD-LLEDTSAVSPEQSVMTLLRSEELEDLIG 271

Query: 230 RSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAF 277
           R    L+ R   I +AR   ++    TL  +  +  ++RER+RQIE  A 
Sbjct: 272 R----LDDRTASIIKARYGIDDGRERTLTEVGKQHGLTRERIRQIEKHAL 317


>gi|313810026|gb|EFS47747.1| sigma-70 region 2 [Propionibacterium acnes HL083PA1]
          Length = 464

 Score = 73.2 bits (178), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 43/137 (31%), Positives = 71/137 (51%), Gaps = 31/137 (22%)

Query: 7   SIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYR---------------------- 42
           +++V G     +  Y+ +I K+ +L   EE  LAKR                        
Sbjct: 203 TVMVAGATADPVKDYLKQIGKVALLNAVEEVDLAKRIEAGLFAGEQLADPDAKIREKDRE 262

Query: 43  ------EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                 E G ++  H L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  
Sbjct: 263 DYEWIAEDGKVAKNH-LLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYT 321

Query: 97  RGFRLATYSMWWIKAAM 113
           +G++ +TY+ WWIK A+
Sbjct: 322 KGYKFSTYATWWIKQAI 338


>gi|284052567|ref|ZP_06382777.1| RNA polymerase sigma factor SigC [Arthrospira platensis str.
           Paraca]
          Length = 232

 Score = 73.2 bits (178), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 29/64 (45%), Positives = 46/64 (71%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           + A   ++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV+KFDP RG+R +TYS 
Sbjct: 168 IQAKDHMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTRGYRFSTYSY 227

Query: 107 WWIK 110
           WWI+
Sbjct: 228 WWIR 231


>gi|302560146|ref|ZP_07312488.1| RNA polymerase sigma (70) factor RpoD [Streptomyces griseoflavus
           Tu4000]
 gi|302477764|gb|EFL40857.1| RNA polymerase sigma (70) factor RpoD [Streptomyces griseoflavus
           Tu4000]
          Length = 332

 Score = 73.2 bits (178), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 64/229 (27%), Positives = 113/229 (49%), Gaps = 16/229 (6%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 100 FIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTYATWWIRQA 159

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   I      +++     ++     +RR++           +P +V A   +L  +   
Sbjct: 160 ITRSIADQSRTIRLPVHLVEE--LGRIRRVQREFNREHGREPEPAEVAA---ELGSTPER 214

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG--QEQVLIEKEERKNRRNMLTR 230
           V+ +        SLN  ++  D+  +Q+ D L+ D      EQ ++     +   +++ R
Sbjct: 215 VVDVLDWARDPVSLNMSVD--DEGETQFGD-LLEDTSAVSPEQSVLTLLRSEELDDLIGR 271

Query: 231 SMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
               L+ R   I + R   E+    TL  +  E  ++RER+RQIE  A 
Sbjct: 272 ----LDQRTASIIKMRYGIEDGRERTLTEVGKEHGLTRERIRQIEKHAL 316


>gi|224088962|ref|XP_002308586.1| predicted protein [Populus trichocarpa]
 gi|222854562|gb|EEE92109.1| predicted protein [Populus trichocarpa]
          Length = 559

 Score = 73.2 bits (178), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 58/232 (25%), Positives = 120/232 (51%), Gaps = 12/232 (5%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ +   LV+ IA  YRG G+ + +++  GN+GL+Q  ++FDP RG+R +TY  +WI+ +
Sbjct: 325 LIKNTHSLVLYIARNYRGMGIAMEDLIQAGNLGLLQGAERFDPTRGYRFSTYVQYWIRKS 384

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           M + + R    ++I    ++     ++ +++   +A+++++ +      +AK   +S ++
Sbjct: 385 MLKIVERHARGIQIPYALSR-----SINKIQKARKALSNSHGRYPDDWEVAKFTGLSLAK 439

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           + S    L    SL+  I         +  +  +  D   Q   E   R++ R  +   +
Sbjct: 440 IESAQKCLRVVASLDQKI-----GEGHYAKYSEFIPDMSIQNPEEAVMRQHMREEIYDLL 494

Query: 233 SVLNPRERRIFEAR-RLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             L+ RE+++   R   ++N P +L  +   F VS+ERVR+IE +   K+++
Sbjct: 495 RGLDSREKQVMVLRYGFKDNQPKSLAEIGRLFRVSKERVRKIEKKIMIKLRD 546


>gi|40353307|gb|AAR84417.1| essential primary sigma 70 factor [Frankia sp. ARgP5ag]
          Length = 217

 Score = 73.2 bits (178), Expect = 4e-11,   Method: Compositional matrix adjust.
 Identities = 51/157 (32%), Positives = 83/157 (52%), Gaps = 15/157 (9%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +LV ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WW
Sbjct: 32  AKRKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 91

Query: 109 IKAAMQEYILRSWSLVKIGT----TAN-----QKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I      ++I      T N     Q++L  +L R         + +L P++V
Sbjct: 92  IRQAITRAIADQARTIRIPVHMVETINKLIRIQRQLLQDLGREPSPEVIAKEMDLTPDKV 151

Query: 160 VAIAKKLNVSESEVISMNCRLAGDES--LNALINSSD 194
             I   L VS+ E +S+   +  +E   L   I   D
Sbjct: 152 REI---LKVSQ-EPVSLETPIGEEEDSHLGDFIEDCD 184


>gi|2398853|dbj|BAA22215.1| plastid RNA polymerase sigma-subunit [Arabidopsis thaliana]
          Length = 571

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 62/234 (26%), Positives = 113/234 (48%), Gaps = 15/234 (6%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV S   LV+ +A  YRG G+   +++  G +G++Q  ++FD  RG++ +TY  +WI+ +
Sbjct: 336 LVKSTRSLVLFLARNYRGMGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKS 395

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           M   + R    V I ++         + R   H+Q      LK    +  A    +++  
Sbjct: 396 MSTMVSRHARGVHIPSS---------IIRTINHIQK-ARKTLKTSHGIKYAADEEIAKLT 445

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQW--QDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
             S+    A ++ L  ++ S DK         +L +  D   +   E   R++ R  +  
Sbjct: 446 GHSVKKIRAANQCLK-VVGSIDKKVGDCFTTKFLEFTPDTTMESPEEAVMRQSARRDIHD 504

Query: 231 SMSVLNPRERRIFEARR-LQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            +  L PRE+++   R  LQ+  P +LE +   F+VS+E +R+IE RA  K+++
Sbjct: 505 LLEGLEPREKQVMVLRYGLQDYRPKSLEEIGKLFKVSKEWIRKIERRAMAKLRD 558


>gi|1173127|sp|P43344|RPOD_SERMA RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
          Length = 215

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 58/222 (26%), Positives = 105/222 (47%), Gaps = 28/222 (12%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I    +     
Sbjct: 5   DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI--PVHMIETI 62

Query: 137 FNLRRLKGHLQAITDNNLKPEQVV--------AIAKKLNVSESEVISMNCRLAGDESLNA 188
             L R+   +         PE++          I K L +++ E ISM   +  DE    
Sbjct: 63  NKLNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAK-EPISMETPIGDDE---- 117

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
                    S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R  
Sbjct: 118 --------DSHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREXKVLRMRFG 166

Query: 249 QE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +     TLE +  +F+V+RER+RQIEA+A +K++   + +V
Sbjct: 167 IDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 208


>gi|320010254|gb|ADW05104.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 333

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 46/141 (32%), Positives = 70/141 (49%), Gaps = 34/141 (24%)

Query: 10  VNGEIG----LSRYIHEIRKIPMLEKQEEYVLAKRYREHG-------------DLSAAHR 52
           V GEI     +  Y+ EI + P+L+  +E  L++   E G             D   A R
Sbjct: 26  VGGEIADRDLVGMYLDEIARTPLLDAAKEVELSQTI-EAGVFAQQILDGVVESDAGGAKR 84

Query: 53  ----------------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                            + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  
Sbjct: 85  EELEALVAESERAKDIFIRSNLRLVVAVARRYPRAGLPLLDLIQEGNAGLVRAVEKFDYA 144

Query: 97  RGFRLATYSMWWIKAAMQEYI 117
           +GF+ +TY+ WWI+ A+   I
Sbjct: 145 KGFKFSTYATWWIRQAITRSI 165


>gi|254384440|ref|ZP_04999781.1| hypothetical protein SSAG_04083 [Streptomyces sp. Mg1]
 gi|194343326|gb|EDX24292.1| hypothetical protein SSAG_04083 [Streptomyces sp. Mg1]
          Length = 1094

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 61/226 (26%), Positives = 114/226 (50%), Gaps = 20/226 (8%)

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA+ + G GL   +++  G +GL++A  KFDP +G++ +TY+ WWI+ +M   +    ++
Sbjct: 276 IALRHAGQGLDHEDLLQHGALGLIRAAVKFDPVKGYKFSTYATWWIRQSMSRAVADEGAV 335

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV-VAIAKKLNVSESEVISMNCRLAG 182
           ++I    +++     +R++    + +         V VA+A  L+V   E I    R   
Sbjct: 336 IRIPVHFHEQ-----IRKVAAAERRLQSEGRPWSAVHVAVACDLSVQRVEEIRRVSRRT- 389

Query: 183 DESLNALINSSDKNSSQWQDWLVYDH--DGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            +SL+ +I     +     D +  D      E + +E+   K+  ++LTR     + R+ 
Sbjct: 390 -DSLDRVIG----DGVHLGDLVALDRPLPSAEHLAMEEMGHKHLLSLLTR----FDARDA 440

Query: 241 RIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           RI   R   +  +  TL++L  EF V+RER+RQ+E +AF   +E +
Sbjct: 441 RILLRRTGLDGGDRSTLDDLGKEFGVTRERIRQVEVKAFAAFREML 486


>gi|239930706|ref|ZP_04687659.1| RNA polymerase principal sigma factor [Streptomyces ghanaensis ATCC
           14672]
 gi|291439071|ref|ZP_06578461.1| sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291341966|gb|EFE68922.1| sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 332

 Score = 73.2 bits (178), Expect = 5e-11,   Method: Compositional matrix adjust.
 Identities = 64/229 (27%), Positives = 113/229 (49%), Gaps = 16/229 (6%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 100 FIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTYATWWIRQA 159

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   I      +++     ++     +RR++         + +P +V A   +L  +   
Sbjct: 160 ITRSIADQSRTIRLPVHLVEE--LGRIRRVQREFNREHGRDPEPAEVAA---ELGSTPER 214

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG--QEQVLIEKEERKNRRNMLTR 230
           V  +        SLN  ++  D+  +Q+ D L+ D      EQ ++     +   +++ R
Sbjct: 215 VTDVLDWARDPVSLNMSVD--DEGETQFGD-LLEDTSAVSPEQSVLTLLRSEELDDLIGR 271

Query: 231 SMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
               L+ R   I + R   E+    TL  +  E  ++RER+RQIE  A 
Sbjct: 272 ----LDQRTASIIKMRYGIEDGRERTLTEVGKEHGLTRERIRQIEKHAL 316


>gi|213616352|ref|ZP_03372178.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 508

 Score = 72.8 bits (177), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 32/78 (41%), Positives = 49/78 (62%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 377 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 436

Query: 109 IKAAMQEYILRSWSLVKI 126
           I+ A+   I      ++I
Sbjct: 437 IRQAITRSIADQARTIRI 454


>gi|302552062|ref|ZP_07304404.1| RNA polymerase sigma factor RpoS [Streptomyces viridochromogenes
           DSM 40736]
 gi|302469680|gb|EFL32773.1| RNA polymerase sigma factor RpoS [Streptomyces viridochromogenes
           DSM 40736]
          Length = 332

 Score = 72.8 bits (177), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 64/229 (27%), Positives = 113/229 (49%), Gaps = 16/229 (6%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 100 FIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTYATWWIRQA 159

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   I      +++     ++     +RR++         + +P +   IA +L  +   
Sbjct: 160 ITRSIADQSRTIRLPVHLVEE--LGRIRRVQREFNREHGRDPEPTE---IAAELGSTPER 214

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG--QEQVLIEKEERKNRRNMLTR 230
           V  +        SLN  ++  D+  +Q+ D L+ D      EQ ++     +   +++ R
Sbjct: 215 VTDVLDWARDPVSLNMSVD--DEGETQFGD-LLEDTSAVSPEQSVLTLLRSEELDDLIGR 271

Query: 231 SMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
               L+ R   I + R   E+    TL  +  E  ++RER+RQIE  A 
Sbjct: 272 ----LDQRTASIIKMRYGIEDGRERTLTEVGKEHGLTRERIRQIEKHAL 316


>gi|82949200|dbj|BAE53364.1| sigma factor [Streptomyces sp. AJ9463]
          Length = 195

 Score = 72.8 bits (177), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 50/185 (27%), Positives = 93/185 (50%), Gaps = 33/185 (17%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------------AAH 51
           Y+ +I K+P+L  ++E  LAKR  E G  +                           A +
Sbjct: 2   YLKQIGKVPLLNAEQEVELAKRI-EAGLFAEDKLANSDKLAPKLKRELEIIAEDGRRAKN 60

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 61  HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 120

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           A+   +      ++I    +   +   L R++  +         PE+   +AK+L+++  
Sbjct: 121 AITRAMADQARTIRI--PVHMVEVINKLARVQRQMLQDLGREPTPEE---LAKELDMTPE 175

Query: 172 EVISM 176
           +VI +
Sbjct: 176 KVIEV 180


>gi|318066969|emb|CBY89099.1| RNA polymerase sigma70 factor [Halomonas salina]
          Length = 366

 Score = 72.8 bits (177), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 31/65 (47%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V +HLRLV+ IA  Y   GLP  ++  EG+IGLM+AV KF+  RG++ +TY+ WW
Sbjct: 301 AKKEMVEAHLRLVISIAQKYPHRGLPFLDLFQEGHIGLMKAVDKFEYRRGYKFSTYATWW 360

Query: 109 IKAAM 113
           I+ A+
Sbjct: 361 IRQAI 365


>gi|270487764|ref|ZP_06204838.1| sigma-70, region 4 [Yersinia pestis KIM D27]
 gi|270336268|gb|EFA47045.1| sigma-70, region 4 [Yersinia pestis KIM D27]
          Length = 215

 Score = 72.8 bits (177), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 60/223 (26%), Positives = 111/223 (49%), Gaps = 30/223 (13%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ 132
           +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I      T N+
Sbjct: 5   DLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK 64

Query: 133 -----KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
                +++   + R +   + + +  L PE    I K L +++ E ISM   +  DE   
Sbjct: 65  LNRISRQMLQEMGR-EPTPEELAERMLMPED--KIRKVLKIAK-EPISMETPIGDDE--- 117

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
                     S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R 
Sbjct: 118 ---------DSHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRF 165

Query: 248 LQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
             +     TLE +  +F+V+RER+RQIEA+A +K++   + +V
Sbjct: 166 GIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 208


>gi|153006912|ref|YP_001381237.1| RNA polymerase sigma-32 subunit RpoH [Anaeromyxobacter sp. Fw109-5]
 gi|152030485|gb|ABS28253.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter sp.
           Fw109-5]
          Length = 238

 Score = 72.8 bits (177), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 42/110 (38%), Positives = 65/110 (59%), Gaps = 1/110 (0%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+   R    L ++ E  LA R R  GD  A   LV  +L LVV +A       L +
Sbjct: 8   LAPYLEAARGRKPLTREAERALALRAR-RGDARAKDELVRHNLALVVMVARKQSRGALRL 66

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            E+V EG +GL++A++KFDP  G R +TY++WWI+A + +Y+ ++ S V+
Sbjct: 67  EELVQEGMLGLLRAIEKFDPNAGTRFSTYAVWWIRAYVWKYLKQARSSVR 116


>gi|329941264|ref|ZP_08290543.1| RNA polymerase principal sigma factor HrdD [Streptomyces
           griseoaurantiacus M045]
 gi|329299795|gb|EGG43694.1| RNA polymerase principal sigma factor HrdD [Streptomyces
           griseoaurantiacus M045]
          Length = 332

 Score = 72.8 bits (177), Expect = 6e-11,   Method: Compositional matrix adjust.
 Identities = 67/230 (29%), Positives = 117/230 (50%), Gaps = 18/230 (7%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 100 FIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTYATWWIRQA 159

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   I      +++     ++     +RR++         + +P +   IA +L  S +E
Sbjct: 160 ITRSIADQSRTIRLPVHLVEE--LGRIRRVQREFNREHGRDPEPAE---IAAELG-SNAE 213

Query: 173 VISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDG--QEQVLIEKEERKNRRNMLT 229
            ++     A D  SLN  ++  D+  +Q+ D L+ D      EQ ++     +   +++ 
Sbjct: 214 RVTDVLDWARDPVSLNMSVD--DEGETQFGD-LLEDTSAVSPEQSVLTLLRSEELDDLIG 270

Query: 230 RSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
           R    L+ R   I + R   E+    TL  +  E  ++RER+RQIE  A 
Sbjct: 271 R----LDQRTASIIKMRYGIEDGRERTLTEVGKEHGLTRERIRQIEKHAL 316


>gi|115452175|ref|NP_001049688.1| Os03g0271100 [Oryza sativa Japonica Group]
 gi|29893614|gb|AAP06868.1| unknown protein [Oryza sativa Japonica Group]
 gi|32351880|dbj|BAC78529.1| plastid sigma factor 2B [Oryza sativa Japonica Group]
 gi|108707414|gb|ABF95209.1| Sigma-70 region 3 family protein, expressed [Oryza sativa Japonica
           Group]
 gi|113548159|dbj|BAF11602.1| Os03g0271100 [Oryza sativa Japonica Group]
 gi|215704451|dbj|BAG93885.1| unnamed protein product [Oryza sativa Japonica Group]
 gi|215765869|dbj|BAG87566.1| unnamed protein product [Oryza sativa Japonica Group]
          Length = 540

 Score = 72.8 bits (177), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 30/80 (37%), Positives = 54/80 (67%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           +S  + +V S++RLV+ IA  + G G+  S+++ EG  GL++  +KFD  +GFR +TYS 
Sbjct: 297 ISCKNTMVKSNVRLVISIAREFEGPGMEFSDLIQEGIQGLVRGAEKFDASKGFRFSTYSH 356

Query: 107 WWIKAAMQEYILRSWSLVKI 126
           WWIK A+++ +L    ++++
Sbjct: 357 WWIKQAIRKSVLEQTQIIRL 376


>gi|55274903|gb|AAV49253.1| RNA polymerase subunit sigma-38 [Escherichia albertii]
          Length = 192

 Score = 72.4 bits (176), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 29/57 (50%), Positives = 43/57 (75%)

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           VKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+
Sbjct: 1   VKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIM 57


>gi|114765238|ref|ZP_01444370.1| RNA polymerase sigma factor protein (sigma-70) [Pelagibaca
           bermudensis HTCC2601]
 gi|114542373|gb|EAU45401.1| RNA polymerase sigma factor protein (sigma-70) [Roseovarius sp.
           HTCC2601]
          Length = 249

 Score = 72.4 bits (176), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 56/266 (21%), Positives = 127/266 (47%), Gaps = 32/266 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +S   H   + P+L  ++E      +++ GD +A   L+ SH R     A  +    + +
Sbjct: 2   MSMSYHSAMREPLLSFEQERAAISGWQDRGDRAALEVLLRSHARQAWSHAARFTDNPVHL 61

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++ +EG +GL++A   FD  +  R ATY+ WW++ A+   + R  +++ I +     R 
Sbjct: 62  EDLAAEGVMGLLRAADSFDRAQDVRFATYAAWWVRNAVSSALSRIKAVIDIPS-----RT 116

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           +     L   +  ++D ++    +V +A +  ++    +  +   AG +    L++S   
Sbjct: 117 Y-----LDAQMGKLSDEDVF---IVQLATRGTLA----LDTHQEDAGRDPAQLLVSS--- 161

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
                      + D +E   ++ + R   R ++  +++ + P E  +   RRL   P TL
Sbjct: 162 -----------EPDPEEHASLQSQRRMLLR-LIDDALARMEPEEVAVIRRRRLAPEPETL 209

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
            +++++  ++++R+RQ+E RA  +++
Sbjct: 210 ADIAADLGITQDRLRQVERRAMMRLR 235


>gi|23978350|dbj|BAC21142.1| principal sigma factor [Xenococcus sp. PCC 7307]
          Length = 203

 Score = 72.4 bits (176), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 58/216 (26%), Positives = 110/216 (50%), Gaps = 17/216 (7%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+
Sbjct: 1   VQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT-DNNLKP-EQVVAIAKKLNVSES 171
              I      +++        L+  + R+K   + ++ +   KP E+ +A   ++ + + 
Sbjct: 61  TRAIADQSRTIRLPV-----HLYETISRIKKTTKLLSQERGRKPTEEEIATRMEMTIEKL 115

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
             I+ + +L    SL   I   +   S+  D++  D +  E  + +   R++  ++L   
Sbjct: 116 RFIAKSAQLPI--SLETPIGKEE--DSRLGDFIEADGETPEDQVSKSLLREDLESVL--- 168

Query: 232 MSVLNPRERRIFEARRLQENP--VTLENLSSEFEVS 265
              L+PRER +   R   ++    TLE +   F V+
Sbjct: 169 -DTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVT 203


>gi|295837882|ref|ZP_06824815.1| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
 gi|197699594|gb|EDY46527.1| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
          Length = 274

 Score = 72.4 bits (176), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 67/244 (27%), Positives = 121/244 (49%), Gaps = 23/244 (9%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           EHG + AA  L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDPERG +  
Sbjct: 46  EHGRVRAA--LIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQFP 103

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           T++M  +   ++ Y   +   V +      +RL     ++    + +T  + +      I
Sbjct: 104 TFAMPTVVGEIKRYFRDNVRTVHV-----PRRLHELWVQVNSAAEDLTTAHGRSPTTAEI 158

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL--VYDHDGQEQVLIEKEE 220
           A++L ++E EV++  C  AG        +++   ++Q  D L  + D  G E   ++  E
Sbjct: 159 AERLRIAEDEVLA--CIEAGRS-----YHATSLEAAQEGDGLPGLLDRLGYEDPALDGVE 211

Query: 221 RKNRRNMLTRSMSVLNP-RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
            ++    L R + V  P RE+RI   R    N +T   +S+E  VS+  V ++ AR+F +
Sbjct: 212 HRD----LVRHLLVQLPEREQRILLLRYY--NNLTQSQISAELGVSQMHVSRLLARSFAR 265

Query: 280 VQES 283
           ++ +
Sbjct: 266 LRSA 269


>gi|125543279|gb|EAY89418.1| hypothetical protein OsI_10924 [Oryza sativa Indica Group]
          Length = 540

 Score = 72.4 bits (176), Expect = 7e-11,   Method: Compositional matrix adjust.
 Identities = 32/87 (36%), Positives = 57/87 (65%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R R +  +S  + +V S++RLV+ IA  + G G+  S+++ EG  GL++  +KFD  +GF
Sbjct: 290 RKRLNYGISCKNTMVKSNVRLVISIAREFEGPGMEFSDLIQEGIQGLVRGAEKFDASKGF 349

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKI 126
           R +TYS WWIK A+++ +L    ++++
Sbjct: 350 RFSTYSHWWIKQAIRKSVLEQTQIIRL 376


>gi|29830237|ref|NP_824871.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29607348|dbj|BAC71406.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 331

 Score = 72.4 bits (176), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 68/231 (29%), Positives = 116/231 (50%), Gaps = 20/231 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 99  FIKSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTYATWWIRQA 158

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   I      +++     ++     +RR++       ++  +PE    IA +L+ + + 
Sbjct: 159 ITRSIADQSRTIRLPVHLVEE--LGRIRRVQREFN--REHGREPEP-AEIAAELDSNPAR 213

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG--QEQ---VLIEKEERKNRRNM 227
           V  +        SLN  ++  D+  +Q+ D L+ D      EQ    L+  EE  +    
Sbjct: 214 VTDVLDWARDPVSLNMHVD--DEGETQFGD-LLEDTSAVSPEQSVLTLLRSEELDDLIGR 270

Query: 228 LT-RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
           L  R+ S++  R   I + R       TL  +  E  ++RER+RQIE  A 
Sbjct: 271 LDQRTASIIKMR-YGIDDGRER-----TLTEVGKEHGLTRERIRQIEKHAL 315


>gi|213418760|ref|ZP_03351826.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
          Length = 162

 Score = 72.4 bits (176), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 32/78 (41%), Positives = 49/78 (62%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 41  AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 100

Query: 109 IKAAMQEYILRSWSLVKI 126
           I+ A+   I      ++I
Sbjct: 101 IRQAITRSIADQARTIRI 118


>gi|213026208|ref|ZP_03340655.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. 404ty]
          Length = 445

 Score = 72.4 bits (176), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 32/78 (41%), Positives = 49/78 (62%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 287 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 346

Query: 109 IKAAMQEYILRSWSLVKI 126
           I+ A+   I      ++I
Sbjct: 347 IRQAITRSIADQARTIRI 364


>gi|257784260|ref|YP_003179477.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Atopobium
           parvulum DSM 20469]
 gi|257472767|gb|ACV50886.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Atopobium
           parvulum DSM 20469]
          Length = 284

 Score = 72.4 bits (176), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 66/277 (23%), Positives = 127/277 (45%), Gaps = 38/277 (13%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           + IP  +K     L  +Y+E  D     +L+ SHL LV  +A  ++  G P+ +++  G 
Sbjct: 29  KGIPAWDKDRTRQLFAQYKETKDSEVRDQLIVSHLNLVRFLASKFKNRGEPLDDLIQVGT 88

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRL 142
           IGL++A+ +F+P+RG    TY+   I   ++ +   + WS+          R+   L+ L
Sbjct: 89  IGLIKAIDRFEPDRGLEFTTYATPTIMGEIKRHFRDKGWSV----------RVPRRLQEL 138

Query: 143 KGHLQAITDNNLKPEQ----VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
              +  +TD+  K  Q    +  IA++L+ +  E++               + SS   SS
Sbjct: 139 SSKINQVTDDLTKELQRSPSIEEIAQRLDTNVEEILEA-------------MESSSAYSS 185

Query: 199 QWQDWLVYDHDGQE------QVLIEKEE--RKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
              +      DG E      Q + E E+    + R +L  ++   +PRE+ I   R ++ 
Sbjct: 186 VPLEGGGSGADGDETPSIIDQYVTEDEDLAGSDDRIVLDEAIRDFSPREQEIIRMRFVE- 244

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             +T   ++ +  +S+ +V ++  R  K++QE I  +
Sbjct: 245 -GLTQVEIAEKLNISQVQVSRLLRRTLKRIQEKIDPE 280


>gi|291445451|ref|ZP_06584841.1| sigma factor [Streptomyces roseosporus NRRL 15998]
 gi|291348398|gb|EFE75302.1| sigma factor [Streptomyces roseosporus NRRL 15998]
          Length = 333

 Score = 72.4 bits (176), Expect = 8e-11,   Method: Compositional matrix adjust.
 Identities = 46/141 (32%), Positives = 70/141 (49%), Gaps = 34/141 (24%)

Query: 10  VNGEIG----LSRYIHEIRKIPMLEKQEEYVLAKRYREHG-------------DLSAAHR 52
           V GEI     +  Y+ EI + P+L+  +E  L++   E G             D   A R
Sbjct: 26  VGGEIADRDLVGMYLDEIARTPLLDAAKEVDLSQTI-EAGVYAQQILDGEVESDAGDAKR 84

Query: 53  ----------------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                            + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  
Sbjct: 85  EELEALVADGERAKDIFIRSNLRLVVAVARRYPRAGLPLLDLIQEGNAGLVRAVEKFDYA 144

Query: 97  RGFRLATYSMWWIKAAMQEYI 117
           +GF+ +TY+ WWI+ A+   I
Sbjct: 145 KGFKFSTYATWWIRQAITRSI 165


>gi|290959686|ref|YP_003490868.1| sigma factor HrdD [Streptomyces scabiei 87.22]
 gi|260649212|emb|CBG72326.1| sigma factor HrdD [Streptomyces scabiei 87.22]
          Length = 332

 Score = 72.4 bits (176), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 64/229 (27%), Positives = 112/229 (48%), Gaps = 16/229 (6%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 100 FIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTYATWWIRQA 159

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   I      +++     ++     +RR++         + +P +   IA +L  +   
Sbjct: 160 ITRSIADQSRTIRLPVHLVEE--LGRIRRVQREFNREHGRDPEPAE---IAAELGSNADR 214

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG--QEQVLIEKEERKNRRNMLTR 230
           V  +        SLN  ++  D   +Q+ D L+ D      EQ ++     +   +++ R
Sbjct: 215 VTDVLDWARDPVSLNMSVD--DDGDTQFGD-LLEDTSAVSPEQSVLTLLRSEELDDLIGR 271

Query: 231 SMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
               L+ R   I + R   E+    TL  +  E  ++RER+RQIE  A 
Sbjct: 272 ----LDQRTASIIKMRYGIEDGRERTLTEVGKEHGLTRERIRQIEKHAL 316


>gi|26665384|dbj|BAC44903.1| principal sigma factor [Gloeobacter violaceus PCC 8105]
          Length = 203

 Score = 72.4 bits (176), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 61/220 (27%), Positives = 110/220 (50%), Gaps = 25/220 (11%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V S+LRLVV IA+ Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+
Sbjct: 1   VQSNLRLVVSIALKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKP-EQVVAIAKKLNVSES 171
              I      +++        L+  + R+K   + ++     KP E+ +A   ++ + + 
Sbjct: 61  TRAIADQSRTIRLPV-----HLYETISRIKKTTKLLSQELGRKPTEEEIATRMEMTIEKL 115

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
             I+ + +L    SL   I   +   S+  D+   + DG      E  E K  +N+L   
Sbjct: 116 RFIAKSAQLPI--SLETPIGKEE--DSRLGDF--SEADG------ETPEDKVAKNLLRED 163

Query: 232 ----MSVLNPRERRIFEARRLQENP--VTLENLSSEFEVS 265
               ++ L+PRER +   R   ++    TLE +   F V+
Sbjct: 164 LEAVLNTLSPRERDVLRLRYGLDDGRMKTLEEIGQLFNVT 203


>gi|330862244|emb|CBX72405.1| RNA polymerase sigma factor rpoD [Yersinia enterocolitica W22703]
          Length = 553

 Score = 72.0 bits (175), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 32/78 (41%), Positives = 49/78 (62%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 417 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 476

Query: 109 IKAAMQEYILRSWSLVKI 126
           I+ A+   I      ++I
Sbjct: 477 IRQAITRSIADQARTIRI 494


>gi|294155544|ref|YP_003559928.1| DNA-directed RNA polymerase, sigma-70 factor [Mycoplasma crocodyli
           MP145]
 gi|291599870|gb|ADE19366.1| DNA-directed RNA polymerase, sigma-70 factor [Mycoplasma crocodyli
           MP145]
          Length = 490

 Score = 72.0 bits (175), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 34/88 (38%), Positives = 57/88 (64%), Gaps = 2/88 (2%)

Query: 28  MLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +L+  EE  LAK   + G     A  +L+  +LRLV+  A  Y+  GL   +++SEGN G
Sbjct: 218 LLKPDEERRLAKLMEKGGFRGKRARDKLIMRNLRLVINNAKKYKNRGLTFIDLISEGNAG 277

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAM 113
           +++AV+K++ E+GF+ +TY+ WWI+ A+
Sbjct: 278 ILKAVQKYNVEKGFKFSTYATWWIRQAI 305


>gi|23978360|dbj|BAC21145.1| principal sigma factor [Pleurocapsa sp. PCC 7314]
          Length = 203

 Score = 72.0 bits (175), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 58/216 (26%), Positives = 110/216 (50%), Gaps = 17/216 (7%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+
Sbjct: 1   VHSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT-DNNLKP-EQVVAIAKKLNVSES 171
              I      +++        L+  + R+K   + ++ +   KP E+ +A   ++ + + 
Sbjct: 61  TRAIADQSRTIRLPV-----HLYETISRIKKTTKLLSQERGRKPTEEEIATRMEMTIEKL 115

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
             I+ + +L    SL   I   +   S+  D++  D +  E  + +   R++  ++L   
Sbjct: 116 RFIAKSAQLPI--SLETPIGKEE--DSRLGDFIEADGETPEDQVSKSLLREDLESVL--- 168

Query: 232 MSVLNPRERRIFEARRLQENP--VTLENLSSEFEVS 265
              L+PRER +   R   ++    TLE +   F V+
Sbjct: 169 -DTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVT 203


>gi|307324239|ref|ZP_07603447.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306889970|gb|EFN20948.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 334

 Score = 72.0 bits (175), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 68/230 (29%), Positives = 118/230 (51%), Gaps = 18/230 (7%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 102 FIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYTKGFKFSTYATWWIRQA 161

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   I      +++     ++     +RR++       ++  +PE    IA +L  S  E
Sbjct: 162 ITRSIADQSRTIRLPVHLVEE--LGRIRRVQREFN--REHGREPEH-AEIAVELG-STME 215

Query: 173 VISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDG--QEQVLIEKEERKNRRNMLT 229
            +S     A D  SLN  ++  D+  +Q+ D L+ D      EQ ++     +   +++ 
Sbjct: 216 RVSDVLDWARDPVSLNMSVD--DEGETQFGD-LLEDTSAVSPEQSVMTLLRSEELEDLIG 272

Query: 230 RSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAF 277
           R    L+ R   I +AR   ++    TL  +  +  ++RER+RQIE  A 
Sbjct: 273 R----LDDRTASIIKARYGIDDGRERTLTEVGKQHGLTRERIRQIEKHAL 318


>gi|270668763|ref|ZP_06222551.1| RNA polymerase sigma factor RpoD [Haemophilus influenzae HK1212]
 gi|270316653|gb|EFA28454.1| RNA polymerase sigma factor RpoD [Haemophilus influenzae HK1212]
          Length = 151

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 32/78 (41%), Positives = 49/78 (62%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 45  AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 104

Query: 109 IKAAMQEYILRSWSLVKI 126
           I+ A+   I      ++I
Sbjct: 105 IRQAITRSIADQARTIRI 122


>gi|254386169|ref|ZP_05001481.1| RNA polymerase sigma subunit [Streptomyces sp. Mg1]
 gi|194345026|gb|EDX25992.1| RNA polymerase sigma subunit [Streptomyces sp. Mg1]
          Length = 325

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 73/312 (23%), Positives = 132/312 (42%), Gaps = 64/312 (20%)

Query: 10  VNGEIG----LSRYIHEIRKIPMLEKQEEY--------------VLAKRYREHGDLSAAH 51
           V GEI     +  Y+ EI + P+L+  +E               +L       G+  A  
Sbjct: 18  VGGEIADRDLVGMYLDEIARTPLLDAAKEVELSQIIEAGVYARQILDGEAEREGEAPARE 77

Query: 52  RL--------------VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
            L              + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +
Sbjct: 78  ELEALAAEGERAKEVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYAK 137

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           GF+ +TY+ WWI+ A+   I      +++     ++     +RR++       ++   PE
Sbjct: 138 GFKFSTYATWWIRQAITRSIADQSRTIRLPVHLVEE--LGRIRRVQREFN--REHGRDPE 193

Query: 158 QVVAIAKKLNVSESEV------------ISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
               IA +L+ +   V            ++M+    GD     L+  +   S +     +
Sbjct: 194 H-TEIAAELDTTAKRVGDVLDWARDPVSLNMSVDDDGDTQFGDLLEDTSAISPEQSVLSL 252

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
              +  E +L + ++R    +++     + + RER             TL  +  +  ++
Sbjct: 253 LRSEELEDLLGKLDQRTA--SIIKMRYGIDDGRER-------------TLTEVGKQHGLT 297

Query: 266 RERVRQIEARAF 277
           RER+RQIE  A 
Sbjct: 298 RERIRQIEKHAL 309


>gi|45128589|gb|AAS55058.1| RpoD [Vibrio parahaemolyticus]
          Length = 492

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 32/78 (41%), Positives = 49/78 (62%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 374 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 433

Query: 109 IKAAMQEYILRSWSLVKI 126
           I+ A+   I      ++I
Sbjct: 434 IRQAITRSIADQARTIRI 451


>gi|182438069|ref|YP_001825788.1| RNA polymerase principal sigma factor hrdD [Streptomyces griseus
           subsp. griseus NBRC 13350]
 gi|326778714|ref|ZP_08237979.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces cf.
           griseus XylebKG-1]
 gi|178466585|dbj|BAG21105.1| RNA polymerase principal sigma factor hrdD [Streptomyces griseus
           subsp. griseus NBRC 13350]
 gi|326659047|gb|EGE43893.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces cf.
           griseus XylebKG-1]
          Length = 333

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 45/140 (32%), Positives = 69/140 (49%), Gaps = 32/140 (22%)

Query: 10  VNGEIG----LSRYIHEIRKIPMLEKQEEYVL------------------------AKRY 41
           V GEI     +  Y+ EI + P+L+  +E  L                        AKR 
Sbjct: 26  VGGEIADRDLVGMYLDEIARTPLLDAAKEVDLSQTIEAGVFAQQILDGEVESTTGDAKRE 85

Query: 42  REHGDLSAAHR----LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
                ++   R     + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +
Sbjct: 86  ELEALVAEGERAKDIFIRSNLRLVVAVARRYPRAGLPLLDLIQEGNAGLVRAVEKFDYAK 145

Query: 98  GFRLATYSMWWIKAAMQEYI 117
           GF+ +TY+ WWI+ A+   I
Sbjct: 146 GFKFSTYATWWIRQAITRSI 165


>gi|318066991|emb|CBY89110.1| RNA polymerase sigma70 factor [Modicisalibacter tunisiensis]
          Length = 373

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 31/65 (47%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 308 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 367

Query: 109 IKAAM 113
           I+ AM
Sbjct: 368 IRQAM 372


>gi|326319203|ref|YP_004236875.1| RpoD subfamily RNA polymerase sigma-70 subunit [Acidovorax avenae
           subsp. avenae ATCC 19860]
 gi|323376039|gb|ADX48308.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidovorax avenae
           subsp. avenae ATCC 19860]
          Length = 878

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 61/244 (25%), Positives = 120/244 (49%), Gaps = 29/244 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+  ++L+L    A  Y   G  + ++  EGN+GL++AV +++  RGFR +TY+ WW
Sbjct: 521 ARDRMTAANLKLAFFHARKYLYSGETLDDLAQEGNVGLLKAVDRYNWRRGFRFSTYATWW 580

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           ++  +  Y+      +++     +K       R+    + + D   +   +  +A+++ +
Sbjct: 581 VRQQISRYVADKARTIRMPVHIYEKAQ--RAERIAQRFEMLAD---RAPSLDELAERMEM 635

Query: 169 SESEVISMNCRLAG-----DES-LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
              ++ ++  R+A      DES ++ LI+   +++     WL    D  E   +      
Sbjct: 636 PRHKLAAL-LRIAPEPSRIDESPVDELISLDARDAY----WLPDPADAVETHQV------ 684

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQ-----ENPVTLENLSSEFEVSRERVRQIEARAF 277
             R  L R +S L+ R+R+     RL+        +TL+ +   F V+RER+RQIEA+A 
Sbjct: 685 --RAALDRYISSLSTRDRKEEHVLRLRYGIGVHEALTLDEVGQRFGVTRERIRQIEAKAI 742

Query: 278 KKVQ 281
           +K++
Sbjct: 743 RKLK 746


>gi|116328490|ref|YP_798210.1| RNA polymerase sigma factor WhiG [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116331220|ref|YP_800938.1| RNA polymerase sigma factor WhiG [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
 gi|116121234|gb|ABJ79277.1| RNA polymerase sigma subunit [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116124909|gb|ABJ76180.1| RNA polymerase sigma subunit [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
          Length = 266

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 76/267 (28%), Positives = 131/267 (49%), Gaps = 29/267 (10%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGL 86
           +Q+E  L K YR+  D      LV  +  LV  +A G    G+P      ++VS G  GL
Sbjct: 10  QQDETELWKSYRDTKDQDIRSYLVEKYSPLVKHVA-GRIAIGMPQNVEFDDLVSYGVFGL 68

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS--WSLVKIGTTANQKRLFFNLRRLKG 144
           + A++KFDP+R  +  TY+M  I+ ++ +  LRS  W    I   A Q      L ++ G
Sbjct: 69  LDAIEKFDPDRLIKFKTYAMTRIRGSIFDE-LRSIDWIPRSIRQKAKQ------LEQIIG 121

Query: 145 HLQAITDNNLKPEQV--VAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSS-Q 199
            L+     N + +QV   AIAK+L +S  E  S+  +++G    SLN +    D+N    
Sbjct: 122 MLE-----NKEGQQVDDDAIAKELGISMEEYNSLLTKISGTSLVSLNDIWFLGDENDEVS 176

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
           + + L    +     +IEKEE K   N++  ++  L  +E+++      ++  +TL+ + 
Sbjct: 177 FMETLESPMNMNPDTIIEKEEIK---NVIVEAIKTLPEKEKKVIVLYYYED--LTLKEIG 231

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQK 286
              EV+  R+ Q+  RA  +++  + K
Sbjct: 232 EVLEVTESRISQLHTRAVSRLRSKLGK 258


>gi|15828925|ref|NP_326285.1| RNA polymerase sigma factor [Mycoplasma pulmonis UAB CTIP]
 gi|14089868|emb|CAC13627.1| DNA-DIRECTED RNA POLYMERASE SIGMA FACTOR (SIGMA-A) [Mycoplasma
           pulmonis]
          Length = 461

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 27/65 (41%), Positives = 46/65 (70%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L+  +LRLV+  A  Y+  GL   +++SEGN G+++AV+KFD  +GF+ +TY+ WW
Sbjct: 214 AKDKLINRNLRLVINNAKKYKNRGLSFIDLISEGNAGIIKAVQKFDESKGFKFSTYATWW 273

Query: 109 IKAAM 113
           I+ ++
Sbjct: 274 IRQSI 278


>gi|6682871|dbj|BAA88922.1| sigma factor [Nicotiana tabacum]
          Length = 502

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 65/259 (25%), Positives = 126/259 (48%), Gaps = 44/259 (16%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  S++RLV+ IA  Y   G  +++++  G IGL++ ++KFD  RGF+++TY  WW
Sbjct: 259 AREKLAMSNVRLVMSIAQRYDTNGTEMADLIQGGLIGLLRGIEKFDHSRGFKISTYVYWW 318

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   ++ +   +++    +++       ++K     + +N + P  +  IA+ LN+
Sbjct: 319 IRQGVSRALVENSRTLRLPIHLHERLSLIRNAKIK-----LKENGITP-SIEKIAECLNM 372

Query: 169 SE----------SEVISMN----CRLAG--DESLNALINSSDKNSSQWQ---DWLVYDHD 209
           S+          S+V S++      L G   E+L++ I  +   +  W    +W++ D  
Sbjct: 373 SQKKVRNATEASSKVFSLDREAFPSLNGLPGETLHSYIADNRLENIPWHGVDEWMLKDE- 431

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPVTLENLSSEFEVSRER 268
                           N+++   S L  RER I      L    +T E++S    +SRER
Sbjct: 432 --------------VNNLIS---STLREREREIVRLYYGLDNECLTWEDISRRIGLSRER 474

Query: 269 VRQIEARAFKKVQESIQKQ 287
           VRQ+   A +K++ + +K+
Sbjct: 475 VRQVGLVALEKLKHAARKR 493


>gi|330946209|gb|EGH47399.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. pisi
           str. 1704B]
          Length = 230

 Score = 72.0 bits (175), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 32/78 (41%), Positives = 49/78 (62%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 77  AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 136

Query: 109 IKAAMQEYILRSWSLVKI 126
           I+ A+   I      ++I
Sbjct: 137 IRQAITRSIADQARTIRI 154


>gi|157833814|pdb|1SIG|A Chain A, Crystal Structure Of A Sigma70 Subunit Fragment From
           Escherichia Coli Rna Polymerase
          Length = 339

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 31/69 (44%), Positives = 46/69 (66%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 266 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 325

Query: 109 IKAAMQEYI 117
           I+ A+   I
Sbjct: 326 IRQAITRSI 334


>gi|17158744|ref|NP_478255.1| group 2 sigma 70-type sigma factor [Nostoc sp. PCC 7120]
 gi|17134693|dbj|BAB77251.1| group 2 sigma 70-type sigma factor [Nostoc sp. PCC 7120]
          Length = 323

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 28/65 (43%), Positives = 46/65 (70%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +++ ++LRLVV IA  Y+   L + +++ EG++GL + V+KFDP RG++ +TY+ WW
Sbjct: 87  AKQKMMVANLRLVVAIAKKYQRRNLELMDLIQEGSLGLERGVEKFDPTRGYKFSTYAYWW 146

Query: 109 IKAAM 113
           I  AM
Sbjct: 147 ISQAM 151


>gi|326566650|gb|EGE16791.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis 12P80B1]
          Length = 585

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 32/78 (41%), Positives = 49/78 (62%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 387 AKKDMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 446

Query: 109 IKAAMQEYILRSWSLVKI 126
           I+ A+   I      ++I
Sbjct: 447 IRQAITRSIADQARTIRI 464


>gi|289805026|ref|ZP_06535655.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. AG3]
          Length = 196

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 31/69 (44%), Positives = 46/69 (66%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 95  AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 154

Query: 109 IKAAMQEYI 117
           I+ A+   I
Sbjct: 155 IRQAITRSI 163


>gi|45128597|gb|AAS55059.1| RpoD [Vibrio parahaemolyticus]
          Length = 492

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 32/78 (41%), Positives = 49/78 (62%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 374 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 433

Query: 109 IKAAMQEYILRSWSLVKI 126
           I+ A+   I      ++I
Sbjct: 434 IRQAITRSIADQARTIRI 451


>gi|255553456|ref|XP_002517769.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
 gi|223543041|gb|EEF44576.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
          Length = 389

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 29/62 (46%), Positives = 46/62 (74%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R+  ++ RLV+ IA  YRG GL + +++ EG+IGL++  ++FDP+RG +L+TY  WWIK 
Sbjct: 179 RITGNYRRLVLSIANRYRGKGLSLQDLIQEGSIGLLRGAERFDPKRGNKLSTYVYWWIKE 238

Query: 112 AM 113
           A+
Sbjct: 239 AI 240


>gi|319777141|ref|YP_004136792.1| putative RNA polymerase sigma factor [Mycoplasma fermentans M64]
 gi|238810060|dbj|BAH69850.1| hypothetical protein [Mycoplasma fermentans PG18]
 gi|318038216|gb|ADV34415.1| Putative RNA polymerase sigma factor [Mycoplasma fermentans M64]
          Length = 489

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 67/267 (25%), Positives = 130/267 (48%), Gaps = 57/267 (21%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L+  +LRLV+  A  Y+  GL   +++SEGN G+++AV K++  +GF+ +TY+ WW
Sbjct: 242 ARDKLIKRNLRLVINNAKKYKNRGLSFIDLISEGNSGIVKAVSKYNVSKGFKFSTYATWW 301

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ-----AITD--------NNLK 155
           I+ A+   +      +++    +       + +++  LQ       TD        N   
Sbjct: 302 IRQAITRAVADQARTIRV--PVHMVETINKITKIERELQQELGYEPTDEMIAERYGNGYD 359

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV-------YDH 208
            E+V  I +K+N+   + IS++ ++              +N S + D++         D+
Sbjct: 360 AEKVRYI-RKINI---DPISLDKQIGK------------ENDSSFSDFVKDESVVNPVDY 403

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR----LQEN----PV-TLENLS 259
             QE+++      +   ++L +S+      + RI   +R    + EN    P+ +LE L+
Sbjct: 404 ASQEELV------ETLNSILEKSL----DDDERILICKRFGVGVDENGNKYPIHSLEKLA 453

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQK 286
            E  VS+ER+RQIE +  +K++ S +K
Sbjct: 454 EERNVSKERIRQIENKILRKLKSSTRK 480


>gi|318056947|ref|ZP_07975670.1| RNA polymerase principal sigma factor [Streptomyces sp. SA3_actG]
 gi|318078687|ref|ZP_07986019.1| RNA polymerase principal sigma factor [Streptomyces sp. SA3_actF]
          Length = 307

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 46/65 (70%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 75  FIRSNLRLVVAVARRYPRAGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTYATWWIRQA 134

Query: 113 MQEYI 117
           +   I
Sbjct: 135 ITRSI 139


>gi|134293382|ref|YP_001117118.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia vietnamiensis
           G4]
 gi|134136539|gb|ABO57653.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia vietnamiensis
           G4]
          Length = 518

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 64/244 (26%), Positives = 118/244 (48%), Gaps = 27/244 (11%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ ++LRLV+ IA  Y   G+ + ++V +G +GLM+A++KF+  RGF+ +TY+ WWI+ A
Sbjct: 285 MLEANLRLVLSIARKYVNRGVDLPDLVQDGCLGLMRAIEKFEYRRGFKFSTYATWWIRQA 344

Query: 113 MQEYIL-RSWSL---VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK--KL 166
           +   +  RS ++   V +G   +Q+     LR  + H +  T   L  +  +A  K   L
Sbjct: 345 VARAVADRSRTIRVPVHVGDQ-SQRVQRHALRFRQRHGRRATPAELAADTGLAEDKLRAL 403

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
               +E +S++  L   E+   L++  +  +S                  E+      R 
Sbjct: 404 LALPAEPLSLDTPLPDAET--GLVDLIEDQTSASP--------------FERLANTRMRE 447

Query: 227 MLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            ++  +  + P E  +   RR       P T + ++ +  +SRERVRQIE RA   ++ +
Sbjct: 448 CVSSLLRSVTPTEADVLR-RRFGLGGAEPDTYDAIAQDAGMSRERVRQIEKRALATLRTA 506

Query: 284 IQKQ 287
            Q +
Sbjct: 507 AQAE 510


>gi|308189916|ref|YP_003922847.1| RNA polymerase sigma factor [Mycoplasma fermentans JER]
 gi|307624658|gb|ADN68963.1| RNA polymerase sigma factor [Mycoplasma fermentans JER]
          Length = 489

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 67/267 (25%), Positives = 130/267 (48%), Gaps = 57/267 (21%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L+  +LRLV+  A  Y+  GL   +++SEGN G+++AV K++  +GF+ +TY+ WW
Sbjct: 242 ARDKLIKRNLRLVINNAKKYKNRGLSFIDLISEGNSGIVKAVSKYNVSKGFKFSTYATWW 301

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ-----AITD--------NNLK 155
           I+ A+   +      +++    +       + +++  LQ       TD        N   
Sbjct: 302 IRQAITRAVADQARTIRV--PVHMVETINKITKIERELQQELGYEPTDEMIAERYGNGYD 359

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV-------YDH 208
            E+V  I +K+N+   + IS++ ++              +N S + D++         D+
Sbjct: 360 AEKVRYI-RKINI---DPISLDKQIGK------------ENDSSFSDFVKDESVVNPVDY 403

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR----LQEN----PV-TLENLS 259
             QE+++      +   ++L +S+      + RI   +R    + EN    P+ +LE L+
Sbjct: 404 ASQEELV------ETLNSILEKSL----DDDERILICKRFGVGVDENGNKYPIHSLEKLA 453

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQK 286
            E  VS+ER+RQIE +  +K++ S +K
Sbjct: 454 EERNVSKERIRQIENKILRKLKSSTRK 480


>gi|302519838|ref|ZP_07272180.1| RNA polymerase sigma factor RpoS [Streptomyces sp. SPB78]
 gi|302428733|gb|EFL00549.1| RNA polymerase sigma factor RpoS [Streptomyces sp. SPB78]
          Length = 341

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 46/65 (70%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 109 FIRSNLRLVVAVARRYPRAGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTYATWWIRQA 168

Query: 113 MQEYI 117
           +   I
Sbjct: 169 ITRSI 173


>gi|295838256|ref|ZP_06825189.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. SPB74]
 gi|197698235|gb|EDY45168.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. SPB74]
          Length = 341

 Score = 71.6 bits (174), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 46/65 (70%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 109 FIRSNLRLVVAVARRYPRAGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTYATWWIRQA 168

Query: 113 MQEYI 117
           +   I
Sbjct: 169 ITRSI 173


>gi|311742672|ref|ZP_07716481.1| RNA polymerase principal sigma factor SigB [Aeromicrobium marinum
           DSM 15272]
 gi|311314300|gb|EFQ84208.1| RNA polymerase principal sigma factor SigB [Aeromicrobium marinum
           DSM 15272]
          Length = 320

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 71/259 (27%), Positives = 112/259 (43%), Gaps = 60/259 (23%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A    + ++LRLVV IA  Y    +P+ ++V EGN GL++AV+KFD  +GF+ +TY+ WW
Sbjct: 87  ALQEFIQANLRLVVSIARKYGRSAMPMLDLVQEGNTGLIRAVEKFDYVKGFKFSTYATWW 146

Query: 109 IKAAMQEYILRSWSLVKIG---------TTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           ++ A+   I +   +V++           TA ++    NL R  G+          PE  
Sbjct: 147 VRQAITRGIAQQARVVRLPVHVVEELNQVTAARR----NLERTLGY---------DPEP- 192

Query: 160 VAIAKKLNVSESEVI----------SMNCRL--AGDESLNALI---NSSDKNSSQWQDWL 204
             I+ +L +    VI          S++  +   GD SL  LI    +   +SS   D  
Sbjct: 193 AEISAELGMDVDRVIDLLSWGRDHVSLDTPVDEDGDTSLGDLIARETAPGPDSSMMSD-- 250

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEF 262
                               R M+ + +  L  RE  I  AR   L      L ++    
Sbjct: 251 ------------------ATRGMIAQLIDHLGEREADIVRARYGLLDGRQQKLADIGKRH 292

Query: 263 EVSRERVRQIEARAFKKVQ 281
            +S ERVRQ+E  A  K++
Sbjct: 293 GISAERVRQLEREALAKLR 311


>gi|330946768|gb|EGH47674.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. pisi
           str. 1704B]
          Length = 184

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 32/78 (41%), Positives = 49/78 (62%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 81  AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 140

Query: 109 IKAAMQEYILRSWSLVKI 126
           I+ A+   I      ++I
Sbjct: 141 IRQAITRSIADQARTIRI 158


>gi|239942002|ref|ZP_04693939.1| RNA polymerase principal sigma factor hrdD [Streptomyces
           roseosporus NRRL 15998]
 gi|239988467|ref|ZP_04709131.1| RNA polymerase principal sigma factor hrdD [Streptomyces
           roseosporus NRRL 11379]
          Length = 308

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 66/231 (28%), Positives = 113/231 (48%), Gaps = 20/231 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 76  FIRSNLRLVVAVARRYPRAGLPLLDLIQEGNAGLVRAVEKFDYAKGFKFSTYATWWIRQA 135

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   I      +++     ++     +RR++       ++   PE    IA +L+ S +E
Sbjct: 136 ITRSIADQSRTIRLPVHLVEE--LGRIRRVQREFN--REHGRDPEH-AEIAAELD-SNAE 189

Query: 173 VISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN---RRNML 228
            +      A D  SLN  ++  D   +Q+ D L      ++   +  E+      R   L
Sbjct: 190 RVGNVLDWARDPVSLNMSVD--DDGDTQFGDLL------EDTSAVSPEQSVMTLLRSEEL 241

Query: 229 TRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAF 277
              +  L+ R   I + R   E+    TL  +  +  ++RER+RQIE  A 
Sbjct: 242 EDLIGKLDNRTASIIKMRYGIEDGRERTLTEVGKQHGLTRERIRQIEKHAL 292


>gi|23978340|dbj|BAC21139.1| principal sigma factor [Stanieria cyanosphaera str. PCC 7437]
          Length = 203

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 58/216 (26%), Positives = 109/216 (50%), Gaps = 17/216 (7%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+
Sbjct: 1   VQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT-DNNLKP-EQVVAIAKKLNVSES 171
              I      +++        L+  + R+K   + ++ +   KP E+ +A   ++ + + 
Sbjct: 61  TRAIADQSRTIRLPV-----HLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKL 115

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
             I+ + +L    SL   I   +   S+  D++  D +  E  + +   R++  N+L   
Sbjct: 116 RFIAKSAQLPI--SLETPIGKEE--DSRLGDFIEADGETPEDQVSKSLLREDLENVL--- 168

Query: 232 MSVLNPRERRIFEARRLQENP--VTLENLSSEFEVS 265
              L+P ER +   R   ++    TLE +   F V+
Sbjct: 169 -DTLSPSERDVLRLRYGLDDGRMKTLEEIGQIFNVT 203


>gi|282865528|ref|ZP_06274579.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces sp.
           ACTE]
 gi|282559572|gb|EFB65123.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces sp.
           ACTE]
          Length = 333

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 68/231 (29%), Positives = 114/231 (49%), Gaps = 20/231 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 101 FIRSNLRLVVAVARRYPRAGLPLLDLIQEGNAGLVRAVEKFDYAKGFKFSTYATWWIRQA 160

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   I      +++     ++     +RR++       ++   PE    IA +L  S +E
Sbjct: 161 ITRSIADQSRTIRLPVHLVEE--LGRIRRVQREFN--REHGRDPEH-AEIAAELG-SNTE 214

Query: 173 VISMNCRLAGDE-SLNALINSSDKNSSQWQDWL----VYDHDGQEQVLIEKEERKNRRNM 227
            +      A D  SLN  ++  D   +Q+ D L        +     L+  EE ++    
Sbjct: 215 RVGNVLDWARDPVSLNMSVD--DDGDTQFGDLLEDTSAVSPEQSVMTLLRSEELEDLIGK 272

Query: 228 L-TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
           L  R+ S++  R R   E  R +    TL  +  +  ++RER+RQIE  A 
Sbjct: 273 LDNRTASII--RMRYGIEDGRER----TLTEVGKQHGLTRERIRQIEKHAL 317


>gi|288553151|ref|YP_003425086.1| sporulation sigma factor SigE [Bacillus pseudofirmus OF4]
 gi|288544311|gb|ADC48194.1| sporulation sigma factor SigE [Bacillus pseudofirmus OF4]
          Length = 237

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 71/267 (26%), Positives = 116/267 (43%), Gaps = 69/267 (25%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL K+    GD +    L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 35  PPLSKEEEAVLLKKL-PTGDKAVRSMLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 93

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+                          
Sbjct: 94  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN-------------------------- 127

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ--DWL 204
                               N + SEV       + DE LN            W   + L
Sbjct: 128 --------------------NKTRSEV-------SFDEPLNI----------DWDGNELL 150

Query: 205 VYDHDGQEQVLIEKE-ERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSE 261
           + D  G E+ +I +  E K  R +L +++  LN RE++I E R     E   T ++++  
Sbjct: 151 LSDVLGTEEDIITRGIEEKVDRKLLVKALHTLNEREKQIMELRFGLAGEEEKTQKDVADM 210

Query: 262 FEVSRERVRQIEARAFKKVQESIQKQV 288
             +S+  + ++E R  K++Q+   K V
Sbjct: 211 LGISQSYISRLEKRIIKRLQKEFNKMV 237


>gi|207723156|ref|YP_002253555.1| sigma factor, ecf;peptidase aspartic, active site;;; protein
           [Ralstonia solanacearum MolK2]
 gi|206588350|emb|CAQ35313.1| sigma factor, ecf;peptidase aspartic, active site;;; protein
           [Ralstonia solanacearum MolK2]
          Length = 229

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 60/206 (29%), Positives = 101/206 (49%), Gaps = 20/206 (9%)

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ- 147
           A++KFDPERGFR +TY+ WWI+ +++  I+     V++    +  R    + R K HL+ 
Sbjct: 29  AIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRL--PVHVIRELNQVLRAKRHLEK 86

Query: 148 -AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN-SSQWQDWLV 205
             I   +   E +  +  K      +V+S+N      E   +L    D +  +   D+L 
Sbjct: 87  SGIDGRDASIEDIAHLLGKTTEEVQDVLSLN------EHTTSLDTPFDLDPGTSLLDFLS 140

Query: 206 YDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN---PVTLENLSSE 261
            +H    +Q +  +E  +  ++ L R    L+ + R + E RR   N   P TLE L++E
Sbjct: 141 DEHGASPDQEVAHRELSQLMKSWLAR----LSDKHRYVVE-RRFGLNHIEPATLEELAAE 195

Query: 262 FEVSRERVRQIEARAFKKVQESIQKQ 287
             ++RERVRQI+  A  K++     Q
Sbjct: 196 MGLTRERVRQIQQEALVKLKRHFASQ 221


>gi|148377531|ref|YP_001256407.1| RNA polymerase sigma factor [Mycoplasma agalactiae PG2]
 gi|148291577|emb|CAL58963.1| DNA directed RNA polymerase sigma factor(Sigma A) [Mycoplasma
           agalactiae PG2]
          Length = 509

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 32/88 (36%), Positives = 57/88 (64%), Gaps = 2/88 (2%)

Query: 28  MLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +L+ +EE+ LA    + G     A  +L+  +LRLV+  A  Y+  GL   +++SEGN G
Sbjct: 239 LLQPEEEFELATEMDKGGFKGKRARDKLIKRNLRLVINNAKKYKNRGLSFIDLISEGNSG 298

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAM 113
           +++AV+K++  +GF+ +TY+ WWI+ A+
Sbjct: 299 IIKAVQKYNVNKGFKFSTYATWWIRQAI 326


>gi|23978369|dbj|BAC21149.1| principal sigma factor [Pseudanabaena sp. PCC 7403]
          Length = 203

 Score = 71.2 bits (173), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 57/216 (26%), Positives = 110/216 (50%), Gaps = 17/216 (7%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+
Sbjct: 1   VQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT-DNNLKP-EQVVAIAKKLNVSES 171
              I      +++        L+  + R+K   + ++ +   KP E+ +A   ++ + + 
Sbjct: 61  TRAIADQSRTIRLPV-----HLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKL 115

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
             I+ + +L    SL   I   +   S+  D++  D +  +  + +   R++  ++L   
Sbjct: 116 RFIAKSAQLP--ISLETPIGKEE--DSRLGDFIESDGETPDDQVAKSLLREDLESVL--- 168

Query: 232 MSVLNPRERRIFEARRLQENP--VTLENLSSEFEVS 265
              L+PRER +   R   ++    TLE +   F V+
Sbjct: 169 -GTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVT 203


>gi|313678638|ref|YP_004056378.1| RNA polymerase sigma factor [Mycoplasma bovis PG45]
 gi|312950821|gb|ADR25416.1| RNA polymerase sigma factor [Mycoplasma bovis PG45]
          Length = 509

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 32/88 (36%), Positives = 57/88 (64%), Gaps = 2/88 (2%)

Query: 28  MLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +L+ +EE+ LA    + G     A  +L+  +LRLV+  A  Y+  GL   +++SEGN G
Sbjct: 239 LLQPEEEFELATEMDKGGFRGKRARDKLIKRNLRLVINNAKKYKNRGLSFIDLISEGNSG 298

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAM 113
           +++AV+K++  +GF+ +TY+ WWI+ A+
Sbjct: 299 IIKAVQKYNVNKGFKFSTYATWWIRQAI 326


>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 = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 31/78 (39%), Positives = 48/78 (61%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 577 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 636

Query: 109 IKAAMQEYILRSWSLVKI 126
           I+ A+   I      ++I
Sbjct: 637 IRQAITRSIADQARTIRI 654


>gi|207723755|ref|YP_002254153.1| rna polymerase sigma d (sigma-70) factor protein [Ralstonia
           solanacearum MolK2]
 gi|206588959|emb|CAQ35921.1| rna polymerase sigma d (sigma-70) factor protein [Ralstonia
           solanacearum MolK2]
          Length = 773

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 31/78 (39%), Positives = 48/78 (61%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 577 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 636

Query: 109 IKAAMQEYILRSWSLVKI 126
           I+ A+   I      ++I
Sbjct: 637 IRQAITRSIADQARTIRI 654


>gi|22135904|gb|AAM91534.1| sigma factor SigC [Arabidopsis thaliana]
          Length = 291

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 61/234 (26%), Positives = 112/234 (47%), Gaps = 15/234 (6%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV S   LV+ +A  YRG G+   +++  G +G++Q  ++FD  RG++ +TY  +WI+ +
Sbjct: 56  LVKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKS 115

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           M   + R    V I ++         + R   H+Q      LK    +  A    +++  
Sbjct: 116 MSTMVSRHARGVHIPSS---------IIRTINHIQK-ARKTLKTSHGIKYAADEEIAKLT 165

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQW--QDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
             S+    A ++ L  ++ S DK         +L +  D   +   E   R++ R  +  
Sbjct: 166 GHSVKKIRAANQCLK-VVGSIDKKVGDCFTTKFLEFTPDTTMESPEEAVMRQSARRDIHD 224

Query: 231 SMSVLNPRERRIFEARR-LQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            +  L PRE+++   R  LQ+  P +LE +    +VS+E +R+IE RA  K+++
Sbjct: 225 LLEGLEPREKQVMVLRYGLQDYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLRD 278


>gi|330984347|gb|EGH82450.1| putative alternative sigma factor RpoH [Pseudomonas syringae pv.
           lachrymans str. M301315]
          Length = 263

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 59/262 (22%), Positives = 125/262 (47%), Gaps = 20/262 (7%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           +IP +++ +  +  + ++  G   A    VT+ L +V  +A+   G    + ++  +G +
Sbjct: 18  QIPSIQEMDNNI--RIFKSTGCRKAHDACVTALLPMVYGLAVANAGRA-EVDDMFQQGAL 74

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
            +M A++KFDP+    + +++  ++  A+    +    L+++  T   K +    RR+  
Sbjct: 75  AVMDALRKFDPDDELNILSWTKLYVSRAINSLCVFGTKLIRVPDT---KTIRLCYRRMGL 131

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD---ESLNALINSSDKNSSQWQ 201
            L+   D  +   +   +A +L VS  +      ++A D        +++  D+    WQ
Sbjct: 132 FLK---DGPINEARSKILANELGVSLEDF-----KIARDLYSSCYEPVLSCGDE---PWQ 180

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
              +   +  E+ +I ++E  +   ++ R M+VLNP+E  +   R LQE PV L  +  +
Sbjct: 181 GHDIKTSETLEEAIIVEDEAAHVTRVVGRLMTVLNPKEAEVIRLRCLQEEPVQLRLVGEQ 240

Query: 262 FEVSRERVRQIEARAFKKVQES 283
              S ER RQ+E  A  K++++
Sbjct: 241 LGFSTERARQVENIAKDKMRKA 262


>gi|291320189|ref|YP_003515450.1| DNA directed RNA polymerase sigma factor [Mycoplasma agalactiae]
 gi|290752521|emb|CBH40493.1| DNA directed RNA polymerase sigma factor(Sigma A) [Mycoplasma
           agalactiae]
          Length = 509

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 32/88 (36%), Positives = 57/88 (64%), Gaps = 2/88 (2%)

Query: 28  MLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +L+ +EE+ LA    + G     A  +L+  +LRLV+  A  Y+  GL   +++SEGN G
Sbjct: 239 LLQPEEEFELATEMDKGGFRGKRARDKLIKRNLRLVINNAKKYKNRGLSFIDLISEGNSG 298

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAM 113
           +++AV+K++  +GF+ +TY+ WWI+ A+
Sbjct: 299 IIKAVQKYNVNKGFKFSTYATWWIRQAI 326


>gi|289751356|ref|ZP_06510734.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis T92]
 gi|289691943|gb|EFD59372.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis T92]
          Length = 470

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 45/141 (31%), Positives = 75/141 (53%), Gaps = 31/141 (21%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGD-LS 48
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+ L 
Sbjct: 216 RKDAELTASADS-VRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSERGEKLP 274

Query: 49  AAHR----------------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           AA R                L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 275 AAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEK 334

Query: 93  FDPERGFRLATYSMWWIKAAM 113
           FD  +G++ +TY+ WWI+ A+
Sbjct: 335 FDYTKGYKFSTYATWWIRQAI 355


>gi|254253854|ref|ZP_04947171.1| DNA-directed RNA polymerase sigma subunit [Burkholderia dolosa
           AUO158]
 gi|124898499|gb|EAY70342.1| DNA-directed RNA polymerase sigma subunit [Burkholderia dolosa
           AUO158]
          Length = 547

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 56/232 (24%), Positives = 109/232 (46%), Gaps = 15/232 (6%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ ++LRLV+ IA  Y   G+ + ++V +G +GLM+A++KF+  RGF+ +TY+ WWI+ A
Sbjct: 314 MLEANLRLVLSIARKYMNRGVDLPDLVQDGCVGLMRAIEKFEYRRGFKFSTYATWWIRQA 373

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +      +++      +  +  ++R     +  T     P +   +A +  + E +
Sbjct: 374 VARAVADRSRTIRVPVHVGDQ--YQRVQRHALRFRQRTGRRATPAE---LAAETGLDEDK 428

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           + ++    A   SL+  +  +D       D +    D       E+      R  +T  +
Sbjct: 429 LRAILALPAEPVSLDTPLPDTDTG---LVDTI---EDQASASPFERLADARMRECVTSLL 482

Query: 233 SVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             + P E  +   RR       P T + ++ +  +SRERVRQIE RA   ++
Sbjct: 483 RSVTPTEADVLR-RRFGLGGAEPDTYDAIAQDAGMSRERVRQIEKRALAALR 533


>gi|193216688|ref|YP_001999930.1| RNA polymerase sigma factor [Mycoplasma arthritidis 158L3-1]
 gi|193002011|gb|ACF07226.1| RNA polymerase sigma-70 factor [Mycoplasma arthritidis 158L3-1]
          Length = 513

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 66/253 (26%), Positives = 121/253 (47%), Gaps = 39/253 (15%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   LV  +LRLV+  A  Y+  GL   +++SEGN G+M+AV K+D ++GF+ +TY+ WW
Sbjct: 260 ARDMLVKRNLRLVINNAKRYKNRGLSFIDLISEGNSGIMKAVSKYDYKKGFKFSTYATWW 319

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   +            A+Q R      R+  H+    +  LK E+ +        
Sbjct: 320 IRQAITRAV------------ADQARTI----RVPVHMVETINKILKIERELQQEFGYPP 363

Query: 169 SESEVISMNCRLAGDESLNAL-----IN----SSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           ++ E+     +  GD +   +     IN    S DKN  + ++    D    E V+   +
Sbjct: 364 TDEEIAK---KFGGDFTAEKVRYIRKINIDPISLDKNIGKEENSSFSDFVKDESVISPND 420

Query: 220 -ERKNRRNMLTRSM--SVLNPRERRIFEARR-LQENPV-------TLENLSSEFEVSRER 268
              +    ++   M  S L+P ++ +   R  + ++P        TL+ L+ E  +S+E+
Sbjct: 421 FASQQELAVILNEMINSSLDPEDQALIRKRYGVGQDPSGVPYRPHTLDELAKELNISKEK 480

Query: 269 VRQIEARAFKKVQ 281
           VR++EA+  +K++
Sbjct: 481 VRKLEAKILRKLK 493


>gi|47459124|ref|YP_015986.1| RNA polymerase sigma factor [Mycoplasma mobile 163K]
 gi|47458453|gb|AAT27775.1| DNA-directed RNA polymerase sigma factor [Mycoplasma mobile 163K]
          Length = 488

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 34/103 (33%), Positives = 61/103 (59%), Gaps = 4/103 (3%)

Query: 28  MLEKQEEYVLAKRYREHGD----LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           +L+K+EE   +K+  E  +      A + L+  +LRLV+  A  Y+  GL   +++SEGN
Sbjct: 214 VLDKEEEIKYSKQIEEDRNGRKGKKAFNALIHHNLRLVINNAKKYKNRGLSFIDLISEGN 273

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            GL++A  K+D  RGF+ +TY+ WW++ A+   +     +V++
Sbjct: 274 AGLIKAATKYDYRRGFKFSTYATWWVRQAITRAVADQARIVRV 316


>gi|26665386|dbj|BAC44904.1| principal sigma factor [Fischerella major NIES-592]
          Length = 203

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 61/217 (28%), Positives = 110/217 (50%), Gaps = 19/217 (8%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+
Sbjct: 1   VQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT-DNNLKP-EQVVAIAKKLNVSES 171
              I      +++        L+  + R+K   + ++ +   KP E+ +A   ++ + + 
Sbjct: 61  TRAIADQSRTIRLPV-----HLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKL 115

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTR 230
             I  + +L    SL   I   +   S+  D++  + DG+     E +  KN  R  L +
Sbjct: 116 RFIVKSAQLPI--SLETPIGKEE--DSRLGDFI--ESDGETP---EDQVSKNLLREDLEK 166

Query: 231 SMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVS 265
            +  L+PRER +   R   ++    TLE +   F V+
Sbjct: 167 VLDSLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVT 203


>gi|302520386|ref|ZP_07272728.1| RNA polymerase sigma-G factor [Streptomyces sp. SPB78]
 gi|318060770|ref|ZP_07979493.1| RNA polymerase sigma factor [Streptomyces sp. SA3_actG]
 gi|318078699|ref|ZP_07986031.1| RNA polymerase sigma factor [Streptomyces sp. SA3_actF]
 gi|333025873|ref|ZP_08453937.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
 gi|302429281|gb|EFL01097.1| RNA polymerase sigma-G factor [Streptomyces sp. SPB78]
 gi|332745725|gb|EGJ76166.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
          Length = 274

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 66/244 (27%), Positives = 120/244 (49%), Gaps = 23/244 (9%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           EHG + AA  L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDP+RG +  
Sbjct: 46  EHGRVRAA--LIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFP 103

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           T++M  +   ++ Y   +   V +      +RL     ++    + +T  + +      I
Sbjct: 104 TFAMPTVVGEIKRYFRDNVRTVHV-----PRRLHELWVQVNSAAEDLTTAHGRSPTTAEI 158

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL--VYDHDGQEQVLIEKEE 220
           A++L + E EV++  C  AG        +++   ++Q  D L  + D  G E   ++  E
Sbjct: 159 AERLRIGEDEVLA--CIEAGRS-----YHATSLEAAQEGDGLPGLLDRLGYEDPALDGVE 211

Query: 221 RKNRRNMLTRSMSVLNP-RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
            ++    L R + V  P RE+RI   R    N +T   +S+E  VS+  V ++ AR+F +
Sbjct: 212 HRD----LVRHLLVQLPEREQRILLLRYY--NNLTQSQISAELGVSQMHVSRLLARSFAR 265

Query: 280 VQES 283
           ++ +
Sbjct: 266 LRSA 269


>gi|89068737|ref|ZP_01156123.1| sigma32-like factor [Oceanicola granulosus HTCC2516]
 gi|89045700|gb|EAR51762.1| sigma32-like factor [Oceanicola granulosus HTCC2516]
          Length = 241

 Score = 70.9 bits (172), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 68/263 (25%), Positives = 116/263 (44%), Gaps = 39/263 (14%)

Query: 22  EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           E  K P+L   +E    ++++  GD ++   L+ SH R     A  +      I ++V+E
Sbjct: 7   EALKEPLLGLDQERQAIEKWQGEGDRASLELLLRSHARQAYAQATRWTDNPSYIEDLVAE 66

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           G I LM+A ++FD  R  R +TY+ WW++ AM E   R  +++ +   A         RR
Sbjct: 67  GMIALMRAAERFDLTREVRFSTYAAWWLRTAMAEAYGRISAVIDVPVKA-----LAEARR 121

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
                +A+   N     VVA+      SE +   M+ RLA  E                 
Sbjct: 122 AG---EALAQRN-----VVALDGGARASEED--DMSDRLACPEPT--------------- 156

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
                     E  +I    R     +L  +++ L+  ER I   R+L + P  ++ L++E
Sbjct: 157 ---------PEDRIIRDSSRDAAARLLHAALASLSETERTILARRKLSDRPAPVDALAAE 207

Query: 262 FEVSRERVRQIEARAFKKVQESI 284
             +S  R+RQIE RA  ++++ +
Sbjct: 208 LSMSPTRLRQIETRAMGRLRQRL 230


>gi|318066901|emb|CBY89065.1| RNA polymerase sigma70 factor [Carnimonas nigrificans]
          Length = 371

 Score = 70.9 bits (172), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 306 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 365

Query: 109 IKAAM 113
           I+ A+
Sbjct: 366 IRQAI 370


>gi|15232364|ref|NP_190960.1| SIGC (RNA POLYMERASE SIGMA-SUBUNIT C); DNA binding / DNA-directed
           RNA polymerase/ sigma factor/ transcription factor
           [Arabidopsis thaliana]
 gi|2353175|gb|AAB69386.1| sigma factor 3 [Arabidopsis thaliana]
 gi|2463554|dbj|BAA22530.1| SigC [Arabidopsis thaliana]
 gi|5478585|dbj|BAA82450.1| sigma factor SigC [Arabidopsis thaliana]
 gi|7630012|emb|CAB88354.1| sigma factor SigC [Arabidopsis thaliana]
 gi|133778870|gb|ABO38775.1| At3g53920 [Arabidopsis thaliana]
 gi|332645638|gb|AEE79159.1| RNApolymerase sigma-subunit C [Arabidopsis thaliana]
          Length = 571

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 61/234 (26%), Positives = 112/234 (47%), Gaps = 15/234 (6%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV S   LV+ +A  YRG G+   +++  G +G++Q  ++FD  RG++ +TY  +WI+ +
Sbjct: 336 LVKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKS 395

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           M   + R    V I ++         + R   H+Q      LK    +  A    +++  
Sbjct: 396 MSTMVSRHARGVHIPSS---------IIRTINHIQK-ARKTLKTSHGIKYAADEEIAKLT 445

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQW--QDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
             S+    A ++ L  ++ S DK         +L +  D   +   E   R++ R  +  
Sbjct: 446 GHSVKKIRAANQCLK-VVGSIDKKVGDCFTTKFLEFTPDTTMESPEEAVMRQSARRDIHD 504

Query: 231 SMSVLNPRERRIFEARR-LQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            +  L PRE+++   R  LQ+  P +LE +    +VS+E +R+IE RA  K+++
Sbjct: 505 LLEGLEPREKQVMVLRYGLQDYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLRD 558


>gi|307776476|pdb|3LES|A Chain A, 2f5 Epitope Scaffold Es2
 gi|307776477|pdb|3LES|B Chain B, 2f5 Epitope Scaffold Es2
 gi|307776478|pdb|3LEV|A Chain A, Hiv-1 Antibody 2f5 In Complex With Epitope Scaffold Es2
          Length = 179

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 32/70 (45%), Positives = 48/70 (68%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   L+ ++LRLVV IA  Y G GL   +++ EGN GL++AV+KF+ +RGF  +TY+ W
Sbjct: 105 AARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRGFAFSTYATW 164

Query: 108 WIKAAMQEYI 117
           WI+ A+   I
Sbjct: 165 WIRQAINRAI 174


>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 = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 31/78 (39%), Positives = 48/78 (61%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 565 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 624

Query: 109 IKAAMQEYILRSWSLVKI 126
           I+ A+   I      ++I
Sbjct: 625 IRQAITRSIADQARTIRI 642


>gi|75812393|ref|YP_320012.1| sigma-70 [Anabaena variabilis ATCC 29413]
 gi|75705149|gb|ABA24823.1| Sigma-70 [Anabaena variabilis ATCC 29413]
          Length = 314

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 42/154 (27%), Positives = 73/154 (47%), Gaps = 39/154 (25%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYRE---------------HGDLS--------------- 48
           Y+ EI K PML  ++E  LA++ ++               H  L+               
Sbjct: 11  YLREISKYPMLTPEQEITLARQVKQMTVVQQHKQVLEEQLHQQLNIQQLAADMGKSETEV 70

Query: 49  ---------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                    A  +++ ++LRLVV IA  YR   L   ++V EG+IGL +AV++FDP RG+
Sbjct: 71  FQILRLGQKAKEKMIAANLRLVVAIAKKYRWSQLEFLDLVQEGSIGLQKAVERFDPNRGY 130

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           + +T + WWI+  + + I    + ++  +  N +
Sbjct: 131 KFSTCAYWWIRQEITKAIANKSTTIRTPSHMNDR 164


>gi|318066953|emb|CBY89091.1| RNA polymerase sigma70 factor [Halomonas koreensis]
          Length = 365

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 300 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 359

Query: 109 IKAAM 113
           I+ A+
Sbjct: 360 IRQAI 364


>gi|318066923|emb|CBY89076.1| RNA polymerase sigma70 factor [Halomonas anticariensis]
          Length = 371

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 306 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 365

Query: 109 IKAAM 113
           I+ A+
Sbjct: 366 IRQAI 370


>gi|282863441|ref|ZP_06272500.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
 gi|282561776|gb|EFB67319.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
          Length = 285

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 64/234 (27%), Positives = 115/234 (49%), Gaps = 21/234 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDPERG +  T++M  +   
Sbjct: 65  LIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQFPTFAMPTVVGE 124

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           ++ Y   +   V +      +RL     ++ G  + +T  + +      IA++L +SE E
Sbjct: 125 IKRYFRDNVRTVHV-----PRRLHELWVQVTGATEDLTTAHGRSPTTAEIAQRLKISEEE 179

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWL--VYDHDGQEQVLIEKEERKNRRNMLTR 230
           V++  C  AG        +++   ++Q  D L  + D  G E   +   E ++    L R
Sbjct: 180 VLA--CIEAGRS-----YHATSLEAAQEGDGLPGLLDRLGYEDPALAGVEHRD----LVR 228

Query: 231 SMSVLNP-RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            + V  P RE+RI   R    N +T   +S+E  VS+  V ++ AR+F +++ +
Sbjct: 229 HLLVQLPEREQRILLLRYY--NNLTQSQISAELGVSQMHVSRLLARSFARLRSA 280


>gi|318066973|emb|CBY89101.1| RNA polymerase sigma70 factor [Halomonas taeanensis]
          Length = 366

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 301 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 360

Query: 109 IKAAM 113
           I+ A+
Sbjct: 361 IRQAI 365


>gi|318066945|emb|CBY89087.1| RNA polymerase sigma70 factor [Halomonas halocynthiae]
          Length = 368

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 303 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 362

Query: 109 IKAAM 113
           I+ A+
Sbjct: 363 IRQAI 367


>gi|318066993|emb|CBY89111.1| RNA polymerase sigma70 factor [Salinicola halophilus]
          Length = 368

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 303 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 362

Query: 109 IKAAM 113
           I+ A+
Sbjct: 363 IRQAI 367


>gi|321309572|ref|YP_004191901.1| RNA polymerase sigma factor rpoD [Mycoplasma haemofelis str.
           Langford 1]
 gi|319801416|emb|CBY92062.1| RNA polymerase sigma factor rpoD [Mycoplasma haemofelis str.
           Langford 1]
          Length = 461

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 30/78 (38%), Positives = 49/78 (62%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  S+LRLV  +A  Y  YG P+ ++V EG  GLM+AV+KF+   G + +TY+ WW
Sbjct: 175 AIKQLTISNLRLVQSVAKKYLNYGFPMEDLVQEGFFGLMKAVQKFNYNLGNKFSTYATWW 234

Query: 109 IKAAMQEYILRSWSLVKI 126
           I+ A+   I   + ++++
Sbjct: 235 IRQAIVRSIAEKYRVIRV 252


>gi|318066957|emb|CBY89093.1| RNA polymerase sigma70 factor [Halomonas maura]
          Length = 365

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 300 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 359

Query: 109 IKAAM 113
           I+ A+
Sbjct: 360 IRQAI 364


>gi|323345486|ref|ZP_08085709.1| RNA polymerase sigma-43 factor [Prevotella oralis ATCC 33269]
 gi|323093600|gb|EFZ36178.1| RNA polymerase sigma-43 factor [Prevotella oralis ATCC 33269]
          Length = 238

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 38/112 (33%), Positives = 67/112 (59%), Gaps = 1/112 (0%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
            G+  +  Y+ EI    +L   EE  LA++  ++GD +A  RL  ++L+ VV IA  Y+ 
Sbjct: 4   TGKSSMKLYLDEIGGESLLTSLEEMKLAEKI-QNGDEAALERLTKANLKFVVFIAKQYQH 62

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            G+ + ++VSEGNIGL+ A KK+ P +  R A ++  +I+  +++ +LR  +
Sbjct: 63  QGVDMEDLVSEGNIGLLYAAKKYTPSKEKRFAPFAAPFIRKQIEQLLLRQGA 114


>gi|318066989|emb|CBY89109.1| RNA polymerase sigma70 factor [Kushneria marisflavi]
          Length = 373

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 308 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 367

Query: 109 IKAAM 113
           I+ A+
Sbjct: 368 IRQAI 372


>gi|318066981|emb|CBY89105.1| RNA polymerase sigma70 factor [Halotalea alkalilenta]
          Length = 370

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 305 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 364

Query: 109 IKAAM 113
           I+ A+
Sbjct: 365 IRQAI 369


>gi|7363220|emb|CAB83107.1| sigma factor 3 [Sinapis alba]
          Length = 567

 Score = 70.5 bits (171), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 61/234 (26%), Positives = 112/234 (47%), Gaps = 15/234 (6%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV S   LV+ +A  YRG G+   +++  G +G++Q  ++FD  RG++ +TY  +WI+ +
Sbjct: 332 LVKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVRYWIRKS 391

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           M   + R    V I   A+  R    +++ +          LK  Q +       +S+  
Sbjct: 392 MSTMVSRHARGVHI--PASIIRTMSQIQKAR--------KTLKTSQGIKYPADEEISKLT 441

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQW--QDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
             S+    A ++ L  ++ S DK         +L +  D   +   E   R++ R  +  
Sbjct: 442 GYSLKKIRAANQCLK-VVGSIDKKVGDCFTTRFLEFTPDPTMESPEEAVMRQSARGEVHN 500

Query: 231 SMSVLNPRERRIFEARR-LQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            +  L PRE+++   R  LQ+ +P +LE +     VS+E +R+IE RA  K+++
Sbjct: 501 LLEGLEPREKQVMVLRYGLQDYSPKSLEEIGKILRVSKEGIRKIERRAMAKLRD 554


>gi|318066943|emb|CBY89086.1| RNA polymerase sigma70 factor [Halomonas halmophila]
          Length = 367

 Score = 70.1 bits (170), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 302 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 361

Query: 109 IKAAM 113
           I+ A+
Sbjct: 362 IRQAI 366


>gi|318066921|emb|CBY89075.1| RNA polymerase sigma70 factor [Halomonas almeriensis]
          Length = 366

 Score = 70.1 bits (170), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 301 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 360

Query: 109 IKAAM 113
           I+ A+
Sbjct: 361 IRQAI 365


>gi|225454599|ref|XP_002264964.1| PREDICTED: hypothetical protein isoform 2 [Vitis vinifera]
          Length = 496

 Score = 70.1 bits (170), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 65/251 (25%), Positives = 122/251 (48%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  S++RLV+ IA  Y   G  ++++V  G IGL++ ++KFD  +GF+++TY  WW
Sbjct: 253 AREKLAMSNVRLVMSIAQRYDNMGAEMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 312

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN--------NLKPEQV- 159
           I+  +   ++ +   +++ +  +++       +++   + IT +        N+  ++V 
Sbjct: 313 IRQGVSRALVENSRTLRLPSHLHERLSLIRNAKIRLEEKGITPSIDRIAECLNMSQKKVR 372

Query: 160 ---VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
               AI+K  ++      S+N  L G E+L++ I      ++ W       H   E  L 
Sbjct: 373 NATEAISKVFSLDREAFPSLNG-LPG-ETLHSYIADVRLENNPW-------HGVDEWAL- 422

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEA-RRLQENPVTLENLSSEFEVSRERVRQIEAR 275
                K+  N L    + L  RER I      L    +T E++S    +SRERVRQ+   
Sbjct: 423 -----KDEVNKLIN--TTLGERERDIIRLYYGLDNECLTWEDISKRIGLSRERVRQVGLV 475

Query: 276 AFKKVQESIQK 286
           A +K++ + +K
Sbjct: 476 ALEKLKNAARK 486


>gi|318066975|emb|CBY89102.1| RNA polymerase sigma70 factor [Halomonas variabilis]
          Length = 368

 Score = 70.1 bits (170), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 303 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 362

Query: 109 IKAAM 113
           I+ A+
Sbjct: 363 IRQAI 367


>gi|225454597|ref|XP_002264928.1| PREDICTED: hypothetical protein isoform 1 [Vitis vinifera]
          Length = 507

 Score = 70.1 bits (170), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 65/251 (25%), Positives = 122/251 (48%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  S++RLV+ IA  Y   G  ++++V  G IGL++ ++KFD  +GF+++TY  WW
Sbjct: 264 AREKLAMSNVRLVMSIAQRYDNMGAEMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 323

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN--------NLKPEQV- 159
           I+  +   ++ +   +++ +  +++       +++   + IT +        N+  ++V 
Sbjct: 324 IRQGVSRALVENSRTLRLPSHLHERLSLIRNAKIRLEEKGITPSIDRIAECLNMSQKKVR 383

Query: 160 ---VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
               AI+K  ++      S+N  L G E+L++ I      ++ W       H   E  L 
Sbjct: 384 NATEAISKVFSLDREAFPSLNG-LPG-ETLHSYIADVRLENNPW-------HGVDEWAL- 433

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEA-RRLQENPVTLENLSSEFEVSRERVRQIEAR 275
                K+  N L    + L  RER I      L    +T E++S    +SRERVRQ+   
Sbjct: 434 -----KDEVNKLIN--TTLGERERDIIRLYYGLDNECLTWEDISKRIGLSRERVRQVGLV 486

Query: 276 AFKKVQESIQK 286
           A +K++ + +K
Sbjct: 487 ALEKLKNAARK 497


>gi|318066987|emb|CBY89108.1| RNA polymerase sigma70 factor [Kushneria indalinina]
          Length = 372

 Score = 70.1 bits (170), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 307 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 366

Query: 109 IKAAM 113
           I+ A+
Sbjct: 367 IRQAI 371


>gi|318066961|emb|CBY89095.1| RNA polymerase sigma70 factor [Halomonas muralis]
          Length = 367

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 302 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 361

Query: 109 IKAAM 113
           I+ A+
Sbjct: 362 IRQAI 366


>gi|318066977|emb|CBY89103.1| RNA polymerase sigma70 factor [Halomonas ventosae]
          Length = 366

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 301 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 360

Query: 109 IKAAM 113
           I+ A+
Sbjct: 361 IRQAI 365


>gi|318066955|emb|CBY89092.1| RNA polymerase sigma70 factor [Halomonas magadiensis]
          Length = 370

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 305 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 364

Query: 109 IKAAM 113
           I+ A+
Sbjct: 365 IRQAI 369


>gi|318066931|emb|CBY89080.1| RNA polymerase sigma70 factor [Halomonas campaniensis]
          Length = 368

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 303 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 362

Query: 109 IKAAM 113
           I+ A+
Sbjct: 363 IRQAI 367


>gi|23978365|dbj|BAC21147.1| principal sigma factor [Leptolyngbya sp. PCC 7375]
          Length = 203

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 58/216 (26%), Positives = 108/216 (50%), Gaps = 17/216 (7%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+
Sbjct: 1   VQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKP-EQVVAIAKKLNVSES 171
              I      +++        L+  + R+K   + ++     KP E+ +A   ++ + + 
Sbjct: 61  TRAIADQSRTIRLPV-----HLYETISRIKKTTKLLSQELGRKPTEEEIATRMEMTIEKL 115

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
             I+ + +L    SL   I   +   S+  D++  D +  E  + +   R++   +L   
Sbjct: 116 RFIAKSAQLP--ISLETPIGKEE--DSRLGDFIESDGETPEDEVSKSLLREDLEGVL--- 168

Query: 232 MSVLNPRERRIFEARRLQENP--VTLENLSSEFEVS 265
            S L+P ER +   R   ++    TLE +   F V+
Sbjct: 169 -STLSPSERDVLRLRYGLDDGRMKTLEEIGQIFNVT 203


>gi|318066929|emb|CBY89079.1| RNA polymerase sigma70 factor [Halomonas boliviensis]
          Length = 368

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 303 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 362

Query: 109 IKAAM 113
           I+ A+
Sbjct: 363 IRQAI 367


>gi|318066995|emb|CBY89112.1| RNA polymerase sigma70 factor [Salinicola salarius]
          Length = 368

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 303 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 362

Query: 109 IKAAM 113
           I+ A+
Sbjct: 363 IRQAI 367


>gi|318066951|emb|CBY89090.1| RNA polymerase sigma70 factor [Halomonas hydrothermalis]
          Length = 370

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 305 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 364

Query: 109 IKAAM 113
           I+ A+
Sbjct: 365 IRQAI 369


>gi|318066937|emb|CBY89083.1| RNA polymerase sigma70 factor [Halomonas desiderata]
          Length = 375

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 310 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 369

Query: 109 IKAAM 113
           I+ A+
Sbjct: 370 IRQAI 374


>gi|318066967|emb|CBY89098.1| RNA polymerase sigma70 factor [Halomonas pantelleriensis]
          Length = 363

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 298 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 357

Query: 109 IKAAM 113
           I+ A+
Sbjct: 358 IRQAI 362


>gi|318066963|emb|CBY89096.1| RNA polymerase sigma70 factor [Halomonas neptunia]
          Length = 368

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 303 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 362

Query: 109 IKAAM 113
           I+ A+
Sbjct: 363 IRQAI 367


>gi|318066935|emb|CBY89082.1| RNA polymerase sigma70 factor [Halomonas cupida]
          Length = 365

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 300 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 359

Query: 109 IKAAM 113
           I+ A+
Sbjct: 360 IRQAI 364


>gi|318066939|emb|CBY89084.1| RNA polymerase sigma70 factor [Halomonas elongata]
          Length = 367

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 302 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 361

Query: 109 IKAAM 113
           I+ A+
Sbjct: 362 IRQAI 366


>gi|318066971|emb|CBY89100.1| RNA polymerase sigma70 factor [Halomonas sulfidaeris]
          Length = 368

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 303 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 362

Query: 109 IKAAM 113
           I+ A+
Sbjct: 363 IRQAI 367


>gi|229051333|ref|ZP_04194847.1| RNA polymerase sigma-43 factor [Bacillus cereus AH676]
 gi|229125362|ref|ZP_04254451.1| RNA polymerase sigma-43 factor [Bacillus cereus 95/8201]
 gi|228658091|gb|EEL13842.1| RNA polymerase sigma-43 factor [Bacillus cereus 95/8201]
 gi|228722026|gb|EEL73457.1| RNA polymerase sigma-43 factor [Bacillus cereus AH676]
          Length = 325

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 72/276 (26%), Positives = 127/276 (46%), Gaps = 37/276 (13%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY--GLPISEVVSEGNIG 85
           +L K+E   L KRY+ HG+      L   +  LV+ IA  Y+     +   ++V EGN G
Sbjct: 50  VLSKEESLHLFKRYK-HGEKDLRDYLFHVNEGLVLSIARNYKNKHPDIEFDDLVQEGNEG 108

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS-LVKIGTTANQKRLFFNLRRLKG 144
           +++A++ F+P+ G+  +TY+ WWI+ +M   I +  S   KI T  NQ    FNL+ ++ 
Sbjct: 109 MLRAMEDFNPDLGYCFSTYAFWWIQKSMLGIIRKKKSGPFKIPTHVNQ----FNLKYVEL 164

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS------------ 192
             + +   N  P  V  + K+LNV+   VI          ++   I++            
Sbjct: 165 EDKYLQRYNRTP-SVEEVVKELNVTRETVIRHKVYYKRATTMTLDIDTINEDVGISTPFF 223

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE-ARRLQEN 251
            DK++    + ++ +    E  LI  E              VLNP+++ +      L + 
Sbjct: 224 DDKSAIPSTNEMIIEDLNYEIWLIFDE--------------VLNPKQKMVLNLCFGLLDG 269

Query: 252 PVTL-ENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            V L + ++    ++ ERV QI+  A KK+++   K
Sbjct: 270 KVYLHKEIAKALMITTERVSQIKDEAIKKLKKCQHK 305


>gi|318066979|emb|CBY89104.1| RNA polymerase sigma70 factor [Halomonas venusta]
          Length = 370

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 305 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 364

Query: 109 IKAAM 113
           I+ A+
Sbjct: 365 IRQAI 369


>gi|318066941|emb|CBY89085.1| RNA polymerase sigma70 factor [Halomonas eurihalina]
          Length = 367

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 302 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 361

Query: 109 IKAAM 113
           I+ A+
Sbjct: 362 IRQAI 366


>gi|239942801|ref|ZP_04694738.1| RNA polymerase sigma factor, sigma F [Streptomyces roseosporus NRRL
           15998]
 gi|239989260|ref|ZP_04709924.1| RNA polymerase sigma factor, sigma F [Streptomyces roseosporus NRRL
           11379]
 gi|291446270|ref|ZP_06585660.1| sigma F [Streptomyces roseosporus NRRL 15998]
 gi|291349217|gb|EFE76121.1| sigma F [Streptomyces roseosporus NRRL 15998]
          Length = 285

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 67/244 (27%), Positives = 119/244 (48%), Gaps = 23/244 (9%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           EH  + AA  L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDPERG +  
Sbjct: 57  EHRRVRAA--LIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQFP 114

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           T++M  +   ++ Y   +   V +      +RL     ++ G  + +T  + +      I
Sbjct: 115 TFAMPTVVGEIKRYFRDNVRTVHV-----PRRLHELWVQVTGATEDLTTAHGRSPTTAEI 169

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL--VYDHDGQEQVLIEKEE 220
           A++L +SE EV++  C  AG        +++   ++Q  D L  + D  G E   +   E
Sbjct: 170 AERLKISEDEVLA--CIEAGRS-----YHATSLEAAQEGDGLPGLLDRLGYEDPALAGVE 222

Query: 221 RKNRRNMLTRSMSVLNP-RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
            ++    L R + V  P RE+RI   R      +T   +S+E  VS+  V ++ AR+F +
Sbjct: 223 HRD----LVRHLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLLARSFAR 276

Query: 280 VQES 283
           ++ +
Sbjct: 277 LRSA 280


>gi|9621765|gb|AAF89531.1|AF160964_1 RNA polymerase sigma factor [Peanut witches'-broom phytoplasma]
          Length = 458

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 70/263 (26%), Positives = 123/263 (46%), Gaps = 40/263 (15%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           YV   +Y  H  +        S+LR+VV IA      G    +++ EGN+GLM+ V KFD
Sbjct: 206 YVFNNQYSSHYGIKQL-----SNLRIVVSIAKKQSERGQYFLDLIHEGNMGLMKTVDKFD 260

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN- 153
             +GF+ +TY+ WWI+ A+   +            A+Q R      R   H+  I + N 
Sbjct: 261 YTKGFKFSTYATWWIRQAITRAV------------ADQSRTI----RCPVHVSDILNKNF 304

Query: 154 -LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             K +    +A+K   +E+  I+   +    E+   +I    K +  +++   +      
Sbjct: 305 AFKSKLTQDLARKARKAENHEIA---KAMNIETKKLMIYKWLKRNDFFRNIYSWWRWFFF 361

Query: 213 QVLIEKEER---------KNRRNMLTRSM-SVLNPRERRIFEARR--LQ-ENPV-TLENL 258
           +   ++  R         +N +  L  S+   L PRE+ + + R   L+ +N V TLE +
Sbjct: 362 RWFYKRSLRYFASWLYVTRNFKKTLEESLEEALTPREQLVLKMRYGILEGDNRVHTLEEV 421

Query: 259 SSEFEVSRERVRQIEARAFKKVQ 281
            ++  V+RER+RQIE +A +K++
Sbjct: 422 GAKLGVTRERIRQIETKALRKLR 444


>gi|318066965|emb|CBY89097.1| RNA polymerase sigma70 factor [Halomonas pacifica]
          Length = 362

 Score = 70.1 bits (170), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 297 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 356

Query: 109 IKAAM 113
           I+ A+
Sbjct: 357 IRQAI 361


>gi|67921071|ref|ZP_00514590.1| Sigma-70 region 2:Sigma-70 region 1.2 [Crocosphaera watsonii WH
           8501]
 gi|67857188|gb|EAM52428.1| Sigma-70 region 2:Sigma-70 region 1.2 [Crocosphaera watsonii WH
           8501]
          Length = 250

 Score = 69.7 bits (169), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 27/67 (40%), Positives = 47/67 (70%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           + A   ++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV+KFDP +G+R +TY+ 
Sbjct: 177 IKAKDEIIKANLRLVVSVAKKYQHRGLELLDLIQEGTLGLEKAVEKFDPVKGYRFSTYAY 236

Query: 107 WWIKAAM 113
           WWI+  +
Sbjct: 237 WWIRQGI 243


>gi|321309570|ref|YP_004191899.1| RNA polymerase sigma factor rpoD [Mycoplasma haemofelis str.
           Langford 1]
 gi|319801414|emb|CBY92060.1| RNA polymerase sigma factor rpoD [Mycoplasma haemofelis str.
           Langford 1]
          Length = 524

 Score = 69.7 bits (169), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 38/101 (37%), Positives = 62/101 (61%), Gaps = 3/101 (2%)

Query: 28  MLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           ML  +EE  LAK   ++ DL   A  +L+TS+LRLV+ IA  Y   G  + ++V EG  G
Sbjct: 213 MLTAEEERKLAK-LMDNPDLRPFAVKQLMTSNLRLVISIAKKYLNRGFSLGDLVQEGVFG 271

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           LM++++KFD + G + +TY+ WWI+ ++   I     +++I
Sbjct: 272 LMKSIQKFDYKFGNKFSTYATWWIRQSITRAIADQARIIRI 312


>gi|318066947|emb|CBY89088.1| RNA polymerase sigma70 factor [Halomonas halodenitrificans]
          Length = 360

 Score = 69.7 bits (169), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 295 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 354

Query: 109 IKAAM 113
           I+ A+
Sbjct: 355 IRQAI 359


>gi|318066983|emb|CBY89106.1| RNA polymerase sigma70 factor [Kushneria aurantia]
          Length = 370

 Score = 69.7 bits (169), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 305 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 364

Query: 109 IKAAM 113
           I+ A+
Sbjct: 365 IRQAI 369


>gi|318066925|emb|CBY89077.1| RNA polymerase sigma70 factor [Halomonas aquamarina]
 gi|318066927|emb|CBY89078.1| RNA polymerase sigma70 factor [Halomonas axialensis]
 gi|318066959|emb|CBY89094.1| RNA polymerase sigma70 factor [Halomonas meridiana]
          Length = 370

 Score = 69.7 bits (169), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 305 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 364

Query: 109 IKAAM 113
           I+ A+
Sbjct: 365 IRQAI 369


>gi|320009625|gb|ADW04475.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 285

 Score = 69.7 bits (169), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 64/234 (27%), Positives = 115/234 (49%), Gaps = 21/234 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDPERG +  T++M  +   
Sbjct: 65  LIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQFPTFAMPTVVGE 124

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           ++ Y   +   V +      +RL     ++ G  + +T  + +      IA++L +SE E
Sbjct: 125 IKRYFRDNVRTVHV-----PRRLHELWVQVTGATEDLTTAHGRSPTTGEIAERLKISEDE 179

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWL--VYDHDGQEQVLIEKEERKNRRNMLTR 230
           V++  C  AG        +++   ++Q  D L  + D  G E   +   E ++    L R
Sbjct: 180 VLA--CIEAGRS-----YHATSLEAAQEGDGLPGLLDRLGYEDPALAGVEHRD----LVR 228

Query: 231 SMSVLNP-RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            + V  P RE+RI   R    N +T   +S+E  VS+  V ++ AR+F +++ +
Sbjct: 229 HLLVQLPEREQRILLLRYY--NNLTQSQISAELGVSQMHVSRLLARSFARLRSA 280


>gi|318066903|emb|CBY89066.1| RNA polymerase sigma70 factor [Chromohalobacter beijerinckii]
          Length = 367

 Score = 69.7 bits (169), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 302 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 361

Query: 109 IKAAM 113
           I+ A+
Sbjct: 362 IRQAI 366


>gi|119717204|ref|YP_924169.1| sigma-70 region 3 domain-containing protein [Nocardioides sp.
           JS614]
 gi|119537865|gb|ABL82482.1| sigma-70 region 3 domain protein [Nocardioides sp. JS614]
          Length = 319

 Score = 69.7 bits (169), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 60/235 (25%), Positives = 117/235 (49%), Gaps = 12/235 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A    +T++LRLVV IA  Y    +P+ +++ EGN GL++AV+KFD  +G++ +TY+ WW
Sbjct: 86  AVDTFITANLRLVVSIARKYGRAQMPMLDLIQEGNTGLIRAVEKFDYTKGYKFSTYATWW 145

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           ++ A+   I +   +V++        +   L ++ G  + +     +  +   IA++L +
Sbjct: 146 VRQAITRGIAQQARVVRLPV-----HVVEELNQVGGARRTLERKLGREPEPREIAEELGM 200

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
               V+ +        SL++ ++  D ++S           G +   I+ E R +R N L
Sbjct: 201 EVDRVLDLMAWGREHVSLDSPVD-EDGDTSLGDLMAQETAPGPDLNFIDVESR-DRLNSL 258

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L+ R   I  +R   +      L ++ ++  +S ERVRQ+E  A +K++
Sbjct: 259 ---VGKLDDRAADIIRSRYGLVDGRQHKLADIGAKHGISAERVRQLEREALQKLR 310


>gi|318066915|emb|CBY89072.1| RNA polymerase sigma70 factor [Chromohalobacter sarecensis]
          Length = 369

 Score = 69.7 bits (169), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 304 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 363

Query: 109 IKAAM 113
           I+ A+
Sbjct: 364 IRQAI 368


>gi|318066919|emb|CBY89074.1| RNA polymerase sigma70 factor [Halomonas alimentaria]
          Length = 362

 Score = 69.7 bits (169), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 297 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 356

Query: 109 IKAAM 113
           I+ A+
Sbjct: 357 IRQAI 361


>gi|45128577|gb|AAS55057.1| RpoD [Vibrio parahaemolyticus]
          Length = 492

 Score = 69.7 bits (169), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 31/78 (39%), Positives = 48/78 (61%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   G    +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 374 AKKEMVEANLRLVISIAKKYTNRGXQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 433

Query: 109 IKAAMQEYILRSWSLVKI 126
           I+ A+   I      ++I
Sbjct: 434 IRQAITRSIADQARTIRI 451


>gi|297737220|emb|CBI26421.3| unnamed protein product [Vitis vinifera]
          Length = 555

 Score = 69.7 bits (169), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 65/251 (25%), Positives = 122/251 (48%), Gaps = 30/251 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  S++RLV+ IA  Y   G  ++++V  G IGL++ ++KFD  +GF+++TY  WW
Sbjct: 312 AREKLAMSNVRLVMSIAQRYDNMGAEMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 371

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN--------NLKPEQV- 159
           I+  +   ++ +   +++ +  +++       +++   + IT +        N+  ++V 
Sbjct: 372 IRQGVSRALVENSRTLRLPSHLHERLSLIRNAKIRLEEKGITPSIDRIAECLNMSQKKVR 431

Query: 160 ---VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
               AI+K  ++      S+N  L G E+L++ I      ++ W       H   E  L 
Sbjct: 432 NATEAISKVFSLDREAFPSLNG-LPG-ETLHSYIADVRLENNPW-------HGVDEWAL- 481

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPVTLENLSSEFEVSRERVRQIEAR 275
                K+  N L    + L  RER I      L    +T E++S    +SRERVRQ+   
Sbjct: 482 -----KDEVNKLIN--TTLGERERDIIRLYYGLDNECLTWEDISKRIGLSRERVRQVGLV 534

Query: 276 AFKKVQESIQK 286
           A +K++ + +K
Sbjct: 535 ALEKLKNAARK 545


>gi|170077819|ref|YP_001734457.1| sigma-70 factor [Synechococcus sp. PCC 7002]
 gi|169885488|gb|ACA99201.1| sigma-70 factor [Synechococcus sp. PCC 7002]
          Length = 328

 Score = 69.7 bits (169), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 60/240 (25%), Positives = 114/240 (47%), Gaps = 31/240 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +++ ++LRLVV IA  Y+   L   +++ EG++GL + V+KFDP +G++ +TY+ WW
Sbjct: 92  AKRKMIEANLRLVVAIAKKYQKRNLEFLDLIQEGSLGLERGVEKFDPTKGYKFSTYAYWW 151

Query: 109 IKAAMQEYILRSWSLVKI---------GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I +    +++              Q++L  +L R     +      L+P Q 
Sbjct: 152 IRQAITRAIAQQGRTIRLPIHITEKLNKIKKTQRQLAQDLGRAATIAEIAEALELEPAQ- 210

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I +   VS    IS++ R+ GD     L++  + +     + + Y+   Q+       
Sbjct: 211 --IREYFRVSRHP-ISLDVRV-GDNQDTELMDLLEDSGESPDNNVTYELLKQD------- 259

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENP-VTLENLSSEFEVSRERVRQIEARAF 277
                   L   ++ L P+++ +   R  L +   ++L  +     +SRERVRQ+E +A 
Sbjct: 260 --------LRDLIADLTPQQQEVIILRFGLNDGKELSLAKIGKRMNLSRERVRQLERQAL 311


>gi|318066905|emb|CBY89067.1| RNA polymerase sigma70 factor [Chromohalobacter canadensis]
          Length = 367

 Score = 69.7 bits (169), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 302 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 361

Query: 109 IKAAM 113
           I+ A+
Sbjct: 362 IRQAI 366


>gi|318066909|emb|CBY89069.1| RNA polymerase sigma70 factor [Chromohalobacter marismortui]
          Length = 367

 Score = 69.7 bits (169), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 302 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 361

Query: 109 IKAAM 113
           I+ A+
Sbjct: 362 IRQAI 366


>gi|318066933|emb|CBY89081.1| RNA polymerase sigma70 factor [Halomonas campisalis]
          Length = 367

 Score = 69.7 bits (169), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 302 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 361

Query: 109 IKAAM 113
           I+ A+
Sbjct: 362 IRQAI 366


>gi|294856621|gb|ADF45248.1| RNA polymerase sigma S factor [Escherichia sp. B827]
 gi|294856623|gb|ADF45249.1| RNA polymerase sigma S factor [Escherichia sp. E1492]
 gi|294856625|gb|ADF45250.1| RNA polymerase sigma S factor [Escherichia sp. E807]
 gi|294856627|gb|ADF45251.1| RNA polymerase sigma S factor [Escherichia sp. H442]
 gi|294856629|gb|ADF45252.1| RNA polymerase sigma S factor [Escherichia sp. M863]
 gi|294856631|gb|ADF45253.1| RNA polymerase sigma S factor [Escherichia sp. TW10509]
 gi|294856633|gb|ADF45254.1| RNA polymerase sigma S factor [Escherichia sp. TW11930]
 gi|294856635|gb|ADF45255.1| RNA polymerase sigma S factor [Escherichia sp. TW11966]
 gi|294856639|gb|ADF45257.1| RNA polymerase sigma S factor [Escherichia sp. TW09231]
 gi|294856641|gb|ADF45258.1| RNA polymerase sigma S factor [Escherichia sp. TW09276]
 gi|294856643|gb|ADF45259.1| RNA polymerase sigma S factor [Escherichia sp. TW09254]
 gi|294856645|gb|ADF45260.1| RNA polymerase sigma S factor [Escherichia sp. TW09266]
 gi|294856647|gb|ADF45261.1| RNA polymerase sigma S factor [Escherichia sp. TA04]
 gi|294856649|gb|ADF45262.1| RNA polymerase sigma S factor [Escherichia sp. B685]
 gi|294856651|gb|ADF45263.1| RNA polymerase sigma S factor [Escherichia sp. TW14182]
 gi|294856653|gb|ADF45264.1| RNA polymerase sigma S factor [Escherichia albertii TW11588]
 gi|294856655|gb|ADF45265.1| RNA polymerase sigma S factor [Escherichia sp. H605]
 gi|294856657|gb|ADF45266.1| RNA polymerase sigma S factor [Escherichia sp. B49]
 gi|294856659|gb|ADF45267.1| RNA polymerase sigma S factor [Escherichia sp. TW09308]
 gi|294856661|gb|ADF45268.1| RNA polymerase sigma S factor [Escherichia sp. B1225]
 gi|294856663|gb|ADF45269.1| RNA polymerase sigma S factor [Escherichia sp. B646]
 gi|294856665|gb|ADF45270.1| RNA polymerase sigma S factor [Escherichia sp. E1118]
 gi|294856667|gb|ADF45271.1| RNA polymerase sigma S factor [Escherichia sp. E1195]
 gi|294856669|gb|ADF45272.1| RNA polymerase sigma S factor [Escherichia sp. E1196]
 gi|294856671|gb|ADF45273.1| RNA polymerase sigma S factor [Escherichia sp. E471]
 gi|294856673|gb|ADF45274.1| RNA polymerase sigma S factor [Escherichia sp. E472]
 gi|294856675|gb|ADF45275.1| RNA polymerase sigma S factor [Escherichia sp. E620]
 gi|294856677|gb|ADF45276.1| RNA polymerase sigma S factor [Escherichia sp. M1108]
 gi|294856679|gb|ADF45277.1| RNA polymerase sigma S factor [Escherichia sp. TA290]
 gi|294856681|gb|ADF45278.1| RNA polymerase sigma S factor [Escherichia sp. TW14263]
 gi|294856683|gb|ADF45279.1| RNA polymerase sigma S factor [Escherichia sp. TW14264]
 gi|294856685|gb|ADF45280.1| RNA polymerase sigma S factor [Escherichia sp. TW14265]
 gi|294856687|gb|ADF45281.1| RNA polymerase sigma S factor [Escherichia sp. TW14266]
 gi|294856689|gb|ADF45282.1| RNA polymerase sigma S factor [Escherichia sp. TW14267]
 gi|294856691|gb|ADF45283.1| RNA polymerase sigma S factor [Escherichia sp. RL325/96]
 gi|294856693|gb|ADF45284.1| RNA polymerase sigma S factor [Escherichia sp. Z205]
 gi|294856695|gb|ADF45285.1| RNA polymerase sigma S factor [Escherichia albertii]
 gi|294856697|gb|ADF45286.1| RNA polymerase sigma S factor [Escherichia albertii]
 gi|294856699|gb|ADF45287.1| RNA polymerase sigma S factor [Escherichia albertii]
 gi|294856701|gb|ADF45288.1| RNA polymerase sigma S factor [Escherichia albertii]
 gi|294856703|gb|ADF45289.1| RNA polymerase sigma S factor [Escherichia albertii]
 gi|294856705|gb|ADF45290.1| RNA polymerase sigma S factor [Escherichia albertii]
 gi|294856707|gb|ADF45291.1| RNA polymerase sigma S factor [Escherichia albertii]
 gi|294856709|gb|ADF45292.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|294856711|gb|ADF45293.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|294856713|gb|ADF45294.1| RNA polymerase sigma S factor [Escherichia fergusonii]
 gi|294856715|gb|ADF45295.1| RNA polymerase sigma S factor [Escherichia fergusonii]
 gi|294856717|gb|ADF45296.1| RNA polymerase sigma S factor [Escherichia fergusonii]
          Length = 157

 Score = 69.7 bits (169), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 27/63 (42%), Positives = 44/63 (69%)

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     
Sbjct: 1   IARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRT 60

Query: 124 VKI 126
           +++
Sbjct: 61  IRL 63


>gi|318066911|emb|CBY89070.1| RNA polymerase sigma70 factor [Chromohalobacter nigrandesensis]
          Length = 367

 Score = 69.7 bits (169), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 302 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 361

Query: 109 IKAAM 113
           I+ A+
Sbjct: 362 IRQAI 366


>gi|318066907|emb|CBY89068.1| RNA polymerase sigma70 factor [Chromohalobacter israelensis]
 gi|318066913|emb|CBY89071.1| RNA polymerase sigma70 factor [Chromohalobacter salexigens]
          Length = 367

 Score = 69.7 bits (169), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 302 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 361

Query: 109 IKAAM 113
           I+ A+
Sbjct: 362 IRQAI 366


>gi|294856637|gb|ADF45256.1| RNA polymerase sigma S factor [Escherichia sp. B1147]
          Length = 157

 Score = 69.7 bits (169), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 27/63 (42%), Positives = 44/63 (69%)

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     
Sbjct: 1   IARRYGNRGLALLDLIKEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRT 60

Query: 124 VKI 126
           +++
Sbjct: 61  IRL 63


>gi|318066917|emb|CBY89073.1| RNA polymerase sigma70 factor [Cobetia marina]
 gi|318066949|emb|CBY89089.1| RNA polymerase sigma70 factor [Halomonas halodurans]
          Length = 364

 Score = 69.7 bits (169), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 45/65 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 299 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 358

Query: 109 IKAAM 113
           I+ A+
Sbjct: 359 IRQAI 363


>gi|318041016|ref|ZP_07972972.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CB0101]
          Length = 323

 Score = 69.7 bits (169), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 56/235 (23%), Positives = 113/235 (48%), Gaps = 23/235 (9%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A+ ++VT++LRLVV +A       L + +++ EG +GL++AV++FDP RG++ +TY+ WW
Sbjct: 88  ASEQMVTANLRLVVSLARRISHRRLDLDDLIQEGTLGLIRAVQRFDPSRGYKFSTYATWW 147

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT--DNNLKPEQVVAIAKKL 166
           I+  M   + +    +++   A+ +     LRR +  L+ +   + NL+        K L
Sbjct: 148 IREGMGRALQQQSRTIRL--PAHMQDRLQRLRRCQMELRQMLGREPNLEELAEATELKPL 205

Query: 167 NVSES-----EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           ++ E+     E +S++     ++ L  L+++    +    D L   H   + V +  E  
Sbjct: 206 DIREALFRAQEPLSLDSGHGPEDDLR-LLDTLRCGAQLPSDQLTAAHLQTDLVALLDELP 264

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           +    +L     +  P              P+ L  ++ +  +SR++ R +E RA
Sbjct: 265 EKEAELLRLRYGIDQP-------------APMNLSAVARQMGLSRDQARGMERRA 306


>gi|26665382|dbj|BAC44902.1| principal sigma factor [Anabaena planctonica TAC421]
          Length = 203

 Score = 69.3 bits (168), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 29/64 (45%), Positives = 45/64 (70%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+
Sbjct: 1   VQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 114 QEYI 117
              I
Sbjct: 61  TRAI 64


>gi|291522675|emb|CBK80968.1| RNA polymerase, sigma subunit, RpsG/SigG [Coprococcus catus GD/7]
          Length = 259

 Score = 69.3 bits (168), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 65/264 (24%), Positives = 128/264 (48%), Gaps = 31/264 (11%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L++ E+ +L KR + H DL A  R +  +LRLV+ +   + G    ++++   G I
Sbjct: 15  KLPLLKEDEKEMLMKRIKSH-DLRARERFINGNLRLVLSVIQRFSGTNENVNDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD  +G R +TY++  I   ++ + LR  S +++  +          + +  
Sbjct: 74  GLIKAIDNFDLTQGVRFSTYAVPMIVGEIRRF-LRDNSAIRVSRSLRDTA----YKAIYA 128

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
               IT NN +P  V+ IA++  + + +++          +L+A+       S       
Sbjct: 129 REALITRNNREP-TVMEIAEETGIPKEDIVF---------ALDAI------QSPMSLYEP 172

Query: 205 VYDHDGQEQVLIEK-EERKNRRN------MLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           VY   G    ++++  +RKN  N       L  +M  L+ RE RI +  R  E    +E 
Sbjct: 173 VYTDGGDALCIMDQVSDRKNGENSWVENLALNDAMKRLSHRENRIIKM-RFYEGKTQME- 230

Query: 258 LSSEFEVSRERVRQIEARAFKKVQ 281
           ++ E  +S+ ++ +IE  A + ++
Sbjct: 231 VADELAISQAQISRIEKSALQNMR 254


>gi|167949416|ref|ZP_02536490.1| RNA polymerase sigma factor RpoD [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 134

 Score = 69.3 bits (168), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 31/69 (44%), Positives = 46/69 (66%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 11  AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 70

Query: 109 IKAAMQEYI 117
           I+ A+   I
Sbjct: 71  IRQAITRSI 79


>gi|284050754|ref|ZP_06380964.1| RNA polymerase sigma factor [Arthrospira platensis str. Paraca]
          Length = 159

 Score = 69.3 bits (168), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 35/131 (26%), Positives = 64/131 (48%), Gaps = 39/131 (29%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDL------------------------------- 47
           Y+HEI ++P+L ++EE +  K+ ++  +L                               
Sbjct: 28  YLHEIGRVPLLTREEEIIYGKKVQQMMNLLEVRDELTKELDRDPTPEEWSAKAGLSESEM 87

Query: 48  --------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                    A  +++ ++LRLVV IA  Y+   +   +++ EG +GL + V+KFDP RG+
Sbjct: 88  TDIINRGRRAKQKMIEANLRLVVSIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPMRGY 147

Query: 100 RLATYSMWWIK 110
           + +TY+ WWI+
Sbjct: 148 KFSTYAYWWIR 158


>gi|121534953|ref|ZP_01666772.1| sigma-70 region 2 domain protein [Thermosinus carboxydivorans Nor1]
 gi|121306552|gb|EAX47475.1| sigma-70 region 2 domain protein [Thermosinus carboxydivorans Nor1]
          Length = 215

 Score = 69.3 bits (168), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 36/104 (34%), Positives = 61/104 (58%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
            ++Y+ E++KI +LE  EE  L + ++  G L    RL+  +  LV K AM +R +   +
Sbjct: 3   FAQYLDELKKIRLLEPAEEAALWRGFKVDGCLDCRRRLIEHYQPLVFKEAMRWRAHEGVV 62

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
            +++ EG +GL++AV+ FDPERG   + Y+   I+  M  Y+ R
Sbjct: 63  MDLIQEGTVGLIEAVENFDPERGVAFSLYAPHRIRGRMLTYLER 106


>gi|32453269|gb|AAP82767.1| sigma 70 [Hydrogenothermus marinus]
          Length = 369

 Score = 69.3 bits (168), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 29/62 (46%), Positives = 43/62 (69%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 307 AAKREMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 366

Query: 108 WI 109
           WI
Sbjct: 367 WI 368


>gi|329936108|ref|ZP_08285907.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
 gi|329304426|gb|EGG48305.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
          Length = 310

 Score = 69.3 bits (168), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 65/235 (27%), Positives = 110/235 (46%), Gaps = 19/235 (8%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RLV  HL LV  +A  YR  G P+ ++     IGL+++V +FDP+RG   +TY+   +  
Sbjct: 89  RLVRMHLPLVEHLARRYRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATPTVVG 148

Query: 112 AMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            ++ +   + W+ V++     + RL      L      ++  + +   V  +A+KL +SE
Sbjct: 149 EIKRHFRDKGWA-VRVPRRLQELRLA-----LTTATAELSQQHGRSPTVHELAEKLAISE 202

Query: 171 SEVISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
            EV      L G ES NA    S D   +      V D  G ++  +E  E +    +L 
Sbjct: 203 EEV------LEGLESANAYSTLSLDVPDTDDDAPAVADRLGADEAALESVEYRASLRLL- 255

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   K++E +
Sbjct: 256 --LEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAKLRERL 306


>gi|168986243|dbj|BAG11803.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H7]
 gi|168986245|dbj|BAG11804.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H7]
 gi|168986247|dbj|BAG11805.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H7]
 gi|168986249|dbj|BAG11806.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H7]
 gi|168986251|dbj|BAG11807.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H7]
 gi|168986253|dbj|BAG11808.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H7]
 gi|168986255|dbj|BAG11809.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H7]
 gi|168986259|dbj|BAG11811.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H6]
 gi|168986261|dbj|BAG11812.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H6]
 gi|258642983|gb|ACV86055.1| RNA polymerase sigma factor [Shigella flexneri]
          Length = 177

 Score = 69.3 bits (168), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 27/55 (49%), Positives = 41/55 (74%)

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           IA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+
Sbjct: 1   IARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIM 55


>gi|148656381|ref|YP_001276586.1| RNA polymerase, sigma 32 subunit, RpoH [Roseiflexus sp. RS-1]
 gi|148568491|gb|ABQ90636.1| RNA polymerase, sigma 32 subunit, RpoH [Roseiflexus sp. RS-1]
          Length = 398

 Score = 69.3 bits (168), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 117/234 (50%), Gaps = 18/234 (7%)

Query: 53  LVTSHLRLVVKIAMGYRGYG--LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           L+  +LRLV KIA  Y  Y   L   +++ EG IGL++A+++FD     RL+TY+++WI+
Sbjct: 162 LMRCNLRLVAKIATRYMPYARHLTFDDLLQEGRIGLLKAIERFDQNCRGRLSTYAVYWIR 221

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            ++Q  +     +V++        +   L RL+   +     + +      +A  L VS 
Sbjct: 222 QSIQRALADQDRMVRLPV-----HIVEQLHRLRKTCEQFRCIHGREPGDAELANALGVSL 276

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNML 228
           ++V S+  R+A   +       +D N+  +   L+ D   +G + +     E++    +L
Sbjct: 277 AKVRSL-WRVAQHHTSIDRPVGADTNT--FLGELIADDREEGPDFIC----EQQLLHAVL 329

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
              +  L+ RER I E R   +     TLE +   F ++RER+RQIE +A K++
Sbjct: 330 REVLGHLSSRERDILERRYGLIDGQTHTLEEIGQIFGLTRERIRQIERKALKRL 383


>gi|296506459|ref|YP_003667693.1| RNA polymerase sigma-43 factor [Bacillus thuringiensis BMB171]
 gi|296327046|gb|ADH09973.1| RNA polymerase sigma-43 factor [Bacillus thuringiensis BMB171]
          Length = 323

 Score = 69.3 bits (168), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 72/267 (26%), Positives = 128/267 (47%), Gaps = 19/267 (7%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY--GLPISEVVSEGNIG 85
           +L K+E   L KRY+ HG+      L   +  LV+ IA  Y+     +   ++V EGN G
Sbjct: 48  VLSKEESLHLFKRYK-HGEKDLRDYLFHVNEGLVLSIARNYKNKHPDIEFDDLVQEGNEG 106

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS-LVKIGTTANQKRLFFNLRRLKG 144
           +++A++ F+P+ G+  +TY+ WWI+ +M   I +  S   KI T  NQ    FNL+ ++ 
Sbjct: 107 MLRAMEDFNPDLGYCFSTYAFWWIQKSMLGIIRKKKSGPFKIPTHVNQ----FNLKYVEL 162

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN---SSQWQ 201
             + +   N  P  V  + K+LNV+   VI          ++   I++ +++   S+ + 
Sbjct: 163 EDKYLQRYNRTP-SVEEVVKELNVTRETVIRHKVYYKRATTMTLDIDTINEDVGISTPFF 221

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE-ARRLQENPVTL-ENLS 259
           D         E ++    E  N    L     VLNP+++ +      L +  V L + ++
Sbjct: 222 DDRSAIPSTNEMII----EDLNYEIWLIFD-EVLNPKQKMVLNLCFGLLDGKVYLHKEIA 276

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQK 286
               ++ ERV QI+  A KK+++   K
Sbjct: 277 KALMITTERVSQIKDEAIKKLKKCQHK 303


>gi|126215762|gb|ABN81001.1| putative RNA polymerase sigma-B factor [Rhodococcus opacus]
          Length = 194

 Score = 69.3 bits (168), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 59/213 (27%), Positives = 104/213 (48%), Gaps = 32/213 (15%)

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A+   +      +++     +
Sbjct: 1   MPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVE 60

Query: 133 KRLFFNLRRLKGHLQ-----AITDNNLKPEQVVA---IAKKLNVSESEVISMNCRLAGDE 184
           +     L R+K  L        TD+ L  E  +    IA  L+ S   V S++  +  DE
Sbjct: 61  Q--VNKLARIKRELHQQLGREATDDELAEESGIPAHKIADLLDHSRDPV-SLDMPVGNDE 117

Query: 185 --SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
              L   I  S+  S+             E  +I      + R++L    + L+ RE+++
Sbjct: 118 EAPLGDFIEDSEATSA-------------ENAVIAGLLHSDVRSVL----ATLDEREQQV 160

Query: 243 FEARRLQEN--PVTLENLSSEFEVSRERVRQIE 273
              R   ++  P TL+ +   F +SRERVRQIE
Sbjct: 161 IRLRYGLDDGQPRTLDQIGKLFGLSRERVRQIE 193


>gi|20151056|pdb|1KU2|A Chain A, Crystal Structure Of Thermus Aquaticus Rna Polymerase
           Sigma Subunit Fragment Containing Regions 1.2 To 3.1
 gi|20151057|pdb|1KU2|B Chain B, Crystal Structure Of Thermus Aquaticus Rna Polymerase
           Sigma Subunit Fragment Containing Regions 1.2 To 3.1
          Length = 241

 Score = 69.3 bits (168), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 32/79 (40%), Positives = 51/79 (64%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   L+ ++LRLVV IA  Y G GL   +++ EGN GL++AV+KF+ +R F+ +TY+ W
Sbjct: 106 AARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYATW 165

Query: 108 WIKAAMQEYILRSWSLVKI 126
           WI+ A+   I      ++I
Sbjct: 166 WIRQAINRAIADQARTIRI 184


>gi|328955594|ref|YP_004372927.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Coriobacterium
           glomerans PW2]
 gi|328455918|gb|AEB07112.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Coriobacterium
           glomerans PW2]
          Length = 262

 Score = 68.9 bits (167), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 66/269 (24%), Positives = 130/269 (48%), Gaps = 27/269 (10%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           +K++ + L +RY+E GD  A  +LV SH+ LV  +A  ++  G P+ +++  G +GL++A
Sbjct: 13  DKEKTHELFRRYKEDGDDDAREKLVMSHMNLVRFLANKFKNRGEPLDDLMQVGYLGLLKA 72

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           + +F+P RG    TY+   I   ++ +   + WS+          R+   L+ L   +  
Sbjct: 73  IDRFEPARGLEFTTYATPTILGEIKRHFRDKGWSV----------RVPRRLQELSAKVNQ 122

Query: 149 ITD---NNL-KPEQVVAIAKKLNVSESEVI-SMNCRLA-GDESLNALINSSDKNSSQWQD 202
            TD     L +  +V  IA+ L+ +  EV+ +M    A     L    +S + ++    D
Sbjct: 123 ATDLLTTELQRSPKVEEIAEYLDATVDEVLEAMESSSAYSSVPLEGTGSSENDDAPSIID 182

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
               D    + VL   ++R     ++  ++   +PRER +   R L+   +T   ++ + 
Sbjct: 183 RYAID----DNVLSFTDDRL----IIEDALESFSPREREVVNLRFLK--GMTQIEIAEQL 232

Query: 263 EVSRERVRQIEARAFKKVQESIQKQVELS 291
            +S+ +V ++  R  KK+Q+ I  +  +S
Sbjct: 233 GISQVQVSRLLRRTLKKIQDRIDPEGVMS 261


>gi|290956130|ref|YP_003487312.1| sigma factor [Streptomyces scabiei 87.22]
 gi|260645656|emb|CBG68747.1| putative sigma factor [Streptomyces scabiei 87.22]
          Length = 1033

 Score = 68.9 bits (167), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 64/249 (25%), Positives = 117/249 (46%), Gaps = 22/249 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  + RLV  +       GL   ++V  G +GLM+A +KFDP +G++ +TY+ WW++ +
Sbjct: 254 LVLHNQRLVHSLIRSCLDQGLEYEDLVQHGVLGLMRAARKFDPAKGYKFSTYATWWVRQS 313

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   I    +L+++    +++     +R++    +A+     +P   V +A + +++   
Sbjct: 314 VSRAIADEGALIRVPVHMHEQ-----MRKVAAAERALAAQG-RPAGNVDVAVQCDMTLDR 367

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           V  +       +SL+ +I              + D  G+ Q L   E       ++   M
Sbjct: 368 VEEIRKLTRRTDSLDRIIGDGAT---------LGDFVGKRQALPSVENDVLHVLLMEDVM 418

Query: 233 SVL---NPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            V+   + R  RI   RRL    E P TL+ L  EF V+RER+RQ+E +A  + +  ++ 
Sbjct: 419 GVVGTFSERSARIL-VRRLGLDGEEPSTLDELGREFGVTRERIRQLEGKARSEFRCRLRA 477

Query: 287 QVELSSSPP 295
              LS   P
Sbjct: 478 AGLLSGHGP 486


>gi|55274905|gb|AAV49254.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 182

 Score = 68.9 bits (167), Expect = 8e-10,   Method: Compositional matrix adjust.
 Identities = 27/55 (49%), Positives = 41/55 (74%)

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           IA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+
Sbjct: 1   IARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIM 55


>gi|78062752|ref|YP_372660.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia sp. 383]
 gi|77970637|gb|ABB12016.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia sp. 383]
          Length = 511

 Score = 68.9 bits (167), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 59/230 (25%), Positives = 114/230 (49%), Gaps = 19/230 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   G+ + ++V +G++GLM+A++KF+  RGF+ +TY+ WW
Sbjct: 274 ATRAMLEANLRLVLSIARKYMNRGVDLPDLVQDGSLGLMRAIEKFEYRRGFKFSTYATWW 333

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   +      +++      +  +  ++R     +  T     P +   +A +  +
Sbjct: 334 IRQAITRAVADRARTIRVPVHVGDQ--YQRVQRHALRFRQRTGRRATPAE---LAAETGL 388

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV--LIEKEERKNRRN 226
            E ++ ++    A   SL+A +  +D    +    L+ D         L +   R+  R+
Sbjct: 389 DEDKLRAVLALPAEPVSLDAPLPDADTGLVE----LIEDQASASPFEQLADTRMRECVRS 444

Query: 227 MLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIE 273
           +L RS++   P E  +   RR       P T + ++ +  +SRERVRQIE
Sbjct: 445 LL-RSVT---PAEADVLR-RRFGLGGTEPDTYDAIAQDAGMSRERVRQIE 489


>gi|239982221|ref|ZP_04704745.1| RNA polymerase sigma factor, sigH [Streptomyces albus J1074]
          Length = 287

 Score = 68.9 bits (167), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 66/235 (28%), Positives = 109/235 (46%), Gaps = 19/235 (8%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDPERG   +TY+   +  
Sbjct: 66  RLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPERGVEFSTYATPTVVG 125

Query: 112 AMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            ++ +   + W+ V++     + RL      L      ++  + +   V  +A+KL +SE
Sbjct: 126 EIKRHFRDKGWA-VRVPRRLQELRL-----SLTSATAELSQRHGRSPTVHELAEKLGISE 179

Query: 171 SEVISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
            EV      L G ES NA    S D   +  +   V D  G E   +E  E    R  L 
Sbjct: 180 EEV------LEGLESANAYSTLSLDVPDTDDESPAVADTLGSEDEALEGVE---YRESLK 230

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 231 PLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLREKL 283


>gi|172063054|ref|YP_001810705.1| RpoD family RNA polymerase sigma factor [Burkholderia ambifaria
           MC40-6]
 gi|171995571|gb|ACB66489.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           ambifaria MC40-6]
          Length = 520

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 55/238 (23%), Positives = 112/238 (47%), Gaps = 15/238 (6%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ ++LRLV+ IA  Y   G+ + ++V +G +GLM+A++KF+  RGF+ +TY+ WWI+ A
Sbjct: 287 MLEANLRLVLSIARKYMNRGVDLPDLVQDGCLGLMRAIEKFEYRRGFKFSTYATWWIRQA 346

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +      +++      +  +  ++R     +  T     P +   +A +  + E +
Sbjct: 347 VARAVADRSRTIRVPVHVGDQ--YQRVQRHALRFRQRTGRRATPAE---LAAETGLPEGK 401

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           + ++    A   SL+  +  ++         L+ D         E+      R  +T  +
Sbjct: 402 LRAVLALPAEPLSLDTPLPDAETGLVD----LIEDQASASP--FERLADTRMRECVTSLL 455

Query: 233 SVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             + P E  +   RR       P T + ++ +  +SRERVRQIE RA   ++ + + +
Sbjct: 456 RSVTPAEADVLR-RRFGLGGAEPDTYDAIAQDAGMSRERVRQIEKRALATLRTAAEAE 512


>gi|289770379|ref|ZP_06529757.1| transcription initiation factor sigma F [Streptomyces lividans
           TK24]
 gi|289700578|gb|EFD68007.1| transcription initiation factor sigma F [Streptomyces lividans
           TK24]
          Length = 287

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 68/250 (27%), Positives = 121/250 (48%), Gaps = 23/250 (9%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           LA    EH  + AA  L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDPE
Sbjct: 53  LAPGTPEHDRVRAA--LIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPE 110

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RG +  T++M  +   ++ Y   +   V +      +RL     ++    + +T    + 
Sbjct: 111 RGVQFPTFAMPTVVGEIKRYFRDNVRTVHV-----PRRLHELWVQVNSATEDLTTAFGRS 165

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL--VYDHDGQEQV 214
                IA++L ++E EV+S  C  AG        +++   ++Q  D L  + D  G E  
Sbjct: 166 PTTAEIAERLRITEEEVLS--CIEAGRS-----YHATSLEAAQEGDGLPGLLDRLGYEDP 218

Query: 215 LIEKEERKNRRNMLTRSMSVLNP-RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
            ++  E ++    L R + V  P RE+RI   R      +T   +S+E  VS+  V ++ 
Sbjct: 219 ALDGVEHRD----LVRHLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLL 272

Query: 274 ARAFKKVQES 283
           AR+F++++ +
Sbjct: 273 ARSFQRLRSA 282


>gi|224146103|ref|XP_002325882.1| predicted protein [Populus trichocarpa]
 gi|222862757|gb|EEF00264.1| predicted protein [Populus trichocarpa]
          Length = 509

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 68/253 (26%), Positives = 122/253 (48%), Gaps = 32/253 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  S++RLV+ IA  Y   G  ++++V  G IGL++ ++KFD  +GF+++TY  WW
Sbjct: 266 AREKLAMSNVRLVMSIAQKYDNMGAEMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 325

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   ++ +   +++    +++       +++   + +T +      +  IA+ LN+
Sbjct: 326 IRQGVSRALVDNSRTLRLPNHLHERLGLIRNAKIRLEEKGVTPS------IDRIAESLNM 379

Query: 169 SE------SEVISMNCRLAGDE--SLNALINSSD-----KNSSQWQDWLVYDHDGQEQVL 215
           S+      +E IS    L  +   SLN L   +       N  +   W    H   E  L
Sbjct: 380 SQRKVRNATEAISKVFSLDREAFPSLNGLPGETHHSYIADNRPENNPW----HGVDEWAL 435

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPVTLENLSSEFEVSRERVRQIEA 274
             KEE     N L    S L  RE+ I      L +  +T E++S    +SRERVRQ+  
Sbjct: 436 --KEE----VNKLID--STLQEREKEIIRLYHGLDQECLTWEDISKRMGLSRERVRQVGL 487

Query: 275 RAFKKVQESIQKQ 287
            A +K++ + +K+
Sbjct: 488 VALEKLKHAARKR 500


>gi|21222438|ref|NP_628217.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
 gi|585925|sp|P37971|RPOF_STRCO RecName: Full=RNA polymerase sigma-F factor
 gi|153455|gb|AAA93052.1| sigma factor [Streptomyces coelicolor A3(2)]
 gi|13122128|emb|CAC32306.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
          Length = 287

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 68/250 (27%), Positives = 121/250 (48%), Gaps = 23/250 (9%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           LA    EH  + AA  L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDPE
Sbjct: 53  LAPGTPEHDRVRAA--LIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPE 110

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RG +  T++M  +   ++ Y   +   V +      +RL     ++    + +T    + 
Sbjct: 111 RGVQFPTFAMPTVVGEIKRYFRDNVRTVHV-----PRRLHELWVQVNSATEDLTTAFGRS 165

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL--VYDHDGQEQV 214
                IA++L ++E EV+S  C  AG        +++   ++Q  D L  + D  G E  
Sbjct: 166 PTTAEIAERLRITEEEVLS--CIEAGRS-----YHATSLEAAQEGDGLPGLLDRLGYEDP 218

Query: 215 LIEKEERKNRRNMLTRSMSVLNP-RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
            ++  E ++    L R + V  P RE+RI   R      +T   +S+E  VS+  V ++ 
Sbjct: 219 ALDGVEHRD----LVRHLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLL 272

Query: 274 ARAFKKVQES 283
           AR+F++++ +
Sbjct: 273 ARSFQRLRSA 282


>gi|256786488|ref|ZP_05524919.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
          Length = 291

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 68/250 (27%), Positives = 121/250 (48%), Gaps = 23/250 (9%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           LA    EH  + AA  L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDPE
Sbjct: 57  LAPGTPEHDRVRAA--LIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPE 114

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RG +  T++M  +   ++ Y   +   V +      +RL     ++    + +T    + 
Sbjct: 115 RGVQFPTFAMPTVVGEIKRYFRDNVRTVHV-----PRRLHELWVQVNSATEDLTTAFGRS 169

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL--VYDHDGQEQV 214
                IA++L ++E EV+S  C  AG        +++   ++Q  D L  + D  G E  
Sbjct: 170 PTTAEIAERLRITEEEVLS--CIEAGRS-----YHATSLEAAQEGDGLPGLLDRLGYEDP 222

Query: 215 LIEKEERKNRRNMLTRSMSVLNP-RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
            ++  E ++    L R + V  P RE+RI   R      +T   +S+E  VS+  V ++ 
Sbjct: 223 ALDGVEHRD----LVRHLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLL 276

Query: 274 ARAFKKVQES 283
           AR+F++++ +
Sbjct: 277 ARSFQRLRSA 286


>gi|318066985|emb|CBY89107.1| RNA polymerase sigma70 factor [Kushneria avicenniae]
          Length = 373

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 44/65 (67%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V + LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 308 AKKEMVEAILRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 367

Query: 109 IKAAM 113
           I+ A+
Sbjct: 368 IRQAI 372


>gi|23978293|dbj|BAC21127.1| principal sigma factor [Arthrospira platensis]
          Length = 203

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 60/217 (27%), Positives = 109/217 (50%), Gaps = 19/217 (8%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V S+LRLVV IA  Y   GL   +++ EG++GL++A +K D E+G++ +TY+ WWI+ A+
Sbjct: 1   VQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKLDHEKGYKFSTYATWWIRQAI 60

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT-DNNLKP-EQVVAIAKKLNVSES 171
              I      +++        L+  + R+K   + ++ +   KP E+ +A   ++ + + 
Sbjct: 61  TRAIADQSRTIRLPVL-----LYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKL 115

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTR 230
             I+ + +L    SL   I   +   S+  D++  + DG+     E +  KN  R  L  
Sbjct: 116 RFIAKSAQLPI--SLETPIGKEE--DSRLGDFI--ESDGETP---EDQVSKNLLREDLES 166

Query: 231 SMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVS 265
            +  L+PRER +   R   ++    TLE +   F V+
Sbjct: 167 VLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVT 203


>gi|9368549|emb|CAB98133.1| unnamed protein product [Mycoplasma genitalium]
          Length = 100

 Score = 68.6 bits (166), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 31/69 (44%), Positives = 48/69 (69%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A ++LVTS+LRLVV IA  +   GL  ++++ EGN+GL++A+ KF+   G + +TY+ WW
Sbjct: 23  AINQLVTSNLRLVVSIAKKHLERGLDFNDLIQEGNLGLLKAISKFNWSLGNKFSTYATWW 82

Query: 109 IKAAMQEYI 117
           IK A+   I
Sbjct: 83  IKQAITRAI 91


>gi|119474993|ref|ZP_01615346.1| RNA polymerase sigma-70 factor family protein [marine gamma
           proteobacterium HTCC2143]
 gi|119451196|gb|EAW32429.1| RNA polymerase sigma-70 factor family protein [marine gamma
           proteobacterium HTCC2143]
          Length = 491

 Score = 68.2 bits (165), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 70/239 (29%), Positives = 112/239 (46%), Gaps = 27/239 (11%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           +V  +LRLV  IA  Y    LP+ E++ EG  GL++AV+KF P  G R +TY+  WI+A 
Sbjct: 253 MVNHNLRLVYHIAKRYNSGTLPMLELIQEGVFGLVRAVEKFQPASGNRFSTYAYLWIEAK 312

Query: 113 MQEYILRSWSLVKIGTTANQK----RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           ++    +  SLV++ ++  Q     R      R  G   +  +   K +   A  + L  
Sbjct: 313 VRLTHEKLNSLVRLPSSNFQDVIKLRRSMEQSRSTGERFSTRNVAAKLDMTQAHVELLLR 372

Query: 169 SESEVISMNCRLAG---DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           ++S+ +S++  + G   D SL+  +       S     LV + D Q QV           
Sbjct: 373 TKSQPLSLDQPVGGEDNDLSLSGTLQLEQPPVSS----LVLNSDMQRQV----------- 417

Query: 226 NMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              T  +S L  RE  I + R    +  P++ E++     +SRERVRQIE  A   ++E
Sbjct: 418 ---TELLSELTSREAYILQHRFGLGDMEPMSRESIGKNIGLSRERVRQIEKAALISLKE 473


>gi|148645064|gb|ABR01057.1| RpoD [uncultured Geobacter sp.]
          Length = 102

 Score = 68.2 bits (165), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 30/60 (50%), Positives = 42/60 (70%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ WWI+ A+   I
Sbjct: 1   LRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQAITRAI 60


>gi|171322339|ref|ZP_02911166.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           MEX-5]
 gi|171092333|gb|EDT37699.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           MEX-5]
          Length = 234

 Score = 68.2 bits (165), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 55/239 (23%), Positives = 113/239 (47%), Gaps = 29/239 (12%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ ++LRLV+ IA  Y   G+ + ++V +G +GLM+A++KF+  RGF+ +TY+ WWI+ A
Sbjct: 1   MLEANLRLVLSIARKYMNRGVDLPDLVQDGCLGLMRAIEKFEYRRGFKFSTYATWWIRQA 60

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA-------KK 165
           +   +      +++      +  +  ++R     +  T     P +++A         + 
Sbjct: 61  VARAVADRSRTIRVPVHVGDQ--YQRVQRHALRFRQRTGRRATPAELIAETGLPEGKLRA 118

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           +    +E +S++  L   E+   L++  +  +S       ++H    ++          R
Sbjct: 119 VLALPAEPLSLDTPLPDAET--GLVDLIEDQASASP----FEHLADTRM----------R 162

Query: 226 NMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             +T  +  + P E  +   RR       P T + ++ +  +SRERVRQIE RA   ++
Sbjct: 163 ECVTSLLRSVTPAEADVLR-RRFGLGGAEPDTYDAIAQDAGMSRERVRQIEKRALATLR 220


>gi|89094249|ref|ZP_01167191.1| RNA polymerase sigma factor [Oceanospirillum sp. MED92]
 gi|89081504|gb|EAR60734.1| RNA polymerase sigma factor [Oceanospirillum sp. MED92]
          Length = 411

 Score = 68.2 bits (165), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 61/245 (24%), Positives = 119/245 (48%), Gaps = 30/245 (12%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +L+  +LRLV  +A+ ++  G+ + +++ EGNIGL++A  +F+   G+R +TY+ W I+ 
Sbjct: 178 KLIEKNLRLVYVVALRFKSSGVSLDDLIQEGNIGLLKAADRFNFVHGYRFSTYAFWCIQN 237

Query: 112 AMQEYILRSWSLV--------KIGTTANQKRLFFN-LRRLKGHLQAITDNNLKPEQVVAI 162
            ++  + +++  +        K+     +   F N   R  G  + +++    PE   A+
Sbjct: 238 VLKTALQKNYHTISRPSYLQEKLSVIKRESVRFLNQYGRYPGTTE-LSELTSIPE---AM 293

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE-ER 221
            +K+    +E +S++  ++               S + +D  V        +  EKE + 
Sbjct: 294 LEKIKSFPAEPLSLSQPVS--------------RSQEGEDLTVESTLEDNAMAAEKETDI 339

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKK 279
             +R ML R    LN RE ++ + R   +     TLE +S +  VS ERVRQ++  A +K
Sbjct: 340 ALKRRMLERMSLRLNEREYKVLKMRFGIDCHTEHTLEEISHQLNVSVERVRQLQKIALEK 399

Query: 280 VQESI 284
           +Q + 
Sbjct: 400 LQTTF 404


>gi|86148201|ref|ZP_01066499.1| RNA polymerase sigma factor [Vibrio sp. MED222]
 gi|85834048|gb|EAQ52208.1| RNA polymerase sigma factor [Vibrio sp. MED222]
          Length = 83

 Score = 68.2 bits (165), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 33/68 (48%), Positives = 42/68 (61%)

Query: 16 LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
          L  YI      PML   EE  LA+R    G++ AA  L+ SHLR VV +A GY GYGLP+
Sbjct: 16 LDSYIRSANSYPMLTPDEERGLAERLHYKGEIDAAKGLILSHLRFVVHVARGYSGYGLPM 75

Query: 76 SEVVSEGN 83
          +++V EGN
Sbjct: 76 ADLVQEGN 83


>gi|257063114|ref|YP_003142786.1| RNA polymerase sigma factor, sigma-70 family [Slackia
           heliotrinireducens DSM 20476]
 gi|256790767|gb|ACV21437.1| RNA polymerase sigma factor, sigma-70 family [Slackia
           heliotrinireducens DSM 20476]
          Length = 269

 Score = 68.2 bits (165), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 42/140 (30%), Positives = 64/140 (45%), Gaps = 33/140 (23%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR-------------------------------EHGDL 47
           Y+ EI + P+L+ QEE  L  + R                                 GD 
Sbjct: 49  YLLEIDRFPLLDSQEEADLVAKIRAGAEAADQLRQASQDGVVLDDAEARRLARIQSDGD- 107

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  +LV + LRLV +IA  Y   G+   ++V EGN+GL++A ++FDP  G   + Y+ W
Sbjct: 108 AAKEQLVGASLRLVARIAKRYIFRGVSFMDLVHEGNMGLIRAAERFDPASGAAFSVYASW 167

Query: 108 WIKAAMQEYILRS-WSLVKI 126
           WI+AA+     R  W    +
Sbjct: 168 WIRAAISRATGRGRWGCFPL 187


>gi|206563110|ref|YP_002233873.1| RNA polymerase sigma factor [Burkholderia cenocepacia J2315]
 gi|198039150|emb|CAR55114.1| RNA polymerase sigma factor [Burkholderia cenocepacia J2315]
          Length = 508

 Score = 68.2 bits (165), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 59/230 (25%), Positives = 113/230 (49%), Gaps = 19/230 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   G+ +S++V +G +GLM+A++KF+  RGF+ +TY+ WW
Sbjct: 271 ATRAMLEANLRLVLSIARKYLNRGVDLSDLVQDGCLGLMRAIEKFEYRRGFKFSTYATWW 330

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   +      +++      +  +  ++R     +  T     P +   +A +  +
Sbjct: 331 IRQAIARAVADRSRTIRVPVHVGDQ--YQRVQRHALRFRQRTGRRATPAE---LAAETGL 385

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV--LIEKEERKNRRN 226
           +E ++ ++    A   SL+  +  +D    +    L+ D         L +   R   R+
Sbjct: 386 AEDKLRAVLALPAEPVSLDTPLPDADTGLVE----LIEDQASASPFEQLADTRMRDCVRS 441

Query: 227 MLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIE 273
           +L RS++   P E  +   RR       P T + ++ +  +SRERVRQIE
Sbjct: 442 LL-RSVT---PTEADVLR-RRFGLGGAEPDTYDAIAQDAGMSRERVRQIE 486


>gi|94499982|ref|ZP_01306517.1| RNA polymerase sigma-A factor [Oceanobacter sp. RED65]
 gi|94427840|gb|EAT12815.1| RNA polymerase sigma-A factor [Oceanobacter sp. RED65]
          Length = 368

 Score = 68.2 bits (165), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 35/116 (30%), Positives = 70/116 (60%), Gaps = 8/116 (6%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           ++IHE++    L KQ + VL +RY ++ +     +LV ++LRL + +A  Y G G+ + E
Sbjct: 115 QHIHELKG--RLYKQAQ-VLKRRYEDYRN-----QLVQANLRLAMHVARQYTGKGMELEE 166

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           ++ EG +GL++  ++++  +G+R  TY+ WWI+ A++  +     +V+I T    +
Sbjct: 167 LIQEGTLGLIKGAERYNINKGYRFTTYAYWWIQQAIKGALSEKRGIVRIPTNVTDR 222


>gi|302559792|ref|ZP_07312134.1| RNA polymerase sigma-F factor [Streptomyces griseoflavus Tu4000]
 gi|302477410|gb|EFL40503.1| RNA polymerase sigma-F factor [Streptomyces griseoflavus Tu4000]
          Length = 298

 Score = 68.2 bits (165), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 66/244 (27%), Positives = 119/244 (48%), Gaps = 23/244 (9%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           EH  + AA  L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDPERG +  
Sbjct: 70  EHARVRAA--LIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQFP 127

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           T++M  +   ++ Y   +   V +      +RL     ++    + +T    +      I
Sbjct: 128 TFAMPTVVGEIKRYFRDNVRTVHV-----PRRLHELWVQVNSATEDLTTAFGRSPSTAEI 182

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL--VYDHDGQEQVLIEKEE 220
           A++L +SE EV+S  C  AG        +++   ++Q  D +  + D  G E   ++  E
Sbjct: 183 AERLRISEDEVLS--CIEAGRS-----YHATSLEAAQEGDGMPGLLDRLGYEDPALDGVE 235

Query: 221 RKNRRNMLTRSMSVLNP-RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
            ++    L R + V  P RE+RI   R      +T   +S+E  VS+  V ++ AR+F++
Sbjct: 236 HRD----LVRHLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLLARSFQR 289

Query: 280 VQES 283
           ++ +
Sbjct: 290 LRSA 293


>gi|167630135|ref|YP_001680634.1| RNA polymerase sigma-e factor [Heliobacterium modesticaldum Ice1]
 gi|167592875|gb|ABZ84623.1| RNA polymerase sigma-e factor [Heliobacterium modesticaldum Ice1]
          Length = 235

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 38/94 (40%), Positives = 56/94 (59%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EEY L ++  E GDL+    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 33  PPLSNDEEYRLLEQL-EQGDLTVKSILIERNLRLVVYIARKFENTGVGIEDLVSIGTIGL 91

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  FDP +  +LATY+   I+  +  Y+ R+
Sbjct: 92  IKAVNTFDPLKKIKLATYASRCIENEILMYLRRN 125


>gi|107026582|ref|YP_624093.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia cenocepacia AU
           1054]
 gi|116692228|ref|YP_837761.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia cenocepacia
           HI2424]
 gi|105895956|gb|ABF79120.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia cenocepacia AU
           1054]
 gi|116650228|gb|ABK10868.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia cenocepacia
           HI2424]
          Length = 514

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 59/230 (25%), Positives = 113/230 (49%), Gaps = 19/230 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   G+ +S++V +G +GLM+A++KF+  RGF+ +TY+ WW
Sbjct: 277 ATRAMLEANLRLVLSIARKYLNRGVDLSDLVQDGCLGLMRAIEKFEYRRGFKFSTYATWW 336

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   +      +++      +  +  ++R     +  T     P +   +A +  +
Sbjct: 337 IRQAIARAVADRSRTIRVPVHVGDQ--YQRVQRHALRFRQRTGRRATPAE---LAAETGL 391

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV--LIEKEERKNRRN 226
           +E ++ ++    A   SL+  +  +D    +    L+ D         L +   R   R+
Sbjct: 392 AEDKLRAVLALPAEPVSLDTPLPDADTGLVE----LIEDQASASPFEQLADTRMRDCVRS 447

Query: 227 MLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIE 273
           +L RS++   P E  +   RR       P T + ++ +  +SRERVRQIE
Sbjct: 448 LL-RSVT---PTEADVLR-RRFGLGGAEPDTYDAIAQDAGMSRERVRQIE 492


>gi|149183912|ref|ZP_01862300.1| sporulation sigma factor SigE [Bacillus sp. SG-1]
 gi|148848376|gb|EDL62638.1| sporulation sigma factor SigE [Bacillus sp. SG-1]
          Length = 239

 Score = 68.2 bits (165), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 38/94 (40%), Positives = 59/94 (62%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL K+   +GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLSKEEEAVLLKKL-PNGDKTARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN 129


>gi|182437344|ref|YP_001825063.1| RNA polymerase sigma factor, sigma F [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|326777954|ref|ZP_08237219.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
 gi|178465860|dbj|BAG20380.1| RNA polymerase sigma factor, sigma F [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|326658287|gb|EGE43133.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
          Length = 292

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 62/234 (26%), Positives = 114/234 (48%), Gaps = 21/234 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDP+RG +  T++M  +   
Sbjct: 72  LIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFPTFAMPTVVGE 131

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           ++ Y   +   V +      +RL     ++ G  + +T  + +      IA++L +SE E
Sbjct: 132 IKRYFRDNVRTVHV-----PRRLHELWVQVTGATEDLTTAHGRSPTTAEIAERLKISEDE 186

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWL--VYDHDGQEQVLIEKEERKNRRNMLTR 230
           V++  C  AG        +++   ++Q  D L  + D  G E   +   E ++    L R
Sbjct: 187 VLA--CIEAGRS-----YHATSLEAAQEGDGLPGLLDRLGYEDPALAGVEHRD----LVR 235

Query: 231 SMSVLNP-RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            + V  P RE+RI   R      +T   +S+E  VS+  V ++ AR+F +++ +
Sbjct: 236 HLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLLARSFARLRSA 287


>gi|229113622|ref|ZP_04243069.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock1-15]
 gi|228669818|gb|EEL25214.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock1-15]
 gi|324323938|gb|ADY24981.1| RNA polymerase sigma-43 factor [Bacillus thuringiensis serovar
           finitimus YBT-020]
          Length = 323

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 69/292 (23%), Positives = 126/292 (43%), Gaps = 59/292 (20%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY--GLPISE 77
           I  I    +L K+E   L KRY+ HG+      L   +  LV+ +A  Y+     +   +
Sbjct: 40  IRGIGNYKVLSKEESLHLFKRYK-HGEKDLRDYLFHVNEGLVLSVARNYKNKHPDIEFDD 98

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS-LVKIGTTANQKRLF 136
           +V EGN G+++A++ F+P+ G+  +TY+ WWI+ +M   I +  S   KI T  NQ    
Sbjct: 99  LVQEGNEGMLRAMEDFNPDLGYCFSTYAFWWIQKSMLGIIRKKKSGPFKIPTHVNQ---- 154

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
           FNL+ ++   + +   N  P  V  + K+LNV+   VI          ++   I++ +++
Sbjct: 155 FNLKYVELEDKYLQRYNRTP-SVEEVVKELNVTRETVIRHKVYYKRATTMTLDIDTINED 213

Query: 197 SS-----------------------QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
                                     ++ WL++D                          
Sbjct: 214 VGISNPFFDDRSAIPSTNEMIIEDLNYEIWLIFD-------------------------E 248

Query: 234 VLNPRERRIFE-ARRLQENPVTL-ENLSSEFEVSRERVRQIEARAFKKVQES 283
           VLNP+++ +      L +  V L + ++    ++ ERV QI+  A KK+++ 
Sbjct: 249 VLNPKQKMVLNLCFGLLDGKVYLHKEIAKALMITTERVSQIKDEAIKKLKKC 300


>gi|23978335|dbj|BAC21137.1| principal sigma factor [Phormidium sp. IAM M-99]
          Length = 203

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 28/64 (43%), Positives = 44/64 (68%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V S+ RLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+
Sbjct: 1   VQSNFRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 114 QEYI 117
              I
Sbjct: 61  TRAI 64


>gi|221212711|ref|ZP_03585688.1| RNA polymerase sigma factor RpoD (Sigma-70) [Burkholderia
           multivorans CGD1]
 gi|221167810|gb|EEE00280.1| RNA polymerase sigma factor RpoD (Sigma-70) [Burkholderia
           multivorans CGD1]
          Length = 522

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 61/230 (26%), Positives = 111/230 (48%), Gaps = 19/230 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   G+ +S++V +G IGLM+A++KF+  RGF+ +TY+ WW
Sbjct: 285 ATRAMLEANLRLVLSIARKYLNRGVDLSDLVQDGCIGLMRAIEKFEYRRGFKFSTYATWW 344

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   +      +++      +     +RR     +  T     P +   +A +  +
Sbjct: 345 IRQAIARAVADRARTIRVPVHVGDQ--HQRVRRQALRFRQRTGRQPTPAE---LAAETGL 399

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV--LIEKEERKNRRN 226
           +E ++ ++    A   SL+  +  +D         L+ D         L     R+  R+
Sbjct: 400 AEDKLRAILALPAEPVSLDTPLPDADTGLVD----LIEDETSASPFEQLAGTRMRECVRS 455

Query: 227 MLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIE 273
           +L RS++   P E  +   RR       P T + ++ +  +SRERVRQIE
Sbjct: 456 LL-RSVT---PTEADVLR-RRFGLGGTEPDTYDAIAKDAGMSRERVRQIE 500


>gi|297200782|ref|ZP_06918179.1| RNA polymerase sigma-E factor [Streptomyces sviceus ATCC 29083]
 gi|197712352|gb|EDY56386.1| RNA polymerase sigma-E factor [Streptomyces sviceus ATCC 29083]
          Length = 285

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 64/244 (26%), Positives = 119/244 (48%), Gaps = 23/244 (9%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           EH  +  A  L+ ++L LV   A  +R    P+ +V+  G IGL+ A+ +FDP+RG +  
Sbjct: 57  EHNRVRTA--LIEANLPLVRYAAARFRSRNEPMEDVIQVGTIGLINAIDRFDPDRGVQFP 114

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           T++M  +   ++ Y   +   V +      +RL     ++ G  + +T    +      I
Sbjct: 115 TFAMPTVVGEIKRYFRDNVRTVHV-----PRRLHELWVQVNGATEDLTTAFGRTPTTAEI 169

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL--VYDHDGQEQVLIEKEE 220
           A++L ++E EV+S  C  AG        +++   ++Q  D L  + D  G E   ++  E
Sbjct: 170 AQRLRITEDEVLS--CIEAGRS-----YHATSLEAAQEGDGLPGLLDRLGYEDPALDGVE 222

Query: 221 RKNRRNMLTRSMSVLNP-RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
            ++    L R + V  P RE+RI   R      +T   +S+E  VS+  V ++ AR+F++
Sbjct: 223 HRD----LVRHLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLLARSFQR 276

Query: 280 VQES 283
           ++ +
Sbjct: 277 LRSA 280


>gi|161521004|ref|YP_001584431.1| RpoD family RNA polymerase sigma factor [Burkholderia multivorans
           ATCC 17616]
 gi|189352818|ref|YP_001948445.1| RNA polymerase sigma 38 subunit [Burkholderia multivorans ATCC
           17616]
 gi|160345054|gb|ABX18139.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           multivorans ATCC 17616]
 gi|189336840|dbj|BAG45909.1| RNA polymerase sigma 38 subunit [Burkholderia multivorans ATCC
           17616]
          Length = 525

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 61/230 (26%), Positives = 111/230 (48%), Gaps = 19/230 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   G+ +S++V +G IGLM+A++KF+  RGF+ +TY+ WW
Sbjct: 288 ATRAMLEANLRLVLSIARKYLNRGVDLSDLVQDGCIGLMRAIEKFEYRRGFKFSTYATWW 347

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   +      +++      +     +RR     +  T     P +   +A +  +
Sbjct: 348 IRQAIARAVADRARTIRVPVHVGDQ--HQRVRRQALRFRQRTGRQPTPAE---LAAETGL 402

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV--LIEKEERKNRRN 226
           +E ++ ++    A   SL+  +  +D         L+ D         L     R+  R+
Sbjct: 403 AEDKLRAILALPAEPVSLDTPLPDADTGLVD----LIEDETSASPFEQLAGTRMRECVRS 458

Query: 227 MLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIE 273
           +L RS++   P E  +   RR       P T + ++ +  +SRERVRQIE
Sbjct: 459 LL-RSVT---PTEADVLR-RRFGLGGTEPDTYDAIAKDAGMSRERVRQIE 503


>gi|294673112|ref|YP_003573728.1| sigma factor [Prevotella ruminicola 23]
 gi|294471705|gb|ADE81094.1| putative sigma factor [Prevotella ruminicola 23]
          Length = 238

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 34/95 (35%), Positives = 61/95 (64%), Gaps = 2/95 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  ++  IR +  L++++E  LA+R +  GD  A  +++ S+L+LVV IA  YR   + +
Sbjct: 14  LESFMARIRGVKALDEEQEVYLAQRIK-AGDTKAEEQMIKSNLKLVVSIANSYRPM-MSM 71

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            +++  GNIGL++AV++F+PE G+R   Y+   I+
Sbjct: 72  EDLIQNGNIGLIKAVREFNPELGYRFVFYASMMIR 106


>gi|115358293|ref|YP_775431.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia ambifaria
           AMMD]
 gi|115283581|gb|ABI89097.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia ambifaria
           AMMD]
          Length = 516

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 55/245 (22%), Positives = 113/245 (46%), Gaps = 29/245 (11%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ ++LRLV+ IA  Y   G+ + ++V +G +GLM+A++KF+  RGF+ +TY+ WWI+ A
Sbjct: 283 MLEANLRLVLSIARKYMNRGVDLPDLVQDGCLGLMRAIEKFEYRRGFKFSTYATWWIRQA 342

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA-------KK 165
           +   +      +++      +  +  ++R     +  T     P ++ A +       + 
Sbjct: 343 VARAVADRSRTIRVPVHVGDQ--YQRVQRHALRFRQRTGRRATPAELAAESGLPEGKLRA 400

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           +    +E +S++  L   E+   L++  +  +S                  E+      R
Sbjct: 401 VLALPAEPLSLDTPLPDAET--GLVDLIEDQASASP--------------FERLADTRMR 444

Query: 226 NMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             +T  +  + P E  +   RR       P T + ++ +  +SRERVRQIE RA   ++ 
Sbjct: 445 ECVTSLLRSVTPAEADVLR-RRFGLGGAEPDTYDAIAQDAGMSRERVRQIEKRALATLRT 503

Query: 283 SIQKQ 287
           + + +
Sbjct: 504 AAEAE 508


>gi|221196694|ref|ZP_03569741.1| RNA polymerase sigma factor RpoD (Sigma-70) [Burkholderia
           multivorans CGD2M]
 gi|221203363|ref|ZP_03576382.1| RNA polymerase sigma factor RpoD (Sigma-70) [Burkholderia
           multivorans CGD2]
 gi|221177297|gb|EEE09725.1| RNA polymerase sigma factor RpoD (Sigma-70) [Burkholderia
           multivorans CGD2]
 gi|221183248|gb|EEE15648.1| RNA polymerase sigma factor RpoD (Sigma-70) [Burkholderia
           multivorans CGD2M]
          Length = 524

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 61/230 (26%), Positives = 111/230 (48%), Gaps = 19/230 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   G+ +S++V +G IGLM+A++KF+  RGF+ +TY+ WW
Sbjct: 287 ATRAMLEANLRLVLSIARKYLNRGVDLSDLVQDGCIGLMRAIEKFEYRRGFKFSTYATWW 346

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   +      +++      +     +RR     +  T     P +   +A +  +
Sbjct: 347 IRQAIARAVADRARTIRVPVHVGDQ--HQRVRRQALRFRQRTGRQPTPAE---LAAETGL 401

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV--LIEKEERKNRRN 226
           +E ++ ++    A   SL+  +  +D         L+ D         L     R+  R+
Sbjct: 402 AEDKLRAILALPAEPVSLDTPLPDADTGLVD----LIEDETSASPFEQLAGARMRECVRS 457

Query: 227 MLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIE 273
           +L RS++   P E  +   RR       P T + ++ +  +SRERVRQIE
Sbjct: 458 LL-RSVT---PAEADVLR-RRFGLGGTEPDTYDAIAKDAGMSRERVRQIE 502


>gi|149921691|ref|ZP_01910139.1| RNA polymerase sigma factor RpoD [Plesiocystis pacifica SIR-1]
 gi|149817429|gb|EDM76901.1| RNA polymerase sigma factor RpoD [Plesiocystis pacifica SIR-1]
          Length = 384

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 67/245 (27%), Positives = 119/245 (48%), Gaps = 27/245 (11%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
              ++LRLVV +A       LP+ +++ EGNIGL++A+++FD  +GFR +TY+ WWI+ +
Sbjct: 154 FAKANLRLVVSLARRLSNGRLPLQDLIQEGNIGLLKAIERFDHRKGFRFSTYASWWIRHS 213

Query: 113 MQEYILRSWSLVKIGT---TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           +   I      V++       +QK     + R++   +A        E+   IA ++ V 
Sbjct: 214 ISRAIYNKGRQVRLPVHVYDVHQK-----ITRVRRRYEAQIGREPTHEE---IANEIGVP 265

Query: 170 ESEVISMNC-RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE---KEERKNRR 225
            ++V  +    L    SL+A ++ +D  S    D L      ++QV      + E     
Sbjct: 266 LAKVEKIAAIELGPIVSLDAPLSRNDDRSG--VDLL------EDQVSPGPGFELELGELE 317

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPV---TLENLSSEFEVSRERVRQIEARAFKKVQE 282
             L  ++S L P E  I   RR   + V   TL  +   + +SRER+RQ++ RA  +++E
Sbjct: 318 EGLEDALSALRPMEADILR-RRYGLDGVEKETLREIGERYALSRERIRQLQERAVSRMRE 376

Query: 283 SIQKQ 287
              ++
Sbjct: 377 EFARR 381


>gi|332982149|ref|YP_004463590.1| RNA polymerase sigma-29 subunit SigE [Mahella australiensis 50-1
           BON]
 gi|332699827|gb|AEE96768.1| RNA polymerase, sigma 29 subunit, SigE [Mahella australiensis 50-1
           BON]
          Length = 239

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 37/106 (34%), Positives = 60/106 (56%), Gaps = 1/106 (0%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EE  + KR  + GD S    L+  +LRLVV IA  +   G+P+ +++S G IGL
Sbjct: 36  PPLSADEEQDIMKRLSD-GDESVKSILIERNLRLVVYIARRFENTGIPVEDLISIGTIGL 94

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           ++AV  FDP++  +LATY+   I+  +  Y+ R+    K   + ++
Sbjct: 95  IKAVNTFDPDKKIKLATYASRCIENEILMYLRRNCRFNKTEVSIDE 140


>gi|308069873|ref|YP_003871478.1| RNA polymerase sigma-35 factor precursor [Paenibacillus polymyxa
           E681]
 gi|305859152|gb|ADM70940.1| RNA polymerase sigma-35 factor precursor [Paenibacillus polymyxa
           E681]
          Length = 246

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 37/94 (39%), Positives = 56/94 (59%), Gaps = 2/94 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+   +EEY+L K     GD +    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 45  PLTRDEEEYLLGKL--SSGDAAVRSMLIERNLRLVVYIARKFENTGINIEDLVSIGAIGL 102

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  FDPE+  +LATY+   I+  +  Y+ R+
Sbjct: 103 IKAVNTFDPEKKIKLATYASRCIENEILMYLRRN 136


>gi|55274907|gb|AAV49255.1| RNA polymerase subunit sigma-38 [Escherichia albertii]
          Length = 189

 Score = 67.8 bits (164), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 25/51 (49%), Positives = 39/51 (76%)

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+
Sbjct: 4   YGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIM 54


>gi|317129289|ref|YP_004095571.1| RNA polymerase, sigma 28 subunit, SigE [Bacillus cellulosilyticus
           DSM 2522]
 gi|315474237|gb|ADU30840.1| RNA polymerase, sigma 28 subunit, SigE [Bacillus cellulosilyticus
           DSM 2522]
          Length = 238

 Score = 67.4 bits (163), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 69/264 (26%), Positives = 114/264 (43%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE  L K+    GD S    L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 36  PPLSKEEEAYLLKKL-PSGDDSVRSVLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 94

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FDPE+  +LATY+   I+  +  Y                      LRR     
Sbjct: 95  IKAVSTFDPEKKIKLATYASRCIENEILMY----------------------LRR----- 127

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
               +N ++ E                      ++ DE LN      D N     D L  
Sbjct: 128 ----NNKIRSE----------------------VSFDEPLNI---DWDGNELLLSDVLGT 158

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEV 264
           + D    ++ +  E K  R +L +++  LN RE++I E R     +   T ++++    +
Sbjct: 159 EED----IITKGIEDKVDRKLLVKALEALNDREKQIMELRFGLAGDEEKTQKDVADMLGI 214

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++Q+   K +
Sbjct: 215 SQSYISRLEKRIIKRLQKEFNKML 238


>gi|170700559|ref|ZP_02891561.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           ambifaria IOP40-10]
 gi|170134549|gb|EDT02875.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           ambifaria IOP40-10]
          Length = 519

 Score = 67.4 bits (163), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 55/245 (22%), Positives = 113/245 (46%), Gaps = 29/245 (11%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ ++LRLV+ IA  Y   G+ + ++V +G +GLM+A++KF+  RGF+ +TY+ WWI+ A
Sbjct: 286 MLEANLRLVLSIARKYMNRGVDLPDLVQDGCLGLMRAIEKFEYRRGFKFSTYATWWIRQA 345

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA-------KK 165
           +   +      +++      +  +  ++R     +  T     P ++ A +       + 
Sbjct: 346 VARAVADRSRTIRVPVHVGDQ--YQRVQRHALRFRQRTGRRATPAELAAESGLPEGKLRA 403

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           +    +E +S++  L   E+   L++  +  +S                  E+      R
Sbjct: 404 VLALPAEPLSLDTPLPDAET--GLVDLIEDQASASP--------------FERLADTRMR 447

Query: 226 NMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             +T  +  + P E  +   RR       P T + ++ +  +SRERVRQIE RA   ++ 
Sbjct: 448 ECVTSLLRSVTPAEADVLR-RRFGLGGAEPDTYDAIAQDAGMSRERVRQIEKRALATLRT 506

Query: 283 SIQKQ 287
           + + +
Sbjct: 507 AAEAE 511


>gi|323704529|ref|ZP_08116107.1| RNA polymerase, sigma 32 subunit, RpoH [Thermoanaerobacterium
           xylanolyticum LX-11]
 gi|323535991|gb|EGB25764.1| RNA polymerase, sigma 32 subunit, RpoH [Thermoanaerobacterium
           xylanolyticum LX-11]
          Length = 339

 Score = 67.4 bits (163), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 62/248 (25%), Positives = 121/248 (48%), Gaps = 19/248 (7%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAM-GYRGYGLPISE--VVSEGNIGLMQAVKKFDPERGF 99
           + G+  A   LV  + +LV+  A   ++ Y L I E  +V  G  GL++A ++FD +R  
Sbjct: 88  QQGNKWALEALVDRNKKLVMSRAYKCFKRYKLNIDEDDLVQYGYFGLIKAAERFDIKRET 147

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           +  TY+ WWI  A++  I     ++++         F  + ++   L    D  L  E +
Sbjct: 148 KFVTYATWWIDQAIKRSICDYGFIIRLPV-----HYFDEINKVLNILSIHFD--LSKEAI 200

Query: 160 VAIAKKLNVSES---EVISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVL 215
           + I ++  +S+    +++ +   +   +SLN  +N +S    ++  D +V   D     +
Sbjct: 201 IKILEENGISKDKYDDIMFVIENVLSIDSLNKYVNPNSGDGDTELLDLIV---DKTNPTV 257

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIE 273
            E+ + K  +  +   +  L  RE+ +   R   +  + +TLE +  EF ++RER+RQIE
Sbjct: 258 EEEIDLKLLKETINNILDTLKSREKEVIRMRFGLDGGDEMTLERIGKEFNITRERIRQIE 317

Query: 274 ARAFKKVQ 281
            +A KK++
Sbjct: 318 EKAIKKLR 325


>gi|228931462|ref|ZP_04094387.1| RNA polymerase sigma-43 factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|229188107|ref|ZP_04315191.1| RNA polymerase sigma-43 factor [Bacillus cereus BGSC 6E1]
 gi|228595348|gb|EEK53084.1| RNA polymerase sigma-43 factor [Bacillus cereus BGSC 6E1]
 gi|228828268|gb|EEM73978.1| RNA polymerase sigma-43 factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
          Length = 323

 Score = 67.4 bits (163), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 75/296 (25%), Positives = 129/296 (43%), Gaps = 59/296 (19%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY--GLPISE 77
           I EI    +L KQE   L +RY+ HG+      L   ++ LV+ IA  Y+     +   +
Sbjct: 40  IKEIGNYQVLSKQESLNLFQRYK-HGEKDLRDYLFHVNVGLVLSIARKYKNKHPDIEFDD 98

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS-LVKIGTTANQKRLF 136
           +V EGN G+++A++ F+P  G+  +TY+  WI+  M   I +  S   KI    NQ    
Sbjct: 99  LVQEGNEGMLRAMEDFNPALGYCFSTYAFCWIQKRMLGIICKKRSGPFKIPNYVNQ---- 154

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC--RLAGDESLN------- 187
           FNL+ ++   + +   N +P  V  + K L+V+   VI  N   + A   +L+       
Sbjct: 155 FNLKYVELEDKYLQMYN-RPPSVEEVVKDLDVTSEIVIRHNVYYKRATTMTLDIDTINED 213

Query: 188 -ALINSSDKNSS-------------QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             + NSS  + S              ++ WL++D                          
Sbjct: 214 IGISNSSHDDKSAIPSINEMVIEDLNYEIWLIFD-------------------------E 248

Query: 234 VLNPRERRIFE-ARRLQENPVTL-ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           VLNP+++ +      L +  V L + ++    ++ ERV QI+  A KK+++   K 
Sbjct: 249 VLNPKQKMVLNLCFGLLDGKVYLHKEIAKALMITTERVSQIKEEAIKKLKKCDYKD 304


>gi|310642979|ref|YP_003947737.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
 gi|309247929|gb|ADO57496.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
          Length = 246

 Score = 67.4 bits (163), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 37/94 (39%), Positives = 56/94 (59%), Gaps = 2/94 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+   +EEY+L K     GD +    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 45  PLTRDEEEYLLGKL--SSGDAAVRSMLIERNLRLVVYIARKFENTGINIEDLVSIGAIGL 102

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  FDPE+  +LATY+   I+  +  Y+ R+
Sbjct: 103 IKAVNTFDPEKKIKLATYASRCIENEILMYLRRN 136


>gi|255566078|ref|XP_002524027.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
 gi|223536754|gb|EEF38395.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
          Length = 508

 Score = 67.4 bits (163), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 64/259 (24%), Positives = 123/259 (47%), Gaps = 44/259 (16%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  S++RLV+ IA  Y   G  ++++V  G IGL++ ++KFD  +GFR++TY  WW
Sbjct: 265 AREKLAMSNVRLVMSIAQRYDNMGAEMADLVQGGLIGLLRGIEKFDSSKGFRISTYVYWW 324

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   ++ +   +++    +++       +++   + +T +      +  IA+ LN+
Sbjct: 325 IRQGVSRALVENSRTLRLPNHLHERLGLIRNAKIRLEEKGVTPS------IDRIAESLNI 378

Query: 169 SE----------SEVISMN----CRLAG--DESLNALINSSDKNSSQWQ---DWLVYDHD 209
           S+          S+V S++      L G   E+ ++ I  +   ++ W    DW + D  
Sbjct: 379 SQKKVRNATEAVSKVFSLDREAFPSLNGLPGETHHSYIADNCLENNPWHGVDDWALKDE- 437

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPVTLENLSSEFEVSRER 268
                        N+   LT     L  RE+ I      L    +T E++S    +SRER
Sbjct: 438 ------------VNKLINLT-----LQEREQEIIRLYYGLDNESLTWEDISKRIGLSRER 480

Query: 269 VRQIEARAFKKVQESIQKQ 287
           VRQ+   A +K++ + +K+
Sbjct: 481 VRQVGLVALEKLKHAARKK 499


>gi|321309571|ref|YP_004191900.1| RNA polymerase sigma factor rpoD [Mycoplasma haemofelis str.
           Langford 1]
 gi|319801415|emb|CBY92061.1| RNA polymerase sigma factor rpoD [Mycoplasma haemofelis str.
           Langford 1]
          Length = 424

 Score = 67.4 bits (163), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 40/65 (61%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  RL   +LRLV   A  Y  YG P+ ++V EG  GL++A+ KFD   G R +TY+ WW
Sbjct: 136 AVKRLTIFNLRLVWSSARKYLNYGFPMEDLVQEGIFGLVKAIHKFDCAFGNRFSTYATWW 195

Query: 109 IKAAM 113
           I+ AM
Sbjct: 196 IRQAM 200


>gi|291454068|ref|ZP_06593458.1| RNA polymerase sigma factor [Streptomyces albus J1074]
 gi|291357017|gb|EFE83919.1| RNA polymerase sigma factor [Streptomyces albus J1074]
          Length = 365

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 65/234 (27%), Positives = 106/234 (45%), Gaps = 17/234 (7%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDPERG   +TY+   +  
Sbjct: 144 RLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPERGVEFSTYATPTVVG 203

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            ++ +       V++     + RL      L      ++  + +   V  +A+KL +SE 
Sbjct: 204 EIKRHFRDKGWAVRVPRRLQELRL-----SLTSATAELSQRHGRSPTVHELAEKLGISEE 258

Query: 172 EVISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           EV      L G ES NA    S D   +  +   V D  G E   +E  E    R  L  
Sbjct: 259 EV------LEGLESANAYSTLSLDVPDTDDESPAVADTLGSEDEALEGVE---YRESLKP 309

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 310 LLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLREKL 361


>gi|291438641|ref|ZP_06578031.1| transcription initiation factor sigma F [Streptomyces ghanaensis
           ATCC 14672]
 gi|291341536|gb|EFE68492.1| transcription initiation factor sigma F [Streptomyces ghanaensis
           ATCC 14672]
          Length = 303

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 64/244 (26%), Positives = 120/244 (49%), Gaps = 23/244 (9%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           EH  + AA  L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDP+RG +  
Sbjct: 75  EHTRVRAA--LIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFP 132

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           T++M  +   ++ Y   +   V +      +RL     ++ G  + +T    +      I
Sbjct: 133 TFAMPTVVGEIKRYFRDNVRTVHV-----PRRLHELWVQVNGATEDLTTAFGRSPSTAEI 187

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL--VYDHDGQEQVLIEKEE 220
           A++L ++E +V+S  C  AG        +++   ++Q  D +  + D  G E   ++  E
Sbjct: 188 AERLRITEEDVLS--CIEAGRS-----YHATSLEAAQEGDGMPGLLDRLGYEDPALDGVE 240

Query: 221 RKNRRNMLTRSMSVLNP-RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
            ++    L R + V  P RE+RI   R      +T   +S+E  VS+  V ++ AR+F++
Sbjct: 241 HRD----LVRHLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLLARSFQR 294

Query: 280 VQES 283
           ++ +
Sbjct: 295 LRSA 298


>gi|170735771|ref|YP_001777031.1| RpoD family RNA polymerase sigma factor [Burkholderia cenocepacia
           MC0-3]
 gi|169817959|gb|ACA92541.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           cenocepacia MC0-3]
          Length = 511

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 59/230 (25%), Positives = 112/230 (48%), Gaps = 19/230 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   G+ +S++V +G +GLM+A++KF+  RGF+ +TY+ WW
Sbjct: 274 ATRAMLEANLRLVLSIARKYLNRGVDLSDLVQDGCLGLMRAIEKFEYRRGFKFSTYATWW 333

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   +      +++      +  +  ++R     +  T     P +   +A +  +
Sbjct: 334 IRQAIARAVADRSRTIRVPVHVGDQ--YQRVQRHALRFRQRTGRRATPAE---LAAETGL 388

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV--LIEKEERKNRRN 226
            E ++ ++    A   SL+  +  +D    +    L+ D         L +   R+  R 
Sbjct: 389 DEGKLRAVLALPAEPVSLDTPLPDADTGLVE----LIEDQASASPFEQLADTRMRECVRA 444

Query: 227 MLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIE 273
           +L RS++   P E  +   RR       P T + ++ +  +SRERVRQIE
Sbjct: 445 LL-RSVT---PTEADVLR-RRFGLGGAEPDTYDAIAQDAGMSRERVRQIE 489


>gi|585927|sp|P37970|RPOF_STRAU RecName: Full=RNA polymerase sigma-F factor
 gi|153450|gb|AAA93050.1| minor sigma-like factor [Streptomyces aureofaciens]
          Length = 297

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 67/245 (27%), Positives = 119/245 (48%), Gaps = 23/245 (9%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
           REH  +  A  L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDPERG + 
Sbjct: 68  REHERVRGA--LIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQF 125

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
            T++M  +   ++ Y   +   V +      +RL     ++    + +T  + +      
Sbjct: 126 PTFAMPTVVGEIKRYFRDNVRTVHV-----PRRLHELWVQVNAATEDLTTLHGRTPTTPE 180

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL--VYDHDGQEQVLIEKE 219
           IA++L +SE EV+S  C  AG        +++   ++Q  D +  + D  G E   +   
Sbjct: 181 IAERLRISEDEVLS--CIEAGRS-----YHATSLEAAQEGDGMPGLLDRLGYEDPELAGV 233

Query: 220 ERKNRRNMLTRSMSVLNP-RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           E ++    L R + V  P RE+RI   R    N +T   +S+E  VS+  V ++ AR+F 
Sbjct: 234 EHRD----LVRHLLVQLPEREQRILLLRYY--NNLTQSQISAELGVSQMHVSRLLARSFA 287

Query: 279 KVQES 283
           +++ +
Sbjct: 288 RLRSA 292


>gi|239930293|ref|ZP_04687246.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 305

 Score = 67.4 bits (163), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 64/244 (26%), Positives = 120/244 (49%), Gaps = 23/244 (9%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           EH  + AA  L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDP+RG +  
Sbjct: 77  EHTRVRAA--LIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFP 134

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           T++M  +   ++ Y   +   V +      +RL     ++ G  + +T    +      I
Sbjct: 135 TFAMPTVVGEIKRYFRDNVRTVHV-----PRRLHELWVQVNGATEDLTTAFGRSPSTAEI 189

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL--VYDHDGQEQVLIEKEE 220
           A++L ++E +V+S  C  AG        +++   ++Q  D +  + D  G E   ++  E
Sbjct: 190 AERLRITEEDVLS--CIEAGRS-----YHATSLEAAQEGDGMPGLLDRLGYEDPALDGVE 242

Query: 221 RKNRRNMLTRSMSVLNP-RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
            ++    L R + V  P RE+RI   R      +T   +S+E  VS+  V ++ AR+F++
Sbjct: 243 HRD----LVRHLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLLARSFQR 296

Query: 280 VQES 283
           ++ +
Sbjct: 297 LRSA 300


>gi|326332710|ref|ZP_08198972.1| RNA polymerase principal sigma factor SigB [Nocardioidaceae
           bacterium Broad-1]
 gi|325949491|gb|EGD41569.1| RNA polymerase principal sigma factor SigB [Nocardioidaceae
           bacterium Broad-1]
          Length = 315

 Score = 67.0 bits (162), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 28/78 (35%), Positives = 51/78 (65%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A    + ++LRLVV IA  Y    +P+ +++ EGN GL++AV+KFD  +G++ +TY+ WW
Sbjct: 82  ATREFINANLRLVVSIARKYGRAQMPMLDLIQEGNTGLIRAVEKFDYTKGYKFSTYATWW 141

Query: 109 IKAAMQEYILRSWSLVKI 126
           ++ A+   I +   +V++
Sbjct: 142 VRQAITRGIAQQARVVRL 159


>gi|1769588|gb|AAB95226.1| sigma factor [Synechococcus sp. PCC 7002]
          Length = 328

 Score = 67.0 bits (162), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 59/240 (24%), Positives = 113/240 (47%), Gaps = 31/240 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +++ ++LRLVV IA   +   L   +++ EG++GL + V+KFDP +G++ +TY+ WW
Sbjct: 92  AKRKMIEANLRLVVAIARNIKKRNLEFLDLIQEGSLGLERGVEKFDPTKGYKFSTYAYWW 151

Query: 109 IKAAMQEYILRSWSLVKI---------GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           I+ A+   I +    +++              Q++L  +L R     +      L+P Q 
Sbjct: 152 IRQAITRAIAQQGRTIRLPIHITEKLNKIKKTQRQLAQDLGRAATIAEIAEALELEPAQ- 210

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I +   VS    IS++ R+ GD     L++  + +     + + Y+   Q+       
Sbjct: 211 --IREYFRVSRHP-ISLDVRV-GDNQDTELMDLLEDSGESPDNNVTYELLKQD------- 259

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENP-VTLENLSSEFEVSRERVRQIEARAF 277
                   L   ++ L P+++ +   R  L +   ++L  +     +SRERVRQ+E +A 
Sbjct: 260 --------LRDLIADLTPQQQEVIILRFGLNDGKELSLAKIGKRMNLSRERVRQLERQAL 311


>gi|21104382|dbj|BAB93461.1| unnamed protein product [Roseateles depolymerans]
          Length = 47

 Score = 67.0 bits (162), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 28/46 (60%), Positives = 37/46 (80%)

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           LVV IA  Y G GLP+S+++ EGN+GLM A+ KF+PERGFR +TY+
Sbjct: 1   LVVSIAKNYLGRGLPMSDLIEEGNLGLMHAIGKFEPERGFRFSTYA 46


>gi|313799121|gb|ADR82155.1| RNA polymerase sigma factor [Mycoplasma sp. 1220]
 gi|313799126|gb|ADR82156.1| RNA polymerase sigma factor [Mycoplasma anatis]
 gi|313799129|gb|ADR82157.1| RNA polymerase sigma factor [Mycoplasma anatis]
          Length = 183

 Score = 67.0 bits (162), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 32/88 (36%), Positives = 54/88 (61%), Gaps = 2/88 (2%)

Query: 28  MLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +L   EE  LAK     G     A  +L+  +LRLV+  A  Y+  GL   +++SEGN G
Sbjct: 9   LLSADEEVELAKTMNLGGFRGKRARDKLIKRNLRLVINNAKKYKNRGLSFIDLISEGNAG 68

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAM 113
           +++A +K++ ++GF+ +TY+ WWI+ A+
Sbjct: 69  ILKAAQKYNVDKGFKFSTYATWWIRQAI 96


>gi|3077738|dbj|BAA25787.1| SigB [Cyanidium caldarium]
          Length = 424

 Score = 67.0 bits (162), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 60/272 (22%), Positives = 116/272 (42%), Gaps = 44/272 (16%)

Query: 49  AAHRLVTSHLRLVVKIAMGYR---------------GYGLP--------------ISEVV 79
           A  RLV S+LRLV+ IA  Y+               G  +P              + +++
Sbjct: 143 ARERLVASNLRLVLAIANRYKLRAVVCSAWKSRSKGGMDMPSHEKVRLQRQHNIFLGDLI 202

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EG +GL++A +KFDP +GF+ +TY+ WWI+ A+Q  +      +++     +      +
Sbjct: 203 QEGALGLIRAAEKFDPSKGFKFSTYATWWIRQAIQRCVSEHSRTIRLPNHVTES--LRQI 260

Query: 140 RRLKGHLQAITDNNLKPEQVVAIA-------KKLNVSESEVISMNCRLAGDESLNALINS 192
            R++  LQ +       E+V           KK+     E  +++     +   ++L  S
Sbjct: 261 YRMRARLQHVLKRPPTDEEVAEACNMTLKRLKKITQHAWETQTLSLEGPPNSEAHSLYKS 320

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQ 249
               +      ++   +   +  +E+   +     + R++     +ER I   R      
Sbjct: 321 QQGEAPLSIGSIIEATEETPEEALERNCMREDVECVLRTLPF---QEREILRLRYGISDD 377

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           E P + E LS+ F++    +R IE+RA +K++
Sbjct: 378 ERPHSTEELSARFQLPVHTIRLIESRALRKLR 409


>gi|297193426|ref|ZP_06910824.1| RNA polymerase sigma-F factor [Streptomyces pristinaespiralis ATCC
           25486]
 gi|197723191|gb|EDY67099.1| RNA polymerase sigma-F factor [Streptomyces pristinaespiralis ATCC
           25486]
          Length = 282

 Score = 67.0 bits (162), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 64/244 (26%), Positives = 117/244 (47%), Gaps = 23/244 (9%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           EH  + AA  L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDP+RG +  
Sbjct: 54  EHSRVRAA--LIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFP 111

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           T++M  +   ++ Y   +   V +      +RL     ++ G  + +T  + +      I
Sbjct: 112 TFAMPTVVGEIKRYFRDNVRTVHV-----PRRLHELWVQVNGATEDLTTAHGRSPTTAEI 166

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL--VYDHDGQEQVLIEKEE 220
           A++L + E EV++  C  AG        +++   ++Q  D +  + D  G E   +   E
Sbjct: 167 AERLKIGEDEVLA--CIEAGRS-----YHATSLEAAQEGDGMPGLLDRLGYEDPALAGVE 219

Query: 221 RKNRRNMLTRSMSVLNP-RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
            ++    L R + V  P RE+RI   R      +T   +S E  VS+  V ++ AR+F +
Sbjct: 220 HRD----LVRHLLVQLPEREQRILMLRYYSN--LTQSQISQELGVSQMHVSRLLARSFAR 273

Query: 280 VQES 283
           ++ +
Sbjct: 274 LRSA 277


>gi|318041750|ref|ZP_07973706.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CB0101]
          Length = 279

 Score = 66.6 bits (161), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 34/88 (38%), Positives = 52/88 (59%), Gaps = 5/88 (5%)

Query: 53  LVTSHLRLVVKIAMGY-----RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           ++  +LRLVV IA  Y     R   L  S+++  G IGL++AV+KFDP  G+  +TY+ W
Sbjct: 55  MIKENLRLVVCIAKPYHARIQRSSALEFSDLLQAGTIGLIRAVEKFDPALGYSFSTYASW 114

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRL 135
           WI+ A++  I  S S +++     Q RL
Sbjct: 115 WIRQAIRREIEASESSIRLSARQQQMRL 142


>gi|297820128|ref|XP_002877947.1| predicted protein [Arabidopsis lyrata subsp. lyrata]
 gi|297323785|gb|EFH54206.1| predicted protein [Arabidopsis lyrata subsp. lyrata]
          Length = 568

 Score = 66.6 bits (161), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 57/233 (24%), Positives = 119/233 (51%), Gaps = 13/233 (5%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ S   LV+ +A  YRG G+   +++  G +G++Q  ++FD  RG++ +TY  +WI+ +
Sbjct: 333 LLKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYWIRKS 392

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           M   + R    V I ++    R    +++ +  L+  T + +K      I+K  ++S  +
Sbjct: 393 MSMMVSRHARGVHIPSSI--IRTINQIQKARKTLK--TSHGIKYPADEDISKLTSLSVKK 448

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLV-YDHDGQEQVLIEKEERKNRRNMLTRS 231
           + + N  L    S+   +   D  S+++ ++      +  E+ ++ +  R++  ++L   
Sbjct: 449 IRAANQCLKVVGSIEKKVG--DCFSTKFLEFTPDTTMESPEEAVMRQSARRDIHDLL--- 503

Query: 232 MSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              L PRE+++   R   +N  P +LE +     VS+E +R+IE RA  K+++
Sbjct: 504 -EGLEPREKQVMVLRYGLQNYRPKSLEEIGKLLRVSKEWIRKIERRAMAKLRD 555


>gi|164690667|dbj|BAF98617.1| putative DNA helicase [Streptomyces argenteolus]
          Length = 1064

 Score = 66.6 bits (161), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 65/262 (24%), Positives = 112/262 (42%), Gaps = 52/262 (19%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  ++RLV      Y G G+   ++V  G +G+M+A +KFDP  G R +TY+ WWI+ A
Sbjct: 156 LVLHNIRLVHAAVAPYLGQGVDREDLVQHGVLGVMRAAEKFDPRAGTRFSTYATWWIRQA 215

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNL-------RRLKGHLQAITDNNLKPEQVVAIAKK 165
           +   +    S ++I        L   +       R L+   Q +      P   V +A +
Sbjct: 216 VSRAVADEGSTIRIPAHVRDVVLKVAVACRRSRERGLRPRPQDLAAELDLPPDTVNLALR 275

Query: 166 LN------------VSESEV-ISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQ 211
           ++            V  +E+ IS+   + G +E+L A          QW DWL+      
Sbjct: 276 VSRPADSLDRVADGVRPAELAISLRDAIPGPEETLRAAF------GRQWVDWLL------ 323

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E +     +   RRN + +                     P TL+++   + V+RER+RQ
Sbjct: 324 EPLPARNADIVRRRNGVIKG-------------------EPQTLKDIGVLYGVTRERIRQ 364

Query: 272 IEARAFKKVQESIQKQVELSSS 293
            E RA   +++ +   V++ +S
Sbjct: 365 NEKRALAVLRDRLGAPVKVPAS 386


>gi|224553606|gb|ACN55041.1| RNA polymerase sigma factor [Escherichia coli]
          Length = 111

 Score = 66.6 bits (161), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 24/47 (51%), Positives = 38/47 (80%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+
Sbjct: 1   GLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIM 47


>gi|224553592|gb|ACN55034.1| RNA polymerase sigma factor [Escherichia coli]
          Length = 111

 Score = 66.6 bits (161), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 24/47 (51%), Positives = 38/47 (80%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+
Sbjct: 1   GLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIM 47


>gi|297616993|ref|YP_003702152.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
 gi|297144830|gb|ADI01587.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
          Length = 241

 Score = 66.6 bits (161), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 70/262 (26%), Positives = 113/262 (43%), Gaps = 63/262 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L  +EE  L +R  E GD      L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 39  PPLSSEEESTLLQRL-EQGDNGVKSTLIEHNLRLVVYIAKKFENTGINIEDLVSIGTIGL 97

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+P +  +LATY+   I+  +  Y                      LRR     
Sbjct: 98  IKAVNTFEPRKNIKLATYASRCIENEILMY----------------------LRR----- 130

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                 NLK    V++ + LNV                         D N     D L  
Sbjct: 131 ------NLKTRAEVSLDEPLNV-----------------------DWDGNELLLSDVLGT 161

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEV 264
           D D   + + E+ E+K    +L++++  L PRE+RI + R   E+    T + ++    +
Sbjct: 162 DGDMIYKTIEEEVEKK----LLSQAILRLPPREKRIIQLRFGLEDGYEKTQKEVADILGI 217

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+  + ++E R  K+++  I+K
Sbjct: 218 SQSYISRLEKRILKRLRREIRK 239


>gi|30024622|dbj|BAC75679.1| sigma F [Streptomyces griseus]
          Length = 293

 Score = 66.6 bits (161), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 61/234 (26%), Positives = 114/234 (48%), Gaps = 20/234 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDP+RG +  T++M  +   
Sbjct: 72  LIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFPTFAMPTVVGE 131

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           ++ Y   + +      + +  RL     ++ G  + +T  + +      IA++L +SE E
Sbjct: 132 IKRYFRDNCA----HPSTSPDRLHELWVQVTGATEDLTTAHGRSPTTAEIAERLKISEDE 187

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWL--VYDHDGQEQVLIEKEERKNRRNMLTR 230
           V++  C  AG        +++   ++Q  D L  + D  G E   +   E ++    L R
Sbjct: 188 VLA--CIEAGRS-----YHATSLEAAQEGDGLPGLLDRLGYEDPALAGVEHRD----LVR 236

Query: 231 SMSVLNP-RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            + V  P RE+RI   R      +T   +S+E  VS+  V ++ AR+F +++ +
Sbjct: 237 HLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLLARSFARLRSA 288


>gi|332196178|gb|AEE34299.1| sigma factor A [Arabidopsis thaliana]
          Length = 498

 Score = 66.6 bits (161), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 37/125 (29%), Positives = 71/125 (56%), Gaps = 6/125 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  S++RLV+ IA  Y   G  +S++V  G IGL++ ++KFD  +GFR++TY  WW
Sbjct: 259 AREKLAMSNVRLVMSIAQRYDNLGAEMSDLVQGGLIGLLRGIEKFDSSKGFRISTYVYWW 318

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   ++ +   +++ T  +++       +L+   + IT +      +  IA+ LN+
Sbjct: 319 IRQGVSRALVDNSRTLRLPTHLHERLGLIRNAKLRLQEKGITPS------IDRIAESLNM 372

Query: 169 SESEV 173
           S+ +V
Sbjct: 373 SQKKV 377


>gi|224553536|gb|ACN55006.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553538|gb|ACN55007.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553540|gb|ACN55008.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553542|gb|ACN55009.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553546|gb|ACN55011.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553548|gb|ACN55012.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553550|gb|ACN55013.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553552|gb|ACN55014.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553554|gb|ACN55015.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553556|gb|ACN55016.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553558|gb|ACN55017.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553560|gb|ACN55018.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553562|gb|ACN55019.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553564|gb|ACN55020.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553566|gb|ACN55021.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553568|gb|ACN55022.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553570|gb|ACN55023.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553572|gb|ACN55024.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553574|gb|ACN55025.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553576|gb|ACN55026.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553578|gb|ACN55027.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553580|gb|ACN55028.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553582|gb|ACN55029.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553584|gb|ACN55030.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553586|gb|ACN55031.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553588|gb|ACN55032.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553594|gb|ACN55035.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553596|gb|ACN55036.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553598|gb|ACN55037.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553600|gb|ACN55038.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553602|gb|ACN55039.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553604|gb|ACN55040.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553608|gb|ACN55042.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553610|gb|ACN55043.1| RNA polymerase sigma factor [Escherichia coli ETEC H10407]
 gi|224553612|gb|ACN55044.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553614|gb|ACN55045.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553616|gb|ACN55046.1| RNA polymerase sigma factor [Escherichia coli]
          Length = 111

 Score = 66.6 bits (161), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 24/47 (51%), Positives = 38/47 (80%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+
Sbjct: 1   GLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIM 47


>gi|29829555|ref|NP_824189.1| RNA polymerase sigma factor, sigH [Streptomyces avermitilis
           MA-4680]
 gi|29606663|dbj|BAC70724.1| putative RNA polymerase sigma factor, sigH [Streptomyces
           avermitilis MA-4680]
          Length = 391

 Score = 66.6 bits (161), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 64/235 (27%), Positives = 107/235 (45%), Gaps = 17/235 (7%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           +RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDPERG   +TY+   + 
Sbjct: 169 NRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPERGVEFSTYATPTVV 228

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
             ++ +       V++     + RL       +     ++  + +   V  +A+KL +SE
Sbjct: 229 GEIKRHFRDKGWAVRVPRRLQELRLALTTATAE-----LSQQHGRSPTVHELAEKLAISE 283

Query: 171 SEVISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
            EV      L G ES NA    S D   +  +   V D  G E   +E  E    R  L 
Sbjct: 284 EEV------LEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVE---YRESLK 334

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 335 PLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLREKL 387


>gi|26665380|dbj|BAC44901.1| principal sigma factor [Chlorogloeopsis fritschii PCC 6912]
          Length = 198

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 57/212 (26%), Positives = 107/212 (50%), Gaps = 19/212 (8%)

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           +VV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+   I  
Sbjct: 1   MVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIAD 60

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAIT-DNNLKP-EQVVAIAKKLNVSESEVISMN 177
               +++        L+  + R+K   + ++ +   KP E+ +A   ++ + +   I+ +
Sbjct: 61  QSRTIRLPV-----HLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKS 115

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLN 236
            +L    SL   I   +   S+  D++  + DG+     E +  KN  R  L + +  L+
Sbjct: 116 AQLPI--SLETPIGKEE--DSRLGDFI--ESDGETP---EDQVSKNLLREDLEKVLDSLS 166

Query: 237 PRERRIFEARRLQENP--VTLENLSSEFEVSR 266
           PRER +   R   ++    TLE +   F V+R
Sbjct: 167 PRERDVLRLRYGLDDGRMKTLEEIGQIFNVTR 198


>gi|256371428|ref|YP_003109252.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Acidimicrobium
           ferrooxidans DSM 10331]
 gi|256008012|gb|ACU53579.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Acidimicrobium
           ferrooxidans DSM 10331]
          Length = 254

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 63/244 (25%), Positives = 113/244 (46%), Gaps = 20/244 (8%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQAVKKFD 94
           +R++  GDL A +RL+  H   +V+        GLP S    ++ S G  GL+ A++KF+
Sbjct: 12  RRFKHDGDLEARNRLL-EHYASLVRFVASRVAVGLPASVDPNDLASYGTFGLIDALEKFE 70

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           PERG +  TY++  IK A+ +  LR+   V     A  K +      L+  L        
Sbjct: 71  PERGIKFETYAITRIKGAIIDE-LRAIDWVPRSVRAKAKSVEQAYAALEARLH------- 122

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +P     +A +L +SE E++++  +++  G   L+ ++ S ++         + D     
Sbjct: 123 RPPTDAEVASELGMSEDELLAIYSKISFLGLVGLDEVVMSGERGEGMTLGDTLADRRQSA 182

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
               E++E   RR ML  S++ L  RE+ +      +    TL  +     V+  R+ QI
Sbjct: 183 GGAFEEQE---RRRMLADSINQLADREKTVLVLYYYE--GFTLAEIGRILGVTESRICQI 237

Query: 273 EARA 276
            ++A
Sbjct: 238 HSKA 241


>gi|27884311|dbj|BAC55891.1| RNA polymerase sigma factor [Streptomyces griseus subsp. griseus]
          Length = 318

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 62/234 (26%), Positives = 106/234 (45%), Gaps = 17/234 (7%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+   +  
Sbjct: 97  RLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATPTVVG 156

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            ++ +       V++     + RL       +     ++  + +   V  +A++L +SE 
Sbjct: 157 EIKRHFRDKGWAVRVPRRLQELRLSLTTATAE-----LSQQHGRSPTVHELAERLGISEE 211

Query: 172 EVISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           EV      L G ES NA    S D   +  +   V D  G E   +E  E    R  L  
Sbjct: 212 EV------LEGLESANAYSTLSLDVPDTDDESPAVADTLGSEDEALEGVE---YRESLKP 262

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 263 LLEALPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLRERL 314


>gi|322384113|ref|ZP_08057831.1| sporulation sigma factor SigE-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321151193|gb|EFX44502.1| sporulation sigma factor SigE-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 233

 Score = 66.6 bits (161), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 37/94 (39%), Positives = 57/94 (60%), Gaps = 2/94 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  ++EEY+L K     GD +    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 32  PLTREEEEYLLGKL--PSGDAAIRAMLIERNLRLVVYIARKFENTGINIEDLVSIGAIGL 89

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  FDPE+  +LATY+   I+  +  Y+ R+
Sbjct: 90  IKAVNTFDPEKKIKLATYASRCIENEILMYLRRN 123


>gi|11993459|gb|AAG42748.1|AF299295_2 RNA polymerase sigma factor [Zymomonas mobilis]
          Length = 763

 Score = 66.2 bits (160), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 54/199 (27%), Positives = 98/199 (49%), Gaps = 12/199 (6%)

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I    +       L R   
Sbjct: 471 GLMKAVGKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI--PVHMIETINKLVRTSR 528

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            +         PE+   +A++L++   +V  +  ++A  E ++      D+  S   D++
Sbjct: 529 QILHEIGREPTPEE---LAERLSMPLEKVRKV-MKIA-KEPISLETPIGDEEDSHLGDFI 583

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEF 262
               D    + ++   + N +  +TR ++ L PRE R+   R         TLE +  +F
Sbjct: 584 ---EDKNAIIPVDAAIQANLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQF 640

Query: 263 EVSRERVRQIEARAFKKVQ 281
            V+RER+RQIEA+A +K++
Sbjct: 641 SVTRERIRQIEAKALRKLK 659


>gi|239980907|ref|ZP_04703431.1| RNA polymerase sigma factor, sigma F [Streptomyces albus J1074]
 gi|291452769|ref|ZP_06592159.1| transcription initiation factor sigma F [Streptomyces albus J1074]
 gi|291355718|gb|EFE82620.1| transcription initiation factor sigma F [Streptomyces albus J1074]
          Length = 294

 Score = 66.2 bits (160), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 64/244 (26%), Positives = 119/244 (48%), Gaps = 23/244 (9%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           EH  + +A  L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDP+RG +  
Sbjct: 66  EHARVRSA--LIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFP 123

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           T++M  +   ++ Y   +   V +      +RL     ++    + +T  + +      I
Sbjct: 124 TFAMPTVVGEIKRYFRDNVRTVHV-----PRRLHELWVQVTSATEDLTTAHGRSPTTAEI 178

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL--VYDHDGQEQVLIEKEE 220
           A++L +SE EV++  C  AG        +++   ++Q  D L  + D  G E   ++  E
Sbjct: 179 AERLRISEDEVLA--CIEAGRS-----YHATSLEAAQEGDGLPGLLDRLGYEDPALDGVE 231

Query: 221 RKNRRNMLTRSMSVLNP-RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
            ++    L R + V  P RE+RI   R      +T   +S+E  VS+  V ++ AR+F +
Sbjct: 232 HRD----LVRHLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLLARSFAR 285

Query: 280 VQES 283
           ++ +
Sbjct: 286 LRSA 289


>gi|254384657|ref|ZP_04999996.1| RNA polymerase sigma factor [Streptomyces sp. Mg1]
 gi|194343541|gb|EDX24507.1| RNA polymerase sigma factor [Streptomyces sp. Mg1]
          Length = 334

 Score = 66.2 bits (160), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 63/234 (26%), Positives = 106/234 (45%), Gaps = 17/234 (7%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+   +  
Sbjct: 113 RLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATPTVVG 172

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            ++ +       V++     + RL      L      ++  + +   V  +A++L +SE 
Sbjct: 173 EIKRHFRDKGWAVRVPRRLQELRL-----SLTTATAELSQQHGRSPTVHELAERLGISEE 227

Query: 172 EVISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           EV      L G ES NA    S D   +  +   V D  G E   +E  E    R  L  
Sbjct: 228 EV------LEGLESANAYSTLSLDVPDTDDESPAVADTLGSEDEALEGVE---YRESLKP 278

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 279 LLEGLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLREKL 330


>gi|300689719|ref|YP_003750714.1| RNA polymerase sigma factor [Ralstonia solanacearum PSI07]
 gi|299076779|emb|CBM09897.1| putative RNA polymerase sigma factor [Ralstonia solanacearum PSI07]
          Length = 907

 Score = 66.2 bits (160), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 70/265 (26%), Positives = 118/265 (44%), Gaps = 38/265 (14%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           RYR+H        ++ ++LRLV+ IA      GL + +++ EGN+GL++AV +FD  RGF
Sbjct: 548 RYRDH--------MMQANLRLVMDIARHRMHSGLRVEDLIQEGNLGLLKAVDRFDWRRGF 599

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           R +T ++WWIK  +   I           TA + RL  ++       Q I+    + E  
Sbjct: 600 RFSTMAIWWIKQQIGRGIF---------DTALEIRLPVHIH------QKISRGRRETESF 644

Query: 160 VAI-AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
             +  K  ++SE   I   C +  D+   A    S+  S +    + Y    +      +
Sbjct: 645 EHVRGKPASLSERATI---CNMTLDKFELAARALSEPLSIEGAQQVGYFKSEESDEPFAR 701

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE-----FEVSRERVRQIE 273
               +   ++   ++ L  ++  +    RL+     LE L+ E       V+RERVRQIE
Sbjct: 702 MSEDDDARLVEEVLTKLKTKDAEVL---RLRFGIGVLEALTLEQIGEILGVTRERVRQIE 758

Query: 274 ARAFKKVQESIQKQV---ELSSSPP 295
           A A +K+     ++     L   PP
Sbjct: 759 AAAMQKLSSPFSREALMKALGRVPP 783


>gi|168986257|dbj|BAG11810.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H6]
          Length = 177

 Score = 66.2 bits (160), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 26/55 (47%), Positives = 40/55 (72%)

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           IA  Y   GL + +++ EGN+GL++AV+KFDPERGF  +TY+ WWI+  ++  I+
Sbjct: 1   IARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFLFSTYATWWIRQTIERAIM 55


>gi|260893401|ref|YP_003239498.1| RNA polymerase, sigma 28 subunit, SigE [Ammonifex degensii KC4]
 gi|260865542|gb|ACX52648.1| RNA polymerase, sigma 28 subunit, SigE [Ammonifex degensii KC4]
          Length = 242

 Score = 66.2 bits (160), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 39/93 (41%), Positives = 58/93 (62%), Gaps = 1/93 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L+ +EE  L KR  E GD S  + LV  +LRLVV IA  Y   G+ + ++VS G+IGL
Sbjct: 38  PPLDAEEEAHLLKRL-EAGDQSVRNTLVERNLRLVVYIARKYESTGINLEDLVSIGSIGL 96

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           ++AV  F+P+R  +LATY+   I+  +  ++ R
Sbjct: 97  IKAVNTFNPQRKVKLATYASRCIENEILMFLRR 129


>gi|229086469|ref|ZP_04218641.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock3-44]
 gi|228696786|gb|EEL49599.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock3-44]
          Length = 239

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 70/264 (26%), Positives = 115/264 (43%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL  +  + GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLTKEEEEVLLNKLPK-GDQAARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I                      +  +  +LRR     
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCI----------------------ENEILMHLRR----- 128

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                               N + SEV       + DE LN      D N     D L  
Sbjct: 129 -------------------NNKNRSEV-------SFDEPLNI---DWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEV 264
           D D    ++ +  E    R++L +++  LN RE++I E R     E   T ++++    +
Sbjct: 160 DED----IITKDLEATVDRHLLMKALHQLNDREKQIMELRFGLAGEEEKTQKDVADMLGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 216 SQSYISRLEKRIIKRLRKEFNKMV 239


>gi|229031536|ref|ZP_04187536.1| RNA polymerase sigma-35 factor [Bacillus cereus AH1271]
 gi|229075661|ref|ZP_04208643.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock4-18]
 gi|229098375|ref|ZP_04229320.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock3-29]
 gi|229104467|ref|ZP_04235134.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock3-28]
 gi|229117401|ref|ZP_04246777.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock1-3]
 gi|229162840|ref|ZP_04290797.1| RNA polymerase sigma-35 factor [Bacillus cereus R309803]
 gi|229174571|ref|ZP_04302101.1| RNA polymerase sigma-35 factor [Bacillus cereus MM3]
 gi|228608876|gb|EEK66168.1| RNA polymerase sigma-35 factor [Bacillus cereus MM3]
 gi|228620722|gb|EEK77591.1| RNA polymerase sigma-35 factor [Bacillus cereus R309803]
 gi|228666011|gb|EEL21477.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock1-3]
 gi|228678909|gb|EEL33119.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock3-28]
 gi|228684992|gb|EEL38925.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock3-29]
 gi|228707437|gb|EEL59628.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock4-18]
 gi|228729825|gb|EEL80805.1| RNA polymerase sigma-35 factor [Bacillus cereus AH1271]
          Length = 239

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 70/264 (26%), Positives = 115/264 (43%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL  +  + GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLTKEEEEVLLNKLPK-GDQAARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I                      +  +  +LRR     
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCI----------------------ENEILMHLRR----- 128

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                               N + SEV       + DE LN      D N     D L  
Sbjct: 129 -------------------NNKNRSEV-------SFDEPLNI---DWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEV 264
           D D    ++ +  E    R++L +++  LN RE++I E R     E   T ++++    +
Sbjct: 160 DDD----IITKDLEATVDRHLLMKALHQLNDREKQIMELRFGLAGEEEKTQKDVADMLGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 216 SQSYISRLEKRIIKRLRKEFNKMV 239


>gi|325973333|ref|YP_004250397.1| RNA polymerase sigma factor rpoD [Mycoplasma suis str. Illinois]
 gi|325989768|ref|YP_004249467.1| RNA polymerase sigma factor [Mycoplasma suis KI3806]
 gi|323574853|emb|CBZ40513.1| RNA polymerase sigma factor [Mycoplasma suis]
 gi|323651935|gb|ADX98017.1| RNA polymerase sigma factor rpoD [Mycoplasma suis str. Illinois]
          Length = 530

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 28/78 (35%), Positives = 48/78 (61%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L+TS+LRLV+ +A  Y   G  + +++ EG  GL +A+ KFD + G + +TY+ WW
Sbjct: 236 AEKQLMTSNLRLVISVAKKYLNCGFNLGDLIQEGVFGLRKAITKFDYKFGNKFSTYATWW 295

Query: 109 IKAAMQEYILRSWSLVKI 126
           I+ A+   I     +++I
Sbjct: 296 IRQAITRSIADQSKIIRI 313


>gi|218289914|ref|ZP_03494104.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
 gi|218240054|gb|EED07240.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
          Length = 259

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 70/275 (25%), Positives = 127/275 (46%), Gaps = 45/275 (16%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           ++P+L   +   L ++ R  GDLSA  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  QLPVLTNAQMRELFEQLRA-GDLSAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEY------ILRSWSLVKIGTTANQKRLFFN 138
           GLM+A+  FD  +  R +TY++  I   ++ Y      I  S SL  I   A Q R    
Sbjct: 74  GLMKAIDNFDLNQNVRFSTYAVPMIVGEIRRYLRDNNPIRVSRSLRDIAYKALQVR---- 129

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
                     +   NL+   +V IA ++N+ + EV+          +L+A+ +      S
Sbjct: 130 --------DMLASKNLREPSIVEIANEMNLPKEEVVF---------ALDAIQDP----VS 168

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRN--------MLTRSMSVLNPRERRIFEARRLQE 250
            ++   +Y HDG + + +  +    R           L  +M  L+ RE++I  A+R  E
Sbjct: 169 MFEP--IY-HDGGDPIYVMDQIHDEREKDSAWVEGIALREAMRKLSDREKKIL-AKRFYE 224

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
               +E ++ E  +S+ +V ++E  A  ++ + IQ
Sbjct: 225 GKTQME-VADEIGISQAQVSRLEKAAIHRMYKHIQ 258


>gi|330375231|gb|AEC12842.1| RNA polymerase sigma factor RpoS [Pseudomonas fluorescens]
          Length = 200

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 58/202 (28%), Positives = 101/202 (50%), Gaps = 16/202 (7%)

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   LR  +   Q 
Sbjct: 1   AVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVYLRAARELTQK 59

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYD 207
           + D+   PE++  + +K       ++ +N R++  D SL      SDK      D L  D
Sbjct: 60  L-DHEPSPEEIANLLEKPVAEVKRMLGLNERVSSVDVSLGP---DSDKT---LLDTLTDD 112

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEV 264
                  L++ ++       + + +S L  ++R +   R   R  E+  TLE++  E  +
Sbjct: 113 RPTDPCELLQDDDLSQS---IDQWLSELTEKQREVVVRRFGLRGHESS-TLEDVGLEIGL 168

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           +RERVRQI+    K+++E ++K
Sbjct: 169 TRERVRQIQVEGLKRLREILEK 190


>gi|297158638|gb|ADI08350.1| RNA polymerase sigma factor, sigma F [Streptomyces bingchenggensis
           BCW-1]
          Length = 277

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 65/244 (26%), Positives = 118/244 (48%), Gaps = 23/244 (9%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           EHG +  A  L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDPERG +  
Sbjct: 49  EHGRVRDA--LIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQFP 106

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           T++M  +   ++ Y   +   V +      +RL     ++ G  + +T  + +      I
Sbjct: 107 TFAMPTVVGEIKRYFRDNVRTVHV-----PRRLHELWVQVNGATEDLTVLHGRSPTTAEI 161

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL--VYDHDGQEQVLIEKEE 220
           A++L + E EV++  C  AG        +++   ++Q  D L  + D  G E   +   E
Sbjct: 162 AERLGLGEDEVLA--CIEAGRS-----YHATSLEAAQEGDGLPGLVDRLGYEDPALAGVE 214

Query: 221 RKNRRNMLTRSMSVLNP-RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
            ++    L R + V  P RE+RI   R      +T   +S+E  VS+  V ++ +R+F +
Sbjct: 215 HRD----LVRHLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLLSRSFAR 268

Query: 280 VQES 283
           ++ +
Sbjct: 269 LRSA 272


>gi|302392455|ref|YP_003828275.1| RNA polymerase, sigma subunit, RpoX/SigF [Acetohalobium arabaticum
           DSM 5501]
 gi|302204532|gb|ADL13210.1| RNA polymerase, sigma subunit, RpoX/SigF [Acetohalobium arabaticum
           DSM 5501]
          Length = 253

 Score = 66.2 bits (160), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 62/240 (25%), Positives = 118/240 (49%), Gaps = 16/240 (6%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A  +LV  +++LV+K+A  +        E+   G+IGL++A+++FD ER  + +TY
Sbjct: 29  GDQKAKDKLVNHNVKLVLKVAHRFANKNYDYEELFQIGSIGLLKAIERFDLERDVKFSTY 88

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           ++  I   ++ + LR    VK+  +   KR    +  +K  L A  + N +P  +  IA+
Sbjct: 89  AVPLIIGEIKRF-LRDDDAVKVSRSL--KRRAHRINEVKESLTA--ELNREP-TIQEIAE 142

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           ++ V + E+++    +    S+ + +  ++ NS +  D L    + QEQ +         
Sbjct: 143 EMEVDKEEIVNALEAVREPTSIYSPVYENEGNSIELVDQLAASSENQEQEI--------D 194

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L   +  L  RER I + R   E   T + ++    VS+ +V ++E +   KV+E +
Sbjct: 195 RLALREVIDELKTRERLILKLRFFDEK--TQQEVADRIGVSQVQVSRLERKIIDKVREEL 252


>gi|225175485|ref|ZP_03729479.1| RNA polymerase, sigma 28 subunit, SigE [Dethiobacter alkaliphilus
           AHT 1]
 gi|225168814|gb|EEG77614.1| RNA polymerase, sigma 28 subunit, SigE [Dethiobacter alkaliphilus
           AHT 1]
          Length = 243

 Score = 65.9 bits (159), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 71/262 (27%), Positives = 117/262 (44%), Gaps = 63/262 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L + EE  L ++ +  GD +    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 41  PPLSQDEEGFLLEKLK-TGDYAVKAVLIERNLRLVVYIARKFENTGILIDDLVSIGTIGL 99

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FDP +  +LATY+   I+                    N+  +F  LRR     
Sbjct: 100 IKAVNTFDPHKNIKLATYASKCIE--------------------NEILMF--LRR----- 132

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
               +N +K E                      ++ DE LN      D N     D L  
Sbjct: 133 ----NNKVKAE----------------------VSFDEPLNV---DWDGNELLLSDVLGT 163

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEV 264
           ++D    ++I+  E +  R +L  ++  LN RE+RI E R   L +   T + ++    +
Sbjct: 164 END----LVIKGIEAEVERKLLYNAIEKLNRREKRIMELRFGLLGQEEKTQKEVAVMLGI 219

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+  + ++E R  K++Q+ I+K
Sbjct: 220 SQSYISRLEKRIIKRLQKEIRK 241


>gi|188589224|ref|YP_001920224.1| RNA polymerase sigma-D factor [Clostridium botulinum E3 str. Alaska
           E43]
 gi|251778902|ref|ZP_04821822.1| RNA polymerase sigma-D factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
 gi|188499505|gb|ACD52641.1| RNA polymerase sigma-D factor [Clostridium botulinum E3 str. Alaska
           E43]
 gi|243083217|gb|EES49107.1| RNA polymerase sigma-D factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
          Length = 242

 Score = 65.9 bits (159), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 65/252 (25%), Positives = 119/252 (47%), Gaps = 43/252 (17%)

Query: 52  RLVTSHLRLVVKIA----MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           ++V  ++ LV  IA    +G   Y +   ++VS G IGLM A+ KF+P++G + ++Y+  
Sbjct: 12  QIVKEYIPLVKYIASRIMIGKNKY-MEYEDLVSYGIIGLMDAISKFNPDKGMKFSSYASI 70

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            IK A+ + I ++  + K             L R    ++++ +  L+   ++ IA+ L 
Sbjct: 71  RIKGAIIDQIRKNRPITKGAMDK--------LNRYNSAIESLQNKLLREPNILEIAQYLE 122

Query: 168 VSESEV---------ISM----NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +S  EV         ISM    N   + DE +N L    DKNS   +  L          
Sbjct: 123 LSLQEVSQIENYINHISMVSLENIIFSDDEEVNLLGIIEDKNSPSPEGEL---------- 172

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
                E K +  +L+ ++ +L  +E+ I      ++  +TL+ + S   VS  RV Q+ A
Sbjct: 173 -----EEKEQLEVLSDAIKLLKEKEQLILNLYYYEK--LTLKEIGSILSVSESRVCQLHA 225

Query: 275 RAFKKVQESIQK 286
           R+   ++E+++K
Sbjct: 226 RSISNLREAMKK 237


>gi|315646039|ref|ZP_07899160.1| sporulation sigma factor SigE [Paenibacillus vortex V453]
 gi|315278800|gb|EFU42114.1| sporulation sigma factor SigE [Paenibacillus vortex V453]
          Length = 240

 Score = 65.9 bits (159), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 36/94 (38%), Positives = 58/94 (61%), Gaps = 2/94 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ +++EE++L K     GD +    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 39  PLTKEEEEFLLKKL--PSGDAATRAMLIERNLRLVVYIARKFENTGINIEDLVSIGAIGL 96

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  FDPE+  +LATY+   I+  +  Y+ R+
Sbjct: 97  IKAVNTFDPEKKIKLATYASRCIENEILMYLRRN 130


>gi|253573548|ref|ZP_04850891.1| RNA polymerase sigma factor [Paenibacillus sp. oral taxon 786 str.
           D14]
 gi|251847076|gb|EES75081.1| RNA polymerase sigma factor [Paenibacillus sp. oral taxon 786 str.
           D14]
          Length = 262

 Score = 65.9 bits (159), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 68/259 (26%), Positives = 129/259 (49%), Gaps = 20/259 (7%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQAVKK 92
           L +R++EHGDL A  +L+  +L +V  ++ G    GLP +    ++ S G +GL+ AV+K
Sbjct: 14  LWERWKEHGDLEAKKQLIEKYLPIVDYVS-GRLAVGLPKNVSKDDLASNGVMGLIDAVEK 72

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL-KGHLQAITD 151
           FD +RG +  TY+ W ++ A+ +  LR    V        K++    + L + +L+++TD
Sbjct: 73  FDYKRGLQFETYASWRVRGAILDG-LRQGDWVPRSVREKAKKIEEGYQHLEQQYLRSVTD 131

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
             +        +  LNVSE E  SM   +A   +L +L +   +  S+ +  L+ D   +
Sbjct: 132 AEM--------SSYLNVSEKEFQSMLQEVAV-MTLCSLEDPIREEESETRLTLLVDEKAK 182

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
                 +E     R  L + +  L  +ER +     L    ++L  ++    +S  R+ Q
Sbjct: 183 NPDYKVRE--FYLRESLAKGIEKLTEKERTVVSL--LYYEDLSLSEIAEVMSLSPSRISQ 238

Query: 272 IEARAFKKVQESIQKQVEL 290
           + ++A  +++ S++KQ +L
Sbjct: 239 LHSKAILRLRGSLEKQRDL 257


>gi|302536824|ref|ZP_07289166.1| RNA polymerase sigma-F factor [Streptomyces sp. C]
 gi|302445719|gb|EFL17535.1| RNA polymerase sigma-F factor [Streptomyces sp. C]
          Length = 332

 Score = 65.9 bits (159), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 63/234 (26%), Positives = 106/234 (45%), Gaps = 17/234 (7%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+   +  
Sbjct: 111 RLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATPTVVG 170

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            ++ +       V++     + RL      L      ++  + +   V  +A++L +SE 
Sbjct: 171 EIKRHFRDKGWAVRVPRRLQELRL-----SLTTATAELSQQHGRSPTVHELAERLGISEE 225

Query: 172 EVISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           EV      L G ES NA    S D   +  +   V D  G E   +E  E    R  L  
Sbjct: 226 EV------LEGLESANAYSTLSLDVPDTDDESPAVADTLGSEDEALEGVE---YRESLKP 276

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 277 LLEGLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLREKL 328


>gi|302552549|ref|ZP_07304891.1| RNA polymerase sigma-B factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302470167|gb|EFL33260.1| RNA polymerase sigma-B factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 289

 Score = 65.9 bits (159), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 64/244 (26%), Positives = 119/244 (48%), Gaps = 23/244 (9%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           EH  +  A  L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDP+RG +  
Sbjct: 61  EHDRVRGA--LIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFP 118

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           T++M  +   ++ Y   +   V +      +RL     ++    + +T +  +      I
Sbjct: 119 TFAMPTVVGEIKRYFRDNVRTVHV-----PRRLHELWVQVNSATEDLTTSFGRTPTTAEI 173

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL--VYDHDGQEQVLIEKEE 220
           A++L ++E EV+S  C  AG        +++   ++Q  D L  + D  G E   ++  E
Sbjct: 174 AERLRITEDEVLS--CIEAGRS-----YHATSLEAAQEGDGLPGLLDRLGYEDPALDGVE 226

Query: 221 RKNRRNMLTRSMSVLNP-RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
            ++    L R + V  P RE+RI   R      +T   +S+E  VS+  V ++ AR+F++
Sbjct: 227 HRD----LVRHLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLLARSFQR 280

Query: 280 VQES 283
           ++ +
Sbjct: 281 LRSA 284


>gi|261405673|ref|YP_003241914.1| sporulation sigma factor SigE [Paenibacillus sp. Y412MC10]
 gi|329922715|ref|ZP_08278267.1| RNA polymerase sigma-E factor [Paenibacillus sp. HGF5]
 gi|261282136|gb|ACX64107.1| RNA polymerase, sigma 28 subunit, SigE [Paenibacillus sp. Y412MC10]
 gi|328942057|gb|EGG38340.1| RNA polymerase sigma-E factor [Paenibacillus sp. HGF5]
          Length = 240

 Score = 65.9 bits (159), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 36/94 (38%), Positives = 58/94 (61%), Gaps = 2/94 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ +++EE++L K     GD +    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 39  PLTKEEEEFLLKKL--PTGDAATRAMLIERNLRLVVYIARKFENTGINIEDLVSIGAIGL 96

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  FDPE+  +LATY+   I+  +  Y+ R+
Sbjct: 97  IKAVNTFDPEKKIKLATYASRCIENEILMYLRRN 130


>gi|239990645|ref|ZP_04711309.1| RNA polymerase sigma factor [Streptomyces roseosporus NRRL 11379]
          Length = 309

 Score = 65.9 bits (159), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 63/234 (26%), Positives = 106/234 (45%), Gaps = 17/234 (7%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+   +  
Sbjct: 88  RLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATPTVVG 147

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            ++ +       V++     + RL      L      ++  + +   V  +A++L +SE 
Sbjct: 148 EIKRHFRDKGWAVRVPRRLQELRL-----SLTTATAELSQQHGRSPTVHELAERLGISEE 202

Query: 172 EVISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           EV      L G ES NA    S D   +  +   V D  G E   +E  E    R  L  
Sbjct: 203 EV------LEGLESANAYSTLSLDVPDTDDESPAVADTLGSEDEALEGVE---YRESLKP 253

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 254 LLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLRERL 305


>gi|5732893|gb|AAD49326.1|AF162936_2 RNA polymerase alternative sigma factor [Streptomyces coelicolor
           A3(2)]
          Length = 354

 Score = 65.9 bits (159), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 66/240 (27%), Positives = 110/240 (45%), Gaps = 29/240 (12%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+   +  
Sbjct: 133 RLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATPTVVG 192

Query: 112 AMQEYIL-RSWSLVKIGTTANQKRLFFN-----LRRLKGHLQAITDNNLKPEQVVAIAKK 165
            ++ +   + W+ V++     + RL        L +L G    + +          +A+K
Sbjct: 193 EIKRHFRDKGWA-VRVPRRLQELRLALTTATAELSQLHGRSPTVHE----------LAEK 241

Query: 166 LNVSESEVISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           L++SE EV      L G ES NA    S D   +  +   V D  G E   +E  E    
Sbjct: 242 LSISEEEV------LEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVE---Y 292

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 293 RESLKPLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLREKL 350


>gi|239944189|ref|ZP_04696126.1| RNA polymerase sigma factor [Streptomyces roseosporus NRRL 15998]
          Length = 284

 Score = 65.9 bits (159), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 63/234 (26%), Positives = 106/234 (45%), Gaps = 17/234 (7%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+   +  
Sbjct: 63  RLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATPTVVG 122

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            ++ +       V++     + RL      L      ++  + +   V  +A++L +SE 
Sbjct: 123 EIKRHFRDKGWAVRVPRRLQELRL-----SLTTATAELSQQHGRSPTVHELAERLGISEE 177

Query: 172 EVISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           EV      L G ES NA    S D   +  +   V D  G E   +E  E    R  L  
Sbjct: 178 EV------LEGLESANAYSTLSLDVPDTDDESPAVADTLGSEDEALEGVE---YRESLKP 228

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 229 LLEDLPPREKRILLLRFF--GNMTQSQIAQEVGISQMHVSRLLARTLAQLRERL 280


>gi|256785278|ref|ZP_05523709.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
          Length = 354

 Score = 65.9 bits (159), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 66/240 (27%), Positives = 110/240 (45%), Gaps = 29/240 (12%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+   +  
Sbjct: 133 RLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATPTVVG 192

Query: 112 AMQEYIL-RSWSLVKIGTTANQKRLFFN-----LRRLKGHLQAITDNNLKPEQVVAIAKK 165
            ++ +   + W+ V++     + RL        L +L G    + +          +A+K
Sbjct: 193 EIKRHFRDKGWA-VRVPRRLQELRLALTTATAELSQLHGRSPTVHE----------LAEK 241

Query: 166 LNVSESEVISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           L++SE EV      L G ES NA    S D   +  +   V D  G E   +E  E    
Sbjct: 242 LSISEEEV------LEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVE---Y 292

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 293 RESLKPLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLREKL 350


>gi|162139704|ref|YP_878335.2| sporulation sigma factor SigE [Clostridium novyi NT]
          Length = 235

 Score = 65.9 bits (159), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 37/94 (39%), Positives = 56/94 (59%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE  L  + R  GD S    L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 33  PPLSKEEEENLVNKIR-AGDDSVRTILIERNLRLVVYIARKFENSGILVEDLISVGTIGL 91

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  FDPE+  +LATY+   I+  +  Y+ R+
Sbjct: 92  IKAVNTFDPEKKIKLATYASRCIENEILMYLRRN 125


>gi|291447660|ref|ZP_06587050.1| RNA polymerase sigma factor [Streptomyces roseosporus NRRL 15998]
 gi|291350607|gb|EFE77511.1| RNA polymerase sigma factor [Streptomyces roseosporus NRRL 15998]
          Length = 318

 Score = 65.5 bits (158), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 63/234 (26%), Positives = 106/234 (45%), Gaps = 17/234 (7%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+   +  
Sbjct: 97  RLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATPTVVG 156

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            ++ +       V++     + RL      L      ++  + +   V  +A++L +SE 
Sbjct: 157 EIKRHFRDKGWAVRVPRRLQELRL-----SLTTATAELSQQHGRSPTVHELAERLGISEE 211

Query: 172 EVISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           EV      L G ES NA    S D   +  +   V D  G E   +E  E    R  L  
Sbjct: 212 EV------LEGLESANAYSTLSLDVPDTDDESPAVADTLGSEDEALEGVE---YRESLKP 262

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 263 LLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLRERL 314


>gi|289769170|ref|ZP_06528548.1| SigH protein [Streptomyces lividans TK24]
 gi|289699369|gb|EFD66798.1| SigH protein [Streptomyces lividans TK24]
          Length = 361

 Score = 65.5 bits (158), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 65/239 (27%), Positives = 107/239 (44%), Gaps = 27/239 (11%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+   +  
Sbjct: 140 RLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATPTVVG 199

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFN-----LRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            ++ +       V++     + RL        L +L G    + +          +A+KL
Sbjct: 200 EIKRHFRDKGWAVRVPRRLQELRLALTTATAELSQLHGRSPTVHE----------LAEKL 249

Query: 167 NVSESEVISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           ++SE EV      L G ES NA    S D   +  +   V D  G E   +E  E    R
Sbjct: 250 SISEEEV------LEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVE---YR 300

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 301 ESLKPLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLREKL 357


>gi|302558487|ref|ZP_07310829.1| RNA polymerase sigma factor [Streptomyces griseoflavus Tu4000]
 gi|302476105|gb|EFL39198.1| RNA polymerase sigma factor [Streptomyces griseoflavus Tu4000]
          Length = 281

 Score = 65.5 bits (158), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 67/240 (27%), Positives = 109/240 (45%), Gaps = 29/240 (12%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+   +  
Sbjct: 60  RLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATPTVVG 119

Query: 112 AMQEYIL-RSWSLVKIGTTANQKRLFFN-----LRRLKGHLQAITDNNLKPEQVVAIAKK 165
            ++ +   + W+ V++     + RL        L +L G          +   V  +A+K
Sbjct: 120 EIKRHFRDKGWA-VRVPRRLQELRLALTTATAELSQLHG----------RSPTVHELAEK 168

Query: 166 LNVSESEVISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           L +SE EV      L G ES NA    S D   +  +   V D  G E   +E  E    
Sbjct: 169 LAISEEEV------LEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVE---Y 219

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 220 RESLKPLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLREKL 277


>gi|320008631|gb|ADW03481.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 320

 Score = 65.5 bits (158), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 63/235 (26%), Positives = 109/235 (46%), Gaps = 19/235 (8%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+   +  
Sbjct: 99  RLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATPTVVG 158

Query: 112 AMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            ++ +   + W+ V++     + RL       +     ++  + +   V  +A++L +SE
Sbjct: 159 EIKRHFRDKGWA-VRVPRRLQELRLSLTTATAE-----LSQQHGRSPTVHELAERLGISE 212

Query: 171 SEVISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
            EV      L G ES NA    S D   +  +   V D  G E   +E  E    R  L 
Sbjct: 213 EEV------LEGLESANAYSTLSLDVPDTDDESPAVADTLGSEDEALEGVE---YRESLK 263

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 264 PLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLRERL 316


>gi|118134194|gb|ABK61238.1| RNA polymerase sigma-E factor [Clostridium novyi NT]
          Length = 230

 Score = 65.5 bits (158), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 37/94 (39%), Positives = 56/94 (59%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE  L  + R  GD S    L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 28  PPLSKEEEENLVNKIR-AGDDSVRTILIERNLRLVVYIARKFENSGILVEDLISVGTIGL 86

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  FDPE+  +LATY+   I+  +  Y+ R+
Sbjct: 87  IKAVNTFDPEKKIKLATYASRCIENEILMYLRRN 120


>gi|251797867|ref|YP_003012598.1| sporulation sigma factor SigE [Paenibacillus sp. JDR-2]
 gi|247545493|gb|ACT02512.1| RNA polymerase, sigma 28 subunit, SigE [Paenibacillus sp. JDR-2]
          Length = 240

 Score = 65.5 bits (158), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 37/94 (39%), Positives = 57/94 (60%), Gaps = 2/94 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  ++EEY+L K     GD +    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 39  PLTREEEEYLLDKL--PSGDTAIRAMLIERNLRLVVYIARKFENTGIHIEDLVSIGAIGL 96

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  FDPE+  +LATY+   I+  +  Y+ R+
Sbjct: 97  IKAVNTFDPEKKIKLATYASRCIENEILMYLRRN 130


>gi|220931758|ref|YP_002508666.1| sporulation sigma factor SigE [Halothermothrix orenii H 168]
 gi|219993068|gb|ACL69671.1| sporulation sigma factor SigE [Halothermothrix orenii H 168]
          Length = 245

 Score = 65.5 bits (158), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 39/91 (42%), Positives = 54/91 (59%), Gaps = 1/91 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE+ EE  L KR  E GD S    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 42  PPLEEDEEDYLLKRLSE-GDNSVRQLLIKHNLRLVVYIARKFSNTGIDIEDLVSIGTIGL 100

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           ++AVK FD  +  +LATY+   I+  +  Y+
Sbjct: 101 IKAVKTFDVNKNIKLATYASRCIENEILMYL 131


>gi|294501014|ref|YP_003564714.1| RNA polymerase sigma-E factor [Bacillus megaterium QM B1551]
 gi|295706363|ref|YP_003599438.1| RNA polymerase sigma-E factor [Bacillus megaterium DSM 319]
 gi|294350951|gb|ADE71280.1| RNA polymerase sigma-E factor [Bacillus megaterium QM B1551]
 gi|294804022|gb|ADF41088.1| RNA polymerase sigma-E factor [Bacillus megaterium DSM 319]
          Length = 239

 Score = 65.5 bits (158), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 38/94 (40%), Positives = 57/94 (60%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K EE VL K+    GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLTKDEEEVLLKKL-PSGDEAARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN 129


>gi|168186813|ref|ZP_02621448.1| RNA polymerase sigma-E factor [Clostridium botulinum C str. Eklund]
 gi|169295137|gb|EDS77270.1| RNA polymerase sigma-E factor [Clostridium botulinum C str. Eklund]
          Length = 235

 Score = 65.5 bits (158), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 37/94 (39%), Positives = 56/94 (59%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE  L  + R  GD S    L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 33  PPLSKEEEESLVAKIR-AGDDSVRTILIERNLRLVVYIARKFENSGVLVEDLISVGTIGL 91

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  FDPE+  +LATY+   I+  +  Y+ R+
Sbjct: 92  IKAVNTFDPEKKIKLATYASRCIENEILMYLRRN 125


>gi|21223610|ref|NP_629389.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
 gi|5912531|emb|CAB56114.2| SigH protein [Streptomyces coelicolor A3(2)]
 gi|9968693|emb|CAC05976.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
          Length = 361

 Score = 65.5 bits (158), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 66/240 (27%), Positives = 110/240 (45%), Gaps = 29/240 (12%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+   +  
Sbjct: 140 RLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATPTVVG 199

Query: 112 AMQEYIL-RSWSLVKIGTTANQKRLFFN-----LRRLKGHLQAITDNNLKPEQVVAIAKK 165
            ++ +   + W+ V++     + RL        L +L G    + +          +A+K
Sbjct: 200 EIKRHFRDKGWA-VRVPRRLQELRLALTTATAELSQLHGRSPTVHE----------LAEK 248

Query: 166 LNVSESEVISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           L++SE EV      L G ES NA    S D   +  +   V D  G E   +E  E    
Sbjct: 249 LSISEEEV------LEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVE---Y 299

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 300 RESLKPLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLREKL 357


>gi|212639647|ref|YP_002316167.1| sporulation sigma factor SigE [Anoxybacillus flavithermus WK1]
 gi|212561127|gb|ACJ34182.1| DNA-directed RNA polymerase specialized sigma subunit sigE
           [Anoxybacillus flavithermus WK1]
          Length = 239

 Score = 65.5 bits (158), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 37/94 (39%), Positives = 58/94 (61%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE +L K+    GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLTKEEEEMLLKKL-PSGDETARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN 129


>gi|229542547|ref|ZP_04431607.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Bacillus
           coagulans 36D1]
 gi|229326967|gb|EEN92642.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Bacillus
           coagulans 36D1]
          Length = 259

 Score = 65.5 bits (158), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 65/275 (23%), Positives = 141/275 (51%), Gaps = 32/275 (11%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSE 81
           K+P  ++ +   L + ++++GD  A   LV  + +LV  +A  Y   R Y   I +V   
Sbjct: 3   KLPQPDQIDVNQLIQSFQQNGDKEAQEILVAHYQKLVESLARKYSKGRAYQEDIFQV--- 59

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLR 140
           G IGL+ A+++FDP  G    ++++  I   ++ ++  ++WS+         +R+     
Sbjct: 60  GIIGLLGAIQRFDPNIGKSFESFAIPTIIGEIKRFLRDKTWSV------HVPRRIKELGP 113

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVI-SMNCR-----LAGDESLNALINSSD 194
           R+K  ++ +T+   +  ++  IA  L +SE EV+ +M        L+ D S+ +    SD
Sbjct: 114 RIKSTVEKLTNELQRSPKIAEIAAHLEISEEEVLEAMEMSKSYHALSVDHSIES---DSD 170

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
            ++    D +  + DG E+V        N+R +L + + VL+ RER++     ++   ++
Sbjct: 171 GSTVTLLDMVGSEDDGYEKV--------NQRLVLEKVLHVLSERERQVIHYTYIEN--LS 220

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
            ++   +  +S+  V +++ RA KK++++I+ +++
Sbjct: 221 QKDTGEKLGISQMHVSRLQRRAIKKLRDAIEGELQ 255


>gi|328883833|emb|CCA57072.1| RNA polymerase sigma factor SigB [Streptomyces venezuelae ATCC
           10712]
          Length = 281

 Score = 65.5 bits (158), Expect = 9e-09,   Method: Compositional matrix adjust.
 Identities = 61/234 (26%), Positives = 112/234 (47%), Gaps = 21/234 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDP+RG +  T++M  +   
Sbjct: 61  LIEANLPLVRYAADRFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFPTFAMPTVVGE 120

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           ++ Y   +   V +      +RL     ++ G  + +T  + +      IA++L + E E
Sbjct: 121 IKRYFRDNVRTVHV-----PRRLHELWVQVNGATEDLTTAHGRSPTTAEIAERLRIGEDE 175

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWL--VYDHDGQEQVLIEKEERKNRRNMLTR 230
           V++  C  AG        +++   ++Q  D L  + D  G E   +   E ++    L R
Sbjct: 176 VLA--CIEAGRS-----YHATSLEAAQEGDGLPGLLDRLGYEDPALAGVEHRD----LVR 224

Query: 231 SMSVLNP-RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            + V  P RE+RI   R      +T   +S E  VS+  V ++ AR+F +++ +
Sbjct: 225 HLLVQLPEREQRILMLRYYSN--LTQSQISQELGVSQMHVSRLLARSFARLRSA 276


>gi|170691127|ref|ZP_02882293.1| sigma-70 region 3 domain protein [Burkholderia graminis C4D1M]
 gi|170144376|gb|EDT12538.1| sigma-70 region 3 domain protein [Burkholderia graminis C4D1M]
          Length = 202

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 50/197 (25%), Positives = 98/197 (49%), Gaps = 12/197 (6%)

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I    +       + R+    
Sbjct: 1   MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI--PVHMIETINKMNRISR-- 56

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           Q + +  L+P+    +A+K+ + E ++  +  ++A  E ++      D + S   D++  
Sbjct: 57  QILQETGLEPDPAT-LAEKMEMPEDKIRKI-MKIAK-EPISMETPIGDDDDSHLGDFI-- 111

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEV 264
             D       +     + R+++   +  L PRE ++   R   E     TLE +  +F+V
Sbjct: 112 -EDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDV 170

Query: 265 SRERVRQIEARAFKKVQ 281
           +RER+RQIEA+A +K++
Sbjct: 171 TRERIRQIEAKALRKLR 187


>gi|225055401|gb|ACN80687.1| Tsr7 [Streptomyces laurentii]
          Length = 336

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 61/234 (26%), Positives = 112/234 (47%), Gaps = 21/234 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDP+RG +  T++M  +   
Sbjct: 116 LIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFPTFAMPTVVGE 175

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           ++ Y   +   V +      +RL     ++ G  + +T  + +      IA++L + E E
Sbjct: 176 IKRYFRDNVRTVHV-----PRRLHELWVQVNGATEDLTTAHGRSPTTAEIAERLKIGEDE 230

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWL--VYDHDGQEQVLIEKEERKNRRNMLTR 230
           V++  C  AG        +++   ++Q  D L  + D  G E   +   E ++    L R
Sbjct: 231 VLA--CIEAGRS-----YHATSLEAAQEGDGLPGLLDRLGYEDPALAGVEHRD----LVR 279

Query: 231 SMSVLNP-RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            + V  P RE+RI   R      +T   +S E  VS+  V ++ AR+F +++ +
Sbjct: 280 HLLVQLPEREQRILMLRYYSN--LTQSQISQELGVSQMHVSRLLARSFARLRSA 331


>gi|224124068|ref|XP_002319237.1| predicted protein [Populus trichocarpa]
 gi|222857613|gb|EEE95160.1| predicted protein [Populus trichocarpa]
          Length = 499

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 68/252 (26%), Positives = 120/252 (47%), Gaps = 32/252 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  S++RLV+ IA      G  ++++V  G IGL++ ++KFD  +GF+++TY  WW
Sbjct: 256 AREKLAMSNVRLVMSIAQKNDNMGAEMADLVQAGLIGLLRGIEKFDSSKGFKISTYVYWW 315

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   ++ +   +++    +++       +++   + +T +      +  IA+ LN+
Sbjct: 316 IRQGVSRALVENPRTLRLPNHLHERLGLIRNAKIRLEEKGVTPS------IDRIAESLNM 369

Query: 169 SE------SEVISMNCRLAGDE--SLNALINSSD-----KNSSQWQDWLVYDHDGQEQVL 215
           S+      +E IS    L  +   SLN L   +       N  +   W    H   E  L
Sbjct: 370 SQRKVRNATEAISKVFSLDREAFPSLNGLPGETHHSYIADNRLENNPW----HGVDEWAL 425

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPVTLENLSSEFEVSRERVRQIEA 274
             KEE     N L  S   L  RER I      L +  +T E++S    +SRERVRQ+  
Sbjct: 426 --KEEV----NKLIDS--ALQEREREIIRLYHGLDKECLTWEDISKRMGLSRERVRQVGL 477

Query: 275 RAFKKVQESIQK 286
            A +K++ + +K
Sbjct: 478 VALEKLKHAARK 489


>gi|239826532|ref|YP_002949156.1| sporulation sigma factor SigE [Geobacillus sp. WCH70]
 gi|239806825|gb|ACS23890.1| RNA polymerase, sigma 28 subunit, SigE [Geobacillus sp. WCH70]
          Length = 239

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 37/94 (39%), Positives = 58/94 (61%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE +L K+    GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLTKEEEEMLIKKL-SSGDETARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN 129


>gi|333024500|ref|ZP_08452564.1| putative RNA polymerase sigma-F factor [Streptomyces sp. Tu6071]
 gi|332744352|gb|EGJ74793.1| putative RNA polymerase sigma-F factor [Streptomyces sp. Tu6071]
          Length = 356

 Score = 65.5 bits (158), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 64/235 (27%), Positives = 110/235 (46%), Gaps = 19/235 (8%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDPERG   +TY+   +  
Sbjct: 135 RLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPERGVEFSTYATPTVVG 194

Query: 112 AMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            ++ +   + W+ V++     + RL      L      ++  + +   V  +A++L++SE
Sbjct: 195 EIKRHFRDKGWA-VRVPRRLQELRL-----SLTSATAELSQQHGRSPTVHELAQRLSISE 248

Query: 171 SEVISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
            EV      L G ES NA    S D   +  +   V D  G E   +E  E    R  L 
Sbjct: 249 EEV------LEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVE---YRESLK 299

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   ++++ +
Sbjct: 300 PLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLRDKL 352


>gi|224553534|gb|ACN55005.1| RNA polymerase sigma factor [Escherichia coli]
          Length = 111

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 24/47 (51%), Positives = 37/47 (78%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  +   I+
Sbjct: 1   GLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIGRAIM 47


>gi|229061510|ref|ZP_04198854.1| RNA polymerase sigma-35 factor [Bacillus cereus AH603]
 gi|229134714|ref|ZP_04263523.1| RNA polymerase sigma-35 factor [Bacillus cereus BDRD-ST196]
 gi|229168645|ref|ZP_04296367.1| RNA polymerase sigma-35 factor [Bacillus cereus AH621]
 gi|228614801|gb|EEK71904.1| RNA polymerase sigma-35 factor [Bacillus cereus AH621]
 gi|228648760|gb|EEL04786.1| RNA polymerase sigma-35 factor [Bacillus cereus BDRD-ST196]
 gi|228717744|gb|EEL69394.1| RNA polymerase sigma-35 factor [Bacillus cereus AH603]
          Length = 232

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 69/264 (26%), Positives = 114/264 (43%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL  +   +GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 30  PPLTKEEEAVLLNKL-PNGDQAARSMLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 88

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I                      +  +  +LRR     
Sbjct: 89  IKAVNTFNPEKKIKLATYASRCI----------------------ENEILMHLRR----- 121

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                               N + SEV       + DE LN      D N     D L  
Sbjct: 122 -------------------NNKNRSEV-------SFDEPLNI---DWDGNELLLSDVLGT 152

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEV 264
           D D    ++ +  E    R++L +++  LN RE++I E R         T ++++    +
Sbjct: 153 DDD----IITKDLEATVDRHLLMKALHQLNDREKQIMELRFGLAGGEEKTQKDVADMLGI 208

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 209 SQSYISRLEKRIIKRLRKEFNKMV 232


>gi|302525186|ref|ZP_07277528.1| RNA polymerase sigma-G factor [Streptomyces sp. AA4]
 gi|302434081|gb|EFL05897.1| RNA polymerase sigma-G factor [Streptomyces sp. AA4]
          Length = 282

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 67/254 (26%), Positives = 114/254 (44%), Gaps = 19/254 (7%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFD 94
           +++ +  D ++  RLV  H   +VK   G  G GLP    + ++V  G  GL+ A++KFD
Sbjct: 40  QQFADKPDQTSRDRLVL-HYAPLVKYVAGRVGTGLPTHVDVGDLVQSGIFGLVDAIEKFD 98

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ-AITDNN 153
           PERG R  TY+M  I+ A+ +  LRS   V     +  K     L RL   L    TD  
Sbjct: 99  PERGLRFETYAMQRIRGAILDD-LRSQDWVPRAVRSKAKETARALERLGARLHRTPTDAE 157

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
           L  E        +++ +        RL    +L  L+ ++ K++    D L    DG   
Sbjct: 158 LAGEM------GISLDDLRDFYGQLRLTSVVALEDLV-AAGKDAGSLVDTL--PDDGAVD 208

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
            +    ++ NRR  L  +++ L  R++ +      +   +TL  +     V+  RV Q+ 
Sbjct: 209 PVAVLVDQDNRRQ-LAEAIAQLTDRDKIVVSLYYFES--LTLAEIGKVLGVTESRVSQLH 265

Query: 274 ARAFKKVQESIQKQ 287
            RA  +++  + +Q
Sbjct: 266 TRAVMRLRAKLMEQ 279


>gi|255527843|ref|ZP_05394691.1| RNA polymerase, sigma 28 subunit, SigK [Clostridium carboxidivorans
           P7]
 gi|296185444|ref|ZP_06853854.1| RNA polymerase sigma-K factor [Clostridium carboxidivorans P7]
 gi|255508454|gb|EET84846.1| RNA polymerase, sigma 28 subunit, SigK [Clostridium carboxidivorans
           P7]
 gi|296050278|gb|EFG89702.1| RNA polymerase sigma-K factor [Clostridium carboxidivorans P7]
          Length = 233

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 35/83 (42%), Positives = 53/83 (63%), Gaps = 2/83 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ +K+EEY L K+++E GDL A + LV  +LRLV  I   Y   G  + +++S G +GL
Sbjct: 30  PLNDKEEEYYL-KKFKE-GDLLAKNILVERNLRLVAHIVKKYSYPGKEVDDLISIGTVGL 87

Query: 87  MQAVKKFDPERGFRLATYSMWWI 109
           ++A+  FD  +G RLATY+   I
Sbjct: 88  IKAIDSFDASKGTRLATYAAKCI 110


>gi|290957490|ref|YP_003488672.1| sigma factor [Streptomyces scabiei 87.22]
 gi|260647016|emb|CBG70115.1| putative sigma factor [Streptomyces scabiei 87.22]
          Length = 388

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 63/234 (26%), Positives = 106/234 (45%), Gaps = 17/234 (7%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+   +  
Sbjct: 167 RLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATPTVVG 226

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            ++ +       V++     + RL       +     ++  + +   V  +A+KL +SE 
Sbjct: 227 EIKRHFRDKGWAVRVPRRLQELRLALTTATAE-----LSQQHGRSPTVHELAEKLAISEE 281

Query: 172 EVISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           EV      L G ES NA    S D   +  +   V D  G E   +E  E    R  L  
Sbjct: 282 EV------LEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVE---YRESLKP 332

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 333 LLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLREKL 384


>gi|182436064|ref|YP_001823783.1| RNA polymerase sigma factor [Streptomyces griseus subsp. griseus
           NBRC 13350]
 gi|326776688|ref|ZP_08235953.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
 gi|178464580|dbj|BAG19100.1| RNA polymerase sigma factor [Streptomyces griseus subsp. griseus
           NBRC 13350]
 gi|326657021|gb|EGE41867.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
          Length = 318

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 63/234 (26%), Positives = 106/234 (45%), Gaps = 17/234 (7%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+   +  
Sbjct: 97  RLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATPTVVG 156

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            ++ +       V++     + RL      L      ++  + +   V  +A++L +SE 
Sbjct: 157 EIKRHFRDKGWAVRVPRRLQELRL-----SLTTATAELSQQHGRSPTVHELAERLGISEE 211

Query: 172 EVISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           EV      L G ES NA    S D   +  +   V D  G E   +E  E    R  L  
Sbjct: 212 EV------LEGLESANAYSTLSLDVPDTDDESPAVADTLGSEDEALEGVE---YRESLKP 262

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 263 LLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLRERL 314


>gi|253682372|ref|ZP_04863169.1| RNA polymerase sigma-E factor [Clostridium botulinum D str. 1873]
 gi|253562084|gb|EES91536.1| RNA polymerase sigma-E factor [Clostridium botulinum D str. 1873]
          Length = 235

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 37/94 (39%), Positives = 56/94 (59%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE  L  + R  GD S    L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 33  PPLSKEEEENLVAKIR-AGDDSVRTILIERNLRLVVYIARKFENSGVLVEDLISVGTIGL 91

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  FDPE+  +LATY+   I+  +  Y+ R+
Sbjct: 92  IKAVNTFDPEKKIKLATYASRCIENEILMYLRRN 125


>gi|160943881|ref|ZP_02091111.1| hypothetical protein FAEPRAM212_01381 [Faecalibacterium prausnitzii
           M21/2]
 gi|158444557|gb|EDP21561.1| hypothetical protein FAEPRAM212_01381 [Faecalibacterium prausnitzii
           M21/2]
 gi|295104730|emb|CBL02274.1| RNA polymerase, sigma 29 subunit, SigE [Faecalibacterium
           prausnitzii SL3/3]
          Length = 234

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 37/94 (39%), Positives = 53/94 (56%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L  ++E  L  R    GD +A   L+T +LRLVV +A  Y   G+P  ++VS G IGL
Sbjct: 33  PPLTPEQEKALLDRM-AAGDAAAREELITHNLRLVVYLAKKYENSGVPAEDLVSIGTIGL 91

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  F P R  +LATY+   I   +  Y+ +S
Sbjct: 92  IKAVNTFTPARSIKLATYASRCIGNEILMYLRKS 125


>gi|163941644|ref|YP_001646528.1| sporulation sigma factor SigE [Bacillus weihenstephanensis KBAB4]
 gi|229013089|ref|ZP_04170254.1| RNA polymerase sigma-35 factor [Bacillus mycoides DSM 2048]
 gi|163863841|gb|ABY44900.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           weihenstephanensis KBAB4]
 gi|228748343|gb|EEL98203.1| RNA polymerase sigma-35 factor [Bacillus mycoides DSM 2048]
 gi|322510149|gb|ADX05463.1| RNA polymerase sigma-35 factor [Bacillus mycoides]
          Length = 239

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 69/264 (26%), Positives = 114/264 (43%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL  +   +GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLTKEEEAVLLNKL-PNGDQAARSMLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I                      +  +  +LRR     
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCI----------------------ENEILMHLRR----- 128

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                               N + SEV       + DE LN      D N     D L  
Sbjct: 129 -------------------NNKNRSEV-------SFDEPLNI---DWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEV 264
           D D    ++ +  E    R++L +++  LN RE++I E R         T ++++    +
Sbjct: 160 DDD----IITKDLEATVDRHLLMKALHQLNDREKQIMELRFGLAGGEEKTQKDVADMLGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 216 SQSYISRLEKRIIKRLRKEFNKMV 239


>gi|318060190|ref|ZP_07978913.1| RNA polymerase sigma factor, sigH [Streptomyces sp. SA3_actG]
 gi|318078835|ref|ZP_07986167.1| RNA polymerase sigma factor, sigH [Streptomyces sp. SA3_actF]
          Length = 356

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 64/235 (27%), Positives = 110/235 (46%), Gaps = 19/235 (8%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDPERG   +TY+   +  
Sbjct: 135 RLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPERGVEFSTYATPTVVG 194

Query: 112 AMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            ++ +   + W+ V++     + RL      L      ++  + +   V  +A++L++SE
Sbjct: 195 EIKRHFRDKGWA-VRVPRRLQELRL-----SLTSATAELSQQHGRSPTVHELAQRLSISE 248

Query: 171 SEVISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
            EV      L G ES NA    S D   +  +   V D  G E   +E  E    R  L 
Sbjct: 249 EEV------LEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVE---YRESLK 299

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   ++++ +
Sbjct: 300 PLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLRDKL 352


>gi|302391540|ref|YP_003827360.1| RNA polymerase, sigma 29 subunit, SigE [Acetohalobium arabaticum
           DSM 5501]
 gi|302203617|gb|ADL12295.1| RNA polymerase, sigma 29 subunit, SigE [Acetohalobium arabaticum
           DSM 5501]
          Length = 247

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 72/263 (27%), Positives = 113/263 (42%), Gaps = 65/263 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  ++E Y+L+K   + GD +    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 43  PLSNEEESYLLSKL--KEGDKAVRSVLIERNLRLVVYIARKFENTGIDIEDLVSIGTIGL 100

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FD  +  +LATY+   I+  +  Y                      LRR     
Sbjct: 101 IKAVNTFDVSKRIKLATYASRCIENEILMY----------------------LRR----- 133

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                NN K  ++                     + DE LN      D N  +  D L  
Sbjct: 134 -----NNKKKSEI---------------------SFDEPLNI---DWDGNELKLSDVLGT 164

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQEN--PVTLENLSSEFE 263
           D D   Q +    E    R +L ++M VL  RER+I   R  L E+   +T + ++    
Sbjct: 165 DMDLIYQYI----EEDVDRELLLQAMEVLTDRERKIMILRFGLGEDREEMTQKEVADILG 220

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+  + ++E R  KK+Q+ I K
Sbjct: 221 ISQSYISRLEKRIIKKLQQEISK 243


>gi|221309406|ref|ZP_03591253.1| sporulation sigma factor SigE [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221313731|ref|ZP_03595536.1| sporulation sigma factor SigE [Bacillus subtilis subsp. subtilis
           str. NCIB 3610]
 gi|221318655|ref|ZP_03599949.1| sporulation sigma factor SigE [Bacillus subtilis subsp. subtilis
           str. JH642]
 gi|221322928|ref|ZP_03604222.1| sporulation sigma factor SigE [Bacillus subtilis subsp. subtilis
           str. SMY]
 gi|255767354|ref|NP_389415.2| sporulation sigma factor SigE [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|296331108|ref|ZP_06873582.1| sporulation sigma factor SigE [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|305674263|ref|YP_003865935.1| sporulation-specific sigma factor sigma-E [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|321315297|ref|YP_004207584.1| sporulation sigma factor SigE [Bacillus subtilis BSn5]
 gi|133472|sp|P06222|RPSE_BACSU RecName: Full=RNA polymerase sigma-E factor; AltName: Full=P31;
           AltName: Full=Sigma-29; AltName: Full=Stage II
           sporulation protein GB; Flags: Precursor
 gi|40169|emb|CAA25620.1| unnamed protein product [Bacillus subtilis]
 gi|225184981|emb|CAB13406.2| RNA polymerase sporulation-specific sigma-29 factor (sigma-E)
           [Bacillus subtilis subsp. subtilis str. 168]
 gi|291484083|dbj|BAI85158.1| sporulation sigma factor SigE [Bacillus subtilis subsp. natto
           BEST195]
 gi|296151752|gb|EFG92627.1| sporulation sigma factor SigE [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|305412507|gb|ADM37626.1| sporulation-specific sigma factor sigma-E [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|320021571|gb|ADV96557.1| sporulation sigma factor SigE [Bacillus subtilis BSn5]
 gi|224259|prf||1012299A spoIIG gene
          Length = 239

 Score = 65.1 bits (157), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 68/264 (25%), Positives = 113/264 (42%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K EE VL  +   +GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLSKDEEQVLLMKL-PNGDQAARAILIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+                          
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN-------------------------- 129

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                               N   SEV       + DE LN      D N     D L  
Sbjct: 130 --------------------NKIRSEV-------SFDEPLNI---DWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEV 264
           D D    ++ +  E    + +L +++  LN RE++I E R   + E   T ++++    +
Sbjct: 160 DDD----IITKDIEANVDKKLLKKALEQLNEREKQIMELRFGLVGEEEKTQKDVADMMGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 216 SQSYISRLEKRIIKRLRKEFNKMV 239


>gi|329938754|ref|ZP_08288150.1| SigF-like sigma factor [Streptomyces griseoaurantiacus M045]
 gi|329302245|gb|EGG46137.1| SigF-like sigma factor [Streptomyces griseoaurantiacus M045]
          Length = 305

 Score = 64.7 bits (156), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 65/244 (26%), Positives = 116/244 (47%), Gaps = 23/244 (9%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           EH  +  A  L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDPERG +  
Sbjct: 77  EHDRVRGA--LIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQFP 134

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           T++M  +   ++ Y   +   V +      +RL     ++    + +T    +      I
Sbjct: 135 TFAMPTVVGEIKRYFRDNVRTVHV-----PRRLHELWVQVNSATEDLTTAFGRSPTTAEI 189

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL--VYDHDGQEQVLIEKEE 220
           A++L + E EV+S  C  AG        +++   ++Q  D L  + D  G E   ++  E
Sbjct: 190 AERLRIGEEEVLS--CIEAGRS-----YHATSLEAAQEGDGLPGLLDRLGYEDPALDGVE 242

Query: 221 RKNRRNMLTRSMSVLNP-RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
            ++    L R + V  P RE+RI   R      +T   +S+E  VS+  V ++ AR+F +
Sbjct: 243 HRD----LVRHLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLLARSFAR 296

Query: 280 VQES 283
           ++ +
Sbjct: 297 LRSA 300


>gi|56964116|ref|YP_175847.1| sporulation sigma factor SigE [Bacillus clausii KSM-K16]
 gi|56910359|dbj|BAD64886.1| DNA-directed RNA polymerase sigma-29 factor sigma-E [Bacillus
           clausii KSM-K16]
          Length = 237

 Score = 64.7 bits (156), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 70/268 (26%), Positives = 117/268 (43%), Gaps = 71/268 (26%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE  L  +    GD +    L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 35  PPLSKEEEAELLGKL-PSGDKAVRSVLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 93

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+                          
Sbjct: 94  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN-------------------------- 127

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ--DWL 204
                               N + SEV       + DE LN            W   + L
Sbjct: 128 --------------------NKTRSEV-------SFDEPLNI----------DWDGNELL 150

Query: 205 VYDHDGQEQVLIEK--EERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSS 260
           + D  G E+ +I +  EER +RR +L +++  L+ RE++I E R     E   T ++++ 
Sbjct: 151 LSDVLGTEEDIITRGIEERVDRR-LLVKALHTLSEREKQIMELRFGLAGEEEKTQKDVAD 209

Query: 261 EFEVSRERVRQIEARAFKKVQESIQKQV 288
              +S+  + ++E R  K++Q+   K V
Sbjct: 210 MLGISQSYISRLEKRIIKRLQKEFSKMV 237


>gi|187935068|ref|YP_001885063.1| RNA polymerase sigma-D factor [Clostridium botulinum B str. Eklund
           17B]
 gi|187723221|gb|ACD24442.1| RNA polymerase sigma-D factor [Clostridium botulinum B str. Eklund
           17B]
          Length = 242

 Score = 64.7 bits (156), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 68/258 (26%), Positives = 121/258 (46%), Gaps = 43/258 (16%)

Query: 46  DLSAAHRLVTSHLRLVVKIA----MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
           D     ++V  ++ LV  IA    +G   Y +   ++VS G IGLM A+ KF+PE+G + 
Sbjct: 6   DNDVKEQIVKEYIPLVKYIASRIMIGKNKY-MEYEDLVSYGIIGLMDAISKFNPEKGMKF 64

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           ++Y+   IK A+ + I ++  + K             L R  G ++A+ +  L+   ++ 
Sbjct: 65  SSYASIRIKGAIIDQIRKNRPITKGAMD--------KLNRYNGAIEALQNKLLREPNILE 116

Query: 162 IAKKLNVSESEV---------ISM----NCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           IAK L +S  EV         ISM    N   + DE +N L    DKNS   +       
Sbjct: 117 IAKYLELSLEEVSQIENYINHISMVSLENIIFSDDEEVNLLGIIEDKNSPSPE------- 169

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
                    + E K +  +L+ ++ +L  +E+ I      ++  +TL+ + +   VS  R
Sbjct: 170 --------GELEEKEKLEVLSDAIKLLKEKEQLILNLYYYEK--LTLKEIGAILSVSESR 219

Query: 269 VRQIEARAFKKVQESIQK 286
           V Q+ AR+   ++E+++K
Sbjct: 220 VCQLHARSISNLREAMKK 237


>gi|219124053|ref|XP_002182327.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217406288|gb|EEC46228.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 317

 Score = 64.7 bits (156), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 64/254 (25%), Positives = 119/254 (46%), Gaps = 32/254 (12%)

Query: 53  LVTSHLRLVVKIAM-----------GYRGYG--LPISEVVSEGNIGLMQAVKKFDPERGF 99
           LV ++L LV  +A              RG G  L + +++ EG +GLM+A ++F+PERG+
Sbjct: 67  LVAANLGLVTALAKRQLSTLQTATEAGRGVGTILTLQDLIQEGTLGLMKAAERFEPERGW 126

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA----ITDNNLK 155
           R +TY+ WW++  + + +  S   +++   A+       +++ K   QA     T ++L 
Sbjct: 127 RFSTYATWWVRQRILKSVSDSSRTIRL--PAHVHGTLQRIQKAKAWFQAHGEEATLSSLA 184

Query: 156 P--EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
              E  V   +    S   V+S+   L G  +        D+N+    D L  D    E+
Sbjct: 185 QYLELPVEKVRLYTDSSRNVMSLETPLKGRSAFK------DENTRTLGDTLASDEKTPEE 238

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQ 271
            +  +  R +  +++T+   VL   E+ +   R   E+    ++E  + +  VSR+R+R 
Sbjct: 239 DVEAQALRLDLEHVMTQ---VLTDVEQNVLRRRFGLEDGTCWSVEETARQLGVSRDRIRL 295

Query: 272 IEARAFKKVQESIQ 285
           +E RA  K++   Q
Sbjct: 296 VETRALNKLRHPQQ 309


>gi|294813860|ref|ZP_06772503.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|326442278|ref|ZP_08217012.1| RNA polymerase sigma factor, sigma F [Streptomyces clavuligerus
           ATCC 27064]
 gi|294326459|gb|EFG08102.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 335

 Score = 64.7 bits (156), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 61/234 (26%), Positives = 112/234 (47%), Gaps = 21/234 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDP+RG +  T++M  +   
Sbjct: 115 LIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFPTFAMPTVVGE 174

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           ++ Y   +   V +      +RL     ++ G  + +T  + +      IA++L + E E
Sbjct: 175 IKRYFRDNVRTVHV-----PRRLHELWVQVNGATEDLTTAHGRIPTTAEIAERLRIGEDE 229

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWL--VYDHDGQEQVLIEKEERKNRRNMLTR 230
           V++  C  AG        +++   ++Q  D L  + D  G E   +   E ++    L R
Sbjct: 230 VLA--CIEAGRS-----YHATSLEAAQEGDGLPGLLDRLGYEDPALAGVEHRD----LVR 278

Query: 231 SMSVLNP-RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            + V  P RE+RI   R      +T   +S E  VS+  V ++ AR+F +++ +
Sbjct: 279 HLLVQLPEREQRILMLRYYSN--LTQSQISQELGVSQMHVSRLLARSFARLRSA 330


>gi|3077740|dbj|BAA25788.1| SigC [Cyanidium caldarium]
          Length = 424

 Score = 64.7 bits (156), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 59/272 (21%), Positives = 116/272 (42%), Gaps = 44/272 (16%)

Query: 49  AAHRLVTSHLRLVVKIAMGYR---------------GYGLP--------------ISEVV 79
           A  RLV S+LRLV+ IA  Y+               G  +P              + +++
Sbjct: 143 ARARLVASNLRLVLAIANRYKSRAVVRSAWKSRSKGGMDMPSHEKVRLQRQHNIFLGDLI 202

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EG +GL++A +KFDP +GF+ +TY+ WWI+ A+Q  +      +++     +      +
Sbjct: 203 QEGALGLIRAAEKFDPSKGFKFSTYATWWIRQAIQRCVSEHSRTIRLPNHVTES--LRQI 260

Query: 140 RRLKGHLQAITDNNLKPEQVVAIA-------KKLNVSESEVISMNCRLAGDESLNALINS 192
            R++  LQ +       E+V           KK+     +  +++     +   ++L  S
Sbjct: 261 YRMRARLQHVLKRPPTDEEVAEACNMTLKRLKKITQHAWKTQTLSLEGPPNNEAHSLYKS 320

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQ 249
               +      ++   +   +  +E+   +     + R++     +ER I   R      
Sbjct: 321 QQGEAPLSIGSIIEATEETPEEALERNCMREDVECVLRTLPF---QEREILRLRYGISDD 377

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           E P + E LS+ F++    +R IE+RA +K++
Sbjct: 378 ERPHSTEELSARFQLPVHTIRLIESRALRKLR 409


>gi|254390382|ref|ZP_05005599.1| RNA polymerase sigma-F factor [Streptomyces clavuligerus ATCC
           27064]
 gi|197704086|gb|EDY49898.1| RNA polymerase sigma-F factor [Streptomyces clavuligerus ATCC
           27064]
          Length = 326

 Score = 64.7 bits (156), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 61/234 (26%), Positives = 112/234 (47%), Gaps = 21/234 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDP+RG +  T++M  +   
Sbjct: 106 LIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFPTFAMPTVVGE 165

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           ++ Y   +   V +      +RL     ++ G  + +T  + +      IA++L + E E
Sbjct: 166 IKRYFRDNVRTVHV-----PRRLHELWVQVNGATEDLTTAHGRIPTTAEIAERLRIGEDE 220

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWL--VYDHDGQEQVLIEKEERKNRRNMLTR 230
           V++  C  AG        +++   ++Q  D L  + D  G E   +   E ++    L R
Sbjct: 221 VLA--CIEAGRS-----YHATSLEAAQEGDGLPGLLDRLGYEDPALAGVEHRD----LVR 269

Query: 231 SMSVLNP-RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            + V  P RE+RI   R      +T   +S E  VS+  V ++ AR+F +++ +
Sbjct: 270 HLLVQLPEREQRILMLRYYSN--LTQSQISQELGVSQMHVSRLLARSFARLRSA 321


>gi|187932801|ref|YP_001885388.1| sporulation sigma factor SigE [Clostridium botulinum B str. Eklund
           17B]
 gi|187720954|gb|ACD22175.1| RNA polymerase sigma-E factor [Clostridium botulinum B str. Eklund
           17B]
          Length = 235

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 36/94 (38%), Positives = 54/94 (57%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K EE  L      HGD S    L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 33  PPLSKDEEETLVNNLM-HGDESIRSTLIERNLRLVVYIARKFENTGVHVEDLISVGTIGL 91

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+
Sbjct: 92  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN 125


>gi|219123705|ref|XP_002182160.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217406121|gb|EEC46061.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 319

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 61/248 (24%), Positives = 117/248 (47%), Gaps = 28/248 (11%)

Query: 53  LVTSHLRLVVKIAM-----------GYRGYG--LPISEVVSEGNIGLMQAVKKFDPERGF 99
           LV ++L LV  +A              RG G  L + +++ EG +GLM+A ++F+PERG+
Sbjct: 69  LVAANLGLVTALAKRQLSTLQTATEAGRGVGTILTLQDLIQEGTLGLMKAAERFEPERGW 128

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ--KRLFFNLRRLKGHLQAITDNNLKP- 156
           R +TY+ WW++  + + +  S   +++    +   +R+       + H +  T ++L   
Sbjct: 129 RFSTYATWWVRQRILKSVSDSSRTIRLPAHVHGTLQRIQKAKAWFRAHGEEATLSSLAQY 188

Query: 157 -EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
            E  V   +    S   V+S+   L G  +        D+N+    D L  D    E+ +
Sbjct: 189 LELPVEKVRLYTDSSRNVMSLETPLKGRSAFK------DENTRTLGDTLASDEKTPEENV 242

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIE 273
             +  R +  +++   + VL   E+ +   R   E+    +LE  + +  +SR+R+R +E
Sbjct: 243 EAQALRLDLEHVM---IKVLTDVEQNVLRRRFGLEDGTSWSLEETAKQLGMSRDRIRLVE 299

Query: 274 ARAFKKVQ 281
           ARA  K++
Sbjct: 300 ARALNKLR 307


>gi|29830728|ref|NP_825362.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29607841|dbj|BAC71897.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 309

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 64/244 (26%), Positives = 117/244 (47%), Gaps = 23/244 (9%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           EH  +  A  L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDP+RG +  
Sbjct: 81  EHSRVRGA--LIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFP 138

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           T++M  +   ++ Y   +   V +      +RL     ++    + +T    +      I
Sbjct: 139 TFAMPTVVGEIKRYFRDNVRTVHV-----PRRLHELWVQVNSATEDLTTAFGRSPTTAEI 193

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL--VYDHDGQEQVLIEKEE 220
           A++L ++E EV+S  C  AG        +++   ++Q  D L  + D  G E   ++  E
Sbjct: 194 AERLRITEEEVLS--CIEAGRS-----YHATSLEAAQEGDGLPGLLDRLGYEDPALDGVE 246

Query: 221 RKNRRNMLTRSMSVLNP-RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
            ++    L R + V  P RE+RI   R      +T   +S+E  VS+  V ++ AR+F +
Sbjct: 247 HRD----LVRHLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLLARSFAR 300

Query: 280 VQES 283
           ++ +
Sbjct: 301 LRSA 304


>gi|188587460|ref|YP_001919005.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|179352147|gb|ACB86417.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 273

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 70/277 (25%), Positives = 135/277 (48%), Gaps = 43/277 (15%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P++  +E   L +R  E GD  A   L+  +LRLV+ +   ++  G  + ++   G +
Sbjct: 15  KLPVISSEETQKLFERL-EQGDEQAKQELINGNLRLVLSVINKFKNRGENLDDLFQVGCL 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++AV  FDP++G + +TY++  I   ++ Y LR  S +++  +           +L G
Sbjct: 74  GLVKAVDNFDPKQGVKFSTYAVPMIMGEIKRY-LRDDSPMRVSRSL----------KLLG 122

Query: 145 HLQAITDNNLKPEQ-----VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
              A     L+ E+     +  +A +LN+S  E++               +NSS +  S 
Sbjct: 123 QEAAKAKEKLRKEKPYEPTIEELASELNISREELVEA-------------LNSSSEPLSL 169

Query: 200 WQDWLVYDHDGQEQVLI-----EKEERKNR--RNM-LTRSMSVLNPRERRIFEARRLQEN 251
           +    VY  D  + VL+     ++EER      NM L  +++ L  R+R I   RR  + 
Sbjct: 170 YDP--VY-SDSTDPVLLVDQIKDEEERLENWVENMTLKEAIAKLPERQRNIVN-RRFFKG 225

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
              +E +S E  +S+ +V ++E  A  ++++ ++++V
Sbjct: 226 QTQVE-VSDELNISQAQVSRLEKSALLQLRKLVKEEV 261


>gi|258645545|ref|ZP_05733014.1| RNA polymerase sigma-F factor [Dialister invisus DSM 15470]
 gi|260402901|gb|EEW96448.1| RNA polymerase sigma-F factor [Dialister invisus DSM 15470]
          Length = 205

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 45/159 (28%), Positives = 78/159 (49%), Gaps = 2/159 (1%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           LS YI  + K   L ++EE  L   Y+  G+L A  +L+  +  LV K A  Y      +
Sbjct: 2   LSEYISSLPKEGKLSREEEARLWDAYKNEGELEARQKLIEHYQLLVFKEATKYPVQETVL 61

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EG +GLM+A +KFD E+G   + Y++  I+  M +++ +  + + +G    +K  
Sbjct: 62  LDLIQEGTVGLMEAAEKFDIEQGVAFSLYAIHRIRGRMLDFLRKGQNDILMGEEQEEK-- 119

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVI 174
            F L+        +TD N     V     +L + E +VI
Sbjct: 120 LFTLQVAPDTAFEVTDRNSLHSAVSMAVSRLPMKEQDVI 158


>gi|188587739|ref|YP_001920535.1| sporulation sigma factor SigE [Clostridium botulinum E3 str. Alaska
           E43]
 gi|251779018|ref|ZP_04821938.1| RNA polymerase sigma-E factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
 gi|188498020|gb|ACD51156.1| RNA polymerase sigma-E factor [Clostridium botulinum E3 str. Alaska
           E43]
 gi|243083333|gb|EES49223.1| RNA polymerase sigma-E factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
          Length = 235

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 36/94 (38%), Positives = 54/94 (57%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K EE  L      HGD S    L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 33  PPLSKDEEETLVNNLM-HGDESIRSTLIERNLRLVVYIARKFENTGVHVEDLISVGTIGL 91

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+
Sbjct: 92  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN 125


>gi|329939708|ref|ZP_08289009.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
 gi|329301278|gb|EGG45173.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
          Length = 387

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 66/240 (27%), Positives = 109/240 (45%), Gaps = 29/240 (12%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+   +  
Sbjct: 166 RLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATPTVVG 225

Query: 112 AMQEYIL-RSWSLVKIGTTANQKRLFFN-----LRRLKGHLQAITDNNLKPEQVVAIAKK 165
            ++ +   + W+ V++     + RL        L +L G    + +          +A+K
Sbjct: 226 EIKRHFRDKGWA-VRVPRRLQELRLALTTATAELSQLHGRSPTVHE----------LAEK 274

Query: 166 LNVSESEVISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           L +SE EV      L G ES NA    S D   +  +   V D  G E   +E  E    
Sbjct: 275 LAISEEEV------LEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVE---Y 325

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 326 RESLKPLLEDLPPREKRILLLRFFAN--MTQSQIAQEVGISQMHVSRLLARTLAQLREKL 383


>gi|225026956|ref|ZP_03716148.1| hypothetical protein EUBHAL_01212 [Eubacterium hallii DSM 3353]
 gi|224955721|gb|EEG36930.1| hypothetical protein EUBHAL_01212 [Eubacterium hallii DSM 3353]
          Length = 275

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 46/159 (28%), Positives = 82/159 (51%), Gaps = 14/159 (8%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ E+ K   L  ++E V+A++    GD +A + L+ ++L   V+IA  Y G GL +S++
Sbjct: 109 YLKEMEKANSLSGEQERVIARKLV-SGDDTARNLLIEANLSRAVEIAKEYEGRGLLLSDL 167

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA----AMQEYILRSWSLVKIGTTANQKR 134
           + EGNIGLM AV +F+P+       +S   I+      ++EY   + S VK+    N+  
Sbjct: 168 IQEGNIGLMVAVNEFEPDIDKDFHAFSEKMIRKHLEETLEEYNSSTRSAVKMANRVNE-- 225

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
               +  +        +   KP +   IA+++ ++E EV
Sbjct: 226 ----MNDIATAFAKEYEREAKPSE---IAERMGITEEEV 257


>gi|52080135|ref|YP_078926.1| sporulation sigma factor SigE [Bacillus licheniformis ATCC 14580]
 gi|52785509|ref|YP_091338.1| sporulation sigma factor SigE [Bacillus licheniformis ATCC 14580]
 gi|319646087|ref|ZP_08000317.1| RNA polymerase sigma-E factor [Bacillus sp. BT1B_CT2]
 gi|52003346|gb|AAU23288.1| RNA polymerase sporulation-specific sigma-29 factor (sigma-E)
           [Bacillus licheniformis ATCC 14580]
 gi|52348011|gb|AAU40645.1| SigE [Bacillus licheniformis ATCC 14580]
 gi|317391837|gb|EFV72634.1| RNA polymerase sigma-E factor [Bacillus sp. BT1B_CT2]
          Length = 239

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 37/94 (39%), Positives = 57/94 (60%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K EE VL  +  + GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLSKDEEQVLLHKLPD-GDQAARAILIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN 129


>gi|228992638|ref|ZP_04152564.1| RNA polymerase sigma-G factor [Bacillus pseudomycoides DSM 12442]
 gi|228998684|ref|ZP_04158271.1| RNA polymerase sigma-G factor [Bacillus mycoides Rock3-17]
 gi|229006186|ref|ZP_04163872.1| RNA polymerase sigma-G factor [Bacillus mycoides Rock1-4]
 gi|228755027|gb|EEM04386.1| RNA polymerase sigma-G factor [Bacillus mycoides Rock1-4]
 gi|228761152|gb|EEM10111.1| RNA polymerase sigma-G factor [Bacillus mycoides Rock3-17]
 gi|228766970|gb|EEM15607.1| RNA polymerase sigma-G factor [Bacillus pseudomycoides DSM 12442]
          Length = 259

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 67/263 (25%), Positives = 124/263 (47%), Gaps = 21/263 (7%)

Query: 25  KIPMLEKQEEYVLAKRYRE--HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           K+P+L+ +E   + K +RE   G++SA  +LV  +LRLV+ +   +   G  + ++   G
Sbjct: 15  KLPVLKNEE---MRKLFREMQSGEISAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVG 71

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            IGLM+++  FD  +  + +TY++  I   ++ Y LR  + +++  +          + L
Sbjct: 72  CIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSLRD----IAYKAL 126

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
           +   + I +N+ +P   + IAK L V+  E++     +    SL   I +   +     D
Sbjct: 127 QVREKLIAENSKEP-TAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGGDPIFVMD 185

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
            L  D    EQ + E          L   M  LN RE+ I   R  Q    T   ++ E 
Sbjct: 186 QLSDDKQRDEQWVEEL--------ALKEGMKRLNDREKMIIRKRFFQGK--TQMEVAEEI 235

Query: 263 EVSRERVRQIEARAFKKVQESIQ 285
            +S+ +V ++E  A K++ ++IQ
Sbjct: 236 GISQAQVSRLEKSAIKQMNKTIQ 258


>gi|197303735|ref|ZP_03168772.1| hypothetical protein RUMLAC_02464 [Ruminococcus lactaris ATCC
           29176]
 gi|197297255|gb|EDY31818.1| hypothetical protein RUMLAC_02464 [Ruminococcus lactaris ATCC
           29176]
          Length = 265

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 36/91 (39%), Positives = 54/91 (59%), Gaps = 2/91 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+   +E+Y   K Y E GDL A H L+  +LRLV  I   Y+  G  + +++S G IGL
Sbjct: 66  PLTPDEEKYYFQK-YTE-GDLEAKHILIERNLRLVAHIVRKYQNLGEEMEDLISIGTIGL 123

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           ++AV  FDPE+G RLA Y+   ++  +  Y+
Sbjct: 124 IKAVISFDPEKGNRLAAYASRCVENEILMYL 154


>gi|254384106|ref|ZP_04999451.1| RNA polymerase sigma-F factor [Streptomyces sp. Mg1]
 gi|194342996|gb|EDX23962.1| RNA polymerase sigma-F factor [Streptomyces sp. Mg1]
          Length = 302

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 62/234 (26%), Positives = 114/234 (48%), Gaps = 21/234 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDP+RG +  T++M  +   
Sbjct: 82  LIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFPTFAMPTVVGE 141

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           ++ Y   +   V +      +RL     ++    + +T  + +      IA++L ++E E
Sbjct: 142 IKRYFRDNVRTVHV-----PRRLHELWVQVNAATEDLTTLHGRTPTTPEIAERLRITEEE 196

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWL--VYDHDGQEQVLIEKEERKNRRNMLTR 230
           V+S  C  AG        +++   ++Q  D L  + D  G E   +   E ++    L R
Sbjct: 197 VLS--CIEAGRS-----YHATSLEAAQEGDGLPGLLDRLGYEDPELAGVEHRD----LVR 245

Query: 231 SMSVLNP-RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            + V  P RE+RI   R    N +T   +S+E  VS+  V ++ AR+F +++ +
Sbjct: 246 HLLVQLPEREQRILLLRYY--NNLTQSQISAELGVSQMHVSRLLARSFARLRSA 297


>gi|308173494|ref|YP_003920199.1| RNA polymerase sporulation-specific sigma-29 factor sigma-E
           [Bacillus amyloliquefaciens DSM 7]
 gi|307606358|emb|CBI42729.1| RNA polymerase sporulation-specific sigma-29 factor (sigma-E)
           [Bacillus amyloliquefaciens DSM 7]
 gi|328553576|gb|AEB24068.1| sporulation sigma factor SigE [Bacillus amyloliquefaciens TA208]
 gi|328911631|gb|AEB63227.1| RNA polymerase sporulation-specific sigma-29 factor (sigma-E)
           [Bacillus amyloliquefaciens LL3]
          Length = 239

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 68/264 (25%), Positives = 113/264 (42%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL  +    GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLSKEEEQVLLLKL-PSGDQAARAILIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+                          
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN-------------------------- 129

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                               N   SEV       + DE LN      D N     D L  
Sbjct: 130 --------------------NKIRSEV-------SFDEPLNI---DWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEV 264
           D D    ++ +  E    + +L +++  LN RE++I E R   + E   T ++++    +
Sbjct: 160 DDD----IITKDIEANVDKKLLKKALEQLNDREKQIMELRFGLIGEEEKTQKDVADMMGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 216 SQSYISRLEKRIIKRLRKEFNKMV 239


>gi|295836570|ref|ZP_06823503.1| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
 gi|295826098|gb|EDY44232.2| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
          Length = 338

 Score = 64.7 bits (156), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 65/241 (26%), Positives = 111/241 (46%), Gaps = 29/241 (12%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           +RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDPERG   +TY+   + 
Sbjct: 116 NRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPERGVEFSTYATPTVV 175

Query: 111 AAMQEYIL-RSWSLVKIGTTANQKRLFFN-----LRRLKGHLQAITDNNLKPEQVVAIAK 164
             ++ +   + W+ V++     + RL        L +L G    + +          +A+
Sbjct: 176 GEIKRHFRDKGWA-VRVPRRLQELRLSLTSATAELSQLHGRSPTVHE----------LAQ 224

Query: 165 KLNVSESEVISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           +L++SE EV      L G ES NA    S D   +  +   V D  G E   +E  E   
Sbjct: 225 RLSISEEEV------LEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVE--- 275

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            R  L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   ++++ 
Sbjct: 276 YRESLKPLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLRDK 333

Query: 284 I 284
           +
Sbjct: 334 L 334


>gi|307328849|ref|ZP_07608019.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306885514|gb|EFN16530.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 277

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 64/244 (26%), Positives = 119/244 (48%), Gaps = 23/244 (9%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           EH  + AA  L+ ++L LV   A  +R    P+ +V+  G IGL+ A+ +FDP+RG +  
Sbjct: 49  EHTRVRAA--LIEANLPLVRYAAARFRSRNEPMEDVIQVGTIGLINAIDRFDPDRGVQFP 106

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           T++M  +   ++ Y   +   V +      +RL     ++ G  + +T  + +      I
Sbjct: 107 TFAMPTVVGEIKRYFRDNVRTVHV-----PRRLHELWVQVNGATEDLTVLHGRSPTTAEI 161

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL--VYDHDGQEQVLIEKEE 220
           A++L +SE EV++  C  AG        +++   ++Q  D L  + D  G E   +   E
Sbjct: 162 AERLKLSEEEVLA--CIEAGRS-----YHATSLEAAQEGDGLPGLVDRLGYEDPALAGVE 214

Query: 221 RKNRRNMLTRSMSVLNP-RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
            ++    L R + V  P RE+RI   R      +T   +S+E  VS+  V ++ +R+F +
Sbjct: 215 HRD----LVRHLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLLSRSFAR 268

Query: 280 VQES 283
           ++ +
Sbjct: 269 LRSA 272


>gi|323449639|gb|EGB05525.1| hypothetical protein AURANDRAFT_60247 [Aureococcus anophagefferens]
          Length = 399

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 40/148 (27%), Positives = 75/148 (50%), Gaps = 25/148 (16%)

Query: 53  LVTSHLRLVV--------------KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           ++ S++RLVV              ++A+   G    + ++V+EG +GL +AV +F+P+RG
Sbjct: 141 MMLSNMRLVVAMARRMQRSLPQASRLAVDRDGGSYALDDLVAEGTLGLAKAVDRFEPDRG 200

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           FR +TY+ WW++ A+Q  I R  ++V +     Q       ++ +   Q + D   +P  
Sbjct: 201 FRFSTYATWWVRQAIQRAI-RRRAVVAVPVHVQQL-----AKKCENATQELRDEYGRPPT 254

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESL 186
              +A ++  SE  +     +LAG  +L
Sbjct: 255 SAELAARVGASEKRL-----KLAGRAAL 277


>gi|294630217|ref|ZP_06708777.1| RNA polymerase sigma-F factor [Streptomyces sp. e14]
 gi|292833550|gb|EFF91899.1| RNA polymerase sigma-F factor [Streptomyces sp. e14]
          Length = 314

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 64/244 (26%), Positives = 118/244 (48%), Gaps = 23/244 (9%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           EH  +  A  L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDP+RG +  
Sbjct: 86  EHARVRGA--LIEANLPLVRYAAGRFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFP 143

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           T++M  +   ++ Y   +   V +      +RL     ++    + +T    +      I
Sbjct: 144 TFAMPTVVGEIKRYFRDNVRTVHV-----PRRLHELWVQVNSATEDLTTAFGRSPTTAEI 198

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL--VYDHDGQEQVLIEKEE 220
           A++L ++E EV+S  C  AG        +++   ++Q  D L  + D  G E   ++  E
Sbjct: 199 AERLRITEEEVLS--CIEAGRS-----YHATSLEAAQEGDGLPGLLDRLGYEDPALDGVE 251

Query: 221 RKNRRNMLTRSMSVLNP-RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
            ++    L R + V  P RE+RI   R      +T   +S+E  VS+  V ++ AR+F++
Sbjct: 252 HRD----LVRHLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLLARSFQR 305

Query: 280 VQES 283
           ++ +
Sbjct: 306 LRSA 309


>gi|229541193|ref|ZP_04430253.1| RNA polymerase, sigma 28 subunit, SigE [Bacillus coagulans 36D1]
 gi|229325613|gb|EEN91288.1| RNA polymerase, sigma 28 subunit, SigE [Bacillus coagulans 36D1]
          Length = 239

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 37/94 (39%), Positives = 58/94 (61%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE +L K+    GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLSKEEEEMLLKKL-PAGDKAARSILIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN 129


>gi|297192165|ref|ZP_06909563.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
 gi|197720190|gb|EDY64098.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
          Length = 349

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 63/234 (26%), Positives = 108/234 (46%), Gaps = 19/234 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  HL LV  +A  +R  G P+ ++     IGL+++V +FDPERG   +TY+   +   
Sbjct: 129 LVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPERGVEFSTYATPTVVGE 188

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +   + W+ V++     + RL       +     ++  + +   V  +A++L +SE 
Sbjct: 189 IKRHFRDKGWA-VRVPRRLQELRLSLTTATAE-----LSQQHGRSPTVHELAERLGISEE 242

Query: 172 EVISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           EV      L G ES NA    S D   +  +   V D  G E   +E  E    R  L  
Sbjct: 243 EV------LEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVE---YRESLKP 293

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 294 LLEGLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLRERL 345


>gi|302535695|ref|ZP_07288037.1| RNA polymerase sigma-B factor [Streptomyces sp. C]
 gi|302444590|gb|EFL16406.1| RNA polymerase sigma-B factor [Streptomyces sp. C]
          Length = 355

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 63/234 (26%), Positives = 114/234 (48%), Gaps = 21/234 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDPERG +  T++M  +   
Sbjct: 135 LIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQFPTFAMPTVVGE 194

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           ++ Y   +   V +      +RL     ++    + +T  + +      IA++L +SE E
Sbjct: 195 IKRYFRDNVRTVHV-----PRRLHELWVQVNAATEDLTTLHGRTPTTPEIAERLRISEDE 249

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWL--VYDHDGQEQVLIEKEERKNRRNMLTR 230
           V+S  C  AG        +++   ++Q  D +  + D  G E   +   E ++    L R
Sbjct: 250 VLS--CIEAGRS-----YHATSLEAAQEGDGMPGLLDRLGYEDPELAGVEHRD----LVR 298

Query: 231 SMSVLNP-RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            + V  P RE+RI   R    N +T   +S+E  VS+  V ++ AR+F +++ +
Sbjct: 299 HLLVQLPEREQRILLLRYY--NNLTQSQISAELGVSQMHVSRLLARSFARLRSA 350


>gi|220932606|ref|YP_002509514.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Halothermothrix
           orenii H 168]
 gi|219993916|gb|ACL70519.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Halothermothrix
           orenii H 168]
          Length = 209

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 31/102 (30%), Positives = 62/102 (60%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           ++ Y+ ++ KI +LE +EE  L  +Y+++ D  A  RL+TS+  LV KI   Y      +
Sbjct: 2   INDYLKQLGKIKILEAEEEKELWIKYKDYNDTEARQRLITSYQPLVFKIVRQYARDNEVV 61

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
            +++ EG +GL+ A+  +D +RG   ++Y++++I+  +  Y+
Sbjct: 62  MDLIQEGTLGLIDAIDSYDHKRGKSFSSYALYYIRGRVINYL 103


>gi|75764482|ref|ZP_00743967.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|74488029|gb|EAO51760.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
          Length = 260

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 67/267 (25%), Positives = 128/267 (47%), Gaps = 28/267 (10%)

Query: 25  KIPMLEKQEEYVLAKRYRE--HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           K+P+L+ +E   + K +RE   G++SA  +LV  +LRLV+ +   +   G  + ++   G
Sbjct: 15  KLPVLKNEE---MRKLFREMQSGEISAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVG 71

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            IGLM+++  FD  +  + +TY++  I   ++ Y LR  + ++      +  L   +  L
Sbjct: 72  CIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRY-LRDNNPIRFCAFLGRYAL---INXL 127

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
           +   + I +N+ +P   + IAK L V+  E++          +L+A+ +        + D
Sbjct: 128 QVREKLIAENSKEP-TAMDIAKVLEVTHEEIVF---------ALDAIQDPVSLFEPIYND 177

Query: 203 W----LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
                 V D    E+   +K+E+      L   M  LN RE+ I   R  Q    T   +
Sbjct: 178 GGDPIFVMDQLSDEK---QKDEQWVEELALKEGMKRLNDREKMIIRKRFFQGK--TQMEV 232

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQ 285
           + E  +S+ +V ++E  A K++ ++IQ
Sbjct: 233 AEEIGISQAQVSRLEKSAIKQMNKTIQ 259


>gi|75764483|ref|ZP_00743968.1| RNA polymerase sigma-E factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|74488030|gb|EAO51761.1| RNA polymerase sigma-E factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
          Length = 224

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 69/264 (26%), Positives = 113/264 (42%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL  +    GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 22  PPLTKEEEEVLLNKL-PKGDQAARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 80

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I                      +  +  +LRR     
Sbjct: 81  IKAVNTFNPEKKIKLATYASRCI----------------------ENEILMHLRR----- 113

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                               N + SEV       + DE LN      D N     D L  
Sbjct: 114 -------------------NNKNRSEV-------SFDEPLNI---DWDGNELLLSDVLGT 144

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEV 264
           D D    ++ +  E    R++L +++  LN RE++I E R         T ++++    +
Sbjct: 145 DDD----IITKDLEATVDRHLLMKALHQLNDREKQIMELRFGLAGGEEKTQKDVADMLGI 200

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 201 SQSYISRLEKRIIKRLRKEFNKMV 224


>gi|229157483|ref|ZP_04285560.1| RNA polymerase sigma-35 factor [Bacillus cereus ATCC 4342]
 gi|228625933|gb|EEK82683.1| RNA polymerase sigma-35 factor [Bacillus cereus ATCC 4342]
          Length = 223

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 69/264 (26%), Positives = 113/264 (42%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL  +    GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 21  PPLTKEEEEVLLNKL-PKGDQAARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 79

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I                      +  +  +LRR     
Sbjct: 80  IKAVNTFNPEKKIKLATYASRCI----------------------ENEILMHLRR----- 112

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                               N + SEV       + DE LN      D N     D L  
Sbjct: 113 -------------------NNKNRSEV-------SFDEPLNI---DWDGNELLLSDVLGT 143

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEV 264
           D D    ++ +  E    R++L +++  LN RE++I E R         T ++++    +
Sbjct: 144 DDD----IITKDLEATVDRHLLMKALHQLNDREKQIMELRFGLAGGEEKTQKDVADMLGI 199

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 200 SQSYISRLEKRIIKRLRKEFNKMV 223


>gi|297588048|ref|ZP_06946692.1| RNA polymerase general stress sigma factor(sigma B) [Finegoldia
           magna ATCC 53516]
 gi|297574737|gb|EFH93457.1| RNA polymerase general stress sigma factor(sigma B) [Finegoldia
           magna ATCC 53516]
          Length = 258

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 59/254 (23%), Positives = 119/254 (46%), Gaps = 18/254 (7%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           +++E  D      LV  +L +   +A  Y G G+   ++     IGL+ A+ ++DP +G+
Sbjct: 20  KFQETRDKKTRDTLVEKNLYIAEILAKKYTGRGIEYDDLYQVACIGLIYAIDRYDPSKGY 79

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
             ++Y+   I   +++Y      ++++     +  L   +   K HL        K   V
Sbjct: 80  EFSSYATPTIVGEIKKYFRDKGWVIRVPRRIQE--LNKKVANAKIHLAQTMQ---KSPTV 134

Query: 160 VAIAKKLNVSESEVISM--NCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLI 216
             IA  L++S  EV+ +    ++   +SL+  I+ SSD   +   D +     G+E   +
Sbjct: 135 EDIADYLSISNEEVLEVLEGAKVYAPQSLDQSIDQSSDDRDTNLSDLI-----GEEDKDM 189

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
            K E    R+++ R M  LN  E++I   R   +    +  ++ E ++S+  V ++E + 
Sbjct: 190 LKFE---NRDLINRCMEDLNEVEKKILLGRYFDKKTQIV--IAEELDISQMTVSRMEKKI 244

Query: 277 FKKVQESIQKQVEL 290
            KK + S+++Q+E 
Sbjct: 245 LKKFKASLKEQLEF 258


>gi|295696452|ref|YP_003589690.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
 gi|295412054|gb|ADG06546.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
          Length = 261

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 67/277 (24%), Positives = 126/277 (45%), Gaps = 45/277 (16%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           ++P+L   E   L   + + GDLSA  RL+  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  QLPVLTNAEMRKLFAEF-QAGDLSARERLIHGNLRLVLSVIQRFNNRGENVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEY------ILRSWSLVKIGTTANQKRLFFN 138
           GLM+A+  FD  +  + +TY++  I   ++ Y      I  S SL  I   A Q R    
Sbjct: 74  GLMKAIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLRDIAYKALQVR---- 129

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
                     +T+  L+   +  I+++LN+ + +V+          +L+A+ +       
Sbjct: 130 --------DQLTNERLREPTITEISEQLNLPKEDVVF---------ALDAIQDPVSLFEP 172

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRN--------MLTRSMSVLNPRERRIFEARRLQE 250
            +       HDG + + +  + R +R           L  +M+ L  RE++I  A R  E
Sbjct: 173 IY-------HDGGDPIYVMDQIRDDRNQDVLWVEEIALREAMNKLGQREQKIL-AMRFFE 224

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
               +E ++ E  +S+ +V ++E  A + +Q+ I+ Q
Sbjct: 225 GKTQME-VAEEIGISQAQVSRLEKSAIQHMQKFIKIQ 260


>gi|23098930|ref|NP_692396.1| sporulation sigma factor SigE [Oceanobacillus iheyensis HTE831]
 gi|22777158|dbj|BAC13431.1| stage II sporulation protein GB (RNA polymerase
           sporulation-specific sigma E factor) [Oceanobacillus
           iheyensis HTE831]
          Length = 239

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 71/270 (26%), Positives = 115/270 (42%), Gaps = 75/270 (27%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L KQEE  L  R    GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLSKQEEQELLIRL-PKGDKAARAMLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  Y                      LRR     
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMY----------------------LRR----- 128

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW--- 203
               +N LK E                      ++ DE LN              DW   
Sbjct: 129 ----NNKLKSE----------------------VSFDEPLNI-------------DWDGN 149

Query: 204 --LVYDHDGQEQVLIEKE-ERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENL 258
             L+ D  G E+ +I K  E    + +L  ++  LN RE++I E R   + E   T +++
Sbjct: 150 ELLLSDVMGTEEDIITKNLESTVDKTLLKSALEKLNAREKQIMELRFGLIGEEEKTQKDV 209

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +    +S+  + ++E +  +++++   K V
Sbjct: 210 ADMLGISQSYISRLEKKIIRRLKKEFNKMV 239


>gi|331269712|ref|YP_004396204.1| FliA/WhiG family RNA polymerase sigma 28 subunit [Clostridium
           botulinum BKT015925]
 gi|329126262|gb|AEB76207.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           botulinum BKT015925]
          Length = 249

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 37/94 (39%), Positives = 56/94 (59%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE  L  + R  GD S    L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 47  PPLSKEEEENLVAKIR-AGDDSVRTILIERNLRLVVYIARKFENSGVLVEDLISVGTIGL 105

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  FDPE+  +LATY+   I+  +  Y+ R+
Sbjct: 106 IKAVNTFDPEKKIKLATYASRCIENEILMYLRRN 139


>gi|258511273|ref|YP_003184707.1| sporulation sigma factor SigE [Alicyclobacillus acidocaldarius
           subsp. acidocaldarius DSM 446]
 gi|257477999|gb|ACV58318.1| RNA polymerase, sigma 28 subunit, SigE [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
          Length = 249

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 39/97 (40%), Positives = 56/97 (57%), Gaps = 1/97 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE  L +R    GD S    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 47  PPLTKEEEQYLLERL-PSGDPSVRSMLIERNLRLVVYIARKFENTGVNIEDLVSIGTIGL 105

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           ++AV  FDP +  +LATY+   I+  +  Y+ R+  L
Sbjct: 106 IKAVNTFDPSKKIKLATYASRCIENEILMYLRRNNKL 142


>gi|328884955|emb|CCA58194.1| RNA polymerase sigma factor [Streptomyces venezuelae ATCC 10712]
          Length = 344

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 64/235 (27%), Positives = 108/235 (45%), Gaps = 19/235 (8%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +LV  HL LV  +A  +R  G P+ ++     IGL+++V +FDPERG   +TY+   +  
Sbjct: 123 QLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPERGVEFSTYATPTVVG 182

Query: 112 AMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            ++ +   + W+ V++     + RL      L      ++  + +   V  +A++L +SE
Sbjct: 183 EIKRHFRDKGWA-VRVPRRLQELRL-----SLTTATAELSQQHGRSPTVHELAERLGISE 236

Query: 171 SEVISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
            EV      L G ES NA    S D   +  +   V D  G E   +E  E    R  L 
Sbjct: 237 EEV------LEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVE---YRESLK 287

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR    ++E +
Sbjct: 288 PLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLASLREKL 340


>gi|312281919|dbj|BAJ33825.1| unnamed protein product [Thellungiella halophila]
          Length = 562

 Score = 64.3 bits (155), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 57/234 (24%), Positives = 113/234 (48%), Gaps = 15/234 (6%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ S   LV+ ++  YRG G+   +++  GN+G++Q  ++FD  RG++ +TY  +WI+ +
Sbjct: 327 LLKSTRSLVLFLSRNYRGLGIAHEDLIQAGNVGVLQGAERFDHTRGYKFSTYVQYWIRKS 386

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           M   + R    V I ++    R    +++ +  L+  T + +K      I+K+   S  +
Sbjct: 387 MSMMVSRHARGVYIPSSV--IRTMSQIQKARKTLK--TSHGIKYPADEEISKETGYSLKK 442

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQW--QDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           + + N  L        ++ S DK         +L +  D   +   E   R++    +  
Sbjct: 443 IRAANQCL-------KVVGSIDKKVGDCFTTKFLEFTPDTTMESPEEAVMRQSAWRDVHD 495

Query: 231 SMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            +  L PRE+++   R   +   P +LE +    +VS+E +R+IE RA  K+++
Sbjct: 496 LLQGLEPREKQVMVLRYGLQGFRPKSLEEIGKLLKVSKEWIRKIERRAMAKLRD 549


>gi|89099620|ref|ZP_01172495.1| sporulation sigma factor SigE [Bacillus sp. NRRL B-14911]
 gi|89085773|gb|EAR64899.1| sporulation sigma factor SigE [Bacillus sp. NRRL B-14911]
          Length = 239

 Score = 63.9 bits (154), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 37/94 (39%), Positives = 57/94 (60%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL  +    GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLSKEEEEVLLIKL-PKGDKAARSMLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN 129


>gi|311068053|ref|YP_003972976.1| sporulation sigma factor SigE [Bacillus atrophaeus 1942]
 gi|310868570|gb|ADP32045.1| sporulation sigma factor SigE [Bacillus atrophaeus 1942]
          Length = 239

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 68/264 (25%), Positives = 112/264 (42%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K EE VL  +    GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLSKDEEQVLLLKL-PSGDQAARAILIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+                          
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN-------------------------- 129

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                               N   SEV       + DE LN      D N     D L  
Sbjct: 130 --------------------NKIRSEV-------SFDEPLNI---DWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEV 264
           D D    ++ +  E    + +L +++  LN RE++I E R   + E   T ++++    +
Sbjct: 160 DDD----IITKDIEANVDKKLLKKALEQLNDREKQIMELRFGLVGEEEKTQKDVADMMGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 216 SQSYISRLEKRIIKRLRKEFNKMV 239


>gi|282861039|ref|ZP_06270104.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
 gi|282563697|gb|EFB69234.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
          Length = 323

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 62/234 (26%), Positives = 105/234 (44%), Gaps = 17/234 (7%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+   +  
Sbjct: 102 RLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATPTVVG 161

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            ++ +       V++     + RL       +     ++    +   V  +A++L +SE 
Sbjct: 162 EIKRHFRDKGWAVRVPRRLQELRLSLTTATAE-----LSQQYGRSPTVHELAERLGISEE 216

Query: 172 EVISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           EV      L G ES NA    S D   +  +   V D  G E   +E  E    R  L  
Sbjct: 217 EV------LEGLESANAYSTLSLDVPDTDDESPAVADTLGSEDEALEGVE---YRESLKP 267

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 268 LLEGLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLRERL 319


>gi|55274889|gb|AAV49247.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 180

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 30/61 (49%), Positives = 41/61 (67%), Gaps = 8/61 (13%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL +        +GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLAL--------LGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 52

Query: 118 L 118
           +
Sbjct: 53  M 53


>gi|253576138|ref|ZP_04853470.1| RNA polymerase sigma-E factor [Paenibacillus sp. oral taxon 786
           str. D14]
 gi|251844481|gb|EES72497.1| RNA polymerase sigma-E factor [Paenibacillus sp. oral taxon 786
           str. D14]
          Length = 240

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 36/94 (38%), Positives = 57/94 (60%), Gaps = 2/94 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  ++EEY+L +     GD +    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 39  PLTREEEEYLLQRL--PSGDSAIRAMLIERNLRLVVYIARKFENTGINIEDLVSIGAIGL 96

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  FDPE+  +LATY+   I+  +  Y+ R+
Sbjct: 97  IKAVNTFDPEKKIKLATYASRCIENEILMYLRRN 130


>gi|290959143|ref|YP_003490325.1| SigF-like sigma factor [Streptomyces scabiei 87.22]
 gi|260648669|emb|CBG71782.1| SigF-like sigma factor [Streptomyces scabiei 87.22]
          Length = 287

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 65/250 (26%), Positives = 119/250 (47%), Gaps = 23/250 (9%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           LA    EH  +  A  L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDP+
Sbjct: 53  LAPGTPEHNRVRGA--LIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPD 110

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RG +  T++M  +   ++ Y   +   V +      +RL     ++    + +T    + 
Sbjct: 111 RGVQFPTFAMPTVIGEIKRYFRDNVRTVHV-----PRRLHELWVQVNSATEDLTTAFGRT 165

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL--VYDHDGQEQV 214
                IA++L ++E EV+S  C  AG        +++   ++Q  D +  + D  G E  
Sbjct: 166 PSTAEIAERLRITEEEVLS--CIEAGRS-----YHATSLEAAQEGDGMPGLLDRLGYEDP 218

Query: 215 LIEKEERKNRRNMLTRSMSVLNP-RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
            ++  E ++    L R + V  P RE+RI   R      +T   +S+E  VS+  V ++ 
Sbjct: 219 ELDGVEHRD----LVRHLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLL 272

Query: 274 ARAFKKVQES 283
           AR+F +++ +
Sbjct: 273 ARSFARLRSA 282


>gi|229019107|ref|ZP_04175942.1| RNA polymerase sigma-35 factor [Bacillus cereus AH1273]
 gi|229025351|ref|ZP_04181769.1| RNA polymerase sigma-35 factor [Bacillus cereus AH1272]
 gi|228735936|gb|EEL86513.1| RNA polymerase sigma-35 factor [Bacillus cereus AH1272]
 gi|228742207|gb|EEL92372.1| RNA polymerase sigma-35 factor [Bacillus cereus AH1273]
          Length = 232

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 69/264 (26%), Positives = 114/264 (43%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL  +  + GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 30  PPLTKEEEEVLLNKLPK-GDQAARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 88

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I                      +  +  +LRR     
Sbjct: 89  IKAVNTFNPEKKIKLATYASRCI----------------------ENEILMHLRR----- 121

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                               N + SEV       + DE LN      D N     D L  
Sbjct: 122 -------------------NNKNRSEV-------SFDEPLNI---DWDGNELLLSDVLGT 152

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEV 264
           D D    ++ +  E    R++L +++  LN RE++I E R         T ++++    +
Sbjct: 153 DDD----IITKDLEATVDRHLLMKALHQLNDREKQIMELRFGLAGGEEKTQKDVADMLGI 208

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 209 SQSYISRLEKRIIKRLRKEFNKMV 232


>gi|299535876|ref|ZP_07049196.1| RNA polymerase sigma-35 factor precursor [Lysinibacillus fusiformis
           ZC1]
 gi|298728628|gb|EFI69183.1| RNA polymerase sigma-35 factor precursor [Lysinibacillus fusiformis
           ZC1]
          Length = 206

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 61/265 (23%), Positives = 117/265 (44%), Gaps = 64/265 (24%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+  ++E  V+A     +GDL A   L+  +LRLVV IA  +   G PI +++S G+IG
Sbjct: 3   VPLSREEEVTVIASFM--NGDLRARDTLIERNLRLVVYIARRFDNTGTPIEDLISIGSIG 60

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A++ F+ ++  +LATY+   I+  +  + LR  S                  R+KG 
Sbjct: 61  LIKAIETFNTDKNIKLATYASRCIENEILMH-LRKTS------------------RMKGE 101

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           +                                    DE LN+    +D N     D L 
Sbjct: 102 VSL----------------------------------DEPLNS---DADGNELLLSDIL- 123

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFE 263
                +E ++++  E+K  R  +  ++++L  RER I E R      V  T + ++    
Sbjct: 124 ---GTEEHIILDNVEKKIERQHMFHAINLLGARERYIMECRFGLNGKVEMTQKEVADHLG 180

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           +S+  + ++E +  + ++E++ + +
Sbjct: 181 ISQSYISRLEKKIIQDLRENLNQPI 205


>gi|266620503|ref|ZP_06113438.1| RNA polymerase sigma-F factor [Clostridium hathewayi DSM 13479]
 gi|288867868|gb|EFD00167.1| RNA polymerase sigma-F factor [Clostridium hathewayi DSM 13479]
          Length = 237

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 62/241 (25%), Positives = 116/241 (48%), Gaps = 16/241 (6%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GD  A  RLVT ++ L+  I   + G G    ++   G+IGLM+A+ KFD     + +T
Sbjct: 13  EGDKEARDRLVTENMGLIWSIVRRFTGRGYDPEDLFQIGSIGLMKAIDKFDMSFDVKFST 72

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y++  I   ++ + LR   ++K+  +  +        R+K   +A+     +   +  IA
Sbjct: 73  YAVPMITGEIKRF-LRDDGMIKVSRSIKEMGT-----RVKCVREALGFTLGREPTIEEIA 126

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
            +L  S+ EV +     A  ESL   +N +D+NS    D +  +   QE++L        
Sbjct: 127 GELGASKEEVAASIEAGAEVESLYRTVNKNDENSILLIDKIEEESSAQEELL-------- 178

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            R +L   ++ L+ ++R I   RR   N  T   ++S   +S+ +V ++E +  K+++E 
Sbjct: 179 NRMVLRELLTGLSDKDREII-IRRYYYNE-TQSQIASHLGISQVQVSRLEKKILKQMREK 236

Query: 284 I 284
           +
Sbjct: 237 L 237


>gi|332976340|gb|EGK13196.1| DNA-directed RNA polymerase sigma subunit SigG [Desmospora sp.
           8437]
          Length = 259

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 68/266 (25%), Positives = 120/266 (45%), Gaps = 28/266 (10%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+ +E   L +  +E GD SA  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKNEEMRALFRSLQEEGDRSAREKLVNGNLRLVLSVIQRFNNRGENVDDLFQVGCI 74

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEY------ILRSWSLVKIGTTANQKRLFFN 138
           GLM+A+  FD  +  + +TY++  I   ++ Y      I  S SL  I   A Q R    
Sbjct: 75  GLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLRDIAYKALQVR---- 130

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
                    ++T  + +   +  I+++LNVS+ EV+     +    SL   I     +  
Sbjct: 131 --------DSLTYRHSREPTIQEISEELNVSKEEVVFALDAIQDPVSLFEPIYQDGGDPI 182

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
              D L  D +        K+        L  +M  LN RE+ I  + R  E    +E +
Sbjct: 183 YVMDQLADDEN--------KDLHWVEEIALREAMGRLNDREKMIL-SMRFFEGKTQME-V 232

Query: 259 SSEFEVSRERVRQIEARAFKKVQESI 284
           + E  +S+ +V ++E  A +++ + I
Sbjct: 233 AEEIGISQAQVSRLEKAAIQQMNKYI 258


>gi|154685948|ref|YP_001421109.1| sporulation sigma factor SigE [Bacillus amyloliquefaciens FZB42]
 gi|154351799|gb|ABS73878.1| SigE [Bacillus amyloliquefaciens FZB42]
          Length = 239

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 68/264 (25%), Positives = 115/264 (43%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL  +    GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLSKEEEQVLLLKL-PSGDQAARAILIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  Y                      LRR     
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMY----------------------LRR----- 128

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
               +N ++ E                      ++ DE LN      D N     D L  
Sbjct: 129 ----NNKIRSE----------------------VSFDEPLNI---DWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEV 264
           D D    ++ +  E    + +L +++  LN RE++I E R   + E   T ++++    +
Sbjct: 160 DDD----IITKDIEANVDKKLLKKALEQLNEREKQIMELRFGLVGEEEKTQKDVADMMGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 216 SQSYISRLEKRIIKRLRKEFNKMV 239


>gi|297202300|ref|ZP_06919697.1| RNA polymerase sigma-F factor [Streptomyces sviceus ATCC 29083]
 gi|297148082|gb|EDY54214.2| RNA polymerase sigma-F factor [Streptomyces sviceus ATCC 29083]
          Length = 381

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 63/236 (26%), Positives = 110/236 (46%), Gaps = 19/236 (8%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           ++LV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+   + 
Sbjct: 159 NQLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATPTVV 218

Query: 111 AAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
             ++ +   + W+ V++     + RL       +     ++  + +   V  +A+KL +S
Sbjct: 219 GEIKRHFRDKGWA-VRVPRRLQELRLSLTTATAE-----LSQQHGRSPTVHELAEKLAIS 272

Query: 170 ESEVISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           E EV      L G ES NA    S D   +  +   V D  G E   +E  E    R  L
Sbjct: 273 EEEV------LEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVE---YRESL 323

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 324 KPLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLREKL 377


>gi|167465670|ref|ZP_02330759.1| sporulation sigma factor SigE [Paenibacillus larvae subsp. larvae
           BRL-230010]
          Length = 196

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 36/88 (40%), Positives = 53/88 (60%), Gaps = 2/88 (2%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EEY+L K     GD +    L+  +LRLVV IA  +   G+ I ++VS G IGL++AV  
Sbjct: 1   EEYLLGKL--PSGDAAIRAMLIERNLRLVVYIARKFENTGINIEDLVSIGAIGLIKAVNT 58

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRS 120
           FDPE+  +LATY+   I+  +  Y+ R+
Sbjct: 59  FDPEKKIKLATYASRCIENEILMYLRRN 86


>gi|239623450|ref|ZP_04666481.1| RNA polymerase [Clostridiales bacterium 1_7_47_FAA]
 gi|239521481|gb|EEQ61347.1| RNA polymerase [Clostridiales bacterium 1_7_47FAA]
          Length = 246

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 64/262 (24%), Positives = 118/262 (45%), Gaps = 64/262 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE +EE  +        D  A   L+  +LRLVV IA  +    + + +++S G IGL
Sbjct: 41  PPLESEEESRMIGLLGGEDDKGARSTLIEHNLRLVVYIAKKFDNTSVGVEDLISIGTIGL 100

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+  F P++  +LATY+   I+  +  Y+ R+          N+ RL           
Sbjct: 101 IKAINTFKPDKNIKLATYASRCIENEILMYLRRN----------NKTRL----------- 139

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                        V+I + LNV             G+E L + I  +D++       ++Y
Sbjct: 140 ------------EVSIDEPLNVD----------WDGNELLLSDILGTDED-------VIY 170

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN----PVTLENLSSEF 262
            HD ++++          +N+L  ++S LNPRER+I E R    N     +T + ++   
Sbjct: 171 -HDIEDEI---------EKNLLNNAISRLNPRERKIVELRYGLTNEDGEEMTQKEVADLL 220

Query: 263 EVSRERVRQIEARAFKKVQESI 284
            +S+  + ++E +  K++++ I
Sbjct: 221 GISQSYISRLEKKIMKRLKKEI 242


>gi|229086468|ref|ZP_04218640.1| RNA polymerase sigma-G factor [Bacillus cereus Rock3-44]
 gi|228696785|gb|EEL49598.1| RNA polymerase sigma-G factor [Bacillus cereus Rock3-44]
          Length = 259

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 67/263 (25%), Positives = 124/263 (47%), Gaps = 21/263 (7%)

Query: 25  KIPMLEKQEEYVLAKRYRE--HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           K+P+L+ +E   + K +RE   G++SA  +LV  +LRLV+ +   +   G  + ++   G
Sbjct: 15  KLPVLKNEE---MRKLFREMQSGEISAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVG 71

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            IGLM+++  FD  +  + +TY++  I   ++ Y LR  + +++  +          + L
Sbjct: 72  CIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSLRD----IAYKAL 126

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
           +   + I +N+ +P   + IAK L V+  E++     +    SL   I +   +     D
Sbjct: 127 QVREKLIAENSKEP-TAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGGDPIFVMD 185

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
            L  D    EQ + E          L   M  LN RE+ I   R  Q    T   ++ E 
Sbjct: 186 QLSDDKQRDEQWVEEL--------ALKEGMKRLNDREKMIIRKRFFQGK--TQMEVAEEI 235

Query: 263 EVSRERVRQIEARAFKKVQESIQ 285
            +S+ +V ++E  A K++ ++IQ
Sbjct: 236 GISQAQVSRLEKSAIKQMNKTIQ 258


>gi|118418349|gb|ABK86768.1| RNA polymerase, sigma 29 subunit, SigE [Bacillus thuringiensis str.
           Al Hakam]
          Length = 248

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 69/264 (26%), Positives = 113/264 (42%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL  +    GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 46  PPLTKEEEEVLLNKL-PKGDQAARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 104

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I                      +  +  +LRR     
Sbjct: 105 IKAVNTFNPEKKIKLATYASRCI----------------------ENEILMHLRR----- 137

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                               N + SEV       + DE LN      D N     D L  
Sbjct: 138 -------------------NNKNRSEV-------SFDEPLNI---DWDGNELLLSDVLGT 168

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEV 264
           D D    ++ +  E    R++L +++  LN RE++I E R         T ++++    +
Sbjct: 169 DDD----IITKDLEATVDRHLLMKALHQLNDREKQIMELRFGLAGGEEKTQKDVADMLGI 224

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 225 SQSYISRLEKRIIKRLRKEFNKMV 248


>gi|21104384|dbj|BAB93462.1| rpoS like gene [Variovorax sp. WFF52]
          Length = 47

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 26/46 (56%), Positives = 35/46 (76%)

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           LVV IA  Y   G+P S+++ EGN+GLM A+ KF+PERGFR +TY+
Sbjct: 1   LVVNIAKAYLNRGVPFSDLIEEGNLGLMHAITKFEPERGFRFSTYA 46


>gi|297580650|ref|ZP_06942576.1| RNA polymerase sigma factor RpoD [Vibrio cholerae RC385]
 gi|297535066|gb|EFH73901.1| RNA polymerase sigma factor RpoD [Vibrio cholerae RC385]
          Length = 477

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 29/69 (42%), Positives = 43/69 (62%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++L LV+ IA  Y   GL   +++ EGNIGLM+AV K +  RG+  +TY+ WW
Sbjct: 404 ANKEMVEANLPLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKSEYRRGYNFSTYATWW 463

Query: 109 IKAAMQEYI 117
           I+ A+   I
Sbjct: 464 IRQAITRSI 472


>gi|313901496|ref|ZP_07834946.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Thermaerobacter
           subterraneus DSM 13965]
 gi|313468234|gb|EFR63698.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Thermaerobacter
           subterraneus DSM 13965]
          Length = 258

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 67/258 (25%), Positives = 118/258 (45%), Gaps = 20/258 (7%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIG 85
           ++QE   L +RYR   D  +   L+  HL LV  +A G     LP    + +++S G  G
Sbjct: 7   QRQERAELWRRYRTAADPESWEALIREHLPLVRYLA-GRLVVHLPPQVELDDLISYGIFG 65

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           LM+A+K++DP RG +  TY+   I+ AM +  LR+   V  G     + +    RRL+  
Sbjct: 66  LMEAIKRYDPSRGVKFETYAYTRIRGAMLDG-LRAMDWVPQGLRRRAREVEACYRRLENR 124

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDW 203
           L        +P +   +A +L ++  E   +   LA     SL+ ++ S   + +   D 
Sbjct: 125 LG-------RPAEDAEVAAELGLTPDEFGELLKDLARTTVISLDDVLRSESDDPAAVLDR 177

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L    D      +      + R  L ++++VL  RER +      +   +T++ ++    
Sbjct: 178 LA---DPGAADPLAAATLADLRQRLAQALAVLPERERLVITLYYYEG--LTVKEIAEVMG 232

Query: 264 VSRERVRQIEARAFKKVQ 281
           VS  RV Q+  RA  +++
Sbjct: 233 VSPSRVSQLHTRAILRLR 250


>gi|34733392|gb|AAP82769.1| sigma 70 [Hydrogenobacter hydrogenophilus]
          Length = 310

 Score = 63.9 bits (154), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 29/61 (47%), Positives = 41/61 (67%), Gaps = 1/61 (1%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V  +LRLVV IA  Y   GL   +++ EGNIGLM+AV K+D  +G++ +TY+ WW
Sbjct: 251 AKQVMVKCNLRLVVSIA-KYVNRGLHFLDLIQEGNIGLMKAVDKYDYRKGYKFSTYATWW 309

Query: 109 I 109
           I
Sbjct: 310 I 310


>gi|323099956|gb|ADX23556.1| RNA polymerase sigma-G factor [Bacillus mycoides]
          Length = 292

 Score = 63.5 bits (153), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 66/267 (24%), Positives = 128/267 (47%), Gaps = 29/267 (10%)

Query: 25  KIPMLEKQEEYVLAKRYRE--HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           K+P+L+ +E   + K +RE   G++SA  +LV  +LRLV+ +   +   G  + ++   G
Sbjct: 48  KLPVLKNEE---MRKLFREMQSGEISAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVG 104

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            IGLM+++  FD  +  + +TY++  I   ++ Y LR  + +++  +          + L
Sbjct: 105 CIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSLRD----IAYKAL 159

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
           +   + I +N+ +P   + IAK L V+  E++          +L+A+ +        + D
Sbjct: 160 QVREKLIAENSKEP-TAMDIAKVLEVTHEEIVF---------ALDAIQDPVSLFEPIYND 209

Query: 203 W----LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
                 V D    E+   +K+E+      L   M  LN RE+ I   R  Q    T   +
Sbjct: 210 GGDPIFVMDQLSDEK---QKDEQWVEELALKEGMKRLNDREKMIIRKRFFQGK--TQMEV 264

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQ 285
           + E  +S+ +V ++E  A K++ ++IQ
Sbjct: 265 AEEIGISQAQVSRLEKSAIKQMNKTIQ 291


>gi|167641125|ref|ZP_02399380.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0193]
 gi|167510905|gb|EDR86296.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0193]
          Length = 239

 Score = 63.5 bits (153), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 69/264 (26%), Positives = 113/264 (42%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL  +    GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLTKEEEEVLLNKL-PKGDQAARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I                      +  +  +LRR     
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCI----------------------ENEILMHLRR----- 128

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                               N + SEV       + DE LN      D N     D L  
Sbjct: 129 -------------------NNKNRSEV-------SFDEPLNI---DWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEV 264
           D D    ++ +  E    R++L +++  LN RE++I E R         T ++++    +
Sbjct: 160 DDD----IITKDLEATVDRHLLMKALHQLNDREKQIMELRFGLAGGEEKTQKDVADMLGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 216 SQSYISRLEKRIIKRLRKKFNKMV 239


>gi|301055395|ref|YP_003793606.1| sporulation sigma factor SigE [Bacillus anthracis CI]
 gi|300377564|gb|ADK06468.1| sporulation sigma factor SigE [Bacillus cereus biovar anthracis
           str. CI]
          Length = 238

 Score = 63.5 bits (153), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 69/264 (26%), Positives = 114/264 (43%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL  +  + GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 36  PPLTKEEEEVLLNKLPK-GDQAARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 94

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I                      +  +  +LRR     
Sbjct: 95  IKAVNTFNPEKKIKLATYASRCI----------------------ENEILMHLRR----- 127

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                               N + SEV       + DE LN      D N     D L  
Sbjct: 128 -------------------NNKNRSEV-------SFDEPLNI---DWDGNELLLSDVLGT 158

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEV 264
           D D    ++ +  E    R++L +++  LN RE++I E R         T ++++    +
Sbjct: 159 DDD----IITKDLEATVDRHLLMKALHQLNDREKQIMELRFGLAGGEEKTQKDVADMLGI 214

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 215 SQSYISRLEKRIIKRLRKEFNKMV 238


>gi|228973923|ref|ZP_04134498.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228980512|ref|ZP_04140822.1| RNA polymerase sigma-G factor [Bacillus thuringiensis Bt407]
 gi|228779332|gb|EEM27589.1| RNA polymerase sigma-G factor [Bacillus thuringiensis Bt407]
 gi|228785789|gb|EEM33793.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
          Length = 289

 Score = 63.5 bits (153), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 66/267 (24%), Positives = 128/267 (47%), Gaps = 29/267 (10%)

Query: 25  KIPMLEKQEEYVLAKRYRE--HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           K+P+L+ +E   + K +RE   G++SA  +LV  +LRLV+ +   +   G  + ++   G
Sbjct: 45  KLPVLKNEE---MRKLFREMQSGEISAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVG 101

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            IGLM+++  FD  +  + +TY++  I   ++ Y LR  + +++  +          + L
Sbjct: 102 CIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSLRD----IAYKAL 156

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
           +   + I +N+ +P   + IAK L V+  E++          +L+A+ +        + D
Sbjct: 157 QVREKLIAENSKEP-TAMDIAKVLEVTHEEIVF---------ALDAIQDPVSLFEPIYND 206

Query: 203 W----LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
                 V D    E+   +K+E+      L   M  LN RE+ I   R  Q    T   +
Sbjct: 207 GGDPIFVMDQLSDEK---QKDEQWVEELALKEGMKRLNDREKMIIRKRFFQGK--TQMEV 261

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQ 285
           + E  +S+ +V ++E  A K++ ++IQ
Sbjct: 262 AEEIGISQAQVSRLEKSAIKQMNKTIQ 288


>gi|224553590|gb|ACN55033.1| RNA polymerase sigma factor [Escherichia coli]
          Length = 111

 Score = 63.5 bits (153), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 23/47 (48%), Positives = 37/47 (78%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           GL + +++ EGN+GL++AV+KFDPERGF  +TY+ WWI+  ++  I+
Sbjct: 1   GLALLDLIEEGNLGLIRAVEKFDPERGFCFSTYATWWIRQTIERAIM 47


>gi|299473209|emb|CBN78785.1| RNA polymerase [Ectocarpus siliculosus]
          Length = 627

 Score = 63.5 bits (153), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 31/75 (41%), Positives = 51/75 (68%), Gaps = 7/75 (9%)

Query: 42  REHGDLSAA-HRLVTSHLRLVVKIA--MGYRGYG----LPISEVVSEGNIGLMQAVKKFD 94
           RE G + AA  R+++ +LRLVV IA    Y+G      + + +++ +G  GL++AV++FD
Sbjct: 227 REIGIMKAARDRMISCNLRLVVHIARRKFYKGASGTLKVSLEDMIQDGTAGLVKAVERFD 286

Query: 95  PERGFRLATYSMWWI 109
           PE+GFR +TY+ WW+
Sbjct: 287 PEKGFRFSTYATWWV 301


>gi|260886518|ref|ZP_05897781.1| RNA polymerase sigma-70 factor [Selenomonas sputigena ATCC 35185]
 gi|330839639|ref|YP_004414219.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Selenomonas
           sputigena ATCC 35185]
 gi|260863661|gb|EEX78161.1| RNA polymerase sigma-70 factor [Selenomonas sputigena ATCC 35185]
 gi|329747403|gb|AEC00760.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Selenomonas
           sputigena ATCC 35185]
          Length = 208

 Score = 63.5 bits (153), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 50/186 (26%), Positives = 85/186 (45%), Gaps = 29/186 (15%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ E+ K+ +L  +EE  L + ++E G+ +A  RL+ S+  LV K A+ +R     I
Sbjct: 3   LEEYLQELEKVELLAPEEEQSLWQAFKERGERAARQRLIESYQPLVFKTALPWR-MSESI 61

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR---------------- 119
            +++ EG +GL++A + FD +RG   + +++  I+  M  ++ +                
Sbjct: 62  MDIIQEGTVGLIEAAENFDWKRGVAFSLFAVHRIRGRMLNFLQKEGSRDVTCMDAPRADG 121

Query: 120 --SWSLVKIGT--TANQKRLFFNLRRLKGHLQAITDNN--------LKPEQVVAIAKKLN 167
              W L+   T   A Q  L F  R L   L  +            LK E +  IA  L+
Sbjct: 122 RAPWELLPDTTPSVAEQAELGFMTRELHRALARLPQKERVVLESVYLKSETIPKIADVLD 181

Query: 168 VSESEV 173
           VS S +
Sbjct: 182 VSASHI 187


>gi|258511274|ref|YP_003184708.1| RNA polymerase, sigma 28 subunit, SigG [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
 gi|257478000|gb|ACV58319.1| RNA polymerase, sigma 28 subunit, SigG [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
          Length = 259

 Score = 63.5 bits (153), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 69/275 (25%), Positives = 126/275 (45%), Gaps = 45/275 (16%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           ++P+L   +   L ++ R  GD SA  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  QLPVLTNAQMRELFEQLRA-GDPSAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEY------ILRSWSLVKIGTTANQKRLFFN 138
           GLM+A+  FD  +  R +TY++  I   ++ Y      I  S SL  I   A Q R    
Sbjct: 74  GLMKAIDNFDLNQNVRFSTYAVPMIVGEIRRYLRDNNPIRVSRSLRDIAYKALQVR---- 129

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
                     +   NL+   +V IA ++N+ + EV+          +L+A+ +      S
Sbjct: 130 --------DMLASKNLREPSIVEIANEMNLPKEEVVF---------ALDAIQDP----VS 168

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRN--------MLTRSMSVLNPRERRIFEARRLQE 250
            ++   +Y HDG + + +  +    R           L  +M  L+ RE++I  A+R  E
Sbjct: 169 MFEP--IY-HDGGDPIYVMDQIHDEREKDSAWVEGIALREAMRKLSDREKKIL-AKRFYE 224

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
               +E ++ E  +S+ +V ++E  A  ++ + IQ
Sbjct: 225 GKTQME-VADEIGISQAQVSRLEKAAIHRMYKHIQ 258


>gi|51892359|ref|YP_075050.1| sporulation sigma factor SigE [Symbiobacterium thermophilum IAM
           14863]
 gi|51856048|dbj|BAD40206.1| RNA polymerase sigma factor similar to B. subtilis SigE
           [Symbiobacterium thermophilum IAM 14863]
          Length = 251

 Score = 63.5 bits (153), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 37/94 (39%), Positives = 56/94 (59%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L  +EE  L +R    GD S  + L+  +LRLVV IA  +   G+ + ++VS G IGL
Sbjct: 49  PPLTGEEEAALLQRL-TQGDESVKNTLIERNLRLVVYIARKFDNTGIWVEDLVSIGTIGL 107

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AVK FDP +  +LATY+   I+  +  Y+ R+
Sbjct: 108 IKAVKTFDPSKRIKLATYASKCIENEILMYLRRA 141


>gi|30021993|ref|NP_833624.1| sporulation sigma factor SigE [Bacillus cereus ATCC 14579]
 gi|30263906|ref|NP_846283.1| sporulation sigma factor SigE [Bacillus anthracis str. Ames]
 gi|42782997|ref|NP_980244.1| sporulation sigma factor SigE [Bacillus cereus ATCC 10987]
 gi|47529336|ref|YP_020685.1| sporulation sigma factor SigE [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49186754|ref|YP_030006.1| sporulation sigma factor SigE [Bacillus anthracis str. Sterne]
 gi|49478442|ref|YP_037966.1| sporulation sigma factor SigE [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|52141583|ref|YP_085245.1| sporulation sigma factor SigE [Bacillus cereus E33L]
 gi|162382776|ref|YP_896275.2| sporulation sigma factor SigE [Bacillus thuringiensis str. Al
           Hakam]
 gi|165872323|ref|ZP_02216960.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0488]
 gi|167636583|ref|ZP_02394877.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0442]
 gi|170688850|ref|ZP_02880053.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0465]
 gi|170708793|ref|ZP_02899229.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0389]
 gi|177654897|ref|ZP_02936614.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0174]
 gi|190566146|ref|ZP_03019065.1| RNA polymerase sigma-29 factor [Bacillus anthracis Tsiankovskii-I]
 gi|196035954|ref|ZP_03103356.1| RNA polymerase sigma-29 factor [Bacillus cereus W]
 gi|196038626|ref|ZP_03105934.1| RNA polymerase sigma-29 factor [Bacillus cereus NVH0597-99]
 gi|196045866|ref|ZP_03113095.1| RNA polymerase sigma-29 factor [Bacillus cereus 03BB108]
 gi|206971306|ref|ZP_03232257.1| RNA polymerase sigma-29 factor [Bacillus cereus AH1134]
 gi|206976716|ref|ZP_03237620.1| RNA polymerase sigma-29 factor [Bacillus cereus H3081.97]
 gi|217961326|ref|YP_002339894.1| sporulation sigma factor SigE [Bacillus cereus AH187]
 gi|218234749|ref|YP_002368704.1| sporulation sigma factor SigE [Bacillus cereus B4264]
 gi|218899058|ref|YP_002447469.1| RNA polymerase sigma-29 factor [Bacillus cereus G9842]
 gi|218905035|ref|YP_002452869.1| RNA polymerase sigma-29 factor [Bacillus cereus AH820]
 gi|222097350|ref|YP_002531407.1| sporulation sigma factor sige [Bacillus cereus Q1]
 gi|225865886|ref|YP_002751264.1| RNA polymerase sigma-29 factor [Bacillus cereus 03BB102]
 gi|227813186|ref|YP_002813195.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. CDC 684]
 gi|228902410|ref|ZP_04066564.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis IBL 4222]
 gi|228909730|ref|ZP_04073553.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis IBL 200]
 gi|228916542|ref|ZP_04080108.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228922657|ref|ZP_04085957.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228928953|ref|ZP_04091985.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228935220|ref|ZP_04098046.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228940993|ref|ZP_04103551.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228947624|ref|ZP_04109914.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228954181|ref|ZP_04116209.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228960122|ref|ZP_04121786.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228966858|ref|ZP_04127902.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           sotto str. T04001]
 gi|228973924|ref|ZP_04134499.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228980513|ref|ZP_04140823.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis Bt407]
 gi|228987049|ref|ZP_04147174.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|229047589|ref|ZP_04193179.1| RNA polymerase sigma-35 factor [Bacillus cereus AH676]
 gi|229071404|ref|ZP_04204626.1| RNA polymerase sigma-35 factor [Bacillus cereus F65185]
 gi|229081157|ref|ZP_04213667.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock4-2]
 gi|229092951|ref|ZP_04224084.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock3-42]
 gi|229111374|ref|ZP_04240927.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock1-15]
 gi|229123418|ref|ZP_04252622.1| RNA polymerase sigma-35 factor [Bacillus cereus 95/8201]
 gi|229129182|ref|ZP_04258155.1| RNA polymerase sigma-35 factor [Bacillus cereus BDRD-Cer4]
 gi|229140553|ref|ZP_04269108.1| RNA polymerase sigma-35 factor [Bacillus cereus BDRD-ST26]
 gi|229146476|ref|ZP_04274847.1| RNA polymerase sigma-35 factor [Bacillus cereus BDRD-ST24]
 gi|229152102|ref|ZP_04280297.1| RNA polymerase sigma-35 factor [Bacillus cereus m1550]
 gi|229180180|ref|ZP_04307524.1| RNA polymerase sigma-35 factor [Bacillus cereus 172560W]
 gi|229186145|ref|ZP_04313314.1| RNA polymerase sigma-35 factor [Bacillus cereus BGSC 6E1]
 gi|229192074|ref|ZP_04319043.1| RNA polymerase sigma-35 factor [Bacillus cereus ATCC 10876]
 gi|229198016|ref|ZP_04324730.1| RNA polymerase sigma-35 factor [Bacillus cereus m1293]
 gi|229601447|ref|YP_002868140.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0248]
 gi|254683386|ref|ZP_05147246.1| sporulation sigma factor SigE [Bacillus anthracis str. CNEVA-9066]
 gi|254721438|ref|ZP_05183227.1| sporulation sigma factor SigE [Bacillus anthracis str. A1055]
 gi|254735943|ref|ZP_05193649.1| sporulation sigma factor SigE [Bacillus anthracis str. Western
           North America USA6153]
 gi|254739808|ref|ZP_05197501.1| sporulation sigma factor SigE [Bacillus anthracis str. Kruger B]
 gi|254750998|ref|ZP_05203037.1| sporulation sigma factor SigE [Bacillus anthracis str. Vollum]
 gi|254757944|ref|ZP_05209971.1| sporulation sigma factor SigE [Bacillus anthracis str. Australia
           94]
 gi|296504398|ref|YP_003666098.1| sporulation sigma factor SigE [Bacillus thuringiensis BMB171]
 gi|49065841|sp|P62177|RP35_BACAN RecName: Full=RNA polymerase sigma-35 factor; Flags: Precursor
 gi|49065842|sp|P62178|RP35_BACCR RecName: Full=RNA polymerase sigma-35 factor; Flags: Precursor
 gi|49065843|sp|P62179|RP35_BACTK RecName: Full=RNA polymerase sigma-35 factor; Flags: Precursor
 gi|40335|emb|CAA40026.1| sigma factor 35 [Bacillus thuringiensis serovar kurstaki]
 gi|19918914|gb|AAL99378.1| sigma factor 35 [Bacillus thuringiensis serovar israelensis]
 gi|29897549|gb|AAP10825.1| RNA polymerase sigma-E factor [Bacillus cereus ATCC 14579]
 gi|30258550|gb|AAP27769.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. Ames]
 gi|42738924|gb|AAS42852.1| RNA polymerase sigma-29 factor [Bacillus cereus ATCC 10987]
 gi|47504484|gb|AAT33160.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49180681|gb|AAT56057.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. Sterne]
 gi|49329998|gb|AAT60644.1| RNA polymerase sporulation-specific sigma E factor [Bacillus
           thuringiensis serovar konkukian str. 97-27]
 gi|51975052|gb|AAU16602.1| RNA polymerase sporulation-specific sigma E factor [Bacillus cereus
           E33L]
 gi|164711999|gb|EDR17539.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0488]
 gi|165973128|gb|ABY76243.1| sigma factor [Bacillus thuringiensis]
 gi|167528006|gb|EDR90812.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0442]
 gi|170126278|gb|EDS95169.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0389]
 gi|170667205|gb|EDT17965.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0465]
 gi|172080408|gb|EDT65495.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0174]
 gi|190563065|gb|EDV17031.1| RNA polymerase sigma-29 factor [Bacillus anthracis Tsiankovskii-I]
 gi|195991603|gb|EDX55569.1| RNA polymerase sigma-29 factor [Bacillus cereus W]
 gi|196023306|gb|EDX61984.1| RNA polymerase sigma-29 factor [Bacillus cereus 03BB108]
 gi|196030349|gb|EDX68948.1| RNA polymerase sigma-29 factor [Bacillus cereus NVH0597-99]
 gi|206734078|gb|EDZ51249.1| RNA polymerase sigma-29 factor [Bacillus cereus AH1134]
 gi|206745026|gb|EDZ56429.1| RNA polymerase sigma-29 factor [Bacillus cereus H3081.97]
 gi|217065302|gb|ACJ79552.1| RNA polymerase sigma-29 factor [Bacillus cereus AH187]
 gi|218162706|gb|ACK62698.1| RNA polymerase sigma-29 factor [Bacillus cereus B4264]
 gi|218537297|gb|ACK89695.1| RNA polymerase sigma-29 factor [Bacillus cereus AH820]
 gi|218544009|gb|ACK96403.1| RNA polymerase sigma-29 factor [Bacillus cereus G9842]
 gi|221241408|gb|ACM14118.1| RNA polymerase sporulation-specific sigma E factor [Bacillus cereus
           Q1]
 gi|225791008|gb|ACO31225.1| RNA polymerase sigma-29 factor [Bacillus cereus 03BB102]
 gi|227003693|gb|ACP13436.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. CDC 684]
 gi|228585495|gb|EEK43599.1| RNA polymerase sigma-35 factor [Bacillus cereus m1293]
 gi|228591400|gb|EEK49250.1| RNA polymerase sigma-35 factor [Bacillus cereus ATCC 10876]
 gi|228597321|gb|EEK54972.1| RNA polymerase sigma-35 factor [Bacillus cereus BGSC 6E1]
 gi|228603389|gb|EEK60866.1| RNA polymerase sigma-35 factor [Bacillus cereus 172560W]
 gi|228631451|gb|EEK88085.1| RNA polymerase sigma-35 factor [Bacillus cereus m1550]
 gi|228637109|gb|EEK93568.1| RNA polymerase sigma-35 factor [Bacillus cereus BDRD-ST24]
 gi|228643114|gb|EEK99390.1| RNA polymerase sigma-35 factor [Bacillus cereus BDRD-ST26]
 gi|228654419|gb|EEL10284.1| RNA polymerase sigma-35 factor [Bacillus cereus BDRD-Cer4]
 gi|228660194|gb|EEL15830.1| RNA polymerase sigma-35 factor [Bacillus cereus 95/8201]
 gi|228672150|gb|EEL27441.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock1-15]
 gi|228690455|gb|EEL44239.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock3-42]
 gi|228702201|gb|EEL54677.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock4-2]
 gi|228711695|gb|EEL63648.1| RNA polymerase sigma-35 factor [Bacillus cereus F65185]
 gi|228723836|gb|EEL75191.1| RNA polymerase sigma-35 factor [Bacillus cereus AH676]
 gi|228772643|gb|EEM21084.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228779333|gb|EEM27590.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis Bt407]
 gi|228785790|gb|EEM33794.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228792957|gb|EEM40515.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           sotto str. T04001]
 gi|228799638|gb|EEM46591.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228805501|gb|EEM52092.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228812144|gb|EEM58475.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228818672|gb|EEM64739.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228824385|gb|EEM70191.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228830760|gb|EEM76365.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228837086|gb|EEM82427.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228843121|gb|EEM88203.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228850019|gb|EEM94850.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis IBL 200]
 gi|228857154|gb|EEN01660.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis IBL 4222]
 gi|229265855|gb|ACQ47492.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0248]
 gi|296325450|gb|ADH08378.1| sporulation sigma factor SigE [Bacillus thuringiensis BMB171]
 gi|308154178|gb|ADA55132.3| sporulation specific sigma factor E [Bacillus thuringiensis serovar
           aizawai]
 gi|308154180|gb|ADA55133.2| sporulation specific sigma factor E [Bacillus thuringiensis serovar
           aizawai]
 gi|324327803|gb|ADY23063.1| sporulation sigma factor SigE [Bacillus thuringiensis serovar
           finitimus YBT-020]
 gi|326941674|gb|AEA17570.1| sporulation sigma factor SigE [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 239

 Score = 63.5 bits (153), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 69/264 (26%), Positives = 114/264 (43%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL  +  + GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLTKEEEEVLLNKLPK-GDQAARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I                      +  +  +LRR     
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCI----------------------ENEILMHLRR----- 128

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                               N + SEV       + DE LN      D N     D L  
Sbjct: 129 -------------------NNKNRSEV-------SFDEPLNI---DWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEV 264
           D D    ++ +  E    R++L +++  LN RE++I E R         T ++++    +
Sbjct: 160 DDD----IITKDLEATVDRHLLMKALHQLNDREKQIMELRFGLAGGEEKTQKDVADMLGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 216 SQSYISRLEKRIIKRLRKEFNKMV 239


>gi|317132580|ref|YP_004091894.1| RNA polymerase, sigma 28 subunit, SigE [Ethanoligenens harbinense
           YUAN-3]
 gi|315470559|gb|ADU27163.1| RNA polymerase, sigma 28 subunit, SigE [Ethanoligenens harbinense
           YUAN-3]
          Length = 242

 Score = 63.5 bits (153), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 35/92 (38%), Positives = 52/92 (56%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           YI+    +P     E+     R  E G+  A +RL+  +LRLVV IA  +   G+ + ++
Sbjct: 31  YINGPDTLPAPLGAEDEAACLRGLEAGEKDAKNRLIEHNLRLVVYIAKKFENTGVGVEDL 90

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           VS G IGL++AV  F P RG +LATY+   I+
Sbjct: 91  VSIGTIGLIKAVNTFCPSRGIKLATYASRCIE 122


>gi|228992639|ref|ZP_04152565.1| RNA polymerase sigma-35 factor [Bacillus pseudomycoides DSM 12442]
 gi|228998685|ref|ZP_04158272.1| RNA polymerase sigma-35 factor [Bacillus mycoides Rock3-17]
 gi|229006188|ref|ZP_04163874.1| RNA polymerase sigma-35 factor [Bacillus mycoides Rock1-4]
 gi|228755029|gb|EEM04388.1| RNA polymerase sigma-35 factor [Bacillus mycoides Rock1-4]
 gi|228761153|gb|EEM10112.1| RNA polymerase sigma-35 factor [Bacillus mycoides Rock3-17]
 gi|228766971|gb|EEM15608.1| RNA polymerase sigma-35 factor [Bacillus pseudomycoides DSM 12442]
          Length = 239

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 69/264 (26%), Positives = 113/264 (42%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL  +    GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLTKEEEEVLLNKL-PKGDQAARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I                      +  +  +LRR     
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCI----------------------ENEILMHLRR----- 128

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                               N + SEV       + DE LN      D N     D L  
Sbjct: 129 -------------------NNKNRSEV-------SFDEPLNI---DWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEV 264
           D D    ++ +  E    R++L +++  LN RE++I E R         T ++++    +
Sbjct: 160 DDD----IITKDLEANVDRHLLKKALHQLNDREKQIMELRFGLAGGEEKTQKDVADMLGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 216 SQSYISRLEKRIIKRLRKEFNKMV 239


>gi|323099955|gb|ADX23555.1| RNA polymerase sigma-35 factor [Bacillus mycoides]
          Length = 239

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 69/264 (26%), Positives = 114/264 (43%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL  +  + GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLTKEEEEVLLNKLPK-GDQAARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I                      +  +  +LRR     
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCI----------------------ENEILMHLRR----- 128

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                               N + SEV       + DE LN      D N     D L  
Sbjct: 129 -------------------NNKNRSEV-------SFDEPLNI---DWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEV 264
           D D    ++ +  E    R++L +++  LN RE++I E R         T ++++    +
Sbjct: 160 DDD----IITKDLEATVDRHLLMKALHQLNDREKQIMELRFGLAGGEEKTQKDVADMLGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 216 SQSYISRLEKRIIKRLRKEFNKMV 239


>gi|291547959|emb|CBL21067.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase
           sigma-70 factor, sigma-B/F/G subfamily [Ruminococcus sp.
           SR1/5]
          Length = 260

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 63/246 (25%), Positives = 114/246 (46%), Gaps = 16/246 (6%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GD +A   L   +  L+  +A  + G G+ + ++   G+IGL++AV KFD     + +T
Sbjct: 13  QGDKAARDLLFEENTGLIYSVAKRFLGRGVEMEDLFQIGSIGLLKAVDKFDMSYDVKFST 72

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y++  I   ++ Y LR   ++K+  +  +     N  R+    +A+T    +      +A
Sbjct: 73  YAVPMIIGEIKRY-LRDDGILKVSRSLKE-----NHYRIYQVREALTRRLEREPTTGEMA 126

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           +++ +S  E++      A  ESL+  I   +       D L    + QE+VL        
Sbjct: 127 EEMGISIEELVMTMESGAEVESLHKTIYQGEGTEISLMDKLPEKENRQEKVL-------- 178

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            R  L   +  L  +ERR+   R  Q N   +E ++ E  VS+ +V ++E R  + +QES
Sbjct: 179 DRIFLEEILGTLEAKERRLIYMRYFQ-NMTQME-IAHELGVSQVQVSRMEKRILRSLQES 236

Query: 284 IQKQVE 289
            +K  E
Sbjct: 237 AEKNKE 242


>gi|229075660|ref|ZP_04208642.1| RNA polymerase sigma-G factor [Bacillus cereus Rock4-18]
 gi|229098374|ref|ZP_04229319.1| RNA polymerase sigma-G factor [Bacillus cereus Rock3-29]
 gi|229117400|ref|ZP_04246776.1| RNA polymerase sigma-G factor [Bacillus cereus Rock1-3]
 gi|228666010|gb|EEL21476.1| RNA polymerase sigma-G factor [Bacillus cereus Rock1-3]
 gi|228684991|gb|EEL38924.1| RNA polymerase sigma-G factor [Bacillus cereus Rock3-29]
 gi|228707436|gb|EEL59627.1| RNA polymerase sigma-G factor [Bacillus cereus Rock4-18]
          Length = 289

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 66/267 (24%), Positives = 128/267 (47%), Gaps = 29/267 (10%)

Query: 25  KIPMLEKQEEYVLAKRYRE--HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           K+P+L+ +E   + K +RE   G++SA  +LV  +LRLV+ +   +   G  + ++   G
Sbjct: 45  KLPVLKNEE---MRKLFREMQSGEISAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVG 101

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            IGLM+++  FD  +  + +TY++  I   ++ Y LR  + +++  +          + L
Sbjct: 102 CIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSLRD----IAYKAL 156

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
           +   + I +N+ +P   + IAK L V+  E++          +L+A+ +        + D
Sbjct: 157 QVREKLIAENSKEP-TAMDIAKVLEVTHEEIVF---------ALDAIQDPVSLFEPIYND 206

Query: 203 W----LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
                 V D    E+   +K+E+      L   M  LN RE+ I   R  Q    T   +
Sbjct: 207 GGDPIFVMDQLSDEK---QKDEQWVEELALKEGMKRLNDREKMIIRKRFFQGK--TQMEV 261

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQ 285
           + E  +S+ +V ++E  A K++ ++IQ
Sbjct: 262 AEEIGISQAQVSRLEKSAIKQMNKTIQ 288


>gi|30021992|ref|NP_833623.1| sporulation sigma factor SigG [Bacillus cereus ATCC 14579]
 gi|206971353|ref|ZP_03232304.1| RNA polymerase sigma-G factor [Bacillus cereus AH1134]
 gi|218899057|ref|YP_002447468.1| RNA polymerase sigma-G factor [Bacillus cereus G9842]
 gi|228902409|ref|ZP_04066563.1| RNA polymerase sigma-G factor [Bacillus thuringiensis IBL 4222]
 gi|228909729|ref|ZP_04073552.1| RNA polymerase sigma-G factor [Bacillus thuringiensis IBL 200]
 gi|228922656|ref|ZP_04085956.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228940992|ref|ZP_04103550.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228954180|ref|ZP_04116208.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228960121|ref|ZP_04121785.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228966857|ref|ZP_04127901.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|229019106|ref|ZP_04175941.1| RNA polymerase sigma-G factor [Bacillus cereus AH1273]
 gi|229025350|ref|ZP_04181768.1| RNA polymerase sigma-G factor [Bacillus cereus AH1272]
 gi|229047588|ref|ZP_04193178.1| RNA polymerase sigma-G factor [Bacillus cereus AH676]
 gi|229071403|ref|ZP_04204625.1| RNA polymerase sigma-G factor [Bacillus cereus F65185]
 gi|229081156|ref|ZP_04213666.1| RNA polymerase sigma-G factor [Bacillus cereus Rock4-2]
 gi|229104466|ref|ZP_04235133.1| RNA polymerase sigma-G factor [Bacillus cereus Rock3-28]
 gi|229111373|ref|ZP_04240926.1| RNA polymerase sigma-G factor [Bacillus cereus Rock1-15]
 gi|229129181|ref|ZP_04258154.1| RNA polymerase sigma-G factor [Bacillus cereus BDRD-Cer4]
 gi|229146475|ref|ZP_04274846.1| RNA polymerase sigma-G factor [Bacillus cereus BDRD-ST24]
 gi|229162839|ref|ZP_04290796.1| RNA polymerase sigma-G factor [Bacillus cereus R309803]
 gi|229180179|ref|ZP_04307523.1| RNA polymerase sigma-G factor [Bacillus cereus 172560W]
 gi|229192073|ref|ZP_04319042.1| RNA polymerase sigma-G factor [Bacillus cereus ATCC 10876]
 gi|296504397|ref|YP_003666097.1| sporulation sigma factor SigG [Bacillus thuringiensis BMB171]
 gi|29897548|gb|AAP10824.1| RNA polymerase sigma-G factor [Bacillus cereus ATCC 14579]
 gi|206734125|gb|EDZ51296.1| RNA polymerase sigma-G factor [Bacillus cereus AH1134]
 gi|218543268|gb|ACK95662.1| RNA polymerase sigma-G factor [Bacillus cereus G9842]
 gi|228591399|gb|EEK49249.1| RNA polymerase sigma-G factor [Bacillus cereus ATCC 10876]
 gi|228603388|gb|EEK60865.1| RNA polymerase sigma-G factor [Bacillus cereus 172560W]
 gi|228620721|gb|EEK77590.1| RNA polymerase sigma-G factor [Bacillus cereus R309803]
 gi|228637108|gb|EEK93567.1| RNA polymerase sigma-G factor [Bacillus cereus BDRD-ST24]
 gi|228654418|gb|EEL10283.1| RNA polymerase sigma-G factor [Bacillus cereus BDRD-Cer4]
 gi|228672149|gb|EEL27440.1| RNA polymerase sigma-G factor [Bacillus cereus Rock1-15]
 gi|228678908|gb|EEL33118.1| RNA polymerase sigma-G factor [Bacillus cereus Rock3-28]
 gi|228702200|gb|EEL54676.1| RNA polymerase sigma-G factor [Bacillus cereus Rock4-2]
 gi|228711694|gb|EEL63647.1| RNA polymerase sigma-G factor [Bacillus cereus F65185]
 gi|228723835|gb|EEL75190.1| RNA polymerase sigma-G factor [Bacillus cereus AH676]
 gi|228735935|gb|EEL86512.1| RNA polymerase sigma-G factor [Bacillus cereus AH1272]
 gi|228742206|gb|EEL92371.1| RNA polymerase sigma-G factor [Bacillus cereus AH1273]
 gi|228792956|gb|EEM40514.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228799637|gb|EEM46590.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228805500|gb|EEM52091.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228818671|gb|EEM64738.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228837085|gb|EEM82426.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228850018|gb|EEM94849.1| RNA polymerase sigma-G factor [Bacillus thuringiensis IBL 200]
 gi|228857153|gb|EEN01659.1| RNA polymerase sigma-G factor [Bacillus thuringiensis IBL 4222]
 gi|296325449|gb|ADH08377.1| sporulation sigma factor SigG [Bacillus thuringiensis BMB171]
 gi|326941673|gb|AEA17569.1| sporulation sigma factor SigG [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 259

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 66/267 (24%), Positives = 128/267 (47%), Gaps = 29/267 (10%)

Query: 25  KIPMLEKQEEYVLAKRYRE--HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           K+P+L+ +E   + K +RE   G++SA  +LV  +LRLV+ +   +   G  + ++   G
Sbjct: 15  KLPVLKNEE---MRKLFREMQSGEISAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVG 71

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            IGLM+++  FD  +  + +TY++  I   ++ Y LR  + +++  +          + L
Sbjct: 72  CIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSLRD----IAYKAL 126

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
           +   + I +N+ +P   + IAK L V+  E++          +L+A+ +        + D
Sbjct: 127 QVREKLIAENSKEP-TAMDIAKVLEVTHEEIVF---------ALDAIQDPVSLFEPIYND 176

Query: 203 W----LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
                 V D    E+   +K+E+      L   M  LN RE+ I   R  Q    T   +
Sbjct: 177 GGDPIFVMDQLSDEK---QKDEQWVEELALKEGMKRLNDREKMIIRKRFFQGK--TQMEV 231

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQ 285
           + E  +S+ +V ++E  A K++ ++IQ
Sbjct: 232 AEEIGISQAQVSRLEKSAIKQMNKTIQ 258


>gi|327438872|dbj|BAK15237.1| DNA-directed RNA polymerase [Solibacillus silvestris StLB046]
          Length = 425

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 71/247 (28%), Positives = 118/247 (47%), Gaps = 40/247 (16%)

Query: 53  LVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           LV ++ +LV KI   Y G    G   +++   G IGL++A +KFD   G++ +TY+ WWI
Sbjct: 184 LVEANRKLVWKIVKHYSGLATVGFDENDMYQVGFIGLLKAAEKFDVSLGYQFSTYATWWI 243

Query: 110 KAAMQEYILRSWSLVKIGTTANQK---------RLFFNLRRLKGHLQAITDNNLKPEQVV 160
           + A+   I    +L++I     +K          L+  L R     + I+    +P  V+
Sbjct: 244 RQAITRGIADYSTLIRIPVHYREKMNKFIKIENELWNELARPATTFE-ISKEMEEPTNVI 302

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD----GQEQVLI 216
               +  +S+S + S++ RL GD          D+N+S  +  LV D +     +E   I
Sbjct: 303 E-ELRFYISQSNLDSLD-RLVGD----------DENTSLGE--LVLDDNLKMPDEEYYKI 348

Query: 217 EKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIE 273
           E       RN +     S L  RE ++   R   +N    TLE +   + ++RER+RQIE
Sbjct: 349 E------LRNTIGEIFQSNLTEREMQVLYYRFGFKNDETKTLEEVGQIYNLTRERIRQIE 402

Query: 274 ARAFKKV 280
           A+A +K+
Sbjct: 403 AKALRKL 409


>gi|169827019|ref|YP_001697177.1| RNA polymerase sigma-35 factor [Lysinibacillus sphaericus C3-41]
 gi|168991507|gb|ACA39047.1| RNA polymerase sigma-35 factor precursor [Lysinibacillus sphaericus
           C3-41]
          Length = 204

 Score = 63.5 bits (153), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 61/265 (23%), Positives = 117/265 (44%), Gaps = 64/265 (24%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+  ++E  V+A   +  GDL A   L+  +LRLVV IA  +   G PI +++S G+IG
Sbjct: 1   MPLSREEEVTVIASFMK--GDLRARDTLIERNLRLVVYIARRFDNTGTPIEDLISIGSIG 58

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A++ F+ ++  +LATY+   I+  +  + LR  S                  R+KG 
Sbjct: 59  LIKAIETFNTDKNIKLATYASRCIENEILMH-LRKTS------------------RMKGE 99

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           +                                    DE LN+    +D N     D L 
Sbjct: 100 VSL----------------------------------DEPLNS---DADGNELLLSDIL- 121

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFE 263
                +E ++++  E+K  R  +  ++++L  RER I E R      V  T + ++    
Sbjct: 122 ---GTEEHIILDNVEKKIERQHMFHAINLLGARERYIMECRFGLNGKVEMTQKEVADHLG 178

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           +S+  + ++E +  + ++E++ + +
Sbjct: 179 ISQSYISRLEKKIIQDLRENLNQPI 203


>gi|308233741|ref|ZP_07664478.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Atopobium vaginae DSM
           15829]
 gi|328943730|ref|ZP_08241195.1| DNA-directed RNA polymerase sigma subunit SigB [Atopobium vaginae
           DSM 15829]
 gi|327491699|gb|EGF23473.1| DNA-directed RNA polymerase sigma subunit SigB [Atopobium vaginae
           DSM 15829]
          Length = 286

 Score = 63.2 bits (152), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 60/261 (22%), Positives = 122/261 (46%), Gaps = 23/261 (8%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           +KQ+   L KRY+E GD  A  +LV +HL L   +A  ++  G  + ++V    IGL++A
Sbjct: 29  DKQKTKELFKRYKETGDEQAREQLVLAHLNLARFLASKFKNRGESLDDLVQVATIGLIKA 88

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           + +FD  RG    T++   I   ++ +   + WS+          R+   L+ L   +  
Sbjct: 89  IDRFDISRGLEFTTFATPTIMGEIKRHFRDKGWSV----------RVPRRLQELSAKVTQ 138

Query: 149 ITDNNLKPEQ----VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
           ++D   +  Q    V  IA+ L VS  EV+          S++  +   D +       +
Sbjct: 139 VSDKLTEKLQRSPSVDEIAQALGVSVDEVLEAMESAHAYSSVSLDVPQGDDDDGTQSSTV 198

Query: 205 VYDHDGQEQVLIEKE-ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  +      L++++ E  + R +L +++   + RE++I   R L+    T   ++ + +
Sbjct: 199 IDKY-----ALVDEDLESSDDRIVLEQAIKDFSEREQQIIRMRFLE--GFTQVEIAQKLQ 251

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++  +  +K QE +
Sbjct: 252 ISQVQVSRLLRKTLQKFQEKL 272


>gi|169351193|ref|ZP_02868131.1| hypothetical protein CLOSPI_01972 [Clostridium spiroforme DSM 1552]
 gi|169292255|gb|EDS74388.1| hypothetical protein CLOSPI_01972 [Clostridium spiroforme DSM 1552]
          Length = 258

 Score = 63.2 bits (152), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 66/274 (24%), Positives = 125/274 (45%), Gaps = 27/274 (9%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           N  II+NG        HE RK   L  +E Y L   Y++  D     +LV  +++LV+ +
Sbjct: 3   NYQIIING-------YHEPRK--KLTTKETYALIDEYQKTKDERIKEKLVNDNIKLVISM 53

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
              +        ++   G IGL++A++ F+     + +TY++  I   M+ Y LR    +
Sbjct: 54  TKRFYNRSDGCDDLFQVGMIGLIKAIENFNTSYDLKFSTYAVPLIIGEMKRY-LRDNHQI 112

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA-IAKKLNVSESEVISMNCRLAGD 183
           KI  +   K + + + ++K        N  + E  +  +AKKL++ +S ++         
Sbjct: 113 KISRSL--KDIAYKILKIKDEYL----NKFQREPTIKELAKKLDIDQSVIVEALLSTNSV 166

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SL   + +SD NS +  D L    D +  VL     + N R  L  ++  L+ +E  + 
Sbjct: 167 ASLQEEVKNSDGNSLKMIDSL---SDEKAGVL-----KTNERIDLYDALKSLSQKEHDVI 218

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
           + R  +   ++   ++ E  +S+ +V +IE +A 
Sbjct: 219 KQRYFE--GLSQSEIAKELFISQAQVSRIEKKAL 250


>gi|160933251|ref|ZP_02080640.1| hypothetical protein CLOLEP_02097 [Clostridium leptum DSM 753]
 gi|156868325|gb|EDO61697.1| hypothetical protein CLOLEP_02097 [Clostridium leptum DSM 753]
          Length = 230

 Score = 63.2 bits (152), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 36/97 (37%), Positives = 58/97 (59%), Gaps = 1/97 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L ++EE  + +R R  G+ +A   L+T +LRLVV IA  +   G  + +++S G IGL
Sbjct: 28  PPLSREEEDEVMERVR-RGEKNAREPLITHNLRLVVYIAKKFDSNGASVEDLISIGTIGL 86

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           ++AV  F PER  +LATY+   I+  +  ++ +S  L
Sbjct: 87  IKAVNTFCPERNIKLATYASRCIENEILMFLRKSSQL 123


>gi|254389000|ref|ZP_05004231.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|294814936|ref|ZP_06773579.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|197702718|gb|EDY48530.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|294327535|gb|EFG09178.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 358

 Score = 63.2 bits (152), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 63/240 (26%), Positives = 107/240 (44%), Gaps = 27/240 (11%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           ++LV  HL LV  +A  +R  G P+ ++     IGL+++V +FDPERG   +TY+   + 
Sbjct: 136 NQLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPERGVEFSTYATPTVV 195

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFN-----LRRLKGHLQAITDNNLKPEQVVAIAKK 165
             ++ +       V++     + RL        L +L G    + +          +A++
Sbjct: 196 GEIKRHFRDKGWAVRVPRRLQELRLALTTATAELSQLHGRSPTVHE----------LAER 245

Query: 166 LNVSESEVISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           L +SE EV      L G ES NA    S D   +  +   V D  G E   +E  E    
Sbjct: 246 LGISEEEV------LEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVE---Y 296

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   ++++ +
Sbjct: 297 RESLKPLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLRDKL 354


>gi|290968733|ref|ZP_06560271.1| sigma-70 region 2 [Megasphaera genomosp. type_1 str. 28L]
 gi|290781386|gb|EFD93976.1| sigma-70 region 2 [Megasphaera genomosp. type_1 str. 28L]
          Length = 217

 Score = 63.2 bits (152), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 33/104 (31%), Positives = 61/104 (58%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+ E++KI +L ++EE  L + Y+E G++ A  RL+  +  LV K  M    +   I
Sbjct: 2   LTSYLEELKKITLLTREEEQTLWRAYKEQGNMQARARLIEQYQPLVFKEVMRLSMHSEWI 61

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
            + + EG +GL++AV+ F  ++G   + Y++  I+  + EY+ R
Sbjct: 62  PDAIQEGTVGLIEAVEHFRIQQGVAFSLYAVHRIRGEILEYLRR 105


>gi|326443307|ref|ZP_08218041.1| sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 351

 Score = 63.2 bits (152), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 63/240 (26%), Positives = 107/240 (44%), Gaps = 27/240 (11%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           ++LV  HL LV  +A  +R  G P+ ++     IGL+++V +FDPERG   +TY+   + 
Sbjct: 129 NQLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPERGVEFSTYATPTVV 188

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFN-----LRRLKGHLQAITDNNLKPEQVVAIAKK 165
             ++ +       V++     + RL        L +L G    + +          +A++
Sbjct: 189 GEIKRHFRDKGWAVRVPRRLQELRLALTTATAELSQLHGRSPTVHE----------LAER 238

Query: 166 LNVSESEVISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           L +SE EV      L G ES NA    S D   +  +   V D  G E   +E  E    
Sbjct: 239 LGISEEEV------LEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVE---Y 289

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   ++++ +
Sbjct: 290 RESLKPLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLRDKL 347


>gi|224553544|gb|ACN55010.1| RNA polymerase sigma factor [Escherichia coli]
          Length = 111

 Score = 63.2 bits (152), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 23/47 (48%), Positives = 37/47 (78%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           GL + +++ EGN+GL++AV+KFDPERGFR +T + WWI+  ++  I+
Sbjct: 1   GLALLDLIEEGNLGLIRAVEKFDPERGFRFSTSATWWIRQTIERAIM 47


>gi|15615119|ref|NP_243422.1| sporulation sigma factor SigE [Bacillus halodurans C-125]
 gi|10175176|dbj|BAB06275.1| RNA polymerase sporulation mother cell-specific (early) sigma-29
           factor [Bacillus halodurans C-125]
          Length = 237

 Score = 63.2 bits (152), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 68/264 (25%), Positives = 111/264 (42%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE  L K+    GD +    L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 35  PPLSKEEEAHLLKKL-PSGDKAVRSMLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 93

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  Y                      LRR     
Sbjct: 94  IKAVNTFNPEKKIKLATYASRCIENEILMY----------------------LRR----- 126

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
               +N ++ E                      ++ DE LN      D N     D L  
Sbjct: 127 ----NNKIRSE----------------------VSFDEPLNI---DWDGNELLLSDVLGT 157

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEV 264
           D D    ++    E K  R +L +++  L  RE++I E R         T ++++    +
Sbjct: 158 DDD----IITRGIEEKVDRKLLMKALHTLTDREKQIMELRFGLAGGEEKTQKDVADLLGI 213

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++Q+   K V
Sbjct: 214 SQSYISRLEKRIIKRLQKEFNKMV 237


>gi|163941643|ref|YP_001646527.1| sporulation sigma factor SigG [Bacillus weihenstephanensis KBAB4]
 gi|229134713|ref|ZP_04263522.1| RNA polymerase sigma-G factor [Bacillus cereus BDRD-ST196]
 gi|163863840|gb|ABY44899.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           weihenstephanensis KBAB4]
 gi|228648759|gb|EEL04785.1| RNA polymerase sigma-G factor [Bacillus cereus BDRD-ST196]
 gi|322510150|gb|ADX05464.1| RNA polymerase sigma-G factor [Bacillus mycoides]
          Length = 292

 Score = 63.2 bits (152), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 66/267 (24%), Positives = 128/267 (47%), Gaps = 29/267 (10%)

Query: 25  KIPMLEKQEEYVLAKRYRE--HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           K+P+L+ +E   + K +RE   G++SA  +LV  +LRLV+ +   +   G  + ++   G
Sbjct: 48  KLPVLKNEE---MRKLFREMQSGEISAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVG 104

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            IGLM+++  FD  +  + +TY++  I   ++ Y LR  + +++  +          + L
Sbjct: 105 CIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSLRD----IAYKAL 159

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
           +   + I +N+ +P   + IAK L V+  E++          +L+A+ +        + D
Sbjct: 160 QVREKLIAENSKEP-TAMDIAKVLEVTHEEIVF---------ALDAIQDPVSLFEPIYND 209

Query: 203 W----LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
                 V D    E+   +K+E+      L   M  LN RE+ I   R  Q    T   +
Sbjct: 210 GGDPIFVMDQLKDEK---QKDEQWVEELALKEGMKRLNDREKMIIRKRFFQGK--TQMEV 264

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQ 285
           + E  +S+ +V ++E  A K++ ++IQ
Sbjct: 265 AEEIGISQAQVSRLEKSAIKQMNKTIQ 291


>gi|126649719|ref|ZP_01721955.1| sporulation sigma factor SigE [Bacillus sp. B14905]
 gi|126593438|gb|EAZ87383.1| sporulation sigma factor SigE [Bacillus sp. B14905]
          Length = 227

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 61/265 (23%), Positives = 117/265 (44%), Gaps = 64/265 (24%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+  ++E  V+A   +  GDL A   L+  +LRLVV IA  +   G PI +++S G+IG
Sbjct: 24  VPLSREEEVTVIASFMK--GDLRARDTLIERNLRLVVYIARRFDNTGTPIEDLISIGSIG 81

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A++ F+ ++  +LATY+   I+  +  + LR  S                  R+KG 
Sbjct: 82  LIKAIETFNTDKNIKLATYASRCIENEILMH-LRKTS------------------RMKGE 122

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           +                                    DE LN+    +D N     D L 
Sbjct: 123 VSL----------------------------------DEPLNS---DADGNELLLSDIL- 144

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFE 263
                +E ++++  E+K  R  +  ++++L  RER I E R      V  T + ++    
Sbjct: 145 ---GTEEHIILDNVEKKIERQHMFHAINLLGARERYIMECRFGLNGKVEMTQKEVADHLG 201

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           +S+  + ++E +  + ++E++ + +
Sbjct: 202 ISQSYISRLEKKIIQDLRENLNQPI 226


>gi|114566372|ref|YP_753526.1| sporulation sigma factor SigE [Syntrophomonas wolfei subsp. wolfei
           str. Goettingen]
 gi|114337307|gb|ABI68155.1| sporulation sigma factor SigE [Syntrophomonas wolfei subsp. wolfei
           str. Goettingen]
          Length = 240

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 37/110 (33%), Positives = 65/110 (59%), Gaps = 7/110 (6%)

Query: 16  LSRYIH-----EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           L R+IH     E+   P+ E++E  ++++   + G +S    L+  +LRLVV IA  +  
Sbjct: 23  LPRFIHYIGSTEVLPAPLREQEEMALISQL--DQGIMSVKATLIEHNLRLVVYIAKKFEN 80

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
            G+ I ++VS G IGL++AV  F+P++  +LATY+   I+  +  Y+ R+
Sbjct: 81  TGINIEDLVSIGTIGLIKAVNTFEPKKNIKLATYASRCIENEILMYLRRN 130


>gi|183220350|ref|YP_001838346.1| RNA polymerase sigma factor WhiG [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Paris)']
 gi|189910466|ref|YP_001962021.1| RNA polymerase sigma factor WhiG [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Ames)']
 gi|167775142|gb|ABZ93443.1| RNA polymerase sigma subunit [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Ames)']
 gi|167778772|gb|ABZ97070.1| RNA polymerase sigma factor for flagellar operon [Leptospira
           biflexa serovar Patoc strain 'Patoc 1 (Paris)']
          Length = 266

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 76/271 (28%), Positives = 126/271 (46%), Gaps = 32/271 (11%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQ 88
           +E  L K+YR   D      LV  +  LV  +A G    G+P      ++VS G  GL+ 
Sbjct: 12  DETDLWKQYRVKKDAEIRSYLVEKYSPLVKHVA-GRIAIGMPQNVEFEDLVSYGVFGLLD 70

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRS--WSLVKIGTTANQKRLFFNLRRLKGHL 146
           A++KFDP R  +  TY+M  I+ ++ +  LRS  W    I   A Q      L  +   L
Sbjct: 71  AIEKFDPSREIKFKTYAMTRIRGSIFDE-LRSVDWIPRSIRQKAKQ------LENIIAML 123

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSS-QWQDW 203
           +      +  E+   IAK+L VS  E  S+  +L+G    SLN +    D+N    + + 
Sbjct: 124 ENKEGKKVDDEE---IAKELGVSMEEYNSLLAKLSGTSLVSLNDIWFLGDENDEVSFMET 180

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L    +     +IEKEE K   N++  ++  L  +E+++      ++  +TL+ +    E
Sbjct: 181 LESPMNMNPDNIIEKEEIK---NVIVEAIQSLPEKEKKVIVLYYYED--LTLKEIGEVLE 235

Query: 264 VSRERVRQIEARA-------FKKVQESIQKQ 287
           V+  R+ Q+  +A         KV+ +IQK+
Sbjct: 236 VTESRISQLHTKAVARLRSKLSKVKSAIQKR 266


>gi|294631337|ref|ZP_06709897.1| RNA polymerase sigma factor [Streptomyces sp. e14]
 gi|292834670|gb|EFF93019.1| RNA polymerase sigma factor [Streptomyces sp. e14]
          Length = 379

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 65/240 (27%), Positives = 109/240 (45%), Gaps = 29/240 (12%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +LV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+   +  
Sbjct: 158 QLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATPTVVG 217

Query: 112 AMQEYIL-RSWSLVKIGTTANQKRLFFN-----LRRLKGHLQAITDNNLKPEQVVAIAKK 165
            ++ +   + W+ V++     + RL        L +L G    + +          +A+K
Sbjct: 218 EIKRHFRDKGWA-VRVPRRLQELRLALTTATAELSQLHGRSPTVHE----------LAEK 266

Query: 166 LNVSESEVISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           L +SE EV      L G ES NA    S D   +  +   V D  G E   +E  E    
Sbjct: 267 LAISEEEV------LEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVE---Y 317

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 318 RESLKPLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLREKL 375


>gi|302554065|ref|ZP_07306407.1| RNA polymerase sigma-G factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302471683|gb|EFL34776.1| RNA polymerase sigma-G factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 381

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 65/240 (27%), Positives = 110/240 (45%), Gaps = 29/240 (12%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +LV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+   +  
Sbjct: 160 QLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATPTVVG 219

Query: 112 AMQEYIL-RSWSLVKIGTTANQKRLFFN-----LRRLKGHLQAITDNNLKPEQVVAIAKK 165
            ++ +   + W+ V++     + RL        L +L G    + +          +A+K
Sbjct: 220 EIKRHFRDKGWA-VRVPRRLQELRLALTTATAELSQLHGRSPTVHE----------LAEK 268

Query: 166 LNVSESEVISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           L++SE EV      L G ES NA    S D   +  +   V D  G E   +E  E    
Sbjct: 269 LSISEEEV------LEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVE---Y 319

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 320 RESLKPLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLREKL 377


>gi|218197356|gb|EEC79783.1| hypothetical protein OsI_21197 [Oryza sativa Indica Group]
          Length = 557

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 62/251 (24%), Positives = 113/251 (45%), Gaps = 14/251 (5%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E +L  R +E        RL+ +   LV  IA  Y G G    +++  G +G++   +K
Sbjct: 305 DEALLRSRLQE--GYCCRERLLVTTEWLVKYIAKTYAGMGTAFEDLLQAGKMGVLNGAEK 362

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD ++G + +TY  +WI+ AM   +  +  ++++       R+   +R+++   +AI  N
Sbjct: 363 FDSQKGCKFSTYVKYWIRKAMLALLAENSGVIQLPA-----RMEGIIRKVREARRAIRYN 417

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA  + VS +     N RLA   S   +   ++    Q   ++    D   
Sbjct: 418 TGRNPPDAEIAALIGVSVA-----NVRLARKCSRRVVSLYTEIGVGQNAKFVEVTPDTSL 472

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
           +   E   R   R  L   +  L PRE  + + R   E+    +LE + S + VS+E +R
Sbjct: 473 EAPDEAMFRMQLRERLLHVLDRLPPREGHVLKLRHGLEDGKCRSLEQIGSIYHVSKEWIR 532

Query: 271 QIEARAFKKVQ 281
           +IE  A  K++
Sbjct: 533 KIEKSAMSKLR 543


>gi|30266005|gb|AAN16080.1| SigB [Listeria seeligeri]
 gi|30266007|gb|AAN16081.1| SigB [Listeria seeligeri]
 gi|66968476|gb|AAY59617.1| SigB [Listeria seeligeri]
 gi|66968478|gb|AAY59618.1| SigB [Listeria seeligeri]
 gi|66968480|gb|AAY59619.1| SigB [Listeria seeligeri]
 gi|66968482|gb|AAY59620.1| SigB [Listeria seeligeri]
 gi|66968484|gb|AAY59621.1| SigB [Listeria seeligeri]
 gi|66968486|gb|AAY59622.1| SigB [Listeria seeligeri]
 gi|313634111|gb|EFS00776.1| RNA polymerase sigma-B factor [Listeria seeligeri FSL N1-067]
 gi|313638716|gb|EFS03817.1| RNA polymerase sigma-B factor [Listeria seeligeri FSL S4-171]
          Length = 259

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 67/269 (24%), Positives = 131/269 (48%), Gaps = 36/269 (13%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  + +LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQENGDQDAQYNLVVHYKKLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +++D   G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEEL 125

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDW 203
           T       Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D 
Sbjct: 126 TRELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDV 182

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE-- 261
           +    DG E+V        N+R +L + + VL+ RE++I +          +EN S +  
Sbjct: 183 VGGTDDGFERV--------NQRMLLEKVLPVLDEREQKILQY-------TFIENRSQKET 227

Query: 262 ---FEVSRERVRQIEARAFKKVQESIQKQ 287
               ++S+  V +I+ +A KK++E++Q +
Sbjct: 228 GELLDISQMHVSRIQRQAIKKLREALQNE 256


>gi|42782996|ref|NP_980243.1| sporulation sigma factor SigG [Bacillus cereus ATCC 10987]
 gi|49186753|ref|YP_030005.1| sporulation sigma factor SigG [Bacillus anthracis str. Sterne]
 gi|49478441|ref|YP_037965.1| sporulation sigma factor SigG [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|52141585|ref|YP_085244.1| sporulation sigma factor SigG [Bacillus cereus E33L]
 gi|118479123|ref|YP_896274.1| sporulation sigma factor SigG [Bacillus thuringiensis str. Al
           Hakam]
 gi|196038711|ref|ZP_03106019.1| RNA polymerase sigma-G factor [Bacillus cereus NVH0597-99]
 gi|222097349|ref|YP_002531406.1| sporulation sigma factor sigg [Bacillus cereus Q1]
 gi|228928952|ref|ZP_04091984.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228935219|ref|ZP_04098045.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228947623|ref|ZP_04109913.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228987048|ref|ZP_04147173.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|229092950|ref|ZP_04224083.1| RNA polymerase sigma-G factor [Bacillus cereus Rock3-42]
 gi|229123417|ref|ZP_04252621.1| RNA polymerase sigma-G factor [Bacillus cereus 95/8201]
 gi|229186144|ref|ZP_04313313.1| RNA polymerase sigma-G factor [Bacillus cereus BGSC 6E1]
 gi|254683387|ref|ZP_05147247.1| sporulation sigma factor SigG [Bacillus anthracis str. CNEVA-9066]
 gi|254739809|ref|ZP_05197502.1| sporulation sigma factor SigG [Bacillus anthracis str. Kruger B]
 gi|254750999|ref|ZP_05203038.1| sporulation sigma factor SigG [Bacillus anthracis str. Vollum]
 gi|254757943|ref|ZP_05209970.1| sporulation sigma factor SigG [Bacillus anthracis str. Australia
           94]
 gi|301055394|ref|YP_003793605.1| RNA polymerase sigma-G factor [Bacillus anthracis CI]
 gi|42738923|gb|AAS42851.1| RNA polymerase sigma-G factor [Bacillus cereus ATCC 10987]
 gi|49180680|gb|AAT56056.1| RNA polymerase sigma-G factor [Bacillus anthracis str. Sterne]
 gi|49329997|gb|AAT60643.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|51975054|gb|AAU16604.1| RNA polymerase sigma-G factor [Bacillus cereus E33L]
 gi|118418348|gb|ABK86767.1| RNA polymerase, sigma subunit, RpsG/SigG [Bacillus thuringiensis
           str. Al Hakam]
 gi|196030434|gb|EDX69033.1| RNA polymerase sigma-G factor [Bacillus cereus NVH0597-99]
 gi|221241407|gb|ACM14117.1| RNA polymerase sigma-G factor [Bacillus cereus Q1]
 gi|228597320|gb|EEK54971.1| RNA polymerase sigma-G factor [Bacillus cereus BGSC 6E1]
 gi|228660193|gb|EEL15829.1| RNA polymerase sigma-G factor [Bacillus cereus 95/8201]
 gi|228690454|gb|EEL44238.1| RNA polymerase sigma-G factor [Bacillus cereus Rock3-42]
 gi|228772642|gb|EEM21083.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228812143|gb|EEM58474.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228824384|gb|EEM70190.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228830759|gb|EEM76364.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|300377563|gb|ADK06467.1| RNA polymerase sigma-G factor [Bacillus cereus biovar anthracis
           str. CI]
 gi|324327802|gb|ADY23062.1| sporulation sigma factor SigG [Bacillus thuringiensis serovar
           finitimus YBT-020]
          Length = 289

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 66/267 (24%), Positives = 127/267 (47%), Gaps = 29/267 (10%)

Query: 25  KIPMLEKQEEYVLAKRYRE--HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           K+P+L+  E   + K +RE   G++SA  +LV  +LRLV+ +   +   G  + ++   G
Sbjct: 45  KLPVLKNDE---MRKLFREMQSGEISAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVG 101

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            IGLM+++  FD  +  + +TY++  I   ++ Y LR  + +++  +          + L
Sbjct: 102 CIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSLRD----IAYKAL 156

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
           +   + I +N+ +P   + IAK L V+  E++          +L+A+ +        + D
Sbjct: 157 QVREKLIAENSKEP-TAMDIAKVLEVTHEEIVF---------ALDAIQDPVSLFEPIYND 206

Query: 203 W----LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
                 V D    E+   +K+E+      L   M  LN RE+ I   R  Q    T   +
Sbjct: 207 GGDPIFVMDQLSDEK---QKDEQWVEELALKEGMKRLNDREKMIIRKRFFQGK--TQMEV 261

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQ 285
           + E  +S+ +V ++E  A K++ ++IQ
Sbjct: 262 AEEIGISQAQVSRLEKSAIKQMNKTIQ 288


>gi|302338101|ref|YP_003803307.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Spirochaeta
           smaragdinae DSM 11293]
 gi|301635286|gb|ADK80713.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Spirochaeta
           smaragdinae DSM 11293]
          Length = 262

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 66/265 (24%), Positives = 127/265 (47%), Gaps = 29/265 (10%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGN 83
           +LE++ E  L + YR   D     R +  +  LV  +A G    G+P      ++V  G 
Sbjct: 5   LLEEKTEAELWELYRNSRDPKIRDRFIEQYSPLVKYVA-GKVAIGMPQNVEFDDLVGFGV 63

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
            GL  A++KFDPE+  +  TY++  I+ A+ +  LRS   V        + +   + RL+
Sbjct: 64  FGLFDAIEKFDPEKHVKFKTYAVTRIRGAIYDE-LRSIDWVPRSVRQKAREIEETIHRLE 122

Query: 144 GHL-QAITDNNLKPEQVVAIAK----KLNVSESEVISMN-CRLAGDESLN-ALINSSDKN 196
             L +A +D  +  E  +++A      L +S + V+S+N     GDE+   A+++  +  
Sbjct: 123 ASLGRAASDKEIADELGISVADFQKLMLKISGTSVLSLNDVWYTGDENDTVAIVDGIESP 182

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
            S   D           ++IEKEE    R ++ +++S L  +E+++      ++  +TL+
Sbjct: 183 QSLNPD-----------IIIEKEE---IRRVIVQAISELPEKEKKVLVLYYYED--LTLK 226

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +    +V+  RV Q+  +A  +++
Sbjct: 227 EIGKVLDVTESRVSQLHTKAIMRLR 251


>gi|152976265|ref|YP_001375782.1| sporulation sigma factor SigE [Bacillus cereus subsp. cytotoxis NVH
           391-98]
 gi|152025017|gb|ABS22787.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           cytotoxicus NVH 391-98]
          Length = 239

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 34/79 (43%), Positives = 50/79 (63%), Gaps = 1/79 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL  +    GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLTKEEEEVLLNKL-PKGDQAARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYS 105
           ++AV  F+PE+  +LATY+
Sbjct: 96  IKAVNTFNPEKKIKLATYA 114


>gi|166031695|ref|ZP_02234524.1| hypothetical protein DORFOR_01395 [Dorea formicigenerans ATCC
           27755]
 gi|166028672|gb|EDR47429.1| hypothetical protein DORFOR_01395 [Dorea formicigenerans ATCC
           27755]
          Length = 244

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 70/260 (26%), Positives = 120/260 (46%), Gaps = 35/260 (13%)

Query: 34  EYVLAKRYREH-GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           ++ +A   R H GD  A  RLV  +  LV  I   +   G+   ++   GNIGL++A+ K
Sbjct: 2   DHTIALIQRSHEGDEEARARLVEENAGLVWCIVKRFHNRGVETEDLFQIGNIGLIKAIDK 61

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD     + +TY++  I   ++ + LR   ++K+  +   K L +    LK  LQ    N
Sbjct: 62  FDLSYDVKFSTYAVPMISGEIKRF-LRDDGMIKVSRSL--KELAYKAYLLKEDLQ----N 114

Query: 153 NLKPEQVVA-IAKKLNVSESEVISMNCRLAGD-ESLNALINSSDKNSSQWQDWLVYDHDG 210
               E  V  ++++L V + E++ M     GD ESL+  I               Y  DG
Sbjct: 115 QWGREPTVGELSERLGVEQEELV-MALDAGGDVESLHKPI---------------YQKDG 158

Query: 211 QEQVLIEKEERKNRRN-------MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           QE  L++K E K+  +       +LT  + VLN  E+R+   R   E   T   +  E  
Sbjct: 159 QEIRLMDKLEEKSEEHEQVLNHIVLTELLGVLNQDEKRLIYLRYFAEQ--TQSQVGRELG 216

Query: 264 VSRERVRQIEARAFKKVQES 283
           +S+ +V ++E +   +++ +
Sbjct: 217 ISQVQVSRMEKKILGQLKNA 236


>gi|229031535|ref|ZP_04187535.1| RNA polymerase sigma-G factor [Bacillus cereus AH1271]
 gi|228729824|gb|EEL80804.1| RNA polymerase sigma-G factor [Bacillus cereus AH1271]
          Length = 289

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 66/267 (24%), Positives = 126/267 (47%), Gaps = 29/267 (10%)

Query: 25  KIPMLEKQEEYVLAKRYRE--HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           K+P+L+  E   + K +RE   G++SA  +LV  +LRLV+ +   +   G  + ++   G
Sbjct: 45  KLPVLKNDE---MRKLFREMQSGEISAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVG 101

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            IGLM+++  FD  +  + +TY++  I   ++ Y LR    +++  +          + L
Sbjct: 102 CIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRY-LRDNDPIRVSRSLRD----IAYKAL 156

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
           +   + I +N+ +P   + IAK L V+  E++          +L+A+ +        + D
Sbjct: 157 QVREKLIAENSKEP-TAMDIAKVLEVTHEEIVF---------ALDAIQDPVSLFEPIYND 206

Query: 203 W----LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
                 V D    E+   +K+E+      L   M  LN RE+ I   R  Q    T   +
Sbjct: 207 GGDPIFVMDQLSDEK---QKDEQWVEELALKEGMKRLNDREKMIIRKRFFQGK--TQMEV 261

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQ 285
           + E  +S+ +V ++E  A K++ ++IQ
Sbjct: 262 AEEIGISQAQVSRLEKSAIKQMNKTIQ 288


>gi|143621|gb|AAA22794.1| sporulation protein [Bacillus subtilis]
          Length = 239

 Score = 63.2 bits (152), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 37/94 (39%), Positives = 56/94 (59%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K EE VL  +   +GD +A   L+   LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLSKDEEQVLLMKL-PNGDQAARAILIERILRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN 129


>gi|49328110|gb|AAT58808.1| hypothetical protein [Oryza sativa Japonica Group]
          Length = 799

 Score = 62.8 bits (151), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 62/251 (24%), Positives = 113/251 (45%), Gaps = 14/251 (5%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E +L  R +E        RL+ +   LV  IA  Y G G    +++  G +G++   +K
Sbjct: 547 DEALLRSRLQE--GYCCRERLLVTTEWLVKYIAKTYAGMGTAFEDLLQAGKMGVLNGAEK 604

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD ++G + +TY  +WI+ AM   +  +  ++++       R+   +R+++   +AI  N
Sbjct: 605 FDSQKGCKFSTYVKYWIRKAMLALLAENSGVIQLPA-----RMEGIIRKVREARRAIRYN 659

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA  + VS +     N RLA   S   +   ++    Q   ++    D   
Sbjct: 660 TGRNPPDAEIAALIGVSVA-----NVRLARKCSRRVVSLYTEIGVGQNAKFVEVTPDTSL 714

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
           +   E   R   R  L   +  L PRE  + + R   E+    +LE + S + VS+E +R
Sbjct: 715 EAPDEAMFRMQLRERLLHVLDRLPPREGHVLKLRHGLEDGKCRSLEQIGSIYHVSKEWIR 774

Query: 271 QIEARAFKKVQ 281
           +IE  A  K++
Sbjct: 775 KIEKSAMSKLR 785


>gi|258514353|ref|YP_003190575.1| sporulation sigma factor SigE [Desulfotomaculum acetoxidans DSM
           771]
 gi|257778058|gb|ACV61952.1| RNA polymerase, sigma 28 subunit, SigE [Desulfotomaculum
           acetoxidans DSM 771]
          Length = 241

 Score = 62.8 bits (151), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 37/94 (39%), Positives = 54/94 (57%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EE +L  R  E GD +    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 39  PPLSIDEESILINRL-ETGDGAVRGVLIERNLRLVVYIARKFENTGISIEDLVSIGTIGL 97

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  FDP +  +LATY+   I+  +  Y+ R+
Sbjct: 98  IKAVNTFDPAKKIKLATYASRCIENEILMYLRRN 131


>gi|161486847|ref|NP_781765.2| sporulation sigma factor SigE [Clostridium tetani E88]
          Length = 235

 Score = 62.8 bits (151), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 36/94 (38%), Positives = 56/94 (59%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L ++EE  L ++   +GD S    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 33  PPLTREEEENLVEKLN-YGDESIRSILIERNLRLVVYIARKFENTGIGIEDLVSVGTIGL 91

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  FDP +  +LATY+   I+  +  Y+ R+
Sbjct: 92  IKAVNTFDPSKKIKLATYASRCIENEILMYLRRN 125


>gi|30263905|ref|NP_846282.1| sporulation sigma factor SigG [Bacillus anthracis str. Ames]
 gi|47778237|ref|YP_020684.2| sporulation sigma factor SigG [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|165872304|ref|ZP_02216941.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0488]
 gi|167641114|ref|ZP_02399369.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0193]
 gi|170688856|ref|ZP_02880059.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0465]
 gi|170708817|ref|ZP_02899253.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0389]
 gi|177654919|ref|ZP_02936636.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0174]
 gi|190565736|ref|ZP_03018655.1| RNA polymerase sigma-G factor [Bacillus anthracis Tsiankovskii-I]
 gi|196035947|ref|ZP_03103349.1| RNA polymerase sigma-G factor [Bacillus cereus W]
 gi|196045922|ref|ZP_03113151.1| RNA polymerase sigma-G factor [Bacillus cereus 03BB108]
 gi|206976720|ref|ZP_03237624.1| RNA polymerase sigma-G factor [Bacillus cereus H3081.97]
 gi|217961324|ref|YP_002339892.1| sporulation sigma factor SigG [Bacillus cereus AH187]
 gi|218233406|ref|YP_002368703.1| sporulation sigma factor SigG [Bacillus cereus B4264]
 gi|218905033|ref|YP_002452867.1| RNA polymerase sigma-G factor [Bacillus cereus AH820]
 gi|225865885|ref|YP_002751263.1| RNA polymerase sigma-G factor [Bacillus cereus 03BB102]
 gi|227813187|ref|YP_002813196.1| RNA polymerase sigma-G factor [Bacillus anthracis str. CDC 684]
 gi|228916541|ref|ZP_04080107.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|229140552|ref|ZP_04269107.1| RNA polymerase sigma-G factor [Bacillus cereus BDRD-ST26]
 gi|229152101|ref|ZP_04280296.1| RNA polymerase sigma-G factor [Bacillus cereus m1550]
 gi|229157482|ref|ZP_04285559.1| RNA polymerase sigma-G factor [Bacillus cereus ATCC 4342]
 gi|229174570|ref|ZP_04302100.1| RNA polymerase sigma-G factor [Bacillus cereus MM3]
 gi|229198015|ref|ZP_04324729.1| RNA polymerase sigma-G factor [Bacillus cereus m1293]
 gi|229602177|ref|YP_002868139.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0248]
 gi|254721437|ref|ZP_05183226.1| sporulation sigma factor SigG [Bacillus anthracis str. A1055]
 gi|30258549|gb|AAP27768.1| RNA polymerase sigma-G factor [Bacillus anthracis str. Ames]
 gi|47551942|gb|AAT33159.2| RNA polymerase sigma-G factor [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|164711980|gb|EDR17520.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0488]
 gi|167510894|gb|EDR86285.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0193]
 gi|170126302|gb|EDS95193.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0389]
 gi|170667211|gb|EDT17971.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0465]
 gi|172080430|gb|EDT65517.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0174]
 gi|190562655|gb|EDV16621.1| RNA polymerase sigma-G factor [Bacillus anthracis Tsiankovskii-I]
 gi|195991596|gb|EDX55562.1| RNA polymerase sigma-G factor [Bacillus cereus W]
 gi|196023362|gb|EDX62040.1| RNA polymerase sigma-G factor [Bacillus cereus 03BB108]
 gi|206745030|gb|EDZ56433.1| RNA polymerase sigma-G factor [Bacillus cereus H3081.97]
 gi|217067470|gb|ACJ81720.1| RNA polymerase sigma-G factor [Bacillus cereus AH187]
 gi|218161363|gb|ACK61355.1| RNA polymerase sigma-G factor [Bacillus cereus B4264]
 gi|218537241|gb|ACK89639.1| RNA polymerase sigma-G factor [Bacillus cereus AH820]
 gi|225788717|gb|ACO28934.1| RNA polymerase sigma-G factor [Bacillus cereus 03BB102]
 gi|227002358|gb|ACP12101.1| RNA polymerase sigma-G factor [Bacillus anthracis str. CDC 684]
 gi|228585494|gb|EEK43598.1| RNA polymerase sigma-G factor [Bacillus cereus m1293]
 gi|228608875|gb|EEK66167.1| RNA polymerase sigma-G factor [Bacillus cereus MM3]
 gi|228625932|gb|EEK82682.1| RNA polymerase sigma-G factor [Bacillus cereus ATCC 4342]
 gi|228631450|gb|EEK88084.1| RNA polymerase sigma-G factor [Bacillus cereus m1550]
 gi|228643113|gb|EEK99389.1| RNA polymerase sigma-G factor [Bacillus cereus BDRD-ST26]
 gi|228843120|gb|EEM88202.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|229266585|gb|ACQ48222.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0248]
          Length = 259

 Score = 62.8 bits (151), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 66/267 (24%), Positives = 127/267 (47%), Gaps = 29/267 (10%)

Query: 25  KIPMLEKQEEYVLAKRYRE--HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           K+P+L+  E   + K +RE   G++SA  +LV  +LRLV+ +   +   G  + ++   G
Sbjct: 15  KLPVLKNDE---MRKLFREMQSGEISAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVG 71

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            IGLM+++  FD  +  + +TY++  I   ++ Y LR  + +++  +          + L
Sbjct: 72  CIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSLRD----IAYKAL 126

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
           +   + I +N+ +P   + IAK L V+  E++          +L+A+ +        + D
Sbjct: 127 QVREKLIAENSKEP-TAMDIAKVLEVTHEEIVF---------ALDAIQDPVSLFEPIYND 176

Query: 203 W----LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
                 V D    E+   +K+E+      L   M  LN RE+ I   R  Q    T   +
Sbjct: 177 GGDPIFVMDQLSDEK---QKDEQWVEELALKEGMKRLNDREKMIIRKRFFQGK--TQMEV 231

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQ 285
           + E  +S+ +V ++E  A K++ ++IQ
Sbjct: 232 AEEIGISQAQVSRLEKSAIKQMNKTIQ 258


>gi|307102796|gb|EFN51063.1| hypothetical protein CHLNCDRAFT_33233 [Chlorella variabilis]
          Length = 288

 Score = 62.8 bits (151), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 61/259 (23%), Positives = 120/259 (46%), Gaps = 33/259 (12%)

Query: 57  HLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           ++RLV+ IA  Y G G+ I +++ EG +GL +++ +FD  +GF+ +TY+ WWI+ ++   
Sbjct: 4   NVRLVINIAKRYVGNGIDIVDLIPEGLVGLSKSLDRFDASKGFKFSTYAHWWIRQSISRA 63

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
           +     +V++ +   +      L R+   + ++T+   +      IA  +++    VI  
Sbjct: 64  VCDQARVVRLPSHVCE-----TLYRINRAITSMTEQRDEMPSYEEIAAAVDLPVRRVIHY 118

Query: 177 --------NCRLAGDESLNALINSSDKNSS--QWQDWLVYDHDGQEQVLIEKEERKNRRN 226
                       A D     L  SS K  +    +D    D D  E+   E+ + ++ R 
Sbjct: 119 LRLSKLPGGAASARDRPTQYLSGSSLKEVTYEALED-CAEDEDPGEEGEEEEAQHESIRQ 177

Query: 227 MLTRSMSVLNPRERRIFEAR-----------------RLQENPVTLENLSSEFEVSRERV 269
           M    +S L  RER I   R                  +    ++L  ++S + +S+ER+
Sbjct: 178 MTDLLLSTLEKRERNILRLRYGLLGWGPAAGGLSWDDNVDGGSMSLGEVASAYGLSKERI 237

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE +A + +++  ++Q+
Sbjct: 238 RQIEDKAMRALRKPWRQQL 256


>gi|300783890|ref|YP_003764181.1| RNA polymerase sigma factor [Amycolatopsis mediterranei U32]
 gi|299793404|gb|ADJ43779.1| RNA polymerase sigma factor [Amycolatopsis mediterranei U32]
          Length = 282

 Score = 62.8 bits (151), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 67/254 (26%), Positives = 116/254 (45%), Gaps = 19/254 (7%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFD 94
           +++ +  D ++  RLV  H   +VK   G  G GLP    + ++V  G  GL+ A++KFD
Sbjct: 40  QQFADSPDQASRDRLVL-HYAPLVKYVAGRVGTGLPTHIDVGDLVQSGIFGLVDAIEKFD 98

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ-AITDNN 153
           PERG R  TY+M  I+ A+ +  LRS   V     +  K     + RL   L    TD  
Sbjct: 99  PERGLRFETYAMQRIRGAILDD-LRSQDWVPRAVRSKAKEAERAMERLGARLHRTPTDAE 157

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
           L  E        + + +        +L    +L  L+ ++ K+S    D L  D D  + 
Sbjct: 158 LAAE------LGIGLDDLRDFYGQLQLTSVVALEDLV-AAGKDSGSLVDTL-PDDDAVDP 209

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
           V +  ++  NRR  L ++++ L  R++ +      +   +TL  +     V+  RV Q+ 
Sbjct: 210 VAVLVDQ-DNRRQ-LAQAIAQLTERDKIVVSLYYFES--LTLAEIGKVLGVTESRVSQLH 265

Query: 274 ARAFKKVQESIQKQ 287
            RA  +++  + +Q
Sbjct: 266 TRAVMRLRAKLVEQ 279


>gi|308205773|gb|ADO19206.1| RNA polymerase sigma factor [Nostoc flagelliforme str. Sunitezuoqi]
          Length = 124

 Score = 62.8 bits (151), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 29/63 (46%), Positives = 44/63 (69%), Gaps = 1/63 (1%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E G L A H ++T++LRLVV +A  YR   L   +++ EG IGL +AV+KF+P RG++ +
Sbjct: 40  EQGQL-AKHLMITANLRLVVAVAKKYRWSNLEFLDLIQEGAIGLQKAVEKFEPNRGYKFS 98

Query: 103 TYS 105
           TY+
Sbjct: 99  TYA 101


>gi|229013088|ref|ZP_04170253.1| RNA polymerase sigma-G factor [Bacillus mycoides DSM 2048]
 gi|229061509|ref|ZP_04198853.1| RNA polymerase sigma-G factor [Bacillus cereus AH603]
 gi|229168644|ref|ZP_04296366.1| RNA polymerase sigma-G factor [Bacillus cereus AH621]
 gi|228614800|gb|EEK71903.1| RNA polymerase sigma-G factor [Bacillus cereus AH621]
 gi|228717743|gb|EEL69393.1| RNA polymerase sigma-G factor [Bacillus cereus AH603]
 gi|228748342|gb|EEL98202.1| RNA polymerase sigma-G factor [Bacillus mycoides DSM 2048]
          Length = 259

 Score = 62.8 bits (151), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 66/267 (24%), Positives = 128/267 (47%), Gaps = 29/267 (10%)

Query: 25  KIPMLEKQEEYVLAKRYRE--HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           K+P+L+ +E   + K +RE   G++SA  +LV  +LRLV+ +   +   G  + ++   G
Sbjct: 15  KLPVLKNEE---MRKLFREMQSGEISAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVG 71

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            IGLM+++  FD  +  + +TY++  I   ++ Y LR  + +++  +          + L
Sbjct: 72  CIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSLRD----IAYKAL 126

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
           +   + I +N+ +P   + IAK L V+  E++          +L+A+ +        + D
Sbjct: 127 QVREKLIAENSKEP-TAMDIAKVLEVTHEEIVF---------ALDAIQDPVSLFEPIYND 176

Query: 203 W----LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
                 V D    E+   +K+E+      L   M  LN RE+ I   R  Q    T   +
Sbjct: 177 GGDPIFVMDQLKDEK---QKDEQWVEELALKEGMKRLNDREKMIIRKRFFQGK--TQMEV 231

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQ 285
           + E  +S+ +V ++E  A K++ ++IQ
Sbjct: 232 AEEIGISQAQVSRLEKSAIKQMNKTIQ 258


>gi|147678181|ref|YP_001212396.1| sporulation sigma factor SigE [Pelotomaculum thermopropionicum SI]
 gi|146274278|dbj|BAF60027.1| DNA-directed RNA polymerase specialized sigma subunit
           [Pelotomaculum thermopropionicum SI]
          Length = 243

 Score = 62.8 bits (151), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 38/94 (40%), Positives = 53/94 (56%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EE  L  R  E GD +    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 41  PPLTTDEESFLISRL-ESGDGAVRSVLIERNLRLVVYIARKFENTGVGIEDLVSIGTIGL 99

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  FDP +  +LATY+   I+  +  Y+ RS
Sbjct: 100 IKAVNTFDPAKKIKLATYASRCIENEILMYLRRS 133


>gi|238924140|ref|YP_002937656.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Eubacterium rectale
           ATCC 33656]
 gi|238875815|gb|ACR75522.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Eubacterium rectale
           ATCC 33656]
 gi|291524873|emb|CBK90460.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Eubacterium
           rectale DSM 17629]
 gi|291529014|emb|CBK94600.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Eubacterium
           rectale M104/1]
          Length = 255

 Score = 62.8 bits (151), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 59/224 (26%), Positives = 107/224 (47%), Gaps = 16/224 (7%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           +RLV      Y G+ +   ++VS G  GL+ A+ KF+ E+  +  TY+   I+ A+ + I
Sbjct: 33  VRLVAGRLSMYLGHNVEYDDLVSYGIFGLIDAIDKFNLEKNVKFETYASLRIRGAILDQI 92

Query: 118 LR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
            +  W    I  T  Q++     R++   ++ I     K      +AK+L++SE E+ S 
Sbjct: 93  RKMDW----IPRTVRQRQ-----RKIDEAIKNIELRTGKTANDADLAKELSISEDELCSW 143

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
             +L    ++ +L    +       D     H  Q + ++ +EE K    ML +S+  L 
Sbjct: 144 QSQLKV-TNVVSLDEFDESGPEPVMDAAHNSHYAQPEEIVTQEELK---TMLVKSLDNLT 199

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            +ERR+ E    ++  +TL+ +S+  EVS  RV Q+  +   K+
Sbjct: 200 EKERRVIELYYYED--LTLKEISNILEVSESRVSQLHTKGLIKM 241


>gi|258514023|ref|YP_003190245.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfotomaculum
           acetoxidans DSM 771]
 gi|257777728|gb|ACV61622.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfotomaculum
           acetoxidans DSM 771]
          Length = 249

 Score = 62.8 bits (151), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 69/254 (27%), Positives = 133/254 (52%), Gaps = 20/254 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQAVKKFDPE 96
           Y  + D  A  +L+  +L LV  ++ G     LPI     ++   G +GL+++++KF+P 
Sbjct: 10  YISNRDKKAREKLILMYLPLVKHLS-GRLAVRLPIGISYEDLEGYGVVGLIESIEKFNPA 68

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +G    T++   I+ A+ + + +   L  +  T  QK    N  R +  L+ I  +N+  
Sbjct: 69  KGVSFETFAYRRIRGAIIDEVRK---LYWVPRTLWQKFQAVNAERER--LRRINGDNVTD 123

Query: 157 EQVVAIAKKLNVSESEV-ISMNC-RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           EQV A    LN+S +E+  + NC       SL+ ++ SSD +S +  + L+ D +  + +
Sbjct: 124 EQVAA---SLNISIAELHKTSNCYNQLNMNSLDEVLTSSDGDSVRLGN-LIPDPNSPDPL 179

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
            + +E+  + R +L  +++ LN ++R +  A   QE  +TL+ +    EVS  RV Q+ A
Sbjct: 180 DVVEEQ--DGRRILAEAVNSLNEKDRLVM-ALYYQER-LTLKEIGQVLEVSESRVCQLHA 235

Query: 275 RAFKKVQESIQKQV 288
           RA  ++++ I++ +
Sbjct: 236 RAMSRLRQKIKEML 249


>gi|88705109|ref|ZP_01102821.1| RNA polymerase sigma factor 70 family protein [Congregibacter
           litoralis KT71]
 gi|88700804|gb|EAQ97911.1| RNA polymerase sigma factor 70 family protein [Congregibacter
           litoralis KT71]
          Length = 439

 Score = 62.8 bits (151), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 31/82 (37%), Positives = 50/82 (60%), Gaps = 1/82 (1%)

Query: 48  SAAHRLVTSH-LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           S A   +T H LRLV  IA  YRG G+   +++ EG +GL++A +K+D  +GFR +TY  
Sbjct: 196 SDARDTLTMHNLRLVYSIAGRYRGKGVNYLDLIQEGTLGLIRAAEKYDHSKGFRFSTYCF 255

Query: 107 WWIKAAMQEYILRSWSLVKIGT 128
            WI  A++ ++  +  L++  T
Sbjct: 256 NWITQAIRRHVGDTGGLIRYPT 277


>gi|28203259|gb|AAO35702.1| RNA polymerase sigma-E factor [Clostridium tetani E88]
          Length = 261

 Score = 62.8 bits (151), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 70/264 (26%), Positives = 119/264 (45%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L ++EE  L ++   +GD S    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 59  PPLTREEEENLVEKLN-YGDESIRSILIERNLRLVVYIARKFENTGIGIEDLVSVGTIGL 117

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FDP +  +LATY+   I+  +  Y                      LRR     
Sbjct: 118 IKAVNTFDPSKKIKLATYASRCIENEILMY----------------------LRR----- 150

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
               +N +K E  ++  + LNV             G+E L + I  +D +       +VY
Sbjct: 151 ----NNKIKSE--ISFYEPLNVDWD----------GNELLLSDILGTDTD-------IVY 187

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEV 264
           D+  +E   ++KE       +L  +M  LN RE++I   R         T + ++    +
Sbjct: 188 DYIEEE---VDKE-------LLLIAMDKLNNREKQIVNLRFGLGGKTEKTQKEVADMLGI 237

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++ I K +
Sbjct: 238 SQSYISRLEKRIIKRLKKEINKMI 261


>gi|126698352|ref|YP_001087249.1| RNA polymerase sigma-F factor [Clostridium difficile 630]
 gi|115249789|emb|CAJ67606.1| RNA polymerase sigma-F factor [Clostridium difficile]
          Length = 254

 Score = 62.8 bits (151), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 61/268 (22%), Positives = 130/268 (48%), Gaps = 32/268 (11%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K P+L  +E   L ++  ++GD  A   L++S+L LV  +   +   G    ++   G+I
Sbjct: 10  KKPLLSHEETLELIEKV-QNGDEEAKEILISSNLGLVRSVVSRFLNIGYDREDLFQLGSI 68

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++++ KFDP+   + +TY++  I   ++ Y LR   ++K+  +  Q  +     + K 
Sbjct: 69  GLIKSIYKFDPKFNVKFSTYAVPMILGEIKRY-LRDDGMIKVSRSLKQIAI-----KAKM 122

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             +A+T    +   +  +AK ++V + +++     +A + + N           ++   +
Sbjct: 123 ESEALTKKLGREPSIEELAKAIDVEKEDLV-----MAMEANFNV----------EYLQGV 167

Query: 205 VYDHDGQEQVLIEK-------EERKNRRNMLTRS-MSVLNPRERRIFEARRLQENPVTLE 256
           +++ +G    LI+K       EE K   N+L +  +  L+ RER+I   R  ++  +T  
Sbjct: 168 IHEEEGSPICLIDKISMKGESEEEKVVDNILLKDILGRLDKRERQIIVLRYFED--MTQS 225

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
            +     +S+ +V +IE +   K++E I
Sbjct: 226 EIGEMLNISQVQVSRIEKKVLSKLKEYI 253


>gi|182418318|ref|ZP_02949613.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           butyricum 5521]
 gi|237666658|ref|ZP_04526643.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium butyricum
           E4 str. BoNT E BL5262]
 gi|182377700|gb|EDT75244.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           butyricum 5521]
 gi|237657857|gb|EEP55412.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium butyricum
           E4 str. BoNT E BL5262]
          Length = 243

 Score = 62.8 bits (151), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 63/257 (24%), Positives = 116/257 (45%), Gaps = 41/257 (15%)

Query: 46  DLSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           ++    +++  ++ LV  IA   M  +   +   ++VS G IGL+ A+ KFD  +G + +
Sbjct: 7   EVDGKEQIIEEYIPLVKYIASRVMFAKNKYMEYEDLVSYGMIGLIDAINKFDNSKGMKFS 66

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           +Y+   IK AM + + ++  + K G      R    +  L+G L       L+      I
Sbjct: 67  SYASIRIKGAMIDELRKNRPISK-GAMDKLNRYNKAIEELQGRL-------LREPTTQEI 118

Query: 163 AKKLNVSESEV---------ISM----NCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
           +  L +S SEV         ISM    +   + DE +N +    DKNS     +L     
Sbjct: 119 SNYLGISSSEVAEIENYINYISMVSLESVIFSDDEDVNLMGVIEDKNSPSPHSYL----- 173

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
                     E K +  +LT+++ +L  ++R I      +   +TL+ +    EVS  RV
Sbjct: 174 ----------EDKEKLEILTQAIELLKEKDRMILNLYYYE--GLTLKEIGKILEVSESRV 221

Query: 270 RQIEARAFKKVQESIQK 286
            Q+ +R+ + ++E ++K
Sbjct: 222 CQLHSRSIRNLRECMKK 238


>gi|125972968|ref|YP_001036878.1| sporulation sigma factor SigE [Clostridium thermocellum ATCC 27405]
 gi|256004765|ref|ZP_05429740.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium thermocellum
           DSM 2360]
 gi|281417179|ref|ZP_06248199.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium thermocellum
           JW20]
 gi|125713193|gb|ABN51685.1| RNA polymerase, sigma 29 subunit, SigE [Clostridium thermocellum
           ATCC 27405]
 gi|255991215|gb|EEU01322.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium thermocellum
           DSM 2360]
 gi|281408581|gb|EFB38839.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium thermocellum
           JW20]
 gi|316940796|gb|ADU74830.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium thermocellum
           DSM 1313]
          Length = 244

 Score = 62.8 bits (151), Expect = 6e-08,   Method: Compositional matrix adjust.
 Identities = 33/94 (35%), Positives = 54/94 (57%), Gaps = 2/94 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+   +E Y+L+K   E  D      L+  +LRLVV IA  +   G+ + ++VS G IGL
Sbjct: 42  PLTNDEENYLLSKL--EKRDFGVKSILIERNLRLVVYIARKFENTGVGVEDLVSIGTIGL 99

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++A+  FDP +  +LATY+   I+  +  Y+ R+
Sbjct: 100 IKAINTFDPNKNIKLATYASRCIENEILMYLRRN 133


>gi|56419662|ref|YP_146980.1| sporulation sigma factor SigE [Geobacillus kaustophilus HTA426]
 gi|56379504|dbj|BAD75412.1| DNA-directed RNA polymerase sigma-29 factor precursor (sigma-E)
           (stage II sporulation protein GB) [Geobacillus
           kaustophilus HTA426]
          Length = 239

 Score = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 37/94 (39%), Positives = 56/94 (59%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE  L  R    GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLTKEEEEQLIARL-AAGDDTARSLLIERNLRLVVYIARKFENTGIHIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN 129


>gi|303242484|ref|ZP_07328964.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302589952|gb|EFL59720.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 252

 Score = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 53/249 (21%), Positives = 120/249 (48%), Gaps = 17/249 (6%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            + + L + ++    +   + +V+ +L L   I+  +   G+   ++    +I L++AV+
Sbjct: 13  DDSHSLFENFKNSQSVEVRNEIVSKYLYLAEIISKKFVNRGIDYEDIYQVASIALIKAVE 72

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           +FDP++G + A+++   +   ++ +     S+++I      +R++   +++    +++T 
Sbjct: 73  RFDPDKGVKFASFATPTLIGEIKRFFRDKASVIRIP-----RRIYEVYQKVSHARESLTQ 127

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDG 210
              +P ++  IAK LN+SE  V+ +       ES NA  + S D+N     D  +++  G
Sbjct: 128 ELSRPPRIDEIAKYLNISEETVMEII------ESNNAHNLQSFDQNVYTDDDLELHETIG 181

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
           +E    EK E    R+ L +S+   N  E+   + R    N  T + ++    VS+  V 
Sbjct: 182 EEDATFEKIE---NRDFLKKSLDKFNDAEKEFIDMRYF--NNRTQKEIAERLGVSQMYVS 236

Query: 271 QIEARAFKK 279
           ++E +   +
Sbjct: 237 RLEKKVLDR 245


>gi|168029696|ref|XP_001767361.1| plastid sigma factor SIG5 [Physcomitrella patens subsp. patens]
 gi|56603661|dbj|BAD80742.1| plastid sigma factor PpSIG5 [Physcomitrella patens]
 gi|162681425|gb|EDQ67852.1| plastid sigma factor SIG5 [Physcomitrella patens subsp. patens]
          Length = 632

 Score = 62.8 bits (151), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 29/68 (42%), Positives = 44/68 (64%), Gaps = 2/68 (2%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYR--GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           +A  +L+  +LRLV+  A  Y      L I ++  EG IGLMQAV KFDP +G+R +TY 
Sbjct: 393 AARTKLIQRNLRLVLSQAYKYHKDSMSLSIQDLCQEGVIGLMQAVDKFDPGKGYRFSTYG 452

Query: 106 MWWIKAAM 113
           ++WI+ ++
Sbjct: 453 IYWIRNSI 460


>gi|254514436|ref|ZP_05126497.1| RNA polymerase sigma factor SigB [gamma proteobacterium NOR5-3]
 gi|219676679|gb|EED33044.1| RNA polymerase sigma factor SigB [gamma proteobacterium NOR5-3]
          Length = 432

 Score = 62.4 bits (150), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 31/87 (35%), Positives = 52/87 (59%), Gaps = 1/87 (1%)

Query: 48  SAAHRLVTSH-LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           S A   +T H LRLV  IA  YRG G+   +++ EG +GL++A +K+D  +GFR +TY  
Sbjct: 189 SDARDTLTMHNLRLVYSIAGRYRGKGVNYLDLIQEGTLGLIRAAEKYDHNKGFRFSTYCF 248

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQK 133
            WI  A++ ++  +  L++  T   ++
Sbjct: 249 NWITQAIRRHVGDTGGLIRYPTHVQEQ 275


>gi|295399723|ref|ZP_06809704.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|312111758|ref|YP_003990074.1| RNA polymerase, sigma 28 subunit, SigE [Geobacillus sp. Y4.1MC1]
 gi|294978126|gb|EFG53723.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|311216859|gb|ADP75463.1| RNA polymerase, sigma 28 subunit, SigE [Geobacillus sp. Y4.1MC1]
          Length = 239

 Score = 62.4 bits (150), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 33/79 (41%), Positives = 51/79 (64%), Gaps = 1/79 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE +L  +  + GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLTKEEEEMLIGKLSD-GDETARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYS 105
           ++AV  F+PE+  +LATY+
Sbjct: 96  IKAVNTFNPEKKIKLATYA 114


>gi|78044685|ref|YP_360875.1| sporulation sigma factor SigE [Carboxydothermus hydrogenoformans
           Z-2901]
 gi|77996800|gb|ABB15699.1| RNA polymerase sigma-E factor [Carboxydothermus hydrogenoformans
           Z-2901]
          Length = 237

 Score = 62.4 bits (150), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 36/100 (36%), Positives = 58/100 (58%), Gaps = 2/100 (2%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           H+I   P+  ++E  +L       GD +A   L+  +LRLVV IA  +   G+ I ++VS
Sbjct: 30  HDILPPPLSSEEENTLLT--LLVQGDAAAKSTLIERNLRLVVYIARKFENTGVNIEDLVS 87

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
            G IGL++AV  F+PE+  +LATY+   I+  +  Y+ R+
Sbjct: 88  IGTIGLIKAVNTFNPEKKIKLATYASRCIENEILMYLRRN 127


>gi|296120653|ref|YP_003628431.1| RNA polymerase sigma factor, sigma-70 family [Planctomyces
           limnophilus DSM 3776]
 gi|296012993|gb|ADG66232.1| RNA polymerase sigma factor, sigma-70 family [Planctomyces
           limnophilus DSM 3776]
          Length = 558

 Score = 62.4 bits (150), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 59/232 (25%), Positives = 92/232 (39%), Gaps = 72/232 (31%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ S+LRLVV IA  +        E++S+GN+ L++A++KFD  RGF+ +TY+ W I   
Sbjct: 383 LIRSNLRLVVSIAKKHSHPTANFFEMISDGNMSLIKAIEKFDYTRGFKFSTYASWAI--- 439

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
                                        +K   ++I   N +         +      E
Sbjct: 440 -----------------------------MKNFARSIPAENTR-------LDRFRTGSEE 463

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           V                + S D  + Q++D +V                  +R  L   +
Sbjct: 464 VF---------------VQSMDPRTDQFRDEIV---------------NYRQREALMGIL 493

Query: 233 SVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             L  RER I   R      + P TLE +     V++ER+RQIEARA KK++
Sbjct: 494 GQLELRERDIIMHRYGLETGQQPQTLEQVGHRLGVTKERIRQIEARALKKLK 545


>gi|295837881|ref|ZP_06824814.1| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
 gi|295826719|gb|EDY46528.2| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
          Length = 286

 Score = 62.4 bits (150), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 64/237 (27%), Positives = 106/237 (44%), Gaps = 23/237 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +   
Sbjct: 65  LIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTVVGE 124

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL   L +    L    D +     V  +AK L VSE 
Sbjct: 125 IKRFFRDTSWS-VRVPRRLQELRL--ALTKTSDELAQKLDRS---PTVPELAKALGVSED 178

Query: 172 EVIS----MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +V+      N   A   SL++     D       D L Y+    E V    E R++ + +
Sbjct: 179 DVVDGLAVGNAYTA--SSLDSPAPEDDGGEGSLADRLGYEDTALEGV----EYRESLKPL 232

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L +    L PRERRI   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 233 LAK----LPPRERRIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 283


>gi|302518878|ref|ZP_07271220.1| RNA polymerase sigma factor RpoS [Streptomyces sp. SPB78]
 gi|302427773|gb|EFK99588.1| RNA polymerase sigma factor RpoS [Streptomyces sp. SPB78]
          Length = 201

 Score = 62.4 bits (150), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 59/211 (27%), Positives = 95/211 (45%), Gaps = 38/211 (18%)

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN--LRRLK 143
           L++AV+KFD  RGF+ +TY+ WWI+ AM   +      +++     +     N  +R  +
Sbjct: 1   LIRAVEKFDYTRGFKFSTYATWWIRQAMSRALADQARTIRVPVHVVE---LINRVVRVQR 57

Query: 144 GHLQAITDNNLKPEQVVAIA----KKLNVSE-----SEVISMNCRLAGDE--SLNALINS 192
           G LQ   +   +P      A     K  V E      E +S++  + G++  +L  LI  
Sbjct: 58  GLLQ---ERGHEPSHAEVAALLGLTKERVGEVLRLAQEPVSLHTPVGGEDEVALGDLIED 114

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN- 251
            D  S      L+      E VL                 S L  RER++ + R   ++ 
Sbjct: 115 GDAPSPPESAALLLLRRHLEDVL-----------------STLGERERQVVQLRYGLDDG 157

Query: 252 -PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            P TLE + + F V+RER+RQIEA+   K++
Sbjct: 158 RPRTLEEIGTLFGVTRERIRQIEAKTLAKLR 188


>gi|52080136|ref|YP_078927.1| sporulation sigma factor SigG [Bacillus licheniformis ATCC 14580]
 gi|52785510|ref|YP_091339.1| sporulation sigma factor SigG [Bacillus licheniformis ATCC 14580]
 gi|319646086|ref|ZP_08000316.1| RNA polymerase sigma-G factor [Bacillus sp. BT1B_CT2]
 gi|52003347|gb|AAU23289.1| RNA polymerase sporulation-specific sigma factor (sigma-G)
           [Bacillus licheniformis ATCC 14580]
 gi|52348012|gb|AAU40646.1| SigG [Bacillus licheniformis ATCC 14580]
 gi|317391836|gb|EFV72633.1| RNA polymerase sigma-G factor [Bacillus sp. BT1B_CT2]
          Length = 259

 Score = 62.4 bits (150), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 62/261 (23%), Positives = 121/261 (46%), Gaps = 16/261 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+ +E   L K+ ++ GD +A  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKNEEMRKLFKQMQDEGDTTAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 74

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD     + +TY++  I   ++ Y LR  + +++  +          + L+ 
Sbjct: 75  GLMKSIDNFDLSHNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSLRD----IAYKALQV 129

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + I++ + +P     IAK+L VS  E++     +    SL   I +   +     D +
Sbjct: 130 RERLISETSREP-TAQEIAKELEVSHEEIVFALDAIQDPVSLFEPIYNDGGDPIYVMDQI 188

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             + +   Q + E          L   M  LN RE+ I   R  Q    T   ++ E  +
Sbjct: 189 SDERNKDSQWIEEL--------ALKEGMRRLNEREKMILRKRFFQGK--TQMEVADEIGI 238

Query: 265 SRERVRQIEARAFKKVQESIQ 285
           S+ +V ++E  A K++ ++I 
Sbjct: 239 SQAQVSRLEKAAIKQMNKNIH 259


>gi|47570318|ref|ZP_00240965.1| RNA polymerase sigma-G factor [Bacillus cereus G9241]
 gi|47553027|gb|EAL11431.1| RNA polymerase sigma-G factor [Bacillus cereus G9241]
          Length = 257

 Score = 62.4 bits (150), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 66/267 (24%), Positives = 126/267 (47%), Gaps = 29/267 (10%)

Query: 25  KIPMLEKQEEYVLAKRYRE--HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           K+P+L   E   + K +RE   G++SA  +LV  +LRLV+ +   +   G  + ++   G
Sbjct: 13  KLPVLXNDE---MRKLFREMQSGEISAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVG 69

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            IGLM+++  FD  +  + +TY++  I   ++ Y LR  + +++  +          + L
Sbjct: 70  CIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSLRD----IAYKAL 124

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
           +   + I +N+ +P   + IAK L V+  E++          +L+A+ +        + D
Sbjct: 125 QVREKLIAENSKEP-TAMDIAKVLEVTHEEIVF---------ALDAIQDPVSLFEPIYND 174

Query: 203 W----LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
                 V D    E+   +K+E+      L   M  LN RE+ I   R  Q    T   +
Sbjct: 175 GGDPIFVMDQLSDEK---QKDEQWVEELALKEGMKRLNDREKMIIRKRFFQGK--TQMEV 229

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQ 285
           + E  +S+ +V ++E  A K++ ++IQ
Sbjct: 230 AEEIGISQAQVSRLEKSAIKQMNKTIQ 256


>gi|224009562|ref|XP_002293739.1| RNA polymerase [Thalassiosira pseudonana CCMP1335]
 gi|220970411|gb|EED88748.1| RNA polymerase [Thalassiosira pseudonana CCMP1335]
          Length = 316

 Score = 62.4 bits (150), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 65/251 (25%), Positives = 118/251 (47%), Gaps = 27/251 (10%)

Query: 48  SAAHRLVTSHLRLVVKIAMGY--RGY--GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           SA   LV S++ LV  +   Y  + Y  G+ I E+V EG++GL++A + FDP +G R +T
Sbjct: 64  SAKQELVASNMGLVHAVVKNYSRKAYYRGITIDELVQEGSLGLIRAAELFDPAKGLRFST 123

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+  WIK  +    +    LV       +++++  +R +   +    D  L  +    IA
Sbjct: 124 YATIWIKGVLSNSRVDEMVLV----PQRERQIWNKIREVSKDVDD-EDGRLSTDM---IA 175

Query: 164 KKLNVSESEV-------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           KKL + +S V        S+N  L+ D    +   S + + S+  + L+ D  G +  L 
Sbjct: 176 KKLGLDKSSVEQNIQRMSSVNNMLSLDYQYASTTRSGETDGSKPFEALMADKSGSDADLA 235

Query: 217 EKEERKNRRNMLTRSMSVLNPRE----RRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           E+ + K   +++   +  LN RE    R ++      E  V  ++ +    ++RE  R +
Sbjct: 236 ERAQFKA--DLVAGLVRNLNEREIQLIRLMYGMHDGHEYSV--KDSAKIMGINRETARLL 291

Query: 273 EARAFKKVQES 283
                KK++E+
Sbjct: 292 HHACLKKLREA 302


>gi|304317194|ref|YP_003852339.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium thermosaccharolyticum DSM 571]
 gi|302778696|gb|ADL69255.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium thermosaccharolyticum DSM 571]
          Length = 241

 Score = 62.4 bits (150), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 33/94 (35%), Positives = 58/94 (61%), Gaps = 2/94 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  ++E +++AK   E GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 40  PLSTEEEIFLIAKM--ESGDNAAKSMLIERNLRLVVYIAKKFENTGVGIEDLISIGTIGL 97

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++A+  F+P +  +LATY+   I+  +  Y+ R+
Sbjct: 98  IKAINTFNPHKKIKLATYASRCIENEILMYLRRN 131


>gi|239929001|ref|ZP_04685954.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291437340|ref|ZP_06576730.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291340235|gb|EFE67191.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 374

 Score = 62.4 bits (150), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 65/240 (27%), Positives = 109/240 (45%), Gaps = 29/240 (12%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +LV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+   +  
Sbjct: 153 QLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATPTVVG 212

Query: 112 AMQEYIL-RSWSLVKIGTTANQKRLFFN-----LRRLKGHLQAITDNNLKPEQVVAIAKK 165
            ++ +   + W+ V++     + RL        L +L G    + +          +A+K
Sbjct: 213 EIKRHFRDKGWA-VRVPRRLQELRLALTTATAELSQLHGRSPTVHE----------LAEK 261

Query: 166 LNVSESEVISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           L +SE EV      L G ES NA    S D   +  +   V D  G E   +E  E    
Sbjct: 262 LAISEEEV------LEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVE---Y 312

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 313 RESLKPLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLREKL 370


>gi|254974392|ref|ZP_05270864.1| RNA polymerase sigma-F factor [Clostridium difficile QCD-66c26]
 gi|255091783|ref|ZP_05321261.1| RNA polymerase sigma-F factor [Clostridium difficile CIP 107932]
 gi|255099887|ref|ZP_05328864.1| RNA polymerase sigma-F factor [Clostridium difficile QCD-63q42]
 gi|255305776|ref|ZP_05349948.1| RNA polymerase sigma-F factor [Clostridium difficile ATCC 43255]
 gi|255313518|ref|ZP_05355101.1| RNA polymerase sigma-F factor [Clostridium difficile QCD-76w55]
 gi|255516203|ref|ZP_05383879.1| RNA polymerase sigma-F factor [Clostridium difficile QCD-97b34]
 gi|255649300|ref|ZP_05396202.1| RNA polymerase sigma-F factor [Clostridium difficile QCD-37x79]
 gi|255654820|ref|ZP_05400229.1| RNA polymerase sigma-F factor [Clostridium difficile QCD-23m63]
 gi|260682470|ref|YP_003213755.1| RNA polymerase sigma-F factor [Clostridium difficile CD196]
 gi|260686069|ref|YP_003217202.1| RNA polymerase sigma-F factor [Clostridium difficile R20291]
 gi|296449564|ref|ZP_06891341.1| RNA polymerase sigma-F factor [Clostridium difficile NAP08]
 gi|296878113|ref|ZP_06902128.1| RNA polymerase sigma-F factor [Clostridium difficile NAP07]
 gi|306519396|ref|ZP_07405743.1| RNA polymerase sigma-F factor [Clostridium difficile QCD-32g58]
 gi|260208633|emb|CBA61376.1| RNA polymerase sigma-F factor [Clostridium difficile CD196]
 gi|260212085|emb|CBE02685.1| RNA polymerase sigma-F factor [Clostridium difficile R20291]
 gi|296261628|gb|EFH08446.1| RNA polymerase sigma-F factor [Clostridium difficile NAP08]
 gi|296430866|gb|EFH16698.1| RNA polymerase sigma-F factor [Clostridium difficile NAP07]
          Length = 254

 Score = 62.4 bits (150), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 61/268 (22%), Positives = 130/268 (48%), Gaps = 32/268 (11%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K P+L  +E   L ++  ++GD  A   L++S+L LV  +   +   G    ++   G+I
Sbjct: 10  KKPLLSHEETLELIEKV-QNGDEEAKEILISSNLGLVRSVVSRFLNIGYDREDLFQLGSI 68

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++++ KFDP+   + +TY++  I   ++ Y LR   ++K+  +  Q  +     + K 
Sbjct: 69  GLIKSIYKFDPKFNVKFSTYAVPMILGEIKRY-LRDDGMIKVSRSLKQIAV-----KAKM 122

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             +A+T    +   +  +AK ++V + +++     +A + + N           ++   +
Sbjct: 123 ESEALTKKLGREPSIEELAKAIDVEKEDLV-----MAMEANFNV----------EYLQGV 167

Query: 205 VYDHDGQEQVLIEK-------EERKNRRNMLTRS-MSVLNPRERRIFEARRLQENPVTLE 256
           +++ +G    LI+K       EE K   N+L +  +  L+ RER+I   R  ++  +T  
Sbjct: 168 IHEEEGSPICLIDKISMKGESEEEKVVDNILLKDILGRLDKRERQIIVLRYFED--MTQS 225

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
            +     +S+ +V +IE +   K++E I
Sbjct: 226 EIGEMLNISQVQVSRIEKKVLSKLKEYI 253


>gi|257438786|ref|ZP_05614541.1| RNA polymerase sigma-E factor [Faecalibacterium prausnitzii A2-165]
 gi|257198754|gb|EEU97038.1| RNA polymerase sigma-E factor [Faecalibacterium prausnitzii A2-165]
          Length = 188

 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 31/76 (40%), Positives = 46/76 (60%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD +A   L+T +LRLVV +A  Y   G+P  +++S G IGL++AV  F P R  +LATY
Sbjct: 4   GDAAARDDLITHNLRLVVYLAKKYENSGVPQEDMISIGTIGLIKAVNTFTPARNIKLATY 63

Query: 105 SMWWIKAAMQEYILRS 120
           +   I   +  Y+ +S
Sbjct: 64  ASRCIGNEILMYLRKS 79


>gi|261419324|ref|YP_003253006.1| sporulation sigma factor SigE [Geobacillus sp. Y412MC61]
 gi|297530706|ref|YP_003671981.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
 gi|319766140|ref|YP_004131641.1| RNA polymerase, sigma 28 subunit, SigE [Geobacillus sp. Y412MC52]
 gi|261375781|gb|ACX78524.1| RNA polymerase, sigma 28 subunit, SigE [Geobacillus sp. Y412MC61]
 gi|297253958|gb|ADI27404.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
 gi|317111006|gb|ADU93498.1| RNA polymerase, sigma 28 subunit, SigE [Geobacillus sp. Y412MC52]
          Length = 239

 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 37/94 (39%), Positives = 56/94 (59%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE  L  R    GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLTKEEEEQLIARL-AAGDDTARSLLIERNLRLVVYIARKFENTGIHIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN 129


>gi|83589703|ref|YP_429712.1| sporulation sigma factor SigE [Moorella thermoacetica ATCC 39073]
 gi|83572617|gb|ABC19169.1| RNA polymerase, sigma 29 subunit, SigE [Moorella thermoacetica ATCC
           39073]
          Length = 243

 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 37/94 (39%), Positives = 54/94 (57%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EE  L  R  E GD +    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 41  PPLSSDEESDLLLRL-EDGDAAVKKVLIERNLRLVVYIARKFENTGVGIEDLVSIGTIGL 99

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  FDP++  +LATY+   I+  +  Y+ R+
Sbjct: 100 IKAVNTFDPKKRIKLATYASRCIENEILMYLRRN 133


>gi|158312828|ref|YP_001505336.1| FliA/WhiG family RNA polymerase sigma factor [Frankia sp. EAN1pec]
 gi|158108233|gb|ABW10430.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Frankia sp.
           EAN1pec]
          Length = 376

 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 68/241 (28%), Positives = 116/241 (48%), Gaps = 30/241 (12%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +LV  HL LV  +A  +R  G P+ ++V    IGL+++V +FDPERG   +TY+   I  
Sbjct: 154 QLVRMHLPLVEYLARRFRNRGEPLDDLVQVATIGLIKSVDRFDPERGVEFSTYATPTIVG 213

Query: 112 AMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT---DNNLKPEQVVA-IAKKL 166
            ++ +   + W++          R+   L+ LK  L   T     +L     V+ IA+ L
Sbjct: 214 EIKRHFRDKGWAI----------RVPRRLQELKLSLTKATSELSQSLGRSPTVSEIARHL 263

Query: 167 NVSESEVISMNCRLAGDESLNA--LINSSDKNSSQWQDWLVYDHDG-QEQVLIEKEERKN 223
            +SE EV      L G ES NA   ++    +S   +   V D  G Q++ L   E R++
Sbjct: 264 EMSEEEV------LEGLESANAYSAVSLDAPDSGDDEAPAVADTLGVQDESLEGVEYRES 317

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            + +L +    L PRE+RI   R      +T   +++E  +S+  V ++ AR   +++  
Sbjct: 318 LKPLLEK----LPPREKRILLLRFFGN--MTQSQIANELGISQMHVSRLLARTLAQLRRG 371

Query: 284 I 284
           +
Sbjct: 372 L 372


>gi|311029937|ref|ZP_07708027.1| sporulation sigma factor SigE [Bacillus sp. m3-13]
          Length = 239

 Score = 62.4 bits (150), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 67/265 (25%), Positives = 116/265 (43%), Gaps = 66/265 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ +++E ++L K    +GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 38  PLSKEEEAHLLIKL--PNGDQAARSILIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+                          
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN-------------------------- 129

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                               N   SEV       + DE LN      D N     D L  
Sbjct: 130 --------------------NKVRSEV-------SFDEPLNI---DWDGNELLLSDVL-- 157

Query: 207 DHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFE 263
              G E+ +I K+   N  R +L +++  LN RE++I E R   +     T ++++    
Sbjct: 158 ---GTEEDIITKDLEANVDRKLLLKALEQLNDREKQIMELRFGLIGGEEKTQKDVADMLG 214

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           +S+  + ++E R  K++++   K V
Sbjct: 215 ISQSYISRLEKRIIKRLRKEFNKMV 239


>gi|23098931|ref|NP_692397.1| sporulation sigma factor SigG [Oceanobacillus iheyensis HTE831]
 gi|22777159|dbj|BAC13432.1| stage III sporulation protein G (RNA polymerase
           sporulation-specific sigma G factor) [Oceanobacillus
           iheyensis HTE831]
          Length = 260

 Score = 62.0 bits (149), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 60/260 (23%), Positives = 122/260 (46%), Gaps = 24/260 (9%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+ +E   L  R +E GD++A   LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKNEEMKKLFVRMQEDGDITAREELVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 74

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD     R +TY++  I   ++ Y LR  + +++  +   + + +   +++ 
Sbjct: 75  GLMKSIDNFDLSHNVRFSTYAVPMIIGEIRRY-LRDNNPIRVSRSL--RDIAYKALQVRE 131

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW- 203
            L + T     P +   IAK++++ +++V+          +L+A+ +        + D  
Sbjct: 132 KLISKTSKEPSPAE---IAKEMDIPQTDVVF---------ALDAIQDPVSLFEPIYNDGG 179

Query: 204 ---LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
               V D    E+   +K+     +  L   M  LN RE+ I   R  Q    T   ++ 
Sbjct: 180 DPIFVMDQISDEK---DKDSSWVDKLSLKEGMHQLNEREKMILNKRFFQGK--TQMEVAD 234

Query: 261 EFEVSRERVRQIEARAFKKV 280
           E  +S+ +V ++E  A  ++
Sbjct: 235 EIGISQAQVSRLEKAAISQM 254


>gi|47777365|gb|AAT37999.1| putative RNA polymerase sigma factor [Oryza sativa Japonica Group]
          Length = 882

 Score = 62.0 bits (149), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 58/232 (25%), Positives = 106/232 (45%), Gaps = 12/232 (5%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RL+ +   LV  IA  Y G G    +++  G +G++   +KFD ++G + +TY  +WI+ 
Sbjct: 647 RLLVTTEWLVKYIAKTYAGMGTAFEDLLQAGKMGVLNGAEKFDSQKGCKFSTYVKYWIRK 706

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           AM   +  +  ++++       R+   +R+++   +AI  N  +      IA  + VS +
Sbjct: 707 AMLALLAENSGVIQLPA-----RMEGIIRKVREARRAIRYNTGRNPPDAEIAALIGVSVA 761

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
                N RLA   S   +   ++    Q   ++    D   +   E   R   R  L   
Sbjct: 762 -----NVRLARKCSRRVVSLYTEIGVGQNAKFVEVTPDTSLEAPDEAMFRMQLRERLLHV 816

Query: 232 MSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +  L PRE  + + R   E+    +LE + S + VS+E +R+IE  A  K++
Sbjct: 817 LDRLPPREGHVLKLRHGLEDGKCRSLEQIGSIYHVSKEWIRKIEKSAMSKLR 868


>gi|313901760|ref|ZP_07835186.1| RNA polymerase, sigma subunit, RpsG/SigG [Thermaerobacter
           subterraneus DSM 13965]
 gi|313467966|gb|EFR63454.1| RNA polymerase, sigma subunit, RpsG/SigG [Thermaerobacter
           subterraneus DSM 13965]
          Length = 261

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 32/93 (34%), Positives = 55/93 (59%), Gaps = 1/93 (1%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           ++P+L  ++  VL +R RE GD  A  +LV  +LRLV+ +   +   G P+ ++   G I
Sbjct: 19  ELPVLSNEQMRVLFRRMRE-GDEEARQQLVQGNLRLVLSVIQRFNHRGEPVDDLFQVGCI 77

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           GLM+A+  FD E+  R +TY++  I   ++ Y+
Sbjct: 78  GLMKAIDNFDLEQNVRFSTYAVPMIIGEIRRYL 110


>gi|222632746|gb|EEE64878.1| hypothetical protein OsJ_19735 [Oryza sativa Japonica Group]
          Length = 1012

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 58/232 (25%), Positives = 106/232 (45%), Gaps = 12/232 (5%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RL+ +   LV  IA  Y G G    +++  G +G++   +KFD ++G + +TY  +WI+ 
Sbjct: 777 RLLVTTEWLVKYIAKTYAGMGTAFEDLLQAGKMGVLNGAEKFDSQKGCKFSTYVKYWIRK 836

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           AM   +  +  ++++       R+   +R+++   +AI  N  +      IA  + VS +
Sbjct: 837 AMLALLAENSGVIQLPA-----RMEGIIRKVREARRAIRYNTGRNPPDAEIAALIGVSVA 891

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
                N RLA   S   +   ++    Q   ++    D   +   E   R   R  L   
Sbjct: 892 -----NVRLARKCSRRVVSLYTEIGVGQNAKFVEVTPDTSLEAPDEAMFRMQLRERLLHV 946

Query: 232 MSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +  L PRE  + + R   E+    +LE + S + VS+E +R+IE  A  K++
Sbjct: 947 LDRLPPREGHVLKLRHGLEDGKCRSLEQIGSIYHVSKEWIRKIEKSAMSKLR 998


>gi|197723819|gb|ACH72689.1| RNA polymerase sigma-37 factor [Listeria marthii]
          Length = 257

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 64/264 (24%), Positives = 129/264 (48%), Gaps = 26/264 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +++D   G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEEL 125

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDW 203
           T       Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D 
Sbjct: 126 TRELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDV 182

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    DG E+V        N+R +L + + VL+ RE++I +   ++    + +      +
Sbjct: 183 VGGTDDGFERV--------NQRMLLEKVLPVLDEREQKILQYTFIENR--SQKETGELLD 232

Query: 264 VSRERVRQIEARAFKKVQESIQKQ 287
           +S+  V +I+ +A KK++E++Q +
Sbjct: 233 ISQMHVSRIQRQAIKKLREALQNE 256


>gi|167770714|ref|ZP_02442767.1| hypothetical protein ANACOL_02060 [Anaerotruncus colihominis DSM
           17241]
 gi|167667309|gb|EDS11439.1| hypothetical protein ANACOL_02060 [Anaerotruncus colihominis DSM
           17241]
          Length = 243

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 32/88 (36%), Positives = 54/88 (61%), Gaps = 2/88 (2%)

Query: 19  YIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           YI+    +P  L ++EE ++ ++  EH D +A   L   +LRLVV IA  +   G+ + +
Sbjct: 32  YINGPETLPAPLSREEEQIVFRKLEEH-DEAAKETLTVHNLRLVVYIAKKFESTGICVED 90

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYS 105
           ++S G IGL++AV  F P++  +LATY+
Sbjct: 91  LISIGTIGLIKAVNTFCPQKNIKLATYA 118


>gi|302520387|ref|ZP_07272729.1| RNA polymerase sigma-B factor [Streptomyces sp. SPB78]
 gi|302429282|gb|EFL01098.1| RNA polymerase sigma-B factor [Streptomyces sp. SPB78]
          Length = 338

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 64/237 (27%), Positives = 106/237 (44%), Gaps = 23/237 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +   
Sbjct: 117 LIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTVVGE 176

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL   L +    L    D +     V  +AK L VSE 
Sbjct: 177 IKRFFRDTSWS-VRVPRRLQELRL--ALTKTSDELAQKLDRS---PTVPELAKALGVSED 230

Query: 172 EVIS----MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +V+      N   A   SL++     D       D L Y+    E V    E R++ + +
Sbjct: 231 DVVDGLAVGNAYTA--SSLDSPAPEDDGGEGSLADRLGYEDTALEGV----EYRESLKPL 284

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L +    L PRERRI   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 285 LAK----LPPRERRIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 335


>gi|319649653|ref|ZP_08003809.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
 gi|317398815|gb|EFV79497.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
          Length = 239

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 35/94 (37%), Positives = 59/94 (62%), Gaps = 2/94 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ +++EE +L K  +  GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 38  PLSKEEEEMLLIKLPK--GDKAARSILIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN 129


>gi|134298554|ref|YP_001112050.1| sporulation sigma factor SigE [Desulfotomaculum reducens MI-1]
 gi|134051254|gb|ABO49225.1| RNA polymerase, sigma 29 subunit, SigE [Desulfotomaculum reducens
           MI-1]
          Length = 241

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 34/79 (43%), Positives = 48/79 (60%), Gaps = 1/79 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EE  L +R  + GDL   + L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 39  PPLSIDEEIDLIERLGD-GDLKVKNVLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGL 97

Query: 87  MQAVKKFDPERGFRLATYS 105
           ++AV  FDP +  +LATY+
Sbjct: 98  IKAVNTFDPHKKIKLATYA 116


>gi|169823706|ref|YP_001691317.1| RNA polymerase sigma B factor [Finegoldia magna ATCC 29328]
 gi|302380124|ref|ZP_07268597.1| RNA polymerase sigma-70 factor, sigma-B/F/G family protein
           [Finegoldia magna ACS-171-V-Col3]
 gi|303234447|ref|ZP_07321085.1| RNA polymerase sigma-70 factor, sigma-B/F/G family protein
           [Finegoldia magna BVS033A4]
 gi|167830511|dbj|BAG07427.1| RNA polymerase sigma B factor [Finegoldia magna ATCC 29328]
 gi|302312066|gb|EFK94074.1| RNA polymerase sigma-70 factor, sigma-B/F/G family protein
           [Finegoldia magna ACS-171-V-Col3]
 gi|302494402|gb|EFL54170.1| RNA polymerase sigma-70 factor, sigma-B/F/G family protein
           [Finegoldia magna BVS033A4]
          Length = 258

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 57/253 (22%), Positives = 119/253 (47%), Gaps = 16/253 (6%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           +++E  D      LV  +L +   +A  Y G G+   ++     IGL+ A+ ++DP +G+
Sbjct: 20  KFQETRDKKTRDTLVEKNLYIAEILAKKYTGRGIEYDDLYQVACIGLIYAIDRYDPSKGY 79

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
             ++Y+   I   +++Y      ++++     +  L   +   K HL        K   V
Sbjct: 80  EFSSYATPTIVGEIKKYFRDKGWVIRVPRRIQE--LNKKVATAKVHLSQTMQ---KSPTV 134

Query: 160 VAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
             IA  L++S  EV+ +    ++   +SL+  I+ S+++       L+    G+E   + 
Sbjct: 135 EDIADYLSISNEEVLEVLEGAKVYAPQSLDQSIDQSNEDRETNLSDLI----GEEDKDML 190

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
           K E    R+++ R M  LN  ER+I   R   +    +  ++ E ++S+  V ++E +  
Sbjct: 191 KFE---NRDLINRCMQDLNKVERKILLGRYFDKKTQIV--IAEELDISQMTVSRMEKKIL 245

Query: 278 KKVQESIQKQVEL 290
           KK + ++++Q+E 
Sbjct: 246 KKFKAALKEQLEF 258


>gi|297157365|gb|ADI07077.1| putative sigma factor [Streptomyces bingchenggensis BCW-1]
          Length = 242

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 62/234 (26%), Positives = 109/234 (46%), Gaps = 19/234 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+   +   
Sbjct: 22  LVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATPTVVGE 81

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +   + W+ V++     + RL      L      ++  + +   V  +A++L++SE 
Sbjct: 82  IKRHFRDKGWA-VRVPRRLQELRL-----SLTTATAELSQRHGRAPTVHELAEQLSISEE 135

Query: 172 EVISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           EV      L G ES NA    S D   +  +   V D  G E   +E  E    R  L  
Sbjct: 136 EV------LEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVE---YRESLKP 186

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  L PRE++I   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 187 LLEDLPPREKKILLLRFF--GNMTQSQIAQEVGISQMHVSRLLARTLAQLRERL 238


>gi|153854402|ref|ZP_01995680.1| hypothetical protein DORLON_01675 [Dorea longicatena DSM 13814]
 gi|149752928|gb|EDM62859.1| hypothetical protein DORLON_01675 [Dorea longicatena DSM 13814]
          Length = 230

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 36/84 (42%), Positives = 51/84 (60%), Gaps = 2/84 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+   +E+Y + K Y E GDL A H L+  +LRLV  I   Y+     + +++S G IGL
Sbjct: 30  PLTAAEEKYYVQK-YTE-GDLEAKHILIERNLRLVAHIVKKYQPPPEEMEDLLSIGTIGL 87

Query: 87  MQAVKKFDPERGFRLATYSMWWIK 110
           M+AV  FDPE+  RLATY+   I+
Sbjct: 88  MKAVVTFDPEKSARLATYAARCIE 111


>gi|111225338|ref|YP_716132.1| SigH putative RNA polymerase sigma factor [Frankia alni ACN14a]
 gi|111152870|emb|CAJ64617.1| SigH putative RNA polymerase sigma factor [Frankia alni ACN14a]
          Length = 299

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 67/241 (27%), Positives = 115/241 (47%), Gaps = 30/241 (12%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +LV  HL LV  +A  +R  G P+ ++V    IGL+++V +FDPERG   +TY+   I  
Sbjct: 77  QLVRMHLPLVEYLARRFRNRGEPLDDLVQVATIGLIKSVDRFDPERGVEFSTYATPTIVG 136

Query: 112 AMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT---DNNL-KPEQVVAIAKKL 166
            ++ +   + W++          R+   L+ LK  L   T      L +   V  IA+ L
Sbjct: 137 EIKRHFRDKGWAI----------RVPRRLQELKLSLTKATSELSQTLGRSPTVSEIARHL 186

Query: 167 NVSESEVISMNCRLAGDESLNA--LINSSDKNSSQWQDWLVYDHDG-QEQVLIEKEERKN 223
            +SE +V      L G ES NA   ++    +S   +   V D  G Q++ L   E R++
Sbjct: 187 QMSEEDV------LEGLESANAYSAVSLDAPDSGDDEAPAVADTLGVQDESLEGVEYRES 240

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            + +L +    L PRE+RI   R      +T   +++E  +S+  V ++ AR   +++  
Sbjct: 241 LKPLLEK----LPPREKRILLLRFFGN--MTQSQIATELGISQMHVSRLLARTLAQLRRG 294

Query: 284 I 284
           +
Sbjct: 295 L 295


>gi|197723817|gb|ACH72688.1| RNA polymerase sigma-37 factor [Listeria marthii]
          Length = 256

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 67/269 (24%), Positives = 130/269 (48%), Gaps = 36/269 (13%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 11  KEKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 70

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +++D   G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +
Sbjct: 71  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEEL 124

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDW 203
           T       Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D 
Sbjct: 125 TRELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDV 181

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE-- 261
           +    DG E+V        N+R +L + + VL+ RE++I +          +EN S +  
Sbjct: 182 VGGTDDGFERV--------NQRMLLEKVLPVLDEREQKILQY-------TFIENRSQKET 226

Query: 262 ---FEVSRERVRQIEARAFKKVQESIQKQ 287
               ++S+  V +I+ +A KK++E++Q +
Sbjct: 227 GELLDISQMHVSRIQRQAIKKLREALQNE 255


>gi|261366888|ref|ZP_05979771.1| RNA polymerase sigma-G factor [Subdoligranulum variabile DSM 15176]
 gi|282571002|gb|EFB76537.1| RNA polymerase sigma-G factor [Subdoligranulum variabile DSM 15176]
          Length = 260

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 64/260 (24%), Positives = 122/260 (46%), Gaps = 18/260 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           ++P+L + E+  L +  R  GD  A  +++  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  QLPVLSETEKSALIRAAR-AGDAEARRKMIQGNLRLVLSVVQKFANRGENLDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FDP    R +TY +  I   ++ + LR  + V++  +   + L ++  R + 
Sbjct: 74  GLIKAIDHFDPSLQVRFSTYGVPMIVGEIRRF-LRDNNAVRVSRSI--RDLAYHSMRARE 130

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            LQ   +N   P ++  IA ++  S   V      +    SL   + S  ++S    D L
Sbjct: 131 ALQ--KENGRDP-KISEIAARVGASPENVAMALESVVEPASLYEPVYSDGEDSFAIVDQL 187

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
            +D  G+E  + +         M   ++  L+ RERRI   R L     T   ++ E  +
Sbjct: 188 -HDATGEESWISDI--------MFRDTVKSLSARERRIIAMRYLGGK--TQMQVAREIGI 236

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ +V ++E  A  +++E I
Sbjct: 237 SQAQVSRLEKGALNRIKEQI 256


>gi|16802936|ref|NP_464421.1| RNA polymerase sigma factor SigB [Listeria monocytogenes EGD-e]
 gi|47094902|ref|ZP_00232516.1| RNA polymerase sigma-B factor [Listeria monocytogenes str. 1/2a
           F6854]
 gi|224499433|ref|ZP_03667782.1| RNA polymerase sigma factor SigB [Listeria monocytogenes Finland
           1988]
 gi|224503136|ref|ZP_03671443.1| RNA polymerase sigma factor SigB [Listeria monocytogenes FSL
           R2-561]
 gi|254827839|ref|ZP_05232526.1| SigB [Listeria monocytogenes FSL N3-165]
 gi|254832139|ref|ZP_05236794.1| RNA polymerase sigma factor SigB [Listeria monocytogenes 10403S]
 gi|254898932|ref|ZP_05258856.1| RNA polymerase sigma factor SigB [Listeria monocytogenes J0161]
 gi|254911580|ref|ZP_05261592.1| RNA polymerase sigma-B factor [Listeria monocytogenes J2818]
 gi|254935906|ref|ZP_05267603.1| RNA polymerase sigma-B factor [Listeria monocytogenes F6900]
 gi|284801225|ref|YP_003413090.1| RNA polymerase sigma factor SigB [Listeria monocytogenes 08-5578]
 gi|284994367|ref|YP_003416135.1| RNA polymerase sigma factor SigB [Listeria monocytogenes 08-5923]
 gi|289434163|ref|YP_003464035.1| RNA polymerase sigma-B factor SigB [Listeria seeligeri serovar 1/2b
           str. SLCC3954]
 gi|315281577|ref|ZP_07870178.1| RNA polymerase sigma-B factor [Listeria marthii FSL S4-120]
 gi|22770508|gb|AAN06629.1|AF497201_1 sigma factor B [Listeria monocytogenes]
 gi|22770512|gb|AAN06631.1|AF497203_1 sigma factor B [Listeria monocytogenes]
 gi|22770532|gb|AAN06641.1|AF497213_1 sigma factor B [Listeria monocytogenes]
 gi|3298587|gb|AAC38791.1| Sigma B [Listeria monocytogenes]
 gi|16410298|emb|CAC98973.1| RNA polymerase sigma-37 factor (sigma-B) [Listeria monocytogenes
           EGD-e]
 gi|47016784|gb|EAL07703.1| RNA polymerase sigma-B factor [Listeria monocytogenes str. 1/2a
           F6854]
 gi|66968488|gb|AAY59623.1| SigB [Listeria seeligeri]
 gi|112363462|gb|ABI16056.1| sigma B [Listeria monocytogenes]
 gi|153582303|emb|CAO79793.1| sigma factor B [Listeria monocytogenes]
 gi|153582305|emb|CAO79794.1| sigma factor B [Listeria monocytogenes]
 gi|223700498|gb|ACN20365.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700502|gb|ACN20368.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700506|gb|ACN20371.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700514|gb|ACN20377.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700518|gb|ACN20380.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700522|gb|ACN20383.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700526|gb|ACN20386.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700530|gb|ACN20389.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700534|gb|ACN20392.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700538|gb|ACN20395.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700542|gb|ACN20398.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700546|gb|ACN20401.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700550|gb|ACN20404.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700554|gb|ACN20407.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700558|gb|ACN20410.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700562|gb|ACN20413.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700566|gb|ACN20416.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700570|gb|ACN20419.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700574|gb|ACN20422.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700578|gb|ACN20425.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700582|gb|ACN20428.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700586|gb|ACN20431.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700590|gb|ACN20434.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700594|gb|ACN20437.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700598|gb|ACN20440.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700602|gb|ACN20443.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700606|gb|ACN20446.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700610|gb|ACN20449.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700614|gb|ACN20452.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700618|gb|ACN20455.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700622|gb|ACN20458.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700626|gb|ACN20461.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700630|gb|ACN20464.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700634|gb|ACN20467.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700638|gb|ACN20470.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700642|gb|ACN20473.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700646|gb|ACN20476.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700650|gb|ACN20479.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700654|gb|ACN20482.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700658|gb|ACN20485.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700662|gb|ACN20488.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700666|gb|ACN20491.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700670|gb|ACN20494.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700674|gb|ACN20497.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700678|gb|ACN20500.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700682|gb|ACN20503.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700686|gb|ACN20506.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700690|gb|ACN20509.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700694|gb|ACN20512.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700698|gb|ACN20515.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700702|gb|ACN20518.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700706|gb|ACN20521.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700710|gb|ACN20524.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700714|gb|ACN20527.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700718|gb|ACN20530.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700722|gb|ACN20533.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700726|gb|ACN20536.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700730|gb|ACN20539.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700734|gb|ACN20542.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700738|gb|ACN20545.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700742|gb|ACN20548.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700746|gb|ACN20551.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700750|gb|ACN20554.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700754|gb|ACN20557.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700758|gb|ACN20560.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700762|gb|ACN20563.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700766|gb|ACN20566.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700770|gb|ACN20569.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700774|gb|ACN20572.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700778|gb|ACN20575.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700782|gb|ACN20578.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700786|gb|ACN20581.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700790|gb|ACN20584.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700794|gb|ACN20587.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700798|gb|ACN20590.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700802|gb|ACN20593.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700806|gb|ACN20596.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700810|gb|ACN20599.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700814|gb|ACN20602.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700818|gb|ACN20605.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700822|gb|ACN20608.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700826|gb|ACN20611.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700830|gb|ACN20614.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700834|gb|ACN20617.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700838|gb|ACN20620.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700842|gb|ACN20623.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700846|gb|ACN20626.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700850|gb|ACN20629.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700854|gb|ACN20632.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700858|gb|ACN20635.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700862|gb|ACN20638.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700866|gb|ACN20641.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700870|gb|ACN20644.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700874|gb|ACN20647.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700878|gb|ACN20650.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700882|gb|ACN20653.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700886|gb|ACN20656.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700890|gb|ACN20659.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700894|gb|ACN20662.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700898|gb|ACN20665.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700902|gb|ACN20668.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700906|gb|ACN20671.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700910|gb|ACN20674.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700914|gb|ACN20677.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700918|gb|ACN20680.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700922|gb|ACN20683.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700926|gb|ACN20686.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700930|gb|ACN20689.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700934|gb|ACN20692.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700938|gb|ACN20695.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700942|gb|ACN20698.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700946|gb|ACN20701.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700950|gb|ACN20704.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700954|gb|ACN20707.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700958|gb|ACN20710.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700962|gb|ACN20713.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700966|gb|ACN20716.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700970|gb|ACN20719.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700974|gb|ACN20722.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700978|gb|ACN20725.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700982|gb|ACN20728.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700986|gb|ACN20731.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700990|gb|ACN20734.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700994|gb|ACN20737.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700998|gb|ACN20740.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|258600220|gb|EEW13545.1| SigB [Listeria monocytogenes FSL N3-165]
 gi|258608494|gb|EEW21102.1| RNA polymerase sigma-B factor [Listeria monocytogenes F6900]
 gi|284056787|gb|ADB67728.1| RNA polymerase sigma factor SigB [Listeria monocytogenes 08-5578]
 gi|284059834|gb|ADB70773.1| RNA polymerase sigma factor SigB [Listeria monocytogenes 08-5923]
 gi|289170407|emb|CBH26947.1| RNA polymerase sigma-B factor SigB [Listeria seeligeri serovar 1/2b
           str. SLCC3954]
 gi|293589526|gb|EFF97860.1| RNA polymerase sigma-B factor [Listeria monocytogenes J2818]
 gi|302034427|gb|ADK92367.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|302034429|gb|ADK92368.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|302034431|gb|ADK92369.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|302034433|gb|ADK92370.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|302034439|gb|ADK92373.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|302034441|gb|ADK92374.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|302034443|gb|ADK92375.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|302034445|gb|ADK92376.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|313614786|gb|EFR88329.1| RNA polymerase sigma-B factor [Listeria marthii FSL S4-120]
          Length = 259

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 64/264 (24%), Positives = 129/264 (48%), Gaps = 26/264 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +++D   G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEEL 125

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDW 203
           T       Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D 
Sbjct: 126 TRELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDV 182

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    DG E+V        N+R +L + + VL+ RE++I +   ++    + +      +
Sbjct: 183 VGGTDDGFERV--------NQRMLLEKVLPVLDEREQKILQYTFIENR--SQKETGELLD 232

Query: 264 VSRERVRQIEARAFKKVQESIQKQ 287
           +S+  V +I+ +A KK++E++Q +
Sbjct: 233 ISQMHVSRIQRQAIKKLREALQNE 256


>gi|46907127|ref|YP_013516.1| RNA polymerase sigma factor SigB [Listeria monocytogenes serotype
           4b str. F2365]
 gi|47092103|ref|ZP_00229896.1| RNA polymerase sigma-B factor [Listeria monocytogenes str. 4b
           H7858]
 gi|217965008|ref|YP_002350686.1| RNA polymerase sigma-B factor [Listeria monocytogenes HCC23]
 gi|226223514|ref|YP_002757621.1| RNA polymerase sigma-37 factor (sigma-B) [Listeria monocytogenes
           Clip81459]
 gi|254823836|ref|ZP_05228837.1| RNA polymerase sigma-B factor [Listeria monocytogenes FSL J1-194]
 gi|254852389|ref|ZP_05241737.1| RNA polymerase sigma-B factor [Listeria monocytogenes FSL R2-503]
 gi|254931278|ref|ZP_05264637.1| RNA polymerase sigma B [Listeria monocytogenes HPB2262]
 gi|254994246|ref|ZP_05276436.1| RNA polymerase sigma factor SigB [Listeria monocytogenes FSL
           J2-064]
 gi|255521165|ref|ZP_05388402.1| RNA polymerase sigma factor SigB [Listeria monocytogenes FSL
           J1-175]
 gi|290892914|ref|ZP_06555904.1| RNA polymerase sigma-B factor [Listeria monocytogenes FSL J2-071]
 gi|300764104|ref|ZP_07074099.1| RNA polymerase sigma-B factor [Listeria monocytogenes FSL N1-017]
 gi|22770514|gb|AAN06632.1|AF497204_1 sigma factor B [Listeria monocytogenes]
 gi|22770518|gb|AAN06634.1|AF497206_1 sigma factor B [Listeria monocytogenes]
 gi|22770520|gb|AAN06635.1|AF497207_1 sigma factor B [Listeria monocytogenes]
 gi|22770522|gb|AAN06636.1|AF497208_1 sigma factor B [Listeria monocytogenes]
 gi|22770524|gb|AAN06637.1|AF497209_1 sigma factor B [Listeria monocytogenes]
 gi|22770526|gb|AAN06638.1|AF497210_1 sigma factor B [Listeria monocytogenes]
 gi|22770528|gb|AAN06639.1|AF497211_1 sigma factor B [Listeria monocytogenes]
 gi|22770530|gb|AAN06640.1|AF497212_1 sigma factor B [Listeria monocytogenes]
 gi|3298584|gb|AAC38789.1| sigma B [Listeria monocytogenes]
 gi|3298589|gb|AAC38792.1| Sigma B [Listeria monocytogenes]
 gi|26000673|gb|AAN75465.1| SigB [Listeria monocytogenes]
 gi|46880394|gb|AAT03693.1| RNA polymerase sigma-B factor [Listeria monocytogenes serotype 4b
           str. F2365]
 gi|47019543|gb|EAL10283.1| RNA polymerase sigma-B factor [Listeria monocytogenes str. 4b
           H7858]
 gi|112960117|gb|ABI27557.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960121|gb|ABI27560.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960125|gb|ABI27563.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960129|gb|ABI27566.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960133|gb|ABI27569.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960137|gb|ABI27572.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960141|gb|ABI27575.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960145|gb|ABI27578.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960149|gb|ABI27581.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960153|gb|ABI27584.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960157|gb|ABI27587.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960161|gb|ABI27590.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960165|gb|ABI27593.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960169|gb|ABI27596.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960173|gb|ABI27599.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960177|gb|ABI27602.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960181|gb|ABI27605.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960185|gb|ABI27608.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960189|gb|ABI27611.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960193|gb|ABI27614.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960197|gb|ABI27617.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960201|gb|ABI27620.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960205|gb|ABI27623.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960209|gb|ABI27626.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960213|gb|ABI27629.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960217|gb|ABI27632.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960221|gb|ABI27635.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960225|gb|ABI27638.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960229|gb|ABI27641.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960233|gb|ABI27644.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960237|gb|ABI27647.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960241|gb|ABI27650.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960245|gb|ABI27653.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960249|gb|ABI27656.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960253|gb|ABI27659.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960257|gb|ABI27662.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960261|gb|ABI27665.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960265|gb|ABI27668.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960269|gb|ABI27671.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960273|gb|ABI27674.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960277|gb|ABI27677.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960281|gb|ABI27680.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960285|gb|ABI27683.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960289|gb|ABI27686.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960293|gb|ABI27689.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960297|gb|ABI27692.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960301|gb|ABI27695.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960305|gb|ABI27698.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960309|gb|ABI27701.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960313|gb|ABI27704.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960317|gb|ABI27707.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960321|gb|ABI27710.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960325|gb|ABI27713.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960329|gb|ABI27716.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960333|gb|ABI27719.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960337|gb|ABI27722.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960341|gb|ABI27725.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960345|gb|ABI27728.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960349|gb|ABI27731.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960353|gb|ABI27734.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960357|gb|ABI27737.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960361|gb|ABI27740.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962434|gb|ABI28932.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962439|gb|ABI28936.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962444|gb|ABI28940.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962449|gb|ABI28944.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962454|gb|ABI28948.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962459|gb|ABI28952.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962464|gb|ABI28956.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962469|gb|ABI28960.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962474|gb|ABI28964.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962479|gb|ABI28968.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962484|gb|ABI28972.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962489|gb|ABI28976.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962494|gb|ABI28980.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962499|gb|ABI28984.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962504|gb|ABI28988.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962509|gb|ABI28992.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962514|gb|ABI28996.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962519|gb|ABI29000.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962524|gb|ABI29004.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962529|gb|ABI29008.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962534|gb|ABI29012.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962539|gb|ABI29016.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962544|gb|ABI29020.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962549|gb|ABI29024.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962554|gb|ABI29028.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962559|gb|ABI29032.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962564|gb|ABI29036.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962569|gb|ABI29040.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962574|gb|ABI29044.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962579|gb|ABI29048.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962584|gb|ABI29052.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962589|gb|ABI29056.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962594|gb|ABI29060.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962599|gb|ABI29064.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962604|gb|ABI29068.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962609|gb|ABI29072.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962614|gb|ABI29076.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962619|gb|ABI29080.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962624|gb|ABI29084.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962629|gb|ABI29088.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962634|gb|ABI29092.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962644|gb|ABI29100.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962649|gb|ABI29104.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962654|gb|ABI29108.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962659|gb|ABI29112.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962664|gb|ABI29116.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962669|gb|ABI29120.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962674|gb|ABI29124.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962679|gb|ABI29128.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962684|gb|ABI29132.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962689|gb|ABI29136.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962694|gb|ABI29140.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962699|gb|ABI29144.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962704|gb|ABI29148.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962709|gb|ABI29152.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962714|gb|ABI29156.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962719|gb|ABI29160.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962724|gb|ABI29164.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962729|gb|ABI29168.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962734|gb|ABI29172.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962739|gb|ABI29176.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962744|gb|ABI29180.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|118084623|gb|ABI16055.2| sigma B [Listeria monocytogenes]
 gi|118084625|gb|ABI16057.2| sigma B [Listeria monocytogenes]
 gi|153582301|emb|CAO79792.1| sigma factor B [Listeria monocytogenes]
 gi|153582307|emb|CAO79795.1| sigma factor B [Listeria monocytogenes]
 gi|217334278|gb|ACK40072.1| RNA polymerase sigma-B factor [Listeria monocytogenes HCC23]
 gi|225875976|emb|CAS04680.1| RNA polymerase sigma-37 factor (sigma-B) [Listeria monocytogenes
           serotype 4b str. CLIP 80459]
 gi|258605695|gb|EEW18303.1| RNA polymerase sigma-B factor [Listeria monocytogenes FSL R2-503]
 gi|290557490|gb|EFD91014.1| RNA polymerase sigma-B factor [Listeria monocytogenes FSL J2-071]
 gi|293582827|gb|EFF94859.1| RNA polymerase sigma B [Listeria monocytogenes HPB2262]
 gi|293593059|gb|EFG00820.1| RNA polymerase sigma-B factor [Listeria monocytogenes FSL J1-194]
 gi|300515094|gb|EFK42146.1| RNA polymerase sigma-B factor [Listeria monocytogenes FSL N1-017]
 gi|302034435|gb|ADK92371.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|302034437|gb|ADK92372.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|307570432|emb|CAR83611.1| RNA polymerase sigma-B factor [Listeria monocytogenes L99]
 gi|313609777|gb|EFR85233.1| RNA polymerase sigma-B factor [Listeria monocytogenes FSL F2-208]
 gi|328467051|gb|EGF38146.1| RNA polymerase sigma factor SigB [Listeria monocytogenes 1816]
 gi|328475458|gb|EGF46224.1| RNA polymerase sigma factor SigB [Listeria monocytogenes 220]
 gi|332311302|gb|EGJ24397.1| RNA polymerase sigma-B factor [Listeria monocytogenes str. Scott A]
          Length = 259

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 67/269 (24%), Positives = 130/269 (48%), Gaps = 36/269 (13%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +++D   G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEEL 125

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDW 203
           T       Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D 
Sbjct: 126 TRELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDV 182

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE-- 261
           +    DG E+V        N+R +L + + VL+ RE++I +          +EN S +  
Sbjct: 183 VGGTDDGFERV--------NQRMLLEKVLPVLDEREQKILQF-------TFIENRSQKET 227

Query: 262 ---FEVSRERVRQIEARAFKKVQESIQKQ 287
               ++S+  V +I+ +A KK++E++Q +
Sbjct: 228 GELLDISQMHVSRIQRQAIKKLREALQNE 256


>gi|318060769|ref|ZP_07979492.1| RNA polymerase sigma factor [Streptomyces sp. SA3_actG]
 gi|318078700|ref|ZP_07986032.1| RNA polymerase sigma factor [Streptomyces sp. SA3_actF]
 gi|333025872|ref|ZP_08453936.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
 gi|332745724|gb|EGJ76165.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
          Length = 367

 Score = 62.0 bits (149), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 64/237 (27%), Positives = 106/237 (44%), Gaps = 23/237 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +   
Sbjct: 146 LIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTVVGE 205

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL   L +    L    D +     V  +AK L VSE 
Sbjct: 206 IKRFFRDTSWS-VRVPRRLQELRL--ALTKTSDELAQKLDRS---PTVPELAKALGVSED 259

Query: 172 EVIS----MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +V+      N   A   SL++     D       D L Y+    E V    E R++ + +
Sbjct: 260 DVVDGLAVGNAYTA--SSLDSPAPEDDGGEGSLADRLGYEDTALEGV----EYRESLKPL 313

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L +    L PRERRI   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 314 LAK----LPPRERRIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 364


>gi|313887713|ref|ZP_07821395.1| putative RNA polymerase sigma-B factor [Peptoniphilus harei
           ACS-146-V-Sch2b]
 gi|312846322|gb|EFR33701.1| putative RNA polymerase sigma-B factor [Peptoniphilus harei
           ACS-146-V-Sch2b]
          Length = 261

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 56/264 (21%), Positives = 122/264 (46%), Gaps = 17/264 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K+E   L K Y E  D      L+  HL +   ++  Y G G+   ++    +IGL+ 
Sbjct: 13  LTKEERKDLFKEYHETKDQEIRDILIEEHLYIAEILSKKYTGRGIDYDDIYQVASIGLIY 72

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++++DPE+GF  ++++   I   +++Y   +   +++      +R+    +++     +
Sbjct: 73  AIERYDPEKGFEFSSFATPTIIGEIKKYFRDNGWTIRVP-----RRIQELSKKISNATVS 127

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           ++    K   +  IA+ L+ +  EV+      ++   +SL+    S D++     D +  
Sbjct: 128 LSQKYQKTPTIDEIAEYLDSTPEEVMEAMEASKVYTPQSLDVTYESGDESEVNLSDLI-- 185

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
              G E+   +K E     +   ++M  L+  ER I   R    N  T   ++ +  +S+
Sbjct: 186 ---GVEEAYFDKIE---SNDFFKKAMENLDEVERTILIDRYF--NKKTQVVIAKKLNISQ 237

Query: 267 ERVRQIEARAFKKVQESIQKQVEL 290
             V +IE +  +K+++ + K +E+
Sbjct: 238 MTVSRIEKKVLEKMRKEVAKTMEV 261


>gi|225175855|ref|ZP_03729848.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Dethiobacter
           alkaliphilus AHT 1]
 gi|225168779|gb|EEG77580.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Dethiobacter
           alkaliphilus AHT 1]
          Length = 268

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 64/269 (23%), Positives = 121/269 (44%), Gaps = 29/269 (10%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+      L K+  + GD  A   L+  +LRLV+ +   ++  G  + ++   G I
Sbjct: 15  KLPVLKSARMKELFKKM-QSGDEHARQELINGNLRLVLSVLQRFKNRGENLDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR------SWSLVKIGTTANQKRLFFN 138
           GLM+AV  F  +     +TY++  I   ++ Y+        S SL  +   A Q R    
Sbjct: 74  GLMKAVDNFSLDHNVHFSTYAVPMIIGEIKRYLRDNNAVRVSRSLKMLAHKAQQSR---- 129

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
                   + +T   L+   +  IA  L+++  EV+     +    SL+  +     +  
Sbjct: 130 --------EELTRKLLREPTLKEIAADLDITPEEVVFAYQAINDPLSLHDPVFQDTTDPV 181

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
              D LV D     ++ +E          L ++M +L+ RERRI E+R  +    T   +
Sbjct: 182 FVMD-LVSDQSSSAEIWVED-------ITLRQAMEILSERERRILESRFFEGRTQT--EI 231

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++E  +S+ +V +IE  A ++V+  + ++
Sbjct: 232 ANEIGISQAQVSRIEKSALRQVRHHLAEE 260


>gi|188585936|ref|YP_001917481.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|179350623|gb|ACB84893.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 239

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 35/97 (36%), Positives = 56/97 (57%), Gaps = 1/97 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L  +EE  L ++ +  GD      L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLTNEEEKDLLEKLK-AGDKKVRSTLIERNLRLVVYIARKFENTGVNIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           ++AV  FDP++  +LATY+   I+  +  Y+ R+  L
Sbjct: 96  IKAVNTFDPQKKIKLATYASKCIENEILMYLRRNNKL 132


>gi|182418945|ref|ZP_02950202.1| RNA polymerase sigma-E factor [Clostridium butyricum 5521]
 gi|237668989|ref|ZP_04528973.1| RNA polymerase sigma-E factor [Clostridium butyricum E4 str. BoNT E
           BL5262]
 gi|182377228|gb|EDT74796.1| RNA polymerase sigma-E factor [Clostridium butyricum 5521]
 gi|237657337|gb|EEP54893.1| RNA polymerase sigma-E factor [Clostridium butyricum E4 str. BoNT E
           BL5262]
          Length = 235

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 35/94 (37%), Positives = 55/94 (58%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K EE  L K+   +GD      L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 33  PPLSKDEEEELLKKLN-NGDEKIRSTLIERNLRLVVYIARKFENTGVYVEDLISVGTIGL 91

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+
Sbjct: 92  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN 125


>gi|182418995|ref|ZP_02950251.1| RNA polymerase sigma-K factor [Clostridium butyricum 5521]
 gi|182377278|gb|EDT74846.1| RNA polymerase sigma-K factor [Clostridium butyricum 5521]
          Length = 232

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 35/96 (36%), Positives = 56/96 (58%), Gaps = 2/96 (2%)

Query: 16  LSRYIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           L+ YI      P+ L+++EE +  K+++E GD SA   L+  +LRLV  I   Y      
Sbjct: 17  LTGYITNNNTFPLPLDEEEEQMYLKKFKE-GDKSAKSILIERNLRLVAHIVKKYSFPNKD 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           + E++S G +GL++A+  FD  +G RLATY+   I+
Sbjct: 76  VDELISIGTVGLIKAIDSFDSSKGTRLATYASRCIE 111


>gi|313619763|gb|EFR91370.1| RNA polymerase sigma-B factor [Listeria innocua FSL S4-378]
          Length = 259

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 64/264 (24%), Positives = 129/264 (48%), Gaps = 26/264 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQENGDEDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +++D   G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEEL 125

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDW 203
           T       Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D 
Sbjct: 126 TRELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDV 182

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    DG E+V        N+R +L + + VL+ RE++I +   ++    + +      +
Sbjct: 183 VGGTDDGFERV--------NQRMLLEKVLPVLDEREQKILQYTFIENR--SQKETGELLD 232

Query: 264 VSRERVRQIEARAFKKVQESIQKQ 287
           +S+  V +I+ +A KK++E++Q +
Sbjct: 233 ISQMHVSRIQRQAIKKLREALQNE 256


>gi|3386359|gb|AAC34827.1| RNA polymerase sigma B [Listeria monocytogenes]
          Length = 266

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 67/269 (24%), Positives = 130/269 (48%), Gaps = 36/269 (13%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 19  KEKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 78

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +++D   G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +
Sbjct: 79  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEEL 132

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDW 203
           T       Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D 
Sbjct: 133 TRELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDV 189

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE-- 261
           +    DG E+V        N+R +L + + VL+ RE++I +          +EN S +  
Sbjct: 190 VGGTDDGFERV--------NQRMLLEKVLPVLDEREQKILQF-------TFIENRSQKET 234

Query: 262 ---FEVSRERVRQIEARAFKKVQESIQKQ 287
               ++S+  V +I+ +A KK++E++Q +
Sbjct: 235 GELLDISQMHVSRIQRQAIKKLREALQNE 263


>gi|313895463|ref|ZP_07829020.1| Sigma-70 region 2 [Selenomonas sp. oral taxon 137 str. F0430]
 gi|312976358|gb|EFR41816.1| Sigma-70 region 2 [Selenomonas sp. oral taxon 137 str. F0430]
          Length = 208

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 32/109 (29%), Positives = 62/109 (56%), Gaps = 3/109 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP- 74
            + Y+ ++  +  L   EE  L + Y+E GD  A  R++ ++  LV +  M YR   LP 
Sbjct: 2   FADYVKKLSAVEKLRPDEERALWRAYKEKGDEGARRRIIEAYQPLVFREVMPYRA--LPA 59

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           + + V EG IGL++AV+++DP RG   + Y++  ++  + +++ R  ++
Sbjct: 60  VMDAVQEGTIGLIEAVERYDPARGVAFSLYAVHRVRGCILDFLRREGTV 108


>gi|307330885|ref|ZP_07610018.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306883426|gb|EFN14479.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 263

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 61/234 (26%), Positives = 109/234 (46%), Gaps = 19/234 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+   +   
Sbjct: 43  LVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATPTVVGE 102

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +   + W+ V++     + RL      L      ++  + +   V  +A++L++SE 
Sbjct: 103 IKRHFRDKGWA-VRVPRRLQELRL-----SLTTATAELSQRHGRAPTVHELAEQLSISEE 156

Query: 172 EVISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           EV      L G ES NA    S D   +  +   V D  G E   +E  E    R  L  
Sbjct: 157 EV------LEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVE---YRESLKP 207

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  L PRE++I   R      +T   ++ E  +S+  V ++ AR   ++++ +
Sbjct: 208 LLEDLPPREKKILLLRFF--GNMTQSQIAQEVGISQMHVSRLLARTLAQLRDKL 259


>gi|296133648|ref|YP_003640895.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           sp. JR]
 gi|296032226|gb|ADG82994.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           potens JR]
          Length = 242

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 34/94 (36%), Positives = 55/94 (58%), Gaps = 2/94 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+   +E Y+++K     GD +    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 41  PLSNAEENYLISKL--ATGDAAVRSVLIERNLRLVVYIARKFENTGVGIEDLVSIGTIGL 98

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  FDP +  +LATY+   I+  +  Y+ R+
Sbjct: 99  IKAVNTFDPAKKIKLATYASRCIENEILMYLRRN 132


>gi|320529893|ref|ZP_08030970.1| sigma-70 region 2 [Selenomonas artemidis F0399]
 gi|320137911|gb|EFW29816.1| sigma-70 region 2 [Selenomonas artemidis F0399]
          Length = 208

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 32/109 (29%), Positives = 62/109 (56%), Gaps = 3/109 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP- 74
            + Y+ ++  +  L   EE  L + Y+E GD  A  R++ ++  LV +  M YR   LP 
Sbjct: 2   FADYVKKLSAVKKLRPDEERALWRAYKEKGDEGARRRIIEAYQPLVFREVMPYRA--LPA 59

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           + + V EG IGL++AV+++DP RG   + Y++  ++  + +++ R  ++
Sbjct: 60  VMDAVQEGTIGLIEAVERYDPARGVAFSLYAVHRVRGCILDFLRREGTV 108


>gi|255022641|ref|ZP_05294627.1| RNA polymerase sigma factor SigB [Listeria monocytogenes FSL
           J1-208]
 gi|22770504|gb|AAN06627.1|AF497199_1 sigma factor B [Listeria monocytogenes]
          Length = 259

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 64/264 (24%), Positives = 129/264 (48%), Gaps = 26/264 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQENGDEDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +++D   G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEEL 125

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDW 203
           T       Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D 
Sbjct: 126 TRELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDV 182

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    DG E+V        N+R +L + + VL+ RE++I +   ++    + +      +
Sbjct: 183 VGGTDDGFERV--------NQRMLLEKVLPVLDEREQKILQFTFIENR--SQKETGELLD 232

Query: 264 VSRERVRQIEARAFKKVQESIQKQ 287
           +S+  V +I+ +A KK++E++Q +
Sbjct: 233 ISQMHVSRIQRQAIKKLREALQNE 256


>gi|315302306|ref|ZP_07873197.1| RNA polymerase sigma-B factor [Listeria ivanovii FSL F6-596]
 gi|313629329|gb|EFR97571.1| RNA polymerase sigma-B factor [Listeria ivanovii FSL F6-596]
          Length = 259

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 64/264 (24%), Positives = 128/264 (48%), Gaps = 26/264 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQEDGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +++D   G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEEL 125

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDW 203
           T       Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D 
Sbjct: 126 TRELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDV 182

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    DG E+V        N+R +L + + VL+ RE++I +   ++    + +      +
Sbjct: 183 VGGTDDGFERV--------NQRMLLEKVLPVLDEREQKILQYTFIENR--SQKETGELLD 232

Query: 264 VSRERVRQIEARAFKKVQESIQKQ 287
           +S+  V +I+ +A KK++E++Q +
Sbjct: 233 ISQMHVSRIQRQAIKKLREALQNE 256


>gi|300814743|ref|ZP_07094991.1| putative RNA polymerase sigma-B factor [Peptoniphilus sp. oral
           taxon 836 str. F0141]
 gi|300511130|gb|EFK38382.1| putative RNA polymerase sigma-B factor [Peptoniphilus sp. oral
           taxon 836 str. F0141]
          Length = 258

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 65/270 (24%), Positives = 127/270 (47%), Gaps = 29/270 (10%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K+E+  L   Y +  D      L+  +L +   ++  Y G G+   ++    +IGL+ 
Sbjct: 10  LTKEEKKELFLEYYKTKDQDLRTILIEEYLYIAEILSKKYIGKGIDYDDIYQVASIGLIY 69

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +V +FDP +G+  ++++   I   +++Y   + W++          R+   ++ L   + 
Sbjct: 70  SVDRFDPTKGYEFSSFATPTIIGEIKKYFRDKGWTI----------RVPRRIQELSKKI- 118

Query: 148 AITDNNLKPE-----QVVAIAKKLNVSESEVI-SMNC-RLAGDESLNALINSSDKNSSQW 200
            I  N L  E      V  IA+ LN S  E+I SM   ++   +SL+ + +S D      
Sbjct: 119 MIAKNKLSQEYQRTPTVEDIAEFLNASPEEIIESMEASKVYTPQSLDIVYDSGDDKKMSL 178

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
           QD +     G+++   +K + K   + L +SM  LN  E+ I   R    N  T   ++ 
Sbjct: 179 QDLI-----GEDEKYFDKIDLK---DFLLKSMKNLNEVEKTILIDRYF--NKKTQIVIAK 228

Query: 261 EFEVSRERVRQIEARAFKKVQESIQKQVEL 290
           +  +S+  V +IE +  +K+++ I+K +E+
Sbjct: 229 KLNISQMTVSRIEKKVLEKMRKEIKKTMEV 258


>gi|152976264|ref|YP_001375781.1| sporulation sigma factor SigG [Bacillus cereus subsp. cytotoxis NVH
           391-98]
 gi|152025016|gb|ABS22786.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           cytotoxicus NVH 391-98]
          Length = 259

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 65/267 (24%), Positives = 127/267 (47%), Gaps = 29/267 (10%)

Query: 25  KIPMLEKQEEYVLAKRYRE--HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           K+P+L+  E   + K +RE   G+ SA  +LV  +LRLV+ +   +   G  + ++   G
Sbjct: 15  KLPVLKNDE---MRKLFREMQSGETSAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVG 71

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            IGLM+++  FD  +  + +TY++  I   ++ Y LR  + +++  +          + L
Sbjct: 72  CIGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSLRD----IAYKAL 126

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
           +   + I +N+ +P   + IA+ L+V+  E++          +L+A+ +        + D
Sbjct: 127 QVREKLIAENSKEP-TAMDIAQVLDVTHEEIVF---------ALDAIQDPVSLFEPIYND 176

Query: 203 W----LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
                 V D    E+   +K+E+      L   M  LN RE+ I   R  Q    T   +
Sbjct: 177 GGDPIFVMDQLSDEK---QKDEQWVEELALKEGMKRLNDREKMIIRKRFFQGK--TQMEV 231

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQ 285
           + E  +S+ +V ++E  A K++ ++IQ
Sbjct: 232 AEEIGISQAQVSRLEKSAIKQMNKTIQ 258


>gi|238800552|gb|ACR56097.1| RNA polymerase sigma factor SigB [Listeria innocua]
          Length = 248

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 64/264 (24%), Positives = 129/264 (48%), Gaps = 26/264 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 1   KEKVYIWIAAYQENGDEDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 60

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +++D   G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +
Sbjct: 61  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEEL 114

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDW 203
           T       Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D 
Sbjct: 115 TRELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDV 171

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    DG E+V        N+R +L + + VL+ RE++I +   ++    + +      +
Sbjct: 172 VGGTDDGFERV--------NQRMLLEKVLPVLDEREQKILQYTFIENR--SQKETGELLD 221

Query: 264 VSRERVRQIEARAFKKVQESIQKQ 287
           +S+  V +I+ +A KK++E++Q +
Sbjct: 222 ISQMHVSRIQRQAIKKLREALQNE 245


>gi|254519267|ref|ZP_05131323.1| sporulation sigma factor SigE [Clostridium sp. 7_2_43FAA]
 gi|226913016|gb|EEH98217.1| sporulation sigma factor SigE [Clostridium sp. 7_2_43FAA]
          Length = 235

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 30/77 (38%), Positives = 48/77 (62%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           HGD S    L+  +LRLVV IA  +   G+ + +++S G IGL++AV  F+PE+  +LAT
Sbjct: 49  HGDESIRDILIERNLRLVVYIARKFENTGVCVEDLISVGTIGLIKAVNTFNPEKKIKLAT 108

Query: 104 YSMWWIKAAMQEYILRS 120
           Y+   I+  +  Y+ R+
Sbjct: 109 YASRCIENEILMYLRRN 125


>gi|3298591|gb|AAC38793.1| Sigma B [Listeria innocua]
          Length = 259

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 64/264 (24%), Positives = 129/264 (48%), Gaps = 26/264 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQENGDEDAQYNLVIHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +++D   G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEEL 125

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDW 203
           T       Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D 
Sbjct: 126 TRELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDV 182

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    DG E+V        N+R +L + + VL+ RE++I +   ++    + +      +
Sbjct: 183 VGGTDDGFERV--------NQRMLLEKVLPVLDEREQKILQYTFIENR--SQKETGELLD 232

Query: 264 VSRERVRQIEARAFKKVQESIQKQ 287
           +S+  V +I+ +A KK++E++Q +
Sbjct: 233 ISQMHVSRIQRQAIKKLREALQNE 256


>gi|326790567|ref|YP_004308388.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium lentocellum DSM
           5427]
 gi|326541331|gb|ADZ83190.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium lentocellum DSM
           5427]
          Length = 239

 Score = 61.6 bits (148), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 67/247 (27%), Positives = 116/247 (46%), Gaps = 30/247 (12%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A + LV  +L LV  +   +   G  + ++   G+IGL++++ KFD     + +
Sbjct: 12  QQGDEIAKNILVQENLGLVWSLVRRFSNRGYDMEDLFQIGSIGLLKSIDKFDLSFNVKFS 71

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I   ++ + LR   ++K+  +   K   + +R LK  L  I + N +P  +  I
Sbjct: 72  TYAVPMIVGEIKRF-LRDDGMIKVSRSL--KETAYKVRILKDEL--IRELNREP-TISEI 125

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK-EER 221
           A  L++   EV+      A  ESLNA+I               Y  DG+   L +K +E 
Sbjct: 126 AAGLDLQVEEVVEALESNAEIESLNAVI---------------YQGDGKPITLSDKIDEV 170

Query: 222 KNRRNMLTRSMSV------LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
              +N L   M +      L P ER I   R  ++   T   ++S  ++S+ +V +IE R
Sbjct: 171 PTLQNSLVDKMILTELIERLLPIEREIIHMRYFEDRTQT--EIASALDISQVQVSRIEKR 228

Query: 276 AFKKVQE 282
             KK++E
Sbjct: 229 ILKKMRE 235


>gi|325288837|ref|YP_004265018.1| RNA polymerase, sigma 29 subunit, SigE [Syntrophobotulus glycolicus
           DSM 8271]
 gi|324964238|gb|ADY55017.1| RNA polymerase, sigma 29 subunit, SigE [Syntrophobotulus glycolicus
           DSM 8271]
          Length = 250

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 31/77 (40%), Positives = 47/77 (61%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GDLS    L+  +LRLVV I+  +   G+ I ++VS G IGL++AV  FDP +  +LAT
Sbjct: 64  KGDLSVKGTLIERNLRLVVYISRKFENTGISIEDLVSIGTIGLIKAVNTFDPTKKIKLAT 123

Query: 104 YSMWWIKAAMQEYILRS 120
           Y+   I+  +  Y+ R+
Sbjct: 124 YASRCIENEILMYLRRN 140


>gi|299538362|ref|ZP_07051645.1| RNA polymerase sigma-F factor [Lysinibacillus fusiformis ZC1]
 gi|298725949|gb|EFI66541.1| RNA polymerase sigma-F factor [Lysinibacillus fusiformis ZC1]
          Length = 247

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 58/243 (23%), Positives = 111/243 (45%), Gaps = 26/243 (10%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A  R+V  + RLV  I   +   G+ + ++   G IGLM++V KFD     + +
Sbjct: 9   QQGDHEARKRMVEGNTRLVWSIVQRFTTRGVELEDLFQIGCIGLMKSVDKFDLTYDVKFS 68

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK----PEQ 158
           TY++  I   +Q + LR   +VK+  +         +R L   ++  TD  +K    P  
Sbjct: 69  TYAVPMIIGEIQRF-LRDDGMVKVSRS---------IRELNFKIRHATDEFIKKNEHPPT 118

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           +  +A+ L V+  E+++ +  L    SL+  +  S+ +S    D          Q+  EK
Sbjct: 119 IQELAQVLGVTTEEIVTASDALRDPASLHEQLYESEGDSITLMD----------QMKDEK 168

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
            E+      L   ++ L PRE+ I   R   +   T   +++   +S+ +V ++E +   
Sbjct: 169 SEQPFDYIPLKEVLTRLEPREQSIIYLRYFSD--CTQTEIANRLGISQVQVSRLEKKILA 226

Query: 279 KVQ 281
           +++
Sbjct: 227 QLK 229


>gi|295696453|ref|YP_003589691.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
 gi|295412055|gb|ADG06547.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
          Length = 242

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 35/79 (44%), Positives = 49/79 (62%), Gaps = 1/79 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L ++EE  L  R  E GD S    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 40  PPLTREEEEALLVRLIE-GDESVRSTLIERNLRLVVYIARKFENTGIYIEDLVSIGTIGL 98

Query: 87  MQAVKKFDPERGFRLATYS 105
           ++AV  FDP++  +LATY+
Sbjct: 99  IKAVNTFDPQKRIKLATYA 117


>gi|323702293|ref|ZP_08113959.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
 gi|323532783|gb|EGB22656.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
          Length = 121

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 38/106 (35%), Positives = 60/106 (56%), Gaps = 3/106 (2%)

Query: 9   IVNGEIGLSRYI-HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           +VNG + L  YI +     P+ E++E Y L +  +  GD SA + LV  +LRLV  I   
Sbjct: 13  VVNGALALVSYITNNTFPQPLTEEEEAYYLEQLAK--GDESARNVLVERNLRLVAHIVKK 70

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           +   G  + +++S G IGL++A+  F  ++G RLATY+   I+  M
Sbjct: 71  FDQTGEDVDDLISIGAIGLIKAINTFKTDKGTRLATYAARCIENEM 116


>gi|237668235|ref|ZP_04528219.1| RNA polymerase sigma-K factor (Sigma-27) [Clostridium butyricum E4
           str. BoNT E BL5262]
 gi|237656583|gb|EEP54139.1| RNA polymerase sigma-K factor (Sigma-27) [Clostridium butyricum E4
           str. BoNT E BL5262]
          Length = 146

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 35/96 (36%), Positives = 56/96 (58%), Gaps = 2/96 (2%)

Query: 16  LSRYIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           L+ YI      P+ L+++EE +  K+++E GD SA   L+  +LRLV  I   Y      
Sbjct: 17  LTGYITNNNTFPLPLDEEEEQMYLKKFKE-GDKSAKSILIERNLRLVAHIVKKYSFPNKD 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           + E++S G +GL++A+  FD  +G RLATY+   I+
Sbjct: 76  VDELISIGTVGLIKAIDSFDSSKGTRLATYASRCIE 111


>gi|292670483|ref|ZP_06603909.1| DNA-directed RNA polymerase sigma subunit RpoH [Selenomonas noxia
           ATCC 43541]
 gi|292647893|gb|EFF65865.1| DNA-directed RNA polymerase sigma subunit RpoH [Selenomonas noxia
           ATCC 43541]
          Length = 205

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 31/95 (32%), Positives = 58/95 (61%), Gaps = 1/95 (1%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L  +EE+ L + Y+E GD SA  R++ ++  LV +  M YR   + + + V EG IGL++
Sbjct: 10  LTPEEEHALWRAYKEEGDESARRRIIEAYQPLVFREVMPYRTMPV-VMDAVQEGTIGLIE 68

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           AV+++DP RG   + Y++  ++  + +++ R  S+
Sbjct: 69  AVERYDPTRGVAFSLYAVHRVRGRILDFLRREGSV 103


>gi|282881777|ref|ZP_06290435.1| RNA polymerase sigma-B factor [Peptoniphilus lacrimalis 315-B]
 gi|281298387|gb|EFA90825.1| RNA polymerase sigma-B factor [Peptoniphilus lacrimalis 315-B]
          Length = 261

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 65/270 (24%), Positives = 127/270 (47%), Gaps = 29/270 (10%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K+E+  L   Y +  D      L+  +L +   ++  Y G G+   ++    +IGL+ 
Sbjct: 13  LTKEEKKELFLEYYKTKDQDLRTILIEEYLYIAEILSKKYIGKGIDYDDIYQVASIGLIY 72

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +V +FDP +G+  ++++   I   +++Y   + W++          R+   ++ L   + 
Sbjct: 73  SVDRFDPTKGYEFSSFATPTIIGEIKKYFRDKGWTI----------RVPRRIQELSKKI- 121

Query: 148 AITDNNLKPE-----QVVAIAKKLNVSESEVI-SMNC-RLAGDESLNALINSSDKNSSQW 200
            I  N L  E      V  IA+ LN S  E+I SM   ++   +SL+ + +S D      
Sbjct: 122 MIAKNKLSQEYQRTPTVEDIAEFLNASPEEIIESMEASKVYTPQSLDIVYDSGDDKKMSL 181

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
           QD +     G+++   +K + K   + L +SM  LN  E+ I   R    N  T   ++ 
Sbjct: 182 QDLI-----GEDEKYFDKIDLK---DFLLKSMKNLNEIEKTILIDRYF--NKKTQIVIAK 231

Query: 261 EFEVSRERVRQIEARAFKKVQESIQKQVEL 290
           +  +S+  V +IE +  +K+++ I+K +E+
Sbjct: 232 KLNISQMTVSRIEKKVLEKMRKEIKKTMEV 261


>gi|225018358|ref|ZP_03707550.1| hypothetical protein CLOSTMETH_02302 [Clostridium methylpentosum
           DSM 5476]
 gi|224948875|gb|EEG30084.1| hypothetical protein CLOSTMETH_02302 [Clostridium methylpentosum
           DSM 5476]
          Length = 245

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 32/79 (40%), Positives = 49/79 (62%), Gaps = 1/79 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K EE V+ ++  E  D  A  +L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 42  PPLTKDEERVVFQKLSEK-DPWARDQLIVHNLRLVVYIAKKFESTGIGVEDLISIGTIGL 100

Query: 87  MQAVKKFDPERGFRLATYS 105
           ++AV  F PE+  +LATY+
Sbjct: 101 IKAVNTFSPEKNIKLATYA 119


>gi|30266009|gb|AAN16082.1| SigB [Listeria ivanovii]
 gi|30266011|gb|AAN16083.1| SigB [Listeria ivanovii]
          Length = 259

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 66/265 (24%), Positives = 127/265 (47%), Gaps = 36/265 (13%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 16  YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 75

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 76  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTREL 129

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +   
Sbjct: 130 QSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGT 186

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE-----F 262
            DG E+V        N+R +L + + VL+ RE++I +          +EN S +      
Sbjct: 187 DDGFERV--------NQRMLLEKVLPVLDEREQKILQY-------TFIENRSQKETGELL 231

Query: 263 EVSRERVRQIEARAFKKVQESIQKQ 287
           ++S+  V +I+ +A KK++E++Q +
Sbjct: 232 DISQMHVSRIQRQAIKKLREALQNE 256


>gi|255525678|ref|ZP_05392611.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium carboxidivorans
           P7]
 gi|296185436|ref|ZP_06853846.1| RNA polymerase sigma-G factor [Clostridium carboxidivorans P7]
 gi|255510664|gb|EET86971.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium carboxidivorans
           P7]
 gi|296050270|gb|EFG89694.1| RNA polymerase sigma-G factor [Clostridium carboxidivorans P7]
          Length = 257

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 67/281 (23%), Positives = 134/281 (47%), Gaps = 59/281 (20%)

Query: 25  KIPMLEKQE--EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           K+P+L+++E  E +L+ R   +GD+S   + + S+LRLV+ +   +   G  + ++   G
Sbjct: 15  KLPVLKEKEMKELLLSMR---NGDVSCREKFIKSNLRLVLSVIQRFNNRGENVDDLFQVG 71

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            IGL++++  FD  +  + +TY++  I   ++ Y LR  + +++  +          R L
Sbjct: 72  CIGLIKSIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNSIRVSRSLRD----IAYRAL 126

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
           +   + I++NN +P  V  IAK+L V   EV+          +L+A+           QD
Sbjct: 127 QVRDRLISENNKEP-TVSQIAKELKVPREEVVF---------ALDAI-----------QD 165

Query: 203 WL-----VYDHDGQEQVLIEKEERKNRRNM---------LTRSMSVLNPRER-----RIF 243
            +     +Y HDG + + +  +   N +NM         +  +M  LN RE+     R F
Sbjct: 166 PVSLFEPIY-HDGGDAIYVMDQISDN-KNMDDSWLENIAIKEAMKKLNDREKLILNLRFF 223

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + R   E       ++ E  +S+ +V ++E  A + +++ +
Sbjct: 224 DGRTQME-------VADEIGISQAQVSRLEKTALRHMRKYV 257


>gi|302876403|ref|YP_003845036.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium cellulovorans
           743B]
 gi|307687066|ref|ZP_07629512.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium cellulovorans
           743B]
 gi|302579260|gb|ADL53272.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium cellulovorans
           743B]
          Length = 427

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 63/241 (26%), Positives = 113/241 (46%), Gaps = 18/241 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYG---LPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           A   LV ++ +LV +IA+ Y+ +       S++   G +GLM+A +KFD  +G + +TY+
Sbjct: 181 ALDNLVNANKKLVWEIALRYKQFSTVSFDNSDMYQAGVLGLMKAAEKFDISKGNQFSTYA 240

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
            WW++ ++   I    + ++I     +K     + +         + N +      +A  
Sbjct: 241 TWWVRQSITRSIADYSTTIRIPVHMREK-----IIKYVSTENKFWNENGRVASKEELANL 295

Query: 166 LNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD-HDGQEQVLIEKEERK 222
           L +S  EV  + +   +A   SL+  I + +   S   +++  D H   E+     EE +
Sbjct: 296 LGISSEEVNYLQVYQDVANLTSLDIPIGADE--GSFLGEFIPDDKHRSPEK---SAEEGE 350

Query: 223 NRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            +R +       L P+E RI   R   +     TLE +     V+RER+RQIEA+A  K+
Sbjct: 351 LKRELKEICEGRLTPKETRILNFRFGFIDGRTHTLEEIGHVENVTRERIRQIEAKAISKL 410

Query: 281 Q 281
           Q
Sbjct: 411 Q 411


>gi|257055039|ref|YP_003132871.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Saccharomonospora
           viridis DSM 43017]
 gi|256584911|gb|ACU96044.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Saccharomonospora
           viridis DSM 43017]
          Length = 295

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 59/238 (24%), Positives = 107/238 (44%), Gaps = 24/238 (10%)

Query: 57  HLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           H   +VK   G  G GLP    +++++  G  GL+ A++KFDPERG R  TY+M  I+ A
Sbjct: 66  HYAPLVKYVAGRVGTGLPTHIDVADLIQSGIFGLVDAIEKFDPERGLRFETYAMQRIRGA 125

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           + +  LRS   V     +  + +     RL   L+    +         +A +L ++  E
Sbjct: 126 ILDD-LRSQDWVPRAVRSRAREIERAHERLGARLRRTPTD-------AEVAAELGITLRE 177

Query: 173 VISM--NCRLAGDESLNALINSS-DKNSSQWQDWLVYDHDGQ---EQVLIEKEERKNRRN 226
           +  +    RL    +L+ L+ +S D  +           DG      VL++++ R+    
Sbjct: 178 LRDLYGQLRLTSVLALDDLMGASKDNGNGTGSPADTLPDDGAVDPAAVLVDQDNRRQ--- 234

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L  +++ LN R+R +      +   +TL  +     V+  RV Q+  RA  +++  +
Sbjct: 235 -LAEAIAQLNERDRIVVSLYYFEN--LTLAEIGKVLGVTESRVSQLHTRAVLRLRAKL 289


>gi|20808064|ref|NP_623235.1| sporulation sigma factor SigE [Thermoanaerobacter tengcongensis
           MB4]
 gi|20516645|gb|AAM24839.1| DNA-directed RNA polymerase sigma subunits (sigma70/sigma32)
           [Thermoanaerobacter tengcongensis MB4]
          Length = 241

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 33/94 (35%), Positives = 57/94 (60%), Gaps = 2/94 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  ++E Y+++K   E GD  A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 40  PLSVEEESYLISKM--EKGDNEAKSILIERNLRLVVYIAKKFENTGVGIEDLISIGTIGL 97

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++A+  F+P +  +LATY+   I+  +  Y+ R+
Sbjct: 98  IKAINTFNPRKKIKLATYASRCIENEILMYLRRN 131


>gi|323706112|ref|ZP_08117681.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
 gi|323534556|gb|EGB24338.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
          Length = 241

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 32/94 (34%), Positives = 57/94 (60%), Gaps = 2/94 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  ++E +++AK   E GD  A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 40  PLSAEEEMFLIAKM--ESGDNEAKSMLIERNLRLVVYIAKKFENTGVGIEDLISIGTIGL 97

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++++  F+P +  +LATY+   I+  +  Y+ R+
Sbjct: 98  IKSINTFNPRKKIKLATYASRCIENEILMYLRRN 131


>gi|254478789|ref|ZP_05092157.1| RNA polymerase sigma-E factor [Carboxydibrachium pacificum DSM
           12653]
 gi|214035301|gb|EEB76007.1| RNA polymerase sigma-E factor [Carboxydibrachium pacificum DSM
           12653]
          Length = 244

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 33/94 (35%), Positives = 57/94 (60%), Gaps = 2/94 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  ++E Y+++K   E GD  A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 43  PLSVEEESYLISKM--EKGDNEAKSILIERNLRLVVYIAKKFENTGVGIEDLISIGTIGL 100

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++A+  F+P +  +LATY+   I+  +  Y+ R+
Sbjct: 101 IKAINTFNPRKKIKLATYASRCIENEILMYLRRN 134


>gi|255026033|ref|ZP_05298019.1| RNA polymerase sigma factor SigB [Listeria monocytogenes FSL
           J2-003]
          Length = 259

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 64/264 (24%), Positives = 129/264 (48%), Gaps = 26/264 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +++D   G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEEL 125

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDW 203
           T       Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D 
Sbjct: 126 TRELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDV 182

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    DG E+V        N+R +L + + VL+ RE++I +   ++    + +      +
Sbjct: 183 VGGTDDGFERV--------NQRMLLEKVLPVLDEREQKILQFTFIENR--SQKETGELLD 232

Query: 264 VSRERVRQIEARAFKKVQESIQKQ 287
           +S+  V +I+ +A KK++E++Q +
Sbjct: 233 ISQMHVSRIQRQAXKKLREALQNE 256


>gi|253580606|ref|ZP_04857870.1| RNA polymerase [Ruminococcus sp. 5_1_39B_FAA]
 gi|251847977|gb|EES75943.1| RNA polymerase [Ruminococcus sp. 5_1_39BFAA]
          Length = 237

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 62/245 (25%), Positives = 118/245 (48%), Gaps = 22/245 (8%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A   +   +  LV  +A  + G  + + ++V  G+IGL++A+ +FD     + +
Sbjct: 12  QQGDKEARDTVFKENAGLVYSMAKRFAGRSVEMEDIVQIGSIGLLKAIDRFDISYDVKFS 71

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV--- 159
           TY++  I   ++ Y LR   ++K+     +     N  R+    +A+ +  L  E +   
Sbjct: 72  TYAVPMIIGEIRRY-LRDDGMLKVSRNLKE-----NCARIYSAREAL-EKELGREPILEE 124

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           VA A +L+V E  V+SM    A  ESL+ +I   D N     D L    +GQ+  L    
Sbjct: 125 VAKATELSVDEV-VMSMESG-AEVESLHKIIYQGDGNDISLMDRLQEKENGQDAAL---- 178

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
                R  L   +  L+ RER++   R  ++  +T   +++E  +S+ +V ++E R  K+
Sbjct: 179 ----NRIFLDEILKKLDARERQLIGMRYFKD--MTQTEIAAEMGISQVQVSRMEKRILKE 232

Query: 280 VQESI 284
           +++ +
Sbjct: 233 LKKQV 237


>gi|16799967|ref|NP_470235.1| RNA polymerase sigma factor SigB [Listeria innocua Clip11262]
 gi|16413344|emb|CAC96126.1| RNA polymerase sigma-37 factor (sigma-B) [Listeria innocua
           Clip11262]
 gi|30266013|gb|AAN16084.1| SigB [Listeria monocytogenes]
          Length = 259

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 64/264 (24%), Positives = 128/264 (48%), Gaps = 26/264 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQEDGDEDAQYNLVIHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +++D   G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEEL 125

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDW 203
           T       Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D 
Sbjct: 126 TRELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDV 182

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    DG E+V        N+R +L + + VL+ RE++I +   ++    + +      +
Sbjct: 183 VGGTDDGFERV--------NQRMLLEKVLPVLDEREQKILQYTFIENR--SQKETGELLD 232

Query: 264 VSRERVRQIEARAFKKVQESIQKQ 287
           +S+  V +I+ +A KK++E++Q +
Sbjct: 233 ISQMHVSRIQRQAIKKLREALQNE 256


>gi|332755592|gb|EGJ85955.1| RNA polymerase sigma factor rpoS domain protein [Shigella flexneri
           2747-71]
          Length = 133

 Score = 61.2 bits (147), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 32/74 (43%), Positives = 50/74 (67%), Gaps = 1/74 (1%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKK 92
           + EGN+GL++AV+K
Sbjct: 120 IEEGNLGLIRAVEK 133


>gi|302385959|ref|YP_003821781.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           saccharolyticum WM1]
 gi|302196587|gb|ADL04158.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           saccharolyticum WM1]
          Length = 240

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 62/241 (25%), Positives = 119/241 (49%), Gaps = 16/241 (6%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GD +A  +LVT +  LV  I   + G G    ++   G+IGLM+A+ KFD     + +T
Sbjct: 16  EGDKAARDQLVTDNFGLVWSIVRRFTGRGYEAEDLFQIGSIGLMKAIDKFDLSYEVKFST 75

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y++  I   ++ + LR   ++K+  +   K +   ++ ++  L  I     +P  V  IA
Sbjct: 76  YAVPMITGEIKRF-LRDDGMIKVSRSI--KEMGLKVKNVREEL--IYRLGREP-TVEEIA 129

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
            ++  S+ EV +     A  ESL   +N +D+NS    D +  +   QE++L        
Sbjct: 130 GEIGASKEEVAASIEAGAEVESLYRSVNKNDENSILLIDKIEEESSAQEELL-------- 181

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            R +L   ++ L+ ++R I   RR   N  T   ++++  +S+ +V ++E +  K+++E 
Sbjct: 182 NRMVLRELLTALSDKDREII-IRRYYYNE-TQSQIAAKLGISQVQVSRLEKKILKQMREK 239

Query: 284 I 284
           +
Sbjct: 240 L 240


>gi|253580726|ref|ZP_04857990.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251848097|gb|EES76063.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 209

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 34/91 (37%), Positives = 54/91 (59%), Gaps = 2/91 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+   QE+Y L K Y+E GD  A + L+  +LRLV  +   Y+G G    +++S G IGL
Sbjct: 7   PLSISQEKYYLQK-YQE-GDSQAKNILIEHNLRLVAHVVKKYQGTGEDTDDLISIGTIGL 64

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           ++AV  F+P++  RL+TY+   I+  +  Y 
Sbjct: 65  IKAVTTFNPQKASRLSTYAARCIENELLMYF 95


>gi|148380490|ref|YP_001255031.1| RNA polymerase sigma-E factor [Clostridium botulinum A str. ATCC
           3502]
 gi|153932419|ref|YP_001384713.1| sporulation sigma factor SigE [Clostridium botulinum A str. ATCC
           19397]
 gi|153937804|ref|YP_001388234.1| sporulation sigma factor SigE [Clostridium botulinum A str. Hall]
 gi|153940530|ref|YP_001391830.1| sporulation sigma factor SigE [Clostridium botulinum F str.
           Langeland]
 gi|168180581|ref|ZP_02615245.1| RNA polymerase sigma-E factor [Clostridium botulinum NCTC 2916]
 gi|170756639|ref|YP_001782077.1| sporulation sigma factor SigE [Clostridium botulinum B1 str. Okra]
 gi|187778871|ref|ZP_02995344.1| hypothetical protein CLOSPO_02466 [Clostridium sporogenes ATCC
           15579]
 gi|226949888|ref|YP_002804979.1| RNA polymerase sigma-E factor [Clostridium botulinum A2 str. Kyoto]
 gi|148289974|emb|CAL84087.1| RNA polymerase sigma-E factor [Clostridium botulinum A str. ATCC
           3502]
 gi|152928463|gb|ABS33963.1| RNA polymerase sigma-E factor [Clostridium botulinum A str. ATCC
           19397]
 gi|152933718|gb|ABS39217.1| RNA polymerase sigma-E factor [Clostridium botulinum A str. Hall]
 gi|152936426|gb|ABS41924.1| RNA polymerase sigma-E factor [Clostridium botulinum F str.
           Langeland]
 gi|169121851|gb|ACA45687.1| RNA polymerase sigma-E factor [Clostridium botulinum B1 str. Okra]
 gi|182668430|gb|EDT80409.1| RNA polymerase sigma-E factor [Clostridium botulinum NCTC 2916]
 gi|187772496|gb|EDU36298.1| hypothetical protein CLOSPO_02466 [Clostridium sporogenes ATCC
           15579]
 gi|226843077|gb|ACO85743.1| RNA polymerase sigma-E factor [Clostridium botulinum A2 str. Kyoto]
 gi|295319856|gb|ADG00234.1| RNA polymerase sigma-E factor [Clostridium botulinum F str. 230613]
 gi|322806803|emb|CBZ04372.1| RNA polymerase sporulation specific sigma factor SigE [Clostridium
           botulinum H04402 065]
          Length = 235

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 47/165 (28%), Positives = 80/165 (48%), Gaps = 10/165 (6%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE    +R   +GD      L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 33  PPLSKEEEEYFVQRLI-NGDEKVRSVLIERNLRLVVYIARKFENTGICIEDLVSVGTIGL 91

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS---------WSLVKIGTTANQKRLFF 137
           ++AV  F P++  +LATY+   I+  +  Y+ R+         +  + I    N+  L  
Sbjct: 92  IKAVNTFKPDKKIKLATYASRCIENEILMYLRRNSKVKAEISFYEPLNIDWDGNELLLSD 151

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            L      +  + ++ +  + ++   KKLN  E E++ +   L G
Sbjct: 152 ILGTDNDEVYNLIEDEVDKQLLLLAMKKLNEREKEIVRLRFGLNG 196


>gi|300854412|ref|YP_003779396.1| putative RNA polymerase sigma-K factor [Clostridium ljungdahlii DSM
           13528]
 gi|300434527|gb|ADK14294.1| predicted RNA polymerase sigma-K factor precursor [Clostridium
           ljungdahlii DSM 13528]
          Length = 233

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 34/84 (40%), Positives = 49/84 (58%), Gaps = 2/84 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ +++EEY L K   E GDL A   LV  +LRLV  I   Y      + E++S G +GL
Sbjct: 30  PLSDEEEEYYLKKL--EQGDLLAKSILVERNLRLVAHIVKKYSYPSKEVDELISIGTVGL 87

Query: 87  MQAVKKFDPERGFRLATYSMWWIK 110
           ++A+  FD  +G RLATY+   I+
Sbjct: 88  IKAIDSFDMSKGTRLATYAAKCIE 111


>gi|293375845|ref|ZP_06622113.1| putative RNA polymerase sigma factor RpoD [Turicibacter sanguinis
           PC909]
 gi|325844994|ref|ZP_08168319.1| RNA polymerase sigma factor RpoD family protein [Turicibacter sp.
           HGF1]
 gi|292645524|gb|EFF63566.1| putative RNA polymerase sigma factor RpoD [Turicibacter sanguinis
           PC909]
 gi|325488967|gb|EGC91357.1| RNA polymerase sigma factor RpoD family protein [Turicibacter sp.
           HGF1]
          Length = 331

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 65/262 (24%), Positives = 121/262 (46%), Gaps = 30/262 (11%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDP 95
           K+YR   D +A   L+ ++  LV KI   Y  +    L   ++ S G  GLM+A++KFD 
Sbjct: 69  KKYRLENDETALEWLIFNNTNLVHKIIGRYTKFYHHKLDYDDLFSVGLEGLMKAIEKFDF 128

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
                 +TY+ +W+K A+   I      ++I        +F ++ ++  + Q   D   +
Sbjct: 129 TFDNNFSTYATYWVKQAVTRTIADEGFTIRIPV-----HMFESINQVMRYEQK-ADQEDE 182

Query: 156 PEQVVAIAKKLNV---SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           P  V  +  +L +       V  +   +    SLN  ++  D++ ++ QD +      + 
Sbjct: 183 PVDVDNLCGELKIPIEKYEAVKRVQTYMLKPTSLNGFVSKEDED-TELQDLI----SNEN 237

Query: 213 QVLIEKEER-----------KNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLS 259
           ++L+E   R           ++ +  + + +  LNPRE+ +   R     E   TLE + 
Sbjct: 238 EMLVEGMSRIYDNPEKQAMDEDLKAYMDKMILSLNPREQFVIIHRFGLNGEEKKTLEEIG 297

Query: 260 SEFEVSRERVRQIEARAFKKVQ 281
               V+RER+RQIEA+A +K++
Sbjct: 298 EIEGVTRERIRQIEAKAMRKLR 319


>gi|168182610|ref|ZP_02617274.1| RNA polymerase sigma-E factor [Clostridium botulinum Bf]
 gi|170759960|ref|YP_001787849.1| sporulation sigma factor SigE [Clostridium botulinum A3 str. Loch
           Maree]
 gi|237795972|ref|YP_002863524.1| sporulation sigma factor SigE [Clostridium botulinum Ba4 str. 657]
 gi|169406949|gb|ACA55360.1| RNA polymerase sigma-E factor [Clostridium botulinum A3 str. Loch
           Maree]
 gi|182674165|gb|EDT86126.1| RNA polymerase sigma-E factor [Clostridium botulinum Bf]
 gi|229261167|gb|ACQ52200.1| RNA polymerase sigma-E factor [Clostridium botulinum Ba4 str. 657]
          Length = 235

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 47/165 (28%), Positives = 80/165 (48%), Gaps = 10/165 (6%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE    +R   +GD      L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 33  PPLSKEEEEYFVQRLI-NGDEKVRSVLIERNLRLVVYIARKFENTGICIEDLVSVGTIGL 91

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS---------WSLVKIGTTANQKRLFF 137
           ++AV  F P++  +LATY+   I+  +  Y+ R+         +  + I    N+  L  
Sbjct: 92  IKAVNTFKPDKKIKLATYASRCIENEILMYLRRNSKVKAEISFYEPLNIDWDGNELLLSD 151

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            L      +  + ++ +  + ++   KKLN  E E++ +   L G
Sbjct: 152 ILGTDNDEVYNLIEDEVDKQLLLLAMKKLNEREKEIVRLRFGLNG 196


>gi|302544115|ref|ZP_07296457.1| RNA polymerase sigma-F factor [Streptomyces hygroscopicus ATCC
           53653]
 gi|302461733|gb|EFL24826.1| RNA polymerase sigma-F factor [Streptomyces himastatinicus ATCC
           53653]
          Length = 284

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 62/243 (25%), Positives = 117/243 (48%), Gaps = 23/243 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++L LV   A  +R    P+ +V+  G IGL+ A+ +FDP RG +  T++M  +   
Sbjct: 62  LIEANLPLVRYAAARFRSRNEPMEDVIQVGTIGLINAIDRFDPGRGVQFPTFAMPTVVGE 121

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           ++ Y   +   V +      +RL     ++ G  + +T  + +      IA++L + E E
Sbjct: 122 IKRYFRDNVRTVHV-----PRRLHELWVQVNGATEDLTVLHGRSPTTAEIAERLGLGEDE 176

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWL--VYDHDGQEQVLIEKEERKNRRNMLTR 230
           V++  C  AG        +++   ++Q  D L  + D  G E   +   E ++    L R
Sbjct: 177 VLA--CIEAGRS-----YHATSLEAAQEGDGLPGLVDRLGYEDPALAGVEHRD----LVR 225

Query: 231 SMSVLNP-RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
            + V  P RE+RI   R      +T   +S+E  VS+  V ++ +R+F +++ +   ++E
Sbjct: 226 HLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLLSRSFARLRSA--NRIE 281

Query: 290 LSS 292
            SS
Sbjct: 282 PSS 284


>gi|22770516|gb|AAN06633.1|AF497205_1 sigma factor B [Listeria monocytogenes]
          Length = 259

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 64/264 (24%), Positives = 128/264 (48%), Gaps = 26/264 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +++D   G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEEL 125

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDW 203
           T       Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D 
Sbjct: 126 TRELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDV 182

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    DG E+V        N+R +L + + VL+ RE++I +   ++    + +      +
Sbjct: 183 VGGTDDGFERV--------NQRMLLEKVLPVLDEREQKILQFTFIENR--SQKETGELLD 232

Query: 264 VSRERVRQIEARAFKKVQESIQKQ 287
           +S+  V +I+ +A KK+ E++Q +
Sbjct: 233 ISQMHVSRIQRQAIKKLLEALQNE 256


>gi|297544885|ref|YP_003677187.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
 gi|296842660|gb|ADH61176.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
          Length = 241

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 33/94 (35%), Positives = 58/94 (61%), Gaps = 2/94 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  ++E Y+++K   E GD  A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 40  PLSMEEETYLVSKM--EKGDNEAKTVLIERNLRLVVYIAKKFENTGVGIEDLISIGTIGL 97

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++A+  F+P++  +LATY+   I+  +  Y+ R+
Sbjct: 98  IKAINTFNPKKKIKLATYASRCIENEILMYLRRN 131


>gi|167628452|ref|YP_001678951.1| RNA polymerase sigma-f factor, putative [Heliobacterium
           modesticaldum Ice1]
 gi|167591192|gb|ABZ82940.1| RNA polymerase sigma-f factor, putative [Heliobacterium
           modesticaldum Ice1]
          Length = 264

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 73/279 (26%), Positives = 132/279 (47%), Gaps = 39/279 (13%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           + P+L  +EE     R  + GD  A  RL+  +LRLV  +   ++  G  + ++   G I
Sbjct: 12  RFPLL-GEEETTRLLRLAKDGDGDARERLIQCNLRLVFNLVQRFQHRGYELEDLFQIGVI 70

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+ KFD     R +TY++  I   ++ + LR  S VK+  + + K +   + R++ 
Sbjct: 71  GLIKAIDKFDLSYNVRFSTYAVPMIVGEIRRF-LRDDSPVKV--SRSYKEIAQRIHRVRQ 127

Query: 145 HLQAITDNNLKPEQVVA-IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
            L    + +L  E  V  IA  +N+   +V+         E+L A+   +  + + +QD 
Sbjct: 128 EL----NGSLGREPTVQEIAGAMNMPVEDVV---------EALEAVQLPTSIHETLYQD- 173

Query: 204 LVYDHDGQEQVLIEK------EERKNRRNM-LTRSMSVLNPRERRIFEARRLQENPVTLE 256
                DG    L+++      EE     ++ L   +S L  RER I E R  Q+   T  
Sbjct: 174 -----DGDPIFLLDQLASVGTEESAWFDHLALKDVLSRLAAREREILEMRFFQDKTQT-- 226

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPP 295
            +++   +S+ ++ +IE  A KK+++       LS +PP
Sbjct: 227 EVATLVGLSQVQISRIERAALKKIRDM------LSQTPP 259


>gi|289746505|ref|ZP_06505883.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           02_1987]
 gi|289687033|gb|EFD54521.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           02_1987]
          Length = 216

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 49/206 (23%), Positives = 98/206 (47%), Gaps = 12/206 (5%)

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           G  ++V+KFD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++ 
Sbjct: 15  GADRSVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQR 72

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L         PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++
Sbjct: 73  ELLQDLGREPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI 127

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEF 262
               D +  V ++       ++ L   +  L+ RE  +   R       P TL+ +   +
Sbjct: 128 ---EDSEAVVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVY 184

Query: 263 EVSRERVRQIEARAFKKVQESIQKQV 288
            V+RER+RQIE++   K++   + QV
Sbjct: 185 GVTRERIRQIESKTMSKLRHPSRSQV 210


>gi|289578665|ref|YP_003477292.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter italicus Ab9]
 gi|289528378|gb|ADD02730.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter italicus Ab9]
          Length = 241

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 33/94 (35%), Positives = 58/94 (61%), Gaps = 2/94 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  ++E Y+++K   E GD  A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 40  PLSVEEETYLVSKM--EKGDNEAKTVLIERNLRLVVYIAKKFENTGVGIEDLISIGTIGL 97

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++A+  F+P++  +LATY+   I+  +  Y+ R+
Sbjct: 98  IKAINTFNPKKKIKLATYASRCIENEILMYLRRN 131


>gi|255030138|ref|ZP_05302089.1| RNA polymerase sigma factor SigB [Listeria monocytogenes LO28]
          Length = 245

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 63/260 (24%), Positives = 126/260 (48%), Gaps = 26/260 (10%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTREL 115

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +   
Sbjct: 116 QSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGT 172

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            DG E+V        N+R +L + + VL+ RE++I +   ++    + +      ++S+ 
Sbjct: 173 DDGFERV--------NQRMLLEKVLPVLDEREQKILQYTFIENR--SQKETGELLDISQM 222

Query: 268 RVRQIEARAFKKVQESIQKQ 287
            V +I+ +A KK++E++Q +
Sbjct: 223 HVSRIQRQAIKKLREALQNE 242


>gi|289642895|ref|ZP_06475030.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Frankia
           symbiont of Datisca glomerata]
 gi|289507278|gb|EFD28242.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Frankia
           symbiont of Datisca glomerata]
          Length = 332

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 67/241 (27%), Positives = 113/241 (46%), Gaps = 30/241 (12%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +LV  HL LV  +A  +R  G P+ ++     IGL+++V +FDPERG   +TY+   I  
Sbjct: 110 QLVRMHLPLVEYLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPERGVEFSTYATPTIVG 169

Query: 112 AMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT---DNNL-KPEQVVAIAKKL 166
            ++ +   + W++          R+   L+ LK  L   T      L +   V  IA  L
Sbjct: 170 EIKRHFRDKGWAI----------RVPRRLQELKLSLTKATSELSQTLGRSPTVSEIAAHL 219

Query: 167 NVSESEVISMNCRLAGDESLNA--LINSSDKNSSQWQDWLVYDHDG-QEQVLIEKEERKN 223
            +SE EV      L G ES NA   ++    +S   +   V D  G Q++ L   E R++
Sbjct: 220 QMSEEEV------LEGLESANAYSAVSLDAPDSGDDEAPAVADTLGVQDESLEGVEYRES 273

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            + +L +    L PRE+RI   R      +T   +++E  +S+  V ++ AR   +++  
Sbjct: 274 LKPLLEK----LPPREKRILLLRFFGN--MTQSQIATELGISQMHVSRLLARTLAQLRRG 327

Query: 284 I 284
           +
Sbjct: 328 L 328


>gi|126650128|ref|ZP_01722361.1| sporulation sigma factor SigF [Bacillus sp. B14905]
 gi|126593300|gb|EAZ87262.1| sporulation sigma factor SigF [Bacillus sp. B14905]
          Length = 263

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 62/261 (23%), Positives = 117/261 (44%), Gaps = 37/261 (14%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A  R+V  + RLV  I   +   G+ + ++   G IGLM++V KFD     + +
Sbjct: 25  QKGDHEARKRMVEGNTRLVWSIVQRFTTRGVELEDLFQIGCIGLMKSVDKFDLSYDVKFS 84

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK----PEQ 158
           TY++  I   +Q + LR   +VK+  +         +R L   ++  TD  +K    P  
Sbjct: 85  TYAVPMIIGEIQRF-LRDDGMVKVSRS---------IRELNFKIRHATDEFIKKNEHPPT 134

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           +  +A+ L V+  E+++ +  L    SL+  +  S+ +S    D          Q+  EK
Sbjct: 135 IQELAQVLGVTTEEIVTASDALRDPASLHEQLYESEGDSITLMD----------QMKDEK 184

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
            E+      L   ++ L PRE+ I   R   +   T   +++   +S+ +V ++E +   
Sbjct: 185 SEQPFDYIPLKEVLTRLEPREQSIIYLRYFSD--CTQTEIANRLGISQVQVSRLEKKILA 242

Query: 279 KV-----------QESIQKQV 288
           ++           QE+I+K +
Sbjct: 243 QLKSWMATSATVEQEAIKKDI 263


>gi|194014382|ref|ZP_03052999.1| RNA polymerase sigma-E factor [Bacillus pumilus ATCC 7061]
 gi|194013408|gb|EDW22973.1| RNA polymerase sigma-E factor [Bacillus pumilus ATCC 7061]
          Length = 239

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 36/94 (38%), Positives = 55/94 (58%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K EE  L  +    GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLSKDEEQELLVKL-PKGDQTARAILIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN 129


>gi|300854418|ref|YP_003779402.1| RNA polymerase sigma-E factor [Clostridium ljungdahlii DSM 13528]
 gi|300434533|gb|ADK14300.1| RNA polymerase sigma-E factor precursor [Clostridium ljungdahlii
           DSM 13528]
          Length = 241

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 34/94 (36%), Positives = 56/94 (59%), Gaps = 2/94 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ +K+EE ++ K     GD      L+  +LRLVV IA  +   G+ + ++VS G IGL
Sbjct: 40  PLSKKEEEDLVLKLV--SGDEKVRSTLIERNLRLVVYIARKFENTGVNVEDLVSVGTIGL 97

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+
Sbjct: 98  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN 131


>gi|157692207|ref|YP_001486669.1| sporulation sigma factor SigE [Bacillus pumilus SAFR-032]
 gi|157680965|gb|ABV62109.1| DNA-directed RNA polymerase sigma subunit SigE [Bacillus pumilus
           SAFR-032]
          Length = 239

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 36/94 (38%), Positives = 55/94 (58%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K EE  L  +    GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLSKDEEQELLVKL-PKGDQTARAILIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN 129


>gi|313115572|ref|ZP_07801031.1| RNA polymerase sigma-E factor [Faecalibacterium cf. prausnitzii
           KLE1255]
 gi|310622087|gb|EFQ05583.1| RNA polymerase sigma-E factor [Faecalibacterium cf. prausnitzii
           KLE1255]
          Length = 234

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 62/220 (28%), Positives = 96/220 (43%), Gaps = 61/220 (27%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L  ++E VL  R     D +A   L+T +LRLVV +A  Y   G+P  +++S G IGL
Sbjct: 33  PPLTPEQEKVLLSRMAAG-DAAARDDLITHNLRLVVYLAKKYESSGVPAEDMISIGTIGL 91

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F PER  +LATY+   I   +  Y+ +S         +N++             
Sbjct: 92  IKAVNTFTPERSIKLATYASRCIGNEILMYLRKS---------SNRR------------- 129

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                      Q  +I + LNV             G+E L + I  SD+N          
Sbjct: 130 -----------QEASIDEPLNVDGD----------GNELLLSDILGSDENQ--------- 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
                   + ++ E+   R +L R++  L+PRER+I E R
Sbjct: 160 --------ISQRLEQDAERAVLRRAVDSLSPRERQIMELR 191


>gi|150019061|ref|YP_001311315.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           beijerinckii NCIMB 8052]
 gi|149905526|gb|ABR36359.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           beijerinckii NCIMB 8052]
          Length = 242

 Score = 60.8 bits (146), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 65/258 (25%), Positives = 115/258 (44%), Gaps = 43/258 (16%)

Query: 46  DLSAAHRLVTSHLRLVVKIA----MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
           D+    +++  ++ LV  IA     G   Y +   ++VS G +GLM A+ KFD  +G + 
Sbjct: 6   DVDGKEQIIQEYIPLVKYIASRVMFGKNKY-MEYEDLVSYGMVGLMDALNKFDDTKGMKF 64

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           ++Y+   IK AM + + R+  + K G      +    +  L+  L     N+        
Sbjct: 65  SSYASIRIKGAMIDELRRNRPISK-GAMDKLNKYNKAVDTLQLELLREPTND-------E 116

Query: 162 IAKKLNVSESEV---------ISM----NCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           IAK L +S SEV         ISM    N   + DE +N +    DKNS     +L    
Sbjct: 117 IAKYLGISMSEVAEIENYINYISMVSLENVIFSDDEDVNLIGIIEDKNSPSPDAYL---- 172

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
                      + K +  +LT+++ +L  ++R +      +   +TL+ + +   VS  R
Sbjct: 173 -----------QDKEQLEILTKAIDLLKEKDRIVLNLYYYE--GLTLKEIGTVLSVSESR 219

Query: 269 VRQIEARAFKKVQESIQK 286
           V Q+ +RA   ++E ++K
Sbjct: 220 VCQLHSRAISSLRECMRK 237


>gi|22770506|gb|AAN06628.1|AF497200_1 sigma factor B [Listeria monocytogenes]
          Length = 259

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 64/264 (24%), Positives = 128/264 (48%), Gaps = 26/264 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQENGDEDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +++D   G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEEL 125

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDW 203
           T       Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D 
Sbjct: 126 TRELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDV 182

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    DG E+V        N+R +L + + VL+ RE++I +   ++    + +      +
Sbjct: 183 VGGTDDGFERV--------NQRMLLEKVLPVLDEREQKILQFTFIENR--SQKETGELLD 232

Query: 264 VSRERVRQIEARAFKKVQESIQKQ 287
           +S+  V +I+ +A KK+ E++Q +
Sbjct: 233 ISQMHVSRIQRQAIKKLLEALQNE 256


>gi|125972969|ref|YP_001036879.1| sporulation sigma factor SigG [Clostridium thermocellum ATCC 27405]
 gi|256004766|ref|ZP_05429741.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium thermocellum
           DSM 2360]
 gi|281417180|ref|ZP_06248200.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           thermocellum JW20]
 gi|125713194|gb|ABN51686.1| RNA polymerase, sigma subunit, RpsG/SigG [Clostridium thermocellum
           ATCC 27405]
 gi|255991216|gb|EEU01323.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium thermocellum
           DSM 2360]
 gi|281408582|gb|EFB38840.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           thermocellum JW20]
 gi|316940795|gb|ADU74829.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium thermocellum
           DSM 1313]
          Length = 257

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 67/277 (24%), Positives = 129/277 (46%), Gaps = 51/277 (18%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L  +++  L +R  + GD SA    +  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLTNEQKKELFERMHK-GDTSAREEFIKGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK- 143
           GL++A+  FD  +  + +TY++  I   ++ Y LR  + +++  +         LR +  
Sbjct: 74  GLIKAIDNFDVTQNVKFSTYAVPMIIGEIRRY-LRDNNAIRVSRS---------LRDIAY 123

Query: 144 GHLQA---ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
             LQA   +T+ N K   +  IAK+L + + EV+          +L+A+ +      S +
Sbjct: 124 KALQAKEKLTNQNSKEPTIEEIAKELGLPKEEVVF---------ALDAIQDPISLFESVY 174

Query: 201 QDWLVYDHDGQEQVLIE---KEERKNRRN-----MLTRSMSVLNPRER-----RIFEARR 247
                  HDG + + +    K+E+ N  N      L+ +M  LN RE+     R F+ R 
Sbjct: 175 -------HDGGDAIYVMDQVKDEKNNDENWLEGIALSEAMRKLNDREKLILNLRFFDGRT 227

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             E       ++ E  +S+ +V ++E  A   +++ I
Sbjct: 228 QME-------VAEEIGISQAQVSRLEKTALMHMRKYI 257


>gi|30266015|gb|AAN16085.1| SigB [Listeria welshimeri]
          Length = 259

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 64/264 (24%), Positives = 128/264 (48%), Gaps = 26/264 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +++D   G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEEL 125

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDW 203
           T       Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D 
Sbjct: 126 TRELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDV 182

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    DG E+V        N+R +L + + VL+ RE+ I +   ++    + +      +
Sbjct: 183 VGGTDDGFERV--------NQRMLLEKVLPVLDEREQMILQYTFIENR--SQKETGELLD 232

Query: 264 VSRERVRQIEARAFKKVQESIQKQ 287
           +S+  V +I+ +A KK++E++Q +
Sbjct: 233 ISQMHVSRIQRQAIKKLREALQNE 256


>gi|239826533|ref|YP_002949157.1| sporulation sigma factor SigG [Geobacillus sp. WCH70]
 gi|239806826|gb|ACS23891.1| RNA polymerase, sigma 28 subunit, SigG [Geobacillus sp. WCH70]
          Length = 259

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 65/261 (24%), Positives = 121/261 (46%), Gaps = 17/261 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+ +E   L KR  E GDL A  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKNEEMRELFKRMHE-GDLEAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD  +  + +TY++  I   ++ Y LR  + +++  +   + + +   +++ 
Sbjct: 74  GLMKSIDNFDLNQNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSL--RDIAYKALQVRE 130

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L + T      E+   IAK L +   EV+     +    SL   I +   +     D L
Sbjct: 131 KLMSETAKEPSAEE---IAKVLGIPHEEVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQL 187

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             + +   Q + E          L   M  LN RE+ I   R  Q    T   ++ E  +
Sbjct: 188 SDERNRDSQWIEEI--------ALKEGMRRLNEREKMIIRKRFFQGK--TQMEVAEEIGI 237

Query: 265 SRERVRQIEARAFKKVQESIQ 285
           S+ +V ++E  A +++ ++IQ
Sbjct: 238 SQAQVSRLEKAAIRQMNKNIQ 258


>gi|167040624|ref|YP_001663609.1| sporulation sigma factor SigE [Thermoanaerobacter sp. X514]
 gi|300914665|ref|ZP_07131981.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X561]
 gi|307724101|ref|YP_003903852.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter sp. X513]
 gi|166854864|gb|ABY93273.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Thermoanaerobacter sp. X514]
 gi|300889600|gb|EFK84746.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X561]
 gi|307581162|gb|ADN54561.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X513]
          Length = 241

 Score = 60.8 bits (146), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 33/94 (35%), Positives = 58/94 (61%), Gaps = 2/94 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  ++E Y+++K   E GD  A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 40  PLSVEEEMYLISKM--EKGDNEAKTVLIERNLRLVVYIAKKFENTGVGIEDLISIGTIGL 97

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++A+  F+P++  +LATY+   I+  +  Y+ R+
Sbjct: 98  IKAINTFNPKKKIKLATYASRCIENEILMYLRRN 131


>gi|332799103|ref|YP_004460602.1| RNA polymerase sigma-28 subunit SigE [Tepidanaerobacter sp. Re1]
 gi|332696838|gb|AEE91295.1| RNA polymerase, sigma 28 subunit, SigE [Tepidanaerobacter sp. Re1]
          Length = 239

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 32/94 (34%), Positives = 54/94 (57%), Gaps = 2/94 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+   +E + L K   + GD +    L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 38  PLTSDEEVFYLKKL--QMGDQTVKTVLIERNLRLVVYIARKFENTGICIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++A+  FDP +  +LATY+   I+  +  Y+ R+
Sbjct: 96  IKAINTFDPNKKIKLATYASKCIENEILMYLRRN 129


>gi|116872297|ref|YP_849078.1| RNA polymerase sigma factor SigB [Listeria welshimeri serovar 6b
           str. SLCC5334]
 gi|55535652|gb|AAV52891.1| SigB [Listeria welshimeri]
 gi|116741175|emb|CAK20295.1| RNA polymerase sigma-37 (sigma-B) [Listeria welshimeri serovar 6b
           str. SLCC5334]
          Length = 259

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 64/264 (24%), Positives = 128/264 (48%), Gaps = 26/264 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +++D   G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEEL 125

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDW 203
           T       Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D 
Sbjct: 126 TRELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDV 182

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    DG E+V        N+R +L + + VL+ RE+ I +   ++    + +      +
Sbjct: 183 VGGTDDGFERV--------NQRMLLEKVLPVLDEREQMILQYTFIENR--SQKETGELLD 232

Query: 264 VSRERVRQIEARAFKKVQESIQKQ 287
           +S+  V +I+ +A KK++E++Q +
Sbjct: 233 ISQMHVSRIQRQAIKKLREALQNE 256


>gi|317121977|ref|YP_004101980.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermaerobacter marianensis DSM 12885]
 gi|315591957|gb|ADU51253.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermaerobacter marianensis DSM 12885]
          Length = 250

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 26/62 (41%), Positives = 40/62 (64%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A  RLV  H+ LV  +A  + G+G  + ++V  G IGL+QA+  FDP RG++ +TY
Sbjct: 12  GDAEARERLVALHMPLVRHVARRFAGFGHEMDDLVQAGTIGLLQAIDGFDPARGYQFSTY 71

Query: 105 SM 106
           ++
Sbjct: 72  AV 73


>gi|229541192|ref|ZP_04430252.1| RNA polymerase, sigma 28 subunit, SigG [Bacillus coagulans 36D1]
 gi|229325612|gb|EEN91287.1| RNA polymerase, sigma 28 subunit, SigG [Bacillus coagulans 36D1]
          Length = 258

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 64/261 (24%), Positives = 123/261 (47%), Gaps = 17/261 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+ +E   L K+    GD SA  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKNEEMRDLLKKMH-AGDASAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD  +  R +TY++  I   ++ Y LR  + +++  +   + + +   +++ 
Sbjct: 74  GLMKSIDNFDLNQNVRFSTYAVPMIIGEIRRY-LRDNNPIRVSRSL--RDIAYKALQVRE 130

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L + T      E+   IA++L+V   +++     +    SL   I +   +     D  
Sbjct: 131 KLMSATSKEPTTEE---IARELDVPHEDIVFALDAIQDPVSLFEPIYNDGGDPIYVMDQ- 186

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           V D   ++   IE+         L   M  LN RE+ I   R  Q    T   ++ E  +
Sbjct: 187 VSDEKNKDSQWIEE-------IALQEGMRRLNEREKMIIRKRFFQGK--TQMEVAEEIGI 237

Query: 265 SRERVRQIEARAFKKVQESIQ 285
           S+ +V ++E  A K++ ++IQ
Sbjct: 238 SQAQVSRLEKAAIKQMNKNIQ 258


>gi|329938753|ref|ZP_08288149.1| SigH-like stress response sigma factor [Streptomyces
           griseoaurantiacus M045]
 gi|329302244|gb|EGG46136.1| SigH-like stress response sigma factor [Streptomyces
           griseoaurantiacus M045]
          Length = 291

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 62/237 (26%), Positives = 106/237 (44%), Gaps = 23/237 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FDP+RG    T++M  +   
Sbjct: 70  LIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDPDRGVEFPTFAMPTVVGE 129

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL   L +    L    D +     V  +A  L VSE 
Sbjct: 130 IKRFFRDTSWS-VRVPRRLQELRL--ALTKASDELSQKLDRS---PTVAELAVVLGVSEE 183

Query: 172 EVIS----MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +V+      N   A   SL++     D       D L Y+    E V    E R++ + +
Sbjct: 184 DVVDGLAVGNAYTAS--SLDSPAPEDDGGEGSLADRLGYEDTALEGV----EYRESLKPL 237

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L +    L PRER+I   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 238 LAK----LPPRERQIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 288


>gi|87306557|ref|ZP_01088704.1| sigma-70 factor [Blastopirellula marina DSM 3645]
 gi|87290736|gb|EAQ82623.1| sigma-70 factor [Blastopirellula marina DSM 3645]
          Length = 556

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 39/124 (31%), Positives = 63/124 (50%), Gaps = 29/124 (23%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRY----------REHGDLSAA-------------- 50
           GL  Y+  + + P+L +++EY L +++          RE  + S A              
Sbjct: 313 GLPSYLASLYEAPLLTREQEYHLFRKFNYLKHHAAKLRESVETSKAKASVMDEIERLYEA 372

Query: 51  -----HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
                +++V S+LRLVV IA  + G      E+VS+GN+ L++AV+KFD  RG + +TY 
Sbjct: 373 AVEVKNQIVQSNLRLVVSIAKRHLGAADEFFELVSDGNMSLIRAVEKFDYSRGNKFSTYC 432

Query: 106 MWWI 109
            W I
Sbjct: 433 SWAI 436


>gi|312111757|ref|YP_003990073.1| RNA polymerase, sigma 28 subunit, SigG [Geobacillus sp. Y4.1MC1]
 gi|311216858|gb|ADP75462.1| RNA polymerase, sigma 28 subunit, SigG [Geobacillus sp. Y4.1MC1]
          Length = 271

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 70/267 (26%), Positives = 115/267 (43%), Gaps = 29/267 (10%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+ +E   L KR  E GDL A  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 27  KLPVLKNEEMRELFKRMHE-GDLEAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGCI 85

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEY------ILRSWSLVKIGTTANQKRLFFN 138
           GLM+++  FD  +  + +TY++  I   ++ Y      I  S SL  I   A Q R    
Sbjct: 86  GLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLRDIAYKALQVR---- 141

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
             +L G          K      IA  L +   EV+     +    SL   I +   +  
Sbjct: 142 -EKLMGEAA-------KEPTTEEIANVLGIPHEEVVFALDAIQDPVSLFEPIYNDGGDPI 193

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
              D L  + +G  Q + E          L   +  LN RE+ I   R  Q    T   +
Sbjct: 194 YVMDQLSDERNGDSQWIEEI--------ALKEGLCRLNEREKMIIRKRFFQGK--TQMEV 243

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQ 285
           + E  +S+ +V ++E  A +++ ++IQ
Sbjct: 244 AEEIGISQAQVSRLEKAAIRQMNKNIQ 270


>gi|317121713|ref|YP_004101716.1| RNA polymerase, sigma subunit, RpsG/SigG [Thermaerobacter
           marianensis DSM 12885]
 gi|315591693|gb|ADU50989.1| RNA polymerase, sigma subunit, RpsG/SigG [Thermaerobacter
           marianensis DSM 12885]
          Length = 261

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 31/93 (33%), Positives = 55/93 (59%), Gaps = 1/93 (1%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           ++P+L  ++  VL +R R+ GD  A  +LV  +LRLV+ +   +   G P+ ++   G I
Sbjct: 19  ELPVLTNEQMRVLFRRMRQ-GDEEARQQLVQGNLRLVLSVIQRFNHRGEPVDDLFQVGCI 77

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           GLM+A+  FD E+  R +TY++  I   ++ Y+
Sbjct: 78  GLMKAIDNFDLEQNVRFSTYAVPMIIGEIRRYL 110


>gi|270659580|ref|ZP_06222335.1| RNA polymerase sigma-32 factor [Haemophilus influenzae HK1212]
 gi|270316998|gb|EFA28670.1| RNA polymerase sigma-32 factor [Haemophilus influenzae HK1212]
          Length = 147

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 44/151 (29%), Positives = 81/151 (53%), Gaps = 8/151 (5%)

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FFNLR+ K  L    +N     +V  +A +L VS+ +VI M  R++G + +   + + D 
Sbjct: 1   FFNLRKTKQRLGWFNEN-----EVDMVANELGVSKEDVIEMESRMSGAD-VGFDLPTDDA 54

Query: 196 NSSQWQDWL-VYDHDGQEQVLIEKEERKNRRN-MLTRSMSVLNPRERRIFEARRLQENPV 253
            +  +   L + D        +E E  +++    L  ++  L+ R + I +AR L +N  
Sbjct: 55  ETETYSPALYLEDKSSNFAAELENENFESQATEQLGAALQSLDARSQDIIKARWLDDNKA 114

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           TL +L++++ VS ER+RQ+E  A KK++ ++
Sbjct: 115 TLHDLAAKYNVSAERIRQLETNALKKLKSAV 145


>gi|332976341|gb|EGK13197.1| DNA-directed RNA polymerase sigma subunit SigE [Desmospora sp.
           8437]
          Length = 240

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 31/79 (39%), Positives = 49/79 (62%), Gaps = 2/79 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  ++EE++L +     GD +    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 39  PLTREEEEHLLIRL--PSGDAAVRAMLIERNLRLVVYIARKFENTGINIEDLVSIGTIGL 96

Query: 87  MQAVKKFDPERGFRLATYS 105
           ++AV  FDP +  +LATY+
Sbjct: 97  IKAVNTFDPSKKIKLATYA 115


>gi|138894663|ref|YP_001125116.1| sporulation sigma factor SigG [Geobacillus thermodenitrificans
           NG80-2]
 gi|134266176|gb|ABO66371.1| Sporulation-specific sigma factor [Geobacillus thermodenitrificans
           NG80-2]
          Length = 264

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 71/267 (26%), Positives = 117/267 (43%), Gaps = 29/267 (10%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+ +E   L +R  E GDL A  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 20  KLPVLKNEEMRELFQRMHE-GDLEAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGCI 78

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEY------ILRSWSLVKIGTTANQKRLFFN 138
           GLM+++  FD  +  + +TY++  I   ++ Y      I  S SL  I   A Q R    
Sbjct: 79  GLMKSIDNFDLNQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLRDIAYKALQVR---- 134

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
             RL G          K      IAK+L V+  EV+     +    SL   I +   +  
Sbjct: 135 -ERLMGE-------TAKEPSTEEIAKELGVAHEEVVLALDAIQDPVSLFEPIYNDGGDPI 186

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
              D L  + +   Q + E          L   +  LN RE+ I   R  Q    T   +
Sbjct: 187 YVMDQLSDERNRDSQWIEEI--------ALKEGLRRLNEREKMIIRKRFFQGK--TQMEV 236

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQ 285
           + E  +S+ +V ++E  A +++ ++IQ
Sbjct: 237 AEEIGISQAQVSRLEKAAIRQMNKNIQ 263


>gi|256379908|ref|YP_003103568.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Actinosynnema mirum
           DSM 43827]
 gi|255924211|gb|ACU39722.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Actinosynnema mirum
           DSM 43827]
          Length = 272

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 63/242 (26%), Positives = 111/242 (45%), Gaps = 22/242 (9%)

Query: 57  HLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           H   +VK   G  G GLP    +++++  G  GL+ A++KF+PERG +  TY+M  I+ A
Sbjct: 43  HYAPLVKYVAGRVGTGLPAHVDVADLIQSGIFGLVDAIEKFEPERGLKFETYAMQRIRGA 102

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ-AITDNNLKPEQVVAIAKKLNVSES 171
           + +  LRS   V     +  + +   L RL G LQ   TD  L  E       K+ + E 
Sbjct: 103 ILDD-LRSQDWVPRSVRSRARDVERALERLGGRLQRTPTDRELAAE------LKIGLGEL 155

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWL--VYDHDGQEQV--LIEKEERKNRRNM 227
             +    +L    +L+ LI +     S        + D   ++ V  L++++ R+     
Sbjct: 156 RELYAQFQLTSVVALDELIAAGRAAGSAGSSLAESLPDEGAEDPVASLVDQDSRRQ---- 211

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L  +++ L  R+R +      +   +TL  +     V+  RV Q+  RA  +++  I +Q
Sbjct: 212 LADAIAQLAERDRVVVTLYYFEN--LTLAEIGKVLGVTESRVCQLHTRAVLRLRTKINEQ 269

Query: 288 VE 289
           +E
Sbjct: 270 LE 271


>gi|167037236|ref|YP_001664814.1| sporulation sigma factor SigE [Thermoanaerobacter pseudethanolicus
           ATCC 33223]
 gi|307266545|ref|ZP_07548078.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|307267688|ref|ZP_07549142.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|320115655|ref|YP_004185814.1| RNA polymerase sigma-E factor [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
 gi|326392136|ref|ZP_08213613.1| RNA polymerase, sigma 28 subunit, SigE [Thermoanaerobacter
           ethanolicus JW 200]
 gi|166856070|gb|ABY94478.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Thermoanaerobacter pseudethanolicus ATCC 33223]
 gi|306917290|gb|EFN47610.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|306918464|gb|EFN48705.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|319928746|gb|ADV79431.1| RNA polymerase sigma-E factor [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
 gi|325991823|gb|EGD50338.1| RNA polymerase, sigma 28 subunit, SigE [Thermoanaerobacter
           ethanolicus JW 200]
          Length = 241

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 33/94 (35%), Positives = 58/94 (61%), Gaps = 2/94 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  ++E Y+++K   E GD  A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 40  PLSVEEEIYLISKM--EKGDNEAKTVLIERNLRLVVYIAKKFENTGVGIEDLISIGTIGL 97

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++A+  F+P++  +LATY+   I+  +  Y+ R+
Sbjct: 98  IKAINTFNPKKKIKLATYASRCIENEILMYLRRN 131


>gi|160880600|ref|YP_001559568.1| sporulation sigma factor SigG [Clostridium phytofermentans ISDg]
 gi|160429266|gb|ABX42829.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           phytofermentans ISDg]
          Length = 260

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 59/254 (23%), Positives = 120/254 (47%), Gaps = 17/254 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+ +E+  L +R ++ GD  A    +  +LRLV+ I   +      + ++   G I
Sbjct: 15  KLPLLKGEEKDALFERIKQ-GDKEARELYIKGNLRLVLSIIQRFSNSNENVDDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A+  FD  +G + +TY++  I   ++ Y LR  + +++  +          + +  
Sbjct: 74  GLMKAIDNFDITQGVKFSTYAVPMIIGEIRRY-LRDNNAIRVSRSLRDTA----YKAIYA 128

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
               +  N+ +P  V  IA ++ +S+ ++++    +    SL   + S   ++    D  
Sbjct: 129 KEMLLKKNDKEP-TVCEIANEVGISQEDIVAALDAIQSPVSLYEPVYSEGGDTLYIMDQ- 186

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           V D   +E+  +E+         L  +M+ L+PRE  I   R  Q    T   ++ E ++
Sbjct: 187 VSDKKNKEENWVEEIS-------LKEAMARLSPRENNIINLRFFQGK--TQMEVAEEIQI 237

Query: 265 SRERVRQIEARAFK 278
           S+ +V ++E  A K
Sbjct: 238 SQAQVSRLEKNALK 251


>gi|313901762|ref|ZP_07835188.1| RNA polymerase, sigma 29 subunit, SigE [Thermaerobacter
           subterraneus DSM 13965]
 gi|313467968|gb|EFR63456.1| RNA polymerase, sigma 29 subunit, SigE [Thermaerobacter
           subterraneus DSM 13965]
          Length = 244

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 59/239 (24%), Positives = 104/239 (43%), Gaps = 63/239 (26%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           H L+  +LRLVV IA  +   G+PI ++VS G IGL++AV  FDP +  +LATY+     
Sbjct: 64  HTLIERNLRLVVYIARKFDNTGIPIEDLVSIGTIGLIKAVNTFDPSKRIKLATYA----- 118

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
                            +   +  +  +LRR             +    V++ + LNV  
Sbjct: 119 -----------------SKCIENEILMHLRRTS-----------RTRYEVSLDEPLNVDW 150

Query: 171 SEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
                      G+E  L+ +I ++D +                 V+    E K  R++L 
Sbjct: 151 E----------GNELLLSDVIPATDGD-----------------VIYRDLEAKVDRHLLH 183

Query: 230 RSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R+++ L PRER I E R    + +  T + ++    +S+  + ++E R   +++  I+K
Sbjct: 184 RALARLTPRERLIMELRFGLVDGIERTQKQVADHLGISQSYISRLEKRIINRLRREIRK 242


>gi|134102478|ref|YP_001108139.1| putative RNA polymerase sigma factor [Saccharopolyspora erythraea
           NRRL 2338]
 gi|133915101|emb|CAM05214.1| putative RNA polymerase sigma factor [Saccharopolyspora erythraea
           NRRL 2338]
          Length = 311

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 59/235 (25%), Positives = 108/235 (45%), Gaps = 16/235 (6%)

Query: 57  HLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           H   +VK   G  G GLP    +S+++  G  GL+ A++KF+PERG +  TY+M  I+ A
Sbjct: 88  HYAPLVKYVAGRVGTGLPSHVEVSDLIQSGIFGLVDAIEKFEPERGLKFETYAMQRIRGA 147

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           + +  LR+   V     +  + +   L RL+  LQ    +    E++     +L+V E  
Sbjct: 148 ILDD-LRAQDWVPRSVRSRARDVERALERLEAKLQRTASDAELAEEL-----ELSVDELR 201

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
            +    ++    +L+ LI +    SS  +       D  E  +    +R +RR  L  ++
Sbjct: 202 ELFAQLQMTSVVALDDLIGAGQTTSSLAE---TLPDDRAEDPVATLVDRDSRRQ-LAEAV 257

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             L+ R+R +      +   +TL  +     V+  RV Q+  RA  +++  + +Q
Sbjct: 258 ERLSDRDRIVVTLYYFEN--LTLAEIGKVLGVTESRVCQLHTRAVLRLRTKLTEQ 310


>gi|119715356|ref|YP_922321.1| FliA/WhiG family RNA polymerase sigma factor [Nocardioides sp.
           JS614]
 gi|119536017|gb|ABL80634.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Nocardioides sp.
           JS614]
          Length = 244

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 34/81 (41%), Positives = 49/81 (60%), Gaps = 5/81 (6%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQAVKK 92
           L +R+++ GD  A  RLV  H   +VK   G    GLP +    ++VS+G IGL+ A+ K
Sbjct: 12  LWERFKQDGDREARDRLVV-HYSPLVKFVAGRVRSGLPPAVEHADLVSDGVIGLLDALDK 70

Query: 93  FDPERGFRLATYSMWWIKAAM 113
           FDPERG +  TY++  I+ AM
Sbjct: 71  FDPERGLQFQTYAVSRIRGAM 91


>gi|291004131|ref|ZP_06562104.1| putative RNA polymerase sigma factor [Saccharopolyspora erythraea
           NRRL 2338]
          Length = 328

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 59/235 (25%), Positives = 108/235 (45%), Gaps = 16/235 (6%)

Query: 57  HLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           H   +VK   G  G GLP    +S+++  G  GL+ A++KF+PERG +  TY+M  I+ A
Sbjct: 105 HYAPLVKYVAGRVGTGLPSHVEVSDLIQSGIFGLVDAIEKFEPERGLKFETYAMQRIRGA 164

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           + +  LR+   V     +  + +   L RL+  LQ    +    E++     +L+V E  
Sbjct: 165 ILDD-LRAQDWVPRSVRSRARDVERALERLEAKLQRTASDAELAEEL-----ELSVDELR 218

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
            +    ++    +L+ LI +    SS  +       D  E  +    +R +RR  L  ++
Sbjct: 219 ELFAQLQMTSVVALDDLIGAGQTTSSLAE---TLPDDRAEDPVATLVDRDSRRQ-LAEAV 274

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             L+ R+R +      +   +TL  +     V+  RV Q+  RA  +++  + +Q
Sbjct: 275 ERLSDRDRIVVTLYYFEN--LTLAEIGKVLGVTESRVCQLHTRAVLRLRTKLTEQ 327


>gi|160939297|ref|ZP_02086648.1| hypothetical protein CLOBOL_04191 [Clostridium bolteae ATCC
           BAA-613]
 gi|158438260|gb|EDP16020.1| hypothetical protein CLOBOL_04191 [Clostridium bolteae ATCC
           BAA-613]
          Length = 240

 Score = 60.5 bits (145), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 62/241 (25%), Positives = 114/241 (47%), Gaps = 16/241 (6%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GD +A  +LV  ++ L+  I   + G G  + ++   G+IGL++A+ KFD     + +T
Sbjct: 16  EGDKAARDQLVMDNVGLIWSIVRRFSGRGYEMEDLFQIGSIGLIKAIDKFDTGFDVKFST 75

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y++  I   ++ + LR   ++K+  +   K L   +R  +   + +T    +   +  IA
Sbjct: 76  YAVPMITGEIKRF-LRDDGMIKVSRSI--KELGVKVRAAR---EEMTYALGREPTIEEIA 129

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
            +L  S  EV +     A  ESL    +S D+NS+   D L  D++  E +L        
Sbjct: 130 GRLGTSREEVAASLEAAAEVESLYRPADSGDENSTYLMDRLAQDNNDHEDLL-------- 181

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            R +L   M  L   +R I   RR   N  T   ++ E  +S+ +V ++E R  K++++ 
Sbjct: 182 NRMVLKDLMEGLEEEQREII-LRRYFYNE-TQTQIAGELGISQVQVSRLEKRILKEMRKK 239

Query: 284 I 284
           +
Sbjct: 240 L 240


>gi|317121712|ref|YP_004101715.1| RNA polymerase, sigma 29 subunit, SigE [Thermaerobacter marianensis
           DSM 12885]
 gi|315591692|gb|ADU50988.1| RNA polymerase, sigma 29 subunit, SigE [Thermaerobacter marianensis
           DSM 12885]
          Length = 245

 Score = 60.1 bits (144), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 59/239 (24%), Positives = 105/239 (43%), Gaps = 63/239 (26%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           H L+  +LRLVV IA  +   G+PI ++VS G IGL++AV  FDP +  +LATY+     
Sbjct: 65  HTLIERNLRLVVYIARKFDNTGIPIEDLVSIGTIGLIKAVNTFDPSKRIKLATYA----- 119

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
                            +   +  +  +LRR             +    V++ + LNV  
Sbjct: 120 -----------------SKCIENEILMHLRRTS-----------RTRYEVSLDEPLNVDW 151

Query: 171 SEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
                      G+E  L+ +I ++D +                 V+    E K  R++L 
Sbjct: 152 E----------GNELLLSDVIPATDGD-----------------VIYRDLEAKVDRHLLY 184

Query: 230 RSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R+++ L+PRER I E R    + +  T + ++    +S+  + ++E R   +++  I+K
Sbjct: 185 RALARLSPRERLIMELRFGLVDGIERTQKQVADRLGISQSYISRLEKRIINRLRREIRK 243


>gi|56419663|ref|YP_146981.1| sporulation sigma factor SigG [Geobacillus kaustophilus HTA426]
 gi|261419325|ref|YP_003253007.1| sporulation sigma factor SigG [Geobacillus sp. Y412MC61]
 gi|297530705|ref|YP_003671980.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
 gi|319766141|ref|YP_004131642.1| RNA polymerase, sigma 28 subunit, SigG [Geobacillus sp. Y412MC52]
 gi|56379505|dbj|BAD75413.1| DNA-directed RNA polymerase sporulation-specific sigma factor
           (sigma-G) [Geobacillus kaustophilus HTA426]
 gi|261375782|gb|ACX78525.1| RNA polymerase, sigma 28 subunit, SigG [Geobacillus sp. Y412MC61]
 gi|297253957|gb|ADI27403.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
 gi|317111007|gb|ADU93499.1| RNA polymerase, sigma 28 subunit, SigG [Geobacillus sp. Y412MC52]
          Length = 259

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 64/261 (24%), Positives = 123/261 (47%), Gaps = 17/261 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+ +E   L +R  E GDL A  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKNEEMRELFRRMHE-GDLEAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD  +  + +TY++  I   ++ Y LR  + +++  +   + + +   +++ 
Sbjct: 74  GLMKSIDNFDLNQNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSL--RDIAYKALQVRE 130

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L + T      E+   IAK+L V+  EV+     +    SL   I +   +     D L
Sbjct: 131 RLMSETAKEPSTEE---IAKELGVAHEEVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQL 187

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             + +   Q + E          L   +  LN RE+ I   R  Q    T   ++ E  +
Sbjct: 188 SDERNRDSQWIEEI--------ALKEGLRRLNEREKMIIRKRFFQGK--TQMEVAEEIGI 237

Query: 265 SRERVRQIEARAFKKVQESIQ 285
           S+ +V ++E  A +++ ++IQ
Sbjct: 238 SQAQVSRLEKAAIRQMNKNIQ 258


>gi|288917890|ref|ZP_06412250.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Frankia sp.
           EUN1f]
 gi|288350679|gb|EFC84896.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Frankia sp.
           EUN1f]
          Length = 392

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 67/241 (27%), Positives = 116/241 (48%), Gaps = 30/241 (12%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +LV  HL LV  +A  +R  G P+ ++V    IGL+++V +FDPERG   +TY+   I  
Sbjct: 170 QLVRMHLPLVEYLARRFRNRGEPLDDLVQVATIGLIKSVDRFDPERGVEFSTYATPTIVG 229

Query: 112 AMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT---DNNLKPEQVVA-IAKKL 166
            ++ +   + W++          R+   L+ LK  L   T     +L     V+ IA+ L
Sbjct: 230 EIKRHFRDKGWAI----------RVPRRLQELKLSLTKATSELSQSLGRSPTVSEIARHL 279

Query: 167 NVSESEVISMNCRLAGDESLNA--LINSSDKNSSQWQDWLVYDHDG-QEQVLIEKEERKN 223
            ++E EV      L G ES NA   ++    +S   +   V D  G Q++ L   E R++
Sbjct: 280 EMTEEEV------LEGLESANAYSAVSLDAPDSGDDEAPAVADTLGVQDESLEGVEYRES 333

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            + +L +    L PRE+RI   R      +T   +++E  +S+  V ++ AR   +++  
Sbjct: 334 LKPLLEK----LPPREKRILLLRFFGN--MTQSQIANELGISQMHVSRLLARTLAQLRRG 387

Query: 284 I 284
           +
Sbjct: 388 L 388


>gi|196247722|ref|ZP_03146424.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
 gi|196212506|gb|EDY07263.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
          Length = 259

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 71/267 (26%), Positives = 117/267 (43%), Gaps = 29/267 (10%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+ +E   L +R  E GDL A  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKNEEMRELFQRMHE-GDLEAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEY------ILRSWSLVKIGTTANQKRLFFN 138
           GLM+++  FD  +  + +TY++  I   ++ Y      I  S SL  I   A Q R    
Sbjct: 74  GLMKSIDNFDLNQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLRDIAYKALQVR---- 129

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
             RL G          K      IAK+L V+  EV+     +    SL   I +   +  
Sbjct: 130 -ERLMGE-------TAKEPSTEEIAKELGVAHEEVVLALDAIQDPVSLFEPIYNDGGDPI 181

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
              D L  + +   Q + E          L   +  LN RE+ I   R  Q    T   +
Sbjct: 182 YVMDQLSDERNRDSQWIEEI--------ALKEGLRRLNEREKMIIRKRFFQGK--TQMEV 231

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQ 285
           + E  +S+ +V ++E  A +++ ++IQ
Sbjct: 232 AEEIGISQAQVSRLEKAAIRQMNKNIQ 258


>gi|256751991|ref|ZP_05492860.1| RNA polymerase, sigma 28 subunit, SigE [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|256749101|gb|EEU62136.1| RNA polymerase, sigma 28 subunit, SigE [Thermoanaerobacter
           ethanolicus CCSD1]
          Length = 236

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 33/94 (35%), Positives = 58/94 (61%), Gaps = 2/94 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  ++E Y+++K   E GD  A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 40  PLSVEEEMYLISKM--EKGDNEAKTVLIERNLRLVVYIAKKFENTGVGIEDLISIGTIGL 97

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++A+  F+P++  +LATY+   I+  +  Y+ R+
Sbjct: 98  IKAINTFNPKKKIKLATYASRCIENEILMYLRRN 131


>gi|119715950|ref|YP_922915.1| sigma-70 region 2 domain-containing protein [Nocardioides sp.
           JS614]
 gi|119536611|gb|ABL81228.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Nocardioides sp.
           JS614]
          Length = 270

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 60/242 (24%), Positives = 109/242 (45%), Gaps = 30/242 (12%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  HL LV   A  +R  G P+ ++V  G IGL+++V +FD +RG   +TY+   I   
Sbjct: 49  LVHLHLPLVEHCARRFRNRGEPLEDLVQVGTIGLIKSVDRFDADRGVEFSTYATPTIIGE 108

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ Y   + W+   I      + L   +      L      +  P +   +A  +  +  
Sbjct: 109 IKRYFRDKGWA---IRVPRRLQELRMQISTASAELTQSLGRSPTPRE---LAGAIGCTVE 162

Query: 172 EVISMNCRLAGDESLNA-------LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           E++       G ES NA         +  D N++   D +  D +G E V I    R++ 
Sbjct: 163 EIVE------GIESSNAYSTLSLDATDDGDDNTASMLDAIGVDDEGLEHVEI----RESL 212

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + +L R    L PRE++I   R  +   +T   ++ E  VS+  V ++  R  ++++ S+
Sbjct: 213 KPLLDR----LEPREKKILLLRFFKN--MTQSQIAEEIGVSQMHVSRLLNRTLEQLRVSL 266

Query: 285 QK 286
           ++
Sbjct: 267 EE 268


>gi|291544789|emb|CBL17898.1| RNA polymerase, sigma subunit, RpsG/SigG [Ruminococcus sp. 18P13]
          Length = 257

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 65/274 (23%), Positives = 122/274 (44%), Gaps = 45/274 (16%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+ +L++ E+  L +  +  G   A  +L+  +LRLV+ +   + G G  I ++   G I
Sbjct: 15  KLTVLKESEKIELLREIQRTGSKEARDKLINGNLRLVLSVIQRFAGRGEDIDDLFQIGVI 74

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD  +  R +TY +  I   ++ + LR ++ +K+  +   + L +   + K 
Sbjct: 75  GLIKAINNFDLSKEVRFSTYCVPMISGELRRF-LRDYNHIKVSRSL--RDLAYKAMQAKE 131

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVI----SMNCRL---------AGDESLNALIN 191
            L A      K   +  IAK+++   S+V+    S+   +         AGD +L  L  
Sbjct: 132 QLTA---EQQKEPTMDEIAKRIDAKRSDVVLALESVTDPVSLYEPVYSDAGD-TLYVLDQ 187

Query: 192 SSDKNS-SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
            SD+NS   W D +                       L  ++  L PRE+RI   R  Q 
Sbjct: 188 ISDQNSVDSWLDEIA----------------------LRDAIKALQPREKRILYLRFFQG 225

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              T   ++ E  +S+ +V ++E  A  +++  +
Sbjct: 226 K--TQVEVAQEIGISQAQVSRLEKGALNQIKGDV 257


>gi|58699689|ref|ZP_00374359.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of
           Drosophila ananassae]
 gi|58533795|gb|EAL58124.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of
           Drosophila ananassae]
          Length = 256

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 33/74 (44%), Positives = 50/74 (67%), Gaps = 2/74 (2%)

Query: 32  QEEYVLAKRYREHG-DLS-AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           QE   L KR ++H  ++S A   ++ ++LRLVV IA  Y   GL + +++ EGNIGLM+A
Sbjct: 118 QEFKELIKRIQKHEREVSEAKQEMIKANLRLVVSIAKKYSKRGLDLLDLIQEGNIGLMKA 177

Query: 90  VKKFDPERGFRLAT 103
           V KFD +RG++ +T
Sbjct: 178 VDKFDYKRGYKFST 191


>gi|302810520|ref|XP_002986951.1| hypothetical protein SELMODRAFT_43614 [Selaginella moellendorffii]
 gi|300145356|gb|EFJ12033.1| hypothetical protein SELMODRAFT_43614 [Selaginella moellendorffii]
          Length = 326

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 60/245 (24%), Positives = 116/245 (47%), Gaps = 29/245 (11%)

Query: 48  SAAHRLVTSHLRLVVKIAMGY--RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           +A ++++  +LRLV   A  Y      L + ++  EG  GLM AV KFDP++G+R +TY+
Sbjct: 87  AARNKMIKHNLRLVAHQARKYFKEELSLSLLDLCQEGVPGLMSAVDKFDPKKGYRFSTYA 146

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
           ++W+K ++     R   +V++      +++   ++R +  L    D     E+V+   K 
Sbjct: 147 VYWVKNSILRAQTRLGHIVRVPYNVAAQKM--TIQRKRAQLSLELDREPTHEEVITELKM 204

Query: 166 LNVSESEVI-------SMNCR--LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
            +    EV+       S+N R  + G+E +++ I+  D+N +Q+ +       G + VL 
Sbjct: 205 DSRRYFEVLRTGAPRRSLNARSKVTGEELIHS-ISDPDENEAQYYNAGAQLRLGMDDVL- 262

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
             +  K + +++ R    L+ +  R F              +     +SRE VR+ E R 
Sbjct: 263 --DSLKPKESLIIRQRYGLDGKGERSF------------TEIGRNLNLSREMVRKYEIRG 308

Query: 277 FKKVQ 281
             K++
Sbjct: 309 MMKLK 313


>gi|308068681|ref|YP_003870286.1| RNA polymerase sigma-D factor (Sigma-28) [Paenibacillus polymyxa
           E681]
 gi|305857960|gb|ADM69748.1| RNA polymerase sigma-D factor (Sigma-28) [Paenibacillus polymyxa
           E681]
          Length = 262

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 65/274 (23%), Positives = 127/274 (46%), Gaps = 50/274 (18%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQAVKK 92
           L ++++EHGD  A  +L+  +L +V  ++ G    GLP +    ++ S G +GL+ A++K
Sbjct: 14  LWEQWKEHGDKEAKKQLIEKYLHIVEYVS-GRLAVGLPKNVSKDDLASNGVMGLIDALEK 72

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG-HLQAITD 151
           FD ERG +  TY+ W ++ A+ +  LR    V        K++    + L+  +L+ ++D
Sbjct: 73  FDYERGLQFETYASWRVRGAILDG-LRQGDWVPRSVREKAKKIEDAYQHLEQRYLRTVSD 131

Query: 152 NNLKPEQVVAIAKKLNVSESE------------VISMNCRLAGDES---LNALINSSDKN 196
             +        +  L+VSE E            ++S+   +  +ES   L+ L++   KN
Sbjct: 132 EEM--------SHYLDVSEKEFQNMIQEVAVMSIVSLEDPIREEESETRLSLLVDEKAKN 183

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
                     DH   E  L         R+ L + +  L  +ER +     L    ++L 
Sbjct: 184 P---------DHKVNEFTL---------RDALAQGIDKLTEKERIVVSL--LYYEDLSLS 223

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
            ++    +S  R+ Q+ ++A  +++ ++ KQ +L
Sbjct: 224 EIAEVMSLSPSRISQLHSKAILRLRATLDKQRDL 257


>gi|239930292|ref|ZP_04687245.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291438640|ref|ZP_06578030.1| sigma L factor [Streptomyces ghanaensis ATCC 14672]
 gi|291341535|gb|EFE68491.1| sigma L factor [Streptomyces ghanaensis ATCC 14672]
          Length = 300

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 63/237 (26%), Positives = 105/237 (44%), Gaps = 23/237 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +   
Sbjct: 79  LIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTVVGE 138

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL   L +    L    D +     V  +A  L VSE 
Sbjct: 139 IKRFFRDTSWS-VRVPRRLQELRL--ALTKTSDELSQKLDRS---PTVTELATALGVSEE 192

Query: 172 EVIS----MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +V+      N   A   SL++     D       D L Y+    E V    E R++ + +
Sbjct: 193 DVVDGLAVGNAYTA--SSLDSPAPEDDGGEGSLADRLGYEDTALEGV----EYRESLKPL 246

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L +    L PRERRI   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 247 LAK----LPPRERRIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 297


>gi|2224777|emb|CAA80617.1| putative pro-sigma factor E [Clostridium acetobutylicum ATCC 824]
          Length = 235

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 35/94 (37%), Positives = 53/94 (56%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K EE  L  +   +GD S    L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 33  PPLSKDEEDDLVNKLV-NGDESIRSILIERNLRLVVYIARKFENTGVGVEDLISVGTIGL 91

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  FDP +  +LATY    I+  +  Y+ R+
Sbjct: 92  IKAVNTFDPTKKIKLATYGSRCIENEILMYLRRN 125


>gi|112962639|gb|ABI29096.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
          Length = 258

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 62/263 (23%), Positives = 127/263 (48%), Gaps = 25/263 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +++D   G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEEL 125

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNC-----RLAGDESLNALINSSDKNSSQWQDWL 204
           T       Q+  IA  + V+E  + +M        L+ D S+ A    SD ++    D +
Sbjct: 126 TRELQSSPQISDIADFIGVTEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVV 182

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               DG E+V        N+R +L + + VL+ RE++I +   ++    + +      ++
Sbjct: 183 GGTDDGFERV--------NQRMLLEKVLPVLDEREQKILQFTFIENR--SQKETGELLDI 232

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           S+  V +I+ +A KK++E++Q +
Sbjct: 233 SQMHVSRIQRQAIKKLREALQNE 255


>gi|15894972|ref|NP_348321.1| sporulation sigma factor SigE [Clostridium acetobutylicum ATCC 824]
 gi|585930|sp|P33657|RPSE_CLOAB RecName: Full=RNA polymerase sigma-E factor
 gi|15024659|gb|AAK79661.1|AE007679_7 DNA-dependent RNA polymerase sigma subunit [Clostridium
           acetobutylicum ATCC 824]
 gi|460971|gb|AAC43309.1| putative sigma factor E [Clostridium acetobutylicum ATCC 824]
 gi|325509109|gb|ADZ20745.1| sporulation sigma factor SigE [Clostridium acetobutylicum EA 2018]
          Length = 235

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 35/94 (37%), Positives = 53/94 (56%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K EE  L  +   +GD S    L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 33  PPLSKDEEDDLVNKLV-NGDESIRSILIERNLRLVVYIARKFENTGVGVEDLISVGTIGL 91

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  FDP +  +LATY    I+  +  Y+ R+
Sbjct: 92  IKAVNTFDPTKKIKLATYGSRCIENEILMYLRRN 125


>gi|304438393|ref|ZP_07398334.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
 gi|304368759|gb|EFM22443.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
          Length = 208

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 31/105 (29%), Positives = 64/105 (60%), Gaps = 3/105 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
            S Y+ ++  +  L  +EE  L + Y+E+GD++A  R++ ++  LV +    YR   LP 
Sbjct: 2   FSAYMKKLSAVQKLAPEEERALWRAYKENGDMAARRRIIEAYQPLVFREVYPYRA--LPA 59

Query: 76  S-EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           + + V EG IGL++AV+++DP+ G   + Y++  ++  +++++ R
Sbjct: 60  AMDAVQEGTIGLIEAVERYDPDYGAAFSLYAVHRVRGRVRDFLRR 104


>gi|255525679|ref|ZP_05392612.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium carboxidivorans
           P7]
 gi|296185437|ref|ZP_06853847.1| RNA polymerase sigma-E factor [Clostridium carboxidivorans P7]
 gi|255510665|gb|EET86972.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium carboxidivorans
           P7]
 gi|296050271|gb|EFG89695.1| RNA polymerase sigma-E factor [Clostridium carboxidivorans P7]
          Length = 235

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 46/165 (27%), Positives = 81/165 (49%), Gaps = 10/165 (6%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE  L  +  + G+      L+  +LRLVV IA  +   G+ + ++VS G IGL
Sbjct: 33  PPLSKKEEDDLVSKL-DGGEEKVRSTLIERNLRLVVYIARKFENTGVNVEDLVSVGTIGL 91

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS---------WSLVKIGTTANQKRLFF 137
           ++AV  FDP +  +LATY+   I+  +  Y+ R+         +  + I    N+  L  
Sbjct: 92  IKAVNTFDPSKKIKLATYASRCIENEILMYLRRNSKVKAEISFYEPLNIDWDGNELLLSD 151

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            L      +  + ++ +  + ++   KKLN  E E++++   L G
Sbjct: 152 ILGTDNDVVYNLIEDEVDKQLLMVAMKKLNDREKEIVNLRFGLNG 196


>gi|255658878|ref|ZP_05404287.1| sigma 70 family protein [Mitsuokella multacida DSM 20544]
 gi|260848826|gb|EEX68833.1| sigma 70 family protein [Mitsuokella multacida DSM 20544]
          Length = 208

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 46/185 (24%), Positives = 86/185 (46%), Gaps = 28/185 (15%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+ E+RK+  L+ +EE  L   ++E GD  A  RL+ S+  LV K A  +      +
Sbjct: 3   LADYLKELRKVKTLDLEEEQALWAAFKERGDEGARQRLIESYQPLVFKQAAPFAQLDCAL 62

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW-------------- 121
            +++ EG +GL++A +++D  RG   + +++  I+  M +++ R                
Sbjct: 63  -DLIQEGTVGLIEAAERYDHTRGVAFSLFAVHRIRGRMMDFLRREGQVDVACMEENLEGG 121

Query: 122 ----SLVKIGTTANQK--------RLFFNLRRLKGHLQAITDN-NLKPEQVVAIAKKLNV 168
               +LV  G +  ++        RL   + RL    +A+ +   L  E    +A  L+V
Sbjct: 122 NLKENLVDTGASVPEQAESHELAHRLHQAMARLPDKERAVLEGMYLSSEDAAGMADALHV 181

Query: 169 SESEV 173
           S S +
Sbjct: 182 SASHI 186


>gi|219112653|ref|XP_002178078.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217410963|gb|EEC50892.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 358

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 27/72 (37%), Positives = 50/72 (69%), Gaps = 4/72 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFDPERGFRLA 102
           L A ++LVTS+LR+V  +   Y   GL       +++ EG I L++A +KF+P+RG++ +
Sbjct: 98  LEAKNQLVTSNLRMVQSVVNTYIRNGLTAQYNAGDMMQEGIIALIRAAEKFEPDRGWKFS 157

Query: 103 TYSMWWIKAAMQ 114
           TY+M+W++A+++
Sbjct: 158 TYAMYWVRASVK 169


>gi|225389924|ref|ZP_03759648.1| hypothetical protein CLOSTASPAR_03674 [Clostridium asparagiforme
           DSM 15981]
 gi|225044004|gb|EEG54250.1| hypothetical protein CLOSTASPAR_03674 [Clostridium asparagiforme
           DSM 15981]
          Length = 223

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 63/260 (24%), Positives = 114/260 (43%), Gaps = 64/260 (24%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           LE +EE  +        D  A   L+  +LRLVV IA  +    + + +++S G IGL++
Sbjct: 20  LEPEEESRMIGMLSGEEDQKARAALIEHNLRLVVYIAKKFDNTSVGVEDLISIGTIGLIK 79

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A+  F P++  +LATY+   I                      +  +   LRR       
Sbjct: 80  AINTFKPDKNIKLATYASRCI----------------------ENEILMYLRR------- 110

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
               N K    V+I + LNV             G+E L + I  +D++       ++Y H
Sbjct: 111 ----NNKTRMEVSIDEPLNVD----------WDGNELLLSDILGTDED-------VIY-H 148

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN----PVTLENLSSEFEV 264
           D ++++          +N+L  ++S LNPRER+I E R    N     +T + ++    +
Sbjct: 149 DIEDEI---------EKNLLNNAISRLNPRERKIVELRYGLTNEDGEEMTQKEVADLLGI 199

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+  + ++E +  K++++ I
Sbjct: 200 SQSYISRLEKKIMKRLRKEI 219


>gi|154484272|ref|ZP_02026720.1| hypothetical protein EUBVEN_01984 [Eubacterium ventriosum ATCC
           27560]
 gi|149734749|gb|EDM50666.1| hypothetical protein EUBVEN_01984 [Eubacterium ventriosum ATCC
           27560]
          Length = 304

 Score = 60.1 bits (144), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 29/75 (38%), Positives = 45/75 (60%), Gaps = 1/75 (1%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ E+  +P L K EE  L  +    GD S + ++V ++L LV KIA  +RG G+   ++
Sbjct: 104 YMEEMEALPNLSKDEEADLIDKLL-AGDTSVSSKIVEANLSLVAKIAESHRGKGVNFGDL 162

Query: 79  VSEGNIGLMQAVKKF 93
           + EGN+GLM AV  +
Sbjct: 163 IQEGNVGLMLAVSDY 177


>gi|88799025|ref|ZP_01114606.1| RNA polymerase sigma factor [Reinekea sp. MED297]
 gi|88778252|gb|EAR09446.1| RNA polymerase sigma factor [Reinekea sp. MED297]
          Length = 339

 Score = 59.7 bits (143), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 61/247 (24%), Positives = 112/247 (45%), Gaps = 23/247 (9%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           LS    L+ S++RLV K+A  +   GL + ++  EG  GL++A+++F  ++  R +TY+ 
Sbjct: 106 LSVREFLIASNIRLVFKVAHRHTERGLSLLDLAQEGQFGLVRALERFRCDKELRFSTYAT 165

Query: 107 WWIKAAMQEYILRSWSLVKIGTT-----ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
            WI   ++  I +    V I T      A   R     ++ +G   ++T+      Q   
Sbjct: 166 HWITQYIRLAIKKQTRTVPIPTNVQDDLARTNRALARAQQQQGRPVSVTEFARLSNQSTD 225

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
            A+ L    + V S++ RL+ D  ++AL            D L  D    E     + ER
Sbjct: 226 AAEHLMSLNAPVQSLDERLSDDSEVSAL------------DLLDSDLARPES----EHER 269

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
            + +  +   ++ L  RE++I   R             ++ +  +SRERVRQ+E +A   
Sbjct: 270 SDNQERVQALLAHLTSREQQILAMRYGIGMGAEYGYREIADQLNLSRERVRQLEKQALGF 329

Query: 280 VQESIQK 286
           ++  ++K
Sbjct: 330 LRAQMEK 336


>gi|29830729|ref|NP_825363.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29607842|dbj|BAC71898.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 307

 Score = 59.7 bits (143), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 63/237 (26%), Positives = 105/237 (44%), Gaps = 23/237 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +   
Sbjct: 86  LIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTVVGE 145

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL   L +    L    D +     V  +A  L VSE 
Sbjct: 146 IKRFFRDTSWS-VRVPRRLQELRL--ALTKASDELSQKLDRS---PTVAELAAVLGVSEE 199

Query: 172 EVIS----MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +V+      N   A   SL++     D       D L Y+    E V    E R++ + +
Sbjct: 200 DVVDGLAVGNAYTAS--SLDSPAPEDDGGEGSLADRLGYEDTALEGV----EYRESLKPL 253

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L +    L PRERRI   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 254 LAK----LPPRERRIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 304


>gi|295399724|ref|ZP_06809705.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|294978127|gb|EFG53724.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
          Length = 271

 Score = 59.7 bits (143), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 70/267 (26%), Positives = 114/267 (42%), Gaps = 29/267 (10%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+ +E   L KR  E GDL A  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 27  KLPVLKNEEMRELFKRMHE-GDLEAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGCI 85

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEY------ILRSWSLVKIGTTANQKRLFFN 138
           GLM+++  FD  +  + +TY++  I   ++ Y      I  S SL  I   A Q R    
Sbjct: 86  GLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLRDIAYKALQVR---- 141

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
             +L G          K      IA  L +   EV+     +    SL   I +   +  
Sbjct: 142 -EKLMGEAA-------KEPTTEEIANVLGIPHEEVVFALDAIQDPVSLFEPIYNDGGDPI 193

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
              D L  +  G  Q + E          L   +  LN RE+ I   R  Q    T   +
Sbjct: 194 YVMDQLSDERSGDNQWIEEI--------ALKEGLCRLNEREKMIIRKRFFQGK--TQMEV 243

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQ 285
           + E  +S+ +V ++E  A +++ ++IQ
Sbjct: 244 AEEIGISQAQVSRLEKAAIRQMNKNIQ 270


>gi|302552550|ref|ZP_07304892.1| RNA polymerase sigma-E factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302470168|gb|EFL33261.1| RNA polymerase sigma-E factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 301

 Score = 59.7 bits (143), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 63/237 (26%), Positives = 105/237 (44%), Gaps = 23/237 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +   
Sbjct: 80  LIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTVVGE 139

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL   L +    L    D +     V  +A  L VSE 
Sbjct: 140 IKRFFRDTSWS-VRVPRRLQELRL--ALTKASDELSQKLDRS---PTVTELASVLGVSEE 193

Query: 172 EVIS----MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +V+      N   A   SL++     D       D L Y+    E V    E R++ + +
Sbjct: 194 DVVDGLAVGNAYTAS--SLDSPAPEDDGGEGSLADRLGYEDTALEGV----EYRESLKPL 247

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L +    L PRERRI   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 248 LAK----LPPRERRIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 298


>gi|163816725|ref|ZP_02208088.1| hypothetical protein COPEUT_02915 [Coprococcus eutactus ATCC 27759]
 gi|158447982|gb|EDP24977.1| hypothetical protein COPEUT_02915 [Coprococcus eutactus ATCC 27759]
          Length = 224

 Score = 59.7 bits (143), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 31/87 (35%), Positives = 53/87 (60%), Gaps = 1/87 (1%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R  + GD++A  RL+T ++ LVV +A  Y G G  + +++  G IGL++AV +FD E   
Sbjct: 9   RLAKEGDITARDRLITENMGLVVSVAKRYIGRGQELEDLIQIGLIGLIKAVDRFDLEYDV 68

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKI 126
             +TYS+  I+  ++ + LR   LV++
Sbjct: 69  MFSTYSVPLIQGEIRRF-LRDDGLVRV 94


>gi|299472548|emb|CBN77333.1| RNA polymerase sigma factor SigD [Ectocarpus siliculosus]
          Length = 825

 Score = 59.7 bits (143), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 40/131 (30%), Positives = 67/131 (51%), Gaps = 9/131 (6%)

Query: 49  AAHRLVTSHLRLV---VKIAMGYRGYG-LPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           A   LV  +L LV   VK  +G   YG     ++  +  +GL++AV+KFDPE+GF  ATY
Sbjct: 110 AKQELVLDNLNLVDIIVKNYVGTFAYGRFTEKDLTQDATVGLIRAVEKFDPEKGFFFATY 169

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA-ITDNNLKPEQVVAIA 163
             WW++  + E +     +V+I  +A  +     ++R++  L+  +     KPE  +A+ 
Sbjct: 170 GRWWVRKYLHEGVQNHNRMVRIPNSAAYR--IAKVKRVRDELEGELGRAPTKPE--IALE 225

Query: 164 KKLNVSESEVI 174
             L V + E  
Sbjct: 226 TDLTVQQVEAC 236


>gi|302874723|ref|YP_003843356.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium cellulovorans
           743B]
 gi|307690664|ref|ZP_07633110.1| sporulation sigma factor SigE [Clostridium cellulovorans 743B]
 gi|302577580|gb|ADL51592.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium cellulovorans
           743B]
          Length = 235

 Score = 59.7 bits (143), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 34/94 (36%), Positives = 54/94 (57%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE  L  +    G  +    L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 33  PPLTKEEEEELVGKL-STGKEAVRSVLIERNLRLVVYIARKFENTGVGVEDLISVGTIGL 91

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  FDPE+  +LATY+   I+  +  Y+ R+
Sbjct: 92  IKAVNTFDPEKKIKLATYASRCIENEILMYLRRN 125


>gi|150016004|ref|YP_001308258.1| sporulation sigma factor SigE [Clostridium beijerinckii NCIMB 8052]
 gi|149902469|gb|ABR33302.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           beijerinckii NCIMB 8052]
          Length = 235

 Score = 59.7 bits (143), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 34/94 (36%), Positives = 54/94 (57%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K EE  L  +    GD +    L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 33  PPLSKDEEEDLVNKLN-GGDENIRSTLIERNLRLVVYIARKFENTGVYVEDLISVGTIGL 91

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+
Sbjct: 92  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN 125


>gi|169831583|ref|YP_001717565.1| sporulation sigma factor SigE [Candidatus Desulforudis audaxviator
           MP104C]
 gi|169638427|gb|ACA59933.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Candidatus
           Desulforudis audaxviator MP104C]
          Length = 241

 Score = 59.7 bits (143), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 37/94 (39%), Positives = 52/94 (55%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EE  L  R  E GD      L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 39  PPLTVDEETGLISRL-EAGDHGVRSTLIERNLRLVVYIARKFESTGVGIEDMVSIGTIGL 97

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  FDP +  +LATY+   I+  +  Y+ R+
Sbjct: 98  IKAVNTFDPRKRIKLATYASRCIENEILMYLRRN 131


>gi|239980906|ref|ZP_04703430.1| RNA polymerase sigma factor, sigma L [Streptomyces albus J1074]
 gi|291452768|ref|ZP_06592158.1| sigma L [Streptomyces albus J1074]
 gi|291355717|gb|EFE82619.1| sigma L [Streptomyces albus J1074]
          Length = 340

 Score = 59.7 bits (143), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 63/237 (26%), Positives = 105/237 (44%), Gaps = 23/237 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +   
Sbjct: 119 LIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTVIGE 178

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL   L +    L    D +     V  +A  L VSE 
Sbjct: 179 IKRFFRDTSWS-VRVPRRLQELRL--ALTKTSDELAQKLDRS---PTVPELAHALGVSEE 232

Query: 172 EVIS----MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +V+      N   A   SL++     D       D L Y+    E V    E R++ + +
Sbjct: 233 DVVDGLAVGNAYTA--SSLDSPAPEDDGGEGSLADRLGYEDTALEGV----EYRESLKPL 286

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L +    L PRERRI   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 287 LAK----LPPRERRIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 337


>gi|22770510|gb|AAN06630.1|AF497202_1 sigma factor B [Listeria monocytogenes]
          Length = 259

 Score = 59.7 bits (143), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 63/264 (23%), Positives = 128/264 (48%), Gaps = 26/264 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +++D   G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEEL 125

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDW 203
                   Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D 
Sbjct: 126 XRELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDV 182

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    DG E+V        N+R +L + + VL+ RE++I +   ++    + +      +
Sbjct: 183 VGGTDDGFERV--------NQRMLLEKVLPVLDEREQKILQYTFIENR--SQKETGELLD 232

Query: 264 VSRERVRQIEARAFKKVQESIQKQ 287
           +S+  V +I+ +A KK++E++Q +
Sbjct: 233 ISQMHVSRIQRQAIKKLREALQNE 256


>gi|323701301|ref|ZP_08112976.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
 gi|323533903|gb|EGB23767.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
          Length = 243

 Score = 59.7 bits (143), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 37/96 (38%), Positives = 55/96 (57%), Gaps = 3/96 (3%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHR--LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           P L   EE  L  R  E GD+  + +  L+  +LRLVV IA  +   G+ I ++VS G I
Sbjct: 39  PPLTSDEENDLIGRLGE-GDIDGSIKSVLIERNLRLVVYIARKFENTGVGIEDLVSIGTI 97

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           GL++AV  FDP +  +LATY+   I+  +  Y+ R+
Sbjct: 98  GLIKAVNTFDPNKKIKLATYASRCIENEILMYLRRN 133


>gi|153953966|ref|YP_001394731.1| sporulation sigma factor SigE [Clostridium kluyveri DSM 555]
 gi|219854580|ref|YP_002471702.1| hypothetical protein CKR_1237 [Clostridium kluyveri NBRC 12016]
 gi|146346847|gb|EDK33383.1| SigE2 [Clostridium kluyveri DSM 555]
 gi|219568304|dbj|BAH06288.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 235

 Score = 59.7 bits (143), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 35/94 (37%), Positives = 54/94 (57%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE  L  R    G+      L+  +LRLVV IA  +   G+ + ++VS G IGL
Sbjct: 33  PPLSKKEEEDLVSRL-VSGNEKVRATLIERNLRLVVYIARKFENTGVNVEDLVSVGTIGL 91

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+
Sbjct: 92  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN 125


>gi|25991939|gb|AAN76997.1|AF481773_1 putative sigma 70 transcription factor [Frankia sp. ACoN24d]
          Length = 185

 Score = 59.7 bits (143), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 54/188 (28%), Positives = 84/188 (44%), Gaps = 32/188 (17%)

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT- 128
           G G+ + ++V EGN+GL++ VKKFD  +G++ +TY+ WWI+ A+   +      ++I   
Sbjct: 2   GRGMTLLDLVQEGNLGLIRPVKKFDYAKGYKFSTYATWWIRQAIGRALADQGRTIRIPVX 61

Query: 129 --------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
                   T  Q++L   L R     +   + ++  EQVV    +L     + +S+   +
Sbjct: 62  VVEQINKITRLQRQLVSTLGREPTDEELALELDMPIEQVV----ELRRYAQDTVSLETSV 117

Query: 181 A--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
              GD  L   I  SD  S    D   Y   G  Q  IE        N+L      LNPR
Sbjct: 118 GDDGDSVLGDFIEDSDATSP--ADAASY---GAMQDEIE--------NVL----GGLNPR 160

Query: 239 ERRIFEAR 246
           ER +   R
Sbjct: 161 EREVMRLR 168


>gi|302389525|ref|YP_003825346.1| RNA polymerase, sigma 29 subunit, SigE [Thermosediminibacter oceani
           DSM 16646]
 gi|302200153|gb|ADL07723.1| RNA polymerase, sigma 29 subunit, SigE [Thermosediminibacter oceani
           DSM 16646]
          Length = 239

 Score = 59.7 bits (143), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 33/94 (35%), Positives = 54/94 (57%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L  +EE +L  +  + GD    + L+  +LRLVV IA  +   G  I +++S G IGL
Sbjct: 37  PPLSSEEEAMLLDKL-QMGDNGVRNVLIERNLRLVVYIARKFENTGAGIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++A+  FDP +  +LATY+   I+  +  Y+ R+
Sbjct: 96  IKAINTFDPHKKIKLATYASRCIENEILMYLRRN 129


>gi|121535239|ref|ZP_01667053.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
 gi|121306124|gb|EAX47052.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
          Length = 234

 Score = 59.7 bits (143), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 35/94 (37%), Positives = 52/94 (55%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EE  L  R  + GD +     +  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 31  PPLTSDEEVFLLSRL-QKGDKAVKSIFIERNLRLVVYIARKFENTGVGIEDLVSIGTIGL 89

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  FDP +  +LATY+   I+  +  Y+ R+
Sbjct: 90  IKAVNTFDPIKRIKLATYASRCIENEILMYLRRN 123


>gi|312194695|ref|YP_004014756.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Frankia sp.
           EuI1c]
 gi|311226031|gb|ADP78886.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Frankia sp.
           EuI1c]
          Length = 393

 Score = 59.7 bits (143), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 62/204 (30%), Positives = 93/204 (45%), Gaps = 36/204 (17%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +LV  HL LV  +A  +R  G P+ ++V    IGL+++V +FDPERG   +TY+   I  
Sbjct: 171 QLVRMHLPLVEYLARRFRNRGEPLDDLVQVATIGLIKSVDRFDPERGVEFSTYATPTIVG 230

Query: 112 AMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT---DNNLKPEQVVA-IAKKL 166
            ++ +   + W++          R+   L+ LK  L   T      L     VA IA  L
Sbjct: 231 EIKRHFRDKGWAI----------RVPRRLQELKLSLTKATSELSQKLGRSPTVAEIAAHL 280

Query: 167 NVSESEVISMNCRLAGDESLNA-------LINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
            ++E EV      L G ES NA         +S D  S    D L      Q++ L   E
Sbjct: 281 EMTEEEV------LEGLESANAYSAVSLDAPDSGDDESPAVADTLGV----QDESLEGVE 330

Query: 220 ERKNRRNMLTRSMSVLNPRERRIF 243
            R++ + +L +    L PRE+RI 
Sbjct: 331 YRESLKPLLEK----LPPREKRIL 350


>gi|308173495|ref|YP_003920200.1| RNA polymerase sporulation-specific sigma factor sigma-G [Bacillus
           amyloliquefaciens DSM 7]
 gi|307606359|emb|CBI42730.1| RNA polymerase sporulation-specific sigma factor (sigma-G)
           [Bacillus amyloliquefaciens DSM 7]
 gi|328553575|gb|AEB24067.1| sporulation sigma factor SigG [Bacillus amyloliquefaciens TA208]
 gi|328911632|gb|AEB63228.1| RNA polymerase sporulation-specific sigma factor (sigma-G)
           [Bacillus amyloliquefaciens LL3]
          Length = 260

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 62/262 (23%), Positives = 121/262 (46%), Gaps = 16/262 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+ +E   L K+ ++ GD SA  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKNEEMRKLFKQLQDEGDDSAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 74

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD     + +TY++  I   ++ Y LR  + +++  +   + + +   +++ 
Sbjct: 75  GLMKSIDNFDLSHNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSL--RDIAYKALQVRE 131

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L + T      E+   IAK L V   E++     +    SL   I +   +     D +
Sbjct: 132 RLISETSREPTAEE---IAKVLEVPHEEIVFALDAIQDPVSLFEPIYNDGGDPIYVMDQI 188

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             + +   Q + E          L   M  LN RE+ I   R  Q    T   ++ E  +
Sbjct: 189 SDERNKDTQWIEEL--------ALKEGMRRLNEREKMILRKRFFQGK--TQMEVAEEIGI 238

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+ +V ++E  A K++ ++I +
Sbjct: 239 SQAQVSRLEKAAIKQMNKNIHQ 260


>gi|303232785|ref|ZP_07319470.1| putative RNA polymerase sigma-B factor [Atopobium vaginae
           PB189-T1-4]
 gi|302481271|gb|EFL44346.1| putative RNA polymerase sigma-B factor [Atopobium vaginae
           PB189-T1-4]
          Length = 287

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 42/150 (28%), Positives = 75/150 (50%), Gaps = 15/150 (10%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           +KQ    L  +++ HGD  A ++LV +HL L   +A  ++  G  + +++    IGL++A
Sbjct: 40  DKQRTRELFIKFKRHGDEEARNQLVLNHLNLARFLASKFKNRGESLDDLIQVATIGLIKA 99

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           + +FD +RG    T++   I   ++ +   RSWS+          R+   L+ L   +  
Sbjct: 100 IDRFDIDRGLEFTTFATPTILGEIKRHFRDRSWSV----------RVPRRLQELSSKVSQ 149

Query: 149 ITDNNLKPEQ----VVAIAKKLNVSESEVI 174
            TD   +  Q    V  IA++L+VS  EV+
Sbjct: 150 ATDMLTEKLQHSPSVEEIARELDVSVDEVL 179


>gi|290959142|ref|YP_003490324.1| SigH-like stress response sigma factor [Streptomyces scabiei 87.22]
 gi|260648668|emb|CBG71781.1| SigH-like stress response sigma factor [Streptomyces scabiei 87.22]
          Length = 306

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 63/237 (26%), Positives = 105/237 (44%), Gaps = 23/237 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +   
Sbjct: 85  LIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTVVGE 144

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL   L +    L    D +     V  +A  L VSE 
Sbjct: 145 IKRFFRDTSWS-VRVPRRLQELRL--ALTKASDELSQKLDRS---PTVTELAAVLGVSEE 198

Query: 172 EVIS----MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +V+      N   A   SL++     D       D L Y+    E V    E R++ + +
Sbjct: 199 DVVDGLAVGNAYTAS--SLDSPAPEDDGGEGSLADRLGYEDTALEGV----EYRESLKPL 252

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L +    L PRERRI   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 253 LAK----LPPRERRIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 303


>gi|224002653|ref|XP_002290998.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220972774|gb|EED91105.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 345

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 50/72 (69%), Gaps = 4/72 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + A ++LV S+LR+V ++   Y   GL       +++ +G + L++A +K++PERGFR +
Sbjct: 83  IEAKNQLVASNLRMVQRVVNLYIRNGLGSEYNAGDLMQDGTMALIRAAEKYEPERGFRFS 142

Query: 103 TYSMWWIKAAMQ 114
           TY+M+WI++A++
Sbjct: 143 TYAMYWIRSAVK 154


>gi|32474462|ref|NP_867456.1| sigma-70 factor [Rhodopirellula baltica SH 1]
 gi|32445000|emb|CAD75002.1| sigma-70 factor [Rhodopirellula baltica SH 1]
          Length = 557

 Score = 59.7 bits (143), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 65/249 (26%), Positives = 109/249 (43%), Gaps = 75/249 (30%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           +++V ++LRLVV IA  +         ++S+GN+ L++AV+KFD  RG + +TY+     
Sbjct: 378 NKIVQANLRLVVSIAKRHVASAEDFFSLISDGNMSLIRAVEKFDYSRGNKFSTYA----- 432

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
                    SW+++K     N  R   N  + +   +A  D      Q            
Sbjct: 433 ---------SWAIMK-----NFARTIPNEFKHRDRFRATPDEMFVAHQ------------ 466

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
                       DE L+  +                    +E V ++      R+  L R
Sbjct: 467 ------------DERLDPYL--------------------EETVQLQ------RQRELAR 488

Query: 231 SMSVLNPRERRIFEAR-RLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK- 286
            +  L+ RE++I  AR  LQ    P+TL+ +  E  V++ERVRQ+EARA  K++++ +  
Sbjct: 489 ILDRLDEREQKIITARFGLQRGVEPLTLKEVGEEMGVTKERVRQLEARALSKLRDAARDA 548

Query: 287 --QVELSSS 293
              VEL +S
Sbjct: 549 KIDVELGAS 557


>gi|327539462|gb|EGF26077.1| sigma-70 factor [Rhodopirellula baltica WH47]
          Length = 557

 Score = 59.3 bits (142), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 65/248 (26%), Positives = 108/248 (43%), Gaps = 75/248 (30%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           ++V ++LRLVV IA  +         ++S+GN+ L++AV+KFD  RG + +TY+      
Sbjct: 379 KIVQANLRLVVSIAKRHVASAEDFFSLISDGNMSLIRAVEKFDYSRGNKFSTYA------ 432

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
                   SW+++K     N  R   N  + +   +A  D      Q             
Sbjct: 433 --------SWAIMK-----NFARTIPNEFKHRDRFRATPDEMFVAHQ------------- 466

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
                      DE L+  +                    +E V ++      R+  L R 
Sbjct: 467 -----------DERLDPYL--------------------EETVQLQ------RQRELARI 489

Query: 232 MSVLNPRERRIFEAR-RLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK-- 286
           +  L+ RE++I  AR  LQ    P+TL+ +  E  V++ERVRQ+EARA  K++++ +   
Sbjct: 490 LDRLDEREQKIITARFGLQRGVEPLTLKEVGEEMGVTKERVRQLEARALSKLRDAARDAK 549

Query: 287 -QVELSSS 293
             VEL +S
Sbjct: 550 IDVELGAS 557


>gi|323490578|ref|ZP_08095784.1| RNA polymerase sigma-B factor [Planococcus donghaensis MPA1U2]
 gi|323395844|gb|EGA88684.1| RNA polymerase sigma-B factor [Planococcus donghaensis MPA1U2]
          Length = 260

 Score = 59.3 bits (142), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 59/249 (23%), Positives = 129/249 (51%), Gaps = 22/249 (8%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           Y++  D  A   LV ++ RLV  IA  Y   + Y   I++V   G +GL+ A++++DP  
Sbjct: 22  YQKTEDEEAQTNLVLNYKRLVESIARKYSNGKSYHEDIAQV---GMLGLLGAIRRYDPSY 78

Query: 98  GFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           G     +++  I   ++ ++  ++W++         +R+     R+K  ++ +T    + 
Sbjct: 79  GRSFEAFAVPTIIGEIKRFLRDKTWAI------HVPRRIKELGPRIKATVEVLTTELQRS 132

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQVL 215
            QV  IA+ L+V E +++     +   +S  AL ++ S +  S      ++D  GQE   
Sbjct: 133 PQVWEIAEYLDVEEDDILEA---MEMGKSYQALSMDHSLEADSDGSTITLFDVVGQED-- 187

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
            +  E+ ++R ++  +M+VL+ RE++I +   +++  ++ +    +  +S+  V +++ +
Sbjct: 188 -DGYEKADQRMLVAEAMNVLSEREKQIIQFTYIEQ--LSQKEAGDKLGISQMHVSRLQRK 244

Query: 276 AFKKVQESI 284
           A KK+QE+I
Sbjct: 245 AIKKLQEAI 253


>gi|302670750|ref|YP_003830710.1| flagellar biosynthesis sigma factor FliA [Butyrivibrio
           proteoclasticus B316]
 gi|302395223|gb|ADL34128.1| flagellar biosynthesis sigma factor FliA [Butyrivibrio
           proteoclasticus B316]
          Length = 257

 Score = 59.3 bits (142), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 63/246 (25%), Positives = 115/246 (46%), Gaps = 33/246 (13%)

Query: 61  VVKIAMG----YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           +VK+  G    Y G+ +   ++V  G  GL+ A+ KFD  +  +  TY+   I+ A+ + 
Sbjct: 32  LVKLVAGRLSMYLGFNVEYDDLVGYGIFGLIDAIDKFDLMKDVKFETYASLRIRGAILDQ 91

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLK---GHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
           I R    +       QK++   +R ++   GH+   TD          IA K+ +SE E 
Sbjct: 92  I-RKMDWIPRTIRQRQKKIEAAIREIERDGGHVA--TD--------AEIAAKMQISEDEY 140

Query: 174 ISM--NCRLAGDESLNALINSS---DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            +     ++ G  SLN  ++      ++S+      V   +      IEKEE K    ML
Sbjct: 141 ANWQNQMKVTGVVSLNEFMDQGADIPEDSNNRSSGFVKPEEA-----IEKEELK---KML 192

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +S+  L  +E+++      +E  +TL+ +S   EVS  RV Q+  +A +K++E +   +
Sbjct: 193 AQSLESLTDKEKKVILLYYYEE--LTLKEISQVLEVSESRVSQLHTKALQKMREKLGDYL 250

Query: 289 ELSSSP 294
            + ++P
Sbjct: 251 GILTNP 256


>gi|302871563|ref|YP_003840199.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
 gi|302574422|gb|ADL42213.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
          Length = 240

 Score = 59.3 bits (142), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 60/243 (24%), Positives = 113/243 (46%), Gaps = 24/243 (9%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           ++GD  A  +L+ S+L LV  +   +   G+ + ++   G IGL++AV +FDP    R +
Sbjct: 14  KNGDKVARQQLIESNLALVWSVVKKFAAKGVELEDLFQIGCIGLIKAVDRFDPSFNVRFS 73

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
           TY++  I   ++ Y LR    +K+      NQ +    +++L+   Q ++DN  +P  + 
Sbjct: 74  TYAVPMIIGEIKRY-LRDDGRIKVSRKIKENQSK----IKKLRN--QFVSDNGREP-TIS 125

Query: 161 AIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            I++   +S  E+  + C  A  E  SL+ +IN  +       D    + D   ++L   
Sbjct: 126 EISQLTGLSSEEI--LLCMDASSEVASLSEVINQEEGKPITLMDLASDEEDYSTKLL--- 180

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                    L   +  L  RER I   R  +    T   ++ +  +S+  V +IE RA +
Sbjct: 181 -----DLMALKEGLKKLKGRERYIIFMRYFKNK--TQSEIAKQLNISQVHVSRIEKRALE 233

Query: 279 KVQ 281
           +++
Sbjct: 234 RIK 236


>gi|298715063|emb|CBJ27770.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Ectocarpus siliculosus]
          Length = 737

 Score = 59.3 bits (142), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 27/69 (39%), Positives = 44/69 (63%), Gaps = 5/69 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYR----GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + A  +LV  +L LVV +A  Y+      G  +  ++ EG IGL++A +++DP +GFR  
Sbjct: 477 MEARQKLVVCNLALVVSLANKYKRSHFDCGC-LQTLIQEGTIGLIRAAERYDPSKGFRFT 535

Query: 103 TYSMWWIKA 111
           TY++WWI+A
Sbjct: 536 TYAIWWIEA 544


>gi|2529271|gb|AAB81191.1| sigma factor [Lysinibacillus sphaericus]
          Length = 263

 Score = 59.3 bits (142), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 58/239 (24%), Positives = 110/239 (46%), Gaps = 18/239 (7%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A  R+V  + RLV  I   +   G+ + ++   G IGLM++V KFD     + +
Sbjct: 25  QQGDHEARKRMVEGNTRLVWSIVQRFTTRGVELEDLFQIGCIGLMKSVDKFDLSYDVKFS 84

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I   +Q + LR   +VK+  +   + L F +R        I  N  +P  +  +
Sbjct: 85  TYAVPMIIGEIQRF-LRDDGMVKVSRSI--RELNFKIRHATDEF--IKRNEHRP-TIQEL 138

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+ L V+  E+++ +  L    SL+  +  S+ +S    D          Q+  EK E+ 
Sbjct: 139 AQVLGVTTEEIVTASDALRDPASLHEQLYESEGDSITLMD----------QMKDEKSEQP 188

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                L   ++ L PRE+ I   R   +   T   +++   +S+ +V ++E +   +++
Sbjct: 189 FDYIPLKEVLTRLEPREQSIIYLRYFSD--CTQTEIANRLGISQVQVSRLEKKILAQLK 245


>gi|302792318|ref|XP_002977925.1| hypothetical protein SELMODRAFT_53596 [Selaginella moellendorffii]
 gi|300154628|gb|EFJ21263.1| hypothetical protein SELMODRAFT_53596 [Selaginella moellendorffii]
          Length = 326

 Score = 59.3 bits (142), Expect = 6e-07,   Method: Compositional matrix adjust.
 Identities = 60/245 (24%), Positives = 116/245 (47%), Gaps = 29/245 (11%)

Query: 48  SAAHRLVTSHLRLVVKIAMGY--RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           +A ++++  +LRLV   A  Y      L + ++  EG  GLM AV KFDP++G+R +TY+
Sbjct: 87  AARNKMIKHNLRLVAHQARKYFKEELSLSLLDLCQEGVPGLMSAVDKFDPKKGYRFSTYA 146

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
           ++W+K ++     R   +V++      +++   ++R +  L    D     E+V+   K 
Sbjct: 147 VYWVKNSILRAQTRLGHIVRVPYNVAAQKM--TIQRKRAQLSLELDREPTHEEVITELKM 204

Query: 166 LNVSESEVI-------SMNCR--LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
            +    EV+       S+N R  + G+E +++ I+  D+N +Q+ +       G + VL 
Sbjct: 205 DSRRYFEVLRTGAPRRSLNARSKVTGEELIHS-ISDPDENEAQYFNAGAQLRLGMDDVL- 262

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
             +  K + +++ R    L+ +  R F              +     +SRE VR+ E R 
Sbjct: 263 --DSLKPKESLIIRQRYGLDGKGERSF------------TEIGRNLNLSREMVRKYEIRG 308

Query: 277 FKKVQ 281
             K++
Sbjct: 309 MMKLK 313


>gi|225462725|ref|XP_002268709.1| PREDICTED: hypothetical protein [Vitis vinifera]
 gi|302143685|emb|CBI22546.3| unnamed protein product [Vitis vinifera]
          Length = 518

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 46/169 (27%), Positives = 85/169 (50%), Gaps = 18/169 (10%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
           V  +R+ E G  +A ++L+  +LRLV+ +   Y      G    ++   G  GL+ A+ +
Sbjct: 268 VQVRRHMEVGQ-AARNKLIKHNLRLVLFVINKYFQEFANGPKFQDLCQAGVKGLITAIDR 326

Query: 93  FDPERGFRLATYSMWWIK-AAMQEYILRSWSLVKIGTTA-------NQKRLFFNLRRLKG 144
           F+P+R FRL+TY ++WI+ A M+   L S++ V  G  +        +  L F L+RL  
Sbjct: 327 FEPKRSFRLSTYGLFWIRHAIMRSMTLSSFTRVSFGLESVRVEIQRAKLELLFKLQRLPT 386

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG--DESLNALIN 191
             + I    + PE+   + +    +   V+S++ R A   +E +N + +
Sbjct: 387 EEEIIEKVGISPERYHEVMR----ASKSVLSLHARHATTQEEYINGITD 431


>gi|23978331|dbj|BAC21136.1| principal sigma factor [Synechococcus leopoliensis]
          Length = 188

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 53/199 (26%), Positives = 100/199 (50%), Gaps = 19/199 (9%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+   I      +++     
Sbjct: 4   GLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV--- 60

Query: 132 QKRLFFNLRRLKGHLQAIT-DNNLKP-EQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
              L+  + R+K   + ++ +   KP E+ +A   ++ + +   I+ + +L    SL   
Sbjct: 61  --HLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLP--ISLETP 116

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFEARRL 248
           I   +   S+  D++  + DG+     E E  KN  R  L   +S L+PRER +   R  
Sbjct: 117 IGKEE--DSRLGDFI--EADGETP---EDEVAKNLLREDLEGVLSTLSPRERDVLRLRYG 169

Query: 249 QENP--VTLENLSSEFEVS 265
            ++    TLE +   F V+
Sbjct: 170 LDDGRMKTLEEIGQLFNVT 188


>gi|83589704|ref|YP_429713.1| sporulation sigma factor SigG [Moorella thermoacetica ATCC 39073]
 gi|83572618|gb|ABC19170.1| RNA polymerase, sigma subunit, RpsG/SigG [Moorella thermoacetica
           ATCC 39073]
          Length = 272

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 66/272 (24%), Positives = 133/272 (48%), Gaps = 41/272 (15%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+  E   L ++  + G+  A  +L+T +LRLV+ +   +   G  + ++   G I
Sbjct: 30  KLPLLKSDEIRQLFQQM-QAGETGAREKLITGNLRLVLSVIQRFTNRGEHVDDLFQVGCI 88

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A+  FD  +  + +TY++  I   ++ Y LR  + +++  +         LR +  
Sbjct: 89  GLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRS---------LRDVAY 138

Query: 145 HLQAITD---NNLKPEQVVA-IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
               I D   N L  E  +A +A++L++ + EVI          +L+A+     +  S +
Sbjct: 139 KALQIRDTLVNKLAREPSLAEVAQQLDLPQEEVIF---------ALDAI----QEPVSLF 185

Query: 201 QDWLVYDHDGQEQVLIEKE--ERKNRRN------MLTRSMSVLNPRERRIFEARRLQENP 252
           +   +Y HDG + + +  +  + KN+ +       +  +M+ LNPRER I   R  +   
Sbjct: 186 EP--IY-HDGGDPIFVMDQIGDEKNQDSSWLENIAIKEAMNKLNPRERLILSLRFFEGK- 241

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            T   ++ E  +S+ +V ++E  A + +++ I
Sbjct: 242 -TQMEVADEIGISQAQVSRLEKAALQHMRKYI 272


>gi|297616583|ref|YP_003701742.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
 gi|297144420|gb|ADI01177.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
          Length = 235

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 35/102 (34%), Positives = 57/102 (55%), Gaps = 1/102 (0%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +  G + L  Y++ +     L ++EE +  ++ RE GD  A H L+  +LRLV  +   +
Sbjct: 13  LTKGMLMLFSYLNNLVFPHPLSEEEERIYLEKTRE-GDEEAKHILIEHNLRLVAHVIKKF 71

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            G G    +++S G IGL++A+  FD  RG RLATY+   I+
Sbjct: 72  EGTGEDTEDLISIGTIGLIKAINTFDYARGTRLATYAARCIE 113


>gi|327438482|dbj|BAK14847.1| DNA-directed RNA polymerase specialized sigma subunit [Solibacillus
           silvestris StLB046]
          Length = 261

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 59/246 (23%), Positives = 119/246 (48%), Gaps = 16/246 (6%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y+  G   +   LV  + +LV  IA  Y        ++V  G +GL+ A+++FDP  G  
Sbjct: 22  YQASGCEESQTNLVLHYQQLVESIARKYSHGKSYYDDIVQVGMLGLLGAIRRFDPSFGRS 81

Query: 101 LATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
              +++  I   ++ ++  ++W +         +R+     R+K  ++A+T +  +   +
Sbjct: 82  FEAFAVPTIVGEIKRFLRDKTWDV------HVPRRIKELGPRIKAAVEALTTSLQRSPSI 135

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
             IA  L V + +V+     +    S  AL ++ S ++ S      ++D  G+E      
Sbjct: 136 TEIATYLEVQDEDVLEA---MEMGRSYQALSMDHSIESDSDGSTVTLFDVVGREDT---G 189

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
            E  NRR ++  +M+VLN RER+I +   L++  ++ +       +S+  V +I+ +A K
Sbjct: 190 YEVTNRRMIVADAMNVLNERERQIIQLTYLEQ--LSQKEAGERLGISQMHVSRIQRKAIK 247

Query: 279 KVQESI 284
           K+Q++I
Sbjct: 248 KLQDAI 253


>gi|160935680|ref|ZP_02083055.1| hypothetical protein CLOBOL_00570 [Clostridium bolteae ATCC
           BAA-613]
 gi|158441424|gb|EDP19134.1| hypothetical protein CLOBOL_00570 [Clostridium bolteae ATCC
           BAA-613]
          Length = 246

 Score = 59.3 bits (142), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 66/275 (24%), Positives = 122/275 (44%), Gaps = 65/275 (23%)

Query: 15  GLSRYIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           G   YI     +P  LE +EE  +        D  A   L+  +LRLVV IA  +    +
Sbjct: 28  GEVHYIGGADILPAPLETEEEGRMISLLGSEDDKEARAALIEHNLRLVVYIAKKFDNTSV 87

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++S G IGL++A+  F P++  +LATY+   I+  +  Y+ R+          N+ 
Sbjct: 88  GVEDLISIGTIGLIKAINTFKPDKNIKLATYASRCIENEILMYLRRN----------NKT 137

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
           RL                        V+I + LNV             G+E L + I  +
Sbjct: 138 RL-----------------------EVSIDEPLNVD----------WDGNELLLSDILGT 164

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-- 251
           D++       ++Y HD ++++          +++L  ++S LNPRER+I E R    N  
Sbjct: 165 DED-------VIY-HDIEDEI---------EKSLLNNAISRLNPRERKIVELRYGLTNED 207

Query: 252 --PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              +T + ++    +S+  + ++E +  K++++ I
Sbjct: 208 GEEMTQKEVADLLGISQSYISRLEKKIMKRLKKEI 242


>gi|23978319|dbj|BAC21133.1| principal sigma factor [Microcystis wesenbergii]
          Length = 188

 Score = 58.9 bits (141), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 49/198 (24%), Positives = 99/198 (50%), Gaps = 17/198 (8%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+   I      +++     
Sbjct: 4   GLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV--- 60

Query: 132 QKRLFFNLRRLKGHLQAIT-DNNLKP-EQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
              L+  + R+K   + ++ +   KP E+ +A   ++ + +   I+ + +L    SL   
Sbjct: 61  --HLYETISRIKKTTKILSQEMRRKPTEEEIATKMEMTIEKLRFIAKSAQLPI--SLETP 116

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   +   S+  D++  D +  E  + +   R++  N+L      L+PRER +   R   
Sbjct: 117 IGKEE--DSRLGDFIEADGETPEDEVSKNLLREDLENVL----DTLSPRERDVLRLRYGL 170

Query: 250 ENP--VTLENLSSEFEVS 265
           ++    TLE +   F V+
Sbjct: 171 DDGRMKTLEEIGQIFNVT 188


>gi|302542626|ref|ZP_07294968.1| putative RNA polymerase sigma factor [Streptomyces hygroscopicus
           ATCC 53653]
 gi|302460244|gb|EFL23337.1| putative RNA polymerase sigma factor [Streptomyces himastatinicus
           ATCC 53653]
          Length = 351

 Score = 58.9 bits (141), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 59/233 (25%), Positives = 104/233 (44%), Gaps = 17/233 (7%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+   +   
Sbjct: 131 LVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATPTVVGE 190

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           ++ +       V++     + RL       +     ++  + +   V  +A+ L +SE E
Sbjct: 191 IKRHFRDKGWAVRVPRRLQELRLSLTTATAE-----LSQRHGRAPTVHELAEHLAISEEE 245

Query: 173 VISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           V      L G ES NA    S D   +  +   V D  G E   +E  E    R  L   
Sbjct: 246 V------LEGLESANAYSTLSLDVPDTDDESPAVADTLGAEDEALEGVE---YRESLKPL 296

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +  L PRE++I   R      +T   ++ E  +S+  V ++ AR   ++++ +
Sbjct: 297 LEDLPPREKKILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLRDRL 347


>gi|325662152|ref|ZP_08150770.1| hypothetical protein HMPREF0490_01508 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|325471601|gb|EGC74821.1| hypothetical protein HMPREF0490_01508 [Lachnospiraceae bacterium
           4_1_37FAA]
          Length = 211

 Score = 58.9 bits (141), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 33/84 (39%), Positives = 51/84 (60%), Gaps = 2/84 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+   +E+Y + K Y E GDL A H L+  +LRLV  I   Y+       +++S G +GL
Sbjct: 10  PLTSAEEQYYMQK-YTE-GDLEAKHILIEHNLRLVAHIVKKYQRPEEDNEDLISIGTVGL 67

Query: 87  MQAVKKFDPERGFRLATYSMWWIK 110
           ++AV  F+PE+G RL+TY+   I+
Sbjct: 68  IKAVITFNPEKGNRLSTYAARCIE 91


>gi|153953795|ref|YP_001394560.1| RNA polymerase sigma factor [Clostridium kluyveri DSM 555]
 gi|219854411|ref|YP_002471533.1| hypothetical protein CKR_1068 [Clostridium kluyveri NBRC 12016]
 gi|146346676|gb|EDK33212.1| RNA polymerase sigma factor [Clostridium kluyveri DSM 555]
 gi|219568135|dbj|BAH06119.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 241

 Score = 58.9 bits (141), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 66/247 (26%), Positives = 113/247 (45%), Gaps = 21/247 (8%)

Query: 46  DLSAAHRLVTSHLRLVVKIA----MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
           +L+    LV  +L LV  IA    +G   Y +   ++VS G +GLM A+ KFD +RG + 
Sbjct: 6   ELNIKEELVKKYLPLVKYIASRVIIGKTKY-IEYEDLVSYGTLGLMDAINKFDKDRGMKF 64

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY+   IK +M + + R+  + K G      R    +  L+G L        +    V 
Sbjct: 65  STYASIRIKGSMIDELRRNSPISK-GAMDKLNRYNAAVEYLQGELG-------REPNSVE 116

Query: 162 IAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           IA KL +S  E++ +          SL  L+ S + N               E+ L EKE
Sbjct: 117 IASKLGISLKEMMEIENYINYISMVSLEDLVFSDEDNIPIMGTIEDTKSPSPERNLEEKE 176

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           + K     L +++ +LN ++  +      +E  +TL+ +     VS  RV Q+ +RA   
Sbjct: 177 KLK----YLAKALELLNEKDNLVLTLYYYEE--LTLKEIGHILNVSESRVCQLHSRAIVH 230

Query: 280 VQESIQK 286
           +++++ K
Sbjct: 231 LRKAMAK 237


>gi|294630218|ref|ZP_06708778.1| RNA polymerase sigma-F factor [Streptomyces sp. e14]
 gi|292833551|gb|EFF91900.1| RNA polymerase sigma-F factor [Streptomyces sp. e14]
          Length = 302

 Score = 58.9 bits (141), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 62/237 (26%), Positives = 105/237 (44%), Gaps = 23/237 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +   
Sbjct: 81  LIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTVVGE 140

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL   L +    L    D +     V  +A  L VSE 
Sbjct: 141 IKRFFRDTSWS-VRVPRRLQELRL--ALTKASDELSQKLDRS---PTVAELAAVLGVSEE 194

Query: 172 EVIS----MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +V+      N   A   SL++     D       D L Y+    E V    E R++ + +
Sbjct: 195 DVVDGLAVGNAYTAS--SLDSPAPEDDGGEGSLADRLGYEDSALEGV----EYRESLKPL 248

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L +    L PRERRI   R      +T   +  E  +S+  V ++  R   ++++ +
Sbjct: 249 LAK----LPPRERRIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLRDGL 299


>gi|219125233|ref|XP_002182890.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217405684|gb|EEC45626.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 312

 Score = 58.9 bits (141), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 28/70 (40%), Positives = 43/70 (61%), Gaps = 5/70 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRG-----YGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           A H LVT++L LV  +     G      G+   E++ EG++GL++A + FDPERG R +T
Sbjct: 60  AKHDLVTANLGLVHAVVNQQYGSLKTHTGITKEELIQEGSLGLLRAAELFDPERGLRFST 119

Query: 104 YSMWWIKAAM 113
           Y++ WIK  +
Sbjct: 120 YAVVWIKGVL 129


>gi|26249146|ref|NP_755186.1| hypothetical protein c3307 [Escherichia coli CFT073]
 gi|26109553|gb|AAN81756.1|AE016765_158 Putative conserved protein [Escherichia coli CFT073]
          Length = 144

 Score = 58.9 bits (141), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 31/73 (42%), Positives = 49/73 (67%), Gaps = 1/73 (1%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 73  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 131

Query: 79  VSEGNIGLMQAVK 91
           + EGN+GL++AV+
Sbjct: 132 IEEGNLGLIRAVE 144


>gi|16078597|ref|NP_389416.1| sporulation sigma factor SigG [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221309407|ref|ZP_03591254.1| sporulation sigma factor SigG [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221313732|ref|ZP_03595537.1| sporulation sigma factor SigG [Bacillus subtilis subsp. subtilis
           str. NCIB 3610]
 gi|221318656|ref|ZP_03599950.1| sporulation sigma factor SigG [Bacillus subtilis subsp. subtilis
           str. JH642]
 gi|221322929|ref|ZP_03604223.1| sporulation sigma factor SigG [Bacillus subtilis subsp. subtilis
           str. SMY]
 gi|321315298|ref|YP_004207585.1| sporulation sigma factor SigG [Bacillus subtilis BSn5]
 gi|133475|sp|P19940|RPSG_BACSU RecName: Full=RNA polymerase sigma-G factor; AltName: Full=Stage
           III sporulation protein G
 gi|143430|gb|AAA22703.1| sporulation-specific sigma factor [Bacillus subtilis]
 gi|580764|emb|CAA40771.1| sigma-G factor [Bacillus subtilis subsp. subtilis str. 168]
 gi|2633906|emb|CAB13407.1| RNA polymerase sporulation-specific sigma factor (sigma-G)
           [Bacillus subtilis subsp. subtilis str. 168]
 gi|320021572|gb|ADV96558.1| sporulation sigma factor SigG [Bacillus subtilis BSn5]
          Length = 260

 Score = 58.9 bits (141), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 61/262 (23%), Positives = 120/262 (45%), Gaps = 16/262 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+ +E   L ++ ++ GD SA  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKNEEMRKLFRQLQDEGDDSAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 74

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD     + +TY++  I   ++ Y LR  + +++  +          + L+ 
Sbjct: 75  GLMKSIDNFDLSHNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSLRD----IAYKALQV 129

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + I++ + +P     IAK L V   E++     +    SL   I +   +     D +
Sbjct: 130 RERLISETSKEP-TAEDIAKVLEVPHEEIVFALDAIQDPVSLFEPIYNDGGDPIYVMDQI 188

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             + +   Q + E          L   M  LN RE+ I   R  Q    T   ++ E  +
Sbjct: 189 SDERNTDSQWIEEL--------ALKEGMRRLNDREKMILRKRFFQGK--TQMEVAEEIGI 238

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+ +V ++E  A K++ ++I +
Sbjct: 239 SQAQVSRLEKAAIKQMNKNIHQ 260


>gi|212639646|ref|YP_002316166.1| sporulation sigma factor SigG [Anoxybacillus flavithermus WK1]
 gi|212561126|gb|ACJ34181.1| DNA-directed RNA polymerase specialized sigma subunit sigG
           [Anoxybacillus flavithermus WK1]
          Length = 259

 Score = 58.9 bits (141), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 65/273 (23%), Positives = 129/273 (47%), Gaps = 41/273 (15%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L K EE     R  + GD+SA  +L+T +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVL-KNEEMRELFRQMQAGDISAREKLITGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD  +  + +TY++  I   ++ Y LR  + +++  +   + + +   +++ 
Sbjct: 74  GLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSL--RDIAYKALQVRE 130

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            + + T      E+   IAK L+V   E++          +L+A+           QD +
Sbjct: 131 KMMSETAKEPTAEE---IAKILDVPHEEIVF---------ALDAI-----------QDPV 167

Query: 205 -----VYDHDGQEQVLIEK-EERKNRRN------MLTRSMSVLNPRERRIFEARRLQENP 252
                +Y+  G    ++++  + KNR         L   +  LN RE+ I   R  Q   
Sbjct: 168 SLFEPIYNDGGDPIYVMDQLSDEKNRDTNWIEEIALKEGLRRLNEREKMIIRKRFFQGK- 226

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            T   ++ E  +S+ +V ++E  A K++ ++IQ
Sbjct: 227 -TQMEVAEEIGISQAQVSRLEKAAIKQMNKNIQ 258


>gi|331090616|ref|ZP_08339467.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium 2_1_46FAA]
 gi|330401056|gb|EGG80651.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium 2_1_46FAA]
          Length = 246

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 30/92 (32%), Positives = 53/92 (57%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           LE +EE  + ++     D  A   L+  +LRLVV IA  +   G+ + +++S G IGL++
Sbjct: 43  LETEEETAVIEKLGTETDDVAKKTLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIK 102

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           A+  F+P +  +LATY+   I+  +  Y+ R+
Sbjct: 103 AINTFNPMKNIKLATYASRCIENEILMYLRRN 134


>gi|226313414|ref|YP_002773308.1| sporulation sigma factor SigE [Brevibacillus brevis NBRC 100599]
 gi|226096362|dbj|BAH44804.1| RNA polymerase sigma-E factor precursor [Brevibacillus brevis NBRC
           100599]
          Length = 240

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 47/76 (61%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD +    L+  +LRLVV IA  +   G+ I ++VS G IGL++AV  FDP++  +LATY
Sbjct: 55  GDPAVRGMLIERNLRLVVYIARKFENTGINIEDLVSIGTIGLIKAVNTFDPDKNIKLATY 114

Query: 105 SMWWIKAAMQEYILRS 120
           +   I+  +  Y+ R+
Sbjct: 115 ASRCIENEILMYLRRN 130


>gi|320009626|gb|ADW04476.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 288

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 63/237 (26%), Positives = 106/237 (44%), Gaps = 23/237 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +   
Sbjct: 67  LIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTVVGE 126

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL   L +    L    D +     V  +AK L VSE 
Sbjct: 127 IKRFFRDTSWS-VRVPRRLQELRL--ALTKTSDELAQKLDRS---PTVPELAKALGVSEE 180

Query: 172 EVIS----MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +V+      N   A   SL++     D       D L Y+    E V    E R++ + +
Sbjct: 181 DVVDGLAVGNAYTA--SSLDSPSPEDDGGEGSLADRLGYEDAALEGV----EYRESLKPL 234

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L +    L PRER+I   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 235 LAK----LAPRERQIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLTQLREGL 285


>gi|23978363|dbj|BAC21146.1| principal sigma factor [Pleurocapsa sp. PCC 7327]
          Length = 188

 Score = 58.9 bits (141), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 49/198 (24%), Positives = 99/198 (50%), Gaps = 17/198 (8%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+   I      +++     
Sbjct: 4   GLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV--- 60

Query: 132 QKRLFFNLRRLKGHLQAIT-DNNLKP-EQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
              L+  + R+K   + ++ +   KP E+ +A   ++ + +   I+ + +L    SL   
Sbjct: 61  --HLYETISRIKKTTKILSQEMRRKPTEEEIATRMEMTIEKLRFIAKSAQLPI--SLETP 116

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   +   S+  D++  D +  E  + +   R++  N+L      L+PRER +   R   
Sbjct: 117 IGKEE--DSRLGDFIEADGETPEDEVSKNLLREDLENVL----DTLSPRERDVLRLRYGL 170

Query: 250 ENP--VTLENLSSEFEVS 265
           ++    TLE +   F V+
Sbjct: 171 DDGRMKTLEEIGQIFNVT 188


>gi|51892950|ref|YP_075641.1| sporulation sigma factor SigF [Symbiobacterium thermophilum IAM
           14863]
 gi|51856639|dbj|BAD40797.1| RNA polymerase sigma factor similar to B. subtilis
           sporulation-specific sigma-F [Symbiobacterium
           thermophilum IAM 14863]
          Length = 255

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 58/237 (24%), Positives = 110/237 (46%), Gaps = 15/237 (6%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A  RLV  +LRLV  +   +   G    ++   G IGL++A+ +FD     R +TY
Sbjct: 27  GDKEARDRLVEGNLRLVRSLVSRFSASGADPEDLFQIGCIGLLKAIDRFDLNYDVRFSTY 86

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           ++  I   ++ + LR    +++  +  Q  L    RR++  L A  + +     V  +A 
Sbjct: 87  AVPLIMGEIRRH-LRDDGPMRVSRSLKQ--LAQQARRVRERLAAQMERD---PTVAEVAA 140

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L VS  EV++    +    S++  ++  D +     D L  D   +E V ++       
Sbjct: 141 ELGVSPEEVVAALDGVRPPTSIHQTVHEGDGDPIYLLDQLAADDGQREGVWLD------- 193

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R  L   ++ L+ RER +   R  ++   T   ++S    S+ +V ++E RA ++++
Sbjct: 194 RVALREGLNQLDERERTVILLRFFRDK--TQTEVASILGCSQVQVSRLERRALERIR 248


>gi|303238906|ref|ZP_07325437.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302593539|gb|EFL63256.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 257

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 65/277 (23%), Positives = 128/277 (46%), Gaps = 51/277 (18%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L   ++ VL +R  + GD SA    +  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLTNDQKKVLFERMHK-GDTSAREEFIKGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK- 143
           GL++A+  FD  +  + +TY++  I   ++ Y+  + S+          R+  +LR +  
Sbjct: 74  GLIKAIDNFDVSQNVKFSTYAVPMIIGEIRRYLRDNNSI----------RVSRSLRDIAY 123

Query: 144 GHLQA---ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
             LQA   +T+ N K   V  I+K+L + + +++          +L+A+ +      S +
Sbjct: 124 KALQAKERLTNKNSKEPTVDDISKELGIPKEDIVF---------ALDAIQDPISLFESVY 174

Query: 201 QDWLVYDHDGQEQVLIE---KEERKNRRN-----MLTRSMSVLNPRER-----RIFEARR 247
                  HDG + + +    K+E+ +  N      L  +M  LN RE+     R F+ R 
Sbjct: 175 -------HDGGDAIYVMDQVKDEKNHDENWLEGIALNEAMRKLNDREKLILNLRFFDGRT 227

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             E       ++ E  +S+ +V ++E  A   +++ I
Sbjct: 228 QME-------VAEEIGISQAQVSRLEKTALMHMRKYI 257


>gi|304404017|ref|ZP_07385679.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
 gi|304346995|gb|EFM12827.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
          Length = 240

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 31/76 (40%), Positives = 47/76 (61%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD +    L+  +LRLVV IA  +   G+ I ++VS G IGL++AV  FDPE+  +LATY
Sbjct: 55  GDTAIRAMLIERNLRLVVYIARKFENTGIHIEDLVSIGAIGLIKAVNTFDPEKKIKLATY 114

Query: 105 SMWWIKAAMQEYILRS 120
           +   I+  +  Y+ R+
Sbjct: 115 ASRCIENEILMYLRRN 130


>gi|296331109|ref|ZP_06873583.1| sporulation sigma factor SigG [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|305674264|ref|YP_003865936.1| sporulation-specific sigma factor sigma-G [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|296151753|gb|EFG92628.1| sporulation sigma factor SigG [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|305412508|gb|ADM37627.1| sporulation-specific sigma factor sigma-G [Bacillus subtilis subsp.
           spizizenii str. W23]
          Length = 260

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 61/262 (23%), Positives = 120/262 (45%), Gaps = 16/262 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+ +E   L ++ ++ GD SA  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKNEEMRKLFRQLQDEGDDSAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 74

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD     + +TY++  I   ++ Y LR  + +++  +          + L+ 
Sbjct: 75  GLMKSIDNFDLSHNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSLRD----IAYKALQV 129

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + I++ + +P     IAK L V   E++     +    SL   I +   +     D +
Sbjct: 130 RERLISETSKEP-TAEDIAKVLEVPHEEIVFALDAIQDPVSLFEPIYNDGGDPIYVMDQI 188

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             + +   Q + E          L   M  LN RE+ I   R  Q    T   ++ E  +
Sbjct: 189 SDERNKDSQWIEEL--------ALKEGMRRLNDREKMILRKRFFQGK--TQMEVAEEIGI 238

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+ +V ++E  A K++ ++I +
Sbjct: 239 SQAQVSRLEKAAIKQMNKNIHQ 260


>gi|282863440|ref|ZP_06272499.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
 gi|282561775|gb|EFB67318.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
          Length = 288

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 63/237 (26%), Positives = 106/237 (44%), Gaps = 23/237 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +   
Sbjct: 67  LIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTVVGE 126

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL   L +    L    D +     V  +AK L VSE 
Sbjct: 127 IKRFFRDTSWS-VRVPRRLQELRL--ALTKASDELAQKLDRS---PTVPELAKALGVSEE 180

Query: 172 EVIS----MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +V+      N   A   SL++     D       D L Y+    E V    E R++ + +
Sbjct: 181 DVVDGLAVGNAYTA--SSLDSPSPEDDGGEGSLADRLGYEDAALEGV----EYRESLKPL 234

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L +    L PRER+I   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 235 LAK----LPPRERQIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLTQLREGL 285


>gi|266626024|ref|ZP_06118959.1| RNA polymerase sigma-E factor [Clostridium hathewayi DSM 13479]
 gi|288862073|gb|EFC94371.1| RNA polymerase sigma-E factor [Clostridium hathewayi DSM 13479]
          Length = 246

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 66/267 (24%), Positives = 113/267 (42%), Gaps = 65/267 (24%)

Query: 22  EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           +I   P+  + E  V+A    E  D SA   L+  +LRLVV IA  +    + + +++S 
Sbjct: 37  DILPAPLDNESEARVIAMLGGED-DQSAKSELIEHNLRLVVYIAKKFDNTSVGVEDLISI 95

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           G IGL++A+  F+P +  +LATY+   I+  +  Y                      LRR
Sbjct: 96  GTIGLIKAINTFNPGKNIKLATYASRCIENEILMY----------------------LRR 133

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
                      N K +  V+I + LNV                         D N     
Sbjct: 134 -----------NNKTKMEVSIDEPLNV-----------------------DWDGNELLLS 159

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR----RLQENPVTLEN 257
           D L  D D    V+ +  E +  RN+L  ++S L+PRER+I E R      +   +T + 
Sbjct: 160 DILGTDED----VIYKDLETEVERNLLNSAISRLSPRERKIVELRFGLSDEEGEEMTQKE 215

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESI 284
           ++    +S+  + ++E +  K++++ I
Sbjct: 216 VADLLGISQSYISRLEKKIMKRLKKEI 242


>gi|167770711|ref|ZP_02442764.1| hypothetical protein ANACOL_02057 [Anaerotruncus colihominis DSM
           17241]
 gi|167667306|gb|EDS11436.1| hypothetical protein ANACOL_02057 [Anaerotruncus colihominis DSM
           17241]
          Length = 263

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 64/273 (23%), Positives = 124/273 (45%), Gaps = 44/273 (16%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+ +L+++E+  L K+ R+ GD  A   ++  +LRLV+ +   +   G  + ++   G I
Sbjct: 22  KLTVLKEKEKIELLKKIRQ-GDQKARQEMINGNLRLVLSVVQKFTNRGENLDDLFQVGCI 80

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FDP +  R +TY +  I   ++ + LR  + V++  +   + L +   + K 
Sbjct: 81  GLIKAIDNFDPNQNVRFSTYGVPMIIGEIRRH-LRDNNSVRVSRSL--RDLAYKAMQAK- 136

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA------------GDESLNALINS 192
             +A+ + N K   V  IAK++   + +V+     +             G +++  +   
Sbjct: 137 --EALINRNSKEPTVEEIAKEMGAKKEDVVLALEAIVEPMSLYDPVYSDGGDTIYVMDQI 194

Query: 193 SDKNS-SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
            DKNS S W D +V+           +E  KN           L  RE++I   R     
Sbjct: 195 GDKNSESDWMDEIVF-----------REAMKN-----------LGDREKQILSLRFF--G 230

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             T   ++ E  +S+ +V ++E  A   V++ I
Sbjct: 231 GKTQMEVAKEIGISQAQVSRLEKGALDWVKKHI 263


>gi|78043932|ref|YP_360874.1| sporulation sigma factor SigG [Carboxydothermus hydrogenoformans
           Z-2901]
 gi|77996047|gb|ABB14946.1| RNA polymerase sigma-G factor [Carboxydothermus hydrogenoformans
           Z-2901]
          Length = 257

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 65/265 (24%), Positives = 123/265 (46%), Gaps = 41/265 (15%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L  QE   L  + +E GD+ A  +L++ +LRLV+ I   +   G  + ++   G I
Sbjct: 15  KLPVLTNQEMKKLFLKVKE-GDMEARQKLISGNLRLVLSIIQRFTNRGEYVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD E+  + +TY++  I   ++ Y LR  + +++  +         LR +  
Sbjct: 74  GLIKAIDNFDLEQNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRS---------LRDVAY 123

Query: 145 HLQAITDNNL----KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
               + DN +    +   V  IA++L V + EV+          +L+A+ +        +
Sbjct: 124 KALQVRDNLVGRFSREPTVSEIAQELKVPQEEVVF---------ALDAIQDPVSLFEPIY 174

Query: 201 QDWLVYDHDGQEQVLIE---KEERKNRRN-----MLTRSMSVLNPRERRIFEARRLQENP 252
           Q       DG + + +    K+E+    N      L  ++  LN RER I +  R  E  
Sbjct: 175 Q-------DGGDPIFVMDQIKDEKNTDHNWLQGIALKEALERLNERERLILKL-RFYEGK 226

Query: 253 VTLENLSSEFEVSRERVRQIEARAF 277
             +E ++ E  +S+ +V ++E  A 
Sbjct: 227 TQME-VAEEIGISQAQVSRLEKAAL 250


>gi|326204637|ref|ZP_08194493.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium papyrosolvens
           DSM 2782]
 gi|325985204|gb|EGD46044.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium papyrosolvens
           DSM 2782]
          Length = 243

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 31/94 (32%), Positives = 53/94 (56%), Gaps = 2/94 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+   +E Y+L K   E  D      L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 42  PLTLDEETYLLNKL--EQSDYGVKSILIERNLRLVVYIARKFENTGVGVEDLISIGTIGL 99

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++A+  F+P +  +LATY+   I+  +  Y+ R+
Sbjct: 100 IKAINTFNPSKNIKLATYASRCIENEILMYLRRN 133


>gi|167757711|ref|ZP_02429838.1| hypothetical protein CLOSCI_00041 [Clostridium scindens ATCC 35704]
 gi|167664593|gb|EDS08723.1| hypothetical protein CLOSCI_00041 [Clostridium scindens ATCC 35704]
          Length = 208

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 32/84 (38%), Positives = 49/84 (58%), Gaps = 2/84 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+   +E Y + K Y E GDL A H L+  +LRLV  I   Y+ +     +++S G IGL
Sbjct: 10  PLTAAEERYYMQK-YTE-GDLEAKHILIERNLRLVAHIVKKYQSFEEDTEDLLSIGTIGL 67

Query: 87  MQAVKKFDPERGFRLATYSMWWIK 110
           ++AV  F+P++  RL TY+   I+
Sbjct: 68  IKAVVTFNPDKCVRLGTYAARCIE 91


>gi|291561536|emb|CBL40335.1| RNA polymerase, sigma subunit, RpsG/SigG [butyrate-producing
           bacterium SS3/4]
          Length = 258

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 58/264 (21%), Positives = 123/264 (46%), Gaps = 31/264 (11%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L  +E+  L +R  ++GD  A    +  +LRLV+ +   + G    + ++   G I
Sbjct: 15  KLPLLTNEEKTDLFRRI-QNGDTDARETYIKGNLRLVLSVIQRFSGSSENLDDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD  +  + +TY++  I   ++ Y LR  + +++      + L     +   
Sbjct: 74  GLIKAIDNFDLSQNVKFSTYAVPMILGEVRRY-LRDNNSIRV-----SRSLRDTAYKALS 127

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + +T  NL+   ++ IA ++ +S+ E+                +++     S ++   
Sbjct: 128 ARELLTKRNLREPTIMEIADEVGISKEEI-------------TYAMDAIQSPVSLYEP-- 172

Query: 205 VYDHDGQEQVLIEK-EERKNRRN------MLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           VY   G    ++++  ++KNR         L+ +M  L  RERRI + R  +    T   
Sbjct: 173 VYTDGGDPLCVMDQISDKKNREENWVEQLSLSEAMKRLPARERRIIDMRFFEGKTQT--E 230

Query: 258 LSSEFEVSRERVRQIEARAFKKVQ 281
           ++ E  +S+ +V ++E  A K ++
Sbjct: 231 VAGEVGISQAQVSRLEKNALKAMK 254


>gi|154685949|ref|YP_001421110.1| sporulation sigma factor SigG [Bacillus amyloliquefaciens FZB42]
 gi|154351800|gb|ABS73879.1| SigG [Bacillus amyloliquefaciens FZB42]
          Length = 260

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 61/262 (23%), Positives = 121/262 (46%), Gaps = 16/262 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+ +E   L ++ ++ GD SA  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKNEEMRKLFRQLQDEGDDSAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 74

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD     + +TY++  I   ++ Y LR  + +++  +   + + +   +++ 
Sbjct: 75  GLMKSIDNFDLSHNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSL--RDIAYKALQVRE 131

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L + T      E+   IAK L V   E++     +    SL   I +   +     D +
Sbjct: 132 RLISETSREPTAEE---IAKVLEVPHEEIVFALDAIQDPVSLFEPIYNDGGDPIYVMDQI 188

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             + +   Q + E          L   M  LN RE+ I   R  Q    T   ++ E  +
Sbjct: 189 SDERNKDTQWIEEL--------ALKEGMRRLNEREKMILRKRFFQGK--TQMEVAEEIGI 238

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+ +V ++E  A K++ ++I +
Sbjct: 239 SQAQVSRLEKAAIKQMNKNIHQ 260


>gi|154503852|ref|ZP_02040912.1| hypothetical protein RUMGNA_01678 [Ruminococcus gnavus ATCC 29149]
 gi|153795451|gb|EDN77871.1| hypothetical protein RUMGNA_01678 [Ruminococcus gnavus ATCC 29149]
          Length = 246

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 31/94 (32%), Positives = 53/94 (56%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE + E  + +R     D  A   L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 41  PPLETERETEVIRRLGSEYDQEAKKMLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGL 100

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++A+  F+P +  +LATY+   I+  +  Y+ R+
Sbjct: 101 IKAINTFNPTKKIKLATYASRCIENEILMYLRRN 134


>gi|283798349|ref|ZP_06347502.1| RNA polymerase sigma-E factor [Clostridium sp. M62/1]
 gi|291073934|gb|EFE11298.1| RNA polymerase sigma-E factor [Clostridium sp. M62/1]
 gi|295092808|emb|CBK78915.1| RNA polymerase, sigma 29 subunit, SigE [Clostridium cf.
           saccharolyticum K10]
          Length = 246

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 69/269 (25%), Positives = 114/269 (42%), Gaps = 65/269 (24%)

Query: 22  EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           +I   P+  K+E  VL +   E  D  A  RL+  +LRLVV IA  +    + + +++S 
Sbjct: 37  DILPAPLDSKEEAEVLGELGTEK-DREAKSRLIEHNLRLVVYIAKKFDNTSVGVEDLISI 95

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           G IGL++A+  F+  +  +LATY+   I+  +  Y                      LRR
Sbjct: 96  GTIGLIKAINTFNTGKNIKLATYASRCIENEILMY----------------------LRR 133

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
                      N K +  V+I + LNV                         D N     
Sbjct: 134 -----------NNKTKLEVSIDEPLNV-----------------------DWDGNELLLS 159

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QEN--PVTLEN 257
           D L  D D    V+    E +  RN+L  ++S LNPRE++I E R     EN   +T + 
Sbjct: 160 DILGTDED----VIYRDLEDEIERNLLNTAISRLNPREKKIVELRFGLNSENGEEMTQKE 215

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ++    +S+  + ++E +  K++++ I K
Sbjct: 216 VADLLGISQSYISRLEKKIMKRLKKEIVK 244


>gi|220929479|ref|YP_002506388.1| sporulation sigma factor SigE [Clostridium cellulolyticum H10]
 gi|219999807|gb|ACL76408.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium cellulolyticum
           H10]
          Length = 243

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 31/94 (32%), Positives = 53/94 (56%), Gaps = 2/94 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+   +E Y+L K   E  D      L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 42  PLTLDEETYLLNKL--EQSDYGVKSILIERNLRLVVYIARKFENTGVGVEDLISIGTIGL 99

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++A+  F+P +  +LATY+   I+  +  Y+ R+
Sbjct: 100 IKAINTFNPSKNIKLATYASRCIENEILMYLRRN 133


>gi|312793875|ref|YP_004026798.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
 gi|312181015|gb|ADQ41185.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
          Length = 240

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 60/243 (24%), Positives = 112/243 (46%), Gaps = 24/243 (9%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           ++GD  A  +L+ S+L LV  +   +   G+ + ++   G IGL++AV +FDP    R +
Sbjct: 14  KNGDKLARQQLIESNLALVWSVVKKFAAKGVELEDLFQIGCIGLIKAVDRFDPSFNVRFS 73

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
           TY++  I   ++ Y LR    +K+      NQ +    +++L+   Q ++ N  +P  + 
Sbjct: 74  TYAVPMIIGEIKRY-LRDDGKIKVSRKIKENQSK----IKKLRN--QFVSSNGREP-TIS 125

Query: 161 AIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            I++   +S  E++   C  A  E  SLN ++N  +       D    + D   ++L   
Sbjct: 126 EISQLTGLSSDEILL--CMDATSEVASLNDVVNQEEGKPITLMDIASDEEDYSTKLL--- 180

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                    L   +  L  RER I   R  +    T   ++ E  +S+  V +IE RA +
Sbjct: 181 -----DLMALKEGLKKLKGRERYIIFMRYFKNK--TQSEIAKELNISQVHVSRIEKRALE 233

Query: 279 KVQ 281
           +++
Sbjct: 234 RIK 236


>gi|169834796|ref|YP_001715634.1| RNA polymerase sigma-E factor [Clostridium botulinum A3 str. Loch
           Maree]
 gi|169408903|gb|ACA57313.1| RNA polymerase sigma-E factor [Clostridium botulinum A3 str. Loch
           Maree]
          Length = 296

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 51/242 (21%), Positives = 113/242 (46%), Gaps = 39/242 (16%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           + L+  +  L+ K+A  Y+   + + ++  +G +G ++AV KFD  +  + +TY+ +WI+
Sbjct: 88  NSLIEKNQNLIFKVANKYKNKNIELQDLTQQGFLGFLKAVDKFDESKKVKFSTYAYYWIE 147

Query: 111 AAMQEYI-LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           A +  +        + I ++       +  R+LKG+   I   +  PE V    +  N S
Sbjct: 148 AEISSFFNFNVDGSLSISSS-------YQHRKLKGYENGILSEDELPELVKNHIQLKNNS 200

Query: 170 ESEVISMNCRLAGDESLNA---LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
               IS++  + G E+ N+   L+  +D N +  +  +V                     
Sbjct: 201 ----ISVDSIVHGKENENSADYLLGKTDINYNNIESKIV--------------------- 235

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++S L+ +E+ I  +R + E     ++++ EF+VS + ++ +   A  K++ +I+K
Sbjct: 236 -MKNALSGLSEKEKSIIISRIIYEKK--YKDIAKEFKVSYQYIQYLYKNAIGKLKRTIKK 292

Query: 287 QV 288
            +
Sbjct: 293 DI 294


>gi|30266017|gb|AAN16086.1| SigB [Listeria welshimeri]
          Length = 259

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 63/264 (23%), Positives = 128/264 (48%), Gaps = 26/264 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+G+  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQENGNQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +++D   G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEEL 125

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDW 203
           T       Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D 
Sbjct: 126 TRELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDV 182

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    DG E+V        N+R +L + + VL+ RE+ I +   ++    + +      +
Sbjct: 183 VGGTDDGFERV--------NQRMLLEKVLPVLDEREQMILQYTFIENR--SQKETGELLD 232

Query: 264 VSRERVRQIEARAFKKVQESIQKQ 287
           +S+  V +I+ +A KK++E++Q +
Sbjct: 233 ISQMHVSRIQRQAIKKLREALQNE 256


>gi|23978358|dbj|BAC21144.1| principal sigma factor [Nodularia sp. PCC 73104]
          Length = 188

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 52/199 (26%), Positives = 100/199 (50%), Gaps = 19/199 (9%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL   +++ EG++GL++A +KFD E+G+R +TY+ WWI+ A+   I      +++     
Sbjct: 4   GLSFQDLIQEGSLGLIRAAEKFDHEKGYRFSTYATWWIRQAITRAIADQSRTIRLPV--- 60

Query: 132 QKRLFFNLRRLKGHLQAIT-DNNLKP-EQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
              L+  + R+K   + ++ +   KP E+ +A   ++ + +   I+ + +L    SL   
Sbjct: 61  --HLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPI--SLETP 116

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFEARRL 248
           I   +   S+  D++  + DG+     E +  KN  R  L + +  L+PRER +   R  
Sbjct: 117 IGKEE--DSRLGDFI--ESDGETP---EDQVSKNLLREDLEKVLDSLSPRERDVLRLRYG 169

Query: 249 QENP--VTLENLSSEFEVS 265
            ++    TLE +   F V+
Sbjct: 170 LDDGRMKTLEEIGQIFNVT 188


>gi|311068054|ref|YP_003972977.1| sporulation sigma factor SigG [Bacillus atrophaeus 1942]
 gi|310868571|gb|ADP32046.1| sporulation sigma factor SigG [Bacillus atrophaeus 1942]
          Length = 260

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 61/262 (23%), Positives = 120/262 (45%), Gaps = 16/262 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+ +E   L ++ ++ GD SA  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKNEEMRKLFRQLQDEGDDSAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 74

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD     + +TY++  I   ++ Y LR  + +++  +          + L+ 
Sbjct: 75  GLMKSIDNFDLSHNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSLRD----IAYKALQV 129

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + I++ + +P     IAK L V   E++     +    SL   I +   +     D +
Sbjct: 130 RERLISETSKEP-TAEDIAKVLEVPHEEIVFALDAIQDPVSLFEPIYNDGGDPIYVMDQI 188

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             + +   Q + E          L   M  LN RE+ I   R  Q    T   ++ E  +
Sbjct: 189 SDERNKDTQWIEEL--------ALKEGMRRLNDREKMILRKRFFQGK--TQMEVAEEIGI 238

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+ +V ++E  A K++ ++I +
Sbjct: 239 SQAQVSRLEKAAIKQMNKNIHQ 260


>gi|158320682|ref|YP_001513189.1| FliA/WhiG family RNA polymerase sigma factor [Alkaliphilus
           oremlandii OhILAs]
 gi|158140881|gb|ABW19193.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           oremlandii OhILAs]
          Length = 176

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 36/96 (37%), Positives = 51/96 (53%), Gaps = 2/96 (2%)

Query: 16  LSRYIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           L  YI      P  L  +EE +  +RY E GD  A + LV  +LRLV  I   Y   G  
Sbjct: 18  LVSYISSTTSFPQPLTAEEESMYLERY-EQGDEEARNILVERNLRLVAHIVKKYSNIGRD 76

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           + +++S G IGL++ +  FD  +G RLATY+   I+
Sbjct: 77  MDDLISIGTIGLIKGITTFDRSKGTRLATYAARCIE 112


>gi|86742435|ref|YP_482835.1| sigma 28 subunit [Frankia sp. CcI3]
 gi|86569297|gb|ABD13106.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Frankia sp. CcI3]
          Length = 338

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 66/241 (27%), Positives = 114/241 (47%), Gaps = 30/241 (12%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +LV  HL LV  +A  +R  G P+ ++V    IGL+++V +FDPERG   +TY+   I  
Sbjct: 116 QLVRMHLPLVEYLARRFRNRGEPLDDLVQVATIGLIKSVDRFDPERGVEFSTYATPTIVG 175

Query: 112 AMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT---DNNLKPEQVVA-IAKKL 166
            ++ +   + W++          R+   L+ LK  L   T      L     V+ IA+ L
Sbjct: 176 EIKRHFRDKGWAI----------RVPRRLQELKLSLTKATSELSQTLGRSPTVSEIARHL 225

Query: 167 NVSESEVISMNCRLAGDESLNA--LINSSDKNSSQWQDWLVYDHDG-QEQVLIEKEERKN 223
            +SE +V      L G ES NA   ++    +S   +   V D  G Q++ L   E R++
Sbjct: 226 QMSEDDV------LEGLESANAYSAVSLDAPDSGDDEAPAVADTLGVQDESLEGVEYRES 279

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            + +L +    L  RE+RI   R      +T   +++E  +S+  V ++ AR   +++  
Sbjct: 280 LKPLLEK----LPAREKRILLLRFFGN--MTQSQIATELGISQMHVSRLLARTLAQLRRG 333

Query: 284 I 284
           +
Sbjct: 334 L 334


>gi|303238907|ref|ZP_07325438.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302593540|gb|EFL63257.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 244

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 31/94 (32%), Positives = 53/94 (56%), Gaps = 2/94 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+   +E Y+L K   E  D      L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 42  PLSNDEESYLLNKL--EKNDYGVKTILIERNLRLVVYIARKFENTGVGVEDLISIGTIGL 99

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++A+  F+P +  +LATY+   I+  +  Y+ R+
Sbjct: 100 IKAINTFNPSKNIKLATYASRCIENEILMYLRRN 133


>gi|325662349|ref|ZP_08150958.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium 4_1_37FAA]
 gi|331086152|ref|ZP_08335234.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|325471351|gb|EGC74574.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium 4_1_37FAA]
 gi|330406311|gb|EGG85825.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 247

 Score = 58.5 bits (140), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 37/112 (33%), Positives = 60/112 (53%), Gaps = 6/112 (5%)

Query: 14  IGLSRYIH-----EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           IG  R IH     E+   P LE +EE  + K      +  A   L+  +LRLVV IA  +
Sbjct: 24  IGTRREIHYIGGSEVLPAP-LEMEEESAVIKELATEYNEKAKKVLIEHNLRLVVYIAKKF 82

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
              G+ + +++S G IGL++A+  F+P +  +LATY+   I+  +  Y+ R+
Sbjct: 83  DNTGIGVEDLISIGTIGLIKAINTFNPTKKIKLATYASRCIENEILMYLRRN 134


>gi|239989259|ref|ZP_04709923.1| RNA polymerase sigma factor, sigma L [Streptomyces roseosporus NRRL
           11379]
          Length = 288

 Score = 58.2 bits (139), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 63/237 (26%), Positives = 106/237 (44%), Gaps = 23/237 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +   
Sbjct: 67  LIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTVVGE 126

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL   L +    L    D +     V  +A+ L VSE 
Sbjct: 127 IKRFFRDTSWS-VRVPRRLQELRL--ALTKTSDELAQKLDRS---PTVPELARALGVSEE 180

Query: 172 EVIS----MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +VI      N   A   SL++     D       D L Y+    E V    E R++ + +
Sbjct: 181 DVIDGLAVGNAYTA--SSLDSPSPEDDGGEGSLADRLGYEDTALEGV----EYRESLKPL 234

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L +    L PRER+I   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 235 LAK----LAPRERQIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 285


>gi|150015999|ref|YP_001308253.1| sporulation sigma factor SigK [Clostridium beijerinckii NCIMB 8052]
 gi|149902464|gb|ABR33297.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           beijerinckii NCIMB 8052]
          Length = 232

 Score = 58.2 bits (139), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 35/105 (33%), Positives = 60/105 (57%), Gaps = 3/105 (2%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           + +I+N  + L+ Y+      P+ L++ EE +  K+++E GD +A   L+  +LRLV  I
Sbjct: 8   IDLILNS-LFLTGYVTNNNTFPLPLDETEEQMYLKKFKE-GDKNAKSILIERNLRLVAHI 65

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              Y      + E++S G +GL++A+  FD  +G RLATY+   I
Sbjct: 66  VKKYSFPNKDVDELISIGTVGLIKAIDSFDAGKGTRLATYASRCI 110


>gi|153953960|ref|YP_001394725.1| sporulation sigma factor SigK [Clostridium kluyveri DSM 555]
 gi|219854574|ref|YP_002471696.1| hypothetical protein CKR_1231 [Clostridium kluyveri NBRC 12016]
 gi|146346841|gb|EDK33377.1| SigE1 [Clostridium kluyveri DSM 555]
 gi|219568298|dbj|BAH06282.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 233

 Score = 58.2 bits (139), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 32/83 (38%), Positives = 48/83 (57%), Gaps = 2/83 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ +++E Y L  R  + GDL A   LV  +LRLV  I   Y   G  + +++S G +GL
Sbjct: 30  PLNDEEERYYL--RKLKEGDLLAKSILVERNLRLVAHIVKKYSYPGKDVDDLISIGTVGL 87

Query: 87  MQAVKKFDPERGFRLATYSMWWI 109
           ++A+  FD  +G RLATY+   I
Sbjct: 88  IKAIDSFDSCKGTRLATYAAKCI 110


>gi|138894662|ref|YP_001125115.1| sporulation sigma factor SigE [Geobacillus thermodenitrificans
           NG80-2]
 gi|196247723|ref|ZP_03146425.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
 gi|134266175|gb|ABO66370.1| RNA polymerase sigma-E factor [Geobacillus thermodenitrificans
           NG80-2]
 gi|196212507|gb|EDY07264.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
          Length = 239

 Score = 58.2 bits (139), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 48/76 (63%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL++AV  F+PE+  +LATY
Sbjct: 54  GDKTARSLLIERNLRLVVYIARKFENTGIHIEDLISIGTIGLIKAVNTFNPEKKIKLATY 113

Query: 105 SMWWIKAAMQEYILRS 120
           +   I+  +  Y+ R+
Sbjct: 114 ASRCIENEILMYLRRN 129


>gi|225568655|ref|ZP_03777680.1| hypothetical protein CLOHYLEM_04733 [Clostridium hylemonae DSM
           15053]
 gi|225162583|gb|EEG75202.1| hypothetical protein CLOHYLEM_04733 [Clostridium hylemonae DSM
           15053]
          Length = 246

 Score = 58.2 bits (139), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 34/99 (34%), Positives = 55/99 (55%), Gaps = 1/99 (1%)

Query: 22  EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           EI   P LE +EE  +        D  A   L+  +LRLVV IA  +   G+ + +++S 
Sbjct: 37  EILPAP-LEAEEESAVINDLGSEYDEKAKKVLIEHNLRLVVYIAKKFDNTGVGVEDLISI 95

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           G IGL++A+  F+PE+  +LATY+   I+  +  Y+ R+
Sbjct: 96  GTIGLIKAINTFNPEKNIKLATYASRCIENEILMYLRRN 134


>gi|2660755|gb|AAC29510.1| sigma-B general stress transcription factor [Bacillus
           licheniformis]
          Length = 265

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 64/267 (23%), Positives = 128/267 (47%), Gaps = 26/267 (9%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K   L K E   L K+Y++  D  A   LV ++  LV  +A  Y        ++   G +
Sbjct: 8   KTTKLTKTEVDTLIKKYQDSQDEDAQLTLVQTYKNLVETLAKKYSKGKSFHEDLCQVGML 67

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLK 143
           GL+ A+K++DP+ G     +++  I   ++ ++  ++WS+         +R+     R+K
Sbjct: 68  GLLGAIKRYDPDVGKSFEAFAIPTIIGEIKRFLRDKTWSV------HVPRRIKELGPRIK 121

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNS 197
             +  +T+   +  +V  IA+ L+V+E EV+ +M        L+ D S+ A    +D ++
Sbjct: 122 MAVDHLTNETQRSPKVDEIAEFLDVTEEEVLETMEMGKSYQALSVDHSIEA---DADGST 178

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
               D +    +G E+V        N++ ML   + VL+ RE++I E   +Q    + + 
Sbjct: 179 VTILDIVGSQEEGYEKV--------NQKLMLESVLHVLSDREKQIIELTYIQNK--SQKE 228

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESI 284
                 +S+  V +++ +A KK++E++
Sbjct: 229 TGDMLGISQMHVSRLQRKAVKKLREAL 255


>gi|332653441|ref|ZP_08419186.1| RNA polymerase sigma-E factor [Ruminococcaceae bacterium D16]
 gi|332518587|gb|EGJ48190.1| RNA polymerase sigma-E factor [Ruminococcaceae bacterium D16]
          Length = 239

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 37/105 (35%), Positives = 59/105 (56%), Gaps = 2/105 (1%)

Query: 19  YIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           YI     +P  L ++EE  L +R  + GD  A   L+  +LRLVV IA  +   G+ I +
Sbjct: 28  YIGGSDTLPTPLSREEEGELMERL-QQGDQRARQTLIEHNLRLVVYIARRFENTGINIED 86

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           ++S G IGL++AV  + P R  +LATY+   I+  +  Y+ ++ S
Sbjct: 87  LISIGTIGLIKAVGTYQPARSIKLATYASRCIENEILMYLRKTSS 131


>gi|21222437|ref|NP_628216.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
 gi|256786489|ref|ZP_05524920.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
 gi|289770380|ref|ZP_06529758.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
 gi|13122198|emb|CAC32374.1| putative RNA polymerase sigma factor [Streptomyces coelicolor
           A3(2)]
 gi|289700579|gb|EFD68008.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
          Length = 318

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 63/237 (26%), Positives = 105/237 (44%), Gaps = 23/237 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +   
Sbjct: 97  LIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTVVGE 156

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL   L +    L    D +     V  +A  L VSE 
Sbjct: 157 IKRFFRDTSWS-VRVPRRLQELRL--ALTKASDELSQKLDRS---PTVGELAAVLGVSEE 210

Query: 172 EVIS----MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +V+      N   A   SL++     D       D L Y+    E V    E R++ + +
Sbjct: 211 DVVDGLAVGNAYTA--SSLDSPAPEDDGGEGSLADRLGYEDTALEGV----EYRESLKPL 264

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L +    L PRERRI   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 265 LAK----LPPRERRIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLSQLREGL 315


>gi|325265256|ref|ZP_08131981.1| RNA polymerase sigma-G factor [Clostridium sp. D5]
 gi|324029435|gb|EGB90725.1| RNA polymerase sigma-G factor [Clostridium sp. D5]
          Length = 259

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 65/263 (24%), Positives = 122/263 (46%), Gaps = 35/263 (13%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+++E+  L  R +  GD  A    +  +LRLV+ +   +        ++   G +
Sbjct: 15  KLPLLKEEEKEALFTRIK-AGDEEAREEYIKGNLRLVLSVIKRFSNSNENADDLFQIGCV 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT---ANQKRLFFNLRR 141
           GLM+AV  FDP R  + +TY++  I   ++ Y LR  + +++  +      K ++     
Sbjct: 74  GLMKAVDHFDPNRLVKFSTYAVPMIIGEIRRY-LRDNNSIRVSRSLRDTAYKAIYAKEGY 132

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL------AGDESLNALINSSDK 195
           +K HL+  T   +  E  + I+K+  V   + I M   L       G ++L  +   SDK
Sbjct: 133 MKKHLKEPTVQEIAEE--IGISKEDIVFALDAIQMPMSLHEPVYSDGGDTLYVMDQVSDK 190

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
            + + ++W+       E++ +E             +M  LN RER I    R  E    +
Sbjct: 191 KNKE-ENWV-------EELSLEA------------AMERLNERERYII-TLRFFEGKTQM 229

Query: 256 ENLSSEFEVSRERVRQIEARAFK 278
           E ++ E ++S+ +V ++E  A K
Sbjct: 230 E-VAEEIKISQAQVSRLEKNALK 251


>gi|197723821|gb|ACH72690.1| RNA polymerase sigma-37 factor [Listeria marthii]
          Length = 238

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 62/256 (24%), Positives = 123/256 (48%), Gaps = 26/256 (10%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTREL 115

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +   
Sbjct: 116 QSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGT 172

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            DG E+V        N+R +L + + VL+ RE++I +   ++    + +      ++S+ 
Sbjct: 173 DDGFERV--------NQRMLLEKVLPVLDEREQKILQYTFIENR--SQKETGELLDISQM 222

Query: 268 RVRQIEARAFKKVQES 283
            V +I+ +A KK++E+
Sbjct: 223 HVSRIQRQAIKKLREA 238


>gi|167628365|ref|YP_001678864.1| RNA polymerase sigma-k factor, putative [Heliobacterium
           modesticaldum Ice1]
 gi|167591105|gb|ABZ82853.1| RNA polymerase sigma-k factor, putative [Heliobacterium
           modesticaldum Ice1]
          Length = 233

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 31/84 (36%), Positives = 51/84 (60%), Gaps = 2/84 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ + +E Y LA R +E GD  A ++L+  +LRLV  +   + G G    +++S G IGL
Sbjct: 32  PLSDTEEAYCLA-RLKE-GDEQARNKLIEHNLRLVAHLVKKFDGTGENNDDLISIGTIGL 89

Query: 87  MQAVKKFDPERGFRLATYSMWWIK 110
           ++A+  FD  +G +LATY+   I+
Sbjct: 90  IKAINTFDASKGTKLATYAARCIE 113


>gi|238924602|ref|YP_002938118.1| sporulation sigma factor SigE [Eubacterium rectale ATCC 33656]
 gi|238876277|gb|ACR75984.1| sporulation sigma factor SigE [Eubacterium rectale ATCC 33656]
          Length = 244

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 58/242 (23%), Positives = 106/242 (43%), Gaps = 64/242 (26%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L+  +LRLVV +A  +   G+ + +++S G IGL++ +  F+PE+  +LATY+   
Sbjct: 61  AKKQLIEHNLRLVVYLAKKFENTGVCVEDLISIGTIGLIKGINTFNPEKKIKLATYASRC 120

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +  Y                      LRR         +N +K E           
Sbjct: 121 IENEILMY----------------------LRR---------NNRVKLE----------- 138

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
                      ++ DE LN      D N     D L  D D    V+ +  E +   ++L
Sbjct: 139 -----------VSFDEPLNT---DWDGNELLLSDILGTDED----VIYKDLETEVEISLL 180

Query: 229 TRSMSVLNPRERRIFEAR----RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            ++M  LN RER+I E R    R++   +T + ++    +S+  + ++E +  +++++ I
Sbjct: 181 KKAMLSLNERERQIIELRFGVNRVENKELTQKEVADILGISQSYISRLEKKIMERLKKEI 240

Query: 285 QK 286
           QK
Sbjct: 241 QK 242


>gi|15895412|ref|NP_348761.1| sigma factor of SigD/WhiG family [Clostridium acetobutylicum ATCC
           824]
 gi|15025135|gb|AAK80101.1|AE007715_6 Sigma factor of SigD/WhiG family [Clostridium acetobutylicum ATCC
           824]
 gi|325509558|gb|ADZ21194.1| Sigma factor of SigD/WhiG family [Clostridium acetobutylicum EA
           2018]
          Length = 241

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 62/212 (29%), Positives = 95/212 (44%), Gaps = 16/212 (7%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           ++V  G IGLM A+KKFD  +G + +TYS   IK AM +  LR  S +  G      R  
Sbjct: 40  DLVGYGMIGLMDALKKFDQSKGMKFSTYSSIRIKGAMIDE-LRKNSPISKGAMDKLNRYN 98

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV--ISMNCRLAGDESLNALINSSD 194
             + RL+  L        +P + + IA  L V   EV  I          SL  LI S D
Sbjct: 99  LVVERLEKELSR------EPTE-LEIASGLGVGRKEVGEIEGYINYISVVSLEDLIFSED 151

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
            +               E+ L EKEE +     L + + +LN ++R +      +   +T
Sbjct: 152 DDMPLIGTIEDEKSPSPEKALEEKEEIE----YLAKGIELLNEKDRMVLSLYYYE--GLT 205

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           L+ + +   VS  RV Q+  RA   +++S++K
Sbjct: 206 LKKIGNILNVSESRVCQLHTRAIMHLRKSLKK 237


>gi|291446269|ref|ZP_06585659.1| sigma L [Streptomyces roseosporus NRRL 15998]
 gi|291349216|gb|EFE76120.1| sigma L [Streptomyces roseosporus NRRL 15998]
          Length = 307

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 62/237 (26%), Positives = 106/237 (44%), Gaps = 23/237 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +   
Sbjct: 86  LIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTVVGE 145

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL   L +    L    D +     V  +A+ L VSE 
Sbjct: 146 IKRFFRDTSWS-VRVPRRLQELRL--ALTKTSDELAQKLDRS---PTVPELARALGVSEE 199

Query: 172 EVIS----MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +V+      N   A   SL++     D       D L Y+    E V    E R++ + +
Sbjct: 200 DVVDGLAVGNAYTA--SSLDSPSPEDDGGEGSLADRLGYEDTALEGV----EYRESLKPL 253

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L +    L PRER+I   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 254 LAK----LAPRERQIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 304


>gi|257470879|ref|ZP_05634969.1| RNA polymerase sigma factor [Fusobacterium ulcerans ATCC 49185]
 gi|317065081|ref|ZP_07929566.1| RNA polymerase sigma factor rpoD [Fusobacterium ulcerans ATCC
           49185]
 gi|313690757|gb|EFS27592.1| RNA polymerase sigma factor rpoD [Fusobacterium ulcerans ATCC
           49185]
          Length = 284

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 34/119 (28%), Positives = 57/119 (47%), Gaps = 9/119 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ E+  + ++  ++E    K  RE    +   +++  +L  V  IA  Y   G+   +V
Sbjct: 61  YLEELSNMEVISDEDENNYLKDLRE----ADKEKVIVKNLNEVASIAFNYVKNGIAYMDV 116

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           V EG +GL++AV  FDP+R      YS +WI   +  YI       K+    N+ + FF
Sbjct: 117 VQEGTVGLIKAVDYFDPDRNGDFKNYSKYWIAREIVLYIEN-----KVADIRNEFKNFF 170


>gi|256396809|ref|YP_003118373.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Catenulispora acidiphila DSM 44928]
 gi|256363035|gb|ACU76532.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Catenulispora acidiphila DSM 44928]
          Length = 353

 Score = 58.2 bits (139), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 61/237 (25%), Positives = 110/237 (46%), Gaps = 30/237 (12%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  HL LV  +A  +R  G P+ ++     IGL+++V +FD ERG   +TY+   +   
Sbjct: 132 LVQMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDTERGVEFSTYATPTVIGE 191

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +   + W+ V++     + RL      L      ++  N +   V  +A+ L +SE 
Sbjct: 192 IKRHFRDKGWA-VRVPRRLQELRL-----SLTSATSELSQRNRRSPTVAELAEYLKISEE 245

Query: 172 EVISMNCRLAGDESLNA-------LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           EV      L G ES NA       +    D++S    D L  + +  E V    E R++ 
Sbjct: 246 EV------LEGLESANAYSTLSLDVSEGGDEDSPAVADSLGSEDEALEGV----EYRESL 295

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           + +L +    L PRE++I   R      +T   ++ E  +S+  V ++ AR  ++++
Sbjct: 296 KPLLEQ----LPPREKKILLLRFFGN--MTQSQIAEEIGISQMHVSRLLARTLEQLR 346


>gi|311898315|dbj|BAJ30723.1| putative RNA polymerase sigma factor [Kitasatospora setae KM-6054]
          Length = 360

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 61/240 (25%), Positives = 112/240 (46%), Gaps = 29/240 (12%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +LV  H+ LV  +A  +R  G P+ ++     IGL+++V +FD ERG   +TY+   I  
Sbjct: 139 QLVRMHIPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDHERGVEFSTYATPTIVG 198

Query: 112 AMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            ++ +   + W+ V++     + RL      L      ++  + +   V  +A+ L +SE
Sbjct: 199 EIKRHFRDKGWA-VRVPRRLQELRL-----SLTTATSELSQRHGRSPTVHELAEHLGISE 252

Query: 171 SEVISMNCRLAGDESLNAL------INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            +V      L G ES NA       +  SD  S    D L    +  E V    E R++ 
Sbjct: 253 EDV------LEGLESANAYSTLSLDVPDSDDESPAVADTLGATDEALEGV----EYRESL 302

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + +L +    L PRE++I   R  +   +T   +++E  +S+  V ++ AR   +++E +
Sbjct: 303 KPLLAQ----LPPREQKILVLRFFRN--MTQSQIAAEVGISQMHVSRLLARTLAQLREKL 356


>gi|1396060|dbj|BAA13043.1| part of principal sigma factor homolog [Synechocystis sp.]
          Length = 186

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 49/198 (24%), Positives = 99/198 (50%), Gaps = 17/198 (8%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+   I      +++     
Sbjct: 2   GLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV--- 58

Query: 132 QKRLFFNLRRLKGHLQAIT-DNNLKP-EQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
              L+  + R+K   + ++ +   KP E+ +A   ++ + +   I+ + +L    SL   
Sbjct: 59  --HLYETISRIKKTTKLLSQEMRRKPTEEEIAEKMEMTIEKLRFIAKSAQLPI--SLETP 114

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   +   S+  D++  D +  E  + +   R++  N+L      L+PRER +   R   
Sbjct: 115 IGKEE--DSRLGDFIEADGETPEDEVSKNLLREDLENVL----DTLSPRERDVLRLRYGL 168

Query: 250 ENP--VTLENLSSEFEVS 265
           ++    TLE +   F V+
Sbjct: 169 DDGRMKTLEEIGQIFNVT 186


>gi|289829788|ref|ZP_06547303.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-3139]
          Length = 158

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 30/75 (40%), Positives = 48/75 (64%), Gaps = 1/75 (1%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKF 93
           + EGN+GL++A +  
Sbjct: 120 IEEGNLGLIRASRSL 134


>gi|299143454|ref|ZP_07036534.1| RNA polymerase sigma-B factor [Peptoniphilus sp. oral taxon 386
           str. F0131]
 gi|298517939|gb|EFI41678.1| RNA polymerase sigma-B factor [Peptoniphilus sp. oral taxon 386
           str. F0131]
          Length = 260

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 65/262 (24%), Positives = 121/262 (46%), Gaps = 20/262 (7%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L+K E   L + Y+ + D      L+  HL +   ++  Y G G+   ++    +IGL+ 
Sbjct: 13  LDKSERKELFEAYKLNKDPEIRDILIEEHLYIAEILSKKYSGRGIDYDDIFQVASIGLIY 72

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSL-VKIGTTANQKRLFFNLRRLKGHL 146
           A+ ++D E+G+  ++++   I   +++Y   + W++ V        K++     +L   L
Sbjct: 73  AIDRYDFEKGYEFSSFATPTIIGEIKKYFRDKGWTIRVPRRIQELSKKINNAKTQLTQEL 132

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWL 204
           Q I         V  IA  L  +  EVI      ++   +SL+    + D N    +  L
Sbjct: 133 QRIP-------TVEDIADYLETTPEEVIEAMEASKVYTPQSLDV---TYDTNGDDKELNL 182

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             D  G+ +   EK E K   + L R+MS LN  ER I   R  ++   T   ++ + ++
Sbjct: 183 A-DLVGENEKYFEKIEMK---DFLERAMSELNDMERTILIERYFEKK--TQVAIAEKLDI 236

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+  + +IE +  KK++E I+K
Sbjct: 237 SQMTISRIEKKVLKKMREEIKK 258


>gi|284033085|ref|YP_003383016.1| B/F/G subfamily RNA polymerase sigma-28 subunit [Kribbella flavida
           DSM 17836]
 gi|283812378|gb|ADB34217.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Kribbella
           flavida DSM 17836]
          Length = 264

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 60/240 (25%), Positives = 110/240 (45%), Gaps = 24/240 (10%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV+ H+ LV  +A  +R  G P  ++V    IGL++A+ +FD +RG   +TY+   I   
Sbjct: 44  LVSLHMPLVEHLARRFRNRGEPYDDLVQVATIGLIKAIDRFDSDRGVEFSTYATPTILGE 103

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ Y   + W+ +++     + RL      L      +T    +   V  ++ +L +S+ 
Sbjct: 104 IKRYFRDKGWA-IRVPRRLQELRL-----SLTAATAELTQELGRAPTVAELSTRLGLSQD 157

Query: 172 EVISMNCRLAGDESLNAL----INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
            VI       G ES NA     +++ D+N +      V D  G E   +E  E    R  
Sbjct: 158 LVIE------GLESANAYNTLSLDAPDQNEADAT--TVLDGLGGEDEALESVE---FRES 206

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   ++ L  RE+RI   R  +   +T   ++ E  +S+  V ++ AR   +++  + K+
Sbjct: 207 LKPLLAQLETREKRILTLRFFR--GMTQSQIAEEIGISQMHVSRLLARTLTELRAGLLKE 264


>gi|226313413|ref|YP_002773307.1| sporulation sigma factor SigG [Brevibacillus brevis NBRC 100599]
 gi|226096361|dbj|BAH44803.1| RNA polymerase sigma-G factor [Brevibacillus brevis NBRC 100599]
          Length = 259

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 62/267 (23%), Positives = 131/267 (49%), Gaps = 29/267 (10%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L  +E   L +R  + G+L+A  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLTNKEMRDLFERL-QSGELAAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A+  FD  +  + +TY++  I   ++ Y LR  + +++  +   + + +   +++ 
Sbjct: 74  GLMKAIDNFDLGQNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSL--RDIAYKALQVRD 130

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW- 203
           +L   T+ + +   ++ I+++LNV++ +V+          +L+A+ +        +QD  
Sbjct: 131 NL---TNKHSREPTIIEISQELNVAKEDVVF---------ALDAIQDPVSLFEPIYQDGG 178

Query: 204 -LVYDHDGQEQVLIEKEERKN----RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
             +Y  D      I  E+ K+        L   M  L  RE+ I  + R  E    +E +
Sbjct: 179 DPIYVMDQ-----ISDEKNKDVTWVEEIALREGMQRLGDREKMIL-SMRFYEGKTQME-V 231

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQ 285
           + E  +S+ +V ++E  A   +Q+ +Q
Sbjct: 232 AEEIGISQAQVSRLEKAAIAHMQKHVQ 258


>gi|83590339|ref|YP_430348.1| sigma 28 (flagella/sporulation) [Moorella thermoacetica ATCC 39073]
 gi|83573253|gb|ABC19805.1| RNA polymerase, sigma subunit, RpoX/SigF [Moorella thermoacetica
           ATCC 39073]
          Length = 270

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 59/263 (22%), Positives = 120/263 (45%), Gaps = 17/263 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           + P+L + E   L +R +  GD  A  RL+  +L+LV  +   +      + ++   G I
Sbjct: 10  RFPLLSEAETDELLRRAK-AGDKEARERLINCNLKLVFNLVQRFEKRNYELEDLFQIGTI 68

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+ KFD     R +TY++  I   ++ + LR  S VK+  +  +     N  R   
Sbjct: 69  GLIKAIDKFDLSYKVRFSTYAVPMILGEIRRF-LRDDSAVKVSRSLKETAFKVNRTR--- 124

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + +     +   +  IA+ L++S  E+I+    +    S++  +   D +     D L
Sbjct: 125 --EELAKKFGREPAIGEIAEALDLSREEIIAALEAVQMPSSIHDTVYQDDGDPIYVLDQL 182

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               DG+E   ++K         L   +  L  + RR+   R  Q+   T   +++   +
Sbjct: 183 A-SEDGEEPEWLDK-------IALKEVLRQLPEKHRRVLVLRFFQDK--TQAEVAARMGL 232

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           S+ ++ +IE +A ++++E +Q +
Sbjct: 233 SQVQISRIERQALQRIRELLQAE 255


>gi|215404668|ref|ZP_03416849.1| RNA polymerase sigma factor [Mycobacterium tuberculosis 02_1987]
 gi|298526173|ref|ZP_07013582.1| hypothetical protein TBAG_01589 [Mycobacterium tuberculosis
           94_M4241A]
 gi|298495967|gb|EFI31261.1| hypothetical protein TBAG_01589 [Mycobacterium tuberculosis
           94_M4241A]
          Length = 197

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 47/201 (23%), Positives = 95/201 (47%), Gaps = 12/201 (5%)

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           ++KFD  +G++ +TY+ WWI+ A+   +      ++I    +   +   L R++  L   
Sbjct: 1   MEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRI--PVHMVEVINKLGRIQRELLQD 58

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
                 PE+   +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D
Sbjct: 59  LGREPTPEE---LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---ED 110

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRE 267
            +  V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RE
Sbjct: 111 SEAVVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRE 170

Query: 268 RVRQIEARAFKKVQESIQKQV 288
           R+RQIE++   K++   + QV
Sbjct: 171 RIRQIESKTMSKLRHPSRSQV 191


>gi|295109522|emb|CBL23475.1| RNA polymerase, sigma 29 subunit, SigE [Ruminococcus obeum A2-162]
          Length = 243

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 32/94 (34%), Positives = 56/94 (59%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  K+E YV++K   E  +  A   L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 39  PLEPKREAYVISKLKTEQ-EQEARSLLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGL 97

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++A+  F+P +  +LATY+   I+  +  Y+ R+
Sbjct: 98  IKAINTFNPVKNIKLATYASRCIENEILMYLRRN 131


>gi|291532045|emb|CBK97630.1| RNA polymerase sigma factor, FliA/WhiG family/RNA polymerase sigma
           factor, sigma-70 family [Eubacterium siraeum 70/3]
          Length = 251

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 45/151 (29%), Positives = 74/151 (49%), Gaps = 15/151 (9%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMG----YRGYGLPISEVVSEGNIGLMQAVKK 92
           L ++YR  GD++  + +V  ++ LV  IA+     Y GY     ++++EG I LM A+  
Sbjct: 12  LLEKYRLTGDMNVRNEIVLMYMDLVKMIAVSMRNIYTGYA-ESDDIINEGVIALMAAIDG 70

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITD 151
           FDPE+  +  TY+   IK A+ +Y LR    V        K+L  N  RL   L +  TD
Sbjct: 71  FDPEKNVKFETYAGIRIKGAVIDY-LRKLDRVPRTLRKLSKQLDDNFARLNSELCRTPTD 129

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
             L        A+ +N++ +++  +    AG
Sbjct: 130 EEL--------AESMNMTTAQLSKLMANTAG 152


>gi|239942800|ref|ZP_04694737.1| RNA polymerase sigma factor, sigma L [Streptomyces roseosporus NRRL
           15998]
          Length = 288

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 62/237 (26%), Positives = 106/237 (44%), Gaps = 23/237 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +   
Sbjct: 67  LIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTVVGE 126

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL   L +    L    D +     V  +A+ L VSE 
Sbjct: 127 IKRFFRDTSWS-VRVPRRLQELRL--ALTKTSDELAQKLDRS---PTVPELARALGVSEE 180

Query: 172 EVIS----MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +V+      N   A   SL++     D       D L Y+    E V    E R++ + +
Sbjct: 181 DVVDGLAVGNAYTA--SSLDSPSPEDDGGEGSLADRLGYEDTALEGV----EYRESLKPL 234

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L +    L PRER+I   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 235 LAK----LAPRERQIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 285


>gi|125975381|ref|YP_001039291.1| RNA polymerase, sigma 28 subunit [Clostridium thermocellum ATCC
           27405]
 gi|281419342|ref|ZP_06250357.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Clostridium
           thermocellum JW20]
 gi|125715606|gb|ABN54098.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Clostridium
           thermocellum ATCC 27405]
 gi|281406962|gb|EFB37225.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Clostridium
           thermocellum JW20]
 gi|316939496|gb|ADU73530.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Clostridium
           thermocellum DSM 1313]
          Length = 252

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 50/251 (19%), Positives = 121/251 (48%), Gaps = 17/251 (6%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L + Y+E   +   +++V+ +L L   +A  +   G+   ++    +I L++AV++FDP+
Sbjct: 18  LFREYKETKSVEVRNKIVSKYLYLSDILAKKFLNRGIDYEDIYQVASIALIKAVERFDPD 77

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +G +  +++   I   ++ Y     S+++I      +R++   +++    +++T    +P
Sbjct: 78  KGVKFISFATPTIIGEIKRYFRDKGSVIRIP-----RRIYEVYQKINHARESLTQELKRP 132

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQVL 215
            ++  +A+ LN+SE  V+ +       ES NA  I S  +N     +  +++  G +   
Sbjct: 133 PRIDELARHLNISEESVVEII------ESYNAYNIQSFSQNVYANDELELHEVIGDQDST 186

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
            E+ E    R+ L +S+   +  E+     R       T ++++ +  VS+  + ++E +
Sbjct: 187 FERIE---NRDFLEKSLDKFSDVEKEFISMRYFDNK--TQKDIAQKMGVSQMYISRLERK 241

Query: 276 AFKKVQESIQK 286
             +K +  + K
Sbjct: 242 VLEKFRRMLAK 252


>gi|297158639|gb|ADI08351.1| RNA polymerase sigma factor, sigma L [Streptomyces bingchenggensis
           BCW-1]
          Length = 276

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 62/237 (26%), Positives = 105/237 (44%), Gaps = 23/237 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +   
Sbjct: 55  LIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTVVGE 114

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL   L +    L    D   +   V  +A  L VSE 
Sbjct: 115 IKRFFRDTSWS-VRVPRRLQELRL--ALTKTSDELSQKLD---RSPTVTELATALGVSEE 168

Query: 172 EVIS----MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +V+      N   A   SL++     D       D L Y+    E V    E R++ + +
Sbjct: 169 DVVDGLAVGNAYTA--SSLDSPSPEDDGGEGSLADRLGYEDSALEGV----EYRESLKPL 222

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L +    L PRER+I   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 223 LAK----LPPRERQIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 273


>gi|291545019|emb|CBL18128.1| RNA polymerase sigma factor, sigma-70 family [Ruminococcus sp.
           18P13]
          Length = 220

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 39/122 (31%), Positives = 65/122 (53%), Gaps = 6/122 (4%)

Query: 57  HLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           +L LV   A  +RG G+   ++ S G IGLM+AV  FD ERG R +TY++  I   ++  
Sbjct: 13  NLGLVHLCANRFRGRGVEYDDLYSAGCIGLMKAVNAFDTERGVRFSTYAVPVILGEIKR- 71

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
           + R    VK+  + + K L   + RL+  L+     + K   V  +A+++ V E+E++  
Sbjct: 72  LFRDGGTVKV--SRSMKELSMRVVRLRDELRM---QSGKEPTVQQLAREMGVEEAEIVQA 126

Query: 177 NC 178
            C
Sbjct: 127 LC 128


>gi|254519266|ref|ZP_05131322.1| sporulation sigma factor SigG [Clostridium sp. 7_2_43FAA]
 gi|226913015|gb|EEH98216.1| sporulation sigma factor SigG [Clostridium sp. 7_2_43FAA]
          Length = 259

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 66/273 (24%), Positives = 130/273 (47%), Gaps = 43/273 (15%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+++E+  L  + R+ GD  A    +  +LRLV+ +   +   G  + ++   G I
Sbjct: 17  KLPILKEKEKRELLLKMRD-GDKGARETFIKGNLRLVLSVIQRFNNRGENVDDLFQVGCI 75

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A+  FD  +  + +TY++  I   ++ Y LR  + +++  +   + + +    ++ 
Sbjct: 76  GLMKAIDNFDLGQNVKFSTYAVPMIIGEIRRY-LRDNNSIRVSRSL--RDIAYKALLVRD 132

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L  I +NN +P  V  IAK+LN+   EV+          +L+A+           QD +
Sbjct: 133 RL--IKENNKEP-TVSQIAKELNLPREEVVF---------ALDAI-----------QDPV 169

Query: 205 -----VYDHDGQEQVLIEKE--ERKNRRN------MLTRSMSVLNPRERRIFEARRLQEN 251
                +Y HDG + + +  +  + KN          +  +M  LN RE+ I   R    N
Sbjct: 170 SLFEPIY-HDGGDAIYVMDQISDSKNSDESWLENISIKEAMKKLNDREKLILTLRFF--N 226

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             T   ++ E  +S+ +V ++E  A K +++ +
Sbjct: 227 GRTQMEVADEIGISQAQVSRLEKTALKHMRKYV 259


>gi|157692208|ref|YP_001486670.1| sporulation sigma factor SigG [Bacillus pumilus SAFR-032]
 gi|194014766|ref|ZP_03053383.1| RNA polymerase sigma-G factor [Bacillus pumilus ATCC 7061]
 gi|157680966|gb|ABV62110.1| DNA-directed RNA polymerase sigma subunit SigG [Bacillus pumilus
           SAFR-032]
 gi|194013792|gb|EDW23357.1| RNA polymerase sigma-G factor [Bacillus pumilus ATCC 7061]
          Length = 259

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 61/260 (23%), Positives = 118/260 (45%), Gaps = 16/260 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+  E   L ++ ++ GD +A  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKNDEMRKLFRQLQDEGDDTAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 74

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD     R +TY++  I   ++ Y LR  + +++  +          + L+ 
Sbjct: 75  GLMKSIDNFDLSHNVRFSTYAVPMIIGEIRRY-LRDNNPIRVSRSLRD----IAYKALQV 129

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + I++ + +P     IAK L V   E++     +    SL   I +   +     D +
Sbjct: 130 RERLISETSKEP-TAEDIAKVLEVPHEEIVFALDAIQDPVSLFEPIYNDGGDPIYVMDQI 188

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             + +   Q + E          L   M  LN RE+ I   R  Q    T   ++ E  +
Sbjct: 189 SDERNKDTQWVEEL--------ALKEGMRRLNDREKMILRKRFFQGK--TQMEVAEEIGI 238

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ +V ++E  A K++ ++I
Sbjct: 239 SQAQVSRLEKAAIKQMNKNI 258


>gi|325106726|ref|YP_004267794.1| RNA polymerase, sigma 32 subunit, RpoH [Planctomyces brasiliensis
           DSM 5305]
 gi|324966994|gb|ADY57772.1| RNA polymerase, sigma 32 subunit, RpoH [Planctomyces brasiliensis
           DSM 5305]
          Length = 332

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 26/65 (40%), Positives = 42/65 (64%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  +    L   E+ S+G I LM AV+KFD +RG+R +TY+ + I  +
Sbjct: 156 LIRANLRLVVSVARKFVTPQLTFDELFSDGVIALMNAVEKFDYDRGYRFSTYAYYSISRS 215

Query: 113 MQEYI 117
           +  +I
Sbjct: 216 LYRFI 220


>gi|197302589|ref|ZP_03167644.1| hypothetical protein RUMLAC_01318 [Ruminococcus lactaris ATCC
           29176]
 gi|197298487|gb|EDY33032.1| hypothetical protein RUMLAC_01318 [Ruminococcus lactaris ATCC
           29176]
          Length = 248

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 31/94 (32%), Positives = 53/94 (56%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE ++E  +  R     D  A   L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 43  PPLENEKEEEVIGRLGTEDDQEAKKLLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGL 102

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++A+  F+P +  +LATY+   I+  +  Y+ R+
Sbjct: 103 IKAINTFNPTKKIKLATYASRCIENEILMYLRRN 136


>gi|254973932|ref|ZP_05270404.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile QCD-66c26]
 gi|255091318|ref|ZP_05320796.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile CIP 107932]
 gi|255312976|ref|ZP_05354559.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile QCD-76w55]
 gi|255515735|ref|ZP_05383411.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile QCD-97b34]
 gi|255648829|ref|ZP_05395731.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile QCD-37x79]
 gi|260682047|ref|YP_003213332.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile CD196]
 gi|260685645|ref|YP_003216778.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile R20291]
 gi|306518943|ref|ZP_07405290.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile QCD-32g58]
 gi|260208210|emb|CBA60565.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile CD196]
 gi|260211661|emb|CBE01928.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile R20291]
          Length = 233

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 68/237 (28%), Positives = 117/237 (49%), Gaps = 19/237 (8%)

Query: 53  LVTSHLRLVVKIAMGY--RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           L+  ++ LV  IA  +   G G    ++V+ G IGL+ A+ KFD E+G + ++YS   IK
Sbjct: 6   LIKENMPLVKSIARKFFIPGKGFEYQDLVNSGVIGLIDAINKFDAEKGAKFSSYSYIKIK 65

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
           +A+ + I     + K   T   K   +N  R+   LQ+     L+      IAK+LNVSE
Sbjct: 66  SAILDEIRNQSPISKHNLTKVNK---YN--RVVEKLQSKL---LREPTSYEIAKELNVSE 117

Query: 171 SEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E+  I  N  +    SLN +I   D N +  QD +    D +E+      E + +  +L
Sbjct: 118 KELHDIESNIDMLNIVSLNYVI-FEDTNET-VQDVI---SDREEEAPENIIEEEEKLEIL 172

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           ++++S LN RE+ I      ++  + L+ +     VS  RV Q+  ++ + ++  I+
Sbjct: 173 SKAISNLNEREKLILSLYYYED--LNLKEIGKVLGVSESRVSQLHRKSIRNLRNKIK 227


>gi|266624907|ref|ZP_06117842.1| RNA polymerase sigma-G factor [Clostridium hathewayi DSM 13479]
 gi|288863210|gb|EFC95508.1| RNA polymerase sigma-G factor [Clostridium hathewayi DSM 13479]
          Length = 258

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 62/264 (23%), Positives = 118/264 (44%), Gaps = 31/264 (11%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L  +E+  L KR  + GD+ A    +  +LRLV+ +   + G    + ++   G I
Sbjct: 15  KLPLLNNEEKEALFKRILD-GDMEAREEYIKGNLRLVLSVIQRFSGSNENVDDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ---KRLFFNLRR 141
           GL++A+  FD  +  R +TY++  I   ++ Y LR  + +++  +      K ++     
Sbjct: 74  GLIKAIDNFDITQNVRFSTYAVPMILGEVRRY-LRDNNSIRVSRSLRDTAYKAIYAKENL 132

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           +K         NLK   ++ IA ++ VS+ ++           +L+A+ N        + 
Sbjct: 133 MK--------KNLKEPTIMEIADEIGVSKEDITY---------ALDAIQNPVSLYEPVYS 175

Query: 202 D----WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           D      V D    ++ L   EE       L  +M  L  RER I + R  +    T   
Sbjct: 176 DGGDPLFVMDQISDKKNL---EENWVEDISLNEAMKRLPERERHIIDMRFFEGKTQT--E 230

Query: 258 LSSEFEVSRERVRQIEARAFKKVQ 281
           ++ E  +S+ +V ++E  A K ++
Sbjct: 231 VAEEIHISQAQVSRLEKNALKSMK 254


>gi|323486720|ref|ZP_08092041.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323692141|ref|ZP_08106384.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
 gi|323400101|gb|EGA92478.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323503715|gb|EGB19534.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
          Length = 246

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 65/269 (24%), Positives = 116/269 (43%), Gaps = 65/269 (24%)

Query: 22  EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           +I   P+  K+E  VL +   E  D  A  +L+  +LRLVV IA  +    + + +++S 
Sbjct: 37  DILPAPLGSKEEAEVLKELGTER-DAQAKSKLIEHNLRLVVYIAKKFDNTSVGVEDLISI 95

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           G+IGL++A+  F+ ++  +LATY+   I+  +  Y                      LRR
Sbjct: 96  GSIGLIKAINTFNIDKNIKLATYASRCIENEILMY----------------------LRR 133

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
                      N K +  V+I + LNV                         D N     
Sbjct: 134 -----------NNKTKMEVSIDEPLNV-----------------------DWDGNELLLS 159

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR----RLQENPVTLEN 257
           D L  D D    V+    E +  +++L  ++S LNPRE++I E R       E+ +T + 
Sbjct: 160 DILGTDED----VIYRDLEDEIEKSLLNTAISRLNPREQKIVELRFGLGTENEDEMTQKE 215

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ++    +S+  + ++E +  K++++ I K
Sbjct: 216 VADLLGISQSYISRLEKKIMKRLKKEIVK 244


>gi|238916673|ref|YP_002930190.1| RNA polymerase sporulation-specific sigma factor [Eubacterium
           eligens ATCC 27750]
 gi|238872033|gb|ACR71743.1| RNA polymerase sporulation-specific sigma factor [Eubacterium
           eligens ATCC 27750]
          Length = 250

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 35/118 (29%), Positives = 61/118 (51%), Gaps = 4/118 (3%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           KN  ++  G++    YI     +P  L   EE    +      D  A H L+  +LRLVV
Sbjct: 24  KNFCLLKQGDV---HYIGGTDILPAPLGASEEQDAIEALGTASDAEAKHTLIEHNLRLVV 80

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
            IA  +   G+ + +++S G IGL++A+  +D ++  +LATY+   I+  +  Y+ R+
Sbjct: 81  YIAKKFDNTGVGVEDLISIGTIGLIKAINSYDKDKNIKLATYASRCIENEILMYLRRN 138


>gi|182437345|ref|YP_001825064.1| RNA polymerase sigma factor, sigma L [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|326777955|ref|ZP_08237220.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
 gi|178465861|dbj|BAG20381.1| RNA polymerase sigma factor, sigma L [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|326658288|gb|EGE43134.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
          Length = 288

 Score = 57.8 bits (138), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 62/237 (26%), Positives = 106/237 (44%), Gaps = 23/237 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +   
Sbjct: 67  LIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTVVGE 126

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL   L +    L    D +     V  +A+ L VSE 
Sbjct: 127 IKRFFRDTSWS-VRVPRRLQELRL--ALTKTSDELAQKLDRS---PTVPELARALGVSEE 180

Query: 172 EVIS----MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +V+      N   A   SL++     D       D L Y+    E V    E R++ + +
Sbjct: 181 DVVDGLAVGNAYTA--SSLDSPSPEDDGGEGSLADRLGYEDAALEGV----EYRESLKPL 234

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L +    L PRER+I   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 235 LAK----LAPRERQIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 285


>gi|331696957|ref|YP_004333196.1| SigB/F/G subfamily RNA polymerase sigma-28 subunit [Pseudonocardia
           dioxanivorans CB1190]
 gi|326951646|gb|AEA25343.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Pseudonocardia dioxanivorans CB1190]
          Length = 288

 Score = 57.4 bits (137), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 27/73 (36%), Positives = 43/73 (58%), Gaps = 1/73 (1%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RLVT HL +V  IA  + G G P+ ++   G +GL+ AV +FDP RG    +Y++  I  
Sbjct: 69  RLVTGHLPVVRHIARRFAGRGEPVDDLEQAGTVGLINAVDRFDPARGVDFLSYAVPTITG 128

Query: 112 AMQEYIL-RSWSL 123
            ++ +   R+WS+
Sbjct: 129 EVRRHFRDRTWSM 141


>gi|310641572|ref|YP_003946330.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
 gi|309246522|gb|ADO56089.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
          Length = 262

 Score = 57.4 bits (137), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 64/274 (23%), Positives = 124/274 (45%), Gaps = 50/274 (18%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQAVKK 92
           L ++++E+GD  A  +L+  +L +V  ++ G    GLP +    ++ S G +GL+ A++K
Sbjct: 14  LWEQWKEYGDKEAKKQLIEKYLHIVEYVS-GRLAVGLPKNVSKDDLASNGVMGLIDALEK 72

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG-HLQAITD 151
           FD ERG +  TY+ W ++ A+ +  LR    V        K++    + L+  +L+ ++D
Sbjct: 73  FDYERGLQFETYASWRVRGAILDG-LRQGDWVPRSVREKAKKIEDAYQHLEQRYLRTVSD 131

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLA---------------GDESLNALINSSDKN 196
             +        +  L+VSE E  SM   +A                +  L+ L++   KN
Sbjct: 132 EEM--------SHYLDVSEKEFQSMIQEVAVMSIVSLEDPIREEESETRLSLLVDEKAKN 183

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
                     DH   E  L         R+ L + +  L  +ER +     L    ++L 
Sbjct: 184 P---------DHKVNEFTL---------RDALAQGIDKLTEKERIVVSL--LYYEDLSLS 223

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
            ++    +S  R+ Q+ ++A  +++ ++ KQ +L
Sbjct: 224 EIAEVMSLSPSRISQLHSKAILRLRATLDKQRDL 257


>gi|229587526|ref|YP_002860564.1| putative DNA-directed RNA polymerase specialized sigma subunit
           [Clostridium botulinum Ba4 str. 657]
 gi|229260255|gb|ACQ51292.1| putative DNA-directed RNA polymerase specialized sigma subunit
           [Clostridium botulinum Ba4 str. 657]
          Length = 296

 Score = 57.4 bits (137), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 47/242 (19%), Positives = 116/242 (47%), Gaps = 39/242 (16%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           + L+  +  L+ K+A  Y+   + + ++  +G +G ++AV KFD  +  + +TY+ +WI+
Sbjct: 88  NSLIEKNENLIFKVANKYKNKNIELQDLTQQGFLGFLKAVDKFDESKKVKFSTYAYYWIE 147

Query: 111 AAMQEYI-LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           A +  +        + I ++       +  R+LKG+   I    L  +++  + K     
Sbjct: 148 AEISSFFNFNVDGSLSISSS-------YQHRKLKGYENGI----LSEDELPKLVKNHIQL 196

Query: 170 ESEVISMNCRLAGDESLNA---LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++  IS++  + G E+ N+   L+  +D N +  +  +V                     
Sbjct: 197 KNNSISVDSIVHGKENENSADYLLGKTDINYNNIESKIV--------------------- 235

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++S L+ +E+ I  +R + E     ++++ EF+VS + ++ +   A +K++++++K
Sbjct: 236 -MENALSGLSDKEKNIIISRIIYEKK--YKDIAKEFKVSYQYIQYLYNNAIEKLRQTVKK 292

Query: 287 QV 288
            +
Sbjct: 293 DI 294


>gi|167750707|ref|ZP_02422834.1| hypothetical protein EUBSIR_01685 [Eubacterium siraeum DSM 15702]
 gi|167656386|gb|EDS00516.1| hypothetical protein EUBSIR_01685 [Eubacterium siraeum DSM 15702]
          Length = 251

 Score = 57.4 bits (137), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 45/151 (29%), Positives = 74/151 (49%), Gaps = 15/151 (9%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMG----YRGYGLPISEVVSEGNIGLMQAVKK 92
           L ++YR  GD++  + +V  ++ LV  IA+     Y GY     ++++EG I LM A+  
Sbjct: 12  LLEKYRLTGDMNVRNEIVLMYMDLVKMIAVSMRNIYTGYA-ESDDIINEGVIALMAAIDG 70

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITD 151
           FDPE+  +  TY+   IK A+ +Y LR    V        K+L  N  RL   L +  TD
Sbjct: 71  FDPEKNVKFETYAGIRIKGAVIDY-LRKLDRVPRTLRKLSKQLDDNFARLNSELCRTPTD 129

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
             L        A+ +N++ +++  +    AG
Sbjct: 130 EEL--------AESMNMTTAQLSKLMANTAG 152


>gi|223986354|ref|ZP_03636363.1| hypothetical protein HOLDEFILI_03674 [Holdemania filiformis DSM
           12042]
 gi|223961703|gb|EEF66206.1| hypothetical protein HOLDEFILI_03674 [Holdemania filiformis DSM
           12042]
          Length = 257

 Score = 57.4 bits (137), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 62/255 (24%), Positives = 120/255 (47%), Gaps = 21/255 (8%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L+ Q+   L  + ++ GDLSA  +L+  +L+LV+ I   +      + ++   G IG
Sbjct: 16  LPVLKSQQMTELFIQLQD-GDLSAKEKLINGNLKLVLSIVQRFAHRTENMDDLFQIGCIG 74

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A+  FD     R +TY++  I   ++ Y LR   ++++  + + K L + + + K  
Sbjct: 75  LIKAIDNFDLSHEVRFSTYAVPMIIGEIKRY-LRDNQMIRV--SRHLKDLAYKVLKEK-- 129

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            +A    N +   +  +A+ + V E ++      L    S+   I + D ++    D + 
Sbjct: 130 -EAFIHANQREPSLAELAEIMGVKEKDIAESLESLQSVVSIFEPIYNDDGDTLYLLDQIK 188

Query: 206 YDHD--GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
            DHD  G+   LI           L  SM  L+ +E +I   R  Q    T   ++SE  
Sbjct: 189 DDHDEIGKLSSLI----------ALKESMKHLSDKEAQIINKRYYQGQTQT--EIASELG 236

Query: 264 VSRERVRQIEARAFK 278
           +S+ +V ++E  A +
Sbjct: 237 ISQAQVSRLEKSALQ 251


>gi|291558216|emb|CBL35333.1| RNA polymerase sigma factor, FliA/WhiG family/RNA polymerase sigma
           factor, sigma-70 family [Eubacterium siraeum V10Sc8a]
          Length = 251

 Score = 57.4 bits (137), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 45/151 (29%), Positives = 74/151 (49%), Gaps = 15/151 (9%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMG----YRGYGLPISEVVSEGNIGLMQAVKK 92
           L ++YR  GD++  + +V  ++ LV  IA+     Y GY     ++++EG I LM A+  
Sbjct: 12  LLEKYRLTGDMNVRNEIVLMYMDLVKMIAVSMRNIYTGYA-ESDDIINEGVIALMAAIDG 70

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITD 151
           FDPE+  +  TY+   IK A+ +Y LR    V        K+L  N  RL   L +  TD
Sbjct: 71  FDPEKNVKFETYAGIRIKGAVIDY-LRKLDRVPRTLRKLSKQLDDNFARLNSELCRTPTD 129

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
             L        A+ +N++ +++  +    AG
Sbjct: 130 EEL--------AESMNMTTAQLSKLMANTAG 152


>gi|302559791|ref|ZP_07312133.1| RNA polymerase sigma-F factor [Streptomyces griseoflavus Tu4000]
 gi|302477409|gb|EFL40502.1| RNA polymerase sigma-F factor [Streptomyces griseoflavus Tu4000]
          Length = 301

 Score = 57.4 bits (137), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 62/237 (26%), Positives = 105/237 (44%), Gaps = 23/237 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +   
Sbjct: 79  LIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTVVGE 138

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL   L +    L    D +     V  +A  L VSE 
Sbjct: 139 IKRFFRDTSWS-VRVPRRLQELRL--ALTKASDELSQKLDRS---PTVPELAAVLGVSEE 192

Query: 172 EVIS----MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +V+      N   A   SL++     D       D L Y+    E V    E R++ + +
Sbjct: 193 DVVDGLAVGNAYTA--SSLDSPAPEDDGGEGSLADRLGYEDTALEGV----EYRESLKPL 246

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L +    L PRER+I   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 247 LAK----LPPRERQIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 297


>gi|168186818|ref|ZP_02621453.1| RNA polymerase sigma-K factor [Clostridium botulinum C str. Eklund]
 gi|169295229|gb|EDS77362.1| RNA polymerase sigma-K factor [Clostridium botulinum C str. Eklund]
          Length = 235

 Score = 57.4 bits (137), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 35/103 (33%), Positives = 59/103 (57%), Gaps = 4/103 (3%)

Query: 9   IVNGEIGLSRYIHEIRKIP--MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           +++G   L+ Y+      P  + EK+E+Y L ++++E GD  A   L+  +LRLV  I  
Sbjct: 10  MIDGMTFLTAYVSNGTSFPQPLNEKEEKYYL-QQFKE-GDALAKGILIERNLRLVAHIVK 67

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            Y      I +++S G +GL++A+  FD ++G RLATY+   I
Sbjct: 68  KYSYPNKDIDDLISIGTVGLIKAIDSFDVDKGTRLATYAARCI 110


>gi|153812463|ref|ZP_01965131.1| hypothetical protein RUMOBE_02862 [Ruminococcus obeum ATCC 29174]
 gi|149831388|gb|EDM86476.1| hypothetical protein RUMOBE_02862 [Ruminococcus obeum ATCC 29174]
          Length = 243

 Score = 57.4 bits (137), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 31/94 (32%), Positives = 56/94 (59%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  K+E YV++ R +   +  A   L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 39  PLEPKREAYVIS-RLKTDQEQEARSLLIEHNLRLVVYIARKFDNTGVGVEDLISIGTIGL 97

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++A+  F+P +  +LATY+   I+  +  Y+ R+
Sbjct: 98  IKAINTFNPVKNIKLATYASRCIENEILMYLRRN 131


>gi|302386724|ref|YP_003822546.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           saccharolyticum WM1]
 gi|302197352|gb|ADL04923.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           saccharolyticum WM1]
          Length = 246

 Score = 57.4 bits (137), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 57/223 (25%), Positives = 92/223 (41%), Gaps = 66/223 (29%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L+ ++E  +        D  A   L+  +LRLVV IA  +    + + +++S G IGL
Sbjct: 41  PPLDNEKEAQIIALLGSDDDQRAKSELIEHNLRLVVYIAKKFDNTSVGVEDLISIGTIGL 100

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+  F+P +  +LATY+   I+  +  Y                      LRR     
Sbjct: 101 IKAINTFNPNKNIKLATYASRCIENEILMY----------------------LRR----- 133

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ--DWL 204
                 N K +  V+I + LNV                               W   + L
Sbjct: 134 ------NNKTKMEVSIDEPLNVD------------------------------WDGNELL 157

Query: 205 VYDHDGQEQVLIEKE-ERKNRRNMLTRSMSVLNPRERRIFEAR 246
           + D  G E+ +I K+ E +  RN+L  ++S L+PRER+I E R
Sbjct: 158 LSDILGTEEDVIYKDLETEVERNLLNTAISRLSPRERKIVELR 200


>gi|168214239|ref|ZP_02639864.1| RNA polymerase sigma-E factor [Clostridium perfringens CPE str.
           F4969]
 gi|170714290|gb|EDT26472.1| RNA polymerase sigma-E factor [Clostridium perfringens CPE str.
           F4969]
          Length = 235

 Score = 57.4 bits (137), Expect = 2e-06,   Method: Compositional matrix adjust.
 Identities = 33/92 (35%), Positives = 55/92 (59%), Gaps = 1/92 (1%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K+EE  L  +  E+ D +    L+  +LRLVV IA  +   G+ + +++S G IGL++
Sbjct: 35  LSKEEEEELVNKLGEN-DEAIRSILIERNLRLVVYIARKFENTGVGVEDLISVGTIGLIK 93

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           AV  F+PE+  +LATY+   I+  +  Y+ R+
Sbjct: 94  AVNTFNPEKKIKLATYASRCIENEILMYLRRN 125


>gi|312135430|ref|YP_004002768.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|311775481|gb|ADQ04968.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor owensensis OL]
          Length = 240

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 59/243 (24%), Positives = 112/243 (46%), Gaps = 24/243 (9%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           ++GD  A  +L+ S+L LV  +   +   G+ + ++   G IGL++AV +FDP    R +
Sbjct: 14  KNGDKVARQQLIESNLALVWSVVKKFAAKGVELEDLFQIGCIGLIKAVDRFDPSFNVRFS 73

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
           TY++  I   ++ Y LR    +K+      NQ +    +++L+   Q ++ N  +P  + 
Sbjct: 74  TYAVPMIIGEIKRY-LRDDGRIKVSRKIKENQGK----IKKLRN--QFVSSNGREP-TIS 125

Query: 161 AIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            I++   +S  E+  + C  A  E  SLN ++N  +       D    + D   ++L   
Sbjct: 126 EISQLTGLSSDEI--LLCLDASSEVASLNEVVNQEEGKPITLMDIASDEEDYSTKLL--- 180

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                    L   +  L  RER I   R  +    T   ++ +  +S+  V +IE RA +
Sbjct: 181 -----DLMALKEGLKKLKGRERYIIFMRYFKNK--TQSEIAKQLNISQVHVSRIEKRALE 233

Query: 279 KVQ 281
           +++
Sbjct: 234 RIK 236


>gi|119514602|gb|ABL76113.1| SigB [Listeria monocytogenes]
 gi|119514606|gb|ABL76115.1| SigB [Listeria monocytogenes]
 gi|119514608|gb|ABL76116.1| SigB [Listeria monocytogenes]
 gi|119514610|gb|ABL76117.1| SigB [Listeria monocytogenes]
 gi|119514614|gb|ABL76119.1| SigB [Listeria monocytogenes]
 gi|119514618|gb|ABL76121.1| SigB [Listeria monocytogenes 690]
 gi|119514626|gb|ABL76125.1| SigB [Listeria monocytogenes]
 gi|119514630|gb|ABL76127.1| SigB [Listeria monocytogenes]
 gi|119514632|gb|ABL76128.1| SigB [Listeria monocytogenes]
          Length = 249

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 62/257 (24%), Positives = 123/257 (47%), Gaps = 26/257 (10%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +++D   G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEEL 125

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDW 203
           T       Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D 
Sbjct: 126 TRELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDV 182

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    DG E+V        N+R +L + + VL+ RE++I +   ++    + +      +
Sbjct: 183 VGGTDDGFERV--------NQRMLLEKVLPVLDEREQKILQYTFIENR--SQKETGELLD 232

Query: 264 VSRERVRQIEARAFKKV 280
           +S+  V +I+ +A KK+
Sbjct: 233 ISQMHVSRIQRQAIKKL 249


>gi|161353798|ref|YP_519128.2| sporulation sigma factor SigE [Desulfitobacterium hafniense Y51]
 gi|219670065|ref|YP_002460500.1| sporulation sigma factor SigE [Desulfitobacterium hafniense DCB-2]
 gi|219540325|gb|ACL22064.1| RNA polymerase, sigma 28 subunit, SigE [Desulfitobacterium
           hafniense DCB-2]
          Length = 249

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 27/60 (45%), Positives = 40/60 (66%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           D+S    L+  +LRLVV IA  +   G+ I ++VS G IGL++AV  FDP++  +LATY+
Sbjct: 65  DVSVRDVLIERNLRLVVYIARKFENTGVGIEDLVSIGTIGLIKAVNTFDPQKKIKLATYA 124


>gi|167755749|ref|ZP_02427876.1| hypothetical protein CLORAM_01264 [Clostridium ramosum DSM 1402]
 gi|167704688|gb|EDS19267.1| hypothetical protein CLORAM_01264 [Clostridium ramosum DSM 1402]
          Length = 258

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 66/273 (24%), Positives = 124/273 (45%), Gaps = 25/273 (9%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           N  +I+NG         E +K   L   E Y L   Y+   + +   RLV  + +LV+ +
Sbjct: 3   NYQVIING-------YQEPKK--RLTTDETYKLIDEYQATKNEAIKDRLVNDNTKLVLSM 53

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  + G    + ++   G IGL++A++ F+   G + +TY++  I   M+ Y LR    +
Sbjct: 54  ARRFYGREDSMDDLFQVGMIGLIKAIENFNTSFGLKFSTYAVPLIIGEMKRY-LRDNHQI 112

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           KI  +   + L + + ++K     IT  N +P  +  +A +L V  S VI          
Sbjct: 113 KISRSI--RDLAYKVLKVKDSY--ITKLNREP-TINELANELEVEPSAVIEALLSTNSVS 167

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   + + D N+ +  D +  D     + ++    R N    L  ++  LN +E R+ +
Sbjct: 168 SLQEEVKNDDGNNLKMIDSITDD-----KTVV---SRTNETIDLYDALKSLNQKEHRVIK 219

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
            R  +   ++   ++ E  +S+ +V +IE +A 
Sbjct: 220 QRYFE--GLSQSEIAKELFISQAQVSRIERKAL 250


>gi|52784380|ref|YP_090209.1| RNA polymerase sigma factor SigB [Bacillus licheniformis ATCC
           14580]
 gi|52346882|gb|AAU39516.1| SigB [Bacillus licheniformis ATCC 14580]
          Length = 264

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 68/283 (24%), Positives = 133/283 (46%), Gaps = 32/283 (11%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K   L K E   L K+Y+E+ D  A   LV ++  LV  +A  Y        ++   G +
Sbjct: 7   KTTKLTKTEVDTLIKKYQENQDEDAQLTLVQTYKNLVETLAKKYSKGKSFHEDLCQVGML 66

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLK 143
           GL+ A+K++DP+ G     +++  I   ++ ++  ++WS+         +R+     R+K
Sbjct: 67  GLLGAIKRYDPDVGKSFEAFAIPTIIGEIKRFLRDKTWSV------HVPRRIKELGPRIK 120

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNS 197
             +  +T    +  +V  IA+ L+V+E EV+ +M        L+ D S+ A    +D ++
Sbjct: 121 MAVDHLTTETQRSPRVDEIAEFLDVTEEEVLETMEMGKSYQALSVDHSIEA---DADGST 177

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
               D +    +G E+V        N++ ML   + VL+ RE++I E   +Q    + + 
Sbjct: 178 VTILDIVGSQEEGYEKV--------NQKLMLESVLHVLSDREKQIIELTYIQNK--SQKE 227

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQKP 300
                 +S+  V +++ +A K+++E+      L+  P +  KP
Sbjct: 228 TGEMLGISQMHVSRLQRKAVKRLREA------LAEDPYMELKP 264


>gi|18310744|ref|NP_562678.1| sporulation sigma factor SigE [Clostridium perfringens str. 13]
 gi|110798939|ref|YP_696448.1| sporulation sigma factor SigE [Clostridium perfringens ATCC 13124]
 gi|110801836|ref|YP_699048.1| sporulation sigma factor SigE [Clostridium perfringens SM101]
 gi|168207289|ref|ZP_02633294.1| RNA polymerase sigma-E factor [Clostridium perfringens E str.
           JGS1987]
 gi|168210605|ref|ZP_02636230.1| RNA polymerase sigma-E factor [Clostridium perfringens B str. ATCC
           3626]
 gi|168217049|ref|ZP_02642674.1| RNA polymerase sigma-E factor [Clostridium perfringens NCTC 8239]
 gi|169342673|ref|ZP_02863714.1| RNA polymerase sigma-E factor [Clostridium perfringens C str.
           JGS1495]
 gi|182625822|ref|ZP_02953588.1| RNA polymerase sigma-E factor [Clostridium perfringens D str.
           JGS1721]
 gi|18145425|dbj|BAB81468.1| probable transcription initiation factor sigma E [Clostridium
           perfringens str. 13]
 gi|110673586|gb|ABG82573.1| RNA polymerase sigma-E factor [Clostridium perfringens ATCC 13124]
 gi|110682337|gb|ABG85707.1| RNA polymerase sigma-E factor [Clostridium perfringens SM101]
 gi|169299179|gb|EDS81249.1| RNA polymerase sigma-E factor [Clostridium perfringens C str.
           JGS1495]
 gi|170661363|gb|EDT14046.1| RNA polymerase sigma-E factor [Clostridium perfringens E str.
           JGS1987]
 gi|170711254|gb|EDT23436.1| RNA polymerase sigma-E factor [Clostridium perfringens B str. ATCC
           3626]
 gi|177908856|gb|EDT71348.1| RNA polymerase sigma-E factor [Clostridium perfringens D str.
           JGS1721]
 gi|182380960|gb|EDT78439.1| RNA polymerase sigma-E factor [Clostridium perfringens NCTC 8239]
          Length = 235

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 33/92 (35%), Positives = 55/92 (59%), Gaps = 1/92 (1%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K+EE  L  +  E+ D +    L+  +LRLVV IA  +   G+ + +++S G IGL++
Sbjct: 35  LSKEEEEELVNKLGEN-DEAIRSILIERNLRLVVYIARKFENTGVGVEDLISVGTIGLIK 93

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           AV  F+PE+  +LATY+   I+  +  Y+ R+
Sbjct: 94  AVNTFNPEKKIKLATYASRCIENEILMYLRRN 125


>gi|331091330|ref|ZP_08340170.1| hypothetical protein HMPREF9477_00813 [Lachnospiraceae bacterium
           2_1_46FAA]
 gi|330404491|gb|EGG84035.1| hypothetical protein HMPREF9477_00813 [Lachnospiraceae bacterium
           2_1_46FAA]
          Length = 206

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 35/84 (41%), Positives = 49/84 (58%), Gaps = 2/84 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+   +E Y L K Y E GDL A H L+  +LRLV  I   Y+       +++S G IGL
Sbjct: 7   PLTASEERYYLQK-YTE-GDLEAKHILIERNLRLVAHIVKKYQHLDEDPEDLLSIGTIGL 64

Query: 87  MQAVKKFDPERGFRLATYSMWWIK 110
           ++AV  F+ E+G RLATY+   I+
Sbjct: 65  IKAVSTFNLEKGNRLATYAARCIE 88


>gi|293401521|ref|ZP_06645664.1| RNA polymerase sigma-G factor [Erysipelotrichaceae bacterium
           5_2_54FAA]
 gi|291305159|gb|EFE46405.1| RNA polymerase sigma-G factor [Erysipelotrichaceae bacterium
           5_2_54FAA]
          Length = 259

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 63/259 (24%), Positives = 127/259 (49%), Gaps = 31/259 (11%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           + +L  +E   L K+Y + GD  A   L+  +L+LV+ I   +      + ++   G IG
Sbjct: 16  LKVLSNEEMKELFKKY-QSGDEQAKEDLIQGNLKLVLSIVQRFSNRCENMDDLFQVGCIG 74

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++++  FD +   R +TY++  I   ++ Y LR   ++++  + + K L + + RLK  
Sbjct: 75  LVKSIDNFDLKHEVRFSTYAVPMIMGEIKRY-LRDNQVIRV--SRHLKDLAYKVFRLKE- 130

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            + I ++  +P  +  +A++L V E +V+     L   +S+ ++               V
Sbjct: 131 -EYIHEHQKEP-TIHWLAEQLQVKEKDVVDA---LDSTQSVVSIFEP------------V 173

Query: 206 YDHDGQEQVLI-----EKEERKNRRNMLT--RSMSVLNPRERRIFEARRLQENPVTLENL 258
           Y+ DG E  L+     +K+E +   N +T  +SM  L  +E+ I + R  Q+   T   +
Sbjct: 174 YNTDGDELYLLDQIKDDKDEIERLSNYMTLKKSMRNLKGKEKDIIQKRYYQDKTQT--EI 231

Query: 259 SSEFEVSRERVRQIEARAF 277
           ++E  +S+ +V ++E  A 
Sbjct: 232 ANELGISQAQVSRLEKNAI 250


>gi|23978307|dbj|BAC21130.1| principal sigma factor [Calothrix brevissima]
          Length = 188

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 46/178 (25%), Positives = 91/178 (51%), Gaps = 17/178 (9%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+   I      +++     
Sbjct: 4   GLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLSV--- 60

Query: 132 QKRLFFNLRRLKGHLQAIT-DNNLKP-EQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
              L+  + R+K   + ++ +   KP E+ +A   ++ + +   I+ + +L    SL   
Sbjct: 61  --HLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLP--ISLETP 116

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFEAR 246
           I   +   S+  D++  + DG+     E +  KN  R  L + +  L+PRER +   R
Sbjct: 117 IGKEE--DSRLGDFI--ESDGETP---EDQVSKNLLREDLEKVLDSLSPRERDVLRLR 167


>gi|52079008|ref|YP_077799.1| RNA polymerase sigma factor SigB [Bacillus licheniformis ATCC
           14580]
 gi|319648688|ref|ZP_08002899.1| RNA polymerase sigma factor [Bacillus sp. BT1B_CT2]
 gi|52002219|gb|AAU22161.1| RNA polymerase sigma-37 factor (sigma-B) [Bacillus licheniformis
           ATCC 14580]
 gi|317389107|gb|EFV69923.1| RNA polymerase sigma factor [Bacillus sp. BT1B_CT2]
          Length = 263

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 68/283 (24%), Positives = 133/283 (46%), Gaps = 32/283 (11%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K   L K E   L K+Y+E+ D  A   LV ++  LV  +A  Y        ++   G +
Sbjct: 6   KTTKLTKTEVDTLIKKYQENQDEDAQLTLVQTYKNLVETLAKKYSKGKSFHEDLCQVGML 65

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLK 143
           GL+ A+K++DP+ G     +++  I   ++ ++  ++WS+         +R+     R+K
Sbjct: 66  GLLGAIKRYDPDVGKSFEAFAIPTIIGEIKRFLRDKTWSV------HVPRRIKELGPRIK 119

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNS 197
             +  +T    +  +V  IA+ L+V+E EV+ +M        L+ D S+ A    +D ++
Sbjct: 120 MAVDHLTTETQRSPRVDEIAEFLDVTEEEVLETMEMGKSYQALSVDHSIEA---DADGST 176

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
               D +    +G E+V        N++ ML   + VL+ RE++I E   +Q    + + 
Sbjct: 177 VTILDIVGSQEEGYEKV--------NQKLMLESVLHVLSDREKQIIELTYIQNK--SQKE 226

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQKP 300
                 +S+  V +++ +A K+++E+      L+  P +  KP
Sbjct: 227 TGEMLGISQMHVSRLQRKAVKRLREA------LAEDPYMELKP 263


>gi|89335089|dbj|BAE84684.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 238

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 27/60 (45%), Positives = 40/60 (66%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           D+S    L+  +LRLVV IA  +   G+ I ++VS G IGL++AV  FDP++  +LATY+
Sbjct: 54  DVSVRDVLIERNLRLVVYIARKFENTGVGIEDLVSIGTIGLIKAVNTFDPQKKIKLATYA 113


>gi|260589594|ref|ZP_05855507.1| RNA polymerase sigma-E factor [Blautia hansenii DSM 20583]
 gi|260540162|gb|EEX20731.1| RNA polymerase sigma-E factor [Blautia hansenii DSM 20583]
          Length = 252

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 40/130 (30%), Positives = 61/130 (46%), Gaps = 14/130 (10%)

Query: 5   NMSIIVNGEIGLS-------------RYIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAA 50
           NM I V G +  S              YI     +P  L  QEE  +       G   A 
Sbjct: 11  NMDICVGGNVKFSGFKGVFLPKKNELHYIGGAEVLPAPLTAQEEGEMLDALAGEGKEEAR 70

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
             L+  +LRLVV IA  +   G+ + +++S G IGL++A+  FDP +  +LATY+   I+
Sbjct: 71  ACLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFDPVKKIKLATYASRCIE 130

Query: 111 AAMQEYILRS 120
             +  Y+ R+
Sbjct: 131 NEILMYLRRN 140


>gi|311897124|dbj|BAJ29532.1| putative RNA polymerase sigma factor [Kitasatospora setae KM-6054]
          Length = 301

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 58/231 (25%), Positives = 110/231 (47%), Gaps = 19/231 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  ++ LV   A+ +R    P+ +VV  G IGL+ A+ +FDP+RG +  TY++  I   
Sbjct: 81  LIEINIPLVRYAAIRFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFPTYALPTILGE 140

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           ++ Y   +     + T    +RL     ++ G ++ +T  + +  +V  IA  L + E +
Sbjct: 141 IKRYFRDN-----VRTMHVPRRLQELWVQVSGAMEELTVAHGRAPKVPEIAANLRIPEED 195

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQ--DWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           V +  C  AG     A + ++ ++       D L Y    ++  L + E R   R++L +
Sbjct: 196 VRA--CLDAGRAYNAASLEAAQEHEGGLALLDRLGY----EDSALTDVEHRDMVRHLLVQ 249

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
               L  RERRI   R      +T   +S+E  +S+  V ++ +R   +++
Sbjct: 250 ----LPERERRIIMLRFFAN--LTQSQISTELGMSQMHVSRLLSRILSRLR 294


>gi|26665390|dbj|BAC44906.1| principal sigma factor [Scytonema sp. IAM M-262]
          Length = 188

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 48/198 (24%), Positives = 99/198 (50%), Gaps = 17/198 (8%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+   I      +++     
Sbjct: 4   GLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV--- 60

Query: 132 QKRLFFNLRRLKGHLQAIT-DNNLKP-EQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
              L+  + R+K   + ++ +   KP E+ +A   ++ + +   I+ + +L    SL   
Sbjct: 61  --HLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPI--SLETP 116

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   +   S+  D++  D +  E  + +   R++    L + +  L+PRER +   R   
Sbjct: 117 IGKEE--DSRLGDFIESDSETPEDQVSKNLLRED----LEKVLDSLSPRERDVLRLRYGL 170

Query: 250 ENP--VTLENLSSEFEVS 265
           ++    TLE +   F V+
Sbjct: 171 DDGRMKTLEEIGQIFNVT 188


>gi|239623681|ref|ZP_04666712.1| RNA polymerase [Clostridiales bacterium 1_7_47_FAA]
 gi|239521712|gb|EEQ61578.1| RNA polymerase [Clostridiales bacterium 1_7_47FAA]
          Length = 239

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 60/238 (25%), Positives = 113/238 (47%), Gaps = 16/238 (6%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GD +A  +LV  ++ L+  I   + G G  + ++   G+IGL++A+ KFD     + +T
Sbjct: 13  EGDKAARDQLVMDNVGLIWSIVRRFSGRGYEMEDLFQIGSIGLIKAIDKFDTGFEVKFST 72

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y++  I   ++ + LR   ++K+  +   K L F +R  +   + +T +  +   +  IA
Sbjct: 73  YAVPMITGEIKRF-LRDDGMIKVSRSI--KELGFKVRAAR---EEMTYSLGREPTIEEIA 126

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
            +L+ S  EV +     A  ESL     + D N+    D L  +++  E++L        
Sbjct: 127 ARLDTSREEVAASMEAGAEVESLYRPTGNGDDNTMFLMDRLEEENNDHEELL-------- 178

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R +L   M  L   +R I   RR   N  T   ++ E  +S+ +V ++E R  K+++
Sbjct: 179 NRMVLKELMEDLGEEQREII-VRRYFYNQ-TQTQIAKELGISQVQVSRLEKRILKEMR 234


>gi|331027965|ref|YP_004421515.1| RNA polymerase sigma factor [Synechococcus phage S-CBS2]
 gi|294805578|gb|ADF42417.1| RNA polymerase sigma factor [Synechococcus phage S-CBS2]
          Length = 261

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 28/95 (29%), Positives = 51/95 (53%), Gaps = 8/95 (8%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGL--------PISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           +L   +LRLV K    Y   G            +++ EG  GL +A  KFDPERG+  AT
Sbjct: 46  KLCQHNLRLVAKFTRAYMKGGTRKLTWGGDETMDLLQEGYFGLRRAANKFDPERGYTFAT 105

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           Y+  W++ A+ +Y +   SL+++  ++ ++  +++
Sbjct: 106 YANAWVRQALGKYHVDKLSLIRVPESSAREIFYYD 140


>gi|311029938|ref|ZP_07708028.1| sporulation sigma factor SigG [Bacillus sp. m3-13]
          Length = 259

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 64/275 (23%), Positives = 130/275 (47%), Gaps = 45/275 (16%)

Query: 25  KIPMLEKQEEYVLAKRYRE--HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           K+P+L+ +E   + K +RE   G+LSA  +LV  +LRLV+ +   +   G  + ++   G
Sbjct: 15  KLPVLKNEE---MRKLFREMQGGELSAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVG 71

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            IGLM+++  FD  +  + +TY++  I   ++ Y LR  + +++  +   + + +   ++
Sbjct: 72  CIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSL--RDIAYKALQV 128

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
           +  L + T      E+   IAK L V   E++          +L+A+           QD
Sbjct: 129 RERLMSETSREPTAEE---IAKVLEVPHEEIVF---------ALDAI-----------QD 165

Query: 203 WL-----VYDHDGQEQVLIEKEERKNRRNM-------LTRSMSVLNPRERRIFEARRLQE 250
            +     +Y+  G    ++++   +  +++       L   M  LN RE+ I   R  Q 
Sbjct: 166 PVSLFEPIYNDGGDPIYVLDQISDEKNKDIQWIEEIALKEGMRRLNDREKLILRKRFFQG 225

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              T   ++ E  +S+ +V ++E  A K++ ++IQ
Sbjct: 226 K--TQMEVADEIGISQAQVSRLEKAAIKQMNKNIQ 258


>gi|119514598|gb|ABL76111.1| SigB [Listeria monocytogenes]
 gi|119514600|gb|ABL76112.1| SigB [Listeria monocytogenes]
 gi|119514604|gb|ABL76114.1| SigB [Listeria monocytogenes]
 gi|119514612|gb|ABL76118.1| SigB [Listeria monocytogenes]
 gi|119514616|gb|ABL76120.1| SigB [Listeria monocytogenes]
 gi|119514620|gb|ABL76122.1| SigB [Listeria monocytogenes]
 gi|119514622|gb|ABL76123.1| SigB [Listeria monocytogenes]
 gi|119514624|gb|ABL76124.1| SigB [Listeria monocytogenes]
 gi|119514628|gb|ABL76126.1| SigB [Listeria monocytogenes]
 gi|119514634|gb|ABL76129.1| SigB [Listeria monocytogenes]
 gi|119514636|gb|ABL76130.1| SigB [Listeria monocytogenes]
 gi|119514638|gb|ABL76131.1| SigB [Listeria monocytogenes]
          Length = 249

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 62/257 (24%), Positives = 123/257 (47%), Gaps = 26/257 (10%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +++D   G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEEL 125

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDW 203
           T       Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D 
Sbjct: 126 TRELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDV 182

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    DG E+V        N+R +L + + VL+ RE++I +   ++    + +      +
Sbjct: 183 VGGTDDGFERV--------NQRMLLEKVLPVLDEREQKILQFTFIENR--SQKETGELLD 232

Query: 264 VSRERVRQIEARAFKKV 280
           +S+  V +I+ +A KK+
Sbjct: 233 ISQMHVSRIQRQAIKKL 249


>gi|313901877|ref|ZP_07835297.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermaerobacter subterraneus DSM 13965]
 gi|313467870|gb|EFR63364.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermaerobacter subterraneus DSM 13965]
          Length = 251

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 24/63 (38%), Positives = 39/63 (61%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GD  A  RLV  H+ LV  +A  +  +G  + +++  G IGL+QA+  FDP RG++ +T
Sbjct: 11  QGDGEARERLVALHMPLVRHVARRFASFGHDLDDLIQAGTIGLLQAIDGFDPSRGYQFST 70

Query: 104 YSM 106
           Y++
Sbjct: 71  YAV 73


>gi|229827370|ref|ZP_04453439.1| hypothetical protein GCWU000182_02758 [Abiotrophia defectiva ATCC
           49176]
 gi|229788308|gb|EEP24422.1| hypothetical protein GCWU000182_02758 [Abiotrophia defectiva ATCC
           49176]
          Length = 268

 Score = 57.4 bits (137), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 68/254 (26%), Positives = 117/254 (46%), Gaps = 35/254 (13%)

Query: 51  HRLVTSHLRLVVKIAMG----YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +L+  +  LV KI  G    Y GY +   ++V  G  GL+ A+ KFD  +G +  TY+ 
Sbjct: 31  EKLIIEYANLV-KIIAGRMSIYLGYNVEYDDLVGYGIFGLIDAIDKFDHVKGVKFETYAS 89

Query: 107 WWIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
             IK A+ + I +  W    I  T  Q++     ++L+   +AI +   +      IA +
Sbjct: 90  LRIKGAILDQIRKMDW----IPRTMRQRQ-----KKLEAAERAIEEKYGRMATDEEIAAE 140

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG---------QEQVLI 216
           L +S  E  S   ++    S++ +I S D    Q  D LV D  G         Q +  +
Sbjct: 141 LGISVDEYGSWQSQV----SMSGII-SLDDYLEQGSD-LVADKSGSKLGISGFEQPEEAV 194

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           EKEE K     L  ++  L  +E+++      +E  +TL+ +S    VS  RV Q+  +A
Sbjct: 195 EKEELKES---LAVAIEGLTEKEQKVIALYYYEE--LTLKEISRVLSVSESRVSQLHTKA 249

Query: 277 FKKVQESIQKQVEL 290
             K++E +   +++
Sbjct: 250 LTKLKEKLGDYIDI 263


>gi|325289982|ref|YP_004266163.1| RNA polymerase, sigma subunit, RpoX/SigF [Syntrophobotulus
           glycolicus DSM 8271]
 gi|324965383|gb|ADY56162.1| RNA polymerase, sigma subunit, RpoX/SigF [Syntrophobotulus
           glycolicus DSM 8271]
          Length = 257

 Score = 57.0 bits (136), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 45/178 (25%), Positives = 90/178 (50%), Gaps = 16/178 (8%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           + P+L++QE   L  +  + GD  A  +L+  +L+L+  +   +   G  + ++   G I
Sbjct: 12  RFPLLKEQEMTELLHK-AQAGDHDAREQLINCNLKLIFNLIQRFTHRGYELEDLFQIGTI 70

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+ KFD   G + +TY++  I   ++ + LR    +K+  +   K L + + R + 
Sbjct: 71  GLIKAIDKFDFSYGVKFSTYAVPMIIGEIRRF-LRDDHPIKVPRSY--KELVYKIHRSRE 127

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
            L    + N +P  V  IA+ LNV   E+++         +L+A+ + +  N + +QD
Sbjct: 128 KLS--LELNREP-TVNEIAQDLNVGSEEIVT---------ALDAVQSPTSINDTLYQD 173


>gi|317502438|ref|ZP_07960602.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|331090300|ref|ZP_08339184.1| hypothetical protein HMPREF1025_02767 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|316896176|gb|EFV18283.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|330401435|gb|EGG81020.1| hypothetical protein HMPREF1025_02767 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 206

 Score = 57.0 bits (136), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 35/94 (37%), Positives = 56/94 (59%), Gaps = 3/94 (3%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+   +E+Y + ++Y E GDL A H L+  +LRLV  +   Y+       +++S G IGL
Sbjct: 7   PLTPSEEKYYI-RKYTE-GDLEAKHILIERNLRLVAHVIKKYQNSEEDPEDLISIGTIGL 64

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  F+P++G RLA Y+   I+  +  Y LRS
Sbjct: 65  IKAVVTFNPDKGNRLAAYASRCIENEILMY-LRS 97


>gi|226327187|ref|ZP_03802705.1| hypothetical protein PROPEN_01052 [Proteus penneri ATCC 35198]
 gi|225204405|gb|EEG86759.1| hypothetical protein PROPEN_01052 [Proteus penneri ATCC 35198]
          Length = 201

 Score = 57.0 bits (136), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 54/213 (25%), Positives = 102/213 (47%), Gaps = 30/213 (14%)

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQ-----KRLFF 137
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I      T N+     +++  
Sbjct: 1   MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQ 60

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + R +   + + +  L PE    I K L +++ E ISM   +  DE             
Sbjct: 61  EMGR-EPSPEELAERMLMPED--KIRKVLKIAK-EPISMETPIGDDED------------ 104

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 105 SHLGDFI---EDTTLELPLDSATSESLRSATHEVLAGLTLREAKVLRMRFGIDMNTDHTL 161

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           E +  +F+V+RER+RQIEA+A +K++   + +V
Sbjct: 162 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 194


>gi|23978298|dbj|BAC21128.1| principal sigma factor [Anabaena variabilis]
 gi|23978312|dbj|BAC21131.1| principal sigma factor [Nostoc linckia]
 gi|23978323|dbj|BAC21134.1| principal sigma factor [Anabaena variabilis]
 gi|23978327|dbj|BAC21135.1| principal sigma factor [Anabaenopsis circularis]
 gi|23978343|dbj|BAC21140.1| principal sigma factor [Chlorogloeopsis sp. PCC 6718]
 gi|23978354|dbj|BAC21143.1| principal sigma factor [Fischerella muscicola]
 gi|23978367|dbj|BAC21148.1| principal sigma factor [Chroococcidiopsis sp. PCC 7431]
 gi|26665388|dbj|BAC44905.1| principal sigma factor [Tolypothrix sp. IAM M-259]
 gi|26665392|dbj|BAC44907.1| principal sigma factor [Fischerella sp. IAM M-263]
 gi|26665394|dbj|BAC44908.1| principal sigma factor [Hapalosiphon sp. IAM M-264]
 gi|26665396|dbj|BAC44909.1| principal sigms factor [Hapalosiphon delicatulus IAM M-266]
 gi|26665398|dbj|BAC44910.1| principal sigma factor [Nostoc entophytum IAM M-267]
          Length = 188

 Score = 57.0 bits (136), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 51/199 (25%), Positives = 100/199 (50%), Gaps = 19/199 (9%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+   I      +++     
Sbjct: 4   GLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV--- 60

Query: 132 QKRLFFNLRRLKGHLQAIT-DNNLKP-EQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
              L+  + R+K   + ++ +   KP E+ +A   ++ + +   I+ + +L    SL   
Sbjct: 61  --HLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPI--SLETP 116

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFEARRL 248
           I   +   S+  D++  + DG+     E +  KN  R  L + +  L+PRER +   R  
Sbjct: 117 IGKEE--DSRLGDFI--ESDGETP---EDQVSKNLLREDLEKVLDSLSPRERDVLRLRYG 169

Query: 249 QENP--VTLENLSSEFEVS 265
            ++    TLE +   F V+
Sbjct: 170 LDDGRMKTLEEIGQIFNVT 188


>gi|317122054|ref|YP_004102057.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Thermaerobacter
           marianensis DSM 12885]
 gi|315592034|gb|ADU51330.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Thermaerobacter
           marianensis DSM 12885]
          Length = 251

 Score = 57.0 bits (136), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 37/102 (36%), Positives = 54/102 (52%), Gaps = 2/102 (1%)

Query: 10  VNGEIGLSRYIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           V G + L  Y+   R  P  L  +EE    +R R HGD  A   L+  +LRLV  IA  +
Sbjct: 14  VRGLLYLVGYLQTGRSFPQPLTPEEEAHYLERMR-HGDERARDVLIERNLRLVAHIAKKF 72

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
              G    +++S G +GL++ V  +DP +G RLATY+   I+
Sbjct: 73  DETGEDPEDLISIGTVGLIKGVDTYDPSKGTRLATYAARCIE 114


>gi|149177082|ref|ZP_01855690.1| sigma-70 factor [Planctomyces maris DSM 8797]
 gi|148844147|gb|EDL58502.1| sigma-70 factor [Planctomyces maris DSM 8797]
          Length = 556

 Score = 57.0 bits (136), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 59/236 (25%), Positives = 104/236 (44%), Gaps = 72/236 (30%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ S+LRLVV IA  +   G    E+VS+GN+ L++A++KFD  +G + +TY+       
Sbjct: 381 LIRSNLRLVVSIAKRHIRPGGNFFEMVSDGNMSLIRAIEKFDYTKGNKFSTYA------- 433

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
                  SW++                  +K + ++I                     +E
Sbjct: 434 -------SWAI------------------MKNYARSIP--------------------AE 448

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
              ++    G+E L     S+D+  SQ+++ L+     Q+Q  +           +   +
Sbjct: 449 YKVLDRFRTGNEEL--FFQSTDERESQYREELI----NQKQHAV-----------IMSIL 491

Query: 233 SVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             L+ RE+ I   R     +  P TLE +   F V++ER+RQ+E+RA KK++   Q
Sbjct: 492 DQLDGREKDILIYRYGLNARNEPQTLEQVGDRFGVTKERIRQLESRALKKLRRITQ 547


>gi|312794377|ref|YP_004027300.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
 gi|312876651|ref|ZP_07736632.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
 gi|311796604|gb|EFR12952.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
 gi|312181517|gb|ADQ41687.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
          Length = 256

 Score = 57.0 bits (136), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 40/180 (22%), Positives = 87/180 (48%), Gaps = 19/180 (10%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L + Y++  D+   + LV  HL +   IA  +   G+   ++     I L+ AV++F+P 
Sbjct: 18  LFEEYQKTKDIKLRNELVNKHLYIAEIIAKKFVNRGIDYEDLYQVACIALINAVERFEPN 77

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +G+R  +++   I   ++ Y     S++++      +R++    ++K   + ++    +P
Sbjct: 78  KGYRFTSFATPTIMGEIKRYFRDRASIIRLP-----RRIYETSAKIKLATEILSTKLKRP 132

Query: 157 EQVVAIAKKLNVSESEVI------------SMNCRLAGDE--SLNALINSSDKNSSQWQD 202
            +V  IA+ LN+S  EV+            S++  +  DE  +L  ++  SD+N  Q ++
Sbjct: 133 PKVEEIAQHLNMSTEEVLEVMEASSSYLPQSLDQTMYEDEEMTLGDVLGKSDENILQVEN 192


>gi|147678403|ref|YP_001212618.1| DNA-directed RNA polymerase specialized sigma subunit
           [Pelotomaculum thermopropionicum SI]
 gi|146274500|dbj|BAF60249.1| DNA-directed RNA polymerase specialized sigma subunit
           [Pelotomaculum thermopropionicum SI]
          Length = 256

 Score = 57.0 bits (136), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 69/261 (26%), Positives = 126/261 (48%), Gaps = 20/261 (7%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQAVKK 92
           L + YR   D    H +V S+L LV  +A G     LP      ++ S G +GL++AV+K
Sbjct: 7   LWREYRRSRDEKLKHEIVMSYLPLVKYLA-GRLAVKLPACIGQEDLESFGILGLLEAVEK 65

Query: 93  FDPERGFRLATYSMWWIKAA-MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           ++P+ G     Y+   I+ A + E+   +W    I  T  QK    +L   +  LQ    
Sbjct: 66  YNPDYGVSFKAYAYNRIRGAIIDEFRKLNW----IPRTMWQK--IQSLNNTRERLQGEAG 119

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
             +  E  +A A  +++ E   ++ +       SL+  +  +D    +W D ++ D +  
Sbjct: 120 ETVTSE-TLAGAMGISLPELHKLAWHASRLSLSSLDETVALADGELVRWGD-MIQDPESP 177

Query: 212 EQV-LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
           + + +IEKEE    R +L +++  L P + R+  +   QE  +TL+ + +  EVS  RV 
Sbjct: 178 DPLDIIEKEE---GRRLLVQAIEEL-PEKDRLVLSLYYQEG-LTLKEIGAVMEVSESRVC 232

Query: 271 QIEARAFKKVQESIQKQVELS 291
           Q+  RA  ++++ +++   LS
Sbjct: 233 QLHTRAINRLRKKLEQASGLS 253


>gi|268611133|ref|ZP_06144860.1| sporulation sigma factor SigE [Ruminococcus flavefaciens FD-1]
          Length = 232

 Score = 57.0 bits (136), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 34/94 (36%), Positives = 54/94 (57%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L +QEE  +  +  E  D +A   L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 30  PPLTRQEEAEVFMKL-EANDPAARKYLIEHNLRLVVYIAKKFESSGVGIEDLVSIGTIGL 88

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  F P +  +LATY+   I+  +  ++ +S
Sbjct: 89  IKAVNTFCPTKNIKLATYASRCIENEILMFLRKS 122


>gi|225028516|ref|ZP_03717708.1| hypothetical protein EUBHAL_02795 [Eubacterium hallii DSM 3353]
 gi|224954159|gb|EEG35368.1| hypothetical protein EUBHAL_02795 [Eubacterium hallii DSM 3353]
          Length = 209

 Score = 57.0 bits (136), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 41/111 (36%), Positives = 61/111 (54%), Gaps = 9/111 (8%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K P+  ++E Y L K YR+ GD  A  +L+  +LRLV  I   Y      + +++S G I
Sbjct: 5   KKPLKAEEERYYL-KMYRD-GDEKAKEKLIEHNLRLVAHIVKKYNSPDRDLDDLISIGTI 62

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVK-IGT 128
           GL++AV  FD  +G RL TY+   I+  +      ++ ILR  SL + IGT
Sbjct: 63  GLIKAVNTFDLNKGGRLVTYAARCIENELLMMIRQEKKILREVSLYEPIGT 113


>gi|160880601|ref|YP_001559569.1| sporulation sigma factor SigE [Clostridium phytofermentans ISDg]
 gi|160429267|gb|ABX42830.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           phytofermentans ISDg]
          Length = 246

 Score = 57.0 bits (136), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 27/75 (36%), Positives = 47/75 (62%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           D+ A   LV  +LRLVV IA  +   G+ + +++S G IGL++A+  F+P++  +LATY+
Sbjct: 60  DVEAKSLLVEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFNPDKNIKLATYA 119

Query: 106 MWWIKAAMQEYILRS 120
              I+  +  Y+ R+
Sbjct: 120 SRCIENEILMYLRRN 134


>gi|28210768|ref|NP_781712.1| RNA polymerase sigma factor [Clostridium tetani E88]
 gi|28203206|gb|AAO35649.1| RNA polymerase sigma factor [Clostridium tetani E88]
          Length = 182

 Score = 57.0 bits (136), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 36/101 (35%), Positives = 52/101 (51%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           I+   I L+ Y+      P   K EE     +  E GD+SA   L+  +LRLV  I   Y
Sbjct: 40  ILGSNILLTAYVTGNNSFPKPLKAEEEKYYLKQLEKGDISAKGVLIERNLRLVAHIVKKY 99

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              G  + +++S G IGL++A+  F  +RG RLATY+   I
Sbjct: 100 SFPGKDMDDLISIGTIGLIKAIDSFKIDRGTRLATYAAKCI 140


>gi|225574676|ref|ZP_03783286.1| hypothetical protein RUMHYD_02753 [Blautia hydrogenotrophica DSM
           10507]
 gi|225038103|gb|EEG48349.1| hypothetical protein RUMHYD_02753 [Blautia hydrogenotrophica DSM
           10507]
          Length = 239

 Score = 57.0 bits (136), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 63/261 (24%), Positives = 123/261 (47%), Gaps = 35/261 (13%)

Query: 34  EYVLAKRYREH-GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           E+ LA   R H GD  A   +   ++ L+  I   ++  G+ + ++   G+IGL++AV K
Sbjct: 4   EHTLALIARAHQGDKEARDTIFEENIGLIWSIVKRFQNRGVELEDLFQIGSIGLLKAVDK 63

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ--KRLFFNLRRLKGHLQAIT 150
           FD     + +TY++  I   ++ + LR   ++K+  +  +   + +    +L+  L    
Sbjct: 64  FDLSYDVKFSTYAVPMISGEIKRF-LRDDGMIKVSRSLKEVCYKAYLAREKLEKELG--- 119

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
               +  Q+  +A ++ + + E++     +A D   N  I S  K         +Y  +G
Sbjct: 120 ----RDPQIAEMAGEIGIPQEELM-----MALDS--NVEIESLQKT--------IYQGEG 160

Query: 211 QEQVLIEK-EERKNR------RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
            +  LI+K EE+KNR      R +L   +  L   ERR+   R  QE   T   ++ E  
Sbjct: 161 NDIRLIDKLEEKKNRQEESLNRILLEEILGQLTVSERRLIYMRYFQERTQT--EIARELG 218

Query: 264 VSRERVRQIEARAFKKVQESI 284
           VS+ +V ++E +  K++++ +
Sbjct: 219 VSQVQVSRMEKKILKRLRDKM 239


>gi|149917001|ref|ZP_01905502.1| DNA-directed RNA polymerase sigma subunit (RpoD) [Plesiocystis
           pacifica SIR-1]
 gi|149822279|gb|EDM81670.1| DNA-directed RNA polymerase sigma subunit (RpoD) [Plesiocystis
           pacifica SIR-1]
          Length = 411

 Score = 57.0 bits (136), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 69/282 (24%), Positives = 123/282 (43%), Gaps = 60/282 (21%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L+   RL    LRLV+ +   YR + +  +  +  G +GL +A+ +F+PERG++ +TY+ 
Sbjct: 159 LATRRRLFADSLRLVISLVHRYRKH-MDFATGMLRGALGLDKAIDRFEPERGWQFSTYAT 217

Query: 107 WWIK-------------------AAMQE---YILRS--WSLVKIGTTA----NQKRLFFN 138
           WWI+                   AA Q    ++++   WS   +  T     NQ    F+
Sbjct: 218 WWIRQNITRSSMDFATALRVPVHAAEQTTRFWMVQQELWSQTGVRPTDEEVLNQANFKFS 277

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           + RL  + +     +L     +  A+   + +S++ S+   L G+ +   +  + D  ++
Sbjct: 278 IERLGDYRRHARTAHLTRRDQLGAAEA--ILDSDIPSL---LEGNPASGWVRAAIDHATA 332

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           Q  D               KE  +  R    R  ++ +   RRI    ++Q N  TL  L
Sbjct: 333 QVDD---------------KEHSRPSRG---RWHAIFS---RRIL-GDQIQNN--TLREL 368

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQKP 300
             EF+++RER+RQ EA+    +   + +  E    PPL   P
Sbjct: 369 GEEFDITRERIRQNEAKLIDFLARRLFRGQE--HLPPLAWGP 408


>gi|117927772|ref|YP_872323.1| RNA polymerase, sigma 28 subunit [Acidothermus cellulolyticus 11B]
 gi|117648235|gb|ABK52337.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Acidothermus
           cellulolyticus 11B]
          Length = 287

 Score = 57.0 bits (136), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 66/240 (27%), Positives = 110/240 (45%), Gaps = 30/240 (12%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV +HL LV  +A  +R  G P  ++V    IGL++A+ +FD ERG   +TY+   I   
Sbjct: 66  LVQTHLPLVEYLARRFRNRGEPHDDLVQVATIGLIKAIDRFDVERGVEFSTYATPTIVGE 125

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD----NNLKPEQVVAIAKKLN 167
           ++ Y   R W++          R+   L+ LK  L   T        +   V  +A  L 
Sbjct: 126 IKRYFRDRGWAI----------RVPRRLQELKMSLAKATSELSQQYGRAPTVSELADHLG 175

Query: 168 VSESEVISMNCRLAGDESLNA--LINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNR 224
           +SE E+      L G ES NA   I+     +       V D  G  ++ L   E R++ 
Sbjct: 176 MSEDEI------LEGLESANAYSTISLDTPETDDADALAVADTLGNIDEALEGVEYRESL 229

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + +L +    L PRE+RI   R  +   +T   +++E  +S+  V ++ AR   +++E +
Sbjct: 230 KPLLEK----LPPREKRILLLRFFRN--MTQSQIAAELGISQMHVSRLLARTLARLREGL 283


>gi|325262838|ref|ZP_08129574.1| RNA polymerase sigma-K factor [Clostridium sp. D5]
 gi|324031932|gb|EGB93211.1| RNA polymerase sigma-K factor [Clostridium sp. D5]
          Length = 212

 Score = 57.0 bits (136), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 32/91 (35%), Positives = 53/91 (58%), Gaps = 2/91 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+   +E+Y + K Y E GDL A H L+  +LRLV  +   Y+       +++S G IGL
Sbjct: 14  PLTPSEEKYYMQK-YTE-GDLQAKHVLIERNLRLVAHVIKKYQYLDEDPEDLISIGTIGL 71

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           ++AV  F+P++G RLA Y+   ++  +  Y+
Sbjct: 72  IKAVVTFNPDKGNRLAAYASKCVENEILMYL 102


>gi|119476594|ref|ZP_01616904.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2143]
 gi|119449850|gb|EAW31086.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2143]
          Length = 194

 Score = 57.0 bits (136), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 52/197 (26%), Positives = 95/197 (48%), Gaps = 16/197 (8%)

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           PERGFR +TY+ WWI+  ++  I+     +++      K L   LR  +   Q + D+  
Sbjct: 1   PERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-VKELNVYLRAARELTQKL-DHEP 58

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            PE++  +  +       ++ +N R+A  D  L A    SDK+     D +   H     
Sbjct: 59  TPEEIAELLDRPVADVKRMLRLNERVASVDTPLGA---DSDKS---LLDTIPDTHVSDPA 112

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVR 270
            +++ ++ K     ++  +  L  ++R +  ARR         TLE +  E  ++RERVR
Sbjct: 113 EMLQDDDMKAS---ISEWIGELTEKQREVV-ARRFGLRGYETSTLEEVGREIGLTRERVR 168

Query: 271 QIEARAFKKVQESIQKQ 287
           QI+  A K++++ ++KQ
Sbjct: 169 QIQVEALKRLRDILEKQ 185


>gi|23978347|dbj|BAC21141.1| principal sigma factor [Oscillatoria sp. PCC 7112]
          Length = 188

 Score = 57.0 bits (136), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 48/198 (24%), Positives = 99/198 (50%), Gaps = 17/198 (8%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+   I      +++     
Sbjct: 4   GLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV--- 60

Query: 132 QKRLFFNLRRLKGHLQAIT-DNNLKP-EQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
              L+  + R+K   + ++ +   KP E+ +A   ++ + +   I+ + +L    SL   
Sbjct: 61  --HLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPI--SLETP 116

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   +   S+  D++  D +  E  + +   R++  ++L      L+PRER +   R   
Sbjct: 117 IGKEE--DSRLGDFIESDGETPEDQVSKNLLREDLESVL----DTLSPRERDVLRLRYGL 170

Query: 250 ENP--VTLENLSSEFEVS 265
           ++    TLE +   F V+
Sbjct: 171 DDGRMKTLEEIGQIFNVT 188


>gi|261405674|ref|YP_003241915.1| sporulation sigma factor SigG [Paenibacillus sp. Y412MC10]
 gi|315646040|ref|ZP_07899161.1| sporulation sigma factor SigG [Paenibacillus vortex V453]
 gi|329922674|ref|ZP_08278226.1| RNA polymerase sigma-G factor [Paenibacillus sp. HGF5]
 gi|261282137|gb|ACX64108.1| RNA polymerase, sigma 28 subunit, SigG [Paenibacillus sp. Y412MC10]
 gi|315278801|gb|EFU42115.1| sporulation sigma factor SigG [Paenibacillus vortex V453]
 gi|328942016|gb|EGG38299.1| RNA polymerase sigma-G factor [Paenibacillus sp. HGF5]
          Length = 260

 Score = 57.0 bits (136), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 62/274 (22%), Positives = 131/274 (47%), Gaps = 42/274 (15%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L   E   L    +++ + SA  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLTNVEMRELFHNLQQNNERSAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGCI 74

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A+  FD  +  + +TY++  I   ++ Y LR  + +++  +   + + +   +++ 
Sbjct: 75  GLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSL--RDIAYKALQVRD 131

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L   T+ N +   +  I++ LNV + +V+          +L+A+           QD +
Sbjct: 132 QL---TNANSREPTIFEISEALNVPKEDVVF---------ALDAI-----------QDPV 168

Query: 205 -----VYDHDGQEQVLIEKE--ERKNR------RNMLTRSMSVLNPRERRIFEARRLQEN 251
                +Y HDG + + +  +  + KN+         L  +M  L  RE+ I  + R  E 
Sbjct: 169 SLFEPIY-HDGGDPIYVMDQISDDKNKDVSWIEEIALREAMHKLGQREKMIL-SMRFYEG 226

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              +E ++ E  +S+ +V ++E  A K++Q+ ++
Sbjct: 227 KTQME-VADEIGISQAQVSRLEKSAIKQMQKHVK 259


>gi|23978302|dbj|BAC21129.1| principal sigma factor [Oscillatoria agardhii]
          Length = 188

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 48/198 (24%), Positives = 99/198 (50%), Gaps = 17/198 (8%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL   +++ EG++GL++A +KF+ E+G++ +TY+ WWI+ A+   I      +++     
Sbjct: 4   GLSFQDLIQEGSLGLIRAAEKFEHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV--- 60

Query: 132 QKRLFFNLRRLKGHLQAIT-DNNLKP-EQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
              L+  + R+K   + ++ +   KP E+ +A   ++ + +   I+ + +L    SL   
Sbjct: 61  --HLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPI--SLETP 116

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   +   S+  D++  D +  E  + +   R++  N+L      L+PRER +   R   
Sbjct: 117 IGKEE--DSRLGDFIESDGETPEDQVSKNLLREDLENVL----DTLSPRERDVLRLRYGL 170

Query: 250 ENP--VTLENLSSEFEVS 265
           ++    TLE +   F V+
Sbjct: 171 DDGRMKTLEEIGQIFNVT 188


>gi|297200783|ref|ZP_06918180.1| RNA polymerase sigma-G factor [Streptomyces sviceus ATCC 29083]
 gi|197712353|gb|EDY56387.1| RNA polymerase sigma-G factor [Streptomyces sviceus ATCC 29083]
          Length = 297

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 62/237 (26%), Positives = 105/237 (44%), Gaps = 23/237 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +   
Sbjct: 76  LIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTVVGE 135

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL   L +    L    D +     V  +A  L VSE 
Sbjct: 136 IKRFFRDTSWS-VRVPRRLQELRL--ALTKASDELSQKLDRS---PTVAELASVLGVSEE 189

Query: 172 EVIS----MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +V+      N   A   SL++     D       D L Y+    E V    E R++ + +
Sbjct: 190 DVVDGLAVGNAYTAS--SLDSPAPEDDGGEGSLADRLGYEDTALEGV----EYRESLKPL 243

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L +    L PRER+I   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 244 LAK----LPPRERQIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 294


>gi|110802253|ref|YP_699047.1| sporulation sigma factor SigG [Clostridium perfringens SM101]
 gi|110682754|gb|ABG86124.1| RNA polymerase sigma-G factor [Clostridium perfringens SM101]
          Length = 257

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 59/266 (22%), Positives = 129/266 (48%), Gaps = 29/266 (10%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+++E   L  +  ++GD SA  + +  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKEKEMKELLLQM-QNGDTSAREKFIKGNLRLVLSVIQRFNNRGENVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD  +  + +TY++  I   ++ Y LR  + +++  +   + + +    ++ 
Sbjct: 74  GLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNTIRVSRSL--RDIAYKALLVRD 130

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L  + +NN +P  V  IAK+L +   +V+          +L+A+     ++     + +
Sbjct: 131 KL--VNENNKEP-TVSQIAKELKIPREDVVF---------ALDAI-----QDPVSLFEPI 173

Query: 205 VYDHDGQEQVLIEKEERKNRRN------MLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
            YD      V+ +  + KN+ +       +  +M  LN RE+ I   R    N  T   +
Sbjct: 174 YYDGGDAIYVMDQISDSKNQDDSWLENIAIKEAMKKLNDREKLILNLRFF--NGRTQMEV 231

Query: 259 SSEFEVSRERVRQIEARAFKKVQESI 284
           + E  +S+ +V ++E  A K +++ +
Sbjct: 232 ADEIGISQAQVSRLEKIALKHMRKYV 257


>gi|51894120|ref|YP_076811.1| RNA polymerase sigma factor related to flagellar biosynthesis
           [Symbiobacterium thermophilum IAM 14863]
 gi|51857809|dbj|BAD41967.1| RNA polymerase sigma factor related to flagellar biosynthesis
           [Symbiobacterium thermophilum IAM 14863]
          Length = 253

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 62/254 (24%), Positives = 118/254 (46%), Gaps = 17/254 (6%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKK 92
           L +R+R+  D +A   LV  +L LV  +A G    G+P      +V   G  GL++A+ +
Sbjct: 6   LWQRWRQSHDTAARDALVQHYLWLVRYVA-GRLMVGMPDHVDQGDVEGHGCFGLLEAIAR 64

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           +DP+RG R  T+++ WI+ A  E       L  +      +R    L R++  L A+   
Sbjct: 65  YDPDRGVRFETFAIPWIRGACLE------GLRAMQWAPALRRRVRQLERVRDELMAVLGR 118

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
                + +A    ++V E+E            SL+  +   D  ++   D  V D +  +
Sbjct: 119 EPSAAE-LAEQMGISVEEAERRLQEAGTLAVLSLDEALAFDDGETTALAD-RVADEEAVD 176

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
             L  + +R  RR +L R+++ L  +E+ +  A   QE  +  E +S    +S+ R+ Q+
Sbjct: 177 PEL--ESQRAERREVLARAIASLTEQEQLVI-ALIYQEGLIAKE-VSEILGLSQARISQV 232

Query: 273 EARAFKKVQESIQK 286
            ++A  +++  + +
Sbjct: 233 HSKAILRLRGKLSR 246


>gi|225574871|ref|ZP_03783481.1| hypothetical protein RUMHYD_02949 [Blautia hydrogenotrophica DSM
           10507]
 gi|225037945|gb|EEG48191.1| hypothetical protein RUMHYD_02949 [Blautia hydrogenotrophica DSM
           10507]
          Length = 230

 Score = 57.0 bits (136), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 31/83 (37%), Positives = 51/83 (61%), Gaps = 2/83 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  ++E Y L K+++E GDL A   L+  +LRLV  +   Y+G    + +++S G IGL
Sbjct: 29  PLTVEEERYYL-KKFQE-GDLKAKDILIERNLRLVAHVVKKYQGLEEDLDDLISIGTIGL 86

Query: 87  MQAVKKFDPERGFRLATYSMWWI 109
           ++AV  FD ++  RL+TY+   I
Sbjct: 87  IKAVSTFDSKKSNRLSTYAARCI 109


>gi|117928753|ref|YP_873304.1| RNA polymerase sigma factor WhiG [Acidothermus cellulolyticus 11B]
 gi|117649216|gb|ABK53318.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Acidothermus
           cellulolyticus 11B]
          Length = 289

 Score = 56.6 bits (135), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 62/260 (23%), Positives = 120/260 (46%), Gaps = 26/260 (10%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFD 94
           +R++E GD     RL+  H   +VK   G  G GLP     +++VS G  GL+ A++KFD
Sbjct: 44  RRFKETGDPELRERLIL-HYSPLVKYVAGRVGVGLPPNIEQADLVSYGIFGLIDAIEKFD 102

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
            +R  +  TY++  IK A+ +  LR+   +        + + +  R ++    A+     
Sbjct: 103 LDRAIKFETYAINRIKGAIIDE-LRAIDWIP-------RSVRYKAREVEKAYAALEHKLH 154

Query: 155 KPEQVVAIAKKLNVSESEV------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           +      +A +L +S  E+      +S    +A DE LN   +  D+ S    D L    
Sbjct: 155 RTPTEAEVAAELGISLDELHAIFSQVSFVNVIALDELLNVGGDRGDRLS--LVDTL---E 209

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D + +  +E  E +  + +L+R+++ L  RE+ +      +   +TL  +     V+  R
Sbjct: 210 DTKAEDPVEAFETEETKYLLSRAINALPEREKIVITLYYYE--GLTLAEIGQVLGVTESR 267

Query: 269 VRQIEARAFKKVQESIQKQV 288
           + Q+  +A  +++  + +Q 
Sbjct: 268 ICQMHTKAVLQLRAKLAEQT 287


>gi|251797866|ref|YP_003012597.1| sporulation sigma factor SigG [Paenibacillus sp. JDR-2]
 gi|247545492|gb|ACT02511.1| RNA polymerase, sigma 28 subunit, SigG [Paenibacillus sp. JDR-2]
          Length = 260

 Score = 56.6 bits (135), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 66/280 (23%), Positives = 126/280 (45%), Gaps = 54/280 (19%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L   E   L    +   + +A  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLTNAEMRELFTALQTQNEWAAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGCI 74

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEY------ILRSWSLVKIGTTANQKRLFFN 138
           GLM+A+  FD  +  + +TY++  I   ++ Y      I  S SL  I   A Q R    
Sbjct: 75  GLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLRDIAYKALQVR---- 130

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
                    ++T+ N +   +  I++ LNV + +V+          +L+A+         
Sbjct: 131 --------DSLTNQNSREPTIFEISEALNVPKEDVVF---------ALDAI--------- 164

Query: 199 QWQDWL-----VYDHDGQEQVLIEKE--ERKNR------RNMLTRSMSVLNPRERRIFEA 245
             QD +     +Y HDG + + +  +  + KN+         L  +M  LN RE+ I  +
Sbjct: 165 --QDPVSLFEPIY-HDGGDPIYVMDQISDDKNKDVSWIEEIALREAMHKLNDREKMIL-S 220

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            R  E    +E ++ E  +S+ +V ++E  A +++Q+ ++
Sbjct: 221 MRFFEGKTQME-VADEIGISQAQVSRLEKSAIQQMQKHVK 259


>gi|85706634|ref|ZP_01037726.1| RNA polymerase sigma subunit [Roseovarius sp. 217]
 gi|85668692|gb|EAQ23561.1| RNA polymerase sigma subunit [Roseovarius sp. 217]
          Length = 830

 Score = 56.6 bits (135), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 57/236 (24%), Positives = 106/236 (44%), Gaps = 27/236 (11%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           SA   L+  HL  V + A      G    +V     +GL ++ ++FDPERG+R   Y+ +
Sbjct: 498 SATEHLIREHLPYVRRFASRNVEEGEEPEDVFQVAFMGLQRSTRRFDPERGYRFLIYATY 557

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQK--RLFFNLRRLKGHL-QAITDNNLKPEQVVAIAK 164
           W++ A+  +     + ++I    N+K  +L   L RL   +  A++D +L        A+
Sbjct: 558 WMRQAIMRWRADEGAAIRIPVHRNEKVTKLDRALDRLDVRVGGAVSDLDL--------AE 609

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L  +  EV    C           I    +  +   DW   D+   E   ++  ++   
Sbjct: 610 ELEWAIDEVRQFRC-----------IPRKAEYPASLDDW---DNLLPEPSEVDVLDQAET 655

Query: 225 RNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFK 278
             ++T +++ L  R+  +   R     ++ +TLE +   + V+RER+RQIEA+   
Sbjct: 656 ERIVTEALADLPERQADVIRMRFGIGHDSEMTLEEIGQIYGVTRERIRQIEAKGLD 711


>gi|297617167|ref|YP_003702326.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
 gi|297145004|gb|ADI01761.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
          Length = 258

 Score = 56.6 bits (135), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 64/258 (24%), Positives = 121/258 (46%), Gaps = 26/258 (10%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAM----GYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           RY++ GD+ A   L+  +  LV  IA         + + + E++S G  GL+ AV +FDP
Sbjct: 12  RYKDEGDIEARDELILHYAGLVKYIAARLFPNLSSHQVELDELISYGIEGLIDAVHRFDP 71

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITDNNL 154
           +R  +  TY++  IK A+ +  LR+   + +      K L      L+  L +A TD  +
Sbjct: 72  KRKVKFETYALARIKGAIIDG-LRAMDWIPVSLRHKAKELEKAYCLLEHRLGRAATDEEM 130

Query: 155 KPEQVVAIAKKLN----VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
             E  ++I +  N    V+ + +I +   + GDE         DKN       ++ D   
Sbjct: 131 ACELGMSIPEFQNLLKEVNLATIIYLEDLIPGDE--------GDKNKRIAD--VIKDERA 180

Query: 211 QEQV-LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
           ++ + LIE EE K    +L  ++++L  +ER +      +   +TL+ +     +S  R+
Sbjct: 181 EDGLELIEFEESK---RLLAEAIALLPEKERTVVTLYYYE--GLTLKEIGEVLGLSESRI 235

Query: 270 RQIEARAFKKVQESIQKQ 287
            Q+  +A  +++  + K+
Sbjct: 236 SQLHTKAILRLRGRLGKK 253


>gi|328883832|emb|CCA57071.1| RNA polymerase sigma factor SigB [Streptomyces venezuelae ATCC
           10712]
          Length = 303

 Score = 56.6 bits (135), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 62/237 (26%), Positives = 105/237 (44%), Gaps = 23/237 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +   
Sbjct: 82  LIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTVVGE 141

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL   L +    L    D +     V  +A  L VSE 
Sbjct: 142 IKRFFRDTSWS-VRVPRRLQELRL--ALTKASDELAQKLDRS---PTVTELAAVLGVSEE 195

Query: 172 EVIS----MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +V+      N   A   SL++     D       D L Y+    E V    E R++ + +
Sbjct: 196 DVVDGLAVGNAYTA--SSLDSPSPEDDGGEGSLADRLGYEDTALEGV----EYRESLKPL 249

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L +    L PRER+I   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 250 LAK----LPPRERQIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 300


>gi|302874716|ref|YP_003843349.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           cellulovorans 743B]
 gi|307690671|ref|ZP_07633117.1| sporulation sigma factor SigK [Clostridium cellulovorans 743B]
 gi|302577573|gb|ADL51585.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           cellulovorans 743B]
          Length = 233

 Score = 56.6 bits (135), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 41/106 (38%), Positives = 61/106 (57%), Gaps = 5/106 (4%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIP--MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           M++IVN  + LS YI      P  + E++E+Y L K   + GDL +   LV  +LRLV  
Sbjct: 7   MNLIVNMTM-LSGYISNGNSFPKPLEEEEEKYHLQKL--KEGDLLSKSILVERNLRLVAH 63

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           I   Y G G    E++S G +GL++A+  F+ ++G RLATY+   I
Sbjct: 64  IVKKYSGVGKDSDELISIGTVGLIKAIDSFNVDKGTRLATYAARCI 109


>gi|89099505|ref|ZP_01172381.1| sigma factor B [Bacillus sp. NRRL B-14911]
 gi|89085891|gb|EAR65016.1| sigma factor B [Bacillus sp. NRRL B-14911]
          Length = 264

 Score = 56.6 bits (135), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 70/264 (26%), Positives = 130/264 (49%), Gaps = 32/264 (12%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLM 87
           K+E   L K Y+E+ D  A   LV ++  LV  IA  Y   R Y   I++V   G IGL+
Sbjct: 12  KEEINELIKAYQENQDEEAQEILVRNYKALVETIARKYSKGRSYHEDIAQV---GIIGLL 68

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHL 146
            A++++D   G     +++  I   ++ ++  ++WS+         +R+     ++K  +
Sbjct: 69  GAIRRYDETFGKSFEAFAVPTIIGEIKRFLRDKTWSV------HVPRRIKELGPKIKTTV 122

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQW 200
           + +T    +  +V  IA ++ VSE EV+ +M        L+ D S+ A    SD  +   
Sbjct: 123 EELTTQLHRSPRVDEIADEIGVSEEEVLEAMEMGKSYQALSVDHSIEA---DSDGGTVTL 179

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
            D +    +G E+V        N+R +L R + VL  RE++I +   L+   ++ ++   
Sbjct: 180 LDIVGNVDEGFEKV--------NQRMVLERVLHVLTDREKQIIQYTYLEN--MSQKDAGD 229

Query: 261 EFEVSRERVRQIEARAFKKVQESI 284
           +  +S+  V +++ RA KK+QE+I
Sbjct: 230 KLGISQMHVSRLQRRAIKKLQEAI 253


>gi|308069872|ref|YP_003871477.1| RNA polymerase sigma-G factor (stage III sporulation protein G)
           [Paenibacillus polymyxa E681]
 gi|305859151|gb|ADM70939.1| RNA polymerase sigma-G factor (Stage III sporulation protein G)
           [Paenibacillus polymyxa E681]
          Length = 260

 Score = 56.6 bits (135), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 65/280 (23%), Positives = 125/280 (44%), Gaps = 54/280 (19%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L   E   L    +++ + SA  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLTNAEMRELFTSLQQNNERSAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGCI 74

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEY------ILRSWSLVKIGTTANQKRLFFN 138
           GLM+A+  FD  +  + +TY++  I   ++ Y      I  S SL  I   A Q R    
Sbjct: 75  GLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLRDIAYKALQVR---- 130

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
                    ++T+ N +   +  I++ LNV + +V+          +L+A+         
Sbjct: 131 --------DSLTNLNSREPTIFEISEALNVPKEDVVF---------ALDAI--------- 164

Query: 199 QWQDWL-----VYDHDGQEQVLIEKEERKNRRN--------MLTRSMSVLNPRERRIFEA 245
             QD +     +Y HDG + + +  +   +R           L  +M  L  RE+ I  +
Sbjct: 165 --QDPVSLFEPIY-HDGGDPIYVMDQISDDRNKDVSWIEEIALREAMHRLGQREKMIL-S 220

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            R  E    +E ++ E  +S+ +V ++E  A +++Q+ ++
Sbjct: 221 MRFYEGKTQME-VADEIGISQAQVSRLEKSAIQQMQKHVK 259


>gi|197723815|gb|ACH72687.1| RNA polymerase sigma-37 factor [Listeria marthii]
          Length = 242

 Score = 56.6 bits (135), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 62/257 (24%), Positives = 123/257 (47%), Gaps = 26/257 (10%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 5   KEKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 64

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +++D   G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +
Sbjct: 65  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEEL 118

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDW 203
           T       Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D 
Sbjct: 119 TRELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDV 175

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    DG E+V        N+R +L + + VL+ RE++I +   ++    + +      +
Sbjct: 176 VGGTDDGFERV--------NQRMLLEKVLPVLDEREQKILQYTFIENR--SQKETGELLD 225

Query: 264 VSRERVRQIEARAFKKV 280
           +S+  V +I+ +A KK+
Sbjct: 226 ISQMHVSRIQRQAIKKL 242


>gi|307328850|ref|ZP_07608020.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306885515|gb|EFN16531.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 276

 Score = 56.6 bits (135), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 62/237 (26%), Positives = 105/237 (44%), Gaps = 23/237 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +   
Sbjct: 55  LIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTVVGE 114

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL   L +    L    D +     V  +A  L VSE 
Sbjct: 115 IKRFFRDTSWS-VRVPRRLQELRL--ALTKASDELSQRLDRS---PTVPELATALGVSEE 168

Query: 172 EVIS----MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +V+      N   A   SL++     D       D L Y+    E V    E R++ + +
Sbjct: 169 DVVDGLAVGNAYTA--SSLDSPSPEDDGGEGSLADRLGYEDSALEGV----EYRESLKPL 222

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L +    L PRER+I   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 223 LAK----LPPRERQIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 273


>gi|158320420|ref|YP_001512927.1| sporulation sigma factor SigE [Alkaliphilus oremlandii OhILAs]
 gi|158140619|gb|ABW18931.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           oremlandii OhILAs]
          Length = 244

 Score = 56.6 bits (135), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 34/95 (35%), Positives = 54/95 (56%), Gaps = 3/95 (3%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHR-LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           P L   EE +L  + +   D S     L+  +LRLVV IA  +   G+ I +++S G IG
Sbjct: 42  PPLSNDEENLLISKLK--SDESTVRTILIERNLRLVVYIARKFENTGIGIEDLISIGTIG 99

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           L++AV  F+PE+  +LATY+   I+  +  Y+ R+
Sbjct: 100 LIKAVNTFNPEKNIKLATYASRCIENEILMYLRRN 134


>gi|158320421|ref|YP_001512928.1| sporulation sigma factor SigG [Alkaliphilus oremlandii OhILAs]
 gi|158140620|gb|ABW18932.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           oremlandii OhILAs]
          Length = 257

 Score = 56.6 bits (135), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 66/266 (24%), Positives = 124/266 (46%), Gaps = 29/266 (10%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           ++P+L+  +  VL  R  + GD SA    +  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  ELPVLKNSQMRVLFDRIHK-GDNSAREEFIQGNLRLVLSVIQRFNNRGEHVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD     R +TY++  I   ++ Y LR  + +++  +          + L+ 
Sbjct: 74  GLIKAIDNFDLSHNVRFSTYAVPMIIGEIRRY-LRDNNSIRVSRSLRDTA----YKALQV 128

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD-- 202
             Q I  N+ +P  +  IA++LN+   +V+          +L+A+ +        +QD  
Sbjct: 129 REQLINKNSKEP-TIAQIAEELNLPREDVVF---------ALDAIQDPVSLFEPIYQDSG 178

Query: 203 --WLVYDHDGQEQVLIEKEERKNRRN--MLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
               V D     QV  EK E +   +   L  +M  LN RE+ I  + R  E    +E +
Sbjct: 179 DAIFVMD-----QVCDEKSEDECWIDGIALREAMRKLNSREKHIL-SLRFFEGRTQME-V 231

Query: 259 SSEFEVSRERVRQIEARAFKKVQESI 284
           + E  +S+ +V ++E  A K +++ I
Sbjct: 232 ADEIGISQAQVSRLEKTALKHMRKYI 257


>gi|258511987|ref|YP_003185421.1| RNA polymerase, sigma 28 subunit, SigK [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
 gi|257478713|gb|ACV59032.1| RNA polymerase, sigma 28 subunit, SigK [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
          Length = 239

 Score = 56.6 bits (135), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 27/73 (36%), Positives = 46/73 (63%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A +RL+  +LRLV  +A  Y   G  + +++S G IGL++AV+ + P++G +LATY
Sbjct: 46  GDADARNRLIEHNLRLVAHLAKKYESSGEEMDDLISIGTIGLIKAVESYRPDKGTKLATY 105

Query: 105 SMWWIKAAMQEYI 117
           +   I+  +  Y+
Sbjct: 106 AARCIENEILMYL 118


>gi|225175484|ref|ZP_03729478.1| RNA polymerase, sigma 28 subunit, SigG [Dethiobacter alkaliphilus
           AHT 1]
 gi|225168813|gb|EEG77613.1| RNA polymerase, sigma 28 subunit, SigG [Dethiobacter alkaliphilus
           AHT 1]
          Length = 277

 Score = 56.6 bits (135), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 65/273 (23%), Positives = 129/273 (47%), Gaps = 41/273 (15%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+  E   L  R RE GD SA  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 34  KLPVLKNDEMRRLFARLRE-GDESAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 92

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD  +  + +TY++  I   ++ Y LR  + +++  +         LR +  
Sbjct: 93  GLIKAIDNFDLGQNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRS---------LRDIAY 142

Query: 145 HLQAITD---NNLKPEQVVA-IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
            +  + D   N    E  ++ IAK+LN+   +++          +L+A+     +  S +
Sbjct: 143 KVLQVRDSLANRFAREPTISEIAKELNLKREDIVF---------ALDAI----QEPVSLF 189

Query: 201 QDWLVYDHDGQEQVLIEKE--ERKNRRN------MLTRSMSVLNPRERRIFEARRLQENP 252
           +   +Y HDG + + +  +  + KN  N       +  ++  LN RE+ I   R  +   
Sbjct: 190 EP--IY-HDGGDPIFVMDQISDDKNHDNKWLEVLAINEALHKLNEREKLILTLRFYRGK- 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            T   ++ E  +S+ +V ++E  A   +++ +Q
Sbjct: 246 -TQMEVADEIGISQAQVSRLEKAALSHLRKHVQ 277


>gi|302389526|ref|YP_003825347.1| RNA polymerase, sigma subunit, RpsG/SigG [Thermosediminibacter
           oceani DSM 16646]
 gi|302200154|gb|ADL07724.1| RNA polymerase, sigma subunit, RpsG/SigG [Thermosediminibacter
           oceani DSM 16646]
          Length = 257

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 67/273 (24%), Positives = 127/273 (46%), Gaps = 47/273 (17%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L   +   L  R ++ GD  A  +L+  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLSNSKMKELFLRVKQ-GDKEAREKLIHGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEY------ILRSWSLVKIGTTANQKRLFFN 138
           GLM+A+  FD  +  + +TY++  I   ++ Y      I  S SL  I   A Q R    
Sbjct: 74  GLMKAIDNFDLNQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLRDIAYKALQVR---- 129

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
                    ++ + N +   +  IAK++N+   E++          +L+A+     +  S
Sbjct: 130 --------DSLVNKNSREPSIEEIAKEMNIPSEEIVM---------ALDAI----QEPIS 168

Query: 199 QWQDWLVYDHDGQEQVLIEK---EERKNRRNMLTRSMSV------LNPRERRIFEARRLQ 249
            ++   +Y HDG + + +     +++ N  N L RS+S+      LN RE+ I   R   
Sbjct: 169 LFEP--IY-HDGGDPIFVMDQISDDKNNDENWL-RSISIKEAMQKLNEREKLILTLRFF- 223

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           E    +E ++ E  +S+ +V ++E  A K +++
Sbjct: 224 EGKTQME-VAQEIGISQAQVSRLEKAALKHLKK 255


>gi|319654668|ref|ZP_08008747.1| sigma factor B [Bacillus sp. 2_A_57_CT2]
 gi|317393584|gb|EFV74343.1| sigma factor B [Bacillus sp. 2_A_57_CT2]
          Length = 264

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 69/268 (25%), Positives = 127/268 (47%), Gaps = 32/268 (11%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLM 87
           K+E   L K Y+ H D  A + LV  +  LV  IA  Y   R Y   I +V   G IGL+
Sbjct: 12  KEETNALIKAYQLHQDEDAQNTLVLQYQNLVEAIARKYSKGRSYHEDIVQV---GIIGLL 68

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHL 146
            A++++D   G     +++  I   ++ ++  ++WS+         +R+     ++K  +
Sbjct: 69  GAIRRYDESFGKTFEAFAVPTIIGEIKRFLRDKTWSV------HVPRRIKELGPKIKATV 122

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQW 200
           + +T    +  +V  IA  L VSE EV+ +M        L+ D S+ A    SD  +   
Sbjct: 123 EELTTELHRSPRVDEIADVLGVSEEEVLEAMEMGKSYQALSVDHSIEA---DSDGGTVTL 179

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
            D +  + +G E+V        N+  +L + + VL+ RE+ I +   L+   ++ +    
Sbjct: 180 LDIVGNEDEGYEKV--------NQMLVLDKVLHVLSEREKLIIQYTYLEN--MSQKEAGD 229

Query: 261 EFEVSRERVRQIEARAFKKVQESIQKQV 288
           +  +S+  V +++ RA KK+QE+I  + 
Sbjct: 230 KLGISQMHVSRLQRRAIKKLQEAIHSET 257


>gi|110799379|ref|YP_696447.1| sporulation sigma factor SigG [Clostridium perfringens ATCC 13124]
 gi|168207288|ref|ZP_02633293.1| RNA polymerase sigma-G factor [Clostridium perfringens E str.
           JGS1987]
 gi|168210606|ref|ZP_02636231.1| RNA polymerase sigma-G factor [Clostridium perfringens B str. ATCC
           3626]
 gi|168214238|ref|ZP_02639863.1| RNA polymerase sigma-G factor [Clostridium perfringens CPE str.
           F4969]
 gi|168217048|ref|ZP_02642673.1| RNA polymerase sigma-G factor [Clostridium perfringens NCTC 8239]
 gi|169342669|ref|ZP_02863710.1| RNA polymerase sigma-G factor [Clostridium perfringens C str.
           JGS1495]
 gi|182625828|ref|ZP_02953594.1| RNA polymerase sigma-G factor [Clostridium perfringens D str.
           JGS1721]
 gi|110674026|gb|ABG83013.1| RNA polymerase sigma-G factor [Clostridium perfringens ATCC 13124]
 gi|169299175|gb|EDS81245.1| RNA polymerase sigma-G factor [Clostridium perfringens C str.
           JGS1495]
 gi|170661342|gb|EDT14025.1| RNA polymerase sigma-G factor [Clostridium perfringens E str.
           JGS1987]
 gi|170711289|gb|EDT23471.1| RNA polymerase sigma-G factor [Clostridium perfringens B str. ATCC
           3626]
 gi|170714329|gb|EDT26511.1| RNA polymerase sigma-G factor [Clostridium perfringens CPE str.
           F4969]
 gi|177908862|gb|EDT71354.1| RNA polymerase sigma-G factor [Clostridium perfringens D str.
           JGS1721]
 gi|182380954|gb|EDT78433.1| RNA polymerase sigma-G factor [Clostridium perfringens NCTC 8239]
          Length = 257

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 62/273 (22%), Positives = 132/273 (48%), Gaps = 43/273 (15%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+++E   L  +  ++GD SA  + +  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKEKEMKELLLQM-QNGDTSAREKFIKGNLRLVLSVIQRFNNRGENVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD  +  + +TY++  I   ++ Y LR  + +++  +   + + +    ++ 
Sbjct: 74  GLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNTIRVSRSL--RDIAYKALLVRD 130

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L  + +NN +P  V  IAK+L +   +V+          +L+A+           QD +
Sbjct: 131 KL--VNENNKEP-TVSQIAKELKIPREDVVF---------ALDAI-----------QDPV 167

Query: 205 -----VYDHDGQEQVLIEKE--ERKNRRN------MLTRSMSVLNPRERRIFEARRLQEN 251
                +Y HDG + + +  +  + KN+ +       +  +M  LN RE+ I   R    N
Sbjct: 168 SLFEPIY-HDGGDAIYVMDQISDSKNQDDSWLENIAIKEAMKKLNDREKLILNLRFF--N 224

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             T   ++ E  +S+ +V ++E  A K +++ +
Sbjct: 225 GRTQMEVADEIGISQAQVSRLEKIALKHMRKYV 257


>gi|158320823|ref|YP_001513330.1| FliA/WhiG family RNA polymerase sigma factor [Alkaliphilus
           oremlandii OhILAs]
 gi|158141022|gb|ABW19334.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           oremlandii OhILAs]
          Length = 256

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 54/244 (22%), Positives = 113/244 (46%), Gaps = 15/244 (6%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + G++ A   LV  +L LV  +   +   G    ++   G IGL++A+KKFD     R +
Sbjct: 27  QSGNMEAQEILVNHNLGLVRSVIRRFANRGYEREDLFQLGCIGLIKAIKKFDTSFDVRFS 86

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I   ++ + LR   ++K+  +  Q        R+K   + +   N +   +  I
Sbjct: 87  TYAVPMIIGEIKRF-LRDDGIIKVSRSLKQ-----TAARVKMTKEKLQKENGREPTLQEI 140

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A  +  ++ E++      A  E L  +I+  D +     D +  +   ++  +I+     
Sbjct: 141 ADDMGATKEEIVMALDSSASPEYLYDVIHQDDGSPIHLIDKISENDTLEDSEVID----- 195

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             R +L  ++S L PRER+I   R  ++   T   ++    +S+ +V +IE +  + +++
Sbjct: 196 --RIVLQEAISKLEPRERQIIFLRYFKDQTQT--QIAQVLGISQVQVSRIEKKVLQNMKD 251

Query: 283 SIQK 286
            ++K
Sbjct: 252 IMKK 255


>gi|320101986|ref|YP_004177577.1| RNA polymerase sigma-32 subunit RpoH [Isosphaera pallida ATCC
           43644]
 gi|319749268|gb|ADV61028.1| RNA polymerase, sigma 32 subunit, RpoH [Isosphaera pallida ATCC
           43644]
          Length = 565

 Score = 56.6 bits (135), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 35/124 (28%), Positives = 65/124 (52%), Gaps = 29/124 (23%)

Query: 15  GLSRYIHEIRKIPMLEKQEEY----------VLAKRYREHGD------------------ 46
           GL  Y+  + ++P+L +++E            LA++ R+  D                  
Sbjct: 325 GLPPYLASLYEVPLLSREQETHLFRKMNFLKYLAQKLRDQVDPARARAGDLDQIEALQEE 384

Query: 47  -LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
            L+  +++++++LRLVV IA  + G      ++VS+GN+ L++AV+KFD  RG + +TY+
Sbjct: 385 ALAVKNQIISANLRLVVSIAKRHVGPSNNFFDLVSDGNMSLIRAVEKFDFARGNKFSTYA 444

Query: 106 MWWI 109
            W I
Sbjct: 445 SWAI 448



 Score = 40.0 bits (92), Expect = 0.41,   Method: Compositional matrix adjust.
 Identities = 29/76 (38%), Positives = 46/76 (60%), Gaps = 5/76 (6%)

Query: 217 EKEERKNRRNM---LTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQ 271
           E E+  N+R M   +   +S L PRE++I  +R        +TLE L  E  +++ERVRQ
Sbjct: 484 EHEQESNQRRMREGVNGMLSKLEPREQKIIVSRFGINGAKEMTLEQLGKELGITKERVRQ 543

Query: 272 IEARAFKKVQESIQKQ 287
           IEARA +K+++  Q++
Sbjct: 544 IEARAQQKLRKIAQEE 559


>gi|256005472|ref|ZP_05430434.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Clostridium
           thermocellum DSM 2360]
 gi|255990527|gb|EEU00647.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Clostridium
           thermocellum DSM 2360]
          Length = 252

 Score = 56.2 bits (134), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 50/251 (19%), Positives = 121/251 (48%), Gaps = 17/251 (6%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L + Y+E   +   +++V+ +L L   +A  +   G+   ++    +I L++AV++FDP+
Sbjct: 18  LFREYKETKSVEVRNKIVSKYLYLSDILAKKFLNRGIDYEDIYQVVSIALIKAVERFDPD 77

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +G +  +++   I   ++ Y     S+++I      +R++   +++    +++T    +P
Sbjct: 78  KGVKFISFATPTIIGEIKRYFRDKGSVIRIP-----RRIYEVYQKINHARESLTQELKRP 132

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQVL 215
            ++  +A+ LN+SE  V+ +       ES NA  I S  +N     +  +++  G +   
Sbjct: 133 PRIDELARHLNISEESVVEII------ESYNAYNIQSFSQNVYANDELELHEVIGDQDST 186

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
            E+ E    R+ L +S+   +  E+     R       T ++++ +  VS+  + ++E +
Sbjct: 187 FERIE---NRDFLEKSLDKFSDVEKEFISMRYFDNK--TQKDIAQKMGVSQMYISRLERK 241

Query: 276 AFKKVQESIQK 286
             +K +  + K
Sbjct: 242 VLEKFRRMLAK 252


>gi|297193425|ref|ZP_06910823.1| sigma L [Streptomyces pristinaespiralis ATCC 25486]
 gi|197723192|gb|EDY67100.1| sigma L [Streptomyces pristinaespiralis ATCC 25486]
          Length = 304

 Score = 56.2 bits (134), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 62/237 (26%), Positives = 105/237 (44%), Gaps = 23/237 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +   
Sbjct: 83  LIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTVVGE 142

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL   L +    L    D +     V  +A  L VSE 
Sbjct: 143 IKRFFRDTSWS-VRVPRRLQELRL--ALTKASDELAQKLDRS---PTVPELAAVLGVSEE 196

Query: 172 EVIS----MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +V+      N   A   SL++     D       D L Y+    E V    E R++ + +
Sbjct: 197 DVVDGLAVGNAYTA--SSLDSPSPEDDGGEGSLADRLGYEDSALEGV----EYRESLKPL 250

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L +    L PRER+I   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 251 LAK----LPPRERQIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 301


>gi|326390169|ref|ZP_08211730.1| RNA polymerase, sigma 28 subunit, SigK [Thermoanaerobacter
           ethanolicus JW 200]
 gi|325993817|gb|EGD52248.1| RNA polymerase, sigma 28 subunit, SigK [Thermoanaerobacter
           ethanolicus JW 200]
          Length = 231

 Score = 56.2 bits (134), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 30/80 (37%), Positives = 48/80 (60%), Gaps = 3/80 (3%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           E++++Y+ A R   +GD  A + L+  +LRLV  +   Y G G  I +++S G IGL++A
Sbjct: 35  EEEKKYLEAYR---NGDEEARNILIERNLRLVAHVVKKYSGTGKDIDDLISIGTIGLIKA 91

Query: 90  VKKFDPERGFRLATYSMWWI 109
           +  FD  +G  LATY+   I
Sbjct: 92  ISTFDSSKGTHLATYAARCI 111


>gi|167040197|ref|YP_001663182.1| FliA/WhiG family RNA polymerase sigma factor [Thermoanaerobacter
           sp. X514]
 gi|300914281|ref|ZP_07131597.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacter sp.
           X561]
 gi|307265137|ref|ZP_07546696.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacter wiegelii
           Rt8.B1]
 gi|307724483|ref|YP_003904234.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter sp. X513]
 gi|326391064|ref|ZP_08212611.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacter
           ethanolicus JW 200]
 gi|166854437|gb|ABY92846.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Thermoanaerobacter sp. X514]
 gi|300889216|gb|EFK84362.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacter sp.
           X561]
 gi|306919759|gb|EFN49974.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacter wiegelii
           Rt8.B1]
 gi|307581544|gb|ADN54943.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X513]
 gi|325992849|gb|EGD51294.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacter
           ethanolicus JW 200]
          Length = 246

 Score = 56.2 bits (134), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 61/259 (23%), Positives = 122/259 (47%), Gaps = 20/259 (7%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
            EK +E +   R  +  D  +  +L+  +  L+  I   +   G  + ++   G IG ++
Sbjct: 6   FEKSDENLELIRAAQKNDKESLEKLILENSGLIWSIVKKFSNRGYELEDLYQIGCIGFVK 65

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++KFD     +L+TY++  I   ++ + LR   L+K+  +  +      L     +++ 
Sbjct: 66  AIQKFDESYNVKLSTYAVPIIMGEIKRF-LRDDGLIKVSRSLKE------LSTKAFYVKE 118

Query: 149 ITDNNLKPEQVV-AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
           I  N L  E  +  IA++LNVS  E+       A  ESL       D  +    D L+ +
Sbjct: 119 ILSNELNREPTINEIAERLNVSPEEIAMAFESAATAESL------YDNATHDEDDRLLIE 172

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
              +E    EKE   + +  L   ++ L PRE++I   R  ++  +T   ++S   +S+ 
Sbjct: 173 MVSEE----EKEVDIDDKLALQMVINKLKPREKQIIFLRYFKD--MTQMEVASVLGISQV 226

Query: 268 RVRQIEARAFKKVQESIQK 286
           +V +IE +  +K+++ +++
Sbjct: 227 QVSRIEKKVLQKLRKELEE 245


>gi|23098085|ref|NP_691551.1| RNA polymerase sigma factor SigB [Oceanobacillus iheyensis HTE831]
 gi|22776310|dbj|BAC12586.1| RNA polymerase general stress sigma factor (sigma B)
           [Oceanobacillus iheyensis HTE831]
          Length = 263

 Score = 56.2 bits (134), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 62/243 (25%), Positives = 114/243 (46%), Gaps = 26/243 (10%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           ++V  +  LV  IA  Y        ++V  G IGL+ AV+++DP  G    ++++  I  
Sbjct: 34  KIVLKYQDLVGSIARKYSKNSAIHEDLVQVGMIGLLAAVRRYDPTYGKSFESFAIPTIIG 93

Query: 112 AMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            ++ +I  ++WS   +      K L   +R  KG  +  TDN   P  V  IAK +  SE
Sbjct: 94  EIKRFIRDKTWS---VHVPRRIKELGPKIR--KGVDELTTDNQKSP-TVAEIAKYIGTSE 147

Query: 171 SEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            EV+ +M        L+ D  + A    SD ++    D +    DG + V         +
Sbjct: 148 EEVLETMEMGQSYKALSVDRKIEA---DSDGSTVAILDLVGNSEDGYDNV--------EQ 196

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R ML + + +L+ RE++I E    +   ++ +       +S+  V +++ R+ +K++E+I
Sbjct: 197 RMMLEKILPILSEREQQILECTYFKN--MSQKETGELLGISQMHVSRLQRRSLRKLREAI 254

Query: 285 QKQ 287
           Q +
Sbjct: 255 QSE 257


>gi|166031221|ref|ZP_02234050.1| hypothetical protein DORFOR_00908 [Dorea formicigenerans ATCC
           27755]
 gi|166029068|gb|EDR47825.1| hypothetical protein DORFOR_00908 [Dorea formicigenerans ATCC
           27755]
          Length = 227

 Score = 56.2 bits (134), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 33/85 (38%), Positives = 50/85 (58%), Gaps = 2/85 (2%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+   +E+Y L K Y E GDL+A H L+  +LRLV  I   Y+       +++S G IG
Sbjct: 28  LPLTASEEQYYLQK-YIE-GDLNAKHILIEHNLRLVAHIVKKYQANVEEAEDLLSIGTIG 85

Query: 86  LMQAVKKFDPERGFRLATYSMWWIK 110
           L++AV  F+P +  RL TY+   I+
Sbjct: 86  LIKAVVTFNPGKNVRLGTYAARCIE 110


>gi|312877562|ref|ZP_07737521.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
 gi|311795637|gb|EFR12007.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
          Length = 240

 Score = 56.2 bits (134), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 59/243 (24%), Positives = 111/243 (45%), Gaps = 24/243 (9%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           ++GD  A  +L+ S+L LV  +   +   G+ + ++   G IGL++AV +F P    R +
Sbjct: 14  KNGDKLARQQLIESNLALVWSVVKKFAAKGVELDDLFQIGCIGLIKAVDRFAPSFNLRFS 73

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
           TY++  I   ++ Y LR    +K+      NQ +    +++L+   Q ++ N  +P  + 
Sbjct: 74  TYAVPMIIGEIKRY-LRDDGKIKVSRKIKENQSK----IKKLRN--QFVSSNGREP-TIS 125

Query: 161 AIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            I++   +S  E++   C  A  E  SLN ++N  +       D    + D   ++L   
Sbjct: 126 EISQLTGLSSDEILL--CMDASSEVASLNEVVNQEEGKPITLMDIASDEEDYSTKLL--- 180

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                    L   +  L  RER I   R  +    T   ++ E  +S+  V +IE RA +
Sbjct: 181 -----DLMALKEGLKKLKGRERYIIFMRYFKNK--TQSEIAKELNISQVHVSRIEKRALE 233

Query: 279 KVQ 281
           +++
Sbjct: 234 RIK 236


>gi|291543210|emb|CBL16319.1| RNA polymerase, sigma 29 subunit, SigE [Ruminococcus sp. 18P13]
          Length = 232

 Score = 56.2 bits (134), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 31/79 (39%), Positives = 44/79 (55%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+ E     R       SA   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 30  PPLSKEAEAEAFARLGTGDAESARQTLIVHNLRLVVYIAKKFESTGIGIEDLISIGTIGL 89

Query: 87  MQAVKKFDPERGFRLATYS 105
           ++AV  F PE+  +LATY+
Sbjct: 90  IKAVNTFCPEKNIKLATYA 108


>gi|218132856|ref|ZP_03461660.1| hypothetical protein BACPEC_00717 [Bacteroides pectinophilus ATCC
           43243]
 gi|217991729|gb|EEC57733.1| hypothetical protein BACPEC_00717 [Bacteroides pectinophilus ATCC
           43243]
          Length = 205

 Score = 56.2 bits (134), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 31/81 (38%), Positives = 46/81 (56%), Gaps = 1/81 (1%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L  +EE +  K+ RE GDL A ++L+  ++RLV  I   Y        +++S G IGL++
Sbjct: 15  LSSEEEKIYLKKCRE-GDLEARNKLIEKNMRLVAHIVKKYACADRDTEDLLSVGTIGLIK 73

Query: 89  AVKKFDPERGFRLATYSMWWI 109
           AV  FD  +  RLATY+   I
Sbjct: 74  AVNTFDMNKSIRLATYAAKCI 94


>gi|93007303|gb|ABE97152.1| Sigma-70 [Pasteuria ramosa]
          Length = 241

 Score = 56.2 bits (134), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 28/68 (41%), Positives = 44/68 (64%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +LRLVV IA  +   G+ I ++VS G IGL++AV  FDPE+  +LATY+   I+  
Sbjct: 64  LIERNLRLVVYIARKFENTGIHIEDLVSTGTIGLIKAVNTFDPEKKIKLATYASRCIENE 123

Query: 113 MQEYILRS 120
           +  ++ R+
Sbjct: 124 ILMFLRRN 131


>gi|302544114|ref|ZP_07296456.1| RNA polymerase sigma-F factor [Streptomyces hygroscopicus ATCC
           53653]
 gi|302461732|gb|EFL24825.1| RNA polymerase sigma-F factor [Streptomyces himastatinicus ATCC
           53653]
          Length = 293

 Score = 56.2 bits (134), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 61/237 (25%), Positives = 105/237 (44%), Gaps = 23/237 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +   
Sbjct: 72  LIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTVVGE 131

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL   L +    L    D   +   V  +A  L VSE 
Sbjct: 132 IKRFFRDTSWS-VRVPRRLQELRL--ALTKASDELAQTLD---RSPTVTELATALGVSEE 185

Query: 172 EVIS----MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +V+      N   A   SL++     +       D L Y+    E V    E R++ + +
Sbjct: 186 DVVDGLAVGNAYTA--SSLDSPSPEDEGGEGSLADRLGYEDSALEGV----EYRESLKPL 239

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L +    L PRER+I   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 240 LAK----LPPRERQIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 290


>gi|28211312|ref|NP_782256.1| RNA polymerase sigma factor for flagellar operon fliA [Clostridium
           tetani E88]
 gi|28203752|gb|AAO36193.1| RNA polymerase sigma factor for flagellar operon fliA [Clostridium
           tetani E88]
          Length = 242

 Score = 56.2 bits (134), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 62/240 (25%), Positives = 114/240 (47%), Gaps = 21/240 (8%)

Query: 53  LVTSHLRLVVKIA----MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           LV  ++ LV  IA    +G   Y +   ++V  G +GLM A++KFDP +G + +TY+   
Sbjct: 13  LVKKYIPLVKYIASRVIIGKTKY-IDYDDLVGYGMLGLMDAMQKFDPSKGMKFSTYASIR 71

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ +M + + R   +  I  +A  K     L R    ++ +   N K  ++  +AK+L++
Sbjct: 72  IRGSMIDELRR---ISPISKSAMDK-----LNRYNEAVEKLQMKNFKEPKLEEVAKELDM 123

Query: 169 SESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           S  EV  I          SL   I S +++ S     +  +    E++L EKE       
Sbjct: 124 SLKEVAQIENYINYISIVSLEDFIFSDEEDMSLMATVVDKNSPSPEKILEEKE----LIE 179

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L ++++ L  R+R +      +   +TL+ +    +VS  RV Q+ +RA   ++  ++K
Sbjct: 180 YLEKAINKLKERDRIVLSLYYYER--LTLKEIGKVLDVSESRVCQLHSRAIVHLRSELKK 237


>gi|18310743|ref|NP_562677.1| sporulation sigma factor SigG [Clostridium perfringens str. 13]
 gi|18145424|dbj|BAB81467.1| probable transcription initiation factor sigma G [Clostridium
           perfringens str. 13]
          Length = 270

 Score = 56.2 bits (134), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 62/273 (22%), Positives = 132/273 (48%), Gaps = 43/273 (15%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+++E   L  +  ++GD SA  + +  +LRLV+ +   +   G  + ++   G I
Sbjct: 28  KLPVLKEKEMKELLLQM-QNGDTSAREKFIKGNLRLVLSVIQRFNNRGENVDDLFQVGCI 86

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD  +  + +TY++  I   ++ Y LR  + +++  +   + + +    ++ 
Sbjct: 87  GLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNTIRVSRSL--RDIAYKALLVRD 143

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L  + +NN +P  V  IAK+L +   +V+          +L+A+           QD +
Sbjct: 144 KL--VNENNKEP-TVSQIAKELKIPREDVVF---------ALDAI-----------QDPV 180

Query: 205 -----VYDHDGQEQVLIEKE--ERKNRRN------MLTRSMSVLNPRERRIFEARRLQEN 251
                +Y HDG + + +  +  + KN+ +       +  +M  LN RE+ I   R    N
Sbjct: 181 SLFEPIY-HDGGDAIYVMDQISDSKNQDDSWLENIAIKEAMKKLNDREKLILNLRFF--N 237

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             T   ++ E  +S+ +V ++E  A K +++ +
Sbjct: 238 GRTQMEVADEIGISQAQVSRLEKIALKHMRKYV 270


>gi|294501013|ref|YP_003564713.1| RNA polymerase sigma-G factor [Bacillus megaterium QM B1551]
 gi|295706362|ref|YP_003599437.1| RNA polymerase sigma-G factor [Bacillus megaterium DSM 319]
 gi|294350950|gb|ADE71279.1| RNA polymerase sigma-G factor [Bacillus megaterium QM B1551]
 gi|294804021|gb|ADF41087.1| RNA polymerase sigma-G factor [Bacillus megaterium DSM 319]
          Length = 259

 Score = 56.2 bits (134), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 63/261 (24%), Positives = 123/261 (47%), Gaps = 17/261 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+ +E   L K+  + GD +A  +LV+ +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKNEEMRKLFKQM-QAGDGTAREKLVSGNLRLVLSVIQRFNNRGEFVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD  +  + +TY++  I   ++ Y LR  + +++  +   + + +   +++ 
Sbjct: 74  GLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSL--RDIAYKALQVRE 130

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L + T      E+   I+K L V   E++     +    SL   I +   +     D L
Sbjct: 131 RLMSETSKEPTAEE---ISKVLEVPHEEIVFALDAIQDPVSLFEPIYNDGGDPIYVMDQL 187

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             D   ++   IE+         L   M  LN RE+ I   R  Q    T   ++ E  +
Sbjct: 188 -SDERNRDSTWIEE-------IALQEGMRRLNEREKLILRKRFFQGK--TQMEVAEEIGI 237

Query: 265 SRERVRQIEARAFKKVQESIQ 285
           S+ +V ++E  A K++ ++IQ
Sbjct: 238 SQAQVSRLEKAAIKQMNKNIQ 258


>gi|218669755|gb|ACL00354.1| Bcp26 [Bacillus phage Bcp1]
          Length = 256

 Score = 56.2 bits (134), Expect = 5e-06,   Method: Compositional matrix adjust.
 Identities = 53/185 (28%), Positives = 88/185 (47%), Gaps = 18/185 (9%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           +L K+E Y L +R  + G+  A   LV  + RLV  +            ++   G IGL+
Sbjct: 16  VLTKEETYELIER-SQAGEEEATESLVEHNARLVTYVVRRKNNPYHEYDDLFQLGMIGLI 74

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK----IGTTANQKRLFFNLRRLK 143
            A+ KFD  +G + +TY++ WI A +  Y+    S++K    IG   N+        +LK
Sbjct: 75  TAIAKFDTSKGLQFSTYAVRWIDAEIGNYLKNRTSILKVPREIGAIVNKILAV----KLK 130

Query: 144 GHLQAITDNNLKPE--QVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQ 199
               AI    LK +  Q+  +   L +  +EVIS++ +     D+SL++++   D N   
Sbjct: 131 NEEPAIIMEKLKLDASQLDNVTIALEIIHNEVISLDKQTGEEKDDSLSSIV-GQDVN--- 186

Query: 200 WQDWL 204
            QDW 
Sbjct: 187 -QDWF 190


>gi|160915288|ref|ZP_02077501.1| hypothetical protein EUBDOL_01297 [Eubacterium dolichum DSM 3991]
 gi|158433087|gb|EDP11376.1| hypothetical protein EUBDOL_01297 [Eubacterium dolichum DSM 3991]
          Length = 239

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 74/284 (26%), Positives = 115/284 (40%), Gaps = 70/284 (24%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEE--YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           I++  +G   Y+H       L+K+ E  Y+ A      G+ +A  +L+  +LRLV  I  
Sbjct: 10  ILSNALGYVGYVHNNTFAQPLDKESETKYIAA---LAKGNQTARDKLIEHNLRLVAHIVK 66

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y        +++S G IGL++AV  F PE+G +L TY+   I+  +  Y          
Sbjct: 67  KYDFKKEATEDLISIGTIGLIKAVDSFKPEKGHKLTTYASKCIENEILMY---------- 116

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
                       LR  K + Q                   NVS +E I+ +     D S 
Sbjct: 117 ------------LRSSKNYFQ-------------------NVSLNEPIATD----KDGSE 141

Query: 187 NALIN--SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
             LI+  +S  ++S   D LV D+       I K         L + M VL+ RE  I  
Sbjct: 142 IMLIDAIASPCDTSIIDDMLVADN-------IVK---------LKQYMHVLDARELEIIT 185

Query: 245 AR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R     +   T   ++ +  +SR  V +IE RAF K+    +K
Sbjct: 186 KRFGLFGQKEATQREIAKQLHISRSYVSRIEKRAFMKLYREFKK 229


>gi|167759902|ref|ZP_02432029.1| hypothetical protein CLOSCI_02266 [Clostridium scindens ATCC 35704]
 gi|167662521|gb|EDS06651.1| hypothetical protein CLOSCI_02266 [Clostridium scindens ATCC 35704]
          Length = 237

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 60/241 (24%), Positives = 111/241 (46%), Gaps = 18/241 (7%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A  RLV  +  LV  I   +   G+   ++   GNIGL++A+ KFD     + +TY
Sbjct: 14  GDEEARARLVEENAGLVWCIVKRFYNRGVEAEDLFQVGNIGLLKAIDKFDMSYDVKFSTY 73

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           ++  I   ++ + LR   ++K+  +   K L +     +  LQ   +   +   +  IA+
Sbjct: 74  AVPMISGEIKRF-LRDDGMIKVSRSL--KELAYKAYLCQERLQ---EQWGRDPTITEIAE 127

Query: 165 KLNVSESEVISMNCRLAGD-ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
            LNV E E ++M    +GD ESL+  I   +    +  D L     G++++L        
Sbjct: 128 SLNV-EREELTMALDASGDIESLHKPIYQKEGQEIRLMDKLPEKEGGEDKIL-------- 178

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
              +L + ++ L+  ER++   R       T   +  E  +S+ +V ++E +  K ++E 
Sbjct: 179 NHMLLQQLLNYLDKDERQLIYLRYFANQTQT--QVGRELGISQVQVSRMEKKILKNLRER 236

Query: 284 I 284
           I
Sbjct: 237 I 237


>gi|330468593|ref|YP_004406336.1| RNA polymerase sigma-70 factor [Verrucosispora maris AB-18-032]
 gi|328811564|gb|AEB45736.1| RNA polymerase sigma-70 factor [Verrucosispora maris AB-18-032]
          Length = 292

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 64/249 (25%), Positives = 117/249 (46%), Gaps = 27/249 (10%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV   L    ++A  YRG G P+ ++     +GL+ AV ++DPERG   A  ++  +   
Sbjct: 46  LVRFALPFAGRLARRYRGRGEPLEDLEQVARLGLVNAVDRYDPERGSFTAYAAITIVGEI 105

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
            + +  R+W  V +      +RL   +  +     A+T    +   V  ++K+L+  E E
Sbjct: 106 KRHFRDRTWG-VHV-----PRRLRDLILEVGQATAALTSELSRAPTVAELSKRLDTPEEE 159

Query: 173 VISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK-EERKNRRNMLT 229
           +++     AG    SLNA +    ++S+++ D +     G+  + +E  ++R     +L 
Sbjct: 160 ILAALESAAGYSPASLNAPVGG--ESSAEFGDLV-----GESDIALESVDDRVTVSGLLH 212

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           R    L  RERRI  A R   N    E +++ F +S+  V ++ +RA   +     +Q  
Sbjct: 213 R----LPWRERRIL-AMRFYGNQTQAE-IAARFGISQMHVSRLLSRALTWL-----RQAM 261

Query: 290 LSSSPPLLQ 298
           L+ +PP  Q
Sbjct: 262 LADAPPPWQ 270


>gi|327441149|dbj|BAK17514.1| DNA-directed RNA polymerase specialized sigma subunit [Solibacillus
           silvestris StLB046]
          Length = 236

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 53/203 (26%), Positives = 85/203 (41%), Gaps = 60/203 (29%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           +GDL A   L+  +LRLVV IA  +     PI +++S G+IGL++A++ F+ ++  +LAT
Sbjct: 49  NGDLHARDMLIERNLRLVVYIARRFDNTSTPIEDLISIGSIGLIKAIETFNLDKNIKLAT 108

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   I+  +  + LR  S                  R+KG                   
Sbjct: 109 YASRCIENEILMH-LRKTS------------------RMKG------------------- 130

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
                           ++ DE LNA    +D N     D L      +E ++    ERK 
Sbjct: 131 ---------------EVSFDEPLNA---DADGNELLLSDIL----GTEEHIITLDVERKI 168

Query: 224 RRNMLTRSMSVLNPRERRIFEAR 246
            R  +  +++ L PRE+ I E R
Sbjct: 169 ERQHMFNAINQLTPREKYIMECR 191


>gi|317132579|ref|YP_004091893.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Ethanoligenens harbinense YUAN-3]
 gi|315470558|gb|ADU27162.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Ethanoligenens harbinense YUAN-3]
          Length = 256

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 56/260 (21%), Positives = 125/260 (48%), Gaps = 24/260 (9%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+ +L + ++  L KR ++ GDL+A   L++ +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLKVLTESQKTALLKRVKQ-GDLAAREELISGNLRLVLSVIQRFTNRGENLDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD  +  R +TY++  I   ++ Y LR  + +++  +   + + +   + K 
Sbjct: 74  GLMKSIDNFDISQNVRFSTYAVPMIIGEIRRY-LRDNNPIRVSRSL--RDIAYKAMQCKE 130

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L    + N +   +  +AK++++ + E++     +    SL   + S   ++    D +
Sbjct: 131 RLM---NANQREPTIEEMAKEMDMPKEEIVMALESVVEPVSLYEPVYSDGGDTIYVMDQI 187

Query: 205 ---VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
                D D  +++             L  ++  L+ RE+RI   R  + +  T   ++SE
Sbjct: 188 GDKTVDSDWLDEI------------TLKEAVGALSEREKRILYLRFFEGH--TQMEVASE 233

Query: 262 FEVSRERVRQIEARAFKKVQ 281
             +S+ +V ++E  A  K++
Sbjct: 234 IGISQAQVSRLEKGALSKIK 253


>gi|284043529|ref|YP_003393869.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
 gi|283947750|gb|ADB50494.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
          Length = 261

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 28/88 (31%), Positives = 50/88 (56%), Gaps = 1/88 (1%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L +RYRE GD     R + S + LV K+A  Y     P+ ++V    +GL++A+ +FDP+
Sbjct: 29  LIRRYRETGDPRCRTRAIESFMPLVHKLARRYHPGPEPLDDLVQVACVGLVKAIDRFDPD 88

Query: 97  RGFRLATYSMWWIKAAMQEYIL-RSWSL 123
            G R A++++  I   ++ +    +WS+
Sbjct: 89  AGPRFASFAIPTITGELRRHFRDTTWSV 116


>gi|312876365|ref|ZP_07736350.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
 gi|311796859|gb|EFR13203.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
          Length = 255

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 51/205 (24%), Positives = 100/205 (48%), Gaps = 8/205 (3%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L  +E+  L KR +E GD  A    +  +LRLV+ +   +   G  + ++   G IG
Sbjct: 14  LPVLSHEEKLELLKRMKE-GDKEARRIFIEGNLRLVLSVVQKFANRGENLDDLFQVGCIG 72

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A+  FD  +  + +TY++  I   ++ Y LR  + ++I  +   K   +   ++K  
Sbjct: 73  LIKAIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNSMRISRSL--KDTAYKALKIK-- 127

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            +    NN K   +  IAK+L++++ E++     +    SL   +   D   + +    +
Sbjct: 128 -EKYISNNQKEPTLEEIAKELSITKEELVFTLDSIQEPISLYEPV-FQDSTDTMYVVEKL 185

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTR 230
           YDH   E V +E+   K+  + LT+
Sbjct: 186 YDHKSSENVWLEEISLKDALSRLTK 210


>gi|310642978|ref|YP_003947736.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
 gi|309247928|gb|ADO57495.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
          Length = 260

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 65/280 (23%), Positives = 125/280 (44%), Gaps = 54/280 (19%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L   E   L    +++ + SA  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLTNAEMRELFTSLQQNNERSAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGCI 74

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEY------ILRSWSLVKIGTTANQKRLFFN 138
           GLM+A+  FD  +  + +TY++  I   ++ Y      I  S SL  I   A Q R    
Sbjct: 75  GLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLRDIAYKALQVR---- 130

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
                    ++T+ N +   +  I++ LNV + +V+          +L+A+         
Sbjct: 131 --------DSLTNLNSREPTIFEISEVLNVPKEDVVF---------ALDAI--------- 164

Query: 199 QWQDWL-----VYDHDGQEQVLIEKEERKNRRN--------MLTRSMSVLNPRERRIFEA 245
             QD +     +Y HDG + + +  +   +R           L  +M  L  RE+ I  +
Sbjct: 165 --QDPVSLFEPIY-HDGGDPIYVMDQISDDRNKDVSWIEEIALREAMHRLGQREKMIL-S 220

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            R  E    +E ++ E  +S+ +V ++E  A +++Q+ ++
Sbjct: 221 MRFYEGKTQME-VADEIGISQAQVSRLEKSAIQQMQKHVK 259


>gi|119384818|ref|YP_915874.1| RNA polymerase, sigma 32 subunit, RpoH [Paracoccus denitrificans
           PD1222]
 gi|119374585|gb|ABL70178.1| RNA polymerase, sigma 32 subunit, RpoH [Paracoccus denitrificans
           PD1222]
          Length = 728

 Score = 56.2 bits (134), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 60/248 (24%), Positives = 112/248 (45%), Gaps = 33/248 (13%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           SA   L+  HL  V + A      G    +V     +GL ++ ++FDPERG+R   Y+ +
Sbjct: 498 SATEHLIREHLPYVRRFASRNVEEGEDPEDVFQVAFMGLQRSTRRFDPERGYRFLIYATY 557

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQK--RLFFNLRRLKGHL-QAITDNNLKPEQVVAIAK 164
           W++ A+  +     + ++I    N+K  +L   L RL   +  A++D        + +AK
Sbjct: 558 WMRQAITRWRSDEGAAIRIPVHRNEKITKLDRALERLDVRVGGAVSD--------LELAK 609

Query: 165 KLNVSESEVI---SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           +L  +  EV    S+       ESL+            W D L       E   ++  + 
Sbjct: 610 ELEWTIDEVTQFRSIPREAEYPESLD-----------DWDDLL------PEPSGVDVFDE 652

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
                ++T +++ L  R+  +   R    +++ +TLE +   + V+RER+RQIEA+   +
Sbjct: 653 AETERIVTDALADLPERQADVIRMRFGIGRDSDMTLEEIGQIYGVTRERIRQIEAKGLDR 712

Query: 280 VQESIQKQ 287
           +    +K+
Sbjct: 713 LSHPGRKR 720


>gi|218289913|ref|ZP_03494103.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
 gi|218240053|gb|EED07239.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
          Length = 179

 Score = 55.8 bits (133), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 29/71 (40%), Positives = 44/71 (61%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +LRLVV IA  +   G+ I ++VS G IGL++AV  FDP +  +LATY+   I+  
Sbjct: 2   LIERNLRLVVYIARKFENTGVNIEDLVSIGTIGLIKAVNTFDPSKKIKLATYASRCIENE 61

Query: 113 MQEYILRSWSL 123
           +  Y+ R+  L
Sbjct: 62  ILMYLRRNNKL 72


>gi|291531057|emb|CBK96642.1| RNA polymerase, sigma 29 subunit, SigE [Eubacterium siraeum 70/3]
          Length = 239

 Score = 55.8 bits (133), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 34/95 (35%), Positives = 54/95 (56%), Gaps = 3/95 (3%)

Query: 27  PMLEKQEEY-VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           P L K+EE   LAK   +  +  A   L+  +LRLVV IA  +   G+ I +++S G IG
Sbjct: 36  PPLSKEEEAKTLAKLNTDFEN--ARETLIVHNLRLVVYIAKKFESTGIGIEDLISIGTIG 93

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           L++AV  F  E+  +LATY+   I+  +  Y+ ++
Sbjct: 94  LIKAVNTFSVEKNIKLATYASRCIENEILMYLRKT 128


>gi|168333394|ref|ZP_02691674.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family protein
           [Epulopiscium sp. 'N.t. morphotype B']
          Length = 249

 Score = 55.8 bits (133), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 60/243 (24%), Positives = 117/243 (48%), Gaps = 18/243 (7%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD+SA   LV  +L LV  +   +   G  + ++   G+IGL+++++KFD +     +
Sbjct: 21  QGGDISAKELLVEQNLGLVWSLVKRFTNRGYDLDDLFQVGSIGLLKSIEKFDLKYPVAFS 80

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I   ++ + LR   L+K+  +   K L    R +K   Q     N +P  +  I
Sbjct: 81  TYAVPMIVGEIKRF-LRDDGLIKVSRSL--KDLASKARNVKEDFQ--RQENREP-TLKEI 134

Query: 163 AKKLNVSESEV-ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           +  LNV   E+ +S+   +   ESLNA++N +   +    + +    D Q+ +       
Sbjct: 135 SDILNVPCEEIAVSLEANMEV-ESLNAVVNPNSSATITLAEKIDQSPDEQKNIF------ 187

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                 L   +  L+  ER+I   R  ++  +T   +++   VS+ ++ +IE R  +K++
Sbjct: 188 --ENIYLKEIIKTLSSVERQIVNYRYFED--LTQLEIANRLGVSQVQISRIEKRVLEKLR 243

Query: 282 ESI 284
           +SI
Sbjct: 244 QSI 246


>gi|229076790|ref|ZP_04209702.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock4-18]
 gi|228706352|gb|EEL58613.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock4-18]
          Length = 252

 Score = 55.8 bits (133), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 37/124 (29%), Positives = 69/124 (55%), Gaps = 8/124 (6%)

Query: 57  HLRLVVKIAMGYRGYG--LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114
           ++ LV+ IA  Y+     +   ++V EGN G+++A++ FDP+ G+  +TY+  WIK +M 
Sbjct: 5   NIGLVLSIARKYKKKHPEIEFDDLVQEGNEGMLRAIEDFDPDLGYCFSTYAYCWIKKSML 64

Query: 115 EYILRSWS-LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
            +I +  S   KI    NQ    FN++ ++   + +  +N  P  V  + K+L+V+  +V
Sbjct: 65  GFICKKKSGPFKIPNYVNQ----FNVKYVEIEDKYLQMHNRIP-TVEEVVKELDVTREKV 119

Query: 174 ISMN 177
           +  N
Sbjct: 120 VRHN 123


>gi|118442872|ref|YP_878340.1| sporulation sigma factor SigK [Clostridium novyi NT]
 gi|118133328|gb|ABK60372.1| DNA-dependent RNA polymerase sigma subunit [Clostridium novyi NT]
          Length = 225

 Score = 55.8 bits (133), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 30/83 (36%), Positives = 48/83 (57%), Gaps = 2/83 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ EK+E+Y L +   + GD  A   L+  +LRLV  I   Y      + +++S G +GL
Sbjct: 21  PLNEKEEKYYLQQF--KQGDALAKGILIERNLRLVAHIVKKYSYPNKDVDDLISIGTVGL 78

Query: 87  MQAVKKFDPERGFRLATYSMWWI 109
           ++A+  FD ++G RLATY+   I
Sbjct: 79  IKAIDSFDVDKGTRLATYAARCI 101


>gi|15615117|ref|NP_243420.1| sporulation sigma factor SigG [Bacillus halodurans C-125]
 gi|10175174|dbj|BAB06273.1| RNA polymerase sporulation forespore-specific (late) sigma-G factor
           [Bacillus halodurans C-125]
          Length = 261

 Score = 55.8 bits (133), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 63/261 (24%), Positives = 119/261 (45%), Gaps = 15/261 (5%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+ QE   L  R  + GD SA   LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKNQEMRELFARL-QSGDTSARETLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD  +  + +TY++  I   ++ Y LR  + +++  +   + + +   +++ 
Sbjct: 74  GLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSL--RDIAYKALQVRD 130

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L        +P  V  IAK+L V + +V+     +    SL   I +   +     D +
Sbjct: 131 QLMGEKQREKEP-TVQEIAKELGVPKEDVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQI 189

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             D +   Q + E          L  +M  LN RE+ I   R  Q    T   ++ E  +
Sbjct: 190 SDDRNKDVQWVDEI--------ALKEAMVRLNDREKLILNMRFYQGK--TQMEVAEEIGI 239

Query: 265 SRERVRQIEARAFKKVQESIQ 285
           S+ +V ++E  A +++ +  Q
Sbjct: 240 SQAQVSRLEKAAIQQMSKHAQ 260


>gi|167749813|ref|ZP_02421940.1| hypothetical protein EUBSIR_00781 [Eubacterium siraeum DSM 15702]
 gi|167657125|gb|EDS01255.1| hypothetical protein EUBSIR_00781 [Eubacterium siraeum DSM 15702]
 gi|291557474|emb|CBL34591.1| RNA polymerase, sigma 29 subunit, SigE [Eubacterium siraeum
           V10Sc8a]
          Length = 239

 Score = 55.8 bits (133), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 34/95 (35%), Positives = 54/95 (56%), Gaps = 3/95 (3%)

Query: 27  PMLEKQEEY-VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           P L K+EE   LAK   +  +  A   L+  +LRLVV IA  +   G+ I +++S G IG
Sbjct: 36  PPLSKEEEAKTLAKLNTDFEN--ARETLIVHNLRLVVYIAKKFESTGIGIEDLISIGTIG 93

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           L++AV  F  E+  +LATY+   I+  +  Y+ ++
Sbjct: 94  LIKAVNTFSVEKNIKLATYASRCIENEILMYLRKT 128


>gi|161898923|gb|ABX80451.1| SigB [Listeria monocytogenes]
          Length = 236

 Score = 55.8 bits (133), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 61/253 (24%), Positives = 120/253 (47%), Gaps = 26/253 (10%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTREL 115

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +   
Sbjct: 116 QSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGT 172

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            DG E+V        N+R +L + + VL+ RE++I +   ++    + +      ++S+ 
Sbjct: 173 DDGFERV--------NQRMLLEKVLPVLDEREQKILQYTFIENR--SQKETGELLDISQM 222

Query: 268 RVRQIEARAFKKV 280
            V +I+ +A KK+
Sbjct: 223 HVSRIQRQAIKKL 235


>gi|161898845|gb|ABX80412.1| SigB [Listeria monocytogenes]
 gi|161898851|gb|ABX80415.1| SigB [Listeria monocytogenes]
 gi|161898853|gb|ABX80416.1| SigB [Listeria monocytogenes]
 gi|161898861|gb|ABX80420.1| SigB [Listeria monocytogenes]
 gi|161898863|gb|ABX80421.1| SigB [Listeria monocytogenes]
 gi|161898867|gb|ABX80423.1| SigB [Listeria monocytogenes]
 gi|161898869|gb|ABX80424.1| SigB [Listeria monocytogenes]
 gi|161898873|gb|ABX80426.1| SigB [Listeria monocytogenes]
 gi|161898875|gb|ABX80427.1| SigB [Listeria monocytogenes]
 gi|161898877|gb|ABX80428.1| SigB [Listeria monocytogenes]
 gi|161898879|gb|ABX80429.1| SigB [Listeria monocytogenes]
 gi|161898887|gb|ABX80433.1| SigB [Listeria monocytogenes]
 gi|161898891|gb|ABX80435.1| SigB [Listeria monocytogenes]
 gi|161898901|gb|ABX80440.1| SigB [Listeria monocytogenes]
 gi|161898911|gb|ABX80445.1| SigB [Listeria monocytogenes]
 gi|161898919|gb|ABX80449.1| SigB [Listeria monocytogenes]
 gi|161898925|gb|ABX80452.1| SigB [Listeria monocytogenes]
 gi|161898927|gb|ABX80453.1| SigB [Listeria monocytogenes]
 gi|161898929|gb|ABX80454.1| SigB [Listeria monocytogenes]
 gi|161898935|gb|ABX80457.1| SigB [Listeria monocytogenes]
 gi|161898941|gb|ABX80460.1| SigB [Listeria monocytogenes]
 gi|161898943|gb|ABX80461.1| SigB [Listeria monocytogenes]
          Length = 237

 Score = 55.8 bits (133), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 61/253 (24%), Positives = 120/253 (47%), Gaps = 26/253 (10%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 3   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 62

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 63  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTREL 116

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +   
Sbjct: 117 QSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGT 173

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            DG E+V        N+R +L + + VL+ RE++I +   ++    + +      ++S+ 
Sbjct: 174 DDGFERV--------NQRMLLEKVLPVLDEREQKILQFTFIENR--SQKETGELLDISQM 223

Query: 268 RVRQIEARAFKKV 280
            V +I+ +A KK+
Sbjct: 224 HVSRIQRQAIKKL 236


>gi|291531212|emb|CBK96797.1| RNA polymerase, sigma subunit, RpsG/SigG [Eubacterium siraeum 70/3]
          Length = 255

 Score = 55.8 bits (133), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 38/150 (25%), Positives = 79/150 (52%), Gaps = 7/150 (4%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+ +L++ E+  L ++ R  GD +A  +L+  +LRLV+ +   + G G    ++   G I
Sbjct: 20  KLKVLKESEKTELLRQMR-SGDPTAREKLINGNLRLVLSVIQRFSGRGENPDDLFQVGCI 78

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A+  F  +   R +TY++  I   ++ Y+  S S   I  + + + L +   + + 
Sbjct: 79  GLMKAIDNFSTDFNVRFSTYAVPMIMGELRRYLRDSGS---IRVSRSMRDLAYKAMQAR- 134

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVI 174
             + +T++N K   +  IAK+++    +V+
Sbjct: 135 --EKLTNDNSKEPTIEQIAKEIDAKREDVV 162


>gi|297529299|ref|YP_003670574.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
 gi|297252551|gb|ADI25997.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
          Length = 245

 Score = 55.8 bits (133), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 50/161 (31%), Positives = 77/161 (47%), Gaps = 19/161 (11%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  ++EE  LA   +  GD  A +RL+  +LRLV  I   +   G  + +++S G IGL
Sbjct: 38  PLSAQEEEKYLALMAK--GDEQARNRLIEHNLRLVAHIVKKFENTGEEVEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK----------IGTTANQKRLF 136
           ++A++ + P +G +LATY+   I+    E ++   SL K          IG       + 
Sbjct: 96  IKAIESYSPGKGTKLATYAARCIE---NEILMHLRSLKKTRKDVSLHEPIGQDKEGNEIS 152

Query: 137 FNLRRLKGHLQAITDN---NLKPEQVVAIAKKLNVSESEVI 174
             L  LK   Q I D    N++ EQV      L+  E EVI
Sbjct: 153 L-LDILKAEGQDIVDEIHLNMELEQVKQYISVLDEREKEVI 192


>gi|326442277|ref|ZP_08217011.1| RNA polymerase sigma factor, sigma L [Streptomyces clavuligerus
           ATCC 27064]
          Length = 292

 Score = 55.8 bits (133), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 62/237 (26%), Positives = 105/237 (44%), Gaps = 23/237 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +   
Sbjct: 71  LIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTVVGE 130

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL   L +    L    D +     V  +A  L VSE 
Sbjct: 131 IKRFFRDTSWS-VRVPRRLQELRL--ALTKASDELAQRLDRS---PTVPELAAVLGVSEE 184

Query: 172 EVIS----MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           EV+      N   A   SL++     D       D L Y+    E V    E R++ + +
Sbjct: 185 EVVDGLAVGNAYTA--SSLDSPSPEDDGGEGSLADRLGYEDTALEGV----EYRESLKPL 238

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L +    L PRER+I   R      +T   +  E  +S+  V ++  R   ++++ +
Sbjct: 239 LAK----LPPRERQIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLRDGL 289


>gi|225389231|ref|ZP_03758955.1| hypothetical protein CLOSTASPAR_02977 [Clostridium asparagiforme
           DSM 15981]
 gi|225044710|gb|EEG54956.1| hypothetical protein CLOSTASPAR_02977 [Clostridium asparagiforme
           DSM 15981]
          Length = 239

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 61/241 (25%), Positives = 111/241 (46%), Gaps = 17/241 (7%)

Query: 42  REH-GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           R H GD +A  +LV  ++ L+  I   + G G  + ++   G+IGLM+A+ KFD     +
Sbjct: 10  RAHEGDKTARDQLVMDNVGLIWSIVRRFAGRGYEMEDLFQIGSIGLMKAIDKFDTTFEVK 69

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY++  I   ++ + LR   ++K+  +  +  L     ++K   + +T    +   + 
Sbjct: 70  FSTYAVPMITGEIKRF-LRDDGMIKVSRSIKELGL-----KVKCAREEMTYELGREPTIE 123

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            IA  + VS  EV +     A  ESL   +  SD N     D L  +++  E ++     
Sbjct: 124 EIAGSVGVSREEVAASMEAGAEVESLYRPVGGSDDNQLCLMDRLEEENNEHEALI----- 178

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
               R +L   +S L   ER I   RR   N  T   ++ +  +S+ +V ++E R  K +
Sbjct: 179 ---NRMVLKELLSSLEEGEREII-VRRYFHNQ-TQTQIAQDLGISQVQVSRLEKRILKAM 233

Query: 281 Q 281
           +
Sbjct: 234 R 234


>gi|307265198|ref|ZP_07546757.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|306919820|gb|EFN50035.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
          Length = 230

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 29/75 (38%), Positives = 43/75 (57%), Gaps = 3/75 (4%)

Query: 38  AKRYRE---HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
            K+Y E   +GD  A + L+  +LRLV  +   Y G G  I +++S G IGL++A+  FD
Sbjct: 36  GKKYLEAYRNGDEEARNILIERNLRLVAHVVKKYSGTGKDIDDLISIGTIGLIKAISTFD 95

Query: 95  PERGFRLATYSMWWI 109
             +G  LATY+   I
Sbjct: 96  SSKGTHLATYAARCI 110


>gi|161898889|gb|ABX80434.1| SigB [Listeria monocytogenes]
 gi|161898893|gb|ABX80436.1| SigB [Listeria monocytogenes]
 gi|161898909|gb|ABX80444.1| SigB [Listeria monocytogenes]
          Length = 236

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 61/253 (24%), Positives = 120/253 (47%), Gaps = 26/253 (10%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTREL 115

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +   
Sbjct: 116 QSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGT 172

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            DG E+V        N+R +L + + VL+ RE++I +   ++    + +      ++S+ 
Sbjct: 173 DDGFERV--------NQRMLLEKVLPVLDEREQKILQFTFIENR--SQKETGELLDISQM 222

Query: 268 RVRQIEARAFKKV 280
            V +I+ +A KK+
Sbjct: 223 HVSRIQRQAIKKL 235


>gi|138896107|ref|YP_001126560.1| sporulation sigma factor SigK [Geobacillus thermodenitrificans
           NG80-2]
 gi|196249000|ref|ZP_03147700.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
 gi|134267620|gb|ABO67815.1| RNA polymerase sigma-K factor [Geobacillus thermodenitrificans
           NG80-2]
 gi|196211876|gb|EDY06635.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
          Length = 237

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 50/161 (31%), Positives = 76/161 (47%), Gaps = 19/161 (11%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  K+EE  L    +  GD  A +RL+  +LRLV  I   +   G  + +++S G IGL
Sbjct: 30  PLSPKEEEKYLELMAK--GDEQARNRLIEHNLRLVAHIVKKFENTGEEVEDLISIGTIGL 87

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK----------IGTTANQKRLF 136
           ++A++ + P +G +LATY+   I+    E ++   SL K          IG       + 
Sbjct: 88  IKAIESYSPNKGTKLATYAARCIE---NEILMHLRSLKKTRKDVSLHEPIGQDKEGNEIS 144

Query: 137 FNLRRLKGHLQAITDN---NLKPEQVVAIAKKLNVSESEVI 174
             L  LK   Q I D    N++ EQV      L+  E EVI
Sbjct: 145 L-LDILKSEGQDIVDEIQLNMELEQVKKYISVLDEREKEVI 184


>gi|260438492|ref|ZP_05792308.1| RNA polymerase sigma-E factor [Butyrivibrio crossotus DSM 2876]
 gi|292809081|gb|EFF68286.1| RNA polymerase sigma-E factor [Butyrivibrio crossotus DSM 2876]
          Length = 207

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 33/78 (42%), Positives = 47/78 (60%), Gaps = 3/78 (3%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           ++EY+  KRY+ +GD  A + L+  +LRLV  I   Y      I E +S G IGL++A+K
Sbjct: 13  EQEYL--KRYK-NGDEEAGNVLILRNLRLVAHIVKHYNFDEKDIEEYLSIGTIGLIKAIK 69

Query: 92  KFDPERGFRLATYSMWWI 109
            FD  +G RLATY+   I
Sbjct: 70  TFDCSKGNRLATYASKCI 87


>gi|251797416|ref|YP_003012147.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Paenibacillus sp.
           JDR-2]
 gi|247545042|gb|ACT02061.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Paenibacillus sp.
           JDR-2]
          Length = 256

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 66/271 (24%), Positives = 118/271 (43%), Gaps = 50/271 (18%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQAVKK 92
           L + ++E GDL A  RL+   L LV  +       GLP +    ++ S G +GL+ A++K
Sbjct: 9   LWRAWKEEGDLEAKKRLIEQFLPLVDYVT-NRMAIGLPKNVLKDDLASNGVMGLIDAIEK 67

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL-KGHLQAITD 151
           FD  RG +  TY+ W I+ ++ +  LR    V        KR+    + L + +L++++D
Sbjct: 68  FDYCRGLQFETYASWRIRGSIIDG-LRQGDWVPRSVREKAKRIEEAYQSLEQKYLRSVSD 126

Query: 152 NNLKPEQVVAIAKKLNVSESEVISM--------NCRL-------AGDESLNALINSSDKN 196
                     I++ LNVSE E  +M         C L         +  L+ LI+   KN
Sbjct: 127 --------AEISQYLNVSEKEFTTMLHEIAITTVCSLEDPIREEESETRLSLLIDERAKN 178

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
                     DH   E  L         ++ L   +  L  +ER +      +E  ++L 
Sbjct: 179 P---------DHKAHEFFL---------KDSLISGIEKLTEKERTVISLFYYEE--LSLS 218

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            ++    +S  R+ Q+ ++A  +++ ++ K 
Sbjct: 219 EIAEVMSLSPSRISQLHSKAILRLRGALAKH 249


>gi|161898913|gb|ABX80446.1| SigB [Listeria monocytogenes]
 gi|161898915|gb|ABX80447.1| SigB [Listeria monocytogenes]
 gi|161898939|gb|ABX80459.1| SigB [Listeria monocytogenes]
          Length = 237

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 61/253 (24%), Positives = 120/253 (47%), Gaps = 26/253 (10%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 3   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 62

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 63  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTREL 116

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +   
Sbjct: 117 QSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGT 173

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            DG E+V        N+R +L + + VL+ RE++I +   ++    + +      ++S+ 
Sbjct: 174 DDGFERV--------NQRMLLEKVLPVLDEREQKILQYTFIENR--SQKETGELLDISQM 223

Query: 268 RVRQIEARAFKKV 280
            V +I+ +A KK+
Sbjct: 224 HVSRIQRQAIKKL 236


>gi|297544535|ref|YP_003676837.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
 gi|296842310|gb|ADH60826.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
          Length = 231

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 43/74 (58%), Gaps = 3/74 (4%)

Query: 39  KRYRE---HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           K+Y E   +GD  A + L+  +LRLV  +   Y G G  I +++S G IGL++A+  FD 
Sbjct: 38  KKYLEAYKNGDEEARNILIERNLRLVAHVVKKYSGTGKDIDDLISIGTIGLIKAISTFDS 97

Query: 96  ERGFRLATYSMWWI 109
            +G  LATY+   I
Sbjct: 98  SKGTHLATYAARCI 111


>gi|291542628|emb|CBL15738.1| RNA polymerase, sigma 29 subunit, SigE [Ruminococcus bromii L2-63]
          Length = 233

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 30/97 (30%), Positives = 54/97 (55%), Gaps = 2/97 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  ++E++++    +  GD  A   L+  +LRLVV IA  +        +++S G IGL
Sbjct: 32  PLTREEEQHIMENIAK--GDSKAREPLIVHNLRLVVYIAKKFETPNASAEDLISIGTIGL 89

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           ++AV  F PE+  +LATY+   I+  +  ++ +S  L
Sbjct: 90  IKAVNTFSPEKNIKLATYASRCIENEILMFLRKSSQL 126


>gi|149183910|ref|ZP_01862298.1| sporulation sigma factor SigG [Bacillus sp. SG-1]
 gi|148848374|gb|EDL62636.1| sporulation sigma factor SigG [Bacillus sp. SG-1]
          Length = 227

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 30/95 (31%), Positives = 55/95 (57%), Gaps = 5/95 (5%)

Query: 25  KIPMLEKQEEYVLAKRYRE--HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           K+P+L+ +E   + K +RE   GD+SA  +LV  +LRLV+ +   +   G  + ++   G
Sbjct: 26  KLPVLKNEE---MRKLFREMQAGDISAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVG 82

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
            IGLM+++  FD  +  R +TY++  I   ++ Y+
Sbjct: 83  CIGLMKSIDNFDLGQNVRFSTYAVPMIIGEIRRYL 117


>gi|289578255|ref|YP_003476882.1| RNA polymerase, sigma 28 subunit, SigK [Thermoanaerobacter italicus
           Ab9]
 gi|289527968|gb|ADD02320.1| RNA polymerase, sigma 28 subunit, SigK [Thermoanaerobacter italicus
           Ab9]
          Length = 231

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 43/74 (58%), Gaps = 3/74 (4%)

Query: 39  KRYRE---HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           K+Y E   +GD  A + L+  +LRLV  +   Y G G  I +++S G IGL++A+  FD 
Sbjct: 38  KKYLEAYKNGDEEARNILIERNLRLVAHVVKKYSGTGKDIDDLISIGTIGLIKAISTFDS 97

Query: 96  ERGFRLATYSMWWI 109
            +G  LATY+   I
Sbjct: 98  SKGTHLATYAARCI 111


>gi|218288661|ref|ZP_03492938.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
 gi|218241318|gb|EED08493.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
          Length = 239

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 27/73 (36%), Positives = 46/73 (63%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A +RL+  +LRLV  +A  Y   G  + +++S G IGL++AV+ + P++G +LATY
Sbjct: 46  GDGDARNRLIEHNLRLVAHLAKKYESSGEEMDDLISIGTIGLIKAVESYRPDKGTKLATY 105

Query: 105 SMWWIKAAMQEYI 117
           +   I+  +  Y+
Sbjct: 106 AARCIENEILMYL 118


>gi|328948495|ref|YP_004365832.1| RNA polymerase, sigma 32 subunit, RpoH [Treponema succinifaciens
           DSM 2489]
 gi|328448819|gb|AEB14535.1| RNA polymerase, sigma 32 subunit, RpoH [Treponema succinifaciens
           DSM 2489]
          Length = 349

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 55/240 (22%), Positives = 107/240 (44%), Gaps = 24/240 (10%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           G++ A +R+   +LR V++I+  + +       E    G IGL++A+K FD       A+
Sbjct: 117 GNVYAFNRMTEMYLRGVLRISYNFAKENYCDFEEAFQNGTIGLIRAIKNFDVTSPNSFAS 176

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y    + + MQ       S   +    +QK   F      G +         PE+ + I 
Sbjct: 177 YYSLSVLSEMQRKYSVKNSFFDLPVHFSQKTFEF-----LGIISKYLAKGKTPEESIGI- 230

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
               +S+   + +N +L         +   D ++  ++++  +D   ++ ++ E     +
Sbjct: 231 ----ISDDFYLEINPKLKM-----YFLPYLDLDAISYENF-AFDIHIEDDIIYE-----S 275

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +  L   +  L  RER++ E R    N   +TLE +   + VSRER+RQIE +A ++++
Sbjct: 276 LKEQLNEVLHTLPERERKVLEMRFGLNNLKQMTLEEVGKYYNVSRERIRQIEKKALRRLR 335


>gi|291522682|emb|CBK80975.1| RNA polymerase, sigma 29 subunit, SigE [Coprococcus catus GD/7]
          Length = 245

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 40/119 (33%), Positives = 65/119 (54%), Gaps = 13/119 (10%)

Query: 11  NGEIGLSRYIHEIRKIPM-LEKQEE-----YVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           NGEI    YI     +P+ LE +EE      +  +  REHG     + L+  +LRLVV I
Sbjct: 23  NGEI---HYISGTDVLPVPLEGEEEKNAIAMLATEAEREHG----RNILIEHNLRLVVYI 75

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           A  +   G  + +++S G IGL++A+  ++P++  +LATY+   I+  +  Y+ RS  L
Sbjct: 76  ARKFDNTGAGMEDLISIGTIGLIKAINSYNPDKNIKLATYASRCIENEILMYLRRSSKL 134


>gi|218673042|ref|ZP_03522711.1| RNA polymerase factor sigma-32 [Rhizobium etli GR56]
          Length = 88

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 28/61 (45%), Positives = 42/61 (68%)

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           RR  L  ++  LN RE +I  ARRL E+  TLE L ++  +S+ERVRQIE+RA +K++ +
Sbjct: 17  RRVWLASALKHLNEREMKIISARRLAEDGATLEELGADLGISKERVRQIESRAMEKLRSA 76

Query: 284 I 284
           +
Sbjct: 77  L 77


>gi|161898883|gb|ABX80431.1| SigB [Listeria monocytogenes]
          Length = 235

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 61/253 (24%), Positives = 120/253 (47%), Gaps = 26/253 (10%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 1   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 60

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 61  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTREL 114

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +   
Sbjct: 115 QSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGT 171

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            DG E+V        N+R +L + + VL+ RE++I +   ++    + +      ++S+ 
Sbjct: 172 DDGFERV--------NQRMLLEKVLPVLDEREQKILQFTFIENR--SQKETGELLDISQM 221

Query: 268 RVRQIEARAFKKV 280
            V +I+ +A KK+
Sbjct: 222 HVSRIQRQAIKKL 234


>gi|30024623|dbj|BAC75680.1| sigma L [Streptomyces griseus]
          Length = 288

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 61/237 (25%), Positives = 105/237 (44%), Gaps = 23/237 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +   
Sbjct: 67  LIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTVVGE 126

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL   L +    L    D +     V  + + L VSE 
Sbjct: 127 IKRFFRDTSWS-VRVPRRLQELRL--ALTKTSDELAQKLDRS---PTVPELVRALGVSEE 180

Query: 172 EVIS----MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +V+      N   A   SL++     D       D L Y+    E V    E R++ + +
Sbjct: 181 DVVDGLAVGNAYTA--SSLDSPSPEDDGGEGSLADRLGYEDAALEGV----EYRESLKPL 234

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L +    L PRER+I   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 235 LAK----LAPRERQIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 285


>gi|312127292|ref|YP_003992166.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor hydrothermalis 108]
 gi|311777311|gb|ADQ06797.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor hydrothermalis 108]
          Length = 240

 Score = 55.8 bits (133), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 57/241 (23%), Positives = 108/241 (44%), Gaps = 20/241 (8%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           ++GD  A  +L+ S+L LV  +   +   G+ + ++   G IGL++AV +FDP    R +
Sbjct: 14  KNGDKLARQQLIESNLALVWSVVKKFAAKGVELEDLFQIGCIGLIKAVDRFDPSFNVRFS 73

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I   ++ Y LR    +K+      +++  N  ++K        N+ +   +  I
Sbjct: 74  TYAVPMIIGEIKRY-LRDDGKIKVS-----RKIKENQGKIKKLRNQFVSNHGREPTISEI 127

Query: 163 AKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
           ++   +S  E+  + C  A  E  SL+ +IN  +       D    + D   ++L     
Sbjct: 128 SQLTGLSSDEI--LLCLDASSEVASLSEVINQEEGKPITLMDIASDEEDYSTKLL----- 180

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                  L   +  L  RER I   R  +    T   ++ E  +S+  V +IE RA +++
Sbjct: 181 ---DLMALKEGLKKLKGRERYIIFMRYFKNK--TQSEIAKELNISQVHVSRIEKRALERI 235

Query: 281 Q 281
           +
Sbjct: 236 K 236


>gi|56421070|ref|YP_148388.1| sporulation sigma factor SigK [Geobacillus kaustophilus HTA426]
 gi|56380912|dbj|BAD76820.1| sporulation mother cell-specific RNA polymerase sigma-27 factor
           precursor (sigma K) (stage IV sporulation protein CB)
           [Geobacillus kaustophilus HTA426]
          Length = 237

 Score = 55.5 bits (132), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 29/84 (34%), Positives = 50/84 (59%), Gaps = 2/84 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  ++EE  LA   +  GD  A +RL+  +LRLV  I   +   G  + +++S G IGL
Sbjct: 30  PLSAQEEEKYLALMAK--GDEQARNRLIEHNLRLVAHIVKKFENTGEEVEDLISIGTIGL 87

Query: 87  MQAVKKFDPERGFRLATYSMWWIK 110
           ++A++ + P +G +LATY+   I+
Sbjct: 88  IKAIESYSPGKGTKLATYAARCIE 111


>gi|254390381|ref|ZP_05005598.1| sigma L [Streptomyces clavuligerus ATCC 27064]
 gi|294813859|ref|ZP_06772502.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|197704085|gb|EDY49897.1| sigma L [Streptomyces clavuligerus ATCC 27064]
 gi|294326458|gb|EFG08101.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 314

 Score = 55.5 bits (132), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 62/237 (26%), Positives = 105/237 (44%), Gaps = 23/237 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +   
Sbjct: 93  LIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTVVGE 152

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL   L +    L    D +     V  +A  L VSE 
Sbjct: 153 IKRFFRDTSWS-VRVPRRLQELRL--ALTKASDELAQRLDRS---PTVPELAAVLGVSEE 206

Query: 172 EVIS----MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           EV+      N   A   SL++     D       D L Y+    E V    E R++ + +
Sbjct: 207 EVVDGLAVGNAYTA--SSLDSPSPEDDGGEGSLADRLGYEDTALEGV----EYRESLKPL 260

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L +    L PRER+I   R      +T   +  E  +S+  V ++  R   ++++ +
Sbjct: 261 LAK----LPPRERQIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLRDGL 311


>gi|148380498|ref|YP_001255039.1| sporulation sigma factor SigK [Clostridium botulinum A str. ATCC
           3502]
 gi|170759231|ref|YP_001787857.1| sporulation sigma factor SigK [Clostridium botulinum A3 str. Loch
           Maree]
 gi|226949896|ref|YP_002804987.1| RNA polymerase sigma-K factor [Clostridium botulinum A2 str. Kyoto]
 gi|237795980|ref|YP_002863532.1| RNA polymerase sigma-K factor [Clostridium botulinum Ba4 str. 657]
 gi|148289982|emb|CAL84095.1| RNA polymerase sigma-28 factor [Clostridium botulinum A str. ATCC
           3502]
 gi|169406220|gb|ACA54631.1| RNA polymerase sigma-70 factor family [Clostridium botulinum A3
           str. Loch Maree]
 gi|226844119|gb|ACO86785.1| RNA polymerase sigma-K factor [Clostridium botulinum A2 str. Kyoto]
 gi|229261319|gb|ACQ52352.1| RNA polymerase sigma-K factor [Clostridium botulinum Ba4 str. 657]
          Length = 234

 Score = 55.5 bits (132), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 31/83 (37%), Positives = 48/83 (57%), Gaps = 2/83 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ +++E+Y L +   + GD  A   LV  +LRLV  I   Y   G  I +++S G +GL
Sbjct: 30  PLSDEEEKYYLDRL--KKGDALAKDILVERNLRLVAHIVKKYSYPGKDIDDLISIGTVGL 87

Query: 87  MQAVKKFDPERGFRLATYSMWWI 109
           ++A+  FD  +G RLATY+   I
Sbjct: 88  IKAIDSFDNSKGTRLATYAARCI 110


>gi|312282679|dbj|BAJ34205.1| unnamed protein product [Thellungiella halophila]
          Length = 511

 Score = 55.5 bits (132), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 59/253 (23%), Positives = 110/253 (43%), Gaps = 45/253 (17%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           +A ++L+  +LRLV+ +   Y      G    ++   G  GL+ A+ +F+P+R FRL+TY
Sbjct: 272 AARNKLIKHNLRLVLFVMNKYFQDFTNGPKFQDLCQAGMRGLITAIDRFEPKRKFRLSTY 331

Query: 105 SMWWIKAAMQEYILRSWSL------------VKIGTTANQKRLFFNLRRLKGHLQAITDN 152
            ++WI+ A    I+RS +             V++     +  L F L RL    + +   
Sbjct: 332 GLFWIRHA----IIRSMTTSNFTRVPFGLESVRVEIYKTKMELLFELGRLPTEDEVVERL 387

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCR--LAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
            + PE+   + +    +   V S+N +  +  +E +N + +          D +  D+  
Sbjct: 388 KISPERYREVLR----AAKPVFSLNSKHSVTQEEFINGITDV---------DGVGADNRR 434

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRER 268
           Q  +L         R  L   +  L P+E  +   R   +     TL  ++    +SRE 
Sbjct: 435 QPAIL---------RLALDDVLDSLKPKESLVIRQRYGLDGKGDRTLGEIAGNLNISREM 485

Query: 269 VRQIEARAFKKVQ 281
           VR+ E +A  K++
Sbjct: 486 VRKHEVKALMKLK 498


>gi|311897125|dbj|BAJ29533.1| putative RNA polymerase sigma factor [Kitasatospora setae KM-6054]
          Length = 296

 Score = 55.5 bits (132), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 55/199 (27%), Positives = 90/199 (45%), Gaps = 21/199 (10%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +L LV   +  +R    P+ ++V  G IGL++A+ +FDP+RG    T++M  +   
Sbjct: 75  LIELNLPLVRYASARFRSRNEPMEDIVQVGTIGLIKAIDRFDPDRGVEFPTFAMPTVVGE 134

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL   L +    L    D +     V  +A  L V+E 
Sbjct: 135 IKRFFRDTSWS-VRVPRRLQELRL--ALTKAGDELSQRLDRS---PTVPELAAYLGVTED 188

Query: 172 EVIS----MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +V+      N   A   SL++     D       D L Y+    E V    E R++ + +
Sbjct: 189 DVVEGLAVGNAYTA--SSLDSTPAEDDGGDGPLADRLGYEDLALEGV----EYRESLKPL 242

Query: 228 LTRSMSVLNPRERRIFEAR 246
           L +    L PRERRI   R
Sbjct: 243 LAK----LPPRERRIIMLR 257


>gi|187778862|ref|ZP_02995335.1| hypothetical protein CLOSPO_02457 [Clostridium sporogenes ATCC
           15579]
 gi|187772487|gb|EDU36289.1| hypothetical protein CLOSPO_02457 [Clostridium sporogenes ATCC
           15579]
          Length = 234

 Score = 55.5 bits (132), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 31/83 (37%), Positives = 48/83 (57%), Gaps = 2/83 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ +++E+Y L +   + GD  A   LV  +LRLV  I   Y   G  I +++S G +GL
Sbjct: 30  PLSDEEEKYYLDRL--KKGDALAKDILVERNLRLVAHIVKKYSYPGKDIDDLISIGTVGL 87

Query: 87  MQAVKKFDPERGFRLATYSMWWI 109
           ++A+  FD  +G RLATY+   I
Sbjct: 88  IKAIDSFDNSKGTRLATYAARCI 110


>gi|51893096|ref|YP_075787.1| sporulation sigma factor SigK [Symbiobacterium thermophilum IAM
           14863]
 gi|51856785|dbj|BAD40943.1| RNA polymerase sigma factor similar to B. subtilis SigK
           [Symbiobacterium thermophilum IAM 14863]
          Length = 236

 Score = 55.5 bits (132), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 30/84 (35%), Positives = 50/84 (59%), Gaps = 2/84 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ E++E   L++   ++GD  A   L+  +LRLV  I   +   G  + +++S G +GL
Sbjct: 32  PLSEEEEAKYLSRL--QNGDEEARAVLIERNLRLVAHIVKKFDNTGEDVDDLISIGTVGL 89

Query: 87  MQAVKKFDPERGFRLATYSMWWIK 110
           ++A+  F PERG RLATY+   I+
Sbjct: 90  IKAIGTFKPERGTRLATYAARCIE 113


>gi|331269717|ref|YP_004396209.1| RNA polymerase sigma-K factor [Clostridium botulinum BKT015925]
 gi|329126267|gb|AEB76212.1| RNA polymerase sigma-K factor [Clostridium botulinum BKT015925]
          Length = 226

 Score = 55.5 bits (132), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 33/102 (32%), Positives = 54/102 (52%), Gaps = 2/102 (1%)

Query: 9   IVNGEIGLSRYIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           +++G   L+ Y+      P  L + EE    K++++ GD  A   L+  +LRLV  I   
Sbjct: 1   MIDGMTFLTAYVSNGTSFPQPLNEDEERYYLKKFKD-GDTLAKGILIERNLRLVAHIVKK 59

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           Y      I +++S G +GL++A+  FD  +G RLATY+   I
Sbjct: 60  YSYPNKDIDDLISIGTVGLIKAIDSFDISKGTRLATYAARCI 101


>gi|258511711|ref|YP_003185145.1| sporulation sigma factor SigF [Alicyclobacillus acidocaldarius
           subsp. acidocaldarius DSM 446]
 gi|257478437|gb|ACV58756.1| RNA polymerase, sigma 28 subunit, SigF [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
          Length = 256

 Score = 55.5 bits (132), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 61/245 (24%), Positives = 109/245 (44%), Gaps = 26/245 (10%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A  RL+  + RLV  +   + G G    ++   G IGLM+AV KFD     + +TY
Sbjct: 34  GDAEARERLIVHNQRLVWAVVQRFLGRGYEAEDLFQIGCIGLMKAVDKFDLSYDVKFSTY 93

Query: 105 SMWWIKAAMQEYILRSWSLVKIG----TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
           ++  I   +Q + LR  S VK+      TA Q R   +  RL   L        +P  + 
Sbjct: 94  AVPMIIGEIQRF-LRDDSTVKVSRSLKETAKQIRHVRD--RLAKEL------GRQP-HIT 143

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            IA+ + +  SE++     L    S++  +  +D +     D          Q+  E+ E
Sbjct: 144 EIAEAMGMEPSEIVFAQEALRAPASIHETVYENDGDPIYLMD----------QIADEETE 193

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            K  +  L   +  L  RER I   R  ++   T  +++    +S+ +V ++E R  +++
Sbjct: 194 GKFDKVELHEIIGRLPERERFIVYMRFFRDK--TQSDVARVLGISQVQVSRLEKRILQQI 251

Query: 281 QESIQ 285
           ++ ++
Sbjct: 252 RQELE 256


>gi|168182618|ref|ZP_02617282.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           Bf]
 gi|182674200|gb|EDT86161.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           Bf]
          Length = 234

 Score = 55.5 bits (132), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 31/83 (37%), Positives = 48/83 (57%), Gaps = 2/83 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ +++E+Y L +   + GD  A   LV  +LRLV  I   Y   G  I +++S G +GL
Sbjct: 30  PLSDEEEKYYLDRL--KKGDALAKDILVERNLRLVAHIVKKYSYPGKDIDDLISIGTVGL 87

Query: 87  MQAVKKFDPERGFRLATYSMWWI 109
           ++A+  FD  +G RLATY+   I
Sbjct: 88  IKAIDSFDNSKGTRLATYAARCI 110


>gi|167037477|ref|YP_001665055.1| sporulation sigma factor SigK [Thermoanaerobacter pseudethanolicus
           ATCC 33223]
 gi|167040139|ref|YP_001663124.1| sporulation sigma factor SigK [Thermoanaerobacter sp. X514]
 gi|256752531|ref|ZP_05493387.1| RNA polymerase, sigma 28 subunit, SigK [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|300914223|ref|ZP_07131539.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X561]
 gi|307724542|ref|YP_003904293.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter sp. X513]
 gi|320115891|ref|YP_004186050.1| RNA polymerase sigma-K factor [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
 gi|166854379|gb|ABY92788.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Thermoanaerobacter sp. X514]
 gi|166856311|gb|ABY94719.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Thermoanaerobacter pseudethanolicus ATCC 33223]
 gi|256748597|gb|EEU61645.1| RNA polymerase, sigma 28 subunit, SigK [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|300889158|gb|EFK84304.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X561]
 gi|307581603|gb|ADN55002.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X513]
 gi|319928982|gb|ADV79667.1| RNA polymerase sigma-K factor [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
          Length = 231

 Score = 55.5 bits (132), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 29/74 (39%), Positives = 43/74 (58%), Gaps = 3/74 (4%)

Query: 39  KRYRE---HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           K+Y E   +GD  A + L+  +LRLV  +   Y G G  I +++S G IGL++A+  FD 
Sbjct: 38  KKYLEAYKNGDEEARNILIERNLRLVAHVVKKYSGTGKDIDDLISIGTIGLIKAISTFDS 97

Query: 96  ERGFRLATYSMWWI 109
            +G  LATY+   I
Sbjct: 98  SKGTHLATYAARCI 111


>gi|319649652|ref|ZP_08003808.1| FliA/WhiG family RNA polymerase [Bacillus sp. 2_A_57_CT2]
 gi|317398814|gb|EFV79496.1| FliA/WhiG family RNA polymerase [Bacillus sp. 2_A_57_CT2]
          Length = 236

 Score = 55.5 bits (132), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 57/241 (23%), Positives = 112/241 (46%), Gaps = 16/241 (6%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD++A  +LV  +LRLV+ +   +   G  + ++   G IGLM+++  FD  +  + +TY
Sbjct: 11  GDITAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGCIGLMKSIDNFDLSQNVKFSTY 70

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           ++  I   ++ Y LR  + +++  +   + + +   +++  L + T      E+   IAK
Sbjct: 71  AVPMIIGEIRRY-LRDNNPIRVSRSL--RDIAYKALQVRERLMSKTSREPTAEE---IAK 124

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L+V   E++     +    SL   I +   +     D L  + +   Q + E       
Sbjct: 125 ELDVPHEEIVFALDAIQDPVSLFEPIYNDGGDPIYVMDQLSDERNKDIQWIEEI------ 178

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              L   M  LN RE+ I   R  Q    T   ++ E  +S+ +V ++E  A K++ ++I
Sbjct: 179 --ALKEGMRRLNEREKLILRKRFFQGK--TQMEVAEEIGISQAQVSRLEKAAIKQMNKNI 234

Query: 285 Q 285
           Q
Sbjct: 235 Q 235


>gi|153938998|ref|YP_001391838.1| sporulation sigma factor SigK [Clostridium botulinum F str.
           Langeland]
 gi|168180573|ref|ZP_02615237.1| RNA polymerase sigma-70 factor family [Clostridium botulinum NCTC
           2916]
 gi|152934894|gb|ABS40392.1| RNA polymerase sigma-70 factor family [Clostridium botulinum F str.
           Langeland]
 gi|182668432|gb|EDT80411.1| RNA polymerase sigma-70 factor family [Clostridium botulinum NCTC
           2916]
 gi|295319864|gb|ADG00242.1| RNA polymerase sigma-70 factor family [Clostridium botulinum F str.
           230613]
          Length = 234

 Score = 55.5 bits (132), Expect = 9e-06,   Method: Compositional matrix adjust.
 Identities = 31/83 (37%), Positives = 48/83 (57%), Gaps = 2/83 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ +++E+Y L +   + GD  A   LV  +LRLV  I   Y   G  I +++S G +GL
Sbjct: 30  PLSDEEEKYYLDRL--KKGDALAKDILVERNLRLVAHIVKKYSYPGKDIDDLISIGTVGL 87

Query: 87  MQAVKKFDPERGFRLATYSMWWI 109
           ++A+  FD  +G RLATY+   I
Sbjct: 88  IKAIDSFDNSKGTRLATYAARCI 110


>gi|255280674|ref|ZP_05345229.1| RNA polymerase sigma-G factor [Bryantella formatexigens DSM 14469]
 gi|255268611|gb|EET61816.1| RNA polymerase sigma-G factor [Bryantella formatexigens DSM 14469]
          Length = 258

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 65/261 (24%), Positives = 125/261 (47%), Gaps = 25/261 (9%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L  +E+  L +R R+ GD+ A    +  +LRLV+ +   +        ++   G I
Sbjct: 15  KLPVLTNEEKEELFERIRQ-GDMEARELYIKGNLRLVLSVIKRFSASNENADDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ---KRLFFNLRR 141
           GLM+A+  F+ E   + +TY++  I   ++ Y LR  + +++  +      K L+     
Sbjct: 74  GLMKAIDNFNTEMDVKFSTYAVPMIIGEIRRY-LRDNNSIRVSRSLRDTAYKALYTREAY 132

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           +K HL+  T N L        A+++ +S  +++      A D ++ + ++  D   S+  
Sbjct: 133 MKKHLKEPTINEL--------AEEIGISREDIV-----FAMD-AIQSPLSLYDPVYSEGG 178

Query: 202 DWL-VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
           D L V D    ++    KEE       L  +M  L+ RER+I   R   E    +E +++
Sbjct: 179 DTLYVMDQISDKK---NKEENWVESLALQEAMKRLSDRERKIINMRFF-EGKTQME-VAA 233

Query: 261 EFEVSRERVRQIEARAFKKVQ 281
           E  +S+ +V ++E  A K ++
Sbjct: 234 EICISQAQVSRLEKSALKSMR 254


>gi|220931759|ref|YP_002508667.1| sporulation sigma factor SigG [Halothermothrix orenii H 168]
 gi|219993069|gb|ACL69672.1| sporulation sigma factor SigG [Halothermothrix orenii H 168]
          Length = 260

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 64/277 (23%), Positives = 135/277 (48%), Gaps = 47/277 (16%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           ++P+L  +E   L K+  + GD SA  +++  +LRLV+ +   +   G  + ++   G I
Sbjct: 14  ELPVLSNEEMRKLFKKM-QQGDWSARQKIINGNLRLVLSVIQRFNNRGENVDDLFQVGCI 72

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD  +  R +TY++  I   ++ Y LR  + +++  +   +   +   ++K 
Sbjct: 73  GLIKAIDNFDLSQNVRFSTYAVPMIIGEIRRY-LRDNNPIRVSRSL--RDTAYKALQMKE 129

Query: 145 HLQAITDNNLKPEQ--VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
            L+     N K E+  +  ++++L +  SE+I          +L+A+           QD
Sbjct: 130 SLK-----NKKSEEPSLKEVSEELGIPRSEIIF---------ALDAI-----------QD 164

Query: 203 WL-----VYDHDGQEQVLI------EKEERKNRRNMLT--RSMSVLNPRERRIFEARRLQ 249
            +     +Y HDG + + +      EK E +N    +     +  L+PRE+ I  A R  
Sbjct: 165 PISLFEPIY-HDGGDPIFVMDQISDEKTEDENWLEGIAVREGLRKLSPREKLIL-AYRFY 222

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E    +E +++E  +S+ +V ++E  A K+++  +++
Sbjct: 223 EGKTQME-VANEIGISQAQVSRLEKAALKRLKRHVKE 258


>gi|37522237|ref|NP_925614.1| RNA polymerase sigma factor SigF [Gloeobacter violaceus PCC 7421]
 gi|35213237|dbj|BAC90609.1| glr2668 [Gloeobacter violaceus PCC 7421]
          Length = 254

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 31/83 (37%), Positives = 48/83 (57%), Gaps = 1/83 (1%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKKFD 94
           +L + Y E    +  + LV  +L LV KIA    RG   P+ ++V  G IGLM+AV++FD
Sbjct: 13  LLLRAYGESPSTALRNELVCRNLGLVRKIAHQLARGSSEPLEDLVQVGAIGLMRAVERFD 72

Query: 95  PERGFRLATYSMWWIKAAMQEYI 117
           P  G   ++++   I+ AMQ Y+
Sbjct: 73  PSLGHAFSSFATPCIRGAMQHYL 95


>gi|167758775|ref|ZP_02430902.1| hypothetical protein CLOSCI_01117 [Clostridium scindens ATCC 35704]
 gi|167663515|gb|EDS07645.1| hypothetical protein CLOSCI_01117 [Clostridium scindens ATCC 35704]
          Length = 247

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 26/72 (36%), Positives = 45/72 (62%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+  +LRLVV IA  +   G+ + +++S G IGL++A+  F+PE+  +LATY+   
Sbjct: 64  AKKTLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFNPEKNIKLATYASRC 123

Query: 109 IKAAMQEYILRS 120
           I+  +  Y+ R+
Sbjct: 124 IENEILMYLRRN 135


>gi|219669461|ref|YP_002459896.1| RNA polymerase, sigma 28 subunit, SigF [Desulfitobacterium
           hafniense DCB-2]
 gi|219539721|gb|ACL21460.1| RNA polymerase, sigma 28 subunit, SigF [Desulfitobacterium
           hafniense DCB-2]
          Length = 261

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 57/267 (21%), Positives = 125/267 (46%), Gaps = 27/267 (10%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           + P+L  +E   L  R  ++GD  A  RL+  +L+L+  +   +   G  + ++   G I
Sbjct: 13  RFPLLSDEEMMDLLHR-AQNGDAEARERLINCNLKLIFNLVQRFSHRGYELEDLFQIGTI 71

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+ KFD   G + +TY++  I   ++ + LR    VK+  +   K L + + + + 
Sbjct: 72  GLIKAIDKFDFTYGVKFSTYAVPMIIGEIRRF-LRDDHPVKVPRS--YKELVYKVNKARE 128

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L A    +     +  IA+ + V   +++S         +L A+ + +  + + +QD  
Sbjct: 129 SLSATLGRD---PTIGEIAESIGVDREDIVS---------ALEAVQSPTSIHDTLYQD-- 174

Query: 205 VYDHDG---QEQVLIEKEERKN--RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
             D D     +Q+ +EK+       +  L   +  L  RE+R+   R  ++   T   ++
Sbjct: 175 --DSDPIYILDQLPMEKDLEAGWFEKIALKEVLDKLPEREKRVLMMRFYEDK--TQSEIA 230

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQK 286
           +   +S+ ++ +IE  A  ++++ + +
Sbjct: 231 ALLNLSQVQISRIERAALHRIRQYLHE 257


>gi|312128428|ref|YP_003993302.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor hydrothermalis 108]
 gi|311778447|gb|ADQ07933.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor hydrothermalis 108]
          Length = 256

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 52/233 (22%), Positives = 111/233 (47%), Gaps = 21/233 (9%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L + Y+    +   + LV  HL +   IA  + G G+   ++     I L+ AV++F+P 
Sbjct: 18  LFEEYQRTKAIELRNELVNKHLYIAEIIAKKFVGRGIDYEDLYQVACIALINAVERFEPN 77

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +G++  +++   I   ++ Y     S++++      +R++    ++K   + ++    +P
Sbjct: 78  KGYKFTSFATPTIMGEIKRYFRDRASIIRLP-----RRIYETSAKIKLATEVLSTKLKRP 132

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ--EQV 214
            +V  IA+ LN+S  EV+ +      + S N L  S D+   + ++  + D  G+  E +
Sbjct: 133 PKVEEIARHLNMSTEEVLEV-----MEASNNYLPQSLDQTMYEDEEMTLGDVLGKSDENI 187

Query: 215 L-IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           L +E  E       + +++  L+P ER   + R  +E   T + ++ E  VS+
Sbjct: 188 LQVENVE------AVKKAIERLSPFEREFVQKRFFEEK--TQKEIAEEMNVSQ 232


>gi|187778769|ref|ZP_02995242.1| hypothetical protein CLOSPO_02364 [Clostridium sporogenes ATCC
           15579]
 gi|187772394|gb|EDU36196.1| hypothetical protein CLOSPO_02364 [Clostridium sporogenes ATCC
           15579]
          Length = 242

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 65/248 (26%), Positives = 115/248 (46%), Gaps = 21/248 (8%)

Query: 45  GDLSAAHRLVTSHLRLVVKIA----MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
            +L     +V  ++ LV  IA    +G   Y +   ++VS G IGLM A+ KFD  +G +
Sbjct: 6   NNLYVKEEIVKKYIPLVKYIASRVIIGKTKY-IEYEDLVSYGMIGLMDALNKFDESKGMK 64

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+   IK +M + + R+  + K G      R    + RL+  L        K   ++
Sbjct: 65  FSTYASIRIKGSMIDELRRNSPISK-GAMDKLNRYNEAIERLQKKLN-------KEPNLI 116

Query: 161 AIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            IA +LN+S  EV  I          SL  LI SS+ +       +  D     +  +E+
Sbjct: 117 QIADELNISLKEVSEIENYINYISVISLEDLIFSSE-DEVPLIGTIKDDKSPSPEKHVEE 175

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
            E   + + L +++ +LN ++R +      +E  +TL+ +     VS  RV Q+ +RA  
Sbjct: 176 NE---QLDYLAKAIELLNEKDRLVVTLYYYEE--LTLKEIGKILSVSESRVCQLHSRAII 230

Query: 279 KVQESIQK 286
            +++++ K
Sbjct: 231 HLKKAMTK 238


>gi|307717588|gb|ADN88847.1| RNA polymerase sigma-37 factor [Listeria seeligeri]
 gi|307717632|gb|ADN88869.1| RNA polymerase sigma-37 factor [Listeria seeligeri]
          Length = 220

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 55/217 (25%), Positives = 104/217 (47%), Gaps = 24/217 (11%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  + +LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQENGDQDAQYNLVVHYKKLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTREL 115

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +   
Sbjct: 116 QSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGT 172

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
            DG E+V        N+R +L + + VL+ RE++I +
Sbjct: 173 DDGFERV--------NQRMLLEKVLPVLDEREQKILQ 201


>gi|295094809|emb|CBK83900.1| RNA polymerase, sigma 29 subunit, SigE [Coprococcus sp. ART55/1]
          Length = 245

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 34/106 (32%), Positives = 56/106 (52%), Gaps = 1/106 (0%)

Query: 19  YIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           YI     +P  LE  EE V+      +   SA   L+  +LRLVV IA  +   G+ I +
Sbjct: 31  YIGGTEVLPAPLEPHEEAVVINELTNNQSDSAKKMLIERNLRLVVYIAKKFDNTGVGIED 90

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           ++S G IGL++A+  F  ++  +LATY+   I+  +  ++ R+  L
Sbjct: 91  LISIGTIGLIKAINTFKNDKNIKLATYASRCIENEILMFLRRNSKL 136


>gi|161898857|gb|ABX80418.1| SigB [Listeria monocytogenes]
          Length = 236

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 61/253 (24%), Positives = 120/253 (47%), Gaps = 26/253 (10%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQENGDEDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTREL 115

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +   
Sbjct: 116 QSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGT 172

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            DG E+V        N+R +L + + VL+ RE++I +   ++    + +      ++S+ 
Sbjct: 173 DDGFERV--------NQRMLLEKVLPVLDEREQKILQFTFIENR--SQKETGELLDISQM 222

Query: 268 RVRQIEARAFKKV 280
            V +I+ +A KK+
Sbjct: 223 HVSRIQRQAIKKL 235


>gi|149183717|ref|ZP_01862127.1| sigma factor B [Bacillus sp. SG-1]
 gi|148848576|gb|EDL62816.1| sigma factor B [Bacillus sp. SG-1]
          Length = 265

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 62/257 (24%), Positives = 126/257 (49%), Gaps = 16/257 (6%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           K Y+E  D  A   LV  +  LV+ IA  Y        ++V  G IGL+ A++++D   G
Sbjct: 20  KAYQEDNDDEAQSNLVLHYENLVISIARKYSKGKSFHEDIVQVGMIGLLGAIRRYDDSFG 79

Query: 99  FRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
                +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T+   +  
Sbjct: 80  KTFEAFAIPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKSTVEELTNTLERSP 133

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQVLI 216
           +V  IA  + V+E EV+     +   +S  AL ++ S +  S+     + D  G    + 
Sbjct: 134 KVEEIADYIGVTEEEVLEA---MEMGKSYQALSVDHSIEADSEGSTVTLLDIVGN---VD 187

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           E  ER N++ +L + + VL+ RER I +   L  + ++ ++   +  +S+  V +++ RA
Sbjct: 188 EGYERINQKLVLEKVLHVLSERERLIIQYTYL--DNLSQKDAGEKLGISQMHVSRLQRRA 245

Query: 277 FKKVQESIQKQVELSSS 293
            KK++E+I  ++  S S
Sbjct: 246 IKKLKEAIDAEMRNSES 262


>gi|114566373|ref|YP_753527.1| sporulation sigma factor SigG [Syntrophomonas wolfei subsp. wolfei
           str. Goettingen]
 gi|114337308|gb|ABI68156.1| RNA polymerase sigma-G factor [Syntrophomonas wolfei subsp. wolfei
           str. Goettingen]
          Length = 234

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 58/241 (24%), Positives = 109/241 (45%), Gaps = 16/241 (6%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            G   A  +L+  ++RLV+ +   +   G  + ++   G IGL++++  FD  +  R +T
Sbjct: 10  QGKTQAREKLIQGNIRLVLSVIQRFTNRGEYVDDLFQVGCIGLIKSIDNFDLSQNVRFST 69

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y++  I   ++ Y LR  + V++  +          + L+   + I DN+ +P  V  IA
Sbjct: 70  YAVPMIIGEIRRY-LRDNNAVRVSRSLRD----IAYKALQVREKLINDNSAEP-TVSQIA 123

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + L+VS  EV+     +    SL   I +   +     D L  +  G EQ L E      
Sbjct: 124 QHLDVSREEVVFALDAIQEPVSLFEPIYNDGGDPILVMDQLSDERSGDEQWLEEIS---- 179

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               +  +M  LN RE+ I   R       T   ++ E  +S+ +V ++E  A K++++ 
Sbjct: 180 ----IKEAMKKLNDREKHIVSLRFFAGK--TQMEVAEEIGISQAQVSRLEKAALKQLRKY 233

Query: 284 I 284
           +
Sbjct: 234 V 234


>gi|331086150|ref|ZP_08335232.1| hypothetical protein HMPREF0987_01535 [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|330406309|gb|EGG85823.1| hypothetical protein HMPREF0987_01535 [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 259

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 59/261 (22%), Positives = 126/261 (48%), Gaps = 23/261 (8%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L  +E+  L  + +E GD +A  R +  +LRLV+ +   +      + ++   G +
Sbjct: 15  KLPLLSNEEKEALFVKIKE-GDEAARERYIKGNLRLVLSVIKRFASSNENVDDLFQIGCV 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT---ANQKRLFFNLRR 141
           GLM+A+  F+ +   + +TY++  I   ++ Y LR  + +++  +      K ++     
Sbjct: 74  GLMKAIDNFNTDLQVKFSTYAVPMIIGEIRRY-LRDNNSIRVSRSLRDTAYKAIYAKEGY 132

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           +K HL+  T        V  IA+++ +++ ++I     +    SLN  + +   ++    
Sbjct: 133 MKRHLKEPT--------VEEIAEEIGIAKEDIIFALDAIQAPMSLNEPVYNDSGDALYVM 184

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           D  + D   +E+  +E          L  +M  LN RER I + R   E    +E ++S+
Sbjct: 185 DQ-ISDKKNREEYWVEGLS-------LEAAMERLNERERFIIQLRFF-EGKTQME-VASQ 234

Query: 262 FEVSRERVRQIEARAFKKVQE 282
            ++S+ +V ++E  A K +++
Sbjct: 235 VKISQAQVSRLEKNALKTMRQ 255


>gi|197302592|ref|ZP_03167647.1| hypothetical protein RUMLAC_01321 [Ruminococcus lactaris ATCC
           29176]
 gi|197298490|gb|EDY33035.1| hypothetical protein RUMLAC_01321 [Ruminococcus lactaris ATCC
           29176]
          Length = 259

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 61/265 (23%), Positives = 124/265 (46%), Gaps = 31/265 (11%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L + E+  L +R  + GD  A    +  +LRLV+ +   +        ++   G +
Sbjct: 14  KLPLLREDEKEELFRRI-QKGDEKAREEYIKGNLRLVLSVIKRFDSSSESADDLFQIGCV 72

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+AV  FDPER  R +TY++  I   ++ Y LR  S +++  +  +   +  +   +G
Sbjct: 73  GLMKAVDNFDPERLVRFSTYAVPMIVGEIRRY-LRDNSSIRVSRSL-RDTAYKAIYAKEG 130

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
           +++      +K   V  IA ++ +++ +V+          +L+A+      +        
Sbjct: 131 YVR----RYMKEPTVQEIADEIGIAKEDVVF---------ALDAVQTPMSLHEP------ 171

Query: 205 VYDHDGQEQVLIEK-EERKNRRN------MLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           VY+  G    ++++  ++KNR         L  +M  LN RER I   R  +    T   
Sbjct: 172 VYNDGGDALYVMDQVSDKKNREENWVEELSLEAAMERLNERERYIISLRFFEGKTQT--E 229

Query: 258 LSSEFEVSRERVRQIEARAFKKVQE 282
           ++ +  +S+ +V ++E  A K +++
Sbjct: 230 VAGQIGISQAQVSRLEKNALKTMRQ 254


>gi|161898933|gb|ABX80456.1| SigB [Listeria monocytogenes]
          Length = 236

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 62/253 (24%), Positives = 119/253 (47%), Gaps = 27/253 (10%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y   G    E    GNIGL+ A++++D
Sbjct: 3   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKY-SQGKSFHEDSQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTREL 115

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +   
Sbjct: 116 QSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGT 172

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            DG E+V        N+R +L + + VL+ RE++I +   ++    + +      ++S+ 
Sbjct: 173 DDGFERV--------NQRMLLEKVLPVLDEREQKILQFTFIENR--SQKETGELLDISQM 222

Query: 268 RVRQIEARAFKKV 280
            V +I+ +A KK+
Sbjct: 223 HVSRIQRQAIKKL 235


>gi|261418447|ref|YP_003252129.1| sporulation sigma factor SigK [Geobacillus sp. Y412MC61]
 gi|319767593|ref|YP_004133094.1| RNA polymerase, sigma 28 subunit, SigK [Geobacillus sp. Y412MC52]
 gi|261374904|gb|ACX77647.1| RNA polymerase, sigma 28 subunit, SigK [Geobacillus sp. Y412MC61]
 gi|317112459|gb|ADU94951.1| RNA polymerase, sigma 28 subunit, SigK [Geobacillus sp. Y412MC52]
          Length = 245

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 29/84 (34%), Positives = 50/84 (59%), Gaps = 2/84 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  ++EE  LA   +  GD  A +RL+  +LRLV  I   +   G  + +++S G IGL
Sbjct: 38  PLSAQEEEKYLALMAK--GDEQARNRLIEHNLRLVAHIVKKFENTGEEVEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIK 110
           ++A++ + P +G +LATY+   I+
Sbjct: 96  IKAIESYSPGKGTKLATYAARCIE 119


>gi|154485093|ref|ZP_02027541.1| hypothetical protein EUBVEN_02816 [Eubacterium ventriosum ATCC
           27560]
 gi|149734046|gb|EDM50165.1| hypothetical protein EUBVEN_02816 [Eubacterium ventriosum ATCC
           27560]
          Length = 258

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 61/262 (23%), Positives = 125/262 (47%), Gaps = 19/262 (7%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L + E+  L K  ++ G+  A  + +  +LRLV+ I   +      + ++   G I
Sbjct: 15  KLPLLTEDEKKELFKEIKK-GNEVAREKYIRGNLRLVLSILQRFSNSNENVDDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++AV  FD     + +TY++  I   ++ Y LR  + +++  +   K + +     K 
Sbjct: 74  GLIKAVDNFDDTLNVKFSTYAVPMISGELKRY-LRDNAAIRVSRSI--KDIAYKAIYCKE 130

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
           ++   T    +   VV IAK++ V   +V+         +++ + ++  D    Q  D L
Sbjct: 131 NIIKTTH---REPTVVEIAKEIGVEPEDVVY------ALDAIQSPVSLYDPVYDQGGDTL 181

Query: 205 -VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
            V D    ++    KEE+     +L  ++  L+ RER+I + R    N  T   ++ E  
Sbjct: 182 YVMDQISDKK---NKEEKWVENIVLNEALKGLSERERKIIDMRFF--NGKTQMEIADEIG 236

Query: 264 VSRERVRQIEARAFKKVQESIQ 285
           +S+ +V ++E  A K +++ ++
Sbjct: 237 ISQAQVSRLEKNALKAMKKYME 258


>gi|150389982|ref|YP_001320031.1| FliA/WhiG family RNA polymerase sigma factor [Alkaliphilus
           metalliredigens QYMF]
 gi|149949844|gb|ABR48372.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           metalliredigens QYMF]
          Length = 258

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 56/255 (21%), Positives = 115/255 (45%), Gaps = 15/255 (5%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            EE +   +  + GDL A  +LV+ +L L+  +   +   G    ++   G+IGL++A++
Sbjct: 17  HEETMTLIQMAQKGDLQAQEKLVSHNLGLIRSVIKRFSNRGYDREDLFQLGSIGLIKAIR 76

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD     R +TY++  I   ++ + LR   ++K+  +  Q        R+K   + +  
Sbjct: 77  KFDISFNVRFSTYAVPMIIGEIKRF-LRDDGIIKVSRSLKQ-----TASRVKVTKEKLFK 130

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +   +  IAK L +++ E++         E L  +I+  D +     D +       
Sbjct: 131 EFGREPTLHEIAKVLEITKEEIVMALDSNMYPEYLYEVIHQDDGSPIHLIDKISETDSLD 190

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           +  +I+K        ML   +  L PRER+I   R  ++   T   ++    +S+ +V +
Sbjct: 191 DSEVIDK-------IMLKEVIGRLEPRERQIIILRYFKDKTQT--EIAKVLGISQVQVSR 241

Query: 272 IEARAFKKVQESIQK 286
           IE +  + +++ + K
Sbjct: 242 IEKKVLQTMKDMMSK 256


>gi|315648111|ref|ZP_07901212.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Paenibacillus vortex
           V453]
 gi|315276757|gb|EFU40100.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Paenibacillus vortex
           V453]
          Length = 262

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 61/270 (22%), Positives = 123/270 (45%), Gaps = 50/270 (18%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQAVKKFDPE 96
           ++E GD  A  +L+  HL +V  ++      GLP +    ++ S G +GL+ A++KFD +
Sbjct: 18  WKEDGDHEAKKKLIEYHLHIVDYVS-SRLAIGLPKNVSKGDLASNGVMGLIDAIEKFDYK 76

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL-KGHLQAITDNNLK 155
           RG +  TY+ W ++ A+ +  LR    V        KR+    ++L + +L++++D+ + 
Sbjct: 77  RGLQFETYASWRVRGAILDS-LRQGDWVPRSVREKAKRIETAYQQLEQKYLRSVSDSEM- 134

Query: 156 PEQVVAIAKKLNVSESE------------VISMNCRLAGDES---LNALINSSDKNSSQW 200
                  +  L+V+E E            + S+   +  +ES   ++ L++   KN    
Sbjct: 135 -------SDYLDVTEKEFRHMLQEVAVMTLTSLEDPIREEESETRMSLLVDEKAKNP--- 184

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
                 DH   E  L         R  L + +  L P+ER +     L    ++L  ++ 
Sbjct: 185 ------DHKVHEFYL---------REALMKGIGKLTPKERTVVSL--LYYEDLSLSEIAE 227

Query: 261 EFEVSRERVRQIEARAFKKVQESIQKQVEL 290
              +S  R+ Q+ ++A  +++ ++ K  +L
Sbjct: 228 VMSLSPSRISQLHSKAILRLRGALDKDRDL 257


>gi|254519270|ref|ZP_05131326.1| sporulation sigma factor SigK [Clostridium sp. 7_2_43FAA]
 gi|226913019|gb|EEH98220.1| sporulation sigma factor SigK [Clostridium sp. 7_2_43FAA]
          Length = 231

 Score = 55.5 bits (132), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 31/84 (36%), Positives = 48/84 (57%), Gaps = 2/84 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ E++EE  L  +  ++GD  A   L+  +LRLV  I   Y      I E++S G +GL
Sbjct: 30  PLDEEEEEQYL--KLLKNGDKEAKSILIERNLRLVAHIVKKYNFPNKDIDELISIGTVGL 87

Query: 87  MQAVKKFDPERGFRLATYSMWWIK 110
           ++A+  FD  +G RLATY+   I+
Sbjct: 88  IKAIDSFDASKGTRLATYASRCIE 111


>gi|18310750|ref|NP_562684.1| sporulation sigma factor SigK [Clostridium perfringens str. 13]
 gi|168214245|ref|ZP_02639870.1| RNA polymerase sigma-70 factor family [Clostridium perfringens CPE
           str. F4969]
 gi|169343581|ref|ZP_02864580.1| RNA polymerase sigma-70 factor family [Clostridium perfringens C
           str. JGS1495]
 gi|170764185|ref|ZP_02633869.2| RNA polymerase sigma-70 factor family [Clostridium perfringens E
           str. JGS1987]
 gi|182420555|ref|ZP_02643878.2| RNA polymerase sigma-70 factor family [Clostridium perfringens NCTC
           8239]
 gi|182625679|ref|ZP_02953448.1| RNA polymerase sigma-70 factor family [Clostridium perfringens D
           str. JGS1721]
 gi|18145431|dbj|BAB81474.1| probable transcription initiation factor sigma K [Clostridium
           perfringens str. 13]
 gi|169298141|gb|EDS80231.1| RNA polymerase sigma-70 factor family [Clostridium perfringens C
           str. JGS1495]
 gi|170660828|gb|EDT13511.1| RNA polymerase sigma-70 factor family [Clostridium perfringens E
           str. JGS1987]
 gi|170714308|gb|EDT26490.1| RNA polymerase sigma-70 factor family [Clostridium perfringens CPE
           str. F4969]
 gi|177909081|gb|EDT71556.1| RNA polymerase sigma-70 factor family [Clostridium perfringens D
           str. JGS1721]
 gi|182379749|gb|EDT77228.1| RNA polymerase sigma-70 factor family [Clostridium perfringens NCTC
           8239]
          Length = 233

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 72/285 (25%), Positives = 118/285 (41%), Gaps = 70/285 (24%)

Query: 9   IVNGEIGLSRYIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           +V  +I L+ Y+      P  L ++EE +  +R ++ GD+ A   LV  +LRLV  I   
Sbjct: 10  LVGSKIFLTGYVTGNSTFPKPLNEKEEKIYLERLKD-GDVEAKRVLVERNLRLVAHIVKK 68

Query: 68  YRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           Y         + +++S G IGL++A+  FD  +G RLATY+   I               
Sbjct: 69  YSSNYQNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATYAAKCID-------------- 114

Query: 125 KIGTTANQKRLFF-NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
                 N+  +FF N ++ KG               V +   + V +           G+
Sbjct: 115 ------NEILMFFRNTKKTKGE--------------VFLQDPIGVDKE----------GN 144

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS-VLNPRERRI 242
           E     I SSD +S                 ++E  E   +   L + MS VL+PRE+ I
Sbjct: 145 EICLIDILSSDSDS-----------------VLEAVENSLQVKELYKKMSDVLSPREKEI 187

Query: 243 FEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            + R   L  +  T   ++    +SR  V +IE +A KK+ +  +
Sbjct: 188 IQMRYGLLDGDIKTQREIAGILGISRSYVSRIEKKALKKLNKEFK 232


>gi|295102494|emb|CBL00039.1| RNA polymerase, sigma subunit, RpsG/SigG [Faecalibacterium
           prausnitzii L2-6]
          Length = 255

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 67/264 (25%), Positives = 121/264 (45%), Gaps = 30/264 (11%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           ++P+L +QE+  L  R R  GD  A   ++  +LRLV+ +   +   G  + ++   G I
Sbjct: 14  ELPILSEQEKRDLLTRAR-AGDKKARQSMIEGNLRLVLSVVQRFSQRGENMDDLFQVGCI 72

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI-----LR-SWSLVKIGTTANQKRLFFN 138
           GL++A+  FDP +  R +TY +  I   ++ ++     LR S SL      A Q R    
Sbjct: 73  GLIKAIDNFDPAQQVRFSTYGVPMIIGEIRRFLRDNNALRVSRSLRDTAYRAMQSR---- 128

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
              L+  L        +   V  IA+K  +S  EV +    +    SL   + +   ++ 
Sbjct: 129 -EELEKQLG-------REPTVDEIAQKTGLSRREVSAALESVVEPLSLEEPVYADGGDAV 180

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
              D  V D DG++  +   + R+        +++ L PRE+RI E R L+    T   +
Sbjct: 181 YVIDQ-VRDPDGEDSWISGLQFRQ--------TVAGLTPREKRIMELRYLKGK--TQMEV 229

Query: 259 SSEFEVSRERVRQIEARAFKKVQE 282
           + E  +S+ +V ++E  A ++  +
Sbjct: 230 AREIGISQAQVSRLEKAALEQFHQ 253


>gi|294673099|ref|YP_003573715.1| RNA polymerase sigma-70 factor family protein [Prevotella
           ruminicola 23]
 gi|294472548|gb|ADE81937.1| RNA polymerase sigma-70 factor family protein [Prevotella
           ruminicola 23]
          Length = 240

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 32/108 (29%), Positives = 59/108 (54%), Gaps = 2/108 (1%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           G + Y+ +I     L  +EE  L +R    GD +A ++L+ ++LR V+  A+      +P
Sbjct: 11  GFNVYLEQIENNQPLTMEEEQELGRRIMA-GDTTARNKLIEANLRFVLTCAIDMATPFVP 69

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           I E+++ GN GL  A  +++P       +Y++  I+ A+ E I R+W+
Sbjct: 70  IEELIAAGNYGLTIAAARYNPSFDNHFCSYAVHHIRRAISEAI-RTWT 116


>gi|313901033|ref|ZP_07834521.1| RNA polymerase sigma-K factor [Clostridium sp. HGF2]
 gi|312953991|gb|EFR35671.1| RNA polymerase sigma-K factor [Clostridium sp. HGF2]
          Length = 242

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 65/246 (26%), Positives = 99/246 (40%), Gaps = 65/246 (26%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           D  A ++L+  +LRLV  I   Y        +++S G IGL++AV  F PE+G +L TY+
Sbjct: 44  DEEARNKLIEHNLRLVAHIVKKYDIKKEQTEDLISIGTIGLIKAVDSFKPEKGHKLTTYA 103

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
              I+  +  Y                      LR  K + Q                  
Sbjct: 104 SKCIENEILMY----------------------LRSSKNYFQ------------------ 123

Query: 166 LNVSESEVISMNCRLAGDESLNALIN--SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
            NVS +E I+ +     D S   LI+  SS ++SS   D +V D+  +            
Sbjct: 124 -NVSLNEPIATD----KDGSEITLIDAISSPEDSSIIDDMIVEDNIAR------------ 166

Query: 224 RRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
               L R + VL+ RE  I   R     +   T   ++ +  +SR  V +IE RAF K+ 
Sbjct: 167 ----LKRYIHVLDARELEIITKRFGLYGQEEETQREIARQLHISRSYVSRIEKRAFMKIY 222

Query: 282 ESIQKQ 287
              QK+
Sbjct: 223 REFQKE 228


>gi|255085668|ref|XP_002505265.1| predicted protein [Micromonas sp. RCC299]
 gi|226520534|gb|ACO66523.1| predicted protein [Micromonas sp. RCC299]
          Length = 477

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 44/71 (61%), Gaps = 5/71 (7%)

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L +S+++ EG  GL  A  KFDP+RG+R +TY+ +WIK A+ + +  S   +++    N+
Sbjct: 116 LSVSDLMQEGCAGLATAADKFDPQRGYRFSTYAFFWIKKAVIDCVGNSGRTIRLPIHVNE 175

Query: 133 KRLFFNLRRLK 143
                N++++K
Sbjct: 176 -----NIQKMK 181


>gi|313901043|ref|ZP_07834531.1| RNA polymerase sigma-G factor [Clostridium sp. HGF2]
 gi|312954001|gb|EFR35681.1| RNA polymerase sigma-G factor [Clostridium sp. HGF2]
          Length = 259

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 57/242 (23%), Positives = 113/242 (46%), Gaps = 30/242 (12%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD SA   L+  +L+LV+ I   +      + ++   G IGL++++  FD +   R +
Sbjct: 32  QQGDESAKETLINGNLKLVLSIVQRFSNRCENMDDLFQVGCIGLVKSIDNFDLKHEVRFS 91

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I   ++ Y LR   ++++  + + K L +   +LK   +     + K   V  +
Sbjct: 92  TYAVPMIMGEIKRY-LRDNQVIRV--SRHLKDLAYRAFKLK---EEYVHKHQKEPSVSWL 145

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK---- 218
           A++L V E +++     L   +S+ ++               VY+ DG E  L+++    
Sbjct: 146 AQQLEVKEKDIVDA---LDSTQSVLSIFEP------------VYNSDGDELFLLDQIKDD 190

Query: 219 ---EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
               ER N    L RS++ L  +E  I + R  Q+  +T   ++ E  +S+ +V ++E  
Sbjct: 191 KDEIERLNNLMALKRSLTRLKGKELDIIQKRYYQD--MTQTEIAGELGISQAQVSRLEKN 248

Query: 276 AF 277
           A 
Sbjct: 249 AI 250


>gi|260892756|ref|YP_003238853.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Ammonifex
           degensii KC4]
 gi|260864897|gb|ACX52003.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Ammonifex
           degensii KC4]
          Length = 245

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 61/245 (24%), Positives = 109/245 (44%), Gaps = 22/245 (8%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A   LV ++L LV K+   + G G    ++   G IGL++A+ +FDP+RG   +
Sbjct: 20  QEGDPQARELLVRANLGLVGKVVRRFAGQGREGEDLFQIGCIGLLKAIDRFDPQRGTCFS 79

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQ--KRLFFNLRRLKGHLQAITDNNLKPEQVV 160
           TY++  I   ++ + LR   ++K+  +  +  +R+      LK  L        +   V 
Sbjct: 80  TYAVATILGEIRRF-LRDDGMLKVSRSLKETSRRVIRTRASLKMALG-------REPSVA 131

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            IA+ L ++  EV+           L   +    + +  W+D L            EKEE
Sbjct: 132 EIAESLGIAVEEVVMALEAGKAPAFLQEPLAGEGEEALCWEDCLSS----------EKEE 181

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                  L  S+  L  RER I   R       T E ++ +  +S+ +V ++E  A +K+
Sbjct: 182 SWLETLSLRESLRRLPAREREIIWWRFF--AGYTQEEVAKQLGISQAQVSRLERNALQKL 239

Query: 281 QESIQ 285
           +E ++
Sbjct: 240 REELE 244


>gi|225574950|ref|ZP_03783560.1| hypothetical protein RUMHYD_03029 [Blautia hydrogenotrophica DSM
           10507]
 gi|225037797|gb|EEG48043.1| hypothetical protein RUMHYD_03029 [Blautia hydrogenotrophica DSM
           10507]
          Length = 225

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 32/94 (34%), Positives = 55/94 (58%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  +QEE V+ K   E  +  A   L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 21  PLDAQQEEKVIQKLGTEQ-EKEAKALLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGL 79

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++A+  F+P +  +LATY+   I+  +  Y+ R+
Sbjct: 80  IKAINTFNPVKKIKLATYASRCIENEILMYLRRN 113


>gi|328958265|ref|YP_004375651.1| RNA polymerase sigma factor SigD [Carnobacterium sp. 17-4]
 gi|328674589|gb|AEB30635.1| RNA polymerase sigma factor SigD [Carnobacterium sp. 17-4]
          Length = 238

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 53/211 (25%), Positives = 108/211 (51%), Gaps = 17/211 (8%)

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           G IGLM A++KFD  +      Y+   IK ++ + I ++  + +  T   +   ++   R
Sbjct: 41  GVIGLMDALEKFDKSKKVPFEGYAYIRIKGSIIDEIRKTAPVSR--TRMGKLNEYY---R 95

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL--AGDESLNALINSSDKNSSQ 199
            K  L+A     ++      I ++L + E  +  ++  +      SL  ++ S D NS +
Sbjct: 96  AKEKLEATL---MRTPTEKEICEELKIDEKALTKIHETVHNLASISLEKVMFSDDGNSIE 152

Query: 200 WQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
             D+L   H+ G E  L++KE    R+ +LT+++S L+ RE+ I     ++E  ++L+ +
Sbjct: 153 LIDFLEDKHETGSEDTLLDKE----RQQLLTKNVSKLDKREQTILNLYYVEE--LSLKEI 206

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           +  F++S  RV QI  +   K++E ++++ +
Sbjct: 207 AYIFDISVPRVSQIHGKMILKLKELMRREYD 237


>gi|89895050|ref|YP_518537.1| hypothetical protein DSY2304 [Desulfitobacterium hafniense Y51]
 gi|89334498|dbj|BAE84093.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 260

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 57/267 (21%), Positives = 125/267 (46%), Gaps = 27/267 (10%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           + P+L  +E   L  R  ++GD  A  RL+  +L+L+  +   +   G  + ++   G I
Sbjct: 12  RFPLLSDEEMMDLLHR-AQNGDAEARERLINCNLKLIFNLVQRFSHRGYELEDLFQIGTI 70

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+ KFD   G + +TY++  I   ++ + LR    VK+  +   K L + + + + 
Sbjct: 71  GLIKAIDKFDFTYGVKFSTYAVPMIIGEIRRF-LRDDHPVKVPRS--YKELVYKVNKARE 127

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L A    +     +  IA+ + V   +++S         +L A+ + +  + + +QD  
Sbjct: 128 SLSATLGRD---PTIGEIAESIGVDREDIVS---------ALEAVQSPTSIHDTLYQD-- 173

Query: 205 VYDHDG---QEQVLIEKEERKN--RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
             D D     +Q+ +EK+       +  L   +  L  RE+R+   R  ++   T   ++
Sbjct: 174 --DSDPIYILDQLPMEKDLEAGWFEKIALKEVLDKLPEREKRVLMMRFYEDK--TQSEIA 229

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQK 286
           +   +S+ ++ +IE  A  ++++ + +
Sbjct: 230 ALLNLSQVQISRIERAALHRIRQYLHE 256


>gi|317970154|ref|ZP_07971544.1| RNA polymerase sigma factor SigF [Synechococcus sp. CB0205]
          Length = 253

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 66/248 (26%), Positives = 116/248 (46%), Gaps = 31/248 (12%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHR--LVTSHLRLVVKIAM-GYRGYGLPISEVVSEGNIG 85
           ++ Q++++L++  +   D + AHR  +V ++L LV K+A       G    ++  EG  G
Sbjct: 3   VQDQQQWLLSRYLK---DPNHAHRNAVVAANLPLVWKVARRESERSGHSFEDLAQEGVRG 59

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYI---LRSWSLVKIGTTANQKRLFFNLRRL 142
           L++AV++FDP  G+ L+T ++ WI+ AM+ Y+    R +S  +      Q+      RR 
Sbjct: 60  LIKAVERFDPSLGYTLSTAAVPWIRGAMRHYLRDRCRVFSGARNVIELLQRGAALQRRRE 119

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVS-----ESEVISMNCRLAGDESLNALINSSDKNS 197
           +  L  + D++L        A+ L  S     E++ +    R+A   SL+     SD  +
Sbjct: 120 QQGLSPMNDSSL--------ARALGCSQQRWQEAQALQTCLRVA---SLDQPGGGSDPET 168

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
              +        GQ   L    ER   R  L R +  L   +RR+  AR LQ+   T ++
Sbjct: 169 PLVEQLSDQQAPGQYGWL----ERCELRRQLWRGLKTLQASQRRLVLARVLQQR--TWQD 222

Query: 258 LSSEFEVS 265
           L +   +S
Sbjct: 223 LGAMAGIS 230


>gi|218133795|ref|ZP_03462599.1| hypothetical protein BACPEC_01684 [Bacteroides pectinophilus ATCC
           43243]
 gi|217991170|gb|EEC57176.1| hypothetical protein BACPEC_01684 [Bacteroides pectinophilus ATCC
           43243]
          Length = 256

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 41/152 (26%), Positives = 75/152 (49%), Gaps = 6/152 (3%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A +RLVT ++ L+  I   + G G  + ++   G+IGL++A+ KFD     R +TY
Sbjct: 18  GDKEARNRLVTENMGLIWSIVKRFTGRGHELEDLFQIGSIGLIKAIDKFDTSYDVRFSTY 77

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           ++  I   ++ + LR   ++K+  +   K +   ++R +  LQ         E    IA+
Sbjct: 78  AVPMITGEVKRF-LRDDGMIKVSRSL--KEIVVKVQRAREQLQKEMGEEPSME---MIAR 131

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKN 196
            ++V E +++      +  ES+   I  SD N
Sbjct: 132 AIDVPEEDIVMALEAGSEIESIYKTIYQSDGN 163


>gi|210610056|ref|ZP_03288235.1| hypothetical protein CLONEX_00421 [Clostridium nexile DSM 1787]
 gi|210152667|gb|EEA83673.1| hypothetical protein CLONEX_00421 [Clostridium nexile DSM 1787]
          Length = 208

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 32/85 (37%), Positives = 49/85 (57%), Gaps = 2/85 (2%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           IP+   +E+Y + K Y E GDL A H L+  +LRLV  +   Y+       +++S G IG
Sbjct: 9   IPLTAAEEQYYIQK-YIE-GDLEAKHILIERNLRLVAHVIKKYQYLDDDPEDLISIGTIG 66

Query: 86  LMQAVKKFDPERGFRLATYSMWWIK 110
           L++AV  F+P +  RL TY+   I+
Sbjct: 67  LIKAVATFNPSKNNRLGTYAARCIE 91


>gi|302535451|ref|ZP_07287793.1| RNA polymerase sigma-E factor [Streptomyces sp. C]
 gi|302444346|gb|EFL16162.1| RNA polymerase sigma-E factor [Streptomyces sp. C]
          Length = 288

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 26/74 (35%), Positives = 42/74 (56%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  +L LV   A  +RG   P+ ++V  G IGL++A+ +FDPERG    T++M  I   
Sbjct: 65  LVELNLSLVKYAARRFRGRSEPMEDIVQVGTIGLIKAINRFDPERGVEFTTFAMPTISGE 124

Query: 113 MQEYILRSWSLVKI 126
           ++ +   +   VK+
Sbjct: 125 IKRFFRDTSWAVKV 138


>gi|167751709|ref|ZP_02423836.1| hypothetical protein EUBSIR_02718 [Eubacterium siraeum DSM 15702]
 gi|167655517|gb|EDR99646.1| hypothetical protein EUBSIR_02718 [Eubacterium siraeum DSM 15702]
 gi|291558002|emb|CBL35119.1| RNA polymerase, sigma subunit, RpsG/SigG [Eubacterium siraeum
           V10Sc8a]
          Length = 261

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 38/150 (25%), Positives = 79/150 (52%), Gaps = 7/150 (4%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+ +L++ E+  L ++ R  GD +A  +L+  +LRLV+ +   + G G    ++   G I
Sbjct: 20  KLKVLKESEKTELLRQMR-SGDPTAREKLINGNLRLVLSVIQRFSGRGENPDDLFQVGCI 78

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A+  F  +   R +TY++  I   ++ Y+  S S   I  + + + L +   + + 
Sbjct: 79  GLMKAIDNFSTDFNVRFSTYAVPMIMGELRRYLRDSGS---IRVSRSMRDLAYKAMQAR- 134

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVI 174
             + +T++N K   +  IAK+++    +V+
Sbjct: 135 --EKLTNDNSKEPTIEQIAKEIDAKREDVV 162


>gi|331269204|ref|YP_004395696.1| FliA/WhiG family RNA polymerase sigma 28 subunit [Clostridium
           botulinum BKT015925]
 gi|329125754|gb|AEB75699.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           botulinum BKT015925]
          Length = 252

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 55/242 (22%), Positives = 112/242 (46%), Gaps = 20/242 (8%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A  +LV  +L LV  I+  +   G    ++   G++GL++A+  FD     + +TY
Sbjct: 27  GDKKAVDQLVQKNLPLVSAISKKFLNRGYEYEDIFQIGSMGLIKAINNFDSSYNVQFSTY 86

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTA--NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           ++  I   ++ +I R   L+K+  +     K+L ++  +L   L      N +P  +  +
Sbjct: 87  AVPMIMGEIKRFI-RDDGLIKVSRSVKYTAKKLHYDKEKLTKQL------NREP-SIEEL 138

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           +K   +S+ E+I  +  +   + L   I+  D +     D +V D  G+   L       
Sbjct: 139 SKFSGISKEEIIFSSEAINEPKYLYDTIHQDDGSPIYLIDKVVVDDKGEIDEL------- 191

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             +  L  ++S L+ R R+I   R  ++  +T   ++    +S+ +V +IE +  K ++E
Sbjct: 192 -DKIALKEALSKLDQRSRQIIILRYFKD--ITQVKVAKMLGISQVQVSRIEKKVLKSMKE 248

Query: 283 SI 284
            +
Sbjct: 249 KL 250


>gi|167750689|ref|ZP_02422816.1| hypothetical protein EUBSIR_01667 [Eubacterium siraeum DSM 15702]
 gi|167656368|gb|EDS00498.1| hypothetical protein EUBSIR_01667 [Eubacterium siraeum DSM 15702]
 gi|291558233|emb|CBL35350.1| RNA polymerase sigma factor, sigma-70 family [Eubacterium siraeum
           V10Sc8a]
          Length = 221

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 66/240 (27%), Positives = 110/240 (45%), Gaps = 33/240 (13%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            +T H  LV  IA  +R  G+   E+ S G +GL++A   FD  RG + +TY++  I   
Sbjct: 9   FITEHFALVHSIAGRFRNRGIEYDELFSAGCVGLVKAGNNFDESRGLKFSTYAVPVIMGE 68

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +++ + R    VK+  + + K L   + RL+  L     N  +P  +  +A+KL ++  E
Sbjct: 69  IKQ-LFRDGGTVKV--SRSLKELSLKICRLRDEL---IKNGEEP-HISVLAEKLGITPEE 121

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
                  LA   SL  +  SS      + D    + +G   + +E E+ K    M  R +
Sbjct: 122 A-----SLALGASLPPVSLSS------YDDE--ENDEGSFDLPVEPEQPKALDRMALRQL 168

Query: 233 -SVLNPRERRIFEARRLQE--NPVTLENLS-SEFEVSRERVRQIEARAFKKVQESIQKQV 288
            S L P +RR+   R  +E     T E L  ++ +VSR           KK+ E ++KQ+
Sbjct: 169 VSRLEPLDRRLIILRYSEECTQSRTAEILGMTQVQVSRRE---------KKILEGLRKQL 219


>gi|331083018|ref|ZP_08332137.1| RNA polymerase sigma-35 factor [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|330399755|gb|EGG79416.1| RNA polymerase sigma-35 factor [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 241

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 39/129 (30%), Positives = 60/129 (46%), Gaps = 14/129 (10%)

Query: 6   MSIIVNGEIGLS-------------RYIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAH 51
           M I V G +  S              YI     +P  L  QEE  +       G   A  
Sbjct: 1   MDICVGGNVKFSGFKGVFLPKKNELHYIGGAEVLPAPLTAQEEGEMLDALAGEGKEEARA 60

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+  +LRLVV IA  +   G+ + +++S G IGL++A+  FDP +  +LATY+   I+ 
Sbjct: 61  CLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFDPVKKIKLATYASRCIEN 120

Query: 112 AMQEYILRS 120
            +  Y+ R+
Sbjct: 121 EILMYLRRN 129


>gi|323487067|ref|ZP_08092375.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323694575|ref|ZP_08108741.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
 gi|323399568|gb|EGA91958.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323501343|gb|EGB17239.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
          Length = 237

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 47/174 (27%), Positives = 83/174 (47%), Gaps = 12/174 (6%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD +A  RLV  ++ LV  I   + G G    ++   G+IGL++A+ KFD     R +TY
Sbjct: 14  GDKAARERLVMDNVGLVWSIVRRFTGRGCETEDLFQIGSIGLIKAIDKFDTSYDVRFSTY 73

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           ++  I   ++ + LR   ++K+  +   K L F +  ++  L          E+   I++
Sbjct: 74  AVPMITGEIKRF-LRDDGMIKVSRSI--KELGFKVSAVRESLSGSLGREPTLEE---ISE 127

Query: 165 KLNVSESEV---ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
            L VS+ EV   +   C++   ESL A   S + N+    D +  + +  E +L
Sbjct: 128 ALEVSKEEVAASLEAGCQV---ESLYAPSGSGEDNTLSLIDKVAEEKEENEMLL 178


>gi|161898897|gb|ABX80438.1| SigB [Listeria monocytogenes]
          Length = 235

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 61/253 (24%), Positives = 119/253 (47%), Gaps = 26/253 (10%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 1   YIWIAAYQEDGDEDAQYNLVIHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 60

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 61  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTREL 114

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +   
Sbjct: 115 QSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGT 171

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            DG E+V        N+R +L + + VL+ RE++I +   ++    + +      ++S+ 
Sbjct: 172 DDGFERV--------NQRMLLEKVLPVLDEREQKILQYTFIENR--SQKETGELLDISQM 221

Query: 268 RVRQIEARAFKKV 280
            V +I+ +A KK+
Sbjct: 222 HVSRIQRQAIKKL 234


>gi|330959578|gb|EGH59838.1| putative RNA polymerase sigma factor [Pseudomonas syringae pv.
           maculicola str. ES4326]
          Length = 532

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 55/207 (26%), Positives = 96/207 (46%), Gaps = 17/207 (8%)

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
           S  N+GL +AV +F PE GFR +T ++ WI  ++   +    S+         +R+  N+
Sbjct: 327 SAANMGLTRAVYRFAPEMGFRFSTIALTWINVSISRDLADQESIRLPEGMHKHRRMIANM 386

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNSS 198
            R         D+     + +A A KL   E +V+      AG + S++     +D + +
Sbjct: 387 LR---------DHPNVSIKTLAEATKL---EQDVVRDLVHFAGGQRSIDTAFQGTDSSEA 434

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLE 256
                L+ D +     + E E+   R+ + +    VL  RE  +   R    +    TL 
Sbjct: 435 DGLHELLADTN--NDFISEIEDDSMRQFVESALGDVLTQREIFVLVNRFGMGDAREKTLA 492

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQES 283
            LS E ++S+ERVRQ+E +A  K+++S
Sbjct: 493 ELSIEMKLSKERVRQLEIQALGKIRDS 519


>gi|312622111|ref|YP_004023724.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
 gi|312202578|gb|ADQ45905.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
          Length = 240

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 56/241 (23%), Positives = 109/241 (45%), Gaps = 20/241 (8%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           ++GD  A  +L+ S+L LV  +   +   G+ + ++   G+IGL++AV +FDP    R +
Sbjct: 14  KNGDKLARQQLIESNLALVWSVVKKFAAKGVELEDLFQIGSIGLIKAVDRFDPSFNVRFS 73

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I   ++ Y LR    +K+      +++  N  ++K        N+ +   +  I
Sbjct: 74  TYAVPMIIGEIKRY-LRDDGKIKVS-----RKIKENQGKIKKLRNQFVSNHGREPTISEI 127

Query: 163 AKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
           ++   +S  E++   C  A  E  SL+ +IN  +       D    + D   ++L     
Sbjct: 128 SQLTGLSNDEILL--CLDASSEVASLSEVINQEEGKPITLMDIASDEEDYSTKLL----- 180

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                  L   +  L  RER I   R  +    T   ++ +  +S+  V +IE RA +++
Sbjct: 181 ---DLMALKEGLKKLKGRERYIIFMRYFKNK--TQSEIAKQLNISQVHVSRIEKRALERI 235

Query: 281 Q 281
           +
Sbjct: 236 K 236


>gi|20807766|ref|NP_622937.1| DNA-directed RNA polymerase specialized sigma subunit
           [Thermoanaerobacter tengcongensis MB4]
 gi|20516321|gb|AAM24541.1| DNA-directed RNA polymerase specialized sigma subunit
           [Thermoanaerobacter tengcongensis MB4]
          Length = 240

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 58/259 (22%), Positives = 126/259 (48%), Gaps = 24/259 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K+EE +   +  ++ D ++  +L+  +  L+  I   +   G  + ++   G IG ++AV
Sbjct: 2   KEEENLELIKLAKNNDKASLEKLILENSGLIWSIVKKFANRGYELEDLYQIGCIGFVKAV 61

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +KFD     + +TY++  I   ++ + LR   L+K+  +  +      L     +++ + 
Sbjct: 62  QKFDESYNVKFSTYAVPIIMGEIKRF-LRDDGLIKVSRSLKE------LSSKAFYMKEVL 114

Query: 151 DNNLKPEQVV-AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
            N L  E  +  IA++LNV+  E+       A  ESL       D  S + +D  + +  
Sbjct: 115 SNELNREPTINEIAERLNVTPEEIAMAFESAATAESL------YDSISHEEEDRQLIEMV 168

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSV--LNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           G ++  ++ EE+      LT  M +  L PRE+++   R  ++  +T   +++   +S+ 
Sbjct: 169 GDKEDSVDLEEK------LTLHMIIDKLKPREKQVIFLRYFKD--MTQTEVANILGISQV 220

Query: 268 RVRQIEARAFKKVQESIQK 286
           +V +IE +  +K+++ ++K
Sbjct: 221 QVSRIEKKVLEKIRKELEK 239


>gi|317499143|ref|ZP_07957420.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium 5_1_63FAA]
 gi|316893556|gb|EFV15761.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 231

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 51/199 (25%), Positives = 82/199 (41%), Gaps = 60/199 (30%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   L+  +LRLVV IA  +   G+ + +++S G IGL++A+  F+P +  +LATY+  
Sbjct: 45  TARSMLIERNLRLVVYIAKKFDNTGIGVEDLISIGTIGLIKAINTFNPAKKIKLATYASR 104

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+  +  Y                      LRR           N K +  V+I + LN
Sbjct: 105 CIENEILMY----------------------LRR-----------NNKTKMEVSIDEPLN 131

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           V                         D N     D L  D D    ++ +  E +  + +
Sbjct: 132 V-----------------------DWDGNELLLSDILGTDED----IIYKDLEHEVDKKL 164

Query: 228 LTRSMSVLNPRERRIFEAR 246
           LTR+M++L  RE+ I E R
Sbjct: 165 LTRAMTILTDREKMIIELR 183


>gi|121488787|emb|CAJ18278.1| sigma 70-type sigma factor [Prosthecochloris aestuarii]
          Length = 165

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 53/178 (29%), Positives = 88/178 (49%), Gaps = 33/178 (18%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA------AMQEYILRSWSLVKIGTTA 130
           ++  EGN+GL++A K+FD  RGF+  +Y++WWI+       A Q  I+R   L ++GT  
Sbjct: 1   DLXXEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSXLQALAEQSRIVR-LPLNRVGTLN 59

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNAL 189
              + +  L +     +   D N K      +A  L++ +S+ ++   ++AG   S++A 
Sbjct: 60  KISKAYSQLEQ-----EYERDPNTK-----ELANVLDM-DSQDVADTLKIAGRHVSVDAP 108

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT----RSMSVLNPRERRIF 243
               D N  +  D  V  HDGQ      K +    ++ LT    RS+SVL PRE  + 
Sbjct: 109 FAQGDDN--RLLD--VLQHDGQ------KPDYSLTKDSLTLEVERSLSVLAPREADVI 156


>gi|260589068|ref|ZP_05854981.1| RNA polymerase sigma-E factor [Blautia hansenii DSM 20583]
 gi|331082498|ref|ZP_08331623.1| hypothetical protein HMPREF0992_00547 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|260540488|gb|EEX21057.1| RNA polymerase sigma-E factor [Blautia hansenii DSM 20583]
 gi|330400476|gb|EGG80106.1| hypothetical protein HMPREF0992_00547 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 208

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 29/83 (34%), Positives = 51/83 (61%), Gaps = 2/83 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  ++E Y L + Y++ G+L A + L+  +LRLV  I   Y+G    + +++S G IGL
Sbjct: 7   PLTSEEESYYL-QEYKQ-GNLEAKNILIERNLRLVAHIVKKYQGAPEEMDDLISIGTIGL 64

Query: 87  MQAVKKFDPERGFRLATYSMWWI 109
           ++A+  FD ++  RL+TY+   I
Sbjct: 65  IKAIHTFDAQKASRLSTYAARCI 87


>gi|254478776|ref|ZP_05092144.1| RNA polymerase sigma-G factor [Carboxydibrachium pacificum DSM
           12653]
 gi|214035288|gb|EEB75994.1| RNA polymerase sigma-G factor [Carboxydibrachium pacificum DSM
           12653]
          Length = 258

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 62/262 (23%), Positives = 125/262 (47%), Gaps = 21/262 (8%)

Query: 25  KIPMLE--KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           K+P+L+  KQ E ++  +   +GD  A    + S+LRLV+ +   +   G  + ++   G
Sbjct: 16  KLPVLKPSKQRELLITMK---NGDKKAREEFINSNLRLVLSVIQRFNNRGESVDDLFQVG 72

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            IGL++A+  FD ++  + +TY++  I   ++ Y LR  + +++  +          + L
Sbjct: 73  CIGLIKAIDNFDLDQNVKFSTYAVPMIIGEIRRY-LRDNTPIRVSRSLRD----IAYKAL 127

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
           +   + +++N+ +P  V  IAK+L++   EV+     +    SL   I     ++    D
Sbjct: 128 QVRDKLVSENSKEP-TVGEIAKELDLPSEEVVMALDAIQEPVSLFEPIYHDGGDAIYVMD 186

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
             V D    ++V +EK         L  ++  LN RE+ I    R  E    +E ++ E 
Sbjct: 187 Q-VSDDKNVDEVWLEK-------IALKEALEKLNEREKMIL-TMRFFEGKTQME-VAKEI 236

Query: 263 EVSRERVRQIEARAFKKVQESI 284
            +S+ +V ++E  A   +++ I
Sbjct: 237 GISQAQVSRLEKAALNHMRKYI 258


>gi|161898931|gb|ABX80455.1| SigB [Listeria monocytogenes]
 gi|161898937|gb|ABX80458.1| SigB [Listeria monocytogenes]
          Length = 237

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 61/253 (24%), Positives = 119/253 (47%), Gaps = 26/253 (10%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 3   YIWIAAYQEDGDEDAQYNLVIHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 62

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 63  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTREL 116

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +   
Sbjct: 117 QSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGT 173

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            DG E+V        N+R +L + + VL+ RE++I +   ++    + +      ++S+ 
Sbjct: 174 DDGFERV--------NQRMLLEKVLPVLDEREQKILQFTFIENR--SQKETGELLDISQM 223

Query: 268 RVRQIEARAFKKV 280
            V +I+ +A KK+
Sbjct: 224 HVSRIQRQAIKKL 236


>gi|20808063|ref|NP_623234.1| sporulation sigma factor SigG [Thermoanaerobacter tengcongensis
           MB4]
 gi|20516644|gb|AAM24838.1| DNA-directed RNA polymerase sigma subunits (sigma70/sigma32)
           [Thermoanaerobacter tengcongensis MB4]
          Length = 264

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 61/260 (23%), Positives = 127/260 (48%), Gaps = 17/260 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+  ++  L  R + +GD  A    + S+LRLV+ +   +   G  + ++   G I
Sbjct: 22  KLPVLKPSKQRELLIRMK-NGDKKAREEFINSNLRLVLSVIQRFNNRGESVDDLFQVGCI 80

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD ++  + +TY++  I   ++ Y LR  + +++  +   + + +   +++ 
Sbjct: 81  GLIKAIDNFDLDQNVKFSTYAVPMIIGEIRRY-LRDNTPIRVSRSL--RDIAYKALQVRD 137

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L  +++N+ +P  V  IAK+L++   EV+     +    SL   I     ++    D  
Sbjct: 138 KL--VSENSKEP-TVGEIAKELDLPSEEVVMALDAIQEPVSLFEPIYHDGGDAIYVMDQ- 193

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           V D    ++V +EK         L  ++  LN RE+ I    R  E    +E ++ E  +
Sbjct: 194 VSDDKNVDEVWLEK-------IALKEALEKLNEREKMIL-TMRFFEGKTQME-VAKEIGI 244

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ +V ++E  A   +++ I
Sbjct: 245 SQAQVSRLEKAALNHMRKYI 264


>gi|255305293|ref|ZP_05349465.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile ATCC 43255]
          Length = 233

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 67/237 (28%), Positives = 116/237 (48%), Gaps = 19/237 (8%)

Query: 53  LVTSHLRLVVKIAMGY--RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           L+  ++ LV  IA  +   G G    ++V+ G IGL+ A+ KFD E+G + ++YS   IK
Sbjct: 6   LIKENMPLVKSIARKFFIPGKGFEYQDLVNSGVIGLIDAINKFDTEKGAKFSSYSYIKIK 65

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
           +A+ + I     + K   T   K   +N  R+   LQ+     L+      IAK+L VSE
Sbjct: 66  SAILDEIRNQSPISKHNLTKVNK---YN--RVVEKLQSKL---LREPTSYEIAKELKVSE 117

Query: 171 SEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E+  I  N  +    SLN +I   D N +  QD +    D +E+      E + +  +L
Sbjct: 118 KELHDIESNIDMLNIVSLNYVI-FEDTNET-VQDVI---SDREEEAPENIIEEEEKLEIL 172

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           ++++S LN RE+ I      ++  + L+ +     VS  RV Q+  ++ + ++  I+
Sbjct: 173 SKAISNLNEREKLILSLYYYED--LNLKEIGKVLGVSESRVSQLHRKSIRNLRNKIK 227


>gi|167767678|ref|ZP_02439731.1| hypothetical protein CLOSS21_02213 [Clostridium sp. SS2/1]
 gi|167710695|gb|EDS21274.1| hypothetical protein CLOSS21_02213 [Clostridium sp. SS2/1]
 gi|291560812|emb|CBL39612.1| RNA polymerase, sigma 29 subunit, SigE [butyrate-producing
           bacterium SSC/2]
          Length = 240

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 51/199 (25%), Positives = 82/199 (41%), Gaps = 60/199 (30%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   L+  +LRLVV IA  +   G+ + +++S G IGL++A+  F+P +  +LATY+  
Sbjct: 54  TARSMLIERNLRLVVYIAKKFDNTGIGVEDLISIGTIGLIKAINTFNPAKKIKLATYASR 113

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+  +  Y                      LRR           N K +  V+I + LN
Sbjct: 114 CIENEILMY----------------------LRR-----------NNKTKMEVSIDEPLN 140

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           V                         D N     D L  D D    ++ +  E +  + +
Sbjct: 141 V-----------------------DWDGNELLLSDILGTDED----IIYKDLEHEVDKKL 173

Query: 228 LTRSMSVLNPRERRIFEAR 246
           LTR+M++L  RE+ I E R
Sbjct: 174 LTRAMTILTDREKMIIELR 192


>gi|126697838|ref|YP_001086735.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile 630]
 gi|255099435|ref|ZP_05328412.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile QCD-63q42]
 gi|115249275|emb|CAJ67088.1| RNA polymerase sigma-28factor for flagellar operon [Clostridium
           difficile]
          Length = 233

 Score = 55.1 bits (131), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 67/237 (28%), Positives = 116/237 (48%), Gaps = 19/237 (8%)

Query: 53  LVTSHLRLVVKIAMGY--RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           L+  ++ LV  IA  +   G G    ++V+ G IGL+ A+ KFD E+G + ++YS   IK
Sbjct: 6   LIKENMPLVKSIARKFFIPGKGFEYQDLVNSGVIGLIDAINKFDAEKGAKFSSYSYIKIK 65

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
           +A+ + I     + K   T   K   +N  R+   LQ+     L+      IAK+L VSE
Sbjct: 66  SAILDEIRNQSPISKHNLTKVNK---YN--RVVEKLQSKL---LREPTSYEIAKELKVSE 117

Query: 171 SEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E+  I  N  +    SLN +I   D N +  QD +    D +E+      E + +  +L
Sbjct: 118 KELHDIESNIDMLNIVSLNYVI-FEDTNET-VQDVI---SDREEEAPENIIEEEEKLEIL 172

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           ++++S LN RE+ I      ++  + L+ +     VS  RV Q+  ++ + ++  I+
Sbjct: 173 SKAISNLNEREKLILSLYYYED--LNLKEIGKVLGVSESRVSQLHRKSIRNLRNKIK 227


>gi|323702540|ref|ZP_08114203.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
 gi|323532514|gb|EGB22390.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
          Length = 260

 Score = 54.7 bits (130), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 68/267 (25%), Positives = 120/267 (44%), Gaps = 35/267 (13%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           + P+L  +E   L K+  + GD  A  RLV  +L+LV  +   +   G  + ++   G I
Sbjct: 13  RFPLLGDKEMRDLIKKA-QAGDADARERLVNCNLKLVFNLVQRFNNRGYELEDLFQIGCI 71

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A+ KFD     + +TY++  I   ++ + LR  S VK+  +   K   + +++ + 
Sbjct: 72  GLMKAIDKFDLSYDVKFSTYAVPMIVGEIRRF-LRDDSPVKVSRSL--KETAYKIQQTRD 128

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L A    +     +  IA++L     EV+S         S+   ++  D +     D L
Sbjct: 129 RLTARLGRD---PSINEIAQELGCHREEVVSALEAAQTPTSIYETLHQDDGDPIYILDQL 185

Query: 205 VYDHDGQ---------EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
               DG          +Q+LIE  ER +R+ +L            R FE +   ++ V L
Sbjct: 186 SGADDGDSPWLEKLAVKQLLIELPER-DRQILLW-----------RFFEDK--TQSEVAL 231

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQE 282
               S+ +VSR     +E +A +K++E
Sbjct: 232 RLGLSQVQVSR-----LERQALRKLKE 253


>gi|317472443|ref|ZP_07931767.1| RNA polymerase sigma-E factor [Anaerostipes sp. 3_2_56FAA]
 gi|316900087|gb|EFV22077.1| RNA polymerase sigma-E factor [Anaerostipes sp. 3_2_56FAA]
          Length = 238

 Score = 54.7 bits (130), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 32/99 (32%), Positives = 57/99 (57%), Gaps = 1/99 (1%)

Query: 22  EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           EI   P+  K+EE ++ K      +  A  +L+  +LRLVV IA  +   G+ + +++S 
Sbjct: 27  EILPAPLEAKEEEKMIHKLGTAE-EPEARAKLIERNLRLVVYIAKKFDNTGIGVEDLISI 85

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           G IGL++A+  F+P +  +LATY+   I+  +  Y+ R+
Sbjct: 86  GTIGLIKAINTFNPAKKIKLATYASRCIENEILMYLRRN 124


>gi|323702739|ref|ZP_08114399.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
 gi|323532256|gb|EGB22135.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
          Length = 232

 Score = 54.7 bits (130), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 37/106 (34%), Positives = 55/106 (51%), Gaps = 1/106 (0%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           ++NG I L  Y+   R    L  +EE  L  R  + GD  A   LV  +LRLV  IA  +
Sbjct: 13  LINGLIFLVSYLSSGRLPDPLSAEEEQELLSRL-QQGDQLARSVLVERNLRLVATIANKH 71

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114
           +  G+   ++   G IGL++AV  F+P R  + ATY+   I+  M+
Sbjct: 72  KDRGIDKQDLFQVGVIGLIKAVNTFNPARTNKFATYAGVCIENEMR 117


>gi|307717634|gb|ADN88870.1| RNA polymerase sigma-37 factor [Listeria seeligeri]
          Length = 220

 Score = 54.7 bits (130), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 55/217 (25%), Positives = 104/217 (47%), Gaps = 24/217 (11%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV ++  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQENGDQDAQYNLVVNYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTREL 115

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +   
Sbjct: 116 QSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGT 172

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
            DG E+V        N+R +L + + VL+ RE++I +
Sbjct: 173 DDGFERV--------NQRMLLEKVLPVLDEREQKILQ 201


>gi|291542453|emb|CBL15563.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Ruminococcus bromii
           L2-63]
          Length = 231

 Score = 54.7 bits (130), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 31/84 (36%), Positives = 48/84 (57%), Gaps = 2/84 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ EKQE   L K    +GD++A + LV  +LRLV  I   Y G      ++VS G IGL
Sbjct: 28  PLTEKQERECLEKS--ANGDIAARNMLVEHNLRLVAHIIKKYYGTQSEQDDLVSIGTIGL 85

Query: 87  MQAVKKFDPERGFRLATYSMWWIK 110
           ++A+  FD  +  +L++Y+   I+
Sbjct: 86  IKAINTFDMNKNIKLSSYASRCIE 109


>gi|224370767|ref|YP_002604931.1| FliA [Desulfobacterium autotrophicum HRM2]
 gi|223693484|gb|ACN16767.1| FliA [Desulfobacterium autotrophicum HRM2]
          Length = 238

 Score = 54.7 bits (130), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 56/222 (25%), Positives = 104/222 (46%), Gaps = 20/222 (9%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           E+VS G++GL+ AV KFD  +   L TY+ + IK A+ +  LRS            + + 
Sbjct: 28  ELVSAGSLGLIDAVDKFDSGKHVSLKTYAQYRIKGAILDE-LRSMD-------TYSRSMR 79

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSD 194
             ++ +   ++AI D    P     +AK L V       M   + G    SL+A I + D
Sbjct: 80  KKIQDISRAVKAIEDKKKGPASDNEVAKLLEVPLESYYDMLTDIHGAAILSLDAFIRTGD 139

Query: 195 KNSS---QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
            ++S   ++Q  +  +H   +  L+++EE K    +L R+++ L  +E+ +      +E 
Sbjct: 140 NDTSSMTRFQAGIKGEHTPAD--LLDREELK---GVLARAVTTLTEKEQLVVSLYYYEE- 193

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
            +TL+ +     ++  R+ QI      K++  I+     S+S
Sbjct: 194 -LTLKEIGEVLTLTESRICQIHTAILIKLKVKIKDYYGSSTS 234


>gi|167745312|ref|ZP_02417439.1| hypothetical protein ANACAC_00003 [Anaerostipes caccae DSM 14662]
 gi|167655033|gb|EDR99162.1| hypothetical protein ANACAC_00003 [Anaerostipes caccae DSM 14662]
          Length = 243

 Score = 54.7 bits (130), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 32/99 (32%), Positives = 57/99 (57%), Gaps = 1/99 (1%)

Query: 22  EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           EI   P+  K+EE ++ K      +  A  +L+  +LRLVV IA  +   G+ + +++S 
Sbjct: 32  EILPAPLEAKEEEKMIHKLGTAE-EPEARAKLIERNLRLVVYIAKKFDNTGIGVEDLISI 90

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           G IGL++A+  F+P +  +LATY+   I+  +  Y+ R+
Sbjct: 91  GTIGLIKAINTFNPAKKIKLATYASRCIENEILMYLRRN 129


>gi|110799358|ref|YP_696454.1| sporulation sigma factor SigK [Clostridium perfringens ATCC 13124]
 gi|110674005|gb|ABG82992.1| RNA polymerase sigma-70 factor family [Clostridium perfringens ATCC
           13124]
          Length = 233

 Score = 54.7 bits (130), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 71/285 (24%), Positives = 119/285 (41%), Gaps = 70/285 (24%)

Query: 9   IVNGEIGLSRYIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           +V  +I L+ Y+      P  L ++EE +  +R ++ GD+ A   LV  +LRLV  I   
Sbjct: 10  LVGSKIFLTGYVTGNSTFPKPLNEKEEKIYLERLKD-GDVEAKRVLVERNLRLVAHIVKK 68

Query: 68  YRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           Y         + +++S G IGL++A+  FD  +G RLATY+   I               
Sbjct: 69  YSSNYQNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATYAAKCID-------------- 114

Query: 125 KIGTTANQKRLFF-NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
                 N+  +FF N ++ KG               V +   + V +           G+
Sbjct: 115 ------NEILMFFRNTKKTKGE--------------VFLQDPIGVDKE----------GN 144

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS-VLNPRERRI 242
           E     I SSD +S                 ++E  E   +   L + MS +L+PRE+ I
Sbjct: 145 EICLIDILSSDSDS-----------------VLEAVENSLQVKELYKKMSDILSPREKEI 187

Query: 243 FEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            + R   L  +  T   +++   +SR  V +IE +A KK+ +  +
Sbjct: 188 IKMRYGLLDGDIKTQREIAAILGISRSYVSRIEKKALKKLNKEFK 232


>gi|297560171|ref|YP_003679145.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
 gi|296844619|gb|ADH66639.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
          Length = 313

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 49/197 (24%), Positives = 95/197 (48%), Gaps = 13/197 (6%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R+V  +  L+ KIA  Y G G P+ ++     +GL++AV+ +DP RG    +Y +  +  
Sbjct: 84  RVVVLYQPLINKIARRYGGRGEPLEDLKQTAMVGLVKAVRGYDPARGKPFISYLLPTVTG 143

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            ++ +       V++     + R+   LRR+ G  Q     + +   V  +++++ + E+
Sbjct: 144 EIKRHFRDHTWAVRVPRRHQENRV--KLRRVTGEFQQA---HARTPTVHELSEEMGLPEA 198

Query: 172 EVISMNCRLAGDESLNAL-INSSDKNSSQWQDWL-VYDHDGQEQVLIEKEERKNRRNMLT 229
           EV  +   +   ES  +L +++ D + S+ Q+   + DH G E   +   +R   R  L 
Sbjct: 199 EVGEL---IQVSESYRSLSLDAPDSSDSEGQEGTRLEDHLGCEDAAL---DRVVERESLK 252

Query: 230 RSMSVLNPRERRIFEAR 246
            +++ L  RER I   R
Sbjct: 253 PALARLPAREREILRLR 269


>gi|331085949|ref|ZP_08335032.1| hypothetical protein HMPREF0987_01335 [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|330406872|gb|EGG86377.1| hypothetical protein HMPREF0987_01335 [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 192

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 29/72 (40%), Positives = 45/72 (62%), Gaps = 1/72 (1%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           ++Y E GDL A H L+  +LRLV  I   Y+       +++S G +GL++AV  F+PE+G
Sbjct: 2   QKYTE-GDLEAKHILIEHNLRLVAHIVKKYQRPEEDNEDLISIGTVGLIKAVITFNPEKG 60

Query: 99  FRLATYSMWWIK 110
            RL+TY+   I+
Sbjct: 61  NRLSTYAARCIE 72


>gi|154498128|ref|ZP_02036506.1| hypothetical protein BACCAP_02109 [Bacteroides capillosus ATCC
           29799]
 gi|150273118|gb|EDN00275.1| hypothetical protein BACCAP_02109 [Bacteroides capillosus ATCC
           29799]
          Length = 240

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 30/79 (37%), Positives = 47/79 (59%), Gaps = 1/79 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K EE  L  R  E G+ +   +L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 38  PPLSKGEEAELIARLDE-GEETVKSQLIERNLRLVVYIARRFENTGVGIEDLISIGTIGL 96

Query: 87  MQAVKKFDPERGFRLATYS 105
           ++A+  + P +  +LATY+
Sbjct: 97  IKAINTYKPAKNIKLATYA 115


>gi|110803132|ref|YP_699053.1| sporulation sigma factor SigK [Clostridium perfringens SM101]
 gi|6715486|gb|AAF26431.1|AF218835_2 RNA polymerase sigma factor SigK [Clostridium perfringens]
 gi|110683633|gb|ABG87003.1| RNA polymerase sigma-70 factor family [Clostridium perfringens
           SM101]
          Length = 233

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 71/285 (24%), Positives = 118/285 (41%), Gaps = 70/285 (24%)

Query: 9   IVNGEIGLSRYIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           +V  +I L+ Y+      P  L ++EE +   R ++ GD+ A   LV  +LRLV  I   
Sbjct: 10  LVGSKIFLTGYVTGNSTFPKPLNEKEEKIYLDRLKD-GDVEAKRVLVERNLRLVAHIVKK 68

Query: 68  YRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           Y         + +++S G IGL++A+  FD  +G RLATY+   I               
Sbjct: 69  YSSNYQNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATYAAKCID-------------- 114

Query: 125 KIGTTANQKRLFF-NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
                 N+  +FF N ++ KG               V +   + V +           G+
Sbjct: 115 ------NEILMFFRNTKKTKGE--------------VFLQDPIGVDKE----------GN 144

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS-VLNPRERRI 242
           E     I SSD +S                 ++E  E   +   L + MS +L+PRE+ I
Sbjct: 145 EICLIDILSSDSDS-----------------VLEAVENSLQVKELYKKMSDILSPREKEI 187

Query: 243 FEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            + R   L  +  T   +++   +SR  V +IE +A KK+ +  +
Sbjct: 188 IKMRYGLLDGDIKTQREIAAILGISRSYVSRIEKKALKKLNKEFK 232


>gi|161898855|gb|ABX80417.1| SigB [Listeria monocytogenes]
          Length = 237

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 61/253 (24%), Positives = 119/253 (47%), Gaps = 26/253 (10%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 3   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 62

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 63  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTREL 116

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D     
Sbjct: 117 QSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVAGGT 173

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            DG E+V        N+R +L + + VL+ RE++I +   ++    + +      ++S+ 
Sbjct: 174 DDGFERV--------NQRMLLEKVLPVLDEREQKILQFTFIENR--SQKETGELLDISQM 223

Query: 268 RVRQIEARAFKKV 280
            V +I+ +A KK+
Sbjct: 224 HVSRIQRQAIKKL 236


>gi|328880278|emb|CCA53517.1| RNA polymerase sigma factor SigB [Streptomyces venezuelae ATCC
           10712]
          Length = 290

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 55/234 (23%), Positives = 106/234 (45%), Gaps = 15/234 (6%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  ++ LVV  A  +R  G  + ++V  G IGL++A+ +FD  R    AT+++ +I   
Sbjct: 63  LIEMNMSLVVYAAGRFRARGDEMEDIVQVGMIGLIKAIDRFDLSREVEFATFAVPYIVGE 122

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           ++ +   S   V +     + R+      L      ++    +  +V  +A  +++SE +
Sbjct: 123 IKRFFRDSTWAVHVPRRLQEARV-----ELAKATDELSSRLGRAPRVAELAPAMDLSEEQ 177

Query: 173 VISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           V+       G    SL+A +   D   S+  D  + D  GQE   IE  E     + L  
Sbjct: 178 VVEAQVAANGYHSTSLDAAVAGGD---SEDDDAALADLIGQEDPAIELFEDF---HTLAP 231

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  L PR+R +   R ++E  +T   +     VS+  V ++ AR  ++++  +
Sbjct: 232 LVEALGPRDRLLLHLRFVEE--LTQSEIGERLGVSQMHVSRLLARNIERLRAGM 283


>gi|317121837|ref|YP_004101840.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Thermaerobacter
           marianensis DSM 12885]
 gi|315591817|gb|ADU51113.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Thermaerobacter
           marianensis DSM 12885]
          Length = 261

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 64/266 (24%), Positives = 120/266 (45%), Gaps = 34/266 (12%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKK 92
           L +RYR   D  +   L+  HL LV  +A G     LP    + +++S G  GLM+A+++
Sbjct: 14  LWRRYRTTADPESWEALIREHLPLVRYLA-GRMIIHLPPQVELDDLISYGIFGLMEAIRR 72

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           +DP RG +  TY+   I+ AM +  LR+   V        + +    RRL+  L    ++
Sbjct: 73  YDPARGVKFETYAYTRIRGAMLDG-LRAMDWVPQTLRRRARDVEACYRRLENRLGRPAND 131

Query: 153 N-------LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           +       LKPE+   + ++L  + + V+S++         + L + SD  ++      V
Sbjct: 132 DEVAAELGLKPEEFAGLLQEL--ARTTVVSLD---------DVLPSDSDDPAA------V 174

Query: 206 YDH--DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
            D   D      ++     + R  L  +++ L  RER +      +   +T++ ++    
Sbjct: 175 LDRLADPGATDPLQAATLADLRRRLADALAGLPERERLVVSLYYYEG--LTVKEIAEVMG 232

Query: 264 VSRERVRQIEARAFKKVQESIQKQVE 289
           VS  RV Q+  RA  +++  +  + E
Sbjct: 233 VSPSRVSQLHTRAILRLRARLGAEEE 258


>gi|161898865|gb|ABX80422.1| SigB [Listeria monocytogenes]
          Length = 237

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 61/253 (24%), Positives = 119/253 (47%), Gaps = 26/253 (10%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 3   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 62

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 63  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTREL 116

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D     
Sbjct: 117 QSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVAGGT 173

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            DG E+V        N+R +L + + VL+ RE++I +   ++    + +      ++S+ 
Sbjct: 174 DDGFERV--------NQRMLLEKVLPVLDEREQKILQYTFIENR--SQKETGELLDISQM 223

Query: 268 RVRQIEARAFKKV 280
            V +I+ +A KK+
Sbjct: 224 HVSRIQRQAIKKL 236


>gi|146344354|ref|YP_001202210.1| putative RNA polymerase sigma factor [Pseudomonas fluorescens
           SBW25]
 gi|146188166|emb|CAM96497.1| putative RNA polymerase sigma factor [Pseudomonas fluorescens
           SBW25]
          Length = 533

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 56/207 (27%), Positives = 98/207 (47%), Gaps = 17/207 (8%)

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
           S  N+GL +AV +F PE GFR +T ++ WI  ++   +    S+         +R+  N+
Sbjct: 328 SAANMGLTRAVYRFAPEMGFRFSTIALTWINVSISRDLADQESIRLPEGMHKHRRMISNM 387

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNSS 198
            R + +   ++ N+L      A A KL   E +V+      AG + S++     +D + +
Sbjct: 388 LRDQPN---VSINSL------AEATKL---EQDVVRDLVHFAGGQRSIDTAFQGTDSSDA 435

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLE 256
                L+ D +     + E E+   R+ + +    VL  RE  +   R    +    TL 
Sbjct: 436 DGLHELLADTN--NDFMSEIEDDSMRQFVESALGDVLTQREIFVIVNRFGMGDAREKTLA 493

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQES 283
            LS E  +S+ERVRQ+E +A  K+++S
Sbjct: 494 ELSVEMNLSKERVRQLEIQALSKIRDS 520


>gi|317471864|ref|ZP_07931199.1| sigma-70 family RNA polymerase sigma factor [Anaerostipes sp.
           3_2_56FAA]
 gi|316900637|gb|EFV22616.1| sigma-70 family RNA polymerase sigma factor [Anaerostipes sp.
           3_2_56FAA]
          Length = 207

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 29/83 (34%), Positives = 48/83 (57%), Gaps = 2/83 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ +++E+Y L K     GD+ A + LV  +LRLV  I   Y  +     +++S G IGL
Sbjct: 7   PLSQEEEQYYLKKS--RLGDMEARNILVEHNLRLVAHIVKKYNNFDRDKDDLISVGTIGL 64

Query: 87  MQAVKKFDPERGFRLATYSMWWI 109
           ++A+  ++ E+G RL TY+   I
Sbjct: 65  IKAINTYNMEKGHRLVTYASRCI 87


>gi|119632740|gb|ABL84377.1| DNA directed RNA polymerase sigma 42 protein [Streptococcus suis]
          Length = 75

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 31/41 (75%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I
Sbjct: 1   DLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAI 41


>gi|150387863|ref|YP_001317912.1| RinA family phage transcriptional regulator [Alkaliphilus
           metalliredigens QYMF]
 gi|149947725|gb|ABR46253.1| phage transcriptional regulator, RinA family [Alkaliphilus
           metalliredigens QYMF]
          Length = 266

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 58/259 (22%), Positives = 124/259 (47%), Gaps = 32/259 (12%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y+E+  +   + LV  +L +   ++  +   G+   ++    ++GL+ A+++FD  RGF 
Sbjct: 30  YQENKKVEVRNELVNRYLYIAEILSKKFLNKGIDYEDIYQVASLGLIYAIERFDLSRGFE 89

Query: 101 LATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
            ++++   I   ++++   + WS +++     +     N  ++  H      N  +   +
Sbjct: 90  FSSFATPTIIGEIKKHFRDKGWS-IRVPRRIQELSKKVNTAKMTLH-----QNLQRTPMI 143

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ----VL 215
             IA+ LN ++ EV+         E++ A    S   + +  D L YD+DG+++    + 
Sbjct: 144 KDIAEYLNCTQEEVM---------EAMEA----SQVYTPKSLD-LTYDNDGEDKDIQLID 189

Query: 216 IEKEERKN-----RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
           +  E+ KN      R+ L ++M  LN  E+++ E R    N  T  N++ E  VS+  V 
Sbjct: 190 LIGEKDKNFDEIENRDFLKKAMRNLNEVEKKVLEDRFF--NSKTQMNVAEELNVSQMTVS 247

Query: 271 QIEARAFKKVQESIQKQVE 289
           ++E R  +K ++ + K +E
Sbjct: 248 RMEKRIIEKFRKELNKSME 266


>gi|291532029|emb|CBK97614.1| RNA polymerase sigma factor, sigma-70 family [Eubacterium siraeum
           70/3]
          Length = 221

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 66/240 (27%), Positives = 110/240 (45%), Gaps = 33/240 (13%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            +T H  LV  IA  +R  G+   E+ S G +GL++A   FD  RG + +TY++  I   
Sbjct: 9   FITEHFALVHSIAGRFRNRGIEYDELFSAGCVGLVKAGNNFDESRGLKFSTYAVPVIMGE 68

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +++ + R    VK+  + + K L   + RL+  L     N  +P  +  +A+KL ++  E
Sbjct: 69  IKQ-LFRDGGTVKV--SRSLKELSLKICRLRDEL---IKNGEEP-HISVLAEKLGITPEE 121

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
                  LA   SL  +  SS      + D    + +G   + +E E+ K    M  R +
Sbjct: 122 A-----SLALGASLPPVSLSS------YDDE--ENDEGSFDLPVEPEQPKALDRMALRQL 168

Query: 233 -SVLNPRERRIFEARRLQE--NPVTLENLS-SEFEVSRERVRQIEARAFKKVQESIQKQV 288
            S L P +RR+   R  +E     T E L  ++ +VSR           KK+ E ++KQ+
Sbjct: 169 VSRLEPIDRRLIILRYSEECTQSRTAEILGMTQVQVSRRE---------KKILEGLRKQL 219


>gi|52080862|ref|YP_079653.1| sporulation sigma factor SigF [Bacillus licheniformis ATCC 14580]
 gi|52786234|ref|YP_092063.1| sporulation sigma factor SigF [Bacillus licheniformis ATCC 14580]
 gi|319645181|ref|ZP_07999414.1| RNA polymerase sigma-F factor [Bacillus sp. BT1B_CT2]
 gi|52004073|gb|AAU24015.1| RNA polymerase sporulation-specific sigma factor (sigma-F)
           [Bacillus licheniformis ATCC 14580]
 gi|52348736|gb|AAU41370.1| SigF [Bacillus licheniformis ATCC 14580]
 gi|317392990|gb|EFV73784.1| RNA polymerase sigma-F factor [Bacillus sp. BT1B_CT2]
          Length = 255

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 58/244 (23%), Positives = 110/244 (45%), Gaps = 28/244 (11%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           ++GD  A   L+  ++RLV  +   +   G    ++   G IGL+++V KFD     R +
Sbjct: 27  QNGDQKARDLLIEKNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKSVDKFDLSYDVRFS 86

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I   +Q +I R    VK+  +   K L   +RR K  L   + +N +   V  I
Sbjct: 87  TYAVPMIIGEIQRFI-RDDGTVKVSRSL--KELGNKIRRAKDEL---SKSNGRIPTVQEI 140

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ-----EQVLIE 217
           A  L +S  EV+     +    S++                 VY++DG      +Q+  +
Sbjct: 141 ADYLEISSEEVVMAQEAVRSPSSIHE---------------TVYENDGDPITLLDQIADQ 185

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
            EE+   +  L  ++  L+ RE+ I   R  ++   T   ++    +S+ +V ++E +  
Sbjct: 186 SEEKWFDKIALKEAIKDLDEREKLIVYLRYYKDK--TQSEVADRLGISQVQVSRLEKKIL 243

Query: 278 KKVQ 281
           K+++
Sbjct: 244 KQIK 247


>gi|238928124|ref|ZP_04659884.1| sigma-70 area 2 domain protein [Selenomonas flueggei ATCC 43531]
 gi|238884084|gb|EEQ47722.1| sigma-70 area 2 domain protein [Selenomonas flueggei ATCC 43531]
          Length = 208

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 28/104 (26%), Positives = 58/104 (55%), Gaps = 1/104 (0%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
            S Y+ ++  +  L  +EE  L + Y++ GD +A  R++ ++  LV +    YR     +
Sbjct: 2   FSTYMKKLSAVKKLTPEEEKKLWRAYKDQGDAAARRRIIEAYQPLVFREVYPYRSLSAAM 61

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
            + V EG IGL++AV+++DP  G   + Y++  ++  + +++ R
Sbjct: 62  -DAVQEGTIGLIEAVERYDPHHGAAFSLYAVHRVRGRIHDFLRR 104


>gi|168180934|ref|ZP_02615598.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum NCTC 2916]
 gi|182668292|gb|EDT80271.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum NCTC 2916]
          Length = 242

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 66/249 (26%), Positives = 115/249 (46%), Gaps = 23/249 (9%)

Query: 45  GDLSAAHRLVTSHLRLVVKIA----MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
            +L     +V  ++ LV  IA    +G   Y +   ++VS G IGLM A+ KFD  +G +
Sbjct: 6   NNLYVKEEIVKKYIPLVKYIASRVIIGKTKY-IEYEDLVSYGMIGLMDALNKFDESKGMK 64

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+   IK +M + + R+  + K G      R    + +L+  L        K   ++
Sbjct: 65  FSTYASIRIKGSMIDELRRNSPISK-GAMDKLNRYNEAIEKLQKKLN-------KEPNLI 116

Query: 161 AIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            IA +LNVS  EV  I          SL  LI SS+         L+     ++    EK
Sbjct: 117 QIADELNVSLKEVSEIENYINYISVISLEDLIFSSEDEVP-----LIGTIKDEKSPSPEK 171

Query: 219 EERKNRR-NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
              +N + + L +++ +LN ++R +      +E  +TL+ +     VS  RV Q+ +RA 
Sbjct: 172 HVEENEQLDYLAKAIELLNEKDRLVVTLYYYEE--LTLKEIGKILNVSESRVCQLHSRAI 229

Query: 278 KKVQESIQK 286
             +++++ K
Sbjct: 230 IHLKKAMAK 238


>gi|293374267|ref|ZP_06620595.1| RNA polymerase sigma-K factor [Turicibacter sanguinis PC909]
 gi|292647100|gb|EFF65082.1| RNA polymerase sigma-K factor [Turicibacter sanguinis PC909]
          Length = 229

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 28/83 (33%), Positives = 48/83 (57%), Gaps = 2/83 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  ++EE+ L      +GD +A  +L+  +LRLV  I   Y+       +++S G IGL
Sbjct: 29  PLSAEEEEHYLT--LMANGDKNAREKLIEHNLRLVAHIVKKYQNQTDDKEDLISIGTIGL 86

Query: 87  MQAVKKFDPERGFRLATYSMWWI 109
           ++A+  F P++G +LATY+   I
Sbjct: 87  IKAIDSFSPDKGTKLATYAARCI 109


>gi|145594674|ref|YP_001158971.1| sigma-70 region 2 domain-containing protein [Salinispora tropica
           CNB-440]
 gi|145304011|gb|ABP54593.1| sigma-70 region 2 domain protein [Salinispora tropica CNB-440]
          Length = 284

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 66/248 (26%), Positives = 115/248 (46%), Gaps = 25/248 (10%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV   L    ++A  YRG G P+ ++     +GL+ AV ++DPERG   A  ++  +   
Sbjct: 46  LVRFALPFAGRLARRYRGRGEPLEDLEQVARLGLVNAVDRYDPERGSFTAYAAITIVGEI 105

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
            + +  R+W  V +      +RL   +  +     A+T    +   V  +A++L   E E
Sbjct: 106 KRHFRDRTWG-VHV-----PRRLRDLILEVGQATAALTSELSRAPTVAELARRLETPEEE 159

Query: 173 VISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           +++     AG    SLNA +    ++S+++ D LV + D     L   ++R     +L R
Sbjct: 160 ILAALESAAGYSPASLNAPVGG--ESSAEFGD-LVGESD---NALESVDDRVTVSGLLHR 213

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
               L  RERRI  A R   N    E +++ F +S+  V ++ +RA   +     +Q  L
Sbjct: 214 ----LPWRERRIL-AMRFYGNQTQAE-IAARFGISQMHVSRLLSRALTWL-----RQAML 262

Query: 291 SSSPPLLQ 298
           + +PP  Q
Sbjct: 263 ADAPPPWQ 270


>gi|302874724|ref|YP_003843357.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium cellulovorans
           743B]
 gi|302577581|gb|ADL51593.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium cellulovorans
           743B]
          Length = 256

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 40/150 (26%), Positives = 79/150 (52%), Gaps = 7/150 (4%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L++ E   L  + +  GD  +  + +  +LRLV+ +   +   G    ++   G I
Sbjct: 14  KLPVLKEHEMRELLDKMKA-GDYISREKFIRGNLRLVLSVIQRFNNRGENADDLFQVGCI 72

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD  +  + +TY++  I   ++ Y LR  + +++  +          R L+ 
Sbjct: 73  GLIKALDNFDLTQNVKFSTYAVPMIIGEIRRY-LRDNNSIRVSRSLRD----IAYRALQV 127

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVI 174
             + +T+NN +P  V  IAK+L+V++ EVI
Sbjct: 128 RDKLLTENNKEP-TVYQIAKELDVAKEEVI 156


>gi|167747049|ref|ZP_02419176.1| hypothetical protein ANACAC_01761 [Anaerostipes caccae DSM 14662]
 gi|167654009|gb|EDR98138.1| hypothetical protein ANACAC_01761 [Anaerostipes caccae DSM 14662]
          Length = 200

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 29/84 (34%), Positives = 49/84 (58%), Gaps = 2/84 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ +++E+Y L K     GD+ A + LV  +LRLV  I   Y  +     +++S G IGL
Sbjct: 7   PLSQEEEQYYLKKS--RLGDMEARNILVEHNLRLVAHIVKKYNNFDRDKDDLISVGTIGL 64

Query: 87  MQAVKKFDPERGFRLATYSMWWIK 110
           ++A+  ++ E+G RL TY+   I+
Sbjct: 65  IKAINTYNLEKGHRLVTYASRCIE 88


>gi|317063373|ref|ZP_07927858.1| RNA polymerase [Fusobacterium ulcerans ATCC 49185]
 gi|313689049|gb|EFS25884.1| RNA polymerase [Fusobacterium ulcerans ATCC 49185]
          Length = 54

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 19/42 (45%), Positives = 35/42 (83%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           +++SEGN+GL+ A++KFD  +GFR +TY++WWIK ++ + ++
Sbjct: 5   DLISEGNLGLIYAIEKFDITKGFRFSTYAVWWIKQSISKAVI 46


>gi|187935615|ref|YP_001885389.1| sporulation sigma factor SigG [Clostridium botulinum B str. Eklund
           17B]
 gi|187723768|gb|ACD24989.1| RNA polymerase sigma-G factor [Clostridium botulinum B str. Eklund
           17B]
          Length = 257

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 41/150 (27%), Positives = 75/150 (50%), Gaps = 7/150 (4%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+PML K++E        + GDLSA    +  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPML-KEKEKKQLLLALKKGDLSARETFIKGNLRLVLSVIQRFNNRGENVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD  +  + +TY++  I   ++ Y LR  + +++  +          + L  
Sbjct: 74  GLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNSIRVSRSLRD----IAYKALIV 128

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVI 174
             + I DNN +P  +  IAK+L +   EV+
Sbjct: 129 RDKFIKDNNKEP-TISQIAKELELPREEVV 157


>gi|161898849|gb|ABX80414.1| SigB [Listeria monocytogenes]
          Length = 236

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 55/217 (25%), Positives = 103/217 (47%), Gaps = 24/217 (11%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 3   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 62

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 63  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTREL 116

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +   
Sbjct: 117 QSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGT 173

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
            DG E+V        N+R +L + + VL+ RE++I +
Sbjct: 174 DDGFERV--------NQRMLLEKVLPVLDEREQKILQ 202


>gi|154500348|ref|ZP_02038386.1| hypothetical protein BACCAP_04015 [Bacteroides capillosus ATCC
           29799]
 gi|150270853|gb|EDM98136.1| hypothetical protein BACCAP_04015 [Bacteroides capillosus ATCC
           29799]
          Length = 256

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 63/269 (23%), Positives = 133/269 (49%), Gaps = 35/269 (13%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+ +L+ +E   L KR +E GD +A   L+  +LRLV+ +   +   G  + ++   G I
Sbjct: 14  KLKVLKNEETVALLKRTKE-GDTAAREELIAGNLRLVLSVIQKFSNRGENVDDLFQVGCI 72

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  F+ +   R +TY +  I   ++ Y LR  S +++  +          + L+ 
Sbjct: 73  GLIKAIDNFNTDLDVRFSTYGVPMIVGEIRRY-LRDNSSMRVSRSMRDT----AYKVLQA 127

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + + ++  +P  +  IAK L++   +V+          +++A+++      S ++   
Sbjct: 128 KEKFMAEHQREP-TMEEIAKMLDLKREDVVF---------AMDAIMDP----VSLYEP-- 171

Query: 205 VYDHDGQEQVLIEKEERKNRRNM---------LTRSMSVLNPRERRIFEARRLQENPVTL 255
           VY  DG + + +  ++ K+ +N          L  ++S L+ RER I  + R  E    +
Sbjct: 172 VY-SDGGDAICV-MDQVKDSKNTDESWLEHIALKEAISHLSDRERHIL-SLRFFEGRTQM 228

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESI 284
           E +S+E  +S+ +V ++E  A  K+++S+
Sbjct: 229 E-VSAEIGISQAQVSRLEKSAIWKIRKSL 256


>gi|23978316|dbj|BAC21132.1| principal sigma factor [Anabaena cylindrica]
          Length = 188

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 50/199 (25%), Positives = 99/199 (49%), Gaps = 19/199 (9%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL   +++ EG++GL++A +K D E+G++ +TY+ WWI+ A+   I      +++     
Sbjct: 4   GLSFQDLIQEGSLGLIRAAEKLDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV--- 60

Query: 132 QKRLFFNLRRLKGHLQAIT-DNNLKP-EQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
              L+  + R+K   + ++ +   KP E+ +A   ++ + +   I+ + +L    SL   
Sbjct: 61  --HLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPI--SLETP 116

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFEARRL 248
           I   +   S+  D++  + DG+     E +  KN  R  L + +  L+PRER +   R  
Sbjct: 117 IGKEE--DSRLGDFI--ESDGETP---EDQVSKNLLREDLEKVLDSLSPRERDVLRLRYG 169

Query: 249 QENP--VTLENLSSEFEVS 265
            ++    TLE +   F V+
Sbjct: 170 LDDGRMKTLEEIGQIFNVT 188


>gi|188588400|ref|YP_001920536.1| sporulation sigma factor SigG [Clostridium botulinum E3 str. Alaska
           E43]
 gi|251778549|ref|ZP_04821469.1| RNA polymerase sigma-G factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
 gi|188498681|gb|ACD51817.1| RNA polymerase sigma-G factor [Clostridium botulinum E3 str. Alaska
           E43]
 gi|243082864|gb|EES48754.1| RNA polymerase sigma-G factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
          Length = 257

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 41/150 (27%), Positives = 75/150 (50%), Gaps = 7/150 (4%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+PML K++E        + GDLSA    +  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPML-KEKEKKQLLLALKKGDLSARETFIKGNLRLVLSVIQRFNNRGENVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD  +  + +TY++  I   ++ Y LR  + +++  +          + L  
Sbjct: 74  GLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNSIRVSRSLRD----IAYKALIV 128

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVI 174
             + I DNN +P  +  IAK+L +   EV+
Sbjct: 129 RDKFIKDNNREP-TISQIAKELELPREEVV 157


>gi|284046869|ref|YP_003397209.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
 gi|283951090|gb|ADB53834.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
          Length = 276

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 55/205 (26%), Positives = 93/205 (45%), Gaps = 27/205 (13%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           +V  HL L   +A  Y   G P+ ++V   ++GL++AV +FDP RG   A+Y++  I   
Sbjct: 54  MVEQHLGLAHHLARRYSDRGEPLDDLVQVASLGLLKAVDRFDPARGVSFASYAVPTILGE 113

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRR-LKGHL-QAITDNNLKPE---QVVAIAKKL 166
           ++ +   R W+   I    + K     +   L GH  ++ T + L  E    V A+ + L
Sbjct: 114 LRRHFRDRGWA---IHVPRDLKEAALRVESALAGHAGRSPTPSQLGKETGLDVEAVLEAL 170

Query: 167 NVSESE-VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
            V+ +   +S++   AG        N  +  ++   D L  D D        + +R   R
Sbjct: 171 EVAGAHRALSLDA-PAG--------NEEEGTTATLVDRLGRDDD--------ELDRAGDR 213

Query: 226 NMLTRSMSVLNPRERRIFEARRLQE 250
             + R  SVL PRER I   R +++
Sbjct: 214 ATIERLASVLEPREREILRLRFVED 238


>gi|161898871|gb|ABX80425.1| SigB [Listeria monocytogenes]
          Length = 229

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 63/252 (25%), Positives = 119/252 (47%), Gaps = 36/252 (14%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D   G  
Sbjct: 1   YQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKS 60

Query: 101 LATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
              +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T       Q+
Sbjct: 61  FEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTRELQSSPQI 114

Query: 160 VAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
             IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +    DG E+
Sbjct: 115 SDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTDDGFER 171

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE-----FEVSRER 268
           V        N+R +L + + VL+ RE++I +          +EN S +      ++S+  
Sbjct: 172 V--------NQRMLLEKVLPVLDEREQKILQF-------TFIENRSQKETGELLDISQMH 216

Query: 269 VRQIEARAFKKV 280
           V +I+ +A KK+
Sbjct: 217 VSRIQRQAIKKL 228


>gi|56963560|ref|YP_175291.1| sporulation sigma factor SigF [Bacillus clausii KSM-K16]
 gi|56909803|dbj|BAD64330.1| DNA-directed RNA polymerase sigma factor sigma-F [Bacillus clausii
           KSM-K16]
          Length = 254

 Score = 54.7 bits (130), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 63/268 (23%), Positives = 125/268 (46%), Gaps = 34/268 (12%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           +K P+ +KQ + ++AK   + GD  A   +V  + RLV  +   +   G    ++   G 
Sbjct: 10  KKKPLSDKQVKELIAKS--QEGDTEARDSIVNHNTRLVWSVVQRFLNRGYEADDLFQIGC 67

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL+++V KFD     + +TY++  I   +Q + LR    VK+  +   K L   +R+ K
Sbjct: 68  IGLIKSVDKFDLSYDVKFSTYAVPMIIGEIQRF-LRDDGTVKVSRSI--KELSNKIRKAK 124

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQ 201
             L   T    +   +  IA+ L V+  E++      AGD   SL+++  +         
Sbjct: 125 DEL---TKTLRRAPTINEIAEHLGVTPEEIV-----FAGDANRSLSSIHET--------- 167

Query: 202 DWLVYDHDGQEQVLIEKEERKNR-----RNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
              VY++DG    L+++    ++     +  L  ++  L  RER I   R  ++   T  
Sbjct: 168 ---VYENDGDPITLLDQIADHSQVKWFDKIALKEAICDLGERERLIVYLRYYKDQ--TQS 222

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
            ++    +S+ +V ++E +  ++++E++
Sbjct: 223 EVAERLGISQVQVSRLEKKILEQMKETM 250


>gi|309775717|ref|ZP_07670714.1| RNA polymerase sigma-K factor [Erysipelotrichaceae bacterium
           3_1_53]
 gi|308916522|gb|EFP62265.1| RNA polymerase sigma-K factor [Erysipelotrichaceae bacterium
           3_1_53]
          Length = 249

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 68/263 (25%), Positives = 106/263 (40%), Gaps = 66/263 (25%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L+K+EE        EH D  A ++L+  +LRLV  I   Y        +++S G IGL++
Sbjct: 28  LDKEEEARCISLLSEH-DEEARNKLIEHNLRLVAHIVKKYDIKKEQTEDLISIGTIGLIK 86

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
            V  F PE+G +L TY+   I+  +  Y                      LR  K + Q 
Sbjct: 87  GVDSFKPEKGHKLTTYASKCIENEILMY----------------------LRSSKNYFQ- 123

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN--SSDKNSSQWQDWLVY 206
                             NVS +E I+ +     D S   LI+  +S +++S   D +V 
Sbjct: 124 ------------------NVSLNEPIATD----KDGSEITLIDAIASPEDTSIIDDMIVE 161

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEV 264
           D+  +                L R + VL+ RE  I   R     +   T   ++ +  +
Sbjct: 162 DNIAR----------------LKRFIHVLDARELEIITKRFGLYGQEEETQREIARQLHI 205

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           SR  V +IE RAF K+    QK+
Sbjct: 206 SRSYVSRIEKRAFMKIYREFQKE 228


>gi|307717606|gb|ADN88856.1| RNA polymerase sigma-37 factor [Listeria innocua]
          Length = 220

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 55/217 (25%), Positives = 104/217 (47%), Gaps = 24/217 (11%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQENGDEDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTREL 115

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA+ + V+E EV+ +M        L+ D S+ A    SD ++    D +   
Sbjct: 116 QSSPQISDIAEFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGT 172

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
            DG E+V        N+R +L + + VL+ RE++I +
Sbjct: 173 DDGFERV--------NQRMLLEKVLPVLDEREQKILQ 201


>gi|161898905|gb|ABX80442.1| SigB [Listeria monocytogenes]
          Length = 236

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 55/217 (25%), Positives = 103/217 (47%), Gaps = 24/217 (11%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 3   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 62

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 63  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTREL 116

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +   
Sbjct: 117 QSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGT 173

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
            DG E+V        N+R +L + + VL+ RE++I +
Sbjct: 174 DDGFERV--------NQRMLLEKVLPVLDEREQKILQ 202


>gi|160878636|ref|YP_001557604.1| FliA/WhiG family RNA polymerase sigma factor [Clostridium
           phytofermentans ISDg]
 gi|160427302|gb|ABX40865.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           phytofermentans ISDg]
          Length = 238

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 54/243 (22%), Positives = 108/243 (44%), Gaps = 16/243 (6%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R  + GD  A  R+VT ++ LV  I   + G G    ++   G+IGLM+A+ KFD     
Sbjct: 8   RLSKQGDKVARDRVVTENVGLVWSIVRRFMGRGHEAEDLFQIGSIGLMKAIDKFDLSYDV 67

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY++  I   ++ + LR   ++K+  +  +      L R     + +   N +   +
Sbjct: 68  KFSTYAVPMITGEIKRF-LRDDGMIKVSRSLKETAGKIRLMR-----ETLESKNGREPTI 121

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I + L +++ EV+      A  ESL   I   D N+    D +    D  ++++    
Sbjct: 122 EEIGEALELAKEEVVMALESGAEVESLYKTIYQGDGNAIFLIDKIEQTDDASDEMI---- 177

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
                   L   M  L+ +E+ I   R  ++   T   ++ +  +S+ +V ++E +  + 
Sbjct: 178 ----DHMALREVMDSLDEKEKDIIRLRYFKDKTQT--EIAKQLGISQVQVSRLERKILRT 231

Query: 280 VQE 282
           ++E
Sbjct: 232 MRE 234


>gi|169334413|ref|ZP_02861606.1| hypothetical protein ANASTE_00813 [Anaerofustis stercorihominis DSM
           17244]
 gi|169259130|gb|EDS73096.1| hypothetical protein ANASTE_00813 [Anaerofustis stercorihominis DSM
           17244]
          Length = 250

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 57/249 (22%), Positives = 123/249 (49%), Gaps = 24/249 (9%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           ++GD ++   L   +  L+  I   Y  Y +   ++   G IGL++A+K+F  E   + +
Sbjct: 23  QNGDKNSLEELTVINTPLINSILKRYLSYSISYDDLFQIGAIGLIKAIKRFSFEFNTKFS 82

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+++ I    + Y  R   ++K+G   N K ++   + ++     +  N ++P  +  +
Sbjct: 83  TYAVYVINGEYKRY-FRDEGIIKVG--RNLKTIYLKTKTIREDY--VKKNGVEP-SIDYL 136

Query: 163 AKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
           ++K+ VS  +V+     CR    ESL+  +N+++       D +  ++D  E++ +EK +
Sbjct: 137 SEKIGVSSEDVLMALEACRQP--ESLSKELNNNENTPILLMDKIKDENDSNEKI-VEKLD 193

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            KN       ++  L  R+R+I   R  +    T + ++    +S+ +V ++E    KK+
Sbjct: 194 LKN-------AIMNLEKRDRQIIVLRYFKNK--TQKEVAEVLGLSQVQVSRLE----KKI 240

Query: 281 QESIQKQVE 289
            E+++K  E
Sbjct: 241 IENMKKTFE 249


>gi|161898859|gb|ABX80419.1| SigB [Listeria monocytogenes]
          Length = 236

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 62/253 (24%), Positives = 118/253 (46%), Gaps = 27/253 (10%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E GD  A + LV  +  LV  IA  Y   G    E    GNIGL+ A++++D
Sbjct: 3   YIWIAAYQEDGDEDAQYNLVIHYKNLVESIARKY-SQGKSFHEDSQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTREL 115

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +   
Sbjct: 116 QSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGT 172

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            DG E+V        N+R +L + + VL+ RE++I +   ++    + +      ++S+ 
Sbjct: 173 DDGFERV--------NQRMLLEKVLPVLDEREQKILQFTFIENR--SQKETGELLDISQM 222

Query: 268 RVRQIEARAFKKV 280
            V +I+ +A KK+
Sbjct: 223 HVSRIQRQAIKKL 235


>gi|295092950|emb|CBK82041.1| DNA-directed RNA polymerase specialized sigma subunit [Coprococcus
           sp. ART55/1]
          Length = 128

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 31/99 (31%), Positives = 59/99 (59%), Gaps = 3/99 (3%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A  +LVT ++ LVV +A  Y G G  + +++  G IGL++A+ +FD +   +L+TY
Sbjct: 14  GDRDARDKLVTDNMGLVVSVARRYVGRGQELEDLIQIGLIGLVKAIDRFDMDYEVKLSTY 73

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           ++  I+  ++ + LR   +VK+  + N K +++   R +
Sbjct: 74  AVPLIQGEIRRF-LRDDGMVKV--SRNLKTIYYRADRYR 109


>gi|325844829|ref|ZP_08168281.1| RNA polymerase sigma-K factor [Turicibacter sp. HGF1]
 gi|325489016|gb|EGC91404.1| RNA polymerase sigma-K factor [Turicibacter sp. HGF1]
          Length = 229

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 28/83 (33%), Positives = 48/83 (57%), Gaps = 2/83 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  ++EE+ L      +GD +A  +L+  +LRLV  I   Y+       +++S G IGL
Sbjct: 29  PLSPEEEEHYLT--LMANGDKNAREKLIEHNLRLVAHIVKKYQNQTDDKEDLISIGTIGL 86

Query: 87  MQAVKKFDPERGFRLATYSMWWI 109
           ++A+  F P++G +LATY+   I
Sbjct: 87  IKAIDSFSPDKGTKLATYAARCI 109


>gi|284042121|ref|YP_003392461.1| RNA polymerase, sigma 32 subunit, RpoH [Conexibacter woesei DSM
           14684]
 gi|283946342|gb|ADB49086.1| RNA polymerase, sigma 32 subunit, RpoH [Conexibacter woesei DSM
           14684]
          Length = 300

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 59/241 (24%), Positives = 106/241 (43%), Gaps = 8/241 (3%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGY-GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           G+  A   LV   + L+  +A  YRG   +  +E++  G +GL+ A+++FDP R     T
Sbjct: 63  GETGARDELVDVFMPLIGSVARLYRGVTSVHRAELMQAGVVGLLTALERFDPSRRAPFWT 122

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WW++ AMQ+ +      V +       R    L R++   +  T  +      V +A
Sbjct: 123 YASWWVRQAMQQVVAELARPVVM-----SDRGLRELARMRAARRDFTRLHDAGPSSVRLA 177

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
               ++   + ++       E+L +    SD++    +     +  G E+      +R  
Sbjct: 178 AATGLTRERIETLLALELVPETLESEPAWSDEDDLARRSGHPLEDPGAEEAFDRVLDRVE 237

Query: 224 RRNMLTRSMSVLNPRERRIFEAR-RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              +L R +  L  RER I  AR  L     TL  ++    +S ERVRQ+E  A  +++ 
Sbjct: 238 CDRLL-RLIGDLRQRERVILHARFGLDGQERTLREVARMVGLSAERVRQLEHEALDELRA 296

Query: 283 S 283
           +
Sbjct: 297 A 297


>gi|326204636|ref|ZP_08194492.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium papyrosolvens
           DSM 2782]
 gi|325985203|gb|EGD46043.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium papyrosolvens
           DSM 2782]
          Length = 257

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 62/278 (22%), Positives = 128/278 (46%), Gaps = 53/278 (19%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L  +++ VL +R  + GD SA    +  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLTNEQKKVLFERMHK-GDNSARDEFINGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK- 143
           GL++A+  FD  +  + +TY++  I   ++ Y LR  + +++  +         LR +  
Sbjct: 74  GLIKAIDNFDVSQNVKFSTYAVPMIIGEIRRY-LRDNNSIRVSRS---------LRDIAY 123

Query: 144 GHLQA---ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
             LQA   +T  N K   +  +A++L + + +++          +L+A+ +      S +
Sbjct: 124 KALQAKERLTTQNSKEPTIAELAQELQLPKEDIVF---------ALDAIQDPISLFESVY 174

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNM---------LTRSMSVLNPRER-----RIFEAR 246
                  HDG + + +  ++  + +N+         L  +M  LN RE+     R FE R
Sbjct: 175 -------HDGGDAIYV-MDQVSDDKNIDENWLETISLKEAMRKLNDREKLILNLRFFEGR 226

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              E       ++ E  +S+ +V ++E  A   +++ I
Sbjct: 227 TQME-------VADEIGISQAQVSRLEKTALMHMKKYI 257


>gi|188011585|gb|ACD45089.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011587|gb|ACD45090.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011589|gb|ACD45091.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011591|gb|ACD45092.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011593|gb|ACD45093.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011595|gb|ACD45094.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011597|gb|ACD45095.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011599|gb|ACD45096.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011601|gb|ACD45097.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011603|gb|ACD45098.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011605|gb|ACD45099.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011607|gb|ACD45100.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011609|gb|ACD45101.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011611|gb|ACD45102.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011613|gb|ACD45103.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011615|gb|ACD45104.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011617|gb|ACD45105.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011619|gb|ACD45106.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011621|gb|ACD45107.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011623|gb|ACD45108.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011625|gb|ACD45109.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011627|gb|ACD45110.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011629|gb|ACD45111.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011631|gb|ACD45112.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011633|gb|ACD45113.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011635|gb|ACD45114.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011637|gb|ACD45115.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011639|gb|ACD45116.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011641|gb|ACD45117.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011643|gb|ACD45118.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011645|gb|ACD45119.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011647|gb|ACD45120.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011649|gb|ACD45121.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011651|gb|ACD45122.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011653|gb|ACD45123.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011655|gb|ACD45124.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011657|gb|ACD45125.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011659|gb|ACD45126.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011661|gb|ACD45127.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011663|gb|ACD45128.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011665|gb|ACD45129.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011667|gb|ACD45130.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011669|gb|ACD45131.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011671|gb|ACD45132.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011673|gb|ACD45133.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011675|gb|ACD45134.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011677|gb|ACD45135.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011679|gb|ACD45136.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011681|gb|ACD45137.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011683|gb|ACD45138.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011685|gb|ACD45139.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011687|gb|ACD45140.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011689|gb|ACD45141.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011691|gb|ACD45142.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011693|gb|ACD45143.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011695|gb|ACD45144.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011697|gb|ACD45145.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011699|gb|ACD45146.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011701|gb|ACD45147.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011703|gb|ACD45148.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011705|gb|ACD45149.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011707|gb|ACD45150.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011709|gb|ACD45151.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011711|gb|ACD45152.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011713|gb|ACD45153.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011715|gb|ACD45154.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011717|gb|ACD45155.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011719|gb|ACD45156.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011721|gb|ACD45157.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011723|gb|ACD45158.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011725|gb|ACD45159.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011727|gb|ACD45160.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011729|gb|ACD45161.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011731|gb|ACD45162.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011733|gb|ACD45163.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011735|gb|ACD45164.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011737|gb|ACD45165.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011739|gb|ACD45166.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011741|gb|ACD45167.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011743|gb|ACD45168.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011745|gb|ACD45169.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011747|gb|ACD45170.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011749|gb|ACD45171.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011751|gb|ACD45172.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011753|gb|ACD45173.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011755|gb|ACD45174.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011757|gb|ACD45175.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011763|gb|ACD45178.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011865|gb|ACD45229.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011871|gb|ACD45232.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011873|gb|ACD45233.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011945|gb|ACD45269.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011947|gb|ACD45270.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011949|gb|ACD45271.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|211906951|gb|ACJ11994.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|211906953|gb|ACJ11995.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|211906955|gb|ACJ11996.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|211906957|gb|ACJ11997.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|211906959|gb|ACJ11998.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|211906961|gb|ACJ11999.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|211906963|gb|ACJ12000.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|281324219|gb|ADA60651.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324223|gb|ADA60653.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324225|gb|ADA60654.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324227|gb|ADA60655.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324229|gb|ADA60656.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324231|gb|ADA60657.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324233|gb|ADA60658.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324235|gb|ADA60659.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324237|gb|ADA60660.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324241|gb|ADA60662.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324243|gb|ADA60663.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324245|gb|ADA60664.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324247|gb|ADA60665.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324249|gb|ADA60666.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324251|gb|ADA60667.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324253|gb|ADA60668.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324255|gb|ADA60669.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324257|gb|ADA60670.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324259|gb|ADA60671.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324261|gb|ADA60672.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324263|gb|ADA60673.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324265|gb|ADA60674.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324267|gb|ADA60675.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324269|gb|ADA60676.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324271|gb|ADA60677.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324275|gb|ADA60679.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324277|gb|ADA60680.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324279|gb|ADA60681.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324281|gb|ADA60682.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324283|gb|ADA60683.1| RNA polymerase sigma factor B [Listeria monocytogenes]
          Length = 222

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 55/217 (25%), Positives = 103/217 (47%), Gaps = 24/217 (11%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 4   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 63

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 64  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTREL 117

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +   
Sbjct: 118 QSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGT 174

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
            DG E+V        N+R +L + + VL+ RE++I +
Sbjct: 175 DDGFERV--------NQRMLLEKVLPVLDEREQKILQ 203


>gi|182418893|ref|ZP_02950150.1| RNA polymerase sigma-G factor [Clostridium butyricum 5521]
 gi|237667291|ref|ZP_04527275.1| RNA polymerase sigma-G factor [Clostridium butyricum E4 str. BoNT E
           BL5262]
 gi|182377176|gb|EDT74744.1| RNA polymerase sigma-G factor [Clostridium butyricum 5521]
 gi|237655639|gb|EEP53195.1| RNA polymerase sigma-G factor [Clostridium butyricum E4 str. BoNT E
           BL5262]
          Length = 257

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 62/261 (23%), Positives = 119/261 (45%), Gaps = 19/261 (7%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+++E+  L  + +  GD SA    +  +LRLV+ +   +   G  I ++   G I
Sbjct: 15  KLPILKEKEKKQLLLQMK-AGDKSARETFIKGNLRLVLSVIQRFNNRGENIDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD  +  + +TY++  I   ++ Y LR  + +++  +          + L  
Sbjct: 74  GLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNSIRVSRSLRD----IAYKALIV 128

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + I DNN +P  +  IAK+L +   EV+     +    SL   I     ++    D +
Sbjct: 129 REKFIKDNNKEP-TISQIAKELELPREEVVFALDAIQDPVSLYEPIYHDGGDAIYVMDQI 187

Query: 205 VYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
               D  E  L          N+ +  +M  L+ RE+ I   R    N  T   ++ E  
Sbjct: 188 SDSKDTDENWL---------ENISIKEAMKKLSDREKLILNLRFF--NGRTQMEVADEIG 236

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A K +++ +
Sbjct: 237 ISQAQVSRLEKTALKHMRKHV 257


>gi|85679193|gb|ABC72013.1| SigB [Listeria monocytogenes]
 gi|85679197|gb|ABC72015.1| SigB [Listeria monocytogenes]
 gi|85679199|gb|ABC72016.1| SigB [Listeria monocytogenes]
 gi|85679201|gb|ABC72017.1| SigB [Listeria monocytogenes]
 gi|85679203|gb|ABC72018.1| SigB [Listeria monocytogenes]
 gi|85679207|gb|ABC72020.1| SigB [Listeria monocytogenes]
 gi|85679209|gb|ABC72021.1| SigB [Listeria monocytogenes]
 gi|85679215|gb|ABC72024.1| SigB [Listeria monocytogenes]
 gi|307717584|gb|ADN88845.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|307717618|gb|ADN88862.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|307717628|gb|ADN88867.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
          Length = 220

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 55/217 (25%), Positives = 103/217 (47%), Gaps = 24/217 (11%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTREL 115

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +   
Sbjct: 116 QSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGT 172

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
            DG E+V        N+R +L + + VL+ RE++I +
Sbjct: 173 DDGFERV--------NQRMLLEKVLPVLDEREQKILQ 201


>gi|161898899|gb|ABX80439.1| SigB [Listeria monocytogenes]
          Length = 229

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 55/217 (25%), Positives = 103/217 (47%), Gaps = 24/217 (11%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTREL 115

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +   
Sbjct: 116 QSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGT 172

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
            DG E+V        N+R +L + + VL+ RE++I +
Sbjct: 173 DDGFERV--------NQRMLLEKVLPVLDEREQKILQ 201


>gi|295695806|ref|YP_003589044.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
 gi|295411408|gb|ADG05900.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
          Length = 238

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 29/84 (34%), Positives = 48/84 (57%), Gaps = 2/84 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ E++EE  L +     GD  A + L+  +LRLV  I   +   G    +++S G IGL
Sbjct: 30  PLSEEEEEQYLKQMAE--GDERARNLLIEHNLRLVAHIVKKFENTGEDTEDLISIGTIGL 87

Query: 87  MQAVKKFDPERGFRLATYSMWWIK 110
           ++A++ F P +G +LATY+   I+
Sbjct: 88  IKAIESFQPHKGTKLATYAARCIE 111


>gi|225629823|ref|ZP_03787747.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of
           Muscidifurax uniraptor]
 gi|225591324|gb|EEH12440.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of
           Muscidifurax uniraptor]
          Length = 95

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 33/87 (37%), Positives = 50/87 (57%)

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
           QD +  +   QE      EE + +  +L  +++ LN R R IF +R L EN  TL+ LS 
Sbjct: 1   QDMIPCNLVSQEVTYQNHEEEELKETILNNALASLNERARDIFISRYLSENIQTLDELSK 60

Query: 261 EFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++ VSRER+RQ+  +A  KV+  IQ +
Sbjct: 61  KYCVSRERIRQLAEQAMAKVKPYIQSE 87


>gi|150390631|ref|YP_001320680.1| sporulation sigma factor SigE [Alkaliphilus metalliredigens QYMF]
 gi|149950493|gb|ABR49021.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           metalliredigens QYMF]
          Length = 244

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 34/106 (32%), Positives = 60/106 (56%), Gaps = 2/106 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EE  L  + + + + +    L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 42  PPLSHDEERFLINKLK-NDESTVRTILIERNLRLVVYIARKFENTGIGVEDLISIGTIGL 100

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           ++AV  F+P++  +LATY+   I+  +  Y LR  S VK+  + ++
Sbjct: 101 IKAVNTFNPDKNIKLATYASRCIENEILMY-LRRNSKVKMEVSFDE 145


>gi|58699678|ref|ZP_00374352.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Drosophila
           ananassae]
 gi|58533807|gb|EAL58132.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Drosophila
           ananassae]
          Length = 93

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 31/78 (39%), Positives = 48/78 (61%)

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
            QE      EE++ +  +L  +++ LN R R IF +R L EN  TL+ LS ++ VSRER+
Sbjct: 8   SQEVTYQNHEEKELKEAILNNALASLNERARDIFISRYLSENIQTLDELSKKYCVSRERI 67

Query: 270 RQIEARAFKKVQESIQKQ 287
           RQ+  +A  KV++ IQ +
Sbjct: 68  RQLAEQAMAKVKQYIQSE 85


>gi|322806877|emb|CBZ04447.1| RNA polymerase sporulation specific sigma factor SigK [Clostridium
           botulinum H04402 065]
          Length = 144

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 30/79 (37%), Positives = 47/79 (59%), Gaps = 2/79 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ +++E+Y L +   + GD  A   LV  +LRLV  I   Y   G  I +++S G +GL
Sbjct: 30  PLSDEEEKYYLDRL--KKGDALAKDILVERNLRLVAHIVKKYSYPGKDIDDLISIGTVGL 87

Query: 87  MQAVKKFDPERGFRLATYS 105
           ++A+  FD  +G RLATY+
Sbjct: 88  IKAIDSFDNSKGTRLATYA 106


>gi|266624394|ref|ZP_06117329.1| RNA polymerase sigma-E factor [Clostridium hathewayi DSM 13479]
 gi|288863758|gb|EFC96056.1| RNA polymerase sigma-E factor [Clostridium hathewayi DSM 13479]
          Length = 216

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 30/84 (35%), Positives = 49/84 (58%), Gaps = 2/84 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  ++E   L  RY+E GD  A   L+  ++RLV  +A  Y+     + +++S G IGL
Sbjct: 7   PLTAREERECL-DRYQE-GDQEARATLIERNMRLVAHVAKKYQNTDYDMEDLLSVGTIGL 64

Query: 87  MQAVKKFDPERGFRLATYSMWWIK 110
           ++AV  F  +RG RLATY+   ++
Sbjct: 65  IKAVNTFHTDRGSRLATYAAKCVE 88


>gi|188011759|gb|ACD45176.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011761|gb|ACD45177.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011765|gb|ACD45179.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011767|gb|ACD45180.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011769|gb|ACD45181.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011771|gb|ACD45182.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011773|gb|ACD45183.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011775|gb|ACD45184.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011777|gb|ACD45185.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011779|gb|ACD45186.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011781|gb|ACD45187.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011783|gb|ACD45188.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011785|gb|ACD45189.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011787|gb|ACD45190.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011789|gb|ACD45191.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011791|gb|ACD45192.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011793|gb|ACD45193.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011795|gb|ACD45194.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011797|gb|ACD45195.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011799|gb|ACD45196.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011801|gb|ACD45197.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011803|gb|ACD45198.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011805|gb|ACD45199.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011807|gb|ACD45200.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011809|gb|ACD45201.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011811|gb|ACD45202.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011813|gb|ACD45203.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011815|gb|ACD45204.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011817|gb|ACD45205.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011819|gb|ACD45206.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011821|gb|ACD45207.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011823|gb|ACD45208.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011825|gb|ACD45209.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011827|gb|ACD45210.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011829|gb|ACD45211.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011831|gb|ACD45212.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011833|gb|ACD45213.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011835|gb|ACD45214.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011837|gb|ACD45215.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011839|gb|ACD45216.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011841|gb|ACD45217.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011843|gb|ACD45218.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011845|gb|ACD45219.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011847|gb|ACD45220.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011849|gb|ACD45221.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011851|gb|ACD45222.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011853|gb|ACD45223.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011855|gb|ACD45224.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011857|gb|ACD45225.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011859|gb|ACD45226.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011861|gb|ACD45227.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011863|gb|ACD45228.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011867|gb|ACD45230.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011869|gb|ACD45231.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011875|gb|ACD45234.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011877|gb|ACD45235.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011879|gb|ACD45236.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011881|gb|ACD45237.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011883|gb|ACD45238.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011885|gb|ACD45239.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011887|gb|ACD45240.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011889|gb|ACD45241.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011891|gb|ACD45242.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011893|gb|ACD45243.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011895|gb|ACD45244.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011899|gb|ACD45246.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011903|gb|ACD45248.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011905|gb|ACD45249.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011907|gb|ACD45250.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011909|gb|ACD45251.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011911|gb|ACD45252.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011913|gb|ACD45253.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011917|gb|ACD45255.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011919|gb|ACD45256.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011921|gb|ACD45257.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011923|gb|ACD45258.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011925|gb|ACD45259.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011927|gb|ACD45260.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011929|gb|ACD45261.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011931|gb|ACD45262.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011933|gb|ACD45263.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011935|gb|ACD45264.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011937|gb|ACD45265.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011939|gb|ACD45266.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011941|gb|ACD45267.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011943|gb|ACD45268.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|281324217|gb|ADA60650.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324221|gb|ADA60652.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324239|gb|ADA60661.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324273|gb|ADA60678.1| RNA polymerase sigma factor B [Listeria monocytogenes]
          Length = 222

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 55/217 (25%), Positives = 103/217 (47%), Gaps = 24/217 (11%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 4   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 63

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 64  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTREL 117

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +   
Sbjct: 118 QSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGT 174

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
            DG E+V        N+R +L + + VL+ RE++I +
Sbjct: 175 DDGFERV--------NQRMLLEKVLPVLDEREQKILQ 203


>gi|78043803|ref|YP_360778.1| RNA polymerase sigma-F factor [Carboxydothermus hydrogenoformans
           Z-2901]
 gi|77995918|gb|ABB14817.1| RNA polymerase sigma-F factor [Carboxydothermus hydrogenoformans
           Z-2901]
          Length = 257

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 61/261 (23%), Positives = 126/261 (48%), Gaps = 25/261 (9%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           + P L +QE   L ++  + GD++A  +L+  +L+LV K+   +   G  + ++   G I
Sbjct: 12  RFPRLGEQEIKELIEKA-QKGDVAAREKLINCNLKLVFKVVERFLHRGYEVEDLFQIGTI 70

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+ KFD ++  + +TY++  I   ++ + LR    ++I  +  +      ++ LK 
Sbjct: 71  GLIKAIDKFDLKQQVKFSTYAVPMIVGEIRRF-LRDDQAIRISRSTKE----LGVKILKE 125

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL---INSSDKNSSQWQ 201
             +A+T    +   +  + + L  S   ++     L   +SL +L   ++  D +     
Sbjct: 126 K-EALTVKLGREPTIAELEETLGYSREAIVEA---LEAGQSLASLFETVHQDDGDPIYLL 181

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
           D +  + D +EQ L+E        N+ +   +S L PRER I   R  +E   T   ++ 
Sbjct: 182 DQIKQEGD-EEQTLLE--------NISIKEVLSKLEPRERYILINRFFKEK--TQMEIAR 230

Query: 261 EFEVSRERVRQIEARAFKKVQ 281
              +S+ +V ++E +A  K++
Sbjct: 231 TLGISQVQVSRLERQALLKLK 251


>gi|297812573|ref|XP_002874170.1| hypothetical protein ARALYDRAFT_489269 [Arabidopsis lyrata subsp.
           lyrata]
 gi|297320007|gb|EFH50429.1| hypothetical protein ARALYDRAFT_489269 [Arabidopsis lyrata subsp.
           lyrata]
          Length = 517

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 58/253 (22%), Positives = 111/253 (43%), Gaps = 45/253 (17%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           +A ++L+  +LRLV+ +   Y      G    ++   G  GL+ A+ +F+P+R FRL+TY
Sbjct: 278 AARNKLIKHNLRLVLFVMNKYFHDFTNGPKFQDLCQAGMRGLITAIDRFEPKRKFRLSTY 337

Query: 105 SMWWIKAAMQEYILRSWSL------------VKIGTTANQKRLFFNLRRLKGHLQAITDN 152
            ++WI+ A    I+RS +             V++     +  L F L RL    + +   
Sbjct: 338 GLFWIRHA----IIRSMTTSNFTRVPFGLESVRVEIFKTKTELLFELGRLPTEDEVVERL 393

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCR--LAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
            + PE+   + +    +   V+S+N +  +  +E +N + +          D +  ++  
Sbjct: 394 KITPERYREVLR----AAKPVLSLNSKHSVTQEEFINGITDV---------DGVGANNSR 440

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRER 268
           Q  +L         R  L   +  L P+E  +   R   +     TL  ++    +SRE 
Sbjct: 441 QPALL---------RLALDDVLDSLKPKESLVIRQRYGLDGKGDRTLGEIAGNLNISREM 491

Query: 269 VRQIEARAFKKVQ 281
           VR+ E +A  K++
Sbjct: 492 VRKHEVKALMKLK 504


>gi|161898841|gb|ABX80410.1| SigB [Listeria monocytogenes]
          Length = 234

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 55/217 (25%), Positives = 103/217 (47%), Gaps = 24/217 (11%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 3   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 62

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 63  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVKELTREL 116

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +   
Sbjct: 117 QSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGT 173

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
            DG E+V        N+R +L + + VL+ RE++I +
Sbjct: 174 DDGFERV--------NQRMLLEKVLPVLDEREQKILQ 202


>gi|159037890|ref|YP_001537143.1| anti-sigma-factor antagonist [Salinispora arenicola CNS-205]
 gi|157916725|gb|ABV98152.1| anti-sigma-factor antagonist [Salinispora arenicola CNS-205]
          Length = 374

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 64/248 (25%), Positives = 114/248 (45%), Gaps = 25/248 (10%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV   L    ++A  YRG G P+ ++     +GL+ AV ++DPERG   A  ++  +   
Sbjct: 46  LVRFALPFAGRLARRYRGRGEPLEDLEQVARLGLVNAVDRYDPERGSFTAYAAITIVGEI 105

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
            + +  R+W  V +      +RL   +  +     A+T    +   V  +A++L   E E
Sbjct: 106 KRHFRDRTWG-VHV-----PRRLRDLILEVGQATAALTSELSRAPTVAELARRLETPEEE 159

Query: 173 VISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           +++     AG    SLNA +    ++S+++ D +    +  E V    ++R     +L R
Sbjct: 160 ILAALESAAGYSPASLNAPVGG--ESSAEFGDLVGESDNALESV----DDRVTVSGLLHR 213

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
               L  RERRI  A R   N    E +++ F +S+  V ++ +RA   +     +Q  L
Sbjct: 214 ----LPWRERRIL-AMRFYGNQTQAE-IAARFGISQMHVSRLLSRALTWL-----RQAML 262

Query: 291 SSSPPLLQ 298
           + +PP  Q
Sbjct: 263 ADAPPPWQ 270


>gi|188011915|gb|ACD45254.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
          Length = 221

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 55/217 (25%), Positives = 103/217 (47%), Gaps = 24/217 (11%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 3   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 62

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 63  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTREL 116

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +   
Sbjct: 117 QSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGT 173

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
            DG E+V        N+R +L + + VL+ RE++I +
Sbjct: 174 DDGFERV--------NQRMLLEKVLPVLDEREQKILQ 202


>gi|188011897|gb|ACD45245.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011901|gb|ACD45247.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|307717586|gb|ADN88846.1| RNA polymerase sigma-37 factor [Listeria seeligeri]
 gi|307717610|gb|ADN88858.1| RNA polymerase sigma-37 factor [Listeria seeligeri]
 gi|307717630|gb|ADN88868.1| RNA polymerase sigma-37 factor [Listeria seeligeri]
 gi|307717636|gb|ADN88871.1| RNA polymerase sigma-37 factor [Listeria ivanovii subsp. ivanovii]
 gi|307717638|gb|ADN88872.1| RNA polymerase sigma-37 factor [Listeria ivanovii subsp.
           londoniensis]
 gi|307717646|gb|ADN88876.1| RNA polymerase sigma-37 factor [Listeria ivanovii subsp. ivanovii]
          Length = 220

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 55/217 (25%), Positives = 103/217 (47%), Gaps = 24/217 (11%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTREL 115

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +   
Sbjct: 116 QSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGT 172

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
            DG E+V        N+R +L + + VL+ RE++I +
Sbjct: 173 DDGFERV--------NQRMLLEKVLPVLDEREQKILQ 201


>gi|253578603|ref|ZP_04855875.1| sporulation sigma factor SigE [Ruminococcus sp. 5_1_39B_FAA]
 gi|251850921|gb|EES78879.1| sporulation sigma factor SigE [Ruminococcus sp. 5_1_39BFAA]
          Length = 238

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 34/120 (28%), Positives = 62/120 (51%), Gaps = 9/120 (7%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           MNR      + G        +++   P+  K+E ++L K      +  A   L+  +LRL
Sbjct: 16  MNRSGEVFYIGG--------NDVLPAPLEPKREAFILQKLGTGQEE-EAKSVLIEHNLRL 66

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  +   G+ + +++S G IGL++A+  F+P +  +LATY+   I+  +  Y+ R+
Sbjct: 67  VVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFNPVKNIKLATYASRCIENEILMYLRRN 126


>gi|261407955|ref|YP_003244196.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Paenibacillus sp.
           Y412MC10]
 gi|329929288|ref|ZP_08283041.1| RNA polymerase sigma factor, FliA/WhiG family [Paenibacillus sp.
           HGF5]
 gi|261284418|gb|ACX66389.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Paenibacillus sp.
           Y412MC10]
 gi|328936657|gb|EGG33100.1| RNA polymerase sigma factor, FliA/WhiG family [Paenibacillus sp.
           HGF5]
          Length = 262

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 60/270 (22%), Positives = 123/270 (45%), Gaps = 50/270 (18%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQAVKKFDPE 96
           ++E GD  A  +L+  HL +V  ++      GLP +    ++ S G +GL+ A++KFD +
Sbjct: 18  WKEDGDHEAKKKLIEYHLHIVDYVS-SRLAIGLPKNVSKGDLASNGVMGLIDAIEKFDYK 76

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL-KGHLQAITDNNLK 155
           RG +  TY+ W ++ A+ +  LR    V        K++    ++L + +L++++D+ + 
Sbjct: 77  RGLQFETYASWRVRGAILDS-LRQGDWVPRSVREKAKKIETAYQQLEQKYLRSVSDSEM- 134

Query: 156 PEQVVAIAKKLNVSESE------------VISMNCRLAGDES---LNALINSSDKNSSQW 200
                  +  L+V+E E            + S+   +  +ES   ++ L++   KN    
Sbjct: 135 -------SDYLDVTEKEFRHMLQEVAVMTLTSLEDPIREEESETRMSLLVDEKAKNP--- 184

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
                 DH   E  L         R  L + +  L P+ER +     L    ++L  ++ 
Sbjct: 185 ------DHKVHEFYL---------REALMKGIGKLTPKERTVVSL--LYYEDLSLSEIAE 227

Query: 261 EFEVSRERVRQIEARAFKKVQESIQKQVEL 290
              +S  R+ Q+ ++A  +++ ++ K  +L
Sbjct: 228 VMSLSPSRISQLHSKAILRLRGALDKDRDL 257


>gi|312135825|ref|YP_004003163.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|311775876|gb|ADQ05363.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor owensensis OL]
          Length = 246

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 61/261 (23%), Positives = 125/261 (47%), Gaps = 21/261 (8%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG----YRGYGLPISEVVSEGNIGLMQ 88
           +E +L +++ +  D     +L+  ++ LV K+  G    Y G  +   ++VS G+IGL+ 
Sbjct: 2   DEALLWEKFIKTKDQKIKEQLIIKYMPLV-KLVAGRMAIYFGGNVEYDDLVSYGSIGLLD 60

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++KFD ++G +  TY+   I+ A+ + + RS   +        K +      ++   + 
Sbjct: 61  AIEKFDSQKGVKFETYAYTRIRGAIIDCV-RSQDFLPRSIRQKAKEIEKAYIEIEREGRT 119

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
            TD          +AK+L +S SE+  +  +++    +   + S  + S + +   + D 
Sbjct: 120 PTDYE--------VAKRLGISISELQKLQEKISS--GMIVSLESFLEQSYESKIGGLEDF 169

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
             Q +  IE EE K   N+L + +  L   ER +      +E  ++++ ++    +S  R
Sbjct: 170 VSQPEHFIENEELK---NVLRQQIDNLMENERMVIMLYYYEE--LSIKEIAKILGISESR 224

Query: 269 VRQIEARAFKKVQESIQKQVE 289
           V Q+  RA  K++ ++QK +E
Sbjct: 225 VSQLHTRALLKLRSALQKYLE 245


>gi|310815187|ref|YP_003963151.1| RNA polymerase, sigma 32 subunit, RpoH [Ketogulonicigenium vulgare
           Y25]
 gi|308753922|gb|ADO41851.1| RNA polymerase, sigma 32 subunit, RpoH [Ketogulonicigenium vulgare
           Y25]
          Length = 809

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 58/245 (23%), Positives = 111/245 (45%), Gaps = 27/245 (11%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           SA   L+  HL  V + A      G    +V     +GL ++ ++FDPERG+R   Y+ +
Sbjct: 579 SATEHLIREHLPYVRRFASRNVDEGEDPEDVFQVAFMGLQRSTRRFDPERGYRFLIYATY 638

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQK--RLFFNLRRLKGHL-QAITDNNLKPEQVVAIAK 164
           W++ A+  +     + ++I    N+K  +L   L RL   +  A++D        + +A+
Sbjct: 639 WMRQAITRWRADEGAAIRIPVHRNEKITKLDRALERLDVRVGGAVSD--------LELAE 690

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L  +  EV      +  +    A ++  D    +  +  V+D    E++L +       
Sbjct: 691 ELEWTIDEVKQFRG-IPREAEYPASLDDWDNLLPEPSEADVFDQTETERILAD------- 742

Query: 225 RNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
                 +++ L  R+  +   R    +E  +TLE +   + V+RER+RQIEA+A   +  
Sbjct: 743 ------ALAELPERQADVLRMRFGIGRETDMTLEEVGQIYGVTRERIRQIEAKALDHLSH 796

Query: 283 SIQKQ 287
             +K+
Sbjct: 797 PGRKR 801


>gi|238916778|ref|YP_002930295.1| phosphatidylserine decarboxylase [Eubacterium eligens ATCC 27750]
 gi|238872138|gb|ACR71848.1| phosphatidylserine decarboxylase [Eubacterium eligens ATCC 27750]
          Length = 252

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 53/225 (23%), Positives = 103/225 (45%), Gaps = 18/225 (8%)

Query: 61  VVKIAMG----YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           +VK+  G    Y GY +   ++V  G  GL+ A+ KFD  +  +  TY+   I+ A+ + 
Sbjct: 32  LVKLVAGRLNMYLGYNVEYDDLVGYGIFGLIDAIDKFDYGKNVKFETYASLRIRGAILDQ 91

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
           I R    +       QKR+   + +++     I  +         +A +L +++ E+   
Sbjct: 92  I-RKMDWIPRSLRQKQKRIEAAMTKIESETGHIASDE-------ELAAELGITQDELSDW 143

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
             ++    +L +L   ++  S    + +   H  Q +  +EKEE K    M+ +++  L 
Sbjct: 144 QGKMKA-SNLISLDEYTEAGSEVKMESVGNSHFDQPEDAMEKEELK---KMMVKAIDSLT 199

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +ER +      +E  +TL+ +S   EVS  RV Q+  +A  K++
Sbjct: 200 EKERSVVVLYYYEE--MTLKEISLTLEVSESRVSQLHTKALNKMK 242


>gi|261366886|ref|ZP_05979769.1| RNA polymerase sigma-E factor [Subdoligranulum variabile DSM 15176]
 gi|282571000|gb|EFB76535.1| RNA polymerase sigma-E factor [Subdoligranulum variabile DSM 15176]
          Length = 237

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 33/94 (35%), Positives = 52/94 (55%), Gaps = 2/94 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  +QE+  L       G  SA   L+T +LRLVV IA  +      I +++S G IGL
Sbjct: 36  PLDPQQEQQALEGLSAGKG--SARDLLITHNLRLVVYIAKKFETPSAGIEDMISIGTIGL 93

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++AV  F+P +  +LATY+   I+  +  Y+ +S
Sbjct: 94  IKAVNTFEPSKNIKLATYASRCIENEILMYLRKS 127


>gi|254729575|ref|YP_003084257.1| RNAP sigma factor [Cyanophage PSS2]
 gi|254211727|gb|ACT65675.1| RNAP sigma factor [Cyanophage PSS2]
 gi|265524923|gb|ACY75815.1| predicted protein [Cyanophage PSS2]
          Length = 284

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 33/92 (35%), Positives = 49/92 (53%), Gaps = 4/92 (4%)

Query: 48  SAAHRLVTSHLRLVVKI-AMGYRGYGLPIS---EVVSEGNIGLMQAVKKFDPERGFRLAT 103
           +A  R+V  +LRLV  I    Y    +  +   E++ EG IGL  A  +FDP  G+R +T
Sbjct: 43  AALQRIVKGNLRLVAAIWKKRYLKRNIAPAHSLEILQEGAIGLNDAAMRFDPSSGYRFST 102

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++ WWI  +M+EY   S  LV+     + K L
Sbjct: 103 FASWWIIKSMKEYQRDSERLVRFKGDMHWKAL 134


>gi|260439092|ref|ZP_05792908.1| RNA polymerase sigma-F factor [Butyrivibrio crossotus DSM 2876]
 gi|292808404|gb|EFF67609.1| RNA polymerase sigma-F factor [Butyrivibrio crossotus DSM 2876]
          Length = 241

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 55/214 (25%), Positives = 92/214 (42%), Gaps = 24/214 (11%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           G+  A   LV  ++ LV  IA  +   G  + ++VS G IGL++A+ KFD      L+TY
Sbjct: 14  GNKEARDMLVMHNMGLVYSIAKRFANRGYEMDDIVSIGTIGLIKAIDKFDLNMDVMLSTY 73

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-AIA 163
           ++  I   ++ +I R   ++KI  +  +    + + + K +L       LK E  +  I+
Sbjct: 74  AVPMISGEIKRFI-RDDGIIKISRSIKENG--WKINQAKDYLS----QKLKREVTIEEIS 126

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY-----DHDGQEQVLIEK 218
           K+  +   +++         ES+   I  SD N     D L       DHD         
Sbjct: 127 KETGICTEDIVVAMEASKDVESIYQTIYQSDGNQIYVVDKLAASAKESDHD--------- 177

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
             +     ML  +M++L   E+ I E R  QE  
Sbjct: 178 --KIMNHVMLEETMNILEKDEKTIIEMRYFQEKT 209


>gi|288572993|ref|ZP_06391350.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Dethiosulfovibrio peptidovorans DSM 11002]
 gi|288568734|gb|EFC90291.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Dethiosulfovibrio peptidovorans DSM 11002]
          Length = 189

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 41/77 (53%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E GD SA   L+ ++  LV  IA  +   G    +++ EG + L++ +  FDP RGFR  
Sbjct: 19  EDGDPSAREDLILAYRPLVFWIAKKFNVGGDIYPDLIQEGMMALIKGIDSFDPSRGFRFT 78

Query: 103 TYSMWWIKAAMQEYILR 119
           TY  + I+  M  Y+ R
Sbjct: 79  TYGYYRIRGQMLNYLQR 95


>gi|211906943|gb|ACJ11990.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|211906945|gb|ACJ11991.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|211906947|gb|ACJ11992.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|211906949|gb|ACJ11993.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
          Length = 222

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 55/217 (25%), Positives = 103/217 (47%), Gaps = 24/217 (11%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 4   YIWIAAYQENGDEDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 63

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 64  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTREL 117

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +   
Sbjct: 118 QSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGT 174

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
            DG E+V        N+R +L + + VL+ RE++I +
Sbjct: 175 DDGFERV--------NQRMLLEKVLPVLDEREQKILQ 203


>gi|161898881|gb|ABX80430.1| SigB [Listeria monocytogenes]
 gi|161898907|gb|ABX80443.1| SigB [Listeria monocytogenes]
          Length = 233

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 60/247 (24%), Positives = 118/247 (47%), Gaps = 26/247 (10%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D   G  
Sbjct: 5   YQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKS 64

Query: 101 LATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
              +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T       Q+
Sbjct: 65  FEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTRELQSSPQI 118

Query: 160 VAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
             IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +    DG E+
Sbjct: 119 SDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTDDGFER 175

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
           V        N+R +L + + VL+ RE++I +   ++    + +      ++S+  V +I+
Sbjct: 176 V--------NQRMLLEKVLPVLDEREQKILQYTFIENR--SQKETGELLDISQMHVSRIQ 225

Query: 274 ARAFKKV 280
            +A KK+
Sbjct: 226 RQAIKKL 232


>gi|167636574|ref|ZP_02394868.1| RNA polymerase sigma-G factor (Stage III sporulation protein G)
           [Bacillus anthracis str. A0442]
 gi|167527997|gb|EDR90803.1| RNA polymerase sigma-G factor (Stage III sporulation protein G)
           [Bacillus anthracis str. A0442]
          Length = 211

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 40/152 (26%), Positives = 80/152 (52%), Gaps = 11/152 (7%)

Query: 25  KIPMLEKQEEYVLAKRYRE--HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           K+P+L+  E   + K +RE   G++SA  +LV  +LRLV+ +   +   G  + ++   G
Sbjct: 15  KLPVLKNDE---MRKLFREMQSGEISAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVG 71

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            IGLM+++  FD  +  + +TY++  I   ++ Y LR  + +++  +          + L
Sbjct: 72  CIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSLRD----IAYKAL 126

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVI 174
           +   + I +N+ +P   + IAK L V+  E++
Sbjct: 127 QVREKLIAENSKEP-TAMDIAKVLEVTHEEIV 157


>gi|291538695|emb|CBL11806.1| RNA polymerase, sigma subunit, RpsG/SigG [Roseburia intestinalis
           XB6B4]
          Length = 259

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/93 (27%), Positives = 54/93 (58%), Gaps = 1/93 (1%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+++E+  L  R ++ GD +A    +  +LRLV+ +   + G    + ++   G I
Sbjct: 15  KLPILKEEEKDALFARIKQ-GDTAARETYIKGNLRLVLSVIKRFSGNHENVDDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           GL++++  FDP  G + +TY++  I   ++ Y+
Sbjct: 74  GLIKSIDNFDPTIGVKFSTYAVPMIIGEIRRYL 106


>gi|114566068|ref|YP_753222.1| sporulation sigma factor SigK [Syntrophomonas wolfei subsp. wolfei
           str. Goettingen]
 gi|114337003|gb|ABI67851.1| sigma 28 (flagella/sporulation) [Syntrophomonas wolfei subsp.
           wolfei str. Goettingen]
          Length = 244

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 33/102 (32%), Positives = 57/102 (55%), Gaps = 3/102 (2%)

Query: 9   IVNGEIGLSRYIH-EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           I+ G + L  Y++ ++   P+ E+ E   L +  R  G   A + L+  +LRLV  +   
Sbjct: 13  ILKGSLCLFAYLNNQVFPQPLSEEDERKCLQEMQR--GGEEARNILIEHNLRLVAHVVKK 70

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           Y   G  + +++S G IGL++A++ ++ ERG RLATY+   I
Sbjct: 71  YESSGEDLEDLISIGTIGLIKAIRTYNFERGVRLATYAARCI 112


>gi|154485092|ref|ZP_02027540.1| hypothetical protein EUBVEN_02815 [Eubacterium ventriosum ATCC
           27560]
 gi|149734045|gb|EDM50164.1| hypothetical protein EUBVEN_02815 [Eubacterium ventriosum ATCC
           27560]
          Length = 244

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/79 (32%), Positives = 45/79 (56%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           K   E+ D  A   L+  +LRLVV IA  +   G+ + +++S G IGL++ +  F P++ 
Sbjct: 51  KNLIENNDEEAKSMLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKGINTFKPDKN 110

Query: 99  FRLATYSMWWIKAAMQEYI 117
            +LATY+   I+  +  Y+
Sbjct: 111 IKLATYASRCIENEILMYL 129


>gi|309778067|ref|ZP_07673006.1| RNA polymerase sigma-G factor [Erysipelotrichaceae bacterium
           3_1_53]
 gi|308914161|gb|EFP59962.1| RNA polymerase sigma-G factor [Erysipelotrichaceae bacterium
           3_1_53]
          Length = 259

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 56/242 (23%), Positives = 114/242 (47%), Gaps = 30/242 (12%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A   L+  +L+LV+ I   +      + ++   G IGL++++  FD +   R +
Sbjct: 32  QQGDEQAKETLINGNLKLVLSIVQRFSNRCENMDDLFQVGCIGLVKSIDNFDLKHEVRFS 91

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I   ++ Y LR   ++++  + + K L +   +LK   +     N K   +  +
Sbjct: 92  TYAVPMIMGEIKRY-LRDNQVIRV--SRHLKDLAYRAFKLK---EEYVHKNQKEPTIAWL 145

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI-----E 217
           A++L V E +++     L   +S+ ++               VY+ DG E  L+     +
Sbjct: 146 AEQLEVKEKDIVDA---LDSTQSVLSIFEP------------VYNSDGDELFLLDQIKDD 190

Query: 218 KEERKNRRNM--LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
           K+E ++  N+  L RS+  L  +E  I + R  Q+  +T   ++ E  +S+ +V ++E  
Sbjct: 191 KDEIEHLNNIMALKRSLKRLKGKELDIIQKRYYQD--MTQTEIAGELGISQAQVSRLEKN 248

Query: 276 AF 277
           A 
Sbjct: 249 AI 250


>gi|302389688|ref|YP_003825509.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermosediminibacter oceani DSM 16646]
 gi|302200316|gb|ADL07886.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermosediminibacter oceani DSM 16646]
          Length = 245

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 68/257 (26%), Positives = 123/257 (47%), Gaps = 40/257 (15%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPE 96
           Y+  GD +   RL+  ++ LV  IA       LP      ++VS G IGL+QA++++D  
Sbjct: 14  YKNTGDSNLKERLIEEYIPLVKHIA-ARLAINLPPCVDYDDLVSAGIIGLLQAIERYDVG 72

Query: 97  RGFRLATYSMWWIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           +G R  T++   I+ AM + + R +W   K   T  + +L   L+     ++   + N+K
Sbjct: 73  KGVRFETFAYTRIRGAMLDELRRLNWIPQK---TMEKAKL---LQDAYSQMEQELNGNVK 126

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
            E    IA+KLN++ +E+      LA       L++  +  S   +D      +G+    
Sbjct: 127 DED---IARKLNITIAELHQTYKELAA----TNLVSLEEIFSVAVED------NGEPVSH 173

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRI-----FEARRLQENPVTLENLSSEFEVSRERVR 270
           +EKEE K    +L  ++  L P+E+ +     +E   L+E  V L NLS        R+ 
Sbjct: 174 VEKEEIK---RILGEAIDRLPPKEKLVIALYYYEGLNLKEISVVL-NLSP------ARIS 223

Query: 271 QIEARAFKKVQESIQKQ 287
           Q+  +A  +++ S+ ++
Sbjct: 224 QLHTKAILRLRGSLSRK 240


>gi|148380599|ref|YP_001255140.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum A str. ATCC 3502]
 gi|153931945|ref|YP_001384886.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum A str. ATCC 19397]
 gi|153937160|ref|YP_001388355.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum A str. Hall]
 gi|168182725|ref|ZP_02617389.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum Bf]
 gi|170754752|ref|YP_001782258.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum B1 str. Okra]
 gi|226950054|ref|YP_002805145.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum A2 str. Kyoto]
 gi|237796081|ref|YP_002863633.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum Ba4 str. 657]
 gi|148290083|emb|CAL84202.1| RNA polymerase sigma factor [Clostridium botulinum A str. ATCC
           3502]
 gi|152927989|gb|ABS33489.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum A str. ATCC 19397]
 gi|152933074|gb|ABS38573.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum A str. Hall]
 gi|169119964|gb|ACA43800.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum B1 str. Okra]
 gi|182674219|gb|EDT86180.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum Bf]
 gi|226840945|gb|ACO83611.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum A2 str. Kyoto]
 gi|229261699|gb|ACQ52732.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum Ba4 str. 657]
          Length = 242

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 65/249 (26%), Positives = 115/249 (46%), Gaps = 23/249 (9%)

Query: 45  GDLSAAHRLVTSHLRLVVKIA----MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
            +L     +V  ++ LV  IA    +G   Y +   ++VS G IGLM A+ KFD  +G +
Sbjct: 6   NNLYVKEEIVKKYIPLVKYIASRVIIGKTKY-IEYEDLVSYGMIGLMDALNKFDESKGMK 64

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+   IK +M + + R+  + K G      R    + +L+  L        K   ++
Sbjct: 65  FSTYASIRIKGSMIDELRRNSPISK-GAMDKLNRYNEAIEKLQKKLN-------KEPNLI 116

Query: 161 AIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            IA +LN+S  EV  I          SL  LI SS+         L+     ++    EK
Sbjct: 117 QIADELNISLKEVSEIENYINYISVISLEDLIFSSEDEVP-----LIGTIKDEKSPSPEK 171

Query: 219 EERKNRR-NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
              +N + + L +++ +LN ++R +      +E  +TL+ +     VS  RV Q+ +RA 
Sbjct: 172 HVEENEQLDYLAKAIELLNEKDRLVVTLYYYEE--LTLKEIGKILNVSESRVCQLHSRAI 229

Query: 278 KKVQESIQK 286
             +++++ K
Sbjct: 230 IHLKKAMAK 238


>gi|134300227|ref|YP_001113723.1| FliA/WhiG family RNA polymerase sigma factor [Desulfotomaculum
           reducens MI-1]
 gi|134052927|gb|ABO50898.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Desulfotomaculum
           reducens MI-1]
          Length = 251

 Score = 54.3 bits (129), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 70/268 (26%), Positives = 122/268 (45%), Gaps = 44/268 (16%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVK 91
           +L ++Y    D  A  +++  HL LV  +A G     LP      ++ S G IGLM+A+ 
Sbjct: 5   LLWEKYITLRDPEARQKIILLHLPLVKHLA-GRVAVKLPSFILREDLESYGVIGLMEALD 63

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR-RLKGHLQAIT 150
           K+DP  G    +Y+   I+ AM + + R   L +     NQ  L  N R RL+     + 
Sbjct: 64  KYDPAMGHSFDSYAYHRIRGAMLDEVRRQNWLPRTAWQKNQ--LLKNTRERLEREQGEVI 121

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
            N +       +AK++ +   EV               LI +++K   Q  D  V  HDG
Sbjct: 122 TNEV-------LAKEMGIPVEEV-------------RQLIFNANKMYIQSLDEEVAGHDG 161

Query: 211 QEQVLIE-------------KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
            +   +E              EE++++R +L  ++  L+ RE+ I  A    E  +TL+ 
Sbjct: 162 SQMSKLELLEDTNSPDPLSIVEEKESKR-LLAEAIETLSEREKLIL-ALYYSEG-LTLKE 218

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQ 285
           +    EVS  RV Q+ ++  K+++++++
Sbjct: 219 IGQVLEVSESRVCQLHSQVMKRLKKTLE 246


>gi|291536437|emb|CBL09549.1| RNA polymerase, sigma subunit, RpsG/SigG [Roseburia intestinalis
           M50/1]
          Length = 259

 Score = 53.9 bits (128), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 26/93 (27%), Positives = 54/93 (58%), Gaps = 1/93 (1%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+++E+  L  R ++ GD +A    +  +LRLV+ +   + G    + ++   G I
Sbjct: 15  KLPILKEEEKDALFARIKQ-GDTAARETYIKGNLRLVLSVIKRFSGNHENVDDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           GL++++  FDP  G + +TY++  I   ++ Y+
Sbjct: 74  GLIKSIDNFDPTIGVKFSTYAVPMIIGEIRRYL 106


>gi|161898837|gb|ABX80408.1| SigB [Listeria monocytogenes]
          Length = 236

 Score = 53.9 bits (128), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 55/217 (25%), Positives = 103/217 (47%), Gaps = 24/217 (11%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 3   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 62

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 63  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVKELTREL 116

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +   
Sbjct: 117 QSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGT 173

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
            DG E+V        N+R +L + + VL+ RE++I +
Sbjct: 174 DDGFERV--------NQRMLLEKVLPVLDEREQKILQ 202


>gi|293376227|ref|ZP_06622470.1| RNA polymerase sigma-E factor [Turicibacter sanguinis PC909]
 gi|325845158|ref|ZP_08168467.1| RNA polymerase sigma-E factor [Turicibacter sp. HGF1]
 gi|292645119|gb|EFF63186.1| RNA polymerase sigma-E factor [Turicibacter sanguinis PC909]
 gi|325488823|gb|EGC91223.1| RNA polymerase sigma-E factor [Turicibacter sp. HGF1]
          Length = 236

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 31/93 (33%), Positives = 56/93 (60%), Gaps = 5/93 (5%)

Query: 17  SRYIHEIR---KIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           ++Y++ IR    +P  L K EE+ +  R+ + GD  A   L+  +LRLVV IA  +   G
Sbjct: 20  NKYVNYIRGNETLPEPLSKDEEFNVLTRF-QGGDERARQTLIEHNLRLVVYIAKKFESSG 78

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           + + +++S G +GL++ V+ F  ++  +LATY+
Sbjct: 79  VNLEDLISIGTLGLIKGVQTFKMDKNIKLATYA 111


>gi|160880817|ref|YP_001559785.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           phytofermentans ISDg]
 gi|160429483|gb|ABX43046.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           phytofermentans ISDg]
          Length = 254

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 56/248 (22%), Positives = 108/248 (43%), Gaps = 59/248 (23%)

Query: 61  VVKIAMG----YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           +VKI  G    Y GY +   ++V  G  GL+ A+ KFD E+G +  TY+   I+ A+ + 
Sbjct: 32  LVKIVAGRLSIYLGYNVEYDDLVGYGTFGLIDAIDKFDCEKGAKFETYASLRIRGAILDQ 91

Query: 117 ILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
           I +  W    I  T  QK+                             K+L+ +  ++ +
Sbjct: 92  IRKMDW----IPRTLRQKQ-----------------------------KRLDAAYQKLET 118

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDW-----LVYDHDGQEQVLIEKE----------- 219
           M  R A DE +   +  + +    WQ+      LV   +  EQ  ++ E           
Sbjct: 119 MYGRQATDEEVAKELEITTEELETWQNQTKISNLVSLDEYMEQGEVKVESIASEDYAQPE 178

Query: 220 ---ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
              E++  + ML +++  L  +E+++      ++  +TL+ +S+  EVS  R+ Q+  +A
Sbjct: 179 KVMEKQELKAMLVKALEYLTEKEKKVIVLYYYED--LTLKEISAVLEVSESRISQLHTKA 236

Query: 277 FKKVQESI 284
            +K+++ +
Sbjct: 237 LQKMRQKL 244


>gi|121534479|ref|ZP_01666302.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
 gi|121306972|gb|EAX47891.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
          Length = 234

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 29/85 (34%), Positives = 49/85 (57%), Gaps = 2/85 (2%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+ EK+E+  L +   + GD  A + L+  +LRLV  I   +   G  + +++S G IG
Sbjct: 30  LPLSEKEEQIYLERL--KAGDEKAKNVLIERNLRLVAHIVKKFDNTGEDVDDLISIGTIG 87

Query: 86  LMQAVKKFDPERGFRLATYSMWWIK 110
           L++A+  FD  +  RLATY+   I+
Sbjct: 88  LIKAINTFDQAKKIRLATYAARCIE 112


>gi|85679195|gb|ABC72014.1| SigB [Listeria monocytogenes]
 gi|85679205|gb|ABC72019.1| SigB [Listeria monocytogenes]
 gi|85679211|gb|ABC72022.1| SigB [Listeria monocytogenes]
 gi|85679213|gb|ABC72023.1| SigB [Listeria monocytogenes]
 gi|307717608|gb|ADN88857.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|307717616|gb|ADN88861.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
          Length = 220

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 55/217 (25%), Positives = 103/217 (47%), Gaps = 24/217 (11%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQENGDEDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTREL 115

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +   
Sbjct: 116 QSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGT 172

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
            DG E+V        N+R +L + + VL+ RE++I +
Sbjct: 173 DDGFERV--------NQRMLLEKVLPVLDEREQKILQ 201


>gi|240144182|ref|ZP_04742783.1| RNA polymerase sigma-G factor [Roseburia intestinalis L1-82]
 gi|257203785|gb|EEV02070.1| RNA polymerase sigma-G factor [Roseburia intestinalis L1-82]
          Length = 259

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 26/93 (27%), Positives = 54/93 (58%), Gaps = 1/93 (1%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+++E+  L  R ++ GD +A    +  +LRLV+ +   + G    + ++   G I
Sbjct: 15  KLPILKEEEKDALFARIKQ-GDTAARETYIKGNLRLVLSVIKRFSGNHENVDDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           GL++++  FDP  G + +TY++  I   ++ Y+
Sbjct: 74  GLIKSIDNFDPTIGVKFSTYAVPMIIGEIRRYL 106


>gi|78045111|ref|YP_359473.1| sporulation sigma factor SigK [Carboxydothermus hydrogenoformans
           Z-2901]
 gi|77997226|gb|ABB16125.1| RNA polymerase sigma-K factor [Carboxydothermus hydrogenoformans
           Z-2901]
          Length = 234

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 28/84 (33%), Positives = 47/84 (55%), Gaps = 2/84 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ E++E Y + +     GD  A   L   +LRLV  I   + G G    +++S G IGL
Sbjct: 30  PLSEEEEAYYIDRLL--QGDREARDVLAERNLRLVAHIVKKFEGTGEATEDLISIGTIGL 87

Query: 87  MQAVKKFDPERGFRLATYSMWWIK 110
           ++A+  F P++G +LATY+   ++
Sbjct: 88  IKAIDTFRPDKGTKLATYAAKCVE 111


>gi|161898895|gb|ABX80437.1| SigB [Listeria monocytogenes]
 gi|161898903|gb|ABX80441.1| SigB [Listeria monocytogenes]
          Length = 237

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 63/259 (24%), Positives = 119/259 (45%), Gaps = 38/259 (14%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 3   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 62

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWS------LVKIGTTANQKRLFFNLRRLKGHLQ 147
              G     +++  I   ++ ++  ++WS      + ++G   N       +  L   LQ
Sbjct: 63  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKINNA-----VEELTRELQ 117

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQ 201
           +         Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    
Sbjct: 118 S-------SPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLL 167

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           D +    DG E+V        N+R +L + + VL+ RE++I +   ++    + +     
Sbjct: 168 DVVGGTDDGFERV--------NQRMLLEKVLPVLDEREQKILQFTFIENR--SQKETGEL 217

Query: 262 FEVSRERVRQIEARAFKKV 280
            ++S+  V +I+ +A KK+
Sbjct: 218 LDISQMHVSRIQRQAIKKL 236


>gi|302386721|ref|YP_003822543.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           saccharolyticum WM1]
 gi|302197349|gb|ADL04920.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           saccharolyticum WM1]
          Length = 258

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 61/260 (23%), Positives = 117/260 (45%), Gaps = 23/260 (8%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L  +E+ VL KR   +GD  A    +  +LRLV+ +   + G    + ++   G I
Sbjct: 15  KLPLLSNEEKEVLFKRIL-NGDKKAREDYIKGNLRLVLSVIQRFSGSNENVDDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ---KRLFFNLRR 141
           GL++A+  FD  +  R +TY++  I   ++ Y LR  + +++  +      K ++     
Sbjct: 74  GLIKAIDNFDITQNVRFSTYAVPMILGEVRRY-LRDNNSIRVSRSLRDTAYKAIYAKENL 132

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           +K         NLK   ++ IA+++ VS+ ++      +    SL   + S   +     
Sbjct: 133 MK--------KNLKEPTLMEIAEEIGVSKEDITYALDAIQSPVSLYEPVYSDGGDPLFVM 184

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           D  + D    E+  +E          L  +M  L  RER I + R  +    T   ++ E
Sbjct: 185 DQ-ISDKKNLEENWVEDIS-------LNEAMRRLPERERHIIDMRFFEGKTQT--EVAEE 234

Query: 262 FEVSRERVRQIEARAFKKVQ 281
             +S+ +V ++E  A K ++
Sbjct: 235 IHISQAQVSRLEKNALKTMK 254


>gi|187935345|ref|YP_001885383.1| sporulation sigma factor SigK [Clostridium botulinum B str. Eklund
           17B]
 gi|187723498|gb|ACD24719.1| RNA polymerase sigma-K factor [Clostridium botulinum B str. Eklund
           17B]
          Length = 232

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 32/84 (38%), Positives = 49/84 (58%), Gaps = 2/84 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ E +EE  L KR ++ GD +A   L+  +LRLV  I   Y      + E++S G +GL
Sbjct: 30  PLNESEEEEYL-KRLKD-GDKTAKGVLIERNLRLVAHIVKKYSFPNKDVDELISIGTVGL 87

Query: 87  MQAVKKFDPERGFRLATYSMWWIK 110
           ++A+  FD  +G RLATY+   I+
Sbjct: 88  IKAIDSFDSGKGTRLATYASRCIE 111


>gi|15894966|ref|NP_348315.1| sporulation sigma factor SigK [Clostridium acetobutylicum ATCC 824]
 gi|15024653|gb|AAK79655.1|AE007679_1 DNA-dependent RNA polymerase sigma subunit [Clostridium
           acetobutylicum ATCC 824]
 gi|528974|gb|AAB94775.1| SigK [Clostridium acetobutylicum]
 gi|325509103|gb|ADZ20739.1| sporulation sigma factor SigK [Clostridium acetobutylicum EA 2018]
          Length = 234

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 30/83 (36%), Positives = 48/83 (57%), Gaps = 2/83 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ E +E+Y L K   + GD  A + L+  +LRLV  I   Y   G  + +++S G IGL
Sbjct: 30  PLSESEEKYYLKKL--KEGDPLAKNILIERNLRLVAHIVKKYSYSGKEVDDLISIGTIGL 87

Query: 87  MQAVKKFDPERGFRLATYSMWWI 109
           ++A+  ++  +G RLATY+   I
Sbjct: 88  IKAIDSYNVSKGTRLATYAARCI 110


>gi|307717596|gb|ADN88851.1| RNA polymerase sigma-37 factor [Listeria innocua]
 gi|307717598|gb|ADN88852.1| RNA polymerase sigma-37 factor [Listeria innocua]
 gi|307717600|gb|ADN88853.1| RNA polymerase sigma-37 factor [Listeria innocua]
 gi|307717602|gb|ADN88854.1| RNA polymerase sigma-37 factor [Listeria innocua]
          Length = 220

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 55/217 (25%), Positives = 103/217 (47%), Gaps = 24/217 (11%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQENGDEDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTREL 115

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +   
Sbjct: 116 QSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGT 172

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
            DG E+V        N+R +L + + VL+ RE++I +
Sbjct: 173 DDGFERV--------NQRMLLEKVLPVLDEREQKILQ 201


>gi|161898917|gb|ABX80448.1| SigB [Listeria monocytogenes]
          Length = 236

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 63/259 (24%), Positives = 119/259 (45%), Gaps = 38/259 (14%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 3   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 62

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWS------LVKIGTTANQKRLFFNLRRLKGHLQ 147
              G     +++  I   ++ ++  ++WS      + ++G   N       +  L   LQ
Sbjct: 63  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELGPKINNA-----VEELTRELQ 117

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQ 201
           +         Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    
Sbjct: 118 S-------SPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLL 167

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           D +    DG E+V        N+R +L + + VL+ RE++I +   ++    + +     
Sbjct: 168 DVVGGTDDGFERV--------NQRMLLEKVLPVLDEREQKILQFTFIENR--SQKETGEL 217

Query: 262 FEVSRERVRQIEARAFKKV 280
            ++S+  V +I+ +A KK+
Sbjct: 218 LDISQMHVSRIQRQAIKKL 236


>gi|307717640|gb|ADN88873.1| RNA polymerase sigma-37 factor [Listeria ivanovii subsp. ivanovii]
          Length = 220

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 55/217 (25%), Positives = 103/217 (47%), Gaps = 24/217 (11%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTREL 115

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +   
Sbjct: 116 QSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGT 172

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
            DG E+V        N+R +L + + VL+ RE++I +
Sbjct: 173 DDGFERV--------NQRMLLEKVLPVLDEREQKILQ 201


>gi|251780405|ref|ZP_04823325.1| RNA polymerase sigma-K factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
 gi|243084720|gb|EES50610.1| RNA polymerase sigma-K factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
          Length = 232

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 32/83 (38%), Positives = 48/83 (57%), Gaps = 2/83 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ E +EE  L KR ++ GD +A   L+  +LRLV  I   Y      + E++S G +GL
Sbjct: 30  PLNESEEEEYL-KRLKD-GDKTAKGVLIERNLRLVAHIVKKYSFPNKDVDELISIGTVGL 87

Query: 87  MQAVKKFDPERGFRLATYSMWWI 109
           ++A+  FD  +G RLATY+   I
Sbjct: 88  IKAIDSFDSGKGTRLATYASRCI 110


>gi|160914280|ref|ZP_02076501.1| hypothetical protein EUBDOL_00290 [Eubacterium dolichum DSM 3991]
 gi|158433907|gb|EDP12196.1| hypothetical protein EUBDOL_00290 [Eubacterium dolichum DSM 3991]
          Length = 233

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 66/260 (25%), Positives = 111/260 (42%), Gaps = 62/260 (23%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           LEK+EE   A    EHGD  A + L+  +LRLVV IA  Y    + + +++S G+IGL++
Sbjct: 33  LEKEEEQA-ALIALEHGDEEARNTLIEHNLRLVVYIAKRYETNPIFMEDLISIGSIGLIK 91

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           AV  F   +  +L TY+   I+  +  + LR  S                          
Sbjct: 92  AVNTFKRNKNIKLVTYASRCIENEILMF-LRKKS-------------------------- 124

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                          +KL VS             DE LN      D N     D L  D 
Sbjct: 125 --------------RRKLEVS------------FDEPLNI---DYDGNELLLSDILGTDD 155

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPVTLENLSSEFEVSRE 267
           D    V+ ++ ER+  +  L ++M  L  RER+I + R  ++   +T ++++    +S+ 
Sbjct: 156 D----VVTKQFEREENKRELLKAMRGLKDRERQILQMRYGIEHEELTQKDIAKRLGISQS 211

Query: 268 RVRQIEARAFKKVQESIQKQ 287
            + ++E R   K++  +++Q
Sbjct: 212 YISRLEKRIIHKLKLQMKQQ 231


>gi|260438830|ref|ZP_05792646.1| RNA polymerase sigma-E factor [Butyrivibrio crossotus DSM 2876]
 gi|292808820|gb|EFF68025.1| RNA polymerase sigma-E factor [Butyrivibrio crossotus DSM 2876]
          Length = 246

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 31/94 (32%), Positives = 53/94 (56%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+   +E  V+A    E+ D  A   L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 42  PLEPAEEAEVIADLGTEY-DTKAKTMLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGL 100

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++A+  FD  +  +LATY+   I+  +  Y+ R+
Sbjct: 101 IKAINSFDINKKIKLATYASRCIENEILMYLRRN 134


>gi|148380489|ref|YP_001255030.1| RNA polymerase sigma-G factor [Clostridium botulinum A str. ATCC
           3502]
 gi|153933176|ref|YP_001384712.1| sporulation sigma factor SigG [Clostridium botulinum A str. ATCC
           19397]
 gi|153936833|ref|YP_001388233.1| sporulation sigma factor SigG [Clostridium botulinum A str. Hall]
 gi|153938804|ref|YP_001391829.1| sporulation sigma factor SigG [Clostridium botulinum F str.
           Langeland]
 gi|148289973|emb|CAL84086.1| RNA polymerase sigma-G factor [Clostridium botulinum A str. ATCC
           3502]
 gi|152929220|gb|ABS34720.1| RNA polymerase sigma-G factor [Clostridium botulinum A str. ATCC
           19397]
 gi|152932747|gb|ABS38246.1| RNA polymerase sigma-G factor [Clostridium botulinum A str. Hall]
 gi|152934700|gb|ABS40198.1| RNA polymerase sigma-G factor [Clostridium botulinum F str.
           Langeland]
 gi|295319855|gb|ADG00233.1| RNA polymerase sigma-G factor [Clostridium botulinum F str. 230613]
 gi|322806802|emb|CBZ04371.1| RNA polymerase sporulation specific sigma factor SigG [Clostridium
           botulinum H04402 065]
          Length = 257

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 62/279 (22%), Positives = 127/279 (45%), Gaps = 55/279 (19%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+ +E   L  R R +G+       +  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKDKEMKKLLVRIR-NGETECREEFIQGNLRLVLSVIKRFNNRGENVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD  +  + +TY++  I   ++ Y LR  + +++  +          + L+ 
Sbjct: 74  GLIKAIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNSIRVSRSLRD----IAYKALQA 128

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + I +NN +P  V  IAK+L +   EV+          +L+A+           QD +
Sbjct: 129 RDKLIKNNNKEP-TVSQIAKELELPREEVVF---------ALDAI-----------QDPV 167

Query: 205 -----VYDHDGQEQVLIEKEERKNRRNM---------LTRSMSVLNPRER-----RIFEA 245
                +Y HDG + + +  ++  + +N+         +  +M  LN RE+     R F+ 
Sbjct: 168 SLFEPIY-HDGGDAIFV-MDQISDTKNIDENWIENISIKEAMKKLNDREKLILNLRFFDG 225

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R   E       ++ E  +S+ +V ++E  A K +++ +
Sbjct: 226 RTQME-------VADEIGISQAQVSRLEKTALKHMRKYV 257


>gi|188588587|ref|YP_001920530.1| sporulation sigma factor SigK [Clostridium botulinum E3 str. Alaska
           E43]
 gi|188498868|gb|ACD52004.1| RNA polymerase sigma-K factor [Clostridium botulinum E3 str. Alaska
           E43]
          Length = 232

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 32/83 (38%), Positives = 48/83 (57%), Gaps = 2/83 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ E +EE  L KR ++ GD +A   L+  +LRLV  I   Y      + E++S G +GL
Sbjct: 30  PLNESEEEEYL-KRLKD-GDKTAKGVLIERNLRLVAHIVKKYSFPNKDVDELISIGTVGL 87

Query: 87  MQAVKKFDPERGFRLATYSMWWI 109
           ++A+  FD  +G RLATY+   I
Sbjct: 88  IKAIDSFDSGKGTRLATYASRCI 110


>gi|322806971|emb|CBZ04541.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           botulinum H04402 065]
          Length = 242

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 65/249 (26%), Positives = 115/249 (46%), Gaps = 23/249 (9%)

Query: 45  GDLSAAHRLVTSHLRLVVKIA----MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
            +L     +V  ++ LV  IA    +G   Y +   ++VS G IGLM A+ KFD  +G +
Sbjct: 6   NNLYVKEEIVKKYIPLVKYIASRVIIGKTKY-IEYEDLVSYGMIGLMDALNKFDESKGMK 64

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+   IK +M + + R+  + K G      R    + +L+  L        K   ++
Sbjct: 65  FSTYASIRIKGSMIDELRRNSPISK-GAMDKLNRYNEAIEKLQKKLN-------KEPNLI 116

Query: 161 AIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            IA +LN+S  EV  I          SL  LI SS+         L+     ++    EK
Sbjct: 117 QIADELNISLKEVSEIENYINYISVISLEDLIFSSEDEVP-----LIGTIKDEKSPSPEK 171

Query: 219 EERKNRR-NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
              +N + + L +++ +LN ++R +      +E  +TL+ +     VS  RV Q+ +RA 
Sbjct: 172 HVEENEQLDYLAKAIELLNEKDRLVVTLYYYEE--LTLKEIGKILNVSESRVCQLHSRAI 229

Query: 278 KKVQESIQK 286
             +++++ K
Sbjct: 230 IHLKKAMAK 238


>gi|311071144|ref|YP_003976067.1| RNA polymerase sigma factor SigB [Bacillus atrophaeus 1942]
 gi|310871661|gb|ADP35136.1| RNA polymerase sigma factor SigB [Bacillus atrophaeus 1942]
          Length = 262

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 68/268 (25%), Positives = 126/268 (47%), Gaps = 28/268 (10%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE-GN 83
           K   L K E   L   Y+ + D SA   LV  +  LV  +A  Y   G    E + + G 
Sbjct: 6   KTTKLTKDEVDRLINEYQTNQDDSAQETLVQVYTNLVEVLAKKY-SKGKSFHEDLRQVGM 64

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRL 142
           IGL+ A+K++DP  G     +++  I   ++ ++  ++WS+         +R+     R+
Sbjct: 65  IGLLGAIKRYDPVVGKSFEAFAIPTIIGEIKRFLRDKTWSV------HVPRRIKELGPRI 118

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKN 196
           K  +  +T    +  +V  IA+ L+VSE EV+ +M        L+ D S+ A    +D +
Sbjct: 119 KMAVDTLTTETQRSPKVEEIAEYLDVSEEEVLETMEMGKSYQALSVDHSIEA---DADGS 175

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           +    D +    DG E+V        N++ ML   + VL+ RE++I +   +Q    + +
Sbjct: 176 TVTILDIVGSQEDGYERV--------NQQMMLKSVLHVLSEREKQIIDLTYIQNK--SQK 225

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
                  +S+  V +++ +A KK++E++
Sbjct: 226 ETGDILGISQMHVSRLQRKAVKKLREAL 253


>gi|125972644|ref|YP_001036554.1| RNA polymerase, sigma 28 subunit [Clostridium thermocellum ATCC
           27405]
 gi|125712869|gb|ABN51361.1| RNA polymerase, sigma subunit, RpoX/SigF [Clostridium thermocellum
           ATCC 27405]
          Length = 246

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 58/241 (24%), Positives = 111/241 (46%), Gaps = 29/241 (12%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  ++ LV  I   ++  G    ++   G IGL++A+ KFD     + +TY++  I   
Sbjct: 27  LVEKNVGLVWSIVRRFQNRGYEAEDIFQIGCIGLIKAINKFDCSYDVKFSTYAVPMIIGE 86

Query: 113 MQEYILRSWSLVKIGTT----ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA-IAKKLN 167
           ++ +I R   ++K+  +    AN+ R+           + I    L  E  V  I+++L 
Sbjct: 87  IKRFI-RDDGMIKVSRSLKELANKARI----------TKEIMSKELGREPTVGEISEQLG 135

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +   EV+         ESL + +   D +S+   D +  + + QE  +++       R  
Sbjct: 136 IPVEEVVMAMEASCTPESLYSTLGEGDNSSTLLIDKIANESENQEVDIVD-------RID 188

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L + +  L PRE++I   R  +E   T   ++    +S+ +V +IE    KK+ E I+K+
Sbjct: 189 LRKVLDTLKPREKQIIVLRYFKEK--TQVQIAKMLGISQVQVSRIE----KKILEEIRKK 242

Query: 288 V 288
           +
Sbjct: 243 I 243


>gi|133473|sp|P26764|RPSF_BACLI RecName: Full=RNA polymerase sigma-F factor; AltName:
           Full=Sporulation sigma factor; AltName: Full=Stage II
           sporulation protein AC
 gi|304173|gb|AAA22797.1| sporulation protein [Bacillus licheniformis]
          Length = 255

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 58/244 (23%), Positives = 110/244 (45%), Gaps = 28/244 (11%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           ++GD  A   L+  ++RLV  +   +   G    ++   G IGL+++V KFD     R +
Sbjct: 27  QNGDQKARDLLIEKNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKSVDKFDLSYDVRFS 86

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I   +Q +I R    VK+  +   K L   +RR K  L   + +N +   V  I
Sbjct: 87  TYAVPMIIGEIQRFI-RDDGTVKVSRSL--KELGNKIRRAKEEL---SKSNGRIPTVQEI 140

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ-----EQVLIE 217
           A  L +S  EV+     +    S++                 VY++DG      +Q+  +
Sbjct: 141 ADYLEISSEEVVMAQEAVRSPSSIHE---------------TVYENDGDPITLLDQIADQ 185

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
            EE+   +  L  ++  L+ RE+ I   R  ++   T   ++    +S+ +V ++E +  
Sbjct: 186 SEEKWFDKIALKEAIKDLDEREKLIVYLRYYKDK--TQSEVADRLGISQVQVSRLEKKIL 243

Query: 278 KKVQ 281
           K+++
Sbjct: 244 KQIK 247


>gi|312794092|ref|YP_004027015.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
 gi|312181232|gb|ADQ41402.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
          Length = 255

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 40/149 (26%), Positives = 79/149 (53%), Gaps = 7/149 (4%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L  +E+  L KR +E GD  A    +  +LRLV+ +   +   G  + ++   G IG
Sbjct: 14  LPVLSHEEKLELLKRMKE-GDKEARRIFIEGNLRLVLSVVQKFANRGENLDDLFQVGCIG 72

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A+  FD  +  + +TY++  I   ++ Y LR  + ++I  +   K   +   ++K  
Sbjct: 73  LIKAIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNSMRISRSL--KDTAYKALKIK-- 127

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVI 174
            +   +NN K   +  IAK+L+V++ E++
Sbjct: 128 -EKYINNNQKEPTLEEIAKELSVTKEELV 155


>gi|325288800|ref|YP_004264981.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Syntrophobotulus
           glycolicus DSM 8271]
 gi|324964201|gb|ADY54980.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Syntrophobotulus
           glycolicus DSM 8271]
          Length = 254

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 63/253 (24%), Positives = 123/253 (48%), Gaps = 29/253 (11%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFDPERGFR 100
           G+LS  +  +  +L LV ++A G     LP      +++  G  GL+ A++K++P RG +
Sbjct: 16  GNLSEEY--IDQYLPLVKRLA-GRLAMSLPSHIEEEDLIGYGVFGLIDALQKYEPSRGVK 72

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQK-----RLFFNLRRLKGHLQAITDNNLK 155
             TY+   I+ AM +  LRS   V    +A QK     + + +L  L+G   +I +    
Sbjct: 73  FETYASLRIRGAMIDG-LRSMDWVP--HSARQKVKKVRQAYIDLENLQGRTPSIEE---- 125

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV- 214
               VA   ++ + E     ++ +     S++ L++    +S      L+ D + QE   
Sbjct: 126 ----VAGFLEIQLEELHTTLLHGQYMTLVSMDQLLDGHSGDSGISPVDLIIDAEAQESFN 181

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
            IEKEE+K    +L R +  L+ +E+ +      +E  +TL+ +++   +S  R+ QI +
Sbjct: 182 NIEKEEQK---QILAREIEKLSEKEKLVIAMYYREE--MTLKEIAAVMNLSESRISQIHS 236

Query: 275 RAFKKVQESIQKQ 287
           +A  +++  + +Q
Sbjct: 237 QAILRLRGYLGRQ 249


>gi|164687591|ref|ZP_02211619.1| hypothetical protein CLOBAR_01232 [Clostridium bartlettii DSM
           16795]
 gi|164603365|gb|EDQ96830.1| hypothetical protein CLOBAR_01232 [Clostridium bartlettii DSM
           16795]
          Length = 255

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 57/251 (22%), Positives = 113/251 (45%), Gaps = 31/251 (12%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           ++GD  A   L++S+L LV  +   +   G    ++   G+IGL++A+ KFDP    + +
Sbjct: 27  QNGDEEAKALLISSNLGLVRSVIGKFSNIGYERDDLFQLGSIGLIKAIYKFDPSYNVKFS 86

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I   ++ Y LR   +VK+  +  Q  +     +++G +               +
Sbjct: 87  TYAVPMILGEIKRY-LRDDGMVKVSRSLKQLAIKV---KMQGEM---------------L 127

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK---- 218
           +KKL       I       G E  + ++      S ++   ++++ +G    LI+K    
Sbjct: 128 SKKLG--RDPTIEELAEAIGVEKEDVVMAIESNFSVEYLQGVIHEEEGSPICLIDKISQK 185

Query: 219 ---EERKNRRNMLTRS-MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
              EE K   N+L +  +  L+ RER+I   R  ++   T   +     +S+ +V +IE 
Sbjct: 186 GEAEEDKVVDNILLKEVLGKLDKRERQIIMLRYFEDK--TQSEIGELLNISQVQVSRIEK 243

Query: 275 RAFKKVQESIQ 285
           +   K++  I+
Sbjct: 244 KVLHKLKLYIE 254


>gi|161898839|gb|ABX80409.1| SigB [Listeria monocytogenes]
          Length = 222

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 55/217 (25%), Positives = 103/217 (47%), Gaps = 24/217 (11%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 1   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 60

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 61  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVKELTREL 114

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +   
Sbjct: 115 QSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGT 171

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
            DG E+V        N+R +L + + VL+ RE++I +
Sbjct: 172 DDGFERV--------NQRMLLEKVLPVLDEREQKILQ 200


>gi|304439070|ref|ZP_07398989.1| RNA polymerase sigma-B factor [Peptoniphilus duerdenii ATCC
           BAA-1640]
 gi|304372429|gb|EFM26016.1| RNA polymerase sigma-B factor [Peptoniphilus duerdenii ATCC
           BAA-1640]
          Length = 260

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 65/259 (25%), Positives = 115/259 (44%), Gaps = 36/259 (13%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y +  D     +L+  +L +   +A  Y G G+   ++    +IGL+ AV ++DP +GF 
Sbjct: 20  YNKTRDPELREKLIEDNLYIAEILAKKYYGRGIDYDDIYQVASIGLIYAVDRYDPSKGFE 79

Query: 101 LATYSMWWIKAAMQEYIL-RSWS------LVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
            ++++   I   +++Y   + W+      + ++    N  R++     L  +LQ      
Sbjct: 80  FSSFATPTIIGEIKKYFRDKGWTIRVPRRIQELSKKINNARVY-----LAQNLQ------ 128

Query: 154 LKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINS-SDKNSSQWQDWLVYDHDG 210
            K   V  IA+ LN +E EV+      R+   +SL+    S SD       D +     G
Sbjct: 129 -KAPTVSDIAEYLNTTEEEVLEAIEASRVYQPQSLDISYESQSDDKEVNLADII-----G 182

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
           Q++   EK E  +    L ++   LN  E+ I   R    N  T   ++ +  +S+  V 
Sbjct: 183 QDEEYFEKIEMNDLMESLFKN---LNEVEKTILVERYF--NRKTQVAIAEQLNISQMTVS 237

Query: 271 QIEARAFKKVQESIQKQVE 289
           +IE    KKV E ++K VE
Sbjct: 238 RIE----KKVLERLKKDVE 252


>gi|302793696|ref|XP_002978613.1| hypothetical protein SELMODRAFT_177039 [Selaginella moellendorffii]
 gi|300153962|gb|EFJ20599.1| hypothetical protein SELMODRAFT_177039 [Selaginella moellendorffii]
          Length = 458

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 32/115 (27%), Positives = 65/115 (56%), Gaps = 4/115 (3%)

Query: 48  SAAHRLVTSHLRLVVKIAMGY-RGYG-LPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           +A ++L+  + RLV+ +A  Y R  G   + ++  EG  GL+ A+  F+P +G R +TY+
Sbjct: 218 AAQNKLIEHNCRLVLFLARRYERDAGSFSLEDLCQEGVKGLIDAMDHFNPGKGTRFSTYA 277

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
           ++WI+ AM   I R+  ++++  +   K++   +R+ +  L+     N   E+V+
Sbjct: 278 IFWIRTAMVRAITRTGQVIRLPFSFAAKKV--EIRKARRELRVELGRNPSDEEVM 330


>gi|153932837|ref|YP_001384784.1| RNA polymerase sigma-K factor [Clostridium botulinum A str. ATCC
           19397]
 gi|170755199|ref|YP_001782157.1| RNA polymerase sigma-K factor [Clostridium botulinum B1 str. Okra]
 gi|152928881|gb|ABS34381.1| RNA polymerase sigma-K factor [Clostridium botulinum A str. ATCC
           19397]
 gi|169120411|gb|ACA44247.1| RNA polymerase sigma-K factor [Clostridium botulinum B1 str. Okra]
          Length = 144

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 30/79 (37%), Positives = 47/79 (59%), Gaps = 2/79 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ +++E+Y L +   + GD  A   LV  +LRLV  I   Y   G  I +++S G +GL
Sbjct: 30  PLSDEEEKYYLDRL--KKGDALAKDILVERNLRLVAHIVKKYSYPGKDIDDLISIGTVGL 87

Query: 87  MQAVKKFDPERGFRLATYS 105
           ++A+  FD  +G RLATY+
Sbjct: 88  IKAIDSFDNSKGTRLATYA 106


>gi|153854689|ref|ZP_01995939.1| hypothetical protein DORLON_01937 [Dorea longicatena DSM 13814]
 gi|149752793|gb|EDM62724.1| hypothetical protein DORLON_01937 [Dorea longicatena DSM 13814]
          Length = 246

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 26/75 (34%), Positives = 47/75 (62%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           D +A   L+  +LRLVV IA  +   G+ + +++S G IGL++A+  F+P++  +LATY+
Sbjct: 60  DENARKILIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFNPDKNIKLATYA 119

Query: 106 MWWIKAAMQEYILRS 120
              I+  +  Y+ R+
Sbjct: 120 SRCIENEILMYLRRN 134


>gi|307717644|gb|ADN88875.1| RNA polymerase sigma-37 factor [Listeria ivanovii subsp.
           londoniensis]
          Length = 220

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 55/217 (25%), Positives = 102/217 (47%), Gaps = 24/217 (11%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQEDGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTREL 115

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +   
Sbjct: 116 QSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSMEA---DSDGSTITLLDVVGGT 172

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
            DG E+V        N+R +L + + VL+ RE++I +
Sbjct: 173 DDGFERV--------NQRMLLEKVLPVLDEREQKILQ 201


>gi|256004731|ref|ZP_05429707.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium thermocellum
           DSM 2360]
 gi|281416836|ref|ZP_06247856.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium thermocellum
           JW20]
 gi|255991324|gb|EEU01430.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium thermocellum
           DSM 2360]
 gi|281408238|gb|EFB38496.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium thermocellum
           JW20]
 gi|316941118|gb|ADU75152.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium thermocellum
           DSM 1313]
          Length = 248

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 58/241 (24%), Positives = 111/241 (46%), Gaps = 29/241 (12%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  ++ LV  I   ++  G    ++   G IGL++A+ KFD     + +TY++  I   
Sbjct: 29  LVEKNVGLVWSIVRRFQNRGYEAEDIFQIGCIGLIKAINKFDCSYDVKFSTYAVPMIIGE 88

Query: 113 MQEYILRSWSLVKIGTT----ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA-IAKKLN 167
           ++ +I R   ++K+  +    AN+ R+           + I    L  E  V  I+++L 
Sbjct: 89  IKRFI-RDDGMIKVSRSLKELANKARI----------TKEIMSKELGREPTVGEISEQLG 137

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +   EV+         ESL + +   D +S+   D +  + + QE  +++       R  
Sbjct: 138 IPVEEVVMAMEASCTPESLYSTLGEGDNSSTLLIDKIANESENQEVDIVD-------RID 190

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L + +  L PRE++I   R  +E   T   ++    +S+ +V +IE    KK+ E I+K+
Sbjct: 191 LRKVLDTLKPREKQIIVLRYFKEK--TQVQIAKMLGISQVQVSRIE----KKILEEIRKK 244

Query: 288 V 288
           +
Sbjct: 245 I 245


>gi|312126848|ref|YP_003991722.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor hydrothermalis 108]
 gi|311776867|gb|ADQ06353.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor hydrothermalis 108]
          Length = 248

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 62/264 (23%), Positives = 127/264 (48%), Gaps = 27/264 (10%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG----YRGYGLPISEVVSEGNIGLMQ 88
           ++ +L +++ +  D     +L+  ++ LV K+  G    Y G  +   ++VS G+IGL+ 
Sbjct: 4   DDALLWEKFIKTKDPKIKEQLIIKYMPLV-KLVAGRMAIYFGGNVEYDDLVSYGSIGLLD 62

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++KFD ++G +  TY+   IK A+ + + RS   +        K +       K +++ 
Sbjct: 63  AIEKFDSQKGVKFETYAYTRIKGAIIDCV-RSQDFLPRSIRQKAKEI------EKAYIEI 115

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ-WQDWL--V 205
             +     +Q   +AK++ +S  E+  +  R++     + +I S D    Q ++  +  +
Sbjct: 116 EKEGKTPTDQ--EVAKRIGISVDELQKLQDRIS-----SGMIISLDSFLEQNYESKIGGL 168

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            D   Q +  IE EE K    +L + +  L   ER +      +E  ++++ ++    VS
Sbjct: 169 EDFVSQPEHFIENEELK---TVLRQQIDNLMENERMVIVLYYYEE--LSIKEIAKVLGVS 223

Query: 266 RERVRQIEARAFKKVQESIQKQVE 289
             RV Q+  RA  K++ ++QK +E
Sbjct: 224 ESRVSQLHTRALLKLRSALQKYLE 247


>gi|226323679|ref|ZP_03799197.1| hypothetical protein COPCOM_01454 [Coprococcus comes ATCC 27758]
 gi|225207863|gb|EEG90217.1| hypothetical protein COPCOM_01454 [Coprococcus comes ATCC 27758]
          Length = 247

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 33/103 (32%), Positives = 54/103 (52%), Gaps = 1/103 (0%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSH-LRLVVKIAMGYRGYGLPISE 77
           YI     +P+    EE   A      G      +L+  H LRLVV IA  +   G+ + +
Sbjct: 32  YIGGTDILPLPLSSEEEGHAISLLGGGQDEEGKKLLIEHNLRLVVYIAKKFDNTGVGVED 91

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++S G IGL++A+  F+PE+  +LATY+   I+  +  Y+ R+
Sbjct: 92  LISIGTIGLIKAINTFNPEKNIKLATYASRCIENEILMYLRRN 134


>gi|168180582|ref|ZP_02615246.1| RNA polymerase sigma-G factor [Clostridium botulinum NCTC 2916]
 gi|168182609|ref|ZP_02617273.1| RNA polymerase sigma-G factor [Clostridium botulinum Bf]
 gi|170757556|ref|YP_001782076.1| sporulation sigma factor SigG [Clostridium botulinum B1 str. Okra]
 gi|170761503|ref|YP_001787848.1| sporulation sigma factor SigG [Clostridium botulinum A3 str. Loch
           Maree]
 gi|187778872|ref|ZP_02995345.1| hypothetical protein CLOSPO_02467 [Clostridium sporogenes ATCC
           15579]
 gi|226949887|ref|YP_002804978.1| sporulation sigma factor SigG [Clostridium botulinum A2 str. Kyoto]
 gi|237795971|ref|YP_002863523.1| sporulation sigma factor SigG [Clostridium botulinum Ba4 str. 657]
 gi|169122768|gb|ACA46604.1| RNA polymerase sigma-G factor [Clostridium botulinum B1 str. Okra]
 gi|169408492|gb|ACA56903.1| RNA polymerase sigma-G factor [Clostridium botulinum A3 str. Loch
           Maree]
 gi|182668579|gb|EDT80558.1| RNA polymerase sigma-G factor [Clostridium botulinum NCTC 2916]
 gi|182674221|gb|EDT86182.1| RNA polymerase sigma-G factor [Clostridium botulinum Bf]
 gi|187772497|gb|EDU36299.1| hypothetical protein CLOSPO_02467 [Clostridium sporogenes ATCC
           15579]
 gi|226842131|gb|ACO84797.1| RNA polymerase sigma-G factor [Clostridium botulinum A2 str. Kyoto]
 gi|229263792|gb|ACQ54825.1| RNA polymerase sigma-G factor [Clostridium botulinum Ba4 str. 657]
          Length = 257

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 62/279 (22%), Positives = 127/279 (45%), Gaps = 55/279 (19%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+ +E   L  R R +G+       +  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKDKEMKKLLVRIR-NGETECREEFIQGNLRLVLSVIKRFNNRGENVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD  +  + +TY++  I   ++ Y LR  + +++  +          + L+ 
Sbjct: 74  GLIKAIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNSIRVSRSLRD----IAYKALQA 128

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + I +NN +P  V  IAK+L +   EV+          +L+A+           QD +
Sbjct: 129 RDKLIKNNNKEP-TVSQIAKELELPREEVVF---------ALDAI-----------QDPV 167

Query: 205 -----VYDHDGQEQVLIEKEERKNRRNM---------LTRSMSVLNPRER-----RIFEA 245
                +Y HDG + + +  ++  + +N+         +  +M  LN RE+     R F+ 
Sbjct: 168 SLFEPIY-HDGGDAIFV-MDQISDTKNVDENWIENISIKEAMKKLNDREKLILNLRFFDG 225

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R   E       ++ E  +S+ +V ++E  A K +++ +
Sbjct: 226 RTQME-------VADEIGISQAQVSRLEKTALKHMRKYV 257


>gi|146295518|ref|YP_001179289.1| FliA/WhiG family RNA polymerase sigma factor [Caldicellulosiruptor
           saccharolyticus DSM 8903]
 gi|145409094|gb|ABP66098.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Caldicellulosiruptor
           saccharolyticus DSM 8903]
          Length = 257

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 48/233 (20%), Positives = 110/233 (47%), Gaps = 21/233 (9%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L + YR+  D++  + LV  HL +   +A  +   G+   ++     + L+ AV++F+P 
Sbjct: 18  LFEEYRKTKDINLRNELVNRHLYIAEIVAKKFINRGIEYDDLYQVACMALINAVERFEPN 77

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +G++  +++   I   ++ Y     SL+++      +R++    ++K   + ++    +P
Sbjct: 78  KGYKFTSFATPTIMGEIKRYFRDRASLIRLP-----RRIYETSAKIKLATEILSAKLKQP 132

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ--- 213
            ++  IA+ + ++  EV+ +      + S N L  S D+   + ++  + D  G+     
Sbjct: 133 PKIEEIAQYIGITPEEVLEV-----MEASNNYLPQSLDQTMYEDEEMTLGDVLGKSDENL 187

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           V IE  E       + +++  L+P ER   + R  +E   T   ++ E +VS+
Sbjct: 188 VQIENTE------TVKKAIDKLSPLEREFVQKRFFEEK--TQREIADEMKVSQ 232


>gi|253682196|ref|ZP_04862993.1| RNA polymerase sigma-K factor [Clostridium botulinum D str. 1873]
 gi|253561908|gb|EES91360.1| RNA polymerase sigma-K factor [Clostridium botulinum D str. 1873]
          Length = 235

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 33/102 (32%), Positives = 53/102 (51%), Gaps = 2/102 (1%)

Query: 9   IVNGEIGLSRYIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           +++G   L+ Y+      P  L + EE    K+++  GD  A   L+  +LRLV  I   
Sbjct: 10  MIDGMTFLTAYVSNGTSFPQPLNEDEERYYLKKFK-GGDALAKGILIERNLRLVAHIVKK 68

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           Y      I +++S G +GL++A+  FD  +G RLATY+   I
Sbjct: 69  YSYPNKDIDDLISIGTVGLIKAIDSFDISKGTRLATYAARCI 110


>gi|170760209|ref|YP_001787962.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum A3 str. Loch Maree]
 gi|169407198|gb|ACA55609.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum A3 str. Loch Maree]
          Length = 242

 Score = 53.9 bits (128), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 65/249 (26%), Positives = 115/249 (46%), Gaps = 23/249 (9%)

Query: 45  GDLSAAHRLVTSHLRLVVKIA----MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
            +L     +V  ++ LV  IA    +G   Y +   ++VS G IGLM A+ KFD  +G +
Sbjct: 6   NNLYVKEEIVKKYIPLVKYIASRVIIGKTKY-IEYEDLVSYGMIGLMDALNKFDESKGMK 64

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+   IK +M + + R+  + K G      R    + +L+  L        K   ++
Sbjct: 65  FSTYASIRIKGSMIDELRRNSPISK-GAMDKLNRYNEAIEKLQKKLN-------KEPNLI 116

Query: 161 AIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            IA +LN+S  EV  I          SL  LI SS+         L+     ++    EK
Sbjct: 117 QIADELNISLKEVSEIENYINYISVISLEDLIFSSEDEVP-----LIGTIKDEKSPSPEK 171

Query: 219 EERKNRR-NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
              +N + + L +++ +LN ++R +      +E  +TL+ +     VS  RV Q+ +RA 
Sbjct: 172 HVEENEQLDYLAKAIELLNEKDRLVVTLYYYEE--LTLKEIGKILNVSESRVCQLHSRAI 229

Query: 278 KKVQESIQK 286
             +++++ K
Sbjct: 230 VHLKKAMVK 238


>gi|332799104|ref|YP_004460603.1| RNA polymerase sigma-28 subunit SigG [Tepidanaerobacter sp. Re1]
 gi|332696839|gb|AEE91296.1| RNA polymerase, sigma 28 subunit, SigG [Tepidanaerobacter sp. Re1]
          Length = 257

 Score = 53.5 bits (127), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 56/250 (22%), Positives = 123/250 (49%), Gaps = 32/250 (12%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD SA  +L++ +LRLV+ +   +   G  + ++   G IGL++A+  FD  +  + +
Sbjct: 32  QKGDKSAREKLISGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLIKAIDNFDLSQNVKFS 91

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I   ++ Y LR  + +++  +          + L+     +T N+ +P  +  +
Sbjct: 92  TYAVPMIIGEIRRY-LRDNNQIRVSRSLRDTA----YKALQVRDSLVTKNSREPS-INEV 145

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE--E 220
           AK++N+   EV+          +L+A+     +  S ++   +Y HDG + + +  +  +
Sbjct: 146 AKEMNMPSEEVVF---------ALDAI----QEPVSLFEP--IY-HDGGDPIFVMDQISD 189

Query: 221 RKNRRNMLTRSMSV------LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
            KN+ +   + +S+      L  RE++I   R   E    +E ++ E  +S+ +V ++E 
Sbjct: 190 EKNQDDQWLQGISIKEAMQRLGEREKKILNLRFF-EGKTQME-VAQEIGISQAQVSRLEK 247

Query: 275 RAFKKVQESI 284
            A K +++ I
Sbjct: 248 AALKHMRKFI 257


>gi|166031185|ref|ZP_02234014.1| hypothetical protein DORFOR_00871 [Dorea formicigenerans ATCC
           27755]
 gi|166029032|gb|EDR47789.1| hypothetical protein DORFOR_00871 [Dorea formicigenerans ATCC
           27755]
          Length = 246

 Score = 53.5 bits (127), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 29/85 (34%), Positives = 49/85 (57%), Gaps = 6/85 (7%)

Query: 42  REHGDLSAAHR------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           R  G L +AH       L+  +LRLVV IA  +   G+ + +++S G IGL++A+  F+P
Sbjct: 50  RAIGYLGSAHDEEARKLLIEHNLRLVVYIAKKFDNTGIGVEDLISIGTIGLIKAINTFNP 109

Query: 96  ERGFRLATYSMWWIKAAMQEYILRS 120
            +  +LATY+   I+  +  Y+ R+
Sbjct: 110 TKNIKLATYASRCIENEILMYLRRN 134


>gi|224110206|ref|XP_002333134.1| predicted protein [Populus trichocarpa]
 gi|222834948|gb|EEE73397.1| predicted protein [Populus trichocarpa]
          Length = 512

 Score = 53.5 bits (127), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 58/248 (23%), Positives = 105/248 (42%), Gaps = 37/248 (14%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           +A ++L+  +LRLV+ +   Y      G    +    G  GL+ A+ +F+P+R FRL+TY
Sbjct: 275 AARNKLIKHNLRLVLFVIKKYFQDFANGTKFQDFCQAGVKGLITAIDRFEPKRRFRLSTY 334

Query: 105 SMWWIK-AAMQEYILRSWSLVKIGTTA-------NQKRLFFNLRRLKGHLQAITDNNLKP 156
            ++WI+ A ++   L S++ V  G  +        +  L+F L+R     + I    + P
Sbjct: 335 GLFWIRHAIIRSMTLSSFTRVSFGLESIRSEIQKAKLELWFQLKRQPMEDEIIEKVRISP 394

Query: 157 EQVVAIAKKLNVSESEVISMNCR-LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
           E+   + +    +   V+S++ R     E     I   D    + Q  L+          
Sbjct: 395 ERYHEVTR----ASKPVLSLHSRHKTTQEEFIGGIADVDGGDDRRQSALL---------- 440

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIE 273
                    R  L   +  L P+E  +   R   +     TL  ++    +SRE VR+ E
Sbjct: 441 ---------RLALDDVLDSLKPKESLVVRQRYGLDGKGDRTLGEIAGNLNISREMVRKHE 491

Query: 274 ARAFKKVQ 281
            +A  K++
Sbjct: 492 VKALMKLK 499


>gi|225075400|ref|ZP_03718599.1| hypothetical protein NEIFLAOT_00405 [Neisseria flavescens
           NRL30031/H210]
 gi|224953218|gb|EEG34427.1| hypothetical protein NEIFLAOT_00405 [Neisseria flavescens
           NRL30031/H210]
          Length = 113

 Score = 53.5 bits (127), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 34/101 (33%), Positives = 61/101 (60%), Gaps = 3/101 (2%)

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFEARRLQ 249
           N+ D+++    DWL  DHD +    + K+     +   L  +++ L+ R  RI E+R LQ
Sbjct: 12  NNDDEDNFAPIDWLA-DHDAEPSRQLSKQAHYALQTEGLQNALAQLDDRSHRIVESRWLQ 70

Query: 250 ENP-VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 71  DDGGLTLHELAAEYGVSAERIRQIEAKAMQKLRGFLAEEAE 111


>gi|307717642|gb|ADN88874.1| RNA polymerase sigma-37 factor [Listeria ivanovii subsp.
           londoniensis]
          Length = 220

 Score = 53.5 bits (127), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 55/217 (25%), Positives = 102/217 (47%), Gaps = 24/217 (11%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQEDGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTREL 115

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +   
Sbjct: 116 QSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGT 172

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
            DG E+V        N+R +L + + VL+ RE++I +
Sbjct: 173 DDGFERV--------NQRMLLEKVLPVLDEREQKILQ 201


>gi|225569422|ref|ZP_03778447.1| hypothetical protein CLOHYLEM_05506 [Clostridium hylemonae DSM
           15053]
 gi|225161630|gb|EEG74249.1| hypothetical protein CLOHYLEM_05506 [Clostridium hylemonae DSM
           15053]
          Length = 237

 Score = 53.5 bits (127), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 59/242 (24%), Positives = 107/242 (44%), Gaps = 18/242 (7%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GD  A  +LV  +  LV  I   +   G    ++   GNIGL++A+ KFD     + +T
Sbjct: 13  QGDEKARAQLVEENAGLVWCIVKRFYNRGAEAEDLFQVGNIGLLKAIDKFDMSYEVKFST 72

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y++  I   ++ + LR   ++K+  +   K L +     +  LQ       +   +  IA
Sbjct: 73  YAVPMISGEIKRF-LRDDGMIKVSRSL--KELSYKAYLCQEKLQEALG---REPTITEIA 126

Query: 164 KKLNVSESEVISMNCRLAGD-ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           + L V   E ++M    +GD ESL+  I   +    +  D L     G+E++L       
Sbjct: 127 EYLEVDREE-LTMALDASGDIESLHKPIYQKEGQEIRLMDKLPEKEGGEEKIL------- 178

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
               +L + +  LN  ER++   R       T   +  E  +S+ +V ++E +  K+++E
Sbjct: 179 -NHMLLQQLLEYLNKDERQLIYLRYFANQ--TQSQVGQELGISQVQVSRLEKKILKRLRE 235

Query: 283 SI 284
            I
Sbjct: 236 RI 237


>gi|220907105|ref|YP_002482416.1| RNA polymerase sigma factor SigF [Cyanothece sp. PCC 7425]
 gi|219863716|gb|ACL44055.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cyanothece
           sp. PCC 7425]
          Length = 263

 Score = 53.5 bits (127), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 67/262 (25%), Positives = 127/262 (48%), Gaps = 30/262 (11%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           Y ++  ++  ++LV  HL LV K+A    R    P  ++V  G +GL+ A+++FDP +G+
Sbjct: 18  YHQNPTIAVRNQLVRLHLGLVRKVAHRLARQCKEPYEDLVQCGCLGLIAAIERFDPSQGY 77

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
             +++++ +I+  +  ++     ++KI     Q  L  + ++++  L  + D     EQV
Sbjct: 78  AFSSFAVPYIRGEILHFLRDRAYMLKIPRRWQQ--LNQDGQKVRQELAKVLDRPPTEEQV 135

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ-------WQDWLVYDHDGQE 212
              A +L VS  E  S+  RLA        IN++  +S+Q         D LV   D QE
Sbjct: 136 ---ASQLQVSPEEWRSV--RLAMRNRTPLSINTTLSSSAQAAGMALTLADLLV---DAQE 187

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           +V   ++ +      L ++++ L  R R++ E        V L +L+ +   SR+ V  I
Sbjct: 188 EV---RQSQTEDSLELYQALAQLEERTRQMIEE-------VFLHHLTRQEVASRKGVSPI 237

Query: 273 EARAFKKVQESIQKQVELSSSP 294
                + +Q+ I++ + L  SP
Sbjct: 238 TVS--RHIQKGIEQLMNLLQSP 257


>gi|318040135|ref|ZP_07972091.1| RNA polymerase sigma factor, sigma-70 family protein [Synechococcus
           sp. CB0101]
          Length = 310

 Score = 53.5 bits (127), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 58/247 (23%), Positives = 108/247 (43%), Gaps = 15/247 (6%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLP-----ISEVVSEGNIGLMQAVKKFDPERGFRL 101
           L A  +LV  +L LV     G     LP      ++ + E  + L++A +KFDP +G+R 
Sbjct: 59  LRAREQLVRHNLGLVAHT-WGRHRCSLPAHDDTTADALQEAALNLVRAAEKFDPAKGYRF 117

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY+ +W++    E+  R+   ++    A +  +     RL    QA T +    E + A
Sbjct: 118 STYATFWVRRGFTEFEQRAKRAIRF--PAEKAAVVLKALRLSQQHQATTGDEPALEWLAA 175

Query: 162 ----IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
                 K ++  +              SL+      D+     +  L       EQ L +
Sbjct: 176 QLKFDGKAMSAEQLAEFIRQWDATRTGSLDGAEEEGDEKGGCSRLDLASLQQAAEQQLTQ 235

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL-SSEFEVSRERVRQIEARA 276
           + + ++    L + MS L+ +E R+   R L+  P++   L  S   + RE++ Q+EA A
Sbjct: 236 EPDPQH--ASLPQLMSCLDEQEHRLIRNRYLRRPPLSPCQLRRSMGGMQREQLEQLEATA 293

Query: 277 FKKVQES 283
             K++++
Sbjct: 294 LDKLRQA 300


>gi|222529665|ref|YP_002573547.1| Sig B/F/G subfamily RNA polymerase sigma-28 factor
           [Caldicellulosiruptor bescii DSM 6725]
 gi|222456512|gb|ACM60774.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor bescii DSM 6725]
          Length = 232

 Score = 53.5 bits (127), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 55/241 (22%), Positives = 107/241 (44%), Gaps = 20/241 (8%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           ++GD  A  +L+ ++L LV  +   +   G+ + ++   G+IGL++AV +FDP    R +
Sbjct: 6   KNGDKLARQQLIENNLALVWSVVKKFAAKGVELEDLFQIGSIGLIKAVDRFDPSFNVRFS 65

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I   ++ Y LR    +K+     +     N  ++K        N+ +   +  I
Sbjct: 66  TYAVPMIIGEIKRY-LRDDGKIKVSRKIKE-----NQGKIKKLRNQFVSNHGREPTISEI 119

Query: 163 AKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
           ++   +S  E++   C  A  E  SL+ +IN  +       D    + D   ++L     
Sbjct: 120 SQLTGLSNDEILL--CLDASSEVASLSEVINQEEGKPITLMDIASDEEDYSTKLL----- 172

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                  L   +  L  RER I   R  +    T   ++ +  +S+  V +IE RA +++
Sbjct: 173 ---DLMALKEGLKKLKGRERYIIFMRYFKNK--TQSEIAKQLNISQVHVSRIEKRALERI 227

Query: 281 Q 281
           +
Sbjct: 228 K 228


>gi|283796413|ref|ZP_06345566.1| RNA polymerase sigma-F factor [Clostridium sp. M62/1]
 gi|291075823|gb|EFE13187.1| RNA polymerase sigma-F factor [Clostridium sp. M62/1]
 gi|295091441|emb|CBK77548.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase
           sigma-70 factor, sigma-B/F/G subfamily [Clostridium cf.
           saccharolyticum K10]
 gi|295114800|emb|CBL35647.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase
           sigma-70 factor, sigma-B/F/G subfamily
           [butyrate-producing bacterium SM4/1]
          Length = 245

 Score = 53.5 bits (127), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 62/240 (25%), Positives = 106/240 (44%), Gaps = 21/240 (8%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD +A  RLV  ++ LV  I   + G G    ++   G+IGL++A+ KFD     R +TY
Sbjct: 20  GDKAARDRLVEENMGLVWSIVRRFAGRGCETEDLFQIGSIGLIKAIDKFDTSYDVRFSTY 79

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR--LKGHLQAITDNNLKPEQVVAI 162
           ++  I   ++ + LR   ++K+  +  +  +  +  R  L G L        +   +  I
Sbjct: 80  AVPMIAGEIRRF-LRDDGMIKVSRSVKEMGIKVSAAREKLAGTLG-------REPTLEEI 131

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A  +  S  EV +     A  ESL A     D N S   D L  +    E+VL       
Sbjct: 132 AGSVGASREEVAASLEAGAQVESLYAPAGGDDTNLS-LLDRLSQESRENEEVL------- 183

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             R +L + +  L  +ER +   R       T   ++ +  +S+ +V ++E R  KK++E
Sbjct: 184 -DRMVLKKLLGSLGEKERELIVRRYFYGQTQT--KIAGQMGISQVQVSRMEKRILKKMRE 240


>gi|161898847|gb|ABX80413.1| SigB [Listeria monocytogenes]
          Length = 233

 Score = 53.5 bits (127), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 60/247 (24%), Positives = 118/247 (47%), Gaps = 26/247 (10%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D   G  
Sbjct: 5   YQENGDEDAQYNLVIHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKS 64

Query: 101 LATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
              +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T       Q+
Sbjct: 65  FEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTRELQSSPQI 118

Query: 160 VAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
             IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +    DG E+
Sbjct: 119 SDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTDDGFER 175

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
           V        N+R +L + + VL+ RE++I +   ++    + +      ++S+  V +I+
Sbjct: 176 V--------NQRMLLEKVLPVLDEREQKILQFTFIENR--SQKETGELLDISQMHVSRIQ 225

Query: 274 ARAFKKV 280
            +A KK+
Sbjct: 226 RQAIKKL 232


>gi|326791409|ref|YP_004309230.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium lentocellum DSM
           5427]
 gi|326542173|gb|ADZ84032.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium lentocellum DSM
           5427]
          Length = 257

 Score = 53.5 bits (127), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 60/260 (23%), Positives = 118/260 (45%), Gaps = 17/260 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L  +++  L K   E GD  A    +  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPILTNEQKETLFKLI-EQGDNKAREEYIRGNLRLVLSVIQRFNNRGEHVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD  +  R +TY++  I   ++ Y LR  + +++  +   +   +   + K 
Sbjct: 74  GLIKAIDNFDVTQNVRFSTYAVPMIIGEIRRY-LRDNNAIRVSRSL--RDTAYKALQTKE 130

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L   T  N K   V  IA +L + + +++     +    SL   +   + ++    D  
Sbjct: 131 QL---TRKNAKEPTVQEIADELGIKKEDIVFALDAIQDPISLFEPVYHDESDTLYIMDQ- 186

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           V D   Q+ V +E          L  +M  +N RE++I   R       T   +++E  +
Sbjct: 187 VSDDKNQDDVWLEN-------IALKEAMKRINDREKQILMLRFFAGK--TQMEVANEIGI 237

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ +V ++E  A K +++ I
Sbjct: 238 SQAQVSRLEKTALKHMKKYI 257


>gi|220931546|ref|YP_002508454.1| sporulation sigma factor SigF [Halothermothrix orenii H 168]
 gi|219992856|gb|ACL69459.1| sporulation sigma factor SigF [Halothermothrix orenii H 168]
          Length = 257

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 55/252 (21%), Positives = 126/252 (50%), Gaps = 32/252 (12%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           ++ D  A  +LV  +LRLV+K+   ++  G    ++   G IGL++A+K FD +RG + +
Sbjct: 27  QNNDQKALDKLVEHNLRLVLKVINRFKSSGYDPQDLFQIGVIGLIKAIKNFDLDRGVKFS 86

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I   ++ +I R   ++K+  +   K++  ++R+ +   +    NN  P  ++ +
Sbjct: 87  TYAVSRIIGEIRLHI-RDDGIIKVSRSL--KKIANDVRKKE--EELKKKNNCSP-SILEL 140

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE----- 217
           +KK   S+ E++     L  +++  ++  +            VY+ DG E  +++     
Sbjct: 141 SKKTGYSKEEIVQA---LEANKAPTSIYET------------VYEDDGSELYVVDNLANE 185

Query: 218 --KEERKNRRNML--TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
              EE+    N +     +  L+ R R+I   R  ++   T + ++ E  VS+ ++ ++E
Sbjct: 186 SKDEEKIPDFNKILLVDLLKKLDERSRKIIYLRYFEDK--TQQEVADEIGVSQVQISRLE 243

Query: 274 ARAFKKVQESIQ 285
            +   K++++++
Sbjct: 244 KKILHKLRDNLE 255


>gi|325264805|ref|ZP_08131534.1| RNA polymerase sigma-E factor [Clostridium sp. D5]
 gi|324030097|gb|EGB91383.1| RNA polymerase sigma-E factor [Clostridium sp. D5]
          Length = 246

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 31/99 (31%), Positives = 56/99 (56%), Gaps = 1/99 (1%)

Query: 22  EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           E+   P+  ++E  V+     E+ D  A   L+  +LRLVV IA  +   G+ + +++S 
Sbjct: 37  EVLPAPLETERETEVIEHLGSEY-DQEAKKLLIEHNLRLVVYIAKKFDNTGVGVEDLISI 95

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           G IGL++A+  F+P +  +LATY+   I+  +  Y+ R+
Sbjct: 96  GTIGLIKAINTFNPTKKIKLATYASRCIENEILMYLRRN 134


>gi|222528460|ref|YP_002572342.1| Sig B/F/G subfamily RNA polymerase sigma-28 factor
           [Caldicellulosiruptor bescii DSM 6725]
 gi|222455307|gb|ACM59569.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor bescii DSM 6725]
          Length = 256

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 51/233 (21%), Positives = 112/233 (48%), Gaps = 21/233 (9%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L + Y++   +   + LV  +L +   IA  + G G+   ++     I L+ AV++F+P 
Sbjct: 18  LFEEYQKTKSIELRNELVNKYLYIAEIIAKKFVGRGIDYEDLYQVACIALINAVERFEPN 77

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +G++  +++   I   ++ Y     S++++      +R++    ++K   + ++    +P
Sbjct: 78  KGYKFTSFATPTIMGEIKRYFRDRASIIRLP-----RRIYETSAKIKLATEVLSTKLKRP 132

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ--EQV 214
            +V  IA+ LN+S  EV+ +      + S N L  S D+   + ++  + D  G+  E +
Sbjct: 133 PKVEEIAQHLNMSAEEVLEV-----MEASNNYLPQSLDQTMYEDEEMTLGDVLGKSDENI 187

Query: 215 L-IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           L +E  E       + +++  L+P ER   + R  +E   T + ++ E  VS+
Sbjct: 188 LQVENVE------AVKKAIERLSPFEREFVQKRFFEEK--TQKEIAEEMNVSQ 232


>gi|312134334|ref|YP_004001672.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|311774385|gb|ADQ03872.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor owensensis OL]
          Length = 256

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 30/140 (21%), Positives = 71/140 (50%), Gaps = 5/140 (3%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L + Y++  D+   + LV  HL +   IA  +   G+   ++     + L+ AV++F+P 
Sbjct: 18  LFEEYQKTKDVKLRNELVNRHLYIAEIIAKKFVNRGIDYDDLYQVACVALINAVERFEPN 77

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +G++  +++   I   ++ Y     S++++      +R++    ++K   + ++    +P
Sbjct: 78  KGYKFTSFATPTIMGEIKRYFRDRASIIRLP-----RRIYETSAKIKLATEVLSTKLKRP 132

Query: 157 EQVVAIAKKLNVSESEVISM 176
            +V  IA+ LN+S  EV+ +
Sbjct: 133 PKVEEIAQHLNMSTEEVLEV 152


>gi|160895354|ref|ZP_02076125.1| hypothetical protein CLOL250_02913 [Clostridium sp. L2-50]
 gi|156863047|gb|EDO56478.1| hypothetical protein CLOL250_02913 [Clostridium sp. L2-50]
          Length = 226

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 67/278 (24%), Positives = 121/278 (43%), Gaps = 67/278 (24%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           I   EI +  +     K P+  K+E Y L  +  + GD  A   L+  ++RLV  IA  Y
Sbjct: 14  IAGAEIDVQTF-----KKPLSPKEEAYFL--KLCKEGDPRARKTLIEYNMRLVAHIAKKY 66

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            G      +++S G IGL++A+  +D ++G RL TY+   I                   
Sbjct: 67  NG-SHENDDLISAGTIGLIKAIDTYDSKKGKRLVTYASRCI------------------- 106

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN-VSESEVISMNCRLAGDESLN 187
              +  L   LR+ + H + ++    +P   +   K+ N +S  ++IS +        L+
Sbjct: 107 ---ENELLMLLRQNRKHAREVS--LFEP---IGTDKEGNEISLMDIISPD----TPSILD 154

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           ++++  D N  Q  D +++    QE VL+      +RR  L+                  
Sbjct: 155 SMVH--DYNLKQLPDCMLHHLTKQEMVLL------SRRYGLS------------------ 188

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             E P T + ++S   +SR  V +IE RA  K++++++
Sbjct: 189 -GEAPCTQKEIASAMGISRSYVSRIEKRALLKLRKALE 225


>gi|167037535|ref|YP_001665113.1| FliA/WhiG family RNA polymerase sigma factor [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|256752057|ref|ZP_05492925.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|320115950|ref|YP_004186109.1| RNA polymerase sigma-F factor [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
 gi|166856369|gb|ABY94777.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Thermoanaerobacter pseudethanolicus ATCC 33223]
 gi|256749067|gb|EEU62103.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|319929041|gb|ADV79726.1| RNA polymerase sigma-F factor [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
          Length = 246

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 59/259 (22%), Positives = 122/259 (47%), Gaps = 20/259 (7%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
            EK +E +   R  +  D  +  +L+  +  L+  I   +   G  + ++   G IG ++
Sbjct: 6   FEKSDENLELIRAAQKNDKESLEKLILENSGLIWSIVKKFSNRGYELEDLYQIGCIGFVK 65

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++KFD     +L+TY++  I   ++ + LR   L+K+  +  +      L     +++ 
Sbjct: 66  AIQKFDESYNVKLSTYAVPIIMGEIKRF-LRDDGLIKVSRSLKE------LSTKAFYVKE 118

Query: 149 ITDNNLKPEQVV-AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
           I  N L  E  +  IA++LNVS  E+       A  ESL       D  +    D L+ +
Sbjct: 119 ILSNELNREPTINEIAERLNVSPEEIAMAFESAATAESL------YDNATHDEDDKLLIE 172

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
              +E    EKE   + +  L   ++ L PRE++I   R  ++  +T   +++   +S+ 
Sbjct: 173 MVSEE----EKEVDIDDKLALQMVINKLKPREKQIIFLRYFKD--MTQMEVANILGISQV 226

Query: 268 RVRQIEARAFKKVQESIQK 286
           +V ++E +  +K+++ +++
Sbjct: 227 QVSRLEKKVLQKLRKELEE 245


>gi|323706111|ref|ZP_08117680.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
 gi|323534555|gb|EGB24337.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
          Length = 256

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 69/281 (24%), Positives = 125/281 (44%), Gaps = 59/281 (20%)

Query: 25  KIPMLE--KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           K+P+L+  KQ+E +L  +   +GD SA    +  +LRLV+ +   +   G  + ++   G
Sbjct: 14  KLPVLKGAKQKELLLRMK---NGDKSAREEFINGNLRLVLSVIQRFNNRGEYVDDLFQVG 70

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY------ILRSWSLVKIGTTANQKRLF 136
            IGL++A+  FD  +  + +TY++  I   ++ Y      I  S SL  +   A Q R  
Sbjct: 71  CIGLIKAIDNFDLNQNVKFSTYAVPMIIGEIRRYLRDNNSIRVSRSLRDVAYKALQVR-- 128

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
                       + + N K   V  IAK+LN+   EV+          +L+A+       
Sbjct: 129 ----------DKLVNENSKEPTVGDIAKELNIPREEVVF---------ALDAI------- 162

Query: 197 SSQWQDWL-----VYDHDGQEQVLIEKE--ERKNRRNM------LTRSMSVLNPRERRIF 243
               QD +     +Y HDG + + +  +  + KN   +      L  ++  LN RE+ I 
Sbjct: 163 ----QDPVSLFEPIY-HDGGDAIYVMDQIGDEKNVDEVWLEQIALKEAIKKLNDREKMIL 217

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              R  E    +E ++ E  +S+ +V ++E  A   +++ I
Sbjct: 218 -TMRFFEGKTQME-VAKEIGISQAQVSRLEKSALSHMRKYI 256


>gi|89099621|ref|ZP_01172496.1| sporulation sigma factor SigG [Bacillus sp. NRRL B-14911]
 gi|89085774|gb|EAR64900.1| sporulation sigma factor SigG [Bacillus sp. NRRL B-14911]
          Length = 259

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 62/270 (22%), Positives = 124/270 (45%), Gaps = 35/270 (12%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+ +E   L K+  E GD  A   LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKNEEMRKLFKQMHE-GDTYARECLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD  +  + +TY++  I   ++ Y LR  + +++  +   + + +   +++ 
Sbjct: 74  GLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSL--RDIAYKALQVRE 130

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L + T      E+   IA+ L V   E++          +L+A+ +        +    
Sbjct: 131 RLMSETSKEPTAEE---IARVLEVPHEEIVF---------ALDAIQDPVSLFEPIY---- 174

Query: 205 VYDHDGQEQVLIEKEERKNRRN---------MLTRSMSVLNPRERRIFEARRLQENPVTL 255
              +DG + + +  ++  + RN          L   M  LN RE+ I   R  Q    T 
Sbjct: 175 ---NDGGDPIFV-MDQLSDERNKDIQWIEEIALKEGMRRLNEREKLILRKRFFQGK--TQ 228

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             ++ E  +S+ +V ++E  A K++ ++IQ
Sbjct: 229 MEVAEEIGISQAQVSRLEKAAIKQMNKNIQ 258


>gi|323486723|ref|ZP_08092043.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323692138|ref|ZP_08106382.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
 gi|323399942|gb|EGA92320.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323503825|gb|EGB19643.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
          Length = 258

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 59/257 (22%), Positives = 111/257 (43%), Gaps = 17/257 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L   E+  L KR  + GD+ A  + +  +LRLV+ +   +      + ++   G I
Sbjct: 15  KLPLLSNDEKEELFKRILD-GDMDAREQYIKGNLRLVLSVIQRFSNSSENVDDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD  +  R +TY++  I   ++ Y LR  + +++  +           R   
Sbjct: 74  GLIKAIDNFDITQNVRFSTYAVPMILGEVKRY-LRDNNSIRVSRSLRDTAYKAIYAR--- 129

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + +   NLK   +  IA ++ VS+  +      +    SL   + +   +     D L
Sbjct: 130 --EGLMKRNLKEPTICEIADEIGVSKESITYALDAIQSPVSLYEPVYTDGGDPLYVMDQL 187

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             D    E+  IE          L  +M  L  RER I + R  +    T   ++ E  +
Sbjct: 188 S-DKKCSEEHWIEDIS-------LNEAMKRLPERERHIIDMRFFEGKTQT--EVAEEIHI 237

Query: 265 SRERVRQIEARAFKKVQ 281
           S+ +V ++E  A K ++
Sbjct: 238 SQAQVSRLEKSALKNMR 254


>gi|317129288|ref|YP_004095570.1| RNA polymerase, sigma 28 subunit, SigG [Bacillus cellulosilyticus
           DSM 2522]
 gi|315474236|gb|ADU30839.1| RNA polymerase, sigma 28 subunit, SigG [Bacillus cellulosilyticus
           DSM 2522]
          Length = 261

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 61/262 (23%), Positives = 119/262 (45%), Gaps = 27/262 (10%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+ +E  VL ++  ++GD  A   LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKNKEMRVLFEKM-QNGDEFAREELVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD  +  + +TY++  I   ++ Y LR  + +++  +         LR +  
Sbjct: 74  GLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRS---------LRDIAY 123

Query: 145 HLQAITDNNLKPEQ------VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
               + DN +  ++      V  IAK L+V + +++     +    SL   I +   +  
Sbjct: 124 KALQVRDNMMNEKKREREPTVQEIAKVLDVPKEDIVFALDAIQDPVSLFEPIYNDGGDPI 183

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
              D +  D     Q + E          L  +M  LN RE+ I + R  Q    T   +
Sbjct: 184 YVMDQISDDKQKDIQWIEEI--------ALKEAMIRLNDREKMILDMRFFQGK--TQMEV 233

Query: 259 SSEFEVSRERVRQIEARAFKKV 280
           + E  +S+ +V ++E  A +++
Sbjct: 234 ADEIGISQAQVSRLEKAAIQQM 255


>gi|169831144|ref|YP_001717126.1| FliA/WhiG family RNA polymerase sigma factor [Candidatus
           Desulforudis audaxviator MP104C]
 gi|169637988|gb|ACA59494.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Candidatus
           Desulforudis audaxviator MP104C]
          Length = 256

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 31/81 (38%), Positives = 46/81 (56%), Gaps = 3/81 (3%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           E+++EYV   R    GD  A + L   +LRLV  I   Y   G    +++S G IGL++A
Sbjct: 57  EEEKEYV---RRMLAGDEHARNILTERNLRLVAHIIKKYDSTGEDTDDLISIGTIGLIKA 113

Query: 90  VKKFDPERGFRLATYSMWWIK 110
           +  F+P +G RLATY+   I+
Sbjct: 114 INTFNPHKGARLATYAARCIE 134


>gi|304404022|ref|ZP_07385684.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
 gi|304347000|gb|EFM12832.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
          Length = 272

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 65/280 (23%), Positives = 125/280 (44%), Gaps = 54/280 (19%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L   E   L    +   + +A  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 27  KLPVLTNAEMRELFTALQTRNERAAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 86

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEY------ILRSWSLVKIGTTANQKRLFFN 138
           GLM+A+  FD  +  + +TY++  I   ++ Y      I  S SL  I   A Q R    
Sbjct: 87  GLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLRDIAYKALQVR---- 142

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
                    ++T+ N +   +  I++ L V + +V+          +L+A+         
Sbjct: 143 --------DSLTNANSREPTIFEISEALGVPKEDVVF---------ALDAI--------- 176

Query: 199 QWQDWL-----VYDHDGQEQVLIEKE--ERKNR------RNMLTRSMSVLNPRERRIFEA 245
             QD +     +Y HDG + + +  +  + KN+         L  +M  LN RE+ I  +
Sbjct: 177 --QDPVSLFEPIY-HDGGDPIYVMDQISDDKNKDISWIEEIALREAMHKLNDREKMIL-S 232

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            R  E    +E ++ E  +S+ +V ++E  A +++Q+ ++
Sbjct: 233 MRFFEGKTQME-VADEIGISQAQVSRLEKSAIQQMQKHVK 271


>gi|325678908|ref|ZP_08158506.1| putative RNA polymerase sigma-F factor [Ruminococcus albus 8]
 gi|324109412|gb|EGC03630.1| putative RNA polymerase sigma-F factor [Ruminococcus albus 8]
          Length = 217

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 51/187 (27%), Positives = 80/187 (42%), Gaps = 27/187 (14%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           +SA   L   +L LV   A  +RG G+   ++   G IGL++A K FD  RG + +TY++
Sbjct: 1   MSAESHLPEDNLGLVHLCANRFRGRGIEYDDLYGAGCIGLLKASKAFDSGRGVKFSTYAV 60

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I   ++  + R    VK+  +  +  L     RL G  Q     N +   V  +AK +
Sbjct: 61  PVILGEIKR-LFRDGGTVKVSRSLKELSL-----RLTGEAQVFAHKNGREPTVEELAKIV 114

Query: 167 NVSESEVISMNCRLAGDESLNA------LINSSDKNSSQWQ------DWLVYDHDGQEQV 214
                +VI         E+LNA      L    D+N +Q        D  + D     QV
Sbjct: 115 GTPVEDVI---------EALNAAQPVISLTVGDDENETQADLPAPAPDEDITDRLALRQV 165

Query: 215 LIEKEER 221
           L E +++
Sbjct: 166 LTELDDK 172


>gi|254479124|ref|ZP_05092475.1| RNA polymerase sigma-K factor [Carboxydibrachium pacificum DSM
           12653]
 gi|214034938|gb|EEB75661.1| RNA polymerase sigma-K factor [Carboxydibrachium pacificum DSM
           12653]
          Length = 234

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 30/82 (36%), Positives = 47/82 (57%), Gaps = 1/82 (1%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L  +EE    + YR  GD  A + L+  +LRLV  +   Y G G  + +++S G IGL++
Sbjct: 35  LSPEEERKYLEAYR-RGDEEARNILIERNLRLVAHVVKKYSGTGRDLDDLISIGTIGLIK 93

Query: 89  AVKKFDPERGFRLATYSMWWIK 110
           A+  +D E+G  LATY+   I+
Sbjct: 94  AIDTYDFEKGTHLATYAAKCIE 115


>gi|283779412|ref|YP_003370167.1| RNA polymerase, sigma 32 subunit, RpoH [Pirellula staleyi DSM 6068]
 gi|283437865|gb|ADB16307.1| RNA polymerase, sigma 32 subunit, RpoH [Pirellula staleyi DSM 6068]
          Length = 374

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 25/64 (39%), Positives = 42/64 (65%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L+  +R+V ++LRLVV IA  +        +++SEG   L++AV+KFD +RGFR +TY+ 
Sbjct: 192 LADRNRIVRANLRLVVSIAKKFSDARNSFDDLLSEGITSLLRAVEKFDYDRGFRFSTYAT 251

Query: 107 WWIK 110
             ++
Sbjct: 252 QAVR 255



 Score = 46.2 bits (108), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 28/70 (40%), Positives = 45/70 (64%), Gaps = 4/70 (5%)

Query: 225 RNMLTRSMSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R  L + +S L+PRER I   R     +E   TL++L+ EF V +ERVRQ+E RA  K++
Sbjct: 301 RRALAKMLSKLDPRERSIIRCRFGLDRKEQVQTLQSLAGEFGVCKERVRQLEMRAISKLR 360

Query: 282 ESIQKQVELS 291
            S+ ++++L+
Sbjct: 361 -SMAEEIDLT 369


>gi|20807708|ref|NP_622879.1| sporulation sigma factor SigK [Thermoanaerobacter tengcongensis
           MB4]
 gi|20516259|gb|AAM24483.1| DNA-directed RNA polymerase sigma subunits (sigma70/sigma32)
           [Thermoanaerobacter tengcongensis MB4]
          Length = 231

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 29/81 (35%), Positives = 48/81 (59%), Gaps = 3/81 (3%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           E++ +Y+ A R    GD  A + L+  +LRLV  +   Y G G  + +++S G IGL++A
Sbjct: 35  EEERKYLEAYR---RGDEEARNILIERNLRLVAHVVKKYSGTGRDLDDLISIGTIGLIKA 91

Query: 90  VKKFDPERGFRLATYSMWWIK 110
           +  +D E+G  LATY+   I+
Sbjct: 92  IDTYDFEKGTHLATYAAKCIE 112


>gi|312623242|ref|YP_004024855.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
 gi|312203709|gb|ADQ47036.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
          Length = 256

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 38/180 (21%), Positives = 87/180 (48%), Gaps = 19/180 (10%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L + Y++   +   + LV  +L +   IA  + G G+   ++     I L+ AV++F+P 
Sbjct: 18  LFEEYQKTKSIELRNELVNRYLYIAEIIAKKFVGRGIDYEDLYQVACIALINAVERFEPN 77

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +G++  +++   I   ++ Y     S++++      +R++    ++K   + ++    +P
Sbjct: 78  KGYKFTSFATPTIMGEIKRYFRDRASIIRLP-----RRIYETSAKIKLATEVLSTKLKRP 132

Query: 157 EQVVAIAKKLNVSESEVI------------SMNCRLAGDE--SLNALINSSDKNSSQWQD 202
            +V  IA+ LN+S  EV+            S++  +  DE  +L  ++  SD+N  Q ++
Sbjct: 133 PKVEEIAQHLNMSTEEVLEVMEASNNYLPQSLDQTMYEDEEMTLGDVLGKSDENILQVEN 192


>gi|291550014|emb|CBL26276.1| RNA polymerase, sigma 29 subunit, SigE [Ruminococcus torques L2-14]
          Length = 264

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 30/94 (31%), Positives = 53/94 (56%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE ++E  + +      D  A   L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 59  PPLENEKEREVVRWLGTDRDEKARKILIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGL 118

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++A+  F+P +  +LATY+   I+  +  Y+ R+
Sbjct: 119 IKAINTFNPSKKIKLATYASRCIENEILMYLRRN 152


>gi|302871380|ref|YP_003840016.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
 gi|302574239|gb|ADL42030.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
          Length = 255

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 39/149 (26%), Positives = 79/149 (53%), Gaps = 7/149 (4%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L  +E++ L KR +E GD  A    +  +LRLV+ +   +   G  + ++   G IG
Sbjct: 14  LPVLSHEEKFELLKRMKE-GDKEARRIFIEGNLRLVLSVVQKFANRGENLDDLFQVGCIG 72

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A+  FD  +  + +TY++  I   ++ Y LR  + ++I  +          + LK  
Sbjct: 73  LIKAIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNSMRISRSLKDTA----YKALKIK 127

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVI 174
            + I  N+ +P  +  IAK+L++++ E++
Sbjct: 128 EKYINKNHREP-TLEEIAKELSITKEELV 155


>gi|297560730|ref|YP_003679704.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
 gi|296845178|gb|ADH67198.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
          Length = 287

 Score = 53.5 bits (127), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 56/226 (24%), Positives = 104/226 (46%), Gaps = 17/226 (7%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRL----VTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           P+ E   E +LA+ +    D   A RL    V  +  LV K+A  Y G G P+ ++    
Sbjct: 29  PVKEIPAEELLAELHGLDDDDPRAVRLREEVVVRYQPLVNKLARRYNGRGEPLEDLKQTA 88

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            +GL++A++ + P+RG    +Y M  +   ++ +       +++     + R+     +L
Sbjct: 89  MVGLVKAIRGYRPDRGKPFISYLMPTVTGEIKRHFRDHTWAIRVPRRHQENRI-----KL 143

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQ 201
           +  L      + +      IAK++ + E EV+ +   +   ES  +L +++ D + S  Q
Sbjct: 144 RQVLNTFQQTHARVPTNAEIAKEMGLDEEEVVEL---VQASESYRSLSLDAPDSSDSDGQ 200

Query: 202 DWL-VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           +   + DH G E    E  ER  +R  L  +++ L  RER I + R
Sbjct: 201 EGSRLEDHLGSED---EGLERVVQRESLKPALARLPEREREILKLR 243


>gi|160914281|ref|ZP_02076502.1| hypothetical protein EUBDOL_00291 [Eubacterium dolichum DSM 3991]
 gi|158433908|gb|EDP12197.1| hypothetical protein EUBDOL_00291 [Eubacterium dolichum DSM 3991]
          Length = 260

 Score = 53.1 bits (126), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 59/240 (24%), Positives = 115/240 (47%), Gaps = 30/240 (12%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD +A   L+  +L+LV+ I   +      + ++   G IGL++++  FD +   R +TY
Sbjct: 34  GDQNAKEELINGNLKLVLSIVQRFANRCENMDDLFQVGCIGLVKSIDHFDLKHEVRFSTY 93

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           ++  I   ++ Y LR   ++++  + + K L +   RLK   +     + K   +  +A+
Sbjct: 94  AVPMIMGEIKRY-LRDNQVLRV--SRHLKDLAYKCFRLK---EEYVHQHQKEPSITWLAE 147

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI-----EKE 219
           +L V E +++      A D + N L        S ++   VY+ DG E  L+     EK+
Sbjct: 148 QLEVREKDIVD-----ALDSTQNVL--------SIFEP--VYNSDGDELYLLDQIRDEKD 192

Query: 220 ERKNRRNMLT--RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
           E     N+L+   S+  L  +E  I + R  Q+  +T   +++E  +S+ +V ++E  A 
Sbjct: 193 EIDLLNNVLSLRSSLKQLKEKELEILDKRYYQD--MTQTEIANELGISQAQVSRLEKSAI 250


>gi|268608170|ref|ZP_06141897.1| sporulation sigma factor SigG [Ruminococcus flavefaciens FD-1]
          Length = 259

 Score = 53.1 bits (126), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 28/102 (27%), Positives = 56/102 (54%), Gaps = 1/102 (0%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           ++ ++++ E+  L +  +  G   A  +L+  +LRLV+ +   + G G  I ++   G I
Sbjct: 15  ELKVMKEDEKMALLREIKATGSKEARDKLIKGNLRLVLSVIQRFTGRGEDIDDLFQIGVI 74

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           GL++A+  FD  +  R +TY +  I   ++ + LR +S VK+
Sbjct: 75  GLIKAINNFDLTKEVRFSTYCVPMISGELRRH-LRDYSHVKV 115


>gi|307717594|gb|ADN88850.1| RNA polymerase sigma-37 factor [Listeria innocua]
 gi|307717604|gb|ADN88855.1| RNA polymerase sigma-37 factor [Listeria innocua]
 gi|307717614|gb|ADN88860.1| RNA polymerase sigma-37 factor [Listeria innocua]
 gi|307717620|gb|ADN88863.1| RNA polymerase sigma-37 factor [Listeria innocua]
 gi|307717622|gb|ADN88864.1| RNA polymerase sigma-37 factor [Listeria innocua]
          Length = 220

 Score = 53.1 bits (126), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 55/217 (25%), Positives = 102/217 (47%), Gaps = 24/217 (11%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQEDGDEDAQYNLVIHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTREL 115

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +   
Sbjct: 116 QSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGT 172

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
            DG E+V        N+R +L + + VL+ RE++I +
Sbjct: 173 DDGFERV--------NQRMLLEKVLPVLDEREQKILQ 201


>gi|219115846|ref|XP_002178718.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217409485|gb|EEC49416.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 217

 Score = 53.1 bits (126), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 25/58 (43%), Positives = 37/58 (63%), Gaps = 1/58 (1%)

Query: 53  LVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           L+ S++RLVV IA  + +       E V EG +GL +A  ++DPERG R ATY+ +W+
Sbjct: 14  LIASNVRLVVSIAKKWAKNAHKAARETVQEGILGLAKAADRYDPERGLRFATYATYWV 71


>gi|291548178|emb|CBL21286.1| RNA polymerase, sigma 29 subunit, SigE [Ruminococcus sp. SR1/5]
          Length = 241

 Score = 53.1 bits (126), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 25/68 (36%), Positives = 43/68 (63%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +LRLVV IA  +   G+ + +++S G IGL++A+  FDP +  +LATY+   I+  
Sbjct: 62  LIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFDPVKNIKLATYASRCIENE 121

Query: 113 MQEYILRS 120
           +  Y+ R+
Sbjct: 122 ILMYLRRN 129


>gi|302391216|ref|YP_003827036.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Acetohalobium
           arabaticum DSM 5501]
 gi|302203293|gb|ADL11971.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Acetohalobium
           arabaticum DSM 5501]
          Length = 235

 Score = 53.1 bits (126), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 34/105 (32%), Positives = 56/105 (53%), Gaps = 2/105 (1%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           S + +G + L  YI      P  L+ +EE     RY E GD  A   L+  ++RLV  I 
Sbjct: 11  SSLADGILVLISYIANNNIFPQPLDDEEEKKYLTRYLE-GDEEAKEVLIEHNMRLVAHIV 69

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
             Y    +   +++S G+IGL++A++ +DP +  +LATY+   I+
Sbjct: 70  KKYNNSNVDKEDLISIGSIGLIKAIETYDPSKKVKLATYASRCIE 114


>gi|303241077|ref|ZP_07327586.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302591337|gb|EFL61076.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 246

 Score = 53.1 bits (126), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 56/250 (22%), Positives = 116/250 (46%), Gaps = 29/250 (11%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A   LV  ++ LV  I   ++  G    ++   G IGL++A+KKFD     + +
Sbjct: 17  KSGDKQAQSILVERNVGLVWSIVKRFQNRGYETDDIYQIGCIGLIKAIKKFDDSFDVKFS 76

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK----PEQ 158
           TY++  I   ++ +I R   ++K+  +         L+ L   ++   +  +K       
Sbjct: 77  TYAVPMIIGEIKRFI-RDDGIIKVSRS---------LKELSNKIRVTKEIMMKELGREPS 126

Query: 159 VVAIAKKLNVSESEVI---SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
           +  I+ +++V+  E++     NC     ESL   +  SD ++    D L  + + +E  L
Sbjct: 127 ISEISLRMDVAAEELVMAMEANC---SPESLYNTVGDSDTSTVLLIDKLNNESNDEEVDL 183

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
           ++K +       L   ++ L PRE++I   R  +E   T   ++    +S+ +V +IE +
Sbjct: 184 VDKID-------LRLVLNTLKPREKQIIILRYFKEK--TQVQIAKMLGISQVQVSRIEKK 234

Query: 276 AFKKVQESIQ 285
              ++++ I+
Sbjct: 235 ILDEIKKKIK 244


>gi|313902394|ref|ZP_07835797.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Thermaerobacter
           subterraneus DSM 13965]
 gi|313467325|gb|EFR62836.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Thermaerobacter
           subterraneus DSM 13965]
          Length = 247

 Score = 53.1 bits (126), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 36/102 (35%), Positives = 53/102 (51%), Gaps = 2/102 (1%)

Query: 10  VNGEIGLSRYIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           V G + L  Y+   R  P  L  +EE    +R R  GD  A   L+  +LRLV  IA  +
Sbjct: 14  VRGLLYLVGYLQTGRSFPQPLSPEEEAHYLERMR-CGDERAREVLIERNLRLVAHIAKKF 72

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
              G    +++S G +GL++ V  +DP +G RLATY+   I+
Sbjct: 73  DETGEDPEDLISIGTVGLIKGVDTYDPSKGTRLATYAARCIE 114


>gi|224992858|gb|ACN76144.1| SigB [Listeria monocytogenes]
 gi|224992860|gb|ACN76145.1| SigB [Listeria monocytogenes]
 gi|224992862|gb|ACN76146.1| SigB [Listeria monocytogenes]
 gi|224992864|gb|ACN76147.1| SigB [Listeria monocytogenes]
 gi|224992866|gb|ACN76148.1| SigB [Listeria monocytogenes]
 gi|224992868|gb|ACN76149.1| SigB [Listeria monocytogenes]
 gi|224992870|gb|ACN76150.1| SigB [Listeria monocytogenes]
 gi|224992872|gb|ACN76151.1| SigB [Listeria monocytogenes]
 gi|224992876|gb|ACN76153.1| SigB [Listeria monocytogenes]
 gi|224992878|gb|ACN76154.1| SigB [Listeria monocytogenes]
 gi|224992880|gb|ACN76155.1| SigB [Listeria monocytogenes]
 gi|224992882|gb|ACN76156.1| SigB [Listeria monocytogenes]
 gi|224992884|gb|ACN76157.1| SigB [Listeria monocytogenes]
 gi|224992888|gb|ACN76159.1| SigB [Listeria monocytogenes]
 gi|224992890|gb|ACN76160.1| SigB [Listeria monocytogenes]
 gi|224992892|gb|ACN76161.1| SigB [Listeria monocytogenes]
 gi|224992894|gb|ACN76162.1| SigB [Listeria monocytogenes]
 gi|224992896|gb|ACN76163.1| SigB [Listeria monocytogenes]
 gi|224992900|gb|ACN76165.1| SigB [Listeria monocytogenes]
          Length = 214

 Score = 53.1 bits (126), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 54/211 (25%), Positives = 101/211 (47%), Gaps = 24/211 (11%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D   G  
Sbjct: 4   YQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKS 63

Query: 101 LATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
              +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T       Q+
Sbjct: 64  FEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTRELQSSPQI 117

Query: 160 VAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
             IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +    DG E+
Sbjct: 118 SDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTDDGFER 174

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           V        N+R +L + + VL+ RE++I +
Sbjct: 175 V--------NQRMLLEKVLPVLDEREQKILQ 197


>gi|255994576|ref|ZP_05427711.1| RNA polymerase sigma-B factor [Eubacterium saphenum ATCC 49989]
 gi|255993289|gb|EEU03378.1| RNA polymerase sigma-B factor [Eubacterium saphenum ATCC 49989]
          Length = 249

 Score = 53.1 bits (126), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 54/220 (24%), Positives = 103/220 (46%), Gaps = 27/220 (12%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           ++Y +  D++  + +V  +L +V  +   Y   G+   ++   G + L+ AV++FD  RG
Sbjct: 8   EKYAKTRDINERNAIVEDYLYIVDILVRKYLNKGVEYDDLYQVGAMALIMAVERFDASRG 67

Query: 99  FRLATYSMWWIKAAMQEYIL-RSWSL-----VKIGTTANQ---KRLFFNLRRLKGHLQAI 149
           F  ++++   I   +++Y   + W L     VK    A Q   + LF  L+R     +  
Sbjct: 68  FEFSSFATPTILGEIKKYFRDKEWKLKVPRSVKEANAAIQSARESLFAKLQRDPTVKEIA 127

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
            + N+K E+V     KL  S     +++  +  D+S       SD   S+++ ++  +  
Sbjct: 128 EEKNMKEEEVA----KLIDSSMAYNTLSLDVTFDDS------GSDSGVSRYEKYMAVEGS 177

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           G E   +E EE      M+   +SVL+ + R IF+ R L+
Sbjct: 178 GIES--LEYEE------MIESILSVLSEKNRYIFKKRFLE 209


>gi|205373280|ref|ZP_03226084.1| sporulation sigma factor SigG [Bacillus coahuilensis m4-4]
          Length = 258

 Score = 53.1 bits (126), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 66/279 (23%), Positives = 121/279 (43%), Gaps = 53/279 (18%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+ +E   L ++  + GD  +  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKNEEMRELFRKM-QAGDTYSREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEY------ILRSWSLVKIGTTANQKRLFFN 138
           GLM+++  FD  +  R +TY++  I   ++ Y      I  S SL  I   A Q R    
Sbjct: 74  GLMKSIDNFDLSQNVRFSTYAVPMIIGEIRRYLRDNNPIRVSRSLRDIAYKALQAR---- 129

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
             +L G          K      IAK L+V   +++          +L+A+         
Sbjct: 130 -EKLMGETS-------KEPTAEEIAKVLDVPHEDIVF---------ALDAI--------- 163

Query: 199 QWQDWL-----VYDHDGQEQVLIEKEERKNRRNM-------LTRSMSVLNPRERRIFEAR 246
             QD +     +Y+  G    ++++   +  R++       L   +  LN RE+ I   R
Sbjct: 164 --QDPVSLFEPIYNDGGDPIFVMDQLSDERNRDVNWIEEIALKEGLRRLNDREKMIIRKR 221

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             Q    T   ++ E  +S+ +V ++E  A K + ++IQ
Sbjct: 222 FFQGK--TQMEVADEIGISQAQVSRLEKAAIKHMNKNIQ 258


>gi|224992874|gb|ACN76152.1| SigB [Listeria monocytogenes]
 gi|224992886|gb|ACN76158.1| SigB [Listeria monocytogenes]
 gi|224992898|gb|ACN76164.1| SigB [Listeria monocytogenes]
 gi|224992902|gb|ACN76166.1| SigB [Listeria monocytogenes]
          Length = 214

 Score = 53.1 bits (126), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 54/211 (25%), Positives = 101/211 (47%), Gaps = 24/211 (11%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D   G  
Sbjct: 4   YQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKS 63

Query: 101 LATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
              +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T       Q+
Sbjct: 64  FEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTRELQSSPQI 117

Query: 160 VAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
             IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +    DG E+
Sbjct: 118 SDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTDDGFER 174

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           V        N+R +L + + VL+ RE++I +
Sbjct: 175 V--------NQRMLLEKVLPVLDEREQKILQ 197


>gi|332977445|gb|EGK14221.1| DNA-directed RNA polymerase sigma subunit SigF [Desmospora sp.
           8437]
          Length = 254

 Score = 53.1 bits (126), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 55/247 (22%), Positives = 115/247 (46%), Gaps = 28/247 (11%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A  RLV  ++RLV  +   +   G    ++   G IGL++AV KFD     + +
Sbjct: 26  QKGDTEARDRLVQHNIRLVWSVVQRFLNRGYEAEDLFQIGCIGLLKAVDKFDLAYDVKFS 85

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I   +Q + LR   +VK+  +   K L   +R++K  +   T    +   +  +
Sbjct: 86  TYAVPMIIGEIQRF-LRDDGMVKVSRSL--KELSNRIRKVKDEM---TKGLGRSPTIQEL 139

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ-----EQVLIE 217
           ++++ V+  E++                  +++  +   +  VY++DG      +Q+  E
Sbjct: 140 SEEMGVTPEEIV--------------FAQEANRTPTSIHE-TVYENDGDPITLMDQIADE 184

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
           +EE    R  L  ++  L  RER I   R  ++   T   ++    +S+ +V ++E +  
Sbjct: 185 EEEGWFDRMALKEAIRQLEERERLIVYLRFFKDQ--TQSEVAQRLGISQVQVSRLEKKII 242

Query: 278 KKVQESI 284
           ++++++I
Sbjct: 243 RRMRDAI 249


>gi|167770367|ref|ZP_02442420.1| hypothetical protein ANACOL_01710 [Anaerotruncus colihominis DSM
           17241]
 gi|167667689|gb|EDS11819.1| hypothetical protein ANACOL_01710 [Anaerotruncus colihominis DSM
           17241]
          Length = 225

 Score = 53.1 bits (126), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 45/179 (25%), Positives = 81/179 (45%), Gaps = 20/179 (11%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           ++ ++ LV   A  ++G G+   ++   G +GL +AV  FDP+RG +L+TY++  I   M
Sbjct: 16  ISENIGLVHSCAHRFKGRGIEYDDLFQAGCMGLCKAVDAFDPQRGVKLSTYAVPVILGEM 75

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
           +  + R    VK+  T  +     +LR  +   Q       +P  V  +A+ + + E +V
Sbjct: 76  RR-LFRDGGAVKVSRTLKE----LSLRIGRAREQLALALGREP-SVSELAQAMELPEEQV 129

Query: 174 ISMNCRLA-------GDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +   C  A        DE     I+  +D    Q  D +  +       ++EK E K+R
Sbjct: 130 VEALCAAAPPLSLTESDEDGGGQIDLPADSPEDQLADVISLNQ------VVEKLEDKDR 182


>gi|225568718|ref|ZP_03777743.1| hypothetical protein CLOHYLEM_04797 [Clostridium hylemonae DSM
           15053]
 gi|225162217|gb|EEG74836.1| hypothetical protein CLOHYLEM_04797 [Clostridium hylemonae DSM
           15053]
          Length = 189

 Score = 53.1 bits (126), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 29/79 (36%), Positives = 46/79 (58%), Gaps = 1/79 (1%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           ++Y E GDL A H L+  +LRLV  I   Y+       +++S G IGL++AV  F+P++ 
Sbjct: 2   QKYTE-GDLEAKHVLIERNLRLVAHIVKKYQSLEEDNEDLLSIGTIGLIKAVVTFNPDKC 60

Query: 99  FRLATYSMWWIKAAMQEYI 117
            RL TY+   I+  +  Y+
Sbjct: 61  VRLGTYAARCIENEILMYL 79


>gi|299472406|emb|CBN77594.1| RpoD family RNA polymerase sigma factor [Ectocarpus siliculosus]
          Length = 242

 Score = 53.1 bits (126), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 52/232 (22%), Positives = 100/232 (43%), Gaps = 37/232 (15%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++ EG I L  A +++DP+RG R  TY+ W ++AA +       + + I      + ++
Sbjct: 15  DLIQEGAIALHLAAERYDPQRGVRFFTYADWSLRAAFERAEASQATTIAI-----PRYVY 69

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
              RRLK    AI   +  P+    +A  L +SE ++  +  R    +S+N ++ SS   
Sbjct: 70  VQKRRLK----AILGQHCGPQTSQDLATSLGISERQLAKLLRRAKDCQSMNRVLVSSGVA 125

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI------FEARRLQE 250
             +    ++      E +L     R +    L   +  L P+E  +         RR + 
Sbjct: 126 LGE----MIPGAQSCEDIL----RRLDAEASLVGLLGTLKPQEEEVIVHRYGLFGRRRKS 177

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQKPRY 302
            P     +++   VSR+ V ++   A +K++ S +            Q+PR+
Sbjct: 178 TPA----VAAVMGVSRQYVGRVHRSALEKMRASFEAD----------QQPRF 215


>gi|307717590|gb|ADN88848.1| RNA polymerase sigma-37 factor [Listeria welshimeri]
 gi|307717592|gb|ADN88849.1| RNA polymerase sigma-37 factor [Listeria welshimeri]
 gi|307717624|gb|ADN88865.1| RNA polymerase sigma-37 factor [Listeria welshimeri]
 gi|307717626|gb|ADN88866.1| RNA polymerase sigma-37 factor [Listeria welshimeri]
          Length = 220

 Score = 53.1 bits (126), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 55/217 (25%), Positives = 102/217 (47%), Gaps = 24/217 (11%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTREL 115

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +   
Sbjct: 116 QSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGT 172

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
            DG E+V        N+R +L + + VL+ RE+ I +
Sbjct: 173 DDGFERV--------NQRMLLEKVLPVLDEREQMILQ 201


>gi|326791235|ref|YP_004309056.1| RNA polymerase, sigma 28 subunit, SigK [Clostridium lentocellum DSM
           5427]
 gi|326541999|gb|ADZ83858.1| RNA polymerase, sigma 28 subunit, SigK [Clostridium lentocellum DSM
           5427]
          Length = 220

 Score = 53.1 bits (126), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 27/84 (32%), Positives = 47/84 (55%), Gaps = 2/84 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  ++E++ L     + GD +A + L+  +LRLV  I   Y      + +++S G IGL
Sbjct: 19  PLSAEEEKHYL--ECYQDGDEAAKNILIERNLRLVAHIVKKYNNINNDVDDLISIGTIGL 76

Query: 87  MQAVKKFDPERGFRLATYSMWWIK 110
           ++ +  FDP +  RLATY+   I+
Sbjct: 77  IKGISSFDPNKCTRLATYAARCIE 100


>gi|121488781|emb|CAJ18275.1| sigma 70-type sigma factor [Chlorobium phaeovibrioides]
          Length = 165

 Score = 53.1 bits (126), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 48/180 (26%), Positives = 91/180 (50%), Gaps = 33/180 (18%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTTA 130
           ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++      Q  I+R   L ++GT  
Sbjct: 1   DLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVR-LPLNRVGTLN 59

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNAL 189
              + +  L +     +   D N K      +A +L++ +S+ ++   ++AG   S++A 
Sbjct: 60  KISKAYSQLEQ-----EYERDPNTK-----ELANQLDM-DSQDVADTLKIAGRHVSVDAP 108

Query: 190 INSSDKN---SSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
               D N        D  + DH   ++ + +E E          RS+SVL PRE  + ++
Sbjct: 109 FAQGDDNRLLDVLQNDGHLPDHGLNRDSLTLEVE----------RSLSVLAPREADVIKS 158


>gi|134298861|ref|YP_001112357.1| sigma-70 region 2 domain-containing protein [Desulfotomaculum
           reducens MI-1]
 gi|134051561|gb|ABO49532.1| sigma-70 region 2 domain protein [Desulfotomaculum reducens MI-1]
          Length = 118

 Score = 53.1 bits (126), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 36/106 (33%), Positives = 56/106 (52%), Gaps = 3/106 (2%)

Query: 9   IVNGEIGLSRYI-HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           +VNG + L  YI +     P+ E +E   LA      GD  A + L   +LRLV  I   
Sbjct: 13  VVNGVMALVSYIANNTFPQPLKEVEEARYLA--LLAEGDEMARNILTERNLRLVAHIVKK 70

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           +   G  + +++S G IGL++A+  F  ++G RLATY+   I+ A+
Sbjct: 71  FDSTGEDVDDLISIGTIGLIKAINTFKADKGTRLATYAARCIENAI 116


>gi|331090017|ref|ZP_08338907.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium 3_1_46FAA]
 gi|330402931|gb|EGG82497.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium 3_1_46FAA]
          Length = 245

 Score = 53.1 bits (126), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 34/110 (30%), Positives = 55/110 (50%), Gaps = 4/110 (3%)

Query: 15  GLSRYIHEIRKI----PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           G  R +H I       P LE   E  +  R        A   L+  +LRLVV IA  +  
Sbjct: 24  GSGREVHYIGGTEVLPPPLEGMRESEMINRLGTEYAEDAKKVLIEHNLRLVVYIAKKFDN 83

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
            G+ + +++S G IGL++A+  F+P +  +LATY+   I+  +  Y+ R+
Sbjct: 84  TGVGVEDLISIGTIGLIKAINTFNPTKKIKLATYASRCIENEILMYLRRN 133


>gi|224992792|gb|ACN76111.1| SigB [Listeria innocua]
 gi|224992796|gb|ACN76113.1| SigB [Listeria innocua]
 gi|224992810|gb|ACN76120.1| SigB [Listeria innocua]
 gi|224992814|gb|ACN76122.1| SigB [Listeria innocua]
 gi|224992832|gb|ACN76131.1| SigB [Listeria innocua]
 gi|224992834|gb|ACN76132.1| SigB [Listeria innocua]
 gi|224992848|gb|ACN76139.1| SigB [Listeria innocua]
 gi|224992850|gb|ACN76140.1| SigB [Listeria innocua]
 gi|224992856|gb|ACN76143.1| SigB [Listeria innocua]
          Length = 214

 Score = 52.8 bits (125), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 54/211 (25%), Positives = 101/211 (47%), Gaps = 24/211 (11%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D   G  
Sbjct: 4   YQENGDEDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKS 63

Query: 101 LATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
              +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T       Q+
Sbjct: 64  FEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTRELQSSPQI 117

Query: 160 VAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
             IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +    DG E+
Sbjct: 118 SDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTDDGFER 174

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           V        N+R +L + + VL+ RE++I +
Sbjct: 175 V--------NQRMLLEKVLPVLDEREQKILQ 197


>gi|225026792|ref|ZP_03715984.1| hypothetical protein EUBHAL_01044 [Eubacterium hallii DSM 3353]
 gi|224955911|gb|EEG37120.1| hypothetical protein EUBHAL_01044 [Eubacterium hallii DSM 3353]
          Length = 245

 Score = 52.8 bits (125), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 62/248 (25%), Positives = 121/248 (48%), Gaps = 25/248 (10%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L K+ +E G+  A   LV  +  L+  +   ++G G    ++   G+IGL++ ++ FD E
Sbjct: 7   LIKQAKE-GNKEAQSILVEENSGLIWSVVKRFQGRGYDKEDLFQIGSIGLLKCIENFDLE 65

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           R  + +TY++  I   ++ + LR   +VK+  +   K   + ++R K H Q +   N +P
Sbjct: 66  RNVKFSTYAVPLIMGEIKRF-LRDDGIVKVSRSL--KEASYKIKREKEHYQKLY--NREP 120

Query: 157 EQVVAIAKKLNVSESEVI-SMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
             +  IA  L++ ES+++ +M    +G E  SL+ +I  S+ +    +D L    D  EQ
Sbjct: 121 -TLKEIAVTLDMDESDILMAME---SGQEVCSLHQVIYQSEGDEIHLEDKLEQQADLIEQ 176

Query: 214 VLIEKEERKNRRNMLTRS-MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
            +          N+  +  +  LN +ER+I   R  Q    T   ++ +  +S+ +V ++
Sbjct: 177 TV---------DNIYVQELLKKLNEQERQIIHMRYFQNQ--TQAAIAKKIGISQVQVSRM 225

Query: 273 EARAFKKV 280
           E +   K+
Sbjct: 226 EKKILNKL 233


>gi|161898843|gb|ABX80411.1| SigB [Listeria monocytogenes]
          Length = 228

 Score = 52.8 bits (125), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 54/211 (25%), Positives = 101/211 (47%), Gaps = 24/211 (11%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D   G  
Sbjct: 6   YQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKS 65

Query: 101 LATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
              +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T       Q+
Sbjct: 66  FEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTRELQSSPQI 119

Query: 160 VAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
             IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +    DG E+
Sbjct: 120 SDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTDDGFER 176

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           V        N+R +L + + VL+ RE++I +
Sbjct: 177 V--------NQRMLLEKVLPVLDEREQKILQ 199


>gi|153938360|ref|YP_001391942.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum F str. Langeland]
 gi|152934256|gb|ABS39754.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum F str. Langeland]
 gi|295319962|gb|ADG00340.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum F str. 230613]
          Length = 242

 Score = 52.8 bits (125), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 57/213 (26%), Positives = 101/213 (47%), Gaps = 18/213 (8%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           ++VS G IGLM A+ KFD  +G + +TY+   IK +M + + R+  + K G      R  
Sbjct: 41  DLVSYGMIGLMDALNKFDESKGMKFSTYASIRIKGSMIDELRRNSPISK-GAMDKLNRYN 99

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV--ISMNCRLAGDESLNALINSSD 194
             + +L+  L        K   ++ IA +LN+S  EV  I          SL  LI SS+
Sbjct: 100 EAIEKLQKKLN-------KEPNLIQIAGELNISLKEVSEIENYINYISVISLEDLIFSSE 152

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRR-NMLTRSMSVLNPRERRIFEARRLQENPV 253
                    L+     ++    EK   +N + + L +++ +LN ++R +      +E  +
Sbjct: 153 DEVP-----LIGTIKDEKSPSPEKHVEENEQLDYLAKAIELLNEKDRLVVTLYYYEE--L 205

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TL+ +     VS  RV Q+ +RA   +++++ K
Sbjct: 206 TLKEIGKILNVSESRVCQLHSRAIIHLKKAMAK 238


>gi|153814605|ref|ZP_01967273.1| hypothetical protein RUMTOR_00819 [Ruminococcus torques ATCC 27756]
 gi|317501234|ref|ZP_07959439.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|145848099|gb|EDK25017.1| hypothetical protein RUMTOR_00819 [Ruminococcus torques ATCC 27756]
 gi|316897410|gb|EFV19476.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
          Length = 246

 Score = 52.8 bits (125), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 34/110 (30%), Positives = 55/110 (50%), Gaps = 4/110 (3%)

Query: 15  GLSRYIHEIRKI----PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           G  R +H I       P LE   E  +  R        A   L+  +LRLVV IA  +  
Sbjct: 25  GSGREVHYIGGTEVLPPPLEGMRESEMINRLGTEYAEDAKKVLIEHNLRLVVYIAKKFDN 84

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
            G+ + +++S G IGL++A+  F+P +  +LATY+   I+  +  Y+ R+
Sbjct: 85  TGVGVEDLISIGTIGLIKAINTFNPTKKIKLATYASRCIENEILMYLRRN 134


>gi|161898921|gb|ABX80450.1| SigB [Listeria monocytogenes]
          Length = 231

 Score = 52.8 bits (125), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 54/211 (25%), Positives = 101/211 (47%), Gaps = 24/211 (11%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D   G  
Sbjct: 6   YQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKS 65

Query: 101 LATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
              +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T       Q+
Sbjct: 66  FEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTRELQSSPQI 119

Query: 160 VAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
             IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +    DG E+
Sbjct: 120 SDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTDDGFER 176

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           V        N+R +L + + VL+ RE++I +
Sbjct: 177 V--------NQRMLLEKVLPVLDEREQKILQ 199


>gi|332970514|gb|EGK09503.1| RNA polymerase sigma factor SigB [Desmospora sp. 8437]
          Length = 261

 Score = 52.8 bits (125), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 59/250 (23%), Positives = 119/250 (47%), Gaps = 16/250 (6%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L +RY+E  D      LV     LV  +A  +     P  ++V  G IGL+ A+K++DP+
Sbjct: 18  LIRRYQEESDEEIQEVLVDHFTPLVETLASKFTKGSEPFEDLVQVGMIGLLAALKRYDPD 77

Query: 97  RGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            G    ++++  I   ++ +I  ++WS+         +R+     R+K   + +T    +
Sbjct: 78  FGKSFESFAVPTIVGEIKRHIRDKTWSV------HVPRRIKELGPRIKKAAEELTIRYQR 131

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQV 214
              V  IA+ L+V+  EV+     +    S NA+ ++S  + +++     + D  G    
Sbjct: 132 SPSVDEIAQYLDVTPEEVLET---MEMGRSYNAVSVDSPIEANNEGSQVTLLDLVGNRDA 188

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
             EK    +++ +L ++  VL  RE+ I   R    + ++ + +  E  +S+  V +++ 
Sbjct: 189 GFEK---VDQQLLLQKAFQVLTDREQAII--RMTFFDNLSQKQVGDELGISQMHVSRLQR 243

Query: 275 RAFKKVQESI 284
           RA  K++E+I
Sbjct: 244 RALGKLREAI 253


>gi|312134672|ref|YP_004002010.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|311774723|gb|ADQ04210.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor owensensis OL]
          Length = 255

 Score = 52.8 bits (125), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 39/149 (26%), Positives = 78/149 (52%), Gaps = 7/149 (4%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L  +E++ L KR +E GD  A    +  +LRLV+ +   +   G  + ++   G IG
Sbjct: 14  LPVLSHEEKFELLKRMKE-GDKEARRIFIEGNLRLVLSVVQKFANRGENLDDLFQVGCIG 72

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A+  FD  +  + +TY++  I   ++ Y LR  + ++I  +          + LK  
Sbjct: 73  LIKAIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNSMRISRSLKDTA----YKALKIK 127

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVI 174
            + I  N  +P  +  IAK+L++++ E++
Sbjct: 128 EKYINKNQREP-TLEEIAKELSITKEELV 155


>gi|320102910|ref|YP_004178501.1| RNA polymerase sigma-28 subunit SigD/FliA/WhiG [Isosphaera pallida
           ATCC 43644]
 gi|319750192|gb|ADV61952.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Isosphaera
           pallida ATCC 43644]
          Length = 273

 Score = 52.8 bits (125), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 54/215 (25%), Positives = 101/215 (46%), Gaps = 17/215 (7%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           G+ + +++S G  GLM A+  FD  RG +  TY +  I+ AM +  LR+   V     + 
Sbjct: 65  GVDLDDLISAGTFGLMDAIDAFDLSRGVKFETYCVPRIRGAMLDE-LRTMDWVPRLVRSK 123

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS--ESEVISMNCRLAGDESLNAL 189
             R    +   +  L+AI   + +P     IA++L V+  E E +++     G  SLN  
Sbjct: 124 HSR----MEEARKALEAI---HGRPPTDAEIAERLGVTPEEFEKMALESNAVGLVSLNKK 176

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
              +D      +  ++ D  G++     + +RK+   M+TR    LN  ER I      +
Sbjct: 177 WYETDSYKDVREIDILEDKKGEDPT--RRLQRKDLMRMVTRG---LNRNERLIIILYYYE 231

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           E  +T++ + +  ++S  RV Q+ +   +++Q  +
Sbjct: 232 E--LTMKEIGATLDLSESRVSQMHSSIIQRLQSQL 264


>gi|291550016|emb|CBL26278.1| RNA polymerase, sigma subunit, RpsG/SigG [Ruminococcus torques
           L2-14]
          Length = 260

 Score = 52.8 bits (125), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 39/154 (25%), Positives = 77/154 (50%), Gaps = 15/154 (9%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L ++E+  L +R R  GD  A    +  +LRLV+ +   +        ++   G +
Sbjct: 15  KLPLLREKEKEELFRRIR-QGDKLAREEYIKGNLRLVLSVMKRFDSSNENADDLFQIGCV 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++AV  FDP+R  + +TY++  I   ++ Y+  + SL          R+  +LR +  
Sbjct: 74  GLVKAVDNFDPDRQVKFSTYAVPMIIGEIRRYLRDNSSL----------RVSRSLRDIAY 123

Query: 145 HL----QAITDNNLKPEQVVAIAKKLNVSESEVI 174
            +    +     N+K   +  IA+++ +S+ EV+
Sbjct: 124 KVIYTREGYIRKNMKEPSIQEIAEEIGLSKEEVV 157


>gi|255505283|ref|ZP_05345211.3| RNA polymerase sigma-E factor [Bryantella formatexigens DSM 14469]
 gi|255268593|gb|EET61798.1| RNA polymerase sigma-E factor [Bryantella formatexigens DSM 14469]
          Length = 249

 Score = 52.8 bits (125), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 28/79 (35%), Positives = 48/79 (60%), Gaps = 2/79 (2%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
           RE G+  A   L+  +LRLVV IA  +   G+ + +++S G IGL++A+  F+P +  +L
Sbjct: 61  RESGE--AKSLLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFNPGKNIKL 118

Query: 102 ATYSMWWIKAAMQEYILRS 120
           ATY+   I+  +  Y+ R+
Sbjct: 119 ATYASRCIENEILMYLRRT 137


>gi|133481|sp|P26768|RPSX_BACTK RecName: Full=Putative RNA polymerase sigma-G factor; AltName:
           Full=ORF3
 gi|580955|emb|CAA40027.1| unnamed protein product [Bacillus thuringiensis serovar kurstaki]
          Length = 125

 Score = 52.8 bits (125), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 28/95 (29%), Positives = 55/95 (57%), Gaps = 5/95 (5%)

Query: 25  KIPMLEKQEEYVLAKRYRE--HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           K+P+L+ +E   + K +RE   G++SA  +LV  +LRLV+ +   +   G  + ++   G
Sbjct: 15  KLPVLKNEE---MRKLFREMQSGEISAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVG 71

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
            IGLM+++  FD  +  + +TY++  I   ++ Y+
Sbjct: 72  CIGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYL 106


>gi|288573001|ref|ZP_06391358.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Dethiosulfovibrio
           peptidovorans DSM 11002]
 gi|288568742|gb|EFC90299.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Dethiosulfovibrio
           peptidovorans DSM 11002]
          Length = 248

 Score = 52.8 bits (125), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 58/211 (27%), Positives = 103/211 (48%), Gaps = 24/211 (11%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL   +++S G +GL+ A+ +F+ ERGF   T+++  I+ A+ + + +     + G    
Sbjct: 46  GLDYEDLISFGLMGLLDAIDRFEIERGFSFQTFAVPRIRGAVLDELRKCDWFSRTGREKL 105

Query: 132 QKRLFFNLRRLKGHLQAIT--DNNLKPEQVVAIAKKLNVSESEVISMNCR---LAGDESL 186
           Q RL     RL   +Q IT  D +LK E  V      + +  E++S+  R   ++ DE  
Sbjct: 106 Q-RLERATERL--MIQGITPDDESLKREMDVD-----DKTYREMLSLASRGYVVSLDE-- 155

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              + S D+   Q  D L Y     ++ L  +EE    R+++  +++ L+ RER +    
Sbjct: 156 ---VMSLDEGDVQKGDLLSYTGASAQEFLENREE----RDLVVGALNRLSERERLVLSMY 208

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAF 277
            L+E  +TL+ +     V+  RV QI  +A 
Sbjct: 209 YLEE--MTLKEIGLVLGVTESRVSQIHGKAI 237


>gi|167770197|ref|ZP_02442250.1| hypothetical protein ANACOL_01540 [Anaerotruncus colihominis DSM
           17241]
 gi|167667519|gb|EDS11649.1| hypothetical protein ANACOL_01540 [Anaerotruncus colihominis DSM
           17241]
          Length = 257

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 61/260 (23%), Positives = 127/260 (48%), Gaps = 30/260 (11%)

Query: 37  LAKRYREHGDLSAAHRLVT--SHLRLVVKIAMG--YRGYGLPISEVVSEGNIGLMQAVKK 92
           L + Y+E G     +R+V   S++   V I M   +  Y   I E+V++G I L+ +V +
Sbjct: 14  LMRLYKETGSQELRNRIVMHYSYIAKSVAIEMNNMFHKYA-TIEEMVNQGVIALIDSVDR 72

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           FDP+ G + +TY+   +K A+ +Y+ +  W   ++   A +    +N   +K     +  
Sbjct: 73  FDPDHGVKFSTYAFTKVKGAIIDYVRKQDWLPRRVRHNAIRVNNAYNDLPMK-----LGR 127

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHD 209
           N  + E    +AK+L++SE E       ++G+   S  +L+    +N +     +++  +
Sbjct: 128 NPTRSE----MAKQLDMSEREFDQCIYEMSGESIFSYESLLADGPQNQN-----MLWPME 178

Query: 210 GQEQVLIEKE---ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           G+   ++  E   + K  R  L  ++  LN +ER +  +    EN +T++ +     VS 
Sbjct: 179 GE---IVNPEGCVDAKELREQLGMAIDSLNEQERHVL-SLYYYEN-LTMKEIGGVLGVSE 233

Query: 267 ERVRQIEARAFKKVQESIQK 286
           +R+ QI  +  +K++  +++
Sbjct: 234 QRIGQINRKLIQKLRNKLEQ 253


>gi|239626528|ref|ZP_04669559.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47_FAA]
 gi|239516674|gb|EEQ56540.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47FAA]
          Length = 209

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 28/80 (35%), Positives = 51/80 (63%), Gaps = 3/80 (3%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           +++EY+  +R +E GD SA   L+  ++RLV  +   Y+G    + +++S G IGL++AV
Sbjct: 12  EEKEYL--ERCKE-GDQSARDMLIEHNMRLVAHVVKKYQGSDYDMEDLLSVGTIGLIKAV 68

Query: 91  KKFDPERGFRLATYSMWWIK 110
             F+ ++G RLATY+   ++
Sbjct: 69  NTFNADKGSRLATYAARCVE 88


>gi|168186139|ref|ZP_02620774.1| RNA polymerase sigma-D factor [Clostridium botulinum C str. Eklund]
 gi|169295860|gb|EDS77993.1| RNA polymerase sigma-D factor [Clostridium botulinum C str. Eklund]
          Length = 242

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 60/243 (24%), Positives = 113/243 (46%), Gaps = 27/243 (11%)

Query: 53  LVTSHLRLVVKIA----MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           +V  ++ LV  IA    +G   Y +   +++  G +GLM A  KFD  +G + +TY+   
Sbjct: 13  IVKKYIPLVKYIASRVIIGKTKY-IEFEDLLGYGMLGLMDAFNKFDKSKGMKFSTYASIR 71

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ +M + I ++  + K    A  K     L +    ++ +   NL    +  IA++L++
Sbjct: 72  IRGSMIDEIRKNSPISK---GAMDK-----LNKYNAAIENLQRKNLSEPNIKDIAQELDM 123

Query: 169 SESEV--ISMNCRLAGDESLNALINSSDKNSS---QWQDWLVYDHDGQEQVLIEKEERKN 223
           + S+V  I          SL  LI S D + S     +D  +   D +E+      ER  
Sbjct: 124 TVSQVGEIENFINYISIVSLEDLIFSDDDDISLIGTIED--INSPDPEEEF-----ERDE 176

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +   L++ + +LN ++R +      +E  +TL+ +     VS  RV Q+ +RA   +++ 
Sbjct: 177 KLEYLSKGLDMLNDKDRTVLSLYYYEE--MTLKEIGKVLGVSESRVCQLHSRAIVHLRKE 234

Query: 284 IQK 286
           + K
Sbjct: 235 LAK 237


>gi|319937135|ref|ZP_08011542.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
 gi|319807501|gb|EFW04094.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
          Length = 230

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 47/176 (26%), Positives = 82/176 (46%), Gaps = 12/176 (6%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY-GLPISEVV 79
           H++ K P+  K+E   L K   + GD  A   L+  +LRLVV +A  Y       I +++
Sbjct: 22  HDVLKAPLKGKEEADALVKL--QQGDAQARDLLIEHNLRLVVYVAKKYDSVQNGSIEDLI 79

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL---------VKIGTTA 130
           S G IGL++AV  F  ++  +LATY+   I+  +  ++ ++  L         + +    
Sbjct: 80  SIGTIGLVKAVNTFKMDKNIKLATYASRCIENEILMFLRKNNKLRQEISLDEPLNVDYDG 139

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
           N+  L   +   K  +Q   ++N + E+       LN  E E++ M   L G + L
Sbjct: 140 NELLLSDIIGTDKDIVQDEIEHNDQKEKFYRALHHLNEREQEILMMRYGLVGHDEL 195


>gi|240144184|ref|ZP_04742785.1| RNA polymerase sigma-E factor [Roseburia intestinalis L1-82]
 gi|257203788|gb|EEV02073.1| RNA polymerase sigma-E factor [Roseburia intestinalis L1-82]
 gi|291536439|emb|CBL09551.1| RNA polymerase, sigma 29 subunit, SigE [Roseburia intestinalis
           M50/1]
 gi|291538693|emb|CBL11804.1| RNA polymerase, sigma 29 subunit, SigE [Roseburia intestinalis
           XB6B4]
          Length = 243

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 32/96 (33%), Positives = 55/96 (57%), Gaps = 3/96 (3%)

Query: 27  PMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           P L  ++E V  +     E G L A  +L+  +LRLVV IA  +   G+ + +++S G I
Sbjct: 37  PPLAGEDEAVCIEMLTSDESGQL-ARKQLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTI 95

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           GL++A+  F+P +  +LATY+   I+  +  Y+ R+
Sbjct: 96  GLIKAINTFNPGKNIKLATYASRCIENEILMYLRRN 131


>gi|309778066|ref|ZP_07673005.1| RNA polymerase sigma-E factor [Erysipelotrichaceae bacterium
           3_1_53]
 gi|313901138|ref|ZP_07834626.1| RNA polymerase sigma-E factor [Clostridium sp. HGF2]
 gi|308914160|gb|EFP59961.1| RNA polymerase sigma-E factor [Erysipelotrichaceae bacterium
           3_1_53]
 gi|312954096|gb|EFR35776.1| RNA polymerase sigma-E factor [Clostridium sp. HGF2]
          Length = 234

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 67/254 (26%), Positives = 113/254 (44%), Gaps = 62/254 (24%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L+K+EE + A    E+GD  A + L+  +LRLVV IA  Y    + + +++S G+IGL++
Sbjct: 35  LDKEEE-LAALIALENGDEEARNTLIEHNLRLVVYIAKRYETNPIFMEDLISIGSIGLIK 93

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           AV  F  ++  +L TY+   I+  +  + LR  S                 RR       
Sbjct: 94  AVNTFKRDKNIKLVTYASRCIENEILMF-LRKKS-----------------RR------- 128

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                           K+ VS  E   +N    G+E L               D L  D 
Sbjct: 129 ----------------KVEVSFDE--PLNIDYDGNELL-------------LSDILGTDD 157

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPVTLENLSSEFEVSRE 267
           D    V  E E+++N+R +L  +MS L  RER+I + R  +Q   +T ++++    +S+ 
Sbjct: 158 DV---VTKEFEKKENKRELL-EAMSTLKERERQILQMRYGIQHEELTQKDIAKRLGISQS 213

Query: 268 RVRQIEARAFKKVQ 281
            + ++E R   K++
Sbjct: 214 YISRLEKRIIAKLK 227


>gi|253682486|ref|ZP_04863283.1| RNA polymerase sigma-F factor [Clostridium botulinum D str. 1873]
 gi|253562198|gb|EES91650.1| RNA polymerase sigma-F factor [Clostridium botulinum D str. 1873]
          Length = 252

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 54/242 (22%), Positives = 111/242 (45%), Gaps = 20/242 (8%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A   LV  +L LV  I+  +   G    ++   G++GL++A+  FD     + +TY
Sbjct: 27  GDKKAVDELVQKNLPLVSSISKKFLNRGYEYEDIFQIGSMGLIKAINNFDSSYDVQFSTY 86

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTA--NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           ++  I   ++ +I R   L+K+  +     K+L ++  +L   L      N +P  +  +
Sbjct: 87  AVPMIMGEIKRFI-RDDGLIKVSRSVKYTAKKLHYDKEKLTKEL------NREP-SLEEL 138

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           +K   +S+ ++I  +  +   + L   I+  D +     D +V D  G+   L       
Sbjct: 139 SKFSGISKEDIIFSSEAINEPKYLYDTIHQDDGSPIYLIDKVVLDDKGEIDEL------- 191

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             +  L  ++S L+ R R+I   R  ++  +T   ++    +S+ +V +IE +  K ++E
Sbjct: 192 -DKIALKEALSKLDQRSRQIIILRYFKD--ITQVKVAKMLGISQVQVSRIEKKVLKSMKE 248

Query: 283 SI 284
            +
Sbjct: 249 KL 250


>gi|254384107|ref|ZP_04999452.1| sigma factor [Streptomyces sp. Mg1]
 gi|194342997|gb|EDX23963.1| sigma factor [Streptomyces sp. Mg1]
          Length = 301

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 56/199 (28%), Positives = 89/199 (44%), Gaps = 21/199 (10%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +   
Sbjct: 80  LIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTVVGE 139

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL   L +    L    D +     V  +A  L VSE 
Sbjct: 140 IKRFFRDTSWS-VRVPRRLQELRL--ALTKASDELAQKLDRS---PTVPELAAVLGVSEE 193

Query: 172 EVIS----MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           EV+      N   A   SL++     +       D L Y+    E V    E R++ + +
Sbjct: 194 EVVDGLAVGNAYTA--SSLDSPSPEDEGGEGSLADRLGYEDTALEGV----EYRESLKPL 247

Query: 228 LTRSMSVLNPRERRIFEAR 246
           L +    L PRER+I   R
Sbjct: 248 LAK----LPPRERQIIMLR 262


>gi|161898885|gb|ABX80432.1| SigB [Listeria monocytogenes]
          Length = 217

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 54/211 (25%), Positives = 101/211 (47%), Gaps = 24/211 (11%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D   G  
Sbjct: 5   YQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKS 64

Query: 101 LATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
              +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T       Q+
Sbjct: 65  FEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTRELQSSPQI 118

Query: 160 VAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
             IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +    DG E+
Sbjct: 119 SDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTDDGFER 175

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           V        N+R +L + + VL+ RE++I +
Sbjct: 176 V--------NQRMLLEKVLPVLDEREQKILQ 198


>gi|220934511|ref|YP_002513410.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thioalkalivibrio sp.
           HL-EbGR7]
 gi|219995821|gb|ACL72423.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thioalkalivibrio sp.
           HL-EbGR7]
          Length = 241

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 55/237 (23%), Positives = 106/237 (44%), Gaps = 25/237 (10%)

Query: 51  HRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +RLV +H+ LV +IA   +G     + + +++  G +GL++A +++D  +G    TY+  
Sbjct: 10  NRLVDAHVPLVKRIAYHLLGRLPSSVQVDDLIQAGVVGLLEAAQQYDATQGASFETYAGI 69

Query: 108 WIKAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            I+ AM + + RS W+          + +  N RR+   ++ + +   +  Q   +A +L
Sbjct: 70  RIRGAMLDEVRRSDWT---------PRSVHRNARRVSEAMRLVENRLGREAQPAEVAAEL 120

Query: 167 NVSESEVISMNCRLAGDESLNALINSSD--KNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            VS  E   M      D +   +++  D  +  S+ +D L     G E    E  +    
Sbjct: 121 GVSLDEYQHM----VSDAASCKVLSFEDIFEPDSEGEDLL----PGDEPSPFEALQSDGF 172

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R  L R +  L  RER +       ++ + L  +     VS  RV Q+  +A  +++
Sbjct: 173 RAALAREVGALPERERLVMSL--YYDDELNLREIGEVLGVSESRVCQLHGQALVRLR 227


>gi|87302171|ref|ZP_01084996.1| RNA polymerase ECF-type (group 3) sigma-E factor [Synechococcus sp.
           WH 5701]
 gi|87283096|gb|EAQ75052.1| RNA polymerase ECF-type (group 3) sigma-E factor [Synechococcus sp.
           WH 5701]
          Length = 318

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 26/82 (31%), Positives = 51/82 (62%), Gaps = 1/82 (1%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG-LPISEVVSEGNIGLMQAVKKFDP 95
           L +R+   GD    +RLV  +L LV ++A+   G   +P+ ++V  G +GL++A++ FDP
Sbjct: 21  LLQRFHSSGDHRLRNRLVELNLPLVRQVAVRQSGSTRVPLDDLVQLGCLGLIRAIEAFDP 80

Query: 96  ERGFRLATYSMWWIKAAMQEYI 117
            R   L+++++ +I+  MQ ++
Sbjct: 81  SRHTALSSFAVLYIRGEMQHHL 102


>gi|225375611|ref|ZP_03752832.1| hypothetical protein ROSEINA2194_01236 [Roseburia inulinivorans DSM
           16841]
 gi|225212590|gb|EEG94944.1| hypothetical protein ROSEINA2194_01236 [Roseburia inulinivorans DSM
           16841]
          Length = 244

 Score = 52.8 bits (125), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 30/99 (30%), Positives = 55/99 (55%), Gaps = 1/99 (1%)

Query: 22  EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           EI   P+  ++E Y +      H +  A   L+  +LRLVV IA  +   G+ + +++S 
Sbjct: 35  EILPPPLEGEREAYCIRMLDGVHAE-RARKELIEHNLRLVVYIAKKFDNTGVGVEDLISI 93

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           G IGL++ +  F+P++  +LATY+   I+  +  Y+ R+
Sbjct: 94  GTIGLIKGINTFNPDKNIKLATYASRCIENEILMYLRRN 132


>gi|291522735|emb|CBK81028.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Coprococcus catus
           GD/7]
          Length = 206

 Score = 52.4 bits (124), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 30/81 (37%), Positives = 47/81 (58%), Gaps = 1/81 (1%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L   +E V  ++Y ++GD+ A   L+  +LRLV  I   Y   G    E++S G +GL++
Sbjct: 8   LSAAQETVYLRQY-QNGDMHARDILIERNLRLVAHIVKKYMNSGKETDEMISVGIVGLVK 66

Query: 89  AVKKFDPERGFRLATYSMWWI 109
           AV  ++ E+G RLATY+   I
Sbjct: 67  AVNTYNFEKGSRLATYAARCI 87


>gi|293401517|ref|ZP_06645660.1| RNA polymerase sigma-E factor [Erysipelotrichaceae bacterium
           5_2_54FAA]
 gi|291305155|gb|EFE46401.1| RNA polymerase sigma-E factor [Erysipelotrichaceae bacterium
           5_2_54FAA]
          Length = 238

 Score = 52.4 bits (124), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 64/259 (24%), Positives = 119/259 (45%), Gaps = 62/259 (23%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           LEK+EE + A    E+GD  A ++L+  +LRLVV IA  Y    + + +++S G+IGL++
Sbjct: 35  LEKEEE-LAALIALENGDEEARNKLIEHNLRLVVYIAKRYETNPIFMEDLISIGSIGLIK 93

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           AV  F  ++  +L TY+   I+                    N+  +F    R K     
Sbjct: 94  AVNTFKRDKNIKLVTYASRCIE--------------------NEILMFL---RKKSR--- 127

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                          +K+ VS  E   +N    G+E L + I  +D +            
Sbjct: 128 ---------------RKVEVSFDE--PLNIDYDGNELLLSDILGTDDDI----------- 159

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPVTLENLSSEFEVSRE 267
                V  E E+++N+R +L  +M+ L  RER+I + R  ++   +T ++++    +S+ 
Sbjct: 160 -----VTKEFEKQENKRELLA-AMATLKDRERQILQMRYGIEHEELTQKDIAKRLGISQS 213

Query: 268 RVRQIEARAFKKVQESIQK 286
            + ++E R  +K++  ++K
Sbjct: 214 YISRLEKRIIQKLKVQMKK 232


>gi|210608671|ref|ZP_03287948.1| hypothetical protein CLONEX_00127 [Clostridium nexile DSM 1787]
 gi|210152928|gb|EEA83934.1| hypothetical protein CLONEX_00127 [Clostridium nexile DSM 1787]
          Length = 247

 Score = 52.4 bits (124), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 26/75 (34%), Positives = 45/75 (60%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           D  A   L+  +LRLVV IA  +   G+ + +++S G IGL++A+  F+P +  +LATY+
Sbjct: 60  DEYAKKVLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFNPTKNIKLATYA 119

Query: 106 MWWIKAAMQEYILRS 120
              I+  +  Y+ R+
Sbjct: 120 SRCIENEILMYLRRN 134


>gi|302391629|ref|YP_003827449.1| RNA polymerase, sigma subunit, RpsG/SigG [Acetohalobium arabaticum
           DSM 5501]
 gi|302203706|gb|ADL12384.1| RNA polymerase, sigma subunit, RpsG/SigG [Acetohalobium arabaticum
           DSM 5501]
          Length = 260

 Score = 52.4 bits (124), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 27/93 (29%), Positives = 52/93 (55%), Gaps = 1/93 (1%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           ++P+L  +E   L K+  ++GD  A   +V  +L+LV+ +   +   G PI ++   G I
Sbjct: 14  ELPVLSNEEMRELFKKM-QNGDREARQTIVGGNLKLVLSVLQRFNNRGEPIDDLFQVGCI 72

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           GLM+A+  FD  R  + +TY++  I   ++ ++
Sbjct: 73  GLMKAIDNFDLSRNVKFSTYAVPMIIGEIRRHL 105


>gi|150390238|ref|YP_001320287.1| FliA/WhiG family RNA polymerase sigma factor [Alkaliphilus
           metalliredigens QYMF]
 gi|149950100|gb|ABR48628.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           metalliredigens QYMF]
          Length = 149

 Score = 52.4 bits (124), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 32/85 (37%), Positives = 48/85 (56%), Gaps = 1/85 (1%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L  +EE +  +RY E GD  A + LV  +LRLV  +   Y        +++S G IGL++
Sbjct: 33  LSPEEEAMYLERY-EQGDEEARNILVERNLRLVAHVVKKYSNVNRDADDLISIGTIGLIK 91

Query: 89  AVKKFDPERGFRLATYSMWWIKAAM 113
           A+  F+  +G RLATY+   I+ AM
Sbjct: 92  AITTFNRGKGTRLATYAARCIEKAM 116


>gi|325662347|ref|ZP_08150956.1| hypothetical protein HMPREF0490_01695 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|325471349|gb|EGC74572.1| hypothetical protein HMPREF0490_01695 [Lachnospiraceae bacterium
           4_1_37FAA]
          Length = 234

 Score = 52.4 bits (124), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 53/229 (23%), Positives = 108/229 (47%), Gaps = 21/229 (9%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L  +E+  L  + +E GD +A  R +  +LRLV+ +   +      + ++   G +
Sbjct: 15  KLPLLSNEEKEALFVKIKE-GDEAARERYIKGNLRLVLSVIKRFASSNENVDDLFQIGCV 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT---ANQKRLFFNLRR 141
           GLM+A+  F+ +   + +TY++  I   ++ Y LR  + +++  +      K ++     
Sbjct: 74  GLMKAIDNFNTDLQVKFSTYAVPMIIGEIRRY-LRDNNSIRVSRSLRDTAYKAIYAKEGY 132

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           +K HL+  T        V  IA+++ +++ ++I     +    SLN  + +   ++    
Sbjct: 133 MKRHLKEPT--------VEEIAEEIGIAKEDIIFALDAIQAPMSLNEPVYNDSGDALYVM 184

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           D  + D   +E+  +E          L  +M  LN RER I + R L+E
Sbjct: 185 DQ-ISDKKNREEYWVEGLS-------LEAAMERLNERERFIIQLRFLKE 225


>gi|255523683|ref|ZP_05390649.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           carboxidivorans P7]
 gi|296186687|ref|ZP_06855089.1| putative RNA polymerase sigma factor WhiG [Clostridium
           carboxidivorans P7]
 gi|255512552|gb|EET88826.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           carboxidivorans P7]
 gi|296048724|gb|EFG88156.1| putative RNA polymerase sigma factor WhiG [Clostridium
           carboxidivorans P7]
          Length = 241

 Score = 52.4 bits (124), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 66/246 (26%), Positives = 107/246 (43%), Gaps = 21/246 (8%)

Query: 47  LSAAHRLVTSHLRLVVKIA----MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           L     LV  ++ LV  IA    +G   Y +   ++VS G +GLM A+ KFD  RG + +
Sbjct: 7   LDVKEELVKKYIPLVKYIASRVIIGKTKY-IEYEDLVSYGMLGLMDAIGKFDNTRGMKFS 65

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TYS   IK AM + I R  S +  G      R    + RL+  L        +P     I
Sbjct: 66  TYSSIRIKGAMIDEI-RKNSPISKGAMDKLNRYNAAVERLQKTLGR------EPSD-KEI 117

Query: 163 AKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
           A +LN++  E+I +          SL  LI S D +            D +     +  E
Sbjct: 118 ANELNITLKEMIEIENYINYISIVSLEDLIFSEDDDIPLIGTI----QDNKSPSPEKSLE 173

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            K     L +++ +LN +++ +      +   +TL+ +     VS  RV Q+ +RA   +
Sbjct: 174 EKEELEYLAKALDLLNEKDKTVLSLYYYE--GLTLKEIGKVLSVSESRVCQLHSRAIVHL 231

Query: 281 QESIQK 286
           + ++QK
Sbjct: 232 RNAMQK 237


>gi|256751992|ref|ZP_05492861.1| RNA polymerase, sigma 28 subunit, SigG [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|256749102|gb|EEU62137.1| RNA polymerase, sigma 28 subunit, SigG [Thermoanaerobacter
           ethanolicus CCSD1]
          Length = 256

 Score = 52.4 bits (124), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 59/260 (22%), Positives = 124/260 (47%), Gaps = 17/260 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+  ++  L +R + +GD  A    +  +LRLV+ +   +   G  + ++   G I
Sbjct: 14  KLPVLKPSKQKELLQRMK-NGDKKAREEFINGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 72

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD ++  + +TY++  I   ++ Y LR  + +++  +          + L+ 
Sbjct: 73  GLIKAIDNFDLDQNVKFSTYAVPMIIGEIRRY-LRDNTPIRVSRSLRD----IAYKALQV 127

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + +++N+ +P  V  IAK+L++   EV+     +    SL   I     ++    D  
Sbjct: 128 RDKLVSENSKEP-TVGEIAKELDLPREEVVMALDAIQEPVSLFEPIYHDGGDAIYVMDQ- 185

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           V D    ++V +EK         L  ++  L+ RE+ I    R  E    +E ++ E  +
Sbjct: 186 VSDDKNMDEVWLEK-------IALKEAIQKLSEREKMIL-TMRFFEGKTQME-VAKEIGI 236

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ +V ++E  A   +++ I
Sbjct: 237 SQAQVSRLEKAALNHMRKYI 256


>gi|4378867|gb|AAD19735.1| sigma-F factor [Zymomonas mobilis subsp. mobilis ZM4]
          Length = 244

 Score = 52.4 bits (124), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 60/235 (25%), Positives = 104/235 (44%), Gaps = 23/235 (9%)

Query: 53  LVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           L+ +HL+LV KIA    G     + + +++  G + L++A   F+  RGF  ATY+   I
Sbjct: 25  LIKTHLQLVRKIAWHVHGRVSSAIEVEDLIQIGMVALIEAANAFE-NRGFAFATYASMRI 83

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + AM +Y +R  +     + A QK L      L   L        +PE    IA+KLN+S
Sbjct: 84  RGAMIDY-MRQHAATARSSIARQKTLNKAREELSATL------GRRPED-AEIAEKLNMS 135

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
            SE      R   D ++N    S D   S        D+  Q   +    ER+  ++ L 
Sbjct: 136 PSE-----YREWADGAINIRQESLDDVYSDHSSIFTDDNADQASEM----EREALQSALA 186

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             +  L  RE  + +   ++E  + L+ +    ++   R+ QI+  A   +++ +
Sbjct: 187 EQIKTLPEREALVLQLYYVEE--LNLKEIGEVLDLGTARISQIKKSAVDHLRQKM 239


>gi|332982148|ref|YP_004463589.1| RNA polymerase sigma subunit RpsG/SigG [Mahella australiensis 50-1
           BON]
 gi|332699826|gb|AEE96767.1| RNA polymerase, sigma subunit, RpsG/SigG [Mahella australiensis
           50-1 BON]
          Length = 257

 Score = 52.4 bits (124), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 64/273 (23%), Positives = 124/273 (45%), Gaps = 43/273 (15%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L  ++   L KR +E GD +A    +  +LRLV+ I   +   G  + ++   G I
Sbjct: 15  KLPVLTDKQMKDLLKRIKE-GDKAAREEFIRGNLRLVLSIIQRFNNRGEHVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD  +  + +TY++  I   ++ Y LR  + +++  +          + L+ 
Sbjct: 74  GLIKAIDNFDLGQNVKFSTYAVPMIIGEIRRY-LRDNNSIRVSRSLRDTA----YKALQV 128

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             Q +  N  +P  V  IAK + +   EV+          +++A+           QD +
Sbjct: 129 REQLVAQNGKEP-TVEEIAKAMELPAEEVVF---------AMDAI-----------QDPI 167

Query: 205 -----VYDHDGQEQVLIEKE--ERKNRRN------MLTRSMSVLNPRERRIFEARRLQEN 251
                VY HDG + + +  +  + KN+ +       L  +M  L+ RE+ I   R  Q  
Sbjct: 168 SLFEPVY-HDGGDAIYVMDQVSDDKNQDDNWLETIALKEAMQKLSEREKTILAMRFFQGR 226

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             T   ++ E  +S+ +V ++E  A   +++ I
Sbjct: 227 --TQMEVAEEIGISQAQVSRLEKSALSHMRKYI 257


>gi|154504525|ref|ZP_02041263.1| hypothetical protein RUMGNA_02029 [Ruminococcus gnavus ATCC 29149]
 gi|153795007|gb|EDN77427.1| hypothetical protein RUMGNA_02029 [Ruminococcus gnavus ATCC 29149]
          Length = 208

 Score = 52.4 bits (124), Expect = 8e-05,   Method: Compositional matrix adjust.
 Identities = 28/80 (35%), Positives = 49/80 (61%), Gaps = 3/80 (3%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           +++EY+  ++Y E GDL A H L+  +LRLV  +   Y+       +++S G IGL++A+
Sbjct: 12  EEKEYI--QKYTE-GDLQAKHILIERNLRLVAHVIKKYQYVDEDPEDLISIGTIGLIKAI 68

Query: 91  KKFDPERGFRLATYSMWWIK 110
             F+P +G RLA Y+   ++
Sbjct: 69  VTFNPSKGNRLAAYASKCVE 88


>gi|302774234|ref|XP_002970534.1| hypothetical protein SELMODRAFT_147096 [Selaginella moellendorffii]
 gi|300162050|gb|EFJ28664.1| hypothetical protein SELMODRAFT_147096 [Selaginella moellendorffii]
          Length = 458

 Score = 52.4 bits (124), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 31/115 (26%), Positives = 65/115 (56%), Gaps = 4/115 (3%)

Query: 48  SAAHRLVTSHLRLVVKIAMGY-RGYG-LPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           +A ++L+  + RLV+ +A  Y R  G   + ++  EG  GL+ A+  F+P +G R +TY+
Sbjct: 218 AAQNKLIEHNCRLVLFLARRYERDAGSFSLEDLCQEGVKGLIDAMDHFNPGKGTRFSTYA 277

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
           ++WI+ A+   I R+  ++++  +   K++   +R+ +  L+     N   E+V+
Sbjct: 278 IFWIRTAIVRAITRTGQVIRLPFSFAAKKV--EIRKARRELRVELGRNPSDEEVM 330


>gi|224005495|ref|XP_002291708.1| plastid RNA polymerase sigma factor [Thalassiosira pseudonana
           CCMP1335]
 gi|220972227|gb|EED90559.1| plastid RNA polymerase sigma factor [Thalassiosira pseudonana
           CCMP1335]
          Length = 541

 Score = 52.4 bits (124), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 60/222 (27%), Positives = 94/222 (42%), Gaps = 43/222 (19%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + E V EG +GL +AV K+DPERG R +TY+  WI          S++  K         
Sbjct: 319 LDEAVQEGMLGLARAVDKYDPERGLRFSTYATHWIT---------SYAAYK--------- 360

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE----------SEVISMNCRLAGDE 184
                + +K HLQ  T     P +  +IAK+L +SE            ++S++  +    
Sbjct: 361 -----KIIKDHLQLGT----TPPEQKSIAKELGISEQRLTTAIRATGSLVSVDAPVISPG 411

Query: 185 SLNALINSSDKNSSQWQDWLVYDH-DGQEQVLIEKEERKNRRNMLTRSMSV-LNPRERRI 242
           S +   +++  + S  Q+ L+ D     E    ++ E    R  L  +M+  L P ER +
Sbjct: 412 SGSYKGSAAGGDGSNSQELLILDTLRCAEPKPEDQVEISFLRQCLENAMATELTPYERDV 471

Query: 243 FEAR---RLQENPVTLENLS-SEFEVSRERVRQIEARAFKKV 280
              R      E     E +      V+   VR  E RAFKK+
Sbjct: 472 LRLRLGLDSGEGKTVREVVEICGGSVTMSDVRSAERRAFKKL 513


>gi|15237896|ref|NP_197800.1| SIGE (SIGMA FACTOR E); DNA binding / DNA-directed RNA polymerase/
           sigma factor/ transcription factor [Arabidopsis
           thaliana]
 gi|4033838|emb|CAA77213.1| sigma-like factor [Arabidopsis thaliana]
 gi|4972299|dbj|BAA78109.1| RNA polymerase sigma subunit SigE [Arabidopsis thaliana]
 gi|10178160|dbj|BAB11572.1| sigma-like factor [Arabidopsis thaliana]
 gi|222423237|dbj|BAH19595.1| AT5G24120 [Arabidopsis thaliana]
 gi|332005876|gb|AED93259.1| RNA polymerase sigma factor [Arabidopsis thaliana]
          Length = 517

 Score = 52.4 bits (124), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 32/95 (33%), Positives = 53/95 (55%), Gaps = 13/95 (13%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           +A ++L+  +LRLV+ +   Y      G    ++   G  GL+ A+ +F+P+R FRL+TY
Sbjct: 278 AARNKLIKHNLRLVLFVMNKYFHEFTNGPKFQDLCQAGMRGLITAIDRFEPKRKFRLSTY 337

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            ++WI+ A    I+RS       TT+N  R+ F L
Sbjct: 338 GLFWIRHA----IIRSM------TTSNFTRVPFGL 362


>gi|255280061|ref|ZP_05344616.1| RNA polymerase sigma-E factor [Bryantella formatexigens DSM 14469]
 gi|255269152|gb|EET62357.1| RNA polymerase sigma-E factor [Bryantella formatexigens DSM 14469]
          Length = 243

 Score = 52.4 bits (124), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 31/83 (37%), Positives = 49/83 (59%), Gaps = 2/83 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  ++E + L K Y+E GDL A   L+  +LRLV  +A  Y+  G    E+++ G IGL
Sbjct: 42  PLTPEEEAWFLQK-YKE-GDLEAKKILIERNLRLVAHVAKKYQKQGEDGEELIAVGTIGL 99

Query: 87  MQAVKKFDPERGFRLATYSMWWI 109
           ++AV  F+  R  +LATY+   +
Sbjct: 100 IKAVSTFNHARTNKLATYAARCV 122


>gi|299822364|ref|ZP_07054250.1| RNA polymerase sigma-B factor [Listeria grayi DSM 20601]
 gi|299815893|gb|EFI83131.1| RNA polymerase sigma-B factor [Listeria grayi DSM 20601]
          Length = 259

 Score = 52.4 bits (124), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 61/261 (23%), Positives = 124/261 (47%), Gaps = 26/261 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y   K Y+E  D  A   LV  +  LV  IA  Y        ++V  G IGL+ A+
Sbjct: 12  KEKVYEWIKLYQETADDDAQTNLVLHYHNLVESIARKYSQGKSFHEDLVQVGVIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           K++DP+ G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +
Sbjct: 72  KRYDPDFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEEL 125

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDW 203
           T       Q+  IA  +  +E E++ +M        L+ D S+ A    SD ++    D 
Sbjct: 126 TRELQSSPQISDIANFIGATEEEILEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDV 182

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    +G EQV        N+R +L + + VL+ RE++I +   ++    + +      +
Sbjct: 183 VGGVDEGFEQV--------NQRMILEKILPVLDEREQKILQYTFIENR--SQKETGELLD 232

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+  V +++ +A KK++E++
Sbjct: 233 ISQMHVSRVQRQAIKKLREAL 253


>gi|315506253|ref|YP_004085140.1| anti-sigma-factor antagonist [Micromonospora sp. L5]
 gi|315412872|gb|ADU10989.1| anti-sigma-factor antagonist [Micromonospora sp. L5]
          Length = 377

 Score = 52.4 bits (124), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 66/249 (26%), Positives = 113/249 (45%), Gaps = 27/249 (10%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV   L    ++A  YRG G P+ ++     +GL+ AV ++DPERG   A  ++  +   
Sbjct: 46  LVRFALPFAGRLARRYRGRGEPLEDLEQVARLGLVNAVDRYDPERGSFTAYAAITIVGEI 105

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA-IAKKLNVSES 171
            + +  R+W +       +  R   +L    G   A   + L     VA ++ +L   E 
Sbjct: 106 KRHFRDRTWGV-------HVPRRLRDLILEVGQATATLTSELSRAPTVAELSARLETPEE 158

Query: 172 EVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E+++     AG    SLNA +    ++S+++ D LV + D     L   ++R     +L 
Sbjct: 159 EILAALESAAGYSPASLNAPVGG--ESSAEFGD-LVGESD---HALESVDDRVTVSGLLH 212

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           R    L  RERRI  A R   N    E +++ F +S+  V ++ +RA   +     +Q  
Sbjct: 213 R----LPWRERRIL-AMRFYGNQTQAE-IAARFGISQMHVSRLLSRALTWL-----RQAM 261

Query: 290 LSSSPPLLQ 298
           L+ +PP  Q
Sbjct: 262 LADAPPPWQ 270


>gi|167769451|ref|ZP_02441504.1| hypothetical protein ANACOL_00781 [Anaerotruncus colihominis DSM
           17241]
 gi|167668419|gb|EDS12549.1| hypothetical protein ANACOL_00781 [Anaerotruncus colihominis DSM
           17241]
          Length = 234

 Score = 52.4 bits (124), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 51/174 (29%), Positives = 74/174 (42%), Gaps = 19/174 (10%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  K+E   L    R  GD  A  RL+  +LRLV  I   Y        +++S G IGL
Sbjct: 27  PLSAKEERECLEGIAR--GDEEAKTRLIEHNLRLVAHIIKKYYSAFKDQDDLISIGTIGL 84

Query: 87  MQAVKKFDPERGFRLATYSMWWI------------KAAMQEYILRSWSLVKIGTTANQKR 134
           ++AV  F PE+G R ATY+   I            K+A   YI       K G +   + 
Sbjct: 85  IKAVSTFKPEKGTRFATYASRCIENEVLMHFRNKKKSAQDVYISDPIDTDKDGNSLTLQ- 143

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVV-AIAKKLNVSESEVISMNCRLAGDESLN 187
              ++     ++    D  +K EQ+   I   L+  E ++I M   L G  SL 
Sbjct: 144 ---DIMAEDDNIVDCIDLRIKSEQLYRFIEGALDERERQIIIMRYGLGGTRSLT 194


>gi|224992794|gb|ACN76112.1| SigB [Listeria innocua]
 gi|224992800|gb|ACN76115.1| SigB [Listeria innocua]
 gi|224992802|gb|ACN76116.1| SigB [Listeria innocua]
 gi|224992804|gb|ACN76117.1| SigB [Listeria innocua]
 gi|224992806|gb|ACN76118.1| SigB [Listeria innocua]
 gi|224992808|gb|ACN76119.1| SigB [Listeria innocua]
 gi|224992812|gb|ACN76121.1| SigB [Listeria innocua]
 gi|224992816|gb|ACN76123.1| SigB [Listeria innocua]
 gi|224992818|gb|ACN76124.1| SigB [Listeria innocua]
 gi|224992820|gb|ACN76125.1| SigB [Listeria innocua]
 gi|224992822|gb|ACN76126.1| SigB [Listeria innocua]
 gi|224992824|gb|ACN76127.1| SigB [Listeria innocua]
 gi|224992826|gb|ACN76128.1| SigB [Listeria innocua]
 gi|224992828|gb|ACN76129.1| SigB [Listeria innocua]
 gi|224992830|gb|ACN76130.1| SigB [Listeria innocua]
 gi|224992836|gb|ACN76133.1| SigB [Listeria innocua]
 gi|224992838|gb|ACN76134.1| SigB [Listeria innocua]
 gi|224992840|gb|ACN76135.1| SigB [Listeria innocua]
 gi|224992842|gb|ACN76136.1| SigB [Listeria innocua]
 gi|224992844|gb|ACN76137.1| SigB [Listeria innocua]
 gi|224992846|gb|ACN76138.1| SigB [Listeria innocua]
 gi|224992852|gb|ACN76141.1| SigB [Listeria innocua]
 gi|224992854|gb|ACN76142.1| SigB [Listeria innocua]
          Length = 214

 Score = 52.4 bits (124), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 54/211 (25%), Positives = 100/211 (47%), Gaps = 24/211 (11%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y+E GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D   G  
Sbjct: 4   YQEDGDEDAQYNLVIHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKS 63

Query: 101 LATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
              +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T       Q+
Sbjct: 64  FEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTRELQSSPQI 117

Query: 160 VAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
             IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +    DG E+
Sbjct: 118 SDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTDDGFER 174

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           V        N+R +L + + VL+ RE++I +
Sbjct: 175 V--------NQRMLLEKVLPVLDEREQKILQ 197


>gi|307717612|gb|ADN88859.1| RNA polymerase sigma-37 factor [Listeria welshimeri]
          Length = 220

 Score = 52.4 bits (124), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 55/217 (25%), Positives = 102/217 (47%), Gaps = 24/217 (11%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTREL 115

Query: 154 LKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               Q+  IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +   
Sbjct: 116 QSSPQISDIAYFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGT 172

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
            DG E+V        N+R +L + + VL+ RE+ I +
Sbjct: 173 DDGFERV--------NQRMLLEKVLPVLDEREQMILQ 201


>gi|222528794|ref|YP_002572676.1| sporulation sigma factor SigG [Caldicellulosiruptor bescii DSM
           6725]
 gi|222455641|gb|ACM59903.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor bescii DSM 6725]
          Length = 255

 Score = 52.4 bits (124), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 60/259 (23%), Positives = 122/259 (47%), Gaps = 17/259 (6%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L  +E+  L KR +E GD  A    +  +LRLV+ +   +   G  + ++   G IG
Sbjct: 14  LPVLSHEEKLELLKRMKE-GDKEARRIFIEGNLRLVLSVVQKFANRGENLDDLFQVGCIG 72

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A+  FD  +  + +TY++  I   ++ Y LR  + ++I  +   K   +   ++K  
Sbjct: 73  LIKAIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNSMRISRSL--KDTAYKALKIK-- 127

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            +   +NN K   +  IAK+L++++ +++     +    SL   +   D   + +    +
Sbjct: 128 -EKYINNNQKEPTLEEIAKELSITKEDLVFALDSIQEPISLYEPV-FQDSTDTMYVVERL 185

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            DH   E V +E+   K+       ++S L  RE+ I   R  +    T   ++    +S
Sbjct: 186 CDHKSCESVWLEEISLKD-------ALSKLTKREKEILYLRYYKGK--TQMEVAKIVGIS 236

Query: 266 RERVRQIEARAFKKVQESI 284
           + +V +IE  A   +++ I
Sbjct: 237 QAQVSRIEKSAIGHIKKYI 255


>gi|302872543|ref|YP_003841179.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
 gi|302575402|gb|ADL43193.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
          Length = 246

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 63/264 (23%), Positives = 127/264 (48%), Gaps = 27/264 (10%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG----YRGYGLPISEVVSEGNIGLMQ 88
           +E +L +++ +  D     +L+  ++ LV K+  G    Y G  +   ++VS G+IGL+ 
Sbjct: 2   DEALLWEKFIKTKDPKIKEQLIIKYMPLV-KLVAGRMAIYFGGNVEYDDLVSYGSIGLLD 60

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++KFD ++G +  TY+   IK A+ + + RS   +        K +      ++   + 
Sbjct: 61  AIEKFDSQKGVKFETYAYTRIKGAIIDCV-RSQDFLPRSIRQKAKEIEKAYIEIEREGRT 119

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ-WQDWL--V 205
            TD+         +AK++ +S SE+  +  +++     + +I S D    Q ++  +  +
Sbjct: 120 PTDDE--------VAKRVGLSISELQKLQEKIS-----SGMIVSLDSFLEQNYESKIGGL 166

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            D   Q +  IE EE K    +L + +  L   ER +      +E  ++++ ++    VS
Sbjct: 167 EDFVSQPEHFIENEELK---EVLRQQIDNLLENERMVIVLYYYEE--LSIKEIAKILGVS 221

Query: 266 RERVRQIEARAFKKVQESIQKQVE 289
             RV Q+  RA  K++ ++QK +E
Sbjct: 222 ESRVSQLHTRALLKLRSALQKYLE 245


>gi|288553150|ref|YP_003425085.1| sporulation sigma factor SigG [Bacillus pseudofirmus OF4]
 gi|288544310|gb|ADC48193.1| sporulation sigma factor SigG [Bacillus pseudofirmus OF4]
          Length = 261

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 64/273 (23%), Positives = 126/273 (46%), Gaps = 39/273 (14%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+  E   L  +  + GD SA   LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKNTEMRELFTQL-QSGDDSAREVLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD  +  + +TY++  I   ++ Y LR  + +++  +   + + +   +++ 
Sbjct: 74  GLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSL--RDIAYKALQVRD 130

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L A      +P  V  IAK L+V + +V+          +L+A+           QD +
Sbjct: 131 QLMAEKKRENEP-TVQEIAKVLDVPKEDVVF---------ALDAI-----------QDPV 169

Query: 205 -----VYDHDGQEQVLIEK--EERKNRRN-----MLTRSMSVLNPRERRIFEARRLQENP 252
                +Y+  G    ++++  +ER    N      L  +M  LN RE+ I   R  Q   
Sbjct: 170 SLFEPIYNDGGDPIFVMDQISDERNKDVNWVEEIALKEAMIRLNDREKMILNMRFFQGK- 228

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            T   ++ E  +S+ +V ++E  A +++ +  Q
Sbjct: 229 -TQMEVADEIGISQAQVSRLEKAAIQQMNKHAQ 260


>gi|153814532|ref|ZP_01967200.1| hypothetical protein RUMTOR_00746 [Ruminococcus torques ATCC 27756]
 gi|317500575|ref|ZP_07958796.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|331089324|ref|ZP_08338225.1| hypothetical protein HMPREF1025_01808 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|145848026|gb|EDK24944.1| hypothetical protein RUMTOR_00746 [Ruminococcus torques ATCC 27756]
 gi|316898008|gb|EFV20058.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|330405505|gb|EGG85037.1| hypothetical protein HMPREF1025_01808 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 260

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 59/243 (24%), Positives = 109/243 (44%), Gaps = 34/243 (13%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A  + +  +LRLV+ +   +        ++   G +GLM+AV  FDP R  + +TY
Sbjct: 34  GDEEAREKYIKGNLRLVLSVIKRFENSSENADDLFQIGCVGLMKAVDHFDPGRMVKFSTY 93

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTT---ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           ++  I   ++ Y LR  S +++  +      K ++     +K H++  T   +  E  + 
Sbjct: 94  AVPMIIGEIRRY-LRDNSPIRVSRSLRDTAYKAIYAKEGYIKRHMKEPTVQEIAEE--IG 150

Query: 162 IAKKLNVSESEVISMNCRL------AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
           IAK+  V   + I M   L       G ++L  +   SDK + + ++W+       E++ 
Sbjct: 151 IAKEEIVYALDAIQMPMSLHEPVYSDGQDALFVMDQVSDKKNKE-ENWI-------EELS 202

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
           +E             +M  LN RER I    R  E    +E ++ +  +S+ +V ++E  
Sbjct: 203 LEA------------AMERLNERERYII-TLRFFEGKTQME-VAEQINISQAQVSRLEKN 248

Query: 276 AFK 278
           A K
Sbjct: 249 ALK 251


>gi|218289600|ref|ZP_03493820.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
 gi|218240250|gb|EED07433.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
          Length = 222

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 54/203 (26%), Positives = 85/203 (41%), Gaps = 24/203 (11%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A  RL+  + RLV  +   + G G    ++   G IGLM+AV KFD     + +TY
Sbjct: 34  GDAEARERLIVHNQRLVWAVVQRFLGRGYEAEDLFQIGCIGLMKAVDKFDLSYDVKFSTY 93

Query: 105 SMWWIKAAMQEYILRSWSLVKIG----TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
           ++  I   +Q + LR  S VK+      TA Q R   +  RL   L        +   + 
Sbjct: 94  AVPMIIGEIQRF-LRDDSTVKVSRSLKETAKQIRHVRD--RLAKELG-------RQPHIT 143

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            IA+ + +  SE++     L    S++  +  +D +     D          Q+  E+ E
Sbjct: 144 EIAEAMGMEPSEIVFAQEALRAPASIHETVYENDGDPIYLMD----------QIADEETE 193

Query: 221 RKNRRNMLTRSMSVLNPRERRIF 243
            K  +  L   +  L  RER  F
Sbjct: 194 GKFDKVELHEIIGRLPERERSSF 216


>gi|297156863|gb|ADI06575.1| RNA polymerase sigma factor WhiG [Streptomyces bingchenggensis
           BCW-1]
          Length = 277

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 63/245 (25%), Positives = 103/245 (42%), Gaps = 20/245 (8%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFD 94
           + Y+  GD     +L+  H   +VK   G    GLP     ++ VS G  GL+ A++KFD
Sbjct: 33  RSYKSTGDGRLREQLIL-HYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEKFD 91

Query: 95  PERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           PER  +  TY++  I+ AM  E     W    I  +  QK     + R    L+A     
Sbjct: 92  PERAIKFETYAITRIRGAMIDELRALDW----IPRSVRQK--ARAVERAYATLEAAL-RR 144

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ--DWLVYDHDGQ 211
              E  VA    + + E   +     LA   +L  L+++S +   +    D L    D  
Sbjct: 145 TPSEAEVAAEMDIGLDELHGVFSQLSLANVVALEDLLHASGEGGERLSLMDTL---EDTA 201

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
               +E  E +  R +L R+++ L  RE+ +      +   +TL  +     V+  RV Q
Sbjct: 202 ADNPVEVAEDRELRRLLARAINTLPEREKTVVTLYYYEG--LTLAEIGQVLGVTESRVSQ 259

Query: 272 IEARA 276
           I  ++
Sbjct: 260 IHTKS 264


>gi|302874610|ref|YP_003843243.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           cellulovorans 743B]
 gi|307690779|ref|ZP_07633225.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           cellulovorans 743B]
 gi|302577467|gb|ADL51479.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           cellulovorans 743B]
          Length = 241

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 56/240 (23%), Positives = 109/240 (45%), Gaps = 21/240 (8%)

Query: 53  LVTSHLRLVVKIA----MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           ++T ++ LV  IA    +G +   +   ++VS G +GLM A+ KFD  +G + ++Y+   
Sbjct: 13  IITKYIPLVKYIASRVIIG-KSKHIEFDDLVSNGILGLMDALNKFDESKGMKFSSYASIR 71

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           IK AM + + R+  +         K     L R    + ++ +  L+   V  IA ++ +
Sbjct: 72  IKGAMIDELRRNSPI--------PKGAMDKLNRYNSAIDSLRNTLLREPTVDEIACEMAI 123

Query: 169 SESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             ++VI +  +       SL  LI S D +               E+ L    E K +  
Sbjct: 124 DIADVIEIENHINYLSVVSLEELIYSEDDDMPLIGTIKDNKSPSPEKDL----EDKEKME 179

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L +++ +LN +++ +      +   +TL+ +    EVS  RV Q+  RA   +++++ K
Sbjct: 180 YLAKAIELLNEKDKLVLNLYYYE--GLTLKEIGKILEVSESRVCQLHTRAIAHLRKNLSK 237


>gi|223994539|ref|XP_002286953.1| plastid RNA polymerase sigma factor [Thalassiosira pseudonana
           CCMP1335]
 gi|220978268|gb|EED96594.1| plastid RNA polymerase sigma factor [Thalassiosira pseudonana
           CCMP1335]
          Length = 298

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 46/75 (61%), Gaps = 3/75 (4%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +L+T ++ LV  IA  Y  Y + +  ++ EG +G+M+A +++DP +GFR +TY   WI+ 
Sbjct: 65  KLITGNVGLVTLIAKRY--YNM-LRNLIQEGYMGIMEAAERYDPSKGFRFSTYGTHWIRQ 121

Query: 112 AMQEYILRSWSLVKI 126
            +   I  S  ++++
Sbjct: 122 RIVRAIAESSRMIRL 136


>gi|238064463|ref|ZP_04609172.1| sigma-70 region 2 domain-containing protein [Micromonospora sp.
           ATCC 39149]
 gi|237886274|gb|EEP75102.1| sigma-70 region 2 domain-containing protein [Micromonospora sp.
           ATCC 39149]
          Length = 305

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 66/249 (26%), Positives = 114/249 (45%), Gaps = 27/249 (10%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV   L    ++A  YRG G P+ ++     +GL+ AV ++DPERG   A  ++  +   
Sbjct: 69  LVRFALPFAGRLARRYRGRGEPLEDLEQVARLGLVNAVDRYDPERGSFTAYAAITIVGEI 128

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA-IAKKLNVSES 171
            + +  R+W +       +  R   +L    G   A   + L     VA +A++L   + 
Sbjct: 129 KRHFRDRTWGV-------HVPRRLRDLILEVGQATATLTSELSRAPTVAELAERLETPQE 181

Query: 172 EVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E+++     AG    SLNA +    ++S+++ D LV + D     L   ++R     +L 
Sbjct: 182 EILAALESAAGYSPASLNAPVGG--ESSAEFGD-LVGESD---NALESVDDRVTISGLLH 235

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           R    L  RERRI  A R   N    E +++ F +S+  V ++ +RA   +     +Q  
Sbjct: 236 R----LPWRERRIL-AMRFYGNQTQAE-IAARFGISQMHVSRLLSRALTWL-----RQAM 284

Query: 290 LSSSPPLLQ 298
           L+ +PP  Q
Sbjct: 285 LADAPPPWQ 293


>gi|224771367|dbj|BAH28625.1| sporulation sigma factor SigK [Clostridium perfringens]
          Length = 196

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 31/86 (36%), Positives = 48/86 (55%), Gaps = 5/86 (5%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGN 83
           P+ EK+E+  L +   ++GD+ A   LV  +LRLV  I   Y         + +++S G 
Sbjct: 17  PLNEKEEKIYLERL--KYGDVEAKRVLVERNLRLVAHIVKKYSSNYQNSKEMDDLISIGT 74

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWI 109
           IGL++A+  FD  +G RLATY+   I
Sbjct: 75  IGLIKAIDSFDTNKGIRLATYAAKCI 100


>gi|302867341|ref|YP_003835978.1| RNA polymerase sigma-70 factor [Micromonospora aurantiaca ATCC
           27029]
 gi|302570200|gb|ADL46402.1| RNA polymerase sigma-70 factor, sigma-B/F/G subfamily
           [Micromonospora aurantiaca ATCC 27029]
          Length = 377

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 66/249 (26%), Positives = 113/249 (45%), Gaps = 27/249 (10%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV   L    ++A  YRG G P+ ++     +GL+ AV ++DPERG   A  ++  +   
Sbjct: 46  LVRFALPFAGRLARRYRGRGEPLEDLEQVARLGLVNAVDRYDPERGSFTAYAAITIVGEI 105

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA-IAKKLNVSES 171
            + +  R+W +       +  R   +L    G   A   + L     VA ++ +L   E 
Sbjct: 106 KRHFRDRTWGV-------HVPRRLRDLILEVGQATATLTSELSRAPTVAELSARLETPEE 158

Query: 172 EVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E+++     AG    SLNA +    ++S+++ D LV + D     L   ++R     +L 
Sbjct: 159 EILAALESAAGYSPASLNAPVGG--ESSAEFGD-LVGESD---HALESVDDRVTVSGLLH 212

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           R    L  RERRI  A R   N    E +++ F +S+  V ++ +RA   +     +Q  
Sbjct: 213 R----LPWRERRIL-AMRFYGNQTQAE-IAARFGISQMHVSRLLSRALTWL-----RQAM 261

Query: 290 LSSSPPLLQ 298
           L+ +PP  Q
Sbjct: 262 LADAPPPWQ 270


>gi|222530110|ref|YP_002573992.1| FliA/WhiG subfamily RNA polymerase sigma-28 factor
           [Caldicellulosiruptor bescii DSM 6725]
 gi|222456957|gb|ACM61219.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Caldicellulosiruptor
           bescii DSM 6725]
          Length = 246

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 62/268 (23%), Positives = 131/268 (48%), Gaps = 35/268 (13%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG----YRGYGLPISEVVSEGNIGLMQ 88
           ++ +L +++ +  D     +L+  ++ LV K+  G    Y G  +   ++VS G+IGL+ 
Sbjct: 2   DDALLWEKFTKTKDPKIKEQLIIKYMPLV-KLVAGRMAIYFGGNVEYDDLVSYGSIGLLD 60

Query: 89  AVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTTANQ-KRLFFNLRR 141
           A++KFD ++G +  TY+   IK A+      Q+++ RS     I   A + +R++  + +
Sbjct: 61  AIEKFDSQKGVKFETYAYTRIKGAIIDCVRSQDFLPRS-----IRQKAKEIERVYIEIEK 115

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
                +  T  N +      +AK++ +S  E+  +  R++    ++  + S  + + + +
Sbjct: 116 -----EGKTPTNQE------VAKRIGISVEELQKLQDRISSGMIIS--LESFLEQNYESK 162

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
              + D   Q +  IE EE    R +L + +  L   ER +      +E  ++++ ++  
Sbjct: 163 IGGLEDFVSQPEHFIENEE---LREVLRQQIDNLLENERMVIVLYYYEE--LSIKEIAKV 217

Query: 262 FEVSRERVRQIEARAFKKVQESIQKQVE 289
             VS  RV Q+  RA  K++ ++QK +E
Sbjct: 218 LGVSESRVSQLHTRALLKLRSALQKYLE 245


>gi|121488769|emb|CAJ18269.1| sigma 70-type sigma factor [Chlorobium limicola]
 gi|121488771|emb|CAJ18270.1| sigma 70-type sigma factor [Chlorobium phaeobacteroides]
          Length = 165

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 17/50 (34%), Positives = 37/50 (74%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + +     +V++
Sbjct: 1   DLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL 50


>gi|121488765|emb|CAJ18267.1| sigma 70-type sigma factor [Chlorobium phaeobacteroides]
          Length = 165

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 17/50 (34%), Positives = 37/50 (74%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + +     +V++
Sbjct: 1   DLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL 50


>gi|121488773|emb|CAJ18271.1| sigma 70-type sigma factor [Chlorobium phaeobacteroides]
          Length = 165

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 17/50 (34%), Positives = 37/50 (74%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + +     +V++
Sbjct: 1   DLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL 50


>gi|15894973|ref|NP_348322.1| sporulation sigma factor SigG [Clostridium acetobutylicum ATCC 824]
 gi|1350864|sp|P33658|RPSG_CLOAB RecName: Full=RNA polymerase sigma-G factor
 gi|15024660|gb|AAK79662.1|AE007679_8 Specialized DNA-dependent RNA polymerase sigma subunit [Clostridium
           acetobutylicum ATCC 824]
 gi|580960|emb|CAA80621.1| putative sigma factor G [Clostridium acetobutylicum ATCC 824]
 gi|706854|gb|AAC43310.1| putative sigma factor G [Clostridium acetobutylicum ATCC 824]
 gi|325509110|gb|ADZ20746.1| sporulation sigma factor SigG [Clostridium acetobutylicum EA 2018]
          Length = 257

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 58/262 (22%), Positives = 123/262 (46%), Gaps = 21/262 (8%)

Query: 25  KIPMLEKQE--EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           K+P+L+++E  E +++ R   +G+ +A  + +  +LRLV+ +   +   G    ++   G
Sbjct: 15  KLPVLKEKEMRELLISMR---NGNTTAREKFIKGNLRLVLSVIQRFNNRGENADDLFQVG 71

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            IGL++++  FD  +  + +TY++  I   ++ Y LR  + +++  +          R L
Sbjct: 72  CIGLIKSIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNSIRVSRSLRD----IAYRAL 126

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
           +   + I+ NN +P  V  IAK+L +   EVI     +    SL   I   D ++    D
Sbjct: 127 QVRDRLISKNNKEP-TVSQIAKELKIPREEVIFALDAIQDPISLFEPIYHDDGDAIYVMD 185

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
            +  + +  +  L     ++  + +  R   +LN    R F+ R   E       ++ E 
Sbjct: 186 QISDNKNLDDSWLQNISIKEAMKKLSDREKMILN---MRFFDGRTQME-------VADEI 235

Query: 263 EVSRERVRQIEARAFKKVQESI 284
            +S+ +V ++E  A K +++ +
Sbjct: 236 GISQAQVSRLEKTALKHMKKYV 257


>gi|291484084|dbj|BAI85159.1| sporulation sigma factor SigG [Bacillus subtilis subsp. natto
           BEST195]
          Length = 237

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 57/250 (22%), Positives = 112/250 (44%), Gaps = 16/250 (6%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L ++ ++ GD SA  +LV  +LRLV+ +   +   G  + ++   G IGLM+++  FD  
Sbjct: 4   LFRQLQDEGDDSAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLS 63

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
              + +TY++  I   ++ Y LR  + +++  +          + L+   + I++ + +P
Sbjct: 64  HNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSLRD----IAYKALQVRERLISETSKEP 118

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
                IAK L V   E++     +    SL   I +   +     D +  + +   Q + 
Sbjct: 119 -TAEDIAKVLEVPHEEIVFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDERNTDSQWIE 177

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           E          L   M  LN RE+ I   R  Q    T   ++ E  +S+ +V ++E  A
Sbjct: 178 EL--------ALKEGMRRLNDREKMILRKRFFQGK--TQMEVAEEIGISQAQVSRLEKAA 227

Query: 277 FKKVQESIQK 286
            K++ ++I +
Sbjct: 228 IKQMNKNIHQ 237


>gi|311898622|dbj|BAJ31030.1| putative RNA polymerase sigma factor [Kitasatospora setae KM-6054]
          Length = 276

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 60/245 (24%), Positives = 108/245 (44%), Gaps = 20/245 (8%)

Query: 39  KRYREHGDLSAAHRL---VTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVK 91
           + Y+E GD    HRL   +  H   +VK   G  G GLP     ++ VS G  GL+ A++
Sbjct: 33  RSYKESGD----HRLRDQLILHYSPLVKYVAGRVGVGLPANVEQADFVSSGVFGLIDAIE 88

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD +R  +  TY++  I+ A+ +  LR+   +        K +      L+  L+    
Sbjct: 89  KFDIDRAIKFETYAISRIRGAIIDE-LRALDWIPRSVRQKAKAVERAYATLEARLRR--- 144

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE  VA    +++ +   I     LA   +L+ L++S+ +   +          G 
Sbjct: 145 TPYDPE--VAAEMGISLDDLHTIFSQLSLANVVALDELLHSAGEGGDRLTLMETLPDSGA 202

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           +  +   E+R+ RR +L  +++ L  RE+ +      +   +TL  +     V+  RV Q
Sbjct: 203 DNPVEIAEDRELRR-LLASAVNTLPEREKTVVTLYYYE--GLTLAEIGQVLGVTESRVSQ 259

Query: 272 IEARA 276
           I  ++
Sbjct: 260 IHTKS 264


>gi|78044674|ref|YP_359860.1| RNA polymerase sigma factor for flagellar operon [Carboxydothermus
           hydrogenoformans Z-2901]
 gi|77996789|gb|ABB15688.1| RNA polymerase sigma factor for flagellar operon [Carboxydothermus
           hydrogenoformans Z-2901]
          Length = 254

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 69/269 (25%), Positives = 128/269 (47%), Gaps = 44/269 (16%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKK 92
           L + YR +  L   + L+  +L LV K++       LP      ++   G IGL++AV+ 
Sbjct: 11  LWREYRRNKSLQLRNELLEYYLPLVRKVSAAM-SLKLPTHLSREDIEGYGIIGLIEAVET 69

Query: 93  FDPERGFRLATYSMWWIKAAM------QEYILRS-WSLVKIGTTANQKRLFFNLRRLKGH 145
           +D  RG +  +Y+   I+AA+      Q ++ RS W  +K  TT+ +  L          
Sbjct: 70  YDQNRGVKFESYASLKIRAAIIDELRKQNFLPRSVWDKIKKVTTSEEMLL---------- 119

Query: 146 LQAITDNNLKPE-QVVAIAKKLNVSESEVISMNCRLA--GDESLNALIN---SSDKNSSQ 199
                 N L  E  V  +A++L VS S+V+ +   +A     SL+ +I+   S D+ +  
Sbjct: 120 ------NALGEEVPVEKVAEQLGVSVSDVLKIKTLIALKNHLSLDEIIDPEGSVDRFAGL 173

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
             D    +    E   +++ E +  R  L R    L+ RER I +   ++E  ++L+ ++
Sbjct: 174 ADD----EKYSPENKFLKRVEIEELREALKR----LSDRERLILQLFYVEE--LSLKEIA 223

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +  ++S  RV QI ++A  K+++ + + V
Sbjct: 224 AVLDISTSRVSQIASKALGKLRKLLNEGV 252


>gi|148242553|ref|YP_001227710.1| putative group 3 RNA polymerase sigma factor [Synechococcus sp.
           RCC307]
 gi|147850863|emb|CAK28357.1| Putative group 3 RNA polymerase sigma factor [Synechococcus sp.
           RCC307]
          Length = 259

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 27/86 (31%), Positives = 48/86 (55%), Gaps = 1/86 (1%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVK 91
           E   L +RY +   L   +RLV +HL LV + A  + +       ++  +G  GL+ AV+
Sbjct: 10  ELLALHRRYGQSRCLKLRNRLVEAHLNLVRQQAARFSQASSACYDDLFQQGCFGLLDAVQ 69

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYI 117
           ++ P+RG+  +TY++  I+  MQ Y+
Sbjct: 70  RYQPQRGYAFSTYAVTLIRGQMQHYL 95


>gi|121488735|emb|CAJ18251.1| sigma 70-type sigma factor [Chlorobium chlorovibrioides]
          Length = 165

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 50/178 (28%), Positives = 88/178 (49%), Gaps = 33/178 (18%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTTA 130
           ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++      Q  I+R   L ++GT  
Sbjct: 1   DLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVR-LPLNRVGTLN 59

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNAL 189
              + +  L +     +   D N K      +A  L++ +S+ ++   ++AG   S++A 
Sbjct: 60  KISKAYSQLEQ-----EYERDPNTK-----ELANLLDM-DSQDVADTLKIAGRHVSVDAP 108

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT----RSMSVLNPRERRIF 243
               D N  +  D L  D    +  L         R+ LT    RS+SVL PRE  + 
Sbjct: 109 FAQGDDN--RLLDVLQNDGHMPDHTL--------NRDSLTLEVERSLSVLAPREADVI 156


>gi|121488749|emb|CAJ18259.1| sigma 70-type sigma factor [Pelodictyon luteolum]
          Length = 165

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 17/50 (34%), Positives = 37/50 (74%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + +     +V++
Sbjct: 1   DLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL 50


>gi|108804004|ref|YP_643941.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108765247|gb|ABG04129.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 257

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 40/134 (29%), Positives = 65/134 (48%), Gaps = 7/134 (5%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY-GLPISEVVSEGNIGLMQAVKKFDP 95
           L   YR+ GD  A  RL  SH  L+  IA  Y G  G P  +++  G +GLM+AV  +DP
Sbjct: 18  LVAAYRDGGDRRALERLFASHGALLKSIARRYAGSSGEPYEDLLQAGYVGLMKAVNGYDP 77

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
             G   ++Y+   ++  ++ + LR   LV+    A+   L+  +     HL         
Sbjct: 78  SSGAAFSSYAYSMMEGEIRHH-LRDSGLVRRPRWASG--LYARVSEATAHLTRELGRPPL 134

Query: 156 PEQVVAIAKKLNVS 169
           PE+V   A++ N++
Sbjct: 135 PEEV---AREANIT 145


>gi|253681759|ref|ZP_04862556.1| RNA polymerase sigma-G factor [Clostridium botulinum D str. 1873]
 gi|253561471|gb|EES90923.1| RNA polymerase sigma-G factor [Clostridium botulinum D str. 1873]
          Length = 257

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 63/273 (23%), Positives = 129/273 (47%), Gaps = 43/273 (15%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+ +E   L  + R+ GD  +  + +  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKDKEMKELLIKMRD-GDYFSREKFIRGNLRLVLSVIQRFNNRGENVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD  +  + +TY++  I   ++ Y LR  + +++  +   + + +   +++ 
Sbjct: 74  GLIKAIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNSIRVSRSL--RDIAYKALQVRD 130

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L  I  +N  P  V  IAK+L +   EV+          +L+A+           QD +
Sbjct: 131 RL--INKDNKDP-NVSQIAKELELPREEVVF---------ALDAI-----------QDPV 167

Query: 205 -----VYDHDGQEQ--VLIEKEERKNRRNMLTRSMSV------LNPRERRIFEARRLQEN 251
                +Y HDG +   V+ +  + KN  +    ++S+      LN RE+ I   R  Q  
Sbjct: 168 SLFEPIY-HDGGDALYVMDQISDSKNADDSWIENISIKEAMKRLNKREKLILNMRFFQGR 226

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             T   ++ E  +S+ +V ++E  A K +++ +
Sbjct: 227 --TQMEVADEIGISQAQVSRLEKTALKHMRKYV 257


>gi|225017509|ref|ZP_03706701.1| hypothetical protein CLOSTMETH_01436 [Clostridium methylpentosum
           DSM 5476]
 gi|224949748|gb|EEG30957.1| hypothetical protein CLOSTMETH_01436 [Clostridium methylpentosum
           DSM 5476]
          Length = 231

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 33/86 (38%), Positives = 48/86 (55%), Gaps = 6/86 (6%)

Query: 27  PMLEKQEE--YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           P+  KQE+  + L K+    GD +A  RL+  +LRLV  IA  Y        +++S G I
Sbjct: 29  PLTLKQEKESFELMKQ----GDSAARDRLIEHNLRLVAHIAKKYYSVTNEQDDLISIGTI 84

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIK 110
           GL++AV  FD  +G R ATY+   I+
Sbjct: 85  GLIKAVGTFDYTKGTRFATYASRCIE 110


>gi|121488745|emb|CAJ18257.1| sigma 70-type sigma factor [Chlorobaculum thiosulfatiphilum]
          Length = 165

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 17/50 (34%), Positives = 37/50 (74%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + +     +V++
Sbjct: 1   DLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL 50


>gi|224116898|ref|XP_002331841.1| predicted protein [Populus trichocarpa]
 gi|222875079|gb|EEF12210.1| predicted protein [Populus trichocarpa]
          Length = 512

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 33/103 (32%), Positives = 59/103 (57%), Gaps = 13/103 (12%)

Query: 48  SAAHRLVTSHLRLVVKIAMGY-RGY--GLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           +A ++L+  +LRLV+ +   Y + Y  G    ++   G  GLM A+ +F+P+R FRL+TY
Sbjct: 275 AARNKLIKHNLRLVLFVINKYFQDYANGPRYQDLCQAGVKGLMTAIDRFEPKRRFRLSTY 334

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
            ++WI+ A    I+RS +L      ++  R+ F L  ++  +Q
Sbjct: 335 GLFWIRHA----IIRSMTL------SSFTRVSFGLESIRSEIQ 367


>gi|188585937|ref|YP_001917482.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|179350624|gb|ACB84894.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 269

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 36/151 (23%), Positives = 78/151 (51%), Gaps = 7/151 (4%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAA-HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           K+P+L   E   L ++ R   D   A  +L+  +LRLV+ +   +   G  + ++   G 
Sbjct: 15  KLPVLNNSEMKELFEKMRVGDDEDEARQKLINGNLRLVLSVIQRFNNRGEYVDDLFQVGC 74

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           +GL++A+  FD  +  + +TY++  I   ++ Y LR  + +++  +   + + +   +++
Sbjct: 75  VGLIKAIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNSIRVSRSL--RDIAYKALQIR 131

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVI 174
             L    + N +   +  IA+KL+VSE +V+
Sbjct: 132 DEL---VEKNSREPAISEIAEKLDVSEEQVV 159


>gi|170764001|ref|ZP_02637018.2| RNA polymerase sigma-K factor [Clostridium perfringens B str. ATCC
           3626]
 gi|170710658|gb|EDT22840.1| RNA polymerase sigma-K factor [Clostridium perfringens B str. ATCC
           3626]
          Length = 152

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 35/105 (33%), Positives = 56/105 (53%), Gaps = 5/105 (4%)

Query: 9   IVNGEIGLSRYIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           +V  +I L+ Y+      P  L ++EE +  +R ++ GD+ A   LV  +LRLV  I   
Sbjct: 10  LVGSKIFLTGYVTGNSTFPKPLNEKEEKIYLERLKD-GDVEAKRVLVERNLRLVAHIVKK 68

Query: 68  YRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           Y         + +++S G IGL++A+  FD  +G RLATY+   I
Sbjct: 69  YSSNYQNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATYAAKCI 113


>gi|307330048|ref|ZP_07609199.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306884309|gb|EFN15344.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 277

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 60/248 (24%), Positives = 107/248 (43%), Gaps = 26/248 (10%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFD 94
           + Y+  GD     +L+  H   +VK   G    GLP     ++ VS G  GL+ A++KFD
Sbjct: 33  RSYKTTGDGRLREQLIL-HYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEKFD 91

Query: 95  PERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           PER  +  TY++  I+ AM       ++I RS              L   LRR     + 
Sbjct: 92  PERAIKFETYAITRIRGAMIDELRALDWIPRSVRQKARAVERAYATLEAQLRRTPSEAEV 151

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
             + ++  E++  +  +L++  + V+++      +E L+      D+ S    D L    
Sbjct: 152 AAEMDISIEELHGVFSQLSL--ANVVAL------EELLHVGGEGGDRLS--LMDTL---E 198

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D      +E  E +  R +L R+++ L  RE+ +      +   +TL  +     V+  R
Sbjct: 199 DTAADNPVEVAEDRELRRLLARAINTLPEREKTVVTLYYYEG--LTLAEIGQVLGVTESR 256

Query: 269 VRQIEARA 276
           V QI  ++
Sbjct: 257 VSQIHTKS 264


>gi|224771349|dbj|BAH28616.1| sporulation sigma factor SigK [Clostridium perfringens]
          Length = 196

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 34/101 (33%), Positives = 54/101 (53%), Gaps = 5/101 (4%)

Query: 13  EIGLSRYIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           +I L+ Y+      P  L ++EE +  +R ++ GD+ A   LV  +LRLV  I   Y   
Sbjct: 1   KIFLTGYVTGNSTFPKPLNEKEEKIYLERLKD-GDIEAKRVLVERNLRLVAHIVKKYSSS 59

Query: 72  ---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
                 + +++S G IGL++A+  FD  +G RLATY+   I
Sbjct: 60  YQNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATYAAKCI 100


>gi|121488532|emb|CAJ18256.1| sigma 70-type sigma factor [Chlorobium limicola]
          Length = 165

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 17/50 (34%), Positives = 37/50 (74%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + +     +V++
Sbjct: 1   DLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL 50


>gi|117929239|ref|YP_873790.1| RNA polymerase, sigma 28 subunit [Acidothermus cellulolyticus 11B]
 gi|117649702|gb|ABK53804.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Acidothermus
           cellulolyticus 11B]
          Length = 297

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 55/212 (25%), Positives = 94/212 (44%), Gaps = 25/212 (11%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS--WSLVKIGTTANQK- 133
           ++ S G + L QA + +DP RG   A ++   I+ A+ +  LRS  W+   +   A Q+ 
Sbjct: 51  DLTSAGMMALAQAARTYDPSRGVPFARFATVRIRGAIIDE-LRSHDWASRSVRVKARQRA 109

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN-S 192
                L  + G L         P Q   +A+ L VS  E+ S      GD     +++  
Sbjct: 110 AAEEELAAVLGRL---------PTQ-AELAEHLGVSVDELASTE----GDVHRAVVLSLQ 155

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
              ++   +  L +   G E VL+ +E    R N L  +++ L PR R + E    QE P
Sbjct: 156 GFADAGTLEGMLPHQDPGPEDVLLNRE----RVNYLLDAVAALPPRLRTVVEGYFFQERP 211

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             +  L+ E  V+  R+ Q+ A A   +++ +
Sbjct: 212 --MAELAEELGVTESRISQMRAEALSLLRDGM 241


>gi|56551522|ref|YP_162361.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Zymomonas mobilis
           subsp. mobilis ZM4]
 gi|56543096|gb|AAV89250.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Zymomonas mobilis
           subsp. mobilis ZM4]
          Length = 247

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 60/235 (25%), Positives = 104/235 (44%), Gaps = 23/235 (9%)

Query: 53  LVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           L+ +HL+LV KIA    G     + + +++  G + L++A   F+  RGF  ATY+   I
Sbjct: 28  LIKTHLQLVRKIAWHVHGRVSSAIEVEDLIQIGMVALIEAANAFE-NRGFAFATYASMRI 86

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + AM +Y +R  +     + A QK L      L   L        +PE    IA+KLN+S
Sbjct: 87  RGAMIDY-MRQHAATARSSIARQKTLNKAREELSATL------GRRPED-AEIAEKLNMS 138

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
            SE      R   D ++N    S D   S        D+  Q   +    ER+  ++ L 
Sbjct: 139 PSE-----YREWADGAINIRQESLDDVYSDHSSIFTDDNADQASEM----EREALQSALA 189

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             +  L  RE  + +   ++E  + L+ +    ++   R+ QI+  A   +++ +
Sbjct: 190 EQIKTLPEREALVLQLYYVEE--LNLKEIGEVLDLGTARISQIKKSAVDHLRQKM 242


>gi|154684976|ref|YP_001420137.1| RNA polymerase sigma factor SigB [Bacillus amyloliquefaciens FZB42]
 gi|126363073|emb|CAM35801.1| RNA polymerase sigma-B factor [Bacillus amyloliquefaciens FZB42]
 gi|154350827|gb|ABS72906.1| SigB [Bacillus amyloliquefaciens FZB42]
          Length = 262

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 64/263 (24%), Positives = 125/263 (47%), Gaps = 18/263 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE-GN 83
           K   L K E   L + ++ H +  A   LV  +  LV  +A  Y   G    E + + G 
Sbjct: 6   KTTKLTKDEVDRLIRDFQTHDNKEAQETLVEVYTNLVEMLAKKY-SKGKSFHEDLRQVGM 64

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRL 142
           IGL+ A+K++DPE G     +++  I   ++ ++  ++WS+         +R+     R+
Sbjct: 65  IGLLGAIKRYDPEVGKSFEAFAIPTIIGEIKRFLRDKTWSV------HVPRRIKELGPRI 118

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQ 201
           K  +  +T    +  +V  IA  L+VSE EV+     +   +S  AL ++ S +  +   
Sbjct: 119 KMAVDQLTTETQRSPKVEEIAAFLDVSEEEVLET---MEMGKSYQALSVDHSIEADADGS 175

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
              + D  G ++   E  ER N++ M+   + VL+ RE++I +   +Q    + +     
Sbjct: 176 TVTILDIVGSQE---EGYERVNQQMMIKSVLHVLSDREKQIIDLTFVQNK--SQKETGDI 230

Query: 262 FEVSRERVRQIEARAFKKVQESI 284
             +S+  V +++ +A KK++E++
Sbjct: 231 LGISQMHVSRLQRKAVKKLREAL 253


>gi|302535694|ref|ZP_07288036.1| RNA polymerase sigma-E factor [Streptomyces sp. C]
 gi|302444589|gb|EFL16405.1| RNA polymerase sigma-E factor [Streptomyces sp. C]
          Length = 300

 Score = 52.0 bits (123), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 60/237 (25%), Positives = 104/237 (43%), Gaps = 23/237 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +   
Sbjct: 79  LIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTVVGE 138

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL   L +    L    D +     V  +A  L V+E 
Sbjct: 139 IKRFFRDTSWS-VRVPRRLQELRL--ALTKASDELAQKLDRS---PTVPELAAVLGVTEE 192

Query: 172 EVIS----MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           EV+      N   A   SL++     +       D L Y+    E V    E R++ + +
Sbjct: 193 EVVDGLAVGNAYTA--SSLDSPSPEDEGGEGSLADRLGYEDSALEGV----EYRESLKPL 246

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L +    L PRER+I   R      +T   +  E  +S+  V ++  R   +++  +
Sbjct: 247 LAK----LPPRERQIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLRTGL 297


>gi|157692327|ref|YP_001486789.1| RNA polymerase sigma factor SigD [Bacillus pumilus SAFR-032]
 gi|157681085|gb|ABV62229.1| DNA-directed RNA polymerase sigma subunit D [Bacillus pumilus
           SAFR-032]
          Length = 255

 Score = 51.6 bits (122), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 65/274 (23%), Positives = 130/274 (47%), Gaps = 43/274 (15%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQ 88
           E+  L  R++E  D +A   L+  ++ LV    +G    GLP S    +++S G +GL  
Sbjct: 7   EDQALWARWKEWKDPAAGDDLMRRYMPLVT-YHVGRISIGLPKSVHKEDLISLGMLGLYD 65

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           A++KFDP R  +  TY+ + I+ A+ + + +  W    +  T+ +K      ++++  ++
Sbjct: 66  ALEKFDPGRDLKFDTYASFRIRGAIIDGLRKEDW----LPRTSREKT-----KKVEAAIE 116

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVI-SMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
            +    L+      +A++L +SE +V+ +MN      E   A + S D+         ++
Sbjct: 117 KLEQRYLRNVTPTEVAEELGMSEQDVVTTMN------EGFFANLLSIDEK--------LH 162

Query: 207 DHDGQE--QVLIEKE-----ERKNRRN----MLTRSMSVLNPRERRIFEARRLQENPVTL 255
           D +  E  QV+I  E     E K  ++     L   M+ L+ +E+ +      +E  +TL
Sbjct: 163 DQEDGENVQVMIRDEKTVTPEEKMLKDELIEQLAEKMTELSEKEKLVISLFYKEE--LTL 220

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
             +     +S  R+ QI ++A  K++  + K ++
Sbjct: 221 TEIGHVLNLSTSRISQIHSKALFKLKHLLDKAIQ 254


>gi|160939772|ref|ZP_02087119.1| hypothetical protein CLOBOL_04663 [Clostridium bolteae ATCC
           BAA-613]
 gi|158437206|gb|EDP14971.1| hypothetical protein CLOBOL_04663 [Clostridium bolteae ATCC
           BAA-613]
          Length = 209

 Score = 51.6 bits (122), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/66 (36%), Positives = 41/66 (62%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD SA   L+  ++RLV  +   Y+G    + +++S G IGL++AV  F+ ++G RLATY
Sbjct: 23  GDQSARDMLIEHNMRLVAHVVKKYQGSDYDMEDLLSVGTIGLIKAVNTFNVDKGSRLATY 82

Query: 105 SMWWIK 110
           +   ++
Sbjct: 83  AARCVE 88


>gi|121488785|emb|CAJ18277.1| sigma 70-type sigma factor [Pelodictyon clathratiforme]
          Length = 165

 Score = 51.6 bits (122), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 17/50 (34%), Positives = 37/50 (74%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + +     +V++
Sbjct: 1   DLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL 50


>gi|325679635|ref|ZP_08159210.1| RNA polymerase sigma-E factor [Ruminococcus albus 8]
 gi|324108665|gb|EGC02906.1| RNA polymerase sigma-E factor [Ruminococcus albus 8]
          Length = 235

 Score = 51.6 bits (122), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 30/92 (32%), Positives = 51/92 (55%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           YI+   K+P    +EE   A       +  A   L+  +LRLVV I+  +   G+ + ++
Sbjct: 24  YINGADKLPPPLTKEEERKAFELFATDEKKAKELLIVHNLRLVVYISRKFENAGVGLEDL 83

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           +S G+IGL++AV  F P++  +LATY+   I+
Sbjct: 84  ISIGSIGLIKAVNTFRPDKNIKLATYASRCIE 115


>gi|302542195|ref|ZP_07294537.1| RNA polymerase sigma factor WhiG [Streptomyces hygroscopicus ATCC
           53653]
 gi|302459813|gb|EFL22906.1| RNA polymerase sigma factor WhiG [Streptomyces himastatinicus ATCC
           53653]
          Length = 277

 Score = 51.6 bits (122), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 64/246 (26%), Positives = 104/246 (42%), Gaps = 22/246 (8%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFD 94
           + Y+  GD     +L+  H   +VK   G    GLP     ++ VS G  GL+ A++KFD
Sbjct: 33  RSYKATGDGRLREQLIL-HYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEKFD 91

Query: 95  PERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           PER  +  TY++  I+ AM  E     W    I  +  QK     + R    L+A     
Sbjct: 92  PERAIKFETYAITRIRGAMIDELRALDW----IPRSVRQKA--RAVERAYATLEAALRRT 145

Query: 154 LKPEQV-VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ--DWLVYDHDG 210
             P +V VA    ++V E   +     LA   +L  L++   +   +    D L    D 
Sbjct: 146 --PTEVEVAAEMDISVDELHGVFSQLSLANVVALEELLHVGGEGGDRLSLMDTL---EDT 200

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                +E  E +  R +L R+++ L  RE+ +      +   +TL  +     V+  RV 
Sbjct: 201 AADNPVEVAEDRELRRLLARAINTLPEREKTVVTLYYYE--GLTLAEIGQVLGVTESRVS 258

Query: 271 QIEARA 276
           QI  ++
Sbjct: 259 QIHTKS 264


>gi|160892593|ref|ZP_02073383.1| hypothetical protein CLOL250_00123 [Clostridium sp. L2-50]
 gi|156865634|gb|EDO59065.1| hypothetical protein CLOL250_00123 [Clostridium sp. L2-50]
          Length = 245

 Score = 51.6 bits (122), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 32/106 (30%), Positives = 53/106 (50%), Gaps = 1/106 (0%)

Query: 19  YIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           YI     +P  LE  EE  +        D      L+  +LRLVV IA  +   G+ + +
Sbjct: 31  YIGGCDVLPAPLEPYEESAMVAGLGNGDDQEIKKILIERNLRLVVYIAKKFDNTGIGVED 90

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           ++S G IGL++A+  F  ++  +LATY+   I+  +  Y+ R+  L
Sbjct: 91  LISIGTIGLIKAINTFKCDKNIKLATYASRCIENEILMYLRRNSKL 136


>gi|304316726|ref|YP_003851871.1| RNA polymerase, sigma 28 subunit, SigK [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
 gi|302778228|gb|ADL68787.1| RNA polymerase, sigma 28 subunit, SigK [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
          Length = 231

 Score = 51.6 bits (122), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 3/74 (4%)

Query: 39  KRYRE---HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           K+Y E   +GD  A + L+  +LRLV  I   Y   G  + +++S G IGL++A+  +D 
Sbjct: 38  KKYFEAYKNGDEEAKNILIERNLRLVAHIVKKYSNTGKDVDDLISIGTIGLIKAISTYDA 97

Query: 96  ERGFRLATYSMWWI 109
            +G  LATY+   I
Sbjct: 98  SKGTHLATYAARCI 111


>gi|289578664|ref|YP_003477291.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter italicus Ab9]
 gi|297544884|ref|YP_003677186.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
 gi|289528377|gb|ADD02729.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter italicus Ab9]
 gi|296842659|gb|ADH61175.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
          Length = 256

 Score = 51.6 bits (122), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 60/260 (23%), Positives = 123/260 (47%), Gaps = 17/260 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+  ++  L  R + +GD  A    +  +LRLV+ +   +   G  + ++   G I
Sbjct: 14  KLPVLKPSKQKELLIRMK-NGDKKAREEFINGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 72

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD ++  + +TY++  I   ++ Y LR  + +++  +          + L+ 
Sbjct: 73  GLIKAIDNFDLDQNVKFSTYAVPMIIGEIRRY-LRDNTPIRVSRSLRD----IAYKALQV 127

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + +++N+ +P  V  IAK+L++   EV+     +    SL   I     ++    D  
Sbjct: 128 RDKLVSENSKEP-TVGEIAKELDLPREEVVMALDAIQEPVSLFEPIYHDGGDAIYVMDQ- 185

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           V D    ++V +EK         L  ++  LN RE+ I   R   E    +E ++ E  +
Sbjct: 186 VSDDKNIDEVWLEK-------IALKEAIQKLNEREKLILTLRFF-EGKTQME-VAKEIGI 236

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ +V ++E  A   +++ I
Sbjct: 237 SQAQVSRLEKAALNHMRKYI 256


>gi|150016005|ref|YP_001308259.1| sporulation sigma factor SigG [Clostridium beijerinckii NCIMB 8052]
 gi|149902470|gb|ABR33303.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           beijerinckii NCIMB 8052]
          Length = 257

 Score = 51.6 bits (122), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 39/150 (26%), Positives = 77/150 (51%), Gaps = 7/150 (4%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+++E+  L  +  + GD +A    +  +LRLV+ +   +   G  I ++   G I
Sbjct: 15  KLPILKEKEKKQLFLQM-QAGDKNARETFIKGNLRLVLSVIQRFNNRGENIDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD  +  + +TY++  I   ++ Y LR  + +++  +          + L  
Sbjct: 74  GLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNSIRVSRSLRD----IAYKALIM 128

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVI 174
             + I DNN +P  +  IAK+L +   EV+
Sbjct: 129 REKFIKDNNKEP-TISQIAKELELPREEVV 157


>gi|224771307|dbj|BAH28595.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771319|dbj|BAH28601.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771321|dbj|BAH28602.1| sporulation sigma factor SigK [Clostridium perfringens]
          Length = 196

 Score = 51.6 bits (122), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 34/101 (33%), Positives = 54/101 (53%), Gaps = 5/101 (4%)

Query: 13  EIGLSRYIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           +I L+ Y+      P  L ++EE +  +R ++ GD+ A   LV  +LRLV  I   Y   
Sbjct: 1   KIFLTGYVTGNSTFPKPLNEKEEKIYLERLKD-GDVEAKRVLVERNLRLVAHIVKKYSSN 59

Query: 72  ---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
                 + +++S G IGL++A+  FD  +G RLATY+   I
Sbjct: 60  YQNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATYAAKCI 100


>gi|254519401|ref|ZP_05131457.1| RNA polymerase [Clostridium sp. 7_2_43FAA]
 gi|226913150|gb|EEH98351.1| RNA polymerase [Clostridium sp. 7_2_43FAA]
          Length = 241

 Score = 51.6 bits (122), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 51/229 (22%), Positives = 106/229 (46%), Gaps = 17/229 (7%)

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           L  ++ +G   Y +   ++VS G +GL+ A+ ++D  +G + ++Y+   IK AM + I +
Sbjct: 24  LASRVMLGKTKY-IEYEDLVSYGIVGLLDAINRYDSTKGMKFSSYATLRIKGAMIDEIRK 82

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV--ISMN 177
              +         K     L +    ++ + +  ++   +  IA +LN+SE EV  +   
Sbjct: 83  CRPI--------SKGAMDKLAKYNECVEKLQNRYMREPSLQEIALELNISEEEVSQVENY 134

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                  SL ++I S D + +  +     +    E+ L    E K +  +L  ++  L  
Sbjct: 135 INYMSIISLESIIYSDDDDVTIMETLEDKNSISPEESL----EDKEKLEILAEAIEKLKD 190

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +++ I      ++  +TL+ +    EVS  RV Q+ +RA + ++  +QK
Sbjct: 191 KDKLILNLYYYEK--LTLKEIGQILEVSESRVCQLHSRAIRNLRAVMQK 237


>gi|89895149|ref|YP_518636.1| sporulation sigma factor SigK [Desulfitobacterium hafniense Y51]
 gi|89334597|dbj|BAE84192.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 248

 Score = 51.6 bits (122), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/62 (37%), Positives = 38/62 (61%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A ++LV  +LRLV  +   + G G    +++S G IGL++ +  FDP +G +LATY+   
Sbjct: 64  ARNKLVEHNLRLVAHLVKKFDGTGEDSDDLISIGTIGLIKGIDTFDPGKGTKLATYAARC 123

Query: 109 IK 110
           I+
Sbjct: 124 IE 125


>gi|332701290|ref|ZP_08421378.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio
           africanus str. Walvis Bay]
 gi|332551439|gb|EGJ48483.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio
           africanus str. Walvis Bay]
          Length = 264

 Score = 51.6 bits (122), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 56/222 (25%), Positives = 103/222 (46%), Gaps = 26/222 (11%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR-SWSLVKIGTTANQK 133
           + E++S G++GLM+A++KF+PE   +  TY+   IK AM + + R  W           +
Sbjct: 64  LGELMSAGSLGLMEALQKFNPELRIKFETYAESRIKGAMLDELRRMDWY---------SR 114

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE---SLNALI 190
            L   LR ++  ++ I     +P  V  IAK+  +SE +V  M   +  ++   SL+A+ 
Sbjct: 115 GLRQRLRLMEHTVREIEQETGRPATVQEIAKRTGLSEKDV-DMGLEMLQNQLCLSLDAIS 173

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
                 S    D   Y      Q LI+K         +T  +  L PRE+ +      +E
Sbjct: 174 ECVASVSDAGVDGDPY-QSAAFQELIDK---------ITLLIDELTPREKLVLSLYYGEE 223

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
             + +   ++  E++  RV Q+ ++A  K+++  + Q  L +
Sbjct: 224 --LNMRETANVMEITEGRVSQLHSQALGKLRKLFKDQYNLDA 263


>gi|284045116|ref|YP_003395456.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Conexibacter woesei
           DSM 14684]
 gi|283949337|gb|ADB52081.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Conexibacter woesei
           DSM 14684]
          Length = 262

 Score = 51.6 bits (122), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 67/260 (25%), Positives = 122/260 (46%), Gaps = 24/260 (9%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKK 92
           L +RY+  GD  A  RLV ++  LV  +A G    GLP     ++++S G IGL+ A+++
Sbjct: 13  LWRRYKASGDGRARERLVVAYSPLVKYVA-GRMASGLPAHVEEADLISYGLIGLISAIER 71

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ-AITD 151
           FD  R  +  TY++  I+ A+ +  LRS   V     A  + +     +L+  LQ A TD
Sbjct: 72  FDLGREIKFETYAIPRIRGAIIDE-LRSLDWVPRSVRAKAREIERANAKLEHKLQRAPTD 130

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQ--DWLVYD 207
             +        A +L++S  E      +++     +L+ L   SD +  Q    D L   
Sbjct: 131 EEM--------AHELDMSMDEFQDALIQISNSTIAALDELWTVSDASGDQISLLDTLQDP 182

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
                + +++  E K+R   +  +++ L  RE+ +  A    EN +TL  +     V+  
Sbjct: 183 DAPDPEKIVDASELKDR---VADAIARLPEREKLVI-ALYYYEN-LTLREIGEVLGVTES 237

Query: 268 RVRQIEARAFKKVQESIQKQ 287
           R+ Q+  +A  +++  +Q +
Sbjct: 238 RISQLHTKAVLRLRSRLQNE 257


>gi|219669565|ref|YP_002460000.1| sporulation sigma factor SigK [Desulfitobacterium hafniense DCB-2]
 gi|219539825|gb|ACL21564.1| RNA polymerase, sigma 28 subunit, SigK [Desulfitobacterium
           hafniense DCB-2]
          Length = 249

 Score = 51.6 bits (122), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 23/62 (37%), Positives = 38/62 (61%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A ++LV  +LRLV  +   + G G    +++S G IGL++ +  FDP +G +LATY+   
Sbjct: 65  ARNKLVEHNLRLVAHLVKKFDGTGEDSDDLISIGTIGLIKGIDTFDPGKGTKLATYAARC 124

Query: 109 IK 110
           I+
Sbjct: 125 IE 126


>gi|163789630|ref|ZP_02184068.1| Sigma factor of SigD/WhiG family protein [Carnobacterium sp. AT7]
 gi|159875162|gb|EDP69228.1| Sigma factor of SigD/WhiG family protein [Carnobacterium sp. AT7]
          Length = 238

 Score = 51.6 bits (122), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 54/209 (25%), Positives = 104/209 (49%), Gaps = 13/209 (6%)

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           G IGLM A++KFD  +      Y+   IK  + + I ++  + +  T   +   ++   R
Sbjct: 41  GVIGLMDALEKFDKSKKVPFEGYAYIRIKGTIIDEIRKTAPVSR--TRMGKLNEYY---R 95

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
            K  L+A        +++ A  K    S +++      LA   SL  ++ S D NS +  
Sbjct: 96  GKEKLEAELMRTPTEKEICAELKIDEKSLAKIHETVHNLAS-VSLEKVMFSDDGNSIELL 154

Query: 202 DWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
           D+L   H+ G E  L++KE    R+++LT+ +  L+ RE+ I     ++E  ++L+ ++ 
Sbjct: 155 DFLEDTHETGSEDTLLDKE----RQHLLTKHVGQLDKREQTILNLIYVEE--LSLKEIAY 208

Query: 261 EFEVSRERVRQIEARAFKKVQESIQKQVE 289
            F++S  RV QI  +   K++ S+ ++ +
Sbjct: 209 IFDISVPRVSQIHGKMILKLKGSMGREYD 237


>gi|333024988|ref|ZP_08453052.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
 gi|332744840|gb|EGJ75281.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
          Length = 316

 Score = 51.6 bits (122), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 61/242 (25%), Positives = 108/242 (44%), Gaps = 30/242 (12%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           H LV  +L LV   A  +R    P+ +++  G IGL++A+ +F+  RG    T++M  I 
Sbjct: 93  HTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRGVEFPTFAMPTII 152

Query: 111 AAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
             ++ +    SWS V++     + RL  +L +    L    D    P +   +A+KL + 
Sbjct: 153 GEIKRFFRDTSWS-VRVPRRLQELRL--DLAKAGDELAQRLDRAPTPSE---LAEKLGIE 206

Query: 170 ESEVISMNCRLAGDESLNALINSS-------DKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
             EVI       G  + NA   SS       D + S   D L Y+    E +    E  +
Sbjct: 207 REEVIE------GMAASNAYTASSLDAQPEEDDSESALADRLGYEDHSLEGI----EYIE 256

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           + + M+ R    L  R+R+I   R +    +T   +  E  +S+  V ++ +R   K+++
Sbjct: 257 SLKPMIAR----LPQRDRKILSLRFVAN--MTQSEIGEELGISQMHVSRLLSRTLVKLRK 310

Query: 283 SI 284
            +
Sbjct: 311 GL 312


>gi|194016072|ref|ZP_03054687.1| RNA polymerase sigma-B factor [Bacillus pumilus ATCC 7061]
 gi|194012427|gb|EDW21994.1| RNA polymerase sigma-B factor [Bacillus pumilus ATCC 7061]
          Length = 262

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 65/259 (25%), Positives = 121/259 (46%), Gaps = 18/259 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE-GNIGLM 87
           L K E   L + Y+ + D  A   LV  +  LV  +A  Y   G    E + + G IGL+
Sbjct: 10  LTKDEVDRLIQSYQSNQDEQAQLTLVECYTNLVDMLAKKY-SKGKSFHEDLRQVGMIGLL 68

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHL 146
            A+K++DP  G     +++  I   ++ ++  ++WS+         +R+     R+K  +
Sbjct: 69  GAIKRYDPLVGKSFEAFAIPTIIGEIKRFLRDKTWSV------HVPRRIKELGPRIKMAV 122

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLV 205
             +T    K  QV  IA+ L+V+E EV+     +   +S  AL ++   +  S+     +
Sbjct: 123 DHLTTETQKSPQVQEIAEYLDVTEEEVLET---MEMGKSYQALSVDQGVEADSEGSTVTI 179

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            D  G ++   E  ER N++ ML   + VL  RE+ I     LQ    + +       +S
Sbjct: 180 LDVVGSQE---EGYERVNQKMMLESVLHVLTDREKEIINLTYLQNK--SQKETGDLLGIS 234

Query: 266 RERVRQIEARAFKKVQESI 284
           +  V +++ +A KK+++++
Sbjct: 235 QMHVSRLQRKAVKKLRDAL 253


>gi|318056726|ref|ZP_07975449.1| SigL-like sigma factor [Streptomyces sp. SA3_actG]
 gi|318075360|ref|ZP_07982692.1| SigL-like sigma factor [Streptomyces sp. SA3_actF]
          Length = 316

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 61/240 (25%), Positives = 108/240 (45%), Gaps = 30/240 (12%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  +L LV   A  +R    P+ +++  G IGL++A+ +F+  RG    T++M  I   
Sbjct: 95  LVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRGVEFPTFAMPTIIGE 154

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL  +L +    L    D    P +   +A+KL +   
Sbjct: 155 IKRFFRDTSWS-VRVPRRLQELRL--DLAKAGDELAQRLDRAPTPSE---LAEKLGIERE 208

Query: 172 EVISMNCRLAGDESLNALINSS-------DKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           EVI       G  + NA   SS       D + S   D L Y+  G E +    E  ++ 
Sbjct: 209 EVIE------GMAASNAYTASSLDAQPEEDDSESALADRLGYEDHGLEGI----EYIESL 258

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + M+ R    L  R+R+I   R +    +T   +  E  +S+  V ++ +R   K+++ +
Sbjct: 259 KPMIAR----LPQRDRKILSLRFVAN--MTQSEIGEELGISQMHVSRLLSRTLVKLRKGL 312


>gi|224771357|dbj|BAH28620.1| sporulation sigma factor SigK [Clostridium perfringens]
          Length = 196

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 34/101 (33%), Positives = 54/101 (53%), Gaps = 5/101 (4%)

Query: 13  EIGLSRYIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           +I L+ Y+      P  L ++EE +  +R ++ GD+ A   LV  +LRLV  I   Y   
Sbjct: 1   KIFLTGYVTGNSTFPKPLNEKEEKIYLERLKD-GDVEAKRVLVERNLRLVAHIVKKYSSN 59

Query: 72  ---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
                 + +++S G IGL++A+  FD  +G RLATY+   I
Sbjct: 60  YQNSKEMDDLISIGTIGLIKAIDSFDTSKGIRLATYAAKCI 100


>gi|312792676|ref|YP_004025599.1| RNA polymerase, sigma 28 subunit, flia/whig [Caldicellulosiruptor
           kristjanssonii 177R1B]
 gi|312179816|gb|ADQ39986.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Caldicellulosiruptor
           kristjanssonii 177R1B]
          Length = 246

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 61/251 (24%), Positives = 120/251 (47%), Gaps = 27/251 (10%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMG----YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
           D     +L+  ++ LV K+  G    Y G  +   ++VS G+IGL+ A++KFD ++G + 
Sbjct: 15  DPKIKEQLIIKYMPLV-KLVAGRMAIYFGGNVEYDDLVSYGSIGLLDAIEKFDSQKGVKF 73

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
            TY+   IK A+ + + RS   +        K +       K +++   +     +Q   
Sbjct: 74  ETYAYTRIKGAIIDCV-RSQDFLPRSIRQKAKEI------EKAYVEIEREGKTPTDQ--E 124

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ-WQDWL--VYDHDGQEQVLIEK 218
           +AK++ +S +E+  +  R++     + +I S D    Q ++  +  + D   Q +  IE 
Sbjct: 125 VAKRVGISVNELQKLQERIS-----SGMIISLDSFLEQNYESKIGGLEDFVSQPEHFIEN 179

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           EE K    +L + +  L   ER +      +E  ++++ ++    VS  RV Q+  RA  
Sbjct: 180 EELK---EVLRQQIENLMENERMVIVLYYYEE--LSIKEIAKVLGVSESRVSQLHTRALL 234

Query: 279 KVQESIQKQVE 289
           K++ ++QK +E
Sbjct: 235 KLKAALQKYLE 245


>gi|312128104|ref|YP_003992978.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor hydrothermalis 108]
 gi|311778123|gb|ADQ07609.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor hydrothermalis 108]
          Length = 255

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 54/221 (24%), Positives = 104/221 (47%), Gaps = 15/221 (6%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L  +E+  L KR +E GD  A    +  +LRLV+ +   +   G  + ++   G IG
Sbjct: 14  LPVLSHEEKLELLKRMKE-GDKEARRIFIEGNLRLVLSVVQKFANRGENLDDLFQVGCIG 72

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A+  FD  +  + +TY++  I   ++ Y LR  + ++I  +          + LK  
Sbjct: 73  LIKAIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNSMRISRSLKDTA----YKALKIK 127

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            + I  N+ +P  +  IAK+L++++ E++     +    SL   +   D   + +    +
Sbjct: 128 EKYINKNHREP-TLEEIAKELSITKEELVFALDSIQEPISLYEPV-FQDSTDTMYVVEKL 185

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
            DH   E V +E+   K+       ++S L  RE+ I   R
Sbjct: 186 CDHKSCENVWLEEISLKD-------ALSKLTKREKEILYLR 219


>gi|163814130|ref|ZP_02205522.1| hypothetical protein COPEUT_00283 [Coprococcus eutactus ATCC 27759]
 gi|158450579|gb|EDP27574.1| hypothetical protein COPEUT_00283 [Coprococcus eutactus ATCC 27759]
          Length = 245

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 31/103 (30%), Positives = 54/103 (52%), Gaps = 1/103 (0%)

Query: 19  YIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           YI     +P  LE  EE ++     +     A   L+  +LRLVV IA  +   G+ I +
Sbjct: 31  YIGGAEILPAPLEPHEEAIVIDELTQKQSEEAKKMLIERNLRLVVYIARKFDNTGVGIED 90

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++S G IGL++A+  F  ++  +LATY+   I+  +  ++ R+
Sbjct: 91  LISIGTIGLIKAINTFKNDKNIKLATYASRCIENEILMFLRRN 133


>gi|224771331|dbj|BAH28607.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771333|dbj|BAH28608.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771337|dbj|BAH28610.1| sporulation sigma factor SigK [Clostridium perfringens]
          Length = 196

 Score = 51.6 bits (122), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 34/101 (33%), Positives = 54/101 (53%), Gaps = 5/101 (4%)

Query: 13  EIGLSRYIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           +I L+ Y+      P  L ++EE +  +R ++ GD+ A   LV  +LRLV  I   Y   
Sbjct: 1   KIFLTGYVTGNSTFPKPLNEKEEKIYLERLKD-GDVEAKRVLVERNLRLVAHIVKKYSSS 59

Query: 72  ---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
                 + +++S G IGL++A+  FD  +G RLATY+   I
Sbjct: 60  YQNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATYAAKCI 100


>gi|224771363|dbj|BAH28623.1| sporulation sigma factor SigK [Clostridium perfringens]
          Length = 196

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 34/101 (33%), Positives = 54/101 (53%), Gaps = 5/101 (4%)

Query: 13  EIGLSRYIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           +I L+ Y+      P  L ++EE +  +R ++ GD+ A   LV  +LRLV  I   Y   
Sbjct: 1   KIFLTGYVTGNSTFPKPLNEKEEKIYLERLKD-GDVEAKRVLVERNLRLVAHIVKKYSSN 59

Query: 72  ---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
                 + +++S G IGL++A+  FD  +G RLATY+   I
Sbjct: 60  YQNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATYAAKCI 100


>gi|167037237|ref|YP_001664815.1| sporulation sigma factor SigG [Thermoanaerobacter pseudethanolicus
           ATCC 33223]
 gi|167040623|ref|YP_001663608.1| sporulation sigma factor SigG [Thermoanaerobacter sp. X514]
 gi|300914664|ref|ZP_07131980.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X561]
 gi|307267689|ref|ZP_07549143.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|307724102|ref|YP_003903853.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter sp. X513]
 gi|320115656|ref|YP_004185815.1| RNA polymerase sigma-G factor [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
 gi|166854863|gb|ABY93272.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Thermoanaerobacter sp. X514]
 gi|166856071|gb|ABY94479.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Thermoanaerobacter pseudethanolicus ATCC 33223]
 gi|300889599|gb|EFK84745.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X561]
 gi|306917291|gb|EFN47611.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|307581163|gb|ADN54562.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X513]
 gi|319928747|gb|ADV79432.1| RNA polymerase sigma-G factor [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
          Length = 256

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 59/260 (22%), Positives = 123/260 (47%), Gaps = 17/260 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+  ++  L +R + +GD  A    +  +LRLV+ +   +   G  + ++   G I
Sbjct: 14  KLPVLKPSKQKELLQRMK-NGDKKAREEFINGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 72

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD  +  + +TY++  I   ++ Y LR  + +++  +          + L+ 
Sbjct: 73  GLIKAIDNFDLNQNVKFSTYAVPMIIGEIRRY-LRDNTPIRVSRSLRD----IAYKALQV 127

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + +++N+ +P  V  IAK+L++   EV+     +    SL   I     ++    D  
Sbjct: 128 RDKLVSENSKEP-TVGEIAKELDLPREEVVMALDAIQEPVSLFEPIYHDGGDAIYVMDQ- 185

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           V D    ++V +EK         L  ++  L+ RE+ I    R  E    +E ++ E  +
Sbjct: 186 VSDDKNMDEVWLEK-------IALKEAIQKLSEREKMIL-TMRFFEGKTQME-VAKEIGI 236

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ +V ++E  A   +++ I
Sbjct: 237 SQAQVSRLEKAALNHMRKYI 256


>gi|302521363|ref|ZP_07273705.1| RNA polymerase sigma-B factor [Streptomyces sp. SPB78]
 gi|302430258|gb|EFL02074.1| RNA polymerase sigma-B factor [Streptomyces sp. SPB78]
          Length = 312

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 61/240 (25%), Positives = 108/240 (45%), Gaps = 30/240 (12%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  +L LV   A  +R    P+ +++  G IGL++A+ +F+  RG    T++M  I   
Sbjct: 91  LVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRGVEFPTFAMPTIIGE 150

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL  +L +    L    D    P +   +A+KL +   
Sbjct: 151 IKRFFRDTSWS-VRVPRRLQELRL--DLAKAGDELAQRLDRAPTPSE---LAEKLGIERE 204

Query: 172 EVISMNCRLAGDESLNALINSS-------DKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           EVI       G  + NA   SS       D + S   D L Y+  G E +    E  ++ 
Sbjct: 205 EVIE------GMAASNAYTASSLDAQPEEDDSESALADRLGYEDHGLEGI----EYIESL 254

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + M+ R    L  R+R+I   R +    +T   +  E  +S+  V ++ +R   K+++ +
Sbjct: 255 KPMIAR----LPQRDRKILSLRFVAN--MTQSEIGEELGISQMHVSRLLSRTLVKLRKGL 308


>gi|253581342|ref|ZP_04858568.1| DNA-directed RNA polymerase sigma subunit RpoD [Fusobacterium
           varium ATCC 27725]
 gi|251836706|gb|EES65240.1| DNA-directed RNA polymerase sigma subunit RpoD [Fusobacterium
           varium ATCC 27725]
          Length = 286

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 31/119 (26%), Positives = 55/119 (46%), Gaps = 9/119 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ E+  + ++  +EE    K   +        +++  +L  V  IA  Y   G+   ++
Sbjct: 61  YLEELSNMEVISDEEESNYLKNISDFD----KEKIIVKNLNEVASIAFYYVKTGIAYMDI 116

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           V EG +GL++AV  FDP++      YS +WI   +  YI       K+    N+ + FF
Sbjct: 117 VQEGTVGLIKAVDYFDPDKNGDFKNYSKYWIVREIVLYIEN-----KVADLRNEFKNFF 170


>gi|224771371|dbj|BAH28627.1| sporulation sigma factor SigK [Clostridium perfringens NCTC 8239]
 gi|224771377|dbj|BAH28630.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771385|dbj|BAH28634.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771387|dbj|BAH28635.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771389|dbj|BAH28636.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771391|dbj|BAH28637.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771407|dbj|BAH28645.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771409|dbj|BAH28646.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771411|dbj|BAH28647.1| sporulation sigma factor SigK [Clostridium perfringens]
          Length = 196

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 31/86 (36%), Positives = 47/86 (54%), Gaps = 5/86 (5%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGN 83
           P+ EK+E+  L +   + GD+ A   LV  +LRLV  I   Y         + +++S G 
Sbjct: 17  PLNEKEEKIYLDRL--KDGDVEAKRVLVERNLRLVAHIVKKYSSNYQNSKEMDDLISIGT 74

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWI 109
           IGL++A+  FD  +G RLATY+   I
Sbjct: 75  IGLIKAIDSFDTNKGIRLATYAAKCI 100


>gi|312876527|ref|ZP_07736510.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Caldicellulosiruptor
           lactoaceticus 6A]
 gi|311796738|gb|EFR13084.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Caldicellulosiruptor
           lactoaceticus 6A]
          Length = 246

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 61/251 (24%), Positives = 120/251 (47%), Gaps = 27/251 (10%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMG----YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
           D     +L+  ++ LV K+  G    Y G  +   ++VS G+IGL+ A++KFD ++G + 
Sbjct: 15  DPKIKEQLIIKYMPLV-KLVAGRMAIYFGGNVEYDDLVSYGSIGLLDAIEKFDSQKGVKF 73

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
            TY+   IK A+ + + RS   +        K +       K +++   +     +Q   
Sbjct: 74  ETYAYTRIKGAIIDCV-RSQDFLPRSIRQKAKEI------EKAYVEIEREGKTPTDQ--E 124

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ-WQDWL--VYDHDGQEQVLIEK 218
           +AK++ +S +E+  +  R++     + +I S D    Q ++  +  + D   Q +  IE 
Sbjct: 125 VAKRVGISVNELQKLKERIS-----SGMIISLDSFLEQNYESKIGGLEDFVSQPEHFIEN 179

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           EE K    +L + +  L   ER +      +E  ++++ ++    VS  RV Q+  RA  
Sbjct: 180 EELK---EVLRQQIENLMENERMVIVLYYYEE--LSIKEIAKVLGVSESRVSQLHTRALL 234

Query: 279 KVQESIQKQVE 289
           K++ ++QK +E
Sbjct: 235 KLKAALQKYLE 245


>gi|283780334|ref|YP_003371089.1| RNA polymerase, sigma 32 subunit, RpoH [Pirellula staleyi DSM 6068]
 gi|283438787|gb|ADB17229.1| RNA polymerase, sigma 32 subunit, RpoH [Pirellula staleyi DSM 6068]
          Length = 556

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 34/124 (27%), Positives = 62/124 (50%), Gaps = 29/124 (23%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRY----------REHGDLSAA-------------- 50
           GL  Y+  + ++P+L +++EY L +++          R+  D ++A              
Sbjct: 314 GLPPYLAALYEVPLLMREQEYHLFRKFNYLKFKATALRDKLDPASARTSVMDEIEHLYEE 373

Query: 51  -----HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
                + +V ++LRLVV IA  +         +VS+GN+ L++A +KFD  RG + +TY+
Sbjct: 374 AVAVKNSIVQANLRLVVSIAKRHVNGSEDFFGLVSDGNMSLIRAAEKFDFSRGNKFSTYA 433

Query: 106 MWWI 109
            W I
Sbjct: 434 SWAI 437



 Score = 38.5 bits (88), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 27/93 (29%), Positives = 50/93 (53%), Gaps = 3/93 (3%)

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR---RLQE 250
           D+  +   +  V   D +   L  +  ++ R+  + + +  L+ RE++I  +R       
Sbjct: 453 DRFRTSQDELFVAKQDNRSDQLGLEHVQQQRQLQVEKILEKLDEREQKIIISRFGLDHSH 512

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            P+TL+ +  E  V++ERVRQIEARA  K++E+
Sbjct: 513 EPLTLKEVGHELGVTKERVRQIEARALNKLREA 545


>gi|205373400|ref|ZP_03226204.1| RNA polymerase sigma factor SigD [Bacillus coahuilensis m4-4]
          Length = 257

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 67/264 (25%), Positives = 128/264 (48%), Gaps = 24/264 (9%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLV---VKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           Q+E VL K + E+ +  A   LV  ++ LV   V+         +   ++ S G +GL+ 
Sbjct: 7   QDELVLWKSWIENRNEEAGDLLVKKYMHLVSFHVQRISSTLPKNISKDDLKSLGMMGLLD 66

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++KFD ER  +  TY+ + I+ ++ +  LR    +   T    K++   + RL+  L  
Sbjct: 67  ALQKFDIERDLKFDTYASFRIRGSIIDG-LRKEDWLPRNTRDKAKKIEKTISRLEQTLM- 124

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVIS-MNCR-LAGDESLNALINSSDKNSSQWQDWLVY 206
                + PE V   AK+L++S  EVI  MN    A   S++ +    +K+S ++Q   + 
Sbjct: 125 ---RKIVPEDV---AKELDMSADEVIQIMNEHFFANVLSMDEMTREEEKDSPKFQ---MQ 175

Query: 207 DHDGQ--EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           D   +  E+ L++ E+ ++    L + +  LN +E+ +       +  +TL  +    ++
Sbjct: 176 DEKSRSPEEELVKSEQIRD----LEQHIRGLNEKEQLVLSL--FYQEELTLTEIGEVLQL 229

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S  R+ QI ++A  K+++ I  Q 
Sbjct: 230 STSRISQIHSKALFKLRKFISTQA 253


>gi|224992798|gb|ACN76114.1| SigB [Listeria innocua]
          Length = 214

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 54/211 (25%), Positives = 99/211 (46%), Gaps = 24/211 (11%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y+E GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D   G  
Sbjct: 4   YQEDGDEDAQYNLVIHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKS 63

Query: 101 LATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
              +++  I   ++ ++  + WS+         +R+     ++K  ++ +T       Q+
Sbjct: 64  FEAFAVPTIVGEIKRFLRDKKWSV------HVPRRIKELGPKIKNAVEELTRELQSSPQI 117

Query: 160 VAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
             IA  + V+E EV+ +M        L+ D S+ A    SD ++    D +    DG E+
Sbjct: 118 SDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTDDGFER 174

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           V        N+R +L + + VL+ RE++I +
Sbjct: 175 V--------NQRMLLEKVLPVLDEREQKILQ 197


>gi|224771305|dbj|BAH28594.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771309|dbj|BAH28596.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771311|dbj|BAH28597.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771313|dbj|BAH28598.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771315|dbj|BAH28599.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771317|dbj|BAH28600.1| sporulation sigma factor SigK [Clostridium perfringens CPE str.
           F4969]
 gi|224771323|dbj|BAH28603.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771325|dbj|BAH28604.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771327|dbj|BAH28605.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771329|dbj|BAH28606.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771335|dbj|BAH28609.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771339|dbj|BAH28611.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771341|dbj|BAH28612.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771343|dbj|BAH28613.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771345|dbj|BAH28614.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771347|dbj|BAH28615.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771351|dbj|BAH28617.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771353|dbj|BAH28618.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771355|dbj|BAH28619.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771359|dbj|BAH28621.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771361|dbj|BAH28622.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771365|dbj|BAH28624.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771369|dbj|BAH28626.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771373|dbj|BAH28628.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771375|dbj|BAH28629.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771379|dbj|BAH28631.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771381|dbj|BAH28632.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771383|dbj|BAH28633.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771393|dbj|BAH28638.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771395|dbj|BAH28639.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771397|dbj|BAH28640.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771399|dbj|BAH28641.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771401|dbj|BAH28642.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771403|dbj|BAH28643.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771405|dbj|BAH28644.1| sporulation sigma factor SigK [Clostridium perfringens]
          Length = 196

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 34/101 (33%), Positives = 54/101 (53%), Gaps = 5/101 (4%)

Query: 13  EIGLSRYIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           +I L+ Y+      P  L ++EE +  +R ++ GD+ A   LV  +LRLV  I   Y   
Sbjct: 1   KIFLTGYVTGNSTFPKPLNEKEEKIYLERLKD-GDVEAKRVLVERNLRLVAHIVKKYSSN 59

Query: 72  ---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
                 + +++S G IGL++A+  FD  +G RLATY+   I
Sbjct: 60  YQNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATYAAKCI 100


>gi|168703207|ref|ZP_02735484.1| sigma-70 factor [Gemmata obscuriglobus UQM 2246]
          Length = 566

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 45/149 (30%), Positives = 67/149 (44%), Gaps = 28/149 (18%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  + RLV   A      G  I ++VS+GN+ LM+AV+KFD  RG + +TY+ W    A
Sbjct: 394 LINCNQRLVYAQAKQKLALGENIDDLVSDGNLSLMRAVEKFDYARGNKFSTYATW----A 449

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH---LQAITDNNLKPEQVVAIAKK---- 165
           + +   RS    K   T  Q       R + GH    +A  D     ++V+A+A +    
Sbjct: 450 IMKNFARSIPDAK---THKQ-------RYMTGHDELFEAKADIRTDEQEVLALADQARAR 499

Query: 166 -------LNVSESEVISMNCRLAGDESLN 187
                  L+    EVI M   L G E + 
Sbjct: 500 VNRLLDHLDARTREVIRMRTGLDGSEEMT 528


>gi|226313041|ref|YP_002772935.1| RNA polymerase sigma-D factor [Brevibacillus brevis NBRC 100599]
 gi|226095989|dbj|BAH44431.1| RNA polymerase sigma-D factor [Brevibacillus brevis NBRC 100599]
          Length = 262

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 31/88 (35%), Positives = 47/88 (53%), Gaps = 5/88 (5%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIG 85
           EK +E+     +++ G   A   L+T  L LV K+A       LP +    +++S G  G
Sbjct: 8   EKAKEFDKWVMWKQEGSREAEVDLITRFLPLVDKVA-NRLAINLPANVDKDDLISYGRFG 66

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAM 113
           L+ A+ KFD  RG +  TY+MW I+ AM
Sbjct: 67  LLDALAKFDHTRGLQFETYAMWRIRGAM 94


>gi|220929478|ref|YP_002506387.1| sporulation sigma factor SigG [Clostridium cellulolyticum H10]
 gi|219999806|gb|ACL76407.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium cellulolyticum
           H10]
          Length = 257

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 61/278 (21%), Positives = 128/278 (46%), Gaps = 53/278 (19%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L  +++  L +R  + GD SA    +  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLTNEQKKELFERMHK-GDNSARDEFIKGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK- 143
           GL++++  FD  +  + +TY++  I   ++ Y+  + S+          R+  +LR +  
Sbjct: 74  GLIKSIDNFDVTQNVKFSTYAVPMIIGEIRRYLRDNNSI----------RVSRSLRDIAY 123

Query: 144 GHLQA---ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
             LQA   +T  N K   +V +A++L + + +++          +L+A+ +      S +
Sbjct: 124 KALQAKERLTTQNSKEPTIVELAQELQLPKEDIVF---------ALDAIQDPISLFESVY 174

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNM---------LTRSMSVLNPRER-----RIFEAR 246
                  HDG + + +  ++  + +N+         L  +M  LN RE+     R FE R
Sbjct: 175 -------HDGGDAIYV-MDQVSDDKNIDENWLETISLKEAMRKLNDREKLILNLRFFEGR 226

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              E       ++ E  +S+ +V ++E  A   +++ I
Sbjct: 227 TQME-------VADEIGISQAQVSRLEKTALMHMKKYI 257


>gi|225389920|ref|ZP_03759644.1| hypothetical protein CLOSTASPAR_03670 [Clostridium asparagiforme
           DSM 15981]
 gi|225044021|gb|EEG54267.1| hypothetical protein CLOSTASPAR_03670 [Clostridium asparagiforme
           DSM 15981]
          Length = 258

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 28/93 (30%), Positives = 52/93 (55%), Gaps = 1/93 (1%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L  +E+ VL KR  + GD  A  + +  +LRLV+ +   + G    I ++   G I
Sbjct: 15  KLPLLSNEEKEVLFKRILD-GDKEAREQYIKGNLRLVLSVIQRFSGNQENIDDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           GL++A+  FD  +  + +TY++  I   ++ Y+
Sbjct: 74  GLIKAIDNFDITQNVKFSTYAVPMILGEVRRYL 106


>gi|326392135|ref|ZP_08213612.1| RNA polymerase, sigma 28 subunit, SigG [Thermoanaerobacter
           ethanolicus JW 200]
 gi|325991822|gb|EGD50337.1| RNA polymerase, sigma 28 subunit, SigG [Thermoanaerobacter
           ethanolicus JW 200]
          Length = 256

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 59/260 (22%), Positives = 123/260 (47%), Gaps = 17/260 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+  ++  L +R + +GD  A    +  +LRLV+ +   +   G  + ++   G I
Sbjct: 14  KLPVLKPSKQKELLQRMK-NGDEKAREEFINGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 72

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD  +  + +TY++  I   ++ Y LR  + +++  +          + L+ 
Sbjct: 73  GLIKAIDNFDLNQNVKFSTYAVPMIIGEIRRY-LRDNTPIRVSRSLRD----IAYKALQV 127

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + +++N+ +P  V  IAK+L++   EV+     +    SL   I     ++    D  
Sbjct: 128 RDKLVSENSKEP-TVGEIAKELDLPREEVVMALDAIQEPVSLFEPIYHDGGDAIYVMDQ- 185

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           V D    ++V +EK         L  ++  L+ RE+ I    R  E    +E ++ E  +
Sbjct: 186 VSDDKNMDEVWLEK-------IALKEAIQKLSEREKMIL-TMRFFEGKTQME-VAKEIGI 236

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ +V ++E  A   +++ I
Sbjct: 237 SQAQVSRLEKAALNHMRKYI 256


>gi|169334386|ref|ZP_02861579.1| hypothetical protein ANASTE_00786 [Anaerofustis stercorihominis DSM
           17244]
 gi|169259103|gb|EDS73069.1| hypothetical protein ANASTE_00786 [Anaerofustis stercorihominis DSM
           17244]
          Length = 233

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 29/83 (34%), Positives = 44/83 (53%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE  + K        +    L+  +LRLVV IA  +      + +++S G IGL
Sbjct: 29  PPLTKEEEQEVLKNLESDETNTTKTILIERNLRLVVYIAKKFDTSSASVEDLISIGTIGL 88

Query: 87  MQAVKKFDPERGFRLATYSMWWI 109
           ++AVK F  E+  +LATY+   I
Sbjct: 89  IKAVKTFKVEKNIKLATYASKCI 111


>gi|331269335|ref|YP_004395827.1| RNA polymerase sigma 28 subunit FliA/WhiG [Clostridium botulinum
           BKT015925]
 gi|329125885|gb|AEB75830.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium botulinum
           BKT015925]
          Length = 242

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 60/232 (25%), Positives = 109/232 (46%), Gaps = 23/232 (9%)

Query: 53  LVTSHLRLVVKIA----MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           +V  ++ LV  IA    +G   Y +   +++  G IGLM A+ KFD  +G + +TY+   
Sbjct: 13  IVKKYIPLVKYIASRVIIGKSKY-IEFEDLLGYGMIGLMDALNKFDESKGMKFSTYASIR 71

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ +M + I ++  + K    A  K     L R    ++ +   NL    +  IA++L +
Sbjct: 72  IRGSMIDEIRKNSPISK---GAMDK-----LNRYNNAIETLQKKNLTEPNIKDIAQELQM 123

Query: 169 SESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE-ERKNRR 225
           + +EV  I          SL  LI S D + S     L+   + ++    EK+ E + R 
Sbjct: 124 TVNEVGEIENFINYISIVSLEDLIFSEDDDIS-----LMGTIEDEKSPNPEKDFEDQERL 178

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
             L +++ +LN +++ +      +   +TL+ + S   VS  RV Q+ +RA 
Sbjct: 179 EYLAKALDMLNDKDKTVLSLYYYE--GMTLKEIGSVLGVSESRVCQLHSRAI 228


>gi|167465669|ref|ZP_02330758.1| sporulation sigma factor SigG [Paenibacillus larvae subsp. larvae
           BRL-230010]
          Length = 260

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 62/276 (22%), Positives = 120/276 (43%), Gaps = 46/276 (16%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L   E   L    +   + +A  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLTNTEMRELFALLQTKNERAAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGCI 74

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEY------ILRSWSLVKIGTTANQKRLFFN 138
           GLM+A+  FD  +  + +TY++  I   ++ Y      I  S SL  I   A Q R    
Sbjct: 75  GLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNPIRVSRSLRDIAYKALQVR---- 130

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
                     +T+ N +   +  I++ LNV + +V+          +L+A+ +       
Sbjct: 131 --------DQLTNRNSREPTIYEISEVLNVPKEDVVF---------ALDAIQDPVSLFEP 173

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRN---------MLTRSMSVLNPRERRIFEARRLQ 249
            +       HDG + + +  ++  + RN          L  +M  L  RE+ I  + R  
Sbjct: 174 IY-------HDGGDPIYV-MDQISDERNKDLFWIEGIALREAMRKLGSREKMIL-SMRFF 224

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           E    +E ++ E  +S+ +V ++E  A  ++Q+ ++
Sbjct: 225 EGKTQME-VADEIGISQAQVSRLEKSAINQMQKHVK 259


>gi|332653369|ref|ZP_08419114.1| RNA polymerase sigma-G factor [Ruminococcaceae bacterium D16]
 gi|332518515|gb|EGJ48118.1| RNA polymerase sigma-G factor [Ruminococcaceae bacterium D16]
          Length = 256

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 60/267 (22%), Positives = 131/267 (49%), Gaps = 31/267 (11%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+ +L+ +E   L +R +E GD  A   L+  +LRLV+ +   +   G  + ++   G I
Sbjct: 14  KLKVLKNEETQALLRRAKE-GDKQAREELIAGNLRLVLSVIHKFANRGENVDDLFQVGCI 72

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD     + +TY +  I   ++ Y LR  S +++ + A +   +  L+  + 
Sbjct: 73  GLIKAIDNFDTSLDVKFSTYGVPMIVGEIRRY-LRDNSAMRV-SRAMRDTAYKVLQAKES 130

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
           ++      + K   V  IA+ L +   EV+          +L+A+++      S ++   
Sbjct: 131 YMA----QHQKEPSVEEIAQMLGIKREEVVF---------ALDAILDP----VSLYEP-- 171

Query: 205 VYDHDGQEQVLIEK-EERKNRRNM------LTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           +Y   G    ++++ ++ +N   M      L  ++S L+ RE++I  A R  ++   +E 
Sbjct: 172 IYSDSGDTVCVMDQVKDSRNTDEMWLEHIALKEAVSRLSEREQKIL-AMRFYQSKTQVE- 229

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESI 284
           +S E  +S+ +V ++E  A +++++ +
Sbjct: 230 VSREIGISQAQVSRLEKNALRQIRKEL 256


>gi|304317193|ref|YP_003852338.1| RNA polymerase, sigma 28 subunit, SigG [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
 gi|302778695|gb|ADL69254.1| RNA polymerase, sigma 28 subunit, SigG [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
          Length = 256

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 37/150 (24%), Positives = 78/150 (52%), Gaps = 7/150 (4%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+  ++  L  R + +GD +A    +  +LRLV+ +   +   G  + ++   G I
Sbjct: 14  KLPVLKGAKQKELLIRMK-NGDKNAREEFINGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 72

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD  +  + +TY++  I   ++ Y LR  + +++  +   + + +   +++ 
Sbjct: 73  GLIKAIDNFDLNQNVKFSTYAVPMIIGEIRRY-LRDNNSIRVSRSL--RDVAYKALQIRD 129

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVI 174
            L    + N K   V  IAK+LN+   EV+
Sbjct: 130 KL---VNENSKEPTVGDIAKELNIPREEVV 156


>gi|164688589|ref|ZP_02212617.1| hypothetical protein CLOBAR_02234 [Clostridium bartlettii DSM
           16795]
 gi|164603002|gb|EDQ96467.1| hypothetical protein CLOBAR_02234 [Clostridium bartlettii DSM
           16795]
          Length = 234

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 27/83 (32%), Positives = 46/83 (55%), Gaps = 1/83 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  ++E Y L    +   +  A   LV  ++RLV  I+  Y   G  + +++S G IGL
Sbjct: 10  PLTPEEEVYYL-NLLKNENNKEAKEVLVQRNMRLVAHISKKYNNSGEELDDLISIGTIGL 68

Query: 87  MQAVKKFDPERGFRLATYSMWWI 109
           ++A+  F+ ++G RLATY+   I
Sbjct: 69  IKAIDTFNVDKGIRLATYASKCI 91


>gi|121488727|emb|CAJ18247.1| sigma 70-type sigma factor [Chlorobium limicola]
          Length = 165

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 17/50 (34%), Positives = 36/50 (72%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           ++++EGN+GL +A K+FD  RGF+  +Y++WWI+ ++ + +     +V++
Sbjct: 1   DLINEGNLGLXKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL 50


>gi|297559507|ref|YP_003678481.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
 gi|296843955|gb|ADH65975.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
          Length = 285

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 45/188 (23%), Positives = 85/188 (45%), Gaps = 11/188 (5%)

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           L+ KIA  Y G G P+ ++     +GL +AV+ +DP RG    +Y +  +   ++ +   
Sbjct: 64  LINKIARRYGGRGEPLEDLKQTAMVGLAKAVRGYDPARGKPFISYLLPTVTGEIKRHFRD 123

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
               V++     + R+   LRR+    Q     + +   +  +A  + + E+EV  +   
Sbjct: 124 HTWAVRVPRRHQENRV--KLRRVTSEFQ---QRHARTPTIAELAHDMGLPEAEVSELTQV 178

Query: 180 LAGDESLNALINSSDKNSSQWQDWL-VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
                SL+  +++ D + S+ Q+   + DH G E   +   +R   R  L  +++ L  R
Sbjct: 179 SESYRSLS--LDAPDSSDSEGQEGTRLEDHLGCEDAAL---DRVVERESLKPALARLPAR 233

Query: 239 ERRIFEAR 246
           ER I   R
Sbjct: 234 EREILRLR 241


>gi|88856926|ref|ZP_01131577.1| RNA polymerase sigma-70 factor [marine actinobacterium PHSC20C1]
 gi|88813802|gb|EAR23673.1| RNA polymerase sigma-70 factor [marine actinobacterium PHSC20C1]
          Length = 244

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 35/111 (31%), Positives = 54/111 (48%), Gaps = 2/111 (1%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           + E  LA R   +G++ A H L  S       ++  + G G+ + ++ SE   GL++A K
Sbjct: 16  EREAALAARI-SNGEMEAVHELAMSGYAWAKSLSHKFTGRGVDLDDLNSEAYFGLVEAAK 74

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            FDP RG R A YS  +++ A+ + I  S   V I   A    L  N  R+
Sbjct: 75  TFDPTRG-RFAGYSTAFVQGAIWKAIRLSGRSVSIPKHAFDAELVGNRDRI 124


>gi|311068169|ref|YP_003973092.1| RNA polymerase sigma factor SigD [Bacillus atrophaeus 1942]
 gi|310868686|gb|ADP32161.1| RNA polymerase sigma factor SigD [Bacillus atrophaeus 1942]
          Length = 254

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 63/272 (23%), Positives = 126/272 (46%), Gaps = 39/272 (14%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQ 88
           E+ VL  R++E  D  A   L+  ++ LV    +G    GLP S    +++S G +GL  
Sbjct: 7   EDQVLWSRWKEWKDPKAGDDLMRRYMPLVT-YHVGRISVGLPKSVHKDDLMSLGMLGLYD 65

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           A++KFDP R  +  TY+ + I+ A+ + + +  W    +  T+ +K      ++++  ++
Sbjct: 66  ALEKFDPSRDLKFDTYASFRIRGAIIDGLRKEDW----LPRTSREKT-----KKVEAAIE 116

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVIS-MNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
            +    L+      IA++L ++E +V+S MN      E   A + S D+         ++
Sbjct: 117 KLEQRYLRNVSPAEIAEELGMTEQDVVSTMN------EGFFANLLSIDEK--------LH 162

Query: 207 DHDGQEQVLIEKEERKN----RRNMLTRSMSVLNPRERRIFEARRL-----QENPVTLEN 257
           D D  E + +   + KN     + M    ++ L  +   + E  +L      +  +TL  
Sbjct: 163 DQDDGENIQVMIRDDKNVPPEEKIMKDELIAQLAEKIHELSEKEQLVVSLFYKEELTLTE 222

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           +     +S  R+ QI ++A  K++  + K ++
Sbjct: 223 IGQVLSLSTSRISQIHSKALFKLKHLLDKVIQ 254


>gi|138895880|ref|YP_001126333.1| sporulation sigma factor SigF [Geobacillus thermodenitrificans
           NG80-2]
 gi|134267393|gb|ABO67588.1| RNA polymerase sigma-F factorr [Geobacillus thermodenitrificans
           NG80-2]
          Length = 252

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 58/256 (22%), Positives = 114/256 (44%), Gaps = 19/256 (7%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           ++ QE   L +R +E GD  A   ++  ++RLV  +   +   G    ++   G IGL++
Sbjct: 14  IKDQEMKELIRRSQE-GDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLK 72

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           +V KFD     + +TY++  I   +Q + LR    VK+  +   K +   +R+ K  L  
Sbjct: 73  SVDKFDLSYDVKFSTYAVPMIIGEIQRF-LRDDGTVKVSRSL--KEMGNKIRKAKDEL-- 127

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
            +    +   +  IA  L VS  EV+     +    S++  +  +D +     D +    
Sbjct: 128 -SKTRGRAPTITEIADHLGVSPEEVVLAQEAVRSPASIHETVYENDGDPITLLDQIA--- 183

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D  E    EK         L +++  L+ RER I   R  ++   T   +++   +S+ +
Sbjct: 184 DADEASWFEK-------IALKKAIEELDERERLIVYLRYYKDQ--TQSEVAARLGISQVQ 234

Query: 269 VRQIEARAFKKVQESI 284
           V ++E +  + ++E +
Sbjct: 235 VSRLEKKILQHIKEKM 250


>gi|320537994|ref|ZP_08037899.1| RNA polymerase sigma factor WhiG [Treponema phagedenis F0421]
 gi|320145151|gb|EFW36862.1| RNA polymerase sigma factor WhiG [Treponema phagedenis F0421]
          Length = 262

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 57/246 (23%), Positives = 114/246 (46%), Gaps = 27/246 (10%)

Query: 41  YREHGDLSAAHRLVTSHLRLV----VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           Y++ G+       +  +  LV     KIA+G  G  +   ++VS G  GL  A+ K+DPE
Sbjct: 18  YKKTGNAKIREFFIIQYAPLVKYVASKIAVGKPG-SIEFDDLVSYGIFGLFDAIDKYDPE 76

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITDNNLK 155
           +  R  TY++  I+ A+ +  LRS   V        K++   +  ++  L ++ TD  + 
Sbjct: 77  KNIRFNTYAVTRIRGAIYDE-LRSIDWVPRSVRQQIKQIEDTIAAIEAKLGRSATDEEIA 135

Query: 156 PEQVVAIAKK----LNVSESEVISM-NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
            E  +++ +     L +S + VIS+ + +  G++S    +  S +  +            
Sbjct: 136 FELNISLEEYHQLLLKISGTSVISLADTKFGGEDSGQIAVGDSIEAPASL---------- 185

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
              V++E+EE K    ++  ++  L+ RE+++      ++  +TL+ +    +V+  RV 
Sbjct: 186 NPDVIVEREEIK---RVIVEAIKELSEREQQVLILYYYED--MTLKEIGKVLKVTESRVS 240

Query: 271 QIEARA 276
           QI   A
Sbjct: 241 QIHTSA 246


>gi|300854419|ref|YP_003779403.1| putative RNA polymerase sigma-G factor [Clostridium ljungdahlii DSM
           13528]
 gi|300434534|gb|ADK14301.1| predicted RNA polymerase sigma-G factor [Clostridium ljungdahlii
           DSM 13528]
          Length = 257

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 60/279 (21%), Positives = 129/279 (46%), Gaps = 55/279 (19%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+ +E   L  +  + GD  +  + +  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKGKEMKELLIKM-QQGDNESREKFIKGNLRLVLSVIQRFNNRGENVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD  +  + +TY++  I   ++ Y LR  + +++  +          + L+ 
Sbjct: 74  GLIKAIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNSIRVSRSLRD----IAYKALQV 128

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + I +NN +P  +  IA++LN+   EV+          +L+A+           QD +
Sbjct: 129 RDKLIRENNKEP-TISQIAEELNIPREEVVF---------ALDAI-----------QDPV 167

Query: 205 -----VYDHDGQEQVLIEKEERKNRRNM---------LTRSMSVLNPRER-----RIFEA 245
                +Y HDG + + +  ++  + +N+         +  +M  LN RE+     R F+ 
Sbjct: 168 SLFEPIY-HDGGDAIYV-MDQISDTKNLDENWLENISIKEAMKKLNDREKLILNLRFFDG 225

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R   E       ++ E  +S+ +V ++E  A + +++ I
Sbjct: 226 RTQME-------VADEIGISQAQVSRLEKTALRHMRKYI 257


>gi|295092809|emb|CBK78916.1| RNA polymerase, sigma subunit, RpsG/SigG [Clostridium cf.
           saccharolyticum K10]
          Length = 258

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 59/257 (22%), Positives = 114/257 (44%), Gaps = 17/257 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L  +E+  L  R  + GD  A  + +  +LRLV+ +   + G    + ++   G I
Sbjct: 15  KLPLLTNEEKEELFARILK-GDREAREQYIKGNLRLVLSVIQRFSGSSENVDDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD  +  R +TY++  I   ++ Y LR  + +++  +           R   
Sbjct: 74  GLIKAIDNFDITQNVRFSTYAVPMILGEVKRY-LRDNNSIRVSRSLRDTAYKAIYAR--- 129

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             +++   NLK   +  IA+++ VS+ ++      +    SL   + +   +     D L
Sbjct: 130 --ESLMKKNLKEPTLCEIAEEVGVSKEDITYALDAIQSPVSLYEPVYTDGGDPLYVMDQL 187

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             D    E+  IE          L+ +M  L  RER I   R  +    T   ++ E  +
Sbjct: 188 S-DKKNSEENWIEDIS-------LSEAMRRLPERERHIIGMRFFEGKTQT--EVAEEIHI 237

Query: 265 SRERVRQIEARAFKKVQ 281
           S+ +V ++E  A K ++
Sbjct: 238 SQAQVSRLEKNALKAMK 254


>gi|153953967|ref|YP_001394732.1| sporulation sigma factor SigG [Clostridium kluyveri DSM 555]
 gi|219854581|ref|YP_002471703.1| hypothetical protein CKR_1238 [Clostridium kluyveri NBRC 12016]
 gi|146346848|gb|EDK33384.1| SigG [Clostridium kluyveri DSM 555]
 gi|219568305|dbj|BAH06289.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 257

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 39/151 (25%), Positives = 78/151 (51%), Gaps = 9/151 (5%)

Query: 25  KIPML-EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           K+P+L EK+ + +L K   + GD  A  + +  +LRLV+ +   +   G  + ++   G 
Sbjct: 15  KLPVLKEKEMKELLIKM--QQGDNDAREKFIKGNLRLVLSVIQRFNNRGENVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD  +  + +TY++  I   ++ Y LR  + +++  +          + L+
Sbjct: 73  IGLIKAIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNSIRVSRSLRD----IAYKALQ 127

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVI 174
              + I +NN +P  +  IAK+L +   EV+
Sbjct: 128 VRDKLIRENNKEP-TISQIAKELELPREEVV 157


>gi|322384112|ref|ZP_08057830.1| sporulation sigma factor SigG-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321151192|gb|EFX44501.1| sporulation sigma factor SigG-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 272

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 57/270 (21%), Positives = 125/270 (46%), Gaps = 34/270 (12%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L   E   L    +   + +A  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 27  KLPVLTNTEMRELFALLQTKNERAAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGCI 86

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A+  FD  +  + +TY++  I   ++ Y LR  + +++  +   + + +   +++ 
Sbjct: 87  GLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSL--RDIAYKALQVRD 143

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L   T+ N +   +  I++ LNV + +V+          +L+A+ +        +    
Sbjct: 144 QL---TNRNSREPTIYEISEVLNVPKEDVVF---------ALDAIQDPVSLFEPIY---- 187

Query: 205 VYDHDGQEQVLIEKEERKNRRN---------MLTRSMSVLNPRERRIFEARRLQENPVTL 255
              HDG + + +  ++  + RN          L  +M  L  RE+ I  + R  E    +
Sbjct: 188 ---HDGGDPIYV-MDQISDERNKDLFWIEGIALREAMRKLGSREKMIL-SMRFFEGKTQM 242

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           E ++ E  +S+ +V ++E  A  ++Q+ ++
Sbjct: 243 E-VADEIGISQAQVSRLEKSAINQMQKHVK 271


>gi|167630813|ref|YP_001681312.1| RNA polymerase, sigma-70 factor family [Heliobacterium
           modesticaldum Ice1]
 gi|167593553|gb|ABZ85301.1| RNA polymerase, sigma-70 factor family [Heliobacterium
           modesticaldum Ice1]
          Length = 252

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 57/264 (21%), Positives = 104/264 (39%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  ++E   +A+     GD  A  +L+T +LRLV  I   Y      I +++S G IGL
Sbjct: 32  PLSAEEEAEYIARTT--GGDAEAREKLITHNLRLVAHICKKYYSNDEEIEDLISIGTIGL 89

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+  F  E+  RL+TY+   I                      +  +  +LR      
Sbjct: 90  IKAINTFKAEKQVRLSTYASRCI----------------------ENEILMHLR------ 121

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                N  +  +VV+  + + + +                       D N   + D L  
Sbjct: 122 -----NKKRDSRVVSFEESVGIDK-----------------------DGNRMTYSDILGT 153

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEV 264
           D D   +++    E ++ +N + R    LN +ER I   R       P T + ++    +
Sbjct: 154 DGDTVAELVERSSEIEDLQNKVRRR---LNKKEREILTLRYGLSDGTPKTQQTVADLLNI 210

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           SR  V +IE R  +K+ +   +++
Sbjct: 211 SRSYVSRIEGRGIRKLMKEYLREI 234


>gi|240145473|ref|ZP_04744074.1| RNA polymerase sigma-27 factor [Roseburia intestinalis L1-82]
 gi|257202447|gb|EEV00732.1| RNA polymerase sigma-27 factor [Roseburia intestinalis L1-82]
 gi|291536032|emb|CBL09144.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Roseburia
           intestinalis M50/1]
          Length = 254

 Score = 51.2 bits (121), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 62/243 (25%), Positives = 112/243 (46%), Gaps = 48/243 (19%)

Query: 61  VVKIAMG----YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           +V++  G    Y GY +   ++VS G  GL+ A+ KFD  +  +  TY+   I+ ++ + 
Sbjct: 32  LVRVVAGRLSMYLGYNVEYEDLVSYGIFGLIDAIDKFDRGKDVKFETYASLRIRGSILDQ 91

Query: 117 ILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE--- 172
           I +  W    I  T  QKR    +      ++  T  N   E+   IA++L + E E   
Sbjct: 92  IRKMDW----IPRTVRQKRK--KIEEAIKQIETKTGRNASDEE---IAQELGIGEEELND 142

Query: 173 ---------VISMN--CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
                    VIS+N      G+  ++A      KN+S         H  Q +  +++EE 
Sbjct: 143 WQTQLNVTNVISLNEFVEQGGEPVMDA------KNNS---------HFIQPEESVQEEEL 187

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           K    +L  S+ +L  +E+++      ++  +TL+ +SS  EVS  RV Q+  +A  K++
Sbjct: 188 K---KVLMESLELLTEKEKKVILLYYYED--LTLKEISSILEVSESRVSQLHTKALLKMR 242

Query: 282 ESI 284
           + +
Sbjct: 243 KKM 245


>gi|160902849|ref|YP_001568430.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Petrotoga mobilis
           SJ95]
 gi|160360493|gb|ABX32107.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Petrotoga mobilis
           SJ95]
          Length = 231

 Score = 50.8 bits (120), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 53/221 (23%), Positives = 105/221 (47%), Gaps = 31/221 (14%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR-SW------SLV 124
            + + +++ EG IGL+Q+ K+++PE+G    TY++  IK +M +Y+ R  W      SLV
Sbjct: 32  NIELEDLIQEGIIGLLQSYKRYNPEKGTSFYTYALKRIKGSMYDYLRRIDWLPKDVRSLV 91

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           K       + L +  +      + I DN        ++A+KL++ +++V  +   L+  +
Sbjct: 92  K-----KYEDLIYECK----DNEYIDDN--------SVAEKLHIEKNDVDKIKFSLSKRQ 134

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
            L       +     W + +  ++D   ++L  K+   ++   LT S+  L  RE+ I  
Sbjct: 135 ILQLDEYFLNNEEDTWLEDIQEENDP--EILAYKDMLHDK---LTESIEKLEEREKLILS 189

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
                   +T + + S  E+S  RV Q+ +    K+++ IQ
Sbjct: 190 LYY--NEGLTFKEIGSVLEISESRVSQLHSVILVKLKKMIQ 228


>gi|317133668|ref|YP_004092982.1| RNA polymerase, sigma 28 subunit, SigK [Ethanoligenens harbinense
           YUAN-3]
 gi|315471647|gb|ADU28251.1| RNA polymerase, sigma 28 subunit, SigK [Ethanoligenens harbinense
           YUAN-3]
          Length = 228

 Score = 50.8 bits (120), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 50/168 (29%), Positives = 73/168 (43%), Gaps = 18/168 (10%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+   +E   LA+   + GD  A   L+  +LRLV+ I   Y        +++S G IGL
Sbjct: 29  PLTAAEERECLARM--QAGDTKAQDMLIEHNLRLVMHIIKKYYANARDQEDLLSVGTIGL 86

Query: 87  MQAVKKFDPERGFRLATYSMWWI------------KAAMQEYILRSWSLVKIGTTANQKR 134
           ++ V  F PE+G RLATY+   I            K+A   YI       K G   NQ  
Sbjct: 87  IKGVITFKPEKGTRLATYAARCIENEILMHFRSQKKSAQDVYISDPIDTDKDG---NQLT 143

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           L  ++   +  +    D  +K E++ A   KL   E  +I M   L G
Sbjct: 144 L-MDVVSCEDTILDDVDLKMKSEKLRAYIVKLPPRERAIIEMRYGLHG 190


>gi|271964601|ref|YP_003338797.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Streptosporangium roseum DSM 43021]
 gi|270507776|gb|ACZ86054.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Streptosporangium roseum DSM 43021]
          Length = 258

 Score = 50.8 bits (120), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 54/234 (23%), Positives = 105/234 (44%), Gaps = 16/234 (6%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R+V  H  L ++IA  YR  G P+ +++    +GLM+A+  FDP  G     Y++  +  
Sbjct: 36  RIVEMHRPLAMEIARRYRYRGEPLEDLLQAAYVGLMKAINGFDPTLGHAFRGYAVVTMTG 95

Query: 112 AMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            ++ +   R+W+ +++     ++R   N  RL   L    D    P  V  +A K+ +SE
Sbjct: 96  EVKRHFRDRTWA-IRVPRVYQERRAELN--RLVADLS--QDLGRAP-TVAELAVKMRISE 149

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            +V+      A   +L+        + +     ++ D D    VL+++E  K        
Sbjct: 150 EDVLLTLDASAAYSALSLDAPLGADDDAAALGDIIPDEDDALGVLVDREAVKP------- 202

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  L  RE+ I   R      +T   +++EF +S+  V +I  +   +++E +
Sbjct: 203 LIDKLPTREKNILLLRFF--GNMTQAEIAAEFGISQMHVSRILRKVLDQLREEL 254


>gi|312621597|ref|YP_004023210.1| RNA polymerase, sigma 28 subunit, flia/whig [Caldicellulosiruptor
           kronotskyensis 2002]
 gi|312202064|gb|ADQ45391.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Caldicellulosiruptor
           kronotskyensis 2002]
          Length = 246

 Score = 50.8 bits (120), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 60/269 (22%), Positives = 126/269 (46%), Gaps = 37/269 (13%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG----YRGYGLPISEVVSEGNIGLMQ 88
           ++ +L +++ +  D     +L+  ++ LV K+  G    Y G  +   ++VS G+IGL+ 
Sbjct: 2   DDALLWEKFTKTKDPKIKEQLIIKYMPLV-KLVAGRMAIYFGGNVEYDDLVSYGSIGLLD 60

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL-----K 143
           A++KFD ++G +  TY+   IK A+            I    NQ  L  ++R+      +
Sbjct: 61  AIEKFDSQKGVKFETYAYTRIKGAI------------IDCVRNQDFLPRSIRQKAKEIER 108

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSS-DKNSSQW 200
            +++   +      Q   +AK++ +S  E+  +  R++     SL + +  + +      
Sbjct: 109 AYIEIEKEGKTPTNQ--EVAKRIGISVEELQKLQDRISSGMIISLESFLEQNYESKIGGL 166

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
           +D++      Q +  IE EE    R +L + +  L   ER +      ++  ++++ ++ 
Sbjct: 167 EDFV-----SQPEHFIENEE---LRKVLRQQIDNLMENERMVIVLYYYED--LSIKEIAK 216

Query: 261 EFEVSRERVRQIEARAFKKVQESIQKQVE 289
              VS  RV Q+  RA  K++ ++QK +E
Sbjct: 217 VLGVSESRVSQLHTRALLKLRSALQKYLE 245


>gi|291087795|ref|ZP_06347503.2| RNA polymerase sigma-G factor [Clostridium sp. M62/1]
 gi|291073935|gb|EFE11299.1| RNA polymerase sigma-G factor [Clostridium sp. M62/1]
          Length = 291

 Score = 50.8 bits (120), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 59/257 (22%), Positives = 114/257 (44%), Gaps = 17/257 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L  +E+  L  R  + GD  A  + +  +LRLV+ +   + G    + ++   G I
Sbjct: 48  KLPLLTNEEKEELFARILK-GDREAREQYIKGNLRLVLSVIQRFSGSSENVDDLFQIGCI 106

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD  +  R +TY++  I   ++ Y LR  + +++  +           R   
Sbjct: 107 GLIKAIDNFDITQNVRFSTYAVPMILGEVKRY-LRDNNSIRVSRSLRDTAYKAIYAR--- 162

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             +++   NLK   +  IA+++ VS+ ++      +    SL   + +   +     D L
Sbjct: 163 --ESLMKKNLKEPTLCEIAEEVGVSKEDITYALDAIQSPVSLYEPVYTDGGDPLYVMDQL 220

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             D    E+  IE          L+ +M  L  RER I   R  +    T   ++ E  +
Sbjct: 221 -SDKKNSEENWIEDIS-------LSEAMRRLPERERHIIGMRFFEGKTQT--EVAEEIHI 270

Query: 265 SRERVRQIEARAFKKVQ 281
           S+ +V ++E  A K ++
Sbjct: 271 SQAQVSRLEKNALKAMK 287


>gi|226329392|ref|ZP_03804910.1| hypothetical protein PROPEN_03297 [Proteus penneri ATCC 35198]
 gi|225202578|gb|EEG84932.1| hypothetical protein PROPEN_03297 [Proteus penneri ATCC 35198]
          Length = 131

 Score = 50.8 bits (120), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 41/127 (32%), Positives = 70/127 (55%), Gaps = 3/127 (2%)

Query: 162 IAKKLNVSESEVISMNCRL-AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
           +A++L VSES+V  M  R+ A D + +   + SD +        + D        IE++ 
Sbjct: 4   VARELGVSESDVREMESRMSAQDMAFDMTADDSDDSHPIAPVLFLEDKSSDFADGIEEDN 63

Query: 221 RKNRR-NMLTRSMSVLNPRERRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFK 278
             N   + LT ++  L+ R + I  AR L + N  TL++L++++ VS ERVRQ+E  A K
Sbjct: 64  WDNHAADKLTSAIETLDERSQDIIRARWLDDDNKSTLQDLATKYGVSAERVRQLEKNAMK 123

Query: 279 KVQESIQ 285
           K++ +I+
Sbjct: 124 KLRLAIE 130


>gi|319788967|ref|YP_004090282.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Ruminococcus
           albus 7]
 gi|315450834|gb|ADU24396.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Ruminococcus
           albus 7]
          Length = 234

 Score = 50.8 bits (120), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 32/81 (39%), Positives = 47/81 (58%), Gaps = 5/81 (6%)

Query: 27  PMLEKQEEYVLAKRYREHG-DLSAAHRLVTSH-LRLVVKIAMGYRGYGLPISEVVSEGNI 84
           P L K EE   AK ++    D   A  L+  H LRLVV I+  +   G  I +++S G+I
Sbjct: 32  PPLTKDEE---AKAFQLFATDEKKARELLIVHNLRLVVYISKKFESTGAGIEDLISIGSI 88

Query: 85  GLMQAVKKFDPERGFRLATYS 105
           GL++AV  F P++  +LATY+
Sbjct: 89  GLIKAVNTFRPDKNIKLATYA 109


>gi|296270865|ref|YP_003653497.1| Sig B/F/G subfamily RNA polymerase sigma-28 [Thermobispora bispora
           DSM 43833]
 gi|296093652|gb|ADG89604.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Thermobispora bispora DSM 43833]
          Length = 259

 Score = 50.8 bits (120), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 59/243 (24%), Positives = 111/243 (45%), Gaps = 30/243 (12%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  H+ LV  +A  +R  G  + ++     IGL++++ +FD  RG   +TY+   I   
Sbjct: 38  LVELHMPLVEYLARRFRNRGEWLDDLTQVATIGLIKSIDRFDLSRGVEFSTYATPTIVGE 97

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +   + W+ V++     + +L      L   +  ++    +   V  +A+ L +SE 
Sbjct: 98  IKRHFRDKGWA-VRVPRRLQELKL-----SLTKAISELSQRESRAPTVAELAEHLQMSEE 151

Query: 172 EVISMNCRLAGDESLNAL-------INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           EV      L G ES NA         +S D+++    D L    +  E V    E R++ 
Sbjct: 152 EV------LEGLESANAYSTVSLDAPDSGDEDAPAVSDSLGIVDESLEGV----EYRESL 201

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + +L R    L PRE+RI   R      +T   +++E  +S+  V ++ AR   +++E +
Sbjct: 202 KPLLER----LPPREKRILLLRFFGN--MTQSQIANELGISQMHVSRLLARTLAQLREGL 255

Query: 285 QKQ 287
             +
Sbjct: 256 TAE 258


>gi|269127892|ref|YP_003301262.1| B/F/G subfamily RNA polymerase sigma-28 subunit [Thermomonospora
           curvata DSM 43183]
 gi|268312850|gb|ACY99224.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Thermomonospora curvata DSM 43183]
          Length = 276

 Score = 50.8 bits (120), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 64/247 (25%), Positives = 115/247 (46%), Gaps = 38/247 (15%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  HL LV  +A  +R  G  + +++    IGL++++ +FD +RG   +TY+   I   
Sbjct: 55  LVELHLPLVEYLARRFRNRGEWLDDLIQVATIGLIKSIDRFDLDRGVEFSTYATPTIVGE 114

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITD---NNLKPEQVVAIAKKLN 167
           ++ +   + W++          R+   L+ LK  L +AI+D      +   V  +A+ L 
Sbjct: 115 IKRHFRDKGWAV----------RVPRRLQELKLSLTKAISDLAQREGRAPTVSELAEHLQ 164

Query: 168 VSESEVISMNCRLAGDESLNAL-------INSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
           +SE EV      L G ES NA         +S D+++    D L    D  E V    E 
Sbjct: 165 MSEEEV------LEGLESANAYSTVSLDAPDSGDEDAPAVADSLGMVDDSLEGV----EY 214

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           R++ + +L +    L  RE+RI   R      +T   +++E  +S+  V ++ AR   ++
Sbjct: 215 RESLKPLLEK----LPAREKRILLLRFFGN--MTQSQIANELGISQMHVSRLLARTLAQL 268

Query: 281 QESIQKQ 287
           +E +  +
Sbjct: 269 REGLTAE 275


>gi|194014777|ref|ZP_03053394.1| RNA polymerase sigma-D factor (Sigma-28) [Bacillus pumilus ATCC
           7061]
 gi|194013803|gb|EDW23368.1| RNA polymerase sigma-D factor (Sigma-28) [Bacillus pumilus ATCC
           7061]
          Length = 255

 Score = 50.8 bits (120), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 65/274 (23%), Positives = 130/274 (47%), Gaps = 43/274 (15%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQ 88
           E+  L  R++E  D +A   L+  ++ LV    +G    GLP S    +++S G +GL  
Sbjct: 7   EDQALWARWKEWKDPAAGDDLMRRYMPLVT-YHVGRISIGLPKSVHKEDLISLGMLGLYD 65

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           A++KFDP R  +  TY+ + I+ A+ + + +  W    +  T+ +K      ++++  ++
Sbjct: 66  ALEKFDPGRDLKFDTYASFRIRGAIIDGLRKEDW----LPRTSREKT-----KKVEAAIE 116

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVI-SMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
            +    L+      +A++L +SE +V+ +MN      E   A + S D+         ++
Sbjct: 117 KLEQRYLRNVTPTEVAEELGMSEQDVVTTMN------EGFFANLLSIDEK--------LH 162

Query: 207 DHDGQE--QVLIEKE-----ERKNRRN----MLTRSMSVLNPRERRIFEARRLQENPVTL 255
           D +  E  QV+I  E     E K  ++     L   M+ L+ +E+ +      +E  +TL
Sbjct: 163 DQEDGENVQVMIRDEKTVTPEEKMLKDELIEQLAEKMTELSEKEKLVISLFYKEE--LTL 220

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
             +     +S  R+ QI ++A  K++  + K ++
Sbjct: 221 TEIGHVLNLSTSRISQIHSKALFKLKYLLDKAIQ 254


>gi|143460|gb|AAA22713.1| 37 kd minor sigma factor (rpoF, sigB; ttg start codon) [Bacillus
           subtilis]
 gi|143463|gb|AAA22715.1| 37 kd minor sigma factor (ttg start codon) [Bacillus subtilis]
 gi|1881283|dbj|BAA19310.1| RNA POLYMERASE SIGMA-B FACTOR (SIGMA-37) [Bacillus subtilis]
          Length = 264

 Score = 50.8 bits (120), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 68/268 (25%), Positives = 124/268 (46%), Gaps = 28/268 (10%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE-GN 83
           K   L K E   L   Y+   D  A   LV  +  LV  +A  Y   G    E + + G 
Sbjct: 8   KTTKLTKDEVDRLISDYQTKQDEQAQETLVRVYTNLVDMLAKKY-SKGKSFHEDLRQVGM 66

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRL 142
           IGL+ A+K++DP  G     +++  I   ++ ++  ++WS+         +R+     R+
Sbjct: 67  IGLLGAIKRYDPVVGKSFEAFAIPTIIGEIKRFLRDKTWSV------HVPRRIKELGPRI 120

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKN 196
           K  +  +T    +  +V  IA+ L+VSE EV+ +M        L+ D S+ A    SD +
Sbjct: 121 KMAVDQLTTETQRSPKVEEIAEFLDVSEEEVLETMEMGKSYQALSVDHSIEA---DSDGS 177

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           +    D +    DG E+V        N++ ML   + VL+ RE++I +   +Q    + +
Sbjct: 178 TVTILDIVGSQEDGYERV--------NQQLMLQSVLHVLSDREKQIIDLTYIQNK--SQK 227

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
                  +S+  V +++ +A KK++E++
Sbjct: 228 ETGDILGISQMHVSRLQRKAVKKLREAL 255


>gi|325677679|ref|ZP_08157331.1| RNA polymerase sigma-K factor [Ruminococcus albus 8]
 gi|324110647|gb|EGC04811.1| RNA polymerase sigma-K factor [Ruminococcus albus 8]
          Length = 231

 Score = 50.8 bits (120), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 26/66 (39%), Positives = 38/66 (57%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD SA  RL++ +LRLV  I   Y        +++S G IGL++AV+ FD  +G R ATY
Sbjct: 49  GDKSARDRLISHNLRLVAHIIKKYYAAASDQDDLISIGTIGLIKAVQTFDYTKGTRFATY 108

Query: 105 SMWWIK 110
               ++
Sbjct: 109 GSRCVE 114


>gi|291563747|emb|CBL42563.1| RNA polymerase, sigma subunit, RpoX/SigF [butyrate-producing
           bacterium SS3/4]
          Length = 239

 Score = 50.8 bits (120), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 59/246 (23%), Positives = 111/246 (45%), Gaps = 25/246 (10%)

Query: 42  REH-GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           R H GD  A  RLV  +  LV  I   + G G    ++   GNIGL++A+  FD E G R
Sbjct: 10  RSHAGDKEARDRLVMENAGLVWSIVRRFIGRGPEPDDLFQIGNIGLIKAIDHFDTELGVR 69

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN---NLKPE 157
            +TY++  I   ++ + LR   ++K+            L+ L G + A  +    +L  E
Sbjct: 70  FSTYAVPMITGEIRRF-LRDDGMIKVSRP---------LKELAGKVGAAREKLEADLGRE 119

Query: 158 QVV-AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
             V  +A+ +  S  EV +     A   S+    ++ D++     D +       ++VL 
Sbjct: 120 PTVEELARSVGASREEVAASMEAGARVGSIYEPFDAGDESGGCLADKIAEKTSENDRVL- 178

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
                   R +L   +S L  +E++I + R  +    T+  ++    +S+ +V ++E + 
Sbjct: 179 -------DRIVLAELLSGLGEKEQQIIKMRYFENMTQTV--IAGRLGISQVQVSRMEKKI 229

Query: 277 FKKVQE 282
            ++++E
Sbjct: 230 LREMRE 235


>gi|218133504|ref|ZP_03462308.1| hypothetical protein BACPEC_01371 [Bacteroides pectinophilus ATCC
           43243]
 gi|217990879|gb|EEC56885.1| hypothetical protein BACPEC_01371 [Bacteroides pectinophilus ATCC
           43243]
          Length = 238

 Score = 50.8 bits (120), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/68 (33%), Positives = 44/68 (64%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +LRLVV IA  +   G+ + +++S G IGL++A+  ++P++  +LATY+   I+  
Sbjct: 67  LIEHNLRLVVYIAKRFDNTGIGVEDLISIGTIGLIKAIHSYNPDKSIKLATYASRCIENE 126

Query: 113 MQEYILRS 120
           +  Y+ R+
Sbjct: 127 ILMYLRRN 134


>gi|196248769|ref|ZP_03147469.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
 gi|196211645|gb|EDY06404.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
          Length = 250

 Score = 50.8 bits (120), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 58/256 (22%), Positives = 114/256 (44%), Gaps = 19/256 (7%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           ++ QE   L +R +E GD  A   ++  ++RLV  +   +   G    ++   G IGL++
Sbjct: 12  IKDQEMKELIRRSQE-GDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLK 70

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           +V KFD     + +TY++  I   +Q + LR    VK+  +   K +   +R+ K  L  
Sbjct: 71  SVDKFDLSYDVKFSTYAVPMIIGEIQRF-LRDDGTVKVSRSL--KEMGNKIRKAKDEL-- 125

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
            +    +   +  IA  L VS  EV+     +    S++  +  +D +     D +    
Sbjct: 126 -SKTRGRAPTITEIADHLGVSPEEVVLAQEAVRSPASIHETVYENDGDPITLLDQIA--- 181

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D  E    EK         L +++  L+ RER I   R  ++   T   +++   +S+ +
Sbjct: 182 DADEASWFEK-------IALKKAIEELDERERLIVYLRYYKDQ--TQSEVAARLGISQVQ 232

Query: 269 VRQIEARAFKKVQESI 284
           V ++E +  + ++E +
Sbjct: 233 VSRLEKKILQHIKEKM 248


>gi|153440|gb|AAC36891.1| minor sigma-like factor [Streptomyces aureofaciens]
 gi|743686|prf||2013252A RNA polymerase:SUBUNIT=sigma factor
          Length = 278

 Score = 50.8 bits (120), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 62/247 (25%), Positives = 106/247 (42%), Gaps = 18/247 (7%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVK 91
           VL + Y++ GD     +L+  H   +VK   G    GLP     ++ VS G  GL+ A++
Sbjct: 31  VLWRSYKDSGDERLREQLIL-HYSPLVKYVAGRVSVGLPPNVEQADFVSSGVFGLIDAIE 89

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD ER  +  TY++  I+ AM +  LR+   +        + +      L+  L+    
Sbjct: 90  KFDIERSIKFETYAITRIRGAMIDE-LRALDWIPRSVRQKARAVERAYATLEAQLR---- 144

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ--DWLVYDHD 209
                E  VA    + V E   +     LA   +L  L++   +   +    D L  DH 
Sbjct: 145 -RTPTEGEVAGEMGIGVEELHTVFSQLSLANVVALEELLHVGGEGGDRLSLMDTL-EDHA 202

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
             + V  E  E +  R +L R+++ L  RE+ +      +   +TL  + +   V+  RV
Sbjct: 203 ADDPV--EVAEDRELRRLLARAINTLPEREKTVVTLYYYEG--LTLAEIGNVLGVTESRV 258

Query: 270 RQIEARA 276
            QI  ++
Sbjct: 259 SQIHTKS 265


>gi|163816759|ref|ZP_02208122.1| hypothetical protein COPEUT_02949 [Coprococcus eutactus ATCC 27759]
 gi|158448016|gb|EDP25011.1| hypothetical protein COPEUT_02949 [Coprococcus eutactus ATCC 27759]
          Length = 207

 Score = 50.8 bits (120), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 59/247 (23%), Positives = 100/247 (40%), Gaps = 67/247 (27%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A   L+  +LRLV  I   Y        +++S G IGL++A+  + PE+G +LA Y
Sbjct: 23  GDNEARRVLIEYNLRLVAHIVKKYSSSVRDPEDLLSIGTIGLIKAIDSYKPEKGCKLAGY 82

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +   I                      +  L  NLR+ K           K  + V++ +
Sbjct: 83  AAKCI----------------------ENELLMNLRQEK-----------KKSREVSMYE 109

Query: 165 KLNVSE--SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
            +   +  +E++ M+           +I++S+  S   +  +  DH              
Sbjct: 110 PIGTDKEGNEIVIMD-----------IISTSE--SCPLEKLITEDH-------------- 142

Query: 223 NRRNMLTRSMS-VLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
              N L   M+ +L PRE  I + R   L E P+T +  +    +SR  V +IE RA  K
Sbjct: 143 --LNHLPSCMNQILTPREYHIIQMRYGILGEAPLTQKETAKILGISRSYVSRIEKRALSK 200

Query: 280 VQESIQK 286
           ++  + K
Sbjct: 201 LRGCLDK 207


>gi|153811113|ref|ZP_01963781.1| hypothetical protein RUMOBE_01504 [Ruminococcus obeum ATCC 29174]
 gi|149833001|gb|EDM88084.1| hypothetical protein RUMOBE_01504 [Ruminococcus obeum ATCC 29174]
          Length = 259

 Score = 50.8 bits (120), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 60/266 (22%), Positives = 121/266 (45%), Gaps = 37/266 (13%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L+  E+  L ++ ++ GD  A  + +  +LRLV+ +   ++       ++   G IG
Sbjct: 16  LPILKSDEKEALFQKIKK-GDSEAREQYIKGNLRLVLSVIKRFQNSNENADDLFQIGCIG 74

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ---KRLFFNLRRL 142
           LM+AV  FD     + +TY++  I   ++ Y LR ++ +++  +      K ++     +
Sbjct: 75  LMKAVDNFDDTLNVKFSTYAVPMIIGEIRRY-LRDYNSIRVSRSLRDIAYKAIYTKENMI 133

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL------AGDESLNALINSSDKN 196
           K +L+  T + +  E  + I K++ V   + I     L       G ++L  +   SD+ 
Sbjct: 134 KKNLKEPTIDEIADE--IGIEKEMIVYALDAIQSPVSLFEPVYSEGGDTLYVMDQISDQK 191

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENPVTL 255
           + +   WL                     N+ L  +M+ LN RE+ I E  R  E    +
Sbjct: 192 NKE-DHWL--------------------ENLSLREAMNRLNQREKHIIEM-RFYEGRTQM 229

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           E ++ E  +S+ +V ++E  A K ++
Sbjct: 230 E-VADEIGISQAQVSRLEKNALKTMK 254


>gi|221308296|ref|ZP_03590143.1| RNA polymerase sigma factor SigB [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221312618|ref|ZP_03594423.1| RNA polymerase sigma factor SigB [Bacillus subtilis subsp. subtilis
           str. NCIB 3610]
 gi|221317541|ref|ZP_03598835.1| RNA polymerase sigma factor SigB [Bacillus subtilis subsp. subtilis
           str. JH642]
 gi|221321817|ref|ZP_03603111.1| RNA polymerase sigma factor SigB [Bacillus subtilis subsp. subtilis
           str. SMY]
 gi|255767137|ref|NP_388354.2| RNA polymerase sigma factor SigB [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|321314147|ref|YP_004206434.1| RNA polymerase sigma factor SigB [Bacillus subtilis BSn5]
 gi|133469|sp|P06574|RPSB_BACSU RecName: Full=RNA polymerase sigma-B factor; AltName: Full=General
           stress protein 84; Short=GSP84; AltName: Full=Sigma-37
 gi|143538|gb|AAA22754.1| sigma-37 RNA polymerase [Bacillus subtilis]
 gi|225184764|emb|CAB12280.2| RNA polymerase sigma-37 factor (sigma(B)) [Bacillus subtilis subsp.
           subtilis str. 168]
 gi|291482882|dbj|BAI83957.1| RNA polymerase sigma factor SigB [Bacillus subtilis subsp. natto
           BEST195]
 gi|320020421|gb|ADV95407.1| RNA polymerase sigma factor SigB [Bacillus subtilis BSn5]
          Length = 262

 Score = 50.8 bits (120), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 68/268 (25%), Positives = 124/268 (46%), Gaps = 28/268 (10%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE-GN 83
           K   L K E   L   Y+   D  A   LV  +  LV  +A  Y   G    E + + G 
Sbjct: 6   KTTKLTKDEVDRLISDYQTKQDEQAQETLVRVYTNLVDMLAKKY-SKGKSFHEDLRQVGM 64

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRL 142
           IGL+ A+K++DP  G     +++  I   ++ ++  ++WS+         +R+     R+
Sbjct: 65  IGLLGAIKRYDPVVGKSFEAFAIPTIIGEIKRFLRDKTWSV------HVPRRIKELGPRI 118

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKN 196
           K  +  +T    +  +V  IA+ L+VSE EV+ +M        L+ D S+ A    SD +
Sbjct: 119 KMAVDQLTTETQRSPKVEEIAEFLDVSEEEVLETMEMGKSYQALSVDHSIEA---DSDGS 175

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           +    D +    DG E+V        N++ ML   + VL+ RE++I +   +Q    + +
Sbjct: 176 TVTILDIVGSQEDGYERV--------NQQLMLQSVLHVLSDREKQIIDLTYIQNK--SQK 225

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
                  +S+  V +++ +A KK++E++
Sbjct: 226 ETGDILGISQMHVSRLQRKAVKKLREAL 253


>gi|296332841|ref|ZP_06875301.1| RNA polymerase sigma factor SigB [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305673187|ref|YP_003864859.1| RNA polymerase sigma factor SigB [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|296150121|gb|EFG91010.1| RNA polymerase sigma factor SigB [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305411431|gb|ADM36550.1| RNA polymerase sigma factor SigB [Bacillus subtilis subsp.
           spizizenii str. W23]
          Length = 262

 Score = 50.8 bits (120), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 67/268 (25%), Positives = 125/268 (46%), Gaps = 28/268 (10%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE-GN 83
           K   L K E   L   Y+ + D  A   LV  +  LV  +A  Y   G    E + + G 
Sbjct: 6   KTTKLTKDEVDRLISDYQTNQDEQAQETLVRVYTNLVDMLAKKY-SKGKSFHEDLRQVGM 64

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRL 142
           IGL+ A+K++DP  G     +++  I   ++ ++  ++WS+         +R+     R+
Sbjct: 65  IGLLGAIKRYDPVVGKSFEAFAIPTIIGEIKRFLRDKTWSV------HVPRRIKELGPRI 118

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNALINSSDKN 196
           K  +  +T    +  +V  IA+ L+VSE EV+ +M        L+ D S+ A    +D +
Sbjct: 119 KMAVDQLTTETQRSPKVEEIAEFLDVSEEEVLETMEMGKSYQALSVDHSIEA---DADGS 175

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           +    D +    DG E+V        N++ ML   + VL+ RE++I +   +Q    + +
Sbjct: 176 TVTILDIVGSQEDGYERV--------NQQMMLQSVLHVLSDREKQIIDLTYIQNK--SQK 225

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
                  +S+  V +++ +A KK++E++
Sbjct: 226 ETGDILGISQMHVSRLQRKAVKKLREAL 253


>gi|315186365|gb|EFU20125.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Spirochaeta
           thermophila DSM 6578]
          Length = 262

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 56/229 (24%), Positives = 106/229 (46%), Gaps = 22/229 (9%)

Query: 61  VVKIAMGYRGYGLPIS----EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           +VK   G    GLP S    +++  G  GL+ A++KFDPE+  +  TY++  I+ A+ + 
Sbjct: 37  LVKYVAGKIAVGLPSSVEFDDLIGFGTFGLLDAIEKFDPEKHVKFKTYAVTRIRGAIYDE 96

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITDNNLKPEQVVAIAKKLNVSESEVIS 175
            LR+   V        K +   L RL+  L +A TD  L        A+++N+S  E+  
Sbjct: 97  -LRAMDWVPRSVRQKSKEIEDALHRLESSLGRAATDEEL--------AREMNMSSRELQK 147

Query: 176 MNCRLAGDE--SLNALINSSDKNSS-QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
              +++     SL  L  + D+N      D L           +E+EE K    ++  ++
Sbjct: 148 TLQKISSTSILSLQELWYTGDENDRVAIADMLEAPQAYDPAARVEREEIK---RVVAEAI 204

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             L  +E+++      ++  +TL+ + +   V+  RV Q+  +A  +++
Sbjct: 205 KELPEKEKKVLVLYYYED--LTLKEIGAILNVTESRVSQLHTKAISRLR 251


>gi|289578314|ref|YP_003476941.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter italicus Ab9]
 gi|297544594|ref|YP_003676896.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
 gi|289528027|gb|ADD02379.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter italicus Ab9]
 gi|296842369|gb|ADH60885.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
          Length = 246

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 59/259 (22%), Positives = 120/259 (46%), Gaps = 20/259 (7%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
            EK ++ +   R  +  D  +  +L+  +  L+  I   +   G  + ++   G +G ++
Sbjct: 6   FEKSDDNLTLIRAAQKNDKESLEKLILENSGLIWSIVKKFSNRGYELEDLYQIGCMGFVK 65

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           AV+KFD     +L+TY++  I   ++ + LR   L+K+  +  +      L     +L+ 
Sbjct: 66  AVQKFDESYNVKLSTYAVPIIMGEIKRF-LRDDGLIKVSRSLKE------LSTKAFYLKE 118

Query: 149 ITDNNLKPEQVV-AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
           +  + L  E  +  IA++L VS  EV       A  ESL       D  +    D L+ +
Sbjct: 119 VLSSELNREPTINEIAERLKVSPEEVAMAFESAATAESL------YDNATHDEDDRLLIE 172

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
              +E    EKE   + +  L   ++ L PRE++I   R  ++  +T   ++S   +S+ 
Sbjct: 173 MVSEE----EKEVDIDDKLALQMVINKLKPREKQIIFLRYFKD--MTQMEIASILGISQV 226

Query: 268 RVRQIEARAFKKVQESIQK 286
           +V +IE +  +K+++ + +
Sbjct: 227 QVSRIEKKVLQKLRKELDE 245


>gi|325290052|ref|YP_004266233.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Syntrophobotulus
           glycolicus DSM 8271]
 gi|324965453|gb|ADY56232.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Syntrophobotulus
           glycolicus DSM 8271]
          Length = 248

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 23/70 (32%), Positives = 42/70 (60%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A ++L+  +LRLV  +   Y G G    +++S G IGL++ +  F+ ++G RLATY+  
Sbjct: 64  NARNKLIEHNLRLVAHLVKKYDGTGEDSDDLISIGTIGLIKGINTFNTDKGTRLATYAAR 123

Query: 108 WIKAAMQEYI 117
            I+  +  Y+
Sbjct: 124 CIENEILMYL 133


>gi|291525265|emb|CBK90852.1| RNA polymerase, sigma subunit, RpsG/SigG [Eubacterium rectale DSM
           17629]
 gi|291529276|emb|CBK94862.1| RNA polymerase, sigma subunit, RpsG/SigG [Eubacterium rectale
           M104/1]
          Length = 259

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 29/102 (28%), Positives = 58/102 (56%), Gaps = 2/102 (1%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+  E+  L ++ ++ GD +A  + +  +LRLV+ +   +  +   + ++   G I
Sbjct: 15  KLPVLKDDEKEELFEKIKK-GDKAAREKYIRGNLRLVLSVIRRFSNHNENMDDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           GLM+++  FDP  G + +TY++  I   ++ Y LR  S  +I
Sbjct: 74  GLMKSIDNFDPTIGVKFSTYAVPMIIGEVRRY-LRDNSAYRI 114


>gi|126651479|ref|ZP_01723683.1| sigma factor B [Bacillus sp. B14905]
 gi|126591732|gb|EAZ85828.1| sigma factor B [Bacillus sp. B14905]
          Length = 261

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 58/257 (22%), Positives = 118/257 (45%), Gaps = 38/257 (14%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y+   D  A   LV  +  LV  IA  Y        ++V  G +GL+ A+++FDP  G  
Sbjct: 22  YQSTEDDEAQTNLVIHYRYLVESIARKYSNGKSYYDDIVQVGMLGLLGAIRRFDPNVGRS 81

Query: 101 LATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
              +++  I   ++ ++  ++W +         +R+     R+K  ++A+T    +   +
Sbjct: 82  FEAFAVPTIVGEIKRFLRDKTWDV------HVPRRIKEIGPRIKSTVEALTIELQRSPSI 135

Query: 160 VAIAKK-----------LNVSES-EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
             IA++           + +S S + +SM+  +  D         SD ++    D L  +
Sbjct: 136 QEIAERLEVAEEEVLEAMEMSRSYQALSMDHSIESD---------SDGSTVTLFDILGRE 186

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            DG E          ++R +++ +M VLN RE++I +   L++  ++ +    +  +S+ 
Sbjct: 187 DDGYEMT--------DKRMIVSEAMVVLNEREKQIIQLTYLEQ--LSQKEAGEQLGISQM 236

Query: 268 RVRQIEARAFKKVQESI 284
            V +I+ +A KK+QE+I
Sbjct: 237 HVSRIQRKAIKKLQEAI 253


>gi|158340491|ref|YP_001521485.1| RNA polymerase sigma-2 subunit [Acaryochloris marina MBIC11017]
 gi|158310732|gb|ABW32346.1| RNA polymerase sigma-2 subunit domain protein [Acaryochloris marina
           MBIC11017]
          Length = 697

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 29/121 (23%), Positives = 62/121 (51%), Gaps = 2/121 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRY-IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLR 59
           M    ++   +  I L  Y +  + + P+ + ++E  L ++ +  G  ++   L+  H+R
Sbjct: 1   MTTTTIASPFSDGIRLPEYLVQFLHRFPIPDPEQELDLIRKAKR-GHETSLSWLMIGHVR 59

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           LV K+A  Y        +++ EG +G+  AV KFD  +G + +TY+  WI+  ++ +  +
Sbjct: 60  LVAKLAKQYAWTLDDAQDLIQEGMLGIRHAVGKFDSTKGCKFSTYARGWIRGYIRRFCYK 119

Query: 120 S 120
           +
Sbjct: 120 N 120


>gi|158319069|ref|YP_001511576.1| FliA/WhiG family RNA polymerase sigma factor [Alkaliphilus
           oremlandii OhILAs]
 gi|158139268|gb|ABW17580.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           oremlandii OhILAs]
          Length = 270

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 58/264 (21%), Positives = 124/264 (46%), Gaps = 34/264 (12%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L K Y    D+   + L+  HL +   ++  +   G+   ++    ++GL+ A++++D  
Sbjct: 30  LFKEYALTRDIEIRNELINRHLYIAEILSKKFLNKGIEYEDIYQVASLGLIYAIERYDVT 89

Query: 97  RGFRLATYSMWWIKAAMQEYIL-RSWSL-VKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           +GF  ++++   I   +++Y   + WS+ V        K++  +   L+  LQ       
Sbjct: 90  KGFEFSSFATPTIIGEIKKYFRDKGWSIRVPRRIQELSKKVNVSKNTLQQTLQ------- 142

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ- 213
           +   V  IA+ LN +E EVI         E++ A    S   + +  D L+YD+DG ++ 
Sbjct: 143 RTPTVKDIAEYLNCTEEEVI---------EAMEA----SQVYTPKSLD-LIYDNDGDDKD 188

Query: 214 -----VLIEKEERKN---RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
                ++ E ++R +    ++   +++  LN  E+++ + R    N  T   +S E  VS
Sbjct: 189 IQLLDLIGELDKRFDDIENKDFFQKAIDKLNEVEKKVLKDRFF--NNKTQMKVSEELNVS 246

Query: 266 RERVRQIEARAFKKVQESIQKQVE 289
           +  V ++E R  +K ++ + + +E
Sbjct: 247 QMTVSRMEKRIIEKFKKELDRSME 270


>gi|256271|gb|AAC60416.1| RpoD3 [Synechococcus]
          Length = 48

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 18/41 (43%), Positives = 30/41 (73%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           +++ EG IG+ + V+KFDP +G+R +TY+ WWI+ A+   I
Sbjct: 2   DLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAI 42


>gi|253578148|ref|ZP_04855420.1| sporulation sigma factor SigG [Ruminococcus sp. 5_1_39B_FAA]
 gi|251850466|gb|EES78424.1| sporulation sigma factor SigG [Ruminococcus sp. 5_1_39BFAA]
          Length = 259

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 63/266 (23%), Positives = 117/266 (43%), Gaps = 35/266 (13%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L  +E+  L +R + +GD  A    +  +LRLV+ +   ++       ++   G I
Sbjct: 15  KLPVLTAEEKAELFRRIK-NGDEQARELYIKGNLRLVLSVIRRFQNSSENADDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ---KRLFFNLRR 141
           GL++A+  FD     + +TY++  I   ++ Y LR  + +++  +      K ++     
Sbjct: 74  GLIKAIDNFDTTLQVKFSTYAVPMIIGEIRRY-LRDNNSIRVSRSLRDIAYKAIYTRENY 132

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL------AGDESLNALINSSDK 195
           +K HL+  T   +  E  + I K++ V   + I     L       G ++L  +   SDK
Sbjct: 133 MKQHLKEPTVTEIAQE--IGIEKEMIVYALDAIQNPVSLFEPVYTEGGDTLYVMDQISDK 190

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
            +                    KEER      L  +M  LN RE+ I E  R  E    +
Sbjct: 191 KN--------------------KEERWIENLALREAMQRLNSREKHIIEL-RFYEGKTQM 229

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           E ++ E  +S+ +V ++E  A K ++
Sbjct: 230 E-VAQEIGISQAQVSRLEKNALKSMR 254


>gi|158339684|ref|YP_001520691.1| RNA polymerase sigma factor domain-containing protein
           [Acaryochloris marina MBIC11017]
 gi|158309925|gb|ABW31541.1| RNA polymerase sigma factor domain protein [Acaryochloris marina
           MBIC11017]
          Length = 400

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 31/121 (25%), Positives = 64/121 (52%), Gaps = 2/121 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEI-RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLR 59
           M   ++S   +  I L  Y+ ++  + P+   +EE  L ++ +  G  ++   L+  H+R
Sbjct: 1   MTAASISSPFSEGIRLPDYLTQLLHRFPVPNPEEELDLIRKAKL-GHETSLSWLMIGHVR 59

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           LV K+A  Y        +++ EG +G+  AV+KFD  +G + +TY+  WI+  ++ +  +
Sbjct: 60  LVSKLAKQYAWTLDDAQDLIQEGMLGIRHAVRKFDSTKGCKFSTYARGWIRGYIRRFCYK 119

Query: 120 S 120
           +
Sbjct: 120 N 120


>gi|261405539|ref|YP_003241780.1| sporulation sigma factor SigK [Paenibacillus sp. Y412MC10]
 gi|315645904|ref|ZP_07899025.1| sporulation sigma factor SigK [Paenibacillus vortex V453]
 gi|329925929|ref|ZP_08280639.1| RNA polymerase sigma-K factor [Paenibacillus sp. HGF5]
 gi|261282002|gb|ACX63973.1| RNA polymerase, sigma 28 subunit, SigK [Paenibacillus sp. Y412MC10]
 gi|315278665|gb|EFU41979.1| sporulation sigma factor SigK [Paenibacillus vortex V453]
 gi|328939580|gb|EGG35929.1| RNA polymerase sigma-K factor [Paenibacillus sp. HGF5]
          Length = 233

 Score = 50.8 bits (120), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 28/84 (33%), Positives = 51/84 (60%), Gaps = 2/84 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ E++E   L +R  E GD  + ++L+  +LRLV  I   +   G  + +++S G IGL
Sbjct: 30  PLTEEEEAKHL-QRMAE-GDPQSRNKLIEHNLRLVAHIVKKFDNTGEDLEDLISIGTIGL 87

Query: 87  MQAVKKFDPERGFRLATYSMWWIK 110
           ++A++ F P +G +LAT++   I+
Sbjct: 88  IKAIESFRPNKGTKLATFAARCIE 111


>gi|282866278|ref|ZP_06275324.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
 gi|282558864|gb|EFB64420.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
          Length = 318

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 47/170 (27%), Positives = 78/170 (45%), Gaps = 20/170 (11%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  +L LV   A  +R    P+ ++V  G IGL++A+ +F+  RG    T++M  I   
Sbjct: 97  LVELNLALVKFAAARFRSRSEPMEDIVQVGTIGLIKAIDRFELSRGVEFPTFAMPTIIGE 156

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL  +L +    L    D   +   VV +A++L ++  
Sbjct: 157 IKRFFRDTSWS-VRVPRRLQELRL--DLAKAGDELAQQLD---RAPTVVELAERLGITHE 210

Query: 172 EVISMNCRLAGDESLNALINSS-------DKNSSQWQDWLVYDHDGQEQV 214
           EV+       G  + NA   SS       D N     D L Y+ +G E +
Sbjct: 211 EVVE------GMTASNAYTASSLDAKPEDDDNEGALADRLGYEDNGLEGI 254


>gi|241761164|ref|ZP_04759253.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Zymomonas mobilis
           subsp. mobilis ATCC 10988]
 gi|241374783|gb|EER64244.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Zymomonas mobilis
           subsp. mobilis ATCC 10988]
          Length = 247

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 59/227 (25%), Positives = 100/227 (44%), Gaps = 23/227 (10%)

Query: 53  LVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           L+ +HL+LV KIA    G     + + +++  G + L++A   F+  RGF  ATY+   I
Sbjct: 28  LIKTHLQLVRKIAWHVHGRVSSAIEVEDLIQIGMVALIEAANAFE-NRGFAFATYASMRI 86

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + AM +Y +R  +     +   QK L      L   L        +PE+   IA+KLN+S
Sbjct: 87  RGAMIDY-MRQHAATARSSIVRQKTLNKAREELSATL------GRRPEE-AEIAEKLNMS 138

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
            SE      R   D ++N    S D   S        D+  Q   +    ER+  ++ L 
Sbjct: 139 PSE-----YREWADGAINIRQESLDDVYSDHSSIFTDDNADQASEM----EREALQSALA 189

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
             +  L  RE  + +   ++E  + L+ +    ++   R+ QI+  A
Sbjct: 190 EQIKTLPEREALVLQLYYVEE--LNLKEIGEVLDLGTARISQIKKSA 234


>gi|254478671|ref|ZP_05092042.1| RNA polymerase sigma-F factor [Carboxydibrachium pacificum DSM
           12653]
 gi|214035358|gb|EEB76061.1| RNA polymerase sigma-F factor [Carboxydibrachium pacificum DSM
           12653]
          Length = 215

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 54/221 (24%), Positives = 109/221 (49%), Gaps = 26/221 (11%)

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           RGY L   ++   G IG ++AV+KFD     + +TY++  I   ++ + LR   L+K+  
Sbjct: 17  RGYEL--EDLYQIGCIGFVKAVQKFDESYNVKFSTYAVPIIMGEIKRF-LRDDGLIKVSR 73

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-AIAKKLNVSESEVISMNCRLAGDESLN 187
           +  +      L     +++ +  N L  E  +  IA++LNV+  E+       A  ESL 
Sbjct: 74  SLKE------LSSKAFYMKEVLSNELNREPTINEIAERLNVTPEEIAMAFESAATAESL- 126

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV--LNPRERRIFEA 245
                 D  S + +D  + +  G ++  ++ EE+      LT  M +  L PRE+++   
Sbjct: 127 -----YDSISHEEEDRQLIEMVGDKEDSVDLEEK------LTLHMIIDKLKPREKQVIFL 175

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R  ++  +T   +++   +S+ +V +IE +  +K+++ ++K
Sbjct: 176 RYFKD--MTQTEVANILGISQVQVSRIEKKVLEKIRKELEK 214


>gi|239827809|ref|YP_002950433.1| sporulation sigma factor SigK [Geobacillus sp. WCH70]
 gi|239808102|gb|ACS25167.1| RNA polymerase, sigma 28 subunit, SigK [Geobacillus sp. WCH70]
          Length = 236

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 28/84 (33%), Positives = 47/84 (55%), Gaps = 2/84 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  K+EE  L  +    GD  A + L+  +LRLV  I   +   G    +++S G IGL
Sbjct: 30  PLSAKEEEKYL--QLMAKGDEQARNILIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGL 87

Query: 87  MQAVKKFDPERGFRLATYSMWWIK 110
           ++A++ + P +G +LATY+   I+
Sbjct: 88  IKAIESYSPGKGTKLATYAARCIE 111


>gi|291538524|emb|CBL11635.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Roseburia
           intestinalis XB6B4]
          Length = 254

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 62/239 (25%), Positives = 109/239 (45%), Gaps = 48/239 (20%)

Query: 61  VVKIAMG----YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           +V++  G    Y GY +   ++VS G  GL+ A+ KFD  +  +  TY+   I+ ++ + 
Sbjct: 32  LVRVVAGRLSMYLGYNVEYEDLVSYGIFGLIDAIDKFDRGKDVKFETYASLRIRGSILDQ 91

Query: 117 ILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE--- 172
           I +  W    I  T  QKR    +      ++  T  N   E+   IA++L + E E   
Sbjct: 92  IRKMDW----IPRTVRQKRK--KIEEAIKQIETKTGRNASDEE---IAQELGIGEEELND 142

Query: 173 ---------VISMN--CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
                    VIS+N      G+  ++A      KN+S         H  Q +  +++EE 
Sbjct: 143 WQTQLNVTNVISLNEFVEQGGEPVMDA------KNNS---------HFIQPEESVQEEEL 187

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           K    +L  S+ +L  +E+++      ++  +TL+ +SS  EVS  RV Q+  +A  K+
Sbjct: 188 K---KVLMESLELLTEKEKKVILLYYYED--MTLKEISSILEVSESRVSQLHTKALLKM 241


>gi|238924598|ref|YP_002938114.1| sporulation sigma factor SigG [Eubacterium rectale ATCC 33656]
 gi|238876273|gb|ACR75980.1| sporulation sigma factor SigG [Eubacterium rectale ATCC 33656]
          Length = 259

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 29/102 (28%), Positives = 58/102 (56%), Gaps = 2/102 (1%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+  E+  L ++ ++ GD +A  + +  +LRLV+ +   +  +   + ++   G I
Sbjct: 15  KLPVLKDDEKEELFEKIKK-GDKAAREKYIRGNLRLVLSVIRRFSNHNENMDDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           GLM+++  FDP  G + +TY++  I   ++ Y LR  S  +I
Sbjct: 74  GLMKSIDNFDPTIGVKFSTYAVPMIIGEVRRY-LRDNSAYRI 114


>gi|158341383|ref|YP_001522549.1| RNA polymerase sigma-24 subunit [Acaryochloris marina MBIC11017]
 gi|158311624|gb|ABW33234.1| RNA polymerase sigma-24 subunit [Acaryochloris marina MBIC11017]
          Length = 423

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 28/79 (35%), Positives = 45/79 (56%), Gaps = 1/79 (1%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A  R +  + RLV K A  YRG  +   ++V+ G +GL  A++KFD  RGF+ +TY
Sbjct: 32  GDRRAEDRFIRKNQRLVFKEAKRYRGL-VDWDDLVNAGTLGLSIAIQKFDLSRGFQFSTY 90

Query: 105 SMWWIKAAMQEYILRSWSL 123
           ++  I+  +++ I     L
Sbjct: 91  AVKPIRTEIRQLICEQRGL 109


>gi|188011951|gb|ACD45272.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
          Length = 222

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 52/212 (24%), Positives = 99/212 (46%), Gaps = 14/212 (6%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 4   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 63

Query: 95  PERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +T   
Sbjct: 64  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEELTREL 117

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQE 212
               Q+  IA  + V+E EV+     +   +S  AL ++ S +  S      + D  G  
Sbjct: 118 QSSPQISDIADFIGVTEEEVLEA---MEMGKSYQALSVDHSIEADSDGSTITLLDVVGGT 174

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
                  ER N+R +L + + VL+ RE++I +
Sbjct: 175 DYGF---ERVNQRMLLEKVLPVLDEREQKILQ 203


>gi|326204040|ref|ZP_08193901.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           papyrosolvens DSM 2782]
 gi|325985807|gb|EGD46642.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           papyrosolvens DSM 2782]
          Length = 138

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 31/96 (32%), Positives = 53/96 (55%), Gaps = 2/96 (2%)

Query: 19  YIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           Y+  +   P  L+ +EE    + Y+ +G   A + L+  +LRLV  I   Y   G    +
Sbjct: 22  YVSNVNSFPQPLKPEEEQYYVEAYK-NGSEDARNILIERNLRLVAHIVKKYGSCGSDSDD 80

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           ++S G IGL++A+  F+ ++G RLATY+   I+ A+
Sbjct: 81  LISIGTIGLIKAISTFNMDKGTRLATYAARCIENAI 116


>gi|271969498|ref|YP_003343694.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Streptosporangium roseum DSM 43021]
 gi|270512673|gb|ACZ90951.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Streptosporangium roseum DSM 43021]
          Length = 266

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 61/243 (25%), Positives = 109/243 (44%), Gaps = 30/243 (12%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  HL LV  +A  +R  G  + ++     IGL++++ +FD  RG   +TY+   I   
Sbjct: 45  LVELHLPLVEYLARRFRNRGEWLDDLTQVATIGLIKSIDRFDLGRGVEFSTYATPTIVGE 104

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +   + W+ V++     + +L      L   +  ++    +   V  +A  L +SE 
Sbjct: 105 IKRHFRDKGWA-VRVPRRLQELKL-----SLTKAISELSQREGRAPTVGELAAFLKMSEE 158

Query: 172 EVISMNCRLAGDESLNAL-------INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           EV      L G ES NA         +S D ++    D L    D  E V    E R++ 
Sbjct: 159 EV------LEGLESANAYSTVSLDAPDSGDDDAPAVADSLGIVDDSLEGV----EYRESL 208

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + +L R    L PRE+RI   R      +T   +++E  +S+  V ++ AR   +++E +
Sbjct: 209 KPLLER----LPPREKRILLLRFF--GNMTQSQIATELGISQMHVSRLLARTLAQLREGL 262

Query: 285 QKQ 287
             +
Sbjct: 263 TAE 265


>gi|47122|emb|CAA48660.1| whiG-Stv [Streptomyces griseocarneus]
          Length = 278

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 61/249 (24%), Positives = 104/249 (41%), Gaps = 28/249 (11%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFD 94
           + Y+  GD     +L+  H   +VK   G    GLP     ++ VS G  GL+ A++KFD
Sbjct: 34  RSYKASGDERLREQLIL-HYSPLVKYVAGRVSVGLPPNVEQADFVSSGIFGLIDAIEKFD 92

Query: 95  PERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           P R  +  TY++  I+ AM       ++I RS              L   LRR     + 
Sbjct: 93  PARAIKFETYAITRIRGAMIDELRALDWIPRSVRQKARAVERAYATLEAELRRTPTEAEV 152

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSSDKNSSQWQDWLVYD 207
             +  +  E++ ++  +L++  + V+++   L AGDE    L            D L   
Sbjct: 153 AAEMGIALEELHSVFSQLSL--ANVVALEDLLHAGDEGGERL---------SLMDTL--- 198

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            D      +E  E    R +L R+++ L  RE+ +      +   +TL  +     V+  
Sbjct: 199 EDTAADDPVEVAEDHELRRLLARAINTLPEREKTVVTLYYYE--GLTLAEIGQVLGVTES 256

Query: 268 RVRQIEARA 276
           RV QI  ++
Sbjct: 257 RVSQIHTKS 265


>gi|15614101|ref|NP_242404.1| sporulation sigma factor SigF [Bacillus halodurans C-125]
 gi|10174155|dbj|BAB05257.1| RNA polymerase sigma-F factor (stage II sporulation protein AC)
           [Bacillus halodurans C-125]
          Length = 252

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 59/247 (23%), Positives = 115/247 (46%), Gaps = 32/247 (12%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A  ++V+ + RLV  +   +   G    ++   G IGL+++V KFD     + +TY
Sbjct: 29  GDQEARDQIVSRNTRLVWSVVQRFLNRGYEADDLFQIGCIGLIKSVDKFDLSYDVKFSTY 88

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           ++  I   +Q + LR    VK+  +   K L   +R+LK  +   T    +   V  IA+
Sbjct: 89  AVPMIIGEIQRF-LRDDGTVKVSRSI--KELGNKIRKLKDDM---TKTLGRTPTVNEIAE 142

Query: 165 KLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           +L ++  EV+      AGD   SL+++  +            VY++DG    L+++ E +
Sbjct: 143 QLEITPEEVV-----FAGDASRSLSSIHET------------VYENDGDPITLLDQLEDQ 185

Query: 223 NR-----RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
           +      +  L  ++  L  RER I   R  ++   T   ++    +S+ +V ++E +  
Sbjct: 186 SETRWFDKIALKEAIHNLEERERLIVYLRYYKDQ--TQSEVAQRLGISQVQVSRLEKKIL 243

Query: 278 KKVQESI 284
           + ++ +I
Sbjct: 244 ETMKANI 250


>gi|242089059|ref|XP_002440362.1| hypothetical protein SORBIDRAFT_09g030350 [Sorghum bicolor]
 gi|241945647|gb|EES18792.1| hypothetical protein SORBIDRAFT_09g030350 [Sorghum bicolor]
          Length = 529

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 21/62 (33%), Positives = 35/62 (56%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RL+ +   LV  IA  Y G G  + +++  G +G++   +KFD  +G R +TY  +WI+ 
Sbjct: 290 RLLVTTEWLVRCIARSYTGMGTALDDLLQAGKMGVLDGAEKFDTRKGCRFSTYVKYWIRK 349

Query: 112 AM 113
            M
Sbjct: 350 GM 351


>gi|167630319|ref|YP_001680818.1| RNA polymerase sigma factor, flia/whig family [Heliobacterium
           modesticaldum Ice1]
 gi|167593059|gb|ABZ84807.1| RNA polymerase sigma factor, flia/whig family [Heliobacterium
           modesticaldum Ice1]
          Length = 266

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 63/254 (24%), Positives = 114/254 (44%), Gaps = 20/254 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQAVKKFDPE 96
           Y++H D +A   L+  +  LV K   G     LP +    +++S G  GLM A++KFD  
Sbjct: 21  YKDHKDPAAREELILIYAPLV-KFVAGRLAISLPPNVEREDLISYGVFGLMDAIEKFDLA 79

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITDNNLK 155
           RG +  TY++  I+ +M +  LR+   V +      + L      L   L +  TD    
Sbjct: 80  RGLKFETYAIARIRGSMLDG-LRAMDWVPVSVRQKTRELEKTYATLSQRLGREATDEE-- 136

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNA--LINSSDKNSSQWQDWLVYDHDGQEQ 213
               VA A  L ++E   +  + +     SL+   L +S   +  +  D L  +   +  
Sbjct: 137 ----VAQALGLTLNEFAKLLQDVQATTIMSLDEYWLTDSDKGDPVRLIDSLADEQVEEPT 192

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
             +E EE    R +L +++  L  +ER +  A    E  +TL+ + +   VS  R+ Q+ 
Sbjct: 193 AALEFEE---TRLLLAQAIDKLPEKERTVI-ALYYYEG-LTLKEIGAVIGVSESRISQLH 247

Query: 274 ARAFKKVQESIQKQ 287
            +A  +++  + +Q
Sbjct: 248 TKAILRLRGQLARQ 261


>gi|218132880|ref|ZP_03461684.1| hypothetical protein BACPEC_00741 [Bacteroides pectinophilus ATCC
           43243]
 gi|217991753|gb|EEC57757.1| hypothetical protein BACPEC_00741 [Bacteroides pectinophilus ATCC
           43243]
          Length = 259

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 27/101 (26%), Positives = 57/101 (56%), Gaps = 2/101 (1%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L+ +E+  L ++  + GD  A  + +  +LRLV+ +   + G G    ++   G IG
Sbjct: 16  LPLLKNEEKDELLRKAID-GDSKAREKYIKGNLRLVLSVIQRFAGNGENADDLFQIGCIG 74

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           LM+A+  FD  +  R +TY++  I   ++ Y +R ++ +++
Sbjct: 75  LMKAIDNFDVTQNVRFSTYAVPMIMGEVRRY-MRDYNSIRV 114


>gi|328885347|emb|CCA58586.1| RNA polymerase sigma factor for flagellar operon [Streptomyces
           venezuelae ATCC 10712]
          Length = 258

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 63/248 (25%), Positives = 106/248 (42%), Gaps = 26/248 (10%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFD 94
           + Y+E GD     +L+  H   +VK   G    GLP     ++ VS G  GL+ A++KFD
Sbjct: 14  RSYKETGDERLREQLIL-HYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEKFD 72

Query: 95  PERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTA-NQKRLFFN----LRRLKGHLQA 148
            ER  +  TY++  I+ AM  E     W    +   A N +R +      LRR     + 
Sbjct: 73  VERAIKFETYAITRIRGAMIDELRALDWIPRSVRQKARNVERAYATLEAQLRRTPSETEV 132

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
             + ++  E + A+  +L        S+   +A +E L+      D+ S    D L    
Sbjct: 133 AAEMDISLEDLHAVFSQL--------SLANVVALEELLHVGGEGGDRLS--LMDTL---E 179

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D      +E  E +  R +L R+++ L  RE+ +      +   +TL  +     V+  R
Sbjct: 180 DTAADNPVEVAEDRELRRLLARAINTLPEREKTVVTLYYYE--GLTLAEIGHVLGVTESR 237

Query: 269 VRQIEARA 276
           V QI  ++
Sbjct: 238 VSQIHTKS 245


>gi|226324647|ref|ZP_03800165.1| hypothetical protein COPCOM_02432 [Coprococcus comes ATCC 27758]
 gi|225207095|gb|EEG89449.1| hypothetical protein COPCOM_02432 [Coprococcus comes ATCC 27758]
          Length = 222

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 30/84 (35%), Positives = 47/84 (55%), Gaps = 1/84 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L  +EE  L +R  +  D  A H L+  +LRLV  +   Y+       +++S G IGL
Sbjct: 6   PPLTPKEESELLRRSAD-SDNEARHILIERNLRLVAHVIKKYQHLEDDTEDLLSIGTIGL 64

Query: 87  MQAVKKFDPERGFRLATYSMWWIK 110
           ++AV  F+P++  RLATY+   I+
Sbjct: 65  IKAVSTFNPDKKARLATYACRCIE 88


>gi|319937136|ref|ZP_08011543.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
 gi|319807502|gb|EFW04095.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
          Length = 259

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 71/278 (25%), Positives = 127/278 (45%), Gaps = 43/278 (15%)

Query: 16  LSRYIHEIRKIPM-----LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           +SRY  EI    +     L  QE   L  +Y +  D +   +LV S+L+LV+ +   Y  
Sbjct: 1   MSRYKVEINGYTIQEYEKLSHQETMNLLDQYHQTNDENIKEKLVLSNLKLVLSLVQKYHQ 60

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
               + ++   G IGL++A+  FD     R +TY++  I   ++ YI R  S ++I  + 
Sbjct: 61  RVSNLDDLFQVGVIGLIKAIDHFDTSLDVRFSTYAVPLIIGEIKRYI-RDNSPMRIPRSM 119

Query: 131 NQ---KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
                K L  N   +K H +  +   L        +K L+V E  ++         E+L+
Sbjct: 120 RDLAYKALLANEEYMKKHHKEASTKEL--------SKILDVDEFLLV---------EALS 162

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE--ERKNR-RNM-----LTRSMSVLNPRE 239
           +  NS    S + Q+      DG  Q+ +E +  +RKN+  +M     L  +M+ L+ +E
Sbjct: 163 S-TNSVTSLSQEVQN------DGNGQIDLESQIPDRKNQMEDMQNSIDLYEAMNHLDEKE 215

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
            +I   R  + +  T   ++ E  +S+ +V +IE +A 
Sbjct: 216 LQIINERYFKGH--TQSEIAKELFISQAQVSRIEKQAL 251


>gi|291563982|emb|CBL42798.1| RNA polymerase, sigma 29 subunit, SigE [butyrate-producing
           bacterium SS3/4]
          Length = 246

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 55/241 (22%), Positives = 103/241 (42%), Gaps = 70/241 (29%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +LRLVV IA  +    + + +++S G IGL++A+  F+P +  +LATY+   I+  
Sbjct: 67  LIEHNLRLVVYIAKKFDNTSVGVEDLISIGTIGLIKAINTFNPTKNIKLATYASRCIENE 126

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +  Y+ R+  +                                         KL VS   
Sbjct: 127 ILMYLRRTSKM-----------------------------------------KLEVS--- 142

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQ--DWLVYDHDGQEQVLIEKE-ERKNRRNMLT 229
                     DE LN            W   + L+ D  G E+ +I K+ E +  +++L 
Sbjct: 143 ---------IDEPLNV----------DWDGNELLLSDILGTEEDVIYKDMEDEVEKDLLK 183

Query: 230 RSMSVLNPRERRIFEAR----RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           +++S L+PRER+I E R    R     +T + ++    +S+  + ++E +   ++++ I 
Sbjct: 184 KAVSRLSPRERKIVELRYGLKRRDGAEMTQKEVADLMGISQSYISRLEKKIMMRLKKEIV 243

Query: 286 K 286
           K
Sbjct: 244 K 244


>gi|283797733|ref|ZP_06346886.1| RNA polymerase sigma-E factor [Clostridium sp. M62/1]
 gi|291074630|gb|EFE11994.1| RNA polymerase sigma-E factor [Clostridium sp. M62/1]
          Length = 205

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 31/80 (38%), Positives = 46/80 (57%), Gaps = 3/80 (3%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           E++ EY+  KR RE GD  A   L+  +LRLV  +   Y+       +++S G IGL++A
Sbjct: 11  EEEREYL--KRCRE-GDEEAKAVLIERNLRLVAHVIKKYQYTDYETEDLLSVGTIGLIKA 67

Query: 90  VKKFDPERGFRLATYSMWWI 109
           V  F  E+G RLATY+   +
Sbjct: 68  VNTFKAEKGSRLATYAAKCV 87


>gi|255545052|ref|XP_002513587.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
 gi|223547495|gb|EEF48990.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
          Length = 501

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 27/84 (32%), Positives = 50/84 (59%), Gaps = 4/84 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           +A ++L+  +LRLV+ +   Y      G    ++   G  GL+ A+ +F+P+R F+L+TY
Sbjct: 264 AARNKLIKHNLRLVMFVMNKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPQRRFQLSTY 323

Query: 105 SMWWIK-AAMQEYILRSWSLVKIG 127
           S++WI+ A ++   L S++ V  G
Sbjct: 324 SLFWIRHAIIRSMTLSSFTKVSFG 347


>gi|310826431|ref|YP_003958788.1| RinA family phage transcriptional regulator [Eubacterium limosum
           KIST612]
 gi|308738165|gb|ADO35825.1| RinA family phage transcriptional regulator [Eubacterium limosum
           KIST612]
          Length = 250

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 58/225 (25%), Positives = 100/225 (44%), Gaps = 24/225 (10%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           + KQE   L   Y++ GD     RL+ + L +   +   Y      + ++     +GLM 
Sbjct: 7   MTKQESKKLFIEYKKTGDKEIRDRLIENFLYIPKLLVKKYAYRSNDVEDIYQVACLGLMY 66

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           AV+++DP+RGF   T++   I   +++Y      ++++     +  L   + R K  L+ 
Sbjct: 67  AVERYDPDRGFEFDTFASPTIIGEIKKYYRDKQWIIRVPRRIQE--LNREINRAKTTLEH 124

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                +K   +  IA  L V+E  VI     + G+        S++  S         + 
Sbjct: 125 ---KLMKTPTISEIADYLEVTEEAVIEA---MEGNNVFYPKSLSTEFES---------NA 169

Query: 209 DGQEQVLI----EKEER-KNRRNM--LTRSMSVLNPRERRIFEAR 246
           DGQE  L+    E++ER +N  N+  L + +  LNP ER I E R
Sbjct: 170 DGQEATLLDLIGEEDERIENIGNVEDLRQRLESLNPVERMIIEER 214


>gi|288555973|ref|YP_003427908.1| sporulation sigma factor SigF [Bacillus pseudofirmus OF4]
 gi|288547133|gb|ADC51016.1| sporulation sigma factor SigF [Bacillus pseudofirmus OF4]
          Length = 256

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 59/253 (23%), Positives = 119/253 (47%), Gaps = 32/253 (12%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A   +V  + RLV  +   +   G    ++   G IGL+++V KFD     + +
Sbjct: 29  QEGDQQARDLIVNRNTRLVWSVVQRFMNRGYEADDLFQIGCIGLIKSVDKFDLSYDVKFS 88

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I   +Q + LR    VK+  +   K L   +R++K  L   T +  +   V  I
Sbjct: 89  TYAVPMIIGEIQRF-LRDDGTVKVSRSI--KELGNKIRKMKDEL---TKSLGRVPTVNEI 142

Query: 163 AKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQ-----EQVL 215
           A++L ++  EV+      AG+   SL ++  +            VY++DG      +Q+ 
Sbjct: 143 AEQLEITPEEVV-----FAGEASRSLTSIHET------------VYENDGDPITLLDQIA 185

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
            + E +   +  L  ++  L+ RER I   R  ++   T   +++   +S+ +V ++E +
Sbjct: 186 DQTETKWFDKIALKEAIRDLDERERLIVFLRYYKDQ--TQSEVATRLGISQVQVSRLEKK 243

Query: 276 AFKKVQESIQKQV 288
             ++++E + +Q+
Sbjct: 244 ILEQMKEVMGEQI 256


>gi|146295967|ref|YP_001179738.1| sporulation sigma factor SigG [Caldicellulosiruptor saccharolyticus
           DSM 8903]
 gi|145409543|gb|ABP66547.1| RNA polymerase, sigma subunit, RpsG/SigG [Caldicellulosiruptor
           saccharolyticus DSM 8903]
          Length = 255

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 25/92 (27%), Positives = 51/92 (55%), Gaps = 1/92 (1%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +PML  +E+  L K+ + +GD  A  + +  +LRLV+ +   +   G  + ++   G IG
Sbjct: 14  LPMLSHEEKIELLKKMK-NGDKEARKQFIEGNLRLVLSVVQKFANRGENLDDLFQVGCIG 72

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           L++A+  FD  +  + +TY++  I   ++ Y+
Sbjct: 73  LIKAIDNFDLSQNVKFSTYAVPMIIGEIRRYL 104


>gi|118443948|ref|YP_877996.1| RNA polymerase sigma factor for flagellar operon fliA [Clostridium
           novyi NT]
 gi|118134404|gb|ABK61448.1| RNA polymerase sigma factor for flagellar operon fliA [Clostridium
           novyi NT]
          Length = 242

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 58/240 (24%), Positives = 109/240 (45%), Gaps = 21/240 (8%)

Query: 53  LVTSHLRLVVKIA----MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           +V  ++ LV  IA    +G   Y +   +++  G +GLM A  KFD  +G + +TY+   
Sbjct: 13  IVKKYIPLVKYIASRVIIGKTKY-IEFEDLLGYGMLGLMDAFNKFDKSKGMKFSTYASIR 71

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ +M + I ++  + K    A  K     L +    ++++   NL    +  IAK+L++
Sbjct: 72  IRGSMIDEIRKNSPISK---GAMDK-----LNKYNSAIESLQKRNLAEPNIKDIAKELDM 123

Query: 169 SESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +  +V  I          SL  LI S D + S        +    E    E+ E   +  
Sbjct: 124 TVKQVGEIENFINYISIVSLEDLIFSEDDDISLMGTIEDINSPNPE----EEYENDEKLE 179

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L++ + +LN ++R +      +E  +TL+ +     VS  RV Q+ +RA   +++ + K
Sbjct: 180 YLSKGLDMLNEKDRTVLSLYYYEE--MTLKEIGKILGVSESRVCQLHSRAIVHLRKELAK 237


>gi|291060074|gb|ADD72809.1| RNA polymerase sigma factor WhiG [Treponema pallidum subsp.
           pallidum str. Chicago]
          Length = 262

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 55/220 (25%), Positives = 103/220 (46%), Gaps = 23/220 (10%)

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           KIA+G  G  +   ++VS G  GL  A+ K+DPE+  R  TY++  I+ A+ +  LRS  
Sbjct: 44  KIAVGKPG-NVEFDDLVSYGIFGLFDAIDKYDPEKNIRFNTYAVTRIRGAIFDE-LRSID 101

Query: 123 LVKIGTTANQKRLFFNLRRLKGHL-QAITDNNLKPEQVVAIAKK----LNVSESEVISM- 176
            V        +++   +  L+  L +A TD  +     + + +     L VS + VIS+ 
Sbjct: 102 WVPRSVRQQTRQIEEAIADLEARLGRAATDTEIACALNIELEEYHQLLLKVSGTSVISLA 161

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
           + +  GDE  +  +  S +  +               V++E+EE K    ++  ++  L+
Sbjct: 162 DSKFGGDERDHVSVGDSIEAPASL----------NPDVIVEREEIK---RIIAEAIRELS 208

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
            RE+++      +E  +TL+ +    +V+  R+ QI   A
Sbjct: 209 QREQQVLILYYYEE--MTLKEIGKVLKVTESRISQIHTSA 246


>gi|169829726|ref|YP_001699884.1| RNA polymerase sigma-B factor [Lysinibacillus sphaericus C3-41]
 gi|168994214|gb|ACA41754.1| RNA polymerase sigma-B factor (Sigma-37) (General stress protein
           84) (GSP84) [Lysinibacillus sphaericus C3-41]
          Length = 261

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 58/257 (22%), Positives = 118/257 (45%), Gaps = 38/257 (14%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y+   D  A   LV  +  LV  IA  Y        ++V  G +GL+ A+++FDP  G  
Sbjct: 22  YQSTEDDEAQTNLVIHYRYLVESIARKYSNGKSYYDDIVQVGMLGLLGAIRRFDPNVGRS 81

Query: 101 LATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
              +++  I   ++ ++  ++W +         +R+     R+K  ++A+T    +   +
Sbjct: 82  FEAFAVPTIVGEIKRFLRDKTWDV------HVPRRIKEIGPRIKTTVEALTIELQRSPSI 135

Query: 160 VAIAKK-----------LNVSES-EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
             IA++           + +S S + +SM+  +  D         SD ++    D L  +
Sbjct: 136 QEIAERLEVAEEEVLEAMEMSRSYQALSMDHSIESD---------SDGSTVTLFDILGRE 186

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            DG E          ++R +++ +M VLN RE++I +   L++  ++ +    +  +S+ 
Sbjct: 187 DDGYEMT--------DKRMIVSEAMVVLNEREKQIIQLTYLEQ--LSQKEAGEQLGISQM 236

Query: 268 RVRQIEARAFKKVQESI 284
            V +I+ +A KK+QE+I
Sbjct: 237 HVSRIQRKAIKKLQEAI 253


>gi|26000679|gb|AAN75199.1| sigma K [Clostridium difficile]
 gi|26000681|gb|AAN75200.1| sigma K [Clostridium difficile CD196]
 gi|26000696|gb|AAN75201.1| sigma K [Clostridium difficile]
 gi|26000698|gb|AAN75202.1| sigma K [Clostridium difficile]
 gi|26000700|gb|AAN75203.1| sigma K [Clostridium difficile]
          Length = 108

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 45/81 (55%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L  +EE     +++   D SA   L+  ++RLV  IA  Y        +++S G IGL++
Sbjct: 11  LTPEEEIEYLTKFKIENDKSAKDTLIERNMRLVAYIAKKYNNSTEDQDDLISIGTIGLIK 70

Query: 89  AVKKFDPERGFRLATYSMWWI 109
           A++ ++ ++G RLATY+   I
Sbjct: 71  AIETYNIDKGTRLATYASRCI 91


>gi|152964789|ref|YP_001360573.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Kineococcus
           radiotolerans SRS30216]
 gi|151359306|gb|ABS02309.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Kineococcus
           radiotolerans SRS30216]
          Length = 267

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 34/122 (27%), Positives = 61/122 (50%), Gaps = 15/122 (12%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  HL L   +A  YR  G P  ++V    +GL++A ++FDP+ G R A Y+   I   
Sbjct: 18  LVLEHLPLARSVAAHYRNRGEPYDDLVQVAYLGLVKAAQRFDPDTGHRFAAYAAPTITGE 77

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +     W++          R    L+ L+  L  + ++   PE+V  +A++L+ + +
Sbjct: 78  VRRHFRDHGWNV----------RPPRRLQELRARL--LAEDADTPEEV--LAQRLDATVA 123

Query: 172 EV 173
           EV
Sbjct: 124 EV 125


>gi|258515296|ref|YP_003191518.1| RNA polymerase, sigma 28 subunit, SigF [Desulfotomaculum
           acetoxidans DSM 771]
 gi|257779001|gb|ACV62895.1| RNA polymerase, sigma 28 subunit, SigF [Desulfotomaculum
           acetoxidans DSM 771]
          Length = 259

 Score = 50.4 bits (119), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 32/109 (29%), Positives = 59/109 (54%), Gaps = 4/109 (3%)

Query: 25  KIPMLEKQE-EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           + P+L+ +E   +LAK   + GD  A  RLV  +L+LV  +   +   G  + ++   G+
Sbjct: 12  RFPLLKDEEMRQLLAKA--KLGDAVARERLVNCNLKLVFNLVKRFNNRGYELEDLFQIGS 69

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           IGLM+A+ KFD     + +TY++  I   ++ + LR  + VK+  +  +
Sbjct: 70  IGLMKAIDKFDLNYDVKFSTYAVPMIVGEIRRF-LRDDNPVKVSRSVKE 117


>gi|312876364|ref|ZP_07736349.1| RNA polymerase, sigma 28 subunit, SigE [Caldicellulosiruptor
           lactoaceticus 6A]
 gi|311796858|gb|EFR13202.1| RNA polymerase, sigma 28 subunit, SigE [Caldicellulosiruptor
           lactoaceticus 6A]
          Length = 244

 Score = 50.4 bits (119), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 28/94 (29%), Positives = 50/94 (53%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EE  +  R    G+      L+  +LRLVV IA  +    + + ++VS G IGL
Sbjct: 41  PPLTPDEEAQILYRIHYQGEEGLKKLLIERNLRLVVYIAKRFENTKVNLEDLVSIGTIGL 100

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++A+  ++P +  +LATY+   I+  +  ++ R+
Sbjct: 101 IKAINTYNPNKNIKLATYASKCIENEILMFLRRN 134


>gi|317969500|ref|ZP_07970890.1| RNA polymerase sigma factor, sigma-70 family protein [Synechococcus
           sp. CB0205]
          Length = 315

 Score = 50.1 bits (118), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 62/258 (24%), Positives = 109/258 (42%), Gaps = 37/258 (14%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLP-----ISEVVSEGNIGLMQAVKKFDPERGFRL 101
           L A  +LV  +L LV     G     LP      ++ + E  + L++A +KFDP +G+R 
Sbjct: 64  LRAREQLVRHNLGLVAHT-WGRHRCSLPAHDDTTADALQEAALNLVRAAEKFDPAKGYRF 122

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY+ +W++    E+  R+   ++    A +  +     RL    QA T +    E + A
Sbjct: 123 STYATFWVRRGFTEFEQRAKRAIRF--PAEKAAVVLKALRLSQQQQATTGDEPSLEWLAA 180

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
             K       +  +MN      E L   I   D   +   D    + DG E+    + + 
Sbjct: 181 QLK------FDGKAMNA-----EQLAEFIRQWDATRTGSLD--GAEDDGDEKGGCSRLDL 227

Query: 222 KN---------------RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL-SSEFEVS 265
            +               +   L + MS L+ +E R+   R L+  P++   L  S   + 
Sbjct: 228 ASLQQAAEQQQTQEPDPQHAALPQLMSCLDEQEHRLIRNRYLRRPPLSPCQLRRSMGGMQ 287

Query: 266 RERVRQIEARAFKKVQES 283
           RE++ Q+EA A  K+++S
Sbjct: 288 REQLEQLEATALNKLRQS 305


>gi|94500298|ref|ZP_01306831.1| flagellar biosynthesis sigma factor [Oceanobacter sp. RED65]
 gi|94427597|gb|EAT12574.1| flagellar biosynthesis sigma factor [Oceanobacter sp. RED65]
          Length = 245

 Score = 50.1 bits (118), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 55/242 (22%), Positives = 114/242 (47%), Gaps = 22/242 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           LV  +  LV +IA   +G  LP    + +++  G IGL++A +K++P +G    TY+   
Sbjct: 19  LVEEYASLVKRIAHHLKGR-LPDSVQVDDLIQSGMIGLIEAAQKYEPSKGASFETYAGIR 77

Query: 109 IKAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           I+ +M + I +  W+          + +  N RR+   ++ +     +  Q   +AK L 
Sbjct: 78  IRGSMLDEIRKGDWA---------PRSVHRNSRRISEAIRYVESQTGRDAQDQEVAKALG 128

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + E E    + +      L +  +  ++   Q  D++ +D +   Q L    + ++ +  
Sbjct: 129 M-ELEEYHQHLQDGAGSRLFSFEDLLEQRGEQESDFMGHDDESPLQDL----QSEHFQQQ 183

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L +++S L  RE+ +      +E  + L+ + +  EVS  RV QI ++A  +++  +Q+ 
Sbjct: 184 LAKAISQLPEREQLVLALYYDEE--LNLKEIGAVLEVSESRVSQIHSQAAHRLRARLQEW 241

Query: 288 VE 289
            E
Sbjct: 242 AE 243


>gi|152965379|ref|YP_001361163.1| RNA polymerase sigma factor WhiG [Kineococcus radiotolerans
           SRS30216]
 gi|151359896|gb|ABS02899.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Kineococcus
           radiotolerans SRS30216]
          Length = 312

 Score = 50.1 bits (118), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 70/268 (26%), Positives = 123/268 (45%), Gaps = 31/268 (11%)

Query: 24  RKIPMLEKQEEYVLAKR-----YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI--- 75
           RK P   +QE+   A R     Y+  GD     +L+  H   +VK   G  G GLP    
Sbjct: 49  RKGPQTPEQEQAEAALRAMWEEYKASGDGVVREKLIM-HYSPLVKYVAGRVGVGLPPNIE 107

Query: 76  -SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            +++VS G  GL+ A++KFD ER  +  TY++  I+ A+ +  LRS   +     +  + 
Sbjct: 108 QADLVSYGIFGLIDAIEKFDIERAIKFETYAISRIRGAIIDE-LRSIDWIPRSVRSKARE 166

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQV-VAIAKKLNVSE-----SEVISMNCRLAGDESLNA 188
           +      L+  L      +  P +V VA   ++ +SE     S+V  +N  +A DE L+ 
Sbjct: 167 VERTYAALEAEL------HRTPTEVEVAARMEIKLSELHHIFSQVSYVNV-VALDELLSV 219

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
                DK S    D L    D + +  ++  E++  + +L+R+++ L  RE+ +      
Sbjct: 220 SGEKGDKLS--LVDTL---EDTKAEDPVQSFEKEETKFLLSRAINQLPEREKIVVTLYYY 274

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARA 276
           +   +TL  +     V+  R+ Q+  +A
Sbjct: 275 E--GLTLAEIGRVLGVTESRICQMHTKA 300


>gi|154686064|ref|YP_001421225.1| RNA polymerase sigma factor SigD [Bacillus amyloliquefaciens FZB42]
 gi|308173610|ref|YP_003920315.1| RNA polymerase sigma-28 factor sigma-D [Bacillus amyloliquefaciens
           DSM 7]
 gi|154351915|gb|ABS73994.1| SigD [Bacillus amyloliquefaciens FZB42]
 gi|307606474|emb|CBI42845.1| RNA polymerase sigma-28 factor (sigma-D) [Bacillus
           amyloliquefaciens DSM 7]
 gi|328553458|gb|AEB23950.1| RNA polymerase sigma factor SigD [Bacillus amyloliquefaciens TA208]
 gi|328911751|gb|AEB63347.1| RNA polymerase sigma factor [Bacillus amyloliquefaciens LL3]
          Length = 254

 Score = 50.1 bits (118), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 63/272 (23%), Positives = 127/272 (46%), Gaps = 39/272 (14%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQ 88
           E+ VL  R++E  D  A   L+  ++ LV    +G    GLP S    +++S G +GL  
Sbjct: 7   EDQVLWSRWKEWKDPKAGDDLMRRYMPLVT-YHVGRISVGLPKSVHKDDLMSLGMLGLYD 65

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           A++KFDP R  +  TY+ + I+ A+ + + +  W    +  T+ +K      ++++  ++
Sbjct: 66  ALEKFDPGRDLKFDTYASFRIRGAIIDGLRKEDW----LPRTSREKT-----KKVEAAIE 116

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVIS-MNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
            +    L+      IA++L ++E +V+S MN      E   A + S D+         ++
Sbjct: 117 KLEQRYLRNVTPSEIAEELGMTEQDVVSTMN------EGFFANLLSIDEK--------LH 162

Query: 207 DHDGQEQVLIEKEERKN----RRNMLTRSMSVLNPRERRIFEARRL-----QENPVTLEN 257
           D D  E + +   + KN     + M    ++ L  +   + E  +L      +  +TL  
Sbjct: 163 DQDDGENIQVMIRDDKNVPPEEKIMKDELIAQLAGKIHELSEKEQLVVSLFYKEELTLTE 222

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           +     +S  R+ QI ++A  K++  ++K ++
Sbjct: 223 IGQVLNLSTSRISQIHSKALFKLKHLLEKVIQ 254


>gi|291559903|emb|CBL38703.1| RNA polymerase, sigma subunit, RpsG/SigG [butyrate-producing
           bacterium SSC/2]
          Length = 258

 Score = 50.1 bits (118), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 29/98 (29%), Positives = 52/98 (53%), Gaps = 1/98 (1%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L ++E+  L +R  E GDL A    +  +LRLV+ I   + G      ++   G IG
Sbjct: 16  LPLLSEEEKEDLFERI-EQGDLLAREHYIKGNLRLVLSIIQRFSGSNENADDLFQVGCIG 74

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           LM+A+  FD     + +TY++  I   ++ Y+  + S+
Sbjct: 75  LMKAIDNFDRNLNVKFSTYAVPMIIGEVKRYLRDNHSM 112


>gi|260886663|ref|ZP_05897926.1| RNA polymerase sigma-27 factor [Selenomonas sputigena ATCC 35185]
 gi|330839507|ref|YP_004414087.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Selenomonas sputigena
           ATCC 35185]
 gi|260863515|gb|EEX78015.1| RNA polymerase sigma-27 factor [Selenomonas sputigena ATCC 35185]
 gi|329747271|gb|AEC00628.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Selenomonas sputigena
           ATCC 35185]
          Length = 252

 Score = 50.1 bits (118), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 65/257 (25%), Positives = 115/257 (44%), Gaps = 35/257 (13%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEG 82
           P  E Q+ + L   YRE        ++V  +L LV  IA G    GLP      ++VS G
Sbjct: 7   PSAEIQDLWAL---YRETRAPEVRDKIVEKYLPLVNIIA-GRVVVGLPAHVDRDDLVSSG 62

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
             GL+ A++++D ERG +  TY    I+ AM +Y LR+   + +      +R    +  L
Sbjct: 63  FFGLLDAIERYDVERGNKFETYGGVRIRGAMLDY-LRTMDWIPVSKRQKIRRYEQAVTTL 121

Query: 143 KGHL-QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           +G L ++ TD+ L        A +L +S+ E             L+ L++ ++  +    
Sbjct: 122 EGRLGRSATDDEL--------AAELKISKKE-------------LHDLVSQTNIATVIPL 160

Query: 202 DWLVYDHDGQEQVLIEKE--ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
           +  V       Q +  +E  E+   R+ L  ++  L  +ER +      +E  +TL+ +S
Sbjct: 161 EEYVRTESPSSQTIDPEENAEKNELRDTLAEAIDQLPEKERTVVSLYYYEE--LTLKEIS 218

Query: 260 SEFEVSRERVRQIEARA 276
               +S  R+ Q+  +A
Sbjct: 219 LILHLSEARISQLHTKA 235


>gi|15614994|ref|NP_243297.1| RNA polymerase sigma factor SigD [Bacillus halodurans C-125]
 gi|10175051|dbj|BAB06150.1| RNA polymerase sigma-D factor [Bacillus halodurans C-125]
          Length = 256

 Score = 50.1 bits (118), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 52/221 (23%), Positives = 113/221 (51%), Gaps = 19/221 (8%)

Query: 72  GLPIS----EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           GLP S    +++S G +GL+ A++KF+P+R  +  TY+ + ++ A+ +  LR    +   
Sbjct: 46  GLPRSVSKDDLISHGMLGLLDALEKFNPDRDLKFDTYASFRVRGAILDG-LRKEDWLPRS 104

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVI-SMNCRLAGD-ES 185
                K++     +L+  L      N+  E+V   AK++ +SE+EV  +M   L  +  S
Sbjct: 105 MREKIKKIEAATEKLEQKL----GRNVSVEEV---AKEVGISENEVSQTMTESLVANLLS 157

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           ++   N SD+  +     +       E+ L+E+ +++    ++    ++LN +E+ +   
Sbjct: 158 MDEKTNDSDREETYTATIIDKQSLSPEEKLLEEAQKEELSQLIA---NILNEKEQLVIGL 214

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +E  +TL  +    ++S  R+ QI ++A  ++Q++++K
Sbjct: 215 FYFEE--LTLTEIGQILKLSTSRISQIHSKALFRLQQALKK 253


>gi|312794093|ref|YP_004027016.1| RNA polymerase, sigma 28 subunit, sige [Caldicellulosiruptor
           kristjanssonii 177R1B]
 gi|312181233|gb|ADQ41403.1| RNA polymerase, sigma 28 subunit, SigE [Caldicellulosiruptor
           kristjanssonii 177R1B]
          Length = 244

 Score = 50.1 bits (118), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 28/94 (29%), Positives = 50/94 (53%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EE  +  R    G+      L+  +LRLVV IA  +    + + ++VS G IGL
Sbjct: 41  PPLTPDEEAQILYRIHYQGEEGLKKLLIERNLRLVVYIAKRFENTKVNLEDLVSIGTIGL 100

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++A+  ++P +  +LATY+   I+  +  ++ R+
Sbjct: 101 IKAINTYNPNKNIKLATYASKCIENEILMFLRRN 134


>gi|332981685|ref|YP_004463126.1| RNA polymerase sigma-27/28 subunit,RpsK/SigK [Mahella australiensis
           50-1 BON]
 gi|332699363|gb|AEE96304.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Mahella
           australiensis 50-1 BON]
          Length = 236

 Score = 50.1 bits (118), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 26/75 (34%), Positives = 40/75 (53%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E GD  A + L+  +LRLV  I   Y        +++S G IGL++ +  FD  +G RLA
Sbjct: 46  EQGDQQAKNILIEHNLRLVAHIVKKYNNAVKDPEDLISIGTIGLIKGITTFDSNKGTRLA 105

Query: 103 TYSMWWIKAAMQEYI 117
           TY+   I+  +  Y+
Sbjct: 106 TYAARCIENEILMYV 120


>gi|318075685|ref|ZP_07983017.1| RNA polymerase sigma factor WhiG [Streptomyces sp. SA3_actF]
          Length = 259

 Score = 50.1 bits (118), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 61/244 (25%), Positives = 104/244 (42%), Gaps = 18/244 (7%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFD 94
           + Y+  GD     +L+  H   +VK   G    GLP     ++ VS G  GL+ A++KFD
Sbjct: 15  RMYKTTGDARLREQLIL-HYSPLVKYVAGRVSVGLPPNVEQADFVSSGVFGLIDAIEKFD 73

Query: 95  PERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
            ER  +  TY++  I+ AM  E     W    I  +  QK    N+ R    L+A     
Sbjct: 74  IERSIKFETYAITRIRGAMIDELRALDW----IPRSVRQKAR--NVERAYATLEAKLHRT 127

Query: 154 LKPEQV-VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             P +V VA    + V +   +     LA   +L  L++   +   +       +  G +
Sbjct: 128 --PTEVEVASEMGVGVEDLHAVFSQLSLANVVALEELLSVGSEGGGRLSIMDTLEDTGAD 185

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
              +E  E +  R +L+R+++ L  RE+ +      +   +TL  +     V+  RV QI
Sbjct: 186 NP-VEVAEGRELRQLLSRAINSLPDREKTVVMLYYYE--GLTLAEIGHVLGVTESRVSQI 242

Query: 273 EARA 276
             ++
Sbjct: 243 HTKS 246


>gi|254974785|ref|ZP_05271257.1| sporulation sigma factor SigK [Clostridium difficile QCD-66c26]
 gi|255100257|ref|ZP_05329234.1| sporulation sigma factor SigK [Clostridium difficile QCD-63q42]
 gi|255306197|ref|ZP_05350369.1| sporulation sigma factor SigK [Clostridium difficile ATCC 43255]
 gi|255313912|ref|ZP_05355495.1| sporulation sigma factor SigK [Clostridium difficile QCD-76w55]
 gi|255516591|ref|ZP_05384267.1| sporulation sigma factor SigK [Clostridium difficile QCD-97b34]
 gi|306519807|ref|ZP_07406154.1| sporulation sigma factor SigK [Clostridium difficile QCD-32g58]
          Length = 130

 Score = 50.1 bits (118), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 45/81 (55%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L  +EE     +++   D SA   L+  ++RLV  IA  Y        +++S G IGL++
Sbjct: 11  LTPEEEIEYLTKFKIENDKSAKDTLIERNMRLVAYIAKKYNNSTEDQDDLISIGTIGLIK 70

Query: 89  AVKKFDPERGFRLATYSMWWI 109
           A++ ++ ++G RLATY+   I
Sbjct: 71  AIETYNIDKGTRLATYASRCI 91


>gi|167767366|ref|ZP_02439419.1| hypothetical protein CLOSS21_01885 [Clostridium sp. SS2/1]
 gi|317497448|ref|ZP_07955768.1| sigma-70 family RNA polymerase sigma factor [Lachnospiraceae
           bacterium 5_1_63FAA]
 gi|167711341|gb|EDS21920.1| hypothetical protein CLOSS21_01885 [Clostridium sp. SS2/1]
 gi|316895234|gb|EFV17396.1| sigma-70 family RNA polymerase sigma factor [Lachnospiraceae
           bacterium 5_1_63FAA]
          Length = 207

 Score = 50.1 bits (118), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 29/84 (34%), Positives = 47/84 (55%), Gaps = 4/84 (4%)

Query: 27  PML-EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           P+L E++  Y++  R    GD++A + LV  +LRLV  I   Y        +++S G IG
Sbjct: 7   PLLPEEERHYLILSR---QGDMNARNLLVEHNLRLVAHIVKKYHNLDREKEDMISIGVIG 63

Query: 86  LMQAVKKFDPERGFRLATYSMWWI 109
           L++A+  +D  +G RL TY+   I
Sbjct: 64  LIKAINTYDISKGHRLVTYAARCI 87


>gi|269792906|ref|YP_003317810.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermanaerovibrio acidaminovorans DSM 6589]
 gi|269100541|gb|ACZ19528.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermanaerovibrio acidaminovorans DSM 6589]
          Length = 187

 Score = 50.1 bits (118), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 28/78 (35%), Positives = 44/78 (56%), Gaps = 6/78 (7%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIA--MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            GD  A   L+ ++  +V  +A  +G R Y     +VV EG +GL++AV  FDP RG R 
Sbjct: 22  QGDQEAREELILAYRPMVFWLARRLGNRAY----QDVVQEGMLGLLEAVDNFDPSRGHRF 77

Query: 102 ATYSMWWIKAAMQEYILR 119
           +TY+ + I+  M  ++ R
Sbjct: 78  STYAYYRIRGRMINFLSR 95


>gi|312128105|ref|YP_003992979.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor hydrothermalis 108]
 gi|311778124|gb|ADQ07610.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor hydrothermalis 108]
          Length = 244

 Score = 50.1 bits (118), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 28/94 (29%), Positives = 50/94 (53%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EE  +  R    G+      L+  +LRLVV IA  +    + + ++VS G IGL
Sbjct: 41  PPLTPDEEAQILYRIHYQGEEGLKKLLIERNLRLVVYIAKRFENTKINLEDLVSIGTIGL 100

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++A+  ++P +  +LATY+   I+  +  ++ R+
Sbjct: 101 IKAINTYNPNKNIKLATYASKCIENEILMFLRRN 134


>gi|302522171|ref|ZP_07274513.1| RNA polymerase sigma-G factor [Streptomyces sp. SPB78]
 gi|318056578|ref|ZP_07975301.1| RNA polymerase sigma factor WhiG [Streptomyces sp. SA3_actG]
 gi|302431066|gb|EFL02882.1| RNA polymerase sigma-G factor [Streptomyces sp. SPB78]
          Length = 279

 Score = 50.1 bits (118), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 62/246 (25%), Positives = 105/246 (42%), Gaps = 18/246 (7%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKK 92
           L + Y+  GD     +L+  H   +VK   G    GLP     ++ VS G  GL+ A++K
Sbjct: 33  LWRMYKTTGDARLREQLIL-HYSPLVKYVAGRVSVGLPPNVEQADFVSSGVFGLIDAIEK 91

Query: 93  FDPERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           FD ER  +  TY++  I+ AM  E     W    I  +  QK    N+ R    L+A   
Sbjct: 92  FDIERSIKFETYAITRIRGAMIDELRALDW----IPRSVRQKAR--NVERAYATLEAKLH 145

Query: 152 NNLKPEQV-VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
               P +V VA    + V +   +     LA   +L  L++   +   +       +  G
Sbjct: 146 RT--PTEVEVASEMGVGVEDLHAVFSQLSLANVVALEELLSVGSEGGGRLSIMDTLEDTG 203

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
            +   +E  E +  R +L+R+++ L  RE+ +      +   +TL  +     V+  RV 
Sbjct: 204 ADNP-VEVAEGRELRQLLSRAINSLPDREKTVVMLYYYE--GLTLAEIGHVLGVTESRVS 260

Query: 271 QIEARA 276
           QI  ++
Sbjct: 261 QIHTKS 266


>gi|323140910|ref|ZP_08075823.1| Sigma-70 region 2 [Phascolarctobacterium sp. YIT 12067]
 gi|322414648|gb|EFY05454.1| Sigma-70 region 2 [Phascolarctobacterium sp. YIT 12067]
          Length = 211

 Score = 50.1 bits (118), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 34/133 (25%), Positives = 67/133 (50%), Gaps = 3/133 (2%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD +A  RL+T++  LV KIA  +R       E++ EG +GL++A + +D +R    + +
Sbjct: 30  GDEAAHQRLMTAYQPLVFKIASSFRLPEADTMELIQEGMVGLLEAAESYDYKRQVAFSLF 89

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA---ITDNNLKPEQVVA 161
           + + I+ +M +Y+  S     +   +   + F     L   L +   +T+ +L  E+V  
Sbjct: 90  ASYRIRGSMVDYLRHSTDKGMLYLDSELSKGFTLSDALPSELASPSEVTEQHLLCEKVAQ 149

Query: 162 IAKKLNVSESEVI 174
              +L + E +V+
Sbjct: 150 AMDRLPLKEQQVL 162


>gi|254381060|ref|ZP_04996425.1| sigma factor [Streptomyces sp. Mg1]
 gi|194339970|gb|EDX20936.1| sigma factor [Streptomyces sp. Mg1]
          Length = 302

 Score = 50.1 bits (118), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 53/221 (23%), Positives = 107/221 (48%), Gaps = 20/221 (9%)

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGT 128
           G G+ I ++V  G IGL++A+ +FDP+R    +T ++ +I   ++ +    +W++     
Sbjct: 93  GGGVDIEDIVQVGTIGLIKAIDRFDPDREVEFSTLALPYISGEIKRFFRDTTWAV----- 147

Query: 129 TANQKRLFFNLR-RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVI----SMNCRLAGD 183
             +  R    LR  L     A+T+   +   V  IA+ L +SE +VI    + N   +G 
Sbjct: 148 --HVPRRLQELRSELAKSQDALTEVFGRAPTVKEIAEHLELSEDDVIEGLVAANGYTSG- 204

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            S++A  +S  + S + +   + +  G+    +E  E  +    L +S   L  R+RRI 
Sbjct: 205 -SIDAATSSRQRTSGETEGRSLAETVGEVDPDMELFEEFHTLAPLLQS---LKERDRRIL 260

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             R  +E  +T   + +E  +S+ +V ++  R   +++ ++
Sbjct: 261 AMRFGEE--MTQAEIGTELGISQMQVSRLLTRVLTRLRTAM 299


>gi|168186812|ref|ZP_02621447.1| RNA polymerase sigma-G factor [Clostridium botulinum C str. Eklund]
 gi|169295146|gb|EDS77279.1| RNA polymerase sigma-G factor [Clostridium botulinum C str. Eklund]
          Length = 256

 Score = 50.1 bits (118), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 63/277 (22%), Positives = 127/277 (45%), Gaps = 51/277 (18%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+++E   L  + ++ GD  +  + V  +LRLV+ +   +   G  + ++   G I
Sbjct: 14  KLPVLKEKEMKELLLKMKD-GDNLSREKFVRGNLRLVLSVIQRFNNRGENVDDLFQVGCI 72

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD  +  + +TY++  I   ++ Y LR  + +++  +         LR +  
Sbjct: 73  GLIKAIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNSIRVSRS---------LRDIAY 122

Query: 145 HLQAITDNNLKPE----QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
               + D  +K E     V  IAK+L++   EV+          +L+A+           
Sbjct: 123 KALQVRDRIIKKENKDPNVSQIAKELDLPREEVVF---------ALDAI----------- 162

Query: 201 QDWL-----VYDHDGQEQVLIEKEERKNR-------RNM-LTRSMSVLNPRERRIFEARR 247
           QD +     +Y HDG + + +  +   N+        N+ +  +M  LN RE+ I   R 
Sbjct: 163 QDPVSLFEPIY-HDGGDALYVMDQISDNKNADESWIENISIKEAMKRLNEREKLILNMRF 221

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            Q    T   ++ E  +S+ +V ++E  A K +++ +
Sbjct: 222 FQGR--TQMEVADEIGISQAQVSRLEKTALKHMRKYV 256


>gi|325111003|ref|YP_004272071.1| RNA polymerase, sigma 32 subunit, RpoH [Planctomyces brasiliensis
           DSM 5305]
 gi|324971271|gb|ADY62049.1| RNA polymerase, sigma 32 subunit, RpoH [Planctomyces brasiliensis
           DSM 5305]
          Length = 555

 Score = 50.1 bits (118), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 24/57 (42%), Positives = 38/57 (66%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           L+ S+LRLVV IA  +        E+VS+GN+ L++A++KFD  +G + +TY+ W I
Sbjct: 380 LIRSNLRLVVSIAKRHFKPQANFFEMVSDGNMSLIRAIEKFDYSQGNKFSTYATWAI 436



 Score = 38.9 bits (89), Expect = 0.84,   Method: Compositional matrix adjust.
 Identities = 23/60 (38%), Positives = 39/60 (65%), Gaps = 4/60 (6%)

Query: 235 LNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE-SIQKQVEL 290
           L+PRER I   R        P TLE +   F V++ER+RQIE+RA  K+++ ++++++E+
Sbjct: 493 LDPRERDIILHRFGLNKGTEPETLEQVGHRFGVTKERIRQIESRALSKLKKIAVEEKLEI 552


>gi|147677561|ref|YP_001211776.1| DNA-directed RNA polymerase specialized sigma subunit
           [Pelotomaculum thermopropionicum SI]
 gi|146273658|dbj|BAF59407.1| DNA-directed RNA polymerase specialized sigma subunit
           [Pelotomaculum thermopropionicum SI]
          Length = 259

 Score = 50.1 bits (118), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 56/258 (21%), Positives = 123/258 (47%), Gaps = 17/258 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           + P+L+ +E   L ++ +  GD  A  +LV  +L+LV  +   ++  G  + ++   G I
Sbjct: 12  RFPLLKDREMRELLQKAK-AGDSYARDKLVNCNLKLVFNLVKRFQNRGYELEDLFQIGCI 70

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A+ KFD     + +TY++  I   ++ + LR  + +K+  +  +K       R++ 
Sbjct: 71  GLMKAIDKFDVSYDVKFSTYAVPMIVGEIRRF-LRDDNPIKVSRSLKEKAY-----RVQQ 124

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
               +T    +   V  ++ +L +S  EV++         S+   ++  D +      +L
Sbjct: 125 ARDLLTARLGREPTVGEVSAELGLSREEVVNALEAAQVPASIYETLHQDDGDPI----YL 180

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           +    G E+  +   E+   + +L +    L  R+R+I   R  ++   T  +++    +
Sbjct: 181 LDQIKGSEEGDVPWLEKITVKELLNK----LPERDRQILAWRFFEDR--TQSDIAKRLGL 234

Query: 265 SRERVRQIEARAFKKVQE 282
           S+ +V ++E +A KK++E
Sbjct: 235 SQVQVSRLERQALKKLKE 252


>gi|167765669|ref|ZP_02437722.1| hypothetical protein CLOSS21_00157 [Clostridium sp. SS2/1]
 gi|167712644|gb|EDS23223.1| hypothetical protein CLOSS21_00157 [Clostridium sp. SS2/1]
          Length = 271

 Score = 50.1 bits (118), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 29/98 (29%), Positives = 52/98 (53%), Gaps = 1/98 (1%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L ++E+  L +R  E GDL A    +  +LRLV+ I   + G      ++   G IG
Sbjct: 29  LPLLSEEEKEDLFERI-EQGDLLAREHYIKGNLRLVLSIIQRFSGSNENADDLFQVGCIG 87

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           LM+A+  FD     + +TY++  I   ++ Y+  + S+
Sbjct: 88  LMKAIDNFDRNLNVKFSTYAVPMIIGEVKRYLRDNHSM 125


>gi|23099454|ref|NP_692920.1| sporulation sigma factor SigK [Oceanobacillus iheyensis HTE831]
 gi|22777683|dbj|BAC13955.1| RNA polymerase sigma 28 (sigam K) factor [Oceanobacillus iheyensis
           HTE831]
          Length = 234

 Score = 50.1 bits (118), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 23/68 (33%), Positives = 41/68 (60%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A ++L+  +LRLV  I   +   G  + +++S G IGL++ V+ F  ++G +LA
Sbjct: 44  QEGDEVARNKLIEHNLRLVAHIVKKFENTGEDMEDLISIGTIGLIKGVESFSTDKGTKLA 103

Query: 103 TYSMWWIK 110
           TY+   I+
Sbjct: 104 TYAARCIE 111


>gi|295836990|ref|ZP_06823923.1| RNA polymerase sigma factor [Streptomyces sp. SPB74]
 gi|197697450|gb|EDY44383.1| RNA polymerase sigma factor [Streptomyces sp. SPB74]
          Length = 312

 Score = 50.1 bits (118), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 60/240 (25%), Positives = 107/240 (44%), Gaps = 30/240 (12%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  +L LV   A  +R    P+ +++  G IGL++A+ +F+  RG    T++M  I   
Sbjct: 91  LVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRGVEFPTFAMPTIIGE 150

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL  +L +    L    D    P +   +A +L +   
Sbjct: 151 IKRFFRDTSWS-VRVPRRLQELRL--DLAKAGDELAQRLDRAPTPSE---LADRLGIERE 204

Query: 172 EVISMNCRLAGDESLNALINSS-------DKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           EVI       G  + NA   SS       D + S   D L Y+  G E +    E  ++ 
Sbjct: 205 EVIE------GMAASNAYTASSLDAQPEEDDSESALADRLGYEDHGLEGI----EYIESL 254

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + M+ R    L  R+R+I   R +    +T   +  E  +S+  V ++ +R   K+++ +
Sbjct: 255 KPMIAR----LPQRDRKILSLRFVAN--MTQSEIGEELGISQMHVSRLLSRTLVKLRKGL 308


>gi|121488747|emb|CAJ18258.1| sigma 70-type sigma factor [Pelodictyon luteolum]
          Length = 165

 Score = 50.1 bits (118), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 16/50 (32%), Positives = 36/50 (72%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           ++++EGN+GL++  K+FD  RGF+  +Y++WWI+ ++ + +     +V++
Sbjct: 1   DLINEGNLGLIKXAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL 50


>gi|302871379|ref|YP_003840015.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
 gi|302574238|gb|ADL42029.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
          Length = 262

 Score = 50.1 bits (118), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 28/94 (29%), Positives = 50/94 (53%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EE  +  R    G+      L+  +LRLVV IA  +    + + ++VS G IGL
Sbjct: 41  PPLTPDEEAQILYRIHYQGEEGLKKLLIERNLRLVVYIARRFENTKVNLEDLVSIGTIGL 100

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++A+  ++P +  +LATY+   I+  +  ++ R+
Sbjct: 101 IKAINTYNPNKNIKLATYASKCIENEILMFLRRN 134


>gi|297605001|ref|NP_001056480.2| Os05g0589200 [Oryza sativa Japonica Group]
 gi|255676623|dbj|BAF18394.2| Os05g0589200 [Oryza sativa Japonica Group]
          Length = 464

 Score = 50.1 bits (118), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 25/81 (30%), Positives = 43/81 (53%), Gaps = 2/81 (2%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E +L  R +E        RL+ +   LV  IA  Y G G    +++  G +G++   +K
Sbjct: 305 DEALLRSRLQE--GYCCRERLLVTTEWLVKYIAKTYAGMGTAFEDLLQAGKMGVLNGAEK 362

Query: 93  FDPERGFRLATYSMWWIKAAM 113
           FD ++G + +TY  +WI+ AM
Sbjct: 363 FDSQKGCKFSTYVKYWIRKAM 383


>gi|239982580|ref|ZP_04705104.1| RNA polymerase sigma factor WhiG [Streptomyces albus J1074]
          Length = 259

 Score = 50.1 bits (118), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 28/77 (36%), Positives = 41/77 (53%), Gaps = 5/77 (6%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFDPE 96
           Y+  GD     +L+  H   +VK   G    GLP     ++ VS G  GL+ A++KFDPE
Sbjct: 16  YKATGDARLREQLIL-HYSPLVKYVAGRVSVGLPPNVEQADFVSSGIFGLIDAIEKFDPE 74

Query: 97  RGFRLATYSMWWIKAAM 113
           R  +  TY++  I+ AM
Sbjct: 75  RSIKFETYAITRIRGAM 91


>gi|251733355|emb|CAR82427.1| RNA polymerase sigma factor [Rhizobium galegae]
          Length = 202

 Score = 50.1 bits (118), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 35/87 (40%), Positives = 50/87 (57%), Gaps = 15/87 (17%)

Query: 13  EIGLSRYIHEIRKI-PMLEKQE-EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           E G+S  I E R+I  M++K E E  +AK+            +V ++LRLV+ IA  Y  
Sbjct: 129 ETGIS--IAEFRRIVSMVQKGEREARIAKK-----------EMVEANLRLVISIAKKYTN 175

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPER 97
            GL   +++ EGNIGLM+AV KF+  R
Sbjct: 176 RGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|223984440|ref|ZP_03634576.1| hypothetical protein HOLDEFILI_01870 [Holdemania filiformis DSM
           12042]
 gi|223963596|gb|EEF67972.1| hypothetical protein HOLDEFILI_01870 [Holdemania filiformis DSM
           12042]
          Length = 232

 Score = 50.1 bits (118), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 32/99 (32%), Positives = 53/99 (53%), Gaps = 7/99 (7%)

Query: 17  SRYIH-----EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           SR++H     ++   P+   +EE  L     E+GD  A   L+  +LRLVV IA  Y   
Sbjct: 17  SRHVHFIQGNDVLPHPLARDEEEAALIAL--ENGDQQARDTLIEHNLRLVVYIAKRYETN 74

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            + + +++S G IGL++AV  F  ++  +L TY+   I+
Sbjct: 75  PIFMEDLISIGTIGLIKAVNTFKRDKNIKLVTYASRCIE 113


>gi|282856209|ref|ZP_06265492.1| RNA polymerase, sigma 28 subunit [Pyramidobacter piscolens W5455]
 gi|282585968|gb|EFB91253.1| RNA polymerase, sigma 28 subunit [Pyramidobacter piscolens W5455]
          Length = 196

 Score = 50.1 bits (118), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 26/75 (34%), Positives = 42/75 (56%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A  +L+ ++  LV  +A  +R  G   S++V EG + L++AV KFD   G R  TY
Sbjct: 22  GDEEAREQLILAYRPLVYWVAKKFRVNGQRFSDLVQEGTLALIRAVDKFDVSLGHRFTTY 81

Query: 105 SMWWIKAAMQEYILR 119
           + + I+  M  ++ R
Sbjct: 82  ACYRIRGQMLNFLQR 96


>gi|293400805|ref|ZP_06644950.1| RNA polymerase sigma-K factor [Erysipelotrichaceae bacterium
           5_2_54FAA]
 gi|291305831|gb|EFE47075.1| RNA polymerase sigma-K factor [Erysipelotrichaceae bacterium
           5_2_54FAA]
          Length = 247

 Score = 49.7 bits (117), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 69/284 (24%), Positives = 119/284 (41%), Gaps = 68/284 (23%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEE-YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           I++  +G   YI     +  L+K+EE + +A    +  D    ++L+  +LRLV  I   
Sbjct: 11  ILSSALGYVGYIRSNSFLQPLDKEEEAHCIAGLSLQ--DEECRNKLIEHNLRLVAHIVKK 68

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y        +++S G IGL++A+  F PE+G +L TY+   I+  +  Y           
Sbjct: 69  YDIKKEQTEDLISIGTIGLIKAIDSFKPEKGHKLTTYASRCIENEILMY----------- 117

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
                      LR  K + Q ++ N+        IA   + SE  +I            +
Sbjct: 118 -----------LRSSKNYFQNVSLND-------PIATDKDGSEITLI------------D 147

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR- 246
           A+  SS + +S  +D +V D+  +                L + + VL+ RE  I   R 
Sbjct: 148 AI--SSPQETSIIEDMVVEDNISK----------------LKQFLHVLDSRELEIITKRF 189

Query: 247 ---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
               ++E   T   ++ +  +SR  V +IE RAF K+    QK+
Sbjct: 190 GLYGVEEE--TQREIAKQLHISRSYVSRIEKRAFMKLYREFQKE 231


>gi|255092173|ref|ZP_05321651.1| sporulation sigma factor SigK [Clostridium difficile CIP 107932]
 gi|255649691|ref|ZP_05396593.1| sporulation sigma factor SigK [Clostridium difficile QCD-37x79]
          Length = 105

 Score = 49.7 bits (117), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 45/81 (55%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L  +EE     +++   D SA   L+  ++RLV  IA  Y        +++S G IGL++
Sbjct: 11  LTPEEEIEYLTKFKIENDKSAKDTLIERNMRLVAYIAKKYNNSTEDQDDLISIGTIGLIK 70

Query: 89  AVKKFDPERGFRLATYSMWWI 109
           A++ ++ ++G RLATY+   I
Sbjct: 71  AIETYNIDKGTRLATYASRCI 91


>gi|331090618|ref|ZP_08339469.1| hypothetical protein HMPREF9477_00112 [Lachnospiraceae bacterium
           2_1_46FAA]
 gi|330401058|gb|EGG80653.1| hypothetical protein HMPREF9477_00112 [Lachnospiraceae bacterium
           2_1_46FAA]
          Length = 259

 Score = 49.7 bits (117), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 61/263 (23%), Positives = 120/263 (45%), Gaps = 35/263 (13%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+++E+  L  R +  GD  A    +  +LRLV+ +   +        ++   G I
Sbjct: 15  KLPLLKEEEKEALFVRIK-AGDEEAKEEYIKGNLRLVLSVIKRFSNSNENPDDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT---ANQKRLFFNLRR 141
           GL++A+  F+ E   + +TY++  I   ++ Y +R  + +++  +      K ++     
Sbjct: 74  GLIKAINNFNTELNVKFSTYAVPMIIGEIRRY-MRDNNSIRVSRSLRDTAYKAIYAKEGY 132

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL------AGDESLNALINSSDK 195
           +K HL+  T   +  E  + I+K+  V   + I M   L       G ++L  +   SDK
Sbjct: 133 MKTHLKEPTIQEIASE--IGISKEEIVQALDAIQMPMSLHEPIYNDGGDTLYVMDQISDK 190

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
            + + ++W+      +E  L E  ER             L  RER+I + R   E    +
Sbjct: 191 KNKE-ENWV------EELSLAEAMER-------------LGERERKIIQMRFF-EGKTQM 229

Query: 256 ENLSSEFEVSRERVRQIEARAFK 278
           E ++ E  +S+ +V ++E  A +
Sbjct: 230 E-IAKEIHISQAQVSRLEKNALE 251


>gi|254422308|ref|ZP_05036026.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp. PCC
           7335]
 gi|196189797|gb|EDX84761.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp. PCC
           7335]
          Length = 259

 Score = 49.7 bits (117), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 26/97 (26%), Positives = 58/97 (59%), Gaps = 1/97 (1%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY-GLPISEVVSEGNIGLMQA 89
           K + + L   Y++   L   +RLV  ++ LV + A  + GY G    +++  G++GL+ A
Sbjct: 10  KNQSFELLSLYQKDRSLQLRNRLVQLNIGLVRQEAYRWLGYSGETFDDLMQIGSLGLINA 69

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           +++FD E+G+  +++++ +I+  +Q Y+    ++V+I
Sbjct: 70  IERFDLEKGYAFSSFAIPYIRGEIQHYLRDKGTVVRI 106


>gi|312898376|ref|ZP_07757766.1| sigma-70 region 2 [Megasphaera micronuciformis F0359]
 gi|310620295|gb|EFQ03865.1| sigma-70 region 2 [Megasphaera micronuciformis F0359]
          Length = 205

 Score = 49.7 bits (117), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 31/112 (27%), Positives = 64/112 (57%), Gaps = 6/112 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           + E++KI +L+  EE  L   Y++ G + +  RL+  +  LV + A+ +      +++V+
Sbjct: 1   MEELQKITLLKPDEEKRLWMAYKDEGCMDSRGRLIEQYQPLVFREALRWHVGEEHMADVL 60

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
            EGN+GL++AV+++D + G   + Y++  I+  + ++      L K G +AN
Sbjct: 61  QEGNLGLIEAVERYDYKLGVAFSIYAVHRIRGEIVDW------LKKEGKSAN 106


>gi|331269711|ref|YP_004396203.1| FliA/WhiG family RNA polymerase sigma 28 subunit [Clostridium
           botulinum BKT015925]
 gi|329126261|gb|AEB76206.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           botulinum BKT015925]
          Length = 242

 Score = 49.7 bits (117), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 61/272 (22%), Positives = 124/272 (45%), Gaps = 43/272 (15%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L+ +E   L  + R+ GD  +  + +  +LRLV+ +   +   G  + ++   G IG
Sbjct: 1   MPVLKDKEMKELLIKMRD-GDYFSREKFIRGNLRLVLSVIQRFNNRGENVDDLFQVGCIG 59

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A+  FD  +  + +TY++  I   ++ Y LR  + +++  +          + L+  
Sbjct: 60  LIKAIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNSIRVSRSLRD----IAYKALQVR 114

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL- 204
            + I  +N  P  V  IAK+L +   EV+          +L+A+           QD + 
Sbjct: 115 DRLINKDNKDP-NVSQIAKELELPREEVVF---------ALDAI-----------QDPVS 153

Query: 205 ----VYDHDGQEQVLIEKEERKNR-------RNM-LTRSMSVLNPRERRIFEARRLQENP 252
               +Y HDG + + +  +   N+        N+ +  +M  LN RE+ I   R  Q   
Sbjct: 154 LFEPIY-HDGGDALYVMDQISDNKSVDDSWIENISIKEAMKRLNEREKLILNMRFFQGR- 211

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            T   ++ E  +S+ +V ++E  A K +++ +
Sbjct: 212 -TQMEVADEIGISQAQVSRLEKTALKHMRKYV 242


>gi|302385749|ref|YP_003821571.1| sigma-70 region 3 domain protein [Clostridium saccharolyticum WM1]
 gi|302196377|gb|ADL03948.1| sigma-70 region 3 domain protein [Clostridium saccharolyticum WM1]
          Length = 203

 Score = 49.7 bits (117), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 35/111 (31%), Positives = 56/111 (50%), Gaps = 3/111 (2%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ E+  IP   + E+  L K   E G   A  RLV  +LR  ++ A  Y G G+ I+++
Sbjct: 9   YLEEMGNIPPCTRDEQERLLKEAAE-GRKEAKKRLVEGNLRTALEYAREYDGRGVLITDL 67

Query: 79  VSEGNIGLMQAVKKFDPERGFRLA--TYSMWWIKAAMQEYILRSWSLVKIG 127
           V E N+ LM AV++F      RLA  +++   I+ A+   +    S  + G
Sbjct: 68  VQEANMALMMAVEEFSAMENGRLAFDSFTGRKIREALTAAVEEQQSACQTG 118


>gi|223975681|gb|ACN32028.1| unknown [Zea mays]
          Length = 565

 Score = 49.7 bits (117), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 21/62 (33%), Positives = 35/62 (56%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RL+ +   LV  IA  Y G G  + +++  G +G++   +KFD  +G R +TY  +WI+ 
Sbjct: 331 RLLVTTEWLVRCIARTYTGMGTALDDLLQAGKMGVLDGAEKFDSRKGCRFSTYVKYWIRK 390

Query: 112 AM 113
            M
Sbjct: 391 GM 392


>gi|291454422|ref|ZP_06593812.1| RNA polymerase sigma factor WhiG [Streptomyces albus J1074]
 gi|291357371|gb|EFE84273.1| RNA polymerase sigma factor WhiG [Streptomyces albus J1074]
          Length = 279

 Score = 49.7 bits (117), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 28/77 (36%), Positives = 41/77 (53%), Gaps = 5/77 (6%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFDPE 96
           Y+  GD     +L+  H   +VK   G    GLP     ++ VS G  GL+ A++KFDPE
Sbjct: 36  YKATGDARLREQLIL-HYSPLVKYVAGRVSVGLPPNVEQADFVSSGIFGLIDAIEKFDPE 94

Query: 97  RGFRLATYSMWWIKAAM 113
           R  +  TY++  I+ AM
Sbjct: 95  RSIKFETYAITRIRGAM 111


>gi|226311983|ref|YP_002771877.1| sporulation sigma factor SigF [Brevibacillus brevis NBRC 100599]
 gi|226094931|dbj|BAH43373.1| RNA polymerase sigma-F factor [Brevibacillus brevis NBRC 100599]
          Length = 251

 Score = 49.7 bits (117), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 59/252 (23%), Positives = 113/252 (44%), Gaps = 36/252 (14%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A   LV S++RLV  +   +   G    ++   G IGL++AV KFD     R +
Sbjct: 26  QAGDTEARELLVNSNIRLVWSVVQRFINRGYEADDLFQIGCIGLLKAVDKFDLSYDVRFS 85

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIG----TTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           TY++  I   +Q + LR    VK+      TAN+      +RR K  L        +   
Sbjct: 86  TYAVPMIIGEIQRF-LRDDGTVKVSRSLKETANK------VRRTKDELYK---QFGRAPT 135

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           +  +A  + ++  EV+                  +++  S   +  V+++DG    LI++
Sbjct: 136 IAEVADAVGITPEEVV--------------FAQEANRAPSSIHE-TVFENDGDPITLIDQ 180

Query: 219 --EERKNR---RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
             +E  N+   +  L  ++S L+ RE+ I   R  ++   T   ++    +S+ +V ++E
Sbjct: 181 IADEGVNKWFEKIALKDAISRLSEREQLIVYLRYYKDQ--TQSEVAERLGISQVQVSRLE 238

Query: 274 ARAFKKVQESIQ 285
            R  + +++ I+
Sbjct: 239 KRILQTIKDQIE 250


>gi|147677461|ref|YP_001211676.1| hypothetical protein PTH_1126 [Pelotomaculum thermopropionicum SI]
 gi|146273558|dbj|BAF59307.1| hypothetical protein [Pelotomaculum thermopropionicum SI]
          Length = 127

 Score = 49.7 bits (117), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 34/105 (32%), Positives = 52/105 (49%), Gaps = 1/105 (0%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +VNG + L  YI      P    +EE     +    G+  A + L   +LRLV  I   +
Sbjct: 13  LVNGLLLLVSYIAN-NTFPQPLSEEEEAKYLKLLNMGNEEARNILTERNLRLVAHIVKKF 71

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
              G    +++S G IGL++A+  F+P +G RLATY+   I+  M
Sbjct: 72  DSTGEDSDDLISIGTIGLIKAINTFNPGKGTRLATYAAKCIENEM 116


>gi|157691239|ref|YP_001485701.1| RNA polymerase sigma factor SigB [Bacillus pumilus SAFR-032]
 gi|157679997|gb|ABV61141.1| DNA-directed RNA polymerase sigma subunit SigB [Bacillus pumilus
           SAFR-032]
          Length = 262

 Score = 49.7 bits (117), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 64/259 (24%), Positives = 121/259 (46%), Gaps = 18/259 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE-GNIGLM 87
           L K E   L + Y+ + D  A   LV  +  LV  +A  Y   G    E + + G IGL+
Sbjct: 10  LTKDEVDRLIQSYQSNQDEQAQLTLVECYTNLVDMLAKKY-SKGKSFHEDLRQVGMIGLL 68

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHL 146
            A+K++DP  G     +++  I   ++ ++  ++WS+         +R+     R+K  +
Sbjct: 69  GAIKRYDPLVGKSFEAFAIPTIIGEIKRFLRDKTWSV------HVPRRIKELGPRIKMAV 122

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLV 205
             +T    K  +V  IA+ L+V+E EV+     +   +S  AL ++   +  S+     +
Sbjct: 123 DHLTTETQKSPKVQEIAEYLDVTEEEVLET---MEMGKSYQALSVDQGVEADSEGSTVTI 179

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            D  G ++   E  ER N++ ML   + VL  RE+ I     LQ    + +       +S
Sbjct: 180 LDVVGSQE---EGYERVNQKMMLESVLHVLTDREKEIINLTYLQNK--SQKETGDLLGIS 234

Query: 266 RERVRQIEARAFKKVQESI 284
           +  V +++ +A KK+++++
Sbjct: 235 QMHVSRLQRKAVKKLRDAL 253


>gi|304404273|ref|ZP_07385935.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
 gi|304347251|gb|EFM13083.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
          Length = 262

 Score = 49.7 bits (117), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 45/162 (27%), Positives = 78/162 (48%), Gaps = 18/162 (11%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS----EVVS 80
           K P L   E++   ++++   D+ A  +L+  +L LV  +       GLP +    ++ S
Sbjct: 5   KTPHLSNIEKW---RKWKTEKDIEAKKQLIEQYLPLVDYVT-SRMAIGLPKTVSKDDLYS 60

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
            G +GL+ A++KFD ERG +  TY+ W I+  + +  LR    V        KR+    +
Sbjct: 61  NGVMGLIDAIEKFDYERGLQFETYASWRIRGGIIDG-LRQGDWVPRSVRDKAKRIEEAYQ 119

Query: 141 RL-KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            L + +L+++TD          I+  LNVSE E   +   +A
Sbjct: 120 LLEQKYLRSVTD--------AEISDYLNVSEKEFTGILQEIA 153


>gi|134298969|ref|YP_001112465.1| FliA/WhiG family RNA polymerase sigma factor [Desulfotomaculum
           reducens MI-1]
 gi|134051669|gb|ABO49640.1| RNA polymerase, sigma subunit, RpoX/SigF [Desulfotomaculum reducens
           MI-1]
          Length = 260

 Score = 49.7 bits (117), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 40/151 (26%), Positives = 76/151 (50%), Gaps = 7/151 (4%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           + P+L  +E   L K+  + G+  A  RLV  +L+LV  +   +   G  + ++   G I
Sbjct: 13  RFPLLGDKEMRGLLKKA-QSGNSEARERLVNCNLKLVFNLVQRFSNRGYELEDLFQIGCI 71

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A+ KFD     + +TY++  I   ++ + LR  S VK+  +   K   + +++ + 
Sbjct: 72  GLMKAIDKFDLSYDVKFSTYAVPMIVGEIRRF-LRDDSPVKVSRSL--KETAYKIQQTRD 128

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
            L A      +   +  IA++L+ S  EV++
Sbjct: 129 RLTARLG---REPSINEIAEELSYSREEVVN 156


>gi|312134671|ref|YP_004002009.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|311774722|gb|ADQ04209.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor owensensis OL]
          Length = 244

 Score = 49.7 bits (117), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 28/94 (29%), Positives = 50/94 (53%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EE  +  R    G+      L+  +LRLVV IA  +    + + ++VS G IGL
Sbjct: 41  PPLTPDEEAQILYRIHYQGEEELKKLLIERNLRLVVYIARRFENTKVNLEDLVSIGTIGL 100

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++A+  ++P +  +LATY+   I+  +  ++ R+
Sbjct: 101 IKAINTYNPNKNIKLATYASKCIENEILMFLRRN 134


>gi|295092257|emb|CBK78364.1| RNA polymerase sigma factor, sigma-70 family [Clostridium cf.
           saccharolyticum K10]
          Length = 220

 Score = 49.7 bits (117), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 50/183 (27%), Positives = 87/183 (47%), Gaps = 21/183 (11%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAM-GYRGYGLP-------ISEVVSEGNIGLMQAVKKFDPE 96
           GD +A   L+ ++L  + KIA+  YR  GL        + ++V EG+IGL+ A+  FD  
Sbjct: 16  GDTAARDILLENNLGFIRKIALEQYRSMGLDENDIGIDLDDLVQEGSIGLLNAIPLFDAG 75

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RG +  TY+   I+ AM + I    +L +       K+     +R+  +L  I  ++ + 
Sbjct: 76  RGMKFLTYAAPAIRNAMTDCI--RAALAQFEQRMVDKKNGPGFQRV--YLDDILSDDERM 131

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH---DGQEQ 213
            ++ AIA     +  ++          E L  L  + DK +++ Q +L+Y +   DG E 
Sbjct: 132 LRIEAIADPHTQTPEQIYIQK------EQLTELYAALDKLTAREQTYLLYRYGFTDGIEH 185

Query: 214 VLI 216
            LI
Sbjct: 186 PLI 188


>gi|225375310|ref|ZP_03752531.1| hypothetical protein ROSEINA2194_00935 [Roseburia inulinivorans DSM
           16841]
 gi|225212799|gb|EEG95153.1| hypothetical protein ROSEINA2194_00935 [Roseburia inulinivorans DSM
           16841]
          Length = 196

 Score = 49.7 bits (117), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 24/66 (36%), Positives = 41/66 (62%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           +GDL A + L+  ++RLV  +A  Y+     + +++S G IGL++AV+ +  + G RLAT
Sbjct: 13  NGDLEARNELIERNMRLVAHVAKKYQNPEDEMEDLISIGTIGLIKAVETYKEDYGSRLAT 72

Query: 104 YSMWWI 109
           Y+   I
Sbjct: 73  YAARCI 78


>gi|159901988|gb|ABX10718.1| RNA polymerase sigma factor [uncultured planctomycete 13FN]
          Length = 391

 Score = 49.7 bits (117), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 25/83 (30%), Positives = 50/83 (60%), Gaps = 8/83 (9%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           M+  +++   A++ R+H        ++ ++LRLVV IA  +    + + E++S+GN+ LM
Sbjct: 196 MVRTEKDLDDARQVRDH--------IIQANLRLVVSIARRFVTDFISLDELISDGNLILM 247

Query: 88  QAVKKFDPERGFRLATYSMWWIK 110
           +AV +F+   GFR +TY+   ++
Sbjct: 248 KAVDRFNFSLGFRFSTYATHAVQ 270



 Score = 35.4 bits (80), Expect = 10.0,   Method: Compositional matrix adjust.
 Identities = 18/54 (33%), Positives = 33/54 (61%), Gaps = 3/54 (5%)

Query: 232 MSVLNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +  L+PRE+ I + R   +  +   TL  +  +  +S+ERVRQ++ RA ++V+E
Sbjct: 322 VDALSPREQTILDMRLGLKADDGGKTLREVGEKLSISKERVRQLQTRAIEQVRE 375


>gi|225028118|ref|ZP_03717310.1| hypothetical protein EUBHAL_02388 [Eubacterium hallii DSM 3353]
 gi|224954588|gb|EEG35797.1| hypothetical protein EUBHAL_02388 [Eubacterium hallii DSM 3353]
          Length = 247

 Score = 49.7 bits (117), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 44/72 (61%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+  +LRLVV IA  +   G+ + +++S G IGL++A++ F  ++  +LATY+   
Sbjct: 64  AKALLIERNLRLVVYIAKKFENTGIGVEDLISIGTIGLIKAIQTFKLDKKIKLATYASRC 123

Query: 109 IKAAMQEYILRS 120
           I+  +  Y+ R+
Sbjct: 124 IENEILMYLRRT 135


>gi|254382042|ref|ZP_04997404.1| RNA polymerase sigma subunit [Streptomyces sp. Mg1]
 gi|194340949|gb|EDX21915.1| RNA polymerase sigma subunit [Streptomyces sp. Mg1]
          Length = 278

 Score = 49.7 bits (117), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 60/248 (24%), Positives = 107/248 (43%), Gaps = 26/248 (10%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFD 94
           + Y+E GD     +L+  H   +VK   G    GLP     ++ VS G  GL+ A++KFD
Sbjct: 34  RAYKESGDERLRQQLIL-HYSPLVKYVAGRVSVGLPPNVEQADFVSSGVFGLIDAIEKFD 92

Query: 95  PERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
            +R  +  TY++  I+ AM       ++I RS              L   LRR     + 
Sbjct: 93  IDRSIKFETYAITRIRGAMIDELRALDWIPRSVRQKARAVERAYATLEAQLRRTPTECEV 152

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
             +  +  E++  +  +L++  + V+++      DE L+      D+ S    D L    
Sbjct: 153 ADEMGIAVEELHTVFSQLSL--ANVVAL------DELLHVGGEGGDRLS--LMDTL---E 199

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D      +E  E +  R +L R+++ L  RE+ +      +   +TL  + +   V+  R
Sbjct: 200 DTAADNPVEVAEGRELRRLLARAINTLPEREKTVVTLYYYEG--LTLAEIGNVLGVTESR 257

Query: 269 VRQIEARA 276
           V QI  ++
Sbjct: 258 VSQIHTKS 265


>gi|253996640|ref|YP_003048704.1| flagellar biosynthesis sigma factor [Methylotenera mobilis JLW8]
 gi|253983319|gb|ACT48177.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Methylotenera mobilis
           JLW8]
          Length = 244

 Score = 49.7 bits (117), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 63/257 (24%), Positives = 118/257 (45%), Gaps = 30/257 (11%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPER 97
           Y  HG       L+  H  LV K+A   +    P   + +++  G +GL+ AV +++   
Sbjct: 2   YTAHGKKDQKDVLLDQHAILVKKLAYQLKAKLPPSVELDDLIQAGMMGLLDAVNRYEDTH 61

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITDNNLKP 156
           G +  TY+   I+ AM +  LRS   +      N + +   + +L+  L Q+ T+N+   
Sbjct: 62  GAQFETYAAQRIRGAMLDE-LRSSDWLPRSIRKNMRDVENAISQLEQQLGQSPTEND--- 117

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD----KNSSQWQDWLVYDHDGQ- 211
                +AKKLN+S +E   M     GD S + LI   D     +   + D    DHD   
Sbjct: 118 -----VAKKLNMSLAEYHEM----LGDCSGHQLIYYEDFHEADSGEHFLDRFQTDHDNDP 168

Query: 212 -EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
            + +LI      + ++ L  ++  L  RE+ +      QE  + L+ + +   VS  RV 
Sbjct: 169 IKGLLI-----GDFKDALIGAIDSLPEREKILLGLYYEQE--LNLKEIGAVMSVSESRVC 221

Query: 271 QIEARAFKKVQESIQKQ 287
           Q+ ++A  +++ +++++
Sbjct: 222 QLHSQAVARLRANLREK 238


>gi|126700257|ref|YP_001089154.1| sporulation sigma factor SigE [Clostridium difficile 630]
 gi|254976236|ref|ZP_05272708.1| sporulation sigma factor SigE [Clostridium difficile QCD-66c26]
 gi|255093623|ref|ZP_05323101.1| sporulation sigma factor SigE [Clostridium difficile CIP 107932]
 gi|255101811|ref|ZP_05330788.1| sporulation sigma factor SigE [Clostridium difficile QCD-63q42]
 gi|255307678|ref|ZP_05351849.1| sporulation sigma factor SigE [Clostridium difficile ATCC 43255]
 gi|255518036|ref|ZP_05385712.1| sporulation sigma factor SigE [Clostridium difficile QCD-97b34]
 gi|255651152|ref|ZP_05398054.1| sporulation sigma factor SigE [Clostridium difficile QCD-37x79]
 gi|255656620|ref|ZP_05402029.1| sporulation sigma factor SigE [Clostridium difficile QCD-23m63]
 gi|260684218|ref|YP_003215503.1| sporulation sigma factor SigE [Clostridium difficile CD196]
 gi|260687877|ref|YP_003219011.1| sporulation sigma factor SigE [Clostridium difficile R20291]
 gi|296449924|ref|ZP_06891688.1| RNA polymerase sigma-E factor [Clostridium difficile NAP08]
 gi|296878306|ref|ZP_06902314.1| RNA polymerase sigma-E factor [Clostridium difficile NAP07]
 gi|306521002|ref|ZP_07407349.1| sporulation sigma factor SigE [Clostridium difficile QCD-32g58]
 gi|115251694|emb|CAJ69529.1| RNA polymerase sigma-E factor [Clostridium difficile]
 gi|260210381|emb|CBA64762.1| RNA polymerase sigma-E factor [Clostridium difficile CD196]
 gi|260213894|emb|CBE05927.1| RNA polymerase sigma-E factor [Clostridium difficile R20291]
 gi|296261194|gb|EFH08025.1| RNA polymerase sigma-E factor [Clostridium difficile NAP08]
 gi|296430604|gb|EFH16443.1| RNA polymerase sigma-E factor [Clostridium difficile NAP07]
          Length = 240

 Score = 49.7 bits (117), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 29/91 (31%), Positives = 50/91 (54%), Gaps = 2/91 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L+ +EE  L ++     D S    L+  +LRLVV I+  +   G+ + +++S G IGL
Sbjct: 38  PPLKPEEEMELLQKL--ETDESVKSILIERNLRLVVYISRKFENTGIDVEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           ++AV  F   +  +LATY+   I+  +  Y+
Sbjct: 96  IKAVNTFKLNKNIKLATYASRCIENEILMYL 126


>gi|289208354|ref|YP_003460420.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thioalkalivibrio sp. K90mix]
 gi|288943985|gb|ADC71684.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thioalkalivibrio sp. K90mix]
          Length = 253

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 58/234 (24%), Positives = 108/234 (46%), Gaps = 25/234 (10%)

Query: 54  VTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           V  H+ LV +IA   M      + + +++  G IGL++A ++F+  +G   ATY+   I+
Sbjct: 23  VAEHIELVHRIAHHLMARLPSSVQVDDLIQAGMIGLLEAARQFEGGQGATFATYAGIRIR 82

Query: 111 AAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
            AM + + RS W+          + +  N R++   +Q +     +  + V +A++L V 
Sbjct: 83  GAMIDELRRSDWT---------PRSVHRNSRKIAEAIQTVEAREGRAARGVEVAEELEVP 133

Query: 170 ESEVISMNCRLAGDESLNAL--INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
             E  SM    AG   L AL  +  +D ++    D ++   +GQE       E    R  
Sbjct: 134 IDEYYSMLQDHAG-AHLFALDDLGGTDGDA----DRVI---EGQEASPSRTIEAGEFREE 185

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           L  ++  L  RER +     ++E  + L  + +   V+  RV QI ++A  +++
Sbjct: 186 LAAALGDLPERERLVLSLYYIEE--LNLREIGAVLGVTESRVSQIRSQAVIRLR 237


>gi|251733367|emb|CAR82433.1| RNA polymerase sigma factor [Agrobacterium vitis]
          Length = 202

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 35/87 (40%), Positives = 50/87 (57%), Gaps = 15/87 (17%)

Query: 13  EIGLSRYIHEIRKI-PMLEKQE-EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           E G+S  I E R+I  M++K E E  +AK+            +V ++LRLV+ IA  Y  
Sbjct: 129 ETGIS--IAEFRRIVSMVQKGEREARIAKK-----------EMVEANLRLVISIAKKYTN 175

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPER 97
            GL   +++ EGNIGLM+AV KF+  R
Sbjct: 176 RGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|307718622|ref|YP_003874154.1| hypothetical protein STHERM_c09340 [Spirochaeta thermophila DSM
           6192]
 gi|306532347|gb|ADN01881.1| hypothetical protein STHERM_c09340 [Spirochaeta thermophila DSM
           6192]
          Length = 262

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 55/229 (24%), Positives = 106/229 (46%), Gaps = 22/229 (9%)

Query: 61  VVKIAMGYRGYGLPIS----EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           +VK   G    GLP S    +++  G  GL+ A++KFDPE+  +  TY++  I+ A+ + 
Sbjct: 37  LVKYVAGKIAVGLPSSVEFDDLIGFGTFGLLDAIEKFDPEKHVKFKTYAVTRIRGAIYDE 96

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITDNNLKPEQVVAIAKKLNVSESEVIS 175
            LR+   V        + +   L RL+  L +A TD  L        A+++N+S  E+  
Sbjct: 97  -LRAMDWVPRSVRQKSREIEDALHRLESSLGRAATDEEL--------AREMNMSSRELQK 147

Query: 176 MNCRLAGDE--SLNALINSSDKNSS-QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
              +++     SL  L  + D+N      D L           +E+EE K    ++  ++
Sbjct: 148 TLQKISSTSILSLQELWYTGDENDRVAIADMLEAPQAYDPAARVEREEIK---RVVAEAI 204

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             L  +E+++      ++  +TL+ + +   V+  RV Q+  +A  +++
Sbjct: 205 KELPEKEKKVLVLYYYED--LTLKEIGAILNVTESRVSQLHTKAISRLR 251


>gi|302871075|ref|YP_003839711.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
 gi|302573934|gb|ADL41725.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
          Length = 256

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 37/180 (20%), Positives = 85/180 (47%), Gaps = 19/180 (10%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L + Y+    +   + LV  +L +   IA  +   G+   ++     + L+ AV++F+P 
Sbjct: 18  LFEEYQRTKAIELRNELVNKYLYIAEIIAKKFVNRGIDYDDLYQVACVALINAVERFEPN 77

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +G++  +++   I   ++ Y     S++++      +RL+    ++K   + ++    +P
Sbjct: 78  KGYKFTSFATPTIMGEIKRYFRDRASIIRLP-----RRLYETSAKIKLVTEMLSSKLKRP 132

Query: 157 EQVVAIAKKLNVSESEVI------------SMNCRLAGDE--SLNALINSSDKNSSQWQD 202
            +V  IA+ LN+S  EV+            S++  +  DE  +L  ++  SD+N  Q ++
Sbjct: 133 PKVEEIAQHLNMSTEEVLEVMEASNSYLPQSLDQTMYEDEEMTLGDVLGKSDENILQIEN 192


>gi|312622917|ref|YP_004024530.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
 gi|312203384|gb|ADQ46711.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
          Length = 255

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 26/92 (28%), Positives = 50/92 (54%), Gaps = 1/92 (1%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L  +E+  L KR +E GD  A    +  +LRLV+ +   +   G  + ++   G IG
Sbjct: 14  LPVLSHEEKLELLKRMKE-GDKEARRIFIEGNLRLVLSVVQKFANRGENLDDLFQVGCIG 72

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           L++A+  FD  +  + +TY++  I   ++ Y+
Sbjct: 73  LIKAIDNFDLSQNVKFSTYAVPMIIGEIRRYL 104


>gi|295109465|emb|CBL23418.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase
           sigma-70 factor, sigma-B/F/G subfamily [Ruminococcus
           obeum A2-162]
          Length = 238

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 59/260 (22%), Positives = 123/260 (47%), Gaps = 33/260 (12%)

Query: 34  EYVLAKRYREH-GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           E  LA   R H GD  A  RL   +  L+   A  + G G+ + ++   G+IGL++AV K
Sbjct: 3   EDTLALIGRAHQGDKEARERLFHENTGLIYCAAKRFLGRGVDMEDLFQIGSIGLLKAVDK 62

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD     + +TY++  I   ++ + LR   ++K+  +  + +  + + R +  L+     
Sbjct: 63  FDTSYDVKFSTYAVPMIIGEIKRF-LRDDGILKVSRSVKENQ--YRIGRKREELEK---- 115

Query: 153 NLKPEQVVAIAKKLNVSE-SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
                    + ++  + E +E + M       E L   +++++   S +Q  ++Y  +G 
Sbjct: 116 --------TLGREPTLGELAESVQMLP-----EELAMTMDAANDVESIYQ--IIYQGEGN 160

Query: 212 EQVLIEK-EERKNRRNMLTRSMSV------LNPRERRIFEARRLQENPVTLENLSSEFEV 264
           E  L++K  E++N  + L   + +      LN  ER++   R  +E  +T   ++ EF V
Sbjct: 161 ELRLLDKIPEKENLHDRLLNKIFLEELLRSLNAEERKLLYMRYFRE--MTQTEVADEFGV 218

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ ++ ++E +   +++  I
Sbjct: 219 SQVQISRMEKKILNRLRAII 238


>gi|297562622|ref|YP_003681596.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
 gi|296847070|gb|ADH69090.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
          Length = 267

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 64/239 (26%), Positives = 109/239 (45%), Gaps = 28/239 (11%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  HL LV  +A  +R  G  + ++     IGL++++ +FD ERG   +TY+   I   
Sbjct: 46  LVELHLPLVEYLARRFRNRGEWLDDLTQVATIGLIKSIDRFDLERGVEFSTYATPTIVGE 105

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITD---NNLKPEQVVAIAKKLN 167
           ++ +   + W++          R+   L+ LK  L +A++D      +   V  +A  L 
Sbjct: 106 IKRHFRDKGWAV----------RVPRRLQELKLSLTKAVSDLSQREGRSPTVAELAAHLQ 155

Query: 168 VSESEVISMNCRLAGDESLNALINSS-DKNSSQWQDW-LVYDHDGQEQVLIEKEERKNRR 225
           ++E EV      L G ES NA    S D   S  +D   V D  G   ++ E  E    R
Sbjct: 156 MTEEEV------LEGLESANAYSTVSLDAPDSGDEDAPAVADSLG---IVDESLEGVEYR 206

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   ++++++
Sbjct: 207 ESLKPLLEQLPPREKRILLLRFF--GNMTQSQIAQELGISQMHVSRLLARTLAQLRQAL 263


>gi|217077805|ref|YP_002335523.1| RNA polymerase sigma factor for flagellar operon [Thermosipho
           africanus TCF52B]
 gi|217037660|gb|ACJ76182.1| RNA polymerase sigma factor for flagellar operon [Thermosipho
           africanus TCF52B]
          Length = 226

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 21/68 (30%), Positives = 43/68 (63%), Gaps = 3/68 (4%)

Query: 53  LVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           LV+ +L  + KIA   +    + + + +++ EG +  +QA++KFDP++G +L +Y +  +
Sbjct: 7   LVSEYLPYIKKIAYDLKRNLPHNVEVDDLIQEGLVAFIQAIEKFDPKKGAKLRSYLLTRV 66

Query: 110 KAAMQEYI 117
           K AM +Y+
Sbjct: 67  KGAMYDYL 74


>gi|256273|gb|AAC60417.1| RpoD4 [Synechococcus]
          Length = 48

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 18/41 (43%), Positives = 31/41 (75%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           +++ EG++GL +AV+KFDP  G++ +TY+ WWI+ +M   I
Sbjct: 2   DLIQEGSLGLERAVEKFDPALGYKFSTYAYWWIRQSMTRAI 42


>gi|162463525|ref|NP_001105185.1| sigma factor protein [Zea mays]
 gi|20159761|gb|AAM12034.1| sigma factor protein [Zea mays]
          Length = 568

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 21/62 (33%), Positives = 35/62 (56%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RL+ +   LV  IA  Y G G  + +++  G +G++   +KFD  +G R +TY  +WI+ 
Sbjct: 334 RLLVTTEWLVRCIARTYTGMGTALDDLLQAGKMGVLDGAEKFDSRKGCRFSTYVKYWIRK 393

Query: 112 AM 113
            M
Sbjct: 394 GM 395


>gi|326791410|ref|YP_004309231.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium lentocellum DSM
           5427]
 gi|326542174|gb|ADZ84033.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium lentocellum DSM
           5427]
          Length = 251

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 28/99 (28%), Positives = 54/99 (54%), Gaps = 5/99 (5%)

Query: 27  PMLEKQEEYVLAKRYREHGDL-----SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           P L + EE +L ++  E  +      +    L+  +LRLVV IA  +   G+ + +++S 
Sbjct: 42  PPLSRDEEEILIQKLIEFAEQEEEIKAIKTTLIERNLRLVVYIARKFENTGIYMEDLISI 101

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           G IGL++++  F P +  +LATY+   I+  +  ++ R+
Sbjct: 102 GTIGLIKSINTFKPCKKIKLATYASRCIENEILMFLRRT 140


>gi|312110136|ref|YP_003988452.1| RNA polymerase, sigma 28 subunit, SigK [Geobacillus sp. Y4.1MC1]
 gi|311215237|gb|ADP73841.1| RNA polymerase, sigma 28 subunit, SigK [Geobacillus sp. Y4.1MC1]
          Length = 236

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 27/84 (32%), Positives = 47/84 (55%), Gaps = 2/84 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  K+EE  L  +    GD  A + L+  +LRLV  I   +   G  + +++S G IGL
Sbjct: 30  PLSAKEEEKYL--QLMAKGDEQARNILIEHNLRLVAHIVKKFENTGEDVEDLISIGTIGL 87

Query: 87  MQAVKKFDPERGFRLATYSMWWIK 110
           ++A++ +   +G +LATY+   I+
Sbjct: 88  IKAIESYSSNKGTKLATYAARCIE 111


>gi|196038743|ref|ZP_03106051.1| RNA polymerase sigma-F factor [Bacillus cereus NVH0597-99]
 gi|196030466|gb|EDX69065.1| RNA polymerase sigma-F factor [Bacillus cereus NVH0597-99]
          Length = 252

 Score = 49.7 bits (117), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 50/190 (26%), Positives = 92/190 (48%), Gaps = 17/190 (8%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           +K P L+ QE   L ++ ++ GD  A   +V S++RLV  +   +   G    ++   G 
Sbjct: 9   KKKPQLKDQELKALIQKSQD-GDQQARDTIVQSNMRLVWSVVQRFLNRGYEPDDLFQIGC 67

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL+++V KFD     + +TY++  I   +Q + LR    VK+  +   K     +R+++
Sbjct: 68  IGLLKSVDKFDLSFDVKFSTYAVPMIIGEIQRF-LRDDGSVKVSRSL--KETGNKIRKMR 124

Query: 144 GHL-----QAITDN------NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
             L     +A T N       L PE+VV +A++ + + S +        GD  +  L   
Sbjct: 125 DELSKEFGRAPTINEVAEALELTPEEVV-LAQEASRAPSSIHETVYENDGD-PITILDQI 182

Query: 193 SDKNSSQWQD 202
           +D++ ++W D
Sbjct: 183 ADQSETKWFD 192


>gi|2529267|gb|AAB81186.1| sigma factor [Paenibacillus polymyxa]
          Length = 251

 Score = 49.3 bits (116), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 58/255 (22%), Positives = 115/255 (45%), Gaps = 44/255 (17%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A   L+ S++RLV  +   +   G    ++   G IGL+++V KFD     + +
Sbjct: 26  QSGDNDARETLINSNIRLVWSVVQRFMNRGYEPDDLFQIGCIGLLKSVDKFDLSYEVKFS 85

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIG----TTANQKRLFFNLRRLKGHLQAITDNNLKP-- 156
           TY++  I   +Q + LR    +K+      TAN+      +R++K  L        KP  
Sbjct: 86  TYAVPMIIGEIQRF-LRDDGTLKVSRSLKETANK------VRKMKDELS-------KPLN 131

Query: 157 --EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ--- 211
               V  +A +L V+  +V+                  ++K  +   +  V+++DG    
Sbjct: 132 RLPTVKEVADELGVTPEDVV--------------FAQEANKPPTSIHE-TVFENDGDPIT 176

Query: 212 --EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
             +Q+  E +ER   +  L  ++  L+ RER I   R  ++   T   ++S   +S+ +V
Sbjct: 177 LMDQIADESQERWFDKLALNEAIDGLSERERLIVYLRYYRDQ--TQSEVASRLGISQVQV 234

Query: 270 RQIEARAFKKVQESI 284
            ++E +  +++++ I
Sbjct: 235 SRLEKKILQQIRDQI 249


>gi|251733365|emb|CAR82432.1| RNA polymerase sigma factor [Agrobacterium rubi]
          Length = 202

 Score = 49.3 bits (116), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 35/87 (40%), Positives = 50/87 (57%), Gaps = 15/87 (17%)

Query: 13  EIGLSRYIHEIRKI-PMLEKQE-EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           E G+S  I E R+I  M++K E E  +AK+            +V ++LRLV+ IA  Y  
Sbjct: 129 ETGIS--IAEFRRIVSMVQKGEREARIAKK-----------EMVEANLRLVISIAKKYTN 175

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPER 97
            GL   +++ EGNIGLM+AV KF+  R
Sbjct: 176 RGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|21104386|dbj|BAB93463.1| putative rpoD gene [Variovorax sp. WFF52]
 gi|21104388|dbj|BAB93464.1| putative rpoD gene [Leptothrix discophora]
 gi|21104390|dbj|BAB93465.1| putative rpoD gene [Sphaerotilus natans]
          Length = 47

 Score = 49.3 bits (116), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 22/46 (47%), Positives = 32/46 (69%)

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           LV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+
Sbjct: 1   LVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYA 46


>gi|251733361|emb|CAR82430.1| RNA polymerase sigma factor [Agrobacterium tumefaciens]
          Length = 202

 Score = 49.3 bits (116), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 35/90 (38%), Positives = 52/90 (57%), Gaps = 15/90 (16%)

Query: 10  VNGEIGLSRYIHEIRKI-PMLEKQE-EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++ E G+S  I E R+I  M++K E E  +AK+            +V ++LRLV+ IA  
Sbjct: 126 LSTETGIS--IAEFRRIVSMVQKGEREARIAKK-----------EMVEANLRLVISIAKK 172

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 173 YTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|157692844|ref|YP_001487306.1| sporulation sigma factor SigF [Bacillus pumilus SAFR-032]
 gi|194016850|ref|ZP_03055463.1| RNA polymerase sigma-F factor [Bacillus pumilus ATCC 7061]
 gi|157681602|gb|ABV62746.1| DNA-directed RNA polymerase sigma subunit SigF [Bacillus pumilus
           SAFR-032]
 gi|194011456|gb|EDW21025.1| RNA polymerase sigma-F factor [Bacillus pumilus ATCC 7061]
          Length = 255

 Score = 49.3 bits (116), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 55/239 (23%), Positives = 108/239 (45%), Gaps = 18/239 (7%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A   LV  ++RLV  +   +   G    ++   G IGL+++V KFD     + +
Sbjct: 27  QDGDQQARDLLVEKNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKSVDKFDLSYDVKFS 86

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I   +Q +I R    VK+  +   K L   +RR +  L   + ++ +   V  I
Sbjct: 87  TYAVPMIIGEIQRFI-RDDGTVKVSRSL--KELGNKIRRARDEL---SKSHGRMPTVQEI 140

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+ L+++  +V+     +    S++  +  +D +     D +  DH          EER 
Sbjct: 141 AEYLDITPEDVVLAQEAVRTPSSIHETVYENDGDPITLLDQIA-DH---------SEERW 190

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             +  L  ++  L  RE+ I   R  ++   T   ++    +S+ +V ++E +  K++Q
Sbjct: 191 FDKIALKEAIKELEEREKLIVYLRYYKDQ--TQSEVAERLGISQVQVSRLEKKILKQIQ 247


>gi|108804196|ref|YP_644133.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108765439|gb|ABG04321.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 258

 Score = 49.3 bits (116), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 26/98 (26%), Positives = 50/98 (51%), Gaps = 1/98 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P  +K     L +RY   GD  A  +++   L L   +A  + G G P+ ++V   ++GL
Sbjct: 6   PRPDKARTRRLLERYHREGDRQAREQVIQEQLPLAEFLARKFAGRGEPLEDLVQVASVGL 65

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSL 123
           ++AV +FD +R    +TY+   I   ++ +   + W++
Sbjct: 66  IKAVDRFDVDRNIEFSTYATPNILGEIKRHFRDKGWAM 103


>gi|299472120|emb|CBN77105.1| RNA polymerase sigma factor [Ectocarpus siliculosus]
          Length = 555

 Score = 49.3 bits (116), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 21/66 (31%), Positives = 41/66 (62%), Gaps = 4/66 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYR----GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           A  R+V +++ L+V +A  +       G   S+V+ EG++ +++A + FDP  G+R +TY
Sbjct: 240 AQERIVGANVGLIVVMARRHHPATMARGTITSDVIQEGSLAVLRAAETFDPRLGYRFSTY 299

Query: 105 SMWWIK 110
           + WW++
Sbjct: 300 AGWWVR 305


>gi|225375609|ref|ZP_03752830.1| hypothetical protein ROSEINA2194_01234 [Roseburia inulinivorans DSM
           16841]
 gi|225212588|gb|EEG94942.1| hypothetical protein ROSEINA2194_01234 [Roseburia inulinivorans DSM
           16841]
          Length = 259

 Score = 49.3 bits (116), Expect = 6e-04,   Method: Compositional matrix adjust.
 Identities = 57/259 (22%), Positives = 124/259 (47%), Gaps = 19/259 (7%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L++ E+  L  R R+ GD  A    +  +LRLV+ +   + G    + ++   G I
Sbjct: 15  KLPILKETEKEALFARIRQ-GDQEAREMYIKGNLRLVLSVIKRFSGSHENLDDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++++  F+P+   + +TY++  I   ++ Y LR  + +++      + L     +   
Sbjct: 74  GLIKSIDNFNPDLQVKFSTYAVPMIIGEIRRY-LRDNNSIRVS-----RSLRDTAYKAIH 127

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + ++ N+ K   +  IA++  V+  ++      L   +++ + ++  D   +   D L
Sbjct: 128 AKEVLSKNSFKEPTLQEIAEESGVAAEDI------LYALDAIQSPVSLYDPVYTDGGDTL 181

Query: 205 -VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
            V D    ++    KEE    +  L+ +M+ L+ RE  I   R   E    +E ++ E  
Sbjct: 182 YVMDQISDKK---NKEENWVEKLSLSDAMNHLSERENFIINLRFF-EGKTQME-VADEIH 236

Query: 264 VSRERVRQIEARAFKKVQE 282
           +S+ +V ++E  A K +++
Sbjct: 237 ISQAQVSRLEKSALKTIRQ 255


>gi|317497563|ref|ZP_07955881.1| sigma-70 region 2 [Lachnospiraceae bacterium 5_1_63FAA]
 gi|316895122|gb|EFV17286.1| sigma-70 region 2 [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 215

 Score = 49.3 bits (116), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 29/98 (29%), Positives = 52/98 (53%), Gaps = 1/98 (1%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L ++E+  L +R  E GDL A    +  +LRLV+ I   + G      ++   G IG
Sbjct: 29  LPLLSEEEKEDLFERI-EQGDLLAREHYIKGNLRLVLSIIQRFSGSSENADDLFQVGCIG 87

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           LM+A+  FD     + +TY++  I   ++ Y+  + S+
Sbjct: 88  LMKAIDNFDRNLNVKFSTYAVPMIIGEVKRYLRDNHSM 125


>gi|150390630|ref|YP_001320679.1| sporulation sigma factor SigG [Alkaliphilus metalliredigens QYMF]
 gi|149950492|gb|ABR49020.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           metalliredigens QYMF]
          Length = 257

 Score = 49.3 bits (116), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 61/269 (22%), Positives = 115/269 (42%), Gaps = 49/269 (18%)

Query: 36  VLAKRYREH-------GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           VL   Y  H       GD SA    +  +LRLV+ +   +   G  + ++   G IGL++
Sbjct: 18  VLKNDYMRHLFGLIKQGDNSAREEFIQGNLRLVLSVIQRFNNRGEHVDDLFQVGCIGLIK 77

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A+  FD     R +TY++  I   ++ Y LR  + +++  +   +   +   +++  L  
Sbjct: 78  AIDNFDLRHNVRFSTYAVPMIIGEIRRY-LRDNNSIRVSRSL--RDTAYKALQVRDQL-- 132

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL---- 204
            T+   K   V  IA  LN+   +V+          +L+A+           QD +    
Sbjct: 133 -TNQKSKEPSVAEIAANLNIPREDVVF---------ALDAI-----------QDPVSLFE 171

Query: 205 -VYDHDGQEQVLIEKEERKNRRN--------MLTRSMSVLNPRERRIFEARRLQENPVTL 255
            +Y HD  + + +  + R  +           L  +M  LN RE+ I   R   E    +
Sbjct: 172 PIY-HDSGDAIFVMDQIRDEKSEDETWIDGIALREAMRRLNNREKHILNLRFF-EGRTQM 229

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESI 284
           E ++ E  +S+ +V ++E  A K ++++I
Sbjct: 230 E-VADEIGISQAQVSRLEKTALKHMRKNI 257


>gi|303239292|ref|ZP_07325820.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302593078|gb|EFL62798.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 236

 Score = 49.3 bits (116), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 33/95 (34%), Positives = 48/95 (50%), Gaps = 2/95 (2%)

Query: 16  LSRYIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           L  Y+  +   P  L   EE    K  +E GD  A + L+  +LRLV  I   Y      
Sbjct: 19  LFGYVSNVNSFPQPLSPDEEQHYIKLLKE-GDEEARNILIERNLRLVAHIVKKYNATIGD 77

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             +++S G IGL++A+  F+ E+G RLATY+   I
Sbjct: 78  CDDLISIGTIGLIKAIATFNHEKGTRLATYAARCI 112


>gi|251733405|emb|CAR82452.1| RNA polymerase sigma factor [Ensifer adhaerens]
 gi|251733407|emb|CAR82453.1| RNA polymerase sigma factor [Ensifer adhaerens]
 gi|251733425|emb|CAR82462.1| RNA polymerase sigma factor [Ensifer adhaerens]
 gi|251733427|emb|CAR82463.1| RNA polymerase sigma factor [Ensifer adhaerens]
 gi|251733429|emb|CAR82464.1| RNA polymerase sigma factor [Ensifer adhaerens]
 gi|251733431|emb|CAR82465.1| RNA polymerase sigma factor [Ensifer adhaerens]
 gi|251733433|emb|CAR82466.1| RNA polymerase sigma factor [Ensifer adhaerens]
 gi|251733435|emb|CAR82467.1| RNA polymerase sigma factor [Ensifer adhaerens]
 gi|251733437|emb|CAR82468.1| RNA polymerase sigma factor [Ensifer adhaerens]
          Length = 202

 Score = 49.3 bits (116), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 35/87 (40%), Positives = 50/87 (57%), Gaps = 15/87 (17%)

Query: 13  EIGLSRYIHEIRKI-PMLEKQE-EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           E G+S  I E R+I  M++K E E  +AK+            +V ++LRLV+ IA  Y  
Sbjct: 129 ETGIS--IAEFRRIVSMVQKGEREARIAKK-----------EMVEANLRLVISIAKKYTN 175

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPER 97
            GL   +++ EGNIGLM+AV KF+  R
Sbjct: 176 RGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|251733387|emb|CAR82443.1| RNA polymerase sigma factor [Sinorhizobium kostiense]
 gi|251733389|emb|CAR82444.1| RNA polymerase sigma factor [Sinorhizobium kostiense]
 gi|251733391|emb|CAR82445.1| RNA polymerase sigma factor [Sinorhizobium kostiense]
          Length = 202

 Score = 49.3 bits (116), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 35/87 (40%), Positives = 50/87 (57%), Gaps = 15/87 (17%)

Query: 13  EIGLSRYIHEIRKI-PMLEKQE-EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           E G+S  I E R+I  M++K E E  +AK+            +V ++LRLV+ IA  Y  
Sbjct: 129 ETGIS--IAEFRRIVSMVQKGEREARIAKK-----------EMVEANLRLVISIAKKYTN 175

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPER 97
            GL   +++ EGNIGLM+AV KF+  R
Sbjct: 176 RGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|121488757|emb|CAJ18263.1| sigma 70-type sigma factor [Chlorobium phaeobacteroides]
          Length = 163

 Score = 49.3 bits (116), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 17/46 (36%), Positives = 33/46 (71%)

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + +     +V++
Sbjct: 1   EGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL 46


>gi|292905274|ref|YP_003541145.1| sigma-70 region 2-containing protein [Anabaena variabilis ATCC
           29413]
 gi|75705012|gb|ABA24687.1| Sigma-70 region 2 [Anabaena variabilis ATCC 29413]
          Length = 240

 Score = 49.3 bits (116), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 24/91 (26%), Positives = 47/91 (51%), Gaps = 1/91 (1%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR-GYGLPISEVVSEGNIGLMQAVKKFDP 95
           L + YR +       R+   H +L  +IA  YR     P+ +++    +G++ A+++FDP
Sbjct: 5   LFREYRNNPTRQLRDRIFNHHYKLACEIAHQYRICCDEPLEDLIQLAGVGMLTAIERFDP 64

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            R    ++++  +IK  ++ Y+    S VKI
Sbjct: 65  SRSNAFSSFACPYIKGEIRHYLRDKASTVKI 95


>gi|118443097|ref|YP_878334.1| sporulation sigma factor SigG [Clostridium novyi NT]
 gi|118133553|gb|ABK60597.1| Specialized DNA-dependent RNA polymerase sigma subunit [Clostridium
           novyi NT]
          Length = 256

 Score = 49.3 bits (116), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 62/278 (22%), Positives = 128/278 (46%), Gaps = 53/278 (19%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+++E   L  + ++ GD  +  + V  +LRLV+ +   +   G  + ++   G I
Sbjct: 14  KLPVLKEKEMKELLLKMKD-GDNLSREKFVRGNLRLVLSVIQRFNNRGENVDDLFQVGCI 72

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD  +  + +TY++  I   ++ Y LR  + +++  +         LR +  
Sbjct: 73  GLIKAIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNSIRVSRS---------LRDIAY 122

Query: 145 HLQAITDNNLKPE----QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
               + D  +K E     V  IAK+L++   EV+          +L+A+           
Sbjct: 123 KALQVRDKIIKKENKDPNVSRIAKELDLPREEVVF---------ALDAI----------- 162

Query: 201 QDWL-----VYDHDGQEQVLIEKEERKNRRNM---------LTRSMSVLNPRERRIFEAR 246
           QD +     +Y HDG + + +  ++  + +N+         +  +M  LN RE+ I   R
Sbjct: 163 QDPVSLFEPIY-HDGGDALYV-MDQISDSKNVDESWIENISIKEAMKRLNEREKMILNMR 220

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             Q    T   ++ E  +S+ +V ++E  A K +++ +
Sbjct: 221 FFQGR--TQMEVADEIGISQAQVSRLEKTALKHMRKYV 256


>gi|308172341|ref|YP_003919046.1| RNA polymerase sigma-37 factor sigma B [Bacillus amyloliquefaciens
           DSM 7]
 gi|307605205|emb|CBI41576.1| RNA polymerase sigma-37 factor (sigma(B)) [Bacillus
           amyloliquefaciens DSM 7]
 gi|328552153|gb|AEB22645.1| RNA polymerase sigma factor SigB [Bacillus amyloliquefaciens TA208]
 gi|328910426|gb|AEB62022.1| RNA polymerase sigma-37 factor (sigma(B)) [Bacillus
           amyloliquefaciens LL3]
          Length = 262

 Score = 49.3 bits (116), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 64/263 (24%), Positives = 124/263 (47%), Gaps = 18/263 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE-GN 83
           K   L K E   L   ++ H +  A   LV  +  LV  +A  Y   G    E + + G 
Sbjct: 6   KTTKLTKDEVDRLILDFQIHDNKEAQETLVEVYTNLVEMLAKKY-SKGKSFHEDLRQVGM 64

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRL 142
           IGL+ A+K++DPE G     +++  I   ++ ++  ++WS+         +R+     R+
Sbjct: 65  IGLLGAIKRYDPEVGKSFEAFAIPTIIGEIKRFLRDKTWSV------HVPRRIKELGPRI 118

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQ 201
           K  +  +T    +  +V  IA  L+VSE EV+     +   +S  AL ++ S +  +   
Sbjct: 119 KMAVDQLTTETQRSPKVEEIAAFLDVSEEEVLET---MEMGKSYQALSVDHSIEADADGS 175

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
              + D  G ++   E  ER N++ M+   + VL+ RE++I +   +Q    + +     
Sbjct: 176 TVTILDIVGSQE---EGYERVNQQMMIKSVLHVLSDREKQIIDLTFVQNK--SQKETGDI 230

Query: 262 FEVSRERVRQIEARAFKKVQESI 284
             +S+  V +++ +A KK++E++
Sbjct: 231 LGISQMHVSRLQRKAVKKLREAL 253


>gi|251733373|emb|CAR82436.1| RNA polymerase sigma factor [Sinorhizobium arboris LMG 14919]
 gi|251733375|emb|CAR82437.1| RNA polymerase sigma factor [Sinorhizobium arboris]
 gi|251733377|emb|CAR82438.1| RNA polymerase sigma factor [Sinorhizobium arboris]
 gi|251733393|emb|CAR82446.1| RNA polymerase sigma factor [Sinorhizobium medicae]
 gi|251733395|emb|CAR82447.1| RNA polymerase sigma factor [Sinorhizobium medicae]
 gi|251733397|emb|CAR82448.1| RNA polymerase sigma factor [Sinorhizobium medicae]
 gi|251733399|emb|CAR82449.1| RNA polymerase sigma factor [Sinorhizobium meliloti]
 gi|251733401|emb|CAR82450.1| RNA polymerase sigma factor [Sinorhizobium meliloti]
 gi|251733403|emb|CAR82451.1| RNA polymerase sigma factor [Sinorhizobium meliloti]
          Length = 202

 Score = 49.3 bits (116), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 35/87 (40%), Positives = 50/87 (57%), Gaps = 15/87 (17%)

Query: 13  EIGLSRYIHEIRKI-PMLEKQE-EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           E G+S  I E R+I  M++K E E  +AK+            +V ++LRLV+ IA  Y  
Sbjct: 129 ETGIS--IAEFRRIVSMVQKGEREARIAKK-----------EMVEANLRLVISIAKKYTN 175

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPER 97
            GL   +++ EGNIGLM+AV KF+  R
Sbjct: 176 RGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|257457436|ref|ZP_05622606.1| RNA polymerase sigma-D factor [Treponema vincentii ATCC 35580]
 gi|257445165|gb|EEV20238.1| RNA polymerase sigma-D factor [Treponema vincentii ATCC 35580]
          Length = 262

 Score = 49.3 bits (116), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 56/229 (24%), Positives = 102/229 (44%), Gaps = 22/229 (9%)

Query: 61  VVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           +VK   G    G+P      ++V  G  GL+ A+ K+DPE+  +  TY++  I+ A+ + 
Sbjct: 37  LVKYVAGKVAVGMPNNVEFDDLVGYGVFGLLDAIDKYDPEKNVKFNTYAVTRIRGAIFDE 96

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITDNNLKPEQVVAIAKKLNVSESEVIS 175
            LRS   V        + +   +  L+  L  A TD+         IA+ L +S  E   
Sbjct: 97  -LRSIDWVPRSVRQQSREIEEVIADLEARLGHAATDSE--------IAEALGMSVEEFHQ 147

Query: 176 MNCRLAGDE--SLNAL-INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           +  +++G    SL  L   + D   +   D +         V++E+EE K    ++  ++
Sbjct: 148 VLLKISGTSIISLTDLRFGADDSEQTPVADSIEAPTSLNPDVIVEREEMK---RIIVDAI 204

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           + L  RE+++      ++  +TL  +    EV+  RV QI   A  K++
Sbjct: 205 NELPDREKKVLIMYYYED--MTLREIGKVLEVTESRVSQIHTSANLKLK 251


>gi|260438829|ref|ZP_05792645.1| RNA polymerase sigma-G factor [Butyrivibrio crossotus DSM 2876]
 gi|292808819|gb|EFF68024.1| RNA polymerase sigma-G factor [Butyrivibrio crossotus DSM 2876]
          Length = 260

 Score = 49.3 bits (116), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 28/102 (27%), Positives = 57/102 (55%), Gaps = 2/102 (1%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L  +E+  L  + + +GD +A  R +  +LRLV+ +   + G G  + ++   G I
Sbjct: 15  KLPLLSTKEKEELIIKVK-NGDKAARERYIKCNLRLVLSVVKRFSGNGENMDDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           GL++A+  FD     + +TY++  I   ++ + LR  S +++
Sbjct: 74  GLIKAIDNFDMSLNVKFSTYAVPMIIGEIRRF-LRDNSQIRV 114


>gi|295836278|ref|ZP_06823211.1| RNA polymerase sigma-27 factor [Streptomyces sp. SPB74]
 gi|197697357|gb|EDY44290.1| RNA polymerase sigma-27 factor [Streptomyces sp. SPB74]
          Length = 279

 Score = 49.3 bits (116), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 59/250 (23%), Positives = 106/250 (42%), Gaps = 34/250 (13%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFDPE 96
           Y+  GD     +L+  H   +VK   G    GLP     ++ VS G  GL+ A++KFD E
Sbjct: 37  YKTTGDARLREQLIL-HYSPLVKYVAGRVSVGLPPNVEQADFVSSGVFGLIDAIEKFDIE 95

Query: 97  RGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTA-NQKRLFFN----LRRLKGHLQAIT 150
           R  +  TY++  I+ AM  E     W    +   A N +R +      LRR     +   
Sbjct: 96  RSIKFETYAITRIRGAMIDELRALDWIPRSVRQKARNVERAYATLEAKLRRTPSEAEVAR 155

Query: 151 DNNLKPEQVVAIAKKLN----VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +  +  E + A+  +L+    V+  E++S+     G  S+   +  +D ++         
Sbjct: 156 EMGVGVEDLHAVFSQLSLANVVALEELLSVGSEGGGRLSIMDTLEDTDADNP-------- 207

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
                    +E  E +  R +L+R+++ L  RE+ +      +   +TL  +     V+ 
Sbjct: 208 ---------VEVAEGRELRRLLSRAINSLPEREKTVVMLYYYE--GLTLAEIGHVLGVTE 256

Query: 267 ERVRQIEARA 276
            RV QI  ++
Sbjct: 257 SRVSQIHTKS 266


>gi|149175161|ref|ZP_01853784.1| sigma-70 factor [Planctomyces maris DSM 8797]
 gi|148846139|gb|EDL60479.1| sigma-70 factor [Planctomyces maris DSM 8797]
          Length = 349

 Score = 49.3 bits (116), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 32/114 (28%), Positives = 57/114 (50%), Gaps = 29/114 (25%)

Query: 26  IPMLEKQEEYVL----------AKRYREHGDLSA---------------AHRL----VTS 56
           +P+L+K++E +L          A++ +   DL +               A RL    + +
Sbjct: 114 VPLLDKEQEVILFRGMNYLKYRAEKLKSQIDLKSPCIGLLDRIEQKLKDARRLRNYIIQA 173

Query: 57  HLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           +LRLVV IA           ++VS+G++ L++AV+ FD +RG R +TY  W ++
Sbjct: 174 NLRLVVSIAKNLTDRANLFEDIVSDGHLPLIRAVEIFDVDRGNRFSTYGTWAVR 227


>gi|323705266|ref|ZP_08116841.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
 gi|323535168|gb|EGB24944.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
          Length = 231

 Score = 49.3 bits (116), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 39/67 (58%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           ++GD  A + L+  +LRLV  +   Y   G  + +++S G IGL++A+  +D  +G  LA
Sbjct: 45  KNGDEEAKNILIERNLRLVAHVVKKYSNAGKDVDDLISIGTIGLIKAILTYDSSKGTHLA 104

Query: 103 TYSMWWI 109
           TY+   I
Sbjct: 105 TYAARCI 111


>gi|251733351|emb|CAR82425.1| RNA polymerase sigma factor [Mesorhizobium loti]
          Length = 202

 Score = 49.3 bits (116), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 23/49 (46%), Positives = 32/49 (65%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 154 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|251733349|emb|CAR82424.1| RNA polymerase sigma factor [Sinorhizobium americanum]
 gi|251733415|emb|CAR82457.1| RNA polymerase sigma factor [Sinorhizobium terangae]
 gi|251733417|emb|CAR82458.1| RNA polymerase sigma factor [Sinorhizobium terangae]
 gi|251733419|emb|CAR82459.1| RNA polymerase sigma factor [Sinorhizobium terangae]
          Length = 202

 Score = 49.3 bits (116), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 35/87 (40%), Positives = 50/87 (57%), Gaps = 15/87 (17%)

Query: 13  EIGLSRYIHEIRKI-PMLEKQE-EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           E G+S  I E R+I  M++K E E  +AK+            +V ++LRLV+ IA  Y  
Sbjct: 129 ETGIS--IAEFRRIVSMVQKGEREARIAKK-----------EMVEANLRLVISIAKKYTN 175

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPER 97
            GL   +++ EGNIGLM+AV KF+  R
Sbjct: 176 RGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|328948392|ref|YP_004365729.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Treponema
           succinifaciens DSM 2489]
 gi|328448716|gb|AEB14432.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Treponema
           succinifaciens DSM 2489]
          Length = 262

 Score = 49.3 bits (116), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 59/256 (23%), Positives = 120/256 (46%), Gaps = 21/256 (8%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGN 83
           +L++ EE  L   Y++   ++   RL+  ++ LV  +A G    G+P S    ++V  G 
Sbjct: 5   ILDENEEAELWHEYKKSKSVAIRDRLIRQYMPLVKWVA-GRVSTGMPDSVEFDDLVGFGQ 63

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
            GL+ A+ KFD ++G +  TY+   I+ A+ +  LR    V        + +   +  L+
Sbjct: 64  FGLLDAINKFDIDKGVKFKTYATTRIRGAIFDE-LRELDWVPRSVRQKSREIEDTIVELE 122

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSS-QW 200
             L     +         IAK +N++E+E  S   +++G    SLN +  S D++     
Sbjct: 123 SKLGRTASD-------AEIAKAMNMTEAEYQSAVMKVSGTSVLSLNDVWYSGDESEHVSI 175

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
            D +   +     V++E+EE    R ++ ++++ L P+  ++       E+ ++ + +  
Sbjct: 176 GDSIEAPNSLNPDVIVEREE---IRRVIIQAINEL-PKNEKMVIVLYYHED-LSFKEIGQ 230

Query: 261 EFEVSRERVRQIEARA 276
              VS  R+ Q+ ++A
Sbjct: 231 VLNVSESRISQLHSKA 246


>gi|251733409|emb|CAR82454.1| RNA polymerase sigma factor [Sinorhizobium saheli]
 gi|251733411|emb|CAR82455.1| RNA polymerase sigma factor [Sinorhizobium saheli]
 gi|251733413|emb|CAR82456.1| RNA polymerase sigma factor [Sinorhizobium saheli]
          Length = 202

 Score = 49.3 bits (116), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 35/87 (40%), Positives = 50/87 (57%), Gaps = 15/87 (17%)

Query: 13  EIGLSRYIHEIRKI-PMLEKQE-EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           E G+S  I E R+I  M++K E E  +AK+            +V ++LRLV+ IA  Y  
Sbjct: 129 ETGIS--IAEFRRIVSMVQKGEREARIAKK-----------EMVEANLRLVISIAKKYTN 175

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPER 97
            GL   +++ EGNIGLM+AV KF+  R
Sbjct: 176 RGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|251733363|emb|CAR82431.1| RNA polymerase sigma factor [Agrobacterium rhizogenes]
 gi|251733369|emb|CAR82434.1| RNA polymerase sigma factor [Rhizobium tropici]
 gi|251733371|emb|CAR82435.1| RNA polymerase sigma factor [Rhizobium tropici]
          Length = 202

 Score = 49.3 bits (116), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 35/87 (40%), Positives = 50/87 (57%), Gaps = 15/87 (17%)

Query: 13  EIGLSRYIHEIRKI-PMLEKQE-EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           E G+S  I E R+I  M++K E E  +AK+            +V ++LRLV+ IA  Y  
Sbjct: 129 ETGIS--ISEFRRIVHMVQKGEREARIAKK-----------EMVEANLRLVISIAKKYTN 175

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPER 97
            GL   +++ EGNIGLM+AV KF+  R
Sbjct: 176 RGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|327537603|gb|EGF24315.1| RNA polymerase ECF-type sigma factor [Rhodopirellula baltica WH47]
          Length = 340

 Score = 49.3 bits (116), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 55/230 (23%), Positives = 98/230 (42%), Gaps = 66/230 (28%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R+V ++LRLV  I   +        +++S+G + L++AV+KFD +RGFR +TY+   ++ 
Sbjct: 164 RIVEANLRLVFSIVKKFVNPNNTFDDLLSDGIVALIRAVEKFDFDRGFRFSTYATQVVRR 223

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
                   S+  V +     QK        ++G LQ +                ++VSE 
Sbjct: 224 -------NSYRTVVLKQQERQK--------VQGGLQDM---------------DIDVSEE 253

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           E                   SS  +  +W       H+ + ++ +   +   R   + R+
Sbjct: 254 E------------------RSSAISEKRW-------HELRSRLSVMLGDLDRREKFIIRA 288

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              L P  R++           TL++L+    VS+ERVRQ+E RA  K++
Sbjct: 289 RFSLGP-HRKVH----------TLQSLADRLGVSKERVRQLERRAMDKLR 327


>gi|251733379|emb|CAR82439.1| RNA polymerase sigma factor [Sinorhizobium fredii]
 gi|251733381|emb|CAR82440.1| RNA polymerase sigma factor [Sinorhizobium fredii]
 gi|251733383|emb|CAR82441.1| RNA polymerase sigma factor [Sinorhizobium fredii]
 gi|251733385|emb|CAR82442.1| RNA polymerase sigma factor [Sinorhizobium fredii]
 gi|251733421|emb|CAR82460.1| RNA polymerase sigma factor [Sinorhizobium xinjiangense]
 gi|251733423|emb|CAR82461.1| RNA polymerase sigma factor [Sinorhizobium xinjiangense]
          Length = 202

 Score = 49.3 bits (116), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 35/87 (40%), Positives = 50/87 (57%), Gaps = 15/87 (17%)

Query: 13  EIGLSRYIHEIRKI-PMLEKQE-EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           E G+S  I E R+I  M++K E E  +AK+            +V ++LRLV+ IA  Y  
Sbjct: 129 ETGIS--IAEFRRIVSMVQKGEREARIAKK-----------EMVEANLRLVISIAKKYTN 175

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPER 97
            GL   +++ EGNIGLM+AV KF+  R
Sbjct: 176 RGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|126698826|ref|YP_001087723.1| sporulation sigma factor SigK [Clostridium difficile 630]
 gi|26000675|gb|AAN75197.1| sigma K [Clostridium difficile]
 gi|26000677|gb|AAN75198.1| sigma K [Clostridium difficile]
          Length = 213

 Score = 49.3 bits (116), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 26/82 (31%), Positives = 46/82 (56%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L  +EE     +++   D SA   L+  ++RLV  IA  Y        +++S G IGL++
Sbjct: 11  LTPEEEIEYLTKFKIENDKSAKDTLIERNMRLVAYIAKKYNNSTEDQDDLISIGTIGLIK 70

Query: 89  AVKKFDPERGFRLATYSMWWIK 110
           A++ ++ ++G RLATY+   I+
Sbjct: 71  AIETYNIDKGTRLATYASRCIE 92


>gi|284043274|ref|YP_003393614.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
 gi|283947495|gb|ADB50239.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
          Length = 258

 Score = 49.3 bits (116), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 40/137 (29%), Positives = 65/137 (47%), Gaps = 9/137 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E+ L +R+ E  D  A   L+   + LV  +A  Y   G P+ ++   G +GL++AV +
Sbjct: 16  DEHELLRRWHEERDEDARRALIERMMPLVRSLARRYANRGEPLDDLEQVGCVGLIKAVDR 75

Query: 93  FDPERGFRLATYSMWWIKAAMQEYIL-RSWSL-VKIGTTANQKRLFFNLRRLK---GHLQ 147
           FD  R  R +T+++  I   ++ +   R+WS+ V  G      R+     RL    G   
Sbjct: 76  FDLSRELRFSTFAVPTILGEIKRHFRDRAWSVRVSRGLQELSARVTREADRLSTKLGRSP 135

Query: 148 AITD----NNLKPEQVV 160
            I D     N  PEQV+
Sbjct: 136 TIEDLAEATNSTPEQVL 152


>gi|255655251|ref|ZP_05400660.1| sporulation sigma factor SigK [Clostridium difficile QCD-23m63]
 gi|296451236|ref|ZP_06892976.1| RNA polymerase sigma-E factor [Clostridium difficile NAP08]
 gi|296880412|ref|ZP_06904375.1| RNA polymerase sigma-E factor [Clostridium difficile NAP07]
 gi|296259842|gb|EFH06697.1| RNA polymerase sigma-E factor [Clostridium difficile NAP08]
 gi|296428653|gb|EFH14537.1| RNA polymerase sigma-E factor [Clostridium difficile NAP07]
          Length = 138

 Score = 49.3 bits (116), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 26/82 (31%), Positives = 46/82 (56%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L  +EE     +++   D SA   L+  ++RLV  IA  Y        +++S G IGL++
Sbjct: 11  LTPEEEIEYLTKFKIENDKSAKDTLIERNMRLVAYIAKKYNNSTEDQDDLISIGTIGLIK 70

Query: 89  AVKKFDPERGFRLATYSMWWIK 110
           A++ ++ ++G RLATY+   I+
Sbjct: 71  AIETYNIDKGTRLATYASRCIE 92


>gi|239827600|ref|YP_002950224.1| sporulation sigma factor SigF [Geobacillus sp. WCH70]
 gi|239807893|gb|ACS24958.1| RNA polymerase, sigma 28 subunit, SigF [Geobacillus sp. WCH70]
          Length = 250

 Score = 49.3 bits (116), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 57/259 (22%), Positives = 116/259 (44%), Gaps = 29/259 (11%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           ++ QE   L +R +E GD  A   ++  ++RLV  +   +   G    ++   G IGL++
Sbjct: 12  IKDQEMKELIRRSQE-GDQEARDEIIEKNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLK 70

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           +V KFD     + +TY++  I   +Q +I R    VK+  +   K +   +R+ K  L  
Sbjct: 71  SVDKFDLSYDVKFSTYAVPMIIGEIQRFI-RDDGTVKVSRSL--KEMGNKIRKAKDEL-- 125

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
            +    +   V  IA  L +S  +V+     +    S++                 VY++
Sbjct: 126 -SKKQGRAPTVTEIADYLEISPEDVVLAQEAIRSPASIHE---------------TVYEN 169

Query: 209 DGQEQVLIEKEERKNR-----RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           DG    L+++    +      +  L +++  L+ RER I   R  ++   T   ++S   
Sbjct: 170 DGDPITLLDQIADSDEVSWFDKIALKKAIEELDERERLIVYLRYYKDQ--TQSEVASRLG 227

Query: 264 VSRERVRQIEARAFKKVQE 282
           +S+ +V ++E +  ++++E
Sbjct: 228 ISQVQVSRLEKKILQQIKE 246


>gi|295696440|ref|YP_003589678.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
 gi|295412042|gb|ADG06534.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
          Length = 256

 Score = 49.3 bits (116), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 58/246 (23%), Positives = 111/246 (45%), Gaps = 22/246 (8%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A   LV  + RLV  +   + G G    ++   G IGLM+A+ KFD     + +
Sbjct: 27  QSGDAGARETLVLFNQRLVWSVVQRFLGRGYEPEDLFQIGCIGLMKAIDKFDLSYDVKFS 86

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I   +Q + LR    VK+  +   K    ++RR +  L        +   +  +
Sbjct: 87  TYAVPMIIGEIQRF-LRDDGTVKVSRSV--KETARHIRRARDELAKRLG---RQPHINEL 140

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A++L +  +EV+     +    S++  +  +D +     D          Q+  E++E+ 
Sbjct: 141 AEELGMDPAEVVFTQDAMRAPASIHETVFENDGDPILLMD----------QIADEEQEKW 190

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             R  LT +++ L  RER I   R  ++   T   ++    +S+ +V ++E    KK+  
Sbjct: 191 FDRLALTDALNRLPERERLIVFLRFFRDK--TQSEVAEVLGISQVQVSRLE----KKILN 244

Query: 283 SIQKQV 288
            I++Q+
Sbjct: 245 RIRRQL 250


>gi|298708236|emb|CBJ48299.1| rpoD [Ectocarpus siliculosus]
          Length = 381

 Score = 49.3 bits (116), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 27/80 (33%), Positives = 46/80 (57%), Gaps = 2/80 (2%)

Query: 49  AAHRLVTSHLRLVVKIAMGYR--GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           A   L   H  LV  +A  Y+     L + ++  EGN+GL++AV+KFD  +G R ++Y++
Sbjct: 113 AQRTLALCHQGLVRSVAYRYKQVSRNLSLDDLTQEGNVGLLEAVEKFDSTKGTRFSSYAV 172

Query: 107 WWIKAAMQEYILRSWSLVKI 126
           + IKA++   I     LV++
Sbjct: 173 FRIKASVLRAIADKDRLVRV 192


>gi|296133019|ref|YP_003640266.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           sp. JR]
 gi|296031597|gb|ADG82365.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           potens JR]
          Length = 262

 Score = 48.9 bits (115), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 47/182 (25%), Positives = 83/182 (45%), Gaps = 25/182 (13%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQAVKK 92
           L  R+++  DL+A  +L+  +  LV  +A G     LP +    +++S G  GL+ A++K
Sbjct: 13  LWDRFKKERDLAAREQLILKYAPLVKYVA-GRLAISLPPNVQQDDLISYGIFGLIDAIEK 71

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+PER  +  TY++  IK A+ +  LRS   +        K L     RL+  L      
Sbjct: 72  FEPERNIKFETYAISRIKGAIWDG-LRSMDWIPYSIRQKAKELEETYARLENELG----- 125

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +P     + + L +++ +  S    L  + S  +L++         +D  V+D DG  
Sbjct: 126 --RPATDEEMCETLGITKQQFYS----LLQETSCTSLLS--------LEDLFVFDRDGTN 171

Query: 213 QV 214
            V
Sbjct: 172 GV 173


>gi|261416067|ref|YP_003249750.1| putative RNA polymerase, sigma 70 family subunit [Fibrobacter
           succinogenes subsp. succinogenes S85]
 gi|261372523|gb|ACX75268.1| putative RNA polymerase, sigma 70 family subunit [Fibrobacter
           succinogenes subsp. succinogenes S85]
 gi|302327561|gb|ADL26762.1| sigma-70 factor family protein [Fibrobacter succinogenes subsp.
           succinogenes S85]
          Length = 376

 Score = 48.9 bits (115), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 75/299 (25%), Positives = 131/299 (43%), Gaps = 43/299 (14%)

Query: 1   MNRKNMSIIVNGEIG----LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTS 56
           +N K+ S I +  I     L  +I  +RKI   +K+E   +  +  E G   A  R +  
Sbjct: 70  VNYKDFSCIFDAVIAAEPLLENFIEYVRKIQPADKKEMVRIQYQLFE-GHEYARKRAIEG 128

Query: 57  HLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           +LR+ V +A  YR    Y   I + + E  + L+ A   + P+     A+Y    I  A+
Sbjct: 129 NLRIAVILA--YRESVAYNKNIVDCIGEACLALVSACNSYKPDEHQTFASY----ISIAV 182

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL-KPEQVVAIAKKLNVSE-- 170
            +Y+ R+  +       N   L    R+L    + I  N L K + ++ +     + E  
Sbjct: 183 FDYLARTIGVPFFSIPVNIVNL---CRKL---YKDIKYNRLGKKDALLYVCSCYGLEEYW 236

Query: 171 SEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE---ERKNRR 225
           S V+   ++     ++ L+ ++++            VY     E  L + E   ERKN +
Sbjct: 237 SNVLYDILHVFFLDEDVLDNVLDN------------VYSESCYENFLTDVENDIERKNVQ 284

Query: 226 NMLTRSMS-VLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            ++ R ++  L  RE  + E R     ++  +L  L S   VSRER+RQIE +A  K++
Sbjct: 285 ILINRCLNECLTDREYNVVEHRYGLNGKDSHSLVELGSHQVVSRERIRQIEKKALTKLE 343


>gi|167464139|ref|ZP_02329228.1| DNA-directed RNA polymerase sigma subunit D [Paenibacillus larvae
           subsp. larvae BRL-230010]
 gi|322382365|ref|ZP_08056272.1| RNA polymerase sigma factor SigD-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321153718|gb|EFX46093.1| RNA polymerase sigma factor SigD-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 262

 Score = 48.9 bits (115), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 50/174 (28%), Positives = 86/174 (49%), Gaps = 18/174 (10%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKK 92
           L K ++E G L A   L+  +L LV  ++      GLP      ++ S G +GLM AV+K
Sbjct: 14  LWKAWKEAGCLEAKQSLLEQYLPLVDYVS-SRMSNGLPRNVAKEDLASFGVLGLMDAVEK 72

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH-LQAITD 151
           FD  RG +  TY+ W I  A+ +  LR    V        K++    ++L+ H L+ +TD
Sbjct: 73  FDHTRGLQFETYASWRILGAVIDG-LRQGDWVPRSLREKAKKIEDAYQKLEQHYLRTVTD 131

Query: 152 NNL------KPEQVVAIAKKLNVSESEVISMNCRLAGDES---LNALINSSDKN 196
             +      + E+   + +++NV  + + S++  +  +ES   L+ LI+   KN
Sbjct: 132 AEISEYLGVEEEEFRQMLQEINV--TSICSVDDPIKEEESETRLSLLIDEKAKN 183


>gi|156636391|gb|ABU92466.1| RpoD [Vibrio vulnificus]
          Length = 202

 Score = 48.9 bits (115), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 23/49 (46%), Positives = 32/49 (65%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 154 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|212638845|ref|YP_002315365.1| sporulation sigma factor SigF [Anoxybacillus flavithermus WK1]
 gi|212560325|gb|ACJ33380.1| Stage II sporulation protein AC, DNA-directed RNA polymerase
           sporulation-specific sigma factor (sigma-F)
           [Anoxybacillus flavithermus WK1]
          Length = 247

 Score = 48.9 bits (115), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 54/242 (22%), Positives = 109/242 (45%), Gaps = 19/242 (7%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R  + GD  A   ++  ++RLV  +   +   G    ++   G IGLM++V KFD     
Sbjct: 20  RRSQQGDQQARDEIIEKNMRLVWSVVQRFLNRGYEPEDLFQIGCIGLMKSVDKFDLSYDV 79

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY++  I   +Q +I R    VK+  +   K +   +R+ K  L   +  N +   V
Sbjct: 80  KFSTYAVPMILGEIQRFI-RDDGSVKVSRSL--KEIGNKIRKAKDEL---SKQNGRVPTV 133

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IA+ L +S  +V+     +    S++  +  +D +     D +  + D    V  +K 
Sbjct: 134 NEIAQFLQISPEDVVLAQEAVRSPTSIHETVYENDGDPITLLDQIADEQD----VWFDK- 188

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
                   L ++M  L+ RER I   R  ++   T   +++   +S+ +V ++E +  ++
Sbjct: 189 ------IALKKAMEELDERERLIVYLRYYKDQ--TQSEVAARLGISQVQVSRLEKKILQQ 240

Query: 280 VQ 281
           ++
Sbjct: 241 MK 242


>gi|156636373|gb|ABU92457.1| RpoD [Vibrio vulnificus]
 gi|156636375|gb|ABU92458.1| RpoD [Vibrio vulnificus]
 gi|156636377|gb|ABU92459.1| RpoD [Vibrio vulnificus]
 gi|156636379|gb|ABU92460.1| RpoD [Vibrio vulnificus]
 gi|156636381|gb|ABU92461.1| RpoD [Vibrio vulnificus]
 gi|156636383|gb|ABU92462.1| RpoD [Vibrio vulnificus]
 gi|156636385|gb|ABU92463.1| RpoD [Vibrio vulnificus]
 gi|156636387|gb|ABU92464.1| RpoD [Vibrio vulnificus]
 gi|156636389|gb|ABU92465.1| RpoD [Vibrio vulnificus]
 gi|156636393|gb|ABU92467.1| RpoD [Vibrio vulnificus]
 gi|156636397|gb|ABU92469.1| RpoD [Vibrio vulnificus]
 gi|156636399|gb|ABU92470.1| RpoD [Vibrio vulnificus]
 gi|156636401|gb|ABU92471.1| RpoD [Vibrio vulnificus]
 gi|156636403|gb|ABU92472.1| RpoD [Vibrio vulnificus]
 gi|156636405|gb|ABU92473.1| RpoD [Vibrio vulnificus]
 gi|156636407|gb|ABU92474.1| RpoD [Vibrio vulnificus]
 gi|156636409|gb|ABU92475.1| RpoD [Vibrio vulnificus]
 gi|156636411|gb|ABU92476.1| RpoD [Vibrio vulnificus]
 gi|156636413|gb|ABU92477.1| RpoD [Vibrio vulnificus]
 gi|156636415|gb|ABU92478.1| RpoD [Vibrio vulnificus]
 gi|156636417|gb|ABU92479.1| RpoD [Vibrio vulnificus MO6-24/O]
 gi|156636419|gb|ABU92480.1| RpoD [Vibrio vulnificus]
 gi|156636421|gb|ABU92481.1| RpoD [Vibrio vulnificus]
 gi|156636423|gb|ABU92482.1| RpoD [Vibrio vulnificus]
 gi|156636425|gb|ABU92483.1| RpoD [Vibrio vulnificus]
 gi|156636427|gb|ABU92484.1| RpoD [Vibrio vulnificus]
 gi|156636429|gb|ABU92485.1| RpoD [Vibrio vulnificus]
 gi|156636435|gb|ABU92488.1| RpoD [Vibrio vulnificus]
 gi|156636437|gb|ABU92489.1| RpoD [Vibrio vulnificus]
 gi|156636439|gb|ABU92490.1| RpoD [Vibrio vulnificus]
 gi|156636441|gb|ABU92491.1| RpoD [Vibrio vulnificus]
 gi|156636443|gb|ABU92492.1| RpoD [Vibrio vulnificus]
 gi|156636445|gb|ABU92493.1| RpoD [Vibrio vulnificus]
 gi|156636447|gb|ABU92494.1| RpoD [Vibrio vulnificus]
          Length = 202

 Score = 48.9 bits (115), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 23/49 (46%), Positives = 32/49 (65%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 154 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|258515964|ref|YP_003192186.1| RNA polymerase, sigma 28 subunit, SigK [Desulfotomaculum
           acetoxidans DSM 771]
 gi|257779669|gb|ACV63563.1| RNA polymerase, sigma 28 subunit, SigK [Desulfotomaculum
           acetoxidans DSM 771]
          Length = 234

 Score = 48.9 bits (115), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 34/103 (33%), Positives = 55/103 (53%), Gaps = 3/103 (2%)

Query: 9   IVNGEIGLSRYI-HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           +VNG + L  YI +     P+ E++E   L   +   GD  A + L   +LRLV  I   
Sbjct: 13  VVNGLLLLVSYIANNTFPQPLSEEEEAKYLQLLF--EGDEHARNVLTERNLRLVAHIVKK 70

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           +        +++S G IGL++AV  ++PE+G +LATY+   I+
Sbjct: 71  FDKTVGDTDDLISIGTIGLIKAVNTYNPEKGTKLATYAARCIE 113


>gi|156636431|gb|ABU92486.1| RpoD [Vibrio vulnificus]
          Length = 202

 Score = 48.9 bits (115), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 23/49 (46%), Positives = 32/49 (65%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 154 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|251733359|emb|CAR82429.1| RNA polymerase sigma factor [Rhizobium leguminosarum]
          Length = 202

 Score = 48.9 bits (115), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 35/87 (40%), Positives = 50/87 (57%), Gaps = 15/87 (17%)

Query: 13  EIGLSRYIHEIRKI-PMLEKQE-EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           E G+S  I E R+I  M++K E E  +AK+            +V ++LRLV+ IA  Y  
Sbjct: 129 ETGIS--ISEFRRIVHMVQKGEREARIAKK-----------EMVEANLRLVISIAKKYTN 175

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPER 97
            GL   +++ EGNIGLM+AV KF+  R
Sbjct: 176 RGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|251733357|emb|CAR82428.1| RNA polymerase sigma factor [Rhizobium giardinii]
          Length = 202

 Score = 48.9 bits (115), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 35/87 (40%), Positives = 50/87 (57%), Gaps = 15/87 (17%)

Query: 13  EIGLSRYIHEIRKI-PMLEKQE-EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           E G+S  I E R+I  M++K E E  +AK+            +V ++LRLV+ IA  Y  
Sbjct: 129 ETGIS--ISEFRRIVHMVQKGEREARIAKK-----------EMVEANLRLVISIAKKYTN 175

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPER 97
            GL   +++ EGNIGLM+AV KF+  R
Sbjct: 176 RGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|167630136|ref|YP_001680635.1| RNA polymerase sigma-g factor, putative [Heliobacterium
           modesticaldum Ice1]
 gi|167592876|gb|ABZ84624.1| RNA polymerase sigma-g factor, putative [Heliobacterium
           modesticaldum Ice1]
          Length = 265

 Score = 48.9 bits (115), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 61/269 (22%), Positives = 125/269 (46%), Gaps = 35/269 (13%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L   E   L +   + G+ SA  +L++ +LRLV+ +   +   G  + ++   G I
Sbjct: 23  KLPVLTNAEMRTLFQAM-QSGERSAREKLISGNLRLVLSVIQRFTNRGEYVDDLFQVGCI 81

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A+  FD  +  + +TY++  I   ++ Y LR  + +++  +   + + +   +++ 
Sbjct: 82  GLMKAIDNFDLGQNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSL--RDIAYKALQVRD 138

Query: 145 HLQAITDNNLKPEQVVA-IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
           HL     N L  E  V  IA  L     EV+          +L+A+     +  S ++  
Sbjct: 139 HLV----NELSREPTVTEIADALGFPREEVVF---------ALDAI----QEPISLFEP- 180

Query: 204 LVYDHDGQEQVLIEKE--ERKNRRNMLTRSMSV------LNPRERRIFEARRLQENPVTL 255
            +Y HDG + + +  +  + KN+       ++V      LN RE+ I   R  +    T 
Sbjct: 181 -IY-HDGGDPIFVMDQIGDEKNQDAQWLEGIAVREALRRLNDREKLILTLRFFEGK--TQ 236

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESI 284
             ++ E  +S+ +V ++E  A   +++ +
Sbjct: 237 MEVADEIGISQAQVSRLEKAALTHMRKHV 265


>gi|257054261|ref|YP_003132093.1| RNA polymerase sigma factor, sigma-70 family [Saccharomonospora
           viridis DSM 43017]
 gi|256584133|gb|ACU95266.1| RNA polymerase sigma factor, sigma-70 family [Saccharomonospora
           viridis DSM 43017]
          Length = 267

 Score = 48.9 bits (115), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 54/235 (22%), Positives = 100/235 (42%), Gaps = 18/235 (7%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RLVT HL L   IA  + G G+   ++V    +GL+ AV +FDP RG    ++++  +  
Sbjct: 42  RLVTGHLPLAEHIAQRFSGRGVAKEDLVQVARVGLINAVDRFDPSRGSDFLSFAVPTVMG 101

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            ++ +   +  ++++      K L  ++      L         P +   IA  L ++  
Sbjct: 102 EVRRHFRDTGWVIRV--PRRLKELHLSINNASTQLSQRLGRAPTPSE---IADHLGLTLE 156

Query: 172 EVISMNCRLAGDESLNALINSS--DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           EV        G E+ NA  + S  +  S+  ++  + D  G+E   +   E       L 
Sbjct: 157 EVFE------GLEAGNAYHSMSLDEVLSADTENLALGDTLGEEDAALAGVENHETLQPLV 210

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + +    P   R   A R   N +T   ++    +S+  V ++ AR  KK++E +
Sbjct: 211 KQL----PERERTILALRFVHN-MTQTQIAERIGISQMHVSRLLARTLKKLREGL 260


>gi|76664996|emb|CAJ17940.1| DNA-directed RNA polymerase sigma subunit [Candidatus Phytoplasma
           solani]
          Length = 110

 Score = 48.9 bits (115), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 24/49 (48%), Positives = 33/49 (67%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A   LV S+ RLVV IA  Y G G+   +++ EGN+GLM+AV KFD ++
Sbjct: 62  AKDSLVESNYRLVVSIAKRYIGRGILFLDLIQEGNMGLMRAVDKFDYQK 110


>gi|32471396|ref|NP_864389.1| RNA polymerase sigma 70 [Rhodopirellula baltica SH 1]
 gi|32443237|emb|CAD72068.1| probable RNA polymerase sigma 70 [Rhodopirellula baltica SH 1]
          Length = 340

 Score = 48.9 bits (115), Expect = 8e-04,   Method: Compositional matrix adjust.
 Identities = 55/230 (23%), Positives = 98/230 (42%), Gaps = 66/230 (28%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R+V ++LRLV  I   +        +++S+G + L++AV+KFD +RGFR +TY+   ++ 
Sbjct: 164 RIVEANLRLVFSIVKKFVNPNNTFDDLLSDGIVALIRAVEKFDFDRGFRFSTYATQVVRR 223

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
                   S+  V +     QK        ++G LQ +                ++VSE 
Sbjct: 224 -------NSYRTVVLKQQERQK--------VQGGLQDM---------------DIDVSEE 253

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           E                   SS  +  +W       H+ + ++ +   +   R   + R+
Sbjct: 254 E------------------RSSAISEKRW-------HELRSRLSVMLGDLDRREKFIIRA 288

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              L P  R++           TL++L+    VS+ERVRQ+E RA  K++
Sbjct: 289 RFSLGP-HRKVH----------TLQSLADRLGVSKERVRQLERRAMDKLR 327


>gi|256379368|ref|YP_003103028.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Actinosynnema mirum DSM 43827]
 gi|255923671|gb|ACU39182.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Actinosynnema mirum DSM 43827]
          Length = 268

 Score = 48.9 bits (115), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 61/244 (25%), Positives = 113/244 (46%), Gaps = 34/244 (13%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LVT HL +   IA  +   G P  ++V    +GL+ AV +FDPERG    ++++  I   
Sbjct: 49  LVTEHLPVARHIARRFGHRGEPHDDLVQVATVGLINAVDRFDPERGSDFLSFAVPTIMGE 108

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           +++Y    SWS V++             RRLK    AI   + +  Q +  A     + S
Sbjct: 109 VRKYFRDSSWS-VRMP------------RRLKELHLAINAGSARLSQELGRAP----TPS 151

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD--------GQEQVLIEK-EERK 222
           E ++ +  L+ +E    L   +  +S+   D LV D          G+E   +E  E+R+
Sbjct: 152 E-LAQHLGLSREEVHEGLAAGNAYHSASLDDLLVADDSSISLGSTLGEEDPELEAIEQRE 210

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +   +L +    L  RERRI   R      +T   ++ +  +S+  V ++ A+  +++++
Sbjct: 211 SLHPLLEK----LPERERRIVVMRFFGN--MTQTQIAQKVGISQMHVSRLLAKTLRQLRD 264

Query: 283 SIQK 286
            +++
Sbjct: 265 GLEQ 268


>gi|159469913|ref|XP_001693104.1| predicted protein [Chlamydomonas reinhardtii]
 gi|158277362|gb|EDP03130.1| predicted protein [Chlamydomonas reinhardtii]
          Length = 525

 Score = 48.9 bits (115), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 27/103 (26%), Positives = 52/103 (50%), Gaps = 5/103 (4%)

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
           Y L   + ++ G  GLM+ + KF P+ G+RL+TY  WWI+ ++++ + R  + +++  + 
Sbjct: 153 YELAFEDALTAGMEGLMRGIHKFRPDSGYRLSTYCTWWIRMSIRKTLSRQSTALQLPLSV 212

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
            Q        RL+     +T     P    A+A +L  S + +
Sbjct: 213 LQSVEALVSARLR-----LTKPGASPPTDEAVAAELGWSMTRI 250


>gi|295399044|ref|ZP_06809026.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|312110351|ref|YP_003988667.1| RNA polymerase, sigma 28 subunit, SigF [Geobacillus sp. Y4.1MC1]
 gi|294978510|gb|EFG54106.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|311215452|gb|ADP74056.1| RNA polymerase, sigma 28 subunit, SigF [Geobacillus sp. Y4.1MC1]
          Length = 250

 Score = 48.9 bits (115), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 58/259 (22%), Positives = 116/259 (44%), Gaps = 19/259 (7%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           R   +L+  E   L +R +E GD  A + ++  ++RLV  +   +   G    ++   G 
Sbjct: 7   RDQTLLKDHEMKKLIRRSQE-GDQQARNEIIQKNMRLVWSVVQRFLNRGYEPDDLFQIGC 65

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL+++V KFD     + +TY++  I   +Q +I R    VK+  +   K     +R+ +
Sbjct: 66  IGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFI-RDDGTVKVSRSL--KETGNKIRKAR 122

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L   +  + +   V  IA  L +S  EV+     +    S++  +  +D +     D 
Sbjct: 123 DEL---SKKHGRAPTVTEIADYLEISPEEVVLAQEAVRSPASIHETVYENDGDPITLLDQ 179

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    D  E    +K         L +++  L+ RER I   R  ++   T   ++S   
Sbjct: 180 IA---DADEASWFDK-------IALKKAIEELDERERLIVYLRYYKDQ--TQSEVASRLG 227

Query: 264 VSRERVRQIEARAFKKVQE 282
           +S+ +V ++E +  ++++E
Sbjct: 228 ISQVQVSRLEKKILQQIKE 246


>gi|226325489|ref|ZP_03801007.1| hypothetical protein COPCOM_03294 [Coprococcus comes ATCC 27758]
 gi|225206232|gb|EEG88586.1| hypothetical protein COPCOM_03294 [Coprococcus comes ATCC 27758]
          Length = 239

 Score = 48.9 bits (115), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 57/251 (22%), Positives = 120/251 (47%), Gaps = 19/251 (7%)

Query: 34  EYVLAKRYREH-GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           ++ +A   R H GD +A  +LV  +  L+  +   + G G    ++   G+IGL++A+ K
Sbjct: 2   DHTIALIRRAHEGDENARAQLVEENTGLIWCVVKRFYGRGTEAEDLFQIGSIGLLKAIDK 61

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD     + +TY++  I   ++ + LR   ++K+  + + K + +   + K   +A+T+ 
Sbjct: 62  FDLGYDVKFSTYAVPMITGEIKRF-LRDDGMLKV--SRSLKEIAYKAYQAK---EALTEK 115

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGD-ESLNALINSSDKNSSQWQDWLVYDHDGQ 211
             +   +  IA++  V + E++ M    AG+ ESL+  +   D N     + +  D  G 
Sbjct: 116 LGREPLLEEIAEETGVEKEELV-MAMEAAGEVESLHRPVGMKDGNEVMLLEKIA-DTGGA 173

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E+ +++         +LT  +  L   ER++   R   +   T   +  E  +S+ +V +
Sbjct: 174 EEKILD-------HLLLTELIKELKKDERKLLYLRYFADKTQT--EIGEELGISQVQVSR 224

Query: 272 IEARAFKKVQE 282
           +E +  K ++E
Sbjct: 225 MEKKILKTMRE 235


>gi|156636395|gb|ABU92468.1| RpoD [Vibrio vulnificus]
 gi|156636449|gb|ABU92495.1| RpoD [Vibrio vulnificus]
 gi|156636451|gb|ABU92496.1| RpoD [Vibrio vulnificus]
 gi|156636453|gb|ABU92497.1| RpoD [Vibrio vulnificus]
 gi|156636459|gb|ABU92500.1| RpoD [Vibrio vulnificus]
 gi|156636463|gb|ABU92502.1| RpoD [Vibrio vulnificus]
 gi|156636465|gb|ABU92503.1| RpoD [Vibrio vulnificus]
 gi|156636467|gb|ABU92504.1| RpoD [Vibrio vulnificus]
 gi|156636469|gb|ABU92505.1| RpoD [Vibrio vulnificus]
 gi|156636471|gb|ABU92506.1| RpoD [Vibrio vulnificus]
 gi|156636473|gb|ABU92507.1| RpoD [Vibrio vulnificus]
 gi|156636477|gb|ABU92509.1| RpoD [Vibrio vulnificus]
 gi|156636479|gb|ABU92510.1| RpoD [Vibrio vulnificus]
 gi|156636481|gb|ABU92511.1| RpoD [Vibrio vulnificus]
 gi|156636483|gb|ABU92512.1| RpoD [Vibrio vulnificus]
 gi|156636485|gb|ABU92513.1| RpoD [Vibrio vulnificus]
 gi|156636487|gb|ABU92514.1| RpoD [Vibrio vulnificus]
 gi|156636489|gb|ABU92515.1| RpoD [Vibrio vulnificus]
 gi|156636491|gb|ABU92516.1| RpoD [Vibrio vulnificus]
 gi|156636493|gb|ABU92517.1| RpoD [Vibrio vulnificus]
          Length = 202

 Score = 48.9 bits (115), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 23/49 (46%), Positives = 32/49 (65%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 154 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|320007063|gb|ADW01913.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 297

 Score = 48.9 bits (115), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 63/244 (25%), Positives = 109/244 (44%), Gaps = 26/244 (10%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISE-VVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + L+  +L LV   A  +R  G   +E ++  G IGL++A+ +FD  R    AT+++ 
Sbjct: 68  ARNTLIEMNLSLVRFAASRFRNRGGDDTEDIIQVGTIGLIKAIDRFDLSREVEFATFAVP 127

Query: 108 WIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           +I   ++ +    +WS   +      + L   L + K  L    D +     V  +A  L
Sbjct: 128 YIVGEIKRFFRDTTWS---VHVPRRLQELRVELAKAKEQLSTKLDRD---PTVAELAAHL 181

Query: 167 NVSESEVI----SMNCRLAGDESLNALINSSDKNSSQ--WQDWLVYDHDGQEQVLIEKEE 220
           ++ E E+I    + N   AG  SL+     SD  S Q  + D L  D  G E V      
Sbjct: 182 DLPEEEIIEGLVAANGYSAG--SLDTPNADSDSGSEQRAYADLLGEDDPGMESV------ 233

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                + L   +  L+ RER+I   R  QE  +T   + +E  VS+  V ++ +R  +++
Sbjct: 234 --ENLHTLAPLLRQLDDRERKIVRMRFGQE--MTQAQIGAELGVSQMHVSRLLSRIVQRL 289

Query: 281 QESI 284
           +  +
Sbjct: 290 RAGM 293


>gi|261417856|ref|YP_003251538.1| sporulation sigma factor SigF [Geobacillus sp. Y412MC61]
 gi|297529524|ref|YP_003670799.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
 gi|319767332|ref|YP_004132833.1| RNA polymerase, sigma 28 subunit, SigF [Geobacillus sp. Y412MC52]
 gi|261374313|gb|ACX77056.1| RNA polymerase, sigma 28 subunit, SigF [Geobacillus sp. Y412MC61]
 gi|297252776|gb|ADI26222.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
 gi|317112198|gb|ADU94690.1| RNA polymerase, sigma 28 subunit, SigF [Geobacillus sp. Y412MC52]
          Length = 252

 Score = 48.9 bits (115), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 56/256 (21%), Positives = 114/256 (44%), Gaps = 19/256 (7%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           ++ QE   L +R +E GD  A   ++  ++RLV  +   +   G    ++   G IGL++
Sbjct: 14  IKDQEMKELIRRSQE-GDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLK 72

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           +V KFD     + +TY++  I   +Q + LR    VK+  +   K +   +R+ K  L  
Sbjct: 73  SVDKFDLSYDVKFSTYAVPMIIGEIQRF-LRDDGTVKVSRSL--KEMGNKIRKAKDEL-- 127

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
            +    +   V  IA  L +S  +V+     +    S++  +  +D +     D +    
Sbjct: 128 -SKTRGRAPTVTEIADHLGISPEDVVLAQEAVRSPTSIHETVYENDGDPITLLDQIA--- 183

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D  E    +K         L +++  L+ RER I   R  ++   T   ++S   +S+ +
Sbjct: 184 DADEASWFDK-------IALKKAIEELDERERLIVYLRYYKDQ--TQSEVASRLGISQVQ 234

Query: 269 VRQIEARAFKKVQESI 284
           V ++E +  + +++ +
Sbjct: 235 VSRLEKKILQHIKDKM 250


>gi|147678180|ref|YP_001212395.1| sporulation sigma factor SigG [Pelotomaculum thermopropionicum SI]
 gi|146274277|dbj|BAF60026.1| DNA-directed RNA polymerase specialized sigma subunit
           [Pelotomaculum thermopropionicum SI]
          Length = 257

 Score = 48.9 bits (115), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 26/93 (27%), Positives = 50/93 (53%), Gaps = 1/93 (1%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L   +   L +   + GD SA  +L+  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLTGSQMKALFEAMHK-GDASARTKLINGNLRLVLSVIQRFTNRGEYVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           GLM+A+  FD  +  + +TY++  I   ++ Y+
Sbjct: 74  GLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYL 106


>gi|331698492|ref|YP_004334731.1| RNA polymerase sigma 28 subunit FliA/WhiG [Pseudonocardia
           dioxanivorans CB1190]
 gi|326953181|gb|AEA26878.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pseudonocardia
           dioxanivorans CB1190]
          Length = 429

 Score = 48.9 bits (115), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 25/78 (32%), Positives = 41/78 (52%), Gaps = 10/78 (12%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           L+ +H   +V+        GLP    +S++V  G  GL+ A+ +FDP RG R  TY+   
Sbjct: 206 LLVAHYGPLVRAVAARMAVGLPASVEVSDLVQAGVFGLLDAIARFDPTRGIRFETYAAQR 265

Query: 109 IKAAM------QEYILRS 120
           I+ AM      Q+++ R+
Sbjct: 266 IRGAMLDELRAQDWVPRT 283


>gi|160942608|ref|ZP_02089853.1| hypothetical protein FAEPRAM212_00082 [Faecalibacterium prausnitzii
           M21/2]
 gi|158446087|gb|EDP23090.1| hypothetical protein FAEPRAM212_00082 [Faecalibacterium prausnitzii
           M21/2]
          Length = 234

 Score = 48.9 bits (115), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 29/68 (42%), Positives = 39/68 (57%), Gaps = 4/68 (5%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS--EVVSEGNIGLMQAVKKFDPERGFRLA 102
           GD +A  +L+  +LRLV  I   Y  Y LP    ++VS G IGLM+AV  FD  R  R +
Sbjct: 51  GDAAAREKLIRHNLRLVAHIVKKY--YALPGDQEDLVSIGTIGLMKAVDTFDATRKARFS 108

Query: 103 TYSMWWIK 110
           TY+   I+
Sbjct: 109 TYASRCIE 116


>gi|156636433|gb|ABU92487.1| RpoD [Vibrio vulnificus]
 gi|156636455|gb|ABU92498.1| RpoD [Vibrio vulnificus]
 gi|156636457|gb|ABU92499.1| RpoD [Vibrio vulnificus]
 gi|156636461|gb|ABU92501.1| RpoD [Vibrio vulnificus]
 gi|156636475|gb|ABU92508.1| RpoD [Vibrio vulnificus]
 gi|156636495|gb|ABU92518.1| RpoD [Vibrio vulnificus]
 gi|156636497|gb|ABU92519.1| RpoD [Vibrio vulnificus]
 gi|156636499|gb|ABU92520.1| RpoD [Vibrio vulnificus]
 gi|156636501|gb|ABU92521.1| RpoD [Vibrio vulnificus]
          Length = 202

 Score = 48.9 bits (115), Expect = 9e-04,   Method: Compositional matrix adjust.
 Identities = 23/49 (46%), Positives = 32/49 (65%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 154 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|225850934|ref|YP_002731168.1| RNA polymerase sigma-D factor (Sigma-28) [Persephonella marina
           EX-H1]
 gi|225645790|gb|ACO03976.1| RNA polymerase sigma-D factor (Sigma-28) [Persephonella marina
           EX-H1]
          Length = 241

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 53/231 (22%), Positives = 106/231 (45%), Gaps = 50/231 (21%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           ++++ G +GL+ A+ K+DP +G +L+TY+   I+  + +      SL K+          
Sbjct: 39  DLINTGVLGLIDAINKYDPSKGVKLSTYAEIRIRGQIID------SLRKLDWVPR----- 87

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVA-------IAKKLN------------VSESEVISMN 177
            N+R+   H++A     L+ EQ +        IA+ L             +S S +IS++
Sbjct: 88  -NVRQKARHIEAAI---LEVEQKLGREATPEEIAEYLGMDVEEYMKYAEKISNSGLISID 143

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
             +  DE         D N+  WQ  ++  +D      +E+EE K    +++  +S LN 
Sbjct: 144 TTVGSDE---------DANTKLWQ--IISINDDTPDKYVEEEELK---KIISDIISKLNE 189

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RER +      +E  ++++ +     ++  R+ QI  +   K++  I+K +
Sbjct: 190 RERLVITLYYYEE--LSMKEIGEVLGLTESRISQIHTKTMMKIKSMIKKYI 238


>gi|160933635|ref|ZP_02081023.1| hypothetical protein CLOLEP_02489 [Clostridium leptum DSM 753]
 gi|156867512|gb|EDO60884.1| hypothetical protein CLOLEP_02489 [Clostridium leptum DSM 753]
          Length = 217

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 42/74 (56%), Gaps = 1/74 (1%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           + S++ LV   A  +RG G+   ++V  G +GL++AV  FD  RG + +TY++  I   M
Sbjct: 8   IESNMGLVHACAKRFRGRGIEYDDLVQAGCLGLVKAVDHFDEGRGLQFSTYAVPVILGEM 67

Query: 114 QEYILRSWSLVKIG 127
           +  + R    +K+G
Sbjct: 68  RR-LFRDGGAIKVG 80


>gi|302537203|ref|ZP_07289545.1| RNA polymerase sigma-G factor [Streptomyces sp. C]
 gi|302446098|gb|EFL17914.1| RNA polymerase sigma-G factor [Streptomyces sp. C]
          Length = 278

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 62/246 (25%), Positives = 113/246 (45%), Gaps = 16/246 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVK 91
           VL + Y++ GD     +L+  H   +VK   G    GLP     ++ VS G  GL+ A++
Sbjct: 31  VLWRSYKDSGDERLREQLIL-HYSPLVKYVAGRVSVGLPPNVEQADFVSSGVFGLIDAIE 89

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAIT 150
           KFD ER  +  TY++  I+ AM +  LR+   +        + +      L+  L +  T
Sbjct: 90  KFDIERSIKFETYAITRIRGAMIDE-LRALDWIPRSVRQKARAVERAYATLEAQLRRTPT 148

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
           +  +  E  +A+ ++L+   S+ +S+   +A +E L+      D+ S    D L    D 
Sbjct: 149 EGEVAGEMGIAV-EELHTVFSQ-LSLANVVALEELLHVGGEGGDRLS--LMDTL---EDT 201

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                +E  E +  R +L R+++ L  RE+ +      +   +TL  + +   V+  RV 
Sbjct: 202 AADNPVEVAEDRELRRLLARAINTLPDREKTVVTLYYYEG--LTLAEIGNVLGVTESRVS 259

Query: 271 QIEARA 276
           QI  ++
Sbjct: 260 QIHTKS 265


>gi|15613848|ref|NP_242151.1| sporulation sigma factor SigK [Bacillus halodurans C-125]
 gi|10173901|dbj|BAB05004.1| RNA polymerase sigma factor (sigma K) precursor [Bacillus
           halodurans C-125]
          Length = 235

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 30/82 (36%), Positives = 46/82 (56%), Gaps = 1/82 (1%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K+EE    KR  E GD  A +RL+  +LRLV  I   +        +++S G IGL++
Sbjct: 31  LSKEEERHYLKRMAE-GDEEARNRLIEHNLRLVAHIVKKFENTREHTEDLISIGTIGLIK 89

Query: 89  AVKKFDPERGFRLATYSMWWIK 110
           A++ F   +G +LATY+   I+
Sbjct: 90  AIESFSEGKGTKLATYAARCIE 111


>gi|158341591|ref|YP_001522756.1| RNA polymerase sigma-24 subunit [Acaryochloris marina MBIC11017]
 gi|158311832|gb|ABW33441.1| RNA polymerase sigma-24 subunit [Acaryochloris marina MBIC11017]
          Length = 423

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 27/79 (34%), Positives = 44/79 (55%), Gaps = 1/79 (1%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A  R +  + RLV   A  YRG  +   ++V+ G +GL  A++KFD  RGF+ +TY
Sbjct: 32  GDRRAEDRFIRKNQRLVFNEAKRYRGL-VDWDDLVNAGTLGLSIAIQKFDLSRGFQFSTY 90

Query: 105 SMWWIKAAMQEYILRSWSL 123
           ++  I+  +++ I     L
Sbjct: 91  AVKPIRTEIRQLICEQRGL 109


>gi|239982297|ref|ZP_04704821.1| RNA polymerase sigma factor [Streptomyces albus J1074]
 gi|291454142|ref|ZP_06593532.1| sigma factor [Streptomyces albus J1074]
 gi|291357091|gb|EFE83993.1| sigma factor [Streptomyces albus J1074]
          Length = 298

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 60/235 (25%), Positives = 107/235 (45%), Gaps = 28/235 (11%)

Query: 61  VVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           +V+ A G   +RG G  + ++V  G IGL++A+ +FD  R     T+++ +I   ++ + 
Sbjct: 77  LVRYAAGRFRHRGPG-EMEDIVQVGTIGLIKAIDRFDLSREVEFTTFAVPYIVGEIKRFF 135

Query: 118 L-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV--- 173
              SW+   +      + L  ++ + K  L A  D   +   V  +A KL  +E EV   
Sbjct: 136 RDTSWA---VHVPRRLQELRVDMAKAKESLAAELD---REPTVKELAAKLERTEEEVVEG 189

Query: 174 -ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ---EQVLIEKEERKNRRNMLT 229
            ++ N   AG  SL+    S D N +      + D  G     Q L+E        + L 
Sbjct: 190 LVAANGYTAG--SLDVPTESGDDNRAGGSPRSLADTLGAPDPAQELVED------LHALA 241

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             +  L+ RERRI E R  QE  +T   + +E  +S+  V ++ +R   +++  +
Sbjct: 242 PLLETLDERERRIVEMRFGQE--LTQSQIGAELGISQMHVSRLLSRILTRLRSGM 294


>gi|294631664|ref|ZP_06710224.1| RNA polymerase sigma factor WhiG [Streptomyces sp. e14]
 gi|292834997|gb|EFF93346.1| RNA polymerase sigma factor WhiG [Streptomyces sp. e14]
          Length = 280

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 63/245 (25%), Positives = 101/245 (41%), Gaps = 20/245 (8%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFD 94
           + Y+  GD     +L+  H   +VK   G    GLP     ++ VS G  GL+ A++KFD
Sbjct: 36  RSYKATGDERLREQLIL-HYSPLVKYVAGRVSVGLPPNVEQADFVSSGVFGLIDAIEKFD 94

Query: 95  PERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
            +R  +  TY++  I+ AM  E     W    I  +  QK    N+ R    L+A     
Sbjct: 95  IDREIKFETYAITRIRGAMIDELRALDW----IPRSVRQKAR--NVERAYATLEARL-RR 147

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL--INSSDKNSSQWQDWLVYDHDGQ 211
              E  VA    + V E   +     LA   +L  L  +   D +   + D L    D  
Sbjct: 148 TPTETEVAGEMGIAVDELHAVFSQLSLANVVALEELLHVGGEDGDGLSFMDTL---EDTA 204

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
               +E  E +  R  L R+++ L  RE+ +      +   +TL  + +   V+  RV Q
Sbjct: 205 ADNPVEVAEDRELRRFLARAINTLPEREKTVVTLYYYEG--LTLAEIGNVLGVTESRVSQ 262

Query: 272 IEARA 276
           I  ++
Sbjct: 263 IHTKS 267


>gi|327439575|dbj|BAK15940.1| DNA-directed RNA polymerase specialized sigma subunit [Solibacillus
           silvestris StLB046]
          Length = 233

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 29/84 (34%), Positives = 47/84 (55%), Gaps = 2/84 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  ++EE V+ +  +  GD SA   L+  ++RLV  +   +      + + +S G IGL
Sbjct: 30  PLSREEEEEVINRFIK--GDESARVELIERNMRLVAHVVKKFHPSHDLLDDYISIGTIGL 87

Query: 87  MQAVKKFDPERGFRLATYSMWWIK 110
           M+AV  F PE+  RLATY+   I+
Sbjct: 88  MKAVSSFTPEKKTRLATYAARCIE 111



 Score = 37.4 bits (85), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 31/94 (32%), Positives = 44/94 (46%), Gaps = 6/94 (6%)

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-- 251
           D  S Q +D L  D    E   IEK ER+     L R +  L+PRE  I   R   +N  
Sbjct: 139 DGQSLQIRDLLQLD----EPSTIEKIERQEDFAQLYRYLDTLDPRELEIISYRYGLQNFD 194

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           P T + ++    +SR  V +IE RA  K+ +  +
Sbjct: 195 PHTQKEIAKRLNISRSYVSRIEKRALIKLYQQFK 228


>gi|238917256|ref|YP_002930773.1| RNA polymerase sporulation-specific sigma factor [Eubacterium
           eligens ATCC 27750]
 gi|238872616|gb|ACR72326.1| RNA polymerase sporulation-specific sigma factor [Eubacterium
           eligens ATCC 27750]
          Length = 258

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 58/270 (21%), Positives = 127/270 (47%), Gaps = 45/270 (16%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L+  +   L  + +  GD  A    +  +LRLV+ I   +   G  + ++   G IG
Sbjct: 16  LPLLKPAQAKELLVKIK-SGDTQARETFIKGNLRLVLSIVQRFSQSGENLDDLFQIGCIG 74

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           +++A+  FD     + +TY++  I   ++ + LR  S +++             R LK  
Sbjct: 75  MIKAIDNFDISLNVQFSTYAVPMIIGEIKRF-LRDNSTIRVS------------RSLKDT 121

Query: 146 -LQAITD------NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
             +AIT        NLK   +  IA+++ +S+++++          +L A+  S     S
Sbjct: 122 AYKAITTRETLMKKNLKEPSITEIAEEIGISKADIVI---------ALEAVTPS----IS 168

Query: 199 QWQDWLVYDHDGQEQVLIEK-EERKNRRNMLTRSMSV------LNPRERRIFEARRLQEN 251
            ++   V++  G    +I++ +++KN  +   R++++      L+PRER+I   R    +
Sbjct: 169 LYEP--VFNDGGDTLYVIDQVKDKKNTEDRWVRNIALQEAINRLSPRERQIIILRFF--D 224

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +T   ++    +S+ +V ++E  A + ++
Sbjct: 225 CLTQTEVAKGLGISQAQVSRLEKCALRDMK 254


>gi|332799375|ref|YP_004460874.1| RNA polymerase sigma-28 subunit SigK [Tepidanaerobacter sp. Re1]
 gi|332697110|gb|AEE91567.1| RNA polymerase, sigma 28 subunit, SigK [Tepidanaerobacter sp. Re1]
          Length = 240

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 27/80 (33%), Positives = 46/80 (57%), Gaps = 3/80 (3%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           E++++Y+L       GD  A + L+  +LRLV  I   +   G  + +++S G IGL++A
Sbjct: 39  EEEKKYIL---LYSKGDEEARNILIEHNLRLVAHIVKKFASTGEDMDDLISIGTIGLIKA 95

Query: 90  VKKFDPERGFRLATYSMWWI 109
           +  F+  +G RLATY+   I
Sbjct: 96  ISTFNYSKGSRLATYAARCI 115


>gi|182435659|ref|YP_001823378.1| RNA polymerase sigma factor WhiG [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|326776293|ref|ZP_08235558.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Streptomyces cf.
           griseus XylebKG-1]
 gi|178464175|dbj|BAG18695.1| putative RNA polymerase sigma factor WhiG [Streptomyces griseus
           subsp. griseus NBRC 13350]
 gi|326656626|gb|EGE41472.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Streptomyces cf.
           griseus XylebKG-1]
          Length = 278

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 61/248 (24%), Positives = 110/248 (44%), Gaps = 26/248 (10%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFD 94
           + Y+  GD     +L+  H   +VK   G    GLP     ++ VS G  GL+ A++KFD
Sbjct: 34  RSYKTTGDERLREQLIL-HYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEKFD 92

Query: 95  PERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTA-NQKRLFFNL----RRLKGHLQA 148
            ER  +  TY++  I+ AM  E     W    +   A N +R +  L    RR     + 
Sbjct: 93  IERAIKFETYAITRIRGAMIDELRALDWIPRSVRQKARNVERAYATLEAQFRRTPSEAEV 152

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
            ++  +  E++ A+  +L++  + V+++      +E L+      D+ S    D L    
Sbjct: 153 ASEMGIALEELHAVFSQLSL--ANVVAL------EELLHVGGEGGDRLS--LMDTL---E 199

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D      +E  E +  R +L R+++ L  RE+ +      +   +TL  + +   V+  R
Sbjct: 200 DTAADNPVEVAEDRELRRLLARAINTLPDREKTVVTLYYYEG--LTLAEIGNVLGVTESR 257

Query: 269 VRQIEARA 276
           V QI  ++
Sbjct: 258 VSQIHTKS 265


>gi|146295966|ref|YP_001179737.1| sporulation sigma factor SigE [Caldicellulosiruptor saccharolyticus
           DSM 8903]
 gi|145409542|gb|ABP66546.1| RNA polymerase, sigma 29 subunit, SigE [Caldicellulosiruptor
           saccharolyticus DSM 8903]
          Length = 246

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 28/94 (29%), Positives = 54/94 (57%), Gaps = 1/94 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  ++E  +L K + E  +      LV  +LRLVV IA  +    + + ++VS G IGL
Sbjct: 44  PLTPEEESEILNKIHYERRE-ELKKVLVERNLRLVVYIARKFENTKINLEDLVSIGTIGL 102

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++A+  ++P++  +LATY+   I+  +  ++ R+
Sbjct: 103 IKAINTYNPDKNIKLATYASKCIENEILMFLRRN 136


>gi|311068942|ref|YP_003973865.1| sporulation sigma factor SigF [Bacillus atrophaeus 1942]
 gi|310869459|gb|ADP32934.1| sporulation sigma factor SigF [Bacillus atrophaeus 1942]
          Length = 255

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 59/250 (23%), Positives = 110/250 (44%), Gaps = 29/250 (11%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L KR ++ GD  A   L+  ++RLV  +   +   G    ++   G IGL+++V KFD  
Sbjct: 22  LIKRSQD-GDQQARDLLIEKNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKSVDKFDLS 80

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
              R +TY++  I   +Q +I R    VK+  +   K L   +RR K  L   +    + 
Sbjct: 81  YDVRFSTYAVPMIIGEIQRFI-RDDGTVKVSRSL--KELGNKIRRAKDEL---SKTYGRV 134

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ----- 211
             V  IA+ L +   +V+     +    S++                 VY++DG      
Sbjct: 135 PTVQEIAEHLEIDAEDVVLAQEAVRAPSSIHE---------------TVYENDGDPITLL 179

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           +Q+    EE+   +  L  ++S L  RE+ I   R  ++   T   ++    +S+ +V +
Sbjct: 180 DQIADHSEEKWFDKIALKEAISDLEEREKLIVYLRYYKDQ--TQSEVAERLGISQVQVSR 237

Query: 272 IEARAFKKVQ 281
           +E +  K+++
Sbjct: 238 LEKKILKQIK 247


>gi|158341138|ref|YP_001522305.1| hypothetical protein AM1_E0222 [Acaryochloris marina MBIC11017]
 gi|158311379|gb|ABW32991.1| hypothetical protein AM1_E0222 [Acaryochloris marina MBIC11017]
          Length = 427

 Score = 48.9 bits (115), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 67/261 (25%), Positives = 120/261 (45%), Gaps = 42/261 (16%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           ++Q +Y L  +  + GDL A  R +  +  LV + A  +RG      ++V+ GN+GL  A
Sbjct: 18  DRQSQYTLIIQA-QAGDLRARDRFIRQNEGLVFQQAHKFRGLA-DWDDLVNAGNLGLAIA 75

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILR--------SWSLVKIGTTANQKRLFFNLRR 141
           ++KFD  +G++ ++Y++  I+  ++  I          S  L +I   +   R+  +L R
Sbjct: 76  IQKFDVAKGYKFSSYAVKVIRTEIRRLIHEFKGISIEISLHLKEIEQASQAIRM--DLDR 133

Query: 142 LKGHLQAITDNNLKPEQVVAIA-KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
            +  +  ++D     +QV+  A  K NV E+   S+N  L  D+    L           
Sbjct: 134 -EPTITELSDETGYSQQVIFNAWNKANVVETA--SLNIPLNDDQGCEQL----------- 179

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
                 D  G +    E  E  +++N + +    L  RE  I  A+R   +  + + + +
Sbjct: 180 ------DVIGVDDRTWEFTETLDQKNYIAQ----LPDREAFIVRAKR---DGFSNKEIGT 226

Query: 261 EFEVSRERVRQI--EARAFKK 279
              +S ERVRQ+  +ARAF K
Sbjct: 227 MLSLSGERVRQLLKQARAFLK 247


>gi|210617641|ref|ZP_03291672.1| hypothetical protein CLONEX_03896 [Clostridium nexile DSM 1787]
 gi|210149188|gb|EEA80197.1| hypothetical protein CLONEX_03896 [Clostridium nexile DSM 1787]
          Length = 237

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 52/195 (26%), Positives = 90/195 (46%), Gaps = 19/195 (9%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R    GD  A  +LV  ++ L+  I   + G G    ++   G+IGL++A+ KFD     
Sbjct: 9   RQSHDGDEKAREQLVEENIGLIWCIVKRFYGRGAEPEDLFQIGSIGLLKAIDKFDMTYDV 68

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY++  I   ++ + LR   ++K+  +   K L +     K  LQ     +   E+ 
Sbjct: 69  KFSTYAVPMISGEIKRF-LRDDGMIKVSRSL--KELSYKAYFAKEKLQEKLGRDPTLEE- 124

Query: 160 VAIAKKLNVSESEVISMNCRLAGD-ESLNALINSSDKNSSQWQDWLVYDHDGQEQVL--- 215
             +A+ + V + E++ M    +G+ ESL+  I   D N  Q  D L      +E+VL   
Sbjct: 125 --LAETMEVEKEELV-MAMESSGEVESLHKPIYQKDGNEIQLMDKLEETGAQEEKVLNQM 181

Query: 216 --------IEKEERK 222
                   +EKEER+
Sbjct: 182 LLAQLLEGLEKEERQ 196


>gi|228992811|ref|ZP_04152736.1| RNA polymerase sigma-F factor [Bacillus pseudomycoides DSM 12442]
 gi|228998857|ref|ZP_04158442.1| RNA polymerase sigma-F factor [Bacillus mycoides Rock3-17]
 gi|229006374|ref|ZP_04164053.1| RNA polymerase sigma-F factor [Bacillus mycoides Rock1-4]
 gi|228754873|gb|EEM04239.1| RNA polymerase sigma-F factor [Bacillus mycoides Rock1-4]
 gi|228760873|gb|EEM09834.1| RNA polymerase sigma-F factor [Bacillus mycoides Rock3-17]
 gi|228766860|gb|EEM15498.1| RNA polymerase sigma-F factor [Bacillus pseudomycoides DSM 12442]
          Length = 252

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 50/190 (26%), Positives = 90/190 (47%), Gaps = 17/190 (8%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           +K P L+  E   L ++ ++ GD  A   +V S++RLV  +   +   G    ++   G 
Sbjct: 9   KKKPQLKDHELKALIQKSQD-GDQQARDTIVQSNMRLVWSVVQRFLNRGYEPDDLFQIGC 67

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL+++V KFD     + +TY++  I   +Q + LR    VK+  +   K     +R++K
Sbjct: 68  IGLLKSVDKFDLSFDVKFSTYAVPMIIGEIQRF-LRDDGSVKVSRSL--KETGNKIRKMK 124

Query: 144 GHL-----QAITDN------NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
             L     +A T N       L PE+VV +A++ + + S +        GD  +  L   
Sbjct: 125 DELSKEYGRAPTINEVAEALELTPEEVV-LAQEASRTPSSIHETVYENDGD-PITILDQI 182

Query: 193 SDKNSSQWQD 202
           +D+  ++W D
Sbjct: 183 ADQTETKWFD 192


>gi|56420843|ref|YP_148161.1| sporulation sigma factor SigF [Geobacillus kaustophilus HTA426]
 gi|56380685|dbj|BAD76593.1| DNA-directed RNA polymerase sporulation-specific sigma factor
           (sigma-F) (stage II sporulation protein AC) [Geobacillus
           kaustophilus HTA426]
          Length = 250

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 56/256 (21%), Positives = 114/256 (44%), Gaps = 19/256 (7%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           ++ QE   L +R +E GD  A   ++  ++RLV  +   +   G    ++   G IGL++
Sbjct: 12  IKDQEMKELIRRSQE-GDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLK 70

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           +V KFD     + +TY++  I   +Q + LR    VK+  +   K +   +R+ K  L  
Sbjct: 71  SVDKFDLSYDVKFSTYAVPMIIGEIQRF-LRDDGTVKVSRSL--KEMGNKIRKAKDEL-- 125

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
            +    +   V  IA  L +S  +V+     +    S++  +  +D +     D +    
Sbjct: 126 -SKTRGRAPTVTEIADHLGISPEDVVLAQEAVRSPTSIHETVYENDGDPITLLDQIA--- 181

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D  E    +K         L +++  L+ RER I   R  ++   T   ++S   +S+ +
Sbjct: 182 DADEASWFDK-------IALKKAIEELDERERLIVYLRYYKDQ--TQSEVASRLGISQVQ 232

Query: 269 VRQIEARAFKKVQESI 284
           V ++E +  + +++ +
Sbjct: 233 VSRLEKKILQHIKDKM 248


>gi|685227|dbj|BAA04283.1| sigma factor [Streptomyces setonii]
          Length = 259

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 54/224 (24%), Positives = 102/224 (45%), Gaps = 19/224 (8%)

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIG 127
           RG G  + ++V  G IGL++A+ +FD  R     ++++ +I   ++ +    SW+   + 
Sbjct: 49  RGSG-DMEDIVQVGTIGLIKAIDRFDLSREVEFTSFAVPYIVGEIKRFFRDTSWA---VH 104

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----ISMNCRLAGD 183
                + L  +L + K  L    D +     V  +A+ L + ESEV    ++ N   AG 
Sbjct: 105 VPRRLQELRVDLAKAKESLAGDLDRD---PTVRELAQDLGIEESEVTEGIVASNGYTAG- 160

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SL+   ++++    Q       D  G+    +E  E     + L   +  L+ RERRI 
Sbjct: 161 -SLDMPTDTAEAGPGQHSGRTFADVLGEPDPAMETVENL---HALAPLLGELDERERRII 216

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           + R  QE  +T   + +E  +S+  V ++ +R   K++  +  Q
Sbjct: 217 DMRFGQE--MTQAQIGAELGISQMHVSRLLSRMLGKLRNGMLTQ 258


>gi|294102492|ref|YP_003554350.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Aminobacterium colombiense DSM 12261]
 gi|293617472|gb|ADE57626.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Aminobacterium colombiense DSM 12261]
          Length = 196

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 25/79 (31%), Positives = 42/79 (53%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
           R H D  A   L+ S+  LV  +A  +        +++ EG + L+++V KF+PER  + 
Sbjct: 25  RCHLDDDAREELIISYRPLVFWLAQKFYVSPSLYPDLIQEGMVALIKSVDKFEPERQLKF 84

Query: 102 ATYSMWWIKAAMQEYILRS 120
            TY+ + IK  M  ++ RS
Sbjct: 85  TTYAFYRIKGQMVNFLQRS 103


>gi|118443643|ref|YP_877879.1| sporulation sigma factor SigF [Clostridium novyi NT]
 gi|118134099|gb|ABK61143.1| RNA polymerase sigma-F factor [Clostridium novyi NT]
          Length = 251

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 52/249 (20%), Positives = 106/249 (42%), Gaps = 34/249 (13%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A   LV  +L LV  I+  +   G    ++   G++GL++A+  FD     + +TY
Sbjct: 26  GDKKALDELVEKNLPLVTAISKKFLNRGYEYEDIFQIGSMGLIKAINNFDSSYNVQFSTY 85

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTA--NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           ++  I   ++ +I R   L+K+  +     ++L F+  +L                    
Sbjct: 86  AVPMIMGEIRRFI-RDDGLIKVSRSVKYTARKLHFDKEKL-------------------- 124

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
            KKLN      +    + +G +    +  +   N  ++    ++  DG    LI+K   K
Sbjct: 125 TKKLN--REPTVEELSKFSGIDKEQIIFATEAINEPKYLYDTIHQDDGSPIYLIDKVVLK 182

Query: 223 NRRNM-------LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
           +   +       L  ++S L+ R R+I   R  ++  +T   ++    +S+ +V +IE +
Sbjct: 183 DESEIDELDKIALKEALSKLDQRSRQIIILRYFKD--ITQVKVAKMLGISQVQVSRIEKK 240

Query: 276 AFKKVQESI 284
             K ++E +
Sbjct: 241 VLKTMKEKL 249


>gi|218133693|ref|ZP_03462497.1| hypothetical protein BACPEC_01562 [Bacteroides pectinophilus ATCC
           43243]
 gi|217991068|gb|EEC57074.1| hypothetical protein BACPEC_01562 [Bacteroides pectinophilus ATCC
           43243]
          Length = 254

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 50/229 (21%), Positives = 102/229 (44%), Gaps = 19/229 (8%)

Query: 61  VVKIAMG----YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           +VK+  G    Y GY +   ++   G  GL+ A+ KFD  +  +  TY+   I+ A+ + 
Sbjct: 32  LVKLVAGRLGMYLGYSVEYDDLCGYGIFGLIDAIDKFDCNKNVKFETYASLRIRGAILDQ 91

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI-TDNNLKPEQVVAIAKKLNVSESEVIS 175
           I R    +       QK++   + +++    ++ TD  L        A++L ++  E   
Sbjct: 92  I-RKMDWIPRSLRQKQKKIDAAMSKIEAQKGSVATDEEL--------AQELGITLDEFND 142

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
              +      ++    +  + +    D +      Q + ++EKEE K    M+  ++S+L
Sbjct: 143 WQGKTKATNLISLDEYTETQGTEAKMDSVTNARFDQPEDVVEKEELK---KMIVEAISLL 199

Query: 236 NPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             +ER +      +E  +TL+ +S   +VS  RV Q+  +A  K++  +
Sbjct: 200 TDKERSVVTLYYYEE--MTLKEISLVLDVSESRVSQLHTKALLKMKSKL 246


>gi|23099294|ref|NP_692760.1| sporulation sigma factor SigF [Oceanobacillus iheyensis HTE831]
 gi|22777523|dbj|BAC13795.1| stage II sporulation protein AC (RNA polymerase sigma-F factor)
           [Oceanobacillus iheyensis HTE831]
          Length = 250

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 25/84 (29%), Positives = 44/84 (52%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R  + GD SA  RLV  ++RLV  +   +   G    ++   G+IGL++++ KFD     
Sbjct: 22  RLSQQGDQSARDRLVEKNIRLVWSVVQRFINRGYDPDDLFQIGSIGLIKSIDKFDLSYDV 81

Query: 100 RLATYSMWWIKAAMQEYILRSWSL 123
           + +TY++  I   +Q +I    S+
Sbjct: 82  KFSTYAVPMIIGEIQRFIRDDGSI 105


>gi|320008281|gb|ADW03131.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Streptomyces
           flavogriseus ATCC 33331]
          Length = 278

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 61/248 (24%), Positives = 110/248 (44%), Gaps = 26/248 (10%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFD 94
           + Y+  GD     +L+  H   +VK   G    GLP     ++ VS G  GL+ A++KFD
Sbjct: 34  RSYKTTGDGRLREQLIL-HYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEKFD 92

Query: 95  PERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTA-NQKRLFFN----LRRLKGHLQA 148
            ER  +  TY++  I+ AM  E     W    +   A N +R +      LRR     + 
Sbjct: 93  IERAIKFETYAITRIRGAMIDELRALDWIPRSVRQKARNVERAYATLEAQLRRTPSEAEV 152

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
            ++  +  E++ A+  +L++  + V+++      +E L+      D+ S    D L    
Sbjct: 153 ASEMGVALEELHAVFSQLSL--ANVVAL------EELLHVGGEGGDRLS--LMDTL---E 199

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D      +E  E +  R +L R+++ L  RE+ +      +   +TL  + +   V+  R
Sbjct: 200 DTAADDPVEVAEDRELRRLLARAINTLPEREKTVVTLYYYE--GLTLAEIGNVLGVTESR 257

Query: 269 VRQIEARA 276
           V QI  ++
Sbjct: 258 VSQIHTKS 265


>gi|294501135|ref|YP_003564835.1| RNA polymerase sigma-F factor [Bacillus megaterium QM B1551]
 gi|295706482|ref|YP_003599557.1| RNA polymerase sigma-F factor [Bacillus megaterium DSM 319]
 gi|464690|sp|P35145|RPSF_BACME RecName: Full=RNA polymerase sigma-F factor; AltName:
           Full=Sporulation sigma factor; AltName: Full=Stage II
           sporulation protein AC
 gi|39654|emb|CAA45288.1| spoIIAC [Bacillus megaterium]
 gi|294351072|gb|ADE71401.1| RNA polymerase sigma-F factor [Bacillus megaterium QM B1551]
 gi|294804141|gb|ADF41207.1| RNA polymerase sigma-F factor [Bacillus megaterium DSM 319]
 gi|383708|prf||1904152C spoIIAC gene
          Length = 253

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 47/185 (25%), Positives = 85/185 (45%), Gaps = 13/185 (7%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L+  E   L KR  + GD  A   +V  ++RLV  +   +   G    ++   G IGL
Sbjct: 12  PYLKDHEVKDLIKR-SQQGDQIARDTIVQKNMRLVWSVVQRFINRGYEPDDLFQIGCIGL 70

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ-----KRLFFNLRR 141
           +++V KFD     + +TY++  I   +Q +I R    VK+  +  +     ++    L +
Sbjct: 71  LKSVDKFDLSYDVKFSTYAVPMIIGEIQRFI-RDDGTVKVSRSLKEMSNKIRKAKDELSK 129

Query: 142 LKGHLQAITDN----NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
           L G +  + +     +L PE+VV +A++ N + S +        GD  +  L   +D   
Sbjct: 130 LLGRVPTVAEVAEHLDLTPEEVV-LAQEANRAPSSIHETVYENDGD-PITLLDQIADHTE 187

Query: 198 SQWQD 202
           ++W D
Sbjct: 188 AKWFD 192


>gi|4102217|gb|AAD11814.1| sigma-like factor [Streptomyces sp. A21]
          Length = 343

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 60/242 (24%), Positives = 107/242 (44%), Gaps = 22/242 (9%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISE-VVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + L+  +L LV   A  +R  G   +E ++  G IGL++A+ +FD  R    AT+++ 
Sbjct: 114 ARNTLIEMNLSLVRFAASRFRNRGGDDTEDIIQVGTIGLIKAIDRFDLSREVEFATFAVP 173

Query: 108 WIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           +I   ++ +    +WS   +      + L   L + K  L A  D +     V  +A +L
Sbjct: 174 YIVGEIKRFFRDTTWS---VHVPRRLQELRVELAKAKEALSADLDRD---PTVAELAARL 227

Query: 167 NVSESEVI----SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           ++SE E+I    + N   AG     +  + S      + D L  D  G E V        
Sbjct: 228 DLSEEEIIEGLVAANGYSAGSLDTPSADSESGNEQRAYADLLGEDDPGMESV-------- 279

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              + L   +  L+ RER I   R  QE  +T   + +E  VS+  V ++ +R  ++++ 
Sbjct: 280 ENLHALAPLLRQLDDRERAIVRMRFGQE--MTQAQIGAELGVSQMHVSRLLSRIVRRLRT 337

Query: 283 SI 284
            +
Sbjct: 338 GM 339


>gi|206900763|ref|YP_002250593.1| SigF [Dictyoglomus thermophilum H-6-12]
 gi|206739866|gb|ACI18924.1| SigF [Dictyoglomus thermophilum H-6-12]
          Length = 235

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 23/65 (35%), Positives = 37/65 (56%), Gaps = 1/65 (1%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           +YRE GD      L+     L+   A  +  YG P+ ++V  G +G ++AV+ +DPE+G 
Sbjct: 11  KYRETGDKKVLEELLEVFDDLIYYWASKFTSYGEPLEDLVQIGYLGFLKAVENYDPEKG- 69

Query: 100 RLATY 104
            L+TY
Sbjct: 70  DLSTY 74


>gi|319937328|ref|ZP_08011735.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
 gi|319807694|gb|EFW04287.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
          Length = 227

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 29/81 (35%), Positives = 45/81 (55%), Gaps = 1/81 (1%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L  QEE  L ++Y + GD  A ++L+  +LRLV  IA  Y        +++S G IGL++
Sbjct: 27  LTPQEENDLLEKYFQ-GDQEARNQLIEHNLRLVAHIAKKYESTKDLQEDLISIGTIGLIK 85

Query: 89  AVKKFDPERGFRLATYSMWWI 109
           AV  + P +  +L TY+   I
Sbjct: 86  AVDSYKPTKATKLGTYAAKCI 106


>gi|297616994|ref|YP_003702153.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
 gi|297144831|gb|ADI01588.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
          Length = 256

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 38/149 (25%), Positives = 76/149 (51%), Gaps = 7/149 (4%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L+ +    L  R +++ D  A   L+  +LRLV+ +   +   G  + ++   G IG
Sbjct: 15  LPVLKNERMRDLFLRVKQN-DRQAREELIRGNLRLVLSVIQRFNHRGEYVDDLFQVGCIG 73

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A+  FD E+  R +TY++  I   ++ Y LR  + V++  +          + L+  
Sbjct: 74  LIKAIDNFDLEQNVRFSTYAVPMIIGEIRRY-LRDNNPVRVSRSLRD----VAYKALQVR 128

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVI 174
            Q + + + +P  +  IA +L VS+ EV+
Sbjct: 129 EQLLAEKSREP-TIAEIADRLEVSQEEVV 156


>gi|296504831|ref|YP_003666531.1| sporulation sigma factor SigK [Bacillus thuringiensis BMB171]
 gi|296325883|gb|ADH08811.1| sporulation sigma factor SigK [Bacillus thuringiensis BMB171]
          Length = 196

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 38/67 (56%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E GD  A + L+  +LRLV  I   +   G    +++S G IGL++A++ +   +G +LA
Sbjct: 2   EQGDAQARNLLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIESYSAGKGTKLA 61

Query: 103 TYSMWWI 109
           TY+   I
Sbjct: 62  TYAARCI 68


>gi|296133647|ref|YP_003640894.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           sp. JR]
 gi|296032225|gb|ADG82993.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           potens JR]
          Length = 257

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 26/93 (27%), Positives = 51/93 (54%), Gaps = 1/93 (1%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L   E   + ++  + GD SA  +L+  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLSSSEMRKIFEQM-QAGDKSARTKLINGNLRLVLSVIQRFTNRGEYVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           GLM+A+  FD  +  + +TY++  I   ++ Y+
Sbjct: 74  GLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYL 106


>gi|225181587|ref|ZP_03735028.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Dethiobacter
           alkaliphilus AHT 1]
 gi|225167695|gb|EEG76505.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Dethiobacter
           alkaliphilus AHT 1]
          Length = 239

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 55/253 (21%), Positives = 113/253 (44%), Gaps = 27/253 (10%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFDP 95
           +Y+E  +      LV  +L LV ++  G    GLP      +++  G +GL++A+++FDP
Sbjct: 9   KYQETKEEGLQETLVEKYLPLV-RLHAGRLALGLPAHVNRDDLLQAGMLGLLEALQRFDP 67

Query: 96  ERGFRLATYSMWWIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
            RG +  +++   I+ AM + + R  W           + +   +R +   +Q +     
Sbjct: 68  TRGVKFESFAALRIRGAMLDELRRLCWV---------PRSVVREMREMDRAVQELATQLG 118

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +      IA+K+ ++  ++            +  +INSS   S +     V   DG E  
Sbjct: 119 REPAEEEIAEKMGITIPQL----------RKITGMINSSSLLSLEDTLLAVPAVDGPEVE 168

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
            +++      R  L  ++  L  R +++  A   QE+ +TL+ +     V+  RV Q+ A
Sbjct: 169 ALDRLIAAEDRQRLAEAIGQLPERHQQLL-ALYYQED-LTLKEVGLVLGVTESRVCQLHA 226

Query: 275 RAFKKVQESIQKQ 287
           R   +++ ++Q +
Sbjct: 227 RIIARLRTALQDE 239


>gi|5360738|dbj|BAA82139.1| sigma factor of sigB family [Streptomyces griseus]
          Length = 259

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 53/224 (23%), Positives = 103/224 (45%), Gaps = 19/224 (8%)

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIG 127
           RG G  + ++V  G IGL++A+ +FD  R     ++++ +I   ++ +    SW+   + 
Sbjct: 49  RGSG-DMEDIVQVGTIGLIKAIDRFDLSREVEFTSFAVPYIVGEIKRFFRDTSWA---VH 104

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----ISMNCRLAGD 183
                + L  +L + K  L  + D +   ++   +A+ L + ESEV    ++ N   AG 
Sbjct: 105 VPRRLQELRVDLAKAKEALAGVLDRDPTAKE---LAEYLGIEESEVTEGIVASNGYTAG- 160

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SL+   ++++    Q       D  G     +E  E     + L   +  L+ RERRI 
Sbjct: 161 -SLDMPTDTAEAGPGQTAGRTFADVLGDPDPAMEAVENL---HALAPLLDELDERERRII 216

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           + R  QE  +T   + +E  +S+  V ++ +R   K++  +  Q
Sbjct: 217 DMRFGQE--MTQAQIGAELGISQMHVSRLLSRMLGKLRTGMLVQ 258


>gi|332975582|gb|EGK12472.1| DNA-directed RNA polymerase sigma subunit SigK [Desmospora sp.
           8437]
          Length = 160

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 28/83 (33%), Positives = 46/83 (55%), Gaps = 2/83 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ EK+EE  L  +    GD  A + L+  +LRLV  I   +        +++S G IGL
Sbjct: 30  PLNEKEEEKYL--KQMAGGDKEARNILIEHNLRLVAHIVKKFENTSEDNEDLISIGTIGL 87

Query: 87  MQAVKKFDPERGFRLATYSMWWI 109
           ++A++ + P +G +LATY+   I
Sbjct: 88  IKAIESYQPNKGTKLATYAARCI 110


>gi|86605313|ref|YP_474076.1| RNA polymerase sigma factor SigF [Synechococcus sp. JA-3-3Ab]
 gi|86553855|gb|ABC98813.1| RNA polymerase sigma factor, group 3 [Synechococcus sp. JA-3-3Ab]
          Length = 299

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 30/92 (32%), Positives = 51/92 (55%), Gaps = 9/92 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR-----GYGLPISEVVSEGNIG 85
           K +   L + Y +  D +  +RLV  +L LV K A  +R     GY     ++V  G IG
Sbjct: 52  KAQTAALLRLYHQTRDPALRNRLVEINLGLVRKEAHHWRNQCDEGY----DDLVQVGCIG 107

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           L+QA+++FD  RG   ++++M +I+  +Q Y+
Sbjct: 108 LIQAIERFDISRGLAFSSFAMPYIRGEIQHYL 139


>gi|291448094|ref|ZP_06587484.1| sporulation sigma factor [Streptomyces roseosporus NRRL 15998]
 gi|1655819|gb|AAB41960.1| sporulation sigma factor [Streptomyces filamentosus]
 gi|291351041|gb|EFE77945.1| sporulation sigma factor [Streptomyces roseosporus NRRL 15998]
          Length = 278

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 61/248 (24%), Positives = 110/248 (44%), Gaps = 26/248 (10%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFD 94
           + Y+  GD     +L+  H   +VK   G    GLP     ++ VS G  GL+ A++KFD
Sbjct: 34  RSYKTTGDERLREQLIL-HYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEKFD 92

Query: 95  PERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTA-NQKRLFFNL----RRLKGHLQA 148
            ER  +  TY++  I+ AM  E     W    +   A N +R +  L    RR     + 
Sbjct: 93  IERAIKFETYAITRIRGAMIDELRALDWIPRSVRQKARNVERAYATLEAQFRRTPSEAEV 152

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
            ++  +  E++ A+  +L++  + V+++      +E L+      D+ S    D L    
Sbjct: 153 ASEMGIALEELHAVFSQLSL--ANVVAL------EELLHVGGEGGDRLS--LMDTL---E 199

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D      +E  E +  R +L R+++ L  RE+ +      +   +TL  + +   V+  R
Sbjct: 200 DTAADNPVEVAEDRELRRLLARAINTLPDREKTVVTLYYYEG--LTLAEIGNVLGVTESR 257

Query: 269 VRQIEARA 276
           V QI  ++
Sbjct: 258 VSQIHTKS 265


>gi|114566052|ref|YP_753206.1| sigma 28 (flagella/sporulation) [Syntrophomonas wolfei subsp.
           wolfei str. Goettingen]
 gi|114336987|gb|ABI67835.1| sigma 28 (flagella/sporulation) [Syntrophomonas wolfei subsp.
           wolfei str. Goettingen]
          Length = 126

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 31/98 (31%), Positives = 55/98 (56%), Gaps = 3/98 (3%)

Query: 9   IVNGEIGLSRYIH-EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           I+ G + L  Y++ ++   P+ E+ E   L +  R  G   A + L+  +LRLV  +   
Sbjct: 13  ILKGSLCLFAYLNNQVFPQPLSEEDERKCLQEMQR--GGEEARNILIEHNLRLVAHVVKK 70

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           Y   G  + +++S G IG ++A++ ++ ERG RLATY+
Sbjct: 71  YESSGEDLEDLISIGTIGPIKAIRTYNFERGVRLATYA 108


>gi|47569335|ref|ZP_00240019.1| RNA polymerase sigma-K factor [Bacillus cereus G9241]
 gi|228967406|ref|ZP_04128439.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           sotto str. T04001]
 gi|47554006|gb|EAL12373.1| RNA polymerase sigma-K factor [Bacillus cereus G9241]
 gi|228792294|gb|EEM39863.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           sotto str. T04001]
          Length = 228

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 38/67 (56%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E GD  A + L+  +LRLV  I   +   G    +++S G IGL++A++ +   +G +LA
Sbjct: 34  EQGDAQARNLLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIESYSAGKGTKLA 93

Query: 103 TYSMWWI 109
           TY+   I
Sbjct: 94  TYAARCI 100


>gi|268610009|ref|ZP_06143736.1| sporulation sigma factor SigK [Ruminococcus flavefaciens FD-1]
          Length = 227

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 31/82 (37%), Positives = 44/82 (53%), Gaps = 1/82 (1%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K EE+ L +R    GD  A  +L+  +LRLV  I   Y        E++S G IGL++
Sbjct: 26  LPKSEEHELFER-SSCGDEYARKKLIEHNLRLVAHIVKKYTSSFDEQDELISIGTIGLIK 84

Query: 89  AVKKFDPERGFRLATYSMWWIK 110
           AV  FD  +G + ATY+   I+
Sbjct: 85  AVSSFDHTKGSKFATYASRCIE 106


>gi|254380542|ref|ZP_04995908.1| sigma factor [Streptomyces sp. Mg1]
 gi|194339453|gb|EDX20419.1| sigma factor [Streptomyces sp. Mg1]
          Length = 304

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 54/226 (23%), Positives = 106/226 (46%), Gaps = 29/226 (12%)

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGT 128
           G GL + +++  G IGL++A+ +FDPER    +T ++ +I   ++ +    +WS+     
Sbjct: 94  GGGLDMDDIIQVGTIGLIKAIDRFDPEREVEFSTLALPYIVGEIKRHFRDTTWSV----- 148

Query: 129 TANQKRLFFNLR-RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVI----SMNCRLAGD 183
             +  R    LR  L    +A+TD   +   V  +A+ L ++E +VI    + N   +G 
Sbjct: 149 --HVPRRLQELRSELAKAQEALTDVLGRAPTVKEVAEHLELTEEQVIDGLVAANGYTSG- 205

Query: 184 ESLNALINSSDKNSSQWQDW-----LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
            SL+A    S+ + S  +       LV D D   ++  +        + L   +  L+ R
Sbjct: 206 -SLDAAAGESETSPSTGRSTRPLADLVGDVDPAMELFEDL-------HTLAPLLRQLDER 257

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +R I + R  Q+   T   + SE  +S+ +V ++ +R   +++  +
Sbjct: 258 DRLILQMRFGQDR--TQAEIGSELGISQMQVSRLLSRTLARLRTGM 301


>gi|256269|gb|AAC60415.1| RpoD2 [Synechococcus]
          Length = 48

 Score = 48.5 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 17/41 (41%), Positives = 30/41 (73%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           +++ EG +GL + V+KFDP +G++ +TY+ WWI+ A+   I
Sbjct: 2   DLIQEGTLGLERGVEKFDPSKGYKFSTYAYWWIRQAITRAI 42


>gi|226311507|ref|YP_002771401.1| RNA polymerase sigma-K factor precursor [Brevibacillus brevis NBRC
           100599]
 gi|226094455|dbj|BAH42897.1| RNA polymerase sigma-K factor precursor [Brevibacillus brevis NBRC
           100599]
          Length = 119

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 27/84 (32%), Positives = 48/84 (57%), Gaps = 2/84 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ + +EE  L  R    GD  A ++L+  +LRLV  I   +   G    +++S G IGL
Sbjct: 30  PLQDTEEEKYL--RLMAKGDPYARNKLIEHNLRLVAHIVKKFENTGEDSEDLISIGTIGL 87

Query: 87  MQAVKKFDPERGFRLATYSMWWIK 110
           ++A++ +  ++G +LATY+   I+
Sbjct: 88  IKAIESYQVDKGTKLATYAARCIE 111


>gi|160939653|ref|ZP_02087001.1| hypothetical protein CLOBOL_04545 [Clostridium bolteae ATCC
           BAA-613]
 gi|158437444|gb|EDP15208.1| hypothetical protein CLOBOL_04545 [Clostridium bolteae ATCC
           BAA-613]
          Length = 258

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 24/80 (30%), Positives = 47/80 (58%), Gaps = 3/80 (3%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFDPER 97
           YR++G     +RL+  +L +V   A+  R   G  L   E++ +G + L++ ++++DP+R
Sbjct: 18  YRKNGSQELRNRLIMHYLPIVRSAAVQLRSMAGSLLEQEELIDQGVLALIECLERYDPDR 77

Query: 98  GFRLATYSMWWIKAAMQEYI 117
           G R  T++   ++ AM +YI
Sbjct: 78  GARFETFAFMRVRGAMIDYI 97


>gi|258514354|ref|YP_003190576.1| sporulation sigma factor SigG [Desulfotomaculum acetoxidans DSM
           771]
 gi|257778059|gb|ACV61953.1| RNA polymerase, sigma 28 subunit, SigG [Desulfotomaculum
           acetoxidans DSM 771]
          Length = 257

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 22/75 (29%), Positives = 42/75 (56%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD SA  +L+  +LRLV+ +   +   G  + ++   G IGLM+A+  FD  +  + +
Sbjct: 32  QQGDTSARPQLINGNLRLVLSVIQRFTNRGEYVDDLFQVGCIGLMKAIDNFDLAQNVKFS 91

Query: 103 TYSMWWIKAAMQEYI 117
           TY++  I   ++ Y+
Sbjct: 92  TYAVPMIIGEIRRYL 106


>gi|153852719|ref|ZP_01994156.1| hypothetical protein DORLON_00138 [Dorea longicatena DSM 13814]
 gi|149754361|gb|EDM64292.1| hypothetical protein DORLON_00138 [Dorea longicatena DSM 13814]
          Length = 237

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 64/249 (25%), Positives = 111/249 (44%), Gaps = 34/249 (13%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A  ++V  +  LV  I   + G G  + ++   G IGL++A+ KFD     + +TY
Sbjct: 14  GDEEARAQIVEENTGLVWCIVRRFTGRGTELEDLFQIGTIGLLKAIDKFDLSYEVKFSTY 73

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH-LQAITDNNLKPE-QVVAI 162
           ++  I   ++ + LR   ++K+  + + K L +     KG+  Q +    L  E  V  +
Sbjct: 74  AVPMISGEIKRF-LRDDGMIKV--SRSLKELSY-----KGYQAQEVLGRKLGREPSVTEL 125

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK---- 218
           A+ L+VS  E+          ESL+                 VY  +GQE  L+EK    
Sbjct: 126 AEYLDVSPEELTMAMDACTDVESLHR---------------PVYKKEGQEISLMEKVGKE 170

Query: 219 ---EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
              EER     +L   ++ L+  ER++   R   E   T   +  E  +S+ +V ++E +
Sbjct: 171 DGAEERVLDHLLLKELLTSLDKEERKLIYLRYFAEKTQT--QIGKEMGISQVQVSRMEKK 228

Query: 276 AFKKVQESI 284
             K ++E I
Sbjct: 229 ILKNLRERI 237


>gi|15639696|ref|NP_219146.1| RNA polymerase sigma factor WhiG [Treponema pallidum subsp.
           pallidum str. Nichols]
 gi|189025934|ref|YP_001933706.1| RNA polymerase sigma factor WhiG [Treponema pallidum subsp.
           pallidum SS14]
 gi|3323011|gb|AAC65675.1| RNA polymerase sigma-28 factor [Treponema pallidum subsp. pallidum
           str. Nichols]
 gi|189018509|gb|ACD71127.1| RNA polymerase sigma-28 factor [Treponema pallidum subsp. pallidum
           SS14]
          Length = 262

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 54/220 (24%), Positives = 102/220 (46%), Gaps = 23/220 (10%)

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           KIA+G  G  +   ++VS G  GL  A+ K+DPE+  R  TY++  I+ A+ +  LRS  
Sbjct: 44  KIAVGKPG-NVEFDDLVSYGIFGLFDAIDKYDPEKNIRFNTYAVTRIRGAIFDE-LRSID 101

Query: 123 LVKIGTTANQKRLFFNLRRLKGHL-QAITDNNLKPEQVVAIAKK----LNVSESEVISM- 176
            V        +++   +  L+  L +  TD  +     + + +     L VS + VIS+ 
Sbjct: 102 WVPRSVRQQTRQIEEAIADLEARLGRXATDTEIACALNIELEEYHQLLLKVSGTSVISLA 161

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
           + +  GDE  +  +  S +  +               V++E+EE K    ++  ++  L+
Sbjct: 162 DSKFGGDERDHVSVGDSIEAPASL----------NPDVIVEREEIK---RIIAEAIRELS 208

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
            RE+++      +E  +TL+ +    +V+  R+ QI   A
Sbjct: 209 QREQQVLILYYYEE--MTLKEIGKVLKVTESRISQIHTSA 246


>gi|160892497|ref|ZP_02073287.1| hypothetical protein CLOL250_00024 [Clostridium sp. L2-50]
 gi|156865538|gb|EDO58969.1| hypothetical protein CLOL250_00024 [Clostridium sp. L2-50]
          Length = 258

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 61/268 (22%), Positives = 118/268 (44%), Gaps = 39/268 (14%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           ++P+L  +E+  L  R  E GD++A    +  +LRLV+ +   +        ++   G I
Sbjct: 15  RLPLLTDKEKDELFDRI-EQGDMAARETFIKGNLRLVLSVIQRFSNSNENPDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD     + +TY++  I    + Y+  + S+          R+  +LR +  
Sbjct: 74  GLIKAIDNFDRSLNVKFSTYAVPMILGECRRYLRDNNSI----------RVSRSLRDIAY 123

Query: 145 HLQAITDNNLKP----EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
                 D  LK       V  IAK+++V+  ++ +         +L+A+        S +
Sbjct: 124 KAIYTKDALLKKLDREPTVDEIAKEIDVAPEDITT---------ALDAISTP----VSLY 170

Query: 201 QDWLVYDHDGQEQVLIEK-EERKNRRN------MLTRSMSVLNPRERRIFEARRLQENPV 253
           +   VY   G    ++++  ++KN+         L  +M  LN RE  I   R  +    
Sbjct: 171 EP--VYQEGGDTLYIVDQLSDKKNKEENWVENISLKEAMKKLNEREYNILRLRFFEGKTQ 228

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           T   ++SE  +S+ +V +IE  A K ++
Sbjct: 229 T--EVASEIAISQAQVSRIEKSAIKSLK 254


>gi|154686587|ref|YP_001421748.1| sporulation sigma factor SigF [Bacillus amyloliquefaciens FZB42]
 gi|308174131|ref|YP_003920836.1| RNA polymerase sporulation-specific sigma factor sigma-F [Bacillus
           amyloliquefaciens DSM 7]
 gi|63146682|emb|CAG28933.1| Sigma F [Bacillus amyloliquefaciens FZB42]
 gi|154352438|gb|ABS74517.1| SigF [Bacillus amyloliquefaciens FZB42]
 gi|307606995|emb|CBI43366.1| RNA polymerase sporulation-specific sigma factor (sigma-F)
           [Bacillus amyloliquefaciens DSM 7]
 gi|328552736|gb|AEB23228.1| sporulation sigma factor SigF [Bacillus amyloliquefaciens TA208]
 gi|328912466|gb|AEB64062.1| RNA polymerase sigma factor [Bacillus amyloliquefaciens LL3]
          Length = 255

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 56/244 (22%), Positives = 105/244 (43%), Gaps = 28/244 (11%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A   L+  ++RLV  +   +   G    ++   G IGL+++V KFD     R +
Sbjct: 27  QEGDQQARDLLIEKNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKSVDKFDLSYDVRFS 86

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I   +Q +I R    VK+  +   K L   +RR K  L   +    +   V  I
Sbjct: 87  TYAVPMIIGEIQRFI-RDDGTVKVSRSL--KELGNKIRRAKDEL---SKTYGRVPTVQEI 140

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ-----EQVLIE 217
           A  L +   +V+     +    S++                 VY++DG      +Q+   
Sbjct: 141 ADHLEIDAEDVVLAQEAVRAPSSIHE---------------TVYENDGDPITLLDQIADH 185

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
            EE+   +  L  ++S L  RE+ I   R  ++   T   ++    +S+ +V ++E +  
Sbjct: 186 SEEKWFDKIALKEAISDLEEREKLIVYLRYYKDQ--TQSEVAERLGISQVQVSRLEKKIL 243

Query: 278 KKVQ 281
           K+++
Sbjct: 244 KQIK 247


>gi|149181668|ref|ZP_01860161.1| sporulation sigma factor SigF [Bacillus sp. SG-1]
 gi|148850646|gb|EDL64803.1| sporulation sigma factor SigF [Bacillus sp. SG-1]
          Length = 253

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 51/177 (28%), Positives = 81/177 (45%), Gaps = 17/177 (9%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L KR +E GD SA   +V  ++RLV  +   +   G    ++   G IGL+++V KFD  
Sbjct: 22  LIKRSQE-GDQSARDTIVQKNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKSVDKFDLS 80

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI-----TD 151
              + +TY++  I   +Q +I R    VK+  +   K +   +RR K  L        T 
Sbjct: 81  YDVKFSTYAVPMIIGEIQRFI-RDDGTVKVSRSL--KEMGNRIRRAKDELSKTFGRVPTV 137

Query: 152 N------NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
           N       L PE+VV +A++ + S S +        GD  +  L   SD +  +W D
Sbjct: 138 NEIAAHLELSPEEVV-MAQEASRSPSSIHETVYENDGD-PITLLDQISDTSDQKWFD 192


>gi|240145516|ref|ZP_04744117.1| RNA polymerase sigma-E factor [Roseburia intestinalis L1-82]
 gi|257202333|gb|EEV00618.1| RNA polymerase sigma-E factor [Roseburia intestinalis L1-82]
          Length = 207

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 28/83 (33%), Positives = 45/83 (54%), Gaps = 2/83 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  +QE   L K  +  G L A + L   ++RLV  +A  Y+     + +++S G IGL
Sbjct: 7   PLTPEQENECLKKLKK--GSLEARNELTLHNMRLVAHVAKKYQNSEEDMEDLISIGTIGL 64

Query: 87  MQAVKKFDPERGFRLATYSMWWI 109
           M+A+  +  + G RLATY+   I
Sbjct: 65  MKAIATYKEDYGSRLATYAARCI 87


>gi|220931430|ref|YP_002508338.1| sporulation sigma factor SigK [Halothermothrix orenii H 168]
 gi|219992740|gb|ACL69343.1| sporulation sigma factor SigK [Halothermothrix orenii H 168]
          Length = 232

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 59/256 (23%), Positives = 103/256 (40%), Gaps = 67/256 (26%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           E++E+Y+  KR R+ GD  A + L+  +LRLV  I   Y        +++S G IGL++ 
Sbjct: 32  EEEEKYI--KRMRQ-GDEEARNILIEHNLRLVAHIVKKYNSVYTDNEDLISIGTIGLIKG 88

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +  +D  +  +LATY+   I                      +  +  +LR +K      
Sbjct: 89  INTYDETKKTKLATYAARCI----------------------ENEILMHLRSVK------ 120

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS-DKNSSQWQDWLVYDH 208
                                        +L+ +  L   I S  D N     D L    
Sbjct: 121 -----------------------------KLSNETLLQESIGSDKDGNDITLMDVL---- 147

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSR 266
           D +E  +I K E+      L   +  L+PRE+++ E R   L    +T + ++S   +SR
Sbjct: 148 DTREDSVINKVEKSIDEEQLYNKLGELSPREKKVLELRYGLLDGKRLTQKEVASILGISR 207

Query: 267 ERVRQIEARAFKKVQE 282
             V +IE +A +++ +
Sbjct: 208 SYVSRIEKKAIQELSD 223


>gi|153487|gb|AAA26829.1| sigma factor (whiG) (put. alt.) (gtg start codon); putative
           [Streptomyces coelicolor]
          Length = 258

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 61/245 (24%), Positives = 104/245 (42%), Gaps = 20/245 (8%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFD 94
           + Y+  GD     +L+  H   +VK   G    GLP     ++ VS G  GL+ A++KFD
Sbjct: 14  RSYKTTGDERLREQLIL-HYSPLVKYVAGRVSVGLPPNVEQADFVSSGVFGLIDAIEKFD 72

Query: 95  PERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
            +R  +  TY++  I+ AM  E     W    I  +  QK    N+ R    L+A     
Sbjct: 73  VDREIKFETYAITRIRGAMIDELRALDW----IPRSVRQKAR--NVERAYATLEARLRRT 126

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ--DWLVYDHDGQ 211
              E  VA+   + V +   +     LA   +L  L+++  +   +    D L    D  
Sbjct: 127 -PSESEVAVEMGIAVEDLHAVFSQLSLANVVALEELLHAGGEGGGRLSLMDTL---EDTA 182

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
               +E  E +  R +L R+++ L  RE+ +      +   +TL  + +   V+  RV Q
Sbjct: 183 ADNPVEVAEDRELRRLLARAINTLPEREKTVVTLYYYE--GLTLAEIGNVLGVTESRVSQ 240

Query: 272 IEARA 276
           I  ++
Sbjct: 241 IHTKS 245


>gi|255315371|ref|ZP_05356954.1| sporulation sigma factor SigE [Clostridium difficile QCD-76w55]
          Length = 240

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 28/91 (30%), Positives = 50/91 (54%), Gaps = 2/91 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L+ +EE  L ++     D +    L+  +LRLVV I+  +   G+ + +++S G IGL
Sbjct: 38  PPLKPEEEMELLQKL--ETDENVKSILIERNLRLVVYISRKFENTGIDVEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           ++AV  F   +  +LATY+   I+  +  Y+
Sbjct: 96  IKAVNTFKLNKNIKLATYASRCIENEILMYL 126


>gi|225174918|ref|ZP_03728915.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Dethiobacter
           alkaliphilus AHT 1]
 gi|225169558|gb|EEG78355.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Dethiobacter
           alkaliphilus AHT 1]
          Length = 231

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 39/135 (28%), Positives = 65/135 (48%), Gaps = 10/135 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRG-YGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           YR+ G      R+V +   L+   A  Y G +G    + V  G  GLM+AV++++  +G 
Sbjct: 14  YRKSGKDEDLERVVEAGRSLIHHFARLYTGGFG---EDAVQAGMEGLMKAVQRYEVGKGT 70

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
             ATY+   +   ++ Y+ +  S  + G+    K L F + RL   +  +     +P  V
Sbjct: 71  AFATYAAHCVMGEIRHYVRKESSYYRPGSI---KDLQFRVARL---VDEVLKETGEPPGV 124

Query: 160 VAIAKKLNVSESEVI 174
             IAK+LNV E  V+
Sbjct: 125 SEIAKRLNVKEEGVV 139


>gi|254383401|ref|ZP_04998753.1| RNA polymerase sigma factor [Streptomyces sp. Mg1]
 gi|194342298|gb|EDX23264.1| RNA polymerase sigma factor [Streptomyces sp. Mg1]
          Length = 311

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 46/175 (26%), Positives = 81/175 (46%), Gaps = 20/175 (11%)

Query: 1   MNRKNMSIIVNGEI-GLSRYIHEIRKIPML-EKQEEYVLAKRYREHGDLSAAHRLVTSHL 58
           MNR +++ +  GE   LS  +   R++  L E   EY   +           + LV  +L
Sbjct: 20  MNRTDLTAVDTGEARALSATL--FRRLAELHEGSPEYSYVR-----------NTLVELNL 66

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
            LV   A  +R    P+ ++V  G IGL++A+ +FDP RG    +++M  I   ++ +  
Sbjct: 67  SLVRYAARRFRARSEPMEDIVQVGTIGLIKAINRFDPGRGVEFTSFAMPTITGEIKRFFR 126

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
            +   VK+     + R    +   K H  A+  +  +P   V +A +L+VS  E+
Sbjct: 127 DTSWAVKVPRRLQELR----IDAAKAH-DALEQDLGRPPSDVELAGRLHVSPEEL 176


>gi|218778853|ref|YP_002430171.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfatibacillum
           alkenivorans AK-01]
 gi|218760237|gb|ACL02703.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfatibacillum
           alkenivorans AK-01]
          Length = 252

 Score = 48.5 bits (114), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 49/217 (22%), Positives = 106/217 (48%), Gaps = 18/217 (8%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++S G +GL+ A+ K+D  RG +  TY+ + I+ AM +  LR+   V        + 
Sbjct: 46  VDDLISAGIMGLLDALDKYDEGRGVKFRTYAEFRIRGAMLDE-LRAMDWVP-------RS 97

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINS 192
           +   ++ ++  +  +     +P     IA +L V      +M  +  G E  SL+  + S
Sbjct: 98  VRKKVQEIEQAVNRVEKRESRPADAEEIANELGVDMDTYQNMLSKAGGIELVSLDEPLWS 157

Query: 193 SD--KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           +D  K+  +    L+ D+   ++ L++ E +K    +L +S+S L P+E++I       +
Sbjct: 158 NDNTKDGRRTHVDLLEDNANPDRDLMDSEFKK----ILAQSISSLTPKEQQILSL--YYQ 211

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           + +TL+ +     ++  R+ QI  +   K++  ++ Q
Sbjct: 212 DELTLKEVGEVMGLTESRICQIHTQCMIKLRSKLKTQ 248


>gi|302544852|ref|ZP_07297194.1| putative RNA polymerase sigma factor [Streptomyces hygroscopicus
           ATCC 53653]
 gi|302462470|gb|EFL25563.1| putative RNA polymerase sigma factor [Streptomyces himastatinicus
           ATCC 53653]
          Length = 315

 Score = 48.1 bits (113), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 45/170 (26%), Positives = 79/170 (46%), Gaps = 20/170 (11%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  +L LV   A  +R    P+ ++V  G IGL++A+ +F+P RG    T++M  I   
Sbjct: 94  LVELNLALVKFAASRFRSRSEPMEDIVQVGTIGLIKAIDRFEPGRGVEFPTFAMPTIVGE 153

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL  +L +    L    D   +   V  +A++L+++ +
Sbjct: 154 IKRFFRDTSWS-VRVPRRLQELRL--DLAKAGDELAQRLD---RAPTVHELAQRLDITTA 207

Query: 172 EVISMNCRLAGDESLNALINSS-------DKNSSQWQDWLVYDHDGQEQV 214
           EV+       G  + NA   SS       D +     D + Y+  G E +
Sbjct: 208 EVVE------GMAASNAYTASSLDAQPEEDDSEGALADRIGYEDHGLEGI 251


>gi|222632729|gb|EEE64861.1| hypothetical protein OsJ_19718 [Oryza sativa Japonica Group]
          Length = 457

 Score = 48.1 bits (113), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 28/99 (28%), Positives = 51/99 (51%), Gaps = 21/99 (21%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLP-------ISEVVSEGNIGLMQAVKKFDPERGFR 100
           +A ++L+  +LRLV+     Y     P         ++   G  GL+ A+ +F+P+RGFR
Sbjct: 219 AARNKLIKHNLRLVLYTINKY----YPDMSNDERFDDICQAGANGLITAIDRFEPKRGFR 274

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
           ++TY+++WI+           S+V+  T +N  R  F +
Sbjct: 275 ISTYALFWIR----------HSIVRAITLSNFTRFPFAM 303


>gi|324998294|ref|ZP_08119406.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily protein
           [Pseudonocardia sp. P1]
          Length = 258

 Score = 48.1 bits (113), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 46/194 (23%), Positives = 88/194 (45%), Gaps = 18/194 (9%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RLVT +L +   IA  +   G P+ ++V    +GL+ A+ +FDP++G    ++++  I  
Sbjct: 33  RLVTGYLPVAQHIARRFNHRGEPLDDLVQVATVGLINAIDRFDPDKGGEFFSFAVPTISG 92

Query: 112 AMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            ++ +   +SWS+         K +  ++      L      + +P +   IA+ L +  
Sbjct: 93  EVRRHFRDQSWSMR---VPRRLKDMHVSINGAVSELSQTLGRSPRPSE---IAEHLGLPV 146

Query: 171 SEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            EV+            SL+ +++S D  ++  +  LV D D +        +R + R  L
Sbjct: 147 PEVLEGLEAAEAYRSSSLDEMLSSEDGGATVGE--LVGDADAE-------LDRVDYRESL 197

Query: 229 TRSMSVLNPRERRI 242
              ++ L PRER I
Sbjct: 198 RPLLAELAPRERTI 211


>gi|302551910|ref|ZP_07304252.1| RNA polymerase sigma-E factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302469528|gb|EFL32621.1| RNA polymerase sigma-E factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 304

 Score = 48.1 bits (113), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 56/240 (23%), Positives = 108/240 (45%), Gaps = 30/240 (12%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  +L LV   A  +R    P+ +++  G IGL++A+ +F+  RG    T++M  I   
Sbjct: 83  LVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRGVEFPTFAMPTIVGE 142

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL  +L +    L    D   +   V  +A++L +S  
Sbjct: 143 IKRFFRDTSWS-VRVPRRLQELRL--DLAKAGDELAQKLD---RAPTVTELAERLGISND 196

Query: 172 EVISMNCRLAGDESLNALINSS-------DKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           EV+       G  + NA   SS       D +     D + Y+  G E +    E  ++ 
Sbjct: 197 EVVE------GMAASNAYTASSLDAQPEEDDSEGALADRIGYEDHGLEGI----EYVESL 246

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + ++      L PR+R+I   R +    +T   +  E  +S+  V ++ +R   ++++ +
Sbjct: 247 KPLIAE----LPPRDRKILSLRFVAG--LTQSEIGEELGISQMHVSRLLSRTLVRLRKGL 300


>gi|238063793|ref|ZP_04608502.1| RNA polymerase sigma factor [Micromonospora sp. ATCC 39149]
 gi|237885604|gb|EEP74432.1| RNA polymerase sigma factor [Micromonospora sp. ATCC 39149]
          Length = 294

 Score = 48.1 bits (113), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 59/240 (24%), Positives = 100/240 (41%), Gaps = 34/240 (14%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R + + L L   +A  Y G G P  ++     +GL++A+ KFDP RG   A Y++  I  
Sbjct: 72  RAIEAWLPLANHLAHRYSGRGEPTDDLAQTAAVGLIKAIDKFDPSRGVDFAGYAIPTIIG 131

Query: 112 AMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV---------VA 161
            ++ +   R+W  +++             RRL+    AI+D N    Q          +A
Sbjct: 132 ELKRHFRDRTWD-IRVP------------RRLQELRLAISDANSTLLQTLGRSPTVADIA 178

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
              KL   E        R     SL+      D+ +++  D L     G E    E  E 
Sbjct: 179 AHLKLTEEEVLEGLEGARAYNAVSLSTPTGDGDR-ATELGDML-----GGEDTEFELAE- 231

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              R  L  +++ L+ RE++I   R      +T   ++ +  VS+  V ++ ARA  K++
Sbjct: 232 --LRVALGPALATLDEREQKILTLRFYGN--LTQSQIADQIGVSQMHVSRLLARALTKLR 287


>gi|182440445|ref|YP_001828164.1| RNA polymerase sigma factor [Streptomyces griseus subsp. griseus
           NBRC 13350]
 gi|326781114|ref|ZP_08240379.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
 gi|178468961|dbj|BAG23481.1| RNA polymerase sigma factor [Streptomyces griseus subsp. griseus
           NBRC 13350]
 gi|326661447|gb|EGE46293.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
          Length = 293

 Score = 48.1 bits (113), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 53/224 (23%), Positives = 103/224 (45%), Gaps = 19/224 (8%)

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIG 127
           RG G  + ++V  G IGL++A+ +FD  R     ++++ +I   ++ +    SW+   + 
Sbjct: 83  RGSG-DMEDIVQVGTIGLIKAIDRFDLSREVEFTSFAVPYIVGEIKRFFRDTSWA---VH 138

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----ISMNCRLAGD 183
                + L  +L + K  L  + D +   ++   +A+ L + ESEV    ++ N   AG 
Sbjct: 139 VPRRLQELRVDLAKAKEALAGVLDRDPTAKE---LAEYLGIEESEVTEGIVASNGYTAG- 194

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SL+   ++++    Q       D  G     +E  E     + L   +  L+ RERRI 
Sbjct: 195 -SLDMPTDTAEAGPGQTAGRTFADVLGDPDPAMEAVENL---HALAPLLDELDERERRII 250

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           + R  QE  +T   + +E  +S+  V ++ +R   K++  +  Q
Sbjct: 251 DMRFGQE--MTQAQIGAELGISQMHVSRLLSRMLGKLRSGMLVQ 292


>gi|16078710|ref|NP_389529.1| RNA polymerase sigma factor SigD [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221309525|ref|ZP_03591372.1| RNA polymerase sigma factor SigD [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221313849|ref|ZP_03595654.1| RNA polymerase sigma factor SigD [Bacillus subtilis subsp. subtilis
           str. NCIB 3610]
 gi|221318772|ref|ZP_03600066.1| RNA polymerase sigma factor SigD [Bacillus subtilis subsp. subtilis
           str. JH642]
 gi|221323044|ref|ZP_03604338.1| RNA polymerase sigma factor SigD [Bacillus subtilis subsp. subtilis
           str. SMY]
 gi|296330862|ref|ZP_06873337.1| RNA polymerase sigma factor SigD [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305674380|ref|YP_003866052.1| RNA polymerase sigma factor sigma-D [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|321315414|ref|YP_004207701.1| RNA polymerase sigma factor SigD [Bacillus subtilis BSn5]
 gi|1350863|sp|P10726|RPSD_BACSU RecName: Full=RNA polymerase sigma-D factor; AltName: Full=Sigma-28
 gi|289304|gb|AAA61470.1| sigma factor 28 [Bacillus subtilis]
 gi|2634019|emb|CAB13520.1| RNA polymerase sigma-28 factor (sigma-D) [Bacillus subtilis subsp.
           subtilis str. 168]
 gi|291484202|dbj|BAI85277.1| RNA polymerase sigma factor SigD [Bacillus subtilis subsp. natto
           BEST195]
 gi|296151867|gb|EFG92741.1| RNA polymerase sigma factor SigD [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305412624|gb|ADM37743.1| RNA polymerase sigma factor sigma-D [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|320021688|gb|ADV96674.1| RNA polymerase sigma factor SigD [Bacillus subtilis BSn5]
          Length = 254

 Score = 48.1 bits (113), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 62/272 (22%), Positives = 126/272 (46%), Gaps = 39/272 (14%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQ 88
           E+ VL  R++E  D  A   L+  ++ LV    +G    GLP S    +++S G +GL  
Sbjct: 7   EDQVLWTRWKEWKDPKAGDDLMRRYMPLVT-YHVGRISVGLPKSVHKDDLMSLGMLGLYD 65

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           A++KFDP R  +  TY+ + I+ A+ + + +  W    +  T+ +K      ++++  ++
Sbjct: 66  ALEKFDPSRDLKFDTYASFRIRGAIIDGLRKEDW----LPRTSREKT-----KKVEAAIE 116

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVIS-MNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
            +    L+      IA++L ++  +V+S MN      E   A + S D+         ++
Sbjct: 117 KLEQRYLRNVSPAEIAEELGMTVQDVVSTMN------EGFFANLLSIDEK--------LH 162

Query: 207 DHDGQEQVLIEKEERKN----RRNMLTRSMSVLNPRERRIFEARRL-----QENPVTLEN 257
           D D  E + +   + KN     + M    ++ L  +   + E  +L      +  +TL  
Sbjct: 163 DQDDGENIQVMIRDDKNVPPEEKIMKDELIAQLAEKIHELSEKEQLVVSLFYKEELTLTE 222

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           +     +S  R+ QI ++A  K++  ++K ++
Sbjct: 223 IGQVLNLSTSRISQIHSKALFKLKNLLEKVIQ 254


>gi|160943880|ref|ZP_02091110.1| hypothetical protein FAEPRAM212_01380 [Faecalibacterium prausnitzii
           M21/2]
 gi|158444556|gb|EDP21560.1| hypothetical protein FAEPRAM212_01380 [Faecalibacterium prausnitzii
           M21/2]
 gi|295104729|emb|CBL02273.1| RNA polymerase, sigma subunit, RpsG/SigG [Faecalibacterium
           prausnitzii SL3/3]
          Length = 255

 Score = 48.1 bits (113), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 59/258 (22%), Positives = 121/258 (46%), Gaps = 24/258 (9%)

Query: 25  KIPML---EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           ++P+L   EK++   LA      GD +A  R+V  +LRLV+ +   +   G  + ++   
Sbjct: 14  QLPVLTEAEKRQLLTLA----HAGDKAARARMVEGNLRLVLSVVQRFAQRGENLDDLFQV 69

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           G IGL++A+  FDP +  R +TY +  I   ++ + LR  + +++  T   +   +   +
Sbjct: 70  GCIGLIKAIDNFDPAQPVRFSTYGVPMIIGEIRRF-LRDNNALRVSRTL--RDTAYRAMQ 126

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
            +  L+         +++ A A    ++  EV +    +    SL+  +  +D   + + 
Sbjct: 127 ARETLEKQLGREPTMDEIAAAA---GLARREVTAALESVVEPLSLDEPV-YTDGGDAMYV 182

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
              V D D +E  +   + R         +++ L+PRE+RI E R L+    T   ++ E
Sbjct: 183 IDQVRDPDSEESWISGLQFRD--------TVAALSPREKRIMELRYLRGK--TQMEVAQE 232

Query: 262 FEVSRERVRQIEARAFKK 279
             +S+ +V ++E  A ++
Sbjct: 233 IGISQAQVSRLEKGALQQ 250


>gi|239944630|ref|ZP_04696567.1| RNA polymerase sigma factor WhiG [Streptomyces roseosporus NRRL
           15998]
 gi|239991094|ref|ZP_04711758.1| RNA polymerase sigma factor WhiG [Streptomyces roseosporus NRRL
           11379]
          Length = 247

 Score = 48.1 bits (113), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 61/248 (24%), Positives = 110/248 (44%), Gaps = 26/248 (10%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFD 94
           + Y+  GD     +L+  H   +VK   G    GLP     ++ VS G  GL+ A++KFD
Sbjct: 3   RSYKTTGDERLREQLIL-HYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEKFD 61

Query: 95  PERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTA-NQKRLFFNL----RRLKGHLQA 148
            ER  +  TY++  I+ AM  E     W    +   A N +R +  L    RR     + 
Sbjct: 62  IERAIKFETYAITRIRGAMIDELRALDWIPRSVRQKARNVERAYATLEAQFRRTPSEAEV 121

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
            ++  +  E++ A+  +L++  + V+++      +E L+      D+ S    D L    
Sbjct: 122 ASEMGIALEELHAVFSQLSL--ANVVAL------EELLHVGGEGGDRLS--LMDTL---E 168

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D      +E  E +  R +L R+++ L  RE+ +      +   +TL  + +   V+  R
Sbjct: 169 DTAADNPVEVAEDRELRRLLARAINTLPDREKTVVTLYYYE--GLTLAEIGNVLGVTESR 226

Query: 269 VRQIEARA 276
           V QI  ++
Sbjct: 227 VSQIHTKS 234


>gi|251796351|ref|YP_003011082.1| sporulation sigma factor SigF [Paenibacillus sp. JDR-2]
 gi|247543977|gb|ACT00996.1| RNA polymerase, sigma 28 subunit, SigF [Paenibacillus sp. JDR-2]
          Length = 251

 Score = 48.1 bits (113), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 58/256 (22%), Positives = 117/256 (45%), Gaps = 42/256 (16%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A   LV  ++RLV  +   +   G    ++   G IGL+++V KFD     + +
Sbjct: 26  QSGDTIARDTLVQCNIRLVWSVVQRFINRGYEPEDLFQIGCIGLLKSVDKFDLSYDVKFS 85

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIG----TTANQKRLFFN-LRRLKGHLQAITDNNLKPE 157
           TY++  I   +Q + LR    +K+      TAN+ R   + L +  G L  +++      
Sbjct: 86  TYAVPMIIGEIQRF-LRDDGTLKVSRSLKETANKVRKMKDELSKTLGRLPTVSE------ 138

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ-----E 212
               +A +L ++  +V+                  ++K  +   +  V+++DG      +
Sbjct: 139 ----VADRLGITPEDVV--------------FAQEANKPPTSIHE-TVFENDGDPITLMD 179

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           Q+  + +ER   +  L  ++  L+ RER I   R  ++   T   ++S   +S+ +V ++
Sbjct: 180 QIADDSQERWFDKLALIEAIEGLSERERLIVYLRYYRDK--TQSEVASRLGISQVQVSRL 237

Query: 273 EARAFKKVQESIQKQV 288
           E    KK+ +SI++Q+
Sbjct: 238 E----KKILQSIREQI 249


>gi|21223976|ref|NP_629755.1| RNA polymerase sigma factor WhiG [Streptomyces coelicolor A3(2)]
 gi|256784937|ref|ZP_05523368.1| RNA polymerase sigma factor WhiG [Streptomyces lividans TK24]
 gi|289768830|ref|ZP_06528208.1| RNA polymerase sigma factor whiG [Streptomyces lividans TK24]
 gi|133480|sp|P17211|RPSW_STRCO RecName: Full=RNA polymerase sigma factor whiG
 gi|153486|gb|AAA26828.1| sigma factor (whiG) (put. alt.); putative [Streptomyces coelicolor]
 gi|3192014|emb|CAA19413.1| RNA polymerase sigma factor WhiG [Streptomyces coelicolor A3(2)]
 gi|289699029|gb|EFD66458.1| RNA polymerase sigma factor whiG [Streptomyces lividans TK24]
          Length = 280

 Score = 48.1 bits (113), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 61/245 (24%), Positives = 104/245 (42%), Gaps = 20/245 (8%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFD 94
           + Y+  GD     +L+  H   +VK   G    GLP     ++ VS G  GL+ A++KFD
Sbjct: 36  RSYKTTGDERLREQLIL-HYSPLVKYVAGRVSVGLPPNVEQADFVSSGVFGLIDAIEKFD 94

Query: 95  PERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
            +R  +  TY++  I+ AM  E     W    I  +  QK    N+ R    L+A     
Sbjct: 95  VDREIKFETYAITRIRGAMIDELRALDW----IPRSVRQKAR--NVERAYATLEARL-RR 147

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ--DWLVYDHDGQ 211
              E  VA+   + V +   +     LA   +L  L+++  +   +    D L    D  
Sbjct: 148 TPSESEVAVEMGIAVEDLHAVFSQLSLANVVALEELLHAGGEGGGRLSLMDTL---EDTA 204

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
               +E  E +  R +L R+++ L  RE+ +      +   +TL  + +   V+  RV Q
Sbjct: 205 ADNPVEVAEDRELRRLLARAINTLPEREKTVVTLYYYEG--LTLAEIGNVLGVTESRVSQ 262

Query: 272 IEARA 276
           I  ++
Sbjct: 263 IHTKS 267


>gi|284044899|ref|YP_003395239.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
 gi|283949120|gb|ADB51864.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
          Length = 273

 Score = 48.1 bits (113), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 57/213 (26%), Positives = 94/213 (44%), Gaps = 17/213 (7%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L +RY   GD  A   L+T  L L  ++A+ Y     P+ ++V   ++GL++AV +F+  
Sbjct: 35  LLERYHLRGDERAREELITRFLPLARQLALRYYHGREPLDDLVQVASVGLVKAVDRFEVR 94

Query: 97  RGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           R    A+Y++  +   ++ Y     W+L  +     ++ L  +  R    LQ        
Sbjct: 95  RTTAFASYAVPVMLGELRRYFRDNGWAL-HVPRGLQERALAVD--RTADRLQVAQGAAPT 151

Query: 156 PEQVVAIAKKLNVSESEVI-SMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
           P Q   IA++L ++  EV+ +M    A D  SL+A   S+D       D L  D    E 
Sbjct: 152 PAQ---IAEQLKLTVEEVVEAMAAARATDTVSLDAPRPSADGERDALVDSLGADDSRLE- 207

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
            L+E       R  +  ++  L  RER I   R
Sbjct: 208 -LVEY------REAIAGALDALPVREREILRLR 233


>gi|169831582|ref|YP_001717564.1| sporulation sigma factor SigG [Candidatus Desulforudis audaxviator
           MP104C]
 gi|169638426|gb|ACA59932.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Candidatus
           Desulforudis audaxviator MP104C]
          Length = 255

 Score = 48.1 bits (113), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 39/154 (25%), Positives = 74/154 (48%), Gaps = 15/154 (9%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L   E   L +   + GD SA  +L+  +LRLV+ +   +   G  + ++   G I
Sbjct: 14  KLPVLTAAEMRQLFQEM-QAGDPSARSKLINGNLRLVLSVIQRFTNRGEFVDDLFQVGCI 72

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD  +  + +TY++  I   ++ Y LR  + +++  +         LR +  
Sbjct: 73  GLIKAIDNFDLGQNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRS---------LRDVAY 122

Query: 145 HLQAITDNNL----KPEQVVAIAKKLNVSESEVI 174
               I DN      +   V  IA++LN+   E++
Sbjct: 123 KALQIRDNLANRFSREPSVSEIAQELNIPREEIV 156


>gi|51892360|ref|YP_075051.1| sporulation sigma factor SigG [Symbiobacterium thermophilum IAM
           14863]
 gi|51856049|dbj|BAD40207.1| RNA polymerase sigma factor similar to B. subtilis SigG
           [Symbiobacterium thermophilum IAM 14863]
          Length = 256

 Score = 48.1 bits (113), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 27/93 (29%), Positives = 50/93 (53%), Gaps = 1/93 (1%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L   +   L  R R  G+ +A   L+T +LRLV+ +   +   G  + ++   G I
Sbjct: 14  KLPVLTNAQMRELFVRMR-SGEKAARDELITGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 72

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           GLM+A+  FD  +  + +TY++  I   ++ Y+
Sbjct: 73  GLMKAIDNFDLGQNVKFSTYAVPMIIGEIRRYL 105


>gi|302389895|ref|YP_003825716.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK
           [Thermosediminibacter oceani DSM 16646]
 gi|302200523|gb|ADL08093.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK
           [Thermosediminibacter oceani DSM 16646]
          Length = 239

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 24/66 (36%), Positives = 39/66 (59%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           +GD  A + L+  +LRLV  I   +   G  + +++S G IGL++A+  F+  +G RLAT
Sbjct: 50  NGDEEARNILIERNLRLVAHIVKKFANTGEDMDDLISIGTIGLIKAITTFNKTKGNRLAT 109

Query: 104 YSMWWI 109
           Y+   I
Sbjct: 110 YAARCI 115


>gi|323484320|ref|ZP_08089687.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323694680|ref|ZP_08108842.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
 gi|323402314|gb|EGA94645.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323501272|gb|EGB17172.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
          Length = 209

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 31/84 (36%), Positives = 48/84 (57%), Gaps = 4/84 (4%)

Query: 27  PMLEKQE-EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           P+   +E EY+  KR +E GD  A   L+  +LRLV  +   Y+     + +++S G IG
Sbjct: 7   PLTASEEREYL--KRCKE-GDEEAKAVLIERNLRLVAHVIKKYQYTDYEMEDLLSVGTIG 63

Query: 86  LMQAVKKFDPERGFRLATYSMWWI 109
           L++AV  F  +RG RLATY+   +
Sbjct: 64  LIKAVNTFKMDRGSRLATYAAKCV 87


>gi|222528793|ref|YP_002572675.1| sporulation sigma factor SigE [Caldicellulosiruptor bescii DSM
           6725]
 gi|222455640|gb|ACM59902.1| RNA polymerase, sigma 28 subunit, SigE [Caldicellulosiruptor bescii
           DSM 6725]
          Length = 244

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 28/94 (29%), Positives = 49/94 (52%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EE  +  +    G       LV  +LRLVV IA  +    + + ++VS G IGL
Sbjct: 41  PPLTPDEEAQILYKIHYQGKEELKKLLVERNLRLVVYIARRFENTKINLEDLVSIGTIGL 100

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++A+  ++P +  +LATY+   I+  +  ++ R+
Sbjct: 101 IKAINTYNPNKNIKLATYASKCIENEILMFLRRN 134


>gi|253576139|ref|ZP_04853471.1| RNA polymerase sigma-G factor [Paenibacillus sp. oral taxon 786
           str. D14]
 gi|251844482|gb|EES72498.1| RNA polymerase sigma-G factor [Paenibacillus sp. oral taxon 786
           str. D14]
          Length = 260

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 59/274 (21%), Positives = 128/274 (46%), Gaps = 42/274 (15%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L   E   L    ++    SA  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLTNAEMRELFHSLQQDHVRSAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 74

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A+  FD  +  + +TY++  I   ++ Y LR  + +++  +   + + +   +++ 
Sbjct: 75  GLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSL--RDIAYKALQMRD 131

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
           +L   T+ N +   +  I++ L + + +V+          +L+A+           QD +
Sbjct: 132 NL---TNQNSREPTIFEISEALGLPKEDVVF---------ALDAI-----------QDPV 168

Query: 205 -----VYDHDGQEQVLIEKE--ERKNR------RNMLTRSMSVLNPRERRIFEARRLQEN 251
                +Y HDG + + +  +  + KN+         L  +M  L  RE+ I  + R  E 
Sbjct: 169 SLFEPIY-HDGGDPIYVMDQISDDKNKDVSWIEEIALREAMQRLGNREKMIL-SMRFFEG 226

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              +E ++ E  +S+ +V ++E  A  ++Q+ ++
Sbjct: 227 KTQME-VADEIGISQAQVSRLEKSAILQMQKHVK 259


>gi|281420137|ref|ZP_06251136.1| RNA polymerase sigma-43 factor [Prevotella copri DSM 18205]
 gi|281405937|gb|EFB36617.1| RNA polymerase sigma-43 factor [Prevotella copri DSM 18205]
          Length = 205

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 20/76 (26%), Positives = 43/76 (56%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           +++V+ +L  V  +A  Y+G G+   ++VSEG + ++ A +KF  +RG     Y+  ++ 
Sbjct: 7   NKIVSENLNYVKSVANQYKGKGVEFDDLVSEGTLAMLMAARKFQADRGTDFVAYAGPFVH 66

Query: 111 AAMQEYILRSWSLVKI 126
            A+ + I +   L ++
Sbjct: 67  KAISQAIDKQSGLYRL 82


>gi|295399263|ref|ZP_06809245.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|294978729|gb|EFG54325.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
          Length = 155

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 27/84 (32%), Positives = 47/84 (55%), Gaps = 2/84 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  K+EE  L  +    GD  A + L+  +LRLV  I   +   G  + +++S G IGL
Sbjct: 30  PLSAKEEEKYL--QLMAKGDEQARNILIEHNLRLVAHIVKKFENTGEDVEDLISIGTIGL 87

Query: 87  MQAVKKFDPERGFRLATYSMWWIK 110
           ++A++ +   +G +LATY+   I+
Sbjct: 88  IKAIESYSSNKGTKLATYAARCIE 111


>gi|125553511|gb|EAY99220.1| hypothetical protein OsI_21178 [Oryza sativa Indica Group]
          Length = 500

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 28/99 (28%), Positives = 51/99 (51%), Gaps = 21/99 (21%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLP-------ISEVVSEGNIGLMQAVKKFDPERGFR 100
           +A ++L+  +LRLV+     Y     P         ++   G  GL+ A+ +F+P+RGFR
Sbjct: 262 AARNKLIKHNLRLVLYTINKY----YPDMSNDERFDDICQAGANGLITAIDRFEPKRGFR 317

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
           ++TY+++WI+           S+V+  T +N  R  F +
Sbjct: 318 ISTYALFWIR----------HSIVRAITLSNFTRFPFAM 346


>gi|153854687|ref|ZP_01995937.1| hypothetical protein DORLON_01935 [Dorea longicatena DSM 13814]
 gi|149752791|gb|EDM62722.1| hypothetical protein DORLON_01935 [Dorea longicatena DSM 13814]
          Length = 258

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 60/262 (22%), Positives = 118/262 (45%), Gaps = 25/262 (9%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L ++E+  L  R +  GD  A    +  +LRLV+ +   +   G    ++   G I
Sbjct: 15  KLPILNEKEKEALFVRIK-AGDQEAKEEYIKGNLRLVLSVIRRFGASGENPDDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  F+ E   + +TY++  I   ++ Y+  + S+          R+  +LR    
Sbjct: 74  GLIKAINNFNTELEVKFSTYAVPMIIGEIRRYMRDNNSI----------RVSRSLRDTAY 123

Query: 145 HLQAITDNNLKPEQ----VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
                 +N +K  Q    V  IA+++ +S+ +++     +    SL   + +   ++   
Sbjct: 124 KAIYAKENYMKKNQKEPTVQEIAEEIGISKEDIVFALDAIQVPMSLQEPVYNDGGDALYV 183

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
            D L  D   +E+  IE          L  +M  L  RER I + R  Q    T   ++ 
Sbjct: 184 MDQLS-DQTNKEEKWIEDLS-------LEEAMKHLGERERYIIKLRFFQGK--TQMEVAD 233

Query: 261 EFEVSRERVRQIEARAFKKVQE 282
           E ++S+ +V ++E  A K +++
Sbjct: 234 EIQISQAQVSRLEKNALKTMRQ 255


>gi|93007309|gb|ABE97157.1| SigF [Pasteuria ramosa]
          Length = 131

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 27/84 (32%), Positives = 46/84 (54%), Gaps = 1/84 (1%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A  RLV+ ++RLV  +   +   G    ++   G IGL++AV KF+ E   + +
Sbjct: 27  QKGDTKARDRLVSHNIRLVWSVVQRFLNRGYESDDIFQIGCIGLLKAVDKFNLEYEVKFS 86

Query: 103 TYSMWWIKAAMQEYILRSWSLVKI 126
           TY++  I   +Q + LR   +VK+
Sbjct: 87  TYAVPMILGEIQRF-LRDDGIVKV 109


>gi|115465727|ref|NP_001056463.1| Os05g0586600 [Oryza sativa Japonica Group]
 gi|30698488|dbj|BAC76601.1| Sig5 [Oryza sativa Japonica Group]
 gi|30698518|dbj|BAC76607.1| plastid sigma factor SIG5 [Oryza sativa Japonica Group]
 gi|113580014|dbj|BAF18377.1| Os05g0586600 [Oryza sativa Japonica Group]
          Length = 500

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 28/99 (28%), Positives = 51/99 (51%), Gaps = 21/99 (21%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLP-------ISEVVSEGNIGLMQAVKKFDPERGFR 100
           +A ++L+  +LRLV+     Y     P         ++   G  GL+ A+ +F+P+RGFR
Sbjct: 262 AARNKLIKHNLRLVLYTINKY----YPDMSNDERFDDICQAGANGLITAIDRFEPKRGFR 317

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
           ++TY+++WI+           S+V+  T +N  R  F +
Sbjct: 318 ISTYALFWIR----------HSIVRAITLSNFTRFPFAM 346


>gi|229086911|ref|ZP_04219070.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock3-44]
 gi|228696421|gb|EEL49247.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock3-44]
          Length = 228

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 38/67 (56%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E GD  A + L+  +LRLV  I   +   G    +++S G IGL++A++ +   +G +LA
Sbjct: 34  EQGDAHARNLLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIESYSAGKGTKLA 93

Query: 103 TYSMWWI 109
           TY+   I
Sbjct: 94  TYAARCI 100


>gi|206975995|ref|ZP_03236905.1| RNA polymerase sigma-27 factor [Bacillus cereus H3081.97]
 gi|206745747|gb|EDZ57144.1| RNA polymerase sigma-27 factor [Bacillus cereus H3081.97]
          Length = 237

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 23/68 (33%), Positives = 39/68 (57%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E GD  A + L+  +LRLV  I   +   G    +++S G IGL++A++ +   +G +LA
Sbjct: 43  EQGDAQARNLLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIESYSAGKGTKLA 102

Query: 103 TYSMWWIK 110
           TY+   I+
Sbjct: 103 TYAARCIE 110


>gi|165973130|gb|ABY76244.1| sigma-K factor [Bacillus thuringiensis]
          Length = 237

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 38/67 (56%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E GD  A + L+  +LRLV  I   +   G    +++S G IGL++A++ +   +G +LA
Sbjct: 43  EQGDAQARNLLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIESYSAGKGTKLA 102

Query: 103 TYSMWWI 109
           TY+   I
Sbjct: 103 TYAARCI 109


>gi|319935952|ref|ZP_08010376.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
 gi|319809066|gb|EFW05562.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
          Length = 241

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 49/180 (27%), Positives = 83/180 (46%), Gaps = 8/180 (4%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A  ++V  +L LV  I   ++       ++   G IGLM+A+  FDP    + +TY
Sbjct: 16  GDEQAKEQVVKDNLGLVWSIVHRFKNSYYDKEDLFQIGCIGLMKAINHFDPSYNVQFSTY 75

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           ++  I   ++ Y  R    +K+  +   K L   + + K  LQA  +NN +P  V  +A+
Sbjct: 76  AVPIIMGEIKRY-FRDDGTIKVSRSL--KELNIKVTKAKEILQA--ENNEEP-TVEEVAR 129

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV--YDHDGQEQVLIEKEERK 222
            L V   +V+          SL+  I   D ++   +D L+   DH   E++ +E E  K
Sbjct: 130 YLEVDVHDVVEAIDSSYYPTSLSEPIYEKDGSTISMEDRLIDKSDHMWFEKIALEMEMEK 189


>gi|296121384|ref|YP_003629162.1| RNA polymerase sigma factor, sigma-70 family [Planctomyces
           limnophilus DSM 3776]
 gi|296013724|gb|ADG66963.1| RNA polymerase sigma factor, sigma-70 family [Planctomyces
           limnophilus DSM 3776]
          Length = 376

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 25/78 (32%), Positives = 49/78 (62%), Gaps = 2/78 (2%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
            ++A +++V ++LRLVV +A    G    ++E+VSEG + L+++V+ FD   G R +TY+
Sbjct: 191 SITARNQIVQANLRLVVALARKCCGSIEQLAELVSEGVMPLIRSVELFDISLGNRFSTYA 250

Query: 106 MWWIKAAMQEYI--LRSW 121
            W ++  M  +   +++W
Sbjct: 251 TWAVRNQMHRHFKKVQTW 268


>gi|16079402|ref|NP_390226.1| sporulation sigma factor SigF [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221310263|ref|ZP_03592110.1| sporulation sigma factor SigF [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221314586|ref|ZP_03596391.1| sporulation sigma factor SigF [Bacillus subtilis subsp. subtilis
           str. NCIB 3610]
 gi|221319509|ref|ZP_03600803.1| sporulation sigma factor SigF [Bacillus subtilis subsp. subtilis
           str. JH642]
 gi|221323785|ref|ZP_03605079.1| sporulation sigma factor SigF [Bacillus subtilis subsp. subtilis
           str. SMY]
 gi|321311821|ref|YP_004204108.1| sporulation sigma factor SigF [Bacillus subtilis BSn5]
 gi|133474|sp|P07860|RPSF_BACSU RecName: Full=RNA polymerase sigma-F factor; AltName:
           Full=Sporulation sigma factor; AltName: Full=Stage II
           sporulation protein AC
 gi|143611|gb|AAA22788.1| sporulation-specific sigma factor [Bacillus subtilis]
 gi|1304000|dbj|BAA12655.1| SpoIIAC [Bacillus subtilis]
 gi|2634780|emb|CAB14277.1| RNA polymerase sporulation-specific sigma factor (sigma-F)
           [Bacillus subtilis subsp. subtilis str. 168]
 gi|291484775|dbj|BAI85850.1| sporulation sigma factor SigF [Bacillus subtilis subsp. natto
           BEST195]
 gi|320018095|gb|ADV93081.1| sporulation sigma factor SigF [Bacillus subtilis BSn5]
          Length = 255

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 56/244 (22%), Positives = 105/244 (43%), Gaps = 28/244 (11%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           ++GD  A   L+  ++RLV  +   +   G    ++   G IGL+++V KFD     R +
Sbjct: 27  QNGDQQARDLLIEKNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKSVDKFDLTYDVRFS 86

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I   +Q +I R    VK+  +   K L   +RR K  L        +   V  I
Sbjct: 87  TYAVPMIIGEIQRFI-RDDGTVKVSRSL--KELGNKIRRAKDELSKTLG---RVPTVQEI 140

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ-----EQVLIE 217
           A  L +   +V+     +    S++                 VY++DG      +Q+   
Sbjct: 141 ADHLEIEAEDVVLAQEAVRAPSSIHE---------------TVYENDGDPITLLDQIADN 185

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
            EE+   +  L  ++S L  RE+ I   R  ++   T   ++    +S+ +V ++E +  
Sbjct: 186 SEEKWFDKIALKEAISDLEEREKLIVYLRYYKDQ--TQSEVAERLGISQVQVSRLEKKIL 243

Query: 278 KKVQ 281
           K+++
Sbjct: 244 KQIK 247


>gi|296332278|ref|ZP_06874740.1| sporulation sigma factor SigF [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|305674979|ref|YP_003866651.1| sporulation sigma factor SigmaF [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|296150592|gb|EFG91479.1| sporulation sigma factor SigF [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|305413223|gb|ADM38342.1| sporulation sigma factor SigmaF [Bacillus subtilis subsp.
           spizizenii str. W23]
          Length = 255

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 56/244 (22%), Positives = 105/244 (43%), Gaps = 28/244 (11%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           ++GD  A   L+  ++RLV  +   +   G    ++   G IGL+++V KFD     R +
Sbjct: 27  QNGDQQARDLLIEKNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKSVDKFDLTYDVRFS 86

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I   +Q +I R    VK+  +   K L   +RR K  L        +   V  I
Sbjct: 87  TYAVPMIIGEIQRFI-RDDGTVKVSRSL--KELGNKIRRAKDELSKTLG---RVPTVQEI 140

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ-----EQVLIE 217
           A  L +   +V+     +    S++                 VY++DG      +Q+   
Sbjct: 141 ADHLEIEAEDVVLAQEAVRAPSSIHE---------------TVYENDGDPITLLDQIADN 185

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
            EE+   +  L  ++S L  RE+ I   R  ++   T   ++    +S+ +V ++E +  
Sbjct: 186 SEEKWFDKIALKEAISDLEEREKLIVYLRYYKDQ--TQSEVAERLGISQVQVSRLEKKIL 243

Query: 278 KKVQ 281
           K+++
Sbjct: 244 KQIK 247


>gi|168335365|ref|ZP_02693459.1| sporulation sigma factor SigE [Epulopiscium sp. 'N.t. morphotype
           B']
          Length = 246

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 34/107 (31%), Positives = 55/107 (51%), Gaps = 6/107 (5%)

Query: 9   IVNGEIGLSRYIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHR-----LVTSHLRLVV 62
           I+  +IG   YI     +P  L K+EE  L  +  E+ D           L+  +LRLVV
Sbjct: 18  ILKNQIGQIHYIGGSEVLPAPLSKEEENELLMQMIEYPDDDEKINEIKKILIERNLRLVV 77

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            IA  +      + +++S G+IGL++A+  F P++  +LATY+   I
Sbjct: 78  YIAKKFENTNKGMEDLISIGSIGLIKAINTFKPDKKIKLATYASRCI 124


>gi|300856558|ref|YP_003781542.1| RNA polymerase sigma-F factor [Clostridium ljungdahlii DSM 13528]
 gi|300436673|gb|ADK16440.1| RNA polymerase sigma-F factor [Clostridium ljungdahlii DSM 13528]
          Length = 251

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 52/252 (20%), Positives = 110/252 (43%), Gaps = 34/252 (13%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           +Y + GD  A ++LV  +L LV  I+  +   G    ++   G +GLM+AV  F+ E   
Sbjct: 21  KYAKKGDKDALNKLVELNLPLVASISKKFLNRGYEYEDIFQIGCMGLMKAVNNFNEEYNV 80

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTA--NQKRLFFNLRRLKGHLQAITDNNLKPE 157
           + +TY++  I   ++ + LR   ++K+  +     K++ ++                   
Sbjct: 81  KFSTYAVPMILGEIKRF-LRDDGMIKVSRSVKNTAKKIHYDRE----------------- 122

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
              A+ KKLN      I      +G E    +  +   +S Q+    ++  DG   +LI+
Sbjct: 123 ---ALTKKLN--REPTIQELAEYSGVEVEELIFATESASSLQYLYDTIHQDDGSPVLLID 177

Query: 218 KEERKNRRNM-------LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
           K     + ++       L  +++ L+ + R+I   R  ++   T   ++    +++ +V 
Sbjct: 178 KISENPKEDVEMVDKIALKEALNNLDVKSRQIIMLRYFKDK--TQVQVAKMLGINQVQVS 235

Query: 271 QIEARAFKKVQE 282
           +IE +  K ++E
Sbjct: 236 RIEKKVLKTMRE 247


>gi|288942618|ref|YP_003444858.1| RNA polymerase sigma-28 subunit FliA/WhiG [Allochromatium vinosum
           DSM 180]
 gi|288897990|gb|ADC63826.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Allochromatium vinosum
           DSM 180]
          Length = 248

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 60/251 (23%), Positives = 111/251 (44%), Gaps = 35/251 (13%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQAVKKFDPE 96
           Y   GD +A  RLV+ H+ LV +IA       LP S    +++  G +GL++A ++F   
Sbjct: 10  YASAGDEAA--RLVSEHVDLVRRIAHHLVAR-LPASVQVEDLIQSGMVGLIEAARQFQTG 66

Query: 97  RGFRLATYSMWWIKAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           +G   ATY+   ++ AM + + R+ W+          + +  N RR+   +  +     +
Sbjct: 67  QGATFATYAGIRVRGAMIDELRRADWT---------PRSVHRNSRRIAEAIHQVESREGR 117

Query: 156 PEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
                 IA+ L V+  +   M     +C++ G E L      SD+       +L     G
Sbjct: 118 AASDREIAETLGVTLDDYHGMLQDTASCQILGLEDLFGEDADSDR-------FL----PG 166

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                 E+ ER+     L  +++ L  RER +      +E  + L  + +  +V+  RV 
Sbjct: 167 AGTAPTEQLEREQFAQALAEALADLPERERLVLALYYDEE--LNLREIGAVLDVTESRVS 224

Query: 271 QIEARAFKKVQ 281
           QI ++A  +++
Sbjct: 225 QIRSQALHRLR 235


>gi|251733353|emb|CAR82426.1| RNA polymerase sigma factor [Bradyrhizobium japonicum]
          Length = 205

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 23/49 (46%), Positives = 32/49 (65%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 157 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 205


>gi|297582861|ref|YP_003698641.1| LuxR family transcriptional regulator [Bacillus selenitireducens
           MLS10]
 gi|297141318|gb|ADH98075.1| transcriptional regulator, LuxR family [Bacillus selenitireducens
           MLS10]
          Length = 268

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 61/267 (22%), Positives = 123/267 (46%), Gaps = 36/267 (13%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           +K+ +  +   ++E GD     +LV  +  LV  +A  +        ++V  G IGL+ A
Sbjct: 18  DKERQLKMIAEFQETGDDEIQTQLVLEYENLVHALARKFSRGQRHDEDLVQVGMIGLLAA 77

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           +++FDP  G    ++++  I   ++ +I  ++WS+         +R+     ++K  ++ 
Sbjct: 78  LRRFDPSFGRSFESFAVPTIVGEIKRFIRDKTWSV------HVPRRIKELGPKIKSAVEN 131

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL-----INSSDKNSS-QWQD 202
           +T    +  QV  IA  L VSE E++     +   +S  AL     I + D+ S+    D
Sbjct: 132 LTTELQRSPQVEEIADYLEVSEEEILET---MEMGKSYQALSVDRSIEADDEGSAVTLLD 188

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS--- 259
            +     G EQ         +++ +L ++  VL  RE++I +           EN+S   
Sbjct: 189 LVGSVESGYEQT--------DQQLLLEKAFQVLTDREKQILQL-------TYFENMSQKE 233

Query: 260 --SEFEVSRERVRQIEARAFKKVQESI 284
              +  +S+  V +++ RA +K+++SI
Sbjct: 234 TGEQLGISQMHVSRLQRRALQKLKDSI 260


>gi|89098615|ref|ZP_01171497.1| sigma factor SigD [Bacillus sp. NRRL B-14911]
 gi|89086577|gb|EAR65696.1| sigma factor SigD [Bacillus sp. NRRL B-14911]
          Length = 253

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 51/222 (22%), Positives = 101/222 (45%), Gaps = 22/222 (9%)

Query: 72  GLPIS----EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           GLP +    E+ S G +GL  A++KFDP R  +  TY+ + I+ ++ +  LR    +   
Sbjct: 45  GLPKNVSRDELRSLGLMGLYDALEKFDPTRDLKFDTYASFRIRGSIIDG-LRKEDWLPRS 103

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
           T    K++     RL+ HL       ++      I K++++ E EV ++         L+
Sbjct: 104 TREKAKKIEAAAERLEQHL-------MRKATAAEIGKEVDLHEDEVQTVMSEHFFANVLS 156

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR---SMSVLNPRERRIFE 244
                 D++      +++ DH       +  EE+  +  +L+    ++S LN +E+ +  
Sbjct: 157 MDEQPQDQDEKDGATYILKDHRA-----VVPEEKVAKDELLSEMADAVSCLNEKEQLVIS 211

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
               +E  +TL  +     +S  R+ QI  +A   ++ ++QK
Sbjct: 212 LFYKEE--LTLTEIGQVMGLSTSRISQIHTKAIFSLRHTLQK 251


>gi|30264411|ref|NP_846788.1| sporulation sigma factor SigK [Bacillus anthracis str. Ames]
 gi|47529862|ref|YP_021211.1| sporulation sigma factor SigK [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49187232|ref|YP_030484.1| sporulation sigma factor SigK [Bacillus anthracis str. Sterne]
 gi|49481469|ref|YP_038392.1| sporulation sigma factor SigK [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|52141167|ref|YP_085663.1| sporulation sigma factor SigK [Bacillus cereus E33L]
 gi|163942095|ref|YP_001646979.1| sporulation sigma factor SigK [Bacillus weihenstephanensis KBAB4]
 gi|165873242|ref|ZP_02217852.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0488]
 gi|167634588|ref|ZP_02392908.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0442]
 gi|167638535|ref|ZP_02396811.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0193]
 gi|170687349|ref|ZP_02878566.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0465]
 gi|170707389|ref|ZP_02897843.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0389]
 gi|177653302|ref|ZP_02935554.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0174]
 gi|190566875|ref|ZP_03019791.1| RNA polymerase sigma-27 factor [Bacillus anthracis Tsiankovskii-I]
 gi|196034403|ref|ZP_03101812.1| RNA polymerase sigma-27 factor [Bacillus cereus W]
 gi|196039171|ref|ZP_03106477.1| RNA polymerase sigma-27 factor [Bacillus cereus NVH0597-99]
 gi|196044956|ref|ZP_03112190.1| RNA polymerase sigma-27 factor [Bacillus cereus 03BB108]
 gi|206969450|ref|ZP_03230404.1| RNA polymerase sigma-27 factor [Bacillus cereus AH1134]
 gi|217961829|ref|YP_002340399.1| sporulation sigma factor SigK [Bacillus cereus AH187]
 gi|218231149|ref|YP_002369149.1| sporulation sigma factor SigK [Bacillus cereus B4264]
 gi|218899507|ref|YP_002447918.1| RNA polymerase sigma-27 factor [Bacillus cereus G9842]
 gi|225866320|ref|YP_002751698.1| RNA polymerase sigma-27 factor [Bacillus cereus 03BB102]
 gi|227817116|ref|YP_002817125.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. CDC 684]
 gi|229603939|ref|YP_002868629.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0248]
 gi|254684096|ref|ZP_05147956.1| sporulation sigma factor SigK [Bacillus anthracis str. CNEVA-9066]
 gi|254721930|ref|ZP_05183719.1| sporulation sigma factor SigK [Bacillus anthracis str. A1055]
 gi|254736444|ref|ZP_05194150.1| sporulation sigma factor SigK [Bacillus anthracis str. Western
           North America USA6153]
 gi|254741481|ref|ZP_05199168.1| sporulation sigma factor SigK [Bacillus anthracis str. Kruger B]
 gi|254750920|ref|ZP_05202959.1| sporulation sigma factor SigK [Bacillus anthracis str. Vollum]
 gi|254757752|ref|ZP_05209779.1| sporulation sigma factor SigK [Bacillus anthracis str. Australia
           94]
 gi|300118668|ref|ZP_07056396.1| sporulation sigma factor SigK [Bacillus cereus SJ1]
 gi|49065844|sp|P62180|RP28_BACCR RecName: Full=RNA polymerase sigma-28 factor; Flags: Precursor
 gi|49065845|sp|P62181|RP28_BACTK RecName: Full=RNA polymerase sigma-28 factor; Flags: Precursor
 gi|49065846|sp|P62182|RP28_BACAN RecName: Full=RNA polymerase sigma-28 factor; Flags: Precursor
 gi|580953|emb|CAA40024.1| sigma factor 28 [Bacillus thuringiensis serovar kurstaki]
 gi|19918928|gb|AAL99379.1| sigma factor 28 [Bacillus thuringiensis serovar israelensis]
 gi|30259069|gb|AAP28274.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. Ames]
 gi|47505010|gb|AAT33686.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49181159|gb|AAT56535.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. Sterne]
 gi|49333025|gb|AAT63671.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|51974636|gb|AAU16186.1| RNA polymerase sigma-28 factor [Bacillus cereus E33L]
 gi|163864292|gb|ABY45351.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           weihenstephanensis KBAB4]
 gi|164711001|gb|EDR16568.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0488]
 gi|167513383|gb|EDR88753.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0193]
 gi|167530040|gb|EDR92775.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0442]
 gi|170127633|gb|EDS96506.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0389]
 gi|170668544|gb|EDT19290.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0465]
 gi|172081584|gb|EDT66656.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0174]
 gi|190561866|gb|EDV15835.1| RNA polymerase sigma-27 factor [Bacillus anthracis Tsiankovskii-I]
 gi|195992945|gb|EDX56904.1| RNA polymerase sigma-27 factor [Bacillus cereus W]
 gi|196024444|gb|EDX63117.1| RNA polymerase sigma-27 factor [Bacillus cereus 03BB108]
 gi|196029798|gb|EDX68399.1| RNA polymerase sigma-27 factor [Bacillus cereus NVH0597-99]
 gi|206735138|gb|EDZ52306.1| RNA polymerase sigma-27 factor [Bacillus cereus AH1134]
 gi|217066768|gb|ACJ81018.1| RNA polymerase sigma-27 factor [Bacillus cereus AH187]
 gi|218159106|gb|ACK59098.1| RNA polymerase sigma-27 factor [Bacillus cereus B4264]
 gi|218543613|gb|ACK96007.1| RNA polymerase sigma-27 factor [Bacillus cereus G9842]
 gi|225788740|gb|ACO28957.1| RNA polymerase sigma-27 factor [Bacillus cereus 03BB102]
 gi|227007199|gb|ACP16942.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. CDC 684]
 gi|229268347|gb|ACQ49984.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0248]
 gi|298723917|gb|EFI64631.1| sporulation sigma factor SigK [Bacillus cereus SJ1]
 gi|324328243|gb|ADY23503.1| sporulation sigma factor SigK [Bacillus thuringiensis serovar
           finitimus YBT-020]
 gi|326942122|gb|AEA18018.1| sporulation sigma factor SigK [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 237

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 38/67 (56%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E GD  A + L+  +LRLV  I   +   G    +++S G IGL++A++ +   +G +LA
Sbjct: 43  EQGDAQARNLLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIESYSAGKGTKLA 102

Query: 103 TYSMWWI 109
           TY+   I
Sbjct: 103 TYAARCI 109


>gi|152967736|ref|YP_001363520.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Kineococcus
           radiotolerans SRS30216]
 gi|151362253|gb|ABS05256.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Kineococcus
           radiotolerans SRS30216]
          Length = 326

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 53/237 (22%), Positives = 102/237 (43%), Gaps = 21/237 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L   HL L   +A  + G G P  ++V    IGL++A+ +FDP RG     Y++  +   
Sbjct: 109 LTRRHLPLADHLAARFLGRGEPQDDLVQVATIGLLKALDRFDPSRGVPFGAYAVPTMLGE 168

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +   R W++ ++      +R+    R L    +A+T    +   V  +A++      
Sbjct: 169 IKRHFRDRGWAM-RV-----PRRIQEAGRALGDAREALTHELGRAPTVAELAERTGYDPE 222

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           +V+ +       ES NA         S     LV      +  L   E R+  R +L   
Sbjct: 223 DVVDVL------ESANAYSTLPLDTGSPTS--LVASLGADDDALQNVENREALRPLL--- 271

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            + L  RERRI   R ++   ++   +++E  +S+  V ++  R   +++E +  + 
Sbjct: 272 -AGLPARERRILALRFVRG--MSQSQIAAEVGISQMHVSRLLTRTLAQLREGLGDEA 325


>gi|310642622|ref|YP_003947380.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
 gi|309247572|gb|ADO57139.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
          Length = 251

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 59/251 (23%), Positives = 114/251 (45%), Gaps = 36/251 (14%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A   LV S++RLV  +   +   G    ++   G IGL+++V KFD     + +
Sbjct: 26  QSGDNDARETLVNSNIRLVWSVVQRFMNRGYEPDDLFQIGCIGLLKSVDKFDLSYEVKFS 85

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIG----TTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           TY++  I   +Q + LR    +K+      TAN+      +R++K  L      N  P  
Sbjct: 86  TYAVPMIIGEIQRF-LRDDGTLKVSRSLKETANK------VRKMKDELSKRL--NRLP-T 135

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ-----EQ 213
           V  +A +L V+  +V+                  ++K  +   +  V+++DG      +Q
Sbjct: 136 VKEVADELGVTPEDVV--------------FAQEANKPPTSIHE-TVFENDGDPITLMDQ 180

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
           +  E +ER   +  L  ++  L+ RER I   R  ++   T   ++S   +S+ +V ++E
Sbjct: 181 IADESQERWFDKLALNEAIDGLSERERLIVYLRYYRDQ--TQSEVASRLGISQVQVSRLE 238

Query: 274 ARAFKKVQESI 284
            +  + +++ I
Sbjct: 239 KKILQLIRDQI 249


>gi|297616717|ref|YP_003701876.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
 gi|297144554|gb|ADI01311.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
          Length = 248

 Score = 48.1 bits (113), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 51/240 (21%), Positives = 108/240 (45%), Gaps = 18/240 (7%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A   +  S+L LV      ++       ++   G IGL++A+ +FD   G + +
Sbjct: 20  QAGDRDAEEAVFQSNLGLVYMALERFKNTPYDFEDLFQIGAIGLLKAIARFDFGYGVKFS 79

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA- 161
           TY++  I   ++ Y LR   ++K+  +   K +++ ++  +  L+         E  +  
Sbjct: 80  TYAVPMIIGELKRY-LRDDGILKVQRSI--KEIYYRVKSAQDDLR----REFGKEPTIGE 132

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           IA++L +  ++V+           +  L+   +K         V D +G E +L      
Sbjct: 133 IAERLGLELNDVVMAVEACQPPTYIYNLLPGDEKEQPLPLISKVSDREGTEDLL------ 186

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L  ++  L+PRER +   R  ++   T   ++ +  +S+ +V ++E RA KK++
Sbjct: 187 --EKVALKEAVMRLDPREREVIVRRFFKDE--TQSAIAEDLGISQVQVSRLEKRALKKLR 242


>gi|257438884|ref|ZP_05614639.1| RNA polymerase sigma-K factor [Faecalibacterium prausnitzii A2-165]
 gi|257198699|gb|EEU96983.1| RNA polymerase sigma-K factor [Faecalibacterium prausnitzii A2-165]
          Length = 153

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 33/89 (37%), Positives = 51/89 (57%), Gaps = 7/89 (7%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS--EVVSEGNIGLMQAVKKFDPERGFRLA 102
           GD SA  +++  +LRLV  +A  Y  Y  P    +++S G IGLM+AV  FD  R  R A
Sbjct: 47  GDRSAREKIIRHNLRLVAHVAKKY--YAQPGDQEDLISIGTIGLMKAVDTFDITRKARFA 104

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           TY+   I+ A+   + R+ + ++IGT + 
Sbjct: 105 TYASRCIENAI---LTRANAGLRIGTIST 130


>gi|326201325|ref|ZP_08191197.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium papyrosolvens
           DSM 2782]
 gi|325988893|gb|EGD49717.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium papyrosolvens
           DSM 2782]
          Length = 248

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 60/256 (23%), Positives = 115/256 (44%), Gaps = 18/256 (7%)

Query: 28  MLEKQEEYVLAKRYR-EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           M E  ++ VL    + + GD  A   LV  ++ LV  I   ++  G  + ++   G+IGL
Sbjct: 1   MKETSDDAVLTLIIKAKAGDKQAQSVLVERNVGLVWSIVKRFQNRGYEVDDLFQIGSIGL 60

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+ KFD     + +TY++  I   ++ +I R   ++K+  +   K +    R  K   
Sbjct: 61  IKAINKFDTSYDVKFSTYAVPMIIGEIKRFI-RDDGIIKVSRSL--KEISSKARITK--- 114

Query: 147 QAITDNNLKPEQVV-AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
             I    L  E  +  IA+++N+S  E++         ESL + I   D +     D + 
Sbjct: 115 -EIMSKELGREPTINEIAQRMNISPEELVMAIEAGCTPESLYSTIGDGDNSPILLIDRID 173

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
              +  E  LI+K         + + +  L+ RER+I   R  +E   T   ++    +S
Sbjct: 174 AADNNCEVDLIDK-------IAIRQILDTLDTRERQIIILRYFKEK--TQVQIAKLLGIS 224

Query: 266 RERVRQIEARAFKKVQ 281
           + +V +IE +  + ++
Sbjct: 225 QVQVSRIEKKILRDIK 240


>gi|30022417|ref|NP_834048.1| sporulation sigma factor SigK [Bacillus cereus ATCC 14579]
 gi|228902866|ref|ZP_04067008.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis IBL 4222]
 gi|228910177|ref|ZP_04073996.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis IBL 200]
 gi|228916971|ref|ZP_04080532.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228929384|ref|ZP_04092407.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228935660|ref|ZP_04098474.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228941506|ref|ZP_04104056.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228954625|ref|ZP_04116649.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228960610|ref|ZP_04122256.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228974436|ref|ZP_04135004.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228981030|ref|ZP_04141332.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis Bt407]
 gi|229025805|ref|ZP_04182204.1| RNA polymerase sigma-28 factor [Bacillus cereus AH1272]
 gi|229031990|ref|ZP_04187975.1| RNA polymerase sigma-28 factor [Bacillus cereus AH1271]
 gi|229048046|ref|ZP_04193621.1| RNA polymerase sigma-28 factor [Bacillus cereus AH676]
 gi|229062038|ref|ZP_04199363.1| RNA polymerase sigma-28 factor [Bacillus cereus AH603]
 gi|229071846|ref|ZP_04205059.1| RNA polymerase sigma-28 factor [Bacillus cereus F65185]
 gi|229076014|ref|ZP_04208987.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock4-18]
 gi|229098811|ref|ZP_04229749.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock3-29]
 gi|229104971|ref|ZP_04235627.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock3-28]
 gi|229111812|ref|ZP_04241358.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock1-15]
 gi|229117837|ref|ZP_04247201.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock1-3]
 gi|229123878|ref|ZP_04253071.1| RNA polymerase sigma-28 factor [Bacillus cereus 95/8201]
 gi|229129620|ref|ZP_04258588.1| RNA polymerase sigma-28 factor [Bacillus cereus BDRD-Cer4]
 gi|229141077|ref|ZP_04269619.1| RNA polymerase sigma-28 factor [Bacillus cereus BDRD-ST26]
 gi|229157954|ref|ZP_04286026.1| RNA polymerase sigma-28 factor [Bacillus cereus ATCC 4342]
 gi|229163288|ref|ZP_04291242.1| RNA polymerase sigma-28 factor [Bacillus cereus R309803]
 gi|229169087|ref|ZP_04296802.1| RNA polymerase sigma-28 factor [Bacillus cereus AH621]
 gi|229175013|ref|ZP_04302532.1| RNA polymerase sigma-28 factor [Bacillus cereus MM3]
 gi|229180616|ref|ZP_04307957.1| RNA polymerase sigma-28 factor [Bacillus cereus 172560W]
 gi|229192552|ref|ZP_04319513.1| RNA polymerase sigma-28 factor [Bacillus cereus ATCC 10876]
 gi|229198467|ref|ZP_04325171.1| RNA polymerase sigma-28 factor [Bacillus cereus m1293]
 gi|29897975|gb|AAP11249.1| RNA polymerase sigma-K factor [Bacillus cereus ATCC 14579]
 gi|228584970|gb|EEK43084.1| RNA polymerase sigma-28 factor [Bacillus cereus m1293]
 gi|228590859|gb|EEK48717.1| RNA polymerase sigma-28 factor [Bacillus cereus ATCC 10876]
 gi|228602859|gb|EEK60339.1| RNA polymerase sigma-28 factor [Bacillus cereus 172560W]
 gi|228608474|gb|EEK65777.1| RNA polymerase sigma-28 factor [Bacillus cereus MM3]
 gi|228614315|gb|EEK71425.1| RNA polymerase sigma-28 factor [Bacillus cereus AH621]
 gi|228620195|gb|EEK77067.1| RNA polymerase sigma-28 factor [Bacillus cereus R309803]
 gi|228625514|gb|EEK82269.1| RNA polymerase sigma-28 factor [Bacillus cereus ATCC 4342]
 gi|228642355|gb|EEK98644.1| RNA polymerase sigma-28 factor [Bacillus cereus BDRD-ST26]
 gi|228653737|gb|EEL09607.1| RNA polymerase sigma-28 factor [Bacillus cereus BDRD-Cer4]
 gi|228659592|gb|EEL15239.1| RNA polymerase sigma-28 factor [Bacillus cereus 95/8201]
 gi|228665634|gb|EEL21112.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock1-3]
 gi|228671568|gb|EEL26866.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock1-15]
 gi|228678465|gb|EEL32686.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock3-28]
 gi|228684655|gb|EEL38595.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock3-29]
 gi|228707126|gb|EEL59326.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock4-18]
 gi|228711276|gb|EEL63238.1| RNA polymerase sigma-28 factor [Bacillus cereus F65185]
 gi|228717190|gb|EEL68865.1| RNA polymerase sigma-28 factor [Bacillus cereus AH603]
 gi|228723290|gb|EEL74660.1| RNA polymerase sigma-28 factor [Bacillus cereus AH676]
 gi|228729345|gb|EEL80337.1| RNA polymerase sigma-28 factor [Bacillus cereus AH1271]
 gi|228735513|gb|EEL86109.1| RNA polymerase sigma-28 factor [Bacillus cereus AH1272]
 gi|228778690|gb|EEM26955.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis Bt407]
 gi|228785272|gb|EEM33283.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228799038|gb|EEM46009.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228805071|gb|EEM51666.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228818156|gb|EEM64231.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228824020|gb|EEM69838.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228830290|gb|EEM75904.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228842692|gb|EEM87779.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228849460|gb|EEM94295.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis IBL 200]
 gi|228856740|gb|EEN01258.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis IBL 4222]
          Length = 240

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 38/67 (56%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E GD  A + L+  +LRLV  I   +   G    +++S G IGL++A++ +   +G +LA
Sbjct: 46  EQGDAQARNLLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIESYSAGKGTKLA 105

Query: 103 TYSMWWI 109
           TY+   I
Sbjct: 106 TYAARCI 112


>gi|152976482|ref|YP_001375999.1| sporulation sigma factor SigF [Bacillus cereus subsp. cytotoxis NVH
           391-98]
 gi|152025234|gb|ABS23004.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           cytotoxicus NVH 391-98]
          Length = 252

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 50/190 (26%), Positives = 90/190 (47%), Gaps = 17/190 (8%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           +K P L+  E   L ++ ++ GD  A   +V S++RLV  +   +   G    ++   G 
Sbjct: 9   KKNPQLKDHELKALIQKSQD-GDQGARDTIVQSNMRLVWSVVQRFLNRGYEPDDLFQIGC 67

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL+++V KFD     + +TY++  I   +Q + LR    VK+  +   K     +R++K
Sbjct: 68  IGLLKSVDKFDLSFDVKFSTYAVPMIIGEIQRF-LRDDGSVKVSRSL--KETGNKIRKMK 124

Query: 144 GHL-----QAITDN------NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
             L     +A T N       L PE+VV +A++ + + S +        GD  +  L   
Sbjct: 125 DELSKEYGRAPTINEVAEALELTPEEVV-LAQEASRTPSSIHETVYENDGD-PITILDQI 182

Query: 193 SDKNSSQWQD 202
           +D+  ++W D
Sbjct: 183 ADQAETKWFD 192


>gi|239623611|ref|ZP_04666642.1| conserved hypothetical protein [Clostridiales bacterium
          1_7_47_FAA]
 gi|239521642|gb|EEQ61508.1| conserved hypothetical protein [Clostridiales bacterium
          1_7_47FAA]
          Length = 197

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 29/76 (38%), Positives = 41/76 (53%), Gaps = 1/76 (1%)

Query: 19 YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
          Y+ E+  I  L  QE+  L K     G+  A +RLV   LR V+ +A  Y G  LP+S++
Sbjct: 9  YLEEMGGIAPLTGQEKPELLKETA-KGNAGARNRLVEGSLRHVLNLAAEYEGRELPMSDI 67

Query: 79 VSEGNIGLMQAVKKFD 94
          V E N  LM A  ++D
Sbjct: 68 VQEANTALMLAAIEYD 83


>gi|312622918|ref|YP_004024531.1| RNA polymerase, sigma 28 subunit, sige [Caldicellulosiruptor
           kronotskyensis 2002]
 gi|312203385|gb|ADQ46712.1| RNA polymerase, sigma 28 subunit, SigE [Caldicellulosiruptor
           kronotskyensis 2002]
          Length = 244

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 28/94 (29%), Positives = 49/94 (52%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EE  +  +    G       LV  +LRLVV IA  +    + + ++VS G IGL
Sbjct: 41  PPLTPDEEAQILYKIHYQGKEELKKILVERNLRLVVYIARRFENTKINLEDLVSIGTIGL 100

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++A+  ++P +  +LATY+   I+  +  ++ R+
Sbjct: 101 IKAINTYNPNKNIKLATYASKCIENEILMFLRRN 134


>gi|239623454|ref|ZP_04666485.1| RNA polymerase [Clostridiales bacterium 1_7_47_FAA]
 gi|239521485|gb|EEQ61351.1| RNA polymerase [Clostridiales bacterium 1_7_47FAA]
          Length = 258

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 59/260 (22%), Positives = 116/260 (44%), Gaps = 23/260 (8%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L  +E+  L KR   +GD  A  + +  +LRLV+ +   +      I ++   G I
Sbjct: 15  KLPLLSNEEKEELFKRIL-NGDKDAREQYIKGNLRLVLSVIQRFSNSQENIDDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT---ANQKRLFFNLRR 141
           GL++A+  FD  +  + +TY++  I   ++ Y LR  + +++  +      K L+     
Sbjct: 74  GLIKAIDNFDITQNVKFSTYAVPMILGEVRRY-LRDNNSIRVSRSLRDTAYKALYAR--- 129

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
                + +T  N K   +V IA+++ VS+ ++      +    SL   + +   +     
Sbjct: 130 -----EQLTRVNSKEPTLVEIAQEIGVSKEDITYALDAIQTPVSLYEPVYTDGGDPLYVM 184

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           D  + D    E+  +E          L  +M  L  RER I + R  +    T   ++ E
Sbjct: 185 DQ-ISDKKNLEENWVEDLS-------LVEAMKRLPERERHIIDMRFFEGKTQT--EVAEE 234

Query: 262 FEVSRERVRQIEARAFKKVQ 281
             +S+ +V ++E  A K ++
Sbjct: 235 IHISQAQVSRLEKNALKSMK 254


>gi|65321710|ref|ZP_00394669.1| COG1191: DNA-directed RNA polymerase specialized sigma subunit
           [Bacillus anthracis str. A2012]
 gi|228923092|ref|ZP_04086384.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228948053|ref|ZP_04110338.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228987592|ref|ZP_04147708.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|229013560|ref|ZP_04170693.1| RNA polymerase sigma-28 factor [Bacillus mycoides DSM 2048]
 gi|229019564|ref|ZP_04176380.1| RNA polymerase sigma-28 factor [Bacillus cereus AH1273]
 gi|229081603|ref|ZP_04214099.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock4-2]
 gi|229135165|ref|ZP_04263965.1| RNA polymerase sigma-28 factor [Bacillus cereus BDRD-ST196]
 gi|229146910|ref|ZP_04275274.1| RNA polymerase sigma-28 factor [Bacillus cereus BDRD-ST24]
 gi|229152543|ref|ZP_04280733.1| RNA polymerase sigma-28 factor [Bacillus cereus m1550]
 gi|229186579|ref|ZP_04313740.1| RNA polymerase sigma-28 factor [Bacillus cereus BGSC 6E1]
 gi|228596838|gb|EEK54497.1| RNA polymerase sigma-28 factor [Bacillus cereus BGSC 6E1]
 gi|228630909|gb|EEK87548.1| RNA polymerase sigma-28 factor [Bacillus cereus m1550]
 gi|228636509|gb|EEK92975.1| RNA polymerase sigma-28 factor [Bacillus cereus BDRD-ST24]
 gi|228648293|gb|EEL04328.1| RNA polymerase sigma-28 factor [Bacillus cereus BDRD-ST196]
 gi|228701709|gb|EEL54199.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock4-2]
 gi|228741730|gb|EEL91914.1| RNA polymerase sigma-28 factor [Bacillus cereus AH1273]
 gi|228747720|gb|EEL97590.1| RNA polymerase sigma-28 factor [Bacillus mycoides DSM 2048]
 gi|228772133|gb|EEM20583.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228811639|gb|EEM57975.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228836590|gb|EEM81939.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
          Length = 243

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 38/67 (56%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E GD  A + L+  +LRLV  I   +   G    +++S G IGL++A++ +   +G +LA
Sbjct: 49  EQGDAQARNLLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIESYSAGKGTKLA 108

Query: 103 TYSMWWI 109
           TY+   I
Sbjct: 109 TYAARCI 115


>gi|152976769|ref|YP_001376286.1| sporulation sigma factor SigK [Bacillus cereus subsp. cytotoxis NVH
           391-98]
 gi|152025521|gb|ABS23291.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           cytotoxicus NVH 391-98]
          Length = 237

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 38/67 (56%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E GD  A + L+  +LRLV  I   +   G    +++S G IGL++A++ +   +G +LA
Sbjct: 43  EQGDAQARNLLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIESYSAGKGTKLA 102

Query: 103 TYSMWWI 109
           TY+   I
Sbjct: 103 TYAARCI 109


>gi|299538306|ref|ZP_07051591.1| RNA polymerase sigma-B factor [Lysinibacillus fusiformis ZC1]
 gi|298726508|gb|EFI67098.1| RNA polymerase sigma-B factor [Lysinibacillus fusiformis ZC1]
          Length = 261

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 58/257 (22%), Positives = 116/257 (45%), Gaps = 38/257 (14%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y+   D  A   LV  +  LV  IA  Y        ++V  G +GL+ A+++FDP  G  
Sbjct: 22  YQSTEDDEAQTNLVIHYRYLVESIARKYSNGKSYYDDIVQVGMLGLLGAIRRFDPNVGRS 81

Query: 101 LATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
              +++  I   ++ ++  ++W +         +R+     R+K  ++A+T    +   +
Sbjct: 82  FEAFAVPTIVGEIKRFLRDKTWDV------HVPRRIKELGPRIKSTVEALTIELQRSPSI 135

Query: 160 VAIAKK-----------LNVSES-EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
             IA++           + +S S + +SM+  +  D         SD ++    D L  +
Sbjct: 136 KDIAERLEVAEEEVLEAMEMSRSYQALSMDHSIESD---------SDGSTVTLFDILGRE 186

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            DG E          N+R ++  ++ VLN RE++I +   L++  ++ +       +S+ 
Sbjct: 187 DDGYEMT--------NQRMIVQDALVVLNEREKQIIQLTYLEQ--LSQKEAGERLGISQM 236

Query: 268 RVRQIEARAFKKVQESI 284
            V +I+ +A KK+QE+I
Sbjct: 237 HVSRIQRKAIKKLQEAI 253


>gi|256267|gb|AAC60414.1| RpoD1 [Synechococcus]
          Length = 48

 Score = 47.8 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 17/41 (41%), Positives = 32/41 (78%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+   I
Sbjct: 2   DLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAI 42


>gi|320010407|gb|ADW05257.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 326

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 47/168 (27%), Positives = 78/168 (46%), Gaps = 14/168 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  +L LV   A  +R    P+ ++V  G IGL++A+ +F+  RG    T++M  I   
Sbjct: 103 LVELNLALVKFAASRFRTRSEPMEDIVQVGTIGLIKAIDRFELSRGVEFPTFAMPTIVGE 162

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL  +L +    L    D   +   V  +A +L +S  
Sbjct: 163 IKRFFRDTSWS-VRVPRRLQELRL--DLAKAGDELSQQLD---RAPTVAELADRLGLSRD 216

Query: 172 EVI----SMNCRLAGDESLNALINS-SDKNSSQWQDWLVYDHDGQEQV 214
           EV+    + N   A   SL+A  +   D N     D L Y+ +G E +
Sbjct: 217 EVVEGMAASNAYTA--SSLDAKPDDHGDGNEGALADRLGYEDNGLEGI 262


>gi|168334573|ref|ZP_02692729.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Epulopiscium sp. 'N.t.
           morphotype B']
          Length = 247

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 55/240 (22%), Positives = 107/240 (44%), Gaps = 29/240 (12%)

Query: 54  VTSHLRLVVKIAMG----YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           +  H   +VKI  G    Y    L + +++  G IGL+ A+ K+D ++  +  TY+   I
Sbjct: 23  LIEHYAPLVKIVAGRLGIYLNSYLELDDLLGFGVIGLIDAIDKYDYDKKIKFETYASLRI 82

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK---GHLQAITDNNLKPEQVVAIAKKL 166
           + A+ + I R    V       QK       R++   GH    TD          + K+L
Sbjct: 83  RGAIIDEI-RKLDWVPRSIRQKQKEYIRAYERVEAKIGHSPTDTD----------VRKEL 131

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           N++ESE      +L  D +++ L++  +    ++    +   +  +++     E K    
Sbjct: 132 NINESEY----NKLVHDTNISTLVSIDESELYEFNIEDITTKNPYQEL-----ENKEALE 182

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +L   +  L  RE+ + +    +E  +TL+ +S   E+S  RV QI ++   K++  ++K
Sbjct: 183 ILEHEILALTEREQLLIKLYYYEE--LTLKEISLILEISESRVSQIHSKLMVKLRNKLKK 240


>gi|253576354|ref|ZP_04853684.1| RNA polymerase sigma-F factor [Paenibacillus sp. oral taxon 786
           str. D14]
 gi|251844247|gb|EES72265.1| RNA polymerase sigma-F factor [Paenibacillus sp. oral taxon 786
           str. D14]
          Length = 251

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 58/251 (23%), Positives = 115/251 (45%), Gaps = 32/251 (12%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD +A  RLV  ++RLV  +   +   G    ++   G IGL+++V KFD     + +
Sbjct: 26  QSGDNAARDRLVNCNIRLVWSVVQRFMNRGYEPEDLFQIGCIGLLKSVDKFDLSYDVKFS 85

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I   +Q + LR    +K+  +   K +   +R+ K  L   +    +   V  +
Sbjct: 86  TYAVPMIIGEIQRF-LRDDGTLKVSRSL--KEMANKVRKKKDEL---SKQLGRLPTVKEV 139

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ-----EQVLIE 217
           A +L V+  +V+                  ++K  +   +  V+++DG      +Q+  E
Sbjct: 140 ADELGVTPEDVV--------------FAQEANKPPASIHE-TVFENDGDPITLMDQIADE 184

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
            +ER   +  L  ++  L  RER I   R  ++   T   +++   +S+ +V ++E    
Sbjct: 185 TQERWFDKLALHEAIDGLTDRERLIVYLRYYRDQ--TQSEVATRLGISQVQVSRLE---- 238

Query: 278 KKVQESIQKQV 288
           KK+ +SI+ Q+
Sbjct: 239 KKILQSIRDQI 249


>gi|134298555|ref|YP_001112051.1| sporulation sigma factor SigG [Desulfotomaculum reducens MI-1]
 gi|134051255|gb|ABO49226.1| RNA polymerase, sigma subunit, RpsG/SigG [Desulfotomaculum reducens
           MI-1]
          Length = 257

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 25/93 (26%), Positives = 50/93 (53%), Gaps = 1/93 (1%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+  +   L +   + GD  A  +L+  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKNTQMRTLFEAM-QQGDKDARSQLINGNLRLVLSVIQRFTNRGEYVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           GLM+A+  FD  +  + +TY++  I   ++ Y+
Sbjct: 74  GLMKAIDNFDLGQNVKFSTYAVPMIIGEIRRYL 106


>gi|121535758|ref|ZP_01667560.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
 gi|121305657|gb|EAX46597.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
          Length = 243

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 53/241 (21%), Positives = 109/241 (45%), Gaps = 16/241 (6%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A   ++  ++ LV  I   +   G    ++   G IGLM+A+++FD     + +TY
Sbjct: 17  GDKQAKEYILEHNVNLVRSIVHRFLNRGYEWDDLFQIGCIGLMKAIERFDLNFNVKFSTY 76

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           ++  +   ++ +I R  +  K+      K L + + R +  LQ++     +   +  +AK
Sbjct: 77  AVPMVIGEIRRFI-RDDNPTKVSRPV--KELAYRVYRTQERLQSLLG---REPTIHEVAK 130

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L ++  E++S    +    SL       D +     D +    DGQ+    EK      
Sbjct: 131 ELALAPQEIVSALEAMQPPASLFEQAYHDDGDPISRLDQIA-QCDGQDNAYFEK------ 183

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              L   +S L P+ER +   R  ++   T   +++   +S+ +V +IE +A + +++ +
Sbjct: 184 -LALREVLSRLPPKERYVIHLRFFEDK--TQAEIANMIGLSQVQVSRIEKQALRLIRDLM 240

Query: 285 Q 285
           Q
Sbjct: 241 Q 241


>gi|52080250|ref|YP_079041.1| RNA polymerase sigma factor SigD [Bacillus licheniformis ATCC
           14580]
 gi|52785627|ref|YP_091456.1| RNA polymerase sigma factor SigD [Bacillus licheniformis ATCC
           14580]
 gi|319645970|ref|ZP_08000200.1| RNA polymerase sigma factor [Bacillus sp. BT1B_CT2]
 gi|52003461|gb|AAU23403.1| RNA polymerase sigma-28 factor (sigma-D) [Bacillus licheniformis
           ATCC 14580]
 gi|52348129|gb|AAU40763.1| SigD [Bacillus licheniformis ATCC 14580]
 gi|317391720|gb|EFV72517.1| RNA polymerase sigma factor [Bacillus sp. BT1B_CT2]
          Length = 254

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 39/148 (26%), Positives = 76/148 (51%), Gaps = 15/148 (10%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQ 88
           E+ +L  R++E  D  A   L+  ++ LV    +G    GLP S    ++VS G +GL  
Sbjct: 7   EDQMLWSRWKEWKDPQAGDDLIRRYMPLVT-YHVGRIAVGLPKSVHKDDLVSLGMLGLYD 65

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           A++KFDP R  +  TY+ + I+ A+ + + +  W    +  T+ +K      ++++  ++
Sbjct: 66  ALEKFDPGRDLKFDTYASFRIRGAIIDGLRKEDW----LPRTSREKT-----KKVEAAIE 116

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVIS 175
            +    L+      IA +L +SE +V++
Sbjct: 117 KLEQRYLRNVSPSEIAAELGMSEQDVVT 144


>gi|294501329|ref|YP_003565029.1| RNA polymerase sigma-K factor [Bacillus megaterium QM B1551]
 gi|295706676|ref|YP_003599751.1| RNA polymerase sigma-K factor [Bacillus megaterium DSM 319]
 gi|294351266|gb|ADE71595.1| RNA polymerase sigma-K factor [Bacillus megaterium QM B1551]
 gi|294804335|gb|ADF41401.1| RNA polymerase sigma-K factor [Bacillus megaterium DSM 319]
          Length = 242

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 26/75 (34%), Positives = 42/75 (56%), Gaps = 3/75 (4%)

Query: 39  KRY---REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           KRY    E GD  A + L+  +LRLV  I   +   G    +++S G IGL++A++ +  
Sbjct: 37  KRYLSLMEQGDQEARNLLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIESYSQ 96

Query: 96  ERGFRLATYSMWWIK 110
            +G +LATY+   I+
Sbjct: 97  GKGTKLATYAARCIE 111


>gi|146296669|ref|YP_001180440.1| FliA/WhiG family RNA polymerase sigma factor [Caldicellulosiruptor
           saccharolyticus DSM 8903]
 gi|145410245|gb|ABP67249.1| RNA polymerase, sigma subunit, RpoX/SigF [Caldicellulosiruptor
           saccharolyticus DSM 8903]
          Length = 231

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 55/239 (23%), Positives = 101/239 (42%), Gaps = 17/239 (7%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           ++GD  A   L+ ++L LV  I   +   G+   ++   G IGL++AV +FD     R +
Sbjct: 6   KNGDKKARQELIENNLALVWSIVKKFVVKGIEADDLFQIGCIGLIKAVDRFDLSFNVRFS 65

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I   ++ Y LR    +KI     +     N  +LK         N +   +  I
Sbjct: 66  TYAVPMIIGEIKRY-LRDDGKIKISRKIKE-----NQNKLKRFRDEFLFQNGREPTISEI 119

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           ++   +S+ +++          SLN +IN  +       D +  D D   ++L       
Sbjct: 120 SEATGLSQDDILLCIDASLDVTSLNEVINQEEGKPITLMD-IAADEDYSSRLL------- 171

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                L   +  L  RER I   R  +    T   ++ E  +S+  V +IE +A ++++
Sbjct: 172 -DIMALKEGLRKLKGRERYIIFMRYFKNK--TQSEIAKELNISQVHVSRIEKKALERIK 227


>gi|169831890|ref|YP_001717872.1| FliA/WhiG family RNA polymerase sigma factor [Candidatus
           Desulforudis audaxviator MP104C]
 gi|169638734|gb|ACA60240.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Candidatus
           Desulforudis audaxviator MP104C]
          Length = 257

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 72/266 (27%), Positives = 122/266 (45%), Gaps = 40/266 (15%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIA--MGYRGYGLPISEVVSE-----GNIGLMQAVK 91
           +RYR+  +     +L+  HL LV  IA  +  R    P S +  E     G  GL++AV+
Sbjct: 7   RRYRDTRNSGLREQLIVEHLPLVRLIAGRLAVR----PPSFIAQEDLEGWGIFGLIEAVE 62

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILR-SW---SLVKIGTTANQKRLFFNLRRLKGHLQ 147
           K+DP  G    T++   I+ A+ + + R SW   SL       N+ R    L R  G   
Sbjct: 63  KYDPNHGTDFRTFAYHRIRGAILDEVRRQSWLPRSLWHKLQEINEARA--RLERETG--A 118

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           ++TD          +A  L +++ E   ++ + R     SL+ +  + +  +  W   L+
Sbjct: 119 SVTDAE--------VAASLGMTDLEFHRLANHFRSVSVMSLDDVRTTRNGEAVPWGS-LI 169

Query: 206 YDH---DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
            D    D  EQVL E++ +      L  +++ L  ++R +  A   QE  +TL+ L    
Sbjct: 170 EDTGSPDPLEQVLEEEDHQ-----TLVAAITQLEEKDRLVL-ALYYQEG-LTLKELGRVL 222

Query: 263 EVSRERVRQIEARAFKKVQESIQKQV 288
           EV+  R  Q+ ARA  +++E I + V
Sbjct: 223 EVTESRACQLHARAIARLREKIAQAV 248


>gi|315646368|ref|ZP_07899486.1| sporulation sigma factor SigF [Paenibacillus vortex V453]
 gi|315278011|gb|EFU41331.1| sporulation sigma factor SigF [Paenibacillus vortex V453]
          Length = 251

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 58/251 (23%), Positives = 114/251 (45%), Gaps = 32/251 (12%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A   LV  ++RLV  +   +   G    ++   G IGL+++V KFD     + +
Sbjct: 26  QSGDNVARDTLVNCNIRLVWSVVQRFMNRGYEPDDLFQIGCIGLLKSVDKFDLSYDVKFS 85

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I   +Q + LR    +K+  +   K +   +R+ +  L    D   +   V  +
Sbjct: 86  TYAVPMIIGEIQRF-LRDDGTLKVSRSL--KEMANKVRKKRDELSKQLD---RLPTVKEV 139

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ-----EQVLIE 217
           A++L V+  EV+                  ++K  +   +  V+++DG      +Q+  E
Sbjct: 140 AEELGVTPEEVV--------------FAQEANKPPTSIHE-TVFENDGDPITLMDQIADE 184

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
            +ER   +  L  ++  L  RER I   R  ++   T   ++S   +S+ +V ++E    
Sbjct: 185 SQERWFDKLALNEAIGGLTERERLIVYLRYYRDQ--TQSEVASRLGISQVQVSRLE---- 238

Query: 278 KKVQESIQKQV 288
           KK+ +SI+ ++
Sbjct: 239 KKILQSIRNEI 249


>gi|242089037|ref|XP_002440351.1| hypothetical protein SORBIDRAFT_09g030110 [Sorghum bicolor]
 gi|241945636|gb|EES18781.1| hypothetical protein SORBIDRAFT_09g030110 [Sorghum bicolor]
          Length = 501

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 26/79 (32%), Positives = 48/79 (60%), Gaps = 7/79 (8%)

Query: 48  SAAHRLVTSHLRLV-VKIAMGYRGYGLP--ISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           +A ++L+  +LRLV   I   Y   G      ++   G  GL+ A+ +F+P+RGFR++TY
Sbjct: 262 AARNKLIKHNLRLVPYAINKYYPDMGTDERFDDLCQAGANGLITAIDRFEPKRGFRISTY 321

Query: 105 SMWWIKAAMQEYILRSWSL 123
           +++WI+ +    I+R+ +L
Sbjct: 322 ALFWIRHS----IVRAMTL 336


>gi|225028119|ref|ZP_03717311.1| hypothetical protein EUBHAL_02389 [Eubacterium hallii DSM 3353]
 gi|224954589|gb|EEG35798.1| hypothetical protein EUBHAL_02389 [Eubacterium hallii DSM 3353]
          Length = 278

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 58/262 (22%), Positives = 114/262 (43%), Gaps = 17/262 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           ++P+L  +E+  L  +  E G++ A  + V  +LRLV+ +   +        ++   G I
Sbjct: 34  ELPLLSDEEKENLFIQI-EQGNMDAREQYVKGNLRLVLSVIQRFSSNHEHADDLFQVGCI 92

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A+  FD     + +TY++  I   ++ Y LR  + +++  +          + +  
Sbjct: 93  GLMKAIDNFDRTLNVKFSTYAVPMILGEVRRY-LRDNNSIRVSRSLRDTA----YKAIYA 147

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             Q     N  P  +  ++KK  + E ++I     +A   SL   +   D N   +    
Sbjct: 148 KEQLTKSMNRTP-TIEEVSKKTEIPEEDIIYALDAIATPMSLFEPV-YQDGNDPLFLMDQ 205

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           + D   +E   IE          L  +M+ L+ RE  I E R  +    T   ++ E  +
Sbjct: 206 ICDKKNKEDTWIEHLS-------LQEAMNQLSGREYHIIEKRFFEGKTQT--EVADEISI 256

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+ +V ++E  A K ++  I++
Sbjct: 257 SQAQVSRLEKNALKSIRNFIER 278


>gi|238916719|ref|YP_002930236.1| RNA polymerase sporulation-specific sigma factor [Eubacterium
           eligens ATCC 27750]
 gi|238872079|gb|ACR71789.1| RNA polymerase sporulation-specific sigma factor [Eubacterium
           eligens ATCC 27750]
          Length = 223

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 35/86 (40%), Positives = 48/86 (55%), Gaps = 9/86 (10%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY----RGYGLPISE-VVSEGN 83
           L  QEE  L  + RE GD +A + L+  ++RLV  I   Y    R Y   I+E ++S G 
Sbjct: 14  LSAQEEKELLIKLRE-GDSAARNALIEKNMRLVAHIVKKYTSTERDY---INEDLISVGT 69

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWI 109
           IGL++AV  FD ER  R +TY+   I
Sbjct: 70  IGLIKAVDSFDIERNVRFSTYAAKCI 95


>gi|222097784|ref|YP_002531841.1| sporulation sigma factor sigk [Bacillus cereus Q1]
 gi|221241842|gb|ACM14552.1| RNA polymerase sigma-27 factor [Bacillus cereus Q1]
          Length = 263

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 38/67 (56%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E GD  A + L+  +LRLV  I   +   G    +++S G IGL++A++ +   +G +LA
Sbjct: 69  EQGDAQARNLLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIESYSAGKGTKLA 128

Query: 103 TYSMWWI 109
           TY+   I
Sbjct: 129 TYAARCI 135


>gi|188589198|ref|YP_001920238.1| sporulation sigma factor SigF [Clostridium botulinum E3 str. Alaska
           E43]
 gi|251778416|ref|ZP_04821336.1| RNA polymerase sigma-F factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
 gi|188499479|gb|ACD52615.1| RNA polymerase sigma-F factor [Clostridium botulinum E3 str. Alaska
           E43]
 gi|243082731|gb|EES48621.1| RNA polymerase sigma-F factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
          Length = 251

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 53/252 (21%), Positives = 105/252 (41%), Gaps = 34/252 (13%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A +RL+  +L LV  I+  +   G    ++   G+IGL++A+  FD     + +
Sbjct: 24  KDGDTEAMNRLIEMNLPLVASISKKFLNRGYDYEDIFQIGSIGLVKAINNFDLSYNVKFS 83

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQ--KRLFFNLRRLKGHLQAITDNNLKPEQVV 160
           TY++  I   ++ + LR   ++K+        KR+ F    L                  
Sbjct: 84  TYAVPMIIGEIKRF-LRDDGMIKVSRNVKSLAKRIHFTKEEL------------------ 124

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
              KKLN   S  I      +G +    +       S Q+    ++  DG   +LI+K  
Sbjct: 125 --TKKLN--RSPTIEELAEYSGVDKEEIIFAIESATSLQYLYDTIHQDDGAPVLLIDKLS 180

Query: 221 RKNRRNM-------LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
            K   ++       L  ++  L+ + R+I   R  ++   T   ++    +S+ +V +IE
Sbjct: 181 EKGEDDIGMINKIALKEALRSLDEKARQIIVLRYFKDK--TQVQVAKLLGISQVQVSRIE 238

Query: 274 ARAFKKVQESIQ 285
            +   K+++ ++
Sbjct: 239 KKVLLKMRDKLE 250


>gi|40787125|gb|AAR90090.1| WhiG-like protein [Streptomyces ambofaciens]
          Length = 280

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 61/245 (24%), Positives = 104/245 (42%), Gaps = 20/245 (8%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFD 94
           + Y+  GD     +L+  H   +VK   G    GLP     ++ VS G  GL+ A++KFD
Sbjct: 36  RSYKATGDERLREQLIL-HYSPLVKYVAGRVSVGLPPNVEQADFVSSGVFGLIDAIEKFD 94

Query: 95  PERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
            +R  +  TY++  I+ AM  E     W    I  +  QK    N+ R    L+A     
Sbjct: 95  VDREIKFETYAITRIRGAMIDELRALDW----IPRSVRQKAR--NVERAYTTLEARL-RR 147

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ--DWLVYDHDGQ 211
              E  VA+   + V +   +     LA   +L  L+++  +   +    D L    D  
Sbjct: 148 TPSESEVAVEMGIAVEDLHAVFSQLSLANVVALEELLHAGGEGGGRLSLMDTL---EDTA 204

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
               +E  E +  R +L R+++ L  RE+ +      +   +TL  + +   V+  RV Q
Sbjct: 205 ADNPVEVAEDRELRRLLARAINTLPEREKTVVTLYYYEG--LTLAEIGNVLGVTESRVSQ 262

Query: 272 IEARA 276
           I  ++
Sbjct: 263 IHTKS 267


>gi|294998208|gb|ADF57908.1| sporulation specific sigma factor K [Bacillus thuringiensis serovar
           aizawai]
 gi|308154182|gb|ADF57907.2| sporulation specific sigma factor K [Bacillus thuringiensis serovar
           aizawai]
          Length = 271

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 38/67 (56%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E GD  A + L+  +LRLV  I   +   G    +++S G IGL++A++ +   +G +LA
Sbjct: 77  EQGDAQARNLLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIESYSAGKGTKLA 136

Query: 103 TYSMWWI 109
           TY+   I
Sbjct: 137 TYAARCI 143


>gi|282861385|ref|ZP_06270450.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Streptomyces sp. ACTE]
 gi|282564043|gb|EFB69580.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Streptomyces sp. ACTE]
          Length = 278

 Score = 47.8 bits (112), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 65/248 (26%), Positives = 108/248 (43%), Gaps = 26/248 (10%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFD 94
           + Y+  GD     +L+  H   +VK   G    GLP     ++ VS G  GL+ A++KFD
Sbjct: 34  RSYKSTGDERLREQLIL-HYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEKFD 92

Query: 95  PERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA----- 148
            ER  +  TY++  I+ AM  E     W    I  +  QK    N+ R    L+A     
Sbjct: 93  LERAIKFETYAITRIRGAMIDELRALDW----IPRSVRQK--ARNVERAYATLEAQLRRT 146

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
            T+  +  E  +A+ +  +V     +S+   +A +E L+      D+ S    D L    
Sbjct: 147 PTEAEVAAEMGIALEELHSVFSQ--LSLANVVALEELLHVGGEGGDRLS--LMDTL---E 199

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D      +E  E +  R ML R+++ L  RE+ +      +   +TL  + +   V+  R
Sbjct: 200 DTAADNPVEIAEDRELRRMLARAINTLPEREKTVVTLYYYEG--LTLAEIGNVLGVTESR 257

Query: 269 VRQIEARA 276
           V QI  ++
Sbjct: 258 VSQIHTKS 265


>gi|49183950|ref|YP_027202.1| RNA polymerase sigma factor SigB [Bacillus anthracis str. Sterne]
 gi|49177877|gb|AAT53253.1| RNA polymerase sigma-B factor [Bacillus anthracis str. Sterne]
          Length = 258

 Score = 47.4 bits (111), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 61/271 (22%), Positives = 129/271 (47%), Gaps = 29/271 (10%)

Query: 22  EIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           EI+  P  L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++ 
Sbjct: 3   EIQSQPTNLTKEDVIKLIAEFQQNQCGEAQERLVDHYKNLVYSIAYRYSKGGPMHEDIIQ 62

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNL 139
            G +GL+ A++++D   G     +++  I   +++Y+  ++W +       +  R   +L
Sbjct: 63  VGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGI-------HVPRRIKDL 115

Query: 140 -RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNALI-NS 192
             ++K  ++ +TD+  +  +++ IA  L +SE EV+ +     N R++   SL+ ++ N+
Sbjct: 116 GGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVS---SLDDVVENA 172

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
           SD +S    + +     G EQ          RR +L    +VLN  E+ +     + E  
Sbjct: 173 SDGSSVARIESVGEVEQGYEQT--------ERRLVLKDIFNVLNETEKSVI--HYIFEEN 222

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +  ++      +S+  V +I+ +A  K++++
Sbjct: 223 LNQKDTGERLGISQMHVSRIKRQAISKLKQA 253


>gi|302560279|ref|ZP_07312621.1| RNA polymerase sigma factor [Streptomyces griseoflavus Tu4000]
 gi|302477897|gb|EFL40990.1| RNA polymerase sigma factor [Streptomyces griseoflavus Tu4000]
          Length = 304

 Score = 47.4 bits (111), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 56/237 (23%), Positives = 109/237 (45%), Gaps = 24/237 (10%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  +L LV   A  +R    P+ +++  G IGL++A+ +F+  RG    T++M  I   
Sbjct: 83  LVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRGVEFPTFAMPTIIGE 142

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL  +L +    L    D +     V  +A++L ++  
Sbjct: 143 IKRFFRDTSWS-VRVPRRLQELRL--DLAKAGDELAQQLDRS---PTVAELAERLGITNE 196

Query: 172 EVI----SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           EV+    + N   A   SL+A     D   +   D + Y+  G E +    E  ++ + +
Sbjct: 197 EVVEGMAASNAYTAS--SLDAQPEEDDAEGA-LADRIGYEDHGLEGI----EYVESLKPL 249

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +      L PR+R+I   R +    +T   +  E  +S+  V ++ +R   K+++ +
Sbjct: 250 IAE----LPPRDRKILSLRFVAG--MTQSEIGEELGISQMHVSRLLSRTLVKLRKGL 300


>gi|229093408|ref|ZP_04224513.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock3-42]
 gi|228690002|gb|EEL43805.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock3-42]
          Length = 258

 Score = 47.4 bits (111), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 38/67 (56%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E GD  A + L+  +LRLV  I   +   G    +++S G IGL++A++ +   +G +LA
Sbjct: 46  EQGDAQARNLLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIESYSAGKGTKLA 105

Query: 103 TYSMWWI 109
           TY+   I
Sbjct: 106 TYAARCI 112


>gi|188586048|ref|YP_001917593.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|179350735|gb|ACB85005.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 250

 Score = 47.4 bits (111), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 58/258 (22%), Positives = 118/258 (45%), Gaps = 23/258 (8%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIA--MGYRGY-GLPISEVVSEGNIGLMQAVKKF 93
           L   Y++ GD     +L++ +  LV K    + Y    GL   +++S G IGL+ A+KKF
Sbjct: 5   LITSYQDSGDRQQLEKLISEYSYLVKKQVDKVNYPSISGLNRDDLISFGVIGLIDAIKKF 64

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D  R      Y+   I+ A+ +  LR +  V        K L    R+L+  L     NN
Sbjct: 65  DINRNVPFEAYANIRIRGAILDG-LRKFDFVPRNLREEMKTLHSEYRKLEQKLGRTPTNN 123

Query: 154 LKPEQVVAIAKKLNVSESEVISM----NCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
                   +A ++++SE+E+  +    NC +     L+  I ++++     +D     + 
Sbjct: 124 -------ELAYQMSISEAELDKLWQATNCVIPS--YLSDYI-TAEEGELTLEDIYPDSNS 173

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
              Q  I++   K  +  L +++  L  +E+ +      +E  +TL+ ++   E++  R+
Sbjct: 174 PDPQSRIDE---KTTKQELGQAIDTLPQKEKLVLSLYYYEE--LTLKEIAKILELTESRI 228

Query: 270 RQIEARAFKKVQESIQKQ 287
            Q+ ++A  +++  + K+
Sbjct: 229 SQLHSKAVLRLRGKLAKK 246


>gi|333023850|ref|ZP_08451914.1| putative RNA polymerase sigma-F factor [Streptomyces sp. Tu6071]
 gi|332743702|gb|EGJ74143.1| putative RNA polymerase sigma-F factor [Streptomyces sp. Tu6071]
          Length = 294

 Score = 47.4 bits (111), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 56/218 (25%), Positives = 102/218 (46%), Gaps = 23/218 (10%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL++A+ +FD  R     ++++ +I   ++ Y   S   V +     + R
Sbjct: 88  MEDILQVGTIGLIKAIDRFDLTREAEFTSFAIPYIVGEIKRYFRDSTWAVHVPRRLQELR 147

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG--DESLNALINS 192
           +  +L R K  L    D +     V  +A +LN+SE EVI       G   +SL+   +S
Sbjct: 148 V--DLARAKERLAVELDRD---PGVKELAAELNISEEEVIDGLIAANGYMSDSLDLPADS 202

Query: 193 SD------KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           S       K ++ + D+L  D D   +++   E     R +L      L+ RER + E R
Sbjct: 203 STSGKPDQKTATTYADFL-GDWDPAMELV---ENFTALRPLL----GTLDDRERYLLELR 254

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             QE  +T   + +E  VS+  V ++ +R   K++E +
Sbjct: 255 FGQE--LTQAQIGAELGVSQMHVSRLLSRTLGKLREGL 290


>gi|229917800|ref|YP_002886446.1| RNA polymerase sigma factor SigB [Exiguobacterium sp. AT1b]
 gi|229469229|gb|ACQ71001.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Exiguobacterium sp. AT1b]
          Length = 266

 Score = 47.4 bits (111), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 56/236 (23%), Positives = 119/236 (50%), Gaps = 18/236 (7%)

Query: 53  LVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           L+  +  LV  +A  + RG  +   ++V  G IGL+ A+++FDPE G    ++++  I  
Sbjct: 35  LINRYSDLVEALARKFSRGRAIH-DDLVQVGMIGLLAALRRFDPEFGRSFESFAVPTIIG 93

Query: 112 AMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            ++ +I  ++WS+         +R+     ++K  ++ +T    +  ++  IA  L VS+
Sbjct: 94  EIKRFIRDKTWSV------HVPRRIKELGPKIKKTVEELTTELQRSPRIDEIADHLGVSD 147

Query: 171 SEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
            E++     L   +S  AL ++SS +  ++     + D  G ++      E  ++R +L 
Sbjct: 148 EEILET---LEMGKSYQALSVDSSIEADNEGSTVTLLDLVGSQE---RGYESVDQRLILE 201

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           ++ +VLN RER I E    +   ++ +       +S+  V +++ RA +K++E+I+
Sbjct: 202 KAFNVLNERERAILECAYYKN--MSQKETGELLGISQMHVSRLQRRALEKLREAIK 255


>gi|75761264|ref|ZP_00741246.1| RNA polymerase sigma-K factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|74491246|gb|EAO54480.1| RNA polymerase sigma-K factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
          Length = 271

 Score = 47.4 bits (111), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 38/67 (56%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E GD  A + L+  +LRLV  I   +   G    +++S G IGL++A++ +   +G +LA
Sbjct: 77  EQGDAQARNLLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIESYSAGKGTKLA 136

Query: 103 TYSMWWI 109
           TY+   I
Sbjct: 137 TYAARCI 143


>gi|318041689|ref|ZP_07973645.1| RNA polymerase sigma factor SigF [Synechococcus sp. CB0101]
          Length = 263

 Score = 47.4 bits (111), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 18/46 (39%), Positives = 31/46 (67%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           G    ++  EG  GL++AV++FDP RG  L+T ++ WI+ A++ Y+
Sbjct: 53  GHSFDDLTQEGCFGLIKAVERFDPGRGHSLSTAAVPWIRGAIRHYL 98


>gi|118479504|ref|YP_896655.1| sporulation sigma factor SigK [Bacillus thuringiensis str. Al
           Hakam]
 gi|118418729|gb|ABK87148.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Bacillus
           thuringiensis str. Al Hakam]
          Length = 271

 Score = 47.4 bits (111), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 38/67 (56%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E GD  A + L+  +LRLV  I   +   G    +++S G IGL++A++ +   +G +LA
Sbjct: 77  EQGDAQARNLLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIESYSAGKGTKLA 136

Query: 103 TYSMWWI 109
           TY+   I
Sbjct: 137 TYAARCI 143


>gi|308069565|ref|YP_003871170.1| RNA polymerase sigma-F factor (stage II sporulation protein AC)
           (sporulation sigma factor) [Paenibacillus polymyxa E681]
 gi|305858844|gb|ADM70632.1| RNA polymerase sigma-F factor (Stage II sporulation protein AC)
           (Sporulation sigma factor) [Paenibacillus polymyxa E681]
          Length = 251

 Score = 47.4 bits (111), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 59/251 (23%), Positives = 114/251 (45%), Gaps = 36/251 (14%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A   LV S++RLV  +   +   G    ++   G IGL+++V KFD     + +
Sbjct: 26  QSGDNEARETLVNSNIRLVWSVVQRFMNRGYEPDDLFQIGCIGLLKSVDKFDLSYEVKFS 85

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIG----TTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           TY++  I   +Q + LR    +K+      TAN+      +R++K  L      N  P  
Sbjct: 86  TYAVPMIIGEIQRF-LRDDGTLKVSRSLKETANK------VRKMKDELSKRL--NRLP-T 135

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ-----EQ 213
           V  +A +L V+  +V+                  ++K  +   +  V+++DG      +Q
Sbjct: 136 VKEVADELGVTPEDVV--------------FAQEANKPPTSIHE-TVFENDGDPITLMDQ 180

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
           +  E +ER   +  L  ++  L+ RER I   R  ++   T   ++S   +S+ +V ++E
Sbjct: 181 IADESQERWFDKLALNEAIGGLSERERLIVYLRYYRDQ--TQSEVASRLGISQVQVSRLE 238

Query: 274 ARAFKKVQESI 284
            +  + +++ I
Sbjct: 239 KKILQLIRDQI 249


>gi|228993082|ref|ZP_04153005.1| RNA polymerase sigma-28 factor [Bacillus pseudomycoides DSM 12442]
 gi|228999132|ref|ZP_04158714.1| RNA polymerase sigma-28 factor [Bacillus mycoides Rock3-17]
 gi|229006680|ref|ZP_04164314.1| RNA polymerase sigma-28 factor [Bacillus mycoides Rock1-4]
 gi|228754541|gb|EEM03952.1| RNA polymerase sigma-28 factor [Bacillus mycoides Rock1-4]
 gi|228760749|gb|EEM09713.1| RNA polymerase sigma-28 factor [Bacillus mycoides Rock3-17]
 gi|228766730|gb|EEM15370.1| RNA polymerase sigma-28 factor [Bacillus pseudomycoides DSM 12442]
          Length = 228

 Score = 47.4 bits (111), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 38/67 (56%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E GD  A + L+  +LRLV  I   +   G    +++S G IGL++A++ +   +G +LA
Sbjct: 34  EQGDAHARNLLIEHNLRLVAHIVKKFENTGEDSEDLISIGTIGLIKAIESYSAGKGTKLA 93

Query: 103 TYSMWWI 109
           TY+   I
Sbjct: 94  TYAARCI 100


>gi|11466545|ref|NP_044794.1| transcription initiation factor sigma [Reclinomonas americana]
 gi|2258375|gb|AAD11909.1| transcription initiation factor sigma [Reclinomonas americana]
          Length = 532

 Score = 47.4 bits (111), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 23/81 (28%), Positives = 44/81 (54%), Gaps = 6/81 (7%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYR--GYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           RE+  ++  +R++ +++  +  I+  Y   GY    S+++ EG  G+  A +KF   RG 
Sbjct: 345 RENIKVTLKNRIIFNYMPYITTISKQYVKIGYQAQFSDLIQEGISGVSDAAEKFQLGRGV 404

Query: 100 RLATYSMWWIKAAMQEYILRS 120
           R  TY+ WW    M  Y++++
Sbjct: 405 RFLTYAYWW----MHNYMMKA 421


>gi|30261116|ref|NP_843493.1| RNA polymerase sigma factor SigB [Bacillus anthracis str. Ames]
 gi|47526271|ref|YP_017620.1| RNA polymerase sigma factor SigB [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|65318395|ref|ZP_00391354.1| COG1191: DNA-directed RNA polymerase specialized sigma subunit
           [Bacillus anthracis str. A2012]
 gi|165871654|ref|ZP_02216299.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0488]
 gi|167635453|ref|ZP_02393766.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0442]
 gi|167638886|ref|ZP_02397160.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0193]
 gi|170687593|ref|ZP_02878809.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0465]
 gi|170707965|ref|ZP_02898414.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0389]
 gi|177653505|ref|ZP_02935679.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0174]
 gi|190566700|ref|ZP_03019617.1| RNA polymerase sigma-B factor [Bacillus anthracis Tsiankovskii-I]
 gi|196037492|ref|ZP_03104803.1| RNA polymerase sigma-B factor [Bacillus cereus NVH0597-99]
 gi|227816152|ref|YP_002816161.1| RNA polymerase sigma-B factor [Bacillus anthracis str. CDC 684]
 gi|229604478|ref|YP_002865547.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0248]
 gi|254682827|ref|ZP_05146688.1| RNA polymerase sigma factor SigB [Bacillus anthracis str.
           CNEVA-9066]
 gi|254725613|ref|ZP_05187395.1| RNA polymerase sigma factor SigB [Bacillus anthracis str. A1055]
 gi|254734239|ref|ZP_05191952.1| RNA polymerase sigma factor SigB [Bacillus anthracis str. Western
           North America USA6153]
 gi|254740112|ref|ZP_05197804.1| RNA polymerase sigma factor SigB [Bacillus anthracis str. Kruger B]
 gi|254753453|ref|ZP_05205489.1| RNA polymerase sigma factor SigB [Bacillus anthracis str. Vollum]
 gi|254758550|ref|ZP_05210577.1| RNA polymerase sigma factor SigB [Bacillus anthracis str. Australia
           94]
 gi|17369088|sp|Q9K5J6|RPSB_BACAN RecName: Full=RNA polymerase sigma-B factor
 gi|8670945|emb|CAB95034.1| sigB [Bacillus anthracis]
 gi|30254730|gb|AAP24979.1| RNA polymerase sigma-B factor [Bacillus anthracis str. Ames]
 gi|47501419|gb|AAT30095.1| RNA polymerase sigma-B factor [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|164712555|gb|EDR18087.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0488]
 gi|167513016|gb|EDR88388.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0193]
 gi|167529071|gb|EDR91825.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0442]
 gi|170127125|gb|EDS96003.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0389]
 gi|170668406|gb|EDT19153.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0465]
 gi|172081309|gb|EDT66383.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0174]
 gi|190562252|gb|EDV16220.1| RNA polymerase sigma-B factor [Bacillus anthracis Tsiankovskii-I]
 gi|196031734|gb|EDX70330.1| RNA polymerase sigma-B factor [Bacillus cereus NVH0597-99]
 gi|227003869|gb|ACP13612.1| RNA polymerase sigma-B factor [Bacillus anthracis str. CDC 684]
 gi|229268886|gb|ACQ50523.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0248]
          Length = 257

 Score = 47.4 bits (111), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 61/271 (22%), Positives = 129/271 (47%), Gaps = 29/271 (10%)

Query: 22  EIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           EI+  P  L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++ 
Sbjct: 2   EIQSQPTNLTKEDVIKLIAEFQQNQCGEAQERLVDHYKNLVYSIAYRYSKGGPMHEDIIQ 61

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNL 139
            G +GL+ A++++D   G     +++  I   +++Y+  ++W +       +  R   +L
Sbjct: 62  VGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGI-------HVPRRIKDL 114

Query: 140 -RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNALI-NS 192
             ++K  ++ +TD+  +  +++ IA  L +SE EV+ +     N R++   SL+ ++ N+
Sbjct: 115 GGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVS---SLDDVVENA 171

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
           SD +S    + +     G EQ          RR +L    +VLN  E+ +     + E  
Sbjct: 172 SDGSSVARIESVGEVEQGYEQT--------ERRLVLKDIFNVLNETEKSVI--HYIFEEN 221

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +  ++      +S+  V +I+ +A  K++++
Sbjct: 222 LNQKDTGERLGISQMHVSRIKRQAISKLKQA 252


>gi|126700256|ref|YP_001089153.1| sporulation sigma factor SigG [Clostridium difficile 630]
 gi|254976235|ref|ZP_05272707.1| sporulation sigma factor SigG [Clostridium difficile QCD-66c26]
 gi|255093622|ref|ZP_05323100.1| sporulation sigma factor SigG [Clostridium difficile CIP 107932]
 gi|255101810|ref|ZP_05330787.1| sporulation sigma factor SigG [Clostridium difficile QCD-63q42]
 gi|255307677|ref|ZP_05351848.1| sporulation sigma factor SigG [Clostridium difficile ATCC 43255]
 gi|255315370|ref|ZP_05356953.1| sporulation sigma factor SigG [Clostridium difficile QCD-76w55]
 gi|255518035|ref|ZP_05385711.1| sporulation sigma factor SigG [Clostridium difficile QCD-97b34]
 gi|255651151|ref|ZP_05398053.1| sporulation sigma factor SigG [Clostridium difficile QCD-37x79]
 gi|255656619|ref|ZP_05402028.1| sporulation sigma factor SigG [Clostridium difficile QCD-23m63]
 gi|260684217|ref|YP_003215502.1| sporulation sigma factor SigG [Clostridium difficile CD196]
 gi|260687876|ref|YP_003219010.1| sporulation sigma factor SigG [Clostridium difficile R20291]
 gi|296449925|ref|ZP_06891689.1| RNA polymerase sigma-G factor [Clostridium difficile NAP08]
 gi|296878307|ref|ZP_06902315.1| RNA polymerase sigma-G factor [Clostridium difficile NAP07]
 gi|306521001|ref|ZP_07407348.1| sporulation sigma factor SigG [Clostridium difficile QCD-32g58]
 gi|115251693|emb|CAJ69528.1| RNA polymerase sigma-G factor [Clostridium difficile]
 gi|260210380|emb|CBA64761.1| RNA polymerase sigma-G factor [Clostridium difficile CD196]
 gi|260213893|emb|CBE05925.1| RNA polymerase sigma-G factor [Clostridium difficile R20291]
 gi|296261195|gb|EFH08026.1| RNA polymerase sigma-G factor [Clostridium difficile NAP08]
 gi|296430605|gb|EFH16444.1| RNA polymerase sigma-G factor [Clostridium difficile NAP07]
          Length = 257

 Score = 47.4 bits (111), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 22/75 (29%), Positives = 41/75 (54%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           ++GD  A  + V  +LRLV+ +   +   G  I ++   G IGL++A+  FD  +  R +
Sbjct: 32  KNGDEEARQQFVRGNLRLVLSVIKKFNNRGENIDDLFQIGCIGLIKAIDNFDLSQNVRFS 91

Query: 103 TYSMWWIKAAMQEYI 117
           TY++  I   ++ Y+
Sbjct: 92  TYAVPMIIGEIRRYL 106


>gi|261419446|ref|YP_003253128.1| RNA polymerase sigma factor SigD [Geobacillus sp. Y412MC61]
 gi|319766261|ref|YP_004131762.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacillus sp.
           Y412MC52]
 gi|261375903|gb|ACX78646.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacillus sp.
           Y412MC61]
 gi|317111127|gb|ADU93619.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacillus sp.
           Y412MC52]
          Length = 251

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 60/249 (24%), Positives = 113/249 (45%), Gaps = 21/249 (8%)

Query: 44  HG-DLSAAHRLVTSHLRLV---VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           HG D  AA  LV  ++ LV   V+         +P  E+VS G +GL  A++KFDP R  
Sbjct: 18  HGRDRHAAEELVQRYMPLVFYHVQRLSATLPSSVPKDELVSLGLVGLYDALEKFDPSRDL 77

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG-HLQAITDNNLKPEQ 158
           +  TY+ + I+ A+ +  LR    +        K++   + RL+  H++++T        
Sbjct: 78  KFDTYASFRIRGAILDG-LRKEDWLPRSMRDKAKKIEGAIERLEQRHMRSVTAKE----- 131

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              IA +L ++E EV     + A  E+  +      + +    + L+   D +  +  E+
Sbjct: 132 ---IAAELGMTEEEV-----QAAASETFFSHWLPLGQTTVDEDEGLLSVRDDRAPLPEEQ 183

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
             ++     L  ++  LN +E+ +      +E  +T   + S   +S  R+ QI A+A  
Sbjct: 184 IVKQEMIEKLAEAIGQLNEKEQLVISLFYKEE--LTFTEIGSLLHLSTSRISQIHAKALW 241

Query: 279 KVQESIQKQ 287
           K++   +K+
Sbjct: 242 KLRRFFEKE 250


>gi|30022159|ref|NP_833790.1| sporulation sigma factor SigF [Bacillus cereus ATCC 14579]
 gi|30264150|ref|NP_846527.1| sporulation sigma factor SigF [Bacillus anthracis str. Ames]
 gi|42783188|ref|NP_980435.1| sporulation sigma factor SigF [Bacillus cereus ATCC 10987]
 gi|47529588|ref|YP_020937.1| sporulation sigma factor SigF [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|47568126|ref|ZP_00238830.1| sigma-B, putative [Bacillus cereus G9241]
 gi|49186981|ref|YP_030233.1| sporulation sigma factor SigF [Bacillus anthracis str. Sterne]
 gi|49478518|ref|YP_038132.1| sporulation sigma factor SigF [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|52141420|ref|YP_085409.1| sporulation sigma factor SigF [Bacillus cereus E33L]
 gi|65321467|ref|ZP_00394426.1| COG1191: DNA-directed RNA polymerase specialized sigma subunit
           [Bacillus anthracis str. A2012]
 gi|75762406|ref|ZP_00742276.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|118479276|ref|YP_896427.1| sporulation sigma factor SigF [Bacillus thuringiensis str. Al
           Hakam]
 gi|165871124|ref|ZP_02215774.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0488]
 gi|167633745|ref|ZP_02392069.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0442]
 gi|167639441|ref|ZP_02397712.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0193]
 gi|170687128|ref|ZP_02878346.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0465]
 gi|170705887|ref|ZP_02896350.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0389]
 gi|177652593|ref|ZP_02935009.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0174]
 gi|190565830|ref|ZP_03018749.1| RNA polymerase sigma-F factor [Bacillus anthracis Tsiankovskii-I]
 gi|196035002|ref|ZP_03102409.1| RNA polymerase sigma-F factor [Bacillus cereus W]
 gi|196045861|ref|ZP_03113090.1| RNA polymerase sigma-F factor [Bacillus cereus 03BB108]
 gi|206971277|ref|ZP_03232228.1| RNA polymerase sigma-F factor [Bacillus cereus AH1134]
 gi|206977400|ref|ZP_03238296.1| RNA polymerase sigma-F factor [Bacillus cereus H3081.97]
 gi|217961566|ref|YP_002340136.1| sporulation sigma factor SigF [Bacillus cereus AH187]
 gi|218234550|ref|YP_002368877.1| sporulation sigma factor SigF [Bacillus cereus B4264]
 gi|218899234|ref|YP_002447645.1| RNA polymerase sigma-F factor [Bacillus cereus G9842]
 gi|218905210|ref|YP_002453044.1| RNA polymerase sigma-F factor [Bacillus cereus AH820]
 gi|222097523|ref|YP_002531580.1| sporulation sigma factor sigf [Bacillus cereus Q1]
 gi|225866059|ref|YP_002751437.1| RNA polymerase sigma-F factor [Bacillus cereus 03BB102]
 gi|227816852|ref|YP_002816861.1| RNA polymerase sigma-F factor [Bacillus anthracis str. CDC 684]
 gi|228902583|ref|ZP_04066734.1| RNA polymerase sigma-F factor [Bacillus thuringiensis IBL 4222]
 gi|228909904|ref|ZP_04073725.1| RNA polymerase sigma-F factor [Bacillus thuringiensis IBL 200]
 gi|228916713|ref|ZP_04080278.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228922825|ref|ZP_04086123.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228929122|ref|ZP_04092149.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228935394|ref|ZP_04098212.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228941224|ref|ZP_04103777.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228947793|ref|ZP_04110080.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228954358|ref|ZP_04116384.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228960339|ref|ZP_04121992.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228967106|ref|ZP_04128142.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228974156|ref|ZP_04134726.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228980748|ref|ZP_04141053.1| RNA polymerase sigma-F factor [Bacillus thuringiensis Bt407]
 gi|228987264|ref|ZP_04147385.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|229019284|ref|ZP_04176110.1| RNA polymerase sigma-F factor [Bacillus cereus AH1273]
 gi|229025528|ref|ZP_04181938.1| RNA polymerase sigma-F factor [Bacillus cereus AH1272]
 gi|229047765|ref|ZP_04193345.1| RNA polymerase sigma-F factor [Bacillus cereus AH676]
 gi|229071577|ref|ZP_04204795.1| RNA polymerase sigma-F factor [Bacillus cereus F65185]
 gi|229081330|ref|ZP_04213833.1| RNA polymerase sigma-F factor [Bacillus cereus Rock4-2]
 gi|229093131|ref|ZP_04224253.1| RNA polymerase sigma-F factor [Bacillus cereus Rock3-42]
 gi|229111546|ref|ZP_04241097.1| RNA polymerase sigma-F factor [Bacillus cereus Rock1-15]
 gi|229123596|ref|ZP_04252791.1| RNA polymerase sigma-F factor [Bacillus cereus 95/8201]
 gi|229129353|ref|ZP_04258324.1| RNA polymerase sigma-F factor [Bacillus cereus BDRD-Cer4]
 gi|229140809|ref|ZP_04269354.1| RNA polymerase sigma-F factor [Bacillus cereus BDRD-ST26]
 gi|229146647|ref|ZP_04275014.1| RNA polymerase sigma-F factor [Bacillus cereus BDRD-ST24]
 gi|229152275|ref|ZP_04280468.1| RNA polymerase sigma-F factor [Bacillus cereus m1550]
 gi|229157657|ref|ZP_04285732.1| RNA polymerase sigma-F factor [Bacillus cereus ATCC 4342]
 gi|229186319|ref|ZP_04313484.1| RNA polymerase sigma-F factor [Bacillus cereus BGSC 6E1]
 gi|229192285|ref|ZP_04319250.1| RNA polymerase sigma-F factor [Bacillus cereus ATCC 10876]
 gi|229198196|ref|ZP_04324905.1| RNA polymerase sigma-F factor [Bacillus cereus m1293]
 gi|229603990|ref|YP_002868374.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0248]
 gi|254683842|ref|ZP_05147702.1| sporulation sigma factor SigF [Bacillus anthracis str. CNEVA-9066]
 gi|254721677|ref|ZP_05183466.1| sporulation sigma factor SigF [Bacillus anthracis str. A1055]
 gi|254736189|ref|ZP_05193895.1| sporulation sigma factor SigF [Bacillus anthracis str. Western
           North America USA6153]
 gi|254744078|ref|ZP_05201761.1| sporulation sigma factor SigF [Bacillus anthracis str. Kruger B]
 gi|254754142|ref|ZP_05206177.1| sporulation sigma factor SigF [Bacillus anthracis str. Vollum]
 gi|254758168|ref|ZP_05210195.1| sporulation sigma factor SigF [Bacillus anthracis str. Australia
           94]
 gi|296504567|ref|YP_003666267.1| sporulation sigma factor SigF [Bacillus thuringiensis BMB171]
 gi|301055569|ref|YP_003793780.1| sporulation sigma factor SigF [Bacillus anthracis CI]
 gi|29897716|gb|AAP10991.1| RNA polymerase sigma-F factor [Bacillus cereus ATCC 14579]
 gi|30258795|gb|AAP28013.1| RNA polymerase sigma-F factor [Bacillus anthracis str. Ames]
 gi|42739116|gb|AAS43043.1| RNA polymerase sigma-F factor [Bacillus cereus ATCC 10987]
 gi|47504736|gb|AAT33412.1| RNA polymerase sigma-F factor [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|47555116|gb|EAL13463.1| sigma-B, putative [Bacillus cereus G9241]
 gi|49180908|gb|AAT56284.1| RNA polymerase sigma-F factor [Bacillus anthracis str. Sterne]
 gi|49330074|gb|AAT60720.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|51974889|gb|AAU16439.1| RNA polymerase sigma-F factor [Bacillus cereus E33L]
 gi|74490099|gb|EAO53445.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|118418501|gb|ABK86920.1| RNA polymerase, sigma subunit, RpoX/SigF [Bacillus thuringiensis
           str. Al Hakam]
 gi|164713043|gb|EDR18570.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0488]
 gi|167512500|gb|EDR87875.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0193]
 gi|167531151|gb|EDR93838.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0442]
 gi|170129427|gb|EDS98291.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0389]
 gi|170668745|gb|EDT19490.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0465]
 gi|172081928|gb|EDT66996.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0174]
 gi|190562749|gb|EDV16715.1| RNA polymerase sigma-F factor [Bacillus anthracis Tsiankovskii-I]
 gi|195992541|gb|EDX56502.1| RNA polymerase sigma-F factor [Bacillus cereus W]
 gi|196023301|gb|EDX61979.1| RNA polymerase sigma-F factor [Bacillus cereus 03BB108]
 gi|206734049|gb|EDZ51220.1| RNA polymerase sigma-F factor [Bacillus cereus AH1134]
 gi|206744391|gb|EDZ55802.1| RNA polymerase sigma-F factor [Bacillus cereus H3081.97]
 gi|217063378|gb|ACJ77628.1| RNA polymerase sigma-F factor [Bacillus cereus AH187]
 gi|218162507|gb|ACK62499.1| RNA polymerase sigma-F factor [Bacillus cereus B4264]
 gi|218540139|gb|ACK92537.1| RNA polymerase sigma-F factor [Bacillus cereus AH820]
 gi|218540957|gb|ACK93351.1| RNA polymerase sigma-F factor [Bacillus cereus G9842]
 gi|221241581|gb|ACM14291.1| RNA polymerase sigma-F factor [Bacillus cereus Q1]
 gi|225790809|gb|ACO31026.1| RNA polymerase sigma-F factor [Bacillus cereus 03BB102]
 gi|227007915|gb|ACP17658.1| RNA polymerase sigma-F factor [Bacillus anthracis str. CDC 684]
 gi|228585356|gb|EEK43465.1| RNA polymerase sigma-F factor [Bacillus cereus m1293]
 gi|228591235|gb|EEK49089.1| RNA polymerase sigma-F factor [Bacillus cereus ATCC 10876]
 gi|228597113|gb|EEK54768.1| RNA polymerase sigma-F factor [Bacillus cereus BGSC 6E1]
 gi|228625614|gb|EEK82366.1| RNA polymerase sigma-F factor [Bacillus cereus ATCC 4342]
 gi|228631237|gb|EEK87873.1| RNA polymerase sigma-F factor [Bacillus cereus m1550]
 gi|228636817|gb|EEK93280.1| RNA polymerase sigma-F factor [Bacillus cereus BDRD-ST24]
 gi|228642599|gb|EEK98885.1| RNA polymerase sigma-F factor [Bacillus cereus BDRD-ST26]
 gi|228653958|gb|EEL09825.1| RNA polymerase sigma-F factor [Bacillus cereus BDRD-Cer4]
 gi|228659731|gb|EEL15376.1| RNA polymerase sigma-F factor [Bacillus cereus 95/8201]
 gi|228671928|gb|EEL27221.1| RNA polymerase sigma-F factor [Bacillus cereus Rock1-15]
 gi|228690280|gb|EEL44073.1| RNA polymerase sigma-F factor [Bacillus cereus Rock3-42]
 gi|228701952|gb|EEL54435.1| RNA polymerase sigma-F factor [Bacillus cereus Rock4-2]
 gi|228711513|gb|EEL63470.1| RNA polymerase sigma-F factor [Bacillus cereus F65185]
 gi|228723557|gb|EEL74922.1| RNA polymerase sigma-F factor [Bacillus cereus AH676]
 gi|228735810|gb|EEL86395.1| RNA polymerase sigma-F factor [Bacillus cereus AH1272]
 gi|228741969|gb|EEL92143.1| RNA polymerase sigma-F factor [Bacillus cereus AH1273]
 gi|228772493|gb|EEM20938.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228778917|gb|EEM27179.1| RNA polymerase sigma-F factor [Bacillus thuringiensis Bt407]
 gi|228785496|gb|EEM33505.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228792475|gb|EEM40041.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228799363|gb|EEM46327.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228805290|gb|EEM51883.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228811780|gb|EEM58114.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228818383|gb|EEM64455.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228824146|gb|EEM69960.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228830412|gb|EEM76022.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228836880|gb|EEM82223.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228842900|gb|EEM87983.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228849739|gb|EEM94572.1| RNA polymerase sigma-F factor [Bacillus thuringiensis IBL 200]
 gi|228857024|gb|EEN01533.1| RNA polymerase sigma-F factor [Bacillus thuringiensis IBL 4222]
 gi|229268398|gb|ACQ50035.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0248]
 gi|296325619|gb|ADH08547.1| sporulation sigma factor SigF [Bacillus thuringiensis BMB171]
 gi|300377738|gb|ADK06642.1| sporulation sigma factor SigF [Bacillus cereus biovar anthracis
           str. CI]
 gi|324327980|gb|ADY23240.1| sporulation sigma factor SigF [Bacillus thuringiensis serovar
           finitimus YBT-020]
 gi|326941847|gb|AEA17743.1| sporulation sigma factor SigF [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 252

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 49/190 (25%), Positives = 91/190 (47%), Gaps = 17/190 (8%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           +K P L+  E   L ++ ++ GD  A   +V S++RLV  +   +   G    ++   G 
Sbjct: 9   KKKPQLKDHELKALIQKSQD-GDQQARDTIVQSNMRLVWSVVQRFLNRGYEPDDLFQIGC 67

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL+++V KFD     + +TY++  I   +Q + LR    VK+  +   K     +R+++
Sbjct: 68  IGLLKSVDKFDLSFDVKFSTYAVPMIIGEIQRF-LRDDGSVKVSRSL--KETGNKIRKMR 124

Query: 144 GHL-----QAITDN------NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
             L     +A T N       L PE+VV +A++ + + S +        GD  +  L   
Sbjct: 125 DELSKEFGRAPTINEVAEALELTPEEVV-LAQEASRAPSSIHETVYENDGD-PITILDQI 182

Query: 193 SDKNSSQWQD 202
           +D++ ++W D
Sbjct: 183 ADQSETKWFD 192


>gi|42783467|ref|NP_980714.1| sporulation sigma factor SigK [Bacillus cereus ATCC 10987]
 gi|42739396|gb|AAS43322.1| RNA polymerase sigma-27 factor [Bacillus cereus ATCC 10987]
          Length = 265

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 23/67 (34%), Positives = 38/67 (56%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E GD  A + L+  +LRLV  I   +   G    +++S G IGL++A++ +   +G +LA
Sbjct: 71  EQGDAQARNLLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIESYSAGKGTKLA 130

Query: 103 TYSMWWI 109
           TY+   I
Sbjct: 131 TYAARCI 137


>gi|239930843|ref|ZP_04687796.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 308

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 58/238 (24%), Positives = 107/238 (44%), Gaps = 26/238 (10%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  +L LV   A  +R    P+ +++  G IGL++A+ +F+  RG    T++M  I   
Sbjct: 87  LVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFEMSRGVEFPTFAMPTIIGE 146

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL  +L +    L    D   +   V  +A++L ++  
Sbjct: 147 IKRFFRDTSWS-VRVPRRLQELRL--DLAKAGDELAQQLD---RAPTVAELAERLGITND 200

Query: 172 EVI----SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV-LIEKEERKNRRN 226
           EV+    + N   A   SL+A     D   +   D + Y+  G E +  IE         
Sbjct: 201 EVVEGMAASNAYTAS--SLDAQPEEDDAEGA-LADRIGYEDHGLEGIEYIES-------- 249

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   ++ L PR+R+I   R +    +T   +  E  +S+  V ++ +R   K++  +
Sbjct: 250 -LKPLIAELPPRDRKILSLRFVAG--MTQSEIGEELGISQMHVSRLLSRTLVKLRRGL 304


>gi|52144331|ref|YP_082499.1| RNA polymerase sigma factor SigB [Bacillus cereus E33L]
 gi|51977800|gb|AAU19350.1| RNA polymerase sigma-B factor [Bacillus cereus E33L]
          Length = 258

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 61/271 (22%), Positives = 129/271 (47%), Gaps = 29/271 (10%)

Query: 22  EIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           EI+  P  L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++ 
Sbjct: 3   EIQSQPTNLTKEDVIKLIAEFQQNQCGEAQERLVDHYKNLVYSIAYRYSKGGPMHEDIIQ 62

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNL 139
            G +GL+ A++++D   G     +++  I   +++Y+  ++W +       +  R   +L
Sbjct: 63  VGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGI-------HVPRRIKDL 115

Query: 140 -RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNALI-NS 192
             ++K  ++ +TD+  +  +++ IA  L +SE EV+ +     N R++   SL+ ++ N+
Sbjct: 116 GGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVS---SLDDVVENA 172

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
           SD +S    + +     G EQ          RR +L    +VLN  E+ +     + E  
Sbjct: 173 SDGSSVARIESVGEVEQGYEQT--------ERRLVLEDIFNVLNETEKSVI--HYIFEEN 222

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +  ++      +S+  V +I+ +A  K++++
Sbjct: 223 LNQKDTGERLGISQMHVSRIKRQAISKLKQA 253


>gi|303282119|ref|XP_003060351.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226457822|gb|EEH55120.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 425

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 17/38 (44%), Positives = 25/38 (65%)

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           L +S++  EG  GL QA  KFDP RG++ +TY+  W +
Sbjct: 96  LSVSDLAQEGCAGLAQAADKFDPSRGYKFSTYAYNWTR 133


>gi|196035080|ref|ZP_03102486.1| RNA polymerase sigma-B factor [Bacillus cereus W]
 gi|195992144|gb|EDX56106.1| RNA polymerase sigma-B factor [Bacillus cereus W]
          Length = 257

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 61/271 (22%), Positives = 129/271 (47%), Gaps = 29/271 (10%)

Query: 22  EIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           EI+  P  L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++ 
Sbjct: 2   EIQSQPTNLTKEDVIKLIAEFQQNQCGEAQERLVDHYKNLVYSIAYRYSKGGPMHEDIIQ 61

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNL 139
            G +GL+ A++++D   G     +++  I   +++Y+  ++W +       +  R   +L
Sbjct: 62  VGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGI-------HVPRRIKDL 114

Query: 140 -RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNALI-NS 192
             ++K  ++ +TD+  +  +++ IA  L +SE EV+ +     N R++   SL+ ++ N+
Sbjct: 115 GGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVS---SLDDVVENA 171

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
           SD +S    + +     G EQ          RR +L    +VLN  E+ +     + E  
Sbjct: 172 SDGSSVARIESVGEVEQGYEQT--------ERRLVLEDIFNVLNETEKSVI--HYIFEEN 221

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +  ++      +S+  V +I+ +A  K++++
Sbjct: 222 LNQKDTGERLGISQMHVSRIKRQAISKLKQA 252


>gi|72160963|ref|YP_288620.1| RNA polymerase sigma factor [Thermobifida fusca YX]
 gi|71914695|gb|AAZ54597.1| RNA polymerase sigma factor [Thermobifida fusca YX]
          Length = 267

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 57/240 (23%), Positives = 112/240 (46%), Gaps = 30/240 (12%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  HL LV  +A  +R  G  + ++     IGL++++ +FD  RG   +TY+   I   
Sbjct: 46  LVELHLPLVEYLARRFRNRGEWLDDLTQVATIGLIKSIDRFDLSRGVEFSTYATPTIVGE 105

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +   + W+ V++     + +L      L   +  ++  + +   V  +A+ L +SE 
Sbjct: 106 IKRHFRDKGWA-VRVPRRLQELKL-----SLTKAVSELSQRHGRAPTVAELAEYLKMSEE 159

Query: 172 EVISMNCRLAGDESLNAL-------INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           EV      L G ES NA         ++ D+++    D L    +  E V    E R++ 
Sbjct: 160 EV------LEGLESANAYSTVSLDAPDNGDEDAPAVADSLGIMDESLEGV----EYRESL 209

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + +L R    L PRE++I   R      +T   +++E  +S+  V ++ AR   ++++++
Sbjct: 210 KPLLER----LPPREKKILLLRFF--GNMTQSQIAAELGISQMHVSRLLARTLAQLRQAL 263


>gi|125973527|ref|YP_001037437.1| sporulation sigma factor SigK [Clostridium thermocellum ATCC 27405]
 gi|256003345|ref|ZP_05428336.1| RNA polymerase, sigma 28 subunit, SigK [Clostridium thermocellum
           DSM 2360]
 gi|281417730|ref|ZP_06248750.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           thermocellum JW20]
 gi|125713752|gb|ABN52244.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Clostridium
           thermocellum ATCC 27405]
 gi|255992635|gb|EEU02726.1| RNA polymerase, sigma 28 subunit, SigK [Clostridium thermocellum
           DSM 2360]
 gi|281409132|gb|EFB39390.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           thermocellum JW20]
 gi|316940233|gb|ADU74267.1| RNA polymerase, sigma 28 subunit, SigK [Clostridium thermocellum
           DSM 1313]
          Length = 236

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 33/101 (32%), Positives = 48/101 (47%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           I+N    L  YI  +   P     EE        + GD  A + L+  +LRLV  I   Y
Sbjct: 12  ILNNIFFLLGYISNVNSFPQPLSPEEEQHYLDLLKKGDEEARNILIERNLRLVAHIVKKY 71

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
                   +++S G IGL++A+  F+ E+G RLATY+   I
Sbjct: 72  SSTINDSDDLISIGTIGLIKAISTFNHEKGTRLATYAARCI 112


>gi|229086642|ref|ZP_04218811.1| RNA polymerase sigma-F factor [Bacillus cereus Rock3-44]
 gi|228696724|gb|EEL49540.1| RNA polymerase sigma-F factor [Bacillus cereus Rock3-44]
          Length = 252

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 49/188 (26%), Positives = 89/188 (47%), Gaps = 17/188 (9%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           +K P L+  E   L ++ ++ GD  A   +V S++RLV  +   +   G    ++   G 
Sbjct: 9   KKKPQLKDHELKALIQKSQD-GDQGARDTIVQSNMRLVWSVVQRFLNRGYEPDDLFQIGC 67

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL+++V KFD     + +TY++  I   +Q + LR    VK+  +   K     +R++K
Sbjct: 68  IGLLKSVDKFDLSFEVKFSTYAVPMIIGEIQRF-LRDDGSVKVSRSL--KETGNKIRKMK 124

Query: 144 GHL-----QAITDN------NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
             L     +A T N       L PE+VV +A++ + + S +        GD  +  L   
Sbjct: 125 DELSKEYGRAPTINEVAEALELTPEEVV-LAQEASRTPSSIHETVYENDGD-PITILDQI 182

Query: 193 SDKNSSQW 200
           +D+  ++W
Sbjct: 183 ADQTETKW 190


>gi|325288838|ref|YP_004265019.1| RNA polymerase, sigma subunit, RpsG/SigG [Syntrophobotulus
           glycolicus DSM 8271]
 gi|324964239|gb|ADY55018.1| RNA polymerase, sigma subunit, RpsG/SigG [Syntrophobotulus
           glycolicus DSM 8271]
          Length = 257

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 56/248 (22%), Positives = 118/248 (47%), Gaps = 32/248 (12%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD +   +L+  +LRLV+ +   +   G  + ++   G IGLM+A+  FD  +  + +TY
Sbjct: 34  GDGTIREQLIKGNLRLVLSVIQRFSNRGEHVDDLFQVGCIGLMKAIDNFDLSQNVKFSTY 93

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           ++  I   ++ Y LR  + +++  +   + + +   +++  L   T+ + +P  +  IA 
Sbjct: 94  AVPMIIGEIRRY-LRDNNSIRVSRSL--RDIAYKALQIRDKLA--TECSREP-TIQEIAA 147

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE--ERK 222
           KL   + EVI          +L+A+     +  S ++   +Y HDG + + +  +  + K
Sbjct: 148 KLETPQEEVIL---------ALDAI----QEPVSLFEP--IY-HDGGDPIYVMDQIGDHK 191

Query: 223 NRRNMLTRSMSV------LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
               +   S+S+      L  RE+RI   R  Q    T   ++ E  +S+ +V ++E  A
Sbjct: 192 QSDRIWLESLSIKEGIERLGEREKRIISLRFFQGK--TQMEVAEEIGISQAQVSRLEKAA 249

Query: 277 FKKVQESI 284
            K +++ +
Sbjct: 250 LKHMRKHV 257


>gi|291525957|emb|CBK91544.1| RNA polymerase sigma factor, sigma-70 family [Eubacterium rectale
           DSM 17629]
          Length = 224

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 23/76 (30%), Positives = 42/76 (55%), Gaps = 1/76 (1%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RLVT ++ L+  +   +R  G+   ++   G +GL +A ++FD  +GF  +TY++  I  
Sbjct: 8   RLVTENINLIYLVMKRFRNRGVDREDLFQIGAVGLTKAAQRFDESKGFAFSTYAVPLIIG 67

Query: 112 AMQEYILRSWSLVKIG 127
            +Q + LR   +V I 
Sbjct: 68  EIQRF-LRDDGMVHIS 82


>gi|169831385|ref|YP_001717367.1| FliA/WhiG family RNA polymerase sigma factor [Candidatus
           Desulforudis audaxviator MP104C]
 gi|169638229|gb|ACA59735.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Candidatus
           Desulforudis audaxviator MP104C]
          Length = 257

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 25/91 (27%), Positives = 49/91 (53%), Gaps = 1/91 (1%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+L+ +E   L  R  + GD+ A   L+ ++L+LV  +   + G G    ++   G IGL
Sbjct: 13  PLLKDRETRRLL-RLSQQGDVLARETLINANLKLVCNVIRRFEGRGYDPDDLFQIGCIGL 71

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           ++A+ KFD     + +TY++  I   ++ ++
Sbjct: 72  IKAIDKFDLRFKVKFSTYAVPMIIGEIRRFL 102


>gi|150021309|ref|YP_001306663.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermosipho
           melanesiensis BI429]
 gi|149793830|gb|ABR31278.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermosipho
           melanesiensis BI429]
          Length = 226

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 19/69 (27%), Positives = 45/69 (65%), Gaps = 3/69 (4%)

Query: 52  RLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           +++  +L  + +IA   +    + + I +++ EG IGL+QA+++++P++G +L +Y +  
Sbjct: 6   KIIQEYLPYIKRIAYDLKKNLPHNIEIDDLIQEGLIGLLQAIERYNPKKGAKLRSYILTR 65

Query: 109 IKAAMQEYI 117
           +K AM +Y+
Sbjct: 66  VKGAMYDYL 74


>gi|317133468|ref|YP_004092782.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Ethanoligenens
           harbinense YUAN-3]
 gi|315471447|gb|ADU28051.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Ethanoligenens
           harbinense YUAN-3]
          Length = 248

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 25/83 (30%), Positives = 47/83 (56%), Gaps = 3/83 (3%)

Query: 41  YREHGDLSAAHRLVTSH---LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           YRE     A +RLV  +   +R +V   M   G      ++ S G IGL++A++KFD ++
Sbjct: 16  YRETRSREARNRLVLHYGWLVRAIVHRVMSVSGSYAESDDLTSCGTIGLIKAIEKFDSDK 75

Query: 98  GFRLATYSMWWIKAAMQEYILRS 120
           G + +T++ + I+  + +++ RS
Sbjct: 76  GVQFSTFATYRIRGEILDFVRRS 98


>gi|229180352|ref|ZP_04307695.1| RNA polymerase sigma-F factor [Bacillus cereus 172560W]
 gi|228603099|gb|EEK60577.1| RNA polymerase sigma-F factor [Bacillus cereus 172560W]
          Length = 252

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 49/190 (25%), Positives = 91/190 (47%), Gaps = 17/190 (8%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           +K P L+  E   L ++ ++ GD  A   +V S++RLV  +   +   G    ++   G 
Sbjct: 9   KKKPQLKDHELKALIQKSQD-GDQQARDTIVQSNMRLVWSVVQRFLNRGYEPDDLFQIGC 67

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL+++V KFD     + +TY++  I   +Q + LR    VK+  +   K     +R+++
Sbjct: 68  IGLLKSVDKFDLSFDVKFSTYAVPMIIGEIQRF-LRDDGSVKVSRSL--KETGNKIRKMR 124

Query: 144 GHL-----QAITDN------NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
             L     +A T N       L PE+VV +A++ + + S +        GD  +  L   
Sbjct: 125 DELSKEFGRAPTINEVAEALELTPEEVV-LAQEASRAPSSIHETVYENDGD-PITILDQI 182

Query: 193 SDKNSSQWQD 202
           +D++ ++W D
Sbjct: 183 ADQSEAKWFD 192


>gi|163941815|ref|YP_001646699.1| sporulation sigma factor SigF [Bacillus weihenstephanensis KBAB4]
 gi|229013283|ref|ZP_04170424.1| RNA polymerase sigma-F factor [Bacillus mycoides DSM 2048]
 gi|229061746|ref|ZP_04199079.1| RNA polymerase sigma-F factor [Bacillus cereus AH603]
 gi|229134882|ref|ZP_04263689.1| RNA polymerase sigma-F factor [Bacillus cereus BDRD-ST196]
 gi|229168817|ref|ZP_04296536.1| RNA polymerase sigma-F factor [Bacillus cereus AH621]
 gi|163864012|gb|ABY45071.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           weihenstephanensis KBAB4]
 gi|228614665|gb|EEK71771.1| RNA polymerase sigma-F factor [Bacillus cereus AH621]
 gi|228648557|gb|EEL04585.1| RNA polymerase sigma-F factor [Bacillus cereus BDRD-ST196]
 gi|228717492|gb|EEL69156.1| RNA polymerase sigma-F factor [Bacillus cereus AH603]
 gi|228748050|gb|EEL97914.1| RNA polymerase sigma-F factor [Bacillus mycoides DSM 2048]
          Length = 252

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 49/190 (25%), Positives = 91/190 (47%), Gaps = 17/190 (8%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           +K P L+  E   L ++ ++ GD  A   +V S++RLV  +   +   G    ++   G 
Sbjct: 9   KKKPQLKDHELKALIQKSQD-GDQQARDTIVQSNMRLVWSVVQRFLNRGYEPDDLFQIGC 67

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL+++V KFD     + +TY++  I   +Q + LR    VK+  +   K     +R+++
Sbjct: 68  IGLLKSVDKFDLSFDVKFSTYAVPMIIGEIQRF-LRDDGSVKVSRSL--KETGNKVRKMR 124

Query: 144 GHL-----QAITDN------NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
             L     +A T N       L PE+VV +A++ + + S +        GD  +  L   
Sbjct: 125 DELSKEFGRAPTINEVAQALELTPEEVV-LAQEASRAPSSIHETVYENDGD-PITILDQI 182

Query: 193 SDKNSSQWQD 202
           +D++ ++W D
Sbjct: 183 ADQSETKWFD 192


>gi|291439213|ref|ZP_06578603.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291342108|gb|EFE69064.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 304

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 58/238 (24%), Positives = 107/238 (44%), Gaps = 26/238 (10%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  +L LV   A  +R    P+ +++  G IGL++A+ +F+  RG    T++M  I   
Sbjct: 83  LVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFEMSRGVEFPTFAMPTIIGE 142

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL  +L +    L    D   +   V  +A++L ++  
Sbjct: 143 IKRFFRDTSWS-VRVPRRLQELRL--DLAKAGDELAQQLD---RAPTVAELAERLGITND 196

Query: 172 EVI----SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV-LIEKEERKNRRN 226
           EV+    + N   A   SL+A     D   +   D + Y+  G E +  IE         
Sbjct: 197 EVVEGMAASNAYTAS--SLDAQPEEDDAEGA-LADRIGYEDHGLEGIEYIES-------- 245

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   ++ L PR+R+I   R +    +T   +  E  +S+  V ++ +R   K++  +
Sbjct: 246 -LKPLIAELPPRDRKILSLRFVAG--MTQSEIGEELGISQMHVSRLLSRTLVKLRRGL 300


>gi|317055222|ref|YP_004103689.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit [Ruminococcus
           albus 7]
 gi|315447491|gb|ADU21055.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Ruminococcus
           albus 7]
          Length = 127

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 26/70 (37%), Positives = 37/70 (52%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A   L+  +LRLV  I   Y        +++S G IGL++AV+ FD  +G R ATY
Sbjct: 48  GDAGARDTLIRHNLRLVAHIIKKYYANSSDQDDLISIGTIGLIKAVQTFDYTKGTRFATY 107

Query: 105 SMWWIKAAMQ 114
               ++ A Q
Sbjct: 108 GSRCVENATQ 117


>gi|291527309|emb|CBK92895.1| RNA polymerase sigma factor, sigma-70 family [Eubacterium rectale
           M104/1]
          Length = 224

 Score = 47.4 bits (111), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 23/76 (30%), Positives = 42/76 (55%), Gaps = 1/76 (1%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RLVT ++ L+  +   +R  G+   ++   G +GL +A ++FD  +GF  +TY++  I  
Sbjct: 8   RLVTENINLIYLVMKRFRNRGVDREDLFQIGAVGLTKAAQRFDESKGFAFSTYAVPLIIG 67

Query: 112 AMQEYILRSWSLVKIG 127
            +Q + LR   +V I 
Sbjct: 68  EIQRF-LRDDGMVHIS 82


>gi|229543758|ref|ZP_04432818.1| RNA polymerase, sigma 28 subunit, SigK [Bacillus coagulans 36D1]
 gi|229328178|gb|EEN93853.1| RNA polymerase, sigma 28 subunit, SigK [Bacillus coagulans 36D1]
          Length = 241

 Score = 47.0 bits (110), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 28/81 (34%), Positives = 43/81 (53%), Gaps = 1/81 (1%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L   EE    KR  E GD  A + L+  +LRLV  I   +   G    +++S G IGL++
Sbjct: 31  LSASEERKYLKRMAE-GDADARNILIEHNLRLVAHIVKKFENTGEDTEDLISIGTIGLIK 89

Query: 89  AVKKFDPERGFRLATYSMWWI 109
           A++ +   +G +LATY+   I
Sbjct: 90  AIESYSEGKGTKLATYAARCI 110


>gi|330466807|ref|YP_004404550.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily protein
           [Verrucosispora maris AB-18-032]
 gi|328809778|gb|AEB43950.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily protein
           [Verrucosispora maris AB-18-032]
          Length = 273

 Score = 47.0 bits (110), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 59/240 (24%), Positives = 100/240 (41%), Gaps = 34/240 (14%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R + + L L   +A  Y G G P  ++     +GL++A+ KFDP RG   A Y++  I  
Sbjct: 51  RAIEAWLPLANHLAHRYSGRGEPTDDLAQTAAVGLIKAIDKFDPTRGVDFAGYAIPTIIG 110

Query: 112 AMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV---------VA 161
            ++ +   R+W  +++             RRL+    AI+D N    Q          +A
Sbjct: 111 ELKRHFRDRTWD-IRVP------------RRLQELRLAISDANSSLLQTLGRSPTVADIA 157

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
              KL   E        R     SL+      D+ +++  D L     G E    E  E 
Sbjct: 158 AHLKLTEEEVLEGLEGARAYNAVSLSTPTGDGDR-ATELGDML-----GGEDSEFELAE- 210

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              R  L  +++ L+ RE++I   R      +T   ++ +  VS+  V ++ ARA  K++
Sbjct: 211 --LRVALGPALATLDEREQKILTLRFYGN--LTQSQIAEQIGVSQMHVSRLLARALTKLR 266


>gi|313624456|gb|EFR94462.1| RNA polymerase sigma-B factor [Listeria innocua FSL J1-023]
          Length = 215

 Score = 47.0 bits (110), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 53/223 (23%), Positives = 109/223 (48%), Gaps = 36/223 (16%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRL 135
           ++V  GNIGL+ A++++D   G     +++  I   ++ ++  ++WS+         +R+
Sbjct: 14  DLVQVGNIGLLGAIRRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRI 67

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVI-SMNC-----RLAGDESLNAL 189
                ++K  ++ +T       Q+  IA  + V+E EV+ +M        L+ D S+ A 
Sbjct: 68  KELGPKIKNAVEELTRELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA- 126

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
              SD ++    D +    DG E+V        N+R +L + + VL+ RE++I +     
Sbjct: 127 --DSDGSTITLLDVVGGTDDGFERV--------NQRMLLEKVLPVLDEREQKILQY---- 172

Query: 250 ENPVTLENLSSE-----FEVSRERVRQIEARAFKKVQESIQKQ 287
                +EN S +      ++S+  V +I+ +A KK++E++Q +
Sbjct: 173 ---TFIENRSQKETGELLDISQMHVSRIQRQAIKKLREALQNE 212


>gi|270620051|ref|ZP_06221855.1| RNA polymerase sigma-32 factor [Haemophilus influenzae HK1212]
 gi|270317775|gb|EFA29151.1| RNA polymerase sigma-32 factor [Haemophilus influenzae HK1212]
          Length = 108

 Score = 47.0 bits (110), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 21/57 (36%), Positives = 38/57 (66%)

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L  ++  L+ R + I +AR L +N  TL +L++++ VS ER+RQ+E  A KK++ ++
Sbjct: 50  LGAALQSLDARSQDIIKARWLDDNKATLHDLAAKYNVSAERIRQLETNALKKLKSAV 106


>gi|238924921|ref|YP_002938437.1| RNA polymerase sigma-F factor [Eubacterium rectale ATCC 33656]
 gi|238876596|gb|ACR76303.1| RNA polymerase sigma-F factor [Eubacterium rectale ATCC 33656]
          Length = 224

 Score = 47.0 bits (110), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 23/76 (30%), Positives = 42/76 (55%), Gaps = 1/76 (1%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RLVT ++ L+  +   +R  G+   ++   G +GL +A ++FD  +GF  +TY++  I  
Sbjct: 8   RLVTENINLIYLVMKRFRNRGVDREDLFQIGAVGLTKAAQRFDESKGFAFSTYAVPLIIG 67

Query: 112 AMQEYILRSWSLVKIG 127
            +Q + LR   +V I 
Sbjct: 68  EIQRF-LRDDGMVHIS 82


>gi|229031716|ref|ZP_04187709.1| RNA polymerase sigma-F factor [Bacillus cereus AH1271]
 gi|228729600|gb|EEL80587.1| RNA polymerase sigma-F factor [Bacillus cereus AH1271]
          Length = 252

 Score = 47.0 bits (110), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 49/190 (25%), Positives = 91/190 (47%), Gaps = 17/190 (8%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           +K P L+  E   L ++ ++ GD  A   +V S++RLV  +   +   G    ++   G 
Sbjct: 9   KKKPQLKDHELKALIQQSQD-GDQQARDTIVQSNMRLVWSVVQRFLNRGYEPDDLFQIGC 67

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL+++V KFD     + +TY++  I   +Q + LR    VK+  +   K     +R+++
Sbjct: 68  IGLLKSVDKFDLSFDVKFSTYAVPMIIGEIQRF-LRDDGSVKVSRSL--KETGNKIRKMR 124

Query: 144 GHL-----QAITDN------NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
             L     +A T N       L PE+VV +A++ + + S +        GD  +  L   
Sbjct: 125 DELSKEFGRAPTINEVAEALELTPEEVV-LAQEASRAPSSIHETVYENDGD-PITILDQI 182

Query: 193 SDKNSSQWQD 202
           +D++ ++W D
Sbjct: 183 ADQSETKWFD 192


>gi|297530579|ref|YP_003671854.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
 gi|297253831|gb|ADI27277.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
          Length = 251

 Score = 47.0 bits (110), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 60/249 (24%), Positives = 113/249 (45%), Gaps = 21/249 (8%)

Query: 44  HG-DLSAAHRLVTSHLRLV---VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           HG D  AA  LV  ++ LV   V+         +P  E+VS G +GL  A++KFDP R  
Sbjct: 18  HGRDRHAAEELVQRYMPLVFYHVQRLSATLPSSVPKDELVSLGLVGLYDALEKFDPSRDL 77

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG-HLQAITDNNLKPEQ 158
           +  TY+ + I+ A+ +  LR    +        K++   + RL+  H++++T        
Sbjct: 78  KFDTYASFRIRGAILDG-LRKEDWLPRSMRDKAKKIEEAIERLEQRHMRSVTAKE----- 131

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              IA +L ++E EV     + A  E+  +      + +    + L+   D +  +  E+
Sbjct: 132 ---IAAELGMTEEEV-----QAAASETFFSHWLPLGQTTVDEDEGLLSVRDDRAPLPEEQ 183

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
             ++     L  ++  LN +E+ +      +E  +T   + S   +S  R+ QI A+A  
Sbjct: 184 IVKQEMIEKLAEAIGQLNEKEQLVISLFYKEE--LTFTEIGSLLHLSTSRISQIHAKALW 241

Query: 279 KVQESIQKQ 287
           K++   +K+
Sbjct: 242 KLRRFFEKE 250


>gi|56419781|ref|YP_147099.1| RNA polymerase sigma factor SigD [Geobacillus kaustophilus HTA426]
 gi|56379623|dbj|BAD75531.1| DNA-directed RNA polymerase sigma-28 factor (sigma-D) [Geobacillus
           kaustophilus HTA426]
          Length = 251

 Score = 47.0 bits (110), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 60/249 (24%), Positives = 113/249 (45%), Gaps = 21/249 (8%)

Query: 44  HG-DLSAAHRLVTSHLRLV---VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           HG D  AA  LV  ++ LV   V+         +P  E+VS G +GL  A++KFDP R  
Sbjct: 18  HGRDRHAAEELVQRYMPLVFYHVQRLSATLPSSVPKDELVSLGLVGLYDALEKFDPSRDL 77

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG-HLQAITDNNLKPEQ 158
           +  TY+ + I+ A+ +  LR    +        K++   + RL+  H++++T        
Sbjct: 78  KFDTYASFRIRGAILDG-LRKEDWLPRSMRDKAKKIEEAIERLEQRHMRSVTAKE----- 131

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              IA +L ++E EV     + A  E+  +      + +    + L+   D +  +  E+
Sbjct: 132 ---IAAELGMTEEEV-----QAAASETFFSHWLPLGQTTVDEDEGLLAVRDDRAPLPEEQ 183

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
             ++     L  ++  LN +E+ +      +E  +T   + S   +S  R+ QI A+A  
Sbjct: 184 IVKQEMIEKLAEAIGQLNEKEQLVISLFYKEE--LTFTEIGSLLHLSTSRISQIHAKALW 241

Query: 279 KVQESIQKQ 287
           K++   +K+
Sbjct: 242 KLRRFFEKE 250


>gi|318040084|ref|ZP_07972040.1| RNA polymerase sigma factor, sigma-70 family protein [Synechococcus
           sp. CB0101]
          Length = 310

 Score = 47.0 bits (110), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 59/258 (22%), Positives = 106/258 (41%), Gaps = 37/258 (14%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLP-----ISEVVSEGNIGLMQAVKKFDPERGFRL 101
           L A  +LV  +L LV     G     LP      ++ + E  + L++A +KFDP +G+R 
Sbjct: 59  LRAREQLVRHNLGLVAHT-WGRHRCSLPAHDDTTADALQEAALNLVRAAEKFDPAKGYRF 117

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY+ +W++    E+  R+   ++    A +  +     RL    QA T +    E + A
Sbjct: 118 STYATFWVRRGFTEFEQRAKRAIRF--PAEKAAVVLKALRLSQQHQASTGDEPSLEWLAA 175

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
             K            + +    E L   I   D   +   D    + DG E+    + + 
Sbjct: 176 QLK-----------FDGKAMSAEQLAEFIRQWDATRTGSLD--GAEDDGDEKGGCTRLDL 222

Query: 222 KN---------------RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL-SSEFEVS 265
            +               +   L + MS L+ +E R+   R L+  P++   L  S   + 
Sbjct: 223 ASLQQAAEQQQTQEPDPQHAALPQLMSCLDEQEHRLIRNRYLRRPPLSPCQLRRSMGGMQ 282

Query: 266 RERVRQIEARAFKKVQES 283
            ER+ Q+EA A  K++++
Sbjct: 283 GERLEQLEATALDKLRQA 300


>gi|166031183|ref|ZP_02234012.1| hypothetical protein DORFOR_00869 [Dorea formicigenerans ATCC
           27755]
 gi|166029030|gb|EDR47787.1| hypothetical protein DORFOR_00869 [Dorea formicigenerans ATCC
           27755]
          Length = 278

 Score = 47.0 bits (110), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 54/257 (21%), Positives = 116/257 (45%), Gaps = 23/257 (8%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+++E+  L  R +  GD  A    +  +LRLV+ +   +        ++   G I
Sbjct: 33  KLPILKEEEKEALFARIK-AGDDEAKEEYIKGNLRLVLSVIKRFHSSNENPDDLFQIGCI 91

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ---KRLFFNLRR 141
           GL++A+  F+ E   + +TY++  I   ++ Y +R  S +++  +      K ++     
Sbjct: 92  GLIKAINNFNTELDVKFSTYAVPMIIGEIRRY-MRDNSSIRVSRSLRDTAYKAIYAKENY 150

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           +K         N++   V  IA+++ +++ +++     +    SL   + S   ++    
Sbjct: 151 VK--------QNMREPTVQEIAQEIGIAKEDIVYALDAIQAPMSLQEPVYSDGGDALYVM 202

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           D  + DH  +E+  +E          L  +M  LN RER I   R    +  T   ++ +
Sbjct: 203 DQ-ISDHKNKEEKWVESLS-------LQAAMEHLNERERYIISLRFF--DGRTQMEVARD 252

Query: 262 FEVSRERVRQIEARAFK 278
             +S+ +V ++E  A +
Sbjct: 253 VGISQAQVSRLEKNALR 269


>gi|296132610|ref|YP_003639857.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           sp. JR]
 gi|296031188|gb|ADG81956.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           potens JR]
          Length = 245

 Score = 47.0 bits (110), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 28/79 (35%), Positives = 45/79 (56%), Gaps = 2/79 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ E++E+  L     E GD  A + L+  +LRLV  I   + G      +++S G IGL
Sbjct: 42  PLSEEEEQKYL--ELLEKGDEEARNVLIERNLRLVAHIVKKFDGALDDNDDLISIGTIGL 99

Query: 87  MQAVKKFDPERGFRLATYS 105
           ++A+  F+  +G RLATY+
Sbjct: 100 IKAINTFNRYKGTRLATYA 118


>gi|164686360|ref|ZP_02210390.1| hypothetical protein CLOBAR_02798 [Clostridium bartlettii DSM
           16795]
 gi|164601962|gb|EDQ95427.1| hypothetical protein CLOBAR_02798 [Clostridium bartlettii DSM
           16795]
          Length = 257

 Score = 47.0 bits (110), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 20/75 (26%), Positives = 40/75 (53%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A  + V  +LRLV+ +   +   G  + ++   G +GL++A+  FD  +  R +
Sbjct: 32  KQGDEDARQKFVKGNLRLVLSVIQKFNNRGENVDDLFQIGCVGLIKAIDNFDLSQNVRFS 91

Query: 103 TYSMWWIKAAMQEYI 117
           TY++  I   ++ Y+
Sbjct: 92  TYAVPMIIGEIRRYL 106


>gi|302554440|ref|ZP_07306782.1| RNA polymerase sigma-G factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302472058|gb|EFL35151.1| RNA polymerase sigma-G factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 280

 Score = 47.0 bits (110), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 60/243 (24%), Positives = 103/243 (42%), Gaps = 16/243 (6%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFD 94
           + Y+  GD     +L+  H   +VK   G    GLP     ++ VS G  GL+ A++KFD
Sbjct: 36  RSYKATGDERLREQLIL-HYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEKFD 94

Query: 95  PERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
            +R  +  TY++  I+ AM  E     W    I  +  QK    N+ R    L+A     
Sbjct: 95  IDREIKFETYAITRIRGAMIDELRALDW----IPRSVRQKAR--NVERAYATLEARL-RR 147

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
              E  VA    + V E   +     LA   +L  L+++  +           +    + 
Sbjct: 148 TPTEGEVAAEMGIGVEELHAVFSQLSLANVVALEELLHAGGEGGDGLSVMDTLEDTAADN 207

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
            +   E+R+ RR +L R+++ L  RE+ +      +   +TL  + +   V+  RV QI 
Sbjct: 208 PVEVAEDRELRR-LLARAINTLPEREKTVVTLYYYEG--LTLAEIGNVLGVTESRVSQIH 264

Query: 274 ARA 276
            ++
Sbjct: 265 TKS 267


>gi|260438776|ref|ZP_05792592.1| RNA polymerase sigma-27 factor [Butyrivibrio crossotus DSM 2876]
 gi|292808765|gb|EFF67970.1| RNA polymerase sigma-27 factor [Butyrivibrio crossotus DSM 2876]
          Length = 255

 Score = 47.0 bits (110), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 54/228 (23%), Positives = 105/228 (46%), Gaps = 18/228 (7%)

Query: 61  VVKIAMG----YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           +VK+  G    Y GY +   ++VS G  GL+ A+ KFD  +  +  TY+   I+  + + 
Sbjct: 32  LVKLVAGRLSMYLGYNVEYEDLVSYGIFGLIDAIDKFDYGKNVKFETYASLRIRGEILDQ 91

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
           I R    +       QK+    +   +  L+     N   E++ A A  L++ E      
Sbjct: 92  I-RKMDWIPRSVREKQKK----IDSARTRLETENGKNATDEELAA-ALDLSLDELNNWQG 145

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
             +++   SL+  +    + S +        H  Q + ++EKEE   +   ++ ++S L 
Sbjct: 146 QTKVSNLVSLDEFVEQGSELSMETAG---NSHFEQPERVVEKEELAVK---ISEALSHLT 199

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +E+ +      +E  +TL+ +S+  EVS  RV Q+  +A  K+++S+
Sbjct: 200 EKEKMVVTLYYYEE--MTLKEISNVMEVSESRVSQLHTKALVKLKKSL 245


>gi|229163011|ref|ZP_04290967.1| RNA polymerase sigma-F factor [Bacillus cereus R309803]
 gi|229174749|ref|ZP_04302273.1| RNA polymerase sigma-F factor [Bacillus cereus MM3]
 gi|228608739|gb|EEK66037.1| RNA polymerase sigma-F factor [Bacillus cereus MM3]
 gi|228620417|gb|EEK77287.1| RNA polymerase sigma-F factor [Bacillus cereus R309803]
          Length = 252

 Score = 47.0 bits (110), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 49/190 (25%), Positives = 91/190 (47%), Gaps = 17/190 (8%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           +K P L+  E   L ++ ++ GD  A   +V S++RLV  +   +   G    ++   G 
Sbjct: 9   KKKPQLKDHELKALIQQSQD-GDQQARDTIVQSNMRLVWSVVQRFLNRGYEPDDLFQIGC 67

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL+++V KFD     + +TY++  I   +Q + LR    VK+  +   K     +R+++
Sbjct: 68  IGLLKSVDKFDLSFDVKFSTYAVPMIIGEIQRF-LRDDGSVKVSRSL--KETGNKIRKMR 124

Query: 144 GHL-----QAITDN------NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
             L     +A T N       L PE+VV +A++ + + S +        GD  +  L   
Sbjct: 125 DELSKEFGRAPTINEVAEALELTPEEVV-LAQEASRAPSSIHETVYENDGD-PITILDQI 182

Query: 193 SDKNSSQWQD 202
           +D++ ++W D
Sbjct: 183 ADQSETKWFD 192


>gi|15834951|ref|NP_296710.1| RNA polymerase sigma factor sigma-28 [Chlamydia muridarum Nigg]
 gi|270285123|ref|ZP_06194517.1| RNA polymerase sigma factor sigma-28 [Chlamydia muridarum Nigg]
 gi|270289144|ref|ZP_06195446.1| RNA polymerase sigma factor sigma-28 [Chlamydia muridarum Weiss]
 gi|301336518|ref|ZP_07224720.1| RNA polymerase sigma factor sigma-28 [Chlamydia muridarum
           MopnTet14]
 gi|7190373|gb|AAF39194.1| RNA polymerase sigma factor, sigma-70 family [Chlamydia muridarum
           Nigg]
          Length = 253

 Score = 47.0 bits (110), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 58/243 (23%), Positives = 115/243 (47%), Gaps = 23/243 (9%)

Query: 51  HR--LVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           HR  L+ ++L LV  +A      G+P    I ++ + G  GL++AV++FDPE+  R  +Y
Sbjct: 21  HRDFLIEAYLPLVKNVAHRLAS-GMPSHVKIEDLYASGVEGLVRAVERFDPEKSKRFESY 79

Query: 105 SMWWIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           +++ IKAA+ + + +  W    +   AN         RL   + A+     K      + 
Sbjct: 80  ALFIIKAAIIDDLRKQDWVPRSVYQRAN---------RLADAMDALRQTLGKEPTDGDLC 130

Query: 164 KKLNVSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           + LN+S+ E+     + R A   SLN   +  D++     +  + D   +    + +  +
Sbjct: 131 EYLNISQQELSHWFSSSRPALVLSLNDDFSCQDEDEGLALEERIADERAENGYDVIR--K 188

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           K   ++LT ++  L+ +ER++       +  + L+ +     VS  RV QI ++A  K++
Sbjct: 189 KEAISILTEALLSLDEKERQVMALYYYDD--LVLKEIGKILGVSESRVSQIHSKALLKLR 246

Query: 282 ESI 284
            ++
Sbjct: 247 GTL 249


>gi|153955768|ref|YP_001396533.1| sporulation sigma factor SigF [Clostridium kluyveri DSM 555]
 gi|146348626|gb|EDK35162.1| RNA polymerase sigma-F factor [Clostridium kluyveri DSM 555]
          Length = 251

 Score = 47.0 bits (110), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 57/255 (22%), Positives = 110/255 (43%), Gaps = 35/255 (13%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L K  RE GD  A ++LV  +L LV  I+  +   G    ++   G +GLM+AV  FD  
Sbjct: 19  LIKCARE-GDKEALNKLVELNLPLVSAISKKFLNRGYEYEDIFQIGCMGLMKAVNNFDET 77

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA--NQKRLFFNLRRLKGHLQAITDNNL 154
              + +TY++  I   ++ + LR   ++K+  +     K+L ++                
Sbjct: 78  YNVKFSTYAVPMILGEIKRF-LRDDGMIKVSRSIKNTAKKLHYDRE-------------- 122

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
                 A+ KKLN      I      +G ++   L  +   NS Q+    ++  DG   +
Sbjct: 123 ------ALTKKLN--REPTIEELAEYSGVKTEELLFATESTNSLQYLYDTIHQDDGSPVL 174

Query: 215 LIEKEERKNRRNM-------LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           LI+K     + ++       L  ++  L+ + R+I   R  ++   T   ++    +++ 
Sbjct: 175 LIDKISENPKEDVEVIDRIALKEALRNLDVKSRQIIMLRYFKDK--TQVQVAKMLGINQV 232

Query: 268 RVRQIEARAFKKVQE 282
           +V +IE +  K ++E
Sbjct: 233 QVSRIEKKVLKTMRE 247


>gi|253682632|ref|ZP_04863429.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           D str. 1873]
 gi|253562344|gb|EES91796.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           D str. 1873]
          Length = 242

 Score = 47.0 bits (110), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 59/241 (24%), Positives = 113/241 (46%), Gaps = 23/241 (9%)

Query: 53  LVTSHLRLVVKIA----MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           +V  ++ LV  IA    +G   Y +   +++  G IGLM A+ KFD  +G + +TY+   
Sbjct: 13  IVKKYIPLVKYIASRVIIGKSKY-IEFEDLLGYGMIGLMDALNKFDESKGMKFSTYASIR 71

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ +M + I ++  + K    A  K     L +    ++ +   NL    +  IA++L +
Sbjct: 72  IRGSMIDEIRKNSPISK---GAMDK-----LNKYNSAIETLQKRNLTEPNIKDIAEELEM 123

Query: 169 SESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE-ERKNRR 225
           + +EV  I          SL  LI S D + S     L+   + ++    EK+ E + R 
Sbjct: 124 TVNEVGEIENFINYISVVSLEDLIFSEDDDIS-----LMGTIEDEKSPNPEKDFEDQERL 178

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             L +++ +LN +++ +      +   +TL+ +     VS  RV Q+ +RA   +++ + 
Sbjct: 179 EYLAKALDMLNDKDKTVLSLYYYE--GMTLKEIGIVLGVSESRVCQLHSRAIVHLRKMLG 236

Query: 286 K 286
           K
Sbjct: 237 K 237


>gi|161723249|ref|YP_095808.2| flagellar biosynthesis sigma factor [Legionella pneumophila subsp.
           pneumophila str. Philadelphia 1]
 gi|307610482|emb|CBX00054.1| sigma factor 28 [Legionella pneumophila 130b]
          Length = 238

 Score = 47.0 bits (110), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 53/236 (22%), Positives = 109/236 (46%), Gaps = 27/236 (11%)

Query: 53  LVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           LV +H  LV +IA   +G     + + +++  G +GL++A + +D  +G    TY+   I
Sbjct: 18  LVKTHATLVKRIAHHLLGRLPQSVQLDDLIQSGMLGLLEAARHYDSSKGASFETYAGIRI 77

Query: 110 KAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHL-QAITDNNLKPEQVVAIAKKLN 167
           +  M + + R+ W  V      N + +   +R L+  L +   DN +  E  V++    +
Sbjct: 78  RGHMLDEVRRNDW--VPRSVYRNSRMISDAVRILEHKLGREAKDNEIAEELGVSLDDYHD 135

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + +    S++  L G + L               D +++DH+G      E      R +M
Sbjct: 136 MLQD---SISSHLYGFDDLGV------------TDDVLFDHEGNGST--EPHRNVMRSDM 178

Query: 228 LTRSMSVLN--PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           + R   V++  PR+ R+  +   +++ + L+ +    EVS  R+ QI ++A  +++
Sbjct: 179 MNRLTQVIDSLPRKERLVLSLYYEQD-LNLKEIGEILEVSESRISQILSQATHRIR 233


>gi|197303315|ref|ZP_03168355.1| hypothetical protein RUMLAC_02038 [Ruminococcus lactaris ATCC
           29176]
 gi|197297599|gb|EDY32159.1| hypothetical protein RUMLAC_02038 [Ruminococcus lactaris ATCC
           29176]
          Length = 237

 Score = 47.0 bits (110), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 57/249 (22%), Positives = 112/249 (44%), Gaps = 20/249 (8%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R   HGD  A  +LV  ++ LV  +   + G G    ++   G+IGL++A+ KFD     
Sbjct: 9   RKSHHGDKEAREQLVKENVGLVWCVVKRFYGRGAEPEDLFQIGSIGLLKAIDKFDLSYDV 68

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY++  I   ++ + LR   ++K+  +   K+L +   + K   + +T+   +   +
Sbjct: 69  QFSTYAVPMISGEIRRF-LRDDGMIKVSRSL--KKLSYKCGKKK---EELTERMGREPTM 122

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +A  L   + E++         ES+   I+    +     D L      +E +L    
Sbjct: 123 EELATSLGTEKEELVQAMEAATEVESIYRPIHQEGDSQLSILDRLEEKSRPEEHLL---- 178

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
                R ML++ +  L+  ER++   R  QE   T   +     +S+ +V ++E    KK
Sbjct: 179 ----NRMMLSQILDGLDKEERQLIYLRYFQEK--TQAAVGEILGISQVQVSRME----KK 228

Query: 280 VQESIQKQV 288
           + E ++KQ+
Sbjct: 229 ILERMRKQM 237


>gi|86609923|ref|YP_478685.1| RNA polymerase sigma factor SigF [Synechococcus sp.
           JA-2-3B'a(2-13)]
 gi|86558465|gb|ABD03422.1| RNA polymerase sigma factor, group 3 [Synechococcus sp.
           JA-2-3B'a(2-13)]
          Length = 293

 Score = 47.0 bits (110), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 27/86 (31%), Positives = 50/86 (58%), Gaps = 9/86 (10%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR-----GYGLPISEVVSEGNIGLMQAVK 91
           L + Y ++ D +  +RLV  +L LV K A  +R     GY     ++V  G +GL+QA++
Sbjct: 52  LLRLYHQNRDPALRNRLVEMNLGLVRKEAHHWRNQCNEGY----DDLVQVGCLGLIQAIE 107

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYI 117
           +FD  RG   +++++ +I+  +Q Y+
Sbjct: 108 RFDISRGLAFSSFALPYIRGEIQHYL 133


>gi|238917528|ref|YP_002931045.1| RNA polymerase sporulation-specific sigma factor [Eubacterium
           eligens ATCC 27750]
 gi|238872888|gb|ACR72598.1| RNA polymerase sporulation-specific sigma factor [Eubacterium
           eligens ATCC 27750]
          Length = 249

 Score = 47.0 bits (110), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 55/239 (23%), Positives = 110/239 (46%), Gaps = 30/239 (12%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           + D  A  +LVT +L L+  I   ++G G    ++   G IGL++A+  F+ +     +T
Sbjct: 23  NNDKEAREKLVTDNLGLIWNIIKRFKGRGTEQEDLFQIGCIGLIKAIDNFNLDMDVAFST 82

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y++  I   ++ + LR   +VK+  +  +  +     +  G L+    + L  E  V   
Sbjct: 83  YAVPMITGEIRRF-LRDDGMVKVSRSIKENAV--KSMKAAGQLR----DTLGCEPTV--- 132

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK- 222
                   E I+  C L+  E +   +++S +  S ++   +Y  DG E +L++K E K 
Sbjct: 133 --------EQIAAACELSV-EDITLSMSASMEVESIYK--TIYQGDGSEVMLMDKLEDKA 181

Query: 223 ------NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
                 + +  L + M  L+ RE+ +   R    +  T   ++ EF +S+ +V ++E +
Sbjct: 182 DIGETASSKVALVQLMETLSQREKELIRMRYY--DDYTQMQVAKEFGISQVQVSRMEKK 238


>gi|225418674|ref|ZP_03761863.1| hypothetical protein CLOSTASPAR_05898 [Clostridium asparagiforme
           DSM 15981]
 gi|225041795|gb|EEG52041.1| hypothetical protein CLOSTASPAR_05898 [Clostridium asparagiforme
           DSM 15981]
          Length = 216

 Score = 47.0 bits (110), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 23/65 (35%), Positives = 37/65 (56%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A   L+  ++RLV  +   Y+     I +++S G IGL++AV  F  ++G RLATY
Sbjct: 29  GDQLARDVLIERNMRLVAHVVKKYQSPDYDIEDLLSVGTIGLIKAVNTFKVDKGSRLATY 88

Query: 105 SMWWI 109
           +   +
Sbjct: 89  AAKCV 93


>gi|219856135|ref|YP_002473257.1| hypothetical protein CKR_2792 [Clostridium kluyveri NBRC 12016]
 gi|219569859|dbj|BAH07843.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 254

 Score = 47.0 bits (110), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 57/255 (22%), Positives = 110/255 (43%), Gaps = 35/255 (13%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L K  RE GD  A ++LV  +L LV  I+  +   G    ++   G +GLM+AV  FD  
Sbjct: 22  LIKCARE-GDKEALNKLVELNLPLVSAISKKFLNRGYEYEDIFQIGCMGLMKAVNNFDET 80

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA--NQKRLFFNLRRLKGHLQAITDNNL 154
              + +TY++  I   ++ + LR   ++K+  +     K+L ++                
Sbjct: 81  YNVKFSTYAVPMILGEIKRF-LRDDGMIKVSRSIKNTAKKLHYDRE-------------- 125

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
                 A+ KKLN      I      +G ++   L  +   NS Q+    ++  DG   +
Sbjct: 126 ------ALTKKLN--REPTIEELAEYSGVKTEELLFATESTNSLQYLYDTIHQDDGSPVL 177

Query: 215 LIEKEERKNRRNM-------LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           LI+K     + ++       L  ++  L+ + R+I   R  ++   T   ++    +++ 
Sbjct: 178 LIDKISENPKEDVEVIDRIALKEALRNLDVKSRQIIMLRYFKDK--TQVQVAKMLGINQV 235

Query: 268 RVRQIEARAFKKVQE 282
           +V +IE +  K ++E
Sbjct: 236 QVSRIEKKVLKTMRE 250


>gi|205373764|ref|ZP_03226566.1| sporulation sigma factor SigF [Bacillus coahuilensis m4-4]
          Length = 244

 Score = 47.0 bits (110), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 43/169 (25%), Positives = 78/169 (46%), Gaps = 12/169 (7%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD+ A   +V  ++RLV  +   +   G    ++   G+IGL+++V KFD     + +
Sbjct: 27  QDGDVDARDMIVNRNMRLVWSVVQRFLNRGYEPDDLFQIGSIGLLKSVDKFDLSYDVKFS 86

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIG----TTANQKR-----LFFNLRRLKGHLQAITDNN 153
           TY++  I   +Q +I R    VK+      T N+ R     L   L R+    +      
Sbjct: 87  TYAVPMIIGEIQRFI-RDDGTVKVSRSLKETGNKIRRAKEELSKTLNRVPTISELADFLE 145

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
           + PE+VV +A++ + + S +        GD  +  L   +D+N  +W D
Sbjct: 146 ITPEEVV-LAQEASRTPSSIHETVYENDGD-PITLLDQIADQNDQKWFD 192


>gi|160880422|ref|YP_001559390.1| FliA/WhiG family RNA polymerase sigma factor [Clostridium
           phytofermentans ISDg]
 gi|160429088|gb|ABX42651.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           phytofermentans ISDg]
          Length = 207

 Score = 47.0 bits (110), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 27/83 (32%), Positives = 44/83 (53%), Gaps = 2/83 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  K+E  +L +   + G+  A   L+  +LRLV  I   Y        +++S G IGL
Sbjct: 7   PLSAKEENEMLLQC--KAGNKVARDTLIERNLRLVAHIVKKYNTPDRETDDLISIGTIGL 64

Query: 87  MQAVKKFDPERGFRLATYSMWWI 109
           ++++  FD  +G RLATY+   I
Sbjct: 65  IKSIDTFDSTKGIRLATYASRCI 87


>gi|268612026|ref|ZP_06145753.1| anti-sigma F factor [Ruminococcus flavefaciens FD-1]
          Length = 219

 Score = 46.6 bits (109), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 22/53 (41%), Positives = 34/53 (64%)

Query: 57  HLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           +L LV   A  +R  G+   E+ S G +GL++AVK FDP+RG + +TY++  I
Sbjct: 13  NLGLVHLCANRFRNRGIEYEELYSAGCVGLLKAVKAFDPDRGAQFSTYAVPVI 65


>gi|326503440|dbj|BAJ86226.1| predicted protein [Hordeum vulgare subsp. vulgare]
 gi|326503904|dbj|BAK02738.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 496

 Score = 46.6 bits (109), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 27/92 (29%), Positives = 54/92 (58%), Gaps = 16/92 (17%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP-------ISEVVSEGNIGLMQAVK 91
           +R R+ G  +A ++L+  +LRLV+     Y     P        +++   G  GL+ A+ 
Sbjct: 250 RRLRDVGR-AARNKLIKHNLRLVLYAINKY----YPDMTGDERFADLCQAGANGLITAID 304

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           +F+P+RGFR++TY+++WI+ +    ++R+ +L
Sbjct: 305 RFEPKRGFRISTYALFWIRHS----VVRAMTL 332


>gi|326789987|ref|YP_004307808.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium lentocellum DSM
           5427]
 gi|326540751|gb|ADZ82610.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium lentocellum DSM
           5427]
          Length = 274

 Score = 46.6 bits (109), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 24/84 (28%), Positives = 45/84 (53%), Gaps = 3/84 (3%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
           GD  A  RL+ ++  L+ K++M +   R   +   ++V EG IGL+ A +K+D       
Sbjct: 13  GDSKALERLLEANKGLIYKVSMKFYTERDNAIDQDDLVQEGRIGLIVAAEKYDINGDVPF 72

Query: 102 ATYSMWWIKAAMQEYILRSWSLVK 125
           A+Y+ +WI   M  ++    +++K
Sbjct: 73  ASYAYYWIYQKMHRFMYPKRNMIK 96


>gi|15642066|ref|NP_231698.1| flagellar biosynthesis sigma factor [Vibrio cholerae O1 biovar El
           Tor str. N16961]
 gi|121586929|ref|ZP_01676709.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae 2740-80]
 gi|121727398|ref|ZP_01680537.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae V52]
 gi|147674794|ref|YP_001217593.1| flagellar biosynthesis sigma factor [Vibrio cholerae O395]
 gi|153213706|ref|ZP_01948958.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae 1587]
 gi|153821715|ref|ZP_01974382.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae B33]
 gi|153826072|ref|ZP_01978739.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae MZO-2]
 gi|153828895|ref|ZP_01981562.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae 623-39]
 gi|227082193|ref|YP_002810744.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae M66-2]
 gi|229507844|ref|ZP_04397349.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           BX 330286]
 gi|229511920|ref|ZP_04401399.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           B33]
 gi|229513722|ref|ZP_04403184.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           TMA 21]
 gi|229519056|ref|ZP_04408499.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           RC9]
 gi|229522025|ref|ZP_04411442.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           TM 11079-80]
 gi|229524074|ref|ZP_04413479.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           bv. albensis VL426]
 gi|229528916|ref|ZP_04418306.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           12129(1)]
 gi|229607389|ref|YP_002878037.1| flagellar biosynthesis sigma factor [Vibrio cholerae MJ-1236]
 gi|254226075|ref|ZP_04919673.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae V51]
 gi|254286814|ref|ZP_04961767.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae AM-19226]
 gi|254849153|ref|ZP_05238503.1| flagellar biosynthesis sigma factor [Vibrio cholerae MO10]
 gi|297579572|ref|ZP_06941500.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae RC385]
 gi|298497906|ref|ZP_07007713.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae MAK 757]
 gi|9656612|gb|AAF95212.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae O1 biovar El Tor str. N16961]
 gi|121548865|gb|EAX58908.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae 2740-80]
 gi|121630290|gb|EAX62688.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae V52]
 gi|124115767|gb|EAY34587.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae 1587]
 gi|125621387|gb|EAZ49723.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae V51]
 gi|126520813|gb|EAZ78036.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae B33]
 gi|146316677|gb|ABQ21216.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae O395]
 gi|148875601|gb|EDL73736.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae 623-39]
 gi|149740189|gb|EDM54342.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae MZO-2]
 gi|150423105|gb|EDN15053.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae AM-19226]
 gi|227010081|gb|ACP06293.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae M66-2]
 gi|227013963|gb|ACP10173.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae O395]
 gi|229332690|gb|EEN98176.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           12129(1)]
 gi|229337655|gb|EEO02672.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           bv. albensis VL426]
 gi|229340950|gb|EEO05955.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           TM 11079-80]
 gi|229343745|gb|EEO08720.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           RC9]
 gi|229348903|gb|EEO13860.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           TMA 21]
 gi|229351885|gb|EEO16826.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           B33]
 gi|229355349|gb|EEO20270.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           BX 330286]
 gi|229370044|gb|ACQ60467.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           MJ-1236]
 gi|254844858|gb|EET23272.1| flagellar biosynthesis sigma factor [Vibrio cholerae MO10]
 gi|297537166|gb|EFH75999.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae RC385]
 gi|297542239|gb|EFH78289.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae MAK 757]
 gi|327484600|gb|AEA79007.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           LMA3894-4]
          Length = 244

 Score = 46.6 bits (109), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 62/253 (24%), Positives = 112/253 (44%), Gaps = 31/253 (12%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFD 94
           A  Y ++G+L++    +  +  LV +IA    G   P   I +++  G +GL++A K +D
Sbjct: 4   ALTYDQYGNLNSQQLFLEKYSVLVKRIAHHLIGRLPPSVLIEDLIQAGMVGLLEAQKNYD 63

Query: 95  PERGFRLATYSMWWIKAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
             +G    TY+   I+ AM + I R  W  V      + + +   +  L+G L      N
Sbjct: 64  GSKGASFETYAGIRIRGAMLDDIRRGDW--VPRSVHKHNREISQAIAVLEGEL------N 115

Query: 154 LKPEQVVAIAKKLNVS----ESEVISMNC-RLAGDESLNALINSSDKNSSQWQDWLVYDH 208
             P     +AK LN+S     S ++ +NC R+ G E L      SD   S ++       
Sbjct: 116 RDPTD-AEVAKFLNMSLEQYHSVLMDINCSRIVGIEDLGV----SDDAISPFE------- 163

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           +G++         ++ R  L  S+  L  RE  +      +E  + L+ +     VS  R
Sbjct: 164 EGEDNSPFHGVAEESFRKALVESIKSLPEREALVLSLYYDEE--LNLKEIGEVLGVSESR 221

Query: 269 VRQIEARAFKKVQ 281
           V QI +++ ++++
Sbjct: 222 VSQILSQSMQRLR 234


>gi|317132447|ref|YP_004091761.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Ethanoligenens harbinense YUAN-3]
 gi|315470426|gb|ADU27030.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Ethanoligenens harbinense YUAN-3]
          Length = 237

 Score = 46.6 bits (109), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 27/82 (32%), Positives = 44/82 (53%), Gaps = 1/82 (1%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD +A  +LV  +L LV   A  + G G+   ++   G +GL++AV  FD  RG + +TY
Sbjct: 17  GDAAAQTQLVEENLGLVHAAARHFNGKGIEYDDLYQAGCMGLVKAVTGFDITRGVQFSTY 76

Query: 105 SMWWIKAAMQEYILRSWSLVKI 126
           ++  I   M+  + R    VK+
Sbjct: 77  AVPVIMGEMRR-LFRDDGPVKV 97


>gi|295849257|gb|ADG45292.1| sigma 70 factor-like protein [uncultured bacterium]
          Length = 173

 Score = 46.6 bits (109), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 22/53 (41%), Positives = 35/53 (66%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           ++ ++LRLVV IA  +    + + E+VSEG + LM+AV  FD  RG + +TY+
Sbjct: 25  IIRANLRLVVSIARRHLRGSVSLMELVSEGTMTLMRAVDSFDAHRGHKFSTYA 77


>gi|153803716|ref|ZP_01958302.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           MZO-3]
 gi|124120749|gb|EAY39492.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           MZO-3]
          Length = 242

 Score = 46.6 bits (109), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 62/253 (24%), Positives = 112/253 (44%), Gaps = 31/253 (12%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFD 94
           A  Y ++G+L++    +  +  LV +IA    G   P   I +++  G +GL++A K +D
Sbjct: 4   ALTYDQYGNLNSQQLFLEKYSVLVKRIAHHLIGRLPPSVLIEDLIQAGMVGLLEAQKNYD 63

Query: 95  PERGFRLATYSMWWIKAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
             +G    TY+   I+ AM + I R  W  V      + + +   +  L+G L      N
Sbjct: 64  GSKGASFETYAGIRIRGAMLDDIRRGDW--VPRSVHKHNREISQAIAVLEGEL------N 115

Query: 154 LKPEQVVAIAKKLNVS----ESEVISMNC-RLAGDESLNALINSSDKNSSQWQDWLVYDH 208
             P     +AK LN+S     S ++ +NC R+ G E L      SD   S ++       
Sbjct: 116 RDPTD-AEVAKFLNMSLEQYHSVLMDINCSRIVGIEDLGV----SDDAISPFE------- 163

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           +G++         ++ R  L  S+  L  RE  +      +E  + L+ +     VS  R
Sbjct: 164 EGEDNSPFHGVAEESFRKALVESIKSLPEREALVLSLYYDEE--LNLKEIGEVLGVSESR 221

Query: 269 VRQIEARAFKKVQ 281
           V QI +++ ++++
Sbjct: 222 VSQILSQSMQRLR 234


>gi|167758779|ref|ZP_02430906.1| hypothetical protein CLOSCI_01121 [Clostridium scindens ATCC 35704]
 gi|167663519|gb|EDS07649.1| hypothetical protein CLOSCI_01121 [Clostridium scindens ATCC 35704]
          Length = 258

 Score = 46.6 bits (109), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 56/257 (21%), Positives = 118/257 (45%), Gaps = 23/257 (8%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+++E+  L  R +  GD  A    +  +LRLV+ +   + G      ++   G I
Sbjct: 15  KLPILKEEEKEALFARIK-AGDAEAKEEYIKGNLRLVLSVIKRFGGSNENPDDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT---ANQKRLFFNLRR 141
           GL++A+  F+ E   + +TY++  I   ++ Y +R  + +++  +      K ++     
Sbjct: 74  GLIKAINNFNTELDVKFSTYAVPMIIGEIRRY-MRDNNSIRVSRSLRDTAYKAIYAKENY 132

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           +K         NLK   V  IA+++ +S+ +++     +    SL   + +   ++    
Sbjct: 133 IK--------QNLKEPTVQEIAEEIGISKEDIVFALDAIQVPMSLQEPVYNDGGDALYVM 184

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           D  + D   +E+  +E          L  +M  L  RER I + R   E    +E ++ E
Sbjct: 185 DQ-ISDTKNKEEKWVEDLS-------LEAAMQHLGERERYIIKLRFF-EGKTQME-VADE 234

Query: 262 FEVSRERVRQIEARAFK 278
            ++S+ +V ++E  A +
Sbjct: 235 IKISQAQVSRLEKNALR 251


>gi|260893400|ref|YP_003239497.1| RNA polymerase, sigma 28 subunit, SigG [Ammonifex degensii KC4]
 gi|260865541|gb|ACX52647.1| RNA polymerase, sigma 28 subunit, SigG [Ammonifex degensii KC4]
          Length = 256

 Score = 46.6 bits (109), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 25/93 (26%), Positives = 51/93 (54%), Gaps = 1/93 (1%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L  Q+   L +  +  GD +A   L+  +LRLV+ +   +   G  + ++   G I
Sbjct: 14  KLPVLTAQQMCRLFEAMK-RGDGNARSELIKGNLRLVLSVVQRFANRGEHLDDLFQVGCI 72

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           GL++A+  FD ++  + +TY++  I   ++ Y+
Sbjct: 73  GLIKAIDNFDLDQNVKFSTYAVPMIIGEIRRYL 105


>gi|164686361|ref|ZP_02210391.1| hypothetical protein CLOBAR_02799 [Clostridium bartlettii DSM
           16795]
 gi|164601963|gb|EDQ95428.1| hypothetical protein CLOBAR_02799 [Clostridium bartlettii DSM
           16795]
          Length = 231

 Score = 46.6 bits (109), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 21/57 (36%), Positives = 37/57 (64%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           L+  +LRLVV I+  +   G+ + +++S G IGL++AV  F+ ++  +LATY+   I
Sbjct: 53  LIERNLRLVVYISRKFENTGIDMEDLISIGTIGLIKAVNTFNLDKNIKLATYASRCI 109


>gi|158340157|ref|YP_001521327.1| sigma-28 subunit [Acaryochloris marina MBIC11017]
 gi|158310398|gb|ABW32013.1| sigma-28 subunit [Acaryochloris marina MBIC11017]
          Length = 421

 Score = 46.6 bits (109), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 24/73 (32%), Positives = 44/73 (60%), Gaps = 1/73 (1%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD     R +  + RLV K A  YRG     +++V+ GN GL +A++KFD  +G + ++Y
Sbjct: 32  GDRRTEDRFIRKNQRLVFKEANRYRGLD-DWNDLVTAGNWGLARAIEKFDVSKGCKFSSY 90

Query: 105 SMWWIKAAMQEYI 117
           ++  I+  +Q+++
Sbjct: 91  AVKVIRTEIQQFL 103


>gi|188586278|ref|YP_001917823.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|179350965|gb|ACB85235.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 253

 Score = 46.6 bits (109), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 45/175 (25%), Positives = 88/175 (50%), Gaps = 21/175 (12%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L K++++ GD  A   ++  ++ LV  +   + G G+   ++   G +GL++A+ KFD  
Sbjct: 18  LIKKWQQKGDREARKIIIEENINLVKSVVKRFVGSGIEEEDLTQLGLMGLIKAIDKFDYR 77

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +  R +TY++  I   ++ + LR    +K+  + N K LF   + +K  L       L+ 
Sbjct: 78  KEVRFSTYAVPLIIGEIKTF-LRDDHPIKV--SRNLKELFNRSKEVKRWLTL----KLRR 130

Query: 157 EQVVA-IAKKLNVSES----------EVISMNCRLAGD---ESLNALINSSDKNS 197
           E  ++ +A +L VS+           E+IS++  ++ +   ES  ALI++   NS
Sbjct: 131 EPTISEVADELEVSKEELATAEEANQELISLDKPVSDEHNHESEKALIDTIPDNS 185


>gi|207743453|ref|YP_002259845.1| hypothetical alternative rna sigma factor rpos (partial sequence)
           protein [Ralstonia solanacearum IPO1609]
 gi|206594850|emb|CAQ61777.1| hypothetical alternative rna sigma factor rpos (partial sequence)
           protein [Ralstonia solanacearum IPO1609]
          Length = 184

 Score = 46.6 bits (109), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 26/73 (35%), Positives = 43/73 (58%), Gaps = 1/73 (1%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++ I   P+L   EE   + R +  G+ +A   ++  +LRLVV IA GY   G+ + E+
Sbjct: 112 YLNRISIKPLLTPAEELHFSTRAKA-GEFAARQVMIERNLRLVVSIAKGYLKQGVRLMEM 170

Query: 79  VSEGNIGLMQAVK 91
           +SEGN G+M  ++
Sbjct: 171 ISEGNRGVMPPLQ 183


>gi|222112349|ref|YP_002554613.1| sigma-70 region 4 domain-containing protein [Acidovorax ebreus
           TPSY]
 gi|221731793|gb|ACM34613.1| sigma-70 region 4 domain protein [Acidovorax ebreus TPSY]
          Length = 893

 Score = 46.6 bits (109), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 25/57 (43%), Positives = 35/57 (61%), Gaps = 1/57 (1%)

Query: 226 NMLTRSMSVLNPRERRIFEAR-RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           + +  +   LN  ER IF AR   +  P TL+ +S +  VSRERVRQIE + FKK++
Sbjct: 339 DGIVEAAQCLNENERGIFAARLGFRCEPHTLQQISDQIGVSRERVRQIEVKIFKKIR 395


>gi|218896055|ref|YP_002444466.1| RNA polymerase sigma-B factor [Bacillus cereus G9842]
 gi|218544560|gb|ACK96954.1| RNA polymerase sigma-B factor [Bacillus cereus G9842]
          Length = 257

 Score = 46.6 bits (109), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 55/231 (23%), Positives = 110/231 (47%), Gaps = 27/231 (11%)

Query: 22  EIRKIPMLEKQEEYV-LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           EI+  P    +E+ + L   ++++    A  RLV  +  LV  IA  Y   G    +++ 
Sbjct: 2   EIQSQPTTLTKEDVIKLIAEFQQNQCNEAQERLVDHYKNLVYSIAYRYSKGGPMHEDIIQ 61

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNL 139
            G +GL+ A++++D   G     +++  I   +++Y+  ++W +       +  R   +L
Sbjct: 62  VGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGI-------HVPRRIKDL 114

Query: 140 -RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNALI-NS 192
             ++K  ++ +TD+  +  +++ IA  L +SE EV+ +     N R++   SL+ ++ NS
Sbjct: 115 GGKIKLAIEELTDHLQRSPKIIEIANHLGLSEEEVLEIMDAKNNYRVS---SLDDVVENS 171

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           SD +S    + +     G EQ          RR +L    +VLN  E+ + 
Sbjct: 172 SDGSSVARIESVGEVEQGYEQT--------ERRLVLEDIFNVLNDTEKSVI 214


>gi|121488737|emb|CAJ18252.1| sigma 70-type sigma factor [Chlorobium limicola]
          Length = 165

 Score = 46.6 bits (109), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 16/49 (32%), Positives = 33/49 (67%)

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           + +EGN+GL +A  +FD  RGF+  +Y++WWI+ ++ + +     +V++
Sbjct: 2   LXNEGNLGLXKAXXRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL 50


>gi|306021726|gb|ADM80299.1| RNA-polymerase sigma subunit [Geobacillus pallidus]
          Length = 256

 Score = 46.6 bits (109), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 64/275 (23%), Positives = 122/275 (44%), Gaps = 51/275 (18%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQ 88
           +E V   ++  H D  A + LV  ++ LV +  +     GLP +    +++S G +GL  
Sbjct: 9   DERVYWDKWFRHRDQDAGNMLVKKYMPLV-RYHVSRISVGLPKNVDKDDLISFGLMGLYD 67

Query: 89  AVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTTANQKRLFFNLRRL 142
           A++KFDP R  +  TY+ + I+ A+      ++++ RS+        A  +RL     R 
Sbjct: 68  ALEKFDPTRDLKFDTYASFRIRGAILDGLRKEDWLPRSFREKAKKVEAAIERLEQKYHRN 127

Query: 143 KGHLQAITDNNLKPEQVVAI------AKKLNVSE-----SEVISMNCRLAGDESLNALIN 191
               +   +  + PE+VV +      A  L++ E      E   MN  L  D++L     
Sbjct: 128 VTPNEVAEELGMTPEEVVHVVNENFFANVLSIDEQLHDQEEGEQMNIVLKDDKTLTP--- 184

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
                               E+ L+++E  ++    LT+ +S LN +E+ +      +E 
Sbjct: 185 --------------------EEHLLKEELFEH----LTKLISQLNDKEQLVLSLFYKEE- 219

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +TL  + +   +S  R+ QI ++A  K++ ++ K
Sbjct: 220 -LTLTEIGNVLNLSTSRISQIHSKALYKLKGTLVK 253


>gi|297538886|ref|YP_003674655.1| FliA/WhiG subfamily RNA polymerase sigma-28 factor [Methylotenera
           sp. 301]
 gi|297258233|gb|ADI30078.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Methylotenera sp. 301]
          Length = 244

 Score = 46.6 bits (109), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 59/255 (23%), Positives = 113/255 (44%), Gaps = 26/255 (10%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPER 97
           Y  HG       L+  H  LV K+A   +    P   + +++  G +GL+ A+ +++   
Sbjct: 2   YTIHGKKDQKDELLNKHAVLVKKLAYQLKAKLPPSVELDDLIQAGMMGLLDAINRYEDTH 61

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G +  TY+   I+ +M +  LRS   +      + + +   + +L+  L        KP 
Sbjct: 62  GAQFETYAAQRIRGSMLDE-LRSADWLPRSVRKSMRDVEIAISQLEQQLG-------KPP 113

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD----KNSSQWQDWLVYDHDGQE- 212
               +AKKL +S S+   M     GD S + LI   D    +N   + D    D  G   
Sbjct: 114 TENEVAKKLQLSLSDYYDM----LGDCSGHQLIYYEDFHESENGEHFLDRFNADTTGDPI 169

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           + L+E     + R  L  +++ L  RE+ +      QE  + L+ + +   VS  RV Q+
Sbjct: 170 KSLLE----GDFREALVGAITALPEREKILMGLYYEQE--LNLKEIGAVMNVSESRVCQL 223

Query: 273 EARAFKKVQESIQKQ 287
            ++A  +++ +++++
Sbjct: 224 HSQAVARLRSNLKEK 238


>gi|218905533|ref|YP_002453367.1| RNA polymerase sigma-K factor [Bacillus cereus AH820]
 gi|218535778|gb|ACK88176.1| RNA polymerase sigma-K factor [Bacillus cereus AH820]
          Length = 149

 Score = 46.6 bits (109), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 23/68 (33%), Positives = 39/68 (57%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E GD  A + L+  +LRLV  I   +   G    +++S G IGL++A++ +   +G +LA
Sbjct: 43  EQGDAQARNLLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIESYSAGKGTKLA 102

Query: 103 TYSMWWIK 110
           TY+   I+
Sbjct: 103 TYAARCIE 110


>gi|150015700|ref|YP_001307954.1| sporulation sigma factor SigF [Clostridium beijerinckii NCIMB 8052]
 gi|149902165|gb|ABR32998.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           beijerinckii NCIMB 8052]
          Length = 251

 Score = 46.6 bits (109), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 58/252 (23%), Positives = 117/252 (46%), Gaps = 34/252 (13%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A + L+  +L LV  I+  +   G    ++   G+IGL++A+  FD     + +TY
Sbjct: 26  GDTDAMNTLIEMNLPLVSSISKKFLNRGYDYEDIFQIGSIGLVKAINNFDLNYNVKFSTY 85

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           ++  I   ++ + LR   ++K+  + N K L    R++    + +T    +   +  +A 
Sbjct: 86  AVPMIIGEIKRF-LRDDGMIKV--SRNVKSL---ARKIHFQKEILTKKLKRSPTIEELAD 139

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK--EERK 222
             NV + E++               I SS  NS Q+    ++  DG   +LI+K  E+  
Sbjct: 140 YANVDKEEILFA-------------IESS--NSLQYLYDTIHQDDGAPVLLIDKLSEKSA 184

Query: 223 NRRNM-----LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
           +  N+     L  +++ L+ + ++I   R  ++   T   ++    +S+ +V +IE    
Sbjct: 185 DDENLIEKIALKEALNSLDNKAKQIIMLRYFKDK--TQVQVAKMLGISQVQVSRIE---- 238

Query: 278 KKVQESIQKQVE 289
           KKV   ++K++E
Sbjct: 239 KKVLAEMRKKLE 250


>gi|295094135|emb|CBK83226.1| RNA polymerase sigma factor, sigma-70 family [Coprococcus sp.
           ART55/1]
          Length = 220

 Score = 46.6 bits (109), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 29/94 (30%), Positives = 49/94 (52%), Gaps = 8/94 (8%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAM-GYRGYGLP-------ISEVVSEGNIGLMQAVK 91
           R  + GD +A   L+  +L  + KIA+  YR  GL        + +++ EG+IGL+ A+ 
Sbjct: 11  RLAQKGDTAARDILLEKNLGFIRKIALEQYRNMGLDENDIGIDLDDLMQEGSIGLLNAIP 70

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            FD  RG +  TY+   ++ AM + I  +  L +
Sbjct: 71  LFDAGRGMKFLTYAAPALRNAMTDCIRAALGLFE 104


>gi|21224822|ref|NP_630601.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
 gi|3559995|emb|CAA20617.1| putative RNA polymerase sigma factor [Streptomyces coelicolor
           A3(2)]
          Length = 266

 Score = 46.6 bits (109), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 55/254 (21%), Positives = 109/254 (42%), Gaps = 39/254 (15%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           EH +L    R+V + L +  ++A  +R  G    ++     +GL++AV ++DPERG    
Sbjct: 32  EHDELR--DRIVEAWLPMAERLAGRFRSRGESFEDLRQVAALGLVKAVDRYDPERGNAFE 89

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           +Y++  I   ++ +       + +     + R   N  R  G   + T    +P  V  I
Sbjct: 90  SYAVPTITGEIKRHFRDHMWTLHVPRRVQELR---NRVRFAGQDLSQTIPGRRP-TVAEI 145

Query: 163 AKKLNVSESEV------------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
           A++  +SE +V            +S++  L G E   +L ++            +   D 
Sbjct: 146 AERAELSEEDVRVGLEALESFTALSLDAELPGSEDGYSLGDA------------LGAPDP 193

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
               ++++E  K+R       ++ L PRER I   R    N +T   ++ +  +S+  V 
Sbjct: 194 ALDTVVDREAVKDR-------LAALPPRERAILYMRFF--NDMTQSRIAEQLGISQMHVS 244

Query: 271 QIEARAFKKVQESI 284
           ++  R   +V+E +
Sbjct: 245 RLITRCCDRVREQV 258


>gi|324997618|ref|ZP_08118730.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily protein
           [Pseudonocardia sp. P1]
          Length = 277

 Score = 46.6 bits (109), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 41/158 (25%), Positives = 69/158 (43%), Gaps = 22/158 (13%)

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL- 118
           +V  IA  YR  G P  ++   G IGL+ A+ +FDPE+G     Y++  I   ++ +   
Sbjct: 53  VVRHIAGRYRHRGEPADDLEQVGAIGLLNALDRFDPEQGTPFLAYAVPTITGEIRRHFRD 112

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVI---- 174
           R+WS+        ++   F  R  +   +    +   P +V  +A+ L  S  EVI    
Sbjct: 113 RTWSM-----RVPRRLKDFQTRMTRAQEELAVRHGRAP-KVSELAEHLGTSREEVIEGLQ 166

Query: 175 --------SMNCRLAGD--ESLNALINSSDKNSSQWQD 202
                   S++ RLAGD    L  ++  +D      +D
Sbjct: 167 AQDSYRSDSLD-RLAGDTESPLGEIVGGADAGIGTVED 203


>gi|54025575|ref|YP_119817.1| putative sigma factor [Nocardia farcinica IFM 10152]
 gi|54017083|dbj|BAD58453.1| putative sigma factor [Nocardia farcinica IFM 10152]
          Length = 315

 Score = 46.6 bits (109), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 52/232 (22%), Positives = 105/232 (45%), Gaps = 18/232 (7%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L++  + L   IA  + G G P  ++     +GL+ AV +FDP RG    ++++  I   
Sbjct: 95  LISRCVPLADHIARKFSGRGEPFDDLTQVARVGLVHAVDRFDPARGSNFLSFAVPTIMGE 154

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ Y    +W++ ++     +  L     R+   +  ++ +  +      IA +L V   
Sbjct: 155 VRRYFRDHTWAM-RVPRRVKETHL-----RIGAAIDTLSQSLGRSPTAKEIAAELRVDPD 208

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK-EERKNRRNMLTR 230
           EV      +AG+    + I+++     +  D  + D  G+E+   E+ EE    R +L  
Sbjct: 209 EVT--QAVIAGNAYQPSSIDAA--ALGRESDASLLDTLGEEEAQFERVEEYVAIRPLL-- 262

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             + L  RERRI   R  +   +T   ++ +  +S+  V +I A+   +++E
Sbjct: 263 --AGLPERERRILTMRFFES--MTQTQIAKQMGISQMHVSRILAKTLARLRE 310


>gi|313113343|ref|ZP_07798935.1| sigma-70 region 2 [Faecalibacterium cf. prausnitzii KLE1255]
 gi|310624319|gb|EFQ07682.1| sigma-70 region 2 [Faecalibacterium cf. prausnitzii KLE1255]
          Length = 167

 Score = 46.2 bits (108), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 29/71 (40%), Positives = 42/71 (59%), Gaps = 4/71 (5%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS--EVVSEGNIGLMQAVKKFDPERGFRLA 102
           GD +A  +L+  +LRLV  I   Y  Y LP    +++S G IGLM+AV  FD +R  R +
Sbjct: 52  GDPAAREKLIRHNLRLVAHIVKKY--YALPGDQDDLISIGTIGLMKAVDTFDSDRRARFS 109

Query: 103 TYSMWWIKAAM 113
           TY+   I+ A+
Sbjct: 110 TYASRCIENAI 120


>gi|290957086|ref|YP_003488268.1| sporulation-specific sigma factor WhiG [Streptomyces scabiei 87.22]
 gi|260646612|emb|CBG69709.1| sporulation-specific sigma factor WhiG [Streptomyces scabiei 87.22]
          Length = 258

 Score = 46.2 bits (108), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 61/245 (24%), Positives = 102/245 (41%), Gaps = 20/245 (8%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFD 94
           + Y+  GD     +L+  H   +VK   G    GLP     ++ VS G  GL+ A++KFD
Sbjct: 14  RTYKTSGDERLREQLIL-HYSPLVKYVAGRVSVGLPANVEQADFVSSGVFGLIDAIEKFD 72

Query: 95  PERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
            +R  +  TY++  I+ AM  E     W    I  +  QK    N+ R    L++     
Sbjct: 73  IDREIKFETYAITRIRGAMIDELRALDW----IPRSVRQKAR--NVERAYATLESRL-RR 125

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ--DWLVYDHDGQ 211
              E  VA    + V E   +     LA   +L  L+++  +   +    D L    D  
Sbjct: 126 TPSEGEVAAEMGIAVDELHAVFSQLSLANVVALEELLHAGGEGGDRLSLMDTL---EDTA 182

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
               +E  E +  R  L R+++ L  RE+ +      +   +TL  + +   V+  RV Q
Sbjct: 183 ADDPVEVAEDRELRRFLARAINTLPEREKTVVTLYYYE--GLTLAEIGNVLGVTESRVSQ 240

Query: 272 IEARA 276
           I  ++
Sbjct: 241 IHTKS 245


>gi|187934214|ref|YP_001885077.1| sporulation sigma factor SigF [Clostridium botulinum B str. Eklund
           17B]
 gi|187722367|gb|ACD23588.1| RNA polymerase sigma-F factor [Clostridium botulinum B str. Eklund
           17B]
          Length = 251

 Score = 46.2 bits (108), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 53/251 (21%), Positives = 105/251 (41%), Gaps = 34/251 (13%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A +RL+  +L LV  I+  +   G    ++   G+IGL++A+  FD     + +TY
Sbjct: 26  GDNEAMNRLIEMNLPLVASISKKFLNRGYDYEDIFQIGSIGLVKAINNFDLSYNVKFSTY 85

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQ--KRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           ++  I   ++ + LR   ++K+        KR+ F    L                    
Sbjct: 86  AVPMIIGEIKRF-LRDDGMIKVSRNVKSLAKRIHFTKEEL-------------------- 124

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
            KKLN   S  I      +G +    +       S Q+    ++  DG   +LI+K   K
Sbjct: 125 TKKLN--RSPTIEELAEYSGVDKEEIIFAIESATSLQYLYDTIHQDDGAPVLLIDKLSEK 182

Query: 223 NRRNM-------LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
              ++       L  ++  L+ + R+I   R  ++   T   ++    +S+ +V +IE +
Sbjct: 183 GEDDIGMINKIALKEALRSLDEKARQIIVLRYFKDK--TQVQVAKLLGISQVQVSRIEKK 240

Query: 276 AFKKVQESIQK 286
              +++E +++
Sbjct: 241 VLLRMREKLEE 251


>gi|160935677|ref|ZP_02083052.1| hypothetical protein CLOBOL_00567 [Clostridium bolteae ATCC
           BAA-613]
 gi|158441421|gb|EDP19131.1| hypothetical protein CLOBOL_00567 [Clostridium bolteae ATCC
           BAA-613]
          Length = 258

 Score = 46.2 bits (108), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 58/269 (21%), Positives = 123/269 (45%), Gaps = 41/269 (15%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L  +E+  L +R  + GD  A  + +  +LRLV+ +   +      I ++   G I
Sbjct: 15  KLPLLSNEEKEELFQRILD-GDKEAREQYIKGNLRLVLSVIQRFSNSQENIDDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT---ANQKRLFFNLRR 141
           GL++A+  FD  +  + +TY++  I   ++ Y LR  + +++  +      K L+     
Sbjct: 74  GLIKAIDNFDITQNVKFSTYAVPMILGEVRRY-LRDNNSIRVSRSLRDTAYKALYAR--- 129

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
                + +T  N K   ++ IA+++ VS+             E +   +++     S ++
Sbjct: 130 -----EQLTRTNSKEPTLMEIAQEIGVSK-------------EDITYALDAIQTPVSLYE 171

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNM---------LTRSMSVLNPRERRIFEARRLQENP 252
              VY  DG + + +  ++  +++N+         L  +M  L  RER I + R  +   
Sbjct: 172 P--VY-TDGGDPLFV-MDQISDKKNLEENWVEDLSLVEAMKRLPERERHIIDMRFFEGKT 227

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            T   ++ E  +S+ +V ++E  A K ++
Sbjct: 228 QT--EVAQEIHISQAQVSRLEKNALKSMK 254


>gi|160933256|ref|ZP_02080645.1| hypothetical protein CLOLEP_02102 [Clostridium leptum DSM 753]
 gi|156868330|gb|EDO61702.1| hypothetical protein CLOLEP_02102 [Clostridium leptum DSM 753]
          Length = 260

 Score = 46.2 bits (108), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 56/236 (23%), Positives = 109/236 (46%), Gaps = 17/236 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+  +LRLV+ +   +   G  + ++   G IGL++A+  FD  +  R +TY +  
Sbjct: 42  AREELINGNLRLVLSVIQRFTNRGENLDDLFQVGCIGLIKAIDNFDISQDVRFSTYGVPM 101

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I   ++ + LR  + V++  +   +   +   ++K  L   T NN +P  +  IAK+L +
Sbjct: 102 IIGEIRRF-LRDNNSVRVSRSL--RDTAYKAMQVKERL--TTQNNKEP-SIEEIAKELEL 155

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            + +V+     +    SL   +  SD N + +    V D +     L E   ++  RN  
Sbjct: 156 PKEDVVLALEAIVEPVSLYEPV-FSDGNDTIFVMDQVGDKNDDNNWLDEIALKEAIRN-- 212

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                 L PRE++I   R  Q    T   ++ E  +S+ +V ++E  + ++++  I
Sbjct: 213 ------LGPREKKILNLRFFQGK--TQMEVAKEIGISQAQVSRLEKGSLERIKNHI 260


>gi|332799331|ref|YP_004460830.1| RNA polymerase sigma-28 subunit SigF [Tepidanaerobacter sp. Re1]
 gi|332697066|gb|AEE91523.1| RNA polymerase, sigma 28 subunit, SigF [Tepidanaerobacter sp. Re1]
          Length = 240

 Score = 46.2 bits (108), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 56/245 (22%), Positives = 117/245 (47%), Gaps = 32/245 (13%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           G+  A   LV+ +L LV  I   +   G    ++   G+IGL++A++KFD     + +TY
Sbjct: 16  GEKKARDELVSLNLGLVWSIVKRFNNRGYEPEDLFQIGSIGLLKAIEKFDFSYDVKFSTY 75

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-AIA 163
           ++  I   ++ YI R    +K+  +   K L + +++ +  L     N L  E  +  I+
Sbjct: 76  AVPMIMGEIRRYI-RDDKPIKVSRSL--KELGYKIQKTQEELT----NTLDREPTINEIS 128

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK-EERK 222
            ++ V   E++         E+  +L++ +D         +VY  DG    LI++  E +
Sbjct: 129 DEMEVPVEEIV------MAMEASQSLVSLND---------VVYQDDGSPIYLIDQLNENE 173

Query: 223 NRRNM------LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
            + N+      L  ++S L+  ER+I   R  ++  +T  +++ +  +++ +V ++E + 
Sbjct: 174 YQENLLHDKIALKEALSKLDRDERQIITLRYFKD--MTQIDVAKKLNMTQVQVSRLERKV 231

Query: 277 FKKVQ 281
             KV+
Sbjct: 232 LTKVK 236


>gi|154249080|ref|YP_001409905.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Fervidobacterium
           nodosum Rt17-B1]
 gi|154153016|gb|ABS60248.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Fervidobacterium
           nodosum Rt17-B1]
          Length = 233

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 53/225 (23%), Positives = 104/225 (46%), Gaps = 21/225 (9%)

Query: 53  LVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           ++  ++ +V KIA   +    Y + I +++ EG I L+QA +K+DP  G    T++   +
Sbjct: 7   VIQEYIPMVTKIARDLKINLPYNVEIDDLIQEGVIALLQAAEKYDPRYGATFKTFAYTRV 66

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           K AM +Y+ +   L K     N ++   ++++    L    + N +      +++ L + 
Sbjct: 67  KGAMIDYLRKLDYLPK-----NVRQ---DIKKFDRELLNFYEQNKRLPTYDEMSEILGID 118

Query: 170 ESEVISMNCRLAGDESLN--ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
             EV  +   LA  +SLN    +  SD+NS    D         E+ + E   +      
Sbjct: 119 VEEVEEIYRELALKQSLNLDQYLFESDENSYGSIDI------KSEENVKENAWKSILHEQ 172

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           L  +++ L+ +E+ I   R   E+ ++L+ ++    V+  RV QI
Sbjct: 173 LVEAINKLDEKEKIILSMRF--EHELSLKEIAEVLGVTESRVSQI 215


>gi|52629120|gb|AAU27861.1| flagellar biosynthesis sigma factor FliA [Legionella pneumophila
           subsp. pneumophila str. Philadelphia 1]
          Length = 262

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 53/236 (22%), Positives = 109/236 (46%), Gaps = 27/236 (11%)

Query: 53  LVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           LV +H  LV +IA   +G     + + +++  G +GL++A + +D  +G    TY+   I
Sbjct: 42  LVKTHATLVKRIAHHLLGRLPQSVQLDDLIQSGMLGLLEAARHYDSSKGASFETYAGIRI 101

Query: 110 KAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHL-QAITDNNLKPEQVVAIAKKLN 167
           +  M + + R+ W  V      N + +   +R L+  L +   DN +  E  V++    +
Sbjct: 102 RGHMLDEVRRNDW--VPRSVYRNSRMISDAVRILEHKLGREAKDNEIAEELGVSLDDYHD 159

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + +    S++  L G + L               D +++DH+G      E      R +M
Sbjct: 160 MLQD---SISSHLYGFDDLGV------------TDDVLFDHEGNGST--EPHRNVMRSDM 202

Query: 228 LTRSMSVLN--PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           + R   V++  PR+ R+  +   +++ + L+ +    EVS  R+ QI ++A  +++
Sbjct: 203 MNRLTQVIDSLPRKERLVLSLYYEQD-LNLKEIGEILEVSESRISQILSQATHRIR 257


>gi|323701302|ref|ZP_08112977.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
 gi|323533904|gb|EGB23768.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
          Length = 257

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 24/93 (25%), Positives = 50/93 (53%), Gaps = 1/93 (1%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L   +   L +   + G+  A ++L+  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLTNSQMRTLFEAM-QQGNKEARNQLINGNLRLVLSVIQRFTNRGEYVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           GLM+A+  FD  +  + +TY++  I   ++ Y+
Sbjct: 74  GLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYL 106


>gi|295109704|emb|CBL23657.1| RNA polymerase, sigma subunit, RpsG/SigG [Ruminococcus obeum
           A2-162]
          Length = 259

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 27/101 (26%), Positives = 57/101 (56%), Gaps = 2/101 (1%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L+++E+  L +R ++ GD  A  + +  +LRLV+ +   ++       ++   G IG
Sbjct: 16  LPILKQEEKDELFRRIKQ-GDTKAREQYIKGNLRLVLSVIRRFQNSNENPDDLFQIGCIG 74

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           LM+AV  FD     + +TY++  I   ++ Y LR ++ +++
Sbjct: 75  LMKAVDNFDDTLMVKFSTYAVPMIIGEIRRY-LRDYNSIRV 114


>gi|225019126|ref|ZP_03708318.1| hypothetical protein CLOSTMETH_03078 [Clostridium methylpentosum
           DSM 5476]
 gi|224948099|gb|EEG29308.1| hypothetical protein CLOSTMETH_03078 [Clostridium methylpentosum
           DSM 5476]
          Length = 288

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 53/239 (22%), Positives = 112/239 (46%), Gaps = 23/239 (9%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L++ +L+LV+ +   +   G  + ++   G IGL++A+  FD  +  R +TY++  
Sbjct: 70  AREKLISGNLKLVLSVIQRFTNRGENLDDLFQVGCIGLIKAIDNFDISQNVRFSTYAVPM 129

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I   ++ Y LR  + V++  +   K   +   + K   + +T  +LK   +  I++++ V
Sbjct: 130 IIGEIRRY-LRDNNSVRVSRSL--KDTAYKAMQAK---EKLTTAHLKEPTIDEISQEMGV 183

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ---EQVLIEKEERKNRR 225
              +V+     +    SL   + S   ++    D +    D +   +++ I KE  KN  
Sbjct: 184 RREDVVLALESIVDPVSLYEPVYSDGGDTIYVMDQIGDKSDDKNWLDEIAI-KEAIKN-- 240

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                    LN RE++I   R    N  T   ++ +  +S+ +V ++E  A  ++++SI
Sbjct: 241 ---------LNEREKKILSLRFF--NGKTQVEVAEDIGISQAQVSRLEKGALDRIKKSI 288


>gi|282862754|ref|ZP_06271815.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
 gi|282562440|gb|EFB67981.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
          Length = 298

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 62/244 (25%), Positives = 109/244 (44%), Gaps = 26/244 (10%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISE-VVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + L+  +L LV   A  +R  G   +E ++  G IGL++A+ +FD  R    AT+++ 
Sbjct: 69  ARNTLIEMNLSLVRYAASRFRNRGGDDTEDIIQVGTIGLIKAIDRFDLSREVEFATFAVP 128

Query: 108 WIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           +I   ++ +    +WS   +      + L   L + K  L A  D +     V  +A  L
Sbjct: 129 YIVGEIKRFFRDTTWS---VHVPRRLQELRVELAKAKETLSAQLDRD---PTVAELATHL 182

Query: 167 NVSESEVI----SMNCRLAGDESLNALINSSDKNSSQ--WQDWLVYDHDGQEQVLIEKEE 220
           ++ E E+I    + N   AG  SL+     S+  + Q  + D L  D  G E V      
Sbjct: 183 DLPEEEIIEGLVAANGYSAG--SLDTPSADSESGNEQRAYADLLGEDDPGMESV------ 234

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                + L   +  L+ RER I   R  QE  +T   + +E  VS+  V ++ +R  +++
Sbjct: 235 --ENLHALAPLLRQLDDRERTIVRMRFGQE--MTQAQIGAELGVSQMHVSRLLSRIVQRL 290

Query: 281 QESI 284
           +  +
Sbjct: 291 RTGM 294


>gi|56963382|ref|YP_175113.1| sporulation sigma factor SigK [Bacillus clausii KSM-K16]
 gi|56909625|dbj|BAD64152.1| DNA-directed RNA polymerase sigma-27 factor sigma-K [Bacillus
           clausii KSM-K16]
          Length = 235

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 26/84 (30%), Positives = 48/84 (57%), Gaps = 2/84 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ ++ E+  LA+     GD SA + L+  +LRLV  I   +      + +++S G IGL
Sbjct: 30  PLSKEDEKKYLARM--AEGDASARNMLIEHNLRLVAHIVKKFENTREDVEDLISIGTIGL 87

Query: 87  MQAVKKFDPERGFRLATYSMWWIK 110
           ++A++ +   +G +LATY+   I+
Sbjct: 88  IKAIESYSEGKGTKLATYAARCIE 111


>gi|326443735|ref|ZP_08218469.1| RNA polymerase sigma factor WhiG [Streptomyces clavuligerus ATCC
           27064]
          Length = 258

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 61/248 (24%), Positives = 104/248 (41%), Gaps = 26/248 (10%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFD 94
           + Y+  GD     +L+  H   +VK   G    GLP     ++ VS G  GL+ A++KFD
Sbjct: 14  RSYKVTGDERLREQLIL-HYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEKFD 72

Query: 95  PERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
            ER  +  TY++  I+ AM       ++I RS              L   LRR     + 
Sbjct: 73  IERSIKFETYAITRIRGAMIDELRALDWIPRSVRQKARAVERAYATLEAQLRRTPSEGEV 132

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
             +  +  E++ A+  +L        S+   +A +E L+      D+ S    D L    
Sbjct: 133 AEEMGIAVEELHAVFSQL--------SLANVVALEELLHVGGEGGDRLS--LMDTL---E 179

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D      +E  E +  R +L R+++ L  RE+ +      +   +TL  + +   V+  R
Sbjct: 180 DTAADDPVEVAEGRELRRLLARAINTLPDREKTVVTLYYYE--GLTLAEIGNVLGVTESR 237

Query: 269 VRQIEARA 276
           V QI  ++
Sbjct: 238 VSQIHTKS 245


>gi|323490161|ref|ZP_08095381.1| RNA polymerase sigma-D factor (Sigma-28) [Planococcus donghaensis
           MPA1U2]
 gi|323396209|gb|EGA89035.1| RNA polymerase sigma-D factor (Sigma-28) [Planococcus donghaensis
           MPA1U2]
          Length = 252

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 60/259 (23%), Positives = 117/259 (45%), Gaps = 27/259 (10%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLM 87
           +EE V    +++H D  A   LV  +L LV  +   +    LP +    +V S    GL+
Sbjct: 8   KEELVCWSDWQQHRDPDAGEYLVEQYLPLVDYVIQRFM-ISLPKTVEKDDVRSYAYEGLL 66

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRS-WSLVKIGTTANQ-KRLFFNLRRLKGH 145
            A+ KF+ ER  +  TY+ W IK A+ + + +S W    +     + ++ F  L +  G 
Sbjct: 67  DALSKFNIERDLKFETYASWRIKGAIIDGLRQSDWLPRSVRDKVKKIEKAFLLLEQQSG- 125

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
             +++D          ++  L ++++E+     +   + +L+ +I+  D N  +    + 
Sbjct: 126 -VSVSDEE--------VSSYLGITKAEL----NKTVSEAALSTMISMDDDNFEEQGKLVN 172

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
           Y  D  E+ L E    + R+  L R++  L  +E+        +E  +T   ++    VS
Sbjct: 173 YHVDSPERHLSE----QMRKESLVRAIERLPEKEKITVSLCYFEEMKLT--EIAEILNVS 226

Query: 266 RERVRQIEARAFKKVQESI 284
             RV Q+ ++A  ++  SI
Sbjct: 227 VSRVSQLHSKAMLRLHASI 245


>gi|257866395|ref|ZP_05646048.1| RNA polymerase sigma factor whiG [Enterococcus casseliflavus EC30]
 gi|257873089|ref|ZP_05652742.1| RNA polymerase sigma factor whiG [Enterococcus casseliflavus EC10]
 gi|257800353|gb|EEV29381.1| RNA polymerase sigma factor whiG [Enterococcus casseliflavus EC30]
 gi|257807253|gb|EEV36075.1| RNA polymerase sigma factor whiG [Enterococcus casseliflavus EC10]
          Length = 235

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 51/211 (24%), Positives = 97/211 (45%), Gaps = 20/211 (9%)

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA-NQKRLFFNLR 140
           G IGLM A++KFDP +     +Y+   IK A+ + + +   + +    A NQ   F+  R
Sbjct: 40  GVIGLMDALRKFDPSKKVPFESYAAIRIKGAIIDEVRKHAKISRYKMAAVNQ---FYQAR 96

Query: 141 RLKGHLQAITDNNLKPEQV-VAIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNS 197
           +         + +LK E     I K+L +++S++  I  +       SL   + +  +  
Sbjct: 97  QE-------LEQSLKREATDTEICKQLGINQSQLADIYESLHYLASVSLEDTLFAYQEEG 149

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
              +D +    +  E+ L+ +E    +R  L   +  L  RE+ I      +E  +TL+ 
Sbjct: 150 MTLKDMVRDPAENVEETLVAEE----KRTALVACIKKLGEREQLILSLYYTEE--LTLKE 203

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           ++   EVS  RV QI  +   K++  I++++
Sbjct: 204 IAEILEVSIPRVSQIHGKTIAKLRTLIEEEL 234


>gi|297191780|ref|ZP_06909178.1| sporulation sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
 gi|197721703|gb|EDY65611.1| sporulation sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
          Length = 278

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 58/244 (23%), Positives = 101/244 (41%), Gaps = 18/244 (7%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFD 94
           + Y+  GD     +L+  H   +VK   G    GLP     ++ VS G  GL+ A++KFD
Sbjct: 34  RSYKATGDGRLREQLIL-HYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEKFD 92

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
            ER  +  TY++  I+ AM +  LR+   +        + +      L+  L+       
Sbjct: 93  IERSIKFETYAITRIRGAMIDE-LRALDWIPRSVRQKARAVERAYATLEAQLR-----RT 146

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ--DWLVYDHDGQE 212
             E  VA    + V E   +     LA   +L  L++   +   +    D L    D   
Sbjct: 147 PSESEVAAEMGITVDELHSVFSQLSLANVVALEELLHVGGEGGERLSLMDTL---EDTAA 203

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
              +E  E +  R +L R+++ L  RE+ +      +   +TL  + +   V+  RV QI
Sbjct: 204 DNPVEVAEGRELRRLLARAINTLPDREKTVVTLYYYE--GLTLAEIGNVLGVTESRVSQI 261

Query: 273 EARA 276
             ++
Sbjct: 262 HTKS 265


>gi|167755748|ref|ZP_02427875.1| hypothetical protein CLORAM_01263 [Clostridium ramosum DSM 1402]
 gi|237734714|ref|ZP_04565195.1| sporulation sigma factor sigE [Mollicutes bacterium D7]
 gi|167704687|gb|EDS19266.1| hypothetical protein CLORAM_01263 [Clostridium ramosum DSM 1402]
 gi|229382042|gb|EEO32133.1| sporulation sigma factor sigE [Coprobacillus sp. D7]
          Length = 231

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 31/90 (34%), Positives = 48/90 (53%), Gaps = 3/90 (3%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY-GLPISEVV 79
           H+I   P+   +E+  L K     GD  A   L+  +LRLVV +A  Y       I +++
Sbjct: 21  HDILPPPLKGIEEKEALEKL--GAGDNDARDLLIEHNLRLVVYVAKRYDTTQNGGIEDLI 78

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           S G IGL++A+  F P++  +LATY+   I
Sbjct: 79  SIGTIGLVKAINTFKPDKNIKLATYASRCI 108


>gi|325508641|gb|ADZ20277.1| RNA polymerase sigma factor [Clostridium acetobutylicum EA 2018]
          Length = 219

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 34/143 (23%), Positives = 72/143 (50%), Gaps = 9/143 (6%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGY--RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           +++  +++V  ++ LV  IA  Y  R   L + ++V  G I ++ AV+ FD  +G + +T
Sbjct: 5   NINERNKVVEKYMTLVKSIARKYINRSGTLELEDMVQSGAISMINAVENFDYNKGVKFST 64

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   ++  M+ Y  ++     I  +  Q++   +LRR+K         N K   +  I+
Sbjct: 65  YARHCVEGGMKNYCKKNEL---IHLSEYQRK---DLRRIKKLFDEKQLEN-KDIDITEIS 117

Query: 164 KKLNVSESEVISMNCRLAGDESL 186
            +L + + + I++ C L  D+ +
Sbjct: 118 AELGIEKEKAINLICFLNKDKYI 140


>gi|312135662|ref|YP_004003000.1| RNA polymerase sigma factor, sigma-70 family [Caldicellulosiruptor
           owensensis OL]
 gi|311775713|gb|ADQ05200.1| RNA polymerase sigma factor, sigma-70 family [Caldicellulosiruptor
           owensensis OL]
          Length = 302

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 27/82 (32%), Positives = 48/82 (58%), Gaps = 9/82 (10%)

Query: 50  AHRLVTSHLRLVVKIAMGY----RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
             +LV  +++LV  +A  +    +GY   + ++VSEG IGL+ A + +DPE+G   +TY+
Sbjct: 10  TQKLVADNIKLVYHVANKFMPCPKGYCYEVDDLVSEGYIGLVVAARNYDPEKG-SFSTYA 68

Query: 106 MWWIKA----AMQEYILRSWSL 123
              I++    ++ +Y L S SL
Sbjct: 69  CKVIESKIRKSLPKYRLTSVSL 90


>gi|308070013|ref|YP_003871618.1| RNA polymerase sigma-28 factor precursor [Paenibacillus polymyxa
           E681]
 gi|305859292|gb|ADM71080.1| RNA polymerase sigma-28 factor precursor [Paenibacillus polymyxa
           E681]
          Length = 233

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 27/84 (32%), Positives = 49/84 (58%), Gaps = 2/84 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ EK+E   L K + E G+  + + L+  +LRLV  I   +   G  + +++S G IGL
Sbjct: 30  PLTEKEEARHL-KLFAE-GNAHSRNTLIEHNLRLVAHIVKKFDNTGEDLEDLISIGTIGL 87

Query: 87  MQAVKKFDPERGFRLATYSMWWIK 110
           ++A++ F   +G +LAT++   I+
Sbjct: 88  IKAIESFQTGKGTKLATFAARCIE 111


>gi|294815383|ref|ZP_06774026.1| RNA polymerase sigma factor whiG [Streptomyces clavuligerus ATCC
           27064]
 gi|294327982|gb|EFG09625.1| RNA polymerase sigma factor whiG [Streptomyces clavuligerus ATCC
           27064]
          Length = 278

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 61/248 (24%), Positives = 104/248 (41%), Gaps = 26/248 (10%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFD 94
           + Y+  GD     +L+  H   +VK   G    GLP     ++ VS G  GL+ A++KFD
Sbjct: 34  RSYKVTGDERLREQLIL-HYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEKFD 92

Query: 95  PERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
            ER  +  TY++  I+ AM       ++I RS              L   LRR     + 
Sbjct: 93  IERSIKFETYAITRIRGAMIDELRALDWIPRSVRQKARAVERAYATLEAQLRRTPSEGEV 152

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
             +  +  E++ A+  +L        S+   +A +E L+      D+ S    D L    
Sbjct: 153 AEEMGIAVEELHAVFSQL--------SLANVVALEELLHVGGEGGDRLS--LMDTL---E 199

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D      +E  E +  R +L R+++ L  RE+ +      +   +TL  + +   V+  R
Sbjct: 200 DTAADDPVEVAEGRELRRLLARAINTLPDREKTVVTLYYYE--GLTLAEIGNVLGVTESR 257

Query: 269 VRQIEARA 276
           V QI  ++
Sbjct: 258 VSQIHTKS 265


>gi|260893856|ref|YP_003239953.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Ammonifex degensii
           KC4]
 gi|260865997|gb|ACX53103.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Ammonifex degensii
           KC4]
          Length = 252

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 61/259 (23%), Positives = 116/259 (44%), Gaps = 34/259 (13%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPE 96
           Y++ G+ ++   LV  +L LV K  +G     LP    + ++   G +GL+ A++++DP 
Sbjct: 10  YKQRGNTTSKEELVRRYLPLV-KYLVGRLAVRLPPWVSLEDIEGAGILGLLAAMERYDPS 68

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT------ 150
           +G    +Y+ + I  AM + + R W+                 RR    +QA+       
Sbjct: 69  QGVEFESYARYRIWGAMLDEV-RRWARFS--------------RRTWQQMQAVLKVQERW 113

Query: 151 --DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
             +   +P +V  +A++L    ++V  +    A   S +     S +  S W+++L  D 
Sbjct: 114 EREKGCRP-KVEDVAQELGWEPAQVDRLGRYFAAFNSFSLEEVRSAEGRSPWEEFLA-DP 171

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
            GQ+ +    E+    R  L  ++  L  R + I  A   QE  +TL  +     +S  R
Sbjct: 172 KGQDPLEELLEKEDLGR--LAEAIGRLEERLQLIL-ALYYQEG-LTLREIGEVLGISESR 227

Query: 269 VRQIEARAFKKVQESIQKQ 287
           V Q+ +RA  K++E + ++
Sbjct: 228 VCQLHSRALTKLREILAEE 246


>gi|15894509|ref|NP_347858.1| RNA polymerase sigma factor [Clostridium acetobutylicum ATCC 824]
 gi|15024150|gb|AAK79198.1|AE007635_12 RNA polymerase sigma factor [Clostridium acetobutylicum ATCC 824]
          Length = 227

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 34/143 (23%), Positives = 72/143 (50%), Gaps = 9/143 (6%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGY--RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           +++  +++V  ++ LV  IA  Y  R   L + ++V  G I ++ AV+ FD  +G + +T
Sbjct: 13  NINERNKVVEKYMTLVKSIARKYINRSGTLELEDMVQSGAISMINAVENFDYNKGVKFST 72

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   ++  M+ Y  ++     I  +  Q++   +LRR+K         N K   +  I+
Sbjct: 73  YARHCVEGGMKNYCKKNEL---IHLSEYQRK---DLRRIKKLFDEKQLEN-KDIDITEIS 125

Query: 164 KKLNVSESEVISMNCRLAGDESL 186
            +L + + + I++ C L  D+ +
Sbjct: 126 AELGIEKEKAINLICFLNKDKYI 148


>gi|229075781|ref|ZP_04208758.1| RNA polymerase sigma-F factor [Bacillus cereus Rock4-18]
 gi|229098543|ref|ZP_04229484.1| RNA polymerase sigma-F factor [Bacillus cereus Rock3-29]
 gi|229104680|ref|ZP_04235342.1| RNA polymerase sigma-F factor [Bacillus cereus Rock3-28]
 gi|229117569|ref|ZP_04246941.1| RNA polymerase sigma-F factor [Bacillus cereus Rock1-3]
 gi|228665889|gb|EEL21359.1| RNA polymerase sigma-F factor [Bacillus cereus Rock1-3]
 gi|228678744|gb|EEL32959.1| RNA polymerase sigma-F factor [Bacillus cereus Rock3-28]
 gi|228684865|gb|EEL38802.1| RNA polymerase sigma-F factor [Bacillus cereus Rock3-29]
 gi|228707333|gb|EEL59529.1| RNA polymerase sigma-F factor [Bacillus cereus Rock4-18]
          Length = 252

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 49/190 (25%), Positives = 89/190 (46%), Gaps = 17/190 (8%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           +K P L+  E   L ++  + GD  A   +V S++RLV  +   +   G    ++   G 
Sbjct: 9   KKKPQLKDHELKALIQK-SQGGDQQARDTIVQSNMRLVWSVVQRFLNRGYEPDDLFQIGC 67

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL+++V KFD     + +TY++  I   +Q + LR    VK+  +   K     +R+++
Sbjct: 68  IGLLKSVDKFDLSFDVKFSTYAVPMIIGEIQRF-LRDDGSVKVSRSL--KETGNKIRKMR 124

Query: 144 GHL-----QAITDN------NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
             L     +A T N       L PE+VV +A++ +   S +        GD  +  L   
Sbjct: 125 DELSKEFGRAPTINEVAEALELTPEEVV-LAQEASRPPSSIHETVYENDGD-PITILDQI 182

Query: 193 SDKNSSQWQD 202
           +D++ ++W D
Sbjct: 183 ADQSETKWFD 192


>gi|146295930|ref|YP_001179701.1| sporulation sigma factor SigK [Caldicellulosiruptor saccharolyticus
           DSM 8903]
 gi|145409506|gb|ABP66510.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK
           [Caldicellulosiruptor saccharolyticus DSM 8903]
          Length = 220

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 29/93 (31%), Positives = 52/93 (55%), Gaps = 5/93 (5%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP--ISEVVSEGNI 84
           P+ +++EE  L K +   G + A + L+  +LRLV  IA  Y     P    +++S G I
Sbjct: 13  PLSDEEEEMHLKKMW--EGAIEARNILIEKNLRLVAHIAKKYT-LSFPNLTDDIISVGTI 69

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           GL++A++ +  E+  RL+TY+   I+  +  Y+
Sbjct: 70  GLIKAIETYSQEKNTRLSTYAAKCIENEILMYL 102


>gi|310643126|ref|YP_003947884.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
 gi|309248076|gb|ADO57643.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
          Length = 233

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 27/84 (32%), Positives = 49/84 (58%), Gaps = 2/84 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ EK+E   L K + E G+  + + L+  +LRLV  I   +   G  + +++S G IGL
Sbjct: 30  PLTEKEEARHL-KLFAE-GNAHSRNTLIEHNLRLVAHIVKKFDNTGEDLEDLISIGTIGL 87

Query: 87  MQAVKKFDPERGFRLATYSMWWIK 110
           ++A++ F   +G +LAT++   I+
Sbjct: 88  IKAIESFQTGKGTKLATFAARCIE 111


>gi|225862940|ref|YP_002748318.1| RNA polymerase sigma-B factor [Bacillus cereus 03BB102]
 gi|225786058|gb|ACO26275.1| RNA polymerase sigma-B factor [Bacillus cereus 03BB102]
          Length = 257

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 60/271 (22%), Positives = 129/271 (47%), Gaps = 29/271 (10%)

Query: 22  EIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           EI+  P  L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++ 
Sbjct: 2   EIQSQPTNLTKEDVIKLIAEFQQNQCGEAQERLVNHYKNLVYSIAYRYSKGGPMHEDIIQ 61

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNL 139
            G +GL+ A++++D   G     +++  I   +++Y+  ++W +       +  R   +L
Sbjct: 62  VGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGI-------HVPRRIKDL 114

Query: 140 -RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNALI-NS 192
             ++K  ++ +TD+  +  +++ IA  L +SE EV+ +     N R++   SL+ ++ N+
Sbjct: 115 GGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVS---SLDDVVENA 171

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
           SD +S    + +     G E+          RR +L    +VLN  E+ +     + E  
Sbjct: 172 SDGSSVARIESVGEVEQGYEET--------ERRLVLKDIFNVLNETEKSVI--HYIFEEN 221

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +  ++      +S+  V +I+ +A  K++++
Sbjct: 222 LNQKDTGERLGISQMHVSRIKRQAISKLKQA 252


>gi|297561355|ref|YP_003680329.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
 gi|296845803|gb|ADH67823.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
          Length = 285

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 46/197 (23%), Positives = 92/197 (46%), Gaps = 13/197 (6%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R+V  +  LV K+A  Y G G P+ ++     +GL++A+  F+P+RG    +Y +  +  
Sbjct: 56  RVVVLYQPLVNKLARRYNGRGEPLDDLQQTAMLGLVKAIHGFNPDRGKPFISYLLPTVTG 115

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            ++ +       V++     + R+     +L+  L      + +   V  +++++ + E+
Sbjct: 116 EIKRHFRDHTWAVRVSRRHQENRI-----KLRQALNDFQQAHARTPTVHELSEEMGLPEA 170

Query: 172 EVISMNCRLAGDESLNAL-INSSDKNSSQWQDWL-VYDHDGQEQVLIEKEERKNRRNMLT 229
           EV  +   +   ES  +L +++ D + S  Q+   + DH G E    E  E   +R  L 
Sbjct: 171 EVGEL---IQVSESYRSLSLDAPDTSDSDGQEGTRLEDHLGSED---EGLELVVQRESLK 224

Query: 230 RSMSVLNPRERRIFEAR 246
            +++ L  RER I   R
Sbjct: 225 PALARLPEREREILMLR 241


>gi|212638647|ref|YP_002315167.1| RNA polymerase sporulation-specific sigma factor (sigma-K), SpoIVCB
           [Anoxybacillus flavithermus WK1]
 gi|212560127|gb|ACJ33182.1| RNA polymerase sporulation-specific sigma factor (sigma-K), SpoIVCB
           [Anoxybacillus flavithermus WK1]
          Length = 129

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 48/81 (59%), Gaps = 1/81 (1%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L+ +EE +  K+  + GD +A ++L+  +LRLV  I   +   G    +++S G IGL++
Sbjct: 31  LDAKEEAMYLKQMAK-GDENARNKLIEHNLRLVAHIVKKFENTGEDPEDLISIGTIGLIK 89

Query: 89  AVKKFDPERGFRLATYSMWWI 109
           A++ +   +G +LATY+   I
Sbjct: 90  AIESYSTGKGTKLATYAARCI 110


>gi|329941096|ref|ZP_08290375.1| SigL-like sigma factor [Streptomyces griseoaurantiacus M045]
 gi|329299627|gb|EGG43526.1| SigL-like sigma factor [Streptomyces griseoaurantiacus M045]
          Length = 319

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 35/125 (28%), Positives = 61/125 (48%), Gaps = 7/125 (5%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           H LV  +L LV   A  +R    P+ +++  G IGL++A+ +F+  RG    T++M  I 
Sbjct: 96  HTLVELNLALVKFAAARFRTRSEPMEDIIQVGTIGLIKAIDRFELSRGVEFPTFAMPTII 155

Query: 111 AAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
             ++ +    SWS V++     + RL  +L +    L    D   +   V  +A +L +S
Sbjct: 156 GEIKRFFRDTSWS-VRVPRRLQELRL--DLAKAGDELAQQLD---RAPTVTELADRLGLS 209

Query: 170 ESEVI 174
             EV+
Sbjct: 210 NEEVV 214


>gi|300787087|ref|YP_003767378.1| RNA polymerase sigma factor [Amycolatopsis mediterranei U32]
 gi|299796601|gb|ADJ46976.1| RNA polymerase sigma factor [Amycolatopsis mediterranei U32]
          Length = 263

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 31/106 (29%), Positives = 52/106 (49%), Gaps = 10/106 (9%)

Query: 28  MLEKQEEYVLAKR-YREHGDLSAAH--------RLVTSHLRLVVKIAMGYRGYGLPISEV 78
           +L + +EY   +  ++E G L  A         +LVT  L L   IA  + G G P  ++
Sbjct: 8   LLHRPDEYAHCEPLFQELGSLDTADPRRDVVRSKLVTELLPLAEHIATRFSGRGEPREDL 67

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS-WSL 123
           V    IGL+ AV +FDP RG    ++++  I   ++ +   + WS+
Sbjct: 68  VQVARIGLINAVDRFDPARGHDFLSFAVPTIMGEVRRHFRDTGWSV 113


>gi|154503856|ref|ZP_02040916.1| hypothetical protein RUMGNA_01682 [Ruminococcus gnavus ATCC 29149]
 gi|153795455|gb|EDN77875.1| hypothetical protein RUMGNA_01682 [Ruminococcus gnavus ATCC 29149]
          Length = 259

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 53/235 (22%), Positives = 110/235 (46%), Gaps = 16/235 (6%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GD  A  + +  +LRLV+ +   +        ++   G +GLM+AV  FDP R  + +T
Sbjct: 33  EGDEDAREQYIKGNLRLVLSVIKRFSSSSENADDLFQIGCVGLMKAVDHFDPSRLVKFST 92

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y++  I   ++ Y LR  + +++  +  +   +  +   +G ++  +    K   V  IA
Sbjct: 93  YAVPMIIGEIRRY-LRDNNSIRVSRSL-RDTAYKAIYAKEGFVKKYS----KEPTVQEIA 146

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           +++ +S+ +++     +    SL+  + S   ++    D  V D   +E+  +E+     
Sbjct: 147 EEIGISKEDIVFALDAIQMPVSLHEPVYSDGGDTLYIMDQ-VSDKKNREENWVEELS--- 202

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
               L  +M  LN RER I + R   E    +E ++ + ++S+ +V ++E  A K
Sbjct: 203 ----LEAAMERLNERERFIIQLRFF-EGKTQME-VAEQIQISQAQVSRLEKNALK 251


>gi|2529275|gb|AAB81194.1| sigma factor [Geobacillus stearothermophilus]
          Length = 250

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 55/256 (21%), Positives = 114/256 (44%), Gaps = 19/256 (7%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           ++ QE   L +R +E GD  A   ++  ++RLV  +   +   G    ++   G IGL++
Sbjct: 12  IKDQEMKELIRRSQE-GDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLK 70

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           +V KFD     + +TY++  I   +Q + LR    VK+  +   K +   +R+ K  L  
Sbjct: 71  SVDKFDLSYDVKFSTYAVPMIIGEIQRF-LRDDGTVKVSRSL--KEMGNKIRKAKDEL-- 125

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
            +    +   +  IA  L +S  +V+     +    S++  +  +D +     D +    
Sbjct: 126 -SKTRGRSPTITEIADHLGISPEDVVLAQEAVRLPTSIHETVYENDGDPITLLDQIA--- 181

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D  E    +K         L +++  L+ RER I   R  ++   T   ++S   +S+ +
Sbjct: 182 DADEASWFDK-------IALKKAIEELDERERLIVYLRYYRDR--TQSEVASRLGISQVQ 232

Query: 269 VRQIEARAFKKVQESI 284
           V ++E +  + +++ +
Sbjct: 233 VSRLEKKILQHIKDKM 248


>gi|75761672|ref|ZP_00741618.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|74490828|gb|EAO54098.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
          Length = 258

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 55/231 (23%), Positives = 110/231 (47%), Gaps = 27/231 (11%)

Query: 22  EIRKIPMLEKQEEYV-LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           EI+  P    +E+ + L   ++++    A  RLV  +  LV  IA  Y   G    +++ 
Sbjct: 3   EIQSQPTTLTKEDVIKLIAEFQQNQCNEAQERLVDHYKNLVYSIAYRYSKGGPMHEDIIQ 62

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNL 139
            G +GL+ A++++D   G     +++  I   +++Y+  ++W +       +  R   +L
Sbjct: 63  VGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGI-------HVPRRIKDL 115

Query: 140 -RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNALI-NS 192
             ++K  ++ +TD+  +  +++ IA  L +SE EV+ +     N R++   SL+ ++ NS
Sbjct: 116 GGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVS---SLDDVVENS 172

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           SD +S    + +     G EQ          RR +L    +VLN  E+ + 
Sbjct: 173 SDGSSVARIESVGEVEQGYEQT--------ERRLVLEDIFNVLNDMEKSVI 215


>gi|218515736|ref|ZP_03512576.1| RNA polymerase sigma factor RpoD [Rhizobium etli 8C-3]
          Length = 191

 Score = 46.2 bits (108), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 30/91 (32%), Positives = 47/91 (51%), Gaps = 5/91 (5%)

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QE 250
            D+  S   D++    D    + I+   + N R   TR ++ L PRE R+   R      
Sbjct: 90  GDEEDSHLGDFI---EDKNALLPIDAAIQANLRETTTRVLASLTPREERVLRMRFGIGMN 146

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              TLE +  +F V+RER+RQIEA+A +K++
Sbjct: 147 TDHTLEEVGQQFSVTRERIRQIEAKALRKLK 177


>gi|323703189|ref|ZP_08114842.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
 gi|323531848|gb|EGB21734.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
          Length = 251

 Score = 46.2 bits (108), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 64/248 (25%), Positives = 120/248 (48%), Gaps = 18/248 (7%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFDPERGFRL 101
           D  A  +L+  +L LV  +A G     LP      ++   G IGLM+A+ KFD   G   
Sbjct: 15  DERARQQLILHYLPLVKHLA-GRLAVKLPSFIQREDLEGYGVIGLMEALDKFDHTMGNSF 73

Query: 102 ATYSMWWIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
             Y+   I+ A+ + + R +W    +  TA QK    +L++ +  L+      + P++++
Sbjct: 74  DAYAYHRIRGAILDQVRRQNW----LPRTAWQK--LQHLKQTRERLERELGGAV-PDEIL 126

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
           A    ++V E   ++ +       SL+  +  SD +  +  D LV D  G    L   EE
Sbjct: 127 AREMGISVDELNHLASSAGKMYLMSLDEEVPGSDGSVVRKLD-LVED-TGSPDPLSIVEE 184

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           ++NR+ +L R++  L  R++ I      +   +TL+ +    EVS  RV Q+  +  +K+
Sbjct: 185 KENRK-LLARAIEKLGQRDQLILSLYYTE--GLTLKEIGQVLEVSESRVCQLHGQVMRKL 241

Query: 281 QESIQKQV 288
           ++++Q+ +
Sbjct: 242 RKTLQEML 249


>gi|295835999|ref|ZP_06822932.1| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
 gi|295825822|gb|EFG64505.1| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
          Length = 297

 Score = 46.2 bits (108), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 53/218 (24%), Positives = 102/218 (46%), Gaps = 23/218 (10%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G +GL++A+ +FD  R     ++++ +I   ++ Y   S   V +     + R
Sbjct: 91  MEDILQVGTVGLIKAIDRFDLTREAEFTSFAIPYIVGEIKRYFRDSTWAVHVPRRLQELR 150

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG--DESLNALINS 192
           +  +L R K  L    D +     V  +A +L +SE EVI       G   +SL+   +S
Sbjct: 151 V--DLARAKERLAVDLDRD---PGVKELAAELGISEDEVIDGLIAANGYMSDSLDLPADS 205

Query: 193 SD------KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           +       K ++ + D+L  D D   +++   E+    R +L      L+ RER + E R
Sbjct: 206 TTSGKPDQKTATTYADFL-GDWDPAMELV---EDFTALRPLL----GTLDDRERYLLELR 257

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             QE  +T   + +E  VS+  V ++ +R   K++E +
Sbjct: 258 FGQE--LTQAQIGAELGVSQMHVSRLLSRTLGKLREGL 293


>gi|291535996|emb|CBL09108.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Roseburia
           intestinalis M50/1]
          Length = 192

 Score = 46.2 bits (108), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 23/65 (35%), Positives = 37/65 (56%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           G L A + L   ++RLV  +A  Y+     + +++S G IGLM+A+  +  + G RLATY
Sbjct: 8   GSLEARNELTLHNMRLVAHVAKKYQNSEEDMEDLISIGTIGLMKAIATYKEDYGSRLATY 67

Query: 105 SMWWI 109
           +   I
Sbjct: 68  AARCI 72


>gi|255505890|ref|ZP_05348671.3| RNA polymerase sigma-F factor [Bryantella formatexigens DSM 14469]
 gi|255265373|gb|EET58578.1| RNA polymerase sigma-F factor [Bryantella formatexigens DSM 14469]
          Length = 238

 Score = 46.2 bits (108), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 24/83 (28%), Positives = 46/83 (55%), Gaps = 1/83 (1%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GD +A  +LV  +L LV  IA  + G G  + ++   G+IGL++A+  F+     + +T
Sbjct: 13  QGDKAAREQLVEENLGLVFTIAKRFTGRGTDVEDLFQIGSIGLLKAIDNFNLSYDVKFST 72

Query: 104 YSMWWIKAAMQEYILRSWSLVKI 126
           Y++  I   ++ + LR   ++K+
Sbjct: 73  YAVPMIAGEIRRF-LRDDGMLKV 94


>gi|196044126|ref|ZP_03111362.1| RNA polymerase sigma-B factor [Bacillus cereus 03BB108]
 gi|218902186|ref|YP_002450020.1| RNA polymerase sigma-B factor [Bacillus cereus AH820]
 gi|196024765|gb|EDX63436.1| RNA polymerase sigma-B factor [Bacillus cereus 03BB108]
 gi|218534787|gb|ACK87185.1| RNA polymerase sigma-B factor [Bacillus cereus AH820]
          Length = 257

 Score = 46.2 bits (108), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 60/271 (22%), Positives = 129/271 (47%), Gaps = 29/271 (10%)

Query: 22  EIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           EI+  P  L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++ 
Sbjct: 2   EIQSQPTNLTKEDVIKLIAEFQQNQCGEAQERLVDHYKNLVYSIAYRYSKGGPMHEDIIQ 61

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNL 139
            G +GL+ A++++D   G     +++  I   +++Y+  ++W +       +  R   +L
Sbjct: 62  VGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGI-------HVPRRIKDL 114

Query: 140 -RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNALI-NS 192
             ++K  ++ +TD+  +  +++ IA  L +SE EV+ +     N R++   SL+ ++ N+
Sbjct: 115 GGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVS---SLDDVVENA 171

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
           SD +S    + +     G E+          RR +L    +VLN  E+ +     + E  
Sbjct: 172 SDGSSVARIESVGEVEQGYEET--------ERRLVLKDIFNVLNETEKSVI--HYIFEEN 221

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +  ++      +S+  V +I+ +A  K++++
Sbjct: 222 LNQKDTGERLGISQMHVSRIKRQAISKLKQA 252


>gi|295104067|emb|CBL01611.1| RNA polymerase sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii SL3/3]
          Length = 220

 Score = 45.8 bits (107), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 29/94 (30%), Positives = 49/94 (52%), Gaps = 8/94 (8%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAM-GYRGYGLP-------ISEVVSEGNIGLMQAVK 91
           R  + GD +A   L+  +L  + KIA+  YR  GL        + +++ EG+IGL+ A+ 
Sbjct: 11  RLAQKGDTAARDILLEKNLGFIRKIALEQYRNMGLDENDIGIDLDDLMQEGSIGLLNAIP 70

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            FD  RG +  TY+   ++ AM + I  +  L +
Sbjct: 71  LFDAGRGMKFLTYAAPALRNAMTDCIRAALGLFE 104


>gi|284990614|ref|YP_003409168.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Geodermatophilus obscurus DSM 43160]
 gi|284063859|gb|ADB74797.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Geodermatophilus obscurus DSM 43160]
          Length = 360

 Score = 45.8 bits (107), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 57/238 (23%), Positives = 102/238 (42%), Gaps = 20/238 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  HL LV   A  +   G P  +++  G +GL+ A+ +FDP RG    ++++  I   
Sbjct: 140 LVEEHLPLVRHFARRFSNRGEPFDDLLQVGTLGLIAAIDRFDPTRGVEFLSFAVPTITGE 199

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +   + WS   +      + L  +L    G L         P +   +A+ L +  +
Sbjct: 200 IKRHFRDQGWS---VRVPRRLQELHLSLNAAVGELAQKNGRAPTPSE---LAEHLGIPRA 253

Query: 172 EVISMNCRLAGDESLNALINSS-DKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLT 229
           EV      L G    NA  +SS D+  S   D        G+E   +E  E    R  L 
Sbjct: 254 EV------LEGLAVANAYRSSSLDERLSGEDDSPTLAATLGEEDSALEGVE---YRESLQ 304

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             ++ +  RERRI   R      +T   ++++  +S+  V ++ ++   K++E + K 
Sbjct: 305 PLLATIPARERRILILRFFGN--MTQSQIAADIGISQMHVSRLLSQTLAKLREGLLKD 360


>gi|118476614|ref|YP_893765.1| RNA polymerase sigma factor SigB [Bacillus thuringiensis str. Al
           Hakam]
 gi|301052635|ref|YP_003790846.1| sigma factor B [Bacillus anthracis CI]
 gi|118415839|gb|ABK84258.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Bacillus thuringiensis
           str. Al Hakam]
 gi|300374804|gb|ADK03708.1| sigma factor B [Bacillus cereus biovar anthracis str. CI]
          Length = 258

 Score = 45.8 bits (107), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 60/271 (22%), Positives = 129/271 (47%), Gaps = 29/271 (10%)

Query: 22  EIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           EI+  P  L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++ 
Sbjct: 3   EIQSQPTNLTKEDVIKLIAEFQQNQCGEAQERLVDHYKNLVYSIAYRYSKGGPMHEDIIQ 62

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNL 139
            G +GL+ A++++D   G     +++  I   +++Y+  ++W +       +  R   +L
Sbjct: 63  VGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGI-------HVPRRIKDL 115

Query: 140 -RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNALI-NS 192
             ++K  ++ +TD+  +  +++ IA  L +SE EV+ +     N R++   SL+ ++ N+
Sbjct: 116 GGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVS---SLDDVVENA 172

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
           SD +S    + +     G E+          RR +L    +VLN  E+ +     + E  
Sbjct: 173 SDGSSVARIESVGEVEQGYEET--------ERRLVLKDIFNVLNETEKSVI--HYIFEEN 222

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +  ++      +S+  V +I+ +A  K++++
Sbjct: 223 LNQKDTGERLGISQMHVSRIKRQAISKLKQA 253


>gi|154500630|ref|ZP_02038668.1| hypothetical protein BACCAP_04303 [Bacteroides capillosus ATCC
           29799]
 gi|150270519|gb|EDM97828.1| hypothetical protein BACCAP_04303 [Bacteroides capillosus ATCC
           29799]
          Length = 221

 Score = 45.8 bits (107), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 28/82 (34%), Positives = 45/82 (54%), Gaps = 1/82 (1%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L+ +EE +  +R    GDL A + L+  +LRLV  I   Y        +++S G IGL++
Sbjct: 36  LKAEEERMYLERC-AAGDLEARNILIEHNLRLVAHIIKKYYTQTDDQDDLISIGTIGLIK 94

Query: 89  AVKKFDPERGFRLATYSMWWIK 110
            +  F P++  RLATY+   I+
Sbjct: 95  GISTFKPDKNVRLATYASRCIE 116


>gi|319644916|ref|ZP_07999149.1| RNA polymerase sigma factor [Bacillus sp. BT1B_CT2]
 gi|317392725|gb|EFV73519.1| RNA polymerase sigma factor [Bacillus sp. BT1B_CT2]
          Length = 241

 Score = 45.8 bits (107), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 3/74 (4%)

Query: 39  KRYRE---HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           K+Y E    GD  A + L+  +LRLV  I   +   G    +++S G IGL++A++ +  
Sbjct: 37  KKYLELMAQGDEHARNMLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIESYSA 96

Query: 96  ERGFRLATYSMWWI 109
            +G +LATY+   I
Sbjct: 97  GKGTKLATYAARCI 110


>gi|126653890|ref|ZP_01725737.1| DNA-directed RNA polymerase sigma-27 factor sigma-K [Bacillus sp.
           B14905]
 gi|126589615|gb|EAZ83754.1| DNA-directed RNA polymerase sigma-27 factor sigma-K [Bacillus sp.
           B14905]
          Length = 235

 Score = 45.8 bits (107), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 63/264 (23%), Positives = 107/264 (40%), Gaps = 70/264 (26%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K+EE    +R+   GD  A   L+  ++RLV  +   +      + + +S G IGLM+AV
Sbjct: 33  KEEEAACIERFLG-GDEQARLDLIERNMRLVAHVVKKFHPKHEQLDDYISIGTIGLMKAV 91

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           + + P++  RLATY+   I                      +  +  +LR  K       
Sbjct: 92  ESYTPDKKTRLATYAARCI----------------------ENEILMHLRTQK------- 122

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
                      + K +++ E         +  D+  NAL         Q +D L  D   
Sbjct: 123 ----------KVQKDVSLFEP--------IGTDKDGNAL---------QIRDLLQCD--- 152

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRER 268
            E+   EK E K     L   + +L+ RE  I   R    Q++ +T + +++   +SR  
Sbjct: 153 -EESATEKIEHKEHVAQLYHYLHMLDERELEIVTLRYGLNQQDALTQKEIAARLNISRSY 211

Query: 269 VRQIEARA-------FKKVQESIQ 285
           V +IE RA       +K+ Q+SI+
Sbjct: 212 VSRIEKRALIKLYQLYKRDQKSIE 235


>gi|305644360|gb|ADM53781.1| RNA polymerase sigma factor [Aeromonas hydrophila]
 gi|305644362|gb|ADM53782.1| RNA polymerase sigma factor [Aeromonas hydrophila]
          Length = 176

 Score = 45.8 bits (107), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 47/194 (24%), Positives = 81/194 (41%), Gaps = 28/194 (14%)

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I    +       L R+  
Sbjct: 1   GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI--PVHMIETINKLNRISR 58

Query: 145 HLQAITDNNLKPEQVV--------AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
            +         PE++          I K L +++ E ISM   +  DE            
Sbjct: 59  QMLQEMGREPNPEELAMRMGMPEDKIRKVLKIAK-EPISMETPIGDDE------------ 105

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVT 254
            S   D++    D    +  +    ++ RN     ++ L  RE ++   R   +     T
Sbjct: 106 DSHLGDFI---EDTTLALPADAATSESLRNATREVLAGLTAREAKVLRMRFGIDMNTDHT 162

Query: 255 LENLSSEFEVSRER 268
           LE +  +F+V+RER
Sbjct: 163 LEEVGKQFDVTRER 176


>gi|150390456|ref|YP_001320505.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Alkaliphilus
           metalliredigens QYMF]
 gi|149950318|gb|ABR48846.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Alkaliphilus
           metalliredigens QYMF]
          Length = 243

 Score = 45.8 bits (107), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 60/254 (23%), Positives = 119/254 (46%), Gaps = 31/254 (12%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMG--YRGYG--LPISEVVSEGNIGLMQAVKK 92
           L + Y+++ DL   + L+  ++ LV KI  G  Y  YG  +   ++VS G  GL+ A++K
Sbjct: 6   LWQHYKQNHDLQTKNELIEKYIALV-KIIAGRLYTSYGSNVDYDDLVSYGIFGLIDAIEK 64

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITD 151
           FD  +  +  TY+   I+ A+ +  LR+   V        K++     + +  L +++ D
Sbjct: 65  FDINKNVKFETYAQIRIRGAIIDQ-LRNLDWVPRSIRQKSKKIEDAYAKAENRLGRSVLD 123

Query: 152 NNLKPEQVVAIA---KKL-NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
             +  E  ++I    + L  ++   ++S+  RL+  ++ +  I   D+N           
Sbjct: 124 FEVAQELEMSIGDFHRTLQQINSFNIVSLEERLS--DTHHNQIPIGDEN----------- 170

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            D  EQ++  KEER     +L  S+  L+ RE+ +      +    T + +    +VS  
Sbjct: 171 -DLPEQIICNKEERL----LLRSSIESLSEREKTVVTLYYYE--GFTYKEIGQVLDVSES 223

Query: 268 RVRQIEARAFKKVQ 281
           RV Q+ ++A  +++
Sbjct: 224 RVSQLHSKAIVRLK 237


>gi|311894139|dbj|BAJ26547.1| putative RNA polymerase sigma factor [Kitasatospora setae KM-6054]
          Length = 281

 Score = 45.8 bits (107), Expect = 0.007,   Method: Compositional matrix adjust.
 Identities = 57/217 (26%), Positives = 96/217 (44%), Gaps = 24/217 (11%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQK 133
           + ++V  G +GL++AV  FDP+RG    TY++  I   ++ +    SW L ++  +  Q+
Sbjct: 56  LDDIVQVGTVGLIKAVDGFDPDRGVEFVTYAIPTISGEIKRFFRDTSWPL-RVPRSV-QE 113

Query: 134 RLFFNLR---RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNA 188
           R    +R   RL+  L  + D          +A +L+V+E E        RL   +SL++
Sbjct: 114 RYLAAVRASDRLEQALGRLPDT-------AELAAELHVTEDEAAEGLEAGRLCRCDSLDS 166

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
           L    D  S      L+    G +  L    E    R M T  +S L  RER +   R  
Sbjct: 167 L---RDDGSDDAGSALINRLGGCDPEL----EVAELRVMATPFLSRLPERERTVLLLRFW 219

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
               +T   +++   VS+  V +I A     ++E I+
Sbjct: 220 --GGLTQSEIAARIGVSQMHVSRILAATLAGLRERIE 254


>gi|256784015|ref|ZP_05522446.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
          Length = 266

 Score = 45.8 bits (107), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 55/257 (21%), Positives = 108/257 (42%), Gaps = 45/257 (17%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           EH +L    R+V + L +  ++A  +R  G    ++     +GL++AV ++DPERG    
Sbjct: 32  EHDELR--DRIVEAWLPMAERLAGRFRSRGESFEDLRQVAALGLVKAVDRYDPERGNAFE 89

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           +Y++  I   ++ +       + +     + R   N  R  G   + T    +P  V  I
Sbjct: 90  SYAVPTITGEIKRHFRDHMWTLHVPRRVQELR---NRVRFAGQDLSQTIPGRRP-TVAEI 145

Query: 163 AKKLNVSESEV------------ISMNCRLAGDE---SLNALINSSDKNSSQWQDWLVYD 207
           A++  +SE +V            +S++  L G E   SL   + + D             
Sbjct: 146 AERAELSEEDVRVGLEALESFTALSLDAELPGSEDGYSLGDALGAPDPALD--------- 196

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
                  ++++E  K+R       ++ L PRER I   R   +  +T   ++ +  +S+ 
Sbjct: 197 ------TVVDREAVKDR-------LAALPPRERAILYMRFFDD--MTQSRIAEQLGISQM 241

Query: 268 RVRQIEARAFKKVQESI 284
            V ++  R   +V+E +
Sbjct: 242 HVSRLITRCCDRVREQV 258


>gi|317470325|ref|ZP_07929717.1| RNA polymerase sigma-G factor [Anaerostipes sp. 3_2_56FAA]
 gi|316902189|gb|EFV24111.1| RNA polymerase sigma-G factor [Anaerostipes sp. 3_2_56FAA]
          Length = 258

 Score = 45.8 bits (107), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 63/264 (23%), Positives = 117/264 (44%), Gaps = 33/264 (12%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L  +E+  L  R  E GD  A  + +  +LRLV+ +   + G      ++   G IG
Sbjct: 16  LPLLTNEEKEELFIRI-EQGDQEAREQYIKGNLRLVLSVIQRFSGSNENADDLFQVGCIG 74

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           LM+A+  FD     + +TY++  I   ++ Y+  +          N  R+  +LR +   
Sbjct: 75  LMKAIDNFDRSLNVKFSTYAVPMIIGEVRRYLRDN----------NSMRVSRSLRDIA-- 122

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSES-EVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            +AIT          A+ KK N   + E I+    +  ++ L AL ++     S ++   
Sbjct: 123 YKAITAKE-------ALTKKFNKEPTIEAIAEEIEMKKEDVLFAL-DAIATPLSLYEP-- 172

Query: 205 VYDHDGQEQVLIEK-EERKNRRNM------LTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           VY   G    L+++ +++KN+  +      L  +M  L  RE  I   R       T   
Sbjct: 173 VYQDGGDTLFLMDQVKDKKNKEELWVESIALKDAMEHLPEREYNIIRLRFFDGKTQT--E 230

Query: 258 LSSEFEVSRERVRQIEARAFKKVQ 281
           ++ E  +S+ +V ++E  A K ++
Sbjct: 231 VADEISISQAQVSRLEKNALKHMK 254


>gi|240146182|ref|ZP_04744783.1| RNA polymerase sigma-F factor [Roseburia intestinalis L1-82]
 gi|257201716|gb|EEV00001.1| RNA polymerase sigma-F factor [Roseburia intestinalis L1-82]
 gi|291536709|emb|CBL09821.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase
           sigma-70 factor, sigma-B/F/G subfamily [Roseburia
           intestinalis M50/1]
          Length = 248

 Score = 45.8 bits (107), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 54/215 (25%), Positives = 96/215 (44%), Gaps = 34/215 (15%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A   L+  +L LV  IA  +   G    E+   G IGLM+AV KFD       +TY
Sbjct: 14  GDKGARDTLIAGNLGLVHTIANRFEHRGHEREELFQIGCIGLMKAVDKFDLSLNLAFSTY 73

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           ++  I   ++ + LR   +VK+  T  +    +   R K  L    +   +P  ++ IA+
Sbjct: 74  AVPVIMGEIRRF-LRDDGMVKVSRTLKENA--YKAGRAKEELWG--ELGREP-GLLEIAE 127

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK--EERK 222
           +  +S  E+I               + S+    S +Q   VY+ DG E +++++  E+ +
Sbjct: 128 RTGLSSGEII-------------MAMESARDVESIYQP--VYEKDGDELLMVDQLCEKEE 172

Query: 223 NRRN-----------MLTRSMSVLNPRERRIFEAR 246
           N R+           ++ + M +L+ RE+ +   R
Sbjct: 173 NGRDEPEKEAVLNRMVIEQLMELLDEREQNLIRCR 207


>gi|219129831|ref|XP_002185083.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217403578|gb|EEC43530.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 435

 Score = 45.8 bits (107), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 18/50 (36%), Positives = 35/50 (70%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           +++ EG IGL +AV +++PE G + +TY+++W++AA+   I     LV++
Sbjct: 184 DLIQEGAIGLARAVDRWNPEIGGKFSTYAVYWVRAAILRCIAERDDLVRV 233


>gi|149174362|ref|ZP_01852989.1| probable RNA polymerase sigma 70 [Planctomyces maris DSM 8797]
 gi|148846907|gb|EDL61243.1| probable RNA polymerase sigma 70 [Planctomyces maris DSM 8797]
          Length = 309

 Score = 45.8 bits (107), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 18/49 (36%), Positives = 30/49 (61%)

Query: 57  HLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           ++RLV  I       G+   E+ S+G + +++A+ KFD  RGFR +TY+
Sbjct: 134 NMRLVASIVKKCTTTGVSFDELFSDGCLTMLKAIDKFDYSRGFRFSTYA 182


>gi|20151162|pdb|1L0O|C Chain C, Crystal Structure Of The Bacillus Stearothermophilus Anti-
           Sigma Factor Spoiiab With The Sporulation Sigma Factor
           Sigmaf
          Length = 243

 Score = 45.8 bits (107), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 38/146 (26%), Positives = 69/146 (47%), Gaps = 7/146 (4%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           ++ QE   L +R +E GD  A   ++  ++RLV  +   +   G    ++   G IGL++
Sbjct: 10  IKDQEMKELIRRSQE-GDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLK 68

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           +V KFD     + +TY++  I   +Q + LR    VK+  +   K +   +R+ K  L  
Sbjct: 69  SVDKFDLSYDVKFSTYAVPMIIGEIQRF-LRDDGTVKVSRSL--KEMGNKIRKAKDEL-- 123

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVI 174
            +    +   V  IA  L +S  +V+
Sbjct: 124 -SKTRGRAPTVTEIADHLGISPEDVV 148


>gi|302389825|ref|YP_003825646.1| RNA polymerase, sigma subunit, RpoX/SigF [Thermosediminibacter
           oceani DSM 16646]
 gi|302200453|gb|ADL08023.1| RNA polymerase, sigma subunit, RpoX/SigF [Thermosediminibacter
           oceani DSM 16646]
          Length = 241

 Score = 45.8 bits (107), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 27/81 (33%), Positives = 45/81 (55%), Gaps = 1/81 (1%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L K+ +E GD  A   LV+ +L LV  I   +   G  I ++   G+IGL++A++KFD  
Sbjct: 9   LLKKAKE-GDQEAKSELVSLNLGLVWSIVKRFTNRGYEIEDLFQIGSIGLLKAIEKFDFS 67

Query: 97  RGFRLATYSMWWIKAAMQEYI 117
              + +TY++  I   ++ YI
Sbjct: 68  YNVKFSTYAVPMIIGEIRRYI 88


>gi|49480184|ref|YP_035252.1| RNA polymerase sigma factor SigB [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|49331740|gb|AAT62386.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           konkukian str. 97-27]
          Length = 258

 Score = 45.8 bits (107), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 60/271 (22%), Positives = 129/271 (47%), Gaps = 29/271 (10%)

Query: 22  EIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           EI+  P  L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++ 
Sbjct: 3   EIQSQPTNLTKEDVIKLIAEFQQNQCDEAQERLVDHYKNLVYSIAYRYSKGGPMHEDIIQ 62

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNL 139
            G +GL+ A++++D   G     +++  I   +++Y+  ++W +       +  R   +L
Sbjct: 63  VGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGI-------HVPRRIKDL 115

Query: 140 -RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNALI-NS 192
             ++K  ++ +TD+  +  +++ IA  L +SE EV+ +     N R++   SL+ ++ N+
Sbjct: 116 GGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVS---SLDDVVENA 172

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
           SD +S    + +     G E+          RR +L    +VLN  E+ +     + E  
Sbjct: 173 SDGSSVARIESVGEVEQGYEET--------ERRLVLKDIFNVLNETEKSVI--HYIFEEN 222

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +  ++      +S+  V +I+ +A  K++++
Sbjct: 223 LNQKDTGERLGISQMHVSRIKRQAISKLKQA 253


>gi|221639440|ref|YP_002525702.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Rhodobacter
           sphaeroides KD131]
 gi|221160221|gb|ACM01201.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Rhodobacter
           sphaeroides KD131]
          Length = 239

 Score = 45.8 bits (107), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 52/236 (22%), Positives = 112/236 (47%), Gaps = 22/236 (9%)

Query: 52  RLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           RLV +H+ LV +IA       G  + I +++  G +GL+ A ++++P  G   A Y+   
Sbjct: 16  RLVRAHMDLVRRIAWNLHARIGRKVEIDDLIQVGYMGLVDASRRYEPREGVTFAAYAAIR 75

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ ++ ++ LRS S +   T   Q+++   ++RL+G L       ++  +   +A +L++
Sbjct: 76  IRGSIMDF-LRSNSALCRTTILMQQKVKAAVQRLEGRL-------MRAPETPEVAAELSM 127

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              E      + AG ++  +L    D  S+     L   HD   +   ++ +    R +L
Sbjct: 128 PVGEYQDWLAQFAGSQT-ASLDEVYDDQSA-----LFEGHDPSAE---DRLQASQMRGLL 178

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +++  +  RE  + +   ++E  + +  +     V+  RV QI+  A ++++  I
Sbjct: 179 RQALGRMPEREALLLQLIFVEE--LNVYEVGEILGVTTGRVSQIKKAAIERLRSLI 232


>gi|154503257|ref|ZP_02040317.1| hypothetical protein RUMGNA_01081 [Ruminococcus gnavus ATCC 29149]
 gi|153796251|gb|EDN78671.1| hypothetical protein RUMGNA_01081 [Ruminococcus gnavus ATCC 29149]
          Length = 238

 Score = 45.8 bits (107), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 49/239 (20%), Positives = 113/239 (47%), Gaps = 16/239 (6%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           +GD  A  +LV  ++ L+  +   + G G+   ++   G+IGL++A+ KFD     + +T
Sbjct: 13  NGDKEAREQLVEENIGLIWCVVKRFYGRGIEAEDLFQIGSIGLIKAIDKFDLSYDVKFST 72

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y++  I   ++ + LR   ++K+  + + K L + + + +   + +TD   +   +  ++
Sbjct: 73  YAVPMISGEIKRF-LRDDGMIKV--SRSLKELSYRIFQTR---EKMTDGLGREPTLEELS 126

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           +++ V + E++         ESL   I+  + +     D L      +E++L        
Sbjct: 127 QEMGVEKEELVQAMEASGEVESLYRPIHQKEGSEISLLDKLEEKEHREEKIL-------- 178

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            R +L + +  L+ +ER +   R   E   T   +  E  +S+ +V ++E +  + ++E
Sbjct: 179 DRMLLGQLLEKLDGQERTLIYLRYFAEK--TQSAVGKEMGISQVQVSRMEKKIIQNLRE 235


>gi|330983153|gb|EGH81256.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. aptata
           str. DSM 50252]
          Length = 70

 Score = 45.8 bits (107), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 23/57 (40%), Positives = 35/57 (61%)

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L +++ VL+ R R I   R L E   TL +L+ ++ VS ER+RQ+E  A  K++ SI
Sbjct: 12  LHQALDVLDERSRDILYQRWLAEEKATLHDLAQKYNVSAERIRQLEKSAMNKLKTSI 68


>gi|167748837|ref|ZP_02420964.1| hypothetical protein ANACAC_03611 [Anaerostipes caccae DSM 14662]
 gi|167651807|gb|EDR95936.1| hypothetical protein ANACAC_03611 [Anaerostipes caccae DSM 14662]
          Length = 275

 Score = 45.8 bits (107), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 63/264 (23%), Positives = 117/264 (44%), Gaps = 33/264 (12%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L  +E+  L  R  E GD  A  + +  +LRLV+ +   + G      ++   G IG
Sbjct: 33  LPLLTNEEKEELFIRI-EQGDQEAREQYIKGNLRLVLSVIQRFSGSNENADDLFQVGCIG 91

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           LM+A+  FD     + +TY++  I   ++ Y+  +          N  R+  +LR +   
Sbjct: 92  LMKAIDNFDRSLNVKFSTYAVPMIIGEVRRYLRDN----------NSMRVSRSLRDIA-- 139

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSES-EVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            +AIT          A+ KK N   + E I+    +  ++ L AL ++     S ++   
Sbjct: 140 YKAITAKE-------ALTKKFNKEPTIEAIAEEIEMKKEDVLFAL-DAIATPLSLYEP-- 189

Query: 205 VYDHDGQEQVLIEK-EERKNRRNM------LTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           VY   G    L+++ +++KN+  +      L  +M  L  RE  I   R       T   
Sbjct: 190 VYQDGGDTLFLMDQVKDKKNKEELWVESIALKDAMEHLPEREYNIIRLRFFDGKTQT--E 247

Query: 258 LSSEFEVSRERVRQIEARAFKKVQ 281
           ++ E  +S+ +V ++E  A K ++
Sbjct: 248 VADEISISQAQVSRLEKNALKHMK 271


>gi|219670064|ref|YP_002460499.1| sporulation sigma factor SigG [Desulfitobacterium hafniense DCB-2]
 gi|219540324|gb|ACL22063.1| RNA polymerase, sigma 28 subunit, SigG [Desulfitobacterium
           hafniense DCB-2]
          Length = 257

 Score = 45.8 bits (107), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 38/150 (25%), Positives = 73/150 (48%), Gaps = 7/150 (4%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L   +   L   Y + G+  A  +L+  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLSSAKMKELFVAY-QSGEKEAREKLIYGNLRLVLSVIQRFTNRGEYVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A+  FD  +  + +TY++  I   ++ Y LR  + +++  +          + L+ 
Sbjct: 74  GLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSLRD----IAYKALQV 128

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVI 174
             Q + + + +P  V  IA KL +   EVI
Sbjct: 129 RDQLVNECSREP-TVSEIADKLTLPREEVI 157


>gi|143615|gb|AAA22791.1| sporulation protein [Bacillus subtilis]
          Length = 195

 Score = 45.8 bits (107), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 46/188 (24%), Positives = 79/188 (42%), Gaps = 21/188 (11%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           ++GD  A   L+  ++RLV  +   +   G    ++   G IGL+++V KFD     R +
Sbjct: 27  QNGDQQARDLLIEKNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKSVDKFDLTYDVRFS 86

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I   +Q +I R    VK+  +   K L   +RR K  L        +   V  I
Sbjct: 87  TYAVPMIIGEIQRFI-RDDGTVKVSRSL--KELGNKIRRAKDELSKTLG---RVPTVQEI 140

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A  L +   +V+     +    S++                 VY++DG    L+ K    
Sbjct: 141 ADHLEIEAEDVVLAQEAVRAPSSIHE---------------TVYENDGDPITLLIKSLTT 185

Query: 223 NRRNMLTR 230
            ++N LT+
Sbjct: 186 QKKNGLTK 193


>gi|52081127|ref|YP_079918.1| sporulation sigma factor SigK [Bacillus licheniformis ATCC 14580]
 gi|52786504|ref|YP_092333.1| sporulation sigma factor SigK [Bacillus licheniformis ATCC 14580]
 gi|52004338|gb|AAU24280.1| RNA polymerase sporulation-specific sigma factor [Bacillus
           licheniformis ATCC 14580]
 gi|52349006|gb|AAU41640.1| SpoIIIC [Bacillus licheniformis ATCC 14580]
          Length = 241

 Score = 45.8 bits (107), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 3/74 (4%)

Query: 39  KRYRE---HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           K+Y E    GD  A + L+  +LRLV  I   +   G    +++S G IGL++A++ +  
Sbjct: 37  KKYLELMAQGDEHARNMLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIESYSA 96

Query: 96  ERGFRLATYSMWWI 109
            +G +LATY+   I
Sbjct: 97  GKGTKLATYAARCI 110


>gi|306821834|ref|ZP_07455426.1| RNA polymerase sigma-B factor [Eubacterium yurii subsp. margaretiae
           ATCC 43715]
 gi|304550141|gb|EFM38140.1| RNA polymerase sigma-B factor [Eubacterium yurii subsp. margaretiae
           ATCC 43715]
          Length = 268

 Score = 45.8 bits (107), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 53/265 (20%), Positives = 114/265 (43%), Gaps = 48/265 (18%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y E  D++  + L+  +L +   ++  Y   G+   ++    ++GL+ A++++D  +GF 
Sbjct: 33  YSEKRDIAIRNELIQRNLYIAEILSKKYINKGIEYEDIYQVASLGLIYAIERYDITKGFE 92

Query: 101 LATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
            ++++   I   +++Y   + WS   I      + L   +  +K  LQ  T    K  ++
Sbjct: 93  FSSFATPTIIGEIKKYFRDKGWS---IRVPRRIQELSKRVNTVKNELQQETH---KTPRI 146

Query: 160 VAIAKKLNVSESEV------------ISMNCRLAG-----DESLNALINSSDKNSSQWQD 202
             IA+KL +++ EV            IS++ +        D +L+ LI   DK+ ++ +D
Sbjct: 147 SDIAEKLGITQEEVLETMDAAGAYAPISLDVKYDNEGEDKDVALHELIGKDDKSFAEIED 206

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
                                  + L   M  L+  E++I   R       T   ++ E 
Sbjct: 207 G----------------------DFLRNVMESLSEVEKKIIMDRYFDNK--TQMTVAKEL 242

Query: 263 EVSRERVRQIEARAFKKVQESIQKQ 287
           ++S+  V ++E +   K+++  +KQ
Sbjct: 243 DISQMTVSRMEKKILTKLKKEYEKQ 267


>gi|261405990|ref|YP_003242231.1| sporulation sigma factor SigF [Paenibacillus sp. Y412MC10]
 gi|329929773|ref|ZP_08283449.1| RNA polymerase sigma-F factor [Paenibacillus sp. HGF5]
 gi|261282453|gb|ACX64424.1| RNA polymerase, sigma 28 subunit, SigF [Paenibacillus sp. Y412MC10]
 gi|328935751|gb|EGG32212.1| RNA polymerase sigma-F factor [Paenibacillus sp. HGF5]
          Length = 251

 Score = 45.8 bits (107), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 56/251 (22%), Positives = 114/251 (45%), Gaps = 32/251 (12%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A   LV  ++RLV  +   +   G    ++   G IGL+++V KFD     + +
Sbjct: 26  QSGDNVARDTLVNCNIRLVWSVVQRFMNRGYEPDDLFQIGCIGLLKSVDKFDLSYDVKFS 85

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I   +Q + LR    +K+  +   K +   +R+ +  L    D   +   V  +
Sbjct: 86  TYAVPMIIGEIQRF-LRDDGTLKVSRSL--KEMANKVRKKRDELSKQLD---RLPTVKEV 139

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ-----EQVLIE 217
           A++L V+  EV+                  ++K  +   +  V+++DG      +Q+  +
Sbjct: 140 AEELGVTPEEVV--------------FAQEANKPPTSIHE-TVFENDGDPITLMDQIADD 184

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
            +ER   +  L  ++  L  RER I   R  ++   T   +++   +S+ +V ++E    
Sbjct: 185 SQERWFDKLALNEAIGGLTERERLIVYLRYYRDQ--TQSEVATRLGISQVQVSRLE---- 238

Query: 278 KKVQESIQKQV 288
           KK+ +SI+ ++
Sbjct: 239 KKILQSIRNEI 249


>gi|319651643|ref|ZP_08005770.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
 gi|317396710|gb|EFV77421.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
          Length = 239

 Score = 45.8 bits (107), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 22/65 (33%), Positives = 37/65 (56%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A + L+  +LRLV  I   +   G    +++S G IGL++A++ +   +G +LATY
Sbjct: 46  GDAHARNMLIEHNLRLVAHIVKKFENTGEDSEDLISIGTIGLIKAIESYSEGKGTKLATY 105

Query: 105 SMWWI 109
           +   I
Sbjct: 106 AARCI 110


>gi|299535719|ref|ZP_07049040.1| RNA polymerase sigma-28 factor precursor [Lysinibacillus fusiformis
           ZC1]
 gi|298728919|gb|EFI69473.1| RNA polymerase sigma-28 factor precursor [Lysinibacillus fusiformis
           ZC1]
          Length = 235

 Score = 45.8 bits (107), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 60/252 (23%), Positives = 101/252 (40%), Gaps = 63/252 (25%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K+EE    +R+   GD  A   L+  ++RLV  +   +      + + +S G IGLM+AV
Sbjct: 33  KEEEAACIERFLG-GDEQARLDLIERNMRLVAHVVKKFHPKHEQLDDYISIGTIGLMKAV 91

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           + + P++  RLATY+   I                      +  +  +LR  K       
Sbjct: 92  ESYTPDKKTRLATYAARCI----------------------ENEILMHLRTQK------- 122

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
                      + K +++ E         +  D+  NAL         Q +D L  D   
Sbjct: 123 ----------KVQKDVSLFEP--------IGTDKDGNAL---------QIRDLLQCD--- 152

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRER 268
            E+   EK E K     L   + +L+ RE  I   R    Q++ +T + +++   +SR  
Sbjct: 153 -EESATEKLEHKEHVAQLYHYLHMLDERELEIVTLRYGLNQQDALTQKEIAARLNISRSY 211

Query: 269 VRQIEARAFKKV 280
           V +IE RA  K+
Sbjct: 212 VSRIEKRALIKL 223


>gi|289767896|ref|ZP_06527274.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
 gi|289698095|gb|EFD65524.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
          Length = 270

 Score = 45.8 bits (107), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 55/257 (21%), Positives = 108/257 (42%), Gaps = 45/257 (17%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           EH +L    R+V + L +  ++A  +R  G    ++     +GL++AV ++DPERG    
Sbjct: 36  EHDELR--DRIVEAWLPMAERLAGRFRSRGESFEDLRQVAALGLVKAVDRYDPERGNAFE 93

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           +Y++  I   ++ +       + +     + R   N  R  G   + T    +P  V  I
Sbjct: 94  SYAVPTITGEIKRHFRDHMWTLHVPRRVQELR---NRVRFAGQDLSQTIPGRRP-TVAEI 149

Query: 163 AKKLNVSESEV------------ISMNCRLAGDE---SLNALINSSDKNSSQWQDWLVYD 207
           A++  +SE +V            +S++  L G E   SL   + + D             
Sbjct: 150 AERAELSEEDVRVGLEALESFTALSLDAELPGSEDGYSLGDALGAPDPALD--------- 200

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
                  ++++E  K+R       ++ L PRER I   R   +  +T   ++ +  +S+ 
Sbjct: 201 ------TVVDREAVKDR-------LAALPPRERAILYMRFFDD--MTQSRIAEQLGISQM 245

Query: 268 RVRQIEARAFKKVQESI 284
            V ++  R   +V+E +
Sbjct: 246 HVSRLITRCCDRVREQV 262


>gi|302522454|ref|ZP_07274796.1| RNA polymerase sigma-F factor [Streptomyces sp. SPB78]
 gi|302431349|gb|EFL03165.1| RNA polymerase sigma-F factor [Streptomyces sp. SPB78]
          Length = 297

 Score = 45.8 bits (107), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 55/218 (25%), Positives = 101/218 (46%), Gaps = 23/218 (10%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL++A+ +FD  R     ++++ +I   ++ Y   S   V +     + R
Sbjct: 91  MEDILQVGTIGLIKAIDRFDLTREAEFTSFAIPYIVGEIKRYFRDSTWAVHVPRRLQELR 150

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG--DESLNALINS 192
           +  +L R K  L    D +     V  +A +L +SE EVI       G   +SL+   +S
Sbjct: 151 V--DLARAKERLAVELDRD---PGVKELAAELGISEEEVIDGLIAANGYMSDSLDLPADS 205

Query: 193 SD------KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           S       K ++ + D+L  D D   +++   E     R +L      L+ RER + E R
Sbjct: 206 STSGKPDQKTATTYADFL-GDWDPAMELV---ENFTALRPLL----GTLDDRERYLLELR 257

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             QE  +T   + +E  VS+  V ++ +R   K++E +
Sbjct: 258 FGQE--LTQAQIGAELGVSQMHVSRLLSRTLGKLREGL 293


>gi|306410397|gb|ADM85820.1| RNA polymerase essential primary sigma 70 factor [Frankia alni]
 gi|306410399|gb|ADM85821.1| RNA polymerase essential primary sigma 70 factor [Frankia alni]
 gi|306410401|gb|ADM85822.1| RNA polymerase essential primary sigma 70 factor [Frankia alni]
 gi|306410403|gb|ADM85823.1| RNA polymerase essential primary sigma 70 factor [Frankia alni]
 gi|306410405|gb|ADM85824.1| RNA polymerase essential primary sigma 70 factor [Frankia sp. CcI3]
 gi|306410407|gb|ADM85825.1| RNA polymerase essential primary sigma 70 factor [Frankia sp. CpI1]
 gi|306410409|gb|ADM85826.1| RNA polymerase essential primary sigma 70 factor [Frankia sp.
           Cj1-82]
          Length = 106

 Score = 45.8 bits (107), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 32/110 (29%), Positives = 58/110 (52%), Gaps = 13/110 (11%)

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TAN-----QKR 134
           +GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I      T N     Q++
Sbjct: 1   LGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRIQRQ 60

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           L  +L R     +   + +L P++V  I   L VS+ E +S+   +  +E
Sbjct: 61  LLQDLGREPSPEEIAKEMDLTPDKVREI---LKVSQ-EPVSLETPIGEEE 106


>gi|296133159|ref|YP_003640406.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           sp. JR]
 gi|296031737|gb|ADG82505.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           potens JR]
          Length = 260

 Score = 45.8 bits (107), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 31/112 (27%), Positives = 58/112 (51%), Gaps = 6/112 (5%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           + P+L  +E   L  + + +GD +A  +LV  +L+LV  +   +   G    ++   G I
Sbjct: 12  RFPLLSDKEMKELLIKAK-NGDQAAREKLVNCNLKLVFNLVQRFCNRGYEPEDLFQIGTI 70

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG----TTANQ 132
           GL++A+ KFD     + +TY++  I   ++ + LR  + VK+      TAN+
Sbjct: 71  GLIKAIDKFDLSYDVKFSTYAVPLIIGEIRRF-LRDDNPVKVSRSVKETANK 121


>gi|291537993|emb|CBL11104.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase
           sigma-70 factor, sigma-B/F/G subfamily [Roseburia
           intestinalis XB6B4]
          Length = 248

 Score = 45.8 bits (107), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 56/215 (26%), Positives = 93/215 (43%), Gaps = 34/215 (15%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A   L+  +L LV  IA  +   G    E+   G IGLM+AV KFD       +TY
Sbjct: 14  GDKGARDTLIAGNLGLVHTIANRFEHRGHEREELFQIGCIGLMKAVDKFDLSLNLAFSTY 73

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           ++  I   ++ + LR   +VK+  T  +    +   R K  L    +   +P  ++ IA+
Sbjct: 74  AVPVIMGEIRRF-LRDDGMVKVSRTLKENA--YKAGRAKEELWG--ELGREP-GLLEIAE 127

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI----EKEE 220
           +  +S  E+I               + S+    S +Q   VY+ DG E +++    EKEE
Sbjct: 128 RTGLSSGEII-------------MAMESARDVESIYQP--VYEKDGDELLMVDQLCEKEE 172

Query: 221 RKN---------RRNMLTRSMSVLNPRERRIFEAR 246
                        R ++ + M +L+ RE+ +   R
Sbjct: 173 NGKDEPEKEAVLNRMVIEQLMELLDEREQNLIRCR 207


>gi|89100825|ref|ZP_01173677.1| SpoIIIC [Bacillus sp. NRRL B-14911]
 gi|89084471|gb|EAR63620.1| SpoIIIC [Bacillus sp. NRRL B-14911]
          Length = 240

 Score = 45.8 bits (107), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 23/70 (32%), Positives = 38/70 (54%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R    GD  A + L+  +LRLV  I   +   G    +++S G IGL++A++ +   +G 
Sbjct: 41  RLMAEGDAHARNMLIEHNLRLVAHIVKKFENTGEDSEDLISIGTIGLIKAIESYSEGKGT 100

Query: 100 RLATYSMWWI 109
           +LATY+   I
Sbjct: 101 KLATYAARCI 110


>gi|258592481|emb|CBE68790.1| RNA polymerase sigma factor whiG (modular protein) [NC10 bacterium
           'Dutch sediment']
          Length = 459

 Score = 45.4 bits (106), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 61/248 (24%), Positives = 109/248 (43%), Gaps = 17/248 (6%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFD 94
           K YR+  D     RL+T+++ LV ++A G     LP    + ++ S G +GL+ AV+ +D
Sbjct: 9   KAYRQTKDPGLRDRLITANISLVRQVA-GRLSLQLPSCVELDDLESAGAVGLVSAVEHYD 67

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P++    ATY+ + I+ A+ +  LR+         A  + +   L RL+       D   
Sbjct: 68  PDQPSEFATYAQYRIRGAILDD-LRAQDFAPRSLRAKAREIQQTLVRLE------VDLGR 120

Query: 155 KP-EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
           +P +  VA A  ++           R     SL+     +D   S    W + D  G++ 
Sbjct: 121 EPSDDEVAAALGMDRETYWRTLGEIRGMVLVSLDEPGVEADGTESDRLIWELPDRAGRDP 180

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
               +  R+ R  +L   +  L  +ER +      +E  +T++ +    EVS  RV QI 
Sbjct: 181 S--TEAARRERVRLLGGIIEALPAQERLVLTLYYFEE--LTMKEIGRVLEVSESRVSQIH 236

Query: 274 ARAFKKVQ 281
             A  +++
Sbjct: 237 TSAILRMR 244


>gi|15613092|ref|NP_241395.1| RNA polymerase sigma factor SigB [Bacillus halodurans C-125]
 gi|10173142|dbj|BAB04248.1| RNA polymerase general stress sigma factor(sigma B) [Bacillus
           halodurans C-125]
          Length = 261

 Score = 45.4 bits (106), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 60/261 (22%), Positives = 124/261 (47%), Gaps = 18/261 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           E Y   + Y++  D     +LV  +  LV  +A  +        +++  G +GL+ A ++
Sbjct: 14  EVYDWIESYQQGADEEIQTKLVKHYEPLVHSLARKFSRSRAHDDDLIQVGMVGLLAAFER 73

Query: 93  FDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           +DP+ G    ++++  I   ++ +I  ++WS   +      K L   +++    L +   
Sbjct: 74  YDPKYGRSFESFAVPTIIGEIKRFIRDKTWS---VHVPRRIKELGPKIKKAADELASELQ 130

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDG 210
            + + E+   IA  L VSE EV+     +   +S  AL ++ S +   +  +  + D  G
Sbjct: 131 RSPRVEE---IADFLGVSEEEVLET---MEMGKSYQALSVDRSLEADPEGGEVTLLDLVG 184

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
           QE    EK    +++ +L ++  VL+ RE++I      +   ++ +       +S+  V 
Sbjct: 185 QEDGGYEK---ADQQMLLEKAFQVLDEREKQILLCTYFEH--LSQKETGHRLGISQMHVS 239

Query: 271 QIEARAFKKVQESIQKQVELS 291
           +++ RA KK+++SI  +VELS
Sbjct: 240 RLQRRALKKLRDSI--RVELS 258


>gi|318059283|ref|ZP_07978006.1| RNA polymerase sigma factor [Streptomyces sp. SA3_actG]
 gi|318075250|ref|ZP_07982582.1| RNA polymerase sigma factor [Streptomyces sp. SA3_actF]
          Length = 294

 Score = 45.4 bits (106), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 55/218 (25%), Positives = 101/218 (46%), Gaps = 23/218 (10%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL++A+ +FD  R     ++++ +I   ++ Y   S   V +     + R
Sbjct: 88  MEDILQVGTIGLIKAIDRFDLTREAEFTSFAIPYIVGEIKRYFRDSTWAVHVPRRLQELR 147

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG--DESLNALINS 192
           +  +L R K  L    D +     V  +A +L +SE EVI       G   +SL+   +S
Sbjct: 148 V--DLARAKERLAVELDRD---PGVKELAAELGISEEEVIDGLIAANGYMSDSLDLPADS 202

Query: 193 SD------KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           S       K ++ + D+L  D D   +++   E     R +L      L+ RER + E R
Sbjct: 203 STSGKPDQKTATTYADFL-GDWDPAMELV---ENFTALRPLL----GTLDDRERYLLELR 254

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             QE  +T   + +E  VS+  V ++ +R   K++E +
Sbjct: 255 FGQE--LTQAQIGAELGVSQMHVSRLLSRTLGKLREGL 290


>gi|317128262|ref|YP_004094544.1| RNA polymerase, sigma 28 subunit, SigK [Bacillus cellulosilyticus
           DSM 2522]
 gi|315473210|gb|ADU29813.1| RNA polymerase, sigma 28 subunit, SigK [Bacillus cellulosilyticus
           DSM 2522]
          Length = 238

 Score = 45.4 bits (106), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 28/85 (32%), Positives = 47/85 (55%), Gaps = 4/85 (4%)

Query: 27  PMLEKQE-EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           P+  K+E EY+   R    GD  A + L+  +LRLV  I   +        +++S G IG
Sbjct: 30  PLNAKEEREYI---RRMNEGDDEARNLLIEHNLRLVAHIVKKFENTREENEDLISIGTIG 86

Query: 86  LMQAVKKFDPERGFRLATYSMWWIK 110
           L++A++ + P +G +LATY+   I+
Sbjct: 87  LIKAIESYSPGKGTKLATYAARCIE 111


>gi|169829306|ref|YP_001699464.1| RNA polymerase sigma-28 factor [Lysinibacillus sphaericus C3-41]
 gi|168993794|gb|ACA41334.1| RNA polymerase sigma-28 factor precursor [Lysinibacillus sphaericus
           C3-41]
          Length = 228

 Score = 45.4 bits (106), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 63/264 (23%), Positives = 107/264 (40%), Gaps = 70/264 (26%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K+EE    +R+   GD  A   L+  ++RLV  +   +      + + +S G IGLM+AV
Sbjct: 26  KEEEAACIERFLG-GDEQARLDLIERNMRLVAHVVKKFHPKHEQLDDYISIGTIGLMKAV 84

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           + + P++  RLATY+   I                      +  +  +LR  K       
Sbjct: 85  ESYTPDKKTRLATYAARCI----------------------ENEILMHLRTQK------- 115

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
                      + K +++ E         +  D+  NAL         Q +D L  D   
Sbjct: 116 ----------KVQKDVSLFEP--------IGTDKDGNAL---------QIRDLLQCD--- 145

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRER 268
            E+   EK E K     L   + +L+ RE  I   R    Q++ +T + +++   +SR  
Sbjct: 146 -EESATEKIEHKEHVAQLYHYLHMLDERELEIVTLRYGLNQQDALTQKEIAARLNISRSY 204

Query: 269 VRQIEARA-------FKKVQESIQ 285
           V +IE RA       +K+ Q+SI+
Sbjct: 205 VSRIEKRALIKLYQLYKRDQKSIE 228


>gi|29830033|ref|NP_824667.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29607143|dbj|BAC71202.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 306

 Score = 45.4 bits (106), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 44/170 (25%), Positives = 76/170 (44%), Gaps = 20/170 (11%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  +L LV   A  +R    P+ +++  G IGL++A+ +F+  RG    T++M  I   
Sbjct: 85  LVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRGVEFPTFAMPTIVGE 144

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL  +L +    L    D   +   V  +A++L +S  
Sbjct: 145 IKRFFRDTSWS-VRVPRRLQELRL--DLAKAGDELAQRLD---RAPTVSELAERLGISNG 198

Query: 172 EVISMNCRLAGDESLNALINSS-------DKNSSQWQDWLVYDHDGQEQV 214
           EV+       G  + NA   SS       D +     D + Y+  G E +
Sbjct: 199 EVVE------GMAASNAYTASSLDAQPEEDDSEGALADRIGYEDHGLEGI 242


>gi|89895640|ref|YP_519127.1| sporulation sigma factor SigG [Desulfitobacterium hafniense Y51]
 gi|89335088|dbj|BAE84683.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 266

 Score = 45.4 bits (106), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 38/150 (25%), Positives = 73/150 (48%), Gaps = 7/150 (4%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L   +   L   Y + G+  A  +L+  +LRLV+ +   +   G  + ++   G I
Sbjct: 24  KLPVLSSAKMKELFVAY-QSGEKEAREKLIYGNLRLVLSVIQRFTNRGEYVDDLFQVGCI 82

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A+  FD  +  + +TY++  I   ++ Y LR  + +++  +          + L+ 
Sbjct: 83  GLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRY-LRDNNPIRVSRSLRD----IAYKALQV 137

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVI 174
             Q + + + +P  V  IA KL +   EVI
Sbjct: 138 RDQLVNECSREP-TVSEIADKLTLPREEVI 166


>gi|239945848|ref|ZP_04697785.1| putative RNA polymerase sigma factor [Streptomyces roseosporus NRRL
           15998]
 gi|239992317|ref|ZP_04712981.1| putative RNA polymerase sigma factor [Streptomyces roseosporus NRRL
           11379]
 gi|291449304|ref|ZP_06588694.1| sigma factor [Streptomyces roseosporus NRRL 15998]
 gi|291352251|gb|EFE79155.1| sigma factor [Streptomyces roseosporus NRRL 15998]
          Length = 298

 Score = 45.4 bits (106), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 60/242 (24%), Positives = 108/242 (44%), Gaps = 22/242 (9%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISE-VVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + L+  +L LV   A  +R  G   +E ++  G IGL++A+ +FD  R    AT+++ 
Sbjct: 69  ARNTLIEMNLSLVRFAASRFRNRGGDDTEDIIQVGTIGLIKAIDRFDLSREVEFATFAVP 128

Query: 108 WIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           +I   ++ +    +WS   +      + L  +L + K  L A  D +     V  +A  L
Sbjct: 129 YIVGEIKRFFRDTTWS---VHVPRRLQELRVDLAKAKEQLSAELDRD---PTVKELATHL 182

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ----DWLVYDHDGQEQVLIEKEERK 222
           ++ E E+I       G  + +    S+D +S Q Q    D L     G E V        
Sbjct: 183 DLPEEEIIEGLVAANGYSAGSLDTPSADSDSGQEQRAYADVLGEADPGMETV-------- 234

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              + L   +  L+ RERRI + R   E  +T   +  E  VS+  V ++ +R  +++++
Sbjct: 235 ENLHTLAPLLEQLDDRERRIVQMRFGAE--MTQSQIGEELGVSQMHVSRLLSRIVQQLRK 292

Query: 283 SI 284
            +
Sbjct: 293 GM 294


>gi|332799203|ref|YP_004460702.1| RNA polymerase sigma-28 subunit FliA/WhiG [Tepidanaerobacter sp.
           Re1]
 gi|332696938|gb|AEE91395.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Tepidanaerobacter sp.
           Re1]
          Length = 246

 Score = 45.4 bits (106), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 47/211 (22%), Positives = 96/211 (45%), Gaps = 32/211 (15%)

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L   +++S G  GLMQA++++D ++G +  TY+   IK ++ +  LR   ++        
Sbjct: 48  LEYEDLISYGVFGLMQAIERYDTKKGIKFETYAYTRIKGSIIDE-LRKTDMIPQDIRKKI 106

Query: 133 KRL---FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA---GDESL 186
           K L   F  + ++ GH  +  D++        I+  L +S+ ++  +   ++   G  S 
Sbjct: 107 KMLQNAFSEMEQILGH--SANDDD--------ISNYLGISKKDLYKIYKEISAAYGVLSF 156

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           + LI   D   +           GQ  +  EKEE K    +L  +++ L P+E+ +    
Sbjct: 157 DELIEYEDVGQAS----------GQPDIQAEKEEVK---EILGNAINQLPPQEKLVITLY 203

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAF 277
             +   +  + ++   E+S+ R+ QI  +A 
Sbjct: 204 YYE--GLNFKEIAEVLELSQGRISQIHTKAI 232


>gi|324325029|gb|ADY20289.1| RNA polymerase sigma factor SigB [Bacillus thuringiensis serovar
           finitimus YBT-020]
          Length = 257

 Score = 45.4 bits (106), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 60/271 (22%), Positives = 129/271 (47%), Gaps = 29/271 (10%)

Query: 22  EIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           EI+  P  L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++ 
Sbjct: 2   EIQSQPTNLTKEDVMKLIAEFQQNQCDEAQERLVEHYKNLVYSIAYRYSKGGPMHEDIIQ 61

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNL 139
            G +GL+ A++++D   G     +++  I   +++Y+  ++W +       +  R   +L
Sbjct: 62  VGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGI-------HVPRRIKDL 114

Query: 140 -RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNALI-NS 192
             ++K  ++ +TD+  +  +++ IA  L +SE EV+ +     N R++   SL+ ++ N+
Sbjct: 115 GGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVS---SLDDVVENA 171

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
           SD +S    + +     G E+          RR +L    +VLN  E+ +     + E  
Sbjct: 172 SDGSSVARIESVGEVEQGYEET--------ERRLVLKDIFNVLNETEKSVI--HYIFEEN 221

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +  ++      +S+  V +I+ +A  K++++
Sbjct: 222 LNQKDTGERLGISQMHVSRIKRQAISKLKQA 252


>gi|254381148|ref|ZP_04996513.1| RNA polymerase sigma factor [Streptomyces sp. Mg1]
 gi|194340058|gb|EDX21024.1| RNA polymerase sigma factor [Streptomyces sp. Mg1]
          Length = 306

 Score = 45.4 bits (106), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 48/218 (22%), Positives = 100/218 (45%), Gaps = 18/218 (8%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           G+ + +V+  G IGL++A+ +FDP+R    +T ++ +I   ++ Y   +   V +     
Sbjct: 99  GIELDDVIQVGTIGLIKAIDRFDPDREVEFSTLALPYITGEIKRYFRDTTWAVHVPRRLQ 158

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG--DESLNAL 189
           + R+      L    + +T+   +   V  IA+ L +SE EVI       G    SL++ 
Sbjct: 159 ELRV-----ELAKCQETLTEVLGRAPSVKEIAEHLELSEEEVIEGLVAANGYSSASLDST 213

Query: 190 INSSDKNSSQWQDWLVYDHDGQ---EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
             ++D+ ++  +   + D  G      VL E        + L   +S L+ R+ +I   R
Sbjct: 214 AGTTDRPAALSEGRPLADTVGDIDPAMVLFEDV------HTLAPLLSELDERDLQILRMR 267

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             +E  +T   + +E  +S+ +V ++  R   +++  +
Sbjct: 268 FARE--MTQAEIGTELGISQMQVSRLLTRILTRLRSGM 303


>gi|182625388|ref|ZP_02953161.1| sigma factor [Clostridium perfringens D str. JGS1721]
 gi|177909385|gb|EDT71837.1| sigma factor [Clostridium perfringens D str. JGS1721]
          Length = 232

 Score = 45.4 bits (106), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 54/248 (21%), Positives = 109/248 (43%), Gaps = 66/248 (26%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLMQAVKKFDPE--R 97
           +HGD  A  +L+ ++ +L+ K+A  +   +   +   +++ EG IG + A  K+D E  +
Sbjct: 16  QHGDKKALDKLLENNDKLIYKVASKFYSDKTSSIEFDDLLQEGRIGFILACSKYDIEYIK 75

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
             +  TY+ +WI   +  +I          TT N                          
Sbjct: 76  KTKFITYAFYWIYQKIHRFI----------TTHNT------------------------- 100

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
                        +E IS+N  ++ +E+ + LINS + +S++ +D        +E+ L  
Sbjct: 101 -------------NEEISLNTPVS-EENQDELINSIESHSNEIKD--------REEELYL 138

Query: 218 KEERKNRRNMLTRSMSVLNPRE-RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
            E R     ++ +  + LN RE  +++      E  ++++ ++  FE S   V+ I+ARA
Sbjct: 139 SELRLELEAVMDKH-NTLNEREILKLYYGWDTDE--LSIDQIADIFETSSSEVKNIKARA 195

Query: 277 FKKVQESI 284
            +K++ S+
Sbjct: 196 IRKLRNSM 203


>gi|302532223|ref|ZP_07284565.1| RNA polymerase sigma-F factor [Streptomyces sp. C]
 gi|302441118|gb|EFL12934.1| RNA polymerase sigma-F factor [Streptomyces sp. C]
          Length = 307

 Score = 45.4 bits (106), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 57/242 (23%), Positives = 110/242 (45%), Gaps = 24/242 (9%)

Query: 53  LVTSHLRLVVKIAMGYR----GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           L+  +L LV   A  +R    G GL + +V+  G IGL++A+ +FD +R    +T ++ +
Sbjct: 77  LIEMNLSLVHYAARRFRARVSGGGLDMDDVIQVGTIGLIKAIDRFDLDREVEFSTLALPY 136

Query: 109 IKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLR-RLKGHLQAITDNNLKPEQVVAIAKKL 166
           I   ++ +    +W++       +  R    LR  L    +++T+   +   V  +A+ L
Sbjct: 137 ITGEIKRHFRDTTWAV-------HVPRRLQELRSELAKAQESLTEALHRAPTVKEVAQHL 189

Query: 167 NVSESEVI----SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
            +SE EVI    + N   +G  SL+    + +   +      + +  G+    +E  E  
Sbjct: 190 GLSEEEVIDGLVAANGYTSG--SLDTADEAEEARGTGRPARALAEKLGESDPAMELFEDF 247

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +    L R    L PRER I   R  QE   T   + +E  +S+ +V ++ +R   +++ 
Sbjct: 248 HTLAPLLRE---LQPRERLILSMRFGQEK--TQAEIGAELHISQMQVSRLLSRTLARLRA 302

Query: 283 SI 284
            +
Sbjct: 303 GM 304


>gi|239628979|ref|ZP_04672010.1| DNA-directed RNA polymerase specialized sigma subunit
           [Clostridiales bacterium 1_7_47_FAA]
 gi|239519125|gb|EEQ58991.1| DNA-directed RNA polymerase specialized sigma subunit
           [Clostridiales bacterium 1_7_47FAA]
          Length = 244

 Score = 45.4 bits (106), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 61/256 (23%), Positives = 114/256 (44%), Gaps = 31/256 (12%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFDPER 97
           YR++G     ++LV  +L +V   A+  R   G  L   ++  +G + LM+ + ++DP +
Sbjct: 4   YRKNGSQELRNKLVLHYLPIVRSAAVQLRTMAGSLLEQEDLTDQGVLALMECLDRYDPGK 63

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL---FFNLRRLKGHLQAITDN-- 152
           G R  TY+   ++ AM +YI RS   V       QK++   F  L   K     + D   
Sbjct: 64  GARFETYAFVRVRGAMIDYI-RSQDWVPHRARNFQKKVDEAFSILSHEKMGEPDVKDVAG 122

Query: 153 --NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
             ++  E+V    K +N   + V+S    L   + + A+    +  +         D DG
Sbjct: 123 YLDMPVEKVENHIKYMN--HASVLSFEAAL---QDMTAIFAKGELEAG--------DMDG 169

Query: 211 Q-EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
           + E+ L  +E       MLT ++  L  +ER +      +E  +    ++    + + RV
Sbjct: 170 KPEESLFYRE----MMEMLTAAIDGLGEKERLVITLYYYEE--LKYSEIAEVMGIGQSRV 223

Query: 270 RQIEARAFKKVQESIQ 285
            QI  +A +K++ S++
Sbjct: 224 CQIHTKAIRKLKSSLE 239


>gi|213422468|ref|ZP_03355534.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. E01-6750]
          Length = 79

 Score = 45.4 bits (106), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 27/61 (44%), Positives = 38/61 (62%), Gaps = 1/61 (1%)

Query: 226 NMLTRSMSVLNPRERRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           N LT +M  L+ R + I  AR L E N  TL+ L+  + VS ERVRQ+E  A KK++ +I
Sbjct: 18  NRLTDAMQGLDERSQDIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAI 77

Query: 285 Q 285
           +
Sbjct: 78  E 78


>gi|257876008|ref|ZP_05655661.1| RNA polymerase sigma factor whiG [Enterococcus casseliflavus EC20]
 gi|257810174|gb|EEV38994.1| RNA polymerase sigma factor whiG [Enterococcus casseliflavus EC20]
          Length = 235

 Score = 45.4 bits (106), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 51/211 (24%), Positives = 96/211 (45%), Gaps = 20/211 (9%)

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA-NQKRLFFNLR 140
           G IGLM A++KFDP +     +Y+   IK A+ + + +   + +    A NQ   F+  R
Sbjct: 40  GVIGLMDALRKFDPSKKVPFESYAAIRIKGAIIDEVRKHAKISRYKMAAVNQ---FYQAR 96

Query: 141 RLKGHLQAITDNNLKPEQV-VAIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNS 197
           +         + +LK E     I K+L +++S++  I  +       SL   + +  +  
Sbjct: 97  QE-------LEQSLKREATDTEICKQLGINQSQLADIYESLHYLASVSLEDTLFAYQEEG 149

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
              +D +    +  E  L+ +E    +R  L   +  L  RE+ I      +E  +TL+ 
Sbjct: 150 MTLKDMVRDPAENVEDTLVAEE----KRTALVACIKKLGEREQLILSLYYTEE--LTLKE 203

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           ++   EVS  RV QI  +   K++  I++++
Sbjct: 204 IAEILEVSIPRVSQIHGKTIAKLRTLIEEEL 234


>gi|77463598|ref|YP_353102.1| sigma factor FliA (sigma-28 group, flagellar) [Rhodobacter
           sphaeroides 2.4.1]
 gi|126462430|ref|YP_001043544.1| FliA/WhiG family RNA polymerase sigma factor [Rhodobacter
           sphaeroides ATCC 17029]
 gi|332558454|ref|ZP_08412776.1| FliA/WhiG family RNA polymerase sigma factor [Rhodobacter
           sphaeroides WS8N]
 gi|77388016|gb|ABA79201.1| sigma factor FliA (Sigma-28 group, flagellar) [Rhodobacter
           sphaeroides 2.4.1]
 gi|126104094|gb|ABN76772.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Rhodobacter
           sphaeroides ATCC 17029]
 gi|332276166|gb|EGJ21481.1| FliA/WhiG family RNA polymerase sigma factor [Rhodobacter
           sphaeroides WS8N]
          Length = 239

 Score = 45.4 bits (106), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 53/243 (21%), Positives = 117/243 (48%), Gaps = 25/243 (10%)

Query: 52  RLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           RLV +H+ LV +IA       G  + I +++  G +GL+ A ++++P  G   A Y+   
Sbjct: 16  RLVRAHMDLVRRIAWNLHARIGRKVEIDDLIQVGYMGLVDASRRYEPREGVSFAAYAAIR 75

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ ++ ++ LRS S +   T   Q+++   ++RL+G L       ++  +   +A +L++
Sbjct: 76  IRGSIMDF-LRSNSALCRTTILMQQKVKAAVQRLEGRL-------MRAPETPEVAAELSM 127

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              E      + AG ++  +L    D  S+     L   HD   +   ++ +    R +L
Sbjct: 128 PVGEYQDWLAQFAGSQT-ASLDEVYDDQSA-----LFEGHDPSAE---DRLQASQMRGLL 178

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ---ESIQ 285
            +++  +  RE  + +   ++E  + +  +     V+  RV QI+  A ++++   +++Q
Sbjct: 179 RQALGRMPEREALLLQLIFVEE--LNVYEVGEILGVTTGRVSQIKKAAIERLRGLIDALQ 236

Query: 286 KQV 288
            +V
Sbjct: 237 GEV 239


>gi|213584001|ref|ZP_03365827.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-0664]
          Length = 148

 Score = 45.4 bits (106), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 44/144 (30%), Positives = 70/144 (48%), Gaps = 27/144 (18%)

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDE--------------SLNALINSSDKNSSQWQD 202
           ++V  +A++L VS  +V  M  R+A  +               +  ++   DK SS + D
Sbjct: 16  DEVEMVARELGVSSKDVREMESRMAAQDMTFDMSSDDESDSQPMAPVLYLQDK-SSNFAD 74

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE-NPVTLENLSSE 261
             + D + +EQ            N LT +M  L+ R + I  AR L E N  TL+ L+  
Sbjct: 75  G-IEDDNWEEQAA----------NRLTDAMQGLDERSQDIIRARWLDEDNKSTLQELADR 123

Query: 262 FEVSRERVRQIEARAFKKVQESIQ 285
           + VS ERVRQ+E  A KK++ +I+
Sbjct: 124 YGVSAERVRQLEKNAMKKLRAAIE 147


>gi|290959865|ref|YP_003491047.1| SigL-like sigma factor [Streptomyces scabiei 87.22]
 gi|260649391|emb|CBG72506.1| SigL-like sigma factor [Streptomyces scabiei 87.22]
          Length = 304

 Score = 45.4 bits (106), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 58/240 (24%), Positives = 107/240 (44%), Gaps = 30/240 (12%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  +L LV   A  +R    P+ +++  G IGL++A+ +F+  RG    T++M  I   
Sbjct: 83  LVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRGVEFPTFAMPTIVGE 142

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL  +L +    L    D   +   V  +A++L ++  
Sbjct: 143 IKRFFRDTSWS-VRVPRRLQELRL--DLAKAGDELAQKLD---RAPTVGELAERLGLTND 196

Query: 172 EVISMNCRLAGDESLNALINSS-------DKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           EV+       G  + NA   SS       D +     D + Y+  G E   IE  E    
Sbjct: 197 EVVE------GMAASNAYTASSLDAQPEEDDSEGALADRIGYEDHGLEG--IEYVES--- 245

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              L   ++ L PR+R+I   R +    +T   +  E  +S+  V ++ +R   ++++ +
Sbjct: 246 ---LKPLIAGLPPRDRQILSLRFVAN--MTQSEIGDELGISQMHVSRLLSRTLVRLRKGL 300


>gi|330874712|gb|EGH08861.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv.
           morsprunorum str. M302280PT]
          Length = 81

 Score = 45.4 bits (106), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 23/57 (40%), Positives = 35/57 (61%)

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L +++ VL+ R R I   R L E   TL +L+ ++ VS ER+RQ+E  A  K++ SI
Sbjct: 23  LHQALDVLDERSRDILYQRWLAEEKATLHDLAQKYNVSAERIRQLEKSAMNKLKTSI 79


>gi|225375354|ref|ZP_03752575.1| hypothetical protein ROSEINA2194_00979 [Roseburia inulinivorans DSM
           16841]
 gi|225212843|gb|EEG95197.1| hypothetical protein ROSEINA2194_00979 [Roseburia inulinivorans DSM
           16841]
          Length = 256

 Score = 45.4 bits (106), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 57/230 (24%), Positives = 109/230 (47%), Gaps = 22/230 (9%)

Query: 61  VVKIAMG----YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           +VK+  G    Y GY +   ++VS G  GL+ A+ KFD  +  +  TY+   I+  + + 
Sbjct: 32  LVKLVAGRLSMYLGYNVEYDDLVSYGIFGLIDAIDKFDLGKEVKFETYASLRIRGTILDQ 91

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
           I R    +       QK++   +++++      T  N   E+   IA++L +SE E+ + 
Sbjct: 92  I-RKMDWIPRTVRQKQKKIDEAIKQVEMR----TGKNASDEE---IAQELGLSEDELTTW 143

Query: 177 NCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV 234
             +L      SLN  +   ++ +    D     H  Q +   +K E +  +  L  S+ V
Sbjct: 144 QSQLKVTNIVSLNEYL---EQGAEPVMDARRNSHFIQPE---DKVEEEELKQKLEESLEV 197

Query: 235 LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L  +ER++      ++  +TL+ +SS  EVS  R+ Q+  +A  K+++ +
Sbjct: 198 LTEKERKVILLYYYED--LTLKEISSILEVSESRISQLHTKALLKMRKKL 245


>gi|304407011|ref|ZP_07388665.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
 gi|304343998|gb|EFM09838.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
          Length = 251

 Score = 45.4 bits (106), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 55/252 (21%), Positives = 112/252 (44%), Gaps = 38/252 (15%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  +   LV  ++RLV  +   +   G    ++   G IGL+++V KFD     + +
Sbjct: 26  QSGDNVSRDTLVHCNIRLVWSVVQRFMNRGYEPEDLFQIGCIGLLKSVDKFDLSYDVKFS 85

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIG----TTANQKRLFFN-LRRLKGHLQAITDNNLKPE 157
           TY++  I   +Q + LR    +K+      TAN+ R   + L +  G L  IT+      
Sbjct: 86  TYAVPMIIGEIQRF-LRDDGTLKVSRSLKETANKVRKMKDELSKTLGRLPTITE------ 138

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ-----E 212
               +A+ L ++  +V+                  ++K  +   +  V+++DG      +
Sbjct: 139 ----VAEGLGITPEDVV--------------FAQEANKPPTSIHE-TVFENDGDPITLMD 179

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           Q+  + +ER   +  L  ++  L  RER I   R  ++   T   ++S   +S+ +V ++
Sbjct: 180 QIADDSQERWFDKLALAEAIEGLAERERLIVYLRYYRDQ--TQSEVASRLGISQVQVSRL 237

Query: 273 EARAFKKVQESI 284
           E +  + +++ I
Sbjct: 238 EKKILQLIKDQI 249


>gi|182418456|ref|ZP_02949750.1| RNA polymerase sigma-F factor [Clostridium butyricum 5521]
 gi|237666966|ref|ZP_04526951.1| RNA polymerase sigma-F factor [Clostridium butyricum E4 str. BoNT E
           BL5262]
 gi|182377838|gb|EDT75382.1| RNA polymerase sigma-F factor [Clostridium butyricum 5521]
 gi|237658165|gb|EEP55720.1| RNA polymerase sigma-F factor [Clostridium butyricum E4 str. BoNT E
           BL5262]
          Length = 252

 Score = 45.4 bits (106), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 63/261 (24%), Positives = 118/261 (45%), Gaps = 39/261 (14%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           LAK+    GD  A ++L+  +L LV  I+  +   G    ++   G+IGL++A+  FD  
Sbjct: 22  LAKK----GDNDAMNKLIEINLPLVASISKKFLNRGYDYEDIFQIGSIGLVKAINNFDLN 77

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
              + +TY++  I   ++ + LR   ++K+  + N K L    R++  + + +T N LK 
Sbjct: 78  YNVKFSTYAVPMIMGEIKRF-LRDDGMIKV--SRNVKSL---ARKIHYYREQLT-NKLK- 129

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
                         S  I      AG E    +      NS Q+    ++  DG   +LI
Sbjct: 130 -------------RSPTIEELAEYAGVEKEEIVFAIESANSLQYLYDTIHQDDGAPVMLI 176

Query: 217 EK-EERKNRRNM-------LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           +K  E+K   ++       L  ++  L+ + R+I   R  ++   T   ++    +S+ +
Sbjct: 177 DKLSEKKGEDDVNLIEKIALKEALRSLDEKARQIIMLRYFKDK--TQIQVAKMLGISQVQ 234

Query: 269 VRQIEARAFKKVQESIQKQVE 289
           V +IE    KKV   ++K++E
Sbjct: 235 VSRIE----KKVLLQMKKKLE 251


>gi|54297695|ref|YP_124064.1| flagellar biosynthesis sigma factor [Legionella pneumophila str.
           Paris]
 gi|53751480|emb|CAH12898.1| sigma factor 28 [Legionella pneumophila str. Paris]
          Length = 238

 Score = 45.4 bits (106), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 52/236 (22%), Positives = 108/236 (45%), Gaps = 27/236 (11%)

Query: 53  LVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           LV +H  LV +IA   +G     + + +++  G +GL++A + +D  +G    TY+   I
Sbjct: 18  LVKTHATLVKRIAHHLLGRLPQSVQLDDLIQSGMLGLLEAARHYDSSKGASFETYAGIRI 77

Query: 110 KAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHL-QAITDNNLKPEQVVAIAKKLN 167
           +  M + + R+ W  V      N + +   +R L+    +   DN +  E  V++    +
Sbjct: 78  RGHMLDEVRRNDW--VPRSVYRNSRMISDAVRILEHKFGREAKDNEIAEELGVSLDDYHD 135

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + +    S++  L G + L               D +++DH+G      E      R +M
Sbjct: 136 MLQD---SISSHLYGFDDLGV------------TDDVLFDHEGNGST--EPHRNVMRSDM 178

Query: 228 LTRSMSVLN--PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           + R   V++  PR+ R+  +   +++ + L+ +    EVS  R+ QI ++A  +++
Sbjct: 179 MNRLTQVIDSLPRKERLVLSLYYEQD-LNLKEIGEILEVSESRISQILSQATHRIR 233


>gi|325264312|ref|ZP_08131043.1| putative RNA polymerase sigma factor RpoD [Clostridium sp. D5]
 gi|324030383|gb|EGB91667.1| putative RNA polymerase sigma factor RpoD [Clostridium sp. D5]
          Length = 288

 Score = 45.4 bits (106), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 20/56 (35%), Positives = 31/56 (55%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
           + +++ EG I L +AV+ FD E+      Y+ +WIK  M+ YI      V+I T A
Sbjct: 46  LDDLMQEGYIALCEAVRHFDSEQAVPFINYAAFWIKQGMKRYIENCCGTVRIPTHA 101


>gi|149183156|ref|ZP_01861605.1| SpoIIIC [Bacillus sp. SG-1]
 gi|148849139|gb|EDL63340.1| SpoIIIC [Bacillus sp. SG-1]
          Length = 238

 Score = 45.4 bits (106), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 26/83 (31%), Positives = 46/83 (55%), Gaps = 2/83 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  ++E+  L  R   +GD  A + L+  +LRLV  I   +   G    +++S G IGL
Sbjct: 30  PLSSQEEKKYL--RKMANGDEDARNILIEHNLRLVAHIVKKFENTGEDPEDLISIGTIGL 87

Query: 87  MQAVKKFDPERGFRLATYSMWWI 109
           ++A++ +   +G +LATY+   I
Sbjct: 88  IKAIESYSEGKGTKLATYAARCI 110


>gi|297157938|gb|ADI07650.1| SigL-like sigma factor [Streptomyces bingchenggensis BCW-1]
          Length = 322

 Score = 45.4 bits (106), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 59/240 (24%), Positives = 106/240 (44%), Gaps = 30/240 (12%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  +L LV   A  +R    P+ ++V  G IGL++A+ +F+  RG    T++M  I   
Sbjct: 101 LVELNLALVKFAASRFRSRSEPMEDIVQVGTIGLIKAIDRFELSRGVEFPTFAMPTIVGE 160

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL  +L +    L    D   +      +A++L ++ +
Sbjct: 161 IKRFFRDTSWS-VRVPRRLQELRL--DLAKAGDELAQRLD---RAPTAGELAERLGLTTA 214

Query: 172 EVISMNCRLAGDESLNALINSS-------DKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           EVI       G  + NA   SS       D       D + Y+  G E   IE  E    
Sbjct: 215 EVIE------GMAASNAYTASSLDAQPEEDDTEGALADRIGYEDHGLEG--IEYVES--- 263

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              L   ++ L+PR+R+I   R +    +T   +  E  +S+  V ++ +R   +++  +
Sbjct: 264 ---LKPLIADLSPRDRKILSLRFVAN--MTQSEIGDELGISQMHVSRLLSRTLVRLRRGL 318


>gi|293375494|ref|ZP_06621773.1| putative RNA polymerase sigma-F factor [Turicibacter sanguinis
           PC909]
 gi|325844950|ref|ZP_08168315.1| RNA polymerase sigma-F factor [Turicibacter sp. HGF1]
 gi|292645894|gb|EFF63925.1| putative RNA polymerase sigma-F factor [Turicibacter sanguinis
           PC909]
 gi|325489000|gb|EGC91389.1| RNA polymerase sigma-F factor [Turicibacter sp. HGF1]
          Length = 236

 Score = 45.4 bits (106), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 43/175 (24%), Positives = 86/175 (49%), Gaps = 17/175 (9%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           M +KQ   ++AK   + GD  A   LVT+H+ LV  +   +    +   ++   G +GL+
Sbjct: 1   MDKKQIHELIAKA--QSGDEEARLTLVTNHMDLVWSVVHKFGHIEVEKDDLFQIGCMGLL 58

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +++ +FD      L+TY++  I   ++ +I R  S +KI  +   K     ++ +K HL 
Sbjct: 59  KSINQFDSSYDTTLSTYAIPLIIGEIKAFI-REQSPIKISRSI--KSNIHKIQEVKDHLN 115

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
            + +   +   +  IA++  +SE ++I          +LNA IN +  ++ + +D
Sbjct: 116 KVLE---REPTIKEIAQETELSEEQIIL---------ALNAPINVTSLDNYERED 158


>gi|225568653|ref|ZP_03777678.1| hypothetical protein CLOHYLEM_04731 [Clostridium hylemonae DSM
           15053]
 gi|225162581|gb|EEG75200.1| hypothetical protein CLOHYLEM_04731 [Clostridium hylemonae DSM
           15053]
          Length = 259

 Score = 45.4 bits (106), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 58/265 (21%), Positives = 121/265 (45%), Gaps = 25/265 (9%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+++E+  L  R +  GD  A    +  +LRLV+ +   + G      ++   G I
Sbjct: 15  KLPILKEEEKEALFARIK-AGDEEAKEEYIKGNLRLVLSVIKRFGGSNENPDDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  F+ E   + +TY++  I   ++ Y+  + S+          R+  +LR    
Sbjct: 74  GLIKAINNFNTELDVKFSTYAVPMIIGEIRRYMRDNNSI----------RVSRSLRDTAY 123

Query: 145 HLQAITDN----NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
                 +N    NLK   V  IA+++ +S+ +++     +    SL   + +   ++   
Sbjct: 124 KAIYAKENYVKRNLKEPTVQEIAEEIGISKEDIVFALDAIQVPMSLQEPVYNDGGDALYV 183

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
            D  + D   +E+  +E          L  +M  L  RER I + R   E    +E ++ 
Sbjct: 184 MDQ-ISDTKNKEEKWVEDLS-------LEAAMEHLGERERYIIKLRFF-EGKTQME-VAE 233

Query: 261 EFEVSRERVRQIEARAFKKVQESIQ 285
           E  +S+ +V ++E  A + +++ ++
Sbjct: 234 EINISQAQVSRLEKNALRVMKQYLE 258


>gi|167461547|ref|ZP_02326636.1| RNA polymerase sigma factor [Paenibacillus larvae subsp. larvae
           BRL-230010]
          Length = 361

 Score = 45.4 bits (106), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 28/88 (31%), Positives = 49/88 (55%), Gaps = 9/88 (10%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKF 93
           ++ RY  H  L     ++ ++ ++V  +A  YR   G GL   ++VS G IGL+QA + +
Sbjct: 1   MSIRYNPH--LGYEDEMIPAYEKMVHSVARKYRSCIGAGLDYDDLVSVGMIGLIQAFRNY 58

Query: 94  DPERGFR----LATYSMWWIKAAMQEYI 117
           DP+R  R     +TY+   IK ++Q ++
Sbjct: 59  DPDRFNRKVSSFSTYAFNMIKWSIQRFL 86


>gi|282864142|ref|ZP_06273199.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
 gi|282561220|gb|EFB66765.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
          Length = 290

 Score = 45.1 bits (105), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 56/232 (24%), Positives = 100/232 (43%), Gaps = 22/232 (9%)

Query: 61  VVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           +V+ A G    RG G  + ++V  G +GL++A+ +FD  R     ++++ +I   ++ + 
Sbjct: 69  LVRFAAGRFRSRGSG-DMEDIVQVGTVGLIKAIDRFDLAREVEFTSFAVPYIVGEIKRFF 127

Query: 118 L-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV--- 173
              +WS   +      + L  +L R K  L    D +     V  +A  L + E EV   
Sbjct: 128 RDTTWS---VHVPRRLQELRVDLARAKETLAVGLDRD---PTVQELAAHLGLDEQEVTDG 181

Query: 174 -ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
            ++ N   AG  SL+    + D            D  G+    +E  E     + L   +
Sbjct: 182 IVAANGYTAG--SLDMPAEAGDPAGRATGGRTFADVLGEPDPAMETVENL---HALAPLL 236

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             L+ RERRI E R  QE  +T   +  E  +S+  V ++  R  +K++  +
Sbjct: 237 EDLDARERRIIEMRFGQE--LTQAQIGDELGISQMHVSRLLGRTLRKLRAGM 286


>gi|295105020|emb|CBL02564.1| DNA-directed RNA polymerase specialized sigma subunit
           [Faecalibacterium prausnitzii SL3/3]
          Length = 157

 Score = 45.1 bits (105), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 26/85 (30%), Positives = 44/85 (51%), Gaps = 8/85 (9%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGY--------RGYGLPISEVVSEGNIGLMQAVKKFD 94
           + GD  A + LV ++LR + K A              G+ ++++V EG++GL+  +  F 
Sbjct: 14  QSGDKWAENALVENNLRFIRKTAYEIWSAQRELNVALGIELNDLVQEGSLGLLGCISSFQ 73

Query: 95  PERGFRLATYSMWWIKAAMQEYILR 119
           P+ G +  TY+   I  AM +YI R
Sbjct: 74  PDYGNKFLTYAAPAIHNAMLDYIRR 98


>gi|295706259|ref|YP_003599334.1| RNA polymerase sigma-D factor [Bacillus megaterium DSM 319]
 gi|294803918|gb|ADF40984.1| RNA polymerase sigma-D factor [Bacillus megaterium DSM 319]
          Length = 253

 Score = 45.1 bits (105), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 65/266 (24%), Positives = 128/266 (48%), Gaps = 34/266 (12%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQ 88
           EE+ + + +RE  D  A + LV  ++ LV    +     GLP +    E+ S G IGL  
Sbjct: 8   EEHKIWQEWRETRDSHAGNMLVKKYMPLV-NYHVQRISVGLPKNIHKEELRSLGLIGLYD 66

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           A++KFD  R  +  TY+ + I+ A+ + + +  W    +  +A +K      +R++   +
Sbjct: 67  ALEKFDYGRDLKFDTYASFRIRGAIIDGLRKEDW----LSRSAREK-----TKRIEQATE 117

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVI-SMNCRLAGDESLNALINSSDKNSSQWQD---- 202
           A+    L+      +AK++ ++E++V+ +MN      E   A + S ++   +++D    
Sbjct: 118 ALEQRYLRRVAPSEVAKEVGMTEADVVHTMN------EGFLANVLSMEEQPKEYEDGEQK 171

Query: 203 WLVYDHDGQEQVLIEKEERKN--RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
           + + D    E+ L  +EE  N  R   L   +  LN +E+ +      +E  +T   ++ 
Sbjct: 172 YTIKD----EKTLSPEEELINDERYQELAEVIEQLNEKEQLVVSLFYKEE--LTFTEIAQ 225

Query: 261 EFEVSRERVRQIEARAFKKVQESIQK 286
              +S  R+ QI ++A  K++ S+ K
Sbjct: 226 LLGLSTSRISQIHSKALFKMRTSLSK 251


>gi|47564960|ref|ZP_00236004.1| sigma-B [Bacillus cereus G9241]
 gi|47558333|gb|EAL16657.1| sigma-B [Bacillus cereus G9241]
          Length = 257

 Score = 45.1 bits (105), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 55/231 (23%), Positives = 110/231 (47%), Gaps = 27/231 (11%)

Query: 22  EIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           EI+  P  L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++ 
Sbjct: 2   EIQSQPTNLTKEDVIKLIAEFQQNQCDEAQERLVEHYKNLVYSIAYRYSKGGPMHEDIIQ 61

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNL 139
            G +GL+ A++++D   G     +++  I   +++Y+  ++W +       +  R   +L
Sbjct: 62  VGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGI-------HVPRRIKDL 114

Query: 140 -RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNALI-NS 192
             ++K  ++ +TD+  +  +++ IA  L +SE EV+ +     N R++   SL+ ++ NS
Sbjct: 115 GGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVS---SLDDVVENS 171

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           SD +S    + +     G E+          RR +L    +VLN  E+ + 
Sbjct: 172 SDGSSVARIESVGEVEQGYEET--------ERRLVLKDIFNVLNDTEKSVI 214


>gi|225174854|ref|ZP_03728851.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Dethiobacter
           alkaliphilus AHT 1]
 gi|225169494|gb|EEG78291.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Dethiobacter
           alkaliphilus AHT 1]
          Length = 219

 Score = 45.1 bits (105), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 23/61 (37%), Positives = 35/61 (57%)

Query: 57  HLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           HL LV  +   Y+G      ++   G IGL++A+KKFDP RG   ATY++  I   ++ Y
Sbjct: 11  HLPLVHSLVKRYQGEYAESDDLFQVGCIGLLKALKKFDPARGNAFATYAVPVIAGEIKMY 70

Query: 117 I 117
           +
Sbjct: 71  L 71


>gi|160944585|ref|ZP_02091813.1| hypothetical protein FAEPRAM212_02099 [Faecalibacterium prausnitzii
           M21/2]
 gi|158444367|gb|EDP21371.1| hypothetical protein FAEPRAM212_02099 [Faecalibacterium prausnitzii
           M21/2]
 gi|295103334|emb|CBL00878.1| RNA polymerase sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii SL3/3]
          Length = 224

 Score = 45.1 bits (105), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 23/74 (31%), Positives = 40/74 (54%), Gaps = 1/74 (1%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            +T +L LV   A  +RG G+   ++ S G +GL++A   FD  RG   +TY++  I   
Sbjct: 11  FITQNLGLVHACAGRFRGRGMEYDDLYSAGCVGLIKAYDNFDESRGVCFSTYAVPVILGE 70

Query: 113 MQEYILRSWSLVKI 126
           +++ + R    VK+
Sbjct: 71  IKK-LFRDGGTVKV 83


>gi|126348076|emb|CAJ89797.1| putative RNA polymerase sigma factor [Streptomyces ambofaciens ATCC
           23877]
          Length = 289

 Score = 45.1 bits (105), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 62/241 (25%), Positives = 110/241 (45%), Gaps = 36/241 (14%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LVT+ L +  +IA  +R  G  I ++     +GL++A+ +FDPERG    +Y++  I   
Sbjct: 56  LVTAWLPMAHRIAGRFRDRGESIEDLRQVAALGLVKAIDRFDPERGA-FESYAVPTITGE 114

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLR-RLKGHLQAITDNNLKPE-QVVAIAKKLNVS 169
           ++ +   R W+L          R    LR +++   + +T N   PE  V A+A    ++
Sbjct: 115 VKRHFRDRMWAL-------RVPRRVQELRNKVRVARRELTQNPGSPEPSVAALAAHTGLT 167

Query: 170 ESEVISMNCRLAGDE--------SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           E EV       AG E        SL+A +++ D   S   D L    DG    +I++E  
Sbjct: 168 EDEVS------AGMEALESFSTLSLDAELSAGDDGYS-LADTLGA-ADGSYDTVIDRESA 219

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           K         +  L  RER I   R  ++  +T   ++    +S+  V ++ +R+  +V+
Sbjct: 220 KE-------GLRRLPERERAILYMRFFED--MTQSRIADRLGISQMHVSRLISRSCARVR 270

Query: 282 E 282
           +
Sbjct: 271 D 271


>gi|297194001|ref|ZP_06911399.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
 gi|297152057|gb|EFH31507.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
          Length = 305

 Score = 45.1 bits (105), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 51/202 (25%), Positives = 91/202 (45%), Gaps = 28/202 (13%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  +L LV   A  +R    P+ +++  G IGL++A+ +F+  RG    T++M  I   
Sbjct: 84  LVELNLALVKFAASRFRTRSEPMEDIIQVGTIGLIKAIDRFELSRGVEFPTFAMPTIIGE 143

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL  +L +    L    D   +   V  +A++L++   
Sbjct: 144 IKRFFRDTSWS-VRVPRRLQELRL--DLAKAGDELSQQLD---RAPTVDELAQRLDIGRD 197

Query: 172 EVISMNCRLAGDESLNALINSS-------DKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           EV+       G  + NA   SS       D +     + + Y+  G E +    E  ++ 
Sbjct: 198 EVVE------GMAASNAYTASSLDAQPEEDDSEGALANRIGYEDHGLEGI----EYIESL 247

Query: 225 RNMLTRSMSVLNPRERRIFEAR 246
           R M+    + L PR+R+I   R
Sbjct: 248 RPMI----ASLPPRDRKILSLR 265


>gi|297197437|ref|ZP_06914834.1| RNA polymerase sigma-E factor [Streptomyces sviceus ATCC 29083]
 gi|197716285|gb|EDY60319.1| RNA polymerase sigma-E factor [Streptomyces sviceus ATCC 29083]
          Length = 298

 Score = 45.1 bits (105), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 52/199 (26%), Positives = 91/199 (45%), Gaps = 26/199 (13%)

Query: 61  VVKIAMG-YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           +V+ A G +RG G  + ++V  G IGL++A+ +F+  R     ++++ +I   ++ +   
Sbjct: 78  LVRFAAGRFRGRGDDMEDIVQTGMIGLIKAIDRFEISREVEFTSFALPYIVGEIKRFFRD 137

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
           +   V +     + R+   L + +  L +  D +     V  +A  +N+SE EVI     
Sbjct: 138 TTWAVHVPRRLQELRV--ELAKAREELASRLDRD---PTVAELATLMNISEKEVI----- 187

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDH-DGQEQVL---IEKEERKNRR----NMLTRS 231
                   A I S+  NSS     L  D  +G E VL   I  EE   R     + L   
Sbjct: 188 -------EAQIASNGYNSSSLDAALTGDGPEGGEAVLADFIGVEEDGLRLVEDFHSLAPL 240

Query: 232 MSVLNPRERRIFEARRLQE 250
           M+ L+ R+R+I   R ++E
Sbjct: 241 MAELSERDRQIIHMRFVEE 259


>gi|166154282|ref|YP_001654400.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis 434/Bu]
 gi|166155157|ref|YP_001653412.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis
           L2b/UCH-1/proctitis]
 gi|301335533|ref|ZP_07223777.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis L2tet1]
 gi|165930270|emb|CAP03756.1| RNA polymerase sigma factor [Chlamydia trachomatis 434/Bu]
 gi|165931145|emb|CAP06710.1| RNA polymerase sigma factor [Chlamydia trachomatis
           L2b/UCH-1/proctitis]
          Length = 253

 Score = 45.1 bits (105), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 61/243 (25%), Positives = 114/243 (46%), Gaps = 23/243 (9%)

Query: 51  HR--LVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           HR  L+ S+L LV  +A      G+P    + ++ + G  GL++AV++FDPE+  R  +Y
Sbjct: 21  HRDVLIESYLPLVKNVAHRLAS-GMPSHVKMEDLYALGVEGLIRAVERFDPEKSKRFESY 79

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITDNNLKPEQVVAIA 163
           +++ IKAA+ +  LR    V         RL   +  L+  L +  TD  L         
Sbjct: 80  ALFIIKAAIIDG-LRKQDWVPRSVYQRANRLADAMDSLRQTLGKEPTDGEL--------C 130

Query: 164 KKLNVSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           + LN+S+ E+     + R A   SLN   +  D +     +  + D   +    + +  +
Sbjct: 131 EYLNISQQELSHWFSSSRPALVLSLNDDFSCQDDDEGLALEERIADERAETGYDVIR--K 188

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           K   ++LT ++  L+ +ER++       +  + L+ +     VS  RV QI ++A  K++
Sbjct: 189 KEAISILTEALLALDEKERQVMALYYYDD--LVLKEIGKILGVSESRVSQIHSKALLKLR 246

Query: 282 ESI 284
            ++
Sbjct: 247 GTL 249


>gi|312794234|ref|YP_004027157.1| RNA polymerase, sigma 70 family subunit [Caldicellulosiruptor
           kristjanssonii 177R1B]
 gi|312181374|gb|ADQ41544.1| putative RNA polymerase, sigma 70 family subunit
           [Caldicellulosiruptor kristjanssonii 177R1B]
          Length = 206

 Score = 45.1 bits (105), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 26/95 (27%), Positives = 49/95 (51%), Gaps = 4/95 (4%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L++Q+E V   +    GD  AA  L+ ++  L++ IA  Y    +   ++  EG + ++Q
Sbjct: 6   LDEQKELVCRIK---QGDKKAAEELIRAYEPLIISIASKYNKPDI-FEDLKQEGAVAILQ 61

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           A +KFD   G    T ++++IK      + RS ++
Sbjct: 62  AAQKFDESLGVSFITLAVYYIKRNTDRCVKRSQTI 96


>gi|225181965|ref|ZP_03735398.1| RNA polymerase, sigma 28 subunit, SigK [Dethiobacter alkaliphilus
           AHT 1]
 gi|225167327|gb|EEG76145.1| RNA polymerase, sigma 28 subunit, SigK [Dethiobacter alkaliphilus
           AHT 1]
          Length = 234

 Score = 45.1 bits (105), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 27/83 (32%), Positives = 44/83 (53%), Gaps = 5/83 (6%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P  EK+   ++AK     GD  A   L+  +LRLV  +   +   G    +++S G +GL
Sbjct: 33  PQEEKKYLALMAK-----GDEEARSILIERNLRLVAHVIKKFENTGEDQEDLISIGTVGL 87

Query: 87  MQAVKKFDPERGFRLATYSMWWI 109
           ++A+  F+  +G RLATY+   I
Sbjct: 88  IKAIDSFNNNKGTRLATYAARCI 110


>gi|158333719|ref|YP_001514891.1| RNA polymerase sigma factor SigF [Acaryochloris marina MBIC11017]
 gi|158303960|gb|ABW25577.1| RNA polymerase sigma factor [Acaryochloris marina MBIC11017]
          Length = 264

 Score = 45.1 bits (105), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 23/88 (26%), Positives = 52/88 (59%), Gaps = 1/88 (1%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL-PISEVVSEGNIGLMQA 89
           K E   L ++Y++       +RLV  +L LV + A  + G+      +++  G++GL++A
Sbjct: 10  KSESLELLQQYQQSSCTELRNRLVQMNLGLVRREAHRWVGHSTESFDDLMQVGSLGLIRA 69

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYI 117
           +++FDP +G   +++++ +I+  +Q Y+
Sbjct: 70  IERFDPFKGHAFSSFAVPYIRGEIQHYL 97


>gi|226225717|ref|YP_002759823.1| RNA polymerase sigma factor for flagellar operon [Gemmatimonas
           aurantiaca T-27]
 gi|226088908|dbj|BAH37353.1| RNA polymerase sigma factor for flagellar operon [Gemmatimonas
           aurantiaca T-27]
          Length = 251

 Score = 45.1 bits (105), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 30/88 (34%), Positives = 45/88 (51%), Gaps = 15/88 (17%)

Query: 45  GDLSAAHRLVTSHLRLVVKIA------MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           G+ SA  RL+  HL LV  +A      +  R       E+VS G IGLM A++ FD  RG
Sbjct: 12  GNPSARDRLLEEHLGLVHHVARQVSRTLAVRA---DFDELVSAGTIGLMTALEGFDASRG 68

Query: 99  FRLATYSMWWIKAAM------QEYILRS 120
              +T++   I+ A+      Q+++ RS
Sbjct: 69  LAFSTFAAPRIRGAILDELRKQDHVPRS 96


>gi|160895319|ref|ZP_02076090.1| hypothetical protein CLOL250_02878 [Clostridium sp. L2-50]
 gi|156863012|gb|EDO56443.1| hypothetical protein CLOL250_02878 [Clostridium sp. L2-50]
          Length = 225

 Score = 45.1 bits (105), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 24/83 (28%), Positives = 45/83 (54%), Gaps = 1/83 (1%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           +GD  A  +L+  +L LV  +A  + G G  I ++   G IGL++ + KF  E   + +T
Sbjct: 13  NGDDHAKEKLIEQNLGLVWSVARRFTGRGYDIEDLFQIGCIGLIKCIDKFSFEYDVKFST 72

Query: 104 YSMWWIKAAMQEYILRSWSLVKI 126
           Y++  I+  ++ + LR    +K+
Sbjct: 73  YAVPLIQGEIRRF-LRDSGAIKV 94


>gi|242089065|ref|XP_002440365.1| hypothetical protein SORBIDRAFT_09g030380 [Sorghum bicolor]
 gi|241945650|gb|EES18795.1| hypothetical protein SORBIDRAFT_09g030380 [Sorghum bicolor]
          Length = 182

 Score = 45.1 bits (105), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 22/61 (36%), Positives = 34/61 (55%), Gaps = 1/61 (1%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LVT+   L   IA  Y G G  + +++  G IG++   +KFD  +G R +TY  +WI+  
Sbjct: 2   LVTTEW-LFSYIARTYTGMGTALDKLLQAGKIGVLDGSEKFDNRKGCRFSTYVKYWIRKG 60

Query: 113 M 113
           M
Sbjct: 61  M 61


>gi|326938732|gb|AEA14628.1| RNA polymerase sigma factor SigB [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 257

 Score = 45.1 bits (105), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 54/231 (23%), Positives = 110/231 (47%), Gaps = 27/231 (11%)

Query: 22  EIRKIPMLEKQEEYV-LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           EI+  P    +E+ + L   ++++    A  RLV  +  LV  IA  Y   G    +++ 
Sbjct: 2   EIQSQPTTLTKEDVIKLIAEFQQNQCNEAQERLVDHYKNLVYSIAYRYSKGGPMHEDIIQ 61

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNL 139
            G +GL+ A++++D   G     +++  I   +++Y+  ++W +       +  R   +L
Sbjct: 62  VGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGI-------HVPRRIKDL 114

Query: 140 -RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNALI-NS 192
             ++K  ++ +TD+  +  +++ IA  L +SE EV+ +     N R++   SL+ ++ NS
Sbjct: 115 GGKIKLAIEELTDHLQRSPKIIEIANHLGLSEEEVLEIMDAKNNYRVS---SLDDVVENS 171

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           SD +S    + +     G E+          RR +L    +VLN  E+ + 
Sbjct: 172 SDGSSVARIESVGEVEQGYEET--------ERRLVLKDIFNVLNDTEKSVI 214


>gi|332297782|ref|YP_004439704.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Treponema
           brennaborense DSM 12168]
 gi|332180885|gb|AEE16573.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Treponema
           brennaborense DSM 12168]
          Length = 262

 Score = 45.1 bits (105), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 47/224 (20%), Positives = 101/224 (45%), Gaps = 22/224 (9%)

Query: 61  VVKIAMGYRGYGLPIS----EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           +VK   G    G+P S    ++V  G  GL+ A+ K+DP++  +  TY++  I+ ++ + 
Sbjct: 37  LVKYVAGKVATGMPGSVEFDDLVGFGQFGLLDAINKYDPDKNVKFKTYAVTRIRGSIFDE 96

Query: 117 ILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
           + +  W    +  +  QK      R ++  + A+     +P     +A  + +SE+E   
Sbjct: 97  LRQLDW----VPRSVRQK-----AREIEDAIVALESRLGRPASDAEVAGSMGISEAEFQQ 147

Query: 176 MNCRLAGDE--SLNAL-INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
              R++G    SLN +  +  D +     D +         V++E+EE    R ++  ++
Sbjct: 148 TVMRVSGTSVLSLNDVWYSGDDSDHVSIGDSIESPASLNPDVIVEREE---IRRVIAEAI 204

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           + L  +E+ +      ++  +T + +     VS  R+ Q+  +A
Sbjct: 205 TELPEKEKMVLVLYYHED--LTFKEIGQVLNVSESRISQLHTKA 246


>gi|114566413|ref|YP_753567.1| RNA polymerase sigma factor [Syntrophomonas wolfei subsp. wolfei
           str. Goettingen]
 gi|114337348|gb|ABI68196.1| putative RNA polymerase sigma factor [Syntrophomonas wolfei subsp.
           wolfei str. Goettingen]
          Length = 260

 Score = 45.1 bits (105), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 55/254 (21%), Positives = 115/254 (45%), Gaps = 19/254 (7%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           R +E+ D+ A  +L+     LV  +A     +    + + E++S G  GL+ A++KFD +
Sbjct: 15  RLKENEDIEARDQLIIHFAHLVKYVASRLAIHLSSLVELDELISYGIEGLIDAIEKFDHK 74

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL---FFNLRRLKGHLQAITDNN 153
           R  +  TY++  I+ +M +  LRS   + +      K L   + N+    G  ++ +D  
Sbjct: 75  RNIKFETYAITRIRGSMIDG-LRSMDWIPVSLRQKSKELEKAYMNVEARLG--RSASDAE 131

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
           +  E        LN+ E  V+  +       SL+  +   D    +    L+ DH+    
Sbjct: 132 VAEEL------GLNLDEFAVLLRDVAATTIISLDDFLPGEDGEQKKRMLDLLEDHNSISA 185

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
              E  E    +++L +++S L  +E+ +      +   +TL+ + +   +S  R+ Q+ 
Sbjct: 186 S--EIVEFNEVKDLLAKAISRLPDKEKLVVYLYYYE--GLTLKEIGATISLSESRISQLH 241

Query: 274 ARAFKKVQESIQKQ 287
            +A  +++ S+ K+
Sbjct: 242 TKAILRLRGSLSKK 255


>gi|257871306|ref|ZP_05650959.1| RNA polymerase sigma-70 subunit [Enterococcus gallinarum EG2]
 gi|257805470|gb|EEV34292.1| RNA polymerase sigma-70 subunit [Enterococcus gallinarum EG2]
          Length = 235

 Score = 45.1 bits (105), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 50/211 (23%), Positives = 97/211 (45%), Gaps = 20/211 (9%)

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA-NQKRLFFNLR 140
           G IGLM A++KFDP +     +Y++  IK A+ + + +   + +    A NQ   F+  R
Sbjct: 40  GVIGLMDALRKFDPSKKVPFESYAVIRIKGAIIDEVRKHAKISRYKMAAVNQ---FYQAR 96

Query: 141 RLKGHLQAITDNNLKPEQV-VAIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNS 197
           +         + +LK E     I K+L +++S++  I  +       SL   + +  +  
Sbjct: 97  QE-------LEQSLKREATDTEICKQLGINQSQLADIYESLHYLASVSLEDTLFAYQEEG 149

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
              +D +    +  E  L+ +E    +R  L   +  L  RE+ I      +E  +TL+ 
Sbjct: 150 MTIKDMVRDPAENVEDTLVAEE----KRTALVACIKKLGEREQIILSLYYTEE--LTLKE 203

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           ++   E+S  RV QI  +   K++  I++++
Sbjct: 204 IAEILEISIPRVSQIHGKTIAKLRTLIEEEL 234


>gi|119511138|ref|ZP_01630256.1| sigma factor SigF [Nodularia spumigena CCY9414]
 gi|119464233|gb|EAW45152.1| sigma factor SigF [Nodularia spumigena CCY9414]
          Length = 261

 Score = 45.1 bits (105), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 25/91 (27%), Positives = 50/91 (54%), Gaps = 1/91 (1%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDP 95
           L   Y ++  +   ++LV  H  LV KIA  +      P  ++   G  GL++A+++FDP
Sbjct: 15  LLHSYHQNPSIKLRNQLVQLHTGLVRKIAHKFSHQCHEPYEDLEQIGYFGLIRAIERFDP 74

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            +G+  +++++ +I+  M  ++    SL+KI
Sbjct: 75  SQGYAFSSFAVPYIRGEMLHFLRDRSSLLKI 105


>gi|218661226|ref|ZP_03517156.1| hypothetical protein RetlI_17598 [Rhizobium etli IE4771]
          Length = 20

 Score = 45.1 bits (105), Expect = 0.013,   Method: Composition-based stats.
 Identities = 18/20 (90%), Positives = 19/20 (95%)

Query: 66 MGYRGYGLPISEVVSEGNIG 85
          MGYRGYGLPI EVVSEGN+G
Sbjct: 1  MGYRGYGLPIGEVVSEGNVG 20


>gi|302878264|ref|YP_003846828.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Gallionella
           capsiferriformans ES-2]
 gi|302581053|gb|ADL55064.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Gallionella
           capsiferriformans ES-2]
          Length = 236

 Score = 45.1 bits (105), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 58/232 (25%), Positives = 103/232 (44%), Gaps = 23/232 (9%)

Query: 60  LVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           LV +IA   M    Y + I +++  G +GL+ A  ++D   G +  TY+   I+ AM + 
Sbjct: 20  LVKRIAHQMMSKLPYSVQIDDIIQAGMMGLLDAATRYDEIHGAQFETYATQRIRGAMLDE 79

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
            LRS   +      + +R+   + RL+  L         P +   IAK+L VS  E   M
Sbjct: 80  -LRSADWLPRSLRRDMRRIEQGVSRLQQKL------GRAPNE-TEIAKELEVSLVEYQQM 131

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDW---LVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
                G +    LI   D      +D+     + +D     L++ +  K+    L R++ 
Sbjct: 132 LQESRGAQ----LIYYEDFQDEDHEDFFERFEFANDTDPLALLQDDRFKSE---LARAID 184

Query: 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           VL  RER +     + E  + L  +   F VS  R+ Q+ ++A  +++ S++
Sbjct: 185 VLPERERLLMAL--IYEQELNLREVGEVFGVSESRISQLHSQAVLRLRGSLK 234


>gi|182438259|ref|YP_001825978.1| putative RNA polymerase sigma factor [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|326778910|ref|ZP_08238175.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
 gi|178466775|dbj|BAG21295.1| putative RNA polymerase sigma factor [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|326659243|gb|EGE44089.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
          Length = 323

 Score = 45.1 bits (105), Expect = 0.013,   Method: Compositional matrix adjust.
 Identities = 57/235 (24%), Positives = 103/235 (43%), Gaps = 20/235 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  +L LV   A  +R    P+ ++V  G IGL++A+ +F+  RG    T++M  I   
Sbjct: 102 LVELNLALVKFAAARFRSRSEPMEDIVQVGTIGLIKAIDRFELSRGVEFPTFAMPTIVGE 161

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL  +L +    L    D   +   V  ++++L +S  
Sbjct: 162 IKRFFRDTSWS-VRVPRRLQELRL--DLAKAGDELSQQLD---RAPTVAELSERLGISPE 215

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQD--WLVYDHDGQEQVLIEKEERKNRRNMLT 229
           EV+       G  + NA   SS     +  D    + D  G E   +E  E       L 
Sbjct: 216 EVVE------GMSASNAYTASSLDAKPEEDDGEGALADRIGYEDHSLEGIEYVESLKPL- 268

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             ++ L  R+R I   R +    +T   +  E  +S+  V ++ +R   K+++ +
Sbjct: 269 --IAALPARDRMILSLRFVSN--MTQSEIGEELNISQMHVSRLLSRTLTKLRKGL 319


>gi|157693076|ref|YP_001487538.1| sporulation sigma factor SigK [Bacillus pumilus SAFR-032]
 gi|157681834|gb|ABV62978.1| DNA-directed RNA polymerase sigma subunit SigK carboxy-terminus
           [Bacillus pumilus SAFR-032]
          Length = 289

 Score = 45.1 bits (105), Expect = 0.014,   Method: Compositional matrix adjust.
 Identities = 22/66 (33%), Positives = 38/66 (57%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A + L+  +LRLV  I   +   G    +++S G IGL++A++ +   +G +LATY
Sbjct: 94  GDEHARNMLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIESYSSGKGTKLATY 153

Query: 105 SMWWIK 110
           +   I+
Sbjct: 154 AARCIE 159


>gi|326490962|dbj|BAJ90342.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 496

 Score = 45.1 bits (105), Expect = 0.014,   Method: Compositional matrix adjust.
 Identities = 27/92 (29%), Positives = 53/92 (57%), Gaps = 16/92 (17%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP-------ISEVVSEGNIGLMQAVK 91
           +R R+ G  +A ++L+  +LRLV+     Y     P        +++   G  GL+ A+ 
Sbjct: 250 RRLRDVGR-AARNKLIKHNLRLVLYAINKY----YPDMTGDERFADLCQAGANGLITAID 304

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           +F+P+RGFR++TY++ WI+ +    ++R+ +L
Sbjct: 305 RFEPKRGFRISTYALSWIRHS----VVRAMTL 332


>gi|206975667|ref|ZP_03236579.1| RNA polymerase sigma-B factor [Bacillus cereus H3081.97]
 gi|206746129|gb|EDZ57524.1| RNA polymerase sigma-B factor [Bacillus cereus H3081.97]
          Length = 257

 Score = 45.1 bits (105), Expect = 0.014,   Method: Compositional matrix adjust.
 Identities = 59/271 (21%), Positives = 128/271 (47%), Gaps = 29/271 (10%)

Query: 22  EIRKIPMLEKQEEYV-LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           EI+  P    +E+ + L   ++++    A  RLV  +  LV  IA  Y   G    +++ 
Sbjct: 2   EIQSQPTTLTKEDVIKLIAEFQQNQCDEAQERLVDHYKNLVYSIAYRYSKGGPMHEDIIQ 61

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNL 139
            G +GL+ A++++D   G     +++  I   +++Y+  ++W +       +  R   +L
Sbjct: 62  VGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGI-------HVPRRIKDL 114

Query: 140 -RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNALI-NS 192
             ++K  ++ +TD   +  +++ IA  L +SE EV+ +     N R++   SL+ ++ N+
Sbjct: 115 GGKIKLAIEELTDCLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVS---SLDDVVENA 171

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
           SD +S    + +     G E+          RR +L    +VLN  E+ +     + E  
Sbjct: 172 SDGSSVARIESVGEVEQGYEET--------ERRLVLKDIFNVLNETEKSVI--HYIFEEN 221

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +  ++      +S+  V +I+ +A  K++++
Sbjct: 222 LNQKDTGERLGISQMHVSRIKRQAISKLKQA 252


>gi|315503089|ref|YP_004081976.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily
           [Micromonospora sp. L5]
 gi|315409708|gb|ADU07825.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Micromonospora sp. L5]
          Length = 273

 Score = 45.1 bits (105), Expect = 0.014,   Method: Compositional matrix adjust.
 Identities = 56/238 (23%), Positives = 103/238 (43%), Gaps = 30/238 (12%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R + + L L   +A  Y G G P  ++     IGL++A+ KFDP RG   A Y++  I  
Sbjct: 51  RAIEAWLPLANHLAHRYSGRGEPNDDLAQTAAIGLIKAIDKFDPSRGVDFAGYAIPTIIG 110

Query: 112 AMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL-------KPEQVVAIA 163
            ++ +   R+W  +++             RRL+    AI+D N        +   V  IA
Sbjct: 111 ELKRHFRDRTWD-IRVP------------RRLQELRLAISDANSTLLQTLGRSPTVADIA 157

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
             L ++E EV+          +++    + D   +     L+   DG+ ++         
Sbjct: 158 AHLKLTEEEVLEGLEGARAYNAVSLSTPTGDGERATELGDLLGGEDGEFEL-------AE 210

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R  L  +++ L+ RE++I   R      +T   ++ +  VS+  V ++ ARA  K++
Sbjct: 211 MRVALGPALATLDQREQKILTLRFYGN--LTQSQIAEQIGVSQMHVSRLLARALTKLR 266


>gi|169350469|ref|ZP_02867407.1| hypothetical protein CLOSPI_01237 [Clostridium spiroforme DSM 1552]
 gi|169292789|gb|EDS74922.1| hypothetical protein CLOSPI_01237 [Clostridium spiroforme DSM 1552]
          Length = 228

 Score = 45.1 bits (105), Expect = 0.014,   Method: Compositional matrix adjust.
 Identities = 33/104 (31%), Positives = 54/104 (51%), Gaps = 3/104 (2%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +S++ NG   LS    +  +IP+  K+E   L + +  +GD  A + L+  +LRLV  IA
Sbjct: 6   LSLLTNG-FFLSYIKSKSFEIPLTPKEEAKYLERFF--NGDQEARNVLIERNLRLVAHIA 62

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             Y        +++S G IGL++AV  +      +LATY+   I
Sbjct: 63  KKYENNKDLQEDLISIGTIGLIKAVDSYKQNHKTKLATYASRCI 106


>gi|302866675|ref|YP_003835312.1| RNA polymerase sigma-70 factor [Micromonospora aurantiaca ATCC
           27029]
 gi|302569534|gb|ADL45736.1| RNA polymerase sigma-70 factor, sigma-B/F/G subfamily
           [Micromonospora aurantiaca ATCC 27029]
          Length = 273

 Score = 45.1 bits (105), Expect = 0.014,   Method: Compositional matrix adjust.
 Identities = 56/238 (23%), Positives = 103/238 (43%), Gaps = 30/238 (12%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R + + L L   +A  Y G G P  ++     IGL++A+ KFDP RG   A Y++  I  
Sbjct: 51  RAIEAWLPLANHLAHRYSGRGEPNDDLAQTAAIGLIKAIDKFDPSRGVDFAGYAIPTIIG 110

Query: 112 AMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL-------KPEQVVAIA 163
            ++ +   R+W  +++             RRL+    AI+D N        +   V  IA
Sbjct: 111 ELKRHFRDRTWD-IRVP------------RRLQELRLAISDANSTLLQTLGRSPTVADIA 157

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
             L ++E EV+          +++    + D   +     L+   DG+ ++         
Sbjct: 158 AHLKLTEEEVLEGLEGARAYNAVSLSTPTGDGERATELGDLLGGEDGEFEL-------AE 210

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R  L  +++ L+ RE++I   R      +T   ++ +  VS+  V ++ ARA  K++
Sbjct: 211 MRVALGPALATLDQREQKILTLRFYGN--LTQSQIAEQIGVSQMHVSRLLARALTKLR 266


>gi|83590422|ref|YP_430431.1| sporulation sigma factor SigK [Moorella thermoacetica ATCC 39073]
 gi|83573336|gb|ABC19888.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Moorella
           thermoacetica ATCC 39073]
          Length = 226

 Score = 45.1 bits (105), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 26/87 (29%), Positives = 48/87 (55%), Gaps = 8/87 (9%)

Query: 27  PMLEKQEEYVLAKRYRE---HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           P+ E++E+     +Y E    GD  A + L+  +LRLV  I   +   G    +++S G 
Sbjct: 32  PLSEEEEQ-----KYLELWLQGDQKARNILIEHNLRLVAHITKKFENTGEDTEDLISIGT 86

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIK 110
           +GL++A+  ++  +G +LATY+   I+
Sbjct: 87  VGLIKAINTYNKAKGTKLATYAARCIE 113


>gi|154482592|ref|ZP_02025040.1| hypothetical protein EUBVEN_00259 [Eubacterium ventriosum ATCC
           27560]
 gi|149736617|gb|EDM52503.1| hypothetical protein EUBVEN_00259 [Eubacterium ventriosum ATCC
           27560]
          Length = 192

 Score = 45.1 bits (105), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 22/65 (33%), Positives = 36/65 (55%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A   L+  +LRLV  +   Y        +++S G +GL++AV  ++P++G RL TY
Sbjct: 4   GDKKAKDILIERNLRLVAHVVKKYYDENRENQDLISIGIVGLIKAVNTYNPDKGNRLVTY 63

Query: 105 SMWWI 109
           +   I
Sbjct: 64  AAKCI 68


>gi|229195303|ref|ZP_04322075.1| RNA polymerase sigma-B factor [Bacillus cereus m1293]
 gi|228588158|gb|EEK46204.1| RNA polymerase sigma-B factor [Bacillus cereus m1293]
          Length = 242

 Score = 44.7 bits (104), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 54/243 (22%), Positives = 116/243 (47%), Gaps = 28/243 (11%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  RLV  +  LV  IA  Y   G    +++  G +GL+ A++++D   G     +++  
Sbjct: 15  AQERLVDHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPT 74

Query: 109 IKAAMQEYIL-RSWSLVKIGTTANQKRLFFNL-RRLKGHLQAITDNNLKPEQVVAIAKKL 166
           I   +++Y+  ++W +       +  R   +L  ++K  ++ +TD+  +  +++ IA  L
Sbjct: 75  IVGEIKKYLRDKTWGI-------HVPRRIKDLGGKIKLAIEELTDHLQRSPKIIEIADHL 127

Query: 167 NVSESEVISM-----NCRLAGDESLNALI-NSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +SE EV+ +     N R++   SL+ ++ N+SD +S    + +     G E+       
Sbjct: 128 GLSEEEVLEIMDAKNNYRVS---SLDDVVENASDGSSVARIESVGEVEQGYEET------ 178

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
              RR +L    +VLN  E+ +     + E  +  ++      +S+  V +I+ +A  K+
Sbjct: 179 --ERRLVLKDIFNVLNETEKSVI--HYIFEENLNQKDTGERLGISQMHVSRIKRQAISKL 234

Query: 281 QES 283
           +++
Sbjct: 235 KQA 237


>gi|188586385|ref|YP_001917930.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|179351072|gb|ACB85342.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 114

 Score = 44.7 bits (104), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 23/68 (33%), Positives = 38/68 (55%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E GD  A   L+  +LRLV  +   +   G    +++S G IGL++A+  ++  +G RLA
Sbjct: 44  EQGDDKAREVLIERNLRLVAHVIKKFENSGEDPEDLISIGTIGLIKAINTYNYRKGTRLA 103

Query: 103 TYSMWWIK 110
           TY+   I+
Sbjct: 104 TYAARCIE 111


>gi|146277655|ref|YP_001167814.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Rhodobacter
           sphaeroides ATCC 17025]
 gi|145555896|gb|ABP70509.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Rhodobacter
           sphaeroides ATCC 17025]
          Length = 239

 Score = 44.7 bits (104), Expect = 0.015,   Method: Compositional matrix adjust.
 Identities = 52/236 (22%), Positives = 111/236 (47%), Gaps = 22/236 (9%)

Query: 52  RLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           RLV +H+ LV +IA       G  + I +++  G +GL+ A ++++P  G   A Y+   
Sbjct: 16  RLVRAHMDLVRRIAWNLHARIGRKVEIDDLIQIGYMGLVDASRRYEPRDGVTFAAYAAIR 75

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ ++ ++ LRS S +   T   Q+++   ++RL+  L       ++  +   +A +L +
Sbjct: 76  IRGSIMDF-LRSNSALCRTTILMQQKVKAAVQRLESRL-------MRAPETPEVAAELGM 127

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              E      + AG ++  +L    D  SS +Q        G E    ++ +    R +L
Sbjct: 128 PVGEYQDWLAQFAGSQT-ASLDEVYDDQSSLFQ--------GSEPSAEDRLQATQMRGLL 178

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +++  +  RE  + +   ++E  + +  ++    V+  RV QI+  A ++++  I
Sbjct: 179 RQALGKMPEREALLLQLIFVEE--MNVYEVAEILGVTTGRVSQIKKAAIERLRGFI 232


>gi|168335364|ref|ZP_02693458.1| sporulation sigma factor SigG [Epulopiscium sp. 'N.t. morphotype
           B']
          Length = 243

 Score = 44.7 bits (104), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 26/100 (26%), Positives = 48/100 (48%), Gaps = 15/100 (15%)

Query: 25  KIPMLEKQEEYVLAKRYREH-------GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           K+P L  Q+        +EH       GD  A    +  +LRLV+ +   +   G  + +
Sbjct: 15  KLPTLTNQQ--------KEHLFELIGAGDNMAREEYIRGNLRLVLSVIQRFNNRGEHVDD 66

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           +   G IGL++A+  FD  +G + +TY++  I   ++ Y+
Sbjct: 67  LFQVGCIGLIKAIDNFDTTQGVKFSTYAVPMIIGEIRRYL 106


>gi|148381038|ref|YP_001255579.1| RNA polymerase sigma-F factor [Clostridium botulinum A str. ATCC
           3502]
 gi|153933259|ref|YP_001385409.1| sporulation sigma factor SigF [Clostridium botulinum A str. ATCC
           19397]
 gi|153935896|ref|YP_001388816.1| sporulation sigma factor SigF [Clostridium botulinum A str. Hall]
 gi|153939970|ref|YP_001392365.1| sporulation sigma factor SigF [Clostridium botulinum F str.
           Langeland]
 gi|170754271|ref|YP_001782722.1| sporulation sigma factor SigF [Clostridium botulinum B1 str. Okra]
 gi|226950516|ref|YP_002805607.1| RNA polymerase sigma-F factor [Clostridium botulinum A2 str. Kyoto]
 gi|148290522|emb|CAL84650.1| RNA polymerase sigma-F factor [Clostridium botulinum A str. ATCC
           3502]
 gi|152929303|gb|ABS34803.1| RNA polymerase sigma-F factor [Clostridium botulinum A str. ATCC
           19397]
 gi|152931810|gb|ABS37309.1| RNA polymerase sigma-F factor [Clostridium botulinum A str. Hall]
 gi|152935866|gb|ABS41364.1| RNA polymerase sigma-F factor [Clostridium botulinum F str.
           Langeland]
 gi|169119483|gb|ACA43319.1| RNA polymerase sigma-F factor [Clostridium botulinum B1 str. Okra]
 gi|226844449|gb|ACO87115.1| RNA polymerase sigma-F factor [Clostridium botulinum A2 str. Kyoto]
 gi|295320356|gb|ADG00734.1| RNA polymerase sigma-F factor [Clostridium botulinum F str. 230613]
 gi|322807388|emb|CBZ04962.1| RNA polymerase sporulation specific sigma factor SigF [Clostridium
           botulinum H04402 065]
          Length = 251

 Score = 44.7 bits (104), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 57/250 (22%), Positives = 114/250 (45%), Gaps = 36/250 (14%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           G+  A  +LV  +L LV  I+  +   G    ++   G IGL++A+  F+ +   + +TY
Sbjct: 26  GNKEALDKLVEVNLPLVSAISKKFLNRGYEYDDIFQIGCIGLVKAINNFETKYNVKFSTY 85

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTT--ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           ++  I   ++ + LR   ++K+  +     K+L ++  +L                    
Sbjct: 86  AVPMIMGEIKRF-LRDDGIIKVSRSIKTAAKKLHYDKEKL-------------------- 124

Query: 163 AKKLNVSES-EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK--- 218
            K+LN   + E +S       DE L A  +SS   S Q+   +++  DG   +LI+K   
Sbjct: 125 CKELNREPTIEELSQFSGYTVDEILMATESSS---SPQYLYDVIHQDDGAPVLLIDKISE 181

Query: 219 ---EERKNRRNM-LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
              E+ K   N+ L  ++  L+ + R+I   R  ++   T   ++ +  +S+ +V +IE 
Sbjct: 182 NTEEDNKIVDNIALKEALKNLDIKSRQIIILRYFKDK--TQIEVAKQLGISQVQVSRIEK 239

Query: 275 RAFKKVQESI 284
           +  K ++E +
Sbjct: 240 KVLKLMKEKL 249


>gi|326791514|ref|YP_004309335.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           lentocellum DSM 5427]
 gi|326542278|gb|ADZ84137.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           lentocellum DSM 5427]
          Length = 249

 Score = 44.7 bits (104), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 57/242 (23%), Positives = 104/242 (42%), Gaps = 37/242 (15%)

Query: 57  HLRLVVKIAMGYRGYGL----PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           H   +VK+  G  G  L       ++V  G +GL+ AV KFDP +  +  TY+   I+ A
Sbjct: 28  HYVYLVKLVAGRLGIYLNQYVDSDDLVGYGVLGLIDAVDKFDPGKNVKFETYASLRIRGA 87

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL------QAITDN-NLKPEQVVAIAKK 165
           + + I R    V       QK +      L+G L      + + D   +  E+   + K+
Sbjct: 88  ILDAI-RKLDWVPRTLRKKQKDIDKAYIELEGRLGRQPLDEEVADFLEISIEEYNELLKE 146

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           +N+  S +IS+      DE +    +  D ++   ++++               E    +
Sbjct: 147 VNI--SSLISI------DEYMYQFESVKDPSAPIPENYI---------------EDTEVK 183

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            ML   +  L  RE+++      +E  +TL+ +S   EVS  RV Q+  +A  +++  +Q
Sbjct: 184 EMLAEFIDSLPEREKKVIFLYYYEE--LTLKEISHVLEVSESRVSQLHTKAVSRLRAYMQ 241

Query: 286 KQ 287
           K 
Sbjct: 242 KH 243


>gi|167756988|ref|ZP_02429115.1| hypothetical protein CLORAM_02537 [Clostridium ramosum DSM 1402]
 gi|167703163|gb|EDS17742.1| hypothetical protein CLORAM_02537 [Clostridium ramosum DSM 1402]
          Length = 228

 Score = 44.7 bits (104), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 32/104 (30%), Positives = 55/104 (52%), Gaps = 3/104 (2%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +S++ NG   +S    +  ++P+  K+EE  L + +  +GD  A + L+  +LRLV  IA
Sbjct: 6   LSLLTNG-FFVSYIKSKSFELPLTAKEEERYLEQFF--NGDKEARNVLIERNLRLVAHIA 62

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             Y        +++S G IGL++AV  +      +LATY+   I
Sbjct: 63  KKYENNKDMQEDLISIGTIGLIKAVDSYKQNHKTKLATYASRCI 106


>gi|302558130|ref|ZP_07310472.1| RNA polymerase sigma factor WhiG [Streptomyces griseoflavus Tu4000]
 gi|302475748|gb|EFL38841.1| RNA polymerase sigma factor WhiG [Streptomyces griseoflavus Tu4000]
          Length = 280

 Score = 44.7 bits (104), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 62/245 (25%), Positives = 101/245 (41%), Gaps = 20/245 (8%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFD 94
           + Y+  GD     +L+  H   +VK   G    GLP      + VS G  GL+ A++KFD
Sbjct: 36  RSYKATGDERLREQLIL-HYSPLVKYVAGRVSVGLPPNVDQGDFVSSGVFGLIDAIEKFD 94

Query: 95  PERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
            +R  +  TY++  I+ AM  E     W    I  +  QK    N+ R    L+A     
Sbjct: 95  VDREIKFETYAITRIRGAMIDELRALDW----IPRSVRQKAR--NVERAYATLEARL-RR 147

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ--DWLVYDHDGQ 211
              E  VA    + V E   +     LA   +L  L++   ++  +    D L    D  
Sbjct: 148 TPSESEVAGELGIAVDELHAVFSQLSLANVVALEELLHVGGESGDRLSLMDTL---EDTA 204

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
               +E  E +  R  L R+++ L  RE+ +      +   +TL  + +   V+  RV Q
Sbjct: 205 ADDPVEVAEDRELRRFLARAINTLPEREKTVVTLYYYEG--LTLAEIGNVLGVTESRVSQ 262

Query: 272 IEARA 276
           I  ++
Sbjct: 263 IHTKS 267


>gi|317056324|ref|YP_004104791.1| Sig B/F/G subfamily RNA polymerase sigma-28 subunit [Ruminococcus
           albus 7]
 gi|315448593|gb|ADU22157.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Ruminococcus
           albus 7]
          Length = 256

 Score = 44.7 bits (104), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 28/88 (31%), Positives = 47/88 (53%), Gaps = 4/88 (4%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           EKQE   L KR  + GD +A  +L+  +LRLV+ +   Y G      ++   G +GL++A
Sbjct: 23  EKQE---LLKRSAD-GDKTAREKLIKGNLRLVLSVLQKYSGGKENPDDLFQVGVVGLIKA 78

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYI 117
           +  FD     R +TY++  I   ++ Y+
Sbjct: 79  IDNFDVGLNVRFSTYAVPMILGEIKRYM 106


>gi|163938900|ref|YP_001643784.1| RNA polymerase sigma factor SigB [Bacillus weihenstephanensis
           KBAB4]
 gi|163861097|gb|ABY42156.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           weihenstephanensis KBAB4]
          Length = 257

 Score = 44.7 bits (104), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 55/231 (23%), Positives = 110/231 (47%), Gaps = 27/231 (11%)

Query: 22  EIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           EI+  P  L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++ 
Sbjct: 2   EIQSQPTDLTKEDVIKLIAEFQQNQCDEAQERLVNHYKNLVYSIAYRYSKGGPMHEDIIQ 61

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNL 139
            G +GL+ A++++D   G     +++  I   +++Y+  ++W +       +  R   +L
Sbjct: 62  VGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGV-------HVPRRIKDL 114

Query: 140 -RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNALI-NS 192
             ++K  ++ +TD+  +  +++ IA  L +SE EV+ +     N +++   SL+ ++ NS
Sbjct: 115 GGKIKLAIEELTDHLQRSPKIIEIANHLGLSEEEVLEIMDAKNNYQVS---SLDDVVENS 171

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           SD +S    + +     G EQ          RR +L    +VLN  E+ + 
Sbjct: 172 SDGSSVARIESVGEVEQGYEQT--------ERRLVLDDIFNVLNDTEKSVI 214


>gi|239941779|ref|ZP_04693716.1| putative RNA polymerase sigma factor [Streptomyces roseosporus NRRL
           15998]
 gi|239988239|ref|ZP_04708903.1| putative RNA polymerase sigma factor [Streptomyces roseosporus NRRL
           11379]
 gi|291445225|ref|ZP_06584615.1| RNA polymerase sigma factor [Streptomyces roseosporus NRRL 15998]
 gi|291348172|gb|EFE75076.1| RNA polymerase sigma factor [Streptomyces roseosporus NRRL 15998]
          Length = 329

 Score = 44.7 bits (104), Expect = 0.016,   Method: Compositional matrix adjust.
 Identities = 58/242 (23%), Positives = 106/242 (43%), Gaps = 30/242 (12%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           + LV  +L LV   A  +R    P+ ++V  G IGL++A+ +F+  RG    T++M  I 
Sbjct: 106 NTLVELNLALVKFAASRFRSRSEPMEDIVQVGTIGLIKAIDRFELSRGVEFPTFAMPTIV 165

Query: 111 AAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
             ++ +    SWS V++     + RL  +L +    L    D   +   V  ++++L ++
Sbjct: 166 GEIKRFFRDTSWS-VRVPRRLQELRL--DLAKAGDELSQQLD---RAPTVAELSERLGIT 219

Query: 170 ESEVISMNCRLAGDESLNALINSS-------DKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
             EV+       G  + NA   SS       D +     D + Y+  G E   IE  E  
Sbjct: 220 PDEVVE------GMSASNAYTASSLDAKPEEDDSEGALADRIGYEDHGLEG--IEYVES- 270

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
                L   ++ L  R+R I   R +    +T   +  E  +S+  V ++ +R   K+++
Sbjct: 271 -----LKPLIAALPARDRMILSLRFVSN--MTQSEIGEELNISQMHVSRLLSRTLTKLRK 323

Query: 283 SI 284
            +
Sbjct: 324 GL 325


>gi|291545415|emb|CBL18523.1| RNA polymerase, sigma subunit, RpsG/SigG [Ruminococcus sp. SR1/5]
          Length = 259

 Score = 44.7 bits (104), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 58/265 (21%), Positives = 120/265 (45%), Gaps = 35/265 (13%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L+++E+  L KR +  GD  A    +  +LRLV+ +   ++       ++   G IG
Sbjct: 16  LPVLDQEEKAELFKRIK-AGDEEARELYIKGNLRLVLSVIRRFQNSSENPDDLFQIGCIG 74

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ---KRLFFNLRRL 142
           L++A+  FD     + +TY++  I   ++ Y LR  + +++  +      K ++     +
Sbjct: 75  LIKAIDNFDTTLQVKFSTYAVPMIIGEIRRY-LRDNNSIRVSRSLRDIAYKTIYTRENYM 133

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL------AGDESLNALINSSDKN 196
           + HL+  T   +  E  + I K++ V   + I     L       G ++L  +   SDK 
Sbjct: 134 RQHLKEPTIAEIADE--IGIDKEMIVYAMDAIQSPVSLFEPVYSEGGDTLYVMDQISDKK 191

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           + + ++W+               E  + R+ + R    L  RER I +  R  E    +E
Sbjct: 192 NLE-ENWV---------------EDISLRDAMNR----LGERERHIIDL-RFYEGKTQME 230

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            ++ E  +S+ +V ++E  A + ++
Sbjct: 231 -VADEIGISQAQVSRLEKHALRSMR 254


>gi|284992377|ref|YP_003410931.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geodermatophilus
           obscurus DSM 43160]
 gi|284065622|gb|ADB76560.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geodermatophilus
           obscurus DSM 43160]
          Length = 266

 Score = 44.7 bits (104), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 50/224 (22%), Positives = 94/224 (41%), Gaps = 15/224 (6%)

Query: 57  HLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           H   +VK   G  G GLP     +++VS G  GL+ A+ ++ P R  +  +Y+M  I+ A
Sbjct: 42  HYAPLVKYVAGRVGSGLPAHVEQADLVSYGTFGLIDAITRYQPSREVKFESYAMARIRGA 101

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           + +  LRS   +        ++    +  L+  LQ         E+ VA    ++V +  
Sbjct: 102 IIDE-LRSTDWIPRSVRMKARQFERTVALLESRLQ-----RSPSEEEVAAEMDMDVEDVR 155

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
                  L    +L+ L++  +  + +  D L        Q + E  E    R +L R++
Sbjct: 156 KFLGQLSLVNVVALDELLSDDEGGAPRLVDTLQDTSALDPQAMAEHSE---ARQLLARAV 212

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
             L  RE+ +      +   +TL ++     V+  R+ Q+  +A
Sbjct: 213 EQLPEREKVVVSLYYFE--GLTLADIGRVLGVTESRICQLHTKA 254


>gi|194017684|ref|ZP_03056294.1| RNA polymerase sigma-K factor [Bacillus pumilus ATCC 7061]
 gi|194010584|gb|EDW20156.1| RNA polymerase sigma-K factor [Bacillus pumilus ATCC 7061]
          Length = 289

 Score = 44.7 bits (104), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 22/66 (33%), Positives = 38/66 (57%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A + L+  +LRLV  I   +   G    +++S G IGL++A++ +   +G +LATY
Sbjct: 94  GDEHARNMLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIESYSSGKGTKLATY 153

Query: 105 SMWWIK 110
           +   I+
Sbjct: 154 AARCIE 159


>gi|302871341|ref|YP_003839977.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
 gi|302574200|gb|ADL41991.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
          Length = 242

 Score = 44.7 bits (104), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 29/93 (31%), Positives = 51/93 (54%), Gaps = 5/93 (5%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP--ISEVVSEGNI 84
           PM  ++EE  L K +   G   A + LV  +LRLV  IA  Y  +  P    +++S G I
Sbjct: 36  PMSSEEEEMYLNKMW--EGCKEARNILVEKNLRLVAHIAKKYT-FSFPNLTDDIISVGTI 92

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           GL++A++ +  ++  +L+TY+   I+  +  Y+
Sbjct: 93  GLIKAIETYSKDKSTKLSTYAAKCIENEILMYL 125


>gi|313115569|ref|ZP_07801028.1| RNA polymerase sigma-G factor [Faecalibacterium cf. prausnitzii
           KLE1255]
 gi|310622084|gb|EFQ05580.1| RNA polymerase sigma-G factor [Faecalibacterium cf. prausnitzii
           KLE1255]
          Length = 255

 Score = 44.7 bits (104), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 55/235 (23%), Positives = 104/235 (44%), Gaps = 29/235 (12%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            ++V  +LRLV+ +   +   G  + ++   G IGL++A+  FDP +  R +TY +  I 
Sbjct: 39  EQMVEGNLRLVLSVVQRFAQRGENLDDLFQVGCIGLIKAIDHFDPAQPVRFSTYGVPMII 98

Query: 111 AAMQEYI-----LR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
             ++ ++     LR S SL      A Q R            +A+     +   +  IA+
Sbjct: 99  GEIRRFLRDNNALRVSRSLRDTAYRAMQSR------------EALEKQLGREPTMDEIAQ 146

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
              ++  EV +    +    SL   +  +D   + +    V D DG++  +   + R+  
Sbjct: 147 AAGLARREVTAALESVVEPISLEEPV-YTDGGDAMYVIDQVRDPDGEDSWISGLQFRQ-- 203

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
                 +++ L PRE+RI E R LQ    T   ++ E  +S+ +V ++E  A  +
Sbjct: 204 ------TVAGLTPREKRIMELRYLQGK--TQMEVAREIGISQAQVSRLEKGALSQ 250


>gi|296501716|ref|YP_003663416.1| RNA polymerase sigma factor SigB [Bacillus thuringiensis BMB171]
 gi|296322768|gb|ADH05696.1| RNA polymerase sigma factor SigB [Bacillus thuringiensis BMB171]
          Length = 257

 Score = 44.7 bits (104), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 55/231 (23%), Positives = 110/231 (47%), Gaps = 27/231 (11%)

Query: 22  EIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           EI+  P  L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++ 
Sbjct: 2   EIQSQPTNLTKEDVIKLIADFQQNQCDEAQERLVEHYKNLVYSIAYRYSKGGPMHEDIIQ 61

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNL 139
            G +GL+ A++++D   G     +++  I   +++Y+  ++W +       +  R   +L
Sbjct: 62  VGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGI-------HVPRRIKDL 114

Query: 140 -RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNALI-NS 192
             ++K  ++ +TD+  +  +++ IA  L +SE EV+ +     N R++   SL+ ++ NS
Sbjct: 115 GGKIKLAIEELTDHLQRSPKIIEIANHLGLSEEEVLEIMDAKNNYRVS---SLDDVVENS 171

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           SD +S    + +     G E+          RR +L    +VLN  E+ + 
Sbjct: 172 SDGSSVARIESVGEVEQGYEET--------ERRLVLKDIFNVLNDTEKSVI 214


>gi|291334306|gb|ADD93967.1| sigma factor FliA sigma 28 group flagellar [uncultured marine
           bacterium MedDCM-OCT-S09-C247]
          Length = 225

 Score = 44.7 bits (104), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 51/230 (22%), Positives = 105/230 (45%), Gaps = 22/230 (9%)

Query: 52  RLVTSHLRLVVKIAMGYRG-YG--LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           +L+  +L +V KIA  Y G  G  + + +++  G +GL++A   + P+       Y+   
Sbjct: 14  QLINDNLDIVKKIAFFYVGRVGKVVEVDDLLQLGMVGLIEAAHNYTPQDDVSFVNYARLR 73

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           +K A+ +Y+ +S +L + GT   ++      R+L+  L        +  +   IAK+L V
Sbjct: 74  VKGAIVDYLRKSSNLCR-GTIRRKQDYERAKRKLEKEL-------FRQPETHEIAKELKV 125

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
             S+++S     A  +       S ++ S  + D+L       E+ +   E     +++L
Sbjct: 126 EVSDLLSWQHDFAASQH-----QSLEEASDAYGDFLFATDKSVEEKIFNGE----LKDIL 176

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
              +  LN ++  + +   ++E  + +  +     VS  RV QI++ A K
Sbjct: 177 RTKLEDLNEQQLMVLQLYYVEE--LNVYEIGEILSVSTGRVSQIKSAAIK 224


>gi|167464009|ref|ZP_02329098.1| RNA polymerase, sigma 28 subunit [Paenibacillus larvae subsp.
           larvae BRL-230010]
          Length = 175

 Score = 44.7 bits (104), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 44/168 (26%), Positives = 77/168 (45%), Gaps = 23/168 (13%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFDPER 97
           Y  H  L    +++ ++ ++V  +A  YR   G GL   ++VS G IGL+QA + +DP+R
Sbjct: 5   YNPH--LGYEDQIIPAYEKMVHSVARKYRSCIGAGLDYDDLVSVGMIGLIQAFRNYDPDR 62

Query: 98  GFR----LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
             R     +TY+   IK ++Q ++            A+++      R ++  L  I    
Sbjct: 63  LNRKVSSFSTYAFNMIKWSIQRFL------------ADKRFSVRVPRSIQNKLTVIWKQG 110

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAG--DESLNALINSSDKNSSQ 199
              E   +IA+K      E+      +AG    SL+  ++SSDK   +
Sbjct: 111 WDQESAESIAEKTGWKLPEIREAQRHIAGWSVASLDQALSSSDKTDEE 158


>gi|17227773|ref|NP_484321.1| RNA polymerase sigma factor SigF [Nostoc sp. PCC 7120]
 gi|17135255|dbj|BAB77801.1| RNA polymerase sigma-37 factor [Nostoc sp. PCC 7120]
          Length = 261

 Score = 44.7 bits (104), Expect = 0.017,   Method: Compositional matrix adjust.
 Identities = 24/91 (26%), Positives = 50/91 (54%), Gaps = 1/91 (1%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKKFDP 95
           L + Y  +  +   +RLV  H  LV K+A  +      P  ++   G  GL++A+++FDP
Sbjct: 15  LLRSYHHNPSIKLRNRLVQLHTGLVRKMAHKFSHQCNEPYEDLEQIGYFGLIRAIERFDP 74

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            +G+  +++++ +I+  M  ++    +L+KI
Sbjct: 75  SQGYAFSSFAVPYIRGEMLHFLRDRSTLLKI 105


>gi|237732926|ref|ZP_04563407.1| sporulation sigma factor sigK [Mollicutes bacterium D7]
 gi|229383995|gb|EEO34086.1| sporulation sigma factor sigK [Coprobacillus sp. D7]
          Length = 223

 Score = 44.7 bits (104), Expect = 0.018,   Method: Compositional matrix adjust.
 Identities = 28/84 (33%), Positives = 45/84 (53%), Gaps = 2/84 (2%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+  K+EE  L + +  +GD  A + L+  +LRLV  IA  Y        +++S G IG
Sbjct: 25  LPLTAKEEERYLEQFF--NGDKEARNVLIERNLRLVAHIAKKYENNKDMQEDLISIGTIG 82

Query: 86  LMQAVKKFDPERGFRLATYSMWWI 109
           L++AV  +      +LATY+   I
Sbjct: 83  LIKAVDSYKQNHKTKLATYASRCI 106


>gi|150388236|ref|YP_001318285.1| FliA/WhiG family RNA polymerase sigma factor [Alkaliphilus
           metalliredigens QYMF]
 gi|149948098|gb|ABR46626.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           metalliredigens QYMF]
          Length = 218

 Score = 44.7 bits (104), Expect = 0.018,   Method: Compositional matrix adjust.
 Identities = 33/119 (27%), Positives = 58/119 (48%), Gaps = 9/119 (7%)

Query: 16  LSRYIHEIR-KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           + + +H++  K PM E +E   L  ++RE  +      L+  +LRLV   A  Y+     
Sbjct: 1   MEKLLHKVNFKEPMTE-EESKRLINQFRELNNEEIRKHLIERNLRLVAYEAYKYKNQ--D 57

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR-----SWSLVKIGT 128
             ++ S G IGL++A+  +DP +  R  TY+   I+  +  YI R      W+ V++  
Sbjct: 58  SEDIFSVGCIGLIKAIDSYDPSKQTRFDTYANRCIQNEILLYIKRLKKGSRWTFVRLDA 116


>gi|307109682|gb|EFN57919.1| hypothetical protein CHLNCDRAFT_141989 [Chlorella variabilis]
          Length = 509

 Score = 44.7 bits (104), Expect = 0.018,   Method: Compositional matrix adjust.
 Identities = 27/85 (31%), Positives = 43/85 (50%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  AA  L  ++  LV  +A  + G GL   ++V+EG + L +A   F P+R  R  T+
Sbjct: 65  GDHRAAAMLAHANRPLVTWLAAKFAGRGLAKEDLVAEGMLALERAAGSFHPDREARFGTF 124

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTT 129
           +   I  A+   I R   +++I  T
Sbjct: 125 AAAAISNALSRAIRRQSRVIRIPET 149


>gi|206968111|ref|ZP_03229067.1| RNA polymerase sigma-B factor [Bacillus cereus AH1134]
 gi|206737031|gb|EDZ54178.1| RNA polymerase sigma-B factor [Bacillus cereus AH1134]
          Length = 257

 Score = 44.7 bits (104), Expect = 0.018,   Method: Compositional matrix adjust.
 Identities = 55/231 (23%), Positives = 109/231 (47%), Gaps = 27/231 (11%)

Query: 22  EIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           EI+  P  L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++ 
Sbjct: 2   EIQSQPTNLTKEDVIKLIADFQQNQCDEAQERLVNHYKNLVYSIAYRYSKGGPMHEDIIQ 61

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNL 139
            G +GL+ A++++D   G     +++  I   +++Y+  ++W +       +  R   +L
Sbjct: 62  VGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGI-------HVPRRIKDL 114

Query: 140 -RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNALI-NS 192
             ++K  ++ +TD   +  +++ IA  L +SE EV+ +     N R++   SL+ ++ NS
Sbjct: 115 GGKIKLAIEELTDRFQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVS---SLDDVVENS 171

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           SD +S    + +     G E+          RR +L    +VLN  E+ + 
Sbjct: 172 SDGSSVARIESVGEVEQGYEET--------ERRLVLKDIFNVLNETEKSVI 214


>gi|187778269|ref|ZP_02994742.1| hypothetical protein CLOSPO_01861 [Clostridium sporogenes ATCC
           15579]
 gi|187771894|gb|EDU35696.1| hypothetical protein CLOSPO_01861 [Clostridium sporogenes ATCC
           15579]
          Length = 251

 Score = 44.7 bits (104), Expect = 0.018,   Method: Compositional matrix adjust.
 Identities = 57/250 (22%), Positives = 114/250 (45%), Gaps = 36/250 (14%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           G+  A  +LV  +L LV  I+  +   G    ++   G IGL++A+  F+ +   + +TY
Sbjct: 26  GNKQALDKLVEVNLPLVSAISKKFLNRGYEYDDIFQIGCIGLVKAINNFETKYNVKFSTY 85

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTT--ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           ++  I   ++ + LR   ++K+  +     K+L ++  +L                    
Sbjct: 86  AVPMIMGEIKRF-LRDDGIIKVSRSIKTAAKKLHYDKEKL-------------------- 124

Query: 163 AKKLNVSES-EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK--- 218
            K+LN   + E +S       DE L A  +SS   S Q+   +++  DG   +LI+K   
Sbjct: 125 CKELNREPTIEELSQFSGYTVDEILMATESSS---SPQYLYDVIHQDDGAPVLLIDKISE 181

Query: 219 ---EERKNRRNM-LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
              E+ K   N+ L  ++  L+ + R+I   R  ++   T   ++ +  +S+ +V +IE 
Sbjct: 182 NTEEDNKIIDNIALKEALKNLDIKSRQIIILRYFKDK--TQIEVAKQLGISQVQVSRIEK 239

Query: 275 RAFKKVQESI 284
           +  K ++E +
Sbjct: 240 KVLKLMKEKL 249


>gi|218232670|ref|YP_002365766.1| RNA polymerase sigma factor SigB [Bacillus cereus B4264]
 gi|218160627|gb|ACK60619.1| RNA polymerase sigma-B factor [Bacillus cereus B4264]
          Length = 257

 Score = 44.7 bits (104), Expect = 0.018,   Method: Compositional matrix adjust.
 Identities = 55/231 (23%), Positives = 109/231 (47%), Gaps = 27/231 (11%)

Query: 22  EIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           EI+  P  L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++ 
Sbjct: 2   EIQSQPTNLTKEDVIKLIADFQQNQCDEAQERLVNHYKNLVYSIAYRYSKGGPMHEDIIQ 61

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNL 139
            G +GL+ A++++D   G     +++  I   +++Y+  ++W +       +  R   +L
Sbjct: 62  VGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGI-------HVPRRIKDL 114

Query: 140 -RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNALI-NS 192
             ++K  ++ +TD   +  +++ IA  L +SE EV+ +     N R++   SL+ ++ NS
Sbjct: 115 GGKIKLAIEELTDRFQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVS---SLDDVVENS 171

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           SD +S    + +     G E+          RR +L    +VLN  E+ + 
Sbjct: 172 SDGSSVARIESVGEVEQGYEET--------ERRLVLKDIFNVLNDTEKSVI 214


>gi|217967265|ref|YP_002352771.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Dictyoglomus
           turgidum DSM 6724]
 gi|217336364|gb|ACK42157.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Dictyoglomus
           turgidum DSM 6724]
          Length = 235

 Score = 44.7 bits (104), Expect = 0.018,   Method: Compositional matrix adjust.
 Identities = 27/130 (20%), Positives = 64/130 (49%), Gaps = 6/130 (4%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           +Y+E GD      L+     L+   A  +  YG P+ +++  G +G ++A++ +DP++G 
Sbjct: 11  KYKETGDKKFLEELLNVFDDLIHYWASKFTSYGEPLEDLIQIGYLGFLKAIENYDPKKG- 69

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
            L+TY   ++   ++ ++      +KI  +    ++  N  ++   ++ + +   +    
Sbjct: 70  ELSTYISHYVLGEIRHHLRDKIDKIKIPRSV---KILIN--KMDNFIKEVWEKENRSPSC 124

Query: 160 VAIAKKLNVS 169
             IAK LN++
Sbjct: 125 EEIAKHLNIT 134


>gi|168179581|ref|ZP_02614245.1| RNA polymerase sigma-F factor [Clostridium botulinum NCTC 2916]
 gi|168181777|ref|ZP_02616441.1| RNA polymerase sigma-F factor [Clostridium botulinum Bf]
 gi|170761116|ref|YP_001788407.1| sporulation sigma factor SigF [Clostridium botulinum A3 str. Loch
           Maree]
 gi|237796543|ref|YP_002864095.1| sporulation sigma factor SigF [Clostridium botulinum Ba4 str. 657]
 gi|169408105|gb|ACA56516.1| RNA polymerase sigma-F factor [Clostridium botulinum A3 str. Loch
           Maree]
 gi|182669805|gb|EDT81781.1| RNA polymerase sigma-F factor [Clostridium botulinum NCTC 2916]
 gi|182675139|gb|EDT87100.1| RNA polymerase sigma-F factor [Clostridium botulinum Bf]
 gi|229260985|gb|ACQ52018.1| RNA polymerase sigma-F factor [Clostridium botulinum Ba4 str. 657]
          Length = 251

 Score = 44.7 bits (104), Expect = 0.018,   Method: Compositional matrix adjust.
 Identities = 57/250 (22%), Positives = 114/250 (45%), Gaps = 36/250 (14%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           G+  A  +LV  +L LV  I+  +   G    ++   G IGL++A+  F+ +   + +TY
Sbjct: 26  GNKEALDKLVEVNLPLVSAISKKFLNRGYEYDDIFQIGCIGLVKAINNFETKYNVKFSTY 85

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTT--ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           ++  I   ++ + LR   ++K+  +     K+L ++  +L                    
Sbjct: 86  AVPMIMGEIKRF-LRDDGIIKVSRSIKTAAKKLHYDKEKL-------------------- 124

Query: 163 AKKLNVSES-EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK--- 218
            K+LN   + E +S       DE L A  +SS   S Q+   +++  DG   +LI+K   
Sbjct: 125 CKELNREPTIEELSQFSGYTVDEILMATESSS---SPQYLYDVIHQDDGAPVLLIDKISE 181

Query: 219 ---EERKNRRNM-LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
              E+ K   N+ L  ++  L+ + R+I   R  ++   T   ++ +  +S+ +V +IE 
Sbjct: 182 NTEEDNKIIDNIALKEALKNLDIKSRQIIILRYFKDK--TQIEVAKQLGISQVQVSRIEK 239

Query: 275 RAFKKVQESI 284
           +  K ++E +
Sbjct: 240 KVLKLMKEKL 249


>gi|332981462|ref|YP_004462903.1| RNA polymerase sigma-28 subunit FliA/WhiG [Mahella australiensis
           50-1 BON]
 gi|332699140|gb|AEE96081.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Mahella australiensis
           50-1 BON]
          Length = 247

 Score = 44.7 bits (104), Expect = 0.018,   Method: Compositional matrix adjust.
 Identities = 48/219 (21%), Positives = 102/219 (46%), Gaps = 29/219 (13%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           G  + +++  G  GL+ A++++DP R  +  TY+   I+ A+ +  LR   ++       
Sbjct: 48  GDDLDDLIGYGVFGLLDAIERYDPSRDVKFETYASHRIRGAIIDN-LRKKDVIPRSVRDK 106

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQV---VAIA-KKLNVSESEVISMNCRLAGDESLN 187
            K    +L  +   L+A +D  +  E V   + I+ ++L+   +++   NC ++ DE   
Sbjct: 107 VK----HLDAVYKQLEATSDKPVSDEDVCRYLGISIEQLDALYADINRFNC-ISLDEIFV 161

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
              N  D  SS+     VYD             R   + +L+ ++S L+ RE+++ +   
Sbjct: 162 DEWNIGDTESSES----VYD-------------RIELKQVLSEAVSKLSDREKQLLQLYY 204

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              + +TL+ +     +S  RV Q+  +A  +++  ++K
Sbjct: 205 Y--DGLTLKEIGKVLGISESRVSQLHTKALLQLRSRLRK 241


>gi|317127083|ref|YP_004093365.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Bacillus
           cellulosilyticus DSM 2522]
 gi|315472031|gb|ADU28634.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Bacillus
           cellulosilyticus DSM 2522]
          Length = 262

 Score = 44.7 bits (104), Expect = 0.018,   Method: Compositional matrix adjust.
 Identities = 57/256 (22%), Positives = 119/256 (46%), Gaps = 34/256 (13%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y+  G+     +LV     LV  +A  +        +++  G IGL+ A+++FDP  G  
Sbjct: 23  YQSTGNKEIQTKLVLEFESLVHALARKFSRGQRHDEDLIQVGMIGLLAAIRRFDPTIGKS 82

Query: 101 LATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
             ++++  I   ++ +I  ++WS+         +R+     ++K  +  +T    +  +V
Sbjct: 83  FESFAVPTIIGEIKRFIRDKTWSV------HVPRRIKEMGPKVKNAVDTLTTQLQRSPKV 136

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNAL-----INSSDKNSSQWQDWLVYDHDGQEQV 214
             IA  ++ SE EV+     +   +S  AL     I + D+ S+     LV   +G    
Sbjct: 137 EEIAAHIDASEEEVLET---MEMGKSYQALSVDRSIEADDEGSAVTLLDLVGSTEG---- 189

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS-----EFEVSRERV 269
                E+ +++ +L ++ +VL+ RE++I        +    ENLS      +  +S+  V
Sbjct: 190 ---GYEKTDQQMLLEKAFTVLSDREKQIL-------HLTYFENLSQKDTGEKLGISQMHV 239

Query: 270 RQIEARAFKKVQESIQ 285
            +++ RA +K++ES++
Sbjct: 240 SRLQRRALQKLRESLK 255


>gi|223700510|gb|ACN20374.1| truncated RNA polymerase sigma factor SigB [Listeria monocytogenes]
          Length = 188

 Score = 44.7 bits (104), Expect = 0.018,   Method: Compositional matrix adjust.
 Identities = 36/145 (24%), Positives = 71/145 (48%), Gaps = 7/145 (4%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +++D   G     +++  I   ++ ++  ++WS+         +R+     ++K  ++ +
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSV------HVPRRIKELGPKIKNAVEEL 125

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVI 174
           T       Q+  IA  + V+E EV+
Sbjct: 126 TRELQSSPQISDIADFIGVTEEEVL 150


>gi|210621718|ref|ZP_03292767.1| hypothetical protein CLOHIR_00712 [Clostridium hiranonis DSM 13275]
 gi|210154600|gb|EEA85606.1| hypothetical protein CLOHIR_00712 [Clostridium hiranonis DSM 13275]
          Length = 252

 Score = 44.7 bits (104), Expect = 0.019,   Method: Compositional matrix adjust.
 Identities = 23/84 (27%), Positives = 48/84 (57%), Gaps = 1/84 (1%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GDL + ++L+  ++ LV K    +    L   ++   G IGL++A+++FDP  G   +
Sbjct: 27  QKGDLKSKNKLIKLNIGLVKKAVSKFSFSSLDNDDLYQLGCIGLVKAIERFDPNLGNMFS 86

Query: 103 TYSMWWIKAAMQEYILRSWSLVKI 126
           +Y++  I+  ++ + LR   ++KI
Sbjct: 87  SYAVPLIEGEIKRF-LRDDGIIKI 109


>gi|28211847|ref|NP_782791.1| sporulation sigma factor SigF [Clostridium tetani E88]
 gi|28204289|gb|AAO36728.1| RNA polymerase sigma-F factor [Clostridium tetani E88]
          Length = 255

 Score = 44.7 bits (104), Expect = 0.019,   Method: Compositional matrix adjust.
 Identities = 58/250 (23%), Positives = 113/250 (45%), Gaps = 32/250 (12%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           ++GD  A  +LV  +L LV  I+  +   G    ++   G +GL++A+  FD     + +
Sbjct: 27  KNGDKKATDKLVELNLPLVSAISKKFLNRGYDYEDIYQIGCMGLVKAINNFDSSYNVKFS 86

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I   ++ +I R   ++K+      + L    R+L  H +              +
Sbjct: 87  TYAVPMIMGEIKRFI-RDDGIIKV-----SRSLKIMARKLYYHRE-------------TL 127

Query: 163 AKKLNVSES-EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK--- 218
            KKL    S E +S    L  +E + A+ +SS+    Q+   +++  DG   +LI+K   
Sbjct: 128 CKKLGREPSIEELSEYTGLEIEEIVYAMESSSN---LQYLHDVIHQDDGAPIMLIDKISE 184

Query: 219 --EERKNRRNMLT--RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
              E  +  N L    ++  L+ + R+I   R  ++   T   ++    +S+ +V +IE 
Sbjct: 185 NYSEDSDIINKLALKEALGKLDAKSRQIIMLRYFKDK--TQIEVAKMLGISQVQVSRIEK 242

Query: 275 RAFKKVQESI 284
           R  K ++E +
Sbjct: 243 RVLKTMKEKL 252


>gi|126659593|ref|ZP_01730724.1| sigma factor SigF [Cyanothece sp. CCY0110]
 gi|126619136|gb|EAZ89874.1| sigma factor SigF [Cyanothece sp. CCY0110]
          Length = 245

 Score = 44.7 bits (104), Expect = 0.019,   Method: Compositional matrix adjust.
 Identities = 24/87 (27%), Positives = 50/87 (57%), Gaps = 1/87 (1%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           Y  +  L   +RLV  +L LV ++A    R    P  ++   G +GL++A+++FDP++G 
Sbjct: 7   YARNPSLELRNRLVERNLGLVRQVAHRISRQCSEPYEDLEQIGYLGLIRAIERFDPQQGC 66

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKI 126
             +++++ +I+  M  Y+    S+++I
Sbjct: 67  AFSSFAIPYIRGEMLHYLRDKGSVMRI 93


>gi|297200169|ref|ZP_06917566.1| RNA polymerase sigma-E factor [Streptomyces sviceus ATCC 29083]
 gi|197713380|gb|EDY57414.1| RNA polymerase sigma-E factor [Streptomyces sviceus ATCC 29083]
          Length = 304

 Score = 44.3 bits (103), Expect = 0.020,   Method: Compositional matrix adjust.
 Identities = 44/167 (26%), Positives = 77/167 (46%), Gaps = 14/167 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  +L LV   A  +R    P+ +++  G IGL++A+ +F+  RG    T++M  I   
Sbjct: 83  LVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRGVEFPTFAMPTIVGE 142

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL  +L +    L    D   +   V  +A +L +S+ 
Sbjct: 143 IKRFFRDTSWS-VRVPRRLQELRL--DLAKAGDELAQKLD---RAPTVAELADRLGLSKE 196

Query: 172 EVI----SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           EV+    + N   A   SL+A     D   +   D + Y+  G E +
Sbjct: 197 EVVEGMAASNAYTAA--SLDAQPEEDDSEGA-LADRIGYEDHGLEGI 240


>gi|94495423|ref|ZP_01302003.1| flagellar-specific RNA polymerase sigma factor [Sphingomonas sp.
           SKA58]
 gi|94424811|gb|EAT09832.1| flagellar-specific RNA polymerase sigma factor [Sphingomonas sp.
           SKA58]
          Length = 243

 Score = 44.3 bits (103), Expect = 0.020,   Method: Compositional matrix adjust.
 Identities = 59/258 (22%), Positives = 106/258 (41%), Gaps = 36/258 (13%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKK 92
           V A  Y + G+ S   RL   ++ LV KIA    G     + + +++  G + L++A   
Sbjct: 8   VGAHTYGKPGEHSP-ERLARQYMPLVRKIAWHVHGRVSTAIEVEDLLQIGMVALVEAANS 66

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK------RLFFNLRRLKGHL 146
           F+ +RG   A Y+   ++ AM +++ R  +L +      ++      RL   L RL    
Sbjct: 67  FE-DRGLGFAAYAQLRVRGAMIDHLRRQATLCRSAMARRKEIAGVRNRLEQQLGRLPTEA 125

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +  ++  L+P                      R A D        S D+  S    W   
Sbjct: 126 EMSSEMGLEPAAY-------------------REAADSVEMVQHTSMDEVYSDQSMWFAD 166

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
             D  +QVL    ER++ +  +   +S L  RE  + +   ++E  + LE +    ++  
Sbjct: 167 VEDRADQVL----ERESLKKAMAACISELPQREAMVLQLYFVEE--MNLEEIGQTLDIGA 220

Query: 267 ERVRQIEARAFKKVQESI 284
            RV QI+  A  K++E +
Sbjct: 221 ARVCQIKKAALDKLREKL 238


>gi|115394497|gb|ABI97158.1| RNA polymerase sigma factor [Fusobacterium necrophorum]
          Length = 185

 Score = 44.3 bits (103), Expect = 0.020,   Method: Compositional matrix adjust.
 Identities = 48/188 (25%), Positives = 88/188 (46%), Gaps = 26/188 (13%)

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG----HLQAITDNNLKPEQ 158
           TY+ WWI+ A+   I      ++I        +   + ++K     +LQ  T  +  PE 
Sbjct: 1   TYAPWWIRQAITRAIADQGRTIRIPV-----HMIETINKIKKEARIYLQE-TGKDATPE- 53

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              +A++L +   +V S+        SL   + S +   S+  D++      ++Q ++  
Sbjct: 54  --ILAERLGMEVEKVKSIQEMNQDPISLETPVGSEE--DSELGDFV------EDQKMLTP 103

Query: 219 EERKNR---RNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIE 273
            E  NR   R  L   +  L+ RE ++   R   ++  P TLE +   F+V+RER+RQIE
Sbjct: 104 YELTNRSLLREQLDSVLGSLSSREEKVLRYRYGLDDGSPKTLEEVGKIFKVTRERIRQIE 163

Query: 274 ARAFKKVQ 281
            +A +K++
Sbjct: 164 VKALRKLR 171


>gi|297202660|ref|ZP_06920057.1| RNA polymerase sigma-G factor [Streptomyces sviceus ATCC 29083]
 gi|197713235|gb|EDY57269.1| RNA polymerase sigma-G factor [Streptomyces sviceus ATCC 29083]
          Length = 280

 Score = 44.3 bits (103), Expect = 0.021,   Method: Compositional matrix adjust.
 Identities = 61/245 (24%), Positives = 109/245 (44%), Gaps = 20/245 (8%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFD 94
           + Y+  GD     +L+  H   +VK   G    GLP     ++ VS G  GL+ A++KFD
Sbjct: 36  RSYKATGDERLREQLIL-HYSPLVKYVAGRVSVGLPPNVEQADFVSSGVFGLIDAIEKFD 94

Query: 95  PERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTA-NQKRLFFNLR-RLKGHLQAITD 151
            +R  +  TY++  I+ AM  E     W    +   A N +R +  L  RL+   +  T+
Sbjct: 95  LDREIKFETYAITRIRGAMIDELRALDWIPRSVRQKARNVERAYATLEARLR---RTPTE 151

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
             +  E  +A+   L+   S+ +S+   +A +E L+  +     +   + D L    D  
Sbjct: 152 GEVAGELGIAV-DDLHAVFSQ-LSLANVVALEELLH--VGGEGGDGLSFMDTL---EDPA 204

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
               +E  E +  R  L R+++ L  RE+ +      +   +TL  + +   V+  RV Q
Sbjct: 205 ADNPVEVAEDRELRRFLARAINTLPEREKTVVTLYYYEG--LTLAEIGNVLGVTESRVSQ 262

Query: 272 IEARA 276
           I  ++
Sbjct: 263 IHTKS 267


>gi|68164561|gb|AAY87290.1| predicted flagellar-specific RNA polymerase sigma factor FliA
           [uncultured bacterium BAC17H8]
          Length = 240

 Score = 44.3 bits (103), Expect = 0.021,   Method: Compositional matrix adjust.
 Identities = 55/230 (23%), Positives = 106/230 (46%), Gaps = 26/230 (11%)

Query: 53  LVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           L+TSH+ LV +IA    G     + I +++  G  GL+ A + +    G   A+Y+   I
Sbjct: 15  LITSHMELVRQIAWHMHGRLHSSIEIEDLIQIGYFGLVTAAQNYTLREGATFASYAGIRI 74

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA-IAKKLNV 168
           + A+ +++ +S +L +  T   QK+     R L+        N L  E   A +A+ + +
Sbjct: 75  RGAIVDHLRKSSNLCRT-TIEMQKKANVAGRELR--------NRLGREPTSAEMAEHMCI 125

Query: 169 SESEVISMNCRLAGDESLNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           SE E+ +       + +  A ++ S D    ++  W     +  E+ + E+E     RN+
Sbjct: 126 SEDEMHNW------EHAFQANVHQSLDSVYDEFSIWFESPENTPEENINEEE----LRNL 175

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
           L  ++  L  RE  + +   ++E  + +  ++   EV+  RV QI+  A 
Sbjct: 176 LKEALRTLPEREALVIQLYYVEE--LNVYEIAEVLEVTTGRVSQIKKSAI 223


>gi|298492777|ref|YP_003722954.1| FliA/WhiG subfamily RNA polymerase sigma 28 subunit ['Nostoc
           azollae' 0708]
 gi|298234695|gb|ADI65831.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily ['Nostoc
           azollae' 0708]
          Length = 263

 Score = 44.3 bits (103), Expect = 0.021,   Method: Compositional matrix adjust.
 Identities = 44/205 (21%), Positives = 103/205 (50%), Gaps = 10/205 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           Y ++  +   ++LV  H  LV K+A  +      P  ++   G +GL++A+++F+P + +
Sbjct: 19  YHQNPSIKLRNQLVEVHKGLVRKMAYKFIHQCNEPYEDLEQIGYLGLIRAIERFNPHQRY 78

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
             +++++ +I+  M  ++    +L+KI      + L+   ++++   +  T +  +P + 
Sbjct: 79  AFSSFAIPYIRGEMLHFLRDHSTLLKI--PRRWQELYNAGQKIR---KQFTLSLGRPPRE 133

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           + IA KLN+S  E     C+LA    +   ++++  N   +Q  L          L++++
Sbjct: 134 IDIATKLNISLQE--WQECKLAVQNRIPLSLDATTANYVDYQITLGDILPCLRTALLQQQ 191

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFE 244
           E +  R  L  ++S+L+ + R + E
Sbjct: 192 EEE--RLQLQGAISMLDDKRRIVVE 214


>gi|210608669|ref|ZP_03287946.1| hypothetical protein CLONEX_00125 [Clostridium nexile DSM 1787]
 gi|210152926|gb|EEA83932.1| hypothetical protein CLONEX_00125 [Clostridium nexile DSM 1787]
          Length = 259

 Score = 44.3 bits (103), Expect = 0.021,   Method: Compositional matrix adjust.
 Identities = 51/259 (19%), Positives = 122/259 (47%), Gaps = 27/259 (10%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+++E+  L  + +  GD  A  + +  +LRLV+ +   +        ++   G I
Sbjct: 15  KLPLLKEEEKNALFAKIK-AGDEGAKEQYIKGNLRLVLSVIKRFTNSNENPDDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  F+ E   + +TY++  I   ++ Y +R  + +++  +  +   +  +   +G
Sbjct: 74  GLIKAINNFNTELDVKFSTYAVPMIIGEIRRY-MRDNNSIRVSRSL-RDTAYKAIYAKEG 131

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
           +++     NL+   +  I++++ +++ +++     +    SLN  + +   ++    D  
Sbjct: 132 YMK----RNLREPTLQEISEEIGIAKEDIVFAMDAIQAPMSLNEPVYNDGGDALYVMDQ- 186

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER-----RIFEARRLQENPVTLENLS 259
           + D   +E+  IE+         L  +M  L  RE+     R FE R   E       ++
Sbjct: 187 ISDKKNKEENWIEEL-------ALQAAMEHLGEREKYIIRLRFFEGRTQME-------VA 232

Query: 260 SEFEVSRERVRQIEARAFK 278
            + ++S+ +V ++E  A K
Sbjct: 233 EDIDISQAQVSRLEKHALK 251


>gi|239928675|ref|ZP_04685628.1| RNA polymerase sigma factor WhiG [Streptomyces ghanaensis ATCC
           14672]
 gi|291436999|ref|ZP_06576389.1| RNA polymerase sigma factor WhiG [Streptomyces ghanaensis ATCC
           14672]
 gi|291339894|gb|EFE66850.1| RNA polymerase sigma factor WhiG [Streptomyces ghanaensis ATCC
           14672]
          Length = 280

 Score = 44.3 bits (103), Expect = 0.022,   Method: Compositional matrix adjust.
 Identities = 62/245 (25%), Positives = 101/245 (41%), Gaps = 20/245 (8%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFD 94
           + Y+  GD     +L+  H   +VK   G    GLP     ++ VS G  GL+ A++KFD
Sbjct: 36  RSYKATGDERLREQLIL-HYSPLVKYVAGRVSVGLPSNVEQADFVSSGIFGLIDAIEKFD 94

Query: 95  PERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
            +R  +  TY++  I+ AM  E     W    I  +  QK    N+ R    L+A     
Sbjct: 95  VDREIKFETYAITRIRGAMIDELRALDW----IPRSVRQKAR--NVERAYATLEARL-RR 147

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ--DWLVYDHDGQ 211
              E  VA    + V E   +     LA   +L  L++   +   +    D L    D  
Sbjct: 148 TPSESEVAGELGIAVEELHAVFSQLSLANVVALEELLHVGGEGGDRLSLMDTL---EDTA 204

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
               +E  E +  R  L R+++ L  RE+ +      +   +TL  + +   V+  RV Q
Sbjct: 205 ADNPVEVAEDRELRRFLVRAINTLPEREKTVVTLYYYEG--LTLAEIGNVLGVTESRVSQ 262

Query: 272 IEARA 276
           I  ++
Sbjct: 263 IHTKS 267


>gi|126348115|emb|CAJ89836.1| putative RNA polymerase sigma factor [Streptomyces ambofaciens ATCC
           23877]
          Length = 295

 Score = 44.3 bits (103), Expect = 0.022,   Method: Compositional matrix adjust.
 Identities = 48/206 (23%), Positives = 96/206 (46%), Gaps = 17/206 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A + L+  ++ LV   A  +RG G  + +VV  G IGL++A+ +F+  R     ++++ +
Sbjct: 64  ARNTLIEMNMSLVRFAAGRFRGRGDDMDDVVQTGMIGLIKAIDRFELSREVEFTSFALPY 123

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I   ++ +   +   V +     + R+   L + +  L +  D   +   V  +A  +N+
Sbjct: 124 IVGEIKRFFRDTTWAVHVPRRLQELRV--ELAKAREELSSRLD---REPTVAELATLMNI 178

Query: 169 SESEVISMNCRLAG--DESLNALI--NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           SE+EV+       G    SL+A +  +  +   S   D++  + DG    L+E       
Sbjct: 179 SENEVVEGQIASNGYNSSSLDAALTGDGPEGGESVLADFIGVEEDGLR--LVED------ 230

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQE 250
            + L   M+ L+ R+R+I   R ++E
Sbjct: 231 FHSLAPLMAELSERDRQIIHMRFVEE 256


>gi|326775053|ref|ZP_08234318.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
 gi|326655386|gb|EGE40232.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
          Length = 300

 Score = 44.3 bits (103), Expect = 0.022,   Method: Compositional matrix adjust.
 Identities = 59/242 (24%), Positives = 108/242 (44%), Gaps = 22/242 (9%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISE-VVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + L+  +L LV   A  +R  G   +E ++  G IGL++A+ +FD  R    AT+++ 
Sbjct: 71  ARNTLIEMNLSLVRFAASRFRNRGGDDTEDIIQVGTIGLIKAIDRFDLSREVEFATFAVP 130

Query: 108 WIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           +I   ++ +    +WS   +      + L  +L + K  L    D +     V  +A  L
Sbjct: 131 YIVGEIKRFFRDTTWS---VHVPRRLQELRVDLAKAKEQLSGELDRD---PTVKELAAHL 184

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ----DWLVYDHDGQEQVLIEKEERK 222
           ++ E E+I       G  + +    S+D +S Q Q    D L     G E V        
Sbjct: 185 DLPEEEIIEGLVAANGYSAGSLDTPSADSDSGQEQRAYADVLGEADPGMETV-------- 236

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              + L   +  L+ RERRI + R   E  +T   + +E  VS+  V ++ +R  +++++
Sbjct: 237 ENLHTLAPLLDQLDERERRIVQMRFGAE--MTQSQIGAELGVSQMHVSRLLSRIVQQLRK 294

Query: 283 SI 284
            +
Sbjct: 295 GM 296


>gi|182434526|ref|YP_001822245.1| putative RNA polymerase sigma factor [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|178463042|dbj|BAG17562.1| putative RNA polymerase sigma factor [Streptomyces griseus subsp.
           griseus NBRC 13350]
          Length = 300

 Score = 44.3 bits (103), Expect = 0.022,   Method: Compositional matrix adjust.
 Identities = 59/242 (24%), Positives = 108/242 (44%), Gaps = 22/242 (9%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISE-VVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + L+  +L LV   A  +R  G   +E ++  G IGL++A+ +FD  R    AT+++ 
Sbjct: 71  ARNTLIEMNLSLVRFAASRFRNRGGDDTEDIIQVGTIGLIKAIDRFDLSREVEFATFAVP 130

Query: 108 WIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           +I   ++ +    +WS   +      + L  +L + K  L    D +     V  +A  L
Sbjct: 131 YIVGEIKRFFRDTTWS---VHVPRRLQELRVDLAKAKEQLSGELDRD---PTVKELAAHL 184

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ----DWLVYDHDGQEQVLIEKEERK 222
           ++ E E+I       G  + +    S+D +S Q Q    D L     G E V        
Sbjct: 185 DLPEEEIIEGLVAANGYSAGSLDTPSADSDSGQEQRAYADVLGEADPGMETV-------- 236

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              + L   +  L+ RERRI + R   E  +T   + +E  VS+  V ++ +R  +++++
Sbjct: 237 ENLHTLAPLLDQLDERERRIVQMRFGAE--MTQSQIGAELGVSQMHVSRLLSRIVQQLRK 294

Query: 283 SI 284
            +
Sbjct: 295 GM 296


>gi|124516296|gb|EAY57804.1| putative RNA polymerase sigma 28 subunit, FliA/WhiG [Leptospirillum
           rubarum]
          Length = 251

 Score = 44.3 bits (103), Expect = 0.022,   Method: Compositional matrix adjust.
 Identities = 49/215 (22%), Positives = 102/215 (47%), Gaps = 17/215 (7%)

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI-LRSWSLVKIGTTAN 131
           L + +++S G  GL+ A ++FDP RG +  T +   I+ AM + I    W    +  +  
Sbjct: 32  LDVDDLISAGMGGLLDAARRFDPSRGIKFKTLAEHRIRGAMLDEIRAADW----MPRSVR 87

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV--ISMNCRLAGDESLNAL 189
           +K    +++++K  L  I     +P +   IA +++++E E   +S++       SL  L
Sbjct: 88  EK--LTHVQQVKTEL--IARYKREPTR-QEIAARMDMTEEEFDRLSVDIEPHHLVSLEDL 142

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           ++  D +S    D L    +G     + + E   +   L +++  L  ++R +      +
Sbjct: 143 MDPEDGDSPSLLDRLSAPQEGDPLASLLQSEVSEK---LCQALDRLPEKQRLVLSLYYYE 199

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           E  +T++ ++    VS  RV QI  +A   +++S+
Sbjct: 200 E--LTMKEVARVVGVSESRVSQIHGQALAALKQSL 232


>gi|30019159|ref|NP_830790.1| RNA polymerase sigma factor SigB [Bacillus cereus ATCC 14579]
 gi|29894702|gb|AAP07991.1| RNA polymerase sigma-B factor [Bacillus cereus ATCC 14579]
          Length = 258

 Score = 44.3 bits (103), Expect = 0.022,   Method: Compositional matrix adjust.
 Identities = 55/231 (23%), Positives = 110/231 (47%), Gaps = 27/231 (11%)

Query: 22  EIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           EI+  P  L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++ 
Sbjct: 3   EIQSQPTNLTKEDVIKLIADFQQNQCDEAQERLVEHYKNLVYSIAYRYSKGGPMHEDIIQ 62

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNL 139
            G +GL+ A++++D   G     +++  I   +++Y+  ++W +       +  R   +L
Sbjct: 63  VGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGI-------HVPRRIKDL 115

Query: 140 -RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNALI-NS 192
             ++K  ++ +TD+  +  +++ IA  L +SE EV+ +     N R++   SL+ ++ NS
Sbjct: 116 GGKIKLAIEELTDHLQRSPRIIEIANHLGLSEEEVLEIMDAKNNYRVS---SLDDVVENS 172

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           SD +S    + +     G E+          RR +L    +VLN  E+ + 
Sbjct: 173 SDGSSVARIESVGEVEQGYEET--------ERRLVLKDIFNVLNDTEKSVI 215


>gi|325263641|ref|ZP_08130375.1| RNA polymerase sigma-F factor [Clostridium sp. D5]
 gi|324031350|gb|EGB92631.1| RNA polymerase sigma-F factor [Clostridium sp. D5]
          Length = 238

 Score = 44.3 bits (103), Expect = 0.022,   Method: Compositional matrix adjust.
 Identities = 45/189 (23%), Positives = 90/189 (47%), Gaps = 17/189 (8%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A  +LV  ++ LV  +   + G G    ++   G+IGL++A+ KFD     + +TY
Sbjct: 14  GDKKAREQLVEENVGLVWCVVKRFYGRGTEAEDLFQIGSIGLLKAIDKFDLSYEVKFSTY 73

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           ++  I   ++ + LR   ++K+  + + K L + + + +   +A+T +  +   +  +A 
Sbjct: 74  AVPMISGEIKRF-LRDDGMIKV--SRSLKELSYKIFQTR---EALTGSLGREPTLEELAN 127

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD---------WLVYDHDGQEQVL 215
            +NV + E++         ESL   I+  + N  +  D           + DH    Q+L
Sbjct: 128 TMNVDKEEIVQAMEAGGEVESLYKPIHQKEGNEIRLVDKLEEKERKEEKILDHMLLAQLL 187

Query: 216 --IEKEERK 222
             ++KEER+
Sbjct: 188 ESLDKEERQ 196


>gi|325567514|ref|ZP_08144181.1| DNA-directed RNA polymerase sigma subunit FliA [Enterococcus
           casseliflavus ATCC 12755]
 gi|325158947|gb|EGC71093.1| DNA-directed RNA polymerase sigma subunit FliA [Enterococcus
           casseliflavus ATCC 12755]
          Length = 235

 Score = 44.3 bits (103), Expect = 0.022,   Method: Compositional matrix adjust.
 Identities = 51/211 (24%), Positives = 95/211 (45%), Gaps = 20/211 (9%)

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA-NQKRLFFNLR 140
           G IGLM A++KFDP +     +Y+   IK A+ + + +   + +    A NQ   F+  R
Sbjct: 40  GVIGLMDALRKFDPSKKVPFESYAAIRIKGAIIDEVRKHAKISRYKMAAVNQ---FYQAR 96

Query: 141 RLKGHLQAITDNNLKPEQV-VAIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNS 197
           +         + +LK E     I K+L +++S++  I  +       SL   + +  +  
Sbjct: 97  QE-------LEQSLKREATDTEICKQLGINQSQLADIYESLHYLASVSLEDTLFAYQEEG 149

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
              +D +    +  E  L+ +E    +R  L   +  L  RE+ I      +E  +TL+ 
Sbjct: 150 MTLKDMVRDPAENVEDTLVAEE----KRTALVACIKKLGEREQLILSLYYTEE--LTLKE 203

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           ++   EVS  RV QI  +   K++  I +++
Sbjct: 204 IAEILEVSIPRVSQIHGKTIAKLRTLIGEEL 234


>gi|15604780|ref|NP_219564.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis
           D/UW-3/CX]
 gi|76788774|ref|YP_327860.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis
           A/HAR-13]
 gi|237802495|ref|YP_002887689.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis
           B/Jali20/OT]
 gi|237804410|ref|YP_002888564.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis
           B/TZ1A828/OT]
 gi|255310863|ref|ZP_05353433.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis 6276]
 gi|255317163|ref|ZP_05358409.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis 6276s]
 gi|255348424|ref|ZP_05380431.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis 70]
 gi|255502966|ref|ZP_05381356.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis 70s]
 gi|255506635|ref|ZP_05382274.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis
           D(s)2923]
 gi|3328455|gb|AAC67652.1| Sigma-28/WhiG Family [Chlamydia trachomatis D/UW-3/CX]
 gi|76167304|gb|AAX50312.1| FliA [Chlamydia trachomatis A/HAR-13]
 gi|231272710|emb|CAX09614.1| RNA polymerase sigma factor [Chlamydia trachomatis B/TZ1A828/OT]
 gi|231273729|emb|CAX10508.1| RNA polymerase sigma factor [Chlamydia trachomatis B/Jali20/OT]
 gi|289525106|emb|CBJ14577.1| RNA polymerase sigma factor [Chlamydia trachomatis Sweden2]
 gi|296434648|gb|ADH16826.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis E/150]
 gi|296435578|gb|ADH17752.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis G/9768]
 gi|296436502|gb|ADH18672.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis
           G/11222]
 gi|296437438|gb|ADH19599.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis
           G/11074]
 gi|296438365|gb|ADH20518.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis
           E/11023]
 gi|297139937|gb|ADH96695.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis G/9301]
 gi|297748191|gb|ADI50737.1| FliA [Chlamydia trachomatis D-EC]
 gi|297749071|gb|ADI51749.1| FliA [Chlamydia trachomatis D-LC]
          Length = 253

 Score = 44.3 bits (103), Expect = 0.023,   Method: Compositional matrix adjust.
 Identities = 66/251 (26%), Positives = 118/251 (47%), Gaps = 39/251 (15%)

Query: 51  HR--LVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           HR  L+ S+L LV  +A      G+P    + ++ + G  GL++AV++FDPE+  R  +Y
Sbjct: 21  HRDVLIESYLPLVKNVAHRLAS-GMPSHVKMEDLYALGVEGLIRAVERFDPEKSKRFESY 79

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITDNNLKPEQVVAIA 163
           +++ IKAA+ +  LR    V         RL   +  L+  L +  TD  L         
Sbjct: 80  ALFIIKAAIIDG-LRKQDWVPRSVYQRANRLADAMDSLRQTLGKEPTDGEL--------C 130

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG---QEQVLIEKEE 220
           + LN+S+ E+           S  AL+ S   + S  QD    D +G   +E++  E+ E
Sbjct: 131 EYLNISQQELSHWFS-----SSRPALVLSLHDDFS-CQD----DDEGLALEERIADERAE 180

Query: 221 -------RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
                  +K   ++LT ++  L+ +ER++       +  + L+ +     VS  RV QI 
Sbjct: 181 TGYDVIRKKEAISILTEALLALDEKERQVMALYYYDD--LVLKEIGKILGVSESRVSQIH 238

Query: 274 ARAFKKVQESI 284
           ++A  K++ ++
Sbjct: 239 SKALLKLRGTL 249


>gi|154816043|emb|CAO85715.1| putative RNA polymerase sigma factor rpoD [Clostridium sp.]
          Length = 75

 Score = 44.3 bits (103), Expect = 0.023,   Method: Compositional matrix adjust.
 Identities = 27/62 (43%), Positives = 39/62 (62%), Gaps = 9/62 (14%)

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPV------TLENLSSEFEVSRERVRQIEARAFKK 279
           + L+  +S L+PRE RI    RL+   V      TLE +  EF ++RER+RQIEARA +K
Sbjct: 4   DTLSNVLSTLSPREERIV---RLRYGLVGDGESRTLEEIGREFNLTRERIRQIEARAIRK 60

Query: 280 VQ 281
           ++
Sbjct: 61  LR 62


>gi|170078529|ref|YP_001735167.1| RNA polymerase sigma factor SigF [Synechococcus sp. PCC 7002]
 gi|5359699|gb|AAD42767.1|AF121848_2 SigF [Synechococcus sp. PCC 7002]
 gi|169886198|gb|ACA99911.1| SigF [Synechococcus sp. PCC 7002]
          Length = 259

 Score = 44.3 bits (103), Expect = 0.023,   Method: Compositional matrix adjust.
 Identities = 37/144 (25%), Positives = 75/144 (52%), Gaps = 10/144 (6%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKKFDP 95
           L + YR+  D+   +++V+ ++ LV K A  + R       +++  G++GL++A+++F  
Sbjct: 19  LLQEYRQSQDVKIRNQIVSLNIGLVRKEAHHWSRQCSENFDDLMQVGSLGLLRAIERFTL 78

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI--TDNN 153
           ERG   ++++  +I+  +Q Y+    S V+I       R    LR+           ++N
Sbjct: 79  ERGNAFSSFANPYIRGEIQHYLRDKSSTVRI------PRRMLQLRQQSNRFIHTFRQEHN 132

Query: 154 LKPEQVVAIAKKLNVSESEVISMN 177
            +P   + IA+ LN+S +E  S+N
Sbjct: 133 RQPS-AIEIAEHLNISVTEWQSIN 155


>gi|86146119|ref|ZP_01064445.1| flagellar biosynthesis sigma factor FliA [Vibrio sp. MED222]
 gi|218708840|ref|YP_002416461.1| flagellar biosynthesis sigma factor [Vibrio splendidus LGP32]
 gi|85836066|gb|EAQ54198.1| flagellar biosynthesis sigma factor FliA [Vibrio sp. MED222]
 gi|218321859|emb|CAV17839.1| RNA polymerase sigma factor for flagellar operon [Vibrio splendidus
           LGP32]
          Length = 244

 Score = 44.3 bits (103), Expect = 0.023,   Method: Compositional matrix adjust.
 Identities = 60/252 (23%), Positives = 106/252 (42%), Gaps = 31/252 (12%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFD 94
           A  Y +H + ++       +  LV +IA    G   P   + +++  G IGL++A + +D
Sbjct: 4   ALTYDQHANHNSQQAFFEKYSVLVKRIAHHLLGRLPPNVLVDDLIQAGMIGLIEAQQNYD 63

Query: 95  PERGFRLATYSMWWIKAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
             +G    TY+   I+ AM + I R  W  V      N + +   +  L+G L      N
Sbjct: 64  GTKGASFETYAGIRIRGAMLDDIRRGDW--VPRSVHKNNREISSAIAELEGTL------N 115

Query: 154 LKPEQVVAIAKKLNVS----ESEVISMNC-RLAGDESLNALINSSDKNSSQWQDWLVYDH 208
             P     +AK + +S     S +  +NC +L G E L      SD       D +  + 
Sbjct: 116 RDPSD-AEVAKHMGLSLDQYHSALTDINCSKLVGIEDLGV----SD-------DVISPNE 163

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D Q+    +    ++ R  L  S+  L  RE  +      +E  + L+ +     VS  R
Sbjct: 164 DSQDNTPFQGVADESFRQALIDSIKQLPEREGLVLSLYYDEE--LNLKEIGEVLGVSESR 221

Query: 269 VRQIEARAFKKV 280
           V QI +++ +++
Sbjct: 222 VSQILSQSMQRL 233


>gi|146296307|ref|YP_001180078.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Caldicellulosiruptor
           saccharolyticus DSM 8903]
 gi|145409883|gb|ABP66887.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG
           [Caldicellulosiruptor saccharolyticus DSM 8903]
          Length = 245

 Score = 44.3 bits (103), Expect = 0.023,   Method: Compositional matrix adjust.
 Identities = 55/260 (21%), Positives = 117/260 (45%), Gaps = 21/260 (8%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQA 89
           +E  L ++Y +  D     +L   ++ LV  IA     Y G  +   ++VS G++GL+ A
Sbjct: 2   DEAFLWEKYSKTKDPKIKEQLTLRYMPLVKLIAGRMAMYFGGNVEYDDLVSYGSLGLLDA 61

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYI-LRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           ++K+D ++G +  TY+   I+ A+ + +  + W    I   A +          K +++ 
Sbjct: 62  IEKYDSQKGVKFETYAYTRIRGAIIDCVRSQDWVPRSIRQKAKEVE--------KAYIEI 113

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
             +  +  ++ VA    L +SE + +          SL   +    + + + +   + D 
Sbjct: 114 EKEGKIPTDEEVAKRTGLTLSEFQKLKEKISSGMILSLEGFL----EQNYEIKIGGLEDF 169

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
               +V IE EE K    +L + +  L+  E+ +      +E  ++++ ++    VS  R
Sbjct: 170 VSHPEVFIENEELK---EVLRQEIENLSENEKMVILLYYFEE--LSIKEIAKILGVSESR 224

Query: 269 VRQIEARAFKKVQESIQKQV 288
           V Q+  RA  K++  ++K +
Sbjct: 225 VSQLHTRALLKLRAKLEKHL 244


>gi|302387774|ref|YP_003823596.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           saccharolyticum WM1]
 gi|302198402|gb|ADL05973.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           saccharolyticum WM1]
          Length = 258

 Score = 44.3 bits (103), Expect = 0.023,   Method: Compositional matrix adjust.
 Identities = 22/71 (30%), Positives = 38/71 (53%), Gaps = 3/71 (4%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV---VSEGNIGLMQAVKKF 93
           L  +Y+   D+   H LV  ++ +V  I++  R   L  ++V   V+EG + +M  ++KF
Sbjct: 13  LLIKYKRTKDIHIKHELVMRYMYMVRSISIQMRDVYLSFAQVEDIVNEGVLTIMSGIEKF 72

Query: 94  DPERGFRLATY 104
           DPE   +  TY
Sbjct: 73  DPEMNVKFETY 83


>gi|226359630|ref|YP_002777408.1| RNA polymerase sigma factor [Rhodococcus opacus B4]
 gi|226238115|dbj|BAH48463.1| RNA polymerase sigma factor [Rhodococcus opacus B4]
          Length = 265

 Score = 44.3 bits (103), Expect = 0.024,   Method: Compositional matrix adjust.
 Identities = 22/72 (30%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++T  L L   IA  + G G    +++    +GL++AV +FDP+RGF   +Y++  I   
Sbjct: 45  IITRCLPLADHIARRFGGRGEAHEDLLQVARLGLVKAVDRFDPDRGFDFVSYAVPTIMGE 104

Query: 113 MQEYILRS-WSL 123
           ++ Y   + WS+
Sbjct: 105 VRRYFRDTGWSM 116


>gi|332653851|ref|ZP_08419595.1| RNA polymerase sigma-E factor [Ruminococcaceae bacterium D16]
 gi|332516937|gb|EGJ46542.1| RNA polymerase sigma-E factor [Ruminococcaceae bacterium D16]
          Length = 231

 Score = 44.3 bits (103), Expect = 0.024,   Method: Compositional matrix adjust.
 Identities = 24/67 (35%), Positives = 36/67 (53%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GDL A + LV  +LRLV  I   Y        +++S G IGL++ +  F  ++  RLAT
Sbjct: 44  QGDLEARNILVEHNLRLVAHIVKKYYAQTGDQDDLISIGTIGLIKGISTFKADKNVRLAT 103

Query: 104 YSMWWIK 110
           Y+   I+
Sbjct: 104 YASRCIE 110


>gi|169334044|ref|ZP_02861237.1| hypothetical protein ANASTE_00437 [Anaerofustis stercorihominis DSM
           17244]
 gi|169258761|gb|EDS72727.1| hypothetical protein ANASTE_00437 [Anaerofustis stercorihominis DSM
           17244]
          Length = 253

 Score = 44.3 bits (103), Expect = 0.024,   Method: Compositional matrix adjust.
 Identities = 56/249 (22%), Positives = 114/249 (45%), Gaps = 33/249 (13%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           ++G+    +  +  +LRLV+ +   +      + ++   G IGL++A+  FD + G + +
Sbjct: 31  KNGEEDLKNEFIRCNLRLVLSVVQRFSNRNENMDDLFQVGCIGLIKAIDNFDVKFGVKFS 90

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I   ++ Y LR    +++  +   K + +   + K   +A  D N    +   I
Sbjct: 91  TYAVPMIIGEVRRY-LRDNGTIRVSRSL--KDMAYKALKYK---EAHKDTNPTNRE---I 141

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK-EER 221
           AKKL V E +             LN  ++S  +  S +    +Y+ +G    LI++  + 
Sbjct: 142 AKKLGVKEKD-------------LNFALDSIVEPCSLYDQ--MYNDNGDSISLIDQVGDE 186

Query: 222 KNRRNMLTRSMSV------LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
           KNR    T  +S+      L  RE+ I   +R       +E +++E  +S+ +V ++E  
Sbjct: 187 KNREENWTEKLSLKEAVEKLKGREKEII-LKRYYLGRTQIE-VANEIGISQAQVSRLEKS 244

Query: 276 AFKKVQESI 284
             +K++  I
Sbjct: 245 GLRKIKNEI 253


>gi|329936708|ref|ZP_08286415.1| RNA polymerase sigma factor WhiG [Streptomyces griseoaurantiacus
           M045]
 gi|329303938|gb|EGG47821.1| RNA polymerase sigma factor WhiG [Streptomyces griseoaurantiacus
           M045]
          Length = 279

 Score = 44.3 bits (103), Expect = 0.024,   Method: Compositional matrix adjust.
 Identities = 56/252 (22%), Positives = 105/252 (41%), Gaps = 35/252 (13%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFD 94
           + Y+  GD     +L+  H   +VK   G    GLP     ++ VS G  GL+ A++K+D
Sbjct: 36  RTYKATGDERLREQLIL-HYSPLVKYVAGRVSVGLPPNVEQADFVSSGVFGLIDAIEKYD 94

Query: 95  PERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTA-NQKRLFFN----LRRLKGHLQA 148
             R  +  TY++  I+ AM  E     W    +   A N +R +      LRR     + 
Sbjct: 95  IGREIKFETYAITRIRGAMIDELRALDWIPRSVRQKARNVERAYTTLEARLRRTPTESEV 154

Query: 149 ITDNNLKPEQVVAIAKKLN----VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             +  ++ + + A+  +L+    V+  E++ +     G   ++ L ++S  N        
Sbjct: 155 AAELGIRVDDLHAVFSQLSLANVVALEEILHIGGEGGGLSLMDTLEDTSADNP------- 207

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
                      +E  E +  R  L R+++ L  RE+ +      +   +TL  + +   V
Sbjct: 208 -----------VEVAEDRELRRFLARAINTLPEREKTVVTLYYFEG--LTLAEIGNVLGV 254

Query: 265 SRERVRQIEARA 276
           +  RV QI  ++
Sbjct: 255 TESRVSQIHTKS 266


>gi|258621167|ref|ZP_05716201.1| flagellar biosynthesis sigma factor FliA [Vibrio mimicus VM573]
 gi|258626709|ref|ZP_05721533.1| flagellar biosynthesis sigma factor FliA [Vibrio mimicus VM603]
 gi|258581005|gb|EEW05930.1| flagellar biosynthesis sigma factor FliA [Vibrio mimicus VM603]
 gi|258586555|gb|EEW11270.1| flagellar biosynthesis sigma factor FliA [Vibrio mimicus VM573]
          Length = 244

 Score = 44.3 bits (103), Expect = 0.024,   Method: Compositional matrix adjust.
 Identities = 61/253 (24%), Positives = 111/253 (43%), Gaps = 31/253 (12%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFD 94
           A  Y ++G+L++    +  +  LV +IA    G   P   I +++  G +GL++A K +D
Sbjct: 4   ALTYDQYGNLNSQQLFLEKYSVLVKRIAHHLIGRLPPSVLIEDLIQAGMVGLLEAQKNYD 63

Query: 95  PERGFRLATYSMWWIKAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
             +G    TY+   I+ AM + I R  W  V      + + +   +  L+G L      N
Sbjct: 64  GSKGASFETYAGIRIRGAMLDDIRRGDW--VPRSVHKHNREISQAIAVLEGEL------N 115

Query: 154 LKPEQVVAIAKKLNVS----ESEVISMNC-RLAGDESLNALINSSDKNSSQWQDWLVYDH 208
             P     +AK L +S     S ++ +NC R+ G E L      SD   S ++       
Sbjct: 116 RDPTD-AEVAKFLEMSLEQYHSVLMDINCSRIVGIEDLGV----SDDAISPFE------- 163

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           +G++         ++ R  L  S+  L  RE  +      +E  + L+ +     VS  R
Sbjct: 164 EGEDNSPFHGVAEESFRKALVESIKSLPEREALVLSLYYDEE--LNLKEIGEVLGVSESR 221

Query: 269 VRQIEARAFKKVQ 281
           V QI +++ ++++
Sbjct: 222 VSQILSQSMQRLR 234


>gi|84388128|ref|ZP_00991024.1| flagellar biosynthesis sigma factor FliA [Vibrio splendidus 12B01]
 gi|84377195|gb|EAP94065.1| flagellar biosynthesis sigma factor FliA [Vibrio splendidus 12B01]
          Length = 244

 Score = 44.3 bits (103), Expect = 0.024,   Method: Compositional matrix adjust.
 Identities = 60/252 (23%), Positives = 106/252 (42%), Gaps = 31/252 (12%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFD 94
           A  Y +H + ++       +  LV +IA    G   P   + +++  G IGL++A + +D
Sbjct: 4   ALTYDQHANHNSQQAFFEKYSVLVKRIAHHLLGRLPPNVLVDDLIQAGMIGLIEAQQNYD 63

Query: 95  PERGFRLATYSMWWIKAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
             +G    TY+   I+ AM + I R  W  V      N + +   +  L+G L      N
Sbjct: 64  GTKGASFETYAGIRIRGAMLDDIRRGDW--VPRSVHKNNREISSAIAELEGAL------N 115

Query: 154 LKPEQVVAIAKKLNVS----ESEVISMNC-RLAGDESLNALINSSDKNSSQWQDWLVYDH 208
             P     +AK + +S     + +  +NC RL G E L      SD       D +  + 
Sbjct: 116 RDPSD-AEVAKHMGLSLDQYHNALTDINCSRLVGIEDLGV----SD-------DVISPNE 163

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D Q+    +    ++ R  L  S+  L  RE  +      +E  + L+ +     VS  R
Sbjct: 164 DSQDNTPFQGVADESFRQALIDSIKQLPEREGLVLSLYYDEE--LNLKEIGEVLGVSESR 221

Query: 269 VRQIEARAFKKV 280
           V QI +++ +++
Sbjct: 222 VSQILSQSMQRL 233


>gi|150389709|ref|YP_001319758.1| FliA/WhiG family RNA polymerase sigma factor [Alkaliphilus
           metalliredigens QYMF]
 gi|150392068|ref|YP_001322117.1| FliA/WhiG family RNA polymerase sigma factor [Alkaliphilus
           metalliredigens QYMF]
 gi|149949571|gb|ABR48099.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           metalliredigens QYMF]
 gi|149951930|gb|ABR50458.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           metalliredigens QYMF]
          Length = 215

 Score = 44.3 bits (103), Expect = 0.025,   Method: Compositional matrix adjust.
 Identities = 32/109 (29%), Positives = 52/109 (47%), Gaps = 8/109 (7%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K PM E +E   L  ++RE  +      L+  +LRLV   A  Y+       ++ S G I
Sbjct: 8   KEPMTE-EESKRLINQFRELNNEEIRKHLIERNLRLVAYEAYKYKNQ--DSEDIFSVGCI 64

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR-----SWSLVKIGT 128
           GL++A+  +DP +  R  TY+   I+  +  YI R      W+ V++  
Sbjct: 65  GLIKAIDSYDPSKQTRFDTYANRCIQNEILLYIKRLKKGSRWTFVRLDA 113


>gi|295101345|emb|CBK98890.1| RNA polymerase sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii L2-6]
          Length = 221

 Score = 44.3 bits (103), Expect = 0.025,   Method: Compositional matrix adjust.
 Identities = 24/83 (28%), Positives = 41/83 (49%), Gaps = 8/83 (9%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIA--------MGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           + GD +A   L+ ++   + K+A        +   G  L   ++   GN+GL +AV KFD
Sbjct: 13  QKGDAAALDSLIDNNKSFIGKVANDLFRSMNLAQSGLNLDTDDLKQAGNLGLWKAVPKFD 72

Query: 95  PERGFRLATYSMWWIKAAMQEYI 117
             RG +  TY+   I+ AM + +
Sbjct: 73  AARGMKFLTYAAPAIRNAMMDMV 95


>gi|290769931|gb|ADD61700.1| putative protein [uncultured organism]
          Length = 259

 Score = 43.9 bits (102), Expect = 0.026,   Method: Compositional matrix adjust.
 Identities = 58/265 (21%), Positives = 119/265 (44%), Gaps = 35/265 (13%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L ++E+  L KR +  GD  A    +  +LRLV+ +   ++       ++   G IG
Sbjct: 16  LPVLNQEEKEELFKRIK-AGDEEARELYIKGNLRLVLSVIRRFQNSSENPDDLFQIGCIG 74

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ---KRLFFNLRRL 142
           L++A+  FD     + +TY++  I   ++ Y LR  + +++  +      K ++     +
Sbjct: 75  LIKAIDNFDTTLQVKFSTYAVPMIVGEIRRY-LRDNNSIRVSRSLRDIAYKTIYTRENYM 133

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL------AGDESLNALINSSDKN 196
           + HL+  T   +  E  + I K++ V   + I     L       G ++L  +   SDK 
Sbjct: 134 RQHLKEPTIAEIADE--IGIDKEMIVYAMDAIQSPVSLFEPVYSEGGDTLYVMDQISDKK 191

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           + + ++W+       E +             L  +M+ L  RER I +  R  E    +E
Sbjct: 192 NRE-ENWV-------EDI------------SLRDAMNRLGERERHIIDL-RFYEGKTQME 230

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            ++ E  +S+ +V ++E  A + ++
Sbjct: 231 -VADEIGISQAQVSRLEKHALRSMR 254


>gi|134100730|ref|YP_001106391.1| RNA polymerase sigma factor [Saccharopolyspora erythraea NRRL 2338]
 gi|291006467|ref|ZP_06564440.1| RNA polymerase sigma factor [Saccharopolyspora erythraea NRRL 2338]
 gi|133913353|emb|CAM03466.1| RNA polymerase sigma factor [Saccharopolyspora erythraea NRRL 2338]
          Length = 268

 Score = 43.9 bits (102), Expect = 0.026,   Method: Compositional matrix adjust.
 Identities = 24/73 (32%), Positives = 40/73 (54%), Gaps = 1/73 (1%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RLVT HL +   IA  +R  G    ++V    +GL++AV +FDP RG    +Y++  I  
Sbjct: 38  RLVTEHLPVAEHIARRFRHRGETHDDLVQVATLGLIKAVDRFDPGRGVGFMSYAVPTIMG 97

Query: 112 AMQEYILRS-WSL 123
            ++ +   + WS+
Sbjct: 98  EVRRHFRDAGWSV 110


>gi|158320542|ref|YP_001513049.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Alkaliphilus
           oremlandii OhILAs]
 gi|158140741|gb|ABW19053.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Alkaliphilus
           oremlandii OhILAs]
          Length = 245

 Score = 43.9 bits (102), Expect = 0.026,   Method: Compositional matrix adjust.
 Identities = 61/263 (23%), Positives = 119/263 (45%), Gaps = 37/263 (14%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMG-YRGYGLPI--SEVVSEGNIGLMQAVKKFDPER 97
           Y+ + D  A   L+  ++RLV  IA   Y  YG  I   ++VS G  GL+ A++KFD  +
Sbjct: 11  YKNNNDSQAKALLIEEYIRLVKFIAGRLYISYGSNIEYDDLVSYGIFGLIDAIEKFDLNK 70

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITDNNLKP 156
             +  TY+   I+ A+ +  LRS   V        K++      L+  L ++ TD     
Sbjct: 71  QVKFETYAQIRIRGAIIDS-LRSLDWVPRSIRQKSKKIEEAYSSLENKLGRSATD----- 124

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL----VYDHDGQE 212
              V +++ L++S  E+  +            L+N++  N    ++ +    +  +  +E
Sbjct: 125 ---VEVSEALDISVKELQEI------------LLNTASFNVISLEEVIFEVGLIGNTAEE 169

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           Q+  +   R+   N L  ++  L  RER++        N +T + +    ++S  RV Q+
Sbjct: 170 QLTEDLICRRETYNNLKDTIVQLPERERQVISLYYY--NNLTYKEIGKVLDISESRVSQL 227

Query: 273 EARAFKKVQESIQKQVELSSSPP 295
            ++A  +++       +L+S+ P
Sbjct: 228 HSKAISRLKS------KLTSNSP 244


>gi|291453672|ref|ZP_06593062.1| SigI protein [Streptomyces albus J1074]
 gi|291356621|gb|EFE83523.1| SigI protein [Streptomyces albus J1074]
          Length = 285

 Score = 43.9 bits (102), Expect = 0.026,   Method: Compositional matrix adjust.
 Identities = 60/240 (25%), Positives = 106/240 (44%), Gaps = 30/240 (12%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  +L LV   A  +R    P+ +++  G IGL++A+ +F+  RG    T++M  I   
Sbjct: 64  LVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRGVEFPTFAMPTIIGE 123

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL  +L +    L    D   +   V  +A +L +S+ 
Sbjct: 124 IKRFFRDTSWS-VRVPRRLQELRL--DLAKAGDELAQKLD---RAPTVRELADRLGLSQE 177

Query: 172 EVISMNCRLAGDESLNALINSS-------DKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           EV+       G  + NA   SS       D +     D + Y+  G E   IE  E    
Sbjct: 178 EVVE------GMAASNAYTASSLDAQPEEDDSEGALADRIGYEDHGIEG--IEYVES--- 226

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              L   ++ L  R+RRI  + R   N +T   +  E  +S+  V ++  R   ++++ +
Sbjct: 227 ---LKPLIAELPARDRRIL-SLRFTAN-MTQSEIGEELGISQMHVSRLLTRTLNRLRKGL 281


>gi|223984205|ref|ZP_03634353.1| hypothetical protein HOLDEFILI_01646 [Holdemania filiformis DSM
           12042]
 gi|223963820|gb|EEF68184.1| hypothetical protein HOLDEFILI_01646 [Holdemania filiformis DSM
           12042]
          Length = 234

 Score = 43.9 bits (102), Expect = 0.026,   Method: Compositional matrix adjust.
 Identities = 64/281 (22%), Positives = 117/281 (41%), Gaps = 67/281 (23%)

Query: 13  EIGLSRYIHEIRKI----PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +I  S +I  IR      P+  ++E+  L +  +  GD+ A   L+  +LRLV  I   +
Sbjct: 10  QIFFSCFIGSIRTTSFPQPLTAEEEQDALQRMAK--GDVEARADLIEHNLRLVAHIVKKF 67

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
                   +++S G IGL++ +  F  ++G +LATY    I                   
Sbjct: 68  DIRREQTEDLISIGTIGLIKGIDTFKVDKGHKLATYVSRCI------------------- 108

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
              +  +  +LR  K   Q  + ++       AI +  + SE  +I              
Sbjct: 109 ---ENEILMHLRNNKHAFQTRSLDD-------AIGQDKDGSELTLID------------- 145

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
           +I + D+             D  +++++E+ +RK     LT+ M +L+ RE  I   R  
Sbjct: 146 VIPAPDQP------------DPIDKLMLEENKRK-----LTQFMGLLDEREHSIIVRRYG 188

Query: 249 QEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            E    +T  +++ +  +SR  V +IE RAF K+  +  K+
Sbjct: 189 LEGHQEMTQRDIARQEHISRSYVSRIEKRAFMKLLRAFMKE 229


>gi|220929439|ref|YP_002506348.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           cellulolyticum H10]
 gi|219999767|gb|ACL76368.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           cellulolyticum H10]
          Length = 254

 Score = 43.9 bits (102), Expect = 0.026,   Method: Compositional matrix adjust.
 Identities = 52/246 (21%), Positives = 107/246 (43%), Gaps = 23/246 (9%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           L K+Y E  D +A  +L+  +  L+  +A     Y G  +   ++V  G  GL+ A++K+
Sbjct: 9   LWKQYIETKDAAAKEKLIIQYAYLIKYVAGRLSIYFGSNVEFDDLVGYGAFGLIDAIEKY 68

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL---FFNLRRLKGHLQAIT 150
           D  +G +  TY+   I+ ++ + I R    V        K L   +  +   KGH    T
Sbjct: 69  DLAKGVKFETYASLRIRGSIIDSI-RDMDWVPRSLRQKNKELEKVYVEIENEKGH--TAT 125

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
           D          +A+K+ +S S+      +L  D +++++++  +     ++  L    + 
Sbjct: 126 DKE--------VAEKMGLSMSDF----YKLLNDVNVSSMMSLDEFMEQNYERGLEIFSES 173

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
            E       E    + +L   +  L  +E+ +      +E  +TL+ +S+   V+  R+ 
Sbjct: 174 TEDKPEASLEFNEMKQLLADCIDKLPEKEKAVITFYYFEE--LTLKEISAIMNVTESRIS 231

Query: 271 QIEARA 276
           Q+  +A
Sbjct: 232 QLHTKA 237


>gi|293376228|ref|ZP_06622471.1| RNA polymerase sigma-G factor [Turicibacter sanguinis PC909]
 gi|325845152|ref|ZP_08168461.1| RNA polymerase sigma-G factor [Turicibacter sp. HGF1]
 gi|292645120|gb|EFF63187.1| RNA polymerase sigma-G factor [Turicibacter sanguinis PC909]
 gi|325488817|gb|EGC91217.1| RNA polymerase sigma-G factor [Turicibacter sp. HGF1]
          Length = 259

 Score = 43.9 bits (102), Expect = 0.026,   Method: Compositional matrix adjust.
 Identities = 27/99 (27%), Positives = 52/99 (52%), Gaps = 1/99 (1%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+ +L   E   L K + ++G++ A   L+  +LRLV+ I   +   G  + ++   G +
Sbjct: 15  KLEVLSNAEMTELFKSF-QNGNVEARESLIKGNLRLVLSIIKKFNHRGENLDDLFQVGCL 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           GLM+A+  FD     + +TY++  I   ++ Y+  + SL
Sbjct: 74  GLMKAIDHFDLSHEVKFSTYAVPMIIGEIRRYLRDNNSL 112


>gi|169351192|ref|ZP_02868130.1| hypothetical protein CLOSPI_01971 [Clostridium spiroforme DSM 1552]
 gi|169292254|gb|EDS74387.1| hypothetical protein CLOSPI_01971 [Clostridium spiroforme DSM 1552]
          Length = 231

 Score = 43.9 bits (102), Expect = 0.027,   Method: Compositional matrix adjust.
 Identities = 29/90 (32%), Positives = 48/90 (53%), Gaps = 3/90 (3%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVV 79
           H++   P+   +E+  L K  +  GD  A   L+  +LRLVV +A  Y       I +++
Sbjct: 21  HDVLPPPLNAFEEKEALEKLAK--GDNDARDLLIEHNLRLVVYVAKRYDTNQNGGIEDLI 78

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           S G IGL++A+  F  ++  +LATY+   I
Sbjct: 79  SIGTIGLVKAINTFKTDKNIKLATYASRCI 108


>gi|312128148|ref|YP_003993022.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor hydrothermalis 108]
 gi|311778167|gb|ADQ07653.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor hydrothermalis 108]
          Length = 219

 Score = 43.9 bits (102), Expect = 0.027,   Method: Compositional matrix adjust.
 Identities = 28/93 (30%), Positives = 50/93 (53%), Gaps = 5/93 (5%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP--ISEVVSEGNI 84
           PM  ++EE  L K +   G   A + L+  +LRLV  IA  Y  +  P    +++S G I
Sbjct: 13  PMSSEEEEMYLNKMW--EGCKEARNILIEKNLRLVAHIAKKYT-FSFPNLTDDIISVGTI 69

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           GL++A++ +   +  +L+TY+   I+  +  Y+
Sbjct: 70  GLIKAIETYSTAKCTKLSTYAAKCIENEILMYL 102


>gi|119897398|ref|YP_932611.1| RNA polymerase sigma factor [Azoarcus sp. BH72]
 gi|119669811|emb|CAL93724.1| RNA polymerase sigma factor [Azoarcus sp. BH72]
          Length = 256

 Score = 43.9 bits (102), Expect = 0.027,   Method: Compositional matrix adjust.
 Identities = 51/247 (20%), Positives = 106/247 (42%), Gaps = 18/247 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           Y   G+L   H LV ++  LV +IA   M      + + +++  G +GL+ A+ +++   
Sbjct: 2   YDAEGNLDKDH-LVVAYAPLVKRIAFQLMAKLPASVEVEDLIQNGMMGLLDAIGRYEEGL 60

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G +  TY++  ++ AM + +  +  L         + L  ++RR++  +  +   + +P 
Sbjct: 61  GAQFETYAVQRVRGAMLDGLRENDWL--------PRSLRRDMRRIESAIHVLEQQHGRPP 112

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A+ L V   E      R+  D   + L+   D    + +D+L       E    E
Sbjct: 113 SETELAESLGVPLPEY----QRMLQDARGHQLVYFEDFTDGEGEDFLDRHLGAHESNPAE 168

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
             E  + R  L R++  L  RE+ +       E  + L  +     V+  RV Q+ ++A 
Sbjct: 169 LLEDADMRANLIRAIDDLPEREKLVMAL--YYEEELNLREIGEVLGVTESRVCQLHSQAV 226

Query: 278 KKVQESI 284
            +++  +
Sbjct: 227 ARLRARV 233


>gi|294813001|ref|ZP_06771644.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|326441452|ref|ZP_08216186.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|294325600|gb|EFG07243.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 306

 Score = 43.9 bits (102), Expect = 0.028,   Method: Compositional matrix adjust.
 Identities = 57/238 (23%), Positives = 107/238 (44%), Gaps = 20/238 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  +L LV   A  +R    P+ ++V  G IGL++A+ +F+  RG    T++M  +   
Sbjct: 85  LVELNLSLVRFAAARFRSRSEPMDDIVQVGTIGLIKAIDRFELSRGVEFPTFAMPTVIGE 144

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL  +L R    L A  D   +   V  +A+ L +   
Sbjct: 145 IKRFFRDTSWS-VRVPRRLQELRL--DLARAGDELTARLD---RSPTVAELAEYLGIGAD 198

Query: 172 EVISMNCRLAGDESLNALINSS--DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           EV+       G  + NA   SS   +  ++  D  + +  G E   +E  E       L 
Sbjct: 199 EVVE------GMVASNAYTPSSLDARPQNEEHDGTLAERIGYEDGGLEGVEYIESLKPL- 251

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             ++ L  R+RRI   R   +  +T  ++  E  +S+ +V ++ +R   +++  +  +
Sbjct: 252 --IAGLPDRDRRILSLRFGAD--MTQSDIGEELGISQMQVSRLLSRTLVRLRRGLTAE 305


>gi|305675234|ref|YP_003866906.1| sporulation sigma factor SigmaK [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|161168469|dbj|BAF93933.1| RNA polymerase sigma factor [Bacillus subtilis subsp. natto]
 gi|291485028|dbj|BAI86103.1| hypothetical protein BSNT_03833 [Bacillus subtilis subsp. natto
           BEST195]
 gi|305413478|gb|ADM38597.1| sporulation sigma factor SigmaK [Bacillus subtilis subsp.
           spizizenii str. W23]
          Length = 242

 Score = 43.9 bits (102), Expect = 0.028,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 3/74 (4%)

Query: 39  KRYRE---HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           K+Y E    GD  A + L+  +LRLV  I   +   G    +++S G IGL++ ++ +  
Sbjct: 38  KKYLELMAKGDEHARNMLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKGIESYSA 97

Query: 96  ERGFRLATYSMWWI 109
            +G +LATY+   I
Sbjct: 98  GKGTKLATYAARCI 111


>gi|121535240|ref|ZP_01667054.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
 gi|121306125|gb|EAX47053.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
          Length = 257

 Score = 43.9 bits (102), Expect = 0.028,   Method: Compositional matrix adjust.
 Identities = 20/75 (26%), Positives = 41/75 (54%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + G+  A  +L+  +LRLV+ +   +   G  + ++   G IGLM+A+  FD  +  + +
Sbjct: 32  QQGNPEAREQLIYGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKAIDNFDLSQNVKFS 91

Query: 103 TYSMWWIKAAMQEYI 117
           TY++  I   ++ Y+
Sbjct: 92  TYAVPMIIGEIRRYL 106


>gi|261367813|ref|ZP_05980696.1| putative RNA polymerase sigma-H factor [Subdoligranulum variabile
           DSM 15176]
 gi|282570611|gb|EFB76146.1| putative RNA polymerase sigma-H factor [Subdoligranulum variabile
           DSM 15176]
          Length = 180

 Score = 43.9 bits (102), Expect = 0.028,   Method: Compositional matrix adjust.
 Identities = 25/73 (34%), Positives = 36/73 (49%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD +A   L+   +  + K A  YR  GL   + V EG IGL QAV+ +    G   A
Sbjct: 13  QQGDDTALAALIARMMPAIRKGAAVYRAPGLDFEDAVQEGLIGLFQAVRGYRSAAGTPFA 72

Query: 103 TYSMWWIKAAMQE 115
           +Y+   I  A Q+
Sbjct: 73  SYAATCIHHAQQD 85


>gi|296333262|ref|ZP_06875715.1| sporulation sigma factor SigK [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|296149460|gb|EFG90356.1| sporulation sigma factor SigK [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
          Length = 241

 Score = 43.9 bits (102), Expect = 0.028,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 3/74 (4%)

Query: 39  KRYRE---HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           K+Y E    GD  A + L+  +LRLV  I   +   G    +++S G IGL++ ++ +  
Sbjct: 37  KKYLELMAKGDEHARNMLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKGIESYSA 96

Query: 96  ERGFRLATYSMWWI 109
            +G +LATY+   I
Sbjct: 97  GKGTKLATYAARCI 110


>gi|168187412|ref|ZP_02622047.1| RNA polymerase sigma-F factor [Clostridium botulinum C str. Eklund]
 gi|169294714|gb|EDS76847.1| RNA polymerase sigma-F factor [Clostridium botulinum C str. Eklund]
          Length = 251

 Score = 43.9 bits (102), Expect = 0.028,   Method: Compositional matrix adjust.
 Identities = 27/105 (25%), Positives = 51/105 (48%), Gaps = 3/105 (2%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A   LV  +L LV  I+  +   G    ++   G++GL++A+  FD     + +TY
Sbjct: 26  GDKKALDELVEKNLPLVSAISKKFLNRGYEYEDIFQIGSMGLIKAINNFDSSYNVQFSTY 85

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTA--NQKRLFFNLRRLKGHLQ 147
           ++  I   ++ +I R   L+K+  +     ++L F+  +L   L 
Sbjct: 86  AVPMIMGEIRRFI-RDDGLIKVSRSVKYTARKLHFDKEKLTKKLH 129


>gi|319651418|ref|ZP_08005547.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
 gi|317396949|gb|EFV77658.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
          Length = 252

 Score = 43.9 bits (102), Expect = 0.028,   Method: Compositional matrix adjust.
 Identities = 55/245 (22%), Positives = 113/245 (46%), Gaps = 28/245 (11%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A  ++V  ++RLV  +   +   G    ++   G IGL+++V KFD     + +
Sbjct: 27  QSGDQGARDKIVQKNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKSVDKFDLSYDVKFS 86

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I   +Q +I R    VK+  +   K +   +R+ K  L        +   V  +
Sbjct: 87  TYAVPMIIGEIQRFI-RDDGTVKVSRSL--KEMGNKIRKAKDELSKTLG---RIPTVTEL 140

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           ++ L +S  ++I     LA + S    I SS   +       VY++DG    L+++ +  
Sbjct: 141 SEFLEISPEDII-----LAQEAS---RIPSSIHET-------VYENDGDPITLLDQIDDG 185

Query: 223 NR-----RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
           N      +  L  ++  L+ RER I   R  ++   T   +++   +S+ +V ++E +  
Sbjct: 186 NEGKWFDKIALKEAIRELDERERLIVYLRYYKDQ--TQSEVAARLGISQVQVSRLEKKIL 243

Query: 278 KKVQE 282
           +++++
Sbjct: 244 QQMKD 248


>gi|257437879|ref|ZP_05613634.1| group2 RNA polymerase sigma factor RpoD6 [Faecalibacterium
           prausnitzii A2-165]
 gi|257199539|gb|EEU97823.1| group2 RNA polymerase sigma factor RpoD6 [Faecalibacterium
           prausnitzii A2-165]
          Length = 221

 Score = 43.9 bits (102), Expect = 0.028,   Method: Compositional matrix adjust.
 Identities = 28/101 (27%), Positives = 49/101 (48%), Gaps = 15/101 (14%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIA--------MGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           + GD +A   L+ ++   + K+A        +   G  L   ++   GN+GL +AV KFD
Sbjct: 13  QKGDAAALDSLIDNNKSFIGKVANDLFRSMNLAQAGLNLDTDDLKQAGNMGLWKAVPKFD 72

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
             RG +  TY+   I+ AM +       +V+   TA ++R+
Sbjct: 73  AARGMKFLTYAAPAIRNAMMD-------MVRDAFTAFEQRM 106


>gi|269836601|ref|YP_003318829.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Sphaerobacter
           thermophilus DSM 20745]
 gi|269785864|gb|ACZ38007.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Sphaerobacter
           thermophilus DSM 20745]
          Length = 264

 Score = 43.9 bits (102), Expect = 0.028,   Method: Compositional matrix adjust.
 Identities = 48/205 (23%), Positives = 91/205 (44%), Gaps = 23/205 (11%)

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++  G IGL++A+ +FDPERG +  T+++  I+ A+ + + R+  LV    TA Q+  
Sbjct: 59  DDLLGYGTIGLIEAIDRFDPERGVKFETFAIQRIRGAIIDAV-RTLDLVP--RTARQR-- 113

Query: 136 FFNLRRLKGHLQAI--TDNNLKPEQVVA--IAKKLNVSESEVISMNCRLAGDESLNALIN 191
               R ++   + I      + PE+ VA  +   ++     +    C      ++  L  
Sbjct: 114 ---ARAIEQAYREIFAATGRMPPEEEVAAHLGMTIDAFRQALQDAAC------AILPLQQ 164

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           S        +D L    D Q    ++   R +  + L  ++  L  R+R I      +E 
Sbjct: 165 SDRDGEGTLEDTL---PDAQATEPLDAAVRSDLVHRLAAALERLPERDRLIVTLYYYEE- 220

Query: 252 PVTLENLSSEFEVSRERVRQIEARA 276
            +TL  +S    ++  RV Q+ +RA
Sbjct: 221 -LTLREISEVLGITESRVSQLLSRA 244


>gi|29829172|ref|NP_823806.1| RNA polymerase sigma factor WhiG [Streptomyces avermitilis MA-4680]
 gi|29606278|dbj|BAC70341.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 280

 Score = 43.9 bits (102), Expect = 0.029,   Method: Compositional matrix adjust.
 Identities = 62/245 (25%), Positives = 100/245 (40%), Gaps = 20/245 (8%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFD 94
           + Y+  GD     +L+  H   +VK   G    GLP     ++ VS G  GL+ A++KFD
Sbjct: 36  RSYKATGDERLREQLIL-HYSPLVKYVAGRVSVGLPPNVEQADFVSSGVFGLIDAIEKFD 94

Query: 95  PERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
             R  +  TY++  I+ AM  E     W    I  +  QK    N+ R    L+A     
Sbjct: 95  IGREIKFETYAITRIRGAMIDELRALDW----IPRSVRQKAR--NVERAYATLEARL-RR 147

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ--DWLVYDHDGQ 211
              E  VA    + V E   +     LA   +L  L++   +   +    D L    D  
Sbjct: 148 TPTEGEVATEMGIAVDELHSVFSQLSLANVVALEELLHVGGEGGDRLSLMDTL---EDTA 204

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
               +E  E +  R  L R+++ L  RE+ +      +   +TL  + +   V+  RV Q
Sbjct: 205 ADNPVEVAEDRELRRFLARAINTLPDREKTVVTLYYYEG--LTLAEIGNVLGVTESRVSQ 262

Query: 272 IEARA 276
           I  ++
Sbjct: 263 IHTKS 267


>gi|312794136|ref|YP_004027059.1| RNA polymerase, sigma 28 subunit, sigk [Caldicellulosiruptor
           kristjanssonii 177R1B]
 gi|312181276|gb|ADQ41446.1| RNA polymerase, sigma 28 subunit, SigK [Caldicellulosiruptor
           kristjanssonii 177R1B]
          Length = 219

 Score = 43.9 bits (102), Expect = 0.029,   Method: Compositional matrix adjust.
 Identities = 28/93 (30%), Positives = 50/93 (53%), Gaps = 5/93 (5%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP--ISEVVSEGNI 84
           PM  ++EE  L K +   G   A + L+  +LRLV  IA  Y  +  P    +++S G I
Sbjct: 13  PMSSEEEEMYLNKMW--EGCKEARNILIEKNLRLVAHIAKKYT-FSFPNLTDDIISVGTI 69

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           GL++A++ +   +  +L+TY+   I+  +  Y+
Sbjct: 70  GLIKAIETYSKAKSTKLSTYAAKCIENEILMYL 102


>gi|310659013|ref|YP_003936734.1| RNA polymerase sigma-28 factor (sigma-d) [Clostridium sticklandii
           DSM 519]
 gi|308825791|emb|CBH21829.1| RNA polymerase sigma-28 factor (sigma-D) [Clostridium sticklandii]
          Length = 247

 Score = 43.9 bits (102), Expect = 0.030,   Method: Compositional matrix adjust.
 Identities = 59/233 (25%), Positives = 101/233 (43%), Gaps = 28/233 (12%)

Query: 61  VVKIAMG----YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           +VKI  G    Y    +   +++S G IGL+ A+ K+DP +  +  TY+   I+ ++ + 
Sbjct: 34  LVKIIAGKLYNYYASNIEYDDLMSYGVIGLIDAIDKYDPTKNIKFETYASIRIRGSIIDQ 93

Query: 117 ILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
           I    W    I  +  QK      + LK   +A+     +      IAK L  SE EV++
Sbjct: 94  IRNLDW----IPRSIRQKS-----KILKDANEALESKYGREASYQEIAKYLGKSEQEVLT 144

Query: 176 MNCRLAGDESLNALINSSDKNSS---QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           +   +      N L    D N S   Q +D  +      E + +  +  K     L R++
Sbjct: 145 L---IEETSVYNVLSIEDDFNESFKIQLKDESL--ESSPEDLTVYNDTVKE----LERTI 195

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           S LN RE+ I      +   +T + +     +S  RV QI ++A  K+++  Q
Sbjct: 196 SELNEREQLIINLYYYE--GLTYKEIGEILNISESRVSQIHSKAISKMRKQFQ 246


>gi|311031586|ref|ZP_07709676.1| sporulation sigma factor SigK [Bacillus sp. m3-13]
          Length = 237

 Score = 43.9 bits (102), Expect = 0.031,   Method: Compositional matrix adjust.
 Identities = 22/65 (33%), Positives = 37/65 (56%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           G+  A + L+  +LRLV  I   +   G    +++S G IGL++A++ F   +G +LATY
Sbjct: 46  GNEEARNLLIEHNLRLVAHIVKKFENTGEDSEDLISIGTIGLIKAIESFHSGKGTKLATY 105

Query: 105 SMWWI 109
           +   I
Sbjct: 106 AARCI 110


>gi|294634080|ref|ZP_06712635.1| RNA polymerase sigma factor [Streptomyces sp. e14]
 gi|292829894|gb|EFF88248.1| RNA polymerase sigma factor [Streptomyces sp. e14]
          Length = 311

 Score = 43.9 bits (102), Expect = 0.031,   Method: Compositional matrix adjust.
 Identities = 60/245 (24%), Positives = 112/245 (45%), Gaps = 30/245 (12%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           SA   LVT+ L +  +IA  +R  G  I ++     +GL++A+ +FDP+RG    +Y++ 
Sbjct: 72  SARDELVTAWLPMAHRIAGRFRDRGESIEDLRQVAALGLVKAIDRFDPDRGA-FESYAVP 130

Query: 108 WIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLR-RLKGHLQAITDNNLKPE-QVVAIAK 164
            I   ++ +   R W+L          R    LR +++   + +T N   PE  V A+A 
Sbjct: 131 TITGEVKRHFRDRMWAL-------RVPRRVQELRNKVRVARRELTQNPGSPEPSVAAVAA 183

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD-WLVYD----HDGQEQVLIEKE 219
              ++E EV   N  +   +S + L  S D   S   D + + D     D    V++++E
Sbjct: 184 HTGLTEDEV---NTGMEALDSFSTL--SLDAEMSTGADGYSLADTLGAADSSYDVVVDRE 238

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
             K         +  L  RER I   R  ++  +T   ++    +S+  V ++ +R+  +
Sbjct: 239 SAKE-------GLRRLPERERAILYMRFFED--MTQSRIADRLGISQMHVSRLISRSCAR 289

Query: 280 VQESI 284
           V++ +
Sbjct: 290 VRDEV 294


>gi|111017120|ref|YP_700092.1| sigma factor, sigma 70 type, group 3 [Rhodococcus jostii RHA1]
 gi|110816650|gb|ABG91934.1| sigma factor, sigma 70 type, group 3 [Rhodococcus jostii RHA1]
          Length = 265

 Score = 43.9 bits (102), Expect = 0.031,   Method: Compositional matrix adjust.
 Identities = 22/72 (30%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++T  L L   IA  + G G    +++    +GL++AV +FDP+RGF   +Y++  I   
Sbjct: 45  VITRCLPLADHIARRFGGRGEAHEDLLQVARLGLVKAVDRFDPDRGFDFVSYAVPTIMGE 104

Query: 113 MQEYILRS-WSL 123
           ++ Y   + WS+
Sbjct: 105 VRRYFRDTGWSM 116


>gi|305644358|gb|ADM53780.1| RNA polymerase sigma factor [Aeromonas hydrophila]
          Length = 176

 Score = 43.9 bits (102), Expect = 0.031,   Method: Compositional matrix adjust.
 Identities = 17/42 (40%), Positives = 27/42 (64%)

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           GLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I
Sbjct: 1   GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 42


>gi|222530382|ref|YP_002574264.1| putative RNA polymerase, sigma 70 family subunit
           [Caldicellulosiruptor bescii DSM 6725]
 gi|222457229|gb|ACM61491.1| putative RNA polymerase, sigma 70 family subunit
           [Caldicellulosiruptor bescii DSM 6725]
          Length = 210

 Score = 43.9 bits (102), Expect = 0.031,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 37/69 (53%), Gaps = 1/69 (1%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  AA  L+ ++  L++ +A  Y    +   ++  EG + ++QA +KFD   G    T 
Sbjct: 23  GDKEAAETLIMAYEPLIISLAAKYNKPDI-FEDLKQEGAVAILQAAQKFDESLGVSFVTL 81

Query: 105 SMWWIKAAM 113
           ++++IK  M
Sbjct: 82  AIYYIKRNM 90


>gi|239981813|ref|ZP_04704337.1| RNA polymerase sigma factor [Streptomyces albus J1074]
          Length = 328

 Score = 43.9 bits (102), Expect = 0.031,   Method: Compositional matrix adjust.
 Identities = 60/240 (25%), Positives = 106/240 (44%), Gaps = 30/240 (12%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  +L LV   A  +R    P+ +++  G IGL++A+ +F+  RG    T++M  I   
Sbjct: 107 LVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRGVEFPTFAMPTIIGE 166

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL  +L +    L    D   +   V  +A +L +S+ 
Sbjct: 167 IKRFFRDTSWS-VRVPRRLQELRL--DLAKAGDELAQKLD---RAPTVRELADRLGLSQE 220

Query: 172 EVISMNCRLAGDESLNALINSS-------DKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           EV+       G  + NA   SS       D +     D + Y+  G E   IE  E    
Sbjct: 221 EVVE------GMAASNAYTASSLDAQPEEDDSEGALADRIGYEDHGIEG--IEYVES--- 269

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              L   ++ L  R+RRI  + R   N +T   +  E  +S+  V ++  R   ++++ +
Sbjct: 270 ---LKPLIAELPARDRRIL-SLRFTAN-MTQSEIGEELGISQMHVSRLLTRTLNRLRKGL 324


>gi|222528749|ref|YP_002572631.1| FliA/WhiG subfamily RNA polymerase sigma-28 factor
           [Caldicellulosiruptor bescii DSM 6725]
 gi|222530717|ref|YP_002574606.1| FliA/WhiG subfamily RNA polymerase sigma-28 factor
           [Caldicellulosiruptor bescii DSM 6725]
 gi|222455596|gb|ACM59858.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor bescii DSM 6725]
 gi|222457564|gb|ACM61825.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor bescii DSM 6725]
          Length = 310

 Score = 43.9 bits (102), Expect = 0.032,   Method: Compositional matrix adjust.
 Identities = 22/66 (33%), Positives = 40/66 (60%), Gaps = 5/66 (7%)

Query: 53  LVTSHLRLVVKIAMGY----RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           L+  +L+LV  +A  +    +GY   + ++VSEG IGL+ A K +DP +G   +TY+   
Sbjct: 17  LIVDNLKLVYHVANKFMPCPKGYYYEVDDLVSEGYIGLVVAAKNYDPAKG-SFSTYACKV 75

Query: 109 IKAAMQ 114
           I++ ++
Sbjct: 76  IESKIK 81


>gi|157371179|ref|YP_001479168.1| flagellar biosynthesis sigma factor [Serratia proteamaculans 568]
 gi|157322943|gb|ABV42040.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Serratia
           proteamaculans 568]
          Length = 240

 Score = 43.9 bits (102), Expect = 0.032,   Method: Compositional matrix adjust.
 Identities = 47/214 (21%), Positives = 95/214 (44%), Gaps = 30/214 (14%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL+ AV+++D  +G    TY++  I+ AM +  LRS   V      + + 
Sbjct: 41  LDDLLQAGGIGLLNAVERYDAMQGTAFTTYAVQRIRGAMLDE-LRSRDWVPRSVRRHARE 99

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   +R+L+  L        +P   V +A+ LN+S             DE    L+++++
Sbjct: 100 VAQVMRQLEQQLG-------RPASEVEVAQTLNLS------------LDEYRQILLDTNN 140

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEE--------RKNRRNMLTRSMSVLNPRERRIFEAR 246
                + +W     +  E +L   EE          N R  +  ++  L  RE+ +    
Sbjct: 141 SQLFSYDEWREEHGESAEPLLEGHEEANPLHHLLEGNLRQRVIDAIEALPEREKMVLTLY 200

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             +E  + L+ + +  +V   RV Q+ ++A K++
Sbjct: 201 YQEE--LNLKEIGAVLDVGESRVSQLHSQAIKRL 232


>gi|308803162|ref|XP_003078894.1| RNA-polymerase sigma factor (ISS) [Ostreococcus tauri]
 gi|116057347|emb|CAL51774.1| RNA-polymerase sigma factor (ISS) [Ostreococcus tauri]
          Length = 485

 Score = 43.9 bits (102), Expect = 0.032,   Method: Compositional matrix adjust.
 Identities = 23/85 (27%), Positives = 44/85 (51%), Gaps = 7/85 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPIS-------EVVSEGNIGLMQAVKKFDPERGFRL 101
           A  +LV++++ L  K+A        P+        +++ EG  GL++A +KFDP  G   
Sbjct: 180 ARQKLVSANIELAAKVATDVFHTFSPMERRSISRQDMIHEGVTGLVRASEKFDPALGCAF 239

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKI 126
           +TY+  W K A+   +L +   +++
Sbjct: 240 STYAYNWTKQAVTRGVLNNGRTIRV 264


>gi|154686834|ref|YP_001421995.1| sporulation sigma factor SigK [Bacillus amyloliquefaciens FZB42]
 gi|154352685|gb|ABS74764.1| SpoIIIC [Bacillus amyloliquefaciens FZB42]
          Length = 240

 Score = 43.9 bits (102), Expect = 0.033,   Method: Compositional matrix adjust.
 Identities = 21/65 (32%), Positives = 36/65 (55%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A + L+  +LRLV  I   +   G    +++S G IGL++ ++ +   +G +LATY
Sbjct: 46  GDEHARNMLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKGIESYSAGKGTKLATY 105

Query: 105 SMWWI 109
           +   I
Sbjct: 106 AARCI 110


>gi|302556940|ref|ZP_07309282.1| RNA polymerase sigma factor [Streptomyces griseoflavus Tu4000]
 gi|302474558|gb|EFL37651.1| RNA polymerase sigma factor [Streptomyces griseoflavus Tu4000]
          Length = 285

 Score = 43.9 bits (102), Expect = 0.033,   Method: Compositional matrix adjust.
 Identities = 59/245 (24%), Positives = 108/245 (44%), Gaps = 34/245 (13%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LVT+ L +  +IA  +R  G  + ++     +GL++A+ +FDP RG    +Y++  I   
Sbjct: 51  LVTAWLPMAHRIAGRFRDRGEAVEDLRQVAALGLVKAIDRFDPSRGA-FESYAVPTITGE 109

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLR-RLKGHLQAITDNNLKPE-QVVAIAKKLNVS 169
           ++ +   R W+L          R    LR +++   + +T +   PE  V AIA    ++
Sbjct: 110 VKRHFRDRMWAL-------RVPRRVQELRNKVRVARRELTQSPGSPEPSVAAIAAHTGLT 162

Query: 170 ESEVISMNCRLAGDESLNALIN-------SSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           E EV       AG E+L +          SSD +     D L    D    V++++E  K
Sbjct: 163 EDEVG------AGMEALESFSTLSLDAELSSDDDGYSLADTLGA-SDSSYDVVVDRESAK 215

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
                    +  L  RER I   R  ++  +T   ++ +  +S+  V ++ +R+  +V+ 
Sbjct: 216 E-------GLRRLPERERAILYMRFFED--MTQSRIADQLGISQMHVSRLISRSCARVRA 266

Query: 283 SIQKQ 287
               Q
Sbjct: 267 DAMGQ 271


>gi|239827399|ref|YP_002950023.1| RNA polymerase, sigma 70 family subunit [Geobacillus sp. WCH70]
 gi|239807692|gb|ACS24757.1| putative RNA polymerase, sigma 70 family subunit [Geobacillus sp.
           WCH70]
          Length = 831

 Score = 43.9 bits (102), Expect = 0.033,   Method: Compositional matrix adjust.
 Identities = 54/254 (21%), Positives = 105/254 (41%), Gaps = 44/254 (17%)

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           + + A  +    +P+ ++  E    L +A +K++PE G     Y    + A +Q Y   +
Sbjct: 583 IYQYAKKFSCETVPMEDLYQEAYFALHKAYEKYNPELGGSFYHYFRRHLFARLQRYKSDN 642

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
            SL++I T            R++  ++   D   + + +      +N+ +S+ I      
Sbjct: 643 LSLIRIPT-----------HRIETLMK--NDQIFEKQLITNEKTNINLLDSDYILFKTNY 689

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQE------QVLI------EKEE-------- 220
              E L +L + +  + ++ + +  ++H   E      QV I      E EE        
Sbjct: 690 ISFEELYSLYDDNAGDEARARIYCYFNHPFYEDTSLKRQVFIDYSYIEEPEECDWLLSEE 749

Query: 221 ----RKNRRNMLTRSMSVL-----NPRERRIFEARR--LQENPVTLENLSSEFEVSRERV 269
                   R +   ++  L     NPR+ +I   R   +    +TL+ +   F VSRER+
Sbjct: 750 RYEEEIENRVLAESAIDYLRNIIKNPRDWKIILYRFGFMTGEEMTLQEIGELFGVSRERI 809

Query: 270 RQIEARAFKKVQES 283
           RQIE +A K +++ 
Sbjct: 810 RQIENKALKHLKKC 823


>gi|108799863|ref|YP_640060.1| RNA polymerase sigma factor SigF [Mycobacterium sp. MCS]
 gi|119868973|ref|YP_938925.1| RNA polymerase sigma factor SigF [Mycobacterium sp. KMS]
 gi|126435506|ref|YP_001071197.1| RNA polymerase sigma factor SigF [Mycobacterium sp. JLS]
 gi|108770282|gb|ABG09004.1| RNA polymerase, sigma 28 subunit [Mycobacterium sp. MCS]
 gi|119695062|gb|ABL92135.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Mycobacterium
           sp. KMS]
 gi|126235306|gb|ABN98706.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Mycobacterium
           sp. JLS]
          Length = 269

 Score = 43.5 bits (101), Expect = 0.033,   Method: Compositional matrix adjust.
 Identities = 37/140 (26%), Positives = 61/140 (43%), Gaps = 23/140 (16%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R+VT  L L   IA  Y   G  + ++V    +GLM AV +FDPE G    ++++  +  
Sbjct: 49  RIVTRCLPLADHIAFRYHRKGENLDDLVQIARVGLMHAVNRFDPENGANFLSFAVPTMLG 108

Query: 112 AMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKG-HLQA------ITDNNLKPEQVVAIA 163
            ++ +     W++                RRLK  H+Q       +T +  +P     +A
Sbjct: 109 EIRRHFRDNGWAM-------------HVPRRLKDLHVQITRATPRLTQSLGRPPTPTDLA 155

Query: 164 KKLNVSESEVISMNCRLAGD 183
            +L     EV+   C +AGD
Sbjct: 156 AELGADRQEVV--ECLVAGD 173


>gi|31747734|gb|AAO38358.1| Lfe160p1 [Leptospirillum ferrooxidans]
          Length = 218

 Score = 43.5 bits (101), Expect = 0.033,   Method: Compositional matrix adjust.
 Identities = 48/212 (22%), Positives = 93/212 (43%), Gaps = 15/212 (7%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++VS G  GL+ A K+FDP RG +  T +   I+ AM + I RS   V          
Sbjct: 13  VDDLVSVGMTGLIDAAKRFDPSRGIKFKTMAEHRIRGAMLDEI-RSADWVPRSVREKASS 71

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINS 192
           +      L+  L    D+       + +AK L++S  E +++   +      S+  L   
Sbjct: 72  VHAVREGLRAALLREPDD-------MEMAKALSMSLDEYLTLENEIEPHHLYSIEDLFEM 124

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            +   S   D +V   +        K E     ++L +++  L  ++R +      +E  
Sbjct: 125 EEGAGSSILDRMVVPGEADPLSEFLKSEEA---SLLEKALDSLPEKQRLVLSLYYYEE-- 179

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++++ +++  EVS  RV QI   A K +++++
Sbjct: 180 LSMKEVAAVLEVSESRVSQIHTLAIKNLKKAL 211


>gi|328912710|gb|AEB64306.1| RNA polymerase sigma factor [Bacillus amyloliquefaciens LL3]
          Length = 242

 Score = 43.5 bits (101), Expect = 0.034,   Method: Compositional matrix adjust.
 Identities = 21/65 (32%), Positives = 36/65 (55%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A + L+  +LRLV  I   +   G    +++S G IGL++ ++ +   +G +LATY
Sbjct: 47  GDEHARNMLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKGIESYSAGKGTKLATY 106

Query: 105 SMWWI 109
           +   I
Sbjct: 107 AARCI 111


>gi|308174363|ref|YP_003921068.1| RNA polymerase sporulation-specific sigma-K factor [Bacillus
           amyloliquefaciens DSM 7]
 gi|307607227|emb|CBI43598.1| RNA polymerase sporulation-specific sigma-K factor precursor
           (Sigma-27) (C-terminal fragment) [Bacillus
           amyloliquefaciens DSM 7]
          Length = 240

 Score = 43.5 bits (101), Expect = 0.034,   Method: Compositional matrix adjust.
 Identities = 21/65 (32%), Positives = 36/65 (55%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A + L+  +LRLV  I   +   G    +++S G IGL++ ++ +   +G +LATY
Sbjct: 46  GDEHARNMLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKGIESYSAGKGTKLATY 105

Query: 105 SMWWI 109
           +   I
Sbjct: 106 AARCI 110


>gi|328554314|gb|AEB24806.1| sporulation sigma factor SigK [Bacillus amyloliquefaciens TA208]
          Length = 241

 Score = 43.5 bits (101), Expect = 0.034,   Method: Compositional matrix adjust.
 Identities = 21/65 (32%), Positives = 36/65 (55%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A + L+  +LRLV  I   +   G    +++S G IGL++ ++ +   +G +LATY
Sbjct: 46  GDEHARNMLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKGIESYSAGKGTKLATY 105

Query: 105 SMWWI 109
           +   I
Sbjct: 106 AARCI 110


>gi|311069177|ref|YP_003974100.1| sporulation sigma factor SigK [Bacillus atrophaeus 1942]
 gi|310869694|gb|ADP33169.1| sporulation sigma factor SigK [Bacillus atrophaeus 1942]
          Length = 242

 Score = 43.5 bits (101), Expect = 0.034,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 3/74 (4%)

Query: 39  KRYRE---HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           K+Y E    GD  A + L+  +LRLV  I   +   G    +++S G IGL++ ++ +  
Sbjct: 38  KKYLELMAKGDEHARNMLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKGIESYSA 97

Query: 96  ERGFRLATYSMWWI 109
            +G +LATY+   I
Sbjct: 98  GKGTKLATYAARCI 111


>gi|163801862|ref|ZP_02195759.1| flagellar biosynthesis sigma factor FliA [Vibrio sp. AND4]
 gi|159174370|gb|EDP59174.1| flagellar biosynthesis sigma factor FliA [Vibrio sp. AND4]
          Length = 244

 Score = 43.5 bits (101), Expect = 0.034,   Method: Compositional matrix adjust.
 Identities = 56/250 (22%), Positives = 106/250 (42%), Gaps = 27/250 (10%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFD 94
           A  Y +HG  ++    +  +  LV +IA    G   P   + +++  G IGL++A + +D
Sbjct: 4   AITYDQHGKFNSQQAFIERYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLIEAKQNYD 63

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +G    TY+   I+ AM + I R    V      N +++   +  L+G   A+  +  
Sbjct: 64  GSKGASFETYAGIRIRGAMLDDI-RKGDWVPRSVHKNNRQINQAIAELEG---ALNRDPF 119

Query: 155 KPEQVVAIAKKLNVSESEVISMNC-RLAGDESL---NALINSSDKNSSQWQDWLVYDHDG 210
             E    +   L+   S +  +NC +L G E L   + +I+ +D+         V D D 
Sbjct: 120 DSEVAEHLGMTLDQYHSALTDINCSKLVGIEDLGVSDDVISPADETDDSNPFKGVAD-DS 178

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
            ++ L+E  ++   R  L  S+                 +  + L+ +     VS  RV 
Sbjct: 179 FKKALVESIKQLPEREALVLSL---------------YYDEELNLKEIGDVLGVSESRVS 223

Query: 271 QIEARAFKKV 280
           QI ++A +++
Sbjct: 224 QILSQAMQRL 233


>gi|1552544|emb|CAA90874.1| sigma factor [Bacillus coagulans]
          Length = 252

 Score = 43.5 bits (101), Expect = 0.034,   Method: Compositional matrix adjust.
 Identities = 45/184 (24%), Positives = 77/184 (41%), Gaps = 14/184 (7%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K EE     R  E GD  A   +V  ++RLV  +   +   G    ++   G IGL+++V
Sbjct: 15  KDEEVKNLIRRTEEGDQEARDLIVEKNIRLVWSVVHRFLNRGYEPDDLFQIGCIGLLKSV 74

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL---- 146
            KFD     + +TY++  I   +Q + LR    VK+  +   K     +R+++  L    
Sbjct: 75  DKFDLSYDVKFSTYAVPMIIGEIQRF-LRDDGTVKVSRSL--KETGNRIRKIRDELTKKL 131

Query: 147 ------QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
                   I      P + V +A++   + S +        GD  +  L   SD+N  +W
Sbjct: 132 GRSPTVHEIASELGMPVEEVVMAQEAGKAPSSIHETVYENDGD-PITLLDQISDQNDQKW 190

Query: 201 QDWL 204
            D +
Sbjct: 191 FDQI 194


>gi|210624023|ref|ZP_03294140.1| hypothetical protein CLOHIR_02092 [Clostridium hiranonis DSM 13275]
 gi|210153230|gb|EEA84236.1| hypothetical protein CLOHIR_02092 [Clostridium hiranonis DSM 13275]
          Length = 255

 Score = 43.5 bits (101), Expect = 0.035,   Method: Compositional matrix adjust.
 Identities = 59/255 (23%), Positives = 115/255 (45%), Gaps = 21/255 (8%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L + Y ++ D+   + L+  HL L   +A  Y   G+   ++    ++ L+ A+ ++D  
Sbjct: 18  LFRLYSDNKDIDIRNILIERHLYLARILAKKYINKGVDYEDIYQVASLALIYAIDRYDIS 77

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +GF  ++++   I   +++Y        K+ T    +R+    +++     AI     + 
Sbjct: 78  KGFEFSSFATPTIIGEIKKYFRD-----KVWTMRVPRRIQELSKKISNAKIAIEQEKKRH 132

Query: 157 EQVVAIAKKLNVSESEVI-SMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
             V  IA+ +   E +V+ +M    +    SL+A   SS  +S    D  + D  G E+ 
Sbjct: 133 PSVKDIAEYIGCREEDVLEAMEASYSYQPVSLDA---SSGDDSE--DDLTLSDRVGVEEK 187

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
                E+K   + L R M  LN  E +I E R       ++  +++E  +S+  V ++E 
Sbjct: 188 DFGNIEQK---DFLNRFMQTLNELEVKILEDRFFHNKTQSV--IATELNISQMTVSRLE- 241

Query: 275 RAFKKVQESIQKQVE 289
              KKV E ++K+ E
Sbjct: 242 ---KKVVEKLRKEYE 253


>gi|168213645|ref|ZP_02639270.1| RNA polymerase sigma factor RpoD [Clostridium perfringens CPE str.
           F4969]
 gi|170714810|gb|EDT26992.1| RNA polymerase sigma factor RpoD [Clostridium perfringens CPE str.
           F4969]
          Length = 227

 Score = 43.5 bits (101), Expect = 0.035,   Method: Compositional matrix adjust.
 Identities = 22/82 (26%), Positives = 44/82 (53%), Gaps = 5/82 (6%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLMQAVKKFDPE--R 97
           + GD  A  +L+ ++ +L+ KIA  +   +   +   +++ EG IGL+ A  K+D E  +
Sbjct: 11  QQGDKKALDKLLENNDKLIYKIANKFYSDKTSSIEFDDLLQEGRIGLILACSKYDIEYIK 70

Query: 98  GFRLATYSMWWIKAAMQEYILR 119
             +  TY+ +WI   +  +I +
Sbjct: 71  RTKFITYAFYWIYQKIHRFITK 92


>gi|291544363|emb|CBL17472.1| DNA-directed RNA polymerase specialized sigma subunit [Ruminococcus
           sp. 18P13]
          Length = 118

 Score = 43.5 bits (101), Expect = 0.035,   Method: Compositional matrix adjust.
 Identities = 28/86 (32%), Positives = 43/86 (50%), Gaps = 2/86 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  K+E    A+     GD  A   L+  +LRLV  +   Y        E++S G +GL
Sbjct: 29  PLSPKEEADCFARL--AQGDSQARAMLIEHNLRLVAHMIKKYYANSKDQDELISIGTMGL 86

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAA 112
           ++AV  FD  +G + ATY+   I+ A
Sbjct: 87  IKAVNTFDAAKGSKFATYAGRCIEKA 112


>gi|229492054|ref|ZP_04385868.1| RNA polymerase sigma-F factor [Rhodococcus erythropolis SK121]
 gi|229321078|gb|EEN86885.1| RNA polymerase sigma-F factor [Rhodococcus erythropolis SK121]
          Length = 259

 Score = 43.5 bits (101), Expect = 0.035,   Method: Compositional matrix adjust.
 Identities = 56/244 (22%), Positives = 111/244 (45%), Gaps = 22/244 (9%)

Query: 45  GDLSAAHRLVTSHLRLVVK----IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           GD +   RL T  + L +     IA+ YRG G  + ++V   ++GL+ AV +FD  +G  
Sbjct: 21  GDDARCERLRTQIIELCLPLTRHIALRYRGRGQALDDLVQAASVGLVSAVNRFDLAKGKD 80

Query: 101 LATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
              +++  +   ++++   R W  V++  +  +  L  N  R      A+T +  +   V
Sbjct: 81  FLAFAIPTMMGEVRKHFRDRGWD-VRVPRSLQENCLALNKAR-----TALTQDLGREPTV 134

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +AK+L V  +EV  +    AGD    A ++++     +     + D  G+    ++  
Sbjct: 135 PELAKELGVEPAEVAEIVA--AGDSYHAASLDAAAVGDGRS----IADALGEFDAALDG- 187

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
              + +  L  ++  L  RER I   R   E  +T   ++ +  VS+  V ++ A++  K
Sbjct: 188 --IDNQETLRPALLALPERERIIVIYRFFGE--LTQAEIAEKIGVSQMHVSRLLAQSLAK 243

Query: 280 VQES 283
           ++ S
Sbjct: 244 LRAS 247


>gi|323705323|ref|ZP_08116898.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
 gi|323535225|gb|EGB25001.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
          Length = 247

 Score = 43.5 bits (101), Expect = 0.035,   Method: Compositional matrix adjust.
 Identities = 38/138 (27%), Positives = 68/138 (49%), Gaps = 14/138 (10%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIA--MGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           R  ++ D S+  +L+  +  L+  I     YRGY     ++   G IG ++A+ KFD   
Sbjct: 17  RKSKNNDKSSMEKLLKENSGLIWSIVKKFSYRGY--EAEDLYQIGCIGFVKAINKFDESY 74

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ--KRLFFNLRRLKGHLQAITDNNLK 155
             +L+TY++  I   ++ + LR   L+K+  +  +   + +F   +L+  L      N +
Sbjct: 75  NVKLSTYAVPIIIGEIKRF-LRDDGLIKVSRSLKELSNKAYFMKDKLEKEL------NRE 127

Query: 156 PEQVVAIAKKLNVSESEV 173
           P  +  IA KL+VS  EV
Sbjct: 128 P-TIQEIASKLDVSAEEV 144


>gi|296125231|ref|YP_003632483.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Brachyspira murdochii
           DSM 12563]
 gi|296017047|gb|ADG70284.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Brachyspira murdochii
           DSM 12563]
          Length = 272

 Score = 43.5 bits (101), Expect = 0.036,   Method: Compositional matrix adjust.
 Identities = 54/242 (22%), Positives = 111/242 (45%), Gaps = 38/242 (15%)

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           + + MG   + +   ++V  G+ GLM A+ K++P R  +  TY++  I+ A+ +  LR  
Sbjct: 53  ISVNMGSHKH-IEFQDLVGFGSFGLMDAIDKYNPNRDIKFKTYAVTRIRGAIYDE-LRKL 110

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             +      + K     + + +  L+A    N+KP++   IA  L +  S+         
Sbjct: 111 DYLPRSIRKDVKE----IEKAREILEARLSRNIKPQE---IADMLGIPISKY-------- 155

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK------------EERKNRRNMLT 229
            +E++   I +S  + S    W V D D  E  +I+              ER++ +N + 
Sbjct: 156 -NETMKRYIEASPTSLSDV--WYVGD-DSDEISVIDTLKSNDKTNPEYLAEREDVKNKIV 211

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES---IQK 286
            ++  L  +E+++       +  +TL+ +    EVS  R+ Q+  +A ++++ S   I+K
Sbjct: 212 AALKKLPEKEKQVLILYYYDD--LTLKEIGKVLEVSESRISQLHTKAIQQLRYSLSEIKK 269

Query: 287 QV 288
           Q+
Sbjct: 270 QL 271


>gi|227500978|ref|ZP_03931027.1| possible DNA-directed RNA polymerase sigma subunit SigB
           [Anaerococcus tetradius ATCC 35098]
 gi|227216751|gb|EEI82149.1| possible DNA-directed RNA polymerase sigma subunit SigB
           [Anaerococcus tetradius ATCC 35098]
          Length = 256

 Score = 43.5 bits (101), Expect = 0.036,   Method: Compositional matrix adjust.
 Identities = 51/251 (20%), Positives = 111/251 (44%), Gaps = 20/251 (7%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           +Y +  D      L+  H+ +V  ++  Y G G+   ++    ++GL+ A++++DP +GF
Sbjct: 19  QYYKTKDKKLRDELIEEHMYIVDILSNKYVGKGIEKDDLYQVASLGLIYAIERYDPSKGF 78

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
             ++++   I   ++ Y      ++++       R   NL +     + I    L+    
Sbjct: 79  AFSSFATPTIMGELKRYFRDKGWVIRV------PRRIQNLYKKINTAKKILPQELQRTPT 132

Query: 160 VA-IAKKLNVSESEVISM--NCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVL 215
           VA IA  L   E  ++      ++   +SL+        +N+    D +     G+E   
Sbjct: 133 VADIADYLGEDEETILETMEASKVYTPQSLDMKYQVQKGENAVDLSDMI-----GEEDKN 187

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
            +  E K   +++ +SM  LN  E+ I E R  +    T  ++++  ++S+  V +IE +
Sbjct: 188 FDSIELK---DLIDKSMERLNDLEKEILELRYYEGR--TQVDIANSLDISQMTVSRIEKK 242

Query: 276 AFKKVQESIQK 286
             +K    ++K
Sbjct: 243 ILQKFSIELEK 253


>gi|312134632|ref|YP_004001970.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|311774683|gb|ADQ04170.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor owensensis OL]
          Length = 242

 Score = 43.5 bits (101), Expect = 0.036,   Method: Compositional matrix adjust.
 Identities = 28/93 (30%), Positives = 50/93 (53%), Gaps = 5/93 (5%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP--ISEVVSEGNI 84
           PM  ++EE  L K +   G   A + L+  +LRLV  IA  Y  +  P    +++S G I
Sbjct: 36  PMSSEEEEMYLNKMW--EGCKEARNILIEKNLRLVAHIAKKYT-FSFPNLTDDIISVGTI 92

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           GL++A++ +   +  +L+TY+   I+  +  Y+
Sbjct: 93  GLIKAIETYSTAKCTKLSTYAAKCIENEILMYL 125


>gi|225619299|ref|YP_002720525.1| RNA polymerase sigma factor WhiG [Brachyspira hyodysenteriae WA1]
 gi|225214118|gb|ACN82852.1| RNA polymerase sigma factor WhiG [Brachyspira hyodysenteriae WA1]
          Length = 275

 Score = 43.5 bits (101), Expect = 0.037,   Method: Compositional matrix adjust.
 Identities = 54/242 (22%), Positives = 111/242 (45%), Gaps = 38/242 (15%)

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           + + MG   + +   ++V  G+ GLM A+ K++P R  +  TY++  I+ A+ +  LR  
Sbjct: 56  ISVNMGSHKH-IEFQDLVGFGSFGLMDAIDKYNPNRDIKFKTYAVTRIRGAIYDE-LRKL 113

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             +      + K     + + +  L+A    N+KP++   IA  L +  S+         
Sbjct: 114 DYLPRSIRKDVKE----IEKAREILEARLSRNIKPQE---IADMLGIPISKY-------- 158

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK------------EERKNRRNMLT 229
            +E++   I +S  + S    W V D D  E  +I+              ER++ +N + 
Sbjct: 159 -NETMKRYIEASPTSLSDV--WYVGD-DSDEISVIDTLKSNDKTNPEYLAEREDVKNKII 214

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES---IQK 286
            ++  L  +E+++       +  +TL+ +    EVS  R+ Q+  +A ++++ S   I+K
Sbjct: 215 AALKKLPEKEQQVLILYYYDD--LTLKEIGKVLEVSESRISQLHTKAIQQLRYSLSEIKK 272

Query: 287 QV 288
           Q+
Sbjct: 273 QL 274


>gi|206603135|gb|EDZ39615.1| Putative RNA polymerase sigma 28 subunit [Leptospirillum sp. Group
           II '5-way CG']
          Length = 251

 Score = 43.5 bits (101), Expect = 0.037,   Method: Compositional matrix adjust.
 Identities = 50/215 (23%), Positives = 101/215 (46%), Gaps = 17/215 (7%)

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI-LRSWSLVKIGTTAN 131
           L I +++S G  GL+ A ++FDP RG +  T +   I+ AM + I    W    +  +  
Sbjct: 32  LDIDDLISAGMGGLLDAARRFDPARGIKFKTLAEHRIRGAMLDEIRAADW----MPRSVR 87

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV--ISMNCRLAGDESLNAL 189
           +K    +++++K  L  I     +P +   IA ++ ++E E   +S++       SL  L
Sbjct: 88  EK--LTHVQQVKTEL--IARYKREPTR-QEIAARMEMTEEEFDRLSVDIEPHHLVSLEDL 142

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           ++  D +S    D L    +G     + + E   +   L +++  L  ++R +      +
Sbjct: 143 MDPEDGDSPSLLDRLSAPQEGDPLASLLQNEVSEK---LCQALDRLPEKQRLVLSLYYYE 199

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           E  +T++ ++    VS  RV QI  +A   +++S+
Sbjct: 200 E--LTMKEVARVVGVSESRVSQIHGQALAALKQSL 232


>gi|220909315|ref|YP_002484626.1| RNA polymerase sigma factor SigF [Cyanothece sp. PCC 7425]
 gi|219865926|gb|ACL46265.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cyanothece
           sp. PCC 7425]
          Length = 262

 Score = 43.5 bits (101), Expect = 0.037,   Method: Compositional matrix adjust.
 Identities = 41/172 (23%), Positives = 82/172 (47%), Gaps = 22/172 (12%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE-VVSEGNIGLMQAVKKFDP 95
           L + Y+++   S  +RLV  +L LV K A  +  Y     E +V  G++GL++A+++FD 
Sbjct: 20  LLQAYQKNPAPSLRNRLVQMNLGLVRKEAHRWLSYSTETYEDLVQVGSLGLIRAIERFDI 79

Query: 96  ERGFRLATYSMWWIKAAMQEY---------ILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
            +G   ++++M +I+  +Q Y         I R W +++   +   + L   L R+    
Sbjct: 80  TKGHAFSSFAMPYIRGEIQHYLRDKSPQVRIPRRWQVLQKQASLVAQELREQLHRVP--- 136

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
              TD+ +      A+A  + + E + + ++       SL+A +   D  S+
Sbjct: 137 ---TDDEM------ALALGIGLQEWQQVKLSSYNRSPLSLDAPVGEDDFGST 179


>gi|159029418|emb|CAO90794.1| unnamed protein product [Microcystis aeruginosa PCC 7806]
          Length = 258

 Score = 43.5 bits (101), Expect = 0.037,   Method: Compositional matrix adjust.
 Identities = 39/180 (21%), Positives = 90/180 (50%), Gaps = 18/180 (10%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK-----IAMGYRGYGLPISEVVSEGNIG 85
           K E   L K+Y++ G+     +++  +L LV +     +   +  Y     ++V  G +G
Sbjct: 10  KLETLTLFKKYQKTGENQLRDQIIRLNLGLVRREAHHWVNQCHENY----EDLVQVGCMG 65

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A+K+FD  +G   +++++ +I+  +Q Y      L   G T    R + +L R   +
Sbjct: 66  LIRAIKRFDSSKGHAFSSFAIPYIRGEIQHY------LRDKGYTVRIPRRWLDLGRQAAN 119

Query: 146 LQAI--TDNNLKPEQV-VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
           ++    T +N +P    +++A  +++ E + + +  +     SL+A +N+ + N++  +D
Sbjct: 120 MRRDFQTIHNRQPNDTEISLALNISLEEWQEVKLAFQNREPLSLDATVNNDEDNNTCLKD 179


>gi|222529010|ref|YP_002572892.1| FliA/WhiG subfamily RNA polymerase sigma-28 factor
           [Caldicellulosiruptor bescii DSM 6725]
 gi|222455857|gb|ACM60119.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor bescii DSM 6725]
          Length = 310

 Score = 43.5 bits (101), Expect = 0.037,   Method: Compositional matrix adjust.
 Identities = 22/66 (33%), Positives = 40/66 (60%), Gaps = 5/66 (7%)

Query: 53  LVTSHLRLVVKIAMGY----RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           L+  +L+LV  +A  +    +GY   + ++VSEG IGL+ A K +DP +G   +TY+   
Sbjct: 17  LIVDNLKLVYHVANKFMPCPKGYYYEVDDLVSEGYIGLVVAAKNYDPAKG-SFSTYACKV 75

Query: 109 IKAAMQ 114
           I++ ++
Sbjct: 76  IESKIK 81


>gi|225574955|ref|ZP_03783565.1| hypothetical protein RUMHYD_03034 [Blautia hydrogenotrophica DSM
           10507]
 gi|225037802|gb|EEG48048.1| hypothetical protein RUMHYD_03034 [Blautia hydrogenotrophica DSM
           10507]
          Length = 259

 Score = 43.5 bits (101), Expect = 0.038,   Method: Compositional matrix adjust.
 Identities = 60/263 (22%), Positives = 112/263 (42%), Gaps = 35/263 (13%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L  +E+  L +R ++ GD  A    +  +LRLV+ +   +        ++   G I
Sbjct: 15  KLPILSNEEKEELFRRIKQ-GDQQAREEYIKGNLRLVLSVIKRFSNSNENADDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ---KRLFFNLRR 141
           GL++A+  FD     + +TY++  I   ++ Y LR  + +++  +      K ++   R 
Sbjct: 74  GLIKAIDNFDTTLDVKFSTYAVPMIIGEIRRY-LRDNNSIRVSRSLRDIAYKAIYAKERI 132

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL------AGDESLNALINSSDK 195
           +K  L+  T   +  E  + I K++ V   + I     L       G ++L  +   SDK
Sbjct: 133 VKEELKEPTIEEISKE--IGIEKEMIVYALDAIQNPVSLFEPVYTEGGDALYVMDQISDK 190

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
            +                    KEE       L  +M  L  RE+ I +  R  E    +
Sbjct: 191 KN--------------------KEEHWVEELSLREAMDRLGEREKHIIDL-RFYEGKTQM 229

Query: 256 ENLSSEFEVSRERVRQIEARAFK 278
           E ++ E  +S+ +V ++E  A K
Sbjct: 230 E-VAREIGISQAQVSRLEKNALK 251


>gi|169351116|ref|ZP_02868054.1| hypothetical protein CLOSPI_01895 [Clostridium spiroforme DSM 1552]
 gi|169292178|gb|EDS74311.1| hypothetical protein CLOSPI_01895 [Clostridium spiroforme DSM 1552]
          Length = 239

 Score = 43.5 bits (101), Expect = 0.038,   Method: Compositional matrix adjust.
 Identities = 37/130 (28%), Positives = 60/130 (46%), Gaps = 6/130 (4%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A   +V  +L LV  I   ++       ++   G IGLM+A+  FD   G + +TY
Sbjct: 16  GDEIAKELVVNQNLGLVWSIVHRFKNNYYDKEDLFQIGCIGLMKAINNFDTNYGVQFSTY 75

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           ++  I   ++ Y  R    +K+  +   K L   + ++K  L  I      P  V AIAK
Sbjct: 76  AVPIIMGEIKRY-FRDDGTIKVSRSL--KELNLKINKVKELL--INQTGQDP-TVEAIAK 129

Query: 165 KLNVSESEVI 174
            LN+   +V+
Sbjct: 130 YLNIDVQDVV 139


>gi|75909293|ref|YP_323589.1| RNA polymerase sigma factor SigF [Anabaena variabilis ATCC 29413]
 gi|75703018|gb|ABA22694.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Anabaena
           variabilis ATCC 29413]
          Length = 261

 Score = 43.5 bits (101), Expect = 0.038,   Method: Compositional matrix adjust.
 Identities = 23/91 (25%), Positives = 50/91 (54%), Gaps = 1/91 (1%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKKFDP 95
           L + Y  +  +   ++LV  H  LV K+A  +      P  ++   G  GL++A+++FDP
Sbjct: 15  LLRSYHHNPSIKLRNKLVQLHTGLVRKMAHKFSHQCNEPYEDLEQIGYFGLIRAIERFDP 74

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            +G+  +++++ +I+  M  ++    +L+KI
Sbjct: 75  SQGYAFSSFAVPYIRGEMLHFLRDRSTLLKI 105


>gi|300854227|ref|YP_003779211.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           ljungdahlii DSM 13528]
 gi|300434342|gb|ADK14109.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           ljungdahlii DSM 13528]
          Length = 241

 Score = 43.5 bits (101), Expect = 0.039,   Method: Compositional matrix adjust.
 Identities = 28/83 (33%), Positives = 45/83 (54%), Gaps = 5/83 (6%)

Query: 47  LSAAHRLVTSHLRLVVKIA----MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           L     LV  +L LV  IA    +G   Y +   ++VS G +GL+ A+ KFD +RG + +
Sbjct: 7   LDIKEELVKKYLPLVKYIASRVIIGKTKY-IEYEDLVSYGMLGLIDAINKFDKDRGMKFS 65

Query: 103 TYSMWWIKAAMQEYILRSWSLVK 125
           TY+   IK +M + + R+  + K
Sbjct: 66  TYASIRIKGSMIDELRRNSPISK 88


>gi|146295621|ref|YP_001179392.1| FliA/WhiG family RNA polymerase sigma factor [Caldicellulosiruptor
           saccharolyticus DSM 8903]
 gi|145409197|gb|ABP66201.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Caldicellulosiruptor saccharolyticus DSM 8903]
          Length = 310

 Score = 43.5 bits (101), Expect = 0.040,   Method: Compositional matrix adjust.
 Identities = 22/66 (33%), Positives = 40/66 (60%), Gaps = 5/66 (7%)

Query: 53  LVTSHLRLVVKIAMGY----RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           L+  +L+LV  +A  +    +GY   + ++VSEG IGL+ A K +DP +G   +TY+   
Sbjct: 17  LIVDNLKLVYHVANKFMPCPKGYYYEVEDLVSEGYIGLVVAAKNYDPTKG-SFSTYACKV 75

Query: 109 IKAAMQ 114
           I++ ++
Sbjct: 76  IESKIK 81


>gi|256390724|ref|YP_003112288.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Catenulispora
           acidiphila DSM 44928]
 gi|256356950|gb|ACU70447.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Catenulispora
           acidiphila DSM 44928]
          Length = 411

 Score = 43.5 bits (101), Expect = 0.040,   Method: Compositional matrix adjust.
 Identities = 26/82 (31%), Positives = 43/82 (52%), Gaps = 5/82 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVK 91
           +L   ++  GDL    RL+  H   +VK   G    GLP     ++ VS G  GL+ A++
Sbjct: 165 ILWDDFKRTGDLGLRERLIL-HYSPLVKYVAGRVRVGLPGALDSADFVSSGIFGLIDAIE 223

Query: 92  KFDPERGFRLATYSMWWIKAAM 113
           +F+P R  +  TY++  I+ A+
Sbjct: 224 RFEPHRHVKFETYAIARIRGAI 245


>gi|163815157|ref|ZP_02206538.1| hypothetical protein COPEUT_01315 [Coprococcus eutactus ATCC 27759]
 gi|158449566|gb|EDP26561.1| hypothetical protein COPEUT_01315 [Coprococcus eutactus ATCC 27759]
          Length = 260

 Score = 43.5 bits (101), Expect = 0.040,   Method: Compositional matrix adjust.
 Identities = 26/93 (27%), Positives = 45/93 (48%), Gaps = 1/93 (1%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P L + E+  L  R  E GD SA    +  +LRLV+ +   +        ++   G I
Sbjct: 15  KLPYLTEDEKNKLFDRM-EQGDESARDEFIEGNLRLVLSVIQRFGSSNENPDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           GL++A+  FD     + +TY++  I    + Y+
Sbjct: 74  GLIKALDNFDRSLNVKFSTYAVPMIIGECRRYL 106


>gi|257065529|ref|YP_003151785.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Anaerococcus
           prevotii DSM 20548]
 gi|256797409|gb|ACV28064.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Anaerococcus
           prevotii DSM 20548]
          Length = 255

 Score = 43.5 bits (101), Expect = 0.041,   Method: Compositional matrix adjust.
 Identities = 18/77 (23%), Positives = 41/77 (53%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y +  DL     L+  H+ +V  ++  Y G G+   ++    ++GL+ AV+++DP +G+ 
Sbjct: 20  YYQTRDLKLRDELIKEHMYIVDILSNKYVGKGIEKDDLYQVASLGLIYAVERYDPTKGYA 79

Query: 101 LATYSMWWIKAAMQEYI 117
            ++++   I   ++ Y 
Sbjct: 80  FSSFATPTIMGELKRYF 96


>gi|256832234|ref|YP_003160961.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Jonesia denitrificans
           DSM 20603]
 gi|256685765|gb|ACV08658.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Jonesia denitrificans
           DSM 20603]
          Length = 283

 Score = 43.5 bits (101), Expect = 0.041,   Method: Compositional matrix adjust.
 Identities = 57/243 (23%), Positives = 107/243 (44%), Gaps = 29/243 (11%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           L+  +  LV  IA G  G  LP     +++VS G  GL+ A+ KFDP R  +  TY+   
Sbjct: 52  LILHYAPLVTMIA-GRVGMKLPNTVEAADLVSYGMFGLIDAIDKFDPSRDIKFETYASTR 110

Query: 109 IKAA-MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA-IAKKL 166
           ++ A + E     W    + + A +        R   HL+    N L  E     IA+ L
Sbjct: 111 VRGAIIDELRALDWIPRSVRSRARE------YDRACEHLE----NTLHREPTSGEIAQHL 160

Query: 167 NVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---R 221
            V E +V  +  +++     +L+ ++++ D+      D +      QE + ++  +   +
Sbjct: 161 GVPEKDVWQLQWQVSSGHVIALDEVVSTGDR-----VDQISAMDSVQETLAVDPAQSFAQ 215

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              R +L +++  LN RER +      +   +TL  +     V+  RV Q+ +    K++
Sbjct: 216 GEMREILAQAVDHLNERERAVVTLYYFRS--MTLSEIGKLLGVTESRVSQMHSAIIVKLR 273

Query: 282 ESI 284
           + +
Sbjct: 274 KQL 276


>gi|331082586|ref|ZP_08331709.1| RNA polymerase sigma-G factor [Lachnospiraceae bacterium 6_1_63FAA]
 gi|330400205|gb|EGG79847.1| RNA polymerase sigma-G factor [Lachnospiraceae bacterium 6_1_63FAA]
          Length = 259

 Score = 43.5 bits (101), Expect = 0.042,   Method: Compositional matrix adjust.
 Identities = 55/264 (20%), Positives = 120/264 (45%), Gaps = 37/264 (14%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           ++P+L  +E+  L  R +E GD  A  + +  +LRLV+ +   +        ++   G +
Sbjct: 15  RLPILTNEEKDALFVRIKE-GDPEAREQYIKGNLRLVLSVIKRFSSSNENADDLFQIGCV 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ---KRLFFNLRR 141
           GL++A+  FD     + +TY++  I   ++ Y LR  + +++  +      K ++     
Sbjct: 74  GLIKAIDNFDTTLNVKFSTYAVPMIIGEIRRY-LRDNNAIRVSRSLRDVAYKAIYAKENY 132

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           +K         NLK   +  IA+++ + + E++          +L+A+        S ++
Sbjct: 133 VK--------QNLKEPTINEIAEEIGIDKEEIVY---------ALDAI----QSPVSLYE 171

Query: 202 DWLVYDHDGQEQVLIEK-EERKNRRN------MLTRSMSVLNPRERRIFEARRLQENPVT 254
              VY   G    ++++  ++KN+ +       L  ++  L+ RE+ I    R  E    
Sbjct: 172 P--VYTEGGDTLYVMDQISDKKNKEDNWIENIALKEALKKLDDREQHIV-TMRFYEGKTQ 228

Query: 255 LENLSSEFEVSRERVRQIEARAFK 278
           +E ++ E  +S+ +V ++E  A K
Sbjct: 229 ME-VAEEIGISQAQVSRLEKHALK 251


>gi|291544496|emb|CBL17605.1| RNA polymerase sigma factor, sigma-70 family [Ruminococcus sp.
           18P13]
          Length = 204

 Score = 43.5 bits (101), Expect = 0.042,   Method: Compositional matrix adjust.
 Identities = 28/102 (27%), Positives = 50/102 (49%), Gaps = 10/102 (9%)

Query: 29  LEKQEEYVLAKRYREHGD----LSAAH------RLVTSHLRLVVKIAMGYRGYGLPISEV 78
           +E++ E  L KR  E  D    LSAA        L++ +++L+   A       +   ++
Sbjct: 1   MEQKREQDLGKRQTERSDEELALSAAKCSDSTAELISRYMKLIWVKANTMANAVVDAEDL 60

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
             EG +GLM A+  FDP R  + +T++   I   M+  ++R+
Sbjct: 61  AQEGMLGLMNAIAHFDPNREIKFSTFADVCITNKMKSALIRT 102


>gi|320012478|gb|ADW07328.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 290

 Score = 43.5 bits (101), Expect = 0.042,   Method: Compositional matrix adjust.
 Identities = 54/234 (23%), Positives = 103/234 (44%), Gaps = 20/234 (8%)

Query: 61  VVKIAMGY---RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           +V+ A G    RG G  + ++V  G IGL++A+ +FD  R     ++++ +I   ++ + 
Sbjct: 69  LVRFAAGRFRNRGSG-DMEDIVQVGTIGLIKAIDRFDLAREVEFTSFAVPYIVGEIKRFF 127

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV---- 173
             +   V +     + R+  +L + K  L    D +     V  +A  L++ E E+    
Sbjct: 128 RDTTWAVHVPRRLQELRV--DLAKAKEALAVELDRD---PTVQELAGYLDLEEEEITEGL 182

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
           ++ N   AG  SL    ++ D            D  G+    +E  E     + L   + 
Sbjct: 183 VAANGYTAG--SLEMPADAGDHAGRTTAGRTYADVLGEPDPAMETVENL---HALAPLLG 237

Query: 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            L+ RERRI + R  QE  +T   +  E  +S+  V ++ +R  +K+ + +  Q
Sbjct: 238 ELDARERRIIDMRFGQE--MTQAQIGDELGISQMHVSRLLSRILRKLHDGMLAQ 289


>gi|317970333|ref|ZP_07971723.1| RNA polymerase sigma factor, sigma-70 family protein [Synechococcus
           sp. CB0205]
          Length = 202

 Score = 43.5 bits (101), Expect = 0.042,   Method: Compositional matrix adjust.
 Identities = 31/122 (25%), Positives = 56/122 (45%), Gaps = 9/122 (7%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           +R++  +     + L+R I   ++ P    Q    + KR      L A  +LV  +L LV
Sbjct: 12  SRRHAPLPERTVLELARTIQRWQQHPAGPTQAPRAIQKR-----GLRARDQLVRHNLALV 66

Query: 62  V----KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
                K   G        ++ + E  + L++A +KFDP R +R +TY+ +WI+  +  + 
Sbjct: 67  GFTWRKQHSGLSPEDAATADALQEAALNLLRAAEKFDPTRSYRFSTYASFWIRRGLLRFC 126

Query: 118 LR 119
            R
Sbjct: 127 QR 128


>gi|330984057|gb|EGH82160.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. lachrymans
           str. M301315]
          Length = 227

 Score = 43.5 bits (101), Expect = 0.042,   Method: Compositional matrix adjust.
 Identities = 27/70 (38%), Positives = 41/70 (58%), Gaps = 6/70 (8%)

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + L   ++ L  RE+ I  AR LQ+   TL +L+++F VS ERVRQ+E+ A KK++    
Sbjct: 161 STLEEGIANLPEREKLIVLARHLQDPRATLADLATKFGVSIERVRQLESSAIKKLRN--- 217

Query: 286 KQVELSSSPP 295
               L+  PP
Sbjct: 218 ---HLAEHPP 224


>gi|317060933|ref|ZP_07925418.1| predicted protein [Fusobacterium sp. D12]
 gi|313686609|gb|EFS23444.1| predicted protein [Fusobacterium sp. D12]
          Length = 149

 Score = 43.5 bits (101), Expect = 0.042,   Method: Compositional matrix adjust.
 Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 4/72 (5%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD+ A + L+  ++ LV KI    R YG    +   EG +    A+ KFD  +  +L++Y
Sbjct: 2   GDIEARNELIEKNINLVHKIN---RMYGSS-EDGFQEGILAFCHAIDKFDETKNVKLSSY 57

Query: 105 SMWWIKAAMQEY 116
           +  WI+  ++ Y
Sbjct: 58  AFHWIRQKIKRY 69


>gi|317055657|ref|YP_004104124.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit [Ruminococcus
           albus 7]
 gi|315447926|gb|ADU21490.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Ruminococcus
           albus 7]
          Length = 218

 Score = 43.5 bits (101), Expect = 0.042,   Method: Compositional matrix adjust.
 Identities = 46/193 (23%), Positives = 81/193 (41%), Gaps = 26/193 (13%)

Query: 57  HLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           +L LV   A  +RG G+   ++   G +GL++A + FD  RG + +TY++  I   ++  
Sbjct: 12  NLGLVHLCANRFRGRGIEYDDLYGAGCMGLVKASRAFDASRGVKFSTYAVPVILGEIKR- 70

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
           + R    VK+  + + K L   + R     Q     N +   V  ++        +VI  
Sbjct: 71  LFRDGGTVKV--SRSLKELSLKITRAS---QTFAHKNGREPTVSELSDITGADPDDVI-- 123

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE---ERKNRRNMLTRSMS 233
                  E+LNA        S       + D DG+ Q  +  E   E    R  L + +S
Sbjct: 124 -------EALNA--------SQPTVSLTIGDEDGESQTDLPTEPPDEDITDRLALRQVLS 168

Query: 234 VLNPRERRIFEAR 246
            L+  +R++ + R
Sbjct: 169 ELSADDRKLIDLR 181


>gi|260589168|ref|ZP_05855081.1| RNA polymerase sigma-G factor [Blautia hansenii DSM 20583]
 gi|260540249|gb|EEX20818.1| RNA polymerase sigma-G factor [Blautia hansenii DSM 20583]
          Length = 266

 Score = 43.5 bits (101), Expect = 0.043,   Method: Compositional matrix adjust.
 Identities = 55/264 (20%), Positives = 120/264 (45%), Gaps = 37/264 (14%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           ++P+L  +E+  L  R +E GD  A  + +  +LRLV+ +   +        ++   G +
Sbjct: 22  RLPILTNEEKDALFVRIKE-GDPEAREQYIKGNLRLVLSVIKRFSSSNENADDLFQIGCV 80

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ---KRLFFNLRR 141
           GL++A+  FD     + +TY++  I   ++ Y LR  + +++  +      K ++     
Sbjct: 81  GLIKAIDNFDTTLNVKFSTYAVPMIIGEIRRY-LRDNNAIRVSRSLRDVAYKAIYAKENY 139

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           +K         NLK   +  IA+++ + + E++          +L+A+        S ++
Sbjct: 140 VK--------QNLKEPTINEIAEEIGIDKEEIVY---------ALDAI----QSPVSLYE 178

Query: 202 DWLVYDHDGQEQVLIEK-EERKNRRN------MLTRSMSVLNPRERRIFEARRLQENPVT 254
              VY   G    ++++  ++KN+ +       L  ++  L+ RE+ I    R  E    
Sbjct: 179 P--VYTEGGDTLYVMDQISDKKNKEDNWIENIALKEALKKLDDREQHIV-TMRFYEGKTQ 235

Query: 255 LENLSSEFEVSRERVRQIEARAFK 278
           +E ++ E  +S+ +V ++E  A K
Sbjct: 236 ME-VAEEIGISQAQVSRLEKHALK 258


>gi|222094730|ref|YP_002528790.1| RNA polymerase sigma factor sigb [Bacillus cereus Q1]
 gi|221238788|gb|ACM11498.1| RNA polymerase sigma-B factor [Bacillus cereus Q1]
          Length = 257

 Score = 43.1 bits (100), Expect = 0.044,   Method: Compositional matrix adjust.
 Identities = 54/231 (23%), Positives = 109/231 (47%), Gaps = 27/231 (11%)

Query: 22  EIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           EI+  P  L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++ 
Sbjct: 2   EIQSQPTTLTKEDVMKLIAEFQQNQCDEAQERLVEHYKNLVYSIAYRYSKGGPMHEDIIQ 61

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNL 139
            G +GL+ A++++D   G     +++  I   +++Y+  ++W +       +  R   +L
Sbjct: 62  VGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGI-------HVPRRIKDL 114

Query: 140 -RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNALI-NS 192
             ++K  ++ +TD   +  +++ IA  L +SE EV+ +     N R++   SL+ ++ N+
Sbjct: 115 GGKIKLAIEELTDRLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVS---SLDDVVENA 171

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           SD +S    + +     G E+          RR +L    +VLN  E+ + 
Sbjct: 172 SDGSSVARIESVGEVEQGYEET--------ERRLVLKDIFNVLNDTEKSVI 214


>gi|148359326|ref|YP_001250533.1| flagellar biosynthesis sigma factor FliA [Legionella pneumophila
           str. Corby]
 gi|296107373|ref|YP_003619073.1| RNA polymerase sigma factor for flagellar operon FliA [Legionella
           pneumophila 2300/99 Alcoy]
 gi|148281099|gb|ABQ55187.1| flagellar biosynthesis sigma factor FliA [Legionella pneumophila
           str. Corby]
 gi|295649274|gb|ADG25121.1| RNA polymerase sigma factor for flagellar operon FliA [Legionella
           pneumophila 2300/99 Alcoy]
          Length = 238

 Score = 43.1 bits (100), Expect = 0.044,   Method: Compositional matrix adjust.
 Identities = 52/236 (22%), Positives = 108/236 (45%), Gaps = 27/236 (11%)

Query: 53  LVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           LV +H  LV +IA   +G     + + +++  G +GL++A + +D  +G    TY+   I
Sbjct: 18  LVKTHATLVKRIAHHLLGRLPQSVQLDDLIQSGMLGLLEAARHYDSSKGASFETYAGIRI 77

Query: 110 KAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHL-QAITDNNLKPEQVVAIAKKLN 167
           +  M + + R+ W  V      N + +   +R L+  L +   DN +  E  V++    +
Sbjct: 78  RGHMLDEVRRNDW--VPRSVYRNSRMISDAVRILEHKLGREAKDNEIAEELGVSLNDYHD 135

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + +    S++  L G + L               D +++D +G      E      R +M
Sbjct: 136 MLQD---SISSHLYGFDDLGV------------TDDILFDDEGNGST--EPHRNVMRSDM 178

Query: 228 LTRSMSVLN--PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           + R   V++  PR+ R+  +   +++ + L+ +    EVS  R+ QI ++A  +++
Sbjct: 179 MNRLTQVIDSLPRKERLVLSLYYEQD-LNLKEIGEILEVSESRISQILSQATHRIR 233


>gi|133478|sp|P12254|RPSK_BACSU RecName: Full=RNA polymerase sigma-K factor; AltName:
           Full=Sigma-27; AltName: Full=Stage IV sporulation
           protein CB; Flags: Precursor
          Length = 294

 Score = 43.1 bits (100), Expect = 0.044,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 3/75 (4%)

Query: 39  KRYRE---HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           K+Y E    GD  A + L+  +LRLV  I   +   G    +++S G IGL++ ++ +  
Sbjct: 38  KKYLELMAKGDEHARNMLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKGIESYSA 97

Query: 96  ERGFRLATYSMWWIK 110
            +G +LATY+   I+
Sbjct: 98  GKGTKLATYAARCIE 112


>gi|217958581|ref|YP_002337129.1| RNA polymerase sigma factor SigB [Bacillus cereus AH187]
 gi|217065197|gb|ACJ79447.1| RNA polymerase sigma-B factor [Bacillus cereus AH187]
          Length = 257

 Score = 43.1 bits (100), Expect = 0.044,   Method: Compositional matrix adjust.
 Identities = 53/231 (22%), Positives = 109/231 (47%), Gaps = 27/231 (11%)

Query: 22  EIRKIPMLEKQEEYV-LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           EI+  P    +E+ + L   ++++    A  RLV  +  LV  IA  Y   G    +++ 
Sbjct: 2   EIQSQPTTLTKEDVIKLIAEFQQNQCDEAQERLVEHYKNLVYSIAYRYSKGGPMHEDIIQ 61

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNL 139
            G +GL+ A++++D   G     +++  I   +++Y+  ++W +       +  R   +L
Sbjct: 62  VGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGI-------HVPRRIKDL 114

Query: 140 -RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNALI-NS 192
             ++K  ++ +TD   +  +++ IA  L +SE EV+ +     N R++   SL+ ++ N+
Sbjct: 115 GGKIKLAIEELTDRLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVS---SLDDVVENA 171

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           SD +S    + +     G E+          RR +L    +VLN  E+ + 
Sbjct: 172 SDGSSVARIESVGEVEQGYEET--------ERRLVLKDIFNVLNDTEKSVI 214


>gi|312622956|ref|YP_004024569.1| RNA polymerase, sigma 28 subunit, sigk [Caldicellulosiruptor
           kronotskyensis 2002]
 gi|312203423|gb|ADQ46750.1| RNA polymerase, sigma 28 subunit, SigK [Caldicellulosiruptor
           kronotskyensis 2002]
          Length = 219

 Score = 43.1 bits (100), Expect = 0.045,   Method: Compositional matrix adjust.
 Identities = 28/93 (30%), Positives = 50/93 (53%), Gaps = 5/93 (5%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP--ISEVVSEGNI 84
           PM  ++EE  L K +   G   A + L+  +LRLV  IA  Y  +  P    +++S G I
Sbjct: 13  PMSPEEEEMYLNKMW--EGCKEARNILIEKNLRLVAHIAKKYT-FSFPNLTDDIISVGTI 69

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           GL++A++ +   +  +L+TY+   I+  +  Y+
Sbjct: 70  GLIKAIETYSSAKCTKLSTYAAKCIENEILMYL 102


>gi|305644356|gb|ADM53779.1| RNA polymerase sigma factor [Aeromonas hydrophila]
          Length = 176

 Score = 43.1 bits (100), Expect = 0.045,   Method: Compositional matrix adjust.
 Identities = 17/42 (40%), Positives = 27/42 (64%)

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           GLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I
Sbjct: 1   GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI 42


>gi|114320145|ref|YP_741828.1| RNA polymerase, sigma 28 subunit [Alkalilimnicola ehrlichii MLHE-1]
 gi|114226539|gb|ABI56338.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Alkalilimnicola
           ehrlichii MLHE-1]
          Length = 242

 Score = 43.1 bits (100), Expect = 0.046,   Method: Compositional matrix adjust.
 Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 4/74 (5%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           L+  H  LV +IA    G   P   + +++  G +GL++A ++FDP +G    TY+   I
Sbjct: 18  LLVQHASLVKRIAHHLAGRLPPSVQLDDLIQAGMVGLLEAARQFDPGQGASFQTYAGIRI 77

Query: 110 KAAMQEYILR-SWS 122
           + AM + I R  W+
Sbjct: 78  RGAMLDEIRRLDWT 91


>gi|186681796|ref|YP_001864992.1| RNA polymerase sigma factor SigF [Nostoc punctiforme PCC 73102]
 gi|186464248|gb|ACC80049.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Nostoc
           punctiforme PCC 73102]
          Length = 261

 Score = 43.1 bits (100), Expect = 0.047,   Method: Compositional matrix adjust.
 Identities = 22/87 (25%), Positives = 49/87 (56%), Gaps = 1/87 (1%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           Y ++  +   ++LV  H  LV K+A  +      P  ++   G  GL++A+++FDP +G+
Sbjct: 19  YHQNPSIKLRNKLVQLHTGLVRKMAHKFSHQCNEPYEDLEQIGYFGLIRAIERFDPSQGY 78

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKI 126
             +++++ +I+  M  ++    +L+KI
Sbjct: 79  AFSSFAVPYIRGEMLHFLRDRSTLLKI 105


>gi|257463359|ref|ZP_05627755.1| RNA polymerase sigma factor RpoS [Fusobacterium sp. D12]
          Length = 155

 Score = 43.1 bits (100), Expect = 0.048,   Method: Compositional matrix adjust.
 Identities = 22/72 (30%), Positives = 38/72 (52%), Gaps = 4/72 (5%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD+ A + L+  ++ LV KI    R YG    +   EG +    A+ KFD  +  +L++Y
Sbjct: 8   GDIEARNELIEKNINLVHKIN---RMYGSS-EDGFQEGILAFCHAIDKFDETKNVKLSSY 63

Query: 105 SMWWIKAAMQEY 116
           +  WI+  ++ Y
Sbjct: 64  AFHWIRQKIKRY 75


>gi|167745425|ref|ZP_02417552.1| hypothetical protein ANACAC_00116 [Anaerostipes caccae DSM 14662]
 gi|317473026|ref|ZP_07932327.1| RNA polymerase sigma-70 factor [Anaerostipes sp. 3_2_56FAA]
 gi|167655146|gb|EDR99275.1| hypothetical protein ANACAC_00116 [Anaerostipes caccae DSM 14662]
 gi|316899509|gb|EFV21522.1| RNA polymerase sigma-70 factor [Anaerostipes sp. 3_2_56FAA]
          Length = 241

 Score = 43.1 bits (100), Expect = 0.048,   Method: Compositional matrix adjust.
 Identities = 22/82 (26%), Positives = 44/82 (53%), Gaps = 1/82 (1%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A  ++V  ++ L+  +   + G G    ++   G+IGL++AV KFD     + +TY
Sbjct: 14  GDQDAREKIVLDNMGLIWSVVKRFTGRGHEPEDLFQIGSIGLLKAVDKFDLSYDVKFSTY 73

Query: 105 SMWWIKAAMQEYILRSWSLVKI 126
           ++  I   ++ + LR   ++K+
Sbjct: 74  AVPMITGEIKRF-LRDDGMIKV 94


>gi|302556969|ref|ZP_07309311.1| RNA polymerase sigma factor [Streptomyces griseoflavus Tu4000]
 gi|302474587|gb|EFL37680.1| RNA polymerase sigma factor [Streptomyces griseoflavus Tu4000]
          Length = 295

 Score = 43.1 bits (100), Expect = 0.048,   Method: Compositional matrix adjust.
 Identities = 44/196 (22%), Positives = 92/196 (46%), Gaps = 20/196 (10%)

Query: 61  VVKIAMG-YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           +V+ A G +RG G  + +VV  G IGL++A+ +F+  R     ++++ +I   ++ +   
Sbjct: 75  LVRFAAGRFRGRGDDMDDVVQTGMIGLIKAIDRFELAREVEFTSFALPYIVGEIKRFFRD 134

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
           +   V +     + R+   L + +  L +  D   +   V  +A  +N++E +V+     
Sbjct: 135 TTWAVHVPRRLQELRV--ELAKAREELASRLD---REPTVAELATLMNITEQQVVEGQIA 189

Query: 180 LAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSV 234
             G    SL+A +     +  ++ + ++ D  G E+    L+E        + L   M+ 
Sbjct: 190 ANGYNSSSLDAALTG---DGPEYGEAVLADFIGVEEEGLRLVED------FHSLAPLMAE 240

Query: 235 LNPRERRIFEARRLQE 250
           L+PR+R I   R ++E
Sbjct: 241 LSPRDREILHLRFVEE 256


>gi|255526140|ref|ZP_05393061.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium carboxidivorans
           P7]
 gi|296187150|ref|ZP_06855547.1| RNA polymerase sigma-F factor [Clostridium carboxidivorans P7]
 gi|255510189|gb|EET86508.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium carboxidivorans
           P7]
 gi|296048185|gb|EFG87622.1| RNA polymerase sigma-F factor [Clostridium carboxidivorans P7]
          Length = 251

 Score = 43.1 bits (100), Expect = 0.049,   Method: Compositional matrix adjust.
 Identities = 54/253 (21%), Positives = 116/253 (45%), Gaps = 32/253 (12%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           +Y  +G+  A ++L+  +L LV  I+  +   G    ++   G +GL++AV  FD +   
Sbjct: 21  KYARNGNKDALNKLIEVNLPLVSAISKKFLNRGYEYEDIFQIGCMGLVKAVNNFDEKYNV 80

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY++  I   ++ +I R   ++K+  +          ++L    +A+T         
Sbjct: 81  KFSTYAVPMILGEIKRFI-RDDGMIKVSRSVKN-----TAKKLHYAKEALTKQ------- 127

Query: 160 VAIAKKLNVSE-SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
             I+++  + E SE   +     G E +   + SS  NS Q+    ++  DG   +LI+K
Sbjct: 128 --ISREPTIEELSEYSGI-----GVEDIIFAMESS--NSLQYLYDTIHQDDGAPVLLIDK 178

Query: 219 EERKNRRN-------MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
               + R+        L  ++  L+ + R+I   R  ++   T   ++    +S+ +V +
Sbjct: 179 LSESSDRDSEIVDRIALKEALKNLDVKSRQIIMLRYFKDK--TQIQVAKMLGISQVQVSR 236

Query: 272 IEARAFKKVQESI 284
           IE +  K ++E++
Sbjct: 237 IEKKVLKVMRENL 249


>gi|238927435|ref|ZP_04659195.1| DNA-directed RNA polymerase sigma subunit D [Selenomonas flueggei
           ATCC 43531]
 gi|238884717|gb|EEQ48355.1| DNA-directed RNA polymerase sigma subunit D [Selenomonas flueggei
           ATCC 43531]
          Length = 252

 Score = 43.1 bits (100), Expect = 0.049,   Method: Compositional matrix adjust.
 Identities = 61/267 (22%), Positives = 123/267 (46%), Gaps = 31/267 (11%)

Query: 28  MLEKQEEY---VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVS 80
           M E+ EE     L + Y     ++  +R+   +L LV ++  G     LP      +++S
Sbjct: 4   MAEQTEEENIEALWQEYEREKTVAVRNRIAEYYLPLV-RLVAGRIAISLPQHVDREDLLS 62

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
            G  GL+ A+++++  RG +  TY+   ++ AM ++ LR+   V +    N K+    + 
Sbjct: 63  SGFFGLLDAIERYELARGNKFETYAGVRVRGAMLDH-LRAKDWVPVSVRQNIKKYEKTVA 121

Query: 141 RLKGHL-QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
           +L+G L +A TD  L  E  ++I ++L+  ES+V S    +  +E L A   +S ++   
Sbjct: 122 QLEGELGRAATDKELAEELNLSI-EELHHLESQV-SAATVIPLEEYLRADTQASLEDGP- 178

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
                           +E  E    +  L  ++  L  +ER +       E  +TL+ ++
Sbjct: 179 ----------------VEHAEWTEVKETLAAAIEKLPEKERTVIALYYYDE--MTLKEIA 220

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQK 286
           +   +S  R+ Q+  +A  +++ S+ +
Sbjct: 221 AILHLSEARISQLHTKAIFRMRGSLAR 247


>gi|188025882|ref|ZP_02960155.2| hypothetical protein PROSTU_02069 [Providencia stuartii ATCC 25827]
 gi|188020848|gb|EDU58888.1| hypothetical protein PROSTU_02069 [Providencia stuartii ATCC 25827]
          Length = 246

 Score = 43.1 bits (100), Expect = 0.050,   Method: Compositional matrix adjust.
 Identities = 47/225 (20%), Positives = 101/225 (44%), Gaps = 34/225 (15%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTANQK 133
           I +++  G IGL+ A+++FD  +G   ATY++  I+ +M  E   R W+   +      +
Sbjct: 45  IDDLIQAGGIGLLHALERFDASQGASFATYAVQRIRGSMLDELRSRDWAPRSV------R 98

Query: 134 RLFFNLRRLKGHL-QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
           R    + ++ G L Q+++ +  + E    IA+ LN+  +E               AL+++
Sbjct: 99  RQAREMAKVIGELEQSLSRSATESE----IAQALNIDVTEY------------RQALLDT 142

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEE--------RKNRRNMLTRSMSVLNPRERRIFE 244
           ++     + +W     +  E  + E +           N R  +  ++  L  RE+ +  
Sbjct: 143 NNSQLYSYDEWHEIHGESCEPAIDESDGGNPLSLLMESNLRAQIIEAIEQLPEREKLVLT 202

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
               +E  + L+ + +  EV   RV Q+ ++A K+++  ++   E
Sbjct: 203 LYYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRLRGRLKSLTE 245


>gi|17226799|gb|AAL37943.1|AF359562_4 SigB [Staphylococcus epidermidis]
          Length = 256

 Score = 43.1 bits (100), Expect = 0.051,   Method: Compositional matrix adjust.
 Identities = 53/247 (21%), Positives = 117/247 (47%), Gaps = 16/247 (6%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           K+++E+ D  A  +LV  + +L+  +A  Y        ++V  G +GL+ A+ +FD    
Sbjct: 21  KQHQENEDSQAQDKLVKHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDLSFD 80

Query: 99  FRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
            +   + +  +   ++ Y+  ++WS+         +R+     R+K     +T+   +  
Sbjct: 81  RKFEAFLVPTVIGEIKRYLRDKTWSV------HVPRRIKEIGPRIKKVSDELTNELERSP 134

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQVLI 216
            +  IA++L VS+ EV+     +   +S NAL ++ S +         + D  GQ+    
Sbjct: 135 SISEIAQRLEVSDEEVLEA---MEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQQD--- 188

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           +  +   +R +L R + +L+ RER+I +   ++   ++ +       +S+  V +++  A
Sbjct: 189 DNYDLTEKRMILERILPILSERERQIIQCTFIE--GLSQKETGERIGLSQMHVSRLQRTA 246

Query: 277 FKKVQES 283
            KK+QE+
Sbjct: 247 IKKLQEA 253


>gi|253998499|ref|YP_003050562.1| flagellar biosynthesis sigma factor [Methylovorus sp. SIP3-4]
 gi|313200585|ref|YP_004039243.1| RNA polymerase sigma-28 subunit FliA/WhiG [Methylovorus sp. MP688]
 gi|253985178|gb|ACT50035.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Methylovorus sp.
           SIP3-4]
 gi|312439901|gb|ADQ84007.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Methylovorus sp.
           MP688]
          Length = 244

 Score = 43.1 bits (100), Expect = 0.051,   Method: Compositional matrix adjust.
 Identities = 53/251 (21%), Positives = 108/251 (43%), Gaps = 16/251 (6%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPER 97
           Y   G  +    L+  H  LV K+A   +    P   + ++V  G +GL+ A+ +++   
Sbjct: 2   YTATGKPNQKDSLLHQHATLVKKLAYQLKAKLPPSVELDDLVQAGMMGLLDAINRYEDTH 61

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G +  TY+   I+ AM +  LR+   +        + +  N+R ++G +  +     +P 
Sbjct: 62  GAQFETYAAQRIRGAMIDE-LRNADWLP-------RSIRKNMRDVEGAINQLEQVLGRPP 113

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +AK+L +S  +   M    +G + L        +    + D  + D  G     I+
Sbjct: 114 TEGEVAKQLKMSLDDYYDMLGECSGHQLLYYEDFHESEGGDHFLDRFLQDDSGNP---IK 170

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
                N R  L  ++  L  RE+ +      QE  + L+ + +   VS  RV Q+ ++A 
Sbjct: 171 GLLDSNFRETLIEAIENLPEREQILMGLYYEQE--LNLKEIGAVMNVSESRVCQLHSQAI 228

Query: 278 KKVQESIQKQV 288
            +++  +++Q+
Sbjct: 229 ARLRAYMKEQL 239


>gi|329735692|gb|EGG71975.1| RNA polymerase sigma-B factor [Staphylococcus epidermidis VCU028]
          Length = 256

 Score = 43.1 bits (100), Expect = 0.051,   Method: Compositional matrix adjust.
 Identities = 53/247 (21%), Positives = 117/247 (47%), Gaps = 16/247 (6%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           K+++E+ D  A  +LV  + +L+  +A  Y        ++V  G +GL+ A+ +FD    
Sbjct: 21  KQHQENEDSQAQDKLVKHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDLSFD 80

Query: 99  FRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
            +   + +  +   ++ Y+  ++WS+         +R+     R+K     +T+   +  
Sbjct: 81  RKFEAFLVPTVIGEIKRYLRDKTWSV------HVPRRIKEIGPRIKKVSDELTNELERSP 134

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQVLI 216
            +  IA++L VS+ EV+     +   +S NAL ++ S +         + D  GQ+    
Sbjct: 135 SISEIAQRLEVSDEEVLEA---MEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQQD--- 188

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           +  +   +R +L R + +L+ RER+I +   ++   ++ +       +S+  V +++  A
Sbjct: 189 DNYDLTEKRMILERILPILSERERQIIQCTFIE--GLSQKETGERIGLSQMHVSRLQRTA 246

Query: 277 FKKVQES 283
            KK+QE+
Sbjct: 247 IKKLQEA 253


>gi|323698081|ref|ZP_08109993.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio sp.
           ND132]
 gi|323458013|gb|EGB13878.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio
           desulfuricans ND132]
          Length = 261

 Score = 43.1 bits (100), Expect = 0.051,   Method: Compositional matrix adjust.
 Identities = 19/45 (42%), Positives = 31/45 (68%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           ++E++S G++GL+ A+ KF+PE G +  TYS   IK AM + + R
Sbjct: 64  LNELISAGSLGLLDALGKFNPELGIKFDTYSENRIKGAMLDELRR 108


>gi|160936421|ref|ZP_02083790.1| hypothetical protein CLOBOL_01313 [Clostridium bolteae ATCC
          BAA-613]
 gi|158440704|gb|EDP18442.1| hypothetical protein CLOBOL_01313 [Clostridium bolteae ATCC
          BAA-613]
          Length = 199

 Score = 43.1 bits (100), Expect = 0.051,   Method: Compositional matrix adjust.
 Identities = 27/76 (35%), Positives = 39/76 (51%), Gaps = 1/76 (1%)

Query: 19 YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
          Y+ E+R I  LE+ +E V        GD  A  RLV   L  V+++   Y    LP+S++
Sbjct: 10 YLEEMRSITPLER-DEMVSVLEGTARGDAGARSRLVEGCLGEVLEMVREYGDSELPLSDL 68

Query: 79 VSEGNIGLMQAVKKFD 94
          V E N  LM A  ++D
Sbjct: 69 VQEANTALMLAAIEYD 84


>gi|154499842|ref|ZP_02037880.1| hypothetical protein BACCAP_03499 [Bacteroides capillosus ATCC
           29799]
 gi|150271440|gb|EDM98697.1| hypothetical protein BACCAP_03499 [Bacteroides capillosus ATCC
           29799]
          Length = 235

 Score = 43.1 bits (100), Expect = 0.051,   Method: Compositional matrix adjust.
 Identities = 24/83 (28%), Positives = 43/83 (51%), Gaps = 1/83 (1%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GD  A  R++  +  L+  I   Y G G+   ++   G +G ++AV+ FDP  G + +T
Sbjct: 14  QGDNDACARMMEENSGLIWSIVRRYYGRGVDPEDLYQLGCMGFLKAVRGFDPAFGCQFST 73

Query: 104 YSMWWIKAAMQEYILRSWSLVKI 126
           Y++  I   ++ + LR    VK+
Sbjct: 74  YAVPKIAGEIRRF-LRDDGAVKV 95


>gi|296121398|ref|YP_003629176.1| RNA polymerase sigma factor, FliA/WhiG family [Planctomyces
           limnophilus DSM 3776]
 gi|296013738|gb|ADG66977.1| RNA polymerase sigma factor, FliA/WhiG family [Planctomyces
           limnophilus DSM 3776]
          Length = 259

 Score = 43.1 bits (100), Expect = 0.052,   Method: Compositional matrix adjust.
 Identities = 18/42 (42%), Positives = 28/42 (66%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           G+ I++++S G  GLM A++ FD ERG +  TY +  I+ AM
Sbjct: 51  GVDINDLISAGVFGLMDAIEAFDMERGVKFETYCVPRIRGAM 92


>gi|269792915|ref|YP_003317819.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermanaerovibrio
           acidaminovorans DSM 6589]
 gi|269100550|gb|ACZ19537.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermanaerovibrio
           acidaminovorans DSM 6589]
          Length = 245

 Score = 43.1 bits (100), Expect = 0.053,   Method: Compositional matrix adjust.
 Identities = 49/219 (22%), Positives = 98/219 (44%), Gaps = 26/219 (11%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL   +++S G +GL+ A+ +FDP RGF   T+++  I+ A+ + + R   + + G    
Sbjct: 46  GLDYDDILSFGVMGLLDAMDRFDPSRGFCFQTFAVPRIRGAILDELRRYDWISRTGRDKL 105

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES------EVISMNCRLAGDES 185
           Q+               + D+        A+ ++L ++E       E+ S +  ++ DE 
Sbjct: 106 QR--LERAMEEAAAEGTLLDDE-------ALMERLGMNEKSYRELLEIASRSYVVSLDEV 156

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L        ++    +D L+ D     Q   E+ ER+    ++ R++  L  RER +  +
Sbjct: 157 LGL------EDGEVKRDGLLEDPSPSPQ---EEVERREELALVRRALEELPERERLLL-S 206

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              QE  +TL+ + +   V+  R  Q+  RA   ++  +
Sbjct: 207 LYYQEG-LTLKEVGAVLGVTESRASQLHGRAIAMLRSKL 244


>gi|251798285|ref|YP_003013016.1| sporulation sigma factor SigK [Paenibacillus sp. JDR-2]
 gi|247545911|gb|ACT02930.1| RNA polymerase, sigma 28 subunit, SigK [Paenibacillus sp. JDR-2]
          Length = 232

 Score = 43.1 bits (100), Expect = 0.053,   Method: Compositional matrix adjust.
 Identities = 20/66 (30%), Positives = 39/66 (59%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           G+  + + L+  +LRLV  I   +   G  + +++S G IGL++A++ F   +G +LAT+
Sbjct: 45  GNAHSRNLLIEHNLRLVAHIVKKFDNTGEDLEDLISIGTIGLIKAIESFQTGKGTKLATF 104

Query: 105 SMWWIK 110
           +   I+
Sbjct: 105 AARCIE 110


>gi|167462564|ref|ZP_02327653.1| sporulation sigma factor SigF [Paenibacillus larvae subsp. larvae
           BRL-230010]
          Length = 251

 Score = 43.1 bits (100), Expect = 0.053,   Method: Compositional matrix adjust.
 Identities = 55/246 (22%), Positives = 114/246 (46%), Gaps = 22/246 (8%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A   LV  ++RLV  +   +   G    ++   G IGL+++V KF+     + +
Sbjct: 26  QSGDTIARDTLVNCNIRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVDKFNLSYEVKFS 85

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I   +Q + LR    +K+  +   K L   +R+ K  L   + N  +   +  +
Sbjct: 86  TYAVPMIIGEIQRF-LRDDGTLKVSRSL--KELANKVRKTKDEL---SKNLERLPTLKEV 139

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A  L ++  EV+        ++ L+++  +  +N   W    + D     Q+  + +E+ 
Sbjct: 140 ANALGITPEEVVFAQ---EANKPLSSIHETVFEND--WDPITLMD-----QIADDSQEKW 189

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             +  L  ++  L+ RER I   R  ++   T   +++   +S+ +V ++E    KK+ +
Sbjct: 190 FDKLALNEAIEGLSERERLIVYLRYFKDQ--TQSEVANRLGISQVQVSRLE----KKILQ 243

Query: 283 SIQKQV 288
           SI+ Q+
Sbjct: 244 SIRNQI 249


>gi|157826497|ref|YP_001495561.1| RNA polymerase sigma factor RpoD [Rickettsia bellii OSU 85-389]
 gi|157801801|gb|ABV78524.1| RNA polymerase sigma factor RpoD [Rickettsia bellii OSU 85-389]
          Length = 81

 Score = 43.1 bits (100), Expect = 0.053,   Method: Compositional matrix adjust.
 Identities = 22/56 (39%), Positives = 35/56 (62%), Gaps = 2/56 (3%)

Query: 232 MSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           ++ L PRE R+   R         TLE +  +F+V+RER+RQIE++A +K+Q  I+
Sbjct: 2   LATLTPREERVLRMRFGIGMNTDHTLEEVGQQFKVTRERIRQIESKALRKLQHPIR 57


>gi|167755690|ref|ZP_02427817.1| hypothetical protein CLORAM_01205 [Clostridium ramosum DSM 1402]
 gi|237734438|ref|ZP_04564919.1| sporulation sigma factor sigF [Mollicutes bacterium D7]
 gi|167704629|gb|EDS19208.1| hypothetical protein CLORAM_01205 [Clostridium ramosum DSM 1402]
 gi|229382668|gb|EEO32759.1| sporulation sigma factor sigF [Coprobacillus sp. D7]
          Length = 240

 Score = 43.1 bits (100), Expect = 0.055,   Method: Compositional matrix adjust.
 Identities = 34/130 (26%), Positives = 59/130 (45%), Gaps = 6/130 (4%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A   +V+ +L LV  I   ++       ++   G IGLM+AV  FD   G + +TY
Sbjct: 16  GDDRAKELVVSQNLGLVWSIVHRFKNNYYDKEDLFQIGCIGLMKAVNNFDTNYGVQFSTY 75

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           ++  I   ++ Y  R    +K+  +  +  L  N  R     + +T+   +   V  IA 
Sbjct: 76  AVPIIMGEIKRY-FRDDGTIKVSRSLKELNLKINKAR-----ELLTNQTGQDPTVEQIAA 129

Query: 165 KLNVSESEVI 174
            L+V   +V+
Sbjct: 130 YLDVDVQDVV 139


>gi|239933011|ref|ZP_04689964.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291441364|ref|ZP_06580754.1| conserved hypothetical protein [Streptomyces ghanaensis ATCC 14672]
 gi|291344259|gb|EFE71215.1| conserved hypothetical protein [Streptomyces ghanaensis ATCC 14672]
          Length = 287

 Score = 42.7 bits (99), Expect = 0.057,   Method: Compositional matrix adjust.
 Identities = 60/245 (24%), Positives = 107/245 (43%), Gaps = 34/245 (13%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LVT+ L +  +IA  +R  G  I ++     +GL++A+ +FDP RG    +Y++  I   
Sbjct: 53  LVTAWLPMAHRIAGRFRDRGESIEDLRQVAALGLVKAIDRFDPGRGA-FESYAVPTITGE 111

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLR-RLKGHLQAITDNNLKPEQVVA-IAKKLNVS 169
           ++ +   R W+L          R    LR +++   + +T N   PE  VA IA    ++
Sbjct: 112 VKRHFRDRMWAL-------RVPRRVQELRNKVRVARRELTQNPGSPEPSVADIAAHTGLT 164

Query: 170 ESEVISMNCRLAGDESLNALIN-------SSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           E EV       AG E+L +          S+D +     D L    D    ++I++E  K
Sbjct: 165 EEEVG------AGMEALESFSTLSLDAELSADDDGYSLADTLGA-SDASYDIVIDRESAK 217

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
                    +  L  RER I   R  ++  +T   ++    +S+  V ++ +R+  +V+ 
Sbjct: 218 E-------GLRRLPERERAILYMRFFED--MTQSRIADRLGISQMHVSRLISRSCARVRA 268

Query: 283 SIQKQ 287
               Q
Sbjct: 269 EAMGQ 273


>gi|115377816|ref|ZP_01465004.1| RNA polymerase sigma factor for flagellar operon [Stigmatella
           aurantiaca DW4/3-1]
 gi|310820297|ref|YP_003952655.1| RNA polymerase sigma-70 factor [Stigmatella aurantiaca DW4/3-1]
 gi|115365148|gb|EAU64195.1| RNA polymerase sigma factor for flagellar operon [Stigmatella
           aurantiaca DW4/3-1]
 gi|309393369|gb|ADO70828.1| RNA polymerase sigma-70 factor [Stigmatella aurantiaca DW4/3-1]
          Length = 260

 Score = 42.7 bits (99), Expect = 0.057,   Method: Compositional matrix adjust.
 Identities = 59/228 (25%), Positives = 105/228 (46%), Gaps = 30/228 (13%)

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L + E+VS G IGL++A  +FDP+ G    T++ + IK A+ +  LR   +++ G     
Sbjct: 16  LELDELVSYGQIGLLEAADRFDPKVGANFLTFAHYRIKGAIFDG-LRKMGILRGGDA--- 71

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
            R  F   R   +L  ++D     EQ      +    + +V  ++  +AG   L  +  +
Sbjct: 72  -RSAFVGERAAAYLGNLSDR----EQ--GGGNRGGSFDDDVNDISNAVAG---LAMVFAT 121

Query: 193 S--DKNSSQWQD-WLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPRERRIFEARRL 248
           S    +S+ + D  L  D        +E E+ K R R  + R    L  +ER++ +    
Sbjct: 122 SLEGADSAGYSDESLPADQ------RLEMEQLKRRVRAAIER----LPDKERQLLQGYYF 171

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPL 296
           Q    TLE   SE   S+    ++ ARA ++++E + ++   +SS  L
Sbjct: 172 QGR--TLEEAGSEIGQSKSWASRLHARAIERLKEFLDEEEAPASSDEL 217


>gi|299535877|ref|ZP_07049197.1| sporulation sigma factor SigG [Lysinibacillus fusiformis ZC1]
 gi|298728629|gb|EFI69184.1| sporulation sigma factor SigG [Lysinibacillus fusiformis ZC1]
          Length = 257

 Score = 42.7 bits (99), Expect = 0.058,   Method: Compositional matrix adjust.
 Identities = 57/258 (22%), Positives = 116/258 (44%), Gaps = 17/258 (6%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L+ +E   L  R  + G+      LV  +LRLV+ I   +   G    ++   G IG
Sbjct: 15  LPILKHEEMKELFIRL-QAGETEIREELVMCNLRLVLSIVGRFAYRGEQADDLFQVGCIG 73

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           LM+A+  FD +   R +TY++  I   ++ + LR    +++  +          + ++  
Sbjct: 74  LMKAIDHFDLKHNVRFSTYAVPMIIGEIRRH-LRDHHALRVSRSLRD----IAYKAMQAK 128

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            Q ITD NL+   +  IA+ +++ + +V+     +    SL   I S   ++    D L 
Sbjct: 129 EQWITD-NLREPTIEEIAEMIDMKKEDVLFALDAIQDPVSLQEPIYSDGGDAVYMMDQLR 187

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            D   ++Q +            +  S+  L+ R++ I  A+R        E ++ E  +S
Sbjct: 188 DDDVSEDQWVAYVS--------VKESLQKLDERQQMIV-AKRFYYGETQTE-IAKELGIS 237

Query: 266 RERVRQIEARAFKKVQES 283
           + ++ ++E  A + +Q+ 
Sbjct: 238 QAQISRLEKNAIETMQKD 255


>gi|294013075|ref|YP_003546535.1| RNA polymerase sigma factor for flagellar operon FliA [Sphingobium
           japonicum UT26S]
 gi|292676405|dbj|BAI97923.1| RNA polymerase sigma factor for flagellar operon FliA [Sphingobium
           japonicum UT26S]
          Length = 245

 Score = 42.7 bits (99), Expect = 0.058,   Method: Compositional matrix adjust.
 Identities = 53/252 (21%), Positives = 116/252 (46%), Gaps = 25/252 (9%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFD 94
           A  Y      S+  RL   ++ LV KIA    G     + I +++  G + L++A   F+
Sbjct: 12  ANTYGRSAHASSPERLARQYMPLVRKIAWHVHGRVSSAIEIEDLLQIGMVALVEAANGFE 71

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR-RLKGHLQAITDNN 153
            +RG   A+Y+   ++ AM +++ R  ++ +  +  +Q++    +R RL+   Q +    
Sbjct: 72  -DRGLGFASYAQMRVRGAMIDHLRRHATMTR--SAMSQRKQLAAIRNRLE---QRLGRAP 125

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
           L+ E    +   L+ +    ++  C +    S++ +   SD++      W     D  + 
Sbjct: 126 LEAEMSAEMG--LDAAAYREVADGCEMVQHTSMDEVY--SDQSM-----WFADVEDRADD 176

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
           ++    ER++ +  L + +  L  RE  + +   ++E  + LE + +  ++   RV QI+
Sbjct: 177 IM----ERESLKGALAQYIGELPQREALVLQLYFVEE--LNLEEIGATLDIGAARVCQIK 230

Query: 274 ARAFKKVQESIQ 285
             A  K++E ++
Sbjct: 231 KAALDKLREKLR 242


>gi|91223562|ref|ZP_01258827.1| flagellar biosynthesis sigma factor [Vibrio alginolyticus 12G01]
 gi|269965686|ref|ZP_06179799.1| flagellar biosynthesis sigma factor FliA [Vibrio alginolyticus 40B]
 gi|91191648|gb|EAS77912.1| flagellar biosynthesis sigma factor [Vibrio alginolyticus 12G01]
 gi|269829754|gb|EEZ83990.1| flagellar biosynthesis sigma factor FliA [Vibrio alginolyticus 40B]
          Length = 244

 Score = 42.7 bits (99), Expect = 0.058,   Method: Compositional matrix adjust.
 Identities = 56/250 (22%), Positives = 106/250 (42%), Gaps = 27/250 (10%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFD 94
           A  Y +HG  ++    +  +  LV +IA    G   P   + +++  G IGL++A + +D
Sbjct: 4   AITYDQHGKFNSQQAFIERYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLIEAQQNYD 63

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +G    TY+   I+ AM +  +R    V      N + +   +  L+G L     +  
Sbjct: 64  GSKGASFETYAGIRIRGAMLDD-MRKGDWVPRSVHKNNREINQAIAELEGELNR---DPT 119

Query: 155 KPEQVVAIAKKLNVSESEVISMNC-RLAGDESL---NALINSSDKNSSQWQDWLVYDHDG 210
             E    +   L+   S +  +NC +L G E L   + +I+ +D+           D   
Sbjct: 120 DSEVATHLGMTLDQYHSALTDINCSKLVGIEDLGVSDDVISPADET----------DDSN 169

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
             + ++++  RK     L  S+  L  RE  +      +E  + L+ +     VS  RV 
Sbjct: 170 PFKGVVDESFRK----ALVESIKQLPEREALVLSLYYDEE--LNLKEIGDVLGVSESRVS 223

Query: 271 QIEARAFKKV 280
           QI ++A +++
Sbjct: 224 QILSQAMQRL 233


>gi|3249725|gb|AAC26665.1| RNA polymerase sigma-like factor [Streptomyces glauceuces]
          Length = 162

 Score = 42.7 bits (99), Expect = 0.058,   Method: Compositional matrix adjust.
 Identities = 49/181 (27%), Positives = 75/181 (41%), Gaps = 30/181 (16%)

Query: 104 YSMWWIKAAMQEYILRSWSLVK--------IGTTANQKRLFFNLRRLKGHLQAI-TDNNL 154
           Y+ WWI+ AM   +      ++        I      +R     R ++   + I  D +L
Sbjct: 1   YATWWIRQAMSRALADQADTIRVPVHVVELINRVVRVQRRLLQERGVEPTAEDIGVDLDL 60

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            PE+V  I   L + +  V           SL+A +   D  S  + D +    DG    
Sbjct: 61  TPERVTDI---LRLGQEPV-----------SLHAPVGEEDDVS--FGDLI---EDGDAAS 101

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
            +E       R  L   +S L  RER++ + R   E+  P TLE +   F V+RER+RQI
Sbjct: 102 PVESAVFLLLREHLEAVLSTLGERERKVVQLRYGLEDGRPRTLEEIGRIFGVTRERIRQI 161

Query: 273 E 273
           E
Sbjct: 162 E 162


>gi|293375374|ref|ZP_06621655.1| putative RNA polymerase sigma-H factor [Turicibacter sanguinis
           PC909]
 gi|325844422|ref|ZP_08168149.1| putative RNA polymerase sigma-H factor [Turicibacter sp. HGF1]
 gi|292645927|gb|EFF63956.1| putative RNA polymerase sigma-H factor [Turicibacter sanguinis
           PC909]
 gi|325489096|gb|EGC91480.1| putative RNA polymerase sigma-H factor [Turicibacter sp. HGF1]
          Length = 200

 Score = 42.7 bits (99), Expect = 0.059,   Method: Compositional matrix adjust.
 Identities = 50/212 (23%), Positives = 84/212 (39%), Gaps = 30/212 (14%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           M  +  +Y L    RE  +  A H ++  +  L+ KIA  Y G G    +   EG +  +
Sbjct: 1   MTVEYNDYELVYLVREQNE-EALHIIIEKYSPLIGKIASSYYGIGYDYQDFFQEGRMAFI 59

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +A+  FD    +   +Y+M  ++ A+               T + +R    L+R  G L 
Sbjct: 60  KAIYSFDENSNYSFYSYAMTCVRNAI---------------TTSYRR----LKRTSG-LD 99

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS----QWQDW 203
            +TD +  P             +SE   +N +L  + ++N     SDK  S    Q   +
Sbjct: 100 QLTDYDEHPLVSTLETPGYYHYDSEYTYLNEKLIIEMAMN-----SDKILSPFEKQCLKY 154

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
            +  H+  E  +I     K   N L+R  S L
Sbjct: 155 FLLGHNYNEIAIILNLSPKKIDNALSRCKSKL 186


>gi|220929692|ref|YP_002506601.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium cellulolyticum
           H10]
 gi|220000020|gb|ACL76621.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium cellulolyticum
           H10]
          Length = 249

 Score = 42.7 bits (99), Expect = 0.059,   Method: Compositional matrix adjust.
 Identities = 23/82 (28%), Positives = 44/82 (53%), Gaps = 1/82 (1%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A   LV  ++ LV  I   ++  G  + ++   G+IGL++A+ KFD     + +TY
Sbjct: 19  GDKQAQSVLVEKNVGLVWSIVKRFQNRGYEVDDLFQIGSIGLIKAINKFDTSYDVKFSTY 78

Query: 105 SMWWIKAAMQEYILRSWSLVKI 126
           ++  I   ++ +I R   ++K+
Sbjct: 79  AVPMIIGEIKRFI-RDDGIIKV 99


>gi|223043961|ref|ZP_03614002.1| RNA polymerase sigma-B factor [Staphylococcus capitis SK14]
 gi|314934140|ref|ZP_07841501.1| RNA polymerase sigma-B factor [Staphylococcus caprae C87]
 gi|222442676|gb|EEE48780.1| RNA polymerase sigma-B factor [Staphylococcus capitis SK14]
 gi|313653045|gb|EFS16806.1| RNA polymerase sigma-B factor [Staphylococcus caprae C87]
          Length = 256

 Score = 42.7 bits (99), Expect = 0.060,   Method: Compositional matrix adjust.
 Identities = 52/247 (21%), Positives = 117/247 (47%), Gaps = 16/247 (6%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           K ++E+ +  A  +LVT + +L+  +A  Y        ++V  G +GL+ A+ +FD    
Sbjct: 21  KEHQENENSQAQDKLVTHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDLSFD 80

Query: 99  FRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
            +   + +  +   ++ Y+  ++WS   +      K +   ++++   L   T+   +  
Sbjct: 81  RKFEAFLVPTVIGEIKRYLRDKTWS---VHVPRRIKEIGPRIKKISDEL---TNELERSP 134

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQVLI 216
            +  IA++L VS+ EV+     +   +S NAL ++ S +         + D  GQ+    
Sbjct: 135 SISEIAQRLEVSDEEVLEA---MEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQQD--- 188

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           +  +   +R +L R + +L+ RER+I +   ++   ++ +       +S+  V +++  A
Sbjct: 189 DNYDLTEKRMILERILPILSDRERQIIQCTFIE--GLSQKETGERIGLSQMHVSRLQRTA 246

Query: 277 FKKVQES 283
            KK+QE+
Sbjct: 247 IKKLQEA 253


>gi|295102468|emb|CBL00013.1| RNA polymerase sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii L2-6]
          Length = 224

 Score = 42.7 bits (99), Expect = 0.061,   Method: Compositional matrix adjust.
 Identities = 25/89 (28%), Positives = 44/89 (49%), Gaps = 1/89 (1%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            +  +L LV   A  +RG G+   ++ S G +GL++A   FD  RG   +TY++  I   
Sbjct: 11  FIEQNLGLVHSCAGRFRGRGIEYDDLYSAGCMGLVKAYDGFDESRGVCFSTYAVPVILGE 70

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           +++ + R    VK+  +  +  L  N  R
Sbjct: 71  IKK-LFRDGGTVKVSRSLKELSLRINAAR 98


>gi|325660705|ref|ZP_08149334.1| RNA polymerase sigma-F factor [Lachnospiraceae bacterium 4_1_37FAA]
 gi|331085570|ref|ZP_08334654.1| RNA polymerase sigma-F factor [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|325473012|gb|EGC76221.1| RNA polymerase sigma-F factor [Lachnospiraceae bacterium 4_1_37FAA]
 gi|330407457|gb|EGG86959.1| RNA polymerase sigma-F factor [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 240

 Score = 42.7 bits (99), Expect = 0.061,   Method: Compositional matrix adjust.
 Identities = 60/257 (23%), Positives = 110/257 (42%), Gaps = 25/257 (9%)

Query: 34  EYVLAKRYREH-GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           ++ +A   R H GD  A  +LV  +  LV  I   + G G    ++   G+IGL++A+ K
Sbjct: 2   DHTIALIQRSHDGDEKAREQLVEENTGLVWCIVKRFFGRGTDSEDLFQIGSIGLLKAIDK 61

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK--RLFFNLRRLKGHLQAIT 150
           FD     + +TY++  I   ++ + LR   ++K+  +  +   + F    RL+       
Sbjct: 62  FDLNYDVKFSTYAVPMISGEIRRF-LRDDGMIKVSRSLKETAYKAFLARERLQ------- 113

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD-ESLNALINSSDKNSSQWQDWLVYDHD 209
                 E  +         E E ++M    +G+ ESL+  I   D N  Q  D L  +  
Sbjct: 114 -KKYNREPTMEELAAELEVEKEELAMALDASGEVESLHKPIYQKDGNEIQLLDKLEEEEG 172

Query: 210 GQEQVLIEKEERKNRRNMLTRS-MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
            +E +L          +ML R  +  L+  ER++   R       T   +  +  +S+ +
Sbjct: 173 QEETIL---------NHMLIRQLLEELDREERQLIYLRYFANQ--TQSEIGKKLGISQVQ 221

Query: 269 VRQIEARAFKKVQESIQ 285
           V ++E +  K ++  IQ
Sbjct: 222 VSRLEKKILKNMRTKIQ 238


>gi|91776300|ref|YP_546056.1| flagellar biosynthesis sigma factor [Methylobacillus flagellatus
           KT]
 gi|91710287|gb|ABE50215.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Methylobacillus
           flagellatus KT]
          Length = 244

 Score = 42.7 bits (99), Expect = 0.061,   Method: Compositional matrix adjust.
 Identities = 53/253 (20%), Positives = 110/253 (43%), Gaps = 20/253 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPE 96
           Y  HG  S    L+  H  LV KIA   +   LP    I +++  G +GL+ A  +++  
Sbjct: 2   YTLHGKTSPKEELLKQHASLVKKIAYQLKA-KLPASVDIDDLIQAGMMGLLDASNRYEDN 60

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
            G +  TY+   I+ +M + + R+  L         + +  N+R ++  +  +     +P
Sbjct: 61  HGAQFETYAAQRIRGSMIDELRRADWL--------PRSVRKNMRDVESAVHLLEQKLGRP 112

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE-QVL 215
                +A++LN+S  +   M    +G + +     S   +   + D    D  G   + L
Sbjct: 113 PTEGELARELNLSMDDFQGMLDDCSGHQLIYYEDFSEQDSGDHFLDRYQSDDSGDPLKAL 172

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
           +      + R  L  ++  L  RE+ +      QE  + L+++ +   VS  RV Q+  +
Sbjct: 173 LS----SDFREALIEAIEALPEREKILMGLYYEQE--MNLKDIGAIMSVSESRVCQLHTQ 226

Query: 276 AFKKVQESIQKQV 288
           A  +++  +++++
Sbjct: 227 AVARLRAKLKEKL 239


>gi|302549129|ref|ZP_07301471.1| RNA polymerase sigma-E factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302466747|gb|EFL29840.1| RNA polymerase sigma-E factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 295

 Score = 42.7 bits (99), Expect = 0.062,   Method: Compositional matrix adjust.
 Identities = 43/195 (22%), Positives = 91/195 (46%), Gaps = 18/195 (9%)

Query: 61  VVKIAMG-YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           +V+ A G +RG G  + ++V  G IGL++A+ +F+  R     ++++ +I   ++ +   
Sbjct: 75  LVRFAAGRFRGRGDDMEDIVQTGMIGLIKAIDRFELSREVEFTSFALPYIVGEIKRFFRD 134

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
           +   V +     + R+  +L + +  L +  D   +   V  +A  +N+SE++V+     
Sbjct: 135 TTWAVHVPRRLQELRV--DLAKAREELASRLD---REPTVAELATLMNISENQVVEGQIA 189

Query: 180 LAG--DESLNALINSSDKNSSQ--WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
             G    SL+A +        +    D++  + DG    L+E        + L   M+ L
Sbjct: 190 ANGYNSSSLDAALTGDGPEGGEAVLADFIGVEEDGLR--LVED------FHSLAPLMAEL 241

Query: 236 NPRERRIFEARRLQE 250
           + R+R+I   R ++E
Sbjct: 242 SERDRQIIHMRFVEE 256


>gi|23099037|ref|NP_692503.1| RNA polymerase sigma factor SigD [Oceanobacillus iheyensis HTE831]
 gi|22777265|dbj|BAC13538.1| RNA polymerase sigma-D factor [Oceanobacillus iheyensis HTE831]
          Length = 258

 Score = 42.7 bits (99), Expect = 0.063,   Method: Compositional matrix adjust.
 Identities = 25/83 (30%), Positives = 47/83 (56%), Gaps = 5/83 (6%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLV----VKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           L  +++ H D  AA++L+ +++ LV     +IA  +    +   ++ S G +GL  A+KK
Sbjct: 12  LWDKWKNHQDGEAANQLINNYMYLVNYHTERIA-SHLPNNVVKDDIRSFGILGLYDALKK 70

Query: 93  FDPERGFRLATYSMWWIKAAMQE 115
           FDP R  +  TY+ + IK ++ +
Sbjct: 71  FDPSRDLKFDTYASFRIKGSIMD 93


>gi|256376481|ref|YP_003100141.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Actinosynnema mirum DSM 43827]
 gi|255920784|gb|ACU36295.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Actinosynnema mirum DSM 43827]
          Length = 294

 Score = 42.7 bits (99), Expect = 0.064,   Method: Compositional matrix adjust.
 Identities = 44/214 (20%), Positives = 87/214 (40%), Gaps = 20/214 (9%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA-MQEYILRSWSLVKIGTTANQKRL 135
           E++S GN+ L+ A K FD  RG   A +++  ++ A M E   + W+          + +
Sbjct: 50  ELMSAGNLALVAAAKSFDDSRGAPFAAFAVVRVRGALMDELRGQDWA---------SRSV 100

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
               R++          + +      IA  + V   EV ++      D   +AL++    
Sbjct: 101 RVKARKMNAVQDEFVSKHGRTPTTAEIAGIMEVETREVTAVQ----DDVQRSALLSLQGF 156

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
                ++ +     G E+ L+ +E    R   L  ++  L  R R +      +E P  +
Sbjct: 157 TGGVLEEVVPERQPGPEETLLGRE----RIGYLHSAIDALPDRLRTVVRGYFFEERP--M 210

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
             ++ E  V   RV Q+ A A   +++ +  Q++
Sbjct: 211 AEIAEELGVHESRVSQLRAEAIALLRDGLNSQLD 244


>gi|312877884|ref|ZP_07737830.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
 gi|311795347|gb|EFR11730.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
          Length = 114

 Score = 42.7 bits (99), Expect = 0.064,   Method: Compositional matrix adjust.
 Identities = 28/93 (30%), Positives = 50/93 (53%), Gaps = 5/93 (5%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP--ISEVVSEGNI 84
           PM  ++EE  L K +   G   A + L+  +LRLV  IA  Y  +  P    +++S G I
Sbjct: 13  PMSSEEEEMYLNKMW--EGCKEARNILIEKNLRLVAHIAKKYT-FSFPNLTDDIISVGTI 69

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           GL++A++ +   +  +L+TY+   I+  +  Y+
Sbjct: 70  GLIKAIETYSKAKSTKLSTYAAKCIENEILMYL 102


>gi|313115504|ref|ZP_07800969.1| putative RNA polymerase sigma-F factor [Faecalibacterium cf.
           prausnitzii KLE1255]
 gi|310622214|gb|EFQ05704.1| putative RNA polymerase sigma-F factor [Faecalibacterium cf.
           prausnitzii KLE1255]
          Length = 223

 Score = 42.7 bits (99), Expect = 0.064,   Method: Compositional matrix adjust.
 Identities = 22/74 (29%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            +  +L LV   A  +RG G+   ++ S G +GL++A   FD  RG   +TY++  I   
Sbjct: 11  FIEQNLGLVHACAGRFRGRGIEYDDLYSAGCMGLVKACDNFDESRGVCFSTYAVPVILGE 70

Query: 113 MQEYILRSWSLVKI 126
           +++ + R    VK+
Sbjct: 71  IKK-LFRDSGTVKV 83


>gi|222528742|ref|YP_002572624.1| sporulation sigma factor SigK [Caldicellulosiruptor bescii DSM
           6725]
 gi|222455589|gb|ACM59851.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor bescii DSM 6725]
          Length = 219

 Score = 42.7 bits (99), Expect = 0.066,   Method: Compositional matrix adjust.
 Identities = 30/93 (32%), Positives = 51/93 (54%), Gaps = 5/93 (5%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP--ISEVVSEGNI 84
           PM  ++EE  L K  RE G   A + L+  +LRLV  IA  Y  +  P    +++S G I
Sbjct: 13  PMSPEEEEMYLNK-MRE-GCKEARNILIEKNLRLVAHIAKKYT-FSFPNLTDDIISVGTI 69

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           GL++A++ +   +  +L+TY+   I+  +  Y+
Sbjct: 70  GLIKAIETYSSAKCTKLSTYAAKCIENEILMYL 102


>gi|297584063|ref|YP_003699843.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus
           selenitireducens MLS10]
 gi|297142520|gb|ADH99277.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus
           selenitireducens MLS10]
          Length = 253

 Score = 42.7 bits (99), Expect = 0.066,   Method: Compositional matrix adjust.
 Identities = 58/257 (22%), Positives = 111/257 (43%), Gaps = 31/257 (12%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPE 96
           + E  D SA  RL+ + L LV    +   G  LP      ++ S G +GL  A++KFD +
Sbjct: 17  WEEKRDRSAGDRLIEAFLPLV-DYHVHRIGVHLPKNVSSDDLRSHGLMGLFDALEKFDRK 75

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN---- 152
           R  +  TY+ + I+ A+            I     +  L   LR     ++ +T++    
Sbjct: 76  RELKFDTYASFRIRGAI------------IDGLRQEDWLPRTLRDKAKKIEQVTESLEQQ 123

Query: 153 ---NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
              N+ P++   IA +  ++E++VI  +        L+  I+   +   Q + +     D
Sbjct: 124 LGRNVSPKE---IADEAGLTEADVIKTSNENFFSHLLS--IDEPTQEGDQTETYASSIAD 178

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
            Q     E   ++   + L  ++  LN +E+ +      +E  +TL  +     +S  R+
Sbjct: 179 QQTLTPAESLSKQADYDELADAIQNLNEKEQLVISLFYYEE--LTLTEIGEALSLSTSRI 236

Query: 270 RQIEARAFKKVQESIQK 286
            QI ++A  K+Q+ + K
Sbjct: 237 SQIHSKAVYKLQQQLHK 253


>gi|283781321|ref|YP_003372076.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pirellula staleyi DSM
           6068]
 gi|283439774|gb|ADB18216.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pirellula staleyi DSM
           6068]
          Length = 261

 Score = 42.7 bits (99), Expect = 0.066,   Method: Compositional matrix adjust.
 Identities = 51/218 (23%), Positives = 97/218 (44%), Gaps = 17/218 (7%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           G+ + +++S G  GLM A+  FD  RG +  TY +  I+ AM +  LR+   V     + 
Sbjct: 53  GVELDDLISAGIFGLMDAIDAFDMTRGVKFETYCVPRIRGAMLDE-LRTMDWVPRLVRSK 111

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQV-VAIAKKLNVSESEVISMNCRLAGDESLNALI 190
             +L    + L+  L         P  V +A   +++V E E +       G  SLN   
Sbjct: 112 ASKLGEATKTLEARL------GRHPTTVELAAQMEMSVPEVEKMVSEASAVGLISLNKKW 165

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV-LNPRERRIFEARRLQ 249
             +D      +  ++ D  G++        R+ ++N L R ++  LN  ER I      +
Sbjct: 166 YETDSYKDVREIDILEDKKGEDPT------RRIQKNDLMRLVTKGLNRNERLIIILYYYE 219

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E  +T++ + +  ++S  RV Q+ +    ++Q  + ++
Sbjct: 220 E--LTMKEIGATLDLSESRVSQMHSSIVSRLQSQLGRR 255


>gi|328951994|ref|YP_004369328.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfobacca
           acetoxidans DSM 11109]
 gi|328452318|gb|AEB08147.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfobacca
           acetoxidans DSM 11109]
          Length = 258

 Score = 42.7 bits (99), Expect = 0.067,   Method: Compositional matrix adjust.
 Identities = 16/41 (39%), Positives = 28/41 (68%)

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           + + +++S G IGL+ A+KKFDP++     TY+ + IK A+
Sbjct: 53  ISLDDLISSGMIGLLDAIKKFDPQKNISFKTYAEFRIKGAI 93


>gi|313116074|ref|ZP_07801498.1| sigma-70 region 2 [Faecalibacterium cf. prausnitzii KLE1255]
 gi|310621671|gb|EFQ05202.1| sigma-70 region 2 [Faecalibacterium cf. prausnitzii KLE1255]
          Length = 221

 Score = 42.7 bits (99), Expect = 0.067,   Method: Compositional matrix adjust.
 Identities = 23/83 (27%), Positives = 40/83 (48%), Gaps = 8/83 (9%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIA--------MGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           + GD +A   L+ ++   + K+A        +   G  L   ++   GN+G  +AV KFD
Sbjct: 13  QKGDATALDSLIENNKSFIGKVANDLFRSMDLAQSGLNLDTDDLKQAGNLGFWKAVPKFD 72

Query: 95  PERGFRLATYSMWWIKAAMQEYI 117
             RG +  TY+   I+ AM + +
Sbjct: 73  AARGMKFLTYAAPAIRNAMMDMV 95


>gi|302037625|ref|YP_003797947.1| flagellar-specific RNA polymerase sigma 28 factor [Candidatus
           Nitrospira defluvii]
 gi|300605689|emb|CBK42022.1| Flagellar-specific RNA polymerase sigma 28 factor [Candidatus
           Nitrospira defluvii]
          Length = 247

 Score = 42.7 bits (99), Expect = 0.067,   Method: Compositional matrix adjust.
 Identities = 60/231 (25%), Positives = 102/231 (44%), Gaps = 36/231 (15%)

Query: 61  VVKIAMGYR-GYGLPI----SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQE 115
           VVK AM +R  + LP      +++S G +GLM A+ K+DP R  +  TY+ + I+ AM +
Sbjct: 27  VVK-AMAHRLAFRLPAYMDAEDLISVGIMGLMDAMDKYDPTREAKFKTYAEFRIRGAMLD 85

Query: 116 YILRSWSLVKIGT----TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            I RS   +        T  QK     L RL            +P     + K+L +S  
Sbjct: 86  EI-RSMDWIPRSVHERITLLQKTYSELLHRLG-----------RPPTDQEVGKELKMSAE 133

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDW-----LVYDHDGQEQVLIEKEERKNRRN 226
           E+     R  G     A++ S D    Q  D      ++ D +  + + +   ER   R+
Sbjct: 134 ELDEFLTRSRG-----AVVISLDDLGVQDADGHKIISVLTDSNQPDPLSVLVNERA--RH 186

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
           +L  ++  L  +ER +      +E  +T++ +    +V+  RV QI ++A 
Sbjct: 187 VLEAAIHDLPEKERLVLSLYYFEE--LTMKEIGQALKVTESRVCQIHSKAI 235


>gi|254454176|ref|ZP_05067613.1| RNA polymerase sigma factor SigA [Octadecabacter antarcticus 238]
 gi|198268582|gb|EDY92852.1| RNA polymerase sigma factor SigA [Octadecabacter antarcticus 238]
          Length = 715

 Score = 42.7 bits (99), Expect = 0.067,   Method: Compositional matrix adjust.
 Identities = 55/227 (24%), Positives = 101/227 (44%), Gaps = 30/227 (13%)

Query: 56  SHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQE 115
           S L  + ++A  +   GL   ++  EG  GL ++V+ F   RG RL TYS + I+  +  
Sbjct: 496 SQLTQLRRLATRFPTEGLEEDDLFQEGYFGLTRSVEMFHAGRGNRLTTYSQYRIRQTIAR 555

Query: 116 YILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
            +    S+V+I      K     +R ++   + ++ N  + +   A+ K   +  +E+  
Sbjct: 556 AVDDHRSVVRIPVHFASK-----VRLIERFGERVSGNISRSDYHCALGKAFQIELAEIQK 610

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER---KNRRNMLTRSM 232
           +       E++  L    D+N       L  D D    + +E  +R   + R+ ++   +
Sbjct: 611 I-------ENIPRLSIEFDEN-------LYSDAD----IELEPFQRVLEQQRQAIIKDFL 652

Query: 233 SVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARA 276
             L  R   I   RR      + +TLE     + V+RER+RQ+EA+A
Sbjct: 653 EDLPERHADII-VRRFGLDGNDEMTLEQCGQVYGVTRERIRQLEAKA 698


>gi|187935479|ref|YP_001884301.1| RNA polymerase sigma-F factor [Clostridium botulinum B str. Eklund
           17B]
 gi|187723632|gb|ACD24853.1| RNA polymerase sigma-F factor [Clostridium botulinum B str. Eklund
           17B]
          Length = 233

 Score = 42.7 bits (99), Expect = 0.068,   Method: Compositional matrix adjust.
 Identities = 25/86 (29%), Positives = 46/86 (53%), Gaps = 6/86 (6%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKF 93
           L + Y+E GD  A ++L+ ++ +LV KI   +       + I ++  EG +GL+ A KK+
Sbjct: 6   LVELYQE-GDKQALNKLIENNKKLVFKIVNKFYINATNSIDIEDLEQEGYMGLIMAAKKY 64

Query: 94  DPERGFR--LATYSMWWIKAAMQEYI 117
           +    +    +TYS +WI   +  +I
Sbjct: 65  NSNMDYHASFSTYSFYWIYQKINSFI 90


>gi|317499023|ref|ZP_07957304.1| RNA polymerase sigma-F factor [Lachnospiraceae bacterium 5_1_63FAA]
 gi|291560723|emb|CBL39523.1| RNA polymerase, sigma subunit, RpoX/SigF [butyrate-producing
           bacterium SSC/2]
 gi|316893673|gb|EFV15874.1| RNA polymerase sigma-F factor [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 241

 Score = 42.7 bits (99), Expect = 0.069,   Method: Compositional matrix adjust.
 Identities = 54/253 (21%), Positives = 112/253 (44%), Gaps = 40/253 (15%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R  + G+ +A  +++ +++ L+  +   +   G    ++   G+IGLM+AV KFD     
Sbjct: 9   RLTKEGNEAAREQIILNNVGLIWSVVRRFTNRGYESEDLFQIGSIGLMKAVDKFDLSYDV 68

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY++  I   ++ + LR   ++K+  +  +     N+ ++    +       +   +
Sbjct: 69  KFSTYAVPMITGEIRRF-LRDDGMIKVSRSLKE-----NVYKIMKAREKFCQQYQREATI 122

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK- 218
             I++   ++  E+++         SL A    S++  S  Q    Y  DG E  L++K 
Sbjct: 123 EEISEITKITREEIVT---------SLEA----SNEVESIHQS--AYQKDGSEISLLDKL 167

Query: 219 ------EERKNRRNMLTRSMSVLNPRER-----RIFEARRLQENPVTLENLSSEFEVSRE 267
                  E+     +L  +M  L  +E+     R FE +  QE       ++  F +S+ 
Sbjct: 168 SKGENESEKVVDHVLLKEAMKHLEQKEQQMIYYRYFEGKTQQE-------IAKIFHISQV 220

Query: 268 RVRQIEARAFKKV 280
           +V +IE R  KK+
Sbjct: 221 QVSRIEKRILKKL 233


>gi|293366035|ref|ZP_06612723.1| RNA polymerase sigma-B factor [Staphylococcus epidermidis
           M23864:W2(grey)]
 gi|291319758|gb|EFE60116.1| RNA polymerase sigma-B factor [Staphylococcus epidermidis
           M23864:W2(grey)]
          Length = 256

 Score = 42.7 bits (99), Expect = 0.069,   Method: Compositional matrix adjust.
 Identities = 53/247 (21%), Positives = 117/247 (47%), Gaps = 16/247 (6%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           K+++E+ D  A  +LV  + +L+  +A  Y        ++V  G +GL+ A+ +FD    
Sbjct: 21  KQHQENEDSQAQDKLVKHYRKLIESLAYRYSKGQSHHEDLVQVGMVGLIGAINRFDLSFD 80

Query: 99  FRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
            +   + +  +   ++ Y+  ++WS+         +R+     R+K     +T+   +  
Sbjct: 81  RKFEVFLVPTVIGEIKRYLRDKTWSV------HVPRRIKEIGPRIKKVSDELTNELERSP 134

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQVLI 216
            +  IA++L VS+ EV+     +   +S NAL ++ S +         + D  GQ+    
Sbjct: 135 SISEIAQRLEVSDEEVLEA---MEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQQD--- 188

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           +  +   +R +L R + +L+ RER+I +   ++   ++ +       +S+  V +++  A
Sbjct: 189 DNYDLTEKRMILERILPILSERERQIIQCTFIE--GLSQKETGERIGLSQMHVSRLQRTA 246

Query: 277 FKKVQES 283
            KK+QE+
Sbjct: 247 IKKLQEA 253


>gi|148976430|ref|ZP_01813136.1| flagellar biosynthesis sigma factor [Vibrionales bacterium SWAT-3]
 gi|145964253|gb|EDK29509.1| flagellar biosynthesis sigma factor [Vibrionales bacterium SWAT-3]
          Length = 244

 Score = 42.7 bits (99), Expect = 0.071,   Method: Compositional matrix adjust.
 Identities = 60/252 (23%), Positives = 105/252 (41%), Gaps = 31/252 (12%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFD 94
           A  Y +H + ++       +  LV +IA    G   P   + +++  G IGL++A + +D
Sbjct: 4   ALTYDQHANHNSQQAFFEKYSVLVKRIAHHLLGRLPPNVLVDDLIQAGMIGLIEAQQNYD 63

Query: 95  PERGFRLATYSMWWIKAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
             +G    TY+   I+ AM + I R  W  V      N + +   +  L+  L      N
Sbjct: 64  GTKGASFETYAGIRIRGAMLDDIRRGDW--VPRSVHKNNREISSAIAELESTL------N 115

Query: 154 LKPEQVVAIAKKLNVS----ESEVISMNC-RLAGDESLNALINSSDKNSSQWQDWLVYDH 208
             P     +AK + +S     S +  +NC RL G E L      SD       D +  + 
Sbjct: 116 RDPSD-AEVAKHMGLSLEQYHSALTDINCSRLVGIEDLGV----SD-------DVISPNE 163

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D Q+    +    ++ R  L  S+  L  RE  +      +E  + L+ +     VS  R
Sbjct: 164 DSQDNAPFQGVADESFRQALIDSIKQLPEREGLVLSLYYDEE--LNLKEIGEVLGVSESR 221

Query: 269 VRQIEARAFKKV 280
           V QI +++ +++
Sbjct: 222 VSQILSQSMQRL 233


>gi|311900244|dbj|BAJ32652.1| putative RNA polymerase sigma factor [Kitasatospora setae KM-6054]
          Length = 310

 Score = 42.7 bits (99), Expect = 0.072,   Method: Compositional matrix adjust.
 Identities = 53/221 (23%), Positives = 97/221 (43%), Gaps = 32/221 (14%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQ 132
           P  +++  G++GL++A+ +FDP  G    TY++  I   ++ +    +WS+       + 
Sbjct: 110 PYEDLLQVGSVGLIKAIDRFDPSLGVEFTTYAVPTIIGEIRRHFRDTTWSV-------HV 162

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVA-IAKKLNVSESEVISMNCRLAGDESLNALIN 191
            R    LR      Q      L  E  VA +A+ L++SE EVI       G  + NA   
Sbjct: 163 PRRLQELRLDLAKAQDALAQTLDREPTVADLAEYLSISEEEVIE------GLAAANAHTA 216

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP-------RERRIFE 244
            S   +S  +       DGQ+    E+  R + R  L  ++  L P       R+R+I  
Sbjct: 217 GSLDLTSPGE------GDGQQPA--ERLGRVDGRFALVENLVALKPLIAQLPERDRQIL- 267

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           A R  E+ +T   + +   +S+  V ++ +R   +++  + 
Sbjct: 268 AMRFSED-LTQSQIGARLGLSQMHVSRLLSRTLARLRTGLD 307


>gi|6010734|gb|AAF01233.1|AF184102_1 mutant RpoS [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
          Length = 119

 Score = 42.7 bits (99), Expect = 0.072,   Method: Compositional matrix adjust.
 Identities = 24/56 (42%), Positives = 34/56 (60%), Gaps = 1/56 (1%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL 
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIARRYGNRGLA 115


>gi|291542064|emb|CBL15174.1| RNA polymerase sigma factor, sigma-70 family [Ruminococcus bromii
           L2-63]
          Length = 219

 Score = 42.7 bits (99), Expect = 0.073,   Method: Compositional matrix adjust.
 Identities = 29/128 (22%), Positives = 60/128 (46%), Gaps = 6/128 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           ++  ++L   ++ LV      + G G+   E+ + G +GL +A+  FD  R  + +TY+ 
Sbjct: 1   MTDKNKLADKNMGLVHACCKRFSGKGIEYEELFASGCLGLAKAINNFDESRNLQFSTYAF 60

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I   ++  + R    +++  T   K L   + RL    +     N +   V  +A++L
Sbjct: 61  PVIMGEIKR-LFRDGGAIRVSRTL--KELSLAISRLNNESKL---KNGRELTVSELAERL 114

Query: 167 NVSESEVI 174
           + SE ++I
Sbjct: 115 DTSEEKII 122


>gi|218245540|ref|YP_002370911.1| RNA polymerase sigma factor SigF [Cyanothece sp. PCC 8801]
 gi|257058577|ref|YP_003136465.1| RNA polymerase sigma factor SigF [Cyanothece sp. PCC 8802]
 gi|218166018|gb|ACK64755.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cyanothece
           sp. PCC 8801]
 gi|256588743|gb|ACU99629.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cyanothece
           sp. PCC 8802]
          Length = 255

 Score = 42.4 bits (98), Expect = 0.075,   Method: Compositional matrix adjust.
 Identities = 50/217 (23%), Positives = 100/217 (46%), Gaps = 18/217 (8%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGF 99
           Y  +  L+  ++LV  H  LV ++A         P  ++   G +GL+ A+++F+P +G 
Sbjct: 17  YSRNPSLALRNQLVELHTGLVRQVAHRISNQCTEPYEDLEQIGYLGLINAIERFNPHQGC 76

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
             +++++ +I+  M  Y+    S+++I      + L+   ++++  L        K ++ 
Sbjct: 77  AFSSFAIPYIRGEMLHYLRDKGSVMRI--PRRWQELYNKGKKVRKQLTTSLGRTPKDQE- 133

Query: 160 VAIAKKLNVSESEVISMNCRLAGDE----SLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
             +A  L VS  E     C LA       SL++ IN +  ++  + + L  DH  Q    
Sbjct: 134 --LADALQVSLEEW--HECELALQNRMLVSLDSTINQNTDSTVSFGETLP-DHRYQ---- 184

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
             K+ ++  R  L R+MS L  + +   E   ++E P
Sbjct: 185 -AKQSQEEDRLQLQRAMSQLEDKTKEAIECVFIKELP 220


>gi|21221509|ref|NP_627288.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
 gi|289771198|ref|ZP_06530576.1| SigI protein [Streptomyces lividans TK24]
 gi|5911753|emb|CAB55836.1| SigI protein [Streptomyces coelicolor A3(2)]
 gi|7672251|emb|CAB89440.1| putative RNA polymerase sigma factor [Streptomyces coelicolor
           A3(2)]
 gi|289701397|gb|EFD68826.1| SigI protein [Streptomyces lividans TK24]
          Length = 304

 Score = 42.4 bits (98), Expect = 0.076,   Method: Compositional matrix adjust.
 Identities = 44/167 (26%), Positives = 77/167 (46%), Gaps = 14/167 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  +L LV   A  +R    P+ +++  G IGL++A+ +F+  RG    T++M  I   
Sbjct: 83  LVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRGVEFPTFAMPTIIGE 142

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL  +L +    L    D   +   V  +A+ L +S+ 
Sbjct: 143 IKRFFRDTSWS-VRVPRRLQELRL--DLAKAGDELAQRLD---RAPTVSELAEHLGLSKD 196

Query: 172 EVI----SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           EV+    + N   A   SL+A     D   +   D + Y+  G E +
Sbjct: 197 EVVEGMAASNAYTAS--SLDAQPEEDDAEGA-LADRIGYEDHGLEGI 240


>gi|169836116|ref|ZP_02869304.1| hypothetical protein cdivTM_03213 [candidate division TM7
          single-cell isolate TM7a]
          Length = 54

 Score = 42.4 bits (98), Expect = 0.077,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 30/46 (65%)

Query: 16 LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
          +S Y+ +I+K  +L ++EEY L KR RE  D  A   L+ S+LRLV
Sbjct: 9  MSLYLSDIQKFDLLSREEEYELLKRIREDNDEQARQLLILSNLRLV 54


>gi|56964115|ref|YP_175846.1| sporulation sigma factor SigG [Bacillus clausii KSM-K16]
 gi|56910358|dbj|BAD64885.1| DNA-directed RNA polymerase sigma factor sigma-G [Bacillus clausii
           KSM-K16]
          Length = 261

 Score = 42.4 bits (98), Expect = 0.077,   Method: Compositional matrix adjust.
 Identities = 54/249 (21%), Positives = 112/249 (44%), Gaps = 38/249 (15%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   LV  +LRLV+ +   +   G  + ++   G IGLM+++  FD  +  + +TY++  
Sbjct: 38  ARETLVNGNLRLVLSVIQRFNNRGENVDDLFQVGCIGLMKSIDNFDLSQNVKFSTYAVPM 97

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I   ++ Y LR  + +++  +   + + +   +++  + A      +P  V  IA  L V
Sbjct: 98  IIGEIRRY-LRDNNPIRVSRSL--RDIAYKALQVRDQMMAEKKREKEP-TVQEIAAVLEV 153

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL-----VYDHDGQEQVLIEK--EER 221
            + +V+          +L+A+           QD +     +Y+  G    ++++  +ER
Sbjct: 154 PKEDVVF---------ALDAI-----------QDPVSLFEPIYNDGGDPIFVMDQISDER 193

Query: 222 KNRRN-----MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
               N      L  +M  LN RE+ I   R  Q    T   ++ E  +S+ +V ++E  A
Sbjct: 194 NKDINWVEEIALKEAMVRLNDREKTILNMRFFQGK--TQMEVAEEIGISQAQVSRLEKGA 251

Query: 277 FKKVQESIQ 285
            +++ + I+
Sbjct: 252 IQQMNKHIE 260


>gi|270262372|ref|ZP_06190644.1| RNA polymerase sigma factor for flagellar operon [Serratia
           odorifera 4Rx13]
 gi|270044248|gb|EFA17340.1| RNA polymerase sigma factor for flagellar operon [Serratia
           odorifera 4Rx13]
          Length = 240

 Score = 42.4 bits (98), Expect = 0.079,   Method: Compositional matrix adjust.
 Identities = 46/216 (21%), Positives = 96/216 (44%), Gaps = 32/216 (14%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL+ AV+++D  +G    TY++  I+ AM +  LRS   V      + + 
Sbjct: 41  LDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDE-LRSRDWVPRSVRRHARE 99

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   +R+L+  L        +P   V +A+ LN+              DE    L+++++
Sbjct: 100 VAQVMRQLEQRLG-------RPASEVEVAQTLNIP------------LDEYRQILLDTNN 140

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNR---------RNMLTRSMSVLNPRERRIFEA 245
                + +W   +H    + L+E  E  N          R  +  ++  L  RE+ +   
Sbjct: 141 SQLFSYDEW-REEHGESAEPLLEGHEEANPLHHLLEGNLRQRVIDAIDALPEREKMVLTL 199

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +E  + L+ + +  +V   RV Q+ ++A K+++
Sbjct: 200 YYQEE--LNLKEIGAVLDVGESRVSQLHSQAIKRLR 233


>gi|94312634|ref|YP_585843.1| RNA polymerase sigma 28 (sigma F) factor [Cupriavidus metallidurans
           CH34]
 gi|93356486|gb|ABF10574.1| RNA polymerase sigma 28 (sigma F) factor [Cupriavidus metallidurans
           CH34]
          Length = 238

 Score = 42.4 bits (98), Expect = 0.080,   Method: Compositional matrix adjust.
 Identities = 63/251 (25%), Positives = 110/251 (43%), Gaps = 33/251 (13%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPE 96
           Y   G L  A  +V SH  LV +IA+      LP    I +++  G IGL+ A K+++  
Sbjct: 2   YTIQGKLEQAD-VVKSHAPLVRRIALQL-AAKLPASVQIDDLIQAGMIGLLDAAKRYEDN 59

Query: 97  RGFRLATYSMWWIKAAMQEYI-LRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITDNNL 154
            G R  TY+   I+ AM + +    W       + + ++    + R +  L Q +  + +
Sbjct: 60  HGARFETYASQRIRGAMLDEVRANDWQ------SRSLRQFTRKIERTQRQLEQKLGRSPI 113

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL-----VYDHD 209
             E    +AK+L +   E   +   + G +    L++  D   S  +D+L     V D  
Sbjct: 114 DSE----VAKELEMGLEEYQELLNEVHGCQ----LLHYEDFERSGEEDFLDRHLGVTDEA 165

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
               VL+E       R+ L R++  L  RE+ +      QE  + L  + +  EV+  RV
Sbjct: 166 NPLTVLME----SGMRDALIRAIEKLPEREKLVLSLCYDQE--LNLREIGAVLEVTESRV 219

Query: 270 RQIEARAFKKV 280
            QI ++A  ++
Sbjct: 220 CQIRSQAITRL 230


>gi|256787303|ref|ZP_05525734.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
          Length = 308

 Score = 42.4 bits (98), Expect = 0.081,   Method: Compositional matrix adjust.
 Identities = 44/167 (26%), Positives = 77/167 (46%), Gaps = 14/167 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  +L LV   A  +R    P+ +++  G IGL++A+ +F+  RG    T++M  I   
Sbjct: 87  LVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRGVEFPTFAMPTIIGE 146

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL  +L +    L    D   +   V  +A+ L +S+ 
Sbjct: 147 IKRFFRDTSWS-VRVPRRLQELRL--DLAKAGDELAQRLD---RAPTVSELAEHLGLSKD 200

Query: 172 EVI----SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           EV+    + N   A   SL+A     D   +   D + Y+  G E +
Sbjct: 201 EVVEGMAASNAYTAS--SLDAQPEEDDAEGA-LADRIGYEDHGLEGI 244


>gi|27468586|ref|NP_765223.1| RNA polymerase sigma factor SigB [Staphylococcus epidermidis ATCC
           12228]
 gi|57867587|ref|YP_189242.1| RNA polymerase sigma factor SigB [Staphylococcus epidermidis RP62A]
 gi|251812213|ref|ZP_04826686.1| DNA-directed RNA polymerase sigma subunit FliA [Staphylococcus
           epidermidis BCM-HMP0060]
 gi|282876523|ref|ZP_06285389.1| RNA polymerase sigma-B factor [Staphylococcus epidermidis SK135]
 gi|27316133|gb|AAO05267.1|AE016749_213 sigma factor B [Staphylococcus epidermidis ATCC 12228]
 gi|57638245|gb|AAW55033.1| RNA polymerase sigma-37 factor [Staphylococcus epidermidis RP62A]
 gi|251804310|gb|EES56967.1| DNA-directed RNA polymerase sigma subunit FliA [Staphylococcus
           epidermidis BCM-HMP0060]
 gi|281294775|gb|EFA87303.1| RNA polymerase sigma-B factor [Staphylococcus epidermidis SK135]
 gi|329726159|gb|EGG62631.1| RNA polymerase sigma-B factor [Staphylococcus epidermidis VCU144]
 gi|329734176|gb|EGG70494.1| RNA polymerase sigma-B factor [Staphylococcus epidermidis VCU045]
          Length = 256

 Score = 42.4 bits (98), Expect = 0.081,   Method: Compositional matrix adjust.
 Identities = 53/247 (21%), Positives = 117/247 (47%), Gaps = 16/247 (6%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           K+++E+ D  A  +LV  + +L+  +A  Y        ++V  G +GL+ A+ +FD    
Sbjct: 21  KQHQENEDSQAQDKLVKHYRKLIESLAYRYSKGQSHHEDLVQVGMVGLIGAINRFDLSFD 80

Query: 99  FRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
            +   + +  +   ++ Y+  ++WS+         +R+     R+K     +T+   +  
Sbjct: 81  RKFEAFLVPTVIGEIKRYLRDKTWSV------HVPRRIKEIGPRIKKVSDELTNELERSP 134

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQVLI 216
            +  IA++L VS+ EV+     +   +S NAL ++ S +         + D  GQ+    
Sbjct: 135 SISEIAQRLEVSDEEVLEA---MEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQQD--- 188

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           +  +   +R +L R + +L+ RER+I +   ++   ++ +       +S+  V +++  A
Sbjct: 189 DNYDLTEKRMILERILPILSERERQIIQCTFIE--GLSQKETGERIGLSQMHVSRLQRTA 246

Query: 277 FKKVQES 283
            KK+QE+
Sbjct: 247 IKKLQEA 253


>gi|89099055|ref|ZP_01171934.1| sporulation sigma factor SigF [Bacillus sp. NRRL B-14911]
 gi|89086185|gb|EAR65307.1| sporulation sigma factor SigF [Bacillus sp. NRRL B-14911]
          Length = 252

 Score = 42.4 bits (98), Expect = 0.084,   Method: Compositional matrix adjust.
 Identities = 38/171 (22%), Positives = 76/171 (44%), Gaps = 12/171 (7%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A   +V  ++RLV  +   +   G    ++   G IGL+++V KFD     + +
Sbjct: 27  QAGDQGARDTIVQKNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKSVDKFDLSYDVKFS 86

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQ-----KRLFFNLRRLKGHLQAITDNN---- 153
           TY++  I   +Q +I R    VK+  +  +     ++    L +  G +  +T+ +    
Sbjct: 87  TYAVPMIIGEIQRFI-RDDGTVKVSRSLKEMGNKIRKAKDELTKTFGRIPTVTELSAYLE 145

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
           + PE ++ +A++   + S +        GD  +  L    D N  +W D +
Sbjct: 146 IPPEDII-LAQEAGRTPSSIHETVYENDGD-PITLLDQIDDGNDGKWFDQI 194


>gi|167933077|ref|ZP_02520164.1| RNA polymerase, sigma 70 subunit, RpoD family protein [candidate
           division TM7 single-cell isolate TM7b]
          Length = 103

 Score = 42.4 bits (98), Expect = 0.085,   Method: Compositional matrix adjust.
 Identities = 24/51 (47%), Positives = 34/51 (66%), Gaps = 2/51 (3%)

Query: 232 MSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
           +S L+ RE++I + R   EN    TLE +  EF V+RER+RQIEA+A  K+
Sbjct: 39  LSSLSDREQKIIKMRFGLENGKSHTLEEVGQEFAVTRERIRQIEAKALAKL 89


>gi|134300490|ref|YP_001113986.1| sporulation sigma factor SigK [Desulfotomaculum reducens MI-1]
 gi|134053190|gb|ABO51161.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Desulfotomaculum reducens MI-1]
          Length = 232

 Score = 42.4 bits (98), Expect = 0.085,   Method: Compositional matrix adjust.
 Identities = 33/105 (31%), Positives = 50/105 (47%), Gaps = 1/105 (0%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           I+NG   L  YI        L  +EE  L  +    GD  A   L+  +LRLV KIA   
Sbjct: 13  ILNGIAILVSYISSGSLPDPLSPEEERELLLKM-ATGDKLAKTILIERNLRLVAKIANKL 71

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           +  G+   ++   G IGL++ V  FD ++  + +TY+   I+  M
Sbjct: 72  KDSGVDKQDLFQVGVIGLIKGVDTFDIKKARKFSTYAGVCIQNEM 116


>gi|331006368|ref|ZP_08329678.1| RNA polymerase sigma factor for flagellar operon [gamma
           proteobacterium IMCC1989]
 gi|330419828|gb|EGG94184.1| RNA polymerase sigma factor for flagellar operon [gamma
           proteobacterium IMCC1989]
          Length = 251

 Score = 42.4 bits (98), Expect = 0.086,   Method: Compositional matrix adjust.
 Identities = 53/208 (25%), Positives = 92/208 (44%), Gaps = 27/208 (12%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL++A KK+D  RG    TY+   I+ A+ + I R    V      N + 
Sbjct: 51  VDDLIQSGMIGLLEAAKKYDGSRGASFETYAGIRIRGAIVDEI-RKGDWVPRSVHRNSRL 109

Query: 135 LFFNLRRLKGHL-QAITDNNLKPEQVVAI----AKKLNVSESEVISMNCRLAGDESLNAL 189
           +   + +L+  L +   D+ +     V I    A   + S S + S++     DES    
Sbjct: 110 ISNTIHQLEASLGRDAKDSEIAEAMGVDIDEYYAMSRDASSSRLFSIDESFESDES---- 165

Query: 190 INSSDKNSSQWQDWLVYDHDG-QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
           + S++KNS       V  HDG Q Q L         ++ L  ++  L  RE+ +      
Sbjct: 166 VISNEKNSP-----FVDPHDGAQHQAL---------KSSLVTAIDKLPEREKLVLSLYYD 211

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARA 276
           +E  + L+ +     V+  RV QI ++A
Sbjct: 212 EE--LNLKEIGQILGVTESRVSQIHSQA 237


>gi|229492301|ref|ZP_04386108.1| RNA polymerase sigma-F factor [Rhodococcus erythropolis SK121]
 gi|229320710|gb|EEN86524.1| RNA polymerase sigma-F factor [Rhodococcus erythropolis SK121]
          Length = 260

 Score = 42.4 bits (98), Expect = 0.087,   Method: Compositional matrix adjust.
 Identities = 35/148 (23%), Positives = 69/148 (46%), Gaps = 19/148 (12%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           L L   +A  Y+G G P  ++     +GL+QAV++FD ++G    ++++  +   ++++ 
Sbjct: 44  LPLATHVARRYQGRGQPFEDLEQVARVGLIQAVQRFDVDKGSDFLSFAVPTVMGEVRKHF 103

Query: 118 L-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV--- 173
               WS V++  +  ++ L  N R L    Q +     +   V  +AK+L++   EV   
Sbjct: 104 RDHGWS-VRVPRSLQERHLALN-RALTTLSQTLG----RAPTVAELAKELDIEPDEVEQG 157

Query: 174 ---------ISMNCRLAGDESLNALINS 192
                      ++   AGD S   LI++
Sbjct: 158 LTAGNSYRTTPLDTASAGDGSGLTLIDT 185


>gi|82776398|ref|YP_402747.1| flagellar biosynthesis sigma factor [Shigella dysenteriae Sd197]
 gi|81240546|gb|ABB61256.1| alternative sigma factor 28 [Shigella dysenteriae Sd197]
          Length = 239

 Score = 42.4 bits (98), Expect = 0.088,   Method: Compositional matrix adjust.
 Identities = 48/221 (21%), Positives = 102/221 (46%), Gaps = 32/221 (14%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL+ AV+++D  +G    TY++  I+ AM +  LRS   V      N + 
Sbjct: 41  LDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQCIRGAMLDE-LRSRDWVPRSVRRNARE 99

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   + +L+   Q +  N  + E    +A++L +  ++   M            L+++++
Sbjct: 100 VAQAIGQLE---QELGRNATETE----VAERLGIDIADYRQM------------LLDTNN 140

Query: 195 KNSSQWQDW---------LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
                + +W         LV D D Q +  +++    N R  +  ++  L  RE+ +   
Sbjct: 141 SQLFSYDEWREEHGDSIELVTD-DYQRENPLQQLLDSNLRQRVMEAIETLPEREKLVLTL 199

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +E  + L+ + +E EV   RV Q+ ++A K+++  + K
Sbjct: 200 YYQEE--LNLKEIGAELEVGESRVSQLHSQAIKRLRTKLGK 238


>gi|253795563|ref|YP_003038659.1| putative RNA polymerase sigma factor [Candidatus Hodgkinia
           cicadicola Dsem]
 gi|253739871|gb|ACT34206.1| putative RNA polymerase sigma factor [Candidatus Hodgkinia
           cicadicola Dsem]
          Length = 373

 Score = 42.4 bits (98), Expect = 0.089,   Method: Compositional matrix adjust.
 Identities = 29/100 (29%), Positives = 46/100 (46%), Gaps = 7/100 (7%)

Query: 46  DLSAAHR-LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           +L AA R LV S   ++  +   Y         + S G  GLM +  +FD   G+R A Y
Sbjct: 164 NLKAAKRSLVGSSASVIADVIKAYPSCDAQDPALASAGRDGLMASANRFDLVSGYRFAAY 223

Query: 105 SMWWIKAAMQEYIL---RSWSLV---KIGTTANQKRLFFN 138
           S WW+K  +  ++L   + W+     ++   A  KRL  +
Sbjct: 224 SKWWVKHNVIAHVLAGAKGWAAASAKQLAGAAKLKRLSLD 263


>gi|319399556|gb|EFV87811.1| RNA polymerase sigma-B factor [Staphylococcus epidermidis FRI909]
          Length = 256

 Score = 42.4 bits (98), Expect = 0.089,   Method: Compositional matrix adjust.
 Identities = 53/247 (21%), Positives = 117/247 (47%), Gaps = 16/247 (6%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           K+++E+ D  A  +LV  + +L+  +A  Y        ++V  G +GL+ A+ +FD    
Sbjct: 21  KQHQENEDSLAQDKLVKHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDLSFD 80

Query: 99  FRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
            +   + +  +   ++ Y+  ++WS+         +R+     R+K     +T+   +  
Sbjct: 81  RKFEAFLVPTVIGEIKRYLRDKTWSV------HVPRRIKEIGPRIKKVSDELTNELERSP 134

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQVLI 216
            +  IA++L VS+ EV+     +   +S NAL ++ S +         + D  GQ+    
Sbjct: 135 SISEIAQRLEVSDEEVLEA---MEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQQD--- 188

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           +  +   +R +L R + +L+ RER+I +   ++   ++ +       +S+  V +++  A
Sbjct: 189 DNYDLTEKRMILERILPILSERERQIIQCTFIE--GLSQKETGERIGLSQMHVSRLQRTA 246

Query: 277 FKKVQES 283
            KK+QE+
Sbjct: 247 IKKLQEA 253


>gi|288555607|ref|YP_003427542.1| sporulation sigma factor SigK [Bacillus pseudofirmus OF4]
 gi|288546767|gb|ADC50650.1| sporulation sigma factor SigK [Bacillus pseudofirmus OF4]
          Length = 235

 Score = 42.4 bits (98), Expect = 0.092,   Method: Compositional matrix adjust.
 Identities = 37/142 (26%), Positives = 66/142 (46%), Gaps = 11/142 (7%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A + L+  +LRLV  I   +        +++S G IGL++A++ +   +G +LA
Sbjct: 44  QEGDAEARNLLIEHNLRLVAHIVKKFENTREDTEDLISIGTIGLIKAIESYSDGKGTKLA 103

Query: 103 TYSMWWIKAAMQEYILRSWSLVK--------IGTT--ANQKRLFFNLRRLKGHLQAITDN 152
           TY+   I+  +  + LR+   VK        IGT    N+  L   L+     +  +   
Sbjct: 104 TYAARCIENEILMH-LRALKKVKKDVSLHDPIGTDKEGNEISLIDVLQEDADDIVDVIQT 162

Query: 153 NLKPEQVVAIAKKLNVSESEVI 174
            ++ +Q+      L+  E EVI
Sbjct: 163 KMEKKQIYEYIHVLDEREKEVI 184


>gi|254519896|ref|ZP_05131952.1| sporulation sigma factor SigF [Clostridium sp. 7_2_43FAA]
 gi|226913645|gb|EEH98846.1| sporulation sigma factor SigF [Clostridium sp. 7_2_43FAA]
          Length = 251

 Score = 42.4 bits (98), Expect = 0.092,   Method: Compositional matrix adjust.
 Identities = 54/249 (21%), Positives = 119/249 (47%), Gaps = 32/249 (12%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           G+  A ++++  +L LV  I+  +   G    ++   G+IGL++A+  FD +   + +TY
Sbjct: 26  GNQDAMNKVIEMNLPLVSSISKKFLNRGYDYEDIFQIGSIGLVKAINNFDDKFNVKFSTY 85

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           ++  I   ++ +I R   ++K+           N++ L   L      +   EQ   + K
Sbjct: 86  AVPMIIGEIKRFI-RDDGIIKVSR---------NVKSLARKL------HFDKEQ---LTK 126

Query: 165 KLNVSES-EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK--EER 221
           KL+   + E +S    +  +E L A+ +S+   S Q+    ++  DG   +LI+K  E+ 
Sbjct: 127 KLDREPTIEELSQFSGVDKEEILFAIESSA---SMQYLYDTIHQDDGAPVLLIDKLSEKG 183

Query: 222 KNRRNMLTR-----SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           ++  +M+ R     ++  L+ + R+I   R  ++   T   ++    +S+ +V +IE + 
Sbjct: 184 EDDSDMINRIALKEALRSLDSKARQIIMLRYFKDK--TQVQVAKMLGISQVQVSRIEKKV 241

Query: 277 FKKVQESIQ 285
              +++ +Q
Sbjct: 242 LVLMKQKLQ 250


>gi|302874980|ref|YP_003843613.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium cellulovorans
           743B]
 gi|307690403|ref|ZP_07632849.1| sporulation sigma factor SigF [Clostridium cellulovorans 743B]
 gi|302577837|gb|ADL51849.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium cellulovorans
           743B]
          Length = 265

 Score = 42.4 bits (98), Expect = 0.092,   Method: Compositional matrix adjust.
 Identities = 42/190 (22%), Positives = 89/190 (46%), Gaps = 27/190 (14%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A + L+  ++ LV  I+  +   G    ++   G +GL++AV  F+ +   + +
Sbjct: 38  QGGDNEALNDLIKKNMPLVAAISKKFLNRGYEYDDIFQIGCMGLIKAVNNFNTDFNVKFS 97

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTT--ANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
           TY++  I   ++ + LR   ++KI  +  A  K+L ++   L   L      N +P  + 
Sbjct: 98  TYAVPMIMGEIKRF-LRDDGIIKISRSIKATAKKLHYDRENLTNIL------NREP-TIE 149

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK-- 218
            ++K   +S+ ++I M    +G              S Q+   +++  DG   +LI+K  
Sbjct: 150 ELSKYSGISKDDII-MATESSG--------------SLQYLYDVIHQDDGSPVLLIDKIS 194

Query: 219 EERKNRRNML 228
           E  ++ ++M+
Sbjct: 195 ETGEDDKDMI 204


>gi|126215794|gb|ABN81017.1| putative sigma factor sigma 70 type group 3 [Rhodococcus opacus]
          Length = 139

 Score = 42.4 bits (98), Expect = 0.092,   Method: Compositional matrix adjust.
 Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++T  L L   IA  + G G    ++     +GL++AV +FDP+RGF   +Y++  I   
Sbjct: 33  VITRCLPLADHIARRFGGRGEAHEDLRQVARLGLVKAVDRFDPDRGFDFVSYAVPTIMGE 92

Query: 113 MQEYILRS-WSL 123
           ++ Y   + WS+
Sbjct: 93  VRRYFRDTGWSM 104


>gi|229543947|ref|ZP_04433006.1| RNA polymerase, sigma 28 subunit, SigF [Bacillus coagulans 36D1]
 gi|229325086|gb|EEN90762.1| RNA polymerase, sigma 28 subunit, SigF [Bacillus coagulans 36D1]
          Length = 252

 Score = 42.4 bits (98), Expect = 0.092,   Method: Compositional matrix adjust.
 Identities = 47/183 (25%), Positives = 80/183 (43%), Gaps = 12/183 (6%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K EE     R  + GD  A   +V  ++RLV  +   +   G    ++   G IGL+++V
Sbjct: 15  KDEEVKNLIRRSQEGDQGARDLIVEKNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKSV 74

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG----TTANQKR-----LFFNLRR 141
            KFD     + +TY++  I   +Q + LR    VK+      T N+ R     L   L R
Sbjct: 75  DKFDLSYDVKFSTYAVPMIIGEIQRF-LRDDGTVKVSRSLKETGNRIRKTRDELTKKLGR 133

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
                +  ++  +  E+VV +A++   + S +        GD  +  L   SD+N  +W 
Sbjct: 134 SPTVHEIASELGMPVEEVV-MAQEAGKAPSSIHETVYENDGD-PITLLDQISDQNDQKWF 191

Query: 202 DWL 204
           D +
Sbjct: 192 DQI 194


>gi|46581631|ref|YP_012439.1| RNA polymerase sigma factor for flagellar operon FliA
           [Desulfovibrio vulgaris str. Hildenborough]
 gi|120601210|ref|YP_965610.1| FliA/WhiG family RNA polymerase sigma factor [Desulfovibrio
           vulgaris DP4]
 gi|46451054|gb|AAS97699.1| RNA polymerase sigma factor for flagellar operon FliA
           [Desulfovibrio vulgaris str. Hildenborough]
 gi|120561439|gb|ABM27183.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Desulfovibrio
           vulgaris DP4]
 gi|311235273|gb|ADP88127.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfovibrio vulgaris RCH1]
          Length = 265

 Score = 42.4 bits (98), Expect = 0.092,   Method: Compositional matrix adjust.
 Identities = 18/45 (40%), Positives = 29/45 (64%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           + E++S G +GLM+A+ KF P+ G R  TY+   I+ AM + + R
Sbjct: 64  LGELISAGTLGLMEALGKFKPQLGIRFETYAESRIRGAMLDELRR 108


>gi|295092920|emb|CBK82011.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Coprococcus sp.
           ART55/1]
          Length = 206

 Score = 42.4 bits (98), Expect = 0.094,   Method: Compositional matrix adjust.
 Identities = 21/66 (31%), Positives = 38/66 (57%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD +A   L+  +LRLV  I+  Y        +++S G IGL++A+  + P++G +L+ Y
Sbjct: 23  GDKAARSILIEYNLRLVAHISRKYNSAVRDPEDLLSIGTIGLIKAIDSYKPDKGCKLSGY 82

Query: 105 SMWWIK 110
           +   I+
Sbjct: 83  AAKCIE 88


>gi|289422613|ref|ZP_06424455.1| RNA polymerase sigma factor, sigma-70 family [Peptostreptococcus
           anaerobius 653-L]
 gi|289156964|gb|EFD05587.1| RNA polymerase sigma factor, sigma-70 family [Peptostreptococcus
           anaerobius 653-L]
          Length = 289

 Score = 42.4 bits (98), Expect = 0.095,   Method: Compositional matrix adjust.
 Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 6/78 (7%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIA------MGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           + GDL A ++++    + V  I       M Y+  GL   ++   G IGL+ AVKKFD  
Sbjct: 50  KEGDLVALNKVIEKKSKYVKGIIKNDYEIMAYKKRGLDQEDLFQSGMIGLLNAVKKFDFR 109

Query: 97  RGFRLATYSMWWIKAAMQ 114
            G +  TY    +K +++
Sbjct: 110 DGIKFDTYLAHNVKYSIK 127


>gi|309789348|ref|ZP_07683938.1| RNA polymerase sigma factor for flagellar operon [Shigella
           dysenteriae 1617]
 gi|308922742|gb|EFP68259.1| RNA polymerase sigma factor for flagellar operon [Shigella
           dysenteriae 1617]
          Length = 229

 Score = 42.4 bits (98), Expect = 0.095,   Method: Compositional matrix adjust.
 Identities = 52/238 (21%), Positives = 109/238 (45%), Gaps = 37/238 (15%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRL V++        + + +++  G IGL+ AV+++D  +G    TY++  I+ AM +  
Sbjct: 19  LRLQVRLPAS-----VELDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQCIRGAMLDE- 72

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           LRS   V      N + +   + +L+   Q +  N  + E    +A++L +  ++   M 
Sbjct: 73  LRSRDWVPRSVRRNAREVAQAIGQLE---QELGRNATETE----VAERLGIDIADYRQM- 124

Query: 178 CRLAGDESLNALINSSDKNSSQWQDW---------LVYDHDGQEQVLIEKEERKNRRNML 228
                      L+++++     + +W         LV D D Q +  +++    N R  +
Sbjct: 125 -----------LLDTNNSQLFSYDEWREEHGDSIELVTD-DYQRENPLQQLLDSNLRQRV 172

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             ++  L  RE+ +      +E  + L+ + +E EV   RV Q+ ++A K+++  + K
Sbjct: 173 MEAIETLPEREKLVLTLYYQEE--LNLKEIGAELEVGESRVSQLHSQAIKRLRTKLGK 228


>gi|225019367|ref|ZP_03708559.1| hypothetical protein CLOSTMETH_03320 [Clostridium methylpentosum
           DSM 5476]
 gi|224947998|gb|EEG29207.1| hypothetical protein CLOSTMETH_03320 [Clostridium methylpentosum
           DSM 5476]
          Length = 221

 Score = 42.4 bits (98), Expect = 0.095,   Method: Compositional matrix adjust.
 Identities = 22/74 (29%), Positives = 39/74 (52%), Gaps = 1/74 (1%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            V  +L LV   A  + G G+   ++ S G +GL++A   FD +RG + +TY++  I   
Sbjct: 11  FVKQNLGLVHSCAHRFTGKGIEYDDLFSAGCMGLVKATDAFDEDRGVKFSTYAVPVILGE 70

Query: 113 MQEYILRSWSLVKI 126
           ++  + R    VK+
Sbjct: 71  IRR-LFRDGGSVKV 83


>gi|28899006|ref|NP_798611.1| flagellar biosynthesis sigma factor [Vibrio parahaemolyticus RIMD
           2210633]
 gi|153836996|ref|ZP_01989663.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus AQ3810]
 gi|260365248|ref|ZP_05777805.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus K5030]
 gi|260878798|ref|ZP_05891153.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus AN-5034]
 gi|260899951|ref|ZP_05908346.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus AQ4037]
 gi|28807225|dbj|BAC60495.1| flagellar-specific RNA polymerase sigma factor FliA [Vibrio
           parahaemolyticus RIMD 2210633]
 gi|149749769|gb|EDM60514.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus AQ3810]
 gi|308094185|gb|EFO43880.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus AN-5034]
 gi|308107226|gb|EFO44766.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus AQ4037]
 gi|308115412|gb|EFO52952.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus K5030]
 gi|328474457|gb|EGF45262.1| flagellar biosynthesis sigma factor [Vibrio parahaemolyticus 10329]
          Length = 244

 Score = 42.4 bits (98), Expect = 0.095,   Method: Compositional matrix adjust.
 Identities = 56/250 (22%), Positives = 103/250 (41%), Gaps = 27/250 (10%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFD 94
           A  Y +HG  ++    +  +  LV +IA    G   P   + +++  G IGL++A + +D
Sbjct: 4   AITYDQHGKFNSQQAFIERYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLIEAQQNYD 63

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +G    TY+   I+ AM +  +R    V      N + +   +  L+G    +  +  
Sbjct: 64  GSKGASFETYAGIRIRGAMLDD-MRKGDWVPRSVHKNNREINQAVAELEG---VLNRDPT 119

Query: 155 KPEQVVAIAKKLNVSESEVISMNC-RLAGDESL---NALINSSDKNSSQWQDWLVYDHDG 210
             E    +   L+   S +  +NC RL G E L   + +I+ +D+         V D   
Sbjct: 120 DSEVAAHLGMSLDQYHSALTDINCSRLVGIEDLGVSDDVISPADETDDSNPFKGVAD--- 176

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                      ++ R  L  S+  L  RE  +      +E  + L+ +     VS  RV 
Sbjct: 177 -----------ESFRKALVESIKQLPEREALVLSLYYDEE--LNLKEIGDVLGVSESRVS 223

Query: 271 QIEARAFKKV 280
           QI ++A +++
Sbjct: 224 QILSQAMQRL 233


>gi|309388843|gb|ADO76723.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Halanaerobium praevalens DSM 2228]
          Length = 251

 Score = 42.0 bits (97), Expect = 0.097,   Method: Compositional matrix adjust.
 Identities = 63/251 (25%), Positives = 119/251 (47%), Gaps = 26/251 (10%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKK 92
           L K+Y+   +  A   ++  +L LV + A+G     LP      ++ S G IGL++A++ 
Sbjct: 7   LWKKYKVDDNQQAREEIILKNLGLV-RYAVGRINIMLPEHIEDQDLESYGIIGLIEAIEN 65

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RG + +T+++  IK  + +Y LRS    K     N +R    +   K   +A T  
Sbjct: 66  FNYQRGVKFSTFALPRIKGEIYDY-LRS----KDWLPDNMRRELKKVDEQKRSYKAKTGK 120

Query: 153 NLKPEQVVAIAKKLNVSES--EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
             KP+Q   ++K   + +S  E I  + +LA     N +  S D + ++  + +  D   
Sbjct: 121 --KPDQ-KELSKLTGIKKSRLEKIERHSQLA-----NWISLSHDFDGTELIELVAADFKQ 172

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
               L EKE      + L + + +L+ +E+ +      +E  +T   ++   E+S  RV 
Sbjct: 173 AVDRLTEKEA----VDFLAKKIDLLSEKEKLVLSLYYYEE--LTQVEIAEIIELSAARVS 226

Query: 271 QIEARAFKKVQ 281
           QI  RA ++++
Sbjct: 227 QIHGRAIRRLR 237


>gi|304407606|ref|ZP_07389258.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
 gi|304343557|gb|EFM09399.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
          Length = 232

 Score = 42.0 bits (97), Expect = 0.099,   Method: Compositional matrix adjust.
 Identities = 20/66 (30%), Positives = 39/66 (59%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           G+  + + L+  +LRLV  I   +   G  + +++S G IGL++A++ F   +G +LAT+
Sbjct: 45  GNQHSRNMLIEHNLRLVAHIVKKFDNTGEDLEDLISIGTIGLIKAIESFQVGKGTKLATF 104

Query: 105 SMWWIK 110
           +   I+
Sbjct: 105 AARCIE 110


>gi|315652062|ref|ZP_07905063.1| hypothetical protein HMPREF0381_2057 [Eubacterium saburreum DSM
          3986]
 gi|315485709|gb|EFU76090.1| hypothetical protein HMPREF0381_2057 [Eubacterium saburreum DSM
          3986]
          Length = 171

 Score = 42.0 bits (97), Expect = 0.10,   Method: Compositional matrix adjust.
 Identities = 23/78 (29%), Positives = 44/78 (56%), Gaps = 1/78 (1%)

Query: 16 LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
          L  Y+ +++ I  ++++E   L      HGD SA +RL+  H+   VK+   + G G  +
Sbjct: 7  LEMYLEDMKAIKEIDEKEIKELTDALL-HGDESARNRLIEGHMMYAVKLIKPFIGCGEEM 65

Query: 76 SEVVSEGNIGLMQAVKKF 93
          S+++SE ++ L  AV ++
Sbjct: 66 SDLISESHLALTMAVMEY 83


>gi|157363480|ref|YP_001470247.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermotoga lettingae
           TMO]
 gi|157314084|gb|ABV33183.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermotoga lettingae
           TMO]
          Length = 236

 Score = 42.0 bits (97), Expect = 0.10,   Method: Compositional matrix adjust.
 Identities = 54/236 (22%), Positives = 107/236 (45%), Gaps = 37/236 (15%)

Query: 61  VVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           V +IAM    + LP    + +++ EG + L+ A++++DP++G  + ++ +  IK AM +Y
Sbjct: 17  VKRIAMDLL-HTLPKNVEVDDLIQEGVLALLSAIRRYDPKKGVSMYSFVVKRIKGAMYDY 75

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
            LR    +      N K +   +  L+ HL        K   +  IA    +S +EV   
Sbjct: 76  -LRKIDWMPRNLRKNVKEVEKAIHELENHLN-------KHPSIEEIALHTGLSTNEV--- 124

Query: 177 NCRLAGDESLNALINSSD----KNSSQWQDWLVYDHDGQE----QVLIEKEERKNRRNML 228
             + A DE++   +   D    +    + D +  D +  E    ++++EK         +
Sbjct: 125 --KRALDETVRKQLLRLDEFIYEGLDSFSDIIKADDEPSENAFREIILEK---------V 173

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             ++  L+ RE+ +   R   E  ++L+ + +   VS  RV QI + +  K++  I
Sbjct: 174 AEAIRTLSKREQLVLSLRF--EQDLSLKEIGTVIGVSESRVSQILSSSLIKIKRYI 227


>gi|294500913|ref|YP_003564613.1| RNA polymerase sigma-D factor [Bacillus megaterium QM B1551]
 gi|294350850|gb|ADE71179.1| RNA polymerase sigma-D factor [Bacillus megaterium QM B1551]
          Length = 253

 Score = 42.0 bits (97), Expect = 0.10,   Method: Compositional matrix adjust.
 Identities = 64/266 (24%), Positives = 127/266 (47%), Gaps = 34/266 (12%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQ 88
           EE+ + + + E  D  A + LV  ++ LV    +     GLP +    E+ S G IGL  
Sbjct: 8   EEHKIWQEWIETRDSHAGNMLVKKYMPLV-NYHVQRISVGLPKNIHKEELRSLGLIGLYD 66

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           A++KFD  R  +  TY+ + I+ A+ + + +  W    +  +A +K      +R++   +
Sbjct: 67  ALEKFDYGRDLKFDTYASFRIRGAIIDGLRKEDW----LSRSAREK-----TKRIEQATE 117

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVI-SMNCRLAGDESLNALINSSDKNSSQWQD---- 202
           A+    L+      +AK++ ++E++V+ +MN      E   A + S ++   +++D    
Sbjct: 118 ALEQRYLRRVAPSEVAKEVGMTEADVVHTMN------EGFLANVLSMEEQPKEYEDGEQK 171

Query: 203 WLVYDHDGQEQVLIEKEERKN--RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
           + + D    E+ L  +EE  N  R   L   +  LN +E+ +      +E  +T   ++ 
Sbjct: 172 YTIKD----EKTLSPEEELINDERYQELAEVIEQLNEKEQLVVSLFYKEE--LTFTEIAQ 225

Query: 261 EFEVSRERVRQIEARAFKKVQESIQK 286
              +S  R+ QI ++A  K++ S+ K
Sbjct: 226 LLGLSTSRISQIHSKALFKMRTSLSK 251


>gi|257438785|ref|ZP_05614540.1| RNA polymerase sigma-G factor [Faecalibacterium prausnitzii A2-165]
 gi|257198753|gb|EEU97037.1| RNA polymerase sigma-G factor [Faecalibacterium prausnitzii A2-165]
          Length = 254

 Score = 42.0 bits (97), Expect = 0.10,   Method: Compositional matrix adjust.
 Identities = 54/233 (23%), Positives = 104/233 (44%), Gaps = 29/233 (12%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++  +LRLV+ +   +   G  + ++   G IGL++A+  FDP +  R +TY +  I   
Sbjct: 41  MIEGNLRLVLSVVQRFAQRGENLDDLFQVGCIGLIKAIDNFDPAQPVRFSTYGVPMIIGE 100

Query: 113 MQEYI-----LR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           ++ ++     LR S SL      A Q R            +A+     +   V  +A++ 
Sbjct: 101 IRRFLRDNNALRVSRSLRDAAYKAMQAR------------EALEKQLGREPTVDEVARQA 148

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +S  EV +    +    SL   +  +D   + +    V D D ++  +   E R+    
Sbjct: 149 GLSRREVNAALESVVEPISLEEPL-YTDGGDAMYVIDQVRDPDSEDSWISGLEFRQ---- 203

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
               +++ L PRE+RI E R L+    T   ++ E  +S+ +V ++E  A ++
Sbjct: 204 ----TVAGLTPREKRIMELRYLKGE--TQMEVAREIGISQAQVSRLEKAALEQ 250


>gi|331092383|ref|ZP_08341209.1| RNA polymerase sigma-F factor [Lachnospiraceae bacterium 2_1_46FAA]
 gi|330401407|gb|EGG80993.1| RNA polymerase sigma-F factor [Lachnospiraceae bacterium 2_1_46FAA]
          Length = 237

 Score = 42.0 bits (97), Expect = 0.10,   Method: Compositional matrix adjust.
 Identities = 27/94 (28%), Positives = 50/94 (53%), Gaps = 2/94 (2%)

Query: 34  EYVLAKRYREH-GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           E+ +A   R H GD  A  +LV  ++ LV  +   + G G    ++   G+IGL++A+ K
Sbjct: 2   EHTIALIKRSHKGDEKARTQLVEENVGLVWCVVKRFYGRGTEPEDLFQIGSIGLLKAIDK 61

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           FD     + +TY++  I   ++ + LR   ++K+
Sbjct: 62  FDLSYDVKFSTYAVPMISGEIKRF-LRDDGMIKV 94


>gi|225389367|ref|ZP_03759091.1| hypothetical protein CLOSTASPAR_03114 [Clostridium asparagiforme
          DSM 15981]
 gi|225044546|gb|EEG54792.1| hypothetical protein CLOSTASPAR_03114 [Clostridium asparagiforme
          DSM 15981]
          Length = 384

 Score = 42.0 bits (97), Expect = 0.10,   Method: Compositional matrix adjust.
 Identities = 25/76 (32%), Positives = 43/76 (56%), Gaps = 1/76 (1%)

Query: 19 YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
          Y+ E+ +I  +  +EE  + +R    G++ A  RLV  +L+ V+ IA  Y G  LP++++
Sbjct: 9  YLEEMGQIAPMSAEEEARILERTAA-GEVQARKRLVEGNLQKVLSIAKEYEGSRLPMADI 67

Query: 79 VSEGNIGLMQAVKKFD 94
          V E N  L  A  ++D
Sbjct: 68 VQEANTALTLAAVEYD 83


>gi|168206182|ref|ZP_02632187.1| sigma factor [Clostridium perfringens E str. JGS1987]
 gi|170662325|gb|EDT15008.1| sigma factor [Clostridium perfringens E str. JGS1987]
          Length = 227

 Score = 42.0 bits (97), Expect = 0.10,   Method: Compositional matrix adjust.
 Identities = 21/80 (26%), Positives = 41/80 (51%), Gaps = 5/80 (6%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPE--R 97
           + GD  A  +L+ ++ +L+ KIA  +       +   +++ EG IG + A  K+D E  +
Sbjct: 11  QQGDKRALDKLLENNDKLIYKIASKFYSEKINAIEFDDLLQEGRIGFILACNKYDCEYIK 70

Query: 98  GFRLATYSMWWIKAAMQEYI 117
             +  TY+ +WI   +  +I
Sbjct: 71  KTKFITYAFYWIYQKIHRFI 90


>gi|296164736|ref|ZP_06847300.1| RNA polymerase sigma-F factor [Mycobacterium parascrofulaceum ATCC
           BAA-614]
 gi|295899907|gb|EFG79349.1| RNA polymerase sigma-F factor [Mycobacterium parascrofulaceum ATCC
           BAA-614]
          Length = 288

 Score = 42.0 bits (97), Expect = 0.10,   Method: Compositional matrix adjust.
 Identities = 56/243 (23%), Positives = 101/243 (41%), Gaps = 32/243 (13%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R+V   L L   +A  +   G  + ++V    +GLM AV +FDP++G     +++  +  
Sbjct: 67  RIVARCLPLADHVASHFARRGEGLDDLVQVARLGLMNAVNRFDPDKGPSFIGFAVPTMMG 126

Query: 112 AMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHL-----QAITDNNLKPEQVVAIAKK 165
            ++ Y    SW +         + L   + R  G L     +A T   L        ++ 
Sbjct: 127 EVRRYFRDYSWGM---RVPRRLRELHVQISRTTGDLAQKLGRAPTAGEL--------SRA 175

Query: 166 LNVSESEVISMNCRLAGD----ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           L V   E++   C +AGD    +SL+A + +    + +    LV D  G     IE    
Sbjct: 176 LEVPHEEIV--ECLVAGDAYRLDSLDAPMGTDSSGTPR----LVADAVGGIDPQIEH--- 226

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              R  L   ++ L  RER +   R  +   +T   ++    VS+ +V +I A   + ++
Sbjct: 227 ITNREALRVLVAALPEREREVLRMRFFES--MTQSQIAERIGVSQMQVSRILAGTLRCLR 284

Query: 282 ESI 284
           E +
Sbjct: 285 EQL 287


>gi|192362157|ref|YP_001982606.1| FliA [Cellvibrio japonicus Ueda107]
 gi|190688322|gb|ACE86000.1| FliA [Cellvibrio japonicus Ueda107]
          Length = 247

 Score = 42.0 bits (97), Expect = 0.10,   Method: Compositional matrix adjust.
 Identities = 45/211 (21%), Positives = 92/211 (43%), Gaps = 16/211 (7%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS-WSLVKIGTTANQK 133
           + +++  G IGL++A +K+D  RG    TY+   I+ A+ + + R  W+          +
Sbjct: 46  VEDLIQAGMIGLIEASQKYDASRGASFETYAGIRIRGAIVDEMRRGDWA---------PR 96

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            +  N RR+   + A+     +      IA +L+V   E   M      D S + L +  
Sbjct: 97  SVHRNGRRISQAMAAVEARTGRDASDTEIAAELDVGLDEYYQM----LQDSSGSRLFSYE 152

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           +    +  +    DH       +E  +R   +  L  ++++L  RER +      +E  +
Sbjct: 153 ETFGEEDSNIDGSDHSSVFASPLESIQRDGLKRALADAIALLPERERLVLALYYDEE--L 210

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L+ +     VS  R+ QI ++A  ++++ +
Sbjct: 211 NLKEIGLVLGVSESRISQIHSQAAARLRQKM 241


>gi|6952813|gb|AAF32414.1| flagellar-specific RNA polymerase sigma factor FliA [Vibrio
           parahaemolyticus]
          Length = 245

 Score = 42.0 bits (97), Expect = 0.10,   Method: Compositional matrix adjust.
 Identities = 56/247 (22%), Positives = 102/247 (41%), Gaps = 27/247 (10%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPER 97
           Y +HG  ++    +  +  LV +IA    G   P   + +++  G IGL++A + +D  +
Sbjct: 8   YDQHGKFNSQQAFIERYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLIEAQQNYDGSK 67

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G    TY+   I+ AM +  +R    V      N + +   +  L+G L     +    E
Sbjct: 68  GASFETYAGIRIRGAMLDD-MRKGDWVPRSVHKNNREINQAVAELEGVLNR---DPTDSE 123

Query: 158 QVVAIAKKLNVSESEVISMNC-RLAGDESL---NALINSSDKNSSQWQDWLVYDHDGQEQ 213
               +   L+   S +  +NC RL G E L   + +I+ +D+         V D      
Sbjct: 124 VAAHLGMSLDQYHSALTDINCSRLVGIEDLGVSDDVISPADETDDSNPFKGVAD------ 177

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
                   ++ R  L  S+  L  RE  +      +E  + L+ +     VS  RV QI 
Sbjct: 178 --------ESFRKALVESIKQLPEREALVLSLYYDEE--LNLKEIGDVLGVSESRVSQIL 227

Query: 274 ARAFKKV 280
           ++A +++
Sbjct: 228 SQAMQRL 234


>gi|15895573|ref|NP_348922.1| sporulation sigma factor SigF [Clostridium acetobutylicum ATCC 824]
 gi|15025312|gb|AAK80262.1|AE007731_7 Sporulation-specific sigma factor F [Clostridium acetobutylicum
           ATCC 824]
 gi|325509722|gb|ADZ21358.1| sporulation sigma factor SigF [Clostridium acetobutylicum EA 2018]
          Length = 252

 Score = 42.0 bits (97), Expect = 0.10,   Method: Compositional matrix adjust.
 Identities = 47/251 (18%), Positives = 113/251 (45%), Gaps = 34/251 (13%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           G+  A ++++ ++L LV  I+  +   G    ++   G +GL++AV  F+ +   + +TY
Sbjct: 27  GNKEALNKIIENNLPLVSAISRKFLNRGYEYDDIFQIGCMGLVKAVNNFNSDYKVKFSTY 86

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTT--ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           ++  I   ++ + LR   ++K+  +  +  ++L ++  +L   L      N +P      
Sbjct: 87  AVPMIMGEIKRF-LRDDGIIKVSRSVKSTARQLHYDREKLVKEL------NREP------ 133

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK---- 218
                      I    + +G +    ++ +    S Q+   +V+  DG   +LI+K    
Sbjct: 134 ----------TIDELSKFSGIDKEEIIMATESTTSMQYLYDVVHQDDGSPVLLIDKLSDP 183

Query: 219 ---EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
              +     + +L + +  L+ + ++I   R  ++   T   +++   +S+ +V +IE R
Sbjct: 184 YSEDSDVIDKIVLKQIIKSLDNKSKQIIMLRYFKDKTQT--QVANMLGISQVQVSRIEKR 241

Query: 276 AFKKVQESIQK 286
             K ++E + K
Sbjct: 242 ILKAIREKLTK 252


>gi|300717210|ref|YP_003742013.1| RNA polymerase sigma factor for flagellar operon [Erwinia
           billingiae Eb661]
 gi|299063046|emb|CAX60166.1| RNA polymerase sigma factor for flagellar operon [Erwinia
           billingiae Eb661]
          Length = 240

 Score = 42.0 bits (97), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 46/210 (21%), Positives = 93/210 (44%), Gaps = 22/210 (10%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTANQK 133
           + +++  G IGL+ AV+++D  +G    TY++  I+ AM  E   R W+          +
Sbjct: 41  LDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDWA---------PR 91

Query: 134 RLFFNLRRLKGHLQAITDN--NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
            +  N R + G +  +  +      EQ VA +  +++ E   I ++         N+ + 
Sbjct: 92  SVRRNAREVAGAMHKVEQSLGRTATEQEVAASLDVSLQEYRQILLDTN-------NSQLF 144

Query: 192 SSDKNSSQWQDWLVYDHDGQEQV-LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           S D+   +  D      DG E+   + +    N R  +  ++  L  RE+ +      +E
Sbjct: 145 SYDEFREEHGDTAELVTDGHEEANPLHQLMEGNLRERVIEAIEALPDREKMVLTLYYQEE 204

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             + L+ + +  EV   RV Q+ ++A K++
Sbjct: 205 --LNLKEIGAVLEVGESRVSQLHSQAIKRL 232


>gi|290962881|ref|YP_003494063.1| sigma factor [Streptomyces scabiei 87.22]
 gi|260652407|emb|CBG75540.1| putative sigma factor [Streptomyces scabiei 87.22]
          Length = 275

 Score = 42.0 bits (97), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 54/234 (23%), Positives = 108/234 (46%), Gaps = 15/234 (6%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +L LV   A  +RG    + ++V  G IGL++A+ +F+  R     T+++ +I   
Sbjct: 49  LIEMNLSLVRYAASRFRGREDSLEDIVQVGTIGLIKAIDRFELSREVEFTTFAVPYIVGE 108

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           ++ +   +   V +     + R+   L R    LQ+         +   +++ +++SE E
Sbjct: 109 IKRFFRDTSWAVHVPRRLQEARV--ELARATDELQSRLGRMPTTRE---LSELMSLSEEE 163

Query: 173 VISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           VI       G    SL+A + S   +     D ++ D  G+E   ++  E  +    L  
Sbjct: 164 VIEARKASNGYNTSSLDAALTSDGGDDG---DAVLGDLIGEEDHALQLVEDFHS---LAP 217

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            ++ L+ RERRI   R ++E   T   ++ E  VS+  V ++ +R  K+++  +
Sbjct: 218 LIAQLDDRERRIIHLRFVEE--WTQSQIAEELGVSQMHVSRLISRIIKRLRTGL 269


>gi|85859187|ref|YP_461389.1| RNA polymerase flagellar sigma factor [Syntrophus aciditrophicus
           SB]
 gi|85722278|gb|ABC77221.1| RNA polymerase flagellar sigma factor [Syntrophus aciditrophicus
           SB]
          Length = 261

 Score = 42.0 bits (97), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 54/236 (22%), Positives = 101/236 (42%), Gaps = 29/236 (12%)

Query: 62  VKIAMGYRGYGLPIS-----EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA-MQE 115
           VK  +G     +PI      +++  G IGLM A++K+D  R  R  TY+   I+ A + E
Sbjct: 41  VKAVVGRMASKIPIDAGDKEDLIHVGIIGLMSAIEKYDTRRNVRFETYAGIRIRGAVLDE 100

Query: 116 YILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
              R W  V     +    +   +  L+  L+   D++        I++ L +S  E   
Sbjct: 101 LRARDW--VPRAVRSRDNEITKAISSLQKILRRAPDDH-------EISEYLGLSIEEYF- 150

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYD-----HDGQEQVLIEKEERKNRRNMLTR 230
              +L  D    +LI+S D        +   D       G    LI   E    R  L +
Sbjct: 151 ---KLLDDSRCISLISSEDLPGDYLDRYSCSDVIRAVEQGSALDLITDHE---FRMQLKK 204

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +M +L  +ER +      +E  +T++ +    +++  RV Q+ ++A  +++ +++K
Sbjct: 205 AMELLPDKERLVLTLYYYEE--LTMKEIGKVLDLTESRVCQLHSQAIFRLRAAVKK 258


>gi|302392368|ref|YP_003828188.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Acetohalobium arabaticum DSM 5501]
 gi|302204445|gb|ADL13123.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Acetohalobium arabaticum DSM 5501]
          Length = 260

 Score = 42.0 bits (97), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 55/259 (21%), Positives = 110/259 (42%), Gaps = 28/259 (10%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPE 96
           ++EH +  A   L+   + LV  +A       LP      ++ + G IGL+ A+++FD  
Sbjct: 16  FKEHNNQQAKEELMLRFMPLVKYVA-NRVAINLPDKFEFEDLQNYGIIGLIDAIERFDHR 74

Query: 97  RGFRLATYSMWWIKAAMQEYILR-SWSLVKIGTTANQ-----KRLFFNLRRLKGHLQAIT 150
           RG + +TY++  I+ ++ + + R  W    I   A Q       L   L RL       T
Sbjct: 75  RGMKFSTYAISRIRGSIIDQLRRLDWVPTTIRRKAKQVAEINSELANKLGRLP------T 128

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
           D  ++ E        L+  E   +     +  + SL++ INS   +     + +  +   
Sbjct: 129 DEEIRQEL------DLDSDEYSQLMSEINIPQETSLDSFINSRQADGVTLIEVIADEDAA 182

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
           + +     EE K    +L  ++  L P+ER++      +   + L  +    EV+  R+ 
Sbjct: 183 RPEQTFRYEEIK---RILGEAIEKLKPQERKVVTLYYYE--GLNLTEIGEVLEVTTARIS 237

Query: 271 QIEARAFKKVQESIQKQVE 289
           Q+  +A  +++  + ++ E
Sbjct: 238 QLHTKAIYRLRGYLSRKKE 256


>gi|251779245|ref|ZP_04822165.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium botulinum E1
           str. 'BoNT E Beluga']
 gi|243083560|gb|EES49450.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium botulinum E1
           str. 'BoNT E Beluga']
          Length = 234

 Score = 42.0 bits (97), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 28/92 (30%), Positives = 48/92 (52%), Gaps = 8/92 (8%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLM 87
           K EE VL     + GD     +L+ ++ +L+ KI   +       + I ++  EG IGLM
Sbjct: 2   KNEELVLL---YQQGDKKELEQLIENNKKLIYKIVNKFYVNETNSIDIEDLEQEGMIGLM 58

Query: 88  QAVKK--FDPERGFRLATYSMWWIKAAMQEYI 117
            A +K  F+ E   + +TY+++WI   + E+I
Sbjct: 59  IAAEKYKFNIENKAKFSTYAIYWIYGRITEFI 90


>gi|172038499|ref|YP_001805000.1| RNA polymerase sigma factor SigF [Cyanothece sp. ATCC 51142]
 gi|171699953|gb|ACB52934.1| group 3 sigma-70 RNA polymerase sigma factor J [Cyanothece sp. ATCC
           51142]
          Length = 282

 Score = 42.0 bits (97), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 54/221 (24%), Positives = 103/221 (46%), Gaps = 18/221 (8%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKKFDP 95
           L   Y  +  L   ++LV  +L LV ++A    R    P  ++   G +GL++A+++FDP
Sbjct: 40  LLSAYARNPSLELRNQLVERNLGLVRQVAHRISRQCSEPYEDLEQIGYLGLIRAIERFDP 99

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           ++G   +++++ +I+  M  Y+    S+++I      + L+   ++++  L   T +  +
Sbjct: 100 QQGCAFSSFAIPYIRGEMLHYLRDKGSVMRI--PRRWQELYNKAKKIRKQL---TVSLKR 154

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDE----SLNALINSSDKNSSQWQDWLVYDHDGQ 211
           P     IA  L V   E     C+LA       SL+A I+ +   S  + D L  D + Q
Sbjct: 155 PPSDWEIADALGVPLEEW--NECQLALQNRLLVSLDATISHNVDCSISFGDTLP-DQEYQ 211

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            +  +E++     R  L R++  L  + +   E   L E P
Sbjct: 212 AKQKLEED-----RLQLQRALGQLEEKTKAAIECVFLHELP 247


>gi|289444245|ref|ZP_06433989.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis T46]
 gi|289417164|gb|EFD14404.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis T46]
          Length = 375

 Score = 42.0 bits (97), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 33/116 (28%), Positives = 55/116 (47%), Gaps = 31/116 (26%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGD-LS 48
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+ L 
Sbjct: 216 RKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSERGEKLP 274

Query: 49  AAHR----------------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           AA R                L+ ++LRLVV +A  Y G G+   +++ EGN+GL++
Sbjct: 275 AAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIR 330


>gi|242241477|ref|ZP_04795922.1| DNA-directed RNA polymerase sigma subunit FliA [Staphylococcus
           epidermidis W23144]
 gi|242235020|gb|EES37331.1| DNA-directed RNA polymerase sigma subunit FliA [Staphylococcus
           epidermidis W23144]
          Length = 256

 Score = 42.0 bits (97), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 53/247 (21%), Positives = 117/247 (47%), Gaps = 16/247 (6%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           K+++E+ D  A  +LV  + +L+  +A  Y        ++V  G +GL+ A+ +FD    
Sbjct: 21  KQHQENEDSLAQDKLVKHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDLSFD 80

Query: 99  FRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
            +   + +  +   ++ Y+  ++WS+         +R+     R+K     +T+   +  
Sbjct: 81  RKFEAFLVPTVIGEIKRYLRDKTWSV------HVPRRIKEIGPRIKKVSDELTNELERSP 134

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQVLI 216
            +  IA++L VS+ EV+     +   +S NAL ++ S +         + D  GQ+    
Sbjct: 135 SISEIAQRLEVSDEEVLEA---MEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQQD--- 188

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           +  +   +R +L R + +L+ RER+I +   ++   ++ +       +S+  V +++  A
Sbjct: 189 DNYDLTEKRMILERILPILSERERQIIQCTFIE--GLSQKETGERIGLSQMHVSRLQRTA 246

Query: 277 FKKVQES 283
            KK+QE+
Sbjct: 247 VKKLQEA 253


>gi|238920292|ref|YP_002933807.1| flagellar biosynthesis sigma factor [Edwardsiella ictaluri 93-146]
 gi|238869861|gb|ACR69572.1| RNA polymerase sigma factor for flagellar operon [Edwardsiella
           ictaluri 93-146]
          Length = 240

 Score = 42.0 bits (97), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 48/224 (21%), Positives = 98/224 (43%), Gaps = 36/224 (16%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL+ AV+++D  +G    TY++  I+ AM +  LRS   V      N + 
Sbjct: 41  LDDLLQAGGIGLLHAVERYDAMQGTAFTTYAIQRIRGAMLDE-LRSRDWVPRSVRRNARG 99

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   ++R +  L  +  ++        IA+++ +S +E   +                 D
Sbjct: 100 VSAAMQRAEQRLGRVPGDS-------EIAQEMGISLAEYQQILL---------------D 137

Query: 195 KNSSQ---WQDWLVYDHDGQEQVLIEKEE--------RKNRRNMLTRSMSVLNPRERRIF 243
            N+SQ   + +W     D  E V+ + EE          + R  +  ++  L  RE+ + 
Sbjct: 138 TNTSQLFSYDEWREEHGDSAEPVVEQSEESNPLHQLLESDLRGRVIAAIEALPEREKLVL 197

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
                +E  + L+ + +  EV   RV Q+ ++A K+++  +  Q
Sbjct: 198 TLYYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRLRTRLLSQ 239


>gi|254392909|ref|ZP_05008077.1| sigma factor of sigB family [Streptomyces clavuligerus ATCC 27064]
 gi|294811525|ref|ZP_06770168.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|326440088|ref|ZP_08214822.1| putative RNA polymerase sigma factor [Streptomyces clavuligerus
           ATCC 27064]
 gi|197706564|gb|EDY52376.1| sigma factor of sigB family [Streptomyces clavuligerus ATCC 27064]
 gi|294324124|gb|EFG05767.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 289

 Score = 42.0 bits (97), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 55/230 (23%), Positives = 101/230 (43%), Gaps = 23/230 (10%)

Query: 61  VVKIAMG-YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL- 118
           +VK A G +R     + +++  G IGL++A+ +F+  R    AT+++ +I   ++ +   
Sbjct: 73  LVKYAAGRFRNRAEQMEDIIQVGTIGLIKAIDRFELSREVEFATFAVPYIVGEIKRFFRD 132

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVI---- 174
            SW+   +      + L  +L +    L    D +    +   +A+ L + E EVI    
Sbjct: 133 TSWA---VHVPRRLQELRIDLAKATDDLSQRLDRSPTTRE---LAEHLGIDEQEVIEGVV 186

Query: 175 SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV 234
           + N   AG   +  L +SSD  +S   D L     G     +E  E       L   +  
Sbjct: 187 AANGYTAGSIDM-PLEDSSDHTTSSLSDRL-----GAPDAGLEIAENVQALKPL---IEE 237

Query: 235 LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L  R+RRI   R  +E  +T   + +E  VS+  V ++  R   +++E +
Sbjct: 238 LGERDRRILRMRFGEE--LTQSEIGAELGVSQMHVSRLLTRITTRLREGL 285


>gi|218887101|ref|YP_002436422.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio vulgaris
           str. 'Miyazaki F']
 gi|218758055|gb|ACL08954.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio vulgaris
           str. 'Miyazaki F']
          Length = 265

 Score = 42.0 bits (97), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 18/45 (40%), Positives = 30/45 (66%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           ++E++S G +GLM+A+ KF P+ G R  TY+   I+ AM + + R
Sbjct: 64  LNELISAGTLGLMEALGKFRPQLGIRFETYAESRIRGAMLDELRR 108


>gi|253574829|ref|ZP_04852169.1| RNA polymerase sigma-K factor [Paenibacillus sp. oral taxon 786
           str. D14]
 gi|251845875|gb|EES73883.1| RNA polymerase sigma-K factor [Paenibacillus sp. oral taxon 786
           str. D14]
          Length = 110

 Score = 42.0 bits (97), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 44/75 (58%), Gaps = 2/75 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ E++E   L +R  E GD  + + L+  +LRLV  I   +   G  + +++S G IGL
Sbjct: 38  PLTEEEETKHL-QRMAE-GDSESRNILIEHNLRLVAHIVKKFDNTGEDLEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRL 101
           ++A++ F P +G +L
Sbjct: 96  IKAIESFRPNKGTKL 110


>gi|317128506|ref|YP_004094788.1| RNA polymerase, sigma 28 subunit, SigF [Bacillus cellulosilyticus
           DSM 2522]
 gi|315473454|gb|ADU30057.1| RNA polymerase, sigma 28 subunit, SigF [Bacillus cellulosilyticus
           DSM 2522]
          Length = 252

 Score = 42.0 bits (97), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 34/132 (25%), Positives = 63/132 (47%), Gaps = 6/132 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + G   A  ++V ++ RLV  +   +   G    ++   G IGL+++V KFD     + +
Sbjct: 28  QDGAQEARDQIVNANTRLVWSVVQRFLNRGYEADDLFQIGCIGLIKSVDKFDLSYDVKFS 87

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I   +Q + LR    VK+  +   K     +R++K  L        +   V  I
Sbjct: 88  TYAVPMIIGEIQRF-LRDDGTVKVSRSI--KESANKIRKMKEELSKTLG---RTPTVNEI 141

Query: 163 AKKLNVSESEVI 174
           A+KL+++  EV+
Sbjct: 142 AEKLDLTPEEVV 153


>gi|302867457|ref|YP_003836094.1| RNA polymerase sigma-70 factor [Micromonospora aurantiaca ATCC
           27029]
 gi|315506134|ref|YP_004085021.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily
           [Micromonospora sp. L5]
 gi|302570316|gb|ADL46518.1| RNA polymerase sigma-70 factor, sigma-B/F/G subfamily
           [Micromonospora aurantiaca ATCC 27029]
 gi|315412753|gb|ADU10870.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Micromonospora sp. L5]
          Length = 269

 Score = 42.0 bits (97), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 54/227 (23%), Positives = 100/227 (44%), Gaps = 20/227 (8%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           L L   +A  Y G G P  ++     +GL++AV +FD  RG   A +++  I   ++ + 
Sbjct: 54  LPLANHLAARYSGRGEPAGDLAQTAALGLIKAVDRFDASRGVDFAGFAIPTILGEIKRHF 113

Query: 118 L-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS--ESEVI 174
             R+W+ +++     + RL     R+      +T    +   V  IA  L+V+  E    
Sbjct: 114 RDRTWN-IRVPRRLQELRL-----RISEANSTLTQTLNRAPTVADIAAHLDVTEEEVLEG 167

Query: 175 SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV 234
               R     SL+  I   D ++++  D L     G E     + E  + R  L  +++ 
Sbjct: 168 LEGARAYNAVSLSTPIGDGD-SATELGDTL-----GTED---NEYELADLRASLGPALAT 218

Query: 235 LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           L+ RE++I   R      +T   +++   VS+  V ++ ARA  K++
Sbjct: 219 LDEREQKILTLRFYGN--LTQSEIAARVGVSQMHVSRLLARALTKLR 263


>gi|225848018|ref|YP_002728181.1| RNA polymerase sigma-D factor (Sigma-28) [Sulfurihydrogenibium
           azorense Az-Fu1]
 gi|225644246|gb|ACN99296.1| RNA polymerase sigma-D factor (Sigma-28) [Sulfurihydrogenibium
           azorense Az-Fu1]
          Length = 240

 Score = 42.0 bits (97), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 47/217 (21%), Positives = 105/217 (48%), Gaps = 19/217 (8%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++  G +GL  A++K+DP +G +L+TY+   I+  + ++ LR    V     +  K L 
Sbjct: 39  DLIQVGVLGLYDALEKYDPSKGIKLSTYAEIRIRGYIIDH-LRQLDWVPRSVRSKIKNLE 97

Query: 137 FNLRRLKGHL--QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINS 192
             + +L+  L  QA T+          IA  L ++  E ++    LA     SL++ ++ 
Sbjct: 98  NKIAQLEAQLGRQAKTEE---------IANYLGMTVEEYMTYAEVLANKVLISLDSDVSK 148

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            D  S    + +  + D  ++V+ EK+ ++   +++   ++ L+ RER +      +E  
Sbjct: 149 DDDESLHLWEVISSNDDTPDKVVEEKQLKEILSDII---LNHLDERERLLISLYYYEE-- 203

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           + ++ ++    ++  RV Q+  +   K++  + K +E
Sbjct: 204 LNMKEIADILGITESRVSQLHTKIMLKLKNLVMKYLE 240


>gi|296101730|ref|YP_003611876.1| flagellar biosynthesis sigma factor [Enterobacter cloacae subsp.
           cloacae ATCC 13047]
 gi|295056189|gb|ADF60927.1| flagellar biosynthesis sigma factor [Enterobacter cloacae subsp.
           cloacae ATCC 13047]
          Length = 239

 Score = 42.0 bits (97), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 50/221 (22%), Positives = 97/221 (43%), Gaps = 32/221 (14%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL+ AV ++D  +G    TY++  I+ AM +  LRS   V      N + 
Sbjct: 41  LDDLLQAGGIGLLNAVDRYDALQGTAFTTYAVQRIRGAMLDE-LRSRDWVPRSVRRNARE 99

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   + +L+   Q +  N  + E    +A++L +   E   M            L+++++
Sbjct: 100 VAHAMGQLE---QELGRNATETE----VAERLGIPVEEYRQM------------LLDTNN 140

Query: 195 KNSSQWQDW---------LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
                + +W         LV D   QE  L    E  N R  +  ++  L  RE+ +   
Sbjct: 141 SQLFSYDEWREEHGDSIELVTDEHQQENPLHHLME-GNLRQRVMEAIEALPEREQLVLTL 199

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +E  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 200 YYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 238


>gi|160943408|ref|ZP_02090642.1| hypothetical protein FAEPRAM212_00899 [Faecalibacterium prausnitzii
           M21/2]
 gi|158445268|gb|EDP22271.1| hypothetical protein FAEPRAM212_00899 [Faecalibacterium prausnitzii
           M21/2]
          Length = 221

 Score = 42.0 bits (97), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 26/90 (28%), Positives = 45/90 (50%), Gaps = 12/90 (13%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIA--------MGYRGYGLPISEVVSEGNIGLM 87
           VLA++    GD +A   L+ ++   + K+A        +   G  L   ++   GN+GL 
Sbjct: 10  VLAQK----GDAAALDSLIDNNKSFIGKVANDLFRSMNLAQSGLNLDTDDLKQAGNLGLW 65

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           +AV KFD  +G +  TY+   I+ AM + +
Sbjct: 66  KAVPKFDAAQGMKFLTYAAPAIRNAMVDMV 95


>gi|206901181|ref|YP_002249992.1| SigD [Dictyoglomus thermophilum H-6-12]
 gi|206740284|gb|ACI19342.1| SigD [Dictyoglomus thermophilum H-6-12]
          Length = 171

 Score = 41.6 bits (96), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 25/65 (38%), Positives = 41/65 (63%), Gaps = 2/65 (3%)

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           R  + R++  L+ RER I + R   ++  P TLE +   F ++RERVRQIE RA +K++ 
Sbjct: 104 RREIERALDALSEREREILKWRYGFKDGKPRTLEEVGKLFNITRERVRQIEERALRKLRH 163

Query: 283 SIQKQ 287
            +Q++
Sbjct: 164 ILQQR 168


>gi|226323675|ref|ZP_03799193.1| hypothetical protein COPCOM_01450 [Coprococcus comes ATCC 27758]
 gi|225207859|gb|EEG90213.1| hypothetical protein COPCOM_01450 [Coprococcus comes ATCC 27758]
          Length = 205

 Score = 41.6 bits (96), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 20/73 (27%), Positives = 39/73 (53%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A  + +  +LRLV+ +   + G      ++   G IGL++A+  F+PE   + +TY
Sbjct: 9   GDEEAKEQYIKGNLRLVLSVIKRFSGSSENPDDLFQIGCIGLIKAINNFNPELEVKFSTY 68

Query: 105 SMWWIKAAMQEYI 117
           ++  I   ++ +I
Sbjct: 69  AVPMIIGEIRRFI 81


>gi|121533733|ref|ZP_01665560.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
 gi|121307724|gb|EAX48639.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
          Length = 252

 Score = 41.6 bits (96), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 23/75 (30%), Positives = 43/75 (57%), Gaps = 6/75 (8%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +L+  +L LV K+  G    GLP      +++S G  GL+ A+++FDP R  +  TY++ 
Sbjct: 30  KLIEKYLPLV-KMVAGRVAIGLPQHIDKEDLISYGFFGLLDAIERFDPSRNIKFETYAVA 88

Query: 108 WIKAAMQEYI-LRSW 121
            I+ ++ + I ++ W
Sbjct: 89  RIRGSIFDAIRVQDW 103


>gi|158340672|ref|YP_001521840.1| RNA polymerase sigma factor [Acaryochloris marina MBIC11017]
 gi|158310913|gb|ABW32526.1| RNA polymerase sigma factor [Acaryochloris marina MBIC11017]
          Length = 440

 Score = 41.6 bits (96), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 53/265 (20%), Positives = 112/265 (42%), Gaps = 41/265 (15%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           ++GD  A   ++ S+L  +      +   G+   E+++EG  GL +A+ ++DP +G  L 
Sbjct: 36  QNGDYEARQTVIYSNLAWICSRGGQFSRKGIDDGELINEGYWGLNRAIDQWDPTKGANLR 95

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TYS        + Y  +S ++ +       K  +  L +LK   +++ ++      V  +
Sbjct: 96  TYS------ERKIYKFQSEAIRQKNHIRLPKSTYEQLSKLKKATESLGED----ATVAQL 145

Query: 163 AKKLNVSE---------SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
           A++  + E         S+ +S+N      E+L  L   +D            D  G   
Sbjct: 146 AEETEIKEKRIRKLQEISQPVSLNSVTGERENLELLDQQAD------------DSLGSLD 193

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
             +  E        L   +  L+PR+R I      +E  ++ + +S    +  ++VR++ 
Sbjct: 194 PALSSE--------LLDLVDKLHPRQREILHLYHWEE--LSFQKISDYLGLPAKQVRKLY 243

Query: 274 ARAFKKVQESIQKQVELSSSPPLLQ 298
            +A   +++ +Q ++      PLL+
Sbjct: 244 KKALDLLRKFLQGEINEFPPLPLLE 268


>gi|1378114|gb|AAB41955.1| whiG [Streptomyces sp.]
          Length = 209

 Score = 41.6 bits (96), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 48/198 (24%), Positives = 85/198 (42%), Gaps = 27/198 (13%)

Query: 57  HLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           H   +VK   G    GLP     ++ VS G  GL+ A++KFD +R  +  TY++  I+ A
Sbjct: 9   HYSPLVKYVAGRVSVGLPPNVEQADFVSSGVFGLIDAIEKFDVDREIKFETYAITRIRGA 68

Query: 113 M-QEYILRSWSLVKIGTTA-NQKRLFFNL----RRLKGHLQAITDNNLKPEQVVAIAKKL 166
           M  E     W    +   A N +R +  L    RR     +  ++  +  E++ A+  +L
Sbjct: 69  MIDELRALDWIPRSVRQKARNVERAYATLEAQFRRTPSEAEVASEMGIALEELHAVFSQL 128

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ--DWLVYDHDGQEQVLIEKEERKNR 224
           +            LA   +L  L+++  +   +    D L    D      +E  E +  
Sbjct: 129 S------------LANVVALEELLHAGGEGGGRLSLMDTL---EDTAADNPVEVAEDREL 173

Query: 225 RNMLTRSMSVLNPRERRI 242
           R +L R+++ L  RE+ +
Sbjct: 174 RRLLARAINTLPDREKTV 191


>gi|21225555|ref|NP_631334.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
 gi|256783425|ref|ZP_05521856.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
 gi|289767301|ref|ZP_06526679.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
 gi|4835317|emb|CAB42939.1| putative RNA polymerase sigma factor [Streptomyces coelicolor
           A3(2)]
 gi|289697500|gb|EFD64929.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
          Length = 295

 Score = 41.6 bits (96), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 47/206 (22%), Positives = 93/206 (45%), Gaps = 17/206 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A + L+  ++ LV   A  +RG G  + ++V  G IGL++A+ +F+  R     ++++ +
Sbjct: 64  ARNTLIEMNMSLVRFAAGRFRGRGNDMEDIVQTGMIGLIKAIDRFELSREVEFTSFALPY 123

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I   ++ +   +   V +     + R+   L R +  L    D   +   V  +A  +N+
Sbjct: 124 IVGEIKRFFRDTTWAVHVPRRLQELRV--ELARAREELSTRLD---REPTVAELATLMNI 178

Query: 169 SESEVISMNCRLAG--DESLNALI--NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            E +VI       G    SL+A +  +  +   S   D++  + DG    L+E       
Sbjct: 179 GEDQVIEGQIASNGYNSSSLDAALTGDGPENGESVLADFIGVEEDGLR--LVED------ 230

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQE 250
            + L   M+ L+ R+R+I   R ++E
Sbjct: 231 FHSLAPLMAELSERDRQIIHLRFVEE 256


>gi|124265243|ref|YP_001019247.1| RNA polymerase sigma factor for flagellar operon [Methylibium
           petroleiphilum PM1]
 gi|124258018|gb|ABM93012.1| RNA polymerase sigma factor for flagellar operon [Methylibium
           petroleiphilum PM1]
          Length = 265

 Score = 41.6 bits (96), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 58/238 (24%), Positives = 104/238 (43%), Gaps = 30/238 (12%)

Query: 57  HLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           H  LV +IA   R   LP    + E++  G IGL +A+ +F+   G    TY+   I+ A
Sbjct: 39  HGALVRRIAKRMRAR-LPANVEMDELLQAGLIGLNEAITRFEESFGASFDTYASRRIEGA 97

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           M +  LR+   +     A+Q       R ++  +QA+    L+P + + +A +L  S   
Sbjct: 98  MLDS-LRAADTLSRDARAHQ-------RAIRAAVQALEHRLLRPPRAMEVASELGWS--- 146

Query: 173 VISMNCRL---------AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           +  ++ RL         AGD  L+ L + +    +  +D L    D     L    +R+ 
Sbjct: 147 LARLHQRLVEAGAAGQRAGDAPLDGLADEASARGA--EDDLHATADDHADPLAAL-QRRQ 203

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R   L  +   L  RE+ +   + + E  +  ++ +    VS  RV Q+ A   +K++
Sbjct: 204 RTTALNAAFDTLEEREQLMM--KMIYERGLDHQDAAESLGVSPSRVSQMHAVVVQKLK 259


>gi|159163074|pdb|1TTY|A Chain A, Solution Structure Of Sigma A Region 4 From Thermotoga
           Maritima
          Length = 87

 Score = 41.6 bits (96), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 23/59 (38%), Positives = 34/59 (57%), Gaps = 2/59 (3%)

Query: 225 RNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R  L + +  L+PRE  +   R   L   P TLE +   F V+RER+RQIE +A +K++
Sbjct: 9   REELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVKALRKLR 67


>gi|168700558|ref|ZP_02732835.1| RNA polymerase sigma factor whiG [Gemmata obscuriglobus UQM 2246]
          Length = 260

 Score = 41.6 bits (96), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 59/256 (23%), Positives = 111/256 (43%), Gaps = 28/256 (10%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           YRE   +   +RLV  +L LV   A         G+ + +++S G  GL+ A+  FD  R
Sbjct: 17  YRERPTVELRNRLVERYLSLVKYNAERIWSRLPDGVELDDLISAGVFGLLDAIDAFDLTR 76

Query: 98  GFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           G +  TY +  I+ AM  E     W    + + A++      +   +  L+A      KP
Sbjct: 77  GVKFETYCVPRIRGAMLDELRTMDWVPRLVRSKASK------MEAARKQLEAALGRPPKP 130

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           E+   +++KL +   ++ S      GD +   L++ + K    W +   Y    +  +L 
Sbjct: 131 EE---LSEKLGIPLEQLESY----VGDATAVNLVSLNKK----WYETDSYKDVREIDILE 179

Query: 217 EKEE-----RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           +K+      R   R+++      LN  ER I      +E  +T++ + +   +S  RV Q
Sbjct: 180 DKKAESPTGRLQNRDLMKLVTRGLNRNERLIVILYYYEE--MTMKEIGATLNLSESRVSQ 237

Query: 272 IEARAFKKVQESIQKQ 287
           + +    ++Q  + K+
Sbjct: 238 MHSSIVARLQSHLAKR 253


>gi|254228448|ref|ZP_04921874.1| RNA polymerase sigma factor, FliA/WhiG family [Vibrio sp. Ex25]
 gi|262393605|ref|YP_003285459.1| RNA polymerase sigma factor for flagellar operon [Vibrio sp. Ex25]
 gi|151939036|gb|EDN57868.1| RNA polymerase sigma factor, FliA/WhiG family [Vibrio sp. Ex25]
 gi|262337199|gb|ACY50994.1| RNA polymerase sigma factor for flagellar operon [Vibrio sp. Ex25]
          Length = 244

 Score = 41.6 bits (96), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 55/250 (22%), Positives = 103/250 (41%), Gaps = 27/250 (10%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFD 94
           A  Y +HG  ++    +  +  LV +IA    G   P   + +++  G IGL++A + +D
Sbjct: 4   AITYDQHGKFNSQQAFIERYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLIEAQQNYD 63

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +G    TY+   I+ AM +  +R    V      N + +   +  L+G L     +  
Sbjct: 64  GSKGASFETYAGIRIRGAMLDD-MRKGDWVPRSVHKNNREINQAIAELEGELNR---DPT 119

Query: 155 KPEQVVAIAKKLNVSESEVISMNC-RLAGDESL---NALINSSDKNSSQWQDWLVYDHDG 210
             E    +   L+   S +  +NC +L G E L   + +I+ +D+         V D   
Sbjct: 120 DSEVATHLGMTLDQYHSALTDINCSKLVGIEDLGVSDDVISPADETDDSNPFKGVAD--- 176

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                      ++ R  L  S+  +  RE  +      +E  + L+ +     VS  RV 
Sbjct: 177 -----------ESFRKALVESIKQIPEREALVLSLYYDEE--LNLKEIGDVLGVSESRVS 223

Query: 271 QIEARAFKKV 280
           QI ++A +++
Sbjct: 224 QILSQAMQRL 233


>gi|117926317|ref|YP_866934.1| FliA/WhiG family RNA polymerase sigma factor [Magnetococcus sp.
           MC-1]
 gi|117610073|gb|ABK45528.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Magnetococcus sp.
           MC-1]
          Length = 260

 Score = 41.6 bits (96), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 44/206 (21%), Positives = 94/206 (45%), Gaps = 13/206 (6%)

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAA-MQEYILRSWSLVKIGTTANQKRLFFNLR 140
           G +GL+ AV KFDP+RG +  TY+ + I+ A + E     W   ++   A+Q +  +N  
Sbjct: 61  GVMGLIDAVSKFDPDRGIKFQTYAEFRIRGAILDELRAIDWVPRQLRQNASQMQEAYN-- 118

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
           +L+           +P + V +A+ L +S +E      ++ G   ++      + +  +W
Sbjct: 119 QLEAKFG-------RPAEDVEVAEHLGISLNEYHEQIDQVRGISIVSFEDIRPNNDDEEW 171

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
            D L    D   Q  +E       R+ +  ++  L  +ER +      +E  +T+  +  
Sbjct: 172 -DVLEVLADPSVQDPVEAIGLMELRHAMADAIETLPEKERLVVTLYYFEE--LTMSEIGE 228

Query: 261 EFEVSRERVRQIEARAFKKVQESIQK 286
              ++  R+ Q+ ++A  +++  I++
Sbjct: 229 VLGLTESRISQLHSKAALRMRARIKR 254


>gi|16332163|ref|NP_442891.1| RNA polymerase sigma factor SigF [Synechocystis sp. PCC 6803]
 gi|1653792|dbj|BAA18703.1| RNA polymerase sigma-37 [Synechocystis sp. PCC 6803]
          Length = 258

 Score = 41.6 bits (96), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 40/166 (24%), Positives = 82/166 (49%), Gaps = 16/166 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE-GNIGLMQA 89
           K E   L K Y E  D+   +R++  +L LV K A  +        E +S+ G +GL++A
Sbjct: 10  KLETLRLFKIYAESHDIGVRNRIMEVNLGLVRKEAHHWTAQCNESFEDLSQVGCLGLIRA 69

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI-------GTTANQKRLFFNLRRL 142
           +++FD  +G   +++++ +++  +Q ++    + V+I       G  A   +  F L+  
Sbjct: 70  IERFDVSKGNAFSSFAIPYVRGEIQHFLRDKSNCVRIPRRWLDLGRQAIAVQQEFRLK-- 127

Query: 143 KGHLQAITDNNLKPEQVVAIAK----KLNVSESEVISMNCRLAGDE 184
             + +A TD  +     V +A     KL +   E++S++ ++ GD+
Sbjct: 128 --YDRAATDEEIAQILAVPLADWQETKLALQNRELVSLDTKVNGDD 171


>gi|238924178|ref|YP_002937694.1| sporulation sigma factor SigK [Eubacterium rectale ATCC 33656]
 gi|238875853|gb|ACR75560.1| sporulation sigma factor SigK [Eubacterium rectale ATCC 33656]
 gi|291529048|emb|CBK94634.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Eubacterium rectale
           M104/1]
          Length = 230

 Score = 41.6 bits (96), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 28/106 (26%), Positives = 52/106 (49%), Gaps = 3/106 (2%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +++II   +I    Y++       LE++ E +   +     D  A   L+  ++RLV  +
Sbjct: 10  DLNIIYYKQIMTGCYVNTFLSPLSLERETECL---KKVAQNDKEAKDELILHNMRLVAHV 66

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
              Y      + E++S G IGL++AV  F  + G R AT+++  I+
Sbjct: 67  TKKYAVSEDEMEELISIGTIGLIKAVSSFKADYGNRFATFAIRCIE 112


>gi|85712287|ref|ZP_01043338.1| flagellar biosynthesis sigma factor FliA [Idiomarina baltica OS145]
 gi|85693914|gb|EAQ31861.1| flagellar biosynthesis sigma factor FliA [Idiomarina baltica OS145]
          Length = 241

 Score = 41.6 bits (96), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 58/264 (21%), Positives = 111/264 (42%), Gaps = 38/264 (14%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           A  Y  H D   A  ++  H  LV +IA   M      + + +++  G IGL++A + FD
Sbjct: 4   AAVYSAHADNRQA--IIEQHTGLVKRIAHHMMARLPASVQVDDLIQSGMIGLLEAARNFD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
             +G    T++   I+ AM + I R  W+          + +  N RR+   ++ + +  
Sbjct: 62  NSKGASFETFAGIRIRGAMLDEIRRGDWA---------PRSVHRNHRRVLEAIRQVENET 112

Query: 154 LKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNA---LINSSDKNSSQWQDWLV 205
            +  + V +A+KL +   E  ++     + R+ G E L      I       + ++    
Sbjct: 113 GRDAKDVEVAEKLEMPLEEYHAILRDVNSGRIIGIEDLGVSEDAIMPEQVTGANYEPQKD 172

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            ++D   + L+E             ++S L  RE  +      +E  + L+ +     VS
Sbjct: 173 VENDAFHRALVE-------------TISGLPEREALVLSLYYDEE--LNLKEIGEVLSVS 217

Query: 266 RERVRQIEARAFKKVQESIQKQVE 289
             RV QI ++A  +++  +Q  VE
Sbjct: 218 ESRVSQIHSQAMMRLKTRMQSWVE 241


>gi|291524907|emb|CBK90494.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Eubacterium rectale
           DSM 17629]
          Length = 230

 Score = 41.6 bits (96), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 28/106 (26%), Positives = 52/106 (49%), Gaps = 3/106 (2%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +++II   +I    Y++       LE++ E +   +     D  A   L+  ++RLV  +
Sbjct: 10  DLNIIYYKQIMTGCYVNTFLSPLSLERETECL---KKVAQNDKEAKDELILHNMRLVAHV 66

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
              Y      + E++S G IGL++AV  F  + G R AT+++  I+
Sbjct: 67  TKKYAVSEDEMEELISIGTIGLIKAVSSFKADYGNRFATFAIRCIE 112


>gi|326203397|ref|ZP_08193262.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Clostridium
           papyrosolvens DSM 2782]
 gi|325986655|gb|EGD47486.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Clostridium
           papyrosolvens DSM 2782]
          Length = 249

 Score = 41.6 bits (96), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 40/219 (18%), Positives = 98/219 (44%), Gaps = 17/219 (7%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E  L   Y   G+    + +V+++L L   ++  +   G+   ++     + L++AV++
Sbjct: 12  DEAQLFSLYISTGNQDYRNEIVSNYLSLAEYLSKKFLNRGVDFDDIYQVACLALIKAVER 71

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F PE+G +  +++   I   ++ +     + +KI      +R++ + + +      +T  
Sbjct: 72  FSPEKGVKFISFATPTILGEIKRFFRDKSTTIKI-----PRRIYESRQGVNKARDELTQK 126

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS--DKNSSQWQDWLVYDHDG 210
             +  +   IA+ + +S   V+ +    AG  S+   ++ S   +N S+  D L YD   
Sbjct: 127 LSRVPRADEIAEYMGISVDTVLEI--LEAGSSSIVKSLDQSINQENDSELGDTLGYDEKT 184

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
            E +        + ++ L ++++  N  E+   + R +Q
Sbjct: 185 YEMI--------DNKDFLEKALTSFNDIEKEFIKYRYIQ 215


>gi|331696322|ref|YP_004332561.1| SigB/F/G subfamily RNA polymerase sigma-28 subunit [Pseudonocardia
           dioxanivorans CB1190]
 gi|326951011|gb|AEA24708.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Pseudonocardia dioxanivorans CB1190]
          Length = 283

 Score = 41.6 bits (96), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 55/238 (23%), Positives = 102/238 (42%), Gaps = 20/238 (8%)

Query: 53  LVTSHLRLVVKIAMGYR-GYGLPISEVVSEGNIGLMQAVKKFDPER-GFRLATYSMWWIK 110
           L+ + L +V  +A+ +  GY     ++V  G +GL+ A+ ++DP+R G  L  Y +  ++
Sbjct: 62  LILAFLPIVRHLALRHSAGYPGGYDDLVQVGTVGLISAIDRWDPDRAGADLLGYLVPCVR 121

Query: 111 AAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
             M  Y   R+W+   +      K L   + +  G L        +P +   +A  L V 
Sbjct: 122 GEMLRYFRDRTWA---VRVPRRLKDLAVAINKATGPLSQQLGRAPRPSE---LAAHLGVD 175

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
            SEV+      AG  S    +   D  + +     + + DG+   L   E R   R +L 
Sbjct: 176 VSEVVEALTAKAGHHSDP--LEPVDPETGESSHERLGELDGE---LDHVEYRHALRPLL- 229

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
                L  RER I   R  ++  +T   ++ E  +S+  V ++ AR+   ++  +  +
Sbjct: 230 ---ESLPERERTILMLRFFRD--MTQTQIAEEIGISQMHVSRLLARSLTTLRAGLAAE 282


>gi|113954054|ref|YP_730869.1| type III sigma factor [Synechococcus sp. CC9311]
 gi|113881405|gb|ABI46363.1| putative type III sigma factor [Synechococcus sp. CC9311]
          Length = 271

 Score = 41.6 bits (96), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 14/30 (46%), Positives = 23/30 (76%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           ++V EG +GL+  +  FDP+RGFR++TY +
Sbjct: 51  DLVQEGCLGLINGMANFDPQRGFRISTYVL 80


>gi|284053375|ref|ZP_06383585.1| RNA polymerase sigma factor SigC [Arthrospira platensis str.
           Paraca]
          Length = 183

 Score = 41.6 bits (96), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 40/178 (22%), Positives = 86/178 (48%), Gaps = 13/178 (7%)

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   I      +++     +K     L ++K   + I+    +   +  IA +L
Sbjct: 2   WWIRQGITRAIATQSRTIRLPVHITEK-----LNKIKKAQRKISQEKSRTATIDDIATEL 56

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++  ++  +  R+    SL   + + DK++ +  D L  +    E++L+    R++   
Sbjct: 57  KMTPDQIREVLLRVPRSVSLETKVGT-DKDT-ELGDLLETEESTPEELLM----RESLYR 110

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            L   ++ L+ +ER + + R      +P +L  +    ++SRERVRQIEA+A +K+++
Sbjct: 111 ELQHILADLSGKERAVIQMRYGLGDGHPYSLAEIGRALDLSRERVRQIEAKALQKLRQ 168


>gi|153818374|ref|ZP_01971041.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae NCTC 8457]
 gi|126511064|gb|EAZ73658.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae NCTC 8457]
          Length = 232

 Score = 41.6 bits (96), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 44/159 (27%), Positives = 74/159 (46%), Gaps = 18/159 (11%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFD 94
           A  Y ++G+L++    +  +  LV +IA    G   P   I +++  G +GL++A K +D
Sbjct: 4   ALTYDQYGNLNSQQLFLEKYSVLVKRIAHHLIGRLPPSVLIEDLIQAGMVGLLEAQKNYD 63

Query: 95  PERGFRLATYSMWWIKAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
             +G    TY+   I+ AM + I R  W  V      + + +   +  L+G L      N
Sbjct: 64  GSKGASFETYAGIRIRGAMLDDIRRGDW--VPRSVHKHNREISQAIAVLEGEL------N 115

Query: 154 LKPEQVVAIAKKLNVS----ESEVISMNC-RLAGDESLN 187
             P     +AK LN+S     S ++ +NC R+ G E L 
Sbjct: 116 RDPTD-AEVAKFLNMSLEQYHSVLMDINCSRIVGIEDLG 153


>gi|148554202|ref|YP_001261784.1| RNA polymerase sigma 28 subunit FliA/WhiG [Sphingomonas wittichii
           RW1]
 gi|148499392|gb|ABQ67646.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Sphingomonas wittichii
           RW1]
          Length = 242

 Score = 41.6 bits (96), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 55/239 (23%), Positives = 107/239 (44%), Gaps = 27/239 (11%)

Query: 53  LVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           LV +H++LV KIA    G     + + +++  G I L++A   ++ +RG   +TY+   +
Sbjct: 24  LVRAHMQLVRKIAWHVHGRVSTAIDVEDLIQIGMIALVEAANGYE-DRGHAFSTYASMRV 82

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + AM +++ R  +L +      +  L       K H ++ +++ L        A+ L + 
Sbjct: 83  RGAMIDHLRRQAALTRSAMAKRRALLTAKADFEKKHGRSPSESEL--------AQALGLD 134

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV--LIEKEERKNRRNM 227
            +   ++      DE+      S D+  S    W     D +E+V   IE+EE       
Sbjct: 135 GAAFHALL-----DETAATYHESIDEVYSDQSMWFA---DVEERVDQTIEREELA---GA 183

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           L   +S L  RE  + +   ++E  + LE +     +   RV QI+  A  K++ S+++
Sbjct: 184 LAEHISELPEREAMVLQLYFVEE--MNLEEIGQTLGIGAARVCQIKKAALDKLRVSLRE 240


>gi|160944734|ref|ZP_02091961.1| hypothetical protein FAEPRAM212_02248 [Faecalibacterium prausnitzii
           M21/2]
 gi|158443918|gb|EDP20922.1| hypothetical protein FAEPRAM212_02248 [Faecalibacterium prausnitzii
           M21/2]
          Length = 221

 Score = 41.6 bits (96), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 28/101 (27%), Positives = 47/101 (46%), Gaps = 15/101 (14%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIA--------MGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           + GD +A   L+ ++   + K A        +   G  L   ++   GN+GL +AV KFD
Sbjct: 13  QKGDAAALDSLIDNNKSFIGKAANDLFRSMNLAQSGLNLDTDDLKQAGNMGLWKAVPKFD 72

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
             RG +  TY+   I  AM +       +V+   TA ++R+
Sbjct: 73  AARGMKFLTYAAPAIHNAMMD-------MVRDAFTAFEQRM 106


>gi|315179524|gb|ADT86438.1| RNA polymerase sigma factor for flagellar operon [Vibrio furnissii
           NCTC 11218]
          Length = 244

 Score = 41.6 bits (96), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 63/253 (24%), Positives = 108/253 (42%), Gaps = 31/253 (12%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFD 94
           A  Y ++G++++    +  +  LV +IA    G   P   I +++  G +GL++A K +D
Sbjct: 4   ALTYDQYGNMNSQKLFLDKYSVLVKRIAHHLIGRLPPSVLIEDLIQAGMVGLLEAQKNYD 63

Query: 95  PERGFRLATYSMWWIKAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
             +G    TY+   I+ AM + I R  W  V      + + +   +  L+G L      N
Sbjct: 64  GSKGASFETYAGIRIRGAMLDDIRRGDW--VPRSVHKHNREIGQAIAVLEGEL------N 115

Query: 154 LKPEQVVAIAKKLNVS----ESEVISMNC-RLAGDESLNALINSSDKNSSQWQDWLVYDH 208
             P     +AK L +S     S +  +NC R+ G E L      +D   S   D    D 
Sbjct: 116 RDPTD-SEVAKHLGMSLDQYHSVLTDINCSRIVGIEDLGV----TDDAISPVDD----DE 166

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D      +  E   + R  L  S+  L  RE  +      +E  + L+ +     VS  R
Sbjct: 167 DNSPFKGVADE---SFRKALVESIKSLPEREALVLSLYYDEE--LNLKEIGEVLGVSESR 221

Query: 269 VRQIEARAFKKVQ 281
           V QI ++A ++++
Sbjct: 222 VSQILSQAMQRLR 234


>gi|289523531|ref|ZP_06440385.1| RNA polymerase sigma factor WhiG [Anaerobaculum hydrogeniformans
           ATCC BAA-1850]
 gi|289503223|gb|EFD24387.1| RNA polymerase sigma factor WhiG [Anaerobaculum hydrogeniformans
           ATCC BAA-1850]
          Length = 189

 Score = 41.6 bits (96), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 21/76 (27%), Positives = 41/76 (53%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A   ++ S+  +V  +A  +        +++ EG + L++AV ++D +RG +  TY
Sbjct: 26  GDEKAREEVIISYRPMVFWLAKKFHVPSDSYQDLIQEGMVALIEAVDRYDAKRGTKFITY 85

Query: 105 SMWWIKAAMQEYILRS 120
           + + IK  M  ++ RS
Sbjct: 86  AYYRIKGRMVNFLERS 101


>gi|32475302|ref|NP_868296.1| RNA polymerase sigma factor whiG [Rhodopirellula baltica SH 1]
 gi|32445843|emb|CAD78574.1| RNA polymerase sigma factor whiG [Rhodopirellula baltica SH 1]
 gi|327540927|gb|EGF27485.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Rhodopirellula baltica
           WH47]
          Length = 272

 Score = 41.6 bits (96), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 47/214 (21%), Positives = 93/214 (43%), Gaps = 15/214 (7%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           G+ + +++S G  GLM A+  +D ERG +  T+ +  I+ AM +  LR    V     + 
Sbjct: 64  GVELDDLISAGMFGLMDAIDAYDTERGVKFETFCVPRIRGAMLDE-LRKMDWVPRLVRSK 122

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
             +L    + L+              Q ++   +++V E E +       G  SLN    
Sbjct: 123 ASKLATATKTLEARF-----GRAPTVQELSAHMEIDVKEVEKMQSEANAVGVVSLNKKWY 177

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV-LNPRERRIFEARRLQE 250
            +D      +  ++ D  G++        R+ ++N L R ++  LN  ER I      +E
Sbjct: 178 ETDSYKDVREIDILEDKKGEDPT------RRVQKNDLMRLVTKGLNRNERLIIILYYYEE 231

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             +T++ + +  ++S  RV Q+      ++Q+ +
Sbjct: 232 --LTMKEIGATLDLSESRVSQMHTAIVNRLQQQL 263


>gi|1419613|emb|CAA67397.1| signma factor 28 [Legionella pneumophila str. Corby]
          Length = 238

 Score = 41.6 bits (96), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 54/240 (22%), Positives = 107/240 (44%), Gaps = 35/240 (14%)

Query: 53  LVTSHLRLVVKI---AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           LV +H  LV +I    +G     + + +++  G +GL++A + +D  +G    TY+   I
Sbjct: 18  LVKTHATLVKRIRHHLLGRLPQSVQLDDLIQSGMLGLLEAARHYDSSKGASFETYAGIRI 77

Query: 110 KAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           +  M + + R+ W  V      N + +   +R L+  L     +N        IA++L V
Sbjct: 78  RGHMLDEVRRNDW--VPRSVYRNSRMISDAVRILEHKLGREAKDN-------EIAEELGV 128

Query: 169 SESEVISM-----NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           S ++  SM     +  L G + L               D +++D +G      E      
Sbjct: 129 SLNDYHSMLQDSISSHLYGFDDLGV------------TDDILFDDEGNGST--EPHRNVM 174

Query: 224 RRNMLTRSMSVLN--PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R +M+ R   V++  PR+ R+  +   +++ + L+ +    EVS  R+ QI ++A  +++
Sbjct: 175 RSDMMNRLTQVIDSLPRKERLVLSLYYEQD-LNLKEIGEILEVSESRISQILSQATHRIR 233


>gi|291549326|emb|CBL25588.1| RNA polymerase sigma-F factor [Ruminococcus torques L2-14]
          Length = 239

 Score = 41.6 bits (96), Expect = 0.16,   Method: Compositional matrix adjust.
 Identities = 50/211 (23%), Positives = 96/211 (45%), Gaps = 32/211 (15%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A   LV  ++ L+  +   + G G    ++   G+IGL++A+ KFD     + +TY
Sbjct: 14  GDKKAREELVEKNIGLIWCVVKRFYGRGAEPEDLFQIGSIGLLKAIDKFDFSYEVQFSTY 73

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK-GHLQAITDNNLKPEQVVAIA 163
           ++  I   ++ + LR   ++K+  +         LR L    LQA      + +    + 
Sbjct: 74  AVPMISGEIRRF-LRDDGMIKVSRS---------LRELSYKSLQA------REKMTRILG 117

Query: 164 KKLNVSE-SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           ++  + E SE + ++C     E +   + SS +  S ++   ++  +G E +L++K E K
Sbjct: 118 REPTLKELSEELQIDC-----EEIVQAMESSVEVESIYKP--IHQKEGSEILLMDKLEEK 170

Query: 223 NR-------RNMLTRSMSVLNPRERRIFEAR 246
           +R       R +L   +  L  +ER I   R
Sbjct: 171 DRQEEKVLDRIVLKEVLETLEAKERTIIYLR 201


>gi|221319748|ref|ZP_03601042.1| RNA polymerase sporulation-specific sigma factor (sigma-K)
           (N-terminal half) [Bacillus subtilis subsp. subtilis
           str. JH642]
          Length = 160

 Score = 41.6 bits (96), Expect = 0.16,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 3/75 (4%)

Query: 39  KRYRE---HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           K+Y E    GD  A + L+  +LRLV  I   +   G    +++S G IGL++ ++ +  
Sbjct: 42  KKYLELMAKGDEHARNMLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKGIESYSA 101

Query: 96  ERGFRLATYSMWWIK 110
            +G +LATY+   I+
Sbjct: 102 GKGTKLATYAARCIE 116


>gi|220903606|ref|YP_002478918.1| RNA polymerase sigma-28 subunit FliA/WhiG [Desulfovibrio
           desulfuricans subsp. desulfuricans str. ATCC 27774]
 gi|219867905|gb|ACL48240.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio
           desulfuricans subsp. desulfuricans str. ATCC 27774]
          Length = 260

 Score = 41.6 bits (96), Expect = 0.16,   Method: Compositional matrix adjust.
 Identities = 18/45 (40%), Positives = 29/45 (64%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           + E++S G +GLM+A+ KF P+ G R  TY+   I+ AM + + R
Sbjct: 60  LGELISSGTLGLMEALGKFRPQLGIRFETYAESRIRGAMLDELRR 104


>gi|54294669|ref|YP_127084.1| flagellar biosynthesis sigma factor [Legionella pneumophila str.
           Lens]
 gi|53754501|emb|CAH15985.1| sigma factor 28 [Legionella pneumophila str. Lens]
          Length = 238

 Score = 41.6 bits (96), Expect = 0.16,   Method: Compositional matrix adjust.
 Identities = 51/236 (21%), Positives = 107/236 (45%), Gaps = 27/236 (11%)

Query: 53  LVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           LV +H  LV +IA   +G     + + +++  G +GL++A + +D  +G    TY+   I
Sbjct: 18  LVKTHATLVKRIAHHLLGRLPQSVQLDDLIQSGMLGLLEAARHYDSSKGASFETYAGIRI 77

Query: 110 KAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHL-QAITDNNLKPEQVVAIAKKLN 167
           +  M + + R+ W  V      N + +   +R L+    +   DN +  E  V++    +
Sbjct: 78  RGHMLDEVRRNDW--VPRSVYRNSRMISDAVRILEHKFGREAKDNEIAEELGVSLNDYHD 135

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + +    S++  L G + L               D +++D +G      E      R +M
Sbjct: 136 MLQD---SISSHLYGFDDLGV------------TDDVLFDDEGNGST--EPHRNVMRSDM 178

Query: 228 LTRSMSVLN--PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           + R   V++  PR+ R+  +   +++ + L+ +    EVS  R+ QI ++A  +++
Sbjct: 179 MNRLTQVIDSLPRKERLVLSLYYEQD-LNLKEIGEILEVSESRISQILSQATHRIR 233


>gi|307293798|ref|ZP_07573642.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Sphingobium
           chlorophenolicum L-1]
 gi|306879949|gb|EFN11166.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Sphingobium
           chlorophenolicum L-1]
          Length = 245

 Score = 41.6 bits (96), Expect = 0.16,   Method: Compositional matrix adjust.
 Identities = 52/251 (20%), Positives = 112/251 (44%), Gaps = 23/251 (9%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFD 94
           A  Y      S+  RL   ++ LV K A    G     + I +++  G + L++A   F+
Sbjct: 12  ANTYGRSAHASSPERLARQYMPLVRKTAWHVHGRVSSAIEIEDLLQIGMVALVEAANGFE 71

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
            +RG   A+Y+   ++ AM +++ R  ++ +    A +K+L     RL+  L       +
Sbjct: 72  -DRGLGFASYAQMRVRGAMIDHLRRHATMTR-SAMAQRKQLAGIRNRLEQKL-----GRI 124

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
             E  ++    L+ +    ++  C +    S++ +   SD++      W     +  + V
Sbjct: 125 PLESEMSAEMGLDPAAYREVADGCEMVQHTSMDEVY--SDQSM-----WFADVEERADDV 177

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
           +    ER++ +  L + +  L  RE  + +   ++E  + LE + +  ++   RV QI+ 
Sbjct: 178 M----ERESLKAALAKCIGDLPQREALVLQLYFVEE--LNLEEIGATLDIGAARVCQIKK 231

Query: 275 RAFKKVQESIQ 285
            A  K++E ++
Sbjct: 232 AALDKLREKLR 242


>gi|221310502|ref|ZP_03592349.1| RNA polymerase sporulation-specific sigma factor (sigma-K)
           (N-terminal half) [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221314826|ref|ZP_03596631.1| RNA polymerase sporulation-specific sigma factor (sigma-K)
           (N-terminal half) [Bacillus subtilis subsp. subtilis
           str. NCIB 3610]
 gi|221324026|ref|ZP_03605320.1| RNA polymerase sporulation-specific sigma factor (sigma-K)
           (N-terminal half) [Bacillus subtilis subsp. subtilis
           str. SMY]
 gi|321312063|ref|YP_004204350.1| sporulation sigma factor SigK [Bacillus subtilis BSn5]
 gi|143642|gb|AAA22804.1| spoIVCB peptide precursor [Bacillus subtilis]
 gi|320018337|gb|ADV93323.1| sporulation sigma factor SigK [Bacillus subtilis BSn5]
          Length = 155

 Score = 41.6 bits (96), Expect = 0.16,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 3/75 (4%)

Query: 39  KRYRE---HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           K+Y E    GD  A + L+  +LRLV  I   +   G    +++S G IGL++ ++ +  
Sbjct: 37  KKYLELMAKGDEHARNMLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKGIESYSA 96

Query: 96  ERGFRLATYSMWWIK 110
            +G +LATY+   I+
Sbjct: 97  GKGTKLATYAARCIE 111


>gi|332994104|gb|AEF04159.1| flagellar biosynthesis sigma factor [Alteromonas sp. SN2]
          Length = 243

 Score = 41.6 bits (96), Expect = 0.16,   Method: Compositional matrix adjust.
 Identities = 60/255 (23%), Positives = 108/255 (42%), Gaps = 38/255 (14%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           A  Y++  D S   +LV  H  LV +IA   M      + + +++  G IGL++A + FD
Sbjct: 5   AAAYQQQTDKS---QLVERHASLVKRIAHHLMARLPASVLVDDLIQSGMIGLLEAARNFD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
             +G    T++   I+ AM + I +  W+          + +  N R +   +  +    
Sbjct: 62  GSKGASFETFAGIRIRGAMLDEIRKGDWT---------PRSVHKNGRAITEAISQVEGET 112

Query: 154 LKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNAL--INSSDKNSSQWQDWLVY 206
            +  + V IA K+NVS  +   M       +L G E L     + S++KN          
Sbjct: 113 GRDARDVDIAAKMNVSMQDYHQMLNEVNAGKLVGIEDLGVSEDVISTEKNRGS------- 165

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
             D   + L++   +K     L  +++ L  RE  +      +E  + L  +    +VS 
Sbjct: 166 --DAPLEDLMQGAFQK----ALAHAITTLPEREAIVLSLYYDEE--LNLREIGEVLDVSE 217

Query: 267 ERVRQIEARAFKKVQ 281
            RV QI ++A  K++
Sbjct: 218 SRVSQIHSQAMLKLK 232


>gi|298528406|ref|ZP_07015810.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfonatronospira
           thiodismutans ASO3-1]
 gi|298512058|gb|EFI35960.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfonatronospira
           thiodismutans ASO3-1]
          Length = 261

 Score = 41.6 bits (96), Expect = 0.16,   Method: Compositional matrix adjust.
 Identities = 19/62 (30%), Positives = 38/62 (61%), Gaps = 4/62 (6%)

Query: 62  VKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           ++I      + LP    +++++S G++GL++A+  FDP +G +L T++   IK AM + +
Sbjct: 47  IRITAARLKHKLPAHVDVNDLISAGSLGLIEALGNFDPTQGIKLETFADNRIKGAMLDEL 106

Query: 118 LR 119
            R
Sbjct: 107 RR 108


>gi|149176711|ref|ZP_01855322.1| RNA polymerase sigma factor whiG [Planctomyces maris DSM 8797]
 gi|148844352|gb|EDL58704.1| RNA polymerase sigma factor whiG [Planctomyces maris DSM 8797]
          Length = 258

 Score = 41.6 bits (96), Expect = 0.16,   Method: Compositional matrix adjust.
 Identities = 17/42 (40%), Positives = 27/42 (64%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           G+ +++++S G  GLM A+  FD ERG +  TY +  I+ AM
Sbjct: 51  GVDLNDLISAGVFGLMDAINAFDLERGVKFETYCVPRIRGAM 92


>gi|242371561|ref|ZP_04817135.1| DNA-directed RNA polymerase sigma subunit FliA [Staphylococcus
           epidermidis M23864:W1]
 gi|242350713|gb|EES42314.1| DNA-directed RNA polymerase sigma subunit FliA [Staphylococcus
           epidermidis M23864:W1]
          Length = 256

 Score = 41.2 bits (95), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 52/247 (21%), Positives = 117/247 (47%), Gaps = 16/247 (6%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           K ++E+ +  A  +LVT + +L+  +A  Y        ++V  G +GL+ A+ +FD    
Sbjct: 21  KEHQENENSQAQDKLVTHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDLSFD 80

Query: 99  FRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
            +   + +  +   ++ Y+  ++WS+         +R+     R+K     +T+   +  
Sbjct: 81  RKFEAFLVPTVIGEIKRYLRDKTWSV------HVPRRIKEIGPRIKKVSDELTNELERSP 134

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQVLI 216
            +  IA++L V++ EV+     +   +S NAL ++ S +         + D  GQ+    
Sbjct: 135 SINEIAERLEVTDEEVLEA---MEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQQD--- 188

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           +  +   +R +L R + +L+ RER+I +   ++   ++ +       +S+  V +++  A
Sbjct: 189 DNYDLTEKRMILERILPILSDRERQIIQCTFIE--GLSQKETGERIGLSQMHVSRLQRTA 246

Query: 277 FKKVQES 283
            KK+QE+
Sbjct: 247 IKKLQEA 253


>gi|255283596|ref|ZP_05348151.1| DNA-directed RNA polymerase specialized sigma subunit [Bryantella
           formatexigens DSM 14469]
 gi|255265858|gb|EET59063.1| DNA-directed RNA polymerase specialized sigma subunit [Bryantella
           formatexigens DSM 14469]
          Length = 191

 Score = 41.2 bits (95), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 33/103 (32%), Positives = 51/103 (49%), Gaps = 16/103 (15%)

Query: 47  LSAAHRLVTSHLRLVVKI--AMGYRGYGLPIS---EVVSEGNIGLMQAVKKFDPERGFRL 101
           ++AA+RL+  HL LV KI  ++ +    LP+    E+   G + L QA   +D ER F  
Sbjct: 5   ITAANRLIVEHLELVPKIVRSLTFSYSHLPVQEYEELTQIGYLALCQAASGYDWERPF-- 62

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           A Y+   I+ A+ +Y    W        A QK LF +L  ++ 
Sbjct: 63  APYARTAIRNAIYDY----WR-----DCARQKNLFCSLDAIQA 96


>gi|254437394|ref|ZP_05050888.1| RNA polymerase sigma factor, sigma-70 family [Octadecabacter
           antarcticus 307]
 gi|198252840|gb|EDY77154.1| RNA polymerase sigma factor, sigma-70 family [Octadecabacter
           antarcticus 307]
          Length = 207

 Score = 41.2 bits (95), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 43/210 (20%), Positives = 102/210 (48%), Gaps = 19/210 (9%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           I +++  G IGL++A +++  + G    +Y++  I+ A+ +Y+ ++ +L         ++
Sbjct: 7   IEDLLQVGLIGLIEAAQRYTRQEGVSFESYAVLRIRGAIYDYLRKNTNL--------GRK 58

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
                + +K  L +++    +      +A+ L++S  E +S   +       N+L +  D
Sbjct: 59  AILTSKAVKAALASLSQKLGREPTQPELAEALSMSLQE-LSKWAQNVNSSYHNSLQDEYD 117

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
           ++S     W   +    E ++    +R   ++ L  ++  L  RE  + +   ++E  + 
Sbjct: 118 EHSL----WFSSNEPTTEHLV----DRGRLKDALLAALVSLPKREALVLQLYYVEE--LN 167

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L  +++  EV+  RV Q+++ AFKK+Q S+
Sbjct: 168 LYEIAAVLEVTPGRVSQLKSAAFKKMQPSL 197


>gi|109899335|ref|YP_662590.1| flagellar biosynthesis sigma factor [Pseudoalteromonas atlantica
           T6c]
 gi|109701616|gb|ABG41536.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Pseudoalteromonas
           atlantica T6c]
          Length = 242

 Score = 41.2 bits (95), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 56/252 (22%), Positives = 108/252 (42%), Gaps = 24/252 (9%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           A  Y++  D +A   LV  H  LV +IA   +      + + +++  G IGL++A + FD
Sbjct: 5   AAAYQQLDDRNA---LVERHAPLVKRIAHHLIARLPASVLVDDLIQAGMIGLLEASRNFD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
             +G    T++   I+ +M + I +  W+          + +  N R +   +  +    
Sbjct: 62  GTKGASFETFAGIRIRGSMLDEIRKGDWT---------PRSVHKNGRAITDAINKVERET 112

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            +  + V IAKKL VS    I    ++ G+ +   +I   D   S  +D +  +      
Sbjct: 113 GRDARDVDIAKKLEVS----IEQYHQMLGEVNAGKIIGMEDLGVS--EDVVTTEQTKGSD 166

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
              E   + + +  L  +++ L  RE  +      +E  + L  +    +VS  RV QI 
Sbjct: 167 TPFEDLLQGSFQKALAHAITTLPEREAIVLSLYYDEE--LNLREIGEVLDVSESRVSQIH 224

Query: 274 ARAFKKVQESIQ 285
           ++A  K++  +Q
Sbjct: 225 SQAMLKLKSKMQ 236


>gi|284041831|ref|YP_003392171.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Conexibacter woesei
           DSM 14684]
 gi|283946052|gb|ADB48796.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Conexibacter woesei
           DSM 14684]
          Length = 262

 Score = 41.2 bits (95), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 24/79 (30%), Positives = 45/79 (56%), Gaps = 5/79 (6%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFD 94
           +RY+  G+ +A   LV ++   +VK   G     +P    +++++S+G  GL+ AV++F+
Sbjct: 15  RRYKGTGERAARDDLVLAY-SPIVKYVAGRVAARMPAHVDVADLISDGFKGLLDAVERFE 73

Query: 95  PERGFRLATYSMWWIKAAM 113
           P RG R   Y+   I+ A+
Sbjct: 74  PVRGVRFEAYADTRIRGAI 92


>gi|261366790|ref|ZP_05979673.1| RNA polymerase sigma-F factor [Subdoligranulum variabile DSM 15176]
 gi|282571621|gb|EFB77156.1| RNA polymerase sigma-F factor [Subdoligranulum variabile DSM 15176]
          Length = 232

 Score = 41.2 bits (95), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 46/195 (23%), Positives = 86/195 (44%), Gaps = 21/195 (10%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            +  +L LV   A  ++G G+   E+ + G +GL++A   FD  RG   +TY++  I   
Sbjct: 14  FIEKNLGLVHACAGRFKGRGIEYEELYAAGCLGLVKACDGFDTSRGVCFSTYAVPVILGE 73

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +++ + R    VK+  +  +  L  N  R +     +     +P  V  +A+ L  +  +
Sbjct: 74  IKK-LFRDGGTVKVSRSLKELSLKINAERER----CLKKTGQEP-GVTQLAEILQTTPEQ 127

Query: 173 VISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           +      LA   SL A+ +  +D+   Q ++W V         +   EE  + R  L   
Sbjct: 128 IA-----LAIRASLPAISLTPTDEEDGQ-REWDVP--------VDSPEESLSDRIGLAEV 173

Query: 232 MSVLNPRERRIFEAR 246
           M  L+P +R++   R
Sbjct: 174 MEKLSPTDRQMIRLR 188


>gi|138894766|ref|YP_001125219.1| RNA polymerase sigma factor SigD [Geobacillus thermodenitrificans
           NG80-2]
 gi|196247611|ref|ZP_03146313.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacillus sp.
           G11MC16]
 gi|134266279|gb|ABO66474.1| RNA polymerase sigma-28 factor (sigma-D) [Geobacillus
           thermodenitrificans NG80-2]
 gi|196212395|gb|EDY07152.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacillus sp.
           G11MC16]
          Length = 253

 Score = 41.2 bits (95), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 25/71 (35%), Positives = 38/71 (53%), Gaps = 3/71 (4%)

Query: 46  DLSAAHRLVTSHLRLV---VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           D  AA  LV  ++ LV   V+         +P  E+VS G +GL  A++KFDP R  +  
Sbjct: 23  DRHAAEELVQRYMPLVSYHVQRLSATLPSSVPKEELVSLGLVGLYDALEKFDPSRDLKFD 82

Query: 103 TYSMWWIKAAM 113
           TY+ + I+ A+
Sbjct: 83  TYASFRIRGAI 93


>gi|307546921|ref|YP_003899400.1| flagellar biosynthesis sigma factor [Halomonas elongata DSM 2581]
 gi|307218945|emb|CBV44215.1| flagellar biosynthesis sigma factor [Halomonas elongata DSM 2581]
          Length = 235

 Score = 41.2 bits (95), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 63/248 (25%), Positives = 111/248 (44%), Gaps = 37/248 (14%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQAVKKFDPERG 98
           E GDL      +  +L LV + A+  +   LP S    +++  G +GL++A+ +FD  +G
Sbjct: 9   EQGDL------LEEYLPLVRRQALALQ-VRLPASIELDDLIQAGTVGLLEALGRFDAAQG 61

Query: 99  FRLATYSMWWIKAAM-QEYILRSW--SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
              +T++   I+ AM  E   R W    V+ G  A  +     +RRL+  L        +
Sbjct: 62  ASFSTFASQRIRGAMLDELRSRDWLPRSVRRGARAADE----AVRRLEQSLG-------R 110

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV- 214
           P +   IA+ L++     I    RL  D +   L+   D  S   +  L  +   +  V 
Sbjct: 111 PPEEAEIAEALDMD----IDAYRRLLSDTNSGQLLPFEDLMSEGGEGRLRDNETAETPVS 166

Query: 215 -LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
            L++ E    RR  LT  +  L  RE ++  A   QE  + L+ + +   V+  RV Q+ 
Sbjct: 167 LLVDDE----RRRQLTAGIEALPERE-KLLMALYYQEE-LNLKEIGAVLGVTESRVCQLH 220

Query: 274 ARAFKKVQ 281
           ++A  +++
Sbjct: 221 SQAVSRLR 228


>gi|182420443|ref|ZP_02641505.2| RNA polymerase sigma factor RpoD [Clostridium perfringens NCTC
           8239]
 gi|182382221|gb|EDT79700.1| RNA polymerase sigma factor RpoD [Clostridium perfringens NCTC
           8239]
          Length = 237

 Score = 41.2 bits (95), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 24/102 (23%), Positives = 51/102 (50%), Gaps = 9/102 (8%)

Query: 23  IRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISEVV 79
           I+++  +  +E  VL     + G+  A   L+ ++ +L+ K+A  +   +   +   +++
Sbjct: 5   IKEVKAMTNEELVVLY----QQGEKKALDELLENNDKLIYKVASKFYSEKTSSIEFDDLL 60

Query: 80  SEGNIGLMQAVKKFDPE--RGFRLATYSMWWIKAAMQEYILR 119
            EG IG + A  K+D E  +  +  TY+ +WI   +  +I R
Sbjct: 61  QEGRIGFILACSKYDIEYIKSTKFITYAFYWIYQKIHRFITR 102


>gi|160893355|ref|ZP_02074142.1| hypothetical protein CLOL250_00905 [Clostridium sp. L2-50]
 gi|156865047|gb|EDO58478.1| hypothetical protein CLOL250_00905 [Clostridium sp. L2-50]
          Length = 200

 Score = 41.2 bits (95), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 37/69 (53%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
           RE  D +A   L+  ++ +V K +      G    +++ EG IGL++A++ FD  +G   
Sbjct: 17  REENDNAAFEYLIKKYMGIVKKESRALYIIGAENEDIIQEGMIGLIKAIRSFDGSKGASF 76

Query: 102 ATYSMWWIK 110
           +T++   IK
Sbjct: 77  STFANLCIK 85


>gi|126649718|ref|ZP_01721954.1| sporulation sigma factor SigG [Bacillus sp. B14905]
 gi|126593437|gb|EAZ87382.1| sporulation sigma factor SigG [Bacillus sp. B14905]
          Length = 257

 Score = 41.2 bits (95), Expect = 0.17,   Method: Compositional matrix adjust.
 Identities = 26/84 (30%), Positives = 44/84 (52%), Gaps = 1/84 (1%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L+ +E   L  R  + G++     LV  +LRLV+ I   +   G    ++   G IG
Sbjct: 15  LPILKHEEMKELFIRL-QAGEIEIREELVMCNLRLVLSIVGRFAYRGEQADDLFQVGCIG 73

Query: 86  LMQAVKKFDPERGFRLATYSMWWI 109
           LM+A+  FD +   R +TY++  I
Sbjct: 74  LMKAIDHFDLKHNVRFSTYAVPMI 97


>gi|167470529|ref|ZP_02335233.1| alternative sigma factor RpoH [Yersinia pestis FV-1]
          Length = 127

 Score = 41.2 bits (95), Expect = 0.18,   Method: Compositional matrix adjust.
 Identities = 24/61 (39%), Positives = 39/61 (63%), Gaps = 1/61 (1%)

Query: 226 NMLTRSMSVLNPRERRIFEARRLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + L+ ++  L+ R + I  AR L  EN  TL+ L+ ++ VS ERVRQ+E  A KK++ +I
Sbjct: 66  DKLSYALEGLDERSQHIIRARWLDDENKSTLQELADQYGVSAERVRQLEKNAMKKLRMAI 125

Query: 285 Q 285
           +
Sbjct: 126 E 126


>gi|254411015|ref|ZP_05024793.1| RNA polymerase sigma factor, sigma-70 family [Microcoleus
           chthonoplastes PCC 7420]
 gi|196182370|gb|EDX77356.1| RNA polymerase sigma factor, sigma-70 family [Microcoleus
           chthonoplastes PCC 7420]
          Length = 260

 Score = 41.2 bits (95), Expect = 0.18,   Method: Compositional matrix adjust.
 Identities = 35/135 (25%), Positives = 70/135 (51%), Gaps = 10/135 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFDPER 97
           Y ++  +   ++LV  +  LV KIA  YR       P  ++V  G +GL++A+++F P++
Sbjct: 17  YSQNPSIELRNQLVRLNSGLVKKIA--YRVSQQCSEPYDDLVQLGYLGLIRAIERFKPDQ 74

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G+  +++++ +I+  M  ++    ++VKI      + L    +R+   L A      +P 
Sbjct: 75  GYAFSSFAVPFIRGEMLHFLRDKGNIVKI--PRRWQELQQEGQRVSKRLTATLG---RPP 129

Query: 158 QVVAIAKKLNVSESE 172
           +   IA+ LN+S  E
Sbjct: 130 KEAEIAQALNISMQE 144


>gi|295095481|emb|CBK84571.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Enterobacter
           cloacae subsp. cloacae NCTC 9394]
          Length = 229

 Score = 41.2 bits (95), Expect = 0.18,   Method: Compositional matrix adjust.
 Identities = 50/221 (22%), Positives = 97/221 (43%), Gaps = 32/221 (14%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL+ AV ++D  +G    TY++  I+ AM +  LRS   V      N + 
Sbjct: 31  LDDLLQAGGIGLLNAVDRYDALQGTAFTTYAVQRIRGAMLDE-LRSRDWVPRSVRRNARE 89

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   + +L+   Q +  N  + E    +A++L +   E   M            L+++++
Sbjct: 90  VAHAMGQLE---QELGRNATETE----VAERLGIPVEEYRQM------------LLDTNN 130

Query: 195 KNSSQWQDW---------LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
                + +W         LV D   QE  L    E  N R  +  ++  L  RE+ +   
Sbjct: 131 SQLFSYDEWREEHGDSIELVTDEHQQENPLHHLLE-GNLRQRVMEAIEALPEREQLVLTL 189

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +E  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 190 YYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 228


>gi|227485765|ref|ZP_03916081.1| possible DNA-directed RNA polymerase sigma subunit SigB
           [Anaerococcus lactolyticus ATCC 51172]
 gi|227236320|gb|EEI86335.1| possible DNA-directed RNA polymerase sigma subunit SigB
           [Anaerococcus lactolyticus ATCC 51172]
          Length = 258

 Score = 41.2 bits (95), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 17/74 (22%), Positives = 40/74 (54%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  HL +V  ++  Y G G+   ++    ++GL+ AV ++DP +G+  ++++   I   
Sbjct: 33  LIEEHLYIVDILSNKYVGKGIEKDDLYQVASLGLINAVDRYDPSKGYAFSSFATPTIMGE 92

Query: 113 MQEYILRSWSLVKI 126
           ++ Y      ++K+
Sbjct: 93  IKRYFRDKGWVIKV 106


>gi|262199287|ref|YP_003270496.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Haliangium
           ochraceum DSM 14365]
 gi|262082634|gb|ACY18603.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Haliangium
           ochraceum DSM 14365]
          Length = 244

 Score = 41.2 bits (95), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 60/255 (23%), Positives = 106/255 (41%), Gaps = 39/255 (15%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA--MGYRGYGLPIS----EV 78
           ++ + E+      A R REH D      L+  H+ L + +A  M  R   LP S    ++
Sbjct: 9   RVQVQERHRRVDAAARKREHCD-----ELIKEHIELALSMARRMARR---LPASVCLDDI 60

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
            S   +GL +A +++D +R      ++   I+ A+ + + RS  L + G  A  +++   
Sbjct: 61  ESAALLGLTEAARRYDDKRREPFMGFAAKRIRGAILDQLRRSDMLTRRGRRAA-RQVAEA 119

Query: 139 LRRLKG-HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            R  +G H +  TD+ L        A +L VS+ E            S+ A +       
Sbjct: 120 ARSFEGEHGRPATDSEL--------ADQLGVSDEEF----------HSVYASVRDVTVTG 161

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
               D ++ D        I   ER+  R  L R++  L+ R R +  A    ++ +TL  
Sbjct: 162 VDDADAILPDDAAATFACI---ERQQLRAALVRALEKLDDRARVVLAA--YYQDGLTLRE 216

Query: 258 LSSEFEVSRERVRQI 272
           +     ++  RV QI
Sbjct: 217 IGQILGITESRVCQI 231


>gi|302549077|ref|ZP_07301419.1| RNA polymerase sigma-G factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302466695|gb|EFL29788.1| RNA polymerase sigma-G factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 287

 Score = 41.2 bits (95), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 60/252 (23%), Positives = 109/252 (43%), Gaps = 34/252 (13%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV   L +  +IA  +R  G  I ++     +GL++AV +FDP RG    +Y++  I   
Sbjct: 53  LVALWLPMAHRIAGRFRDRGESIEDLRQVAALGLVKAVDRFDPSRGA-FESYAVPTITGE 111

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLR-RLKGHLQAITDNNLKPE-QVVAIAKKLNVS 169
           ++ +   R W+L          R    LR +++   + +T N   PE  V A+A    ++
Sbjct: 112 VKRHFRDRMWAL-------RVPRRVQELRNKVRVARRELTQNPGSPEPSVPALAAHTGLT 164

Query: 170 ESEVISMNCRLAGDESLNALIN-------SSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           E EV       AG E+L++          S+D +     D L    D    V++++E  K
Sbjct: 165 EEEVN------AGLEALDSFSTLSLDAELSADDDGYSLADTLGA-SDTSYDVVVDRESAK 217

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
                    +  L  RER I   R  ++  +T   ++ +  +S+  V ++  R+  +V++
Sbjct: 218 E-------GLRRLPERERAILYMRFFED--MTQSRIADQLGISQMHVSRLITRSCARVRD 268

Query: 283 SIQKQVELSSSP 294
            +  Q      P
Sbjct: 269 EVLGQRGAGRGP 280


>gi|284045933|ref|YP_003396273.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
 gi|283950154|gb|ADB52898.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
          Length = 263

 Score = 41.2 bits (95), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 61/255 (23%), Positives = 111/255 (43%), Gaps = 30/255 (11%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           +LA R R +GD  A   L+  HL L   +A  YR     + ++V   ++GL++AV +FDP
Sbjct: 28  MLATRAR-NGDGRAREALIAEHLPLARALARRYRRGSESLDDLVQVASVGLIKAVDRFDP 86

Query: 96  ERGFRLATYSMWWIKAAMQEYILRS-WSL-VKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           +RG   +T++   I   +  +   + W + V  GT    + L   +R     ++  T   
Sbjct: 87  DRGHSFSTFAQPTIVGELLRHFRDTGWGVHVARGT----QELALKVRSAAEAIETETGAV 142

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN------SSDKNSSQWQDWLVYD 207
             P Q   IA++       V+         E+L AL N      ++        D  + D
Sbjct: 143 ATPRQ---IAERTGAELEAVV---------EALGALANRTALSLATPAGHDDEGDATIAD 190

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
             G  +   E       R +L  ++  L  RE+RI   R + +  +T   +++E  VS+ 
Sbjct: 191 TLGDVE---EGYRAAEARALLGPALRHLPEREQRIIRMRFVDD--LTQSEIATEIGVSQM 245

Query: 268 RVRQIEARAFKKVQE 282
           ++ ++  ++  K+ E
Sbjct: 246 QISRLLRQSLDKLHE 260


>gi|147677483|ref|YP_001211698.1| DNA-directed RNA polymerase specialized sigma subunit
           [Pelotomaculum thermopropionicum SI]
 gi|146273580|dbj|BAF59329.1| DNA-directed RNA polymerase specialized sigma subunit
           [Pelotomaculum thermopropionicum SI]
          Length = 243

 Score = 41.2 bits (95), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 25/91 (27%), Positives = 44/91 (48%), Gaps = 1/91 (1%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y + G   +  ++V +  RLV    +G    G    ++V  G  GL++A K++DP RG  
Sbjct: 25  YLQDGSAESLQKVVEAGTRLV-HYFVGLYAPGHSREDLVQSGFEGLLKAAKRYDPGRGVS 83

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
            +TY+   I   ++ +I +  S  + G  A 
Sbjct: 84  FSTYASHCIMGEVRHFIRKEASFSRPGWAAG 114


>gi|904172|gb|AAB38522.1| flagellin sigma factor [Yersinia enterocolitica (type O:8)]
          Length = 229

 Score = 41.2 bits (95), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 46/232 (19%), Positives = 98/232 (42%), Gaps = 38/232 (16%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRL V++        + + +++  G IGL+ AV+++D  +G    TY++  I   + E  
Sbjct: 19  LRLQVRLPAS-----VELDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIAPMLDELR 73

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
            R W+          +RL  N R +   +Q +      P     +A+ L++  +E   + 
Sbjct: 74  QRDWA---------PRRLRRNAREVASAMQKVEQRLGAPATEQEVAQNLDIDLTEYRQI- 123

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR---------RNML 228
                      L+++++     + +W   +H    + ++E  E  N          R  +
Sbjct: 124 -----------LLDTNNSQLFSYDEW-REEHGRTVEPMLEGHEDANPLQHLLEGNLRQRV 171

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++  L  RE+ +      +E  + L+ + +  EV   RV Q+ ++A K++
Sbjct: 172 IEAIEALPEREKMVLTLYYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRL 221


>gi|114566161|ref|YP_753315.1| sigma 28 (flagella/sporulation) [Syntrophomonas wolfei subsp.
           wolfei str. Goettingen]
 gi|114337096|gb|ABI67944.1| sigma 28 (flagella/sporulation) [Syntrophomonas wolfei subsp.
           wolfei str. Goettingen]
          Length = 243

 Score = 41.2 bits (95), Expect = 0.19,   Method: Compositional matrix adjust.
 Identities = 51/248 (20%), Positives = 114/248 (45%), Gaps = 21/248 (8%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R  + GD  A  +L  +++ L+  +   ++       ++   G +GL++A+++FD     
Sbjct: 15  RLAQGGDQEAKAQLYEANVGLIYLVLERFKNTSYDQEDLFQVGAMGLLKAIERFDFSFDV 74

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKI--GTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           R +TY++  I   ++++ LR   +VK+  G      R+ +   +L+G L        +  
Sbjct: 75  RFSTYAVPMIIGEIKKF-LRDDGMVKVQRGIKELYARVRWAQDKLRGDLG-------REP 126

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
            V  IA  L + + +++           ++ ++ S +K      D LV++ +G   +L  
Sbjct: 127 GVNEIASLLEMEKEDIVVAMEACQAPAYIHDVVPSEEKEQLSLLDKLVHE-EGNVAIL-- 183

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
                  +  L  +++ L+ RER +   R  Q+   T+  ++ +  VS+ ++ +IE  A 
Sbjct: 184 ------EKLALREALAKLDERERVVIIRRFFQDETQTV--IAEDLGVSQVQISRIEKSAI 235

Query: 278 KKVQESIQ 285
            K++  +Q
Sbjct: 236 LKLRSLLQ 243


>gi|301165903|emb|CBW25476.1| RNA polymerase sigma factor WhiG [Bacteriovorax marinus SJ]
          Length = 260

 Score = 41.2 bits (95), Expect = 0.20,   Method: Compositional matrix adjust.
 Identities = 27/92 (29%), Positives = 46/92 (50%), Gaps = 11/92 (11%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFD 94
           K YR   D      ++  +  L+  IA       LP    + +++S G IGLM A++KFD
Sbjct: 12  KDYRSTVDPKVKDEIIIEYAPLIKYIAQRIASR-LPSNVELDDLISCGVIGLMDAIEKFD 70

Query: 95  PERGFRLATYSMWWIKAAM------QEYILRS 120
           P R  +  TY+ + I+ ++      Q+++ RS
Sbjct: 71  PSRDNKFKTYAEFRIRGSILDELRAQDWVPRS 102


>gi|295102717|emb|CBL00262.1| RNA polymerase sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii L2-6]
          Length = 221

 Score = 41.2 bits (95), Expect = 0.20,   Method: Compositional matrix adjust.
 Identities = 23/83 (27%), Positives = 40/83 (48%), Gaps = 8/83 (9%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIA--------MGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           + GD +A   L+ ++   + K+A        +   G  L   ++   GN+GL +AV KFD
Sbjct: 13  QKGDAAALDSLIENNKSFIGKVANDLFRSMNLAQSGLNLDTDDLKQAGNLGLWKAVSKFD 72

Query: 95  PERGFRLATYSMWWIKAAMQEYI 117
              G +  TY+   I+ AM + +
Sbjct: 73  AACGMKFLTYAAPAIRNAMMDMV 95


>gi|294629742|ref|ZP_06708302.1| RNA polymerase sigma factor [Streptomyces sp. e14]
 gi|292833075|gb|EFF91424.1| RNA polymerase sigma factor [Streptomyces sp. e14]
          Length = 305

 Score = 41.2 bits (95), Expect = 0.20,   Method: Compositional matrix adjust.
 Identities = 45/170 (26%), Positives = 78/170 (45%), Gaps = 20/170 (11%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  +L LV   A  +R    P+ +++  G IGL++A+ +F+  RG    T++M  I   
Sbjct: 84  LVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRGVEFPTFAMPTIIGE 143

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SWS V++     + RL  +L +    L    D   +   V  +A+ L +S  
Sbjct: 144 IKRFFRDTSWS-VRVPRRLQELRL--DLAKAGDELAQRLD---RAPTVSELAEHLGLSAE 197

Query: 172 EVISMNCRLAGDESLNALINSS-----DKNSSQ--WQDWLVYDHDGQEQV 214
           EV+       G  + NA   SS     ++N S+    D + Y+  G E +
Sbjct: 198 EVVE------GMAASNAYTASSLDAQPEENESEGALADRIGYEDHGIEGI 241


>gi|261340320|ref|ZP_05968178.1| flagellar biosynthesis sigma factor FliA [Enterobacter cancerogenus
           ATCC 35316]
 gi|288317411|gb|EFC56349.1| flagellar biosynthesis sigma factor FliA [Enterobacter cancerogenus
           ATCC 35316]
          Length = 229

 Score = 41.2 bits (95), Expect = 0.20,   Method: Compositional matrix adjust.
 Identities = 49/221 (22%), Positives = 98/221 (44%), Gaps = 32/221 (14%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL+ AV ++D  +G    TY++  I+ AM +  LRS   V      N + 
Sbjct: 31  LDDLLQAGGIGLLNAVDRYDALQGTAFTTYAVQRIRGAMLDE-LRSRDWVPRSVRRNARE 89

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   + +L+   Q +  N  + E    +A++L ++  +   M            L+++++
Sbjct: 90  VAHAMGQLE---QELGRNATETE----VAERLGIAVEDYRQM------------LLDTNN 130

Query: 195 KNSSQWQDW---------LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
                + +W         LV D   QE  L    E  N R  +  ++  L  RE+ +   
Sbjct: 131 SQLFSYDEWREEHGDSIELVTDEHQQENPLHHLME-GNLRQRVMEAIEALPEREQLVLTL 189

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +E  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 190 YYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 228


>gi|294497070|ref|YP_003560770.1| RNA polymerase sigma-B factor [Bacillus megaterium QM B1551]
 gi|295702435|ref|YP_003595510.1| RNA polymerase sigma-B factor [Bacillus megaterium DSM 319]
 gi|294347007|gb|ADE67336.1| RNA polymerase sigma-B factor [Bacillus megaterium QM B1551]
 gi|294800094|gb|ADF37160.1| RNA polymerase sigma-B factor [Bacillus megaterium DSM 319]
          Length = 264

 Score = 41.2 bits (95), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 56/250 (22%), Positives = 118/250 (47%), Gaps = 28/250 (11%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           +R+++  D  A   LV  +  LV  IA  Y +G  L   ++V  G +GL+ A++++D   
Sbjct: 20  ERFQKTQDEEAQSDLVVHYKNLVESIARRYSKGRSLH-EDIVQVGMLGLLGAIRRYDASF 78

Query: 98  GFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           G    ++++  I   ++ ++  ++WS+         +R+     ++K  ++ +T    + 
Sbjct: 79  GRSFESFAVPTIIGEIKRFLRDKTWSV------HVPRRIKELGPKIKAAVEELTTRLQRS 132

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQVL 215
            QV  IA  + V+E E++     +   +S  AL ++ S +  S      + D  G+++  
Sbjct: 133 PQVKEIADHIGVTEEEILET---MEMGQSYQALSVDHSIEADSDGSTVTILDLVGEQESG 189

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS-----SEFEVSRERVR 270
            EK    ++R +L + + VL+ RE+ +            +ENLS      +  +S+  V 
Sbjct: 190 YEK---TDQRLVLEKILHVLSDREKEVI-------RYTFIENLSQKDAGEKLGISQMHVS 239

Query: 271 QIEARAFKKV 280
           +++ RA  K+
Sbjct: 240 RLQRRALDKL 249


>gi|81300593|ref|YP_400801.1| RNA polymerase sigma factor SigF [Synechococcus elongatus PCC 7942]
 gi|81169474|gb|ABB57814.1| group3 RNA polymerase sigma factor SigF [Synechococcus elongatus
           PCC 7942]
          Length = 260

 Score = 41.2 bits (95), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 43/177 (24%), Positives = 85/177 (48%), Gaps = 23/177 (12%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           Y E   ++  +++V  +L LV KIA    R    P  ++   G +GL++A+++F P +G 
Sbjct: 18  YAETPSIALRNQIVQLNLGLVRKIAHRLSRQCSEPYEDLEQIGFMGLIRAIERFQPHQGC 77

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN---LKP 156
             +++++ +I+  +  ++  S   ++I       R +  L+R    L+ +  +       
Sbjct: 78  AFSSFAVPYIRGEILHFLRDSCHSIRI------PRRWQELQRQGQQLREVLRHEWGRAPT 131

Query: 157 EQVVAIAKKLNVSESEVI----------SMNCRL--AGDESLNALINSSDKNSSQWQ 201
           EQ +A A  L+++E + I          S++  L  AGD S+  L+ +    S QWQ
Sbjct: 132 EQELAFALNLSMTEWQEIHLARRNRMPMSLDATLSQAGDSSVT-LVETLPDTSQQWQ 187


>gi|164686436|ref|ZP_02210464.1| hypothetical protein CLOBAR_00001 [Clostridium bartlettii DSM
           16795]
 gi|164604447|gb|EDQ97912.1| hypothetical protein CLOBAR_00001 [Clostridium bartlettii DSM
           16795]
          Length = 256

 Score = 41.2 bits (95), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 52/243 (21%), Positives = 113/243 (46%), Gaps = 30/243 (12%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +L LV  +A  Y   G+   ++   G++ L+ A++++D  +G+  ++++   I   
Sbjct: 35  LIERNLYLVSILAKKYINKGVEFEDLYQVGSLALIYAIERYDISKGYEFSSFATPTIIGE 94

Query: 113 MQEYIL-RSWSL------VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
           +++Y   + W++       ++    N+ +L             +   N K  +V  IA+ 
Sbjct: 95  IKKYFRDKVWTMRVPRRVQELNKKVNEAKLL------------LEQQNKKKPKVNEIAEY 142

Query: 166 LNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           +   E EV+       G +  SL++ +NS   +S + +  L+     QE    + E    
Sbjct: 143 IGCREEEVLEALEASYGYQPVSLDSPVNS---DSEEAEISLIDKIGSQENNFSDIE---- 195

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            ++ + +  S LN  ER IFE R  +E   T   L+ E ++S+  + +IE +  +K+++ 
Sbjct: 196 YKDFIEKFTSKLNELERNIFEGRFFKEK--TQSALAKELDISQMTISRIERKVVQKLRKE 253

Query: 284 IQK 286
            ++
Sbjct: 254 YER 256


>gi|304311117|ref|YP_003810715.1| RNA polymerase sigma factor for flagellar operon (Sigma-F factor)
           [gamma proteobacterium HdN1]
 gi|301796850|emb|CBL45062.1| RNA polymerase sigma factor for flagellar operon (Sigma-F factor)
           [gamma proteobacterium HdN1]
          Length = 244

 Score = 40.8 bits (94), Expect = 0.22,   Method: Compositional matrix adjust.
 Identities = 25/74 (33%), Positives = 41/74 (55%), Gaps = 4/74 (5%)

Query: 53  LVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           LV  HL LV +IA   +G     + + +++  G IGL+ A++K+D  +G    TY+   I
Sbjct: 21  LVEQHLPLVRRIAHHMIGRLPSNVIVDDLIQAGVIGLIDALQKYDTGKGASFETYAGIRI 80

Query: 110 KAAMQEYILRS-WS 122
           + AM + I R  W+
Sbjct: 81  RGAMIDEIRRGEWA 94


>gi|153835421|ref|ZP_01988088.1| RNA polymerase sigma factor for flagellar operon [Vibrio harveyi
           HY01]
 gi|156975413|ref|YP_001446320.1| flagellar biosynthesis sigma factor [Vibrio harveyi ATCC BAA-1116]
 gi|148868042|gb|EDL67225.1| RNA polymerase sigma factor for flagellar operon [Vibrio harveyi
           HY01]
 gi|156527007|gb|ABU72093.1| hypothetical protein VIBHAR_03144 [Vibrio harveyi ATCC BAA-1116]
          Length = 244

 Score = 40.8 bits (94), Expect = 0.22,   Method: Compositional matrix adjust.
 Identities = 58/253 (22%), Positives = 104/253 (41%), Gaps = 33/253 (13%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFD 94
           A  Y +HG  ++    +  +  LV +IA    G   P   + +++  G IGL++A + +D
Sbjct: 4   AITYDQHGKFNSQQAFIERYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLIEAQQNYD 63

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +G    TY+   I+ AM + I R    V      N + +   +  L+G L      N 
Sbjct: 64  GSKGASFETYAGIRIRGAMLDDI-RKGDWVPRSVHKNNREINQAIAELEGVL------NR 116

Query: 155 KP---EQVVAIAKKLNVSESEVISMNC-RLAGDESL---NALINSSDKNSSQWQDWLVYD 207
            P   E    +   L+   S +  +NC +L G E L   + +I+ +D+         V D
Sbjct: 117 DPSDSEVAAHLGMTLDQYHSALTDINCSKLVGIEDLGVSDDVISPADETDDSNPFKGVAD 176

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
                         ++ +  L  S+  L  RE  +      +E  + L+ +     VS  
Sbjct: 177 --------------ESFKKALVESIKQLPEREALVLSLYYDEE--LNLKEIGDVLGVSES 220

Query: 268 RVRQIEARAFKKV 280
           RV QI ++A +++
Sbjct: 221 RVSQILSQAMQRL 233


>gi|226949740|ref|YP_002804831.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           A2 str. Kyoto]
 gi|226840763|gb|ACO83429.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           A2 str. Kyoto]
          Length = 183

 Score = 40.8 bits (94), Expect = 0.22,   Method: Compositional matrix adjust.
 Identities = 15/37 (40%), Positives = 25/37 (67%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           E+  EG +GLM+AV +FD  RG + +TY+  ++  A+
Sbjct: 30  ELFQEGCLGLMKAVNRFDTSRGIKFSTYAYPYVDGAI 66


>gi|239826640|ref|YP_002949264.1| RNA polymerase sigma factor SigD [Geobacillus sp. WCH70]
 gi|239806933|gb|ACS23998.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacillus sp. WCH70]
          Length = 254

 Score = 40.8 bits (94), Expect = 0.22,   Method: Compositional matrix adjust.
 Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 3/77 (3%)

Query: 40  RYREHGDLSAAHRLVTSHLRLV---VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           R+  H D  A  +LV +++ LV   V+         +   E++S G +GL  A++KFDP 
Sbjct: 15  RWIYHRDPQAGDKLVQTYMPLVHYHVQRIAASLPKTISKQELISLGLMGLYDALEKFDPS 74

Query: 97  RGFRLATYSMWWIKAAM 113
           R  +  TY+ + I+ A+
Sbjct: 75  RDLKFDTYASFRIRGAI 91


>gi|87311163|ref|ZP_01093286.1| RNA polymerase sigma factor whiG [Blastopirellula marina DSM 3645]
 gi|87286071|gb|EAQ77982.1| RNA polymerase sigma factor whiG [Blastopirellula marina DSM 3645]
          Length = 261

 Score = 40.8 bits (94), Expect = 0.22,   Method: Compositional matrix adjust.
 Identities = 51/218 (23%), Positives = 102/218 (46%), Gaps = 17/218 (7%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           G+ + +++S G  GLM A+  FD  RG +  TY +  I+ AM +  LR+   V     + 
Sbjct: 52  GVELDDLISAGVFGLMDAIDAFDMSRGVKFETYCVPRIRGAMLDE-LRTMDWVPRLVRSK 110

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQV-VAIAKKLNVSESEVISMNCRLAGDESLNALI 190
             +L    ++L+           +P ++ ++    ++V E E +  +    G  SLN   
Sbjct: 111 ASKLNEANKQLEAKF------GRQPTEIELSAHMGMSVKELEKMISDANAVGLISLNKKW 164

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV-LNPRERRIFEARRLQ 249
             +D     ++D  V + D  E +  E   R+ ++N L R ++  LN  ER I      +
Sbjct: 165 YETD----SYKD--VREIDILEDIKGEDPTRRIQKNDLMRLVTKGLNRNERLIIILYYYE 218

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E  +T++ + +  ++S  RV Q+ +   +++Q  + ++
Sbjct: 219 E--LTMKEIGATLDLSESRVSQMHSSIVQRLQSQLGRR 254


>gi|304316787|ref|YP_003851932.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
 gi|302778289|gb|ADL68848.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
          Length = 247

 Score = 40.8 bits (94), Expect = 0.23,   Method: Compositional matrix adjust.
 Identities = 51/220 (23%), Positives = 95/220 (43%), Gaps = 25/220 (11%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R  ++ D  +  +L+  +  L+  I   +   G    ++   G IG ++A+ KFD     
Sbjct: 17  RKSKNNDKLSLEKLLKENSGLIWSIVKKFSNRGYEAEDLYQIGCIGFVKAINKFDESYNV 76

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-----NL 154
           +L+TY++  I   ++ + LR   L+K+  +         L+ L      I D      N 
Sbjct: 77  KLSTYAVPIILGEIKRF-LRDDGLIKVSRS---------LKELSNKAYYIKDELEKELNR 126

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +P  +  IA KLNVS  E+      +A + +  A     +   S+  + L+ +  G E  
Sbjct: 127 EP-TIQEIASKLNVSAEEI-----AMAFESTATAEYLYDNSQHSEDDNMLLIEKIGSEDN 180

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
             + E++   R +L +    L+ RER+I   R  ++   T
Sbjct: 181 EYDIEDKLALRMVLKK----LDSRERQIIVLRYFKDMTQT 216


>gi|237736225|ref|ZP_04566706.1| RNA polymerase sigma factor [Fusobacterium mortiferum ATCC 9817]
 gi|229421778|gb|EEO36825.1| RNA polymerase sigma factor [Fusobacterium mortiferum ATCC 9817]
          Length = 232

 Score = 40.8 bits (94), Expect = 0.23,   Method: Compositional matrix adjust.
 Identities = 25/92 (27%), Positives = 45/92 (48%), Gaps = 5/92 (5%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
               +  +L LV  IA  Y   G+   +VV EG +GL++ ++ ++ E+      Y  +WI
Sbjct: 37  GEDFIVQNLPLVASIAFNYLREGVAYLDVVQEGTMGLIKGIENYNGEKHGDFENYKKYWI 96

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
              ++E +L   +  KI    N+ + FF  +R
Sbjct: 97  ---IREIVLFINN--KITDIKNEFKSFFKDKR 123


>gi|317048579|ref|YP_004116227.1| FliA/WhiG subfamily RNA polymerase sigma-28 factor [Pantoea sp.
           At-9b]
 gi|316950196|gb|ADU69671.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Pantoea sp.
           At-9b]
          Length = 240

 Score = 40.8 bits (94), Expect = 0.23,   Method: Compositional matrix adjust.
 Identities = 47/218 (21%), Positives = 90/218 (41%), Gaps = 38/218 (17%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTANQK 133
           + +++  G IGL+ AV+++D  +G    TY++  I+ AM  E   R W+          +
Sbjct: 41  LDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDWA---------PR 91

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            +  N R + G +  +     +      +A +LNVS  E   +                 
Sbjct: 92  SVRRNAREVAGAMHQVEQAMGRAATEQEVADQLNVSLEEYRQILL--------------- 136

Query: 194 DKNSSQWQDWLVY--DHDGQEQVLIEKEERKNR---------RNMLTRSMSVLNPRERRI 242
           D N+SQ   +  Y  +H    +++ E  E  N          R  +  ++  L  RE+ +
Sbjct: 137 DTNNSQLFSYDEYREEHGDSAELVTEGHEEANPLHQLMEGNLRERVIEAIEALPEREKLV 196

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                 +E  + L+ + +  EV   RV Q+ ++A K++
Sbjct: 197 LTLYYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRL 232


>gi|145224454|ref|YP_001135132.1| FliA/WhiG family RNA polymerase sigma factor [Mycobacterium gilvum
           PYR-GCK]
 gi|145216940|gb|ABP46344.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Mycobacterium gilvum
           PYR-GCK]
          Length = 270

 Score = 40.8 bits (94), Expect = 0.23,   Method: Compositional matrix adjust.
 Identities = 53/237 (22%), Positives = 98/237 (41%), Gaps = 26/237 (10%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++   L L    A  +RG G    ++    ++GL+ AVK+FDP+ G     Y++  I  
Sbjct: 34  RIIAMTLPLAQHTARRFRGRGQSHDDLFQVASVGLVNAVKRFDPDSGSDFLAYAVPTIMG 93

Query: 112 AMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            ++ Y    SW+ VK+      K L   L + +  L         P +V A    L +  
Sbjct: 94  EVRRYFRDCSWA-VKV--PRRLKDLNSQLAKARAELTQQLGRAPTPSEVAA---HLGIDR 147

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY-----DHDGQEQVLIEKEERKNRR 225
            EV+          S N    S+D  S    D++       + D +   +++ E     R
Sbjct: 148 EEVVQATI-----ASSNYATLSTDSTSGPDGDFVALRETLGEPDARLDAVVDNE---TIR 199

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            ++ +    L PRE+ + + R   E  +T   ++     S+  V ++ A+A   +++
Sbjct: 200 PLIEK----LPPREQAVLKLRFFDE--MTQTQIAERMGYSQMHVSRLLAKALATLRD 250


>gi|303326430|ref|ZP_07356873.1| RNA polymerase sigma factor for flagellar operon FliA
           [Desulfovibrio sp. 3_1_syn3]
 gi|302864346|gb|EFL87277.1| RNA polymerase sigma factor for flagellar operon FliA
           [Desulfovibrio sp. 3_1_syn3]
          Length = 260

 Score = 40.8 bits (94), Expect = 0.24,   Method: Compositional matrix adjust.
 Identities = 18/45 (40%), Positives = 29/45 (64%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           + E++S G +GLM+A+ KF P+ G R  TY+   I+ AM + + R
Sbjct: 60  LGEMISSGTLGLMEALGKFRPQLGIRFETYAENRIRGAMLDELRR 104


>gi|119715014|ref|YP_921979.1| FliA/WhiG family RNA polymerase sigma factor [Nocardioides sp.
           JS614]
 gi|119535675|gb|ABL80292.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Nocardioides sp.
           JS614]
          Length = 285

 Score = 40.8 bits (94), Expect = 0.24,   Method: Compositional matrix adjust.
 Identities = 51/230 (22%), Positives = 98/230 (42%), Gaps = 34/230 (14%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS-WSLVKIGTT-----A 130
           ++ S G + L+QA + FD ERG     Y+   ++ A+ + + R+ W+   +        A
Sbjct: 40  DLTSAGLLALVQAAQAFDAERGVPFNRYAATRVRGAVVDELRRTDWASRSVRRRARELDA 99

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
            + RL   L R              P     +A    +S  EV   +  +A  + L+  +
Sbjct: 100 TRSRLATVLGR--------------PATQAEVADTAGLSVDEVTGNDDDIARAQVLS--L 143

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           ++S+ +     D LV +    +  L    E   R   LT +++ L  R R + E   L E
Sbjct: 144 DASEDDG--IGDTLVGNAPDPQGAL----EHGERLTYLTEAVAELPDRLRLVVEQYFLNE 197

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQKP 300
            P  +  +++   V+  R+ Q+ A A   +++++  +++    P LL  P
Sbjct: 198 RP--MAEIAATLGVTESRISQLRAEALVLLRDALNHELD----PDLLPAP 241


>gi|319893019|ref|YP_004149894.1| RNA polymerase sigma factor SigB [Staphylococcus pseudintermedius
           HKU10-03]
 gi|317162715|gb|ADV06258.1| RNA polymerase sigma factor SigB [Staphylococcus pseudintermedius
           HKU10-03]
          Length = 256

 Score = 40.8 bits (94), Expect = 0.24,   Method: Compositional matrix adjust.
 Identities = 53/248 (21%), Positives = 112/248 (45%), Gaps = 16/248 (6%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y+   D  A  +LV  + +L+  +A  Y        ++V  G +GL+ A+ +FD     +
Sbjct: 23  YQNDEDHEAQEKLVKHYEKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDLSFDRK 82

Query: 101 LATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
              + +  +   ++ Y+  ++WS+         +R+     R+K     +T+   +   +
Sbjct: 83  FEAFLVPTVIGEIKRYLRDKTWSV------HVPRRIKEIGPRIKKVSDELTNELGRSPSI 136

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
             IA++L VS+ +V+     +   +S NAL ++ S +         + D  GQ     + 
Sbjct: 137 SEIAERLEVSDEDVLEA---MEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQHD---DN 190

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
            E   +R +L R + +L  RER I +   +  + ++ +       +S+  V +++  A K
Sbjct: 191 YELTEKRMILERILPILTDREREIIQCTFI--DGLSQKETGERIGLSQMHVSRLQRTAIK 248

Query: 279 KVQESIQK 286
           K+QE+ +K
Sbjct: 249 KLQEAARK 256


>gi|224477054|ref|YP_002634660.1| RNA polymerase sigma factor SigB [Staphylococcus carnosus subsp.
           carnosus TM300]
 gi|222421661|emb|CAL28475.1| sigma factor B [Staphylococcus carnosus subsp. carnosus TM300]
          Length = 256

 Score = 40.8 bits (94), Expect = 0.25,   Method: Compositional matrix adjust.
 Identities = 50/241 (20%), Positives = 112/241 (46%), Gaps = 16/241 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A  +LV  + +L+  +A  Y        ++V  G +GL+ A+ +FD   G +   + + 
Sbjct: 30  DAQDKLVKHYQKLIESLAFKYSKGQSHHEDLVQVGMVGLIGAINRFDINFGRKFEAFLVP 89

Query: 108 WIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            +   ++ Y+  ++WS+         +R+     R+K     +T+   +   +  IA++L
Sbjct: 90  TVIGEIKRYLRDKTWSV------HVPRRIKEIGPRIKKTTDELTNELERSPSISEIAERL 143

Query: 167 NVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
            V++ EV+     +   +S NAL ++ S +         + D  G+++   +  E   +R
Sbjct: 144 EVTDEEVLEA---MEMGQSYNALSVDHSIEADKDGSTVTLLDIMGEQEGGYDLTE---KR 197

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            +L R + +L  RER I +   ++   ++ +       +S+  V +++  A KK+Q++ +
Sbjct: 198 MILERILPILTDREREIIQCTFIE--GLSQKETGERIGLSQMHVSRLQRNAIKKLQQAAK 255

Query: 286 K 286
           K
Sbjct: 256 K 256


>gi|325478815|gb|EGC81925.1| putative RNA polymerase sigma-F factor [Anaerococcus prevotii
           ACS-065-V-Col13]
          Length = 255

 Score = 40.8 bits (94), Expect = 0.25,   Method: Compositional matrix adjust.
 Identities = 21/88 (23%), Positives = 43/88 (48%), Gaps = 6/88 (6%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           EK EEY   +      D      L+  H+ +V  ++  Y G G+   ++    ++GL+ A
Sbjct: 15  EKFEEYYKTR------DKKLRDELIEEHMYIVDILSNKYVGKGIEKDDLYQVASLGLIYA 68

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYI 117
           + +FDP +G+  ++++   I   ++ Y 
Sbjct: 69  IDRFDPTKGYAFSSFATPTIMGELKRYF 96


>gi|315444787|ref|YP_004077666.1| RNA polymerase sigma factor, sigma-70 family [Mycobacterium sp.
           Spyr1]
 gi|315263090|gb|ADT99831.1| RNA polymerase sigma factor, sigma-70 family [Mycobacterium sp.
           Spyr1]
          Length = 270

 Score = 40.8 bits (94), Expect = 0.25,   Method: Compositional matrix adjust.
 Identities = 53/237 (22%), Positives = 98/237 (41%), Gaps = 26/237 (10%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++   L L    A  +RG G    ++    ++GL+ AVK+FDP+ G     Y++  I  
Sbjct: 34  RIIAMTLPLAQHTARRFRGRGQSHDDLFQVASVGLVNAVKRFDPDSGSDFLAYAVPTIMG 93

Query: 112 AMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            ++ Y    SW+ VK+      K L   L + +  L         P +V A    L +  
Sbjct: 94  EVRRYFRDCSWA-VKV--PRRLKDLNSQLAKARAELTQQLGRAPTPSEVAA---HLGIDR 147

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY-----DHDGQEQVLIEKEERKNRR 225
            EV+          S N    S+D  S    D++       + D +   +++ E     R
Sbjct: 148 EEVVQATI-----ASSNYATLSTDSTSGPDGDFVALRETLGEPDARLDAVVDNE---TIR 199

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            ++ +    L PRE+ + + R   E  +T   ++     S+  V ++ A+A   +++
Sbjct: 200 PLIEK----LPPREQAVLKLRFFDE--MTQTQIAERMGYSQMHVSRLLAKALATLRD 250


>gi|291326349|ref|ZP_06124166.2| motility sigma factor FliA [Providencia rettgeri DSM 1131]
 gi|291314661|gb|EFE55114.1| motility sigma factor FliA [Providencia rettgeri DSM 1131]
          Length = 241

 Score = 40.8 bits (94), Expect = 0.25,   Method: Compositional matrix adjust.
 Identities = 46/216 (21%), Positives = 96/216 (44%), Gaps = 34/216 (15%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTANQK 133
           I +++  G IGL+ A+++FD  +G   ATY++  I+ +M  E   R W         + +
Sbjct: 45  IDDLIQAGGIGLLHALERFDVTQGASFATYAVQRIRGSMLDELRSRDW------VPRSVR 98

Query: 134 RLFFNLRRLKGHL-QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
           R    + +  G L Q++  +  +PE    IAK L++  +E               AL+++
Sbjct: 99  RQAREMTKAIGALEQSLGRSATEPE----IAKALDIDLAEY------------RQALLDT 142

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKE--------ERKNRRNMLTRSMSVLNPRERRIFE 244
           ++     + +W     +  E  + E +           + R+ +  ++  L  RE+ +  
Sbjct: 143 NNSQLFSYDEWHEIHGESCEPQMDEDDGGNPLSLLLDSSLRDQIAAAIEQLPEREKMVLT 202

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
               +E  + L+ + +  EV   RV Q+ ++A K++
Sbjct: 203 LYYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRL 236


>gi|304398826|ref|ZP_07380696.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Pantoea sp.
           aB]
 gi|308187260|ref|YP_003931391.1| RNA polymerase sigma factor for flagellar operon [Pantoea vagans
           C9-1]
 gi|304353530|gb|EFM17907.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Pantoea sp.
           aB]
 gi|308057770|gb|ADO09942.1| RNA polymerase sigma factor for flagellar operon [Pantoea vagans
           C9-1]
          Length = 240

 Score = 40.8 bits (94), Expect = 0.25,   Method: Compositional matrix adjust.
 Identities = 50/235 (21%), Positives = 99/235 (42%), Gaps = 43/235 (18%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM-QEY 116
           LRL V++        + + +++  G IGL+ AV+++D  +G    TY++  I+ AM  E 
Sbjct: 29  LRLQVRLPAS-----VELDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDEL 83

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
             R W+          + +  N R + G +  +  +  +      +A++LNVS  E   +
Sbjct: 84  RSRDWA---------PRSVRRNAREVAGAMHRVEQSLGRSASEQEVAQQLNVSMEEYRQI 134

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVY--DHDGQEQVLIEKEERKNR---------R 225
                            D N+SQ   +  Y  +H    +++ E  E  N          R
Sbjct: 135 LL---------------DTNNSQLFSYDEYREEHGDSAELVTEGHEEANPLHQLLEGSLR 179

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             +  ++  L  RE+ +      +E  + L+ + +  +V   RV Q+ ++A K++
Sbjct: 180 ERVIEAIEALPDREKMVLTLYYQEE--LNLKEIGAVLDVGESRVSQLHSQAIKRL 232


>gi|149188102|ref|ZP_01866397.1| flagellar biosynthesis sigma factor [Vibrio shilonii AK1]
 gi|148838090|gb|EDL55032.1| flagellar biosynthesis sigma factor [Vibrio shilonii AK1]
          Length = 243

 Score = 40.8 bits (94), Expect = 0.25,   Method: Compositional matrix adjust.
 Identities = 26/86 (30%), Positives = 42/86 (48%), Gaps = 3/86 (3%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFD 94
           A  Y +H +LS     +  +  LV +IA    G   P   + +++  G IGL++A K +D
Sbjct: 4   ALTYDQHANLSGQQAFLEKYSVLVKRIAHHLIGRLPPNVLVEDLIQAGMIGLIEAQKNYD 63

Query: 95  PERGFRLATYSMWWIKAAMQEYILRS 120
             +G    TY+   I+ AM + I R 
Sbjct: 64  GSKGASFETYAGIRIRGAMLDDIRRG 89


>gi|56752318|ref|YP_173019.1| RNA polymerase sigma factor SigF [Synechococcus elongatus PCC 6301]
 gi|56687277|dbj|BAD80499.1| group3 RNA polymerase sigma factor SigF2 [Synechococcus elongatus
           PCC 6301]
          Length = 275

 Score = 40.8 bits (94), Expect = 0.25,   Method: Compositional matrix adjust.
 Identities = 43/177 (24%), Positives = 85/177 (48%), Gaps = 23/177 (12%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           Y E   ++  +++V  +L LV KIA    R    P  ++   G +GL++A+++F P +G 
Sbjct: 33  YAETPSIALRNQIVQLNLGLVRKIAHRLSRQCSEPYEDLEQIGFMGLIRAIERFQPHQGC 92

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN---LKP 156
             +++++ +I+  +  ++  S   ++I       R +  L+R    L+ +  +       
Sbjct: 93  AFSSFAVPYIRGEILHFLRDSCHSIRI------PRRWQELQRQGQQLREVLRHEWGRAPT 146

Query: 157 EQVVAIAKKLNVSESEVI----------SMNCRL--AGDESLNALINSSDKNSSQWQ 201
           EQ +A A  L+++E + I          S++  L  AGD S+  L+ +    S QWQ
Sbjct: 147 EQELAFALNLSMTEWQEIHLARRNRMPMSLDATLSQAGDSSVT-LVETLPDTSQQWQ 202


>gi|297569692|ref|YP_003691036.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfurivibrio alkaliphilus AHT2]
 gi|296925607|gb|ADH86417.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfurivibrio alkaliphilus AHT2]
          Length = 262

 Score = 40.8 bits (94), Expect = 0.26,   Method: Compositional matrix adjust.
 Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 3/75 (4%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERG 98
           RE  D +    L+ ++  L+  IA        P   + +++S G +GL+ A+ KFDP + 
Sbjct: 22  REQLDPAKREELILNYTPLIKYIASRLASRLPPQVAVDDLISCGIVGLIDAINKFDPAKN 81

Query: 99  FRLATYSMWWIKAAM 113
            +  TY+ + IK AM
Sbjct: 82  VQFKTYAEFRIKGAM 96


>gi|229016304|ref|ZP_04173251.1| RNA polymerase sigma-B factor [Bacillus cereus AH1273]
 gi|229022543|ref|ZP_04179074.1| RNA polymerase sigma-B factor [Bacillus cereus AH1272]
 gi|228738763|gb|EEL89228.1| RNA polymerase sigma-B factor [Bacillus cereus AH1272]
 gi|228744996|gb|EEL95051.1| RNA polymerase sigma-B factor [Bacillus cereus AH1273]
          Length = 224

 Score = 40.8 bits (94), Expect = 0.26,   Method: Compositional matrix adjust.
 Identities = 54/239 (22%), Positives = 113/239 (47%), Gaps = 28/239 (11%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           +V  +  LV  IA  Y   G    +++  G +GL+ A++++D   G     +++  I   
Sbjct: 1   MVDHYKNLVHSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGE 60

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNL-RRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
           +++Y+  ++W +       +  R   +L  ++K  ++ +TD   +  +++ IA  L +SE
Sbjct: 61  IKKYLRDKTWGI-------HVPRRIKDLGGKIKLAIEELTDRLQRSPKIIEIADHLGLSE 113

Query: 171 SEVISM-----NCRLAGDESLNALI-NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            EV+ +     N R++   SL+ ++ NSSD +S    + +     G EQ          R
Sbjct: 114 EEVLEIMDAKNNYRVS---SLDDVVENSSDGSSVARIESVGEVEQGYEQT--------ER 162

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           R +L    +VLN  E+ +       EN +  ++      +S+  V +I+ +A  K++++
Sbjct: 163 RLILDDIFNVLNDTEKSVIHY-IFGEN-LNQKDTGERLGISQMHVSRIKRQAISKLKQA 219


>gi|254387389|ref|ZP_05002636.1| sigma factor [Streptomyces sp. Mg1]
 gi|194346181|gb|EDX27147.1| sigma factor [Streptomyces sp. Mg1]
          Length = 266

 Score = 40.8 bits (94), Expect = 0.26,   Method: Compositional matrix adjust.
 Identities = 49/217 (22%), Positives = 95/217 (43%), Gaps = 12/217 (5%)

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           R  G  I +VV  G IGL++A+ +FDP R    +T +M +I   ++ +   +   V++  
Sbjct: 52  RCDGGDIEDVVQVGTIGLIKAIDRFDPARENEFSTLAMPYITGEIKRHFRDTSWAVRVPR 111

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
              + R+  ++ + K  L    D   +   V  +A  L +++ EV+       G  S + 
Sbjct: 112 RLQELRI--DIAKAKEELTVRLD---RSPTVTDLAGHLGLTDEEVVEGLVAANGHTSGSL 166

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQ-VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
               SD          + D  G+E+  L   E+ +    +L R    L+ RER +   R 
Sbjct: 167 DAPHSDHGDGPTTGHTLADVMGEEEPALALVEDVQALAPLLQR----LSERERSMLRMRF 222

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +E  +T   + +   +S+ +V ++  R    ++ S+
Sbjct: 223 GEE--LTQAQIGTALGISQMQVSRLLNRILAHLRASL 257


>gi|238782801|ref|ZP_04626830.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           bercovieri ATCC 43970]
 gi|238716224|gb|EEQ08207.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           bercovieri ATCC 43970]
          Length = 241

 Score = 40.8 bits (94), Expect = 0.26,   Method: Compositional matrix adjust.
 Identities = 49/210 (23%), Positives = 93/210 (44%), Gaps = 22/210 (10%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTANQK 133
           + +++  G IGL+ A+  FDP++G  L+TY    ++ AM  E   R W   ++ + A + 
Sbjct: 41  LDDLIQAGAIGLLTAIDHFDPKKGIGLSTYITQRVRWAMIDELRERDWVPRRVRSNAREI 100

Query: 134 RLFFN-LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
            +    + +  GH+    D          +A  + V+  E   M   LA   S  + + S
Sbjct: 101 AVIIQRIEQESGHVATEAD----------VANSMGVTLPEYQKM---LADTNS--SQLYS 145

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEE--RKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
            D+   +  D      D Q ++L    E  + N    ++R +  L  RE+ +      QE
Sbjct: 146 LDELQEELADGF-EQSDTQHEMLNPLHEIMKGNLTKQISREIKALPEREQLLLNLYYQQE 204

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             + ++ +S    V+  RV Q+ ++A K++
Sbjct: 205 --LNMKEISVLLNVTETRVSQLHSQAIKRL 232


>gi|284028684|ref|YP_003378615.1| B/F/G subfamily RNA polymerase sigma-28 subunit [Kribbella flavida
           DSM 17836]
 gi|283807977|gb|ADB29816.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Kribbella
           flavida DSM 17836]
          Length = 275

 Score = 40.8 bits (94), Expect = 0.26,   Method: Compositional matrix adjust.
 Identities = 51/251 (20%), Positives = 107/251 (42%), Gaps = 54/251 (21%)

Query: 57  HLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           +L +   IA  +RG G+   ++     +GL++A + ++P  G     Y++  I+  ++ Y
Sbjct: 53  NLGIAHSIASRFRGRGVESDDLDQVAYLGLLKAARSYNPSTGTPFLAYAVPTIRGEVKRY 112

Query: 117 ILR-SWSLVKIGTTANQKRLFFNLRRLKGHL-----QAITDNNLKPEQVVAIAKKLNVSE 170
               SW++          R+   L+ L+G +     Q + D    P  +  +A +L    
Sbjct: 113 FRDCSWTV----------RIPRRLQELQGSIASVRPQLVQDLQRDP-TLEELAAELGTDV 161

Query: 171 S------------EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           +             V+S++  + GD + N     +D+  + +                  
Sbjct: 162 AEVEAAIAADGCFSVLSLDRPVDGDSTANLADTIADEEDTSF------------------ 203

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
            ER     ML   ++ L PRER+I E R ++ +  T  ++ +E  VS+ +V    +R  +
Sbjct: 204 -ERTEAVAMLEPVLNDLTPRERKILELRFIEGH--TQADIGAEIGVSQMQV----SRLLR 256

Query: 279 KVQESIQKQVE 289
            + + +++Q+E
Sbjct: 257 GILDRLREQIE 267


>gi|312126664|ref|YP_003991538.1| RNA polymerase sigma factor, sigma-70 family [Caldicellulosiruptor
           hydrothermalis 108]
 gi|311776683|gb|ADQ06169.1| RNA polymerase sigma factor, sigma-70 family [Caldicellulosiruptor
           hydrothermalis 108]
          Length = 206

 Score = 40.8 bits (94), Expect = 0.26,   Method: Compositional matrix adjust.
 Identities = 20/81 (24%), Positives = 40/81 (49%), Gaps = 1/81 (1%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  AA  L+ ++  L++  A  Y    +   ++  EG   ++QA +KF+   G    
Sbjct: 17  KQGDKKAAEELICAYEPLIISFAAKYNKPEI-FEDLKQEGYCAILQAARKFNVSLGVSFI 75

Query: 103 TYSMWWIKAAMQEYILRSWSL 123
           T ++++IK  M   + R  ++
Sbjct: 76  TLAVYYIKRNMDRCVNRDRTI 96


>gi|91792701|ref|YP_562352.1| flagellar biosynthesis sigma factor [Shewanella denitrificans
           OS217]
 gi|91714703|gb|ABE54629.1| RNA polymerase sigma factor, FliA/WhiG [Shewanella denitrificans
           OS217]
          Length = 239

 Score = 40.8 bits (94), Expect = 0.26,   Method: Compositional matrix adjust.
 Identities = 48/212 (22%), Positives = 97/212 (45%), Gaps = 19/212 (8%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR-SWSLVKIGTTANQK 133
           + +++  G +GL++A  KFD  +G +  T++   I+ AM + I R  W  V      NQ+
Sbjct: 41  LDDLLQAGMMGLLEAASKFDGTKGAKFETFAGIRIRGAMIDEIRRGDW--VPRSVHRNQR 98

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
           R+   +  L+ H         +  +   IA+KL++S  E       +  D S+  +I   
Sbjct: 99  RVAQVIDELEQHFG-------RDARDTEIAEKLDMSLDEY----HHILNDVSVGKIIGIE 147

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D   S  QD ++ +    ++   E  E +  ++ L  ++  L  R+  +       +  +
Sbjct: 148 DLGVS--QDVIITEETSMDESFDELVETQF-QSALVEAIKTLPERDALVLSL--YYDEAL 202

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            L+ + +  EVS  RV QI ++A  +++  ++
Sbjct: 203 NLKEIGAILEVSESRVSQILSQAMLRLKAKLK 234


>gi|254818833|ref|ZP_05223834.1| RNA polymerase sigma factor SigF [Mycobacterium intracellulare ATCC
           13950]
          Length = 242

 Score = 40.8 bits (94), Expect = 0.27,   Method: Compositional matrix adjust.
 Identities = 57/264 (21%), Positives = 109/264 (41%), Gaps = 47/264 (17%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           +Q EY++A R     D  A+H                 RG GL   +++    +GLM AV
Sbjct: 17  RQREYIVA-RCLPLADHVASH--------------FARRGEGL--EDLIQVARLGLMNAV 59

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
            +FDP +G     +++  +   ++ Y    SW +          R+   LR L   +   
Sbjct: 60  NRFDPAKGPSFIGFAVPTMMGEVRRYFRDYSWGM----------RVPRRLRELHVQISRA 109

Query: 150 TDNNL----KPEQVVAIAKKLNVSESEVISMNCRLAGD----ESLNALINSSDKNSSQWQ 201
           T +      +      +++ L V   E++   C +AGD    +SL+A + +    + +  
Sbjct: 110 TADLAQQLGRAPNAGELSQMLEVPREEIV--ECLVAGDAYRLDSLDAPLGADSSGTPRSV 167

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
              V D D Q + +  +E        L   ++ L PRER +   R  +   +T   ++  
Sbjct: 168 ADSVGDIDPQIEHITNREA-------LRALVATLPPRERDVLRMRFFES--MTQSQIAER 218

Query: 262 FEVSRERVRQIEARAFKKVQESIQ 285
             VS+ +V +I A   + +++ ++
Sbjct: 219 IGVSQMQVSRILANTLRCLRDQLE 242


>gi|239907027|ref|YP_002953768.1| RNA polymerase sigma factor for flagellar operon [Desulfovibrio
           magneticus RS-1]
 gi|239796893|dbj|BAH75882.1| RNA polymerase sigma factor for flagellar operon [Desulfovibrio
           magneticus RS-1]
          Length = 264

 Score = 40.8 bits (94), Expect = 0.27,   Method: Compositional matrix adjust.
 Identities = 52/215 (24%), Positives = 102/215 (47%), Gaps = 22/215 (10%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR-SWSLVKIGTTANQK 133
           ++E++S G +GL++A+ +F PE G +  TY+   IK AM + + R  W       +  Q+
Sbjct: 64  LNELISAGAMGLLEALGRFRPELGIKFETYAESRIKGAMLDDLRRMDW------FSRGQR 117

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL-NALINS 192
           +    +R L+   + I +++  P  +  +A+   ++E EV SM     G E+L N L  S
Sbjct: 118 Q---RVRTLEEASRRIENDSGGPASLEQLAEATGLTEREV-SM-----GLEALQNQLCLS 168

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            D  +   ++   Y  +  E    +  E K   + L   +  L PRE+ +      +E  
Sbjct: 169 LDAIT---ENISSYQKNQLENEPYKSAEFKELVDKLASLIDDLTPREKLVLSLYYGEE-- 223

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           + +   S    ++  RV Q+ ++A  ++++  + Q
Sbjct: 224 LNMRETSEVMGITEGRVSQLHSQALARLRQKFKSQ 258


>gi|169827020|ref|YP_001697178.1| sporulation sigma factor SigG [Lysinibacillus sphaericus C3-41]
 gi|168991508|gb|ACA39048.1| RNA polymerase sigma-G factor (Stage III sporulation protein G)
           [Lysinibacillus sphaericus C3-41]
          Length = 257

 Score = 40.8 bits (94), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 56/258 (21%), Positives = 115/258 (44%), Gaps = 17/258 (6%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L+ +E   L  R  + G+      LV  +LRLV+ I   +   G    ++   G IG
Sbjct: 15  LPILKHEEMKELFIRL-QAGETEIREELVMCNLRLVLSIVGRFAYRGEQADDLFQVGCIG 73

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           LM+A+  FD +   R +TY++  I   ++ + LR    +++  +          + ++  
Sbjct: 74  LMKAIDHFDLKHNVRFSTYAVPMIIGEIRRH-LRDHHALRVSRSLRD----IAYKAMQAK 128

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            Q IT+ NL+   +  IA  +++ + +V+     +    SL   I S   ++    D L 
Sbjct: 129 EQWITE-NLREPTIEEIADMIDMKKEDVLFALDAIQDPMSLQEPIYSDGGDAVYMMDQLR 187

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            D   ++Q +            +  S+  L+ R++ I  A+R        E ++ E  +S
Sbjct: 188 DDDVSEDQWVAYVS--------VKESLQKLDERQQMIV-AKRFYYGETQTE-IAKELGIS 237

Query: 266 RERVRQIEARAFKKVQES 283
           + ++ ++E  A + +Q+ 
Sbjct: 238 QAQISRLEKNAIETMQKD 255


>gi|325107978|ref|YP_004269046.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Planctomyces
           brasiliensis DSM 5305]
 gi|324968246|gb|ADY59024.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Planctomyces
           brasiliensis DSM 5305]
          Length = 259

 Score = 40.8 bits (94), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 17/42 (40%), Positives = 27/42 (64%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           G+ +++++S G  GLM A+  FD ERG +  TY +  I+ AM
Sbjct: 52  GVDLNDLMSAGVFGLMDAIDAFDMERGVKFETYCVPRIRGAM 93


>gi|317129180|ref|YP_004095462.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus
           cellulosilyticus DSM 2522]
 gi|315474128|gb|ADU30731.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus
           cellulosilyticus DSM 2522]
          Length = 254

 Score = 40.8 bits (94), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 26/78 (33%), Positives = 42/78 (53%), Gaps = 5/78 (6%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDP 95
           R+ E  D  A  RLV ++L LV    +   G  LP    + ++ S G +GL  A++KFD 
Sbjct: 16  RWSEDRDEVACDRLVQAYLPLV-DYHVQRIGANLPRNVQLDDLRSNGMLGLYDALEKFDE 74

Query: 96  ERGFRLATYSMWWIKAAM 113
           +R  +  TY+ + I+ A+
Sbjct: 75  KRELKFDTYASFRIRGAI 92


>gi|312879616|ref|ZP_07739416.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Aminomonas
           paucivorans DSM 12260]
 gi|310782907|gb|EFQ23305.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Aminomonas
           paucivorans DSM 12260]
          Length = 247

 Score = 40.8 bits (94), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 31/106 (29%), Positives = 54/106 (50%), Gaps = 5/106 (4%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY----GLPISEVVSEGNIGLM 87
            E+  L + YR+        RLV  +L LV  +A G        GL   +++S G +GL+
Sbjct: 3   HEDNQLWEDYRKEPSPELKERLVRRYLPLVRYVA-GRMAVSPPPGLDFEDLLSFGAMGLL 61

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            A+++FD +RGF   T+++  I+ A+ + + R   + + G    QK
Sbjct: 62  DAIERFDLDRGFCFQTFAVPRIRGAILDELRRYDWISRTGREKLQK 107


>gi|94264039|ref|ZP_01287839.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
 gi|94266375|ref|ZP_01290074.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
 gi|93453027|gb|EAT03515.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
 gi|93455550|gb|EAT05737.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
          Length = 256

 Score = 40.8 bits (94), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 15/39 (38%), Positives = 26/39 (66%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           + +++S G +GL+ A+ KFDP +  +  TY+ + IK AM
Sbjct: 52  VDDLISCGIVGLIDAINKFDPAKNVQFKTYAEFRIKGAM 90


>gi|332527910|ref|ZP_08403946.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Rubrivivax
           benzoatilyticus JA2]
 gi|332112486|gb|EGJ12279.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Rubrivivax
           benzoatilyticus JA2]
          Length = 237

 Score = 40.4 bits (93), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 41/206 (19%), Positives = 97/206 (47%), Gaps = 13/206 (6%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL  A+ +FD  +G +  T++   I+ AM +  LR    +  G   +Q+ 
Sbjct: 38  LDDLIQVGMIGLSDALSRFDAAQGVQFETFATQRIRGAMLDE-LRGNDWMSRGDRRHQRS 96

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   + +L+  L    + +        IAK++ +S +E   +  ++ G + +     S D
Sbjct: 97  IEAAVHKLEQKLHRAPNES-------EIAKEMGLSLAEYQELLTKVRGTQLIYLEDMSGD 149

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
                + D  V  HD +   L   ++++ R+ ++    ++ N  ER  +      E+ + 
Sbjct: 150 DGDEDYLDRHV--HDDEANPLGRLQDQRMRQALVD---AIKNLPEREQYVMSMYYEHDMN 204

Query: 255 LENLSSEFEVSRERVRQIEARAFKKV 280
           L+ +++  +V+  RV Q+ +++  ++
Sbjct: 205 LKEIAAVLKVTESRVCQLHSQSIARL 230


>gi|269961637|ref|ZP_06175999.1| flagellar biosynthesis sigma factor FliA [Vibrio harveyi 1DA3]
 gi|269833678|gb|EEZ87775.1| flagellar biosynthesis sigma factor FliA [Vibrio harveyi 1DA3]
          Length = 244

 Score = 40.4 bits (93), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 38/154 (24%), Positives = 67/154 (43%), Gaps = 8/154 (5%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFD 94
           A  Y +HG  ++    +  +  LV +IA    G   P   + +++  G IGL++A + +D
Sbjct: 4   AITYDQHGKFNSQQAFIERYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLIEAQQNYD 63

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +G    TY+   I+ AM + I R    V      N + +   +  L+G L     ++ 
Sbjct: 64  GSKGASFETYAGIRIRGAMLDDI-RKGDWVPRSVHKNNREINQAIAELEGVLNRDPSDS- 121

Query: 155 KPEQVVAIAKKLNVSESEVISMNC-RLAGDESLN 187
             E    +   L+   S +  +NC +L G E L 
Sbjct: 122 --EVAAHLGMTLDQYHSALTDINCSKLVGIEDLG 153


>gi|326204596|ref|ZP_08194452.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           papyrosolvens DSM 2782]
 gi|325985163|gb|EGD46003.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           papyrosolvens DSM 2782]
          Length = 254

 Score = 40.4 bits (93), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 51/247 (20%), Positives = 108/247 (43%), Gaps = 25/247 (10%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMG----YRGYGLPISEVVSEGNIGLMQAVKK 92
           L K+Y E+ + +A  +L+  +  L+  +A G    Y G  +   ++V  G  GL+ A++K
Sbjct: 9   LWKQYIENKEAAAKEKLIIQYAYLIKYVA-GRLSIYFGSNVEFDDLVGYGAFGLIDAIEK 67

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL---FFNLRRLKGHLQAI 149
           +D  +G +  TY+   I+ ++ + I R    V        K L   +  +   KGH    
Sbjct: 68  YDLAKGVKFETYASLRIRGSIIDSI-RDMDWVPRSLRQKNKELEKVYAEIENEKGH--TA 124

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
           TD          +A+K+ +   +      +L  D +++++++  +     ++  L    +
Sbjct: 125 TDKE--------VAEKMGLGMDDF----YKLLNDVNVSSMMSLDEFMEQNYERGLEIFSE 172

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
             E       E    + +L  S+  L  +E+ +      +E  +TL+ +S+   V+  R+
Sbjct: 173 STEDKPEASLEFNEMKQLLADSIDKLPEKEKAVITFYYFEE--LTLKEISAIMSVTESRI 230

Query: 270 RQIEARA 276
            Q+  +A
Sbjct: 231 SQLHTKA 237


>gi|323463926|gb|ADX76079.1| RNA polymerase sigma-B factor [Staphylococcus pseudintermedius
           ED99]
          Length = 256

 Score = 40.4 bits (93), Expect = 0.29,   Method: Compositional matrix adjust.
 Identities = 53/248 (21%), Positives = 111/248 (44%), Gaps = 16/248 (6%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y+   D  A  +LV  + +L+  +A  Y        ++V  G +GL+ A+ +FD     +
Sbjct: 23  YQNDEDHEAQEKLVKHYEKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDLSFDRK 82

Query: 101 LATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
              + +  +   ++ Y+  ++WS+         +R+     R+K     +T+   +   +
Sbjct: 83  FEAFLVPTVIGEIKRYLRDKTWSV------HVPRRIKEIGPRIKKVSDELTNELGRSPSI 136

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
             IA +L VS+ +V+     +   +S NAL ++ S +         + D  GQ     + 
Sbjct: 137 SEIADRLEVSDEDVLEA---MEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQHD---DN 190

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
            E   +R +L R + +L  RER I +   +  + ++ +       +S+  V +++  A K
Sbjct: 191 YELTEKRMILERILPILTDREREIIQCTFI--DGLSQKETGERIGLSQMHVSRLQRTAIK 248

Query: 279 KVQESIQK 286
           K+QE+ +K
Sbjct: 249 KLQEAARK 256


>gi|78184762|ref|YP_377197.1| putative type III sigma factor [Synechococcus sp. CC9902]
 gi|78169056|gb|ABB26153.1| putative type III sigma factor [Synechococcus sp. CC9902]
          Length = 124

 Score = 40.4 bits (93), Expect = 0.29,   Method: Compositional matrix adjust.
 Identities = 22/55 (40%), Positives = 32/55 (58%), Gaps = 3/55 (5%)

Query: 54  VTSHLRLVVKIAMGYRGYGLP--ISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           V  HL L   +AM  R  G P    +++ E  +GL+Q ++KFDP RG R ++Y M
Sbjct: 26  VLQHLGLAHCVAMRQRHRG-PEERDDLLQEACLGLIQGLQKFDPSRGLRPSSYLM 79


>gi|323484667|ref|ZP_08090029.1| sigma-70 region 3 [Clostridium symbiosum WAL-14163]
 gi|323694798|ref|ZP_08108953.1| hypothetical protein HMPREF9475_03817 [Clostridium symbiosum
           WAL-14673]
 gi|323402050|gb|EGA94386.1| sigma-70 region 3 [Clostridium symbiosum WAL-14163]
 gi|323501114|gb|EGB17021.1| hypothetical protein HMPREF9475_03817 [Clostridium symbiosum
           WAL-14673]
          Length = 192

 Score = 40.4 bits (93), Expect = 0.29,   Method: Compositional matrix adjust.
 Identities = 26/85 (30%), Positives = 42/85 (49%), Gaps = 1/85 (1%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
             +GE     Y+ E++ +P    +EE  L       G  SA  RLV   L   V++A  Y
Sbjct: 21  FTSGEDFYQLYLEELKLVPPCSPEEEERLLDEIL-AGSQSAVKRLVEGKLGRAVRMAEEY 79

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKF 93
           R  GL ++++V E NI L+   +++
Sbjct: 80  RDRGLSMNDLVQEANIALLLTAQEY 104


>gi|220932500|ref|YP_002509408.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Halothermothrix orenii
           H 168]
 gi|219993810|gb|ACL70413.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Halothermothrix orenii
           H 168]
          Length = 254

 Score = 40.4 bits (93), Expect = 0.29,   Method: Compositional matrix adjust.
 Identities = 63/270 (23%), Positives = 118/270 (43%), Gaps = 50/270 (18%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV----KIAMGYRGYGLPISEVVSEGNIG 85
           EK E   L + Y+  G   A   L+ ++L LV     ++ M    + +   ++ S G IG
Sbjct: 6   EKVEYLDLWEAYKGKGSQEARKELILNYLPLVKYQVERVKMIIPDF-IEEDDLESYGIIG 64

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKG 144
           L+ A++K+D   G +  TY+   I+ ++ +++ +  W             L  +LRR   
Sbjct: 65  LIDAIEKYDYRLGIKFNTYASRRIRGSIIDHLRKLDW-------------LPHSLRREGK 111

Query: 145 HLQAITDN-----NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
            LQ + D        KP  V  +A K N+S  +V  +  +L           +S K  S 
Sbjct: 112 ELQKVADKLAKELGRKP-TVAELANKTNISREKVTKIYSKL-----------NSAKWVSL 159

Query: 200 WQDW--------LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           ++DW        +  D    +++L    ++K R  +L R++  L+  ER +      +E 
Sbjct: 160 YEDWGESTVFNFIKGDCLPPDRIL----DKKERIKLLARAIDRLSESERTVISLYYYEE- 214

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +T + ++    +S  R+ QI  RA  +++
Sbjct: 215 -LTQKEIAEVMGLSPARISQIHKRAVYRLR 243


>gi|317132052|ref|YP_004091366.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ethanoligenens
           harbinense YUAN-3]
 gi|315470031|gb|ADU26635.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ethanoligenens
           harbinense YUAN-3]
          Length = 245

 Score = 40.4 bits (93), Expect = 0.30,   Method: Compositional matrix adjust.
 Identities = 31/116 (26%), Positives = 50/116 (43%), Gaps = 5/116 (4%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A   LV+S +  +   ++     GL   +++ EG +GL+ AV+ F P+ G     Y
Sbjct: 67  GDRDAMADLVSSFVPFIRAHSVPVAAAGLEADDMMQEGMLGLLGAVRHFCPQNGVPFRAY 126

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
           +   IK  M   + R+         A       +L      L A++  N  PE+VV
Sbjct: 127 AHICIKRRMASAVRRATC-----GKAVPLNYALSLDDQTNALFAVSRTNTDPEEVV 177


>gi|300788069|ref|YP_003768360.1| RNA polymerase sigma factor [Amycolatopsis mediterranei U32]
 gi|299797583|gb|ADJ47958.1| RNA polymerase sigma factor [Amycolatopsis mediterranei U32]
          Length = 273

 Score = 40.4 bits (93), Expect = 0.30,   Method: Compositional matrix adjust.
 Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RL+T HL L   IA  + G G P  +++     GL++AV ++  +RG    ++++  I  
Sbjct: 52  RLITEHLPLAEHIARRFSGRGEPFEDLLQVARTGLIRAVDRYAADRGSDFVSFAVPTIMG 111

Query: 112 AMQEYILR-SWSL 123
            ++ +     WS+
Sbjct: 112 EVRRHFRDVGWSM 124


>gi|256545958|ref|ZP_05473313.1| RNA polymerase sigma-B factor [Anaerococcus vaginalis ATCC 51170]
 gi|256398380|gb|EEU12002.1| RNA polymerase sigma-B factor [Anaerococcus vaginalis ATCC 51170]
          Length = 256

 Score = 40.4 bits (93), Expect = 0.30,   Method: Compositional matrix adjust.
 Identities = 15/72 (20%), Positives = 38/72 (52%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           D    + L+  H+ +V  ++  Y G G+   ++    ++GL+ A+ ++DP +G+  ++++
Sbjct: 26  DKDLRNELIEDHMYIVDILSNKYVGKGIEKDDLYQVASLGLIYAIDRYDPSKGYEFSSFA 85

Query: 106 MWWIKAAMQEYI 117
              I   ++ Y 
Sbjct: 86  TPTIMGELKRYF 97


>gi|229010401|ref|ZP_04167605.1| RNA polymerase sigma-B factor [Bacillus mycoides DSM 2048]
 gi|228750821|gb|EEM00643.1| RNA polymerase sigma-B factor [Bacillus mycoides DSM 2048]
          Length = 224

 Score = 40.4 bits (93), Expect = 0.30,   Method: Compositional matrix adjust.
 Identities = 53/239 (22%), Positives = 114/239 (47%), Gaps = 28/239 (11%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           +V  +  LV  IA  Y   G    +++  G +GL+ A++++D   G     +++  I   
Sbjct: 1   MVNHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGE 60

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNL-RRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
           +++Y+  ++W +       +  R   +L  ++K  ++ +TD+  +  +++ IA  L +SE
Sbjct: 61  IKKYLRDKTWGI-------HVPRRIKDLGGKIKLAIEELTDHLQRSPKIIEIADHLGLSE 113

Query: 171 SEVISM-----NCRLAGDESLNALI-NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            EV+ +     N +++   SL+ ++ NSSD +S    + +     G EQ          R
Sbjct: 114 EEVLEIMDAKNNYQVS---SLDDVVENSSDGSSVARIESVGEVEQGYEQT--------ER 162

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           R +L    +VLN  E+ +       EN +  ++      +S+  V +I+ +A  K++++
Sbjct: 163 RLVLDDIFNVLNDTEKSVIH-YIFGEN-LNQKDTGERLGISQMHVSRIKRQAISKLKQA 219


>gi|226304764|ref|YP_002764722.1| RNA polymerase sigma factor [Rhodococcus erythropolis PR4]
 gi|226183879|dbj|BAH31983.1| RNA polymerase sigma factor [Rhodococcus erythropolis PR4]
          Length = 272

 Score = 40.4 bits (93), Expect = 0.30,   Method: Compositional matrix adjust.
 Identities = 34/148 (22%), Positives = 68/148 (45%), Gaps = 19/148 (12%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           L L   +A  Y+G G P  ++     +GL+QAV++FD ++G    ++++  +   ++++ 
Sbjct: 56  LPLATHVARRYQGRGQPFEDLEQVARVGLVQAVQRFDVDKGSDFLSFAVPTVMGEVRKHF 115

Query: 118 L-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV--- 173
               WS V++  +  ++ L  N R L    Q +     +   V  +A +L++   EV   
Sbjct: 116 RDHGWS-VRVPRSLQERHLALN-RALTSLSQTLG----RAPTVAELATELDIEPDEVEQG 169

Query: 174 ---------ISMNCRLAGDESLNALINS 192
                      ++   AGD S   LI++
Sbjct: 170 LTAGNSYRTTPLDTASAGDGSGLTLIDT 197


>gi|294636855|ref|ZP_06715188.1| flagellar biosynthesis sigma factor FliA [Edwardsiella tarda ATCC
           23685]
 gi|291089930|gb|EFE22491.1| flagellar biosynthesis sigma factor FliA [Edwardsiella tarda ATCC
           23685]
          Length = 240

 Score = 40.4 bits (93), Expect = 0.30,   Method: Compositional matrix adjust.
 Identities = 49/224 (21%), Positives = 95/224 (42%), Gaps = 36/224 (16%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL+ AV+++D  +G    TY++  I+ AM +  LRS   V      N + 
Sbjct: 41  LDDLLQAGGIGLLHAVERYDAMQGTAFTTYAIQRIRGAMLDE-LRSRDWVPRSVRRNARG 99

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   ++R +  L  +  +         IA+++ +  +E   +                 D
Sbjct: 100 VSAAMQRAEQRLGRVPSDG-------EIAQEMGIPLAEYQQILL---------------D 137

Query: 195 KNSSQ---WQDWLVYDHDGQEQVLIEKEERKNRRNML--------TRSMSVLNPRERRIF 243
            NSSQ   + +W     D  E V  E+E     R +L          ++  L  RE+ + 
Sbjct: 138 TNSSQLFSYDEWREEHGDNAEPVWGEEESANPLRQLLESDLRGRVIAAIEALPEREKLVL 197

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
                +E  + L+ + +  EV   RV Q+ ++A K+++  +  Q
Sbjct: 198 TLYYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRLRSRLLSQ 239


>gi|298243403|ref|ZP_06967210.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Ktedonobacter racemifer DSM 44963]
 gi|297556457|gb|EFH90321.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Ktedonobacter racemifer DSM 44963]
          Length = 294

 Score = 40.4 bits (93), Expect = 0.30,   Method: Compositional matrix adjust.
 Identities = 61/254 (24%), Positives = 116/254 (45%), Gaps = 23/254 (9%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS-----EVVSEGNIGLMQAVKKF 93
           +RY+EH      + L+T +  LV ++A+G  G   P S     +++  G IGL+ A+ ++
Sbjct: 12  ERYQEHKSSELRNELITMYAPLV-RLAVGRLGIP-PTSIMDSEDLIGYGMIGLINAIDRY 69

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D  RG R   ++   I+ A+ + I R  + +   + +  +++      L+  L       
Sbjct: 70  DLSRGVRFEAFATPRIRGAVIDQI-RQLNWLPRSSVSRIRQIERTHAELEQQLG------ 122

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSS--DKNSSQWQDWLVYDHDG 210
            +P      AK L+VS      M   ++    SL+A + SS  +  S+   D L    D 
Sbjct: 123 -RPATEAEAAKALDVSVERYRQMLTEMSVSVLSLDAPMGSSIQEDESASLGDML---EDE 178

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
            +Q   E  E +     L+ ++  L PRE+ +      +E  +T++ +S    VS  RV 
Sbjct: 179 SQQDPGEAVEHEELIQSLSAALQHLPPREQLLLSLYYKEE--LTMKEISRIMNVSESRVC 236

Query: 271 QIEARAFKKVQESI 284
           Q+  +A  +++ ++
Sbjct: 237 QLRMQALVRLRSTL 250


>gi|326332872|ref|ZP_08199129.1| RNA polymerase sigma-F factor [Nocardioidaceae bacterium Broad-1]
 gi|325949230|gb|EGD41313.1| RNA polymerase sigma-F factor [Nocardioidaceae bacterium Broad-1]
          Length = 265

 Score = 40.4 bits (93), Expect = 0.31,   Method: Compositional matrix adjust.
 Identities = 27/85 (31%), Positives = 43/85 (50%), Gaps = 7/85 (8%)

Query: 46  DLSAAHR------LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           DLS A R      LV  ++ LV   A  + G G P  ++V  G +GL+ AV ++D  R  
Sbjct: 35  DLSDAERTAAREELVHLNMALVEYCASQFYGRGEPHEDLVQVGVVGLLNAVDRYDLARDV 94

Query: 100 RLATYSMWWIKAAMQEYILRS-WSL 123
             +TY++  I   ++ Y   S W++
Sbjct: 95  EFSTYAVPTILGEIKRYFRDSRWAV 119


>gi|257440909|ref|ZP_05616664.1| RNA polymerase sigma-F factor [Faecalibacterium prausnitzii A2-165]
 gi|257196689|gb|EEU94973.1| RNA polymerase sigma-F factor [Faecalibacterium prausnitzii A2-165]
          Length = 222

 Score = 40.4 bits (93), Expect = 0.31,   Method: Compositional matrix adjust.
 Identities = 24/89 (26%), Positives = 43/89 (48%), Gaps = 1/89 (1%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            +  +L LV   A  +RG G+   ++   G +GL++A   FD  RG   +TY++  I   
Sbjct: 11  FIEQNLGLVHACAGRFRGRGIEYDDLYGAGCMGLVKATDGFDEGRGVCFSTYAVPVILGE 70

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           +++ + R    VK+  +  +  L  N  R
Sbjct: 71  IKK-LFREGGTVKVSRSLKELGLRVNAAR 98


>gi|271500098|ref|YP_003333123.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit [Dickeya
           dadantii Ech586]
 gi|270343653|gb|ACZ76418.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Dickeya
           dadantii Ech586]
          Length = 240

 Score = 40.4 bits (93), Expect = 0.32,   Method: Compositional matrix adjust.
 Identities = 51/239 (21%), Positives = 101/239 (42%), Gaps = 35/239 (14%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM-QEY 116
           LRL V++        + + +++  G IGL+ AV+++D  +G    TY++  I+ AM  E 
Sbjct: 29  LRLQVRLPAS-----VELDDLLQAGGIGLLSAVERYDSLQGTAFTTYAVQRIRGAMLDEL 83

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
             R W+          + +  N R +   +Q    +  +      +A+ LN+S  E   +
Sbjct: 84  RSRDWA---------PRSVRRNAREVAQAMQQAEQSLGRAPTEQEVAQTLNISLEEYRQI 134

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT------R 230
                       L+++++     + +W   +H    + L+E  E  N  N+L       R
Sbjct: 135 ------------LLDTNNSQLFSYDEW-REEHGDSAEALLEGNEDANPLNLLMDVNLRQR 181

Query: 231 SMSVL-NPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            M  + N  ER         +  + L+ + +  EV   RV Q+ ++A K+++  +   V
Sbjct: 182 VMDAIENLPEREKMVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLRAKLMSDV 240


>gi|126697577|ref|YP_001086474.1| RNA polymerase sigma-B factor [Clostridium difficile 630]
 gi|254977353|ref|ZP_05273825.1| RNA polymerase sigma-B factor [Clostridium difficile QCD-66c26]
 gi|255102910|ref|ZP_05331887.1| RNA polymerase sigma-B factor [Clostridium difficile QCD-63q42]
 gi|255308730|ref|ZP_05352901.1| RNA polymerase sigma-B factor [Clostridium difficile ATCC 43255]
 gi|255316437|ref|ZP_05358020.1| RNA polymerase sigma-B factor [Clostridium difficile QCD-76w55]
 gi|255519098|ref|ZP_05386774.1| RNA polymerase sigma-B factor [Clostridium difficile QCD-97b34]
 gi|255652280|ref|ZP_05399182.1| RNA polymerase sigma-B factor [Clostridium difficile QCD-37x79]
 gi|260681780|ref|YP_003213065.1| RNA polymerase sigma-B factor [Clostridium difficile CD196]
 gi|260685377|ref|YP_003216510.1| RNA polymerase sigma-B factor [Clostridium difficile R20291]
 gi|296452670|ref|ZP_06894361.1| RNA polymerase sigma-B factor [Clostridium difficile NAP08]
 gi|296880077|ref|ZP_06904046.1| RNA polymerase sigma-B factor [Clostridium difficile NAP07]
 gi|306521994|ref|ZP_07408341.1| RNA polymerase sigma-B factor [Clostridium difficile QCD-32g58]
 gi|115249014|emb|CAJ66825.1| RNA polymerase sigma-B factor (Sigma-37) [Clostridium difficile]
 gi|260207943|emb|CBA60060.1| RNA polymerase sigma-B factor [Clostridium difficile CD196]
 gi|260211393|emb|CBE01463.1| RNA polymerase sigma-B factor [Clostridium difficile R20291]
 gi|296258452|gb|EFH05356.1| RNA polymerase sigma-B factor [Clostridium difficile NAP08]
 gi|296428944|gb|EFH14822.1| RNA polymerase sigma-B factor [Clostridium difficile NAP07]
          Length = 257

 Score = 40.4 bits (93), Expect = 0.32,   Method: Compositional matrix adjust.
 Identities = 33/142 (23%), Positives = 68/142 (47%), Gaps = 21/142 (14%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y ++ ++   + L+  HL L   +A  Y   G+   ++    ++ L+ A+ ++D E+GF 
Sbjct: 22  YNKNKNVDIRNILIERHLYLARLLAKKYINKGVDFEDIYQVASLALIYAIDRYDVEKGFE 81

Query: 101 LATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ- 158
            ++++   I   +++Y   + W+L          R+    RR++   + I+D  +K EQ 
Sbjct: 82  FSSFATPTIVGEIKKYFRDKVWTL----------RV---PRRIQELSKKISDAKIKLEQE 128

Query: 159 ------VVAIAKKLNVSESEVI 174
                 V  IA  + VSE +V+
Sbjct: 129 NKKHPKVKDIADYIGVSEEDVL 150


>gi|78217835|gb|ABB37184.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Desulfovibrio
           desulfuricans subsp. desulfuricans str. G20]
          Length = 227

 Score = 40.4 bits (93), Expect = 0.33,   Method: Compositional matrix adjust.
 Identities = 17/45 (37%), Positives = 29/45 (64%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           ++E++S G +GLM+A  KF P+ G +  TY+   I+ AM + + R
Sbjct: 26  LNELISAGTLGLMEAFGKFQPKLGIKFDTYAENRIRGAMLDELRR 70


>gi|256783387|ref|ZP_05521818.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
 gi|289767263|ref|ZP_06526641.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
 gi|289697462|gb|EFD64891.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
          Length = 287

 Score = 40.4 bits (93), Expect = 0.33,   Method: Compositional matrix adjust.
 Identities = 60/251 (23%), Positives = 113/251 (45%), Gaps = 46/251 (18%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LVT+ L +  +IA  +R  G  I ++     +GL++A+ +FDPERG    +Y++  I   
Sbjct: 56  LVTAWLPMAHRIAGRFRDRGESIEDLRQVAALGLVKAIDRFDPERGA-FESYAVPTITGE 114

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +   R W+L ++     + R   N  R+     A +  + +P  V A+A    +SE 
Sbjct: 115 VKRHFRDRMWAL-RVPRRVQELR---NKVRVARRELAQSPGSPEP-SVAALAAHTGLSED 169

Query: 172 EV------------ISMNCRL-AGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           EV            +S++  L AGD+  SL   + ++D +         YD       +I
Sbjct: 170 EVGAGMEALESFSTLSLDAELSAGDDGYSLADTLGAADTS---------YD------TVI 214

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           ++E  K         +  L  RER I   R  ++  +T   ++    +S+  V ++ +R+
Sbjct: 215 DRESAKE-------GLRRLPERERAILYMRFFED--MTQSRIADCLGISQMHVSRLISRS 265

Query: 277 FKKVQESIQKQ 287
             +V++    Q
Sbjct: 266 CARVRDEAMGQ 276


>gi|302528260|ref|ZP_07280602.1| RNA polymerase sigma-B factor [Streptomyces sp. AA4]
 gi|302437155|gb|EFL08971.1| RNA polymerase sigma-B factor [Streptomyces sp. AA4]
          Length = 261

 Score = 40.4 bits (93), Expect = 0.33,   Method: Compositional matrix adjust.
 Identities = 25/88 (28%), Positives = 42/88 (47%), Gaps = 3/88 (3%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           LA+   EH  L    RL+  HL L   IA  +   G P  +++    IGL+ AV ++DP 
Sbjct: 22  LAEDTDEHSRLR--RRLIEEHLPLAEHIARRFARRGQPTEDLLQVARIGLINAVDRYDPA 79

Query: 97  RGFRLATYSMWWIKAAMQEYIL-RSWSL 123
           R      +++  +   ++ Y    +WS+
Sbjct: 80  RQTDFVAFAVPTVMGEVRRYFRDHTWSV 107


>gi|288553039|ref|YP_003424974.1| RNA polymerase sigma factor SigD [Bacillus pseudofirmus OF4]
 gi|288544199|gb|ADC48082.1| RNA polymerase sigma factor SigD [Bacillus pseudofirmus OF4]
          Length = 257

 Score = 40.4 bits (93), Expect = 0.33,   Method: Compositional matrix adjust.
 Identities = 53/252 (21%), Positives = 111/252 (44%), Gaps = 26/252 (10%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQAVKKFDPERGFRL 101
           DL A   L+  ++  +V   +     GLP +    ++ S G +GL  A++KF+P R  + 
Sbjct: 21  DLDACDELIRLYMP-IVNYHVQRISVGLPKNVSKDDLTSHGMLGLYDALEKFNPNRDLKF 79

Query: 102 ATYSMWWIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            TY+ + ++ A+ + + +  W    +  +  +K     ++R++  +Q +     +     
Sbjct: 80  DTYASFRVRGAIIDGLRKEDW----LPRSMREK-----IKRVEACIQQLEQEFGRNVSAK 130

Query: 161 AIAKKLNVSESEVIS------MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            +  KL++ E EV        ++  L+ DE  N    S   NS+ +   L+   D Q + 
Sbjct: 131 EVGVKLDMPEEEVYQIMNEHYLSNLLSIDERTNDSDRSDSNNSASYSATLI---DKQTKT 187

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
             E    +  +  L + ++ L+  E+ +       E  +TL  +     +S  R+ QI +
Sbjct: 188 PEESLMFEAVKEELIKGINRLSENEKLVISLFYFDE--LTLTEIGHILNLSTSRISQIHS 245

Query: 275 RAFKKVQESIQK 286
           +A  ++ + I K
Sbjct: 246 KALFRMNQLINK 257


>gi|78221650|ref|YP_383397.1| sigma 28 (flagella/sporulation) [Geobacter metallireducens GS-15]
 gi|78192905|gb|ABB30672.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Geobacter
           metallireducens GS-15]
          Length = 250

 Score = 40.4 bits (93), Expect = 0.33,   Method: Compositional matrix adjust.
 Identities = 29/98 (29%), Positives = 48/98 (48%), Gaps = 14/98 (14%)

Query: 36  VLAKRYREHGDLSAAH---RLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQ 88
            L K Y +    S+A     L+ +HL LV K  +G     LP      +++S   IGL+ 
Sbjct: 3   CLVKAYEQEAQRSSAQSRDELIVTHLPLV-KFLVGRIATQLPPHLDQDDLMSAAVIGLIT 61

Query: 89  AVKKFDPERGFRLATYSMWWIKAAM------QEYILRS 120
           A ++FDP RG +  T++   I+  +      Q+++ RS
Sbjct: 62  AAERFDPSRGVQFKTFAEQRIRGTIIDELRSQDWLTRS 99


>gi|22298280|ref|NP_681527.1| RNA polymerase sigma factor SigF [Thermosynechococcus elongatus
           BP-1]
 gi|22294459|dbj|BAC08289.1| group 3 RNA polymerase sigma factor [Thermosynechococcus elongatus
           BP-1]
          Length = 261

 Score = 40.4 bits (93), Expect = 0.33,   Method: Compositional matrix adjust.
 Identities = 21/82 (25%), Positives = 48/82 (58%), Gaps = 1/82 (1%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKKFDP 95
           L + YR++      +RLV  ++ LV K A  + +       +++  G +GL++A+++FDP
Sbjct: 17  LLQAYRDNPAPELRNRLVELNIGLVRKEAHRWVQCTQESFDDLMQVGTLGLIRAIERFDP 76

Query: 96  ERGFRLATYSMWWIKAAMQEYI 117
            +G   +++++ +I+  +Q Y+
Sbjct: 77  TKGVAFSSFAIPYIRGEIQHYL 98


>gi|312621865|ref|YP_004023478.1| RNA polymerase sigma factor, sigma-70 family
          [Caldicellulosiruptor kronotskyensis 2002]
 gi|312202332|gb|ADQ45659.1| RNA polymerase sigma factor, sigma-70 family
          [Caldicellulosiruptor kronotskyensis 2002]
          Length = 302

 Score = 40.4 bits (93), Expect = 0.33,   Method: Compositional matrix adjust.
 Identities = 17/50 (34%), Positives = 31/50 (62%), Gaps = 4/50 (8%)

Query: 53 LVTSHLRLVVKIAMGY----RGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
          L+  +++LV  +A  +    +GY   + +++SEG IGL+ A K +DP +G
Sbjct: 13 LIADNIKLVYHVANKFMPCPKGYCYEVDDLISEGYIGLVVAAKNYDPAKG 62


>gi|304559365|gb|ADM42029.1| RNA polymerase sigma factor for flagellar operon [Edwardsiella
           tarda FL6-60]
          Length = 237

 Score = 40.4 bits (93), Expect = 0.33,   Method: Compositional matrix adjust.
 Identities = 47/227 (20%), Positives = 94/227 (41%), Gaps = 42/227 (18%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGT 128
           + +++  G IGL+ AV+++D  +G    TY++  I+ AM      ++++ RS      G 
Sbjct: 38  LDDLLQAGGIGLLHAVERYDAMQGTAFTTYAIQRIRGAMLDELRSRDWVPRSVRRNARGV 97

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           +A  +R    L R  G      D+ +  E  + +                    +E    
Sbjct: 98  SAAMQRAEQRLGRTPG------DSEIAQEMGIPL--------------------EEYQQI 131

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML--------TRSMSVLNPRER 240
           L++++      + +W     D  E VL + EE    R +L          ++  L  RE+
Sbjct: 132 LLDTNTSQLFSYDEWREDHGDSAEPVLEQSEEANPLRQLLESDLRGRVIAAIEALPEREK 191

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +      +E  + L+ + +  EV   RV Q+ ++A K+++  +  Q
Sbjct: 192 LVLTLYYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRLRTRLLSQ 236


>gi|269139471|ref|YP_003296172.1| flagellar biosynthesis sigma factor [Edwardsiella tarda EIB202]
 gi|267985132|gb|ACY84961.1| flagellar biosynthesis sigma factor [Edwardsiella tarda EIB202]
          Length = 240

 Score = 40.4 bits (93), Expect = 0.34,   Method: Compositional matrix adjust.
 Identities = 47/227 (20%), Positives = 94/227 (41%), Gaps = 42/227 (18%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGT 128
           + +++  G IGL+ AV+++D  +G    TY++  I+ AM      ++++ RS      G 
Sbjct: 41  LDDLLQAGGIGLLHAVERYDAMQGTAFTTYAIQRIRGAMLDELRSRDWVPRSVRRNARGV 100

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           +A  +R    L R  G      D+ +  E  + +                    +E    
Sbjct: 101 SAAMQRAEQRLGRTPG------DSEIAQEMGIPL--------------------EEYQQI 134

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML--------TRSMSVLNPRER 240
           L++++      + +W     D  E VL + EE    R +L          ++  L  RE+
Sbjct: 135 LLDTNTSQLFSYDEWREDHGDSAEPVLEQSEEANPLRQLLESDLRGRVIAAIEALPEREK 194

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +      +E  + L+ + +  EV   RV Q+ ++A K+++  +  Q
Sbjct: 195 LVLTLYYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRLRTRLLSQ 239


>gi|312792353|ref|YP_004025276.1| RNA polymerase sigma factor, sigma-70 family [Caldicellulosiruptor
           kristjanssonii 177R1B]
 gi|312179493|gb|ADQ39663.1| RNA polymerase sigma factor, sigma-70 family [Caldicellulosiruptor
           kristjanssonii 177R1B]
          Length = 311

 Score = 40.4 bits (93), Expect = 0.34,   Method: Compositional matrix adjust.
 Identities = 26/89 (29%), Positives = 46/89 (51%), Gaps = 10/89 (11%)

Query: 47  LSAAHR--LVTSHLRLVVKIAMGY----RGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           L  A R  L+  +L+LV  IA  +    +GY   + +++SEG  GL+ A + + PE G  
Sbjct: 9   LDKAQRQLLIADNLKLVYHIANKFMPCPKGYMYEVDDLISEGYFGLIVAAQNYKPELGTP 68

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTT 129
             +Y+   I++ ++    RS    K+ +T
Sbjct: 69  FVSYACKVIESRIK----RSLPKYKLSST 93


>gi|322384374|ref|ZP_08058069.1| RNA polymerase sigma factor SigB-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321150809|gb|EFX44249.1| RNA polymerase sigma factor SigB-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 340

 Score = 40.4 bits (93), Expect = 0.34,   Method: Compositional matrix adjust.
 Identities = 24/65 (36%), Positives = 38/65 (58%), Gaps = 7/65 (10%)

Query: 60  LVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFDPERGFR----LATYSMWWIKAA 112
           +V  +A  YR   G GL   ++VS G IGL+QA + +DP+R  R     +TY+   IK +
Sbjct: 1   MVHSVARKYRSCIGAGLDYDDLVSVGMIGLIQAFRNYDPDRLNRKVSSFSTYAFNMIKWS 60

Query: 113 MQEYI 117
           +Q ++
Sbjct: 61  IQRFL 65


>gi|261368117|ref|ZP_05981000.1| RNA polymerase sigma-27 factor [Subdoligranulum variabile DSM
           15176]
 gi|282569875|gb|EFB75410.1| RNA polymerase sigma-27 factor [Subdoligranulum variabile DSM
           15176]
          Length = 147

 Score = 40.4 bits (93), Expect = 0.34,   Method: Compositional matrix adjust.
 Identities = 20/61 (32%), Positives = 34/61 (55%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +LRLV  +   Y        +++S G IGL++AV  FDP R  + ++Y+   I+ A
Sbjct: 58  LIRHNLRLVAHVTKKYFAATASQDDLISIGTIGLIKAVDTFDPVRASKFSSYASRCIENA 117

Query: 113 M 113
           +
Sbjct: 118 I 118


>gi|255094683|ref|ZP_05324161.1| RNA polymerase sigma-B factor [Clostridium difficile CIP 107932]
          Length = 252

 Score = 40.4 bits (93), Expect = 0.34,   Method: Compositional matrix adjust.
 Identities = 33/142 (23%), Positives = 68/142 (47%), Gaps = 21/142 (14%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y ++ ++   + L+  HL L   +A  Y   G+   ++    ++ L+ A+ ++D E+GF 
Sbjct: 22  YNKNKNVDIRNILIERHLYLARLLAKKYINKGVDFEDIYQVASLALIYAIDRYDVEKGFE 81

Query: 101 LATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ- 158
            ++++   I   +++Y   + W+L          R+    RR++   + I+D  +K EQ 
Sbjct: 82  FSSFATPTIVGEIKKYFRDKVWTL----------RV---PRRIQELSKKISDAKIKLEQE 128

Query: 159 ------VVAIAKKLNVSESEVI 174
                 V  IA  + VSE +V+
Sbjct: 129 NKKHPKVKDIADYIGVSEEDVL 150


>gi|332708995|ref|ZP_08428965.1| RNA polymerase sigma factor, sigma-70 family [Lyngbya majuscula 3L]
 gi|332352184|gb|EGJ31754.1| RNA polymerase sigma factor, sigma-70 family [Lyngbya majuscula 3L]
          Length = 258

 Score = 40.4 bits (93), Expect = 0.34,   Method: Compositional matrix adjust.
 Identities = 40/174 (22%), Positives = 90/174 (51%), Gaps = 13/174 (7%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQA 89
           K +   L ++Y+++ D    ++LV  +L LV + A  + +       +++  G IGL+ A
Sbjct: 10  KYQSLTLLQKYQQYPDPELRNQLVALNLGLVRREAHHWVKQCNESYEDLLQVGCIGLIVA 69

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR----LKGH 145
           +++FD  +G   +++++ +I+  +Q Y+      ++I       R +  LR+    +  +
Sbjct: 70  IERFDSTKGIAFSSFAIPYIRGEIQHYLRDRGYSIRI------PRRWLALRQKSVEITQN 123

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI-NSSDKNSS 198
           L+A T N    E+ +A A  +++ E + I++  +     SL+  + +S D+N+S
Sbjct: 124 LRA-TLNRQPTEEEIAAALNISLEEWQEITLAHQNREPLSLDTPVGDSEDRNTS 176


>gi|212697380|ref|ZP_03305508.1| hypothetical protein ANHYDRO_01950 [Anaerococcus hydrogenalis DSM
           7454]
 gi|212675572|gb|EEB35179.1| hypothetical protein ANHYDRO_01950 [Anaerococcus hydrogenalis DSM
           7454]
          Length = 256

 Score = 40.4 bits (93), Expect = 0.34,   Method: Compositional matrix adjust.
 Identities = 15/72 (20%), Positives = 38/72 (52%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           D    + L+  H+ +V  ++  Y G G+   ++    ++GL+ A+ ++DP +G+  ++++
Sbjct: 26  DKDLRNELIEDHMYIVDILSNKYVGKGIEKDDLYQVASLGLIYAIDRYDPSKGYEFSSFA 85

Query: 106 MWWIKAAMQEYI 117
              I   ++ Y 
Sbjct: 86  TPTIMGELKRYF 97


>gi|295104322|emb|CBL01866.1| RNA polymerase sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii SL3/3]
          Length = 221

 Score = 40.4 bits (93), Expect = 0.35,   Method: Compositional matrix adjust.
 Identities = 24/83 (28%), Positives = 39/83 (46%), Gaps = 8/83 (9%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIA--------MGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           + GD +A   L+ ++   + K A        +   G  L   ++   GN+GL +AV KFD
Sbjct: 13  QKGDATALDSLIENNKSFIGKEANDLFRSMNLAQSGLNLDTDDLKQAGNLGLWKAVPKFD 72

Query: 95  PERGFRLATYSMWWIKAAMQEYI 117
             RG +  TY+   I  AM + +
Sbjct: 73  AARGMKFLTYAAPAICNAMMDMV 95


>gi|325677915|ref|ZP_08157557.1| putative RNA polymerase sigma-H factor [Ruminococcus albus 8]
 gi|324110469|gb|EGC04643.1| putative RNA polymerase sigma-H factor [Ruminococcus albus 8]
          Length = 194

 Score = 40.4 bits (93), Expect = 0.35,   Method: Compositional matrix adjust.
 Identities = 25/76 (32%), Positives = 40/76 (52%), Gaps = 3/76 (3%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           D +A   L+  ++ L   IA G     G    I ++V EG + L++AV  + P+RG   A
Sbjct: 24  DKAALTALLLRYVSLTEYIAAGLAPKAGREQMIKDLVQEGMMALLKAVNSYRPDRGAGFA 83

Query: 103 TYSMWWIKAAMQEYIL 118
           TY+   I+ +M  YI+
Sbjct: 84  TYAGVCIRHSMLSYIM 99


>gi|325846834|ref|ZP_08169712.1| putative RNA polymerase sigma-B factor [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
 gi|325481206|gb|EGC84249.1| putative RNA polymerase sigma-B factor [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
          Length = 256

 Score = 40.4 bits (93), Expect = 0.35,   Method: Compositional matrix adjust.
 Identities = 15/72 (20%), Positives = 38/72 (52%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           D    + L+  H+ +V  ++  Y G G+   ++    ++GL+ A+ ++DP +G+  ++++
Sbjct: 26  DKDLRNELIEDHMYIVDILSNKYVGKGIEKDDLYQVASLGLIYAIDRYDPSKGYEFSSFA 85

Query: 106 MWWIKAAMQEYI 117
              I   ++ Y 
Sbjct: 86  TPTIMGELKRYF 97


>gi|229544420|ref|ZP_04433478.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus coagulans
           36D1]
 gi|229324905|gb|EEN90582.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus coagulans
           36D1]
          Length = 257

 Score = 40.4 bits (93), Expect = 0.35,   Method: Compositional matrix adjust.
 Identities = 57/250 (22%), Positives = 113/250 (45%), Gaps = 22/250 (8%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPERGFRL 101
           D  A + LV  ++ LV    +     GLP      ++ S G  GL+ ++ KFDP R  R 
Sbjct: 22  DPEAGNALVKRYMPLV-SFHVQRIAAGLPRNVSKEDLKSLGMFGLLDSLNKFDPSRELRF 80

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
            TY+ + I+ A+ +  LR    +  GT    K       +++  ++++    L+      
Sbjct: 81  DTYASFRIRGAILDG-LRKEDWLSRGTREKAK-------KIESAIESLEQKYLRTVSPKE 132

Query: 162 IAKKLNVSESEVI-SMNCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEK 218
           +A +L + E+EV  +MN +   +  L+     +D +  +     V    + GQ +  +EK
Sbjct: 133 VALELGMEETEVCTTMNEQFFAN-VLSIEETGTDNDEPEAASRFVSGDRNAGQPESELEK 191

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           +E       L  ++  L+ +E+ +      +E   TL  +     +S  R+ QI ++A  
Sbjct: 192 KETVKE---LAEAIRALSEKEQLVLSLFYQEE--CTLTEIGEVMGLSTSRISQIHSKAIY 246

Query: 279 KVQESIQKQV 288
           K++  ++K++
Sbjct: 247 KLRNILEKRL 256


>gi|229131899|ref|ZP_04260765.1| RNA polymerase sigma-B factor [Bacillus cereus BDRD-ST196]
 gi|228651574|gb|EEL07543.1| RNA polymerase sigma-B factor [Bacillus cereus BDRD-ST196]
          Length = 224

 Score = 40.4 bits (93), Expect = 0.37,   Method: Compositional matrix adjust.
 Identities = 54/239 (22%), Positives = 114/239 (47%), Gaps = 28/239 (11%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           +V  +  LV  IA  Y   G    ++V  G +GL+ A++++D   G     +++  I   
Sbjct: 1   MVNHYKNLVYSIAYRYSKGGPMHEDIVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGE 60

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNL-RRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
           +++Y+  ++W +       +  R   +L  ++K  ++ +TD+  +  +++ IA  L +SE
Sbjct: 61  IKKYLRDKTWGV-------HVPRRIKDLGGKIKLAIEELTDHLQRSPKIIEIANHLGLSE 113

Query: 171 SEVISM-----NCRLAGDESLNALI-NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            EV+ +     N +++   SL+ ++ NSSD +S    + +     G EQ          R
Sbjct: 114 EEVLEIMDAKNNYQVS---SLDDVVENSSDGSSVARIESVGEVEQGYEQT--------ER 162

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           R +L    +VLN  E+ +       EN +  ++      +S+  V +I+ +A  K++++
Sbjct: 163 RLVLKDIFNVLNDTEKSVIH-YIFGEN-LNQKDTGERLGISQMHVSRIKRQAISKLKQA 219


>gi|21225590|ref|NP_631369.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
 gi|8347047|emb|CAB93752.1| probable RNA polymerase sigma factor [Streptomyces coelicolor
           A3(2)]
          Length = 299

 Score = 40.4 bits (93), Expect = 0.37,   Method: Compositional matrix adjust.
 Identities = 60/251 (23%), Positives = 113/251 (45%), Gaps = 46/251 (18%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LVT+ L +  +IA  +R  G  I ++     +GL++A+ +FDPERG    +Y++  I   
Sbjct: 56  LVTAWLPMAHRIAGRFRDRGESIEDLRQVAALGLVKAIDRFDPERGA-FESYAVPTITGE 114

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +   R W+L ++     + R   N  R+     A +  + +P  V A+A    +SE 
Sbjct: 115 VKRHFRDRMWAL-RVPRRVQELR---NKVRVARRELAQSPGSPEP-SVAALAAHTGLSED 169

Query: 172 EV------------ISMNCRL-AGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           EV            +S++  L AGD+  SL   + ++D +         YD       +I
Sbjct: 170 EVGAGMEALESFSTLSLDAELSAGDDGYSLADTLGAADTS---------YD------TVI 214

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           ++E  K         +  L  RER I   R  ++  +T   ++    +S+  V ++ +R+
Sbjct: 215 DRESAKE-------GLRRLPERERAILYMRFFED--MTQSRIADCLGISQMHVSRLISRS 265

Query: 277 FKKVQESIQKQ 287
             +V++    Q
Sbjct: 266 CARVRDEAMGQ 276


>gi|225376836|ref|ZP_03754057.1| hypothetical protein ROSEINA2194_02478 [Roseburia inulinivorans DSM
           16841]
 gi|225211332|gb|EEG93686.1| hypothetical protein ROSEINA2194_02478 [Roseburia inulinivorans DSM
           16841]
          Length = 244

 Score = 40.0 bits (92), Expect = 0.38,   Method: Compositional matrix adjust.
 Identities = 25/87 (28%), Positives = 43/87 (49%), Gaps = 1/87 (1%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R  + GD  A  ++V+ +L LV  I   +   G    E+   G IGL++A+  FD     
Sbjct: 9   RQAQDGDKKARDKVVSDNLGLVHAIVRRFEKRGHDREELFQIGCIGLIKAIDHFDLSLNL 68

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKI 126
             +TY++  I   ++ + LR   +VK+
Sbjct: 69  AFSTYAVPMITGEIRRF-LRDDGMVKV 94


>gi|325509467|gb|ADZ21103.1| DNA-dependent RNA polymerase sigma subunit [Clostridium
           acetobutylicum EA 2018]
          Length = 246

 Score = 40.0 bits (92), Expect = 0.38,   Method: Compositional matrix adjust.
 Identities = 21/84 (25%), Positives = 42/84 (50%), Gaps = 2/84 (2%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGY--RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           G   A   L+ S ++ + KIA G+      L + +++ EG I +++A+  +D ++  + +
Sbjct: 16  GSKDAKSFLIDSSMKYIKKIANGFCLNNKSLSLEDLMQEGIIAVIKAINSYDLDKNVKFS 75

Query: 103 TYSMWWIKAAMQEYILRSWSLVKI 126
           TY    I   +   I + +S  KI
Sbjct: 76  TYVYSMINFTLISEIKKKYSYFKI 99


>gi|134102136|ref|YP_001107797.1| RNA polymerase sigma factor [Saccharopolyspora erythraea NRRL 2338]
 gi|291007613|ref|ZP_06565586.1| RNA polymerase sigma factor [Saccharopolyspora erythraea NRRL 2338]
 gi|133914759|emb|CAM04872.1| RNA polymerase sigma factor [Saccharopolyspora erythraea NRRL 2338]
          Length = 280

 Score = 40.0 bits (92), Expect = 0.38,   Method: Compositional matrix adjust.
 Identities = 20/66 (30%), Positives = 33/66 (50%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RLVT HL +   IA  +   G    ++     +GL+ AV +FDP RG    +Y++  I  
Sbjct: 43  RLVTEHLPVAEHIARRFSHRGESQEDLTQVATLGLINAVDRFDPGRGVDFLSYAVPTIMG 102

Query: 112 AMQEYI 117
            ++ + 
Sbjct: 103 EVRRHF 108


>gi|157962130|ref|YP_001502164.1| sigma-70 region 4 domain-containing protein [Shewanella pealeana
           ATCC 700345]
 gi|157847130|gb|ABV87629.1| sigma-70 region 4 domain protein [Shewanella pealeana ATCC 700345]
          Length = 930

 Score = 40.0 bits (92), Expect = 0.38,   Method: Compositional matrix adjust.
 Identities = 19/57 (33%), Positives = 37/57 (64%), Gaps = 1/57 (1%)

Query: 228 LTRSMSVLNPRERRIFEARR-LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            T+++S+L  RE+ I E R     + +TLE + ++F V+RER+RQI+ +   ++ ++
Sbjct: 394 FTQALSLLKDREKEIIELRMGFHGHILTLEEVGTKFGVTRERIRQIQKKHVARIIDT 450


>gi|46240842|dbj|BAD15074.1| RNA polymerase alternative sigma factor [Saccharopolyspora
           erythraea]
          Length = 280

 Score = 40.0 bits (92), Expect = 0.39,   Method: Compositional matrix adjust.
 Identities = 20/66 (30%), Positives = 33/66 (50%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RLVT HL +   IA  +   G    ++     +GL+ AV +FDP RG    +Y++  I  
Sbjct: 43  RLVTEHLPVAEHIARRFSHRGESQEDLTQVATLGLINAVDRFDPGRGVDFLSYAVPTIMG 102

Query: 112 AMQEYI 117
            ++ + 
Sbjct: 103 EVRRHF 108


>gi|238784716|ref|ZP_04628720.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           bercovieri ATCC 43970]
 gi|238714395|gb|EEQ06403.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           bercovieri ATCC 43970]
          Length = 240

 Score = 40.0 bits (92), Expect = 0.40,   Method: Compositional matrix adjust.
 Identities = 44/216 (20%), Positives = 93/216 (43%), Gaps = 34/216 (15%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTANQK 133
           + +++  G IGL+ AV+++D  +G    TY++  I+ AM  E   R W+          +
Sbjct: 41  LDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDWA---------PR 91

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            +  N R +   +Q +     +P     +AK L++  +E   +            L++++
Sbjct: 92  SVRRNAREVASAMQQVEQRVGRPATEQEVAKILDIDLAEYRQI------------LLDTN 139

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEE---------RKNRRNMLTRSMSVLNPRERRIFE 244
           +     + +W   +H    + L+E  E           N R  +  ++  L  RE+ +  
Sbjct: 140 NSQLFSYDEWR-EEHGESVEPLLEGHEDANPLQHLLEGNLRQRVIEAIEALPEREKMVLT 198

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
               +E  + L+ + +  EV   RV Q+ ++A K++
Sbjct: 199 LYYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRL 232


>gi|168704081|ref|ZP_02736358.1| RNA polymerase sigma factor for flagellar operon [Gemmata
           obscuriglobus UQM 2246]
          Length = 247

 Score = 40.0 bits (92), Expect = 0.40,   Method: Compositional matrix adjust.
 Identities = 36/124 (29%), Positives = 56/124 (45%), Gaps = 15/124 (12%)

Query: 53  LVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           L+ SHL LV  +    +G    G+ +  + S G +GL++A  KFDP R  +  T++   I
Sbjct: 25  LIVSHLPLVKHVIGRLIGDVPPGVDVENLESAGVLGLVEAAAKFDPARNAQFKTFAYLRI 84

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + A+ + + R+  L +        RL    R  +     IT        V AIA    +S
Sbjct: 85  RGAIVDEMRRNSPLPQ----HVHARLALVRRACRTLPHPIT--------VEAIAAATGLS 132

Query: 170 ESEV 173
           E EV
Sbjct: 133 EDEV 136


>gi|229165937|ref|ZP_04293702.1| RNA polymerase sigma-B factor [Bacillus cereus AH621]
 gi|228617490|gb|EEK74550.1| RNA polymerase sigma-B factor [Bacillus cereus AH621]
          Length = 224

 Score = 40.0 bits (92), Expect = 0.41,   Method: Compositional matrix adjust.
 Identities = 53/239 (22%), Positives = 114/239 (47%), Gaps = 28/239 (11%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           +V  +  LV  IA  Y   G    +++  G +GL+ A++++D   G     +++  I   
Sbjct: 1   MVNHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGE 60

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNL-RRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
           +++Y+  ++W +       +  R   +L  ++K  ++ +TD+  +  +++ IA  L +SE
Sbjct: 61  IKKYLRDKTWGV-------HVPRRIKDLGGKIKLAIEELTDHLQRSPKIIEIADHLGLSE 113

Query: 171 SEVISM-----NCRLAGDESLNALI-NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            EV+ +     N +++   SL+ ++ NSSD +S    + +     G EQ          R
Sbjct: 114 EEVLEIMDAKNNYQVS---SLDDVVENSSDGSSVARIESVGEVEQGYEQT--------ER 162

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           R +L    +VLN  E+ +       EN +  ++      +S+  V +I+ +A  K++++
Sbjct: 163 RLVLDDIFNVLNDTEKSVIH-YIFGEN-LNQKDTGERLGISQMHVSRIKRQAISKLKQA 219


>gi|226939710|ref|YP_002794783.1| FliA1 [Laribacter hongkongensis HLHK9]
 gi|226714636|gb|ACO73774.1| FliA1 [Laribacter hongkongensis HLHK9]
          Length = 247

 Score = 40.0 bits (92), Expect = 0.41,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 36/63 (57%), Gaps = 3/63 (4%)

Query: 54  VTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           +T HL LV K+A   +      + + ++V  G IGL++A ++FDP +G    T++   I+
Sbjct: 19  ITEHLTLVRKLASMMISRLPASVELDDLVQVGMIGLIEAAQQFDPAQGVLFETFASQRIR 78

Query: 111 AAM 113
            AM
Sbjct: 79  GAM 81


>gi|222151972|ref|YP_002561132.1| sigma factor B [Macrococcus caseolyticus JCSC5402]
 gi|222121101|dbj|BAH18436.1| sigma factor B [Macrococcus caseolyticus JCSC5402]
          Length = 255

 Score = 40.0 bits (92), Expect = 0.41,   Method: Compositional matrix adjust.
 Identities = 54/255 (21%), Positives = 116/255 (45%), Gaps = 28/255 (10%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           K Y++  D  A   LV  + +LV  +A  Y        ++V  G +GL+ A+ +FD    
Sbjct: 19  KLYQDTQDEFAQKELVLHYQKLVESLAYRYSKGQSHHEDLVQVGMVGLLGAINRFDVTFE 78

Query: 99  FRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
            +   + +  +   ++ Y+  ++WS   +      K +   ++R    L   T+   +  
Sbjct: 79  RKFEAFLVPTVIGEIKRYLRDKTWS---VHVPRRIKEIGPKIKRATDEL---TNELGRSP 132

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI- 216
           +++ IA+++  +E EV+     +   +S NAL  S D +       +  D DG    L+ 
Sbjct: 133 KIIEIAQRIEATEEEVLEA---MEMGQSYNAL--SVDHS-------IEADKDGSTVTLLD 180

Query: 217 ------EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                 E  +   +R +L + + +L+ RER I +   L  + ++ +    +  +S+  V 
Sbjct: 181 VMGNTEEGYDLTEKRMILEKVLPILSDREREIIQCTFL--DGLSQKETGEKIGLSQMHVS 238

Query: 271 QIEARAFKKVQESIQ 285
           +++  A KK+++++Q
Sbjct: 239 RLQRTAIKKLRDAVQ 253


>gi|124023131|ref|YP_001017438.1| type III sigma factor [Prochlorococcus marinus str. MIT 9303]
 gi|123963417|gb|ABM78173.1| putative type III sigma factor [Prochlorococcus marinus str. MIT
           9303]
          Length = 269

 Score = 40.0 bits (92), Expect = 0.41,   Method: Compositional matrix adjust.
 Identities = 19/55 (34%), Positives = 33/55 (60%), Gaps = 3/55 (5%)

Query: 54  VTSHLRL--VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           V  HL L  +       RG G  + +++ E  +GL+ A++KFD  RGF++++Y+M
Sbjct: 43  VIEHLGLAHLAATRQATRG-GEELDDLIQEARLGLIMAMEKFDANRGFKVSSYAM 96


>gi|188533568|ref|YP_001907365.1| flagellar biosynthesis sigma factor [Erwinia tasmaniensis Et1/99]
 gi|188028610|emb|CAO96472.1| RNA polymerase sigma factor for flagellar operon [Erwinia
           tasmaniensis Et1/99]
          Length = 240

 Score = 40.0 bits (92), Expect = 0.41,   Method: Compositional matrix adjust.
 Identities = 46/218 (21%), Positives = 93/218 (42%), Gaps = 38/218 (17%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTANQK 133
           + +++  G IGL+ AV+++D  +G    TY++  I+ AM  E   R W+          +
Sbjct: 41  LDDLLQAGGIGLLNAVERYDAMQGTAFTTYAVQRIRGAMLDELRSRDWA---------PR 91

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            +  N R + G +  +     +      +A +L+VS  E   +                 
Sbjct: 92  SVRRNAREVAGAMHRVEQALGRSASEQEVAAQLDVSLEEYRQILL--------------- 136

Query: 194 DKNSSQWQDWLVY--DHDGQEQVLIEKEERKNR---------RNMLTRSMSVLNPRERRI 242
           D N+SQ   +  Y  +H    +++ E  E++N          R+ +  ++  L  RE+ +
Sbjct: 137 DTNNSQLFSFDEYREEHGDSAELVTEGHEQENPLHQLLEGDLRDRVIEAIEALPDREKMV 196

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                 +E  + L+ + +  EV   RV Q+ ++A K++
Sbjct: 197 LTLYYQEE--LNLKEIGAVLEVGESRVSQLHSQAVKRL 232


>gi|455127|gb|AAA22315.1| RNA polymerase sigma-K subunit (cisB) [Bacillus subtilis]
 gi|1303780|dbj|BAA12436.1| SpoIVCB [Bacillus subtilis]
          Length = 156

 Score = 40.0 bits (92), Expect = 0.41,   Method: Compositional matrix adjust.
 Identities = 23/75 (30%), Positives = 41/75 (54%), Gaps = 3/75 (4%)

Query: 39  KRYRE---HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           K+Y E    GD  A + L+  +LRLV  I   +   G    +++S G IGL++ ++ +  
Sbjct: 38  KKYLELMAKGDEHARNMLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKGIESYSA 97

Query: 96  ERGFRLATYSMWWIK 110
            +G ++ATY+   I+
Sbjct: 98  GKGTKVATYAARCIE 112


>gi|95929871|ref|ZP_01312612.1| RNA polymerase, sigma 28 subunit [Desulfuromonas acetoxidans DSM
           684]
 gi|95134167|gb|EAT15825.1| RNA polymerase, sigma 28 subunit [Desulfuromonas acetoxidans DSM
           684]
          Length = 243

 Score = 40.0 bits (92), Expect = 0.42,   Method: Compositional matrix adjust.
 Identities = 54/234 (23%), Positives = 101/234 (43%), Gaps = 20/234 (8%)

Query: 53  LVTSHLRLVVKIAMGYR----GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           LV SH+ LV  +    R    G+ +   ++ S   +GLM A  +FDP RG    T++   
Sbjct: 18  LVKSHMSLVHLVVDRMRAQVPGF-VTKDDMTSAAMMGLMDAATRFDPSRGIMFKTFAERR 76

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+ + I R            Q R+   + +++  L          E+ VA A  + +
Sbjct: 77  IRGAIYDEI-RKMDWFSRSLREKQGRIGKTITQMEHRL-----GRTPEEEEVAEAMDMTL 130

Query: 169 SE-SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
            E   ++   C L G  SLN  ++  D +   + D L  D    +Q + E E        
Sbjct: 131 DEYRHMLGQVCHL-GCVSLNETLDDRD-DGRNFLDLLTDDSPSVQQRIEESELASE---- 184

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           L   +  L+ +ER +      +E  +T + ++   +++  R+ Q+ ++A  K++
Sbjct: 185 LAGQLDKLSEKERLVISLYYYEE--LTQKEIAEVLDLTEGRISQLHSQALVKLK 236


>gi|327441148|dbj|BAK17513.1| DNA-directed RNA polymerase specialized sigma subunit [Solibacillus
           silvestris StLB046]
          Length = 256

 Score = 40.0 bits (92), Expect = 0.42,   Method: Compositional matrix adjust.
 Identities = 26/92 (28%), Positives = 48/92 (52%), Gaps = 1/92 (1%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L+  E   L  R ++ G+     +LV  +LRLV+ I   Y   G    ++   G IG
Sbjct: 15  LPVLKPDEMKDLFIRLQQ-GEWIVREQLVFCNLRLVLSIVGRYAYRGEQADDLFQVGCIG 73

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           L++A+  FD +   R +TY++  I   ++ ++
Sbjct: 74  LLKAIDNFDLKHNVRFSTYAVPMIMGEIRRHL 105


>gi|58696753|ref|ZP_00372293.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of
           Drosophila simulans]
 gi|58537061|gb|EAL60191.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of
           Drosophila simulans]
          Length = 183

 Score = 40.0 bits (92), Expect = 0.42,   Method: Compositional matrix adjust.
 Identities = 24/62 (38%), Positives = 37/62 (59%), Gaps = 7/62 (11%)

Query: 225 RNMLTRSMSVLNPRERRIFEAR-----RLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           R + T  ++ L P+E RI   R       +E+  TLE +   F V+RER+RQIEA+A +K
Sbjct: 112 RGITTNVLATLTPKEERILRMRFGLGKDGKEH--TLEEVGKIFNVTRERIRQIEAKALRK 169

Query: 280 VQ 281
           ++
Sbjct: 170 LK 171


>gi|257451779|ref|ZP_05617078.1| RpoS [Fusobacterium sp. 3_1_5R]
 gi|317058336|ref|ZP_07922821.1| predicted protein [Fusobacterium sp. 3_1_5R]
 gi|313684012|gb|EFS20847.1| predicted protein [Fusobacterium sp. 3_1_5R]
          Length = 201

 Score = 40.0 bits (92), Expect = 0.43,   Method: Compositional matrix adjust.
 Identities = 20/72 (27%), Positives = 38/72 (52%), Gaps = 4/72 (5%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           G++ A + L+  ++ L+ KI    R YG    +   EG +    A+ KFD  +  +L++Y
Sbjct: 16  GNIQARNELIEKNINLIHKIN---RRYGSS-EDGFQEGVLAFCHAIDKFDETKKVKLSSY 71

Query: 105 SMWWIKAAMQEY 116
           +  WI+  ++ Y
Sbjct: 72  AFHWIRQRIKRY 83


>gi|158338094|ref|YP_001519270.1| RNA polymerase sigma factor SigF [Acaryochloris marina MBIC11017]
 gi|158308335|gb|ABW29952.1| RNA polymerase sigma factor, group3 [Acaryochloris marina
           MBIC11017]
          Length = 266

 Score = 40.0 bits (92), Expect = 0.43,   Method: Compositional matrix adjust.
 Identities = 21/87 (24%), Positives = 48/87 (55%), Gaps = 1/87 (1%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           YR+   +   +RLV  ++ LV K+A         P  ++   G +GL+ A+++FDP +G+
Sbjct: 18  YRQKPSVQLRNRLVRLNMGLVRKVAHRLTHQCAEPYEDLEQCGFLGLITAIERFDPSQGY 77

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKI 126
             +++++ +I+  +  ++    + V+I
Sbjct: 78  AFSSFAVPYIRGEILHFLRDRANTVRI 104


>gi|73539441|ref|YP_299808.1| sigma-70 region 4 [Ralstonia eutropha JMP134]
 gi|72122778|gb|AAZ64964.1| Sigma-70 region 4 [Ralstonia eutropha JMP134]
          Length = 238

 Score = 40.0 bits (92), Expect = 0.43,   Method: Compositional matrix adjust.
 Identities = 26/77 (33%), Positives = 40/77 (51%), Gaps = 6/77 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPE 96
           Y   G L  A  +V +H +LV +IA+      LP    I +++  G IGL+ A K+++  
Sbjct: 2   YTIQGKLEQAD-VVKTHAQLVRRIALQL-AAKLPASVQIDDLIQAGMIGLLDAAKRYEDT 59

Query: 97  RGFRLATYSMWWIKAAM 113
            G R  TY+   I+ AM
Sbjct: 60  HGARFETYASQRIRGAM 76


>gi|89094438|ref|ZP_01167378.1| flagellar biosynthesis sigma factor FliA [Oceanospirillum sp.
           MED92]
 gi|89081330|gb|EAR60562.1| flagellar biosynthesis sigma factor FliA [Oceanospirillum sp.
           MED92]
          Length = 236

 Score = 40.0 bits (92), Expect = 0.43,   Method: Compositional matrix adjust.
 Identities = 46/210 (21%), Positives = 90/210 (42%), Gaps = 31/210 (14%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS-WSLVKIGTTANQK 133
           + +++  G IGL++A  K+D  +G    TY+   I+ ++ + + R  W+          +
Sbjct: 38  LDDLIQAGMIGLLEAASKYDASKGASFETYAGIRIRGSIIDEVRRGDWT---------PR 88

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            +  N RR+   +Q I     +      +AK+L +S             DE  N L +S 
Sbjct: 89  SVHRNSRRVTEAIQQIEARTGRDASDSEVAKELGISV------------DEYHNLLKDSL 136

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKE-------ERKNRRNMLTRSMSVLNPRERRIFEAR 246
           D     +++ L  +H+G  +     +       ER+     L+ +++ L  RE+ +    
Sbjct: 137 DSRLFSFEEMLNPEHEGPGESFANDDPGPNKHIEREAFLKALSEAINNLPEREKLVLALY 196

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARA 276
             +E  + L+ +     VS  RV QI ++A
Sbjct: 197 YDEE--LNLKEIGQVLGVSESRVSQIHSQA 224


>gi|239932973|ref|ZP_04689926.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291441326|ref|ZP_06580716.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291344221|gb|EFE71177.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 295

 Score = 40.0 bits (92), Expect = 0.43,   Method: Compositional matrix adjust.
 Identities = 42/195 (21%), Positives = 91/195 (46%), Gaps = 18/195 (9%)

Query: 61  VVKIAMG-YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           +V+ A G +RG G  + ++V  G IGL++A+ +F+  R     ++++ +I   ++ +   
Sbjct: 75  LVRFAAGRFRGRGDDMDDIVQTGMIGLIKAIDRFELSREVEFTSFALPYIVGEIKRFFRD 134

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
           +   V +     + R+   L + +  L +  D   +   V  +A  +N++E +VI     
Sbjct: 135 TTWAVHVPRRLQELRV--ELAKAREELASRLD---REPTVAELATLMNITEDQVIEGQIA 189

Query: 180 LAG--DESLNALI--NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
             G    SL+A +  +  +   +   D++  + +G    L+E        + L   M+ L
Sbjct: 190 ANGYNSSSLDAALTGDGPENGEAVLADFIGVEEEGLR--LVED------FHALAPLMAEL 241

Query: 236 NPRERRIFEARRLQE 250
           + R+R+I   R ++E
Sbjct: 242 SERDRQIIHMRFVEE 256


>gi|302527791|ref|ZP_07280133.1| RNA polymerase sigma-F factor [Streptomyces sp. AA4]
 gi|302436686|gb|EFL08502.1| RNA polymerase sigma-F factor [Streptomyces sp. AA4]
          Length = 243

 Score = 40.0 bits (92), Expect = 0.44,   Method: Compositional matrix adjust.
 Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 1/71 (1%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           VT  L +   IA  + G G P  ++V    IGL+ A+ +F P+RG    ++++  I   +
Sbjct: 23  VTEFLPVAEHIATRFTGRGEPREDLVQVARIGLINAIDRFTPDRGPDFLSFAVPTIMGEI 82

Query: 114 QEYILRS-WSL 123
           + Y   + WS+
Sbjct: 83  RRYFRDTGWSV 93


>gi|332140599|ref|YP_004426337.1| flagellar biosynthesis sigma factor [Alteromonas macleodii str.
           'Deep ecotype']
 gi|327550621|gb|AEA97339.1| flagellar biosynthesis sigma factor [Alteromonas macleodii str.
           'Deep ecotype']
          Length = 243

 Score = 40.0 bits (92), Expect = 0.44,   Method: Compositional matrix adjust.
 Identities = 59/253 (23%), Positives = 105/253 (41%), Gaps = 34/253 (13%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           A  YR+  D S   +LV  H  LV +IA   +      + + +++  G IGL++A + FD
Sbjct: 5   AAAYRQQTDKS---QLVERHASLVKRIAHHLIARLPASVLVDDLIQSGMIGLLEAARNFD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
             +G    T++   I+ AM + I +  W+          + +  N R +   +  +    
Sbjct: 62  GSKGASFETFAGIRIRGAMLDEIRKGDWT---------PRSVHRNGRAITEAISQVESET 112

Query: 154 LKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
            +  +   IA KLNVS  +   M       +L G E L    +      S+  D  + D 
Sbjct: 113 GRDARDSDIADKLNVSLQDYHQMLNEVNAGKLVGIEDLGVSEDVITTEQSRGSDAPLED- 171

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
                 L++   +K     L  +++ L  RE  +      +E  + L  +    +VS  R
Sbjct: 172 ------LMQGAFQK----ALAHAITTLPEREAIVLSLYYDEE--LNLREIGEVLDVSESR 219

Query: 269 VRQIEARAFKKVQ 281
           V QI ++A  K++
Sbjct: 220 VSQIHSQAMLKLK 232


>gi|146312155|ref|YP_001177229.1| flagellar biosynthesis sigma factor [Enterobacter sp. 638]
 gi|145319031|gb|ABP61178.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Enterobacter sp.
           638]
          Length = 239

 Score = 40.0 bits (92), Expect = 0.44,   Method: Compositional matrix adjust.
 Identities = 48/221 (21%), Positives = 99/221 (44%), Gaps = 32/221 (14%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL+ AV ++D  +G    TY++  I+ AM +  LRS   V      N + 
Sbjct: 41  LDDLLQAGGIGLLNAVDRYDALQGTAFTTYAVQRIRGAMLDE-LRSRDWVPRSVRRNARE 99

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   + +L+   Q +  N  + E    +A++L ++  +   M            L+++++
Sbjct: 100 VAHAIGQLE---QELGRNATETE----VAERLGIAVQDYRQM------------LLDTNN 140

Query: 195 KNSSQWQDW---------LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
                + +W         LV D +  E  L +  E  N R  +  ++  L  RE+ +   
Sbjct: 141 SQLFSYDEWREEHGDSVELVTDENQHENPLHQLLE-GNLRQRVMDAIEALPEREQLVLTL 199

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +E  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 200 YYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 238


>gi|126435251|ref|YP_001070942.1| FliA/WhiG family RNA polymerase sigma factor [Mycobacterium sp.
           JLS]
 gi|126235051|gb|ABN98451.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Mycobacterium
           sp. JLS]
          Length = 284

 Score = 40.0 bits (92), Expect = 0.44,   Method: Compositional matrix adjust.
 Identities = 48/213 (22%), Positives = 95/213 (44%), Gaps = 38/213 (17%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           +R+R H        ++T+ + +   IA  + G G P  +V+    IGL++ V ++DP++G
Sbjct: 43  QRWRRH--------IITACVPIADHIAYRFVGRGEPSEDVIQVARIGLIKTVDRYDPDKG 94

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
             LA +++  I+  ++ +   +   V++     + +L     R++  +  ++    +   
Sbjct: 95  HFLA-FAVPTIRGEIRRHFRDNTWTVRVPRKVQETQL-----RMRDAVNTLSQRLNRTPT 148

Query: 159 VVAIAKKLNVSESEVISMNCRLAG--------DESLNALINSSDK-NSSQWQDWLVYDHD 209
            V +A++L+V   E+   +C+ A         D  L    N  D   S Q  D   Y   
Sbjct: 149 GVELAEELDVGSEEL--GDCQAATTAYRPVSLDAPLLTAQNDGDTVGSMQGGDDPGY--- 203

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
           G+ + LI          +L  ++S L+PR R I
Sbjct: 204 GRVEDLI----------LLQEAISDLDPRRRAI 226


>gi|228970817|ref|ZP_04131457.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus thuringiensis
           serovar thuringiensis str. T01001]
 gi|228977391|ref|ZP_04137786.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus thuringiensis
           Bt407]
 gi|228782368|gb|EEM30551.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus thuringiensis
           Bt407]
 gi|228788942|gb|EEM36881.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus thuringiensis
           serovar thuringiensis str. T01001]
          Length = 234

 Score = 40.0 bits (92), Expect = 0.45,   Method: Compositional matrix adjust.
 Identities = 41/166 (24%), Positives = 77/166 (46%), Gaps = 15/166 (9%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL I ++V  G IGL++A + F+ E G++ +TY++  I   + ++I+ S   +K+     
Sbjct: 34  GLEIEDLVQYGMIGLIKARRDFNHELGYQFSTYAIPKIHGEVGKFIMNSHK-IKV----- 87

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
             R  + LR        +    L  E    I K+L V+  EV          +SL  ++ 
Sbjct: 88  -PRALYQLRG------KMMRQGLMEEDGETICKQLEVALPEVKEALQYQPNTKSLQDVMY 140

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
           +S    S  ++ L+ D     QV+ E E+ +N   + +   ++ +P
Sbjct: 141 TSAGGGS--EEILLEDMLEDTQVIEETEQVENHMVLQSFYQTLEHP 184


>gi|332707787|ref|ZP_08427814.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Lyngbya majuscula
           3L]
 gi|332353490|gb|EGJ33003.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Lyngbya majuscula
           3L]
          Length = 260

 Score = 40.0 bits (92), Expect = 0.45,   Method: Compositional matrix adjust.
 Identities = 17/53 (32%), Positives = 33/53 (62%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           P  ++   G IGL++A+++FDP +G   ++ ++ +I+  M  ++    SLVKI
Sbjct: 51  PYEDLEQMGYIGLIRAIERFDPHQGCAFSSLAVPYIRGEMLHFLRDRGSLVKI 103


>gi|228937937|ref|ZP_04100564.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus thuringiensis
           serovar berliner ATCC 10792]
 gi|228821728|gb|EEM67729.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus thuringiensis
           serovar berliner ATCC 10792]
          Length = 210

 Score = 40.0 bits (92), Expect = 0.45,   Method: Compositional matrix adjust.
 Identities = 41/166 (24%), Positives = 77/166 (46%), Gaps = 15/166 (9%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL I ++V  G IGL++A + F+ E G++ +TY++  I   + ++I+ S   +K+     
Sbjct: 10  GLEIEDLVQYGMIGLIKARRDFNHELGYQFSTYAIPKIHGEVGKFIMNSHK-IKV----- 63

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
             R  + LR        +    L  E    I K+L V+  EV          +SL  ++ 
Sbjct: 64  -PRALYQLRG------KMMRQGLMEEDGETICKQLEVALPEVKEALQYQPNTKSLQDVMY 116

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
           +S    S  ++ L+ D     QV+ E E+ +N   + +   ++ +P
Sbjct: 117 TSAGGGS--EEILLEDMLEDTQVIEETEQVENHMVLQSFYQTLEHP 160


>gi|229826254|ref|ZP_04452323.1| hypothetical protein GCWU000182_01626 [Abiotrophia defectiva ATCC
           49176]
 gi|229789124|gb|EEP25238.1| hypothetical protein GCWU000182_01626 [Abiotrophia defectiva ATCC
           49176]
          Length = 280

 Score = 40.0 bits (92), Expect = 0.45,   Method: Compositional matrix adjust.
 Identities = 36/140 (25%), Positives = 70/140 (50%), Gaps = 7/140 (5%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF-DPERGFRLAT 103
           GD  A    +   L  VV+IA G+        E++SEGN+GL+  +K+  + ER  +   
Sbjct: 141 GDEKAEASYIERKLHKVVEIARGFELTEDYFKELISEGNVGLLIGLKELKNLERDDKPIE 200

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           +    I++AMQ++I  S   +++ +TAN   +   +  +    + + + N     +  +A
Sbjct: 201 FIESRIESAMQDFIEES---LEMESTANA--MVAKVNFVSDAAKKMKEMNGSSPTLKELA 255

Query: 164 KKLNVSESEVISMNCRLAGD 183
              N++E+E+  +   L+GD
Sbjct: 256 SYTNLTEAELTDI-IELSGD 274


>gi|228902053|ref|ZP_04066217.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus thuringiensis
           IBL 4222]
 gi|228857479|gb|EEN01975.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus thuringiensis
           IBL 4222]
          Length = 237

 Score = 40.0 bits (92), Expect = 0.45,   Method: Compositional matrix adjust.
 Identities = 41/166 (24%), Positives = 77/166 (46%), Gaps = 15/166 (9%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL I ++V  G IGL++A + F+ E G++ +TY++  I   + ++I+ S   +K+     
Sbjct: 37  GLEIEDLVQYGMIGLIKARRDFNHELGYQFSTYAIPKIHGEVGKFIMNSHK-IKV----- 90

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
             R  + LR        +    L  E    I K+L V+  EV          +SL  ++ 
Sbjct: 91  -PRALYQLRG------KMMRQGLMEEDGETICKQLEVALPEVKEALQYQPNTKSLQDVMY 143

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
           +S    S  ++ L+ D     QV+ E E+ +N   + +   ++ +P
Sbjct: 144 TSAGGGS--EEILLEDMLEDTQVIEETEQVENHMVLQSFYQTLEHP 187


>gi|255606356|ref|XP_002538551.1| RNA polymerase sigma factor for flagellar operon, putative [Ricinus
           communis]
 gi|223511619|gb|EEF23833.1| RNA polymerase sigma factor for flagellar operon, putative [Ricinus
           communis]
          Length = 123

 Score = 40.0 bits (92), Expect = 0.46,   Method: Compositional matrix adjust.
 Identities = 30/119 (25%), Positives = 59/119 (49%), Gaps = 11/119 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           L+T H+ LV ++A   +    P   + ++V  G +GL+ A+ +++   G +  TY++  I
Sbjct: 13  LLTEHMPLVKRLAHQMKAKLPPSVEVDDLVQAGMMGLLDAINRYEENHGAQFETYAVLRI 72

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           + AM +  LRS   +   T A       N+R+++  + A+     +P     +AK L +
Sbjct: 73  RGAMLDE-LRSSDWMPRSTRA-------NMRKVESAMAALQQQLGRPPSESEVAKSLKL 123


>gi|56752504|ref|YP_173205.1| RNA polymerase sigma factor SigF [Synechococcus elongatus PCC 6301]
 gi|81300319|ref|YP_400527.1| RNA polymerase sigma factor SigF [Synechococcus elongatus PCC 7942]
 gi|56687463|dbj|BAD80685.1| group3 RNA polymerase sigma factor SigF1 [Synechococcus elongatus
           PCC 6301]
 gi|81169200|gb|ABB57540.1| group3 RNA polymerase sigma factor SigF [Synechococcus elongatus
           PCC 7942]
          Length = 259

 Score = 40.0 bits (92), Expect = 0.46,   Method: Compositional matrix adjust.
 Identities = 27/90 (30%), Positives = 55/90 (61%), Gaps = 5/90 (5%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG-LPIS--EVVSEGNIGLM 87
           +++ ++L ++Y++  D    +RLV  +L LV + A  YR     P S  E+V  G++GL+
Sbjct: 10  RRQTFLLLRQYQQTRDHRIRNRLVELNLGLVRQEA--YRWVQRCPESFEELVQIGSLGLI 67

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
            A+ +F+ ERG   +++++ +I+  +Q Y+
Sbjct: 68  AAIDRFELERGKAFSSFAVPYIRGEIQHYL 97


>gi|119714600|ref|YP_921565.1| FliA/WhiG family RNA polymerase sigma factor [Nocardioides sp.
           JS614]
 gi|119535261|gb|ABL79878.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Nocardioides sp.
           JS614]
          Length = 300

 Score = 40.0 bits (92), Expect = 0.46,   Method: Compositional matrix adjust.
 Identities = 51/211 (24%), Positives = 85/211 (40%), Gaps = 25/211 (11%)

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           + FDPERG   A Y+M  I+ AM +  LRS            + +     RL   L    
Sbjct: 72  RSFDPERGVPFARYAMPRIRGAMVDE-LRSVDWASRSVRRRAREIEEARARLAATLGEFP 130

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ-WQDWLVYDHD 209
           D+        A+A  L ++  EV  ++      E+    +   D  + Q   + L     
Sbjct: 131 DDE-------AVAAALGMTLDEVNRVDS-----EAARGTVLPLDAGAQQGLAEILPVREA 178

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
           G E+  +  E    R   L  ++  L  R R +     L+E P  +  L++E  V+  RV
Sbjct: 179 GPEERAVHLE----RVRYLADAVEELPERMRLVVRGYFLEERP--MAELAAELGVTESRV 232

Query: 270 RQIEARAFKKVQESIQKQVELSSSPPLLQKP 300
            Q+ A A   +++++ +  +     P L KP
Sbjct: 233 SQVRAEALALLRDALGEAFD-----PHLPKP 258


>gi|331663420|ref|ZP_08364330.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli TA143]
 gi|331059219|gb|EGI31196.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli TA143]
          Length = 239

 Score = 40.0 bits (92), Expect = 0.47,   Method: Compositional matrix adjust.
 Identities = 48/221 (21%), Positives = 101/221 (45%), Gaps = 32/221 (14%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL+ AV+++D  +G    TY++  I+ AM +  LRS   V      N + 
Sbjct: 41  LDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDE-LRSRDWVPRSVRRNARE 99

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   + +L+   Q +  N  + E    +A++L +  ++   M            L+++++
Sbjct: 100 VAQAIGQLE---QELGRNATETE----VAERLGIDIADYRQM------------LLDTNN 140

Query: 195 KNSSQWQDW---------LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
                + +W         LV D D Q +  +++    N R  +  ++  L  RE+ +   
Sbjct: 141 SQLFSYDEWREEHGDSIELVTD-DHQRENPLQQLLDSNLRQRVMEAIETLPEREKLVLTL 199

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +E  + L+ + S  EV   RV Q+ ++A K+++  + K
Sbjct: 200 YYQEE--LNLKEIGSVLEVGESRVSQLHSQAIKRLRTKLGK 238


>gi|317153074|ref|YP_004121122.1| FliA/WhiG family RNA polymerase sigma factor [Desulfovibrio
           aespoeensis Aspo-2]
 gi|316943325|gb|ADU62376.1| RNA polymerase sigma factor, FliA/WhiG family [Desulfovibrio
           aespoeensis Aspo-2]
          Length = 261

 Score = 39.7 bits (91), Expect = 0.49,   Method: Compositional matrix adjust.
 Identities = 17/45 (37%), Positives = 31/45 (68%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           ++E++S G++GL+ A+ K++ +RG +  TYS   IK AM + + R
Sbjct: 64  LNELISAGSLGLLDALGKYNAQRGIKFDTYSENRIKGAMLDELRR 108


>gi|297196321|ref|ZP_06913719.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
 gi|197722899|gb|EDY66807.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
          Length = 307

 Score = 39.7 bits (91), Expect = 0.49,   Method: Compositional matrix adjust.
 Identities = 20/72 (27%), Positives = 40/72 (55%), Gaps = 1/72 (1%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  +L LV   A+ +     P+ +++  G IGL++A+ +FD ER    A++++  +   
Sbjct: 79  LVELNLSLVKFAALRFANRAEPMEDIIQVGTIGLIKAINRFDLEREVEFASFALPTVIGE 138

Query: 113 MQEYIL-RSWSL 123
           ++ +    SWS+
Sbjct: 139 IKRFFRDSSWSV 150


>gi|153814969|ref|ZP_01967637.1| hypothetical protein RUMTOR_01184 [Ruminococcus torques ATCC 27756]
 gi|145847537|gb|EDK24455.1| hypothetical protein RUMTOR_01184 [Ruminococcus torques ATCC 27756]
          Length = 243

 Score = 39.7 bits (91), Expect = 0.49,   Method: Compositional matrix adjust.
 Identities = 22/82 (26%), Positives = 44/82 (53%), Gaps = 1/82 (1%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD +A  +LV  ++ LV  +   +   G    ++   G+IGL++A+ KFD     + +TY
Sbjct: 14  GDKAAREQLVKENVGLVHCVVKRFLERGAEREDLFQIGSIGLLKAIDKFDLTYNVKFSTY 73

Query: 105 SMWWIKAAMQEYILRSWSLVKI 126
           ++  I   ++ + LR   ++K+
Sbjct: 74  AVPLISGEIKRF-LRDDGMIKV 94


>gi|300782223|ref|YP_003762514.1| RNA polymerase sigma factor [Amycolatopsis mediterranei U32]
 gi|299791737|gb|ADJ42112.1| RNA polymerase sigma factor [Amycolatopsis mediterranei U32]
          Length = 259

 Score = 39.7 bits (91), Expect = 0.49,   Method: Compositional matrix adjust.
 Identities = 20/72 (27%), Positives = 37/72 (51%), Gaps = 1/72 (1%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV +HL L   +A  +R     + ++V    +GL+ AV +FDP +G     +++  I   
Sbjct: 38  LVRTHLELARNLARKFRNRDEAMEDLVQIATVGLIHAVDRFDPAQGTDFLAFAVPTISGE 97

Query: 113 MQEYIL-RSWSL 123
           ++ +    SWS+
Sbjct: 98  LRHHFRDNSWSV 109


>gi|260752875|ref|YP_003225768.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Zymomonas mobilis
           subsp. mobilis NCIMB 11163]
 gi|258552238|gb|ACV75184.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Zymomonas mobilis
           subsp. mobilis NCIMB 11163]
          Length = 195

 Score = 39.7 bits (91), Expect = 0.49,   Method: Compositional matrix adjust.
 Identities = 51/210 (24%), Positives = 91/210 (43%), Gaps = 20/210 (9%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G + L++A   F+  RGF  ATY+   I+ AM +Y +R  +     + A QK 
Sbjct: 1   MEDLIQIGMVALIEAANAFE-NRGFAFATYASMRIRGAMIDY-MRQHAATARSSIARQKT 58

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           L      L   L        +PE    IA+KLN+S SE      R   D ++N    S D
Sbjct: 59  LNKAREELSATL------GRRPED-AEIAEKLNMSPSEY-----REWADGAINIRQESLD 106

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
              S        D+  Q   +    ER+  ++ L   +  L  RE  + +   ++E  + 
Sbjct: 107 DVYSDHSSIFTDDNADQASEM----EREALQSALAEQIKTLPEREALVLQLYYVEE--LN 160

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L+ +    ++   R+ QI+  A   +++ +
Sbjct: 161 LKEIGEVLDLGTARISQIKKSAVDHLRQKM 190


>gi|303239104|ref|ZP_07325634.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302593442|gb|EFL63160.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 256

 Score = 39.7 bits (91), Expect = 0.50,   Method: Compositional matrix adjust.
 Identities = 45/181 (24%), Positives = 77/181 (42%), Gaps = 40/181 (22%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++E +L +  RE+       RLV+    +V++    Y        +    G IGL+ A 
Sbjct: 8   KKDESLLEEFIREN------QRLVS----MVIRKQFSYVYNTAEYEDYFQSGCIGLVNAA 57

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           K+F PE G   +TY++  I   +  Y  R +    I ++ N K  ++  + L+       
Sbjct: 58  KRFKPEYGTAFSTYAVSLIAGEIMRY-RRDYCASGIHSSRNIKDKYYRYQALRNR----- 111

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDH 208
                            V+E+E     CR  G +S  LN +IN+ +   S   D ++YD+
Sbjct: 112 ----------------GVAEAEA----CRELGVDSAELNKVINAMEPGYS--LDAVIYDN 149

Query: 209 D 209
           D
Sbjct: 150 D 150


>gi|167462462|ref|ZP_02327551.1| DNA-directed RNA polymerase sigma-37 factor (sigma-B)
           [Paenibacillus larvae subsp. larvae BRL-230010]
 gi|322381881|ref|ZP_08055835.1| RNA polymerase sigma factor SigB-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321154269|gb|EFX46591.1| RNA polymerase sigma factor SigB-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 260

 Score = 39.7 bits (91), Expect = 0.51,   Method: Compositional matrix adjust.
 Identities = 55/210 (26%), Positives = 92/210 (43%), Gaps = 32/210 (15%)

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLR 140
           G + L++  K+FDP  G +   Y M  I   M+ Y+  +SW    I      K   F ++
Sbjct: 62  GQMSLLKLFKQFDPSHGVQFEAYMMKSIIGHMKNYLRDKSWY---IQVPRRIKEKGFQIQ 118

Query: 141 RLKGHLQAITDNNLKPEQ---VVAIAKKLNVSESEVISMNCRLAGDE-----SLNALINS 192
                 QAI    +K E+   V  IA +L +S  E I +   LAG E     SL+  + S
Sbjct: 119 ------QAIDSLTMKLERSPNVDEIANELGLSTEETIEI---LAGRECYHYVSLDMPL-S 168

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
           +++N S   D L    D    V        + R  L  +M  L P E++      +  + 
Sbjct: 169 TEENGSTIGDVLGIQEDEYLHV--------DNRLDLQEAMEHLKPEEKKALILAYI--DG 218

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            +   ++ E ++S+  V +++ RA  K++E
Sbjct: 219 YSQRTIAQELDISQMSVSRMQRRALSKLRE 248


>gi|331697274|ref|YP_004333513.1| SigB/F/G subfamily RNA polymerase sigma-28 subunit [Pseudonocardia
           dioxanivorans CB1190]
 gi|326951963|gb|AEA25660.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Pseudonocardia dioxanivorans CB1190]
          Length = 296

 Score = 39.7 bits (91), Expect = 0.51,   Method: Compositional matrix adjust.
 Identities = 53/234 (22%), Positives = 103/234 (44%), Gaps = 19/234 (8%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           +  HL L   IA  +   G P+ ++     +GL+ AV +FDP RG     +++  I   +
Sbjct: 32  IIEHLPLARHIAKRFSQRGEPLQDLEQVAVLGLINAVDRFDPARGPEFLAFAIPTITGEV 91

Query: 114 QEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
             +   R+W+   I      K L  ++      L         P +   IA +L+V+ S+
Sbjct: 92  LRWFRDRAWT---IRVPRRLKELDMSISTAADRLTQELGRAPTPSE---IAARLDVALSD 145

Query: 173 VI-SMNCRLA-GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           V+ S+  R A    SL+  +++  ++ S     L     G    L+E       R +L+ 
Sbjct: 146 VVESIQAREAYRCVSLDVPLSTESEDESVHNGILARTDPG--VALVED------REVLSP 197

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  L  RE+RI   R  ++  +T   +  E  +S+  V ++   A +++++++
Sbjct: 198 LVDALTEREQRIVLLRFFED--MTQNEIGQEIGISQMHVSRVLTAALERLRQAL 249


>gi|42528183|ref|NP_973281.1| RNA polymerase sigma factor WhiG [Treponema denticola ATCC 35405]
 gi|41819453|gb|AAS13200.1| RNA polymerase sigma-27 factor [Treponema denticola ATCC 35405]
 gi|325474612|gb|EGC77798.1| RNA polymerase sigma-27 factor [Treponema denticola F0402]
          Length = 262

 Score = 39.7 bits (91), Expect = 0.52,   Method: Compositional matrix adjust.
 Identities = 54/246 (21%), Positives = 106/246 (43%), Gaps = 19/246 (7%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKK 92
           L  +Y++  D       +  +  LV  +A G  G G+P      ++V  G  GL+ A++K
Sbjct: 14  LWDKYKKTSDPKIREYFILKYAPLVKYVA-GKVGIGMPTNVEFDDLVGYGVFGLLDAIEK 72

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           +D ++  +  TY++  I+ A+ +  LRS   V        + +   +  L+  L     N
Sbjct: 73  YDLDKNVKFNTYAVNRIRGAIFDE-LRSIDWVPRSVRQKSREIEETIADLEARLGRSASN 131

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ--DWLVYDHDG 210
                + +A A  L++ E   + +        SL  L  S+D +S ++   D +      
Sbjct: 132 -----EEIAYAMGLDIEEYNSLLLKISATSVISLTDLRFSND-DSEEFSVGDIIEAPSSL 185

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
              V++E+E+ K    ++  ++  L  RE+++      ++  +TL  +     V+  RV 
Sbjct: 186 NPDVIVEREDIK---RVIVEAIKELPDREKKVLIMYYYED--MTLREIGEVLHVTESRVS 240

Query: 271 QIEARA 276
           QI   A
Sbjct: 241 QIHTSA 246


>gi|320012666|gb|ADW07516.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 294

 Score = 39.7 bits (91), Expect = 0.52,   Method: Compositional matrix adjust.
 Identities = 49/214 (22%), Positives = 97/214 (45%), Gaps = 18/214 (8%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++   G IGL++A+ +F+  R    AT+++ +I   ++ +   +   V +     + R
Sbjct: 93  MEDITQVGTIGLIKAIDRFELSREVEFATFAVPYIVGEIKRFFRDTTWAVHVPRRLQELR 152

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV----ISMNCRLAGDESLNALI 190
           +   L + K  L    D +     V  +A  L+ +E EV    I+ N   AG  SL+   
Sbjct: 153 V--ELAKAKDELAVRLDRD---PTVKELAAHLDRTEDEVIEGIIASNGYTAG--SLDMPT 205

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           ++ +   +  + +   D  G+    +E  E     + L   +  L+ RERR+ E R  QE
Sbjct: 206 DTGETTGTASRTF--ADILGEPDSAMETVE---NLHALAPLLEQLDDRERRLIEMRFGQE 260

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             +T   + +E +VS+  V ++  R   K++  +
Sbjct: 261 --MTQSQIGAELDVSQMHVSRLLTRTLGKLRAGM 292


>gi|224826337|ref|ZP_03699439.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Lutiella nitroferrum
           2002]
 gi|224601438|gb|EEG07619.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Lutiella nitroferrum
           2002]
          Length = 248

 Score = 39.7 bits (91), Expect = 0.53,   Method: Compositional matrix adjust.
 Identities = 53/247 (21%), Positives = 104/247 (42%), Gaps = 21/247 (8%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           HGD+      V  H  LV KIA   +      + + ++   G IGL++A ++FDP +G +
Sbjct: 17  HGDID-----VELHAPLVKKIAKLLIAKLPASVELDDLAQVGIIGLIEAARQFDPTQGVQ 71

Query: 101 LATYSMWWIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
             T++   I+ AM + + R  W          Q R   + ++++  +  +     +P Q 
Sbjct: 72  FETFASQRIRGAMLDELRREDW-------LPRQARR--HSKQIEDAIHQLEQREGRPPQE 122

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IA  L +  +E  +M     G  SL    +  D++    +  +    D          
Sbjct: 123 SEIADFLGLPLAEYQTMLGECKG-VSLQHFSDFDDEDGVGAEAAVANVADDNAVDPFASL 181

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
              + R  L  ++  L  R++ +      QE  + L+ + +   VS  RV Q+ ++A  +
Sbjct: 182 ADGDFRGALVDAIKALPERDQLVMALYYEQE--LNLKEIGAVLGVSESRVSQLHSQAIAR 239

Query: 280 VQESIQK 286
           V+  +++
Sbjct: 240 VRSKLRE 246


>gi|167766746|ref|ZP_02438799.1| hypothetical protein CLOSS21_01252 [Clostridium sp. SS2/1]
 gi|167711500|gb|EDS22079.1| hypothetical protein CLOSS21_01252 [Clostridium sp. SS2/1]
          Length = 232

 Score = 39.7 bits (91), Expect = 0.53,   Method: Compositional matrix adjust.
 Identities = 21/87 (24%), Positives = 47/87 (54%), Gaps = 1/87 (1%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R  + G+ +A  +++ +++ L+  +   +   G    ++   G+IGLM+AV KFD     
Sbjct: 9   RLTKEGNEAAREQIILNNVGLIWSVVRRFTNRGYESEDLFQIGSIGLMKAVDKFDLSYDV 68

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKI 126
           + +TY++  I   ++ + LR   ++K+
Sbjct: 69  KFSTYAVPMITGEIRRF-LRDDGMIKV 94


>gi|160915290|ref|ZP_02077503.1| hypothetical protein EUBDOL_01299 [Eubacterium dolichum DSM 3991]
 gi|158433089|gb|EDP11378.1| hypothetical protein EUBDOL_01299 [Eubacterium dolichum DSM 3991]
          Length = 240

 Score = 39.7 bits (91), Expect = 0.53,   Method: Compositional matrix adjust.
 Identities = 54/246 (21%), Positives = 108/246 (43%), Gaps = 28/246 (11%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           +GD  A  + V ++  LV  I   +    +   ++   G IGLM+A+  FD     + +T
Sbjct: 15  YGDEEALEQFVEANQPLVYAIVKRFHNRRISQEDLFQIGCIGLMKAIHNFDAAYEVKFST 74

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y++  I   ++ +     S   I  + + K  +  + ++K  L   T    K      IA
Sbjct: 75  YAVPIIMGEIKRFFRDDGS---IRISRSLKEGYLQMLKIKEQL---TQTLGKEPTYAQIA 128

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + +N+   EVI     LA +   N  + S D+         +Y++DG   VL ++ E   
Sbjct: 129 QAMNIEVGEVI-----LAFEA--NQFMYSLDEP--------IYENDGSAIVLEDRVEDPK 173

Query: 224 RRNM-----LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           + ++     L +  + L  RE+ I   R   +  +  E+++    +S+ +V ++E +   
Sbjct: 174 QTDIVMKLSLRKEFARLEQREQLILHYRY--DLNMKQEDIAKRLHISQVQVSRLEKKILW 231

Query: 279 KVQESI 284
           K++E +
Sbjct: 232 KLKERL 237


>gi|326938416|gb|AEA14312.1| sporulation sigma factor SigF [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 243

 Score = 39.7 bits (91), Expect = 0.53,   Method: Compositional matrix adjust.
 Identities = 41/166 (24%), Positives = 77/166 (46%), Gaps = 15/166 (9%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL I ++V  G IGL++A + F+ E G++ +TY++  I   + ++I+ S   +K+     
Sbjct: 43  GLEIEDLVQYGMIGLIKARRDFNHELGYQFSTYAIPKIHGEVGKFIMNSHK-IKV----- 96

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
             R  + LR        +    L  E    I K+L V+  EV          +SL  ++ 
Sbjct: 97  -PRALYQLRG------KMMRQGLMEEDGETICKQLEVALPEVKEALQYQPNTKSLQDVMY 149

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
           +S    S  ++ L+ D     QV+ E E+ +N   + +   ++ +P
Sbjct: 150 TSAGGGS--EEILLEDMLEDTQVIEETEQVENHMVLQSFYQTLEHP 193


>gi|317051537|ref|YP_004112653.1| FliA/WhiG family RNA polymerase sigma factor [Desulfurispirillum
           indicum S5]
 gi|316946621|gb|ADU66097.1| RNA polymerase sigma factor, FliA/WhiG family [Desulfurispirillum
           indicum S5]
          Length = 250

 Score = 39.7 bits (91), Expect = 0.53,   Method: Compositional matrix adjust.
 Identities = 51/222 (22%), Positives = 101/222 (45%), Gaps = 24/222 (10%)

Query: 72  GLP----ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           GLP    + +++S G +GL+ A+ KFD  RG    TY+   I+  + +  LR    +  G
Sbjct: 41  GLPSNIELDDLISIGALGLIDAIDKFDMNRGVLFKTYAESRIRGKILDE-LRKLDWLPRG 99

Query: 128 TTANQKRLFFNLRRLK-GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-- 184
                K L     +L     + ++D  L        A +L + E+EV     +  G    
Sbjct: 100 LRQKNKALDRAYSKLGINEGREVSDGEL--------AAELGIDEAEVQQYISQAGGYTML 151

Query: 185 SLNALINSSDKNSSQWQDWLVYDHD--GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
           SL+  +   D + S     L+ D +  G E+ L    E    +  L + + +L+ +E+++
Sbjct: 152 SLDEQMYDRDGSESGTLSDLIPDRENAGPEEHL----EITQNQEFLKKHIRLLSEKEQQM 207

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                 +E  +T++ + +   ++  RV QI ++A  K+++++
Sbjct: 208 LALYYYEE--LTMKEIGTVLGITESRVSQIHSQALFKLKKAM 247


>gi|302872420|ref|YP_003841056.1| RNA polymerase sigma factor, sigma-70 family [Caldicellulosiruptor
           obsidiansis OB47]
 gi|302575279|gb|ADL43070.1| RNA polymerase sigma factor, sigma-70 family [Caldicellulosiruptor
           obsidiansis OB47]
          Length = 310

 Score = 39.7 bits (91), Expect = 0.54,   Method: Compositional matrix adjust.
 Identities = 21/74 (28%), Positives = 41/74 (55%), Gaps = 6/74 (8%)

Query: 47  LSAAHR--LVTSHLRLVVKIAMGY----RGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           L   HR  L+ ++L+LV  +A  +    +GY   + +++SEG  GL+ A   + PE G  
Sbjct: 9   LDNLHRQLLIANNLKLVYHVANKFMPCPKGYMYEVDDLISEGYFGLVVAANNYKPELGTP 68

Query: 101 LATYSMWWIKAAMQ 114
            ++Y+   I++ ++
Sbjct: 69  FSSYACKVIESKIK 82


>gi|228919826|ref|ZP_04083184.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228839842|gb|EEM85125.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
          Length = 224

 Score = 39.7 bits (91), Expect = 0.54,   Method: Compositional matrix adjust.
 Identities = 53/239 (22%), Positives = 113/239 (47%), Gaps = 28/239 (11%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           +V  +  LV  IA  Y   G    +++  G +GL+ A++++D   G     +++  I   
Sbjct: 1   MVNHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGE 60

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNL-RRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
           +++Y+  ++W +       +  R   +L  ++K  ++ +TD   +  +++ IA  L +SE
Sbjct: 61  IKKYLRDKTWGI-------HVPRRIKDLGGKIKLAIEELTDRLQRSPKIIEIADHLGLSE 113

Query: 171 SEVISM-----NCRLAGDESLNALI-NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            EV+ +     N R++   SL+ ++ NSSD +S    + +     G E+          R
Sbjct: 114 EEVLEIMDAKNNYRVS---SLDDVVENSSDGSSVARIESVGEVEQGYEET--------ER 162

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           R +L    +VLN  E+ +       EN +  ++      +S+  V +I+ +A  K++++
Sbjct: 163 RLVLKDIFNVLNETEKSVIHY-IFGEN-LNQKDTGERLGISQMHVSRIKRQAISKLKQA 219


>gi|108798252|ref|YP_638449.1| RNA polymerase sigma factor SigF [Mycobacterium sp. MCS]
 gi|119867348|ref|YP_937300.1| RNA polymerase sigma factor SigF [Mycobacterium sp. KMS]
 gi|126433912|ref|YP_001069603.1| RNA polymerase sigma factor SigF [Mycobacterium sp. JLS]
 gi|108768671|gb|ABG07393.1| RNA polymerase, sigma 28 subunit [Mycobacterium sp. MCS]
 gi|119693437|gb|ABL90510.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Mycobacterium
           sp. KMS]
 gi|126233712|gb|ABN97112.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Mycobacterium
           sp. JLS]
          Length = 263

 Score = 39.7 bits (91), Expect = 0.55,   Method: Compositional matrix adjust.
 Identities = 52/235 (22%), Positives = 100/235 (42%), Gaps = 15/235 (6%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R+V   L L   IA  + G G P  ++V    +GL+ AV +FD + G    ++++  I  
Sbjct: 43  RIVERCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVIRFDVDAGSDFVSFAVPTIMG 102

Query: 112 AMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            ++ +    SWS VK+     +  L     RL      ++    +      +A++L +  
Sbjct: 103 EVRRHFRDNSWS-VKVPRRLKELHL-----RLGSATAELSQRLGRAPTASELAEELGMDR 156

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            EV+     L    S N L   S  NS       + D  G   + +++ E    R  L  
Sbjct: 157 DEVVEG---LVAGSSYNTLSIDSGGNSGNEDAPAIADTLGDVDLGLDQIE---NREALRP 210

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            ++ L  RER +   R  +   +T   ++    +S+  V ++ A++  ++++ +Q
Sbjct: 211 LLAALPERERMVLLLRFFEN--LTQTQIAERVGISQMHVSRLLAKSLTRLRDQLQ 263


>gi|18311030|ref|NP_562964.1| sporulation sigma factor SigF [Clostridium perfringens str. 13]
 gi|110799417|ref|YP_696728.1| sporulation sigma factor SigF [Clostridium perfringens ATCC 13124]
 gi|110803821|ref|YP_699329.1| sporulation sigma factor SigF [Clostridium perfringens SM101]
 gi|168205856|ref|ZP_02631861.1| RNA polymerase sigma-F factor [Clostridium perfringens E str.
           JGS1987]
 gi|168208750|ref|ZP_02634375.1| RNA polymerase sigma-F factor [Clostridium perfringens B str. ATCC
           3626]
 gi|168212915|ref|ZP_02638540.1| RNA polymerase sigma-F factor [Clostridium perfringens CPE str.
           F4969]
 gi|168215675|ref|ZP_02641300.1| RNA polymerase sigma-F factor [Clostridium perfringens NCTC 8239]
 gi|182623955|ref|ZP_02951743.1| RNA polymerase sigma-F factor [Clostridium perfringens D str.
           JGS1721]
 gi|18145712|dbj|BAB81754.1| RNA polymerase sigma-F factor [Clostridium perfringens str. 13]
 gi|110674064|gb|ABG83051.1| RNA polymerase sigma-F factor [Clostridium perfringens ATCC 13124]
 gi|110684322|gb|ABG87692.1| RNA polymerase sigma-F factor [Clostridium perfringens SM101]
 gi|170662589|gb|EDT15272.1| RNA polymerase sigma-F factor [Clostridium perfringens E str.
           JGS1987]
 gi|170712973|gb|EDT25155.1| RNA polymerase sigma-F factor [Clostridium perfringens B str. ATCC
           3626]
 gi|170715517|gb|EDT27699.1| RNA polymerase sigma-F factor [Clostridium perfringens CPE str.
           F4969]
 gi|177910848|gb|EDT73202.1| RNA polymerase sigma-F factor [Clostridium perfringens D str.
           JGS1721]
 gi|182382022|gb|EDT79501.1| RNA polymerase sigma-F factor [Clostridium perfringens NCTC 8239]
          Length = 251

 Score = 39.7 bits (91), Expect = 0.55,   Method: Compositional matrix adjust.
 Identities = 57/260 (21%), Positives = 119/260 (45%), Gaps = 37/260 (14%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           V+AK     G+  A ++L+  +  LV  I   +   G    ++   G++GL++A+  F+ 
Sbjct: 21  VMAK----EGNKEAMNKLIEVNTPLVSSICKRFTNRGYDYEDIFQIGSMGLVKAINNFND 76

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKI--GTTANQKRLFFNLRRLKGHLQAITDNN 153
               + +TY++  I   ++ + LR   ++K+   T    K+L +N   L   L      N
Sbjct: 77  SFNVKFSTYAVPMIIGEIKRF-LRDDGIIKVSRSTKTLAKKLHYNKEELIKKL------N 129

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
             P  V  +A+   V + EVI             AL ++S   S Q+    ++  +G   
Sbjct: 130 RDP-TVDELAEYSGVDKEEVIV------------ALESAS---SMQYLYDTIHHDEGTPV 173

Query: 214 VLIEK-EERKNRRNMLTR-----SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           +LI+K  E+    +M+ +     ++S L+ + ++I   R  ++   T   ++    +S+ 
Sbjct: 174 LLIDKLSEKGEDDDMVNKIALREAISSLDSKGKQIIMLRYFKDK--TQIQVAKMLGISQV 231

Query: 268 RVRQIEARAFKKVQESIQKQ 287
           +V +IE +  K ++E +++ 
Sbjct: 232 QVSRIEKKVLKIMKEKLEED 251


>gi|313844183|ref|YP_004061846.1| hypothetical protein OlV1_214 [Ostreococcus lucimarinus virus OlV1]
 gi|312599568|gb|ADQ91590.1| hypothetical protein OlV1_214 [Ostreococcus lucimarinus virus OlV1]
          Length = 171

 Score = 39.7 bits (91), Expect = 0.55,   Method: Compositional matrix adjust.
 Identities = 22/75 (29%), Positives = 45/75 (60%), Gaps = 7/75 (9%)

Query: 53  LVTSHLRLVVKIA--MGYRGY----GLPI-SEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           L+ +H++L  K++  + ++ Y    G+    ++ S G  GL++A +KF+PE GF+ +TY+
Sbjct: 28  LIANHVKLAYKVSNDVYFKTYPRQRGIHTRKDINSVGLHGLVRAAQKFNPELGFKFSTYA 87

Query: 106 MWWIKAAMQEYILRS 120
             WI  + +  + R+
Sbjct: 88  YPWIYWSCKNCLRRT 102


>gi|310657328|ref|YP_003935049.1| RNA polymerase sigma-37 factor (sigma-b) [Clostridium sticklandii
           DSM 519]
 gi|308824106|emb|CBH20144.1| RNA polymerase sigma-37 factor (sigma-B) [Clostridium sticklandii]
          Length = 273

 Score = 39.7 bits (91), Expect = 0.55,   Method: Compositional matrix adjust.
 Identities = 51/251 (20%), Positives = 112/251 (44%), Gaps = 18/251 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y E+  +   + LV  HL +   ++  +   G+   ++    ++GL+ A+++FD  +GF 
Sbjct: 37  YSENKAIELRNELVKRHLYIAEILSKKFLNKGIEYEDIYQVASLGLIFAIERFDVSKGFE 96

Query: 101 LATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
            ++++   I   +++Y   + WS   I      + L   +   K +LQ       K E  
Sbjct: 97  FSSFATPTIIGEIKKYFRDKGWS---IRVPRRIQELSKKVNTAKSYLQQELHRVPKIED- 152

Query: 160 VAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
             IAK L+ +E EV+       +   +SL+   ++   +       LV D D    ++  
Sbjct: 153 --IAKYLDCTEEEVLEAIEASHVYKPKSLDLSYDNEGDDKDILLLDLVGDEDKSFNMI-- 208

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
                  ++ +  ++S LN  E +I + R  +    T  +++++  VS+  V ++E +  
Sbjct: 209 -----ENKDFIENALSKLNEIETKIIKDRFFKNK--TQMHVANDLGVSQMTVSRMEKKIL 261

Query: 278 KKVQESIQKQV 288
            K+++  +K +
Sbjct: 262 AKLKKDYEKSL 272


>gi|302539934|ref|ZP_07292276.1| stress response/stationary phase sigma factor SigF [Streptomyces
           hygroscopicus ATCC 53653]
 gi|302457552|gb|EFL20645.1| stress response/stationary phase sigma factor SigF [Streptomyces
           himastatinicus ATCC 53653]
          Length = 274

 Score = 39.7 bits (91), Expect = 0.55,   Method: Compositional matrix adjust.
 Identities = 49/197 (24%), Positives = 87/197 (44%), Gaps = 15/197 (7%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R+V + + +  ++A  YR  G  + ++     +GL++AVK++DPE G   A +++  +  
Sbjct: 48  RVVEAWMPMAQRLARQYRNRGESLEDLEQVAALGLVKAVKRYDPEHGTAFAGFAVPTVVG 107

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            ++ +      ++ +     + R    +R     L    D+   P +  AIA++  +SE 
Sbjct: 108 EIKRHFRDHLWVLHVPRRVQELR--NRVRAAHRELSHSLDDATVPTE--AIAERTGLSEK 163

Query: 172 EV-ISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           EV I M    +    SL+A +  +D   S     L     GQE       +R+  R  L 
Sbjct: 164 EVRIGMEAMGSFTPLSLDAQLTGADDGYS-----LADTLGGQEPAYDRVVDREAVRPGLG 218

Query: 230 RSMSVLNPRERRIFEAR 246
           R    L  RER+I   R
Sbjct: 219 R----LPARERQILYMR 231


>gi|229817514|ref|ZP_04447796.1| hypothetical protein BIFANG_02777 [Bifidobacterium angulatum DSM
           20098]
 gi|229785303|gb|EEP21417.1| hypothetical protein BIFANG_02777 [Bifidobacterium angulatum DSM
           20098]
          Length = 621

 Score = 39.7 bits (91), Expect = 0.56,   Method: Compositional matrix adjust.
 Identities = 22/64 (34%), Positives = 33/64 (51%)

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           LT  +   + RE  I   R + E P TL+ +  EF ++RERVRQIE     ++   +  +
Sbjct: 139 LTMLLFSFDEREYAIATQRLMAEQPSTLDEIGKEFNITRERVRQIEKALRNEITTLLDGE 198

Query: 288 VELS 291
             LS
Sbjct: 199 FHLS 202


>gi|56460225|ref|YP_155506.1| flagellar biosynthesis sigma factor [Idiomarina loihiensis L2TR]
 gi|56179235|gb|AAV81957.1| DNA-directed RNA polymerase specialized sigma 28 subunit
           [Idiomarina loihiensis L2TR]
          Length = 241

 Score = 39.7 bits (91), Expect = 0.56,   Method: Compositional matrix adjust.
 Identities = 56/246 (22%), Positives = 102/246 (41%), Gaps = 30/246 (12%)

Query: 53  LVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           ++  H  LV +IA   M      + + +++  G IGL++A + FD  +G    T++   I
Sbjct: 17  IIEQHTGLVKRIAHHMMARLPASVQVDDLIQAGMIGLLEAARNFDNSKGASFETFAGIRI 76

Query: 110 KAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           + AM + I R  W+          + +  N RR+   ++ + +   +  +   +A KLN+
Sbjct: 77  RGAMLDEIRRGDWA---------PRSVHRNHRRVLEAIRQVENETGRDAKDTEVAAKLNM 127

Query: 169 SESEVISM-----NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
              E   +       R+ G E L     S D    +      Y  + Q+ V     E   
Sbjct: 128 GMDEYHHILRDVSTGRIVGIEDLGV---SEDAIMPEQVTGSAY--EPQKDV-----ENAA 177

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               L  ++S L  RE  +      +E  + L+ +     VS  RV QI ++A  +++  
Sbjct: 178 FHKALVSTISSLPEREALVLSLYYDEE--LNLKEIGEVLSVSESRVSQIHSQAMLRLKSR 235

Query: 284 IQKQVE 289
           +Q  VE
Sbjct: 236 MQNWVE 241


>gi|84514822|ref|ZP_01002185.1| sigma factor FliA (Sigma-28 group, flagellar) [Loktanella
           vestfoldensis SKA53]
 gi|84510981|gb|EAQ07435.1| sigma factor FliA (Sigma-28 group, flagellar) [Loktanella
           vestfoldensis SKA53]
          Length = 239

 Score = 39.7 bits (91), Expect = 0.56,   Method: Compositional matrix adjust.
 Identities = 45/208 (21%), Positives = 98/208 (47%), Gaps = 21/208 (10%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
             +++  G IGL++A +++    G     Y++  ++ A+ +Y+ ++ +L +  T A  K 
Sbjct: 39  FDDLLQVGLIGLIEAAQRYTRREGVSFENYAVLRVRGAIYDYLRKNSNLGR-KTIATTKV 97

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI-NSS 193
           + F    L   L         P +V        ++E+  +++    A ++SLN+   NS 
Sbjct: 98  VKFAQAELSQKL------GRAPTRV-------ELAEAVSMTIGELNAWEQSLNSSYQNSL 144

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
                ++  W   +    EQ+L    +R   ++ L  ++  L  RE  + +   ++E  +
Sbjct: 145 QDEYDEYSMWFSAEEPPAEQLL----DRGRLKDALLIALKSLPQREALVLQLYYVEE--L 198

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +  +++  EV+  RV Q+++ AFKK+Q
Sbjct: 199 NIYEIAAILEVTPGRVSQLKSMAFKKMQ 226


>gi|307264896|ref|ZP_07546458.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|306920154|gb|EFN50366.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
          Length = 246

 Score = 39.7 bits (91), Expect = 0.56,   Method: Compositional matrix adjust.
 Identities = 55/256 (21%), Positives = 114/256 (44%), Gaps = 37/256 (14%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE---VVSEGNIGLMQAVKKFDP 95
           K Y  + D +  + ++  ++ LV  I        +  SE   ++++G IGL+ A++K+ P
Sbjct: 10  KTYNSNKDPNLRNEIIIKYMPLVKHIVKKLIISDITQSEYEDLINQGVIGLIDAIEKYQP 69

Query: 96  ERGFRLATYSMWWIKAAMQEYILR-SW-------SLVKIGTTANQKRLFFNLRRLKGHLQ 147
            +G +  TY+   I+  + +Y+ R  W          KI  T    +  +N    +  ++
Sbjct: 70  SKGVKFETYATLRIRGEIIDYLRRKDWMPRSLKKKYKKIEETVETLQQKYN---REPTVE 126

Query: 148 AITD-NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
            IT+   L    V+     +NV  S + S+   +  +  L+A+ N   KN          
Sbjct: 127 EITEACGLNETDVLKTLSYINV--SNINSLEEAIENNLKLHAISNVELKNP--------- 175

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
               +E+VL ++ +RK     L  ++  L  +ER +      ++  +  +++S    ++ 
Sbjct: 176 ----EEEVLYKELKRK-----LASAIESLPDKERLVITLYYYED--LNYKDISKILNLTE 224

Query: 267 ERVRQIEARAFKKVQE 282
            R+ QI  +A K+++E
Sbjct: 225 SRISQIHTKAIKRIRE 240


>gi|307243701|ref|ZP_07525841.1| sigma-70, region 4 [Peptostreptococcus stomatis DSM 17678]
 gi|306492910|gb|EFM64923.1| sigma-70, region 4 [Peptostreptococcus stomatis DSM 17678]
          Length = 289

 Score = 39.7 bits (91), Expect = 0.57,   Method: Compositional matrix adjust.
 Identities = 47/242 (19%), Positives = 106/242 (43%), Gaps = 44/242 (18%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAM------GYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           +GD SA ++ + S +  + KI         ++  GL   ++   G +G++ A+ KFD   
Sbjct: 49  NGDRSARNKFILSKIDYIRKIVTCDNEIKSFKARGLDDDDLFQTGVMGVLCAIDKFDFRP 108

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G ++ TY    +K +++    R +  + +   AN      ++ ++      + ++ +   
Sbjct: 109 GVKVKTYINNNVKYSIKN-TYRKYGSISVSREAN------SIYKICSSQMDLLEDKIDSR 161

Query: 158 QVVAIAKKLNVSESE-------VISMNC--RLAGDESLNA------------LINSSDKN 196
           +++ I+++ N+  S        V S NC  R   D  L+             L+N + + 
Sbjct: 162 KILKISRETNIPPSRLEYGIMAVKSRNCQYRYDNDGCLDTDLVSMEKYSRKVLMNYNQEA 221

Query: 197 SSQWQDWLVYDH----DGQEQVLI------EKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
             ++  WLV +     +G+E ++I      +K +++  R +   + SV N + R + + R
Sbjct: 222 KRKFNYWLVMEAISRLEGKENLVIKEIYINDKTQKEVARQLGCSTTSVGNIKRRALEKIR 281

Query: 247 RL 248
            +
Sbjct: 282 YM 283


>gi|304570578|ref|YP_386879.2| sigma-70 factor [Desulfovibrio desulfuricans subsp. desulfuricans
           str. G20]
          Length = 265

 Score = 39.7 bits (91), Expect = 0.57,   Method: Compositional matrix adjust.
 Identities = 17/45 (37%), Positives = 29/45 (64%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           ++E++S G +GLM+A  KF P+ G +  TY+   I+ AM + + R
Sbjct: 64  LNELISAGTLGLMEAFGKFQPKLGIKFDTYAENRIRGAMLDELRR 108


>gi|301029374|ref|ZP_07192470.1| flagellar biosynthesis sigma factor [Escherichia coli MS 196-1]
 gi|299877729|gb|EFI85940.1| flagellar biosynthesis sigma factor [Escherichia coli MS 196-1]
          Length = 239

 Score = 39.7 bits (91), Expect = 0.57,   Method: Compositional matrix adjust.
 Identities = 47/221 (21%), Positives = 102/221 (46%), Gaps = 32/221 (14%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL+ AV+++D  +G    TY++  I+ AM +  LRS   V      N + 
Sbjct: 41  LDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDE-LRSRDWVPRSVRRNARE 99

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   + +L+   Q +  N+ + E    +A++L +  ++   M            L+++++
Sbjct: 100 VAQAIGQLE---QELGRNSTETE----VAERLGIDIADYRQM------------LLDTNN 140

Query: 195 KNSSQWQDW---------LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
                + +W         LV D D Q +  +++    N R  +  ++  L  RE+ +   
Sbjct: 141 SQLFSYDEWREEHGDSIELVTD-DHQRENPLQQLLDSNLRQRVMEAIETLPEREKLVLTL 199

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +E  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 200 YYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 238


>gi|37525878|ref|NP_929222.1| flagellar biosynthesis sigma factor [Photorhabdus luminescens
           subsp. laumondii TTO1]
 gi|36785307|emb|CAE14248.1| RNA polymerase sigma factor for flagellar operon (Sigma-F factor)
           (Sigma-27) (Sigma-28) [Photorhabdus luminescens subsp.
           laumondii TTO1]
          Length = 240

 Score = 39.7 bits (91), Expect = 0.57,   Method: Compositional matrix adjust.
 Identities = 44/214 (20%), Positives = 92/214 (42%), Gaps = 30/214 (14%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL+ AV++FD  +G    TY++  I+ AM +  LRS          N + 
Sbjct: 41  LDDLLQAGGIGLLNAVERFDSLQGTAFTTYAVQRIRGAMLDE-LRSRDWAPRSVRRNARE 99

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   +R+L+  L        +P     +AK+L +   E   +            L+++++
Sbjct: 100 VTHIIRKLEQDLG-------RPASEQEVAKELKIDLVEYRQI------------LLDTNN 140

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEE--------RKNRRNMLTRSMSVLNPRERRIFEAR 246
                + +W     +  E V+ E  E          + R  +  ++  L  RE+ +    
Sbjct: 141 SQLFSYDEWHEMHGESCEPVIEEGHETNPLQQLLESDVRQRVIEAIDSLPEREKMVLTLY 200

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             +E  + L+ + +  EV   R+ Q+ ++A K++
Sbjct: 201 YQEE--LNLKEIGAVLEVGESRISQLHSQAIKRL 232


>gi|291617817|ref|YP_003520559.1| FliA [Pantoea ananatis LMG 20103]
 gi|291152847|gb|ADD77431.1| FliA [Pantoea ananatis LMG 20103]
          Length = 240

 Score = 39.7 bits (91), Expect = 0.58,   Method: Compositional matrix adjust.
 Identities = 46/218 (21%), Positives = 91/218 (41%), Gaps = 38/218 (17%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTANQK 133
           + +++  G IGL+ AV+++D  +G    TY++  I+ AM  E   R W+          +
Sbjct: 41  LDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDWA---------PR 91

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            +  N R + G +  +     +      +A++LNVS  E   +                 
Sbjct: 92  SVRRNAREVAGAMHQVEQMLGRAASEQEVAQQLNVSIEEYRQILL--------------- 136

Query: 194 DKNSSQWQDWLVY--DHDGQEQVLIEKEERKNR---------RNMLTRSMSVLNPRERRI 242
           D N+SQ   +  Y  +H    +++ E  E  N          R  +  ++  L  RE+ +
Sbjct: 137 DTNNSQLFSYDEYREEHGDSAELVTEGHEEANPLHQLMEGSLRERVIEAIEALPEREKMV 196

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                 +E  + L+ + +  +V   RV Q+ ++A K++
Sbjct: 197 LTLYYQEE--LNLKEIGAVLDVGESRVSQLHSQAIKRL 232


>gi|51892300|ref|YP_074991.1| putative RNA polymerase sigma factor SigI [Symbiobacterium
           thermophilum IAM 14863]
 gi|51855989|dbj|BAD40147.1| RNA polymerase sigma factor [Symbiobacterium thermophilum IAM
           14863]
          Length = 251

 Score = 39.7 bits (91), Expect = 0.58,   Method: Compositional matrix adjust.
 Identities = 25/84 (29%), Positives = 44/84 (52%), Gaps = 2/84 (2%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS--EVVSEGNIGLMQAVKKFDPERGFRLA 102
           GD +A   L+ ++  LV+++     G  L +   E VS G I L +A+ KFDPERG    
Sbjct: 31  GDKAAREELIRAYTPLVLRVGSQVTGRYLRVGRDEEVSVGLIALNEAIDKFDPERGNAFI 90

Query: 103 TYSMWWIKAAMQEYILRSWSLVKI 126
            ++   I+  + ++  R+   V++
Sbjct: 91  PFAEMVIRRRLVDFYRRNAGRVEV 114


>gi|88813218|ref|ZP_01128458.1| flagellar biosynthesis sigma factor FliA [Nitrococcus mobilis
           Nb-231]
 gi|88789540|gb|EAR20667.1| flagellar biosynthesis sigma factor FliA [Nitrococcus mobilis
           Nb-231]
          Length = 240

 Score = 39.7 bits (91), Expect = 0.59,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 40/75 (53%), Gaps = 6/75 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           LV  H  LV +IA    G  LP    + +++  G IGL++A +++D  +G    TY+   
Sbjct: 19  LVVRHAPLVKRIAHHLAGR-LPASVLVDDLIQAGMIGLLEAARQYDATQGASFQTYAAIR 77

Query: 109 IKAAMQEYILR-SWS 122
           I+ AM + I R  W+
Sbjct: 78  IRGAMLDEIRRLDWT 92


>gi|323356683|ref|YP_004223079.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Microbacterium testaceum StLB037]
 gi|323273054|dbj|BAJ73199.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Microbacterium testaceum StLB037]
          Length = 538

 Score = 39.7 bits (91), Expect = 0.59,   Method: Compositional matrix adjust.
 Identities = 20/41 (48%), Positives = 29/41 (70%), Gaps = 1/41 (2%)

Query: 237 PRERRIFEAR-RLQENPVTLENLSSEFEVSRERVRQIEARA 276
           PRE++I   R   +  P TL  ++ EF++SRER+RQIE+RA
Sbjct: 177 PREQKILRMRVGFEGAPRTLAEIAREFDLSRERIRQIESRA 217


>gi|314055297|ref|YP_004063635.1| RNA-polymerase sigma factor-possible host origin [Ostreococcus
           tauri virus 2]
 gi|313575188|emb|CBI70201.1| RNA-polymerase sigma factor-possible host origin [Ostreococcus
           tauri virus 2]
          Length = 172

 Score = 39.7 bits (91), Expect = 0.59,   Method: Compositional matrix adjust.
 Identities = 22/75 (29%), Positives = 45/75 (60%), Gaps = 7/75 (9%)

Query: 53  LVTSHLRLVVKIA--MGYRGY----GLPI-SEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           L+ +H++L  K++  + ++ Y    G+    ++ S G  GL++A +KF+PE GF+ +TY+
Sbjct: 28  LIANHVKLAYKVSNDVYFKTYPRQRGIHTRKDINSVGLHGLVRAAQKFNPELGFKFSTYA 87

Query: 106 MWWIKAAMQEYILRS 120
             WI  + +  + R+
Sbjct: 88  YPWIYWSCKNCLRRT 102


>gi|108799609|ref|YP_639806.1| RNA polymerase, sigma 28 subunit [Mycobacterium sp. MCS]
 gi|119868720|ref|YP_938672.1| FliA/WhiG family RNA polymerase sigma factor [Mycobacterium sp.
           KMS]
 gi|108770028|gb|ABG08750.1| RNA polymerase, sigma 28 subunit [Mycobacterium sp. MCS]
 gi|119694809|gb|ABL91882.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Mycobacterium
           sp. KMS]
          Length = 284

 Score = 39.7 bits (91), Expect = 0.60,   Method: Compositional matrix adjust.
 Identities = 48/213 (22%), Positives = 94/213 (44%), Gaps = 38/213 (17%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           +R+R H        ++T+ + +   IA  + G G P  +V+    IGL++ V ++DP++G
Sbjct: 43  ERWRRH--------IITACVPIADHIAYRFVGRGEPSEDVIQVARIGLIKTVDRYDPDKG 94

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
             LA +++  I+  ++ +   +   V++     + +L     R++  +  ++    +   
Sbjct: 95  HFLA-FAVPTIRGEIRRHFRDNTWTVRVPRKVQETQL-----RMRDAVNTLSQRLNRTPT 148

Query: 159 VVAIAKKLNVSESEVISMNCRLAG--------DESLNALINSSDK-NSSQWQDWLVYDHD 209
            V +A +L+V   E+   +C+ A         D  L    N  D   S Q  D   Y   
Sbjct: 149 GVELADELDVGSEEL--GDCQAATTAYRPVSLDAPLLTAQNDGDTVGSMQGGDDPGY--- 203

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
           G+ + LI          +L  ++S L+PR R I
Sbjct: 204 GRVEDLI----------LLQEAISDLDPRRRAI 226


>gi|303248004|ref|ZP_07334270.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfovibrio fructosovorans JJ]
 gi|302490561|gb|EFL50466.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfovibrio fructosovorans JJ]
          Length = 225

 Score = 39.7 bits (91), Expect = 0.60,   Method: Compositional matrix adjust.
 Identities = 16/39 (41%), Positives = 26/39 (66%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           + E++S G +GL++A+ +F PE G +  TY+   IK AM
Sbjct: 25  LGELLSAGAMGLLEALGRFRPELGIKFETYAESRIKGAM 63


>gi|332753464|gb|EGJ83844.1| RNA polymerase sigma factor rpoS domain protein [Shigella flexneri
           4343-70]
          Length = 114

 Score = 39.7 bits (91), Expect = 0.61,   Method: Compositional matrix adjust.
 Identities = 21/47 (44%), Positives = 31/47 (65%), Gaps = 1/47 (2%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARRAL-RGDVASRRRMIESNLRLVVKIA 106


>gi|74317198|ref|YP_314938.1| RNA polymerase sigma-70 factor [Thiobacillus denitrificans ATCC
           25259]
 gi|74056693|gb|AAZ97133.1| RNA polymerase sigma-70 factor [Thiobacillus denitrificans ATCC
           25259]
          Length = 236

 Score = 39.7 bits (91), Expect = 0.61,   Method: Compositional matrix adjust.
 Identities = 54/248 (21%), Positives = 109/248 (43%), Gaps = 25/248 (10%)

Query: 45  GDLSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
           G  S+    +T +  LV +IA   M      + + +++  G IGLM AV +FD  +G + 
Sbjct: 3   GKPSSQDEQITKYAPLVKRIAYHMMARLPASVEVDDLIQVGLIGLMDAVSRFDGTQGAQF 62

Query: 102 ATYSMWWIKAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +Y+   I+ AM + +  + W    +     QK      R+++  +  +   + K     
Sbjct: 63  ESYATQRIRGAMLDELREADW----LPRHVRQKS-----RQIEAAIHKLEQRHGKAPSES 113

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALI---NSSDKNSSQWQDWLVYDHDGQEQVLIE 217
            I+ +L +   +  SM     GD   + L+   + SD++S+ + +  + D       ++E
Sbjct: 114 EISAELGIPIDQYQSM----LGDVKCSQLLYYEDFSDEDSASFLERYLVDGSNDPLAVLE 169

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
            E     R  L  ++  L  RER +       E  + L+ + +   VS  RV Q+ ++A 
Sbjct: 170 DE---GFRASLIAAIHHLPERERSMMGM--YYEQDMNLKEIGAVLGVSESRVCQLHSQAV 224

Query: 278 KKVQESIQ 285
            +++  ++
Sbjct: 225 ARLRAQLK 232


>gi|237734715|ref|ZP_04565196.1| sporulation sigma factor sigG [Mollicutes bacterium D7]
 gi|229382043|gb|EEO32134.1| sporulation sigma factor sigG [Coprobacillus sp. D7]
          Length = 97

 Score = 39.7 bits (91), Expect = 0.62,   Method: Composition-based stats.
 Identities = 27/102 (26%), Positives = 50/102 (49%), Gaps = 9/102 (8%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           N  +I+NG         E +K   L   E Y L   Y+   + +   RLV  + +LV+ +
Sbjct: 3   NYQVIING-------YQEPKK--RLTTDETYKLIDEYQATKNEAIKDRLVNDNTKLVLSM 53

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           A  + G    + ++   G IGL++A++ F+   G + +TY++
Sbjct: 54  ARRFYGREDSMDDLFQVGMIGLIKAIENFNTSFGLKFSTYAV 95


>gi|15895322|ref|NP_348671.1| DNA-dependent RNA polymerase sigma subunit [Clostridium
           acetobutylicum ATCC 824]
 gi|15025038|gb|AAK80011.1|AE007708_7 DNA-dependent RNA polymerase sigma subunit [Clostridium
           acetobutylicum ATCC 824]
          Length = 237

 Score = 39.7 bits (91), Expect = 0.62,   Method: Compositional matrix adjust.
 Identities = 21/84 (25%), Positives = 42/84 (50%), Gaps = 2/84 (2%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGY--RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           G   A   L+ S ++ + KIA G+      L + +++ EG I +++A+  +D ++  + +
Sbjct: 18  GSKDAKSFLIDSSMKYIKKIANGFCLNNKSLSLEDLMQEGIIAVIKAINSYDLDKNVKFS 77

Query: 103 TYSMWWIKAAMQEYILRSWSLVKI 126
           TY    I   +   I + +S  KI
Sbjct: 78  TYVYSMINFTLISEIKKKYSYFKI 101


>gi|167037640|ref|YP_001665218.1| RNA polymerase sigma-28 subunit FliA/WhiG [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|167040301|ref|YP_001663286.1| RNA polymerase sigma-28 subunit FliA/WhiG [Thermoanaerobacter sp.
           X514]
 gi|256750769|ref|ZP_05491654.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|300914385|ref|ZP_07131701.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X561]
 gi|307724379|ref|YP_003904130.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter sp. X513]
 gi|320116055|ref|YP_004186214.1| FliA/WhiG family RNA polymerase sigma factor [Thermoanaerobacter
           brockii subsp. finnii Ako-1]
 gi|166854541|gb|ABY92950.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermoanaerobacter sp.
           X514]
 gi|166856474|gb|ABY94882.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|256750352|gb|EEU63371.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|300889320|gb|EFK84466.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X561]
 gi|307581440|gb|ADN54839.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X513]
 gi|319929146|gb|ADV79831.1| RNA polymerase sigma factor, FliA/WhiG family [Thermoanaerobacter
           brockii subsp. finnii Ako-1]
          Length = 246

 Score = 39.7 bits (91), Expect = 0.62,   Method: Compositional matrix adjust.
 Identities = 57/260 (21%), Positives = 115/260 (44%), Gaps = 45/260 (17%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE---VVSEGNIGLMQAVKKFDP 95
           K Y  + D +  + ++  ++ LV  I        +  SE   ++++G IGL+ A++K+ P
Sbjct: 10  KTYNSNKDPNLRNEIIIKYMPLVKHIVKKLIISDITQSEYEDLINQGVIGLIDAIEKYQP 69

Query: 96  ERGFRLATYSMWWIKAAMQEYI-LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
            +G +  TY+   I+  + +Y+  + W                  R LK   + I     
Sbjct: 70  SKGVKFETYATLRIRGEIIDYLRKKDWM----------------PRSLKKKYRKI----- 108

Query: 155 KPEQVVAIAKKLNVSES-EVISMNCRLAGDESLNAL--INSSDKNS------SQWQDWLV 205
             E V  + +K N   + E I+  C L   + L  L  IN S+ NS      + ++   +
Sbjct: 109 -EETVETLQQKYNREPTVEEITEACGLNETDVLKTLSYINVSNINSLEEAIENNFKLHAI 167

Query: 206 YD---HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
            D    + +E+VL ++ +RK     L  ++  L  +ER +      ++  +  +++S   
Sbjct: 168 SDVELKNPEEEVLYKELKRK-----LANAIENLPDKERLVITLYYYED--LNYKDISKIL 220

Query: 263 EVSRERVRQIEARAFKKVQE 282
            ++  R+ QI  +A K+++E
Sbjct: 221 NLTESRISQIHTKAIKRIRE 240


>gi|295399836|ref|ZP_06809817.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|312111652|ref|YP_003989968.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacillus sp.
           Y4.1MC1]
 gi|294978239|gb|EFG53836.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|311216753|gb|ADP75357.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacillus sp.
           Y4.1MC1]
          Length = 254

 Score = 39.7 bits (91), Expect = 0.62,   Method: Compositional matrix adjust.
 Identities = 22/71 (30%), Positives = 39/71 (54%), Gaps = 3/71 (4%)

Query: 46  DLSAAHRLVTSHLRLV---VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           D  A ++LV +++ LV   V+         +   E++S G +GL  A++KFDP R  +  
Sbjct: 21  DPQAGNKLVQTYMPLVHYHVQRIAASLPKNISKQELISLGLVGLYDALEKFDPSRDLKFD 80

Query: 103 TYSMWWIKAAM 113
           TY+ + I+ A+
Sbjct: 81  TYASFRIRGAI 91


>gi|328885789|emb|CCA59028.1| hypothetical protein SVEN_5742 [Streptomyces venezuelae ATCC 10712]
          Length = 750

 Score = 39.3 bits (90), Expect = 0.63,   Method: Compositional matrix adjust.
 Identities = 21/41 (51%), Positives = 23/41 (56%)

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
           S  + RER I   R   E P T   L   FEVSRERVRQ+E
Sbjct: 256 STWDERERTIAARRIFAEQPETFAALGDRFEVSRERVRQLE 296


>gi|307131576|ref|YP_003883592.1| RNA polymerase sigma-28 (sigma F) factor [Dickeya dadantii 3937]
 gi|306529105|gb|ADM99035.1| RNA polymerase, sigma 28 (sigma F) factor [Dickeya dadantii 3937]
          Length = 240

 Score = 39.3 bits (90), Expect = 0.63,   Method: Compositional matrix adjust.
 Identities = 51/240 (21%), Positives = 101/240 (42%), Gaps = 37/240 (15%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM-QEY 116
           LRL V++        + + +++  G IGL+ AV+++D  +G    TY++  I+ AM  E 
Sbjct: 29  LRLQVRLPAS-----VELDDLLQAGGIGLLSAVERYDSLQGTAFTTYAVQRIRGAMLDEL 83

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
             R W+          + +  N R +   +Q    +  +      +A+ LN+S  E   +
Sbjct: 84  RSRDWA---------PRSVRRNAREVAQAMQQAEQSLGRAPTEQEVAQTLNISLEEYRQI 134

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT------R 230
                       L+++++     + +W   +H    + L+E  E  N  N L       R
Sbjct: 135 ------------LLDTNNSQLFSYDEW-REEHGDSAEALLEGNEEANPLNQLMDVNLRQR 181

Query: 231 SMSVLN--PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            M  +   P   ++      QE  + L+ + +  EV   RV Q+ ++A K+++  +   V
Sbjct: 182 VMDAIESLPEREKMVLTLYYQEE-LNLKEIGAVLEVGESRVSQLHSQAIKRLRAKLMSDV 240


>gi|327394234|dbj|BAK11656.1| RNA polymerase sigma factor for flagellar operon FliA [Pantoea
           ananatis AJ13355]
          Length = 230

 Score = 39.3 bits (90), Expect = 0.63,   Method: Compositional matrix adjust.
 Identities = 50/235 (21%), Positives = 98/235 (41%), Gaps = 43/235 (18%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM-QEY 116
           LRL V++        + + +++  G IGL+ AV+++D  +G    TY++  I+ AM  E 
Sbjct: 19  LRLQVRLPAS-----VELDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDEL 73

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
             R W+          + +  N R + G +  +     +      +A++LNVS  E   +
Sbjct: 74  RSRDWA---------PRSVRRNAREVAGAMHQVEQMLGRAASEQEVAQQLNVSIEEYRQI 124

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVY--DHDGQEQVLIEKEERKNR---------R 225
                            D N+SQ   +  Y  +H    +++ E  E  N          R
Sbjct: 125 LL---------------DTNNSQLFSYDEYREEHGDSAELVTEGHEEANPLHQLMEGSLR 169

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             +  ++  L  RE+ +      +E  + L+ + +  +V   RV Q+ ++A K++
Sbjct: 170 ERVIEAIEALPEREKMVLTLYYQEE--LNLKEIGAVLDVGESRVSQLHSQAIKRL 222


>gi|253990087|ref|YP_003041443.1| flagellar biosynthesis sigma factor [Photorhabdus asymbiotica
           subsp. asymbiotica ATCC 43949]
 gi|253781537|emb|CAQ84700.1| rna polymerase sigma factor for flagellar operon (sigma-f factor
           (sigma-27) (sigma-28) [Photorhabdus asymbiotica]
          Length = 244

 Score = 39.3 bits (90), Expect = 0.64,   Method: Compositional matrix adjust.
 Identities = 44/214 (20%), Positives = 92/214 (42%), Gaps = 30/214 (14%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL+ AV++FD  +G    TY++  I+ AM +  LRS          N + 
Sbjct: 45  LDDLLQAGGIGLLNAVERFDSLQGTAFTTYAVQRIRGAMLDE-LRSRDWAPRSVRRNARE 103

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   +R+L+  L        +P     +AK+L +   E   +            L+++++
Sbjct: 104 VTQTIRKLEQDLG-------RPASEQEVAKELKIDLVEYRQI------------LLDTNN 144

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEE--------RKNRRNMLTRSMSVLNPRERRIFEAR 246
                + +W     +  E V+ E  E          + R  +  ++  L  RE+ +    
Sbjct: 145 SQLFSYDEWHEMHGESCEPVIEEGHETNPLQQLLESDVRQRVIDAIDSLPEREKMVLTLY 204

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             +E  + L+ + +  EV   R+ Q+ ++A K++
Sbjct: 205 YQEE--LNLKEIGAVLEVGESRISQLHSQAIKRL 236


>gi|116694211|ref|YP_728422.1| DNA-directed RNA polymerase sigma subunit / flagellum specific
           [Ralstonia eutropha H16]
 gi|113528710|emb|CAJ95057.1| DNA-directed RNA polymerase sigma subunit / flagellum specific
           [Ralstonia eutropha H16]
          Length = 238

 Score = 39.3 bits (90), Expect = 0.65,   Method: Compositional matrix adjust.
 Identities = 26/77 (33%), Positives = 40/77 (51%), Gaps = 6/77 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPE 96
           Y   G L  A  +V +H +LV +IA+      LP    I +++  G IGL+ A K+++  
Sbjct: 2   YTIQGKLEQAD-VVKAHAQLVRRIALQLAAR-LPASVQIDDLIQAGMIGLLDAAKRYEDT 59

Query: 97  RGFRLATYSMWWIKAAM 113
            G R  TY+   I+ AM
Sbjct: 60  HGARFETYASQRIRGAM 76


>gi|323705419|ref|ZP_08116994.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
 gi|323535321|gb|EGB25097.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
          Length = 246

 Score = 39.3 bits (90), Expect = 0.66,   Method: Compositional matrix adjust.
 Identities = 22/81 (27%), Positives = 41/81 (50%), Gaps = 3/81 (3%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPE 96
           +Y +  D S+   ++  ++ LV  I        L      +++S+G IGL+ AV K+D  
Sbjct: 11  KYEKQKDGSSKEDIIIKYMPLVKHIVKRICLSELSKEDTDDLISQGMIGLIDAVNKYDVS 70

Query: 97  RGFRLATYSMWWIKAAMQEYI 117
           +G +  TY+   IK  + +Y+
Sbjct: 71  KGVKFETYASIRIKGEIIDYL 91


>gi|256831228|ref|YP_003159956.1| RNA polymerase sigma-28 subunit FliA/WhiG [Desulfomicrobium
           baculatum DSM 4028]
 gi|256580404|gb|ACU91540.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfomicrobium
           baculatum DSM 4028]
          Length = 267

 Score = 39.3 bits (90), Expect = 0.66,   Method: Compositional matrix adjust.
 Identities = 17/45 (37%), Positives = 29/45 (64%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           +S+++S G +GLM+A+ KF PE   R  T++   I+ AM + + R
Sbjct: 68  LSDLISAGTLGLMEALGKFQPELNIRFETFADSRIRGAMLDELRR 112


>gi|119714598|ref|YP_921563.1| sigma-70 region 4 domain-containing protein [Nocardioides sp.
           JS614]
 gi|119535259|gb|ABL79876.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Nocardioides sp.
           JS614]
          Length = 278

 Score = 39.3 bits (90), Expect = 0.66,   Method: Compositional matrix adjust.
 Identities = 48/211 (22%), Positives = 89/211 (42%), Gaps = 20/211 (9%)

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
           S G + L+QA + FDPERG   A Y+   I+ A+ +  LRS            + +    
Sbjct: 39  SAGLLALVQAARAFDPERGVPFAGYASTRIRGALVDE-LRSVDWASRSVRRRAREIEAAR 97

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN-SS 198
            RL   L    D+        A+A+ L ++  E+   +  +A      A++   D   ++
Sbjct: 98  ARLAATLGQFPDD-------AAVAEALGITPEEIGKADSEVA-----RAVVLPLDAGPNA 145

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
            + + L     G E+  +  E    R   L  ++  L  R R +     + + P+    L
Sbjct: 146 GFVESLAGRDPGPEEEALHAE----RAQYLAAAIEELPERLRHVVRGYFVAQRPMA--EL 199

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           ++E  VS  R+ Q+ A A   +++++ +  E
Sbjct: 200 AAELGVSESRISQLRAEALVLLRDALAEAFE 230


>gi|331088539|ref|ZP_08337452.1| hypothetical protein HMPREF1025_01035 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|330407801|gb|EGG87295.1| hypothetical protein HMPREF1025_01035 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 239

 Score = 39.3 bits (90), Expect = 0.67,   Method: Compositional matrix adjust.
 Identities = 22/82 (26%), Positives = 44/82 (53%), Gaps = 1/82 (1%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD +A  +LV  ++ LV  +   +   G    ++   G+IGL++A+ KFD     + +TY
Sbjct: 14  GDKAAREQLVKENVGLVHCVVKRFLERGAEREDLFQIGSIGLLKAIDKFDLTYNVKFSTY 73

Query: 105 SMWWIKAAMQEYILRSWSLVKI 126
           ++  I   ++ + LR   ++K+
Sbjct: 74  AVPLISGEIKRF-LRDDGMIKV 94


>gi|157161393|ref|YP_001458711.1| flagellar biosynthesis sigma factor [Escherichia coli HS]
 gi|157067073|gb|ABV06328.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           HS]
          Length = 239

 Score = 39.3 bits (90), Expect = 0.67,   Method: Compositional matrix adjust.
 Identities = 47/221 (21%), Positives = 101/221 (45%), Gaps = 32/221 (14%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL+ AV+++D  +G    TY++  I+ AM +  LRS   V      N + 
Sbjct: 41  LDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDE-LRSRDWVPRSVRRNARE 99

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   + +L+   Q +  N  + E    +A++L +  ++   M            L+++++
Sbjct: 100 VVQAIGQLE---QELGRNATETE----VAERLGIDIADYRQM------------LLDTNN 140

Query: 195 KNSSQWQDW---------LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
                + +W         LV D D Q +  +++    N R  +  ++  L  RE+ +   
Sbjct: 141 SQLFSYDEWREEHGDSIELVTD-DHQRENPLQQLLDSNLRQRVMEAIETLPEREKLVLTL 199

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +E  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 200 YYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 238


>gi|88704270|ref|ZP_01101984.1| RNA polymerase sigma factor for flagellar operon [Congregibacter
           litoralis KT71]
 gi|88701321|gb|EAQ98426.1| RNA polymerase sigma factor for flagellar operon [Congregibacter
           litoralis KT71]
          Length = 236

 Score = 39.3 bits (90), Expect = 0.67,   Method: Compositional matrix adjust.
 Identities = 59/251 (23%), Positives = 108/251 (43%), Gaps = 46/251 (18%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYR-GYGLP----ISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           S+A  LV   L LV KI  G R    LP    + +++  G IGL++A + +D  +G   A
Sbjct: 13  SSADALVREFLPLVKKI--GLRLAAKLPAEIEVDDLMQVGLIGLLRARESYDASQGASFA 70

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+   IK AM + I R+   +        +++   + R    L         P Q   I
Sbjct: 71  TYAGIRIKGAMLDEI-RAHDWLPRSVQTQLRQVSVAIERADARLG-------HPAQDADI 122

Query: 163 AKKLNVSESEVISMNCRLA---------GDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
           A +L++  +E   ++ +LA           E+ NA++N+ +           +D  G+E 
Sbjct: 123 AAELDMPLAEYQQLSGQLACARMTHIEDSAEAENAVLNTVNP----------FDEVGEE- 171

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
                      R  L  S++ L  +ER +      ++  + L+ + +   VS  RV Q+ 
Sbjct: 172 ---------GFREALAESVAQLPEKERLMMSLYYAED--LNLKEIGAVLGVSESRVSQLH 220

Query: 274 ARAFKKVQESI 284
            +A  +++ ++
Sbjct: 221 GQALARLRVTL 231


>gi|304316881|ref|YP_003852026.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
 gi|302778383|gb|ADL68942.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
          Length = 246

 Score = 39.3 bits (90), Expect = 0.68,   Method: Compositional matrix adjust.
 Identities = 15/43 (34%), Positives = 28/43 (65%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           + +++S+G IGL+ AV K+D  +G +  TY+   IK  + +Y+
Sbjct: 49  VDDLISQGMIGLIDAVNKYDISKGVKFETYASIRIKGEIIDYL 91


>gi|197301393|ref|ZP_03166474.1| hypothetical protein RUMLAC_00124 [Ruminococcus lactaris ATCC
           29176]
 gi|197299550|gb|EDY34069.1| hypothetical protein RUMLAC_00124 [Ruminococcus lactaris ATCC
           29176]
          Length = 206

 Score = 39.3 bits (90), Expect = 0.68,   Method: Compositional matrix adjust.
 Identities = 22/77 (28%), Positives = 41/77 (53%), Gaps = 1/77 (1%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L K +R +GD      L+  +  +V K A     +G    +++ EG IGL++AV+ +DP+
Sbjct: 12  LIKDFR-NGDREIMDHLMMKYKAMVRKKARAMYLFGGENEDLIQEGMIGLIKAVRDYDPD 70

Query: 97  RGFRLATYSMWWIKAAM 113
           +G   A+++   +   M
Sbjct: 71  QGASFASFAELCVSRQM 87


>gi|317501595|ref|ZP_07959789.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|316897012|gb|EFV19089.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
          Length = 239

 Score = 39.3 bits (90), Expect = 0.68,   Method: Compositional matrix adjust.
 Identities = 22/82 (26%), Positives = 44/82 (53%), Gaps = 1/82 (1%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD +A  +LV  ++ LV  +   +   G    ++   G+IGL++A+ KFD     + +TY
Sbjct: 14  GDKAAREQLVKENVGLVHCVVKRFLERGAEREDLFQIGSIGLLKAIDKFDLTYNVKFSTY 73

Query: 105 SMWWIKAAMQEYILRSWSLVKI 126
           ++  I   ++ + LR   ++K+
Sbjct: 74  AVPLISGEIKRF-LRDDGMIKV 94


>gi|158337871|ref|YP_001519047.1| RNA polymerase sigma factor SigF [Acaryochloris marina MBIC11017]
 gi|158308112|gb|ABW29729.1| RNA polymerase sigma factor, group 3 [Acaryochloris marina
           MBIC11017]
          Length = 265

 Score = 39.3 bits (90), Expect = 0.68,   Method: Compositional matrix adjust.
 Identities = 21/88 (23%), Positives = 51/88 (57%), Gaps = 3/88 (3%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIA--MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           YR+   +   +RLV  ++ LV K+A  + ++    P  ++   G +GL+ A+++FDP +G
Sbjct: 18  YRQKPSVQLRNRLVRLNMGLVRKVAHRLAHQ-CAEPYEDLEQCGFLGLITAIERFDPTQG 76

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKI 126
           +  +++++ +I+  +  ++    + V+I
Sbjct: 77  YAFSSFAVPYIRGEILHFLRDRANTVRI 104


>gi|169834851|ref|YP_001715950.1| putative sporulation sigma factor SigK [Clostridium botulinum A3
           str. Loch Maree]
 gi|169408958|gb|ACA57368.1| putative sporulation sigma factor SigK [Clostridium botulinum A3
           str. Loch Maree]
          Length = 271

 Score = 39.3 bits (90), Expect = 0.70,   Method: Compositional matrix adjust.
 Identities = 46/221 (20%), Positives = 96/221 (43%), Gaps = 31/221 (14%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW----SLVKIG 127
           G+   +++ +  +G ++A++KFD  +G  L+TY+       M+ YIL S     +++K+ 
Sbjct: 64  GMEFDDLLIDAKLGFLKALEKFDINKGNALSTYAT----HCMRNYILNSIRVNNNMIKLS 119

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
           +    KR+  + ++ K ++  +   N K           N+        N RL       
Sbjct: 120 SREVNKRIKLS-KKFKANI--LNKGNYKFN--------YNIYNKIFSQHNVRLIDTHEYQ 168

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           + ++    NSS  Q+         E++ +EKE+++     +  ++ +L+  E  I     
Sbjct: 169 SYLD----NSSIEQEI------SSEEMFMEKEQKRFNTRQIISALKILDKTELFIIVHYF 218

Query: 248 --LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
               +   TL  LS    +  E  R+I+ +A  K++   +K
Sbjct: 219 GLFNKKKRTLRELSKRLNIGYENTRKIKGKALSKIECHFKK 259


>gi|311030733|ref|ZP_07708823.1| sporulation sigma factor SigF [Bacillus sp. m3-13]
          Length = 251

 Score = 39.3 bits (90), Expect = 0.70,   Method: Compositional matrix adjust.
 Identities = 20/75 (26%), Positives = 38/75 (50%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + G+  A   +V  ++RLV  +   +   G    ++   G IGL+++V KFD     + +
Sbjct: 26  QSGEQEARDTIVQKNMRLVWSVVQRFMNRGYEPDDLFQIGCIGLLKSVDKFDLSYDVKFS 85

Query: 103 TYSMWWIKAAMQEYI 117
           TY++  I   +Q +I
Sbjct: 86  TYAVPMIIGEIQRFI 100


>gi|302544308|ref|ZP_07296650.1| RNA polymerase sigma-F factor [Streptomyces hygroscopicus ATCC
           53653]
 gi|302461926|gb|EFL25019.1| RNA polymerase sigma-F factor [Streptomyces himastatinicus ATCC
           53653]
          Length = 288

 Score = 39.3 bits (90), Expect = 0.70,   Method: Compositional matrix adjust.
 Identities = 51/229 (22%), Positives = 100/229 (43%), Gaps = 13/229 (5%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +L LV   A  +R   + + +VV  G IGL++A+ +FD  R     T+++ +I   
Sbjct: 47  LIELNLSLVRYAARRFRNRSVEMEDVVQVGTIGLIKAIDRFDLSREVEFTTFAVPYIVGE 106

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SW+   +      + L  +L +    L    D   +      +A+ LN+SE 
Sbjct: 107 IKRFFRDTSWA---VHVPRRLQELRIDLAKANEELFQRFD---RSPTTTELAEHLNLSED 160

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           EV+      +   S ++L   +D  +   +     D  G+    +E  E  +    L   
Sbjct: 161 EVLD-GLVASNGYSTSSLDAPADPETGTTRVTTYADRIGEVDPAMEVVENLHALKPLVEQ 219

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
              L  R+RRI + R  +E  +T   + +E  VS+  V ++  ++  ++
Sbjct: 220 ---LGERDRRILQMRFGEE--MTQSEIGAELGVSQMHVSRLLTKSLTRL 263


>gi|169827282|ref|YP_001697440.1| RNA polymerase sigma-F factor [Lysinibacillus sphaericus C3-41]
 gi|168991770|gb|ACA39310.1| RNA polymerase sigma-F factor (Stage II sporulation protein AC)
           (Sporulation sigma factor) [Lysinibacillus sphaericus
           C3-41]
          Length = 195

 Score = 39.3 bits (90), Expect = 0.70,   Method: Compositional matrix adjust.
 Identities = 44/199 (22%), Positives = 89/199 (44%), Gaps = 26/199 (13%)

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M++V KFD     + +TY++  I   +Q + LR   +VK+  +         +R L   +
Sbjct: 1   MKSVDKFDLSYDVKFSTYAVPMIIGEIQRF-LRDDGMVKVSRS---------IRELNFKI 50

Query: 147 QAITDNNLK----PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
           +  TD  +K    P  +  +A+ L V+  E+++ +  L    SL+  +  S+ +S    D
Sbjct: 51  RHATDEFIKRNEHPPTIQELAQVLGVTTEEIVTASDALRDPASLHEQLYESEGDSITLMD 110

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
                     Q+  EK E+      L   ++ L PRE+ I   R   +   T   +++  
Sbjct: 111 ----------QMKDEKSEQPFDYIPLKEVLTRLEPREQSIIYLRYFSD--CTQTEIANRL 158

Query: 263 EVSRERVRQIEARAFKKVQ 281
            +S+ +V ++E +   +++
Sbjct: 159 GISQVQVSRLEKKILAQLK 177


>gi|251789202|ref|YP_003003923.1| flagellar biosynthesis sigma factor [Dickeya zeae Ech1591]
 gi|247537823|gb|ACT06444.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Dickeya zeae Ech1591]
          Length = 240

 Score = 39.3 bits (90), Expect = 0.71,   Method: Compositional matrix adjust.
 Identities = 51/240 (21%), Positives = 101/240 (42%), Gaps = 37/240 (15%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM-QEY 116
           LRL V++        + + +++  G IGL+ AV+++D  +G    TY++  I+ AM  E 
Sbjct: 29  LRLQVRLPAS-----VELDDLLQAGGIGLLSAVERYDSLQGTAFTTYAVQRIRGAMLDEL 83

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
             R W+          + +  N R +   +Q    +  +      +A+ LN+S  E   +
Sbjct: 84  RSRDWA---------PRSVRRNAREVAQAMQQAEQSLGRAPSEQEVAQTLNISLEEYRQI 134

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT------R 230
                       L+++++     + +W   +H    + L+E  E  N  N L       R
Sbjct: 135 ------------LLDTNNSQLFSYDEW-REEHGDSAEALLEGNEDANPLNQLMDVSLRQR 181

Query: 231 SMSVLN--PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            M  +   P   ++      QE  + L+ + +  EV   RV Q+ ++A K+++  +   V
Sbjct: 182 VMDAIENLPEREKMVLTLYYQEE-LNLKEIGAVLEVGESRVSQLHSQAIKRLRAKLMSDV 240


>gi|304438454|ref|ZP_07398394.1| DNA-directed RNA polymerase sigma subunit FliA [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
 gi|304368537|gb|EFM22222.1| DNA-directed RNA polymerase sigma subunit FliA [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
          Length = 256

 Score = 39.3 bits (90), Expect = 0.71,   Method: Compositional matrix adjust.
 Identities = 62/266 (23%), Positives = 121/266 (45%), Gaps = 30/266 (11%)

Query: 28  MLEKQEEYVLA--KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSE 81
           M E  EE + A  K Y     +   +R+   +L LV ++  G     LP      +++S 
Sbjct: 9   MAEPIEEDIEALWKAYETEKTIEVRNRIAEYYLPLV-RLVAGRIAISLPQHVDREDLLSS 67

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           G  GL+ A+++++  RG +  TY+   ++ A+ ++ LR+   + +    N KR    +  
Sbjct: 68  GFFGLLDAIERYELTRGNKFETYAGVRVRGAILDH-LRAKDWIPVSVRQNIKRYEKAVAH 126

Query: 142 LKGHL-QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
           L+G L +  TD  L  E  ++I ++L+  ES+V S    +  +E L      +D  +S  
Sbjct: 127 LEGTLGRTATDQELAEEMDLSI-EELHRLESQV-SAATVIPLEEYLR-----TDAQASL- 178

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
                   DG     +E  E    +  L  ++  L  +ER +       E  +TL+ +++
Sbjct: 179 -------EDGP----VEHAEWTEIKETLAAAIEKLPEKERTVVALYYYDE--MTLKEIAA 225

Query: 261 EFEVSRERVRQIEARAFKKVQESIQK 286
              +S  R+ Q+  +A  +++ S+ +
Sbjct: 226 VLHLSEARISQLHTKAIFRMRGSLAR 251


>gi|300722632|ref|YP_003711922.1| sigma F (sigma 28) factor of RNA polymerase [Xenorhabdus
           nematophila ATCC 19061]
 gi|297629139|emb|CBJ89735.1| sigma F (sigma 28) factor of RNA polymerase, transcription of late
           flagellar genes (class 3a and 3b operons) [Xenorhabdus
           nematophila ATCC 19061]
          Length = 240

 Score = 39.3 bits (90), Expect = 0.71,   Method: Compositional matrix adjust.
 Identities = 52/230 (22%), Positives = 99/230 (43%), Gaps = 33/230 (14%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRL V++        + + +++  G IGL+ AV++FD  +G    TY++  I+ AM +  
Sbjct: 29  LRLQVRLPAS-----VELDDLLQAGGIGLLNAVERFDSMQGTAFTTYAVQRIRGAMLDE- 82

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           LRS          N + +   +R+L+  L          EQ VA   K+N+ E   I   
Sbjct: 83  LRSRDWAPRSVRRNAREVTQTIRKLEQEL-----GRPASEQEVAKELKINLIEYRQI--- 134

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM--SVL 235
                      L+++++     + +W     +  E V+ E+ E    + +L   +   V+
Sbjct: 135 -----------LLDTNNSQLFSYDEWHEIHGESCEPVIEEEHETNPLQQLLEGDLRQRVI 183

Query: 236 N-----PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N     P   ++      QE  + L+ + +   V   RV Q+ ++A K++
Sbjct: 184 NIIESLPEREKMVLTLYYQEE-LNLKEIGAVLNVGESRVSQLHSQAIKRL 232


>gi|304399206|ref|ZP_07381073.1| sigma-70 region 1.2 [Pantoea sp. aB]
 gi|304353260|gb|EFM17640.1| sigma-70 region 1.2 [Pantoea sp. aB]
          Length = 113

 Score = 39.3 bits (90), Expect = 0.72,   Method: Compositional matrix adjust.
 Identities = 21/47 (44%), Positives = 30/47 (63%), Gaps = 1/47 (2%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA
Sbjct: 61  YLGEIGYSPLLTAEEEVFFARRAL-RGDIPSRRRMIESNLRLVVKIA 106


>gi|166368033|ref|YP_001660306.1| RNA polymerase sigma factor SigF [Microcystis aeruginosa NIES-843]
 gi|166090406|dbj|BAG05114.1| group 3 RNA polymerase sigma factor [Microcystis aeruginosa
           NIES-843]
          Length = 258

 Score = 39.3 bits (90), Expect = 0.72,   Method: Compositional matrix adjust.
 Identities = 34/134 (25%), Positives = 70/134 (52%), Gaps = 10/134 (7%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT-ANQKRL 135
           ++V  G++GL++A+++FD  +G   +++++ +I+  +Q ++      V+I     +  R 
Sbjct: 57  DLVQVGSMGLIRAIERFDSSKGHAFSSFAIPYIRGEIQHHLRDKSYTVRIPRRWLDLGRQ 116

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSS 193
             N+RR     Q I  +N +P     I++ LN+S  E   +       E  SL+  +N+ 
Sbjct: 117 ATNVRR---DFQTI--HNRQPND-TEISRALNISSEEWQEVKLAFQNREPLSLDVTVNND 170

Query: 194 DKNSSQWQDWLVYD 207
           + N++  +D LV D
Sbjct: 171 EDNNTCLKD-LVPD 183


>gi|310658943|ref|YP_003936664.1| RNA polymerase subunit alpha domain-containing protein [Clostridium
           sticklandii DSM 519]
 gi|308825721|emb|CBH21759.1| RNA polymerase, alpha subunit domain protein [Clostridium
           sticklandii]
          Length = 911

 Score = 39.3 bits (90), Expect = 0.73,   Method: Composition-based stats.
 Identities = 22/46 (47%), Positives = 31/46 (67%), Gaps = 3/46 (6%)

Query: 235 LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           LN RE  +   +R+Q    TLE++  E  V+RER+RQIEA+A KK+
Sbjct: 302 LNEREYNVL-LQRIQGK--TLEDVGLEMNVTRERIRQIEAKAIKKL 344


>gi|171741952|ref|ZP_02917759.1| hypothetical protein BIFDEN_01055 [Bifidobacterium dentium ATCC
           27678]
 gi|283456904|ref|YP_003361468.1| RNA polymerase sigma factor [Bifidobacterium dentium Bd1]
 gi|171277566|gb|EDT45227.1| hypothetical protein BIFDEN_01055 [Bifidobacterium dentium ATCC
           27678]
 gi|283103538|gb|ADB10644.1| RNA polymerase sigma factor [Bifidobacterium dentium Bd1]
          Length = 596

 Score = 39.3 bits (90), Expect = 0.74,   Method: Compositional matrix adjust.
 Identities = 17/46 (36%), Positives = 29/46 (63%)

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
           L+ ++  L+ RE +IF  R L E P + + +  +  ++RER+RQIE
Sbjct: 116 LSSAICDLDEREYKIFNERFLMEEPRSFKAIGGDLGITRERIRQIE 161


>gi|114777586|ref|ZP_01452567.1| RNA polymerase sigma factor for flagellar operon [Mariprofundus
           ferrooxydans PV-1]
 gi|114552057|gb|EAU54574.1| RNA polymerase sigma factor for flagellar operon [Mariprofundus
           ferrooxydans PV-1]
          Length = 243

 Score = 39.3 bits (90), Expect = 0.74,   Method: Compositional matrix adjust.
 Identities = 25/101 (24%), Positives = 49/101 (48%), Gaps = 14/101 (13%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
             ++++ G +GL+   ++FD  R  +  T+  + ++ AM +Y LR++  +  G   + K 
Sbjct: 41  FDDLINAGVLGLLDGAQRFDHSRDVQFKTFVSYRVRGAMIDY-LRAFDWMPRGLRDHAKE 99

Query: 135 L---FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   F  L ++ G          +P +   IAK LN+S  E
Sbjct: 100 MQTAFQQLEQVYG----------RPAEETEIAKHLNISLDE 130


>gi|3249731|gb|AAC26668.1| RNA polymerase sigma-like factor [Streptomyces spectabilis]
          Length = 161

 Score = 39.3 bits (90), Expect = 0.74,   Method: Compositional matrix adjust.
 Identities = 47/175 (26%), Positives = 73/175 (41%), Gaps = 19/175 (10%)

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI+ AM   +      +++     +  L   + R++  +         PE+V A  
Sbjct: 1   YATWWIRQAMSRAMADQARTIRVPVHVVE--LINRVVRVQRRMLQERGYEPSPEEVAA-- 56

Query: 164 KKLNVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEE 220
             L++    V     RLA +  SL+A +   D       D  + D   DG     +E   
Sbjct: 57  -HLDLPHERV--RGLRLAQEPVSLHAPVGEED-------DVALGDLIEDGDAASPVESAA 106

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIE 273
               R  L   +S L  RER++ + R       P TLE +   F V+RER+RQIE
Sbjct: 107 FLLLREHLEAVLSTLGERERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIE 161


>gi|20807860|ref|NP_623031.1| DNA-directed RNA polymerase specialized sigma subunit
           [Thermoanaerobacter tengcongensis MB4]
 gi|254478885|ref|ZP_05092249.1| RNA polymerase sigma factor, FliA/WhiG family [Carboxydibrachium
           pacificum DSM 12653]
 gi|20516424|gb|AAM24635.1| DNA-directed RNA polymerase specialized sigma subunit
           [Thermoanaerobacter tengcongensis MB4]
 gi|214035198|gb|EEB75908.1| RNA polymerase sigma factor, FliA/WhiG family [Carboxydibrachium
           pacificum DSM 12653]
          Length = 246

 Score = 39.3 bits (90), Expect = 0.74,   Method: Compositional matrix adjust.
 Identities = 23/87 (26%), Positives = 44/87 (50%), Gaps = 4/87 (4%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE---VVSEGNIGLMQAVKKFDP 95
           K Y    D  A + ++  +L LV  I        +  SE   ++ +G +GL+ A++K+ P
Sbjct: 10  KVYNLQKDPDARNEIIVKYLPLVKHIVKKLVISDIAQSEYEDLIHQGILGLIDAIEKYQP 69

Query: 96  ERGFRLATYSMWWIKAAMQEYI-LRSW 121
           ++G +  TY+   I+  + +Y+  R W
Sbjct: 70  DKGVKFETYATLRIRGEIIDYLRKRDW 96


>gi|291436144|ref|ZP_06575534.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291339039|gb|EFE65995.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 282

 Score = 39.3 bits (90), Expect = 0.75,   Method: Compositional matrix adjust.
 Identities = 52/240 (21%), Positives = 110/240 (45%), Gaps = 23/240 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           +V + L +  ++A  +R  G    ++     +GL++AV ++DPE G    +Y++  I   
Sbjct: 56  IVEAWLPMADRLAGRFRSRGESFDDLRQVAALGLVKAVDRYDPELGNAFESYAVPTITGE 115

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLR-RLKGHLQAIT-DNNLKPEQVVAIAKKLNVS 169
           ++ +     W+L       +  R    LR R++   Q ++   + +P  V  IA+  ++S
Sbjct: 116 IKRHFRDHMWTL-------HVPRRVQELRNRVRSASQDLSLSGSGRPPTVAEIAEHADLS 168

Query: 170 ESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E +V +    L      SL+A + S D   S   D L    D     ++++E  + R   
Sbjct: 169 EEDVRTGQGALDSFTALSLDAELTSGDDGYS-LGDTLGA-PDPALDTVVDREAVRER--- 223

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
               ++ L  RE+ I   R   +  +T  ++++E  +S+  V ++ +R   +++E + + 
Sbjct: 224 ----LAALPEREQAILYMRFFGD--MTQSSIAAELGISQMHVSRLISRCCGRIREQVMRD 277


>gi|218548541|ref|YP_002382332.1| flagellar biosynthesis sigma factor [Escherichia fergusonii ATCC
           35469]
 gi|218356082|emb|CAQ88699.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia fergusonii
           ATCC 35469]
 gi|324113640|gb|EGC07615.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           fergusonii B253]
 gi|325496958|gb|EGC94817.1| flagellar biosynthesis sigma factor [Escherichia fergusonii ECD227]
          Length = 238

 Score = 39.3 bits (90), Expect = 0.76,   Method: Compositional matrix adjust.
 Identities = 51/236 (21%), Positives = 105/236 (44%), Gaps = 37/236 (15%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM-QEY 116
           LRL V++        + + +++  G IGL+ AV ++D  +G    TY++  I+ AM  E 
Sbjct: 29  LRLQVRLPAS-----VELDDLLQAGGIGLLNAVDRYDALQGTAFTTYAVQRIRGAMLDEL 83

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
             R W+   +   A +      + +  G L+     N    +V   AK+L +S  E   M
Sbjct: 84  RSRDWAPRSVRRNARE------VAQAIGQLEQELGRNASETEV---AKRLGISTEEYRQM 134

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS---MS 233
                       L+++++     + +W   +H    +++ E+ ++ N  + L  S     
Sbjct: 135 ------------LLDTNNSQLFSYDEW-REEHGDSAELITEEHQQANPLHQLLESDLRQQ 181

Query: 234 VLNPRERRIFEARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           V++  E R+ E  +L      +  + L+ + +  EV   RV Q+ ++A K+++  +
Sbjct: 182 VMDAIE-RLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLRSKL 236


>gi|153812846|ref|ZP_01965514.1| hypothetical protein RUMOBE_03253 [Ruminococcus obeum ATCC 29174]
 gi|149831058|gb|EDM86147.1| hypothetical protein RUMOBE_03253 [Ruminococcus obeum ATCC 29174]
          Length = 107

 Score = 39.3 bits (90), Expect = 0.77,   Method: Compositional matrix adjust.
 Identities = 26/95 (27%), Positives = 49/95 (51%), Gaps = 2/95 (2%)

Query: 42  REH-GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           R H GD  A   L   +  L+  +A  + G G  + ++   G+IGL++AV KFD     +
Sbjct: 11  RAHQGDKEARDILFHENTGLIYSVAHRFLGRGAEMEDLFQIGSIGLLKAVDKFDLSYDVK 70

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +TY++  I   ++ + LR   ++K+  +  +K +
Sbjct: 71  FSTYAVPMIAGEIKRF-LRDDGMLKVSRSIKRKSI 104


>gi|15618277|ref|NP_224562.1| RNA polymerase sigma factor sigma-28 [Chlamydophila pneumoniae
           CWL029]
 gi|15835895|ref|NP_300419.1| RNA polymerase sigma factor sigma-28 [Chlamydophila pneumoniae
           J138]
 gi|16752677|ref|NP_444944.1| RNA polymerase sigma factor sigma-28 [Chlamydophila pneumoniae
           AR39]
 gi|33241705|ref|NP_876646.1| RNA polymerase sigma factor sigma-28 [Chlamydophila pneumoniae
           TW-183]
 gi|4376638|gb|AAD18506.1| Sigma-28/WhiG Family [Chlamydophila pneumoniae CWL029]
 gi|7189319|gb|AAF38240.1| RNA polymerase sigma factor, sigma-70 family [Chlamydophila
           pneumoniae AR39]
 gi|8978734|dbj|BAA98570.1| sigma-28/WhiG family [Chlamydophila pneumoniae J138]
 gi|33236214|gb|AAP98303.1| transcription initiation factor sigmaD protein [Chlamydophila
           pneumoniae TW-183]
 gi|269303237|gb|ACZ33337.1| RNA polymerase sigma factor, FliA [Chlamydophila pneumoniae LPCoLN]
          Length = 257

 Score = 39.3 bits (90), Expect = 0.79,   Method: Compositional matrix adjust.
 Identities = 51/222 (22%), Positives = 106/222 (47%), Gaps = 23/222 (10%)

Query: 72  GLP----ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR-SWSLVKI 126
           G+P      ++ + G  GL++AV++++PER  R   Y+++ IKAA+ + + +  W    +
Sbjct: 46  GMPSHVKTEDLYASGVEGLVRAVERYNPERSRRFEGYAVFLIKAAIIDDLRKQDWVPRSV 105

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS--MNCRLAGDE 184
              AN         +L G + ++  +  K    + + + LN+S+ E+    ++ R A   
Sbjct: 106 HQKAN---------KLSGAMDSLRQSLGKEPTDLELCEYLNISQQELSGWFVSARPALIV 156

Query: 185 SLNALINS-SDKNSSQWQDWLVYDHDGQEQV-LIEKEERKNRRNMLTRSMSVLNPRERRI 242
           SLN    S SD+ +    +  + D   +    +++K+E       L  ++  L  +ER++
Sbjct: 157 SLNEEWPSQSDEGAGMALEERIPDERAETGYDVVDKQEFS---LCLANAIQELEEKERKV 213

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                 +E  + L+ +     VS  RV QI ++A  K++ ++
Sbjct: 214 MALYYYEE--LVLKEIGKVLGVSESRVSQIHSKALLKLRAAL 253


>gi|117924589|ref|YP_865206.1| sigma-70 region 4 domain-containing protein [Magnetococcus sp.
           MC-1]
 gi|117608345|gb|ABK43800.1| sigma-70 region 4 domain protein [Magnetococcus sp. MC-1]
          Length = 187

 Score = 39.3 bits (90), Expect = 0.79,   Method: Compositional matrix adjust.
 Identities = 26/70 (37%), Positives = 45/70 (64%), Gaps = 3/70 (4%)

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +R ML R+M  L+ RE ++   R   EN +  E+++   +++RERVR IEA+A KK++  
Sbjct: 121 KRIMLGRAMQHLSAREAQVVNMR--MEN-LRYEDVAKVMKITRERVRIIEAKASKKIKAV 177

Query: 284 IQKQVELSSS 293
           I++  E S++
Sbjct: 178 IEQIKESSTT 187


>gi|333003010|gb|EGK22564.1| RNA polymerase sigma factor for flagellar operon [Shigella flexneri
           VA-6]
          Length = 239

 Score = 39.3 bits (90), Expect = 0.80,   Method: Compositional matrix adjust.
 Identities = 47/221 (21%), Positives = 101/221 (45%), Gaps = 32/221 (14%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL+ AV+++D  +G    TY++  I+ AM +  LRS   V      N + 
Sbjct: 41  LDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDE-LRSRDWVPRSVRRNARE 99

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   + +L+   Q +  N  + E    +A++L +  ++   M            L+++++
Sbjct: 100 VAQAIGQLE---QELGRNATETE----VAERLGIDIADYRQM------------LLDTNN 140

Query: 195 KNSSQWQDW---------LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
                + +W         LV D D Q +  +++    N R  +  ++  L  RE+ +   
Sbjct: 141 SQLFSYDEWREEHGDSIELVTD-DHQRENPLQQLLDSNLRQRVMEAIETLPEREKLVLTL 199

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +E  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 200 YYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 238


>gi|331657967|ref|ZP_08358929.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli TA206]
 gi|331056215|gb|EGI28224.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli TA206]
          Length = 239

 Score = 39.3 bits (90), Expect = 0.80,   Method: Compositional matrix adjust.
 Identities = 47/221 (21%), Positives = 102/221 (46%), Gaps = 32/221 (14%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL+ AV+++D  +G    TY++  I+ AM +  LRS   V      N + 
Sbjct: 41  LDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDE-LRSRDWVPRSVRRNARE 99

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   + +L+   Q +  N  + E    +A++L +  ++   M            L+++++
Sbjct: 100 VAQAIGQLE---QELGRNATETE----VAERLGIDIADYRQM------------LLDTNN 140

Query: 195 KNSSQWQDW---------LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
                + +W         LV D D Q +  +++    N R  +  ++ +L  RE+ +   
Sbjct: 141 SQLFSYDEWREEHGDSIELVTD-DHQRENPLQQLLDSNLRQRVMEAIEMLPEREKLVLTL 199

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +E  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 200 YYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 238


>gi|182412226|ref|YP_001817292.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Opitutus terrae
           PB90-1]
 gi|177839440|gb|ACB73692.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Opitutus terrae
           PB90-1]
          Length = 262

 Score = 39.3 bits (90), Expect = 0.80,   Method: Compositional matrix adjust.
 Identities = 34/140 (24%), Positives = 60/140 (42%), Gaps = 40/140 (28%)

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR-SWSLVKIGTTANQKR 134
            ++ S G  GL+ AV+KFDPE+G   A+Y+   I+ A+ + + R  W           +R
Sbjct: 59  DDLYSVGVTGLIAAVRKFDPEQGCTFASYAAMRIRGAVLDELRRMDWC---------PRR 109

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
                R+LK             E ++ + +KL            R A DE + + +  + 
Sbjct: 110 ARARSRKLK-------------ETIIEVEQKLG-----------RAASDEEICSALGLTQ 145

Query: 195 KNSSQWQD------WLVYDH 208
           K+ ++W +      +L  DH
Sbjct: 146 KDYAKWVEDARPVTFLAIDH 165


>gi|94968665|ref|YP_590713.1| sigma 28 [Candidatus Koribacter versatilis Ellin345]
 gi|94550715|gb|ABF40639.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Candidatus
           Koribacter versatilis Ellin345]
          Length = 262

 Score = 39.3 bits (90), Expect = 0.80,   Method: Compositional matrix adjust.
 Identities = 47/223 (21%), Positives = 93/223 (41%), Gaps = 33/223 (14%)

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR-SWSLVKIGTTAN 131
           +PI ++++ G +GL+ A  K+D E+  +  +Y+ + I+ A+ + +    WS         
Sbjct: 44  VPIEDLINAGILGLIDAAGKYDSEKNVQFQSYAKFRIRGAILDSLRDLDWS--------- 94

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
            + L    R L+     +T     P     +A++L +       +   L G         
Sbjct: 95  PRDLRRKARALEAAELRLTSETGHPPLEDELARELGMDLDGFRELTRELEG--------- 145

Query: 192 SSDKNSSQWQDWLVYDHDGQE-QVLIEKEE--------RKNRRNMLTRSMSVLNPRERRI 242
                 S  Q+ L  +  G+E +V++E  E        R     +L  ++  L  RER++
Sbjct: 146 ---LGISSLQEGLPAEGFGEEREVVVESHEESPLDAFLRSENHELLVEAIEQLPARERQV 202

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
                 +E  +T++ +     V   RV QI ++A  +V+  +Q
Sbjct: 203 LALYYFEE--LTMKEVGDVLGVGESRVSQIHSQALTRVRARLQ 243


>gi|226310092|ref|YP_002769986.1| RNA polymerase sigma-B factor [Brevibacillus brevis NBRC 100599]
 gi|226093040|dbj|BAH41482.1| RNA polymerase sigma-B factor [Brevibacillus brevis NBRC 100599]
          Length = 262

 Score = 39.3 bits (90), Expect = 0.81,   Method: Compositional matrix adjust.
 Identities = 64/267 (23%), Positives = 122/267 (45%), Gaps = 41/267 (15%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP--ERG 98
           Y E  D +   +LV ++  LV  +A  +    +   ++V  G IGL+ + ++FDP  ER 
Sbjct: 22  YGETKDPTIQEQLVRAYTPLVESLAKKFVRGQVMYEDLVQVGLIGLLASFRRFDPSFERT 81

Query: 99  FRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           F   ++++  I   ++ YI  ++WS   +      K L   ++R+   +  +T    +  
Sbjct: 82  FE--SFAIPTIVGEIKRYIRDKTWS---VYVPRRVKELSPKIKRV---VDELTIKLQRSP 133

Query: 158 QVVAIAKKLNVSES---EVISMN---CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
           Q+  IA  L VSE    E + M      L+ D  L A +   D N+    D +    +G 
Sbjct: 134 QIADIANSLGVSEEAILETLEMGRSYHSLSMDSELEADL---DGNTISLLDLVGTMEEGY 190

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE-----FEVSR 266
             V         +  ML R++ +L+ RE+ I +    Q       NLS +       +S+
Sbjct: 191 GAV--------EQNLMLERALQILDHREKEIIQLTFYQ-------NLSQKQAGDIMGMSQ 235

Query: 267 ERVRQIEARAFKKVQESIQ-KQVELSS 292
             + +++ RA  K++E+++ +Q+E ++
Sbjct: 236 MHISRLQRRALGKLREALRVEQLETAT 262


>gi|318075206|ref|ZP_07982538.1| sigma factor [Streptomyces sp. SA3_actF]
          Length = 293

 Score = 39.3 bits (90), Expect = 0.81,   Method: Compositional matrix adjust.
 Identities = 19/65 (29%), Positives = 36/65 (55%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV + L +  +IA  YRG G  + ++     +GL++AV +FDPE      TY++  ++  
Sbjct: 41  LVEAWLPMAHRIAGRYRGRGESLEDLCQVAALGLLRAVDRFDPEVSDAFETYAVPTMQGE 100

Query: 113 MQEYI 117
           ++ + 
Sbjct: 101 LKRHF 105


>gi|229587513|ref|YP_002860551.1| putative sporulation sigma factor SigK [Clostridium botulinum Ba4
           str. 657]
 gi|229260138|gb|ACQ51175.1| putative sporulation sigma factor SigK [Clostridium botulinum Ba4
           str. 657]
          Length = 271

 Score = 39.3 bits (90), Expect = 0.81,   Method: Compositional matrix adjust.
 Identities = 46/221 (20%), Positives = 96/221 (43%), Gaps = 31/221 (14%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW----SLVKIG 127
           G+   +++ +  +G ++A++KFD  +G  L+TY+       M+ YIL S     +++K+ 
Sbjct: 64  GMEFDDLLIDAKLGFLKALEKFDINKGNALSTYAT----HCMRNYILNSIRVNNNMIKLS 119

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
           +    KR+  + ++ K ++  +   N K           N+        N RL       
Sbjct: 120 SREVNKRIKLS-KKFKANI--LNKGNYKFN--------YNIYNKIFSQHNVRLIDTHEYQ 168

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF--EA 245
           + ++    NSS  Q+         E++ +EKE+++     +  ++ +L+  E  I     
Sbjct: 169 SYLD----NSSIEQEI------SSEEMFMEKEQKRFNTRQIISALKILDKTELFIIVHYF 218

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
               +   TL  LS    +  E  R+I+ +A  K++   +K
Sbjct: 219 GLFNKKKRTLRELSKRLNIGYENTRKIKGKALSKIECYFKK 259


>gi|326332685|ref|ZP_08198948.1| putative stress response/stationary phase sigma factor SigF
           [Nocardioidaceae bacterium Broad-1]
 gi|325949513|gb|EGD41590.1| putative stress response/stationary phase sigma factor SigF
           [Nocardioidaceae bacterium Broad-1]
          Length = 176

 Score = 38.9 bits (89), Expect = 0.82,   Method: Compositional matrix adjust.
 Identities = 19/61 (31%), Positives = 35/61 (57%), Gaps = 1/61 (1%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  HL +   +A  Y G G+ + ++     +GL++A +++DPE+G  L +Y++   K  
Sbjct: 18  LVVRHLPVARSLAARYSGRGIEVEDLRQAARMGLVKAARRYDPEQGAFL-SYAVPMAKGE 76

Query: 113 M 113
           M
Sbjct: 77  M 77


>gi|326389454|ref|ZP_08211021.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermoanaerobacter
           ethanolicus JW 200]
 gi|325994459|gb|EGD52884.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermoanaerobacter
           ethanolicus JW 200]
          Length = 246

 Score = 38.9 bits (89), Expect = 0.83,   Method: Compositional matrix adjust.
 Identities = 56/256 (21%), Positives = 114/256 (44%), Gaps = 37/256 (14%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE---VVSEGNIGLMQAVKKFDP 95
           K Y  + D +  + ++  ++ LV  I        +  SE   ++++G IGL+ A++K+ P
Sbjct: 10  KTYNSNKDPNLRNEIIIKYMPLVKHIVKKLIISDITQSEYEDLINQGVIGLIDAIEKYQP 69

Query: 96  ERGFRLATYSMWWIKAAMQEYILR-SW-------SLVKIGTTANQKRLFFNLRRLKGHLQ 147
            +G +  TY+   I+  + +Y+ R  W          KI  T    +  +N    +  ++
Sbjct: 70  SKGVKFETYATLRIRGEIIDYLRRKDWMPRSLKKKYKKIEETVETLQQKYN---REPTVE 126

Query: 148 AITD-NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
            IT+   L    V+     +NV  S V S+   +  +  L+A+ N   KN          
Sbjct: 127 EITEACGLNEIDVLKTLSYINV--SNVNSLEEAIENNFKLHAISNVELKNP--------- 175

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
               +E+VL ++ +RK     L  ++  L  +ER +      ++  +  +++S    ++ 
Sbjct: 176 ----EEEVLYKELKRK-----LASAIESLPDKERLVITLYYYED--LNYKDISKILNLTE 224

Query: 267 ERVRQIEARAFKKVQE 282
            R+ QI  +A K+++E
Sbjct: 225 SRISQIHTKAIKRIRE 240


>gi|307152337|ref|YP_003887721.1| FliA/WhiG subfamily RNA polymerase sigma-28 factor [Cyanothece sp.
           PCC 7822]
 gi|306982565|gb|ADN14446.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cyanothece
           sp. PCC 7822]
          Length = 257

 Score = 38.9 bits (89), Expect = 0.84,   Method: Compositional matrix adjust.
 Identities = 41/180 (22%), Positives = 85/180 (47%), Gaps = 11/180 (6%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P  ++   G +GL++A+++F+P++G   +++++ +++  +  Y+    S+++I      +
Sbjct: 53  PYEDLEQVGYLGLIRAIERFNPQQGCAFSSFAIPYVRGEILHYLRDRGSVMRI--PRRWQ 110

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            L+   ++L+  L        K  +   IA+ L VS  E     C+LA     N L+ S 
Sbjct: 111 DLYTKGKKLRKQLAQTLGRQPKESE---IAQALGVSYQE--WNECQLALQ---NRLLVSL 162

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEER-KNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
           D   +Q  D ++   D       + ++R +  R  L R+MS L  + +   E   L + P
Sbjct: 163 DATINQVHDGVITFGDTLPDPKSQGQQRMQEDRLQLQRAMSQLEDKTKAAIECVFLWDLP 222


>gi|91211141|ref|YP_541127.1| flagellar biosynthesis sigma factor [Escherichia coli UTI89]
 gi|117624064|ref|YP_852977.1| flagellar biosynthesis sigma factor [Escherichia coli APEC O1]
 gi|218558780|ref|YP_002391693.1| flagellar biosynthesis sigma factor [Escherichia coli S88]
 gi|237705878|ref|ZP_04536359.1| flagellar biosynthesis sigma factor FliA [Escherichia sp.
           3_2_53FAA]
 gi|91072715|gb|ABE07596.1| flagellar biosynthesis; alternative sigma factor 28; regulation of
           flagellar operons [Escherichia coli UTI89]
 gi|115513188|gb|ABJ01263.1| flagellar biosynthesis sigma factor FliA [Escherichia coli APEC O1]
 gi|218365549|emb|CAR03276.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli S88]
 gi|226900635|gb|EEH86894.1| flagellar biosynthesis sigma factor FliA [Escherichia sp.
           3_2_53FAA]
 gi|294492788|gb|ADE91544.1| flagellar operon sigma factor FliA [Escherichia coli IHE3034]
 gi|323952417|gb|EGB48290.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli H252]
 gi|323956319|gb|EGB52062.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli H263]
          Length = 239

 Score = 38.9 bits (89), Expect = 0.84,   Method: Compositional matrix adjust.
 Identities = 47/221 (21%), Positives = 101/221 (45%), Gaps = 32/221 (14%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL+ AV+++D  +G    TY++  I+ AM +  LRS   V      N + 
Sbjct: 41  LDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDE-LRSRDWVPRSVRRNARE 99

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   + +L+   Q +  N  + E    +A++L +  ++   M            L+++++
Sbjct: 100 VAQAIGQLE---QELGRNATETE----VAERLGIDIADYRQM------------LLDTNN 140

Query: 195 KNSSQWQDW---------LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
                + +W         LV D D Q +  +++    N R  +  ++  L  RE+ +   
Sbjct: 141 SQLFSYDEWREEHGDSIELVTD-DHQRENPLQQLLDSNLRQRVMETIETLPEREKLVLTL 199

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +E  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 200 YYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 238


>gi|238794024|ref|ZP_04637642.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           intermedia ATCC 29909]
 gi|238726656|gb|EEQ18192.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           intermedia ATCC 29909]
          Length = 240

 Score = 38.9 bits (89), Expect = 0.84,   Method: Compositional matrix adjust.
 Identities = 47/218 (21%), Positives = 94/218 (43%), Gaps = 38/218 (17%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTANQK 133
           + +++  G IGL+ AV+++D  +G    TY++  I+ AM  E   R W+          +
Sbjct: 41  LDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDWA---------PR 91

Query: 134 RLFFNLRRLKGHLQAITDNNLKP--EQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
            +  N R +   +Q +     +P  EQ VA    ++++E   I ++             N
Sbjct: 92  SVRRNAREVASAMQKVEQRVGRPATEQEVAQILDIDLAEYRQILLDTN-----------N 140

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEE---------RKNRRNMLTRSMSVLNPRERRI 242
           S   +  +W++    +H    + L+E  E           N R  +  ++  L  RE+ +
Sbjct: 141 SQLFSYDEWRE----EHGESVEPLLEGHEDANPLQHLLEGNLRQRVIEAIEALPEREKMV 196

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                 +E  + L+ + +  EV   RV Q+ ++A K++
Sbjct: 197 LTLYYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRL 232


>gi|300928953|ref|ZP_07144457.1| flagellar biosynthesis sigma factor [Escherichia coli MS 187-1]
 gi|300463107|gb|EFK26600.1| flagellar biosynthesis sigma factor [Escherichia coli MS 187-1]
          Length = 229

 Score = 38.9 bits (89), Expect = 0.86,   Method: Compositional matrix adjust.
 Identities = 47/221 (21%), Positives = 102/221 (46%), Gaps = 32/221 (14%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL+ AV+++D  +G    TY++  I+ AM +  LRS   V      N + 
Sbjct: 31  LDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDE-LRSRDWVPRSVRRNARE 89

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   + +L+   Q +  N  + E    +A++L +  ++   M            L+++++
Sbjct: 90  VAQAIGQLE---QELGRNATETE----VAERLGIDIADYRQM------------LLDTNN 130

Query: 195 KNSSQWQDW---------LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
                + +W         LV D D Q +  +++    N R  +  ++ +L  RE+ +   
Sbjct: 131 SQLFSYDEWREEHGDSIELVTD-DHQRENPLQQLLDSNLRQRVMEAIEMLPEREKLVLTL 189

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +E  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 190 YYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 228


>gi|33322911|gb|AAQ07192.1|AF496500_1 RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           lactis]
          Length = 141

 Score = 38.9 bits (89), Expect = 0.86,   Method: Compositional matrix adjust.
 Identities = 25/60 (41%), Positives = 36/60 (60%), Gaps = 3/60 (5%)

Query: 225 RNMLTRSMS-VLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++ L+  M   L  RE ++ + R   EN  P TLE +     V+RERVRQIEA+A KK++
Sbjct: 69  KDQLSSMMGEFLTDREAKVLKLRFGLENDEPHTLEEVGRSLGVTRERVRQIEAKAVKKLK 128


>gi|3249719|gb|AAC26662.1| RNA polymerase sigma-like factor [Streptomyces lividans TK24]
          Length = 162

 Score = 38.9 bits (89), Expect = 0.89,   Method: Compositional matrix adjust.
 Identities = 46/175 (26%), Positives = 75/175 (42%), Gaps = 18/175 (10%)

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI+ AM   +      +++     +  L   + R++  +         P++V   A
Sbjct: 1   YATWWIRQAMSRALADQARTIRVPVHVVE--LINRVVRVQRRMLQERGCEPTPQEV---A 55

Query: 164 KKLNVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEE 220
             L+++  E +    RLA +  SL+A +   D       D  + D   DG     +E   
Sbjct: 56  AHLDLA-PERVGEVLRLAQEPVSLHAPVGEED-------DVALGDLIEDGDAASPVESAA 107

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIE 273
               R  L   +S L  RER++ + R       P TLE +   F V+RER+RQIE
Sbjct: 108 FLLLRQHLEAVLSTLGERERKVVQLRYGLADGRPRTLEEIGRLFGVTRERIRQIE 162


>gi|1588993|prf||2209422A fliA gene
          Length = 237

 Score = 38.9 bits (89), Expect = 0.89,   Method: Compositional matrix adjust.
 Identities = 48/234 (20%), Positives = 97/234 (41%), Gaps = 43/234 (18%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRL V++        + + +++  G IGL+ AV+++D  +G    TY++  I   + E  
Sbjct: 28  LRLQVRLPAS-----VELDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIAPMLDELR 82

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
            R W+          +R+  N R +   +Q +      P     +A+ L++  +E   + 
Sbjct: 83  QRDWA---------PRRIRRNAREVASAMQKVEQRLGAPATEQEVAQNLDIDLTEYRQI- 132

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                      L+++++     + +W   +H    + ++E  E  N    L       N 
Sbjct: 133 -----------LLDTNNSQLFSYDEW-REEHGRTVEPMLEGHEDANPLQHLLEG----NL 176

Query: 238 RERRIFEARRLQE-----------NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           R+ R+ EA  L E             + L+ + +  EV   RV Q+ ++A K++
Sbjct: 177 RQ-RVIEAEALPEREKMVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRL 229


>gi|238758082|ref|ZP_04619262.1| RNA polymerase sigma factor for flagellar operon [Yersinia aldovae
           ATCC 35236]
 gi|238703620|gb|EEP96157.1| RNA polymerase sigma factor for flagellar operon [Yersinia aldovae
           ATCC 35236]
          Length = 240

 Score = 38.9 bits (89), Expect = 0.90,   Method: Compositional matrix adjust.
 Identities = 47/233 (20%), Positives = 100/233 (42%), Gaps = 39/233 (16%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM-QEY 116
           LRL V++        + + +++  G IGL+ AV+++D  +G    TY++  I+ AM  E 
Sbjct: 29  LRLQVRLPAS-----VELDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDEL 83

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
             R W+          + +  N R +   +Q +     +P     +A+ L++  SE   +
Sbjct: 84  RSRDWA---------PRSVRRNAREVATAMQKVEQRVGRPATEQEVAQTLDIELSEYRQI 134

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---------RKNRRNM 227
                       L+++++     + +W   +H    + L+E  E           N R  
Sbjct: 135 ------------LLDTNNSQLFSYDEWR-EEHGESVEPLLEGHEDANPLQHLLEGNLRQR 181

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           +  ++  L  RE+ +      +E  + L+ + +  +V   RV Q+ ++A K++
Sbjct: 182 VIDAIEALPDREKMVLTLYYQEE--LNLKEIGAVLDVGESRVSQLHSQAIKRL 232


>gi|158334762|ref|YP_001515934.1| hypothetical protein AM1_1596 [Acaryochloris marina MBIC11017]
 gi|158305003|gb|ABW26620.1| hypothetical protein AM1_1596 [Acaryochloris marina MBIC11017]
          Length = 51

 Score = 38.9 bits (89), Expect = 0.90,   Method: Composition-based stats.
 Identities = 14/28 (50%), Positives = 23/28 (82%)

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYS 105
           ++ EG IGL ++V+KFDP +G+R +TY+
Sbjct: 23  LIQEGTIGLRRSVEKFDPTKGYRFSTYA 50


>gi|220927856|ref|YP_002504765.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Clostridium
           cellulolyticum H10]
 gi|219998184|gb|ACL74785.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Clostridium
           cellulolyticum H10]
          Length = 249

 Score = 38.9 bits (89), Expect = 0.90,   Method: Compositional matrix adjust.
 Identities = 18/94 (19%), Positives = 47/94 (50%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E  L  +Y   G+L   + +V+++L L   ++  +   G+   ++     + L+ AV++
Sbjct: 12  DEVQLFSQYISTGNLEYRNEIVSNYLSLAEYLSKKFLNRGVDFDDIYQVACLALINAVER 71

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           F P++G +  +++   I   ++ +     + +KI
Sbjct: 72  FSPDKGVKFISFATPTILGEIKRFFRDKSTTIKI 105


>gi|5327289|emb|CAB46360.1| FliA, sigma 28 [Xenorhabdus nematophila]
 gi|139522465|gb|ABO77651.1| FliA [Xenorhabdus nematophila]
          Length = 230

 Score = 38.9 bits (89), Expect = 0.92,   Method: Compositional matrix adjust.
 Identities = 52/230 (22%), Positives = 99/230 (43%), Gaps = 33/230 (14%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRL V++        + + +++  G IGL+ AV++FD  +G    TY++  I+ AM +  
Sbjct: 19  LRLQVRLPAS-----VELDDLLQAGGIGLLNAVERFDSMQGTAFTTYAVQRIRGAMLDE- 72

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           LRS          N + +   +R+L+  L          EQ VA   K+N+ E   I   
Sbjct: 73  LRSRDWAPRSVRRNAREVTQTIRKLEQEL-----GRPASEQEVAKELKINLIEYRQI--- 124

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM--SVL 235
                      L+++++     + +W     +  E V+ E+ E    + +L   +   V+
Sbjct: 125 -----------LLDTNNSQLFSYDEWHEIHGESCEPVIEEEHETNPLQQLLEGDLRQRVI 173

Query: 236 N-----PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N     P   ++      QE  + L+ + +   V   RV Q+ ++A K++
Sbjct: 174 NIIESLPEREKMVLTLYYQEE-LNLKEIGAVLNVGESRVSQLHSQAIKRL 222


>gi|282854097|ref|ZP_06263434.1| sigma-70, region 4 [Propionibacterium acnes J139]
 gi|282583550|gb|EFB88930.1| sigma-70, region 4 [Propionibacterium acnes J139]
 gi|314923070|gb|EFS86901.1| sigma-70, region 4 [Propionibacterium acnes HL001PA1]
 gi|314966840|gb|EFT10939.1| sigma-70, region 4 [Propionibacterium acnes HL082PA2]
 gi|314981182|gb|EFT25276.1| sigma-70, region 4 [Propionibacterium acnes HL110PA3]
 gi|315092002|gb|EFT63978.1| sigma-70, region 4 [Propionibacterium acnes HL110PA4]
 gi|315093239|gb|EFT65215.1| sigma-70, region 4 [Propionibacterium acnes HL060PA1]
 gi|315103504|gb|EFT75480.1| sigma-70, region 4 [Propionibacterium acnes HL050PA2]
 gi|327327666|gb|EGE69442.1| RNA polymerase sigma factor [Propionibacterium acnes HL103PA1]
          Length = 270

 Score = 38.9 bits (89), Expect = 0.93,   Method: Compositional matrix adjust.
 Identities = 19/67 (28%), Positives = 39/67 (58%), Gaps = 6/67 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           +V +H R   + A+ YR     + +++  G +GL +A++++D  RG R +T +  WI+  
Sbjct: 71  IVLTHAR---QAAVSYR---CSVEDLIQAGCVGLGEAIERYDVRRGARFSTVAWTWIRRR 124

Query: 113 MQEYILR 119
           + E ++R
Sbjct: 125 IGEEVVR 131


>gi|123442749|ref|YP_001006726.1| flagellar biosynthesis sigma factor [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|332161358|ref|YP_004297935.1| flagellar biosynthesis sigma factor [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|122089710|emb|CAL12562.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           enterocolitica subsp. enterocolitica 8081]
 gi|318605283|emb|CBY26781.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           enterocolitica subsp. palearctica Y11]
 gi|325665588|gb|ADZ42232.1| flagellar biosynthesis sigma factor [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|330859514|emb|CBX69857.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           enterocolitica W22703]
          Length = 240

 Score = 38.9 bits (89), Expect = 0.93,   Method: Compositional matrix adjust.
 Identities = 46/232 (19%), Positives = 99/232 (42%), Gaps = 37/232 (15%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM-QEY 116
           LRL V++        + + +++  G IGL+ AV+++D  +G    TY++  I+ AM  E 
Sbjct: 29  LRLQVRLPAS-----VELDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDEL 83

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
             R W+          + +  N R +   +Q +     +P     +A+ L++  +E   +
Sbjct: 84  RSRDWA---------PRSVRRNAREVASAMQKVEQRLGRPATEQEVAQNLDIDLTEYRQI 134

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE--------RKNRRNML 228
                       L+++++     + +W     +  E +L   E+          N R  +
Sbjct: 135 ------------LLDTNNSQLFSYDEWREEHGESVEPMLEGHEDANPLQHLLEGNLRQRV 182

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++  L  RE+ +      +E  + L+ + +  EV   RV Q+ ++A K++
Sbjct: 183 IEAIEALPEREKMVLTLYYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRL 232


>gi|160896045|ref|YP_001561627.1| RNA polymerase sigma 28 subunit FliA/WhiG [Delftia acidovorans
           SPH-1]
 gi|160361629|gb|ABX33242.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Delftia acidovorans
           SPH-1]
          Length = 237

 Score = 38.9 bits (89), Expect = 0.93,   Method: Compositional matrix adjust.
 Identities = 53/233 (22%), Positives = 106/233 (45%), Gaps = 18/233 (7%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           L+  H+ LV +IA+       P   + +++  G IGL +A+ +F+ E+G +  T++   I
Sbjct: 13  LIRRHVPLVRRIALHMIAKLPPNVELDDLIQVGMIGLAEALSRFESEQGVQFETFASQRI 72

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + AM +  LR    +   +  +QK +   L RL+   Q +    L+ E    IA +L + 
Sbjct: 73  RGAMLDE-LREGDWMSRSSRKSQKDIEHALHRLE---QRLGRTPLESE----IADELGMD 124

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNML 228
             +  S+  ++ G + +     S       + +  V D       L+    R +R R  L
Sbjct: 125 LDDYQSLLGKVRGTQLVYLEDMSGGDEGEDFLERHVADSGADPFALL----RDHRLRVAL 180

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             ++  L  RE+ I       E+ + L+ +++   V+  RV Q+ ++A  +++
Sbjct: 181 VEAIKALPEREQYIMGM--YYEHDMNLKEIAAVLGVTESRVCQLHSQAIARLR 231


>gi|300935898|ref|ZP_07150854.1| flagellar biosynthesis sigma factor [Escherichia coli MS 21-1]
 gi|300458917|gb|EFK22410.1| flagellar biosynthesis sigma factor [Escherichia coli MS 21-1]
 gi|307626601|gb|ADN70905.1| flagellar biosynthesis sigma factor [Escherichia coli UM146]
 gi|315286624|gb|EFU46057.1| flagellar biosynthesis sigma factor [Escherichia coli MS 110-3]
          Length = 229

 Score = 38.9 bits (89), Expect = 0.94,   Method: Compositional matrix adjust.
 Identities = 51/238 (21%), Positives = 108/238 (45%), Gaps = 37/238 (15%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRL V++        + + +++  G IGL+ AV+++D  +G    TY++  I+ AM +  
Sbjct: 19  LRLQVRLPAS-----VELDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDE- 72

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           LRS   V      N + +   + +L+   Q +  N  + E    +A++L +  ++   M 
Sbjct: 73  LRSRDWVPRSVRRNAREVAQAIGQLE---QELGRNATETE----VAERLGIDIADYRQM- 124

Query: 178 CRLAGDESLNALINSSDKNSSQWQDW---------LVYDHDGQEQVLIEKEERKNRRNML 228
                      L+++++     + +W         LV D D Q +  +++    N R  +
Sbjct: 125 -----------LLDTNNSQLFSYDEWREEHGDSIELVTD-DHQRENPLQQLLDSNLRQRV 172

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             ++  L  RE+ +      +E  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 173 METIETLPEREKLVLTLYYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 228


>gi|238798562|ref|ZP_04642039.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           mollaretii ATCC 43969]
 gi|238717582|gb|EEQ09421.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           mollaretii ATCC 43969]
          Length = 240

 Score = 38.9 bits (89), Expect = 0.94,   Method: Compositional matrix adjust.
 Identities = 44/216 (20%), Positives = 92/216 (42%), Gaps = 34/216 (15%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTANQK 133
           + +++  G IGL+ AV+++D  +G    TY++  I+ AM  E   R W+          +
Sbjct: 41  LDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDWA---------PR 91

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            +  N R +   +Q +     +P     +AK L++   E   +            L++++
Sbjct: 92  SVRRNAREVASAMQQVEQRVGRPATEQEVAKILDIDLVEYRQI------------LLDTN 139

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEE---------RKNRRNMLTRSMSVLNPRERRIFE 244
           +     + +W   +H    + L+E  E           N R  +  ++  L  RE+ +  
Sbjct: 140 NSQLFSYDEWR-EEHGESVEPLLEGHEDANPLQHLLEGNLRQRVIEAIEALPEREKMVLT 198

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
               +E  + L+ + +  EV   RV Q+ ++A K++
Sbjct: 199 LYYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRL 232


>gi|15802357|ref|NP_288383.1| flagellar biosynthesis sigma factor [Escherichia coli O157:H7
           EDL933]
 gi|15831915|ref|NP_310688.1| flagellar biosynthesis sigma factor [Escherichia coli O157:H7 str.
           Sakai]
 gi|26248189|ref|NP_754229.1| flagellar biosynthesis sigma factor [Escherichia coli CFT073]
 gi|49176170|ref|NP_416432.3| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli str.
           K-12 substr. MG1655]
 gi|74311731|ref|YP_310150.1| flagellar biosynthesis sigma factor [Shigella sonnei Ss046]
 gi|89108757|ref|AP_002537.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli str.
           K-12 substr. W3110]
 gi|110642027|ref|YP_669757.1| flagellar biosynthesis sigma factor [Escherichia coli 536]
 gi|157158016|ref|YP_001463226.1| flagellar biosynthesis sigma factor [Escherichia coli E24377A]
 gi|170019740|ref|YP_001724694.1| flagellar biosynthesis sigma factor [Escherichia coli ATCC 8739]
 gi|170081570|ref|YP_001730890.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli str.
           K-12 substr. DH10B]
 gi|170684004|ref|YP_001743321.1| flagellar biosynthesis sigma factor [Escherichia coli SMS-3-5]
 gi|187776391|ref|ZP_02802353.2| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4196]
 gi|188025223|ref|ZP_02776870.2| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4113]
 gi|189010650|ref|ZP_02808323.2| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4076]
 gi|189402557|ref|ZP_02783240.2| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4401]
 gi|189403603|ref|ZP_02796533.2| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4486]
 gi|189404441|ref|ZP_02789463.2| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4501]
 gi|189405427|ref|ZP_02815329.2| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC869]
 gi|189406256|ref|ZP_02827273.2| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC508]
 gi|191168296|ref|ZP_03030089.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           B7A]
 gi|191173335|ref|ZP_03034865.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           F11]
 gi|193066383|ref|ZP_03047431.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           E22]
 gi|193071158|ref|ZP_03052082.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           E110019]
 gi|194429934|ref|ZP_03062444.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           B171]
 gi|194439580|ref|ZP_03071653.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           101-1]
 gi|208810387|ref|ZP_03252263.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4206]
 gi|209399914|ref|YP_002271036.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4115]
 gi|209919344|ref|YP_002293428.1| flagellar biosynthesis sigma factor [Escherichia coli SE11]
 gi|215487127|ref|YP_002329558.1| flagellar biosynthesis sigma factor [Escherichia coli O127:H6 str.
           E2348/69]
 gi|218554506|ref|YP_002387419.1| flagellar biosynthesis sigma factor [Escherichia coli IAI1]
 gi|218689915|ref|YP_002398127.1| flagellar biosynthesis sigma factor [Escherichia coli ED1a]
 gi|218695529|ref|YP_002403196.1| flagellar biosynthesis sigma factor [Escherichia coli 55989]
 gi|218699514|ref|YP_002407143.1| flagellar biosynthesis sigma factor [Escherichia coli IAI39]
 gi|218705417|ref|YP_002412936.1| flagellar biosynthesis sigma factor [Escherichia coli UMN026]
 gi|238901131|ref|YP_002926927.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli BW2952]
 gi|253773125|ref|YP_003035956.1| flagellar biosynthesis sigma factor [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254793572|ref|YP_003078409.1| flagellar biosynthesis sigma factor [Escherichia coli O157:H7 str.
           TW14359]
 gi|260844326|ref|YP_003222104.1| RNA polymerase, sigma 28 factor [Escherichia coli O103:H2 str.
           12009]
 gi|260855902|ref|YP_003229793.1| RNA polymerase, sigma 28 factor [Escherichia coli O26:H11 str.
           11368]
 gi|260868514|ref|YP_003234916.1| RNA polymerase, sigma 28 factor [Escherichia coli O111:H- str.
           11128]
 gi|291283099|ref|YP_003499917.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O55:H7 str. CB9615]
 gi|293405408|ref|ZP_06649400.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           FVEC1412]
 gi|293410281|ref|ZP_06653857.1| conserved hypothetical protein [Escherichia coli B354]
 gi|293446304|ref|ZP_06662726.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           B088]
 gi|298381052|ref|ZP_06990651.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           FVEC1302]
 gi|307314171|ref|ZP_07593781.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Escherichia
           coli W]
 gi|312967123|ref|ZP_07781341.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           2362-75]
 gi|312973866|ref|ZP_07788038.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           1827-70]
 gi|331642544|ref|ZP_08343679.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli H736]
 gi|331668616|ref|ZP_08369464.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli TA271]
 gi|331673440|ref|ZP_08374208.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli TA280]
 gi|331677807|ref|ZP_08378482.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli H591]
 gi|331683474|ref|ZP_08384075.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli H299]
 gi|332278907|ref|ZP_08391320.1| transcription initiation factor alternative sigma factor 28
           [Shigella sp. D9]
 gi|84028136|sp|P0AEM8|FLIA_ECO57 RecName: Full=RNA polymerase sigma factor for flagellar operon;
           AltName: Full=Sigma-27; AltName: Full=Sigma-28; AltName:
           Full=Sigma-F factor
 gi|84028137|sp|P0AEM7|FLIA_ECOL6 RecName: Full=RNA polymerase sigma factor for flagellar operon;
           AltName: Full=Sigma-27; AltName: Full=Sigma-28; AltName:
           Full=Sigma-F factor
 gi|84028138|sp|P0AEM6|FLIA_ECOLI RecName: Full=RNA polymerase sigma factor for flagellar operon;
           AltName: Full=Sigma-27; AltName: Full=Sigma-28; AltName:
           Full=Sigma-F factor
 gi|12516023|gb|AAG56937.1|AE005415_2 flagellar biosynthesis; alternative sigma factor 28; regulation of
           flagellar operons [Escherichia coli O157:H7 str. EDL933]
 gi|26108593|gb|AAN80796.1|AE016762_49 RNA polymerase sigma factor for flagellar operon [Escherichia coli
           CFT073]
 gi|556180|gb|AAC37011.1| sigma factor 28 [Escherichia coli]
 gi|687650|gb|AAC43543.1| sigma F [Escherichia coli]
 gi|1736581|dbj|BAA15742.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli str.
           K12 substr. W3110]
 gi|1788231|gb|AAC74989.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli str.
           K-12 substr. MG1655]
 gi|13362129|dbj|BAB36084.1| transcription initiation factor alternative sigma factor 28
           [Escherichia coli O157:H7 str. Sakai]
 gi|73855208|gb|AAZ87915.1| alternative sigma factor 28 [Shigella sonnei Ss046]
 gi|110343619|gb|ABG69856.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           536]
 gi|157080046|gb|ABV19754.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           E24377A]
 gi|169754668|gb|ACA77367.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Escherichia coli ATCC
           8739]
 gi|169889405|gb|ACB03112.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli str.
           K-12 substr. DH10B]
 gi|170521722|gb|ACB19900.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           SMS-3-5]
 gi|187767374|gb|EDU31218.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4196]
 gi|188014157|gb|EDU52279.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4113]
 gi|188999325|gb|EDU68311.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4076]
 gi|189354876|gb|EDU73295.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4401]
 gi|189359713|gb|EDU78132.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4486]
 gi|189365564|gb|EDU83980.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4501]
 gi|189370194|gb|EDU88610.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC869]
 gi|189375693|gb|EDU94109.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC508]
 gi|190901668|gb|EDV61424.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           B7A]
 gi|190906452|gb|EDV66061.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           F11]
 gi|192925968|gb|EDV80614.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           E22]
 gi|192955553|gb|EDV86032.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           E110019]
 gi|194412023|gb|EDX28335.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           B171]
 gi|194421489|gb|EDX37503.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           101-1]
 gi|208724903|gb|EDZ74610.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4206]
 gi|209161314|gb|ACI38747.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4115]
 gi|209748392|gb|ACI72503.1| transcription initiation factor alternative sigma factor 28
           [Escherichia coli]
 gi|209748394|gb|ACI72504.1| transcription initiation factor alternative sigma factor 28
           [Escherichia coli]
 gi|209748396|gb|ACI72505.1| transcription initiation factor alternative sigma factor 28
           [Escherichia coli]
 gi|209912603|dbj|BAG77677.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           SE11]
 gi|215265199|emb|CAS09588.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli O127:H6
           str. E2348/69]
 gi|218352261|emb|CAU98017.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli 55989]
 gi|218361274|emb|CAQ98858.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli IAI1]
 gi|218369500|emb|CAR17267.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli IAI39]
 gi|218427479|emb|CAR08375.2| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli ED1a]
 gi|218432514|emb|CAR13407.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli UMN026]
 gi|222033663|emb|CAP76404.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           LF82]
 gi|238863498|gb|ACR65496.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli BW2952]
 gi|253324169|gb|ACT28771.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254592972|gb|ACT72333.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli O157:H7
           str. TW14359]
 gi|257754551|dbj|BAI26053.1| RNA polymerase, sigma 28 factor [Escherichia coli O26:H11 str.
           11368]
 gi|257759473|dbj|BAI30970.1| RNA polymerase, sigma 28 factor [Escherichia coli O103:H2 str.
           12009]
 gi|257764870|dbj|BAI36365.1| RNA polymerase, sigma 28 factor [Escherichia coli O111:H- str.
           11128]
 gi|260448961|gb|ACX39383.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Escherichia coli DH1]
 gi|284921835|emb|CBG34908.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           042]
 gi|290762972|gb|ADD56933.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O55:H7 str. CB9615]
 gi|291323134|gb|EFE62562.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           B088]
 gi|291427616|gb|EFF00643.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           FVEC1412]
 gi|291470749|gb|EFF13233.1| conserved hypothetical protein [Escherichia coli B354]
 gi|298278494|gb|EFI20008.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           FVEC1302]
 gi|306906140|gb|EFN36658.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Escherichia
           coli W]
 gi|307553936|gb|ADN46711.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           ABU 83972]
 gi|309702217|emb|CBJ01534.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           ETEC H10407]
 gi|310332461|gb|EFP99696.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           1827-70]
 gi|312288587|gb|EFR16489.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           2362-75]
 gi|315061222|gb|ADT75549.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli W]
 gi|315617855|gb|EFU98453.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           3431]
 gi|320191897|gb|EFW66544.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC1212]
 gi|320194366|gb|EFW68997.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           WV_060327]
 gi|320198616|gb|EFW73216.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           EC4100B]
 gi|323158594|gb|EFZ44608.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           E128010]
 gi|323165278|gb|EFZ51066.1| RNA polymerase sigma factor for flagellar operon [Shigella sonnei
           53G]
 gi|323180827|gb|EFZ66367.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           1180]
 gi|323186802|gb|EFZ72122.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           RN587/1]
 gi|323378201|gb|ADX50469.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Escherichia coli KO11]
 gi|323937197|gb|EGB33477.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli E1520]
 gi|323940415|gb|EGB36606.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli E482]
 gi|323948197|gb|EGB44185.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli H120]
 gi|323961971|gb|EGB57570.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli H489]
 gi|323968339|gb|EGB63746.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli M863]
 gi|323972715|gb|EGB67916.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli TA007]
 gi|323977897|gb|EGB72983.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli TW10509]
 gi|324118976|gb|EGC12865.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli E1167]
 gi|326342331|gb|EGD66112.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. 1044]
 gi|326344837|gb|EGD68584.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. 1125]
 gi|327253053|gb|EGE64707.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           STEC_7v]
 gi|331039342|gb|EGI11562.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli H736]
 gi|331063810|gb|EGI35721.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli TA271]
 gi|331069638|gb|EGI41025.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli TA280]
 gi|331074267|gb|EGI45587.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli H591]
 gi|331079689|gb|EGI50886.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli H299]
 gi|332089656|gb|EGI94758.1| RNA polymerase sigma factor for flagellar operon [Shigella boydii
           5216-82]
 gi|332101259|gb|EGJ04605.1| transcription initiation factor alternative sigma factor 28
           [Shigella sp. D9]
 gi|332343648|gb|AEE56982.1| RNA polymerase sigma factor for flagellar operon protein
           [Escherichia coli UMNK88]
 gi|332756073|gb|EGJ86426.1| RNA polymerase sigma factor for flagellar operon [Shigella flexneri
           4343-70]
 gi|333003239|gb|EGK22785.1| RNA polymerase sigma factor for flagellar operon [Shigella flexneri
           K-218]
 gi|333004180|gb|EGK23712.1| RNA polymerase sigma factor for flagellar operon [Shigella flexneri
           K-272]
 gi|333017792|gb|EGK37099.1| RNA polymerase sigma factor for flagellar operon [Shigella flexneri
           K-227]
          Length = 239

 Score = 38.9 bits (89), Expect = 0.94,   Method: Compositional matrix adjust.
 Identities = 47/221 (21%), Positives = 101/221 (45%), Gaps = 32/221 (14%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL+ AV+++D  +G    TY++  I+ AM +  LRS   V      N + 
Sbjct: 41  LDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDE-LRSRDWVPRSVRRNARE 99

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   + +L+   Q +  N  + E    +A++L +  ++   M            L+++++
Sbjct: 100 VAQAIGQLE---QELGRNATETE----VAERLGIDIADYRQM------------LLDTNN 140

Query: 195 KNSSQWQDW---------LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
                + +W         LV D D Q +  +++    N R  +  ++  L  RE+ +   
Sbjct: 141 SQLFSYDEWREEHGDSIELVTD-DHQRENPLQQLLDSNLRQRVMEAIETLPEREKLVLTL 199

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +E  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 200 YYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 238


>gi|302556917|ref|ZP_07309259.1| stress response/stationary phase sigma factor SigF [Streptomyces
           griseoflavus Tu4000]
 gi|302474535|gb|EFL37628.1| stress response/stationary phase sigma factor SigF [Streptomyces
           griseoflavus Tu4000]
          Length = 263

 Score = 38.9 bits (89), Expect = 0.95,   Method: Compositional matrix adjust.
 Identities = 20/72 (27%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LVT+ L +  +IA+ +RG G  + ++     +GL++AV  +DP RG     Y++  +   
Sbjct: 41  LVTAWLPMAERIAVRFRGRGEALEDLYQVAALGLVKAVDHYDPARGNAFEAYAVPTVTGE 100

Query: 113 MQEYIL-RSWSL 123
           ++ +     W+L
Sbjct: 101 IKRHFRDHMWTL 112


>gi|331653330|ref|ZP_08354335.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli M718]
 gi|323174562|gb|EFZ60183.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           LT-68]
 gi|331049428|gb|EGI21500.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli M718]
          Length = 239

 Score = 38.9 bits (89), Expect = 0.95,   Method: Compositional matrix adjust.
 Identities = 47/221 (21%), Positives = 101/221 (45%), Gaps = 32/221 (14%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL+ AV+++D  +G    TY++  I+ AM +  LRS   V      N + 
Sbjct: 41  LDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDE-LRSRDWVPRSVRRNARE 99

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   + +L+   Q +  N  + E    +A++L +  ++   M            L+++++
Sbjct: 100 VAQAIGQLE---QELGRNATETE----VAERLGIDIADYRQM------------LLDTNN 140

Query: 195 KNSSQWQDW---------LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
                + +W         LV D D Q +  +++    N R  +  ++  L  RE+ +   
Sbjct: 141 SQLFSYDEWREEHGDSIELVTD-DHQRENPLQQLLDSNLRQRVMEAIETLPEREKLVLTL 199

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +E  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 200 YYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 238


>gi|229918653|ref|YP_002887299.1| RNA polymerase sigma factor SigD [Exiguobacterium sp. AT1b]
 gi|229470082|gb|ACQ71854.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Exiguobacterium sp.
           AT1b]
          Length = 256

 Score = 38.9 bits (89), Expect = 0.95,   Method: Compositional matrix adjust.
 Identities = 55/244 (22%), Positives = 105/244 (43%), Gaps = 19/244 (7%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQAVKKFDPERGFRL 101
           D+  A+ L+ +H   ++   +      LP S    E+ S G +GL  A+ K+DPE   + 
Sbjct: 17  DMDTANELL-AHYEFLIHYHVQRMIVTLPKSVERDELKSLGYMGLYDALMKYDPEHNNKF 75

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ-AITDNNLKPEQVV 160
            TY+ + I+ A+ +  LR    +        K++     +L+  L  A T + L      
Sbjct: 76  DTYAAFRIRGAIIDG-LRKVDWLPRSVREKVKKIDHVAEQLEQSLHRAPTKSEL------ 128

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
           A A  L +SE E        A   S++  +   ++       +   D +  E  L+++E 
Sbjct: 129 ASACDLPISEIERTMAEGYFANMLSIDEAVTLQEEGKVMSVTYFDPDSEKPEDTLLQRE- 187

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                ++L   +  L+ +ER +       E  +TL  +    E+S  R+ QI ++A K +
Sbjct: 188 ---LIDVLAAEVDHLSEKERLVVSLFYFDE--LTLTEIGEVLELSTSRISQIHSKALKTL 242

Query: 281 QESI 284
           + ++
Sbjct: 243 KHAL 246


>gi|238788344|ref|ZP_04632138.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           frederiksenii ATCC 33641]
 gi|238723590|gb|EEQ15236.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           frederiksenii ATCC 33641]
          Length = 240

 Score = 38.9 bits (89), Expect = 0.96,   Method: Compositional matrix adjust.
 Identities = 47/218 (21%), Positives = 94/218 (43%), Gaps = 38/218 (17%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTANQK 133
           + +++  G IGL+ AV+++D  +G    TY++  I+ AM  E   R W+          +
Sbjct: 41  LDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDWA---------PR 91

Query: 134 RLFFNLRRLKGHLQAITDNNLKP--EQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
            +  N R +   +Q +     +P  EQ VA    ++++E   I ++             N
Sbjct: 92  SVRRNAREVASAMQKVEQRLGRPATEQEVAQILDIDLAEYRQILLDTN-----------N 140

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEE---------RKNRRNMLTRSMSVLNPRERRI 242
           S   +  +W++    +H    + L+E  E           N R  +  ++  L  RE+ +
Sbjct: 141 SQLFSYDEWRE----EHGESVEPLLEGHEDANPLQHLLEGNLRQRVIEAIEALPEREKMV 196

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                 +E  + L+ + +  EV   RV Q+ ++A K++
Sbjct: 197 LTLYYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRL 232


>gi|317057764|ref|YP_004106231.1| LuxR family transcriptional regulator [Ruminococcus albus 7]
 gi|315450033|gb|ADU23597.1| transcriptional regulator, LuxR family [Ruminococcus albus 7]
          Length = 195

 Score = 38.9 bits (89), Expect = 0.97,   Method: Compositional matrix adjust.
 Identities = 21/68 (30%), Positives = 37/68 (54%), Gaps = 1/68 (1%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R + +  R+   IA G  G    + ++V EG + L++AV  + P+RG   A Y+   I+ 
Sbjct: 34  RYMGTAERIAAGIAPG-AGREQTVKDLVQEGMMALLRAVNSYRPDRGAGFAAYAGVCIRH 92

Query: 112 AMQEYILR 119
           +M  YI++
Sbjct: 93  SMLSYIMK 100


>gi|242238998|ref|YP_002987179.1| flagellar biosynthesis sigma factor [Dickeya dadantii Ech703]
 gi|242131055|gb|ACS85357.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Dickeya dadantii
           Ech703]
          Length = 240

 Score = 38.9 bits (89), Expect = 0.97,   Method: Compositional matrix adjust.
 Identities = 50/223 (22%), Positives = 97/223 (43%), Gaps = 32/223 (14%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL+ AV+++D  +G    TY++  I+ AM +  LRS          N + 
Sbjct: 41  LDDLLQAGGIGLLSAVERYDSLQGTAFTTYAVQRIRGAMLDE-LRSRDWAPRSVRRNARE 99

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVI-SMNCRLAGDESLNALINSS 193
           +   +R              + EQ++  A     +E EV  S+N  L  +E    L++++
Sbjct: 100 VAHAMR--------------QAEQLLGRAP----TEQEVAQSLNISL--EEYRQILLDTN 139

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERK--------NRRNMLTRSMSVLNPRERRIFEA 245
           +     + +W     D  E +L   EE          N R  +  ++  L  RE+ +   
Sbjct: 140 NSQLFSYDEWREEHGDSAEALLEGNEEANPLHQLMDVNLRQRVMEAIENLPEREKMVLTL 199

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
              +E  + L+ + +  EV   RV Q+ ++A K+++  +   V
Sbjct: 200 YYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRLRVKLMNDV 240


>gi|328880523|emb|CCA53762.1| RNA polymerase sigma factor SigB [Streptomyces venezuelae ATCC
           10712]
          Length = 325

 Score = 38.9 bits (89), Expect = 0.98,   Method: Compositional matrix adjust.
 Identities = 39/169 (23%), Positives = 74/169 (43%), Gaps = 15/169 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  +L LV   A  +R       ++V  G +GL++A+ +FDP RG    ++++  +   
Sbjct: 74  LVELNLSLVKYAATRFRHSSENWEDLVQVGTVGLIKAINRFDPARGNEFMSFALPTVLGE 133

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL-KPEQVVAIAKKLNVSE 170
           ++ ++   SWS+       +  R    LR          +  L +P     ++ +L+++E
Sbjct: 134 IRRHLRDTSWSV-------HVPRRLQELRLDVAKANDALEQELGRPPTAAELSDRLHITE 186

Query: 171 SEVISMNCRLAGD----ESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
            E+     R+A +     SL+  ++  D         L  D D  E+VL
Sbjct: 187 DEL--REGRIAANGFASRSLDVPVDDEDAGPGMLARCLGSDDDAFEKVL 233


>gi|308205502|gb|ADO18992.1| RNA polymerase sigma 70 subunit [Nostoc flagelliforme str.
           Sunitezuoqi]
          Length = 165

 Score = 38.9 bits (89), Expect = 0.98,   Method: Compositional matrix adjust.
 Identities = 20/55 (36%), Positives = 31/55 (56%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           H    A  ++VT++LRLVV IA  Y+   L   +++ EG +GL + V+K    R 
Sbjct: 76  HQGERAKQKMVTANLRLVVAIAKKYQNRNLEFLDLIQEGTLGLYRGVEKLIQTRA 130


>gi|90411040|ref|ZP_01219054.1| flagellar biosynthesis sigma factor FliA [Photobacterium profundum
           3TCK]
 gi|90328253|gb|EAS44564.1| flagellar biosynthesis sigma factor FliA [Photobacterium profundum
           3TCK]
          Length = 240

 Score = 38.9 bits (89), Expect = 0.99,   Method: Compositional matrix adjust.
 Identities = 52/235 (22%), Positives = 104/235 (44%), Gaps = 33/235 (14%)

Query: 60  LVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           LV +IA   MG     + + +++  G IGL++A + +DP +G    T++   I+ AM + 
Sbjct: 24  LVKRIAYHLMGRLPSSVQVEDLIQSGMIGLLEAQQNYDPTKGASFETFAGIRIRGAMLDD 83

Query: 117 ILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV-VAIAKKLNVSESE-- 172
           I R  W           + ++ N RR+   + A+ +N L  +     IA+ L ++  +  
Sbjct: 84  IRRGDWV---------PRSVYKNNRRITEAM-ALLENKLGRDPTDTEIAEHLEMTLDQYH 133

Query: 173 --VISMNC-RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             +  +NC RL G + L              +D +  +   +E +  +     N R  L 
Sbjct: 134 QALNDVNCGRLVGMDDLGV-----------SEDAVTTEASREENLPFQGVVDDNFRQSLA 182

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            ++  L  RE  +      +E  + L+ + +   VS  R+ QI ++A ++++  +
Sbjct: 183 DAIKTLPEREALVLSLYYDEE--LNLKEIGAVVGVSESRICQIHSQAMQRLRSKL 235


>gi|320647130|gb|EFX15963.1| flagellar biosynthesis sigma factor [Escherichia coli O157:H- str.
           493-89]
 gi|320652413|gb|EFX20711.1| flagellar biosynthesis sigma factor [Escherichia coli O157:H- str.
           H 2687]
          Length = 228

 Score = 38.9 bits (89), Expect = 1.00,   Method: Compositional matrix adjust.
 Identities = 51/238 (21%), Positives = 108/238 (45%), Gaps = 37/238 (15%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRL V++        + + +++  G IGL+ AV+++D  +G    TY++  I+ AM +  
Sbjct: 19  LRLQVRLPAS-----VELDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDE- 72

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           LRS   V      N + +   + +L+   Q +  N  + E    +A++L +  ++   M 
Sbjct: 73  LRSRDWVPRSVRRNAREVAQAIGQLE---QELGRNATETE----VAERLGIDIADYRQM- 124

Query: 178 CRLAGDESLNALINSSDKNSSQWQDW---------LVYDHDGQEQVLIEKEERKNRRNML 228
                      L+++++     + +W         LV D D Q +  +++    N R  +
Sbjct: 125 -----------LLDTNNSQLFSYDEWREEHGDSIELVTD-DHQRENPLQQLLDSNLRQRV 172

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             ++  L  RE+ +      +E  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 173 MEAIETLPEREKLVLTLYYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 228


>gi|56964009|ref|YP_175740.1| RNA polymerase sigma factor SigD [Bacillus clausii KSM-K16]
 gi|56910252|dbj|BAD64779.1| DNA-directed RNA polymerase sigma-28 factor sigma-D [Bacillus
           clausii KSM-K16]
          Length = 254

 Score = 38.9 bits (89), Expect = 1.00,   Method: Compositional matrix adjust.
 Identities = 54/229 (23%), Positives = 97/229 (42%), Gaps = 32/229 (13%)

Query: 72  GLPIS----EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           GLP S    E+ S    GL+ A+ KFD +R  +  TY+ + I+ A+            I 
Sbjct: 41  GLPSSISKDELKSHALSGLLDAIAKFDSKRALKFDTYASFRIRGAI------------ID 88

Query: 128 TTANQKRLFFNLRRLKGHLQAITDN-------NLKPEQVVAIAKKLNVSESEVISMNCRL 180
               + RL   +R     L+ IT+        ++ P +V A A  L   E E +      
Sbjct: 89  GLRKEDRLPRTIRDKVKKLEQITEQLEQEKGRSVLPGEVAA-AMGLPEKEIEALKREQFA 147

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDG--QEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           +   SL+ +++ +D        +   D      +  L+E++ RK    M+      L   
Sbjct: 148 SHTLSLDDVMHMNDHLDPSAVAYQFEDEQAIMPDDKLVEEDTRKELAEMIKE----LGRN 203

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+ + +    +E  ++L  +     +S  R+ QI ARA  K+++ +QK+
Sbjct: 204 EQLVIQLSYYEE--LSLTEIGRILNLSTSRISQIHARAIAKLRKGLQKK 250


>gi|188495466|ref|ZP_03002736.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           53638]
 gi|293415233|ref|ZP_06657876.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           B185]
 gi|331647515|ref|ZP_08348607.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli M605]
 gi|188490665|gb|EDU65768.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           53638]
 gi|281178984|dbj|BAI55314.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           SE15]
 gi|291432881|gb|EFF05860.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           B185]
 gi|330911730|gb|EGH40240.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           AA86]
 gi|331043239|gb|EGI15377.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli M605]
          Length = 239

 Score = 38.9 bits (89), Expect = 1.00,   Method: Compositional matrix adjust.
 Identities = 47/221 (21%), Positives = 101/221 (45%), Gaps = 32/221 (14%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL+ AV+++D  +G    TY++  I+ AM +  LRS   V      N + 
Sbjct: 41  LDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDE-LRSRDWVPRSVRRNARE 99

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   + +L+   Q +  N  + E    +A++L +  ++   M            L+++++
Sbjct: 100 VAQAIGQLE---QELGRNATETE----VAERLGIDIADYRQM------------LLDTNN 140

Query: 195 KNSSQWQDW---------LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
                + +W         LV D D Q +  +++    N R  +  ++  L  RE+ +   
Sbjct: 141 SQLFSYDEWREEHGDSIELVTD-DHQRENPLQQLLDNNLRQRVMEAIETLPEREKLVLTL 199

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +E  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 200 YYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 238


>gi|319787083|ref|YP_004146558.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pseudoxanthomonas
           suwonensis 11-1]
 gi|317465595|gb|ADV27327.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pseudoxanthomonas
           suwonensis 11-1]
          Length = 248

 Score = 38.9 bits (89), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 23/71 (32%), Positives = 38/71 (53%), Gaps = 5/71 (7%)

Query: 54  VTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           V  H  LV +IA  +    LP    + +++  G IGL++A + +DPE+G    TY+   I
Sbjct: 20  VVRHADLVRRIAH-HLAARLPASVEVDDLIQAGMIGLIEASRSYDPEQGASFETYASIRI 78

Query: 110 KAAMQEYILRS 120
           + +M + I R 
Sbjct: 79  RGSMIDEIRRG 89


>gi|310777972|ref|YP_003966305.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ilyobacter
           polytropus DSM 2926]
 gi|309747295|gb|ADO81957.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ilyobacter
           polytropus DSM 2926]
          Length = 203

 Score = 38.9 bits (89), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 19/68 (27%), Positives = 34/68 (50%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           ++GD  A  ++   +   V   A  Y   G    ++V EG IGL++A++ +D E+     
Sbjct: 15  QNGDQEAVRKVFDYYKNFVFLKAKNYFLIGADRDDLVQEGMIGLLKAIRAYDTEKAASFK 74

Query: 103 TYSMWWIK 110
           T++   IK
Sbjct: 75  TFATICIK 82


>gi|221635447|ref|YP_002523323.1| RNA polymerase sigma-D factor (Sigma-28) [Thermomicrobium roseum
           DSM 5159]
 gi|221157679|gb|ACM06797.1| RNA polymerase sigma-D factor (Sigma-28) [Thermomicrobium roseum
           DSM 5159]
          Length = 262

 Score = 38.9 bits (89), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 16/49 (32%), Positives = 30/49 (61%), Gaps = 1/49 (2%)

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
            +++  G IGL++A+ +FD  RG +  TY+   I+ A+ +  LR+  +V
Sbjct: 54  DDLIGYGTIGLLEALDRFDDTRGVKFETYAAMRIRGAILD-ALRTLDIV 101


>gi|110805895|ref|YP_689415.1| flagellar biosynthesis sigma factor [Shigella flexneri 5 str. 8401]
 gi|195939226|ref|ZP_03084608.1| flagellar biosynthesis sigma factor [Escherichia coli O157:H7 str.
           EC4024]
 gi|208816591|ref|ZP_03257711.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4045]
 gi|208820391|ref|ZP_03260711.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4042]
 gi|217328583|ref|ZP_03444664.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. TW14588]
 gi|227885651|ref|ZP_04003456.1| flagellar biosynthesis sigma factor [Escherichia coli 83972]
 gi|256017880|ref|ZP_05431745.1| flagellar biosynthesis sigma factor [Shigella sp. D9]
 gi|256022420|ref|ZP_05436285.1| flagellar biosynthesis sigma factor [Escherichia sp. 4_1_40B]
 gi|261227583|ref|ZP_05941864.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli O157:H7
           str. FRIK2000]
 gi|261255813|ref|ZP_05948346.1| RNA polymerase, sigma 28 factor [Escherichia coli O157:H7 str.
           FRIK966]
 gi|300818654|ref|ZP_07098862.1| flagellar biosynthesis sigma factor [Escherichia coli MS 107-1]
 gi|300822306|ref|ZP_07102447.1| flagellar biosynthesis sigma factor [Escherichia coli MS 119-7]
 gi|300899176|ref|ZP_07117454.1| flagellar biosynthesis sigma factor [Escherichia coli MS 198-1]
 gi|300904809|ref|ZP_07122636.1| flagellar biosynthesis sigma factor [Escherichia coli MS 84-1]
 gi|300917364|ref|ZP_07134033.1| flagellar biosynthesis sigma factor [Escherichia coli MS 115-1]
 gi|300925015|ref|ZP_07140938.1| flagellar biosynthesis sigma factor [Escherichia coli MS 182-1]
 gi|300951546|ref|ZP_07165380.1| flagellar biosynthesis sigma factor [Escherichia coli MS 116-1]
 gi|300956562|ref|ZP_07168843.1| flagellar biosynthesis sigma factor [Escherichia coli MS 175-1]
 gi|300982291|ref|ZP_07176001.1| flagellar biosynthesis sigma factor [Escherichia coli MS 200-1]
 gi|300993927|ref|ZP_07180602.1| flagellar biosynthesis sigma factor [Escherichia coli MS 45-1]
 gi|301018228|ref|ZP_07182743.1| flagellar biosynthesis sigma factor [Escherichia coli MS 69-1]
 gi|301050723|ref|ZP_07197582.1| flagellar biosynthesis sigma factor [Escherichia coli MS 185-1]
 gi|301305263|ref|ZP_07211360.1| flagellar biosynthesis sigma factor [Escherichia coli MS 124-1]
 gi|301327712|ref|ZP_07220918.1| flagellar biosynthesis sigma factor [Escherichia coli MS 78-1]
 gi|301645559|ref|ZP_07245489.1| flagellar biosynthesis sigma factor [Escherichia coli MS 146-1]
 gi|306814254|ref|ZP_07448420.1| flagellar biosynthesis sigma factor [Escherichia coli NC101]
 gi|307138589|ref|ZP_07497945.1| flagellar biosynthesis sigma factor [Escherichia coli H736]
 gi|309795968|ref|ZP_07690381.1| flagellar biosynthesis sigma factor [Escherichia coli MS 145-7]
 gi|110615443|gb|ABF04110.1| flagellar biosynthesis sigma factor FliA [Shigella flexneri 5 str.
           8401]
 gi|208730934|gb|EDZ79623.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4045]
 gi|208740514|gb|EDZ88196.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4042]
 gi|217317930|gb|EEC26357.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. TW14588]
 gi|227837224|gb|EEJ47690.1| flagellar biosynthesis sigma factor [Escherichia coli 83972]
 gi|300297591|gb|EFJ53976.1| flagellar biosynthesis sigma factor [Escherichia coli MS 185-1]
 gi|300307268|gb|EFJ61788.1| flagellar biosynthesis sigma factor [Escherichia coli MS 200-1]
 gi|300316625|gb|EFJ66409.1| flagellar biosynthesis sigma factor [Escherichia coli MS 175-1]
 gi|300357213|gb|EFJ73083.1| flagellar biosynthesis sigma factor [Escherichia coli MS 198-1]
 gi|300399815|gb|EFJ83353.1| flagellar biosynthesis sigma factor [Escherichia coli MS 69-1]
 gi|300403277|gb|EFJ86815.1| flagellar biosynthesis sigma factor [Escherichia coli MS 84-1]
 gi|300406428|gb|EFJ89966.1| flagellar biosynthesis sigma factor [Escherichia coli MS 45-1]
 gi|300415410|gb|EFJ98720.1| flagellar biosynthesis sigma factor [Escherichia coli MS 115-1]
 gi|300418834|gb|EFK02145.1| flagellar biosynthesis sigma factor [Escherichia coli MS 182-1]
 gi|300449221|gb|EFK12841.1| flagellar biosynthesis sigma factor [Escherichia coli MS 116-1]
 gi|300525189|gb|EFK46258.1| flagellar biosynthesis sigma factor [Escherichia coli MS 119-7]
 gi|300528826|gb|EFK49888.1| flagellar biosynthesis sigma factor [Escherichia coli MS 107-1]
 gi|300839469|gb|EFK67229.1| flagellar biosynthesis sigma factor [Escherichia coli MS 124-1]
 gi|300845756|gb|EFK73516.1| flagellar biosynthesis sigma factor [Escherichia coli MS 78-1]
 gi|301076168|gb|EFK90974.1| flagellar biosynthesis sigma factor [Escherichia coli MS 146-1]
 gi|305852413|gb|EFM52864.1| flagellar biosynthesis sigma factor [Escherichia coli NC101]
 gi|308120418|gb|EFO57680.1| flagellar biosynthesis sigma factor [Escherichia coli MS 145-7]
 gi|312946514|gb|ADR27341.1| flagellar biosynthesis sigma factor [Escherichia coli O83:H1 str.
           NRG 857C]
 gi|315136559|dbj|BAJ43718.1| RNA polymerase sigma factor [Escherichia coli DH1]
 gi|315257247|gb|EFU37215.1| flagellar biosynthesis sigma factor [Escherichia coli MS 85-1]
 gi|315290288|gb|EFU49666.1| flagellar biosynthesis sigma factor [Escherichia coli MS 153-1]
 gi|315296505|gb|EFU55802.1| flagellar biosynthesis sigma factor [Escherichia coli MS 16-3]
 gi|320641770|gb|EFX11158.1| flagellar biosynthesis sigma factor [Escherichia coli O157:H7 str.
           G5101]
 gi|320658015|gb|EFX25777.1| flagellar biosynthesis sigma factor [Escherichia coli O55:H7 str.
           3256-97 TW 07815]
 gi|320658587|gb|EFX26281.1| flagellar biosynthesis sigma factor [Escherichia coli O55:H7 str.
           USDA 5905]
 gi|320668485|gb|EFX35312.1| flagellar biosynthesis sigma factor [Escherichia coli O157:H7 str.
           LSU-61]
 gi|323152745|gb|EFZ39017.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           EPECa14]
 gi|323186302|gb|EFZ71652.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           1357]
 gi|324007273|gb|EGB76492.1| flagellar biosynthesis sigma factor [Escherichia coli MS 57-2]
 gi|324013514|gb|EGB82733.1| flagellar biosynthesis sigma factor [Escherichia coli MS 60-1]
 gi|324017957|gb|EGB87176.1| flagellar biosynthesis sigma factor [Escherichia coli MS 117-3]
          Length = 229

 Score = 38.9 bits (89), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 51/238 (21%), Positives = 108/238 (45%), Gaps = 37/238 (15%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRL V++        + + +++  G IGL+ AV+++D  +G    TY++  I+ AM +  
Sbjct: 19  LRLQVRLPAS-----VELDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDE- 72

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           LRS   V      N + +   + +L+   Q +  N  + E    +A++L +  ++   M 
Sbjct: 73  LRSRDWVPRSVRRNAREVAQAIGQLE---QELGRNATETE----VAERLGIDIADYRQM- 124

Query: 178 CRLAGDESLNALINSSDKNSSQWQDW---------LVYDHDGQEQVLIEKEERKNRRNML 228
                      L+++++     + +W         LV D D Q +  +++    N R  +
Sbjct: 125 -----------LLDTNNSQLFSYDEWREEHGDSIELVTD-DHQRENPLQQLLDSNLRQRV 172

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             ++  L  RE+ +      +E  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 173 MEAIETLPEREKLVLTLYYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 228


>gi|168069803|ref|XP_001786584.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162660945|gb|EDQ48604.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 406

 Score = 38.9 bits (89), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 51/192 (26%), Positives = 84/192 (43%), Gaps = 29/192 (15%)

Query: 42  REHGD---LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF-DPER 97
           R H D   L      +T +LRLV   A  Y  Y     +VVSEG IGL+ A  ++ D   
Sbjct: 3   RNHPDNPLLGPRDAFITQNLRLVHMCAKRY-AYNRGYDDVVSEGTIGLILAYDRYSDATV 61

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
            F  +T++  +I+  ++ Y  RS      GT +  +R   N RR       I +  L+ +
Sbjct: 62  AF--STFAATYIRGYIRNY-FRSLR----GTVSVPRRTLDNSRR-------IAEAGLEDK 107

Query: 158 QVVAIAKKLNV----SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
               +A+ L +    +E  +  +    +G    +  IN+  K+   + D  V D +    
Sbjct: 108 APETVAEALGIAVKHAEDALYYLAVTESGSRDYDEEINA--KSVHTFDDDTVPDVNA--- 162

Query: 214 VLIEKEERKNRR 225
             IE++  KN+R
Sbjct: 163 -FIERQVPKNQR 173


>gi|318061849|ref|ZP_07980570.1| sigma factor [Streptomyces sp. SA3_actG]
          Length = 295

 Score = 38.9 bits (89), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 19/65 (29%), Positives = 36/65 (55%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV + L +  +IA  YRG G  + ++     +GL++AV +FDPE      TY++  ++  
Sbjct: 41  LVEAWLPMAHRIAGRYRGRGESLEDLCQVAALGLLRAVDRFDPEVSDAFETYAVPTMQGE 100

Query: 113 MQEYI 117
           ++ + 
Sbjct: 101 LKRHF 105


>gi|311279128|ref|YP_003941359.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Enterobacter cloacae
           SCF1]
 gi|308748323|gb|ADO48075.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Enterobacter cloacae
           SCF1]
          Length = 243

 Score = 38.9 bits (89), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 51/232 (21%), Positives = 105/232 (45%), Gaps = 37/232 (15%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRL V++        + + +++  G IGL+ AV+++D  +G    TY++  I+ AM +  
Sbjct: 29  LRLQVRLPAS-----VELDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDE- 82

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           LRS   V      N + +   + +L+   Q +  N  + E    +A++L ++  E   M 
Sbjct: 83  LRSRDWVPRSVRRNAREVAQAMGQLE---QELGRNATETE----VAQRLGIAVEEYRQM- 134

Query: 178 CRLAGDESLNALINSSDKNSSQWQDW---------LVYDHDGQEQVLIEKEERKNRRNML 228
                      L+++++     + +W         LV + + QE  L +  E  N R  +
Sbjct: 135 -----------LLDTNNSQLFSYDEWREEHGDSIELVTEENQQENPLHQLME-SNLRQRV 182

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++  L  RE+ +      +E  + L+ + +  +V   RV Q+ ++A K++
Sbjct: 183 IEAIEALPEREQLVLTLYYQEE--LNLKEIGAVLDVGESRVSQLHSQAIKRL 232


>gi|302671184|ref|YP_003831144.1| RNA polymerase sigma factor sigma-70 family protein [Butyrivibrio
           proteoclasticus B316]
 gi|302395657|gb|ADL34562.1| RNA polymerase sigma factor sigma-70 family [Butyrivibrio
           proteoclasticus B316]
          Length = 207

 Score = 38.9 bits (89), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 25/86 (29%), Positives = 39/86 (45%), Gaps = 2/86 (2%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            EE +L+   R+  D  A   ++  +  LV K A      G    +++ EG IGL +AV+
Sbjct: 11  DEELILS--IRDGDDPGAVDHIMNKYKNLVRKKAASMFALGADKDDLIQEGMIGLFKAVR 68

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYI 117
            +D  R    AT++   I   M   I
Sbjct: 69  DYDCGRDASFATFAELCISRQMYSAI 94


>gi|284053747|ref|ZP_06383957.1| RNA polymerase sigma factor [Arthrospira platensis str. Paraca]
          Length = 179

 Score = 38.9 bits (89), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 38/173 (21%), Positives = 82/173 (47%), Gaps = 13/173 (7%)

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I ++   +++     +K     ++R++  L      N  P +   IAK L
Sbjct: 2   WWIRQAITRAIAQNSRTIRLPIHITEK--LNKIKRVQRELFQQYGRNATPTE---IAKAL 56

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++  S++   +  LA    ++  +   D   ++ QD L  +    +  + ++  R++ ++
Sbjct: 57  DLEPSQI--RDYLLASRHPVSLDLRVGDNQDTELQDLLEDESASADSYVTQQLLRQDLKD 114

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
           M    M+ L P++R +   R    +   ++L  +  +  +SRERVRQ+E +A 
Sbjct: 115 M----MADLTPQQREVLTLRYGLNDGKEMSLSKVGVQMNISRERVRQLENQAL 163


>gi|325922773|ref|ZP_08184506.1| DNA-directed RNA polymerase specialized sigma subunit [Xanthomonas
           gardneri ATCC 19865]
 gi|325546748|gb|EGD17869.1| DNA-directed RNA polymerase specialized sigma subunit [Xanthomonas
           gardneri ATCC 19865]
          Length = 128

 Score = 38.9 bits (89), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 41/75 (54%), Gaps = 5/75 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           A+ +VT H  LV +IA  +    LP S    +++  G IGL++A + +D E+G    TY+
Sbjct: 23  ANDIVTQHADLVRRIAH-HLAARLPASVEVDDLIQAGMIGLIEASRSYDSEQGASFETYA 81

Query: 106 MWWIKAAMQEYILRS 120
              I+ +M + I R 
Sbjct: 82  SIRIRGSMIDEIRRG 96


>gi|302556259|ref|ZP_07308601.1| RNA polymerase sigma-B factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302473877|gb|EFL36970.1| RNA polymerase sigma-B factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 281

 Score = 38.9 bits (89), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 51/231 (22%), Positives = 109/231 (47%), Gaps = 25/231 (10%)

Query: 61  VVKIAMG-YRGYGLP--ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           +V+ A G +R  G P  + ++V  G IGL++A+ +FD  R     ++++ +I   ++ + 
Sbjct: 65  LVRFAAGRFRSRG-PEEMEDIVQVGMIGLIKAIDRFDLSREAEFTSFAVPYIVGEIKRFF 123

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
             +   V +     + R+   L R    L++      +   V  +++ +++ E EV    
Sbjct: 124 RDTTWAVHVPRRLQEARV--QLARATEELRSRLG---RTPTVKELSELMSLPEQEV--RE 176

Query: 178 CRLAGD----ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
            R+A +     SL+A I+ SD   +  QD++  +    E  L+E        + L   ++
Sbjct: 177 ARIAANGYNSSSLDATISGSDDGEAALQDFIGAEDQAME--LVED------FHALAPLLA 228

Query: 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L+ R+R I   R ++E  +T   +     VS+ +V ++ +R   +++E +
Sbjct: 229 ELDERDRHIIRMRFVEE--LTQAQIGERLGVSQMQVSRLLSRTLARLREGM 277


>gi|323341369|ref|ZP_08081613.1| DNA-directed RNA polymerase sigma subunit FliA [Lactobacillus
           ruminis ATCC 25644]
 gi|323091246|gb|EFZ33874.1| DNA-directed RNA polymerase sigma subunit FliA [Lactobacillus
           ruminis ATCC 25644]
          Length = 250

 Score = 38.9 bits (89), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 52/213 (24%), Positives = 102/213 (47%), Gaps = 27/213 (12%)

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR--SWSLVKIGTTANQKRLFFNL 139
           G IGL+ A++KFD  +      Y+   I+ A+ + + R    S  K+G   +    F+  
Sbjct: 53  GVIGLIDAMQKFDSSKKVPFENYAAIRIRGAIIDEVRRHSKISRYKMGNVNS----FYQA 108

Query: 140 RR-LKGHLQ-AITDNNLKPEQVVAIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDK 195
           ++ L+  ++  +TD          I KK+ ++ S++  I  + +     SL + + S++ 
Sbjct: 109 KQELEQEMKREVTDKE--------IMKKMGITSSQLGDIYDSIQYLSSVSLESTLYSNND 160

Query: 196 NSSQWQDWLVYDH--DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
            +   QD L       G+++++  K+ERK     L  ++  L+ RE+ +       E   
Sbjct: 161 ETVMVQDTLRDSKAPSGEKELM--KQERKKE---LIEAIKRLSEREQLVLSL--YYEEDA 213

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TL+ +++  +VS  RV QI  RA  K++  I++
Sbjct: 214 TLKEIAAILDVSIARVSQIHGRAIAKIRGYIEE 246


>gi|108756900|ref|YP_630657.1| FliA/WhiG family RNA polymerase sigma factor [Myxococcus xanthus DK
           1622]
 gi|108460780|gb|ABF85965.1| RNA polymerase sigma factor, FliA/WhiG/SigD family [Myxococcus
           xanthus DK 1622]
          Length = 278

 Score = 38.9 bits (89), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 15/41 (36%), Positives = 28/41 (68%)

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           L + E+++ G IGL++A ++FDP+ G    T++ + IK A+
Sbjct: 33  LELDELLAYGQIGLLEAAERFDPKVGANFLTFAHYRIKGAI 73


>gi|110678161|ref|YP_681168.1| RNA polymerase sigma factor, putative [Roseobacter denitrificans
           OCh 114]
 gi|109454277|gb|ABG30482.1| RNA polymerase sigma factor, putative [Roseobacter denitrificans
           OCh 114]
          Length = 1005

 Score = 38.9 bits (89), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 24/62 (38%), Positives = 40/62 (64%), Gaps = 6/62 (9%)

Query: 231 SMSVLNPRERRIFEAR----RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +S LN R++ I + R    R Q    TLE ++S+++V+RER+RQIE +A +K++    K
Sbjct: 466 CISTLNDRQQDILQRRYGINRGQTE--TLEQVASDYDVTRERIRQIEKKAKQKLETKRTK 523

Query: 287 QV 288
           +V
Sbjct: 524 KV 525


>gi|82543610|ref|YP_407557.1| flagellar biosynthesis sigma factor [Shigella boydii Sb227]
 gi|81245021|gb|ABB65729.1| alternative sigma factor 28 [Shigella boydii Sb227]
 gi|320176074|gb|EFW51142.1| RNA polymerase sigma factor for flagellar operon [Shigella
           dysenteriae CDC 74-1112]
 gi|320184751|gb|EFW59543.1| RNA polymerase sigma factor for flagellar operon [Shigella flexneri
           CDC 796-83]
          Length = 239

 Score = 38.5 bits (88), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 47/221 (21%), Positives = 100/221 (45%), Gaps = 32/221 (14%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL+ AV+++D  +G    TY++  I+ AM +  LRS   V      N + 
Sbjct: 41  LDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDE-LRSRDWVPRSVRRNARE 99

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   + +L+   Q +  N  + E    +A++L +  ++   M            L+++++
Sbjct: 100 VAQAIGQLE---QELGRNATETE----VAERLGIDIADYRQM------------LLDTNN 140

Query: 195 KNSSQWQDW---------LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
                + +W         LV D D Q +  +++    N R  +  ++  L  RE+ +   
Sbjct: 141 SQLFSYDEWREEHGDSIELVTD-DHQRENPLQQLLDSNLRQRVMEAIETLPEREKLVLTL 199

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +E  + L+ + +  EV   RV Q+ ++A K++   + K
Sbjct: 200 YYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRLSTKLGK 238


>gi|261886011|ref|ZP_06010050.1| RNA polymerase sigma factor RpoD [Campylobacter fetus subsp.
           venerealis str. Azul-94]
          Length = 190

 Score = 38.5 bits (88), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 34/103 (33%), Positives = 51/103 (49%), Gaps = 14/103 (13%)

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDG---QEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           SL A I S D    ++ D+ V D       EQ+L     + + +  +   +  LN RE+ 
Sbjct: 81  SLEAPIGSED--DGKYGDF-VEDKTNLSPMEQIL-----KGDLKEQIDEVLDQLNDREKA 132

Query: 242 IFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 133 VIRMRFGLLEDESDRTLEEIGKELNVTRERVRQIESSAIKKLK 175


>gi|213419842|ref|ZP_03352908.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
          Length = 115

 Score = 38.5 bits (88), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 16/35 (45%), Positives = 27/35 (77%)

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           TLE +  +F+V+RER+RQIEA+A +K++   + +V
Sbjct: 74  TLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 108


>gi|56962590|ref|YP_174316.1| RNA polymerase sigma factor SigB [Bacillus clausii KSM-K16]
 gi|56908828|dbj|BAD63355.1| DNA-directed RNA polymerase general stress sigma factor sigma-B
           [Bacillus clausii KSM-K16]
          Length = 261

 Score = 38.5 bits (88), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 59/264 (22%), Positives = 124/264 (46%), Gaps = 32/264 (12%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLM 87
           K + Y+  ++Y++ G   A  +LV     LV  ++  +   R Y   + +V   G +GL+
Sbjct: 12  KDDIYLWIEQYQKTGSEEAQIKLVNHFEALVRSLSRKFSKGREYDEDLYQV---GMVGLL 68

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHL 146
            A+K+++ + G    ++++  +   ++ +I  ++WS+         +R+     ++K   
Sbjct: 69  AAMKRYNEDYGRSFESFAVPTVVGEIKRFIRDKTWSV------HVPRRIKELGPKIKKAA 122

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLV 205
             +T    +   V  IA+ L V+E EV+     +   +S  AL +N   +   +  +  +
Sbjct: 123 DTLTIELQRSPYVHEIAEYLQVTEEEVLET---MEMSKSYQALSVNRPLEADQEGGEVTL 179

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS-----S 260
            D  G E+   E+ ++K    +L ++  VLN RE+ I +           ENLS      
Sbjct: 180 LDLVGNEEAGYEQADQKL---LLEKAFEVLNEREKDILQC-------TYYENLSQKETGE 229

Query: 261 EFEVSRERVRQIEARAFKKVQESI 284
           +  +S+  V +++ RA +K+++SI
Sbjct: 230 KLGISQMHVSRLQRRALQKLRDSI 253


>gi|307328229|ref|ZP_07607407.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306886063|gb|EFN17071.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 307

 Score = 38.5 bits (88), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 53/239 (22%), Positives = 103/239 (43%), Gaps = 31/239 (12%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +L LV   A  +    + + ++V  G IGL++A+ +FD  R     T+++ +I   
Sbjct: 83  LIELNLSLVRYAARRFHNRSVEMEDIVQVGTIGLIKAIDRFDLSREVEFTTFAVPYIVGE 142

Query: 113 MQEYIL-RSWSL--------VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           ++ +    SW++        ++I      + LF  L R              P     +A
Sbjct: 143 IKRFFRDTSWAVHVPRRLQELRIDLAKANEELFQRLDR-------------SP-TTAELA 188

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY-DHDGQEQVLIEKEERK 222
           + L +SE EV+  +  +A +  L + +++  +  S       Y D  G     +E  E  
Sbjct: 189 EHLQLSEDEVV--DGLVASNGYLTSSLDAPAEQESGATRVTTYADRFGDVDPAMEAVENL 246

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +    L      L  R+RRI + R  +E  +T   + +E  VS+  V ++ +RA  +++
Sbjct: 247 HALKPLVEE---LGERDRRILQLRFGEE--MTQSEIGAELGVSQMHVSRLLSRALSRLR 300


>gi|213610106|ref|ZP_03369932.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 103

 Score = 38.5 bits (88), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 16/35 (45%), Positives = 27/35 (77%)

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           TLE +  +F+V+RER+RQIEA+A +K++   + +V
Sbjct: 62  TLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 96


>gi|254459646|ref|ZP_05073062.1| flagellar-specific RNA polymerase sigma factor [Rhodobacterales
           bacterium HTCC2083]
 gi|206676235|gb|EDZ40722.1| flagellar-specific RNA polymerase sigma factor [Rhodobacteraceae
           bacterium HTCC2083]
          Length = 219

 Score = 38.5 bits (88), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 51/225 (22%), Positives = 102/225 (45%), Gaps = 43/225 (19%)

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL----VKIGTTANQKR--L 135
           G +GL++A +++  + G    +Y++  ++ A+ +++ ++ +L    +KI    N+ R  L
Sbjct: 26  GLMGLIEAAQRYTRQEGISFESYAVIRVRGAINDFLRKNSALSRKSMKINKEVNEARNKL 85

Query: 136 FFNLRRL-KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
             +L R  +GH                +AK + +S  E  +    L          NSS 
Sbjct: 86  VHDLGRAPEGH---------------EVAKAVGLSLDEFTAWEQTL----------NSSY 120

Query: 195 KNSSQWQDWLVYDHD----GQEQVLIEKE-ERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
            NS Q +    YD            IE+E +R   +  L  ++  L  RE  + +   ++
Sbjct: 121 HNSIQDE----YDEHSMWFATADAPIEQELDRARLKEALLYALKTLPEREALVLQLYYVE 176

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSP 294
           E  + L  +++  +V+  RV QI++ AFKK+Q  ++  ++ S + 
Sbjct: 177 E--LNLFEIAAVLDVTSGRVSQIKSSAFKKMQPLLKDYIDNSQAA 219


>gi|166712012|ref|ZP_02243219.1| RNA polymerase sigma factor [Xanthomonas oryzae pv. oryzicola
           BLS256]
 gi|289666124|ref|ZP_06487705.1| RNA polymerase sigma factor [Xanthomonas campestris pv. vasculorum
           NCPPB702]
          Length = 255

 Score = 38.5 bits (88), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 5/75 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           A+ +VT H  LV +IA  +    LP    + +++  G IGL++A + +D E+G    TY+
Sbjct: 21  ANDVVTQHADLVRRIAH-HLAARLPASVEVDDLIQAGMIGLIEASRSYDSEQGASFETYA 79

Query: 106 MWWIKAAMQEYILRS 120
              I+ +M + I R 
Sbjct: 80  SIRIRGSMIDEIRRG 94


>gi|289670573|ref|ZP_06491648.1| RNA polymerase sigma factor [Xanthomonas campestris pv. musacearum
           NCPPB4381]
          Length = 255

 Score = 38.5 bits (88), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 5/75 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           A+ +VT H  LV +IA  +    LP    + +++  G IGL++A + +D E+G    TY+
Sbjct: 21  ANDVVTQHADLVRRIAH-HLAARLPASVEVDDLIQAGMIGLIEASRSYDSEQGASFETYA 79

Query: 106 MWWIKAAMQEYILRS 120
              I+ +M + I R 
Sbjct: 80  SIRIRGSMIDEIRRG 94


>gi|289808389|ref|ZP_06539018.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. AG3]
          Length = 148

 Score = 38.5 bits (88), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 16/35 (45%), Positives = 27/35 (77%)

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           TLE +  +F+V+RER+RQIEA+A +K++   + +V
Sbjct: 107 TLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 141


>gi|291461239|ref|ZP_06027789.2| RNA polymerase sigma factor [Fusobacterium periodonticum ATCC
           33693]
 gi|291378120|gb|EFE85638.1| RNA polymerase sigma factor [Fusobacterium periodonticum ATCC
           33693]
          Length = 259

 Score = 38.5 bits (88), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 22/64 (34%), Positives = 37/64 (57%), Gaps = 2/64 (3%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V  +L+ V +IA+     G+   ++  EG IGLM+A + F+ ++ F+L  Y  ++I  AM
Sbjct: 69  VEKNLKKVYQIALYMLRDGILYQDLTQEGVIGLMKAHELFEDDKDFKL--YKDYYIARAM 126

Query: 114 QEYI 117
             YI
Sbjct: 127 FNYI 130


>gi|21242677|ref|NP_642259.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. citri str.
           306]
 gi|294664736|ref|ZP_06730065.1| RNA polymerase sigma factor [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 10535]
 gi|21108148|gb|AAM36795.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. citri str.
           306]
 gi|292605490|gb|EFF48812.1| RNA polymerase sigma factor [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 10535]
          Length = 255

 Score = 38.5 bits (88), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 5/75 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           A+ +VT H  LV +IA  +    LP    + +++  G IGL++A + +D E+G    TY+
Sbjct: 21  ANDVVTQHADLVRRIAH-HLAARLPASVEVDDLIQAGMIGLIEASRSYDSEQGASFETYA 79

Query: 106 MWWIKAAMQEYILRS 120
              I+ +M + I R 
Sbjct: 80  SIRIRGSMIDEIRRG 94


>gi|149201624|ref|ZP_01878598.1| sigma factor FliA (Sigma-28 group, flagellar) [Roseovarius sp.
           TM1035]
 gi|149144672|gb|EDM32701.1| sigma factor FliA (Sigma-28 group, flagellar) [Roseovarius sp.
           TM1035]
          Length = 242

 Score = 38.5 bits (88), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 23/85 (27%), Positives = 45/85 (52%), Gaps = 3/85 (3%)

Query: 52  RLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           RLV  H+ LV ++A    G  G  + I +++  G +GL+ A +++    G   A Y+   
Sbjct: 16  RLVEQHMPLVQRLAWHFHGRVGRFIEIDDLLQAGYLGLIDASQRYSVCDGVSFAAYATIR 75

Query: 109 IKAAMQEYILRSWSLVKIGTTANQK 133
           I+ ++ +++ R+ +L +   T  QK
Sbjct: 76  IRGSIIDHLRRNSNLCRNSITMRQK 100


>gi|78047533|ref|YP_363708.1| RNA polymerase sigma factor for flagellar operon FliA [Xanthomonas
           campestris pv. vesicatoria str. 85-10]
 gi|325928018|ref|ZP_08189235.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Xanthomonas
           perforans 91-118]
 gi|78035963|emb|CAJ23654.1| RNA polymerase sigma factor for flagellar operon FliA [Xanthomonas
           campestris pv. vesicatoria str. 85-10]
 gi|325541614|gb|EGD13139.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Xanthomonas
           perforans 91-118]
          Length = 255

 Score = 38.5 bits (88), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 5/75 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           A+ +VT H  LV +IA  +    LP    + +++  G IGL++A + +D E+G    TY+
Sbjct: 21  ANDVVTQHADLVRRIAH-HLAARLPASVEVDDLIQAGMIGLIEASRSYDSEQGASFETYA 79

Query: 106 MWWIKAAMQEYILRS 120
              I+ +M + I R 
Sbjct: 80  SIRIRGSMIDEIRRG 94


>gi|317492397|ref|ZP_07950826.1| FliA/WhiG family RNA polymerase sigma factor [Enterobacteriaceae
           bacterium 9_2_54FAA]
 gi|316919736|gb|EFV41066.1| FliA/WhiG family RNA polymerase sigma factor [Enterobacteriaceae
           bacterium 9_2_54FAA]
          Length = 240

 Score = 38.5 bits (88), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 50/239 (20%), Positives = 104/239 (43%), Gaps = 37/239 (15%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRL V++        + + +++  G IGL+ AV+++D  +G    TY++  I+ AM +  
Sbjct: 29  LRLQVRLPAS-----VELDDLLQAGGIGLLHAVERYDAMQGTAFTTYAVQRIRGAMLDE- 82

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQ-AITDNNLKPEQVVAIAKKLNVSESEVISM 176
           LRS   V      N + +   ++R +  L  A T+          IA++L++   E   +
Sbjct: 83  LRSRDWVPRSVRRNAREVSAAMQRAEQRLHRAPTETE--------IAQELDMPLVEYQQI 134

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML-------- 228
                       L++++  +   + +W     D  E V  + E+    + +L        
Sbjct: 135 ------------LLDTNTSHLFSYDEWREEHGDSAEPVFQQHEDANPLKQLLEGDLRQRV 182

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             ++  L  RE+ +      +E  + L+ + +  EV   RV Q+ ++A K+++  +  Q
Sbjct: 183 IAAIEALPEREKLVLTLYYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLASQ 239


>gi|260776433|ref|ZP_05885328.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           coralliilyticus ATCC BAA-450]
 gi|260607656|gb|EEX33921.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           coralliilyticus ATCC BAA-450]
          Length = 244

 Score = 38.5 bits (88), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 57/252 (22%), Positives = 106/252 (42%), Gaps = 31/252 (12%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFD 94
           A  Y ++ +  +    +  +  LV +IA    G   P   + +++  G IGL++A K +D
Sbjct: 4   ALTYDQYANQDSQRAFLEKYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLLEAQKNYD 63

Query: 95  PERGFRLATYSMWWIKAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
             +G    TY+   I+ AM + I R  W  V      N + +   + +L+G L      N
Sbjct: 64  GSKGASFETYAGIRIRGAMLDDIRRGDW--VPRSVHKNSREISQAIAQLEGEL------N 115

Query: 154 LKPEQVVAIAKKLNVS----ESEVISMN-CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
             P     +AK+L +S     S +  +N  RL G + L              +D + ++ 
Sbjct: 116 RDPTD-AEVAKRLEMSLEQYHSALTDINSSRLIGIDDLGV-----------SEDAISHED 163

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
             +E +  +    +  R  L  S+  L  RE  +      +E  + L+ +     VS  R
Sbjct: 164 ADEENIPFQGVADEYFRTALVESIKSLPEREALVLSLYYDEE--LNLKEIGEVIGVSESR 221

Query: 269 VRQIEARAFKKV 280
           V QI +++ +++
Sbjct: 222 VSQILSQSMQRL 233


>gi|238752744|ref|ZP_04614214.1| RNA polymerase sigma factor for flagellar operon [Yersinia rohdei
           ATCC 43380]
 gi|238709075|gb|EEQ01323.1| RNA polymerase sigma factor for flagellar operon [Yersinia rohdei
           ATCC 43380]
          Length = 240

 Score = 38.5 bits (88), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 51/235 (21%), Positives = 102/235 (43%), Gaps = 43/235 (18%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM-QEY 116
           LRL V++        + + +++  G IGL+ AV+++D  +G    TY++  I+ AM  E 
Sbjct: 29  LRLQVRLPAS-----VELDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDEL 83

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP--EQVVAIAKKLNVSESEVI 174
             R W+          + +  N R +   +Q +     +P  EQ VA   +++++E   I
Sbjct: 84  RSRDWA---------PRSVRRNAREVASAMQKVEQRLGRPATEQEVAQNLEIDLAEYRQI 134

Query: 175 SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---------RKNRR 225
            ++             NS   +  +W++    +H    + L+E  E           N R
Sbjct: 135 LLDTN-----------NSQLFSYDEWRE----EHGESVEPLLEGHEDANPLQHLLEGNLR 179

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             +  ++  L  RE+ +      +E  + L+ + +  EV   RV Q+ ++A K++
Sbjct: 180 QRVIDAIEALPEREKMVLTLYYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRL 232


>gi|83589646|ref|YP_429655.1| sigma 28 (flagella/sporulation) [Moorella thermoacetica ATCC 39073]
 gi|83572560|gb|ABC19112.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Moorella
           thermoacetica ATCC 39073]
          Length = 255

 Score = 38.5 bits (88), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 47/209 (22%), Positives = 96/209 (45%), Gaps = 26/209 (12%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS-W---SLVKIGTTANQ 132
           +++  G +GL++AV ++DP RG    T++   I+ A+ + + R+ W   SL++    A+Q
Sbjct: 51  DLLGYGIVGLLEAVDRYDPSRGVNFETFASQRIRGAILDALRRAHWAPRSLIEKLRRASQ 110

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE----SLNA 188
             ++  L + +G    ++D         A+A+ L ++E+E+  +  R  G +    SL  
Sbjct: 111 --VYRQLEQEQGG--EVSDG--------AVARALGITEAELRELMER--GSQMAILSLED 156

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +   +      +  L+ D    + V I   E+   R  L  ++  L  ++R +      
Sbjct: 157 FLLDQEGEEGTTRGELLADPGSPDPVGI--YEQGELRRALAAALENLKEKDRLVLTLYYY 214

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAF 277
           +   +TL+ +     +S  RV Q+  RA 
Sbjct: 215 E--GLTLKEIGKVLGISESRVCQLHGRAI 241


>gi|58582244|ref|YP_201260.1| RNA polymerase sigma factor FliA [Xanthomonas oryzae pv. oryzae
           KACC10331]
 gi|84624137|ref|YP_451509.1| RNA polymerase sigma factor FliA [Xanthomonas oryzae pv. oryzae
           MAFF 311018]
 gi|188576807|ref|YP_001913736.1| RNA polymerase sigma factor FliA [Xanthomonas oryzae pv. oryzae
           PXO99A]
 gi|188577000|ref|YP_001913929.1| RNA polymerase sigma factor FliA [Xanthomonas oryzae pv. oryzae
           PXO99A]
 gi|6969595|gb|AAF33832.1|AF226282_6 RNA polymerase sigma factor FliA [Xanthomonas oryzae pv. oryzae]
 gi|58426838|gb|AAW75875.1| RNA polymerase sigma factor FliA [Xanthomonas oryzae pv. oryzae
           KACC10331]
 gi|84368077|dbj|BAE69235.1| RNA polymerase sigma factor FliA [Xanthomonas oryzae pv. oryzae
           MAFF 311018]
 gi|188521259|gb|ACD59204.1| RNA polymerase sigma factor FliA [Xanthomonas oryzae pv. oryzae
           PXO99A]
 gi|188521452|gb|ACD59397.1| RNA polymerase sigma factor FliA [Xanthomonas oryzae pv. oryzae
           PXO99A]
          Length = 251

 Score = 38.5 bits (88), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 40/75 (53%), Gaps = 5/75 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           A  +VT H  LV +IA  +    LP    + +++  G IGL++A + +D E+G    TY+
Sbjct: 17  ADNVVTQHADLVRRIAH-HLAARLPASVEVDDLIQAGMIGLIEASRSYDSEQGASFETYA 75

Query: 106 MWWIKAAMQEYILRS 120
              I+ +M + I R 
Sbjct: 76  SIRIRGSMIDEIRRG 90


>gi|330862243|emb|CBX72404.1| RNA polymerase sigma factor rpoD [Yersinia enterocolitica W22703]
          Length = 113

 Score = 38.5 bits (88), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 16/35 (45%), Positives = 27/35 (77%)

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           TLE +  +F+V+RER+RQIEA+A +K++   + +V
Sbjct: 72  TLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 106


>gi|332675354|gb|AEE72170.1| RNA polymerase sigma factor [Propionibacterium acnes 266]
          Length = 266

 Score = 38.5 bits (88), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 15/49 (30%), Positives = 30/49 (61%)

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           Y   + +++  G IGL +A++++D  RG R +T +  WI+  + E ++R
Sbjct: 83  YRCSVEDLIQAGCIGLGEAIERYDVRRGARFSTVAWTWIRRRIGEEVVR 131


>gi|289523542|ref|ZP_06440396.1| RNA polymerase sigma factor [Anaerobaculum hydrogeniformans ATCC
           BAA-1850]
 gi|289503234|gb|EFD24398.1| RNA polymerase sigma factor [Anaerobaculum hydrogeniformans ATCC
           BAA-1850]
          Length = 251

 Score = 38.5 bits (88), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 40/161 (24%), Positives = 78/161 (48%), Gaps = 15/161 (9%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL   +++S G +GL+ A+ ++DP RG    T++   I+ A+ +  LR +  +  G    
Sbjct: 51  GLSQDDLLSFGAMGLLDAIDRYDPSRGVSFNTFAFSRIRGAILDE-LRRYDWLSRGARDK 109

Query: 132 QKRL-----FFNLRRLKGHLQAITDNNLKPEQVV-----AIAKKLNVSESEVISMNCRLA 181
            +RL       N + LK + + + +     E+ +      +++   VS  EVIS++    
Sbjct: 110 IQRLEKAIAEMNEQGLKANDEMLMEKLQMDEKELRWLYELMSRSYVVSLDEVISLD---E 166

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           GD   +AL+  +  N  ++ + +  D D  +  L + EER+
Sbjct: 167 GDVERSALVPDTSPNPEEYMEAM-EDCDTLKGALEKLEERE 206


>gi|126664990|ref|ZP_01735973.1| flagellar biosynthesis sigma factor FliA [Marinobacter sp. ELB17]
 gi|126630360|gb|EBA00975.1| flagellar biosynthesis sigma factor FliA [Marinobacter sp. ELB17]
          Length = 246

 Score = 38.5 bits (88), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 58/244 (23%), Positives = 103/244 (42%), Gaps = 44/244 (18%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQAVKKFDPERGFRLAT 103
           S A  L+  H  LV KIA+      LP S    +++  G IGL++A +++   +G    T
Sbjct: 16  SDASWLIEEHAPLVKKIALHLLAR-LPSSVQLEDLMQAGMIGLLEASQRYTTGKGATFET 74

Query: 104 YSMWWIKAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           Y+   I+ AM + I +  W           + +  N RR+   ++A+     +    V +
Sbjct: 75  YAGIRIRGAMVDEIRKGDWV---------PRSVHRNSRRISSAIKAVEGREGRESHDVEV 125

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A +L+++ SE  S  C    D +   L +  + N S              ++ IE+ E  
Sbjct: 126 AAELDMTLSEYHS--C--LADSNSGRLFSLDELNDSG-------------ELPIEQSETD 168

Query: 223 NR----------RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           +           RN L  ++  L  RE+ +      +E  + L  + +  +VS  RV QI
Sbjct: 169 DNPLHGVSEFAFRNSLAAAIETLPEREKLVLSLYYQEE--LNLREIGAVLDVSESRVSQI 226

Query: 273 EARA 276
            ++A
Sbjct: 227 HSQA 230


>gi|126659553|ref|ZP_01730685.1| sigma factor SigF [Cyanothece sp. CCY0110]
 gi|126619192|gb|EAZ89929.1| sigma factor SigF [Cyanothece sp. CCY0110]
          Length = 258

 Score = 38.5 bits (88), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 33/140 (23%), Positives = 71/140 (50%), Gaps = 23/140 (16%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY---------ILRSWSLVKIG 127
           ++V  G++GL++A+++F  E+G   +++++ +I+  +Q Y         I R W  +++G
Sbjct: 57  DLVQVGSLGLIRAIERFSIEKGHAFSSFAIPYIRGEIQHYLRDKKYTVRIPRRW--LELG 114

Query: 128 -TTANQKRLF---FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-- 181
             + N +R F   FN +     +  + + +LK  Q +    KL     E +S++ +++  
Sbjct: 115 RQSMNVRREFREKFNRQPTDSEIAQVLEISLKEWQEI----KLAFQNREPVSLDVKVSSE 170

Query: 182 --GDESLNALINSSDKNSSQ 199
             G  SL  L+  ++  S Q
Sbjct: 171 GEGQTSLGDLVPDANYRSFQ 190


>gi|307824496|ref|ZP_07654721.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Methylobacter tundripaludum SV96]
 gi|307734480|gb|EFO05332.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Methylobacter tundripaludum SV96]
          Length = 237

 Score = 38.5 bits (88), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 49/237 (20%), Positives = 100/237 (42%), Gaps = 31/237 (13%)

Query: 54  VTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           V  H  LV +IA   +G     + + +++  G +GL++A+K +D  +G    TY+   I+
Sbjct: 14  VMQHAPLVKRIAYHLLGRLPDSVQVDDLIQAGMLGLLEAIKNYDASQGASFDTYAGIRIR 73

Query: 111 AAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
            +M + + RS W+          + +    R +   ++ I +   +  + V +AK L ++
Sbjct: 74  GSMLDEVRRSDWT---------PRSVHKKSRMVSDAIRTIENKTGREARDVDVAKYLGIA 124

Query: 170 ESEV-----ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
             E       S +CR+   E L        ++   + D  +   +G     ++   R+  
Sbjct: 125 IDEYNHILQDSSSCRVFSVEELA-------QDGDHYMDETLSHEEGP----VDGLSREGF 173

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +  L  ++  L  RER +      +E    L  +     +S  RV QI  +A  +++
Sbjct: 174 QQALANAIMGLPERERLVISLYYDEE--FNLREIGEVLNISESRVSQICTQAVLRLR 228


>gi|295798118|emb|CAX68947.1| RNA polymerase sigma factor 70 [uncultured bacterium]
          Length = 259

 Score = 38.5 bits (88), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 24/88 (27%), Positives = 48/88 (54%), Gaps = 5/88 (5%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLM 87
           + ++ L K+Y++         +V  ++ LV  +A G    GLP     +++VS G +GL 
Sbjct: 3   EADFKLWKKYKQRRTKLLREEIVRKYMYLVKYVA-GRVAIGLPSNVEFNDLVSYGLLGLF 61

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQE 115
            A++K+D  +G +  TY++  I+ A+ +
Sbjct: 62  DAIEKYDVMQGNKFETYAVSRIRGAIMD 89


>gi|266623350|ref|ZP_06116285.1| RNA polymerase sigma factor WhiG [Clostridium hathewayi DSM 13479]
 gi|288864870|gb|EFC97168.1| RNA polymerase sigma factor WhiG [Clostridium hathewayi DSM 13479]
          Length = 131

 Score = 38.5 bits (88), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 20/80 (25%), Positives = 41/80 (51%), Gaps = 3/80 (3%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE---VVSEGNIGLMQAVKKFDPER 97
           Y ++G     ++L+   L +V   A   RG     +E   ++ +G + LM+ + ++D  +
Sbjct: 18  YLKNGSQELRNKLIVHFLPIVRSAAAQLRGMAGSFTEEEDLIDQGVLALMECLDRYDASK 77

Query: 98  GFRLATYSMWWIKAAMQEYI 117
           G +  TY+   ++ AM +YI
Sbjct: 78  GAQFETYAFIRVRGAMIDYI 97


>gi|23097664|ref|NP_691130.1| positive control sigma-like factor [Oceanobacillus iheyensis
           HTE831]
 gi|22775887|dbj|BAC12165.1| sigma factor-like positive control facor [Oceanobacillus iheyensis
           HTE831]
          Length = 170

 Score = 38.5 bits (88), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 29/86 (33%), Positives = 45/86 (52%), Gaps = 5/86 (5%)

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERK---NRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
           S +Q  ++YD D    + IE  ERK   N + M+T  + VL+PRER+ +     Q    +
Sbjct: 76  SAYQRRVIYDMDLLPSLEIEPTERKLTENEKVMITEILLVLSPRERQCYLLHMAQ--GWS 133

Query: 255 LENLSSEFEVSRERVRQIEARAFKKV 280
           +  +S E  + +  V+Q   RA KKV
Sbjct: 134 MGEISEELNIGKSSVQQFIQRAKKKV 159


>gi|114562377|ref|YP_749890.1| flagellar biosynthesis sigma factor [Shewanella frigidimarina NCIMB
           400]
 gi|114333670|gb|ABI71052.1| RNA polymerase, sigma 28 subunit [Shewanella frigidimarina NCIMB
           400]
          Length = 239

 Score = 38.5 bits (88), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 49/212 (23%), Positives = 97/212 (45%), Gaps = 19/212 (8%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR-SWSLVKIGTTANQK 133
           + +++  G +GL++A  KFD  +G +  T++   I+ AM + I R  W  V      N +
Sbjct: 41  LDDLLQAGMMGLLEASSKFDNSKGAKFETFAGIRIRGAMIDEIRRGDW--VPRSVHRNNR 98

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            +   +  L G L     N+ +      IA+KL++S  E       +  D S+  +I   
Sbjct: 99  LVAHAIDEL-GQLLGRDANDTE------IAEKLDMSLDEY----HHILNDVSVGKIIGIE 147

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D   S  QD L+ D++  ++      E +  ++ L  ++  L  R+  +       +  +
Sbjct: 148 DLGVS--QDVLITDNESPDETFDSLAEIQ-FQSALVEAIKTLPERDALVLSL--YYDEAL 202

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            L+ + +  EVS  RV QI ++A  +++  ++
Sbjct: 203 NLKEIGAILEVSESRVSQILSQAMLRLKAKLK 234


>gi|33322905|gb|AAQ07189.1|AF496497_1 RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           lactis]
          Length = 167

 Score = 38.5 bits (88), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 23/58 (39%), Positives = 34/58 (58%), Gaps = 2/58 (3%)

Query: 225 RNMLTRSMSVLNPRERRIFEAR-RLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           ++ L   +  L  RE  +   R  L + NP TLE +   F V+RER+RQIEA+A +K+
Sbjct: 96  KDQLAEVLDTLTDREENVLRLRFGLDDGNPRTLEEVGRVFGVTRERIRQIEAKALRKL 153


>gi|315108409|gb|EFT80385.1| sigma-70, region 4 [Propionibacterium acnes HL030PA2]
          Length = 270

 Score = 38.5 bits (88), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 15/49 (30%), Positives = 30/49 (61%)

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           Y   + +++  G IGL +A++++D  RG R +T +  WI+  + E ++R
Sbjct: 83  YRCSVEDLIQAGCIGLGEAIERYDVRRGARFSTVAWTWIRRRIGEEVVR 131


>gi|85859095|ref|YP_461297.1| putative cytoplasmic protein [Syntrophus aciditrophicus SB]
 gi|85722186|gb|ABC77129.1| hypothetical cytosolic protein [Syntrophus aciditrophicus SB]
          Length = 94

 Score = 38.5 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 17/35 (48%), Positives = 24/35 (68%)

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           P TLE +     V+RER+RQIEA+A KK+Q   ++
Sbjct: 44  PFTLEEVGDMMGVTRERIRQIEAKALKKLQHKKRR 78


>gi|332096706|gb|EGJ01697.1| RNA polymerase sigma factor for flagellar operon [Shigella boydii
           3594-74]
          Length = 229

 Score = 38.5 bits (88), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 51/238 (21%), Positives = 107/238 (44%), Gaps = 37/238 (15%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRL V++        + + +++  G IGL+ AV+++D  +G    TY++  I+ AM +  
Sbjct: 19  LRLQVRLPAS-----VELDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDE- 72

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           LRS   V      N + +   + +L+   Q +  N  + E    +A++L +  ++   M 
Sbjct: 73  LRSRDWVPRSVRRNAREVAQAIGQLE---QELGRNATETE----VAERLGIDIADYRQM- 124

Query: 178 CRLAGDESLNALINSSDKNSSQWQDW---------LVYDHDGQEQVLIEKEERKNRRNML 228
                      L+++++     + +W         LV D D Q +  +++    N R  +
Sbjct: 125 -----------LLDTNNSQLFSYDEWREEHGDSIELVTD-DHQRENPLQQLLDSNLRQRV 172

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             ++  L  RE+ +      +E  + L+ + +  EV   RV Q+ ++A K++   + K
Sbjct: 173 MEAIETLPEREKLVLTLYYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRLSTKLGK 228


>gi|50842442|ref|YP_055669.1| RNA polymerase sigma factor [Propionibacterium acnes KPA171202]
 gi|50840044|gb|AAT82711.1| RNA polymerase sigma factor [Propionibacterium acnes KPA171202]
 gi|315105463|gb|EFT77439.1| sigma-70, region 4 [Propionibacterium acnes HL030PA1]
          Length = 270

 Score = 38.5 bits (88), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 15/49 (30%), Positives = 30/49 (61%)

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           Y   + +++  G IGL +A++++D  RG R +T +  WI+  + E ++R
Sbjct: 83  YRCSVEDLIQAGCIGLGEAIERYDVRRGARFSTVAWTWIRRRIGEEVVR 131


>gi|222833283|gb|EEE71760.1| predicted protein [Populus trichocarpa]
          Length = 152

 Score = 38.5 bits (88), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 27/77 (35%), Positives = 39/77 (50%), Gaps = 6/77 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPE 96
           Y   G L  A  +V SH  LV +IA+      LP    I +++  G IGL+ A K+++  
Sbjct: 2   YTIQGKLEQAD-VVKSHAPLVRRIALQLAAK-LPASVQIDDLIQAGMIGLLDAAKRYEDN 59

Query: 97  RGFRLATYSMWWIKAAM 113
            G R  TY+   I+ AM
Sbjct: 60  HGARFETYASQRIRGAM 76


>gi|188592109|ref|YP_001796707.1| RNA polymerase sigma factor for flagellar operon; sigma-70 factor
           family; sigma-f factor; sigma-27; sigma-28 [Cupriavidus
           taiwanensis LMG 19424]
 gi|170938483|emb|CAP63470.1| RNA polymerase sigma factor for flagellar operon; sigma-70 factor
           family; Sigma-F factor; Sigma-27; Sigma-28 [Cupriavidus
           taiwanensis LMG 19424]
          Length = 238

 Score = 38.5 bits (88), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 26/77 (33%), Positives = 39/77 (50%), Gaps = 6/77 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPE 96
           Y   G L  A  +V +H  LV +IA+      LP    I +++  G IGL+ A K+++  
Sbjct: 2   YTIQGKLEQAD-VVKAHAPLVRRIALQLAAR-LPASVQIDDLIQAGMIGLLDAAKRYEDT 59

Query: 97  RGFRLATYSMWWIKAAM 113
            G R  TY+   I+ AM
Sbjct: 60  HGARFETYASQRIRGAM 76


>gi|314918186|gb|EFS82017.1| sigma-70, region 4 [Propionibacterium acnes HL050PA1]
          Length = 270

 Score = 38.5 bits (88), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 15/49 (30%), Positives = 30/49 (61%)

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           Y   + +++  G IGL +A++++D  RG R +T +  WI+  + E ++R
Sbjct: 83  YRCSVEDLIQAGCIGLGEAIERYDVRRGARFSTVAWTWIRRRIGEEVVR 131


>gi|289425371|ref|ZP_06427148.1| sigma-70, region 4 [Propionibacterium acnes SK187]
 gi|289427143|ref|ZP_06428859.1| sigma-70, region 4 [Propionibacterium acnes J165]
 gi|295130519|ref|YP_003581182.1| sigma-70, region 4 [Propionibacterium acnes SK137]
 gi|289154349|gb|EFD03037.1| sigma-70, region 4 [Propionibacterium acnes SK187]
 gi|289159612|gb|EFD07800.1| sigma-70, region 4 [Propionibacterium acnes J165]
 gi|291375175|gb|ADD99029.1| sigma-70, region 4 [Propionibacterium acnes SK137]
 gi|313764535|gb|EFS35899.1| sigma-70, region 4 [Propionibacterium acnes HL013PA1]
 gi|313772426|gb|EFS38392.1| sigma-70, region 4 [Propionibacterium acnes HL074PA1]
 gi|313792224|gb|EFS40325.1| sigma-70, region 4 [Propionibacterium acnes HL110PA1]
 gi|313801827|gb|EFS43061.1| sigma-70, region 4 [Propionibacterium acnes HL110PA2]
 gi|313807437|gb|EFS45924.1| sigma-70, region 4 [Propionibacterium acnes HL087PA2]
 gi|313809944|gb|EFS47665.1| sigma-70, region 4 [Propionibacterium acnes HL083PA1]
 gi|313813018|gb|EFS50732.1| sigma-70, region 4 [Propionibacterium acnes HL025PA1]
 gi|313816077|gb|EFS53791.1| sigma-70, region 4 [Propionibacterium acnes HL059PA1]
 gi|313818482|gb|EFS56196.1| sigma-70, region 4 [Propionibacterium acnes HL046PA2]
 gi|313825126|gb|EFS62840.1| sigma-70, region 4 [Propionibacterium acnes HL063PA1]
 gi|313827695|gb|EFS65409.1| sigma-70, region 4 [Propionibacterium acnes HL063PA2]
 gi|313830275|gb|EFS67989.1| sigma-70, region 4 [Propionibacterium acnes HL007PA1]
 gi|313834076|gb|EFS71790.1| sigma-70, region 4 [Propionibacterium acnes HL056PA1]
 gi|313838653|gb|EFS76367.1| sigma-70, region 4 [Propionibacterium acnes HL086PA1]
 gi|314915531|gb|EFS79362.1| sigma-70, region 4 [Propionibacterium acnes HL005PA4]
 gi|314920001|gb|EFS83832.1| sigma-70, region 4 [Propionibacterium acnes HL050PA3]
 gi|314932014|gb|EFS95845.1| sigma-70, region 4 [Propionibacterium acnes HL067PA1]
 gi|314955884|gb|EFT00284.1| sigma-70, region 4 [Propionibacterium acnes HL027PA1]
 gi|314958197|gb|EFT02300.1| sigma-70, region 4 [Propionibacterium acnes HL002PA1]
 gi|314960081|gb|EFT04183.1| sigma-70, region 4 [Propionibacterium acnes HL002PA2]
 gi|314962882|gb|EFT06982.1| sigma-70, region 4 [Propionibacterium acnes HL082PA1]
 gi|314967752|gb|EFT11851.1| sigma-70, region 4 [Propionibacterium acnes HL037PA1]
 gi|314973281|gb|EFT17377.1| sigma-70, region 4 [Propionibacterium acnes HL053PA1]
 gi|314975956|gb|EFT20051.1| sigma-70, region 4 [Propionibacterium acnes HL045PA1]
 gi|314978286|gb|EFT22380.1| sigma-70, region 4 [Propionibacterium acnes HL072PA2]
 gi|314984025|gb|EFT28117.1| sigma-70, region 4 [Propionibacterium acnes HL005PA1]
 gi|314988208|gb|EFT32299.1| sigma-70, region 4 [Propionibacterium acnes HL005PA2]
 gi|314990010|gb|EFT34101.1| sigma-70, region 4 [Propionibacterium acnes HL005PA3]
 gi|315078096|gb|EFT50147.1| sigma-70, region 4 [Propionibacterium acnes HL053PA2]
 gi|315080726|gb|EFT52702.1| sigma-70, region 4 [Propionibacterium acnes HL078PA1]
 gi|315084397|gb|EFT56373.1| sigma-70, region 4 [Propionibacterium acnes HL027PA2]
 gi|315085736|gb|EFT57712.1| sigma-70, region 4 [Propionibacterium acnes HL002PA3]
 gi|315088845|gb|EFT60821.1| sigma-70, region 4 [Propionibacterium acnes HL072PA1]
 gi|315096194|gb|EFT68170.1| sigma-70, region 4 [Propionibacterium acnes HL038PA1]
 gi|315098455|gb|EFT70431.1| sigma-70, region 4 [Propionibacterium acnes HL059PA2]
 gi|327326110|gb|EGE67900.1| RNA polymerase sigma factor [Propionibacterium acnes HL096PA2]
 gi|327332019|gb|EGE73756.1| RNA polymerase sigma factor [Propionibacterium acnes HL096PA3]
 gi|327443222|gb|EGE89876.1| sigma-70, region 4 [Propionibacterium acnes HL013PA2]
 gi|327446006|gb|EGE92660.1| sigma-70, region 4 [Propionibacterium acnes HL043PA2]
 gi|327448014|gb|EGE94668.1| sigma-70, region 4 [Propionibacterium acnes HL043PA1]
 gi|327450862|gb|EGE97516.1| sigma-70, region 4 [Propionibacterium acnes HL087PA3]
 gi|327453061|gb|EGE99715.1| sigma-70, region 4 [Propionibacterium acnes HL092PA1]
 gi|327453790|gb|EGF00445.1| sigma-70, region 4 [Propionibacterium acnes HL083PA2]
 gi|328753549|gb|EGF67165.1| sigma-70, region 4 [Propionibacterium acnes HL020PA1]
 gi|328754281|gb|EGF67897.1| sigma-70, region 4 [Propionibacterium acnes HL087PA1]
 gi|328754466|gb|EGF68082.1| sigma-70, region 4 [Propionibacterium acnes HL025PA2]
 gi|328760671|gb|EGF74238.1| RNA polymerase sigma factor [Propionibacterium acnes HL099PA1]
          Length = 270

 Score = 38.5 bits (88), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 15/49 (30%), Positives = 30/49 (61%)

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           Y   + +++  G IGL +A++++D  RG R +T +  WI+  + E ++R
Sbjct: 83  YRCSVEDLIQAGCIGLGEAIERYDVRRGARFSTVAWTWIRRRIGEEVVR 131


>gi|300864899|ref|ZP_07109744.1| RNA polymerase sigma factor SigF [Oscillatoria sp. PCC 6506]
 gi|300337103|emb|CBN54894.1| RNA polymerase sigma factor SigF [Oscillatoria sp. PCC 6506]
          Length = 292

 Score = 38.5 bits (88), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 28/126 (22%), Positives = 61/126 (48%), Gaps = 21/126 (16%)

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY---------ILRSWSLVKIGTTANQ 132
           G+IGL++A+++FD  +G   +++++ +I+  +Q Y         + R W  ++  +++  
Sbjct: 99  GSIGLIRAIERFDMSKGNAFSSFAIPYIRGEIQHYLRDKSPSVRVPRHWLTLERQSSSIV 158

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
           K L   L R    ++            VA A  ++V E + I + CR     SL+A +  
Sbjct: 159 KDLQVRLNRHPTDIE------------VATALNISVGEWQEIKLACRNRSPLSLDAPLQD 206

Query: 193 SDKNSS 198
            ++ ++
Sbjct: 207 EEEGAT 212


>gi|269103161|ref|ZP_06155858.1| RNA polymerase sigma factor for flagellar operon [Photobacterium
           damselae subsp. damselae CIP 102761]
 gi|268163059|gb|EEZ41555.1| RNA polymerase sigma factor for flagellar operon [Photobacterium
           damselae subsp. damselae CIP 102761]
          Length = 240

 Score = 38.5 bits (88), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 51/238 (21%), Positives = 104/238 (43%), Gaps = 23/238 (9%)

Query: 53  LVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            +  H  LV +IA   M      + I +++  G IGL++A + +DP +G    T++   I
Sbjct: 17  FIARHSSLVKRIAHHLMARLPPNILIEDLIQAGMIGLLEAQQNYDPTKGASFETFAGIRI 76

Query: 110 KAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           + AM + I R  W  V      N +R+   + +L+  L    +++   E +    ++ + 
Sbjct: 77  RGAMLDDIRRGDW--VPRSVYKNSRRISEAMAQLEHELGRDPNDHEVAEHLEMSLEQYHQ 134

Query: 169 SESEVISMNC-RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + ++V   NC RL G + L              +D +  D   +E +  +     + R  
Sbjct: 135 ALNDV---NCGRLVGIDDLGI-----------SEDAVANDELLEENLPFQGVVDDSFRQA 180

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L  ++  L  RE  +      +E  + L+ + +   VS  R+ QI  +A ++++  ++
Sbjct: 181 LAEAIKTLPEREALVLSLYYDEE--LNLKEIGAVIGVSESRICQIHTQAMQRLKAKLK 236


>gi|260437950|ref|ZP_05791766.1| RNA polymerase sigma-H factor [Butyrivibrio crossotus DSM 2876]
 gi|292809701|gb|EFF68906.1| RNA polymerase sigma-H factor [Butyrivibrio crossotus DSM 2876]
          Length = 205

 Score = 38.5 bits (88), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 23/87 (26%), Positives = 44/87 (50%), Gaps = 2/87 (2%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E ++AK +   GD  AA  L+  +  LV K    Y   G    +++ EG +GL +A++ 
Sbjct: 12  DEELVAKYH--SGDEKAADYLIEKYKNLVRKNVRSYYLAGADNEDLLQEGMLGLFKAIRD 69

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILR 119
           ++P+R     T++   +   ++  I R
Sbjct: 70  YNPDRDALFMTFASLCVSRHIRSTITR 96


>gi|302531661|ref|ZP_07284003.1| RNA polymerase sigma-B factor [Streptomyces sp. AA4]
 gi|302440556|gb|EFL12372.1| RNA polymerase sigma-B factor [Streptomyces sp. AA4]
          Length = 258

 Score = 38.5 bits (88), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  HL L   +A  +R     + ++V    +GL+ AV ++DP +G     +++  I   
Sbjct: 37  LVREHLELARNLARKFRNRDEAMDDLVQIATVGLIHAVDRYDPTQGTDFLAFAVPTISGE 96

Query: 113 MQEYIL-RSWSL 123
           ++ +    SWS+
Sbjct: 97  LRHHFRDNSWSV 108


>gi|259908158|ref|YP_002648514.1| flagellar biosynthesis sigma factor [Erwinia pyrifoliae Ep1/96]
 gi|224963780|emb|CAX55281.1| RNA polymerase sigma factor for flagellar operon [Erwinia
           pyrifoliae Ep1/96]
 gi|283478078|emb|CAY73994.1| RNA polymerase sigma factor FliA/RpoD [Erwinia pyrifoliae DSM
           12163]
 gi|310767931|gb|ADP12881.1| flagellar biosynthesis sigma factor [Erwinia sp. Ejp617]
          Length = 240

 Score = 38.5 bits (88), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 47/220 (21%), Positives = 92/220 (41%), Gaps = 42/220 (19%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTANQK 133
           + +++  G IGL+ AV+++D  +G    TY++  I+ AM  E   R W+          +
Sbjct: 41  LDDLLQAGGIGLLNAVERYDAMQGTAFTTYAVQRIRGAMLDELRSRDWA---------PR 91

Query: 134 RLFFNLRRLKGHLQAITD--NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
            +  N R + G +  +         EQ VA    + + E   I +               
Sbjct: 92  SVRRNAREVAGAMHQVEQALGRTATEQEVAAQLDVPLEEYRQILL--------------- 136

Query: 192 SSDKNSSQWQDWLVY--DHDGQEQVLIEKEERKNR---------RNMLTRSMSVLNPRER 240
             D N+SQ   +  Y  +H    +++ E  E++N          R+ +  ++  L  RE+
Sbjct: 137 --DTNNSQLFSFDEYREEHGDSAELVTEGHEQENPLHQLLEGDLRDRVIEAIDGLPEREK 194

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            +      +E  + L+ + +  EV   RV Q+ ++A K++
Sbjct: 195 MVLTLYYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRL 232


>gi|254506869|ref|ZP_05119008.1| flagellar biosynthesis sigma factor FliA [Vibrio parahaemolyticus
           16]
 gi|219550154|gb|EED27140.1| flagellar biosynthesis sigma factor FliA [Vibrio parahaemolyticus
           16]
          Length = 220

 Score = 38.1 bits (87), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 49/213 (23%), Positives = 89/213 (41%), Gaps = 28/213 (13%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS-WSLVKIGTTANQK 133
           + +++  G IGL++A K +D  +G    TY+   I+ AM + I R  W  V      + +
Sbjct: 20  VEDLIQAGMIGLLEAQKNYDGTKGASFETYAGIRIRGAMLDDIRRGDW--VPRSVHKHSR 77

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS----ESEVISMNC-RLAGDESLNA 188
            +   +  L+G L      N  P     +A+ L +S     + +  +NC RL G E L  
Sbjct: 78  EISQAISVLEGEL------NRDPTD-AEVAQHLGLSLTQYHTALTDINCSRLVGIEDLGV 130

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
                       +D +  D D +     +    +  R  L  S+  L  RE  +      
Sbjct: 131 -----------SEDVITPDGDEEANTPFQGVADEYFRKALIDSIKSLPEREALVLSLYYD 179

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +E  + L+ +     VS  RV QI +++ ++++
Sbjct: 180 EE--LNLKEIGDVIGVSESRVSQILSQSMQRLR 210


>gi|327330175|gb|EGE71924.1| RNA polymerase sigma factor [Propionibacterium acnes HL097PA1]
          Length = 270

 Score = 38.1 bits (87), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 15/49 (30%), Positives = 30/49 (61%)

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           Y   + +++  G IGL +A++++D  RG R +T +  WI+  + E ++R
Sbjct: 83  YRCSVEDLIQAGCIGLGEAIERYDVRRGARFSTVAWTWIRRRIGEEVVR 131


>gi|312879625|ref|ZP_07739425.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Aminomonas
           paucivorans DSM 12260]
 gi|310782916|gb|EFQ23314.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Aminomonas
           paucivorans DSM 12260]
          Length = 210

 Score = 38.1 bits (87), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 31/92 (33%), Positives = 48/92 (52%), Gaps = 3/92 (3%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR-GYGLPISEVVSEGNIGLM 87
           LE +EE  L  R  + GD  A  RL+ ++  LV  +A  +R  YG    ++V EG + L+
Sbjct: 27  LEPEEEERLWSRCCQ-GDEEARERLILAYRPLVFWLAKRFRVPYGT-YPDLVQEGMLALI 84

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
            AV  FD  R  R  TY+ + ++  M  ++ R
Sbjct: 85  FAVDHFDALRKNRFITYAYYRVRGRMINFLQR 116


>gi|319649539|ref|ZP_08003695.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
 gi|317398701|gb|EFV79383.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
          Length = 251

 Score = 38.1 bits (87), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 55/221 (24%), Positives = 99/221 (44%), Gaps = 30/221 (13%)

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++ S G +GL  A++KFDP R  +  TY+ + I+ A+ +  LR    +   T    K++
Sbjct: 53  DDIRSLGLMGLYDALEKFDPARDLKFDTYASFRIRGAILDG-LRKEDWLPRSTRDKAKKI 111

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS-MNCRLAGDESLNALINSSD 194
              + +L+  L       ++   V  IA++  + E EV S MN      E   A I S D
Sbjct: 112 DAAIEKLEQRL-------MRNATVHEIAEEAEMQEDEVYSVMN------EHFYANILSID 158

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKE---ERKNRRNMLTRSMS----VLNPRERRIFEARR 247
           +           + DG   +  EK    E K  +N L   M+     LN +E+ +     
Sbjct: 159 EQPD------ADEKDGSYSIKDEKAIIPEEKVLKNELLEEMAEKILQLNEKEQMVLSLFY 212

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +E  +TL  +     +S  R+ QI +++  K+++ ++K +
Sbjct: 213 KEE--LTLTEIGEVMGLSTSRISQIHSKSIFKLRQLLEKAI 251


>gi|323499559|ref|ZP_08104529.1| flagellar biosynthesis sigma factor [Vibrio sinaloensis DSM 21326]
 gi|323315432|gb|EGA68473.1| flagellar biosynthesis sigma factor [Vibrio sinaloensis DSM 21326]
          Length = 244

 Score = 38.1 bits (87), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 57/252 (22%), Positives = 104/252 (41%), Gaps = 31/252 (12%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFD 94
           A  Y ++ + ++    +  +  LV +IA    G   P   + +++  G IGL++A K +D
Sbjct: 4   ALTYDQYANQNSQRAFLEKYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLLEAQKNYD 63

Query: 95  PERGFRLATYSMWWIKAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
             +G    TY+   I+ AM + I R  W  V      + + +   +  L+G L      N
Sbjct: 64  GSKGASFETYAGIRIRGAMLDDIRRGDW--VPRSVHKHNREISQAISVLEGEL------N 115

Query: 154 LKPEQVVAIAKKLNVS----ESEVISMNC-RLAGDESLNALINSSDKNSSQWQDWLVYDH 208
             P     +A+ L +S     S +  +NC RL G E L              +D +  + 
Sbjct: 116 RDPTD-AEVAQHLGMSLAQYHSALADINCSRLVGIEDLGV-----------SEDVISPED 163

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D +     +    +  R  L  S+  L  RE  +      +E  + L+ +     VS  R
Sbjct: 164 DDEANTPFQGVADEYFRKALVDSIKALPEREALVLSLYYDEE--LNLKEIGDVIGVSESR 221

Query: 269 VRQIEARAFKKV 280
           V QI +++ +++
Sbjct: 222 VSQILSQSMQRL 233


>gi|189916711|gb|ACE62866.1| RNA polymerase sigma 70 factor [Xylella fastidiosa]
 gi|189916713|gb|ACE62867.1| RNA polymerase sigma 70 factor [Xylella fastidiosa]
 gi|189916715|gb|ACE62868.1| RNA polymerase sigma 70 factor [Xylella fastidiosa]
          Length = 161

 Score = 38.1 bits (87), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 21/52 (40%), Positives = 35/52 (67%), Gaps = 2/52 (3%)

Query: 232 MSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 95  LAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 146


>gi|313837242|gb|EFS74956.1| sigma-70, region 4 [Propionibacterium acnes HL037PA2]
 gi|314927738|gb|EFS91569.1| sigma-70, region 4 [Propionibacterium acnes HL044PA1]
 gi|314972014|gb|EFT16112.1| sigma-70, region 4 [Propionibacterium acnes HL037PA3]
 gi|328907208|gb|EGG26974.1| sigma-70, region 4 [Propionibacterium sp. P08]
          Length = 270

 Score = 38.1 bits (87), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 14/49 (28%), Positives = 30/49 (61%)

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           Y   + +++  G +GL +A++++D  RG R +T +  WI+  + E ++R
Sbjct: 83  YRCSVEDLIQSGCVGLGEAIERYDERRGARFSTVAWTWIRRRIGEEVVR 131


>gi|160946612|ref|ZP_02093815.1| hypothetical protein PEPMIC_00570 [Parvimonas micra ATCC 33270]
 gi|158446996|gb|EDP23991.1| hypothetical protein PEPMIC_00570 [Parvimonas micra ATCC 33270]
          Length = 254

 Score = 38.1 bits (87), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 51/254 (20%), Positives = 116/254 (45%), Gaps = 23/254 (9%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L + Y E+       +L+  +L +   +A  Y   G+   ++    ++GL+ A+ ++D  
Sbjct: 16  LFREYFENPTPELRDKLIEKNLYMAEILAKKYVNRGIDYDDLFQVASLGLIYAIDRYDIS 75

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLF---FNLRRLKGHLQAITD 151
           +GF  ++++M  I   ++ Y      ++++      N K++    ++L +  G    I D
Sbjct: 76  KGFEFSSFAMPTIVGEIKRYFRDKGWVIRVPRRIQENSKKVNNAKYHLTQELGRTPTIKD 135

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
                   +A   +L+  E   I    ++   +SL+    +SD   S+ +D  + D  G+
Sbjct: 136 --------IADYVELSEEEVLEIMEASKVYTPQSLDQSFENSD---SEDKDTNLIDIVGE 184

Query: 212 EQVLIEKE-ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
           E    +KE +  + ++ + +++  L   E++I   R  ++   T   L+ E  +S+  V 
Sbjct: 185 E----DKEFDFIDNQDFIRKTLDKLTEVEKQIILGRYFEQK--TQVALAKELNISQMTVS 238

Query: 271 QIEARAFKKVQESI 284
           ++E +A  K +E +
Sbjct: 239 RLEKKALAKFREEL 252


>gi|167768028|ref|ZP_02440081.1| hypothetical protein CLOSS21_02571 [Clostridium sp. SS2/1]
 gi|317498378|ref|ZP_07956673.1| sigma-70 region 2 [Lachnospiraceae bacterium 5_1_63FAA]
 gi|167710357|gb|EDS20936.1| hypothetical protein CLOSS21_02571 [Clostridium sp. SS2/1]
 gi|291561028|emb|CBL39828.1| Sigma-70 region 3./Sigma-70 region 2 [butyrate-producing bacterium
           SSC/2]
 gi|316894272|gb|EFV16459.1| sigma-70 region 2 [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 256

 Score = 38.1 bits (87), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 40/151 (26%), Positives = 79/151 (52%), Gaps = 15/151 (9%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P  E+Q+E + A    E GD  A   ++ S L  +++IA  + G G+   ++V EGNIG
Sbjct: 97  LPGEEEQKELIHA-WLVEKGDGEA---VIESFLPQILEIARTHTGKGVLFGDLVQEGNIG 152

Query: 86  LMQAVKKF---DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
           L++A+  +   D E GF      +   K+A+++ IL + ++ + G+ +  + +     RL
Sbjct: 153 LLEAMAIYQGKDAE-GF------LAHAKSAVEDSILDAIAIQR-GSDSVGEAMAIKANRL 204

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
                 ++    +  ++  +AK L+++E EV
Sbjct: 205 DDASTFLSKELGREPKIEELAKYLSMTEEEV 235


>gi|312140062|ref|YP_004007398.1| sigma-70 factor [Rhodococcus equi 103S]
 gi|311889401|emb|CBH48717.1| sigma-70 factor [Rhodococcus equi 103S]
          Length = 289

 Score = 38.1 bits (87), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 20/72 (27%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RL  + L +  ++A  YR  G+P +E+     + L+ A ++FDP RG     Y++  ++ 
Sbjct: 66  RLCVAALPMAYRVAGRYRNRGVPTAELRQVAALALVGAARRFDPSRGTDFIPYAVTSVRG 125

Query: 112 AMQEYILR-SWS 122
            +++Y    +WS
Sbjct: 126 EIRKYFRDFTWS 137


>gi|189916709|gb|ACE62865.1| RNA polymerase sigma 70 factor [Xylella fastidiosa]
          Length = 161

 Score = 38.1 bits (87), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 21/52 (40%), Positives = 35/52 (67%), Gaps = 2/52 (3%)

Query: 232 MSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 95  LAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 146


>gi|159795060|pdb|2P7V|B Chain B, Crystal Structure Of The Escherichia Coli Regulator Of
           Sigma 70, Rsd, In Complex With Sigma 70 Domain 4
          Length = 68

 Score = 38.1 bits (87), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 16/35 (45%), Positives = 27/35 (77%)

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           TLE +  +F+V+RER+RQIEA+A +K++   + +V
Sbjct: 27  TLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 61


>gi|266621294|ref|ZP_06114229.1| DNA-directed RNA polymerase sigma subunit [Clostridium hathewayi
          DSM 13479]
 gi|288867054|gb|EFC99352.1| DNA-directed RNA polymerase sigma subunit [Clostridium hathewayi
          DSM 13479]
          Length = 188

 Score = 38.1 bits (87), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 18/54 (33%), Positives = 31/54 (57%)

Query: 45 GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
          G+  A  RL+  +L   +K A  Y G G+ ++++V+E N+ L  AV +F  + G
Sbjct: 25 GNEGAKKRLIEGNLEAALKCAKEYDGKGVLLTDLVAEANMALTMAVTEFLTDAG 78


>gi|119718035|ref|YP_925000.1| sigma-70 region 2 domain-containing protein [Nocardioides sp.
           JS614]
 gi|119538696|gb|ABL83313.1| sigma-70 region 2 domain protein [Nocardioides sp. JS614]
          Length = 257

 Score = 38.1 bits (87), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 16/65 (24%), Positives = 36/65 (55%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  ++ + V     +RG G+   ++     +GL++AVK FDP+RG    ++++  I+  
Sbjct: 35  LIRLNMAVAVDATRRFRGRGIATDDLEQVAYVGLVKAVKGFDPDRGHDFLSFAIPTIRGE 94

Query: 113 MQEYI 117
           ++ + 
Sbjct: 95  VRRHF 99


>gi|188997568|ref|YP_001931819.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Sulfurihydrogenibium
           sp. YO3AOP1]
 gi|188932635|gb|ACD67265.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Sulfurihydrogenibium
           sp. YO3AOP1]
          Length = 242

 Score = 38.1 bits (87), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 48/214 (22%), Positives = 102/214 (47%), Gaps = 25/214 (11%)

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           G +GL  A++KFDP +G + +TY+   ++  + ++ LR    +      N +    NL  
Sbjct: 44  GVLGLYDALEKFDPAKGVKFSTYAEIRVRGYILDH-LRQLDWI----PRNIRNKVKNLEN 98

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
               L+       KPE+   IA+ L +S  E +     +  ++++N ++ S D + S+  
Sbjct: 99  KIVELETKLGREAKPEE---IAEYLGMSLEEYM-----IYAEKAVNKILISLDSDVSKDD 150

Query: 202 D-----WLVY--DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
           D     W V   + D  E+ + EK+ ++   +++   M+ L+ RE+ I      ++  + 
Sbjct: 151 DESLHLWEVISTNDDTPEKYVEEKQLKEILSDII---MNKLDEREKLIVTLYYYED--LN 205

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           ++ ++     +  RV Q+  +   K+++ I+K V
Sbjct: 206 MKEIAEILGCTESRVSQLHTKIMLKIRKLIEKYV 239


>gi|14994233|gb|AAK73284.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
          Length = 144

 Score = 38.1 bits (87), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 21/52 (40%), Positives = 35/52 (67%), Gaps = 2/52 (3%)

Query: 232 MSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 78  LAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 129


>gi|292488613|ref|YP_003531497.1| RNA polymerase sigma factor FliA/RpoD [Erwinia amylovora CFBP1430]
 gi|292899773|ref|YP_003539142.1| RNA polymerase sigma factor for flagellar operon (sigma-F factor)
           [Erwinia amylovora ATCC 49946]
 gi|291199621|emb|CBJ46740.1| RNA polymerase sigma factor for flagellar operon (sigma-F factor)
           [Erwinia amylovora ATCC 49946]
 gi|291554044|emb|CBA21132.1| RNA polymerase sigma factor FliA/RpoD [Erwinia amylovora CFBP1430]
 gi|312172755|emb|CBX81011.1| RNA polymerase sigma factor FliA/RpoD [Erwinia amylovora ATCC
           BAA-2158]
          Length = 240

 Score = 38.1 bits (87), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 47/220 (21%), Positives = 92/220 (41%), Gaps = 42/220 (19%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTANQK 133
           + +++  G IGL+ AV+++D  +G    TY++  I+ AM  E   R W+          +
Sbjct: 41  LDDLLQAGGIGLLNAVERYDAMQGTAFTTYAVQRIRGAMLDELRSRDWA---------PR 91

Query: 134 RLFFNLRRLKGHLQAITD--NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
            +  N R + G +  +         EQ VA    + + E   I +               
Sbjct: 92  SVRRNAREVAGAMHQVEQALGRTATEQEVAAQLDVPLEEYRQILL--------------- 136

Query: 192 SSDKNSSQWQDWLVY--DHDGQEQVLIEKEERKNR---------RNMLTRSMSVLNPRER 240
             D N+SQ   +  Y  +H    +++ E  E++N          R+ +  ++  L  RE+
Sbjct: 137 --DTNNSQLFSFDEYREEHGDSAELVTEGHEQENPLHQLLEGDLRDRVIEAIDGLPEREK 194

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            +      +E  + L+ + +  EV   RV Q+ ++A K++
Sbjct: 195 MVLTLYYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRL 232


>gi|51596050|ref|YP_070241.1| flagellar biosynthesis sigma factor [Yersinia pseudotuberculosis IP
           32953]
 gi|153949581|ref|YP_001401249.1| flagellar biosynthesis sigma factor [Yersinia pseudotuberculosis IP
           31758]
 gi|170024605|ref|YP_001721110.1| flagellar biosynthesis sigma factor [Yersinia pseudotuberculosis
           YPIII]
 gi|186895155|ref|YP_001872267.1| flagellar biosynthesis sigma factor [Yersinia pseudotuberculosis
           PB1/+]
 gi|51589332|emb|CAH20954.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           pseudotuberculosis IP 32953]
 gi|152961076|gb|ABS48537.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           pseudotuberculosis IP 31758]
 gi|169751139|gb|ACA68657.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Yersinia
           pseudotuberculosis YPIII]
 gi|186698181|gb|ACC88810.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Yersinia
           pseudotuberculosis PB1/+]
          Length = 240

 Score = 38.1 bits (87), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 43/216 (19%), Positives = 92/216 (42%), Gaps = 34/216 (15%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTANQK 133
           + +++  G IGL+ AV+++D  +G    TY++  I+ AM  E   R W+          +
Sbjct: 41  LDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDWA---------PR 91

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            +  N R +   +Q +     +P     +A+ L++   E   +            L++++
Sbjct: 92  SVRRNAREVASAMQQVEQRVGRPATEQEVAQVLDIGLVEYRQI------------LLDTN 139

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEE---------RKNRRNMLTRSMSVLNPRERRIFE 244
           +     + +W   +H    + L+E  E           N R  +  ++  L  RE+ +  
Sbjct: 140 NSQLFSYDEWR-EEHGESVEPLLEGHEDANPLKHLLEGNLRQRVIEAIEALPEREKMVLT 198

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
               +E  + L+ + +  EV   RV Q+ ++A K++
Sbjct: 199 LYYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRL 232


>gi|325674464|ref|ZP_08154152.1| stress response/stationary phase sigma factor SigF [Rhodococcus
           equi ATCC 33707]
 gi|325554724|gb|EGD24398.1| stress response/stationary phase sigma factor SigF [Rhodococcus
           equi ATCC 33707]
          Length = 269

 Score = 38.1 bits (87), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 20/72 (27%), Positives = 39/72 (54%), Gaps = 1/72 (1%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RL  + L +  ++A  YR  G+P +E+     + L+ A ++FDP RG     Y++  ++ 
Sbjct: 46  RLCVAALPMAYRVAGRYRNRGVPTAELRQVAALALVGAARRFDPSRGTDFIPYAVTSVRG 105

Query: 112 AMQEYILR-SWS 122
            +++Y    +WS
Sbjct: 106 EIRKYFRDFTWS 117


>gi|332654157|ref|ZP_08419901.1| RNA polymerase sigma-F factor [Ruminococcaceae bacterium D16]
 gi|332517243|gb|EGJ46848.1| RNA polymerase sigma-F factor [Ruminococcaceae bacterium D16]
          Length = 239

 Score = 38.1 bits (87), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 22/83 (26%), Positives = 43/83 (51%), Gaps = 1/83 (1%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GD  A  +++  +  L+  +   Y G G+   ++   G +G ++AV+ FDP  G + +T
Sbjct: 16  EGDNRACEQVLEENNGLIWSVVRRYYGRGVEPDDLYQLGCLGFLKAVRGFDPAFGTQFST 75

Query: 104 YSMWWIKAAMQEYILRSWSLVKI 126
           Y++  I   ++ + LR    VK+
Sbjct: 76  YAVPKIAGEIRRF-LRDDGAVKV 97


>gi|189916717|gb|ACE62869.1| RNA polymerase sigma 70 factor [Xylella fastidiosa]
          Length = 161

 Score = 38.1 bits (87), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 21/52 (40%), Positives = 35/52 (67%), Gaps = 2/52 (3%)

Query: 232 MSVLNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++ L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 95  LAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 146


>gi|29833942|ref|NP_828576.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29611067|dbj|BAC75111.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 264

 Score = 38.1 bits (87), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 18/65 (27%), Positives = 35/65 (53%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           +V + L +  +IA  YRG G    ++     +GL++AV ++DP RG    +Y++  I   
Sbjct: 41  IVRAWLPMAERIAWRYRGRGESTEDLCQVAAVGLVKAVDRYDPARGNAFESYAVPTITGE 100

Query: 113 MQEYI 117
           ++ + 
Sbjct: 101 IKRHF 105


>gi|164415557|gb|ABY53195.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415559|gb|ABY53196.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415561|gb|ABY53197.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415563|gb|ABY53198.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415565|gb|ABY53199.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415567|gb|ABY53200.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415569|gb|ABY53201.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415571|gb|ABY53202.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415573|gb|ABY53203.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415575|gb|ABY53204.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415577|gb|ABY53205.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415579|gb|ABY53206.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415581|gb|ABY53207.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415583|gb|ABY53208.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415585|gb|ABY53209.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415587|gb|ABY53210.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415589|gb|ABY53211.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415591|gb|ABY53212.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415593|gb|ABY53213.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
          Length = 166

 Score = 38.1 bits (87), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 21/49 (42%), Positives = 33/49 (67%), Gaps = 2/49 (4%)

Query: 235 LNPRERRIFEAR-RLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           L PRE ++   R  +  N   TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 103 LTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLR 151


>gi|78485092|ref|YP_391017.1| sigma 28 (flagella/sporulation) [Thiomicrospira crunogena XCL-2]
 gi|78363378|gb|ABB41343.1| sigma 28 (Flagella/Sporulation) [Thiomicrospira crunogena XCL-2]
          Length = 241

 Score = 38.1 bits (87), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 26/84 (30%), Positives = 44/84 (52%), Gaps = 6/84 (7%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPERGF 99
           H   S A   + + L LV +IA   +G  LP    + +++  G IGL+++ +KFD  +G 
Sbjct: 11  HKQTSGAAINIEAFLPLVKRIAYHLKGR-LPDSVMVDDLIQSGIIGLIESSQKFDATQGA 69

Query: 100 RLATYSMWWIKAAMQEYILRS-WS 122
              TY+   I+ AM + I +  W+
Sbjct: 70  SFETYAGIRIRGAMLDEIRKGDWT 93


>gi|307327205|ref|ZP_07606393.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306887096|gb|EFN18094.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 272

 Score = 38.1 bits (87), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 32/155 (20%), Positives = 74/155 (47%), Gaps = 20/155 (12%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R+V + + +  ++A  YR  G  + ++     +GL++AVK++DPE G   A +++  I  
Sbjct: 48  RVVEAWMPMAERLARQYRNRGESLEDLEQVAALGLVKAVKRYDPEHGTAFAGFAVPTIVG 107

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLR-RLK-GHLQAITDNNLKPEQVVAIAKKLNVS 169
            ++ +      ++ +       R   +LR R++  H +     + +P +   IA++  ++
Sbjct: 108 EIKRHFRDHLWVLHV------PRRVQDLRNRVRAAHRELSHSADDRPPRTQDIAERTGLT 161

Query: 170 ESEV------------ISMNCRLAGDESLNALINS 192
           E EV            +S++ +L G +   +L ++
Sbjct: 162 EKEVRAGMEAMGSFTPLSLDAQLTGSDDGYSLADT 196


>gi|154484618|ref|ZP_02027066.1| hypothetical protein EUBVEN_02334 [Eubacterium ventriosum ATCC
           27560]
 gi|149734466|gb|EDM50383.1| hypothetical protein EUBVEN_02334 [Eubacterium ventriosum ATCC
           27560]
          Length = 237

 Score = 38.1 bits (87), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 54/235 (22%), Positives = 103/235 (43%), Gaps = 36/235 (15%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GD  A  +++  +  L+  I   +   G    ++   G IG+++A+ +FD E     +T
Sbjct: 12  QGDKLARDKILIENTGLIWSIVRRFLNRGHEGEDLFQIGCIGMLKAIDRFDTEFDVAFST 71

Query: 104 YSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV- 160
           Y++  I   ++ +I R   +VKI      NQ ++         H + I  N  K E  + 
Sbjct: 72  YAVPMIAGEIRRFI-RDDGIVKISRKIKENQMKIM--------HQREIYINEKKQEPTIE 122

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDK------NSSQWQDWLVYDHDGQEQV 214
            + K  ++++ E++     +A D S N  + S DK      ++    D    D + +E V
Sbjct: 123 ELEKVCDLTKEEIV-----MAMDASRN--VESIDKEMYSKDSAYTLMDLAEDDTNIEETV 175

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ---ENPVTLENLSSEFEVSR 266
           L         + M+ + M +L  +ER+I   R  +   ++ V  E   ++ +VSR
Sbjct: 176 L--------NKIMVQQLMDMLESKERKIINLRYFKNKTQSQVAKEMGMTQVQVSR 222


>gi|212634384|ref|YP_002310909.1| flagellar biosynthesis sigma factor [Shewanella piezotolerans WP3]
 gi|212555868|gb|ACJ28322.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4 [Shewanella
           piezotolerans WP3]
          Length = 239

 Score = 38.1 bits (87), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 47/213 (22%), Positives = 93/213 (43%), Gaps = 29/213 (13%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS-WSLVKIGTTANQK 133
           + +++  G +GL++A  KFD  +G +  T++   I+ +M + I R  W  V      NQ+
Sbjct: 41  LDDLLQAGMMGLLEASSKFDGSKGAKFETFAGIRIRGSMLDEIRRGDW--VPRSVHRNQR 98

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNA 188
           R+   +  L+   Q +  +   PE    IA++L +S  E  S+       ++ G E L  
Sbjct: 99  RVAQVIDELE---QELGRDARDPE----IAERLEMSLDEYYSILNDVSVGKVVGIEDLGV 151

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            ++            +V   D  + V  E        + L  ++ +L  R+  +      
Sbjct: 152 AVD------------VVNHEDNHDDVAYESLAEVEFHSALVAAIKLLPERDALVLSL--Y 197

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +  + L+ + +  EVS  RV QI ++A  +++
Sbjct: 198 YDEALNLKEIGAILEVSESRVSQIHSQAMLRLK 230


>gi|225871941|ref|YP_002753395.1| flagellar operon sigma factor FliA [Acidobacterium capsulatum ATCC
           51196]
 gi|225792596|gb|ACO32686.1| flagellar operon sigma factor FliA [Acidobacterium capsulatum ATCC
           51196]
          Length = 336

 Score = 38.1 bits (87), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 43/203 (21%), Positives = 89/203 (43%), Gaps = 15/203 (7%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI-LRSWSLVKIGTTANQK 133
           + ++VS G +GL+ A++KFDP +  +  +Y+ + I+ A+ + + +  WS          +
Sbjct: 105 LDDLVSAGVVGLLDAMRKFDPAKKVQFRSYAQFRIRGAILDSLRMLDWS---------PR 155

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            L    R ++  ++A+T    +  Q   +A ++ +   E   +   L G E     +  S
Sbjct: 156 ELRRKGRAVEEAIRAVTARLGRAPQESEVAGEMGLPLHEYQQLLGELKGLEIGTLHVERS 215

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           + +  +   +L  D +        K E + R   L  ++  L  RER +      +E  +
Sbjct: 216 EDSGEEELAFLPNDPEDDPLFRCLKGEMRER---LMAAIDALPERERLVMTLYYYEE--M 270

Query: 254 TLENLSSEFEVSRERVRQIEARA 276
           T++ +     V   RV Q+ + A
Sbjct: 271 TMKEIGLTLGVVESRVSQMHSSA 293


>gi|302343749|ref|YP_003808278.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfarculus baarsii DSM 2075]
 gi|301640362|gb|ADK85684.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfarculus baarsii DSM 2075]
          Length = 260

 Score = 38.1 bits (87), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 13/39 (33%), Positives = 26/39 (66%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           + +++  G +GL+ AV KFDPE+  +  TY+ + ++ A+
Sbjct: 54  MEDLIGAGVLGLIDAVDKFDPEKNVKFKTYAEFRVRGAI 92


>gi|226364233|ref|YP_002782015.1| RNA polymerase sigma factor [Rhodococcus opacus B4]
 gi|226242722|dbj|BAH53070.1| RNA polymerase sigma factor [Rhodococcus opacus B4]
          Length = 285

 Score = 38.1 bits (87), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 29/114 (25%), Positives = 52/114 (45%), Gaps = 18/114 (15%)

Query: 22  EIRKIPMLEKQEEYVLAK---RYREH-------GDLSAA--------HRLVTSHLRLVVK 63
           EIR+IP   K      ++   +YR+        G L+A+         RL+   L L   
Sbjct: 13  EIRRIPARTKPTHRTASRERDQYRDVPAQCAAIGRLAASDPRRELLRQRLIERCLPLAEH 72

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           IA  + G G P+ +++    +GL++AV +FD   G    +Y++  I   ++ + 
Sbjct: 73  IARRFLGRGEPLDDLIQVARLGLVKAVDRFDARCGASFVSYAVPTITGEVRRHF 126


>gi|169629597|ref|YP_001703246.1| RNA polymerase sigma factor SigF [Mycobacterium abscessus ATCC
           19977]
 gi|169241564|emb|CAM62592.1| Alternative sigma factor SigF [Mycobacterium abscessus]
          Length = 272

 Score = 38.1 bits (87), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 56/242 (23%), Positives = 100/242 (41%), Gaps = 33/242 (13%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           +VT  L L   +A  +   G  + +++    +GL+ AV +FDPE+G   A++  + +   
Sbjct: 53  IVTRCLPLADNVARHFDRRGEDLEDLIQVARVGLLNAVNRFDPEKG---ASFLGFAVPTM 109

Query: 113 MQE----YILRSWSL-VKIGTTANQKRLFFNLRRLKGHLQ-AITDNNLKPEQVVAIAKKL 166
           M E    +    WSL V         ++      L   LQ A T   L        A +L
Sbjct: 110 MGEVRRHFRDHGWSLHVPRAIRDRHAQISRATAELTQELQRAPTAGEL--------AAEL 161

Query: 167 NVSESEVISMNCRLAGD----ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
            +   EV+     +A D    +S+ A ++  D+ S    D L  +    E V   +  R 
Sbjct: 162 GIDREEVV--ESLIAADAYQPQSIEAPLSHGDQESKHLSDLLGNEDPALEHVTNREAVRP 219

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              N+  R  +VL   E R F+        +T   ++++  VS+  V +I +   + ++E
Sbjct: 220 LLANLPLRERTVL---ELRFFKG-------MTQSQIAAQIGVSQMHVSRILSDTLRYLRE 269

Query: 283 SI 284
            +
Sbjct: 270 QM 271


>gi|317970336|ref|ZP_07971726.1| RNA polymerase sigma factor SigF [Synechococcus sp. CB0205]
          Length = 138

 Score = 38.1 bits (87), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 19/54 (35%), Positives = 30/54 (55%), Gaps = 1/54 (1%)

Query: 52  RLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           R    HL L  + A  Y R +G+PI E++S    GL +   +FD  +G+R ++Y
Sbjct: 11  RFACQHLGLARQQAHRYARRWGIPIEELLSPAYEGLCKGAAQFDAAKGYRPSSY 64


>gi|302549049|ref|ZP_07301391.1| RNA polymerase sigma-B factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302466667|gb|EFL29760.1| RNA polymerase sigma-B factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 263

 Score = 38.1 bits (87), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 31/124 (25%), Positives = 62/124 (50%), Gaps = 10/124 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV + L +  +IA+ +RG G  + ++     +GL++AV  +DP RG     Y++  +   
Sbjct: 41  LVEAWLPMAERIAVRFRGRGEALEDLYQVAALGLVKAVDHYDPARGNAFEAYAVPTVTGE 100

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLR-RLKGHLQAITDNNLKPEQVVA-IAKKLNVS 169
           ++ +     W+L       +  R   +LR R++  ++ ++   L     VA IA+  +++
Sbjct: 101 IKRHFRDHMWTL-------HVPRRVQDLRNRVRHAVKELSQTTLGRAPTVAEIAEYAHLT 153

Query: 170 ESEV 173
           E EV
Sbjct: 154 EGEV 157


>gi|227498999|ref|ZP_03929136.1| RNA polymerase [Acidaminococcus sp. D21]
 gi|226904448|gb|EEH90366.1| RNA polymerase [Acidaminococcus sp. D21]
          Length = 232

 Score = 38.1 bits (87), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 24/68 (35%), Positives = 36/68 (52%), Gaps = 2/68 (2%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK--KF 93
           VL KR +E GD  A   L+  +  LV K    Y   G    ++V EG IGL +A++  +F
Sbjct: 14  VLLKRIQEEGDGKAQDILLARYKELVKKKTSLYYMAGAERDDIVQEGMIGLFKAIRDYRF 73

Query: 94  DPERGFRL 101
           D +  F++
Sbjct: 74  DQKASFKV 81


>gi|302670826|ref|YP_003830786.1| RNA polymerase sigma factor sigma-70 family protein [Butyrivibrio
           proteoclasticus B316]
 gi|302395299|gb|ADL34204.1| RNA polymerase sigma factor sigma-70 family [Butyrivibrio
           proteoclasticus B316]
          Length = 258

 Score = 38.1 bits (87), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 25/85 (29%), Positives = 40/85 (47%), Gaps = 11/85 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLA-KRYRE----HGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           L+ Y+  ++++P      EY    KR  E     GD  A  +L+   L LVV +A  Y  
Sbjct: 81  LNDYLESLKELP------EYTDGEKRAIEMSAISGDKEAQSKLIECFLPLVVDVARMYTE 134

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDP 95
            G+ + +++ EGN  L + V   D 
Sbjct: 135 QGVYLEDLIGEGNFALTKGVTMLDA 159


>gi|212709528|ref|ZP_03317656.1| hypothetical protein PROVALCAL_00570 [Providencia alcalifaciens DSM
           30120]
 gi|212687866|gb|EEB47394.1| hypothetical protein PROVALCAL_00570 [Providencia alcalifaciens DSM
           30120]
          Length = 242

 Score = 38.1 bits (87), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 44/220 (20%), Positives = 96/220 (43%), Gaps = 34/220 (15%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTANQK 133
           I +++  G IGL+ A+++FD   G   ATY++  I+ +M  E   R W         + +
Sbjct: 45  IDDLIQAGGIGLLHALERFDASLGASFATYAVQRIRGSMLDELRSRDW------VPRSVR 98

Query: 134 RLFFNLRRLKGHL-QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
           R    + +  G L Q++  +  +PE    IAK L++  +E                L+++
Sbjct: 99  RQAREMTKAIGELEQSLGRSATEPE----IAKALDIDLAEY------------RQVLLDT 142

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEE--------RKNRRNMLTRSMSVLNPRERRIFE 244
           ++     + +W     +  E  + E +           + ++ +  ++  L  RE+ +  
Sbjct: 143 NNSQLFSYDEWHEVHGESCEPSMDEDDGGNPLSLLMESSLKDQIVAAIEQLPEREKMVLT 202

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
               +E  + L+ + +  EV   RV Q+ ++A K+++  +
Sbjct: 203 LYYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRLRSKL 240


>gi|330721193|gb|EGG99303.1| RNA polymerase sigma factor for flagellar operon [gamma
           proteobacterium IMCC2047]
          Length = 246

 Score = 38.1 bits (87), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 51/228 (22%), Positives = 100/228 (43%), Gaps = 21/228 (9%)

Query: 53  LVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           LV  H  LV +IA   M      + ++++V  G +GL++A +KFD  +G    T++   +
Sbjct: 22  LVEQHAPLVKRIAHHLMARLPSTVQLNDLVQSGMVGLLEAAQKFDASKGASFETFAGIRV 81

Query: 110 KAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           + AM + + +  W+          + +  N RR+   ++A+     +      +A ++ +
Sbjct: 82  RGAMLDDVRKDDWA---------PRSVHRNARRVSEAIKAVEGRTGRDASDQEVAAEMGI 132

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +  +     AG       + S D+ + Q  D  +           E  +R+  ++ L
Sbjct: 133 PLEDYYAYLQDSAGTR-----LFSYDEVTEQ-DDSSILLAASATPTPHENVQRQAFKDNL 186

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
            +++  L  RER +  A   QE  + L+ + S   VS  RV QI ++A
Sbjct: 187 AQAIEALPERERMVL-ALYYQEE-LNLKEIGSVLGVSESRVSQIHSQA 232


>gi|90406802|ref|ZP_01214994.1| flagellar biosynthesis sigma factor FliA [Psychromonas sp. CNPT3]
 gi|90312039|gb|EAS40132.1| flagellar biosynthesis sigma factor FliA [Psychromonas sp. CNPT3]
          Length = 235

 Score = 38.1 bits (87), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 3/75 (4%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           R  G  +    L+  H  LV KIA   M      + + +++  G IGL++A + FD  +G
Sbjct: 3   RVQGYYTDTAELIEKHTGLVQKIAYHLMARLPASVLVDDLLQSGMIGLLEAARNFDGSKG 62

Query: 99  FRLATYSMWWIKAAM 113
               T+S   I+ AM
Sbjct: 63  ASFETFSGIRIRGAM 77


>gi|238764885|ref|ZP_04625825.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           kristensenii ATCC 33638]
 gi|238696904|gb|EEP89681.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           kristensenii ATCC 33638]
          Length = 240

 Score = 37.7 bits (86), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 46/218 (21%), Positives = 94/218 (43%), Gaps = 38/218 (17%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTANQK 133
           + +++  G IGL+ AV+++D  +G    TY++  I+ AM  E   R W+          +
Sbjct: 41  LDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDWA---------PR 91

Query: 134 RLFFNLRRLKGHLQAITDNNLKP--EQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
            +  N R +   +Q +     +P  EQ VA    ++++E   I ++             N
Sbjct: 92  SVRRNAREVASAMQKVEQRLGRPATEQEVAQILDIDLAEYRQILLDTN-----------N 140

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEE---------RKNRRNMLTRSMSVLNPRERRI 242
           S   +  +W++    +H    + ++E  E           N R  +  ++  L  RE+ +
Sbjct: 141 SQLFSYDEWRE----EHGESVEPMLEGHEDANPLQHLLEGNLRQRVIEAIEALPEREKMV 196

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                 +E  + L+ + +  EV   RV Q+ ++A K++
Sbjct: 197 LTLYYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRL 232


>gi|289809217|ref|ZP_06539846.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. AG3]
          Length = 52

 Score = 37.7 bits (86), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 23/49 (46%), Positives = 30/49 (61%), Gaps = 1/49 (2%)

Query: 226 NMLTRSMSVLNPRERRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIE 273
           N LT +M  L+ R + I  AR L E N  TL+ L+  + VS ERVRQ+E
Sbjct: 2   NRLTDAMQGLDERSQDIIRARWLDEDNKSTLQELADRYGVSAERVRQLE 50


>gi|119491111|ref|ZP_01623269.1| Sigma 32 (RpoH) [Lyngbya sp. PCC 8106]
 gi|119453656|gb|EAW34816.1| Sigma 32 (RpoH) [Lyngbya sp. PCC 8106]
          Length = 304

 Score = 37.7 bits (86), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 35/134 (26%), Positives = 66/134 (49%), Gaps = 15/134 (11%)

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ-----KRLF 136
           G IGL+QA+++FD  +G   +++++ +I+  +  Y+     L+++    +Q      +L 
Sbjct: 105 GCIGLIQAIERFDLTKGCAFSSFAVPYIRGEILHYLRDKSLLIRVPRRCSQLKQEAAKLV 164

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAK----KLNVSESEVISMNCRLAGD----ESLNA 188
             L+  K H +  TD  +     ++I K    KL V  S V+S++  L  +      L  
Sbjct: 165 ILLQE-KLHRKP-TDLEIANSLGISIEKWNQVKLTVKNSSVLSLDIPLNDEFNEKHCLGE 222

Query: 189 LINSSDKNSSQWQD 202
           LI  S+ N+S  Q+
Sbjct: 223 LIVDSNPNASMSQE 236


>gi|213028661|ref|ZP_03343108.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. 404ty]
          Length = 88

 Score = 37.7 bits (86), Expect = 1.9,   Method: Composition-based stats.
 Identities = 16/35 (45%), Positives = 27/35 (77%)

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           TLE +  +F+V+RER+RQIEA+A +K++   + +V
Sbjct: 47  TLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 81


>gi|289578405|ref|YP_003477032.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter italicus Ab9]
 gi|297544681|ref|YP_003676983.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
 gi|289528118|gb|ADD02470.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter italicus Ab9]
 gi|296842456|gb|ADH60972.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
          Length = 246

 Score = 37.7 bits (86), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 48/219 (21%), Positives = 100/219 (45%), Gaps = 42/219 (19%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI-LRSWSLVKIGTTANQKRL 135
           +++++G +GL+ A++K+ P +G +  TY+   I+  + +Y+  + W              
Sbjct: 51  DLINQGVLGLIDAIEKYQPSKGVKFETYATLRIRGEIIDYLRKKDWM------------- 97

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES-EVISMNCRLAGDESLNAL--INS 192
               R LK   + I       E V  + +K N   + E I+  C L   + L  L  IN 
Sbjct: 98  ---PRSLKKKYKKI------EETVETLQQKYNREPTVEEITEACGLNETDVLKTLSYINV 148

Query: 193 SDKNS------SQWQDWLVYD---HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           S+ NS      + ++   + D    + +E+VL ++ +RK     L  ++  L  +ER + 
Sbjct: 149 SNINSLEEAIENNFKLHAISDVELKNPEEEVLYKELKRK-----LANAIKNLPDKERLVI 203

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
                ++  +  +++S    ++  R+ QI  +A K+++E
Sbjct: 204 TLYYYED--LNYKDISKILNLTESRISQIHTKAIKRIRE 240


>gi|225569957|ref|ZP_03778982.1| hypothetical protein CLOHYLEM_06052 [Clostridium hylemonae DSM
           15053]
 gi|225161427|gb|EEG74046.1| hypothetical protein CLOHYLEM_06052 [Clostridium hylemonae DSM
           15053]
          Length = 274

 Score = 37.7 bits (86), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 60/278 (21%), Positives = 127/278 (45%), Gaps = 57/278 (20%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMG----YRGYGLPISEVVSEGNIGLMQAVKK 92
           L + YR+ G L     +   +L +V  IA+     Y G+   + ++V+EG I LM+A+ K
Sbjct: 19  LLELYRKTGSLEVKQEIALRYLYIVKSIAVQMRNVYAGFS-QVEDIVNEGVIMLMKAIDK 77

Query: 93  FDPERGFRLATYSMWWIKAAM------QEYILR----SWSLVKIGTTANQKRLFFNLRRL 142
           ++ ++  +  TY    I+  +      Q++I R    S+  +K  +      +F+     
Sbjct: 78  YEADKNAKFETYVSKRIRGMIIDIARKQDWIPRTVRKSYRDIKEASA-----VFY----- 127

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR----LAGDESLNALINSS---DK 195
                  +++  +PE     A++L    SE++ M+      + G  SL ++++     ++
Sbjct: 128 -------SEHGREPE-----AEEL----SELLHMDIEKFRDIMGKASLFSVLSLDMVLEE 171

Query: 196 NSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
              Q++   +     +EQ    L++KE     R+ML   +  L   E+ +     ++E  
Sbjct: 172 TKEQYRSIQIPSDKKEEQPEAHLMDKE----FRHMLADGIRSLKENEQTVISLYYMEE-- 225

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
           + ++ ++    VS  R+ QI A A +K++E   ++ +L
Sbjct: 226 LNMKEIAGILHVSEPRISQIHAGAIRKLREYFTEKTKL 263


>gi|1706832|sp|P52621|FLIA_YEREN RecName: Full=RNA polymerase sigma factor for flagellar operon;
           AltName: Full=Sigma-27; AltName: Full=Sigma-28; AltName:
           Full=Sigma-F factor
 gi|790557|gb|AAC43394.1| FliA [Yersinia enterocolitica (type O:9)]
          Length = 230

 Score = 37.7 bits (86), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 46/232 (19%), Positives = 99/232 (42%), Gaps = 37/232 (15%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM-QEY 116
           LRL V++        + + +++  G IGL+ AV+++D  +G    TY++  I+ AM  E 
Sbjct: 19  LRLQVRLPAS-----VELDDLLQAGGIGLLNAVERYDRLQGTAFTTYAVQRIRGAMLDEL 73

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
             R W+          + +  N R +   +Q +     +P     +A+ L++  +E   +
Sbjct: 74  RSRDWA---------PRSVRRNAREVASAMQKVEQRLGRPATEQEVAQNLDIDLTEYRQI 124

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE--------RKNRRNML 228
                       L+++++     + +W     +  E +L   E+          N R  +
Sbjct: 125 ------------LLDTNNSQLFSYDEWREEHGESVEPMLEGHEDANPLQHLLEGNLRQRV 172

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++  L  RE+ +      +E  + L+ + +  EV   RV Q+ ++A K++
Sbjct: 173 IEAIEALPEREKMVLTLYYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRL 222


>gi|283785667|ref|YP_003365532.1| flagellar-specific Sigma F (Sigma 28) factor [Citrobacter rodentium
           ICC168]
 gi|282949121|emb|CBG88728.1| flagellar-specific Sigma F (Sigma 28) factor [Citrobacter rodentium
           ICC168]
          Length = 239

 Score = 37.7 bits (86), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 49/221 (22%), Positives = 98/221 (44%), Gaps = 32/221 (14%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL+ AV ++D  +G    TY++  I+ AM +  LRS   V      N + 
Sbjct: 41  LDDLLQAGGIGLLNAVDRYDALQGTAFTTYAVQRIRGAMLDE-LRSRDWVPRSVRRNARE 99

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   + +L+   Q +  N  + E    +A++L +   E   M            L+++++
Sbjct: 100 VAQAMGQLE---QELGRNATETE----VAERLGIPVEEYRQM------------LLDTNN 140

Query: 195 KNSSQWQDW---------LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
                + +W         LV +   QE  L +  E  N R  +  ++  L  RE+ +   
Sbjct: 141 SQLFSYDEWREEHGDSIELVTEEHQQENPLQQLLE-SNLRQRVMDAIEALPEREQLVLTL 199

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +E  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 200 YYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 238


>gi|193222293|emb|CAL61487.2| RNA polymerase sigma factor for flagellar operon (Sigma-F factor)
           (Sigma-27) (Sigma-28) [Herminiimonas arsenicoxydans]
          Length = 243

 Score = 37.7 bits (86), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 50/241 (20%), Positives = 111/241 (46%), Gaps = 20/241 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           LV+ H  LV K+A   +    P   + +++  G IGL+ AV +++   G +  TY++  I
Sbjct: 13  LVSEHAPLVKKLAHQMKAKLPPSVEVDDLIQAGMIGLLDAVGRYEETHGAQFETYAVQRI 72

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + AM +  LRS   +        + +  N+R+++  + ++     +P     +AK+L +S
Sbjct: 73  RGAMLDE-LRSSDWMP-------RSMRQNMRKIEVAMNSLQQKLGRPPNESEVAKQLKLS 124

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV--YDHDGQEQVLIEKEERKNRRNM 227
            ++       L  D   + L+   D + S+  +  +  Y  D     L +       R+ 
Sbjct: 125 LADYQD----LLSDGGGHQLVYYEDFHDSEDNEHFLDRYCTDESPDPL-QNLMNTGFRSA 179

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +  ++  L  RE+ +      QE  + L+ + +   V+  RV Q+ ++A  +++ +++++
Sbjct: 180 VIAAIEALPEREKILMSLYYEQE--MNLKEIGAVMGVTESRVSQLHSQAIARMRANLREK 237

Query: 288 V 288
            
Sbjct: 238 A 238


>gi|37680648|ref|NP_935257.1| flagellar biosynthesis sigma factor [Vibrio vulnificus YJ016]
 gi|37199396|dbj|BAC95228.1| polar Flagellar-specific RNA polymerase sigma factor FliA [Vibrio
           vulnificus YJ016]
          Length = 245

 Score = 37.7 bits (86), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 58/252 (23%), Positives = 104/252 (41%), Gaps = 31/252 (12%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFD 94
           A  Y +H ++++    +  +  LV +IA    G   P   + +++  G IGL++A + +D
Sbjct: 5   ALTYDQHANVNSQKLFIERYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLIEAQQNYD 64

Query: 95  PERGFRLATYSMWWIKAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
             +G    TY+   I+ AM + I R  W  V      + + +   +  L+G L      N
Sbjct: 65  ASKGASFETYAGIRIRGAMLDDIRRGDW--VPRSVHKSNREISQAIAELEGLL------N 116

Query: 154 LKPEQVVAIAKKLNVS----ESEVISMNC-RLAGDESLNALINSSDKNSSQWQDWLVYDH 208
             P     +AK + +S       +  +NC RL G E L      SD       D +    
Sbjct: 117 RDPTD-AEVAKHMGLSLEQYHGALTDINCSRLIGIEDLGV----SD-------DVITSVE 164

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D +     +    +  R  L  S+  L  RE  +      +E  + L+ +     VS  R
Sbjct: 165 DSENNTPFKGVADEYFRKALVESIKQLPEREALVLSLYYDEE--LNLKEIGEILSVSESR 222

Query: 269 VRQIEARAFKKV 280
           V QI +++ +++
Sbjct: 223 VSQILSQSMQRL 234


>gi|270157125|ref|ZP_06185782.1| RNA polymerase sigma-28 factor FliA [Legionella longbeachae D-4968]
 gi|289164470|ref|YP_003454608.1| sigma factor 28 [Legionella longbeachae NSW150]
 gi|269989150|gb|EEZ95404.1| RNA polymerase sigma-28 factor FliA [Legionella longbeachae D-4968]
 gi|288857643|emb|CBJ11483.1| sigma factor 28 [Legionella longbeachae NSW150]
          Length = 238

 Score = 37.7 bits (86), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 20/71 (28%), Positives = 39/71 (54%), Gaps = 3/71 (4%)

Query: 53  LVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           LV +H  LV +IA   +G    G+ + +++  G +GL++A + +D  +G    TY+   I
Sbjct: 18  LVKNHALLVKRIAHHLLGRLPQGIQLDDLIQAGMLGLLEAARHYDSSKGASFETYAGIRI 77

Query: 110 KAAMQEYILRS 120
           +  M + + R+
Sbjct: 78  RGYMLDEVRRN 88


>gi|330961077|gb|EGH61337.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv.
           maculicola str. ES4326]
          Length = 167

 Score = 37.7 bits (86), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 15/28 (53%), Positives = 24/28 (85%)

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 126 TLEEVGKQFDVTRERIRQIEAKALRKLR 153


>gi|292669753|ref|ZP_06603179.1| DNA-directed RNA polymerase sigma subunit FliA [Selenomonas noxia
           ATCC 43541]
 gi|292648550|gb|EFF66522.1| DNA-directed RNA polymerase sigma subunit FliA [Selenomonas noxia
           ATCC 43541]
          Length = 251

 Score = 37.7 bits (86), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 50/242 (20%), Positives = 101/242 (41%), Gaps = 35/242 (14%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           +  H   +V++  G     LP      +++S G  GL+ A+++++  RG +  TY+   +
Sbjct: 31  IAEHYLPLVRLVAGRIAISLPQHVDREDLLSSGFFGLLDAIERYELARGNKFETYAGVRV 90

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITDNNLKPEQVVAIAK---- 164
           + AM ++ LR+   + +    N K+    +  L+G L +  TD  L  E  + I      
Sbjct: 91  RGAMLDH-LRAKDWIPVSVRQNIKKYEKAVAHLEGELGRTATDEELAEELDLTIEGLHHL 149

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +  VS + VI +   L  D   +                     DG     +E  E    
Sbjct: 150 EGQVSAATVIPLEEYLRTDSPTSL-------------------EDGP----VEHAEWTEV 186

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +  L  ++  L  +ER +       E  +TL+ +++   +S  R+ Q+  +A  +++ S+
Sbjct: 187 KETLAAAIEKLPEKERTVITLYYYDE--MTLKEIAAILHLSEARISQLHTKAIFRMRGSL 244

Query: 285 QK 286
            +
Sbjct: 245 AR 246


>gi|254973714|ref|ZP_05270186.1| RNA polymerase factor sigma-70 [Clostridium difficile QCD-66c26]
 gi|255091104|ref|ZP_05320582.1| RNA polymerase factor sigma-70 [Clostridium difficile CIP 107932]
 gi|255099216|ref|ZP_05328193.1| RNA polymerase factor sigma-70 [Clostridium difficile QCD-63q42]
 gi|255304999|ref|ZP_05349171.1| RNA polymerase factor sigma-70 [Clostridium difficile ATCC 43255]
 gi|255312759|ref|ZP_05354342.1| RNA polymerase factor sigma-70 [Clostridium difficile QCD-76w55]
 gi|255515519|ref|ZP_05383195.1| RNA polymerase factor sigma-70 [Clostridium difficile QCD-97b34]
 gi|255648612|ref|ZP_05395514.1| RNA polymerase factor sigma-70 [Clostridium difficile QCD-37x79]
 gi|255654145|ref|ZP_05399554.1| RNA polymerase factor sigma-70 [Clostridium difficile QCD-23m63]
          Length = 215

 Score = 37.7 bits (86), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 1/79 (1%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           +Q+EY +  R  E GD  A   ++T +   V   A  Y   G    +++ EG IGL +AV
Sbjct: 16  QQDEYNIVLRASE-GDKIALEYIITKYRNFVKAKAKSYFLIGADKEDIIQEGMIGLYKAV 74

Query: 91  KKFDPERGFRLATYSMWWI 109
           + FD  +      ++   I
Sbjct: 75  RDFDGSKTNSFKCFAEICI 93


>gi|54308132|ref|YP_129152.1| flagellar biosynthesis sigma factor [Photobacterium profundum SS9]
 gi|46912558|emb|CAG19350.1| Putative flagellar-specific RNA polymerase sigma factor, FliA
           [Photobacterium profundum SS9]
          Length = 240

 Score = 37.7 bits (86), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 51/231 (22%), Positives = 99/231 (42%), Gaps = 25/231 (10%)

Query: 60  LVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           LV +IA   MG     + + +++  G IGL++A + +DP +G    T++   I+ AM + 
Sbjct: 24  LVKRIAYHLMGRLPPSVQVEDLIQSGMIGLLEAQQNYDPTKGASFETFAGIRIRGAMLDD 83

Query: 117 ILRS-WSLVKIGTTANQKRLFFNLRRLKGHL-QAITDNNLKPEQVVAIAKKLNVSESEVI 174
           I R  W  V      N +R+   + +L+  L +  TD  +       +   L+     + 
Sbjct: 84  IRRGDW--VPRSVYKNNRRITEAMAQLENKLGRDPTDTEIAEH----LEMTLDQYHQALN 137

Query: 175 SMNC-RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
            +NC RL G + L              +D +  +   +E +  +     N R  L  ++ 
Sbjct: 138 DVNCGRLVGMDDLGV-----------SEDAVTTEASREENLPFQGVVDDNFRQSLADAIK 186

Query: 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L  RE  +      +E  + L+ +     VS  R+ QI ++A ++++  +
Sbjct: 187 TLPEREALVLSLYYDEE--LNLKEIGVVVGVSESRICQIHSQAMQRLRSKL 235


>gi|313820245|gb|EFS57959.1| sigma-70 region 2 [Propionibacterium acnes HL036PA1]
 gi|313822945|gb|EFS60659.1| sigma-70 region 2 [Propionibacterium acnes HL036PA2]
 gi|314925132|gb|EFS88963.1| sigma-70 region 2 [Propionibacterium acnes HL036PA3]
          Length = 228

 Score = 37.7 bits (86), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 15/49 (30%), Positives = 30/49 (61%)

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           Y   + +++  G IGL +A++++D  RG R +T +  WI+  + E ++R
Sbjct: 83  YRCSVEDLIQAGCIGLGEAIERYDVRRGARFSTVAWTWIRRRIGEEVVR 131


>gi|118618107|ref|YP_906439.1| RNA polymerase sigma factor SigF [Mycobacterium ulcerans Agy99]
 gi|183981270|ref|YP_001849561.1| alternate RNA polymerase sigma factor SigF [Mycobacterium marinum
           M]
 gi|118570217|gb|ABL04968.1| alternate RNA polymerase sigma factor SigF [Mycobacterium ulcerans
           Agy99]
 gi|183174596|gb|ACC39706.1| alternate RNA polymerase sigma factor SigF [Mycobacterium marinum
           M]
          Length = 262

 Score = 37.7 bits (86), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 53/239 (22%), Positives = 102/239 (42%), Gaps = 19/239 (7%)

Query: 51  HR--LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           HR  +V   L L   IA  + G G P  ++V    +GL+ AV +FD E G    ++++  
Sbjct: 39  HRDTIVERCLPLADHIARRFEGRGEPRDDLVQVARVGLVNAVVRFDVETGSDFVSFAVPT 98

Query: 109 IKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           I   ++ +    SWS VK+     +  L     RL      ++    +      +A +L 
Sbjct: 99  IMGEVRRHFRDNSWS-VKVPRRLKELHL-----RLGAATAELSQRLGRAPTATELAAELE 152

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK-EERKNRRN 226
           +  +EV+     L    S N L   S   S       + D  G     +++ E+R++ R 
Sbjct: 153 MDRAEVVEG---LVAGSSYNTLSIDSGSGSEDDDARAIADTLGDMDAGLDRIEDRESLRP 209

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           +L      L  RER +   R    + +T   ++    +S+  V ++ A++  ++++ ++
Sbjct: 210 LL----EALPERERTVLVLRFF--DSMTQTQIAERVGISQMHVSRLLAKSLARLRDQLE 262


>gi|332305676|ref|YP_004433527.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Glaciecola agarilytica
           4H-3-7+YE-5]
 gi|332173005|gb|AEE22259.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Glaciecola agarilytica
           4H-3-7+YE-5]
          Length = 242

 Score = 37.7 bits (86), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 54/252 (21%), Positives = 107/252 (42%), Gaps = 24/252 (9%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           A  Y++  D +A   LV  H  LV +IA   +      + + +++  G IGL++A + FD
Sbjct: 5   AAAYQQLDDRNA---LVERHAPLVKRIAHHLIARLPASVLVDDLIQAGMIGLLEASRNFD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
             +G    T++   I+ +M + I +  W+          + +  N R +   +  +    
Sbjct: 62  GSKGASFETFAGIRIRGSMLDEIRKGDWT---------PRSVHKNGRAITDAINKVERET 112

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            +  + V IAKKL VS    I    ++  + +   +I   D   +  +D +  +      
Sbjct: 113 GRDARDVDIAKKLEVS----IEQYHQMLSEVNAGKIIGMEDLGVT--EDVVTTEQTKGSD 166

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
              E   + + +  L  +++ L  RE  +      +E  + L  +    +VS  RV QI 
Sbjct: 167 TPFEDLLQGSFQKALAHAITTLPEREAIVLSLYYDEE--LNLREIGEVLDVSESRVSQIH 224

Query: 274 ARAFKKVQESIQ 285
           ++A  K++  +Q
Sbjct: 225 SQAMLKLKSKMQ 236


>gi|27365297|ref|NP_760825.1| flagellar biosynthesis sigma factor [Vibrio vulnificus CMCP6]
 gi|320155681|ref|YP_004188060.1| RNA polymerase sigma factor for flagellar operon [Vibrio vulnificus
           MO6-24/O]
 gi|27361444|gb|AAO10352.1| RNA polymerase sigma factor for flagellar operon [Vibrio vulnificus
           CMCP6]
 gi|319930993|gb|ADV85857.1| RNA polymerase sigma factor for flagellar operon [Vibrio vulnificus
           MO6-24/O]
          Length = 244

 Score = 37.7 bits (86), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 58/252 (23%), Positives = 104/252 (41%), Gaps = 31/252 (12%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFD 94
           A  Y +H ++++    +  +  LV +IA    G   P   + +++  G IGL++A + +D
Sbjct: 4   ALTYDQHANVNSQKLFIERYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLIEAQQNYD 63

Query: 95  PERGFRLATYSMWWIKAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
             +G    TY+   I+ AM + I R  W  V      + + +   +  L+G L      N
Sbjct: 64  ASKGASFETYAGIRIRGAMLDDIRRGDW--VPRSVHKSNREISQAIAELEGLL------N 115

Query: 154 LKPEQVVAIAKKLNVS----ESEVISMNC-RLAGDESLNALINSSDKNSSQWQDWLVYDH 208
             P     +AK + +S       +  +NC RL G E L      SD       D +    
Sbjct: 116 RDPTD-AEVAKHMGLSLEQYHGALTDINCSRLIGIEDLGV----SD-------DVITSVE 163

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D +     +    +  R  L  S+  L  RE  +      +E  + L+ +     VS  R
Sbjct: 164 DSENNTPFKGVADEYFRKALVESIKQLPEREALVLSLYYDEE--LNLKEIGEILSVSESR 221

Query: 269 VRQIEARAFKKV 280
           V QI +++ +++
Sbjct: 222 VSQILSQSMQRL 233


>gi|108804234|ref|YP_644171.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108765477|gb|ABG04359.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 264

 Score = 37.7 bits (86), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 17/42 (40%), Positives = 29/42 (69%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           G+   ++VS G +GL++AV+ FDP RG +  TY++  I+ A+
Sbjct: 69  GVEQEDLVSWGVVGLLKAVETFDPARGAKFETYAISKIRWAI 110


>gi|284007149|emb|CBA72430.1| flagellar biosynthesis sigma factor [Arsenophonus nasoniae]
          Length = 243

 Score = 37.7 bits (86), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 16/48 (33%), Positives = 28/48 (58%), Gaps = 1/48 (2%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM-QEYILRSW 121
           + ++V  G IGL+ A+++FD  +G    TY++  ++ AM  E   R W
Sbjct: 44  LDDLVQAGGIGLLDALERFDASQGTAFTTYAVQRVRGAMLDELRARDW 91


>gi|167949417|ref|ZP_02536491.1| RNA polymerase sigma factor RpoD [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 128

 Score = 37.7 bits (86), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 15/28 (53%), Positives = 24/28 (85%)

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 86  TLEEVGKQFDVTRERIRQIEAKALRKLR 113


>gi|118465934|ref|YP_882149.1| RNA polymerase sigma factor SigF [Mycobacterium avium 104]
 gi|118167221|gb|ABK68118.1| RNA polymerase sigma-F factor [Mycobacterium avium 104]
          Length = 269

 Score = 37.7 bits (86), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 59/273 (21%), Positives = 114/273 (41%), Gaps = 43/273 (15%)

Query: 22  EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           E+R++P   +  EY   +R RE        R+V   L L   +A  +   G  + ++V  
Sbjct: 31  ELRRMPA--ESHEY---RRQRE--------RIVARCLPLADHVASHFARRGEGLDDLVQV 77

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLR 140
             +GLM AV +FDP +G     +++  +   ++ Y    SW +          R+   LR
Sbjct: 78  ARLGLMNAVNRFDPAKGPSFIGFAVPTMMGEVRRYFRDYSWGM----------RVPRRLR 127

Query: 141 RLKGHLQAITDNNL----KPEQVVAIAKKLNVSESEVISMNCRLAGD----ESLNALINS 192
            L   +   T +      +      +++ L V   E++   C +AGD    +SL+A   +
Sbjct: 128 ELHVQISRTTADLAQQLGRAPNAGELSQVLEVPREEIV--ECLVAGDAYRLDSLDAPQGA 185

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
               + +     V D D Q + +  +E        L   ++ L  RER +   R  +   
Sbjct: 186 DSSGTPRSVADSVGDIDPQIEHITNRE-------ALRVLVATLPHREREVLRMRFFES-- 236

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           +T   ++    VS+ +V +I A   + +++ ++
Sbjct: 237 MTQSQIAERIGVSQMQVSRILANTLRCLRDQLE 269


>gi|291613029|ref|YP_003523186.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Sideroxydans
           lithotrophicus ES-1]
 gi|291583141|gb|ADE10799.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Sideroxydans
           lithotrophicus ES-1]
          Length = 247

 Score = 37.7 bits (86), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 47/213 (22%), Positives = 94/213 (44%), Gaps = 18/213 (8%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G +GL+ A  ++D  RG +  TY+   I+ AM + +         G     + 
Sbjct: 49  VDDLIQAGMMGLLDAASRYDELRGAQFETYAAQRIRGAMLDELR--------GADWLPRS 100

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           L  ++RR++  +  +     K      IA++L VS  E   M     G +    L+   D
Sbjct: 101 LRRDMRRIETAVSRLQQQMGKTPNETEIARELGVSLHEYQQMLQEGRGAQ----LLYYED 156

Query: 195 KNSSQWQDWLV-YDHDGQEQVL-IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            +  + +D+   ++  G    L + ++ER   R  L  ++  L  RER++       E  
Sbjct: 157 FHGEEGEDFFERFEFSGDSNPLELLQDERF--REALIHAIERLPERERQMMGMH--YEQD 212

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + L  +     VS  RV Q+ ++A  +++ S++
Sbjct: 213 MNLREIGEVMGVSESRVCQLHSQAVARLRASMK 245


>gi|41407572|ref|NP_960408.1| RNA polymerase sigma factor SigF [Mycobacterium avium subsp.
           paratuberculosis K-10]
 gi|41395925|gb|AAS03791.1| SigF_1 [Mycobacterium avium subsp. paratuberculosis K-10]
          Length = 269

 Score = 37.7 bits (86), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 59/273 (21%), Positives = 114/273 (41%), Gaps = 43/273 (15%)

Query: 22  EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           E+R++P   +  EY   +R RE        R+V   L L   +A  +   G  + ++V  
Sbjct: 31  ELRRMPA--ESHEY---RRQRE--------RIVARCLPLADHVASHFARRGEGLDDLVQV 77

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLR 140
             +GLM AV +FDP +G     +++  +   ++ Y    SW +          R+   LR
Sbjct: 78  ARLGLMNAVNRFDPAKGPSFIGFAVPTMMGEVRRYFRDYSWGM----------RVPRRLR 127

Query: 141 RLKGHLQAITDNNL----KPEQVVAIAKKLNVSESEVISMNCRLAGD----ESLNALINS 192
            L   +   T +      +      +++ L V   E++   C +AGD    +SL+A   +
Sbjct: 128 ELHVQISRTTADLAQQLGRAPNAGELSQVLEVPREEIV--ECLVAGDAYRLDSLDAPQGA 185

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
               + +     V D D Q + +  +E        L   ++ L  RER +   R  +   
Sbjct: 186 DSSGTPRSVADSVGDIDPQIEHITNRE-------ALRVLVATLPHREREVLRMRFFES-- 236

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           +T   ++    VS+ +V +I A   + +++ ++
Sbjct: 237 MTQSQIAERIGVSQMQVSRILANTLRCLRDQLE 269


>gi|197294375|ref|YP_001798916.1| RNA polymerase sigma factor [Candidatus Phytoplasma australiense]
 gi|171853702|emb|CAM11593.1| RNA polymerase sigma factor [Candidatus Phytoplasma australiense]
          Length = 151

 Score = 37.7 bits (86), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 31/123 (25%), Positives = 61/123 (49%), Gaps = 9/123 (7%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGY--GLPISEVVSEGNIGLMQAVKKFDPERGF 99
           +   +L+   +L+  H  LV KIA  ++ +   L   ++  EG +GL++++  ++ + G+
Sbjct: 12  KNKNNLAIRDQLIKMHFPLVKKIANKFKYFPKSLQREDLYQEGILGLIKSLDNYE-DLGY 70

Query: 100 RLATYSMWWIKAAMQEYI--LRSWSL-VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
               Y+   IK  + E I  L++ S  +K+     Q     N+   +   Q+I +NNL P
Sbjct: 71  DFIAYATPTIKGEITELIRGLQTTSTPIKVFRKEKQTS---NIPFEENQPQSINNNNLNP 127

Query: 157 EQV 159
            Q+
Sbjct: 128 HQI 130


>gi|330465518|ref|YP_004403261.1| hypothetical protein VAB18032_07705 [Verrucosispora maris
           AB-18-032]
 gi|328808489|gb|AEB42661.1| hypothetical protein VAB18032_07705 [Verrucosispora maris
           AB-18-032]
          Length = 237

 Score = 37.7 bits (86), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 29/125 (23%), Positives = 63/125 (50%), Gaps = 14/125 (11%)

Query: 186 LNALINSSDKNSSQWQD-----WLVYDHDGQEQVLIEKEER---KNRRNMLTRSMSVLNP 237
           L+A +N+ D++  QW D     +  YD+DG+   + +  ER   + RR++  +    +  
Sbjct: 2   LDAALNARDEHGRQWSDARWGCYAFYDYDGEPIYVGQTNERLRARVRRHLTNQRTDAVAM 61

Query: 238 RERRIFEARRLQENPV-TLENLSS----EFEVSRERVRQIEARAF-KKVQESIQKQVELS 291
           R   +FE   ++  P+   E+++     ++  +++R+  +E  A+ K ++ES  K +   
Sbjct: 62  RILDVFEVAEMELWPLWEFEDVAGKRHPDYAAAQQRLNAVEYTAYLKAIRESRFKAILNE 121

Query: 292 SSPPL 296
             PP+
Sbjct: 122 KIPPV 126


>gi|303240258|ref|ZP_07326777.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302592168|gb|EFL61897.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 256

 Score = 37.7 bits (86), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 55/253 (21%), Positives = 110/253 (43%), Gaps = 27/253 (10%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG----YRGYGLPISEVVSEGNIGL 86
           KQ+E  + ++Y +  D +   +L+  +   ++K   G    Y G  +   +++  G  GL
Sbjct: 7   KQQE--MWRQYSDTKDPAIKEKLIIEYSH-IIKYVAGRLSIYFGSNVEYDDLIGYGVFGL 63

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK---RLFFNLRRLK 143
           + A+ KFD  +G +  TY+   I+ A+ + I R    V        K   R++  +    
Sbjct: 64  IDAINKFDINKGVKFETYASLRIRGAIIDSI-RELDWVPRSLRQKNKELERVYTEVENEL 122

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
           GH  + TD          +A+KL VS  E      +L  + +L++LI+  +     ++  
Sbjct: 123 GH--SATDQE--------VAQKLGVSVDEF----YKLLNEVNLSSLISLEEFLEQNYEAG 168

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +      +E       E    R +L  ++  L  +E+ +      ++  +TL+ +S   +
Sbjct: 169 VNIAGGCKEDRPEGYMEITELREILVDAIGKLPEKEKTVVSFYYFED--LTLKEISEIMK 226

Query: 264 VSRERVRQIEARA 276
           VS  R+ Q+  +A
Sbjct: 227 VSESRISQLHTKA 239


>gi|269925713|ref|YP_003322336.1| sigma-70 region 4 domain protein [Thermobaculum terrenum ATCC
           BAA-798]
 gi|269789373|gb|ACZ41514.1| sigma-70 region 4 domain protein [Thermobaculum terrenum ATCC
           BAA-798]
          Length = 785

 Score = 37.7 bits (86), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 18/51 (35%), Positives = 35/51 (68%), Gaps = 1/51 (1%)

Query: 233 SVLNPRERRIFEAR-RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           ++ +PR RR+ EAR  +    +TL+ + +E ++S+ERVRQ+E R  + +++
Sbjct: 332 TIKSPRVRRVLEARFGVSGKILTLQEIGAELKLSKERVRQLEERGLRLIRK 382


>gi|290475011|ref|YP_003467895.1| sigma F (sigma 28) factor of RNA polymerase, transcription of late
           flagellar genes (class 3a and 3b operons) [Xenorhabdus
           bovienii SS-2004]
 gi|289174328|emb|CBJ81122.1| sigma F (sigma 28) factor of RNA polymerase, transcription of late
           flagellar genes (class 3a and 3b operons) [Xenorhabdus
           bovienii SS-2004]
          Length = 240

 Score = 37.7 bits (86), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 51/230 (22%), Positives = 99/230 (43%), Gaps = 33/230 (14%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRL V++        + + +++  G IGL+ AV++FD  +G    TY++  I+ AM +  
Sbjct: 29  LRLQVRLPAS-----VELDDLLQAGGIGLLNAVERFDSLQGTAFTTYAVQRIRGAMLDE- 82

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           LRS          N + +   +R+L+  L          EQ VA   K+N+ E   I   
Sbjct: 83  LRSRDWAPRSVRRNAREVTQTIRKLEQEL-----GRPASEQEVAKELKINLIEYRQI--- 134

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML-----TRSM 232
                      L+++++     + +W     +  E V+ ++ E    + +L      R +
Sbjct: 135 -----------LLDTNNSQLFSYDEWHEIHGESCEPVIEDEHETNPLQQLLEGDLRQRVI 183

Query: 233 SVLN--PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            V+   P   ++      QE  + L+ + +   V   RV Q+ ++A K++
Sbjct: 184 DVIESLPEREKMVLTLYYQEE-LNLKEIGAVLNVGESRVSQLHSQAIKRL 232


>gi|111021699|ref|YP_704671.1| sigma factor, sigma 70 type, group 3 [Rhodococcus jostii RHA1]
 gi|110821229|gb|ABG96513.1| sigma factor, sigma 70 type, group 3 [Rhodococcus jostii RHA1]
          Length = 249

 Score = 37.7 bits (86), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 18/67 (26%), Positives = 34/67 (50%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            RL+   L L   IA  + G G P+ +++    +GL++AV +FD   G    +Y++  I 
Sbjct: 23  QRLIERCLPLAEHIARRFHGRGEPLDDLIQVARLGLVKAVDRFDARCGANFVSYAVPTIT 82

Query: 111 AAMQEYI 117
             ++ + 
Sbjct: 83  GEVRRHF 89


>gi|56966075|pdb|1TLH|B Chain B, T4 Asia Bound To Sigma70 Region 4
          Length = 81

 Score = 37.7 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 16/35 (45%), Positives = 27/35 (77%)

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           TLE +  +F+V+RER+RQIEA+A +K++   + +V
Sbjct: 40  TLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 74


>gi|283832678|ref|ZP_06352419.1| flagellar biosynthesis sigma factor FliA [Citrobacter youngae ATCC
           29220]
 gi|291072353|gb|EFE10462.1| flagellar biosynthesis sigma factor FliA [Citrobacter youngae ATCC
           29220]
          Length = 229

 Score = 37.4 bits (85), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 47/220 (21%), Positives = 96/220 (43%), Gaps = 30/220 (13%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL+ AV ++D  +G    TY++  I+ AM +  LRS   V      N + 
Sbjct: 31  LDDLLQAGGIGLLNAVDRYDALQGTAFTTYAVQRIRGAMLDE-LRSRDWVPRSVRRNARE 89

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   + +L+   Q +  N  + E    +A++L +   E   M            L+++++
Sbjct: 90  VAQAMGQLE---QELGRNATETE----VAERLAIPVQEYRQM------------LLDTNN 130

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERK--------NRRNMLTRSMSVLNPRERRIFEAR 246
                + +W     D  E V  E ++          N R  +  ++  L  RE+ +    
Sbjct: 131 SQLFSYDEWREEHGDSIELVTEEHQQENPLQQLLEGNLRQRVMDAIEALPEREKLVLTLY 190

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             +E  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 191 YQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 228


>gi|39998144|ref|NP_954095.1| RNA polymerase sigma factor for flagellar operon [Geobacter
           sulfurreducens PCA]
 gi|39985090|gb|AAR36445.1| RNA polymerase sigma factor for flagellar operon [Geobacter
           sulfurreducens PCA]
          Length = 250

 Score = 37.4 bits (85), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 28/98 (28%), Positives = 47/98 (47%), Gaps = 14/98 (14%)

Query: 36  VLAKRYREHGDLSAAH---RLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQ 88
            + K Y +    S A     L+ +HL LV K  +G     LP      +++S   IGL+ 
Sbjct: 3   CMLKAYEQEAQRSVAQTRDELIVNHLPLV-KFLVGRIASQLPPHLDQEDLMSAAIIGLIT 61

Query: 89  AVKKFDPERGFRLATYSMWWIKAAM------QEYILRS 120
           A ++FDP RG +  T++   I+  +      Q+++ RS
Sbjct: 62  AAERFDPTRGVQFKTFAEQRIRGTIIDELRSQDWLTRS 99


>gi|312138386|ref|YP_004005722.1| sigma-70 factor [Rhodococcus equi 103S]
 gi|311887725|emb|CBH47037.1| putative sigma-70 factor [Rhodococcus equi 103S]
          Length = 262

 Score = 37.4 bits (85), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 19/66 (28%), Positives = 32/66 (48%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R+V   L L   IA  +   G  + ++     +GL+ AV +FDP +G   A Y++  I  
Sbjct: 42  RIVAQSLPLARNIARRFSSRGEEMDDLYQVACVGLINAVDRFDPAQGSSFAAYAVPTIMG 101

Query: 112 AMQEYI 117
            ++ Y 
Sbjct: 102 EVRRYF 107


>gi|325674621|ref|ZP_08154308.1| DNA-directed RNA polymerase sigma subunit SigB [Rhodococcus equi
           ATCC 33707]
 gi|325554207|gb|EGD23882.1| DNA-directed RNA polymerase sigma subunit SigB [Rhodococcus equi
           ATCC 33707]
          Length = 262

 Score = 37.4 bits (85), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 19/66 (28%), Positives = 32/66 (48%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R+V   L L   IA  +   G  + ++     +GL+ AV +FDP +G   A Y++  I  
Sbjct: 42  RIVAQSLPLARNIARRFSSRGEEMDDLYQVACVGLINAVDRFDPAQGSSFAAYAVPTIMG 101

Query: 112 AMQEYI 117
            ++ Y 
Sbjct: 102 EVRRYF 107


>gi|226326542|ref|ZP_03802060.1| hypothetical protein PROPEN_00392 [Proteus penneri ATCC 35198]
 gi|225205141|gb|EEG87495.1| hypothetical protein PROPEN_00392 [Proteus penneri ATCC 35198]
          Length = 244

 Score = 37.4 bits (85), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 54/229 (23%), Positives = 107/229 (46%), Gaps = 31/229 (13%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRL VK+        + + +++  G IGL+ AV+++D  +G    TY++  I+ +M +  
Sbjct: 33  LRLQVKLPAS-----VELDDLLQAGGIGLLNAVERYDSMQGAAFTTYAVQRIRGSMLDE- 86

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP--EQVVAIAKKLNVSESEVIS 175
           LRS          N + +  ++ +L+  L        +P  EQ VA   ++ ++E   I 
Sbjct: 87  LRSRDWAPRSVRRNAREVTHSIHQLEQDLG-------RPPLEQEVADHLQIELAEYRQIL 139

Query: 176 M---NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE-QVLIEKEERKNRRNMLTRS 231
           +   N +L   +  + +   S + S   QD    DHD    Q+L+E + R+     +  +
Sbjct: 140 LDTNNSQLFSYDEWHEIYGESCEPS---QD---EDHDDNPLQMLLESDIRQR----VIDA 189

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + +L  RE+ +      +E  + L+ + +   V   RV Q+ ++A K++
Sbjct: 190 IELLPEREKMVLTLYYQEE--LNLKEIGAVLNVGESRVSQLHSQAIKRL 236


>gi|10834759|gb|AAG23813.1|AF274004_5 SigB [Staphylococcus epidermidis]
          Length = 246

 Score = 37.4 bits (85), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 45/209 (21%), Positives = 97/209 (46%), Gaps = 14/209 (6%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           K+++E+ D  A  +LV  + +L+  +A  Y        ++V  G +GL+ A+ +FD    
Sbjct: 21  KQHQENEDSQAQDKLVKHYRKLIESLAYRYSKGQSHHEDLVQVGMVGLIGAINRFDLSFD 80

Query: 99  FRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
            +   + +  +   ++ Y+  ++WS+         +R+     R+K     +T+   +  
Sbjct: 81  RKFEAFLVPTVIGEIKRYLRDKTWSV------HVPRRIKEIGPRIKKVSDELTNELERSP 134

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQVLI 216
            +  IA++L VS+ EV+     +   +S NAL ++ S +         + D  GQ+    
Sbjct: 135 SISEIAQRLEVSDEEVLEA---MEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQQD--- 188

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           +  +   +R +L   + +L+ RER+I + 
Sbjct: 189 DNYDLTEKRMILECILPILSERERQIIQC 217


>gi|323493327|ref|ZP_08098450.1| flagellar biosynthesis sigma factor [Vibrio brasiliensis LMG 20546]
 gi|323312413|gb|EGA65554.1| flagellar biosynthesis sigma factor [Vibrio brasiliensis LMG 20546]
          Length = 244

 Score = 37.4 bits (85), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 56/252 (22%), Positives = 105/252 (41%), Gaps = 31/252 (12%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFD 94
           A  Y ++ + ++    +  +  LV +IA    G   P   + +++  G IGL++A K +D
Sbjct: 4   ALTYEQYANQNSQRAFLEKYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLLEAQKNYD 63

Query: 95  PERGFRLATYSMWWIKAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
             +G    TY+   I+ AM + I R  W  V      + + +   +  L+G L      N
Sbjct: 64  GSKGASFETYAGIRIRGAMLDDIRRGDW--VPRSVHKHNREVSQAISELEGQL------N 115

Query: 154 LKPEQVVAIAKKLNVS----ESEVISMNC-RLAGDESLNALINSSDKNSSQWQDWLVYDH 208
             P     +A+ + +S     + +  +NC RL G E L              +D +  D 
Sbjct: 116 RDPSD-AEVAQHMGISLEQYHTILTDINCSRLVGIEDLGV-----------SEDVISPDD 163

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
             +E +  +    +  R  L  S+  L  RE  +      +E  + L+ +     VS  R
Sbjct: 164 RDEENLPFQGVADEYFRKALIDSIKSLPEREALVLSLYYDEE--LNLKEIGEVIGVSESR 221

Query: 269 VRQIEARAFKKV 280
           V QI +++ +++
Sbjct: 222 VSQILSQSMQRL 233


>gi|300871802|ref|YP_003786675.1| RNA polymerase sigma factor [Brachyspira pilosicoli 95/1000]
 gi|300689503|gb|ADK32174.1| RNA polymerase sigma factor [Brachyspira pilosicoli 95/1000]
          Length = 270

 Score = 37.4 bits (85), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 47/233 (20%), Positives = 98/233 (42%), Gaps = 41/233 (17%)

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQE----------YILRSWS 122
           +   ++V  G +GL+ A++K+DP +  +  TY+   IK ++ +           I R   
Sbjct: 61  IEFDDLVGYGALGLIDAIEKYDPNKEVKFKTYATTRIKGSIYDELRKIDKLPRSIRREIK 120

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            ++I     + +L  N+       Q I D    P   +    + ++  S          G
Sbjct: 121 DIEIAREFLESKLGRNVNS-----QEIADTMGIPLSKINETMRYSIEASTTSLSEVWYHG 175

Query: 183 DE----SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           D+    S+   + +SDKN+ ++                   ERK+ +  +  ++  L  +
Sbjct: 176 DDSDEISIMDTLKASDKNNPEYL-----------------AERKDVQKKIVEALDKLPEK 218

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES---IQKQV 288
           ER +      ++  +TL+ +    +VS  RV Q+  +A ++++ S   I+KQ+
Sbjct: 219 ERSVLILYYYED--LTLKEIGKVLDVSESRVSQLHTKAVQQLRYSLSEIKKQL 269


>gi|298507081|gb|ADI85804.1| RNA polymerase sigma-28 factor for flagellar operon [Geobacter
           sulfurreducens KN400]
          Length = 250

 Score = 37.4 bits (85), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 28/98 (28%), Positives = 47/98 (47%), Gaps = 14/98 (14%)

Query: 36  VLAKRYREHGDLSAAH---RLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQ 88
            + K Y +    S A     L+ +HL LV K  +G     LP      +++S   IGL+ 
Sbjct: 3   CMLKAYEQEAQRSVAQTRDELIVNHLPLV-KFLVGRIASQLPPHLDQEDLMSAAIIGLIT 61

Query: 89  AVKKFDPERGFRLATYSMWWIKAAM------QEYILRS 120
           A ++FDP RG +  T++   I+  +      Q+++ RS
Sbjct: 62  AAERFDPTRGVQFKTFAEQRIRGTIIDELRSQDWLTRS 99


>gi|264676583|ref|YP_003276489.1| RNA polymerase, sigma 28 subunit [Comamonas testosteroni CNB-2]
 gi|262207095|gb|ACY31193.1| RNA polymerase, sigma 28 subunit [Comamonas testosteroni CNB-2]
          Length = 239

 Score = 37.4 bits (85), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 50/233 (21%), Positives = 108/233 (46%), Gaps = 18/233 (7%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           L+  H+ LV +IA+       P   + +++  G IGL +A+ +F+ E+G +  T++   I
Sbjct: 13  LIRQHVPLVRRIALHMIAKLPPNVELDDLIQVGMIGLAEALSRFESEQGVQFDTFASQRI 72

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + AM +  LR    +   +  +QK +   L RL+  L        +P     IA +L ++
Sbjct: 73  RGAMLDE-LREGDWMSRSSRKSQKEIEQALNRLEQRLG-------RPPLESEIAAELGMA 124

Query: 170 ESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
             +  S+  ++ G +   L  +      +   + +  V D  G +   + +++R   R+ 
Sbjct: 125 LDDYQSLLGKVRGTQLVYLEDIGGGDGDDGDDYLERHVAD-SGADPFALLRDQRM--RSA 181

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           L  ++  L  RE+ +       E+ + L+ +++   V+  RV Q+ ++A  ++
Sbjct: 182 LVEAIKTLPEREQYVMGM--YYEHDMNLKEIAAVLGVTESRVCQLHSQAIARL 232


>gi|29840191|ref|NP_829297.1| RNA polymerase sigma factor sigma-28 [Chlamydophila caviae GPIC]
 gi|29834539|gb|AAP05175.1| RNA polymerase sigma factor, sigma-70 family [Chlamydophila caviae
           GPIC]
          Length = 257

 Score = 37.4 bits (85), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 27/90 (30%), Positives = 48/90 (53%), Gaps = 11/90 (12%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPE 96
           Y E  ++     L+  +L LV K  +     G+P      ++ + G  GL++AV++FDPE
Sbjct: 16  YWETQEIEYRDTLIDFYLHLV-KCVVHRLISGMPSHVKTEDLYASGVEGLVRAVERFDPE 74

Query: 97  RGFRLATYSMWWIKAAM------QEYILRS 120
           +  R   Y+++ IKAA+      Q+++ RS
Sbjct: 75  KSRRFEGYALFLIKAAIIDDLRKQDWVPRS 104


>gi|221069309|ref|ZP_03545414.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Comamonas testosteroni
           KF-1]
 gi|220714332|gb|EED69700.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Comamonas testosteroni
           KF-1]
          Length = 239

 Score = 37.4 bits (85), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 50/233 (21%), Positives = 108/233 (46%), Gaps = 18/233 (7%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           L+  H+ LV +IA+       P   + +++  G IGL +A+ +F+ E+G +  T++   I
Sbjct: 13  LIRQHVPLVRRIALHMIAKLPPNVELDDLIQVGMIGLAEALSRFESEQGVQFDTFASQRI 72

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + AM +  LR    +   +  +QK +   L RL+  L        +P     IA +L ++
Sbjct: 73  RGAMLDE-LREGDWMSRSSRKSQKEIEQALNRLEQRLG-------RPPLESEIAAELGMA 124

Query: 170 ESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
             +  S+  ++ G +   L  +      +   + +  V D  G +   + +++R   R+ 
Sbjct: 125 LDDYQSLLGKVRGTQLVYLEDIGGGDGDDGDDYLERHVAD-SGADPFALLRDQRM--RSA 181

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           L  ++  L  RE+ +       E+ + L+ +++   V+  RV Q+ ++A  ++
Sbjct: 182 LVEAIKALPEREQYVMGM--YYEHDMNLKEIAAVLGVTESRVCQLHSQAIARL 232


>gi|330938480|gb|EGH42083.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. pisi
           str. 1704B]
          Length = 82

 Score = 37.4 bits (85), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 15/28 (53%), Positives = 24/28 (85%)

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 41  TLEEVGKQFDVTRERIRQIEAKALRKLR 68


>gi|322833177|ref|YP_004213204.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Rahnella sp. Y9602]
 gi|321168378|gb|ADW74077.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Rahnella sp. Y9602]
          Length = 240

 Score = 37.4 bits (85), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 46/220 (20%), Positives = 91/220 (41%), Gaps = 40/220 (18%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTANQK 133
           + +++  G IGL+ AV++FD  +G    TY++  I+ AM  E   R W           +
Sbjct: 41  LDDLLQAGGIGLLNAVERFDAMQGTAFTTYAVQRIRGAMLDELRSRDWV---------PR 91

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            +  N R +   + +      +P     +A+ L++   E   +                 
Sbjct: 92  SVRRNAREVSQAMHSAEQKLGRPPSEGEVAQVLDIPIEEYRQILM--------------- 136

Query: 194 DKNSSQ---WQDWLVYDHDGQEQVLIEKEERKNR---------RNMLTRSMSVLNPRERR 241
           D NSSQ   + +W   +H    + L+E  E  N          R+ +  ++  L  RE+ 
Sbjct: 137 DTNSSQLFSYDEWR-EEHGDTAEALMEGHEEANPLHHLLEGNLRHRVMEAIDALPEREKL 195

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +      +E  + L+ + +  +V   RV Q+ ++A K+++
Sbjct: 196 VLTLYYQEE--LNLKEIGAVLDVGESRVSQLHSQAIKRLR 233


>gi|299534757|ref|ZP_07048087.1| RNA polymerase sigma factor SigD [Lysinibacillus fusiformis ZC1]
 gi|298729845|gb|EFI70390.1| RNA polymerase sigma factor SigD [Lysinibacillus fusiformis ZC1]
          Length = 256

 Score = 37.4 bits (85), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 27/91 (29%), Positives = 44/91 (48%), Gaps = 7/91 (7%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEG 82
           P+L   +E  L  R+    D  A   L+  ++ LV    +   G GLP S    ++ S G
Sbjct: 4   PIL--NDEQKLWNRWIHERDPDAGDLLIKKYISLV-SYHVQRIGAGLPKSVSRDDLTSLG 60

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
            +GL  A+ KFD  R  +  TY+ + ++ A+
Sbjct: 61  MVGLFDALNKFDINRDLKFDTYASFRVRGAI 91


>gi|237731968|ref|ZP_04562449.1| flagellar biosynthesis sigma factor [Citrobacter sp. 30_2]
 gi|226907507|gb|EEH93425.1| flagellar biosynthesis sigma factor [Citrobacter sp. 30_2]
          Length = 239

 Score = 37.4 bits (85), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 47/220 (21%), Positives = 95/220 (43%), Gaps = 30/220 (13%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL+ AV ++D  +G    TY++  I+ AM +  LRS   V      N + 
Sbjct: 41  LDDLLQAGGIGLLNAVDRYDALQGTAFTTYAVQRIRGAMLDE-LRSRDWVPRSVRRNARE 99

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   + +L+   Q +  N  + E    +A +L +   E   M            L+++++
Sbjct: 100 VAQAMGQLE---QELGRNATETE----VAARLAIPVQEYRQM------------LLDTNN 140

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERK--------NRRNMLTRSMSVLNPRERRIFEAR 246
                + +W     D  E V  E ++          N R  +  ++  L  RE+ +    
Sbjct: 141 SQLFSYDEWREEHGDSIELVTEEHQQENPLQQLLEGNLRQRVMDAIEALPEREKLVLTLY 200

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             +E  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 201 YQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 238


>gi|126697623|ref|YP_001086520.1| RNA polymerase factor sigma-70 [Clostridium difficile 630]
 gi|260681829|ref|YP_003213114.1| RNA polymerase factor sigma-70 [Clostridium difficile CD196]
 gi|260685427|ref|YP_003216560.1| RNA polymerase factor sigma-70 [Clostridium difficile R20291]
 gi|296449816|ref|ZP_06891583.1| DNA-directed RNA polymerase sigma subunit SigH [Clostridium
           difficile NAP08]
 gi|296877880|ref|ZP_06901900.1| DNA-directed RNA polymerase sigma subunit SigH [Clostridium
           difficile NAP07]
 gi|115249060|emb|CAJ66871.1| RNA polymerase factor sigma-70 [Clostridium difficile]
 gi|260207992|emb|CBA60155.1| RNA polymerase sigma-H factor [Clostridium difficile CD196]
 gi|260211443|emb|CBE01550.1| RNA polymerase sigma-H factor [Clostridium difficile R20291]
 gi|296261303|gb|EFH08131.1| DNA-directed RNA polymerase sigma subunit SigH [Clostridium
           difficile NAP08]
 gi|296431077|gb|EFH16904.1| DNA-directed RNA polymerase sigma subunit SigH [Clostridium
           difficile NAP07]
          Length = 220

 Score = 37.4 bits (85), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 1/79 (1%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           +Q+EY +  R  E GD  A   ++T +   V   A  Y   G    +++ EG IGL +AV
Sbjct: 21  QQDEYNIVLRASE-GDKIALEYIITKYRNFVKAKAKSYFLIGADKEDIIQEGMIGLYKAV 79

Query: 91  KKFDPERGFRLATYSMWWI 109
           + FD  +      ++   I
Sbjct: 80  RDFDGSKTNSFKCFAEICI 98


>gi|302538372|ref|ZP_07290714.1| RNA polymerase sigma-E factor [Streptomyces sp. C]
 gi|302447267|gb|EFL19083.1| RNA polymerase sigma-E factor [Streptomyces sp. C]
          Length = 323

 Score = 37.4 bits (85), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 14/43 (32%), Positives = 26/43 (60%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           + ++V  G IGL++A+ +FDP R    AT +M +I   ++ + 
Sbjct: 107 VDDLVQVGTIGLIKAIDRFDPARENEFATLAMPYITGEIKRHF 149


>gi|254775435|ref|ZP_05216951.1| RNA polymerase sigma factor SigF [Mycobacterium avium subsp. avium
           ATCC 25291]
          Length = 242

 Score = 37.4 bits (85), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 59/273 (21%), Positives = 114/273 (41%), Gaps = 43/273 (15%)

Query: 22  EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           E+R++P   +  EY   +R RE        R+V   L L   +A  +   G  + ++V  
Sbjct: 4   ELRRMPA--ESHEY---RRQRE--------RIVARCLPLADHVASHFARRGEGLDDLVQV 50

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLR 140
             +GLM AV +FDP +G     +++  +   ++ Y    SW +          R+   LR
Sbjct: 51  ARLGLMNAVNRFDPAKGPSFIGFAVPTMMGEVRRYFRDYSWGM----------RVPRRLR 100

Query: 141 RLKGHLQAITDNNL----KPEQVVAIAKKLNVSESEVISMNCRLAGD----ESLNALINS 192
            L   +   T +      +      +++ L V   E++   C +AGD    +SL+A   +
Sbjct: 101 ELHVQISRTTADLAQQLGRAPNAGELSQVLEVPREEIV--ECLVAGDAYRLDSLDAPQGA 158

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
               + +     V D D Q + +  +E        L   ++ L  RER +   R  +   
Sbjct: 159 DSSGTPRSVADSVGDIDPQIEHITNRE-------ALRVLVATLPHREREVLRMRFFES-- 209

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           +T   ++    VS+ +V +I A   + +++ ++
Sbjct: 210 MTQSQIAERIGVSQMQVSRILANTLRCLRDQLE 242


>gi|254425398|ref|ZP_05039116.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp. PCC
           7335]
 gi|196192887|gb|EDX87851.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp. PCC
           7335]
          Length = 246

 Score = 37.4 bits (85), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 14/53 (26%), Positives = 33/53 (62%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           P  ++   G IGL++++++FDP +G   +++++ +I+  M  ++    + VKI
Sbjct: 37  PYEDLEQIGYIGLIRSIERFDPGQGCAFSSFAVPYIRGEMLHFLRDRGTTVKI 89


>gi|113473821|ref|YP_718084.1| RNA polymerase sigma factor (RpoD) [Sphingomonas sp. KA1]
 gi|112821501|dbj|BAF03372.1| Probable RNA polymerase sigma factor (RpoD) [Sphingomonas sp. KA1]
          Length = 328

 Score = 37.4 bits (85), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 20/64 (31%), Positives = 37/64 (57%), Gaps = 2/64 (3%)

Query: 226 NMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +LT ++S L+ RE R+   R         TL+ +  EF V+ +R+RQIE +A ++++  
Sbjct: 52  GVLTAALSCLSAREERVIRLRFGLGGHGEWTLQQIGDEFGVNPQRIRQIEMKALRRLRHQ 111

Query: 284 IQKQ 287
            +K+
Sbjct: 112 FRKR 115


>gi|332800097|ref|YP_004461596.1| ECF subfamily RNA polymerase sigma-24 subunit SigH
           [Tepidanaerobacter sp. Re1]
 gi|332697832|gb|AEE92289.1| RNA polymerase, sigma-24 subunit, SigH, ECF subfamily
           [Tepidanaerobacter sp. Re1]
          Length = 215

 Score = 37.4 bits (85), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 26/95 (27%), Positives = 42/95 (44%), Gaps = 9/95 (9%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           +GD  A   L+  +   V   A  Y   G    +++ EG IGL +A++ F+PE   RL++
Sbjct: 27  NGDHEALEYLINKYKNFVKSKARSYFLIGADREDIIQEGMIGLYKAIRDFNPE---RLSS 83

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           +       A  E  +    +  I T   QK +  N
Sbjct: 84  FR------AFAELCITRQIITAIKTATRQKHIPLN 112


>gi|170780849|ref|YP_001709181.1| putative sigma factor [Clavibacter michiganensis subsp.
           sepedonicus]
 gi|169155417|emb|CAQ00524.1| putative sigma factor [Clavibacter michiganensis subsp.
           sepedonicus]
          Length = 337

 Score = 37.4 bits (85), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 48/240 (20%), Positives = 108/240 (45%), Gaps = 27/240 (11%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           +V  HL L  ++A  + G     S++   G +GL++A +++DP  G    ++++  I   
Sbjct: 91  IVLDHLELADQLARQHSGRAHDWSDLRQVGYLGLVKAARRYDPGFGAPFVSFAIPTISGE 150

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           ++ ++  +  +V         R    ++ L+  L A+         V A+ ++L  + ++
Sbjct: 151 IKRHLRDNGWMV---------RPPRQIQELRHALLAV---------VPALTQRLGRTPTD 192

Query: 173 V-ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG--QEQVLIEKEE---RKNRRN 226
             ++ +     +E + AL   S    +   D  V++H+G      L   +    R  R  
Sbjct: 193 AELAAHTGHPREEVMEALAAHSSLRPASL-DHTVHEHEGISLADTLGADDPGYARAERTV 251

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +L  +  VL+ R+RRI   R + E   +   +++E  V++ +V ++ AR    ++  + +
Sbjct: 252 LLDAARGVLSERDRRILHLRFVDE--CSQSEIAAELGVTQMQVSRLLARILGALRAELTR 309


>gi|306518735|ref|ZP_07405082.1| RNA polymerase factor sigma-70 [Clostridium difficile QCD-32g58]
          Length = 205

 Score = 37.4 bits (85), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 23/79 (29%), Positives = 37/79 (46%), Gaps = 1/79 (1%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           +Q+EY +  R  E GD  A   ++T +   V   A  Y   G    +++ EG IGL +AV
Sbjct: 16  QQDEYNIVLRASE-GDKIALEYIITKYRNFVKAKAKSYFLIGADKEDIIQEGMIGLYKAV 74

Query: 91  KKFDPERGFRLATYSMWWI 109
           + FD  +      ++   I
Sbjct: 75  RDFDGSKTNSFKCFAEICI 93


>gi|163856407|ref|YP_001630705.1| flagellar-specific RNA polymerase sigma factor [Bordetella petrii
           DSM 12804]
 gi|163260135|emb|CAP42436.1| flagellar-specific RNA polymerase sigma factor [Bordetella petrii]
          Length = 246

 Score = 37.4 bits (85), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 45/215 (20%), Positives = 95/215 (44%), Gaps = 15/215 (6%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL+ A +++      +  TY+   I+ AM +  LRS   +     +  KR
Sbjct: 32  LDDLIQAGMIGLLDAARRYQETPDAQFETYATARIRGAMLDE-LRSQDWLPRSVRSKGKR 90

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN-ALINSS 193
           +   ++R +  L       ++P     IA +L +   E  +M     G + L+   I S+
Sbjct: 91  IEAAIQRKEHEL-------MRPPSESEIADELELPLDEYQAMLNDARGIQILHYDDIGSN 143

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D +   W+D +  D  G     ++     + R  L  ++  L  RE+ +       E  +
Sbjct: 144 DPDERGWRD-VPADSGGDP---LDALLTGDLRRALVNAIETLPEREKLVLSL--CYEQGL 197

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            L+ + +  EV+  RV Q+ ++A  +++  +++  
Sbjct: 198 NLKEIGAVLEVTEARVCQLRSQATARIRARLKEDA 232


>gi|121488755|emb|CAJ18262.1| sigma 70-type sigma factor [Chlorobium phaeobacteroides]
          Length = 165

 Score = 37.4 bits (85), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 13/50 (26%), Positives = 29/50 (58%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           +  +EG  G ++A K+ D  RGF+  +Y++WW + +  + +     +V++
Sbjct: 1   DXXNEGXXGXIKAAKRXDETRGFKFISYAVWWXRQSXLQALAEQSRIVRL 50


>gi|331002428|ref|ZP_08325946.1| hypothetical protein HMPREF0491_00808 [Lachnospiraceae oral taxon
          107 str. F0167]
 gi|330410244|gb|EGG89678.1| hypothetical protein HMPREF0491_00808 [Lachnospiraceae oral taxon
          107 str. F0167]
          Length = 172

 Score = 37.4 bits (85), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 19/79 (24%), Positives = 44/79 (55%), Gaps = 3/79 (3%)

Query: 16 LSRYIHEIRKI-PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
          L  Y+ +++ I P+ E +++ +L       GD +A +RL+ +H+    ++   + G G  
Sbjct: 7  LEMYLEDMKNIKPLDEAKKDDLLKALCT--GDNNAKNRLIEAHMMYATELVQPFMGCGQE 64

Query: 75 ISEVVSEGNIGLMQAVKKF 93
          + +++SE ++ L  AV ++
Sbjct: 65 VMDLISESHLALTMAVTEY 83


>gi|169840343|ref|ZP_02873531.1| RNA polymerase factor sigma-32 [candidate division TM7 single-cell
           isolate TM7a]
          Length = 54

 Score = 37.4 bits (85), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 20/49 (40%), Positives = 29/49 (59%), Gaps = 5/49 (10%)

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +LFFNLR ++  L A++     P++  AIA  L V  SEV+ M  R+ G
Sbjct: 1   QLFFNLRSMRKSLSALS-----PKEAQAIADDLGVKLSEVLEMEQRMTG 44


>gi|284041500|ref|YP_003391840.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Conexibacter woesei
           DSM 14684]
 gi|283945721|gb|ADB48465.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Conexibacter woesei
           DSM 14684]
          Length = 270

 Score = 37.4 bits (85), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 63/267 (23%), Positives = 113/267 (42%), Gaps = 29/267 (10%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNI 84
           +  ++   L ++Y+E GD +   RLV +   +V K  +  +   +P    + + +S G  
Sbjct: 11  ISAEDALALWRQYKESGDRAVRDRLVLTFAPMV-KYIVYKKVREIPARCEVEDFISCGLE 69

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR-SW---SLVKIGTTANQKRLFFNLR 140
            L+ +++++DPE+G  L  +S   I  A+ + + R  W   SL +     NQ R  F   
Sbjct: 70  ALIHSIERYDPEKGATLEQFSWTRIHGAVLDELRRQDWAPRSLRRWERDINQAREHF--- 126

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
            +  H +  +   L    +     +L   E E+++ +       SLN L+ S D+ + + 
Sbjct: 127 -IGVHSRRPSREELAG-ALGTTPAELRAREDEIVASDV-----TSLNTLVLSDDETAIER 179

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTR---SMSVLNPRERRIFEARRLQENPVTLEN 257
            D LV      E    + E    R     R   +   L  RER +  A  L    +TL  
Sbjct: 180 IDTLV-----SEDRFADPEHHTARDQAKMRFREAFERLPRREREV--AVLLYVKNLTLRE 232

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESI 284
           +     VS  RV QI  +  + ++E +
Sbjct: 233 IGGILGVSESRVCQIHGQLKRMLKEEL 259


>gi|326566649|gb|EGE16790.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis 12P80B1]
          Length = 48

 Score = 37.4 bits (85), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 15/28 (53%), Positives = 24/28 (85%)

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TLE +  +F+V+RER+RQIEA+A +K++
Sbjct: 6   TLEEVGKQFDVTRERIRQIEAKALRKLR 33


>gi|194365639|ref|YP_002028249.1| RNA polymerase sigma-28 subunit, FliA/WhiG [Stenotrophomonas
           maltophilia R551-3]
 gi|194348443|gb|ACF51566.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Stenotrophomonas
           maltophilia R551-3]
          Length = 247

 Score = 37.4 bits (85), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 27/87 (31%), Positives = 47/87 (54%), Gaps = 6/87 (6%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQAVKKF 93
           A +YRE    SAA+ ++  H  LV +IA  +    LP S    +++  G +GL++A + +
Sbjct: 4   AAQYREV-QRSAANEVIAQHSDLVRRIAH-HLAARLPASVEVDDLIQAGMMGLIEASRSY 61

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRS 120
           D ++G    TY+   I+ +M + I R 
Sbjct: 62  DADQGASFETYASIRIRGSMIDEIRRG 88


>gi|256783362|ref|ZP_05521793.1| RNA polymerase secondary sigma factor [Streptomyces lividans TK24]
 gi|289767236|ref|ZP_06526614.1| RNA polymerase secondary sigma factor [Streptomyces lividans TK24]
 gi|289697435|gb|EFD64864.1| RNA polymerase secondary sigma factor [Streptomyces lividans TK24]
          Length = 263

 Score = 37.4 bits (85), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 18/67 (26%), Positives = 36/67 (53%), Gaps = 1/67 (1%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           L +  +IA+ +RG G  + ++     +GL++AV  +DPERG     Y++  +   ++ + 
Sbjct: 46  LPMAERIAVRFRGRGENLEDLYQVAALGLVKAVDHYDPERGHAFEAYAVPTVTGEIKRHF 105

Query: 118 L-RSWSL 123
               W+L
Sbjct: 106 RDHMWTL 112


>gi|254523268|ref|ZP_05135323.1| RNA polymerase sigma factor [Stenotrophomonas sp. SKA14]
 gi|219720859|gb|EED39384.1| RNA polymerase sigma factor [Stenotrophomonas sp. SKA14]
          Length = 247

 Score = 37.4 bits (85), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 27/87 (31%), Positives = 47/87 (54%), Gaps = 6/87 (6%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQAVKKF 93
           A +YRE    SAA+ ++  H  LV +IA  +    LP S    +++  G +GL++A + +
Sbjct: 4   AAQYREV-QRSAANEVIAQHSDLVRRIAH-HLAARLPASVEVDDLIQAGMMGLIEASRSY 61

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRS 120
           D ++G    TY+   I+ +M + I R 
Sbjct: 62  DADQGASFETYTSIRIRGSMIDEIRRG 88


>gi|21225616|ref|NP_631395.1| RNA polymerase secondary sigma factor [Streptomyces coelicolor
           A3(2)]
 gi|2687404|gb|AAC01582.1| putative RNA polymerase secondary sigma factor [Streptomyces
           coelicolor A3(2)]
 gi|8246836|emb|CAB92887.1| putative RNA polymerase secondary sigma factor [Streptomyces
           coelicolor A3(2)]
          Length = 263

 Score = 37.0 bits (84), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 18/67 (26%), Positives = 36/67 (53%), Gaps = 1/67 (1%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           L +  +IA+ +RG G  + ++     +GL++AV  +DPERG     Y++  +   ++ + 
Sbjct: 46  LPMAERIAVRFRGRGENLEDLYQVAALGLVKAVDHYDPERGHAFEAYAVPTVTGEIKRHF 105

Query: 118 L-RSWSL 123
               W+L
Sbjct: 106 RDHMWTL 112


>gi|282599758|ref|ZP_05971750.2| motility sigma factor FliA [Providencia rustigianii DSM 4541]
 gi|282567697|gb|EFB73232.1| motility sigma factor FliA [Providencia rustigianii DSM 4541]
          Length = 242

 Score = 37.0 bits (84), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 17/48 (35%), Positives = 28/48 (58%), Gaps = 1/48 (2%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM-QEYILRSW 121
           I +++  G IGL+ A+++FD   G   ATY++  I+ +M  E   R W
Sbjct: 45  IDDLIQAGGIGLLHALERFDASLGASFATYAVQRIRGSMLDELRSRDW 92


>gi|158341129|ref|YP_001522296.1| RNA polymerase sigma factor domain-containing protein
           [Acaryochloris marina MBIC11017]
 gi|158311370|gb|ABW32982.1| RNA polymerase sigma factor domain protein [Acaryochloris marina
           MBIC11017]
          Length = 476

 Score = 37.0 bits (84), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 59/286 (20%), Positives = 118/286 (41%), Gaps = 44/286 (15%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           I  I + P L  ++E  L  + ++ GD  A   ++ S+L  +  +       G+   E++
Sbjct: 14  IATIARHPNLSPEQEAELILKAQD-GDNDARQTVIYSNLAWICSMGGSLSRKGIEDGELI 72

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
           SEG  GL +A+ ++  E+G  + T+S   I      Y  +S ++ +       K  +  L
Sbjct: 73  SEGYFGLNKAIDQWSSEKGANIRTFSRDKI------YKFQSEAVHQKNHIRLPKSTYEQL 126

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSE---------SEVISMNCRLAGDESLNALI 190
            +LK     + ++      V  +A+   + E         S+ +S+N      E+L  L 
Sbjct: 127 SKLKKATAVLGED----ATVAQLAEGTEIKEKRIRTLQEISQPVSLNSVTGTRENLELLD 182

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D            D  G     +  E        L   +  L+PR+R I      +E
Sbjct: 183 QQAD------------DCQGSLDPALSSE--------LLDLVDKLHPRQREILHLYHWEE 222

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPL 296
             ++ + +S    +  ++VR++  +A   +++ +Q   E++  PPL
Sbjct: 223 --LSFQKISDYLGLPAKKVRKLYKQALDLLRKFLQG--EINEFPPL 264


>gi|119485331|ref|ZP_01619659.1| sigma factor SigF [Lyngbya sp. PCC 8106]
 gi|119457087|gb|EAW38213.1| sigma factor SigF [Lyngbya sp. PCC 8106]
          Length = 259

 Score = 37.0 bits (84), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 28/98 (28%), Positives = 51/98 (52%), Gaps = 7/98 (7%)

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++  G IGL++A+++FD  +G   +++++ +I+  +Q Y LR  SL          R 
Sbjct: 56  DDLLQVGCIGLIRAIERFDLSKGHAFSSFAIPYIRGEIQHY-LRDKSL-----PLRVPRH 109

Query: 136 FFNLRRLKGHLQAITDNNLKPEQV-VAIAKKLNVSESE 172
           +  L+R    L       LK +     IA+ LN+SE+E
Sbjct: 110 WLTLQRQGMKLAQELQVKLKRQPTDTEIARGLNISETE 147


>gi|148273835|ref|YP_001223396.1| putative RNA polymerase sigma factor SigF [Clavibacter
           michiganensis subsp. michiganensis NCPPB 382]
 gi|147831765|emb|CAN02734.1| putative RNA polymerase sigma factor, SigF-homolog (stress
           response/stationary phase sigma factor) [Clavibacter
           michiganensis subsp. michiganensis NCPPB 382]
          Length = 335

 Score = 37.0 bits (84), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 47/240 (19%), Positives = 111/240 (46%), Gaps = 27/240 (11%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           +V  HL L  ++A  + G     S++   G +GL++A +++DP  G    ++++  I   
Sbjct: 89  IVLDHLELADQLARQHSGRAHDWSDLRQVGYLGLVKAARRYDPGFGAPFVSFAIPTISGE 148

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           ++ ++  +  +V         R   +++ L+  L A+         V A+ ++L  + ++
Sbjct: 149 IKRHLRDNGWVV---------RPPRHVQELRHALLAV---------VPALTQRLGRTPTD 190

Query: 173 V-ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG---QEQVLIEKE--ERKNRRN 226
             ++ +   A +E + AL   S    +   D+ V++ +G    + +  +     R  R  
Sbjct: 191 AELAAHTGHAREEVVEALAAHSSLRPASL-DFTVHEDEGISLADTIGADDPGYARAERTV 249

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +L  +  VL+ R+RRI   R + E   +   +++E  V++ +V ++ AR    ++  + +
Sbjct: 250 LLDAARGVLSDRDRRILHLRFVDE--CSQSEIAAELGVTQMQVSRLLARILGALRAELTR 307


>gi|197285477|ref|YP_002151349.1| flagellar biosynthesis sigma factor [Proteus mirabilis HI4320]
 gi|6959882|gb|AAF33246.1|AF221596_2 FliA [Proteus mirabilis]
 gi|194682964|emb|CAR43378.1| RNA polymerase sigma factor for flagellar operon [Proteus mirabilis
           HI4320]
          Length = 240

 Score = 37.0 bits (84), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 53/230 (23%), Positives = 106/230 (46%), Gaps = 33/230 (14%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM-QEY 116
           LRL VK+        + + +++  G IGL+ AV+++D  +G    TY++  I+ +M  E 
Sbjct: 29  LRLQVKLPAS-----VELDDLLQAGGIGLLNAVERYDSMQGAAFTTYAVQRIRGSMLDEL 83

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP--EQVVAIAKKLNVSESEVI 174
             R W+          + +  N R +   +  +  +  +P  EQ VA   ++ ++E   I
Sbjct: 84  RSRDWA---------PRSVRRNAREVTQSIHQLEQDLGRPPSEQEVADHLQIELAEYRQI 134

Query: 175 SM---NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE-QVLIEKEERKNRRNMLTR 230
            +   N +L   +  + +   S + S   QD    DHD    Q+L+E + R+     +  
Sbjct: 135 LLDTNNSQLFSYDEWHEIYGESCEPS---QD---EDHDDNPLQMLLESDIRQR----VID 184

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           ++ +L  RE+ +      +E  + L+ + +   V   RV Q+ ++A K++
Sbjct: 185 AIELLPEREKMVLTLYYQEE--LNLKEIGAVLNVGESRVSQLHSQAIKRL 232


>gi|330684827|gb|EGG96520.1| RNA polymerase sigma-B factor [Staphylococcus epidermidis VCU121]
          Length = 256

 Score = 37.0 bits (84), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 50/247 (20%), Positives = 113/247 (45%), Gaps = 16/247 (6%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           K ++E  +  A  +LV  + +L+  +A  Y        ++V  G +GL+ A+ +FD    
Sbjct: 21  KEHQEDQNSGAQDKLVRHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDLSFD 80

Query: 99  FRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
            +   + +  +   ++ Y+  ++WS+         +R+     R+K     +T+   +  
Sbjct: 81  RKFEAFLVPTVIGEIKRYLRDKTWSV------HVPRRIKEIGPRIKKVSDELTNELERSP 134

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQVLI 216
            +  IA +L V++ EV+     +   +S NAL ++ S +         + D  GQ+    
Sbjct: 135 SISEIAARLEVTDEEVLEA---IEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQQD--- 188

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           +  +   +R +L R + +L+ RE+ I +   ++   ++ +       +S+  V +++  A
Sbjct: 189 DNYDLTEKRMILERILPILSDREKEIIQCTFIE--GLSQKETGERIGLSQMHVSRLQRTA 246

Query: 277 FKKVQES 283
            KK+QE+
Sbjct: 247 IKKLQEA 253


>gi|283850718|ref|ZP_06368005.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio sp.
           FW1012B]
 gi|283573961|gb|EFC21934.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio sp.
           FW1012B]
          Length = 264

 Score = 37.0 bits (84), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 55/240 (22%), Positives = 105/240 (43%), Gaps = 26/240 (10%)

Query: 54  VTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           +  H    +KI        LP    + E++S G +GL++A+ +F PE G +  TY+   I
Sbjct: 39  IVRHYSPKIKIVASRLKAKLPQSVEMGELLSAGAMGLIEALGRFRPELGIKFETYAESRI 98

Query: 110 KAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           K +M + + R  W       +  Q+     +R L+   + I +++ K   V  +A+   +
Sbjct: 99  KGSMLDDLRRMDW------FSRGQRH---RVRTLEEASRRIENDSGKAATVEQLAEATGL 149

Query: 169 SESEVISMNCRLAGDESL-NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +E EV        G E+L N L  S D  +   ++   Y  +  E    +  E K   + 
Sbjct: 150 TEREVTQ------GLEALQNQLCLSLDAIT---ENISSYQKNQLENEPYKSAEFKELVDK 200

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   +  L PRE+ +      +E  + +   S    ++  RV Q+ ++A  ++++  + Q
Sbjct: 201 LASLIDDLTPREKLVLSLYYGEE--LNMRETSEVMGITEGRVSQLHSQALARLRQKFKAQ 258


>gi|239927803|ref|ZP_04684756.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 220

 Score = 37.0 bits (84), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 50/230 (21%), Positives = 105/230 (45%), Gaps = 23/230 (10%)

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSW 121
           ++A  +R  G    ++     +GL++AV ++DPE G    +Y++  I   ++ +     W
Sbjct: 4   RLAGRFRSRGESFDDLRQVAALGLVKAVDRYDPELGNAFESYAVPTITGEIKRHFRDHMW 63

Query: 122 SLVKIGTTANQKRLFFNLR-RLKGHLQAIT-DNNLKPEQVVAIAKKLNVSESEVISMNCR 179
           +L       +  R    LR R++   Q ++   + +P  V  IA+  ++SE +V +    
Sbjct: 64  TL-------HVPRRVQELRNRVRSASQDLSLSGSGRPPTVAEIAEHADLSEEDVRTGQGA 116

Query: 180 LAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
           L      SL+A + S D   S   D L    D     ++++E  + R       ++ L  
Sbjct: 117 LDSFTALSLDAELTSGDDGYS-LGDTLGA-PDPALDTVVDREAVRER-------LAALPE 167

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           RE+ I   R   +  +T  ++++E  +S+  V ++ +R   +++E + + 
Sbjct: 168 REQAILYMRFFGD--MTQSSIAAELGISQMHVSRLISRCCGRIREQVMRD 215


>gi|227355968|ref|ZP_03840360.1| RNA polymerase sigma factor for flagellar operon [Proteus mirabilis
           ATCC 29906]
 gi|227163956|gb|EEI48858.1| RNA polymerase sigma factor for flagellar operon [Proteus mirabilis
           ATCC 29906]
          Length = 244

 Score = 37.0 bits (84), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 53/230 (23%), Positives = 106/230 (46%), Gaps = 33/230 (14%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM-QEY 116
           LRL VK+        + + +++  G IGL+ AV+++D  +G    TY++  I+ +M  E 
Sbjct: 33  LRLQVKLPAS-----VELDDLLQAGGIGLLNAVERYDSMQGAAFTTYAVQRIRGSMLDEL 87

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP--EQVVAIAKKLNVSESEVI 174
             R W+          + +  N R +   +  +  +  +P  EQ VA   ++ ++E   I
Sbjct: 88  RSRDWA---------PRSVRRNAREVTQSIHQLEQDLGRPPSEQEVADHLQIELAEYRQI 138

Query: 175 SM---NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE-QVLIEKEERKNRRNMLTR 230
            +   N +L   +  + +   S + S   QD    DHD    Q+L+E + R+     +  
Sbjct: 139 LLDTNNSQLFSYDEWHEIYGESCEPS---QD---EDHDDNPLQMLLESDIRQR----VID 188

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           ++ +L  RE+ +      +E  + L+ + +   V   RV Q+ ++A K++
Sbjct: 189 AIELLPEREKMVLTLYYQEE--LNLKEIGAVLNVGESRVSQLHSQAIKRL 236


>gi|239637364|ref|ZP_04678346.1| RNA polymerase sigma-B factor [Staphylococcus warneri L37603]
 gi|239596964|gb|EEQ79479.1| RNA polymerase sigma-B factor [Staphylococcus warneri L37603]
          Length = 256

 Score = 37.0 bits (84), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 50/247 (20%), Positives = 113/247 (45%), Gaps = 16/247 (6%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           K ++E  +  A  +LV  + +L+  +A  Y        ++V  G +GL+ A+ +FD    
Sbjct: 21  KEHQEDQNSGAQDKLVRHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGAINRFDLSFD 80

Query: 99  FRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
            +   + +  +   ++ Y+  ++WS+         +R+     R+K     +T+   +  
Sbjct: 81  RKFEAFLVPTVIGEIKRYLRDKTWSV------HVPRRIKEIGPRIKKVSDELTNELERSP 134

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQVLI 216
            +  IA +L V++ EV+     +   +S NAL ++ S +         + D  GQ+    
Sbjct: 135 SISEIAARLEVTDEEVLEA---MEMGQSYNALSVDHSIEADKDGSTVTLLDIMGQQD--- 188

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           +  +   +R +L R + +L+ RE+ I +   ++   ++ +       +S+  V +++  A
Sbjct: 189 DNYDLTEKRMILERILPILSDREKEIIQCTFIE--GLSQKETGERIGLSQMHVSRLQRTA 246

Query: 277 FKKVQES 283
            KK+QE+
Sbjct: 247 IKKLQEA 253


>gi|229074589|ref|ZP_04207614.1| RNA polymerase sigma-B factor [Bacillus cereus Rock4-18]
 gi|229095607|ref|ZP_04226590.1| RNA polymerase sigma-B factor [Bacillus cereus Rock3-29]
 gi|229114558|ref|ZP_04243973.1| RNA polymerase sigma-B factor [Bacillus cereus Rock1-3]
 gi|228668908|gb|EEL24335.1| RNA polymerase sigma-B factor [Bacillus cereus Rock1-3]
 gi|228687817|gb|EEL41712.1| RNA polymerase sigma-B factor [Bacillus cereus Rock3-29]
 gi|228708547|gb|EEL60695.1| RNA polymerase sigma-B factor [Bacillus cereus Rock4-18]
          Length = 203

 Score = 37.0 bits (84), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 40/175 (22%), Positives = 86/175 (49%), Gaps = 26/175 (14%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRL 135
           +++  G +GL+ A++++D   G     +++  I   +++Y+  ++W +       +  R 
Sbjct: 4   DIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGI-------HVPRR 56

Query: 136 FFNLR-RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNAL 189
             +L  ++K  ++ +TD+  +  +++ IA  L +SE EV+ +     N R++   SL+ +
Sbjct: 57  IKDLGGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVS---SLDDV 113

Query: 190 I-NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           + NSSD +S    + +     G EQ          RR +L    +VLN  E+ + 
Sbjct: 114 VENSSDGSSVARIESVGEVEQGYEQT--------ERRLVLEDIFNVLNETEKSVI 160


>gi|297197353|ref|ZP_06914750.1| RNA polymerase sigma-B factor [Streptomyces sviceus ATCC 29083]
 gi|197714848|gb|EDY58882.1| RNA polymerase sigma-B factor [Streptomyces sviceus ATCC 29083]
          Length = 263

 Score = 37.0 bits (84), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 33/139 (23%), Positives = 65/139 (46%), Gaps = 15/139 (10%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV   L +  +IA+ +RG G  + ++     +GL++AV  +DP RG     Y++  +   
Sbjct: 41  LVELWLPMAERIAVRFRGRGESLEDLYQVAALGLVKAVDHYDPARGSAFEAYAVPTVTGE 100

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLR-RLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
           ++ +     W+L       +  R   +LR R++   + ++    +   V  IA++ +++E
Sbjct: 101 IKRHFRDHMWTL-------HVPRRVQDLRNRVRQASKELSQTPGRAPTVAEIAERAHLTE 153

Query: 171 SEVISMNCRLAGDESLNAL 189
            EV       AG E+L   
Sbjct: 154 DEV------RAGAEALECF 166


>gi|190574220|ref|YP_001972065.1| putative RNA polymerase sigma factor for flagellar regulon FliA
           [Stenotrophomonas maltophilia K279a]
 gi|190012142|emb|CAQ45765.1| putative RNA polymerase sigma factor for flagellar regulon FliA
           [Stenotrophomonas maltophilia K279a]
          Length = 247

 Score = 37.0 bits (84), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 27/87 (31%), Positives = 47/87 (54%), Gaps = 6/87 (6%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQAVKKF 93
           A +YRE    SAA+ ++  H  LV +IA  +    LP S    +++  G +GL++A + +
Sbjct: 4   AAQYREV-QRSAANEVIAQHSDLVRRIAH-HLAARLPASVEVDDLIQAGMMGLIEASRSY 61

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRS 120
           D ++G    TY+   I+ +M + I R 
Sbjct: 62  DADQGASFETYASIRIRGSMIDEIRRG 88


>gi|228906737|ref|ZP_04070609.1| RNA polymerase sigma-B factor [Bacillus thuringiensis IBL 200]
 gi|228964059|ref|ZP_04125186.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228795629|gb|EEM43109.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228852914|gb|EEM97696.1| RNA polymerase sigma-B factor [Bacillus thuringiensis IBL 200]
          Length = 203

 Score = 37.0 bits (84), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 40/175 (22%), Positives = 86/175 (49%), Gaps = 26/175 (14%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRL 135
           +++  G +GL+ A++++D   G     +++  I   +++Y+  ++W +       +  R 
Sbjct: 4   DIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGI-------HVPRR 56

Query: 136 FFNLR-RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNAL 189
             +L  ++K  ++ +TD+  +  +++ IA  L +SE EV+ +     N R++   SL+ +
Sbjct: 57  IKDLGGKIKLAIEELTDHLQRSPKIIEIANHLGLSEEEVLEIMDAKNNYRVS---SLDDV 113

Query: 190 I-NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           + NSSD +S    + +     G EQ          RR +L    +VLN  E+ + 
Sbjct: 114 VENSSDGSSVARIESVGEVEQGYEQT--------ERRLVLEDIFNVLNDTEKSVI 160


>gi|320107038|ref|YP_004182628.1| RNA polymerase sigma 28 subunit FliA/WhiG [Terriglobus saanensis
           SP1PR4]
 gi|319925559|gb|ADV82634.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Terriglobus saanensis
           SP1PR4]
          Length = 294

 Score = 37.0 bits (84), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 50/224 (22%), Positives = 101/224 (45%), Gaps = 23/224 (10%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI-LRSWSLVKIGTTANQK 133
           + ++++ G IGL+ A  KFD  +  +  +Y+ + I+ A+ + +    WS          +
Sbjct: 87  LDDLIAAGMIGLIDAFSKFDHSKKVQFKSYAQFRIRGAILDSLRTLDWS---------PR 137

Query: 134 RLFFNLRRLKGHLQAITD--NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNAL 189
            L    R ++  ++A+T     +  EQ   IA+++N+S SE   +   L G E  SL+A 
Sbjct: 138 ELRRKGRAVEEAIRAVTQRFGCVPAEQ--EIAREMNLSLSEYQGLLGELKGLEIGSLHA- 194

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
               ++     ++ L Y     E   + +  +   +  L  ++  L  RER +      +
Sbjct: 195 ----ERGEDSGEEELAYVPGSPEDGPLFRCLKGELKQHLMEAIDDLPERERMVLTLYYYE 250

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E  +T++ +     V   RV QI + A  +++ S+ +    +SS
Sbjct: 251 E--LTMKEVGLTLGVVESRVSQIHSSAVARLRVSLAELANKTSS 292


>gi|205352349|ref|YP_002226150.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 287/91]
 gi|205272130|emb|CAR36983.1| RNA polymerase sigma transcription factor for flagellar operon
           [Salmonella enterica subsp. enterica serovar Gallinarum
           str. 287/91]
 gi|326627399|gb|EGE33742.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 9]
          Length = 239

 Score = 37.0 bits (84), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 48/221 (21%), Positives = 100/221 (45%), Gaps = 32/221 (14%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL+ AV ++D  +G    TY++  I+ AM +  LRS   V      N + 
Sbjct: 41  LDDLLQAGGIGLLNAVDRYDALQGTAFTTYAVQRIRGAMLDE-LRSRDWVPRSVRRNARE 99

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   + +L+   Q +  N  + E    +A++L +  +E   M            L+++++
Sbjct: 100 VAQAMGQLE---QKLGRNATETE----VAERLGIPVAEYRQM------------LLDTNN 140

Query: 195 KNSSQWQDW---------LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
                + +W         LV +   QE  L +  E   R+ ++  ++  L  RE+ +   
Sbjct: 141 SQLFSYDEWREEHGDSIELVTEEHQQENPLHQLLEGDLRQRVMD-AIESLPEREQLVLTL 199

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +E  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 200 YYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 238


>gi|167745714|ref|ZP_02417841.1| hypothetical protein ANACAC_00407 [Anaerostipes caccae DSM 14662]
 gi|317472694|ref|ZP_07932009.1| RNA polymerase sigma-H factor [Anaerostipes sp. 3_2_56FAA]
 gi|167655026|gb|EDR99155.1| hypothetical protein ANACAC_00407 [Anaerostipes caccae DSM 14662]
 gi|316899871|gb|EFV21870.1| RNA polymerase sigma-H factor [Anaerostipes sp. 3_2_56FAA]
          Length = 192

 Score = 37.0 bits (84), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 34/126 (26%), Positives = 57/126 (45%), Gaps = 7/126 (5%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A   L+  +  LV + +  +   G    +++ EG IGL +AVK +D E+    +T+
Sbjct: 19  GDDRAMDFLLNRYGGLVRRESRKFFLAGADEEDLIQEGMIGLFKAVKNYDDEKNASFSTF 78

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +   +K   Q Y   + S  K     N     FN +   G      + +  PEQV  + +
Sbjct: 79  ASLCVKR--QIYTTVTASKRKKHGPLNNYISLFNEQ---GEEDQFMEEDTNPEQV--LIQ 131

Query: 165 KLNVSE 170
           K N+S+
Sbjct: 132 KENISD 137


>gi|299531273|ref|ZP_07044683.1| RNA polymerase, sigma 28 subunit [Comamonas testosteroni S44]
 gi|298720680|gb|EFI61627.1| RNA polymerase, sigma 28 subunit [Comamonas testosteroni S44]
          Length = 239

 Score = 37.0 bits (84), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 50/233 (21%), Positives = 107/233 (45%), Gaps = 18/233 (7%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           L+  H+ LV +IA+       P   + +++  G IGL +A+ +F+ E+G +  T++   I
Sbjct: 13  LIRQHVPLVRRIALHMIAKLPPNVELDDLIQVGMIGLAEALSRFESEQGVQFDTFASQRI 72

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + AM +  LR    +   +  +QK +   L RL+  L        +P     IA +L ++
Sbjct: 73  RGAMLDE-LREGDWMSRSSRKSQKEIEQALNRLEQRLG-------RPPLESEIAAELGMA 124

Query: 170 ESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
             +  S+  ++ G +   L  +      +   + +  V D  G +   + ++ R   R+ 
Sbjct: 125 LDDYQSLLGKVRGTQLVYLEDIGGGDGDDGDDYLERHVAD-SGADPFALLRDHRM--RSA 181

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           L  ++  L  RE+ +       E+ + L+ +++   V+  RV Q+ ++A  ++
Sbjct: 182 LVEAIKALPEREQYVMGM--YYEHDMNLKEIAAVLGVTESRVCQLHSQAIARL 232


>gi|124268265|ref|YP_001022269.1| DNA-directed RNA polymerase specialized sigma subunit [Methylibium
           petroleiphilum PM1]
 gi|124261040|gb|ABM96034.1| DNA-directed RNA polymerase specialized sigma subunit [Methylibium
           petroleiphilum PM1]
          Length = 237

 Score = 37.0 bits (84), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 43/206 (20%), Positives = 91/206 (44%), Gaps = 13/206 (6%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           I +++  G IGL  A+ +FD  +G +  T++   I+ AM +  LR    +  G    Q+ 
Sbjct: 38  IDDLIQVGLIGLTDAMSRFDSAQGVQFETFATQRIRGAMLDE-LRGSDWMSRGNRKQQRE 96

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   + +L+  L         P +   IAK++ +S ++   +  ++ G + +     S D
Sbjct: 97  IEVAVHKLQQQL------GRAPAE-SEIAKQMGLSLADYQELLGKVRGTQLVYLEDMSGD 149

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
              + + D  V D +     L++       R  L  ++  L  RE+  F      E  + 
Sbjct: 150 DGDNDFLDRHVADENENPVALLQDH---RMRLALIEAIKTLPEREQ--FVMGMYYEQDMN 204

Query: 255 LENLSSEFEVSRERVRQIEARAFKKV 280
           L+ +++   V+  RV Q+ +++  ++
Sbjct: 205 LKEIAAVLGVTESRVCQLHSQSIARL 230


>gi|161613481|ref|YP_001587446.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|167993526|ref|ZP_02574620.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar 4,[5],12:i:- str.
           CVM23701]
 gi|168234127|ref|ZP_02659185.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Kentucky str. CDC 191]
 gi|168244804|ref|ZP_02669736.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL486]
 gi|168259759|ref|ZP_02681732.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Hadar str. RI_05P066]
 gi|168822997|ref|ZP_02834997.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Weltevreden str.
           HI_N05-537]
 gi|194445382|ref|YP_002041220.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Newport str. SL254]
 gi|194450090|ref|YP_002046006.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL476]
 gi|194471287|ref|ZP_03077271.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Kentucky str. CVM29188]
 gi|197251137|ref|YP_002146068.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
 gi|197362055|ref|YP_002141692.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. AKU_12601]
 gi|198242943|ref|YP_002215131.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Dublin str. CT_02021853]
 gi|200390898|ref|ZP_03217509.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Virchow str. SL491]
 gi|213053507|ref|ZP_03346385.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. E00-7866]
 gi|213650343|ref|ZP_03380396.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. J185]
 gi|213855803|ref|ZP_03384043.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. M223]
 gi|238912471|ref|ZP_04656308.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Tennessee str. CDC07-0191]
 gi|289824078|ref|ZP_06543676.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-3139]
 gi|56127386|gb|AAV76892.1| RNA polymerase sigma transcription factor for flagellar operon
           [Salmonella enterica subsp. enterica serovar Paratyphi A
           str. ATCC 9150]
 gi|161362845|gb|ABX66613.1| hypothetical protein SPAB_01198 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|194404045|gb|ACF64267.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Newport str. SL254]
 gi|194408394|gb|ACF68613.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL476]
 gi|194457651|gb|EDX46490.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Kentucky str. CVM29188]
 gi|197093532|emb|CAR58994.1| RNA polymerase sigma transcription factor for flagellar operon
           [Salmonella enterica subsp. enterica serovar Paratyphi A
           str. AKU_12601]
 gi|197214840|gb|ACH52237.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Agona str. SL483]
 gi|197937459|gb|ACH74792.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Dublin str.
           CT_02021853]
 gi|199603343|gb|EDZ01889.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Virchow str. SL491]
 gi|205328422|gb|EDZ15186.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar 4,[5],12:i:- str.
           CVM23701]
 gi|205331884|gb|EDZ18648.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Kentucky str. CDC 191]
 gi|205336383|gb|EDZ23147.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL486]
 gi|205340661|gb|EDZ27425.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Weltevreden str.
           HI_N05-537]
 gi|205350810|gb|EDZ37441.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Hadar str. RI_05P066]
 gi|312912946|dbj|BAJ36920.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhimurium str. T000240]
 gi|321224599|gb|EFX49662.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Typhimurium str.
           TN061786]
 gi|322616949|gb|EFY13857.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315996572]
 gi|322618189|gb|EFY15081.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-1]
 gi|322625859|gb|EFY22678.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-3]
 gi|322626311|gb|EFY23121.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-4]
 gi|322632726|gb|EFY29471.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-1]
 gi|322639068|gb|EFY35761.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-2]
 gi|322640509|gb|EFY37162.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 531954]
 gi|322647255|gb|EFY43754.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. NC_MB110209-0054]
 gi|322649897|gb|EFY46318.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. OH_2009072675]
 gi|322655505|gb|EFY51813.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. CASC_09SCPH15965]
 gi|322660283|gb|EFY56521.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 19N]
 gi|322662964|gb|EFY59171.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 81038-01]
 gi|322668149|gb|EFY64308.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. MD_MDA09249507]
 gi|322674091|gb|EFY70185.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 414877]
 gi|322675556|gb|EFY71630.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 366867]
 gi|322683032|gb|EFY79048.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 413180]
 gi|322686726|gb|EFY82704.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 446600]
 gi|323195385|gb|EFZ80565.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609458-1]
 gi|323199276|gb|EFZ84371.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556150-1]
 gi|323204441|gb|EFZ89447.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609460]
 gi|323207531|gb|EFZ92479.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 507440-20]
 gi|323211856|gb|EFZ96687.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556152]
 gi|323217516|gb|EGA02235.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB101509-0077]
 gi|323219591|gb|EGA04075.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB102109-0047]
 gi|323223594|gb|EGA07909.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB110209-0055]
 gi|323231538|gb|EGA15651.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB111609-0052]
 gi|323235981|gb|EGA20060.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009083312]
 gi|323240551|gb|EGA24594.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009085258]
 gi|323245443|gb|EGA29443.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315731156]
 gi|323253976|gb|EGA37800.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008282]
 gi|323255497|gb|EGA39258.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008283]
 gi|323262094|gb|EGA45657.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008284]
 gi|323266217|gb|EGA49707.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008285]
 gi|323270674|gb|EGA54115.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008287]
 gi|326622879|gb|EGE29224.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Dublin str. 3246]
          Length = 229

 Score = 37.0 bits (84), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 48/221 (21%), Positives = 100/221 (45%), Gaps = 32/221 (14%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL+ AV ++D  +G    TY++  I+ AM +  LRS   V      N + 
Sbjct: 31  LDDLLQAGGIGLLNAVDRYDALQGTAFTTYAVQRIRGAMLDE-LRSRDWVPRSVRRNARE 89

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   + +L+   Q +  N  + E    +A++L +  +E   M            L+++++
Sbjct: 90  VAQAMGQLE---QELGRNATETE----VAERLGIPVAEYRQM------------LLDTNN 130

Query: 195 KNSSQWQDW---------LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
                + +W         LV +   QE  L +  E   R+ ++  ++  L  RE+ +   
Sbjct: 131 SQLFSYDEWREEHGDSIELVTEEHQQENPLHQLLEGDLRQRVMD-AIESLPEREQLVLTL 189

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +E  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 190 YYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 228


>gi|34496477|ref|NP_900692.1| RNA polymerase sigma factor for flagellar operon [Chromobacterium
           violaceum ATCC 12472]
 gi|34102331|gb|AAQ58697.1| RNA polymerase sigma factor for flagellar operon [Chromobacterium
           violaceum ATCC 12472]
          Length = 248

 Score = 37.0 bits (84), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 15/45 (33%), Positives = 29/45 (64%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           + ++V  G IGL++A ++FDP +G +  T++   I+ AM + + R
Sbjct: 46  LGDLVQVGMIGLIEAARQFDPAQGVQFETFASQRIRGAMLDELRR 90


>gi|119716157|ref|YP_923122.1| sigma-70 region 4 domain-containing protein [Nocardioides sp.
           JS614]
 gi|119536818|gb|ABL81435.1| sigma-70 region 4 domain protein [Nocardioides sp. JS614]
          Length = 282

 Score = 37.0 bits (84), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R+V  +  +   +A  +R  G+P  ++      GL +AV +FDPE    L TY++  I+ 
Sbjct: 61  RVVVINRGVADAVAARFRNRGIPQEDLRQVAYEGLTKAVHRFDPELRNDLLTYAVPTIRG 120

Query: 112 AMQEYIL-RSWSL 123
            +Q Y   + W++
Sbjct: 121 ELQRYFRDQGWTV 133


>gi|290956233|ref|YP_003487415.1| sigma factor [Streptomyces scabiei 87.22]
 gi|260645759|emb|CBG68850.1| putative sigma factor [Streptomyces scabiei 87.22]
          Length = 262

 Score = 37.0 bits (84), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 53/256 (20%), Positives = 112/256 (43%), Gaps = 51/256 (19%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ + L +  ++A  +R  G    ++    ++GL++AV ++DPE G    +Y++  I  
Sbjct: 38  RIIEAWLPMAERLAGRFRSRGESYEDLRQVASLGLVKAVDRYDPELGNAFESYAVPTITG 97

Query: 112 AMQEYILRS-WSLVKIGTTANQKRLFFNLR-RLKGHLQAI--TDNNLKPEQVVAIAKKLN 167
            ++ +     W+L       +  R   +LR R++   Q +  T +  +P  V  IA+  N
Sbjct: 98  EIKRHFRDHMWTL-------HVPRRVQDLRNRVRFATQDLSQTISGRRP-TVAEIAEHAN 149

Query: 168 VSESEV------------ISMNCRLAGDE---SLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +SE +V            +S++  L G E   SL+  + S+D                  
Sbjct: 150 MSEEDVRVGLEALESFTALSLDAELPGSEDGYSLSDALGSADPAL--------------- 194

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
             ++++E  K R       ++ L  RER I   R   +  +T   ++ E  +S+  V ++
Sbjct: 195 DTVVDREAVKPR-------LAALPERERAILYMRFFGD--MTQSRIADELGISQMHVSRL 245

Query: 273 EARAFKKVQESIQKQV 288
            +R   ++++ + +  
Sbjct: 246 ISRCCDRLRDQVMRDA 261


>gi|116626504|ref|YP_828660.1| FliA/WhiG family RNA polymerase sigma factor [Candidatus Solibacter
           usitatus Ellin6076]
 gi|116229666|gb|ABJ88375.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Candidatus
           Solibacter usitatus Ellin6076]
          Length = 251

 Score = 37.0 bits (84), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 56/249 (22%), Positives = 105/249 (42%), Gaps = 37/249 (14%)

Query: 52  RLVTSHL---RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           RL+  HL   RL+ +         + + ++VS G +GL+ A+  FD     +L TY+ + 
Sbjct: 17  RLILEHLPQVRLIARRIQERLPESISLDDLVSTGVLGLISAIDNFDASHNVKLKTYAEYK 76

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA-KKLN 167
           I+ A+ +      SL  +     QKR     R+ K           + E  +A+A ++L+
Sbjct: 77  IRGAILD------SLRGLDWAPRQKR-----RKSK-----------QIEAAIAVAEQRLH 114

Query: 168 VSES-EVISMNCRLAGDESLNALINSSDKNSS--------QWQDWLVYDHDGQEQVLIEK 218
            S   E I+    +  DE    L+     N +        Q +D L Y  DG + +    
Sbjct: 115 ASPGEEEIAGELGITVDEYHEWLVEIRGLNVASLEYAGNEQGRDLLHYIPDGSDNLPSTL 174

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
            ER     +L  S+  +   ER +      +E  +TL  ++    +   R+ Q++++A  
Sbjct: 175 LERSELERLLASSIDGIPAIERTVLSLYFHEE--LTLREIAQVVNLHESRISQLKSQAIL 232

Query: 279 KVQESIQKQ 287
           +++  +  Q
Sbjct: 233 RLRGQMASQ 241


>gi|24374722|ref|NP_718765.1| flagellar biosynthesis sigma factor [Shewanella oneidensis MR-1]
 gi|24349382|gb|AAN56209.1|AE015759_1 RNA polymerase sigma-27 factor [Shewanella oneidensis MR-1]
          Length = 237

 Score = 37.0 bits (84), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 53/223 (23%), Positives = 100/223 (44%), Gaps = 39/223 (17%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS-WSLVKIGTTANQK 133
           + +++  G +GL++A  KFD  +G +  T++   I+ AM + I R  W           +
Sbjct: 41  LDDLLQAGMMGLLEASSKFDGGKGAKFETFAGIRIRGAMLDEIRRGDWV---------PR 91

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVA-------IAKKLNVSESEVISMNCRLAGDESL 186
            +  N RR+    QAI     + EQV+        IA+KL+++  E       +  D S+
Sbjct: 92  SVHRNNRRIA---QAID----ELEQVLGRDARDTEIAEKLDMTLDEY----HHILNDVSV 140

Query: 187 NALINSSDKNSSQWQDWLVYDH---DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
             +I   D   S  +D L       DG  +VL E +      + L  ++ +L  R+  + 
Sbjct: 141 GKIIGIEDLGVS--EDILTTSDNVSDGTFEVLAETQ----FHSALVEAIKILPERDALVL 194

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                 +  + L+ + +  EVS  RV QI ++A  +++  +++
Sbjct: 195 SL--YYDEALNLKEIGAILEVSESRVSQILSQAMLRLKGKLKQ 235


>gi|218439022|ref|YP_002377351.1| RNA polymerase sigma factor SigF [Cyanothece sp. PCC 7424]
 gi|218171750|gb|ACK70483.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cyanothece
           sp. PCC 7424]
          Length = 257

 Score = 37.0 bits (84), Expect = 3.8,   Method: Compositional matrix adjust.
 Identities = 41/183 (22%), Positives = 86/183 (46%), Gaps = 17/183 (9%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P  ++   G +GL++A+++F+P++G   +++++ +I+  +  Y+    S+++I      +
Sbjct: 53  PYEDLEQVGYLGLIRAIERFNPQQGSAFSSFAIPYIRGEILHYLRDRGSVMRI--PRRWQ 110

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE----SLNAL 189
            L+   ++L+  L        +  +   IA+ L +S  E     C+LA       SL+A 
Sbjct: 111 DLYTKGKKLRKELAQTLGRQPRESE---IAQALGISSQEW--NECQLALQNRLLVSLDAT 165

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           +N +      + D L  D   Q Q  I+++     R  L ++MS L  + +   E   L 
Sbjct: 166 VNQAHDGMISFGDTLP-DPKSQGQQKIQED-----RLQLQKAMSQLEDKTKAAIECVFLW 219

Query: 250 ENP 252
           + P
Sbjct: 220 DLP 222


>gi|16760902|ref|NP_456519.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. CT18]
 gi|16765294|ref|NP_460909.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|29141406|ref|NP_804748.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
 gi|62180530|ref|YP_216947.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|161936245|ref|YP_150204.2| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. ATCC 9150]
 gi|194736051|ref|YP_002114988.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. CVM19633]
 gi|195873263|ref|ZP_02696436.2| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Newport str. SL317]
 gi|197263158|ref|ZP_03163232.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA23]
 gi|197301170|ref|ZP_02664251.2| RNA polymerase sigma factor for flagellar operon (Sigma-F factor)
           [Salmonella enterica subsp. enterica serovar
           Schwarzengrund str. SL480]
 gi|204931059|ref|ZP_03221885.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Javiana str.
           GA_MM04042433]
 gi|205357293|ref|ZP_02346566.2| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA29]
 gi|207856530|ref|YP_002243181.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Enteritidis str. P125109]
 gi|224583543|ref|YP_002637341.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Paratyphi C strain RKS4594]
 gi|289810757|ref|ZP_06541386.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. AG3]
 gi|61224055|sp|P0A2E8|FLIA_SALTY RecName: Full=RNA polymerase sigma factor for flagellar operon;
           AltName: Full=Sigma-27; AltName: Full=Sigma-28; AltName:
           Full=Sigma-F factor
 gi|61224057|sp|P0A2E9|FLIA_SALTI RecName: Full=RNA polymerase sigma factor for flagellar operon;
           AltName: Full=Sigma-27; AltName: Full=Sigma-28; AltName:
           Full=Sigma-F factor
 gi|25331353|pir||AF0750 RNA polymerase sigma transcription factor for flagellar operon fliA
           [imported] - Salmonella enterica subsp. enterica serovar
           Typhi (strain CT18)
 gi|556579|dbj|BAA00389.1| sigma factor [Salmonella enterica subsp. enterica serovar
           Typhimurium]
 gi|4115509|dbj|BAA36397.1| FliA [Salmonella enterica subsp. enterica serovar Typhimurium]
 gi|16420491|gb|AAL20868.1| sigma F (sigma 28) factor of RNA polymerase [Salmonella enterica
           subsp. enterica serovar Typhimurium str. LT2]
 gi|16503199|emb|CAD05705.1| RNA polymerase sigma transcription factor for flagellar operon
           [Salmonella enterica subsp. enterica serovar Typhi]
 gi|29137033|gb|AAO68597.1| RNA polymerase sigma transcription factor for flagellar operon
           [Salmonella enterica subsp. enterica serovar Typhi str.
           Ty2]
 gi|62128163|gb|AAX65866.1| sigma F (sigma 28) factor of RNA polymerase, transcription of late
           flagellar genes (class 3a and 3b operons) [Salmonella
           enterica subsp. enterica serovar Choleraesuis str.
           SC-B67]
 gi|194711553|gb|ACF90774.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Schwarzengrund str.
           CVM19633]
 gi|195634506|gb|EDX52858.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Newport str. SL317]
 gi|197241413|gb|EDY24033.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA23]
 gi|197288040|gb|EDY27427.1| RNA polymerase sigma factor for flagellar operon (Sigma-F factor)
           [Salmonella enterica subsp. enterica serovar
           Schwarzengrund str. SL480]
 gi|204320103|gb|EDZ05308.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Javiana str.
           GA_MM04042433]
 gi|205322652|gb|EDZ10491.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA29]
 gi|206708333|emb|CAR32636.1| RNA polymerase sigma transcription factor for flagellar operon
           [Salmonella enterica subsp. enterica serovar Enteritidis
           str. P125109]
 gi|224468070|gb|ACN45900.1| flagellar biosynthesis sigma factor FliA [Salmonella enterica
           subsp. enterica serovar Paratyphi C strain RKS4594]
 gi|261247122|emb|CBG24945.1| RNA polymerase sigma transcription factor for flagellar operon
           [Salmonella enterica subsp. enterica serovar Typhimurium
           str. D23580]
 gi|267993942|gb|ACY88827.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 14028S]
 gi|301158470|emb|CBW17980.1| RNA polymerase sigma transcription factor for flagellar operon
           [Salmonella enterica subsp. enterica serovar Typhimurium
           str. SL1344]
 gi|320085426|emb|CBY95207.1| RNA polymerase sigma factor rpoD Sigma-70 [Salmonella enterica
           subsp. enterica serovar Weltevreden str. 2007-60-3289-1]
 gi|322715006|gb|EFZ06577.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. A50]
 gi|323130234|gb|ADX17664.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 4/74]
 gi|323250213|gb|EGA34105.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2009159199]
 gi|332988845|gb|AEF07828.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhimurium str. UK-1]
          Length = 239

 Score = 37.0 bits (84), Expect = 3.8,   Method: Compositional matrix adjust.
 Identities = 48/221 (21%), Positives = 100/221 (45%), Gaps = 32/221 (14%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL+ AV ++D  +G    TY++  I+ AM +  LRS   V      N + 
Sbjct: 41  LDDLLQAGGIGLLNAVDRYDALQGTAFTTYAVQRIRGAMLDE-LRSRDWVPRSVRRNARE 99

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   + +L+   Q +  N  + E    +A++L +  +E   M            L+++++
Sbjct: 100 VAQAMGQLE---QELGRNATETE----VAERLGIPVAEYRQM------------LLDTNN 140

Query: 195 KNSSQWQDW---------LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
                + +W         LV +   QE  L +  E   R+ ++  ++  L  RE+ +   
Sbjct: 141 SQLFSYDEWREEHGDSIELVTEEHQQENPLHQLLEGDLRQRVMD-AIESLPEREQLVLTL 199

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +E  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 200 YYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 238


>gi|120554892|ref|YP_959243.1| FliA/WhiG family RNA polymerase sigma factor [Marinobacter
           aquaeolei VT8]
 gi|120324741|gb|ABM19056.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Marinobacter
           aquaeolei VT8]
          Length = 247

 Score = 37.0 bits (84), Expect = 3.8,   Method: Compositional matrix adjust.
 Identities = 29/124 (23%), Positives = 56/124 (45%), Gaps = 13/124 (10%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           L+  H  LV KIA+       P   + +++  G IGL++A +++   +G    TY+   I
Sbjct: 21  LIEEHAPLVKKIALHLMARLPPSVQLEDLMQAGMIGLLEAAQRYSSGKGATFETYAGIRI 80

Query: 110 KAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           + AM + I +  W           + +  N RR+   ++ + D   +  Q   +A++L +
Sbjct: 81  RGAMVDEIRKGDWV---------PRSVHRNARRIASAIKQVEDRTGREAQDAEVAEELGI 131

Query: 169 SESE 172
              E
Sbjct: 132 GLDE 135


>gi|161502922|ref|YP_001570034.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:-- str. RSK2980]
 gi|160864269|gb|ABX20892.1| hypothetical protein SARI_00981 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 229

 Score = 37.0 bits (84), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 46/221 (20%), Positives = 100/221 (45%), Gaps = 32/221 (14%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL+ AV ++D  +G    TY++  I+ AM +  LRS   V      N + 
Sbjct: 31  LDDLLQAGGIGLLNAVDRYDALQGTAFTTYAVQRIRGAMLDE-LRSRDWVPRSVRRNARE 89

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   + +L+   Q +  N  + E    +A++L +   E   M            L+++++
Sbjct: 90  VAQAMGQLE---QELGRNATETE----VAERLGIPVEEYRQM------------LLDTNN 130

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS---------MSVLNPRERRIFEA 245
                + +W   +H    +++ E+ +++N  + L  S         +  L  RE+ +   
Sbjct: 131 SQLFSYDEW-REEHGDSIELVTEEHQKENPLHQLLESDLRQRVMGAIESLPEREQLVLTL 189

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +E  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 190 YYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 228


>gi|320120593|gb|EFE29148.2| RNA polymerase sigma-H factor [Filifactor alocis ATCC 35896]
          Length = 227

 Score = 37.0 bits (84), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 26/80 (32%), Positives = 43/80 (53%), Gaps = 5/80 (6%)

Query: 19 YIHEIRKIPMLEKQEEYV-LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
          Y  ++  IP  E +E+ V LA++    GD  A   + T ++ LV   A  Y   G    +
Sbjct: 16 YSVDLDNIPQEEWEEQIVHLAQK----GDSYAIDYIFTKYMGLVRSKAKLYFLVGADKED 71

Query: 78 VVSEGNIGLMQAVKKFDPER 97
          +V EG IGL +A++ F+P++
Sbjct: 72 IVQEGLIGLHKAIRDFNPDK 91


>gi|228899672|ref|ZP_04063925.1| RNA polymerase sigma-B factor [Bacillus thuringiensis IBL 4222]
 gi|228859981|gb|EEN04388.1| RNA polymerase sigma-B factor [Bacillus thuringiensis IBL 4222]
          Length = 203

 Score = 37.0 bits (84), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 40/175 (22%), Positives = 86/175 (49%), Gaps = 26/175 (14%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRL 135
           +++  G +GL+ A++++D   G     +++  I   +++Y+  ++W +       +  R 
Sbjct: 4   DIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGI-------HVPRR 56

Query: 136 FFNLR-RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNAL 189
             +L  ++K  ++ +TD+  +  +++ IA  L +SE EV+ +     N R++   SL+ +
Sbjct: 57  IKDLGGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVS---SLDDV 113

Query: 190 I-NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           + NSSD +S    + +     G EQ          RR +L    +VLN  E+ + 
Sbjct: 114 VENSSDGSSVARIESVGEVEQGYEQT--------ERRLVLEDIFNVLNDMEKSVI 160


>gi|237653596|ref|YP_002889910.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thauera sp. MZ1T]
 gi|237624843|gb|ACR01533.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thauera sp. MZ1T]
          Length = 257

 Score = 36.6 bits (83), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 53/251 (21%), Positives = 110/251 (43%), Gaps = 26/251 (10%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           Y  HG L     LV ++  LV +IA   M      + + +++  G +GL+ A+ +++   
Sbjct: 2   YDAHGKLDKGG-LVENYAPLVKRIAYQLMSRLPASVDVDDLIQNGMMGLLDALGRYEQGL 60

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G +  TY++  I+ AM + +  +  L         + L  ++RR++  + ++   N +P 
Sbjct: 61  GAQFETYAVQRIRGAMLDGLRENDWL--------PRSLRRDMRRIEAAIHSLEQQNGRPP 112

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ---- 213
               +A  L++   +      R+  D   + L+   D N  +  D+L   H  QE     
Sbjct: 113 SESELAAALDLPLEDY----QRMLQDARGHQLVYLEDFNREEDDDYLDR-HLAQEGNDPL 167

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
            L+E  + + R   L  ++  L  RE+ +      +E  + L  +     V+  RV Q+ 
Sbjct: 168 TLLEDTDLRRR---LVGAIEHLPEREQLVMALYYDEE--LNLREIGEVLGVTESRVCQLH 222

Query: 274 ARAFKKVQESI 284
           ++A  +++  +
Sbjct: 223 SQAVARLRACV 233


>gi|213583576|ref|ZP_03365402.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-0664]
          Length = 201

 Score = 36.6 bits (83), Expect = 4.1,   Method: Compositional matrix adjust.
 Identities = 48/223 (21%), Positives = 101/223 (45%), Gaps = 32/223 (14%)

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           + + +++  G IGL+ AV ++D  +G    TY++  I+ AM +  LRS   V      N 
Sbjct: 1   MELDDLLQAGGIGLLNAVDRYDALQGTAFTTYAVQRIRGAMLDE-LRSRDWVPRSVRRNA 59

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
           + +   + +L+   Q +  N  + E    +A++L +  +E   M            L+++
Sbjct: 60  REVAQAMGQLE---QELGRNATETE----VAERLGIPVAEYRQM------------LLDT 100

Query: 193 SDKNSSQWQDW---------LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           ++     + +W         LV +   QE  L +  E   R+ ++  ++  L  RE+ + 
Sbjct: 101 NNSQLFSYDEWREEHGDSIELVTEEHQQENPLHQLLEGDLRQRVMD-AIESLPEREQLVL 159

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                +E  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 160 TLYYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 200


>gi|118443284|ref|YP_877182.1| RNA polymerase factor sigma-70 [Clostridium novyi NT]
 gi|118133740|gb|ABK60784.1| RNA polymerase sigma-H factor [Clostridium novyi NT]
          Length = 219

 Score = 36.6 bits (83), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 24/95 (25%), Positives = 41/95 (43%), Gaps = 9/95 (9%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           +GD+ A   L+  +   V   A  Y   G    ++  EG IGL +A++ F P+   +L++
Sbjct: 30  NGDIKAQEYLINKYKNFVKAKAKSYFLVGADKEDIYQEGMIGLYKAIRDFKPD---KLSS 86

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           +       A  E  +    +  I T   QK +  N
Sbjct: 87  FK------AFAELCVTRQIITAIKTATRQKHIPLN 115


>gi|152980386|ref|YP_001353773.1| RNA polymerase sigma factor for flagellar operon [Janthinobacterium
           sp. Marseille]
 gi|151280463|gb|ABR88873.1| RNA polymerase sigma factor for flagellar operon [Janthinobacterium
           sp. Marseille]
          Length = 243

 Score = 36.6 bits (83), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 3/69 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           S  + LV  H  LV K+A   +    P   + +++  G IGL+ AV +++   G +  TY
Sbjct: 8   SDKNHLVGEHAPLVKKLAHQMKAKLPPSVEVDDLIQAGMIGLLDAVSRYEETHGAQFETY 67

Query: 105 SMWWIKAAM 113
           ++  I+ AM
Sbjct: 68  AVQRIRGAM 76


>gi|315101187|gb|EFT73163.1| sigma-70, region 4 [Propionibacterium acnes HL046PA1]
          Length = 270

 Score = 36.6 bits (83), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 14/49 (28%), Positives = 29/49 (59%)

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           Y   + +++  G IGL + ++++D  RG R +T +  WI+  + E ++R
Sbjct: 83  YRCSVEDLIQAGCIGLGETIERYDVRRGARFSTVAWTWIRRRIGEEVVR 131


>gi|288561068|ref|YP_003424554.1| DnaK-related protein [Methanobrevibacter ruminantium M1]
 gi|288543778|gb|ADC47662.1| DnaK-related protein [Methanobrevibacter ruminantium M1]
          Length = 584

 Score = 36.6 bits (83), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 29/98 (29%), Positives = 55/98 (56%), Gaps = 11/98 (11%)

Query: 155 KPEQVVAIAKKLNVSESEVISMNCR-LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
           +P+  VAI  KL V ++ ++ ++ + L+ ++ L+A  +SS++ SS+       D+   E 
Sbjct: 443 RPKGEVAIQVKLKVDKNGIMGLSAKELSTNKKLSATFDSSNRMSSEEIKKAGLDN---EN 499

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           +L + EE+  +RN       ++N  E  IFE ++L EN
Sbjct: 500 LLSDYEEKIKQRN-------IINDAEEVIFEGKKLIEN 530


>gi|327481248|gb|AEA84558.1| flagellar biosynthesis sigma factor [Pseudomonas stutzeri DSM 4166]
          Length = 241

 Score = 36.6 bits (83), Expect = 4.4,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 36/69 (52%), Gaps = 3/69 (4%)

Query: 48  SAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
            A +RL+  +  LV +IA   +      + + +++  G IGL++A KK+D  +G    TY
Sbjct: 10  DAQYRLIDQYAPLVKRIAYHLLARLPASVQVDDLIQAGMIGLLEAAKKYDAGKGASFETY 69

Query: 105 SMWWIKAAM 113
           +   I+  M
Sbjct: 70  AGIRIRGTM 78


>gi|319944142|ref|ZP_08018420.1| DNA-directed RNA polymerase sigma subunit FliA [Lautropia mirabilis
           ATCC 51599]
 gi|319742636|gb|EFV95045.1| DNA-directed RNA polymerase sigma subunit FliA [Lautropia mirabilis
           ATCC 51599]
          Length = 241

 Score = 36.6 bits (83), Expect = 4.4,   Method: Compositional matrix adjust.
 Identities = 47/207 (22%), Positives = 92/207 (44%), Gaps = 15/207 (7%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL+ AV +FD   G +  T++M  ++ AM +  LR+   +      +Q  
Sbjct: 41  LDDLIQAGLIGLVDAVSRFDAAMGVQFDTFAMQRVRGAMLDE-LRNADWMPRSVRKSQ-- 97

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS- 193
                R ++  + A+     +P Q   IA +L V   E   +     G + L    ++S 
Sbjct: 98  -----RSIEQAIHAVEQRLGRPAQEREIADELQVPLEEYQRLLSSAKGSQLLYFEDSASE 152

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D + S+ +  L  D    ++ L    E    R  L  ++  L  RE+ +     ++E  +
Sbjct: 153 DDDESRIEQMLPDDAPTPDRRL----EDARFRESLVAAIDGLPEREKLLMNLYYVEE--L 206

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKV 280
           TL+ +     V+  RV Q+ ++A  ++
Sbjct: 207 TLKEIGEVLGVTESRVSQLHSQAVARL 233


>gi|289758832|ref|ZP_06518210.1| predicted protein [Mycobacterium tuberculosis T85]
 gi|289714396|gb|EFD78408.1| predicted protein [Mycobacterium tuberculosis T85]
          Length = 170

 Score = 36.6 bits (83), Expect = 4.4,   Method: Compositional matrix adjust.
 Identities = 31/129 (24%), Positives = 62/129 (48%), Gaps = 7/129 (5%)

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +  V ++    
Sbjct: 41  LAKEMDITPEKVLEIQQYAREPISLDQTIG--DEGDSQLGDFI---EDSEAVVAVDAVSF 95

Query: 222 KNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
              ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K
Sbjct: 96  TLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSK 155

Query: 280 VQESIQKQV 288
           ++   + QV
Sbjct: 156 LRHPSRSQV 164


>gi|300717856|ref|YP_003742659.1| peptide ABC transporter permease [Erwinia billingiae Eb661]
 gi|299063692|emb|CAX60812.1| peptide ABC transporter, permease protein [Erwinia billingiae
           Eb661]
          Length = 322

 Score = 36.6 bits (83), Expect = 4.4,   Method: Compositional matrix adjust.
 Identities = 26/88 (29%), Positives = 40/88 (45%), Gaps = 19/88 (21%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL------------SAAHRLVTSHLRLVV 62
           G  +Y   IR + +LEKQ+EYV A R    G L            S    L T HL + +
Sbjct: 194 GWMQYARTIRSLTLLEKQKEYVQASRVSGGGTLHIMFAHILPNVISPLSVLATLHLGMAI 253

Query: 63  --KIAMGYRGYGLP-----ISEVVSEGN 83
             +  + + G G+P     +  +++EGN
Sbjct: 254 LTEATLSFLGVGMPPDQPSLGTLINEGN 281


>gi|73532520|dbj|BAE19818.1| RNA polymerase sigma factor for flagellar operon [Edwardsiella
           tarda]
          Length = 168

 Score = 36.6 bits (83), Expect = 4.4,   Method: Compositional matrix adjust.
 Identities = 25/102 (24%), Positives = 48/102 (47%), Gaps = 6/102 (5%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM------QEYILRSWSLVKIGT 128
           + +++  G IGL+ AV+++D  +G    TY++  I+ AM      ++++ RS      G 
Sbjct: 13  LDDLLQAGGIGLLHAVERYDAMQGTAFTTYAIQRIRGAMLDELRSRDWVPRSVRRNARGV 72

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
           +A  +R    L R  G  +   +  +  E+   I    N S+
Sbjct: 73  SAAMQRAEQRLGRTPGDSEIAQEMGIPLEEYQQILLDTNTSQ 114


>gi|300857263|ref|YP_003782247.1| RNA polymerase sigma-H factor [Clostridium ljungdahlii DSM 13528]
 gi|300437378|gb|ADK17145.1| RNA polymerase sigma-H factor [Clostridium ljungdahlii DSM 13528]
          Length = 213

 Score = 36.6 bits (83), Expect = 4.5,   Method: Compositional matrix adjust.
 Identities = 30/116 (25%), Positives = 53/116 (45%), Gaps = 12/116 (10%)

Query: 24  RKI-PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           RK+ P  EK +E ++ +  +  GD+SA   L+  +   V   +  Y   G    ++  EG
Sbjct: 9   RKVSPFEEKLDEEIVIEAKK--GDVSAQEYLINKYGNFVKSKSKSYFLIGADKEDIYQEG 66

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
            IGL +A++ F P+   +L+++       A  E  +    +  I T   QK +  N
Sbjct: 67  MIGLYKAIRDFKPD---KLSSFK------AFAELCVTRQIITAIKTATRQKHIPLN 113


>gi|47168808|pdb|1RP3|A Chain A, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma
           Complex, Sigma-28FLGM
 gi|47168810|pdb|1RP3|C Chain C, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma
           Complex, Sigma-28FLGM
 gi|47168812|pdb|1RP3|E Chain E, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma
           Complex, Sigma-28FLGM
 gi|47168814|pdb|1RP3|G Chain G, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma
           Complex, Sigma-28FLGM
 gi|47169132|pdb|1SC5|A Chain A, Sigma-28(Flia)FLGM COMPLEX
          Length = 239

 Score = 36.6 bits (83), Expect = 4.5,   Method: Compositional matrix adjust.
 Identities = 56/241 (23%), Positives = 108/241 (44%), Gaps = 35/241 (14%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           L+  +L LV  IA   + + LP    I +++S G IGL++AV     E   R   Y    
Sbjct: 17  LILKYLPLVKAIATNIKKH-LPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIKLR 75

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITDNNLKPEQVVAIAKKLN 167
           IK A+ +Y LRS           ++R+   + +LK  L +  TD          +AK+L 
Sbjct: 76  IKGAIYDY-LRSLDFGSRQVREKERRIKEVVEKLKEKLGREPTDEE--------VAKELG 126

Query: 168 VSESEV------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           +S  E+      I+ +  L+ +E            +  + + +    + +E+V+     +
Sbjct: 127 ISTEELFKTLDKINFSYILSLEEVFRDF-------ARDYSELIPSSTNVEEEVI-----K 174

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +     +  ++S L  RE+ + +    +E P   + ++   E S  RV Q++A+A ++++
Sbjct: 175 RELTEKVKEAVSKLPEREKLVIQLIFYEELPA--KEVAKILETSVSRVSQLKAKALERLR 232

Query: 282 E 282
           E
Sbjct: 233 E 233


>gi|103488379|ref|YP_617940.1| RNA polymerase, sigma 28 subunit [Sphingopyxis alaskensis RB2256]
 gi|98978456|gb|ABF54607.1| RNA polymerase, sigma 28 subunit [Sphingopyxis alaskensis RB2256]
          Length = 248

 Score = 36.6 bits (83), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 57/260 (21%), Positives = 112/260 (43%), Gaps = 29/260 (11%)

Query: 29  LEKQEEYVLA--KRYREHGDLSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGN 83
           +E  E++  A  +  R HG   +   LVT +  LV KIA            + +++  G 
Sbjct: 3   IEPAEQFAGAPGRALRPHGYGESVDALVTEYAPLVRKIAWQVFSRVSRTSELDDLIQTGL 62

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           I L++A + ++ ERGF  ATY+   I+ AM + + R      +G +A         +RL+
Sbjct: 63  IALIEASRHYE-ERGFAFATYASTRIRGAMIDQLRRE---ADVGRSA-----MVAAKRLQ 113

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQ 201
               A+    L+      +A  L+++  +  ++  N       SL+ L            
Sbjct: 114 ATRAALEQQLLRAPTAAEMAVALDMAAEDYFALERNATHGRSTSLDELT----------- 162

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           D   +    ++ +  ++ E+++    L + +  L+ RE+ + +    +E  + L  +   
Sbjct: 163 DIGAFLAADEDALADDRCEQEDLMGALRQCVGRLSEREQLVLQLYFFEE--LNLHEIGLT 220

Query: 262 FEVSRERVRQIEARAFKKVQ 281
            +VS  R+ QI+  A  KV+
Sbjct: 221 LDVSAARICQIKREAMIKVE 240


>gi|120598267|ref|YP_962841.1| flagellar biosynthesis sigma factor [Shewanella sp. W3-18-1]
 gi|120558360|gb|ABM24287.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Shewanella sp.
           W3-18-1]
          Length = 237

 Score = 36.6 bits (83), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 49/215 (22%), Positives = 95/215 (44%), Gaps = 25/215 (11%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS-WSLVKIGTTANQK 133
           + +++  G +GL++A  KFD  +G +  T++   I+ AM + I R  W  V      N +
Sbjct: 41  LDDLLQAGMMGLLEASSKFDGGKGAKFETFAGIRIRGAMLDEIRRGDW--VPRSVHRNNR 98

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
           R+   +  L+  L        +  +   IA+KL+++  E       +  D S+  +I   
Sbjct: 99  RVAQAIDELEKELG-------RDARDTEIAEKLDMTLDEY----HHILNDVSVGKIIGIE 147

Query: 194 DKNSSQWQDWLVY---DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           D   S  QD L       DG  + L E +      + L  ++ +L  R+  +       +
Sbjct: 148 DLGVS--QDILTLSDRSDDGSFEALAETQ----FHSALVEAIKLLPERDALVLSL--YYD 199

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             + L+ + +  EVS  RV QI ++A  +++  ++
Sbjct: 200 EALNLKEIGAILEVSESRVSQILSQAMLRLKAKLK 234


>gi|238789522|ref|ZP_04633307.1| RNA polymerase sigma factor [Yersinia frederiksenii ATCC 33641]
 gi|238722472|gb|EEQ14127.1| RNA polymerase sigma factor [Yersinia frederiksenii ATCC 33641]
          Length = 531

 Score = 36.6 bits (83), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 20/49 (40%), Positives = 32/49 (65%), Gaps = 1/49 (2%)

Query: 233 SVLNPRERRIFEAR-RLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           S+   R+R I   R  + E+P TL  ++ +  +SRERVRQI+ RAF+++
Sbjct: 167 SLSKERDRDILLMRLGMDEHPHTLAEIAIKLGISRERVRQIQERAFRRL 215


>gi|146282908|ref|YP_001173061.1| flagellar biosynthesis sigma factor [Pseudomonas stutzeri A1501]
 gi|145571113|gb|ABP80219.1| flagellar biosynthesis sigma factor FliA [Pseudomonas stutzeri
           A1501]
          Length = 241

 Score = 36.6 bits (83), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 20/69 (28%), Positives = 36/69 (52%), Gaps = 3/69 (4%)

Query: 48  SAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
            A +RL+  +  LV +IA   +      + + +++  G IGL++A KK+D  +G    TY
Sbjct: 10  DAQYRLIDQYAPLVKRIAYHLLARLPASVQVDDLIQAGMIGLLEAAKKYDAGKGASFETY 69

Query: 105 SMWWIKAAM 113
           +   I+  M
Sbjct: 70  AGIRIRGTM 78


>gi|206558549|ref|YP_002229309.1| flagellar biosynthesis sigma factor [Burkholderia cenocepacia
           J2315]
 gi|198034586|emb|CAR50452.1| RNA polymerase sigma factor for flagellar regulon FliA
           [Burkholderia cenocepacia J2315]
          Length = 243

 Score = 36.6 bits (83), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 48/231 (20%), Positives = 97/231 (41%), Gaps = 19/231 (8%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           L+LV K+        + + +++  G IGLM A  ++  ++G +  TY+   I+ AM +  
Sbjct: 26  LQLVAKMPAS-----VDLDDLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDE- 79

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           LRS   +        + +   + +++ HL        +      IA+ LN+   E   M 
Sbjct: 80  LRSNDWLPRSLRKTSREVEHAVHQVEQHLG-------RSASETEIAQHLNMPLDEYQGML 132

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
             L G + +         +   + D    DH      L++    ++ R  L  ++  L  
Sbjct: 133 QDLHGSQLIYYEDFDRAADDEPFLDRYRVDHADPLSALLD----EHLREALVEAIERLPE 188

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RE+ +       E  + L  + +  EVS  RV Q+ ++A  +++  +++Q 
Sbjct: 189 REKLLMSL--YYERGLNLREIGAVLEVSESRVCQLHSQAVARLRARLREQA 237


>gi|116748823|ref|YP_845510.1| FliA/WhiG family RNA polymerase sigma factor [Syntrophobacter
           fumaroxidans MPOB]
 gi|116697887|gb|ABK17075.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Syntrophobacter
           fumaroxidans MPOB]
          Length = 279

 Score = 36.6 bits (83), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 50/231 (21%), Positives = 97/231 (41%), Gaps = 31/231 (13%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI-LRSW---SLVKIGTTA 130
           I +++S G IGL+ AV K+D  +G     Y+   I+ AM + I    W   SL + G   
Sbjct: 60  IDDLISAGVIGLIDAVDKYDSGQGIPFKFYAKIRIRGAMLDEIRAMDWVPRSLRQKGNVL 119

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG----DESL 186
             +R F  L +  G   +        EQV   A +LN+   +   +   + G     E++
Sbjct: 120 --ERTFSALEQKLGRCPS-------DEQV---AGELNIGIEDYHRLLDEIKGISFLPENI 167

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           N  +  + ++ S   D          + L +   R+  +  L  ++  L  +E+ +    
Sbjct: 168 NEALLENGESGSLASD---------SEELFQHAYRQEIQRHLADAIRTLTEKEQLVLSLY 218

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLL 297
              E  +T++ + +    +  R+ QI  +A  K++  + K++     PP +
Sbjct: 219 YYDE--LTMKEVGTALGYTESRISQIHTKAIIKLRSRLAKRLTADDLPPYI 267


>gi|219670137|ref|YP_002460572.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfitobacterium
           hafniense DCB-2]
 gi|219540397|gb|ACL22136.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfitobacterium
           hafniense DCB-2]
          Length = 248

 Score = 36.6 bits (83), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 13/38 (34%), Positives = 24/38 (63%)

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
            +++  G  GL+ A+++FDP RG +  TY+   I+ A+
Sbjct: 43  DDLIGYGVFGLLDALERFDPVRGVKFETYATLRIRGAI 80


>gi|297195554|ref|ZP_06912952.1| sigma factor [Streptomyces pristinaespiralis ATCC 25486]
 gi|197721376|gb|EDY65284.1| sigma factor [Streptomyces pristinaespiralis ATCC 25486]
          Length = 291

 Score = 36.6 bits (83), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 51/237 (21%), Positives = 103/237 (43%), Gaps = 22/237 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +L LV   A  +R     + +++  G IGL++A+ +F+  R    AT+++ +I   
Sbjct: 68  LIELNLALVKYAAGRFRNRAEQMEDIIQVGTIGLIKAIDRFELSREVEFATFAVPYIIGE 127

Query: 113 MQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ +    SW+   +      + L  +L +    L    D+         +A+ L + E 
Sbjct: 128 IKRFFRDTSWA---VHVPRRLQELRIDLAKAVDELSQKLDHT---PTTAELAEHLGMDEE 181

Query: 172 EVI----SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E+I    + N   AG   +  + ++SD  +    D L     G     +E  E       
Sbjct: 182 EIIEGVVASNGYTAGSIDM-PMDDASDHGAVPLSDRL-----GAPDAELEIAENVQALKP 235

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L      L+ R+R+I + R  +E  +T   + +E  VS+  V ++ +R   +++E +
Sbjct: 236 LIEE---LDERDRQILQMRFGEE--MTQSEIGAELGVSQMHVSRLLSRITARLREGL 287


>gi|89895713|ref|YP_519200.1| hypothetical protein DSY2967 [Desulfitobacterium hafniense Y51]
 gi|89335161|dbj|BAE84756.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 248

 Score = 36.6 bits (83), Expect = 5.0,   Method: Compositional matrix adjust.
 Identities = 13/38 (34%), Positives = 24/38 (63%)

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
            +++  G  GL+ A+++FDP RG +  TY+   I+ A+
Sbjct: 43  DDLIGYGVFGLLDALERFDPVRGVKFETYATLRIRGAI 80


>gi|228932399|ref|ZP_04095281.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228984185|ref|ZP_04144367.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|229183301|ref|ZP_04310530.1| RNA polymerase sigma-B factor [Bacillus cereus BGSC 6E1]
 gi|228600171|gb|EEK57762.1| RNA polymerase sigma-B factor [Bacillus cereus BGSC 6E1]
 gi|228775472|gb|EEM23856.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228827335|gb|EEM73087.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
          Length = 203

 Score = 36.6 bits (83), Expect = 5.1,   Method: Compositional matrix adjust.
 Identities = 44/215 (20%), Positives = 105/215 (48%), Gaps = 28/215 (13%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRL 135
           +++  G +GL+ A++++D   G     +++  I   +++Y+  ++W +       +  R 
Sbjct: 4   DIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGI-------HVPRR 56

Query: 136 FFNLR-RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNAL 189
             +L  ++K  ++ +TD+  +  +++ IA  L +SE EV+ +     N R++   SL+ +
Sbjct: 57  IKDLGGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVS---SLDDV 113

Query: 190 I-NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
           + N+SD +S    + +     G E+          RR +L    +VLN  E+ +     +
Sbjct: 114 VENASDGSSVARIESVGEVEQGYEET--------ERRLVLKDIFNVLNETEKSVI--HYI 163

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            E  +  ++      +S+  V +I+ +A  K++++
Sbjct: 164 FEENLNQKDTGERLGISQMHVSRIKRQAISKLKQA 198


>gi|15606452|ref|NP_213832.1| RNA polymerase sigma factor FliA [Aquifex aeolicus VF5]
 gi|2983663|gb|AAC07229.1| RNA polymerase sigma factor FliA [Aquifex aeolicus VF5]
          Length = 236

 Score = 36.6 bits (83), Expect = 5.1,   Method: Compositional matrix adjust.
 Identities = 56/241 (23%), Positives = 108/241 (44%), Gaps = 35/241 (14%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           L+  +L LV  IA   + + LP    I +++S G IGL++AV     E   R   Y    
Sbjct: 14  LILKYLPLVKAIATNIKKH-LPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIKLR 72

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITDNNLKPEQVVAIAKKLN 167
           IK A+ +Y LRS           ++R+   + +LK  L +  TD          +AK+L 
Sbjct: 73  IKGAIYDY-LRSLDFGSRQVREKERRIKEVVEKLKEKLGREPTDEE--------VAKELG 123

Query: 168 VSESEV------ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           +S  E+      I+ +  L+ +E            +  + + +    + +E+V+     +
Sbjct: 124 ISTEELFKTLDKINFSYILSLEEVFRDF-------ARDYSELIPSSTNVEEEVI-----K 171

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +     +  ++S L  RE+ + +    +E P   + ++   E S  RV Q++A+A ++++
Sbjct: 172 RELTEKVKEAVSKLPEREKLVIQLIFYEELPA--KEVAKILETSVSRVSQLKAKALERLR 229

Query: 282 E 282
           E
Sbjct: 230 E 230


>gi|138897001|ref|YP_001127454.1| sigma-B general stress transcription factor [Geobacillus
           thermodenitrificans NG80-2]
 gi|134268514|gb|ABO68709.1| Sigma-B general stress transcription factor [Geobacillus
           thermodenitrificans NG80-2]
          Length = 258

 Score = 36.6 bits (83), Expect = 5.1,   Method: Compositional matrix adjust.
 Identities = 44/207 (21%), Positives = 99/207 (47%), Gaps = 27/207 (13%)

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           G +  ++ ++ +DP +G    +Y+M  +   M+ Y+      +++      +R+  N  +
Sbjct: 64  GRLSFLRLLEHYDPNQGTSFESYAMKSLIGYMKNYLRDKAWYIQV-----PRRVKENGSK 118

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-----SLNALINSSDKN 196
           ++  +  +T    +   +  IA  L +S  E I +   LAG +     S++A +   +K+
Sbjct: 119 VQKAIDELTVTLERSPNIEEIANHLGLSVEETIEI---LAGRDHYQAISIDAPVQDGEKD 175

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA--RRLQENPVT 254
           ++   ++L  D   + + LIE+ +       L  ++  L+ +ER + EA  RR +    T
Sbjct: 176 ATTIGEFLA-DDTNEVEALIERLD-------LQEAIGKLSEQERIVIEAVFRRGE----T 223

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQ 281
             +L+    VS+  + +I+ RA +K++
Sbjct: 224 QRSLAKRLGVSQMTISRIQKRAIEKLK 250


>gi|262273680|ref|ZP_06051493.1| putative RNA polymerase sigma-38 factor [Grimontia hollisae CIP
           101886]
 gi|262222095|gb|EEY73407.1| putative RNA polymerase sigma-38 factor [Grimontia hollisae CIP
           101886]
          Length = 78

 Score = 36.6 bits (83), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 20/56 (35%), Positives = 34/56 (60%), Gaps = 4/56 (7%)

Query: 235 LNPRERRIFEARR---LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           LNP++R +  ARR   L     TLE++  E  ++RERVRQI+    +++++ +  Q
Sbjct: 12  LNPKQREVL-ARRFGLLGHEASTLEDVGREIGLTRERVRQIQVEGLRRLRDMLTHQ 66


>gi|293395614|ref|ZP_06639897.1| DNA-directed RNA polymerase sigma subunit FliA [Serratia odorifera
           DSM 4582]
 gi|291421933|gb|EFE95179.1| DNA-directed RNA polymerase sigma subunit FliA [Serratia odorifera
           DSM 4582]
          Length = 240

 Score = 36.2 bits (82), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 43/214 (20%), Positives = 94/214 (43%), Gaps = 30/214 (14%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL+ AV+++D  +G    TY++  I+ AM +  LRS   V      + + 
Sbjct: 41  LDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDE-LRSRDWVPRSVRRHARD 99

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   ++RL+  L        +P   + +A+ +N+S ++   +            L+++++
Sbjct: 100 VAQAMQRLEQQLG-------RPAGELEVAQAMNMSLADYRQI------------LMDTNN 140

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM--------SVLNPRERRIFEAR 246
                + +W     +  E +L    E      +L  S+          L  RE+ +    
Sbjct: 141 SQLFSYDEWREEQGESAEPLLEGHAEANPLHQLLEGSLRQRVIDAIEALPEREKLVLTLY 200

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             +E  + L+ + +  EV   RV Q+ ++A K++
Sbjct: 201 YQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRL 232


>gi|119718669|ref|YP_925634.1| sigma-70 region 4 domain-containing protein [Nocardioides sp.
           JS614]
 gi|119539330|gb|ABL83947.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Nocardioides sp.
           JS614]
          Length = 300

 Score = 36.2 bits (82), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 15/34 (44%), Positives = 21/34 (61%)

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           S G + L+QA + FDPERG   A Y+   I+ A+
Sbjct: 47  SAGLLALVQAARAFDPERGVPFAGYASTRIRGAL 80


>gi|146293655|ref|YP_001184079.1| flagellar biosynthesis sigma factor [Shewanella putrefaciens CN-32]
 gi|145565345|gb|ABP76280.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Shewanella
           putrefaciens CN-32]
 gi|319427054|gb|ADV55128.1| RNA polymerase sigma-28 factor for flagellar operon, FliA
           [Shewanella putrefaciens 200]
          Length = 237

 Score = 36.2 bits (82), Expect = 5.4,   Method: Compositional matrix adjust.
 Identities = 49/215 (22%), Positives = 95/215 (44%), Gaps = 25/215 (11%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS-WSLVKIGTTANQK 133
           + +++  G +GL++A  KFD  +G +  T++   I+ AM + I R  W  V      N +
Sbjct: 41  LDDLLQAGMMGLLEASSKFDGGKGAKFETFAGIRIRGAMLDEIRRGDW--VPRSVHRNNR 98

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
           R+   +  L+  L        +  +   IA+KL+++  E       +  D S+  +I   
Sbjct: 99  RVAQAIDELEQELG-------RDARDTEIAEKLDMTLDEY----HHILNDVSVGKIIGIE 147

Query: 194 DKNSSQWQDWLVY---DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           D   S  QD L       DG  + L E +      + L  ++ +L  R+  +       +
Sbjct: 148 DLGVS--QDILTLSDRSDDGSFEALAETQ----FHSALVEAIKLLPERDALVLSL--YYD 199

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             + L+ + +  EVS  RV QI ++A  +++  ++
Sbjct: 200 EALNLKEIGAILEVSESRVSQILSQAMLRLKAKLK 234


>gi|297196439|ref|ZP_06913837.1| sigma factor [Streptomyces pristinaespiralis ATCC 25486]
 gi|197722266|gb|EDY66174.1| sigma factor [Streptomyces pristinaespiralis ATCC 25486]
          Length = 292

 Score = 36.2 bits (82), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 20/76 (26%), Positives = 41/76 (53%), Gaps = 1/76 (1%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A + L+  ++ LV  +A  +R       ++V  G IGL++A+ +FD  R    AT+++ +
Sbjct: 67  ARNTLIEMNISLVRYVARRFRNRAESDEDIVQVGTIGLIKAIDRFDLSREVEFATFAVPY 126

Query: 109 IKAAMQEYIL-RSWSL 123
           I   ++ +    SW++
Sbjct: 127 ILGEIKRFFRDTSWAV 142


>gi|254246774|ref|ZP_04940095.1| Sigma-70 region 3 [Burkholderia cenocepacia PC184]
 gi|124871550|gb|EAY63266.1| Sigma-70 region 3 [Burkholderia cenocepacia PC184]
          Length = 306

 Score = 36.2 bits (82), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 48/231 (20%), Positives = 96/231 (41%), Gaps = 19/231 (8%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           L+LV K+        + + +++  G IGLM A  ++  ++G +  TY+   I+ AM +  
Sbjct: 89  LQLVAKMPAS-----VDLDDLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDE- 142

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           LRS   +        + +   + +++ HL        +      IA+ LN+   E   M 
Sbjct: 143 LRSNDWLPRSLRKTSREVEHAVHQVEQHLG-------RSASETEIAQHLNMPLDEYQGML 195

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
             L G + +         +   + D    DH      L++     + R  L  ++  L  
Sbjct: 196 QDLHGSQLIYYEDFDRAADDEPFLDRYRVDHADPLSALLD----DHLREALVEAIERLPE 251

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RE+ +       E  + L  + +  EVS  RV Q+ ++A  +++  +++Q 
Sbjct: 252 REKLLMSL--YYERGLNLREIGAVLEVSESRVCQLHSQAVARLRARLREQA 300


>gi|332533108|ref|ZP_08408977.1| RNA polymerase sigma factor for flagellar operon [Pseudoalteromonas
           haloplanktis ANT/505]
 gi|332037390|gb|EGI73844.1| RNA polymerase sigma factor for flagellar operon [Pseudoalteromonas
           haloplanktis ANT/505]
          Length = 236

 Score = 36.2 bits (82), Expect = 5.6,   Method: Compositional matrix adjust.
 Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 4/74 (5%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           +V  H  LV K+A        P   + +++  G IGL++A K FD  +G    T++   I
Sbjct: 12  IVEKHASLVKKVACHLIARLPPSVQLDDLIQSGMIGLIEASKNFDATKGASFETFAGIRI 71

Query: 110 KAAMQEYILR-SWS 122
           + AM + + R  W+
Sbjct: 72  RGAMLDEMRRGDWA 85


>gi|228950124|ref|ZP_04112308.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|229120608|ref|ZP_04249853.1| RNA polymerase sigma-B factor [Bacillus cereus 95/8201]
 gi|228662893|gb|EEL18488.1| RNA polymerase sigma-B factor [Bacillus cereus 95/8201]
 gi|228809547|gb|EEM55984.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
          Length = 203

 Score = 36.2 bits (82), Expect = 5.6,   Method: Compositional matrix adjust.
 Identities = 44/215 (20%), Positives = 105/215 (48%), Gaps = 28/215 (13%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRL 135
           +++  G +GL+ A++++D   G     +++  I   +++Y+  ++W +       +  R 
Sbjct: 4   DIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGI-------HVPRR 56

Query: 136 FFNLR-RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNAL 189
             +L  ++K  ++ +TD+  +  +++ IA  L +SE EV+ +     N R++   SL+ +
Sbjct: 57  IKDLGGKIKLAIEELTDHLQRSPKIIEIANHLGLSEEEVLEIMDAKNNYRVS---SLDDV 113

Query: 190 I-NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
           + N+SD +S    + +     G E+          RR +L    +VLN  E+ +     +
Sbjct: 114 VENASDGSSVARIESVGEVEKGYEET--------ERRLVLKDIFNVLNETEKSVI--HYI 163

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            E  +  ++      +S+  V +I+ +A  K++++
Sbjct: 164 FEENLNQKDTGERLGISQMHVSRIKRQAISKLKQA 198


>gi|226944861|ref|YP_002799934.1| motility sigma factor 28 [Azotobacter vinelandii DJ]
 gi|226719788|gb|ACO78959.1| motility sigma factor 28 [Azotobacter vinelandii DJ]
          Length = 231

 Score = 36.2 bits (82), Expect = 5.6,   Method: Compositional matrix adjust.
 Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL+ A+ ++D  +G   AT++   ++ AM +  LRS   V      N + 
Sbjct: 38  LDDLIQAGTIGLLDALSRYDAAQGASFATFASQRVRGAMLDE-LRSRDWVPRSVRRNARA 96

Query: 135 LFFNLRRLKGHL 146
           L   LR+L+  L
Sbjct: 97  LEDTLRQLEQRL 108


>gi|229171759|ref|ZP_04299331.1| RNA polymerase sigma-B factor [Bacillus cereus MM3]
 gi|228611656|gb|EEK68906.1| RNA polymerase sigma-B factor [Bacillus cereus MM3]
          Length = 203

 Score = 36.2 bits (82), Expect = 5.6,   Method: Compositional matrix adjust.
 Identities = 39/175 (22%), Positives = 86/175 (49%), Gaps = 26/175 (14%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRL 135
           +++  G +GL+ A++++D   G     +++  I   +++Y+  ++W +       +  R 
Sbjct: 4   DIIQVGMLGLLGAIRRYDCSIGNAFEPFAIPTIVGEIKKYLRDKTWGI-------HVPRR 56

Query: 136 FFNLR-RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNAL 189
             +L  ++K  ++ +TD+  +  +++ IA  L +SE EV+ +     N R++   SL+ +
Sbjct: 57  IKDLGGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVS---SLDDV 113

Query: 190 I-NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           + NSSD +S    + +     G E+          RR +L    +VLN  E+ + 
Sbjct: 114 VENSSDGSSVARIESVGEVEQGYEET--------ERRLVLKDIFNVLNETEKSVI 160


>gi|157145286|ref|YP_001452605.1| flagellar biosynthesis sigma factor [Citrobacter koseri ATCC
           BAA-895]
 gi|157082491|gb|ABV12169.1| hypothetical protein CKO_01023 [Citrobacter koseri ATCC BAA-895]
          Length = 229

 Score = 36.2 bits (82), Expect = 5.6,   Method: Compositional matrix adjust.
 Identities = 53/238 (22%), Positives = 105/238 (44%), Gaps = 37/238 (15%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRL V++        + + +++  G IGL+ AV ++D  +G    TY++  I+ AM +  
Sbjct: 19  LRLQVRLPAS-----VELDDLLQAGGIGLLNAVDRYDALQGTAFTTYAVQRIRGAMLDE- 72

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           LRS   V      N + +   + +L+   Q +  N  + E    +A++L +   E   M 
Sbjct: 73  LRSRDWVPRSVRRNAREVAQAMGQLE---QELGRNATETE----VAERLAIPVEEYRQM- 124

Query: 178 CRLAGDESLNALINSSDKNSSQWQDW---------LVYDHDGQEQVLIEKEERKNRRNML 228
                      L+++++     + +W         LV +   QE  L +  E  N R  +
Sbjct: 125 -----------LLDTNNSQLFSYDEWREEHGDSIELVTEEHQQENPLQQLLE-SNLRQRV 172

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             ++  L  RE+ +      +E  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 173 MDAIESLPEREQLVLTLYYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 228


>gi|90021809|ref|YP_527636.1| flagellar protein FliS [Saccharophagus degradans 2-40]
 gi|89951409|gb|ABD81424.1| RNA polymerase sigma factor, FliA/WhiG [Saccharophagus degradans
           2-40]
          Length = 250

 Score = 36.2 bits (82), Expect = 5.6,   Method: Compositional matrix adjust.
 Identities = 47/214 (21%), Positives = 95/214 (44%), Gaps = 20/214 (9%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS-WSLVKIGTTANQK 133
           I +++  G +GL++A +K+D  +G    TYS   I+ A+ + + R  W+          +
Sbjct: 48  IEDLIQAGMLGLLEAAQKYDASKGASFETYSGIRIRGAIVDEMRRGDWA---------PR 98

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            +  N RR+   +  +   + +  +   IA+++ +S  E  +M  R +    L +   + 
Sbjct: 99  SVHRNSRRVAEAIATVEARHGRDARDHEIAEEMGLSLDEYYAM-ARDSASTRLFSYEETY 157

Query: 194 DKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           + + S++ ++   D      EQV      R      L  ++  L  RER +      QE 
Sbjct: 158 ENDESRFDEYEPSDGLRGPSEQV-----HRNALYTDLVAAIGKLPERERLVLSLYYEQE- 211

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            + L+ +     VS  RV QI ++A  +++  +Q
Sbjct: 212 -MNLKEIGLVLGVSESRVSQIHSQAALRLKSRMQ 244


>gi|196249822|ref|ZP_03148518.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
 gi|196210698|gb|EDY05461.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
          Length = 256

 Score = 36.2 bits (82), Expect = 5.7,   Method: Compositional matrix adjust.
 Identities = 44/207 (21%), Positives = 99/207 (47%), Gaps = 27/207 (13%)

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           G +  ++ ++ +DP +G    +Y+M  +   M+ Y+      +++      +R+  N  +
Sbjct: 62  GRLSFLRLLEHYDPNQGTSFESYAMKSLIGYMKNYLRDKAWYIQV-----PRRVKENGSK 116

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-----SLNALINSSDKN 196
           ++  +  +T    +   +  IA  L +S  E I +   LAG +     S++A +   +K+
Sbjct: 117 VQKAIDELTVTLERSPNIEEIANHLGLSVEETIEI---LAGRDHYQAISIDAPVQDGEKD 173

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA--RRLQENPVT 254
           ++   ++L  D   + + LIE+ +       L  ++  L+ +ER + EA  RR +    T
Sbjct: 174 ATTIGEFLA-DDTNEVEALIERLD-------LQEAIGKLSEQERIVIEAVFRRGE----T 221

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQ 281
             +L+    VS+  + +I+ RA +K++
Sbjct: 222 QRSLAKRLGVSQMTISRIQKRAIEKLK 248


>gi|72161291|ref|YP_288948.1| RNA polymerase sigma-B factor [Thermobifida fusca YX]
 gi|71915023|gb|AAZ54925.1| RNA polymerase sigma-B factor [Thermobifida fusca YX]
          Length = 307

 Score = 36.2 bits (82), Expect = 5.7,   Method: Compositional matrix adjust.
 Identities = 21/88 (23%), Positives = 42/88 (47%), Gaps = 2/88 (2%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +L   H  +  +IA  YR  G P  ++     +GL  A++ FDP  G    +Y++  +  
Sbjct: 85  KLTELHAPVARRIARQYRNRGEPEEDLRQVAMVGLYNAIRNFDPAYGKEFISYALPMMTG 144

Query: 112 AMQEYIL-RSWSLVKIGTTANQKRLFFN 138
            ++ +   R+W+ +++     +KR   N
Sbjct: 145 EVKRHFRDRTWA-IRVPRKYQEKRAELN 171


>gi|238756654|ref|ZP_04617944.1| RNA polymerase sigma factor for flagellar operon [Yersinia ruckeri
           ATCC 29473]
 gi|238705123|gb|EEP97550.1| RNA polymerase sigma factor for flagellar operon [Yersinia ruckeri
           ATCC 29473]
          Length = 240

 Score = 36.2 bits (82), Expect = 5.8,   Method: Compositional matrix adjust.
 Identities = 42/215 (19%), Positives = 93/215 (43%), Gaps = 32/215 (14%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM-QEYILRSWSLVKIGTTANQK 133
           + +++  G IGL+ AV+++D  +G    TY++  I+ AM  E   R W+          +
Sbjct: 41  LDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDWA---------PR 91

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            +  N R +   ++ +     +P     +A+ L++S  E   +            L++++
Sbjct: 92  SVRRNAREVAQAMRQVEQKVGRPASEQEVAQILDISLVEYRQI------------LLDTN 139

Query: 194 DKNSSQWQDWLVYDHDGQEQVL--------IEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           +     + +W     +  E VL        +++    N R  +  ++  L  RE+ +   
Sbjct: 140 NSQLFSYDEWREEHGESVEPVLDGLDDANPLQQLLEGNLRQRVIEAIEALPEREKMVLTL 199

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
              +E  + L+ + +  EV   RV Q+ ++A K++
Sbjct: 200 YYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRL 232


>gi|311030102|ref|ZP_07708192.1| RNA polymerase sigma factor SigD [Bacillus sp. m3-13]
          Length = 254

 Score = 36.2 bits (82), Expect = 5.8,   Method: Compositional matrix adjust.
 Identities = 17/46 (36%), Positives = 27/46 (58%), Gaps = 4/46 (8%)

Query: 72  GLPIS----EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           GLP S    E+ S   +GL  A++KFDP R  +  TY+ + I+ ++
Sbjct: 46  GLPKSVKREELKSLAFVGLFDAIEKFDPSRDLKFDTYASFRIRGSI 91


>gi|237808347|ref|YP_002892787.1| sigma-70 region 4 domain-containing protein [Tolumonas auensis DSM
           9187]
 gi|237500608|gb|ACQ93201.1| sigma-70 region 4 domain protein [Tolumonas auensis DSM 9187]
          Length = 913

 Score = 36.2 bits (82), Expect = 5.9,   Method: Composition-based stats.
 Identities = 19/47 (40%), Positives = 27/47 (57%)

Query: 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           V N +E      R L  N  TLE L + + V+RER+RQ+E+ A  K+
Sbjct: 401 VKNEKELATIVCRLLSNNKKTLEELGAIYGVTRERIRQLESLAIAKL 447


>gi|119775415|ref|YP_928155.1| flagellar biosynthesis sigma factor [Shewanella amazonensis SB2B]
 gi|119767915|gb|ABM00486.1| RNA polymerase sigma factor, FliA/WhiG [Shewanella amazonensis
           SB2B]
          Length = 239

 Score = 36.2 bits (82), Expect = 5.9,   Method: Compositional matrix adjust.
 Identities = 47/207 (22%), Positives = 92/207 (44%), Gaps = 17/207 (8%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL++A  KFD  +G +  T++   I+ AM + I R    V      NQ+R
Sbjct: 41  LDDLLQAGMIGLLEASAKFDGGKGAKFETFAGIRIRGAMLDEI-RKGDWVPRSVHRNQRR 99

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   +  L+  L        +  +   IA++L++S  E       +  D S+  +I   D
Sbjct: 100 VAQVIDELEQELG-------RDARDTEIAERLDMSMEEY----HHILNDVSVGKIIGIED 148

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
              S   D LV D + Q   + +   +   +  L  ++  L  R+  +       +  + 
Sbjct: 149 LGVS--HDVLVPDGE-QTNDIYDDLAQSQFQQALADAIRQLPERDALVLSL--YYDEALN 203

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQ 281
           L+ + +  +VS  RV QI ++A  +++
Sbjct: 204 LKEIGAILDVSESRVCQIHSQAMLRLK 230


>gi|256393983|ref|YP_003115547.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Catenulispora acidiphila DSM 44928]
 gi|256360209|gb|ACU73706.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Catenulispora acidiphila DSM 44928]
          Length = 265

 Score = 36.2 bits (82), Expect = 5.9,   Method: Compositional matrix adjust.
 Identities = 41/188 (21%), Positives = 79/188 (42%), Gaps = 18/188 (9%)

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           +GL++AV  FDP+ G    TY+   I   ++ +   +   V +   A +  L      ++
Sbjct: 73  LGLVKAVDNFDPDYGATFLTYATPMIAGEVRRHFRDTTWHVHVPRRAQENAL-----AVR 127

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQ 201
              + +T    +      I ++L++S  EV       A     SL+  +  +D + +   
Sbjct: 128 AVERELTQQLGRAPSAAEIGRRLDLSADEVAEAYEASAAHHTASLDVPVAMADGDGASLG 187

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA---RRLQENPVTLENL 258
           D L  +  G + V+         R  L   ++ L+PR++RI      R + +  +  E  
Sbjct: 188 DLLGDEDPGFDSVV--------DREALKPLLAELSPRDKRILLMKFFRNMSQAQIGAEIG 239

Query: 259 SSEFEVSR 266
            S+ +VSR
Sbjct: 240 VSQMQVSR 247


>gi|296168913|ref|ZP_06850582.1| RNA polymerase sigma-F factor [Mycobacterium parascrofulaceum ATCC
           BAA-614]
 gi|295896382|gb|EFG76035.1| RNA polymerase sigma-F factor [Mycobacterium parascrofulaceum ATCC
           BAA-614]
          Length = 262

 Score = 36.2 bits (82), Expect = 6.0,   Method: Compositional matrix adjust.
 Identities = 51/236 (21%), Positives = 103/236 (43%), Gaps = 17/236 (7%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           ++V   L L   IA  + G G P  ++V    +GL+ AV +FD + G    ++++  I  
Sbjct: 42  KIVERCLPLADHIARRFEGRGEPRDDLVQVARVGLVNAVVRFDVDAGSDFVSFAVPTIMG 101

Query: 112 AMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            ++ +    SWS VK+      +RL     RL      ++    +      +A +L +  
Sbjct: 102 EVRRHFRDNSWS-VKV-----PRRLKELHLRLGTATAELSQRLGRAPTATELAAELGMDR 155

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK-EERKNRRNMLT 229
            EV+     L    S N L   S   S + +   + D  G     +++ E++++ R +L 
Sbjct: 156 EEVVEG---LVAGSSYNTLSIDSGGGSDEDEARAIADTLGDVDTGLDRIEDQESLRPLL- 211

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
                L  RER +   R  +   +T   ++    +S+  V ++ A++  ++++ +Q
Sbjct: 212 ---EALPERERTVLVLRFFES--MTQTQIAERVGISQMHVSRLLAKSLTRLRDQLQ 262


>gi|317126839|ref|YP_004093121.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Bacillus
           cellulosilyticus DSM 2522]
 gi|315471787|gb|ADU28390.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Bacillus
           cellulosilyticus DSM 2522]
          Length = 217

 Score = 36.2 bits (82), Expect = 6.1,   Method: Compositional matrix adjust.
 Identities = 27/98 (27%), Positives = 42/98 (42%), Gaps = 9/98 (9%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y   GD SA   L+  +   V   A  Y   G    ++V EG IGL +A++ F   +G +
Sbjct: 25  YVREGDSSALEYLINKYKNFVRAKARSYFLIGADHEDIVQEGMIGLYKAIRDF---KGDK 81

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           L+++       A  E  +    +  I T   QK +  N
Sbjct: 82  LSSFK------AFAELCITRQIITAIKTATRQKHIPLN 113


>gi|228913674|ref|ZP_04077301.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|229090035|ref|ZP_04221286.1| RNA polymerase sigma-B factor [Bacillus cereus Rock3-42]
 gi|228693265|gb|EEL46975.1| RNA polymerase sigma-B factor [Bacillus cereus Rock3-42]
 gi|228845962|gb|EEM90986.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
          Length = 196

 Score = 36.2 bits (82), Expect = 6.1,   Method: Compositional matrix adjust.
 Identities = 45/210 (21%), Positives = 102/210 (48%), Gaps = 28/210 (13%)

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLR 140
           G +GL+ A++++D   G     +++  I   +++Y+  ++W +       +  R   +L 
Sbjct: 2   GMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGI-------HVPRRIKDLG 54

Query: 141 -RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNALI-NSS 193
            ++K  ++ +TD+  +  +++ IA  L +SE EV+ +     N R++   SL+ ++ N+S
Sbjct: 55  GKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVS---SLDDVVENAS 111

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D +S    + +     G EQ          RR +L    +VLN  E+ +     + E  +
Sbjct: 112 DGSSVARIESVGEVEQGYEQT--------ERRLVLKDIFNVLNETEKSVI--HYIFEENL 161

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQES 283
             ++      +S+  V +I+ +A  K++++
Sbjct: 162 NQKDTGERLGISQMHVSRIKRQAISKLKQA 191


>gi|239933042|ref|ZP_04689995.1| RNA polymerase secondary sigma factor [Streptomyces ghanaensis ATCC
           14672]
 gi|291441393|ref|ZP_06580783.1| conserved hypothetical protein [Streptomyces ghanaensis ATCC 14672]
 gi|291344288|gb|EFE71244.1| conserved hypothetical protein [Streptomyces ghanaensis ATCC 14672]
          Length = 263

 Score = 36.2 bits (82), Expect = 6.1,   Method: Compositional matrix adjust.
 Identities = 20/72 (27%), Positives = 38/72 (52%), Gaps = 1/72 (1%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV + L +  +IA+ +RG G  + ++     +GL++AV  +DP RG     Y++  I   
Sbjct: 41  LVQAWLPMAERIAVRFRGRGEALEDLYQVAALGLVKAVDHYDPVRGNAFEAYAVPTITGE 100

Query: 113 MQEYIL-RSWSL 123
           ++ +     W+L
Sbjct: 101 IKRHFRDHMWTL 112


>gi|229108567|ref|ZP_04238180.1| RNA polymerase sigma-B factor [Bacillus cereus Rock1-15]
 gi|228674898|gb|EEL30129.1| RNA polymerase sigma-B factor [Bacillus cereus Rock1-15]
          Length = 203

 Score = 36.2 bits (82), Expect = 6.2,   Method: Compositional matrix adjust.
 Identities = 46/215 (21%), Positives = 106/215 (49%), Gaps = 28/215 (13%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRL 135
           +++  G +GL+ A++++D   G     +++  I   +++Y+  ++W +       +  R 
Sbjct: 4   DIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGI-------HVPRR 56

Query: 136 FFNLR-RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNAL 189
             +L  ++K  ++ +TD+  +  +++ IA  L +SE EV+ +     N R++   SL+ +
Sbjct: 57  IKDLGGKIKLAIEELTDHLQRSPKIIEIANHLGLSEEEVLEIMDAKNNYRVS---SLDDV 113

Query: 190 I-NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
           + NSSD +S    + +     G E+          RR +L    +VLN  E+ +      
Sbjct: 114 VENSSDGSSVARIESVGEVEQGYEET--------ERRLVLKDIFNVLNDTEKSVIHY-IF 164

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +EN +  ++      +S+  V +I+ +A  K++++
Sbjct: 165 REN-LNQKDTGERLGISQMHVSRIKRQAISKLKQA 198


>gi|254387242|ref|ZP_05002505.1| sigma factor [Streptomyces sp. Mg1]
 gi|194346050|gb|EDX27016.1| sigma factor [Streptomyces sp. Mg1]
          Length = 272

 Score = 36.2 bits (82), Expect = 6.2,   Method: Compositional matrix adjust.
 Identities = 12/45 (26%), Positives = 28/45 (62%)

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           + + ++V  G IGL++A+ ++DPER    +T ++ +I   ++ + 
Sbjct: 64  IDMDDIVQVGTIGLIKAIDRYDPEREVEFSTLALPYITGEIKRHF 108


>gi|158319526|ref|YP_001512033.1| RNA polymerase factor sigma-70 [Alkaliphilus oremlandii OhILAs]
 gi|158139725|gb|ABW18037.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Alkaliphilus
           oremlandii OhILAs]
          Length = 213

 Score = 36.2 bits (82), Expect = 6.3,   Method: Compositional matrix adjust.
 Identities = 26/94 (27%), Positives = 41/94 (43%), Gaps = 9/94 (9%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GDL A   L+  +   V   A  Y   G    ++V EG IGL +A++ F P+   +L+++
Sbjct: 27  GDLEALEYLIKKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDFKPD---KLSSF 83

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
                  A  E  +    +  I T   QK +  N
Sbjct: 84  R------AFAELCITRQIITAIKTATRQKHIPLN 111


>gi|291165889|gb|EFE27936.1| hypothetical protein HMPREF0389_01188 [Filifactor alocis ATCC
           35896]
          Length = 217

 Score = 36.2 bits (82), Expect = 6.3,   Method: Compositional matrix adjust.
 Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 1/48 (2%)

Query: 82  GNIGLMQAVKKFDPERGFRLAT-YSMWWIKAAMQEYILRSWSLVKIGT 128
           G IG+   V + DP  G ++   Y  W +    Q+Y LR W + K GT
Sbjct: 169 GIIGINHFVAEGDPNHGIKITCIYKEWKVTKGGQKYTLRDWKVEKFGT 216


>gi|78064851|ref|YP_367620.1| flagellar biosynthesis sigma factor [Burkholderia sp. 383]
 gi|77965596|gb|ABB06976.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Burkholderia sp.
           383]
          Length = 244

 Score = 36.2 bits (82), Expect = 6.3,   Method: Compositional matrix adjust.
 Identities = 50/233 (21%), Positives = 98/233 (42%), Gaps = 23/233 (9%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           L+LV K+        + + +++  G IGLM A  ++  ++G +  TY+   I+ AM +  
Sbjct: 27  LQLVAKMPAS-----VDLDDLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDE- 80

Query: 118 LRS--WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
           LRS  W    +  T+         R ++  +  +  N  +      IA+ LN+   E   
Sbjct: 81  LRSNDWLPRSLRKTS---------REVEHAVHQVEQNLGRSASETEIAQHLNMPLDEYQG 131

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
           M   L G + +         +   + D    DH      L++    ++ R  L  ++  L
Sbjct: 132 MLQDLHGSQLIYYEDFDRAADDEPFLDRYRVDHADPLSALLD----EHLREALVEAIERL 187

Query: 236 NPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
             RE+ +       E  + L  + +  EVS  RV Q+ ++A  +++  +++Q 
Sbjct: 188 PEREKLLMSL--YYERGLNLREIGAVLEVSESRVCQLHSQAVARLRARLREQA 238


>gi|313895821|ref|ZP_07829375.1| RNA polymerase sigma factor, FliA/WhiG family [Selenomonas sp. oral
           taxon 137 str. F0430]
 gi|320529404|ref|ZP_08030492.1| putative RNA polymerase sigma factor WhiG [Selenomonas artemidis
           F0399]
 gi|312975246|gb|EFR40707.1| RNA polymerase sigma factor, FliA/WhiG family [Selenomonas sp. oral
           taxon 137 str. F0430]
 gi|320138370|gb|EFW30264.1| putative RNA polymerase sigma factor WhiG [Selenomonas artemidis
           F0399]
          Length = 246

 Score = 36.2 bits (82), Expect = 6.4,   Method: Compositional matrix adjust.
 Identities = 27/102 (26%), Positives = 51/102 (50%), Gaps = 6/102 (5%)

Query: 61  VVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           +V++  G     LP      +++S G  GL+ A+++++  RG +  TY+   ++ AM ++
Sbjct: 33  LVRLVAGRIAISLPQHVDREDLLSSGFFGLLDAIERYELTRGNKFETYAGVRVRGAMLDH 92

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHL-QAITDNNLKPE 157
            LRS   + +    N K+    +  L+G L +  TD  L  E
Sbjct: 93  -LRSKDWIPVSVRQNIKKYEKAVASLEGKLGRTATDEELAAE 133


>gi|107024379|ref|YP_622706.1| flagellar biosynthesis sigma factor [Burkholderia cenocepacia AU
           1054]
 gi|116688295|ref|YP_833918.1| flagellar biosynthesis sigma factor [Burkholderia cenocepacia
           HI2424]
 gi|170731608|ref|YP_001763555.1| flagellar biosynthesis sigma factor [Burkholderia cenocepacia
           MC0-3]
 gi|105894568|gb|ABF77733.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Burkholderia
           cenocepacia AU 1054]
 gi|116646384|gb|ABK07025.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Burkholderia
           cenocepacia HI2424]
 gi|169814850|gb|ACA89433.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia
           cenocepacia MC0-3]
          Length = 243

 Score = 36.2 bits (82), Expect = 6.5,   Method: Compositional matrix adjust.
 Identities = 48/231 (20%), Positives = 96/231 (41%), Gaps = 19/231 (8%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           L+LV K+        + + +++  G IGLM A  ++  ++G +  TY+   I+ AM +  
Sbjct: 26  LQLVAKMPAS-----VDLDDLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDE- 79

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           LRS   +        + +   + +++ HL        +      IA+ LN+   E   M 
Sbjct: 80  LRSNDWLPRSLRKTSREVEHAVHQVEQHLG-------RSASETEIAQHLNMPLDEYQGML 132

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
             L G + +         +   + D    DH      L++     + R  L  ++  L  
Sbjct: 133 QDLHGSQLIYYEDFDRAADDEPFLDRYRVDHADPLSALLD----DHLREALVEAIERLPE 188

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RE+ +       E  + L  + +  EVS  RV Q+ ++A  +++  +++Q 
Sbjct: 189 REKLLMSL--YYERGLNLREIGAVLEVSESRVCQLHSQAVARLRARLREQA 237


>gi|260598417|ref|YP_003210988.1| flagellar biosynthesis sigma factor [Cronobacter turicensis z3032]
 gi|260217594|emb|CBA31853.1| RNA polymerase sigma factor for flagellar operon [Cronobacter
           turicensis z3032]
          Length = 239

 Score = 36.2 bits (82), Expect = 6.6,   Method: Compositional matrix adjust.
 Identities = 47/213 (22%), Positives = 100/213 (46%), Gaps = 16/213 (7%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL+ AV+++D  +G    TY++  I+ AM +  LRS   V      N + 
Sbjct: 41  LDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDE-LRSRDWVPRSVRRNARE 99

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   + +L+   Q +  N  + E    +A++L++   E   M       ++ N+ + S D
Sbjct: 100 VAQAIGQLE---QELGRNATELE----VAERLSIPLEEYRQMLL-----DTNNSQLFSYD 147

Query: 195 KNSSQWQDWL-VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           +   +  D + +   D Q +  + +    N R  +  ++  L  RE+ +      +E  +
Sbjct: 148 EWREEHGDSIELVTEDNQNENPLHQLLEGNLRERVMEAIESLPEREQMVLTLYYQEE--L 205

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 206 NLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 238


>gi|257056691|ref|YP_003134523.1| RNA polymerase sigma factor, sigma-70 family [Saccharomonospora
           viridis DSM 43017]
 gi|256586563|gb|ACU97696.1| RNA polymerase sigma factor, sigma-70 family [Saccharomonospora
           viridis DSM 43017]
          Length = 266

 Score = 36.2 bits (82), Expect = 6.6,   Method: Compositional matrix adjust.
 Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 1/72 (1%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++T  L L   IA  + G G P  ++V    +GL+ A+ +FD  RG     +++  I   
Sbjct: 48  IITRCLPLAEHIARRFVGRGEPRDDLVQVARLGLLNAIDRFDASRGTEFVAFAVPTIMGE 107

Query: 113 MQEYIL-RSWSL 123
           ++ +    SW++
Sbjct: 108 VRRHFRDSSWAV 119


>gi|239995147|ref|ZP_04715671.1| flagellar biosynthesis sigma factor [Alteromonas macleodii ATCC
           27126]
          Length = 243

 Score = 36.2 bits (82), Expect = 6.8,   Method: Compositional matrix adjust.
 Identities = 54/253 (21%), Positives = 103/253 (40%), Gaps = 34/253 (13%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           A  Y++  D +   +LV  H  LV +IA   +      + + +++  G IGL++A + FD
Sbjct: 5   AAAYQQQTDKA---QLVERHAPLVKRIAHHLIARLPASVLVDDLIQSGMIGLLEAARNFD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
             +G    T++   I+ AM + I +  W+          + +  N R +   +  +    
Sbjct: 62  GSKGASFETFAGIRIRGAMLDEIRKGDWT---------PRSVHRNGRAITEAISQVESET 112

Query: 154 LKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
            +  +   IA KLNVS  +   M       +L G E L              +D +  + 
Sbjct: 113 GRDARDSDIADKLNVSLQDYHQMLNEVNAGKLVGIEDLGV-----------SEDVISTEQ 161

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           +      +E   +   +  L  +++ L  RE  +      +E  + L  +    +VS  R
Sbjct: 162 NRGSDAPLEDLMQGAFQKALAHAITTLPEREAIVLSLYYDEE--LNLREIGEVLDVSESR 219

Query: 269 VRQIEARAFKKVQ 281
           V QI ++A  K++
Sbjct: 220 VSQIHSQAMLKLK 232


>gi|156933482|ref|YP_001437398.1| flagellar biosynthesis sigma factor [Cronobacter sakazakii ATCC
           BAA-894]
 gi|156531736|gb|ABU76562.1| hypothetical protein ESA_01300 [Cronobacter sakazakii ATCC BAA-894]
          Length = 229

 Score = 35.8 bits (81), Expect = 7.1,   Method: Compositional matrix adjust.
 Identities = 51/230 (22%), Positives = 107/230 (46%), Gaps = 21/230 (9%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRL V++        + + +++  G IGL+ AV+++D  +G    TY++  I+ AM +  
Sbjct: 19  LRLQVRLPAS-----VELDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDE- 72

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           LRS   V      N + +   + +L+   Q +  N  + E    +A++L++   E   M 
Sbjct: 73  LRSRDWVPRSVRRNAREVAQAIGQLE---QELGRNATELE----VAERLSIPLEEYRQML 125

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWL-VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
                 ++ N+ + S D+   +  D + +   D Q +  + +    N R  +  ++  L 
Sbjct: 126 L-----DTNNSQLFSYDEWREEHGDSIELVTEDNQNENPLHQLLESNLRERVMEAIESLP 180

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            RE+ +      +E  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 181 EREQMVLTLYYQEE--LNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 228


>gi|74055051|gb|AAZ95856.1| FliA [Aeromonas hydrophila]
          Length = 239

 Score = 35.8 bits (81), Expect = 7.1,   Method: Compositional matrix adjust.
 Identities = 55/249 (22%), Positives = 102/249 (40%), Gaps = 26/249 (10%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKF 93
           A+ Y  H D   ++ LV  H  LV +IA       LP    + +++  G IGL++A + F
Sbjct: 4   AQAYLRHQD---SYVLVERHAPLVKRIAQHLLAR-LPSSVLLDDLIQAGMIGLLEASRNF 59

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           D  +G    TY+   I+ +M + I R  W           + +  N R +   ++ +   
Sbjct: 60  DGSKGASFETYAGIRIRGSMLDEIRRGDWV---------PRSVHRNSRSIAEAIENVEQA 110

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           + +  +   +A ++ VS  E  +M      D S   +I   D   S  +D + +  D   
Sbjct: 111 HGRDARDTEVAAQMGVSLGEYHTM----LQDVSCGKIIGIEDLGVS--EDVIGHPDDAAS 164

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
               ++   +  +  L   +  L  RE  +      +E  + L  +     VS  RV QI
Sbjct: 165 NSGFDELAAERFQGALAEHIGRLPEREALVLSLYYDEE--LNLREIGEVLNVSESRVSQI 222

Query: 273 EARAFKKVQ 281
            ++A  +++
Sbjct: 223 HSQAMHRLR 231


>gi|269795656|ref|YP_003315111.1| RNA polymerase sigma-28 subunit SigD/FliA/WhiG [Sanguibacter
           keddieii DSM 10542]
 gi|269097841|gb|ACZ22277.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Sanguibacter
           keddieii DSM 10542]
          Length = 345

 Score = 35.8 bits (81), Expect = 7.1,   Method: Compositional matrix adjust.
 Identities = 58/255 (22%), Positives = 112/255 (43%), Gaps = 21/255 (8%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQAVKKFD 94
           + Y+   D     RL+  +  LV  +A    G  LP +    ++VS G  GL+ A++KF+
Sbjct: 101 REYKACADAPTRERLILHYAPLVTSVA-SRVGMKLPSTVEHADLVSYGMFGLIDAIEKFE 159

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ-AITDNN 153
            +R  +  TY+   I+ A+ +  LR+   V     +  + +      L+  L  A TD  
Sbjct: 160 LDREIKFETYATSRIRGAILDE-LRANDWVPRSVRSKARAVDRAHAELEARLHRAPTD-- 216

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQ 211
             PE    IA+ + ++ SE+ S+   ++     +L+ +  + D+        L   H  +
Sbjct: 217 --PE----IAEHMEIALSELRSIRHLVSTVNLVALDEVFGAGDQVEPVGH--LDTGHGAR 268

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
                   E K  + +L+++M  L  RE +I       E  +TL  + +   V+  R+ Q
Sbjct: 269 STDPARTFESKETKFLLSQAMDQLGERE-KIMLVLYYYEG-MTLAEIGAVLGVTESRISQ 326

Query: 272 IEARAFKKVQESIQK 286
           +   A  +++E + +
Sbjct: 327 MHTAAMGRLREKLSR 341


>gi|329904712|ref|ZP_08273913.1| RNA polymerase sigma factor for flagellar operon [Oxalobacteraceae
           bacterium IMCC9480]
 gi|327547856|gb|EGF32614.1| RNA polymerase sigma factor for flagellar operon [Oxalobacteraceae
           bacterium IMCC9480]
          Length = 244

 Score = 35.8 bits (81), Expect = 7.2,   Method: Compositional matrix adjust.
 Identities = 47/238 (19%), Positives = 105/238 (44%), Gaps = 19/238 (7%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           S  + L+  H  LV ++A   +    P   + +++  G IGL  A+ +++   G +  TY
Sbjct: 8   SDKNHLLVQHAPLVKRLAHQMKAKLPPSVEVDDLIQAGMIGLFDAINRYEDTHGAQFETY 67

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           ++  I+ +M +  LRS   +        + +  N+R+++  +QA+     +      +AK
Sbjct: 68  AVQRIRGSMLDE-LRSSDWLP-------RSMRQNMRKIEVAMQALQQKLGRAPLEAEVAK 119

Query: 165 KLNVSESEVISMNCRLAGDESL--NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
            + +S +E  ++     G + +      +SS+ N      +     D   Q L+      
Sbjct: 120 HMKLSLAEYQNLLGEGGGHQLVYYEDFHDSSEGNEHFLDRYCTDLSDNPLQSLL----NA 175

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             R+ + R++  L  RE+ +      QE  + L+ + +   V+  R+ Q+ ++A  ++
Sbjct: 176 GFRDAVIRAIEALPEREKILMGLYYEQE--MNLKEIGAVLGVTESRISQLHSQAIARM 231


>gi|212639538|ref|YP_002316058.1| RNA polymerase sigma factor SigD [Anoxybacillus flavithermus WK1]
 gi|212561018|gb|ACJ34073.1| DNA-directed RNA polymerase specialized sigma subunit
           [Anoxybacillus flavithermus WK1]
          Length = 243

 Score = 35.8 bits (81), Expect = 7.3,   Method: Compositional matrix adjust.
 Identities = 25/94 (26%), Positives = 47/94 (50%), Gaps = 10/94 (10%)

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           +GL  A++KFDP R  +  TY+ + I+ A+ +  LR    +        K++   + RL+
Sbjct: 52  LGLYDALEKFDPSRDLKFDTYASFRIRGAILDG-LRKEDWLPRSVREKAKKIEATIERLQ 110

Query: 144 G-HLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
             H++ ++           +A  LN+SE EV ++
Sbjct: 111 QMHMRDVSAKE--------VADALNISEDEVYAV 136


>gi|229101713|ref|ZP_04232430.1| RNA polymerase sigma-B factor [Bacillus cereus Rock3-28]
 gi|228681661|gb|EEL35821.1| RNA polymerase sigma-B factor [Bacillus cereus Rock3-28]
          Length = 203

 Score = 35.8 bits (81), Expect = 7.3,   Method: Compositional matrix adjust.
 Identities = 39/175 (22%), Positives = 86/175 (49%), Gaps = 26/175 (14%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRL 135
           +++  G +GL+ A++++D   G     +++  I   +++Y+  ++W +       +  R 
Sbjct: 4   DIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGI-------HVPRR 56

Query: 136 FFNLR-RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNAL 189
             +L  ++K  ++ +TD+  +  +++ IA  L +SE EV+ +     N R++   SL+ +
Sbjct: 57  IKDLGGKIKLAIEELTDHLQRSPKIIEIANHLGLSEEEVLEIMDAKNNYRVS---SLDDV 113

Query: 190 I-NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           + N+SD +S    + +     G EQ          RR +L    +VLN  E+ + 
Sbjct: 114 VENASDGSSVARIESVGEVEQGYEQT--------ERRLVLNDIFNVLNETEKSVI 160


>gi|293392778|ref|ZP_06637096.1| DNA-directed RNA polymerase sigma subunit RpoS [Serratia odorifera
           DSM 4582]
 gi|291424637|gb|EFE97848.1| DNA-directed RNA polymerase sigma subunit RpoS [Serratia odorifera
           DSM 4582]
          Length = 119

 Score = 35.8 bits (81), Expect = 7.4,   Method: Compositional matrix adjust.
 Identities = 21/56 (37%), Positives = 34/56 (60%), Gaps = 4/56 (7%)

Query: 235 LNPRERRIFEARR---LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           LN ++R +  ARR   L     TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 55  LNAKQREVL-ARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQMQ 109


>gi|326942736|gb|AEA18632.1| sporulation sigma factor SigF [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 248

 Score = 35.8 bits (81), Expect = 7.6,   Method: Compositional matrix adjust.
 Identities = 38/125 (30%), Positives = 59/125 (47%), Gaps = 13/125 (10%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL I ++   G IGL++A   FD E G + +TY++  I   +   I R    VK+     
Sbjct: 50  GLDIEDLTQFGMIGLIKARDNFDLEYGCKFSTYAVPKIIGEIGRAI-RDHQKVKV----- 103

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
           Q+ ++     +KG    I   NL+ E    IA  LN   S V +      G +SLN +++
Sbjct: 104 QRSVY----SIKG---KILRQNLEYEIPEEIASILNEDVSVVSNALHYQPGTQSLNKVVH 156

Query: 192 SSDKN 196
            S+ N
Sbjct: 157 QSNGN 161


>gi|228957370|ref|ZP_04119129.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|229028783|ref|ZP_04184888.1| RNA polymerase sigma-B factor [Bacillus cereus AH1271]
 gi|228732530|gb|EEL83407.1| RNA polymerase sigma-B factor [Bacillus cereus AH1271]
 gi|228802319|gb|EEM49177.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
          Length = 203

 Score = 35.8 bits (81), Expect = 7.7,   Method: Compositional matrix adjust.
 Identities = 39/175 (22%), Positives = 86/175 (49%), Gaps = 26/175 (14%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRL 135
           +++  G +GL+ A++++D   G     +++  I   +++Y+  ++W +       +  R 
Sbjct: 4   DIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGI-------HVPRR 56

Query: 136 FFNLR-RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNAL 189
             +L  ++K  ++ +TD+  +  +++ IA  L +SE EV+ +     N R++   SL+ +
Sbjct: 57  IKDLGGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVS---SLDDV 113

Query: 190 I-NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           + NSSD +S    + +     G E+          RR +L    +VLN  E+ + 
Sbjct: 114 VENSSDGSSVARIESVGEVEQGYEET--------ERRLVLKDIFNVLNDTEKSVI 160


>gi|207109684|ref|ZP_03243846.1| RNA polymerase sigma factor RpoD [Helicobacter pylori
           HPKX_438_CA4C1]
          Length = 84

 Score = 35.8 bits (81), Expect = 7.7,   Method: Compositional matrix adjust.
 Identities = 22/50 (44%), Positives = 30/50 (60%), Gaps = 3/50 (6%)

Query: 235 LNPRERRIFEAR---RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 21  LNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 70


>gi|197250155|ref|YP_002147819.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
 gi|197213858|gb|ACH51255.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
          Length = 68

 Score = 35.8 bits (81), Expect = 7.8,   Method: Compositional matrix adjust.
 Identities = 22/59 (37%), Positives = 35/59 (59%), Gaps = 4/59 (6%)

Query: 232 MSVLNPRERRIFEARR---LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           M  LN ++R +  ARR   L     TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 1   MFELNAKQREVL-ARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 58


>gi|228943596|ref|ZP_04106021.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228976443|ref|ZP_04136903.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228981654|ref|ZP_04141950.1| RNA polymerase sigma factor [Bacillus thuringiensis Bt407]
 gi|228778139|gb|EEM26410.1| RNA polymerase sigma factor [Bacillus thuringiensis Bt407]
 gi|228783244|gb|EEM31363.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228816045|gb|EEM62245.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
          Length = 232

 Score = 35.8 bits (81), Expect = 8.0,   Method: Compositional matrix adjust.
 Identities = 38/125 (30%), Positives = 59/125 (47%), Gaps = 13/125 (10%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL I ++   G IGL++A   FD E G + +TY++  I   +   I R    VK+     
Sbjct: 34  GLDIEDLTQFGMIGLIKARDNFDLEYGCKFSTYAVPKIIGEIGRAI-RDHQKVKV----- 87

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
           Q+ ++     +KG    I   NL+ E    IA  LN   S V +      G +SLN +++
Sbjct: 88  QRSVY----SIKG---KILRQNLEYEIPEEIASILNEDVSVVSNALHYQPGTQSLNKVVH 140

Query: 192 SSDKN 196
            S+ N
Sbjct: 141 QSNGN 145


>gi|91200244|emb|CAJ73289.1| strongly similar to RNA polymerase sigma factor for flagellar
           operon [Candidatus Kuenenia stuttgartiensis]
          Length = 259

 Score = 35.8 bits (81), Expect = 8.1,   Method: Compositional matrix adjust.
 Identities = 52/241 (21%), Positives = 106/241 (43%), Gaps = 19/241 (7%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +LVT +L LV  +   +  Y LP      +++  G IGL++A ++FDP    +  T+++ 
Sbjct: 28  KLVTENLSLVKYVVNKFIIY-LPSFVDKEDLIEYGVIGLLEASERFDPCMDTKFGTFAVS 86

Query: 108 WIKAAMQEYI-LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            I+ A+ +++  + W    +    +  R  +        L+   + +  PE++ A   K+
Sbjct: 87  RIRGAILDHLRAQDWLPRSVREKVSLAREAY------ATLEQKLNRHPLPEEIAA-ELKI 139

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRR 225
           + +E E + +        SL  +   S+  + +    L  D   G     IE EE K   
Sbjct: 140 DTAEWEKLLVEINFGMFLSLEEMNAKSEDGNKEAVGMLFADSKIGDPLSNIETEEEK--- 196

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            +L  ++  L  RE+ +      ++  + L  +S   ++S  RV QI  +    ++  ++
Sbjct: 197 ELLVAAIKELPAREKLVITLYYYED--LMLREISQMLDISESRVSQIHHQGLFMLRSKVR 254

Query: 286 K 286
           K
Sbjct: 255 K 255


>gi|153803628|ref|ZP_01958214.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae MZO-3]
 gi|124120837|gb|EAY39580.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae MZO-3]
          Length = 193

 Score = 35.8 bits (81), Expect = 8.1,   Method: Compositional matrix adjust.
 Identities = 50/204 (24%), Positives = 89/204 (43%), Gaps = 28/204 (13%)

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRL 142
           +GL++A K +D  +G    TY+   I+ AM + I R  W  V      + + +   +  L
Sbjct: 2   VGLLEAQKNYDGSKGASFETYAGIRIRGAMLDDIRRGDW--VPRSVHKHNREISQAIAVL 59

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVS----ESEVISMNC-RLAGDESLNALINSSDKNS 197
           +G L      N  P     +AK LN+S     S ++ +NC R+ G E L      SD   
Sbjct: 60  EGEL------NRDPTD-AEVAKFLNMSLEQYHSVLMDINCSRIVGIEDLGV----SDDAI 108

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           S ++       +G++         ++ R  L  S+  L  RE  +      +E  + L+ 
Sbjct: 109 SPFE-------EGEDNSPFHGVAEESFRKALVESIKSLPEREALVLSLYYDEE--LNLKE 159

Query: 258 LSSEFEVSRERVRQIEARAFKKVQ 281
           +     VS  RV QI +++ ++++
Sbjct: 160 IGEVLGVSESRVSQILSQSMQRLR 183


>gi|313647806|gb|EFS12252.1| RNA polymerase sigma factor rpoS domain protein [Shigella flexneri
           2a str. 2457T]
          Length = 76

 Score = 35.8 bits (81), Expect = 8.3,   Method: Compositional matrix adjust.
 Identities = 21/56 (37%), Positives = 34/56 (60%), Gaps = 4/56 (7%)

Query: 235 LNPRERRIFEARR---LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           LN ++R +  ARR   L     TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 12  LNAKQREVL-ARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 66


>gi|20151058|pdb|1KU3|A Chain A, Crystal Structure Of Thermus Aquaticus Rna Polymerase
           Sigma Subunit Fragment, Region 4
 gi|20151059|pdb|1KU7|A Chain A, Crystal Structure Of Thermus Aquatics Rna Polymerase
           Sigmaa Subunit Region 4 Bound To-35 Element Dna
 gi|20151062|pdb|1KU7|D Chain D, Crystal Structure Of Thermus Aquatics Rna Polymerase
           Sigmaa Subunit Region 4 Bound To-35 Element Dna
          Length = 73

 Score = 35.8 bits (81), Expect = 8.3,   Method: Compositional matrix adjust.
 Identities = 20/56 (35%), Positives = 36/56 (64%), Gaps = 2/56 (3%)

Query: 228 LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           L +++S L+ RE  + + R+  +     TLE + + F V+RER+RQIE +A +K++
Sbjct: 4   LEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLK 59


>gi|242280062|ref|YP_002992191.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio
           salexigens DSM 2638]
 gi|242122956|gb|ACS80652.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio
           salexigens DSM 2638]
          Length = 263

 Score = 35.8 bits (81), Expect = 8.4,   Method: Compositional matrix adjust.
 Identities = 16/45 (35%), Positives = 29/45 (64%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           + E++S G++GL++++ KF PE   +  TY+   IK AM + + R
Sbjct: 64  LGELISAGSLGLVESLGKFRPELKIKFETYAENRIKGAMLDELRR 108


>gi|315445714|ref|YP_004078593.1| RNA polymerase sigma factor, sigma-70 family [Mycobacterium sp.
           Spyr1]
 gi|315264017|gb|ADU00759.1| RNA polymerase sigma factor, sigma-70 family [Mycobacterium sp.
           Spyr1]
          Length = 262

 Score = 35.8 bits (81), Expect = 8.6,   Method: Compositional matrix adjust.
 Identities = 59/258 (22%), Positives = 106/258 (41%), Gaps = 23/258 (8%)

Query: 37  LAKRYREHGDL---SAA-----HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           +A  +RE  +L   SAA      R+V   L L   IA  + G G P  ++V    +GL+ 
Sbjct: 19  VADMFRELAELEEGSAAFQRQRDRIVERCLPLADHIARRFDGRGEPRDDLVQVARVGLVN 78

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           AV +FD   G    ++++  I   ++ +    SWS VK+      K L   L      L 
Sbjct: 79  AVIRFDVNAGSDFVSFAVPTIMGEVRRHFRDNSWS-VKV--PRRLKELHLRLGAATAELS 135

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                   P +   +A +L +   EV+     L    S N L   S   S       + D
Sbjct: 136 QRLGRAPTPSE---LAAELEMDRDEVVEG---LVAGSSYNTLSIDSGGGSGNEDAPAIAD 189

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
             G   + +++ E    R  L   ++ L  RER +   R  +   +T   ++    +S+ 
Sbjct: 190 TLGDVDLTLDQIE---NREALRPLLAALPERERTVLVLRFFES--MTQTQIAERVGISQM 244

Query: 268 RVRQIEARAFKKVQESIQ 285
            V ++ A++  ++++ ++
Sbjct: 245 HVSRLLAKSLTRLRDQLE 262


>gi|228943728|ref|ZP_04106130.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228976238|ref|ZP_04136717.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228977712|ref|ZP_04138098.1| RNA polymerase sigma-B factor [Bacillus thuringiensis Bt407]
 gi|229042834|ref|ZP_04190570.1| RNA polymerase sigma-B factor [Bacillus cereus AH676]
 gi|229143711|ref|ZP_04272133.1| RNA polymerase sigma-B factor [Bacillus cereus BDRD-ST24]
 gi|228639767|gb|EEK96175.1| RNA polymerase sigma-B factor [Bacillus cereus BDRD-ST24]
 gi|228726494|gb|EEL77715.1| RNA polymerase sigma-B factor [Bacillus cereus AH676]
 gi|228782010|gb|EEM30202.1| RNA polymerase sigma-B factor [Bacillus thuringiensis Bt407]
 gi|228783483|gb|EEM31583.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228815947|gb|EEM62170.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
          Length = 203

 Score = 35.8 bits (81), Expect = 8.7,   Method: Compositional matrix adjust.
 Identities = 39/175 (22%), Positives = 86/175 (49%), Gaps = 26/175 (14%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRL 135
           +++  G +GL+ A++++D   G     +++  I   +++Y+  ++W +       +  R 
Sbjct: 4   DIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGI-------HVPRR 56

Query: 136 FFNLR-RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLNAL 189
             +L  ++K  ++ +TD+  +  +++ IA  L +SE EV+ +     N R++   SL+ +
Sbjct: 57  IKDLGGKIKLAIEELTDHLQRSPKIIEIANHLGLSEEEVLEIMDAKNNYRVS---SLDDV 113

Query: 190 I-NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           + NSSD +S    + +     G E+          RR +L    +VLN  E+ + 
Sbjct: 114 VENSSDGSSVARIESVGEVEQGYEET--------ERRLVLKDIFNVLNDTEKSVI 160


>gi|83647839|ref|YP_436274.1| flagellar biosynthesis sigma factor FliA [Hahella chejuensis KCTC
           2396]
 gi|83635882|gb|ABC31849.1| flagellar biosynthesis sigma factor FliA [Hahella chejuensis KCTC
           2396]
          Length = 275

 Score = 35.8 bits (81), Expect = 8.8,   Method: Compositional matrix adjust.
 Identities = 14/43 (32%), Positives = 27/43 (62%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           + +++  G IGL++A +K+D  +G +  TY+   I+ AM + I
Sbjct: 76  VEDLIQAGMIGLLEAAQKYDAGKGAKFETYAGIRIRGAMVDEI 118


>gi|291562040|emb|CBL40856.1| RNA polymerase sigma factor, sigma-70 family [butyrate-producing
           bacterium SS3/4]
          Length = 265

 Score = 35.8 bits (81), Expect = 8.9,   Method: Compositional matrix adjust.
 Identities = 10/45 (22%), Positives = 28/45 (62%)

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           + + + V+EG + +++ +  +DP++  + +TY    ++ AM +Y+
Sbjct: 51  MQMEDAVNEGVVAIIKGIDMYDPDKNIKFSTYITTRVRGAMLDYV 95


>gi|210623158|ref|ZP_03293612.1| hypothetical protein CLOHIR_01562 [Clostridium hiranonis DSM 13275]
 gi|210153791|gb|EEA84797.1| hypothetical protein CLOHIR_01562 [Clostridium hiranonis DSM 13275]
          Length = 216

 Score = 35.8 bits (81), Expect = 8.9,   Method: Compositional matrix adjust.
 Identities = 21/80 (26%), Positives = 39/80 (48%), Gaps = 1/80 (1%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           +++EEY + KR   +GD  A   ++  +   V   A  Y   G    +++ EG IGL +A
Sbjct: 16  QQKEEYEIVKR-AANGDRMALEYIMAKYKNFVRVKAKSYFLIGADREDIIQEGMIGLYKA 74

Query: 90  VKKFDPERGFRLATYSMWWI 109
           ++ FD  +     +++   I
Sbjct: 75  IRDFDETKAHSFRSFAEVCI 94


>gi|145225367|ref|YP_001136045.1| RNA polymerase sigma factor SigF [Mycobacterium gilvum PYR-GCK]
 gi|145217853|gb|ABP47257.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Mycobacterium
           gilvum PYR-GCK]
          Length = 262

 Score = 35.8 bits (81), Expect = 8.9,   Method: Compositional matrix adjust.
 Identities = 60/259 (23%), Positives = 108/259 (41%), Gaps = 25/259 (9%)

Query: 37  LAKRYREHGDL---SAA-----HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           +A  +RE  +L   SAA      R+V   L L   IA  + G G P  ++V    +GL+ 
Sbjct: 19  VADMFRELAELEEGSAAFQRQRDRIVERCLPLADHIARRFDGRGEPRDDLVQVARVGLVN 78

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           AV +FD   G    ++++  I   ++ +    SWS VK+      K L   L      L 
Sbjct: 79  AVIRFDVTAGSDFVSFAVPTIMGEVRRHFRDNSWS-VKV--PRRLKELHLRLGAATAELS 135

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                   P +   +A +L +   EV+     L    S N L   S   S       + D
Sbjct: 136 QRLGRAPTPSE---LAAELEMDRDEVVEG---LVAGSSYNTLSIDSGGGSGNEDAPAIAD 189

Query: 208 HDGQEQVLIEK-EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
             G   + +++ E R+  R +L    + L  RER +   R  +   +T   ++    +S+
Sbjct: 190 TLGDVDLTLDQIENREALRPLL----AALPERERTVLVLRFFES--MTQTQIAERVGISQ 243

Query: 267 ERVRQIEARAFKKVQESIQ 285
             V ++ A++  ++++ ++
Sbjct: 244 MHVSRLLAKSLTRLRDQLE 262


>gi|119470003|ref|ZP_01612808.1| flagellar biosynthesis sigma factor [Alteromonadales bacterium
           TW-7]
 gi|119446713|gb|EAW27986.1| flagellar biosynthesis sigma factor [Alteromonadales bacterium
           TW-7]
          Length = 240

 Score = 35.4 bits (80), Expect = 9.3,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 6/75 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           +V  H  LV K+A       LP S    +++  G IGL++A K FD  +G    T++   
Sbjct: 16  IVEKHASLVKKVACHLIAR-LPASVQLDDLIQSGMIGLIEASKSFDATKGASFETFAGIR 74

Query: 109 IKAAMQEYILRS-WS 122
           I+ AM + + R  W+
Sbjct: 75  IRGAMLDEMRRGDWA 89


>gi|167587836|ref|ZP_02380224.1| flagellar biosynthesis sigma factor [Burkholderia ubonensis Bu]
          Length = 244

 Score = 35.4 bits (80), Expect = 9.4,   Method: Compositional matrix adjust.
 Identities = 48/231 (20%), Positives = 97/231 (41%), Gaps = 19/231 (8%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           L+LV K+        + + +++  G IGLM A  ++  ++G +  TY+   I+ AM +  
Sbjct: 27  LQLVAKMPAS-----VDLDDLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDE- 80

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           LRS   +        + +   + +++ HL        +      IA+ LN+   E   M 
Sbjct: 81  LRSNDWLPRSLRKTSREVEHAVHQVEQHLG-------RAASEAEIAQHLNMPLDEYQGML 133

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
             L G + +         +   + D    DH      L++    ++ R  L  ++  L  
Sbjct: 134 QDLHGSQLIYYEDFDRAADDEPFLDRYRVDHADPLSSLLD----EHLREALIEAIERLPE 189

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RE+ +       E  + L  + +  EVS  RV Q+ ++A  +++  +++Q 
Sbjct: 190 REKLLMSL--YYERGLNLREIGAVLEVSESRVCQLHSQAVARLRARLREQA 238


>gi|239815268|ref|YP_002944178.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Variovorax
           paradoxus S110]
 gi|239801845|gb|ACS18912.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Variovorax
           paradoxus S110]
          Length = 272

 Score = 35.4 bits (80), Expect = 9.5,   Method: Compositional matrix adjust.
 Identities = 24/82 (29%), Positives = 45/82 (54%), Gaps = 4/82 (4%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHL---RLVVKIAMGYRGYG-LPISEVVSEGNIGLMQAVK 91
            L +R+RE GD  A  +L+  HL   R++   A G R +  +  ++      +GL++AV 
Sbjct: 15  ALWRRWREEGDEGARAQLIEHHLPYARMMAAAAYGRRTHNEVEFADYHQLARLGLIEAVD 74

Query: 92  KFDPERGFRLATYSMWWIKAAM 113
           +FDP +G +  T++   ++ A+
Sbjct: 75  RFDPAQGAQFKTFAAKRVQGAI 96


>gi|291165879|gb|EFE27926.1| RNA polymerase sigma-B factor [Filifactor alocis ATCC 35896]
          Length = 273

 Score = 35.4 bits (80), Expect = 9.5,   Method: Compositional matrix adjust.
 Identities = 14/74 (18%), Positives = 41/74 (55%), Gaps = 1/74 (1%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           + L+  +L +   ++  Y   G+   ++    ++GL+ A++++D  +GF+ ++++   I 
Sbjct: 45  NELIQKNLYIAEILSKKYLNKGIEYDDIFQVASLGLILAIERYDVTKGFKFSSFATPTII 104

Query: 111 AAMQEYIL-RSWSL 123
             +++Y   + WS+
Sbjct: 105 GEIKKYFRDKGWSI 118


>gi|289754805|ref|ZP_06514183.1| predicted protein [Mycobacterium tuberculosis EAS054]
 gi|289695392|gb|EFD62821.1| predicted protein [Mycobacterium tuberculosis EAS054]
          Length = 473

 Score = 35.4 bits (80), Expect = 9.5,   Method: Compositional matrix adjust.
 Identities = 34/122 (27%), Positives = 58/122 (47%), Gaps = 32/122 (26%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGD-LS 48
           RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+ L 
Sbjct: 218 RKDAELTASADS-VRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSERGEKLP 276

Query: 49  AAHR----------------LVTSHLRLVVKIAMGYRGYGLPISEVV-SEGNIGLMQAVK 91
           AA R                L+ ++LRLVV +A  Y G G+   +++  +  +GL++AV+
Sbjct: 277 AAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIPGKATLGLIRAVE 336

Query: 92  KF 93
           KF
Sbjct: 337 KF 338


>gi|251765105|sp|Q1LWB0|TXB1A_DANRE RecName: Full=Tax1-binding protein 1 homolog A
 gi|148725290|emb|CAK04430.2| novel protein similar to vertebrate Tax1 (human T-cell leukemia
           virus type I) binding protein 1 (TAX1BP1) [Danio rerio]
          Length = 781

 Score = 35.4 bits (80), Expect = 9.5,   Method: Compositional matrix adjust.
 Identities = 28/99 (28%), Positives = 52/99 (52%), Gaps = 1/99 (1%)

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
           ++ L  + DG   +L+  EE +     L +++ +L  +ER   + ++ Q+N    ++L  
Sbjct: 138 EELLTVEDDGNSDILVRVEEVQQECKELQKALRLLT-QERDQLQEKQRQQNQELQKSLIE 196

Query: 261 EFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQK 299
           E E ++ RVRQ+E    K  Q+++ K+ EL      LQK
Sbjct: 197 EKEEAQSRVRQLEQDLLKITQKAVLKETELDCLRDKLQK 235


>gi|42543555|pdb|1RIO|H Chain H, Structure Of Bacteriophage Lambda Ci-Ntd In Complex With
           Sigma-Region4 Of Thermus Aquaticus Bound To Dna
          Length = 73

 Score = 35.4 bits (80), Expect = 9.6,   Method: Compositional matrix adjust.
 Identities = 20/56 (35%), Positives = 36/56 (64%), Gaps = 2/56 (3%)

Query: 228 LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           L +++S L+ RE  + + R+  +     TLE + + F V+RER+RQIE +A +K++
Sbjct: 4   LEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLK 59


>gi|330828816|ref|YP_004391768.1| RNA polymerase sigma factor [Aeromonas veronii B565]
 gi|328803952|gb|AEB49151.1| RNA polymerase sigma factor [Aeromonas veronii B565]
          Length = 225

 Score = 35.4 bits (80), Expect = 9.7,   Method: Compositional matrix adjust.
 Identities = 24/72 (33%), Positives = 36/72 (50%), Gaps = 5/72 (6%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           LV  H  LV +IA       LP    + +++  G IGL++A + FD  +G    TY+   
Sbjct: 2   LVERHAPLVKRIAQHLLAR-LPSSVLLDDLIQAGMIGLLEASRNFDGSKGASFETYAGIR 60

Query: 109 IKAAMQEYILRS 120
           I+ AM + I R 
Sbjct: 61  IRGAMLDEIRRG 72


>gi|320354339|ref|YP_004195678.1| RNA polymerase sigma-28 subunit SigD/FliA/WhiG [Desulfobulbus
           propionicus DSM 2032]
 gi|320122841|gb|ADW18387.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Desulfobulbus
           propionicus DSM 2032]
          Length = 244

 Score = 35.4 bits (80), Expect = 9.7,   Method: Compositional matrix adjust.
 Identities = 11/37 (29%), Positives = 24/37 (64%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           +++S   +GL+ A  KFDP +G +  T++ + ++ A+
Sbjct: 41  DMISAAMVGLVDAANKFDPTKGVKFKTFAEYRVRGAI 77


>gi|228912145|ref|ZP_04075860.1| RNA polymerase sigma factor [Bacillus thuringiensis IBL 200]
 gi|228847482|gb|EEM92421.1| RNA polymerase sigma factor [Bacillus thuringiensis IBL 200]
          Length = 232

 Score = 35.4 bits (80), Expect = 9.7,   Method: Compositional matrix adjust.
 Identities = 38/125 (30%), Positives = 58/125 (46%), Gaps = 13/125 (10%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL I ++   G IGL++A   FD E G + +TY++  I   +   I R    VK+     
Sbjct: 34  GLDIEDLTQFGMIGLIKARDNFDLEYGCKFSTYAVPKIIGEIGRAI-RDHQKVKV----- 87

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
           Q+ ++     +KG    I   NL  E    IA  LN   S V +      G +SLN +++
Sbjct: 88  QRSVY----SVKG---KILRQNLGDEIPEEIASILNEDVSVVSNALHYQPGTQSLNKVVH 140

Query: 192 SSDKN 196
            S+ N
Sbjct: 141 QSNGN 145


>gi|72161738|ref|YP_289395.1| RNA polymerase sigma factor [Thermobifida fusca YX]
 gi|71915470|gb|AAZ55372.1| RNA polymerase sigma factor [Thermobifida fusca YX]
          Length = 308

 Score = 35.4 bits (80), Expect = 9.7,   Method: Compositional matrix adjust.
 Identities = 23/86 (26%), Positives = 42/86 (48%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  ++ LV + A  YR  G P+ ++   G +GLM+A+K FDP  G     Y +  +   
Sbjct: 89  LVRLYMPLVRREARRYRNRGEPMDDLYQVGMLGLMKAIKGFDPSYGKPFVAYLLPMVTGE 148

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFN 138
           ++ +   +   V++     ++R   N
Sbjct: 149 LKRHFRDTTWAVRVPRVHQERRSELN 174


>gi|304399205|ref|ZP_07381072.1| sigma-70 region 3 domain protein [Pantoea sp. aB]
 gi|304353259|gb|EFM17639.1| sigma-70 region 3 domain protein [Pantoea sp. aB]
          Length = 172

 Score = 35.4 bits (80), Expect = 9.8,   Method: Compositional matrix adjust.
 Identities = 21/56 (37%), Positives = 34/56 (60%), Gaps = 4/56 (7%)

Query: 235 LNPRERRIFEARR---LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           LN ++R +  ARR   L     TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 108 LNAKQREVL-ARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQAQ 162


>gi|229189193|ref|ZP_04316217.1| RNA polymerase sigma-B factor [Bacillus cereus ATCC 10876]
 gi|228594237|gb|EEK52032.1| RNA polymerase sigma-B factor [Bacillus cereus ATCC 10876]
          Length = 203

 Score = 35.4 bits (80), Expect = 9.8,   Method: Compositional matrix adjust.
 Identities = 40/177 (22%), Positives = 83/177 (46%), Gaps = 30/177 (16%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLV---KIGTTANQ 132
           +++  G IGL+ A++++D   G     +++  I   +++Y+  ++W +    +I     +
Sbjct: 4   DIIQVGMIGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVPRRIKDLGGK 63

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM-----NCRLAGDESLN 187
            RL          ++ +TD   +  +++ IA  L +SE EV+ +     N R++   SL+
Sbjct: 64  IRL---------AIEELTDRLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVS---SLD 111

Query: 188 ALI-NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            ++ NSSD +S    + +     G E+          RR +L    +VLN  E+ + 
Sbjct: 112 DVVENSSDGSSVARIESVGEVEQGYEET--------ERRLVLKDIFNVLNETEKSVI 160


>gi|271969632|ref|YP_003343828.1| hypothetical protein Sros_8441 [Streptosporangium roseum DSM 43021]
 gi|270512807|gb|ACZ91085.1| hypothetical protein Sros_8441 [Streptosporangium roseum DSM 43021]
          Length = 615

 Score = 35.4 bits (80), Expect = 9.9,   Method: Compositional matrix adjust.
 Identities = 21/65 (32%), Positives = 34/65 (52%), Gaps = 2/65 (3%)

Query: 211 QEQVLIEKEERKNRR--NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           +E V   +  R +R    ++    + L+ R+R I   R       TL++L+  F V+RER
Sbjct: 112 EESVAQVRPSRPDRPLPELIDEVFAALDDRQRAIARDRLYASQRATLDDLAQRFSVTRER 171

Query: 269 VRQIE 273
           +RQIE
Sbjct: 172 IRQIE 176


>gi|284050443|ref|ZP_06380653.1| RNA polymerase sigma factor SigF [Arthrospira platensis str.
           Paraca]
 gi|291567732|dbj|BAI90004.1| group 3 RNA polymerase sigma factor SigF [Arthrospira platensis
           NIES-39]
          Length = 261

 Score = 35.4 bits (80), Expect = 10.0,   Method: Compositional matrix adjust.
 Identities = 11/41 (26%), Positives = 29/41 (70%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           +++  G IGL++A+++FD  +G   +++++ +I+  +Q Y+
Sbjct: 57  DLLQVGCIGLIRAIERFDMSKGHAFSSFAIPYIRGEIQHYL 97


>gi|117919807|ref|YP_868999.1| flagellar biosynthesis sigma factor [Shewanella sp. ANA-3]
 gi|117612139|gb|ABK47593.1| RNA polymerase, sigma 28 subunit [Shewanella sp. ANA-3]
          Length = 237

 Score = 35.4 bits (80), Expect = 10.0,   Method: Compositional matrix adjust.
 Identities = 53/218 (24%), Positives = 96/218 (44%), Gaps = 39/218 (17%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS-WSLVKIGTTANQK 133
           + +++  G +GL++A  KFD  +G +  T++   I+ AM + I R  W           +
Sbjct: 41  LDDLLQAGMMGLLEASSKFDGGKGAKFETFAGIRIRGAMLDEIRRGDWV---------PR 91

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVA-------IAKKLNVSESEVISMNCRLAGDESL 186
            +  N RR+    QAI +     EQV+        IA+KL+++  E       +  D S+
Sbjct: 92  SVHRNNRRVA---QAIDE----LEQVLGRDARDTEIAEKLDMTLDEY----HHILNDVSV 140

Query: 187 NALINSSDKNSSQWQDWLVYDH---DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
             +I   D   S  QD L       DG  + L E +      + L  ++ +L  R+  + 
Sbjct: 141 GKIIGIEDLGVS--QDILTSSDNVSDGTYEALAETQ----FHSALVEAIKLLPERDALVL 194

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                 +  + L+ + +  EVS  RV QI ++A  +++
Sbjct: 195 SL--YYDEALNLKEIGAILEVSESRVSQILSQAMLRLK 230


>gi|126175111|ref|YP_001051260.1| flagellar biosynthesis sigma factor [Shewanella baltica OS155]
 gi|153001435|ref|YP_001367116.1| flagellar biosynthesis sigma factor [Shewanella baltica OS185]
 gi|160876160|ref|YP_001555476.1| flagellar biosynthesis sigma factor [Shewanella baltica OS195]
 gi|217972633|ref|YP_002357384.1| flagellar biosynthesis sigma factor [Shewanella baltica OS223]
 gi|304409942|ref|ZP_07391561.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Shewanella
           baltica OS183]
 gi|307302345|ref|ZP_07582103.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Shewanella
           baltica BA175]
 gi|125998316|gb|ABN62391.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Shewanella
           baltica OS155]
 gi|151366053|gb|ABS09053.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella baltica
           OS185]
 gi|160861682|gb|ABX50216.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella baltica
           OS195]
 gi|217497768|gb|ACK45961.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella baltica
           OS223]
 gi|304351351|gb|EFM15750.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Shewanella
           baltica OS183]
 gi|306914383|gb|EFN44804.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Shewanella
           baltica BA175]
 gi|315268356|gb|ADT95209.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella baltica
           OS678]
          Length = 237

 Score = 35.4 bits (80), Expect = 10.0,   Method: Compositional matrix adjust.
 Identities = 48/212 (22%), Positives = 94/212 (44%), Gaps = 19/212 (8%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS-WSLVKIGTTANQK 133
           + +++  G +GL++A  KFD  +G +  T++   I+ AM + I R  W  V      N +
Sbjct: 41  LDDLLQAGMMGLLEASSKFDGGKGAKFETFAGIRIRGAMLDEIRRGDW--VPRSVHRNNR 98

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
           ++   +  L+   QA+  +    E    IA+KL+++  E       +  D S+  +I   
Sbjct: 99  KVAHAIDELE---QALGRDARDTE----IAEKLDMTLDEY----HHILNDVSVGKIIGIE 147

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D   S  QD L    D  +    E        + L  ++ +L  R+  +       +  +
Sbjct: 148 DLGVS--QDILTVS-DRSDDDSFEALAENQFHSALVEAIKLLPERDALVLSL--YYDEAL 202

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            L+ + +  EVS  RV QI ++A  +++  ++
Sbjct: 203 NLKEIGAILEVSESRVSQILSQAMLRLKAKLK 234


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


Results from round 2




>gi|254780611|ref|YP_003065024.1| RNA polymerase factor sigma-32 [Candidatus Liberibacter asiaticus
           str. psy62]
 gi|254040288|gb|ACT57084.1| RNA polymerase factor sigma-32 [Candidatus Liberibacter asiaticus
           str. psy62]
          Length = 302

 Score =  394 bits (1013), Expect = e-108,   Method: Composition-based stats.
 Identities = 302/302 (100%), Positives = 302/302 (100%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL
Sbjct: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS
Sbjct: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL
Sbjct: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER
Sbjct: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQKP 300
           RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQKP
Sbjct: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQKP 300

Query: 301 RY 302
           RY
Sbjct: 301 RY 302


>gi|315121811|ref|YP_004062300.1| RNA polymerase factor sigma-32 [Candidatus Liberibacter
           solanacearum CLso-ZC1]
 gi|313495213|gb|ADR51812.1| RNA polymerase factor sigma-32 [Candidatus Liberibacter
           solanacearum CLso-ZC1]
          Length = 300

 Score =  344 bits (882), Expect = 1e-92,   Method: Composition-based stats.
 Identities = 247/289 (85%), Positives = 269/289 (93%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+R+NMSI+++GEIGL RYIHEI+KIPMLEKQEEY+LAKRY EH DL+A H+LVTSHLRL
Sbjct: 1   MSRRNMSIMIDGEIGLRRYIHEIKKIPMLEKQEEYMLAKRYHEHHDLNAVHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VVKIAMGYRGYGLPISEV+SEGNIGLMQAVKKFDPERGFRLATY +WWIKAA+QEYILRS
Sbjct: 61  VVKIAMGYRGYGLPISEVISEGNIGLMQAVKKFDPERGFRLATYGIWWIKAAIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVKIGTTANQKRLFFNLRRLKG LQA+ D NLKPEQVV IA KLNVSE+EVISMNCRL
Sbjct: 121 WSLVKIGTTANQKRLFFNLRRLKGRLQAVNDTNLKPEQVVEIATKLNVSEAEVISMNCRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GDESLN L+NSSDK+SSQWQD LVY+HD QEQ LI+KEERKNRRNMLTRSMS LNPRER
Sbjct: 181 SGDESLNVLMNSSDKDSSQWQDLLVYNHDSQEQTLIDKEERKNRRNMLTRSMSTLNPRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           RIFEARRL ENP TLENLSSEF VSRER+RQIEARAF+KVQ S+QKQ E
Sbjct: 241 RIFEARRLNENPSTLENLSSEFAVSRERIRQIEARAFEKVQASVQKQTE 289


>gi|327190963|gb|EGE58017.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli
           CNPAF512]
          Length = 332

 Score =  340 bits (872), Expect = 2e-91,   Method: Composition-based stats.
 Identities = 213/288 (73%), Positives = 247/288 (85%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R  +  I  GE GL+RY+ EIRK PMLE Q+EY+LAKRY EHGD  AAH+LVTSHLRL
Sbjct: 31  MARNTLPSITAGEAGLNRYLDEIRKFPMLEPQQEYMLAKRYAEHGDRDAAHKLVTSHLRL 90

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EVVSEGN+GLMQAVKKFDPERGFRLATY+MWWIKA++QEYILRS
Sbjct: 91  VAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRS 150

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLRRLKG +QAI D +LKPE V  IA KLNVSE EVISMN RL
Sbjct: 151 WSLVKMGTTANQKRLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKLNVSEEEVISMNRRL 210

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA I +++ +S QWQDWLV DHD QE VLIE++E + RR ML+++MSVLN RER
Sbjct: 211 SGDASLNAPIKAAEGDSGQWQDWLVDDHDSQEDVLIEQDELETRRRMLSKAMSVLNERER 270

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RIFEARRL E PVTLE+LS+EF++SRERVRQIE RAF+KVQ++++K+ 
Sbjct: 271 RIFEARRLAEEPVTLEDLSAEFDISRERVRQIEVRAFEKVQDAVRKEA 318


>gi|190893168|ref|YP_001979710.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CIAT
           652]
 gi|190698447|gb|ACE92532.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CIAT
           652]
          Length = 302

 Score =  332 bits (853), Expect = 3e-89,   Method: Composition-based stats.
 Identities = 213/288 (73%), Positives = 247/288 (85%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R  +  I  GE GL+RY+ EIRK PMLE Q+EY+LAKRY EHGD  AAH+LVTSHLRL
Sbjct: 1   MARNTLPSITAGEAGLNRYLDEIRKFPMLEPQQEYMLAKRYAEHGDRDAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EVVSEGN+GLMQAVKKFDPERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLRRLKG +QAI D +LKPE V  IA KLNVSE EVISMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKLNVSEEEVISMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA I +++ +S QWQDWLV DHD QE VLIE++E + RR ML+++MSVLN RER
Sbjct: 181 SGDASLNAPIKAAEGDSGQWQDWLVDDHDSQEDVLIEQDELETRRRMLSKAMSVLNERER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RIFEARRL E PVTLE+LS+EF++SRERVRQIE RAF+KVQ++++K+ 
Sbjct: 241 RIFEARRLAEEPVTLEDLSAEFDISRERVRQIEVRAFEKVQDAVRKEA 288


>gi|86358940|ref|YP_470832.1| RNA polymerase factor sigma-32 [Rhizobium etli CFN 42]
 gi|86283042|gb|ABC92105.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CFN
           42]
          Length = 302

 Score =  331 bits (848), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 211/288 (73%), Positives = 246/288 (85%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R  +  I  GE GL+RY+ EIRK PMLE Q+EY+LAKRY EHGD  AAH+LVTSHLRL
Sbjct: 1   MARNTLPSITAGEAGLNRYLDEIRKFPMLEPQQEYMLAKRYAEHGDRDAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EVVSEGN+GLMQAVKKFDPERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WS VK+GTTANQKRLFFNLRRLKG +QAI D +LKPE V  IA KLNVSE EVISMN RL
Sbjct: 121 WSAVKMGTTANQKRLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKLNVSEEEVISMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA I +++ +S QWQDWLV DH+ QE VLIE++E + RR ML ++MSVLN RER
Sbjct: 181 SGDASLNAPIKAAEGDSGQWQDWLVDDHESQEDVLIEQDELETRRRMLAKAMSVLNERER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RIFEARRL E+PVTLE+LS+EF++SRERVRQIE RAF+KVQ++++K+ 
Sbjct: 241 RIFEARRLAEDPVTLEDLSAEFDISRERVRQIEVRAFEKVQDAVRKEA 288


>gi|74099847|gb|AAZ99132.1| RpoH [Rhizobium leguminosarum]
          Length = 302

 Score =  330 bits (847), Expect = 1e-88,   Method: Composition-based stats.
 Identities = 212/288 (73%), Positives = 245/288 (85%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R  +  I  GE GL+RY+ EIRK PMLE Q+EY+LAKRY EHGD  AAH+LVTSHLRL
Sbjct: 1   MARNTLPSITAGEAGLNRYLDEIRKFPMLEPQQEYMLAKRYAEHGDRDAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EVVSEGN+GLMQAVKKFD ERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDAERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLRRLKG +QAI D +LKPE V  IA KLNVSE EVISMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKLNVSEEEVISMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA I +++ +S QWQDWLV DHD QE VLIE++E   RR ML ++MSVLN RER
Sbjct: 181 SGDASLNAPIKAAEGDSGQWQDWLVDDHDSQEDVLIEQDELDTRRRMLAKAMSVLNERER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RIFEARRL E+PVTLE+LS+EF++SRERVRQIE RAF+KVQ++++K+ 
Sbjct: 241 RIFEARRLAEDPVTLEDLSTEFDISRERVRQIEVRAFEKVQDAVRKEA 288


>gi|116253507|ref|YP_769345.1| RNA polymerase factor sigma-32 [Rhizobium leguminosarum bv. viciae
           3841]
 gi|115258155|emb|CAK09256.1| putative RNA polymerase sigma-32 factor [Rhizobium leguminosarum
           bv. viciae 3841]
          Length = 302

 Score =  330 bits (846), Expect = 2e-88,   Method: Composition-based stats.
 Identities = 211/288 (73%), Positives = 244/288 (84%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R  +  I  GE GL+RY+ EIRK PMLE Q+EY+LAKRY EHGD  AAH+LVTSHLRL
Sbjct: 1   MARNTLPSITAGEAGLNRYLDEIRKFPMLEPQQEYMLAKRYAEHGDRDAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EVVSEGN+GLMQAVKKFD ERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDAERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLRRLKG +QAI D +LKPE V  IA KLNVSE EVISMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKLNVSEEEVISMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA I +++ +  QWQDWLV DHD QE VLIE++E   RR ML ++MSVLN RER
Sbjct: 181 SGDASLNAPIKAAEGDGGQWQDWLVDDHDSQEDVLIEQDELDTRRRMLAKAMSVLNERER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RIFEARRL E+PVTLE+LS+EF++SRERVRQIE RAF+KVQ++++K+ 
Sbjct: 241 RIFEARRLAEDPVTLEDLSTEFDISRERVRQIEVRAFEKVQDAVRKEA 288


>gi|209550663|ref|YP_002282580.1| RNA polymerase factor sigma-32 [Rhizobium leguminosarum bv.
           trifolii WSM2304]
 gi|209536419|gb|ACI56354.1| RNA polymerase, sigma 32 subunit, RpoH [Rhizobium leguminosarum bv.
           trifolii WSM2304]
          Length = 302

 Score =  329 bits (845), Expect = 3e-88,   Method: Composition-based stats.
 Identities = 211/289 (73%), Positives = 245/289 (84%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R  +  I  GE GL+RY+ EIRK PMLE Q+EY+LAKRY EHGD  AAH+LVTSHLRL
Sbjct: 1   MARNTLPSITAGEAGLNRYLDEIRKFPMLEPQQEYMLAKRYAEHGDRDAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EVVSEGN+GLMQAVKKFD ERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDAERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLRRLKG +QAI D +LKPE V  IA KL VSE EVISMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKLKVSEEEVISMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA I +++ +S QWQDWLV DHD QE VLIE++E   RR ML ++MSVLN RER
Sbjct: 181 SGDASLNAPIKAAEGDSGQWQDWLVDDHDSQEDVLIEQDELDTRRRMLAKAMSVLNERER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           RIFEARRL E+PVTLE+LS+EF++SRERVRQIE RAF+KVQ++++K+ +
Sbjct: 241 RIFEARRLAEDPVTLEDLSTEFDISRERVRQIEVRAFEKVQDAVRKEAQ 289


>gi|222149598|ref|YP_002550555.1| RNA polymerase factor sigma-32 [Agrobacterium vitis S4]
 gi|221736580|gb|ACM37543.1| alternative sigma factor RpoH [Agrobacterium vitis S4]
          Length = 300

 Score =  328 bits (842), Expect = 6e-88,   Method: Composition-based stats.
 Identities = 214/288 (74%), Positives = 242/288 (84%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R ++  I  GE GL+RY+ EIRK PMLE Q EY+LAKRY EHGD  AAHRLVTSHLRL
Sbjct: 1   MARNSLPSITAGEGGLNRYLDEIRKFPMLEPQVEYMLAKRYAEHGDRDAAHRLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EVVSEGN+GLMQAVKKFDPERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLRRLKG +QAI + +LKP+QV  IA KL VSE EVISMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRRLKGKIQAIEEGDLKPDQVTEIATKLKVSEEEVISMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA I +S+  S QWQDWLV DHD QE  LIE++E + RRNML+R+M VLN RER
Sbjct: 181 SGDASLNAPIRASEGESGQWQDWLVDDHDSQEDTLIEQDELETRRNMLSRAMGVLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RIF ARRL E PVTLE LSSEF++SRERVRQIE RAF+KVQ+++QK  
Sbjct: 241 RIFAARRLAEEPVTLEELSSEFDISRERVRQIEVRAFEKVQDAVQKDA 288


>gi|241206034|ref|YP_002977130.1| RNA polymerase factor sigma-32 [Rhizobium leguminosarum bv.
           trifolii WSM1325]
 gi|240859924|gb|ACS57591.1| RNA polymerase, sigma 32 subunit, RpoH [Rhizobium leguminosarum bv.
           trifolii WSM1325]
          Length = 302

 Score =  328 bits (842), Expect = 6e-88,   Method: Composition-based stats.
 Identities = 210/288 (72%), Positives = 243/288 (84%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R  +  I  GE GL+RY+ EIRK PMLE Q+EY+LAKRY EHGD  AAH+LVTSHLRL
Sbjct: 1   MARNTLPSITAGEAGLNRYLDEIRKFPMLEPQQEYMLAKRYAEHGDRDAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EVVSEGN+GLMQAVKKFD ERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDAERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLRRLKG +QAI D +LKPE V  IA KL VSE EVISMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKLKVSEEEVISMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA I +++ +  QWQDWLV DHD QE VLIE++E   RR ML ++MSVLN RER
Sbjct: 181 SGDASLNAPIKAAEGDGGQWQDWLVDDHDSQEDVLIEQDELDTRRRMLAKAMSVLNERER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RIFEARRL E+PVTLE+LS+EF++SRERVRQIE RAF+KVQ++++K+ 
Sbjct: 241 RIFEARRLAEDPVTLEDLSTEFDISRERVRQIEVRAFEKVQDAVRKEA 288


>gi|325293796|ref|YP_004279660.1| RNA polymerase sigma-32 factor [Agrobacterium sp. H13-3]
 gi|1710644|sp|P50507|RP32_AGRTU RecName: Full=RNA polymerase sigma-32 factor
 gi|1143324|dbj|BAA09439.1| sigma-32 homolog [Agrobacterium tumefaciens]
 gi|325061649|gb|ADY65340.1| RNA polymerase sigma-32 factor [Agrobacterium sp. H13-3]
          Length = 300

 Score =  328 bits (841), Expect = 8e-88,   Method: Composition-based stats.
 Identities = 214/292 (73%), Positives = 244/292 (83%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R ++  I  GE GL+RY+ EIRK PMLE QEEY+L KRY EHGD  AAH+LVTSHLRL
Sbjct: 1   MARNSLPTITAGEAGLNRYLDEIRKFPMLEPQEEYMLGKRYAEHGDRDAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EVVSEGN+GLMQAVKKFDPERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLRRLKG +QAI D +LKPE V  IA KL VSE EVISMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRRLKGRIQAIDDGDLKPEHVKEIATKLQVSEEEVISMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA I +S+  S QWQDWLV DH+ QE VLIE++E + RR ML ++M VLN RER
Sbjct: 181 HGDASLNAPIKASEGESGQWQDWLVDDHESQEAVLIEQDELETRRRMLAKAMGVLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
           RIFEARRL E+PVTLE LSSEF++SRERVRQIE RAF+KVQE++QK+   ++
Sbjct: 241 RIFEARRLAEDPVTLEELSSEFDISRERVRQIEVRAFEKVQEAVQKEALEAA 292


>gi|10952458|gb|AAG24943.1|AF128845_2 RpoH [Sinorhizobium meliloti]
          Length = 301

 Score =  327 bits (840), Expect = 9e-88,   Method: Composition-based stats.
 Identities = 207/293 (70%), Positives = 246/293 (83%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R  +  I  GE GL+RY+ EIRK PMLE QEEY+LAKRY+EH D  AAH+LVTSHLRL
Sbjct: 1   MARNTLPTIAAGEGGLNRYLDEIRKFPMLEPQEEYMLAKRYQEHDDRKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVKKF+P+RGFRLATY+MWWIKAA+QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKKFEPDRGFRLATYAMWWIKAAIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLRRLKG +QA+ + +LKPEQV  IA  L VSE EV+SMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRRLKGRIQALDEGDLKPEQVKEIATTLKVSEEEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA I +S+ +S QWQDWLV DHD QEQ+LIE++E ++RR +L  +M VLN RER
Sbjct: 181 SGDASLNAPIKASEGDSGQWQDWLVDDHDNQEQILIEQDELESRRALLANAMKVLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           RIFEARRL E P+TLE+LS+EF++SRERVRQIE RAF+KVQE+++K     +S
Sbjct: 241 RIFEARRLTEEPITLEDLSTEFDISRERVRQIEVRAFEKVQEAVRKAALERAS 293


>gi|15889716|ref|NP_355397.1| RNA polymerase factor sigma-32 [Agrobacterium tumefaciens str. C58]
 gi|15157628|gb|AAK88182.1| RNA polymerase sigma-32 factor [Agrobacterium tumefaciens str. C58]
          Length = 300

 Score =  327 bits (840), Expect = 9e-88,   Method: Composition-based stats.
 Identities = 214/292 (73%), Positives = 244/292 (83%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R ++  I  GE GL+RY+ EIRK PMLE QEEY+L KRY EHGD  AAH+LVTSHLRL
Sbjct: 1   MARNSLPTITAGEAGLNRYLDEIRKFPMLEPQEEYMLGKRYAEHGDRDAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EVVSEGN+GLMQAVKKFDPERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLRRLKG +QAI D +LKPE V  IA KL VSE EVISMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRRLKGRIQAIDDGDLKPEHVKEIATKLQVSEEEVISMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA I +S+  S QWQDWLV DH+ QE VLIE++E + RR ML ++M VLN RER
Sbjct: 181 HGDASLNAPIKASEGESGQWQDWLVDDHESQEAVLIEQDELETRRRMLAKAMGVLNERER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
           RIFEARRL E+PVTLE LSSEF++SRERVRQIE RAF+KVQE++QK+   ++
Sbjct: 241 RIFEARRLAEDPVTLEELSSEFDISRERVRQIEVRAFEKVQEAVQKEALEAA 292


>gi|15966479|ref|NP_386832.1| RNA polymerase factor sigma-32 [Sinorhizobium meliloti 1021]
 gi|307300484|ref|ZP_07580264.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium meliloti
           BL225C]
 gi|307318349|ref|ZP_07597784.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium meliloti
           AK83]
 gi|15075750|emb|CAC47305.1| RNA polymerase sigma factor (Sigma-32) [Sinorhizobium meliloti
           1021]
 gi|306896031|gb|EFN26782.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium meliloti
           AK83]
 gi|306904650|gb|EFN35234.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium meliloti
           BL225C]
          Length = 301

 Score =  327 bits (840), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 207/293 (70%), Positives = 246/293 (83%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R  +  I  GE GL+RY+ EIRK PMLE QEEY+LAKRY+EH D  AAH+LVTSHLRL
Sbjct: 1   MARNTLPTIAAGEGGLNRYLDEIRKFPMLEPQEEYMLAKRYQEHDDRKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVKKF+P+RGFRLATY+MWWIKAA+QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKKFEPDRGFRLATYAMWWIKAAIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLRRLKG +QA+ + +LKPEQV  IA  L VSE EV+SMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRRLKGRIQALDEGDLKPEQVKEIATTLKVSEEEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA I +S+ +S QWQDWLV DHD QEQ+LIE++E ++RR +L  +M VLN RER
Sbjct: 181 SGDASLNAPIKASEGDSGQWQDWLVDDHDNQEQILIEQDELESRRALLANAMKVLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           RIFEARRL E P+TLE+LS+EF++SRERVRQIE RAF+KVQE+++K     +S
Sbjct: 241 RIFEARRLTEEPITLEDLSTEFDISRERVRQIEVRAFEKVQEAVRKAALERAS 293


>gi|10129883|dbj|BAB13517.1| sigma factor [Sinorhizobium meliloti]
          Length = 301

 Score =  327 bits (840), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 206/293 (70%), Positives = 246/293 (83%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R  +  I  GE GL+RY+ EIRK PMLE QEEY+LAKRY+EH D  AAH+LVTSHLRL
Sbjct: 1   MARNTLPTIAAGEGGLNRYLDEIRKFPMLEPQEEYMLAKRYQEHDDRKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVKKF+P+RGFRLATY+MWWIKAA+QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKKFEPDRGFRLATYAMWWIKAAIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLRRLKG +QA+ + +LKPEQV  IA  L VSE +V+SMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRRLKGRIQALDEGDLKPEQVKEIATTLKVSEEKVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA I +S+ +S QWQDWLV DHD QEQ+LIE++E ++RR +L  +M VLN RER
Sbjct: 181 SGDASLNAPIKASEGDSGQWQDWLVDDHDNQEQILIEQDELESRRGLLANAMKVLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           RIFEARRL E P+TLE+LS+EF++SRERVRQIE RAF+KVQE+++K     +S
Sbjct: 241 RIFEARRLTEEPITLEDLSTEFDISRERVRQIEVRAFEKVQEAVRKAALERAS 293


>gi|150397812|ref|YP_001328279.1| RNA polymerase factor sigma-32 [Sinorhizobium medicae WSM419]
 gi|150029327|gb|ABR61444.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium medicae
           WSM419]
          Length = 301

 Score =  327 bits (838), Expect = 1e-87,   Method: Composition-based stats.
 Identities = 205/286 (71%), Positives = 244/286 (85%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R  +  I  GE GL+RY+ EIRK PMLE QEEY+LAKRY+EH D  AAH+LVTSHLRL
Sbjct: 1   MARNTLPTIAAGEGGLNRYLDEIRKFPMLEPQEEYMLAKRYQEHDDRKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVKKF+P+RGFRLATY+MWWIKAA+QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKKFEPDRGFRLATYAMWWIKAAIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLRRLKG +QA+ + +LKPEQV  IA  L VSE EVISMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRRLKGRIQALDEGDLKPEQVKEIATTLKVSEDEVISMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA I +S+ +S QWQDWLV ++D QEQ+LIE++E  NRR +L  ++ VLN RER
Sbjct: 181 SGDASLNAPIKASEGDSGQWQDWLVDENDNQEQILIEQDELDNRRALLANALKVLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           RIFEARRL E+P+TLE+LS+EF++SRERVRQIE RAF+KVQE+++K
Sbjct: 241 RIFEARRLTEDPITLEDLSTEFDISRERVRQIEVRAFEKVQEAVRK 286


>gi|227823295|ref|YP_002827267.1| RNA polymerase factor sigma-32 [Sinorhizobium fredii NGR234]
 gi|227342296|gb|ACP26514.1| RNA polymerase sigma factor, sigma-70 family [Sinorhizobium fredii
           NGR234]
          Length = 301

 Score =  325 bits (834), Expect = 5e-87,   Method: Composition-based stats.
 Identities = 206/286 (72%), Positives = 243/286 (84%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R  +  I  GE GL+RY+ EIRK PMLE QEEY+LAKRY+EH D SAAH+LVTSHLRL
Sbjct: 1   MARSTLPSIAAGEGGLNRYLDEIRKFPMLEPQEEYMLAKRYQEHDDRSAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVKKF+P+RGFRLATY+MWWIKAA+QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVMSEGNVGLMQAVKKFEPDRGFRLATYAMWWIKAAIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLRRLKG +QA+ + +LKPEQV  IA  L VSE EV+SMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRRLKGRIQALDEGDLKPEQVKEIATTLKVSEDEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA I +S+ +S QWQDWLV +HD QE++LIE++E  +RR +L  +M VLN RER
Sbjct: 181 SGDASLNAPIKASEGDSGQWQDWLVDEHDNQEEILIEQDELDSRRALLASAMKVLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           RIFEARRL E PVTLE LS+EF++SRERVRQIE RAF+KVQE+++K
Sbjct: 241 RIFEARRLTEEPVTLEELSTEFDISRERVRQIEVRAFEKVQEAVRK 286


>gi|222086841|ref|YP_002545375.1| alternative sigma factor RpoH [Agrobacterium radiobacter K84]
 gi|221724289|gb|ACM27445.1| alternative sigma factor RpoH [Agrobacterium radiobacter K84]
          Length = 302

 Score =  324 bits (830), Expect = 1e-86,   Method: Composition-based stats.
 Identities = 216/288 (75%), Positives = 242/288 (84%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R  +  I  GE GL+RY+ EIRK PMLE QEEY+LAKRY EH D  AAHRLVTSHLRL
Sbjct: 1   MARNTLPSIAAGEAGLNRYLDEIRKFPMLEPQEEYMLAKRYAEHADREAAHRLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EVVSEGN+GLMQAVKKFDPERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLRRLKG +QAI + +LKPE V  IA KL VSE EVISMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRRLKGRIQAIDEGDLKPEHVSEIATKLKVSEEEVISMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA I +S+  S QWQDWLV DH+ QE VLIE++E   RR ML R+MSVLN RER
Sbjct: 181 SGDASLNAPIKASEGESGQWQDWLVDDHESQEAVLIEQDELDTRRRMLARAMSVLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RIFEARRL E+PVTLE+LSSEF++SRERVRQIE RAF+KVQE++QK  
Sbjct: 241 RIFEARRLSEDPVTLEDLSSEFDISRERVRQIEVRAFEKVQEAVQKDA 288


>gi|163758761|ref|ZP_02165848.1| RNA polymerase sigma factor [Hoeflea phototrophica DFL-43]
 gi|162284051|gb|EDQ34335.1| RNA polymerase sigma factor [Hoeflea phototrophica DFL-43]
          Length = 300

 Score =  323 bits (829), Expect = 2e-86,   Method: Composition-based stats.
 Identities = 197/292 (67%), Positives = 244/292 (83%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M + ++  I  GE GL+RY+ EIR+ PMLE QEEY+LAKR+ +H D  AAH+LVTSHLRL
Sbjct: 1   MAQTSLPTISAGENGLNRYLAEIRRFPMLEPQEEYMLAKRFLQHEDTKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVKKFDPERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLR++K  +QA+ D +L+P+QV  IA KLNVSE EVISMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRKVKSKIQAVEDGDLRPDQVAEIATKLNVSEEEVISMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA I +S+  S QWQDWLV + D QE +L+E++E ++RR ML  ++ VLN RE+
Sbjct: 181 SGDASLNAPIKASEGESGQWQDWLVDESDSQEDMLVEQDELESRRAMLKSALEVLNEREK 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
           RIFEARRL+++P+TLE+LS EF++SRERVRQIE RAF+KVQ+++QK    S 
Sbjct: 241 RIFEARRLRDDPITLEDLSGEFDISRERVRQIEVRAFEKVQDAVQKAAAASD 292


>gi|254473077|ref|ZP_05086475.1| alternative sigma factor RpoH [Pseudovibrio sp. JE062]
 gi|211957798|gb|EEA93000.1| alternative sigma factor RpoH [Pseudovibrio sp. JE062]
          Length = 297

 Score =  322 bits (826), Expect = 4e-86,   Method: Composition-based stats.
 Identities = 195/290 (67%), Positives = 238/290 (82%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           +N+  +  GE GLSRY+ EIRK PML+ QEEY+LAKRYREH +  AA +LV SHLRLV K
Sbjct: 3   RNLPALTGGEGGLSRYLDEIRKFPMLQPQEEYMLAKRYREHDEPKAAEKLVNSHLRLVAK 62

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IAMGYRGYGLP+ EV+SEGN+GLMQAVK+F+P++GFRLATY+MWWIKA++QEYILR+WSL
Sbjct: 63  IAMGYRGYGLPLGEVISEGNVGLMQAVKRFEPDKGFRLATYAMWWIKASIQEYILRTWSL 122

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VK+GTTANQKRLFFNLRR+KG +QA  D +L+PEQV  IA  L V+E+EV+SMN RL GD
Sbjct: 123 VKMGTTANQKRLFFNLRRVKGKIQAFEDGDLRPEQVQQIATTLGVTENEVVSMNRRLGGD 182

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SLNA + SS+  SS+WQDWLV D + QE VL E+EE   RR+ML  +MSVLN RE RIF
Sbjct: 183 SSLNAPLRSSEGESSEWQDWLVDDSESQEAVLAEQEEYDVRRDMLKNAMSVLNERETRIF 242

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           EARRL ENP+TLE LS+EF VSRERVRQIE RAF+KVQ+++Q+     ++
Sbjct: 243 EARRLSENPITLEELSTEFGVSRERVRQIEVRAFEKVQKAVQESAMAMAA 292


>gi|328542558|ref|YP_004302667.1| RNA polymerase sigma factor [polymorphum gilvum SL003B-26A1]
 gi|326412304|gb|ADZ69367.1| RNA polymerase sigma factor [Polymorphum gilvum SL003B-26A1]
          Length = 296

 Score =  322 bits (826), Expect = 4e-86,   Method: Composition-based stats.
 Identities = 193/293 (65%), Positives = 238/293 (81%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           +N+ ++  GE GLSRY+ EIR+ PMLE QEEY+LAKRY+EH D +AA RLV SHLRLV K
Sbjct: 3   QNVPMLTAGEGGLSRYLDEIRRFPMLEPQEEYMLAKRYKEHDDPAAAERLVNSHLRLVAK 62

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IAMGYRGYGLP+ EVVSEGN+GLMQAVK+F+P++GFRLATY+MWWIKAA+QEYILRSWSL
Sbjct: 63  IAMGYRGYGLPLGEVVSEGNVGLMQAVKRFEPDKGFRLATYAMWWIKAAIQEYILRSWSL 122

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VK+GTTANQKRLFFNLRRLKG +QA+ + +LKPEQV  IA KL V E +V+SMN RLAGD
Sbjct: 123 VKMGTTANQKRLFFNLRRLKGRIQALEEGDLKPEQVQEIATKLGVPEEDVVSMNRRLAGD 182

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SLNA I +++ +S +WQDWLV + + QE +L  +EE   RR +L  +M +L  RERRIF
Sbjct: 183 ASLNAPIRAAEADSGEWQDWLVDESESQETLLANQEELDIRRKLLGDAMDILTERERRIF 242

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPL 296
           EARRL E+P+TLE LS+EF VSRERVRQIE RAF+K+Q++++K       P L
Sbjct: 243 EARRLAEDPITLEELSTEFGVSRERVRQIEVRAFEKIQKAVRKSARDLEQPSL 295


>gi|110635485|ref|YP_675693.1| RNA polymerase factor sigma-32 [Mesorhizobium sp. BNC1]
 gi|110286469|gb|ABG64528.1| RNA polymerase, sigma 32 subunit, RpoH [Chelativorans sp. BNC1]
          Length = 308

 Score =  321 bits (824), Expect = 6e-86,   Method: Composition-based stats.
 Identities = 200/297 (67%), Positives = 248/297 (83%), Gaps = 4/297 (1%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           + +  IV+GE GL+RY+ EIR+ PML+ +EEY+LAKRYREH D  AAH+LVTSHLRLV K
Sbjct: 3   QTLPSIVSGEGGLTRYLEEIRRFPMLQPEEEYMLAKRYREHDDTDAAHKLVTSHLRLVAK 62

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IAMGYRGYGLPI EV+SEGN+GLMQAVKKF+PERGFRLATY+MWWIKAA+QEYILRSWSL
Sbjct: 63  IAMGYRGYGLPIGEVISEGNVGLMQAVKKFEPERGFRLATYAMWWIKAAIQEYILRSWSL 122

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VK+GTTANQKRLFFNLR++KG +QA+ + +L PEQV  IA +LNVSE EVISMN RL+GD
Sbjct: 123 VKMGTTANQKRLFFNLRKVKGKIQALDEGDLNPEQVSEIATRLNVSEEEVISMNRRLSGD 182

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SLNA I +++  S +WQDWLV +H+ QE++L+E++E ++RR ML  +M VLN RERRIF
Sbjct: 183 ASLNAPIRATEGESGEWQDWLVDEHENQEEMLVEQDELESRRRMLEDAMDVLNDRERRIF 242

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI----QKQVELSSSPPL 296
           EARRL + P+TLE LS EF++SRERVRQIE RAF+KVQE++    ++Q +   S PL
Sbjct: 243 EARRLSDEPMTLEELSGEFDISRERVRQIEVRAFEKVQEAVKASAKRQAQALRSAPL 299


>gi|153008567|ref|YP_001369782.1| RNA polymerase factor sigma-32 [Ochrobactrum anthropi ATCC 49188]
 gi|151560455|gb|ABS13953.1| RNA polymerase, sigma 32 subunit, RpoH [Ochrobactrum anthropi ATCC
           49188]
          Length = 303

 Score =  321 bits (824), Expect = 7e-86,   Method: Composition-based stats.
 Identities = 194/278 (69%), Positives = 234/278 (84%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M + N+  I +G+ GL+RY+ EIR+ PMLE QEEY+LAKRY EH D  AAHRLVTSHLRL
Sbjct: 1   MAQMNLPSITSGDGGLTRYLEEIRRFPMLEPQEEYMLAKRYHEHTDPKAAHRLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVK+F+PERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLR++K  +QA+ D +L P+QV  IA KL VSE EV+SMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRKMKSKIQALDDGDLNPDQVKQIATKLKVSEDEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA + +S+  S +WQDWLV D   QEQVLIE++E +NRR+ML ++M  LN RER
Sbjct: 181 SGDASLNAPLRASEGESGEWQDWLVDDSSSQEQVLIEQDELENRRSMLEQAMDTLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           RIFEARRL ++P+TLE+LSSEF +SRERVRQIE RAF+
Sbjct: 241 RIFEARRLSDDPMTLEDLSSEFGISRERVRQIEVRAFE 278


>gi|298292657|ref|YP_003694596.1| RNA polymerase, sigma 32 subunit, RpoH [Starkeya novella DSM 506]
 gi|296929168|gb|ADH89977.1| RNA polymerase, sigma 32 subunit, RpoH [Starkeya novella DSM 506]
          Length = 303

 Score =  320 bits (822), Expect = 1e-85,   Method: Composition-based stats.
 Identities = 189/299 (63%), Positives = 237/299 (79%), Gaps = 1/299 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R  MS+  + E GLSRY+ EIR+ PMLE QEEY+LAKR+REH D  AAH+LVTSHLRL
Sbjct: 1   MARSAMSLP-SAEGGLSRYLAEIRRFPMLEPQEEYMLAKRWREHEDPEAAHKLVTSHLRL 59

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPISEV+SEGN+GLMQAVK+F+P++GFRLATY+MWWIKA++QEYILRS
Sbjct: 60  VAKIAMGYRGYGLPISEVISEGNVGLMQAVKRFEPDKGFRLATYAMWWIKASIQEYILRS 119

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTA QK+LFFNLR+ K  + A+ D +L+P+QV  IA KL V+E EV+ MN RL
Sbjct: 120 WSLVKMGTTAAQKKLFFNLRKAKSQISALEDGDLRPDQVQQIATKLGVTEQEVVDMNRRL 179

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA +    +   +WQDWL  D D QE  L + EE  NRR+ L  ++SVLN RER
Sbjct: 180 SGDASLNAPLRGDVEGGGEWQDWLADDRDDQETTLADLEETDNRRSALAGALSVLNERER 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQK 299
           RIFEARRL ++P+TLE+L+SEF VSRERVRQIE RAF+KVQ+++  +V    + P+ ++
Sbjct: 240 RIFEARRLSDDPMTLEDLASEFGVSRERVRQIEVRAFEKVQKAVIDRVHAMETAPMRRE 298


>gi|239832766|ref|ZP_04681095.1| alternative sigma factor RpoH [Ochrobactrum intermedium LMG 3301]
 gi|239825033|gb|EEQ96601.1| alternative sigma factor RpoH [Ochrobactrum intermedium LMG 3301]
          Length = 303

 Score =  320 bits (821), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 193/278 (69%), Positives = 234/278 (84%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M + N+  I +G+ GL+RY+ EIR+ PMLE QEEY+LAKRY EH D  AAH+LVTSHLRL
Sbjct: 1   MAQMNLPSITSGDGGLTRYLEEIRRFPMLEPQEEYMLAKRYHEHTDPKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVK+F+PERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLR++K  +QA+ D +L P+QV  IA KLNVSE EV+SMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRKMKSKIQALDDGDLNPDQVKQIATKLNVSEDEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA + +S+  S +WQDWLV D   QEQ+LIE++E  NRR+ML ++M  LN RER
Sbjct: 181 SGDASLNAPLRASEGESGEWQDWLVDDSSSQEQILIEQDELDNRRSMLEQAMDTLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           RIFEARRL ++P+TLE+LSSEF +SRERVRQIE RAF+
Sbjct: 241 RIFEARRLSDDPMTLEDLSSEFSISRERVRQIEVRAFE 278


>gi|319781136|ref|YP_004140612.1| RNA polymerase sigma factor RpoH [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
 gi|317167024|gb|ADV10562.1| RNA polymerase sigma factor RpoH [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
          Length = 303

 Score =  320 bits (820), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 200/283 (70%), Positives = 248/283 (87%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           +++  IV+GE GLSRY+ EIR+ PML+ QEEY+LAKRY EH D SAAH+LVTSHLRLV K
Sbjct: 3   QSLPSIVSGEGGLSRYLEEIRRFPMLQPQEEYMLAKRYAEHEDTSAAHKLVTSHLRLVAK 62

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IAMGYRGYGLPI EV+SEGN+GLMQAVKKF+PERGFRLATY+MWWIKA++QEYILRSWSL
Sbjct: 63  IAMGYRGYGLPIGEVISEGNVGLMQAVKKFEPERGFRLATYAMWWIKASIQEYILRSWSL 122

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VK+GTTANQKRLFFNLR++KG +QA+ D +LKP+Q+  IA +LNVSE+EV+SMN RL+GD
Sbjct: 123 VKMGTTANQKRLFFNLRKVKGKIQALDDGDLKPDQIAEIATRLNVSEAEVVSMNRRLSGD 182

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SLNA I +S+  S +WQDWLV DH+ QE++LIE++E +NRR ML+ +++VLN RERRIF
Sbjct: 183 ASLNAPIRASEGESGEWQDWLVDDHESQEEMLIEQDELENRRGMLSGALAVLNERERRIF 242

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           EARRL E P+TLE LSSEF++SRERVRQIE RAF+KVQ++++ 
Sbjct: 243 EARRLAEEPLTLEELSSEFDISRERVRQIEVRAFEKVQDAVKA 285


>gi|13473215|ref|NP_104782.1| RNA polymerase factor sigma-32 [Mesorhizobium loti MAFF303099]
 gi|14023963|dbj|BAB50568.1| sigma factor [Mesorhizobium loti MAFF303099]
          Length = 303

 Score =  320 bits (820), Expect = 2e-85,   Method: Composition-based stats.
 Identities = 197/283 (69%), Positives = 248/283 (87%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           +++  IV+GE GLSRY+ EIR+ PML+ QEEY+LAKRY EH D SAAH+LVTSHLRLV K
Sbjct: 3   QSLPSIVSGEGGLSRYLEEIRRFPMLQPQEEYMLAKRYAEHEDTSAAHKLVTSHLRLVAK 62

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IAMGYRGYGLPI EV+SEGN+GLMQAVKKF+PERGFRLATY+MWWIKA++QEYILRSWSL
Sbjct: 63  IAMGYRGYGLPIGEVISEGNVGLMQAVKKFEPERGFRLATYAMWWIKASIQEYILRSWSL 122

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VK+GTTANQKRLFFNLR++KG +QA+ D +LKP+Q+  IA +LNV+E+EV+SMN RL+GD
Sbjct: 123 VKMGTTANQKRLFFNLRKVKGKIQALDDGDLKPDQIAEIATRLNVTEAEVVSMNRRLSGD 182

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SLNA I +++  S +WQDWLV DH+ QE++LIE++E +NRR ML+ +++VLN RERRIF
Sbjct: 183 ASLNAPIRATEGESGEWQDWLVDDHESQEEMLIEQDELENRRGMLSGALAVLNERERRIF 242

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           EARRL E P+TLE LS+EF++SRERVRQIE RAF+KVQ++++ 
Sbjct: 243 EARRLAEEPLTLEELSAEFDISRERVRQIEVRAFEKVQDAVKA 285


>gi|118588309|ref|ZP_01545718.1| RNA polymerase sigma factor [Stappia aggregata IAM 12614]
 gi|118439015|gb|EAV45647.1| RNA polymerase sigma factor [Stappia aggregata IAM 12614]
          Length = 294

 Score =  319 bits (819), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 195/291 (67%), Positives = 233/291 (80%), Gaps = 1/291 (0%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           +N+  +  GE GLSRY+ EIRK PML+ QEEY+LAKRY+EH D  AA RLV SHLRLV K
Sbjct: 3   QNVPTLTAGEGGLSRYLDEIRKFPMLQPQEEYMLAKRYKEHEDPEAAERLVNSHLRLVAK 62

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IAMGYRGYGLPI EVVSEGN+GLMQAVK+F+P++GFRLATY+MWWIKAA+QEYILRSWSL
Sbjct: 63  IAMGYRGYGLPIGEVVSEGNVGLMQAVKRFEPDKGFRLATYAMWWIKAAIQEYILRSWSL 122

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VK+GTTANQKRLFFNLRRLKG +QA+ + +LKP QV  IA KL VSE EV+SMN RL GD
Sbjct: 123 VKMGTTANQKRLFFNLRRLKGKIQALDEGDLKPHQVSEIATKLGVSEEEVVSMNRRLGGD 182

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SLNA +  ++ ++ +WQDWLV + D QE +L  +EE   RR ML  +M VLN RERRIF
Sbjct: 183 ASLNAPVR-AEADAGEWQDWLVDESDSQETLLANQEELDMRRKMLNDAMDVLNERERRIF 241

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSP 294
           EARRL E+P+TLE+LS EF VSRERVRQIE RAF+KVQ++++        P
Sbjct: 242 EARRLSEDPMTLEDLSGEFGVSRERVRQIEVRAFEKVQKAVRNSARTMDQP 292


>gi|260461535|ref|ZP_05809782.1| RNA polymerase, sigma 32 subunit, RpoH [Mesorhizobium opportunistum
           WSM2075]
 gi|259032605|gb|EEW33869.1| RNA polymerase, sigma 32 subunit, RpoH [Mesorhizobium opportunistum
           WSM2075]
          Length = 303

 Score =  319 bits (818), Expect = 3e-85,   Method: Composition-based stats.
 Identities = 198/283 (69%), Positives = 248/283 (87%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           +++  IV+GE GLSRY+ EIR+ PML+ QEEY+LAKRY EH D SAAH+LVTSHLRLV K
Sbjct: 3   QSLPSIVSGEGGLSRYLEEIRRFPMLQPQEEYMLAKRYAEHEDTSAAHKLVTSHLRLVAK 62

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IAMGYRGYGLPI EV+SEGN+GLMQAVKKF+PERGFRLATY+MWWIKA++QEYILRSWSL
Sbjct: 63  IAMGYRGYGLPIGEVISEGNVGLMQAVKKFEPERGFRLATYAMWWIKASIQEYILRSWSL 122

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VK+GTTANQKRLFFNLR++KG +QA+ D +LKP+Q+  IA +LNVSE+EV+SMN RL+GD
Sbjct: 123 VKMGTTANQKRLFFNLRKVKGKIQALDDGDLKPDQIAEIATRLNVSEAEVVSMNRRLSGD 182

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SLNA I +++  S +WQDWLV DH+ QE++LIE++E +NRR ML+ +++VLN RERRIF
Sbjct: 183 ASLNAPIRATEGESGEWQDWLVDDHESQEEMLIEQDELENRRGMLSGALAVLNDRERRIF 242

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           EARRL E P+TLE LS+EF++SRERVRQIE RAF+KVQ++++ 
Sbjct: 243 EARRLAEEPLTLEELSAEFDISRERVRQIEVRAFEKVQDAVKA 285


>gi|158425877|ref|YP_001527169.1| RNA polymerase factor sigma-32 [Azorhizobium caulinodans ORS 571]
 gi|158332766|dbj|BAF90251.1| sigma-70 factor [Azorhizobium caulinodans ORS 571]
          Length = 300

 Score =  318 bits (816), Expect = 5e-85,   Method: Composition-based stats.
 Identities = 185/288 (64%), Positives = 230/288 (79%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M     + I + E GL+RY+ EIR+ PMLE QEEY+LAK +REHGD  AAH+LVTSHLRL
Sbjct: 1   MAGSRQAPIPSAEGGLTRYLEEIRRFPMLEPQEEYMLAKSWREHGDRDAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPISEV+SEGN+GLMQAVK+F+PE+GFRLATY+MWWI+A++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPISEVISEGNVGLMQAVKRFEPEKGFRLATYAMWWIRASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTA QK+LFFNLR+ K  + A+ + +L+P+QV  IA KL V+E +V+ MN RL
Sbjct: 121 WSLVKMGTTAAQKKLFFNLRKAKSQISALEEGDLRPDQVKQIATKLGVTEQDVVDMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA +        +WQDWL  DH  QE  L+E EE  NRR  L+ +++VLNPRER
Sbjct: 181 SGDASLNAPLREDGDGGGEWQDWLQDDHQDQETNLVESEELDNRRTALSSALAVLNPRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RIFEARRL E+PVTLE L++EF VSRERVRQIE RAF+KVQ+++  +V
Sbjct: 241 RIFEARRLSEDPVTLEELAAEFGVSRERVRQIEVRAFEKVQKAVVDKV 288


>gi|49475181|ref|YP_033222.1| RNA polymerase factor sigma-32 [Bartonella henselae str. Houston-1]
 gi|49237986|emb|CAF27191.1| RNA polymerase sigma-32 factor [Bartonella henselae str. Houston-1]
          Length = 294

 Score =  318 bits (815), Expect = 8e-85,   Method: Composition-based stats.
 Identities = 188/286 (65%), Positives = 236/286 (82%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M   N+  +  G+ GLSRY+ E+R+ PMLE QEEY+LA+RYR+H DL AAH+LVTSHLRL
Sbjct: 1   MAHMNLLSVTTGDGGLSRYLEEVRRFPMLEPQEEYMLAQRYRKHNDLKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIA+GYRGYGLPI EV+SEGN+GLM+AVK+F+PERGFRLATY++WWIKA++QEY+LRS
Sbjct: 61  VAKIAVGYRGYGLPIGEVISEGNVGLMKAVKRFEPERGFRLATYAIWWIKASIQEYVLRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLR+LK  LQA+ + +L  EQV  IA +LNV+E EV+SMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRKLKSRLQALDNGDLNAEQVKEIAIQLNVTEDEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA + + +  +S+WQDWLV D + QEQ LIE+ E +NRR+MLT ++  LN RE+
Sbjct: 181 GGDTSLNAPLRTKEGENSEWQDWLVDDSNNQEQTLIEQNELENRRSMLTNALDNLNEREK 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           RIF+ARRL + P+TLE LSSEF +SRERVRQIE RAF+K+Q SI+ 
Sbjct: 241 RIFKARRLSDIPLTLEELSSEFNISRERVRQIEMRAFEKIQNSIKA 286


>gi|27382448|ref|NP_773977.1| RNA polymerase factor sigma-32 [Bradyrhizobium japonicum USDA 110]
 gi|1834373|emb|CAA70697.1| rpoH2 [Bradyrhizobium japonicum]
 gi|27355619|dbj|BAC52602.1| sigma32-like transcription factor [Bradyrhizobium japonicum USDA
           110]
          Length = 299

 Score =  317 bits (813), Expect = 1e-84,   Method: Composition-based stats.
 Identities = 188/285 (65%), Positives = 232/285 (81%), Gaps = 1/285 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R     ++NGE GLSRY+ EIRK PMLE Q+EY+LAKR+REH D  AAH+LVTSHLRL
Sbjct: 1   MARTAALPVLNGESGLSRYLAEIRKFPMLEPQQEYMLAKRWREHDDRDAAHQLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPISEVVSEGN+GLMQAVK+F+PE+GFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQK+LFFNLR+ K  + A+ + +L+P+QV  IAK+L V++ +VI MN RL
Sbjct: 121 WSLVKMGTTANQKKLFFNLRKAKSKINALDEGDLRPDQVATIAKRLGVTDQDVIDMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA I   D  + +WQDWLV +   QE ++ E EE  +RR+ L  +M VLNPRER
Sbjct: 181 GGDASLNAPIRD-DGEAGEWQDWLVDNTPNQEAMMAEHEEYDHRRDALNGAMGVLNPRER 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           RIFEARRL + P+TLE+L++EF VSRERVRQIE RAF+KVQ +++
Sbjct: 240 RIFEARRLADEPMTLEDLAAEFGVSRERVRQIEVRAFEKVQSAVK 284


>gi|307944600|ref|ZP_07659940.1| alternative sigma factor RpoH [Roseibium sp. TrichSKD4]
 gi|307772349|gb|EFO31570.1| alternative sigma factor RpoH [Roseibium sp. TrichSKD4]
          Length = 294

 Score =  317 bits (812), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 191/291 (65%), Positives = 235/291 (80%), Gaps = 1/291 (0%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           +N+ ++  GE GLSRY+ EIRK P+L+ QEEY+LAKRY+EH D  AA RLV SHLRLV K
Sbjct: 3   QNVPMLTAGEGGLSRYLDEIRKFPLLQPQEEYMLAKRYKEHADPEAAERLVNSHLRLVAK 62

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IAMGYRGYGLPI EVVSEGN+GLMQAVK+F+P++GFRLATY+MWWIKAA+QEYILRSWSL
Sbjct: 63  IAMGYRGYGLPIGEVVSEGNVGLMQAVKRFEPDKGFRLATYAMWWIKAAIQEYILRSWSL 122

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VK+GTTANQKRLFFNLRRLKG +QA+ + +LKP QV  IA KL VSE EVISMN RL GD
Sbjct: 123 VKMGTTANQKRLFFNLRRLKGKIQALEEGDLKPHQVQEIATKLGVSEEEVISMNRRLGGD 182

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SLN+ +  ++ ++ +WQDWLV + D QE +L  +EE   RR +L+++M  LN RERRIF
Sbjct: 183 TSLNSPVR-AEADAGEWQDWLVDEADSQETLLANQEELDQRRELLSQAMDELNERERRIF 241

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSP 294
            ARRL E+P+TLE+LS+EF VSRERVRQIE RAF+KVQ++++        P
Sbjct: 242 TARRLSEDPITLEDLSTEFGVSRERVRQIEVRAFEKVQKAVKNSARAKELP 292


>gi|319898405|ref|YP_004158498.1| RNA polymerase sigma-32 factor [Bartonella clarridgeiae 73]
 gi|319402369|emb|CBI75908.1| RNA polymerase sigma-32 factor [Bartonella clarridgeiae 73]
          Length = 305

 Score =  316 bits (811), Expect = 2e-84,   Method: Composition-based stats.
 Identities = 187/285 (65%), Positives = 231/285 (81%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M   N+   +  + GLSRY+ E+R+ P+LE QEEY+LAKRY EH D  AAH+LVTSHLRL
Sbjct: 1   MAHINLPSFIANDSGLSRYLEEVRRFPVLEPQEEYMLAKRYHEHNDPKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGNIGLMQAVK+F+PERGFRLATY+MWWIKA++QEY+LRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVISEGNIGLMQAVKRFEPERGFRLATYAMWWIKASIQEYVLRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVKIGTTANQKRLFFNLR+LK  LQ     +L  EQV  IA +L V+E EV+SMN RL
Sbjct: 121 WSLVKIGTTANQKRLFFNLRKLKNKLQMFDSGDLNAEQVKEIATRLKVTEDEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA + ++   S +WQDWLV D + QEQ+LIE++E +NR +ML ++M  LN RE+
Sbjct: 181 SGDASLNAPLLTNKGESYEWQDWLVDDSNSQEQILIEQDELENRHSMLIQAMDNLNEREK 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           RIF+ARRL++ P+TLE LS+EF +SRERVRQIE RAF+K+Q SI+
Sbjct: 241 RIFKARRLRDEPMTLEELSNEFNISRERVRQIEMRAFEKIQNSIK 285


>gi|209886261|ref|YP_002290118.1| alternative sigma factor RpoH [Oligotropha carboxidovorans OM5]
 gi|209874457|gb|ACI94253.1| alternative sigma factor RpoH [Oligotropha carboxidovorans OM5]
          Length = 299

 Score =  315 bits (809), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 193/288 (67%), Positives = 229/288 (79%), Gaps = 1/288 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R     I+NGE GLS Y+ EIRK PMLE QEEY+LAKR+REH D  AAH+LVTSHLRL
Sbjct: 1   MARTATLPILNGESGLSHYLAEIRKFPMLEPQEEYMLAKRWREHDDRDAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPISEVVSEGN+GLMQAVK+F+PE+GFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQK+LFFNLR+ K  + A+ D ++  +QV  IAK+L V+E +VI MN RL
Sbjct: 121 WSLVKMGTTANQKKLFFNLRKAKSKISALEDGDMHEDQVKLIAKRLGVTERDVIDMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA I   D    +WQDWLV     QE ++ E EE  +RRN LT +M VLNPRER
Sbjct: 181 GGDASLNAPIRD-DGEPGEWQDWLVDTSPNQETIMAESEEYDHRRNALTGAMGVLNPRER 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RIFEARRL E P+TLE+L++EF VSRERVRQIE RAF+KVQ +++  V
Sbjct: 240 RIFEARRLAEEPMTLEDLAAEFGVSRERVRQIEVRAFEKVQAAVKSTV 287


>gi|114707401|ref|ZP_01440298.1| RNA polymerase sigma factor [Fulvimarina pelagi HTCC2506]
 gi|114537282|gb|EAU40409.1| RNA polymerase sigma factor [Fulvimarina pelagi HTCC2506]
          Length = 304

 Score =  315 bits (809), Expect = 3e-84,   Method: Composition-based stats.
 Identities = 192/288 (66%), Positives = 240/288 (83%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M + N+  I +GE GL+RY+ EIR+ PML+  EEY+LAKRY EH D +AAH+LVTSHLRL
Sbjct: 1   MAQMNLPSIASGEGGLNRYLEEIRRFPMLQPDEEYMLAKRYAEHDDRNAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EVVSEGN+GLMQAVK+FDPERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKRFDPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLR++K  +QA+ D +L P+QV  IA +L VS+ EVISMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRKMKSRIQALEDGDLNPDQVKQIATQLGVSDDEVISMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLN+ + +++  S +WQDWLV +++ QE VL +++E   RR ML R+M +LN RER
Sbjct: 181 SGDASLNSPLRATEGESGEWQDWLVDENESQEDVLAQQDELDQRRGMLKRAMGILNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RIFEARRL E+P+TLE LS EF++SRERVRQIE RAF+KVQ+++Q+ V
Sbjct: 241 RIFEARRLSEDPITLEALSGEFDISRERVRQIEVRAFEKVQKAVQENV 288


>gi|17986661|ref|NP_539295.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 1 str. 16M]
 gi|62290526|ref|YP_222319.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 1 str. 9-941]
 gi|82700442|ref|YP_415016.1| RNA polymerase factor sigma-32 [Brucella melitensis biovar Abortus
           2308]
 gi|189024748|ref|YP_001935516.1| RNA polymerase factor sigma-32 [Brucella abortus S19]
 gi|225853116|ref|YP_002733349.1| RNA polymerase factor sigma-32 [Brucella melitensis ATCC 23457]
 gi|237816032|ref|ZP_04595028.1| alternative sigma factor RpoH [Brucella abortus str. 2308 A]
 gi|254689824|ref|ZP_05153078.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 6 str. 870]
 gi|254694316|ref|ZP_05156144.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 3 str. Tulya]
 gi|254697972|ref|ZP_05159800.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 2 str.
           86/8/59]
 gi|254730858|ref|ZP_05189436.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 4 str. 292]
 gi|256045266|ref|ZP_05448160.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|256114225|ref|ZP_05454970.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 3 str.
           Ether]
 gi|256258077|ref|ZP_05463613.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 9 str. C68]
 gi|256263396|ref|ZP_05465928.1| sigma-70 factor [Brucella melitensis bv. 2 str. 63/9]
 gi|260547226|ref|ZP_05822964.1| sigma-70 factor family protein [Brucella abortus NCTC 8038]
 gi|260565841|ref|ZP_05836324.1| sigma-70 factor family protein [Brucella melitensis bv. 1 str. 16M]
 gi|260755355|ref|ZP_05867703.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 6 str. 870]
 gi|260758577|ref|ZP_05870925.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 4 str. 292]
 gi|260762409|ref|ZP_05874746.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 2 str.
           86/8/59]
 gi|260884371|ref|ZP_05895985.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 9 str. C68]
 gi|261214622|ref|ZP_05928903.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 3 str. Tulya]
 gi|265991691|ref|ZP_06104248.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|265995528|ref|ZP_06108085.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 3 str.
           Ether]
 gi|297248928|ref|ZP_06932636.1| alternative sigma factor RpoH [Brucella abortus bv. 5 str. B3196]
 gi|17982279|gb|AAL51559.1| RNA polymerase sigma-32 factor [Brucella melitensis bv. 1 str. 16M]
 gi|62196658|gb|AAX74958.1| RNA polymerase sigma-70 factor family protein [Brucella abortus bv.
           1 str. 9-941]
 gi|82616543|emb|CAJ11621.1| Sigma-70 factor family:Sigma-70 region 2:Sigma-70 region 4
           [Brucella melitensis biovar Abortus 2308]
 gi|189020320|gb|ACD73042.1| Sigma-70 factor family [Brucella abortus S19]
 gi|225641481|gb|ACO01395.1| alternative sigma factor RpoH [Brucella melitensis ATCC 23457]
 gi|237788695|gb|EEP62907.1| alternative sigma factor RpoH [Brucella abortus str. 2308 A]
 gi|260095591|gb|EEW79469.1| sigma-70 factor family protein [Brucella abortus NCTC 8038]
 gi|260151214|gb|EEW86309.1| sigma-70 factor family protein [Brucella melitensis bv. 1 str. 16M]
 gi|260668895|gb|EEX55835.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 4 str. 292]
 gi|260672835|gb|EEX59656.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 2 str.
           86/8/59]
 gi|260675463|gb|EEX62284.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 6 str. 870]
 gi|260873899|gb|EEX80968.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 9 str. C68]
 gi|260916229|gb|EEX83090.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 3 str. Tulya]
 gi|262766812|gb|EEZ12430.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 3 str.
           Ether]
 gi|263002647|gb|EEZ15050.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|263093393|gb|EEZ17462.1| sigma-70 factor [Brucella melitensis bv. 2 str. 63/9]
 gi|297174061|gb|EFH33418.1| alternative sigma factor RpoH [Brucella abortus bv. 5 str. B3196]
 gi|326409662|gb|ADZ66727.1| Sigma-70 factor family [Brucella melitensis M28]
 gi|326539369|gb|ADZ87584.1| alternative sigma factor RpoH [Brucella melitensis M5-90]
          Length = 303

 Score =  315 bits (809), Expect = 4e-84,   Method: Composition-based stats.
 Identities = 191/278 (68%), Positives = 232/278 (83%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M +  +  I +G+ GL+RY+ EIR+ PMLE QEEY+LAKRY EH D  AAH+LVTSHLRL
Sbjct: 1   MAQMKLPSITSGDGGLTRYLEEIRRFPMLEPQEEYMLAKRYHEHADPKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVK+F+PERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLR++K  +QA+ D +L P+QV  IA KLNVSE EV+SMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRKMKSKIQALDDGDLNPDQVKQIATKLNVSEDEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA + +S+  S +WQDWLV D + QEQVLIE++E ++RR+ML ++M  LN RER
Sbjct: 181 SGDASLNAPLRASEGESGEWQDWLVDDSNSQEQVLIEQDELESRRSMLEQAMETLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
            IFEARRL E P+TLE+LS EF +SRERVRQIE RAF+
Sbjct: 241 HIFEARRLAEEPMTLEDLSGEFGISRERVRQIEVRAFE 278


>gi|306844673|ref|ZP_07477258.1| alternative sigma factor RpoH [Brucella sp. BO1]
 gi|306274845|gb|EFM56615.1| alternative sigma factor RpoH [Brucella sp. BO1]
          Length = 303

 Score =  315 bits (809), Expect = 4e-84,   Method: Composition-based stats.
 Identities = 193/278 (69%), Positives = 234/278 (84%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M +  +  I +G+ GL+RY+ EIR+ PMLE QEEY+LAKRY EH D  AAH+LVTSHLRL
Sbjct: 1   MAQMKLPSITSGDGGLTRYLEEIRRFPMLEPQEEYMLAKRYHEHADPKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVK+F+PERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLR++K  +QA+ D +L P+QV  IA KLNVSE EV+SMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRKMKSKIQALDDGDLNPDQVKQIATKLNVSEDEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA + +S+  S +WQDWLV D + QEQVLIE++E ++RR+ML ++M  LN RER
Sbjct: 181 SGDASLNAPLRASEGESGEWQDWLVDDSNSQEQVLIEQDELESRRSMLEQAMETLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           RIFEARRL E P+TLE+LSSEF +SRERVRQIE RAF+
Sbjct: 241 RIFEARRLAEEPMTLEDLSSEFGISRERVRQIEVRAFE 278


>gi|254719685|ref|ZP_05181496.1| RNA polymerase factor sigma-32 [Brucella sp. 83/13]
 gi|265984700|ref|ZP_06097435.1| RNA polymerase factor sigma-32 [Brucella sp. 83/13]
 gi|306840038|ref|ZP_07472825.1| alternative sigma factor RpoH [Brucella sp. NF 2653]
 gi|264663292|gb|EEZ33553.1| RNA polymerase factor sigma-32 [Brucella sp. 83/13]
 gi|306404852|gb|EFM61144.1| alternative sigma factor RpoH [Brucella sp. NF 2653]
          Length = 303

 Score =  315 bits (808), Expect = 4e-84,   Method: Composition-based stats.
 Identities = 192/278 (69%), Positives = 233/278 (83%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M +  +  I +G+ GL+RY+ EIR+ PMLE QEEY+LAKRY EH D  AAH+LVTSHLRL
Sbjct: 1   MAQMKLPSITSGDGGLTRYLEEIRRFPMLEPQEEYMLAKRYHEHADPKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVK+F+PERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLR++K  +QA+ D +L P+QV  IA KLNVSE EV+SMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRKMKSKIQALDDGDLNPDQVKQIATKLNVSEDEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA + +S+  S +WQDWLV D + QEQVLIE++E ++RR+ML ++M  LN RER
Sbjct: 181 SGDASLNAPLRASEGESGEWQDWLVDDSNSQEQVLIEQDELESRRSMLEQAMETLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           RIFEARRL E P+TLE+LS EF +SRERVRQIE RAF+
Sbjct: 241 RIFEARRLAEEPMTLEDLSGEFGISRERVRQIEVRAFE 278


>gi|23502510|ref|NP_698637.1| RNA polymerase factor sigma-32 [Brucella suis 1330]
 gi|161619585|ref|YP_001593472.1| RNA polymerase factor sigma-32 [Brucella canis ATCC 23365]
 gi|163845234|ref|YP_001622889.1| RNA polymerase factor sigma-32 [Brucella suis ATCC 23445]
 gi|225628222|ref|ZP_03786256.1| alternative sigma factor RpoH [Brucella ceti str. Cudo]
 gi|254708479|ref|ZP_05170307.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M163/99/10]
 gi|254708670|ref|ZP_05170481.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis B2/94]
 gi|254714517|ref|ZP_05176328.1| RNA polymerase factor sigma-32 [Brucella ceti M644/93/1]
 gi|254717415|ref|ZP_05179226.1| RNA polymerase factor sigma-32 [Brucella ceti M13/05/1]
 gi|256030196|ref|ZP_05443810.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M292/94/1]
 gi|256061694|ref|ZP_05451831.1| RNA polymerase factor sigma-32 [Brucella neotomae 5K33]
 gi|256160370|ref|ZP_05458060.1| RNA polymerase factor sigma-32 [Brucella ceti M490/95/1]
 gi|256255578|ref|ZP_05461114.1| RNA polymerase factor sigma-32 [Brucella ceti B1/94]
 gi|260167873|ref|ZP_05754684.1| RNA polymerase factor sigma-32 [Brucella sp. F5/99]
 gi|260568745|ref|ZP_05839213.1| sigma-70 factor family protein [Brucella suis bv. 4 str. 40]
 gi|261219245|ref|ZP_05933526.1| RNA polymerase factor sigma-32 [Brucella ceti M13/05/1]
 gi|261222781|ref|ZP_05937062.1| RNA polymerase factor sigma-32 [Brucella ceti B1/94]
 gi|261315977|ref|ZP_05955174.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M163/99/10]
 gi|261316160|ref|ZP_05955357.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis B2/94]
 gi|261322306|ref|ZP_05961503.1| RNA polymerase factor sigma-32 [Brucella ceti M644/93/1]
 gi|261325699|ref|ZP_05964896.1| RNA polymerase factor sigma-32 [Brucella neotomae 5K33]
 gi|261757310|ref|ZP_06001019.1| sigma-70 factor family [Brucella sp. F5/99]
 gi|265987224|ref|ZP_06099781.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M292/94/1]
 gi|265998739|ref|ZP_06111296.1| RNA polymerase factor sigma-32 [Brucella ceti M490/95/1]
 gi|23348506|gb|AAN30552.1| RNA polymerase sigma-70 factor family protein [Brucella suis 1330]
 gi|161336396|gb|ABX62701.1| alternative sigma factor RpoH [Brucella canis ATCC 23365]
 gi|163675957|gb|ABY40067.1| alternative sigma factor RpoH [Brucella suis ATCC 23445]
 gi|225616068|gb|EEH13116.1| alternative sigma factor RpoH [Brucella ceti str. Cudo]
 gi|260154129|gb|EEW89211.1| sigma-70 factor family protein [Brucella suis bv. 4 str. 40]
 gi|260921365|gb|EEX88018.1| RNA polymerase factor sigma-32 [Brucella ceti B1/94]
 gi|260924334|gb|EEX90902.1| RNA polymerase factor sigma-32 [Brucella ceti M13/05/1]
 gi|261294996|gb|EEX98492.1| RNA polymerase factor sigma-32 [Brucella ceti M644/93/1]
 gi|261295383|gb|EEX98879.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis B2/94]
 gi|261301679|gb|EEY05176.1| RNA polymerase factor sigma-32 [Brucella neotomae 5K33]
 gi|261305003|gb|EEY08500.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M163/99/10]
 gi|261737294|gb|EEY25290.1| sigma-70 factor family [Brucella sp. F5/99]
 gi|262553428|gb|EEZ09197.1| RNA polymerase factor sigma-32 [Brucella ceti M490/95/1]
 gi|264659421|gb|EEZ29682.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M292/94/1]
          Length = 303

 Score =  315 bits (808), Expect = 4e-84,   Method: Composition-based stats.
 Identities = 192/278 (69%), Positives = 233/278 (83%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M +  +  I +G+ GL+RY+ EIR+ PMLE QEEY+LAKRY EH D  AAH+LVTSHLRL
Sbjct: 1   MAQMKLPSITSGDGGLTRYLEEIRRFPMLEPQEEYMLAKRYHEHADPKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVK+F+PERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLR++K  +QA+ D +L P+QV  IA KLNVSE EV+SMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRKMKSKIQALDDGDLNPDQVKQIATKLNVSEDEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA + +S+  S +WQDWLV D + QEQVLIE++E ++RR+ML ++M  LN RER
Sbjct: 181 SGDASLNAPLRASEGESGEWQDWLVDDSNSQEQVLIEQDELESRRSMLEQAMETLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           RIFEARRL E P+TLE+LS EF +SRERVRQIE RAF+
Sbjct: 241 RIFEARRLAEEPMTLEDLSGEFGISRERVRQIEVRAFE 278


>gi|115522843|ref|YP_779754.1| RNA polymerase factor sigma-32 [Rhodopseudomonas palustris BisA53]
 gi|115516790|gb|ABJ04774.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodopseudomonas palustris
           BisA53]
          Length = 299

 Score =  315 bits (808), Expect = 5e-84,   Method: Composition-based stats.
 Identities = 186/285 (65%), Positives = 227/285 (79%), Gaps = 1/285 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R     ++NGE GLSRY+ EIRK PMLE Q+EY+LAKR+REH D  AAH LVTSHLRL
Sbjct: 1   MARAATLPVLNGESGLSRYLAEIRKFPMLEPQQEYMLAKRWREHDDRDAAHHLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPISEVVSEGN+GLMQAVK+F+PE+GFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQK+LFFNLR+ K  + A+ + ++ P+QV  IA +L V+E +V+ MN RL
Sbjct: 121 WSLVKMGTTANQKKLFFNLRKAKSKISALDEGDMHPDQVKLIATRLGVTEQDVVDMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA I   D    +WQDWLV     QE V+ E EE  +RR  L  ++ VLNPRER
Sbjct: 181 GGDASLNAPIRD-DGEPGEWQDWLVDHSPSQEAVMAEHEELDHRRAALNGAIGVLNPRER 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           RIFEARRL ++P+TLE+L++EF VSRERVRQIE RAF+KVQ +++
Sbjct: 240 RIFEARRLADDPMTLEDLAAEFGVSRERVRQIEVRAFEKVQAAVK 284


>gi|306841398|ref|ZP_07474101.1| alternative sigma factor RpoH [Brucella sp. BO2]
 gi|306288583|gb|EFM59932.1| alternative sigma factor RpoH [Brucella sp. BO2]
          Length = 303

 Score =  315 bits (808), Expect = 5e-84,   Method: Composition-based stats.
 Identities = 192/278 (69%), Positives = 233/278 (83%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M +  +  I +G+ GL+RY+ EIR+ PMLE QEEY+LAKRY EH D  AAH+LVTSHLRL
Sbjct: 1   MAQMKLPSITSGDGGLTRYLEEIRRFPMLEPQEEYMLAKRYHEHADPKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVK+F+PERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLR++K  +QA+ D +L P+QV  IA KLNVSE EV+SMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRKMKSKIQALDDGDLNPDQVKQIATKLNVSEDEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA + +S+  S +WQDWLV D + QEQVLIE++E ++RR+ML ++M  LN RER
Sbjct: 181 SGDASLNAPLRASEGESGEWQDWLVDDSNSQEQVLIEQDELESRRSMLEQAMETLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           RIFEARRL E P+TLE+LS EF +SRERVRQIE RAF+
Sbjct: 241 RIFEARRLAEEPMTLEDLSGEFGISRERVRQIEVRAFE 278


>gi|299134310|ref|ZP_07027503.1| RNA polymerase, sigma 32 subunit, RpoH [Afipia sp. 1NLS2]
 gi|298591057|gb|EFI51259.1| RNA polymerase, sigma 32 subunit, RpoH [Afipia sp. 1NLS2]
          Length = 299

 Score =  315 bits (807), Expect = 6e-84,   Method: Composition-based stats.
 Identities = 192/288 (66%), Positives = 230/288 (79%), Gaps = 1/288 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R     ++NGE GLS Y+ EIRK PMLE QEEY+LAKR+REH D  AAHRLVTSHLRL
Sbjct: 1   MARTATLPVLNGESGLSHYLAEIRKFPMLEPQEEYMLAKRWREHDDRDAAHRLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPISEVVSEGN+GLMQAVK+F+PE+GFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQK+LFFNLR+ K  + A+ + +++ +QV  IAK+L V+E +VI MN RL
Sbjct: 121 WSLVKMGTTANQKKLFFNLRKAKSKISALEEGDMREDQVKLIAKRLGVTERDVIDMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA I   D    +WQDWLV     QE ++ E EE  +RRN LT +M VLNPRER
Sbjct: 181 GGDASLNAPIRD-DGEPGEWQDWLVDTSPNQEAIMAESEEYDHRRNALTGAMGVLNPRER 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RIFEARRL E P+TLE+L++EF VSRERVRQIE RAF+KVQ +++  V
Sbjct: 240 RIFEARRLAEEPMTLEDLAAEFGVSRERVRQIEVRAFEKVQAAVKSTV 287


>gi|316931591|ref|YP_004106573.1| RNA polymerase sigma 32 subunit RpoH [Rhodopseudomonas palustris
           DX-1]
 gi|315599305|gb|ADU41840.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodopseudomonas palustris
           DX-1]
          Length = 299

 Score =  315 bits (807), Expect = 6e-84,   Method: Composition-based stats.
 Identities = 186/285 (65%), Positives = 226/285 (79%), Gaps = 1/285 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R     ++NGE GL+RY+ EIRK PMLE ++EY+LAKR+REHGD  AAH+LVTSHLRL
Sbjct: 1   MARAATLPVLNGESGLARYLAEIRKFPMLEPEQEYMLAKRWREHGDRDAAHQLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPISEVVSEGN+GLMQAVK+F+PE+GFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQK+LFFNLR+ K  + A+ + +L P+ V  IA +L V+E +V+ MN RL
Sbjct: 121 WSLVKMGTTANQKKLFFNLRKAKSKISALDEGDLHPDHVKLIASRLGVTEQDVVDMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA I   D    +WQDWLV     QE VL E EE   RR  L  ++ VLNPRER
Sbjct: 181 GGDASLNAPIRD-DGEPGEWQDWLVDQSPSQEAVLAEHEELDQRRAALNGAIQVLNPRER 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           RIFEARRL + P+TLE+L++EF VSRERVRQIE RAF+KVQ +++
Sbjct: 240 RIFEARRLADEPMTLEDLAAEFGVSRERVRQIEVRAFEKVQSAVK 284


>gi|146338455|ref|YP_001203503.1| RNA polymerase factor sigma-32 [Bradyrhizobium sp. ORS278]
 gi|146191261|emb|CAL75266.1| sigma H (sigma 32) factor of RNA polymerase; transcription of heat
           shock and stress proteins [Bradyrhizobium sp. ORS278]
          Length = 299

 Score =  314 bits (804), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 187/296 (63%), Positives = 232/296 (78%), Gaps = 1/296 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R     ++NGE GL+RY+ EIRK PMLE QEEY+LAKR+REH D  AAH+LVTSHLRL
Sbjct: 1   MARTATLPVLNGESGLARYLSEIRKFPMLEPQEEYMLAKRWREHDDSDAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPISEVVSEGN+GLMQAVK+F+PE+GFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQK+LFFNLR+ K  + A+ + +L+P+QV  IAK+L V++ +VI MN RL
Sbjct: 121 WSLVKMGTTANQKKLFFNLRKAKSKISALDEGDLRPDQVKLIAKRLGVTDQDVIDMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA I   D  + +WQDWLV     QE ++ E EE  +RR  L  ++ VLN RER
Sbjct: 181 GGDASLNAPIRD-DGEAGEWQDWLVDTSPNQEAIMAEHEEYDHRRQALNGAIGVLNARER 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPL 296
           RIFEARRL + P+TLE+L++EF VSRERVRQIE RAF+KVQ +++  +    +  L
Sbjct: 240 RIFEARRLADEPMTLEDLAAEFGVSRERVRQIEVRAFEKVQSAVKGAIAKQEAAAL 295


>gi|148560551|ref|YP_001259508.1| RNA polymerase factor sigma-32 [Brucella ovis ATCC 25840]
 gi|294850906|ref|ZP_06791582.1| alternative sigma factor RpoH [Brucella sp. NVSL 07-0026]
 gi|148371808|gb|ABQ61787.1| alternative sigma factor RpoH [Brucella ovis ATCC 25840]
 gi|294821549|gb|EFG38545.1| alternative sigma factor RpoH [Brucella sp. NVSL 07-0026]
          Length = 303

 Score =  314 bits (804), Expect = 1e-83,   Method: Composition-based stats.
 Identities = 191/278 (68%), Positives = 232/278 (83%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M +  +  I +G+ GL+RY+ EIR+ PMLE QEEY+LAKRY EH D  AAH+LVTSHLRL
Sbjct: 1   MAQMKLPSITSGDGGLTRYLEEIRRFPMLEPQEEYMLAKRYHEHADPKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGL I EV+SEGN+GLMQAVK+F+PERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLSIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLR++K  +QA+ D +L P+QV  IA KLNVSE EV+SMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRKMKSKIQALDDGDLNPDQVKQIATKLNVSEDEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA + +S+  S +WQDWLV D + QEQVLIE++E ++RR+ML ++M  LN RER
Sbjct: 181 SGDASLNAPLRASEGESGEWQDWLVDDSNSQEQVLIEQDELESRRSMLEQAMETLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           RIFEARRL E P+TLE+LS EF +SRERVRQIE RAF+
Sbjct: 241 RIFEARRLAEEPMTLEDLSGEFGISRERVRQIEVRAFE 278


>gi|39933444|ref|NP_945720.1| RNA polymerase factor sigma-32 [Rhodopseudomonas palustris CGA009]
 gi|192288802|ref|YP_001989407.1| RNA polymerase factor sigma-32 [Rhodopseudomonas palustris TIE-1]
 gi|39647290|emb|CAE25811.1| RNA polymerase sigma 32 subunit, RpoH, stress response sigma factor
           [Rhodopseudomonas palustris CGA009]
 gi|192282551|gb|ACE98931.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodopseudomonas palustris
           TIE-1]
          Length = 299

 Score =  313 bits (803), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 189/285 (66%), Positives = 227/285 (79%), Gaps = 1/285 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R     I+NGE GL+RY+ EIRK PMLE Q+EY+LAKR+REHGD  AAH+LVTSHLRL
Sbjct: 1   MARAATLPILNGESGLARYLAEIRKFPMLEPQQEYMLAKRWREHGDRDAAHQLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPISEVVSEGN+GLMQAVK+F+PE+GFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQK+LFFNLR+ K  + A+ + +L P+QV  IA +L V+E +V+ MN RL
Sbjct: 121 WSLVKMGTTANQKKLFFNLRKAKSKISALDEGDLHPDQVKLIATRLGVTEQDVVDMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA I   D    +WQDWLV     QE V+ E EE   RR  L  ++ VLNPRER
Sbjct: 181 GGDASLNAPIRD-DGEPGEWQDWLVDQSPSQEAVMAEHEELDQRRAALNGAIQVLNPRER 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           RIFEARRL + P+TLE+L+SEF VSRERVRQIE RAF+KVQ +++
Sbjct: 240 RIFEARRLADEPMTLEDLASEFGVSRERVRQIEVRAFEKVQSAVK 284


>gi|315498780|ref|YP_004087584.1| RNA polymerase, sigma 32 subunit, rpoh [Asticcacaulis excentricus
           CB 48]
 gi|315416792|gb|ADU13433.1| RNA polymerase, sigma 32 subunit, RpoH [Asticcacaulis excentricus
           CB 48]
          Length = 344

 Score =  313 bits (803), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 175/285 (61%), Positives = 221/285 (77%), Gaps = 3/285 (1%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
             +++ + GL+RY+ EIRK PML K EE++LAKR+ EH D  AAH+LVTSHLRLV KIAM
Sbjct: 60  PSVLSPDGGLNRYLSEIRKFPMLAKDEEFMLAKRWAEHADPKAAHKLVTSHLRLVAKIAM 119

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           GYRGYGLPI EV+SEGN+GLMQAVKKFDP++GFRLATY+MWWIKAA+QEY+LRSWSLVK+
Sbjct: 120 GYRGYGLPIGEVISEGNVGLMQAVKKFDPDKGFRLATYAMWWIKAAIQEYVLRSWSLVKM 179

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DES 185
           GTTA QK+LFFNLR++K  + A+ + +++ EQV  IA KL VSE +VISMN R++  D S
Sbjct: 180 GTTAAQKKLFFNLRKVKSEISALEEGDMRHEQVAQIATKLGVSEDDVISMNRRMSSPDSS 239

Query: 186 LNALINSSDKNSSQWQDWLVYDH-DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           LNA +  S+ + S+WQDWL  D    QE VL + EE K R ++L  +M  LN RER I  
Sbjct: 240 LNAPLRVSEGD-SEWQDWLADDSTPSQETVLADSEEYKLRMSLLEEAMGELNERERAILT 298

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           ARRLQENP TLE+L+  F VSRERVRQIE RAF+K+Q+++    +
Sbjct: 299 ARRLQENPTTLEDLADRFGVSRERVRQIEVRAFEKLQKAMMASAQ 343


>gi|319408110|emb|CBI81763.1| RNA polymerase sigma-32 factor [Bartonella schoenbuchensis R1]
          Length = 308

 Score =  313 bits (802), Expect = 2e-83,   Method: Composition-based stats.
 Identities = 185/288 (64%), Positives = 235/288 (81%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M   N+  I+ G+ GL+RY+ EIR+ PML+ +EEY+LAKRYREH D  AAH+LVTSHLRL
Sbjct: 1   MAHVNLPSIIAGDGGLNRYLEEIRRFPMLKPKEEYMLAKRYREHDDPKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIA+GYRGYGLPI EV+SEGNIGLMQAVK+F+PERGFRLATY+MWWIKA++QEY+LRS
Sbjct: 61  VAKIAIGYRGYGLPIGEVISEGNIGLMQAVKRFEPERGFRLATYAMWWIKASIQEYVLRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLR+LK  LQA+ + +L  EQV  IA +LNV+E EV+SMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRKLKNKLQALDNGDLNAEQVKEIATRLNVTEDEVVSMNHRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA + + +   ++WQDWLV D + QEQ+LIE++E +NRR+ML  ++  LN RE+
Sbjct: 181 SGDTSLNAPLRTKEGEKTEWQDWLVDDSNSQEQILIEQDELENRRSMLIHAIDNLNEREK 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            IF+ARRL +  +TLE LS+ F +SRERVRQIE RAF+KV+ SI+  +
Sbjct: 241 HIFKARRLSDESLTLEELSNTFNISRERVRQIEMRAFEKVRNSIKAAI 288


>gi|90418989|ref|ZP_01226900.1| sigma factor [Aurantimonas manganoxydans SI85-9A1]
 gi|90337069|gb|EAS50774.1| sigma factor [Aurantimonas manganoxydans SI85-9A1]
          Length = 303

 Score =  312 bits (801), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 194/285 (68%), Positives = 235/285 (82%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M + N+  I +GE GLSRY+ EIR+ PMLE QEEY+LAKRY EH D  AAHRLVTSHLRL
Sbjct: 1   MAQANLPSISSGEAGLSRYLEEIRRFPMLEPQEEYMLAKRYAEHDDRDAAHRLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EVVSEGN+GLMQAVK+FDPERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKRFDPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLR++K  +QA+ + +L+P+QV  IA  L VS+ EV+SMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRKMKSRIQALDEGDLRPDQVSQIATNLGVSDEEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA + +++  S +WQDWLV D + QE +L   +E   RR ML ++M VLN RER
Sbjct: 181 SGDASLNAPLRATEGESGEWQDWLVDDSETQEDLLARNDELDQRRGMLQQAMGVLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           RIFEARRL E+P+TLE LS EFE+SRERVRQIE RAF+KVQ++++
Sbjct: 241 RIFEARRLAEDPLTLETLSGEFEISRERVRQIEVRAFEKVQKAVR 285


>gi|148257972|ref|YP_001242557.1| RNA polymerase factor sigma-32 [Bradyrhizobium sp. BTAi1]
 gi|146410145|gb|ABQ38651.1| RNA polymerase, sigma 32 subunit, RpoH [Bradyrhizobium sp. BTAi1]
          Length = 299

 Score =  312 bits (801), Expect = 3e-83,   Method: Composition-based stats.
 Identities = 185/296 (62%), Positives = 230/296 (77%), Gaps = 1/296 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R     ++NGE GL+RY+ EIRK PMLE QEEY+LAKR+REH D  AA +LVTSHLRL
Sbjct: 1   MARTATLPVLNGESGLARYLAEIRKFPMLEPQEEYMLAKRWREHDDSDAAQKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPISEVVSEGN+GLMQAVK+F+PE+GFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQK+LFFNLR+ K  + A+ + +L P+QV  IAK+L V++ +V+ MN RL
Sbjct: 121 WSLVKMGTTANQKKLFFNLRKAKSRISALDEGDLHPDQVKLIAKRLGVTDQDVVDMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA I   D  + +WQDWLV     QE ++ E EE  +RR  L  ++ VLN RER
Sbjct: 181 GGDASLNAPIRD-DGEAGEWQDWLVDTSPNQEAIMAEHEEYDHRRQALNGAIGVLNARER 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPL 296
           RIFEARRL + P+TLE+L++EF VSRERVRQIE RAF+KVQ +++  +    +  L
Sbjct: 240 RIFEARRLADEPMTLEDLAAEFGVSRERVRQIEVRAFEKVQSAVKGAIAKQEAAAL 295


>gi|254703436|ref|ZP_05165264.1| RNA polymerase factor sigma-32 [Brucella suis bv. 3 str. 686]
 gi|261754065|ref|ZP_05997774.1| RNA polymerase factor sigma-32 [Brucella suis bv. 3 str. 686]
 gi|261743818|gb|EEY31744.1| RNA polymerase factor sigma-32 [Brucella suis bv. 3 str. 686]
          Length = 300

 Score =  312 bits (800), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 191/273 (69%), Positives = 231/273 (84%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +  I +G+ GL+RY+ EIR+ PMLE QEEY+LAKRY EH D  AAH+LVTSHLRLV KIA
Sbjct: 3   LPSITSGDGGLTRYLEEIRRFPMLEPQEEYMLAKRYHEHADPKAAHKLVTSHLRLVAKIA 62

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
           MGYRGYGLPI EV+SEGN+GLMQAVK+F+PERGFRLATY+MWWIKA++QEYILRSWSLVK
Sbjct: 63  MGYRGYGLPIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWWIKASIQEYILRSWSLVK 122

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           +GTTANQKRLFFNLR++K  +QA+ D +L P+QV  IA KLNVSE EV+SMN RL+GD S
Sbjct: 123 MGTTANQKRLFFNLRKMKSKIQALDDGDLNPDQVKQIATKLNVSEDEVVSMNRRLSGDAS 182

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           LNA + +S+  S +WQDWLV D + QEQVLIE++E ++RR+ML ++M  LN RERRIFEA
Sbjct: 183 LNAPLRASEGESGEWQDWLVDDSNSQEQVLIEQDELESRRSMLEQAMETLNDRERRIFEA 242

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           RRL E P+TLE+LS EF +SRERVRQIE RAF+
Sbjct: 243 RRLAEEPMTLEDLSGEFGISRERVRQIEVRAFE 275


>gi|86747581|ref|YP_484077.1| RNA polymerase factor sigma-32 [Rhodopseudomonas palustris HaA2]
 gi|86570609|gb|ABD05166.1| sigma 32 (RpoH) [Rhodopseudomonas palustris HaA2]
          Length = 299

 Score =  312 bits (800), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 185/285 (64%), Positives = 226/285 (79%), Gaps = 1/285 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R     ++NGE GL+RY+ EIRK PMLE Q+EY+ AKR+REH D  AAH LVTSHLRL
Sbjct: 1   MARAATLPVLNGESGLARYLAEIRKFPMLEPQQEYMFAKRWREHDDRDAAHHLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPISEVVSEGN+GLMQAVK+F+P++GFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPDKGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQK+LFFNLR+ K  + A+ + ++ P+QV  IAK+L V+E +VI MN RL
Sbjct: 121 WSLVKMGTTANQKKLFFNLRKAKSKISALDEGDMHPDQVKLIAKRLGVTEQDVIDMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA I   D    +WQDWLV     QE V+ E EE  +RR  L  ++ VLNPRER
Sbjct: 181 GGDASLNAPIRD-DGEPGEWQDWLVDQSPNQEAVMAEHEELDHRRAALNGAIGVLNPRER 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           RIFEARRL + P+TLE+L++EF VSRERVRQIE RAF+KVQ +++
Sbjct: 240 RIFEARRLADEPMTLEDLAAEFGVSRERVRQIEVRAFEKVQSAVK 284


>gi|256370062|ref|YP_003107573.1| RNA polymerase factor sigma-32 [Brucella microti CCM 4915]
 gi|256000225|gb|ACU48624.1| RNA polymerase factor sigma-32 [Brucella microti CCM 4915]
          Length = 303

 Score =  312 bits (800), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 191/278 (68%), Positives = 232/278 (83%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M +  +  I +G+ GL+RY+ EIR+ PMLE QEEY+LAKRY EH D  AAH+LVTSHLRL
Sbjct: 1   MAQMKLPSITSGDGGLTRYLEEIRRFPMLEPQEEYMLAKRYHEHADPKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVK+F+PERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLR++K  +QA+ D +L P+QV  IA KLNVSE EV+SMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRKMKSKIQALDDGDLNPDQVKQIATKLNVSEDEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA + +S+  S +WQD LV D + QEQVLIE++E ++RR+ML ++M  LN RER
Sbjct: 181 SGDASLNAPLRASEGESGEWQDRLVDDSNSQEQVLIEQDELESRRSMLEQAMETLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           RIFEARRL E P+TLE+LS EF +SRERVRQIE RAF+
Sbjct: 241 RIFEARRLAEEPMTLEDLSGEFGISRERVRQIEVRAFE 278


>gi|90422128|ref|YP_530498.1| RNA polymerase factor sigma-32 [Rhodopseudomonas palustris BisB18]
 gi|90104142|gb|ABD86179.1| sigma 32 (RpoH) [Rhodopseudomonas palustris BisB18]
          Length = 299

 Score =  312 bits (800), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 186/285 (65%), Positives = 227/285 (79%), Gaps = 1/285 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R     ++NGE GLSRY+ EIRK PMLE Q+EY+ AKR+REH D  AAH LVTSHLRL
Sbjct: 1   MARAATLPVLNGESGLSRYLAEIRKFPMLEPQQEYMFAKRWREHDDRDAAHHLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPISEVVSEGN+GLMQAVK+F+PE+GFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQK+LFFNLR+ K  + A+ + ++ P+QV  IAK+L V+E +V+ MN RL
Sbjct: 121 WSLVKMGTTANQKKLFFNLRKAKSKISALDEGDMHPDQVKLIAKRLGVTEQDVVDMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA I   D    +WQDWLV     QE ++ E EE  +RR  LT ++ VLNPRER
Sbjct: 181 GGDASLNAPIRD-DGEPGEWQDWLVDHSPNQEAIMAEHEELDHRRAALTGAIGVLNPRER 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           RIFEARRL + P+TLE+L++EF VSRERVRQIE RAF+KVQ +++
Sbjct: 240 RIFEARRLADEPMTLEDLAAEFGVSRERVRQIEVRAFEKVQSAVK 284


>gi|312114652|ref|YP_004012248.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodomicrobium vannielii
           ATCC 17100]
 gi|311219781|gb|ADP71149.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodomicrobium vannielii
           ATCC 17100]
          Length = 308

 Score =  312 bits (800), Expect = 4e-83,   Method: Composition-based stats.
 Identities = 180/286 (62%), Positives = 223/286 (77%), Gaps = 1/286 (0%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
            V    GL+RY+ EIR+ PMLE Q+EY+LAKR++EH D  AA +LVTSHLRLV +IAMGY
Sbjct: 6   SVAASGGLARYLEEIRRFPMLEPQQEYMLAKRWQEHEDAKAAQKLVTSHLRLVARIAMGY 65

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           RGYGLPI EV+SEGN+GLMQAVK+FDP++GFRLATY+MWWI+AA+QEYILRSWSLVK+GT
Sbjct: 66  RGYGLPIGEVISEGNVGLMQAVKRFDPDKGFRLATYAMWWIRAAIQEYILRSWSLVKMGT 125

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           TA+QK+LFFNLR+ K  LQA+ + +L+P+QV  IA  L V E +V+SMN RL GD SLNA
Sbjct: 126 TASQKKLFFNLRKAKSQLQALEEGDLRPDQVKTIATNLGVPEEDVVSMNRRLGGDASLNA 185

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +  +D  S +WQDWLV +   QE  L E EE   RR  L  +M  LN RERRIF ARRL
Sbjct: 186 PLR-ADSESGEWQDWLVDEGPNQETQLAESEELSRRREYLGAAMDSLNERERRIFTARRL 244

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSP 294
            ++P+TLE LSSEF VSRER+RQIE RAF+KVQ+++QK    + +P
Sbjct: 245 ADDPLTLEELSSEFNVSRERIRQIEVRAFEKVQKAVQKAALKAEAP 290


>gi|91974840|ref|YP_567499.1| RNA polymerase factor sigma-32 [Rhodopseudomonas palustris BisB5]
 gi|91681296|gb|ABE37598.1| RNA polymerase sigma factor RpoH [Rhodopseudomonas palustris BisB5]
          Length = 299

 Score =  312 bits (799), Expect = 5e-83,   Method: Composition-based stats.
 Identities = 184/285 (64%), Positives = 225/285 (78%), Gaps = 1/285 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R     ++NGE GL+RY+ EIRK PMLE Q+EY+ AKR+REH D  AAH LVTSHLRL
Sbjct: 1   MARAATLPVLNGESGLARYLAEIRKFPMLEPQQEYMFAKRWREHDDRDAAHHLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPISEVVSEGN+GLMQAVK+F+P++GFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPDKGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQK+LFFNLR+ K  + A+ + ++ P+QV  IA +L V+E +VI MN RL
Sbjct: 121 WSLVKMGTTANQKKLFFNLRKAKSKISALDEGDMHPDQVKLIATRLGVTEQDVIDMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA I   D    +WQDWLV     QE V+ E EE  +RR  L  ++ VLNPRER
Sbjct: 181 GGDASLNAPIRD-DGEPGEWQDWLVDQSPSQEAVMAEHEELDHRRAALNGAIGVLNPRER 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           RIFEARRL + P+TLE+L++EF VSRERVRQIE RAF+KVQ +++
Sbjct: 240 RIFEARRLADEPMTLEDLAAEFGVSRERVRQIEVRAFEKVQSAVK 284


>gi|319405171|emb|CBI78776.1| RNA polymerase sigma-32 factor [Bartonella sp. AR 15-3]
          Length = 305

 Score =  311 bits (798), Expect = 6e-83,   Method: Composition-based stats.
 Identities = 185/285 (64%), Positives = 232/285 (81%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M   N+   +  +  L+RY+ EIR+ P+LE QEEY+LAKRY EH D  AAH+LVTSHLRL
Sbjct: 1   MAHINLPSFIANDNSLNRYLEEIRRFPILEPQEEYMLAKRYHEHNDPKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIA+GYRGYGLPI EV+SEGNIGLMQAVK+F+PERGFRLATY+MWWIKA++QEY+LRS
Sbjct: 61  VAKIAIGYRGYGLPIGEVISEGNIGLMQAVKRFEPERGFRLATYAMWWIKASIQEYVLRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVKIGTTANQKRLFFNLR+LK  LQ +   +L  +QV  IA +L V+E EV+SMN RL
Sbjct: 121 WSLVKIGTTANQKRLFFNLRKLKNKLQMLDSGDLNAQQVKEIATRLKVTEDEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA + ++   S +WQDWLV D + QEQ+LIE++E +NR ++L ++M  LN RE+
Sbjct: 181 SGDASLNAPLLTNKGESYEWQDWLVDDSNNQEQILIEQDELENRYSLLIQAMDNLNEREK 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           RIF+ARRL++ P+TLE LS+EF +SRERVRQIEARAF+KVQ SI+
Sbjct: 241 RIFKARRLRDEPLTLEELSNEFNISRERVRQIEARAFEKVQNSIK 285


>gi|319406710|emb|CBI80343.1| RNA polymerase sigma-32 factor [Bartonella sp. 1-1C]
          Length = 305

 Score =  311 bits (798), Expect = 7e-83,   Method: Composition-based stats.
 Identities = 181/285 (63%), Positives = 231/285 (81%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M   N+   +  + GL+RY+ EIR+ P+LE QEEY+LAKRY E+ D  AAH+LVTSHLRL
Sbjct: 1   MAHINLPSFIANDNGLNRYLEEIRRFPVLEPQEEYMLAKRYHEYNDPKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIA+GYRGYGLPI EV+SEGNIGLMQAVK+F+PERGFRLATY+MWWIKA++QEY+LRS
Sbjct: 61  VAKIAIGYRGYGLPIGEVISEGNIGLMQAVKRFEPERGFRLATYAMWWIKASIQEYVLRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVKIGTTANQKRLFFNLR+LK  LQ + + +L  +QV  IA +L V+E EV+SMN RL
Sbjct: 121 WSLVKIGTTANQKRLFFNLRKLKNKLQMLDNGDLNAQQVKEIATRLKVTEDEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA + ++   S +WQDWL+ D + QEQ LIE++E +NR ++L  +M  LN RE+
Sbjct: 181 NGDASLNAPLLTNKGESYEWQDWLIDDSNNQEQTLIEQDELENRYSILIHAMDNLNEREK 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           RIF+ARRL+++P+TLE LS+EF +SRERVRQIEARAF+K++  I+
Sbjct: 241 RIFKARRLRDDPLTLEELSNEFNISRERVRQIEARAFEKIKNFIK 285


>gi|300023529|ref|YP_003756140.1| RNA polymerase, sigma 32 subunit, RpoH [Hyphomicrobium
           denitrificans ATCC 51888]
 gi|299525350|gb|ADJ23819.1| RNA polymerase, sigma 32 subunit, RpoH [Hyphomicrobium
           denitrificans ATCC 51888]
          Length = 296

 Score =  310 bits (796), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 183/293 (62%), Positives = 227/293 (77%), Gaps = 1/293 (0%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
             K +  +  G +GLSRY+ EIRK PML   EEY+LAKR+++H D  AA +LVTSHLRLV
Sbjct: 3   ATKGLPTLAGGSLGLSRYLEEIRKFPMLAPNEEYMLAKRWQQHEDSDAAEKLVTSHLRLV 62

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            +IAMGYRGYGLPI EV+SEGN+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSW
Sbjct: 63  ARIAMGYRGYGLPIGEVISEGNVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSW 122

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
           SLVK+GTTA QK+LFFNLRR K  LQA+ D +L+PE V AIA KL V E +V+SMN RL 
Sbjct: 123 SLVKMGTTAAQKKLFFNLRRAKSQLQALDDGDLRPEHVKAIATKLGVPEEDVVSMNRRLG 182

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           GD SLNA I  ++  S +WQDWLV D   QE  L+E EE + R++ L+ ++SVLN RERR
Sbjct: 183 GDASLNAPIR-AESESGEWQDWLVDDTPTQEDRLVEDEELRRRKSYLSSALSVLNDRERR 241

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSP 294
           +FE RRL E P TLE LS+EF VSRER+RQIE RAF+KVQ+++      + +P
Sbjct: 242 VFEQRRLAEEPATLEELSAEFGVSRERIRQIEVRAFEKVQKAVTSTARRAEAP 294


>gi|49473931|ref|YP_031973.1| RNA polymerase factor sigma-32 [Bartonella quintana str. Toulouse]
 gi|49239434|emb|CAF25783.1| RNA polymerase sigma-32 factor [Bartonella quintana str. Toulouse]
          Length = 294

 Score =  310 bits (796), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 191/286 (66%), Positives = 234/286 (81%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M   N+  +  G+ GL+RY+ E+R+ P+LE +EEY+LA+RYR+H DL AAHRLVTSHLRL
Sbjct: 1   MAHINLLSVTTGDGGLNRYLEEVRRFPILEPKEEYMLAQRYRQHNDLKAAHRLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVK+F+PERG RLATY++WWIKA++QEY+LRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKRFEPERGLRLATYAIWWIKASIQEYVLRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVKIGTTANQKRLFFNLR+LK  LQ +   +L  EQV  IA +LNV+E EVISMN RL
Sbjct: 121 WSLVKIGTTANQKRLFFNLRKLKSRLQVLDKGDLNAEQVKEIATQLNVTEDEVISMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA + + +  +S+WQDWLV D + QEQ LIE+ E +NRR+MLT +MS LN RE+
Sbjct: 181 CGDTSLNAPLRTQEGENSEWQDWLVDDSNNQEQTLIEQSELENRRSMLTYAMSNLNEREK 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           RIF+ARRL + P+TLE LSSEF +SRERVRQIE RAF+KVQ SI+ 
Sbjct: 241 RIFKARRLSDKPLTLEELSSEFNISRERVRQIEMRAFEKVQNSIKA 286


>gi|154245929|ref|YP_001416887.1| RNA polymerase factor sigma-32 [Xanthobacter autotrophicus Py2]
 gi|154160014|gb|ABS67230.1| RNA polymerase, sigma 32 subunit, RpoH [Xanthobacter autotrophicus
           Py2]
          Length = 300

 Score =  310 bits (796), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 190/294 (64%), Positives = 232/294 (78%), Gaps = 1/294 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M +     I + E GLSRY+ EIR+ PMLE QEEY+LAK +REHGD  AAHRLVTSHLRL
Sbjct: 1   MAQPKSMSIPSAEGGLSRYLEEIRRFPMLEPQEEYMLAKSWREHGDRDAAHRLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPISEV+SEGN+GLMQAVK+F+PE+GFRLATY+MWWI+A++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPISEVISEGNVGLMQAVKRFEPEKGFRLATYAMWWIRASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTA QK+LFFNLR+ K  + A+ D +LKPE V  IA KL V+E +V+ MN RL
Sbjct: 121 WSLVKMGTTAAQKKLFFNLRKAKSQISALEDGDLKPEHVKQIATKLGVTEQDVVDMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLN+ I   D    +WQDWLV +   QE+ L E EE  NRR  L+ ++SVLN RER
Sbjct: 181 SGDASLNSPIR-EDSEGGEWQDWLVDERLDQEEQLAESEELDNRRAALSGALSVLNDRER 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSP 294
           RIFEARRL E+P+TLE+L+SEF VSRERVRQIE RAF+KVQ+++  +V    +P
Sbjct: 240 RIFEARRLSEDPMTLEDLASEFGVSRERVRQIEVRAFEKVQKAVMDKVRQVEAP 293


>gi|319403703|emb|CBI77288.1| RNA polymerase sigma-32 factor [Bartonella rochalimae ATCC
           BAA-1498]
          Length = 305

 Score =  310 bits (795), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 184/285 (64%), Positives = 231/285 (81%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M   N+   +  + GL+RY+ EIR+ P+LE QEEY+LAKRYRE+ D  AAH+LVTSHLRL
Sbjct: 1   MAHINLPSFIANDNGLNRYLEEIRRFPVLEPQEEYMLAKRYREYNDPKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIA+GYRGYGLPI EV+SEGNIGLMQAVK+F+PERGFRLATY+MWWIKA++QEY+LRS
Sbjct: 61  VAKIAIGYRGYGLPIGEVISEGNIGLMQAVKRFEPERGFRLATYAMWWIKASIQEYVLRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVKIGTTANQKRLFFNLR+LK  LQ + + +L  +QV  IA +L V+E EV+SMN RL
Sbjct: 121 WSLVKIGTTANQKRLFFNLRKLKNKLQMLDNGDLNAQQVKEIATRLKVTEDEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA + ++   S +WQDWLV D + QEQ LIE+ E +NR ++L  +M  LN RE+
Sbjct: 181 NGDASLNAPLLTNKGESYEWQDWLVDDSNNQEQTLIEQNELENRYSILIHAMDNLNEREK 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           RIF+ARRL+++P+TLE LS+EF +SRERVRQIEARAF+K+Q  I+
Sbjct: 241 RIFKARRLRDDPLTLEELSNEFNISRERVRQIEARAFEKIQNFIK 285


>gi|163867808|ref|YP_001609012.1| RNA polymerase factor sigma-32 [Bartonella tribocorum CIP 105476]
 gi|161017459|emb|CAK01017.1| RNA polymerase sigma-32 factor [Bartonella tribocorum CIP 105476]
          Length = 294

 Score =  310 bits (795), Expect = 1e-82,   Method: Composition-based stats.
 Identities = 192/285 (67%), Positives = 235/285 (82%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M   N+  I+ G+ GL+RY+ E+R+ PMLE +EEY+LA+RYREH DL AAHRLVTSHLRL
Sbjct: 1   MAHMNLLSIITGDGGLNRYLEEVRRFPMLEPKEEYMLAQRYREHNDLKAAHRLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V K+AMGYRGYGLPI EV+SEGNIGLMQAVK+F+PERGFRLATY++WWIKA++QEY+LRS
Sbjct: 61  VAKVAMGYRGYGLPIGEVISEGNIGLMQAVKRFEPERGFRLATYAIWWIKASIQEYVLRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLR+LK  LQA+   +L  EQV  IA +LNV+E EV+SMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRKLKNKLQALDSGDLNTEQVKEIATQLNVTEDEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA + + +  +S+ QDWLV + + QEQ+LIEK E +NRR ML  +M+ LN RER
Sbjct: 181 GGDTSLNAPLRTKEGENSELQDWLVDESNNQEQILIEKSELENRRFMLVNAMNNLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           RIF+ARRL + P+TLE LSSEF +SRERVRQIE RAF+KVQ SI+
Sbjct: 241 RIFKARRLNDIPLTLEELSSEFNISRERVRQIEMRAFEKVQNSIR 285


>gi|92118359|ref|YP_578088.1| RNA polymerase factor sigma-32 [Nitrobacter hamburgensis X14]
 gi|91801253|gb|ABE63628.1| RNA polymerase, sigma 32 subunit, RpoH [Nitrobacter hamburgensis
           X14]
          Length = 299

 Score =  309 bits (793), Expect = 3e-82,   Method: Composition-based stats.
 Identities = 187/285 (65%), Positives = 227/285 (79%), Gaps = 1/285 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R     I+NGE GLSRY+ EIRK PMLE  +EY+ AKR+REH D  AAH LVTSHLRL
Sbjct: 1   MARTATVPILNGESGLSRYLAEIRKFPMLEPHQEYMFAKRWREHDDREAAHHLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPISEVVSEGN+GLMQAVK+F+PE+GFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQK+LFFNLR+ K  + A+ + ++ P+QV  IAK+L V+E +V+ MN RL
Sbjct: 121 WSLVKMGTTANQKKLFFNLRKAKSKISALEEGDMHPDQVKLIAKRLGVTEQDVVDMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA I   D  + +WQDWLV     QE ++ E EE  +RR  LT +M VLNPRER
Sbjct: 181 GGDASLNAPIRD-DGEAGEWQDWLVDHSPTQEAIMAEHEELNHRRQALTGAMGVLNPRER 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           RIFEARRL + P+TLE+L++EF VSRERVRQIE RAF+KVQ +++
Sbjct: 240 RIFEARRLADEPMTLEDLAAEFNVSRERVRQIEVRAFEKVQSAVK 284


>gi|75676615|ref|YP_319036.1| RNA polymerase factor sigma-32 [Nitrobacter winogradskyi Nb-255]
 gi|74421485|gb|ABA05684.1| RNA polymerase, sigma 32 subunit, RpoH [Nitrobacter winogradskyi
           Nb-255]
          Length = 299

 Score =  309 bits (791), Expect = 4e-82,   Method: Composition-based stats.
 Identities = 187/285 (65%), Positives = 227/285 (79%), Gaps = 1/285 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R     ++NGE GLSRY+ EIRK PMLE  EEY+ AKR REH D  AAH LVTSHLRL
Sbjct: 1   MARTATLPVLNGENGLSRYLSEIRKFPMLEPHEEYMFAKRLREHDDRDAAHHLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPISEVVSEGN+GLMQAVK+F+PE+GFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQK+LFFNLR+ K  + A+ + +++P+QV  IAK+L V+E +V+ MN RL
Sbjct: 121 WSLVKMGTTANQKKLFFNLRKAKSKISALDEGDMRPDQVKLIAKRLGVTEQDVVDMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA I   D  + +WQDWLV     QE ++ E EE  +RR  LT +M VLNPRER
Sbjct: 181 GGDASLNAPIRD-DGEAGEWQDWLVDQSPNQEAIMAEHEEFDHRRRALTGAMGVLNPRER 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           RIFEARRL + P+TLE+L++EF VSRERVRQIE RAF+KVQ +++
Sbjct: 240 RIFEARRLADEPMTLEDLAAEFNVSRERVRQIEVRAFEKVQSAVK 284


>gi|240850016|ref|YP_002971409.1| RNA polymerase sigma-32 factor [Bartonella grahamii as4aup]
 gi|240267139|gb|ACS50727.1| RNA polymerase sigma-32 factor [Bartonella grahamii as4aup]
          Length = 294

 Score =  309 bits (791), Expect = 5e-82,   Method: Composition-based stats.
 Identities = 191/285 (67%), Positives = 234/285 (82%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M   N+  +  G+ GL+RY+ E+R  PML+ +EEY+LA+RYREH DL AAHRLVTSHLRL
Sbjct: 1   MAHMNLLSVTAGDGGLNRYLEEVRHFPMLDPKEEYMLAQRYREHNDLKAAHRLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVK+F+PERGFRLATY++WWIKA++QEY+LRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKRFEPERGFRLATYAIWWIKASIQEYVLRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLR+LK  LQA+ + +L  EQV  IA +LNVSE EVISMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRKLKSKLQALDNGDLNAEQVKEIATQLNVSEDEVISMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA + + +  +S+ QDWLV + + QEQVLIEK E +NRR+ML  +M  LN RE+
Sbjct: 181 GGDTSLNAPLRTKEGENSELQDWLVDESNDQEQVLIEKSELENRRSMLINAMDNLNEREK 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           RIF+ARRL + P+TLE LS EF +SRERVRQIE RAF+KVQ+SI+
Sbjct: 241 RIFKARRLNDIPLTLEELSGEFNISRERVRQIEMRAFEKVQDSIR 285


>gi|154252606|ref|YP_001413430.1| RNA polymerase sigma-32 subunit RpoH [Parvibaculum lavamentivorans
           DS-1]
 gi|154156556|gb|ABS63773.1| RNA polymerase, sigma 32 subunit, RpoH [Parvibaculum
           lavamentivorans DS-1]
          Length = 340

 Score =  308 bits (789), Expect = 7e-82,   Method: Composition-based stats.
 Identities = 180/281 (64%), Positives = 220/281 (78%), Gaps = 2/281 (0%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           ++   N E  LSRY+ EIRK PMLE QEEY+LAKR+REH D  AAH+LVTSHLRLV KIA
Sbjct: 44  LAPAPNPEGSLSRYLQEIRKFPMLEPQEEYMLAKRWREHEDTEAAHQLVTSHLRLVAKIA 103

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
           MGYRGYGLPI EV+SEGN+GLMQAVK+F+PERGFRLATY+MWWI+A++QEYILRSWSLVK
Sbjct: 104 MGYRGYGLPIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWWIRASIQEYILRSWSLVK 163

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DE 184
           +GTTA QK+LFFNLR++KG +QAI + +L PEQV  I+ +L V+E EVISMN RL+G D 
Sbjct: 164 MGTTAAQKKLFFNLRKVKGQIQAIEEGDLHPEQVKVISDRLGVTEDEVISMNRRLSGPDN 223

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SLNA +   D    +WQDWLV D   QE  L E EE   RR ML  +M+ LN RE  I  
Sbjct: 224 SLNAPLRQ-DSEGGEWQDWLVDDTADQEATLGEAEELDQRREMLAAAMATLNEREMHILT 282

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            RRL++ P TLE+LS E+ +SRERVRQIE RAF+K+Q++++
Sbjct: 283 ERRLKDEPATLEDLSQEYGISRERVRQIEVRAFEKLQKAMK 323


>gi|103487228|ref|YP_616789.1| RNA polymerase factor sigma-32 [Sphingopyxis alaskensis RB2256]
 gi|98977305|gb|ABF53456.1| RNA polymerase sigma factor RpoH [Sphingopyxis alaskensis RB2256]
          Length = 300

 Score =  305 bits (783), Expect = 3e-81,   Method: Composition-based stats.
 Identities = 172/290 (59%), Positives = 221/290 (76%), Gaps = 7/290 (2%)

Query: 2   NRKNMSIIVN---GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHL 58
           N+ N+  +V    GE  L+RY+ EIRK P+L  ++EY+LAKR++EHGD  AA +LVTSHL
Sbjct: 3   NKSNVPAVVPALGGEASLNRYLAEIRKFPLLTPEQEYMLAKRFQEHGDNEAAAQLVTSHL 62

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLV KIAMGYRGYGLP+SE++SEGNIGLMQ VKKFDPERGFRLATY+MWWI+A++QE+IL
Sbjct: 63  RLVAKIAMGYRGYGLPVSELISEGNIGLMQGVKKFDPERGFRLATYAMWWIRASIQEFIL 122

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
           RSWSLVK+GTTA QK+LFFNLRR+K +L+A  D +L PE V  IA  L V+E EV+SMN 
Sbjct: 123 RSWSLVKMGTTAAQKKLFFNLRRMKNNLEAFEDGDLSPEHVAKIATDLGVTEDEVVSMNR 182

Query: 179 RLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
           R+A  GD SLN  +   +   SQWQD L  D   Q++ + E +ER  R ++LT ++  LN
Sbjct: 183 RMAMGGDTSLNVPM--GEDGDSQWQDLLGDDGPLQDERVAEAQERDVRHDLLTEALETLN 240

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            RER I   RRL ++P TLE+LS  ++VSRERVRQIE RAF+K+Q+++ K
Sbjct: 241 ERERHILTERRLTDDPKTLEDLSQLYDVSRERVRQIEVRAFEKLQKAMLK 290


>gi|121602451|ref|YP_988610.1| RNA polymerase factor sigma-32 [Bartonella bacilliformis KC583]
 gi|120614628|gb|ABM45229.1| RNA polymerase sigma-32 factor [Bartonella bacilliformis KC583]
          Length = 303

 Score =  305 bits (783), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 186/286 (65%), Positives = 231/286 (80%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M   ++  I   + GLSRY+ EIR+ P+LE +EEY+L KRY EH DL AAH+LVTSHLRL
Sbjct: 1   MAHISLPSIAANDGGLSRYLEEIRRFPILEPKEEYMLVKRYNEHNDLKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIA+GYRGYGLP+ EV+SEGNIGLMQAVK+F+PERGFRLATY+MWWIKA++QEY+LRS
Sbjct: 61  VAKIAIGYRGYGLPMGEVISEGNIGLMQAVKRFEPERGFRLATYAMWWIKASIQEYVLRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVKIGTT NQKRLFFNLR+LK  LQA+ +  L  EQV  IA +LNV+E EV+SMN RL
Sbjct: 121 WSLVKIGTTTNQKRLFFNLRKLKSKLQALDNGELNTEQVKEIATRLNVTEDEVVSMNHRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA + +++   S+WQD LV +   QEQVLIEK+E +NRR++L  +M+ LN RE+
Sbjct: 181 SGDTSLNAPLRTNEDEHSEWQDCLVDEASSQEQVLIEKDELENRRSLLIHAMANLNEREK 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           RIFEARRL +  +TLE LSSEF +SRERVRQIE RAF+KVQ+ ++ 
Sbjct: 241 RIFEARRLSDEVLTLEELSSEFNISRERVRQIEMRAFEKVQDFVRA 286


>gi|304393314|ref|ZP_07375242.1| alternative sigma factor RpoH [Ahrensia sp. R2A130]
 gi|303294321|gb|EFL88693.1| alternative sigma factor RpoH [Ahrensia sp. R2A130]
          Length = 300

 Score =  305 bits (783), Expect = 4e-81,   Method: Composition-based stats.
 Identities = 190/295 (64%), Positives = 231/295 (78%), Gaps = 1/295 (0%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
             +  I     GL RY+ EIRK PML+  EEY+L KRY EH D  AAH++VTSHLRLV K
Sbjct: 3   NTLPSISASGNGLQRYMEEIRKFPMLKPDEEYMLGKRYSEHDDTEAAHKMVTSHLRLVAK 62

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IAMGYRGYGLP+SEV+SEGN+GLMQAVKKFDPE+GFRLATY+MWWIKA++QEY+LRSWSL
Sbjct: 63  IAMGYRGYGLPVSEVISEGNVGLMQAVKKFDPEKGFRLATYAMWWIKASIQEYVLRSWSL 122

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VK+GTTANQKRLFFNLR+LKG L+A+ +  LK E V  IA  L VS  EV SMN RL+GD
Sbjct: 123 VKMGTTANQKRLFFNLRKLKGKLKALEEGELKQENVEKIASTLGVSHDEVRSMNQRLSGD 182

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SLNA I +++  S QWQDWLV D + QEQ+LI+++E   RR+ML  +M VLN RE+RIF
Sbjct: 183 ASLNAPIKAAEGESGQWQDWLVDDSESQEQMLIKQDELDVRRDMLAEAMDVLNDREKRIF 242

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI-QKQVELSSSPPLL 297
            ARRL+E+P+TLE LS EF++SRERVRQIE RAF+KVQ+++     EL+   P L
Sbjct: 243 MARRLEEDPLTLEVLSGEFDISRERVRQIEVRAFEKVQKAMVTANKELAKPAPQL 297


>gi|170752008|ref|YP_001758268.1| RNA polymerase factor sigma-32 [Methylobacterium radiotolerans JCM
           2831]
 gi|170658530|gb|ACB27585.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium
           radiotolerans JCM 2831]
          Length = 297

 Score =  305 bits (781), Expect = 6e-81,   Method: Composition-based stats.
 Identities = 185/286 (64%), Positives = 228/286 (79%), Gaps = 2/286 (0%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           ++  E GLSRY+ EIRK PMLE  EE+ LAK +R+ GD  AAHRLVTSHLRLV KIAMGY
Sbjct: 7   VLANEGGLSRYLDEIRKFPMLEPSEEFTLAKAWRDAGDREAAHRLVTSHLRLVAKIAMGY 66

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           RGYGLPI EVVSEGN+GLMQAVK+FDP++GFRLATY+MWWIKAA+QEYILRSWSLVK+GT
Sbjct: 67  RGYGLPIGEVVSEGNVGLMQAVKRFDPDKGFRLATYAMWWIKAAIQEYILRSWSLVKMGT 126

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           TANQK+LFFNLR+ KG + A+ + +LKP+QV  IA +L V E +VI MN RL+GD SLNA
Sbjct: 127 TANQKKLFFNLRKAKGKISALDEGDLKPDQVKQIATRLGVPEQDVIDMNRRLSGDTSLNA 186

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +   ++   +WQDWLV +   QE VL  ++E +NR + L  ++ VLNPRERRIFEARRL
Sbjct: 187 PLR--EEGEGEWQDWLVDNSPSQETVLAREQEGQNRLSALKDALGVLNPRERRIFEARRL 244

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSP 294
            E+P+TLE+LS EF VSRERVRQIE RAF+KVQE++++ +     P
Sbjct: 245 AEDPITLEDLSGEFGVSRERVRQIEVRAFEKVQEAVKRNIATRELP 290


>gi|170744871|ref|YP_001773526.1| RNA polymerase factor sigma-32 [Methylobacterium sp. 4-46]
 gi|168199145|gb|ACA21092.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium sp. 4-46]
          Length = 296

 Score =  304 bits (780), Expect = 8e-81,   Method: Composition-based stats.
 Identities = 188/280 (67%), Positives = 229/280 (81%), Gaps = 2/280 (0%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           ++  E GLSRY+ EIR+ PMLE  EEY+LAK +REHGD  AAH+LVTSHLRLV KIAMGY
Sbjct: 7   VLANEGGLSRYLDEIRRFPMLEPTEEYMLAKSWREHGDREAAHKLVTSHLRLVAKIAMGY 66

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           RGYGLPI EVVSEGN+GLMQAVK+FDP++GFRLATY+MWWIKAA+QEYILRSWSLVK+GT
Sbjct: 67  RGYGLPIGEVVSEGNVGLMQAVKRFDPDKGFRLATYAMWWIKAAIQEYILRSWSLVKMGT 126

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           TANQK+LFFNLR+ KG + A+ + +L+PEQV  IA +L V E +VI MN RL+GD SLNA
Sbjct: 127 TANQKKLFFNLRKAKGRISALDEGDLRPEQVKQIATRLGVPEQDVIEMNRRLSGDASLNA 186

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +   ++   +WQDWLV D   QE VL  +EE +NR   L  ++SVLNPRERRIFEARRL
Sbjct: 187 PLR--EEGEGEWQDWLVDDSPSQEAVLAREEEGQNRLAALRDALSVLNPRERRIFEARRL 244

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            E P+TLE+LSSEF VSRERVRQIE RAF+KVQ+++++ +
Sbjct: 245 AEEPITLEDLSSEFGVSRERVRQIEVRAFEKVQDAVKRNL 284


>gi|220927320|ref|YP_002502622.1| RNA polymerase factor sigma-32 [Methylobacterium nodulans ORS 2060]
 gi|219951927|gb|ACL62319.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium nodulans
           ORS 2060]
          Length = 296

 Score =  304 bits (780), Expect = 9e-81,   Method: Composition-based stats.
 Identities = 187/280 (66%), Positives = 229/280 (81%), Gaps = 2/280 (0%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           ++  E GLSRY+ EIR+ PMLE  EEY+LAK +REHGD  AAH+LVTSHLRLV KIAMGY
Sbjct: 7   VLANEGGLSRYLDEIRRFPMLEPTEEYMLAKSWREHGDREAAHKLVTSHLRLVAKIAMGY 66

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           RGYGLPI EVVSEGN+GLMQAVK+FDP++GFRLATY+MWWIKAA+QEYILRSWSLVK+GT
Sbjct: 67  RGYGLPIGEVVSEGNVGLMQAVKRFDPDKGFRLATYAMWWIKAAIQEYILRSWSLVKMGT 126

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           TANQK+LFFNLR+ KG + A+ + +L+PEQV  IA +L V E +VI MN RL+GD SLNA
Sbjct: 127 TANQKKLFFNLRKAKGRISALDEGDLRPEQVKQIATRLGVPEQDVIDMNRRLSGDASLNA 186

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +   ++   +WQDWLV D   QE VL  +EE +NR   L  ++SVLNPRERRIFEARRL
Sbjct: 187 PLR--EEGEGEWQDWLVDDSPSQEAVLAREEEGQNRLAALRDALSVLNPRERRIFEARRL 244

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            E P+TLE+LS+EF VSRERVRQIE RAF+KVQ+++++ +
Sbjct: 245 AEEPITLEDLSTEFGVSRERVRQIEVRAFEKVQDAVKRNL 284


>gi|162148038|ref|YP_001602499.1| RNA polymerase factor sigma-32 [Gluconacetobacter diazotrophicus
           PAl 5]
 gi|161786615|emb|CAP56197.1| putative RNA polymerase sigma-32 factor [Gluconacetobacter
           diazotrophicus PAl 5]
          Length = 325

 Score =  304 bits (779), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 172/289 (59%), Positives = 220/289 (76%), Gaps = 3/289 (1%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           +  +  + V  E  LSRY+ +IRK PML  ++E  L++R+++ GD  AAH LVTSHLRLV
Sbjct: 30  SMASSVLNVGPESNLSRYLQDIRKFPMLSPEDEQRLSRRWKDKGDTEAAHALVTSHLRLV 89

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            KIAMGYRGYGLP+ E++SEGNIG+MQAV++FDP+RGFRLATY+MWWI+AA+QEYIL SW
Sbjct: 90  AKIAMGYRGYGLPLGELISEGNIGMMQAVRRFDPDRGFRLATYAMWWIRAAIQEYILHSW 149

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
           SLVK+GTTA QK+LFFNLRRLKG +QAI D +LKPEQV  IA+ L V E +VI+MN RL+
Sbjct: 150 SLVKMGTTAAQKKLFFNLRRLKGQMQAIDDGDLKPEQVNKIAESLGVPEQDVINMNRRLS 209

Query: 182 G-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
             D SLNA + +   +  +WQDWLV +HD QEQ L E EE   R+ +L  +M  LN RER
Sbjct: 210 APDHSLNAPLRA--DSEGEWQDWLVDEHDNQEQTLAENEEFSGRKALLDNAMKTLNDRER 267

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
            I   RRL+++P TLE LS  + +SRERVRQIE RAF+KVQ +++ +VE
Sbjct: 268 HILTERRLKDDPATLEELSHTYNISRERVRQIEVRAFEKVQAAMKAEVE 316


>gi|296445492|ref|ZP_06887449.1| RNA polymerase, sigma 32 subunit, RpoH [Methylosinus trichosporium
           OB3b]
 gi|296257058|gb|EFH04128.1| RNA polymerase, sigma 32 subunit, RpoH [Methylosinus trichosporium
           OB3b]
          Length = 294

 Score =  304 bits (778), Expect = 1e-80,   Method: Composition-based stats.
 Identities = 181/296 (61%), Positives = 235/296 (79%), Gaps = 3/296 (1%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
             N    ++G+ GLSRY+ EIR+ PMLE ++EY+LAKR+REH D +AA +LVTSHLRLV 
Sbjct: 1   MANALPTLSGDSGLSRYLAEIRRFPMLEPEQEYMLAKRWREHEDPNAAQKLVTSHLRLVA 60

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           KIAMGYRGYGLPI E+VSEGN+GLMQAVK+F+PERGFRLATY+MWWI+A++QEYILRSWS
Sbjct: 61  KIAMGYRGYGLPIGEIVSEGNVGLMQAVKRFEPERGFRLATYAMWWIRASIQEYILRSWS 120

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           LVK+GTTA+QK+LFFNLR+ K  + A  D +L PE V  IA++L V+  +VI MN R++G
Sbjct: 121 LVKMGTTASQKKLFFNLRKAKSKISAFEDGDLTPEHVGEIARRLGVTNQDVIEMNRRMSG 180

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
           D SLNA +   ++   +WQDWLV D   QE++L+++EE  NR + L  +++VLNPRERRI
Sbjct: 181 DASLNAPLR--EEGEGEWQDWLVDDSSDQERILVDQEEAGNRLDALRGALTVLNPRERRI 238

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK-QVELSSSPPLL 297
           FEARRL E+PVTLE+LS+EF VSRERVRQIE RAF+KVQ +++    +L + P  +
Sbjct: 239 FEARRLSEDPVTLEDLSTEFGVSRERVRQIEVRAFEKVQSAVRAGMAQLEALPAPM 294


>gi|114327512|ref|YP_744669.1| RNA polymerase sigma-32 factor [Granulibacter bethesdensis CGDNIH1]
 gi|114315686|gb|ABI61746.1| RNA polymerase sigma-32 factor [Granulibacter bethesdensis CGDNIH1]
          Length = 375

 Score =  303 bits (777), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 168/282 (59%), Positives = 216/282 (76%), Gaps = 3/282 (1%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           I +  E  LSRY+ EIRK PML  +EE  L++R+R+  D+ AAHRLVTSHLRLV KIAMG
Sbjct: 76  IKIAPEGNLSRYLQEIRKYPMLTPEEELDLSRRWRDTEDMGAAHRLVTSHLRLVAKIAMG 135

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           YRGYGLP+ E++SEGN+G+MQAV++FDP+RGFRLATY+MWWI+AA+QEYIL SWSLVK+G
Sbjct: 136 YRGYGLPVGELISEGNVGMMQAVRRFDPDRGFRLATYAMWWIRAAIQEYILHSWSLVKMG 195

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESL 186
           TTA QK+LFFNLRRLKG +QAI D +LKPEQV  IA  LNV E +V+ MN R++  D SL
Sbjct: 196 TTAAQKKLFFNLRRLKGQMQAIDDGDLKPEQVSKIATSLNVPEQDVVQMNRRMSAPDHSL 255

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           NA +    +   +WQDWLV D + QE VL + EE   R+ +L  ++  LN RER I   R
Sbjct: 256 NAPLRQ--EGEGEWQDWLVDDAETQETVLADTEELGGRKTLLANALKTLNDRERHILTER 313

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RL++ P TLE+LS  + +SRERVRQIE RAF+K+Q++++ +V
Sbjct: 314 RLKDEPTTLEDLSQHYNISRERVRQIEVRAFEKLQKAMKAEV 355


>gi|85707639|ref|ZP_01038705.1| RNA polymerase sigma factor [Erythrobacter sp. NAP1]
 gi|85689173|gb|EAQ29176.1| RNA polymerase sigma factor [Erythrobacter sp. NAP1]
          Length = 298

 Score =  303 bits (776), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 162/288 (56%), Positives = 216/288 (75%), Gaps = 3/288 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M++  +  + +GE  L+RY+ EI+K P+L  ++EY+LAKRY EH D  AA +LV+SHLRL
Sbjct: 1   MSKATVPAL-SGEQSLNRYLSEIKKYPVLTAEQEYMLAKRYAEHEDPEAASQLVSSHLRL 59

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLP+S+++SEGN+GLMQ VKKF+P+RGFRLATY+MWWIKA++QEYILRS
Sbjct: 60  VAKIAMGYRGYGLPVSDLISEGNVGLMQGVKKFEPDRGFRLATYAMWWIKASIQEYILRS 119

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR- 179
           WSLVK+GTTA QK+LFFNLRR+K  L+A  D++L P+ V  IA  L V E EV++MN R 
Sbjct: 120 WSLVKMGTTAAQKKLFFNLRRMKKQLEAYEDSDLHPDDVTKIATDLGVPEQEVVNMNRRM 179

Query: 180 -LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
            + GD SLN  + + +  S +WQDWL  D   Q++ + + EE + R  ML  +M  LN R
Sbjct: 180 MMGGDGSLNTPMRNGEDGSGEWQDWLTDDRPLQDETVADAEEAEVRHEMLVEAMDSLNER 239

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E+ I   RRL E P TLE LS  ++VSRER+RQIE RAF+K+Q+++Q+
Sbjct: 240 EQHILTERRLTEKPQTLEELSQVYDVSRERIRQIEVRAFEKLQKAMQR 287


>gi|258543198|ref|YP_003188631.1| RNA polymerase factor sigma-32 [Acetobacter pasteurianus IFO
           3283-01]
 gi|256634276|dbj|BAI00252.1| DNA-directed RNA polymerase Heat shock sigma factor RpoH
           [Acetobacter pasteurianus IFO 3283-01]
 gi|256637336|dbj|BAI03305.1| DNA-directed RNA polymerase Heat shock sigma factor RpoH
           [Acetobacter pasteurianus IFO 3283-03]
 gi|256640388|dbj|BAI06350.1| DNA-directed RNA polymerase Heat shock sigma factor RpoH
           [Acetobacter pasteurianus IFO 3283-07]
 gi|256643445|dbj|BAI09400.1| DNA-directed RNA polymerase Heat shock sigma factor RpoH
           [Acetobacter pasteurianus IFO 3283-22]
 gi|256646500|dbj|BAI12448.1| DNA-directed RNA polymerase Heat shock sigma factor RpoH
           [Acetobacter pasteurianus IFO 3283-26]
 gi|256649553|dbj|BAI15494.1| DNA-directed RNA polymerase Heat shock sigma factor RpoH
           [Acetobacter pasteurianus IFO 3283-32]
 gi|256652539|dbj|BAI18473.1| DNA-directed RNA polymerase Heat shock sigma factor RpoH
           [Acetobacter pasteurianus IFO 3283-01-42C]
 gi|256655597|dbj|BAI21524.1| DNA-directed RNA polymerase Heat shock sigma factor RpoH
           [Acetobacter pasteurianus IFO 3283-12]
          Length = 319

 Score =  303 bits (776), Expect = 2e-80,   Method: Composition-based stats.
 Identities = 176/281 (62%), Positives = 220/281 (78%), Gaps = 3/281 (1%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V  E  LSRY+ EIRK P+L  +EE  L++ +R+ GD+ AAH+LVTSHLRLV KIAMGYR
Sbjct: 31  VGPENNLSRYLQEIRKYPLLTPEEELSLSRLWRDKGDVKAAHQLVTSHLRLVAKIAMGYR 90

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYGLPI+E++SEGNIG+MQAVK+FDPE+GFRLATY+MWWI+AA+QEYIL SWSLVK+GTT
Sbjct: 91  GYGLPINELISEGNIGMMQAVKRFDPEKGFRLATYAMWWIRAAIQEYILHSWSLVKMGTT 150

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNA 188
           A QK+LFFNLRRLKG +QAI D +LKPEQV  IA  L VSE +V+ MN R+A  D SLNA
Sbjct: 151 AAQKKLFFNLRRLKGQMQAIDDGDLKPEQVNKIATTLGVSEQDVVDMNRRMAAPDHSLNA 210

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            + +     S+WQD LV DH  QE V  E EE   R+ +L+ +M  LN RERRIF  RRL
Sbjct: 211 PMRA--DQDSEWQDRLVDDHTNQEDVYAENEELSGRKALLSSAMENLNERERRIFTERRL 268

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           +++P TLE L+ E+ +SRERVRQIE RAF+KVQ +++K+V+
Sbjct: 269 KDDPSTLEELAHEYGISRERVRQIEVRAFEKVQAAMKKEVQ 309


>gi|329114085|ref|ZP_08242849.1| RNA polymerase sigma-32 factor [Acetobacter pomorum DM001]
 gi|326696624|gb|EGE48301.1| RNA polymerase sigma-32 factor [Acetobacter pomorum DM001]
          Length = 319

 Score =  302 bits (775), Expect = 3e-80,   Method: Composition-based stats.
 Identities = 176/281 (62%), Positives = 220/281 (78%), Gaps = 3/281 (1%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V  E  LSRY+ EIRK P+L  +EE  L++ +R+ GD+ AAH+LVTSHLRLV KIAMGYR
Sbjct: 31  VGPENNLSRYLQEIRKYPLLTPEEELSLSRLWRDKGDVKAAHQLVTSHLRLVAKIAMGYR 90

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYGLPI+E++SEGNIG+MQAVK+FDPE+GFRLATY+MWWI+AA+QEYIL SWSLVK+GTT
Sbjct: 91  GYGLPINELISEGNIGMMQAVKRFDPEKGFRLATYAMWWIRAAIQEYILHSWSLVKMGTT 150

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNA 188
           A QK+LFFNLRRLKG +QAI D +LKPEQV  IA  L VSE +V+ MN R+A  D SLNA
Sbjct: 151 AAQKKLFFNLRRLKGQMQAIDDGDLKPEQVNKIATTLGVSEQDVVDMNRRMAAPDHSLNA 210

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            + +     S+WQD LV DH  QE V  E EE   R+ +L+ +M  LN RERRIF  RRL
Sbjct: 211 PMRA--DQDSEWQDRLVDDHTNQEDVYAENEELSGRKALLSSAMENLNERERRIFTERRL 268

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           +++P TLE L+ E+ +SRERVRQIE RAF+KVQ +++K+V+
Sbjct: 269 KDDPSTLEELAHEYGISRERVRQIEVRAFEKVQAAMKKEVQ 309


>gi|218528993|ref|YP_002419809.1| RNA polymerase factor sigma-32 [Methylobacterium chloromethanicum
           CM4]
 gi|240137510|ref|YP_002961981.1| RNA polymerase sigma-32 (sigma H) factor [Methylobacterium
           extorquens AM1]
 gi|254559688|ref|YP_003066783.1| RNA polymerase sigma-32 [Methylobacterium extorquens DM4]
 gi|218521296|gb|ACK81881.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium
           chloromethanicum CM4]
 gi|240007478|gb|ACS38704.1| RNA polymerase sigma-32 (sigma H) factor [Methylobacterium
           extorquens AM1]
 gi|254266966|emb|CAX22766.1| RNA polymerase sigma-32 (sigma H) factor [Methylobacterium
           extorquens DM4]
          Length = 297

 Score =  302 bits (774), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 184/286 (64%), Positives = 227/286 (79%), Gaps = 2/286 (0%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           ++  E GLSRY+ EIRK PMLE  EE+ LAK +R+ GD  AAHRLVTSHLRLV KIAMGY
Sbjct: 7   VLANEGGLSRYLDEIRKFPMLEPAEEFTLAKSWRDDGDREAAHRLVTSHLRLVAKIAMGY 66

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           RGYGLPISEVVSEGN+GLMQAVK+FDP++GFRLATY+MWWIKAA+QEYILRSWSLVK+GT
Sbjct: 67  RGYGLPISEVVSEGNVGLMQAVKRFDPDKGFRLATYAMWWIKAAIQEYILRSWSLVKMGT 126

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           TANQK+LFFNLR+ KG + A+ + +L+P+QV  IA  L V   +VI MN RL+GD SLNA
Sbjct: 127 TANQKKLFFNLRKAKGRISALDEGDLRPDQVQHIATSLGVPAQDVIDMNRRLSGDTSLNA 186

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +   ++   +WQDWLV +   QE VL  +EE +NR + L  ++ VLNPRERRIFEARRL
Sbjct: 187 PLR--EEGEGEWQDWLVDNSPSQETVLAREEEGRNRLSALRDALGVLNPRERRIFEARRL 244

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSP 294
            ++P+TLE+LS EF VSRERVRQIE RAF+KVQE++++ +     P
Sbjct: 245 ADDPITLEDLSGEFGVSRERVRQIEVRAFEKVQEAVKRNLATRELP 290


>gi|182677344|ref|YP_001831490.1| RNA polymerase, sigma 32 subunit, RpoH [Beijerinckia indica subsp.
           indica ATCC 9039]
 gi|182633227|gb|ACB94001.1| RNA polymerase, sigma 32 subunit, RpoH [Beijerinckia indica subsp.
           indica ATCC 9039]
          Length = 299

 Score =  302 bits (774), Expect = 4e-80,   Method: Composition-based stats.
 Identities = 179/278 (64%), Positives = 228/278 (82%), Gaps = 2/278 (0%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +++GE GL+RY++EIR+ PMLE QEEY+LAKR+REH D  AA RLVTSHLRLV KIAMGY
Sbjct: 7   MISGESGLTRYLNEIRRFPMLEPQEEYMLAKRWREHEDPDAAQRLVTSHLRLVAKIAMGY 66

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           RGYGLPI EVVSEGN+GLMQAVK+F+P++GFRLATY+MWWI+A++QEYILRSWSLVK+GT
Sbjct: 67  RGYGLPIGEVVSEGNVGLMQAVKRFEPDKGFRLATYAMWWIRASIQEYILRSWSLVKMGT 126

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           TA+QK+LFFNLR+ K  + A+ + +L+P+QV  IA +L V+  EVI MN R++GD SLNA
Sbjct: 127 TASQKKLFFNLRKAKSQISALDEGDLRPDQVALIATRLGVTGQEVIDMNRRMSGDASLNA 186

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +   ++   +WQDWLV D   QE VL ++EE  NR   L +++ VLNPRERRIFEARRL
Sbjct: 187 PLR--EEGEGEWQDWLVDDQANQEHVLADQEESANRLGALRQALDVLNPRERRIFEARRL 244

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            ++PVTLE LS EF++SRERVRQIE RAF+KVQ +++ 
Sbjct: 245 ADDPVTLEALSDEFDISRERVRQIEVRAFEKVQAAVKA 282


>gi|329890478|ref|ZP_08268821.1| alternative sigma factor RpoH [Brevundimonas diminuta ATCC 11568]
 gi|328845779|gb|EGF95343.1| alternative sigma factor RpoH [Brevundimonas diminuta ATCC 11568]
          Length = 294

 Score =  302 bits (773), Expect = 5e-80,   Method: Composition-based stats.
 Identities = 173/290 (59%), Positives = 218/290 (75%), Gaps = 4/290 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M    ++++ + E GLSRY+ EIRK PML K EE++LAKR+ EH D  AAHRLVTSHLRL
Sbjct: 1   MANNTLTVM-SPEQGLSRYLTEIRKFPMLTKDEEFMLAKRWSEHQDPEAAHRLVTSHLRL 59

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVKKFDP++GFRLATY+MWWI+A++QEYILRS
Sbjct: 60  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKKFDPDKGFRLATYAMWWIRASIQEYILRS 119

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTA QK+LFFNLR+ K  + A  + +L PE + AIA KL VSE EV +MN RL
Sbjct: 120 WSLVKMGTTAAQKKLFFNLRKAKSQISAFEEGDLHPEHLTAIATKLGVSEEEVTNMNRRL 179

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            GD SLNA + +     S+WQDWL  D    QE  L E EE+  R ++L  +M  L  RE
Sbjct: 180 GGDASLNAPLRA--DGESEWQDWLADDDAVSQETQLAENEEKSIRMSLLQEAMEELTDRE 237

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           + I   RRL+++PVTLE L+ ++ VSRERVRQIE RAF+K+Q++++   E
Sbjct: 238 KHILTERRLKDDPVTLEELAGQYGVSRERVRQIEVRAFEKLQKAMRAAAE 287


>gi|163850434|ref|YP_001638477.1| RNA polymerase factor sigma-32 [Methylobacterium extorquens PA1]
 gi|163662039|gb|ABY29406.1| RNA polymerase sigma factor RpoH [Methylobacterium extorquens PA1]
          Length = 297

 Score =  302 bits (773), Expect = 6e-80,   Method: Composition-based stats.
 Identities = 184/286 (64%), Positives = 227/286 (79%), Gaps = 2/286 (0%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           ++  E GLSRY+ EIRK PMLE  EE+ LAK +R+ GD  AAHRLVTSHLRLV KIAMGY
Sbjct: 7   VLANEGGLSRYLDEIRKFPMLEPAEEFTLAKSWRDDGDREAAHRLVTSHLRLVAKIAMGY 66

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           RGYGLPISEVVSEGN+GLMQAVK+FDP++GFRLATY+MWWIKAA+QEYILRSWSLVK+GT
Sbjct: 67  RGYGLPISEVVSEGNVGLMQAVKRFDPDKGFRLATYAMWWIKAAIQEYILRSWSLVKMGT 126

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           TANQK+LFFNLR+ KG + A+ + +L+P+QV  IA  L V   +VI MN RL+GD SLNA
Sbjct: 127 TANQKKLFFNLRKAKGRISALDEGDLRPDQVQHIATSLGVPAQDVIDMNRRLSGDTSLNA 186

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +   ++   +WQDWLV +   QE VL  +EE +NR + L  ++ VLNPRERRIFEARRL
Sbjct: 187 PLR--EEGEGEWQDWLVDNSPSQETVLAREEEGRNRLSALRDALGVLNPRERRIFEARRL 244

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSP 294
            ++P+TLE+LS EF VSRERVRQIE RAF+KVQE++++ +     P
Sbjct: 245 ADDPITLEDLSGEFGVSRERVRQIEVRAFEKVQEAVKRNLATRELP 290


>gi|85373062|ref|YP_457124.1| RNA polymerase factor sigma-32 [Erythrobacter litoralis HTCC2594]
 gi|84786145|gb|ABC62327.1| RNA polymerase sigma-32 factor [Erythrobacter litoralis HTCC2594]
          Length = 301

 Score =  301 bits (772), Expect = 6e-80,   Method: Composition-based stats.
 Identities = 164/279 (58%), Positives = 211/279 (75%), Gaps = 2/279 (0%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           + GE  L+RY+ EI+K P+L  ++EY+LAKRY+EH D  AA +LV+SHLRLV KIAMGYR
Sbjct: 12  LGGEQSLNRYLSEIKKYPVLTAEQEYMLAKRYQEHEDPEAAAQLVSSHLRLVAKIAMGYR 71

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYGLP+S+++SEGN+GLMQ VKKF+P+RGFRLATY+MWWIKA+MQE+ILRSWSLVK+GTT
Sbjct: 72  GYGLPVSDLISEGNVGLMQGVKKFEPDRGFRLATYAMWWIKASMQEFILRSWSLVKMGTT 131

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR--LAGDESLN 187
           A QK+LFFNLRR+K  L+A  D +L PE V  IA  L V E EVI+MN R  + GD SLN
Sbjct: 132 AAQKKLFFNLRRMKKQLEAYEDTDLSPEDVTKIATDLGVPEQEVINMNRRMMMGGDGSLN 191

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             + + +  S +WQDWL  D   Q++ +   EE + R  ML  +M  LN RE+ I   RR
Sbjct: 192 TPMRNGEDGSGEWQDWLTDDRPLQDETVANAEEAQVRHEMLVEAMDALNEREQHILTERR 251

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           L ENP TLE LS  ++VSRER+RQIE RAF+K+Q+++Q+
Sbjct: 252 LTENPQTLEELSQVYDVSRERIRQIEVRAFEKLQKAMQR 290


>gi|83592446|ref|YP_426198.1| RNA polymerase factor sigma-32 [Rhodospirillum rubrum ATCC 11170]
 gi|83575360|gb|ABC21911.1| Sigma 32 (RpoH) [Rhodospirillum rubrum ATCC 11170]
          Length = 299

 Score =  301 bits (772), Expect = 7e-80,   Method: Composition-based stats.
 Identities = 167/285 (58%), Positives = 212/285 (74%), Gaps = 3/285 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M      + +  E  L+RY+  IRK PML  +EEY LA+R R+ GD  AAHRLVTSHLRL
Sbjct: 1   MATVAPGLSIGPESNLTRYLQNIRKFPMLAPEEEYTLAQRLRDSGDSEAAHRLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLP+ EV+SEGN+GLMQAVK+FDPERGFRLATY+MWWI+AA+QEYIL S
Sbjct: 61  VAKIAMGYRGYGLPMGEVISEGNVGLMQAVKRFDPERGFRLATYAMWWIRAAIQEYILHS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTA QK+LFFNLR++KG LQ + + ++ P++V  IA KL V E +VI+MN RL
Sbjct: 121 WSLVKMGTTAAQKKLFFNLRKMKGQLQLMDEGDMHPDKVTQIATKLGVPEQDVINMNRRL 180

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +  D SLNA +        +WQDWLV + D QE  L E +E   RR +L+ ++  LN RE
Sbjct: 181 SSPDHSLNAPVRM--DGDGEWQDWLVDESDDQETTLAESQEMGQRRALLSGALKSLNERE 238

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R I   RRL+++PVTLE+LS  + +SRERVRQIE RAF+K+Q+ +
Sbjct: 239 RHILTQRRLRDDPVTLEDLSQHYGISRERVRQIEVRAFEKLQKWM 283


>gi|217978453|ref|YP_002362600.1| RNA polymerase, sigma 32 subunit, RpoH [Methylocella silvestris
           BL2]
 gi|217503829|gb|ACK51238.1| RNA polymerase, sigma 32 subunit, RpoH [Methylocella silvestris
           BL2]
          Length = 303

 Score =  301 bits (772), Expect = 7e-80,   Method: Composition-based stats.
 Identities = 177/278 (63%), Positives = 232/278 (83%), Gaps = 2/278 (0%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +++GE GL+RY++EIR+ PMLE Q+EY+LAKR+REH D  AAH+LVTSHLRLV KIAMGY
Sbjct: 7   MISGESGLARYLNEIRRFPMLEPQQEYMLAKRWREHADSDAAHKLVTSHLRLVAKIAMGY 66

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           RGYGLPISEVVSEGN+GLMQAVK+F+PE+GFRLATY+MWWI+A++QEYILRSWSLVK+GT
Sbjct: 67  RGYGLPISEVVSEGNVGLMQAVKRFEPEKGFRLATYAMWWIRASIQEYILRSWSLVKMGT 126

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           TA+QK+LFFNLR++K  + A+ + +L+PE V  IA +L VS+ +VI MN R++GD SLNA
Sbjct: 127 TASQKKLFFNLRKVKSQISALEEGDLRPEHVDKIAHRLGVSKQDVIDMNRRMSGDASLNA 186

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +   ++   +WQDWLV D   QE++L+++EE  NR   L  +++VLN RERRIFEARRL
Sbjct: 187 PLR--EEGEGEWQDWLVDDSASQEKLLVDREETDNRLGALHTALNVLNDRERRIFEARRL 244

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            ++P+TLE LS EF++SRERVRQIE RAF+KVQ +++ 
Sbjct: 245 ADDPMTLEALSDEFDISRERVRQIEVRAFEKVQSAVKA 282


>gi|326386899|ref|ZP_08208513.1| RNA polymerase factor sigma-32 [Novosphingobium nitrogenifigens DSM
           19370]
 gi|326208579|gb|EGD59382.1| RNA polymerase factor sigma-32 [Novosphingobium nitrogenifigens DSM
           19370]
          Length = 300

 Score =  301 bits (771), Expect = 8e-80,   Method: Composition-based stats.
 Identities = 168/291 (57%), Positives = 219/291 (75%), Gaps = 7/291 (2%)

Query: 1   MNRKNMSIIV---NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSH 57
           M+ +N ++ V   +GE  L+RY+ EIRK P+L  ++EY+LAKRY+EHGD  AA +LVTSH
Sbjct: 1   MSEQNKALSVPALSGEASLNRYLTEIRKFPLLTAEQEYMLAKRYQEHGDPQAAAQLVTSH 60

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLV KIAMGYRGYGLP+SE++SEGNIGLMQ VKKFDP+RGFRLATY+MWWIKA++QE+I
Sbjct: 61  LRLVAKIAMGYRGYGLPVSELISEGNIGLMQGVKKFDPDRGFRLATYAMWWIKASIQEFI 120

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           LRSWSLVK+GTTA QK+LFFNLRR+K +L+A  D++L P+ V  IA  L V E++V+SMN
Sbjct: 121 LRSWSLVKMGTTAAQKKLFFNLRRMKKNLEAFEDSDLHPDDVKKIATDLGVPEADVVSMN 180

Query: 178 CRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
            R+   GD SLN  +   +     WQDWL  +   Q++ + + EE + R ++L  +M  L
Sbjct: 181 RRMMMGGDASLNVPLR--EDGEGSWQDWLADERPLQDEAVADAEEAQVRHDLLVEAMQDL 238

Query: 236 NPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           N RER I   RRL + P TLE LS  + VSRERVRQIE RAF+K+Q++IQ+
Sbjct: 239 NDRERHILIDRRLVDEPKTLEELSQVYHVSRERVRQIEVRAFEKLQKAIQR 289


>gi|294085881|ref|YP_003552641.1| RNA polymerase sigma-32 subunit RpoH [Candidatus Puniceispirillum
           marinum IMCC1322]
 gi|292665456|gb|ADE40557.1| RNA polymerase, sigma 32 subunit, RpoH [Candidatus Puniceispirillum
           marinum IMCC1322]
          Length = 312

 Score =  301 bits (771), Expect = 9e-80,   Method: Composition-based stats.
 Identities = 172/287 (59%), Positives = 226/287 (78%), Gaps = 2/287 (0%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           R  M  I + +  LSRY+ +IR  PMLE ++EY+LAK ++E GD+ +AH+LVTSHLRLV 
Sbjct: 9   RSTMPAI-SPDGNLSRYLEQIRAFPMLEPKQEYMLAKAWKEKGDVESAHQLVTSHLRLVA 67

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           KIAMGYRGYGLP+++++SEGN+G+M AVKKF+PE+GFRLATY+MWWIKAA+QEYILRSWS
Sbjct: 68  KIAMGYRGYGLPVADLISEGNLGMMHAVKKFEPEKGFRLATYAMWWIKAAIQEYILRSWS 127

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           LVKIGTTA QK+LFFNLRR+KG +QAI + +LKPEQV  IA +LNV+E+EV+SMN R+AG
Sbjct: 128 LVKIGTTAGQKKLFFNLRRIKGQIQAIDEGDLKPEQVTHIADELNVTEAEVMSMNQRMAG 187

Query: 183 -DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
            D SLN  ++   + + +WQDWL  D   QE    E EE   R N++  +M  LN RE+R
Sbjct: 188 NDRSLNVPLSRDGEGTGEWQDWLEDDTVDQETSFAEHEEYSARANLMMDAMKGLNEREQR 247

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           I +ARRL E P+TLE+L+ EF VSRER+RQIE RAF+K+Q++++ + 
Sbjct: 248 ILQARRLAEPPLTLEDLAGEFNVSRERIRQIEVRAFEKLQKAVRDKA 294


>gi|188580210|ref|YP_001923655.1| RNA polymerase factor sigma-32 [Methylobacterium populi BJ001]
 gi|179343708|gb|ACB79120.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium populi
           BJ001]
          Length = 297

 Score =  301 bits (771), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 184/286 (64%), Positives = 227/286 (79%), Gaps = 2/286 (0%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           ++  E GLSRY+ EIRK PMLE  EE+ LAK +R+ GD  AAHRLVTSHLRLV KIAMGY
Sbjct: 7   VLANEGGLSRYLDEIRKFPMLEPAEEFTLAKSWRDEGDREAAHRLVTSHLRLVAKIAMGY 66

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           RGYGLPISEVVSEGN+GLMQAVK+FDP++GFRLATY+MWWIKAA+QEYILRSWSLVK+GT
Sbjct: 67  RGYGLPISEVVSEGNVGLMQAVKRFDPDKGFRLATYAMWWIKAAIQEYILRSWSLVKMGT 126

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           TANQK+LFFNLR+ KG + A+ + +L+P+QV  IA  L V   +VI MN RL+GD SLNA
Sbjct: 127 TANQKKLFFNLRKAKGRISALDEGDLRPDQVQQIATSLGVPTQDVIDMNRRLSGDTSLNA 186

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +   ++   +WQDWLV +   QE VL  +EE +NR + L  ++ VLNPRERRIFEARRL
Sbjct: 187 PLR--EEGEGEWQDWLVDNSPSQETVLAREEEGRNRLSALRDALGVLNPRERRIFEARRL 244

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSP 294
            ++P+TLE+LS EF VSRERVRQIE RAF+KVQE++++ +     P
Sbjct: 245 ADDPITLEDLSGEFGVSRERVRQIEVRAFEKVQEAVKRNLATRELP 290


>gi|77462968|ref|YP_352472.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides 2.4.1]
 gi|126461842|ref|YP_001042956.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides ATCC 17029]
 gi|221638824|ref|YP_002525086.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides KD131]
 gi|332557843|ref|ZP_08412165.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides WS8N]
 gi|1769585|gb|AAC46050.1| RpoH [Rhodobacter sphaeroides]
 gi|77387386|gb|ABA78571.1| sigma factor RpoH1 (Sigma-32 group, heat shock) [Rhodobacter
           sphaeroides 2.4.1]
 gi|126103506|gb|ABN76184.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacter sphaeroides
           ATCC 17029]
 gi|221159605|gb|ACM00585.1| RNA polymerase sigma factor [Rhodobacter sphaeroides KD131]
 gi|332275555|gb|EGJ20870.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides WS8N]
          Length = 298

 Score =  300 bits (770), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 171/287 (59%), Positives = 218/287 (75%), Gaps = 1/287 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+        + E GL+RY+ EIRK P+LE +EEY+LAKR+ +H D  AAH+LVTSHLRL
Sbjct: 1   MSTYTSLPAPSPEQGLNRYMQEIRKFPLLEPEEEYMLAKRWVDHQDNRAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
             KIAMGYRGYGLP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRS
Sbjct: 61  AAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTT+ QK+LFFNLR+ K  L A+ + +L+PE V  IAK L VSE+EVI MN RL
Sbjct: 121 WSLVKLGTTSAQKKLFFNLRKAKAKLGALEEGDLRPENVAQIAKDLGVSETEVIDMNRRL 180

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D SLNA I S  + S+QWQDWL  +   Q     E++E + RR +L +SMSVLN RE
Sbjct: 181 SGSDASLNATIGSDGEGSTQWQDWLEDEDSDQAADYAERDELEIRRELLAQSMSVLNDRE 240

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           + I   RRL ++PVTLE LS  + VSRER+RQIE RAF+K+Q  +++
Sbjct: 241 KDILVQRRLTDDPVTLEELSEGYGVSRERIRQIEVRAFEKLQAKMRE 287


>gi|302382389|ref|YP_003818212.1| RNA polymerase, sigma 32 subunit, RpoH [Brevundimonas subvibrioides
           ATCC 15264]
 gi|302193017|gb|ADL00589.1| RNA polymerase, sigma 32 subunit, RpoH [Brevundimonas subvibrioides
           ATCC 15264]
          Length = 295

 Score =  300 bits (769), Expect = 1e-79,   Method: Composition-based stats.
 Identities = 171/290 (58%), Positives = 216/290 (74%), Gaps = 3/290 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M       +++ E GLSRY+ EIRK PML K EE++LAKR+ EH D  +AHRLVTSHLRL
Sbjct: 1   MAAMKSLAVMSPEQGLSRYLTEIRKFPMLTKDEEFMLAKRWSEHQDSESAHRLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVKKFDP++GFRLATY+MWWI+A++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKKFDPDKGFRLATYAMWWIRASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTA QK+LFFNLR+ K  + A  + +L+PE + AIA KL VSE EV +MN RL
Sbjct: 121 WSLVKMGTTAAQKKLFFNLRKAKSQISAFEEGDLRPEHLAAIATKLGVSEEEVTNMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            GD SLNA +       S+WQDWL  D+   QE  L + EE+  R  +L  +M  L  RE
Sbjct: 181 GGDASLNAPLRV--DGESEWQDWLSDDNAVSQETALADSEEKSLRMGLLQEAMGELTERE 238

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           + I   RRL+++PVTLE L+ ++ VSRERVRQIE RAF+K+Q++++   E
Sbjct: 239 KHILTERRLKDDPVTLEELAGQYGVSRERVRQIEVRAFEKLQKAMRAAAE 288


>gi|296536196|ref|ZP_06898318.1| DNA-directed RNA polymerase sigma subunit RpoH [Roseomonas
           cervicalis ATCC 49957]
 gi|296263478|gb|EFH09981.1| DNA-directed RNA polymerase sigma subunit RpoH [Roseomonas
           cervicalis ATCC 49957]
          Length = 295

 Score =  300 bits (769), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 168/290 (57%), Positives = 220/290 (75%), Gaps = 3/290 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M      I +  E  LSRY+ EIRK PML  +EE+ LAK ++EHGD  AAH+LVTSHLRL
Sbjct: 1   MASTTSMIPIAPEGNLSRYLQEIRKFPMLTPEEEFRLAKDWKEHGDQKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLP+ E++SEGN+G+MQAV++FDP+RGFRLATY+MWWI+AA+QEYIL S
Sbjct: 61  VAKIAMGYRGYGLPVGELISEGNVGMMQAVRRFDPDRGFRLATYAMWWIRAAIQEYILHS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTA QK+LFFNLRRLKG + A+ + +L+PEQV  IA+ L V E +V+SMN RL
Sbjct: 121 WSLVKMGTTAAQKKLFFNLRRLKGQMAALEEGDLQPEQVEKIARVLQVPEQDVVSMNRRL 180

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           A  D SLNA + +   +  +WQDWLV + + QE  + E+++  NRR +L  ++  LN RE
Sbjct: 181 ASPDNSLNAPVRA--DSEGEWQDWLVDESESQETEIAERQDMSNRRELLGEALKTLNERE 238

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           R I   RRL++ P TLE LS ++ +SRERVRQIE RAF+K+Q+S++ Q+ 
Sbjct: 239 RHILIERRLKDEPTTLEELSQQYNISRERVRQIEVRAFEKLQKSMKSQIM 288


>gi|144897893|emb|CAM74757.1| RNA polymerase sigma-32 factor [Magnetospirillum gryphiswaldense
           MSR-1]
          Length = 288

 Score =  300 bits (769), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 176/289 (60%), Positives = 220/289 (76%), Gaps = 3/289 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M     S+ +  E  LSRY+ EIRK PMLE  EEY LAKRYREHGD  AA RL+TSHLRL
Sbjct: 1   MTAIPTSLSLAPEGNLSRYLQEIRKFPMLEPTEEYQLAKRYREHGDFEAADRLITSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLP+ E++SEGN+G+MQAVK+FDP+RGFRLATY+MWWI+AA+QEYIL S
Sbjct: 61  VAKIAMGYRGYGLPLGELISEGNVGMMQAVKRFDPDRGFRLATYAMWWIRAAVQEYILHS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTA QK+LFFNLR+LKG +QA+ + +L  E V +IA KLNV E++VI+MN RL
Sbjct: 121 WSLVKMGTTAAQKKLFFNLRKLKGQMQAMDEGDLPQETVTSIATKLNVPENDVINMNRRL 180

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           A  D SLNA +        +WQDWLV + D QE  L +++ER  R  +L+ ++  LN RE
Sbjct: 181 ASPDHSLNAPVRM--DGEGEWQDWLVDESDDQETELADRQERGIRSKLLSTALDTLNERE 238

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           R I   RRL E+P TLE+LS ++ +SRERVRQIE RAF+K+Q+SI+  V
Sbjct: 239 RSILSQRRLTEDPATLEDLSQQYGISRERVRQIEVRAFEKLQKSIRASV 287


>gi|330993273|ref|ZP_08317209.1| RNA polymerase sigma-32 factor [Gluconacetobacter sp. SXCC-1]
 gi|329759675|gb|EGG76183.1| RNA polymerase sigma-32 factor [Gluconacetobacter sp. SXCC-1]
          Length = 298

 Score =  300 bits (768), Expect = 2e-79,   Method: Composition-based stats.
 Identities = 169/299 (56%), Positives = 221/299 (73%), Gaps = 3/299 (1%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
             + ++I   E  LS+Y+ +IRK PML  +EE  L++R+++ GD  AAH+LVTSHLRLV 
Sbjct: 1   MASSALISGPENNLSKYLRDIRKFPMLSPEEELRLSRRWKDKGDTEAAHKLVTSHLRLVA 60

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           KIAMGYRGYGLP+ E++SEGNIG+MQAV++FDP+RGFRLATY+MWWI+AA+QEYIL SWS
Sbjct: 61  KIAMGYRGYGLPVGELISEGNIGMMQAVRRFDPDRGFRLATYAMWWIRAAIQEYILHSWS 120

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           LVKIGTTA QK+LFFNLRRLKG +QAI D +L+PEQV  IA+ L V E +V++MN RLA 
Sbjct: 121 LVKIGTTAAQKKLFFNLRRLKGQMQAIDDGDLRPEQVNKIAQSLGVPEQDVVNMNRRLAA 180

Query: 183 -DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
            D SLNA +        +WQDWLV D+D QE+ L + EE   R+ +L  ++  LN RER 
Sbjct: 181 PDHSLNAPLRM--DGEGEWQDWLVDDNDNQEETLAQSEEYSGRQALLANALKTLNERERH 238

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQKP 300
           I   RRL++ P TLE+LS  + +SRERVRQIE RAF+K+Q +++ +V    +    Q P
Sbjct: 239 ILTERRLKDEPATLEDLSHVYNISRERVRQIEVRAFEKLQAAMKAEVAARRARHGEQAP 297


>gi|254294740|ref|YP_003060763.1| RNA polymerase factor sigma-32 [Hirschia baltica ATCC 49814]
 gi|254043271|gb|ACT60066.1| RNA polymerase, sigma 32 subunit, RpoH [Hirschia baltica ATCC
           49814]
          Length = 295

 Score =  299 bits (765), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 170/288 (59%), Positives = 223/288 (77%), Gaps = 3/288 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M + + SI ++ E GLSRY+ EIRK P+LEK +E++LA R+R+H D  AA ++VTSHLRL
Sbjct: 1   MAQLSTSIALSPEQGLSRYLTEIRKYPLLEKDQEFMLANRWRDHEDPEAAEKMVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVKKFDP++GFRLATY+MWWI+A++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKKFDPDKGFRLATYAMWWIRASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTA QK+LFFNLRRLKG +QA+ + +L+PE V  IA +LNVSE+EVISMN R+
Sbjct: 121 WSLVKLGTTAAQKKLFFNLRRLKGEIQALEEGDLRPENVAEIATRLNVSETEVISMNRRM 180

Query: 181 -AGDESLNALINSSDKNSSQWQDWLVYD-HDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
             GD SLNA I  +D +  +W DWL  D    Q +   + +E   R ++L  +M  LN R
Sbjct: 181 TGGDASLNAPIGGADGD-GEWMDWLSDDNQQNQAEEYEQNDEFSTRMSLLETAMEGLNER 239

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E+ I   RRL++ P TLE LS+ + VSRER+RQIE RAF+K+Q+++++
Sbjct: 240 EKHIIAERRLKDEPSTLEELSAVYNVSRERIRQIEVRAFEKLQKAMKE 287


>gi|114569135|ref|YP_755815.1| RNA polymerase factor sigma-32 [Maricaulis maris MCS10]
 gi|114339597|gb|ABI64877.1| RNA polymerase, sigma 32 subunit, RpoH [Maricaulis maris MCS10]
          Length = 295

 Score =  299 bits (765), Expect = 5e-79,   Method: Composition-based stats.
 Identities = 171/284 (60%), Positives = 219/284 (77%), Gaps = 3/284 (1%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S+ ++ E GLS Y+ EIR+ PMLEK EE++L KR+REH D  AA +LVTSHLRLV KIAM
Sbjct: 6   SMTLSPEQGLSSYLSEIRRFPMLEKDEEFMLGKRWREHEDGGAAEKLVTSHLRLVAKIAM 65

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           GYRGYGLPI+EV+SEGN+GLMQAVKKFDP++GFRLATY+MWWI+A++QEYILRSWSLVK+
Sbjct: 66  GYRGYGLPIAEVISEGNVGLMQAVKKFDPDKGFRLATYAMWWIRASIQEYILRSWSLVKM 125

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DES 185
           GTTA QK+LFFNLRR+K  +QA+ + +LKP+QV AIA KL V+  EV+SMN RL+G D S
Sbjct: 126 GTTAAQKKLFFNLRRMKSQMQALDEGDLKPDQVEAIATKLGVTNDEVMSMNGRLSGPDAS 185

Query: 186 LNALINSSDKNSSQWQDWLVYDH-DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           LNA +  ++    QWQDWL  D  + QE  L E +E   R  +L  +M  LN RE+ I +
Sbjct: 186 LNAPLRGTEGE-GQWQDWLSDDTAESQEDELAESDEFDTRMQLLQSAMGELNEREQHILQ 244

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            RRL E+P TLE L+  + VSRER+RQIE RAF+K+Q++++   
Sbjct: 245 ERRLSEDPKTLEELAEHYGVSRERIRQIEVRAFEKLQKAMKAMA 288


>gi|332185869|ref|ZP_08387616.1| alternative sigma factor RpoH [Sphingomonas sp. S17]
 gi|332014227|gb|EGI56285.1| alternative sigma factor RpoH [Sphingomonas sp. S17]
          Length = 301

 Score =  298 bits (764), Expect = 6e-79,   Method: Composition-based stats.
 Identities = 167/279 (59%), Positives = 212/279 (75%), Gaps = 4/279 (1%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           + GE  L+RY+ EI+K P+L  ++EY+LAKR++EHGD  AA +LVTSHLRLV KIAMGYR
Sbjct: 14  LGGEQSLNRYLAEIKKFPILAPEQEYMLAKRFQEHGDPEAAAQLVTSHLRLVAKIAMGYR 73

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYGLP SE++SEGNIGLMQ VKKF+P+RGFRLATY+MWWI+A++QEYILRSWSLVK+GTT
Sbjct: 74  GYGLPTSELISEGNIGLMQGVKKFEPDRGFRLATYAMWWIRASIQEYILRSWSLVKMGTT 133

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
           A QK+LFFNLRR+K  L A  D +L+PE V  IA  L V+E EVISMN R+A  GD SLN
Sbjct: 134 AAQKKLFFNLRRMKSKLDAFEDGDLRPEDVTKIATDLGVNEDEVISMNRRMAMGGDTSLN 193

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             ++  +    QWQDWL  D   Q+ V+ E++E   R +ML  +M  LN RE+ I   RR
Sbjct: 194 --VSMREDGEGQWQDWLADDAPLQDSVVAEQQEADVRHDMLVSAMDDLNDREKHILTERR 251

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           L ++P TLE LS  + VSRERVRQIE RAF+K+Q+++ +
Sbjct: 252 LTDDPKTLEELSQVYGVSRERVRQIEVRAFEKLQKAMMR 290


>gi|146277611|ref|YP_001167770.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides ATCC 17025]
 gi|145555852|gb|ABP70465.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacter sphaeroides
           ATCC 17025]
          Length = 298

 Score =  298 bits (764), Expect = 7e-79,   Method: Composition-based stats.
 Identities = 169/287 (58%), Positives = 217/287 (75%), Gaps = 1/287 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+        + E GL+RY+ EIRK P+LE +EEY+LAKR+ +H D  AAHRLVTSHLRL
Sbjct: 1   MSSYTSLPAPSPEQGLNRYMQEIRKFPLLEPEEEYMLAKRWVDHQDNRAAHRLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
             KIAMGYRGYGLP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRS
Sbjct: 61  AAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTT+ QK+LFFNLR+ K  L A+ + +L+PE V  IAK L+V+E+EVI MN RL
Sbjct: 121 WSLVKLGTTSAQKKLFFNLRKAKAKLGALEEGDLRPENVAQIAKDLSVTEAEVIDMNRRL 180

Query: 181 -AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            A D SLNA I S    ++QWQDWL  +   Q     E++E + RR +L ++MSVLN RE
Sbjct: 181 SASDASLNATIGSDGDGATQWQDWLEDEDSDQASDYAERDELEIRRELLAQAMSVLNDRE 240

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           + I   RRL ++PVTLE LS  + VSRER+RQIE RAF+K+Q  +++
Sbjct: 241 KDILVQRRLTDDPVTLEELSDGYGVSRERIRQIEVRAFEKLQARMRE 287


>gi|148552989|ref|YP_001260571.1| RNA polymerase factor sigma-32 [Sphingomonas wittichii RW1]
 gi|148498179|gb|ABQ66433.1| RNA polymerase sigma factor RpoH [Sphingomonas wittichii RW1]
          Length = 301

 Score =  297 bits (762), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 169/279 (60%), Positives = 210/279 (75%), Gaps = 4/279 (1%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           + GE  L+RY+ EIRK P+L  +EEY+LAKR++EHGD  AA RLVTSHLRLV KIAMGYR
Sbjct: 14  LGGEQSLNRYLAEIRKFPLLTAEEEYMLAKRFQEHGDPEAATRLVTSHLRLVAKIAMGYR 73

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYGLP SE++SEGNIGLMQ VKKF+P+RGFRLATY+MWWIKA++QEYILRSWSLVK+GTT
Sbjct: 74  GYGLPASELISEGNIGLMQGVKKFEPDRGFRLATYAMWWIKASIQEYILRSWSLVKMGTT 133

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL--AGDESLN 187
           A QK+LFFNLRR+K  L+A  D +LKPE +  IA  L VSE EV SMN R+   GD SLN
Sbjct: 134 AAQKKLFFNLRRMKSQLEAFEDGDLKPEDLKKIATDLGVSEEEVTSMNRRMSMGGDASLN 193

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             ++ ++    +WQD LV     Q++ L E EE+  R NML  +++ LN RE+ I   RR
Sbjct: 194 --VSMNEDGEGEWQDMLVDQGPLQDERLAEVEEKSVRHNMLNEALAALNDREKHILVERR 251

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           L + P TLE LS  + VSRERVRQIE RAF K+Q+++ +
Sbjct: 252 LVDEPKTLEELSQVYGVSRERVRQIEVRAFDKLQKAMMR 290


>gi|149187051|ref|ZP_01865358.1| RNA polymerase sigma factor [Erythrobacter sp. SD-21]
 gi|148829340|gb|EDL47784.1| RNA polymerase sigma factor [Erythrobacter sp. SD-21]
          Length = 319

 Score =  297 bits (762), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 161/279 (57%), Positives = 211/279 (75%), Gaps = 2/279 (0%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           + GE  L+RY+ EI+K P+L +++EY+LAKRY EHGD  AA +LVTSHLRLV KIAMGYR
Sbjct: 30  LGGEQSLNRYLSEIKKFPILTQEQEYMLAKRYEEHGDSEAAAQLVTSHLRLVSKIAMGYR 89

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYGLP+S+++SEGN+GLMQ VKKF+ +RGFRLATY+MWWIKA++QEYILRSWSLVK+GTT
Sbjct: 90  GYGLPVSDLISEGNVGLMQGVKKFEADRGFRLATYAMWWIKASIQEYILRSWSLVKMGTT 149

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR--LAGDESLN 187
           A QK+LFFNLRR+K +L A  D +L P+ V  IA  L V E EV++MN R  + GD SLN
Sbjct: 150 AAQKKLFFNLRRMKKNLDAYEDTDLHPDDVQKIATDLGVPEQEVVNMNRRMMMGGDGSLN 209

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             + + ++ S +W DWL  D   Q++ + + EE++ R  ML  +M  LN RE+ I   RR
Sbjct: 210 VPMRNGEEGSGEWMDWLTDDRPLQDETVADAEEKEVRHEMLGEAMEALNEREQHILTERR 269

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           L ENP TLE LS  + VSRER+RQIE RAF+K+Q++++ 
Sbjct: 270 LTENPQTLEELSQVYNVSRERIRQIEVRAFEKLQKAMKA 308


>gi|254419521|ref|ZP_05033245.1| alternative sigma factor RpoH [Brevundimonas sp. BAL3]
 gi|196185698|gb|EDX80674.1| alternative sigma factor RpoH [Brevundimonas sp. BAL3]
          Length = 286

 Score =  297 bits (761), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 171/281 (60%), Positives = 214/281 (76%), Gaps = 3/281 (1%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ E GLSRY+ EIRK PML K EE++LAKR+ EH D  AAHRLVTSHLRLV KIAMGYR
Sbjct: 1   MSPEQGLSRYLTEIRKFPMLTKDEEFMLAKRWSEHQDPEAAHRLVTSHLRLVAKIAMGYR 60

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYGLPI EV+SEGN+GLMQAVKKFDP++GFRLATY+MWWI+A++QEYILRSWSLVK+GTT
Sbjct: 61  GYGLPIGEVISEGNVGLMQAVKKFDPDKGFRLATYAMWWIRASIQEYILRSWSLVKMGTT 120

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
           A QK+LFFNLR+ K  + A  + +L PE + AIA KL VSE EV +MN RL GD SLNA 
Sbjct: 121 AAQKKLFFNLRKAKSQISAFEEGDLHPEHLAAIATKLGVSEEEVTNMNRRLGGDASLNAP 180

Query: 190 INSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
           + +     S+WQDWL  D    QE  L + EE+  R ++L  +M  L  RE+ I   RRL
Sbjct: 181 LRA--DGESEWQDWLADDTAVSQETQLADDEEKGIRMSLLQEAMEELTDREKHILTERRL 238

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           +++PVTLE L+ ++ VSRERVRQIE RAF+K+Q++++   E
Sbjct: 239 KDDPVTLEELAGQYGVSRERVRQIEVRAFEKLQKAMRAAAE 279


>gi|114797392|ref|YP_759060.1| RNA polymerase factor sigma-32 [Hyphomonas neptunium ATCC 15444]
 gi|114737566|gb|ABI75691.1| alternative sigma factor RpoH [Hyphomonas neptunium ATCC 15444]
          Length = 298

 Score =  297 bits (761), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 169/289 (58%), Positives = 220/289 (76%), Gaps = 3/289 (1%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S+ ++ E G+SRY+ EIRK PMLEK EE++LA+R+ EH D  AA ++VTSHLRLV KIAM
Sbjct: 9   SVALSPEQGMSRYLSEIRKFPMLEKNEEFMLARRWHEHEDTEAAEKMVTSHLRLVAKIAM 68

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           GYRGYGLP++EV+SEGN+GLMQAVKKFDP++GFRLATY+MWWI+AA+QEYILRSWSLVK+
Sbjct: 69  GYRGYGLPMAEVISEGNVGLMQAVKKFDPDKGFRLATYAMWWIRAAIQEYILRSWSLVKL 128

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DES 185
           GTTA QK+LFFNLRRLKG +QA+ + +LKPEQ   IA+KLNV+E+EV SMN R++G D S
Sbjct: 129 GTTAAQKKLFFNLRRLKGEMQALEEGDLKPEQARLIAEKLNVTETEVYSMNGRMSGSDAS 188

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           LN  +        +WQDWL  D  G  +     +E   R  +LT++M  L+ RER I   
Sbjct: 189 LNVPM--GTDGDMEWQDWLADDEPGTAETFANSQELDARMTLLTQAMEDLSERERHILTE 246

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSP 294
           RRL + P TLE LS ++ VSRER+RQIE RAF+K+Q+++++  +    P
Sbjct: 247 RRLVDEPKTLEELSEQYNVSRERIRQIEVRAFEKLQKAMKRMAKEQGLP 295


>gi|209965020|ref|YP_002297935.1| RNA polymerase sigma-32 factor [Rhodospirillum centenum SW]
 gi|209958486|gb|ACI99122.1| RNA polymerase sigma-32 factor [Rhodospirillum centenum SW]
          Length = 294

 Score =  297 bits (761), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 175/282 (62%), Positives = 222/282 (78%), Gaps = 3/282 (1%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           ++N E  L+RY+ EIRK PMLE +EEY+LAK +REHGD  AAHRLVTSHLRLV KIAMGY
Sbjct: 10  VINSESNLARYLQEIRKFPMLEAEEEYMLAKSWREHGDTDAAHRLVTSHLRLVAKIAMGY 69

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           RGYGLP+SE++SEGN+G+MQAVK+FDP+RGFRLATY+MWWI+AA+QEYIL SWSLVK+GT
Sbjct: 70  RGYGLPLSELISEGNVGMMQAVKRFDPDRGFRLATYAMWWIRAAIQEYILHSWSLVKMGT 129

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN 187
           TA QK+LFFNLR+LKG +QAI + +L PE V  IA+ L+V ES+V++MN RLA  D SLN
Sbjct: 130 TAAQKKLFFNLRKLKGQMQAIDEGDLHPETVRKIAETLDVPESDVVNMNRRLASPDHSLN 189

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           A +        +WQDWLV + + QE  L E+EE   R+ +L  +M  LN RER I   RR
Sbjct: 190 APLRV--DGEGEWQDWLVDESESQEIRLGEREELGKRKALLAEAMKTLNDRERHILVERR 247

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           L++NP TLE+LS ++ +SRERVRQIE RAF+K+Q++I+   E
Sbjct: 248 LRDNPTTLEDLSQQYGISRERVRQIEVRAFEKLQKAIRSAAE 289


>gi|260434077|ref|ZP_05788048.1| alternative sigma factor RpoH [Silicibacter lacuscaerulensis
           ITI-1157]
 gi|260417905|gb|EEX11164.1| alternative sigma factor RpoH [Silicibacter lacuscaerulensis
           ITI-1157]
          Length = 298

 Score =  297 bits (761), Expect = 1e-78,   Method: Composition-based stats.
 Identities = 169/297 (56%), Positives = 218/297 (73%), Gaps = 5/297 (1%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N KN+ +    E GL+RY+ EIRK P+LE +EEY+LAKR+ E  D  AAH+LVTSHLRL 
Sbjct: 3   NYKNLPVPTP-EGGLNRYLQEIRKFPLLEPEEEYMLAKRWVEDHDTEAAHKLVTSHLRLA 61

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            KIAMGYRGYGLP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSW
Sbjct: 62  AKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSW 121

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL- 180
           SLVK+GTT+ QK+LFFNLR+ K  + A+ D +L P+ V  IA  L V+E EVISMN R+ 
Sbjct: 122 SLVKLGTTSAQKKLFFNLRKAKARIGALEDGDLHPDNVKQIAHDLGVTEDEVISMNRRMS 181

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA + S  + + QWQDWL  +   Q      +EE + RR +L  ++ VLN RE+
Sbjct: 182 GGDASLNATVGSEGEGTMQWQDWLEDESADQAGDYETREELEVRRELLAEALEVLNDREK 241

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLL 297
            I   RRL + PVTLE LSS++ VSRER+RQIE RAF+K+Q+ ++   EL+    +L
Sbjct: 242 DILTQRRLMDQPVTLEELSSQYNVSRERIRQIEVRAFEKLQKKMR---ELAREKGML 295


>gi|323137119|ref|ZP_08072198.1| RNA polymerase, sigma 32 subunit, RpoH [Methylocystis sp. ATCC
           49242]
 gi|322397477|gb|EFX99999.1| RNA polymerase, sigma 32 subunit, RpoH [Methylocystis sp. ATCC
           49242]
          Length = 294

 Score =  297 bits (760), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 177/292 (60%), Positives = 228/292 (78%), Gaps = 5/292 (1%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           ++ V  E GL+RY+ EIR+ PMLE Q+EY+LAKR+REH D  AA  LVTSHLRLV KIAM
Sbjct: 3   NLPVIAEGGLARYLAEIRRFPMLEPQQEYMLAKRWREHEDPKAAQELVTSHLRLVAKIAM 62

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           GYRGYGLPI E++SEGN+GLMQAVK+F+P+RGFRLATY+MWWI+A++QEYILRSWSLVK+
Sbjct: 63  GYRGYGLPIGEIISEGNVGLMQAVKRFEPDRGFRLATYAMWWIRASIQEYILRSWSLVKM 122

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
           GTTA+QK+LFFNLR+ K  + A  + +++PE V  IA +L VS+ +VI MN R+ GD SL
Sbjct: 123 GTTASQKKLFFNLRKAKSRISAFEEGDMRPENVEKIATRLGVSQQDVIEMNRRMGGDASL 182

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           NA +   ++   +WQDWLV D + QE++L+ +EE  NR   L  ++ VLNPRERRIFEAR
Sbjct: 183 NAPLR--EEGEGEWQDWLVDDSEDQERILVAQEENNNRLKALRGALDVLNPRERRIFEAR 240

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK---QVELSSSPP 295
           RL ++PVTLE LS EF VSRERVRQIE RAF+KVQ +++    ++E +   P
Sbjct: 241 RLADDPVTLEQLSEEFGVSRERVRQIEVRAFEKVQAAVRSGVARIEAAHHAP 292


>gi|209542656|ref|YP_002274885.1| RNA polymerase factor sigma-32 [Gluconacetobacter diazotrophicus
           PAl 5]
 gi|209530333|gb|ACI50270.1| RNA polymerase, sigma 32 subunit, RpoH [Gluconacetobacter
           diazotrophicus PAl 5]
          Length = 295

 Score =  297 bits (760), Expect = 2e-78,   Method: Composition-based stats.
 Identities = 172/281 (61%), Positives = 217/281 (77%), Gaps = 3/281 (1%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V  E  LSRY+ +IRK PML  ++E  L++R+++ GD  AAH LVTSHLRLV KIAMGYR
Sbjct: 8   VGPESNLSRYLQDIRKFPMLSPEDEQRLSRRWKDKGDTEAAHALVTSHLRLVAKIAMGYR 67

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYGLP+ E++SEGNIG+MQAV++FDP+RGFRLATY+MWWI+AA+QEYIL SWSLVK+GTT
Sbjct: 68  GYGLPLGELISEGNIGMMQAVRRFDPDRGFRLATYAMWWIRAAIQEYILHSWSLVKMGTT 127

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNA 188
           A QK+LFFNLRRLKG +QAI D +LKPEQV  IA+ L V E +VI+MN RL+  D SLNA
Sbjct: 128 AAQKKLFFNLRRLKGQMQAIDDGDLKPEQVNKIAESLGVPEQDVINMNRRLSAPDHSLNA 187

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            + +   +  +WQDWLV +HD QEQ L E EE   R+ +L  +M  LN RER I   RRL
Sbjct: 188 PLRA--DSEGEWQDWLVDEHDNQEQTLAENEEFSGRKALLDNAMKTLNDRERHILTERRL 245

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           +++P TLE LS  + +SRERVRQIE RAF+KVQ +++ +VE
Sbjct: 246 KDDPATLEELSHTYNISRERVRQIEVRAFEKVQAAMKAEVE 286


>gi|167644630|ref|YP_001682293.1| RNA polymerase factor sigma-32 [Caulobacter sp. K31]
 gi|167347060|gb|ABZ69795.1| RNA polymerase, sigma 32 subunit, RpoH [Caulobacter sp. K31]
          Length = 295

 Score =  296 bits (758), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 171/288 (59%), Positives = 222/288 (77%), Gaps = 5/288 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M   ++S++ + + GLSRY+ EIRK PML K EE++LA+R++EH D  AAH++VTSHLRL
Sbjct: 1   MAVSSLSVM-SPDGGLSRYLTEIRKFPMLPKDEEFMLAQRWKEHQDSEAAHKMVTSHLRL 59

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVKKF+P++GFRLATY+MWWI+A++QEYILRS
Sbjct: 60  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKKFEPDKGFRLATYAMWWIRASIQEYILRS 119

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTA QK+LFFNLR+ K  + A  D +L P+QV  IA KL V +SEVISMN RL
Sbjct: 120 WSLVKMGTTAAQKKLFFNLRKAKSQIAAFQDGDLHPDQVSYIATKLGVLDSEVISMNRRL 179

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYD-HDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
            G D SLNA + +     S+WQDWL  D    QE V+ E +E+  R  +L  +M  L  R
Sbjct: 180 GGPDASLNAPLRA--DGESEWQDWLADDNQVSQETVVAENQEKSMRMTLLEEAMVELTDR 237

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ER I   RRL+++P TLE+L++E+ VSRERVRQIE RAF+K+Q+S+++
Sbjct: 238 ERHILTERRLKDDPTTLEDLATEYGVSRERVRQIEVRAFEKLQKSMRE 285


>gi|94497521|ref|ZP_01304090.1| sigma 32 (RpoH) [Sphingomonas sp. SKA58]
 gi|94422938|gb|EAT07970.1| sigma 32 (RpoH) [Sphingomonas sp. SKA58]
          Length = 310

 Score =  296 bits (758), Expect = 3e-78,   Method: Composition-based stats.
 Identities = 165/290 (56%), Positives = 216/290 (74%), Gaps = 6/290 (2%)

Query: 1   MNRKNMSII--VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHL 58
           M + N+  +  + GE  L+RY+ EIRK P+L  ++EY+LAKRY+EH D  AA +LVTSHL
Sbjct: 8   MAKSNVPAVPALGGEASLNRYLSEIRKFPLLTPEQEYMLAKRYQEHQDPEAAAQLVTSHL 67

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLV KIAMGYRGYGLP+SE++SEGNIGLMQ VKKF+ +RGFRLATY+MWWI+A++QE+IL
Sbjct: 68  RLVAKIAMGYRGYGLPVSELISEGNIGLMQGVKKFEADRGFRLATYAMWWIRASIQEFIL 127

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
           RSWSLVK+GTTA QK+LFFNLRR+K +++A  D +L+PE V  IA  L VSE +VISMN 
Sbjct: 128 RSWSLVKMGTTAAQKKLFFNLRRMKNNIEAFEDGDLRPEDVTKIATDLGVSEDDVISMNR 187

Query: 179 RLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
           R+A  GD SLN  +   +    QWQDWL      Q++ + +++E+  R +ML  +M  LN
Sbjct: 188 RMAMGGDTSLNVPMR--EDGEGQWQDWLADTDPLQDERVADEQEKVQRHDMLVEAMDDLN 245

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            RE+ I   RRL E P TLE LS  + VSRERVRQIE RAF+K+Q+++ +
Sbjct: 246 DREKHILAERRLAEEPKTLEELSQVYGVSRERVRQIEVRAFEKLQKAMMR 295


>gi|148261701|ref|YP_001235828.1| RNA polymerase factor sigma-32 [Acidiphilium cryptum JF-5]
 gi|326405194|ref|YP_004285276.1| RNA polymerase sigma factor RpoH [Acidiphilium multivorum AIU301]
 gi|146403382|gb|ABQ31909.1| RNA polymerase, sigma 32 subunit, RpoH [Acidiphilium cryptum JF-5]
 gi|325052056|dbj|BAJ82394.1| RNA polymerase sigma factor RpoH [Acidiphilium multivorum AIU301]
          Length = 296

 Score =  295 bits (757), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 170/281 (60%), Positives = 217/281 (77%), Gaps = 3/281 (1%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +   E  L+RY+ EIRK PML  +EE  LA+ +R++ D +AAH+LVTSHLRLV KIAMGY
Sbjct: 1   MAPSEGNLARYLQEIRKFPMLSPEEEDRLARAWRDNEDQAAAHKLVTSHLRLVAKIAMGY 60

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           RGYGLP+ E++SEGN+G+MQAVK+FDPERGFRLATY+MWWI+AA+QEYIL SWSLVK+GT
Sbjct: 61  RGYGLPLGELISEGNVGMMQAVKRFDPERGFRLATYAMWWIRAAIQEYILHSWSLVKMGT 120

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLN 187
           TA QK+LFFNLRRLKG +QAI D +++PEQV  IA+ L V E +V+SMN RL A D SLN
Sbjct: 121 TAAQKKLFFNLRRLKGQMQAIEDGDMQPEQVEKIARVLGVPEQDVVSMNRRLTAPDHSLN 180

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           A I        +WQDWLV D D QE+ + + EE   RR +L  ++  LN RER I   RR
Sbjct: 181 APIRM--DGEGEWQDWLVDDADSQEEAIGDHEEMTGRRALLATALKTLNDRERHILIQRR 238

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           L+++P TLE+LS ++ +SRERVRQIE RAF+K+Q+S++ QV
Sbjct: 239 LKDDPTTLEDLSQQYNISRERVRQIEVRAFEKLQKSMKAQV 279


>gi|296114957|ref|ZP_06833602.1| RNA polymerase factor sigma-32 [Gluconacetobacter hansenii ATCC
           23769]
 gi|295978475|gb|EFG85208.1| RNA polymerase factor sigma-32 [Gluconacetobacter hansenii ATCC
           23769]
          Length = 299

 Score =  295 bits (757), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 173/286 (60%), Positives = 220/286 (76%), Gaps = 3/286 (1%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
            + +I+   E  LS+Y+ +IRK PML  +EE  L++ ++E GD  AAH+LVTSHLRLV K
Sbjct: 3   SSSAILSGPENNLSKYLRDIRKFPMLSPEEELKLSRLWKEKGDTEAAHKLVTSHLRLVAK 62

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IAMGYRGYGLP+ E++SEGNIG+MQAV++FDPERGFRLATY+MWWI+AA+QEYIL SWSL
Sbjct: 63  IAMGYRGYGLPVGELISEGNIGMMQAVRRFDPERGFRLATYAMWWIRAAIQEYILHSWSL 122

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG- 182
           VKIGTTA QK+LFFNLRRLKG +QAI D +L+PEQV  IAK L V E +V++MN RL+  
Sbjct: 123 VKIGTTAAQKKLFFNLRRLKGQMQAIDDGDLQPEQVDKIAKSLGVPEQDVVNMNRRLSAP 182

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
           D SLNA + +   +  +WQDWLV DHD QEQ L E EE   R+ +L  +M  LN RER I
Sbjct: 183 DHSLNAPLRT--DSEGEWQDWLVDDHDNQEQTLAENEEYSGRKALLANAMQSLNERERHI 240

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
              RRL+++P TLE+LS  + +SRERVRQIE RAF+KVQ +++ +V
Sbjct: 241 LTERRLKDDPATLEDLSHVYNISRERVRQIEVRAFEKVQNAMKAEV 286


>gi|259417918|ref|ZP_05741837.1| alternative sigma factor RpoH [Silicibacter sp. TrichCH4B]
 gi|259346824|gb|EEW58638.1| alternative sigma factor RpoH [Silicibacter sp. TrichCH4B]
          Length = 298

 Score =  295 bits (757), Expect = 4e-78,   Method: Composition-based stats.
 Identities = 166/299 (55%), Positives = 219/299 (73%), Gaps = 5/299 (1%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N  N+    + E GL+RY+ EIRK P+LE +EEY+LAKR+ E  D  AAH++VTSHLRL 
Sbjct: 3   NYANLPAP-SPEGGLNRYLQEIRKFPLLEPEEEYMLAKRWVEEQDTEAAHKMVTSHLRLA 61

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            KIAMGYRGYGLP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSW
Sbjct: 62  AKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSW 121

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL- 180
           SLVK+GTT+ QK+LFFNLR+ K  + A+ D +L+PE V  IA  L V+E EVISMN R+ 
Sbjct: 122 SLVKLGTTSAQKKLFFNLRKAKARIGALEDGDLRPEAVKKIATDLGVTEDEVISMNRRMS 181

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA++     ++ QWQDWL  +   Q      ++E + RR +L  +MSVLN RE+
Sbjct: 182 GGDASLNAMVGGDGDSTMQWQDWLEDEGADQAGDYEAQDELQARRELLAEAMSVLNDREK 241

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQK 299
            I   RRL +   TLE LS +++VSRER+RQIE RAF+K+Q+ ++   EL++   +LQ 
Sbjct: 242 DILTQRRLADQAKTLEELSVQYDVSRERIRQIEVRAFEKLQKKMR---ELAAGKGMLQP 297


>gi|260575497|ref|ZP_05843496.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacter sp. SW2]
 gi|259022417|gb|EEW25714.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacter sp. SW2]
          Length = 298

 Score =  295 bits (756), Expect = 5e-78,   Method: Composition-based stats.
 Identities = 167/287 (58%), Positives = 219/287 (76%), Gaps = 1/287 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+        + E GL+RY+ EIRK P+LE +EEY+LAKR+ +H D +AAH++VTSHLRL
Sbjct: 1   MSTYTNLPAPSPEQGLNRYMQEIRKFPLLEPEEEYMLAKRWVDHQDATAAHKMVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
             KIAMGYRGYGLP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRS
Sbjct: 61  AAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTT+ QK+LFFNLR+ K  + A+ + +L+PE V  IA  LNVSE+EVI MN RL
Sbjct: 121 WSLVKLGTTSAQKKLFFNLRKAKAKVGALEEGDLRPENVARIAHDLNVSETEVIDMNRRL 180

Query: 181 -AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
             GD SLNA + S  + S+QWQDWL  +   Q     E+ E + RR +L ++M+VLN RE
Sbjct: 181 SGGDASLNATVGSDGEGSTQWQDWLEDEDSDQANDYAERNELEMRRALLVQAMAVLNDRE 240

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           + I   RRL + PVTLE+LS+ + VSRER+RQIE RAF+K+QE +++
Sbjct: 241 KDILMQRRLADEPVTLEDLSASYGVSRERIRQIEVRAFEKLQERMRE 287


>gi|84688065|ref|ZP_01015924.1| RNA polymerase sigma factor [Maritimibacter alkaliphilus HTCC2654]
 gi|84663915|gb|EAQ10420.1| RNA polymerase sigma factor [Rhodobacterales bacterium HTCC2654]
          Length = 298

 Score =  295 bits (756), Expect = 5e-78,   Method: Composition-based stats.
 Identities = 169/298 (56%), Positives = 221/298 (74%), Gaps = 5/298 (1%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N + +      E GL+RY+ +IRK PMLE +EEY+LAKR+ +H D  AAH+LVTSHLRL 
Sbjct: 3   NYQTLPAPTP-EGGLNRYLQDIRKFPMLEPEEEYMLAKRWVDHQDTDAAHQLVTSHLRLA 61

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            KIAMGYRGYGLP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSW
Sbjct: 62  AKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSW 121

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL- 180
           SLVK+GTT+ QK+LFFNLR+ K  + A+ D +L+PE V  IA  LNV+E EVISMN R+ 
Sbjct: 122 SLVKLGTTSAQKKLFFNLRKAKARIGALEDGDLRPENVAQIAHDLNVTEEEVISMNRRMS 181

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA I +   ++ QWQDWL  +   Q     +++E   RR ML ++M VLN RE+
Sbjct: 182 GGDASLNATITNDGDSTMQWQDWLEDEDADQAGDYEQRDELTVRREMLAQAMDVLNDREK 241

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQ 298
            I   RRL +  VTLE+LS +++VSRER+RQIE RAF+K+Q+ +Q   EL+S   + +
Sbjct: 242 DILTQRRLSDETVTLEDLSGQYDVSRERIRQIEVRAFEKLQKRMQ---ELASEKGMAE 296


>gi|197103875|ref|YP_002129252.1| heat shock sigma factor RpoH [Phenylobacterium zucineum HLK1]
 gi|196477295|gb|ACG76823.1| heat shock sigma factor RpoH [Phenylobacterium zucineum HLK1]
          Length = 295

 Score =  295 bits (756), Expect = 5e-78,   Method: Composition-based stats.
 Identities = 178/287 (62%), Positives = 222/287 (77%), Gaps = 4/287 (1%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           N   +++ E GLSRY+ EIRK PML K EE++LAKR++EH D  AAHRLVTSHLRLV KI
Sbjct: 4   NALAVMSPEGGLSRYLTEIRKFPMLAKDEEFMLAKRWQEHQDPEAAHRLVTSHLRLVAKI 63

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           AMGYRGYGLPI EV+SEGN+GLMQAVKKFDP++GFRLATY+MWWI+A++QEYILRSWSLV
Sbjct: 64  AMGYRGYGLPIGEVISEGNVGLMQAVKKFDPDKGFRLATYAMWWIRASIQEYILRSWSLV 123

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GD 183
           K+GTTA QK+LFFNLR+ K  + A+ + +L+PEQV  IA KL V + EVISMN RLA GD
Sbjct: 124 KMGTTAAQKKLFFNLRKAKSEISALEEGDLRPEQVRQIATKLGVLDEEVISMNRRLAGGD 183

Query: 184 ESLNALINSSDKNSSQWQDWLVY-DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
            SLN+ + +   + S+WQDWLV  D   QE V+ E EER  R  +L  +M+ L  RER I
Sbjct: 184 ASLNSPLRA--DSESEWQDWLVDEDTPSQESVVAEAEERGIRMELLQEAMAELTDRERHI 241

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
              RRL++ P TLE L+S++ VSRERVRQIE RAF+K+Q+S++   E
Sbjct: 242 LTERRLKDEPTTLEELASQYGVSRERVRQIEVRAFEKLQKSMRAAAE 288


>gi|58038976|ref|YP_190940.1| RNA polymerase factor sigma-32 [Gluconobacter oxydans 621H]
 gi|58001390|gb|AAW60284.1| Heat shock sigma factor RpoH [Gluconobacter oxydans 621H]
          Length = 297

 Score =  295 bits (756), Expect = 6e-78,   Method: Composition-based stats.
 Identities = 176/283 (62%), Positives = 216/283 (76%), Gaps = 3/283 (1%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           I V  E  L+RY+ EIRK P+L  QEE  L++R+R+  D SAAHRLVTSHLRLV KIAMG
Sbjct: 7   ISVGPENNLTRYLQEIRKFPLLTPQEELDLSRRWRKDEDTSAAHRLVTSHLRLVAKIAMG 66

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           YRGYGLP++E++SEGNIG+MQAV++FDPERGFRLATY+MWWI+AAMQEYIL SWSLVK+G
Sbjct: 67  YRGYGLPVNELISEGNIGMMQAVRRFDPERGFRLATYAMWWIRAAMQEYILHSWSLVKMG 126

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESL 186
           TTA QK+LFFNLRRLKG +QAI D +LKPEQV +IA  L V E +V+SMN RLA  D SL
Sbjct: 127 TTAAQKKLFFNLRRLKGQMQAIDDGDLKPEQVNSIATTLGVPEQDVVSMNQRLAAPDHSL 186

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           NA +        +WQDWLV DH+ QEQ     EE   R+ +L +++  LN RER I   R
Sbjct: 187 NAPLRI--DGEGEWQDWLVDDHENQEQTYAASEEFTGRKALLDQALMTLNERERHILSER 244

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           RL+E P TLE LS  + VSRER+RQIEARA +K+Q+++  +VE
Sbjct: 245 RLKEEPSTLEELSHHYNVSRERIRQIEARAMEKLQKAMAAEVE 287


>gi|304320253|ref|YP_003853896.1| RNA polymerase sigma factor [Parvularcula bermudensis HTCC2503]
 gi|303299155|gb|ADM08754.1| RNA polymerase sigma factor [Parvularcula bermudensis HTCC2503]
          Length = 304

 Score =  295 bits (755), Expect = 6e-78,   Method: Composition-based stats.
 Identities = 168/279 (60%), Positives = 220/279 (78%), Gaps = 2/279 (0%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ E GL+RY+ EIRK P+LE+ EEY+LAKR++EH D  AA RL+TSHLRLV KIAMGYR
Sbjct: 13  LSPEGGLNRYLAEIRKFPLLERDEEYMLAKRFKEHEDPDAAQRLITSHLRLVAKIAMGYR 72

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYGLP  EV+SEGN+GLMQAVKKFDP++GFRL+TY+MWWI+A++QEYILRSWSLVKIGTT
Sbjct: 73  GYGLPTGEVISEGNVGLMQAVKKFDPDKGFRLSTYAMWWIRASIQEYILRSWSLVKIGTT 132

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNA 188
           A QK+LFFNLR+LKG + A+ + +++PE+V  IA +L V+E EVISMN R+AG D SLN+
Sbjct: 133 AAQKKLFFNLRKLKGQIDAVDEGDMRPEEVELIATRLGVTEDEVISMNRRMAGSDNSLNS 192

Query: 189 LINSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
            + S     ++WQDWLV ++    E  L++ +E + R  +L  +M  LN RER I   RR
Sbjct: 193 PMRSDGDGGAEWQDWLVDENAVNAESQLVKDDEFETRMELLQEAMVDLNDRERHILTERR 252

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           L ENP TLE LS E+ VSRER+RQIE RAF+K+Q+++++
Sbjct: 253 LTENPKTLEELSGEYGVSRERIRQIEVRAFEKLQKAMKR 291


>gi|23015588|ref|ZP_00055360.1| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Magnetospirillum magnetotacticum
           MS-1]
          Length = 296

 Score =  295 bits (755), Expect = 7e-78,   Method: Composition-based stats.
 Identities = 176/286 (61%), Positives = 223/286 (77%), Gaps = 3/286 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M     S+ +  E  L+RY+ +IRK PML  +EEY+LAKR+REHGDL AA+RLVTSHLRL
Sbjct: 1   MTAIASSLSLAPEGNLTRYLQDIRKFPMLPPEEEYLLAKRFREHGDLPAANRLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLP+ E++SEGN+G+MQAV++FDPERGFRLATY+MWWI+AA+QEYIL S
Sbjct: 61  VAKIAMGYRGYGLPLGELISEGNVGMMQAVRRFDPERGFRLATYAMWWIRAAIQEYILHS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTA QK+LFFNLR+LKG +QAI + ++  E V  IA KL V+E EVI+MN RL
Sbjct: 121 WSLVKMGTTAAQKKLFFNLRKLKGQMQAIEEGDMSAENVAKIATKLEVTEDEVITMNRRL 180

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +  D SLNA + +  +   +WQDWLV DH+ QE  L E+EE   RR MLT +++ LN RE
Sbjct: 181 SSPDHSLNAPVRT--EGEGEWQDWLVDDHEDQETELGEREEMGQRRGMLTSALAALNDRE 238

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           R I   RRL E+P TLE+LS  + +SRERVRQIE RAF+K+Q+S++
Sbjct: 239 RAILIQRRLTEDPATLEDLSQRYGISRERVRQIEVRAFEKLQKSVK 284


>gi|295688294|ref|YP_003591987.1| RNA polymerase sigma 32 factor subunit RpoH [Caulobacter segnis
           ATCC 21756]
 gi|295430197|gb|ADG09369.1| RNA polymerase, sigma 32 subunit, RpoH [Caulobacter segnis ATCC
           21756]
          Length = 295

 Score =  295 bits (755), Expect = 7e-78,   Method: Composition-based stats.
 Identities = 170/288 (59%), Positives = 225/288 (78%), Gaps = 5/288 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M   ++S++ + + GLSRY+ EIRK PML K EE++LA+R++EH D  AAH++VTSHLRL
Sbjct: 1   MAVNSLSVM-SPDGGLSRYLTEIRKFPMLSKDEEFMLAQRWKEHQDPQAAHKMVTSHLRL 59

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVKKF+P++GFRLATY+MWWI+A++QEYILRS
Sbjct: 60  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKKFEPDKGFRLATYAMWWIRASIQEYILRS 119

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTA QK+LFFNLR+ K  + A  + +L+PEQV AIA KL V +SEVISMN RL
Sbjct: 120 WSLVKMGTTAAQKKLFFNLRKAKSQIAAFQEGDLRPEQVSAIATKLGVLDSEVISMNRRL 179

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           +G D SLNA + S   + S+WQDWL  +    QE  + E EE+  R ++L  +M  L  R
Sbjct: 180 SGPDASLNAPLRS--DSESEWQDWLADEEQVSQETRVAEDEEKSLRMSLLEEAMVELTDR 237

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ER I   RRL+++P TLE L++++ VSRERVRQIE RAF+K+Q+++++
Sbjct: 238 ERHILTERRLKDDPTTLEELAAQYGVSRERVRQIEVRAFEKLQKTMRE 285


>gi|260425792|ref|ZP_05779772.1| alternative sigma factor RpoH [Citreicella sp. SE45]
 gi|260423732|gb|EEX16982.1| alternative sigma factor RpoH [Citreicella sp. SE45]
          Length = 298

 Score =  294 bits (754), Expect = 9e-78,   Method: Composition-based stats.
 Identities = 170/286 (59%), Positives = 217/286 (75%), Gaps = 2/286 (0%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N  N+    + E GLSRY+ EIRK P+LE +EEY+LAKR+ E  D  +AH+LVTSHLRL 
Sbjct: 3   NYANLPAP-SPEAGLSRYLSEIRKFPLLEPEEEYMLAKRWVEDQDAPSAHKLVTSHLRLA 61

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            KIAMGYRGYGLP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSW
Sbjct: 62  AKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSW 121

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL- 180
           SLVK+GTT+ QK+LFFNLR+ K  + A+ + +L+PE V  IA  L VS+ EVISMN RL 
Sbjct: 122 SLVKLGTTSAQKKLFFNLRKAKSRIGALEEGDLRPEHVEKIATDLGVSKDEVISMNRRLS 181

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA + S D +S QWQDWL  +   Q     E+ E + RR +L ++M VLN RE+
Sbjct: 182 GGDASLNATVGSDDDSSMQWQDWLEDEGADQASDYAERNELEARRALLAQAMDVLNDREK 241

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            I   RRL E PVTLE+LSS ++VSRER+RQIE RAF+K+Q+ +++
Sbjct: 242 DILTQRRLAEQPVTLEDLSSVYDVSRERIRQIEVRAFEKLQKRMRE 287


>gi|83592357|ref|YP_426109.1| RNA polymerase factor sigma-32 [Rhodospirillum rubrum ATCC 11170]
 gi|83575271|gb|ABC21822.1| Sigma 32 (RpoH) [Rhodospirillum rubrum ATCC 11170]
          Length = 306

 Score =  294 bits (753), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 159/278 (57%), Positives = 204/278 (73%), Gaps = 3/278 (1%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V+ E GLSRY+ EI++ PML  +EE++LAKR ++ GD  AAHRLVTSHLRLV KIAMGYR
Sbjct: 11  VSDEGGLSRYLTEIKRFPMLTPEEEFMLAKRLQDEGDRDAAHRLVTSHLRLVAKIAMGYR 70

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
            YGLP+S++V+EGN+GLM+AVKKF+ +RGFRLATY+MWWIKA++ EYIL SWSLVK+GT 
Sbjct: 71  HYGLPVSDLVAEGNMGLMKAVKKFEADRGFRLATYAMWWIKASINEYILNSWSLVKVGTV 130

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNA 188
           A QK+LFFNLRRLK  L    + +L PE V  IA +L V+E++V+ MN RLAG D SLN 
Sbjct: 131 AAQKKLFFNLRRLKAKLGVYEEGDLSPEDVKTIATQLKVTEADVVMMNRRLAGPDASLNV 190

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +   +  S    D L+ + D QE+V    EE+     +L  ++S L  RER I  ARRL
Sbjct: 191 PV--GEDQSMDRMDLLMDEGDNQEEVYAAHEEQSLGNRLLKDALSTLTERERHIITARRL 248

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +  PVTLE L  E+ VSRERVRQIE RAF+K+Q +++K
Sbjct: 249 RSEPVTLEELGGEYGVSRERVRQIENRAFEKLQTAVRK 286


>gi|83312286|ref|YP_422550.1| RNA polymerase factor sigma-32 [Magnetospirillum magneticum AMB-1]
 gi|82947127|dbj|BAE51991.1| DNA-directed RNA polymerase, sigma subunit [Magnetospirillum
           magneticum AMB-1]
          Length = 296

 Score =  294 bits (753), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 175/287 (60%), Positives = 222/287 (77%), Gaps = 3/287 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M     S+ +  E  L+RY+ +IRK PML  +EEY+LAKR+REHGDL AA+RLVTSHLRL
Sbjct: 1   MTAIASSLSLAPEGNLTRYLQDIRKFPMLPPEEEYLLAKRFREHGDLPAANRLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLP+ E++SEGN+G+MQAV++FDPERGFRLATY+MWWI+AA+QEYIL S
Sbjct: 61  VAKIAMGYRGYGLPLGELISEGNVGMMQAVRRFDPERGFRLATYAMWWIRAAIQEYILHS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTA QK+LFFNLR+LKG +QAI + ++  E V  IA KL V+E EV++MN RL
Sbjct: 121 WSLVKMGTTAAQKKLFFNLRKLKGQMQAIEEGDMSAENVAKIATKLEVTEDEVVTMNRRL 180

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +  D SLNA + +  +   +WQDWLV DH+ QE  L E+EE   RR MLT ++  LN RE
Sbjct: 181 SSPDHSLNAPVRA--EGEGEWQDWLVDDHEDQETELGEREELGQRRQMLTSALEALNDRE 238

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R I   RRL E+P TLE+LS  + +SRERVRQIE RAF+K+Q+S++ 
Sbjct: 239 RAILIQRRLTEDPATLEDLSQRYGISRERVRQIEVRAFEKLQKSVKS 285


>gi|119384948|ref|YP_916004.1| RNA polymerase factor sigma-32 [Paracoccus denitrificans PD1222]
 gi|119374715|gb|ABL70308.1| RNA polymerase, sigma 32 subunit, RpoH [Paracoccus denitrificans
           PD1222]
          Length = 301

 Score =  294 bits (753), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 168/288 (58%), Positives = 214/288 (74%), Gaps = 2/288 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M         + E GL+RY+ EIRK P+LE +EEY+LAK + +H D  AA RLVTSHLRL
Sbjct: 1   MANYTNLPAPSPEQGLNRYLQEIRKFPLLEPEEEYMLAKAWVDHQDAEAAQRLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
             KIAMGYRGYGLP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRS
Sbjct: 61  AAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTT+ QK+LFFNLR+ K  L A+ + +L+PE V  IA  LNV+E EVI MN RL
Sbjct: 121 WSLVKMGTTSAQKKLFFNLRKAKSKLGALEEGDLRPENVTQIAHDLNVTEQEVIDMNRRL 180

Query: 181 -AGDESLNALINSSDKNSS-QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
            +GD SLNA + S D  S+ QWQDWL  +   Q +   E +E   RR ML  +M VLN R
Sbjct: 181 SSGDASLNATVGSGDGESTAQWQDWLEDEDANQAEAFAEADELSARREMLIAAMDVLNDR 240

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E+ I   RRL+++P+TLE+LS+ + VSRER+RQIE RAF+K+Q  I++
Sbjct: 241 EKDILMERRLRDDPMTLEDLSTRYGVSRERIRQIEVRAFEKLQNRIRE 288


>gi|114763110|ref|ZP_01442536.1| RNA polymerase sigma factor [Pelagibaca bermudensis HTCC2601]
 gi|114544163|gb|EAU47172.1| RNA polymerase sigma factor [Roseovarius sp. HTCC2601]
          Length = 298

 Score =  294 bits (753), Expect = 1e-77,   Method: Composition-based stats.
 Identities = 171/286 (59%), Positives = 214/286 (74%), Gaps = 1/286 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M++       + E GLSRY+ EIRK P+LE +EEY+LAKR+ E  D  +AHRLVTSHLRL
Sbjct: 1   MSKYANLPAPSPEAGLSRYLSEIRKFPLLEPEEEYMLAKRWVEDQDAESAHRLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
             KIAMGYRGYGLP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRS
Sbjct: 61  AAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTT+ QK+LFFNLR+ K  + A+ D +L+PE V  IA  L V+  EVISMN RL
Sbjct: 121 WSLVKLGTTSAQKKLFFNLRKAKSRIGALEDGDLRPEHVERIATDLGVTHDEVISMNRRL 180

Query: 181 -AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
             GD SLNA + S D++S QWQDWL  +   Q     E+ E + RR +LT +M VLN RE
Sbjct: 181 SGGDASLNATVGSDDESSMQWQDWLEDESADQAGDYAERNELEARRELLTEAMDVLNERE 240

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           R I   RRL E PVTLE LS  ++VSRER+RQIE RAF+K+Q+ ++
Sbjct: 241 RDILTQRRLAEQPVTLEELSGVYDVSRERIRQIEVRAFEKLQKRMR 286


>gi|163747420|ref|ZP_02154772.1| RNA polymerase sigma factor [Oceanibulbus indolifex HEL-45]
 gi|161379273|gb|EDQ03690.1| RNA polymerase sigma factor [Oceanibulbus indolifex HEL-45]
          Length = 298

 Score =  294 bits (752), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 163/285 (57%), Positives = 216/285 (75%), Gaps = 2/285 (0%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N  N+      E GL+RY+ EIRK P+LE +EEY+LAKR+ E  D  AAHR+VTSHLRL 
Sbjct: 3   NYANLPAPTP-EGGLNRYMQEIRKFPLLEPEEEYMLAKRWVEEQDTEAAHRMVTSHLRLA 61

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            KIAMGYRGYGLP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSW
Sbjct: 62  AKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSW 121

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL- 180
           SLVK+GTT+ QK+LFFNLR+ K  + A+ + +L+PE V  IA +L V+E+EV+SMN R+ 
Sbjct: 122 SLVKLGTTSGQKKLFFNLRKAKNKIGALEEGDLRPENVTEIATQLGVTEAEVVSMNRRMS 181

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA + S  + + QWQDWL  +   Q     E++E + RR ML  ++ VLN RE+
Sbjct: 182 GGDASLNATVGSEGEGTMQWQDWLEDEDADQAGDYAERDELETRREMLADALDVLNDREK 241

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            I   RRL +  VTLE+LS++++VSRER+RQIE RAF+K+Q+ ++
Sbjct: 242 DILTQRRLSDETVTLEDLSTQYDVSRERIRQIEVRAFEKLQKRMR 286


>gi|329849869|ref|ZP_08264715.1| alternative sigma factor RpoH [Asticcacaulis biprosthecum C19]
 gi|328841780|gb|EGF91350.1| alternative sigma factor RpoH [Asticcacaulis biprosthecum C19]
          Length = 299

 Score =  293 bits (751), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 172/288 (59%), Positives = 222/288 (77%), Gaps = 5/288 (1%)

Query: 1   MNRKNMSII--VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHL 58
           +   N+S    ++ + GL+RY+ EIRK PML K EE++LAKR++EH D  AAH+LVTSHL
Sbjct: 7   LTTSNLSSTPALSPDGGLNRYLSEIRKFPMLAKDEEFMLAKRWQEHQDPKAAHKLVTSHL 66

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLV KIAMGYRGYGLP+ EV+SEGN+GLMQAVKKFD +RGFRLATY+MWWIKA++QEY+L
Sbjct: 67  RLVAKIAMGYRGYGLPVGEVISEGNVGLMQAVKKFDADRGFRLATYAMWWIKASIQEYVL 126

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
           RSWSLVK+GTTA QK+LFFNLR++K  + A+ + +L+ EQV  IA KL VSE++VI+MN 
Sbjct: 127 RSWSLVKMGTTAAQKKLFFNLRKVKSEISALEEGDLRHEQVEQIATKLGVSETDVINMNR 186

Query: 179 RLAG-DESLNALINSSDKNSSQWQDWLVYD-HDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
           R++  D SLNA I +S+   S+WQDWLV D    QE VL + EE   R  +L  +M  LN
Sbjct: 187 RMSSPDSSLNAPIRASEGE-SEWQDWLVDDKQVSQETVLADSEEYSQRMGLLEAAMGELN 245

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            RER I   RRL+++P TLE+L+  F VSRERVRQIE RAF+K+Q+++
Sbjct: 246 AREREILTERRLKDSPTTLEDLAERFGVSRERVRQIEVRAFEKLQKAM 293


>gi|159045149|ref|YP_001533943.1| RNA polymerase factor sigma-32 [Dinoroseobacter shibae DFL 12]
 gi|157912909|gb|ABV94342.1| RNA polymerase [Dinoroseobacter shibae DFL 12]
          Length = 298

 Score =  293 bits (751), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 165/286 (57%), Positives = 214/286 (74%), Gaps = 1/286 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M         + E GL+RY+ EIRK PMLE +EEY+LAKR+ +H D  AAH++VTSHLRL
Sbjct: 1   MASYTNLPAPSPEQGLNRYLQEIRKFPMLEPEEEYMLAKRWVDHEDTEAAHKMVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
             KIAMGYRGYGLP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRS
Sbjct: 61  AAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTT+ QK+LFFNLR+ K  + A+ + +L+PE V  IA  LNV+E EVISMN R+
Sbjct: 121 WSLVKLGTTSAQKKLFFNLRKAKNRIGALEEGDLRPENVARIANDLNVTEDEVISMNRRM 180

Query: 181 -AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
             GD SLNA+I S  + +++WQDWL  +   Q     EK+E   RR +L  +M VLN RE
Sbjct: 181 SGGDASLNAMIGSDGEGATEWQDWLEDEDADQADDFAEKDELMVRRELLAEAMGVLNDRE 240

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + I   RRL++ P TLE LS  + VSRER+RQIE RAF+K+Q++++
Sbjct: 241 KDILMKRRLEDKPATLEELSEVYGVSRERIRQIEVRAFEKLQKAMR 286


>gi|294678332|ref|YP_003578947.1| RNA polymerase sigma-32 factor [Rhodobacter capsulatus SB 1003]
 gi|294477152|gb|ADE86540.1| RNA polymerase sigma-32 factor-2 [Rhodobacter capsulatus SB 1003]
          Length = 299

 Score =  293 bits (751), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 172/279 (61%), Positives = 216/279 (77%), Gaps = 2/279 (0%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
            + E GL+RY+ EIRK P+LE +EEY+LAK + +H D  AAHRLVTSHLRL  KIAMGYR
Sbjct: 10  PSPEQGLNRYLQEIRKFPLLEPEEEYMLAKAWVDHQDPKAAHRLVTSHLRLAAKIAMGYR 69

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYGLP +EV+SE N+GLMQAVK+FDPERGFRLATY+MWWI+AA+QEYILRSWSLVK+GTT
Sbjct: 70  GYGLPQAEVISEANVGLMQAVKRFDPERGFRLATYAMWWIRAAIQEYILRSWSLVKLGTT 129

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNA 188
           + QK+LFFNLR+ K  + A+ + +L+P+ V  IA  LNVSE +VI MN RLAG D SLNA
Sbjct: 130 SAQKKLFFNLRKAKSKIGALDEGDLRPDAVAKIAHDLNVSEDDVIEMNRRLAGSDASLNA 189

Query: 189 LINSSDKNS-SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
            + +SD  S +QWQDWL  +   Q +   E +E + RR ML  +M VLN RER I  ARR
Sbjct: 190 QVGASDGESATQWQDWLEDEDADQAEAYAEADELQARRAMLVAAMDVLNERERDILMARR 249

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           L++ PVTLE LSS+++VSRER+RQIE RAF+K+Q  ++ 
Sbjct: 250 LRDEPVTLEELSSQYDVSRERIRQIEVRAFEKLQGRMKA 288


>gi|310815299|ref|YP_003963263.1| alternative sigma factor RpoH [Ketogulonicigenium vulgare Y25]
 gi|308754034|gb|ADO41963.1| alternative sigma factor RpoH [Ketogulonicigenium vulgare Y25]
          Length = 298

 Score =  293 bits (751), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 163/285 (57%), Positives = 211/285 (74%), Gaps = 1/285 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+        + E GLSRY+ EIRK PMLE ++EY+LA+ + +HGD  AAH+LVTSHLRL
Sbjct: 1   MSTYTNLPAPSPEQGLSRYLQEIRKFPMLEPEQEYMLARNWVDHGDTQAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
             KIAMGYRGYGLP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRS
Sbjct: 61  AAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTT+ QK+LFFNLR+ K  + A+ + +L+PE V  IA  L V E EV++MN RL
Sbjct: 121 WSLVKLGTTSAQKKLFFNLRKAKARIGALEEGDLRPEHVQRIAHDLGVPEEEVVNMNRRL 180

Query: 181 -AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
             GD SLNA++   D +S+QWQDWL  +   Q      ++E   RR +L  +M  LN RE
Sbjct: 181 SGGDASLNAMVGGDDDSSTQWQDWLEDEDSDQAADFEARDELDARRVLLEAAMEDLNDRE 240

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R +   RRLQ+ PVTLE LS ++ VSRER+RQIE RAF+K+Q+ +
Sbjct: 241 RDVLMMRRLQDPPVTLEELSEKYSVSRERIRQIEVRAFEKLQKRM 285


>gi|2384764|gb|AAC97123.1| heat shock sigma factor [Rhodobacter capsulatus]
          Length = 299

 Score =  293 bits (750), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 171/279 (61%), Positives = 214/279 (76%), Gaps = 2/279 (0%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
            + E GL+RY+ EIRK P+LE +EEY+LAK + +H D  AAHRLVTSHLRL  KIAMGYR
Sbjct: 10  PSPEQGLNRYLQEIRKFPLLEPEEEYMLAKAWVDHQDPKAAHRLVTSHLRLAAKIAMGYR 69

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYGLP +EV+SE N+GLMQAVK+FDPERGFRLATY+MWWI+AA+QEYILRSWSLVK+GTT
Sbjct: 70  GYGLPQAEVISEANVGLMQAVKRFDPERGFRLATYAMWWIRAAIQEYILRSWSLVKLGTT 129

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNA 188
           + QK+LFFNLR+ K  + A  + +L+P+ V  IA  LNVSE +VI MN RLAG D SLNA
Sbjct: 130 SAQKKLFFNLRKAKSKIGAFEEGDLRPDAVAKIAHDLNVSEGDVIEMNRRLAGSDASLNA 189

Query: 189 LINSSDKNS-SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
            + + D  S +QWQDWL  +   Q +   E +E + RR ML  +M VLN RER I  ARR
Sbjct: 190 QVGAGDGESATQWQDWLEDEDADQAEAYAEADELQARRAMLVAAMDVLNERERDILMARR 249

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           L++ PVTLE LSS+++VSRER+RQIE RAF+K+Q  ++ 
Sbjct: 250 LRDEPVTLEELSSQYDVSRERIRQIEVRAFEKLQGRMKA 288


>gi|89067929|ref|ZP_01155373.1| RNA polymerase sigma factor [Oceanicola granulosus HTCC2516]
 gi|89046527|gb|EAR52583.1| RNA polymerase sigma factor [Oceanicola granulosus HTCC2516]
          Length = 297

 Score =  293 bits (750), Expect = 2e-77,   Method: Composition-based stats.
 Identities = 168/287 (58%), Positives = 215/287 (74%), Gaps = 2/287 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M   N+    + E GL+RY+ EIR+ PMLE +EEY+LAKR+ +H D  AAH+LVTSHLRL
Sbjct: 1   MPTNNLPAP-SPEQGLNRYLQEIRRFPMLEPEEEYMLAKRWVDHEDTDAAHKLVTSHLRL 59

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
             KIAMGYRGYGLP +EV+SE N+GLMQAVK+FDPERGFRLATY+MWWI+A++QEYILRS
Sbjct: 60  AAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPERGFRLATYAMWWIRASIQEYILRS 119

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTT+ QK+LFFNLR+ K  + A+ + +L+PE V  IA  L V+E+EVISMN RL
Sbjct: 120 WSLVKLGTTSAQKKLFFNLRKAKARIGALEEGDLRPENVAQIANDLGVTETEVISMNRRL 179

Query: 181 -AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
             GD SLNA+I +   +++QWQDWL  +   Q     E++E   RR +L  +M VLN RE
Sbjct: 180 SGGDASLNAMIGTEGDSATQWQDWLEDESADQAGDYEERDELSTRRELLGEAMDVLNDRE 239

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           + I   RRLQ+  VTLE LS ++ VSRER+RQIE RAF K+Q  +Q+
Sbjct: 240 KDILTQRRLQDQAVTLEELSGQYGVSRERIRQIEVRAFDKLQARMQQ 286


>gi|99080404|ref|YP_612558.1| RNA polymerase factor sigma-32 [Ruegeria sp. TM1040]
 gi|99036684|gb|ABF63296.1| RNA polymerase, sigma 32 subunit, RpoH [Ruegeria sp. TM1040]
          Length = 299

 Score =  293 bits (750), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 168/298 (56%), Positives = 220/298 (73%), Gaps = 5/298 (1%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N  N+    + E GL+RY+ EIRK P+LE +EEY+LAKR+ E  D  AAH++VTSHLRL 
Sbjct: 3   NYANLPAP-SPEGGLNRYLQEIRKFPLLEPEEEYMLAKRWVEEQDTEAAHKMVTSHLRLA 61

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            KIAMGYRGYGLP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSW
Sbjct: 62  AKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSW 121

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL- 180
           SLVK+GTT+ QK+LFFNLR+ K  + A+ D +L+PE V  IA  L V+E EVISMN R+ 
Sbjct: 122 SLVKLGTTSAQKKLFFNLRKAKARIGALEDGDLRPEVVKKIATDLGVTEDEVISMNRRMS 181

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA++ S   ++ QWQDWL  +   Q      ++E + RR +L  +MSVLN RE+
Sbjct: 182 GGDASLNAMVGSDGDSTMQWQDWLEDEDADQAGDYEARDELQARRELLAEAMSVLNDREK 241

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQ 298
            I   RRL E   TLE LS +++VSRER+RQIE RAF+K+Q+ ++   EL++   +LQ
Sbjct: 242 DILTQRRLAEQAKTLEELSVQYDVSRERIRQIEVRAFEKLQKKMR---ELAAGKGMLQ 296


>gi|239977584|sp|P0CAW9|RP32_CAUCR RecName: Full=RNA polymerase sigma-32 factor
 gi|239977655|sp|B8H3C3|RP32_CAUCN RecName: Full=RNA polymerase sigma-32 factor
 gi|1262200|gb|AAC43981.1| RpoH [Caulobacter vibrioides]
 gi|1588870|prf||2209377A heat shock sigma factor 32
          Length = 295

 Score =  293 bits (750), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 168/288 (58%), Positives = 222/288 (77%), Gaps = 5/288 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M   ++S++ + + GLSRY+ EIRK PML K EE++LA+R++EH D  AAH++VTSHLRL
Sbjct: 1   MAVNSLSVM-SPDGGLSRYLTEIRKFPMLSKDEEFMLAQRWKEHQDPQAAHKMVTSHLRL 59

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVKKF+PE+GFRLATY+MWWI+A++QEYILRS
Sbjct: 60  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKKFEPEKGFRLATYAMWWIRASIQEYILRS 119

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTA QK+LFFNLR+ K  + A  + +L P+QV  IA KL V +SEVISMN RL
Sbjct: 120 WSLVKMGTTAAQKKLFFNLRKAKSQIAAFQEGDLHPDQVSQIATKLGVLDSEVISMNRRL 179

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           +G D SLNA + +     S+WQDWL  +    QE  + E EE+  R ++L  +M  L  R
Sbjct: 180 SGPDASLNAPLRA--DGESEWQDWLADEEQVSQETRVAEDEEKSLRMSLLEEAMVELTDR 237

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ER I   RRL+++P TLE L++++ VSRERVRQIE RAF+K+Q+++++
Sbjct: 238 ERHILTERRLKDDPTTLEELAAQYGVSRERVRQIEVRAFEKLQKTMRE 285


>gi|16127328|ref|NP_421892.1| RNA polymerase factor sigma-32 [Caulobacter crescentus CB15]
 gi|221236131|ref|YP_002518568.1| RNA polymerase factor sigma-32 [Caulobacter crescentus NA1000]
 gi|13424754|gb|AAK25060.1| heat shock sigma factor RpoH [Caulobacter crescentus CB15]
 gi|220965304|gb|ACL96660.1| RNA polymerase sigma-32 factor [Caulobacter crescentus NA1000]
          Length = 298

 Score =  292 bits (749), Expect = 3e-77,   Method: Composition-based stats.
 Identities = 168/288 (58%), Positives = 222/288 (77%), Gaps = 5/288 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M   ++S++ + + GLSRY+ EIRK PML K EE++LA+R++EH D  AAH++VTSHLRL
Sbjct: 4   MAVNSLSVM-SPDGGLSRYLTEIRKFPMLSKDEEFMLAQRWKEHQDPQAAHKMVTSHLRL 62

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVKKF+PE+GFRLATY+MWWI+A++QEYILRS
Sbjct: 63  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKKFEPEKGFRLATYAMWWIRASIQEYILRS 122

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTA QK+LFFNLR+ K  + A  + +L P+QV  IA KL V +SEVISMN RL
Sbjct: 123 WSLVKMGTTAAQKKLFFNLRKAKSQIAAFQEGDLHPDQVSQIATKLGVLDSEVISMNRRL 182

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           +G D SLNA + +     S+WQDWL  +    QE  + E EE+  R ++L  +M  L  R
Sbjct: 183 SGPDASLNAPLRA--DGESEWQDWLADEEQVSQETRVAEDEEKSLRMSLLEEAMVELTDR 240

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ER I   RRL+++P TLE L++++ VSRERVRQIE RAF+K+Q+++++
Sbjct: 241 ERHILTERRLKDDPTTLEELAAQYGVSRERVRQIEVRAFEKLQKTMRE 288


>gi|307293092|ref|ZP_07572938.1| RNA polymerase, sigma 32 subunit, RpoH [Sphingobium
           chlorophenolicum L-1]
 gi|306881158|gb|EFN12374.1| RNA polymerase, sigma 32 subunit, RpoH [Sphingobium
           chlorophenolicum L-1]
          Length = 304

 Score =  291 bits (746), Expect = 6e-77,   Method: Composition-based stats.
 Identities = 162/279 (58%), Positives = 210/279 (75%), Gaps = 4/279 (1%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           + GE  L+RY+ EIRK P+L  ++EY+LAKRY EH D  AA +LVTSHLRLV KIAMGYR
Sbjct: 13  LGGEASLNRYLSEIRKFPILTPEQEYMLAKRYAEHADSEAAAQLVTSHLRLVAKIAMGYR 72

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYGLP+SE++SEGNIGLMQ VKKF+P+RGFRLATY+MWWI+A++QE+ILRSWSLVK+GTT
Sbjct: 73  GYGLPVSELISEGNIGLMQGVKKFEPDRGFRLATYAMWWIRASIQEFILRSWSLVKMGTT 132

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
           A QK+LFFNLRR+K +++A  D +L P+ V  IA  L V+E +VISMN R+A  GD SLN
Sbjct: 133 AAQKKLFFNLRRMKNNIEAFEDGDLHPDDVKKIATDLGVTEEDVISMNRRMAMGGDTSLN 192

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             +   +    QWQDWL      Q++ + +++E + R +ML  +M  LN RE+ I   RR
Sbjct: 193 VPMR--EDGEGQWQDWLADTDPLQDERVADRQESELRHDMLVEAMDDLNDREKHILAERR 250

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           L E P TLE LS  + VSRERVRQIE RAF+K+Q+++ +
Sbjct: 251 LAEEPKTLEELSQVYGVSRERVRQIEVRAFEKLQKAMMR 289


>gi|89055891|ref|YP_511342.1| RNA polymerase factor sigma-32 [Jannaschia sp. CCS1]
 gi|88865440|gb|ABD56317.1| RNA polymerase, sigma 32 subunit, RpoH [Jannaschia sp. CCS1]
          Length = 298

 Score =  291 bits (746), Expect = 7e-77,   Method: Composition-based stats.
 Identities = 165/286 (57%), Positives = 216/286 (75%), Gaps = 2/286 (0%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N  N+    + E GL+RY+ EIRK PMLE +EEY+LAK + E  D  AAH++VTSHLRL 
Sbjct: 3   NYANLPAP-SPEGGLNRYLQEIRKFPMLEPEEEYMLAKAWAEKEDTEAAHKMVTSHLRLA 61

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            KIAMGYRGYGLP +EV+SE N+GLMQAVKKFDPE+GFRLATY+MWWI+AA+QEY+LRSW
Sbjct: 62  AKIAMGYRGYGLPQAEVISEANVGLMQAVKKFDPEKGFRLATYAMWWIRAAIQEYVLRSW 121

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL- 180
           S+VK+GTT+ QK+LFFNLR+ K  + A+ + +L+PE V  IA  L V+E+EV+SMN R+ 
Sbjct: 122 SMVKLGTTSAQKKLFFNLRKAKARIGALEEGDLRPENVERIANDLGVTEAEVVSMNRRMS 181

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA + S D+ S+QWQDWL  +   Q     E++E ++R  ++  +M VLN RE+
Sbjct: 182 GGDASLNATVGSEDEGSAQWQDWLEDEDADQATDYAERDEFQSRMALMAEAMEVLNDREK 241

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            I   RRLQE  VTLE+LS  + VSRERVRQIE RAF+K+Q+ +++
Sbjct: 242 DILTQRRLQEKAVTLEDLSGVYNVSRERVRQIEVRAFEKLQKRMRE 287


>gi|254464548|ref|ZP_05077959.1| alternative sigma factor RpoH [Rhodobacterales bacterium Y4I]
 gi|206685456|gb|EDZ45938.1| alternative sigma factor RpoH [Rhodobacterales bacterium Y4I]
          Length = 298

 Score =  291 bits (746), Expect = 8e-77,   Method: Composition-based stats.
 Identities = 164/297 (55%), Positives = 218/297 (73%), Gaps = 5/297 (1%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N  N+      E GL+RY+ EIRK P+LE +EEY+LAKR+ E  D ++AH++VTSHLRL 
Sbjct: 3   NYANLPAPTP-EGGLNRYLQEIRKFPLLEPEEEYMLAKRWVEEQDAASAHKMVTSHLRLA 61

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            KIAMGYRGYGLP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSW
Sbjct: 62  AKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSW 121

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL- 180
           SLVK+GTT+ QK+LFFNLR+ K  + A+ D +L+PE V  IA  L V+E EVISMN R+ 
Sbjct: 122 SLVKLGTTSAQKKLFFNLRKAKARIGALEDGDLRPENVKRIATDLGVTEDEVISMNRRMS 181

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA + S  + + QWQDWL  +   Q      ++E + RR +L  ++ VLN RE+
Sbjct: 182 GGDASLNATVGSEGEGTMQWQDWLEDEDADQAGDYEARDELEARRELLAEALDVLNDREK 241

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLL 297
            I   RRL +  VTLE+LS+++ VSRER+RQIE RAF+K+Q+ ++   EL+    +L
Sbjct: 242 DILTQRRLMDQAVTLEDLSAQYNVSRERIRQIEVRAFEKLQKKMR---ELAGEKGML 295


>gi|1184690|gb|AAB01724.1| RNA polymerase sigma 32 subunit [Caulobacter crescentus CB15]
          Length = 295

 Score =  291 bits (746), Expect = 8e-77,   Method: Composition-based stats.
 Identities = 168/288 (58%), Positives = 221/288 (76%), Gaps = 5/288 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M   ++S++ + + GLSRY+ EIRK PML K EE++LA+R++EH D  AAH++VTSHLRL
Sbjct: 1   MAVNSLSVM-SPDGGLSRYLTEIRKFPMLSKDEEFMLAQRWKEHQDPQAAHKMVTSHLRL 59

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVKKF+PE+GFRLATY+MWWI+A++QEYILRS
Sbjct: 60  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKKFEPEKGFRLATYAMWWIRASIQEYILRS 119

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTA QK+LFFNLR+ K  + A  + +L P+QV  IA KL V +SEVISMN RL
Sbjct: 120 WSLVKMGTTAAQKKLFFNLRKAKSQIAAFQEGDLHPDQVSQIATKLGVLDSEVISMNRRL 179

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           +G D SLNA +       S+WQDWL  +    QE  + E EE+  R ++L  +M  L  R
Sbjct: 180 SGPDASLNAPLRR--DGESEWQDWLADEEQVSQETRVAEDEEKSLRMSLLEEAMVELTDR 237

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ER I   RRL+++P TLE L++++ VSRERVRQIE RAF+K+Q+++++
Sbjct: 238 ERHILTERRLKDDPTTLEELAAQYGVSRERVRQIEVRAFEKLQKTMRE 285


>gi|110679109|ref|YP_682116.1| RNA polymerase factor sigma-32 [Roseobacter denitrificans OCh 114]
 gi|109455225|gb|ABG31430.1| RNA polymerase sigma-32 factor [Roseobacter denitrificans OCh 114]
          Length = 298

 Score =  291 bits (745), Expect = 9e-77,   Method: Composition-based stats.
 Identities = 168/294 (57%), Positives = 217/294 (73%), Gaps = 2/294 (0%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N  N+      E GL+RY+ EIRK P+LE QEEY+LAKR+ E  D  AAH++VTSHLRL 
Sbjct: 3   NYANLPAPTP-EGGLNRYMQEIRKFPLLEPQEEYMLAKRWVEEQDTEAAHKMVTSHLRLA 61

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            KIAMGYRGYGLP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSW
Sbjct: 62  AKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSW 121

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL- 180
           SLVK+GTT+ QK+LFFNLR+ K  + A+ + +L P+ V  IAK L V+E+EVISMN R+ 
Sbjct: 122 SLVKLGTTSGQKKLFFNLRKAKNKIGALEEGDLHPDNVARIAKDLGVTETEVISMNRRMS 181

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA + S  + + QWQDWL  +   Q      ++E + RR +L  +MSVLN RER
Sbjct: 182 GGDASLNATVGSEGEGTMQWQDWLEDEDADQAGDYEARDELEARRELLADAMSVLNDRER 241

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSP 294
            I + RRL E  VTLE+LS+E+ VSRER+RQIE RAF+K+Q+ ++   +    P
Sbjct: 242 DILQQRRLSEQTVTLEDLSAEYNVSRERIRQIEVRAFEKLQKKMRDLAKEKGMP 295


>gi|87201057|ref|YP_498314.1| RNA polymerase factor sigma-32 [Novosphingobium aromaticivorans DSM
           12444]
 gi|87136738|gb|ABD27480.1| RNA polymerase, sigma 32 subunit, RpoH [Novosphingobium
           aromaticivorans DSM 12444]
          Length = 299

 Score =  290 bits (744), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 164/279 (58%), Positives = 211/279 (75%), Gaps = 4/279 (1%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           + GE  L+RY+ EIRK P+L  ++EY+LAKR++EH D  AA +LVTSHLRLV KIAMGYR
Sbjct: 13  LGGEASLNRYLSEIRKFPVLTAEQEYMLAKRFQEHQDPEAAAQLVTSHLRLVAKIAMGYR 72

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYGLP+SE++SEGNIGLMQ VKKF+P+RGFRLATY+MWWIKA+MQE+ILRSWSLVK+GTT
Sbjct: 73  GYGLPVSELISEGNIGLMQGVKKFEPDRGFRLATYAMWWIKASMQEFILRSWSLVKMGTT 132

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL--AGDESLN 187
           A QK+LFFNLRR+K +L+A  D++L P+ V  IA  L V E EV++MN R+   GD SLN
Sbjct: 133 AAQKKLFFNLRRMKKNLEAFEDSDLHPDDVRKIATDLGVPEQEVVNMNRRMMMGGDASLN 192

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             ++  +     WQDWL  D   Q++ + + EE + R  +L  +M  LN RER I   RR
Sbjct: 193 --VSMREDGEGSWQDWLTDDRPLQDETVADAEEAQYRHELLVEAMESLNERERHILTDRR 250

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           L ++P TLE LS  + VSRERVRQIE RAF+K+Q++IQ+
Sbjct: 251 LIDDPKTLEELSQVYNVSRERVRQIEVRAFEKLQKAIQR 289


>gi|294011928|ref|YP_003545388.1| RNA polymerase sigma-32 factor [Sphingobium japonicum UT26S]
 gi|292675258|dbj|BAI96776.1| RNA polymerase sigma-32 factor [Sphingobium japonicum UT26S]
          Length = 304

 Score =  290 bits (744), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 162/279 (58%), Positives = 210/279 (75%), Gaps = 4/279 (1%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           + GE  L+RY+ EIRK P+L  ++EY+LAKRY EH D  AA +LVTSHLRLV KIAMGYR
Sbjct: 13  LGGEASLNRYLSEIRKFPILTPEQEYMLAKRYAEHQDSEAAAQLVTSHLRLVAKIAMGYR 72

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYGLP+SE++SEGNIGLMQ VKKF+P+RGFRLATY+MWWI+A++QE+ILRSWSLVK+GTT
Sbjct: 73  GYGLPVSELISEGNIGLMQGVKKFEPDRGFRLATYAMWWIRASIQEFILRSWSLVKMGTT 132

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
           A QK+LFFNLRR+K +++A  D +L P+ V  IA  L V+E +VISMN R+A  GD SLN
Sbjct: 133 AAQKKLFFNLRRMKNNIEAFEDGDLHPDDVKKIATDLGVTEEDVISMNRRMAMGGDTSLN 192

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             +   +    QWQDWL      Q++ + +++E + R +ML  +M  LN RE+ I   RR
Sbjct: 193 VPMR--EDGEGQWQDWLADSDPLQDERVADRQESELRHDMLVEAMDDLNDREKHILAERR 250

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           L E P TLE LS  + VSRERVRQIE RAF+K+Q+++ +
Sbjct: 251 LAEEPKTLEELSQVYGVSRERVRQIEVRAFEKLQKAMMR 289


>gi|126727088|ref|ZP_01742925.1| RNA polymerase sigma factor [Rhodobacterales bacterium HTCC2150]
 gi|126703516|gb|EBA02612.1| RNA polymerase sigma factor [Rhodobacterales bacterium HTCC2150]
          Length = 289

 Score =  290 bits (744), Expect = 1e-76,   Method: Composition-based stats.
 Identities = 165/281 (58%), Positives = 211/281 (75%), Gaps = 1/281 (0%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
            + E GL+RY+ EIRK PMLE +EEY+LAK + EH D  AAHRLVTSHLRL  KIAMGYR
Sbjct: 4   PSPEQGLNRYMQEIRKFPMLEPEEEYMLAKNWVEHQDSGAAHRLVTSHLRLAAKIAMGYR 63

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYGLP +EVVSE N+GLMQAVKKFDPE+GFRL+TY+MWWI+A++QEY+LRSWSLVK+GTT
Sbjct: 64  GYGLPQAEVVSEANVGLMQAVKKFDPEKGFRLSTYAMWWIRASIQEYVLRSWSLVKLGTT 123

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNA 188
           + QK+LFFNLR+ K  + A+ + +L+PE V  IA  LNV+E+EVISMN R+  GD SLN 
Sbjct: 124 SAQKKLFFNLRKAKNRIGALEEGDLRPENVAKIASDLNVTETEVISMNRRMSGGDASLNV 183

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +    + ++QWQDWL  D   Q     +++E   RR ++ ++M+VLN RE+ I   RRL
Sbjct: 184 QVGGDGEGTAQWQDWLADDSADQAGDYEKQDELDTRRELMAQAMAVLNDREKEILMERRL 243

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           Q+ P TLE LS  F VSRER+RQIE RAF+K+Q  ++   E
Sbjct: 244 QDKPKTLEELSEVFSVSRERIRQIEVRAFEKLQTEMRSLAE 284


>gi|254477747|ref|ZP_05091133.1| alternative sigma factor RpoH [Ruegeria sp. R11]
 gi|214031990|gb|EEB72825.1| alternative sigma factor RpoH [Ruegeria sp. R11]
          Length = 298

 Score =  290 bits (743), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 160/298 (53%), Positives = 217/298 (72%), Gaps = 5/298 (1%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N  N+      E GL+RY+ EIRK P+LE +EEY+LAKR+ E  D ++AH++VTSHLRL 
Sbjct: 3   NYANLPAPTP-EGGLNRYLQEIRKFPLLEPEEEYMLAKRWVEEQDANSAHKMVTSHLRLA 61

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            KIAMGYRGYGLP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSW
Sbjct: 62  AKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSW 121

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL- 180
           SLVK+GTT+ QK+LFFNLR+ K  + A+ + +L P+ V  IA  L V+E EVISMN R+ 
Sbjct: 122 SLVKLGTTSAQKKLFFNLRKAKARIGALEEGDLHPDSVKKIATDLGVTEDEVISMNRRMS 181

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA + +  + + QWQDWL  +   Q      ++E + RR +L  ++ VLN RE+
Sbjct: 182 GGDASLNATVGTEGEGAMQWQDWLEDEDADQAGDYEARDELEARRELLASALEVLNDREK 241

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQ 298
            I   RRL +   TLE+LS+++ VSRER+RQIE RAF+K+Q+ ++   EL++   +L 
Sbjct: 242 DILTQRRLADQAKTLEDLSTQYGVSRERIRQIEVRAFEKLQKKMR---ELAAQKGMLP 296


>gi|84500884|ref|ZP_00999119.1| RNA polymerase sigma factor [Oceanicola batsensis HTCC2597]
 gi|84390951|gb|EAQ03369.1| RNA polymerase sigma factor [Oceanicola batsensis HTCC2597]
          Length = 298

 Score =  290 bits (743), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 162/290 (55%), Positives = 215/290 (74%), Gaps = 4/290 (1%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
            + E GL+RY+ EIRK P+LE +EEY+LAKR+ E  D  AAH++VTSHLRL  KIAMGYR
Sbjct: 10  PSPEGGLNRYLQEIRKFPLLEPEEEYMLAKRWVEEQDTEAAHKMVTSHLRLAAKIAMGYR 69

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYGLP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSWSLVK+GTT
Sbjct: 70  GYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTT 129

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNA 188
           + QK+LFFNLR+ K  + A+ + +L P+ V  IA  L V+E+EVISMN R+  GD SLNA
Sbjct: 130 SAQKKLFFNLRKAKARIGALEEGDLHPDNVKQIANDLGVTEAEVISMNRRMSGGDASLNA 189

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +    +++ +WQDWL  +   Q     E++E  +RR +L  +M+VLN RER I   RRL
Sbjct: 190 TVGMDAESAMEWQDWLEDEEADQAGDYAERDEMDSRRELLAEAMAVLNDRERDILTQRRL 249

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQ 298
            E  +TLE+LS ++ VSRER+RQIE RAF+K+Q  ++   EL+    +L 
Sbjct: 250 SEETITLEDLSEQYGVSRERIRQIEVRAFEKLQLQMR---ELAQEKGMLP 296


>gi|163733965|ref|ZP_02141406.1| RNA polymerase sigma factor [Roseobacter litoralis Och 149]
 gi|161392501|gb|EDQ16829.1| RNA polymerase sigma factor [Roseobacter litoralis Och 149]
          Length = 298

 Score =  290 bits (743), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 167/294 (56%), Positives = 217/294 (73%), Gaps = 2/294 (0%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N  N+      E GL+RY+ EIRK P+LE QEEY+LAKR+ E  D  AAH++VTSHLRL 
Sbjct: 3   NYANLPAPTP-EGGLNRYMQEIRKFPLLEPQEEYMLAKRWVEEQDTEAAHKMVTSHLRLA 61

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            KIAMGYRGYGLP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSW
Sbjct: 62  AKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSW 121

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL- 180
           SLVK+GTT+ QK+LFFNLR+ K  + A+ + +L P+ V  IAK L V+E+EVISMN R+ 
Sbjct: 122 SLVKLGTTSGQKKLFFNLRKAKNKIGALEEGDLHPDNVARIAKDLGVTETEVISMNRRMS 181

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA + S  + + QWQDWL  +   Q      ++E + RR +L  +MSVLN RE+
Sbjct: 182 GGDASLNATVGSEGEGTMQWQDWLEDEGADQAGDYEARDELEARRELLADAMSVLNDREK 241

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSP 294
            I + RRL E  VTLE+LS+E+ VSRER+RQIE RAF+K+Q+ ++   +    P
Sbjct: 242 DILQQRRLSEKTVTLEDLSAEYNVSRERIRQIEVRAFEKLQKKMRDLAKEKGMP 295


>gi|163738663|ref|ZP_02146077.1| RNA polymerase, sigma 32 subunit, RpoH [Phaeobacter gallaeciensis
           BS107]
 gi|163742952|ref|ZP_02150335.1| RNA polymerase sigma factor [Phaeobacter gallaeciensis 2.10]
 gi|161383635|gb|EDQ08021.1| RNA polymerase sigma factor [Phaeobacter gallaeciensis 2.10]
 gi|161387991|gb|EDQ12346.1| RNA polymerase, sigma 32 subunit, RpoH [Phaeobacter gallaeciensis
           BS107]
          Length = 298

 Score =  290 bits (742), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 162/297 (54%), Positives = 218/297 (73%), Gaps = 5/297 (1%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N  N+      E GL+RY+ EIRK P+LE +EEY+LAKR+ E  D ++AH++VTSHLRL 
Sbjct: 3   NYANLPAPTP-EGGLNRYLQEIRKFPLLEPEEEYMLAKRWVEEQDSASAHKMVTSHLRLA 61

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            KIAMGYRGYGLP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSW
Sbjct: 62  AKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSW 121

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL- 180
           SLVK+GTT+ QK+LFFNLR+ K  + A+ + +L P+ V  IA  L V+E+EVISMN R+ 
Sbjct: 122 SLVKLGTTSAQKKLFFNLRKAKARIGALEEGDLHPDSVKKIATDLGVTETEVISMNRRMS 181

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA + S  + + QWQDWL  +   Q      ++E + RR +L  ++ VLN RE+
Sbjct: 182 GGDASLNATVGSEGEGTMQWQDWLEDEDADQAGDYEARDELEARRELLASALEVLNDREK 241

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLL 297
            I   RRL +   TLE+LS+++ VSRER+RQIE RAF+K+Q+ ++   EL+S   +L
Sbjct: 242 DILTQRRLADQAKTLEDLSTQYGVSRERIRQIEVRAFEKLQKKMR---ELASEKGML 295


>gi|254511947|ref|ZP_05124014.1| alternative sigma factor RpoH [Rhodobacteraceae bacterium KLH11]
 gi|221535658|gb|EEE38646.1| alternative sigma factor RpoH [Rhodobacteraceae bacterium KLH11]
          Length = 298

 Score =  290 bits (742), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 163/297 (54%), Positives = 217/297 (73%), Gaps = 5/297 (1%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N  N+      E GL+RY+ EIRK P+LE +EEY+LAKR+ E  D  AAH++VTSHLRL 
Sbjct: 3   NYSNLPAPTP-EGGLNRYMQEIRKFPLLEPEEEYMLAKRWVEEQDTEAAHKMVTSHLRLA 61

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            KIAMGYRGYGLP +EV+SE N+GLMQAVKKFDPE+GFRLATY+MWWI+A++QEY+LRSW
Sbjct: 62  AKIAMGYRGYGLPQAEVISEANVGLMQAVKKFDPEKGFRLATYAMWWIRASIQEYVLRSW 121

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL- 180
           S+VK+GTT+ QK+LFFNLR+ K  + A+ + +L+PE V  IA+ L V+E EVISMN R+ 
Sbjct: 122 SMVKLGTTSAQKKLFFNLRKAKARIGALEEGDLRPENVARIAEDLGVTEEEVISMNRRMS 181

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA + S  + + QWQDWL  +   Q      ++E + RR +L  ++ VLN RE+
Sbjct: 182 GGDASLNATVGSEGEGTMQWQDWLEDEDADQAGDYEARDELEARRELLAAALDVLNDREK 241

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLL 297
            I   RRL +  VTLE LS+++ VSRER+RQIE RAF+K+Q+ ++   EL+    +L
Sbjct: 242 DILTQRRLMDQVVTLEELSTQYNVSRERIRQIEVRAFEKLQKKMR---ELAREKGML 295


>gi|126729201|ref|ZP_01745015.1| RNA polymerase sigma factor [Sagittula stellata E-37]
 gi|126710191|gb|EBA09243.1| RNA polymerase sigma factor [Sagittula stellata E-37]
          Length = 298

 Score =  290 bits (742), Expect = 2e-76,   Method: Composition-based stats.
 Identities = 166/285 (58%), Positives = 213/285 (74%), Gaps = 2/285 (0%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N  N+    + E GLSRY+ EIRK P+LE ++EY+LAKR+ E  D  AAH+LVTSHLRL 
Sbjct: 3   NYANLPAP-SPEAGLSRYLQEIRKFPLLEPEQEYMLAKRWVEDEDTQAAHQLVTSHLRLA 61

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            KIAMGYRGYGLP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSW
Sbjct: 62  AKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSW 121

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL- 180
           SLVK+GTT+ QK+LFFNLR+ K  + A+ D +L+PE V  IA  L V++ EVISMN RL 
Sbjct: 122 SLVKLGTTSAQKKLFFNLRKAKSRIGALEDGDLRPEHVEKIATDLGVTQDEVISMNRRLS 181

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA + S  + + QWQDWL  +   Q     E+ E + RR +L ++M VLN RER
Sbjct: 182 GGDASLNATVGSEGEGTMQWQDWLEDEDADQAGEYAERNELEARRALLEQAMDVLNDRER 241

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            I   RRL +  VTLE LS +++VSRER+RQIE RAF+K+Q+ ++
Sbjct: 242 DILSQRRLSDQAVTLEELSGQYDVSRERIRQIEVRAFEKLQKRMR 286


>gi|288962535|ref|YP_003452830.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
 gi|288914801|dbj|BAI76286.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
          Length = 296

 Score =  289 bits (741), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 173/287 (60%), Positives = 223/287 (77%), Gaps = 3/287 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M   +    +  E  LSRY+ EIRK PMLE + EY+LAKR+++H D  AAH+LVTSHLRL
Sbjct: 1   MATGSNLPAIGSESNLSRYLQEIRKFPMLEPEREYMLAKRWQQHEDSGAAHQLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLP+SE++SEGN+G+MQAVK+FDP+RGFRLATY+MWWI+AA+QEYIL S
Sbjct: 61  VAKIAMGYRGYGLPLSELISEGNVGMMQAVKRFDPDRGFRLATYAMWWIRAAIQEYILHS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTA QK+LFFNLRRLKG +QAI + +L PEQV AIA KL+V E +V++MN RL
Sbjct: 121 WSLVKMGTTAAQKKLFFNLRRLKGQMQAIEEGDLSPEQVQAIATKLDVPEQDVVNMNRRL 180

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           A  D SLNA + +  ++  +WQD+LV +   QE  L ++EE   RR +L  +M+ LN RE
Sbjct: 181 ASPDHSLNAPLRA--ESEGEWQDFLVDESASQEIALADREELGKRRKLLVEAMTGLNERE 238

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R I   RRL+E P TLE+LS ++ +SRERVRQIE RAF+K+Q++I+ 
Sbjct: 239 RDILTERRLREAPTTLEDLSQKYGISRERVRQIEVRAFEKLQKAIKA 285


>gi|126738732|ref|ZP_01754428.1| RNA polymerase sigma factor [Roseobacter sp. SK209-2-6]
 gi|126719913|gb|EBA16620.1| RNA polymerase sigma factor [Roseobacter sp. SK209-2-6]
          Length = 298

 Score =  289 bits (741), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 164/299 (54%), Positives = 217/299 (72%), Gaps = 5/299 (1%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N  N+      E GL+RY+ EIRK P+LE +EEY+LAK + E  D  AAH++VTSHLRL 
Sbjct: 3   NYANLPAPTP-EGGLNRYMQEIRKFPLLEPEEEYMLAKAWVEKEDTGAAHKMVTSHLRLA 61

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            KIAMGYRGYGLP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSW
Sbjct: 62  AKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSW 121

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL- 180
           SLVK+GTT+ QK+LFFNLR+ K  + A+ + +L+PE V  IA  L V+E EVISMN R+ 
Sbjct: 122 SLVKLGTTSAQKKLFFNLRKAKARIGALEEGDLRPENVAQIAHDLGVTEEEVISMNRRMS 181

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA + S  + + QWQDWL  +   Q      ++E + RR +L ++M VLN RE+
Sbjct: 182 GGDASLNATVGSEGEGTMQWQDWLEDEDADQAGDYEARDELEARRELLVQAMEVLNDREK 241

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQK 299
            I   RRL +   TLE+LS E+ VSRER+RQIE RAF+K+Q+ ++   +L+S   +L +
Sbjct: 242 DILTQRRLSDQATTLEDLSGEYGVSRERIRQIEVRAFEKLQKKMR---DLASEKGMLAR 297


>gi|86137868|ref|ZP_01056444.1| RNA polymerase sigma factor [Roseobacter sp. MED193]
 gi|85825460|gb|EAQ45659.1| RNA polymerase sigma factor [Roseobacter sp. MED193]
          Length = 298

 Score =  289 bits (741), Expect = 3e-76,   Method: Composition-based stats.
 Identities = 164/297 (55%), Positives = 218/297 (73%), Gaps = 5/297 (1%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N  N+      E GL+RY+ EIRK P+LE +EEY+LAK + E  D  AAHR+VTSHLRL 
Sbjct: 3   NYANLPAPTP-EGGLNRYMQEIRKFPLLEPEEEYMLAKAWVEKEDSGAAHRMVTSHLRLA 61

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            KIAMGYRGYGLP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEY+LRSW
Sbjct: 62  AKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYVLRSW 121

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL- 180
           S+VK+GTT+ QK+LFFNLR+ K  + A+ + +L+PE V  IA  L V+E EVISMN R+ 
Sbjct: 122 SMVKLGTTSAQKKLFFNLRKAKARIGALEEGDLRPENVAKIAHDLGVTEDEVISMNRRMS 181

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA + S  + + QWQDWL  +   Q      ++E + RR +L +++ VLN RE+
Sbjct: 182 GGDASLNATVGSEGEGTMQWQDWLEDEDADQAGDYEARDELEARRELLGQALEVLNDREK 241

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLL 297
            I   RRL EN  TLE LS+++ VSRER+RQIE RAF+K+Q+ ++   EL+S+  +L
Sbjct: 242 DILTKRRLAENVQTLEELSAQYSVSRERIRQIEVRAFEKLQKKMR---ELASAKGML 295


>gi|126733180|ref|ZP_01748927.1| RNA polymerase sigma-32 factor [Roseobacter sp. CCS2]
 gi|126716046|gb|EBA12910.1| RNA polymerase sigma-32 factor [Roseobacter sp. CCS2]
          Length = 298

 Score =  289 bits (740), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 165/286 (57%), Positives = 213/286 (74%), Gaps = 2/286 (0%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N KN+      E GL+RY+ EIRK PMLE ++EY+LAKR+ +H D  AAH++VTSHLRL 
Sbjct: 3   NYKNLPAPTP-EGGLNRYMQEIRKFPMLEPEQEYMLAKRWVDHEDTDAAHQMVTSHLRLA 61

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            KIAMGYRGYGLP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSW
Sbjct: 62  AKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSW 121

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL- 180
           SLVK+GTT+ QK+LFFNLR+ K  + A+ D +L+PE V  IA  L V+E EVISMN RL 
Sbjct: 122 SLVKLGTTSAQKKLFFNLRKAKNRIGALEDGDLRPENVERIANDLGVTEQEVISMNRRLS 181

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA +++  + ++QWQDWL  +           +E   RR +L  +M VLN RE+
Sbjct: 182 GGDASLNATVSADGEGAAQWQDWLEDESANTAADYEASDELTARRELLAEAMEVLNDREK 241

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            I   RRL E  VTLE+LS +++VSRER+RQIE RAF+K+Q  +Q+
Sbjct: 242 DILMQRRLSEETVTLEDLSGQYDVSRERIRQIEVRAFEKLQAKMQE 287


>gi|163794484|ref|ZP_02188455.1| RNA polymerase sigma-32 factor [alpha proteobacterium BAL199]
 gi|159180208|gb|EDP64731.1| RNA polymerase sigma-32 factor [alpha proteobacterium BAL199]
          Length = 298

 Score =  289 bits (740), Expect = 4e-76,   Method: Composition-based stats.
 Identities = 177/278 (63%), Positives = 221/278 (79%), Gaps = 3/278 (1%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
            ++ E  LSRY+ EIRK PMLE  EEYVLAK +REH D+ +AH+LVTSHLRLV KIAMGY
Sbjct: 10  SISVEGNLSRYLQEIRKFPMLEPGEEYVLAKSWREHDDVESAHKLVTSHLRLVAKIAMGY 69

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           RGYGLP++E++SEGN+G+MQAVK+FDPERGFRLATY+MWWI+A++QEYIL SWSLVK+GT
Sbjct: 70  RGYGLPLAELISEGNVGMMQAVKRFDPERGFRLATYAMWWIRASIQEYILHSWSLVKMGT 129

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN 187
           TA QK+LFFNLRRLKG +QAI D +L PE+V AIA+KL+VSE++V+SMN RLA  D SLN
Sbjct: 130 TAAQKKLFFNLRRLKGQMQAIEDGDLSPERVTAIAEKLDVSEADVVSMNRRLASPDHSLN 189

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           A +        +WQDWLV +   QE    E EE   RR +L  +M  LN RER I   RR
Sbjct: 190 APLRQ--DGEGEWQDWLVDEGQNQEVSFAEDEELSKRRRLLNVAMETLNDRERHILTERR 247

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L++NP TLE+LS E+++SRERVRQIE RAF+K+Q++I+
Sbjct: 248 LRDNPTTLEDLSQEYDISRERVRQIEVRAFEKLQKAIK 285


>gi|330814385|ref|YP_004358624.1| RNA polymerase sigma factor RpoH [Candidatus Pelagibacter sp.
           IMCC9063]
 gi|327487480|gb|AEA81885.1| RNA polymerase sigma factor RpoH [Candidatus Pelagibacter sp.
           IMCC9063]
          Length = 300

 Score =  289 bits (739), Expect = 5e-76,   Method: Composition-based stats.
 Identities = 163/290 (56%), Positives = 220/290 (75%), Gaps = 3/290 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           + + N+  +   E   S Y+ +IRK PML+  EEYVLAK +RE GD  AAH+LVTSHLRL
Sbjct: 5   LTKTNLPTLTP-EGSFSSYLSKIRKFPMLDAAEEYVLAKNWREQGDKDAAHKLVTSHLRL 63

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLP+SE+VSEGNIGLMQAV+KFDPE+GFRLATY+MWWIKA++QEY+LRS
Sbjct: 64  VAKIAMGYRGYGLPVSELVSEGNIGLMQAVRKFDPEKGFRLATYAMWWIKASIQEYVLRS 123

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVKIGTT+ QK+LFFNL+++K  + A    N+ PE +  IA +L+V E EV+SMN RL
Sbjct: 124 WSLVKIGTTSAQKKLFFNLKKIKNQIFAAEQGNMLPEHITEIATQLDVREDEVVSMNQRL 183

Query: 181 AGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           AG E SLNA +   + + ++WQDW+V ++  QE  + +K+E   R+++L  ++ VL+ RE
Sbjct: 184 AGHEHSLNAPVG-GEDSDAEWQDWVVDENADQELQISQKQELNQRQSLLKNALHVLDERE 242

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           + I   RRL + P TLE LS + +VSRER+RQIE RAF+KVQ+++ + ++
Sbjct: 243 KEILHNRRLIDEPKTLEELSQKHKVSRERIRQIENRAFEKVQKAMLENIK 292


>gi|56696293|ref|YP_166650.1| RNA polymerase factor sigma-32 [Ruegeria pomeroyi DSS-3]
 gi|56678030|gb|AAV94696.1| RNA polymerase sigma-32 factor [Ruegeria pomeroyi DSS-3]
          Length = 298

 Score =  289 bits (739), Expect = 5e-76,   Method: Composition-based stats.
 Identities = 162/298 (54%), Positives = 215/298 (72%), Gaps = 4/298 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M           E GL+RY+ EIRK P+LE +EEY+LAKR+ E  D  +AH++VTSHLRL
Sbjct: 1   MANYTTLPAPTPEGGLNRYMQEIRKFPLLEPEEEYMLAKRWVEEQDAESAHKMVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
             KIAMGYRGYGLP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+AA+QEYILRS
Sbjct: 61  AAKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRAAIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTT+ QK+LFFNLR+ K  + A+ + +L+PE V  IA  L VSE +VISMN R+
Sbjct: 121 WSLVKLGTTSAQKKLFFNLRKAKAKIGALEEGDLRPENVARIAHDLGVSEDDVISMNRRM 180

Query: 181 -AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
             GD SLNA + S  + + QWQDWL  +   Q      ++E + RR +L  ++ VLN RE
Sbjct: 181 SGGDASLNATVGSEGEGTMQWQDWLEDEDADQAADYEARDELEARRELLASALDVLNERE 240

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLL 297
           + +   RRL +  VTLE+LS+++ VSRER+RQIE RAF+K+Q+ ++   EL+    +L
Sbjct: 241 KDVLTQRRLLDQTVTLEDLSAQYNVSRERIRQIEVRAFEKLQKRMR---ELAREKGML 295


>gi|218670385|ref|ZP_03520056.1| RNA polymerase factor sigma-32 [Rhizobium etli GR56]
          Length = 266

 Score =  289 bits (739), Expect = 5e-76,   Method: Composition-based stats.
 Identities = 192/251 (76%), Positives = 221/251 (88%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           AKRY EHGD  AAH+LVTSHLRLV KIAMGYRGYGLPI EVVSEGN+GLMQAVKKFDPER
Sbjct: 2   AKRYAEHGDRDAAHKLVTSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPER 61

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           GFRLATY+MWWIKA++QEYILRSWSLVK+GTTANQKRLFFNLRRLKG +QAI D +LKPE
Sbjct: 62  GFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQKRLFFNLRRLKGRIQAIDDGDLKPE 121

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
            V  IA KLNVSE EVISMN RL+GD SLNA I +++ +S QWQDWLV DHD QE VLIE
Sbjct: 122 HVSEIATKLNVSEEEVISMNRRLSGDASLNAPIKAAEGDSGQWQDWLVDDHDSQEDVLIE 181

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
           ++E + RR ML+++MSVLN RERRIFEARRL E PVTLE+LS+EF++SRERVRQIE RAF
Sbjct: 182 QDELETRRRMLSKAMSVLNERERRIFEARRLAEEPVTLEDLSAEFDISRERVRQIEVRAF 241

Query: 278 KKVQESIQKQV 288
           +KVQ++++K+ 
Sbjct: 242 EKVQDAVRKEA 252


>gi|254462386|ref|ZP_05075802.1| alternative sigma factor RpoH [Rhodobacterales bacterium HTCC2083]
 gi|206678975|gb|EDZ43462.1| alternative sigma factor RpoH [Rhodobacteraceae bacterium HTCC2083]
          Length = 298

 Score =  288 bits (738), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 165/286 (57%), Positives = 214/286 (74%), Gaps = 2/286 (0%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N  N+      E GL+RY+ EIRK PMLE +EEY+LAK + E  D +AAH++VTSHLRL 
Sbjct: 3   NYANLPAPTP-EGGLNRYMQEIRKFPMLEPEEEYMLAKSWVEKQDTAAAHKMVTSHLRLA 61

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            KIAMGYRGYGLP +EVVSE N+GLMQAVK+FDPE+GFRL+TY+MWWI+AA+QEYILRSW
Sbjct: 62  AKIAMGYRGYGLPQAEVVSEANVGLMQAVKRFDPEKGFRLSTYAMWWIRAAIQEYILRSW 121

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL- 180
           SLVK+GTT+ QK+LFFNLR+ K  + A+ + +++PE V  IA  L V+E+EVISMN R+ 
Sbjct: 122 SLVKLGTTSAQKKLFFNLRKAKNRIGALEEGDMRPENVARIAHDLGVTETEVISMNRRMS 181

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA + S  + + QWQDWL  +   Q      ++E + RR ML  +M VLN RE+
Sbjct: 182 GGDASLNAQVGSEGEGTMQWQDWLEDEDADQAGDYEARDELEARREMLADAMDVLNDREK 241

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            I   RRL + PVTLE+LS +++VSRER+RQIE RAF+K+QE ++ 
Sbjct: 242 DILVQRRLSDKPVTLEDLSGQYDVSRERIRQIEVRAFEKLQERMRS 287


>gi|83941135|ref|ZP_00953597.1| RNA polymerase sigma factor [Sulfitobacter sp. EE-36]
 gi|83846955|gb|EAP84830.1| RNA polymerase sigma factor [Sulfitobacter sp. EE-36]
          Length = 298

 Score =  288 bits (738), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 164/285 (57%), Positives = 214/285 (75%), Gaps = 2/285 (0%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N  N+      E GL+RY+ EIRK P+LE +EEY+LAKR+ E  D  AAHR+VTSHLRL 
Sbjct: 3   NYANLPAPTP-EGGLNRYMQEIRKFPLLEPEEEYMLAKRWVEEQDTEAAHRMVTSHLRLA 61

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            KIAMGYRGYGLP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSW
Sbjct: 62  AKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSW 121

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL- 180
           SLVK+GTT+ QK+LFFNLR+ K  + A+ + +L P+ V  IA  L V+E+EVISMN R+ 
Sbjct: 122 SLVKLGTTSGQKKLFFNLRKAKNRIGALEEGDLHPDNVKRIATDLGVTETEVISMNRRMS 181

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA + S  + + QWQDWL  +   Q     E++E + RR ML  ++ VLN RE+
Sbjct: 182 GGDASLNATVGSEGEGTMQWQDWLEDEDADQATDYEERDELETRREMLAEALDVLNDREK 241

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            I   RRL +  VTLE+LSS+++VSRER+RQIE RAF+K+Q+ ++
Sbjct: 242 DILTQRRLSDQTVTLEDLSSQYDVSRERIRQIEVRAFEKLQKRMR 286


>gi|254700317|ref|ZP_05162145.1| RNA polymerase factor sigma-32 [Brucella suis bv. 5 str. 513]
 gi|261750811|ref|ZP_05994520.1| RNA polymerase factor sigma-32 [Brucella suis bv. 5 str. 513]
 gi|261740564|gb|EEY28490.1| RNA polymerase factor sigma-32 [Brucella suis bv. 5 str. 513]
          Length = 262

 Score =  288 bits (738), Expect = 6e-76,   Method: Composition-based stats.
 Identities = 180/262 (68%), Positives = 219/262 (83%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M +  +  I +G+ GL+RY+ EIR+ PMLE QEEY+LAKRY EH D  AAH+LVTSHLRL
Sbjct: 1   MAQMKLPSITSGDGGLTRYLEEIRRFPMLEPQEEYMLAKRYHEHADPKAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EV+SEGN+GLMQAVK+F+PERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVISEGNVGLMQAVKRFEPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLR++K  +QA+ D +L P+QV  IA KLNVSE EV+SMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRKMKSKIQALDDGDLNPDQVKQIATKLNVSEDEVVSMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +GD SLNA + +S+  S +WQDWLV D + QEQVLIE++E ++RR+ML ++M  LN RER
Sbjct: 181 SGDASLNAPLRASEGESGEWQDWLVDDSNSQEQVLIEQDELESRRSMLEQAMETLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEF 262
           RIFEARRL E P+TLE+LS EF
Sbjct: 241 RIFEARRLAEEPMTLEDLSGEF 262


>gi|83949442|ref|ZP_00958175.1| RNA polymerase sigma factor [Roseovarius nubinhibens ISM]
 gi|83837341|gb|EAP76637.1| RNA polymerase sigma factor [Roseovarius nubinhibens ISM]
          Length = 298

 Score =  288 bits (737), Expect = 7e-76,   Method: Composition-based stats.
 Identities = 160/286 (55%), Positives = 210/286 (73%), Gaps = 2/286 (0%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N  N+      E GL+RY+ EIRK P+LE +EEY+LAK + E  D  AAHR+VTSHLRL 
Sbjct: 3   NYANLPAPTP-EGGLNRYLQEIRKFPLLEPEEEYMLAKAWVEKQDTEAAHRMVTSHLRLA 61

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            KIAMGYRGYGLP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSW
Sbjct: 62  AKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSW 121

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL- 180
           S+VK+GTT+ QK+LFFNLR+ K  + A+ + ++ P+ V  IA  L V+E EVISMN R+ 
Sbjct: 122 SMVKLGTTSAQKKLFFNLRKAKARIGALEEGDMHPDNVKRIATDLGVTEDEVISMNRRMS 181

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA + S  + + QWQDWL  +   Q     ++ E + R  +LT +M VLN RE+
Sbjct: 182 GGDASLNATVGSEGEGTMQWQDWLEDEDADQAGDYEKRNEMETRLELLTEAMDVLNDREK 241

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            I   RRL +  VTLE+LS+E+ VSRER+RQIE RAF+K+Q+ ++ 
Sbjct: 242 DILSQRRLNDETVTLEDLSTEYGVSRERIRQIEVRAFEKLQKRMRS 287


>gi|254501465|ref|ZP_05113616.1| alternative sigma factor RpoH [Labrenzia alexandrii DFL-11]
 gi|222437536|gb|EEE44215.1| alternative sigma factor RpoH [Labrenzia alexandrii DFL-11]
          Length = 269

 Score =  288 bits (737), Expect = 9e-76,   Method: Composition-based stats.
 Identities = 182/268 (67%), Positives = 217/268 (80%), Gaps = 1/268 (0%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           ML+ QEEY+LAKRY+EH D  AA RLV SHLRLV KIAMGYRGYGLPI EVVSEGN+GLM
Sbjct: 1   MLQPQEEYMLAKRYKEHEDPEAAERLVNSHLRLVAKIAMGYRGYGLPIGEVVSEGNVGLM 60

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           QAVK+F+P++GFRLATY+MWWIKAA+QEYILRSWSLVK+GTTANQKRLFFNLRRLKG +Q
Sbjct: 61  QAVKRFEPDKGFRLATYAMWWIKAAIQEYILRSWSLVKMGTTANQKRLFFNLRRLKGKIQ 120

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
           A+ + +LKP QV  IA +L VSE EV+SMN RL GD SLNA I  ++ ++ +WQDWLV +
Sbjct: 121 ALEEGDLKPHQVQEIATRLGVSEEEVVSMNRRLGGDASLNAPIR-AEADAGEWQDWLVDE 179

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            D QE +L  +EE   RR ML+ +M VLN RERRIFEARRL E+P+TLE+LS EF VSRE
Sbjct: 180 SDSQETLLANQEELDMRRKMLSDAMDVLNDRERRIFEARRLSEDPMTLEDLSGEFGVSRE 239

Query: 268 RVRQIEARAFKKVQESIQKQVELSSSPP 295
           RVRQIE RAF+KVQ++++         P
Sbjct: 240 RVRQIEVRAFEKVQKAVRNSARTLDQQP 267


>gi|149202313|ref|ZP_01879286.1| RNA polymerase sigma factor [Roseovarius sp. TM1035]
 gi|149144411|gb|EDM32442.1| RNA polymerase sigma factor [Roseovarius sp. TM1035]
          Length = 298

 Score =  287 bits (736), Expect = 1e-75,   Method: Composition-based stats.
 Identities = 164/286 (57%), Positives = 215/286 (75%), Gaps = 2/286 (0%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N  N+      E GL+RY+ EIRK P+LE +EEY+LAKR+ E  D  AAH++VTSHLRL 
Sbjct: 3   NYNNLPAPTP-EGGLNRYMQEIRKFPLLEPEEEYMLAKRWAEEQDTEAAHKMVTSHLRLA 61

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            KIAMGYRGYGLP +EV+SE N+GLMQAVK+FDPERGFRLATY+MWWI+A++QEYILRSW
Sbjct: 62  AKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPERGFRLATYAMWWIRASIQEYILRSW 121

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
           SLVK+GTT+ QK+LFFNLR+ K  + A+ + +++P+ V  IA  L V+E+EVISMN R+A
Sbjct: 122 SLVKLGTTSAQKKLFFNLRKAKAKIGALEEGDMRPDVVKKIATDLGVTEAEVISMNQRMA 181

Query: 182 G-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           G D SLNA + +  + S QWQDWL  +   Q      ++E   RR +L ++M VLN RER
Sbjct: 182 GADASLNATVGAEGEGSMQWQDWLEDEDADQAGDYERRDELDARRELLVQAMDVLNERER 241

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            I   RRL +  VTLE+LS+E++VSRER+RQIE RAF+K+Q+ ++ 
Sbjct: 242 DILTQRRLSDETVTLEDLSAEYDVSRERIRQIEVRAFEKLQKRMRA 287


>gi|254441831|ref|ZP_05055324.1| alternative sigma factor RpoH [Octadecabacter antarcticus 307]
 gi|198251909|gb|EDY76224.1| alternative sigma factor RpoH [Octadecabacter antarcticus 307]
          Length = 298

 Score =  287 bits (735), Expect = 2e-75,   Method: Composition-based stats.
 Identities = 160/286 (55%), Positives = 213/286 (74%), Gaps = 1/286 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+        + E GL+RY+ EIRK PMLE  EEY+LAKR+ +H D  AAH++VTSHLRL
Sbjct: 1   MSSYTNLPAPSPEQGLNRYMQEIRKFPMLEPDEEYMLAKRWVDHEDTDAAHKMVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
             KIAMGYRGYGLP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEY+LRS
Sbjct: 61  AAKIAMGYRGYGLPTAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYVLRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WS+VK+GTT+ QK+LFFNLR+ K  + A+ + +L+PE V  IA  L V+E+EV+SMN R+
Sbjct: 121 WSMVKLGTTSAQKKLFFNLRKAKNRIGALEEGDLRPENVQRIANDLGVTEAEVVSMNRRM 180

Query: 181 -AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
             GD SLNA + S  + + QWQDWL  +   Q     +++E + RR ++  +M VLN RE
Sbjct: 181 SGGDASLNATVGSDGEGTMQWQDWLEDESADQAGDYEDRDELQQRRELMAEAMDVLNDRE 240

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + I   RRL E  VTLE+LS ++ VSRER+RQIE RAF+K+Q+ +Q
Sbjct: 241 KDILMQRRLAEKTVTLEDLSGQYSVSRERIRQIEVRAFEKLQKKMQ 286


>gi|84515395|ref|ZP_01002757.1| RNA polymerase sigma factor [Loktanella vestfoldensis SKA53]
 gi|84510678|gb|EAQ07133.1| RNA polymerase sigma factor [Loktanella vestfoldensis SKA53]
          Length = 303

 Score =  286 bits (733), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 169/284 (59%), Positives = 212/284 (74%), Gaps = 2/284 (0%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           + KN+      E GL+RY+ EIRK PMLE +EEY+LAKR+ +H D  AAH++VTSHLRL 
Sbjct: 8   DYKNLPAPTP-EGGLNRYMQEIRKFPMLEPEEEYMLAKRWVDHEDTEAAHKMVTSHLRLA 66

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            KIAMGYRGYGLP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSW
Sbjct: 67  AKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSW 126

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL- 180
           SLVK+GTT+ QK+LFFNLR+ K  + A+ + +L+PE V  IA  L V+E EVISMN RL 
Sbjct: 127 SLVKMGTTSAQKKLFFNLRKAKNRIGALEEGDLRPENVKQIANDLGVTEDEVISMNRRLS 186

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA I S  + S QWQDWL  D         E +E   RR +L  +M++LNPRE+
Sbjct: 187 GGDASLNAQIGSDGEGSMQWQDWLEDDSANTAADYEEHDELDARRALLVEAMTLLNPREK 246

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            I   RRL E  VTLE+LS+ +EVSRER+RQIE RAF+K+Q  +
Sbjct: 247 DILVQRRLAEETVTLEDLSARYEVSRERIRQIEVRAFEKLQSRM 290


>gi|254456610|ref|ZP_05070039.1| alternative sigma factor RpoH [Candidatus Pelagibacter sp.
           HTCC7211]
 gi|207083612|gb|EDZ61038.1| alternative sigma factor RpoH [Candidatus Pelagibacter sp.
           HTCC7211]
          Length = 297

 Score =  286 bits (732), Expect = 3e-75,   Method: Composition-based stats.
 Identities = 156/284 (54%), Positives = 214/284 (75%), Gaps = 4/284 (1%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
              N    +  E GLS Y+ +I+K PML  +EEY+LAK ++  G++ AA +LVTSHLRLV
Sbjct: 4   TYNNNLPALTNEGGLSAYLEQIKKFPMLAAEEEYMLAKNWKTTGNVKAAEKLVTSHLRLV 63

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            KIAMGY+GYGLP++E++SEGN+GLMQAVKKF+PE+GFRLATY+MWWIKA++QEYILRSW
Sbjct: 64  AKIAMGYKGYGLPVNEMISEGNVGLMQAVKKFEPEKGFRLATYAMWWIKASIQEYILRSW 123

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
           SLVKIGTT  QK+LFFNL+++K  +   T+ +L+ E V  IA KL+VS+ EV+SMN RL+
Sbjct: 124 SLVKIGTTTAQKKLFFNLKKIKNQIAPQTEGDLRNEHVNEIANKLDVSKEEVVSMNRRLS 183

Query: 182 GDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           G E SLNA +    ++  +WQDWLV      +     +EE + R+++L  S+ VLN RER
Sbjct: 184 GKEFSLNAQVG---EDGDEWQDWLVDKELDHDLKFAHQEEMEQRKDLLKNSIKVLNDRER 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            I  +RRL ++P TLE+LS ++++SRERVRQIE +AF+K+Q+ +
Sbjct: 241 EILYSRRLNDDPTTLEDLSKKYKISRERVRQIENKAFEKLQKHM 284


>gi|56551645|ref|YP_162484.1| RNA polymerase factor sigma-32 [Zymomonas mobilis subsp. mobilis
           ZM4]
 gi|241761228|ref|ZP_04759316.1| RNA polymerase, sigma 32 subunit, RpoH [Zymomonas mobilis subsp.
           mobilis ATCC 10988]
 gi|260752767|ref|YP_003225660.1| RNA polymerase factor sigma-32 [Zymomonas mobilis subsp. mobilis
           NCIMB 11163]
 gi|59803027|sp|P50512|RP32_ZYMMO RecName: Full=RNA polymerase sigma-32 factor
 gi|56543219|gb|AAV89373.1| RNA polymerase, sigma 32 subunit, RpoH [Zymomonas mobilis subsp.
           mobilis ZM4]
 gi|241374135|gb|EER63632.1| RNA polymerase, sigma 32 subunit, RpoH [Zymomonas mobilis subsp.
           mobilis ATCC 10988]
 gi|258552130|gb|ACV75076.1| RNA polymerase, sigma 32 subunit, RpoH [Zymomonas mobilis subsp.
           mobilis NCIMB 11163]
          Length = 302

 Score =  285 bits (731), Expect = 4e-75,   Method: Composition-based stats.
 Identities = 172/291 (59%), Positives = 215/291 (73%), Gaps = 7/291 (2%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           + G+  L+ Y+ +IRK P+L+ +EEY+LAKR++EH D  AA RLVTSHLRLV KIAMGYR
Sbjct: 14  LGGDQSLNHYLADIRKFPILKPEEEYMLAKRFQEHQDPKAASRLVTSHLRLVAKIAMGYR 73

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYGLP+SE++SEGNIGLMQ VKKFDPERGFRLATY++WWIKA++QEYILRSWSLVK+GTT
Sbjct: 74  GYGLPVSELISEGNIGLMQGVKKFDPERGFRLATYAIWWIKASIQEYILRSWSLVKMGTT 133

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
           A QK+LFFNLRRLK ++ A  D +LKP++V +IA  L VS  EV++MN R+A  GD SLN
Sbjct: 134 AAQKKLFFNLRRLKSNMNAFEDGDLKPDEVDSIATNLGVSNEEVVNMNRRMAMGGDSSLN 193

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +    Q QDWLV     Q+Q + E+EE   R  +L  +M  LN RE+ I   RR
Sbjct: 194 --ITMREDGEGQMQDWLVDQEPLQDQQIEEEEESLVRHKLLIEAMDKLNDREKHILTERR 251

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQ 298
           L +NP TLE LS  + VSRERVRQIE RAF K+Q++I   +EL+    LL 
Sbjct: 252 LSDNPKTLEELSQVYGVSRERVRQIEVRAFDKLQKAI---MELAGDRKLLP 299


>gi|255263634|ref|ZP_05342976.1| alternative sigma factor RpoH [Thalassiobium sp. R2A62]
 gi|255105969|gb|EET48643.1| alternative sigma factor RpoH [Thalassiobium sp. R2A62]
          Length = 298

 Score =  285 bits (730), Expect = 5e-75,   Method: Composition-based stats.
 Identities = 163/287 (56%), Positives = 214/287 (74%), Gaps = 1/287 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+        + E GL+RY+ EIRK PMLE +EEY+LAK + E+ D  +AH+LVTSHLRL
Sbjct: 1   MSTYTNLPAPSPEQGLNRYLQEIRKFPMLEPEEEYMLAKSWVENEDSKSAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
             KIAMGYRGYGLP +EV+SE N+GLMQAVKKFDPE+GFRL+TY+MWWI+AA+QEY+LRS
Sbjct: 61  AAKIAMGYRGYGLPQAEVISEANVGLMQAVKKFDPEKGFRLSTYAMWWIRAAIQEYVLRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WS+VK+GTT+ QK+LFFNLR+ K  + A+ D +L+PE V  IA  L V+E EVI+MN RL
Sbjct: 121 WSMVKLGTTSAQKKLFFNLRKAKSRIGALEDGDLRPEHVERIANDLGVNEQEVINMNRRL 180

Query: 181 -AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
             GD SLNA + S  + + QWQDWL  +   Q      K+E  +RR +L  +MSVLN RE
Sbjct: 181 SGGDASLNAQVGSEGEGTMQWQDWLEDEDADQAGDYEAKDELDSRRELLADAMSVLNDRE 240

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           + I   RRLQ+  +TLE LS +++VSRER+RQIE RAF+K+Q+ +++
Sbjct: 241 KDILMQRRLQDKAITLEELSGQYDVSRERIRQIEVRAFEKLQKKMRE 287


>gi|83859148|ref|ZP_00952669.1| RNA polymerase sigma factor [Oceanicaulis alexandrii HTCC2633]
 gi|83852595|gb|EAP90448.1| RNA polymerase sigma factor [Oceanicaulis alexandrii HTCC2633]
          Length = 296

 Score =  285 bits (730), Expect = 6e-75,   Method: Composition-based stats.
 Identities = 170/297 (57%), Positives = 222/297 (74%), Gaps = 4/297 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M     ++ ++ E GLSRY+ EIRK PMLEK +E++LAKR++EH D  AAH+LVTSHLRL
Sbjct: 1   MANMKTALTMSPEAGLSRYLAEIRKFPMLEKDQEFMLAKRWQEHEDSDAAHQLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI+EV+SEGN+GLMQAVKKFDP++GFRLATY+MWWI+A++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIAEVISEGNVGLMQAVKKFDPDKGFRLATYAMWWIRASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTA QK+LFFNLRR+K  ++A+ + +L+P+QV  IA KL V++ +VISMN RL
Sbjct: 121 WSLVKMGTTAAQKKLFFNLRRMKSQMRALDEGDLRPDQVEEIATKLGVTDDDVISMNRRL 180

Query: 181 AG-DESLNALINSSDKNSSQWQDW-LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           +G D SLNA + +     ++WQDW    D D  E  L E +E   R  +L  +M  LN R
Sbjct: 181 SGPDASLNAPMRA--DGEAEWQDWLADDDADDAEDELAESDEFSMRMTLLQEAMGALNER 238

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPP 295
           E+ I + RRL E P TLE+L+  + VSRER+RQIE RAF+K+Q  +++  E     P
Sbjct: 239 EQNIIQERRLTEEPKTLEDLAQVYGVSRERIRQIEVRAFEKLQNEMKRLAEERGLMP 295


>gi|1143379|dbj|BAA09444.1| sigma-32 homolog [Zymomonas mobilis]
          Length = 302

 Score =  285 bits (729), Expect = 7e-75,   Method: Composition-based stats.
 Identities = 172/291 (59%), Positives = 215/291 (73%), Gaps = 7/291 (2%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           + G+  L+ Y+ +IRK P+L+ +EEY+LAKR++EH D  AA RLVTSHLRLV KIAMGYR
Sbjct: 14  LGGDQSLNHYLADIRKFPILKPEEEYMLAKRFQEHQDPKAASRLVTSHLRLVAKIAMGYR 73

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYGLP+SE++SEGNIGLMQ VKKFDPERGFRLATY++WWIKA++QEYILRSWSLVK+GTT
Sbjct: 74  GYGLPVSELISEGNIGLMQGVKKFDPERGFRLATYAIWWIKASIQEYILRSWSLVKMGTT 133

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLN 187
           A QK+LFFNLRRLK ++ A  D +LKP++V +IA  L VS  EV++MN R+A  GD SLN
Sbjct: 134 AAQKKLFFNLRRLKSNMNAFEDGDLKPDEVDSIATNLGVSNEEVVNMNRRMAMGGDSSLN 193

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +    Q QDWLV     Q+Q + E+EE   R  +L  +M  LN RE+ I   RR
Sbjct: 194 --ITMREDGEGQMQDWLVDQEPLQDQQIEEEEESLVRHKLLIEAMDRLNDREKHILTERR 251

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQ 298
           L +NP TLE LS  + VSRERVRQIE RAF K+Q++I   +EL+    LL 
Sbjct: 252 LSDNPKTLEELSQVYGVSRERVRQIEVRAFDKLQKAI---MELAGDRKLLP 299


>gi|254486865|ref|ZP_05100070.1| alternative sigma factor RpoH [Roseobacter sp. GAI101]
 gi|214043734|gb|EEB84372.1| alternative sigma factor RpoH [Roseobacter sp. GAI101]
          Length = 298

 Score =  284 bits (727), Expect = 1e-74,   Method: Composition-based stats.
 Identities = 163/284 (57%), Positives = 214/284 (75%), Gaps = 2/284 (0%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N  N+      E GL+RY+ EIRK P+LE +EEY+LAKR+ E  D  AAHR+VTSHLRL 
Sbjct: 3   NYANLPAPTP-EGGLNRYMQEIRKFPLLEPEEEYMLAKRWVEEQDTEAAHRMVTSHLRLA 61

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            KIAMGYRGYGLP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSW
Sbjct: 62  AKIAMGYRGYGLPQAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSW 121

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL- 180
           SLVK+GTT+ QK+LFFNLR+ K  + A+ + +++PE V  IA  L V+E+EV+SMN R+ 
Sbjct: 122 SLVKLGTTSGQKKLFFNLRKAKNRIGALEEGDMRPENVSRIATDLGVTEAEVVSMNRRMS 181

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLNA + S  + + QWQDWL  +   Q     E+EE + RR ML  ++ VLN RE+
Sbjct: 182 GGDASLNATVGSEGEGTMQWQDWLEDEDADQAGDYEEREELETRREMLAEALEVLNDREK 241

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            I   RRL +  +TLE+LSS+++VSRER+RQIE RAF+K+Q+ +
Sbjct: 242 DILTQRRLSDETITLEDLSSQYDVSRERIRQIEVRAFEKLQKRM 285


>gi|288962386|ref|YP_003452681.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
 gi|288914652|dbj|BAI76137.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
          Length = 293

 Score =  283 bits (725), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 155/280 (55%), Positives = 205/280 (73%), Gaps = 2/280 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+        +    LSRYI++  + P+L  ++EY+LAK + EHGD+ AAHRLVTSHLRL
Sbjct: 1   MSTAIALRSPDAGESLSRYINDTHRYPVLTAEDEYMLAKAWTEHGDVDAAHRLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VVKIA GYRGYGLP+S++++EGN+GLM AVKKF+PERGFRL+TY+MWWIKA++Q+YILRS
Sbjct: 61  VVKIAGGYRGYGLPLSDLIAEGNLGLMTAVKKFEPERGFRLSTYAMWWIKASIQDYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVKIGTTA QK+LFF+L RLK  L      +L P+ V +IA  L V E +V++MN RL
Sbjct: 121 WSLVKIGTTAAQKKLFFSLGRLKRKLGEYGGGDLHPDSVTSIATDLAVPEDDVVAMNRRL 180

Query: 181 AGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +    SLNA   S++ +S +WQD L  D    E+ L+E+ E + R  +L  +M VLN RE
Sbjct: 181 SAPVASLNAP-MSAEGDSGEWQDLLADDRPSVEESLVERGEARQRSALLHEAMGVLNDRE 239

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           R I  +RRL ++P+TLE+LS  + VSRER+RQIE RAF+K
Sbjct: 240 RDILTSRRLSDSPLTLEDLSVRYGVSRERIRQIEERAFEK 279


>gi|23014972|ref|ZP_00054764.1| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Magnetospirillum magnetotacticum
           MS-1]
          Length = 292

 Score =  283 bits (724), Expect = 2e-74,   Method: Composition-based stats.
 Identities = 145/287 (50%), Positives = 214/287 (74%), Gaps = 5/287 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+  N+  +V G+ GL++Y+ +I++ P+L  +EE++LAKR+ ++ D  AAH+LVTSHLRL
Sbjct: 1   MSVANLP-VVAGDDGLAKYLRDIKEFPVLAPEEEFMLAKRWVDYEDTEAAHKLVTSHLRL 59

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIA+GYR YGLP+++++SEGNIGLM+AVKKF+P+RGFRLATY+MWWIKA++ E++L S
Sbjct: 60  VAKIALGYRHYGLPVADLISEGNIGLMRAVKKFEPDRGFRLATYAMWWIKASLNEFVLNS 119

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WS+VKIGT A QK+LFFNLRR+K  L+ +   +L PE V  IA++L+V E +V++MN R+
Sbjct: 120 WSMVKIGTLAAQKKLFFNLRRIKSRLRLLESGDLAPEHVTTIARELDVDERDVVAMNRRM 179

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           AG D SLN  +    +  ++ QD +  + D QE  L ++EE    R ++ R++  L  RE
Sbjct: 180 AGRDSSLNTPVG---EGGAEIQDLMADEADNQETSLAKREELSKGRTLIARALDSLTERE 236

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R +F  RRL+++P+TLE L   + VSRER+RQIE +AF+KV++ +Q 
Sbjct: 237 REVFVERRLRDDPLTLEELGGRYGVSRERIRQIEVKAFEKVRDLVQA 283


>gi|144898533|emb|CAM75397.1| Sigma-70 region 2:Sigma-70 region 4 [Magnetospirillum
           gryphiswaldense MSR-1]
          Length = 290

 Score =  283 bits (724), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 148/280 (52%), Positives = 208/280 (74%), Gaps = 4/280 (1%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           R  +  I   + GLS+Y+ EIR  P+LE ++EY+LAKR+ ++ D +AAH+LVTSHLRLV 
Sbjct: 2   RATVPAISADDSGLSKYLREIRDFPVLEPEQEYMLAKRWVDYEDTAAAHQLVTSHLRLVA 61

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           KIAMGYR YGLP+++++SEGN+GLM+AVKKF+PERGFRL+TY+MWWIKA++ E++L SWS
Sbjct: 62  KIAMGYRHYGLPMADLISEGNLGLMRAVKKFEPERGFRLSTYAMWWIKASLNEFVLNSWS 121

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           LVKIGT A QK+LFFNLR++K  L+ +    L P  V AIAK+L VSE++V++MN R+ G
Sbjct: 122 LVKIGTLAAQKKLFFNLRKVKTKLRLLDATELAPADVRAIAKELGVSETDVVNMNRRMGG 181

Query: 183 -DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
            D SLN  +    ++ ++  + L  + D QE  L + EE    R ++ ++++ LN RER 
Sbjct: 182 RDSSLNTPVG---ESGTEIIELLPDETDNQETGLAKHEELSKGRKLIAQALTSLNERERE 238

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           IF  RRL++ P+TLE L + F VSRER+RQIE +AF+KV+
Sbjct: 239 IFVERRLRDEPLTLEELGARFGVSRERIRQIEVKAFEKVR 278


>gi|254453399|ref|ZP_05066836.1| alternative sigma factor RpoH [Octadecabacter antarcticus 238]
 gi|198267805|gb|EDY92075.1| alternative sigma factor RpoH [Octadecabacter antarcticus 238]
          Length = 298

 Score =  283 bits (724), Expect = 3e-74,   Method: Composition-based stats.
 Identities = 159/274 (58%), Positives = 208/274 (75%), Gaps = 1/274 (0%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E GL+RY+ EIRK PMLE  EEY+LAKR+ +H D  AAH++VTSHLRL  KIAMGYRGYG
Sbjct: 13  EQGLNRYMQEIRKFPMLEPDEEYMLAKRWVDHEDTEAAHKMVTSHLRLAAKIAMGYRGYG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP +EV+SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEY+LRSWS+VK+GTT+ Q
Sbjct: 73  LPTAEVISEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYVLRSWSMVKLGTTSAQ 132

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALIN 191
           K+LFFNLR+ K  + A+ + +L+PE V  IA  L V+E+EV+SMN R+  GD SLNA + 
Sbjct: 133 KKLFFNLRKAKNRIGALEEGDLRPENVQRIATDLGVTEAEVVSMNRRMSGGDASLNATVG 192

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           S  + + QWQDWL  +   Q      ++E   RR ++  +M VLN RE+ I   RRL E 
Sbjct: 193 SDGEGTMQWQDWLEDESADQAGDYEARDELTQRRELMAEAMEVLNDREKDILMQRRLAEK 252

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            VTLE+LS ++ VSRER+RQIE RAF+K+Q+ +Q
Sbjct: 253 TVTLEDLSGQYSVSRERIRQIEVRAFEKLQKKMQ 286


>gi|71083311|ref|YP_266030.1| RNA polymerase factor sigma-32 [Candidatus Pelagibacter ubique
           HTCC1062]
 gi|71062424|gb|AAZ21427.1| RNA polymerase sigma-32 factor (rpoH) RP303 [Candidatus
           Pelagibacter ubique HTCC1062]
          Length = 293

 Score =  282 bits (723), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 158/285 (55%), Positives = 217/285 (76%), Gaps = 6/285 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           MN  N+  + N E GLS Y+ +I+K PML  +EEY+LAK ++  G++ AA +LVTSHLRL
Sbjct: 1   MN-SNLPALSN-EGGLSAYLEQIKKFPMLAAEEEYMLAKNWKATGNVKAAEKLVTSHLRL 58

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLP++E++SEGN+GLMQAVKKF+PE+GFRLATY+MWWI+A++QEYILRS
Sbjct: 59  VAKIAMGYRGYGLPVNEMISEGNVGLMQAVKKFEPEKGFRLATYAMWWIRASIQEYILRS 118

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVKIGTT  QK+LFFNL+++K  +   ++ +L+PE V  IA KL+V++ EVISMN RL
Sbjct: 119 WSLVKIGTTTAQKKLFFNLKKIKNQIAPQSEGDLRPEHVTEIANKLDVNKDEVISMNRRL 178

Query: 181 AGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G E SLNA +    ++  +WQDWLV      +     +EE   R+N+L  S+ +LN RE
Sbjct: 179 SGKEFSLNAQVG---EDGDEWQDWLVDKELDHDLKFAHQEEMGQRQNLLKDSIKILNERE 235

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + I  +RRL + P TLE+LS ++++SRERVRQIE +AF+K+Q+ +
Sbjct: 236 KEILYSRRLNDEPTTLEDLSKKYKISRERVRQIENKAFEKLQKHM 280


>gi|83311906|ref|YP_422170.1| RNA polymerase factor sigma-32 [Magnetospirillum magneticum AMB-1]
 gi|82946747|dbj|BAE51611.1| RNA polymerase sigma-32 factor [Magnetospirillum magneticum AMB-1]
          Length = 292

 Score =  282 bits (723), Expect = 4e-74,   Method: Composition-based stats.
 Identities = 147/287 (51%), Positives = 214/287 (74%), Gaps = 5/287 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+  N+  +V G+ GL++Y+ +I++ P+L  +EE++LAKR+ ++ D  AAHRLVTSHLRL
Sbjct: 1   MSVANLP-VVAGDDGLAKYLRDIKEFPVLAPEEEFMLAKRWVDYEDTDAAHRLVTSHLRL 59

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIA+GYR YGLP+++++SEGNIGLM+AVKKF+P+RGFRLATY+MWWIKA++ E++L S
Sbjct: 60  VAKIALGYRHYGLPVADLISEGNIGLMRAVKKFEPDRGFRLATYAMWWIKASLNEFVLNS 119

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WS+VKIGT A QK+LFFNLRR+K  L+ +   +L PE V  IA++L+V E +V++MN R+
Sbjct: 120 WSMVKIGTLAAQKKLFFNLRRIKSRLRLLEAGDLAPEHVATIARELDVDERDVVAMNRRM 179

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           AG D SLNA +    +  ++ QD +  + D QE    ++EE    R ++ R++  L  RE
Sbjct: 180 AGRDSSLNAPVG---EGGTEIQDLMADEADNQETAYGKREELSKGRVLIARALDSLTERE 236

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R +F  RRL+++PVTLE L   + VSRER+RQIE +AF+KV++ +Q 
Sbjct: 237 REVFVERRLRDDPVTLEELGGRYGVSRERIRQIEVKAFEKVRDLVQA 283


>gi|91762259|ref|ZP_01264224.1| RNA polymerase sigma factor [Candidatus Pelagibacter ubique
           HTCC1002]
 gi|91718061|gb|EAS84711.1| RNA polymerase sigma factor [Candidatus Pelagibacter ubique
           HTCC1002]
          Length = 293

 Score =  282 bits (721), Expect = 6e-74,   Method: Composition-based stats.
 Identities = 157/285 (55%), Positives = 217/285 (76%), Gaps = 6/285 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           MN  N+  + N E GLS Y+ +I+K PML  +EEY+LAK ++  G++ AA +LVTSHLRL
Sbjct: 1   MN-SNLPALSN-EGGLSAYLEQIKKFPMLAAEEEYMLAKNWKATGNVKAAEKLVTSHLRL 58

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLP++E++SEGN+GLMQAVKKF+PE+GFRLATY+MWWI+A++QEYILRS
Sbjct: 59  VAKIAMGYRGYGLPVNEMISEGNVGLMQAVKKFEPEKGFRLATYAMWWIRASIQEYILRS 118

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVKIGTT  QK+LFFNL+++K  +   ++ +L+PE V  IA KL+V++ EVISMN RL
Sbjct: 119 WSLVKIGTTTAQKKLFFNLKKIKNQIAPQSEGDLRPEHVTEIANKLDVNKDEVISMNRRL 178

Query: 181 AGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G E SLNA +    ++  +WQDWLV      +     +EE   R+N+L  S+ +LN RE
Sbjct: 179 SGKEFSLNAQVG---EDGDEWQDWLVDKELDHDLKFAHQEEMGQRQNLLKDSIKILNERE 235

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + I  +RRL + P TLE+LS ++++SRER+RQIE +AF+K+Q+ +
Sbjct: 236 KEILYSRRLNDEPTTLEDLSKKYKISRERIRQIENKAFEKLQKHM 280


>gi|262277481|ref|ZP_06055274.1| alternative sigma factor RpoH [alpha proteobacterium HIMB114]
 gi|262224584|gb|EEY75043.1| alternative sigma factor RpoH [alpha proteobacterium HIMB114]
          Length = 300

 Score =  281 bits (719), Expect = 9e-74,   Method: Composition-based stats.
 Identities = 165/287 (57%), Positives = 215/287 (74%), Gaps = 2/287 (0%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           K    +++ +     Y+ +IRK PML+  EEY+LAK +RE GD  +AH+LVTSHLRLV K
Sbjct: 7   KTNLPVLSPDGSFDSYLQKIRKFPMLDAAEEYILAKNWREKGDKESAHKLVTSHLRLVAK 66

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA GYRGYGLP+SE+VSEGNIGLM AVKKFDPERGFRLATY+MWWIKA+MQEYILRSWSL
Sbjct: 67  IATGYRGYGLPMSELVSEGNIGLMTAVKKFDPERGFRLATYAMWWIKASMQEYILRSWSL 126

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VKIGTTA QK+LFFNLR++K  +      +L PEQV  IA +L+V+E EV SM+ R+ G 
Sbjct: 127 VKIGTTAAQKKLFFNLRKMKNQIMRSDQTDLLPEQVTEIANRLDVTEDEVNSMDQRMKGP 186

Query: 184 E-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
           E SLNA I S ++  S+WQDW+V ++  QE  +  ++E   R+ +L ++MS+LN RE+ I
Sbjct: 187 EASLNATI-SGEEGESEWQDWVVDENADQELQIAHRQETNKRKALLDKAMSILNEREKEI 245

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
              RRL E P TLE LS ++ +SRER+RQIE RAF+K+Q+ + +Q +
Sbjct: 246 LFDRRLNEEPKTLEELSQKYNISRERIRQIENRAFEKLQKEMLEQAK 292


>gi|296284608|ref|ZP_06862606.1| RNA polymerase factor sigma-32 [Citromicrobium bathyomarinum JL354]
          Length = 280

 Score =  280 bits (717), Expect = 2e-73,   Method: Composition-based stats.
 Identities = 158/269 (58%), Positives = 205/269 (76%), Gaps = 2/269 (0%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           + EI+K P+L  ++EY+LAKRY EH D  AA +LV+SHLRLV KIAMGYRGYGLP+S+++
Sbjct: 1   MSEIKKFPVLTAEQEYMLAKRYEEHEDPEAAAQLVSSHLRLVAKIAMGYRGYGLPVSDLI 60

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
           SEGN+GLMQ VKKF+P+RGFRLATY+MWWIKA++QEYILRSWSLVK+GTTA QK+LFFNL
Sbjct: 61  SEGNVGLMQGVKKFEPDRGFRLATYAMWWIKASIQEYILRSWSLVKMGTTAAQKKLFFNL 120

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR--LAGDESLNALINSSDKNS 197
           RR+K +L A  D +L P+ V  IA  L V E EVI+MN R  + GD SLN  +   ++N+
Sbjct: 121 RRMKKNLDAYEDTDLHPDDVKKIATDLGVPEQEVINMNRRMLMGGDSSLNVSMRGDEENA 180

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           SQWQDWL  D   Q++   + +E + R  ML  +M  LN RE+ I   RRL E+P TLE 
Sbjct: 181 SQWQDWLTDDRPLQDETTADTQEAQVRHAMLLEAMDSLNDREKHILTERRLTEDPQTLEE 240

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LS  ++VSRER+RQIE RAF+K+Q+++Q+
Sbjct: 241 LSKVYDVSRERIRQIEVRAFEKLQKAMQR 269


>gi|283797719|ref|ZP_06346872.1| RNA polymerase sigma factor RpoD [Clostridium sp. M62/1]
 gi|291074616|gb|EFE11980.1| RNA polymerase sigma factor RpoD [Clostridium sp. M62/1]
 gi|295092057|emb|CBK78164.1| RNA polymerase, sigma 70 subunit, RpoD [Clostridium cf.
           saccharolyticum K10]
          Length = 372

 Score =  279 bits (715), Expect = 3e-73,   Method: Composition-based stats.
 Identities = 88/284 (30%), Positives = 144/284 (50%), Gaps = 13/284 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +M   V+ E  +  Y+ EI K+P+L  +EE  LAKR  E GD SA  RL  ++LRLVV I
Sbjct: 92  SMPEGVSIEDPVRMYLKEIGKVPLLTPEEEIDLAKRM-EMGDESAKKRLAEANLRLVVSI 150

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y G G+   +++ EGN+GL++AV+K+D  +GF+ +TY+ WWI+ A+   I      +
Sbjct: 151 AKRYVGRGMQFLDLIQEGNLGLIKAVEKYDYSKGFKFSTYATWWIRQAITRSIADQARTI 210

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I     +      + RL    + +     +      +A+KL++    V  +        
Sbjct: 211 RIPVHMVE-----TINRLIRTSRQLLQELGREPSAEELAEKLDMPVERVREIMKISQDPV 265

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   I   ++  S   D++  DH    QV ++          L   +  L  RE+++  
Sbjct: 266 SLETPI--GEEEDSHLGDFIQDDHV---QVPVDAATYTLLHEQLMEVLDTLTDREQKVLR 320

Query: 245 ARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R   ++  P TLE +  EF V+RER+RQIEA+A +K++   + 
Sbjct: 321 LRFGLDDGRPRTLEEVGREFNVTRERIRQIEAKALRKLRHPSRS 364


>gi|291520418|emb|CBK75639.1| RNA polymerase, sigma 70 subunit, RpoD [Butyrivibrio fibrisolvens
           16/4]
          Length = 376

 Score =  279 bits (713), Expect = 5e-73,   Method: Composition-based stats.
 Identities = 87/284 (30%), Positives = 139/284 (48%), Gaps = 13/284 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           ++   V+ E  +  Y+ EI K+P+L  +EE  LA++  E GD  A ++L  ++LRLVV I
Sbjct: 95  SVPDSVSIEDPVRMYLKEIGKVPLLSAEEEVELAQKM-EDGDQEAKNKLAEANLRLVVSI 153

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y G G+   +++ EGN+GLM+AV+KFD  +G++ +TY+ WWI+ A+   I      +
Sbjct: 154 AKRYVGRGMLFLDLIQEGNLGLMKAVEKFDYHKGYKFSTYATWWIRQAITRAIADQARTI 213

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I     +      L R+   L         PE    IA  + ++   V  +        
Sbjct: 214 RIPVHMVE--TINKLIRVSRQLLQEYGREPTPE---EIAAAMGITVDRVHEILKISQEPV 268

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   I   ++  S   D+L    D    V  E       +  L   +  L  RE+R+  
Sbjct: 269 SLETPI--GEEEDSHLGDFLP---DENVPVPAEAATFTLLKEQLHEVLDTLTEREQRVLI 323

Query: 245 ARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R   E+    TLE +  EF V+RER+RQIEA+A +K++   + 
Sbjct: 324 LRFGLEDGKARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRS 367


>gi|210620870|ref|ZP_03292287.1| hypothetical protein CLOHIR_00230 [Clostridium hiranonis DSM 13275]
 gi|210155082|gb|EEA86088.1| hypothetical protein CLOHIR_00230 [Clostridium hiranonis DSM 13275]
          Length = 388

 Score =  277 bits (710), Expect = 1e-72,   Method: Composition-based stats.
 Identities = 89/280 (31%), Positives = 146/280 (52%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ +  +  Y+ EI KIP+L+  EE   AKR  E GD  A  RLV ++LRLVV IA  Y 
Sbjct: 113 ISIDDPVRMYLKEIGKIPLLKPHEEVEYAKRMHE-GDELAKQRLVEANLRLVVSIAKRYV 171

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD E+GF+ +TY+ WWI+ A+   I      ++I   
Sbjct: 172 GRGMLFLDLIQEGNLGLIKAVEKFDYEKGFKFSTYATWWIRQAITRAIADQARTIRIPVH 231

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L      + KPE    IAK++++S  +V  +        SL   
Sbjct: 232 MVE--TINKLMRVSRQLLQELGRDAKPE---EIAKEMDLSVEKVREIMKIAQDPVSLETP 286

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++  D      +          +  +   +  LN RE+++ + R   
Sbjct: 287 I--GEEEDSHLGDFIPDDDAPAPDI---SAAYSLLKEQIDEVLGSLNEREQKVLKLRFGL 341

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+    TLE +  EF+V+RER+RQIEA+A +K++   + +
Sbjct: 342 EDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSK 381


>gi|291533682|emb|CBL06795.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Megamonas hypermegale
           ART12/1]
          Length = 329

 Score =  277 bits (709), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 86/280 (30%), Positives = 137/280 (48%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           +N +  +  Y+ EI ++P+L   EE  LAKR  E GDL A  RL  ++LRLVV IA  Y 
Sbjct: 60  INIDDPVRMYLKEIGRVPLLSADEEIKLAKRM-EDGDLEAQKRLAEANLRLVVSIAKRYV 118

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 119 GRGMLFLDLIQEGNLGLIKAVEKFDYNKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 178

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L         PE    IAK+++VS   V  +        SL   
Sbjct: 179 MVE--TINKLIRVSRQLLQSLGREPSPE---EIAKEMDVSVDRVREIMKIAQEPVSLETP 233

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++    D       E       +  L   +  L  RE ++   R   
Sbjct: 234 I--GEEEDSHLGDFI---EDHDAPAPAEAASFVLLKEQLEDVLDTLTEREEKVLRLRFGL 288

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 289 DDGRARTLEEVGQNFGVTRERIRQIEAKALRKLRHPSRSK 328


>gi|296133798|ref|YP_003641045.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermincola sp.
           JR]
 gi|296032376|gb|ADG83144.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermincola
           potens JR]
          Length = 366

 Score =  277 bits (708), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 85/280 (30%), Positives = 136/280 (48%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           +  +  +  Y+ EI ++P+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y 
Sbjct: 91  IGIDDPVRMYLKEIGRVPLLTAEEEVELAKRM-ETGDEEAKRRLAEANLRLVVSIAKRYV 149

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G GL   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 150 GRGLLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 209

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L         PE    IA ++++    V  +        SL   
Sbjct: 210 MVE--TINKLIRVSRQLLQELGREPTPE---EIAAEMDIPVDRVREIMKIAQEPVSLETP 264

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++    D       E       R  L   +  L PRE ++   R   
Sbjct: 265 I--GEEEDSHLGDFI---EDQDAPAPAEAASFILLREQLEEVLETLTPREEKVLRLRFGL 319

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 320 DDGRSRTLEEVGQEFGVTRERIRQIEAKALRKLRHPSRSK 359


>gi|218133123|ref|ZP_03461927.1| hypothetical protein BACPEC_00985 [Bacteroides pectinophilus ATCC
           43243]
 gi|217991996|gb|EEC58000.1| hypothetical protein BACPEC_00985 [Bacteroides pectinophilus ATCC
           43243]
          Length = 448

 Score =  277 bits (708), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 88/279 (31%), Positives = 141/279 (50%), Gaps = 13/279 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V+ E  +  Y+ EI K+P+L  +EE  LAKR  E+GD+ A +RL  ++LRLVV IA  Y 
Sbjct: 173 VSIEDPVRMYLKEIGKVPLLSAEEEIELAKRM-ENGDVEAKNRLAEANLRLVVSIAKRYV 231

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV KFD  +GF+ +TY+ WWI+ A+   I      ++I   
Sbjct: 232 GRGMLFLDLIQEGNLGLIKAVDKFDFRKGFKFSTYATWWIRQAITRAIADQARTIRIPVH 291

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L         PE    IAK++++    V  +        SL   
Sbjct: 292 MVE--TINKLLRVSRQLLQELGREPTPE---EIAKEMDIPVERVREIQKISQEPVSLETP 346

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++  D      V  E+      +  L   +  L  RE+++   R   
Sbjct: 347 I--GEEEDSHLGDFIQDD---NVPVPAEEAASTILKEQLVEVLGTLTEREQKVLRLRFGL 401

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ++    TLE +  EF V+RER+RQIEA+A +K++   + 
Sbjct: 402 DDGRARTLEEVGREFNVTRERIRQIEAKALRKLRHPSRS 440


>gi|323484375|ref|ZP_08089742.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323692387|ref|ZP_08106623.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
 gi|323402369|gb|EGA94700.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323503527|gb|EGB19353.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
          Length = 372

 Score =  277 bits (708), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 82/280 (29%), Positives = 142/280 (50%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           VN +  +  Y+ EI K+P+L  +EE  LAK+  E G+  A  RL  ++LRLVV IA  Y 
Sbjct: 97  VNIDDPVRMYLKEIGKVPLLSPEEEIELAKQM-EMGNEYAKKRLAEANLRLVVSIAKRYV 155

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+K+D  +GF+ +TY+ WWI+ A+   I      ++I   
Sbjct: 156 GRGMQFLDLIQEGNLGLIKAVEKYDYSKGFKFSTYATWWIRQAITRSIADQARTIRIPVH 215

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      + RL    + +     +      +A+++++    V  +        SL   
Sbjct: 216 MVE-----TINRLIRTSRQLLQELGREPHPEEVAERMDMPVERVREIMKISQDPVSLETP 270

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++  DH    QV ++          L   +  L  RE+++   R   
Sbjct: 271 I--GEEEDSHLGDFIQDDHV---QVPLDAATFTLLHEQLMEVLDTLTDREQKVLRLRFGL 325

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  P TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 326 DDGRPRTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 365


>gi|326791438|ref|YP_004309259.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           lentocellum DSM 5427]
 gi|326542202|gb|ADZ84061.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           lentocellum DSM 5427]
          Length = 363

 Score =  277 bits (708), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 83/286 (29%), Positives = 147/286 (51%), Gaps = 13/286 (4%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
            N+   ++ +  +  Y+ EI K+P+L  ++E +LA+R ++ GD  A  +L  ++LRLVV 
Sbjct: 82  SNLPDGISIDDPVRMYLKEIGKVPLLSAEQEIILAQRMQD-GDQEAKKKLAEANLRLVVS 140

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      
Sbjct: 141 IAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQART 200

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           ++I     +      L R+   L      + +PE    IAK++++  S+V  +       
Sbjct: 201 IRIPVHMVE--TINKLMRVSRQLLQELGRDPQPE---EIAKRMDMPVSKVREIMKISQEP 255

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SL   I   ++  S   D++  +      V  E       +  L   +  L  RE+++ 
Sbjct: 256 VSLETPI--GEEEDSHLGDFIPDED---IPVPAEAAAFTLLKEQLIEVLDTLTEREQKVL 310

Query: 244 EARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             R   ++    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 311 RLRFGLDDGRARTLEEVGKEFSVTRERIRQIEAKALRKLRHPSRSK 356


>gi|166030947|ref|ZP_02233776.1| hypothetical protein DORFOR_00628 [Dorea formicigenerans ATCC
           27755]
 gi|166029214|gb|EDR47971.1| hypothetical protein DORFOR_00628 [Dorea formicigenerans ATCC
           27755]
          Length = 382

 Score =  277 bits (708), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 89/290 (30%), Positives = 144/290 (49%), Gaps = 15/290 (5%)

Query: 1   MNRKNMSII--VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHL 58
           M + ++S+   ++ E  +  Y+ EI K+P+L   EE  LAKR  E GD  A  RL  ++L
Sbjct: 96  MEKIDLSVPDGISIEDPVRMYLKEIGKVPLLSADEEVELAKRMAE-GDEDAKKRLAEANL 154

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I 
Sbjct: 155 RLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYHKGFKFSTYATWWIRQAITRAIA 214

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
                ++I     +      L R+   L         PE    IA +L++    V  +  
Sbjct: 215 DQARTIRIPVHMVE--TINKLIRVSRQLLQELGREPTPE---EIAAELDMPVERVREILK 269

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
                 SL   I   ++  S   D++  D      V  E   +   +  L   +  L  R
Sbjct: 270 ISQEPVSLETPI--GEEEDSHLGDFIQDD---NVPVPAEAAAQTLLKEQLDEVLDTLTER 324

Query: 239 ERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E+++   R   ++    TLE +  EF+V+RER+RQIEA+A +K++   + 
Sbjct: 325 EQKVLRLRFGMDDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRS 374


>gi|85714568|ref|ZP_01045555.1| RNA polymerase sigma factor [Nitrobacter sp. Nb-311A]
 gi|85698453|gb|EAQ36323.1| RNA polymerase sigma factor [Nitrobacter sp. Nb-311A]
          Length = 272

 Score =  277 bits (708), Expect = 2e-72,   Method: Composition-based stats.
 Identities = 172/258 (66%), Positives = 209/258 (81%), Gaps = 1/258 (0%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           MLE  EEY+ AKR REH D  AAH LVTSHLRLV KIAMGYRGYGLPISEVVSEGN+GLM
Sbjct: 1   MLEPHEEYMFAKRLREHDDRDAAHHLVTSHLRLVAKIAMGYRGYGLPISEVVSEGNVGLM 60

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           QAVK+F+PE+GFRLATY+MWWIKA++QEYILRSWSLVK+GTTANQK+LFFNLR+ K  + 
Sbjct: 61  QAVKRFEPEKGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQKKLFFNLRKAKSKIS 120

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
           A+ + +++P+QV  IA++L V+E +V+ MN RL GD SLNA I   D  + +WQDWLV  
Sbjct: 121 ALDEGDMRPDQVKLIARRLGVTEQDVVDMNRRLGGDASLNAPIRD-DGEAGEWQDWLVDQ 179

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
              QE V+ E EE  +RR  LT +M VLNPRERRIFEARRL + P+TLE+L++EF VSRE
Sbjct: 180 SPTQEAVMAEHEEFDHRRRALTGAMGVLNPRERRIFEARRLADEPMTLEDLAAEFNVSRE 239

Query: 268 RVRQIEARAFKKVQESIQ 285
           RVRQIE RAF+KVQ +++
Sbjct: 240 RVRQIEVRAFEKVQSAVK 257


>gi|253580849|ref|ZP_04858112.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251847919|gb|EES75886.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 375

 Score =  276 bits (706), Expect = 3e-72,   Method: Composition-based stats.
 Identities = 88/279 (31%), Positives = 142/279 (50%), Gaps = 13/279 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V+ E  +  Y+ EI K+P+L  +EE  LAKR  E+GD +A  RL  ++LRLVV IA  Y 
Sbjct: 100 VSIEDPVRMYLKEIGKVPLLSAEEEIELAKRM-ENGDEAAKKRLAEANLRLVVSIAKRYV 158

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 159 GRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 218

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L         PE    IAK++++S   V  +        SL   
Sbjct: 219 MVE--TINKLIRVSRQLLQELGREPTPE---EIAKEMDMSVERVREILKISQEPVSLETP 273

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++  D      V  +       +  L   +S L  RE+++   R   
Sbjct: 274 I--GEEEDSHLGDFIQDD---NVPVPADAAAFTLLKEQLVEVLSTLTDREQKVLRLRFGL 328

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ++    TLE +  EF V+RER+RQIEA+A +K++   + 
Sbjct: 329 DDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRS 367


>gi|255282119|ref|ZP_05346674.1| RNA polymerase sigma factor RpoD [Bryantella formatexigens DSM
           14469]
 gi|255267438|gb|EET60643.1| RNA polymerase sigma factor RpoD [Bryantella formatexigens DSM
           14469]
          Length = 374

 Score =  276 bits (706), Expect = 4e-72,   Method: Composition-based stats.
 Identities = 90/280 (32%), Positives = 142/280 (50%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V+ E  +  Y+ EI  +P+L  +EE  LAKR  E GD  A  RL+ ++LRLVV IA  Y 
Sbjct: 99  VSTEDPVRMYLKEIGNVPLLTTEEEVELAKRV-EAGDEEAKKRLIEANLRLVVSIAKKYV 157

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+P  +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I  +   +++   
Sbjct: 158 GRGMPFLDLIQEGNMGLMKAVDKFDYAKGFKFSTYATWWIRQAITRGIADTGRTIRVPVH 217

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +        R+   L         PE+V   A++LNV  S V  +        SL+  
Sbjct: 218 MVE--TINKTLRMTRTLLQELGREPTPEEV---AERLNVPVSRVREVLKISRDPVSLDTP 272

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL- 248
           I   +++ S   D++  D         +       R  L  ++  L  RER++ + R   
Sbjct: 273 I--GEEDDSHLGDFIEDDS---ALSPSDSAAFSMLREELGTALESLTDRERQVVQLRFGL 327

Query: 249 -QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
                 TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 328 IDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 367


>gi|257869538|ref|ZP_05649191.1| RNA polymerase sigma-43 factor [Enterococcus gallinarum EG2]
 gi|257803702|gb|EEV32524.1| RNA polymerase sigma-43 factor [Enterococcus gallinarum EG2]
          Length = 368

 Score =  275 bits (704), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 80/276 (28%), Positives = 135/276 (48%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++P+L  +EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGRVPLLTAEEEVALALKI-EEGDQEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L         PE++ A   ++++   +V  +        SL   I   
Sbjct: 215 -TINKLIRIQRQLLQDLGREPTPEEIGA---EMDLPTEKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D       E    +  +  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDQDATSPAEHAAYELLKEQLEDVLDTLTDREENVLRLRFGIDDGR 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 361


>gi|315640587|ref|ZP_07895693.1| RNA polymerase sigma factor rpoD [Enterococcus italicus DSM 15952]
 gi|315483615|gb|EFU74105.1| RNA polymerase sigma factor rpoD [Enterococcus italicus DSM 15952]
          Length = 368

 Score =  275 bits (704), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 81/276 (29%), Positives = 135/276 (48%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++P+L   EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGRVPLLTAAEEVELALKI-EEGDQEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L         PE++ A   ++++S  +V  +        SL   I   
Sbjct: 215 -TINKLIRIQRQLLQDLGREPTPEEIGA---EMDLSTEKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D       E    +  +  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDQDATSPAEHAAYELLKEQLEDVLDTLTDREENVLRLRFGIDDGR 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 361


>gi|121534199|ref|ZP_01666024.1| RNA polymerase, sigma 70 subunit, RpoD family [Thermosinus
           carboxydivorans Nor1]
 gi|121307302|gb|EAX48219.1| RNA polymerase, sigma 70 subunit, RpoD family [Thermosinus
           carboxydivorans Nor1]
          Length = 368

 Score =  275 bits (704), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 83/280 (29%), Positives = 138/280 (49%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ +  +  Y+ EI ++P+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y 
Sbjct: 93  ISIDDPVRMYLKEIGRVPLLTAEEEIQLAKRM-EQGDEEAKRRLAEANLRLVVSIAKRYV 151

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 152 GRGMLFLDLIQEGNLGLIKAVEKFDYNKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 211

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L         PE    IA+++++S   V  +        SL   
Sbjct: 212 MVE--TINKLIRVSRQLLQEKGREPTPE---EIAREMDISVERVREIMKIAQEPVSLETP 266

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++    D       E       +  L   +  L PRE ++   R   
Sbjct: 267 I--GEEEDSHLGDFI---EDQDAPAPAEAASFMLLKEQLEEVLETLTPREEKVLRLRFGL 321

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 322 DDGRARTLEEVGQYFGVTRERIRQIEAKALRKLRHPSRSK 361


>gi|289450258|ref|YP_003475183.1| RNA polymerase sigma factor RpoD [Clostridiales genomosp. BVAB3
           str. UPII9-5]
 gi|289184805|gb|ADC91230.1| RNA polymerase sigma factor RpoD [Clostridiales genomosp. BVAB3
           str. UPII9-5]
          Length = 353

 Score =  275 bits (704), Expect = 5e-72,   Method: Composition-based stats.
 Identities = 83/289 (28%), Positives = 147/289 (50%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  + S ++N +  +  Y+ EI K+P+L  +EE  LA+  +E G   A  RL  ++LRL
Sbjct: 69  LNIDDSSDVMNVDDPVRMYLKEIGKVPLLNAEEEKDLARAMKE-GSQEAKDRLCEANLRL 127

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV KFD E+GF+ +TY+ WWI+ A+   I   
Sbjct: 128 VVSIAKRYVGRGMQFLDLIQEGNLGLIKAVDKFDYEKGFKFSTYATWWIRQAITRAIADQ 187

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      + +L    + +     +  +V  +A+++ +S  +V  +    
Sbjct: 188 ARTIRIPVHMVE-----TINKLIRVQRQLLQELGREPEVEELAQEMGISPEKVREIQKIS 242

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   ++  S   D++  D         ++      +  L   +S L PRE 
Sbjct: 243 QEPVSLEKPI--GEEEDSHLGDFIPDDD---APSPADQAAFTLLKEQLLEILSGLTPREE 297

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++   R   ++    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 298 KVLRLRFGLDDGRSRTLEEVGREFNVTRERIRQIEAKALRKMRHPSRSK 346


>gi|313903305|ref|ZP_07836697.1| RNA polymerase, sigma 70 subunit, RpoD [Thermaerobacter
           subterraneus DSM 13965]
 gi|313466393|gb|EFR61915.1| RNA polymerase, sigma 70 subunit, RpoD [Thermaerobacter
           subterraneus DSM 13965]
          Length = 432

 Score =  275 bits (704), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 84/285 (29%), Positives = 140/285 (49%), Gaps = 13/285 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +M   V  +  +  Y+ EI +IP+L  ++E  LAKR  E GD  A  +L+ ++LRLVV I
Sbjct: 152 SMPDGVALDDPVRMYLKEIGRIPLLTPEQEIELAKRI-EQGDEEAKRKLIQANLRLVVSI 210

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y G G+   +++ EGN+GL++A +KFD  +GF+ +TY+ WWI+ A+   I      +
Sbjct: 211 AKRYVGRGMLFLDLIQEGNLGLIKAAEKFDYRKGFKFSTYATWWIRQAITRAIADQARTI 270

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I     +      L R++  L         PE    IAK++ +   +V  +        
Sbjct: 271 RIPVHMVE--TINKLIRVQRQLVQELGREPTPE---EIAKEMGIEPEKVREIMKIAQEPV 325

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   I   ++  S   D++    D       E   +   R  L   +  L  RE+++  
Sbjct: 326 SLETPI--GEEEDSHLGDFI---EDEDALAPAEAASQLLLREQLEDVLHTLTDREQKVLR 380

Query: 245 ARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 381 LRFGLDDGRQRTLEEVGQIFGVTRERIRQIEAKALRKLRHPSRSK 425


>gi|78044024|ref|YP_359316.1| RNA polymerase sigma factor RpoD [Carboxydothermus hydrogenoformans
           Z-2901]
 gi|77996139|gb|ABB15038.1| RNA polymerase sigma factor RpoD [Carboxydothermus hydrogenoformans
           Z-2901]
          Length = 370

 Score =  275 bits (703), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 84/277 (30%), Positives = 142/277 (51%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI ++P+L  +EE  LAKR +E GD  A  +L  ++LRLVV IA  Y G G
Sbjct: 98  DDPVRMYLKEIGRVPLLTPEEEIELAKR-KEEGDEEAKRKLAEANLRLVVSIAKRYVGRG 156

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I     +
Sbjct: 157 MLFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 216

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 L R+  +L         PE    IAK++ +SE +V  +        SL   I  
Sbjct: 217 --TINKLIRVSRNLLQELGREPTPE---EIAKEMGISEDKVREIMKIAQEPVSLETPI-- 269

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            ++  S   D++    D   +  +E+      R  L   +  L  RE+++   R   ++ 
Sbjct: 270 GEEEDSHLGDFV---EDPDAKAPVEEASYTLLREQLDEVLKTLTEREQKVLRLRFGLDDG 326

Query: 253 --VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 327 RARTLEEVGQIFGVTRERIRQIEAKALRKLRHPSRSK 363


>gi|317122932|ref|YP_004102935.1| RNA polymerase, sigma 70 subunit, RpoD [Thermaerobacter marianensis
           DSM 12885]
 gi|315592912|gb|ADU52208.1| RNA polymerase, sigma 70 subunit, RpoD [Thermaerobacter marianensis
           DSM 12885]
          Length = 433

 Score =  275 bits (703), Expect = 6e-72,   Method: Composition-based stats.
 Identities = 84/285 (29%), Positives = 140/285 (49%), Gaps = 13/285 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +M   V  +  +  Y+ EI +IP+L  ++E  LAKR  E GD  A  +L+ ++LRLVV I
Sbjct: 153 SMPDGVALDDPVRMYLKEIGRIPLLTPEQEIELAKRI-EQGDEEAKRKLIQANLRLVVSI 211

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y G G+   +++ EGN+GL++A +KFD  +GF+ +TY+ WWI+ A+   I      +
Sbjct: 212 AKRYVGRGMLFLDLIQEGNLGLIKAAEKFDYRKGFKFSTYATWWIRQAITRAIADQARTI 271

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I     +      L R++  L         PE    IAK++ +   +V  +        
Sbjct: 272 RIPVHMVE--TINKLIRVQRQLVQELGREPTPE---EIAKEMGIEPEKVREIMKIAQEPV 326

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   I   ++  S   D++    D       E   +   R  L   +  L  RE+++  
Sbjct: 327 SLETPI--GEEEDSHLGDFI---EDEDALAPAEAASQLLLREQLEDVLHTLTDREQKVLR 381

Query: 245 ARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 382 LRFGLDDGRQRTLEEVGQVFGVTRERIRQIEAKALRKLRHPSRSK 426


>gi|167768032|ref|ZP_02440085.1| hypothetical protein CLOSS21_02575 [Clostridium sp. SS2/1]
 gi|317498375|ref|ZP_07956670.1| RNA polymerase sigma factor RpoD [Lachnospiraceae bacterium
           5_1_63FAA]
 gi|167710361|gb|EDS20940.1| hypothetical protein CLOSS21_02575 [Clostridium sp. SS2/1]
 gi|291561030|emb|CBL39830.1| RNA polymerase, sigma 70 subunit, RpoD [butyrate-producing
           bacterium SSC/2]
 gi|316894269|gb|EFV16456.1| RNA polymerase sigma factor RpoD [Lachnospiraceae bacterium
           5_1_63FAA]
          Length = 363

 Score =  275 bits (703), Expect = 7e-72,   Method: Composition-based stats.
 Identities = 83/279 (29%), Positives = 138/279 (49%), Gaps = 13/279 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V+ E  +  Y+ EI K+P+L   EE  LA+R  E GD +A  +L  ++LRLVV IA  Y 
Sbjct: 88  VSIEDPVRMYLKEIGKVPLLSADEEIKLAQRM-EEGDEAAKKKLAEANLRLVVSIAKRYV 146

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 147 GRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 206

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L         PE    IA+++++    V  +        SL   
Sbjct: 207 MVE--TINKLIRVSRQLLQELGREPSPE---EIAEEMDIPVERVREILKISQEPVSLETP 261

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++    D    V  +       +  L   +  L  RE+++   R   
Sbjct: 262 I--GEEEDSHLGDFI---QDENVPVPADAAAFTLLKEQLDEVLGTLTEREQKVLRLRFGL 316

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ++    TLE +  EF V+RER+RQIEA+A +K++   + 
Sbjct: 317 DDSRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRS 355


>gi|169830688|ref|YP_001716670.1| RNA polymerase sigma factor RpoD [Candidatus Desulforudis
           audaxviator MP104C]
 gi|169637532|gb|ACA59038.1| RNA polymerase, sigma 70 subunit, RpoD family [Candidatus
           Desulforudis audaxviator MP104C]
          Length = 360

 Score =  275 bits (703), Expect = 7e-72,   Method: Composition-based stats.
 Identities = 87/280 (31%), Positives = 144/280 (51%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V+ +  +  Y+ EI +IP+L  +EE  LA+R  E GD  A  RL+ ++LRLVV IA  Y 
Sbjct: 85  VDIDDPVRMYLKEIGRIPLLTPEEEVSLARRM-EAGDDEAKRRLIEANLRLVVSIAKRYV 143

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD ++G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 144 GRGMLFLDLIQEGNLGLIKAVEKFDYKKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 203

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L         PE    IA+++++SE +V  +        SL   
Sbjct: 204 MVE--TINKLIRISRQLLQELGREPLPE---EIAREMDISEDKVREIQKIAQEPVSLETP 258

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++    D   Q   E+      R  L   +  L  RE+R+   R   
Sbjct: 259 I--GEEEDSHLGDFI---EDQDAQAPAEEASFTLLREQLDDVLKTLTEREQRVLRLRFGL 313

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++    TLE +  EF V+RER+RQIEA+  +K++   + +
Sbjct: 314 DDGRARTLEEVGQEFGVTRERIRQIEAKTLRKLRHPSRSK 353


>gi|312876451|ref|ZP_07736435.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
 gi|311796809|gb|EFR13154.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
          Length = 419

 Score =  274 bits (702), Expect = 9e-72,   Method: Composition-based stats.
 Identities = 89/286 (31%), Positives = 143/286 (50%), Gaps = 13/286 (4%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           +N+   +  +  +  Y+ EI KIP+L  +EE  LAKR  E GD  A  RL  ++LRLVV 
Sbjct: 138 ENLPEGIAIDDPVRMYLKEIGKIPLLTPEEEIELAKRI-EQGDEEAKKRLAEANLRLVVS 196

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      
Sbjct: 197 IAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQART 256

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           ++I     +      L R+   L         PE    IAK++N+   +V  +       
Sbjct: 257 IRIPVHMVE--TINKLVRVSRQLLQEKGREPTPE---EIAKEMNMPVEKVREILKIAQEP 311

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SL   I   ++  S   D++  D         E       +  L   +  LN RE+++ 
Sbjct: 312 VSLETPI--GEEEDSHLGDFIPDDD---ALAPSEAAAYSMLKEQLLEVLDSLNEREKKVL 366

Query: 244 EARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           + R   E+    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 367 KLRFGLEDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 412


>gi|297617785|ref|YP_003702944.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Syntrophothermus
           lipocalidus DSM 12680]
 gi|297145622|gb|ADI02379.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Syntrophothermus
           lipocalidus DSM 12680]
          Length = 361

 Score =  274 bits (702), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 81/277 (29%), Positives = 143/277 (51%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI ++P+L  +EE  LAKR  E+GD  A  +LV ++LRLVV IA  Y G G
Sbjct: 89  DDPVRMYLKEIGRVPLLSAEEEIELAKRI-ENGDEDAKRKLVEANLRLVVSIAKRYVGRG 147

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +   +++ EGN+GLM+AV+KFD  +G++ +TY+ WWI+ A+   I      ++I     +
Sbjct: 148 MLFLDLIQEGNLGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 207

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 + +L    +A+     +      +A+++++    V+ +        SL   I  
Sbjct: 208 -----TINKLSRIQRALLQKLGREPTPAEVAEEMDIPVERVMEIMKVAQEPVSLETPI-- 260

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN- 251
            +++ S   D++  +     +   E       R  L   +S L  RE ++   R   ++ 
Sbjct: 261 GEEDDSHLGDFITDED---AESPEESASFVLLREHLDGILSTLTDREEKVLRLRFGLDDG 317

Query: 252 -PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            P TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 318 RPRTLEEVGQEFGVTRERIRQIEAKALRKLRHPSRSK 354


>gi|147677242|ref|YP_001211457.1| RNA polymerase sigma factor RpoD [Pelotomaculum thermopropionicum
           SI]
 gi|146273339|dbj|BAF59088.1| DNA-directed RNA polymerase, sigma subunit [Pelotomaculum
           thermopropionicum SI]
          Length = 363

 Score =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 86/280 (30%), Positives = 144/280 (51%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V  +  +  Y+ EI ++P+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y 
Sbjct: 88  VGIDDPVRMYLKEIGRVPLLTPEEEVELAKRM-EKGDEEAKRRLAEANLRLVVSIAKRYV 146

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 147 GRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 206

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R++  L      +  PE    IAK++N++E +V  +        SL   
Sbjct: 207 MVE--TINKLVRVQRQLLQELGRDPSPE---EIAKEMNITEDKVREILKIAQEPVSLETP 261

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++    D + +   E+      R  L   +  L  RE+R+   R   
Sbjct: 262 I--GEEEDSHLGDFI---EDHEARAPAEEASFTLLREQLDEVLKTLTEREQRVLRLRFGL 316

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++    TLE +  +F V+RER+RQIEA+  +K++   + +
Sbjct: 317 DDGRARTLEEVGQKFGVTRERIRQIEAKTLRKLRHPSRSK 356


>gi|153853334|ref|ZP_01994743.1| hypothetical protein DORLON_00730 [Dorea longicatena DSM 13814]
 gi|149754120|gb|EDM64051.1| hypothetical protein DORLON_00730 [Dorea longicatena DSM 13814]
          Length = 369

 Score =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 86/279 (30%), Positives = 138/279 (49%), Gaps = 13/279 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ E  +  Y+ EI K+P+L  +EE  LAKR  + GD  A  RL  ++LRLVV IA  Y 
Sbjct: 94  ISIEDPVRMYLKEIGKVPLLSAEEEVELAKRMAD-GDEEAKKRLAEANLRLVVSIAKRYV 152

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I   
Sbjct: 153 GRGMLFLDLIQEGNLGLIKAVEKFDYHKGFKFSTYATWWIRQAITRAIADQARTIRIPVH 212

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L         PE    IA +L++    V  +        SL   
Sbjct: 213 MVE--TINKLIRVSRQLLQELGREPTPE---EIAAELDMPVERVREILKISQEPVSLETP 267

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++  D      V  E   +   +  L   +  L  RE+++   R   
Sbjct: 268 I--GEEEDSHLGDFIQDD---NVPVPAEAAAQTLLKEQLDEVLDTLTEREQKVLRLRFGM 322

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +    TLE +  EF+V+RER+RQIEA+A +K++   + 
Sbjct: 323 NDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRS 361


>gi|317473637|ref|ZP_07932926.1| RNA polymerase sigma factor RpoD [Anaerostipes sp. 3_2_56FAA]
 gi|316898927|gb|EFV20952.1| RNA polymerase sigma factor RpoD [Anaerostipes sp. 3_2_56FAA]
          Length = 364

 Score =  274 bits (701), Expect = 1e-71,   Method: Composition-based stats.
 Identities = 83/279 (29%), Positives = 138/279 (49%), Gaps = 13/279 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V+ E  +  Y+ EI K+P+L   EE  LA+R  E GD  A  +L  ++LRLVV IA  Y 
Sbjct: 89  VSIEDPVRMYLKEIGKVPLLSADEEIRLAQRM-EEGDEEAKKKLAEANLRLVVSIAKRYV 147

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 148 GRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 207

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L         PE    IA+++++    V  +        SL   
Sbjct: 208 MVE--TINKLIRVSRQLLQELGREPLPE---EIAEEMDIPVDRVREILKISQEPVSLETP 262

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++  D      V  +       +  L+  +  L  RE+++   R   
Sbjct: 263 I--GEEEDSHLGDFIQDD---NVPVPADAAAFTLLKEQLSEVLGTLTEREQKVLRLRFGL 317

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ++    TLE +  EF V+RER+RQIEA+A +K++   + 
Sbjct: 318 DDSRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRS 356


>gi|199598416|ref|ZP_03211835.1| RNA polymerase sigma factor RpoD [Lactobacillus rhamnosus HN001]
 gi|258508506|ref|YP_003171257.1| RNA polymerase sigma factor RpoD [Lactobacillus rhamnosus GG]
 gi|199590735|gb|EDY98822.1| RNA polymerase sigma factor RpoD [Lactobacillus rhamnosus HN001]
 gi|257148433|emb|CAR87406.1| RNA polymerase sigma factor [Lactobacillus rhamnosus GG]
 gi|259649816|dbj|BAI41978.1| RNA polymerase sigma factor RpoD [Lactobacillus rhamnosus GG]
          Length = 416

 Score =  273 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 80/289 (27%), Positives = 137/289 (47%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+  +    V     +  Y+ EI ++ +L   EE  LA +  E GD  A  RL  ++LRL
Sbjct: 132 MSDMSAPSGVKINDPVRMYLKEIGRVSLLTADEEVALALKI-EQGDQEAKQRLAEANLRL 190

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 191 VVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQ 250

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE++ A   ++++   +V  +    
Sbjct: 251 ARTIRIPVHMVE--TINKLIRIQRQLLQDLGREPTPEEIGA---EMDMPTEKVREILKIA 305

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D       +    +  +  L   +  L  RE 
Sbjct: 306 QEPVSLETPI--GEEDDSHLGDFI---EDQDATSPEDHASYELLKEQLESVLDTLTDREE 360

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 361 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 409


>gi|56963455|ref|YP_175186.1| RNA polymerase sigma factor RpoD [Bacillus clausii KSM-K16]
 gi|56909698|dbj|BAD64225.1| DNA-directed RNA polymerase major sigma-43 factor sigma-A [Bacillus
           clausii KSM-K16]
          Length = 373

 Score =  273 bits (700), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 83/289 (28%), Positives = 144/289 (49%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   +     +  Y+ EI ++P+L  +EE  LAKR  E GD  A  RL  ++LRL
Sbjct: 89  LNDLSVPPGIKINDPVRMYLKEIGRVPLLSAEEEIDLAKRI-EQGDEEAKKRLAEANLRL 147

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ WWI+ A+   I   
Sbjct: 148 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYDKGFKFSTYATWWIRQAITRAIADQ 207

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE+V    K++++S  +V  +    
Sbjct: 208 ARTIRIPVHMVE--TINKLIRVQRQLLQDYGREPTPEEV---GKEMDLSPDKVREILKIA 262

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D +     +    +  +  L   +  L  RE 
Sbjct: 263 QEPVSLETPI--GEEDDSHLGDFI---EDQEALAPSDAAAYELLKEQLEDVLDTLTDREE 317

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 318 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 366


>gi|83955694|ref|ZP_00964274.1| RNA polymerase sigma factor [Sulfitobacter sp. NAS-14.1]
 gi|83839988|gb|EAP79164.1| RNA polymerase sigma factor [Sulfitobacter sp. NAS-14.1]
          Length = 279

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 157/267 (58%), Positives = 205/267 (76%), Gaps = 1/267 (0%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           + EIRK P+LE +EEY+LAKR+ E  D  AAHR+VTSHLRL  KIAMGYRGYGLP +EV+
Sbjct: 1   MQEIRKFPLLEPEEEYMLAKRWVEEQDTEAAHRMVTSHLRLAAKIAMGYRGYGLPQAEVI 60

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
           SE N+GLMQAVK+FDPE+GFRLATY+MWWI+A++QEYILRSWSLVK+GTT+ QK+LFFNL
Sbjct: 61  SEANVGLMQAVKRFDPEKGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSGQKKLFFNL 120

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSSDKNSS 198
           R+ K  + A+ + +L P+ V  IA  L V+E+EVISMN R+  GD SLNA + S  + + 
Sbjct: 121 RKAKNRIGALEEGDLHPDNVKRIATDLGVTETEVISMNRRMSGGDASLNATVGSEGEGTM 180

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           QWQDWL  +   Q     E++E + RR ML  ++ VLN RE+ I   RRL +  VTLE+L
Sbjct: 181 QWQDWLEDEDADQATDYEERDELETRREMLAEALDVLNDREKDILTQRRLSDQTVTLEDL 240

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQ 285
           SS+++VSRER+RQIE RAF+K+Q+ ++
Sbjct: 241 SSQYDVSRERIRQIEVRAFEKLQKRMR 267


>gi|125973412|ref|YP_001037322.1| RNA polymerase sigma factor RpoD [Clostridium thermocellum ATCC
           27405]
 gi|125713637|gb|ABN52129.1| RNA polymerase, sigma 38 subunit, RpoS [Clostridium thermocellum
           ATCC 27405]
          Length = 358

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 86/280 (30%), Positives = 138/280 (49%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ +  +  Y+ EI K+P+L  +EE  LA R  E GD  A  RL  ++LRLVV IA  Y 
Sbjct: 83  ISIDDPVRMYLKEIGKVPLLTAEEEIELAHRI-EQGDAEAKRRLAEANLRLVVSIAKRYV 141

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I   
Sbjct: 142 GRGMLFLDLIQEGNLGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVH 201

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L         PE    IAK++N+   +V  +        SL   
Sbjct: 202 MVE--TINKLIRVSRQLLQELGREPHPE---EIAKEMNMPVEKVREIMKISQEPVSLETP 256

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++  D         E       +  L   +  L PRE ++   R   
Sbjct: 257 I--GEEEDSHLGDFIPDDD---APAPSEAAAFTLLKEQLVDVLDTLTPREEKVLRLRFGL 311

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 312 DDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 351


>gi|222528719|ref|YP_002572601.1| RpoD subfamily RNA polymerase sigma-70 factor [Caldicellulosiruptor
           bescii DSM 6725]
 gi|222455566|gb|ACM59828.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor bescii DSM 6725]
          Length = 417

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 89/286 (31%), Positives = 143/286 (50%), Gaps = 13/286 (4%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           +N+   +  +  +  Y+ EI KIP+L  +EE  LAKR  E GD  A  RL  ++LRLVV 
Sbjct: 136 ENLPEGIAIDDPVRMYLKEIGKIPLLTPEEEIELAKRI-EQGDEEAKKRLAEANLRLVVS 194

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      
Sbjct: 195 IAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQART 254

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           ++I     +      L R+   L         PE    IAK++N+   +V  +       
Sbjct: 255 IRIPVHMVE--TINKLVRVSRQLLQEKGREPTPE---EIAKEMNMPVEKVREILKIAQEP 309

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SL   I   ++  S   D++  D         E       +  L   +  LN RE+++ 
Sbjct: 310 VSLETPI--GEEEDSHLGDFIPDDD---ALAPSEAAAYSMLKEQLLEVLDSLNEREKKVL 364

Query: 244 EARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           + R   E+    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 365 KLRFGLEDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 410


>gi|294622679|ref|ZP_06701641.1| RNA polymerase sigma factor RpoD [Enterococcus faecium U0317]
 gi|291597877|gb|EFF29007.1| RNA polymerase sigma factor RpoD [Enterococcus faecium U0317]
          Length = 369

 Score =  273 bits (699), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 79/276 (28%), Positives = 135/276 (48%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L  +EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 98  DPVRMYLKEIGRVSLLTAEEEVALALKI-EEGDQEAKQRLAEANLRLVVSIAKRYVGRGM 156

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 157 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 215

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L         PE++ A   ++++   +V  +        SL   I   
Sbjct: 216 -TINKLIRIQRQLLQDLGREPTPEEIGA---EMDLPTEKVREILKIAQEPVSLETPI--G 269

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D +     E    +  +  L   +  L  RE  +   R   ++  
Sbjct: 270 EEDDSHLGDFI---EDQEATSPAEHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGR 326

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 327 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 362


>gi|281417615|ref|ZP_06248635.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           thermocellum JW20]
 gi|281409017|gb|EFB39275.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           thermocellum JW20]
          Length = 358

 Score =  273 bits (698), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 86/280 (30%), Positives = 138/280 (49%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ +  +  Y+ EI K+P+L  +EE  LA R  E GD  A  RL  ++LRLVV IA  Y 
Sbjct: 83  ISIDDPVRMYLKEIGKVPLLTAEEEIELAHRI-EQGDAEAKRRLAEANLRLVVSIAKRYV 141

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I   
Sbjct: 142 GRGMLFLDLIQEGNLGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVH 201

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L         PE    IAK++N+   +V  +        SL   
Sbjct: 202 MVE--TINKLIRVSRQLLQELGREPHPE---EIAKEMNMPVEKVREIMKISQEPVSLETP 256

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++  D         E       +  L   +  L PRE ++   R   
Sbjct: 257 I--GEEEDSHLGDFIPDDD---APAPSEAAAFTLLKEQLVDVLDTLTPREEKVLRLRFGL 311

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 312 DDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 351


>gi|1519632|gb|AAC44890.1| sigma 70-type sigma factor SigA [Heliobacillus mobilis]
          Length = 333

 Score =  273 bits (698), Expect = 2e-71,   Method: Composition-based stats.
 Identities = 84/280 (30%), Positives = 136/280 (48%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V  +  +  Y+ EI ++P+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y 
Sbjct: 58  VGIDDPVRMYLKEIGRVPLLSAEEEIELAKRM-EDGDEEAKRRLAEANLRLVVSIAKRYV 116

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 117 GRGMLFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 176

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L         PE    IAK++++    V  +        SL   
Sbjct: 177 MVE--TINKLIRVSRQLLQEFGREPNPE---EIAKEMDIPVDRVREIMKIAQEPVSLETP 231

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++    D       E       +  L   +  L  RE ++   R   
Sbjct: 232 I--GEEEDSHLGDFI---EDQDAPAPAEAASFILLKEQLEEVLETLTAREMKVLRLRFGL 286

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 287 DDGRSRTLEEVGQEFGVTRERIRQIEAKALRKLRHPSRSK 326


>gi|85704966|ref|ZP_01036066.1| RNA polymerase sigma factor [Roseovarius sp. 217]
 gi|85670288|gb|EAQ25149.1| RNA polymerase sigma factor [Roseovarius sp. 217]
          Length = 279

 Score =  273 bits (698), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 161/268 (60%), Positives = 206/268 (76%), Gaps = 1/268 (0%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           + EIRK P+LE +EEY+LAKR+ E  D  AAH++VTSHLRL  KIAMGYRGYGLP +EV+
Sbjct: 1   MQEIRKFPLLEPEEEYMLAKRWVEEQDTEAAHKMVTSHLRLAAKIAMGYRGYGLPQAEVI 60

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
           SE N+GLMQAVK+FDPERGFRLATY+MWWI+A++QEYILRSWSLVK+GTT+ QK+LFFNL
Sbjct: 61  SEANVGLMQAVKRFDPERGFRLATYAMWWIRASIQEYILRSWSLVKLGTTSAQKKLFFNL 120

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSS 198
           R+ K  + A+ D +++PE V  IA  L V+E+EVISMN R+AG D SLNA + S  + S 
Sbjct: 121 RKAKAKIGALEDGDMRPEVVKKIATDLGVTEAEVISMNQRMAGADASLNATVGSEGEGSM 180

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           QWQDWL  +   Q      ++E   RR +LT +M VLN RER I   RRL +  VTLE+L
Sbjct: 181 QWQDWLEDEDADQAGDYERRDEMDARRELLTMAMDVLNERERDILTQRRLSDETVTLEDL 240

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQK 286
           S+E++VSRER+RQIE RAF+K+Q+ ++ 
Sbjct: 241 SAEYDVSRERIRQIEVRAFEKLQKRMRA 268


>gi|291563082|emb|CBL41898.1| RNA polymerase, sigma 70 subunit, RpoD [butyrate-producing
           bacterium SS3/4]
          Length = 374

 Score =  273 bits (698), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 81/281 (28%), Positives = 141/281 (50%), Gaps = 13/281 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           +  +  +  Y+ EI K+P+L   EE  LAK+  E GD  A  +L  S+LRLVV IA  Y 
Sbjct: 98  IGVDDPVRMYLKEIGKVPLLSPDEEIELAKKI-ELGDEEAKKKLAESNLRLVVSIAKRYA 156

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+ + +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 157 GRGMQLLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 216

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      + RL    + +     +      +AK+L++    V  +        SL   
Sbjct: 217 MVE-----TINRLVRTQRQLVQKLGREATPEELAKELDMPVERVREIMKISQDPVSLETP 271

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++    D   +V  +          L   +S L  RE+++   R   
Sbjct: 272 I--GEEEDSHLGDFI---QDNNVEVPADAATYTLLHEQLMDVLSTLTEREQKVLRLRFGL 326

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           ++  P TLE +  +F V+RER+RQIEA+A +K++   + ++
Sbjct: 327 DDGRPRTLEEVGRQFNVTRERIRQIEAKALRKLRHPSRSKI 367


>gi|257867642|ref|ZP_05647295.1| RNA polymerase sigma-43 factor [Enterococcus casseliflavus EC30]
 gi|257873971|ref|ZP_05653624.1| RNA polymerase sigma-43 factor [Enterococcus casseliflavus EC10]
 gi|257876550|ref|ZP_05656203.1| RNA polymerase sigma-43 factor [Enterococcus casseliflavus EC20]
 gi|325571155|ref|ZP_08146727.1| DNA-directed RNA polymerase sigma subunit RpoD [Enterococcus
           casseliflavus ATCC 12755]
 gi|257801725|gb|EEV30628.1| RNA polymerase sigma-43 factor [Enterococcus casseliflavus EC30]
 gi|257808135|gb|EEV36957.1| RNA polymerase sigma-43 factor [Enterococcus casseliflavus EC10]
 gi|257810716|gb|EEV39536.1| RNA polymerase sigma-43 factor [Enterococcus casseliflavus EC20]
 gi|325156240|gb|EGC68426.1| DNA-directed RNA polymerase sigma subunit RpoD [Enterococcus
           casseliflavus ATCC 12755]
          Length = 368

 Score =  273 bits (698), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 80/276 (28%), Positives = 135/276 (48%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++P+L  +EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGRVPLLTAEEEVALALKI-EEGDQEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L         PE++ A   ++++   +V  +        SL   I   
Sbjct: 215 -TINKLIRIQRQLLQDLGREPTPEEIGA---EMDLPTEKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D       E    +  +  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDQDATSPAEHAAYELLKEQLEDVLDTLTDREENVLRLRFGIDDGR 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 361


>gi|256004390|ref|ZP_05429371.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           thermocellum DSM 2360]
 gi|255991674|gb|EEU01775.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           thermocellum DSM 2360]
 gi|316940353|gb|ADU74387.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           thermocellum DSM 1313]
          Length = 358

 Score =  273 bits (698), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 86/280 (30%), Positives = 138/280 (49%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ +  +  Y+ EI K+P+L  +EE  LA R  E GD  A  RL  ++LRLVV IA  Y 
Sbjct: 83  ISIDDPVRMYLKEIGKVPLLTAEEEIELAHRM-EQGDAEAKRRLAEANLRLVVSIAKRYV 141

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I   
Sbjct: 142 GRGMLFLDLIQEGNLGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVH 201

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L         PE    IAK++N+   +V  +        SL   
Sbjct: 202 MVE--TINKLIRVSRQLLQELGREPHPE---EIAKEMNMPVEKVREIMKISQEPVSLETP 256

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++  D         E       +  L   +  L PRE ++   R   
Sbjct: 257 I--GEEEDSHLGDFIPDDD---APAPSEAAAFTLLKEQLVDVLDTLTPREEKVLRLRFGL 311

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 312 DDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 351


>gi|167747159|ref|ZP_02419286.1| hypothetical protein ANACAC_01873 [Anaerostipes caccae DSM 14662]
 gi|167654119|gb|EDR98248.1| hypothetical protein ANACAC_01873 [Anaerostipes caccae DSM 14662]
          Length = 370

 Score =  273 bits (698), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 83/279 (29%), Positives = 138/279 (49%), Gaps = 13/279 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V+ E  +  Y+ EI K+P+L   EE  LA+R  E GD  A  +L  ++LRLVV IA  Y 
Sbjct: 95  VSIEDPVRMYLKEIGKVPLLSADEEIRLAQRM-EEGDEEAKKKLAEANLRLVVSIAKRYV 153

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 154 GRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 213

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L         PE    IA+++++    V  +        SL   
Sbjct: 214 MVE--TINKLIRVSRQLLQELGREPLPE---EIAEEMDIPVDRVREILKISQEPVSLETP 268

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++  D      V  +       +  L+  +  L  RE+++   R   
Sbjct: 269 I--GEEEDSHLGDFIQDD---NVPVPADAAAFTLLKEQLSEVLGTLTEREQKVLRLRFGL 323

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ++    TLE +  EF V+RER+RQIEA+A +K++   + 
Sbjct: 324 DDSRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRS 362


>gi|160881641|ref|YP_001560609.1| RpoD family RNA polymerase sigma factor [Clostridium
           phytofermentans ISDg]
 gi|160430307|gb|ABX43870.1| RNA polymerase, sigma 70 subunit, RpoD family [Clostridium
           phytofermentans ISDg]
          Length = 372

 Score =  272 bits (697), Expect = 3e-71,   Method: Composition-based stats.
 Identities = 87/279 (31%), Positives = 141/279 (50%), Gaps = 13/279 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ E  +  Y+ EI K+P+L   EE VLA+R  E GD +A  RL  ++LRLVV IA  Y 
Sbjct: 97  ISTEDPVRMYLKEIGKVPLLSADEEIVLAQRM-EQGDKNAKKRLAEANLRLVVSIAKRYV 155

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 156 GRGMQFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 215

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R++  L         PE+V   AK++N+    V  +        SL   
Sbjct: 216 MVE--TINKLIRVQRQLLQELGREPFPEEV---AKEMNIPVERVREIQKISQEPVSLETP 270

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++  D      V  E       +  L   +  L  RE+++   R   
Sbjct: 271 I--GEEEDSHLGDFIQDD---NVPVPAEAAAFTLLKEQLMEVLGTLTDREQKVLRLRFGL 325

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ++    TLE +  EF V+RER+RQIEA+A +K++   + 
Sbjct: 326 DDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRS 364


>gi|69249285|ref|ZP_00604924.1| Sigma-70 region 1.1:Sigma-70 region 3:Sigma-70 region 2:Sigma-70
           region 4:Sigma-70 region 1.2 [Enterococcus faecium DO]
 gi|257877975|ref|ZP_05657628.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,230,933]
 gi|257881238|ref|ZP_05660891.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,231,502]
 gi|257884904|ref|ZP_05664557.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,231,501]
 gi|257889826|ref|ZP_05669479.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,231,410]
 gi|258616539|ref|ZP_05714309.1| RNA polymerase sigma factor RpoD [Enterococcus faecium DO]
 gi|260559026|ref|ZP_05831212.1| RNA polymerase sigma-43 factor [Enterococcus faecium C68]
 gi|261207559|ref|ZP_05922244.1| RNA polymerase sigma-43 factor [Enterococcus faecium TC 6]
 gi|289565071|ref|ZP_06445524.1| RNA polymerase sigma factor rpoD [Enterococcus faecium D344SRF]
 gi|293556716|ref|ZP_06675279.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1039]
 gi|293563374|ref|ZP_06677823.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1162]
 gi|293568034|ref|ZP_06679372.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1071]
 gi|294614871|ref|ZP_06694766.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1636]
 gi|294618226|ref|ZP_06697809.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1679]
 gi|314939477|ref|ZP_07846711.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133a04]
 gi|314941108|ref|ZP_07848006.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133C]
 gi|314949892|ref|ZP_07853194.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0082]
 gi|314951693|ref|ZP_07854736.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133A]
 gi|314993960|ref|ZP_07859287.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133B]
 gi|314996911|ref|ZP_07861912.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133a01]
 gi|68194219|gb|EAN08744.1| Sigma-70 region 1.1:Sigma-70 region 3:Sigma-70 region 2:Sigma-70
           region 4:Sigma-70 region 1.2 [Enterococcus faecium DO]
 gi|257812203|gb|EEV40961.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,230,933]
 gi|257816896|gb|EEV44224.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,231,502]
 gi|257820742|gb|EEV47890.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,231,501]
 gi|257826186|gb|EEV52812.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,231,410]
 gi|260074783|gb|EEW63099.1| RNA polymerase sigma-43 factor [Enterococcus faecium C68]
 gi|260077942|gb|EEW65648.1| RNA polymerase sigma-43 factor [Enterococcus faecium TC 6]
 gi|289163078|gb|EFD10925.1| RNA polymerase sigma factor rpoD [Enterococcus faecium D344SRF]
 gi|291589255|gb|EFF21065.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1071]
 gi|291592333|gb|EFF23947.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1636]
 gi|291595506|gb|EFF26816.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1679]
 gi|291601048|gb|EFF31337.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1039]
 gi|291604635|gb|EFF34120.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E1162]
 gi|313588970|gb|EFR67815.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133a01]
 gi|313591562|gb|EFR70407.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133B]
 gi|313596157|gb|EFR75002.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133A]
 gi|313600109|gb|EFR78952.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133C]
 gi|313641279|gb|EFS05859.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0133a04]
 gi|313643734|gb|EFS08314.1| RNA polymerase sigma factor RpoD [Enterococcus faecium TX0082]
          Length = 369

 Score =  272 bits (697), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 79/276 (28%), Positives = 135/276 (48%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L  +EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 98  DPVRMYLKEIGRVSLLTAEEEVALALKI-EEGDQEAKQRLAEANLRLVVSIAKRYVGRGM 156

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 157 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 215

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L         PE++ A   ++++   +V  +        SL   I   
Sbjct: 216 -TINKLIRIQRQLLQDLGREPTPEEIGA---EMDLPTEKVREILKIAQEPVSLETPI--G 269

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D +     E    +  +  L   +  L  RE  +   R   ++  
Sbjct: 270 EEDDSHLGDFI---EDQEATSPAEHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGR 326

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 327 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 362


>gi|229825330|ref|ZP_04451399.1| hypothetical protein GCWU000182_00684 [Abiotrophia defectiva ATCC
           49176]
 gi|229790702|gb|EEP26816.1| hypothetical protein GCWU000182_00684 [Abiotrophia defectiva ATCC
           49176]
          Length = 409

 Score =  272 bits (697), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 84/287 (29%), Positives = 146/287 (50%), Gaps = 13/287 (4%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
            ++++ +  +  +  Y+ EI   P+L   EE  LAK+  E GD  A  RL  S+LRLVV 
Sbjct: 127 DDITLSIMSDDPVKIYLKEIGNYPLLSMDEEVELAKKIAE-GDQYATDRLTESNLRLVVS 185

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y G GL   +++ EGN+GL++AV KFD  +G++ +TY+ WWI+ A+   I      
Sbjct: 186 IAKKYVGRGLSFLDLIQEGNLGLIKAVDKFDYSKGYKFSTYATWWIRQAITRSIADQSRT 245

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           ++I    ++  +     R+   L          E    IAK++N+   +V  +    A  
Sbjct: 246 IRIPVHMSE--VINKAYRISRSLLQELGREPTEE---EIAKEMNLPVEKVREIMKISADP 300

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SL+  I   +++ S   D++  D     +   +       ++ + + ++ L+ RE+R+ 
Sbjct: 301 ISLDTPI--GEEDDSHLGDFIKDDTIMGPE---DAAAYTMLQDQIQKLLTTLSEREQRVL 355

Query: 244 EARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
             R   L     TLE +  EF V+RER+RQIEA+A +K++   + ++
Sbjct: 356 ILRFGLLDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLRHPNRARM 402


>gi|229552308|ref|ZP_04441033.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           rhamnosus LMS2-1]
 gi|229314290|gb|EEN80263.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           rhamnosus LMS2-1]
          Length = 416

 Score =  272 bits (697), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 80/289 (27%), Positives = 137/289 (47%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+  +    V     +  Y+ EI ++ +L   EE  LA +  E GD  A  RL  ++LRL
Sbjct: 132 MSDMSAPSGVKINDPVRMYLKEIGRVSLLTADEEVALALKI-EQGDQEAKQRLAEANLRL 190

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 191 VVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQ 250

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE++ A   ++++   +V  +    
Sbjct: 251 ARTIRIPVHMVE--TINKLIRIQRQLLQDLGREPTPEEIGA---EMDMPTEKVREILKIA 305

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D       +    +  +  L   +  L  RE 
Sbjct: 306 QEPVSLETPI--GEEDDSHLGDFI---EDQDATSPEDHASYELLKEQLESVLDTLTDREE 360

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 361 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 409


>gi|312128161|ref|YP_003993035.1| RNA polymerase, sigma 70 subunit, rpod subfamily
           [Caldicellulosiruptor hydrothermalis 108]
 gi|312134621|ref|YP_004001959.1| RNA polymerase, sigma 70 subunit, rpod subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|312792985|ref|YP_004025908.1| RNA polymerase, sigma 70 subunit, rpod subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
 gi|311774672|gb|ADQ04159.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|311778180|gb|ADQ07666.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor hydrothermalis 108]
 gi|312180125|gb|ADQ40295.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
          Length = 417

 Score =  272 bits (697), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 89/286 (31%), Positives = 143/286 (50%), Gaps = 13/286 (4%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           +N+   +  +  +  Y+ EI KIP+L  +EE  LAKR  E GD  A  RL  ++LRLVV 
Sbjct: 136 ENLPEGIAIDDPVRMYLKEIGKIPLLTPEEEIELAKRI-EQGDEEAKKRLAEANLRLVVS 194

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      
Sbjct: 195 IAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQART 254

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           ++I     +      L R+   L         PE    IAK++N+   +V  +       
Sbjct: 255 IRIPVHMVE--TINKLVRVSRQLLQEKGREPTPE---EIAKEMNMPVEKVREILKIAQEP 309

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SL   I   ++  S   D++  D         E       +  L   +  LN RE+++ 
Sbjct: 310 VSLETPI--GEEEDSHLGDFIPDDD---ALAPSEAAAYSMLKEQLLEVLDSLNEREKKVL 364

Query: 244 EARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           + R   E+    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 365 KLRFGLEDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 410


>gi|27380342|ref|NP_771871.1| RNA polymerase factor sigma-32 [Bradyrhizobium japonicum USDA 110]
 gi|1613784|gb|AAC44755.1| sigma32-like factor RpoH1 [Bradyrhizobium japonicum]
 gi|27353506|dbj|BAC50496.1| sigma32-like factor [Bradyrhizobium japonicum USDA 110]
          Length = 308

 Score =  272 bits (697), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 161/295 (54%), Positives = 210/295 (71%), Gaps = 1/295 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M         + + GLS+Y+ EIRK P+L  ++E   A+R+REH D  AA+ LVTSHLRL
Sbjct: 1   MFNNAALPAPSVDAGLSKYLVEIRKFPLLTPEQELAYARRWREHRDRDAAYHLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAM YRGYGLPI+E+VSEGNIGLMQAV++FDP+RG RLATY+MWWI+A++QEYILRS
Sbjct: 61  VAKIAMRYRGYGLPIAEIVSEGNIGLMQAVRRFDPDRGVRLATYAMWWIRASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVKI  +A+QK+LFF LRR K  + A+ D +L+PEQV  IA++L V+E +V++M+ RL
Sbjct: 121 WSLVKIAASASQKKLFFKLRRAKSAISALQDGDLRPEQVRLIAERLKVAERDVVAMDRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD SLN  I+  D+   Q  DWLV      E  L E++E K RR  L  +++ LN RER
Sbjct: 181 RGDASLNVPIHDEDEG-GQTLDWLVDPAPTCEITLAEEQEAKQRRLALANALANLNARER 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPP 295
            IF AR L E   TLE L++E+ VSRERVRQIE RAF+KV+ ++      ++ PP
Sbjct: 240 NIFTARWLNEESTTLEELAAEYGVSRERVRQIEERAFQKVKAAMLTSRHEANGPP 294


>gi|331082069|ref|ZP_08331197.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|330405664|gb|EGG85194.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 374

 Score =  272 bits (697), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 89/290 (30%), Positives = 145/290 (50%), Gaps = 15/290 (5%)

Query: 1   MNRKNMSII--VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHL 58
           M   ++S+   V+ E  +  Y+ EI K+P+L  +EE  LA+R  E GD SA  RL  ++L
Sbjct: 88  MENIDLSVPEGVSIEDPVRMYLKEIGKVPLLSAEEEITLAQRM-EEGDESAKKRLAEANL 146

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I 
Sbjct: 147 RLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIA 206

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
                ++I     +      L R+   L         PE    IA+++N+S   V  +  
Sbjct: 207 DQARTIRIPVHMVE--TINKLIRVSRQLLQELGREPHPE---EIAEEMNMSVERVREILK 261

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
                 SL   I   ++  S   D++  D      V  +       +  L   +  L  R
Sbjct: 262 ISQEPVSLETPI--GEEEDSHLGDFIQDD---NVPVPADAAAFTLLKEQLVEVLGTLTER 316

Query: 239 ERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E+++   R   ++    TLE +  EF V+RER+RQIEA+A +K++   + 
Sbjct: 317 EQKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRS 366


>gi|322373396|ref|ZP_08047932.1| RNA polymerase sigma factor RpoD [Streptococcus sp. C150]
 gi|321278438|gb|EFX55507.1| RNA polymerase sigma factor RpoD [Streptococcus sp. C150]
          Length = 369

 Score =  272 bits (697), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 84/276 (30%), Positives = 139/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE  LA    E+GDL A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGVVPLLSNEEEKELAIAV-ENGDLEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA+++ ++  +V  +        SL   I   
Sbjct: 215 -TINKLVREQRNLLQELGQDPTPEQ---IAERMGMTPDKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 361


>gi|323703334|ref|ZP_08114984.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfotomaculum
           nigrificans DSM 574]
 gi|323531697|gb|EGB21586.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfotomaculum
           nigrificans DSM 574]
          Length = 367

 Score =  272 bits (696), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 84/280 (30%), Positives = 140/280 (50%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           +  +  +  Y+ EI ++P+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y 
Sbjct: 92  IGIDDPVRMYLKEIGRVPLLSPEEEVELAKRM-EQGDEEAKRRLAEANLRLVVSIAKRYV 150

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 151 GRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 210

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L         PE    IAK++N+S  +V  +        SL   
Sbjct: 211 MVE--TINKLIRVSRQLLQELGREPTPE---EIAKEMNISGDKVREIMKIAQEPVSLETP 265

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++    D   +   E+      R  L   +  L  RE+++   R   
Sbjct: 266 I--GEEEDSHLGDFI---EDADARAPAEEASFTLLREQLDEVLKTLTDREQKVLRLRFGL 320

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++    TLE +  +F V+RER+RQIEA+  +K++   + +
Sbjct: 321 DDGRARTLEEVGQKFGVTRERIRQIEAKTLRKLRHPSRSK 360


>gi|67458885|ref|YP_246509.1| RNA polymerase factor sigma-32 [Rickettsia felis URRWXCal2]
 gi|67004418|gb|AAY61344.1| RNA polymerase sigma-32 factor [Rickettsia felis URRWXCal2]
          Length = 293

 Score =  272 bits (696), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 146/285 (51%), Positives = 201/285 (70%), Gaps = 1/285 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M     ++ ++ E G   Y+ +I KIP L ++EE++LAK Y E  DL AAH+LVTSHL+L
Sbjct: 1   MTNNINALAISSESGFYSYLQKINKIPSLTQEEEFLLAKSYLEENDLQAAHKLVTSHLKL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIA GYR YGLPI+E+VSEGNIGLMQAVKKF+PE GFRL+TY+MWWIKAA+QEYIL+S
Sbjct: 61  VAKIASGYRTYGLPITELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKAAIQEYILKS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTA QK+LFF+L ++K  +  +    +  +  + IA +L VS +EV  MN R+
Sbjct: 121 WSLVKMGTTAAQKKLFFSLNKIKHKITNLYSRAITADDFIQIADELGVSVNEVSEMNTRI 180

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D SLN  INS D  S +  + L       E + I K++   +R +L+ +M +LN RE
Sbjct: 181 SGPDLSLNNPINSDDAESGELIELLPETRPTPETIAINKQDSTGKRKLLSNAMKILNDRE 240

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            RIF  R+L + P TL+ LS+E+ +S+ER+RQIE  AF+K+++ I
Sbjct: 241 LRIFTERKLTDTPKTLDILSNEYNISKERIRQIENTAFEKIKKFI 285


>gi|253573701|ref|ZP_04851044.1| LOW QUALITY PROTEIN: DNA-directed RNA polymerase [Paenibacillus sp.
           oral taxon 786 str. D14]
 gi|251847229|gb|EES75234.1| LOW QUALITY PROTEIN: DNA-directed RNA polymerase [Paenibacillus sp.
           oral taxon 786 str. D14]
          Length = 325

 Score =  272 bits (696), Expect = 4e-71,   Method: Composition-based stats.
 Identities = 84/285 (29%), Positives = 141/285 (49%), Gaps = 13/285 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
            +   +  +  +  Y+ EI ++P+L  +EE  LA+R  E+GD  A  RL  ++LRLVV I
Sbjct: 45  TLPPGIKIDDPVRMYLKEIGRVPLLSAEEEIELAQRI-ENGDEEAKRRLAEANLRLVVSI 103

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      +
Sbjct: 104 ARRYVGRGMVFLDLIQEGNMGLIKAVEKFDYSKGFKFSTYATWWIRQAITRAIADQARTI 163

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I     +      L R+   L         PE    IAK+++++  +V  +        
Sbjct: 164 RIPVHMVE--TINKLIRVSRQLLQEIGREPTPE---EIAKEMDLTPDKVREIMKIAQEPV 218

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   I   ++N S   D++    D       E    +  +  L   +  L  RE  +  
Sbjct: 219 SLETPI--GEENDSNLGDFI---EDHDAPAPAEAAAYELLKEQLEEVLDTLTEREENVLR 273

Query: 245 ARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R   ++    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 274 LRFGMDDGRTRTLEEVGKEFGVTRERIRQIEAKALRKLRHPSRSK 318


>gi|260588574|ref|ZP_05854487.1| RNA polymerase sigma factor RpoD [Blautia hansenii DSM 20583]
 gi|260541049|gb|EEX21618.1| RNA polymerase sigma factor RpoD [Blautia hansenii DSM 20583]
          Length = 330

 Score =  272 bits (696), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 89/290 (30%), Positives = 145/290 (50%), Gaps = 15/290 (5%)

Query: 1   MNRKNMSII--VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHL 58
           M   ++S+   V+ E  +  Y+ EI K+P+L  +EE  LA+R  E GD SA  RL  ++L
Sbjct: 44  MENIDLSVPEGVSIEDPVRMYLKEIGKVPLLSAEEEITLAQRM-EEGDESAKKRLAEANL 102

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I 
Sbjct: 103 RLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIA 162

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
                ++I     +      L R+   L         PE    IA+++N+S   V  +  
Sbjct: 163 DQARTIRIPVHMVE--TINKLIRVSRQLLQELGREPHPE---EIAEEMNMSVERVREILK 217

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
                 SL   I   ++  S   D++  D      V  +       +  L   +  L  R
Sbjct: 218 ISQEPVSLETPI--GEEEDSHLGDFIQDD---NVPVPADAAAFTLLKEQLVEVLGTLTER 272

Query: 239 ERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E+++   R   ++    TLE +  EF V+RER+RQIEA+A +K++   + 
Sbjct: 273 EQKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRS 322


>gi|312622967|ref|YP_004024580.1| RNA polymerase, sigma 70 subunit, rpod subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
 gi|312203434|gb|ADQ46761.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
          Length = 417

 Score =  272 bits (696), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 89/286 (31%), Positives = 143/286 (50%), Gaps = 13/286 (4%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           +N+   +  +  +  Y+ EI KIP+L  +EE  LAKR  E GD  A  RL  ++LRLVV 
Sbjct: 136 ENLPEGIAIDDPVRMYLKEIGKIPLLTPEEEIELAKRI-EQGDEEAKKRLAEANLRLVVS 194

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      
Sbjct: 195 IAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQART 254

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           ++I     +      L R+   L         PE    IAK++N+   +V  +       
Sbjct: 255 IRIPVHMVE--TINKLVRVSRQLLQEKGREPTPE---EIAKEMNMPVEKVREILKIAQEP 309

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SL   I   ++  S   D++  D         E       +  L   +  LN RE+++ 
Sbjct: 310 VSLETPI--GEEEDSHLGDFIPDDD---ALAPSEAAAYSMLKEQLLEVLDSLNEREKKVL 364

Query: 244 EARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           + R   E+    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 365 KLRFGLEDGRARTLEEVGREFNVTRERIRQIEAKALRKLRHPSRSK 410


>gi|312863004|ref|ZP_07723242.1| RNA polymerase sigma factor RpoD [Streptococcus vestibularis F0396]
 gi|311100540|gb|EFQ58745.1| RNA polymerase sigma factor RpoD [Streptococcus vestibularis F0396]
          Length = 369

 Score =  272 bits (696), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 84/276 (30%), Positives = 140/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE  LA    E+GDL A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGVVPLLSNEEEKELAIAV-ENGDLEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA++++++  +V  +        SL   I   
Sbjct: 215 -TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 361


>gi|227551146|ref|ZP_03981195.1| DNA-directed RNA polymerase sigma subunit RpoD [Enterococcus
           faecium TX1330]
 gi|257887737|ref|ZP_05667390.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,141,733]
 gi|257896230|ref|ZP_05675883.1| RNA polymerase sigma-43 factor [Enterococcus faecium Com12]
 gi|257898868|ref|ZP_05678521.1| RNA polymerase sigma-43 factor [Enterococcus faecium Com15]
 gi|293379528|ref|ZP_06625670.1| RNA polymerase sigma factor RpoD [Enterococcus faecium PC4.1]
 gi|293570226|ref|ZP_06681295.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E980]
 gi|227179708|gb|EEI60680.1| DNA-directed RNA polymerase sigma subunit RpoD [Enterococcus
           faecium TX1330]
 gi|257823791|gb|EEV50723.1| RNA polymerase sigma-43 factor [Enterococcus faecium 1,141,733]
 gi|257832795|gb|EEV59216.1| RNA polymerase sigma-43 factor [Enterococcus faecium Com12]
 gi|257836780|gb|EEV61854.1| RNA polymerase sigma-43 factor [Enterococcus faecium Com15]
 gi|291609633|gb|EFF38894.1| RNA polymerase sigma factor RpoD [Enterococcus faecium E980]
 gi|292641837|gb|EFF60005.1| RNA polymerase sigma factor RpoD [Enterococcus faecium PC4.1]
          Length = 369

 Score =  272 bits (696), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 79/276 (28%), Positives = 135/276 (48%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L  +EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 98  DPVRMYLKEIGRVSLLTAEEEVALALKI-EEGDQEAKQRLAEANLRLVVSIAKRYVGRGM 156

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 157 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 215

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L         PE++ A   ++++   +V  +        SL   I   
Sbjct: 216 -TINKLIRIQRQLLQDLGREPTPEEIGA---EMDLPTEKVREILKIAQEPVSLETPI--G 269

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D +     E    +  +  L   +  L  RE  +   R   ++  
Sbjct: 270 EEDDSHLGDFI---EDQEATSPAEHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGR 326

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 327 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 362


>gi|167630065|ref|YP_001680564.1| RNA polymerase sigma factor rpod [Heliobacterium modesticaldum
           Ice1]
 gi|167592805|gb|ABZ84553.1| RNA polymerase sigma factor rpod [Heliobacterium modesticaldum
           Ice1]
          Length = 371

 Score =  272 bits (696), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 84/280 (30%), Positives = 137/280 (48%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V  +  +  Y+ EI ++P+L  +EE  LAKR  E GD +A  RL  ++LRLVV IA  Y 
Sbjct: 96  VGIDDPVRMYLKEIGRVPLLSAEEEIELAKRM-EEGDEAAKRRLAEANLRLVVSIAKRYV 154

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 155 GRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 214

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L         PE    IAK++++    V  +        SL   
Sbjct: 215 MVE--TINKLIRVSRQLLQEYGREPMPE---EIAKEMDIPVERVREIMKIAQEPVSLETP 269

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++    D       E       +  L   +  L  RE ++   R   
Sbjct: 270 I--GEEEDSHLGDFI---EDQDAPAPAEAASFILLKEQLEEVLETLTAREMKVLRLRFGL 324

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 325 DDGRSRTLEEVGQEFGVTRERIRQIEAKALRKLRHPSRSK 364


>gi|116494985|ref|YP_806719.1| RNA polymerase sigma factor RpoD [Lactobacillus casei ATCC 334]
 gi|191638497|ref|YP_001987663.1| RNA polymerase sigma factor RpoD [Lactobacillus casei BL23]
 gi|227535009|ref|ZP_03965058.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           paracasei subsp. paracasei ATCC 25302]
 gi|301066553|ref|YP_003788576.1| DNA-directed RNA polymerase sigma70/sigma32 subunit [Lactobacillus
           casei str. Zhang]
 gi|116105135|gb|ABJ70277.1| RNA polymerase, sigma 70 subunit, RpoD [Lactobacillus casei ATCC
           334]
 gi|190712799|emb|CAQ66805.1| RNA polymerase sigma factor [Lactobacillus casei BL23]
 gi|227187324|gb|EEI67391.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           paracasei subsp. paracasei ATCC 25302]
 gi|300438960|gb|ADK18726.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Lactobacillus casei str. Zhang]
 gi|327382532|gb|AEA54008.1| RNA polymerase, sigma 70 subunit, RpoD [Lactobacillus casei LC2W]
 gi|327385729|gb|AEA57203.1| RNA polymerase, sigma 70 subunit, RpoD [Lactobacillus casei BD-II]
          Length = 422

 Score =  272 bits (696), Expect = 5e-71,   Method: Composition-based stats.
 Identities = 80/289 (27%), Positives = 137/289 (47%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+  +    V     +  Y+ EI ++ +L   EE  LA +  E GD  A  RL  ++LRL
Sbjct: 138 MSDMSAPSGVKINDPVRMYLKEIGRVSLLTADEEVALALKI-EQGDQEAKQRLAEANLRL 196

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 197 VVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQ 256

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE++ A   ++++   +V  +    
Sbjct: 257 ARTIRIPVHMVE--TINKLIRIQRQLLQDLGREPTPEEIGA---EMDMPTEKVREILKIA 311

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D       +    +  +  L   +  L  RE 
Sbjct: 312 QEPVSLETPI--GEEDDSHLGDFI---EDQDATSPEDHASYELLKEQLESVLDTLTDREE 366

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 367 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 415


>gi|55823393|ref|YP_141834.1| RNA polymerase sigma factor RpoD [Streptococcus thermophilus
           CNRZ1066]
 gi|116628187|ref|YP_820806.1| RNA polymerase sigma factor RpoD [Streptococcus thermophilus LMD-9]
 gi|55739378|gb|AAV63019.1| DNA directed RNA polymerase sigma 42 protein [Streptococcus
           thermophilus CNRZ1066]
 gi|116101464|gb|ABJ66610.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Streptococcus thermophilus LMD-9]
 gi|312278801|gb|ADQ63458.1| RNA polymerase sigma factor [Streptococcus thermophilus ND03]
          Length = 369

 Score =  272 bits (695), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 84/276 (30%), Positives = 140/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE  LA    E+GDL A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGVVPLLSNEEEKELAIAV-ENGDLEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA++++++  +V  +        SL   I   
Sbjct: 215 -TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 361


>gi|228476995|ref|ZP_04061633.1| RNA polymerase sigma factor RpoD [Streptococcus salivarius SK126]
 gi|322516348|ref|ZP_08069273.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           vestibularis ATCC 49124]
 gi|228251014|gb|EEK10185.1| RNA polymerase sigma factor RpoD [Streptococcus salivarius SK126]
 gi|322125081|gb|EFX96474.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           vestibularis ATCC 49124]
          Length = 369

 Score =  272 bits (695), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 84/276 (30%), Positives = 140/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE  LA    E+GDL A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGVVPLLSNEEEKELAIAV-ENGDLEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA++++++  +V  +        SL   I   
Sbjct: 215 -TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 361


>gi|302871329|ref|YP_003839965.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor obsidiansis OB47]
 gi|302574188|gb|ADL41979.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor obsidiansis OB47]
          Length = 417

 Score =  272 bits (695), Expect = 6e-71,   Method: Composition-based stats.
 Identities = 89/286 (31%), Positives = 143/286 (50%), Gaps = 13/286 (4%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           +N+   +  +  +  Y+ EI KIP+L  +EE  LAKR  E GD  A  RL  ++LRLVV 
Sbjct: 136 ENLPEGIAIDDPVRMYLKEIGKIPLLTPEEEIELAKRI-EQGDEEAKKRLAEANLRLVVS 194

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      
Sbjct: 195 IAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQART 254

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           ++I     +      L R+   L         PE    IAK++N+   +V  +       
Sbjct: 255 IRIPVHMVE--TINKLVRVSRQLLQEKGREPTPE---EIAKEMNMPVEKVREILKIAQEP 309

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SL   I   ++  S   D++  D         E       +  L   +  LN RE+++ 
Sbjct: 310 VSLETPI--GEEEDSHLGDFIPDDD---ALAPSEAAAYSMLKEQLLEVLDSLNEREKKVL 364

Query: 244 EARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           + R   E+    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 365 KLRFGLEDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 410


>gi|163815580|ref|ZP_02206953.1| hypothetical protein COPEUT_01755 [Coprococcus eutactus ATCC 27759]
 gi|158449217|gb|EDP26212.1| hypothetical protein COPEUT_01755 [Coprococcus eutactus ATCC 27759]
          Length = 399

 Score =  272 bits (695), Expect = 7e-71,   Method: Composition-based stats.
 Identities = 84/281 (29%), Positives = 140/281 (49%), Gaps = 13/281 (4%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           I    +  +  Y+ +I K+P+L  +EE  LAKR  E GD +A  +L  S+LRLVV IA  
Sbjct: 121 ISSTTQDPVKMYLKDIGKVPLLSAEEEIELAKRM-EAGDEAAKKKLAESNLRLVVSIAKR 179

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I 
Sbjct: 180 YVGRGMLFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIP 239

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
               +      + R+   L         PE+V  +   + + +  V  +        SL 
Sbjct: 240 VHMVE--TINKVTRVSRDLLQKLGREPLPEEVGEV---MGLPKERVQEIMKIAQEPVSLE 294

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   ++  S   D++    D      +E   +      L   +S L  RE+R+ + R 
Sbjct: 295 TPI--GEEEDSHLGDFI---QDESIPTPVEATNQTLLHEQLDDVVSTLTEREQRVIKLRF 349

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             ++  P TLE +  EF V+RER+RQIEA+A +K++   + 
Sbjct: 350 GWDDGRPRTLEEVGKEFNVTRERIRQIEAKALRKLRHPNRS 390


>gi|266623970|ref|ZP_06116905.1| RNA polymerase sigma factor RpoD [Clostridium hathewayi DSM 13479]
 gi|288864209|gb|EFC96507.1| RNA polymerase sigma factor RpoD [Clostridium hathewayi DSM 13479]
          Length = 345

 Score =  271 bits (694), Expect = 8e-71,   Method: Composition-based stats.
 Identities = 85/291 (29%), Positives = 144/291 (49%), Gaps = 15/291 (5%)

Query: 1   MNRKNMSII--VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHL 58
           M   ++S+   ++ E  +  Y+ EI K+P+L   +E  LAK+  E GD  A  +L  ++L
Sbjct: 58  MEHIDLSVPEGISVEDPVRMYLKEIGKVPLLSSDDEIELAKKI-ELGDELAKEKLTEANL 116

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I 
Sbjct: 117 RLVVSIAKRYVGRGMQFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIA 176

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
                ++I     +      L R+   L         PE+V   A ++++    V  +  
Sbjct: 177 DQARTIRIPVHMVE--TINRLVRVSRQLLQELGREPSPEEV---ASRVDMPVERVREIMK 231

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
                 SL   I   ++  S   D++  D   Q  V  +          L   +  L  R
Sbjct: 232 VSQEPVSLETPI--GEEEDSHLGDFIQDD---QVAVPADAATFTMLHEQLMEVLDTLTER 286

Query: 239 ERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+++   R   ++  P TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 287 EQKVLRLRFGLDDGRPRTLEEVGREFNVTRERIRQIEAKALRKLRHPSRSK 337


>gi|55821465|ref|YP_139907.1| RNA polymerase sigma factor RpoD [Streptococcus thermophilus LMG
           18311]
 gi|55737450|gb|AAV61092.1| DNA directed RNA polymerase sigma 42 protein [Streptococcus
           thermophilus LMG 18311]
          Length = 369

 Score =  271 bits (694), Expect = 8e-71,   Method: Composition-based stats.
 Identities = 84/276 (30%), Positives = 140/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE  LA    E+GDL A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGVVPLLSNEEEKKLAIAV-ENGDLEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA++++++  +V  +        SL   I   
Sbjct: 215 -TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 361


>gi|219670224|ref|YP_002460659.1| RNA polymerase sigma factor RpoD [Desulfitobacterium hafniense
           DCB-2]
 gi|219540484|gb|ACL22223.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Desulfitobacterium hafniense DCB-2]
          Length = 372

 Score =  271 bits (694), Expect = 9e-71,   Method: Composition-based stats.
 Identities = 86/280 (30%), Positives = 138/280 (49%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V  +  +  Y+ EI ++P+L  +EE  LAKR  E GD SA  RL  ++LRLVV IA  Y 
Sbjct: 97  VGIDDPVRMYLKEIGRVPLLTAEEEIELAKRM-EQGDESAKRRLAEANLRLVVSIAKRYV 155

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I   
Sbjct: 156 GRGMLFLDLIQEGNLGLIKAVEKFDYVKGFKFSTYATWWIRQAITRAIADQARTIRIPVH 215

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L         PE    IA ++++S   V  +        SL   
Sbjct: 216 MVE--TINKLIRVSRQLLQELGREPTPE---EIAVQMDISVERVREIMKIAQEPVSLETP 270

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++  +         E       +  L   +  L PRE ++   R   
Sbjct: 271 I--GEEEDSHLGDFIPDED---APAPSEAASFILLKEQLEEVLETLTPREEKVLRLRFGL 325

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 326 DDGRTRTLEEVGQEFGVTRERIRQIEAKALRKLRHPSRSK 365


>gi|260583936|ref|ZP_05851684.1| RNA polymerase sigma-43 factor [Granulicatella elegans ATCC 700633]
 gi|260158562|gb|EEW93630.1| RNA polymerase sigma-43 factor [Granulicatella elegans ATCC 700633]
          Length = 374

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 81/289 (28%), Positives = 136/289 (47%), Gaps = 14/289 (4%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           +   +S  V     +  Y+ EI ++P+L   EE  LA R ++ GD  A   L  ++LRLV
Sbjct: 90  DETALSSNVKINDSVRMYLKEIGRVPLLSADEEVNLALRIQQ-GDQEAKQELAEANLRLV 148

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA  Y G G+   +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I    
Sbjct: 149 VSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDHTKGFKFSTYATWWIRQAITRAIADQA 208

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             ++I     +      L R++  L         PE++ A   ++++   +V  +     
Sbjct: 209 RTIRIPVHMVE--TINKLVRIQRQLLQDLGREPTPEEIGA---EMDLPTEKVREILKIAQ 263

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              SL   I   +++ S   D++  D         E       +  L   +  L  RE  
Sbjct: 264 EPVSLETPI--GEEDDSHLGDFIEDD---NATSPAEHTAYALLKEQLDEVLEQLTDREEN 318

Query: 242 IFEARRLQE---NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +   R   +      TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 319 VLRLRFGLDKNGEIRTLEQVGQVFGVTRERIRQIEAKALRKLRHPSRSK 367


>gi|310827637|ref|YP_003959994.1| RNA polymerase [Eubacterium limosum KIST612]
 gi|308739371|gb|ADO37031.1| RNA polymerase [Eubacterium limosum KIST612]
          Length = 395

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 83/285 (29%), Positives = 137/285 (48%), Gaps = 13/285 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           ++   V+    +  Y+ EI K+P+L  ++E  +AKR  E GD  A   L  ++LRLVV I
Sbjct: 115 DLGDSVSVNDPVRLYLKEIGKVPLLTAEQEMGIAKRM-EAGDDEAKKELAEANLRLVVSI 173

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      +
Sbjct: 174 AKRYVGRGMSFLDLIQEGNLGLIKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTI 233

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I     +      L R+   L         P     I K++  SE +V  +        
Sbjct: 234 RIPVHMVE--TINKLIRVSRQLLQELGREPTP---AEIGKEMGFSEEKVREIQKIAQDPV 288

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   I   ++  S   D++  D         E       +  L   ++ L  RE ++  
Sbjct: 289 SLETPI--GEEEDSHLGDFIEDD---NAPAPSEAASYALLKEQLMEVLNTLTEREEKVLR 343

Query: 245 ARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R   ++    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 344 LRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 388


>gi|302391478|ref|YP_003827298.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acetohalobium
           arabaticum DSM 5501]
 gi|302203555|gb|ADL12233.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acetohalobium
           arabaticum DSM 5501]
          Length = 358

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 88/280 (31%), Positives = 143/280 (51%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V  +  +  Y+ EI K+ +L  +EE  LAKR  E GD+ A   LV ++LRLVV IA  Y 
Sbjct: 83  VGIDDPVRMYLKEIGKVDLLTAEEEVELAKRM-EEGDMEAKRMLVEANLRLVVSIAKKYV 141

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 142 GRGMLFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRSIADQARTIRIPVH 201

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      + R+  HL         PE    IA+++++SE +V  +        SL   
Sbjct: 202 MVE--TINKVIRVSRHLLQELGREPTPE---EIAEEMDLSEEKVREVLKISQEPVSLETP 256

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++  D      V          +  L   +  L+ RE+R+ E R   
Sbjct: 257 I--GEEEDSHLGDFIEDDDAPAPSV---AASHMMLQEQLDEVLDTLSDREKRVLELRFGV 311

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 312 EDGRSRTLEEVGKEFGVTRERIRQIEAKALRKLRHPSRSK 351


>gi|225575013|ref|ZP_03783623.1| hypothetical protein RUMHYD_03093 [Blautia hydrogenotrophica DSM
           10507]
 gi|225037764|gb|EEG48010.1| hypothetical protein RUMHYD_03093 [Blautia hydrogenotrophica DSM
           10507]
          Length = 374

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 87/279 (31%), Positives = 138/279 (49%), Gaps = 13/279 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V+ E  +  Y+ EI K+ +L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y 
Sbjct: 99  VSIEDPVRMYLKEIGKVNLLTAEEEIELAKRM-EEGDEDAKKRLAEANLRLVVSIAKRYV 157

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 158 GRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 217

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L         PE    IAK++ +S   V  +        SL   
Sbjct: 218 MVE--TINKLIRVSRQLLQELGREPTPE---EIAKEMEMSVDRVREILKISQEPVSLETP 272

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++  D      V  +       +  L   +S L  RE+++   R   
Sbjct: 273 I--GEEEDSHLGDFIQDD---NVPVPADAAAFTLLKEQLVEVLSTLTDREQKVLRLRFGL 327

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ++    TLE +  EF V+RER+RQIEA+A +K++   + 
Sbjct: 328 DDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRS 366


>gi|258539717|ref|YP_003174216.1| RNA polymerase sigma factor RpoD [Lactobacillus rhamnosus Lc 705]
 gi|257151393|emb|CAR90365.1| RNA polymerase sigma factor [Lactobacillus rhamnosus Lc 705]
          Length = 416

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 80/289 (27%), Positives = 137/289 (47%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+  +    V     +  Y+ EI ++ +L   EE  LA +  E GD  A  RL  ++LRL
Sbjct: 132 MSDMSAPSGVKINDPVRMYLKEIGRVSLLTTDEEVALALKI-EQGDQEAKQRLAEANLRL 190

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 191 VVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQ 250

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE++ A   ++++   +V  +    
Sbjct: 251 ARTIRIPVHMVE--TINKLIRIQRQLLQDLGREPTPEEIGA---EMDMPTEKVREILKIA 305

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D       +    +  +  L   +  L  RE 
Sbjct: 306 QEPVSLETPI--GEEDDSHLGDFI---EDQDATSPEDHASYELLKEQLESVLDTLTDREE 360

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 361 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 409


>gi|259503187|ref|ZP_05746089.1| RNA polymerase sigma factor [Lactobacillus antri DSM 16041]
 gi|259168844|gb|EEW53339.1| RNA polymerase sigma factor [Lactobacillus antri DSM 16041]
          Length = 380

 Score =  271 bits (693), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 81/289 (28%), Positives = 137/289 (47%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M   +    V     +  Y+ EI ++ +L   EE  LA R  E GD  A  +L  ++LRL
Sbjct: 96  MKDTSAPTGVKINDPVRMYLKEIGRVNLLTADEEVKLALRI-EQGDEVAKQQLAEANLRL 154

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GLM+AV+KFD  RGF+ +TY+ WWI+ A+   I   
Sbjct: 155 VVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRRGFKFSTYATWWIRQAITRAIADQ 214

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE++ A   ++++   +V ++    
Sbjct: 215 ARTIRIPVHMVE--TINKLIRIQRQLLQDLGREPLPEEIGA---EMDMPTEKVRNILKIA 269

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D       +    +  +  L   +  L  RE 
Sbjct: 270 QEPVSLETPI--GEEDDSHLGDFI---EDQDATSPADHAAYEMMKKQLENVLDTLTDREE 324

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 325 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 373


>gi|111035800|emb|CAL29427.1| RNA polymerase sigma-32 factor [Wolbachia endosymbiont of
           Onchocerca volvulus]
          Length = 297

 Score =  270 bits (692), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 124/289 (42%), Positives = 198/289 (68%), Gaps = 2/289 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  + +++ +NG   L +YI E++K P+L ++EE  LAK + ++ ++S+AH+L+TSHL L
Sbjct: 1   MLIQALNLCINGSASLMQYIAEVQKFPILSQEEETRLAKNWHQYKNISSAHKLITSHLNL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VVKIAM ++ YGL + +++ EGNIGLM AVKKF+P  GFR +TY++WWI+A+++++IL+S
Sbjct: 61  VVKIAMKFKNYGLLLMDLIMEGNIGLMHAVKKFNPNLGFRFSTYAVWWIEASIKDFILKS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN-LKPEQVVAIAKKLNVSESEVISMNCR 179
           WS +KIGTT  Q++LFF+LR++K  +   T+   L  E++ AI+ +L VSE +VI M+ R
Sbjct: 121 WSFIKIGTTQAQRKLFFSLRKIKKRILQYTNRETLSNEEIKAISNELAVSEGDVIQMSYR 180

Query: 180 LA-GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           LA  D+SLN+ +   D +  + QD +  +   QE      EE++ +  +L  +++ LN R
Sbjct: 181 LAYKDQSLNSCLKVGDGSKKELQDMIPCNSVSQEVTYQNHEEKELKETILNNALANLNER 240

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R IF +R L EN  TL+ L  ++ VSRER+RQ+  +A  KV++ IQ +
Sbjct: 241 SRDIFISRYLSENTQTLDELGKKYNVSRERIRQLAEQAMSKVKQYIQSE 289


>gi|291541030|emb|CBL14141.1| RNA polymerase, sigma 70 subunit, RpoD [Roseburia intestinalis
           XB6B4]
          Length = 397

 Score =  270 bits (692), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 87/279 (31%), Positives = 137/279 (49%), Gaps = 13/279 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V+ E  +  Y+ EI K+P+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y 
Sbjct: 122 VSIEDPVRMYLKEIGKVPLLSAEEEIELAKRM-ELGDQEAKKRLAEANLRLVVSIAKRYV 180

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 181 GRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 240

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L         PE    IA ++N+    V  +        SL   
Sbjct: 241 MVE--TINKLIRVSRQLLQELGREPTPE---EIAAEMNMPVERVREILKISQEPVSLETP 295

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++  D      V  +       +  L   +  L  RE+++   R   
Sbjct: 296 I--GEEEDSHLGDFIQDD---NVPVPADAAAFTLLKEQLEEVLGTLTEREQKVLTLRFGL 350

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E+    TLE +  EF V+RER+RQIEA+A +K++   + 
Sbjct: 351 EDGRARTLEEVGREFNVTRERIRQIEAKALRKLRHPSRS 389


>gi|89895793|ref|YP_519280.1| RNA polymerase sigma factor RpoD [Desulfitobacterium hafniense Y51]
 gi|89335241|dbj|BAE84836.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 367

 Score =  270 bits (692), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 86/280 (30%), Positives = 138/280 (49%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V  +  +  Y+ EI ++P+L  +EE  LAKR  E GD SA  RL  ++LRLVV IA  Y 
Sbjct: 92  VGIDDPVRMYLKEIGRVPLLTAEEEIELAKRM-EQGDESAKRRLAEANLRLVVSIAKRYV 150

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I   
Sbjct: 151 GRGMLFLDLIQEGNLGLIKAVEKFDYVKGFKFSTYATWWIRQAITRAIADQARTIRIPVH 210

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L         PE    IA ++++S   V  +        SL   
Sbjct: 211 MVE--TINKLIRVSRQLLQELGREPTPE---EIAVQMDISVERVREIMKIAQEPVSLETP 265

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++  +         E       +  L   +  L PRE ++   R   
Sbjct: 266 I--GEEEDSHLGDFIPDED---APAPSEAASFILLKEQLEEVLETLTPREEKVLRLRFGL 320

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 321 DDGRTRTLEEVGQEFGVTRERIRQIEAKALRKLRHPSRSK 360


>gi|146319082|ref|YP_001198794.1| RNA polymerase sigma factor RpoD [Streptococcus suis 05ZYH33]
 gi|146321288|ref|YP_001200999.1| RNA polymerase sigma factor RpoD [Streptococcus suis 98HAH33]
 gi|223932503|ref|ZP_03624504.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptococcus
           suis 89/1591]
 gi|253752138|ref|YP_003025279.1| RNA polymerase sigma factor RpoD [Streptococcus suis SC84]
 gi|253753963|ref|YP_003027104.1| RNA polymerase sigma factor RpoD [Streptococcus suis P1/7]
 gi|253755898|ref|YP_003029038.1| RNA polymerase sigma factor RpoD [Streptococcus suis BM407]
 gi|330833083|ref|YP_004401908.1| RNA polymerase sigma factor RpoD [Streptococcus suis ST3]
 gi|145689888|gb|ABP90394.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Streptococcus suis 05ZYH33]
 gi|145692094|gb|ABP92599.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Streptococcus suis 98HAH33]
 gi|223898774|gb|EEF65134.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptococcus
           suis 89/1591]
 gi|251816427|emb|CAZ52060.1| RNA polymerase sigma factor RpoD [Streptococcus suis SC84]
 gi|251818362|emb|CAZ56188.1| RNA polymerase sigma factor RpoD [Streptococcus suis BM407]
 gi|251820209|emb|CAR46610.1| RNA polymerase sigma factor RpoD [Streptococcus suis P1/7]
 gi|292558723|gb|ADE31724.1| RNA polymerase sigma factor rpoD [Streptococcus suis GZ1]
 gi|319758521|gb|ADV70463.1| RNA polymerase sigma factor RpoD [Streptococcus suis JS14]
 gi|329307306|gb|AEB81722.1| RNA polymerase sigma factor RpoD [Streptococcus suis ST3]
          Length = 372

 Score =  270 bits (692), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 84/283 (29%), Positives = 139/283 (49%), Gaps = 13/283 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S        +  Y+ EI  +P+L  +EE  LA    E GD  A  RL  ++LRLVV IA 
Sbjct: 93  STSAKVNDPVRMYLKEIGVVPLLTNEEEQELALAV-EAGDPEAKQRLAEANLRLVVSIAK 151

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y G G+   +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I
Sbjct: 152 RYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI 211

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
                +      L R + +L      +  PEQ   IA++++++  +V  +        SL
Sbjct: 212 PVHMVE--TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPEKVREILKIAQEPVSL 266

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              I   +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R
Sbjct: 267 ETPI--GEEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLR 321

Query: 247 RLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              ++    TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 322 FGLDDGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 364


>gi|261367093|ref|ZP_05979976.1| RNA polymerase sigma factor RpoD [Subdoligranulum variabile DSM
           15176]
 gi|282571217|gb|EFB76752.1| RNA polymerase sigma factor RpoD [Subdoligranulum variabile DSM
           15176]
          Length = 364

 Score =  270 bits (692), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 81/279 (29%), Positives = 138/279 (49%), Gaps = 14/279 (5%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKIAMGYRG 70
           +  +  Y+ EI ++P+L  +EE  LA + +  G     A  RL  ++LRLVV IA  Y G
Sbjct: 89  DDPVKVYLKEIGRVPLLTPEEEIDLALKIQAGGPEGEKAKQRLSEANLRLVVSIAKRYVG 148

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I    
Sbjct: 149 RGMQFLDLIQEGNLGLIKAVEKFDHTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 208

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
            +      + ++K     +            IA++L++S  +V  +        SL   I
Sbjct: 209 VE-----TINKVKKVSSQLLHEYGHDPSAEEIAERLDMSVDKVREIMRVAQEPVSLETPI 263

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
              ++  S   D++  D      V  E   +   +  L   +  L PRE ++   R   E
Sbjct: 264 --GEEEDSHLGDFIPDDD---APVPAEAASQTLLKEQLADVLKTLTPREEKVLRLRFGLE 318

Query: 251 N--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +  P TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 319 DGRPRTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 357


>gi|255659373|ref|ZP_05404782.1| RNA polymerase sigma factor RpoD [Mitsuokella multacida DSM 20544]
 gi|260848459|gb|EEX68466.1| RNA polymerase sigma factor RpoD [Mitsuokella multacida DSM 20544]
          Length = 373

 Score =  270 bits (692), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 83/279 (29%), Positives = 135/279 (48%), Gaps = 13/279 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V+ +  +  Y+ EI ++P+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y 
Sbjct: 98  VSIDDPVRMYLKEIGRVPLLTAEEEVALAKRM-EAGDEEAQKRLAEANLRLVVSIAKRYV 156

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 157 GRGMLFLDLIQEGNLGLIKAVEKFDYNKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 216

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L         PE    IAK++ +    V  +        SL   
Sbjct: 217 MVE--TINKLIRVSRQLLQQLGREPTPE---EIAKEMEIGVDRVREIMKIAQEPVSLETP 271

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++    D       +       +  L   +  L PRE ++   R   
Sbjct: 272 I--GEEEDSHLGDFI---EDQDAPAPADAASFMLLKEQLEDVLDTLTPREEKVLRLRFGL 326

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ++    TLE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 327 DDGRARTLEEVGQNFGVTRERIRQIEAKALRKLRHPSRS 365


>gi|260886856|ref|ZP_05898119.1| RNA polymerase sigma factor RpoD [Selenomonas sputigena ATCC 35185]
 gi|330839344|ref|YP_004413924.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Selenomonas
           sputigena ATCC 35185]
 gi|260863455|gb|EEX77955.1| RNA polymerase sigma factor RpoD [Selenomonas sputigena ATCC 35185]
 gi|329747108|gb|AEC00465.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Selenomonas
           sputigena ATCC 35185]
          Length = 375

 Score =  270 bits (692), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 82/279 (29%), Positives = 132/279 (47%), Gaps = 13/279 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ +  +  Y+ EI ++P+L   EE  LAKR  E GD  A   L  ++LRLVV IA  Y 
Sbjct: 100 ISIDDPVRMYLKEIGRVPLLSADEEIALAKRM-EAGDEEAQKELAEANLRLVVSIAKRYV 158

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 159 GRGMLFLDLIQEGNLGLIKAVEKFDYNKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 218

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L         PE    IA+ + +S   V  +        SL   
Sbjct: 219 MVE--TINKLIRVSRQLLQQLGREPSPE---EIAEAMEISVERVREIMKIAQEPVSLETP 273

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++    D       E       +  L   +  L  RE R+   R   
Sbjct: 274 I--GEEEDSHLGDFI---EDQDAPAPAEAASFMLLKEQLEEVLDTLTEREERVLRLRFGL 328

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ++    TLE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 329 DDGRARTLEEVGQNFGVTRERIRQIEAKALRKLRHPSRS 367


>gi|58584688|ref|YP_198261.1| DNA-directed RNA polymerase sigma 32 subunit [Wolbachia
           endosymbiont strain TRS of Brugia malayi]
 gi|58419004|gb|AAW71019.1| DNA-directed RNA polymerase sigma 32 subunit, RpoH subfamily
           [Wolbachia endosymbiont strain TRS of Brugia malayi]
          Length = 297

 Score =  270 bits (692), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 130/289 (44%), Positives = 199/289 (68%), Gaps = 2/289 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M    +S+ +NG   L++YI E+RK PML ++EE  LAK + +  D+S+AH+L+TSHL L
Sbjct: 1   MLIPKVSLCINGSTNLTQYITEVRKFPMLSQEEEVRLAKSWNQCKDISSAHKLITSHLNL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VVKIAM ++ YGL + +++ EGN+GL+ AVKKF+P+ GFR +TY++WWI+A+++++IL+S
Sbjct: 61  VVKIAMKFKNYGLLLMDLIMEGNMGLIHAVKKFNPDLGFRFSTYAVWWIEASIKDFILKS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN-LKPEQVVAIAKKLNVSESEVISMNCR 179
           WS VKIGTT  Q+RLFF+LR++K  +   T+   L  E++ AI+ +L+VSE +VI MN R
Sbjct: 121 WSFVKIGTTQAQRRLFFSLRKIKKRILQYTNRETLNNEEIKAISNELSVSEGDVIQMNYR 180

Query: 180 LA-GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           LA  D+SLN  I     +  + QD +  +   QE     +EE++ +  +L  +++ LN R
Sbjct: 181 LACKDQSLNNCIKVGGDSKKELQDMIPCNSVNQEVTYQNREEKELKETILNNALASLNER 240

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R IF +R L EN  TL+ LS ++ VSRER+RQ+  +A  KV++ IQ +
Sbjct: 241 SRDIFISRYLSENTQTLDELSKKYCVSRERIRQLAEQAMSKVKQHIQSE 289


>gi|240147091|ref|ZP_04745692.1| RNA polymerase sigma factor RpoD [Roseburia intestinalis L1-82]
 gi|257200737|gb|EEU99021.1| RNA polymerase sigma factor RpoD [Roseburia intestinalis L1-82]
 gi|291536629|emb|CBL09741.1| RNA polymerase, sigma 70 subunit, RpoD [Roseburia intestinalis
           M50/1]
          Length = 397

 Score =  270 bits (692), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 87/279 (31%), Positives = 137/279 (49%), Gaps = 13/279 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V+ E  +  Y+ EI K+P+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y 
Sbjct: 122 VSIEDPVRMYLKEIGKVPLLSAEEEIELAKRM-ELGDQEAKKRLAEANLRLVVSIAKRYV 180

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 181 GRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 240

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L         PE    IA ++N+    V  +        SL   
Sbjct: 241 MVE--TINKLIRVSRQLLQELGREPTPE---EIAAEMNMPVERVREILKISQEPVSLETP 295

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++  D      V  +       +  L   +  L  RE+++   R   
Sbjct: 296 I--GEEEDSHLGDFIQDD---NVPVPADAAAFTLLKEQLEEVLGTLTEREQKVLTLRFGL 350

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E+    TLE +  EF V+RER+RQIEA+A +K++   + 
Sbjct: 351 EDGRARTLEEVGREFNVTRERIRQIEAKALRKLRHPSRS 389


>gi|225026959|ref|ZP_03716151.1| hypothetical protein EUBHAL_01215 [Eubacterium hallii DSM 3353]
 gi|224955724|gb|EEG36933.1| hypothetical protein EUBHAL_01215 [Eubacterium hallii DSM 3353]
          Length = 422

 Score =  270 bits (692), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 86/278 (30%), Positives = 142/278 (51%), Gaps = 13/278 (4%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           N E  +  Y+ EI +IP+L  +EE  LAKR  E GD  A  +L  ++LRL V IA  Y G
Sbjct: 147 NAEDPVRMYLKEIGRIPLLSSEEEIELAKRM-EEGDEEAKKKLSEANLRLTVSIAKRYSG 205

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ ++   I      ++I    
Sbjct: 206 RGMQFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQSITRAIADQARTIRIPVHM 265

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
            +      + R    L         PE    IA+ +N+    V+ ++       SL   I
Sbjct: 266 VE--TMNRVNRTSRRLLQEYGREPTPE---EIAEAMNLPVERVLEISKISQEPVSLETPI 320

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
              ++  S   D++  +H     V  ++      R  L + M  L+ RE+++   R   E
Sbjct: 321 --GEEEDSHLGDFIQDEH---IPVPADEAAHTLLREQLEKVMDTLSEREQKVLALRFGLE 375

Query: 251 N--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +  P TLE +  EF+V+RER+RQIEA+A +K++   + 
Sbjct: 376 DGKPHTLEEVGREFQVTRERIRQIEAKALRKLRHPTRS 413


>gi|28378605|ref|NP_785497.1| RNA polymerase sigma factor RpoD [Lactobacillus plantarum WCFS1]
 gi|300768133|ref|ZP_07078038.1| RNA polymerase sigma factor rpoD [Lactobacillus plantarum subsp.
           plantarum ATCC 14917]
 gi|308180761|ref|YP_003924889.1| RNA polymerase sigma factor RpoD [Lactobacillus plantarum subsp.
           plantarum ST-III]
 gi|28271441|emb|CAD64346.1| DNA-directed RNA polymerase, sigma factor 42 [Lactobacillus
           plantarum WCFS1]
 gi|300494197|gb|EFK29360.1| RNA polymerase sigma factor rpoD [Lactobacillus plantarum subsp.
           plantarum ATCC 14917]
 gi|308046252|gb|ADN98795.1| RNA polymerase sigma factor RpoD [Lactobacillus plantarum subsp.
           plantarum ST-III]
          Length = 368

 Score =  270 bits (692), Expect = 1e-70,   Method: Composition-based stats.
 Identities = 79/276 (28%), Positives = 133/276 (48%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L   EE  LA R  E GD SA   L  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGRVDLLTADEEVALALRI-EQGDESAKQELAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L         PE++ A   ++++   +V  +        SL   I   
Sbjct: 215 -TINKLIRIQRQLLQDLGREPTPEEIGA---EMDMPTEKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D       +    +  +  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDQDATSPADAAAYELLKEQLEGVLDTLTDREENVLRLRFGLDDGR 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 361


>gi|169334166|ref|ZP_02861359.1| hypothetical protein ANASTE_00560 [Anaerofustis stercorihominis DSM
           17244]
 gi|169258883|gb|EDS72849.1| hypothetical protein ANASTE_00560 [Anaerofustis stercorihominis DSM
           17244]
          Length = 403

 Score =  270 bits (692), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 80/276 (28%), Positives = 136/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI K+ +L  +EE  LA++  E GD+ A  +L  ++LRLVV IA  Y   G+
Sbjct: 133 DPVRMYLKEIGKVDLLSAEEELDLAQKI-ESGDVEARKKLCEANLRLVVSIAKRYVNRGM 191

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 192 SFLDLIQEGNLGLLKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 250

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                + +LK   + +  +  +      IAK++ + E +V  +        SL   I   
Sbjct: 251 ----TINKLKRVQRMLIQDLGRDPNSHEIAKEMGLPEEKVRDIMKISQDPVSLETPI--G 304

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-- 251
           ++  S   D++  D         E       R  L   +  L  RE ++   R   E+  
Sbjct: 305 EEEDSHLGDFIPDDD---AVAPEEAASYMLLRTQLFEVLKTLTDREAKVLILRFGLEDGR 361

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           P TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 362 PRTLEEVGDIFCVTRERIRQIEAKALRKLRHPTRSK 397


>gi|227529171|ref|ZP_03959220.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           vaginalis ATCC 49540]
 gi|227350896|gb|EEJ41187.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           vaginalis ATCC 49540]
          Length = 380

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 81/289 (28%), Positives = 136/289 (47%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M   +    V     +  Y+ EI ++ +L   EE  LA R  E GD  A   L  ++LRL
Sbjct: 96  MKDTSAPTGVKINDPVRMYLKEIGRVNLLSADEEVALALRI-EQGDEEAKQELAEANLRL 154

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GLM+AV+KFD  RGF+ +TY+ WWI+ A+   I   
Sbjct: 155 VVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRRGFKFSTYATWWIRQAITRAIADQ 214

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE++ A   ++++   +V ++    
Sbjct: 215 ARTIRIPVHMVE--TINKLIRIQRQLLQDLGREPLPEEIGA---EMDMPTEKVRNILKIA 269

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D       +    +  +  L   +  L  RE 
Sbjct: 270 QEPVSLETPI--GEEDDSHLGDFI---EDQDATSPADHAAYEMMKKQLENVLDTLTDREE 324

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 325 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 373


>gi|302024138|ref|ZP_07249349.1| RNA polymerase sigma factor RpoD [Streptococcus suis 05HAS68]
          Length = 372

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 84/283 (29%), Positives = 139/283 (49%), Gaps = 13/283 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S        +  Y+ EI  +P+L  +EE  LA    E GD  A  RL  ++LRLVV IA 
Sbjct: 93  STSAKVNDPVRMYLKEIGVVPLLTNEEEQELALAV-EAGDPEAKQRLAEANLRLVVSIAK 151

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y G G+   +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I
Sbjct: 152 RYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI 211

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
                +      L R + +L      +  PEQ   IA++++++  +V  +        SL
Sbjct: 212 PVHMVE--TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPEKVREILKIAQEPVSL 266

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              I   +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R
Sbjct: 267 ETPI--GEEDDSHLGDFI---EDEIIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLR 321

Query: 247 RLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              ++    TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 322 FGLDDGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 364


>gi|295397565|ref|ZP_06807644.1| RNA polymerase sigma factor rpoD [Aerococcus viridans ATCC 11563]
 gi|294974189|gb|EFG49937.1| RNA polymerase sigma factor rpoD [Aerococcus viridans ATCC 11563]
          Length = 374

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 80/289 (27%), Positives = 140/289 (48%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           ++  +++  V     +  Y+ EI ++ +L   EE  LA+R  E GD  A   L  ++LRL
Sbjct: 90  IDPTSVASDVKINDPVRMYLKEIGRVELLTADEEVSLAQRI-EQGDPVAKQELAEANLRL 148

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 149 VVSIAKRYVGRGMSFLDLIQEGNMGLMKAVEKFDYHKGFKFSTYATWWIRQAITRAIADQ 208

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE++ A   ++++   +V  +    
Sbjct: 209 ARTIRIPVHMVE--TINKLVRIQRQLLQDLGREPTPEEIGA---EMDLPTEKVRDILKIA 263

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D       +    +  +  L   +  L  RE 
Sbjct: 264 QEPVSLETPI--GEEDDSHLGDFI---EDHDATSPDDYTSAELLKEQLNEVLDTLTDREE 318

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   E+    TLE +  +F V+RER+RQIEA+A +K++   + +
Sbjct: 319 NVLRLRFGLEDGQSKTLEQVGQQFGVTRERIRQIEAKALRKLRHPSRSK 367


>gi|322389216|ref|ZP_08062777.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           parasanguinis ATCC 903]
 gi|321144121|gb|EFX39538.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           parasanguinis ATCC 903]
          Length = 369

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 84/276 (30%), Positives = 139/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE  LA    E GDL A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGVVPLLTNEEEQELAI-LVEQGDLEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA++++++  +V  +        SL   I   
Sbjct: 215 -TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 361


>gi|167758408|ref|ZP_02430535.1| hypothetical protein CLOSCI_00748 [Clostridium scindens ATCC 35704]
 gi|167664305|gb|EDS08435.1| hypothetical protein CLOSCI_00748 [Clostridium scindens ATCC 35704]
          Length = 371

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 88/290 (30%), Positives = 144/290 (49%), Gaps = 15/290 (5%)

Query: 1   MNRKNMSII--VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHL 58
           M + ++S+   ++ E  +  Y+ EI K+P+L  +EE  LAKR  + GD  A  RL  ++L
Sbjct: 85  MEKIDLSVPDGISIEDPVRMYLKEIGKVPLLTAEEEVDLAKRMAD-GDEEAKKRLAEANL 143

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I 
Sbjct: 144 RLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYHKGFKFSTYATWWIRQAITRAIA 203

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
                ++I     +      L R+   L         PE    IA +L++    V  +  
Sbjct: 204 DQARTIRIPVHMVE--TINKLIRVSRQLLQELGREPTPE---EIAAQLDMPVERVREILK 258

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
                 SL   I   ++  S   D++  D      V  E   +   +  L   +  L  R
Sbjct: 259 ISQEPVSLETPI--GEEEDSHLGDFIQDD---NVPVPAEAAAQTLLKEQLDEVLDTLTER 313

Query: 239 ERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E+++   R    +    TLE +  EF+V+RER+RQIEA+A +K++   + 
Sbjct: 314 EQKVLRLRFGMNDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRS 363


>gi|222151460|ref|YP_002560616.1| RNA polymerase sigma factor SigA [Macrococcus caseolyticus
           JCSC5402]
 gi|222120585|dbj|BAH17920.1| RNA polymerase sigma factor SigA [Macrococcus caseolyticus
           JCSC5402]
          Length = 366

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 80/276 (28%), Positives = 136/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 95  DPVRMYLKEIGRVNLLSAEEEIELAKRI-EQGDEEAKARLAEANLRLVVSIAKRYVGRGM 153

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 154 LFLDLIQEGNMGLIKAVEKFDFTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 212

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L      +  PE    I +++++   +V  +        SL   I   
Sbjct: 213 -TINKLIRVQRQLLQDLGRDPSPE---EIGEEMDLPAEKVREILKIAQEPVSLETPI--G 266

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   Q   +    +  +  L   +  L  RE  +   R   ++  
Sbjct: 267 EEDDSHLGDFI---EDQDAQSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGR 323

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 324 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 359


>gi|163790450|ref|ZP_02184881.1| RNA polymerase sigma factor RpoD [Carnobacterium sp. AT7]
 gi|159874354|gb|EDP68427.1| RNA polymerase sigma factor RpoD [Carnobacterium sp. AT7]
          Length = 373

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 79/276 (28%), Positives = 135/276 (48%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L   EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 102 DPVRMYLKEIGRVNLLTAAEEVELAIKI-EEGDQEARQRLAEANLRLVVSIAKRYVGRGM 160

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV+KFD ++GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 161 QFLDLIQEGNMGLMKAVEKFDYKKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 219

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L         PE++ A   ++++   +V  +        SL   I   
Sbjct: 220 -TINKLIRIQRQLLQDLGREPTPEEIGA---EMDLPTEKVREILKIAQEPVSLETPI--G 273

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D       E    +  +  L   +  L  RE  +   R   ++  
Sbjct: 274 EEDDSHLGDFI---EDHDATSPAENAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGR 330

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 331 NRTLEDVGKVFGVTRERIRQIEAKALRKLRHPSRSK 366


>gi|239827752|ref|YP_002950376.1| RNA polymerase sigma factor RpoD [Geobacillus sp. WCH70]
 gi|239808045|gb|ACS25110.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus sp.
           WCH70]
          Length = 374

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 83/289 (28%), Positives = 143/289 (49%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++P+L  +EE  LAKR  E GD  A  RL  ++LRL
Sbjct: 90  LNDLSVPPGVKINDPVRMYLKEIGRVPLLSAEEEIELAKRI-EQGDEEAKRRLTEANLRL 148

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I   
Sbjct: 149 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQ 208

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    IA++++++  +V  +    
Sbjct: 209 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPTPE---EIAEEMDLTPEKVREILKIA 263

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D +     E    +  +  L   +  L  RE 
Sbjct: 264 QEPVSLETPI--GEEDDSHLGDFI---EDQEATSPSEHAAYELLKEQLEDVLDTLTDREE 318

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 319 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 367


>gi|229824058|ref|ZP_04450127.1| hypothetical protein GCWU000282_01362 [Catonella morbi ATCC 51271]
 gi|229786412|gb|EEP22526.1| hypothetical protein GCWU000282_01362 [Catonella morbi ATCC 51271]
          Length = 379

 Score =  270 bits (691), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 80/286 (27%), Positives = 136/286 (47%), Gaps = 13/286 (4%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           K  +  +     +  Y+ EI  +P+L  +EE  LA R +  GD  A   L  ++LRLVV 
Sbjct: 98  KTATSKLKVSDPVRMYLKEIGNVPLLSAEEEINLAVRIQ-GGDDIAKQELAEANLRLVVS 156

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y G G+   +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      
Sbjct: 157 IAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDHTKGFKFSTYATWWIRQAITRAIADQART 216

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           ++I     +      L R++  L         PE++ A   ++++   +V  +       
Sbjct: 217 IRIPVHMVE--TINKLVRVQRQLLQDLGREPTPEEIGA---EMDLPTEKVREILKIAQEP 271

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SL   I   +++ S   D++  +     +V          R  L   +  L  RE  + 
Sbjct: 272 VSLETPI--GEEDDSHLGDFIEDEGAMSPEVFTSSALL---REQLEDVLDTLTDREENVL 326

Query: 244 EARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 327 RLRFGLDDGNIRTLEQVGKVFGVTRERIRQIEAKALRKLRHPSRSK 372


>gi|212638699|ref|YP_002315219.1| RNA polymerase sigma factor RpoD [Anoxybacillus flavithermus WK1]
 gi|212560179|gb|ACJ33234.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Anoxybacillus flavithermus WK1]
          Length = 372

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 83/289 (28%), Positives = 142/289 (49%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++P+L  +EE  LAKR  E GD  A  RL  ++LRL
Sbjct: 88  LNDLSVPPGVKINDPVRMYLKEIGRVPLLSAEEEIELAKRI-EQGDEEAKRRLAEANLRL 146

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I   
Sbjct: 147 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQ 206

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    IA++++++  +V  +    
Sbjct: 207 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPSPE---EIAEEMDLTPEKVREILKIA 261

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D       E    +  +  L   +  L  RE 
Sbjct: 262 QEPVSLETPI--GEEDDSHLGDFI---EDQDATSPAEHAAYELLKEQLEDVLDTLTDREE 316

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 317 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 365


>gi|15927141|ref|NP_374674.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus N315]
 gi|20178083|sp|Q99TT5|RPOD_STAAN RecName: Full=RNA polymerase sigma factor rpoD
 gi|13701359|dbj|BAB42653.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           N315]
          Length = 368

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 81/276 (29%), Positives = 137/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L  QEE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGRVNLLSAQEEIELAKRI-EQGDEVAKSRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 LFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L      +  PE    I +++++   +V  +        SL   I   
Sbjct: 215 -TINKLIRVQRQLLQDLGRDPAPE---EIGEEMDLPAEKVREVLKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D + Q   +    +  +  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGR 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 361


>gi|119776597|ref|YP_929337.1| RNA polymerase factor sigma-32 [Shewanella amazonensis SB2B]
 gi|119769097|gb|ABM01668.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella amazonensis
           SB2B]
          Length = 285

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 113/285 (39%), Positives = 178/285 (62%), Gaps = 7/285 (2%)

Query: 4   KNMSIIVN-GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           ++M+++V  G   L  YIH +  +PMLE ++EY LAKR +E GDL AA +L+ SHLR VV
Sbjct: 6   QSMALMVPQGASSLEAYIHSVNSMPMLEAEQEYQLAKRLQETGDLQAAKQLIMSHLRFVV 65

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y GYGLP ++++ EGNIGLM+AVK+FDP+ G RL ++++ WIKA + EY+L++W 
Sbjct: 66  HVAKSYSGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYVLKNWR 125

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L   +D     ++V  +A+ L VS+ +V  M  R+A 
Sbjct: 126 IVKVATTKAQRKLFFNLRKAKQRLGWFSD-----DEVAMVAENLGVSKDDVTEMESRMAA 180

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLNPRERR 241
            +    L+N  D +        + DH       IE +  + N +N L  ++  L+ R + 
Sbjct: 181 QDQAFDLVNDHDDDEGFAPVHYLEDHSSDLAANIENDNWESNAQNRLIAAIKTLDERSQH 240

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           I  AR L ++ VTL+ L+ +++VS ER+RQ+E  A  K++  ++ 
Sbjct: 241 ILRARWLDDDKVTLQELAEQYQVSAERIRQLEKNAMNKLKARMEA 285


>gi|227513300|ref|ZP_03943349.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           buchneri ATCC 11577]
 gi|227083501|gb|EEI18813.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           buchneri ATCC 11577]
          Length = 389

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 79/276 (28%), Positives = 133/276 (48%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L   EE  LAKR  E GD  A   L  ++LRLVV IA  Y G G+
Sbjct: 118 DPVRMYLKEIGRVSLLSADEEINLAKRI-ESGDEEAKQELAEANLRLVVSIAKRYVGRGM 176

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 177 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 235

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L         PE++ A   ++++   +V  +        SL   I   
Sbjct: 236 -TINKLIRIQRQLLQDLGREPLPEEIGA---EMDMPTEKVREILKIAQEPVSLETPI--G 289

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D       +    +  +  L   +  L  RE  +   R   ++  
Sbjct: 290 EEDDSHLGDFI---EDQDATSPADHAAYELLKEQLESVLDTLTDREENVLRLRFGLDDGR 346

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 347 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 382


>gi|197103427|ref|YP_002128805.1| RNA polymerase sigma 32 subunit(heat shock sigma factor)
           [Phenylobacterium zucineum HLK1]
 gi|196480703|gb|ACG80230.1| RNA polymerase sigma 32 subunit(heat shock sigma factor)
           [Phenylobacterium zucineum HLK1]
          Length = 316

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 162/278 (58%), Positives = 211/278 (75%), Gaps = 4/278 (1%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           + + E GL RY+ EIRK P+L K EEY+LAKR+REH D  AAHRLVTSHLRL  KIA+ Y
Sbjct: 7   LPSAEGGLRRYLTEIRKYPLLGKDEEYMLAKRWREHEDPEAAHRLVTSHLRLSAKIALSY 66

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           RGYGLP+ EV+SEGN+GLM AVKKFDP++GFRLATY++WWI+AA+QEYILRSWSLVK+GT
Sbjct: 67  RGYGLPLGEVISEGNLGLMHAVKKFDPDKGFRLATYAIWWIRAAIQEYILRSWSLVKLGT 126

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLN 187
           +A QK+LFFNLRR K  + A++D +LKP+QV AIA +L V+E EV++M+ RLA  D SLN
Sbjct: 127 SAVQKKLFFNLRRAKARISALSDGDLKPDQVKAIASRLGVNEEEVVNMDRRLASRDASLN 186

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR-NMLTRSMSVLNPRERRIFEAR 246
           + + +  +   +W D L  +     +  + + E +  R ++L ++M  LN RERRIF AR
Sbjct: 187 SPLAADAEQ--EWLDVLEDEAAVDPEAAVAEAEERALRMDLLAQAMQTLNARERRIFTAR 244

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           RLQ+ P  LE+L+ +F VSRERVRQIE RAF+KVQ  +
Sbjct: 245 RLQDPPALLEDLAKDFGVSRERVRQIEVRAFEKVQAFV 282


>gi|227544906|ref|ZP_03974955.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           reuteri CF48-3A]
 gi|300910067|ref|ZP_07127527.1| RNA polymerase sigma factor rpoD [Lactobacillus reuteri SD2112]
 gi|227185118|gb|EEI65189.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           reuteri CF48-3A]
 gi|300892715|gb|EFK86075.1| RNA polymerase sigma factor rpoD [Lactobacillus reuteri SD2112]
          Length = 380

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 81/289 (28%), Positives = 136/289 (47%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M   +    V     +  Y+ EI ++ +L   EE  LA R  E GD  A   L  ++LRL
Sbjct: 96  MKDTSAPTGVKINDPVRMYLKEIGRVNLLTADEEVQLALRI-EKGDEVAKQELAEANLRL 154

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GLM+AV+KFD  RGF+ +TY+ WWI+ A+   I   
Sbjct: 155 VVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRRGFKFSTYATWWIRQAITRAIADQ 214

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE++ A   ++++   +V ++    
Sbjct: 215 ARTIRIPVHMVE--TINKLIRIQRQLLQDLGREPLPEEIGA---EMDMPTEKVRNILKIA 269

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D       +    +  +  L   +  L  RE 
Sbjct: 270 QEPVSLETPI--GEEDDSHLGDFI---EDQDATSPADHAAYEMMKKQLENVLDTLTDREE 324

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 325 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 373


>gi|226324578|ref|ZP_03800096.1| hypothetical protein COPCOM_02362 [Coprococcus comes ATCC 27758]
 gi|225207026|gb|EEG89380.1| hypothetical protein COPCOM_02362 [Coprococcus comes ATCC 27758]
          Length = 371

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 89/290 (30%), Positives = 145/290 (50%), Gaps = 15/290 (5%)

Query: 1   MNRKNMSII--VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHL 58
           M + ++S+   ++ E  +  Y+ EI K+P+L  +EE  LAKR  + GD  A  RL  ++L
Sbjct: 85  MEKIDLSVPDGISIEDPVRMYLKEIGKVPLLSAEEEIELAKRMAD-GDEEAKKRLAEANL 143

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV IA  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ WWI+ A+   I 
Sbjct: 144 RLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYQKGFKFSTYATWWIRQAITRAIA 203

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
                ++I     +      L R+   L         PE    IA +L++    V  +  
Sbjct: 204 DQARTIRIPVHMVE--TINKLIRVSRQLLQELGREPTPE---EIAAELDMPVDRVREILK 258

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
                 SL   I   ++  S   D++  D      V  E   +   +  L   +S L  R
Sbjct: 259 ISQEPVSLETPI--GEEEDSHLGDFIQDD---NVPVPAEAAAQTLLKEQLDEVLSTLTER 313

Query: 239 ERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E+++   R         TLE +  EF+V+RER+RQIEA+A +K++   + 
Sbjct: 314 EQKVLRLRFGMSDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRS 363


>gi|262282856|ref|ZP_06060623.1| RNA polymerase sigma factor RpoD [Streptococcus sp. 2_1_36FAA]
 gi|262261108|gb|EEY79807.1| RNA polymerase sigma factor RpoD [Streptococcus sp. 2_1_36FAA]
          Length = 370

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 83/276 (30%), Positives = 138/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE  LA    E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 98  DPVRMYLKEIGVVPLLTNEEEQELAI-LVEQGDTEAKQRLAEANLRLVVSIAKRYVGRGM 156

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 157 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 215

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA++++++  +V  +        SL   I   
Sbjct: 216 -TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSLETPI--G 269

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 270 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 326

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 327 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 362


>gi|332362696|gb|EGJ40494.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK49]
          Length = 370

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 84/276 (30%), Positives = 139/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE  LA    E GDL A  RL  ++LRLVV IA  Y G G+
Sbjct: 98  DPVRMYLKEIGVVPLLSNEEEQELAI-LVEQGDLEAKQRLAEANLRLVVSIAKRYVGRGM 156

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 157 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 215

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA++++++  +V  +        SL   I   
Sbjct: 216 -TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSLETPI--G 269

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 270 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 326

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 327 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 362


>gi|227510293|ref|ZP_03940342.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           brevis subsp. gravesensis ATCC 27305]
 gi|227524444|ref|ZP_03954493.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           hilgardii ATCC 8290]
 gi|227088403|gb|EEI23715.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           hilgardii ATCC 8290]
 gi|227189945|gb|EEI70012.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           brevis subsp. gravesensis ATCC 27305]
          Length = 389

 Score =  270 bits (690), Expect = 2e-70,   Method: Composition-based stats.
 Identities = 79/276 (28%), Positives = 133/276 (48%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L   EE  LAKR  E GD  A   L  ++LRLVV IA  Y G G+
Sbjct: 118 DPVRMYLKEIGRVSLLSADEEINLAKRI-ESGDEEAKQELAEANLRLVVSIAKRYVGRGM 176

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 177 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 235

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L         PE++ A   ++++   +V  +        SL   I   
Sbjct: 236 -TINKLIRIQRQLLQDLGREPLPEEIGA---EMDMPTEKVREILKIAQEPVSLETPI--G 289

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D       +    +  +  L   +  L  RE  +   R   ++  
Sbjct: 290 EEDDSHLGDFI---EDQDATSPADHAAYELLKEQLESVLDTLTDREENVLRLRFGLDDGR 346

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 347 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 382


>gi|315303191|ref|ZP_07873849.1| RNA polymerase sigma factor RpoD [Listeria ivanovii FSL F6-596]
 gi|313628434|gb|EFR96909.1| RNA polymerase sigma factor RpoD [Listeria ivanovii FSL F6-596]
          Length = 386

 Score =  270 bits (690), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 83/288 (28%), Positives = 141/288 (48%), Gaps = 15/288 (5%)

Query: 4   KNMSIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
            +MS+    +I   +  Y+ EI ++ +L   EE  LAKR  E GD+ A  RL  ++LRLV
Sbjct: 103 TDMSVPPGVKINDPVRMYLKEIGRVDLLTADEEIALAKRI-EAGDIEAKGRLAEANLRLV 161

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA  Y G G+   +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I    
Sbjct: 162 VSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQA 221

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             ++I     +      L R++  L      +  PE    I +++++   +V  +     
Sbjct: 222 RTIRIPVHMVE--TINKLIRVQRSLLQDLGRDPSPE---EIGEEMDLPTEKVREILKIAQ 276

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              SL   I   +++ S   D++    D       +    +  +  L   +  L  RE  
Sbjct: 277 EPVSLETPI--GEEDDSHLGDFI---EDQDATSPSDHAAYELLKEQLEDVLDTLTDREEN 331

Query: 242 IFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 332 VLRLRFGLDDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSK 379


>gi|157151547|ref|YP_001450555.1| RNA polymerase sigma factor RpoD [Streptococcus gordonii str.
           Challis substr. CH1]
 gi|157076341|gb|ABV11024.1| RNA polymerase sigma factor [Streptococcus gordonii str. Challis
           substr. CH1]
          Length = 370

 Score =  270 bits (690), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 83/276 (30%), Positives = 138/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE  LA    E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 98  DPVRMYLKEIGVVPLLTNEEEQELAI-LVEQGDTEAKQRLAEANLRLVVSIAKRYVGRGM 156

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 157 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 215

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA++++++  +V  +        SL   I   
Sbjct: 216 -TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSLETPI--G 269

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 270 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 326

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 327 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 362


>gi|15613939|ref|NP_242242.1| RNA polymerase sigma factor RpoD [Bacillus halodurans C-125]
 gi|12643264|sp|O66381|RPOD_BACHD RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-43; AltName: Full=Sigma-A
 gi|10173992|dbj|BAB05095.1| RNA polymerase major sigma factor [Bacillus halodurans C-125]
          Length = 372

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 82/289 (28%), Positives = 142/289 (49%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++P+L  +EE  LA R  E GD  A  RL  ++LRL
Sbjct: 88  LNDLSVPPGVKINDPVRMYLKEIGRVPLLTAEEEIELATRI-EQGDEEAKRRLAEANLRL 146

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 147 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYNKGFKFSTYATWWIRQAITRAIADQ 206

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE+V   A++++++  +V  +    
Sbjct: 207 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPSPEEV---AEEMDLTPEKVREILKIA 261

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D       +    +  +  L   +  L  RE 
Sbjct: 262 QEPVSLETPI--GEEDDSHLGDFI---EDQDALAPSDAAAYELLKEQLEDVLDTLTDREE 316

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 317 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 365


>gi|304439790|ref|ZP_07399688.1| DNA-directed RNA polymerase sigma subunit RpoD [Peptoniphilus
           duerdenii ATCC BAA-1640]
 gi|304371777|gb|EFM25385.1| DNA-directed RNA polymerase sigma subunit RpoD [Peptoniphilus
           duerdenii ATCC BAA-1640]
          Length = 370

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 89/290 (30%), Positives = 148/290 (51%), Gaps = 15/290 (5%)

Query: 1   MNRKNMSII--VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHL 58
           ++++++S+   ++ +  +  Y+ EI KIP+L   EE V+AKR  E GD  AA  L  ++L
Sbjct: 84  LSKEDLSVPKGISVDDPVRMYLKEIGKIPLLTADEEVVIAKRM-EKGDREAARELAEANL 142

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV IA  Y G G+   +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I 
Sbjct: 143 RLVVSIAKRYVGRGMSFLDLIQEGNLGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIA 202

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
                ++I     +      L R++  L      +  PE    IA+++N+    V  +  
Sbjct: 203 DQARTIRIPVHMVE--TINKLVRIQRQLVQDLGRDPSPE---EIAEEMNIDVERVREIQK 257

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
                 SL   I   ++  S   D++  +     Q   +       R  L   +  L  R
Sbjct: 258 IAQEPVSLETPI--GEEEDSHLGDFIPDEEIQSPQ---DAATFTLLREQLGDVLDTLTDR 312

Query: 239 ERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E+++   R   E+    TLE +  EF+V+RER+RQIEA+A +K++   + 
Sbjct: 313 EKKVLTLRFGLEDGRNRTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRS 362


>gi|291546785|emb|CBL19893.1| RNA polymerase, sigma 70 subunit, RpoD [Ruminococcus sp. SR1/5]
          Length = 375

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 85/279 (30%), Positives = 138/279 (49%), Gaps = 13/279 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V+ E  +  Y+ EI K+ +L   EE  LAKR  E GD +A  RL  ++LRLVV IA  Y 
Sbjct: 100 VSIEDPVRMYLKEIGKVSLLSADEEIELAKRM-EKGDEAAKKRLAEANLRLVVSIAKRYV 158

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 159 GRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 218

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L         PE    IA+++++    V  +        SL   
Sbjct: 219 MVE--TINKLIRVSRQLLQELGREPTPE---EIAEEMDMPVDRVREILKISQEPVSLETP 273

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++  D      V  +       +  L   +S L  RE+++   R   
Sbjct: 274 I--GEEEDSHLGDFIQDD---NVPVPADAAAFTLLKEQLVEVLSTLTDREQKVLRLRFGL 328

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ++    TLE +  EF V+RER+RQIEA+A +K++   + 
Sbjct: 329 DDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRS 367


>gi|239631415|ref|ZP_04674446.1| DNA-directed RNA polymerase [Lactobacillus paracasei subsp.
           paracasei 8700:2]
 gi|239525880|gb|EEQ64881.1| DNA-directed RNA polymerase [Lactobacillus paracasei subsp.
           paracasei 8700:2]
          Length = 352

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 80/289 (27%), Positives = 137/289 (47%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+  +    V     +  Y+ EI ++ +L   EE  LA +  E GD  A  RL  ++LRL
Sbjct: 68  MSDMSAPSGVKINDPVRMYLKEIGRVSLLTADEEVALALKI-EQGDQEAKQRLAEANLRL 126

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 127 VVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQ 186

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE++ A   ++++   +V  +    
Sbjct: 187 ARTIRIPVHMVE--TINKLIRIQRQLLQDLGREPTPEEIGA---EMDMPTEKVREILKIA 241

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D       +    +  +  L   +  L  RE 
Sbjct: 242 QEPVSLETPI--GEEDDSHLGDFI---EDQDATSPEDHASYELLKEQLESVLDTLTDREE 296

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 297 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 345


>gi|27468166|ref|NP_764803.1| RNA polymerase sigma factor RpoD [Staphylococcus epidermidis ATCC
           12228]
 gi|57867102|ref|YP_188703.1| RNA polymerase sigma factor RpoD [Staphylococcus epidermidis RP62A]
 gi|251810978|ref|ZP_04825451.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           epidermidis BCM-HMP0060]
 gi|282876013|ref|ZP_06284880.1| RNA polymerase sigma factor RpoD [Staphylococcus epidermidis SK135]
 gi|293366478|ref|ZP_06613155.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           epidermidis M23864:W2(grey)]
 gi|47606037|sp|Q8CP24|RPOD_STAES RecName: Full=RNA polymerase sigma factor rpoD
 gi|81674470|sp|Q5HNY7|RPOD_STAEQ RecName: Full=RNA polymerase sigma factor rpoD
 gi|27315712|gb|AAO04847.1|AE016748_81 RNA polymerase sigma factor [Staphylococcus epidermidis ATCC 12228]
 gi|57637760|gb|AAW54548.1| RNA polymerase sigma-70 factor [Staphylococcus epidermidis RP62A]
 gi|251805488|gb|EES58145.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           epidermidis BCM-HMP0060]
 gi|281295038|gb|EFA87565.1| RNA polymerase sigma factor RpoD [Staphylococcus epidermidis SK135]
 gi|291319247|gb|EFE59616.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           epidermidis M23864:W2(grey)]
 gi|319400897|gb|EFV89116.1| RNA polymerase sigma factor rpoD [Staphylococcus epidermidis
           FRI909]
 gi|329725345|gb|EGG61828.1| RNA polymerase sigma factor RpoD [Staphylococcus epidermidis
           VCU144]
 gi|329735301|gb|EGG71593.1| RNA polymerase sigma factor RpoD [Staphylococcus epidermidis
           VCU045]
 gi|329737328|gb|EGG73582.1| RNA polymerase sigma factor RpoD [Staphylococcus epidermidis
           VCU028]
          Length = 368

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 81/276 (29%), Positives = 137/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L  QEE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGRVNLLSAQEEIELAKRI-EQGDEIAKSRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 LFLDLIQEGNMGLIKAVEKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L      +  PE    I +++++   +V  +        SL   I   
Sbjct: 215 -TINKLIRVQRQLLQDLGRDPAPE---EIGEEMDLPPEKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D + Q   +    +  +  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGR 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 361


>gi|312867612|ref|ZP_07727818.1| RNA polymerase sigma factor RpoD [Streptococcus parasanguinis
           F0405]
 gi|311096675|gb|EFQ54913.1| RNA polymerase sigma factor RpoD [Streptococcus parasanguinis
           F0405]
          Length = 369

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 84/276 (30%), Positives = 139/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE  LA    E GDL A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGVVPLLTNEEEQELAI-LVEQGDLEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA++++++  +V  +        SL   I   
Sbjct: 215 -TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 361


>gi|148543974|ref|YP_001271344.1| RNA polymerase sigma factor RpoD [Lactobacillus reuteri DSM 20016]
 gi|184153369|ref|YP_001841710.1| RNA polymerase sigma factor RpoD [Lactobacillus reuteri JCM 1112]
 gi|227364887|ref|ZP_03848933.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           reuteri MM2-3]
 gi|325682488|ref|ZP_08162005.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           reuteri MM4-1A]
 gi|148531008|gb|ABQ83007.1| RNA polymerase, sigma 70 subunit, RpoD [Lactobacillus reuteri DSM
           20016]
 gi|183224713|dbj|BAG25230.1| RNA polymerase sigma-43 factor RpoD [Lactobacillus reuteri JCM
           1112]
 gi|227070091|gb|EEI08468.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           reuteri MM2-3]
 gi|324978327|gb|EGC15277.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           reuteri MM4-1A]
          Length = 380

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 81/289 (28%), Positives = 136/289 (47%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M   +    V     +  Y+ EI ++ +L   EE  LA R  E GD  A   L  ++LRL
Sbjct: 96  MKDTSAPTGVKINDPVRMYLKEIGRVNLLTADEEVQLALRI-EKGDEVAKQELAEANLRL 154

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GLM+AV+KFD  RGF+ +TY+ WWI+ A+   I   
Sbjct: 155 VVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRRGFKFSTYATWWIRQAITRAIADQ 214

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE++ A   ++++   +V ++    
Sbjct: 215 ARTIRIPVHMVE--TINKLIRIQRQLLQDLGREPLPEEIGA---EMDMPTEKVRNILKIA 269

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D       +    +  +  L   +  L  RE 
Sbjct: 270 QEPVSLETPI--GEEDDSHLGDFI---EDQDATSPADHAAYEMMKKQLENVLDTLTDREE 324

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 325 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 373


>gi|1943995|dbj|BAA19494.1| sigA=sigma70 [Staphylococcus aureus]
          Length = 368

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 81/276 (29%), Positives = 137/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L  QEE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGRVNLLSAQEEIELAKRI-EQGDEVAKSRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 LFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIAHQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L      +  PE    I +++++   +V  +        SL   I   
Sbjct: 215 -TINKLIRVQRQLLQDLGRDPAPE---EIGEEMDLPAEKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D + Q   +    +  +  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGR 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 361


>gi|291550178|emb|CBL26440.1| RNA polymerase, sigma 70 subunit, RpoD [Ruminococcus torques L2-14]
          Length = 373

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 86/290 (29%), Positives = 142/290 (48%), Gaps = 15/290 (5%)

Query: 1   MNRKNMSII--VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHL 58
           M   ++S+   V+ E  +  Y+ EI K+P+L  + E  LA+R  E GD  A   L  ++L
Sbjct: 87  MENIDLSVPEGVSIEDPVRMYLKEIGKVPLLSAEREIELAQRM-EEGDEEAKKELAEANL 145

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I 
Sbjct: 146 RLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYHKGYKFSTYATWWIRQAITRAIA 205

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
                ++I     +      L R+   L         PE    IAK++++    V  +  
Sbjct: 206 DQARTIRIPVHMVE--TINKLIRVSRQLLQELGREPLPE---EIAKEMDMPVERVREILK 260

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
                 SL   I   ++  S   D++  D      V  E   +   +  L   +  L  R
Sbjct: 261 ISQEPVSLETPI--GEEEDSHLGDFIQDD---NVPVPAEAAAQTLLKEQLDEVLDTLTER 315

Query: 239 ERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E+++   R    +    TLE +  EF+V+RER+RQIEA+A +K++   + 
Sbjct: 316 EQKVLRLRFGMNDGRARTLEEVGREFDVTRERIRQIEAKALRKLRHPSRS 365


>gi|299822900|ref|ZP_07054786.1| DNA-directed RNA polymerase sigma subunit RpoD [Listeria grayi DSM
           20601]
 gi|299816429|gb|EFI83667.1| DNA-directed RNA polymerase sigma subunit RpoD [Listeria grayi DSM
           20601]
          Length = 389

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 83/288 (28%), Positives = 142/288 (49%), Gaps = 15/288 (5%)

Query: 4   KNMSIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
            +MS+    +I   +  Y+ EI ++ +L   EE  LAKR  E GD+ A  RL  ++LRLV
Sbjct: 106 TDMSVPPGVKINDPVRMYLKEIGRVNLLTADEEVALAKRI-ETGDIEAKGRLAEANLRLV 164

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA  Y G G+   +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I    
Sbjct: 165 VSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQA 224

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             ++I     +      L R++  L      +  PE    I +++++   +V  +     
Sbjct: 225 RTIRIPVHMVE--TINKLIRVQRSLLQDLGRDPSPE---EIGEEMDLPTEKVREILKIAQ 279

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              SL   I   +++ S   D++    D +     +    +  +  L   +  L  RE  
Sbjct: 280 EPVSLETPI--GEEDDSHLGDFI---EDQEATSPSDHAAYELLKEQLEDVLDTLTDREEN 334

Query: 242 IFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 335 VLRLRFGLDDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSK 382


>gi|220932077|ref|YP_002508985.1| RNA polymerase, sigma 70 subunit, RpoD family [Halothermothrix
           orenii H 168]
 gi|219993387|gb|ACL69990.1| RNA polymerase, sigma 70 subunit, RpoD family [Halothermothrix
           orenii H 168]
          Length = 358

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 87/280 (31%), Positives = 137/280 (48%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V  +  +  Y+ EI K+P+L  +EE  LAKR  E GD  A   LV ++LRLVV IA  Y 
Sbjct: 83  VGIDDPVRMYLKEIGKVPLLTAEEEVDLAKRI-EQGDEQAKRELVEANLRLVVSIAKKYV 141

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 142 GRGMSFLDLIQEGNMGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 201

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L         PE    I +++ +   +V  +        SL   
Sbjct: 202 MVE--TINKLIRVSRQLLQEKGREPTPE---EIGEEMGMPAEKVREILKIAQEPVSLETP 256

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++    D               R  L   +  L  RE+R+ E R   
Sbjct: 257 I--GEEEDSHLGDFI---EDEDAPAPASAASFTLLREQLDDVLDTLTDREKRVLELRFGL 311

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+  P TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 312 EDGRPRTLEEVGKEFGVTRERIRQIEAKALRKLRHPSRSK 351


>gi|70726356|ref|YP_253270.1| RNA polymerase sigma factor RpoD [Staphylococcus haemolyticus
           JCSC1435]
 gi|68447080|dbj|BAE04664.1| RNA polymerase sigma factor [Staphylococcus haemolyticus JCSC1435]
          Length = 368

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 81/276 (29%), Positives = 137/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L  QEE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGRVNLLSAQEEIELAKRI-EQGDEIAKSRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 LFLDLIQEGNMGLIKAVEKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L      +  PE    I +++++   +V  +        SL   I   
Sbjct: 215 -TINKLIRVQRQLLQDLGRDPAPE---EIGEEMDLPPEKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D + Q   +    +  +  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGR 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 361


>gi|15924551|ref|NP_372085.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus Mu50]
 gi|21283242|ref|NP_646330.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus MW2]
 gi|49483810|ref|YP_041034.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus MRSA252]
 gi|49486397|ref|YP_043618.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus MSSA476]
 gi|57651954|ref|YP_186458.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus COL]
 gi|82751164|ref|YP_416905.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus RF122]
 gi|87162254|ref|YP_494216.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus USA300_FPR3757]
 gi|88195369|ref|YP_500173.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus NCTC 8325]
 gi|148268045|ref|YP_001246988.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus JH9]
 gi|150394113|ref|YP_001316788.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus JH1]
 gi|151221676|ref|YP_001332498.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus str. Newman]
 gi|156979879|ref|YP_001442138.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus Mu3]
 gi|161509790|ref|YP_001575449.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus USA300_TCH1516]
 gi|221140019|ref|ZP_03564512.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus str. JKD6009]
 gi|253314932|ref|ZP_04838145.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus str. CF-Marseille]
 gi|253732214|ref|ZP_04866379.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus USA300_TCH959]
 gi|253733189|ref|ZP_04867354.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus TCH130]
 gi|255006347|ref|ZP_05144948.2| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus Mu50-omega]
 gi|257428347|ref|ZP_05604745.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus 65-1322]
 gi|257433672|ref|ZP_05610030.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus E1410]
 gi|257436586|ref|ZP_05612630.1| transcription initiation factor sigma plaC [Staphylococcus aureus
           subsp. aureus M876]
 gi|257793637|ref|ZP_05642616.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus A9781]
 gi|258411063|ref|ZP_05681343.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus A9763]
 gi|258420133|ref|ZP_05683088.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A9719]
 gi|258423989|ref|ZP_05686871.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus A9635]
 gi|258443599|ref|ZP_05691938.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A8115]
 gi|258448720|ref|ZP_05696832.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus A6224]
 gi|258450610|ref|ZP_05698672.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A5948]
 gi|258453537|ref|ZP_05701515.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A5937]
 gi|262049137|ref|ZP_06022014.1| RNA polymerase sigma factor [Staphylococcus aureus D30]
 gi|262051223|ref|ZP_06023447.1| RNA polymerase sigma factor [Staphylococcus aureus 930918-3]
 gi|269203189|ref|YP_003282458.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus ED98]
 gi|282893062|ref|ZP_06301296.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A8117]
 gi|282904143|ref|ZP_06312031.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus C160]
 gi|282905970|ref|ZP_06313825.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus Btn1260]
 gi|282908880|ref|ZP_06316698.1| RNA polymerase sigma factor RpoS [Staphylococcus aureus subsp.
           aureus WW2703/97]
 gi|282911199|ref|ZP_06319001.1| RNA polymerase sigma factor RpoS [Staphylococcus aureus subsp.
           aureus WBG10049]
 gi|282914368|ref|ZP_06322154.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus M899]
 gi|282916831|ref|ZP_06324589.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus D139]
 gi|282919337|ref|ZP_06327072.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus C427]
 gi|282920110|ref|ZP_06327835.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A9765]
 gi|282924662|ref|ZP_06332330.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus C101]
 gi|282928194|ref|ZP_06335799.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A10102]
 gi|283770637|ref|ZP_06343529.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus H19]
 gi|283958325|ref|ZP_06375776.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus A017934/97]
 gi|284024620|ref|ZP_06379018.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus 132]
 gi|293503442|ref|ZP_06667289.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus 58-424]
 gi|293510459|ref|ZP_06669165.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus M809]
 gi|293530999|ref|ZP_06671681.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus M1015]
 gi|294848592|ref|ZP_06789338.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A9754]
 gi|295406684|ref|ZP_06816489.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A8819]
 gi|295428139|ref|ZP_06820771.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus EMRSA16]
 gi|296275817|ref|ZP_06858324.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus MR1]
 gi|297207720|ref|ZP_06924155.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus ATCC 51811]
 gi|297245734|ref|ZP_06929599.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A8796]
 gi|297590895|ref|ZP_06949533.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus MN8]
 gi|300911801|ref|ZP_07129244.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus TCH70]
 gi|304380850|ref|ZP_07363510.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus ATCC BAA-39]
 gi|60390420|sp|Q6G905|RPOD_STAAS RecName: Full=RNA polymerase sigma factor rpoD
 gi|60390434|sp|Q6GGD8|RPOD_STAAR RecName: Full=RNA polymerase sigma factor rpoD
 gi|60393872|sp|P0A0I8|RPOD_STAAM RecName: Full=RNA polymerase sigma factor rpoD
 gi|60393873|sp|P0A0I9|RPOD_STAAW RecName: Full=RNA polymerase sigma factor rpoD
 gi|60393874|sp|P0A0J0|RPOD_STAA8 RecName: Full=RNA polymerase sigma factor rpoD
 gi|81694388|sp|Q5HFJ9|RPOD_STAAC RecName: Full=RNA polymerase sigma factor rpoD
 gi|153069|gb|AAB59090.1| sigma factor [Staphylococcus aureus]
 gi|14247332|dbj|BAB57723.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           Mu50]
 gi|21204682|dbj|BAB95378.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           MW2]
 gi|49241939|emb|CAG40633.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           MRSA252]
 gi|49244840|emb|CAG43300.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           MSSA476]
 gi|57286140|gb|AAW38234.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus COL]
 gi|82656695|emb|CAI81122.1| RNA polymerase sigma factor [Staphylococcus aureus RF122]
 gi|87128228|gb|ABD22742.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus USA300_FPR3757]
 gi|87202927|gb|ABD30737.1| RNA polymerase sigma factor, putative [Staphylococcus aureus subsp.
           aureus NCTC 8325]
 gi|147741114|gb|ABQ49412.1| RNA polymerase, sigma 70 subunit, RpoD family [Staphylococcus
           aureus subsp. aureus JH9]
 gi|149946565|gb|ABR52501.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus JH1]
 gi|150374476|dbj|BAF67736.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           str. Newman]
 gi|156722014|dbj|BAF78431.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           Mu3]
 gi|160368599|gb|ABX29570.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus USA300_TCH1516]
 gi|253724003|gb|EES92732.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus USA300_TCH959]
 gi|253728729|gb|EES97458.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus TCH130]
 gi|257275188|gb|EEV06675.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus 65-1322]
 gi|257281765|gb|EEV11902.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus E1410]
 gi|257283937|gb|EEV14060.1| transcription initiation factor sigma plaC [Staphylococcus aureus
           subsp. aureus M876]
 gi|257787609|gb|EEV25949.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus A9781]
 gi|257840213|gb|EEV64677.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus A9763]
 gi|257843844|gb|EEV68238.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A9719]
 gi|257845610|gb|EEV69642.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus A9635]
 gi|257851005|gb|EEV74948.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A8115]
 gi|257857998|gb|EEV80887.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus A6224]
 gi|257861768|gb|EEV84567.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A5948]
 gi|257864268|gb|EEV87018.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A5937]
 gi|259160860|gb|EEW45880.1| RNA polymerase sigma factor [Staphylococcus aureus 930918-3]
 gi|259162806|gb|EEW47371.1| RNA polymerase sigma factor [Staphylococcus aureus D30]
 gi|262075479|gb|ACY11452.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus ED98]
 gi|269941051|emb|CBI49435.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           TW20]
 gi|282313497|gb|EFB43892.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus C101]
 gi|282317147|gb|EFB47521.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus C427]
 gi|282319318|gb|EFB49670.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus D139]
 gi|282321549|gb|EFB51874.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus M899]
 gi|282324894|gb|EFB55204.1| RNA polymerase sigma factor RpoS [Staphylococcus aureus subsp.
           aureus WBG10049]
 gi|282327144|gb|EFB57439.1| RNA polymerase sigma factor RpoS [Staphylococcus aureus subsp.
           aureus WW2703/97]
 gi|282331262|gb|EFB60776.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus Btn1260]
 gi|282590001|gb|EFB95083.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A10102]
 gi|282594458|gb|EFB99443.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A9765]
 gi|282595761|gb|EFC00725.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus C160]
 gi|282764380|gb|EFC04506.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A8117]
 gi|283460784|gb|EFC07874.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus H19]
 gi|283470839|emb|CAQ50050.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Staphylococcus aureus subsp. aureus ST398]
 gi|283790474|gb|EFC29291.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus A017934/97]
 gi|285817243|gb|ADC37730.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus 04-02981]
 gi|290920267|gb|EFD97333.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus M1015]
 gi|291095108|gb|EFE25373.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus 58-424]
 gi|291466823|gb|EFF09343.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus M809]
 gi|294824618|gb|EFG41041.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A9754]
 gi|294968431|gb|EFG44455.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A8819]
 gi|295128497|gb|EFG58131.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus EMRSA16]
 gi|296887737|gb|EFH26635.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus ATCC 51811]
 gi|297177385|gb|EFH36637.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A8796]
 gi|297575781|gb|EFH94497.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus MN8]
 gi|298694843|gb|ADI98065.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           ED133]
 gi|300886047|gb|EFK81249.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus TCH70]
 gi|302333237|gb|ADL23430.1| RNA polymerase sigma-70 factor RpoD [Staphylococcus aureus subsp.
           aureus JKD6159]
 gi|302751392|gb|ADL65569.1| RNA polymerase sigma-70 factor RpoD [Staphylococcus aureus subsp.
           aureus str. JKD6008]
 gi|304340577|gb|EFM06511.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus ATCC BAA-39]
 gi|312437970|gb|ADQ77041.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           aureus subsp. aureus TCH60]
 gi|312829949|emb|CBX34791.1| RNA polymerase sigma factor rpoD (Sigma-A) (Sigma-43)
           [Staphylococcus aureus subsp. aureus ECT-R 2]
 gi|315129839|gb|EFT85829.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus CGS03]
 gi|315195463|gb|EFU25850.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus CGS00]
 gi|315198744|gb|EFU29072.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus CGS01]
 gi|320140554|gb|EFW32408.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus MRSA131]
 gi|320144091|gb|EFW35860.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus MRSA177]
 gi|323440459|gb|EGA98171.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus O11]
 gi|323443233|gb|EGB00851.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus O46]
 gi|329314237|gb|AEB88650.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus T0131]
 gi|329727416|gb|EGG63872.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus 21172]
 gi|329728458|gb|EGG64895.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus 21189]
          Length = 368

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 81/276 (29%), Positives = 137/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L  QEE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGRVNLLSAQEEIELAKRI-EQGDEVAKSRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 LFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L      +  PE    I +++++   +V  +        SL   I   
Sbjct: 215 -TINKLIRVQRQLLQDLGRDPAPE---EIGEEMDLPAEKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D + Q   +    +  +  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGR 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 361


>gi|331701385|ref|YP_004398344.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Lactobacillus
           buchneri NRRL B-30929]
 gi|329128728|gb|AEB73281.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Lactobacillus
           buchneri NRRL B-30929]
          Length = 414

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 78/276 (28%), Positives = 133/276 (48%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L   +E  LAKR  E GD  A   L  ++LRLVV IA  Y G G+
Sbjct: 143 DPVRMYLKEIGRVSLLSADQEISLAKRI-EAGDEEAKQELAEANLRLVVSIAKRYVGRGM 201

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 202 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 260

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L         PE++ A   ++++   +V  +        SL   I   
Sbjct: 261 -TINKLIRIQRQLLQDLGREPLPEEIGA---EMDMPTEKVREILKIAQEPVSLETPI--G 314

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D       +    +  +  L   +  L  RE  +   R   ++  
Sbjct: 315 EEDDSHLGDFI---EDQDATSPADHAAYELLKEQLESVLDTLTDREENVLRLRFGLDDGR 371

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 372 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 407


>gi|157964378|ref|YP_001499202.1| RNA polymerase factor sigma-32 [Rickettsia massiliae MTU5]
 gi|157844154|gb|ABV84655.1| RNA polymerase sigma-32 factor [Rickettsia massiliae MTU5]
          Length = 310

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 145/285 (50%), Positives = 198/285 (69%), Gaps = 1/285 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M     ++ ++ E G   Y+ +I KIP L ++EE +LAK Y E  DL AAH+LVTSHL+L
Sbjct: 18  MTNNINALAISSESGFYSYLQKINKIPSLTQEEELLLAKSYLEGNDLQAAHKLVTSHLKL 77

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIA GYR YGLPI+E+VSEGNIGLMQAVKKF+PE GFRL+TY+MWWIKAA+QEYIL+S
Sbjct: 78  VAKIASGYRTYGLPITELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKAAIQEYILKS 137

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTA QK+LFF+L ++K  +  +    +  +    IA +L VS +EV  MN R+
Sbjct: 138 WSLVKMGTTAAQKKLFFSLNKVKHKITNLYSRAITTDDFAQIADELGVSVNEVSEMNTRI 197

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D SLN  INS D  S +  + L       E + I K+   ++R +L+ +M +LN RE
Sbjct: 198 SGPDLSLNNSINSDDAESGELIELLPETRPTPEAMAINKQNSTSKRQLLSNAMKILNDRE 257

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            RI   R+L + P TL+ LS+E+ +S+ER+RQIE  AF+K+++ I
Sbjct: 258 LRILTERKLTDTPKTLDILSNEYNISKERIRQIENTAFEKIKKFI 302


>gi|295399207|ref|ZP_06809189.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|312110191|ref|YP_003988507.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus sp.
           Y4.1MC1]
 gi|294978673|gb|EFG54269.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|311215292|gb|ADP73896.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus sp.
           Y4.1MC1]
          Length = 377

 Score =  269 bits (689), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 83/289 (28%), Positives = 143/289 (49%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++P+L  +EE  LAKR  E GD  A  RL  ++LRL
Sbjct: 93  LNDLSVPPGVKINDPVRMYLKEIGRVPLLSAEEEIELAKRI-EQGDEEAKRRLTEANLRL 151

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I   
Sbjct: 152 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQ 211

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    IA++++++  +V  +    
Sbjct: 212 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPTPE---EIAEEMDLTPEKVREILKIA 266

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D +     E    +  +  L   +  L  RE 
Sbjct: 267 QEPVSLETPI--GEEDDSHLGDFI---EDQEATSPSEHAAYELLKEQLEDVLDTLTDREE 321

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 322 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 370


>gi|319892618|ref|YP_004149493.1| RNA polymerase sigma factor RpoD [Staphylococcus pseudintermedius
           HKU10-03]
 gi|317162314|gb|ADV05857.1| RNA polymerase sigma factor RpoD [Staphylococcus pseudintermedius
           HKU10-03]
 gi|323464344|gb|ADX76497.1| RNA polymerase sigma factor SigA [Staphylococcus pseudintermedius
           ED99]
          Length = 369

 Score =  269 bits (688), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 81/276 (29%), Positives = 137/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L  QEE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 98  DPVRMYLKEIGRVDLLSAQEEIELAKRI-EQGDEVAKARLAEANLRLVVSIAKRYVGRGM 156

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 157 LFLDLIQEGNMGLIKAVEKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 215

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L      +  PE    I +++++   +V  +        SL   I   
Sbjct: 216 -TINKLIRVQRQLLQDLGRDPAPE---EIGEEMDLPPEKVREILKIAQEPVSLETPI--G 269

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D + Q   +    +  +  L   +  L  RE  +   R   ++  
Sbjct: 270 EEDDSHLGDFI---EDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGR 326

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 327 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 362


>gi|228476045|ref|ZP_04060753.1| RNA polymerase sigma factor RpoD [Staphylococcus hominis SK119]
 gi|314936318|ref|ZP_07843665.1| RNA polymerase sigma factor RpoD [Staphylococcus hominis subsp.
           hominis C80]
 gi|228269868|gb|EEK11348.1| RNA polymerase sigma factor RpoD [Staphylococcus hominis SK119]
 gi|313654937|gb|EFS18682.1| RNA polymerase sigma factor RpoD [Staphylococcus hominis subsp.
           hominis C80]
          Length = 368

 Score =  269 bits (688), Expect = 3e-70,   Method: Composition-based stats.
 Identities = 81/276 (29%), Positives = 137/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L  QEE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGRVNLLSAQEEIELAKRI-EQGDEVAKSRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 LFLDLIQEGNMGLIKAVEKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L      +  PE    I +++++   +V  +        SL   I   
Sbjct: 215 -TINKLIRVQRQLLQDLGRDPAPE---EIGEEMDLPPEKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D + Q   +    +  +  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGR 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 361


>gi|327458597|gb|EGF04945.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK1057]
          Length = 370

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 84/276 (30%), Positives = 139/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE  LA    E GDL A  RL  ++LRLVV IA  Y G G+
Sbjct: 98  DPVRMYLKEIGVVPLLSNEEEQELAI-LVEQGDLEAKQRLAEANLRLVVSIAKRYVGRGM 156

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 157 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 215

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA++++++  +V  +        SL   I   
Sbjct: 216 -TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSLETPI--G 269

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 270 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 326

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 327 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 362


>gi|227892546|ref|ZP_04010351.1| RNA polymerase sigma factor RpoD [Lactobacillus ultunensis DSM
           16047]
 gi|227865667|gb|EEJ73088.1| RNA polymerase sigma factor RpoD [Lactobacillus ultunensis DSM
           16047]
          Length = 370

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 81/284 (28%), Positives = 135/284 (47%), Gaps = 13/284 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +    V     +  Y+ EI ++P+L   +E  LAKR  E GD  A   L  ++LRLVV I
Sbjct: 90  SAPSSVRMNDPVRMYLKEIGRVPLLTADQEIALAKRI-EAGDEEAKQELAEANLRLVVSI 148

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y G G+   +++ EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      +
Sbjct: 149 AKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTI 208

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I     +      L +++  L         PE++ A   ++NV  ++V  +        
Sbjct: 209 RIPVHMVE--TINKLIKIQRQLLQDLGREPTPEEIGA---EMNVPTNKVRDILKIAQEPV 263

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   I   +++ S   D++    D       +    +  +  L + +  L  RE  +  
Sbjct: 264 SLETPI--GEEDDSHLGDFI---EDKDATSPEQHASYEMLKEQLEQVLETLTDREENVLR 318

Query: 245 ARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R   ++    TLE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 319 LRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRS 362


>gi|323480687|gb|ADX80126.1| RNA polymerase sigma factor rpoD (Sigma-42) [Enterococcus faecalis
           62]
          Length = 356

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 79/276 (28%), Positives = 133/276 (48%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L   EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 85  DPVRMYLKEIGRVQLLTAAEEVELALKI-EEGDQEAKQRLAEANLRLVVSIAKRYVGRGM 143

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 144 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 202

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L         PE++ A   ++++   +V  +        SL   I   
Sbjct: 203 -TINKLIRIQRQLLQDLGREPTPEEIGA---EMDLPTEKVREILKIAQEPVSLETPI--G 256

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D       E    +  +  L   +  L  RE  +   R   ++  
Sbjct: 257 EEDDSHLGDFI---EDQDATSPAEHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGR 313

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 314 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 349


>gi|312143990|ref|YP_003995436.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Halanaerobium sp.
           'sapolanicus']
 gi|311904641|gb|ADQ15082.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Halanaerobium sp.
           'sapolanicus']
          Length = 360

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 87/280 (31%), Positives = 140/280 (50%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V  +  +  Y+ EI K+ +L   EE +LAKR  E GD  A  +LV ++LRLVV IA  Y 
Sbjct: 85  VGIDDPVRMYLKEIGKVDLLTADEEVMLAKRM-EQGDEWAKQQLVEANLRLVVSIAKKYV 143

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GLM+AV+KFD  +G++ +TY+ WWI+ A+   I      +++   
Sbjct: 144 GRGMLFLDLIQEGNMGLMKAVEKFDYTKGYKFSTYATWWIRQAITRSIADQARTIRVPVH 203

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L        KPE    I +++++S  +V  +        SL   
Sbjct: 204 MVE--TINKLIRVSRQLLQEKGREPKPE---EIGEEMDISAEKVREIMKIAQEPVSLETP 258

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++    D               +  L   +  L  RE+R+ E R   
Sbjct: 259 I--GEEEDSHLGDFI---EDEDSPAPASAASYILLKEQLDGVLDTLTEREKRVLELRFGI 313

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+  P TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 314 EDGRPRTLEEVGKEFGVTRERIRQIEAKALRKLRHPSRSK 353


>gi|302386569|ref|YP_003822391.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           saccharolyticum WM1]
 gi|302197197|gb|ADL04768.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           saccharolyticum WM1]
          Length = 401

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 84/280 (30%), Positives = 140/280 (50%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ E  +  Y+ EI K+P+L  ++E  LAK+  E GD  A  RL  ++LRLVV IA  Y 
Sbjct: 125 ISVEDPVRMYLKEIGKVPLLSSEDEIELAKKI-ELGDDDAKQRLTEANLRLVVSIAKRYV 183

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 184 GRGMQFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 243

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L         PE++ A A   ++    V  +        SL   
Sbjct: 244 MVE--TINRLVRVSRQLLQELGREPVPEEIAARA---DMQVDRVREIMKVSQEPVSLETP 298

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++    D Q  V  +          L   +  L  RE+++ + R   
Sbjct: 299 I--GEEEDSHLGDFI---QDEQVAVPADAATFTMLHEQLMEVLDTLTEREQKVLKLRFGL 353

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  P TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 354 DDGRPRTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 393


>gi|22537572|ref|NP_688423.1| RNA polymerase sigma factor RpoD [Streptococcus agalactiae 2603V/R]
 gi|25011538|ref|NP_735933.1| RNA polymerase sigma factor RpoD [Streptococcus agalactiae NEM316]
 gi|76788342|ref|YP_330069.1| RNA polymerase sigma factor RpoD [Streptococcus agalactiae A909]
 gi|77409561|ref|ZP_00786243.1| RNA polymerase sigma-70 factor [Streptococcus agalactiae COH1]
 gi|77412516|ref|ZP_00788814.1| RNA polymerase sigma-70 factor [Streptococcus agalactiae CJB111]
 gi|77414847|ref|ZP_00790961.1| RNA polymerase sigma-70 factor [Streptococcus agalactiae 515]
 gi|22534455|gb|AAN00296.1|AE014257_3 RNA polymerase sigma-70 factor [Streptococcus agalactiae 2603V/R]
 gi|24413077|emb|CAD47155.1| RNA polymerase major sigma factor RpoD [Streptococcus agalactiae
           NEM316]
 gi|76563399|gb|ABA45983.1| RNA polymerase sigma factor RpoD [Streptococcus agalactiae A909]
 gi|77159097|gb|EAO70294.1| RNA polymerase sigma-70 factor [Streptococcus agalactiae 515]
 gi|77161430|gb|EAO72443.1| RNA polymerase sigma-70 factor [Streptococcus agalactiae CJB111]
 gi|77171826|gb|EAO75013.1| RNA polymerase sigma-70 factor [Streptococcus agalactiae COH1]
          Length = 369

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 84/276 (30%), Positives = 139/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE  LA    E GDL A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGVVPLLTNEEEKELAVAVAE-GDLMAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA++++++  +V  +        SL   I   
Sbjct: 215 -TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 361


>gi|309388945|gb|ADO76825.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Halanaerobium
           praevalens DSM 2228]
          Length = 364

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 80/285 (28%), Positives = 140/285 (49%), Gaps = 13/285 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           ++    + +  +  Y+ EI K+ +L  +EE  LAKR  E G+  A  +LV ++LRLVV I
Sbjct: 84  SIPKSASIDDPVRMYLKEIGKVDLLTAEEEVELAKRM-EQGEEWAKQQLVQANLRLVVSI 142

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y G G+   +++ EGN+GLM+AV KFD  +G++ +TY+ WWI+ A+   I      +
Sbjct: 143 AKKYVGRGMLFLDLIQEGNMGLMKAVDKFDYTKGYKFSTYATWWIRQAITRSIADQARTI 202

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           ++     +      + +L    + +     +  +   I  ++++S  +V  +        
Sbjct: 203 RVPVHMVE-----TINKLIRVSRQLLQEKGREPKDEEIGAEMDISAEKVREIMKISQDPV 257

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   I   ++  S   D++    D               +  L   +  L  RE+R+ E
Sbjct: 258 SLETPI--GEEEDSHLGDFI---EDVDSPAPASAASYILLKEQLNDVLDTLTDREKRVLE 312

Query: 245 ARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R   E+  P TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 313 LRFGIEDGRPRTLEEVGKEFGVTRERIRQIEAKALRKLRHPSRSK 357


>gi|256847131|ref|ZP_05552577.1| RNA polymerase sigma factor RpoS [Lactobacillus coleohominis
           101-4-CHN]
 gi|256715795|gb|EEU30770.1| RNA polymerase sigma factor RpoS [Lactobacillus coleohominis
           101-4-CHN]
          Length = 381

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 77/276 (27%), Positives = 133/276 (48%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L   +E  LA R  E GD +A   L  ++LRLVV IA  Y G G+
Sbjct: 110 DPVRMYLKEIGRVNLLTADQEVELALRI-EKGDETAKQELAEANLRLVVSIAKRYVGRGM 168

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 169 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 227

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L         PE++ A   ++++   +V  +        SL   I   
Sbjct: 228 -TINKLIRIQRQLLQDLGREPLPEEIGA---EMDMPTKKVRDILKIAQEPVSLETPI--G 281

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D       +    +  +  L   +  L  RE  +   R   ++  
Sbjct: 282 EEDDSHLGDFI---EDHDATSPADHAAYEMMKKQLENVLDTLTDREENVLRLRFGLDDGR 338

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 339 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 374


>gi|296876770|ref|ZP_06900818.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           parasanguinis ATCC 15912]
 gi|296432272|gb|EFH18071.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           parasanguinis ATCC 15912]
          Length = 369

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 84/276 (30%), Positives = 139/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE  LA    E GDL A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGVVPLLTNEEEQELAI-LVEQGDLEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA++++++  +V  +        SL   I   
Sbjct: 215 -TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 361


>gi|257425686|ref|ZP_05602110.1| transcription initiation factor sigma plaC [Staphylococcus aureus
           subsp. aureus 55/2053]
 gi|257271380|gb|EEV03526.1| transcription initiation factor sigma plaC [Staphylococcus aureus
           subsp. aureus 55/2053]
          Length = 368

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 81/276 (29%), Positives = 136/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L  QEE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGRVNLLSAQEEIELAKRI-EQGDEVAKSRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 LFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L         PE    I +++++   +V  +        SL   I   
Sbjct: 215 -TINKLIRVQRQLLQDLGREPAPE---EIGEEMDLPAEKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D + Q   +    +  +  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGR 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 361


>gi|3062909|dbj|BAA25730.1| SigA [Bacillus sp.]
          Length = 372

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 82/289 (28%), Positives = 142/289 (49%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++P+L  +EE  LA R  E GD  A  RL  ++LRL
Sbjct: 88  LNDLSVPPGVKINDPVRMYLKEIGRVPLLTAEEEIELATRI-EQGDEEAKRRLAEANLRL 146

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 147 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYNKGFKFSTYATWWIRQAITRAIADQ 206

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE+V   A++++++  +V  +    
Sbjct: 207 ARTIRIPVHMVE--TINKLIRVQRQLLQDVGREPSPEEV---AEEMDLTPEKVREILKIA 261

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D       +    +  +  L   +  L  RE 
Sbjct: 262 QEPVSLETPI--GEEDDSHLGDFI---EDQDALAPSDAAAYELLKEQLEDVLDTLTDREE 316

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 317 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 365


>gi|242242833|ref|ZP_04797278.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           epidermidis W23144]
 gi|242233734|gb|EES36046.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           epidermidis W23144]
          Length = 368

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 80/276 (28%), Positives = 137/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L  QEE  LAK+  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGRVNLLSAQEEIELAKKI-EQGDEIAKSRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 LFLDLIQEGNMGLIKAVEKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L      +  PE    I +++++   +V  +        SL   I   
Sbjct: 215 -TINKLIRVQRQLLQDLGRDPAPE---EIGEEMDLPPEKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D + Q   +    +  +  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGR 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 361


>gi|255972833|ref|ZP_05423419.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis T1]
 gi|255963851|gb|EET96327.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis T1]
          Length = 368

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 79/276 (28%), Positives = 133/276 (48%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L   EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGRVQLLTAAEEVELALKI-EEGDQEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L         PE++ A   ++++   +V  +        SL   I   
Sbjct: 215 -TINKLIRIQRQLLQDLGREPTPEEIGA---EMDLPTEKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D       E    +  +  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDQDATSPAEHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGR 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 361


>gi|160893000|ref|ZP_02073788.1| hypothetical protein CLOL250_00537 [Clostridium sp. L2-50]
 gi|156865083|gb|EDO58514.1| hypothetical protein CLOL250_00537 [Clostridium sp. L2-50]
          Length = 377

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 85/279 (30%), Positives = 137/279 (49%), Gaps = 13/279 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V+ E  +  Y+ EI K+P+L  +EE  LAKR  E GD  A  +L  ++LRLVV IA  Y 
Sbjct: 102 VSIEDPVRMYLKEIGKVPLLSAEEEIELAKRM-EEGDEQAKQKLAEANLRLVVSIAKRYV 160

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 161 GRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 220

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L        +PE    IA  +++    V  +        SL   
Sbjct: 221 MVE--TINKLIRVSRQLLQELGREPQPE---EIADVMDIPVERVREILKISQEPVSLETP 275

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++  D      V  +       +  L   +  L  RE+++   R   
Sbjct: 276 I--GEEEDSHLGDFIPDD---NMPVPADAAAFTLLKEQLVEVLDTLTEREKKVLTLRFGL 330

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E+    TLE +  EF V+RER+RQIEA+A +K++   + 
Sbjct: 331 EDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRS 369


>gi|312869100|ref|ZP_07729274.1| RNA polymerase sigma factor RpoD [Lactobacillus oris PB013-T2-3]
 gi|311095346|gb|EFQ53616.1| RNA polymerase sigma factor RpoD [Lactobacillus oris PB013-T2-3]
          Length = 380

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 80/289 (27%), Positives = 137/289 (47%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M   +    V     +  Y+ EI ++ +L   EE  LA R  E GD  A  +L  ++LRL
Sbjct: 96  MKDTSAPTGVKINDPVRMYLKEIGRVNLLTADEEVKLALRI-EQGDEVAKQQLAEANLRL 154

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GLM+AV+KFD  RGF+ +TY+ WWI+ A+   I   
Sbjct: 155 VVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRRGFKFSTYATWWIRQAITRAIADQ 214

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE++ A   ++++   ++ ++    
Sbjct: 215 ARTIRIPVHMVE--TINKLIRIQRQLLQDLGREPLPEEIGA---EMDMPTEKIRNILKIA 269

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D       +    +  +  L   +  L  RE 
Sbjct: 270 QEPVSLETPI--GEEDDSHLGDFI---EDQDATSPADHAAYEMMKKQLENVLDTLTDREE 324

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 325 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 373


>gi|259046798|ref|ZP_05737199.1| RNA polymerase sigma-43 factor [Granulicatella adiacens ATCC 49175]
 gi|259036566|gb|EEW37821.1| RNA polymerase sigma-43 factor [Granulicatella adiacens ATCC 49175]
          Length = 374

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 78/277 (28%), Positives = 131/277 (47%), Gaps = 14/277 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++P+L   EE  LA R +E GD  A   L  ++LRLVV IA  Y G G+
Sbjct: 102 DSVRMYLKEIGRVPLLSADEEVALALRIQE-GDTEAKQELAEANLRLVVSIAKRYVGRGM 160

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+ V+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 161 QFLDLIQEGNMGLMKTVEKFDHTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 219

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L         PE++ A   ++++   +V  +        SL   I   
Sbjct: 220 -TINKLVRVQRQLLQDLGREPTPEEIGA---EMDLPTEKVREILKIAQEPVSLETPI--G 273

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--- 250
           +++ S   D++  D         +       +  L   +  L  RE  +   R   +   
Sbjct: 274 EEDDSHLGDFIEDD---NATSPADHTAYALLKEQLDEVLEQLTDREENVLRLRFGLDKNG 330

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 331 EIRTLEQVGQVFGVTRERIRQIEAKALRKLRHPSRSK 367


>gi|56421017|ref|YP_148335.1| RNA polymerase sigma factor RpoD [Geobacillus kaustophilus HTA426]
 gi|261417657|ref|YP_003251339.1| RNA polymerase sigma factor RpoD [Geobacillus sp. Y412MC61]
 gi|297529352|ref|YP_003670627.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus sp.
           C56-T3]
 gi|319767537|ref|YP_004133038.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus sp.
           Y412MC52]
 gi|56380859|dbj|BAD76767.1| DNA-directed RNA polymerase major sigma-43 factor (sigma-A)
           [Geobacillus kaustophilus HTA426]
 gi|261374114|gb|ACX76857.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus sp.
           Y412MC61]
 gi|297252604|gb|ADI26050.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus sp.
           C56-T3]
 gi|317112403|gb|ADU94895.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacillus sp.
           Y412MC52]
          Length = 375

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 83/289 (28%), Positives = 142/289 (49%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++P+L  +EE  LAKR  E GD  A  RL  ++LRL
Sbjct: 91  LNDLSVPPGVKINDPVRMYLKEIGRVPLLSAEEEIELAKRI-EQGDEEAKRRLTEANLRL 149

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I   
Sbjct: 150 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQ 209

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    IA++++++  +V  +    
Sbjct: 210 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPTPE---EIAEEMDLTPEKVREILKIA 264

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D       E    +  +  L   +  L  RE 
Sbjct: 265 QEPVSLETPI--GEEDDSHLGDFI---EDQDATSPSEHAAYELLKEQLEDVLDTLTDREE 319

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 320 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 368


>gi|146295919|ref|YP_001179690.1| RpoD family RNA polymerase sigma factor [Caldicellulosiruptor
           saccharolyticus DSM 8903]
 gi|145409495|gb|ABP66499.1| RNA polymerase, sigma 70 subunit, RpoD [Caldicellulosiruptor
           saccharolyticus DSM 8903]
          Length = 411

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 89/286 (31%), Positives = 143/286 (50%), Gaps = 13/286 (4%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           +N+   +  +  +  Y+ EI KIP+L  +EE  LAKR  E GD  A  RL  ++LRLVV 
Sbjct: 130 ENLPEGIAIDDPVRMYLKEIGKIPLLTPEEEIELAKRI-EQGDEEAKKRLAEANLRLVVS 188

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      
Sbjct: 189 IAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQART 248

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           ++I     +      L R+   L         PE    IAK++N+   +V  +       
Sbjct: 249 IRIPVHMVE--TINKLVRVSRQLLQEKGREPTPE---EIAKEMNMPVEKVREILKIAQEP 303

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SL   I   ++  S   D++  D         E       +  L   +  LN RE+++ 
Sbjct: 304 VSLETPI--GEEEDSHLGDFIPDDD---ALAPSEAAAYSMLKEQLLEVLDSLNEREKKVL 358

Query: 244 EARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           + R   E+    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 359 KLRFGLEDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 404


>gi|77406972|ref|ZP_00783989.1| RNA polymerase sigma-70 factor [Streptococcus agalactiae H36B]
 gi|77174413|gb|EAO77265.1| RNA polymerase sigma-70 factor [Streptococcus agalactiae H36B]
          Length = 369

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 84/276 (30%), Positives = 139/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE  LA    E GDL A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGVVPLLTNEEEKELAVAVAE-GDLMAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA++++++  +V  +        SL   I   
Sbjct: 215 -TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 361


>gi|315029422|gb|EFT41354.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX4000]
          Length = 368

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 80/276 (28%), Positives = 133/276 (48%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L   EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGRVQLLTAAEEVELALKI-EEGDQEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L         PE++ A   ++++   +V  +        SL   I   
Sbjct: 215 -TINKLIRIQRQLLQDLGREPTPEEIGA---EMDLPTEKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D       E    +  +  L   +  L  RE  +   R   +N  
Sbjct: 269 EEDDSHLGDFI---EDQDATSPAEHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDNGR 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 361


>gi|227904114|ref|ZP_04021919.1| RNA polymerase sigma factor RpoD [Lactobacillus acidophilus ATCC
           4796]
 gi|227868133|gb|EEJ75554.1| RNA polymerase sigma factor RpoD [Lactobacillus acidophilus ATCC
           4796]
          Length = 370

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 81/284 (28%), Positives = 135/284 (47%), Gaps = 13/284 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +    V     +  Y+ EI ++P+L   +E  LAKR  E GD  A   L  ++LRLVV I
Sbjct: 90  SAPSSVRMNDPVRMYLKEIGRVPLLTADQEIALAKRI-ESGDEEAKQELAEANLRLVVSI 148

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y G G+   +++ EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      +
Sbjct: 149 AKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTI 208

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I     +      L R++  L         PE++ A   ++N+  ++V  +        
Sbjct: 209 RIPVHMVE--TINKLIRIQRQLLQDLGREPTPEEIGA---EMNMPTNKVRDILKIAQEPV 263

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   I   +++ S   D++    D       +    +  +  L + +  L  RE  +  
Sbjct: 264 SLETPI--GEEDDSHLGDFI---EDKDATSPEQHASYEMLKEQLEQVLETLTDREENVLR 318

Query: 245 ARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R   ++    TLE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 319 LRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRS 362


>gi|229543825|ref|ZP_04432884.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacillus
           coagulans 36D1]
 gi|229324964|gb|EEN90640.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacillus
           coagulans 36D1]
          Length = 377

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 82/289 (28%), Positives = 141/289 (48%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++ +L   EE  LAKR  E GD  A  RL  ++LRL
Sbjct: 93  LNDLSVPPGVKINDPVRMYLKEIGRVDLLSADEEIELAKRI-EQGDEEAKRRLAEANLRL 151

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD ++G++ +TY+ WWI+ A+   I   
Sbjct: 152 VVSIAKRYVGRGMQFLDLIQEGNMGLIKAVEKFDYKKGYKFSTYATWWIRQAITRAIADQ 211

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    IA+++++S  +V  +    
Sbjct: 212 ARTIRIPVHMVE--TINKLIRVQRSLLQDLGREPTPE---EIAEEMDISPDKVREIIKIA 266

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D       +    +  +  L   +  L  RE 
Sbjct: 267 QEPVSLETPI--GEEDDSHLGDFI---EDQDATSPSDHAAYELLKEQLEDVLDTLTDREE 321

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 322 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 370


>gi|157803973|ref|YP_001492522.1| RNA polymerase factor sigma-32 [Rickettsia canadensis str. McKiel]
 gi|157785236|gb|ABV73737.1| hypothetical protein A1E_04050 [Rickettsia canadensis str. McKiel]
          Length = 296

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 147/287 (51%), Positives = 201/287 (70%), Gaps = 1/287 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M     ++ ++ E G   Y+ +I KIP L ++EE++LAK Y E  DL AAH+LVTSHL+L
Sbjct: 1   MTNNINALAISSESGFYSYLQKINKIPSLTQEEEFLLAKSYLEENDLKAAHKLVTSHLKL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIA GYR YGLPI+E+VSEGNIGLMQAVKKF+PE GFRL+TY+MWWIKAA+QEYIL+S
Sbjct: 61  VAKIASGYRTYGLPITELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKAAIQEYILKS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTA QK+LFF+L ++K  +  +    +  +  V IA +L VS +EV  MN R+
Sbjct: 121 WSLVKMGTTAAQKKLFFSLNKVKHKITNLYSRAITTDDFVQIADELGVSVNEVSEMNTRI 180

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D SLN  INS D  S +  + L       E + I K+    ++++L  +M +LN RE
Sbjct: 181 SGPDLSLNNSINSDDTESGELIELLPETRPTPEAMAINKQNYTTKKHLLASAMKILNDRE 240

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            RI   R+L++ P TL+ LSSE+ +S+ER+RQIE  AF+K+++ I K
Sbjct: 241 LRILTERKLKDTPKTLDILSSEYNISKERIRQIENTAFEKIKKFILK 287


>gi|223044379|ref|ZP_03614413.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Staphylococcus capitis SK14]
 gi|222442248|gb|EEE48359.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Staphylococcus capitis SK14]
          Length = 368

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 80/276 (28%), Positives = 137/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L  QEE  LAK+  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGRVNLLSAQEEIELAKKI-EQGDEVAKSRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 LFLDLIQEGNMGLIKAVEKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L      +  PE    I +++++   +V  +        SL   I   
Sbjct: 215 -TINKLIRVQRQLLQDLGRDPAPE---EIGEEMDLPPEKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D + Q   +    +  +  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGR 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 361


>gi|138896056|ref|YP_001126509.1| RNA polymerase sigma factor RpoD [Geobacillus thermodenitrificans
           NG80-2]
 gi|196248949|ref|ZP_03147649.1| RNA polymerase, sigma 70 subunit, RpoD family [Geobacillus sp.
           G11MC16]
 gi|134267569|gb|ABO67764.1| RNA polymerase sigma factor RpoD [Geobacillus thermodenitrificans
           NG80-2]
 gi|196211825|gb|EDY06584.1| RNA polymerase, sigma 70 subunit, RpoD family [Geobacillus sp.
           G11MC16]
          Length = 375

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 83/289 (28%), Positives = 143/289 (49%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++P+L  +EE  LAKR  E GD  A  RL  ++LRL
Sbjct: 91  LNDLSVPPGVKINDPVRMYLKEIGRVPLLSAEEEIELAKRI-EQGDEEAKRRLTEANLRL 149

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I   
Sbjct: 150 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQ 209

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    IA++++++  +V  +    
Sbjct: 210 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPTPE---EIAEEMDLTPEKVREILKIA 264

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D +     E    +  +  L   +  L  RE 
Sbjct: 265 QEPVSLETPI--GEEDDSHLGDFI---EDQEATSPSEHAAYELLKEQLEDVLDTLTDREE 319

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 320 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 368


>gi|125717671|ref|YP_001034804.1| RNA polymerase sigma factor RpoD [Streptococcus sanguinis SK36]
 gi|125497588|gb|ABN44254.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32),
           putative [Streptococcus sanguinis SK36]
 gi|324990502|gb|EGC22438.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK353]
 gi|324995458|gb|EGC27370.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK678]
 gi|325688386|gb|EGD30405.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK72]
 gi|325690016|gb|EGD32020.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK115]
 gi|325693940|gb|EGD35858.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK150]
 gi|327461509|gb|EGF07840.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK1]
 gi|327468857|gb|EGF14329.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK330]
 gi|327489365|gb|EGF21158.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK1058]
 gi|332361594|gb|EGJ39398.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK1056]
 gi|332363116|gb|EGJ40903.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK355]
 gi|332365901|gb|EGJ43657.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK1059]
          Length = 370

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 84/276 (30%), Positives = 139/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE  LA    E GDL A  RL  ++LRLVV IA  Y G G+
Sbjct: 98  DPVRMYLKEIGVVPLLSNEEEQELAI-LVEQGDLEAKQRLAEANLRLVVSIAKRYVGRGM 156

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 157 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 215

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA++++++  +V  +        SL   I   
Sbjct: 216 -TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSLETPI--G 269

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 270 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 326

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 327 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 362


>gi|156972625|ref|YP_001443532.1| RNA polymerase factor sigma-32 [Vibrio harveyi ATCC BAA-1116]
 gi|156524219|gb|ABU69305.1| hypothetical protein VIBHAR_00277 [Vibrio harveyi ATCC BAA-1116]
          Length = 285

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 112/284 (39%), Positives = 168/284 (59%), Gaps = 8/284 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++   + +  +  L  YI  +   PML  +EE  LA+R    G++ AA  L+ SHLR 
Sbjct: 1   MTKEAYPMALVTQDSLDSYIRSVNSYPMLTPEEERGLAERLHYKGEIDAAKGLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A GY GYGLP++++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VKI TT  Q++LFFNLR+ K  L    +      +V  +A++L V  SEV  M  RL
Sbjct: 121 WRIVKIATTKAQRKLFFNLRKSKKRLGWFNNG-----EVETVARELGVEPSEVREMESRL 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE---ERKNRRNMLTRSMSVLNP 237
           A  +S   +    D NS+ +   + Y  D    V    E      +  N L  +++ L+ 
Sbjct: 176 AAVDSTFDMPMDDDDNSNSYTAPMFYLEDKSSDVADNIEAANWETHTNNRLGHALASLDE 235

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R +RI  +R L ++  TL++L+ EF VS ER+RQ+E  A KK++
Sbjct: 236 RSQRIVRSRWLDDDKATLQDLADEFGVSAERIRQLEKNAMKKLK 279


>gi|312874241|ref|ZP_07734275.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LEAF 2052A-d]
 gi|311090311|gb|EFQ48721.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LEAF 2052A-d]
          Length = 382

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 81/288 (28%), Positives = 134/288 (46%), Gaps = 13/288 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N       V     +  Y+ EI ++P+L   +E  LAKR  E+ D  A   L  ++LRL
Sbjct: 98  LNDMTAPSSVRMNDPVRMYLKEIGRVPLLNADQEIDLAKRI-ENNDDDAKQELAEANLRL 156

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I   
Sbjct: 157 VVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQ 216

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE++ A   ++++S  +V  +    
Sbjct: 217 ARTIRIPVHMVE--TINKLIRIQRQLLQDLGREPTPEEIGA---EMDMSTDKVREILKIA 271

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D       +    +  +  L   +  L  RE 
Sbjct: 272 QEPVSLETPI--GEEDDSHLGDFI---EDKDATSPEQHASYELLKEQLEEVLDTLTDREE 326

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +   R    +    TLE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 327 NVLRLRFGLNDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRS 374


>gi|58337478|ref|YP_194063.1| RNA polymerase sigma factor RpoD [Lactobacillus acidophilus NCFM]
 gi|58254795|gb|AAV43032.1| RNA polymerase sigma factor [Lactobacillus acidophilus NCFM]
          Length = 356

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 81/284 (28%), Positives = 135/284 (47%), Gaps = 13/284 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +    V     +  Y+ EI ++P+L   +E  LAKR  E GD  A   L  ++LRLVV I
Sbjct: 76  SAPSSVRMNDPVRMYLKEIGRVPLLTADQEIALAKRI-ESGDEEAKQELAEANLRLVVSI 134

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y G G+   +++ EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      +
Sbjct: 135 AKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTI 194

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I     +      L R++  L         PE++ A   ++N+  ++V  +        
Sbjct: 195 RIPVHMVE--TINKLIRIQRQLLQDLGREPTPEEIGA---EMNMPTNKVRDILKIAQEPV 249

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   I   +++ S   D++    D       +    +  +  L + +  L  RE  +  
Sbjct: 250 SLETPI--GEEDDSHLGDFI---EDKDATSPEQHASYEMLKEQLEQVLETLTDREENVLR 304

Query: 245 ARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R   ++    TLE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 305 LRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRS 348


>gi|258446806|ref|ZP_05694960.1| transcription initiation factor sigma plaC [Staphylococcus aureus
           A6300]
 gi|257854381|gb|EEV77330.1| transcription initiation factor sigma plaC [Staphylococcus aureus
           A6300]
          Length = 368

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 81/276 (29%), Positives = 137/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L  QEE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGRVNLLSAQEEIELAKRI-EQGDEVAKSRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 LFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L      +  PE    I +++++   +V  +        SL   I   
Sbjct: 215 -TINKLIRVQRQLLQDLGRDPAPE---EIGEEMDLPAEKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D + Q   +    +  +  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGR 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 361


>gi|258437393|ref|ZP_05689377.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A9299]
 gi|257848598|gb|EEV72586.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus A9299]
          Length = 368

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 81/276 (29%), Positives = 137/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L  QEE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGRVNLLSAQEEIELAKRI-EQGDEVAKSRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 LFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L      +  PE    I +++++   +V  +        SL   I   
Sbjct: 215 -TINKLIRVQRQLLQDLGRDPAPE---EIGEEMDLPAEKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D + Q   +    +  +  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGR 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 361


>gi|90961886|ref|YP_535802.1| RNA polymerase sigma factor RpoD [Lactobacillus salivarius UCC118]
 gi|90821080|gb|ABD99719.1| RNA polymerase sigma factor [Lactobacillus salivarius UCC118]
          Length = 372

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 78/276 (28%), Positives = 133/276 (48%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L   EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 101 DPVRMYLKEIGRVNLLTADEEVALALKI-EEGDQEAKQRLAEANLRLVVSIAKRYVGRGM 159

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 160 SFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 218

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  +         PE++ A   ++++   +V  +        SL   I   
Sbjct: 219 -TINKLIRIQRQMLQDLGREPMPEEIGA---EMDMPTEKVREILKIAQEPVSLETPI--G 272

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D       E    +  +  L   +  L  RE  +   R   ++  
Sbjct: 273 EEDDSHLGDFI---EDQDATSPAEHAAYELLKEQLESVLDTLTDREENVLRLRFGLDDGR 329

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 330 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 365


>gi|29376087|ref|NP_815241.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis V583]
 gi|227518714|ref|ZP_03948763.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0104]
 gi|227553323|ref|ZP_03983372.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis HH22]
 gi|229545861|ref|ZP_04434586.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX1322]
 gi|229550053|ref|ZP_04438778.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis ATCC 29200]
 gi|255975889|ref|ZP_05426475.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis T2]
 gi|256619027|ref|ZP_05475873.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis ATCC 4200]
 gi|256762453|ref|ZP_05503033.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis T3]
 gi|256853088|ref|ZP_05558458.1| RNA polymerase sigma-43 factor [Enterococcus faecalis T8]
 gi|256958944|ref|ZP_05563115.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis DS5]
 gi|256961963|ref|ZP_05566134.1| sigma 42 [Enterococcus faecalis Merz96]
 gi|256965161|ref|ZP_05569332.1| sigma 42 [Enterococcus faecalis HIP11704]
 gi|257078975|ref|ZP_05573336.1| sigma 42 [Enterococcus faecalis JH1]
 gi|257082587|ref|ZP_05576948.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis E1Sol]
 gi|257085220|ref|ZP_05579581.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis Fly1]
 gi|257086781|ref|ZP_05581142.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis D6]
 gi|257089848|ref|ZP_05584209.1| RNA polymerase sigma factor rpoD [Enterococcus faecalis CH188]
 gi|257416057|ref|ZP_05593051.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis AR01/DG]
 gi|257419260|ref|ZP_05596254.1| RNA polymerase sigma factor rpoD [Enterococcus faecalis T11]
 gi|257422656|ref|ZP_05599646.1| RNA polymerase sigma-43 factor [Enterococcus faecalis X98]
 gi|293383032|ref|ZP_06628950.1| RNA polymerase sigma-43 factor [Enterococcus faecalis R712]
 gi|293389479|ref|ZP_06633936.1| RNA polymerase sigma-43 factor [Enterococcus faecalis S613]
 gi|294779115|ref|ZP_06744526.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis PC1.1]
 gi|300860473|ref|ZP_07106560.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TUSoD Ef11]
 gi|307271055|ref|ZP_07552338.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX4248]
 gi|307273262|ref|ZP_07554508.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0855]
 gi|307274998|ref|ZP_07556161.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX2134]
 gi|307278111|ref|ZP_07559195.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0860]
 gi|307289068|ref|ZP_07569024.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0109]
 gi|307292033|ref|ZP_07571902.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0411]
 gi|312900723|ref|ZP_07760020.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0470]
 gi|312903270|ref|ZP_07762450.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0635]
 gi|312907497|ref|ZP_07766488.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis DAPTO 512]
 gi|312910115|ref|ZP_07768962.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis DAPTO 516]
 gi|312951455|ref|ZP_07770352.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0102]
 gi|30179886|sp|P52329|RPOD_ENTFA RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-42
 gi|29343549|gb|AAO81311.1| RNA polymerase sigma-43 factor [Enterococcus faecalis V583]
 gi|227073834|gb|EEI11797.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0104]
 gi|227177552|gb|EEI58524.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis HH22]
 gi|229304757|gb|EEN70753.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis ATCC 29200]
 gi|229309016|gb|EEN75003.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX1322]
 gi|255968761|gb|EET99383.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis T2]
 gi|256598554|gb|EEU17730.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis ATCC 4200]
 gi|256683704|gb|EEU23399.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis T3]
 gi|256711547|gb|EEU26585.1| RNA polymerase sigma-43 factor [Enterococcus faecalis T8]
 gi|256949440|gb|EEU66072.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis DS5]
 gi|256952459|gb|EEU69091.1| sigma 42 [Enterococcus faecalis Merz96]
 gi|256955657|gb|EEU72289.1| sigma 42 [Enterococcus faecalis HIP11704]
 gi|256987005|gb|EEU74307.1| sigma 42 [Enterococcus faecalis JH1]
 gi|256990617|gb|EEU77919.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis E1Sol]
 gi|256993250|gb|EEU80552.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis Fly1]
 gi|256994811|gb|EEU82113.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis D6]
 gi|256998660|gb|EEU85180.1| RNA polymerase sigma factor rpoD [Enterococcus faecalis CH188]
 gi|257157885|gb|EEU87845.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis ARO1/DG]
 gi|257161088|gb|EEU91048.1| RNA polymerase sigma factor rpoD [Enterococcus faecalis T11]
 gi|257164480|gb|EEU94440.1| RNA polymerase sigma-43 factor [Enterococcus faecalis X98]
 gi|291079697|gb|EFE17061.1| RNA polymerase sigma-43 factor [Enterococcus faecalis R712]
 gi|291081096|gb|EFE18059.1| RNA polymerase sigma-43 factor [Enterococcus faecalis S613]
 gi|294453840|gb|EFG22231.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis PC1.1]
 gi|295112959|emb|CBL31596.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Enterococcus sp. 7L76]
 gi|300849512|gb|EFK77262.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TUSoD Ef11]
 gi|306497031|gb|EFM66579.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0411]
 gi|306499777|gb|EFM69138.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0109]
 gi|306505508|gb|EFM74694.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0860]
 gi|306508446|gb|EFM77553.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX2134]
 gi|306510247|gb|EFM79271.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0855]
 gi|306512553|gb|EFM81202.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX4248]
 gi|310626525|gb|EFQ09808.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis DAPTO 512]
 gi|310630611|gb|EFQ13894.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0102]
 gi|310633146|gb|EFQ16429.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0635]
 gi|311289388|gb|EFQ67944.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis DAPTO 516]
 gi|311292204|gb|EFQ70760.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0470]
 gi|315027303|gb|EFT39235.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX2137]
 gi|315033932|gb|EFT45864.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0017]
 gi|315036941|gb|EFT48873.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0027]
 gi|315144454|gb|EFT88470.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX2141]
 gi|315147227|gb|EFT91243.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX4244]
 gi|315150574|gb|EFT94590.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0012]
 gi|315152521|gb|EFT96537.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0031]
 gi|315155799|gb|EFT99815.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0043]
 gi|315158034|gb|EFU02051.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0312]
 gi|315160483|gb|EFU04500.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0645]
 gi|315163977|gb|EFU07994.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX1302]
 gi|315169073|gb|EFU13090.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX1341]
 gi|315169690|gb|EFU13707.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX1342]
 gi|315172348|gb|EFU16365.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX1346]
 gi|315575904|gb|EFU88095.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0309B]
 gi|315577570|gb|EFU89761.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0630]
 gi|315580556|gb|EFU92747.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX0309A]
 gi|327535095|gb|AEA93929.1| RNA polymerase sigma factor rpoD [Enterococcus faecalis OG1RF]
 gi|329571347|gb|EGG53034.1| RNA polymerase sigma factor RpoD [Enterococcus faecalis TX1467]
          Length = 368

 Score =  269 bits (688), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 79/276 (28%), Positives = 133/276 (48%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L   EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGRVQLLTAAEEVELALKI-EEGDQEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L         PE++ A   ++++   +V  +        SL   I   
Sbjct: 215 -TINKLIRIQRQLLQDLGREPTPEEIGA---EMDLPTEKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D       E    +  +  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDQDATSPAEHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGR 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 361


>gi|297584635|ref|YP_003700415.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacillus
           selenitireducens MLS10]
 gi|297143092|gb|ADH99849.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacillus
           selenitireducens MLS10]
          Length = 371

 Score =  268 bits (687), Expect = 4e-70,   Method: Composition-based stats.
 Identities = 81/289 (28%), Positives = 142/289 (49%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   +     +  Y+ EI ++P+L  +EE  LAKR  E  D  A  RL  ++LRL
Sbjct: 87  LNDLSVPPGIKINDPVRMYLKEIGRVPLLSAKEEVELAKRIEED-DEEAKRRLAEANLRL 145

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 146 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYNKGFKFSTYATWWIRQAITRAIADQ 205

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE+V   +K++ ++  +V  +    
Sbjct: 206 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPTPEEV---SKEMELTPDKVREILKIA 260

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D +     +    +  +  L   +  L  RE 
Sbjct: 261 QEPVSLETPI--GEEDDSHLGDFI---EDQEALAPSDAAAYELLKEQLEDVLDTLTDREE 315

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 316 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 364


>gi|288555754|ref|YP_003427689.1| RNA polymerase sigma factor RpoD [Bacillus pseudofirmus OF4]
 gi|288546914|gb|ADC50797.1| RNA polymerase sigma factor SigD [Bacillus pseudofirmus OF4]
          Length = 372

 Score =  268 bits (687), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 83/289 (28%), Positives = 144/289 (49%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   +     +  Y+ EI ++P+L  QEE  LAKR  E GD  A  RL  ++LRL
Sbjct: 88  LNDLSVPPGIKINDPVRMYLKEIGRVPLLSAQEEIELAKRI-EQGDEEAKRRLAEANLRL 146

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD E+G++ +TY+ WWI+ A+   I   
Sbjct: 147 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYEKGYKFSTYATWWIRQAITRAIADQ 206

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE+V   A+++ ++  +V  +    
Sbjct: 207 ARTIRIPVHMVE--TINKLIRVQRQLLQDFGREPTPEEV---AEEMELTPEKVREILKIA 261

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D +     +    +  +  L   +  L  RE 
Sbjct: 262 QEPVSLETPI--GEEDDSHLGDFI---EDQEALAPSDAAAYELLKEQLEDVLDTLTDREE 316

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 317 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 365


>gi|226311661|ref|YP_002771555.1| RNA polymerase sigma factor [Brevibacillus brevis NBRC 100599]
 gi|226094609|dbj|BAH43051.1| RNA polymerase sigma factor [Brevibacillus brevis NBRC 100599]
          Length = 376

 Score =  268 bits (687), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 80/276 (28%), Positives = 136/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++P+L  +EE  LA+R  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 105 DPVRMYLKEIGRVPLLSAEEEIKLAQRI-EQGDEEAKRRLAEANLRLVVSIAKRYVGRGM 163

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 164 LFLDLIQEGNMGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 222

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R+   L         PE    IA+K++++  +V  +        SL   I   
Sbjct: 223 -TINKLIRVSRQLLQELGREPMPE---EIAEKMDLTPEKVREIMKIAQEPVSLETPI--G 276

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D       +    +  +  L   +  L  RE  +   R   ++  
Sbjct: 277 EEDDSHLGDFI---EDQDALEPSDAAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGR 333

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 334 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 369


>gi|167772125|ref|ZP_02444178.1| hypothetical protein ANACOL_03499 [Anaerotruncus colihominis DSM
           17241]
 gi|167665923|gb|EDS10053.1| hypothetical protein ANACOL_03499 [Anaerotruncus colihominis DSM
           17241]
          Length = 361

 Score =  268 bits (687), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 80/280 (28%), Positives = 137/280 (48%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           +N +  +  Y+ EI ++P+L   EE  LA R  + GD+ A  RL  ++LRLVV IA  Y 
Sbjct: 86  INIDDPVKVYLKEIGRVPLLSADEEIDLAVRMAQ-GDIDARKRLSEANLRLVVSIAKRYV 144

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I   
Sbjct: 145 GRGMQFLDLIQEGNLGLIKAVEKFDHTKGFKFSTYATWWIRQAITRAIADQARTIRIPVH 204

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      + ++K     +   N        I+ +L++   +V  +        SL   
Sbjct: 205 MVE-----TINKVKKVSSLLLHKNGHEPTAEEISAELDMPVDKVREIMRVAQEPVSLETP 259

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++  +                 R  L+  +  L PRE ++   R   
Sbjct: 260 I--GEEEDSHLGDFIPDEDAPAPDT---AASHTLLREQLSEVLQTLTPREEKVLRLRFGL 314

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 315 EDGRSRTLEEVGREFNVTRERIRQIEAKALRKLRHPSRSK 354


>gi|332686632|ref|YP_004456406.1| RNA polymerase sigma factor RpoD [Melissococcus plutonius ATCC
           35311]
 gi|332370641|dbj|BAK21597.1| RNA polymerase sigma factor RpoD [Melissococcus plutonius ATCC
           35311]
          Length = 369

 Score =  268 bits (687), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 79/276 (28%), Positives = 135/276 (48%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L  +EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 98  DPVRMYLKEIGRVQLLTAEEEVELALKI-EEGDQEAKQRLAEANLRLVVSIAKRYVGRGM 156

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 157 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 215

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L         PE++ A   ++++   +V  +        SL   I   
Sbjct: 216 -TINKLIRIQRQLLQDLGREPTPEEIGA---EMDLPTEKVREILKIAQEPVSLETPI--G 269

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D +     E    +  +  L   +  L  RE  +   R   ++  
Sbjct: 270 EEDDSHLGDFI---EDQEATSPAEHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGR 326

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 327 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 362


>gi|225570457|ref|ZP_03779482.1| hypothetical protein CLOHYLEM_06558 [Clostridium hylemonae DSM
           15053]
 gi|225160654|gb|EEG73273.1| hypothetical protein CLOHYLEM_06558 [Clostridium hylemonae DSM
           15053]
          Length = 370

 Score =  268 bits (687), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 86/279 (30%), Positives = 137/279 (49%), Gaps = 13/279 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ E  +  Y+ EI K+P+L   EE  LAKR  + GD  A  RL  ++LRLVV IA  Y 
Sbjct: 95  ISIEDPVRMYLKEIGKVPLLTADEEVDLAKRMAD-GDEEAKKRLAEANLRLVVSIAKRYV 153

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I   
Sbjct: 154 GRGMLFLDLIQEGNLGLIKAVEKFDYHKGFKFSTYATWWIRQAITRAIADQARTIRIPVH 213

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L         PE    IA +L++    V  +        SL   
Sbjct: 214 MVE--TINKLIRVSRQLLQELGREPTPE---EIAAELDMPVERVREILKISQEPVSLETP 268

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++  D      V  E   +   +  L   +  L  RE+++   R   
Sbjct: 269 I--GEEEDSHLGDFIQDD---NVPVPAEAAAQTLLKEQLDEVLDTLTEREQKVLRLRFGM 323

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +    TLE +  EF+V+RER+RQIEA+A +K++   + 
Sbjct: 324 NDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRS 362


>gi|167750934|ref|ZP_02423061.1| hypothetical protein EUBSIR_01919 [Eubacterium siraeum DSM 15702]
 gi|167656113|gb|EDS00243.1| hypothetical protein EUBSIR_01919 [Eubacterium siraeum DSM 15702]
 gi|291557421|emb|CBL34538.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Eubacterium siraeum
           V10Sc8a]
          Length = 358

 Score =  268 bits (687), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 80/277 (28%), Positives = 137/277 (49%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI ++P+L  +EE  LA R  + GD  A  RL  ++LRLVV IA  Y G G
Sbjct: 86  DDPVKIYLKEIGRVPLLTAEEEIELATRMAQ-GDKYARKRLSEANLRLVVSIAKRYVGRG 144

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I     +
Sbjct: 145 MQFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRSIADQARTIRIPVHMVE 204

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 + ++K     +   N        IA +L ++   V  +        SL   I  
Sbjct: 205 -----TITKVKKVSSQLLHENGHEPTPQEIADRLGITVDRVREILRISQDPVSLETPI-- 257

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN- 251
            ++  S   D++  +             R   +  L+  +  L PRE ++   R   E+ 
Sbjct: 258 GEEEDSHLGDFIPDEDAPAPAE---AASRTLLKEQLSEILGTLTPREEKVLRLRFGLEDG 314

Query: 252 -PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            P TLE +  EF+V+RER+RQIEA+A +K++   + +
Sbjct: 315 RPRTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSK 351


>gi|291531112|emb|CBK96697.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Eubacterium siraeum 70/3]
          Length = 358

 Score =  268 bits (687), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 80/277 (28%), Positives = 137/277 (49%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI ++P+L  +EE  LA R  + GD  A  RL  ++LRLVV IA  Y G G
Sbjct: 86  DDPVKIYLKEIGRVPLLTAEEEIELATRMAQ-GDKYARKRLSEANLRLVVSIAKRYVGRG 144

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I     +
Sbjct: 145 MQFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRSIADQARTIRIPVHMVE 204

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 + ++K     +   N        IA +L ++   V  +        SL   I  
Sbjct: 205 -----TITKVKKVSSQLLHENGHEPTPQEIADRLGITVDRVREILRISQDPVSLETPI-- 257

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN- 251
            ++  S   D++  +             R   +  L+  +  L PRE ++   R   E+ 
Sbjct: 258 GEEEDSHLGDFIPDEDAPAPAE---AASRTLLKEQLSEILGTLTPREEKVLRLRFGLEDG 314

Query: 252 -PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            P TLE +  EF+V+RER+RQIEA+A +K++   + +
Sbjct: 315 RPRTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSK 351


>gi|319947289|ref|ZP_08021522.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           australis ATCC 700641]
 gi|319746531|gb|EFV98791.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           australis ATCC 700641]
          Length = 370

 Score =  268 bits (687), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 84/276 (30%), Positives = 139/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE  LA    E GDL A  RL  ++LRLVV IA  Y G G+
Sbjct: 98  DPVRMYLKEIGVVPLLTNEEEQELAI-LVEQGDLEAKQRLAEANLRLVVSIAKRYVGRGM 156

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 157 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 215

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA++++++  +V  +        SL   I   
Sbjct: 216 -TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSLETPI--G 269

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 270 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 326

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 327 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 362


>gi|254556820|ref|YP_003063237.1| RNA polymerase sigma factor RpoD [Lactobacillus plantarum JDM1]
 gi|254045747|gb|ACT62540.1| RNA polymerase sigma factor RpoD [Lactobacillus plantarum JDM1]
          Length = 368

 Score =  268 bits (687), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 79/276 (28%), Positives = 133/276 (48%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L   EE  LA R  E GD SA   L  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGRVDLLTADEEVALALRI-EQGDESAKQELAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L         PE++ A   ++++   +V  +        SL   I   
Sbjct: 215 -TINKLIRIQRQLLQDLGREPTPEEIGA---EMDMPTEKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D       +    +  +  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDQDATSPADAAAYELLKEQLEGVLDTLTNREENVLRLRFGLDDGR 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 361


>gi|194467797|ref|ZP_03073783.1| RNA polymerase, sigma 70 subunit, RpoD family [Lactobacillus
           reuteri 100-23]
 gi|194452650|gb|EDX41548.1| RNA polymerase, sigma 70 subunit, RpoD family [Lactobacillus
           reuteri 100-23]
          Length = 380

 Score =  268 bits (687), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 81/289 (28%), Positives = 136/289 (47%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M   +    V     +  Y+ EI ++ +L   EE  LA R  E GD  A   L  ++LRL
Sbjct: 96  MKDTSAPTGVKINDPVRMYLKEIGRVNLLTADEEVQLALRI-EKGDEVAKQELAEANLRL 154

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GLM+AV+KFD  RGF+ +TY+ WWI+ A+   I   
Sbjct: 155 VVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRRGFKFSTYATWWIRQAITRAIADQ 214

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE++ A   ++++   +V ++    
Sbjct: 215 ARTIRIPVHMVE--TINKLIRIQRQLLQDLGREPLPEEIGA---EMDMPTEKVRNILKIA 269

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D       +    +  +  L   +  L  RE 
Sbjct: 270 QEPVSLETPI--GEEDDSHLGDFI---EDQDATSPADHAAYEMMKKQLENVLDTLTDREE 324

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 325 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 373


>gi|104774139|ref|YP_619119.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
 gi|103423220|emb|CAI98048.1| RNA polymerase sigma factor RpoD (Sigma-A) [Lactobacillus
           delbrueckii subsp. bulgaricus ATCC 11842]
          Length = 372

 Score =  268 bits (687), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 83/288 (28%), Positives = 135/288 (46%), Gaps = 13/288 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N       +     +  Y+ EI +  +L  +EE  LAKR  E GD  A   L  ++LRL
Sbjct: 88  LNNMAAPTGMKMNDPVRMYLKEIGRFNLLTSEEEVALAKRI-EAGDEEAKQELAEANLRL 146

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I   
Sbjct: 147 VVSIAKRYVGRGMNFLDLIQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQ 206

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L      + +PE    IA ++++   +V       
Sbjct: 207 ARTIRIPVHMVE--TINKLIRIQRQLLQDLGRDPEPE---EIAAEMDLPVKKVREALKVA 261

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D       +    +  R+ L   +  L  RE 
Sbjct: 262 QEPVSLETPI--GEEDDSHLGDFI---EDKDTTSPEQHAASEMLRDQLAEVLDTLTDREE 316

Query: 241 RIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +   R   ++  P TLE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 317 NVLRLRFGLDDGNPRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRS 364


>gi|769798|emb|CAA60113.1| sigma 42 [Enterococcus faecalis]
          Length = 368

 Score =  268 bits (687), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 79/276 (28%), Positives = 134/276 (48%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L   EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGRVQLLTAAEEVELALKI-EEGDQEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++ +L         PE++ A   ++++   +V  +        SL   I   
Sbjct: 215 -TINKLIRMQRNLLQDLGREPTPEEIGA---EMDLPTEKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D       E    +  +  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDQDATSPAEHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGR 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 361


>gi|259500591|ref|ZP_05743493.1| RNA polymerase sigma factor rpoD [Lactobacillus iners DSM 13335]
 gi|302191282|ref|ZP_07267536.1| RNA polymerase sigma factor RpoD [Lactobacillus iners AB-1]
 gi|309805231|ref|ZP_07699283.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LactinV
           09V1-c]
 gi|309807583|ref|ZP_07701535.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LactinV
           01V1-a]
 gi|312871770|ref|ZP_07731858.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LEAF 3008A-a]
 gi|312875648|ref|ZP_07735649.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LEAF 2053A-b]
 gi|325912054|ref|ZP_08174452.1| RNA polymerase sigma factor RpoD [Lactobacillus iners UPII 143-D]
 gi|259167975|gb|EEW52470.1| RNA polymerase sigma factor rpoD [Lactobacillus iners DSM 13335]
 gi|308165465|gb|EFO67696.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LactinV
           09V1-c]
 gi|308169189|gb|EFO71255.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LactinV
           01V1-a]
 gi|311088902|gb|EFQ47345.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LEAF 2053A-b]
 gi|311092712|gb|EFQ51068.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LEAF 3008A-a]
 gi|325476004|gb|EGC79172.1| RNA polymerase sigma factor RpoD [Lactobacillus iners UPII 143-D]
          Length = 382

 Score =  268 bits (687), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 81/288 (28%), Positives = 134/288 (46%), Gaps = 13/288 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N       V     +  Y+ EI ++P+L   +E  LAKR  E+ D  A   L  ++LRL
Sbjct: 98  LNDMTAPSSVRMNDPVRMYLKEIGRVPLLNADQEIDLAKRI-ENNDDEAKQELAEANLRL 156

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I   
Sbjct: 157 VVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQ 216

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE++ A   ++++S  +V  +    
Sbjct: 217 ARTIRIPVHMVE--TINKLIRIQRQLLQDLGREPTPEEIGA---EMDMSTDKVREILKIA 271

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D       +    +  +  L   +  L  RE 
Sbjct: 272 QEPVSLETPI--GEEDDSHLGDFI---EDKDATSPEQHASYELLKEQLEEVLDTLTDREE 326

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +   R    +    TLE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 327 NVLRLRFGLNDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRS 374


>gi|227890913|ref|ZP_04008718.1| RNA polymerase sigma factor RpoD [Lactobacillus salivarius ATCC
           11741]
 gi|227867322|gb|EEJ74743.1| RNA polymerase sigma factor RpoD [Lactobacillus salivarius ATCC
           11741]
          Length = 372

 Score =  268 bits (687), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 78/276 (28%), Positives = 133/276 (48%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L   EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 101 DPVRMYLKEIGRVNLLTADEEVALALKI-EEGDQEAKQRLAEANLRLVVSIAKRYVGRGM 159

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 160 SFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 218

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  +         PE++ A   ++++   +V  +        SL   I   
Sbjct: 219 -TINKLIRIQRQMLQDLGREPMPEEIGA---EMDMPTEKVREILKIAQEPVSLETPI--G 272

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D       E    +  +  L   +  L  RE  +   R   ++  
Sbjct: 273 EEDDSHLGDFI---EDQDATSPAEHAAYELLKEQLESVLDTLTDREENVLRLRFGLDDGR 329

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 330 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 365


>gi|160937106|ref|ZP_02084469.1| hypothetical protein CLOBOL_01996 [Clostridium bolteae ATCC
           BAA-613]
 gi|158440007|gb|EDP17755.1| hypothetical protein CLOBOL_01996 [Clostridium bolteae ATCC
           BAA-613]
          Length = 378

 Score =  268 bits (687), Expect = 5e-70,   Method: Composition-based stats.
 Identities = 83/280 (29%), Positives = 138/280 (49%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V+ E  +  Y+ EI KIP+L  ++E  LAK+  E GD  A  RL  S+LRLVV IA  Y 
Sbjct: 102 VSLEDPVRMYLKEIGKIPLLGMEDEVELAKKM-ELGDPEARKRLAESNLRLVVSIAKRYV 160

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 161 GRGMQFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 220

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      + RL    + +     +      IA +L++    V  +        SL   
Sbjct: 221 MVE-----TINRLVRTSRQLLQELGREPTTEEIAARLDLPVERVSEIMKMSQEPVSLETP 275

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++  D      V  +          L   +  L  RE+++   R   
Sbjct: 276 I--GEEEDSHLGDFIQDD---NVLVPQDAAAFTLLHEQLMEVLLTLTEREQKVLRLRFGL 330

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  P TLE +  +F V+RER+RQIEA+A +K++   + +
Sbjct: 331 DDGRPRTLEEVGKQFNVTRERIRQIEAKALRKLRHPSRSK 370


>gi|83589488|ref|YP_429497.1| RNA polymerase sigma factor RpoD [Moorella thermoacetica ATCC
           39073]
 gi|83572402|gb|ABC18954.1| RNA polymerase, sigma 70 subunit, RpoD [Moorella thermoacetica ATCC
           39073]
          Length = 361

 Score =  268 bits (687), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 87/280 (31%), Positives = 140/280 (50%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V  +  +  Y+ EI ++P+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y 
Sbjct: 86  VAIDDPVRMYLKEIGRVPLLTPEEEIELAKRM-EAGDEEAKRRLAEANLRLVVSIAKRYV 144

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 145 GRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 204

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R++  L         PE    IA ++++    V  +        SL   
Sbjct: 205 MVE--TINKLIRVQRQLLQELGREPTPE---EIAHEMDIPVERVREIQKIAQEPVSLETP 259

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++    D   Q   E       R  L   ++ L PRE+R+   R   
Sbjct: 260 I--GEEEDSHLGDFI---EDEDAQAPAEAASFMLLREQLEEVLNSLTPREKRVLRLRFGL 314

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 315 DDGRARTLEEVGQEFGVTRERIRQIEAKALRKLRHPSRSK 354


>gi|163803403|ref|ZP_02197278.1| RNA polymerase sigma factor [Vibrio sp. AND4]
 gi|159172807|gb|EDP57652.1| RNA polymerase sigma factor [Vibrio sp. AND4]
          Length = 285

 Score =  268 bits (686), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 113/284 (39%), Positives = 168/284 (59%), Gaps = 8/284 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  S+ +  +  L  YI      PML   EE  LA+R    G++ AA  L+ SHLR 
Sbjct: 1   MTKEAYSMALVTQDSLDSYIRSANSYPMLTADEERGLAERLHYKGEIDAAKGLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A GY GYGLP++++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L    +      +V  +A++L V  SEV  M  RL
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKSKKRLGWFNNG-----EVETVARELGVEPSEVREMESRL 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE---ERKNRRNMLTRSMSVLNP 237
           A  +S   +    D NS+ +   +VY  D    V    E      +  N L  +++ L+ 
Sbjct: 176 AAVDSTFDMPMDDDDNSNSYTAPMVYLEDKSSDVADNIEAANWEAHTNNRLGHALASLDE 235

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R +RI  +R L ++  TL++L+ EF VS ER+RQ+E  A KK++
Sbjct: 236 RSQRIVRSRWLDDDKSTLQDLADEFGVSAERIRQLEKNAMKKLK 279


>gi|324993240|gb|EGC25160.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK405]
          Length = 370

 Score =  268 bits (686), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 84/276 (30%), Positives = 139/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE  LA    E GDL A  RL  ++LRLVV IA  Y G G+
Sbjct: 98  DPVRMYLKEIGVVPLLSNEEEQELAI-LVEQGDLEAKQRLAEANLRLVVSIAKRYVGRGM 156

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 157 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 215

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA++++++  +V  +        SL   I   
Sbjct: 216 -TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSLETPI--G 269

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 270 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 326

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 327 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 362


>gi|293365255|ref|ZP_06611972.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           oralis ATCC 35037]
 gi|306829363|ref|ZP_07462553.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus mitis
           ATCC 6249]
 gi|291316705|gb|EFE57141.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           oralis ATCC 35037]
 gi|304428449|gb|EFM31539.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus mitis
           ATCC 6249]
          Length = 369

 Score =  268 bits (686), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 84/283 (29%), Positives = 141/283 (49%), Gaps = 13/283 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S        +  Y+ EI  +P+L  +EE  LA    E GD+ A  RL  ++LRLVV IA 
Sbjct: 90  STSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAV-EAGDIEAKQRLAEANLRLVVSIAK 148

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y G G+   +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I
Sbjct: 149 RYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI 208

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
                +      L R + +L      +  PEQ   IA++++++  +V  +        SL
Sbjct: 209 PVHMVE--TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSL 263

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              I   +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R
Sbjct: 264 ETPI--GEEDDSHLGDFI---EDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLR 318

Query: 247 RLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              ++    TLE++   F V+RER+RQIEA+A +K+++  + +
Sbjct: 319 FGLDDGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRQPSRSK 361


>gi|190571331|ref|YP_001975689.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Culex
           quinquefasciatus Pel]
 gi|190357603|emb|CAQ55044.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Culex
           quinquefasciatus Pel]
          Length = 297

 Score =  268 bits (686), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 132/283 (46%), Positives = 198/283 (69%), Gaps = 2/283 (0%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           ++ VN    L +YI E+RK PML ++EE  LAK ++E+ D+S+AHRL+TSHL LVVKIAM
Sbjct: 7   NLCVNSSTNLMQYIAEVRKFPMLSQEEEVRLAKNWQEYQDISSAHRLITSHLNLVVKIAM 66

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            ++ YGL + ++V EGN+GLM AVKKF+P+ GFR +TY++WWI+A+M+++IL+SWSLVKI
Sbjct: 67  KFKNYGLLLMDLVMEGNMGLMHAVKKFNPDLGFRFSTYAVWWIEASMKDFILKSWSLVKI 126

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNN-LKPEQVVAIAKKLNVSESEVISMNCRLA-GDE 184
           GTT  Q+RLFF+LR++K  +   T+   L  E++ AI+ +L+VSE +V+ M+ RLA  D+
Sbjct: 127 GTTQAQRRLFFSLRKIKKRILQYTNRETLSKEEIKAISNELSVSEEDVVQMSYRLACKDQ 186

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SLN  I   D +  + QD +  +   QE      EE+  +  +L+ +++ LN R R IF 
Sbjct: 187 SLNNCIKIGDDSKKELQDMIPCNLVSQEVAYQNHEEKALKETILSNALASLNERSRDIFI 246

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +R L EN  TL+ LS ++ VSRER+RQ+  +A  KV++ I+ +
Sbjct: 247 SRYLSENTQTLDELSKKYCVSRERIRQLAEQAMSKVKQHIKSE 289


>gi|315924365|ref|ZP_07920587.1| DNA-directed RNA polymerase sigma subunit RpoD [Pseudoramibacter
           alactolyticus ATCC 23263]
 gi|315622244|gb|EFV02203.1| DNA-directed RNA polymerase sigma subunit RpoD [Pseudoramibacter
           alactolyticus ATCC 23263]
          Length = 396

 Score =  268 bits (686), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 83/287 (28%), Positives = 138/287 (48%), Gaps = 13/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +++++  VN    +  Y+ EI ++ +L   EE  +AKR    GD  A   L  ++LRLVV
Sbjct: 114 KEDLTENVNVNDPVRLYLKEIGRVSLLTADEEMAIAKRMA-AGDEDAKKELAEANLRLVV 172

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I     
Sbjct: 173 SIAKRYVGRGMSFLDLIQEGNLGLIKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQAR 232

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            ++I     +      L R+   L         P     I K++  SE +V  +      
Sbjct: 233 TIRIPVHMVE--TINKLIRVSRQLLQEYGREPTP---AEIGKEMGFSEDKVREIQKIAQD 287

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             SL   I   ++  S   D++  D         E       +  L   +S L  RE ++
Sbjct: 288 PVSLETPI--GEEEDSHLGDFIPDDE---APAPSEAASYALLKEQLIDVLSTLTDREEKV 342

Query: 243 FEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              R   ++    TLE +  EF+V+RER+RQIEA+A +K++   + +
Sbjct: 343 LRLRFGLDDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSK 389


>gi|282882556|ref|ZP_06291177.1| RNA polymerase sigma factor RpoD [Peptoniphilus lacrimalis 315-B]
 gi|281297698|gb|EFA90173.1| RNA polymerase sigma factor RpoD [Peptoniphilus lacrimalis 315-B]
          Length = 361

 Score =  268 bits (686), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 87/280 (31%), Positives = 142/280 (50%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ +  +  Y+ EI KIP+L   EE  +AKR  E+GD SA   L  ++LRLVV IA  Y 
Sbjct: 86  ISVDDPVRMYLKEIGKIPLLTGDEEVEIAKRM-ENGDNSAKKELAEANLRLVVSIAKRYV 144

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I   
Sbjct: 145 GRGMSFLDLIQEGNLGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVH 204

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R++  L      +  PE    IAK++N+   +V  +        SL   
Sbjct: 205 MVE--TINKLVRVQRQLVQELGRDPLPE---EIAKEMNIEVEKVREIQKIAQEPVSLETP 259

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++  +     Q   +       R  L+  +  L  RE+++   R   
Sbjct: 260 I--GEEEDSHLGDFIPDEEILSPQ---DAATFTLLREQLSTVLETLTDREKKVLTLRFGL 314

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 315 DDGRARTLEEVGKEFAVTRERIRQIEAKAIRKLRHPSRSK 354


>gi|322391830|ref|ZP_08065295.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           peroris ATCC 700780]
 gi|321145310|gb|EFX40706.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           peroris ATCC 700780]
          Length = 381

 Score =  268 bits (686), Expect = 6e-70,   Method: Composition-based stats.
 Identities = 84/283 (29%), Positives = 141/283 (49%), Gaps = 13/283 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S        +  Y+ EI  +P+L  +EE  LA    E GD+ A  RL  ++LRLVV IA 
Sbjct: 102 STSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAV-EAGDVEAKQRLAEANLRLVVSIAK 160

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y G G+   +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I
Sbjct: 161 RYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI 220

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
                +      L R + +L      +  PEQ   IA++++++  +V  +        SL
Sbjct: 221 PVHMVE--TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSL 275

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              I   +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R
Sbjct: 276 ETPI--GEEDDSHLGDFI---EDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLR 330

Query: 247 RLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              ++    TLE++   F V+RER+RQIEA+A +K+++  + +
Sbjct: 331 FGLDDGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRQPSRSK 373


>gi|292670108|ref|ZP_06603534.1| DNA-directed RNA polymerase sigma subunit RpoD [Selenomonas noxia
           ATCC 43541]
 gi|292648296|gb|EFF66268.1| DNA-directed RNA polymerase sigma subunit RpoD [Selenomonas noxia
           ATCC 43541]
          Length = 370

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 86/281 (30%), Positives = 140/281 (49%), Gaps = 13/281 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V+ +  +  Y+ EI  +P+L  +EE  LA+R  E GD  A HRL  ++LRLVV IA  Y 
Sbjct: 95  VSLDDPVRMYLKEIGHVPLLTAEEEVALAQRM-EAGDEEARHRLEEANLRLVVSIAKRYV 153

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 154 GRGMLFLDLIQEGNLGLLKAVEKFDYSKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 213

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L      +  PE+V   A+++ +S + V  +        SL   
Sbjct: 214 MVE--TINKLVRISRQLLQELGRDPHPEEV---AREMGISVARVHEIMKIAQEPVSLETP 268

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++    D       E       R  L   +  L  RE+ +   R   
Sbjct: 269 I--GEEEDSHLGDFI---EDEAAPAPAEAASFMLLREQLEEVLETLTDREKNVLRLRFGL 323

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           E+    TLE +   F V+RER+RQIEA+A +K++   + +V
Sbjct: 324 EDGRSRTLEEVGQSFGVTRERIRQIEAKALRKLRHPSRSKV 364


>gi|270292885|ref|ZP_06199096.1| RNA polymerase sigma-70 factor [Streptococcus sp. M143]
 gi|306825379|ref|ZP_07458719.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus sp.
           oral taxon 071 str. 73H25AP]
 gi|315613017|ref|ZP_07887928.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis ATCC 49296]
 gi|322374450|ref|ZP_08048964.1| RNA polymerase sigma-70 factor [Streptococcus sp. C300]
 gi|331266528|ref|YP_004326158.1| RNA polymerase sigma factor RpoD (sigma-70 factor, Sigma-A)
           [Streptococcus oralis Uo5]
 gi|270278864|gb|EFA24710.1| RNA polymerase sigma-70 factor [Streptococcus sp. M143]
 gi|304432317|gb|EFM35293.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus sp.
           oral taxon 071 str. 73H25AP]
 gi|315315127|gb|EFU63168.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis ATCC 49296]
 gi|321279950|gb|EFX56989.1| RNA polymerase sigma-70 factor [Streptococcus sp. C300]
 gi|326683200|emb|CBZ00818.1| RNA polymerase sigma factor RpoD (sigma-70 factor, Sigma-A)
           [Streptococcus oralis Uo5]
          Length = 369

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 84/283 (29%), Positives = 141/283 (49%), Gaps = 13/283 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S        +  Y+ EI  +P+L  +EE  LA    E GD+ A  RL  ++LRLVV IA 
Sbjct: 90  STSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAV-EAGDIEAKQRLAEANLRLVVSIAK 148

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y G G+   +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I
Sbjct: 149 RYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI 208

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
                +      L R + +L      +  PEQ   IA++++++  +V  +        SL
Sbjct: 209 PVHMVE--TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSL 263

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              I   +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R
Sbjct: 264 ETPI--GEEDDSHLGDFI---EDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLR 318

Query: 247 RLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              ++    TLE++   F V+RER+RQIEA+A +K+++  + +
Sbjct: 319 FGLDDGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRQPSRSK 361


>gi|242373866|ref|ZP_04819440.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           epidermidis M23864:W1]
 gi|242348420|gb|EES40022.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           epidermidis M23864:W1]
          Length = 368

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 80/276 (28%), Positives = 137/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L  QEE  LAK+  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGRVNLLSAQEEIELAKKI-EQGDEIAKSRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 LFLDLIQEGNMGLIKAVEKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L      +  PE    I +++++   +V  +        SL   I   
Sbjct: 215 -TINKLIRVQRQLLQDLGRDPAPE---EIGEEMDLPPEKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D + Q   +    +  +  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGR 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 361


>gi|323352412|ref|ZP_08087547.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis VMC66]
 gi|322121844|gb|EFX93585.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis VMC66]
 gi|325696737|gb|EGD38625.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK160]
 gi|328945882|gb|EGG40032.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK1087]
          Length = 370

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 84/276 (30%), Positives = 139/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE  LA    E GDL A  RL  ++LRLVV IA  Y G G+
Sbjct: 98  DPVRMYLKEIGVVPLLSNEEEQELAI-LVEQGDLEAKQRLAEANLRLVVSIAKRYVGRGM 156

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 157 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 215

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA++++++  +V  +        SL   I   
Sbjct: 216 -TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSLETPI--G 269

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 270 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 326

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 327 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 362


>gi|313608766|gb|EFR84582.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           F2-208]
          Length = 374

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 83/288 (28%), Positives = 141/288 (48%), Gaps = 15/288 (5%)

Query: 4   KNMSIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
            +MS+    +I   +  Y+ EI ++ +L   EE  LAKR  E GD+ A  RL  ++LRLV
Sbjct: 91  TDMSVPPGVKINDPVRMYLKEIGRVDLLTADEEIALAKRI-EAGDIEAKGRLAEANLRLV 149

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA  Y G G+   +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I    
Sbjct: 150 VSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQA 209

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             ++I     +      L R++  L      +  PE    I +++++   +V  +     
Sbjct: 210 RTIRIPVHMVE--TINKLIRVQRSLLQDLGRDPSPE---EIGEEMDLPTEKVREILKIAQ 264

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              SL   I   +++ S   D++    D       +    +  +  L   +  L  RE  
Sbjct: 265 EPVSLETPI--GEEDDSHLGDFI---EDQDATSPSDHAAYELLKEQLEDVLDTLTDREEN 319

Query: 242 IFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 320 VLRLRFGLDDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSK 367


>gi|164688099|ref|ZP_02212127.1| hypothetical protein CLOBAR_01744 [Clostridium bartlettii DSM
           16795]
 gi|164602512|gb|EDQ95977.1| hypothetical protein CLOBAR_01744 [Clostridium bartlettii DSM
           16795]
          Length = 385

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 92/291 (31%), Positives = 154/291 (52%), Gaps = 15/291 (5%)

Query: 1   MNRKNMSII--VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHL 58
           M++ ++S+   ++ +  +  Y+ EI KIP+L+  EE   AKR  E GD  A  RLV ++L
Sbjct: 99  MDKIDLSLPKGISIDDPVRMYLKEIGKIPLLKPHEEIEYAKRMLE-GDEIAKQRLVEANL 157

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV IA  Y G G+   +++ EGN+GL++AV+KFD ERGF+ +TY+ WWI+ A+   I 
Sbjct: 158 RLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYERGFKFSTYATWWIRQAITRAIA 217

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
                ++I     +      L R+   L      + KPE    IAK++++SE +V  +  
Sbjct: 218 DQARTIRIPVHMVE--TINKLIRVSRQLLQELGRDPKPE---EIAKEMDMSEEKVREIMK 272

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
                 SL   I   ++  S   D++  +                 ++ +   +  LN R
Sbjct: 273 IAQDPVSLETPI--GEEEDSHLGDFIPDEDALAPAE---AAAYSLLKDQIEEVLGSLNER 327

Query: 239 ERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+++ + R   E+    TLE +  EF+V+RER+RQIEA+A +K++   + +
Sbjct: 328 EQKVLKLRFGLEDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSK 378


>gi|314933733|ref|ZP_07841098.1| RNA polymerase sigma factor RpoD [Staphylococcus caprae C87]
 gi|313653883|gb|EFS17640.1| RNA polymerase sigma factor RpoD [Staphylococcus caprae C87]
          Length = 368

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 80/276 (28%), Positives = 137/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L  QEE  LAK+  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGRVNLLSAQEEIELAKKI-EQGDEVAKSRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 LFLDLIQEGNMGLIKAVEKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L      +  PE    I +++++   +V  +        SL   I   
Sbjct: 215 -TINKLIRVQRQLLQDLGRDPAPE---EIGEEMDLPPEKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D + Q   +    +  +  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGR 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 361


>gi|34580656|ref|ZP_00142136.1| RNA polymerase sigma-32 factor [Rickettsia sibirica 246]
 gi|28262041|gb|EAA25545.1| RNA polymerase sigma-32 factor [Rickettsia sibirica 246]
          Length = 293

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 144/285 (50%), Positives = 198/285 (69%), Gaps = 1/285 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M     ++ ++ E G   Y+ +I KIP L ++EE +LAK Y E  DL AAH+LVTSHL+L
Sbjct: 1   MTNNINALAISSESGFYSYLQKINKIPSLTQEEELLLAKSYLEGNDLQAAHKLVTSHLKL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIA GYR YGLP++E+VSEGNIGLMQAVKKF+P  GFRL+TY+MWWIKAA+QEYIL+S
Sbjct: 61  VAKIASGYRTYGLPMTELVSEGNIGLMQAVKKFNPALGFRLSTYAMWWIKAAIQEYILKS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTA QK+LFF+L ++K  +  +    +  +  V IA +L VS +EV  MN R+
Sbjct: 121 WSLVKMGTTAAQKKLFFSLNKVKHKITNLYSRAITTDDFVQIADELGVSVNEVSEMNTRI 180

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D SLN  INS D  S +  + L       E + I K+   ++R +L+ +M +LN RE
Sbjct: 181 SGPDLSLNNSINSDDAESGELIELLPETRPTPETMAINKQNSTSKRQLLSNAMKILNDRE 240

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            RI   R+L + P TL+ LS+E+ +S+ER+RQIE  AF+K+++ I
Sbjct: 241 LRILTERKLTDTPKTLDILSNEYNISKERIRQIENTAFEKIKKFI 285


>gi|89100479|ref|ZP_01173341.1| RNA polymerase sigma factor [Bacillus sp. NRRL B-14911]
 gi|89084822|gb|EAR63961.1| RNA polymerase sigma factor [Bacillus sp. NRRL B-14911]
          Length = 374

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 83/289 (28%), Positives = 140/289 (48%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++ +L  QEE  LAKR  E GD  A  RL  ++LRL
Sbjct: 90  LNDLSVPPGVKINDPVRMYLKEIGRVDLLSAQEEISLAKRI-EEGDEEAKRRLAEANLRL 148

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I   
Sbjct: 149 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQ 208

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    IA+ ++++  +V  +    
Sbjct: 209 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPTPE---EIAEDMDLTPDKVREILKIA 263

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D       E    +  +  L   +  L  RE 
Sbjct: 264 QEPVSLETPI--GEEDDSHLGDFI---EDQDATSPSEHAAYELLKEQLEDVLDTLTDREE 318

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 319 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 367


>gi|291542495|emb|CBL15605.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Ruminococcus bromii
           L2-63]
          Length = 367

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 81/280 (28%), Positives = 139/280 (49%), Gaps = 13/280 (4%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
            V+ +  +  Y+ EI ++P+L   EE  LA R  + GD++A  RL  ++LRLVV IA  Y
Sbjct: 90  SVSVDDPVKVYLKEIGRVPLLSSDEEINLAIRIAD-GDVAAKQRLSEANLRLVVSIAKRY 148

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I  
Sbjct: 149 LGRGMQFLDLIQEGNLGLIKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPV 208

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
              +      + ++K     +   N        IA ++++   +V  +        SL  
Sbjct: 209 HMVE-----TINKVKKVQSQLLHQNGHEPSADEIAAEIDMPVDKVREIMRVAQEPVSLET 263

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            I   ++  S   D++            +       R  L+  +S L PRE ++ + R  
Sbjct: 264 PI--GEEEDSHLGDFIPD---NDAPAPADAASHTMLREQLSDVLSTLTPREAKVLKLRFG 318

Query: 249 QENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            E+    TLE +  EF V+RER+RQIEA+A +K++   + 
Sbjct: 319 LEDGRSRTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRS 358


>gi|257430984|ref|ZP_05607364.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus 68-397]
 gi|257278414|gb|EEV09050.1| RNA polymerase sigma factor rpoD [Staphylococcus aureus subsp.
           aureus 68-397]
          Length = 342

 Score =  268 bits (686), Expect = 7e-70,   Method: Composition-based stats.
 Identities = 81/276 (29%), Positives = 137/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L  QEE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 71  DPVRMYLKEIGRVNLLSAQEEIELAKRI-EQGDEVAKSRLAEANLRLVVSIAKRYVGRGM 129

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 130 LFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 188

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L      +  PE    I +++++   +V  +        SL   I   
Sbjct: 189 -TINKLIRVQRQLLQDLGRDPAPE---EIGEEMDLPAEKVREILKIAQEPVSLETPI--G 242

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D + Q   +    +  +  L   +  L  RE  +   R   ++  
Sbjct: 243 EEDDSHLGDFI---EDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGR 299

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 300 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 335


>gi|268610742|ref|ZP_06144469.1| RNA polymerase sigma factor RpoD [Ruminococcus flavefaciens FD-1]
          Length = 360

 Score =  268 bits (685), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 83/288 (28%), Positives = 140/288 (48%), Gaps = 16/288 (5%)

Query: 5   NMSIIVNG---EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
            M++   G   +  +  Y+ EI ++P+L  +EE  LA+R  + GD  A  RL  ++LRLV
Sbjct: 77  EMALSTEGIAIDDPVKIYLKEIGRVPLLTTEEEIELAQRMAK-GDRYAKKRLSEANLRLV 135

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I    
Sbjct: 136 VSIAKKYVGRGMQFLDLIQEGNLGLIKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQA 195

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             ++I     +      + ++K     +   N        IA KLN+   +V  +     
Sbjct: 196 RTIRIPVHMVE-----TITKVKKVSSQLLHENGHDPSPEEIADKLNMPVDKVREIMRVAQ 250

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              SL   I   ++  S   D++            E       +  L   +S L  RE +
Sbjct: 251 DPVSLETPI--GEEEDSHLGDFIPD---DDAPAPAEAASHTLLKEQLNEVLSTLTDREAK 305

Query: 242 IFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           + + R   E+    TLE +   F+V+RER+RQIEA+A +K++   + +
Sbjct: 306 VLKLRFGLEDGKSRTLEEVGQRFDVTRERIRQIEAKALRKLRHPSRSK 353


>gi|225174152|ref|ZP_03728151.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dethiobacter
           alkaliphilus AHT 1]
 gi|225169937|gb|EEG78732.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dethiobacter
           alkaliphilus AHT 1]
          Length = 372

 Score =  268 bits (685), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 88/276 (31%), Positives = 138/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI KIP+L   EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 101 DPVRMYLKEIGKIPLLSSDEEIALAKRM-EAGDEEAKRRLAEANLRLVVSIAKKYVGRGM 159

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 160 LFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 218

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R+   L         P+    IA  +N+SE  V  +        SL   I   
Sbjct: 219 -TINKLIRVSRQLVQELGREPAPD---EIAHVMNISEERVREILKIAQEPVSLETPI--G 272

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   Q   E    +  +  L   +  L PRE+++   R   E+  
Sbjct: 273 EEDDSHLGDFI---EDQDVQAPAEAAAFELLKEQLDDVLETLTPREKKVLTLRFGLEDGR 329

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++  ++ +
Sbjct: 330 SRTLEEVGQVFGVTRERIRQIEAKALRKLRHPMRSK 365


>gi|134300301|ref|YP_001113797.1| RNA polymerase sigma factor RpoD [Desulfotomaculum reducens MI-1]
 gi|134053001|gb|ABO50972.1| RNA polymerase, sigma 70 subunit, RpoD [Desulfotomaculum reducens
           MI-1]
          Length = 367

 Score =  268 bits (685), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 82/280 (29%), Positives = 140/280 (50%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           +  +  +  Y+ EI ++P+L  +EE  LAKR  E G+  A  RL  ++LRLVV IA  Y 
Sbjct: 92  IGIDDPVRMYLKEIGRVPLLSPEEEVDLAKRM-EQGEEEAKRRLAEANLRLVVSIAKRYV 150

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 151 GRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 210

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L         PE    IAK++++S  +V  +        SL   
Sbjct: 211 MVE--TINKLIRVSRQLLQELGREPSPE---EIAKEMDISGEKVREILKIAQEPVSLETP 265

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++    D   +   E+      R  L   +  L  RE+++   R   
Sbjct: 266 I--GEEEDSHLGDFI---EDADARAPAEEASFTLLREQLDEVLKTLTDREQKVLRLRFGL 320

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++    TLE +  +F V+RER+RQIEA+  +K++   + +
Sbjct: 321 DDGRARTLEEVGQKFGVTRERIRQIEAKTLRKLRHPSRSK 360


>gi|319745370|gb|EFV97681.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           agalactiae ATCC 13813]
          Length = 380

 Score =  268 bits (685), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 84/276 (30%), Positives = 139/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE  LA    E GDL A  RL  ++LRLVV IA  Y G G+
Sbjct: 108 DPVRMYLKEIGVVPLLTNEEEKELAVAVAE-GDLMAKQRLAEANLRLVVSIAKRYVGRGM 166

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 167 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 225

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA++++++  +V  +        SL   I   
Sbjct: 226 -TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSLETPI--G 279

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 280 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 336

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 337 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 372


>gi|266625476|ref|ZP_06118411.1| RNA polymerase sigma factor RpoD [Clostridium hathewayi DSM 13479]
 gi|288862622|gb|EFC94920.1| RNA polymerase sigma factor RpoD [Clostridium hathewayi DSM 13479]
          Length = 381

 Score =  268 bits (685), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 82/280 (29%), Positives = 142/280 (50%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           +  E  +  Y+ EI  +P+L   EE  LAKR +  GD  A  RL+ ++LRLVV IA  Y 
Sbjct: 107 IGTEDPVRMYLKEIGTVPLLSADEELRLAKR-KADGDEDAKERLIEANLRLVVSIAKRYT 165

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   ++V EGN+GL++ V+KFD  +G++L+TY+ WWI+ ++   +      +++   
Sbjct: 166 GRGMSFLDLVQEGNLGLIKGVEKFDYTKGYKLSTYATWWIRQSVTRALADQARTIRVPVH 225

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      + ++    + +T        V  +A  L++SE +V+ +        SL   
Sbjct: 226 MVE-----TINKMSKMQRKLTLELGYEPSVTELADALDMSEDKVMEIMQIAREPASLETP 280

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   +++ S   D++    D          E    R  +   +  L  RER++   R   
Sbjct: 281 I--GEEDDSNLGDFVA---DNNVVTPEGNVESVMLREHIDALLGDLKERERQVIVLRFGL 335

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+  P TLE +  EF V+RER+RQIEA+A +K++  ++ +
Sbjct: 336 EDGHPRTLEEVGKEFNVTRERIRQIEAKALRKLRNPVRSK 375


>gi|184155321|ref|YP_001843661.1| RNA polymerase sigma factor RpoD [Lactobacillus fermentum IFO 3956]
 gi|227514580|ref|ZP_03944629.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           fermentum ATCC 14931]
 gi|260662165|ref|ZP_05863061.1| RNA polymerase sigma factor RpoD [Lactobacillus fermentum 28-3-CHN]
 gi|183226665|dbj|BAG27181.1| RNA polymerase sigma factor RpoD [Lactobacillus fermentum IFO 3956]
 gi|227086991|gb|EEI22303.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           fermentum ATCC 14931]
 gi|260553548|gb|EEX26440.1| RNA polymerase sigma factor RpoD [Lactobacillus fermentum 28-3-CHN]
          Length = 380

 Score =  268 bits (685), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 78/286 (27%), Positives = 134/286 (46%), Gaps = 13/286 (4%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
                 +     +  Y+ EI ++ +L   EE  LA R  E GD +A   L  ++LRLVV 
Sbjct: 99  TTAPSSIKINDPVRMYLKEIGRVNLLTADEEVALALRI-EKGDETAKQELAEANLRLVVS 157

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y G G+   +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      
Sbjct: 158 IAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQART 217

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           ++I     +      L R++  L         PE++ A   ++++   +V  +       
Sbjct: 218 IRIPVHMVE--TINKLIRIQRQLLQDLGREPLPEEIGA---EMDMDTQKVRDILKISQEP 272

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SL   I   +++ S   D++    D       +    +  +  L   +  L  RE  + 
Sbjct: 273 VSLETPI--GEEDDSHLGDFI---EDHDATSPADHAAYEMMKKQLENVLDTLTDREENVL 327

Query: 244 EARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 328 RLRFGLDDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSK 373


>gi|329733136|gb|EGG69473.1| RNA polymerase sigma factor RpoD [Staphylococcus aureus subsp.
           aureus 21193]
          Length = 314

 Score =  268 bits (685), Expect = 8e-70,   Method: Composition-based stats.
 Identities = 81/276 (29%), Positives = 137/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L  QEE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 43  DPVRMYLKEIGRVNLLSAQEEIELAKRI-EQGDEVAKSRLAEANLRLVVSIAKRYVGRGM 101

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 102 LFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 160

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L      +  PE    I +++++   +V  +        SL   I   
Sbjct: 161 -TINKLIRVQRQLLQDLGRDPAPE---EIGEEMDLPAEKVREILKIAQEPVSLETPI--G 214

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D + Q   +    +  +  L   +  L  RE  +   R   ++  
Sbjct: 215 EEDDSHLGDFI---EDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGR 271

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 272 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 307


>gi|229586560|ref|YP_002845061.1| RNA polymerase factor sigma-32 [Rickettsia africae ESF-5]
 gi|228021610|gb|ACP53318.1| RNA polymerase sigma-32 factor [Rickettsia africae ESF-5]
          Length = 293

 Score =  268 bits (685), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 145/285 (50%), Positives = 199/285 (69%), Gaps = 1/285 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M     ++ ++ E G   Y+ +I KIP L ++EE +LAK Y E  DL AAH+LVTSHL+L
Sbjct: 1   MTNNINALAISSESGFYSYLQKINKIPSLTQEEELLLAKSYLEGNDLQAAHKLVTSHLKL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIA GYR YGLP++E+VSEGNIGLMQAVKKF+PE GFRL+TY+MWWIKAA+QEYIL+S
Sbjct: 61  VAKIASGYRTYGLPMTELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKAAIQEYILKS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTA QK+LFF+L ++K  +  +    +  +  V IA +L VS +EV  MN R+
Sbjct: 121 WSLVKMGTTAAQKKLFFSLNKVKHKITNLYSRTITTDDFVQIADELGVSVNEVSEMNTRI 180

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D SLN  INS D  S +  + L       E + I K+   ++R +L+ +M +LN RE
Sbjct: 181 SGPDLSLNNSINSDDAESGELIELLPETRPTPETMAINKQNSTSKRQLLSNAMKILNDRE 240

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            RI   R+L + P TL+ LS+E+ +S+ER+RQIE  AF+K+++ I
Sbjct: 241 LRILTERKLTDTPKTLDILSNEYNISKERIRQIENTAFEKIKKFI 285


>gi|322385457|ref|ZP_08059101.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           cristatus ATCC 51100]
 gi|321270195|gb|EFX53111.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           cristatus ATCC 51100]
          Length = 370

 Score =  268 bits (685), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 84/276 (30%), Positives = 139/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE  LA    E GDL A  RL  ++LRLVV IA  Y G G+
Sbjct: 98  DPVRMYLKEIGVVPLLSNEEEQELAI-LVEQGDLEAKQRLAEANLRLVVSIAKRYVGRGM 156

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 157 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 215

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA++++++  +V  +        SL   I   
Sbjct: 216 -TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSLETPI--G 269

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 270 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 326

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 327 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 362


>gi|300214611|gb|ADJ79027.1| RNA polymerase sigma factor [Lactobacillus salivarius CECT 5713]
          Length = 372

 Score =  268 bits (685), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 78/276 (28%), Positives = 133/276 (48%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L   EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 101 DPVRMYLKEIGRVNLLTADEEVALALKI-EEGDQEAKQRLAEANLRLVVSIAKRYVGRGM 159

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 160 SFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 218

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  +         PE++ A   ++++   +V  +        SL   I   
Sbjct: 219 -TINKLIRIQRQMLQDLGREPMPEEIGA---EMDMPTEKVREILKIAQEPVSLETPI--G 272

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D       E    +  +  L   +  L  RE  +   R   ++  
Sbjct: 273 EEDDSHLGDFI---EDQDATSPAEHAAYELLKEQLESVLDTLTDREENVLRLRFGLDDGR 329

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 330 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 365


>gi|238650752|ref|YP_002916605.1| RNA polymerase factor sigma-32 [Rickettsia peacockii str. Rustic]
 gi|238624850|gb|ACR47556.1| RNA polymerase factor sigma-32 [Rickettsia peacockii str. Rustic]
          Length = 293

 Score =  268 bits (685), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 146/285 (51%), Positives = 199/285 (69%), Gaps = 1/285 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M     ++ ++ E G   Y+ +I KIP L ++EE +LAK Y E  DL AAH+LVTSHL+L
Sbjct: 1   MTNNINALAISSESGFYSYLQKINKIPSLTQEEELLLAKSYLEGNDLQAAHKLVTSHLKL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIA GYR YGLPI+E+VSEGNIGLMQAVKKF+PE GFRL+TY+MWWIKAA+QEYIL+S
Sbjct: 61  VAKIASGYRTYGLPITELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKAAIQEYILKS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTA QK+LFF+L ++K  +  +    +  +  V IA +L VS +EV  MN R+
Sbjct: 121 WSLVKMGTTAAQKKLFFSLNKVKHKITNLYSRAITTDDFVQIADELGVSVNEVSEMNTRI 180

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D SLN  INS D  S +  + L       E + I K+   ++R +L+ +M +LN RE
Sbjct: 181 SGPDLSLNNSINSDDAESGELIELLPETRPTPEAMAINKQNSTSKRQLLSNAMKILNDRE 240

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            RI   R+L + P TL+ LS+E+ +S+ER+RQIE  AF+K+++ I
Sbjct: 241 LRILTERKLTDTPKTLDILSNEYNISKERIRQIENTAFEKIKKFI 285


>gi|51891726|ref|YP_074417.1| RNA polymerase sigma factor RpoD [Symbiobacterium thermophilum IAM
           14863]
 gi|51855415|dbj|BAD39573.1| RNA polymerase major sigma factor [Symbiobacterium thermophilum IAM
           14863]
          Length = 388

 Score =  268 bits (685), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 79/277 (28%), Positives = 135/277 (48%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI ++P+L  +EE + A+R  E GD  A  +L  ++LRLVV IA  Y G G
Sbjct: 116 DDPVRMYLKEIGRVPLLTAEEEIMYAERI-EKGDEEAKRKLAEANLRLVVSIAKRYVGRG 174

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     +
Sbjct: 175 MQFLDLIQEGNLGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 234

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 L R+   L         PE++ A+   +++    V  +        SL   I  
Sbjct: 235 --TINKLIRVTRQLVQELGREPTPEEIAAV---MDIPVERVREIQKIAQEPVSLETPI-- 287

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            ++  S   D++    D       E       +  L   +  L PRE ++   R   ++ 
Sbjct: 288 GEEEDSHLGDFI---EDQDAPAPAEAASFTLLKEQLEEVLESLTPREEKVLRLRFGLDDG 344

Query: 253 --VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 345 RARTLEEVGQVFGVTRERIRQIEAKALRKLRHPSRSK 381


>gi|327473233|gb|EGF18653.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           sanguinis SK408]
          Length = 370

 Score =  268 bits (685), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 84/276 (30%), Positives = 139/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE  LA    E GDL A  RL  ++LRLVV IA  Y G G+
Sbjct: 98  DPVRMYLKEIGVVPLLSNEEEQELAI-LVEKGDLEAKQRLAEANLRLVVSIAKRYVGRGM 156

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 157 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 215

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA++++++  +V  +        SL   I   
Sbjct: 216 -TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSLETPI--G 269

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 270 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 326

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 327 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 362


>gi|227878689|ref|ZP_03996603.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus JV-V01]
 gi|256843283|ref|ZP_05548771.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus
           125-2-CHN]
 gi|256850360|ref|ZP_05555788.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus MV-1A-US]
 gi|262046492|ref|ZP_06019454.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus MV-3A-US]
 gi|293380134|ref|ZP_06626221.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus 214-1]
 gi|295693058|ref|YP_003601668.1| RNA polymerase sigma factor [Lactobacillus crispatus ST1]
 gi|312978174|ref|ZP_07789918.1| RNA polymerase sigma-43 factor [Lactobacillus crispatus CTV-05]
 gi|227861704|gb|EEJ69309.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus JV-V01]
 gi|256614703|gb|EEU19904.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus
           125-2-CHN]
 gi|256712757|gb|EEU27750.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus MV-1A-US]
 gi|260573363|gb|EEX29921.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus MV-3A-US]
 gi|290923304|gb|EFE00220.1| RNA polymerase sigma factor RpoD [Lactobacillus crispatus 214-1]
 gi|295031164|emb|CBL50643.1| RNA polymerase sigma factor [Lactobacillus crispatus ST1]
 gi|310894892|gb|EFQ43962.1| RNA polymerase sigma-43 factor [Lactobacillus crispatus CTV-05]
          Length = 370

 Score =  268 bits (685), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 81/284 (28%), Positives = 135/284 (47%), Gaps = 13/284 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +    V     +  Y+ EI ++P+L   +E  LAKR  E GD  A   L  ++LRLVV I
Sbjct: 90  SAPSSVRMNDPVRMYLKEIGRVPLLTADQEIALAKRI-ESGDEEAKQELAEANLRLVVSI 148

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y G G+   +++ EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      +
Sbjct: 149 AKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTI 208

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I     +      L R++  L         PE++ A   ++N+  ++V  +        
Sbjct: 209 RIPVHMVE--TINKLIRIQRQLLQDLGREPTPEEIGA---EMNMPTNKVRDILKIAQEPV 263

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   I   +++ S   D++    D       +    +  +  L + +  L  RE  +  
Sbjct: 264 SLETPI--GEEDDSHLGDFI---EDKDATSPEQHASYEMLKEQLEQVLETLTDREENVLR 318

Query: 245 ARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R   ++    TLE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 319 LRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRS 362


>gi|91205341|ref|YP_537696.1| RNA polymerase factor sigma-32 [Rickettsia bellii RML369-C]
 gi|91068885|gb|ABE04607.1| RNA polymerase sigma-32 factor [Rickettsia bellii RML369-C]
          Length = 294

 Score =  268 bits (685), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 150/285 (52%), Positives = 203/285 (71%), Gaps = 1/285 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M     ++ ++ E G   Y+ +I KIP L ++EE++LAK Y E  DL AAH+LVTSHL+L
Sbjct: 1   MTSNINALAISSESGFYSYLQKINKIPSLTQEEEFLLAKSYLEQNDLQAAHKLVTSHLKL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIA GYR YGLP++E+VSEGNIGLMQAVKKF+PE GFRL+TY+MWWIKAA+QEYIL+S
Sbjct: 61  VAKIATGYRTYGLPVTELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKAAIQEYILKS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTA QK+LFF+L ++K  +  +    +  +  V IA +L VS SEV  MN RL
Sbjct: 121 WSLVKMGTTAAQKKLFFSLSKIKNKITNLYSRAITSDDFVQIADELGVSVSEVSDMNIRL 180

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D SLN  IN+ D +S +  + L       E + I KE+  ++R +L+ +M VLN RE
Sbjct: 181 SGSDLSLNNTINNDDASSGELIELLPETRPSPEAIAISKEDMTHKRALLSSAMKVLNARE 240

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            RI   R+LQ+ P TL+ LSSE+ +S+ER+RQIE  AF+K+++ I
Sbjct: 241 LRILTERKLQDTPKTLDVLSSEYNISKERIRQIENTAFEKIKKFI 285


>gi|309803186|ref|ZP_07697283.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LactinV
           11V1-d]
 gi|309806578|ref|ZP_07700575.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LactinV
           03V1-b]
 gi|312872984|ref|ZP_07733044.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LEAF
           2062A-h1]
 gi|315653573|ref|ZP_07906493.1| RNA polymerase sigma factor rpoD [Lactobacillus iners ATCC 55195]
 gi|325912624|ref|ZP_08175007.1| RNA polymerase sigma factor RpoD [Lactobacillus iners UPII 60-B]
 gi|329920166|ref|ZP_08276997.1| RNA polymerase sigma factor RpoD [Lactobacillus iners SPIN 1401G]
 gi|308164694|gb|EFO66944.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LactinV
           11V1-d]
 gi|308166998|gb|EFO69180.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LactinV
           03V1-b]
 gi|311091506|gb|EFQ49890.1| RNA polymerase sigma factor RpoD [Lactobacillus iners LEAF
           2062A-h1]
 gi|315488935|gb|EFU78577.1| RNA polymerase sigma factor rpoD [Lactobacillus iners ATCC 55195]
 gi|325478045|gb|EGC81174.1| RNA polymerase sigma factor RpoD [Lactobacillus iners UPII 60-B]
 gi|328936620|gb|EGG33064.1| RNA polymerase sigma factor RpoD [Lactobacillus iners SPIN 1401G]
          Length = 382

 Score =  268 bits (685), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 81/288 (28%), Positives = 134/288 (46%), Gaps = 13/288 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N       V     +  Y+ EI ++P+L   +E  LAKR  E+ D  A   L  ++LRL
Sbjct: 98  LNDMTAPSSVRMNDPVRMYLKEIGRVPLLNADQEIDLAKRI-ENNDDEAKQELAEANLRL 156

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I   
Sbjct: 157 VVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQ 216

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE++ A   ++++S  +V  +    
Sbjct: 217 ARTIRIPVHMVE--TINKLIRIQRQLLQDLGREPTPEEIGA---EMDMSTDKVREILKIA 271

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D       +    +  +  L   +  L  RE 
Sbjct: 272 QEPVSLETPI--GEEDDSHLGDFI---EDKDATSPEQHASYELLKEQLEEVLDTLTDREE 326

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +   R    +    TLE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 327 NVLRLRFGLNDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRS 374


>gi|289167835|ref|YP_003446104.1| DNA-dependent RNA Polymerase sigma factor rpoD [Streptococcus mitis
           B6]
 gi|288907402|emb|CBJ22239.1| DNA-dependent RNA Polymerase sigma factor rpoD [Streptococcus mitis
           B6]
          Length = 369

 Score =  268 bits (685), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 85/283 (30%), Positives = 140/283 (49%), Gaps = 13/283 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S        +  Y+ EI  +P+L  +EE  LA    E GD+ A  RL  ++LRLVV IA 
Sbjct: 90  STSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAV-EAGDIEAKQRLAEANLRLVVSIAK 148

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y G G+   +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I
Sbjct: 149 RYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI 208

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
                +      L R + +L         PEQ   IA+K++++  +V  +        SL
Sbjct: 209 PVHMVE--TINKLVREQRNLLQEYGQEPTPEQ---IAEKMDMTPDKVREILKIAQEPVSL 263

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              I   +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R
Sbjct: 264 ETPI--GEEDDSHLGDFI---EDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLR 318

Query: 247 RLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              ++    TLE++   F V+RER+RQIEA+A +K+++  + +
Sbjct: 319 FGLDDGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRQPSRSK 361


>gi|238854653|ref|ZP_04644983.1| RNA polymerase sigma factor RpoD [Lactobacillus jensenii 269-3]
 gi|260664404|ref|ZP_05865256.1| RNA polymerase sigma factor RpoS [Lactobacillus jensenii SJ-7A-US]
 gi|282932956|ref|ZP_06338353.1| RNA polymerase sigma factor RpoD [Lactobacillus jensenii 208-1]
 gi|238832443|gb|EEQ24750.1| RNA polymerase sigma factor RpoD [Lactobacillus jensenii 269-3]
 gi|260561469|gb|EEX27441.1| RNA polymerase sigma factor RpoS [Lactobacillus jensenii SJ-7A-US]
 gi|281302991|gb|EFA95196.1| RNA polymerase sigma factor RpoD [Lactobacillus jensenii 208-1]
          Length = 364

 Score =  268 bits (685), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 79/284 (27%), Positives = 135/284 (47%), Gaps = 13/284 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +    V     +  Y+ EI ++P+L   EE  LAKR ++ GD  A   L  ++LRLVV I
Sbjct: 84  SAPASVRMNDPVRMYLKEIGRVPLLNADEEITLAKRIQD-GDEEAKQELAEANLRLVVSI 142

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y G G+   +++ EGN+GLM+AV KF+ + GF+ +TY+ WWI+ A+   I      +
Sbjct: 143 AKRYVGRGMQFLDLIQEGNMGLMKAVDKFNYKLGFKFSTYATWWIRQAITRAIADQARTI 202

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I     +      L R++  L         PE++ A   ++++   +V  +        
Sbjct: 203 RIPVHMVE--TINKLIRIQRQLLQDLGREPTPEEIGA---EMDMGTDKVRDILKIAQEPV 257

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   I   +++ S   D++    D       +    +  +  L   +  L  RE  +  
Sbjct: 258 SLETPI--GEEDDSHLGDFI---EDKDATSPEQHASYEMLKEQLEEVLDTLTDREENVLR 312

Query: 245 ARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R   ++    TLE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 313 LRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRS 356


>gi|323466388|gb|ADX70075.1| RNA polymerase sigma factor [Lactobacillus helveticus H10]
          Length = 370

 Score =  268 bits (685), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 81/284 (28%), Positives = 136/284 (47%), Gaps = 13/284 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +    V     +  Y+ EI ++P+L   +E  LAKR  E GD  A   L  ++LRLVV I
Sbjct: 90  SAPSSVRMNDPVRMYLKEIGRVPLLTADQEIALAKRI-EEGDEEAKQELAEANLRLVVSI 148

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y G G+   +++ EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      +
Sbjct: 149 AKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTI 208

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I     +      L R++  L         PE++ A   ++N+  ++V ++        
Sbjct: 209 RIPVHMVE--TINKLIRIQRQLLQDLGREPTPEEIGA---EMNMPTNKVRNILKIAQEPV 263

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   I   +++ S   D++    D       +    +  +  L + +  L  RE  +  
Sbjct: 264 SLETPI--GEEDDSHLGDFI---EDKDATSPEQHASYEMLKEQLEQVLETLTDREENVLR 318

Query: 245 ARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R   ++    TLE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 319 LRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRS 362


>gi|325263837|ref|ZP_08130570.1| RNA polymerase sigma factor RpoD [Clostridium sp. D5]
 gi|324030875|gb|EGB92157.1| RNA polymerase sigma factor RpoD [Clostridium sp. D5]
          Length = 369

 Score =  268 bits (685), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 86/290 (29%), Positives = 142/290 (48%), Gaps = 15/290 (5%)

Query: 1   MNRKNMSII--VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHL 58
           M   ++S+   ++ E  +  Y+ EI K+P+L  + E  LA+R  E GD  A   L  ++L
Sbjct: 83  MENIDLSVPDGISIEDPVRMYLKEIGKVPLLSAEREIELAQRM-EDGDEDAKKELAEANL 141

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I 
Sbjct: 142 RLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYHKGYKFSTYATWWIRQAITRAIA 201

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
                ++I     +      L R+   L         PE    IAK+L++    V  +  
Sbjct: 202 DQARTIRIPVHMVE--TINKLIRVSRQLLQELGREPTPE---EIAKELDMPVERVREILK 256

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
                 SL   I   ++  S   D++  D      V  E   +   +  L   +  L  R
Sbjct: 257 ISQEPVSLETPI--GEEEDSHLGDFIQDD---NVPVPAEAAAQTLLKEQLDEVLDTLTER 311

Query: 239 ERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E+++   R    +    TLE +  EF+V+RER+RQIEA+A +K++   + 
Sbjct: 312 EQKVLRLRFGMNDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRS 361


>gi|309800318|ref|ZP_07694490.1| RNA polymerase sigma factor RpoD [Streptococcus infantis SK1302]
 gi|308116065|gb|EFO53569.1| RNA polymerase sigma factor RpoD [Streptococcus infantis SK1302]
          Length = 369

 Score =  268 bits (685), Expect = 9e-70,   Method: Composition-based stats.
 Identities = 84/283 (29%), Positives = 141/283 (49%), Gaps = 13/283 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S        +  Y+ EI  +P+L  +EE  LA    E GD+ A  RL  ++LRLVV IA 
Sbjct: 90  STSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAV-EAGDIEAKQRLAEANLRLVVSIAK 148

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y G G+   +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I
Sbjct: 149 RYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI 208

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
                +      L R + +L      +  PEQ   IA++++++  +V  +        SL
Sbjct: 209 PVHMVE--TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSL 263

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              I   +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R
Sbjct: 264 ETPI--GEEDDSHLGDFI---EDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLR 318

Query: 247 RLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              ++    TLE++   F V+RER+RQIEA+A +K+++  + +
Sbjct: 319 FGLDDGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRQPSRSK 361


>gi|239637627|ref|ZP_04678599.1| RNA polymerase sigma factor RpoD [Staphylococcus warneri L37603]
 gi|239596845|gb|EEQ79370.1| RNA polymerase sigma factor RpoD [Staphylococcus warneri L37603]
 gi|330686029|gb|EGG97652.1| RNA polymerase sigma factor RpoD [Staphylococcus epidermidis
           VCU121]
          Length = 367

 Score =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 81/276 (29%), Positives = 137/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L  QEE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 96  DPVRMYLKEIGRVDLLSAQEEIELAKRI-EQGDEIAKSRLAEANLRLVVSIAKRYVGRGM 154

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 155 LFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 213

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L      +  PE    I +++++   +V  +        SL   I   
Sbjct: 214 -TINKLIRVQRQLLQDLGRDPAPE---EIGEEMDLPPEKVREILKIAQEPVSLETPI--G 267

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D + Q   +    +  +  L   +  L  RE  +   R   ++  
Sbjct: 268 EEDDSHLGDFI---EDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGR 324

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 325 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 360


>gi|13377878|gb|AAK20883.1|AF334761_4 RNA polymerase sigma-32 [Aeromonas hydrophila]
          Length = 284

 Score =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 107/286 (37%), Positives = 168/286 (58%), Gaps = 9/286 (3%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           ++ M++I  G   L  YI  +  IP+L   EE  LA+R ++ GDL AA +LV SHLR VV
Sbjct: 6   QRTMALIPQG--SLEGYIQAVNSIPVLTADEERELAERLQQGGDLEAARQLVMSHLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y GYGLP +++V EGNIGLM+AVK+FDP  G RL ++++ WIKA + EY+LR+W 
Sbjct: 64  HVAKSYAGYGLPQADLVQEGNIGLMKAVKRFDPTVGVRLVSFAVHWIKADIHEYVLRNWR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L   +      ++V A+A +L VS ++V  M  R++ 
Sbjct: 124 MVKVATTKAQRKLFFNLRKSKKRLGWFSH-----DEVQAVAAELGVSPTDVTEMEARMSN 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPRERR 241
            +    L+   +          + D        IE +   +     L+ +++ L+ R + 
Sbjct: 179 YDQAFDLVGDDEDEGGFAPVHYLEDKSSDLAATIENDNWDDHATRRLSSALATLDERSQH 238

Query: 242 IFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           I  AR L ++   TL+ L+  + VS ERVRQ+E  A KK++++++ 
Sbjct: 239 IIRARWLDDDSKTTLQELADTYGVSAERVRQLEKNALKKLKDAMEA 284


>gi|303238871|ref|ZP_07325402.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302593504|gb|EFL63221.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 359

 Score =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 81/280 (28%), Positives = 139/280 (49%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ +  +  Y+ EI K+P+L   EE  LA++  E GD  +  RL  ++LRLVV IA  Y 
Sbjct: 84  ISIDDPVRMYLKEIGKVPLLSADEEIQLAQKM-EKGDSESKRRLAEANLRLVVSIAKRYV 142

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 143 GRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 202

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      + +L    + +     K  Q   IAK++N+   +V  +        SL   
Sbjct: 203 MVE-----TINKLIRVSRQLLQELGKEPQPEEIAKEMNMPVEKVREIMKISQEPVSLETP 257

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++  D         E       +  L   +  L PRE ++   R   
Sbjct: 258 I--GEEEDSHLGDFIPDDD---APAPSEAAAFTLLKEQLIDVLDTLTPREEKVLRLRFGL 312

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 313 DDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 352


>gi|301301338|ref|ZP_07207482.1| RNA polymerase sigma factor RpoD [Lactobacillus salivarius
           ACS-116-V-Col5a]
 gi|300851066|gb|EFK78806.1| RNA polymerase sigma factor RpoD [Lactobacillus salivarius
           ACS-116-V-Col5a]
          Length = 372

 Score =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 78/276 (28%), Positives = 133/276 (48%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L   EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 101 DPVRMYLKEIGRVNLLTADEEVALALKI-EEGDQEAKQRLAEANLRLVVSIAKRYVGRGM 159

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 160 SFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 218

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  +         PE++ A   ++++   +V  +        SL   I   
Sbjct: 219 -TINKLIRIQRQMLQDLGREPMPEEIGA---EMDMPTEKVREILKIAQEPVSLETPI--G 272

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D       E    +  +  L   +  L  RE  +   R   ++  
Sbjct: 273 EEDDSHLGDFI---EDQDATSPAEHAAYELLKEQLESVLDTLTDREENVLRLRFGLDDGR 329

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 330 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 365


>gi|288961334|ref|YP_003451673.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
 gi|288913642|dbj|BAI75129.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
          Length = 287

 Score =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 145/269 (53%), Positives = 196/269 (72%), Gaps = 2/269 (0%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y+ + RK   L  + E  LA R+ +H D +A  RLV SHLRLVVK+A GY GYGLP+
Sbjct: 1   MQLYLQDARKYQYLTPELELELAARWHDHQDPAALDRLVGSHLRLVVKMARGYLGYGLPL 60

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           +++V+EGN+GLMQA +KFDP +GFR ATY+ WW++AA+QEY+L +WSLVKIGTTA QK+L
Sbjct: 61  ADLVAEGNVGLMQAAQKFDPGKGFRFATYASWWVRAAIQEYVLHNWSLVKIGTTAGQKKL 120

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FF+LRRLK  +Q +   +L PE V +IA +LNVS++EV+ MN RL  D SLN  +  S+ 
Sbjct: 121 FFSLRRLKARMQELDSGDLSPEAVESIATELNVSKAEVVEMNRRLGNDRSLN--VGLSED 178

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
             ++WQD L  D   QE VL + EER+ R+  L   + VL+ RERRI  ARRL++ P+TL
Sbjct: 179 GDAEWQDLLADDRPDQETVLADSEERRRRQQFLKLGLGVLDDRERRILVARRLRDEPLTL 238

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESI 284
           E LS  F+VSRERVRQ+E RAF+K+Q+++
Sbjct: 239 EELSQTFQVSRERVRQLEVRAFEKLQKAV 267


>gi|15892330|ref|NP_360044.1| RNA polymerase factor sigma-32 [Rickettsia conorii str. Malish 7]
 gi|15619475|gb|AAL02945.1| RNA polymerase sigma-32 factor [Rickettsia conorii str. Malish 7]
          Length = 293

 Score =  268 bits (685), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 146/285 (51%), Positives = 199/285 (69%), Gaps = 1/285 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M     ++ ++ E G   Y+ +I KIP L ++EE +LAK Y E  DL AAH+LVTSHL+L
Sbjct: 1   MTNNINALAISSESGFYSYLQKINKIPSLTQEEELLLAKSYLEGNDLQAAHKLVTSHLKL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIA GYR YGLPI+E+VSEGNIGLMQAVKKF+PE GFRL+TY+MWWIKAA+QEYIL+S
Sbjct: 61  VAKIASGYRTYGLPITELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKAAIQEYILKS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTA QK+LFF+L ++K  +  +    +  +  V IA +L VS +EV  MN R+
Sbjct: 121 WSLVKMGTTAAQKKLFFSLNKVKHKITNLYSRAITTDDFVQIADELGVSVNEVSEMNTRI 180

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D SLN  INS D  S +  + L       E + I K+   ++R +L+ +M +LN RE
Sbjct: 181 SGPDLSLNNSINSDDAESGELIELLPETRPTPEAMAINKQNSTSKRQLLSNAMKILNDRE 240

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            RI   R+L + P TL+ LS+E+ +S+ER+RQIE  AF+K+++ I
Sbjct: 241 LRILTERKLTDTPKTLDILSNEYNISKERIRQIENTAFEKIKKFI 285


>gi|269961508|ref|ZP_06175871.1| RNA polymerase sigma -32 factor [Vibrio harveyi 1DA3]
 gi|269833737|gb|EEZ87833.1| RNA polymerase sigma -32 factor [Vibrio harveyi 1DA3]
          Length = 285

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 111/284 (39%), Positives = 169/284 (59%), Gaps = 8/284 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++   + +  +  L  YI  +   PML  +EE  LA+R   +G++ AA  L+ SHLR 
Sbjct: 1   MTKEAYPMALVTQDSLDSYIRSVNSYPMLTPEEERGLAERLHYNGEIDAAKGLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A GY GYGLP++++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VKI TT  Q++LFFNLR+ K  L    +      +V  +A++L V  SEV  M  RL
Sbjct: 121 WRIVKIATTKAQRKLFFNLRKSKKRLGWFNNG-----EVETVARELGVEPSEVREMESRL 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE---ERKNRRNMLTRSMSVLNP 237
           A  +S   +    D +++ +   +VY  D    V    E      +  N L  +++ L+ 
Sbjct: 176 AAVDSTFDMPMDDDDSANSYTAPMVYLEDKSSDVADNIEAANWETHTNNRLGHALASLDE 235

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R +RI  +R L +   TL++L+ EF VS ER+RQ+E  A KK++
Sbjct: 236 RSQRIVRSRWLDDEKATLQDLADEFGVSAERIRQLEKNAMKKLK 279


>gi|307709167|ref|ZP_07645626.1| RNA polymerase sigma factor rpoD [Streptococcus mitis SK564]
 gi|307620113|gb|EFN99230.1| RNA polymerase sigma factor rpoD [Streptococcus mitis SK564]
          Length = 369

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 84/283 (29%), Positives = 141/283 (49%), Gaps = 13/283 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S        +  Y+ EI  +P+L  +EE  LA    E GD+ A  RL  ++LRLVV IA 
Sbjct: 90  STSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAV-EAGDIEAKQRLAEANLRLVVSIAK 148

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y G G+   +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I
Sbjct: 149 RYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI 208

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
                +      L R + +L      +  PEQ   IA++++++  +V  +        SL
Sbjct: 209 PVHMVE--TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSL 263

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              I   +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R
Sbjct: 264 ETPI--GEEDDSHLGDFI---EDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLR 318

Query: 247 RLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              ++    TLE++   F V+RER+RQIEA+A +K+++  + +
Sbjct: 319 FGLDDGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRQPSRSK 361


>gi|307705133|ref|ZP_07642010.1| RNA polymerase sigma factor rpoD [Streptococcus mitis SK597]
 gi|307621329|gb|EFO00389.1| RNA polymerase sigma factor rpoD [Streptococcus mitis SK597]
          Length = 369

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 84/283 (29%), Positives = 141/283 (49%), Gaps = 13/283 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S        +  Y+ EI  +P+L  +EE  LA    E GD+ A  RL  ++LRLVV IA 
Sbjct: 90  STSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAV-EAGDIEAKQRLAEANLRLVVSIAK 148

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y G G+   +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I
Sbjct: 149 RYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI 208

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
                +      L R + +L      +  PEQ   IA++++++  +V  +        SL
Sbjct: 209 PVHMVE--TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSL 263

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              I   +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R
Sbjct: 264 ETPI--GEEDDSHLGDFI---EDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLR 318

Query: 247 RLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              ++    TLE++   F V+RER+RQIEA+A +K+++  + +
Sbjct: 319 FGLDDGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRQPSRSK 361


>gi|319651585|ref|ZP_08005712.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
 gi|317396652|gb|EFV77363.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
          Length = 374

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 82/289 (28%), Positives = 139/289 (48%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRL
Sbjct: 90  LNDLSVPPGVKINDPVRMYLKEIGRVDLLSAEEEIALANRI-EEGDEEAKRRLAEANLRL 148

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 149 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQ 208

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    IA+ ++++  +V  +    
Sbjct: 209 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPTPE---EIAEDMDLTPDKVREILKIA 263

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D       E    +  +  L   +  L  RE 
Sbjct: 264 QEPVSLETPI--GEEDDSHLGDFI---EDQDATSPSEHAAYELLKEQLEDVLDTLTDREE 318

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 319 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 367


>gi|170724574|ref|YP_001758600.1| RNA polymerase factor sigma-32 [Shewanella woodyi ATCC 51908]
 gi|169809921|gb|ACA84505.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella woodyi ATCC
           51908]
          Length = 283

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 112/288 (38%), Positives = 176/288 (61%), Gaps = 7/288 (2%)

Query: 1   MNRKNMSIIVN-GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLR 59
           M  ++M++ V  G   L  Y+H    I MLE ++EY LAKR +E GDL AA +L+ SHLR
Sbjct: 1   MTNQSMALTVPHGSGSLEAYVHSAHNISMLEPEQEYELAKRLQETGDLQAAKQLIMSHLR 60

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
            VV +A GY GYGLP ++++ EGNIGLM+AVK+FDP+ G RL ++++ WIKA + EY+L+
Sbjct: 61  FVVHVAKGYSGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYVLK 120

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
           +W +VK+ TT  Q++LFFNLR+ K  L   +D     E+V  +A  L VS+++V  M  R
Sbjct: 121 NWRIVKVATTKAQRKLFFNLRKSKKRLGWFSD-----EEVGMVADNLGVSKADVTEMESR 175

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLNPR 238
           +A  +    L + +D +        + DH       +E +  + N +  L  ++  L+ R
Sbjct: 176 MAAQDPAFDLASDNDDDQDFSPVHYLEDHSSDLASQVENDNLESNNQARLLSAIKTLDER 235

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + I +AR L E+  TL+ L++ ++VS ER+RQ+E  A  K++  ++ 
Sbjct: 236 SQHILQARWLNEDKTTLQELAATYQVSAERIRQLEKNAMNKLKGRMEA 283


>gi|315038507|ref|YP_004032075.1| RNA polymerase sigma factor RpoD [Lactobacillus amylovorus GRL
           1112]
 gi|325956923|ref|YP_004292335.1| RNA polymerase sigma factor RpoD [Lactobacillus acidophilus 30SC]
 gi|312276640|gb|ADQ59280.1| RNA polymerase sigma factor RpoD [Lactobacillus amylovorus GRL
           1112]
 gi|325333488|gb|ADZ07396.1| RNA polymerase sigma factor RpoD [Lactobacillus acidophilus 30SC]
 gi|327183703|gb|AEA32150.1| RNA polymerase sigma factor RpoD [Lactobacillus amylovorus GRL
           1118]
          Length = 370

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 81/284 (28%), Positives = 135/284 (47%), Gaps = 13/284 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +    V     +  Y+ EI ++P+L   +E  LAKR  E GD  A   L  ++LRLVV I
Sbjct: 90  SAPSSVRMNDPVRMYLKEIGRVPLLTADQEIALAKRI-EAGDEEAKQELAEANLRLVVSI 148

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y G G+   +++ EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      +
Sbjct: 149 AKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTI 208

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I     +      L R++  L         PE++ A   ++N+  ++V  +        
Sbjct: 209 RIPVHMVE--TINKLIRIQRQLLQDLGREPTPEEIGA---EMNMPTNKVRDILKIAQEPV 263

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   I   +++ S   D++    D       +    +  +  L + +  L  RE  +  
Sbjct: 264 SLETPI--GEEDDSHLGDFI---EDKDATSPEQHASYEMLKEQLEQVLETLTDREENVLR 318

Query: 245 ARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R   ++    TLE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 319 LRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRS 362


>gi|300813859|ref|ZP_07094164.1| RNA polymerase sigma factor RpoD [Peptoniphilus sp. oral taxon 836
           str. F0141]
 gi|300512046|gb|EFK39241.1| RNA polymerase sigma factor RpoD [Peptoniphilus sp. oral taxon 836
           str. F0141]
          Length = 361

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 86/280 (30%), Positives = 142/280 (50%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ +  +  Y+ EI KIP+L   EE  +AKR  E+GD SA   L  ++LRLVV IA  Y 
Sbjct: 86  ISVDDPVRMYLKEIGKIPLLTGDEEVEIAKRM-ENGDNSAKKELAEANLRLVVSIAKRYV 144

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I   
Sbjct: 145 GRGMSFLDLIQEGNLGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVH 204

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R++  L      +  PE    IAK++++   +V  +        SL   
Sbjct: 205 MVE--TINKLVRVQRQLVQELGRDPLPE---EIAKEMSIDVEKVREIQKIAQEPVSLETP 259

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++  +     Q   +       R  L+  +  L  RE+++   R   
Sbjct: 260 I--GEEEDSHLGDFIPDEEILSPQ---DAATFTLLREQLSTVLETLTDREKKVLTLRFGL 314

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 315 DDGRARTLEEVGKEFAVTRERIRQIEAKAIRKLRHPSRSK 354


>gi|326803636|ref|YP_004321454.1| RNA polymerase sigma factor RpoD [Aerococcus urinae
           ACS-120-V-Col10a]
 gi|326651510|gb|AEA01693.1| RNA polymerase sigma factor RpoD [Aerococcus urinae
           ACS-120-V-Col10a]
          Length = 401

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 83/286 (29%), Positives = 139/286 (48%), Gaps = 13/286 (4%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           +  + S  V     +  Y+ EI ++ +L   EE  LAKR  E GD  A   L  ++LRLV
Sbjct: 117 SASSTSSKVKTNDPVRMYLKEIGRVDLLTADEEVALAKRI-EAGDPVAKQELAEANLRLV 175

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA  Y G G+   +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I    
Sbjct: 176 VSIAKRYVGRGMSFLDLIQEGNMGLMKAVEKFDYTKGFKFSTYATWWIRQAITRSIADQA 235

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             ++I     +      L R++  L         PE++ A   ++++   +V ++     
Sbjct: 236 RTIRIPVHMVE--TINKLVRIQRQLLQELGREPTPEEIGA---EMDLPTEKVRNIMKISQ 290

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              SL   I   +++ S   D++  +   Q      +E     +  L   +  L  RE  
Sbjct: 291 EPVSLETPI--GEEDDSHLGDFIEDNDAMQPDEYTNQELL---KEQLNEVLDTLTDREEN 345

Query: 242 IFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           +   R   E+    TLE +  +F V+RER+RQIEA+A +K++   +
Sbjct: 346 VLRLRFGLEDGQTKTLEQVGQQFGVTRERIRQIEAKALRKLRHPSR 391


>gi|16800559|ref|NP_470827.1| RNA polymerase sigma factor RpoD [Listeria innocua Clip11262]
 gi|116872885|ref|YP_849666.1| RNA polymerase sigma factor RpoD [Listeria welshimeri serovar 6b
           str. SLCC5334]
 gi|217964400|ref|YP_002350078.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43) [Listeria
           monocytogenes HCC23]
 gi|290894216|ref|ZP_06557185.1| rpoD protein [Listeria monocytogenes FSL J2-071]
 gi|20140102|sp|Q92BQ6|RPOD_LISIN RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-43
 gi|16413964|emb|CAC96722.1| RNA polymerase sigma factor RpoD [Listeria innocua Clip11262]
 gi|116741763|emb|CAK20887.1| RNA polymerase sigma factor RpoD (Sigma-A) [Listeria welshimeri
           serovar 6b str. SLCC5334]
 gi|217333670|gb|ACK39464.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43) [Listeria
           monocytogenes HCC23]
 gi|290556213|gb|EFD89758.1| rpoD protein [Listeria monocytogenes FSL J2-071]
 gi|307571035|emb|CAR84214.1| RNA polymerase sigma factor [Listeria monocytogenes L99]
 gi|313623755|gb|EFR93895.1| RNA polymerase sigma factor RpoD [Listeria innocua FSL J1-023]
          Length = 374

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 83/288 (28%), Positives = 141/288 (48%), Gaps = 15/288 (5%)

Query: 4   KNMSIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
            +MS+    +I   +  Y+ EI ++ +L   EE  LAKR  E GD+ A  RL  ++LRLV
Sbjct: 91  TDMSVPPGVKINDPVRMYLKEIGRVDLLTADEEIALAKRI-EAGDIEAKGRLAEANLRLV 149

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA  Y G G+   +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I    
Sbjct: 150 VSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQA 209

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             ++I     +      L R++  L      +  PE    I +++++   +V  +     
Sbjct: 210 RTIRIPVHMVE--TINKLIRVQRSLLQDLGRDPSPE---EIGEEMDLPTEKVREILKIAQ 264

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              SL   I   +++ S   D++    D       +    +  +  L   +  L  RE  
Sbjct: 265 EPVSLETPI--GEEDDSHLGDFI---EDQDATSPSDHAAYELLKEQLEDVLDTLTDREEN 319

Query: 242 IFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 320 VLRLRFGLDDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSK 367


>gi|309810147|ref|ZP_07703992.1| RNA polymerase sigma factor RpoD [Lactobacillus iners SPIN
           2503V10-D]
 gi|308169419|gb|EFO71467.1| RNA polymerase sigma factor RpoD [Lactobacillus iners SPIN
           2503V10-D]
          Length = 382

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 81/288 (28%), Positives = 134/288 (46%), Gaps = 13/288 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N       V     +  Y+ EI ++P+L   +E  LAKR  E+ D  A   L  ++LRL
Sbjct: 98  LNDMTAPSSVRMNDPVRMYLKEIGRVPLLNADQEIDLAKRI-ENNDDEAKQELAEANLRL 156

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I   
Sbjct: 157 VVSIAKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQ 216

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE++ A   ++++S  +V  +    
Sbjct: 217 ARTIRIPVHMVE--TINKLIRIQRQLLQDLGREPTPEEIGA---EMDMSTDKVREILKIA 271

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D       +    +  +  L   +  L  RE 
Sbjct: 272 QEPVSLETPI--GEEDDSHLGDFI---EDKDATSPEQHASYELLKEQLEEVLDTLTDREE 326

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +   R    +    TLE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 327 NVLRLRFGLNDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRS 374


>gi|16803494|ref|NP_464979.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes EGD-e]
 gi|46907682|ref|YP_014071.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes serotype
           4b str. F2365]
 gi|47092744|ref|ZP_00230530.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes str. 4b
           H7858]
 gi|47095405|ref|ZP_00233015.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes str. 1/2a
           F6854]
 gi|224499695|ref|ZP_03668044.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes Finland
           1988]
 gi|224501605|ref|ZP_03669912.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           R2-561]
 gi|226224055|ref|YP_002758162.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes Clip81459]
 gi|254824487|ref|ZP_05229488.1| RNA polymerase subunit sigma [Listeria monocytogenes FSL J1-194]
 gi|254827742|ref|ZP_05232429.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           N3-165]
 gi|254829787|ref|ZP_05234442.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes 10403S]
 gi|254852080|ref|ZP_05241428.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           R2-503]
 gi|254898380|ref|ZP_05258304.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes J0161]
 gi|254912128|ref|ZP_05262140.1| sigma 43 subunit of RNA polymerase [Listeria monocytogenes J2818]
 gi|254932639|ref|ZP_05265998.1| RNA polymerase subunit sigma [Listeria monocytogenes HPB2262]
 gi|254936456|ref|ZP_05268153.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes F6900]
 gi|254994146|ref|ZP_05276336.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           J2-064]
 gi|255029176|ref|ZP_05301127.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes LO28]
 gi|255522085|ref|ZP_05389322.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           J1-175]
 gi|284801841|ref|YP_003413706.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes 08-5578]
 gi|284994983|ref|YP_003416751.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes 08-5923]
 gi|315282349|ref|ZP_07870778.1| RNA polymerase sigma factor RpoD [Listeria marthii FSL S4-120]
 gi|1710684|sp|P52331|RPOD_LISMO RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-43
 gi|664756|gb|AAC43306.1| sigma 43 subunit of RNA polymerase [Listeria monocytogenes]
 gi|16410883|emb|CAC99532.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes EGD-e]
 gi|46880950|gb|AAT04248.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes serotype
           4b str. F2365]
 gi|47016226|gb|EAL07149.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes str. 1/2a
           F6854]
 gi|47018932|gb|EAL09679.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes str. 4b
           H7858]
 gi|225876517|emb|CAS05226.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes serotype
           4b str. CLIP 80459]
 gi|258600121|gb|EEW13446.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           N3-165]
 gi|258605378|gb|EEW17986.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           R2-503]
 gi|258609048|gb|EEW21656.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes F6900]
 gi|284057403|gb|ADB68344.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes 08-5578]
 gi|284060450|gb|ADB71389.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes 08-5923]
 gi|293584198|gb|EFF96230.1| RNA polymerase subunit sigma [Listeria monocytogenes HPB2262]
 gi|293590099|gb|EFF98433.1| sigma 43 subunit of RNA polymerase [Listeria monocytogenes J2818]
 gi|293593725|gb|EFG01486.1| RNA polymerase subunit sigma [Listeria monocytogenes FSL J1-194]
 gi|313614010|gb|EFR87725.1| RNA polymerase sigma factor RpoD [Listeria marthii FSL S4-120]
 gi|328465497|gb|EGF36726.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes 1816]
 gi|332311895|gb|EGJ24990.1| RNA polymerase sigma factor rpoD [Listeria monocytogenes str. Scott
           A]
 gi|1093602|prf||2104269C RNA polymerase:SUBUNIT=sigma
          Length = 374

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 83/288 (28%), Positives = 141/288 (48%), Gaps = 15/288 (5%)

Query: 4   KNMSIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
            +MS+    +I   +  Y+ EI ++ +L   EE  LAKR  E GD+ A  RL  ++LRLV
Sbjct: 91  TDMSVPPGVKINDPVRMYLKEIGRVDLLTADEEIALAKRI-EAGDIEAKGRLAEANLRLV 149

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA  Y G G+   +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I    
Sbjct: 150 VSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQA 209

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             ++I     +      L R++  L      +  PE    I +++++   +V  +     
Sbjct: 210 RTIRIPVHMVE--TINKLIRVQRSLLQDLGRDPSPE---EIGEEMDLPTEKVREILKIAQ 264

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              SL   I   +++ S   D++    D       +    +  +  L   +  L  RE  
Sbjct: 265 EPVSLETPI--GEEDDSHLGDFI---EDQDATSPSDHAAYELLKEQLEDVLDTLTDREEN 319

Query: 242 IFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 320 VLRLRFGLDDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSK 367


>gi|73662504|ref|YP_301285.1| RNA polymerase sigma factor RpoD [Staphylococcus saprophyticus
           subsp. saprophyticus ATCC 15305]
 gi|72495019|dbj|BAE18340.1| RNA polymerase sigma factor A [Staphylococcus saprophyticus subsp.
           saprophyticus ATCC 15305]
          Length = 368

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 80/276 (28%), Positives = 137/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L  QEE  LAK+  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGRVNLLNAQEEIELAKKI-EQGDEVAKSRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 LFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L      +  PE    I +++++   +V  +        SL   I   
Sbjct: 215 -TINKLIRVQRQLLQDLGRDPAPE---EIGEEMDLPPEKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D + Q   +    +  +  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGR 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 361


>gi|313903914|ref|ZP_07837294.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Eubacterium
           cellulosolvens 6]
 gi|313471063|gb|EFR66385.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Eubacterium
           cellulosolvens 6]
          Length = 373

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 90/290 (31%), Positives = 142/290 (48%), Gaps = 15/290 (5%)

Query: 1   MNRKNMSII--VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHL 58
           M   ++S+   V+ E  +  Y+ EI K+P+L   EE  LAKR  E GD  A  RL  ++L
Sbjct: 87  MENIDLSVPEGVSIEDPVRMYLKEIGKVPLLSADEEIELAKRM-EEGDEVAKKRLAEANL 145

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I 
Sbjct: 146 RLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIA 205

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
                ++I     +      L R+   L         PE    IAK +N+S   V  +  
Sbjct: 206 DQARTIRIPVHMVE--TINKLIRVSRQLLQEYGREPTPE---EIAKNMNMSVERVREILK 260

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
                 SL   I   ++  S   D++    D    V  +       +  L   +  L  R
Sbjct: 261 ISQEPVSLETPI--GEEEDSHLGDFI---QDENVPVPADAAAFTMLKEQLEEVLGTLAER 315

Query: 239 ERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E+++   R   ++    TLE +  EF V+RER+RQIEA+A +K++   + 
Sbjct: 316 EQKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRS 365


>gi|160935059|ref|ZP_02082445.1| hypothetical protein CLOLEP_03935 [Clostridium leptum DSM 753]
 gi|156866512|gb|EDO59884.1| hypothetical protein CLOLEP_03935 [Clostridium leptum DSM 753]
          Length = 365

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 82/281 (29%), Positives = 136/281 (48%), Gaps = 13/281 (4%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
            V  +  +  Y+ EI ++P+L  +EE  LA R  E GD SA  RL  ++LRLVV IA  Y
Sbjct: 89  SVAIDDPVKVYLKEIGRVPLLSPEEEIDLAIRISE-GDESAKKRLSEANLRLVVSIAKRY 147

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I  
Sbjct: 148 LGRGMQFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPV 207

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
              +      + ++K     +   N        IA +L++   +V  +        SL  
Sbjct: 208 HMVE-----TINKVKKVSSQLLHTNGHEPTADEIALELDMPVDKVREIMRVAQEPVSLET 262

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            I   ++  S   D++  D                 +  L   +  L PRE ++   R  
Sbjct: 263 PI--GEEEDSHLGDFIPDDDAPAPADAASHILL---KEQLAEVLDTLTPREEKVLRLRFG 317

Query: 249 QENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            E+    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 318 LEDGRSRTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 358


>gi|322376488|ref|ZP_08050981.1| RNA polymerase sigma-70 factor [Streptococcus sp. M334]
 gi|321282295|gb|EFX59302.1| RNA polymerase sigma-70 factor [Streptococcus sp. M334]
          Length = 369

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 84/283 (29%), Positives = 141/283 (49%), Gaps = 13/283 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S        +  Y+ EI  +P+L  +EE  LA    E GD+ A  RL  ++LRLVV IA 
Sbjct: 90  STSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAV-EAGDIEAKQRLAEANLRLVVSIAK 148

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y G G+   +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I
Sbjct: 149 RYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI 208

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
                +      L R + +L      +  PEQ   IA++++++  +V  +        SL
Sbjct: 209 PVHMVE--TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSL 263

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              I   +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R
Sbjct: 264 ETPI--GEEDDSHLGDFI---EDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLR 318

Query: 247 RLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              ++    TLE++   F V+RER+RQIEA+A +K+++  + +
Sbjct: 319 FGLDDGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRQPSRSK 361


>gi|322387734|ref|ZP_08061343.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           infantis ATCC 700779]
 gi|321141601|gb|EFX37097.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           infantis ATCC 700779]
          Length = 369

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 85/283 (30%), Positives = 140/283 (49%), Gaps = 13/283 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S        +  Y+ EI  +P+L  +EE  LA    E GD+ A  RL  ++LRLVV IA 
Sbjct: 90  STSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAV-EAGDVEAKQRLAEANLRLVVSIAK 148

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y G G+   +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I
Sbjct: 149 RYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI 208

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
                +      L R + +L         PEQ   IA+K++++  +V  +        SL
Sbjct: 209 PVHMVE--TINKLVREQRNLLQEYGQEPTPEQ---IAEKMDMTPDKVREILKIAQEPVSL 263

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              I   +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R
Sbjct: 264 ETPI--GEEDDSHLGDFI---EDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLR 318

Query: 247 RLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              ++    TLE++   F V+RER+RQIEA+A +K+++  + +
Sbjct: 319 FGLDDGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRQPSRSK 361


>gi|224476669|ref|YP_002634275.1| RNA polymerase sigma factor RpoD [Staphylococcus carnosus subsp.
           carnosus TM300]
 gi|222421276|emb|CAL28090.1| RNA polymerase sigma factor SigA [Staphylococcus carnosus subsp.
           carnosus TM300]
          Length = 369

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 81/276 (29%), Positives = 137/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L  QEE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 98  DPVRMYLKEIGRVDLLNAQEEIELAKRI-EQGDEVAKARLAEANLRLVVSIAKRYVGRGM 156

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 157 LFLDLIQEGNMGLIKAVEKFDFSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 215

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L      +  PE    I +++++   +V  +        SL   I   
Sbjct: 216 -TINKLIRVQRQLLQDLGRDPAPE---EIGEEMDLPPEKVREILKIAQEPVSLETPI--G 269

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D + Q   +    +  +  L   +  L  RE  +   R   ++  
Sbjct: 270 EEDDSHLGDFI---EDQEVQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGR 326

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 327 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 362


>gi|167463432|ref|ZP_02328521.1| RNA polymerase sigma factor RpoD [Paenibacillus larvae subsp.
           larvae BRL-230010]
          Length = 375

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 81/285 (28%), Positives = 138/285 (48%), Gaps = 13/285 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
            +   +     +  Y+ EI ++P+L  ++E  LAKR  E GD  A  RL  ++LRLVV I
Sbjct: 95  TLPPGIKINDPVRMYLKEIGRVPLLSAEDEVELAKRI-EQGDEEAKRRLTEANLRLVVSI 153

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      +
Sbjct: 154 AKRYVGRGMLFLDLIQEGNMGLIKAVEKFDHTKGYKFSTYATWWIRQAITRAIADQARTI 213

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I     +      L R+   L         PE    IAK++ +S  +V  +        
Sbjct: 214 RIPVHMVE--TINKLIRVSRQLLQELGREPTPE---EIAKEMELSTDKVREIMKIAQEPV 268

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   I   +++ S   D++    D +     +    +  +  L   +  L  RE  +  
Sbjct: 269 SLETPI--GEEDDSHLGDFI---EDQEALAPADAAAYELLKEQLEDVLDTLTEREENVLR 323

Query: 245 ARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 324 LRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 368


>gi|289434736|ref|YP_003464608.1| RNA polymerase sigma factor RpoD [Listeria seeligeri serovar 1/2b
           str. SLCC3954]
 gi|289170980|emb|CBH27522.1| RNA polymerase sigma factor RpoD [Listeria seeligeri serovar 1/2b
           str. SLCC3954]
 gi|313633237|gb|EFS00106.1| RNA polymerase sigma factor RpoD [Listeria seeligeri FSL N1-067]
          Length = 374

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 80/276 (28%), Positives = 135/276 (48%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L   EE  LAKR  E GD+ A  RL  ++LRLVV IA  Y G G+
Sbjct: 103 DPVRMYLKEIGRVNLLTADEEIALAKRI-EAGDIEAKGRLAEANLRLVVSIAKRYVGRGM 161

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 162 LFLDLIQEGNMGLMKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 220

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L      +  PE    I +++++   +V  +        SL   I   
Sbjct: 221 -TINKLIRVQRSLLQDLGRDPSPE---EIGEEMDLPTEKVREILKIAQEPVSLETPI--G 274

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D       +    +  +  L   +  L  RE  +   R   ++  
Sbjct: 275 EEDDSHLGDFI---EDQDATSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGR 331

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 332 TRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSK 367


>gi|299144149|ref|ZP_07037229.1| RNA polymerase sigma factor RpoD [Peptoniphilus sp. oral taxon 386
           str. F0131]
 gi|298518634|gb|EFI42373.1| RNA polymerase sigma factor RpoD [Peptoniphilus sp. oral taxon 386
           str. F0131]
          Length = 383

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 84/291 (28%), Positives = 147/291 (50%), Gaps = 15/291 (5%)

Query: 1   MNRKNMSII--VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHL 58
           ++++++S+   ++ +  +  Y+ EI KIP+L   EE  +A+R  E GD  A   L  ++L
Sbjct: 97  LSKEDLSVPKGISVDDPVRMYLKEIGKIPLLTGDEEIDIAQRM-EVGDEDAKQELAEANL 155

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV IA  Y G G+   +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I 
Sbjct: 156 RLVVSIAKRYVGRGMSFLDLIQEGNLGLMKAVEKFDYTKGFKFSTYATWWIRQAITRAIA 215

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
                ++I     +      L R++  L      +  PE    I K++N+   +V  +  
Sbjct: 216 DQARTIRIPVHMVE--TINKLVRVQRQLVQELGRDPLPE---EIGKEMNLEVEKVREIQK 270

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
                 SL   I   ++  S   D++  D         +       +  L   +  L  R
Sbjct: 271 IAQEPVSLETPI--GEEEDSHLGDFIPDDEILS---PSDAATFTLLKEQLEDVLQTLTDR 325

Query: 239 ERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+++   R   ++    TLE +  EF+V+RER+RQIEA+A +K++   + +
Sbjct: 326 EKKVLTLRFGLDDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSK 376


>gi|260893571|ref|YP_003239668.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ammonifex
           degensii KC4]
 gi|260865712|gb|ACX52818.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ammonifex
           degensii KC4]
          Length = 369

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 86/277 (31%), Positives = 141/277 (50%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI +IP+L  +EE  LAKR  E GD  A  RL+ ++LRLVV IA  Y G G
Sbjct: 97  DDPVRMYLKEIGRIPLLTPEEEIELAKRM-EQGDEEAKRRLIEANLRLVVSIAKRYVGRG 155

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I     +
Sbjct: 156 MLFLDLIQEGNLGLIKAVEKFDWRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 215

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 L R+   L         PE    IA+K+ +S  +V  +        SL   I  
Sbjct: 216 --TINKLVRVSRQLVQELGREPTPE---EIAEKMGISPEKVREIMKVAQEPVSLETPI-- 268

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            ++  S   D++    D + Q   E+      R  L   +  L PRE+++   R   ++ 
Sbjct: 269 GEEEDSHLGDFI---EDQEAQAPAEEASYALLREQLNEVLQSLTPREQKVLRLRFGLDDG 325

Query: 253 --VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE +  +F V+RER+RQIEA+  +K++   + +
Sbjct: 326 RARTLEEVGQKFGVTRERIRQIEAKTLRKLRHPSRSK 362


>gi|315223009|ref|ZP_07864888.1| RNA polymerase sigma factor RpoD [Streptococcus anginosus F0211]
 gi|319939161|ref|ZP_08013525.1| RNA polymerase sigma factor rpoD [Streptococcus anginosus 1_2_62CV]
 gi|315187959|gb|EFU21695.1| RNA polymerase sigma factor RpoD [Streptococcus anginosus F0211]
 gi|319812211|gb|EFW08477.1| RNA polymerase sigma factor rpoD [Streptococcus anginosus 1_2_62CV]
          Length = 370

 Score =  267 bits (684), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 84/276 (30%), Positives = 139/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE  LA    E GDL A  RL  ++LRLVV IA  Y G G+
Sbjct: 98  DPVRMYLKEIGVVPLLTNEEEQELAV-LVEQGDLEAKQRLAEANLRLVVSIAKRYVGRGM 156

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 157 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 215

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA++++++  +V  +        SL   I   
Sbjct: 216 -TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSLETPI--G 269

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 270 EEDDSHLGDFI---EDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLRFGLDDGK 326

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 327 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 362


>gi|307706485|ref|ZP_07643293.1| RNA polymerase sigma factor rpoD [Streptococcus mitis SK321]
 gi|307708623|ref|ZP_07645087.1| RNA polymerase sigma factor RpoD [Streptococcus mitis NCTC 12261]
 gi|307615372|gb|EFN94581.1| RNA polymerase sigma factor RpoD [Streptococcus mitis NCTC 12261]
 gi|307618125|gb|EFN97284.1| RNA polymerase sigma factor rpoD [Streptococcus mitis SK321]
          Length = 369

 Score =  267 bits (683), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 84/283 (29%), Positives = 141/283 (49%), Gaps = 13/283 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S        +  Y+ EI  +P+L  +EE  LA    E GD+ A  RL  ++LRLVV IA 
Sbjct: 90  STSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAV-EAGDIEAKQRLAEANLRLVVSIAK 148

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y G G+   +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I
Sbjct: 149 RYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI 208

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
                +      L R + +L      +  PEQ   IA++++++  +V  +        SL
Sbjct: 209 PVHMVE--TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSL 263

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              I   +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R
Sbjct: 264 ETPI--GEEDDSHLGDFI---EDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLR 318

Query: 247 RLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              ++    TLE++   F V+RER+RQIEA+A +K+++  + +
Sbjct: 319 FGLDDGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRQPSRSK 361


>gi|256851182|ref|ZP_05556571.1| RNA polymerase sigma factor RpoS [Lactobacillus jensenii 27-2-CHN]
 gi|260660606|ref|ZP_05861521.1| RNA polymerase sigma factor RpoS [Lactobacillus jensenii 115-3-CHN]
 gi|282934648|ref|ZP_06339891.1| RNA polymerase sigma factor RpoD [Lactobacillus jensenii 208-1]
 gi|297206047|ref|ZP_06923442.1| RNA polymerase sigma factor rpoD [Lactobacillus jensenii JV-V16]
 gi|256616244|gb|EEU21432.1| RNA polymerase sigma factor RpoS [Lactobacillus jensenii 27-2-CHN]
 gi|260548328|gb|EEX24303.1| RNA polymerase sigma factor RpoS [Lactobacillus jensenii 115-3-CHN]
 gi|281301223|gb|EFA93524.1| RNA polymerase sigma factor RpoD [Lactobacillus jensenii 208-1]
 gi|297149173|gb|EFH29471.1| RNA polymerase sigma factor rpoD [Lactobacillus jensenii JV-V16]
          Length = 364

 Score =  267 bits (683), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 79/284 (27%), Positives = 135/284 (47%), Gaps = 13/284 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +    V     +  Y+ EI ++P+L   EE  LAKR ++ GD  A   L  ++LRLVV I
Sbjct: 84  SAPASVRMNDPVRMYLKEIGRVPLLNADEEIALAKRIQD-GDEEAKQELAEANLRLVVSI 142

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y G G+   +++ EGN+GLM+AV KF+ + GF+ +TY+ WWI+ A+   I      +
Sbjct: 143 AKRYVGRGMQFLDLIQEGNMGLMKAVDKFNYKLGFKFSTYATWWIRQAITRAIADQARTI 202

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I     +      L R++  L         PE++ A   ++++   +V  +        
Sbjct: 203 RIPVHMVE--TINKLIRIQRQLLQDLGREPTPEEIGA---EMDMGTDKVRDILKIAQEPV 257

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   I   +++ S   D++    D       +    +  +  L   +  L  RE  +  
Sbjct: 258 SLETPI--GEEDDSHLGDFI---EDKDATSPEQHASYEMLKEQLEEVLDTLTDREENVLR 312

Query: 245 ARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R   ++    TLE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 313 LRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRS 356


>gi|116514229|ref|YP_813135.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC BAA-365]
 gi|116093544|gb|ABJ58697.1| RNA polymerase, sigma 70 subunit, RpoD [Lactobacillus delbrueckii
           subsp. bulgaricus ATCC BAA-365]
          Length = 372

 Score =  267 bits (683), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 80/275 (29%), Positives = 131/275 (47%), Gaps = 13/275 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI +  +L  +EE  LAKR  E GD  A   L  ++LRLVV IA  Y G G+
Sbjct: 101 DPVRMYLKEIGRFNLLTSEEEVALAKRI-EAGDEEAKQELAEANLRLVVSIAKRYVGRGM 159

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 160 NFLDLIQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 218

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++         + +PE    IA ++++   +V           SL   I   
Sbjct: 219 -TINKLIRIQRQFLQDLGRDPEPE---EIAAEMDLPVKKVREALKVAQEPVSLETPI--G 272

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-- 251
           +++ S   D++    D       +    +  ++ L   +  L  RE  +   R   ++  
Sbjct: 273 EEDDSHLGDFI---EDKDATSPEQHAASEMLKDQLAEVLDTLTDREENVLRLRFGLDDGN 329

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           P TLE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 330 PRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRS 364


>gi|188585841|ref|YP_001917386.1| RNA polymerase, sigma 70 subunit, RpoD family [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|179350528|gb|ACB84798.1| RNA polymerase, sigma 70 subunit, RpoD family [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 360

 Score =  267 bits (683), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 82/277 (29%), Positives = 141/277 (50%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
              +  Y+ EI KIP+L   +E  LAK+  E GD  A  +L  ++LRLVV IA  Y G G
Sbjct: 88  SDPVRMYLKEIGKIPLLSPDDEIELAKKI-EEGDEGAKRKLAEANLRLVVSIAKKYVGRG 146

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I     +
Sbjct: 147 MLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 206

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 L R+   L         PE    IA+++++SE +V  +        SL   I  
Sbjct: 207 --TINKLIRVSRQLVQELGREPLPE---EIAEQMDMSEDKVREILKIAQEPVSLETPI-- 259

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            +++ S   D++    D   +   +    +  +  L   +  L PRE+++   R   ++ 
Sbjct: 260 GEEDDSHLGDFI---EDQDAKPPADAAAFELLKGQLEEVLDSLTPREQKVLRLRFGLDDG 316

Query: 253 --VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE +   F V+RER+RQIEA+A +K++  ++ +
Sbjct: 317 KTRTLEEVGKHFGVTRERIRQIEAKALRKLRHPMRSK 353


>gi|153816193|ref|ZP_01968861.1| hypothetical protein RUMTOR_02441 [Ruminococcus torques ATCC 27756]
 gi|145846528|gb|EDK23446.1| hypothetical protein RUMTOR_02441 [Ruminococcus torques ATCC 27756]
          Length = 383

 Score =  267 bits (683), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 88/290 (30%), Positives = 142/290 (48%), Gaps = 15/290 (5%)

Query: 1   MNRKNMSII--VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHL 58
           M   ++S+   V+ E  +  Y+ EI K+P+L  + E  LAKR  E GD  A   L  ++L
Sbjct: 97  MENIDLSVPEGVSIEDPVRMYLKEIGKVPLLSAEREIELAKRM-EEGDEDAKKELAEANL 155

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I 
Sbjct: 156 RLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYHKGYKFSTYATWWIRQAITRAIA 215

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
                ++I     +      L R+   L         PE    IAK+L++    V  +  
Sbjct: 216 DQARTIRIPVHMVE--TINKLIRVSRQLLQELGREPLPE---EIAKELDMPVERVREILK 270

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
                 SL   I   ++  S   D++  D      V  E   +   +  L   +  L  R
Sbjct: 271 ISQEPVSLETPI--GEEEDSHLGDFIQDD---NVPVPAEAAAQTLLKEQLDEVLDTLTER 325

Query: 239 ERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E+++   R    +    TLE +  EF+V+RER+RQIEA+A +K++   + 
Sbjct: 326 EQKVLRLRFGMNDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRS 375


>gi|325290508|ref|YP_004266689.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Syntrophobotulus
           glycolicus DSM 8271]
 gi|324965909|gb|ADY56688.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Syntrophobotulus
           glycolicus DSM 8271]
          Length = 392

 Score =  267 bits (683), Expect = 1e-69,   Method: Composition-based stats.
 Identities = 83/280 (29%), Positives = 136/280 (48%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V  +  +  Y+ EI ++P+L  +EE  LAK   E GD  A  RL  ++LRLVV IA  Y 
Sbjct: 117 VGIDDPVRMYLKEIGRVPLLTAEEEIELAKSM-EAGDEMAKRRLAEANLRLVVSIAKRYV 175

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I   
Sbjct: 176 GRGMLFLDLIQEGNLGLIKAVEKFDFRKGFKFSTYATWWIRQAITRAIADQARTIRIPVH 235

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L      +  PE+    AK +++ E  V  +        SL   
Sbjct: 236 MVE--TINKLIRVNRQLLQELGRDPTPEET---AKVMDIPEERVREIMKIAQEPVSLETP 290

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++  +         E       +  L   +  L  RE ++   R   
Sbjct: 291 I--GEEEDSHLGDFIPDED---APAPSEAASFLLLKEQLEEVLETLTSREEKVLRLRFGL 345

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 346 DDGRTRTLEEVGQEFGVTRERIRQIEAKALRKLRHPSRSK 385


>gi|1710683|sp|P52328|RPSD2_BACSP RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A
 gi|149623|gb|AAA25264.1| RNA polymerase sigma-subunit [Leptospira borgpetersenii]
          Length = 377

 Score =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 80/285 (28%), Positives = 137/285 (48%), Gaps = 13/285 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           ++   +     +  Y+ EI ++P+L   +E  LAKR   +GD  A  RL  ++LRLVV I
Sbjct: 97  SLPPGIKINDPVRMYLKEIGRVPLLSADDEVELAKRIM-NGDEEAKRRLAEANLRLVVSI 155

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      +
Sbjct: 156 AKRYVGRGMLFLDLIQEGNMGLIKAVEKFDHNKGFKFSTYATWWIRQAITRAIADQARTI 215

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I     +      L R+   L         PE    IA ++ +S  +V  +        
Sbjct: 216 RIPVHMVE--TINKLIRVSRQLLQELGREPTPE---EIAAEMELSVEKVREIMKIAQEPV 270

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   I   +++ S   D++    D +     +    +  +  L   +  L  RE  +  
Sbjct: 271 SLETPI--GEEDDSHLGDFI---EDQEALTPADAAAYELLKEQLEDVLDTLTEREENVLR 325

Query: 245 ARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 LRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 370


>gi|313890499|ref|ZP_07824127.1| RNA polymerase sigma factor RpoD [Streptococcus pseudoporcinus SPIN
           20026]
 gi|332523157|ref|ZP_08399409.1| RNA polymerase sigma factor RpoD [Streptococcus porcinus str.
           Jelinkova 176]
 gi|313121016|gb|EFR44127.1| RNA polymerase sigma factor RpoD [Streptococcus pseudoporcinus SPIN
           20026]
 gi|332314421|gb|EGJ27406.1| RNA polymerase sigma factor RpoD [Streptococcus porcinus str.
           Jelinkova 176]
          Length = 369

 Score =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 83/276 (30%), Positives = 138/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE  LA    E GD+ A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGVVPLLTGEEEKELAIAVAE-GDVDAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA+++ ++  +V  +        SL   I   
Sbjct: 215 -TINKLVREQRNLLQELGQDPTPEQ---IAERMEMTPDKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 361


>gi|260101316|ref|ZP_05751553.1| RNA polymerase sigma factor rpoD [Lactobacillus helveticus DSM
           20075]
 gi|260084901|gb|EEW69021.1| RNA polymerase sigma factor rpoD [Lactobacillus helveticus DSM
           20075]
          Length = 370

 Score =  267 bits (683), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 80/284 (28%), Positives = 135/284 (47%), Gaps = 13/284 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +    V     +  Y+ EI ++P++   +E  LAKR  E GD  A   L  ++LRLVV I
Sbjct: 90  SAPSSVRMNDPVRMYLKEIGRVPLITADQEIALAKRI-EEGDEEAKQELAEANLRLVVSI 148

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y G G+   +++ EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      +
Sbjct: 149 AKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYCLGFKFSTYATWWIRQAITRAIADQARTI 208

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I     +      L R++  L         PE++ A   ++N+  ++V  +        
Sbjct: 209 RIPVHMVE--TINKLIRIQRQLLQDLGREPTPEEIGA---EMNMPTNKVRDILKIAQEPV 263

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   I   +++ S   D++    D       +    +  +  L + +  L  RE  +  
Sbjct: 264 SLETPI--GEEDDSHLGDFI---EDKDATSPEQHASYEMLKEQLEQVLETLTDREENVLR 318

Query: 245 ARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R   ++    TLE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 319 LRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRS 362


>gi|297588502|ref|ZP_06947145.1| DNA-directed RNA polymerase sigma subunit RpoD [Finegoldia magna
           ATCC 53516]
 gi|297573875|gb|EFH92596.1| DNA-directed RNA polymerase sigma subunit RpoD [Finegoldia magna
           ATCC 53516]
          Length = 389

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 86/280 (30%), Positives = 139/280 (49%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           +N +  +  Y+ EI KIP+L  +EE  LA+   E+G   A  +L  ++LRLVV IA  Y 
Sbjct: 114 INVDDPVKMYLKEIGKIPLLSAEEEVKLAQEM-ENGSKRAKKKLAEANLRLVVSIAKRYV 172

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GLM+AV KFD  RGF+ +TY+ WWI+ A+   I      ++I   
Sbjct: 173 GRGMSFLDLIQEGNLGLMKAVDKFDYTRGFKFSTYATWWIRQAITRAIADQARTIRIPVH 232

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      + RL    + +  +  +      IAK++ +   +V  +        SL   
Sbjct: 233 MVE-----TINRLVRIERQLLQDLGRDPTNEEIAKEMGIEVEKVREVRKIAQEPVSLETP 287

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL- 248
           I   ++  S   D++  D         E       R  L   ++ LN RER++   R   
Sbjct: 288 I--GEEEDSHLGDFIEDD---TAIAPDEAANFTMLREELEGILNTLNERERKVLALRFGL 342

Query: 249 -QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
               P TLE +  +F+V+RER+RQIEA+A +K++   + Q
Sbjct: 343 VDGTPRTLEEVGKDFDVTRERIRQIEAKALRKLKHPSRSQ 382


>gi|289550668|ref|YP_003471572.1| RNA polymerase sigma factor RpoD [Staphylococcus lugdunensis
           HKU09-01]
 gi|315658163|ref|ZP_07911035.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           lugdunensis M23590]
 gi|289180200|gb|ADC87445.1| RNA polymerase sigma factor RpoD [Staphylococcus lugdunensis
           HKU09-01]
 gi|315496492|gb|EFU84815.1| DNA-directed RNA polymerase sigma subunit RpoD [Staphylococcus
           lugdunensis M23590]
          Length = 368

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 81/276 (29%), Positives = 137/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L  QEE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGRVNLLNAQEEIELAKRI-EQGDEIAKSRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 LFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L      +  PE    I +++++   +V  +        SL   I   
Sbjct: 215 -TINKLIRVQRQLLQDLGRDPAPE---EIGEEMDLPPEKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D + Q   +    +  +  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGR 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 361


>gi|317128328|ref|YP_004094610.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacillus
           cellulosilyticus DSM 2522]
 gi|315473276|gb|ADU29879.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacillus
           cellulosilyticus DSM 2522]
          Length = 372

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 80/289 (27%), Positives = 143/289 (49%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   +     +  Y+ EI ++P+L   EE  LAK+  E GD  A  RL  ++LRL
Sbjct: 88  LNDLSVPPGIKINDPVRMYLKEIGRVPLLSASEEIDLAKKI-EDGDEEAKRRLAEANLRL 146

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I   
Sbjct: 147 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYNKGYKFSTYATWWIRQAITRAIADQ 206

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE+V   +K+++++  +V  +    
Sbjct: 207 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPSPEEV---SKEMDLTPDKVREILKIA 261

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D +     +    +  +  L   +  L  RE 
Sbjct: 262 QEPVSLETPI--GEEDDSHLGDFI---EDQEALAPSDAAAYELLKEQLEDVLDTLTDREE 316

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 317 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 365


>gi|161507646|ref|YP_001577600.1| RNA polymerase sigma factor RpoD [Lactobacillus helveticus DPC
           4571]
 gi|160348635|gb|ABX27309.1| RNA polymerase sigma factor [Lactobacillus helveticus DPC 4571]
          Length = 356

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 80/284 (28%), Positives = 135/284 (47%), Gaps = 13/284 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +    V     +  Y+ EI ++P++   +E  LAKR  E GD  A   L  ++LRLVV I
Sbjct: 76  SAPSSVRMNDPVRMYLKEIGRVPLITADQEIALAKRI-EEGDEEAKQELAEANLRLVVSI 134

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y G G+   +++ EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      +
Sbjct: 135 AKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYCLGFKFSTYATWWIRQAITRAIADQARTI 194

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I     +      L R++  L         PE++ A   ++N+  ++V  +        
Sbjct: 195 RIPVHMVE--TINKLIRIQRQLLQDLGREPTPEEIGA---EMNMPTNKVRDILKIAQEPV 249

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   I   +++ S   D++    D       +    +  +  L + +  L  RE  +  
Sbjct: 250 SLETPI--GEEDDSHLGDFI---EDKDATSPEQHASYEMLKEQLEQVLETLTDREENVLR 304

Query: 245 ARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R   ++    TLE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 305 LRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRS 348


>gi|24379277|ref|NP_721232.1| RNA polymerase sigma factor RpoD [Streptococcus mutans UA159]
 gi|290580718|ref|YP_003485110.1| DNA-dependent RNA polymerase sigma subunit [Streptococcus mutans
           NN2025]
 gi|18202024|sp|O33662|RPOD_STRMU RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-42
 gi|24377195|gb|AAN58538.1|AE014923_2 DNA-dependent RNA polymerase sigma subunit; major sigma factor
           (sigma 70/42) [Streptococcus mutans UA159]
 gi|2258087|dbj|BAA21507.1| sigma 42 protein [Streptococcus mutans]
 gi|254997617|dbj|BAH88218.1| DNA-dependent RNA polymerase sigma subunit [Streptococcus mutans
           NN2025]
          Length = 371

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 84/276 (30%), Positives = 141/276 (51%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE  LA    E+GDL A  RL  ++LRLVV IA  Y G G+
Sbjct: 99  DPVRMYLKEIGVVPLLTNEEEKELAIAV-ENGDLEAKQRLAEANLRLVVSIAKRYVGRGM 157

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 158 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 216

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA++++++  +V  +        SL   I   
Sbjct: 217 -TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSLETPI--G 270

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 271 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 327

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F+V+RER+RQIEA+A +K++   + +
Sbjct: 328 MRTLEDVGKVFDVTRERIRQIEAKALRKLRHPSRSK 363


>gi|313618909|gb|EFR90770.1| RNA polymerase sigma factor RpoD [Listeria innocua FSL S4-378]
          Length = 374

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 83/288 (28%), Positives = 141/288 (48%), Gaps = 15/288 (5%)

Query: 4   KNMSIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
            +MS+    +I   +  Y+ EI ++ +L   EE  LAKR  E GD+ A  RL  ++LRLV
Sbjct: 91  TDMSVPPGVKINDPVRMYLKEIGRVDLLTADEEIALAKRI-EVGDIEAKGRLAEANLRLV 149

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA  Y G G+   +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I    
Sbjct: 150 VSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQA 209

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             ++I     +      L R++  L      +  PE    I +++++   +V  +     
Sbjct: 210 RTIRIPVHMVE--TINKLIRVQRSLLQDLGRDPSPE---EIGEEMDLPTEKVREILKIAQ 264

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              SL   I   +++ S   D++    D       +    +  +  L   +  L  RE  
Sbjct: 265 EPVSLETPI--GEEDDSHLGDFI---EDQDATSPSDHAAYELLKEQLEDVLDTLTDREEN 319

Query: 242 IFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 320 VLRLRFGLDDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSK 367


>gi|307243281|ref|ZP_07525452.1| RNA polymerase sigma factor RpoD [Peptostreptococcus stomatis DSM
           17678]
 gi|306493409|gb|EFM65391.1| RNA polymerase sigma factor RpoD [Peptostreptococcus stomatis DSM
           17678]
          Length = 384

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 86/280 (30%), Positives = 146/280 (52%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ +  +  Y+ EI KIP+L+  EE   AKR  E GD  A  +LV ++LRLVV IA  Y 
Sbjct: 109 ISIDDPVRMYLKEIGKIPLLKPHEEVEYAKRMAE-GDEFAKQKLVEANLRLVVSIAKRYV 167

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD ++G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 168 GRGMLFLDLIQEGNLGLIKAVEKFDYKKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 227

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L      + KP+    IAK++N++E +V  +        SL   
Sbjct: 228 MVE--TINKLIRVSRQLLQELGRDPKPD---EIAKEMNMTEEKVREIMKIAQDPVSLETP 282

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++            E       +  +   ++ LN RE+ + + R   
Sbjct: 283 I--GEEEDSHLGDFIPD---EDAPAPAEAAAYSLLKEQIEDVLNTLNDREQNVLKLRFGL 337

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+    TLE +  EF+V+RER+RQIEA+A +K++   + +
Sbjct: 338 EDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSK 377


>gi|289578734|ref|YP_003477361.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter italicus Ab9]
 gi|289528447|gb|ADD02799.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter italicus Ab9]
          Length = 357

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 85/280 (30%), Positives = 140/280 (50%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ +  +  Y+ EI KIP+L  +EE  LAKR  E GD  A  RL+ ++LRLVV IA  Y 
Sbjct: 82  ISIDDPVRMYLKEIGKIPLLTPEEEIELAKRI-EQGDEEAKKRLIEANLRLVVSIAKRYV 140

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 141 GRGMLFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 200

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R++  L         PE    +AK++ + E +V  +        SL   
Sbjct: 201 MVE--TINKLIRIQRQLLQELGREPTPE---ELAKEMGMPEEKVREIMKIAQEPVSLETP 255

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++            E       +  L   +  L PRE ++   R   
Sbjct: 256 I--GEEEDSHLGDFIPD---EDAPAPAEAAAFTMLKEQLMDVLDTLTPREEKVLRLRFGL 310

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 311 DDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 350


>gi|306833811|ref|ZP_07466936.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus bovis
           ATCC 700338]
 gi|304424005|gb|EFM27146.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus bovis
           ATCC 700338]
          Length = 369

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 83/276 (30%), Positives = 138/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE  LA      GDL A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGVVPLLTSEEEKELAVAVA-TGDLQAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA++++++  +V  +        SL   I   
Sbjct: 215 -TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 361


>gi|157825543|ref|YP_001493263.1| RNA polymerase factor sigma-32 [Rickettsia akari str. Hartford]
 gi|157799501|gb|ABV74755.1| RNA polymerase factor sigma-32 [Rickettsia akari str. Hartford]
          Length = 293

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 143/285 (50%), Positives = 197/285 (69%), Gaps = 1/285 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M     ++ ++ E G   Y+ +I  IP L ++EE++LAK Y E  DL AAH+LVTSHL+L
Sbjct: 1   MTNNINALAISSESGFYNYLQKINNIPSLTQEEEFLLAKSYLEENDLQAAHKLVTSHLKL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIA GYR YG+PI+E+VSEGNIGLMQAVKKF+PE GFRL+TY+MWWIKAA+QEYIL+S
Sbjct: 61  VAKIASGYRTYGIPITELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKAAIQEYILKS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTA QK+LFF+L ++K  +  +    +  +    IA +L VS +EV  MN R+
Sbjct: 121 WSLVKMGTTAAQKKLFFSLNKVKHKITNLYSRAITTDDFAKIADELGVSVNEVSEMNTRI 180

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D SLN  INS D  S +  + L       E + I K+   ++R +L  +M +LN RE
Sbjct: 181 SGPDLSLNNSINSDDAASGELIELLPETRPTPEAMAINKQNFTSKRKLLANAMKILNDRE 240

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            RI   R+L + P TL+ LS+E+ +S+ER+RQIE  AF+K+++ I
Sbjct: 241 LRILTERKLTDTPTTLDILSNEYNISKERIRQIENTAFEKIKKFI 285


>gi|322383680|ref|ZP_08057431.1| RNA polymerase sigma factor RpoD-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321151892|gb|EFX44835.1| RNA polymerase sigma factor RpoD-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 354

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 81/285 (28%), Positives = 138/285 (48%), Gaps = 13/285 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
            +   +     +  Y+ EI ++P+L  ++E  LAKR  E GD  A  RL  ++LRLVV I
Sbjct: 74  TLPPGIKINDPVRMYLKEIGRVPLLSAEDEVELAKRI-EQGDEEAKRRLTEANLRLVVSI 132

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      +
Sbjct: 133 AKRYVGRGMLFLDLIQEGNMGLIKAVEKFDHTKGYKFSTYATWWIRQAITRAIADQARTI 192

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I     +      L R+   L         PE    IAK++ +S  +V  +        
Sbjct: 193 RIPVHMVE--TINKLIRVSRQLLQELGREPTPE---EIAKEMELSTDKVREIMKIAQEPV 247

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   I   +++ S   D++    D +     +    +  +  L   +  L  RE  +  
Sbjct: 248 SLETPI--GEEDDSHLGDFI---EDQEALAPADAAAYELLKEQLEDVLDTLTEREENVLR 302

Query: 245 ARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 303 LRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 347


>gi|295110289|emb|CBL24242.1| RNA polymerase, sigma 70 subunit, RpoD [Ruminococcus obeum A2-162]
          Length = 376

 Score =  267 bits (682), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 84/279 (30%), Positives = 135/279 (48%), Gaps = 13/279 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V+ E  +  Y+ EI K+ +L   EE  LAKR  E GD  A  RL  ++LRLVV IA  Y 
Sbjct: 101 VSIEDPVRMYLKEIGKVSLLTADEEIELAKRM-EQGDEEAKKRLAEANLRLVVSIAKRYV 159

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 160 GRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 219

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L         PE    IA+++ +    V  +        SL   
Sbjct: 220 MVE--TINKLIRVSRQLLQELGREPTPE---EIAEEMKMPVERVREILKISQEPVSLETP 274

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++  D      V  +       +  L   +  L  RE+++   R   
Sbjct: 275 I--GEEEDSHLGDFIQDD---NVPVPADAAAFTLLKEQLIEVLGTLTEREQKVLRLRFGL 329

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ++    TLE +  EF V+RER+RQIEA+A +K++   + 
Sbjct: 330 DDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRS 368


>gi|258516189|ref|YP_003192411.1| RNA polymerase sigma factor RpoD [Desulfotomaculum acetoxidans DSM
           771]
 gi|257779894|gb|ACV63788.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfotomaculum
           acetoxidans DSM 771]
          Length = 359

 Score =  266 bits (681), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 83/280 (29%), Positives = 141/280 (50%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           +  +  +  Y+ EI ++P+L  +EE  LAKR  E G+  A  RL  ++LRLVV IA  Y 
Sbjct: 84  IGIDDPVRMYLKEIGRVPLLSSEEEVELAKRM-EMGEEEAKRRLAEANLRLVVSIAKRYV 142

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 143 GRGMLFLDLIQEGNMGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 202

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L         PE    IAK++N++E +V  +        SL   
Sbjct: 203 MVE--TINKLIRVSRQLLQELGREPMPE---EIAKEMNITEDKVREIMKIAQEPVSLETP 257

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++    D   +   E+      R  L   +  L  RE+++   R   
Sbjct: 258 I--GEEEDSHLGDFI---EDHDARAPAEEASFTLLREQLDDVLKTLTDREQKVLRLRFGL 312

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++    TLE +  +F V+RER+RQIEA+  +K++   + +
Sbjct: 313 DDGRARTLEEVGQKFGVTRERIRQIEAKTLRKLRHPSRSK 352


>gi|260438482|ref|ZP_05792298.1| RNA polymerase sigma factor RpoD [Butyrivibrio crossotus DSM 2876]
 gi|292809071|gb|EFF68276.1| RNA polymerase sigma factor RpoD [Butyrivibrio crossotus DSM 2876]
          Length = 370

 Score =  266 bits (681), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 83/279 (29%), Positives = 135/279 (48%), Gaps = 13/279 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ E  +  Y+ EI K+P+L   EE  LAKR  E GD  A  +L  ++LRLVV IA  Y 
Sbjct: 95  ISIEDPVRMYLKEIGKVPLLSADEEIELAKRM-ELGDEEAKKKLAEANLRLVVSIAKRYV 153

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 154 GRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 213

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L         P     IA ++++    V  +        SL   
Sbjct: 214 MVE--TINKLIRVSRQLLQELGREPSP---QEIADEMDIPVERVREILKISQEPVSLETP 268

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++  D      V  E       +  L   +  L  RE+++ + R   
Sbjct: 269 I--GEEEDSHLGDFIQDD---NVPVPAEAAAFTLLKEQLNEVLGTLTEREQKVLKLRFGL 323

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E+    TLE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 324 EDGRARTLEEVGKVFNVTRERIRQIEAKALRKLRHPSRS 362


>gi|157828283|ref|YP_001494525.1| RNA polymerase factor sigma-32 [Rickettsia rickettsii str. 'Sheila
           Smith']
 gi|165932987|ref|YP_001649776.1| RNA polymerase factor sigma-32 [Rickettsia rickettsii str. Iowa]
 gi|157800764|gb|ABV76017.1| RNA polymerase factor sigma-32 [Rickettsia rickettsii str. 'Sheila
           Smith']
 gi|165908074|gb|ABY72370.1| RNA polymerase sigma-32 factor [Rickettsia rickettsii str. Iowa]
          Length = 293

 Score =  266 bits (681), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 144/285 (50%), Positives = 198/285 (69%), Gaps = 1/285 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M     ++ ++ E G   Y+ +I KIP L ++EE +LAK Y E  DL AAH+LVTSHL+L
Sbjct: 1   MTNNINALAISSESGFYSYLQKINKIPSLTQEEELLLAKSYLEGNDLQAAHKLVTSHLKL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIA GYR YGLPI+E+VSEGNIGLMQAVKKF+PE GFRL+TY+MWWIKAA+QEYIL+S
Sbjct: 61  VAKIASGYRTYGLPITELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKAAIQEYILKS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTT  QK+LFF+L ++K  +  +    +  +  V IA +L VS +EV  MN R+
Sbjct: 121 WSLVKMGTTTAQKKLFFSLNKVKHKITNLYSRAITTDDFVQIADELGVSVNEVSEMNTRI 180

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D SLN  IN+ D  S +  + L       E + I K+   ++R +L+ +M +LN RE
Sbjct: 181 SGPDLSLNNSINNDDAESGELIELLPETRPTPEAMAINKQNSTSKRQLLSNAMKILNDRE 240

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            RI   R+L + P TL+ LS+E+ +S+ER+RQIE  AF+K+++ I
Sbjct: 241 LRILTERKLTDTPKTLDILSNEYNISKERIRQIENTAFEKIKKFI 285


>gi|297544972|ref|YP_003677274.1| RpoD subfamily RNA polymerase sigma-70 subunit [Thermoanaerobacter
           mathranii subsp. mathranii str. A3]
 gi|296842747|gb|ADH61263.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
          Length = 357

 Score =  266 bits (681), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 85/280 (30%), Positives = 140/280 (50%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ +  +  Y+ EI KIP+L  +EE  LAKR  E GD  A  RL+ ++LRLVV IA  Y 
Sbjct: 82  ISIDDPVRMYLKEIGKIPLLTPEEEIELAKRI-EQGDEEAKKRLIEANLRLVVSIAKRYV 140

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 141 GRGMLFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 200

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R++  L         PE    +AK++ + E +V  +        SL   
Sbjct: 201 MVE--TINKLIRVQRQLLQELGREPTPE---ELAKEMGMPEEKVREIMKIAQEPVSLETP 255

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++            E       +  L   +  L PRE ++   R   
Sbjct: 256 I--GEEEDSHLGDFIPD---EDAPAPAEAAAFTMLKEQLMDVLDTLTPREEKVLRLRFGL 310

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 311 DDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 350


>gi|288905580|ref|YP_003430802.1| RNA polymerase major sigma factor [Streptococcus gallolyticus
           UCN34]
 gi|306831670|ref|ZP_07464827.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           gallolyticus subsp. gallolyticus TX20005]
 gi|325978609|ref|YP_004288325.1| RNA polymerase sigma factor rpoD [Streptococcus gallolyticus subsp.
           gallolyticus ATCC BAA-2069]
 gi|288732306|emb|CBI13876.1| RNA polymerase major sigma factor [Streptococcus gallolyticus
           UCN34]
 gi|304426095|gb|EFM29210.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           gallolyticus subsp. gallolyticus TX20005]
 gi|325178537|emb|CBZ48581.1| RNA polymerase sigma factor rpoD [Streptococcus gallolyticus subsp.
           gallolyticus ATCC BAA-2069]
          Length = 369

 Score =  266 bits (681), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 83/276 (30%), Positives = 138/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE  LA      GDL A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGVVPLLTSEEEKELAVAVA-AGDLQAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA++++++  +V  +        SL   I   
Sbjct: 215 -TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 361


>gi|4587113|dbj|BAA76622.1| RpoT [Mycobacterium leprae]
          Length = 576

 Score =  266 bits (681), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 79/320 (24%), Positives = 147/320 (45%), Gaps = 45/320 (14%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------------------- 42
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR                     
Sbjct: 263 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSERGTKL 321

Query: 43  ------------EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
                         GD  A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV
Sbjct: 322 PTAQRRDMMWICRDGDR-AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAV 380

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L    
Sbjct: 381 EKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDL 438

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
                PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D 
Sbjct: 439 GREPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDS 490

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRER 268
           +  V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER
Sbjct: 491 EAVVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRER 550

Query: 269 VRQIEARAFKKVQESIQKQV 288
           +RQIE++   K++   + QV
Sbjct: 551 IRQIESKTMSKLRHPSRSQV 570


>gi|328465879|gb|EGF37062.1| RNA polymerase sigma factor RpoD [Lactobacillus helveticus MTCC
           5463]
          Length = 370

 Score =  266 bits (681), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 80/284 (28%), Positives = 135/284 (47%), Gaps = 13/284 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +    V     +  Y+ EI ++P++   +E  LAKR  E GD  A   L  ++LRLVV I
Sbjct: 90  SAPSSVRMNDPVRMYLKEIGRVPLITADQEIALAKRI-EEGDEEAKQELAEANLRLVVSI 148

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y G G+   +++ EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      +
Sbjct: 149 AKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYCLGFKFSTYATWWIRQAITRAIADQARTI 208

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I     +      L R++  L         PE++ A   ++N+  ++V  +        
Sbjct: 209 RIPVHMVE--TINKLIRIQRQLLQDLGREPTPEEIGA---EMNMPTNKVRDILKIAQEPV 263

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   I   +++ S   D++    D       +    +  +  L + +  L  RE  +  
Sbjct: 264 SLETPI--GEEDDSHLGDFI---EDKDATSPEQHASYEMLKEQLEQVLETLTDREENVLR 318

Query: 245 ARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R   ++    TLE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 319 LRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRS 362


>gi|158320313|ref|YP_001512820.1| RpoD family RNA polymerase sigma factor [Alkaliphilus oremlandii
           OhILAs]
 gi|158140512|gb|ABW18824.1| RNA polymerase, sigma 70 subunit, RpoD family [Alkaliphilus
           oremlandii OhILAs]
          Length = 372

 Score =  266 bits (681), Expect = 2e-69,   Method: Composition-based stats.
 Identities = 88/280 (31%), Positives = 145/280 (51%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           VN +  +  Y+ EI K+P+L  +EE  LAKR  + GD  A  RLV ++LRLVV IA  Y 
Sbjct: 97  VNIDDPVRMYLKEIGKVPLLSAEEEIELAKRM-DAGDEEAKKRLVEANLRLVVSIAKRYV 155

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ WWI+ A+   I      ++I   
Sbjct: 156 GRGMLFLDLIQEGNLGLIKAVEKFDYKKGFKFSTYATWWIRQAITRAIADQARTIRIPVH 215

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L      + KPE    IA ++++SE +V  +        SL   
Sbjct: 216 MVE--TINKLIRVSRQLLQELGRDPKPE---EIAAEMDLSEEKVREILKIAQEPVSLETP 270

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++            E       +  L   +  L PRE+++   R   
Sbjct: 271 I--GEEEDSHLGDFIPD---EDAPAPAEAAAFSLLKEQLVEVLDTLTPREQKVLRLRFGL 325

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++    TLE +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 326 DDGRARTLEEVGKKFDVTRERIRQIEAKALRKLRHPSRSK 365


>gi|241896072|ref|ZP_04783368.1| DNA-directed RNA polymerase sigma subunit RpoD [Weissella
           paramesenteroides ATCC 33313]
 gi|241870672|gb|EER74423.1| DNA-directed RNA polymerase sigma subunit RpoD [Weissella
           paramesenteroides ATCC 33313]
          Length = 378

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 80/276 (28%), Positives = 137/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L   EE  LA+R  E GD +A   L  ++LRLVV IA  Y G G+
Sbjct: 107 DPVRMYLKEIGRVSLLTGDEEVSLAERI-EAGDETAKQELAEANLRLVVSIAKRYVGRGM 165

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 166 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 224

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++ +L         PE++ A   +++V+  +V  +        SL   I   
Sbjct: 225 -TINKLIRIQRNLLQDLGREPTPEEIGA---EMDVATEKVRDILKIAQEPVSLETPI--G 278

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D +     +    +  +  L   +  L  RE  +   R   E+  
Sbjct: 279 EEDDSHLGDFI---EDNEAVSPADSAAYQMLKEQLESVLDTLTDREENVLRLRFGLEDGR 335

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 336 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 371


>gi|300765597|ref|ZP_07075576.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           N1-017]
 gi|300513698|gb|EFK40766.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           N1-017]
          Length = 374

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 83/288 (28%), Positives = 141/288 (48%), Gaps = 15/288 (5%)

Query: 4   KNMSIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
            +MS+    +I   +  Y+ EI ++ +L   EE  LAKR  E GD+ A  RL  ++LRLV
Sbjct: 91  TDMSVPPGVKINDPVRMYLKEIGRVDLLTADEEIALAKRI-EAGDIEAKGRLAEANLRLV 149

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA  Y G G+   +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I    
Sbjct: 150 VSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQA 209

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             ++I     +      L R++  L      +  PE    I +++++   +V  +     
Sbjct: 210 RTIRIPVHMVE--TINKLIRVQRSLLQDLGRDPSPE---EIGEEMDLPTEKVREILKIAQ 264

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              SL   I   +++ S   D++    D       +    +  +  L   +  L  RE  
Sbjct: 265 EPVSLETPI--GEEDDSHLGDFI---EDQDATSPSDHAAYELLKEQLEDVLDTLTDREEN 319

Query: 242 IFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 320 VLRLRFGLDDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSK 367


>gi|329117418|ref|ZP_08246135.1| RNA polymerase sigma factor RpoD [Streptococcus parauberis NCFD
           2020]
 gi|326907823|gb|EGE54737.1| RNA polymerase sigma factor RpoD [Streptococcus parauberis NCFD
           2020]
          Length = 369

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 83/276 (30%), Positives = 138/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE  LA    + GDL A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGVVPLLTGEEEKELAVAV-DEGDLEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA+++ ++  +V  +        SL   I   
Sbjct: 215 -TINKLVREQRNLLQELGQDPTPEQ---IAERMEMTPDKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 361


>gi|291166412|gb|EFE28458.1| RNA polymerase sigma factor RpoD [Filifactor alocis ATCC 35896]
          Length = 372

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 83/280 (29%), Positives = 144/280 (51%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ +  +  Y+ EI KI +L  +EE  LA++  + G   A  +LV ++LRLVV IA  Y 
Sbjct: 97  ISVDDPVRMYLKEIGKISLLSAEEEIELAQKM-DQGSELAKKKLVEANLRLVVSIAKRYV 155

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I   
Sbjct: 156 GRGMLFLDLIQEGNLGLIKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVH 215

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R++  L        +PE    I+K +++S  ++  +        SL   
Sbjct: 216 MVE--TINKLIRVQRQLLQELGREPRPE---EISKVMDMSVEKIREIQKISQEPVSLETP 270

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++  D         E       +  L   +S LN RE+++ + R   
Sbjct: 271 I--GEEEDSHLGDFIPDDD---ALAPSEAAAYSLLKEQLEEVLSTLNEREQKVLKLRFGL 325

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+    TLE +  EF+V+RER+RQIEA+A +K++   + +
Sbjct: 326 EDGRTRTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSK 365


>gi|328957491|ref|YP_004374877.1| RNA polymerase sigma factor RpoD [Carnobacterium sp. 17-4]
 gi|328673815|gb|AEB29861.1| RNA polymerase sigma factor RpoD [Carnobacterium sp. 17-4]
          Length = 373

 Score =  266 bits (681), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 79/276 (28%), Positives = 135/276 (48%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L   EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 102 DPVRMYLKEIGRVNLLTAAEEVELAIKI-EEGDQEARQRLAEANLRLVVSIAKRYVGRGM 160

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV+KFD ++GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 161 QFLDLIQEGNMGLMKAVEKFDYKKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 219

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L         PE++ A   ++++   +V  +        SL   I   
Sbjct: 220 -TINKLIRIQRQLLQDLGREPTPEEIGA---EMDLPTEKVREILKIAQEPVSLETPI--G 273

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D       E    +  +  L   +  L  RE  +   R   ++  
Sbjct: 274 EEDDSHLGDFI---EDHDATSPAENAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGR 330

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 331 NRTLEDVGKVFGVTRERIRQIEAKALRKLRHPSRSK 366


>gi|153813734|ref|ZP_01966402.1| hypothetical protein RUMOBE_04167 [Ruminococcus obeum ATCC 29174]
 gi|149830174|gb|EDM85267.1| hypothetical protein RUMOBE_04167 [Ruminococcus obeum ATCC 29174]
          Length = 330

 Score =  266 bits (680), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 84/279 (30%), Positives = 135/279 (48%), Gaps = 13/279 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V+ E  +  Y+ EI K+ +L   EE  LAKR  E GD  A  RL  ++LRLVV IA  Y 
Sbjct: 55  VSIEDPVRMYLKEIGKVSLLTADEEIELAKRM-EQGDEEAKKRLAEANLRLVVSIAKRYV 113

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 114 GRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 173

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L         PE    IA+++ +    V  +        SL   
Sbjct: 174 MVE--TINKLIRVSRQLLQELGREPTPE---EIAEEMKMPVDRVREILKISQEPVSLETP 228

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++  D      V  +       +  L   +  L  RE+++   R   
Sbjct: 229 I--GEEEDSHLGDFIQDD---NVPVPADAAAFTLLKEQLIEVLGTLTEREQKVLRLRFGL 283

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ++    TLE +  EF V+RER+RQIEA+A +K++   + 
Sbjct: 284 DDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRS 322


>gi|255026189|ref|ZP_05298175.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           J2-003]
          Length = 361

 Score =  266 bits (680), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 83/288 (28%), Positives = 141/288 (48%), Gaps = 15/288 (5%)

Query: 4   KNMSIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
            +MS+    +I   +  Y+ EI ++ +L   EE  LAKR  E GD+ A  RL  ++LRLV
Sbjct: 78  TDMSVPPGVKINDPVRMYLKEIGRVDLLTADEEIALAKRI-EAGDIEAKGRLAEANLRLV 136

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA  Y G G+   +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I    
Sbjct: 137 VSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQA 196

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             ++I     +      L R++  L      +  PE    I +++++   +V  +     
Sbjct: 197 RTIRIPVHMVE--TINKLIRVQRSLLQDLGRDPSPE---EIGEEMDLPTEKVREILKIAQ 251

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              SL   I   +++ S   D++    D       +    +  +  L   +  L  RE  
Sbjct: 252 EPVSLETPI--GEEDDSHLGDFI---EDQDATSPSDHAAYELLKEQLEDVLDTLTDREEN 306

Query: 242 IFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 307 VLRLRFGLDDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSK 354


>gi|225026302|ref|ZP_03715494.1| hypothetical protein EUBHAL_00543 [Eubacterium hallii DSM 3353]
 gi|224956366|gb|EEG37575.1| hypothetical protein EUBHAL_00543 [Eubacterium hallii DSM 3353]
          Length = 367

 Score =  266 bits (680), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 83/279 (29%), Positives = 144/279 (51%), Gaps = 13/279 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V+ E  +  Y+ EI  IP+L  +EE  LA+R  E GD  A  +L+ ++LRLVV IA  Y 
Sbjct: 92  VSLEDPVRMYLKEIGNIPLLTAEEEVFLAQRI-EKGDEQARKQLIEANLRLVVSIAKKYV 150

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GLM+AV+KFD ++G + +TYS WWI+ A+   I  +   +++   
Sbjct: 151 GRGMSFLDLIQEGNMGLMKAVEKFDYKKGNKFSTYSTWWIRQAITRGIADTAKTIRVPVH 210

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      + +     + +     +      IAKK+N+  +++  +        SL+  
Sbjct: 211 MVE-----TINKTLRTSRMLLQELGREPTNEEIAKKMNMPVAKIDEILKTSRDPVSLDTP 265

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  SQ  D++    D      ++       +  L  +M+ L  RER + + R   
Sbjct: 266 I--GEEEDSQLGDFI---EDESLLSPVDSASFSMLKEELEEAMASLTERERNVIKLRFGL 320

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ++    TLE +  EF V+RER+RQIEA+A +K++   + 
Sbjct: 321 DDGKTRTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRS 359


>gi|205374117|ref|ZP_03226917.1| RNA polymerase sigma factor RpoD [Bacillus coahuilensis m4-4]
          Length = 337

 Score =  266 bits (680), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 82/289 (28%), Positives = 141/289 (48%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++ +L  +EE  LA+R  E GD  A  RL  ++LRL
Sbjct: 53  LNDLSVPPGVKINDPVRMYLKEIGRVDLLSAEEEISLAERI-EQGDEEAKRRLAEANLRL 111

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 112 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQ 171

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    I +++++   +V  +    
Sbjct: 172 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPSPE---EIGEEMDLPPEKVREILKIA 226

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D + Q   E    +  +  L   +  L  RE 
Sbjct: 227 QEPVSLETPI--GEEDDSHLGDFI---EDSEAQSPSEHAAYELLKEQLEDVLDTLTDREE 281

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 282 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 330


>gi|126699059|ref|YP_001087956.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile 630]
 gi|115250496|emb|CAJ68320.1| RNA polymerase sigma factor SigA1 (sigma-43) [Clostridium
           difficile]
          Length = 390

 Score =  266 bits (680), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 86/280 (30%), Positives = 144/280 (51%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ +  +  Y+ EI KIP+L+  EE   A+R  E GD  A  RLV ++LRLVV IA  Y 
Sbjct: 115 ISIDDPVRMYLKEIGKIPLLKPHEEVEFARRMHE-GDEIAKQRLVEANLRLVVSIAKRYV 173

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 174 GRGMLFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 233

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L      + KPE    IAK++ ++E +V  +        SL   
Sbjct: 234 MVE--TINKLIRVSRQLLQELGRDPKPE---EIAKEMEMTEDKVREIMKIAQDPVSLETP 288

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++            E       +  +   +  LN RE+++ + R   
Sbjct: 289 I--GEEEDSHLGDFIPD---DDAPAPAEAAAYSLLKEQIEDVLGSLNDREQKVLKLRFGL 343

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+    TLE +  EF+V+RER+RQIEA+A +K++   + +
Sbjct: 344 EDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSK 383


>gi|327440913|dbj|BAK17278.1| DNA-directed RNA polymerase, sigma subunit [Solibacillus silvestris
           StLB046]
          Length = 375

 Score =  266 bits (680), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 80/289 (27%), Positives = 141/289 (48%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++ +L   +E  LA+R  E GD  A  RL  ++LRL
Sbjct: 91  LNDLSVPPGVKINDPVRMYLKEIGRVDLLSADQEIRLAERI-EQGDEEARKRLAEANLRL 149

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 150 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDHRKGFKFSTYATWWIRQAITRAIADQ 209

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    I ++++++  +V  +    
Sbjct: 210 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPSPE---EIGEEMDLTPEKVREILKIA 264

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D + Q   +    +  +  L   +  L  RE 
Sbjct: 265 QEPVSLETPI--GEEDDSHLGDFI---EDSEAQSPSDHAAYELLKEQLEDVLDTLTDREE 319

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 320 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 368


>gi|323498063|ref|ZP_08103069.1| RNA polymerase factor sigma-32 [Vibrio sinaloensis DSM 21326]
 gi|323316871|gb|EGA69876.1| RNA polymerase factor sigma-32 [Vibrio sinaloensis DSM 21326]
          Length = 285

 Score =  266 bits (680), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 110/287 (38%), Positives = 167/287 (58%), Gaps = 8/287 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  +   + V  +  L  YI ++   PML   EE  LA+R    G++ AA  L+ SHLR 
Sbjct: 1   MTNQAYPMAVVTQDSLDSYIRKVNSYPMLTADEERELAERLHYDGEIEAAKGLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A GY GYGLP++++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VKI TT  Q++LFFNLR+ K  L    +      +V  +AK+L V  +EV  M  RL
Sbjct: 121 WRIVKIATTKAQRKLFFNLRKSKKRLGWFNNG-----EVETVAKELGVEPAEVREMESRL 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE---ERKNRRNMLTRSMSVLNP 237
           A  +S   +    D + S +   ++Y  D    V    E      +  N L+ +++ L+ 
Sbjct: 176 AAQDSTFEMPTDDDDSVSSYTAPVLYLEDKASDVADNVEAANWEAHTNNRLSLALASLDE 235

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R + I  +R L +N  TL+ L+  + VS ER+RQ+E  A KK++ ++
Sbjct: 236 RSQHIVRSRWLDDNKSTLQELAETYSVSAERIRQLEKNAMKKLKTAV 282


>gi|15900942|ref|NP_345546.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae TIGR4]
 gi|15903023|ref|NP_358573.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae R6]
 gi|111657922|ref|ZP_01408632.1| hypothetical protein SpneT_02000898 [Streptococcus pneumoniae
           TIGR4]
 gi|116516638|ref|YP_816435.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae D39]
 gi|148985044|ref|ZP_01818287.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP3-BS71]
 gi|148989116|ref|ZP_01820506.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP6-BS73]
 gi|148994179|ref|ZP_01823494.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae
           SP9-BS68]
 gi|148998339|ref|ZP_01825781.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP11-BS70]
 gi|149003984|ref|ZP_01828792.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP14-BS69]
 gi|149006254|ref|ZP_01829966.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae
           SP18-BS74]
 gi|149013172|ref|ZP_01833989.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP19-BS75]
 gi|149019675|ref|ZP_01834994.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP23-BS72]
 gi|168483147|ref|ZP_02708099.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae CDC1873-00]
 gi|168487460|ref|ZP_02711968.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae CDC1087-00]
 gi|168488915|ref|ZP_02713114.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae SP195]
 gi|168494506|ref|ZP_02718649.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae CDC3059-06]
 gi|168576202|ref|ZP_02722096.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae MLV-016]
 gi|169833634|ref|YP_001694498.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae
           Hungary19A-6]
 gi|182684177|ref|YP_001835924.1| RNA polymerase sigma factor [Streptococcus pneumoniae CGSP14]
 gi|221231817|ref|YP_002510969.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae ATCC
           700669]
 gi|225854569|ref|YP_002736081.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae JJA]
 gi|225856717|ref|YP_002738228.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae P1031]
 gi|225858886|ref|YP_002740396.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae 70585]
 gi|225861039|ref|YP_002742548.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae
           Taiwan19F-14]
 gi|237650028|ref|ZP_04524280.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae CCRI
           1974]
 gi|237821736|ref|ZP_04597581.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae CCRI
           1974M2]
 gi|298230104|ref|ZP_06963785.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae str.
           Canada MDR_19F]
 gi|298255542|ref|ZP_06979128.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae str.
           Canada MDR_19A]
 gi|298502915|ref|YP_003724855.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           pneumoniae TCH8431/19A]
 gi|303256088|ref|ZP_07342108.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae BS455]
 gi|303260611|ref|ZP_07346576.1| RNA polymerase sigma factor [Streptococcus pneumoniae SP-BS293]
 gi|303263023|ref|ZP_07348956.1| RNA polymerase sigma factor [Streptococcus pneumoniae SP14-BS292]
 gi|303264870|ref|ZP_07350786.1| RNA polymerase sigma factor [Streptococcus pneumoniae BS397]
 gi|303266910|ref|ZP_07352787.1| RNA polymerase sigma factor [Streptococcus pneumoniae BS457]
 gi|303269116|ref|ZP_07354896.1| RNA polymerase sigma factor [Streptococcus pneumoniae BS458]
 gi|307067745|ref|YP_003876711.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Streptococcus pneumoniae AP200]
 gi|307127396|ref|YP_003879427.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae 670-6B]
 gi|61234224|sp|P0A4I9|RPOD_STRPN RecName: Full=RNA polymerase sigma factor rpoD
 gi|61234230|sp|P0A4J0|RPOD_STRR6 RecName: Full=RNA polymerase sigma factor rpoD
 gi|2108331|emb|CAA72252.1| rpoD [Streptococcus pneumoniae]
 gi|14972548|gb|AAK75186.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae TIGR4]
 gi|15458593|gb|AAK99783.1| RNA polymerase sigmA FACTOR 70 [Streptococcus pneumoniae R6]
 gi|116077214|gb|ABJ54934.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae D39]
 gi|147755736|gb|EDK62781.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP11-BS70]
 gi|147758043|gb|EDK65049.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP14-BS69]
 gi|147762031|gb|EDK68993.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae
           SP18-BS74]
 gi|147763023|gb|EDK69967.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP19-BS75]
 gi|147922742|gb|EDK73859.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP3-BS71]
 gi|147925339|gb|EDK76417.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP6-BS73]
 gi|147927422|gb|EDK78452.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae
           SP9-BS68]
 gi|147931050|gb|EDK82030.1| RNA polymerase sigma-70 factor [Streptococcus pneumoniae SP23-BS72]
 gi|168996136|gb|ACA36748.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae Hungary19A-6]
 gi|172043392|gb|EDT51438.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae CDC1873-00]
 gi|182629511|gb|ACB90459.1| RNA polymerase sigma factor [Streptococcus pneumoniae CGSP14]
 gi|183569691|gb|EDT90219.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae CDC1087-00]
 gi|183572434|gb|EDT92962.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae SP195]
 gi|183575600|gb|EDT96128.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae CDC3059-06]
 gi|183577989|gb|EDT98517.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae MLV-016]
 gi|220674277|emb|CAR68818.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae ATCC
           700669]
 gi|225720127|gb|ACO15981.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae 70585]
 gi|225722225|gb|ACO18078.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae JJA]
 gi|225725305|gb|ACO21157.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae P1031]
 gi|225728137|gb|ACO23988.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae Taiwan19F-14]
 gi|298238510|gb|ADI69641.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           pneumoniae TCH8431/19A]
 gi|301794192|emb|CBW36610.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae INV104]
 gi|301800046|emb|CBW32640.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae OXC141]
 gi|301802035|emb|CBW34765.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae INV200]
 gi|302596935|gb|EFL64061.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae BS455]
 gi|302635850|gb|EFL66352.1| RNA polymerase sigma factor [Streptococcus pneumoniae SP14-BS292]
 gi|302638261|gb|EFL68731.1| RNA polymerase sigma factor [Streptococcus pneumoniae SP-BS293]
 gi|302641365|gb|EFL71732.1| RNA polymerase sigma factor [Streptococcus pneumoniae BS458]
 gi|302643543|gb|EFL73813.1| RNA polymerase sigma factor [Streptococcus pneumoniae BS457]
 gi|302645558|gb|EFL75789.1| RNA polymerase sigma factor [Streptococcus pneumoniae BS397]
 gi|306409282|gb|ADM84709.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Streptococcus pneumoniae AP200]
 gi|306484458|gb|ADM91327.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae 670-6B]
 gi|327389372|gb|EGE87717.1| RNA polymerase sigma factor rpoD [Streptococcus pneumoniae GA04375]
 gi|332073431|gb|EGI83910.1| RNA polymerase sigma factor rpoD [Streptococcus pneumoniae GA17570]
 gi|332075028|gb|EGI85499.1| RNA polymerase sigma factor rpoD [Streptococcus pneumoniae GA17545]
 gi|332075404|gb|EGI85873.1| RNA polymerase sigma factor rpoD [Streptococcus pneumoniae GA41301]
 gi|332200548|gb|EGJ14620.1| RNA polymerase sigma factor rpoD [Streptococcus pneumoniae GA41317]
 gi|332201555|gb|EGJ15625.1| RNA polymerase sigma factor rpoD [Streptococcus pneumoniae GA47368]
 gi|332202930|gb|EGJ16998.1| RNA polymerase sigma factor rpoD [Streptococcus pneumoniae GA47901]
          Length = 369

 Score =  266 bits (680), Expect = 3e-69,   Method: Composition-based stats.
 Identities = 84/283 (29%), Positives = 141/283 (49%), Gaps = 13/283 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S        +  Y+ EI  +P+L  +EE  LA    E GD+ A  RL  ++LRLVV IA 
Sbjct: 90  STSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAV-EAGDIEAKQRLAEANLRLVVSIAK 148

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y G G+   +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I
Sbjct: 149 RYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI 208

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
                +      L R + +L      +  PEQ   IA++++++  +V  +        SL
Sbjct: 209 PVHMVE--TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSL 263

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              I   +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R
Sbjct: 264 ETPI--GEEDDSHLGDFI---EDEVIENPVDYTTRIVLREQLDEILDTLTDREENVLRLR 318

Query: 247 RLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              ++    TLE++   F V+RER+RQIEA+A +K+++  + +
Sbjct: 319 FGLDDGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRQPSRSK 361


>gi|171779914|ref|ZP_02920818.1| hypothetical protein STRINF_01701 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
 gi|171281262|gb|EDT46697.1| hypothetical protein STRINF_01701 [Streptococcus infantarius subsp.
           infantarius ATCC BAA-102]
          Length = 369

 Score =  266 bits (680), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 83/276 (30%), Positives = 138/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE  LA      GDL A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGVVPLLSSEEEKELAVAVA-AGDLQAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA++++++  +V  +        SL   I   
Sbjct: 215 -TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 361


>gi|81428494|ref|YP_395494.1| RNA polymerase sigma factor RpoD [Lactobacillus sakei subsp. sakei
           23K]
 gi|78610136|emb|CAI55185.1| DNA-directed RNA polymerase sigma factor, sigma A (Primary sigma
           factor) [Lactobacillus sakei subsp. sakei 23K]
          Length = 369

 Score =  265 bits (679), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 84/288 (29%), Positives = 141/288 (48%), Gaps = 15/288 (5%)

Query: 4   KNMSIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           K+MS     +I   +  Y+ EI ++ +L  Q+E  LA R  E GD  A  RL  ++LRLV
Sbjct: 86  KDMSAPTGIKINDPVRMYLKEIGRVSLLNAQQEVDLALRI-EQGDQEAKQRLAEANLRLV 144

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA  Y G G+   +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I    
Sbjct: 145 VSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDHRKGFKFSTYATWWIRQAITRAIADQA 204

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             ++I     +      L R++  L         PE++ A   +++++  +V  +     
Sbjct: 205 RTIRIPVHMVE--TINKLIRIQRQLLQDLGREPTPEEIGA---EMDMNTDKVREILKIAQ 259

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              SL   I   +++ S   D++    D       E    +  +  L   +  L  RE  
Sbjct: 260 EPVSLETPI--GEEDDSHLGDFI---EDQDATSPEEHASYELLKEQLESVLDTLTDREEN 314

Query: 242 IFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 315 VLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 362


>gi|320547037|ref|ZP_08041336.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           equinus ATCC 9812]
 gi|320448322|gb|EFW89066.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           equinus ATCC 9812]
          Length = 369

 Score =  265 bits (679), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 84/276 (30%), Positives = 138/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE  LA      GDL A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGVVPLLSSEEEKELAVAVA-AGDLQAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA+++++S  +V  +        SL   I   
Sbjct: 215 -TINKLVREQRNLLQELGQDPTPEQ---IAERMDMSPDKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 361


>gi|167037157|ref|YP_001664735.1| RNA polymerase sigma factor RpoD [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|167039957|ref|YP_001662942.1| RNA polymerase sigma factor RpoD [Thermoanaerobacter sp. X514]
 gi|256751255|ref|ZP_05492135.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter ethanolicus CCSD1]
 gi|300915505|ref|ZP_07132817.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter sp. X561]
 gi|307266219|ref|ZP_07547761.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|307724719|ref|YP_003904470.1| RpoD subfamily RNA polymerase sigma-70 subunit [Thermoanaerobacter
           sp. X513]
 gi|320115576|ref|YP_004185735.1| RNA polymerase sigma factor RpoD [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
 gi|326390577|ref|ZP_08212133.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter ethanolicus JW 200]
 gi|166854197|gb|ABY92606.1| RNA polymerase, sigma 70 subunit, RpoD family [Thermoanaerobacter
           sp. X514]
 gi|166855991|gb|ABY94399.1| RNA polymerase, sigma 70 subunit, RpoD family [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|256749810|gb|EEU62834.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter ethanolicus CCSD1]
 gi|300888457|gb|EFK83607.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter sp. X561]
 gi|306918749|gb|EFN48981.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|307581780|gb|ADN55179.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter sp. X513]
 gi|319928667|gb|ADV79352.1| RNA polymerase sigma factor RpoD [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
 gi|325993402|gb|EGD51838.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter ethanolicus JW 200]
          Length = 357

 Score =  265 bits (679), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 85/280 (30%), Positives = 140/280 (50%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ +  +  Y+ EI KIP+L  +EE  LAKR  E GD  A  RL+ ++LRLVV IA  Y 
Sbjct: 82  ISIDDPVRMYLKEIGKIPLLTPEEEIELAKRI-EQGDEEAKKRLIEANLRLVVSIAKRYV 140

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 141 GRGMLFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 200

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R++  L         PE    +AK++ + E +V  +        SL   
Sbjct: 201 MVE--TINKLIRVQRQLLQELGREPTPE---ELAKEMGMPEEKVREIMKIAQEPVSLETP 255

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++            E       +  L   +  L PRE ++   R   
Sbjct: 256 I--GEEEDSHLGDFIPD---EDAPAPAEAAAFTMLKEQLMDVLDTLTPREEKVLRLRFGL 310

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 311 DDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 350


>gi|302386858|ref|YP_003822680.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           saccharolyticum WM1]
 gi|302197486|gb|ADL05057.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           saccharolyticum WM1]
          Length = 380

 Score =  265 bits (679), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 82/280 (29%), Positives = 144/280 (51%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           +  E  +  Y+ EI  +P+L  +EE  LAKR +  GD  A  RL+ ++LRLVV IA  Y 
Sbjct: 106 IGTEDPVRMYLKEIGTVPLLNAEEELRLAKR-KADGDDDAKERLIEANLRLVVSIAKRYT 164

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   ++V EGN+GL++ V+KFD  +G++L+TY+ WWI+ ++   +      +++   
Sbjct: 165 GRGMSFLDLVQEGNLGLIKGVEKFDYTKGYKLSTYATWWIRQSVTRALADQARTIRVPVH 224

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      + ++    + +T        V  +A+ L++SE +V+ +        SL   
Sbjct: 225 MVE-----TINKMSKMQRKLTLELGYEPSVSELAEALDMSEDKVMEIMQIAREPASLETP 279

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   +++ S   D++    D          E    R  +   +  L  RER++   R   
Sbjct: 280 I--GEEDDSNLGDFVA---DNNVVTPEGNVESVMLREHIDALLGDLKERERQVIVLRFGL 334

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+  P TLE +  EF V+RER+RQIEA+A +K++  ++ +
Sbjct: 335 EDGHPRTLEEVGKEFNVTRERIRQIEAKALRKLRNPVRSK 374


>gi|239947881|ref|ZP_04699634.1| alternative sigma factor RpoH [Rickettsia endosymbiont of Ixodes
           scapularis]
 gi|239922157|gb|EER22181.1| alternative sigma factor RpoH [Rickettsia endosymbiont of Ixodes
           scapularis]
          Length = 293

 Score =  265 bits (679), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 146/285 (51%), Positives = 199/285 (69%), Gaps = 1/285 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M     ++ ++ E G   Y+ +I KIP L ++EE++LAK Y E  DL AAH+LVTSHL+L
Sbjct: 1   MTNNINALAISSESGFYSYLQKINKIPSLTQEEEFLLAKSYLEENDLQAAHKLVTSHLKL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIA GYR YGLPI+E+VSEGNIGLMQAVKKF+PE GFRL+TY+MWWIKAA+QEYIL+S
Sbjct: 61  VAKIASGYRTYGLPITELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKAAIQEYILKS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTA QK+LFF+L ++K  +  +    +  +    IA +L VS +EV  MN R+
Sbjct: 121 WSLVKMGTTAAQKKLFFSLNKVKHKITNLYSRAITTDDFAQIADELGVSINEVSEMNTRI 180

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D SLN  INS D  S +  + L       E + I K+   ++R +L+ +M +LN RE
Sbjct: 181 SGPDLSLNNSINSDDAESGELIELLPETRPTPEAMAINKQNSTSKRKLLSNAMKILNDRE 240

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            RI   R+L + P TL+ LSSE+ +S+ER+RQIE  AF+K+++ I
Sbjct: 241 LRILTERKLTDTPKTLDILSSEYNISKERIRQIENTAFEKIKKFI 285


>gi|283769573|ref|ZP_06342469.1| RNA polymerase sigma factor RpoD [Bulleidia extructa W1219]
 gi|283103841|gb|EFC05227.1| RNA polymerase sigma factor RpoD [Bulleidia extructa W1219]
          Length = 413

 Score =  265 bits (679), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 81/282 (28%), Positives = 141/282 (50%), Gaps = 12/282 (4%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           I       +  Y+ EI ++P+L+  EE  +AK+  E GD  A + L++S+LRLVV IA  
Sbjct: 134 ISATSGDSVKMYLKEIGRVPLLKASEEIEIAKKI-EQGDEEARNVLISSNLRLVVSIAKK 192

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I 
Sbjct: 193 YVGRGMQFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIP 252

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
               +      L R++  L         PE++ A  +   +S  +V  +        SL 
Sbjct: 253 VHMVE--TINKLTRVERSLVQELSREPTPEEISACLE--GISADKVREIKKIALDPVSLE 308

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I   +++ S   D++    D       +    +  ++ +   +S L  RE ++   R 
Sbjct: 309 TPI--GEEDDSHLGDFI---EDKDALSPDQYASNQLLKDEINDVLSGLTEREEKVLRLRF 363

Query: 248 LQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              +    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 364 GLYDGRTRTLEEVGREFNVTRERIRQIEAKALRKLKHPNRSK 405


>gi|120600694|ref|YP_965268.1| RNA polymerase factor sigma-32 [Shewanella sp. W3-18-1]
 gi|146291400|ref|YP_001181824.1| RNA polymerase factor sigma-32 [Shewanella putrefaciens CN-32]
 gi|120560787|gb|ABM26714.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella sp. W3-18-1]
 gi|145563090|gb|ABP74025.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella putrefaciens
           CN-32]
 gi|319428373|gb|ADV56447.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella putrefaciens
           200]
          Length = 285

 Score =  265 bits (679), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 110/290 (37%), Positives = 172/290 (59%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSI---IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSH 57
           M  +  S+   +  G   L  YIH +  I ML+ + EY LAKR +E GDL AA +L+ SH
Sbjct: 1   MTFQTQSMALTVPQGSSSLEAYIHSVTSISMLDAEAEYELAKRLQETGDLQAAKQLIMSH 60

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LR VV +A GY GYGLP ++++ EGNIGLM+AVK+FDP+ G RL ++++ WIKA + EY+
Sbjct: 61  LRFVVHVAKGYSGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYV 120

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           L++W +VK+ TT  Q++LFFN+R+ K  L   +D     E+V  +A+ L VS+++V  M 
Sbjct: 121 LKNWRIVKVATTKAQRKLFFNIRKAKKRLGWFSD-----EEVTMVAENLGVSKADVTEME 175

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLN 236
            R+A  +    L + +D          + DH       IE +  + N +  L  ++  L+
Sbjct: 176 SRMAAQDPAFDLTSDNDDEQDFAPVHYLEDHSSDLAENIENDNWESNAQGRLLSAIKTLD 235

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R + I  AR L ++  TL+ L+  ++VS ER+RQ+E  A  K++  ++ 
Sbjct: 236 ERSQHILRARWLDDDKTTLQELAETYQVSAERIRQLEKNAMNKLKACMEA 285


>gi|15827492|ref|NP_301755.1| RNA polymerase sigma factor [Mycobacterium leprae TN]
 gi|221229969|ref|YP_002503385.1| RNA polymerase sigma factor [Mycobacterium leprae Br4923]
 gi|699190|gb|AAA62955.1| rpoT [Mycobacterium leprae]
 gi|4587111|dbj|BAA76621.1| RpoT [Mycobacterium leprae]
 gi|13093042|emb|CAC31403.1| RNA polymerase sigma factor [Mycobacterium leprae]
 gi|219933076|emb|CAR71117.1| RNA polymerase sigma factor [Mycobacterium leprae Br4923]
          Length = 574

 Score =  265 bits (679), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 79/320 (24%), Positives = 147/320 (45%), Gaps = 45/320 (14%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------------------- 42
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR                     
Sbjct: 261 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSERGTKL 319

Query: 43  ------------EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
                         GD  A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV
Sbjct: 320 PTAQRRDMMWICRDGDR-AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAV 378

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L    
Sbjct: 379 EKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDL 436

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
                PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D 
Sbjct: 437 GREPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDS 488

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRER 268
           +  V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER
Sbjct: 489 EAVVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRER 548

Query: 269 VRQIEARAFKKVQESIQKQV 288
           +RQIE++   K++   + QV
Sbjct: 549 IRQIESKTMSKLRHPSRSQV 568


>gi|168491966|ref|ZP_02716109.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae CDC0288-04]
 gi|183573791|gb|EDT94319.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Streptococcus pneumoniae CDC0288-04]
          Length = 369

 Score =  265 bits (679), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 84/283 (29%), Positives = 141/283 (49%), Gaps = 13/283 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S        +  Y+ EI  +P+L  +EE  LA    E GD+ A  RL  ++LRLVV IA 
Sbjct: 90  STSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAV-EAGDIEAKQRLAEANLRLVVSIAK 148

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y G G+   +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I
Sbjct: 149 RYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI 208

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
                +      L R + +L      +  PEQ   IA++++++  +V  +        SL
Sbjct: 209 PVHMVE--TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSL 263

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              I   +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R
Sbjct: 264 ETPI--GEEDDSHLGDFI---EDEVIENPVDYTTRIVLREQLDEILDTLTDREENVLRLR 318

Query: 247 RLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              ++    TLE++   F V+RER+RQIEA+A +K+++  + +
Sbjct: 319 FGLDDGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRQPSRSK 361


>gi|197301814|ref|ZP_03166884.1| hypothetical protein RUMLAC_00540 [Ruminococcus lactaris ATCC
           29176]
 gi|197299254|gb|EDY33784.1| hypothetical protein RUMLAC_00540 [Ruminococcus lactaris ATCC
           29176]
          Length = 372

 Score =  265 bits (679), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 84/279 (30%), Positives = 137/279 (49%), Gaps = 13/279 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V+ E  +  Y+ EI K+P+L  + E  LA+R  E GD  A   L  ++LRLVV IA  Y 
Sbjct: 97  VSIEDPVRMYLKEIGKVPLLSAEREIELAQRM-EEGDEEAKKELAEANLRLVVSIAKRYV 155

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 156 GRGMLFLDLIQEGNLGLIKAVEKFDYHKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 215

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L         PE    IAK++++    V  +        SL   
Sbjct: 216 MVE--TINKLIRVSRQLLQELGREPLPE---EIAKEMDMPVERVREILKISQEPVSLETP 270

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++  D      V  E   +   +  L   +  L  RE+++   R   
Sbjct: 271 I--GEEEDSHLGDFIQDD---NVPVPAEAAAQTLLKEQLDEVLDTLTEREQKVLRLRFGM 325

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +    TLE +  EF+V+RER+RQIEA+A +K++   + 
Sbjct: 326 NDGRARTLEEVGREFDVTRERIRQIEAKALRKLRHPSRS 364


>gi|118586868|ref|ZP_01544302.1| DNA-directed RNA polymerase RpoD, sigma subunit, Sigma-42
           [Oenococcus oeni ATCC BAA-1163]
 gi|71466858|emb|CAH41003.1| rpoD protein [Oenococcus oeni]
 gi|118432700|gb|EAV39432.1| DNA-directed RNA polymerase RpoD, sigma subunit, Sigma-42
           [Oenococcus oeni ATCC BAA-1163]
          Length = 458

 Score =  265 bits (679), Expect = 4e-69,   Method: Composition-based stats.
 Identities = 78/278 (28%), Positives = 137/278 (49%), Gaps = 14/278 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKIAMGYRGY 71
             +  Y+ EI ++ +L   +E  +AKR  + G     A   L  ++LRLVV IA  Y G 
Sbjct: 183 DPVRMYLKEIGRVSLLNADQEVAIAKRIEKGGSDGERARQELAEANLRLVVSIAKRYVGR 242

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           G+   +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     
Sbjct: 243 GMHFLDLIQEGNMGLMKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMV 302

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
           +      L R++  L      +  PE++ A   ++ ++  +V  +        SL   I 
Sbjct: 303 E--TINKLIRIQRTLIQDLGRDPMPEEIGA---EMELTADKVREIQKIAQEPVSLETPI- 356

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             +++ S   D++    D + +  IE    +  ++ L   +  L  RE  +   R   E+
Sbjct: 357 -GEEDDSHLGDFI---EDNEGESPIESTSDQMLKDQLEEVLGTLTEREENVLRLRFGLED 412

Query: 252 P--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
               TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 413 GKTRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSK 450


>gi|331003577|ref|ZP_08327074.1| hypothetical protein HMPREF0491_01936 [Lachnospiraceae oral taxon
           107 str. F0167]
 gi|330412418|gb|EGG91809.1| hypothetical protein HMPREF0491_01936 [Lachnospiraceae oral taxon
           107 str. F0167]
          Length = 409

 Score =  265 bits (679), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 83/280 (29%), Positives = 144/280 (51%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V  E  +  Y+ EI  +P+L   EE  LAKR ++ GD  A  RL+ ++LRLVV IA  Y 
Sbjct: 134 VGTEDPVRMYLKEIGTVPLLTANEELELAKR-KQDGDEYAKQRLIEANLRLVVSIAKRYT 192

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   ++V EGN+GL++ V+KFD  +GF+L+TY+ WWI+ ++   +      +++   
Sbjct: 193 GRGMSFLDLVQEGNLGLIKGVEKFDYTKGFKLSTYATWWIRQSVTRALADQARTIRVPVH 252

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      + ++    + +T        V  +A +L ++E +V+ +        SL   
Sbjct: 253 MVE-----TINKMSKMQRKLTLELGYEPSVTELANELGMTEEKVMEIMQIAREPASLETP 307

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   +++ S   D++    D          E    R  +   +  L  RER++   R   
Sbjct: 308 I--GEEDDSNLGDFVA---DANVLTPEGNVESVMLREHIDTLLGDLKERERQVIVLRFGL 362

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+  P TLE +  EF+V+RER+RQIEA+A +K++  ++ +
Sbjct: 363 EDGHPRTLEEVGKEFKVTRERIRQIEAKALRKLRNPVRSK 402


>gi|254975009|ref|ZP_05271481.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           QCD-66c26]
 gi|255092397|ref|ZP_05321875.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile CIP
           107932]
 gi|255100481|ref|ZP_05329458.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           QCD-63q42]
 gi|255306421|ref|ZP_05350592.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile ATCC
           43255]
 gi|255314137|ref|ZP_05355720.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           QCD-76w55]
 gi|255516815|ref|ZP_05384491.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           QCD-97b34]
 gi|255649917|ref|ZP_05396819.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           QCD-37x79]
 gi|260683071|ref|YP_003214356.1| RNA polymerase factor sigma-43 [Clostridium difficile CD196]
 gi|260686669|ref|YP_003217802.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           R20291]
 gi|306520001|ref|ZP_07406348.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           QCD-32g58]
 gi|260209234|emb|CBA62522.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           CD196]
 gi|260212685|emb|CBE03759.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           R20291]
          Length = 388

 Score =  265 bits (678), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 86/280 (30%), Positives = 144/280 (51%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ +  +  Y+ EI KIP+L+  EE   A+R  E GD  A  RLV ++LRLVV IA  Y 
Sbjct: 113 ISIDDPVRMYLKEIGKIPLLKPHEEVEFARRMHE-GDEIAKQRLVEANLRLVVSIAKRYV 171

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 172 GRGMLFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 231

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L      + KPE    IAK++ ++E +V  +        SL   
Sbjct: 232 MVE--TINKLIRVSRQLLQELGRDPKPE---EIAKEMEMTEDKVREIMKIAQDPVSLETP 286

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++            E       +  +   +  LN RE+++ + R   
Sbjct: 287 I--GEEEDSHLGDFIPD---DDAPAPAEAAAYSLLKEQIEDVLGSLNDREQKVLKLRFGL 341

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+    TLE +  EF+V+RER+RQIEA+A +K++   + +
Sbjct: 342 EDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSK 381


>gi|116492861|ref|YP_804596.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Pediococcus pentosaceus ATCC 25745]
 gi|116103011|gb|ABJ68154.1| RNA polymerase, sigma 70 subunit, RpoD [Pediococcus pentosaceus
           ATCC 25745]
          Length = 379

 Score =  265 bits (678), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 77/276 (27%), Positives = 134/276 (48%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L   +E  LA R  E GD  A   L  ++LRLVV IA  Y G G+
Sbjct: 108 DPVRMYLKEIGRVSLLTADQEVELALRI-EKGDPRARQELAEANLRLVVSIAKRYVGRGM 166

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV+KFD ++GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 167 QFLDLIQEGNMGLMKAVEKFDYQKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 225

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L         PE++ A   ++++   +V  +        SL   I   
Sbjct: 226 -TINKLIRIQRQLLQDLGREPMPEEIGA---EMDMPSDKVREILKIAQEPVSLETPI--G 279

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D +     +    +  +  L   +  L  RE  +   R   ++  
Sbjct: 280 EEDDSHLGDFI---EDQEATSPADHAAYELLKEQLEGVLDTLTDREENVLRLRFGLDDGR 336

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 337 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 372


>gi|169824520|ref|YP_001692131.1| RNA polymerase sigma A factor [Finegoldia magna ATCC 29328]
 gi|302380672|ref|ZP_07269137.1| RNA polymerase sigma factor RpoD [Finegoldia magna ACS-171-V-Col3]
 gi|303233690|ref|ZP_07320344.1| RNA polymerase sigma factor RpoD [Finegoldia magna BVS033A4]
 gi|167831325|dbj|BAG08241.1| RNA polymerase sigma A factor [Finegoldia magna ATCC 29328]
 gi|302311615|gb|EFK93631.1| RNA polymerase sigma factor RpoD [Finegoldia magna ACS-171-V-Col3]
 gi|302495124|gb|EFL54876.1| RNA polymerase sigma factor RpoD [Finegoldia magna BVS033A4]
          Length = 388

 Score =  265 bits (678), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 86/280 (30%), Positives = 138/280 (49%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           +N +  +  Y+ EI KIP+L   EE  LA+   E+G   A  +L  ++LRLVV IA  Y 
Sbjct: 113 INVDDPVKMYLKEIGKIPLLSADEEVQLAQEM-ENGSKRAKKKLAEANLRLVVSIAKRYV 171

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GLM+AV KFD  RGF+ +TY+ WWI+ A+   I      ++I   
Sbjct: 172 GRGMSFLDLIQEGNLGLMKAVDKFDYTRGFKFSTYATWWIRQAITRAIADQARTIRIPVH 231

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      + RL    + +  +  +      IAK++ +   +V  +        SL   
Sbjct: 232 MVE-----TINRLVRIERQLLQDLGRDPTNEEIAKEMGIEVEKVREVRKIAQEPVSLETP 286

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL- 248
           I   ++  S   D++  D         E       R  L   ++ LN RER++   R   
Sbjct: 287 I--GEEEDSHLGDFIEDD---TAIAPDEAANFTMLREELEGILNTLNERERKVLALRFGL 341

Query: 249 -QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
               P TLE +  +F+V+RER+RQIEA+A +K++   + Q
Sbjct: 342 VDGTPRTLEEVGKDFDVTRERIRQIEAKALRKLKHPSRSQ 381


>gi|325662013|ref|ZP_08150632.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|331085863|ref|ZP_08334946.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|325471676|gb|EGC74895.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|330406786|gb|EGG86291.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 370

 Score =  265 bits (678), Expect = 5e-69,   Method: Composition-based stats.
 Identities = 90/290 (31%), Positives = 145/290 (50%), Gaps = 15/290 (5%)

Query: 1   MNRKNMSII--VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHL 58
           M + ++S+   ++ E  +  Y+ EI K+P+L  +EE  LA+R  E GD  A  RL  ++L
Sbjct: 84  MEKIDLSVPDGISIEDPVRMYLKEIGKVPLLSAEEEIELARRM-EEGDEDAKKRLAEANL 142

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I 
Sbjct: 143 RLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYNKGFKFSTYATWWIRQAITRAIA 202

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
                ++I     +      L R+   L         PE    IAK+L++    V  +  
Sbjct: 203 DQARTIRIPVHMVE--TINKLIRVSRQLLQELGREPLPE---EIAKELDMPVDRVREILK 257

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
                 SL   I   ++  S   D++  D      V  E       +  L   +S L  R
Sbjct: 258 ISQEPVSLETPI--GEEEDSHLGDFIQDD---NVPVPAEAAAATLLKEQLDEVLSTLTDR 312

Query: 239 ERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E+++   R    +    TLE +  EF+V+RER+RQIEA+A +K++   + 
Sbjct: 313 EQKVLRLRFGMNDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRS 362


>gi|269103879|ref|ZP_06156576.1| RNA polymerase sigma factor RpoH [Photobacterium damselae subsp.
           damselae CIP 102761]
 gi|268163777|gb|EEZ42273.1| RNA polymerase sigma factor RpoH [Photobacterium damselae subsp.
           damselae CIP 102761]
          Length = 287

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 110/291 (37%), Positives = 169/291 (58%), Gaps = 8/291 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+ +  S+ +     L  YI  + + PML  ++E  LA+R    GD+ AA  LV SHLR 
Sbjct: 1   MSTEMPSMALVAADSLDSYIQAVNRYPMLTAEQEKELAERLHFDGDIDAAKALVMSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA GY GYGLP+++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + E++LR+
Sbjct: 61  VVHIARGYSGYGLPMADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEFVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L    +     E++  +A +L V  SEV  M  RL
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKSKKRLGWFNN-----EEINMVADQLGVEPSEVREMESRL 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNP 237
           A  ++   + N  D           Y  D    V     E     +  N L+++++ L+ 
Sbjct: 176 AAQDATFEMSNDDDDRDFTPTAPAYYLEDKSSDVARSYEESNWETHATNRLSQALAGLDE 235

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           R + I  +R L E+  TL++L+  F VS ER+RQ+E  A KK++E++   +
Sbjct: 236 RSQFIVRSRWLDEDKSTLQDLADRFGVSAERIRQLEKNAMKKLKEAVGDDI 286


>gi|320530863|ref|ZP_08031900.1| RNA polymerase sigma factor RpoD [Selenomonas artemidis F0399]
 gi|320136897|gb|EFW28842.1| RNA polymerase sigma factor RpoD [Selenomonas artemidis F0399]
          Length = 370

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 86/281 (30%), Positives = 139/281 (49%), Gaps = 13/281 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V+ +  +  Y+ EI  +P+L  +EE  LA+   E GD  A HRL  ++LRLVV IA  Y 
Sbjct: 95  VSLDDPVRMYLKEIGHVPLLTAEEEVELAQLM-EAGDEEARHRLEEANLRLVVSIAKRYV 153

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 154 GRGMLFLDLIQEGNLGLLKAVEKFDYSKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 213

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L      + +PE    IAK++ +S + V  +        SL   
Sbjct: 214 MVE--TINKLVRISRQLLQELGRDPRPE---EIAKEMGISVARVHEIMKIAQEPVSLETP 268

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++    D       E       R  L   +  L  RE+ +   R   
Sbjct: 269 I--GEEEDSHLGDFI---EDEAAPAPAEAASFMLLREQLEEVLETLTDREKNVLRLRFGL 323

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           E+    TLE +   F V+RER+RQIEA+A +K++   + +V
Sbjct: 324 EDGRSRTLEEVGQSFGVTRERIRQIEAKALRKLRHPSRSKV 364


>gi|313897089|ref|ZP_07830636.1| RNA polymerase sigma factor RpoD [Selenomonas sp. oral taxon 137
           str. F0430]
 gi|312974536|gb|EFR40004.1| RNA polymerase sigma factor RpoD [Selenomonas sp. oral taxon 137
           str. F0430]
          Length = 370

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 86/281 (30%), Positives = 139/281 (49%), Gaps = 13/281 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V+ +  +  Y+ EI  +P+L  +EE  LA+   E GD  A HRL  ++LRLVV IA  Y 
Sbjct: 95  VSLDDPVRMYLKEIGHVPLLTAEEEVELAQLM-EAGDEEARHRLEEANLRLVVSIAKRYV 153

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 154 GRGMLFLDLIQEGNLGLLKAVEKFDYSKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 213

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L      + +PE    IAK++ +S + V  +        SL   
Sbjct: 214 MVE--TINKLVRISRQLLQELGRDPRPE---EIAKEMGISVARVHEIMKIAQEPVSLETP 268

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++    D       E       R  L   +  L  RE+ +   R   
Sbjct: 269 I--GEEEDSHLGDFI---EDEAAPAPAEAASFMLLREQLEEVLETLTDREKNVLRLRFGL 323

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           E+    TLE +   F V+RER+RQIEA+A +K++   + +V
Sbjct: 324 EDGRSRTLEEVGQSFGVTRERIRQIEAKALRKLRHPSRSKV 364


>gi|28899727|ref|NP_799332.1| RNA polymerase factor sigma-32 [Vibrio parahaemolyticus RIMD
           2210633]
 gi|260879104|ref|ZP_05891459.1| alternative sigma factor RpoH [Vibrio parahaemolyticus AN-5034]
 gi|28807979|dbj|BAC61216.1| RNA polymerase sigma-32 factor [Vibrio parahaemolyticus RIMD
           2210633]
 gi|308089656|gb|EFO39351.1| alternative sigma factor RpoH [Vibrio parahaemolyticus AN-5034]
 gi|328472446|gb|EGF43312.1| RNA polymerase factor sigma-32 [Vibrio parahaemolyticus 10329]
          Length = 286

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 112/285 (39%), Positives = 168/285 (58%), Gaps = 9/285 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++   + +  +  L  YI  +   PML   EE  LA+R    G++ AA  L+ SHLR 
Sbjct: 1   MTKEAYPMALVTQDSLDSYIRSVNSYPMLTADEERELAERLHYKGEIEAAKGLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A GY GYGLP++++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VKI TT  Q++LFFNLR+ K  L    +      +V  +A++L V  SEV  M  RL
Sbjct: 121 WRIVKIATTKAQRKLFFNLRKSKKRLGWFNNG-----EVETVARELGVEPSEVREMESRL 175

Query: 181 AGDES-LNALINSSDKNSSQWQDWLVYDHDGQEQVL--IEKEERKNRR-NMLTRSMSVLN 236
           A  +S  +   +  D  +S +   ++Y  D    V   IE    +    N L  +++ L+
Sbjct: 176 AAVDSTFDMPTDDDDSATSSYTAPMLYLEDKSSDVADNIEAANWEMHTNNRLGHALASLD 235

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R +RI  +R L +   TL++L+ EF VS ER+RQ+E  A KK++
Sbjct: 236 ERSQRIVRSRWLDDEKATLQDLADEFGVSAERIRQLEKNAMKKLK 280


>gi|91227498|ref|ZP_01261835.1| RNA polymerase sigma factor [Vibrio alginolyticus 12G01]
 gi|262392915|ref|YP_003284769.1| RNA polymerase sigma factor RpoH [Vibrio sp. Ex25]
 gi|269968648|ref|ZP_06182645.1| RNA polymerase sigma -32 factor [Vibrio alginolyticus 40B]
 gi|91188522|gb|EAS74814.1| RNA polymerase sigma factor [Vibrio alginolyticus 12G01]
 gi|262336509|gb|ACY50304.1| RNA polymerase sigma factor RpoH [Vibrio sp. Ex25]
 gi|269826735|gb|EEZ81072.1| RNA polymerase sigma -32 factor [Vibrio alginolyticus 40B]
          Length = 285

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 111/284 (39%), Positives = 167/284 (58%), Gaps = 8/284 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++   + +  +  L  YI  +   PML   EE  LA+R    G++ AA  L+ SHLR 
Sbjct: 1   MTKEAYPMALVTQDSLDSYIRSVNSYPMLTADEERELAERLHYKGEIEAAKGLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A GY GYGLP++++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VKI TT  Q++LFFNLR+ K  L    +      +V  +A++L V  SEV  M  RL
Sbjct: 121 WRIVKIATTKAQRKLFFNLRKSKKRLGWFNNG-----EVETVARELGVEPSEVREMESRL 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE---ERKNRRNMLTRSMSVLNP 237
           A  +S   +    D +S+ +   ++Y  D    V    E      +  N L  +++ L+ 
Sbjct: 176 AAVDSTFDMPTDEDDSSNAYTAPMLYLEDKSSDVADNIEAANWEMHTNNRLGHALASLDE 235

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R +RI  +R L +   TL++L+ EF VS ER+RQ+E  A KK++
Sbjct: 236 RSQRIVRSRWLDDEKATLQDLADEFGVSAERIRQLEKNAMKKLK 279


>gi|116491026|ref|YP_810570.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Oenococcus oeni PSU-1]
 gi|290890507|ref|ZP_06553582.1| hypothetical protein AWRIB429_0972 [Oenococcus oeni AWRIB429]
 gi|116091751|gb|ABJ56905.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Oenococcus oeni PSU-1]
 gi|290479903|gb|EFD88552.1| hypothetical protein AWRIB429_0972 [Oenococcus oeni AWRIB429]
          Length = 458

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 79/278 (28%), Positives = 137/278 (49%), Gaps = 14/278 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKIAMGYRGY 71
             +  Y+ EI ++ +L   +E  +AKR  + G     A   L  ++LRLVV IA  Y G 
Sbjct: 183 DPVRMYLKEIGRVSLLNADQEVAIAKRIEKGGSDGERARQELAEANLRLVVSIAKRYVGR 242

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           G+   +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     
Sbjct: 243 GMHFLDLIQEGNMGLMKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMV 302

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
           +      L R++  L      +  PE++ A   ++ ++  +V  +        SL   I 
Sbjct: 303 E--TINKLIRIQRTLIQDLGRDPMPEEIGA---EMELTADKVREIQKIAQEPVSLETPI- 356

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             ++N S   D++    D + +  IE    +  ++ L   +  L  RE  +   R   E+
Sbjct: 357 -GEENDSHLGDFI---EDNEGESPIESTSDQMLKDQLEEVLGTLTEREENVLRLRFGLED 412

Query: 252 P--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
               TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 413 GKTRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSK 450


>gi|300173322|ref|YP_003772488.1| RNA polymerase sigma factor RpoD [Leuconostoc gasicomitatum LMG
           18811]
 gi|299887701|emb|CBL91669.1| RNA polymerase sigma factor RpoD [Leuconostoc gasicomitatum LMG
           18811]
          Length = 432

 Score =  265 bits (678), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 80/276 (28%), Positives = 136/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L+  EE  +AKR  E GD+ A   L  ++LRLVV IA  Y G G+
Sbjct: 157 DPVRMYLKEIGRVNLLKGDEEINIAKRI-EDGDIEAKQELAEANLRLVVSIAKRYVGRGM 215

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 216 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 274

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L         PE++ A   +++++  +V  +        SL   I   
Sbjct: 275 -TINKLIRIQRQLLQDLGREPLPEEIGA---EMDLTPDKVREILKIAQEPVSLETPI--G 328

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D +     +    +  R  L   +  L  RE  +   R   E+  
Sbjct: 329 EEDDSHLGDFI---EDNEAVSPADSAAYEMLREQLESVLETLTDREENVLRLRFGLEDGR 385

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 386 TRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSK 421


>gi|313888947|ref|ZP_07822607.1| RNA polymerase sigma factor RpoD [Peptoniphilus harei
           ACS-146-V-Sch2b]
 gi|312845120|gb|EFR32521.1| RNA polymerase sigma factor RpoD [Peptoniphilus harei
           ACS-146-V-Sch2b]
          Length = 362

 Score =  265 bits (677), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 86/290 (29%), Positives = 143/290 (49%), Gaps = 15/290 (5%)

Query: 2   NRKNMSII--VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLR 59
            ++++S+   V  +  +  Y+ EI KI +L  +EE  +AKR  E GD  A   L  ++LR
Sbjct: 77  TKEDLSVPKGVTVDDPVRMYLKEIGKISLLTAEEEVEIAKRM-EEGDELAKKELAEANLR 135

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           LVV IA  Y G G+   +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I  
Sbjct: 136 LVVSIAKRYVGRGMSFLDLIQEGNLGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIAD 195

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
               ++I     +      L R++  L      +  PE    IA ++N+    V  +   
Sbjct: 196 QARTIRIPVHMVE--TINKLVRVQRQLVQDLGRDPLPE---EIAAEMNLDVERVREIQKI 250

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
                SL   I   ++  S   D++  D     Q   +       +  L   +  L  RE
Sbjct: 251 AQEPVSLETPI--GEEEDSHLGDFIPDDEILSPQ---DAATFTLLKEQLNTVLETLTDRE 305

Query: 240 RRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +++   R   ++    TLE +  EF+V+RER+RQIEA+A +K++   + +
Sbjct: 306 KKVLTLRFGLDDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSK 355


>gi|20808174|ref|NP_623345.1| RNA polymerase sigma factor RpoD [Thermoanaerobacter tengcongensis
           MB4]
 gi|20516766|gb|AAM24949.1| DNA-directed RNA polymerase sigma subunits (sigma70/sigma32)
           [Thermoanaerobacter tengcongensis MB4]
          Length = 372

 Score =  265 bits (677), Expect = 6e-69,   Method: Composition-based stats.
 Identities = 88/291 (30%), Positives = 146/291 (50%), Gaps = 15/291 (5%)

Query: 1   MNRKNMSII--VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHL 58
           +N  ++S+   V+ +  +  Y+ EI KIP+L  +EE  LAKR  E GD  A  RL+ ++L
Sbjct: 86  LNLDDLSLPEGVSIDDPVRMYLKEIGKIPLLTPEEEIELAKRI-EQGDEEAKKRLIEANL 144

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I 
Sbjct: 145 RLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIA 204

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
                ++I     +      L R++  L         PE    +AK++ + E +V  +  
Sbjct: 205 DQARTIRIPVHMVE--TINKLIRVQRQLLQELGREPTPE---ELAKEMGMPEEKVREILK 259

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
                 SL   I   ++  S   D++            E       +  L   +  L PR
Sbjct: 260 IAQEPVSLETPI--GEEEDSHLGDFIPD---EDAPAPAEAAAYTMLKEQLMDVLDTLTPR 314

Query: 239 ERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E ++   R   ++    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 315 EEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 365


>gi|323127013|gb|ADX24310.1| RNA polymerase sigma factor RpoD [Streptococcus dysgalactiae subsp.
           equisimilis ATCC 12394]
          Length = 369

 Score =  265 bits (677), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 85/276 (30%), Positives = 139/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE VLA    E GDL A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGVVPLLTSEEEKVLAVAVAE-GDLEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA+++ ++  +V  +        SL   I   
Sbjct: 215 -TINKLVREQRNLLQELGQDPTPEQ---IAERMEMTPDKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 361


>gi|313884259|ref|ZP_07818025.1| RNA polymerase sigma factor RpoD [Eremococcus coleocola
           ACS-139-V-Col8]
 gi|312620706|gb|EFR32129.1| RNA polymerase sigma factor RpoD [Eremococcus coleocola
           ACS-139-V-Col8]
          Length = 376

 Score =  265 bits (677), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 78/277 (28%), Positives = 132/277 (47%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
              +  Y+ EI ++ +L    E  LAKR  E GD  A   L  ++LRLVV IA  Y G G
Sbjct: 104 SDPVRMYLKEIGRVDLLSADAEISLAKRI-EDGDELAKQELAEANLRLVVSIAKRYVGRG 162

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +   +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     +
Sbjct: 163 MSFLDLIQEGNMGLMKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 222

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 L R++ +L         PE++ A   ++++   +V  +        SL   I  
Sbjct: 223 --TINKLVRVQRNLLQDLGREPTPEEIGA---EMDLPTEKVREILKISQEPVSLETPI-- 275

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            +++ S   D++  +     +           R  L   +  L  RE  +   R   ++ 
Sbjct: 276 GEEDDSHLGDFIEDEGAMSPESFT---SSSLLREQLEDVLDTLTDREENVLRLRFGLDDG 332

Query: 253 --VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 333 NIRTLEQVGKVFGVTRERIRQIEAKALRKLRHPSRSK 369


>gi|227890104|ref|ZP_04007909.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           johnsonii ATCC 33200]
 gi|227849548|gb|EEJ59634.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           johnsonii ATCC 33200]
          Length = 372

 Score =  265 bits (677), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 79/284 (27%), Positives = 132/284 (46%), Gaps = 13/284 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +    V     +  Y+ EI ++ +L   +E  LAKR  E GD  A   L  ++LRLVV I
Sbjct: 92  SAPSSVRMNDPVRMYLKEIGRVSLLNADQEIALAKRI-ESGDEEAKQELAEANLRLVVSI 150

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y G G+   +++ EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      +
Sbjct: 151 AKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTI 210

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I     +      L R++  L         PE++ A   ++++   +V  +        
Sbjct: 211 RIPVHMVE--TINKLIRIQRQLLQDLGREPTPEEIGA---EMDMPTDKVREILKIAQEPV 265

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   I   +++ S   D++    D       +    +  +  L   +  L  RE  +  
Sbjct: 266 SLETPI--GEEDDSHLGDFI---EDKDATSPEQHASYELLKEQLEEVLDTLTDREENVLR 320

Query: 245 ARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R   ++    TLE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 321 LRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRS 364


>gi|306820486|ref|ZP_07454120.1| DNA-directed RNA polymerase sigma subunit RpoD [Eubacterium yurii
           subsp. margaretiae ATCC 43715]
 gi|304551472|gb|EFM39429.1| DNA-directed RNA polymerase sigma subunit RpoD [Eubacterium yurii
           subsp. margaretiae ATCC 43715]
          Length = 538

 Score =  265 bits (677), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 84/273 (30%), Positives = 144/273 (52%), Gaps = 13/273 (4%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           N +  +  Y+ EI KI +L  +EE+ L++   + GD  A  ++V ++LRLVV IA  Y G
Sbjct: 264 NVDDPVRMYLKEIGKIQLLTVEEEHRLSELMVK-GDEYAKMKIVEANLRLVVSIAKRYVG 322

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I    
Sbjct: 323 RGMLFLDLIQEGNLGLIKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 382

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
            +      L R+   L      + +PE    IA+++ +S+ ++  +        SL   I
Sbjct: 383 VE--TINKLIRINRQLVQELGRDPRPE---EIAEQMGMSQDKIREIMKIAQEPVSLETPI 437

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
              ++  S   D++  D     Q   E       R  + + +  L  RERR+ + R   +
Sbjct: 438 --GEEEDSHLGDFIPDDD---AQAPSEAAAYSLLREQIEQVLCTLTDRERRVLKLRFGLD 492

Query: 251 N--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +  P TLE +  EF+V+RER+RQIEA+A +K++
Sbjct: 493 DGRPRTLEEVGKEFDVTRERIRQIEAKALRKLR 525


>gi|317500513|ref|ZP_07958736.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|331089388|ref|ZP_08338287.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|316898102|gb|EFV20150.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|330404756|gb|EGG84294.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 370

 Score =  265 bits (677), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 88/290 (30%), Positives = 142/290 (48%), Gaps = 15/290 (5%)

Query: 1   MNRKNMSII--VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHL 58
           M   ++S+   V+ E  +  Y+ EI K+P+L  + E  LAKR  E GD  A   L  ++L
Sbjct: 84  MENIDLSVPEGVSIEDPVRMYLKEIGKVPLLSAEREIELAKRM-EEGDEDAKKELAEANL 142

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I 
Sbjct: 143 RLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYHKGYKFSTYATWWIRQAITRAIA 202

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
                ++I     +      L R+   L         PE    IAK+L++    V  +  
Sbjct: 203 DQARTIRIPVHMVE--TINKLIRVSRQLLQELGREPLPE---EIAKELDMPVERVREILK 257

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
                 SL   I   ++  S   D++  D      V  E   +   +  L   +  L  R
Sbjct: 258 ISQEPVSLETPI--GEEEDSHLGDFIQDD---NVPVPAEAAAQTLLKEQLDEVLDTLTER 312

Query: 239 ERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E+++   R    +    TLE +  EF+V+RER+RQIEA+A +K++   + 
Sbjct: 313 EQKVLRLRFGMNDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRS 362


>gi|296112139|ref|YP_003622521.1| RNA polymerase sigma factor [Leuconostoc kimchii IMSNU 11154]
 gi|295833671|gb|ADG41552.1| RNA polymerase sigma factor [Leuconostoc kimchii IMSNU 11154]
          Length = 432

 Score =  265 bits (677), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 80/276 (28%), Positives = 136/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L+  EE  +AKR  E GD+ A   L  ++LRLVV IA  Y G G+
Sbjct: 157 DPVRMYLKEIGRVNLLKGDEEINIAKRI-EDGDVEAKQELAEANLRLVVSIAKRYVGRGM 215

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 216 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 274

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L         PE++ A   +++++  +V  +        SL   I   
Sbjct: 275 -TINKLIRIQRQLLQDLGREPLPEEIGA---EMDLTPDKVREILKIAQEPVSLETPI--G 328

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D +     +    +  R  L   +  L  RE  +   R   E+  
Sbjct: 329 EEDDSHLGDFI---EDNEAISPADSAAYEMLREQLESVLETLTDREENVLRLRFGLEDGR 385

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 386 TRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSK 421


>gi|326693497|ref|ZP_08230502.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Leuconostoc argentinum KCTC 3773]
          Length = 432

 Score =  265 bits (677), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 80/276 (28%), Positives = 137/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L+  EE  +AKR  E GD+ A   L  ++LRLVV IA  Y G G+
Sbjct: 157 DPVRMYLKEIGRVNLLKGDEEINIAKRI-EAGDVEAKQELAEANLRLVVSIAKRYVGRGM 215

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 216 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 274

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L         PE++ A   +++++  +V  +        SL   I   
Sbjct: 275 -TINKLIRIQRQLLQDLGREPLPEEIGA---EMDLTPDKVREILKIAQEPVSLETPI--G 328

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D +     +    +  R+ L   +  L  RE  +   R   E+  
Sbjct: 329 EEDDSHLGDFI---EDNEAISPADSAAYEMLRDQLESVLETLTDREENVLRLRFGLEDGR 385

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 386 TRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSK 421


>gi|238916620|ref|YP_002930137.1| RNA polymerase primary sigma factor [Eubacterium eligens ATCC
           27750]
 gi|238871980|gb|ACR71690.1| RNA polymerase primary sigma factor [Eubacterium eligens ATCC
           27750]
          Length = 434

 Score =  265 bits (677), Expect = 7e-69,   Method: Composition-based stats.
 Identities = 83/276 (30%), Positives = 134/276 (48%), Gaps = 13/276 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI K+P+L   EE   AKR  E GD  A  RL  ++LRLVV IA  Y G G
Sbjct: 162 DDPVRMYLKEIGKVPLLSADEEIEYAKRM-EEGDEEAKKRLAEANLRLVVSIAKRYVGRG 220

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +   +++ EGN+GL++AV+K+D  +GF+ +TY+ WWI+ A+   I      ++I     +
Sbjct: 221 MQFLDLIQEGNLGLIKAVEKYDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 280

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 L R++  L         PE    IA+ +++    V  +        SL   I  
Sbjct: 281 --TINKLVRVQRQLLQELGREPSPE---EIAENMDIPVERVREIQKISQEPVSLETPI-- 333

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            ++  S   D++  D      V  E       +  L   +  L  RE+++   R   ++ 
Sbjct: 334 GEEEDSHLGDFIQDD---NVPVPAEAAASTLLKEQLVEVLGTLTEREQKVLRLRFGMDDG 390

Query: 253 --VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              TLE +  EF V+RER+RQIEA+A +K++   + 
Sbjct: 391 RARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRS 426


>gi|222152854|ref|YP_002562031.1| RNA polymerase sigma factor RpoD [Streptococcus uberis 0140J]
 gi|222113667|emb|CAR41594.1| RNA polymerase sigma factor RpoD [Streptococcus uberis 0140J]
          Length = 369

 Score =  265 bits (677), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 82/276 (29%), Positives = 136/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L   EE  LA      GD+ A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGVVPLLTSDEEKELAIAVA-AGDVDAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA+++ ++  +V  +        SL   I   
Sbjct: 215 -TINKLVREQRNLLQELGQDPTPEQ---IAERMEMTPDKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 361


>gi|255655465|ref|ZP_05400874.1| RNA polymerase sigma factor (sigma-43) [Clostridium difficile
           QCD-23m63]
 gi|296451458|ref|ZP_06893195.1| DNA-directed RNA polymerase sigma subunit RpoD [Clostridium
           difficile NAP08]
 gi|296880193|ref|ZP_06904159.1| DNA-directed RNA polymerase sigma subunit RpoD [Clostridium
           difficile NAP07]
 gi|296259725|gb|EFH06583.1| DNA-directed RNA polymerase sigma subunit RpoD [Clostridium
           difficile NAP08]
 gi|296428782|gb|EFH14663.1| DNA-directed RNA polymerase sigma subunit RpoD [Clostridium
           difficile NAP07]
          Length = 388

 Score =  265 bits (677), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 86/280 (30%), Positives = 144/280 (51%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ +  +  Y+ EI KIP+L+  EE   A+R  E GD  A  RLV ++LRLVV IA  Y 
Sbjct: 113 ISIDDPVRMYLKEIGKIPLLKPHEEVEFARRMHE-GDEIAKQRLVEANLRLVVSIAKRYV 171

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 172 GRGMLFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 231

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L      + KPE    IAK++ ++E +V  +        SL   
Sbjct: 232 MVE--TINKLIRVSRQLLQELGRDPKPE---EIAKEMEMTEDKVREIMKIAQDPVSLETP 286

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++            E       +  +   +  LN RE+++ + R   
Sbjct: 287 I--GEEEDSHLGDFIPD---DDAPAPAEAAAYSLLKEQIEDVLGSLNDREQKVLKLRFGL 341

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+    TLE +  EF+V+RER+RQIEA+A +K++   + +
Sbjct: 342 EDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSK 381


>gi|51473499|ref|YP_067256.1| RNA polymerase factor sigma-32 [Rickettsia typhi str. Wilmington]
 gi|51459811|gb|AAU03774.1| RNA polymerase sigma 32 subunit (heat shock sigma factor)
           [Rickettsia typhi str. Wilmington]
          Length = 293

 Score =  265 bits (677), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 144/285 (50%), Positives = 199/285 (69%), Gaps = 1/285 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M     ++ ++ E G   Y+ +I KIP L ++EE++LAK Y E  DL AAH+LVTSHL+L
Sbjct: 1   MTNNINALAISSESGFYSYLQKINKIPSLTQEEEFLLAKSYLEENDLQAAHKLVTSHLKL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIA GY+ YGLPI+E+VSEGNIGLMQAVKKF+PE GFRL+TY+MWWIKA++QEYIL+S
Sbjct: 61  VAKIASGYKTYGLPITELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKASIQEYILKS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTA QK+LFF+L ++K  +  +    +  +    IA +L VS  EV  MN R+
Sbjct: 121 WSLVKMGTTAAQKKLFFSLNKVKHKITNLYSRAITTDDFAQIADELGVSVHEVSEMNTRI 180

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D SLN  INS D  S +  + L       E + I K+   ++R +L+ +M +LN RE
Sbjct: 181 SGPDLSLNNSINSDDVESGELIELLPETRPTPEAMAINKQNYTSKRKLLSNAMQILNDRE 240

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            RI + R+L + P TL+ LSSE+ +S+ER+RQIE  AF+K+++ I
Sbjct: 241 LRILKDRKLTDTPKTLDILSSEYNISKERIRQIENTAFEKIKKFI 285


>gi|304437691|ref|ZP_07397643.1| DNA-directed RNA polymerase sigma subunit SigA [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
 gi|304369324|gb|EFM22997.1| DNA-directed RNA polymerase sigma subunit SigA [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
          Length = 370

 Score =  265 bits (677), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 86/281 (30%), Positives = 140/281 (49%), Gaps = 13/281 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ +  +  Y+ EI  +P+L  +EE  LA+R  E GD  A HRL  ++LRLVV IA  Y 
Sbjct: 95  ISLDDPVRMYLKEIGHVPLLTAEEEVALAQRM-EAGDEEARHRLEEANLRLVVSIAKRYV 153

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 154 GRGMLFLDLIQEGNLGLLKAVEKFDYSKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 213

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L      + +PE    IAK++ +S + V  +        SL   
Sbjct: 214 MVE--TINKLVRISRQLLQELGRDPRPE---EIAKEMGISVARVHEIMKIAQEPVSLETP 268

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++    D       E       R  L   +  L  RE+ +   R   
Sbjct: 269 I--GEEEDSHLGDFI---EDEAAPAPAEAASFMLLREQLEEVLETLTDREKNVLRLRFGL 323

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           E+    TLE +   F V+RER+RQIEA+A +K++   + +V
Sbjct: 324 EDGRSRTLEEVGQSFGVTRERIRQIEAKALRKLRHPSRSKV 364


>gi|238927758|ref|ZP_04659518.1| DNA-directed RNA polymerase sigma subunit SigA [Selenomonas
           flueggei ATCC 43531]
 gi|238884474|gb|EEQ48112.1| DNA-directed RNA polymerase sigma subunit SigA [Selenomonas
           flueggei ATCC 43531]
          Length = 383

 Score =  265 bits (677), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 85/281 (30%), Positives = 139/281 (49%), Gaps = 13/281 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ +  +  Y+ EI  +P+L  +EE  LA+R  E GD  A HRL  ++LRLVV IA  Y 
Sbjct: 108 ISLDDPVRMYLKEIGHVPLLTAEEEVALAQRM-EAGDEEARHRLEEANLRLVVSIAKRYV 166

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 167 GRGMLFLDLIQEGNLGLLKAVEKFDYSKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 226

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L      +  PE    IAK++ ++ + V  +        SL   
Sbjct: 227 MVE--TINKLVRISRQLLQELGRDPHPE---EIAKEMGITVARVHEIMKIAQEPVSLETP 281

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++    D       E       R  L   +  L  RE+ +   R   
Sbjct: 282 I--GEEEDSHLGDFI---EDEAAPAPAEAASFMLLREQLEEVLETLTDREKNVLRLRFGL 336

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           E+    TLE +   F V+RER+RQIEA+A +K++   + +V
Sbjct: 337 EDGRSRTLEEVGQSFGVTRERIRQIEAKALRKLRHPSRSKV 377


>gi|323704675|ref|ZP_08116253.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
 gi|323536137|gb|EGB25910.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
          Length = 357

 Score =  265 bits (677), Expect = 8e-69,   Method: Composition-based stats.
 Identities = 87/280 (31%), Positives = 139/280 (49%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           +N +  +  Y+ EI KIP+L   EE  LAKR  E GD  A  RL  ++LRLVV IA  Y 
Sbjct: 82  INIDDPVRMYLKEIGKIPLLSPDEEIELAKRI-EKGDEEAKKRLTEANLRLVVSIAKRYV 140

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KF+  +GF+ +TY+ WWI+ A+   I      ++I   
Sbjct: 141 GRGMLFLDLIQEGNLGLLKAVEKFNYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVH 200

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L      +  PE    IAK++++S  +V  +        SL   
Sbjct: 201 MVE--TINKLIRVSRQLLQELGRDPLPE---EIAKEMDMSVDKVREIMKIAQEPVSLETP 255

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++            E       +  L   +  L PRE ++   R   
Sbjct: 256 I--GEEEDSHLGDFIPD---EDAPAPAEAAAFTMLKEQLIDVLDTLTPREEKVLRLRFGL 310

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 311 DDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 350


>gi|322411497|gb|EFY02405.1| RNA polymerase sigma factor RpoD [Streptococcus dysgalactiae subsp.
           dysgalactiae ATCC 27957]
          Length = 369

 Score =  264 bits (676), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 85/276 (30%), Positives = 139/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE VLA    E GDL A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGVVPLLTSEEEKVLAVAVAE-GDLEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA+++ ++  +V  +        SL   I   
Sbjct: 215 -TINKLVREQRNLLQELGQDPTPEQ---IAERMEMTPDKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 361


>gi|154484558|ref|ZP_02027006.1| hypothetical protein EUBVEN_02272 [Eubacterium ventriosum ATCC
           27560]
 gi|149734406|gb|EDM50323.1| hypothetical protein EUBVEN_02272 [Eubacterium ventriosum ATCC
           27560]
          Length = 429

 Score =  264 bits (676), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 79/280 (28%), Positives = 139/280 (49%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V  E  +  Y+ EI  +P+L   EE  LAKR +  GD+ A  +L+ ++LRLVV IA  Y 
Sbjct: 153 VGTEDPVRMYLKEIGTVPLLTADEELELAKR-KTEGDIVAKEKLIEANLRLVVSIAKRYT 211

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   ++V EGN+GL++ V+KFD  +G++L+TY+ WWI+ ++   +      +++   
Sbjct: 212 GRGMSFLDLVQEGNLGLIKGVEKFDYTKGYKLSTYATWWIRQSVTRALADHARTIRVPVH 271

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      + R+    + +T           +A  L+++E +V+ +        SL   
Sbjct: 272 MVE-----TINRMSKMQRKLTLELGYEPSTKELATALDMTEEKVLEIMQIAREPASLETP 326

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL- 248
           I   +++ S   D++    D          E    R  +   +  L  RER +   R   
Sbjct: 327 I--GEEDDSNLGDFVA---DNNTVTPEANIESVMLREHIDVLLQDLKDREREVIILRFGL 381

Query: 249 -QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              +P TLE +   F V+RER+RQIEA+A +K++  ++ +
Sbjct: 382 RDGHPRTLEEVGKIFNVTRERIRQIEAKALRKLRNPVRSK 421


>gi|47679387|gb|AAT36674.1| DNA-directed RNA polymerase sigma A subunit [Oenococcus oeni PSU-1]
          Length = 465

 Score =  264 bits (676), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 79/278 (28%), Positives = 137/278 (49%), Gaps = 14/278 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKIAMGYRGY 71
             +  Y+ EI ++ +L   +E  +AKR  + G     A   L  ++LRLVV IA  Y G 
Sbjct: 190 DPVRMYLKEIGRVSLLNADQEVAIAKRIEKGGSDGERARQELAEANLRLVVSIAKRYVGR 249

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           G+   +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     
Sbjct: 250 GMHFLDLIQEGNMGLMKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMV 309

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
           +      L R++  L      +  PE++ A   ++ ++  +V  +        SL   I 
Sbjct: 310 E--TINKLIRIQRTLIQDLGRDPMPEEIGA---EMELTADKVREIQKIAQEPVSLETPI- 363

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             ++N S   D++    D + +  IE    +  ++ L   +  L  RE  +   R   E+
Sbjct: 364 -GEENDSHLGDFI---EDNEGESPIESTSDQMLKDQLEEVLGTLTEREENVLRLRFGLED 419

Query: 252 P--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
               TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 420 GKTRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSK 457


>gi|300812189|ref|ZP_07092631.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus PB2003/044-T3-4]
 gi|300496825|gb|EFK31905.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus PB2003/044-T3-4]
          Length = 373

 Score =  264 bits (676), Expect = 9e-69,   Method: Composition-based stats.
 Identities = 80/275 (29%), Positives = 135/275 (49%), Gaps = 13/275 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             + +Y+  I ++ +L   EE  LAKR  E GD  A   L +++LRLVV IA  Y G G+
Sbjct: 102 DPVRQYLKRIGRVSLLSGDEEVQLAKRI-EAGDQEAKDELTSANLRLVVSIAKRYVGRGM 160

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD + GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 161 SFLDLIQEGNMGLMKAVDKFDYQLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 219

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L      + +PE    IA ++++   +V  +        SL   I   
Sbjct: 220 -TINKLIRIQRQLLQDLGRDPEPE---EIAAEMDLPVKKVREVLKVAQEPVSLETPI--G 273

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-- 251
           +++ S   D++    D       +    +  ++ L   +  L  RE  +   R   ++  
Sbjct: 274 EEDDSHLGDFI---EDKDATSPEQHAASEMLKDQLAEVLDTLTDREENVLRLRFGLDDGN 330

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           P TLE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 331 PRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRS 365


>gi|160941160|ref|ZP_02088497.1| hypothetical protein CLOBOL_06053 [Clostridium bolteae ATCC
           BAA-613]
 gi|158435721|gb|EDP13488.1| hypothetical protein CLOBOL_06053 [Clostridium bolteae ATCC
           BAA-613]
          Length = 381

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 80/280 (28%), Positives = 143/280 (51%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           +  E  +  Y+ EI  +P+L   EE  LA+R +  GD  A  RL+ ++LRLVV IA  Y 
Sbjct: 107 IGTEDPVRMYLKEIGTVPLLTADEELDLAQR-KADGDEFAKERLIEANLRLVVSIAKRYT 165

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   ++V EGN+GL++ V+KFD  +G++L+TY+ WWI+ ++   +      +++   
Sbjct: 166 GRGMSFLDLVQEGNLGLIKGVEKFDYTKGYKLSTYATWWIRQSVTRALADQARTIRVPVH 225

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      + ++    + +T        V  +A+ L+++E +V+ +        SL   
Sbjct: 226 MVE-----TINKMSKMQRKLTLELGYEPSVTELAEALDMTEDKVMEIMQIAREPASLETP 280

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   +++ S   D++    D          E    R  +   +  L  RER++   R   
Sbjct: 281 I--GEEDDSNLGDFVA---DNNVVTPEGNVESVMLREHIDALLGDLKERERQVIVLRFGL 335

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+  P TLE +  EF V+RER+RQIEA+A +K++  ++ +
Sbjct: 336 EDGHPRTLEEVGKEFNVTRERIRQIEAKALRKLRNPVRSK 375


>gi|254230128|ref|ZP_04923524.1| alternative sigma factor RpoH [Vibrio sp. Ex25]
 gi|151937373|gb|EDN56235.1| alternative sigma factor RpoH [Vibrio sp. Ex25]
          Length = 284

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 111/284 (39%), Positives = 167/284 (58%), Gaps = 8/284 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++   + +  +  L  YI  +   PML   EE  LA+R    G++ AA  L+ SHLR 
Sbjct: 1   MTKEAYPMALVTQDSLDSYIRSVNSYPMLTADEERELAERLHYKGEIEAAKGLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A GY GYGLP++++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VKI TT  Q++LFFNLR+ K  L    +      +V  +A++L V  SEV  M  RL
Sbjct: 121 WRIVKIATTKAQRKLFFNLRKSKKRLGWFNNG-----EVETVARELGVEPSEVREMESRL 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE---ERKNRRNMLTRSMSVLNP 237
           A  +S   +    D +S+ +   ++Y  D    V    E      +  N L  +++ L+ 
Sbjct: 176 AAVDSTFDMPTDEDDSSNAYTAPMLYLEDKSSDVADNIEAANWEMHTNNRLGHALASLDE 235

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R +RI  +R L +   TL++L+ EF VS ER+RQ+E  A KK++
Sbjct: 236 RSQRIVRSRWLDDEKATLQDLADEFGVSAERIRQLEKNAMKKLK 279


>gi|42519241|ref|NP_965171.1| RNA polymerase sigma factor RpoD [Lactobacillus johnsonii NCC 533]
 gi|41583529|gb|AAS09137.1| RNA polymerase sigma factor RpoD [Lactobacillus johnsonii NCC 533]
 gi|329667249|gb|AEB93197.1| RNA polymerase sigma factor RpoD [Lactobacillus johnsonii DPC 6026]
          Length = 372

 Score =  264 bits (676), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 79/284 (27%), Positives = 132/284 (46%), Gaps = 13/284 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +    V     +  Y+ EI ++ +L   +E  LAKR  E GD  A   L  ++LRLVV I
Sbjct: 92  SAPSSVRMNDPVRMYLKEIGRVSLLNADQEIALAKRI-ESGDEEAKQELAEANLRLVVSI 150

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y G G+   +++ EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      +
Sbjct: 151 AKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTI 210

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I     +      L R++  L         PE++ A   ++++   +V  +        
Sbjct: 211 RIPVHMVE--TINKLIRIQRQLLQDLGREPTPEEIGA---EMDMPTDKVREILKIAQEPV 265

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   I   +++ S   D++    D       +    +  +  L   +  L  RE  +  
Sbjct: 266 SLETPI--GEEDDSHLGDFI---EDKDATSPEQHASYELLKEQLEEVLDTLTDREENVLR 320

Query: 245 ARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R   ++    TLE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 321 LRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRS 364


>gi|331090835|ref|ZP_08339681.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           2_1_46FAA]
 gi|330399694|gb|EGG79356.1| RNA polymerase sigma factor rpoD [Lachnospiraceae bacterium
           2_1_46FAA]
          Length = 370

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 88/279 (31%), Positives = 140/279 (50%), Gaps = 13/279 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ E  +  Y+ EI K+P+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y 
Sbjct: 95  ISIEDPVRMYLKEIGKVPLLSAEEEIELAKRMAE-GDEDAKKRLAEANLRLVVSIAKRYV 153

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD E+GF+ +TY+ WWI+ A+   I      ++I   
Sbjct: 154 GRGMLFLDLIQEGNLGLIKAVEKFDYEKGFKFSTYATWWIRQAITRAIADQARTIRIPVH 213

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L         PE    IA++L++    V  +        SL   
Sbjct: 214 MVE--TINKLIRVSRQLLQELGREPSPE---EIAEELDMPVERVREILKISQEPVSLETP 268

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++  D      V  E       +  L   ++ L  RE+++   R   
Sbjct: 269 I--GEEEDSHLGDFIQDD---NVPVPAEAAAATLLKEQLGEVLNTLTDREQKVLRLRFGM 323

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +    TLE +  EF+V+RER+RQIEA+A +K++   + 
Sbjct: 324 NDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRS 362


>gi|313123888|ref|YP_004034147.1| RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           bulgaricus ND02]
 gi|312280451|gb|ADQ61170.1| RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           bulgaricus ND02]
          Length = 373

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 80/275 (29%), Positives = 135/275 (49%), Gaps = 13/275 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             + +Y+  I ++ +L   EE  LAKR  E GD  A   L +++LRLVV IA  Y G G+
Sbjct: 102 DPVRQYLKRIGRVSLLSGDEEVQLAKRI-EAGDQEAKDELTSANLRLVVSIAKRYVGRGM 160

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD + GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 161 SFLDLIQEGNMGLMKAVDKFDYQLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 219

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L      + +PE    IA ++++   +V  +        SL   I   
Sbjct: 220 -TINKLIRIQRQLLQDLGRDPEPE---EIAAEMDLPVKKVREVLKVAQEPVSLETPI--G 273

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-- 251
           +++ S   D++    D       +    +  ++ L   +  L  RE  +   R   ++  
Sbjct: 274 EEDDSHLGDFI---EDKDATSPEQHAASEMLKDQLAEVLDTLTDREENVLRLRFGLDDGN 330

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           P TLE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 331 PRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRS 365


>gi|288958414|ref|YP_003448755.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
 gi|288910722|dbj|BAI72211.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
          Length = 323

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 142/278 (51%), Positives = 195/278 (70%), Gaps = 3/278 (1%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++      L+RYI E ++ P+L    E  LA  +RE G+  A  +LV SHLRLV+KIA G
Sbjct: 32  LLTGENASLTRYIEESKRFPILAPDVERDLAIAWRERGNPRALEQLVGSHLRLVIKIARG 91

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           + GYGL + ++V+EGN+GLMQA +KFDP+RGFR ATY+ WWI+AA+QEYIL SWSLVK+G
Sbjct: 92  FGGYGLSLVDLVAEGNVGLMQAAQKFDPQRGFRFATYATWWIRAAIQEYILHSWSLVKMG 151

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESL 186
           TTA QK+LFFNLRRLK  +  +   +L PE V  IA +L+V E+EV+ MN RLA  D SL
Sbjct: 152 TTAAQKKLFFNLRRLKSQMAELEQGDLSPETVATIAAELDVPETEVVEMNRRLAANDSSL 211

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           +A +  S    + W + L  D   Q+ +L + +E   RR ++ +++  L+PRERRI   R
Sbjct: 212 DATL--STDGETNWLELLADDRPTQDAMLADADELALRRRLVGQALDRLDPRERRILFER 269

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           RL+++P TLE LS +F VSRERVRQIE RAF+K+Q+++
Sbjct: 270 RLKDDPSTLEALSQQFSVSRERVRQIEVRAFEKLQKAV 307


>gi|251782161|ref|YP_002996463.1| RNA polymerase sigma factor RpoD [Streptococcus dysgalactiae subsp.
           equisimilis GGS_124]
 gi|242390790|dbj|BAH81249.1| RNA polymerase sigma factor [Streptococcus dysgalactiae subsp.
           equisimilis GGS_124]
          Length = 369

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 84/276 (30%), Positives = 138/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE V A    E GDL A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGVVPLLTSEEEKVFAVAVAE-GDLEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA+++ ++  +V  +        SL   I   
Sbjct: 215 -TINKLVREQRNLLQELGQDPTPEQ---IAERMEMTPDKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 361


>gi|172056869|ref|YP_001813329.1| RpoD family RNA polymerase sigma factor [Exiguobacterium sibiricum
           255-15]
 gi|171989390|gb|ACB60312.1| RNA polymerase, sigma 70 subunit, RpoD family [Exiguobacterium
           sibiricum 255-15]
          Length = 361

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 79/289 (27%), Positives = 139/289 (48%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++ +L  ++E  LAKR  E  D  A  RL  ++LRL
Sbjct: 77  LNDLSVPPGVKINDPVRMYLKEIGRVDLLNAEDEVELAKRI-EQNDEEAKKRLAEANLRL 135

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I   
Sbjct: 136 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQ 195

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    I+K++ ++  +V  +    
Sbjct: 196 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPTPE---EISKEMEITPEKVREILKIA 250

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D       +    +  +  L   +  L  RE 
Sbjct: 251 QEPVSLETPI--GEEDDSHLGDFI---EDQDATAPQDAAAYELLKEQLEDVLDTLTDREE 305

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 306 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 354


>gi|315635212|ref|ZP_07890490.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Aggregatibacter
           segnis ATCC 33393]
 gi|315476174|gb|EFU66928.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Aggregatibacter
           segnis ATCC 33393]
          Length = 283

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 103/285 (36%), Positives = 171/285 (60%), Gaps = 6/285 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+++  ++++  +  L  YI    + PML  +EE  LA+R   + D+ AA +LV SHLR 
Sbjct: 2   MDKETQTMMLVPQGSLEAYIRAANEYPMLTAEEEKELAERLYYNEDIEAAKKLVLSHLRF 61

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 62  VIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 121

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L    +N     +V  +A +L VS  +V+ M  R+
Sbjct: 122 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNEN-----EVDMVANELGVSPQDVVEMESRM 176

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            G D + +   +  D+ +     +L          L  +       + L  +++ L+ R 
Sbjct: 177 TGADVAFDLPTDDHDEETYAPALYLEDKGSNFAAELENENYEAQATDQLVVALNNLDARS 236

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + I +AR L E   TL++L++++ +S ERVRQ+E  A KK++ ++
Sbjct: 237 QDIIKARWLDETKATLQDLAAKYNISAERVRQLETNALKKLKSAV 281


>gi|331269992|ref|YP_004396484.1| RpoD family RNA polymerase sigma-70 subunit [Clostridium botulinum
           BKT015925]
 gi|329126542|gb|AEB76487.1| RNA polymerase, sigma 70 subunit, RpoD family [Clostridium
           botulinum BKT015925]
          Length = 368

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 82/280 (29%), Positives = 138/280 (49%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ +  +  Y+ EI K+P+L   EE  LA+R  E GD+ A  +L  ++LRLVV IA  Y 
Sbjct: 93  ISIDDPVRMYLKEIGKVPLLSPDEEINLAQRI-EDGDMYAKKKLAEANLRLVVSIAKRYV 151

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 152 GRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 211

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L        +PE    IAK + +   +V  +        SL   
Sbjct: 212 MVE--TINKLIRVSRQLLQELGREPQPE---EIAKIMEMPVDKVREIMKIAQEPVSLETP 266

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++      +     E       +  L   +  L PRE ++   R   
Sbjct: 267 I--GEEEDSHLGDFIPD---DEAPAPAEAAAFTMLKEQLINVLDTLTPREEKVLRLRFGL 321

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 322 DDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 361


>gi|239626722|ref|ZP_04669753.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47_FAA]
 gi|239516868|gb|EEQ56734.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47FAA]
          Length = 374

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 82/280 (29%), Positives = 136/280 (48%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V+ E  +  Y+ EI KIP+L  +EE  LAK   E G   A  RL  S+LRLVV IA  Y 
Sbjct: 98  VSLEDPVRMYLKEIGKIPLLSMEEEIELAKSM-ELGSEDARKRLAESNLRLVVSIAKRYV 156

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 157 GRGMQFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 216

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      + RL    + +     +      IA + ++    V  +        SL   
Sbjct: 217 MVE-----TINRLVRTSRQLLQELGREPTTEEIAARADLPVERVSEIMKMAQEPVSLETP 271

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++  D      V  +          L   +  L  RE+++ + R   
Sbjct: 272 I--GEEEDSHLGDFIQDD---NVMVPQDAAAFTLLHEQLMEVLLTLTEREQKVLKLRFGL 326

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  P TLE +  +F V+RER+RQIEA+A +K++   + +
Sbjct: 327 DDGRPRTLEEVGRQFNVTRERIRQIEAKALRKLRHPSRSK 366


>gi|308069922|ref|YP_003871527.1| RNA polymerase sigma factor rpoD (Sigma-A) [Paenibacillus polymyxa
           E681]
 gi|310643031|ref|YP_003947789.1| RNA polymerase sigma factor rpod [Paenibacillus polymyxa SC2]
 gi|305859201|gb|ADM70989.1| RNA polymerase sigma factor rpoD (Sigma-A) [Paenibacillus polymyxa
           E681]
 gi|309247981|gb|ADO57548.1| RNA polymerase sigma factor rpoD [Paenibacillus polymyxa SC2]
          Length = 377

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 81/285 (28%), Positives = 139/285 (48%), Gaps = 13/285 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           ++   +     +  Y+ EI ++P+L   +E  LAKR   +GD  A  RL  ++LRLVV I
Sbjct: 97  SLPPGIKINDPVRMYLKEIGRVPLLSADDEVELAKRI-NNGDEEAKRRLAEANLRLVVSI 155

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y G G+   +++ EGN+GL++AV+KFD E+GF+ +TY+ WWI+ A+   I      +
Sbjct: 156 AKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYEKGFKFSTYATWWIRQAITRAIADQARTI 215

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I     +      L R+   L         PE+V A   ++ +S  +V  +        
Sbjct: 216 RIPVHMVE--TINKLIRVSRQLLQELGREPTPEEVAA---EMELSVEKVREIMKIAQEPV 270

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   I   +++ S   D++    D +     +    +  +  L   +  L  RE  +  
Sbjct: 271 SLETPI--GEEDDSHLGDFI---EDQEALAPADAAAYELLKEQLEDVLDTLTEREENVLR 325

Query: 245 ARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 LRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 370


>gi|170017101|ref|YP_001728020.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Leuconostoc citreum KM20]
 gi|169803958|gb|ACA82576.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Leuconostoc citreum KM20]
          Length = 432

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 80/276 (28%), Positives = 137/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L+  EE  +AKR  E GD+ A   L  ++LRLVV IA  Y G G+
Sbjct: 157 DPVRMYLKEIGRVNLLKGDEEINIAKRI-EDGDVEAKQELAEANLRLVVSIAKRYVGRGM 215

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 216 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 274

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L         PE++ A   +++++  +V  +        SL   I   
Sbjct: 275 -TINKLIRIQRQLLQDLGREPLPEEIGA---EMDLTPDKVREILKIAQEPVSLETPI--G 328

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D +     +    +  R+ L   +  L  RE  +   R   E+  
Sbjct: 329 EEDDSHLGDFI---EDNEAISPADSAAYEMLRDQLESVLETLTDREENVLRLRFGLEDGR 385

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 386 TRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSK 421


>gi|304317433|ref|YP_003852578.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacterium thermosaccharolyticum DSM 571]
 gi|302778935|gb|ADL69494.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacterium thermosaccharolyticum DSM 571]
          Length = 357

 Score =  264 bits (675), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 87/280 (31%), Positives = 139/280 (49%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           +N +  +  Y+ EI KIP+L   EE  LAKR  E GD  A  RL  ++LRLVV IA  Y 
Sbjct: 82  INIDDPVRMYLKEIGKIPLLSPDEEIELAKRI-EKGDEEAKKRLTEANLRLVVSIAKRYV 140

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KF+  +GF+ +TY+ WWI+ A+   I      ++I   
Sbjct: 141 GRGMQFLDLIQEGNLGLLKAVEKFNYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVH 200

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L      +  PE    IAK++++S  +V  +        SL   
Sbjct: 201 MVE--TINKLIRVSRQLLQELGRDPLPE---EIAKEMDMSVDKVREIMKIAQEPVSLETP 255

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++            E       +  L   +  L PRE ++   R   
Sbjct: 256 I--GEEEDSHLGDFIPD---EDAPAPAEAAAFTMLKEQLIDVLDTLTPREEKVLRLRFGL 310

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 311 DDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 350


>gi|116629751|ref|YP_814923.1| RNA polymerase sigma factor RpoD [Lactobacillus gasseri ATCC 33323]
 gi|238853400|ref|ZP_04643779.1| RNA polymerase sigma factor RpoD [Lactobacillus gasseri 202-4]
 gi|282851794|ref|ZP_06261157.1| RNA polymerase sigma factor RpoD [Lactobacillus gasseri 224-1]
 gi|300361838|ref|ZP_07058015.1| RNA polymerase sigma factor rpoD [Lactobacillus gasseri JV-V03]
 gi|311110607|ref|ZP_07712004.1| RNA polymerase sigma-43 factor [Lactobacillus gasseri MV-22]
 gi|116095333|gb|ABJ60485.1| RNA polymerase, sigma 70 subunit, RpoD [Lactobacillus gasseri ATCC
           33323]
 gi|238833972|gb|EEQ26230.1| RNA polymerase sigma factor RpoD [Lactobacillus gasseri 202-4]
 gi|282557036|gb|EFB62635.1| RNA polymerase sigma factor RpoD [Lactobacillus gasseri 224-1]
 gi|300354457|gb|EFJ70328.1| RNA polymerase sigma factor rpoD [Lactobacillus gasseri JV-V03]
 gi|311065761|gb|EFQ46101.1| RNA polymerase sigma-43 factor [Lactobacillus gasseri MV-22]
          Length = 373

 Score =  263 bits (674), Expect = 1e-68,   Method: Composition-based stats.
 Identities = 79/284 (27%), Positives = 132/284 (46%), Gaps = 13/284 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +    V     +  Y+ EI ++ +L   +E  LAKR  E GD  A   L  ++LRLVV I
Sbjct: 93  SAPSSVRMNDPVRMYLKEIGRVSLLNADQEIALAKRI-EAGDEEAKQELAEANLRLVVSI 151

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y G G+   +++ EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      +
Sbjct: 152 AKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTI 211

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I     +      L R++  L         PE++ A   ++++   +V  +        
Sbjct: 212 RIPVHMVE--TINKLIRIQRQLLQDLGREPTPEEIGA---EMDMPTDKVREILKIAQEPV 266

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   I   +++ S   D++    D       +    +  +  L   +  L  RE  +  
Sbjct: 267 SLETPI--GEEDDSHLGDFI---EDKDATSPEQHASYELLKEQLEEVLDTLTDREENVLR 321

Query: 245 ARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R   ++    TLE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 322 LRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRS 365


>gi|270291312|ref|ZP_06197534.1| RNA polymerase primary sigma factor [Pediococcus acidilactici 7_4]
 gi|304385062|ref|ZP_07367408.1| RNA polymerase sigma factor rpoD [Pediococcus acidilactici DSM
           20284]
 gi|270280158|gb|EFA25994.1| RNA polymerase primary sigma factor [Pediococcus acidilactici 7_4]
 gi|304329256|gb|EFL96476.1| RNA polymerase sigma factor rpoD [Pediococcus acidilactici DSM
           20284]
          Length = 379

 Score =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 78/276 (28%), Positives = 134/276 (48%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L   EE  LA R  E GD  A   L  ++LRLVV IA  Y G G+
Sbjct: 108 DPVRMYLKEIGRVSLLTADEEVALALRI-EKGDERAKQELAEANLRLVVSIAKRYVGRGM 166

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV+KFD ++GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 167 QFLDLIQEGNMGLMKAVEKFDYQKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 225

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L         PE++ A   ++++   +V  +        SL   I   
Sbjct: 226 -TINKLIRIQRQLLQDLGREPMPEEIGA---EMDMPSDKVREILKIAQEPVSLETPI--G 279

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D +     +    +  +  L   +  L  RE  +   R   ++  
Sbjct: 280 EEDDSHLGDFI---EDQEATSPADHAAYELLKEQLEGVLDTLTDREENVLRLRFGLDDGR 336

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 337 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 372


>gi|167462413|ref|ZP_02327502.1| RNA polymerase sigma factor RpoD [Paenibacillus larvae subsp.
           larvae BRL-230010]
          Length = 367

 Score =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 83/276 (30%), Positives = 133/276 (48%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L   +E  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 96  DSVRMYLKEIGRVHLLTADDEIELAKRIME-GDEEAKQRLAEANLRLVVSIARRYVGRGM 154

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV+KFD  +G++ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 155 LFLDLIQEGNMGLMKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 213

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R+   L         PE    IAK++ +S  +V  +        SL   I   
Sbjct: 214 -TINKLIRVSRQLLLELGREPTPE---EIAKEMELSTDKVREIMKISQEPVSLETPI--G 267

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           ++N S   D++    D       +    +  +  L   +  L  RE  +   R   E+  
Sbjct: 268 EENDSNLGDFI---EDQDALAPADAASYELLKEQLEHVLDTLTEREENVLRLRFGLEDGR 324

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 325 SRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 360


>gi|251791618|ref|YP_003006339.1| RNA polymerase factor sigma-32 [Dickeya zeae Ech1591]
 gi|247540239|gb|ACT08860.1| RNA polymerase, sigma 32 subunit, RpoH [Dickeya zeae Ech1591]
          Length = 285

 Score =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 103/290 (35%), Positives = 162/290 (55%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M +   +  +  +  L  YI      PML  +EE  LA+R   HGDL AA +L+ SHLR 
Sbjct: 1   MTKDMQTFALVPQGSLEGYIRAANAYPMLTAEEERALAERLHYHGDLDAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A  Y GYGLP ++++ EGNIGLM+AV++F+P+ G RL ++++ WIKA + EY+LR+
Sbjct: 61  VIHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPDVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVEMVARELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNP 237
           A  +         D    Q    ++Y  D        + E     +  + LT ++  L+ 
Sbjct: 176 AAQDMTFDPSPEDDAQPGQPMAPMLYLQDKSSDFADGIEEDNWETHAADKLTYALEGLDE 235

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L ++   TL+ L+  + VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQHIIRARWLDDDNKSTLQELADHYGVSAERVRQLEKNAMKKLRAAIEA 285


>gi|325125918|gb|ADY85248.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus 2038]
          Length = 373

 Score =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 80/275 (29%), Positives = 131/275 (47%), Gaps = 13/275 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             + +Y+  I ++ +L   EE  LAKR    GD  A   L  ++LRLVV IA  Y G G+
Sbjct: 102 DPVRQYLKRIGRVSLLSGDEEVQLAKRIG-AGDQEAKDELTNANLRLVVSIAKRYVGRGM 160

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 161 SFLDLIQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 219

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L      + +PE    IA ++++   +V           SL   I   
Sbjct: 220 -TINKLIRIQRQLLQDLGRDPEPE---EIAAEMDLPVKKVREALKVAQEPVSLETPI--G 273

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-- 251
           +++ S   D++    D       +    +  R+ L   +  L  RE  +   R   ++  
Sbjct: 274 EEDDSHLGDFI---EDKDATSPEQHAASEMLRDQLAEVLDTLTDREENVLRLRFGLDDGN 330

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           P TLE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 331 PRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRS 365


>gi|157373363|ref|YP_001471963.1| RNA polymerase factor sigma-32 [Shewanella sediminis HAW-EB3]
 gi|157315737|gb|ABV34835.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella sediminis
           HAW-EB3]
          Length = 285

 Score =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 109/290 (37%), Positives = 174/290 (60%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSI---IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSH 57
           M  +  S+   + +G   L  Y+H    I ML+ ++EY LAKR +E GDL AA +L+ SH
Sbjct: 1   MTNQTQSMALTVPHGSGSLEAYVHSAHNISMLQPEQEYELAKRLQETGDLQAAKQLIMSH 60

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LR VV +A GY GYGLP ++++ EGNIGLM+AVK+FDP  G RL ++++ WIKA + EY+
Sbjct: 61  LRFVVHVAKGYSGYGLPQADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWIKAEIHEYV 120

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           L++W +VK+ TT  Q++LFFNLR+ K  L   +D     E+V  +A  L VS+++V  M 
Sbjct: 121 LKNWRIVKVATTKAQRKLFFNLRKSKKRLGWFSD-----EEVGMVADNLGVSKADVTEME 175

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLN 236
            R+A  +    L + +D +        + DH       +E +  + + +  L  ++  L+
Sbjct: 176 SRMAAQDPAFDLASDNDDDHDFAPMHYLEDHSSDLASQVENDNLEASNQARLLSAIKTLD 235

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R + I +AR L E+  TL+ L++ ++VS ER+RQ+E  A  K++  ++ 
Sbjct: 236 ERSQHILQARWLNEDKTTLQELAATYQVSAERIRQLEKNAMNKLKGRMEA 285


>gi|195977963|ref|YP_002123207.1| RNA polymerase sigma factor RpoD [Streptococcus equi subsp.
           zooepidemicus MGCS10565]
 gi|195974668|gb|ACG62194.1| RNA polymerase sigma factor RpoD [Streptococcus equi subsp.
           zooepidemicus MGCS10565]
          Length = 369

 Score =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 83/276 (30%), Positives = 137/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L   EE VLA      GD+ A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGVVPLLTSDEEKVLAVAVA-AGDMEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA+++ ++  +V  +        SL   I   
Sbjct: 215 -TINKLVREQRNLLQELGQDPTPEQ---IAERMEMTPDKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 361


>gi|210615118|ref|ZP_03290449.1| hypothetical protein CLONEX_02663 [Clostridium nexile DSM 1787]
 gi|210150426|gb|EEA81435.1| hypothetical protein CLONEX_02663 [Clostridium nexile DSM 1787]
          Length = 370

 Score =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 89/290 (30%), Positives = 145/290 (50%), Gaps = 15/290 (5%)

Query: 1   MNRKNMSII--VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHL 58
           M + ++S+   ++ E  +  Y+ EI K+P+L  +EE  LAKR  E GD  A  RL  ++L
Sbjct: 84  MEKIDLSVPDGISIEDPVRMYLKEIGKVPLLSAEEEIELAKRMAE-GDEDAKKRLAEANL 142

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV IA  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ WWI+ A+   I 
Sbjct: 143 RLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYQKGFKFSTYATWWIRQAITRAIA 202

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
                ++I     +      L R+   L         PE    IA++L++    V  +  
Sbjct: 203 DQARTIRIPVHMVE--TINKLIRVSRQLLQELGREPLPE---EIAEELDMPVERVREILK 257

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
                 SL   I   ++  S   D++  D      V  E       +  L   +  L  R
Sbjct: 258 ISQEPVSLETPI--GEEEDSHLGDFIQDD---NVPVPAEAAAATLLKEQLGEVLDTLTDR 312

Query: 239 ERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E+++   R    +    TLE +  EF+V+RER+RQIEA+A +K++   + 
Sbjct: 313 EQKVLRLRFGMNDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRS 362


>gi|268319377|ref|YP_003293033.1| DNA-directed RNA polymerase sigma factor RpoD (Sigma-70)
           [Lactobacillus johnsonii FI9785]
 gi|262397752|emb|CAX66766.1| DNA-directed RNA polymerase sigma factor RpoD (Sigma-70)
           [Lactobacillus johnsonii FI9785]
          Length = 372

 Score =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 79/284 (27%), Positives = 132/284 (46%), Gaps = 13/284 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +    V     +  Y+ EI ++ +L   +E  LAKR  E GD  A   L  ++LRLVV I
Sbjct: 92  SAPSSVRMNDPVRMYLKEIGRVSLLNADQEIALAKRI-ESGDEEAKQELAEANLRLVVSI 150

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y G G+   +++ EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      +
Sbjct: 151 AKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTI 210

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I     +      L R++  L         PE++ A   ++++   +V  +        
Sbjct: 211 RIPVHMVE--TINKLIRIQRQLLQDLGREPTPEEIGA---EMDMPTDKVREILKIAQEPV 265

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   I   +++ S   D++    D       +    +  +  L   +  L  RE  +  
Sbjct: 266 SLETPI--GEEDDSHLGDFI---EDKDATSPEQHASYELLKEQLEEVLDTLTDREENVLR 320

Query: 245 ARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R   ++    TLE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 321 LRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRS 364


>gi|157963788|ref|YP_001503822.1| RNA polymerase factor sigma-32 [Shewanella pealeana ATCC 700345]
 gi|157848788|gb|ABV89287.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella pealeana ATCC
           700345]
          Length = 285

 Score =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 110/285 (38%), Positives = 176/285 (61%), Gaps = 7/285 (2%)

Query: 4   KNMSIIVN-GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           ++M+++V      L  Y+H    IPMLE  +EY LAKR +E GDL AA +L+ SHLR VV
Sbjct: 6   QSMALMVPQSSGSLESYVHSAHNIPMLEADKEYELAKRLQETGDLQAAKQLIMSHLRFVV 65

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A GY GYGLP ++++ EGNIGLM+AVK+FDP+ G RL ++++ WIKA + EY+L++W 
Sbjct: 66  HVAKGYSGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYVLKNWR 125

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L   +D+     +V  +A+ L VS+++V  M  R+A 
Sbjct: 126 IVKVATTKAQRKLFFNLRKAKKRLGWFSDS-----EVGMVAESLGVSKADVTEMESRMAA 180

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE-ERKNRRNMLTRSMSVLNPRERR 241
            +    L + +D          + DH       +E +   +N +  L  ++  L+ R + 
Sbjct: 181 QDPAFDLASDNDDEQDYAPMHYLEDHSSDLASQVENDNWEQNNQARLLSAIKTLDERSQH 240

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           I +AR L E+  TL++L++ ++VS ER+RQ+E  A  K++  ++ 
Sbjct: 241 ILKARWLDEDKTTLQDLAATYQVSAERIRQLEKNAMNKLKGCMEA 285


>gi|19745866|ref|NP_607002.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS8232]
 gi|19748016|gb|AAL97501.1| putative RNA polymerase sigma 42 protein [Streptococcus pyogenes
           MGAS8232]
          Length = 369

 Score =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 83/276 (30%), Positives = 138/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE  LA    + GDL A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGVVPLLTSEEEKELAVAVAK-GDLMAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA+++ ++  +V  +        SL   I   
Sbjct: 215 -TINKLVREQRNLLQELGQDPTPEQ---IAERMEMTPDKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 361


>gi|332289156|ref|YP_004420008.1| RNA polymerase factor sigma-32 [Gallibacterium anatis UMN179]
 gi|330432052|gb|AEC17111.1| RNA polymerase factor sigma-32 [Gallibacterium anatis UMN179]
          Length = 281

 Score =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 103/284 (36%), Positives = 165/284 (58%), Gaps = 5/284 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++++  +  L  YI    + PML  +EE  LA+R   H D+ AA +L+ SHLR 
Sbjct: 1   MTKEMQNMMLVPQGSLEGYIRAANEYPMLTAEEEKELAERLYYHQDVDAAKKLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ IA GY GYGLP ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VIHIARGYSGYGLPQADLIQEGNVGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L     N     +V  +A +L VS  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNAN-----EVDMVANELGVSAEDVQEMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +G +    L     + +     +L          L E+       + L+ ++  L+ R R
Sbjct: 176 SGIDMAFDLPTDDSEETYSPALYLEDKSSNFAAELEEENFENQATDQLSEALEQLDERSR 235

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            I + R L +N  TL+ L+  + VS ER+RQ+E+ A KK++ ++
Sbjct: 236 HIIQTRWLDDNKATLQELADHYGVSAERIRQLESNALKKLRNAV 279


>gi|311031650|ref|ZP_07709740.1| RNA polymerase sigma factor RpoD [Bacillus sp. m3-13]
          Length = 374

 Score =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 81/289 (28%), Positives = 138/289 (47%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N   +   V     +  Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRL
Sbjct: 90  LNDLTVPPGVKINDPVRMYLKEIGRVDLLSAEEEISLANRI-EEGDEEAKRRLAEANLRL 148

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 149 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQ 208

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    IA+ ++++  +V  +    
Sbjct: 209 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPSPE---EIAEDMDLTPDKVREILKIA 263

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D       +    +  +  L   +  L  RE 
Sbjct: 264 QEPVSLETPI--GEEDDSHLGDFI---EDQDATSPSDHAAYELLKEQLEDVLDTLTDREE 318

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 319 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 367


>gi|127514531|ref|YP_001095728.1| RNA polymerase factor sigma-32 [Shewanella loihica PV-4]
 gi|126639826|gb|ABO25469.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella loihica PV-4]
          Length = 285

 Score =  263 bits (674), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 111/289 (38%), Positives = 173/289 (59%), Gaps = 9/289 (3%)

Query: 1   MNRKNMSI---IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSH 57
           M  +  S+   +      L  YIH    IPMLE  EEY LAKR +E GD+ AA +L+ SH
Sbjct: 1   MTNQTQSMALMVPQSSSSLEAYIHSAHNIPMLEANEEYELAKRLQETGDIQAAKQLIMSH 60

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LR V+ +A GY GYGLP ++++ EGNIGLM+AVK+FDP+ G RL ++++ WIKA + EY+
Sbjct: 61  LRFVIHVAKGYAGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYV 120

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           L++W +VK+ TT  Q++LFFNLR+ K  L   +D     E+V  +A+ L VS+S+V  M 
Sbjct: 121 LKNWRIVKVATTKAQRKLFFNLRKAKKRLGWFSD-----EEVTMVAENLGVSKSDVTEME 175

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLN 236
            R+A  +    L + +D +        + DH       +E +  + + +  L  ++  L+
Sbjct: 176 SRMAAQDPAFDLASDNDDDQDYAPVHYLEDHSSDIASQVENDNFEADNQTRLLAAIKTLD 235

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            R + I +AR L E   TL+ L++ ++VS ER+RQ+E  A  K++  ++
Sbjct: 236 ERSQHILQARWLDEEKTTLQELAATYQVSAERIRQLEKNAMNKLKGRME 284


>gi|113972098|ref|YP_735891.1| RNA polymerase factor sigma-32 [Shewanella sp. MR-4]
 gi|114049328|ref|YP_739878.1| RNA polymerase factor sigma-32 [Shewanella sp. MR-7]
 gi|117922401|ref|YP_871593.1| RNA polymerase factor sigma-32 [Shewanella sp. ANA-3]
 gi|113886782|gb|ABI40834.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella sp. MR-4]
 gi|113890770|gb|ABI44821.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella sp. MR-7]
 gi|117614733|gb|ABK50187.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella sp. ANA-3]
          Length = 285

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 108/290 (37%), Positives = 172/290 (59%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSI---IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSH 57
           M  +  S+   +  G   L  YIH +  + ML+ + EY LAKR +E GDL AA +L+ SH
Sbjct: 1   MTFQTQSMALTVPQGSSSLEAYIHSVTSMTMLDAETEYELAKRLQETGDLQAAKQLIMSH 60

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LR VV +A GY GYGLP ++++ EGNIGLM+AVK+FDP+ G RL ++++ WIKA + EY+
Sbjct: 61  LRFVVHVAKGYSGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYV 120

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           L++W +VK+ TT  Q++LFFN+R+ K  L   +D     ++V  +A+ L VS+++V  M 
Sbjct: 121 LKNWRIVKVATTKAQRKLFFNIRKAKTRLGWFSD-----DEVAMVAENLGVSKADVTEME 175

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLN 236
            R+A  +    L + +D          + DH       IE +  + N +  L  ++  L+
Sbjct: 176 SRMAAQDPAFDLSSDNDDEQDFAPVHYLEDHSSDLAENIENDNWESNAQGRLLSAIKTLD 235

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R + I  AR L ++  TL+ L+  ++VS ER+RQ+E  A  K++  ++ 
Sbjct: 236 ERSQHILRARWLDDDKTTLQELAETYQVSAERIRQLEKNAMNKLKACMEA 285


>gi|239626154|ref|ZP_04669185.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47_FAA]
 gi|239520384|gb|EEQ60250.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47FAA]
          Length = 381

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 80/280 (28%), Positives = 143/280 (51%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           +  E  +  Y+ EI  +P+L   EE  LA+R +  GD  A  RL+ ++LRLVV IA  Y 
Sbjct: 107 IGTEDPVRMYLKEIGTVPLLTADEELNLAQR-KADGDDYAKERLIEANLRLVVSIAKRYT 165

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   ++V EGN+GL++ V+KFD  +G++L+TY+ WWI+ ++   +      +++   
Sbjct: 166 GRGMSFLDLVQEGNLGLIKGVEKFDYTKGYKLSTYATWWIRQSVTRALADQARTIRVPVH 225

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      + ++    + +T        V  +A+ L+++E +V+ +        SL   
Sbjct: 226 MVE-----TINKMSKMQRKLTLELGYEPSVTELAEALDMTEDKVMEIMQIAREPASLETP 280

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   +++ S   D++    D          E    R  +   +  L  RER++   R   
Sbjct: 281 I--GEEDDSNLGDFVA---DNNVVTPEGNVESVMLREHIDALLGDLKERERQVIVLRFGL 335

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+  P TLE +  EF V+RER+RQIEA+A +K++  ++ +
Sbjct: 336 EDGHPRTLEEVGKEFNVTRERIRQIEAKALRKLRNPVRSK 375


>gi|15674827|ref|NP_269001.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes M1 GAS]
 gi|50913963|ref|YP_059935.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS10394]
 gi|71903245|ref|YP_280048.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS6180]
 gi|71910413|ref|YP_281963.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS5005]
 gi|94988285|ref|YP_596386.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS9429]
 gi|94990164|ref|YP_598264.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS10270]
 gi|94992161|ref|YP_600260.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS2096]
 gi|94994083|ref|YP_602181.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS10750]
 gi|139474032|ref|YP_001128748.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes str.
           Manfredo]
 gi|209559154|ref|YP_002285626.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes NZ131]
 gi|306827613|ref|ZP_07460893.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           pyogenes ATCC 10782]
 gi|13621959|gb|AAK33722.1| putative RNA polymerase sigma 42 protein [Streptococcus pyogenes M1
           GAS]
 gi|50903037|gb|AAT86752.1| RNA polymerase sigma factor rpoD [Streptococcus pyogenes MGAS10394]
 gi|71802340|gb|AAX71693.1| RNA polymerase sigma factor [Streptococcus pyogenes MGAS6180]
 gi|71853195|gb|AAZ51218.1| RNA polymerase sigma factor [Streptococcus pyogenes MGAS5005]
 gi|94541793|gb|ABF31842.1| RNA polymerase sigma factor [Streptococcus pyogenes MGAS9429]
 gi|94543672|gb|ABF33720.1| RNA polymerase sigma factor rpoD [Streptococcus pyogenes MGAS10270]
 gi|94545669|gb|ABF35716.1| RNA polymerase sigma factor rpoD [Streptococcus pyogenes MGAS2096]
 gi|94547591|gb|ABF37637.1| RNA polymerase sigma factor rpoD [Streptococcus pyogenes MGAS10750]
 gi|134272279|emb|CAM30532.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes str.
           Manfredo]
 gi|209540355|gb|ACI60931.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes NZ131]
 gi|304430176|gb|EFM33205.1| DNA-directed RNA polymerase sigma subunit RpoD [Streptococcus
           pyogenes ATCC 10782]
          Length = 369

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 83/276 (30%), Positives = 138/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE  LA    + GDL A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGVVPLLTSEEEKELAVAVAK-GDLMAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA+++ ++  +V  +        SL   I   
Sbjct: 215 -TINKLVREQRNLLQELGQDPTPEQ---IAERMEMTPDKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 361


>gi|261405623|ref|YP_003241864.1| RpoD subfamily RNA polymerase sigma-70 factor [Paenibacillus sp.
           Y412MC10]
 gi|329925852|ref|ZP_08280581.1| RNA polymerase sigma factor RpoD [Paenibacillus sp. HGF5]
 gi|261282086|gb|ACX64057.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Paenibacillus sp.
           Y412MC10]
 gi|328939598|gb|EGG35946.1| RNA polymerase sigma factor RpoD [Paenibacillus sp. HGF5]
          Length = 377

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 80/285 (28%), Positives = 137/285 (48%), Gaps = 13/285 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           ++   +     +  Y+ EI ++P+L   +E  LA R  E GD  A  RL  ++LRLVV I
Sbjct: 97  SLPPGIKINDPVRMYLKEIGRVPLLSADDEIELANRI-EQGDEEAKRRLAEANLRLVVSI 155

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ WWI+ A+   I      +
Sbjct: 156 AKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYKKGFKFSTYATWWIRQAITRAIADQARTI 215

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I     +      L R+   L         PE    IA ++ +S  +V  +        
Sbjct: 216 RIPVHMVE--TINKLIRVSRQLLQELGREPSPE---EIAAEMELSVEKVREIMKIAQEPV 270

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   I   +++ S   D++    D +     +    +  +  L   +  L  RE  +  
Sbjct: 271 SLETPI--GEEDDSHLGDFI---EDQEALAPADAAAYELLKEQLEDVLDTLTEREENVLR 325

Query: 245 ARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 LRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 370


>gi|323340800|ref|ZP_08081052.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           ruminis ATCC 25644]
 gi|323091923|gb|EFZ34543.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           ruminis ATCC 25644]
          Length = 373

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 78/276 (28%), Positives = 134/276 (48%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 102 DPVRMYLKEIGRVNLLTAEEEKKLALRI-EEGDEEAKQRLAEANLRLVVSIAKRYVGRGM 160

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 161 SFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 219

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  +         PE++ A   ++N+   +V  +        SL   I   
Sbjct: 220 -TINKLIRIQRQMLQDLGREPIPEEIGA---EMNLPTEKVREILKIAQEPVSLETPI--G 273

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D       +    +  +  +   +  L  RE  +   R   ++  
Sbjct: 274 EEDDSHLGDFI---EDHAATSPADHAAYELLKEQIESVLDTLTDREENVLRLRFGLDDGR 330

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 331 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 366


>gi|294501280|ref|YP_003564980.1| RNA polymerase sigma factor [Bacillus megaterium QM B1551]
 gi|295706627|ref|YP_003599702.1| RNA polymerase sigma factor [Bacillus megaterium DSM 319]
 gi|294351217|gb|ADE71546.1| RNA polymerase sigma factor [Bacillus megaterium QM B1551]
 gi|294804286|gb|ADF41352.1| RNA polymerase sigma factor [Bacillus megaterium DSM 319]
          Length = 377

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 82/289 (28%), Positives = 140/289 (48%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++ +L  +EE  LAKR  E GD  A  RL  ++LRL
Sbjct: 93  LNDLSVPPGVKINDPVRMYLKEIGRVDLLSAEEEINLAKRI-EEGDEEAKRRLAEANLRL 151

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I   
Sbjct: 152 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQ 211

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    IA+ ++++  +V  +    
Sbjct: 212 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPSPE---EIAEDMDLTPEKVREILKIA 266

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D       E    +  +  L   +  L  RE 
Sbjct: 267 QEPVSLETPI--GEEDDSHLGDFI---EDQDATSPSEHAAYELLKEQLEDVLDTLTDREE 321

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 322 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 370


>gi|225868705|ref|YP_002744653.1| RNA polymerase sigma factor RpoD [Streptococcus equi subsp.
           zooepidemicus]
 gi|225701981|emb|CAW99541.1| RNA polymerase sigma factor RpoD [Streptococcus equi subsp.
           zooepidemicus]
          Length = 369

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 83/276 (30%), Positives = 137/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L   EE VLA      GD+ A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGVVPLLTSDEEKVLAVAVA-AGDMEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA+++ ++  +V  +        SL   I   
Sbjct: 215 -TINKLVREQRNLLQELGQDPTPEQ---IAERMEMTPDKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 361


>gi|167622231|ref|YP_001672525.1| RNA polymerase factor sigma-32 [Shewanella halifaxensis HAW-EB4]
 gi|167352253|gb|ABZ74866.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella halifaxensis
           HAW-EB4]
          Length = 285

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 111/284 (39%), Positives = 173/284 (60%), Gaps = 7/284 (2%)

Query: 4   KNMSIIVN-GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           + M+++V      L  Y+H    IPMLE   EY LAKR +E GDL AA +L+ SHLR VV
Sbjct: 6   QTMALMVPQSSGSLESYVHSAHNIPMLEADTEYELAKRLQETGDLQAAKQLIMSHLRFVV 65

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A GY GYGLP ++++ EGNIGLM+AVK+FDP+ G RL ++++ WIKA + EY+L++W 
Sbjct: 66  HVAKGYSGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYVLKNWR 125

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L   +D+     +V  +A  L VS+++V  M  R+A 
Sbjct: 126 IVKVATTKAQRKLFFNLRKAKKRLGWFSDS-----EVGMVADSLGVSKADVTEMESRMAA 180

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE-ERKNRRNMLTRSMSVLNPRERR 241
            +    L + +D          + DH       +E +   +N +  L  ++  L+ R + 
Sbjct: 181 QDPAFDLASDNDDEHDYAPMHYLEDHSSDLASQVESDNWEQNNQARLLSAIKTLDERSQH 240

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           I +AR L E+  TL++L+S ++VS ER+RQ+E  A  K++  ++
Sbjct: 241 ILKARWLDEDKTTLQDLASTYQVSAERIRQLEKNAMSKLKGCME 284


>gi|302389497|ref|YP_003825318.1| RNA polymerase, sigma 70 subunit, RpoD [Thermosediminibacter oceani
           DSM 16646]
 gi|302200125|gb|ADL07695.1| RNA polymerase, sigma 70 subunit, RpoD [Thermosediminibacter oceani
           DSM 16646]
          Length = 367

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 85/280 (30%), Positives = 138/280 (49%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V  +  +  Y+ EI KIP+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y 
Sbjct: 92  VAIDDPVRMYLKEIGKIPLLTPEEEIELAKRI-EKGDKEAKRRLAEANLRLVVSIAKRYV 150

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 151 GRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 210

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L      +  PE    IA+++ +   +V  +        SL   
Sbjct: 211 MVE--TINKLIRVSRQLLQELGRDPTPE---EIAEEMELPVEKVREIMKIAQEPVSLETP 265

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++  +              +  R  L   +  L PRE ++   R   
Sbjct: 266 I--GEEEDSHLGDFIPDEEAQAPAD---AAAYRLLREQLEDVLETLTPREEKVLRLRFGL 320

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  P TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 321 DDGKPRTLEEVGQVFGVTRERIRQIEAKALRKLRHPSRSK 360


>gi|322384625|ref|ZP_08058303.1| RNA polymerase sigma factor RpoD-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321150510|gb|EFX43991.1| RNA polymerase sigma factor RpoD-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 371

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 83/276 (30%), Positives = 133/276 (48%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L   +E  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 100 DSVRMYLKEIGRVHLLTADDEIELAKRIME-GDEEAKQRLAEANLRLVVSIARRYVGRGM 158

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV+KFD  +G++ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 159 LFLDLIQEGNMGLMKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 217

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R+   L         PE    IAK++ +S  +V  +        SL   I   
Sbjct: 218 -TINKLIRVSRQLLLELGREPTPE---EIAKEMELSTDKVREIMKISQEPVSLETPI--G 271

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           ++N S   D++    D       +    +  +  L   +  L  RE  +   R   E+  
Sbjct: 272 EENDSNLGDFI---EDQDALAPADAASYELLKEQLEHVLDTLTEREENVLRLRFGLEDGR 328

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 329 SRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 364


>gi|251793696|ref|YP_003008426.1| RNA polymerase factor sigma-32 [Aggregatibacter aphrophilus NJ8700]
 gi|247535093|gb|ACS98339.1| alternative sigma factor RpoH [Aggregatibacter aphrophilus NJ8700]
          Length = 282

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 102/285 (35%), Positives = 168/285 (58%), Gaps = 6/285 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+++  ++++  +  L  YI    + PML  +EE  LA+R     D+ AA +LV SHLR 
Sbjct: 1   MDKETQTMMLVPQGSLEAYIRAANEYPMLTAEEEKELAERLYYQEDIDAAKKLVLSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K      ++N     +V  +A +L VS  +V+ M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRFGWFSEN-----EVDMVANELGVSPQDVVEMESRM 175

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            G D + +   +  D+ +     +L          L  +       + L  ++  L+ R 
Sbjct: 176 TGADVAFDLPTDDHDEETYAPALYLEDKGSNFAAELENENYEAQATDRLAVALDNLDARS 235

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + I +AR L E   TL++L+ ++ +S ERVRQ+E  A KK++ ++
Sbjct: 236 QDIIKARWLDETKATLQDLAEKYNISAERVRQLETNALKKLKSAV 280


>gi|225870339|ref|YP_002746286.1| RNA polymerase sigma factor RpoD [Streptococcus equi subsp. equi
           4047]
 gi|225699743|emb|CAW93506.1| RNA polymerase sigma factor RpoD [Streptococcus equi subsp. equi
           4047]
          Length = 369

 Score =  263 bits (673), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 83/276 (30%), Positives = 137/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L   EE VLA      GD+ A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGVVPLLTSDEEKVLAVAVA-AGDMEAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA+++ ++  +V  +        SL   I   
Sbjct: 215 -TINKLVREQRNLLQELGQDPTPEQ---IAERMEMTPDKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 361


>gi|260655747|ref|ZP_05861216.1| RNA polymerase major sigma factor [Jonquetella anthropi E3_33 E1]
 gi|260629363|gb|EEX47557.1| RNA polymerase major sigma factor [Jonquetella anthropi E3_33 E1]
          Length = 969

 Score =  263 bits (672), Expect = 2e-68,   Method: Composition-based stats.
 Identities = 76/277 (27%), Positives = 134/277 (48%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
              +  Y+ +I K+ +L+  EE  LAKR  E GD +A   ++ ++LRLVV IA  Y G G
Sbjct: 697 SDPVRMYLRDIGKVSLLDAAEEVALAKRV-EAGDETAKDEIINANLRLVVSIAKKYIGRG 755

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +   +++ EGN+GL++AV+KFD  RGF+ +TY+ WWI+ A+   I      ++I     +
Sbjct: 756 MQFLDLIQEGNLGLIRAVEKFDYRRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 815

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 + ++    + +     +      IA ++ +    V  +        SL   I  
Sbjct: 816 -----TINKMVRISRQLVQKLGREPSDEEIAAEMKIEPERVEEIKRISQMPVSLETPI-- 868

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            ++  SQ  D++    D       +       +  +   ++ L+ RER +   R   E+ 
Sbjct: 869 GEEEDSQLGDFI---EDRSLPSPEDVAADNLLQEQIEEMLNALSDREREVLRYRFGLEDG 925

Query: 253 V--TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 926 RSYTLEEVGRRFGVTRERIRQIEAKALRKLRHPSRSK 962


>gi|54307376|ref|YP_128396.1| RNA polymerase factor sigma-32 [Photobacterium profundum SS9]
 gi|46911796|emb|CAG18594.1| putative RNA polymerase sigma-32 factor [Photobacterium profundum
           SS9]
          Length = 282

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 110/285 (38%), Positives = 172/285 (60%), Gaps = 10/285 (3%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
             +M++I  G   L  YI  + + PML  ++E  LA+R    GD+ AA  LV SH+R VV
Sbjct: 1   MSSMALIFAG--SLDSYIQTVNRHPMLSAEQEKELAERLHYDGDIEAAKGLVMSHMRFVV 58

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A GY GYGLPI++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W 
Sbjct: 59  HVARGYSGYGLPIADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWR 118

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L    +      +V  +A++L V+ SEV  M  RLA 
Sbjct: 119 IVKVATTKAQRKLFFNLRKSKKRLGWFNN-----AEVEMVAEQLGVNPSEVREMESRLAA 173

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNPRE 239
            +    L N  D   + +   + +  D    V +  EE     +  N L+ +++ L+ R 
Sbjct: 174 QDPAFELPNEDDDRDAGYTAPVYFLEDKSSDVALSYEENNWENHTNNRLSNALAGLDERS 233

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + I  +R L +   TL++L++ + +S ERVRQ+E  A KK++E++
Sbjct: 234 QHIVRSRWLDDEKTTLQDLANHYGISAERVRQLEKNAMKKLKEAV 278


>gi|15604172|ref|NP_220687.1| RNA polymerase factor sigma-32 [Rickettsia prowazekii str. Madrid
           E]
 gi|3860864|emb|CAA14764.1| RNA POLYMERASE SIGMA-32 FACTOR (rpoH) [Rickettsia prowazekii]
 gi|292571903|gb|ADE29818.1| RNA polymerase sigma-32 factor [Rickettsia prowazekii Rp22]
          Length = 293

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 143/285 (50%), Positives = 199/285 (69%), Gaps = 1/285 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M     ++ ++ E G   Y+ +I KIP L ++EE++LAK Y E  DL AAH+LVTSHL+L
Sbjct: 1   MTNNINALAISSESGFYSYLQKINKIPSLTQEEEFLLAKSYLEENDLQAAHKLVTSHLKL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIA  Y+ YGLPI+E+VSEGNIGLMQAVKKF+PE GFRL+TY+MWWIKA++QEYIL+S
Sbjct: 61  VAKIASSYKTYGLPITELVSEGNIGLMQAVKKFNPELGFRLSTYAMWWIKASIQEYILKS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTA QK+LFF+L ++K  +  +    +  +    IA +L VS +EV  MN R+
Sbjct: 121 WSLVKMGTTAAQKKLFFSLNKVKHKITNLYSRAITTDDFAQIADELGVSVNEVSEMNTRI 180

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D SLN  INS D  S +  + L       E + I K+   ++R +L+ +M +LN RE
Sbjct: 181 SGPDLSLNNSINSDDVESGELIELLPELRPTPEAMAINKQNYTSKRKLLSNAMQILNDRE 240

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            RI + R+L + P TL+ LSSE+ +S+ER+RQIE  AF+K+++ I
Sbjct: 241 LRILKDRKLTDTPKTLDILSSEYNISKERIRQIENTAFEKIKKFI 285


>gi|315652381|ref|ZP_07905370.1| RNA polymerase sigma factor rpoD [Eubacterium saburreum DSM 3986]
 gi|315485355|gb|EFU75748.1| RNA polymerase sigma factor rpoD [Eubacterium saburreum DSM 3986]
          Length = 410

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 83/280 (29%), Positives = 144/280 (51%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V  E  +  Y+ EI  +P+L   EE  LAKR ++ GD  A  RL+ ++LRLVV IA  Y 
Sbjct: 135 VGTEDPVRMYLKEIGTVPLLTANEELELAKR-KQDGDEYAKQRLIEANLRLVVSIAKRYT 193

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   ++V EGN+GL++ V+KFD  +GF+L+TY+ WWI+ ++   +      +++   
Sbjct: 194 GRGMSFLDLVQEGNLGLIKGVEKFDYTKGFKLSTYATWWIRQSVTRALADQARTIRVPVH 253

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      + ++    + +T        V  +A  L+++E +V+ +        SL   
Sbjct: 254 MVE-----TINKMSKMQRKLTLELGYEPSVTELANALDMTEEKVMEIMQIAREPASLETP 308

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   +++ S   D++    D          E    R  +   +  L  RER++   R   
Sbjct: 309 I--GEEDDSNLGDFVA---DSNVLTPEGNVESVMLREHIDTLLGDLKERERQVIVLRFGL 363

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+  P TLE +  EF+V+RER+RQIEA+A +K++  ++ +
Sbjct: 364 EDGHPRTLEEVGKEFKVTRERIRQIEAKALRKLRNPVRSK 403


>gi|332799075|ref|YP_004460574.1| RpoD subfamily RNA polymerase sigma-70 [Tepidanaerobacter sp. Re1]
 gi|332696810|gb|AEE91267.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Tepidanaerobacter
           sp. Re1]
          Length = 374

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 83/277 (29%), Positives = 139/277 (50%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI K+P+L  +EE +L+KR  E GD  A  RL  ++LRLVV IA  Y G G
Sbjct: 102 DDPVRMYLKEIGKVPLLSAEEEIMLSKRI-EEGDKEAKRRLAEANLRLVVSIAKKYVGRG 160

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +   +++ EGN+GLM+AV+KFD ++G++ +TY+ WWI+ A+   I      ++I     +
Sbjct: 161 MLFLDLIQEGNLGLMKAVEKFDYKKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 220

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 L R++  L      +  PE    IA+++ +   +V  +        SL   I  
Sbjct: 221 --TINKLIRIQRQLLQELGRDPLPE---EIAEEMELPVEKVREIMKIAQEPVSLATPI-- 273

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN- 251
            ++  S   D++  D                 +  L   +  L PRE ++   R   ++ 
Sbjct: 274 GEEEDSFLGDFIPDDEALAPAD---AAAYLLLKEQLEDVLETLTPREEKVLRLRFGLDDG 330

Query: 252 -PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            P TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 331 RPRTLEEVGQVFGVTRERIRQIEAKALRKLRHPSRSK 367


>gi|21910055|ref|NP_664323.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes MGAS315]
 gi|28896247|ref|NP_802597.1| RNA polymerase sigma factor RpoD [Streptococcus pyogenes SSI-1]
 gi|21904246|gb|AAM79126.1| putative RNA polymerase sigma 42 protein RpoD [Streptococcus
           pyogenes MGAS315]
 gi|28811498|dbj|BAC64430.1| putative RNA polymerase sigma 42 protein [Streptococcus pyogenes
           SSI-1]
          Length = 369

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 83/276 (30%), Positives = 138/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE  LA    + GDL A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGVVPLLTSEEEKELAVAVAK-GDLMAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA+++ ++  +V  +        SL   I   
Sbjct: 215 -TINKLVREQRNLLQELGQDPTPEQ---IAERMEMTPDKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 269 EEDDSHLGDFI---EDEVIENPVDYTTRVVLREQLDEVLDTLTDREENVLRLRFGLDDGK 325

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 326 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 361


>gi|90412724|ref|ZP_01220725.1| RNA polymerase sigma factor [Photobacterium profundum 3TCK]
 gi|90326299|gb|EAS42718.1| RNA polymerase sigma factor [Photobacterium profundum 3TCK]
          Length = 286

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 108/287 (37%), Positives = 172/287 (59%), Gaps = 8/287 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  S+ +     L  YI  + + PML  ++E  LA+R    GD+ AA  LV SH+R 
Sbjct: 1   MAKEMSSMALVSTGSLDSYIQTVNRHPMLTVEQEKELAERLHYDGDIEAAKGLVMSHMRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A GY GYGLP+++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARGYSGYGLPMADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L    +      +V  +A++L V+ SEV  M  RL
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKSKKRLGWFNN-----AEVEMVAEQLGVNPSEVREMESRL 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNP 237
           A  +    L N  D   + +   + +  D    V +  EE     +  N L+ +++ L+ 
Sbjct: 176 AAQDPAFELPNEDDDRDAGYTAPVYFLEDKASDVALSYEENNWENHTNNRLSNALAGLDE 235

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R + I  +R L +   TL++L++ + +S ERVRQ+E  A KK++E++
Sbjct: 236 RSQHIVRSRWLDDEKTTLQDLANHYGISAERVRQLEKNAMKKLKEAV 282


>gi|312865945|ref|ZP_07726166.1| RNA polymerase sigma factor RpoD [Streptococcus downei F0415]
 gi|311098349|gb|EFQ56572.1| RNA polymerase sigma factor RpoD [Streptococcus downei F0415]
          Length = 338

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 84/276 (30%), Positives = 139/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE  LA    E GDL A  RL  ++LRLVV IA  Y G G+
Sbjct: 66  DPVRMYLKEIGIVPLLTNEEEKELAIAAAE-GDLMAKQRLAEANLRLVVSIAKRYVGRGM 124

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 125 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 183

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA++++++  +V  +        SL   I   
Sbjct: 184 -TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSLETPI--G 237

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R   ++  
Sbjct: 238 EEDDSHLGDFI---EDEVIENPVDYTTRIVLREQLNEVLDTLTDREENVLRLRFGLDDGK 294

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE++   F V+RER+RQIEA+A +K++   + +
Sbjct: 295 MRTLEDVGKVFNVTRERIRQIEAKALRKLRHPSRSK 330


>gi|295424882|ref|ZP_06817597.1| RNA polymerase sigma factor rpoD [Lactobacillus amylolyticus DSM
           11664]
 gi|295065448|gb|EFG56341.1| RNA polymerase sigma factor rpoD [Lactobacillus amylolyticus DSM
           11664]
          Length = 368

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 80/284 (28%), Positives = 137/284 (48%), Gaps = 13/284 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +    V     +  Y+ EI ++P+L   +E  LAKR  E+GD  A   L  ++LRLVV I
Sbjct: 88  SAPSSVRMNDPVRMYLKEIGRVPLLNADKEIALAKRI-ENGDEEAKQELAEANLRLVVSI 146

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y G G+   +++ EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I      +
Sbjct: 147 AKRYVGRGMSFLDLIQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQARTI 206

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I     +      L R++  L         PE++ A   ++++  ++V  +        
Sbjct: 207 RIPVHMVE--TINKLIRIQRQLLQDLGREPTPEEIGA---EMDMPTNKVRDILKIAQEPV 261

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   I   +++ S   D++    D +     +    +  +  L  ++  L  RE  +  
Sbjct: 262 SLETPI--GEEDDSHLGDFI---EDKEATSPEQHASYEMLKEQLEETLDTLTDREENVLR 316

Query: 245 ARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R   ++    TLE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 317 LRFGLDDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRS 360


>gi|317132028|ref|YP_004091342.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ethanoligenens
           harbinense YUAN-3]
 gi|315470007|gb|ADU26611.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ethanoligenens
           harbinense YUAN-3]
          Length = 372

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 79/277 (28%), Positives = 138/277 (49%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI ++P+L  +EE  LAKR  E GD++A  RL  ++LRLVV IA  Y G G
Sbjct: 100 DDPVKVYLKEIGRVPLLSGEEEIELAKRMGE-GDVAARKRLSEANLRLVVSIAKRYVGRG 158

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I     +
Sbjct: 159 MQFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 218

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 + ++    + +     +  Q   IA+ + +S  +V  +        SL   I  
Sbjct: 219 -----TINKVVRVERQLLQELGRQPQAEEIAELMGMSVDKVREIMKVAQEPVSLETPI-- 271

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN- 251
            ++  S   D++            E       +  L   +  L  RE ++   R   ++ 
Sbjct: 272 GEEEDSHLGDFIPD---DDAPAPAEAASHTLLKEQLGDVLKTLTQREAKVLRLRFGLDDG 328

Query: 252 -PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            P TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 329 RPRTLEEVGREFNVTRERIRQIEAKALRKLRHPSRSK 365


>gi|229916320|ref|YP_002884966.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Exiguobacterium
           sp. AT1b]
 gi|229467749|gb|ACQ69521.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Exiguobacterium
           sp. AT1b]
          Length = 364

 Score =  263 bits (672), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 81/289 (28%), Positives = 140/289 (48%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   +     +  Y+ EI ++ +L  ++E  LAKR  E GD  A  RL  ++LRL
Sbjct: 80  LNDLSVPPGIKINDPVRMYLKEIGRVDLLSAKDETELAKRI-EQGDEEAKKRLAEANLRL 138

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 139 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYMKGFKFSTYATWWIRQAITRAIADQ 198

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    IAK++ ++  +V  +    
Sbjct: 199 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPSPE---EIAKEMELTPEKVREILKIA 253

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D       +    +  +  L   +  L  RE 
Sbjct: 254 QEPVSLETPI--GEEDDSHLGDFI---EDQDAMAPQDAAAYELLKEQLEDVLDTLTDREE 308

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 309 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 357


>gi|269792833|ref|YP_003317737.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermanaerovibrio
           acidaminovorans DSM 6589]
 gi|269100468|gb|ACZ19455.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermanaerovibrio
           acidaminovorans DSM 6589]
          Length = 387

 Score =  262 bits (671), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 82/277 (29%), Positives = 135/277 (48%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
              +  Y+ EI +IP+L  +EE  LAK   E GD  A  +LV ++LRLVV IA  Y G G
Sbjct: 115 SDPVRMYLREIGRIPLLSPEEEVELAKGV-EAGDKRAKEKLVEANLRLVVSIAKKYIGRG 173

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I     +
Sbjct: 174 MLFLDLIQEGNLGLIRAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 233

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 + +L    + +     +      IA+++ V+   V  +        SL   I  
Sbjct: 234 -----TINKLIRISRVLVQRLGREPSAEEIAQEMGVTVDRVEEIQKIAQEPVSLETPI-- 286

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            ++  SQ  D+L    D       E    +  R  L   +  L  RE+ +   R   E+ 
Sbjct: 287 GEEEDSQLGDFL---EDKDLPSPDEAAANQILREQLEEMLEDLTDREKEVLRLRFGLEDG 343

Query: 253 --VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 344 HSHTLEEVGRRFGVTRERIRQIEAKALRKLRHPSRSK 380


>gi|310659059|ref|YP_003936780.1| RNA polymerase sigma factor rpod [Clostridium sticklandii DSM 519]
 gi|308825837|emb|CBH21875.1| RNA polymerase sigma factor RpoD [Clostridium sticklandii]
          Length = 376

 Score =  262 bits (671), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 85/280 (30%), Positives = 145/280 (51%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V+ +  +  Y+ EI KIP+L  +EE  LA++    GD  A  +LV ++LRLVV IA  Y 
Sbjct: 101 VSIDDPVRMYLKEIGKIPLLSAEEEIDLAEKMGY-GDEIAKKKLVEANLRLVVSIAKRYV 159

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ WWI+ A+   I      ++I   
Sbjct: 160 GRGMLFLDLIQEGNLGLIKAVEKFDYKKGFKFSTYATWWIRQAITRAIADQARTIRIPVH 219

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L      + KPE    +AK++++ E ++  +        SL   
Sbjct: 220 MVE--TINKLIRVHRQLLQEYGRDPKPE---ELAKEMDMPEEKIREIMKIAQEPVSLETP 274

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++            E       +  L   +  LN RE+++ + R   
Sbjct: 275 I--GEEEDSHLGDFIPD---DDAPAPAEAAAYSLLKEQLEDVLCTLNEREQKVLKLRFGL 329

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+    TLE +  EF+V+RER+RQIEA+A +K++   + +
Sbjct: 330 EDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSK 369


>gi|116618341|ref|YP_818712.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Leuconostoc mesenteroides subsp. mesenteroides ATCC
           8293]
 gi|116097188|gb|ABJ62339.1| RNA polymerase, sigma 70 subunit, RpoD [Leuconostoc mesenteroides
           subsp. mesenteroides ATCC 8293]
          Length = 432

 Score =  262 bits (671), Expect = 3e-68,   Method: Composition-based stats.
 Identities = 80/276 (28%), Positives = 137/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L+  EE  +AKR  E+GD+ A   L  ++LRLVV IA  Y G G+
Sbjct: 157 DPVRMYLKEIGRVNLLKGNEEIDIAKRI-ENGDVEAKQELAEANLRLVVSIAKRYVGRGM 215

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 216 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 274

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L         PE++ A   +++++  +V  +        SL   I   
Sbjct: 275 -TINKLIRIQRQLLQDLGREPLPEEIGA---EMDLTADKVREILKIAQEPVSLETPI--G 328

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D +     +    +  R  L   +  L  RE  +   R   E+  
Sbjct: 329 EEDDSHLGDFI---EDNEAVSPADSAAYEMLREQLESVLDTLTDREENVLRLRFGLEDGR 385

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 386 TRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSK 421


>gi|300812183|ref|ZP_07092625.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus PB2003/044-T3-4]
 gi|300496819|gb|EFK31899.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus PB2003/044-T3-4]
          Length = 372

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 80/288 (27%), Positives = 139/288 (48%), Gaps = 13/288 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  +    +     +  Y+ EI ++ +L  +EE  LAKR  E GD  A   L  ++LRL
Sbjct: 88  LNNMDAPTGMKMNDPVRMYLKEIGRVNLLTSEEEVALAKRI-EAGDEEAKQELAEANLRL 146

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GLM+AV KFD   G++ +TY+ WWI+ A+   I   
Sbjct: 147 VVSIAKRYVGRGMNFLDLIQEGNMGLMKAVDKFDYRLGYKFSTYATWWIRQAITRAIADQ 206

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L      + +PE++ A   ++++   +V  +    
Sbjct: 207 ARTIRIPVHMVE--TINKLIRIQRQLLQDLGRDPEPEEIGA---EMDLPVKKVREILKIC 261

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D       +    +  +  L   +  L+ RE 
Sbjct: 262 QEPVSLETPI--GEEDDSNLGDFI---EDKDAMSPEQHAANEMLKEQLAEVLDTLSDREE 316

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +   R   ++    TLE +   FEV+RER+RQIEA+A +K++   + 
Sbjct: 317 EVLRLRFGLDDGKARTLEEVGQHFEVTRERIRQIEAKALRKLRHPSRS 364


>gi|307700837|ref|ZP_07637862.1| RNA polymerase sigma factor RpoD [Mobiluncus mulieris FB024-16]
 gi|307613832|gb|EFN93076.1| RNA polymerase sigma factor RpoD [Mobiluncus mulieris FB024-16]
          Length = 614

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 71/305 (23%), Positives = 143/305 (46%), Gaps = 39/305 (12%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREH---------------------- 44
               +  Y+ +I K+ +L  ++E  LAKR     Y EH                      
Sbjct: 313 TSDPVKDYLKQIGKVALLNAEQEVNLAKRIEAGLYAEHLLKTEQDSMTPKHARELHWVVQ 372

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
             ++A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY
Sbjct: 373 DGVNAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYSKGYKFSTY 432

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + WWI+ A+   +      +++     +  +   L R++  +         P+    +A+
Sbjct: 433 ATWWIRQAITRAMADQARTIRVPVHMVE--VINKLARVQRQMLQDLGREPTPD---ELAR 487

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L+++  +V+ +        SL+  +   +   S++ D +    D +  V  +       
Sbjct: 488 ELDMTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFVML 542

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +  L R +  L+ RE  +   R    +  P TL+++   + V+RER+RQIE++   K++ 
Sbjct: 543 QEQLQRVLDTLSEREAGVIAMRYGLNDGVPKTLDDIGHRYGVTRERIRQIESKTMSKLRH 602

Query: 283 SIQKQ 287
             + Q
Sbjct: 603 PARSQ 607


>gi|154502790|ref|ZP_02039850.1| hypothetical protein RUMGNA_00604 [Ruminococcus gnavus ATCC 29149]
 gi|153796673|gb|EDN79093.1| hypothetical protein RUMGNA_00604 [Ruminococcus gnavus ATCC 29149]
          Length = 371

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 87/290 (30%), Positives = 141/290 (48%), Gaps = 15/290 (5%)

Query: 1   MNRKNMSII--VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHL 58
           M   ++S+   V+ E  +  Y+ EI K+P+L    E  LA+R  E GD  A   L  ++L
Sbjct: 85  MENIDLSVPDGVSIEDPVRMYLKEIGKVPLLSADREIELAQRM-EEGDEDAKKELAEANL 143

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I 
Sbjct: 144 RLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYHKGYKFSTYATWWIRQAITRAIA 203

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
                ++I     +      L R+   L         PE    IAK+L++    V  +  
Sbjct: 204 DQARTIRIPVHMVE--TINKLIRVSRQLLQELGREPLPE---EIAKELDMPVERVREILK 258

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
                 SL   I   ++  S   D++  D      V  E   +   +  L   +  L  R
Sbjct: 259 ISQEPVSLETPI--GEEEDSHLGDFIQDD---NVPVPAEAAAQTLLKEQLDEVLDTLTER 313

Query: 239 ERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E+++   R    +    TLE +  EF+V+RER+RQIEA+A +K++   + 
Sbjct: 314 EQKVLRLRFGMNDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRS 363


>gi|271502546|ref|YP_003335572.1| RNA polymerase sigma-32 subunit RpoH [Dickeya dadantii Ech586]
 gi|270346101|gb|ACZ78866.1| RNA polymerase, sigma 32 subunit, RpoH [Dickeya dadantii Ech586]
          Length = 285

 Score =  262 bits (671), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 103/290 (35%), Positives = 161/290 (55%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M +   +  +  +  L  YI      PML   EE  LA+R   HGDL AA +L+ SHLR 
Sbjct: 1   MTKDMQTFALVPQGSLEGYIRAANAYPMLTADEERALAERLHYHGDLDAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A  Y GYGLP ++++ EGNIGLM+AV++F+P+ G RL ++++ WIKA + EY+LR+
Sbjct: 61  VIHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPDVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVELVARELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNP 237
           A  +         D    Q    ++Y  D        + E     +  + LT ++  L+ 
Sbjct: 176 AAQDMTFDPSPEDDAQPGQPMAPMLYLQDKSSDFADGIEEDNWETHAADKLTYALEGLDE 235

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L ++   TL+ L+  + VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQHIIRARWLDDDNKSTLQELADHYGVSAERVRQLEKNAMKKLRAAIEA 285


>gi|227875511|ref|ZP_03993651.1| RNA polymerase sigma factor SigA [Mobiluncus mulieris ATCC 35243]
 gi|269977243|ref|ZP_06184216.1| RNA polymerase principal sigma factor HrdB [Mobiluncus mulieris
           28-1]
 gi|306818820|ref|ZP_07452542.1| DNA-directed RNA polymerase sigma subunit RpoD [Mobiluncus mulieris
           ATCC 35239]
 gi|227843847|gb|EEJ54016.1| RNA polymerase sigma factor SigA [Mobiluncus mulieris ATCC 35243]
 gi|269934546|gb|EEZ91107.1| RNA polymerase principal sigma factor HrdB [Mobiluncus mulieris
           28-1]
 gi|304648506|gb|EFM45809.1| DNA-directed RNA polymerase sigma subunit RpoD [Mobiluncus mulieris
           ATCC 35239]
          Length = 614

 Score =  262 bits (670), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 71/305 (23%), Positives = 143/305 (46%), Gaps = 39/305 (12%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREH---------------------- 44
               +  Y+ +I K+ +L  ++E  LAKR     Y EH                      
Sbjct: 313 TSDPVKDYLKQIGKVALLNAEQEVNLAKRIEAGLYAEHLLKTEQDSMTPKHARELHWVVQ 372

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
             ++A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY
Sbjct: 373 DGVNAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYSKGYKFSTY 432

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + WWI+ A+   +      +++     +  +   L R++  +         P+    +A+
Sbjct: 433 ATWWIRQAITRAMADQARTIRVPVHMVE--VINKLARVQRQMLQDLGREPTPD---ELAR 487

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L+++  +V+ +        SL+  +   +   S++ D +    D +  V  +       
Sbjct: 488 ELDMTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFVML 542

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +  L R +  L+ RE  +   R    +  P TL+++   + V+RER+RQIE++   K++ 
Sbjct: 543 QEQLQRVLDTLSEREAGVIAMRYGLNDGVPKTLDDIGHRYGVTRERIRQIESKTMSKLRH 602

Query: 283 SIQKQ 287
             + Q
Sbjct: 603 PARSQ 607


>gi|224542125|ref|ZP_03682664.1| hypothetical protein CATMIT_01300 [Catenibacterium mitsuokai DSM
           15897]
 gi|224524962|gb|EEF94067.1| hypothetical protein CATMIT_01300 [Catenibacterium mitsuokai DSM
           15897]
          Length = 418

 Score =  262 bits (670), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 80/289 (27%), Positives = 140/289 (48%), Gaps = 14/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           MN+   ++ +N    +  Y+ EI ++ +L  ++E  LAKR  E GD  A   L  ++LRL
Sbjct: 134 MNQLGSNVKIN--DPVKMYLKEIGRVDLLTHEQEIELAKRILE-GDEQAKKELAAANLRL 190

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 191 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQ 250

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L          E++        ++ ++V  +    
Sbjct: 251 ARTIRIPVHMVE--TINKLTRIQRQLVQELGREPTAEEIAEKMD--GMTPAKVREIQKIS 306

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++  +           E  K+    L   +  L  RE 
Sbjct: 307 LEPVSLETPI--GEEDDSHLGDFIEDEGAMSPDDYASNELLKDE---LNEVLLELTDREE 361

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++   R   ++    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 362 KVLRLRFGLDDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLKHPSRSK 410


>gi|332975851|gb|EGK12729.1| DNA-directed RNA polymerase sigma subunit SigA [Desmospora sp.
           8437]
          Length = 372

 Score =  262 bits (670), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 82/276 (29%), Positives = 137/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++P+L  +EE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 101 DPVRMYLKEIGRVPLLSAEEEVELAKRI-EEGDEEAKRRLAEANLRLVVSIAKRYVGRGM 159

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 160 LFLDLIQEGNMGLIKAVEKFDFRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 218

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R+   L         PE    IA+++++S  +V  +        SL   I   
Sbjct: 219 -TINKLIRVSRQLLQELGREPSPE---EIAEEMDLSPEKVREIMKIAQEPVSLETPI--G 272

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++        Q   +    +  +  L   +  L+ RE  +   R   ++  
Sbjct: 273 EEDDSHLGDFIPD---DDAQAPADAAAYELLKEQLKDVLDTLSDREENVLRLRFGLDDGR 329

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 330 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 365


>gi|242241268|ref|YP_002989449.1| RNA polymerase factor sigma-32 [Dickeya dadantii Ech703]
 gi|242133325|gb|ACS87627.1| RNA polymerase, sigma 32 subunit, RpoH [Dickeya dadantii Ech703]
          Length = 285

 Score =  262 bits (670), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 102/290 (35%), Positives = 161/290 (55%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M +   +  +  +  L  YI      PML  +EE  LA+R   HGDL AA +L+ SHLR 
Sbjct: 1   MTKDMQTFALVPQGSLEGYIRAANAYPMLTAEEERALAERLHYHGDLDAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A  Y GYGLP ++++ EGNIGLM+AV++F+P+ G RL ++++ WIKA + EY+LR+
Sbjct: 61  VIHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPDVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKRRLGWFNQ-----DEVELVARELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNP 237
           A  +         D    Q    ++Y  D        + E     +  + L  ++  L+ 
Sbjct: 176 AAQDMTYDPTPDDDAQPGQPMAPMLYLQDKSSDFADGIEEDNWETHAADKLAYALEGLDE 235

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L ++   TL+ L+  + VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQHIIRARWLDDDNKSTLQELADYYGVSAERVRQLEKNAMKKLRAAIEA 285


>gi|126172428|ref|YP_001048577.1| RNA polymerase factor sigma-32 [Shewanella baltica OS155]
 gi|153002659|ref|YP_001368340.1| RNA polymerase factor sigma-32 [Shewanella baltica OS185]
 gi|217975235|ref|YP_002359986.1| RNA polymerase factor sigma-32 [Shewanella baltica OS223]
 gi|304412289|ref|ZP_07393897.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella baltica OS183]
 gi|307306073|ref|ZP_07585818.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella baltica BA175]
 gi|125995633|gb|ABN59708.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella baltica OS155]
 gi|151367277|gb|ABS10277.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella baltica OS185]
 gi|217500370|gb|ACK48563.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella baltica OS223]
 gi|304349324|gb|EFM13734.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella baltica OS183]
 gi|306910946|gb|EFN41373.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella baltica BA175]
          Length = 285

 Score =  262 bits (670), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 110/290 (37%), Positives = 171/290 (58%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSI---IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSH 57
           M  +  S+   +  G   L  YIH +  I ML+ + EY LAKR +E GDL AA +L+ SH
Sbjct: 1   MTFQTQSMALTVPQGASSLEAYIHSVTSISMLDAEAEYELAKRLQETGDLQAAKQLIMSH 60

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LR VV +A GY GYGLP ++++ EGNIGLM+AVK+FDP+ G RL ++++ WIKA + EY+
Sbjct: 61  LRFVVHVAKGYSGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYV 120

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           L++W +VK+ TT  Q++LFFN+R+ K  L   +D      +V  +A+ L VS+++V  M 
Sbjct: 121 LKNWRIVKVATTKAQRKLFFNIRKAKKRLGWFSD-----AEVTMVAENLGVSKADVTEME 175

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLN 236
            R+A  +    L N  D+         + DH       IE +  + N +  L  ++  L+
Sbjct: 176 SRMAAQDPAFDLTNDQDEEHDFAPVHYLEDHSSDLAENIENDNWESNAQGRLLSAIKTLD 235

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R + I  AR L ++  TL+ L+  ++VS ER+RQ+E  A  K++  ++ 
Sbjct: 236 ERSQHILRARWLDDDKTTLQELAETYQVSAERIRQLEKNAMNKLKACMEA 285


>gi|330447179|ref|ZP_08310829.1| alternative sigma factor RpoH [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
 gi|328491370|dbj|GAA05326.1| alternative sigma factor RpoH [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
          Length = 286

 Score =  262 bits (670), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 107/287 (37%), Positives = 170/287 (59%), Gaps = 8/287 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+++  ++ +     L  YI  + + PML  + E  LA+R     D++AA  LV SHLR 
Sbjct: 1   MSKEMSAMALVSTDSLDSYIQTVNRYPMLTPEREKELAERLHYDDDINAAKALVMSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA GY GYGLPI++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHIARGYSGYGLPIADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L    +     E+V  +A++L V   EV  M  RL
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKSKKRLGWFNN-----EEVNMVAEQLGVEPEEVREMESRL 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNP 237
           A  +    + N  D   +       +  D    V +  EE     +  N L+++++ L+ 
Sbjct: 176 AAQDPTFEMQNDDDDRDAAPMAPAYFLEDKSSDVALTYEENNWENHANNRLSQALASLDE 235

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R + I  +R L ++  TL++L+  + VS ER+RQ+E  A KK+++++
Sbjct: 236 RSQHIVRSRWLDDDKSTLQDLADSYGVSAERIRQLEKNAMKKLKDAV 282


>gi|194397936|ref|YP_002037704.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae G54]
 gi|194357603|gb|ACF56051.1| RNA polymerase sigma factor RpoD [Streptococcus pneumoniae G54]
          Length = 369

 Score =  262 bits (670), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 84/283 (29%), Positives = 140/283 (49%), Gaps = 13/283 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S        +  Y+ EI  +P+L  +EE  LA    E GD+ A  RL  ++LRLVV IA 
Sbjct: 90  STSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAV-EAGDIEAKQRLAEANLRLVVSIAK 148

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y G G+   +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I
Sbjct: 149 RYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI 208

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
                +      L R + +L      +  PEQ   IA++++++  +V  +        SL
Sbjct: 209 PVHMVE--TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSL 263

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              I   +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R
Sbjct: 264 ETPI--GEEDDSHLGDFI---EDEVIENPVDYTTRIVLREQLDEILDTLTDREENVLRLR 318

Query: 247 RLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              ++    TLE++   F V+RER+RQIEA+A +K ++  + +
Sbjct: 319 FGLDDGKMRTLEDVGKVFNVTRERIRQIEAKALRKXRQPSRSK 361


>gi|24376056|ref|NP_720099.1| RNA polymerase factor sigma-32 [Shewanella oneidensis MR-1]
 gi|24351072|gb|AAN57543.1|AE015890_4 RNA polymerase sigma-32 factor [Shewanella oneidensis MR-1]
          Length = 285

 Score =  262 bits (670), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 108/290 (37%), Positives = 172/290 (59%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSI---IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSH 57
           M  +  S+   +  G   L  YIH +  + ML+ + EY LAKR +E GDL AA +L+ SH
Sbjct: 1   MTFQTQSMALTVPQGSSSLEAYIHSVTSMNMLDAETEYELAKRLQETGDLQAAKQLIMSH 60

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LR VV +A GY GYGLP ++++ EGNIGLM+AVK+FDP+ G RL ++++ WIKA + EY+
Sbjct: 61  LRFVVHVAKGYAGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYV 120

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           L++W +VK+ TT  Q++LFFN+R+ K  L   +D     ++V  +A+ L VS+++V  M 
Sbjct: 121 LKNWRIVKVATTKAQRKLFFNIRKAKTRLGWFSD-----DEVTMVAENLGVSKADVTEME 175

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLN 236
            R+A  +    L + +D          + DH       IE +  + N +  L  ++  L+
Sbjct: 176 SRMAAQDPAFDLSSDNDDEHDFAPVHYLEDHSSDLAENIENDNWESNAQGRLLSAIKTLD 235

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R + I  AR L ++  TL+ L+  ++VS ER+RQ+E  A  K++  ++ 
Sbjct: 236 ERSQHILRARWLDDDKTTLQELAETYQVSAERIRQLEKNAMNKLKACMEA 285


>gi|323490072|ref|ZP_08095293.1| RNA polymerase sigma factor RpoD [Planococcus donghaensis MPA1U2]
 gi|323396368|gb|EGA89193.1| RNA polymerase sigma factor RpoD [Planococcus donghaensis MPA1U2]
          Length = 384

 Score =  262 bits (670), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 81/289 (28%), Positives = 141/289 (48%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++ +L+ +EE  LAK   E GD  A  RL  ++LRL
Sbjct: 100 LNDLSVPPGVKINDPVRMYLKEIGRVDLLKAEEEVRLAKLI-EQGDEEAKKRLAEANLRL 158

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 159 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYSKGFKFSTYATWWIRQAITRAIADQ 218

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L      +  PE    I +++++   +V  +    
Sbjct: 219 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGRDPSPE---EIGEEMDLLPEKVREILKIA 273

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D   Q   +    +  +  L   +  L  RE 
Sbjct: 274 QEPVSLETPI--GEEDDSHLGDFI---EDSDAQSPSDHAAYELLKEQLEDVLDTLTDREE 328

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 329 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 377


>gi|228993035|ref|ZP_04152958.1| RNA polymerase sigma factor [Bacillus pseudomycoides DSM 12442]
 gi|228999085|ref|ZP_04158667.1| RNA polymerase sigma factor [Bacillus mycoides Rock3-17]
 gi|229006633|ref|ZP_04164267.1| RNA polymerase sigma factor [Bacillus mycoides Rock1-4]
 gi|228754494|gb|EEM03905.1| RNA polymerase sigma factor [Bacillus mycoides Rock1-4]
 gi|228760702|gb|EEM09666.1| RNA polymerase sigma factor [Bacillus mycoides Rock3-17]
 gi|228766683|gb|EEM15323.1| RNA polymerase sigma factor [Bacillus pseudomycoides DSM 12442]
          Length = 373

 Score =  262 bits (670), Expect = 4e-68,   Method: Composition-based stats.
 Identities = 80/289 (27%), Positives = 140/289 (48%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRL
Sbjct: 89  LNDLSVPPGVKINDPVRMYLKEIGRVDLLSAEEEIRLATRI-EEGDEEAKRRLAEANLRL 147

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 148 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQ 207

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    I ++++++  +V  +    
Sbjct: 208 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPSPE---EIGEEMDLAPEKVREILKIA 262

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D +     +    +  +  L   +  L  RE 
Sbjct: 263 QEPVSLETPI--GEEDDSHLGDFI---EDQEATSPADHAAYELLKEQLEDVLDTLTDREE 317

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 318 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 366


>gi|28211633|ref|NP_782577.1| RNA polymerase sigma factor RpoD [Clostridium tetani E88]
 gi|28204075|gb|AAO36514.1| RNA polymerase sigma factor rpoD [Clostridium tetani E88]
          Length = 366

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 83/280 (29%), Positives = 138/280 (49%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ +  +  Y+ EI K+P+L  +EE  LA+R  E G+L A  +L  ++LRLVV IA  Y 
Sbjct: 91  ISIDDPVRMYLKEIGKVPLLTSEEEVDLAQRI-EAGELKARKKLAEANLRLVVSIAKRYV 149

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 150 GRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 209

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L         PE    IAK++ +S   V  +        SL   
Sbjct: 210 MVE--TINKLIRVSRQLLQELGREPTPE---EIAKEMEISVDRVREIMKIAQEPVSLETP 264

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++            E       +  L   +  L PRE ++   R   
Sbjct: 265 I--GEEEDSHLGDFIPD---DDALAPAEAAAFTMLKEQLINVLDTLTPREEKVLRLRFGL 319

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 320 DDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 359


>gi|282856776|ref|ZP_06266037.1| RNA polymerase sigma factor RpoD [Pyramidobacter piscolens W5455]
 gi|282585399|gb|EFB90706.1| RNA polymerase sigma factor RpoD [Pyramidobacter piscolens W5455]
          Length = 642

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 74/277 (26%), Positives = 132/277 (47%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
              +  Y+ EI K+P+L  ++E  LA +  E GD  A  +++ ++LRLVV IA  Y G G
Sbjct: 370 SDPVRMYLREIGKVPLLSGEKERELAIKV-EAGDAEAKQQIIDANLRLVVSIAKKYIGRG 428

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     +
Sbjct: 429 MLFLDLIQEGNLGLIRAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 488

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 + ++    + +     +      IA ++ +    V  +        SL   I  
Sbjct: 489 -----TINKMVRISRQLVQKLGREPSDEEIAHEMEIESGRVEEIRRIAQLPVSLETPI-- 541

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            ++  SQ  D++    D       +          +   +  L+ RER +   R   E+ 
Sbjct: 542 GEEEDSQLGDFI---EDRNMPSPEDAAAGNLLHEQIEEMLDALSDREREVLRYRFGLEDG 598

Query: 253 V--TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 599 RSYTLEEVGRRFGVTRERIRQIEAKALRKLRHPSRSK 635


>gi|167755652|ref|ZP_02427779.1| hypothetical protein CLORAM_01167 [Clostridium ramosum DSM 1402]
 gi|237734400|ref|ZP_04564881.1| RNA polymerase sigma factor rpoD [Mollicutes bacterium D7]
 gi|167704591|gb|EDS19170.1| hypothetical protein CLORAM_01167 [Clostridium ramosum DSM 1402]
 gi|229382630|gb|EEO32721.1| RNA polymerase sigma factor rpoD [Coprobacillus sp. D7]
          Length = 417

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 78/289 (26%), Positives = 136/289 (47%), Gaps = 12/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +++  +   V     +  Y+ EI ++ +L   EE  LAK+  E GD  A   L  ++LRL
Sbjct: 131 LDQNQLGSNVKINDPVKMYLKEIGRVELLTHDEEIDLAKKILE-GDEDAKKELAAANLRL 189

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 190 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQ 249

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L          E++        ++  +V  +    
Sbjct: 250 ARTIRIPVHMVE--TINKLTRIQRQLIQELGREPSAEEIAEKMD--GMTPEKVREIQKIS 305

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++  +           E  K+    L   +  L  RE 
Sbjct: 306 LEPVSLETPI--GEEDDSHLGDFIEDEGAMSPDDYAANELLKDE---LNEVLLELTDREE 360

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++   R   ++    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 361 KVLRLRFGLDDGRTRTLEEVGKEFSVTRERIRQIEAKALRKLKHPSRSK 409


>gi|27364575|ref|NP_760103.1| RNA polymerase factor sigma-32 [Vibrio vulnificus CMCP6]
 gi|37678299|ref|NP_932908.1| RNA polymerase factor sigma-32 [Vibrio vulnificus YJ016]
 gi|320154977|ref|YP_004187356.1| RNA polymerase sigma factor RpoH [Vibrio vulnificus MO6-24/O]
 gi|29611852|sp|Q8DD54|RP32_VIBVU RecName: Full=RNA polymerase sigma-32 factor
 gi|27360694|gb|AAO09630.1| alternative sigma factor RpoH [Vibrio vulnificus CMCP6]
 gi|37197038|dbj|BAC92879.1| RNA polymerase sigma-32 factor [Vibrio vulnificus YJ016]
 gi|319930289|gb|ADV85153.1| RNA polymerase sigma factor RpoH [Vibrio vulnificus MO6-24/O]
          Length = 285

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 110/287 (38%), Positives = 167/287 (58%), Gaps = 8/287 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  +   + +  +  L  YI  +   PML   EE  LA+R    G++ AA  L+ SHLR 
Sbjct: 1   MTTQAYPMALVTQDSLDGYIRSVNSYPMLTADEERDLAERLHYKGEIEAAKGLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A GY GYGLP++++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VKI TT  Q++LFFNLR+ K  L    +      +V  +A++L V  +EV  M  RL
Sbjct: 121 WRIVKIATTKAQRKLFFNLRKSKKRLGWFNNG-----EVETVARELGVEPAEVREMESRL 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE---ERKNRRNMLTRSMSVLNP 237
           A  +S   L N  D +SS     ++Y  D    V    E      +  N L  +++ L+ 
Sbjct: 176 AAVDSTFDLPNEEDDSSSVSTAPVLYLEDKSSDVADNLEAQNWEAHTNNRLAMALASLDE 235

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R + I  +R L ++  TL++L+  + VS ER+RQ+E  A KK++ ++
Sbjct: 236 RSQHIVRSRWLDDDKATLQDLAEMYGVSAERIRQLEKNAMKKLKMAV 282


>gi|307128894|ref|YP_003880910.1| RNA polymerase sigma-32 (sigma H) factor [Dickeya dadantii 3937]
 gi|306526423|gb|ADM96353.1| RNA polymerase, sigma 32 (sigma H) factor [Dickeya dadantii 3937]
          Length = 285

 Score =  262 bits (670), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 104/290 (35%), Positives = 162/290 (55%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M +   +  +  +  L  YI      PML  +EE  LA+R   HGDL AA +L+ SHLR 
Sbjct: 1   MTKDMQTFALVPQGSLEGYIRAANAYPMLTAEEERALAERLHYHGDLDAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VIHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVELVARELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNP 237
           A  +         D    Q    ++Y  D        + E     +  + LT ++  L+ 
Sbjct: 176 AAQDMTFDPSPEDDAQPGQPMAPMLYLQDKSSDFADGIEEDNWETHAADKLTYALEGLDE 235

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L ++   TL+ L+  + VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQHIIRARWLDDDNKSTLQELADHYGVSAERVRQLEKNAMKKLRAAIEA 285


>gi|325125919|gb|ADY85249.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus 2038]
          Length = 372

 Score =  262 bits (669), Expect = 5e-68,   Method: Composition-based stats.
 Identities = 82/288 (28%), Positives = 136/288 (47%), Gaps = 13/288 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N       +     +  Y+ EI +  +L  +EE  LAKR  E GD  A   L  ++LRL
Sbjct: 88  LNNMAAPTGMKMNDPVRMYLKEIGRFNLLTSEEEVALAKRI-EAGDEEAKQELAEANLRL 146

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GLM+AV KFD   GF+ +TY+ WWI+ A+   I   
Sbjct: 147 VVSIAKRYVGRGMNFLDLIQEGNMGLMKAVDKFDYRLGFKFSTYATWWIRQAITRAIADQ 206

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L      + +PE    IA ++++   +V  +    
Sbjct: 207 ARTIRIPVHMVE--TINKLIRIQRQLLQDLGRDPEPE---EIAAEMDLPVKKVREILKIC 261

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D       +    +  +  L   +  L+ RE 
Sbjct: 262 QEPVSLETPI--GEEDDSNLGDFI---EDKDAMSPEQHAANEMLKEQLAEVLDTLSDREE 316

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +   R   ++    TLE +   FEV+RER+RQIEA+A +K++   + 
Sbjct: 317 EVLRLRFGLDDGKSRTLEEVGQHFEVTRERIRQIEAKALRKLRHPSRS 364


>gi|113461681|ref|YP_719750.1| RNA polymerase factor sigma-32 [Haemophilus somnus 129PT]
 gi|112823724|gb|ABI25813.1| RNA polymerase, sigma 32 subunit, RpoH [Haemophilus somnus 129PT]
          Length = 280

 Score =  262 bits (669), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 104/286 (36%), Positives = 171/286 (59%), Gaps = 10/286 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           MN++  ++++  +  +  YIH     PML  +EE  LA+R   H DL AA  L+ SHLR 
Sbjct: 1   MNKETQAMMLVPQGSIEGYIHAAYDYPMLTAEEEKELAERLYYHQDLDAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L   +D      +V  +A +L VS+ +V+ M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFSDK-----EVDMVANELGVSKEDVLEMESRM 175

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLNPR 238
            G D   +  +   D + S      + D        +E E  +    + +  +++ L+ R
Sbjct: 176 TGSDVGFDLPV---DDDESYAPALYLEDKSSNFAAELENENFETQAADQVANALAELDER 232

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + I ++R L +   TL +L++++ +S ERVRQ+E  A KK++ ++
Sbjct: 233 SQDIIKSRWLDDEKATLHDLAAKYNISAERVRQLETNALKKLKSAV 278


>gi|114567027|ref|YP_754181.1| sigma 38 (RpoS) [Syntrophomonas wolfei subsp. wolfei str.
           Goettingen]
 gi|114337962|gb|ABI68810.1| sigma 38 (RpoS) [Syntrophomonas wolfei subsp. wolfei str.
           Goettingen]
          Length = 358

 Score =  262 bits (669), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 83/277 (29%), Positives = 143/277 (51%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI ++P+L   +E  LA+R  E GD  A  +LV ++LRLVV IA  Y G G
Sbjct: 86  DDPVRMYLKEIGRVPLLIAAQEIDLAQRI-EEGDEEAKRQLVEANLRLVVSIAKRYVGRG 144

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +   +++ EGN+GLM+AV+KFD  +G++ +TY+ WWI+ A+   I      ++I     +
Sbjct: 145 MLFLDLIQEGNLGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 204

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 L R++  L  I      P     +A++++++   VI +        SL   I  
Sbjct: 205 --TINKLSRVQRSLLQILGREPTP---AEVAEEMDIAVDRVIEIMKVAQEPVSLETPI-- 257

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN- 251
            +++ S   D++    D + +   E       R  L   ++ L  RE ++   R   ++ 
Sbjct: 258 GEEDDSHLGDFI---TDEEAESPEESASFVLLREHLDGILNTLTEREEKVLRLRFGLDDG 314

Query: 252 -PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            P TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 315 RPRTLEEVGQEFGVTRERIRQIEAKALRKLRHPSRSK 351


>gi|307703796|ref|ZP_07640737.1| RNA polymerase sigma factor RpoD [Streptococcus oralis ATCC 35037]
 gi|307622631|gb|EFO01627.1| RNA polymerase sigma factor RpoD [Streptococcus oralis ATCC 35037]
          Length = 318

 Score =  262 bits (669), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 84/283 (29%), Positives = 141/283 (49%), Gaps = 13/283 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S        +  Y+ EI  +P+L  +EE  LA    E GD+ A  RL  ++LRLVV IA 
Sbjct: 39  STSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAV-EAGDIEAKQRLAEANLRLVVSIAK 97

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y G G+   +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I
Sbjct: 98  RYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI 157

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
                +      L R + +L      +  PEQ   IA++++++  +V  +        SL
Sbjct: 158 PVHMVE--TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSL 212

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              I   +++ S   D++    D   +  ++   R   R  L   +  L  RE  +   R
Sbjct: 213 ETPI--GEEDDSHLGDFI---EDEVIENPVDYTTRIVLREQLDEVLDTLTDREENVLRLR 267

Query: 247 RLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              ++    TLE++   F V+RER+RQIEA+A +K+++  + +
Sbjct: 268 FGLDDGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRQPSRSK 310


>gi|225388546|ref|ZP_03758270.1| hypothetical protein CLOSTASPAR_02282 [Clostridium asparagiforme
           DSM 15981]
 gi|225045391|gb|EEG55637.1| hypothetical protein CLOSTASPAR_02282 [Clostridium asparagiforme
           DSM 15981]
          Length = 381

 Score =  262 bits (669), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 80/280 (28%), Positives = 144/280 (51%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           +  E  +  Y+ EI  +P+L   EE  LA+R +  GD +A  RL+ ++LRLVV IA  Y 
Sbjct: 107 IGTEDPVRMYLKEIGTVPLLTADEELQLAQR-KAEGDEAAKERLIEANLRLVVSIAKRYT 165

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   ++V EGN+GL++ V+KFD  +G++L+TY+ WWI+ ++   +      +++   
Sbjct: 166 GRGMSFLDLVQEGNLGLIKGVEKFDYTKGYKLSTYATWWIRQSVTRALADQARTIRVPVH 225

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      + ++    + +T        V  +A+ L+++E +V+ +        SL   
Sbjct: 226 MVE-----TINKMSKMQRKLTLELGYEPSVTELAEALDMTEDKVMEIMQIAREPASLETP 280

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   +++ S   D++    D          E    R  +   +  L  RER++   R   
Sbjct: 281 I--GEEDDSNLGDFVA---DNNVVTPEGNVESVMLREHIDALLGDLKERERQVIVLRFGL 335

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+  P TLE +  EF V+RER+RQIEA+A +K++  ++ +
Sbjct: 336 EDGHPRTLEEVGKEFNVTRERIRQIEAKALRKLRNPVRSK 375


>gi|160877394|ref|YP_001556710.1| RNA polymerase factor sigma-32 [Shewanella baltica OS195]
 gi|160862916|gb|ABX51450.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella baltica OS195]
 gi|315269598|gb|ADT96451.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella baltica OS678]
          Length = 285

 Score =  262 bits (669), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 110/290 (37%), Positives = 171/290 (58%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSI---IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSH 57
           M  +  S+   +  G   L  YIH +  I ML+ + EY LAKR +E GDL AA +L+ SH
Sbjct: 1   MTFQTQSMALTVPQGASSLEAYIHSVTSISMLDAEAEYELAKRLQETGDLQAAKQLIMSH 60

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LR VV +A GY GYGLP ++++ EGNIGLM+AVK+FDP+ G RL ++++ WIKA + EY+
Sbjct: 61  LRFVVHVAKGYSGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYV 120

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           L++W +VK+ TT  Q++LFFN+R+ K  L   +D      +V  +A+ L VS+++V  M 
Sbjct: 121 LKNWRIVKVATTKAQRKLFFNIRKAKKRLGWFSD-----AEVTMVAENLGVSKADVTEME 175

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLN 236
            R+A  +    L N  D+         + DH       IE +  + N +  L  ++  L+
Sbjct: 176 SRMAAQDPAFDLTNDQDEEHDFAPVHYLEDHSSDLAENIENDNWESNAQGRLLSAIKTLD 235

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R + I  AR L ++  TL+ L+  ++VS ER+RQ+E  A  K++  ++ 
Sbjct: 236 ERSQHILHARWLDDDKTTLQELAETYQVSAERIRQLEKNAMNKLKACMEA 285


>gi|229825188|ref|ZP_04451257.1| hypothetical protein GCWU000182_00540 [Abiotrophia defectiva ATCC
           49176]
 gi|229790560|gb|EEP26674.1| hypothetical protein GCWU000182_00540 [Abiotrophia defectiva ATCC
           49176]
          Length = 372

 Score =  262 bits (669), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 83/279 (29%), Positives = 141/279 (50%), Gaps = 13/279 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ E  +  Y+ EI K+P+L+  EE  LAK   E GD  A  +L  ++LRLVV IA  Y 
Sbjct: 97  ISTEDPVRMYLKEIGKVPLLDMDEEIKLAKSMAE-GDDEARKKLTEANLRLVVSIAKRYL 155

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWIK ++   I      ++I   
Sbjct: 156 GRGMQFLDLIQEGNMGLIKAVEKFDYTKGYKFSTYATWWIKQSITRAIADQARTIRIPVH 215

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      + +L    + +T    +  Q   I K+LN+   +V S+        S    
Sbjct: 216 MVE-----TINKLIRAQRQLTQTLGREPQPEEIGKELNMEPEKVRSIMKIAQEPVSFETP 270

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++  D +      +E       +  L   +  L  RE R+ + R   
Sbjct: 271 I--GEEEDSHIGDFIPDDSNM---APVEAATHAILKEQLEEVLDSLTEREARVIKLRFGL 325

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E+    TLE +  EF V+RER+RQIE++A +K+++  + 
Sbjct: 326 EDGRTRTLEEVGKEFNVTRERIRQIESKALRKLRQPSRS 364


>gi|283795510|ref|ZP_06344663.1| RNA polymerase sigma factor RpoD [Clostridium sp. M62/1]
 gi|291077175|gb|EFE14539.1| RNA polymerase sigma factor RpoD [Clostridium sp. M62/1]
          Length = 377

 Score =  262 bits (669), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 83/280 (29%), Positives = 146/280 (52%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           +  E  +  Y+ EI  +P+L  +EE  LAKR +  GD+SA  RL+ ++LRLVV IA  Y 
Sbjct: 103 IGTEDPVRMYLKEIGTVPLLSAEEELRLAKR-KAEGDVSAKERLIEANLRLVVSIAKRYT 161

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   ++V EGN+GL++ V+KFD  +G++L+TY+ WWI+ ++   +      +++   
Sbjct: 162 GRGMSFLDLVQEGNLGLIKGVEKFDYTKGYKLSTYATWWIRQSVTRALADQARTIRVPVH 221

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      + ++    + +T        V  ++  L++SE +V+ +        SL   
Sbjct: 222 MVE-----TINKMSKMQRKLTLELGYEPSVAELSAALDMSEDKVMEIMQIAREPASLETP 276

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   +++ S   D++    DG         E    R  +   +  L  RER++   R   
Sbjct: 277 I--GEEDDSNLGDFVA---DGNVVTPEGNVESVMLREHIDALLGDLKERERQVIVLRFGL 331

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+  P TLE +  EF V+RER+RQIEA+A +K++  ++ +
Sbjct: 332 EDGHPRTLEEVGKEFNVTRERIRQIEAKALRKLRNPVRSK 371


>gi|170718627|ref|YP_001783826.1| RNA polymerase factor sigma-32 [Haemophilus somnus 2336]
 gi|168826756|gb|ACA32127.1| RNA polymerase, sigma 32 subunit, RpoH [Haemophilus somnus 2336]
          Length = 280

 Score =  262 bits (669), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 105/286 (36%), Positives = 171/286 (59%), Gaps = 10/286 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           MN++  ++++  +  +  YIH     PML  +EE  LA+R   H DL AA  L+ SHLR 
Sbjct: 1   MNKETQAMMLVPQGSIEGYIHAAYDYPMLTAEEEKELAERLYYHQDLDAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L   +D      +V  +A +L VS+ +V+ M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFSDK-----EVDMVANELGVSKEDVLEMESRM 175

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLNPR 238
            G D   +  +   D + S      + D        +E E  +    + +  +++ L+ R
Sbjct: 176 TGSDVGFDLPV---DDDESYAPALYLEDKSSNFAAELENENFETQAADQVANALAELDER 232

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            R I ++R L +   TL +L++++ +S ERVRQ+E  A KK++ ++
Sbjct: 233 SRDIIKSRWLDDEKATLHDLAAKYNISAERVRQLETNALKKLKSAV 278


>gi|319935434|ref|ZP_08009871.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
 gi|319809650|gb|EFW06063.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
          Length = 422

 Score =  262 bits (669), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 78/277 (28%), Positives = 136/277 (49%), Gaps = 14/277 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L   EE  LAKR  E GD  A  +L  ++LRLVV IA  Y G G+
Sbjct: 149 DPVKMYLKEIGRVELLSHDEEIDLAKRILE-GDEEAKKKLAAANLRLVVSIAKRYVGRGM 207

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 208 LFLDLIQEGNMGLIKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 266

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN-VSESEVISMNCRLAGDESLNALINS 192
                + +L    + +     +      IA+K++ ++  +V  +        SL   I  
Sbjct: 267 ----TINKLTRVQRQLIQELGREPLAEEIAEKMDGMTPEKVREIQKISLEPVSLETPI-- 320

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            +++ S   D++  +           E  K+    L   +  L  RE ++   R   ++ 
Sbjct: 321 GEEDDSHLGDFIEDEGAMSPDDYAANELLKDE---LNEVLLELTDREEKVLRLRFGLDDG 377

Query: 253 --VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 378 RTRTLEEVGKEFNVTRERIRQIEAKALRKLKHPSRSK 414


>gi|52424080|ref|YP_087217.1| RNA polymerase factor sigma-32 [Mannheimia succiniciproducens
           MBEL55E]
 gi|52306132|gb|AAU36632.1| RpoD protein [Mannheimia succiniciproducens MBEL55E]
          Length = 282

 Score =  262 bits (669), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 103/285 (36%), Positives = 168/285 (58%), Gaps = 6/285 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++++  +  +  YI    + PML  +EE  LA+R     DL AA +L+ SHLR 
Sbjct: 1   MTKETQTMMLVPQGSIEAYIRAANEYPMLSAEEEKELAERLYYQEDLEAAKKLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L   +DN L       +A +L V++ +VI M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFSDNEL-----DLVANELGVTKEDVIEMESRM 175

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            G D   +   + S++ +     +L          L  +       + L+ +M  L+ R 
Sbjct: 176 TGADVGFDLPTDDSEEETFAPSMYLEDKSSNFAAELESENFETQAIDQLSNAMENLDERS 235

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + I +AR L +   TL  L++++ +S ERVRQ+E  A KK++ ++
Sbjct: 236 KDIIQARWLDDTKATLHELAAKYNISAERVRQLETNALKKLKSAV 280


>gi|152976724|ref|YP_001376241.1| RNA polymerase sigma factor RpoD [Bacillus cereus subsp. cytotoxis
           NVH 391-98]
 gi|152025476|gb|ABS23246.1| RNA polymerase, sigma 70 subunit, RpoD family [Bacillus cytotoxicus
           NVH 391-98]
          Length = 373

 Score =  262 bits (669), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 80/289 (27%), Positives = 140/289 (48%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRL
Sbjct: 89  LNDLSVPPGVKINDPVRMYLKEIGRVDLLSAEEEIQLATRI-EEGDEEAKRRLAEANLRL 147

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 148 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQ 207

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    I ++++++  +V  +    
Sbjct: 208 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPTPE---EIGEEMDLAPEKVREILKIA 262

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D +     +    +  +  L   +  L  RE 
Sbjct: 263 QEPVSLETPI--GEEDDSHLGDFI---EDQEATSPADHAAYELLKEQLEDVLDTLTDREE 317

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 318 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 366


>gi|332638574|ref|ZP_08417437.1| RNA polymerase sigma factor [Weissella cibaria KACC 11862]
          Length = 377

 Score =  262 bits (669), Expect = 6e-68,   Method: Composition-based stats.
 Identities = 79/276 (28%), Positives = 136/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L   EE  LA+R  E GD +A   L  ++LRLVV IA  Y G G+
Sbjct: 106 DPVRMYLKEIGRVSLLTGDEEVALAERI-EQGDDTAKQELAEANLRLVVSIAKRYVGRGM 164

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 165 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 223

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++ +L         PE++ A   ++++   +V  +        SL   I   
Sbjct: 224 -TINKLIRIQRNLLQDLGREPTPEEIGA---EMDIVTDKVRDILKIAQEPVSLETPI--G 277

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D +     +    +  +  L   +  L  RE  +   R   E+  
Sbjct: 278 EEDDSHLGDFI---EDNEAISPADSAAYQMLKEQLESVLDTLTDREENVLRLRFGLEDGR 334

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 335 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 370


>gi|227431669|ref|ZP_03913702.1| DNA-directed RNA polymerase sigma subunit RpoD [Leuconostoc
           mesenteroides subsp. cremoris ATCC 19254]
 gi|227352572|gb|EEJ42765.1| DNA-directed RNA polymerase sigma subunit RpoD [Leuconostoc
           mesenteroides subsp. cremoris ATCC 19254]
          Length = 432

 Score =  262 bits (669), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 80/276 (28%), Positives = 137/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L+  EE  +AKR  E+GD+ A   L  ++LRLVV IA  Y G G+
Sbjct: 157 DPVRMYLKEIGRVNLLKGNEEIDIAKRI-ENGDVEAKQELAEANLRLVVSIAKRYVGRGM 215

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 216 QFLDLIQEGNMGLMKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 274

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L         PE++ A   +++++  +V  +        SL   I   
Sbjct: 275 -TINKLIRIQRQLLQDLGREPLPEEIGA---EIDLTADKVREILKIAQEPVSLETPI--G 328

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D +     +    +  R  L   +  L  RE  +   R   E+  
Sbjct: 329 EEDDSHLGDFI---EDNEAVSPADSAAYEMLREQLESVLDTLTDREENVLRLRFGLEDGR 385

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 386 TRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSK 421


>gi|238927759|ref|ZP_04659519.1| possible DNA-directed RNA polymerase sigma subunit SigA
           [Selenomonas flueggei ATCC 43531]
 gi|238884475|gb|EEQ48113.1| possible DNA-directed RNA polymerase sigma subunit SigA
           [Selenomonas flueggei ATCC 43531]
          Length = 382

 Score =  262 bits (669), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 78/275 (28%), Positives = 136/275 (49%), Gaps = 13/275 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI ++P+L  +EE  LA+R  E GD +A HRL  ++LRLVV IA  Y G G
Sbjct: 109 DDPVRMYLKEIGRVPLLTAEEEVELARRM-EAGDEAARHRLEEANLRLVVSIAKRYAGRG 167

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I     +
Sbjct: 168 MMFLDLIQEGNLGLLKAVEKFDYSKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 227

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                   R+   L      +  PE    IA ++ +S + V  +        SL   I  
Sbjct: 228 --TINKYIRISRQLLQELGRDPTPE---EIAHRMGLSVARVREIMKISQEPVSLETPI-- 280

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QE 250
            ++  ++  D++            +       +  ++  ++ L PRE  +   R      
Sbjct: 281 GEEEDTRLSDFIED---EAAPDPADAASMLLLKEQISEVLTTLAPREAEVLRLRFGLVDG 337

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              TLE +   F V+RER+RQIEA+A +K++  ++
Sbjct: 338 RSRTLEEVGQNFGVTRERIRQIEAKALRKLRHPVR 372


>gi|30264362|ref|NP_846739.1| RNA polymerase sigma factor RpoD [Bacillus anthracis str. Ames]
 gi|47529811|ref|YP_021160.1| RNA polymerase sigma factor RpoD [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49187190|ref|YP_030442.1| RNA polymerase sigma factor RpoD [Bacillus anthracis str. Sterne]
 gi|49481307|ref|YP_038350.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|52141207|ref|YP_085621.1| RNA polymerase sigma factor RpoD [Bacillus cereus E33L]
 gi|65321666|ref|ZP_00394625.1| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Bacillus anthracis str. A2012]
 gi|118479464|ref|YP_896615.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis str. Al
           Hakam]
 gi|165872043|ref|ZP_02216683.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0488]
 gi|167634513|ref|ZP_02392833.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0442]
 gi|167638663|ref|ZP_02396939.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0193]
 gi|170687516|ref|ZP_02878733.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0465]
 gi|170707362|ref|ZP_02897816.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0389]
 gi|196046412|ref|ZP_03113638.1| RNA polymerase sigma-43 factor [Bacillus cereus 03BB108]
 gi|218905429|ref|YP_002453263.1| RNA polymerase sigma-43 factor [Bacillus cereus AH820]
 gi|225866273|ref|YP_002751651.1| RNA polymerase sigma-43 factor [Bacillus cereus 03BB102]
 gi|228929335|ref|ZP_04092360.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228935612|ref|ZP_04098427.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228948006|ref|ZP_04110292.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|229093361|ref|ZP_04224468.1| RNA polymerase sigma factor [Bacillus cereus Rock3-42]
 gi|229123831|ref|ZP_04253025.1| RNA polymerase sigma factor [Bacillus cereus 95/8201]
 gi|229186532|ref|ZP_04313694.1| RNA polymerase sigma factor [Bacillus cereus BGSC 6E1]
 gi|229601154|ref|YP_002868581.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0248]
 gi|254684050|ref|ZP_05147910.1| RNA polymerase sigma factor RpoD [Bacillus anthracis str.
           CNEVA-9066]
 gi|254736399|ref|ZP_05194105.1| RNA polymerase sigma factor RpoD [Bacillus anthracis str. Western
           North America USA6153]
 gi|254741437|ref|ZP_05199124.1| RNA polymerase sigma factor RpoD [Bacillus anthracis str. Kruger B]
 gi|254757799|ref|ZP_05209826.1| RNA polymerase sigma factor RpoD [Bacillus anthracis str. Australia
           94]
 gi|30259020|gb|AAP28225.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. Ames]
 gi|47504959|gb|AAT33635.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49181117|gb|AAT56493.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. Sterne]
 gi|49332863|gb|AAT63509.1| RNA polymerase sigma-43 factor [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|51974676|gb|AAU16226.1| RNA polymerase sigma-43 factor [Bacillus cereus E33L]
 gi|118418689|gb|ABK87108.1| RNA polymerase sigma-43 factor [Bacillus thuringiensis str. Al
           Hakam]
 gi|164712174|gb|EDR17711.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0488]
 gi|167513511|gb|EDR88881.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0193]
 gi|167529965|gb|EDR92700.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0442]
 gi|170127606|gb|EDS96479.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0389]
 gi|170668711|gb|EDT19457.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0465]
 gi|196022882|gb|EDX61563.1| RNA polymerase sigma-43 factor [Bacillus cereus 03BB108]
 gi|218536133|gb|ACK88531.1| RNA polymerase sigma-43 factor [Bacillus cereus AH820]
 gi|225787167|gb|ACO27384.1| RNA polymerase sigma-43 factor [Bacillus cereus 03BB102]
 gi|228596963|gb|EEK54621.1| RNA polymerase sigma factor [Bacillus cereus BGSC 6E1]
 gi|228659652|gb|EEL15298.1| RNA polymerase sigma factor [Bacillus cereus 95/8201]
 gi|228690017|gb|EEL43818.1| RNA polymerase sigma factor [Bacillus cereus Rock3-42]
 gi|228811696|gb|EEM58031.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228824052|gb|EEM69869.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228830349|gb|EEM75961.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|229265562|gb|ACQ47199.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. A0248]
          Length = 373

 Score =  261 bits (668), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 80/289 (27%), Positives = 140/289 (48%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRL
Sbjct: 89  LNDLSVPPGVKINDPVRMYLKEIGRVDLLSAEEEIRLATRI-EEGDEEAKRRLAEANLRL 147

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 148 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQ 207

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    I ++++++  +V  +    
Sbjct: 208 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPSPE---EIGEEMDLAPEKVREILKIA 262

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D +     +    +  +  L   +  L  RE 
Sbjct: 263 QEPVSLETPI--GEEDDSHLGDFI---EDQEATSPADHAAYELLKEQLEDVLDTLTDREE 317

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 318 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 366


>gi|315645989|ref|ZP_07899110.1| RNA polymerase, sigma 70 subunit, RpoD subfamily protein
           [Paenibacillus vortex V453]
 gi|315278750|gb|EFU42064.1| RNA polymerase, sigma 70 subunit, RpoD subfamily protein
           [Paenibacillus vortex V453]
          Length = 376

 Score =  261 bits (668), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 80/285 (28%), Positives = 137/285 (48%), Gaps = 13/285 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           ++   +     +  Y+ EI ++P+L   +E  LA R  E GD  A  RL  ++LRLVV I
Sbjct: 96  SLPPGIKINDPVRMYLKEIGRVPLLSADDEIELANRI-EQGDEEAKRRLAEANLRLVVSI 154

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ WWI+ A+   I      +
Sbjct: 155 AKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYKKGFKFSTYATWWIRQAITRAIADQARTI 214

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I     +      L R+   L         PE    IA ++ +S  +V  +        
Sbjct: 215 RIPVHMVE--TINKLIRVSRQLLQELGREPSPE---EIAAEMELSVEKVREIMKIAQEPV 269

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   I   +++ S   D++    D +     +    +  +  L   +  L  RE  +  
Sbjct: 270 SLETPI--GEEDDSHLGDFI---EDQEALAPADAAAYELLKEQLEDVLDTLTEREENVLR 324

Query: 245 ARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 325 LRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 369


>gi|148270473|ref|YP_001244933.1| RpoD family RNA polymerase sigma factor [Thermotoga petrophila
           RKU-1]
 gi|170289132|ref|YP_001739370.1| RpoD family RNA polymerase sigma factor [Thermotoga sp. RQ2]
 gi|147736017|gb|ABQ47357.1| RNA polymerase, sigma 70 subunit, RpoD family [Thermotoga
           petrophila RKU-1]
 gi|170176635|gb|ACB09687.1| RNA polymerase, sigma 70 subunit, RpoD family [Thermotoga sp. RQ2]
          Length = 407

 Score =  261 bits (668), Expect = 7e-68,   Method: Composition-based stats.
 Identities = 81/276 (29%), Positives = 138/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI KIP+L   +E  LA+R  + GD  A  +L+TS+LRLVV IA  Y G GL
Sbjct: 129 DSIKMYLKEIGKIPLLTPAQERELARR-AQMGDKKAKEKLITSNLRLVVSIAKRYMGRGL 187

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGNIGL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 188 SFQDLIQEGNIGLLKAVEKFDWRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 246

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                + +L    +     + +   +  +AK +     ++  +        SL + I   
Sbjct: 247 ----TINKLNRLRREYYQKHGEEPSIEELAKMMGKPPEKIKEILEAAKETISLESPI--G 300

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQEN 251
           +   S  +D++  D     +   ++  R   R  L + +  L+PRE  +   R   L   
Sbjct: 301 EDEDSSIEDFVADDSIASPK---KEAMRMLMREELEKVLKTLSPREAMVLRMRYGLLDGK 357

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           P TLE +   F V+RER+RQIE +A +K++   + +
Sbjct: 358 PKTLEEVGQYFNVTRERIRQIEVKALRKLRHPSRSK 393


>gi|304403970|ref|ZP_07385632.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Paenibacillus
           curdlanolyticus YK9]
 gi|304346948|gb|EFM12780.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Paenibacillus
           curdlanolyticus YK9]
          Length = 377

 Score =  261 bits (668), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 80/276 (28%), Positives = 134/276 (48%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++P+L   +E  LAKR  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 106 DPVRMYLKEIGRVPLLSADDEVELAKRI-EKGDEEAKRRLAEANLRLVVSIAKRYVGRGM 164

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 165 LFLDLIQEGNMGLIKAVEKFDHTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 223

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R+   L         PE    IA ++ +S  +V  +        SL   I   
Sbjct: 224 -TINKLIRVSRQLLQELGREPAPE---EIAAEMELSTDKVREIMKIAQEPVSLETPI--G 277

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D +     +    +  +  L   +  L  RE  +   R   ++  
Sbjct: 278 EEDDSHLGDFI---EDQEALAPADAAAYELLKEQLEDVLDTLTEREENVLRLRFGLDDGR 334

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 335 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 370


>gi|317124635|ref|YP_004098747.1| RNA polymerase, sigma 70 subunit, RpoD [Intrasporangium calvum DSM
           43043]
 gi|315588723|gb|ADU48020.1| RNA polymerase, sigma 70 subunit, RpoD [Intrasporangium calvum DSM
           43043]
          Length = 587

 Score =  261 bits (668), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 71/303 (23%), Positives = 137/303 (45%), Gaps = 38/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR--------------------------YREHGDL 47
             +  Y+ +I K+ +L  ++E  LAKR                          +      
Sbjct: 289 DPVKDYLKQIGKVALLNAEQEVELAKRIEAGLFAEEKLNSGEKIDMKLKRELWWIAQDGK 348

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ W
Sbjct: 349 KAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATW 408

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L+
Sbjct: 409 WIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKELD 463

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++  +V+ +        SL+  +   +   S++ D +    D +  V  +       +  
Sbjct: 464 MTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQEQ 518

Query: 228 LTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   +
Sbjct: 519 LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSR 578

Query: 286 KQV 288
            QV
Sbjct: 579 SQV 581


>gi|289423762|ref|ZP_06425557.1| RNA polymerase sigma factor RpoD [Peptostreptococcus anaerobius
           653-L]
 gi|289155801|gb|EFD04471.1| RNA polymerase sigma factor RpoD [Peptostreptococcus anaerobius
           653-L]
          Length = 385

 Score =  261 bits (668), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 85/280 (30%), Positives = 145/280 (51%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ +  +  Y+ EI KIP+L+  EE   A+   E GD  +  +LV ++LRLVV IA  Y 
Sbjct: 110 ISIDDPVRMYLKEIGKIPLLKPHEEVEFARLMSE-GDERSKQKLVEANLRLVVSIAKRYV 168

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD ++G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 169 GRGMLFLDLIQEGNLGLIKAVEKFDYKKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 228

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L      + KPE    IAK +N+SE +V  +        SL   
Sbjct: 229 MVE--TINKLIRVSRQLLQELGRDPKPE---EIAKVMNMSEDKVREIMKIAQDPVSLETP 283

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++            E       +  +   ++ LN RE+++ + R   
Sbjct: 284 I--GEEEDSHLGDFIPD---EDAPAPAEAAAYSLLKEQIEEVLNTLNDREQKVLKLRFGL 338

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+    TLE +  EF+V+RER+RQIEA+A +K++   + +
Sbjct: 339 EDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSK 378


>gi|325686026|gb|EGD28084.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           delbrueckii subsp. lactis DSM 20072]
          Length = 372

 Score =  261 bits (668), Expect = 8e-68,   Method: Composition-based stats.
 Identities = 80/288 (27%), Positives = 139/288 (48%), Gaps = 13/288 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  +    +     +  Y+ EI ++ +L  +EE  LAKR  E GD  A   L  ++LRL
Sbjct: 88  LNNMDAPTGMKMNDPVRMYLKEIGRVNLLTSEEEVALAKRI-EAGDEEAKQELAEANLRL 146

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GLM+AV KFD   G++ +TY+ WWI+ A+   I   
Sbjct: 147 VVSIAKRYVGRGMNFLDLIQEGNMGLMKAVDKFDYRLGYKFSTYATWWIRQAITRAIADQ 206

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L      + +PE++ A   ++++   +V  +    
Sbjct: 207 ARTIRIPVHMVE--TINKLIRIQRQLLQDLGRDPEPEEIGA---EMDLPVKKVREILKLC 261

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D       +    +  +  L   +  L+ RE 
Sbjct: 262 QEPVSLETPI--GEEDDSNLGDFI---EDKDAMSPEQHAANEMLKEQLAEVLDTLSDREE 316

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +   R   ++    TLE +   FEV+RER+RQIEA+A +K++   + 
Sbjct: 317 EVLRLRFGLDDGKARTLEEVGQHFEVTRERIRQIEAKALRKLRHPSRS 364


>gi|313123889|ref|YP_004034148.1| RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           bulgaricus ND02]
 gi|312280452|gb|ADQ61171.1| RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           bulgaricus ND02]
          Length = 372

 Score =  261 bits (667), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 80/288 (27%), Positives = 140/288 (48%), Gaps = 13/288 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  +    +     +  Y+ EI ++ +L  +EE  LAKR  E GD  A   L  ++LRL
Sbjct: 88  LNNMDAPTGMKMNDPVRMYLKEIGRVNLLTSEEEVALAKRI-EAGDEEAKQELAEANLRL 146

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GLM+AV KFD   G++ +TY+ WWI+ A+   I   
Sbjct: 147 VVSIAKRYVGRGMNFLDLIQEGNMGLMKAVDKFDYRLGYKFSTYATWWIRQAITRAIADQ 206

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L      + +PE++ A   ++++  ++V  +    
Sbjct: 207 ARTIRIPVHMVE--TINKLIRIQRQLLQDLGRDPEPEEIGA---EMDLPVNKVREILKLC 261

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D       +    +  +  L   +  L+ RE 
Sbjct: 262 QEPVSLETPI--GEEDDSNLGDFI---EDKDAMSPEQHAANEMLKEQLAEVLDTLSDREE 316

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +   R   ++    TLE +   FEV+RER+RQIEA+A +K++   + 
Sbjct: 317 EVLRLRFGLDDGKARTLEEVGQHFEVTRERIRQIEAKALRKLRHPSRS 364


>gi|196034883|ref|ZP_03102290.1| RNA polymerase sigma-43 factor [Bacillus cereus W]
 gi|195992422|gb|EDX56383.1| RNA polymerase sigma-43 factor [Bacillus cereus W]
          Length = 373

 Score =  261 bits (667), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 80/289 (27%), Positives = 139/289 (48%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRL
Sbjct: 89  LNDLSVPPGVKINDPVRMYLKEIGRVDLLSAEEEIRLATRI-EEGDEEAKRRLAEANLRL 147

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 148 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQ 207

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    I ++++++  +V  +    
Sbjct: 208 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPSPE---EIGEEMDLAPEKVREILKIA 262

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   ++  S   D++    D +     +    +  +  L   +  L  RE 
Sbjct: 263 QEPVSLETPI--GEEGDSHLGDFI---EDQEATSPADHAAYELLKEQLEDVLDTLTDREE 317

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 318 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 366


>gi|163942050|ref|YP_001646934.1| RNA polymerase sigma factor RpoD [Bacillus weihenstephanensis
           KBAB4]
 gi|229013514|ref|ZP_04170648.1| RNA polymerase sigma factor [Bacillus mycoides DSM 2048]
 gi|229019517|ref|ZP_04176334.1| RNA polymerase sigma factor [Bacillus cereus AH1273]
 gi|229025758|ref|ZP_04182158.1| RNA polymerase sigma factor [Bacillus cereus AH1272]
 gi|229061987|ref|ZP_04199313.1| RNA polymerase sigma factor [Bacillus cereus AH603]
 gi|229135118|ref|ZP_04263920.1| RNA polymerase sigma factor [Bacillus cereus BDRD-ST196]
 gi|229169042|ref|ZP_04296758.1| RNA polymerase sigma factor [Bacillus cereus AH621]
 gi|163864247|gb|ABY45306.1| RNA polymerase, sigma 70 subunit, RpoD family [Bacillus
           weihenstephanensis KBAB4]
 gi|228614451|gb|EEK71560.1| RNA polymerase sigma factor [Bacillus cereus AH621]
 gi|228648347|gb|EEL04380.1| RNA polymerase sigma factor [Bacillus cereus BDRD-ST196]
 gi|228717296|gb|EEL68969.1| RNA polymerase sigma factor [Bacillus cereus AH603]
 gi|228735541|gb|EEL86136.1| RNA polymerase sigma factor [Bacillus cereus AH1272]
 gi|228741773|gb|EEL91956.1| RNA polymerase sigma factor [Bacillus cereus AH1273]
 gi|228747751|gb|EEL97620.1| RNA polymerase sigma factor [Bacillus mycoides DSM 2048]
          Length = 375

 Score =  261 bits (667), Expect = 9e-68,   Method: Composition-based stats.
 Identities = 80/289 (27%), Positives = 140/289 (48%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRL
Sbjct: 91  LNDLSVPPGVKINDPVRMYLKEIGRVDLLSAEEEIRLATRI-EEGDEEAKRRLAEANLRL 149

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 150 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQ 209

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    I ++++++  +V  +    
Sbjct: 210 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPSPE---EIGEEMDLAPEKVREILKIA 264

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D +     +    +  +  L   +  L  RE 
Sbjct: 265 QEPVSLETPI--GEEDDSHLGDFI---EDQEATSPADHAAYELLKEQLEDVLDTLTDREE 319

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 320 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 368


>gi|261819465|ref|YP_003257571.1| RNA polymerase factor sigma-32 [Pectobacterium wasabiae WPP163]
 gi|261603478|gb|ACX85964.1| RNA polymerase, sigma 32 subunit, RpoH [Pectobacterium wasabiae
           WPP163]
          Length = 285

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 102/290 (35%), Positives = 162/290 (55%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M +   +  +  +  L  YI      PML  +EE  LA+R    GDL AA  L+ SHLR 
Sbjct: 1   MTKDMQTFTLVPQGSLEGYIRAANAYPMLTAEEERALAERLHYQGDLEAAKHLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VIHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKTRLGWFNQ-----DEVELVARELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNP 237
           A  +         D +  +    ++Y  D        + E     +  + LT ++  L+ 
Sbjct: 176 AAQDMTFDPTPEEDSHDGKAMSPMLYLQDKSSDFAGGIEEDNWDTHAADKLTYALEGLDE 235

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L ++   TL+ L+ ++ VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQHIIRARWLDDDNKSTLQELADQYGVSAERVRQLEKNAMKKLRAAIEA 285


>gi|229086862|ref|ZP_04219022.1| RNA polymerase sigma factor [Bacillus cereus Rock3-44]
 gi|228696437|gb|EEL49262.1| RNA polymerase sigma factor [Bacillus cereus Rock3-44]
          Length = 373

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 80/289 (27%), Positives = 140/289 (48%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRL
Sbjct: 89  LNDLSVPPGVKINDPVRMYLKEIGRVDLLSAEEEIRLATRI-EEGDEEAKRRLAEANLRL 147

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 148 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQ 207

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    I ++++++  +V  +    
Sbjct: 208 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPSPE---EIGEEMDLAPEKVREILKIA 262

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D +     +    +  +  L   +  L  RE 
Sbjct: 263 QEPVSLETPI--GEEDDSHLGDFI---EDQEATSPADHAAYELLKEQLEDVLDTLTDREE 317

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 318 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 366


>gi|254721884|ref|ZP_05183673.1| RNA polymerase sigma factor RpoD [Bacillus anthracis str. A1055]
          Length = 373

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 80/289 (27%), Positives = 140/289 (48%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRL
Sbjct: 89  LNDLSVPPGVKINDPVRMYLKEIGRVDLLSAEEEIRLATRI-EEGDEEAKRRLAEANLRL 147

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 148 VVSIAKRYVGRGILFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQ 207

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    I ++++++  +V  +    
Sbjct: 208 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPSPE---EIGEEMDLAPEKVREILKIA 262

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D +     +    +  +  L   +  L  RE 
Sbjct: 263 QEPVSLETPI--GEEDDSHLGDFI---EDQEATSPADHAAYELLKEQLEDVLDTLTDREE 317

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 318 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 366


>gi|229098765|ref|ZP_04229703.1| RNA polymerase sigma factor [Bacillus cereus Rock3-29]
 gi|229104924|ref|ZP_04235581.1| RNA polymerase sigma factor [Bacillus cereus Rock3-28]
 gi|229117789|ref|ZP_04247154.1| RNA polymerase sigma factor [Bacillus cereus Rock1-3]
 gi|228665652|gb|EEL21129.1| RNA polymerase sigma factor [Bacillus cereus Rock1-3]
 gi|228678498|gb|EEL32718.1| RNA polymerase sigma factor [Bacillus cereus Rock3-28]
 gi|228684609|gb|EEL38549.1| RNA polymerase sigma factor [Bacillus cereus Rock3-29]
          Length = 375

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 80/289 (27%), Positives = 140/289 (48%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRL
Sbjct: 91  LNDLSVPPGVKINDPVRMYLKEIGRVDLLSAEEEIRLATRI-EEGDEEAKRRLAEANLRL 149

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 150 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQ 209

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    I ++++++  +V  +    
Sbjct: 210 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPSPE---EIGEEMDLAPEKVREILKIA 264

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D +     +    +  +  L   +  L  RE 
Sbjct: 265 QEPVSLETPI--GEEDDSHLGDFI---EDQEATSPADHAAYELLKEQLEDVLDTLTDREE 319

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 320 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 368


>gi|229174966|ref|ZP_04302486.1| RNA polymerase sigma factor [Bacillus cereus MM3]
 gi|228608634|gb|EEK65936.1| RNA polymerase sigma factor [Bacillus cereus MM3]
          Length = 375

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 80/289 (27%), Positives = 140/289 (48%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRL
Sbjct: 91  LNDLSVPPGVKINDPVRMYLKEIGRVDLLSAEEEIRLATRI-EEGDEEAKRRLAEANLRL 149

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 150 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQ 209

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    I ++++++  +V  +    
Sbjct: 210 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPSPE---EIGEEMDLAPEKVREILKIA 264

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D +     +    +  +  L   +  L  RE 
Sbjct: 265 QEPVSLETPI--GEEDDSHLGDFI---EDQEATSPADHAAYELLKEQLEDVLDTLTDREE 319

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 320 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 368


>gi|253682266|ref|ZP_04863063.1| RNA polymerase sigma factor RpoD [Clostridium botulinum D str.
           1873]
 gi|253561978|gb|EES91430.1| RNA polymerase sigma factor RpoD [Clostridium botulinum D str.
           1873]
          Length = 368

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 82/280 (29%), Positives = 138/280 (49%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ +  +  Y+ EI K+P+L   EE  LA+R  E GD+ A  +L  ++LRLVV IA  Y 
Sbjct: 93  ISIDDPVRMYLKEIGKVPLLSPDEEISLAQRI-EDGDMYAKKKLAEANLRLVVSIAKRYV 151

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 152 GRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 211

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L        +PE    IAK + +   +V  +        SL   
Sbjct: 212 MVE--TINKLIRVSRQLLQELGREPQPE---EIAKIMEMPVDKVREIMKIAQEPVSLETP 266

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++      +     E       +  L   +  L PRE ++   R   
Sbjct: 267 I--GEEEDSHLGDFIPD---DEAPAPAEAAAFTMLKEQLINVLDTLTPREEKVLRLRFGL 321

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 322 DDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 361


>gi|229031941|ref|ZP_04187928.1| RNA polymerase sigma factor [Bacillus cereus AH1271]
 gi|228729405|gb|EEL80395.1| RNA polymerase sigma factor [Bacillus cereus AH1271]
          Length = 375

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 80/289 (27%), Positives = 140/289 (48%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRL
Sbjct: 91  LNDLSVPPGVKINDPVRMYLKEIGRVDLLSAEEEIRLATRI-EDGDEEAKRRLAEANLRL 149

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 150 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQ 209

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    I ++++++  +V  +    
Sbjct: 210 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPSPE---EIGEEMDLAPEKVREILKIA 264

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D +     +    +  +  L   +  L  RE 
Sbjct: 265 QEPVSLETPI--GEEDDSHLGDFI---EDQEATSPADHAAYELLKEQLEDVLDTLTDREE 319

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 320 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 368


>gi|227817068|ref|YP_002817077.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. CDC 684]
 gi|227007300|gb|ACP17043.1| RNA polymerase sigma-43 factor [Bacillus anthracis str. CDC 684]
          Length = 373

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 80/289 (27%), Positives = 140/289 (48%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRL
Sbjct: 89  LNDLSVPPGVKINDPVRMYLKEIGRVDLLSAEEEIRLATRI-EEGDEEAKRRLAEANLRL 147

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 148 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQ 207

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    I ++++++  +V  +    
Sbjct: 208 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPSPE---EIGEEMDLAPEKVREILKIA 262

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D +     +    +  +  L   +  L  RE 
Sbjct: 263 QEPVSLETPI--GEEDDSHLGDFI---EDQEATSPADHAAYELLKEQLEDVLDTLTDREE 317

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 318 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 366


>gi|301155494|emb|CBW14960.1| RNA polymerase, sigma 32 (sigma H) factor [Haemophilus
           parainfluenzae T3T1]
          Length = 280

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 106/284 (37%), Positives = 168/284 (59%), Gaps = 6/284 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           MN++   ++V  +  +  YI    + PML  +EE  LA+R    GD+ AA +LV SHLR 
Sbjct: 1   MNKETQMMLVP-QGSIEGYIRAANEYPMLTAEEEKSLAERLYYDGDIEAAKKLVLSHLRF 59

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 60  VIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 119

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L    +N     +V  +A +L VS+ +VI M  R+
Sbjct: 120 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNEN-----EVDMVANELGVSKEDVIEMESRM 174

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            G +    L    D  +     +L          L  +   +     L  +++ L+ R +
Sbjct: 175 TGADVGFDLPTDDDDEAYVPSLYLEDKSSNFAAELESENFEEQATEKLGTALANLDERSQ 234

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            I +AR L +   TL +L++++ VS ER+RQ+EA A KK++ ++
Sbjct: 235 EIIKARWLDDEKATLHDLAAKYNVSAERIRQLEANALKKLKSAV 278


>gi|42783418|ref|NP_980665.1| RNA polymerase sigma factor RpoD [Bacillus cereus ATCC 10987]
 gi|47567855|ref|ZP_00238563.1| RNA polymerase sigma factor rpoD [Bacillus cereus G9241]
 gi|217961783|ref|YP_002340353.1| RNA polymerase sigma factor RpoD [Bacillus cereus AH187]
 gi|228916924|ref|ZP_04080486.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228987542|ref|ZP_04147661.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|229141030|ref|ZP_04269573.1| RNA polymerase sigma factor [Bacillus cereus BDRD-ST26]
 gi|229157906|ref|ZP_04285980.1| RNA polymerase sigma factor [Bacillus cereus ATCC 4342]
 gi|229163237|ref|ZP_04291192.1| RNA polymerase sigma factor [Bacillus cereus R309803]
 gi|229198419|ref|ZP_04325125.1| RNA polymerase sigma factor [Bacillus cereus m1293]
 gi|301055785|ref|YP_003793996.1| RNA polymerase sigma factor [Bacillus anthracis CI]
 gi|42739347|gb|AAS43273.1| RNA polymerase sigma-43 factor [Bacillus cereus ATCC 10987]
 gi|47555532|gb|EAL13875.1| RNA polymerase sigma factor rpoD [Bacillus cereus G9241]
 gi|217066780|gb|ACJ81030.1| RNA polymerase sigma-43 factor [Bacillus cereus AH187]
 gi|228585119|gb|EEK43231.1| RNA polymerase sigma factor [Bacillus cereus m1293]
 gi|228620300|gb|EEK77171.1| RNA polymerase sigma factor [Bacillus cereus R309803]
 gi|228625565|gb|EEK82318.1| RNA polymerase sigma factor [Bacillus cereus ATCC 4342]
 gi|228642463|gb|EEK98751.1| RNA polymerase sigma factor [Bacillus cereus BDRD-ST26]
 gi|228772274|gb|EEM20721.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228842748|gb|EEM87834.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|300377954|gb|ADK06858.1| RNA polymerase sigma factor [Bacillus cereus biovar anthracis str.
           CI]
 gi|324328197|gb|ADY23457.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis serovar
           finitimus YBT-020]
          Length = 375

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 80/289 (27%), Positives = 140/289 (48%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRL
Sbjct: 91  LNDLSVPPGVKINDPVRMYLKEIGRVDLLSAEEEIRLATRI-EEGDEEAKRRLAEANLRL 149

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 150 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQ 209

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    I ++++++  +V  +    
Sbjct: 210 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPSPE---EIGEEMDLAPEKVREILKIA 264

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D +     +    +  +  L   +  L  RE 
Sbjct: 265 QEPVSLETPI--GEEDDSHLGDFI---EDQEATSPADHAAYELLKEQLEDVLDTLTDREE 319

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 320 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 368


>gi|253686510|ref|YP_003015700.1| RNA polymerase, sigma 32 subunit, RpoH [Pectobacterium carotovorum
           subsp. carotovorum PC1]
 gi|251753088|gb|ACT11164.1| RNA polymerase, sigma 32 subunit, RpoH [Pectobacterium carotovorum
           subsp. carotovorum PC1]
          Length = 285

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 102/290 (35%), Positives = 162/290 (55%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M +   +  +  +  L  YI      PML  +EE  LA+R    GDL AA  L+ SHLR 
Sbjct: 1   MTKDMQTFTLVPQGSLEGYIRAANAYPMLTAEEERALAERLHYQGDLDAAKHLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VIHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKTRLGWFNQ-----DEVELVARELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNP 237
           A  +         D +  +    ++Y  D        + E     +  + LT ++  L+ 
Sbjct: 176 AAQDMTFDPTPEEDSHDGKAMSPMLYLQDKSSDFADGIEEDNWDTHAADKLTYALEGLDE 235

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L ++   TL+ L+ ++ VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQHIIRARWLDDDNKSTLQELADQYGVSAERVRQLEKNAMKKLRAAIEA 285


>gi|225412271|ref|ZP_03761460.1| hypothetical protein CLOSTASPAR_05493 [Clostridium asparagiforme
           DSM 15981]
 gi|225042189|gb|EEG52435.1| hypothetical protein CLOSTASPAR_05493 [Clostridium asparagiforme
           DSM 15981]
          Length = 376

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 83/280 (29%), Positives = 141/280 (50%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ +  +  Y+ EI KIP+L+ + E  LA++  E GD  AA RL  S+LRLVV IA  Y 
Sbjct: 100 ISLQDPVRMYLKEIGKIPLLDMEAEIRLARQM-EEGDREAAKRLAESNLRLVVSIAKRYV 158

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 159 GRGMQFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRSIADQARTIRIPVH 218

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +     N+ RL    + +     +      IA +  +S   V  +        SL   
Sbjct: 219 MVE-----NINRLVRTSRQLLQELGREPTTEEIAARAEMSVERVSEILKMSQEPVSLETP 273

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++  D      V  +          L   ++ L  RE+++   R   
Sbjct: 274 I--GEEEDSHLGDFIQDD---NVTVPQDAATYTLLHEQLMEVLTTLTEREQKVLRLRFGL 328

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  P TLE +  EF+V+RER+RQIEA+A +K++   + +
Sbjct: 329 DDGRPRTLEEVGREFKVTRERIRQIEAKALRKLRHPSRSK 368


>gi|50123263|ref|YP_052430.1| RNA polymerase factor sigma-32 [Pectobacterium atrosepticum
           SCRI1043]
 gi|49613789|emb|CAG77240.1| RNA polymerase sigma-32 factor [Pectobacterium atrosepticum
           SCRI1043]
          Length = 285

 Score =  261 bits (667), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 102/290 (35%), Positives = 162/290 (55%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M +   +  +  +  L  YI      PML  +EE  LA+R    GDL AA  L+ SHLR 
Sbjct: 1   MTKDMQTFTLVPQGSLEGYIRAANAYPMLTAEEERALAERLHYQGDLEAAKHLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VIHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKAKTRLGWFNQ-----DEVELVARELGVTTKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNP 237
           A  +         D +  +    ++Y  D        + E     +  + LT ++  L+ 
Sbjct: 176 AAQDMTFDPTPEEDSHDGKAMSPMLYLQDKSSDFADGIEEDNWDTHAADKLTYALEGLDE 235

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L ++   TL+ L+ ++ VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQHIIRARWLDDDNKSTLQELADQYGVSAERVRQLEKNAMKKLRAAIEA 285


>gi|229828460|ref|ZP_04454529.1| hypothetical protein GCWU000342_00522 [Shuttleworthia satelles DSM
           14600]
 gi|229793054|gb|EEP29168.1| hypothetical protein GCWU000342_00522 [Shuttleworthia satelles DSM
           14600]
          Length = 614

 Score =  260 bits (666), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 83/318 (26%), Positives = 136/318 (42%), Gaps = 51/318 (16%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------------HGD------- 46
           VN +  +  Y+ EI K+ +L  +EE  LA++  +                 GD       
Sbjct: 299 VNIDDPVRMYLKEIGKVHLLTAEEEVDLAQKMEKGLKADEQIEILREEIRSGDLSEEDMM 358

Query: 47  ----------------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
                             A  +L  ++LRLVV IA  Y G G+   +++ EGN+GL++AV
Sbjct: 359 NLEAQIKILKNDSAVGERAKQKLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAV 418

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +KFD  +G++ +TY+ WWI+ A+   I      ++I     +      L R+   L    
Sbjct: 419 EKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE--TINKLIRVSRQLLQEL 476

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
                PE    IA+++  +   V  +        SL   I   ++  S   D++    D 
Sbjct: 477 GREPSPE---EIAREMETTPDRVREILKISQEPVSLETPI--GEEEDSHLGDFI---QDE 528

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRER 268
              V  E       +  L   +  L  RER++   R   E+    TLE +  EF V+RER
Sbjct: 529 NAPVPAEAATFTLLKEQLNEVLDTLTERERKVLILRFGLEDGRGRTLEEVGKEFNVTRER 588

Query: 269 VRQIEARAFKKVQESIQK 286
           +RQIEA+A +K++   + 
Sbjct: 589 IRQIEAKALRKLRHPSRS 606


>gi|302874342|ref|YP_003842975.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           cellulovorans 743B]
 gi|307689391|ref|ZP_07631837.1| RNA polymerase sigma factor RpoD [Clostridium cellulovorans 743B]
 gi|302577199|gb|ADL51211.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           cellulovorans 743B]
          Length = 363

 Score =  260 bits (666), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 82/277 (29%), Positives = 137/277 (49%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI K+P+L  + E  LA+R  E GD +A  +L  ++LRLVV IA  Y G G
Sbjct: 91  DDPVRMYLKEIGKVPLLSPETEIELAERI-EAGDPAAKKKLAEANLRLVVSIAKRYVGRG 149

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     +
Sbjct: 150 MLFLDLIQEGNLGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 209

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 L R+   L      +  PE    +A+K+ +   +VI +        SL   I  
Sbjct: 210 --TINKLLRITRQLVQELGRDPLPE---ELAEKMEMPVDKVIEIRKIAQEPVSLETPI-- 262

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            ++  S   D++            E       +  L   +  L PRE ++   R   ++ 
Sbjct: 263 GEEEDSHLGDFIPD---DDAPAPAEAAAFTMLKEQLINVLDTLTPREEKVLRLRFGLDDG 319

Query: 253 --VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 320 RARTLEEVGREFNVTRERIRQIEAKALRKLRHPSRSK 356


>gi|317494584|ref|ZP_07952997.1| alternative sigma factor RpoH [Enterobacteriaceae bacterium
           9_2_54FAA]
 gi|316917514|gb|EFV38860.1| alternative sigma factor RpoH [Enterobacteriaceae bacterium
           9_2_54FAA]
          Length = 283

 Score =  260 bits (666), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 106/288 (36%), Positives = 168/288 (58%), Gaps = 7/288 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  Y+      PML  +EE  L +R    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLTLVPQGSLEAYVRAANTYPMLTAEEEKELGERLHYEGDLDAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEMGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VSE +V+ M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVELVARELGVSEKDVLEMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE-ERKNRRNMLTRSMSVLNPRE 239
           A  +    + N  D++S       + D        IE +    +  + LT +M  L+ R 
Sbjct: 176 AAQDMAFDMSNDDDESSPAAPVLFLQDKSSDFANDIEDDNWDSHAADKLTLAMEGLDERS 235

Query: 240 RRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           + I  AR L ++   TL+ L+ ++ VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 QHIIRARWLDDDNKATLQELADQYGVSAERVRQLEKNAMKKLRAAIEA 283


>gi|281412780|ref|YP_003346859.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermotoga
           naphthophila RKU-10]
 gi|281373883|gb|ADA67445.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermotoga
           naphthophila RKU-10]
          Length = 407

 Score =  260 bits (666), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 81/276 (29%), Positives = 138/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI KIP+L   +E  LA+R  + GD  A  +L+TS+LRLVV IA  Y G GL
Sbjct: 129 DSIKMYLKEIGKIPLLTPAQERELARR-AQMGDKKAKEKLITSNLRLVVSIAKRYMGRGL 187

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGNIGL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 188 SFQDLIQEGNIGLLKAVEKFDWRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 246

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                + +L    +     + +   +  +AK +     ++  +        SL + I   
Sbjct: 247 ----TINKLNRLRREYYQKHGEEPSIEELAKMMGKPPEKIKEILEAAKETISLESPI--G 300

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQEN 251
           +   S  +D++  D     +   ++  R   R  L + +  L+PRE  +   R   L   
Sbjct: 301 EDEDSSIEDFVADDSIASPK---KEAMRMLMREELEKVLKTLSPREAMVLRMRYGLLDGK 357

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           P TLE +   F V+RER+RQIE +A +K++   + +
Sbjct: 358 PKTLEEVGQYFNVTRERIRQIEVKALRKLRHPSRSK 393


>gi|15644200|ref|NP_229250.1| RNA polymerase sigma-A factor [Thermotoga maritima MSB8]
 gi|6831649|sp|P77994|RPOD_THEMA RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A
 gi|4982015|gb|AAD36519.1|AE001796_11 RNA polymerase sigma-A factor [Thermotoga maritima MSB8]
          Length = 399

 Score =  260 bits (666), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 81/276 (29%), Positives = 138/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI KIP+L   +E  LA+R  + GD  A  +L+TS+LRLVV IA  Y G GL
Sbjct: 121 DSIKMYLKEIGKIPLLTPAQERELARR-AQMGDKKAKEKLITSNLRLVVSIAKRYMGRGL 179

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGNIGL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 180 SFQDLIQEGNIGLLKAVEKFDWRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 238

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                + +L    +     + +   +  +AK +     ++  +        SL + I   
Sbjct: 239 ----TINKLNRLRREYYQKHGEEPSIEELAKMMGKPPEKIKEILEAAKETISLESPI--G 292

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQEN 251
           +   S  +D++  D     +   ++  R   R  L + +  L+PRE  +   R   L   
Sbjct: 293 EDEDSSIEDFVADDSIASPK---KEAMRMLMREELEKVLKTLSPREAMVLRMRYGLLDGK 349

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           P TLE +   F V+RER+RQIE +A +K++   + +
Sbjct: 350 PKTLEEVGQYFNVTRERIRQIEVKALRKLRHPSRSK 385


>gi|218885581|ref|YP_002434902.1| RNA polymerase, sigma 70 family subunit [Desulfovibrio vulgaris
           str. 'Miyazaki F']
 gi|218756535|gb|ACL07434.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio
           vulgaris str. 'Miyazaki F']
          Length = 474

 Score =  260 bits (666), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 108/286 (37%), Positives = 173/286 (60%), Gaps = 7/286 (2%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
            +    L  Y+ EI + P+L+  EE+ LA+R +E GD  AA RLVTSHLRLVVKIAM ++
Sbjct: 189 ASTRDSLHLYLREISRFPLLKPDEEFDLARRVQEQGDSDAAFRLVTSHLRLVVKIAMDFQ 248

Query: 70  GYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
              +  + +++ EGN+GLM+AV KFDPE+G + + Y+ +WIKA + ++I+ +W +VKIGT
Sbjct: 249 RRWMQNVLDLIQEGNVGLMRAVNKFDPEKGIKFSYYAAFWIKAYILKFIMDNWRMVKIGT 308

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLN 187
           T  Q++LF+NL + +  L A             +++KLNV+  +VI M  RL + D SL+
Sbjct: 309 TQAQRKLFYNLNKERQRLIA----QGYDPDATILSEKLNVTVEQVIEMEQRLDSSDMSLD 364

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             +   D   +   D+L     G E+ L   E  +  ++ +   +  L+ +E  I + R 
Sbjct: 365 ITVG-EDSGGATRMDFLPALGPGIEETLANSEIARMVQDRVQTILPKLSDKEAYILQHRL 423

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           L E PVTL  +  +++++RERVRQIEAR  +K+++ + K++   SS
Sbjct: 424 LSEQPVTLREIGEKYDITRERVRQIEARLLQKLRDHLFKEIRDFSS 469


>gi|206971344|ref|ZP_03232295.1| RNA polymerase sigma-43 factor [Bacillus cereus AH1134]
 gi|218899458|ref|YP_002447869.1| RNA polymerase sigma-43 factor [Bacillus cereus G9842]
 gi|228902815|ref|ZP_04066960.1| RNA polymerase sigma factor [Bacillus thuringiensis IBL 4222]
 gi|228910126|ref|ZP_04073946.1| RNA polymerase sigma factor [Bacillus thuringiensis IBL 200]
 gi|228941457|ref|ZP_04104008.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228954576|ref|ZP_04116601.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228967357|ref|ZP_04128392.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228974388|ref|ZP_04134957.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228980981|ref|ZP_04141284.1| RNA polymerase sigma factor [Bacillus thuringiensis Bt407]
 gi|229071795|ref|ZP_04205010.1| RNA polymerase sigma factor [Bacillus cereus F65185]
 gi|229081552|ref|ZP_04214050.1| RNA polymerase sigma factor [Bacillus cereus Rock4-2]
 gi|229180570|ref|ZP_04307912.1| RNA polymerase sigma factor [Bacillus cereus 172560W]
 gi|229192502|ref|ZP_04319465.1| RNA polymerase sigma factor [Bacillus cereus ATCC 10876]
 gi|206734116|gb|EDZ51287.1| RNA polymerase sigma-43 factor [Bacillus cereus AH1134]
 gi|218541635|gb|ACK94029.1| RNA polymerase sigma-43 factor [Bacillus cereus G9842]
 gi|228591079|gb|EEK48935.1| RNA polymerase sigma factor [Bacillus cereus ATCC 10876]
 gi|228602994|gb|EEK60473.1| RNA polymerase sigma factor [Bacillus cereus 172560W]
 gi|228701757|gb|EEL54245.1| RNA polymerase sigma factor [Bacillus cereus Rock4-2]
 gi|228711390|gb|EEL63350.1| RNA polymerase sigma factor [Bacillus cereus F65185]
 gi|228778772|gb|EEM27036.1| RNA polymerase sigma factor [Bacillus thuringiensis Bt407]
 gi|228785438|gb|EEM33448.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228792392|gb|EEM39959.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228805233|gb|EEM51827.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228818238|gb|EEM64312.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228849643|gb|EEM94477.1| RNA polymerase sigma factor [Bacillus thuringiensis IBL 200]
 gi|228856824|gb|EEN01339.1| RNA polymerase sigma factor [Bacillus thuringiensis IBL 4222]
 gi|326942074|gb|AEA17970.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 375

 Score =  260 bits (666), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 80/289 (27%), Positives = 140/289 (48%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRL
Sbjct: 91  LNDLSVPPGVKINDPVRMYLKEIGRVDLLSAEEEIRLATRI-EEGDEEAKRRLAEANLRL 149

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 150 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQ 209

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    I ++++++  +V  +    
Sbjct: 210 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPSPE---EIGEEMDLAPEKVREILKIA 264

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D +     +    +  +  L   +  L  RE 
Sbjct: 265 QEPVSLETPI--GEEDDSHLGDFI---EDQEATSPADHAAYELLKEQLEDVLDTLTDREE 319

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 320 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 368


>gi|5030433|gb|AAC44889.2| sigma 70-type sigma factor SigA [Thermotoga maritima]
          Length = 407

 Score =  260 bits (666), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 81/276 (29%), Positives = 138/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI KIP+L   +E  LA+R  + GD  A  +L+TS+LRLVV IA  Y G GL
Sbjct: 129 DSIKMYLKEIGKIPLLTPAQERELARR-AQMGDKKAKEKLITSNLRLVVSIAKRYMGRGL 187

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGNIGL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 188 SFQDLIQEGNIGLLKAVEKFDWRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 246

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                + +L    +     + +   +  +AK +     ++  +        SL + I   
Sbjct: 247 ----TINKLNRLRREYYQKHGEEPSIEELAKMMGKPPEKIKEILEAAKETISLESPI--G 300

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQEN 251
           +   S  +D++  D     +   ++  R   R  L + +  L+PRE  +   R   L   
Sbjct: 301 EDEDSSIEDFVADDSIASPK---KEAMRMLMREELEKVLKTLSPREAMVLRMRYGLLDGK 357

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           P TLE +   F V+RER+RQIE +A +K++   + +
Sbjct: 358 PKTLEEVGQYFNVTRERIRQIEVKALRKLRHPSRSK 393


>gi|30022370|ref|NP_834001.1| RNA polymerase sigma factor RpoD [Bacillus cereus ATCC 14579]
 gi|218232261|ref|YP_002369099.1| RNA polymerase sigma factor RpoD [Bacillus cereus B4264]
 gi|228923044|ref|ZP_04086337.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228960557|ref|ZP_04122206.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|229048011|ref|ZP_04193587.1| RNA polymerase sigma factor [Bacillus cereus AH676]
 gi|229111765|ref|ZP_04241313.1| RNA polymerase sigma factor [Bacillus cereus Rock1-15]
 gi|229129569|ref|ZP_04258539.1| RNA polymerase sigma factor [Bacillus cereus BDRD-Cer4]
 gi|229146877|ref|ZP_04275242.1| RNA polymerase sigma factor [Bacillus cereus BDRD-ST24]
 gi|229152492|ref|ZP_04280684.1| RNA polymerase sigma factor [Bacillus cereus m1550]
 gi|296504786|ref|YP_003666486.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis BMB171]
 gi|29897928|gb|AAP11202.1| RNA polymerase sigma factor rpoD [Bacillus cereus ATCC 14579]
 gi|218160218|gb|ACK60210.1| RNA polymerase sigma-43 factor [Bacillus cereus B4264]
 gi|228631100|gb|EEK87737.1| RNA polymerase sigma factor [Bacillus cereus m1550]
 gi|228636705|gb|EEK93170.1| RNA polymerase sigma factor [Bacillus cereus BDRD-ST24]
 gi|228653886|gb|EEL09754.1| RNA polymerase sigma factor [Bacillus cereus BDRD-Cer4]
 gi|228671759|gb|EEL27055.1| RNA polymerase sigma factor [Bacillus cereus Rock1-15]
 gi|228723468|gb|EEL74837.1| RNA polymerase sigma factor [Bacillus cereus AH676]
 gi|228799157|gb|EEM46125.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228836677|gb|EEM82025.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|296325838|gb|ADH08766.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis BMB171]
          Length = 375

 Score =  260 bits (666), Expect = 1e-67,   Method: Composition-based stats.
 Identities = 80/289 (27%), Positives = 140/289 (48%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRL
Sbjct: 91  LNDLSVPPGVKINDPVRMYLKEIGRVDLLSAEEEIRLATRI-EEGDEEAKRRLAEANLRL 149

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 150 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQ 209

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    I ++++++  +V  +    
Sbjct: 210 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPSPE---EIGEEMDLAPEKVREILKIA 264

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D +     +    +  +  L   +  L  RE 
Sbjct: 265 QEPVSLETPI--GEEDDSHLGDFI---EDQEATSPADHAAYELLKEQLEDVLDTLTDREE 319

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 320 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 368


>gi|91794849|ref|YP_564500.1| RNA polymerase factor sigma-32 [Shewanella denitrificans OS217]
 gi|91716851|gb|ABE56777.1| RNA polymerase sigma factor RpoH [Shewanella denitrificans OS217]
          Length = 284

 Score =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 106/284 (37%), Positives = 172/284 (60%), Gaps = 7/284 (2%)

Query: 4   KNMSIIVN-GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           ++MS+ V  G   L  YI  +  I ML  ++E  LAKR +E GDL AA +L+ SHLR VV
Sbjct: 6   QSMSLTVPRGSSSLEAYIQSVTSINMLGAEDEQALAKRLQETGDLQAAKQLIMSHLRFVV 65

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A GY GYGLP ++++ EGNIGLM+AVK+FDP+ G RL ++++ WIKA + EY+L++W 
Sbjct: 66  HVAKGYAGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYVLKNWR 125

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFN+R+ K  L   +D      +V  +A+ L VS+++V  M  R+A 
Sbjct: 126 IVKVATTKAQRKLFFNIRKSKKRLGWFSD-----AEVTMVAENLGVSKADVTEMESRMAA 180

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLNPRERR 241
            +    + + +D  +       + DH       +E    + N ++ L  ++  L+ R + 
Sbjct: 181 QDPAFDIASDNDDETDFSPVHYLEDHSSDVAQQVENANWESNSQSRLFSAIKTLDERSQH 240

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           I +AR L ++  TL+ L+  ++VS ER+RQ+E  A  K++  ++
Sbjct: 241 ILQARWLDDDKTTLQELAETYQVSAERIRQLEKNAMNKLKACME 284


>gi|160878392|ref|YP_001557360.1| RpoD family RNA polymerase sigma factor [Clostridium
           phytofermentans ISDg]
 gi|160427058|gb|ABX40621.1| RNA polymerase, sigma 70 subunit, RpoD family [Clostridium
           phytofermentans ISDg]
          Length = 371

 Score =  260 bits (666), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 78/291 (26%), Positives = 146/291 (50%), Gaps = 15/291 (5%)

Query: 2   NRKNMSIIVN--GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLR 59
           + +++S + +   +  + +Y+ EI   P+L   EE  LAK+  E GD  A   L  S+LR
Sbjct: 85  DTEDLSAMTSTISDDPVKQYLKEIGSYPLLSVAEEIELAKKI-EAGDNMAKQILAESNLR 143

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           LVV IA  Y G GL   +++ EGN+GL++AV KFD  +G++ +TY+ WWI+ A+   I  
Sbjct: 144 LVVSIAKRYVGRGLSFLDLIQEGNLGLIKAVDKFDYNKGYKFSTYATWWIRQAITRSIAD 203

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
               ++I    ++      + +     + +     +      +A  +N+   +V  +   
Sbjct: 204 QSRTIRIPVHMSEV-----INKTYRVSRNLLQELGREPSEQELADAMNLPIEKVREILKV 258

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            A   SL+  I   +++ S   D++  D     +   +       ++ +++ +  L  RE
Sbjct: 259 SADPISLDTPI--GEEDDSHLGDFIKDDTIMGPE---DAASYAVLQDQISKLLDTLTERE 313

Query: 240 RRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +R+   R   ++    TLE +  EF V+RER+RQIEA+A +K++   + ++
Sbjct: 314 QRVLILRFGLQDGRSRTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRARM 364


>gi|160947542|ref|ZP_02094709.1| hypothetical protein PEPMIC_01477 [Parvimonas micra ATCC 33270]
 gi|158446676|gb|EDP23671.1| hypothetical protein PEPMIC_01477 [Parvimonas micra ATCC 33270]
          Length = 382

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 85/280 (30%), Positives = 142/280 (50%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
            N +  +  Y+ EI KIP+L   EE +LA+   E GD+ A  +L  ++LRLVV IA  Y 
Sbjct: 107 FNIDDPVKMYLKEIGKIPLLSADEERILAENM-EAGDIEAKKKLAETNLRLVVSIAKRYV 165

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GLM+AV+KFD  RGF+ +TY+ WWI+ A+   I      ++I   
Sbjct: 166 GRGMQFLDLIQEGNMGLMKAVEKFDFRRGFKFSTYATWWIRQAITRSIADQARTIRIPVH 225

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      + +L    + +     +      I++ + +   +V  +        SL   
Sbjct: 226 MVE-----TINKLVRIERQLVQELGREPTNEEISEHMGIEVDKVNEIRKIAQEPVSLETP 280

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   +++ S   D++    D       E       +  L + +S L+ RE+++ E R   
Sbjct: 281 I--GEEDDSHLGDFI---EDETAIAPDEAANFSMLKEQLNQVLSTLSDREKKVLELRFGL 335

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +  P TLE +  EFEV+RER+RQIEA+A +K++   + Q
Sbjct: 336 NDGTPRTLEEVGKEFEVTRERIRQIEAKALRKLKHPSRSQ 375


>gi|168187756|ref|ZP_02622391.1| RNA polymerase sigma factor RpoD [Clostridium botulinum C str.
           Eklund]
 gi|169294399|gb|EDS76532.1| RNA polymerase sigma factor RpoD [Clostridium botulinum C str.
           Eklund]
          Length = 368

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 81/280 (28%), Positives = 138/280 (49%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ +  +  Y+ EI K+P+L   EE  LA+R  E G++ A  +L  ++LRLVV IA  Y 
Sbjct: 93  ISIDDPVRMYLKEIGKVPLLTPDEEVDLAQRI-EAGEMYAKKKLAEANLRLVVSIAKRYV 151

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 152 GRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 211

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L        +PE    IAK + +   +V  +        SL   
Sbjct: 212 MVE--TINKLIRVSRQLLQELGREPQPE---EIAKIMEMPVDKVREIMKIAQEPVSLETP 266

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++      +     E       +  L   +  L PRE ++   R   
Sbjct: 267 I--GEEEDSHLGDFIPD---DEAPAPAEAAAFTMLKEQLINVLDTLTPREEKVLRLRFGL 321

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 322 DDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 361


>gi|218513990|ref|ZP_03510830.1| RNA polymerase factor sigma-32 [Rhizobium etli 8C-3]
          Length = 217

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 166/217 (76%), Positives = 184/217 (84%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M R  +  I  GE GL+RY+ EIRK PMLE Q+EY+LAKRY EHGD  AAH+LVTSHLRL
Sbjct: 1   MARNTLPSITAGEAGLNRYLDEIRKFPMLEPQQEYMLAKRYAEHGDRDAAHKLVTSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V KIAMGYRGYGLPI EVVSEGN+GLMQAVKKFDPERGFRLATY+MWWIKA++QEYILRS
Sbjct: 61  VAKIAMGYRGYGLPIGEVVSEGNVGLMQAVKKFDPERGFRLATYAMWWIKASIQEYILRS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSLVK+GTTANQKRLFFNLRRLKG +QAI D +LKPE V  IA KLNVSE EVISMN RL
Sbjct: 121 WSLVKMGTTANQKRLFFNLRRLKGRIQAIDDGDLKPEHVSEIATKLNVSEEEVISMNRRL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           +GD SLNA I +++ +S QWQDWLV DHD QE VLIE
Sbjct: 181 SGDASLNAPIKAAEGDSGQWQDWLVDDHDSQEDVLIE 217


>gi|145637130|ref|ZP_01792792.1| RNA polymerase sigma factor [Haemophilus influenzae PittHH]
 gi|145640200|ref|ZP_01795784.1| RNA polymerase sigma factor [Haemophilus influenzae R3021]
 gi|229846357|ref|ZP_04466465.1| RNA polymerase factor sigma-32 [Haemophilus influenzae 7P49H1]
 gi|145269575|gb|EDK09516.1| RNA polymerase sigma factor [Haemophilus influenzae PittHH]
 gi|145274786|gb|EDK14648.1| RNA polymerase sigma factor [Haemophilus influenzae 22.4-21]
 gi|229810450|gb|EEP46168.1| RNA polymerase factor sigma-32 [Haemophilus influenzae 7P49H1]
 gi|309972570|gb|ADO95771.1| RNA polymerase sigma-32 factor [Haemophilus influenzae R2846]
          Length = 281

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 104/285 (36%), Positives = 169/285 (59%), Gaps = 7/285 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+++   ++V  +  +  YI    + PML  +EE  LA+R   H DL AA +L+ SHLR 
Sbjct: 1   MDKETQMMLVP-QGSIEGYIRAANEYPMLTAEEEKELAERLYYHEDLDAAKKLILSHLRF 59

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 60  VIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 119

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L    +N     +V  +A +L VS+ +VI M  R+
Sbjct: 120 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNEN-----EVDMVANELGVSKEDVIEMESRM 174

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D   +   + ++  +     +L          L  +         L  ++  L+ R 
Sbjct: 175 SGADVGFDLPTDDAETETYSPALYLEDKSSNFAAALENENFESQATEQLGAALQSLDARS 234

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + I +AR L +N  TL +L++++ VS ER+RQ+E  A KK++ ++
Sbjct: 235 QDIIKARWLDDNKATLHDLAAKYNVSAERIRQLETNALKKLKSAV 279


>gi|260913469|ref|ZP_05919947.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Pasteurella
           dagmatis ATCC 43325]
 gi|260632409|gb|EEX50582.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Pasteurella
           dagmatis ATCC 43325]
          Length = 281

 Score =  260 bits (665), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 101/284 (35%), Positives = 167/284 (58%), Gaps = 5/284 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           MN++  ++++  +  L  YI    + PML  +EE  LA+R     DL AA +L+ SHLR 
Sbjct: 1   MNKETQTMMLVPQGSLEGYIRAANEYPMLTAEEEKELAERLYYQEDLEAAKKLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L    +N     +V  +A +L V+  +V+ M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNEN-----EVEMVANELGVTPEDVMEMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            G +    L     + +     +L          L ++         L+ ++  L+ R  
Sbjct: 176 TGSDVAFDLPTDDSEETYSPALYLEDKGSNFAAELEDENYETQATEQLSVALEGLDERSL 235

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            I ++R L +N  TL++L++++ +S ERVRQ+E  A KK++ ++
Sbjct: 236 DIIKSRWLDDNKATLQDLAAKYNISAERVRQLETNALKKLKSAV 279


>gi|148652168|ref|YP_001279261.1| RNA polymerase factor sigma-32 [Psychrobacter sp. PRwf-1]
 gi|148571252|gb|ABQ93311.1| RNA polymerase, sigma 32 subunit, RpoH [Psychrobacter sp. PRwf-1]
          Length = 372

 Score =  260 bits (664), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 109/272 (40%), Positives = 166/272 (61%), Gaps = 7/272 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           I L  Y++ + +IP+L  ++E  LA RY + GD+ AA  LV SHLR V+ IA  Y GYGL
Sbjct: 94  INLGAYMNSVHQIPILTTEQEQELAHRYYDDGDVEAARILVMSHLRFVIHIARSYSGYGL 153

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P ++++ EGN+GLM+AVK+FDP +G RL ++++ WIKA + E+++R+W +VK+ TT   +
Sbjct: 154 PQADLIQEGNLGLMKAVKRFDPNKGVRLVSFAVHWIKAEIHEFVIRNWRIVKVATTKAHR 213

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINS 192
           +LFFNLR LK      T+N L  E+  AIA  LNV+  +V+ M  RL   D S  A  ++
Sbjct: 214 KLFFNLRSLKK-----TNNQLTLEEADAIAADLNVTRKQVLEMESRLTSYDASFEAQ-ST 267

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            D++        + D     +++ + +  +N  N L  +M  L+ R R I E R L E  
Sbjct: 268 DDEDGHYAPQLFLEDGVDPAEMVEDADWEENNTNALMDAMDTLDERSRDIVEQRWLSEQK 327

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL  L++ + +S ERVRQIE  A  K++E++
Sbjct: 328 STLHELAAVYNISAERVRQIEKNAMDKIREAM 359


>gi|325579283|ref|ZP_08149239.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Haemophilus
           parainfluenzae ATCC 33392]
 gi|325159518|gb|EGC71652.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Haemophilus
           parainfluenzae ATCC 33392]
          Length = 293

 Score =  260 bits (664), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 106/284 (37%), Positives = 168/284 (59%), Gaps = 6/284 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           MN++   ++V  +  +  YI    + PML  +EE  LA+R    GD+ AA +LV SHLR 
Sbjct: 14  MNKETQMMLVP-QGSIEAYIRAANEYPMLTAEEEKSLAERLYYDGDIEAAKKLVLSHLRF 72

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 73  VIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 132

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L    +N     +V  +A +L VS+ +VI M  R+
Sbjct: 133 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNEN-----EVDMVANELGVSKEDVIEMESRM 187

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            G +    L    D  +     +L          L  +   +     L  +++ L+ R +
Sbjct: 188 TGADVGFDLPTDDDDEAYVPSLYLEDKSSNFAAELESENFEEQATEKLGTALANLDERSQ 247

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            I +AR L +   TL +L++++ VS ER+RQ+EA A KK++ ++
Sbjct: 248 DIIKARWLDDEKATLHDLAAKYNVSAERIRQLEANALKKLKSAV 291


>gi|288916958|ref|ZP_06411330.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EUN1f]
 gi|288351667|gb|EFC85872.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EUN1f]
          Length = 392

 Score =  260 bits (664), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 83/307 (27%), Positives = 141/307 (45%), Gaps = 39/307 (12%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------------REHGDLSA- 49
                 +  Y+ EI K+P+L  +EE  LAKR                    +   DL A 
Sbjct: 89  APTSDPVRMYLKEIGKVPLLTAEEEVDLAKRIEAGLFASEKLAVATKKTSPQMRRDLEAI 148

Query: 50  -------AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
                    +LV ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +
Sbjct: 149 ERDGQIAKRKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFS 208

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I     +      L R++  L         PE    I
Sbjct: 209 TYATWWIRQAITRAIADQARTIRIPVHMVE--TINKLIRIQRQLLQDLGREPSPE---EI 263

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           AK+++++  +V  +        SL   I   ++  S   D++    D    V ++     
Sbjct: 264 AKEMDLTPDKVREILKVSQEPVSLETPI--GEEEDSHLGDFI---EDCDAVVPVDAASFI 318

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             +  L   +  L+ RE+++ + R      +P TLE +  EF V+RER+RQIE++   K+
Sbjct: 319 LLQEQLDSVLHTLSDREKKVIQLRFGLTDGHPRTLEEVGREFGVTRERIRQIESKTLSKL 378

Query: 281 QESIQKQ 287
           +   + Q
Sbjct: 379 RHPSRSQ 385


>gi|300854008|ref|YP_003778992.1| putative RNA polymerase sigma factor [Clostridium ljungdahlii DSM
           13528]
 gi|300434123|gb|ADK13890.1| predicted RNA polymerase sigma factor [Clostridium ljungdahlii DSM
           13528]
          Length = 354

 Score =  260 bits (664), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 87/292 (29%), Positives = 141/292 (48%), Gaps = 17/292 (5%)

Query: 2   NRKNMSIIVNGEIGLS----RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSH 57
           N KN+ + V   I +      Y+ EI K+P+L  +EE  LAKR  E GD  A  +L  ++
Sbjct: 67  NEKNLDLSVPDGIAIDDPVRMYLKEIGKVPLLLPEEEISLAKRI-EEGDQIAKKKLAEAN 125

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I
Sbjct: 126 LRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAI 185

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
                 ++I     +      L R+   L         PE+V  I   + +   +V  + 
Sbjct: 186 ADQARTIRIPVHMVE--TINKLVRVSRQLLQELGREPHPEEVAQI---MEMPVDKVREIM 240

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                  SL   I   ++  S   D++      +     E       +  L   +  L P
Sbjct: 241 KIAQEPVSLETPI--GEEEDSHLGDFIPD---DEAPAPAEAAAFTMLKEQLINVLDTLTP 295

Query: 238 RERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           RE ++   R   ++    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 296 REEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 347


>gi|225018167|ref|ZP_03707359.1| hypothetical protein CLOSTMETH_02104 [Clostridium methylpentosum
           DSM 5476]
 gi|224949164|gb|EEG30373.1| hypothetical protein CLOSTMETH_02104 [Clostridium methylpentosum
           DSM 5476]
          Length = 372

 Score =  260 bits (664), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 81/280 (28%), Positives = 136/280 (48%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           +N +  +  Y+ EI K+P+L  +EE  LA++    GD  A  RL  ++LRLVV IA  Y 
Sbjct: 97  INIDDPVKVYLKEIGKVPLLTAEEEIDLAQKMS-AGDPYARKRLSEANLRLVVSIAKRYV 155

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I   
Sbjct: 156 GRGMQFLDLIQEGNLGLIKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVH 215

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      + ++K     +   N        IA++L++   +V  +        SL   
Sbjct: 216 MVE-----TINKVKKVSSQLLHKNGHEASAEEIAEELDMPVDKVREIMRVSQEPVSLETP 270

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++            E       R  L   +  L  RE ++   R   
Sbjct: 271 I--GEEEDSHLSDFIPD---DDAPAPAEAASHTLLREQLGDVLGTLTEREEKVLRLRFGL 325

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 326 EDGRSRTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 365


>gi|111221463|ref|YP_712257.1| RNA polymerase essential primary sigma 70 factor [Frankia alni
           ACN14a]
 gi|111148995|emb|CAJ60675.1| RNA polymerase essential primary sigma 70 factor [Frankia alni
           ACN14a]
          Length = 409

 Score =  260 bits (664), Expect = 2e-67,   Method: Composition-based stats.
 Identities = 83/307 (27%), Positives = 141/307 (45%), Gaps = 39/307 (12%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------------REHGDLSA- 49
                 +  Y+ EI K+P+L  +EE  LAKR                    +   DL A 
Sbjct: 106 APTSDPVRMYLKEIGKVPLLTAEEEVDLAKRIEAGLFASEKLAVATKKTSPQMRRDLEAI 165

Query: 50  -------AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
                    +LV ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +
Sbjct: 166 ERDGQIAKRKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFS 225

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I     +      L R++  L         PE    I
Sbjct: 226 TYATWWIRQAITRAIADQARTIRIPVHMVE--TINKLIRIQRQLLQDLGREPSPE---EI 280

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           AK+++++  +V  +        SL   I   ++  S   D++    D    V ++     
Sbjct: 281 AKEMDLTPDKVREILKVSQEPVSLETPI--GEEEDSHLGDFI---EDCDAVVPVDAASFI 335

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             +  L   +  L+ RE+++ + R      +P TLE +  EF V+RER+RQIE++   K+
Sbjct: 336 LLQEQLDSVLHTLSDREKKVIQLRFGLTDGHPRTLEEVGREFGVTRERIRQIESKTLSKL 395

Query: 281 QESIQKQ 287
           +   + Q
Sbjct: 396 RHPSRSQ 402


>gi|304437692|ref|ZP_07397644.1| DNA-directed RNA polymerase sigma subunit SigA [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
 gi|304369325|gb|EFM22998.1| DNA-directed RNA polymerase sigma subunit SigA [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
          Length = 381

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 78/275 (28%), Positives = 135/275 (49%), Gaps = 13/275 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI ++P+L  +EE  LA+R  E GD +A HRL  ++LRLVV IA  Y G G
Sbjct: 108 DDPVRMYLKEIGRVPLLTAEEEVDLARRM-EAGDETARHRLEEANLRLVVSIAKRYVGRG 166

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I     +
Sbjct: 167 MMFLDLIQEGNLGLLKAVEKFDYSKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 226

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                   R+   L      +  PE    IA ++ +S + V  +        SL   I  
Sbjct: 227 --TINKYIRVSRQLLQELGRDPTPE---EIAHRMGLSVARVREIMKISQEPVSLETPI-- 279

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QE 250
            ++  +   D++            +       +  ++  ++ L PRE  +   R      
Sbjct: 280 GEEEDTHLSDFIED---EAAPDPADAASMLLLKEQISEVLTTLAPREAEVLRLRFGLVDG 336

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              TLE +   F V+RER+RQIEA+A +K++  ++
Sbjct: 337 RSRTLEEVGQNFGVTRERIRQIEAKALRKLRHPVR 371


>gi|291543225|emb|CBL16334.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Ruminococcus sp. 18P13]
          Length = 360

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 82/288 (28%), Positives = 140/288 (48%), Gaps = 16/288 (5%)

Query: 5   NMSIIVNG---EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
            M++   G   +  +  Y+ EI ++P+L  +EE  LA+R  + GD  A  RL  ++LRLV
Sbjct: 77  EMALSTEGIAIDDPVKIYLKEIGRVPLLSAEEEIELAQRMSK-GDSYAKKRLSEANLRLV 135

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA  Y G G+   +++ EGN+GL++AV KFD  +GF+ +TY+ WWI+ A+   I    
Sbjct: 136 VSIAKKYVGRGMQFLDLIQEGNLGLIKAVDKFDYTKGFKFSTYATWWIRQAITRAIADQA 195

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             ++I     +      + ++K  +  +            IA++L +   +V  +     
Sbjct: 196 RTIRIPVHMVE-----TITKVKKIISQLLHETGHEPTADEIAERLEMPVEKVREIMRIAQ 250

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              SL   I   ++  S   D++            E       +  L   +S L  RE +
Sbjct: 251 DPVSLETPI--GEEEDSHLGDFIPD---DDAPAPAEAASLILLKEQLNEVLSTLTEREAK 305

Query: 242 IFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           + + R   E+    TLE +  EFEV+RER+RQIEA+A +K++   + +
Sbjct: 306 VLKLRFGLEDGRSRTLEEVGREFEVTRERIRQIEAKALRKLRHPSRSK 353


>gi|293391201|ref|ZP_06635535.1| alternative sigma factor RpoH [Aggregatibacter
           actinomycetemcomitans D7S-1]
 gi|290951735|gb|EFE01854.1| alternative sigma factor RpoH [Aggregatibacter
           actinomycetemcomitans D7S-1]
          Length = 282

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 103/285 (36%), Positives = 170/285 (59%), Gaps = 6/285 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+++  ++++  +  +  YI    + PML  +EE  LA+R     D+ AA +LV SHLR 
Sbjct: 1   MDKETQTMMLVPQGSIEAYIRAANEYPMLTAEEEKELAERLYYKEDIEAAKKLVLSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L    +N     +V  +A +L VS  +V+ M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNEN-----EVDMVANELGVSPQDVMEMESRM 175

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            G D + +   +  D+ +     +L          L  +       + L  ++  L+ R 
Sbjct: 176 TGADVAFDLPGDEHDEETYAPALYLEDKSSNFAAELENENYEAQATDQLAVALDNLDARS 235

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + I +AR L E   TL++L++++ +S ERVRQ+EA A KK++ ++
Sbjct: 236 QDIIKARWLDETKATLQDLAAKYNISAERVRQLEANALKKLKSAV 280


>gi|254519856|ref|ZP_05131912.1| transcription initiation factor sigma A [Clostridium sp. 7_2_43FAA]
 gi|226913605|gb|EEH98806.1| transcription initiation factor sigma A [Clostridium sp. 7_2_43FAA]
          Length = 370

 Score =  260 bits (664), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 82/277 (29%), Positives = 136/277 (49%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI K+P+L  +EE  LA R  E GD  A  +L  ++LRLVV IA  Y G G
Sbjct: 98  DDPVRMYLKEIGKVPLLSSEEEIELANRI-EQGDQRAKKKLAEANLRLVVSIAKRYVGRG 156

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     +
Sbjct: 157 MLFLDLIQEGNLGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 216

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 L R++  L      +  PE    I+K +++   +V  +        SL   I  
Sbjct: 217 --TINKLIRVQRQLLQELGRDPFPE---EISKVMDLPVDKVREIQKIAQEPVSLETPI-- 269

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            ++  S   D++            E       +  L   +  L PRE ++   R   ++ 
Sbjct: 270 GEEEDSHLGDFIPD---DDALAPAEAAAFTMLKEQLINVLDTLTPREEKVLRLRFGLDDG 326

Query: 253 --VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 327 RARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 363


>gi|260774824|ref|ZP_05883726.1| RNA polymerase sigma factor [Vibrio coralliilyticus ATCC BAA-450]
 gi|260609249|gb|EEX35404.1| RNA polymerase sigma factor [Vibrio coralliilyticus ATCC BAA-450]
          Length = 285

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 110/287 (38%), Positives = 169/287 (58%), Gaps = 8/287 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  +   + V  +  L  YI  +   PML  +EE  LA+R   +G++ AA  L+ SHLR 
Sbjct: 1   MTNQAYPMAVVTQDSLDSYIRTVNGYPMLTAEEERGLAERLHYNGEIEAAKGLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A GY GYGLP++++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VKI TT  Q++LFFNLR+ K  L    +      +V  +A++L V  SEV  M  RL
Sbjct: 121 WRIVKIATTKAQRKLFFNLRKSKKRLGWFNNG-----EVETVARELGVEPSEVREMESRL 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE---ERKNRRNMLTRSMSVLNP 237
           A  ++   + N  D +   +   ++Y  D    V    E      +  N L+ ++S L+ 
Sbjct: 176 AAQDAAFEMQNDDDDSGVSYTAPMLYLEDKASDVADNVEAANWEAHTNNRLSLALSSLDE 235

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R + I  +R L++N  TL+ L+  + VS ER+RQ+E  A KK++ ++
Sbjct: 236 RSQHIVRSRWLEDNKSTLQELAETYSVSAERIRQLEKNAMKKLKAAV 282


>gi|86739990|ref|YP_480390.1| sigma 38 [Frankia sp. CcI3]
 gi|86566852|gb|ABD10661.1| RNA polymerase, sigma 70 subunit, RpoD [Frankia sp. CcI3]
          Length = 409

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 83/307 (27%), Positives = 141/307 (45%), Gaps = 39/307 (12%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------------REHGDLSA- 49
                 +  Y+ EI K+P+L  +EE  LAKR                    +   DL A 
Sbjct: 106 APTSDPVRMYLKEIGKVPLLTAEEEVDLAKRIEAGLFASEKLAVATKKTSPQMRRDLEAI 165

Query: 50  -------AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
                    +LV ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +
Sbjct: 166 ERDGQIAKRKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFS 225

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I     +      L R++  L         PE    I
Sbjct: 226 TYATWWIRQAITRAIADQARTIRIPVHMVE--TINKLIRIQRQLLQDLGREPSPE---EI 280

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           AK+++++  +V  +        SL   I   ++  S   D++    D    V ++     
Sbjct: 281 AKEMDLTPDKVREILKVSQEPVSLETPI--GEEEDSHLGDFI---EDCDAVVPVDAASFI 335

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             +  L   +  L+ RE+++ + R      +P TLE +  EF V+RER+RQIE++   K+
Sbjct: 336 LLQEQLDSVLHTLSDREKKVIQLRFGLTDGHPRTLEEVGREFGVTRERIRQIESKTLSKL 395

Query: 281 QESIQKQ 287
           +   + Q
Sbjct: 396 RHPSRSQ 402


>gi|329123705|ref|ZP_08252265.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Haemophilus
           aegyptius ATCC 11116]
 gi|327469904|gb|EGF15369.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Haemophilus
           aegyptius ATCC 11116]
          Length = 281

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 105/285 (36%), Positives = 170/285 (59%), Gaps = 7/285 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+++   ++V  +  +  YI    + PML  +EE  LA+R   H DL AA +L+ SHLR 
Sbjct: 1   MDKETQMMLVP-QGSIEGYIRAANEYPMLTAEEEKELAERLYYHEDLDAAKKLILSHLRF 59

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A GY GYGLP ++++ EGNIGLM+AVK+F+PE G RLA++++ WIKA + EY+LR+
Sbjct: 60  VIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLASFAVHWIKAEIHEYVLRN 119

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L    +N     +V  +A +L VS+ +VI M  R+
Sbjct: 120 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNEN-----EVDMVANELGVSKEDVIEMESRM 174

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D   +   + ++  +     +L          L  +         L  ++  L+ R 
Sbjct: 175 SGADVGFDLPTDDAETETYSPALYLEDKSSNFAAELENENFESQATEQLGAALQSLDARS 234

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + I +AR L +N  TL +L++++ VS ER+RQ+E  A KK++ ++
Sbjct: 235 QDIIKARWLDDNKATLHDLAAKYNVSAERIRQLETNALKKLKSAV 279


>gi|325686025|gb|EGD28083.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           delbrueckii subsp. lactis DSM 20072]
          Length = 373

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 79/275 (28%), Positives = 134/275 (48%), Gaps = 13/275 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             + +Y+  I ++ +L   EE  LAKR  E GD  A   L +++LRLVV IA  Y G G+
Sbjct: 102 DPVRQYLKRIGRVSLLSGDEEVQLAKRI-EAGDQEAKDELTSANLRLVVSIAKRYVGRGM 160

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD + GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 161 SFLDLIQEGNMGLMKAVGKFDYQLGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 219

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L      + +PE    IA ++++   +V  +        SL   I   
Sbjct: 220 -TINKLIRIQRQLLQDLGRDPEPE---EIAAEMDLPVKKVREVLKVAQEPVSLETPI--G 273

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-- 251
           +++ S   D++    D       +    +  ++ L   +  L   E  +   R   ++  
Sbjct: 274 EEDDSHLGDFI---EDKDATSPEQHAASEMLKDQLAEVLDTLTDSEENVLRLRFGLDDGN 330

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           P TLE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 331 PRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRS 365


>gi|158313963|ref|YP_001506471.1| RpoD family RNA polymerase sigma factor [Frankia sp. EAN1pec]
 gi|158109368|gb|ABW11565.1| RNA polymerase, sigma 70 subunit, RpoD family [Frankia sp. EAN1pec]
          Length = 409

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 83/307 (27%), Positives = 141/307 (45%), Gaps = 39/307 (12%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------------REHGDLSA- 49
                 +  Y+ EI K+P+L  +EE  LAKR                    +   DL A 
Sbjct: 106 APTSDPVRMYLKEIGKVPLLTAEEEVDLAKRIEAGLFASEKLAVATKKTSPQMRRDLEAI 165

Query: 50  -------AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
                    +LV ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +
Sbjct: 166 ERDGQIAKRKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFS 225

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I     +      L R++  L         PE    I
Sbjct: 226 TYATWWIRQAITRAIADQARTIRIPVHMVE--TINKLIRIQRQLLQDLGREPSPE---EI 280

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           AK+++++  +V  +        SL   I   ++  S   D++    D    V ++     
Sbjct: 281 AKEMDLTPDKVREILKVSQEPVSLETPI--GEEEDSHLGDFI---EDCDAVVPVDAASFI 335

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             +  L   +  L+ RE+++ + R      +P TLE +  EF V+RER+RQIE++   K+
Sbjct: 336 LLQEQLDSVLHTLSDREKKVIQLRFGLTDGHPRTLEEVGREFGVTRERIRQIESKTLSKL 395

Query: 281 QESIQKQ 287
           +   + Q
Sbjct: 396 RHPSRSQ 402


>gi|42520871|ref|NP_966786.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Drosophila
           melanogaster]
 gi|42410611|gb|AAS14720.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Drosophila
           melanogaster]
          Length = 297

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 127/289 (43%), Positives = 196/289 (67%), Gaps = 2/289 (0%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M     ++ V+    L +YI  ++K PML ++EE  LAK + ++ D+S+AH+L+TSHL L
Sbjct: 1   MLTSMANLCVDSRTNLMQYIARVQKFPMLSQEEEVRLAKNWNQYKDVSSAHKLITSHLNL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VVKIAM ++ YGL + ++V EGN+GLM AVKKF+P+ GFR +TY++WWI+A+++++IL+S
Sbjct: 61  VVKIAMKFKNYGLLLMDLVMEGNMGLMHAVKKFNPDLGFRFSTYAVWWIEASIKDFILKS 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN-LKPEQVVAIAKKLNVSESEVISMNCR 179
           WS VKIGTT  Q+RLFF+LR++K  +   T+   L  E++ AI+ +L+VSE +V+ MN R
Sbjct: 121 WSFVKIGTTQAQRRLFFSLRKIKKRILQYTNRETLNNEEIKAISNELSVSEGDVLQMNYR 180

Query: 180 LA-GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           +A  D+SLN  I   D +  + QD +  +   QE      EE++ +  +L  +++ LN R
Sbjct: 181 MACKDQSLNDCIKIGDDSKRELQDMIPCNLVSQEVTYQNHEEKELKETILNNALASLNER 240

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R IF +R L EN  TL+ LS ++ VSRER+RQ+  +A  KV++ IQ +
Sbjct: 241 ARDIFISRYLSENIQTLDELSKKYCVSRERIRQLAEQAMAKVKQYIQSE 289


>gi|261250002|ref|ZP_05942579.1| RNA polymerase sigma factor RpoH [Vibrio orientalis CIP 102891]
 gi|260939506|gb|EEX95491.1| RNA polymerase sigma factor RpoH [Vibrio orientalis CIP 102891]
          Length = 285

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 108/287 (37%), Positives = 164/287 (57%), Gaps = 8/287 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  +   +    +  L  YI      PML  +EE  LA+R    G++ AA  L+ SHLR 
Sbjct: 1   MTSQAYPMAAVTQDSLDSYIRSANSYPMLTPEEERDLAERLHYDGEIEAAKGLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A GY GYGLP++++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VKI TT  Q++LFFNLR+ K  L    +      +V  +A++L V  SEV  M  RL
Sbjct: 121 WRIVKIATTKAQRKLFFNLRKSKKRLGWFNNG-----EVETVARELGVEPSEVREMESRL 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE---ERKNRRNMLTRSMSVLNP 237
           A  ++   +    D+  + +   +VY  D    V    E      +  N L+ ++  L+ 
Sbjct: 176 AAQDATFEMPTDDDETGTSYTAPMVYLEDKASDVADHVEASNWEAHTNNRLSLALKSLDD 235

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R + I  +R L +N  TL+ L+  + VS ER+RQ+E  A KK++ ++
Sbjct: 236 RSQHIVRSRWLDDNKSTLQELAETYSVSAERIRQLEKNAMKKLKAAV 282


>gi|237809745|ref|YP_002894185.1| RNA polymerase, sigma 32 subunit, RpoH [Tolumonas auensis DSM 9187]
 gi|237502006|gb|ACQ94599.1| RNA polymerase, sigma 32 subunit, RpoH [Tolumonas auensis DSM 9187]
          Length = 284

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 107/286 (37%), Positives = 168/286 (58%), Gaps = 9/286 (3%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           ++N+ ++  G   L  YI  +  IPML  ++E  LA++ +  GDL AA +LV SHLR VV
Sbjct: 6   QRNLVLVPQG--SLEGYIQAVNSIPMLTAEKERALAEQLQNDGDLEAARQLVMSHLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA  Y GYGLP ++++ EGNIGLM+AVK+FDP  G RL ++++ WIKA + EY+LR+W 
Sbjct: 64  HIARTYSGYGLPQADLIQEGNIGLMKAVKRFDPTVGVRLVSFAVHWIKAEIHEYVLRNWR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L          ++V A+A++L VS  +V  M  R++G
Sbjct: 124 MVKVATTKAQRKLFFNLRKTKKRLGWFNQ-----DEVRAVAEELGVSPEDVTEMESRMSG 178

Query: 183 -DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
            D S +   +   +++     +L         V        +  + L  ++  L+ R ++
Sbjct: 179 LDHSFDGYDDDDSESNFAPAQYLEDKSSDLATVYENNNWDTHAEHRLAYALQGLDERSQQ 238

Query: 242 IFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           I  AR L E+   TL+ L+  + VS ERVRQ+E  A KK+++ ++ 
Sbjct: 239 IVRARWLDEDNKQTLQELADRYGVSAERVRQLEKNALKKLKDVLEA 284


>gi|311898773|dbj|BAJ31181.1| putative RNA polymerase major sigma factor [Kitasatospora setae
           KM-6054]
          Length = 541

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 75/314 (23%), Positives = 143/314 (45%), Gaps = 40/314 (12%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------- 41
           + +++       +  Y+ +I K+P+L  ++E  LAKR                       
Sbjct: 233 QQVAVAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLSQADKLAPKLKR 292

Query: 42  -----REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                 E G   A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  
Sbjct: 293 ELEIIAEDG-RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYT 351

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  +         P
Sbjct: 352 KGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTP 409

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           E    +AK+L+++  +VI +        SL+  +   +   S++ D +    D +  V  
Sbjct: 410 E---ELAKELDMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPA 461

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEA 274
           +       +  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE+
Sbjct: 462 DAVSFTLLQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIES 521

Query: 275 RAFKKVQESIQKQV 288
           +   K++   + QV
Sbjct: 522 KTMSKLRHPSRSQV 535


>gi|150390747|ref|YP_001320796.1| RpoD family RNA polymerase sigma factor [Alkaliphilus
           metalliredigens QYMF]
 gi|149950609|gb|ABR49137.1| RNA polymerase, sigma 70 subunit, RpoD family [Alkaliphilus
           metalliredigens QYMF]
          Length = 372

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 87/285 (30%), Positives = 142/285 (49%), Gaps = 13/285 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           NM   V  +  +  Y+ EI K+P+L   EE  LA R  E GD  A  +LV ++LRLVV I
Sbjct: 92  NMLKGVIIDDPVRMYLKEIGKVPLLTGPEEIDLATRM-EAGDELAKKKLVEANLRLVVSI 150

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      +
Sbjct: 151 AKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTI 210

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I     +      L R+   L        KPE    IAK++++ E +V  +        
Sbjct: 211 RIPVHMVE--TINKLIRVSRQLLQEFGREPKPE---EIAKEMDLPEEKVREILKIAQEPV 265

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   I   ++  S   D++            E       +  L   +  L PRE+++  
Sbjct: 266 SLETPI--GEEEDSHLGDFIPD---DDAPAPAEAAAFSLLKEQLIEVLDTLTPREQKVLR 320

Query: 245 ARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R   ++    TLE +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 321 LRFGLDDGRARTLEEVGKKFDVTRERIRQIEAKALRKLRHPSRSK 365


>gi|145631055|ref|ZP_01786830.1| RNA polymerase factor sigma-32 [Haemophilus influenzae R3021]
 gi|148827424|ref|YP_001292177.1| RNA polymerase factor sigma-32 [Haemophilus influenzae PittGG]
 gi|144983340|gb|EDJ90822.1| RNA polymerase factor sigma-32 [Haemophilus influenzae R3021]
 gi|148718666|gb|ABQ99793.1| RNA polymerase sigma factor [Haemophilus influenzae PittGG]
 gi|301168923|emb|CBW28517.1| RNA polymerase, sigma 32 (sigma H) factor [Haemophilus influenzae
           10810]
          Length = 281

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 104/285 (36%), Positives = 170/285 (59%), Gaps = 7/285 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+++   ++V  +  +  YI    + PML  +EE  LA+R   H DL AA +L+ SHLR 
Sbjct: 1   MDKETQMMLVP-QGSIEGYIRAANEYPMLTAEEEKELAERLYYHEDLDAAKKLILSHLRF 59

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 60  VIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 119

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L    +N     +V  +A +L VS+ +VI M  R+
Sbjct: 120 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNEN-----EVDMVANELGVSKEDVIEMESRM 174

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D   +   + ++  +     +L          L  +         L+ ++  L+ R 
Sbjct: 175 SGADVGFDLPTDDAETETYSPALYLEDKSSNFAAELENENFESQATEQLSAALQSLDARS 234

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + I +AR L +N  TL +L++++ VS ER+RQ+E  A KK++ ++
Sbjct: 235 QDIIKARWLDDNKATLHDLAAKYNVSAERIRQLETNALKKLKSAV 279


>gi|16272227|ref|NP_438438.1| RNA polymerase factor sigma-32 [Haemophilus influenzae Rd KW20]
 gi|68248876|ref|YP_247988.1| RNA polymerase factor sigma-32 [Haemophilus influenzae 86-028NP]
 gi|260580848|ref|ZP_05848673.1| alternative sigma factor RpoH [Haemophilus influenzae RdAW]
 gi|319896604|ref|YP_004134797.1| RNA polymerase sigma-32 factor [Haemophilus influenzae F3031]
 gi|1173123|sp|P44404|RP32_HAEIN RecName: Full=RNA polymerase sigma-32 factor
 gi|1573235|gb|AAC21935.1| RNA polymerase sigma-32 factor (rpoH) [Haemophilus influenzae Rd
           KW20]
 gi|68057075|gb|AAX87328.1| RNA polymerase sigma-32 factor [Haemophilus influenzae 86-028NP]
 gi|260092471|gb|EEW76409.1| alternative sigma factor RpoH [Haemophilus influenzae RdAW]
 gi|317432106|emb|CBY80457.1| RNA polymerase sigma-32 factor [Haemophilus influenzae F3031]
          Length = 281

 Score =  259 bits (663), Expect = 3e-67,   Method: Composition-based stats.
 Identities = 104/285 (36%), Positives = 169/285 (59%), Gaps = 7/285 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+++   ++V  +  +  YI    + PML  +EE  LA+R   H DL AA +L+ SHLR 
Sbjct: 1   MDKETQMMLVP-QGSIEGYIRAANEYPMLTAEEEKELAERLYYHEDLDAAKKLILSHLRF 59

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 60  VIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 119

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L    +N     +V  +A +L VS+ +VI M  R+
Sbjct: 120 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNEN-----EVDMVANELGVSKEDVIEMESRM 174

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D   +   + ++  +     +L          L  +         L  ++  L+ R 
Sbjct: 175 SGADVGFDLPTDDAETETYSPALYLEDKSSNFAAELENENFESQATEQLGAALQSLDARS 234

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + I +AR L +N  TL +L++++ VS ER+RQ+E  A KK++ ++
Sbjct: 235 QDIIKARWLDDNKATLHDLAAKYNVSAERIRQLETNALKKLKSAV 279


>gi|315647917|ref|ZP_07901018.1| RNA polymerase, sigma 70 subunit, RpoD subfamily protein
           [Paenibacillus vortex V453]
 gi|315276563|gb|EFU39906.1| RNA polymerase, sigma 70 subunit, RpoD subfamily protein
           [Paenibacillus vortex V453]
          Length = 316

 Score =  259 bits (662), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 80/285 (28%), Positives = 137/285 (48%), Gaps = 13/285 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           ++   +     +  Y+ EI ++P+L   EE  L+KR  E GD  A  RL  ++LRLVV I
Sbjct: 36  SLPPGIKISDPVRMYLKEIGRVPLLSADEEVELSKRI-EEGDEEAKRRLAEANLRLVVSI 94

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      +
Sbjct: 95  ARRYAGRGMQFLDLIQEGNMGLIKAVEKFDYSKGFKFSTYATWWIRQAITRSIADQARTI 154

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I     +      L R+   L         PE    I K+++++  +V  +        
Sbjct: 155 RIPVHMVE--TINKLVRVSRQLLQELGREPTPE---EIGKEMDITPEKVREIQKVSQEPV 209

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   +   +++ S   D++    D       +    +  +  L   +  L  RE  +  
Sbjct: 210 SLETPV--GEESDSNLGDFI---EDQDALAPADAAAFELLKEQLEEVLDTLTEREENVLR 264

Query: 245 ARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R   E+    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 265 LRFGLEDGRTRTLEEVGQVFGVTRERIRQIEAKALRKLRHPSRSK 309


>gi|295695448|ref|YP_003588686.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacillus tusciae
           DSM 2912]
 gi|295411050|gb|ADG05542.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacillus tusciae
           DSM 2912]
          Length = 379

 Score =  259 bits (662), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 80/276 (28%), Positives = 136/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++P+L  +EE  LAKR  E GD  A   L+ ++LRLVV IA  Y G G+
Sbjct: 108 DPVRMYLKEIGRVPLLSAEEEIELAKRI-EQGDEEAKAALIKANLRLVVSIAKRYVGRGM 166

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 167 LFLDLIQEGNLGLIKAVEKFDFRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 225

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R+   L      +  PE    IA+++++S  +V  +        SL   I   
Sbjct: 226 -TINKLIRVSRQLLQELGRDPTPE---EIAEEMDMSPDKVREIMKIAQEPVSLETPI--G 279

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++            +    +  +  L   +  L  RE  +   R   ++  
Sbjct: 280 EEDDSHLGDFIPD---DDALAPADAAAYELLKEQLEDVLDTLTEREENVLRLRFGLDDGR 336

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 337 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 372


>gi|261407775|ref|YP_003244016.1| RpoD subfamily RNA polymerase sigma-70 factor [Paenibacillus sp.
           Y412MC10]
 gi|329927238|ref|ZP_08281536.1| RNA polymerase sigma factor RpoD [Paenibacillus sp. HGF5]
 gi|261284238|gb|ACX66209.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Paenibacillus sp.
           Y412MC10]
 gi|328938638|gb|EGG35021.1| RNA polymerase sigma factor RpoD [Paenibacillus sp. HGF5]
          Length = 316

 Score =  259 bits (662), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 81/285 (28%), Positives = 137/285 (48%), Gaps = 13/285 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           ++   +     +  Y+ EI ++P+L   EE  L+KR  E GD  A  RL  ++LRLVV I
Sbjct: 36  SLPPGIKISDPVRMYLKEIGRVPLLSADEEVELSKRI-EEGDEEAKRRLAEANLRLVVSI 94

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      +
Sbjct: 95  ARRYAGRGMQFLDLIQEGNMGLIKAVEKFDYSKGFKFSTYATWWIRQAITRSIADQARTI 154

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I     +      L R+   L         PE    I K++++S  +V  +        
Sbjct: 155 RIPVHMVE--TINKLVRVSRQLLQELGREPTPE---EIGKEMDISPEKVREIQKVSQEPV 209

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   +   +++ S   D++    D       +    +  +  L   +  L  RE  +  
Sbjct: 210 SLETPV--GEESDSNLGDFI---EDQDALAPADAAAFELLKEQLEEVLDTLTEREENVLR 264

Query: 245 ARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R   E+    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 265 LRFGLEDGRTRTLEEVGQVFGVTRERIRQIEAKALRKLRHPSRSK 309


>gi|145639818|ref|ZP_01795419.1| RNA polymerase sigma factor [Haemophilus influenzae PittII]
 gi|145271036|gb|EDK10952.1| RNA polymerase sigma factor [Haemophilus influenzae PittII]
 gi|309750314|gb|ADO80298.1| RNA polymerase sigma-32 factor [Haemophilus influenzae R2866]
          Length = 281

 Score =  259 bits (662), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 104/285 (36%), Positives = 170/285 (59%), Gaps = 7/285 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+++   ++V  +  +  YI    + PML  +EE  LA+R   H DL AA +L+ SHLR 
Sbjct: 1   MDKETQMMLVP-QGSIEGYIRAANEYPMLTAEEEKELAERLYYHEDLDAAKKLILSHLRF 59

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 60  VIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 119

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L    +N     +V  +A +L VS+ +VI M  R+
Sbjct: 120 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNEN-----EVDMVANELGVSKEDVIEMESRM 174

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D   +   + ++  +     +L          L  +         L+ ++  L+ R 
Sbjct: 175 SGADVGFDLPTDDAETETYSPSLYLEDKSSNFAAELENENFESQATEQLSAALQSLDARS 234

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + I +AR L +N  TL +L++++ VS ER+RQ+E  A KK++ ++
Sbjct: 235 QDIIKARWLDDNKATLHDLAAKYNVSAERIRQLETNALKKLKSAV 279


>gi|261866928|ref|YP_003254850.1| RNA polymerase factor sigma-32 [Aggregatibacter
           actinomycetemcomitans D11S-1]
 gi|261412260|gb|ACX81631.1| alternative sigma factor RpoH [Aggregatibacter
           actinomycetemcomitans D11S-1]
          Length = 282

 Score =  259 bits (662), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 102/285 (35%), Positives = 169/285 (59%), Gaps = 6/285 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+++  ++++  +  +  YI    + PML  +EE  LA+R     D+ AA +LV SHLR 
Sbjct: 1   MDKETQTMMLVPQGSIEAYIRAANEYPMLTAEEEKELAERLYYKEDIEAAKKLVLSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L    +N     +V  +A +L VS  +V+ M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNEN-----EVDMVANELGVSPQDVMEMESRM 175

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            G D + +   +  D+ +     +L          L  +       + L  ++  L+ R 
Sbjct: 176 TGADVAFDLPGDEHDEETYAPALYLEDKSSNFAAELENENYEAQATDQLAVALDNLDARS 235

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + I +AR L E   TL++L++++ +S ERVRQ+E  A KK++ ++
Sbjct: 236 QDIIKARWLDETKATLQDLAAKYNISAERVRQLETNALKKLKSAV 280


>gi|319775860|ref|YP_004138348.1| RNA polymerase sigma-32 factor [Haemophilus influenzae F3047]
 gi|317450451|emb|CBY86667.1| RNA polymerase sigma-32 factor [Haemophilus influenzae F3047]
          Length = 281

 Score =  259 bits (662), Expect = 4e-67,   Method: Composition-based stats.
 Identities = 105/285 (36%), Positives = 170/285 (59%), Gaps = 7/285 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+++   ++V  +  +  YI    + PML  +EE  LA+R   H DL AA +L+ SHLR 
Sbjct: 1   MDKETQMMLVP-QGSIEGYIRAANEYPMLTAEEEKELAERLYYHEDLDAAKKLILSHLRF 59

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A GY GYGLP ++++ EGNIGLM+AVK+F+PE G RLA++++ WIKA + EY+LR+
Sbjct: 60  VIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLASFAVHWIKAEIHEYVLRN 119

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L    +N     +V  +A +L VS+ +VI M  R+
Sbjct: 120 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNEN-----EVDMVANELGVSKEDVIEMESRM 174

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D   +   + ++  +     +L          L  +         L  ++  L+ R 
Sbjct: 175 SGADVGFDLPTDDAETETYSPALYLEDKSSNFAAELENENFESQATEQLGVALQSLDARS 234

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + I +AR L +N  TL +L++++ VS ER+RQ+E  A KK++ ++
Sbjct: 235 QDIIKARWLDDNKATLHDLAAKYNVSAERIRQLETNALKKLKSAV 279


>gi|52786447|ref|YP_092276.1| RNA polymerase sigma factor RpoD [Bacillus licheniformis ATCC
           14580]
 gi|163119552|ref|YP_079858.2| RNA polymerase sigma factor RpoD [Bacillus licheniformis ATCC
           14580]
 gi|319644974|ref|ZP_07999207.1| RNA polymerase sigma factor rpoD [Bacillus sp. BT1B_CT2]
 gi|52348949|gb|AAU41583.1| SigA [Bacillus licheniformis ATCC 14580]
 gi|145903060|gb|AAU24220.2| RNA polymerase major sigma-43 factor (sigma-A) [Bacillus
           licheniformis ATCC 14580]
 gi|317392783|gb|EFV73577.1| RNA polymerase sigma factor rpoD [Bacillus sp. BT1B_CT2]
          Length = 373

 Score =  258 bits (661), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 79/289 (27%), Positives = 140/289 (48%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++ +L  +EE   AK+  E GD  +  RL  ++LRL
Sbjct: 89  LNDLSVPPGVKINDPVRMYLKEIGRVNLLSAKEEIEYAKKI-EEGDEESKRRLAEANLRL 147

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GLM+AV+KFD  +G++ +TY+ WWI+ A+   I   
Sbjct: 148 VVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQ 207

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    IA+ ++++  +V  +    
Sbjct: 208 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPTPE---EIAEDMDLTPEKVREILKIA 262

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D +     +    +  +  L   +  L  RE 
Sbjct: 263 QEPVSLETPI--GEEDDSHLGDFI---EDQEATSPSDHAAYELLKEQLEDVLDTLTDREE 317

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 318 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 366


>gi|46579995|ref|YP_010803.1| sigma 70 family protein [Desulfovibrio vulgaris str. Hildenborough]
 gi|120602593|ref|YP_966993.1| sigma-70 region 2 domain-containing protein [Desulfovibrio vulgaris
           DP4]
 gi|46449411|gb|AAS96062.1| sigma 70 family protein [Desulfovibrio vulgaris str. Hildenborough]
 gi|120562822|gb|ABM28566.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfovibrio vulgaris DP4]
 gi|311234006|gb|ADP86860.1| RNA polymerase sigma factor, sigma-70 family [Desulfovibrio
           vulgaris RCH1]
          Length = 356

 Score =  258 bits (661), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 112/289 (38%), Positives = 177/289 (61%), Gaps = 7/289 (2%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           + +  G+  L  Y+ EI + PML+ +EEY LAKR RE GD  AA RLV+SHLRLVVKIAM
Sbjct: 68  ATVSTGKDSLHLYLREISRFPMLKPEEEYELAKRVRETGDGDAAFRLVSSHLRLVVKIAM 127

Query: 67  GYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            ++   +  + +++ EGN+GLM+AV KFDPE+G + + Y+ +WIKA + ++I+ +W +VK
Sbjct: 128 DFQRRWMQNVLDLIQEGNVGLMRAVNKFDPEKGIKFSYYAAFWIKAYILKFIMDNWRMVK 187

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDE 184
           IGTT  Q++LF+NL + +  L               ++++LNV++ +V+ M  RL A D 
Sbjct: 188 IGTTQAQRKLFYNLNKERQKLIL----QGYDPDAATLSERLNVTKEQVVEMEQRLDASDV 243

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL+  +      +S+  D+L     G E  L   E     +N L   +  L+ +E  I +
Sbjct: 244 SLDIPVGDEGGGASR-MDFLPALGPGIEDALSNHEIASMVQNRLQSIIPKLSDKEVDILQ 302

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
            R L E PVTL  +  +++++RERVRQIEAR  +K+++ + K+++  SS
Sbjct: 303 NRLLSEEPVTLREIGEKYDITRERVRQIEARLLQKIRDHLFKEIKDFSS 351


>gi|260582846|ref|ZP_05850631.1| alternative sigma factor RpoH [Haemophilus influenzae NT127]
 gi|260094059|gb|EEW77962.1| alternative sigma factor RpoH [Haemophilus influenzae NT127]
          Length = 281

 Score =  258 bits (661), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 104/285 (36%), Positives = 169/285 (59%), Gaps = 7/285 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+++   ++V  +  +  YI    + PML  +EE  LA+R   H DL AA +L+ SHLR 
Sbjct: 1   MDKETQMMLVP-QGSIEGYIRAANEYPMLTAEEEKELAERLYYHEDLDAAKKLILSHLRF 59

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 60  VIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 119

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L    +N     +V  +A +L VS+ +VI M  R+
Sbjct: 120 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNEN-----EVDMVANELGVSKEDVIEMESRM 174

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D   +   + ++  +     +L          L  +         L  ++  L+ R 
Sbjct: 175 SGADVGFDLPTDDAETETYSPSLYLEDKSSNFAAELENENFESQATEQLGVALQSLDARS 234

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + I +AR L +N  TL +L++++ VS ER+RQ+E  A KK++ ++
Sbjct: 235 QDIIKARWLDDNKATLHDLAAKYNVSAERIRQLETNALKKLKSAV 279


>gi|227113845|ref|ZP_03827501.1| RNA polymerase factor sigma-32 [Pectobacterium carotovorum subsp.
           brasiliensis PBR1692]
          Length = 285

 Score =  258 bits (661), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 102/290 (35%), Positives = 162/290 (55%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M +   +  +  +  L  YI      PML  +EE  LA+R    GDL AA  L+ SHLR 
Sbjct: 1   MTKDMQTFTLVPQGSLEGYIRAANAYPMLTAEEERALAERLHYQGDLEAAKHLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VIHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKSKTRLGWFNQ-----DEVELVARELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNP 237
           A  +         D +  +    ++Y  D        + E     +  + LT ++  L+ 
Sbjct: 176 AAQDMTFDPTPEEDSHDGKAMSPMLYLQDKSSDFADGIEEDNWETHAADKLTYALEGLDE 235

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L ++   TL+ L+ ++ VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQHIIRARWLDDDNKSTLQELADQYGVSAERVRQLEKNAMKKLRAAIEA 285


>gi|222097738|ref|YP_002531795.1| RNA polymerase sigma factor rpod [Bacillus cereus Q1]
 gi|221241796|gb|ACM14506.1| RNA polymerase sigma-43 factor [Bacillus cereus Q1]
          Length = 375

 Score =  258 bits (661), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 79/289 (27%), Positives = 139/289 (48%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRL
Sbjct: 91  LNDLSVPPGVKINDPVRMYLKEIGRVDLLSAEEEIRLATRI-EEGDEEAKRRLAEANLRL 149

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++A +KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 150 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAGEKFDYRKGFKFSTYATWWIRQAITRAIADQ 209

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    I ++++++  +V  +    
Sbjct: 210 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPSPE---EIGEEMDLAPEKVREILKIA 264

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D +     +    +  +  L   +  L  RE 
Sbjct: 265 QEPVSLETPI--GEEDDSHLGDFI---EDQEATSPADHAAYELLKEQLEDVLDTLTDREE 319

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 320 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 368


>gi|227329284|ref|ZP_03833308.1| RNA polymerase factor sigma-32 [Pectobacterium carotovorum subsp.
           carotovorum WPP14]
          Length = 285

 Score =  258 bits (661), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 102/290 (35%), Positives = 162/290 (55%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M +   +  +  +  L  YI      PML  +EE  LA+R    GDL AA  L+ SHLR 
Sbjct: 1   MTKDMQTFTLVPQGSLEGYIRAANAYPMLTAEEERALAERLHYQGDLDAAKHLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VIHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKSKTRLGWFNQ-----DEVELVARELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNP 237
           A  +         D +  +    ++Y  D        + E     +  + LT ++  L+ 
Sbjct: 176 AAQDMTFDPTPEEDSHDGKAMSPMLYLQDKSSDFADGIEEDNWETHAADKLTYALEGLDE 235

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L ++   TL+ L+ ++ VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQHIIRARWLDDDNKSTLQELADKYGVSAERVRQLEKNAMKKLRAAIEA 285


>gi|323484891|ref|ZP_08090246.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323693741|ref|ZP_08107938.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
 gi|323401772|gb|EGA94115.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323502192|gb|EGB18057.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
          Length = 374

 Score =  258 bits (661), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 81/280 (28%), Positives = 143/280 (51%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           +  E  +  Y+ EI  +P+L   EE  LAKR +  GD +A  RL+ ++LRLVV IA  Y 
Sbjct: 100 IGTEDPVRMYLKEIGTVPLLSADEELRLAKR-KAEGDDNAKERLIEANLRLVVSIAKRYT 158

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   ++V EGN+GL++ V+KFD  +G++L+TY+ WWI+ ++   +      +++   
Sbjct: 159 GRGMSFLDLVQEGNLGLIKGVEKFDYTKGYKLSTYATWWIRQSVTRALADQARTIRVPVH 218

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      + ++    + +T        V  +++ L +SE +V+ +        SL   
Sbjct: 219 MVE-----TINKMSKMQRKLTLELGYEPSVAELSEALEMSEDKVMEIMQIAREPASLETP 273

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   +++ S   D++    D          E    R  +   +  L  RER++   R   
Sbjct: 274 I--GEEDDSNLGDFVA---DSNVVTPEGNVESVMLREHIDALLGDLKERERQVIVLRFGL 328

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+  P TLE +  EF V+RER+RQIEA+A +K++  ++ +
Sbjct: 329 EDGHPRTLEEVGKEFNVTRERIRQIEAKALRKLRNPVRSK 368


>gi|299535819|ref|ZP_07049140.1| RNA polymerase sigma factor [Lysinibacillus fusiformis ZC1]
 gi|298729019|gb|EFI69573.1| RNA polymerase sigma factor [Lysinibacillus fusiformis ZC1]
          Length = 375

 Score =  258 bits (661), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 80/289 (27%), Positives = 142/289 (49%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++ +L  ++E  LA+R  E GD  A  RL  ++LRL
Sbjct: 91  LNDLSVPPGVKINDPVRMYLKEIGRVDLLSAEQEIALAERI-EQGDEEARKRLAEANLRL 149

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 150 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQ 209

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    I ++++++  +V  +    
Sbjct: 210 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPSPE---EIGEEMDLTPEKVREILKIA 264

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D + Q   +    +  +  L   +  L  RE 
Sbjct: 265 QEPVSLETPI--GEEDDSHLGDFI---EDSEAQSPSDHAAYELLKEQLEDVLDTLTDREE 319

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 320 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 368


>gi|218288616|ref|ZP_03492893.1| RNA polymerase, sigma 70 subunit, RpoD family [Alicyclobacillus
           acidocaldarius LAA1]
 gi|258511944|ref|YP_003185378.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
 gi|218241273|gb|EED08448.1| RNA polymerase, sigma 70 subunit, RpoD family [Alicyclobacillus
           acidocaldarius LAA1]
 gi|257478670|gb|ACV58989.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
          Length = 368

 Score =  258 bits (661), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 80/277 (28%), Positives = 135/277 (48%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
              +  Y+ EI ++P+L  QEE  LAKR  E GD  A  RL  ++LRLVV IA  Y G G
Sbjct: 96  SDPVRMYLKEIGRVPLLSAQEEIELAKRI-EQGDEEAKQRLAEANLRLVVSIAKRYVGRG 154

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I     +
Sbjct: 155 MLFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 214

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 L R+   L         PE    IA +++++  +V  +        SL   I  
Sbjct: 215 --TINKLIRVSRQLLQELGREPTPE---EIAAEMDLTPEKVREIQKIAQEPVSLETPI-- 267

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            +++ S   D++      +     +    +  +  L   +  L  RE  +   R   ++ 
Sbjct: 268 GEEDDSHLGDFIPD---DEAPAPADAAAYELLKEQLEDVLDTLTEREENVLRLRFGLDDG 324

Query: 253 --VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 325 RTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 361


>gi|145628599|ref|ZP_01784399.1| RNA polymerase sigma factor [Haemophilus influenzae 22.1-21]
 gi|145632513|ref|ZP_01788247.1| RNA polymerase sigma factor [Haemophilus influenzae 3655]
 gi|148825451|ref|YP_001290204.1| RNA polymerase factor sigma-32 [Haemophilus influenzae PittEE]
 gi|144979069|gb|EDJ88755.1| RNA polymerase sigma factor [Haemophilus influenzae 22.1-21]
 gi|144986708|gb|EDJ93260.1| RNA polymerase sigma factor [Haemophilus influenzae 3655]
 gi|148715611|gb|ABQ97821.1| RNA polymerase sigma factor [Haemophilus influenzae PittEE]
          Length = 281

 Score =  258 bits (661), Expect = 5e-67,   Method: Composition-based stats.
 Identities = 104/285 (36%), Positives = 169/285 (59%), Gaps = 7/285 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+++   ++V  +  +  YI    + PML  +EE  LA+R   H DL AA +L+ SHLR 
Sbjct: 1   MDKETQMMLVP-QGSIEGYIRAANEYPMLTAEEEKELAERLYYHEDLDAAKKLILSHLRF 59

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 60  VIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 119

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L    +N     +V  +A +L VS+ +VI M  R+
Sbjct: 120 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNEN-----EVDMVANELGVSKEDVIEMESRM 174

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D   +   + ++  +     +L          L  +         L  ++  L+ R 
Sbjct: 175 SGADVGFDLPTDDAETETYSPSLYLEDKSSNFAAELENENFESQATEQLGVALQSLDARS 234

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + I +AR L +N  TL +L++++ VS ER+RQ+E  A KK++ ++
Sbjct: 235 QDIIKARWLDDNKATLHDLAAKYNVSAERIRQLETNALKKLKSAV 279


>gi|288574624|ref|ZP_06392981.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dethiosulfovibrio
           peptidovorans DSM 11002]
 gi|288570365|gb|EFC91922.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dethiosulfovibrio
           peptidovorans DSM 11002]
          Length = 381

 Score =  258 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 75/275 (27%), Positives = 141/275 (51%), Gaps = 13/275 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  IP+L + +E  LAKR  E GD  A  +L+ ++LRLVV IA  Y G G+
Sbjct: 110 DPVRMYLREIGTIPLLNQPQEVELAKRV-EMGDDEAKSQLIEANLRLVVSIAKKYMGRGM 168

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL++AV+KFD  RG++ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 169 LFLDLIQEGNLGLIRAVEKFDYSRGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 227

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                + ++    + +  +  +      IA ++ +  ++V+ +        SL + +   
Sbjct: 228 ----TINKVMRASRNLVQSLGREPTDEEIAAEMGIEPAKVVQIRKVAQEPISLESPV--G 281

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           +++ S+  D++    D       +    +  R+ L   +  L  RE+++   R   ++  
Sbjct: 282 EEDDSELGDFI---EDKDMISPDDSTSMEFLRDQLDDVLEGLTDREKQVLRLRFGFDDGQ 338

Query: 254 --TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             TLE++   F V+RER+RQIEA+A +K++   + 
Sbjct: 339 CYTLEDVGRRFGVTRERIRQIEAKALRKLRHPSRS 373


>gi|15603449|ref|NP_246523.1| RNA polymerase factor sigma-32 [Pasteurella multocida subsp.
           multocida str. Pm70]
 gi|12721979|gb|AAK03668.1| RpoH [Pasteurella multocida subsp. multocida str. Pm70]
          Length = 281

 Score =  258 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 105/286 (36%), Positives = 169/286 (59%), Gaps = 9/286 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           MN+   ++++  +  +  YI    + PML  +EE  LA+R     DL AA +L+ SHLR 
Sbjct: 1   MNKDTQTMMLVPQGSIEAYIRAANEYPMLTAEEEKELAERLYYQEDLEAAKKLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L    +N     +V  +A +L VS ++V+ M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNEN-----EVEMVANELGVSPADVMEMESRM 175

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLNPR 238
            G D + +      D   +      + D        +E E  +      L+ ++  L+ R
Sbjct: 176 TGADVAFDLPT--DDNEETYSPSLYLEDKGSNFAAELENENYEAQATEQLSVALEGLDER 233

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              I +AR L EN  TL++L++++ +S ERVRQ+E  A KK++ ++
Sbjct: 234 SLDIIKARWLDENKATLQDLAAKYNISAERVRQLETNALKKLKSAV 279


>gi|314960003|gb|EFT04105.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL002PA2]
          Length = 511

 Score =  258 bits (661), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 76/318 (23%), Positives = 143/318 (44%), Gaps = 41/318 (12%)

Query: 2   NRKNMSIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRY------------------ 41
           +    +++V G     +  Y+ +I K+ +L   EE  LAKR                   
Sbjct: 198 DEPEQTVMVAGATADPVKDYLKQIGKVALLNAVEEVDLAKRIEAGLFAGEQLADPDAKIR 257

Query: 42  -REHGDLS--------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
            ++  D          A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 258 EKDREDYEWIAEDGKVAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEK 317

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWIK A+   +      ++I     +  +   L R++  +      
Sbjct: 318 FDYTKGYKFSTYATWWIKQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGR 375

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE    +A +L+++  +VI +        SL+  +   +   S++ D +    D + 
Sbjct: 376 EPTPE---ELASELDMTAEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEA 427

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVR 270
            V  +       +  L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 428 IVPADAVNFTLLQEQLHDVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIR 487

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 488 QIESKTMSKLRHPSRSQV 505


>gi|291522137|emb|CBK80430.1| RNA polymerase, sigma 70 subunit, RpoD [Coprococcus catus GD/7]
          Length = 365

 Score =  258 bits (660), Expect = 6e-67,   Method: Composition-based stats.
 Identities = 76/276 (27%), Positives = 145/276 (52%), Gaps = 13/276 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           +  +  +  Y+ EI  IP+L  +EE  LAK  +E G   AA ++  ++LRLVV IA  Y 
Sbjct: 89  IRTDDPVRMYLKEIGNIPLLTPEEEVELAKEMKE-GSKQAAKKMAEANLRLVVSIAKRYV 147

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++A++K+D  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 148 GRGMQFLDLIQEGNVGLIKAIEKYDYTKGYKFSTYATWWIRQAITRSIADQARTIRIPVH 207

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      + +L    +++T    +   V  IA+ +++  + V  +   +    SL   
Sbjct: 208 MVE-----TMNKLTKVQRSLTQELGREPSVEEIAENVHMDVNRVREILKLVQETVSLETP 262

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           + S ++  S   D++  DH     +  ++      ++ +   +  LN RE+++   R   
Sbjct: 263 VGSEEE--SHLADFIEDDH---TPLPSDEAAFGQLKDDIRSVLDKLNEREQKVLRMRFGL 317

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           ++    TLE +  E  V+RER+RQIEA+A +K+++S
Sbjct: 318 DDGKEHTLEEVGQELHVTRERIRQIEAKALRKLRQS 353


>gi|169829158|ref|YP_001699316.1| RNA polymerase sigma factor rpoD [Lysinibacillus sphaericus C3-41]
 gi|168993646|gb|ACA41186.1| RNA polymerase sigma factor rpoD (Sigma-A) (Sigma-43)
           [Lysinibacillus sphaericus C3-41]
          Length = 375

 Score =  258 bits (660), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 80/289 (27%), Positives = 142/289 (49%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++ +L  ++E  LA+R  E GD  A  RL  ++LRL
Sbjct: 91  LNDLSVPPGVKINDPVRMYLKEIGRVDLLSAEQEIKLAERI-EQGDEEARKRLAEANLRL 149

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 150 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQ 209

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    I ++++++  +V  +    
Sbjct: 210 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPSPE---EIGEEMDLTPEKVREILKIA 264

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D + Q   +    +  +  L   +  L  RE 
Sbjct: 265 QEPVSLETPI--GEEDDSHLGDFI---EDSEAQSPSDHAAYELLKEQLEDVLDTLTDREE 319

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 320 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 368


>gi|255525304|ref|ZP_05392244.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           carboxidivorans P7]
 gi|296188172|ref|ZP_06856564.1| RNA polymerase sigma factor RpoD [Clostridium carboxidivorans P7]
 gi|255510976|gb|EET87276.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           carboxidivorans P7]
 gi|296047298|gb|EFG86740.1| RNA polymerase sigma factor RpoD [Clostridium carboxidivorans P7]
          Length = 361

 Score =  258 bits (660), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 84/293 (28%), Positives = 144/293 (49%), Gaps = 17/293 (5%)

Query: 1   MNRKNMSIIVNGEIGLS----RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTS 56
           ++ K++ + V   I +      Y+ EI K+P+L  +EE  LA+R  E+GD  A  +L  +
Sbjct: 73  VDEKDLDLSVPEGIAIDDPVRMYLKEIGKVPLLAPEEEISLAQRI-ENGDQIAKKKLAEA 131

Query: 57  HLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           +LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   
Sbjct: 132 NLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRA 191

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
           I      ++I     +      L R+   L        +PE+V  I   + +   +V  +
Sbjct: 192 IADQARTIRIPVHMVE--TINKLIRVSRQLLQELGREPQPEEVAKI---MEMPVDKVREI 246

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
                   SL   I   ++  S   D++      +     E       +  L   +  L 
Sbjct: 247 MKIAQEPVSLETPI--GEEEDSHLGDFIPD---DEAPAPAEAAAFTMLKEQLINVLDTLT 301

Query: 237 PRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           PRE ++   R   ++    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 302 PREEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 354


>gi|311277614|ref|YP_003939845.1| RNA polymerase, sigma 32 subunit, RpoH [Enterobacter cloacae SCF1]
 gi|308746809|gb|ADO46561.1| RNA polymerase, sigma 32 subunit, RpoH [Enterobacter cloacae SCF1]
          Length = 285

 Score =  258 bits (660), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 108/290 (37%), Positives = 162/290 (55%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +     L  YI      PML   EE  LA++    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQNLALAPVGNLESYIRAANAWPMLSADEERALAEKLHYQGDLEAAKKLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHIARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVEMVARELGVSSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQ---EQVLIEKEERKNRRNMLTRSMSVLNP 237
           A  +    L    D    Q    ++Y  D        + +    +   N LT +M  L+ 
Sbjct: 176 AAQDMTFDLGPDDDAQDGQPMAPVLYLQDKSSNFADGIEDDNWEEQAANKLTDAMQGLDE 235

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L E+   TL+ L+  + VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQDIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 285


>gi|304415276|ref|ZP_07395971.1| RNA polymerase sigma 32 (sigma H) factor [Candidatus Regiella
           insecticola LSR1]
 gi|304282866|gb|EFL91334.1| RNA polymerase sigma 32 (sigma H) factor [Candidatus Regiella
           insecticola LSR1]
          Length = 285

 Score =  258 bits (660), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 108/290 (37%), Positives = 170/290 (58%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+++  ++ +  + GL  YI      PML  +EE  LA+R   HGDLSAA +L+ SHLR 
Sbjct: 1   MSKEIRTLALISQGGLDAYIRTSNTYPMLTAEEEQELAERLHYHGDLSAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  +A  Y GYGLP ++++ EGNIGLM+AV++F+P  G RL ++++ WIKA + EY+LR+
Sbjct: 61  VTHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPAIGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +AK+L VS+ +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKSKQRLGWFNQ-----DEVEMVAKELGVSKKDVHEMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNP 237
           +  +    L    D    Q    ++Y  D       + EE     +  + L+ ++  L+ 
Sbjct: 176 SAQDMTFDLSPDDDTRDGQLVAPVLYLQDRNSDFAGDVEEDNWDNHAVDKLSFALEKLDE 235

Query: 238 RERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L  +N  TL+ L++++ VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQHIIRARWLNDDNKATLQELANQYGVSAERVRQLEKNAMKKLRLAIEA 285


>gi|240169695|ref|ZP_04748354.1| RNA polymerase sigma factor [Mycobacterium kansasii ATCC 12478]
          Length = 518

 Score =  258 bits (660), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 79/319 (24%), Positives = 148/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------REHGDL- 47
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+  
Sbjct: 205 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMAEMAERGEKL 263

Query: 48  ----------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 264 PAAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 323

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 324 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 381

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 382 REPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 433

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 434 AVVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 493

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 494 RQIESKTMSKLRHPSRSQV 512


>gi|213018727|ref|ZP_03334535.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Culex
           quinquefasciatus JHB]
 gi|212995678|gb|EEB56318.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Culex
           quinquefasciatus JHB]
          Length = 281

 Score =  258 bits (660), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 129/272 (47%), Positives = 193/272 (70%), Gaps = 2/272 (0%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +YI E+RK PML ++EE  LAK ++E+ D+S+AHRL+TSHL LVVKIAM ++ YGL + +
Sbjct: 2   QYIAEVRKFPMLSQEEEVRLAKNWQEYQDISSAHRLITSHLNLVVKIAMKFKNYGLLLMD 61

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +V EGN+GLM AVKKF+P+ GFR +TY++WWI+A+M+++IL+SWSLVKIGTT  Q+RLFF
Sbjct: 62  LVMEGNMGLMHAVKKFNPDLGFRFSTYAVWWIEASMKDFILKSWSLVKIGTTQAQRRLFF 121

Query: 138 NLRRLKGHLQAITDNN-LKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALINSSDK 195
           +LR++K  +   T+   L  E++ AI+ +L+VSE +V+ M+ RLA  D+SLN  I   D 
Sbjct: 122 SLRKIKKRILQYTNRETLSKEEIKAISNELSVSEEDVVQMSYRLACKDQSLNNCIKIGDD 181

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
           +  + QD +  +   QE      EE+  +  +L+ +++ LN R R IF +R L EN  TL
Sbjct: 182 SKKELQDMIPCNLVSQEVAYQNHEEKALKETILSNALASLNERSRDIFISRYLSENTQTL 241

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           + LS ++ VSRER+RQ+  +A  KV++ I+ +
Sbjct: 242 DELSKKYCVSRERIRQLAEQAMSKVKQHIKSE 273


>gi|269121540|ref|YP_003309717.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sebaldella
           termitidis ATCC 33386]
 gi|268615418|gb|ACZ09786.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sebaldella
           termitidis ATCC 33386]
          Length = 387

 Score =  258 bits (660), Expect = 7e-67,   Method: Composition-based stats.
 Identities = 82/284 (28%), Positives = 146/284 (51%), Gaps = 13/284 (4%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           ++ I++ +  +  Y+ EI +IP+L  +EE  LA++  E+ D  A  +L+ S+LRLVV IA
Sbjct: 108 LAEIMDVDEPIKMYLREIGQIPLLTYEEEIALAQKVLEN-DEEAKQKLIESNLRLVVSIA 166

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             +   GL + +++ EGN+GLM+AV+KF+ E+GF+ +TY+ WWI+ A+   I      ++
Sbjct: 167 KKHTNRGLKMLDLIQEGNMGLMKAVEKFEYEKGFKFSTYATWWIRQAITRAIADQGRTIR 226

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           I        +   + ++K   + I     K      +AKKL +   +V S+        S
Sbjct: 227 IPVH-----MIETINKIKKESRIILQETGKEATAEELAKKLEIPVDKVKSILEMNQDPIS 281

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L   + S  +  S+  D++  D         +   R   +  L   +  L+ RE  +   
Sbjct: 282 LETPVGS--EEDSELGDFVEDDKFLN---PYDATTRVLLKEQLDGVLKTLSEREEMVLRY 336

Query: 246 RRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           R   ++  P TLE +   F V+RER+RQIE +A +K++   +++
Sbjct: 337 RYGLDDGSPKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRRK 380


>gi|134096067|ref|YP_001101142.1| sigma H factor [Herminiimonas arsenicoxydans]
 gi|133739970|emb|CAL63021.1| RNA polymerase sigma-32 factor [Herminiimonas arsenicoxydans]
          Length = 298

 Score =  258 bits (660), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 135/284 (47%), Positives = 182/284 (64%), Gaps = 11/284 (3%)

Query: 6   MSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           MS+  +G +G +  YI  + ++PML  +EE  LAKR R+  DL AA +LV SHLRLVV I
Sbjct: 17  MSLGFSGALGNIDAYISAVNRLPMLTHEEEISLAKRLRDDNDLGAAQKLVLSHLRLVVSI 76

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A GY GYGLP ++++ EGNIGLM+AVK+FDP++G RL +YSM WIKA M EYIL++W LV
Sbjct: 77  ARGYLGYGLPHADLIQEGNIGLMKAVKRFDPDQGVRLVSYSMHWIKAEMHEYILKNWRLV 136

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-D 183
           K+ TT  Q++LFFNLR  K  L A+T     P+QV A+AK LNV   EVI M  RL+G D
Sbjct: 137 KVATTKAQRKLFFNLRSHKTGLDAMT-----PDQVEALAKTLNVKREEVIEMETRLSGRD 191

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            +L A  +  D   +    +L  D     +VL  +   + +   L+ ++  L+PR RRI 
Sbjct: 192 IALEAPTDDEDDKFA-PIAYLSSDSQEPTRVLESQRYDRLQTEGLSSALGKLDPRSRRIV 250

Query: 244 EARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           EAR L  +     TL  L++EF VS ER+RQIE  A KK++ S+
Sbjct: 251 EARWLANDDGSGATLHELANEFGVSAERIRQIETVALKKMKGSL 294


>gi|225024603|ref|ZP_03713795.1| hypothetical protein EIKCOROL_01480 [Eikenella corrodens ATCC
           23834]
 gi|224942617|gb|EEG23826.1| hypothetical protein EIKCOROL_01480 [Eikenella corrodens ATCC
           23834]
          Length = 283

 Score =  258 bits (660), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 117/289 (40%), Positives = 181/289 (62%), Gaps = 8/289 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           MN      I +G   L +YIH +  IP+L  +EE+ LA R +  GDL AA +L+ SHLR+
Sbjct: 1   MNNAFALPIPSGHGSLEQYIHTVNSIPLLTAEEEHSLAVR-QLQGDLEAAKKLILSHLRV 59

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+ILR+
Sbjct: 60  VVSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPNRGARLFSFAVHWIKAEIHEFILRN 119

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +V++ TT  Q++LFFNLR ++  + A++     PE+   IA  L V   EV+ M  R+
Sbjct: 120 WRMVRVATTKPQRKLFFNLRSMRKSMNALS-----PEEAQTIADDLGVKMDEVLEMEQRM 174

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            G D +L    + SD++S    DWL        Q + +K     +   L  +++ L+ R 
Sbjct: 175 TGKDIALLPDNSDSDEDSYAPIDWLADTRSEPTQQIAQKARYAMQTEGLQNALAQLDDRS 234

Query: 240 RRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           RRI E+R LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++
Sbjct: 235 RRIVESRWLQDDGGLTLHELAAEYGVSAERIRQIEAKAIQKLRGFMSEE 283


>gi|291484966|dbj|BAI86041.1| RNA polymerase sigma factor [Bacillus subtilis subsp. natto
           BEST195]
          Length = 371

 Score =  258 bits (660), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 79/289 (27%), Positives = 140/289 (48%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++ +L  +EE   AK+  E GD  +  RL  ++LRL
Sbjct: 87  LNDLSVPPGVKINDPVRMYLKEIGRVNLLSAKEEIAYAKKI-EEGDEESKRRLAEANLRL 145

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GLM+AV+KFD  +G++ +TY+ WWI+ A+   I   
Sbjct: 146 VVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQ 205

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    IA+ ++++  +V  +    
Sbjct: 206 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPTPE---EIAEDMDLTPEKVREILKIA 260

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D +     +    +  +  L   +  L  RE 
Sbjct: 261 QEPVSLETPI--GEEDDSHLGDFI---EDQEATSPSDHAAYELLKEQLEDVLDTLTDREE 315

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 316 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 364


>gi|320530862|ref|ZP_08031899.1| RNA polymerase sigma factor RpoD [Selenomonas artemidis F0399]
 gi|320136896|gb|EFW28841.1| RNA polymerase sigma factor RpoD [Selenomonas artemidis F0399]
          Length = 381

 Score =  258 bits (659), Expect = 8e-67,   Method: Composition-based stats.
 Identities = 81/275 (29%), Positives = 137/275 (49%), Gaps = 13/275 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI ++P+L  +EE  LA+R  E GD SA HRL  ++LRLVV IA  Y G G
Sbjct: 108 DDPVRMYLKEIGRVPLLTAEEEVELARRM-EAGDASARHRLEEANLRLVVSIAKRYVGRG 166

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I     +
Sbjct: 167 MLFLDLIQEGNLGLLKAVEKFDYSKGYKFSTYATWWIRQAITRALADQARTIRIPVHMVE 226

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 L R+   L      +   E    IAK++ +S   V  +        SL   +  
Sbjct: 227 --TINKLVRVSRSLLQELGRDATAE---EIAKEMGLSVVRVREIMKIAQEPVSLETPV-- 279

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            ++  S   D++    D       +       +  ++  +  L PRE  +   R   E+ 
Sbjct: 280 GEEEDSHLGDFI---EDEAALDPADAASMMLLKEQISEVLKTLAPREAEVLRLRFGLEDG 336

Query: 253 --VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              TLE +   F V+RER+RQIEA+A +K++  ++
Sbjct: 337 RSRTLEEVGQSFGVTRERIRQIEAKALRKLRHPVR 371


>gi|145635177|ref|ZP_01790882.1| RNA polymerase sigma factor [Haemophilus influenzae PittAA]
 gi|145267598|gb|EDK07597.1| RNA polymerase sigma factor [Haemophilus influenzae PittAA]
          Length = 281

 Score =  258 bits (659), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 104/285 (36%), Positives = 168/285 (58%), Gaps = 7/285 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+++   ++V  +  +  YI    + PML  +EE  LA+R   H DL AA +L+ SHLR 
Sbjct: 1   MDKETQMMLVP-QGSIEGYIRAANEYPMLTAEEEKELAERLYYHEDLDAAKKLILSHLRF 59

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 60  VIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 119

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L    +N     +V  +A +L VS+ +VI M  R+
Sbjct: 120 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNEN-----EVDMVANELGVSKEDVIEMESRM 174

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D   +   + ++        +L          L  +         L  ++  L+ R 
Sbjct: 175 SGADVGFDLPTDDAETEIYSPSLYLEDKSSNFAAELENENFESQATEQLNTALQSLDARS 234

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + I +AR L +N  TL +L++++ VS ER+RQ+E  A KK++ ++
Sbjct: 235 QDIIKARWLDDNKATLHDLAAKYNVSAERIRQLETNALKKLKSAV 279


>gi|156936376|ref|YP_001440292.1| RNA polymerase factor sigma-32 [Cronobacter sakazakii ATCC BAA-894]
 gi|260599762|ref|YP_003212333.1| RNA polymerase factor sigma-32 [Cronobacter turicensis z3032]
 gi|156534630|gb|ABU79456.1| hypothetical protein ESA_04276 [Cronobacter sakazakii ATCC BAA-894]
 gi|260218939|emb|CBA34294.1| RNA polymerase sigma-32 factor [Cronobacter turicensis z3032]
          Length = 285

 Score =  258 bits (659), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 106/290 (36%), Positives = 166/290 (57%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +     L  YI      PML   EE  LA++    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLALAPVGNLDSYIRAANAWPMLSADEERALAEKLHYQGDLEAAKKLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVEMVARELGVSSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQ---EQVLIEKEERKNRRNMLTRSMSVLNP 237
           A  +    +    D   SQ    +++  D        + +    ++  + LT +M  L+ 
Sbjct: 176 AAQDMTFDMSPDDDAGDSQPMAPVLFLQDKSSNFADGIEDDNWEEHAADKLTDAMQGLDE 235

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R ++I  AR L E+   TL+ L++ + VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQQIIRARWLDEDNKSTLQELANRYGVSAERVRQLEKNAMKKLRAAIEA 285


>gi|328885546|emb|CCA58785.1| RNA polymerase sigma factor RpoD [Streptomyces venezuelae ATCC
           10712]
          Length = 567

 Score =  258 bits (659), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 75/314 (23%), Positives = 143/314 (45%), Gaps = 40/314 (12%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------- 41
           + +++       +  Y+ +I K+P+L  ++E  LAKR                       
Sbjct: 259 QQVAVAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANSDKLAPKLKR 318

Query: 42  -----REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                 E G   A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  
Sbjct: 319 ELEIIAEDG-RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYT 377

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  +         P
Sbjct: 378 KGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTP 435

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           E    +AK+L+++  +VI +        SL+  +   +   S++ D +    D +  V  
Sbjct: 436 E---ELAKELDMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPA 487

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEA 274
           +       +  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE+
Sbjct: 488 DAVSFTLLQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIES 547

Query: 275 RAFKKVQESIQKQV 288
           +   K++   + QV
Sbjct: 548 KTMSKLRHPSRSQV 561


>gi|256825489|ref|YP_003149449.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Kytococcus sedentarius
           DSM 20547]
 gi|256688882|gb|ACV06684.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Kytococcus sedentarius
           DSM 20547]
          Length = 594

 Score =  258 bits (659), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 73/303 (24%), Positives = 139/303 (45%), Gaps = 38/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYR---------EHGDL----------------- 47
             +  Y+ +I K+ +L  ++E  LAKR             GD                  
Sbjct: 296 DAVKDYLKQIGKVALLNAEQEVDLAKRIEAGLFAEQRLNSGDKIDAKLKRELWWVASDGK 355

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ W
Sbjct: 356 NAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATW 415

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L+
Sbjct: 416 WIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKELD 470

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++  +V+ +        SL+  +   +   S++ D +    D +  V  +       +  
Sbjct: 471 MTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPSDAVSFTLLQEQ 525

Query: 228 LTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   +
Sbjct: 526 LHSVLDTLSEREAGVVSMRFGLADGQPKTLDEIGRVYGVTRERIRQIESKTMSKLRHPSR 585

Query: 286 KQV 288
            QV
Sbjct: 586 SQV 588


>gi|118444745|ref|YP_878546.1| RNA polymerase sigma factor RpoD [Clostridium novyi NT]
 gi|118135201|gb|ABK62245.1| RNA polymerase sigma-70 factor [Clostridium novyi NT]
          Length = 368

 Score =  258 bits (659), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 81/280 (28%), Positives = 138/280 (49%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ +  +  Y+ EI K+P+L   EE  LA+R  E G++ A  +L  ++LRLVV IA  Y 
Sbjct: 93  ISIDDPVRMYLKEIGKVPLLTPDEEIDLAQRI-EEGEMYAKKKLAEANLRLVVSIAKRYV 151

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 152 GRGMLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 211

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R+   L        +PE    IAK + +   +V  +        SL   
Sbjct: 212 MVE--TINKLIRVSRQLLQELGREPQPE---EIAKIMEMPVDKVREIMKIAQEPVSLETP 266

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++      +     E       +  L   +  L PRE ++   R   
Sbjct: 267 I--GEEEDSHLGDFIPD---DEAPAPAEAAAFTMLKEQLINVLDTLTPREEKVLRLRFGL 321

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 322 DDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 361


>gi|212637488|ref|YP_002314013.1| RNA polymerase factor sigma-32 [Shewanella piezotolerans WP3]
 gi|212558972|gb|ACJ31426.1| RNA polymerase sigma-32 factor [Shewanella piezotolerans WP3]
          Length = 285

 Score =  258 bits (659), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 109/284 (38%), Positives = 174/284 (61%), Gaps = 7/284 (2%)

Query: 4   KNMSIIVN-GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           + M+++V      L  YIH    I ML+ ++E+ LAKR +E GDLSAA  L+ SHLR VV
Sbjct: 6   QTMALMVPQSSGSLESYIHSAHSISMLDAEKEHELAKRLQETGDLSAAKELIMSHLRFVV 65

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A GY GYGLP ++++ EGNIGLM+AVK+FDP+ G RL ++++ WIKA + EY+L++W 
Sbjct: 66  HVAKGYSGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYVLKNWR 125

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L   +DN     +V  +A+ L VS+++V  M  R+A 
Sbjct: 126 IVKVATTKAQRKLFFNLRKTKKRLGWFSDN-----EVGMVAESLGVSKADVTEMESRMAA 180

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE-ERKNRRNMLTRSMSVLNPRERR 241
            +    L + +D          + DH       +E +   ++ +  L  ++  L+ R + 
Sbjct: 181 QDPAFDLASDNDDEQDYAPMHYLEDHSSDLASQVENDNWEQSNQTRLLSAIKTLDERSQH 240

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           I +AR L E+  TL+ L++ ++VS ER+RQ+E  A  K++  ++
Sbjct: 241 ILQARWLNEDKTTLQELAATYQVSAERIRQLEKNAMNKLKGRME 284


>gi|40143|emb|CAA27538.1| unnamed protein product [Bacillus subtilis]
 gi|143454|gb|AAA22709.1| RNA polymerase sigma-43 factor [Bacillus subtilis]
 gi|1303833|dbj|BAA12489.1| RpoD [Bacillus subtilis]
          Length = 371

 Score =  258 bits (659), Expect = 9e-67,   Method: Composition-based stats.
 Identities = 78/289 (26%), Positives = 140/289 (48%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++ +L  +EE   A++  E GD  +  RL  ++LRL
Sbjct: 87  LNDLSVPPGVKINDPVRMYLKEIGRVNLLSAKEEIAYAQKI-EEGDEESKRRLAEANLRL 145

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GLM+AV+KFD  +G++ +TY+ WWI+ A+   I   
Sbjct: 146 VVSIAKRYVGRGMLFLDLIHEGNMGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQ 205

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    IA+ ++++  +V  +    
Sbjct: 206 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPTPE---EIAEDMDLTPEKVREILKIA 260

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D +     +    +  +  L   +  L  RE 
Sbjct: 261 QEPVSLETPI--GEEDDSHLGDFI---EDQEATSPSDHAAYELLKEQLEDVLDTLTDREE 315

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 316 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 364


>gi|257453679|ref|ZP_05618966.1| RNA polymerase factor sigma-32 [Enhydrobacter aerosaccus SK60]
 gi|257448913|gb|EEV23869.1| RNA polymerase factor sigma-32 [Enhydrobacter aerosaccus SK60]
          Length = 393

 Score =  258 bits (659), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 112/278 (40%), Positives = 167/278 (60%), Gaps = 7/278 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + L  YI+ + +IP+L  ++E  LA RY + GD+ AA  LV SHLR V+ IA  Y GYGL
Sbjct: 119 VNLGAYINAVHQIPILTAEQEQELAHRYTDEGDVEAARLLVMSHLRFVIHIARSYSGYGL 178

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P  +++ EGN+GLM+AVK+FDP +G RL ++++ WIKA + E+++R+W +VK+ TT   +
Sbjct: 179 PQGDLIQEGNVGLMKAVKRFDPNKGVRLVSFAVHWIKAEIHEFVIRNWRIVKVATTKAHR 238

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINS 192
           +LFFNLR LK      T+N L  E+  AIAK LNV+  +V+ M  RL   D S  A  + 
Sbjct: 239 KLFFNLRSLKK-----TNNQLTLEEAEAIAKDLNVTVKQVLEMESRLTSYDASFEAQSDD 293

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            D+     Q +L  D      ++ + +  +N  + L  +M  L+ R R I + R L E  
Sbjct: 294 EDEGRYAPQYFL-EDAADPADMVEDADWEENNNSALMEAMEDLDDRSRDIVQQRWLNEQK 352

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
            TL  L++E+ +S ERVRQIE  A  K++E++     L
Sbjct: 353 ATLHELAAEYNISAERVRQIEKNAMDKIKEAMLANTHL 390


>gi|313838731|gb|EFS76445.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL086PA1]
          Length = 511

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 76/318 (23%), Positives = 143/318 (44%), Gaps = 41/318 (12%)

Query: 2   NRKNMSIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRY------------------ 41
           +    +++V G     +  Y+ +I K+ +L   EE  LAKR                   
Sbjct: 198 DEPEQTVMVAGATADPVKDYLKQIGKVALLNAVEEVDLAKRIEAGLFAGEQLADPDAKIR 257

Query: 42  -REHGDLS--------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
            ++  D          A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 258 EKDREDYEWIAEDGKVAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEK 317

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWIK A+   +      ++I     +  +   L R++  +      
Sbjct: 318 FDYTKGYKFSTYATWWIKQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGR 375

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE    +A +L+++  +VI +        SL+  +   +   S++ D +    D + 
Sbjct: 376 EPTPE---ELASELDMTAEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEA 427

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVR 270
            V  +       +  L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 428 IVPADAVNFTLLQEQLHDVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIR 487

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 488 QIESKTMSKLRHPSRSQV 505


>gi|126652263|ref|ZP_01724442.1| RNA polymerase sigma factor RpoD [Bacillus sp. B14905]
 gi|126590995|gb|EAZ85107.1| RNA polymerase sigma factor RpoD [Bacillus sp. B14905]
          Length = 375

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 80/289 (27%), Positives = 142/289 (49%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++ +L  ++E  LA+R  E GD  A  RL  ++LRL
Sbjct: 91  LNDLSVPPGVKINDPVRMYLKEIGRVDLLSAEQEIALAERI-EQGDEEARKRLAEANLRL 149

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 150 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQ 209

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    I ++++++  +V  +    
Sbjct: 210 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPSPE---EIGEEMDLTPEKVREILKIA 264

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D + Q   +    +  +  L   +  L  RE 
Sbjct: 265 QEPVSLETPI--GEEDDSHLGDFI---EDSEAQSPSDHAAYELLKEQLEDVIDTLTDREE 319

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 320 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 368


>gi|300705271|ref|YP_003746874.1| RNA polymerase sigma h (sigma 32) factor; transcription of heat
           shock and stress proteins [Ralstonia solanacearum
           CFBP2957]
 gi|299072935|emb|CBJ44291.1| RNA polymerase sigma H (sigma 32) factor; transcription of heat
           shock and stress proteins [Ralstonia solanacearum
           CFBP2957]
          Length = 306

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 120/287 (41%), Positives = 174/287 (60%), Gaps = 12/287 (4%)

Query: 7   SIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           ++   G +G L  YI  + ++PML  +EE  LA+ Y   GDL AA RLV SHLRLVV IA
Sbjct: 23  ALAFPGSLGNLDAYIQSVNRVPMLTAEEEQQLARDYHATGDLDAARRLVLSHLRLVVSIA 82

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGLP ++++ EGNIGLM+AVK+FDP++G RL +Y++ WIKA M EYIL++W +VK
Sbjct: 83  RQYLGYGLPHADLIQEGNIGLMKAVKRFDPDQGVRLVSYAIHWIKAEMHEYILKNWRMVK 142

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDE 184
           + TT  Q++LFFNLR  K             +++ A+A++LNV  +EV  M  RL  GD 
Sbjct: 143 VATTKAQRKLFFNLRSHK----QDAHATFTSDEIDAVAQELNVKGAEVREMETRLSGGDI 198

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           +L   I+  ++ S     +L   H+   +VL  +   + +   +  +++ L+ R RRI E
Sbjct: 199 ALEGHIDDGEE-SFAPIAYLADTHNEPTRVLETRGHDRLQSEGIETALAKLDDRSRRIIE 257

Query: 245 ARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           AR L          TL  L+ EF VS ER+RQIE+ A KK++ ++Q 
Sbjct: 258 ARWLNVNDDGSGGATLHELADEFGVSAERIRQIESAAMKKMKGALQA 304


>gi|320527310|ref|ZP_08028495.1| RNA polymerase sigma factor RpoD [Solobacterium moorei F0204]
 gi|320132334|gb|EFW24879.1| RNA polymerase sigma factor RpoD [Solobacterium moorei F0204]
          Length = 468

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 78/276 (28%), Positives = 141/276 (51%), Gaps = 12/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++P+L+ ++E  +AKR  E GD  A + L++S+LRLVV IA  Y G G+
Sbjct: 195 DPVKMYLKEIGRVPLLKPEDEPEIAKRI-EEGDEEARNILISSNLRLVVSIAKKYVGRGM 253

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 254 LFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 312

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L      +   E++    +   +S  +V  +        SL   I   
Sbjct: 313 -TINKLTRVQRQLVQELGRDPSAEEISQRME--GISPEKVREIQKIALEPVSLETPI--G 367

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D +     +    +  ++ +   +S L  RE ++   R    +  
Sbjct: 368 EEDDSHLGDFI---EDKEALSPDQYASNQLLKDEINSVLSGLTEREEKVLRLRFGLYDGR 424

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 425 TRTLEEVGREFSVTRERIRQIEAKALRKLKHPSRSK 460


>gi|163748787|ref|ZP_02156039.1| RNA polymerase sigma factor [Shewanella benthica KT99]
 gi|161331561|gb|EDQ02366.1| RNA polymerase sigma factor [Shewanella benthica KT99]
          Length = 286

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 110/283 (38%), Positives = 173/283 (61%), Gaps = 8/283 (2%)

Query: 6   MSIIVN-GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           M+++V  G   L  Y+H    I MLE  +EY LAKR +E GD+ AA +L+ SHLR VV +
Sbjct: 8   MALVVPHGSGSLEAYVHSAHNISMLEADQEYELAKRLQETGDIQAAKQLIMSHLRFVVHV 67

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A GY GYGLP ++++ EGNIGLM+AVK+FDP  G RL ++++ WIKA + EY+L++W +V
Sbjct: 68  AKGYAGYGLPQADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWIKAEIHEYVLKNWRIV 127

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           K+ TT  Q++LFFNLR+ K  L   +D      +V  +A+ L VS+++V  M  R+A  +
Sbjct: 128 KVATTKAQRKLFFNLRKAKKRLGWFSD-----AEVGMVAENLGVSKADVTEMESRMAAQD 182

Query: 185 SLNALINSSDKN-SSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLNPRERRI 242
               L++ SD +         + DH       +E +  + + +  L  ++  L+ R + I
Sbjct: 183 PAFDLVSDSDDDIQDYAPALYLEDHSSDLASQVETDNLEASNQTRLLAAIKTLDERSQHI 242

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            +AR L E+  TL+ L++ ++VS ER+RQ+E  A  K++  I+
Sbjct: 243 LQARWLNEDKTTLQELAATYQVSAERIRQLEKNAMNKLKGCIE 285


>gi|317486415|ref|ZP_07945242.1| alternative sigma factor RpoH [Bilophila wadsworthia 3_1_6]
 gi|316922325|gb|EFV43584.1| alternative sigma factor RpoH [Bilophila wadsworthia 3_1_6]
          Length = 403

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 103/294 (35%), Positives = 177/294 (60%), Gaps = 7/294 (2%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           +++++  + + +  L  Y+ E+ + PML+  EE+ LA+R ++ GD  AA RLV+SHLRLV
Sbjct: 110 SQQHLPSLSSSKDSLHLYLREVSRFPMLKPDEEFDLARRVQKTGDSDAAFRLVSSHLRLV 169

Query: 62  VKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VKIAM ++   +  + +++ EGN+GLM+AV KFDP++G + + Y+ +WI+A + ++I+ +
Sbjct: 170 VKIAMDFQRRWMQNVLDLIQEGNVGLMRAVNKFDPDKGIKFSYYAAFWIRAYILKFIMDN 229

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VKIGTT  Q++LF+NL R +  L A             +A++L V E +++ M  RL
Sbjct: 230 WRMVKIGTTQAQRKLFYNLNRERQKLIA----EGFDPDAATLAERLGVGEDQIVEMQQRL 285

Query: 181 -AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            A D SL+A +   +  S+   D+L     G E+ L   E  +  ++ +   +  L+ +E
Sbjct: 286 DASDMSLDATVGD-ESGSATRMDFLPALGPGIEESLAGMEIAELLQSKIRDILPSLSEKE 344

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
             I E R L ++PVTL  +   + V+RERVRQ+EAR  +K++  +   ++  S 
Sbjct: 345 AYILEHRLLTDDPVTLREIGERYNVTRERVRQLEARLLQKLKTHLSTDIQDFSE 398


>gi|229844972|ref|ZP_04465109.1| RNA polymerase factor sigma-32 [Haemophilus influenzae 6P18H1]
 gi|229812106|gb|EEP47798.1| RNA polymerase factor sigma-32 [Haemophilus influenzae 6P18H1]
          Length = 281

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 104/285 (36%), Positives = 169/285 (59%), Gaps = 7/285 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+++   ++V  +  +  YI    + PML  +EE  LA+R   H DL AA +L+ SHLR 
Sbjct: 1   MDKETQMMLVP-QGSIEGYIRAANEYPMLTAEEEKELAERLYYHEDLDAAKKLILSHLRF 59

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 60  VIHVARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 119

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L    +N     +V  +A +L VS+ +VI M  R+
Sbjct: 120 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNEN-----EVDMVANELGVSKEDVIEMESRM 174

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D   +   + ++  +     +L          L  +         L  ++  L+ R 
Sbjct: 175 SGADVGFDLPTDDAETETYSPSLYLEDKSSNFAAELENENFESQATEQLGVALQSLDVRS 234

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + I +AR L +N  TL +L++++ VS ER+RQ+E  A KK++ ++
Sbjct: 235 QDIIKARWLDDNKATLHDLAAKYNVSAERIRQLETNALKKLKSAV 279


>gi|251796255|ref|YP_003010986.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Paenibacillus sp.
           JDR-2]
 gi|247543881|gb|ACT00900.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Paenibacillus sp.
           JDR-2]
          Length = 376

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 80/276 (28%), Positives = 136/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++P+L   +E  LA+R  E+GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 105 DPVRMYLKEIGRVPLLSADDEIELARRI-ENGDEEAKRRLAEANLRLVVSIAKRYVGRGM 163

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL++AV+KFD ++GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 164 LFLDLIQEGNMGLIKAVEKFDHQKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 222

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R+   L         PE    IA ++ +S  +V  +        SL   I   
Sbjct: 223 -TINKLIRVSRQLLQELGREPTPE---EIAAEMELSTDKVREIMKIAQEPVSLETPI--G 276

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D +     +    +  +  L   +  L  RE  +   R   ++  
Sbjct: 277 EEDDSHLGDFI---EDQEALAPADAAAYELLKEQLEDVLDTLTEREENVLRLRFGLDDGR 333

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 334 TRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 369


>gi|255068324|ref|ZP_05320179.1| alternative sigma factor RpoH [Neisseria sicca ATCC 29256]
 gi|261365915|ref|ZP_05978798.1| alternative sigma factor RpoH [Neisseria mucosa ATCC 25996]
 gi|255047443|gb|EET42907.1| alternative sigma factor RpoH [Neisseria sicca ATCC 29256]
 gi|288565493|gb|EFC87053.1| alternative sigma factor RpoH [Neisseria mucosa ATCC 25996]
          Length = 287

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 117/289 (40%), Positives = 185/289 (64%), Gaps = 7/289 (2%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N   + +I +G   L +YIH +  IPML  +EE  LA+R ++ GDL+AA +L+ SHLR+V
Sbjct: 3   NAFALPVIHSGNGSLEQYIHTVNSIPMLTPEEESQLAER-QQKGDLNAAKQLILSHLRVV 61

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+ILR+W
Sbjct: 62  VSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPSRGARLFSFAVHWIKAEIHEFILRNW 121

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            LV++ TT  Q++LFFNLR ++ +L A++     P++   IA  L V  SEV+ M  R+ 
Sbjct: 122 RLVRVATTKPQRKLFFNLRSMRKNLNALS-----PKEAQDIADDLGVKLSEVMEMEQRMT 176

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           G +      N+ D++S    DWL        + L ++     +   L  +++ L+ R RR
Sbjct: 177 GHDIAIMADNNDDEDSFAPIDWLADHDAEPSRQLSKQAHYALQTEGLQNALAQLDDRSRR 236

Query: 242 IFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           I E+R LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 237 IVESRWLQDDGGLTLHELAAEYGVSAERIRQIEAKAMQKLRGFLAEEAE 285


>gi|320539367|ref|ZP_08039036.1| RNA polymerase, sigma 32 (sigma H) factor [Serratia symbiotica str.
           Tucson]
 gi|320030492|gb|EFW12502.1| RNA polymerase, sigma 32 (sigma H) factor [Serratia symbiotica str.
           Tucson]
          Length = 285

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 104/290 (35%), Positives = 163/290 (56%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  YI      PML  +EE  LA+R    GDL AA +L+ +HLR 
Sbjct: 1   MTKEMQTLALVPQGSLEAYIRAANTYPMLTAEEERDLAERLHYQGDLGAAKQLILAHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VAHIARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVELVARELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER---KNRRNMLTRSMSVLNP 237
           A  +         +    Q    ++Y  D       + EE     N  + L  ++  L+ 
Sbjct: 176 AAQDMTFDPAPDDETRDGQSLAPVLYLQDKSSDFAEDIEEDNWESNAADKLAYALEGLDE 235

Query: 238 RERRIFEARRLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L  +N  TL+ L+ ++ VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQHIIRARWLDNDNKSTLQELADQYGVSAERVRQLEKNAMKKLKMAIEA 285


>gi|223985702|ref|ZP_03635749.1| hypothetical protein HOLDEFILI_03055 [Holdemania filiformis DSM
           12042]
 gi|223962313|gb|EEF66778.1| hypothetical protein HOLDEFILI_03055 [Holdemania filiformis DSM
           12042]
          Length = 408

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 77/285 (27%), Positives = 140/285 (49%), Gaps = 12/285 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           + S  V     +  Y+ EI ++P+L  ++E  +A+R +  GD  A   L++S+LRLVV I
Sbjct: 125 SSSPYVRINDPVKMYLKEIGRVPLLNPEDEPEIARRIQ-AGDEEAKRILISSNLRLVVSI 183

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      +
Sbjct: 184 AKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTI 243

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I     +      L R++  L          E++    +  N++  +V  +        
Sbjct: 244 RIPVHMVE--TINKLTRVQRQLVQDLGREPTAEEIAEKME--NITPDKVREIQKIALEPV 299

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   I   +++ S   D++    D       +    +  ++ +   +  L  RE ++  
Sbjct: 300 SLETPI--GEEDDSHLGDFI---EDKDAMSPDQYANNQLLKDEINNVLQGLTEREEKVLR 354

Query: 245 ARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R    +    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 355 LRFGLYDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLKHPTRSK 399


>gi|183982025|ref|YP_001850316.1| RNA polymerase sigma factor SigA [Mycobacterium marinum M]
 gi|183175351|gb|ACC40461.1| RNA polymerase sigma factor SigA [Mycobacterium marinum M]
          Length = 501

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 78/319 (24%), Positives = 148/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------------- 41
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR                     
Sbjct: 188 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMAELTDRGEKL 246

Query: 42  --REHGDL--------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
              +  D+         A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 247 PAAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 306

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 307 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 364

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 365 REPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 416

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 417 AVVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 476

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 477 RQIESKTMSKLRHPSRSQV 495


>gi|262202178|ref|YP_003273386.1| RNA polymerase sigma factor RpoD [Gordonia bronchialis DSM 43247]
 gi|262085525|gb|ACY21493.1| RNA polymerase sigma factor RpoD [Gordonia bronchialis DSM 43247]
          Length = 489

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 79/319 (24%), Positives = 148/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGDL- 47
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+  
Sbjct: 176 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLFATERLRRIMESGEKI 234

Query: 48  ----------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 235 TTAQKRDLNWISRDGNRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 294

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 295 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 352

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 353 REPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 404

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 405 AVVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 464

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 465 RQIESKTMSKLRHPSRSQV 483


>gi|239994826|ref|ZP_04715350.1| RNA polymerase sigma factor [Alteromonas macleodii ATCC 27126]
          Length = 284

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 110/284 (38%), Positives = 166/284 (58%), Gaps = 6/284 (2%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N ++M++ V     +  YI  +  I ML  +EE  LA R RE  DL AA +LV SHLR V
Sbjct: 4   NLQSMALSVPHSGSIEGYIQAVSSIDMLSAEEERELAVRLREDEDLQAARKLVMSHLRFV 63

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA  Y GYGLP ++++ EGNIGLM+AVK+FDP  G RL ++++ WIKA + E++L++W
Sbjct: 64  VHIAKSYSGYGLPQADLIQEGNIGLMKAVKRFDPTVGVRLVSFAVHWIKAEIHEFVLKNW 123

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            +VK+ TT  Q++LFFNLR+ K  L   T      ++V  +A +L VS  EV+ M  R++
Sbjct: 124 RIVKVATTKAQRKLFFNLRKAKKRLGWFTH-----DEVQTVANELGVSTKEVLQMEARMS 178

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRER 240
             +    L    D+  +      + D     E  +I  +        L  ++  L+ R +
Sbjct: 179 SQDQAFDLTADEDETGNFAPVQYLEDKSSDVETDVINNDWDTAASKRLYSAIKTLDERSQ 238

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            I E R L +N +TL++L+ +++VS ERVRQIE  A KK+Q ++
Sbjct: 239 DIIETRWLADNKITLQDLADKYQVSAERVRQIEKNAMKKLQAAM 282


>gi|117928637|ref|YP_873188.1| RNA polymerase, sigma 28 subunit [Acidothermus cellulolyticus 11B]
 gi|117649100|gb|ABK53202.1| RNA polymerase, sigma 70 subunit, RpoD [Acidothermus cellulolyticus
           11B]
          Length = 495

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 71/303 (23%), Positives = 138/303 (45%), Gaps = 38/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR--------------------------YREHGDL 47
             +  Y+ +I K+P+L  ++E  LAKR                          +      
Sbjct: 197 DPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEEKLNSGEELSPELRKDLEWIAEDGR 256

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ W
Sbjct: 257 RAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATW 316

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   +      ++I     +  +   L R++  +      +  PE    +A +L+
Sbjct: 317 WIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGRDPTPE---ELAVELD 371

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++  +V+ +        SL+  +   +   S++ D +    D +  V  +       +  
Sbjct: 372 MTPEKVMEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAIVPSDAVSFTLLQEQ 426

Query: 228 LTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   +
Sbjct: 427 LHSVLETLSEREAGVVSMRFGLTDGQPKTLDEIGRVYGVTRERIRQIESKTMSKLRHPSR 486

Query: 286 KQV 288
            QV
Sbjct: 487 SQV 489


>gi|313897367|ref|ZP_07830910.1| RNA polymerase sigma factor RpoD [Clostridium sp. HGF2]
 gi|312957737|gb|EFR39362.1| RNA polymerase sigma factor RpoD [Clostridium sp. HGF2]
          Length = 398

 Score =  257 bits (658), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 78/276 (28%), Positives = 141/276 (51%), Gaps = 12/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L+ +EE  +A+R +  GD  A  +L++++LRLVV IA  Y G G+
Sbjct: 124 DPVKMYLKEIGRVELLDPKEEPEIARRIQ-AGDEEAKKKLISANLRLVVSIAKKYVGRGM 182

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 183 LFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 241

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L      +   E++   AK  N+S  +V  +        SL   I   
Sbjct: 242 -TINKLTRIQRQLVQDLGRDPSAEEIA--AKMENISPEKVREIQKIALEPVSLETPI--G 296

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D +     E    +  ++ +   +  L  RE ++   R    +  
Sbjct: 297 EEDDSHLGDFI---EDKEALSPDEYANNQLLKDEINTVLQGLTEREEKVLRLRFGLYDGR 353

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 354 TRTLEEVGKEFNVTRERIRQIEAKALRKLKHPTRSK 389


>gi|292489953|ref|YP_003532845.1| RNA polymerase sigma-32 factor [Erwinia amylovora CFBP1430]
 gi|292900984|ref|YP_003540353.1| RNA polymerase sigma-32 factor [Erwinia amylovora ATCC 49946]
 gi|291200832|emb|CBJ47966.1| RNA polymerase sigma-32 factor [Erwinia amylovora ATCC 49946]
 gi|291555392|emb|CBA23800.1| RNA polymerase sigma-32 factor [Erwinia amylovora CFBP1430]
 gi|312174141|emb|CBX82394.1| RNA polymerase sigma-32 factor [Erwinia amylovora ATCC BAA-2158]
          Length = 284

 Score =  257 bits (657), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 104/289 (35%), Positives = 163/289 (56%), Gaps = 8/289 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +     L  YI      PML  +EE  LA+R    GDL AA  L+ SHLR 
Sbjct: 1   MTKEMQTLAIAPLGNLDSYIRAANAWPMLTAEEEKALAERLHYQGDLEAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKAKQRLGWFNQ-----DEVEMVARELGVSSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNS-SQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPR 238
           A  +         +    S      + D        IE++  ++   + L+ +M  L+ R
Sbjct: 176 AAQDMTFDPTPDDEGEGRSMAPMLYLQDKSSDFANGIEEDNWEDHAADKLSDAMQGLDER 235

Query: 239 ERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + I  AR L ++   TL+ L+ ++ VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 SQHIIRARWLDDDNKTTLQELADQYGVSAERVRQLEKNAMKKLRVAIEA 284


>gi|289642669|ref|ZP_06474809.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia symbiont
           of Datisca glomerata]
 gi|289507499|gb|EFD28458.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia symbiont
           of Datisca glomerata]
          Length = 392

 Score =  257 bits (657), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 83/307 (27%), Positives = 141/307 (45%), Gaps = 39/307 (12%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------------REHGDLSA- 49
                 +  Y+ EI K+P+L  +EE  LAKR                    +   DL A 
Sbjct: 89  APTSDPVRMYLKEIGKVPLLTAEEEVDLAKRIEAGLFASEKLAAATRKTSPQMRRDLEAI 148

Query: 50  -------AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
                    +LV ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +
Sbjct: 149 ERDGQIAKRKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFS 208

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I     +      L R++  L         PE    I
Sbjct: 209 TYATWWIRQAVTRAIADQARTIRIPVHMVE--TINKLIRIQRQLLQDLGREPSPE---EI 263

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           AK+++++  +V  +        SL   I   ++  S   D++    D    V ++     
Sbjct: 264 AKEMDLTPDKVREILKVSQEPVSLETPI--GEEEDSHLGDFI---EDCDAVVPVDAASFI 318

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             +  L   +  L+ RE+++ + R      +P TLE +  EF V+RER+RQIE++   K+
Sbjct: 319 LLQEQLDSVLHTLSDREKKVIQLRFGLTDGHPRTLEEVGREFGVTRERIRQIESKTLSKL 378

Query: 281 QESIQKQ 287
           +   + Q
Sbjct: 379 RHPSRSQ 385


>gi|221310444|ref|ZP_03592291.1| RNA polymerase sigma factor RpoD [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221314767|ref|ZP_03596572.1| RNA polymerase sigma factor RpoD [Bacillus subtilis subsp. subtilis
           str. NCIB 3610]
 gi|221319690|ref|ZP_03600984.1| RNA polymerase sigma factor RpoD [Bacillus subtilis subsp. subtilis
           str. JH642]
 gi|221323967|ref|ZP_03605261.1| RNA polymerase sigma factor RpoD [Bacillus subtilis subsp. subtilis
           str. SMY]
 gi|255767573|ref|NP_390399.2| RNA polymerase sigma factor RpoD [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|296333322|ref|ZP_06875775.1| RNA polymerase sigma factor RpoD [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305675173|ref|YP_003866845.1| RNA polymerase major sigma-43 factor (sigma-A) [Bacillus subtilis
           subsp. spizizenii str. W23]
 gi|321312003|ref|YP_004204290.1| RNA polymerase sigma factor RpoD [Bacillus subtilis BSn5]
 gi|251757327|sp|P06224|RPOD_BACSU RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-43; AltName: Full=Sigma-A
 gi|225185201|emb|CAB14450.2| RNA polymerase major sigma-43 factor (sigma-A) [Bacillus subtilis
           subsp. subtilis str. 168]
 gi|296149520|gb|EFG90416.1| RNA polymerase sigma factor RpoD [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305413417|gb|ADM38536.1| RNA polymerase major sigma-43 factor (sigma-A) [Bacillus subtilis
           subsp. spizizenii str. W23]
 gi|320018277|gb|ADV93263.1| RNA polymerase sigma factor RpoD [Bacillus subtilis BSn5]
          Length = 371

 Score =  257 bits (657), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 78/289 (26%), Positives = 140/289 (48%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++ +L  +EE   A++  E GD  +  RL  ++LRL
Sbjct: 87  LNDLSVPPGVKINDPVRMYLKEIGRVNLLSAKEEIAYAQKI-EEGDEESKRRLAEANLRL 145

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GLM+AV+KFD  +G++ +TY+ WWI+ A+   I   
Sbjct: 146 VVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQ 205

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    IA+ ++++  +V  +    
Sbjct: 206 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPTPE---EIAEDMDLTPEKVREILKIA 260

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D +     +    +  +  L   +  L  RE 
Sbjct: 261 QEPVSLETPI--GEEDDSHLGDFI---EDQEATSPSDHAAYELLKEQLEDVLDTLTDREE 315

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 316 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 364


>gi|294782673|ref|ZP_06747999.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. 1_1_41FAA]
 gi|294481314|gb|EFG29089.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. 1_1_41FAA]
          Length = 500

 Score =  257 bits (657), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 80/285 (28%), Positives = 143/285 (50%), Gaps = 13/285 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           N+      +  +  Y+ EI ++P+L   EE   AK+  E GD  A+ +L+ S+LRLVV I
Sbjct: 219 NLGNSAKVDEPIKMYLREIGQVPLLTHDEEIEYAKKAYE-GDEEASQKLIESNLRLVVSI 277

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  +   GL + +++ EGNIGLM+AV+KF+  +G++ +TY+ WWI+ A+   I      +
Sbjct: 278 AKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTI 337

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I        +   + ++K   +       K      +A++L +   ++ ++        
Sbjct: 338 RIPVH-----MIETINKIKKESRIYLQETGKDASPEILAERLGMEVEKIKAIQEMNQEPI 392

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   + S  +  S+  D++    D +     E   R   R  L   +  L+PRE ++  
Sbjct: 393 SLETPVGS--EEDSELGDFV---EDQKTTSPYEATNRAILREELDGVLKTLSPREEKVLR 447

Query: 245 ARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R   ++  P TLE +   F V+RER+RQIE +A +K++   +K+
Sbjct: 448 YRYGLDDSSPKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRKK 492


>gi|297626466|ref|YP_003688229.1| RNA polymerase principal sigma factor HrdB [Propionibacterium
           freudenreichii subsp. shermanii CIRM-BIA1]
 gi|296922231|emb|CBL56801.1| RNA polymerase principal sigma factor HrdB [Propionibacterium
           freudenreichii subsp. shermanii CIRM-BIA1]
          Length = 509

 Score =  257 bits (657), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 76/318 (23%), Positives = 143/318 (44%), Gaps = 41/318 (12%)

Query: 2   NRKNMSIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRY------------------ 41
           +     ++V G     +  Y+ +I K+ +L   +E  LAKR                   
Sbjct: 196 DEPEQQVMVAGATADPVKDYLKQIGKVALLNAAQEVDLAKRIEAGLFAGEQLTKNGDKIA 255

Query: 42  -REHGDLS--------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
             + GD          A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 256 RADRGDYEWITEDGHRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEK 315

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWIK A+   +      ++I     +  +   L R++  +      
Sbjct: 316 FDYTKGYKFSTYATWWIKQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGR 373

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE    +AK+L+++  +V+ +        SL+  +   +   S++ D +    D + 
Sbjct: 374 EPTPE---ELAKELDMTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEA 425

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVR 270
            V  +       +  L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 426 VVPADAVNFTLLQEQLHDVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIR 485

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 486 QIESKTMSKLRHPSRSQV 503


>gi|89076088|ref|ZP_01162448.1| RNA polymerase sigma factor [Photobacterium sp. SKA34]
 gi|89048240|gb|EAR53822.1| RNA polymerase sigma factor [Photobacterium sp. SKA34]
          Length = 286

 Score =  257 bits (657), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 106/287 (36%), Positives = 172/287 (59%), Gaps = 8/287 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+++  ++ +     L  YI  + + PML  + E  LA+R     D+++A  LV SHLR 
Sbjct: 1   MSQEMSAMALVSTESLDSYIQTVNRYPMLTPEREKELAERLHYDDDINSAKALVMSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA GY GYGLPI++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHIARGYSGYGLPIADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L    +     ++V  +A++L V  S+V  M  RL
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKSKKRLGWFNN-----DEVNMVAEQLGVEPSDVREMESRL 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNP 237
           A  +    + N  D+  +       Y  D    V +  EE     +  N L+++++ L+ 
Sbjct: 176 AAQDPTFEMQNDDDERDTTPVAPAYYLEDKSSDVALTYEENNWENHANNRLSQALASLDE 235

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R + I  +R L +   TL++L++ + VS ER+RQ+E  A KK+++++
Sbjct: 236 RSQHIVRSRWLDDEKSTLQDLANNYGVSAERIRQLEKNAMKKLKDAV 282


>gi|253576089|ref|ZP_04853421.1| RNA polymerase sigma-subunit [Paenibacillus sp. oral taxon 786 str.
           D14]
 gi|251844432|gb|EES72448.1| RNA polymerase sigma-subunit [Paenibacillus sp. oral taxon 786 str.
           D14]
          Length = 374

 Score =  257 bits (657), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 81/285 (28%), Positives = 140/285 (49%), Gaps = 13/285 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           ++   +     +  Y+ EI ++P+L   +E  LAKR  E+GD  A  RL  ++LRLVV I
Sbjct: 94  SLPPGIKINDPVRMYLKEIGRVPLLSADDEMELAKRI-ENGDEEAKRRLAEANLRLVVSI 152

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ WWI+ A+   I      +
Sbjct: 153 AKRYVGRGMLFLDLIQEGNMGLIKAVEKFDHKKGFKFSTYATWWIRQAITRAIADQARTI 212

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I     +      L R+   L         PE    IA ++++S  +V  +        
Sbjct: 213 RIPVHMVE--TINKLIRVSRQLLQELGREPAPE---EIAAEMDLSVEKVREIMKIAQEPV 267

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   I   +++ S   D++    D +     +    +  +  L   +  L  RE  +  
Sbjct: 268 SLETPI--GEEDDSHLGDFI---EDQEALAPADAAAYELLKEQLEDVLDTLTEREENVLR 322

Query: 245 ARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 323 LRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 367


>gi|313897024|ref|ZP_07830571.1| RNA polymerase sigma factor RpoD [Selenomonas sp. oral taxon 137
           str. F0430]
 gi|312974471|gb|EFR39939.1| RNA polymerase sigma factor RpoD [Selenomonas sp. oral taxon 137
           str. F0430]
          Length = 381

 Score =  257 bits (657), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 81/275 (29%), Positives = 137/275 (49%), Gaps = 13/275 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI ++P+L  +EE  LA+R  E GD SA HRL  ++LRLVV IA  Y G G
Sbjct: 108 DDPVRMYLKEIGRVPLLTAEEEVELARRM-EAGDASARHRLEEANLRLVVSIAKRYVGRG 166

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I     +
Sbjct: 167 MLFLDLIQEGNLGLLKAVEKFDYSKGYKFSTYATWWIRQAITRALADQARTIRIPVHMVE 226

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 L R+   L      +   E    IAK++ +S   V  +        SL   +  
Sbjct: 227 --TINKLVRVSRSLLQELGRDATAE---EIAKEMGLSVVRVREIMKIAQEPVSLETPV-- 279

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            ++  S   D++    D       +       +  ++  +  L PRE  +   R   E+ 
Sbjct: 280 GEEEDSHLGDFI---EDEAALDPADAASMMLLKEQISEVLKTLAPREAEVLRLRFGLEDG 336

Query: 253 --VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              TLE +   F V+RER+RQIEA+A +K++  ++
Sbjct: 337 RSRTLEEVGQSFGVTRERIRQIEAKALRKLRHPVR 371


>gi|152965499|ref|YP_001361283.1| RNA polymerase sigma factor [Kineococcus radiotolerans SRS30216]
 gi|151360016|gb|ABS03019.1| RNA polymerase, sigma 70 subunit, RpoD family [Kineococcus
           radiotolerans SRS30216]
          Length = 502

 Score =  257 bits (657), Expect = 1e-66,   Method: Composition-based stats.
 Identities = 72/313 (23%), Positives = 140/313 (44%), Gaps = 38/313 (12%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR----------------------- 40
           + +S        +  Y+ +I K+ +L  ++E  LAKR                       
Sbjct: 194 QQVSTAGATADPVKDYLKQIGKVALLNAEQEVELAKRIEAGLFAEEKLHSGEDIDSIFKR 253

Query: 41  ---YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
              +       A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +
Sbjct: 254 ELWWISEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTK 313

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  +         PE
Sbjct: 314 GYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE 371

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +AK+L+++  +V+ +        SL+  +   +   S++ D +    D +  V  +
Sbjct: 372 ---ELAKELDMTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPAD 423

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEAR 275
                  +  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++
Sbjct: 424 AVSFTLLQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESK 483

Query: 276 AFKKVQESIQKQV 288
              K++   + QV
Sbjct: 484 TMSKLRHPSRSQV 496


>gi|218710915|ref|YP_002418536.1| RNA polymerase factor sigma-32 [Vibrio splendidus LGP32]
 gi|218323934|emb|CAV20295.1| RNA polymerase sigma-32 factor [Vibrio splendidus LGP32]
          Length = 303

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 107/287 (37%), Positives = 164/287 (57%), Gaps = 8/287 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  +   + +  +  L  YI      PML   EE  LA+R    G++ AA  L+ SHLR 
Sbjct: 19  MANQAYQMALVTQDSLDSYIRSANSYPMLTPDEERGLAERLHYKGEIDAAKGLILSHLRF 78

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A GY GYGLP++++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 79  VVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 138

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VKI TT  Q++LFFNLR+ K  L    +      +V  +A++L V  SEV  M  RL
Sbjct: 139 WRIVKIATTKAQRKLFFNLRKSKKRLGWFNNG-----EVETVARELGVEPSEVREMESRL 193

Query: 181 -AGDESLNALINSSDKNS--SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
            A D +  A ++  D  S  +    +L        + +       +  N L  ++  L+ 
Sbjct: 194 AAQDATFEAPMDDDDGGSAYTAPVYYLEDKASDVAETVEAANWESHTNNRLGLALKSLDE 253

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R + I  +R L +N  TL++L+  + +S ERVRQ+E  A KK+++++
Sbjct: 254 RSQHIVRSRWLDDNKATLQDLADTYSISAERVRQLEKNAMKKLKQAV 300


>gi|222100016|ref|YP_002534584.1| RNA polymerase sigma factor rpoD [Thermotoga neapolitana DSM 4359]
 gi|221572406|gb|ACM23218.1| RNA polymerase sigma factor rpoD [Thermotoga neapolitana DSM 4359]
          Length = 392

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 81/276 (29%), Positives = 136/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI KIP+L   +E  LA+R  + GD  A  +L+TS+LRLVV IA  Y G GL
Sbjct: 114 DSIKMYLKEIGKIPLLTPAQERELARR-AQMGDKKAKEKLITSNLRLVVSIAKRYMGRGL 172

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGNIGL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 173 SFQDLIQEGNIGLLKAVEKFDWRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 231

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                + +L    +       +   V  +AK +     ++  +        SL + I   
Sbjct: 232 ----TINKLNRLRREYYQKYGEEPSVEELAKMMGKPPEKIKEILEAAKETISLESPI--G 285

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQEN 251
           +   S  +D++  +         ++  R   R  L + +  L+PRE  +   R   L   
Sbjct: 286 EDEDSSIEDFVADESV---PSPKKEAMRMLMREELEKVLKTLSPREAMVLRMRYGLLDGK 342

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           P TLE +   F V+RER+RQIE +A +K++   + +
Sbjct: 343 PKTLEEVGQYFNVTRERIRQIEVKALRKLRHPSRSK 378


>gi|308174309|ref|YP_003921014.1| RpoD [Bacillus amyloliquefaciens DSM 7]
 gi|307607173|emb|CBI43544.1| RpoD [Bacillus amyloliquefaciens DSM 7]
 gi|328554255|gb|AEB24747.1| RNA polymerase sigma factor RpoD [Bacillus amyloliquefaciens TA208]
 gi|328912652|gb|AEB64248.1| RNA polymerase sigma factor rpoD [Bacillus amyloliquefaciens LL3]
          Length = 373

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 78/289 (26%), Positives = 140/289 (48%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++ +L  +EE   A++  E GD  +  RL  ++LRL
Sbjct: 89  LNDLSVPPGVKINDPVRMYLKEIGRVNLLSAKEEITYAQKI-EEGDEESKRRLAEANLRL 147

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GLM+AV+KFD  +G++ +TY+ WWI+ A+   I   
Sbjct: 148 VVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQ 207

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    IA+ ++++  +V  +    
Sbjct: 208 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPTPE---EIAEDMDLTPEKVREILKIA 262

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D +     +    +  +  L   +  L  RE 
Sbjct: 263 QEPVSLETPI--GEEDDSHLGDFI---EDQEATSPSDHAAYELLKEQLEDVLDTLTDREE 317

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 318 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 366


>gi|189184203|ref|YP_001937988.1| RNA polymerase factor sigma-32 [Orientia tsutsugamushi str. Ikeda]
 gi|189180974|dbj|BAG40754.1| heat shock sigma factor RpoH [Orientia tsutsugamushi str. Ikeda]
          Length = 299

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 132/282 (46%), Positives = 191/282 (67%), Gaps = 2/282 (0%)

Query: 4   KNMSIIVN-GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
            N+ I  +  + G   Y+ +I +IP L  +EEY+LAK Y E  +L AAH LV SHL+LV 
Sbjct: 6   DNLPISASDTDNGFYIYLQKINRIPSLTAEEEYMLAKSYFEQNNLKAAHSLVKSHLKLVA 65

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           KIA+ YRGYGLP+ ++VSEGNIGL+QAVKK++PE GFRL+TY++WWIKAA+Q+YILRSWS
Sbjct: 66  KIALSYRGYGLPVVDLVSEGNIGLLQAVKKYNPELGFRLSTYAIWWIKAAIQDYILRSWS 125

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA- 181
           LVK+GTTA QK+LFFNL ++K  +  +    +       IA +  VS +EV  +N RL+ 
Sbjct: 126 LVKLGTTAAQKKLFFNLGKIKNKITKLHARAINSSDYKQIADESGVSIAEVSEVNQRLSN 185

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
            D SLN  I+  + ++++  + +      QE +L  +++   ++ +L  ++  L  RE  
Sbjct: 186 SDLSLNTPISYHEDDATELVELVPEHRPNQEIILANQQDLNLKQEVLQNALQTLTQRELY 245

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           I  AR+LQ+ P TLE LS  F VS+ER+RQIE++AF+K+Q+ 
Sbjct: 246 IIRARKLQDEPDTLEKLSLHFNVSKERIRQIESKAFEKLQQY 287


>gi|309775524|ref|ZP_07670524.1| RNA polymerase sigma factor RpoD [Erysipelotrichaceae bacterium
           3_1_53]
 gi|308916618|gb|EFP62358.1| RNA polymerase sigma factor RpoD [Erysipelotrichaceae bacterium
           3_1_53]
          Length = 397

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 78/276 (28%), Positives = 142/276 (51%), Gaps = 12/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L+ +EE  +A+R ++ GD  A  +L++++LRLVV IA  Y G G+
Sbjct: 123 DPVKMYLKEIGRVELLDPKEEPEIAQRIQD-GDEEAKKKLISANLRLVVSIAKKYVGRGM 181

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 182 LFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 240

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L      +   E++   AK  N+S  +V  +        SL   I   
Sbjct: 241 -TINKLTRIQRQLVQDLGRDPSAEEIA--AKMENISPEKVREIQKIALEPVSLETPI--G 295

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D +     E    +  ++ +   +  L  RE ++   R    +  
Sbjct: 296 EEDDSHLGDFI---EDKEALSPDEYANNQLLKDEINTVLQGLTEREEKVLRLRFGLYDGR 352

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 353 TRTLEEVGKEFNVTRERIRQIEAKALRKLKHPTRSK 388


>gi|219558712|ref|ZP_03537788.1| RNA polymerase sigma factor [Mycobacterium tuberculosis T17]
          Length = 530

 Score =  257 bits (657), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 79/319 (24%), Positives = 148/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------REHGDL- 47
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+  
Sbjct: 217 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSERGEKL 275

Query: 48  ----------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 276 PGIHHRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 335

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 336 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 393

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 394 REPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 445

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 446 AVVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 505

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 506 RQIESKTMSKLRHPSRSQV 524


>gi|311069121|ref|YP_003974044.1| RNA polymerase sigma factor RpoD [Bacillus atrophaeus 1942]
 gi|310869638|gb|ADP33113.1| RNA polymerase sigma factor RpoD [Bacillus atrophaeus 1942]
          Length = 373

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 78/289 (26%), Positives = 140/289 (48%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++ +L  +EE   A++  E GD  +  RL  ++LRL
Sbjct: 89  LNDLSVPPGVKINDPVRMYLKEIGRVNLLSAKEEITYAQKI-EEGDEESKRRLAEANLRL 147

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GLM+AV+KFD  +G++ +TY+ WWI+ A+   I   
Sbjct: 148 VVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQ 207

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    IA+ ++++  +V  +    
Sbjct: 208 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPTPE---EIAEDMDLTPEKVREILKIA 262

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D +     +    +  +  L   +  L  RE 
Sbjct: 263 QEPVSLETPI--GEEDDSHLGDFI---EDQEATSPSDHAAYELLKEQLEDVLDTLTDREE 317

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 318 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 366


>gi|50842515|ref|YP_055742.1| RNA polymerase sigma factor [Propionibacterium acnes KPA171202]
 gi|289425323|ref|ZP_06427100.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes SK187]
 gi|289427207|ref|ZP_06428923.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes J165]
 gi|295130592|ref|YP_003581255.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes SK137]
 gi|50840117|gb|AAT82784.1| RNA polymerase principal sigma factor HrdB [Propionibacterium acnes
           KPA171202]
 gi|289154301|gb|EFD02989.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes SK187]
 gi|289159676|gb|EFD07864.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes J165]
 gi|291377120|gb|ADE00975.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes SK137]
 gi|332675432|gb|AEE72248.1| RNA polymerase principal sigma factor HrdB [Propionibacterium acnes
           266]
          Length = 506

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 76/318 (23%), Positives = 143/318 (44%), Gaps = 41/318 (12%)

Query: 2   NRKNMSIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRY------------------ 41
           +    +++V G     +  Y+ +I K+ +L   EE  LAKR                   
Sbjct: 193 DEPEQTVMVAGATADPVKDYLKQIGKVALLNAVEEVDLAKRIEAGLFAGEQLADPDAKIR 252

Query: 42  -REHGDLS--------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
            ++  D          A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 253 EKDREDYEWIAEDGKVAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEK 312

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWIK A+   +      ++I     +  +   L R++  +      
Sbjct: 313 FDYTKGYKFSTYATWWIKQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGR 370

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE    +A +L+++  +VI +        SL+  +   +   S++ D +    D + 
Sbjct: 371 EPTPE---ELASELDMTAEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEA 422

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVR 270
            V  +       +  L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 423 IVPADAVNFTLLQEQLHDVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIR 482

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 483 QIESKTMSKLRHPSRSQV 500


>gi|332531759|ref|ZP_08407644.1| RNA polymerase sigma factor RpoH [Pseudoalteromonas haloplanktis
           ANT/505]
 gi|332038735|gb|EGI75177.1| RNA polymerase sigma factor RpoH [Pseudoalteromonas haloplanktis
           ANT/505]
          Length = 287

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 109/285 (38%), Positives = 169/285 (59%), Gaps = 12/285 (4%)

Query: 6   MSIIVNGE-IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           M++ V  +   +  Y+  +  IPML+ ++E  LAKR +E GDLSAA +L+ SHLR V  I
Sbjct: 8   MALTVGQQSASMDGYLQAVSTIPMLKVEQEQELAKRLQEEGDLSAAKQLIMSHLRFVAHI 67

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y GYGLP ++++ EGNIGLM+AVK+FDP  G RL ++++ WIKA + E++L++W +V
Sbjct: 68  AKSYSGYGLPQADLIQEGNIGLMKAVKRFDPTVGVRLVSFAVHWIKAEIHEFVLKNWRIV 127

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-D 183
           K+ TT  Q++LFFNLR+ K  L           +V  +A +L VSE EV  M  R++G D
Sbjct: 128 KVATTKAQRKLFFNLRKNKKRLGWFNQ-----AEVSTVASELGVSEKEVREMESRMSGQD 182

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM----LTRSMSVLNPRE 239
              +   + +D   +     + Y  DG    L +  E++  +      L  ++  L+ R 
Sbjct: 183 MGFDLTGDDNDDAPTSTYSPVQYLTDGAAD-LADDVEQEQWKEQAHTRLFSALKTLDERS 241

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + I  AR L ++  TL+ L+ ++ VS ERVRQ+E  A KK+Q ++
Sbjct: 242 QDIVSARWLSDDKATLQELAQKYSVSAERVRQLEKTAMKKLQSAM 286


>gi|312880428|ref|ZP_07740228.1| RNA polymerase, sigma 70 subunit, RpoD [Aminomonas paucivorans DSM
           12260]
 gi|310783719|gb|EFQ24117.1| RNA polymerase, sigma 70 subunit, RpoD [Aminomonas paucivorans DSM
           12260]
          Length = 387

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 82/277 (29%), Positives = 133/277 (48%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
              +  Y+ EI KIP+L  +EE  LAK   E G   +  +LV ++LRLVV IA  Y G G
Sbjct: 115 SDPVRMYLREIGKIPLLTPEEEVELAKGV-EAGHAPSKAKLVEANLRLVVSIAKKYIGRG 173

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I     +
Sbjct: 174 MLFLDLIQEGNLGLIRAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 233

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 + +L    + +     +      IA ++ +    V  +        SL   I  
Sbjct: 234 -----TINKLIRVSRQLVQRLGREPTAEEIAGEMEIPAERVEEIQRIAQEPVSLETPI-- 286

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN- 251
            ++  SQ  D+L    D       E    +  R  L   +  L  RER +   R   E+ 
Sbjct: 287 GEEEDSQLGDFL---EDKDLPSPEEAAASQILREQLEEMLEDLTDREREVLRLRFGLEDG 343

Query: 252 -PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            P TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 344 HPHTLEEVGRRFGVTRERIRQIEAKALRKLRHPSRSK 380


>gi|320531403|ref|ZP_08032370.1| RNA polymerase sigma factor RpoD [Actinomyces sp. oral taxon 171
           str. F0337]
 gi|320136375|gb|EFW28356.1| RNA polymerase sigma factor RpoD [Actinomyces sp. oral taxon 171
           str. F0337]
          Length = 537

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 74/304 (24%), Positives = 138/304 (45%), Gaps = 39/304 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREHG----------------------D 46
             +  Y+ +I K+ +L  ++E  LAKR     Y EH                        
Sbjct: 238 DPVKDYLKQIGKVALLNAEQEVELAKRIEAGLYAEHRLAEKGNDLPAKLRRELHWVAQDG 297

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ 
Sbjct: 298 QRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYAT 357

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +A +L
Sbjct: 358 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAVEL 412

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +V+ +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 413 DMTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 467

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 468 QLHAVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 527

Query: 285 QKQV 288
           + QV
Sbjct: 528 RSQV 531


>gi|118618666|ref|YP_906998.1| RNA polymerase sigma factor [Mycobacterium ulcerans Agy99]
 gi|118570776|gb|ABL05527.1| RNA polymerase sigma factor SigA [Mycobacterium ulcerans Agy99]
          Length = 501

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 78/319 (24%), Positives = 148/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------------- 41
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR                     
Sbjct: 188 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMAELTDRGEKL 246

Query: 42  --REHGDL--------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
              +  D+         A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 247 PAAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 306

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 307 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 364

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 365 REPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 416

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 417 AVVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 476

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 477 RQIESKTMSKLRHPSRSQV 495


>gi|221133912|ref|ZP_03560217.1| RNA polymerase, sigma 32 subunit, RpoH [Glaciecola sp. HTCC2999]
          Length = 283

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 113/281 (40%), Positives = 167/281 (59%), Gaps = 7/281 (2%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M++ +     +  YI  +  IPML   EE  LA+R    GDL+AA  LV SHLR VV IA
Sbjct: 7   MALTIPQSGSIESYIQSVSNIPMLSADEEKSLAERLFNEGDLTAARELVMSHLRFVVHIA 66

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGL  +++V EGNIGLM+AVK+FDP  G RL ++++ WIKA + E++L++W +VK
Sbjct: 67  KSYSGYGLAQADLVQEGNIGLMKAVKRFDPNVGVRLVSFAVHWIKAEIHEFVLKNWRIVK 126

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DE 184
           + TT  Q++LFFNLR+ K  L   T       +V  +A++L VSE EV+ M  R+   D 
Sbjct: 127 VATTKAQRKLFFNLRKSKKRLGWFTHK-----EVQKVAEELGVSEKEVLQMEARMGSQDT 181

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           + +   +  D NS+      + D     E  +I  +   N    L  ++  L+ R + I 
Sbjct: 182 AFDLSSDDGDDNSNFSPAQYLEDKSENVEAAVINADYDSNASARLYSAIKTLDERSQYII 241

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           E R L +N +TL++L++++EVS ERVRQIE  A KK+Q ++
Sbjct: 242 ETRWLNDNKMTLQDLAAKYEVSAERVRQIEKNAMKKIQAAM 282


>gi|153953576|ref|YP_001394341.1| hypothetical protein CKL_0942 [Clostridium kluyveri DSM 555]
 gi|219854198|ref|YP_002471320.1| hypothetical protein CKR_0855 [Clostridium kluyveri NBRC 12016]
 gi|146346457|gb|EDK32993.1| RpoD2 [Clostridium kluyveri DSM 555]
 gi|219567922|dbj|BAH05906.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 354

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 83/293 (28%), Positives = 142/293 (48%), Gaps = 17/293 (5%)

Query: 1   MNRKNMSIIVNGEIGLS----RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTS 56
           +N KN+ + V   I +      Y+ EI K+P+L  +EE  LAK+  E GD  A  +L  +
Sbjct: 66  LNEKNLDLSVPEGIAIDDPVRMYLKEIGKVPLLLPEEEMSLAKKI-EEGDQIAKKKLAEA 124

Query: 57  HLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           +LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   
Sbjct: 125 NLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYRKGFKFSTYATWWIRQAITRA 184

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
           I      ++I     +      + +L    + +     +      +AK + +   +V  +
Sbjct: 185 IADQARTIRIPVHMVE-----TINKLIRVSRQLLQELGREPHAEEVAKIMEMPVDKVREI 239

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
                   SL   I   ++  S   D++      +     E       +  L   +  L 
Sbjct: 240 MKIAQEPVSLETPI--GEEEDSHLGDFIPD---DEAPAPAEAAAFTMLKEQLINVLDTLT 294

Query: 237 PRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           PRE ++   R   ++    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 295 PREEKVLRLRFGLDDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 347


>gi|84495969|ref|ZP_00994823.1| RNA polymerase sigma factor [Janibacter sp. HTCC2649]
 gi|84382737|gb|EAP98618.1| RNA polymerase sigma factor [Janibacter sp. HTCC2649]
          Length = 546

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 71/303 (23%), Positives = 137/303 (45%), Gaps = 38/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYR---------EHGDL----------------- 47
             +  Y+ +I K+ +L  ++E  LAKR             GD                  
Sbjct: 248 DPVKDYLKQIGKVALLNAEQEVELAKRIEAGLFGEERLNSGDKIDMKLKRELWWIAQDGK 307

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ W
Sbjct: 308 NAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATW 367

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   +      ++I     +  +   L R++  +         PE    +A +L+
Sbjct: 368 WIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAIELD 422

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++  +V+ +        SL+  +   +   S++ D +    D +  V  +       +  
Sbjct: 423 MTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQEQ 477

Query: 228 LTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   +
Sbjct: 478 LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSR 537

Query: 286 KQV 288
            Q 
Sbjct: 538 SQA 540


>gi|300718824|ref|YP_003743627.1| RNA polymerase sigma-32 factor [Erwinia billingiae Eb661]
 gi|299064660|emb|CAX61780.1| RNA polymerase sigma-32 factor [Erwinia billingiae Eb661]
          Length = 284

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 104/289 (35%), Positives = 164/289 (56%), Gaps = 8/289 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +     L  YI      PML  +EE  LA+R    GDL AA  L+ SHLR 
Sbjct: 1   MTKEMQTLAIAPLGNLDSYIRAANVWPMLTAEEEKALAERLHYQGDLEAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          E+V  +A++L V+  +V+ M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKAKQRLGWFNQ-----EEVEMVARELGVTSKDVLEMESRM 175

Query: 181 AGDESLNALINSSDKNS-SQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPR 238
           A  +         +    S      + D        IE++  ++   + L+ +M  L+ R
Sbjct: 176 AAQDMTFDPTPDDEGEGRSMAPMLYLQDKSSDFADGIEEDNWESHAADKLSDAMQGLDER 235

Query: 239 ERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + I  AR L ++   TL+ L+ ++ VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 SQNIIRARWLDDDNKTTLQELADQYGVSAERVRQLEKNAMKKLRVAIEA 284


>gi|90581423|ref|ZP_01237218.1| RNA polymerase sigma factor [Vibrio angustum S14]
 gi|90437400|gb|EAS62596.1| RNA polymerase sigma factor [Vibrio angustum S14]
          Length = 286

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 105/287 (36%), Positives = 171/287 (59%), Gaps = 8/287 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+++  ++ +     L  YI  + + PML  + E  LA+R     D+++A  LV SHLR 
Sbjct: 1   MSQEMSAMALVSTESLDSYIQTVNRYPMLTPEREKELAERLHYDDDINSAKALVMSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA GY GYGLPI++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHIARGYSGYGLPIADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L    +     ++V  +A++L V  S+V  M  RL
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKSKKRLGWFNN-----DEVNMVAEQLGVEPSDVREMESRL 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNP 237
           A  +    + N  D+  +       Y  D    + +  EE     +  N L+++++ L+ 
Sbjct: 176 AAQDPTFEMQNDDDERDTTPVAPAYYLEDKSSDLALTYEENNWENHANNRLSQALASLDE 235

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R + I  +R L +   TL++L+  + VS ER+RQ+E  A KK+++++
Sbjct: 236 RSQHIVRSRWLDDEKSTLQDLADNYGVSAERIRQLEKNAMKKLKDAV 282


>gi|229525043|ref|ZP_04414448.1| RNA polymerase sigma factor RpoH [Vibrio cholerae bv. albensis
           VL426]
 gi|229338624|gb|EEO03641.1| RNA polymerase sigma factor RpoH [Vibrio cholerae bv. albensis
           VL426]
          Length = 286

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 106/288 (36%), Positives = 168/288 (58%), Gaps = 9/288 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  +   + +  +  L  YI  +   PML   EE  LA+R    GD+ AA  L+ SHLR 
Sbjct: 1   MTNQAYPMALVSQDSLDSYIRSVNGYPMLSADEERELAERLHYKGDIDAAKGLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A GY GYGLP++++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VKI TT  Q++LFFNLR+ K  L    +      +V  +A++L V  +EV  M  RL
Sbjct: 121 WRIVKIATTKAQRKLFFNLRKSKKRLGWFNNG-----EVETVARELGVEPAEVREMESRL 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNP 237
           A  ++   +    D+N   +   ++Y  D    +   L  +    +    L+ +++ L+ 
Sbjct: 176 AAQDAAFEMSAEDDENGMAYTAPVLYLEDKHSDLADNLAAENWEAHTTQRLSMALASLDE 235

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R + I  AR L ++   TL++L+  + VS ER+RQ+E  A +K++E++
Sbjct: 236 RSQHIVRARWLDDDNKTTLQDLAEMYGVSAERIRQLEKNAMRKLKEAV 283


>gi|298369543|ref|ZP_06980860.1| alternative sigma factor RpoH [Neisseria sp. oral taxon 014 str.
           F0314]
 gi|298282100|gb|EFI23588.1| alternative sigma factor RpoH [Neisseria sp. oral taxon 014 str.
           F0314]
          Length = 287

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 115/288 (39%), Positives = 179/288 (62%), Gaps = 7/288 (2%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N   +  + +G   L +YIH +  IPML  +EE  LA+R ++ GDL AA +L+ SHLR+V
Sbjct: 3   NAFALPAVHSGNGSLEQYIHTVNSIPMLSAEEESSLAER-QQKGDLEAAKQLILSHLRVV 61

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+ILR+W
Sbjct: 62  VSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPSRGARLFSFAVHWIKAEIHEFILRNW 121

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            LV++ TT  Q++LFFNLR ++  L A++     P++   IA  L V  SEV+ M  R+ 
Sbjct: 122 RLVRVATTKPQRKLFFNLRSMRKSLNALS-----PKEAQEIADDLGVKLSEVLEMEQRMT 176

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
             +      NS D++S    DWL        + L ++     +   L  +++ L+ R RR
Sbjct: 177 SHDIGIMADNSDDEDSFAPIDWLADHDAEPSRQLAKQAHYALQTEGLQNALAQLDDRSRR 236

Query: 242 IFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           I E+R LQ++  +TL  L+ E+ VS ER+RQIEA+A +K++  + ++ 
Sbjct: 237 IVESRWLQDDGGLTLHELADEYGVSAERIRQIEAKAMQKLRGFLAEEA 284


>gi|290967746|ref|ZP_06559301.1| RNA polymerase sigma factor RpoD [Megasphaera genomosp. type_1 str.
           28L]
 gi|290782262|gb|EFD94835.1| RNA polymerase sigma factor RpoD [Megasphaera genomosp. type_1 str.
           28L]
          Length = 423

 Score =  257 bits (656), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 79/291 (27%), Positives = 132/291 (45%), Gaps = 23/291 (7%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL-----------SAAHRLVTSHL 58
           +N +  +  Y+ EI ++P+L   EE  LAK   +  D             A  +L  ++L
Sbjct: 137 INIDDPVRMYLKEIGRVPLLSADEEITLAKAIEKGNDENATVADKKNGIDAKKKLTDANL 196

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV IA  Y G G+   +++ EGN+GL++AV KFD  +G++ +TY+ WWI+ A+   I 
Sbjct: 197 RLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVDKFDYSKGYKFSTYATWWIRQAITRAIA 256

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
                ++I     +      L R+   L      +  PE    IA+K+ +    V  +  
Sbjct: 257 DQARTIRIPVHMVE--TINKLIRISRQLIQEKGRDPLPE---EIAEKMEIPVERVREIMK 311

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
                 SL   I   ++  S   D++    D +     +       +  +    S L  R
Sbjct: 312 IAQEPVSLETPI--GEEEDSHLGDFI---EDQEAVAPDDAASFILLKEQIEEVFSCLTDR 366

Query: 239 ERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ER++   R       P TLE +   F V+RER+RQIE +A  K++   +++
Sbjct: 367 ERKVLYLRFGLKDGRPRTLEEVGQYFNVTRERIRQIEGKALGKLRNWGKRE 417


>gi|284990384|ref|YP_003408938.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geodermatophilus
           obscurus DSM 43160]
 gi|284063629|gb|ADB74567.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geodermatophilus
           obscurus DSM 43160]
          Length = 429

 Score =  256 bits (655), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 80/319 (25%), Positives = 148/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHG--- 45
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G   
Sbjct: 116 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVDLAKRIEAGLYGAERLRQAEEEGQKL 174

Query: 46  --------------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 175 SPQMRRDLNWIVRDGERAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 234

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 235 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 292

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 293 REPTPE---ELAKEMDITPDKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 344

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ LT  +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 345 AVVAVDAVSFTLMQDQLTSVLQTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 404

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 405 RQIESKTMSKLRHPSRSQV 423


>gi|227872476|ref|ZP_03990816.1| DNA-directed RNA polymerase sigma subunit SigA [Oribacterium sinus
           F0268]
 gi|227841677|gb|EEJ51967.1| DNA-directed RNA polymerase sigma subunit SigA [Oribacterium sinus
           F0268]
          Length = 385

 Score =  256 bits (655), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 83/280 (29%), Positives = 146/280 (52%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           +  E  +  Y+ EI  +P+L  +EEY LA + ++ GD  A  RL+ ++LRLVV IA  Y 
Sbjct: 110 IGTEDPVRMYLKEIGTVPLLTAEEEYALAMK-KQEGDEYAKQRLIEANLRLVVSIAKRYT 168

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   ++V EGN+GL++ V+KFDPE+GF+L+TY+ WWI+ ++   +      +++   
Sbjct: 169 GRGMSFLDLVQEGNLGLIKGVEKFDPEKGFKLSTYATWWIRQSVTRALADQARTIRVPVH 228

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      + ++    + +T        V  +A+ L+++E +V  +        SL   
Sbjct: 229 MVE-----TINKMSKMQRKLTLELGYEPSVKELAEHLDMTEEKVQEIMQIAREPASLETP 283

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   +++ S   D++    D          E    R  +   +  L  RER++   R   
Sbjct: 284 I--GEEDDSNLGDFVA---DTNVLSPEGNVESVMLREHIDTLLGDLKERERQVIVLRFGL 338

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+  P TLE +  EF V+RER+RQIEA+A +K++  ++ +
Sbjct: 339 EDGHPRTLEEVGKEFNVTRERIRQIEAKALRKLRNPVRSK 378


>gi|258622821|ref|ZP_05717838.1| RNA polymerase sigma -32 factor [Vibrio mimicus VM573]
 gi|258584882|gb|EEW09614.1| RNA polymerase sigma -32 factor [Vibrio mimicus VM573]
          Length = 286

 Score =  256 bits (655), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 109/289 (37%), Positives = 169/289 (58%), Gaps = 11/289 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  +   + +  +  L  YI  +   PML   EE  LA+R    GD+ AA  L+ SHLR 
Sbjct: 1   MTNQAYPMALVSQDSLDSYIRSVNGYPMLSADEERELAERLHYKGDIDAAKGLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A GY GYGLP++++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VKI TT  Q++LFFNLR+ K  L    +      +V  +A++L V  SEV  M  RL
Sbjct: 121 WRIVKIATTKAQRKLFFNLRKSKKRLGWFNNG-----EVETVARELGVEPSEVREMESRL 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR----NMLTRSMSVLN 236
           A  ++   +    D+N   +   ++Y  D     L +  E +N        L+ +++ L+
Sbjct: 176 AAQDAAFEMSAEDDENGMAYTAPVLYLEDKHSD-LADNLEAENWEAHTTQRLSMALASLD 234

Query: 237 PRERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            R + I  AR L ++   TL++L+  + VS ER+RQ+E  A +K++E++
Sbjct: 235 ERSQHIVRARWLDDDNKTTLQDLAEMYGVSAERIRQLEKNAMRKLKEAV 283


>gi|148284686|ref|YP_001248776.1| RNA polymerase factor sigma-32 [Orientia tsutsugamushi str.
           Boryong]
 gi|146740125|emb|CAM80313.1| RNA polymerase sigma-32 factor [Orientia tsutsugamushi str.
           Boryong]
          Length = 299

 Score =  256 bits (655), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 132/282 (46%), Positives = 191/282 (67%), Gaps = 2/282 (0%)

Query: 4   KNMSIIVN-GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
            N+ I  +  + G   Y+ +I +IP L  +EEY+LAK Y E  +L AAH LV SHL+LV 
Sbjct: 6   DNLPISASDTDNGFYIYLQKINRIPSLTAEEEYMLAKSYFEQNNLKAAHSLVKSHLKLVA 65

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           KIA+ YRGYGLP+ ++VSEGNIGL+QAVKK++PE GFRL+TY++WWIKAA+Q+YILRSWS
Sbjct: 66  KIALSYRGYGLPVVDLVSEGNIGLLQAVKKYNPELGFRLSTYAIWWIKAAIQDYILRSWS 125

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA- 181
           LVK+GTTA QK+LFFNL ++K  +  +    +       IA +  VS +EV  +N RL+ 
Sbjct: 126 LVKLGTTAAQKKLFFNLGKIKNKITKMHARAINSSDYKQIADESGVSIAEVSEVNQRLSN 185

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
            D SLN  I+  + ++++  + +      QE +L  +++   ++ +L  ++  L  RE  
Sbjct: 186 SDLSLNTPISYHEDDATELVELVPEHRPNQEIILANQQDLNLKKEVLENALQTLTQRELY 245

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           I  AR+LQ+ P TLE LS  F VS+ER+RQIE++AF+K+Q+ 
Sbjct: 246 IIRARKLQDEPDTLEKLSLHFNVSKERIRQIESKAFEKLQQY 287


>gi|289570879|ref|ZP_06451106.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis T17]
 gi|289544633|gb|EFD48281.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis T17]
          Length = 528

 Score =  256 bits (655), Expect = 2e-66,   Method: Composition-based stats.
 Identities = 79/319 (24%), Positives = 148/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------REHGDL- 47
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+  
Sbjct: 215 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSERGEKL 273

Query: 48  ----------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 274 PGIHHRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 333

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 334 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 391

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 392 REPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 443

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 444 AVVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 503

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 504 RQIESKTMSKLRHPSRSQV 522


>gi|168335371|ref|ZP_02693465.1| RNA polymerase, sigma 70 subunit, RpoD family protein [Epulopiscium
           sp. 'N.t. morphotype B']
          Length = 364

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 82/280 (29%), Positives = 142/280 (50%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V+ +  +  Y+ EI K+P+L   +E  LAKR  E GD  A  RL  ++LRLVV IA  Y 
Sbjct: 89  VSIDDPVRMYLKEIGKVPLLSADDEIKLAKRM-ESGDEEARKRLAEANLRLVVSIAKRYV 147

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 148 GRGMLFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 207

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      L R++  L      + +PE    IA+++ +S ++V  +        +L   
Sbjct: 208 MVE--TINKLMRIQRQLLQELGRDPQPE---EIAREMELSVNKVREIMKISQEPVALETP 262

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  +   D+L            E       +  L   +  L  RE+++ + R   
Sbjct: 263 I--GEEEDTNLGDFLAD---EDAPAPAEAAAFTLLKEQLIEVLDTLTDREQKVLKLRFGL 317

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 318 DDGRARTLEEVGREFNVTRERIRQIEAKALRKLRHPSRSK 357


>gi|154686781|ref|YP_001421942.1| RNA polymerase sigma factor RpoD [Bacillus amyloliquefaciens FZB42]
 gi|154352632|gb|ABS74711.1| RpoD [Bacillus amyloliquefaciens FZB42]
          Length = 373

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 78/289 (26%), Positives = 140/289 (48%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++ +L  +EE   A++  E GD  +  RL  ++LRL
Sbjct: 89  LNDLSVPPGVKINDPVRMYLKEIGRVNLLSAKEEITYAQKI-EEGDEESKRRLAEANLRL 147

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GLM+AV+KFD  +G++ +TY+ WWI+ A+   I   
Sbjct: 148 VVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQ 207

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    IA+ ++++  +V  +    
Sbjct: 208 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPTPE---EIAEDMDLTPEKVREILKIA 262

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D +     +    +  +  L   +  L  RE 
Sbjct: 263 QEPVSLETPI--GEEDDSHLGDFI---EDQEATSPSDHAAYELLKEQLEDVLDTLTDREE 317

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 318 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 366


>gi|152980759|ref|YP_001354832.1| RNA polymerase sigma-32 factor [Janthinobacterium sp. Marseille]
 gi|151280836|gb|ABR89246.1| RNA polymerase sigma-32 factor [Janthinobacterium sp. Marseille]
          Length = 298

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 130/292 (44%), Positives = 182/292 (62%), Gaps = 11/292 (3%)

Query: 2   NRKNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           N   +++  +G +G +  YI  + ++PML  +EE  LA+R R+  DL AA +LV SHLRL
Sbjct: 13  NSNMLALGFSGALGNIDAYISAVNRLPMLTHEEEMSLARRLRDENDLGAAQKLVLSHLRL 72

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA GY GYGLP ++++ EGNIGLM+AVK+FDP++G RL +YSM WIKA M EYIL++
Sbjct: 73  VVSIARGYLGYGLPHADLIQEGNIGLMKAVKRFDPDQGVRLVSYSMHWIKAEMHEYILKN 132

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W LVK+ TT  Q++LFFNLR  K  L     +++ P+QV  +AK LNV   EVI M  RL
Sbjct: 133 WRLVKVATTKAQRKLFFNLRSHKTGL-----DSMTPDQVDELAKTLNVKREEVIEMETRL 187

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D +L A  +  D   +    +L  D     +VL  ++  + +   L+ ++  L+ R 
Sbjct: 188 SGRDIALEAPTDDEDDKFA-PIAYLSSDMQEPTKVLESQQFDRLQTEGLSNALGKLDARS 246

Query: 240 RRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RRI EAR L     +  TL  L+ EF VS ER+RQIEA A KK++ S+    
Sbjct: 247 RRIVEARWLANDDGSGATLHELADEFGVSAERIRQIEAVALKKMKGSLAAYA 298


>gi|187934045|ref|YP_001885115.1| RNA polymerase sigma factor RpoD [Clostridium botulinum B str.
           Eklund 17B]
 gi|187722198|gb|ACD23419.1| RNA polymerase sigma factor RpoD [Clostridium botulinum B str.
           Eklund 17B]
          Length = 374

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 81/277 (29%), Positives = 136/277 (49%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI K+P+L  ++E   AKR  E GD  A  +L  ++LRLVV IA  Y G G
Sbjct: 102 DDPVRMYLKEIGKVPLLSSEQEIDYAKRI-EEGDPVAKKKLAEANLRLVVSIAKRYVGRG 160

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     +
Sbjct: 161 MLFLDLIQEGNLGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 220

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 L R++  L      +  PE    I+K + +   +V  +        SL   I  
Sbjct: 221 --TINKLIRVQRQLLQELGRDPFPE---EISKVMELPVDKVREIQKIAQEPVSLETPI-- 273

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            ++  S   D++      +     E       +  L   +  L PRE ++   R   ++ 
Sbjct: 274 GEEEDSHLGDFIPD---DEAPAPAEAAAFTMLKEQLINVLDTLTPREEKVLRLRFGLDDG 330

Query: 253 --VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 331 RARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 367


>gi|254750874|ref|ZP_05202913.1| RNA polymerase sigma factor RpoD [Bacillus anthracis str. Vollum]
          Length = 359

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 80/282 (28%), Positives = 137/282 (48%), Gaps = 13/282 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRL
Sbjct: 89  LNDLSVPPGVKINDPVRMYLKEIGRVDLLSAEEEIRLATRI-EEGDEEAKRRLAEANLRL 147

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 148 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQ 207

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    I ++++++  +V  +    
Sbjct: 208 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPSPE---EIGEEMDLAPEKVREILKIA 262

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D +     +    +  +  L   +  L  RE 
Sbjct: 263 QEPVSLETPI--GEEDDSHLGDFI---EDQEATSPADHAAYELLKEQLEDVLDTLTDREE 317

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKV 280
            +   R   ++    TLE +   F V+RER+RQIEA+A +K+
Sbjct: 318 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 359


>gi|188587782|ref|YP_001920276.1| RNA polymerase sigma factor RpoD [Clostridium botulinum E3 str.
           Alaska E43]
 gi|251778486|ref|ZP_04821406.1| RNA polymerase sigma factor RpoD [Clostridium botulinum E1 str.
           'BoNT E Beluga']
 gi|188498063|gb|ACD51199.1| RNA polymerase sigma factor RpoD [Clostridium botulinum E3 str.
           Alaska E43]
 gi|243082801|gb|EES48691.1| RNA polymerase sigma factor RpoD [Clostridium botulinum E1 str.
           'BoNT E Beluga']
          Length = 374

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 81/277 (29%), Positives = 136/277 (49%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI K+P+L  ++E   AKR  E GD  A  +L  ++LRLVV IA  Y G G
Sbjct: 102 DDPVRMYLKEIGKVPLLSSEQEIDYAKRI-EEGDPVAKKKLAEANLRLVVSIAKRYVGRG 160

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     +
Sbjct: 161 MLFLDLIQEGNLGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 220

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 L R++  L      +  PE    I+K + +   +V  +        SL   I  
Sbjct: 221 --TINKLIRVQRQLLQELGRDPFPE---EISKVMELPVDKVREIQKIAQEPVSLETPI-- 273

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            ++  S   D++      +     E       +  L   +  L PRE ++   R   ++ 
Sbjct: 274 GEEEDSHLGDFIPD---DEAPAPAEAAAFTMLKEQLINVLDTLTPREEKVLRLRFGLDDG 330

Query: 253 --VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 331 RARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 367


>gi|220927994|ref|YP_002504903.1| RNA polymerase sigma factor RpoD [Clostridium cellulolyticum H10]
 gi|219998322|gb|ACL74923.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           cellulolyticum H10]
          Length = 359

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 84/280 (30%), Positives = 139/280 (49%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V+ +  +  Y+ EI K+P+L   EE  LA R  E+GD+ A  RL  ++LRLVV IA  Y 
Sbjct: 84  VSIDDPVRMYLKEIGKVPLLTADEEIDLAHRM-ENGDIEAKRRLAEANLRLVVSIAKRYV 142

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  RGF+ +TY+ WWI+ A+   I      ++I   
Sbjct: 143 GRGMQFLDLIQEGNLGLIKAVEKFDYRRGFKFSTYATWWIRQAITRAIADQARTIRIPVH 202

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      + +L    + +     +  Q   IAK++ +S  +V  +        SL   
Sbjct: 203 MVE-----TINKLIRVSRQLLQELGREPQPDEIAKEIGMSVDKVREIMKISQEPVSLETP 257

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++            E       +  L   +  L PRE ++   R   
Sbjct: 258 I--GEEEDSHLGDFIPD---DDAPAPAEAAAFTLLKEQLIDVLDTLTPREEKVLRLRFGL 312

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 313 DDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 352


>gi|292670109|ref|ZP_06603535.1| DNA-directed RNA polymerase sigma subunit RpoD [Selenomonas noxia
           ATCC 43541]
 gi|292648297|gb|EFF66269.1| DNA-directed RNA polymerase sigma subunit RpoD [Selenomonas noxia
           ATCC 43541]
          Length = 382

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 83/275 (30%), Positives = 136/275 (49%), Gaps = 13/275 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI ++P+L   EE  LA+R  E GD SA HRL  ++LRLVV IA  Y G G
Sbjct: 109 DDPVRMYLKEIGRVPLLTADEEIELARRM-EAGDESARHRLEEANLRLVVSIAKRYVGRG 167

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I     +
Sbjct: 168 MLFLDLIQEGNLGLLKAVEKFDYSKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 227

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                   R+   L      +   E+V   AK++ +S   V  +        SL   I  
Sbjct: 228 --TINKYIRISRQLLQDLGRDPTAEEV---AKEMGLSTLRVREIMKIAQEPVSLETPI-- 280

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            ++  S   D++    D       +       +  +T  +  L PRE  +   R   E+ 
Sbjct: 281 GEEEDSHLGDFI---EDEAALDPADAASVMLLKEQITEVLQTLAPREAEVLRLRFGLEDG 337

Query: 253 --VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              TLE +   F V+RER+RQIEA+A +K++  ++
Sbjct: 338 RSRTLEEVGQSFGVTRERIRQIEAKALRKLRHPVR 372


>gi|331001843|ref|ZP_08325365.1| hypothetical protein HMPREF0491_00227 [Lachnospiraceae oral taxon
           107 str. F0167]
 gi|330412817|gb|EGG92200.1| hypothetical protein HMPREF0491_00227 [Lachnospiraceae oral taxon
           107 str. F0167]
          Length = 389

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 86/289 (29%), Positives = 150/289 (51%), Gaps = 15/289 (5%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD---LSAAHRLVTSHLRL 60
            +++  V+ E  +  Y+ EI KIP+L   +E  LAK+  +  +     AA R+  S+LRL
Sbjct: 104 DDLNDYVSIEDPIKMYLKEIGKIPLLNVDDEMDLAKKISDPDESIRKEAAKRMAESNLRL 163

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+ + +++ EGN+GL++AV+KFD ++GF+ +TY+ WWI+ A+   I   
Sbjct: 164 VVSIAKRYMGRGMQLLDLIQEGNLGLLRAVEKFDYKKGFKFSTYATWWIRQAITRSIADQ 223

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L + +  L  I      PE+V   AK++N+S  +V  +    
Sbjct: 224 ARTIRIPVHMVE--TINRLIKTQRKLVQILGREPSPEEV---AKEMNISVPKVREIMSFA 278

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               S+   I   D++ S   D+L    D   +V +         + L   + +L  RE+
Sbjct: 279 LEPVSMETPI--GDEDDSHLGDFL---QDYNAKVPVNFAMDVLLHDQLMDVIKLLTEREQ 333

Query: 241 RIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++   R   E+  P TLE +   F ++RER+RQIEA++ +K++   + +
Sbjct: 334 KVILLRFGLEDGKPRTLEEVGKVFGITRERIRQIEAKSLRKLRNPSKSK 382


>gi|157693020|ref|YP_001487482.1| RNA polymerase sigma factor RpoD [Bacillus pumilus SAFR-032]
 gi|157681778|gb|ABV62922.1| DNA-directed RNA polymerase sigma subunit SigA [Bacillus pumilus
           SAFR-032]
          Length = 373

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 78/289 (26%), Positives = 140/289 (48%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++ +L  +EE   A++  E GD  +  RL  ++LRL
Sbjct: 89  LNDLSVPPGVKINDPVRMYLKEIGRVNLLSAKEEITYAQKI-EEGDEESKRRLAEANLRL 147

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GLM+AV+KFD  +G++ +TY+ WWI+ A+   I   
Sbjct: 148 VVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQ 207

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    IA+ ++++  +V  +    
Sbjct: 208 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPTPE---EIAEDMDLTPEKVREILKIA 262

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D +     +    +  +  L   +  L  RE 
Sbjct: 263 QEPVSLETPI--GEEDDSHLGDFI---EDQEATSPSDHAAYELLKEQLEDVLDTLTDREE 317

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 318 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 366


>gi|329295846|ref|ZP_08253182.1| RNA polymerase factor sigma-32 [Plautia stali symbiont]
          Length = 285

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 103/290 (35%), Positives = 164/290 (56%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +     L  Y+      P+L  +EE  LA+R    GDL AA  L+ SHLR 
Sbjct: 1   MTKEMQNLAIAPLGNLESYVRAANNWPVLTAEEEKALAERLHYQGDLDAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHIARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK  TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V+ M  R+
Sbjct: 121 WRIVKAATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVEMVARELGVSSKDVLEMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNP 237
           A  +    + +  D    +    ++Y  D        + E     +  + L+ +M  L+ 
Sbjct: 176 AAQDMTFDMSSDDDAGEGKPMAPVLYLQDKTSDFADGIEEDNWDAHAADKLSDAMLSLDE 235

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L ++   TL+ L+ ++ VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQHIIRARWLDDDNKTTLQELADQYGVSAERVRQLEKNAMKKLRMAIEA 285


>gi|23099399|ref|NP_692865.1| RNA polymerase sigma factor RpoD [Oceanobacillus iheyensis HTE831]
 gi|22777628|dbj|BAC13900.1| RNA polymerase sigma-43(-A) factor [Oceanobacillus iheyensis
           HTE831]
          Length = 380

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 78/289 (26%), Positives = 137/289 (47%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++ + +     +  Y+ EI ++ +L   EE  LA    E GD  A  RL  ++LRL
Sbjct: 96  LNDLSVPLGIKINDPVRMYLKEIGRVNLLSAAEEIDLASSI-EEGDEEAKRRLAEANLRL 154

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 155 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQ 214

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    I +++ +   +V  +    
Sbjct: 215 ARTIRIPVHMVE--TINKLIRVQRSLLQDLGREPTPE---EIGEEMELGPDKVRDILKIA 269

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D +     +    +  +  L   +  L  RE 
Sbjct: 270 QEPVSLETPI--GEEDDSHLGDFI---EDQEAISPSDHAAYELLKEQLEDVLDTLTDREE 324

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   ++    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 325 NVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 373


>gi|241758558|ref|ZP_04756675.1| alternative sigma factor RpoH [Neisseria flavescens SK114]
 gi|241321301|gb|EER57461.1| alternative sigma factor RpoH [Neisseria flavescens SK114]
          Length = 287

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 117/291 (40%), Positives = 187/291 (64%), Gaps = 8/291 (2%)

Query: 1   MNRK-NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLR 59
           MN+   + +I +G   L +YIH +  IPML  +EE  LA+R ++ GDL+AA +L+ SHLR
Sbjct: 1   MNKAFALPVIHSGNGSLEQYIHTVNSIPMLTAEEETQLAER-QQKGDLNAAKQLILSHLR 59

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           +VV IA GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+ILR
Sbjct: 60  VVVSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPSRGARLFSFAVHWIKAEIHEFILR 119

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
           +W LV++ TT  Q++LFFNLR ++ +L A++     P++   IA  L V  SEV+ M  R
Sbjct: 120 NWRLVRVATTKPQRKLFFNLRSMRKNLNALS-----PKEAQEIANDLGVKLSEVLEMEQR 174

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           + G +      N+ D+++    DWL        + L ++     +   L  +++ L+ R 
Sbjct: 175 MTGHDIGIMAENNDDEDNFAPIDWLADHDAEPSRQLSKQAHYALQTEGLQNALAQLDDRS 234

Query: 240 RRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           RRI E+R LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 235 RRIVESRWLQDDGGLTLHELAAEYGVSAERIRQIEAKAMQKLRGFLAEEAE 285


>gi|258625092|ref|ZP_05720011.1| RNA polymerase sigma -32 factor [Vibrio mimicus VM603]
 gi|258582643|gb|EEW07473.1| RNA polymerase sigma -32 factor [Vibrio mimicus VM603]
          Length = 286

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 107/289 (37%), Positives = 169/289 (58%), Gaps = 11/289 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  +   + +  +  L  YI  +   PML   EE  LA+R    GD+ AA  L+ SHLR 
Sbjct: 1   MTNQAYPMALVSQDSLDSYIRSVNGYPMLSADEERELAERLHYKGDIDAAKGLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A GY GYGLP++++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L    +      +V  +A++L V  +EV  M  RL
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKSKKRLGWFNNG-----EVETVARELGVEPAEVREMESRL 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR----NMLTRSMSVLN 236
           A  ++   +    D+N   +   ++Y  D     L +  E +N        L+ +++ L+
Sbjct: 176 AAQDAAFEMSAEDDENGMAYTAPVLYLEDKHSD-LADNLEAENWEAHTTQRLSMALASLD 234

Query: 237 PRERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            R + I  AR L ++   TL++L+  + VS ER+RQ+E  A +K++E++
Sbjct: 235 ERSQHIVRARWLDDDNKTTLQDLAEMYGVSAERIRQLEKNAMRKLKEAV 283


>gi|259910110|ref|YP_002650466.1| RNA polymerase factor sigma-32 [Erwinia pyrifoliae Ep1/96]
 gi|224965732|emb|CAX57264.1| RNA polymerase sigma-32 factor [Erwinia pyrifoliae Ep1/96]
 gi|283480207|emb|CAY76123.1| RNA polymerase sigma-32 factor [Erwinia pyrifoliae DSM 12163]
 gi|310765698|gb|ADP10648.1| RNA polymerase factor sigma-32 [Erwinia sp. Ejp617]
          Length = 284

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 103/289 (35%), Positives = 161/289 (55%), Gaps = 8/289 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +     L  YI      PML  +EE  LA+R    G L AA  L+ SHLR 
Sbjct: 1   MTKEMQTLAIAPLGNLDSYIRAANAWPMLTAEEEKALAERLHYQGCLEAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKAKQRLGWFNQ-----DEVEMVARELGVSSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNS-SQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPR 238
           A  +         +    S      + D        IE++  ++   + L  +M  L+ R
Sbjct: 176 AAQDMTFDPTPDDEGEGRSMAPMLYLQDKSSDFANGIEEDNWEDHAADKLNDAMQGLDER 235

Query: 239 ERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + I  AR L ++   TL+ L+ ++ VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 SQHIIRARWLDDDNKTTLQELADQYGVSAERVRQLEKNAMKKLRVAIEA 284


>gi|242281118|ref|YP_002993247.1| RNA polymerase, sigma 70 family subunit [Desulfovibrio salexigens
           DSM 2638]
 gi|242124012|gb|ACS81708.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio
           salexigens DSM 2638]
          Length = 322

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 118/285 (41%), Positives = 176/285 (61%), Gaps = 8/285 (2%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V  +  L  Y+ EI + P+LE  EE+ LAK+ +E+GD  AA RLV+SHLRLVVKIAM ++
Sbjct: 36  VATKDPLHLYLQEISRFPLLEPDEEFRLAKQVQENGDQQAAFRLVSSHLRLVVKIAMDFQ 95

Query: 70  GYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
              +  + +++ EGN+GLM+AV KFDP++G + + Y+ +WIKA + +YI+ +W +VKIGT
Sbjct: 96  RRWMQNVLDLIQEGNVGLMKAVNKFDPDKGIKFSYYAAFWIKAYILKYIMDNWRMVKIGT 155

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLN 187
           T  Q++LF+NL + +  LQA+            ++KKLNVSE E+  M+ RLA  D SLN
Sbjct: 156 TQTQRKLFYNLNKERQRLQAL----GFDPTTSELSKKLNVSEEEITEMDQRLAKNDLSLN 211

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             +   + + +   D+L     G E+ L  KE      + L   +  LN +E+ I   R 
Sbjct: 212 --LKFGEDSEATRMDFLPDLGPGVEETLANKEISTLLLDQLRAIVPNLNEKEQVILNDRL 269

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
           L ++P TL  +  EF V+RERVRQIEAR  KK++E + + V+  S
Sbjct: 270 LSDSPRTLREIGEEFGVTRERVRQIEARLLKKLREHLAESVKDFS 314


>gi|282854019|ref|ZP_06263356.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes J139]
 gi|282583472|gb|EFB88852.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes J139]
 gi|314922986|gb|EFS86817.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL001PA1]
 gi|314966763|gb|EFT10862.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL082PA2]
 gi|314981097|gb|EFT25191.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL110PA3]
 gi|315091922|gb|EFT63898.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL110PA4]
 gi|315093321|gb|EFT65297.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL060PA1]
 gi|327327588|gb|EGE69364.1| RNA polymerase principal sigma factor HrdB [Propionibacterium acnes
           HL103PA1]
          Length = 510

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 76/318 (23%), Positives = 143/318 (44%), Gaps = 41/318 (12%)

Query: 2   NRKNMSIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRY------------------ 41
           +    +++V G     +  Y+ +I K+ +L   EE  LAKR                   
Sbjct: 197 DEPEQTVMVAGATADPVKDYLKQIGKVALLNAVEEVDLAKRIEAGLFAGEQLADPDAKIR 256

Query: 42  -REHGDLS--------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
            ++  D          A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 257 EKDREDYEWIAEDGKVAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEK 316

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWIK A+   +      ++I     +  +   L R++  +      
Sbjct: 317 FDYTKGYKFSTYATWWIKQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGR 374

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE    +A +L+++  +VI +        SL+  +   +   S++ D +    D + 
Sbjct: 375 EPTPE---ELANELDMTAEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEA 426

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVR 270
            V  +       +  L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 427 IVPADAVNFTLLQEQLHDVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIR 486

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 487 QIESKTMSKLRHPSRSQV 504


>gi|261380105|ref|ZP_05984678.1| alternative sigma factor RpoH [Neisseria subflava NJ9703]
 gi|284797325|gb|EFC52672.1| alternative sigma factor RpoH [Neisseria subflava NJ9703]
          Length = 287

 Score =  256 bits (655), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 117/291 (40%), Positives = 187/291 (64%), Gaps = 8/291 (2%)

Query: 1   MNRK-NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLR 59
           MN+   + +I +G   L +YIH +  IPML  +EE  LA+R ++ GDL+AA +L+ SHLR
Sbjct: 1   MNKAFALPVIHSGNGSLEQYIHTVNSIPMLTAEEETQLAER-QQKGDLNAAKQLILSHLR 59

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           +VV IA GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+ILR
Sbjct: 60  VVVSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPSRGARLFSFAVHWIKAEIHEFILR 119

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
           +W LV++ TT  Q++LFFNLR ++ +L A++     P++   IA  L V  SEV+ M  R
Sbjct: 120 NWRLVRVATTKPQRKLFFNLRSMRKNLNALS-----PKEAQEIADDLGVKLSEVLEMEQR 174

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           + G +      N+ D+++    DWL        + L ++     +   L  +++ L+ R 
Sbjct: 175 MTGHDIGIMAENNDDEDNFAPIDWLADHDAEPSRQLSKQAHYALQTEGLQNALAQLDDRS 234

Query: 240 RRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           RRI E+R LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 235 RRIVESRWLQDDGGLTLHELAAEYGVSAERIRQIEAKAMQKLRGFLAEEAE 285


>gi|260890619|ref|ZP_05901882.1| RNA polymerase sigma factor RpoD [Leptotrichia hofstadii F0254]
 gi|260859664|gb|EEX74164.1| RNA polymerase sigma factor RpoD [Leptotrichia hofstadii F0254]
          Length = 392

 Score =  256 bits (654), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 80/284 (28%), Positives = 143/284 (50%), Gaps = 13/284 (4%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M+  ++ +  +  Y+ EI +IP+L  +EE   A+R   +G+  A  +L+ S+LRLVV IA
Sbjct: 113 MAESMDVDEPIKMYLREIGQIPLLSYEEEIDYAQRVL-NGEEEAKQKLIESNLRLVVSIA 171

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             +   GL + +++ EGN+GLM+AV+KF+ E+GF+ +TY+ WWI+ A+   I      ++
Sbjct: 172 KKHTNRGLKMLDLIQEGNMGLMKAVEKFEYEKGFKFSTYATWWIRQAITRAIADQGRTIR 231

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           I        +   + ++K   + I     K      +A+KL +   +V S+        S
Sbjct: 232 IPVH-----MIETINKIKKESRIILQETGKEPTAEELAEKLELPVEKVKSILEMNQDPIS 286

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L   + S  +  S+  D++  D         +   R   +  L   +  LN RE  +   
Sbjct: 287 LETPVGS--EEDSELGDFVEDDKFAN---PYDATTRVLLKEQLDEVLKTLNEREEMVLRY 341

Query: 246 RRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           R   ++    TLE +   F V+RER+RQIE +A +K++   +++
Sbjct: 342 RYGLDDGSQKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRRK 385


>gi|224827256|ref|ZP_03700350.1| RNA polymerase, sigma 32 subunit, RpoH [Lutiella nitroferrum 2002]
 gi|224600545|gb|EEG06734.1| RNA polymerase, sigma 32 subunit, RpoH [Lutiella nitroferrum 2002]
          Length = 287

 Score =  256 bits (654), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 115/293 (39%), Positives = 173/293 (59%), Gaps = 7/293 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M       + +    L +YI  +  +P+L  +EE  LA R     DL AA +LV SHLR+
Sbjct: 1   MTATFALPVPSSSGSLEQYIQIVNSVPLLSAEEENELANRLHAQNDLEAAKKLVLSHLRV 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA GY GYGLP ++++ EGNIGLM+AVK+F+P RG RL ++++ WIKA + E+ILR+
Sbjct: 61  VVSIARGYAGYGLPQADLIQEGNIGLMKAVKRFEPNRGVRLFSFAVHWIKAEIHEFILRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W LV++ TT  Q++LFFNLR +K    A+TD+  +      IA  L V   EV  M  R+
Sbjct: 121 WRLVRVATTKPQRKLFFNLRSMKKSFAALTDSEARV-----IADDLGVKPEEVREMETRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +G + +  L + +D       DWL        + L +K     +   L +++S L+ R R
Sbjct: 176 SG-QDVALLADDNDDEGFAPIDWLADSDHEPTRQLEKKAFDHLQTAGLEQALSSLDARSR 234

Query: 241 RIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
           RI EAR L ++   TL  L++EF VS ER+RQIEA+A  K++ ++ ++  + +
Sbjct: 235 RIIEARWLADDSGATLHELAAEFGVSAERIRQIEAKALTKMKAALSERAAIEA 287


>gi|319441597|ref|ZP_07990753.1| RNA polymerase sigma factor [Corynebacterium variabile DSM 44702]
          Length = 536

 Score =  256 bits (654), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 78/319 (24%), Positives = 152/319 (47%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------REHGDL- 47
            RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR              +E G+  
Sbjct: 223 ARKDAELTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYATYKMEQIKESGEKV 281

Query: 48  ----------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 282 SPMQKRDLREIDRDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 341

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 342 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 399

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++E +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 400 REPTPE---ELAKEMDITEDKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 451

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERV 269
             + ++       ++ L   +  L+ RE  + + R    +  P TL+ +   + V+RER+
Sbjct: 452 AVIAVDAVSFTLLQDQLQDVLHTLSEREAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERI 511

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 512 RQIESKTMSKLRHPSRSQV 530


>gi|269794902|ref|YP_003314357.1| RNA polymerase sigma-70 subunit RpoD [Sanguibacter keddieii DSM
           10542]
 gi|269097087|gb|ACZ21523.1| RNA polymerase, sigma 70 subunit, RpoD [Sanguibacter keddieii DSM
           10542]
          Length = 516

 Score =  256 bits (654), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 73/304 (24%), Positives = 139/304 (45%), Gaps = 39/304 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE--------------------------HGD- 46
             +  Y+ +I K+ +L  ++E  LAKR                              GD 
Sbjct: 217 DPVKDYLKQIGKVALLNAEQEVDLAKRIEAGLFAEERLSAPDASFAPKARRELEWIAGDG 276

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 277 RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 336

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L
Sbjct: 337 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKEL 391

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +V+ +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 392 DMTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 446

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L + +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 447 QLHQVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 506

Query: 285 QKQV 288
           + QV
Sbjct: 507 RSQV 510


>gi|208779746|ref|ZP_03247090.1| alternative sigma factor RpoH [Francisella novicida FTG]
 gi|208744201|gb|EDZ90501.1| alternative sigma factor RpoH [Francisella novicida FTG]
          Length = 292

 Score =  256 bits (654), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 105/286 (36%), Positives = 175/286 (61%), Gaps = 7/286 (2%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
             K  ++ V  +  LS Y++ +  +P+L  ++E  LA+RY+   DL AA +LV SHLR V
Sbjct: 9   ATKTKTLPVVSDNNLSAYLNFVNTLPVLSLEQEQELARRYKYKKDLDAAQQLVLSHLRFV 68

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            KIA  + GYGL I++++ EGNIGLM+AV KFDP++G RL ++++ WIKA M +Y+L++W
Sbjct: 69  TKIARNFSGYGLSIADLIQEGNIGLMKAVSKFDPDQGVRLVSFAVHWIKAEMHDYVLKNW 128

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL- 180
            +VK+ TT  Q++LFFNLR +K  +  ++      E +  +A++L V E  VI M  R+ 
Sbjct: 129 KIVKVATTKAQRKLFFNLRSIKDKIGWLS-----SEDIKELAEELGVKEETVIEMEKRMC 183

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            GD SL+      D   +  Q   + D     E  +++++   N + ++   +S  + R 
Sbjct: 184 QGDASLDLPYTDDDGEQTSQQSLYLEDKSSNIEHQVVQQDYYDNFKAIVKDVLSGFDTRT 243

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + I  +R L +N  TL++L++++ +S ERVRQIE  A  K++++I+
Sbjct: 244 KDIIMSRYLLDNKATLQDLAAKYNISAERVRQIEEDALAKLKKAIK 289


>gi|34499661|ref|NP_903876.1| RNA polymerase factor sigma-32 [Chromobacterium violaceum ATCC
           12472]
 gi|34105511|gb|AAQ61866.1| RNA polymerase sigma-32 factor [Chromobacterium violaceum ATCC
           12472]
          Length = 287

 Score =  256 bits (654), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 121/294 (41%), Positives = 180/294 (61%), Gaps = 9/294 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           MN      + +    L +YI  +  IPML  ++E  LA R+++  DL AA ++V SHLR+
Sbjct: 1   MNTTFALPVPSTSGSLEQYIQAVNSIPMLTPEQETELATRFQQENDLEAARQMVLSHLRV 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV ++ GY GYGL  ++++ EGNIGLM+AVK+F+P RG RL ++++ WIKA + E+ILR+
Sbjct: 61  VVSVSRGYAGYGLQQADLIQEGNIGLMKAVKRFEPGRGVRLFSFAIHWIKAEIHEFILRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W LV+I TT  Q++LFFNLR +K    A+++   K     +IA+ L V   EV  M  R+
Sbjct: 121 WRLVRIATTKPQRKLFFNLRSMKSGFSALSEQEAK-----SIAEDLGVKPEEVREMEIRM 175

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            G D SL  L +S D++S    DWL   H    + L  +     +   L  ++S L+PR 
Sbjct: 176 TGQDVSL--LADSDDEDSYAPIDWLADSHSEPTRALERRAFDMLQSEGLEYALSTLDPRS 233

Query: 240 RRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
           RRI EAR L ++   TL  L++EF VS ER+RQIEA+A  K++ ++ + V L +
Sbjct: 234 RRIVEARWLADDSGATLHELAAEFGVSAERIRQIEAKALSKMKAALSEGVVLDN 287


>gi|332142899|ref|YP_004428637.1| RNA polymerase sigma factor [Alteromonas macleodii str. 'Deep
           ecotype']
 gi|332143056|ref|YP_004428794.1| RNA polymerase sigma factor [Alteromonas macleodii str. 'Deep
           ecotype']
 gi|327552921|gb|AEA99639.1| RNA polymerase sigma factor [Alteromonas macleodii str. 'Deep
           ecotype']
 gi|327553078|gb|AEA99796.1| RNA polymerase sigma factor [Alteromonas macleodii str. 'Deep
           ecotype']
          Length = 284

 Score =  256 bits (654), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 110/284 (38%), Positives = 166/284 (58%), Gaps = 6/284 (2%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N ++M++ V     +  YI  +  I ML  +EE  LA R RE  DL AA +LV SHLR V
Sbjct: 4   NLQSMALSVPHSGSIEGYIQAVSSIDMLSAEEERELAVRLREDEDLQAARKLVMSHLRFV 63

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA  Y GYGLP ++++ EGNIGLM+AVK+FDP  G RL ++++ WIKA + E++L++W
Sbjct: 64  VHIAKSYSGYGLPQADLIQEGNIGLMKAVKRFDPTVGVRLVSFAVHWIKAEIHEFVLKNW 123

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            +VK+ TT  Q++LFFNLR+ K  L   T      ++V  +A +L VS  EV+ M  R++
Sbjct: 124 RIVKVATTKAQRKLFFNLRKAKKRLGWFTH-----DEVQTVANELGVSTKEVLQMEARMS 178

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRER 240
             +    L    D+  +      + D     E  +I  +        L  ++  L+ R +
Sbjct: 179 SQDQAFDLSADEDETGNFAPVQFLEDKSSDVETDVINNDWDTAASKRLYSAIKTLDDRSQ 238

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            I E R L +N +TL++L+ +++VS ERVRQIE  A KK+Q ++
Sbjct: 239 DIIETRWLADNKITLQDLADKYQVSAERVRQIEKNAMKKLQAAM 282


>gi|296129901|ref|YP_003637151.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cellulomonas
           flavigena DSM 20109]
 gi|296021716|gb|ADG74952.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cellulomonas
           flavigena DSM 20109]
          Length = 495

 Score =  256 bits (654), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 73/304 (24%), Positives = 139/304 (45%), Gaps = 39/304 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY----------REHGD----------------- 46
             +  Y+ +I K+ +L  ++E  LAKR            E  D                 
Sbjct: 196 DPVKDYLKQIGKVALLNAEQEVELAKRIEAGLFAEEKLAETRDSLEPKLRRELEWIAQDG 255

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 256 RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 315

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L
Sbjct: 316 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKEL 370

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +V+ +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 371 DMTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 425

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L + +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 426 QLHQVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 485

Query: 285 QKQV 288
           + QV
Sbjct: 486 RSQV 489


>gi|290473624|ref|YP_003466496.1| sigma H (sigma 32) factor of RNA polymerase; transcription of heat
           shock and stress proteins [Xenorhabdus bovienii SS-2004]
 gi|289172929|emb|CBJ79700.1| sigma H (sigma 32) factor of RNA polymerase; transcription of heat
           shock and stress proteins [Xenorhabdus bovienii SS-2004]
          Length = 285

 Score =  256 bits (654), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 103/290 (35%), Positives = 169/290 (58%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  Y+      PML  +EE  LA+R    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLALVPQGSLEGYVRASNAYPMLSAEEEKELAERLHYQGDLDAAKKLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARSYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +AK+L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKAKQRLGWFNQ-----DEVDLVAKELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNP 237
           +  +    + ++ D + SQ    ++Y  D        + E     +  + L+ ++  L+ 
Sbjct: 176 SAQDMAFDMSSNDDSHDSQPVAPVLYLQDKASDFADGIEEDNWENHAADKLSMAIEGLDE 235

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L ++   TL+ L+ ++ VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQDIIRARWLDDDNKSTLQELADKYGVSAERVRQLEKNAMKKLRLAIEA 285


>gi|296269171|ref|YP_003651803.1| RpoD subfamily RNA polymerase sigma-70 [Thermobispora bispora DSM
           43833]
 gi|296091958|gb|ADG87910.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobispora
           bispora DSM 43833]
          Length = 367

 Score =  256 bits (654), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 86/315 (27%), Positives = 145/315 (46%), Gaps = 38/315 (12%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------REHG-- 45
            + ++          +  Y+ EI K+P+L  +EE  LAK               +  G  
Sbjct: 58  FDEEDFDSGAPTNDLVRIYLREIGKVPLLTAEEEVELAKAIEAGLFAEDKLCEKKAAGIE 117

Query: 46  ----------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
                      + A  RL+ ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD 
Sbjct: 118 CPELEDLVWEGIRAKQRLIEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDY 177

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            +G++ +TY+ WWI+ A+   I      ++I     +      L R++  L         
Sbjct: 178 TKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE--TINKLVRVQRQLHQDLGREPT 235

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
           PE    IAK++++    V+ +        SL + I   D +     D++    D    V 
Sbjct: 236 PE---EIAKEMDLPVERVVEIQRIAQEPVSLQSPIGEEDSD---LGDFI---EDADAVVP 286

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIE 273
           +E       ++ L   +S L+ RE+RI + R      +P TLE +  EF V+RER+RQIE
Sbjct: 287 LEAAAFILLQDHLDDILSTLSEREQRIIQLRFGLADGHPRTLEEVGREFGVTRERIRQIE 346

Query: 274 ARAFKKVQESIQKQV 288
           ++   K++   + QV
Sbjct: 347 SKTLAKLRHPTRAQV 361


>gi|284008659|emb|CBA75293.1| RNA polymerase sigma-32 factor [Arsenophonus nasoniae]
          Length = 292

 Score =  256 bits (654), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 105/290 (36%), Positives = 168/290 (57%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M +   S+ +  +  +  Y+      PML  +EE   AKR   HGDL+AA +L+ SHLR 
Sbjct: 8   MTKDMQSLALIPQGSIEAYVRSANAYPMLTAEEEQEYAKRLHYHGDLNAAKQLILSHLRF 67

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 68  VIHIARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 127

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  +     N     +V  +AK+L V+  +V  M  R+
Sbjct: 128 WRIVKVATTKAQRKLFFNLRKNKKRIGWFNQN-----EVDMVAKELGVTSKDVREMESRM 182

Query: 181 AGDE---SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
           A  +    +N   +S +  +     +L          + E     +  + LT+++S L+ 
Sbjct: 183 AAQDMAFDMNDDDDSGENTTIAPVLYLQDKSSDFADSIEEDNWENHATDKLTQALSTLDE 242

Query: 238 RERRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L + N  TL++L+ ++ VS ERVRQ+E  A KK++  ++ 
Sbjct: 243 RSQDIIRARWLDDENKTTLQDLADKYSVSAERVRQLEKNAMKKLRLVMEA 292


>gi|256827331|ref|YP_003151290.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Cryptobacterium curtum
           DSM 15641]
 gi|256583474|gb|ACU94608.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Cryptobacterium curtum
           DSM 15641]
          Length = 422

 Score =  256 bits (654), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 87/315 (27%), Positives = 143/315 (45%), Gaps = 43/315 (13%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY----------------------- 41
           + SI +     +  Y+ EI K+P+L   EE  LA +                        
Sbjct: 109 DTSITMLTGDPVRMYLKEIGKVPLLTAAEEIDLAMKIEAGVEAGEQLEAAEADNAEELSR 168

Query: 42  REHG--------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           REH          L A  +L+ ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KF
Sbjct: 169 REHRRLTRIEAVGLDAKQQLIEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKF 228

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D  +GF+ +TY+ WWI+ A+   I      ++I     +      L R++  L       
Sbjct: 229 DYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE--TINKLVRIQRQLLQELGRE 286

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
             PE    IA++++++   V  +        SL   I   ++  SQ  D++  D      
Sbjct: 287 PTPE---EIAEEMDLTPDRVREIQKISQEPVSLETPI--GEEEDSQLGDFIEDD---AAV 338

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQ 271
           V  +       +  LT+ +  L  RER++   R   E+  P TLE +  EF V+RER+RQ
Sbjct: 339 VPPDAASFSMLQEQLTKVLDGLAERERKVISLRFGLEDGHPRTLEEVGREFGVTRERIRQ 398

Query: 272 IEARAFKKVQESIQK 286
           IE++   K++   + 
Sbjct: 399 IESKTLAKLRHPSRS 413


>gi|1710646|sp|P50509|RP32_PROMI RecName: Full=RNA polymerase sigma-32 factor
 gi|1143374|dbj|BAA09441.1| sigma-32 homolog [Proteus mirabilis]
          Length = 284

 Score =  256 bits (654), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 110/288 (38%), Positives = 168/288 (58%), Gaps = 8/288 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  S+ +  +  +  YI      PML  +EE  LA+R    GDL AA  L+ SHLR 
Sbjct: 1   MTQEMQSLALVPQGSIEAYIRAANSYPMLTAEEEKELAERLHYEGDLEAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A  Y GYGLP ++++ EGNIGLM+AV+ F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VIHVARSYSGYGLPQADLIQEGNIGLMKAVRHFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT +Q++LFFNLR+ K  L          ++V  +AK+L VSES+V  M  R+
Sbjct: 121 WRIVKVATTKSQRKLFFNLRKNKKRLGWFNQ-----DEVELVAKELGVSESDVREMESRM 175

Query: 181 -AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPR 238
            A D + +   + SD          + D        IE++   N   + LT ++  L+ R
Sbjct: 176 SAQDMAFDMSADDSDDPHPVAPVLFLEDKSSDFADGIEEDNWDNHAADRLTLAIKTLDER 235

Query: 239 ERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            + I  AR L  +N  TL+ L+ ++ VS ERVRQ+E  A KK++ +I+
Sbjct: 236 SQDIIRARWLEDDNKSTLQELADKYGVSAERVRQLEKNAMKKLRLAIE 283


>gi|299068068|emb|CBJ39282.1| RNA polymerase sigma H (sigma 32) factor; transcription of heat
           shock and stress proteins [Ralstonia solanacearum CMR15]
          Length = 306

 Score =  256 bits (654), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 119/287 (41%), Positives = 176/287 (61%), Gaps = 12/287 (4%)

Query: 7   SIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           ++   G +G L  YI  + ++PML  +EE  LA+ Y   GDL AA RLV SHLRLVV IA
Sbjct: 23  ALAFPGSLGNLDAYIQSVNRVPMLTAEEEQQLARDYHATGDLDAARRLVLSHLRLVVSIA 82

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGLP ++++ EGN+GLM+AVK+FDP++G RL +Y++ WIKA M EYIL++W +VK
Sbjct: 83  RQYLGYGLPHADLIQEGNVGLMKAVKRFDPDQGVRLVSYAIHWIKAEMHEYILKNWRMVK 142

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDE 184
           + TT  Q++LFFNLR  K +  A        +++ A+A++L+V  +EV  M  RL  GD 
Sbjct: 143 VATTKAQRKLFFNLRSHKQNAHA----TFTSDEIDAVAQELDVKGAEVREMETRLSGGDI 198

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           +L   I+  ++ S     +L   H+   +VL  +   + +   +  +++ L+ R RRI E
Sbjct: 199 ALEGQIDDGEE-SFAPIAYLADTHNEPTRVLEGRGLDRLQSEGIETALAKLDDRSRRIIE 257

Query: 245 ARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           AR L          TL  L+ EF VS ER+RQIE+ A KK++ ++Q 
Sbjct: 258 ARWLHVNDDGSGGATLHELADEFGVSAERIRQIESAAMKKMKGALQS 304


>gi|90407357|ref|ZP_01215542.1| RpoD protein [Psychromonas sp. CNPT3]
 gi|90311508|gb|EAS39608.1| RpoD protein [Psychromonas sp. CNPT3]
          Length = 282

 Score =  256 bits (654), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 112/286 (39%), Positives = 167/286 (58%), Gaps = 6/286 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M +K  S+ +  +  +  YI  + K  ML   EE  LA+R    GDL AA +LV SHLR 
Sbjct: 1   MIKKIDSMGLVPQGSIEAYIQSVNKFAMLSASEEKALAERLFYEGDLDAAKKLVMSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  IA  Y GYGL I++++ EGN+GLM+AVK+FDP  G RL ++++ WIKA + EY++R+
Sbjct: 61  VAYIAKSYAGYGLAIADLIQEGNVGLMKAVKRFDPTVGVRLVSFAVHWIKAEIHEYVIRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VKI TT  Q++LFFNLR+ K  L   +      ++V  +A  LNVS  +V+ M  RL
Sbjct: 121 WRVVKIATTKAQRKLFFNLRKAKKRLGWFSK-----DEVENVANNLNVSTKDVLEMESRL 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE-ERKNRRNMLTRSMSVLNPRE 239
            G +    L    D  +       + D +    +L+E E  + N +  L  ++S L+ R 
Sbjct: 176 NGHDYSFDLTGDDDDENCFAPVQYLEDKNADVALLVEVENSQSNMKRQLHSALSSLDERS 235

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + I  +R L E   TL +L++ + +S ERVRQ+EA A KK+Q ++Q
Sbjct: 236 QDIISSRWLNEPKATLHDLAARYSISAERVRQLEANAIKKLQSNMQ 281


>gi|313764456|gb|EFS35820.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL013PA1]
 gi|313772162|gb|EFS38128.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL074PA1]
 gi|313792142|gb|EFS40243.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL110PA1]
 gi|313801905|gb|EFS43139.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL110PA2]
 gi|313807517|gb|EFS46004.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL087PA2]
 gi|313815995|gb|EFS53709.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL059PA1]
 gi|313818559|gb|EFS56273.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL046PA2]
 gi|313820326|gb|EFS58040.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL036PA1]
 gi|313822867|gb|EFS60581.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL036PA2]
 gi|313825201|gb|EFS62915.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL063PA1]
 gi|313827777|gb|EFS65491.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL063PA2]
 gi|313830354|gb|EFS68068.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL007PA1]
 gi|313833727|gb|EFS71441.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL056PA1]
 gi|314915449|gb|EFS79280.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL005PA4]
 gi|314918269|gb|EFS82100.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL050PA1]
 gi|314920081|gb|EFS83912.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL050PA3]
 gi|314925214|gb|EFS89045.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL036PA3]
 gi|314931603|gb|EFS95434.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL067PA1]
 gi|314955756|gb|EFT00156.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL027PA1]
 gi|314958170|gb|EFT02273.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL002PA1]
 gi|314962801|gb|EFT06901.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL082PA1]
 gi|314967832|gb|EFT11931.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL037PA1]
 gi|314973358|gb|EFT17454.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL053PA1]
 gi|314976037|gb|EFT20132.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL045PA1]
 gi|314978425|gb|EFT22519.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL072PA2]
 gi|314983942|gb|EFT28034.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL005PA1]
 gi|314988126|gb|EFT32217.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL005PA2]
 gi|314989931|gb|EFT34022.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL005PA3]
 gi|315080641|gb|EFT52617.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL078PA1]
 gi|315084314|gb|EFT56290.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL027PA2]
 gi|315085657|gb|EFT57633.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL002PA3]
 gi|315088921|gb|EFT60897.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL072PA1]
 gi|315095903|gb|EFT67879.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL038PA1]
 gi|315098534|gb|EFT70510.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL059PA2]
 gi|315101108|gb|EFT73084.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL046PA1]
 gi|315105654|gb|EFT77630.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL030PA1]
 gi|315108328|gb|EFT80304.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL030PA2]
 gi|327326185|gb|EGE67975.1| RNA polymerase principal sigma factor HrdB [Propionibacterium acnes
           HL096PA2]
 gi|327330255|gb|EGE72004.1| RNA polymerase principal sigma factor HrdB [Propionibacterium acnes
           HL097PA1]
 gi|327331940|gb|EGE73677.1| RNA polymerase principal sigma factor HrdB [Propionibacterium acnes
           HL096PA3]
 gi|327443141|gb|EGE89795.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL013PA2]
 gi|327445925|gb|EGE92579.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL043PA2]
 gi|327448095|gb|EGE94749.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL043PA1]
 gi|327450784|gb|EGE97438.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL087PA3]
 gi|327453139|gb|EGE99793.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL092PA1]
 gi|327453872|gb|EGF00527.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL083PA2]
 gi|328753472|gb|EGF67088.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL020PA1]
 gi|328754202|gb|EGF67818.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL087PA1]
 gi|328754546|gb|EGF68162.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL025PA2]
 gi|328760854|gb|EGF74420.1| RNA polymerase principal sigma factor HrdB [Propionibacterium acnes
           HL099PA1]
          Length = 511

 Score =  256 bits (654), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 76/318 (23%), Positives = 143/318 (44%), Gaps = 41/318 (12%)

Query: 2   NRKNMSIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRY------------------ 41
           +    +++V G     +  Y+ +I K+ +L   EE  LAKR                   
Sbjct: 198 DEPEQTVMVAGATADPVKDYLKQIGKVALLNAVEEVDLAKRIEAGLFAGEQLADPDAKIR 257

Query: 42  -REHGDLS--------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
            ++  D          A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 258 EKDREDYEWIAEDGKVAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEK 317

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWIK A+   +      ++I     +  +   L R++  +      
Sbjct: 318 FDYTKGYKFSTYATWWIKQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGR 375

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE    +A +L+++  +VI +        SL+  +   +   S++ D +    D + 
Sbjct: 376 EPTPE---ELASELDMTAEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEA 427

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVR 270
            V  +       +  L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 428 IVPADAVNFTLLQEQLHDVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIR 487

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 488 QIESKTMSKLRHPSRSQV 505


>gi|15640181|ref|NP_229808.1| RNA polymerase factor sigma-32 [Vibrio cholerae O1 biovar El Tor
           str. N16961]
 gi|121591866|ref|ZP_01679036.1| RNA polymerase sigma-32 factor [Vibrio cholerae 2740-80]
 gi|147674371|ref|YP_001218271.1| RNA polymerase factor sigma-32 [Vibrio cholerae O395]
 gi|153214854|ref|ZP_01949662.1| RNA polymerase sigma-32 factor [Vibrio cholerae 1587]
 gi|153803613|ref|ZP_01958199.1| RNA polymerase sigma-32 factor [Vibrio cholerae MZO-3]
 gi|153818953|ref|ZP_01971620.1| RNA polymerase sigma-32 factor [Vibrio cholerae NCTC 8457]
 gi|153824136|ref|ZP_01976803.1| RNA polymerase sigma-32 factor [Vibrio cholerae B33]
 gi|153826296|ref|ZP_01978963.1| RNA polymerase sigma-32 factor [Vibrio cholerae MZO-2]
 gi|153830006|ref|ZP_01982673.1| RNA polymerase sigma-32 factor [Vibrio cholerae 623-39]
 gi|227080385|ref|YP_002808936.1| RNA polymerase sigma-32 factor [Vibrio cholerae M66-2]
 gi|229508425|ref|ZP_04397929.1| RNA polymerase sigma factor RpoH [Vibrio cholerae BX 330286]
 gi|229508894|ref|ZP_04398384.1| RNA polymerase sigma factor RpoH [Vibrio cholerae B33]
 gi|229515820|ref|ZP_04405278.1| RNA polymerase sigma factor RpoH [Vibrio cholerae TMA 21]
 gi|229517008|ref|ZP_04406454.1| RNA polymerase sigma factor RpoH [Vibrio cholerae RC9]
 gi|229520061|ref|ZP_04409489.1| RNA polymerase sigma factor RpoH [Vibrio cholerae TM 11079-80]
 gi|229527110|ref|ZP_04416504.1| RNA polymerase sigma factor RpoH [Vibrio cholerae 12129(1)]
 gi|229606698|ref|YP_002877346.1| RNA polymerase factor sigma-32 [Vibrio cholerae MJ-1236]
 gi|254291956|ref|ZP_04962737.1| RNA polymerase sigma-32 factor [Vibrio cholerae AM-19226]
 gi|254851536|ref|ZP_05240886.1| RNA polymerase sigma-32 factor [Vibrio cholerae MO10]
 gi|255743901|ref|ZP_05417856.1| RNA polymerase sigma factor RpoH [Vibrio cholera CIRS 101]
 gi|262163699|ref|ZP_06031440.1| RNA polymerase sigma factor RpoH [Vibrio mimicus VM223]
 gi|262172906|ref|ZP_06040584.1| RNA polymerase sigma factor RpoH [Vibrio mimicus MB-451]
 gi|262190731|ref|ZP_06048960.1| RNA polymerase sigma factor RpoH [Vibrio cholerae CT 5369-93]
 gi|262404885|ref|ZP_06081439.1| RNA polymerase sigma factor RpoH [Vibrio sp. RC586]
 gi|297581813|ref|ZP_06943734.1| RNA polymerase sigma-32 factor [Vibrio cholerae RC385]
 gi|298501088|ref|ZP_07010888.1| alternative sigma factor RpoH [Vibrio cholerae MAK 757]
 gi|12644296|sp|P50511|RP32_VIBCH RecName: Full=RNA polymerase sigma-32 factor
 gi|9654552|gb|AAF93327.1| RNA polymerase sigma-32 factor [Vibrio cholerae O1 biovar El Tor
           str. N16961]
 gi|121546267|gb|EAX56564.1| RNA polymerase sigma-32 factor [Vibrio cholerae 2740-80]
 gi|124115097|gb|EAY33917.1| RNA polymerase sigma-32 factor [Vibrio cholerae 1587]
 gi|124120852|gb|EAY39595.1| RNA polymerase sigma-32 factor [Vibrio cholerae MZO-3]
 gi|126510515|gb|EAZ73109.1| RNA polymerase sigma-32 factor [Vibrio cholerae NCTC 8457]
 gi|126518343|gb|EAZ75566.1| RNA polymerase sigma-32 factor [Vibrio cholerae B33]
 gi|146316254|gb|ABQ20793.1| RNA polymerase sigma-32 factor [Vibrio cholerae O395]
 gi|148874491|gb|EDL72626.1| RNA polymerase sigma-32 factor [Vibrio cholerae 623-39]
 gi|149739964|gb|EDM54143.1| RNA polymerase sigma-32 factor [Vibrio cholerae MZO-2]
 gi|150422166|gb|EDN14132.1| RNA polymerase sigma-32 factor [Vibrio cholerae AM-19226]
 gi|227008273|gb|ACP04485.1| RNA polymerase sigma-32 factor [Vibrio cholerae M66-2]
 gi|227011849|gb|ACP08059.1| RNA polymerase sigma-32 factor [Vibrio cholerae O395]
 gi|229335341|gb|EEO00824.1| RNA polymerase sigma factor RpoH [Vibrio cholerae 12129(1)]
 gi|229342849|gb|EEO07839.1| RNA polymerase sigma factor RpoH [Vibrio cholerae TM 11079-80]
 gi|229346071|gb|EEO11043.1| RNA polymerase sigma factor RpoH [Vibrio cholerae RC9]
 gi|229347083|gb|EEO12044.1| RNA polymerase sigma factor RpoH [Vibrio cholerae TMA 21]
 gi|229354011|gb|EEO18944.1| RNA polymerase sigma factor RpoH [Vibrio cholerae B33]
 gi|229354698|gb|EEO19620.1| RNA polymerase sigma factor RpoH [Vibrio cholerae BX 330286]
 gi|229369353|gb|ACQ59776.1| RNA polymerase sigma factor RpoH [Vibrio cholerae MJ-1236]
 gi|254847241|gb|EET25655.1| RNA polymerase sigma-32 factor [Vibrio cholerae MO10]
 gi|255738384|gb|EET93774.1| RNA polymerase sigma factor RpoH [Vibrio cholera CIRS 101]
 gi|261893982|gb|EEY39968.1| RNA polymerase sigma factor RpoH [Vibrio mimicus MB-451]
 gi|262027915|gb|EEY46579.1| RNA polymerase sigma factor RpoH [Vibrio mimicus VM223]
 gi|262033375|gb|EEY51884.1| RNA polymerase sigma factor RpoH [Vibrio cholerae CT 5369-93]
 gi|262348969|gb|EEY98108.1| RNA polymerase sigma factor RpoH [Vibrio sp. RC586]
 gi|297533907|gb|EFH72747.1| RNA polymerase sigma-32 factor [Vibrio cholerae RC385]
 gi|297540122|gb|EFH76183.1| alternative sigma factor RpoH [Vibrio cholerae MAK 757]
 gi|327483048|gb|AEA77455.1| RNA polymerase sigma factor RpoH [Vibrio cholerae LMA3894-4]
          Length = 286

 Score =  256 bits (654), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 108/289 (37%), Positives = 169/289 (58%), Gaps = 11/289 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  +   + +  +  L  YI  +   PML   EE  LA+R    GD+ AA  L+ SHLR 
Sbjct: 1   MTNQAYPMALVSQDSLDSYIRSVNGYPMLSADEERELAERLHYKGDIDAAKGLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A GY GYGLP++++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VKI TT  Q++LFFNLR+ K  L    +      +V  +A++L V  +EV  M  RL
Sbjct: 121 WRIVKIATTKAQRKLFFNLRKSKKRLGWFNNG-----EVETVARELGVEPAEVREMESRL 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR----NMLTRSMSVLN 236
           A  ++   +    D+N   +   ++Y  D     L +  E +N        L+ +++ L+
Sbjct: 176 AAQDAAFEMSAEDDENGMAYTAPVLYLEDKHSD-LADNLEAENWEAHTTQRLSMALASLD 234

Query: 237 PRERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            R + I  AR L ++   TL++L+  + VS ER+RQ+E  A +K++E++
Sbjct: 235 ERSQHIVRARWLDDDNKTTLQDLAEMYGVSAERIRQLEKNAMRKLKEAV 283


>gi|313812944|gb|EFS50658.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL025PA1]
          Length = 511

 Score =  256 bits (654), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 76/318 (23%), Positives = 143/318 (44%), Gaps = 41/318 (12%)

Query: 2   NRKNMSIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRY------------------ 41
           +    +++V G     +  Y+ +I K+ +L   EE  LAKR                   
Sbjct: 198 DEPEQTVMVAGATADPVKDYLKQIGKVALLNAVEEVDLAKRIEAGLFAGEQLADPDAKIR 257

Query: 42  -REHGDLS--------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
            ++  D          A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 258 EKDREDYEWIAEDGKVAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEK 317

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWIK A+   +      ++I     +  +   L R++  +      
Sbjct: 318 FDYTKGYKFSTYATWWIKQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGR 375

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE    +A +L+++  +VI +        SL+  +   +   S++ D +    D + 
Sbjct: 376 EPTPE---ELASELDMTAEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEA 427

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVR 270
            V  +       +  L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 428 IVPADAVNFTLLQEQLHDVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIR 487

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 488 QIESKTMSKLRHPSRSQV 505


>gi|319639187|ref|ZP_07993938.1| RNA polymerase sigma-32 factor [Neisseria mucosa C102]
 gi|317399371|gb|EFV80041.1| RNA polymerase sigma-32 factor [Neisseria mucosa C102]
          Length = 287

 Score =  256 bits (654), Expect = 3e-66,   Method: Composition-based stats.
 Identities = 117/291 (40%), Positives = 187/291 (64%), Gaps = 8/291 (2%)

Query: 1   MNRK-NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLR 59
           MN+   + +I +G   L +YIH +  IPML  +EE  LA+R ++ GDL+AA +L+ SHLR
Sbjct: 1   MNKAFALPVIHSGNGSLEQYIHTVNSIPMLTAEEETQLAER-QQKGDLNAAKQLILSHLR 59

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           +VV IA GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+ILR
Sbjct: 60  VVVSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPSRGARLFSFAVHWIKAEIHEFILR 119

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
           +W LV++ TT  Q++LFFNLR ++ +L A++     P++   IA  L V  SEV+ M  R
Sbjct: 120 NWRLVRVATTKPQRKLFFNLRSMRKNLSALS-----PKEAQEIADDLGVKLSEVLEMEQR 174

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           + G +      N+ D+++    DWL        + L ++     +   L  +++ L+ R 
Sbjct: 175 MTGHDIGIMAENNDDEDNFAPIDWLADHDAEPSRQLSKQAHYALQTEGLQNALAQLDDRS 234

Query: 240 RRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           RRI E+R LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 235 RRIVESRWLQDDGGLTLHELAAEYGVSAERIRQIEAKAMQKLRGFLAEEAE 285


>gi|271963879|ref|YP_003338075.1| RNA polymerase sigma factor RpoD [Streptosporangium roseum DSM
           43021]
 gi|270507054|gb|ACZ85332.1| RNA polymerase sigma factor RpoD [Streptosporangium roseum DSM
           43021]
          Length = 392

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 82/296 (27%), Positives = 137/296 (46%), Gaps = 37/296 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREH------------------------GDLSAAHRLV 54
           Y+ EI ++P+L  +EE  LAK                                 A  RL+
Sbjct: 102 YLREIGRVPLLTAEEEVELAKSIEAGLFAEDKLTSVVSRLAFPEFKELVWQGTRAKQRLI 161

Query: 55  TSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114
            ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+ 
Sbjct: 162 EANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAIT 221

Query: 115 EYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVI 174
             I      ++I     +      L R++  L         PE    IA ++++    VI
Sbjct: 222 RAIADQARTIRIPVHMVE--TINKLVRVQRQLHQDLGREPAPE---EIALEMDLPIDRVI 276

Query: 175 SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV 234
            +        SL + I   D +     D++    D    V +E       ++ L   ++ 
Sbjct: 277 EIQRIAQEPVSLQSPIGEEDSD---LGDFI---EDADAVVPMEAAAFIMLQDQLDDILAT 330

Query: 235 LNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           L+ RE+RI + R      +P TLE +  EF V+RER+RQIE++   K++   + Q+
Sbjct: 331 LSDREQRIIQLRFGLADGHPRTLEEVGREFGVTRERIRQIESKTLAKLRHPTRAQM 386


>gi|329766845|ref|ZP_08258374.1| hypothetical protein HMPREF0428_00071 [Gemella haemolysans M341]
 gi|328838571|gb|EGF88177.1| hypothetical protein HMPREF0428_00071 [Gemella haemolysans M341]
          Length = 361

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 84/281 (29%), Positives = 137/281 (48%), Gaps = 15/281 (5%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR---EHGDLSAAHRLVTSHLRLVVKIAM 66
           +     +  Y+ EI K+P+L K++E  L+K      E     A   L  ++LRLVV IA 
Sbjct: 82  IRTNDPVRMYLKEIGKVPLLSKEKELELSKIIETGTEAEKEQAKKDLAEANLRLVVSIAK 141

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I
Sbjct: 142 RYVGRGMLFLDLIQEGNMGLIKAVEKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI 201

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
                +      L R++  L        KPE    IAKK+N++  +V  +        SL
Sbjct: 202 PVHMVE--TINRLIRIQRQLLQDLGREPKPE---EIAKKMNMTPEKVREILKIAQEPVSL 256

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              I   +++ S   D++    D   Q  +E    +  +  L   +  L  RE  + + R
Sbjct: 257 ETPI--GEEDDSHLGDFI---EDKDAQSPVEHAANELLKEQLEEILETLTDREENVLKLR 311

Query: 247 RL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
                    TLE + S F V+RER+RQIEA+A +K++   +
Sbjct: 312 FGLKDGKTHTLEEVGSAFGVTRERIRQIEAKAIRKLKHPSK 352


>gi|315103424|gb|EFT75400.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL050PA2]
          Length = 510

 Score =  256 bits (654), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 76/318 (23%), Positives = 143/318 (44%), Gaps = 41/318 (12%)

Query: 2   NRKNMSIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRY------------------ 41
           +    +++V G     +  Y+ +I K+ +L   EE  LAKR                   
Sbjct: 197 DEPEQTVMVAGATADPVKDYLKQIGKVALLNAVEEVDLAKRIEAGLFAGEQLADPDAKIR 256

Query: 42  -REHGDLS--------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
            ++  D          A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 257 EKDREDYEWIAEDGKVAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEK 316

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWIK A+   +      ++I     +  +   L R++  +      
Sbjct: 317 FDYTKGYKFSTYATWWIKQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGR 374

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE    +A +L+++  +VI +        SL+  +   +   S++ D +    D + 
Sbjct: 375 EPTPE---ELANELDMTAEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEA 426

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVR 270
            V  +       +  L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 427 IVPADAVNFTLLQEQLHDVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIR 486

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 487 QIESKTMSKLRHPSRSQV 504


>gi|308371101|ref|ZP_07423832.2| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu003]
 gi|308379284|ref|ZP_07485758.2| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu010]
 gi|308405944|ref|ZP_07494511.2| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu012]
 gi|308329814|gb|EFP18665.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu003]
 gi|308357496|gb|EFP46347.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu010]
 gi|308365045|gb|EFP53896.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu012]
 gi|323718698|gb|EGB27860.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           CDC1551A]
          Length = 530

 Score =  255 bits (653), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 79/319 (24%), Positives = 148/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------REHGDL- 47
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+  
Sbjct: 217 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSERGEKL 275

Query: 48  ----------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 276 PAAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 335

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 336 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 393

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 394 REPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 445

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 446 AVVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 505

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 506 RQIESKTMSKLRHPSRSQV 524


>gi|15672535|ref|NP_266709.1| RNA polymerase sigma factor RpoD [Lactococcus lactis subsp. lactis
           Il1403]
 gi|281491019|ref|YP_003352999.1| RNA polymerase sigma factor RpoD [Lactococcus lactis subsp. lactis
           KF147]
 gi|12723439|gb|AAK04651.1|AE006289_2 major RNA polymerase sigma factor [Lactococcus lactis subsp. lactis
           Il1403]
 gi|281374777|gb|ADA64297.1| RNA polymerase sigma factor RpoD (Sigma-42) [Lactococcus lactis
           subsp. lactis KF147]
 gi|326406054|gb|ADZ63125.1| RNA polymerase sigma factor RpoD [Lactococcus lactis subsp. lactis
           CV56]
          Length = 447

 Score =  255 bits (653), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 81/279 (29%), Positives = 138/279 (49%), Gaps = 14/279 (5%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD--LSAAHRLVTSHLRLVVKIAMGYRG 70
           +  +  Y+ EI + P++   EE  LA+     G+    A   L  ++LRLVV IA  Y G
Sbjct: 173 DDPVRMYLKEIGRYPLISLDEETKLAEAIIAGGEGAEFAKQMLAEANLRLVVSIAKRYSG 232

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            G+   +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    
Sbjct: 233 RGMQFLDLIQEGNMGLMKAVDKFDHTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 292

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
            +      L R++ +L      +  PE    I K+L+++  +V  +        SL   I
Sbjct: 293 VE--TINKLIRVQRNLLQELGRDPSPE---EIGKELHMAPDKVREVLKIAQEPVSLETPI 347

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
              +++ S   D++  D     +  ++   R   R  L   M  L  RE  +   R   +
Sbjct: 348 --GEEDDSHLGDFIEDD---VIESPVDYTNRILLREQLDEVMDTLTDREENVLRMRFGLD 402

Query: 251 NP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +    TLE++  +F+V+RER+RQIEA+A KK++   + +
Sbjct: 403 DGRMHTLEDVGKQFKVTRERIRQIEAKAIKKLRHPRRSK 441


>gi|116511352|ref|YP_808568.1| RNA polymerase sigma factor RpoD [Lactococcus lactis subsp.
           cremoris SK11]
 gi|125623388|ref|YP_001031871.1| RNA polymerase sigma factor RpoD [Lactococcus lactis subsp.
           cremoris MG1363]
 gi|116107006|gb|ABJ72146.1| RNA polymerase, sigma 70 subunit, RpoD [Lactococcus lactis subsp.
           cremoris SK11]
 gi|124492196|emb|CAL97125.1| RNA polymerase sigma factor rpoD (Sigma-42) [Lactococcus lactis
           subsp. cremoris MG1363]
 gi|300070136|gb|ADJ59536.1| RNA polymerase sigma factor RpoD [Lactococcus lactis subsp.
           cremoris NZ9000]
          Length = 447

 Score =  255 bits (653), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 81/279 (29%), Positives = 138/279 (49%), Gaps = 14/279 (5%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD--LSAAHRLVTSHLRLVVKIAMGYRG 70
           +  +  Y+ EI + P++   EE  LA+     G+    A   L  ++LRLVV IA  Y G
Sbjct: 173 DDPVRMYLKEIGRYPLISLDEETKLAEAIIAGGEGAEFAKQMLAEANLRLVVSIAKRYSG 232

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            G+   +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    
Sbjct: 233 RGMQFLDLIQEGNMGLMKAVDKFDHTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 292

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
            +      L R++ +L      +  PE    I K+L+++  +V  +        SL   I
Sbjct: 293 VE--TINKLIRVQRNLLQELGRDPSPE---EIGKELHMAPDKVREVLKIAQEPVSLETPI 347

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
              +++ S   D++  D     +  ++   R   R  L   M  L  RE  +   R   +
Sbjct: 348 --GEEDDSHLGDFIEDD---VIESPVDYTNRILLREQLDEVMDTLTDREENVLRMRFGLD 402

Query: 251 NP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +    TLE++  +F+V+RER+RQIEA+A KK++   + +
Sbjct: 403 DGRMHTLEDVGKQFKVTRERIRQIEAKAIKKLRHPRRSK 441


>gi|114321809|ref|YP_743492.1| RNA polymerase, sigma 32 subunit, RpoH [Alkalilimnicola ehrlichii
           MLHE-1]
 gi|114228203|gb|ABI58002.1| RNA polymerase, sigma 32 subunit, RpoH [Alkalilimnicola ehrlichii
           MLHE-1]
          Length = 285

 Score =  255 bits (653), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 107/281 (38%), Positives = 166/281 (59%), Gaps = 9/281 (3%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           N+   V  E     YIH + +IP+L  +EE+ LA+RYR  GDL AA  LV SHLR VV I
Sbjct: 12  NLPTPVGSE---EAYIHAVNQIPVLSAEEEHELAERYRLQGDLDAARALVLSHLRFVVHI 68

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  YRGYGLP+ +++ EGN+GLM+AVK+FDP +G RL ++++ WI+A + EY+LR+W +V
Sbjct: 69  ARSYRGYGLPLGDIIQEGNVGLMKAVKRFDPAQGVRLVSFAVHWIRAEIHEYVLRNWRIV 128

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           K+ TT  Q++LFFNLR  + HL  +T      E+V A+A+ L V    V  M  R+ G++
Sbjct: 129 KVATTKAQRKLFFNLRSGRKHLGWLT-----SEEVDAMARDLGVKPETVREMEARMTGND 183

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIF 243
           +        D          + D        +E+ + +  R+  L ++++ L+ R + I 
Sbjct: 184 TTFDPTPGQDDEGIHAPVAYLEDKRYDPATAVEEADWEQHRDQNLHQALAGLDERSQDIL 243

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             R L E   TL+ L+  ++VS ER+RQ+E  A  +++ ++
Sbjct: 244 ARRWLSERKATLKELAEHYQVSAERIRQLEKNAMGRLKTAL 284


>gi|326564381|gb|EGE14609.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis 12P80B1]
          Length = 371

 Score =  255 bits (653), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 107/272 (39%), Positives = 158/272 (58%), Gaps = 7/272 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + L  YI+ + +IP+L  +EE  LA+RY   GD+ AA  LV SHLR V+ IA  Y GYGL
Sbjct: 97  VNLGAYINTVHQIPILTPEEERALAERYYHDGDVEAARLLVMSHLRFVIHIARSYSGYGL 156

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
             ++++ EGN+GLM+AVK+FDP +G RL ++++ WIKA + E+++++W +VK+ TT   +
Sbjct: 157 SQADLIQEGNLGLMKAVKRFDPNKGVRLVSFAVHWIKAEIHEFVIKNWRIVKVATTKAHR 216

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINS 192
           +LFFNLR LK      + N L  ++  AIA  LNV+  +V+ M  RL   D S  A   S
Sbjct: 217 KLFFNLRSLKK-----SSNQLTLDEATAIANDLNVTVKQVLEMESRLTSYDASFEAQD-S 270

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            D          + D      V+ E +  +N    L  +M  L+ R R I   R L +  
Sbjct: 271 DDDEGRYAPQLFLEDAVNPADVVEEADWEENTTTALKDAMETLDERSRDIITQRWLADQK 330

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL  L++ + +S ERVRQIE  A  K++E+I
Sbjct: 331 STLHELAATYNISAERVRQIEKNAMNKIKEAI 362


>gi|315078017|gb|EFT50068.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL053PA2]
          Length = 511

 Score =  255 bits (653), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 76/318 (23%), Positives = 143/318 (44%), Gaps = 41/318 (12%)

Query: 2   NRKNMSIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRY------------------ 41
           +    +++V G     +  Y+ +I K+ +L   EE  LAKR                   
Sbjct: 198 DEPEQTVMVAGATADPVKDYLKQIGKVALLNAVEEVDLAKRIEAGLFAGEQLADPDAKIR 257

Query: 42  -REHGDLS--------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
            ++  D          A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 258 EKDREDYEWIAEDGKVAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEK 317

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWIK A+   +      ++I     +  +   L R++  +      
Sbjct: 318 FDYTKGYKFSTYATWWIKQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGR 375

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE    +A +L+++  +VI +        SL+  +   +   S++ D +    D + 
Sbjct: 376 EPTPE---ELASELDMTAEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEA 427

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVR 270
            V  +       +  L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 428 IVPADAVNFTLLQEQLHDVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIR 487

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 488 QIESKTMSKLRHPSRSQV 505


>gi|296171852|ref|ZP_06852951.1| RNA polymerase sigma factor rpoD [Mycobacterium parascrofulaceum
           ATCC BAA-614]
 gi|295893936|gb|EFG73705.1| RNA polymerase sigma factor rpoD [Mycobacterium parascrofulaceum
           ATCC BAA-614]
          Length = 503

 Score =  255 bits (653), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 80/319 (25%), Positives = 148/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------REHGDL- 47
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E GD  
Sbjct: 190 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMAEMAERGDKL 248

Query: 48  ----------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 249 PAAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 308

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 309 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 366

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 367 REPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 418

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 419 AVVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 478

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 479 RQIESKTMSKLRHPSRSQV 497


>gi|254821650|ref|ZP_05226651.1| RNA polymerase sigma factor [Mycobacterium intracellulare ATCC
           13950]
          Length = 488

 Score =  255 bits (653), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 80/319 (25%), Positives = 148/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGDL- 47
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E GD  
Sbjct: 175 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTEMTERGDKL 233

Query: 48  ----------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 234 PAAQRRDMQWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 293

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 294 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 351

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 352 REPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 403

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 404 AVVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 463

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 464 RQIESKTMSKLRHPSRSQV 482


>gi|315127793|ref|YP_004069796.1| RNA polymerase factor sigma-32 [Pseudoalteromonas sp. SM9913]
 gi|315016307|gb|ADT69645.1| RNA polymerase factor sigma-32 [Pseudoalteromonas sp. SM9913]
          Length = 287

 Score =  255 bits (653), Expect = 4e-66,   Method: Composition-based stats.
 Identities = 108/285 (37%), Positives = 169/285 (59%), Gaps = 12/285 (4%)

Query: 6   MSIIVNGE-IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           M++ V  +   +  Y+  +  IPML+ ++E  LAK+ +E GDLSAA +L+ SHLR V  I
Sbjct: 8   MALTVGQQSASMDGYLQAVSTIPMLKVEQEQELAKKLQEEGDLSAAKQLIMSHLRFVAHI 67

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y GYGLP ++++ EGNIGLM+AVK+FDP  G RL ++++ WIKA + E++L++W +V
Sbjct: 68  AKSYSGYGLPQADLIQEGNIGLMKAVKRFDPSVGVRLVSFAVHWIKAEIHEFVLKNWRIV 127

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-D 183
           K+ TT  Q++LFFNLR+ K  L           +V  +A +L VSE EV  M  R++G D
Sbjct: 128 KVATTKAQRKLFFNLRKNKKRLGWFNQ-----AEVSTVASELGVSEKEVREMESRMSGQD 182

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM----LTRSMSVLNPRE 239
              +   + +D   +     + Y  DG    L +  E++  +      L  ++  L+ R 
Sbjct: 183 MGFDLTGDDNDDAPTSTYSPVQYLTDGSAD-LADDIEQQQWQEQSHTRLFSALKTLDERS 241

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + I  AR L ++  TL+ L+ ++ VS ERVRQ+E  A KK+Q ++
Sbjct: 242 QDIVSARWLSDDKATLQELAEKYSVSAERVRQLEKTAMKKLQSAM 286


>gi|291454591|ref|ZP_06593981.1| RNA polymerase sigma factor RpoD [Streptomyces albus J1074]
 gi|581664|emb|CAA53564.1| sigma factor (RNA polymerase subunit) [Streptomyces griseus]
 gi|291357540|gb|EFE84442.1| RNA polymerase sigma factor RpoD [Streptomyces albus J1074]
          Length = 510

 Score =  255 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 75/304 (24%), Positives = 139/304 (45%), Gaps = 40/304 (13%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------------REHGD 46
             +  Y+ +I K+P+L  ++E  LAKR                             E G 
Sbjct: 212 DPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANADKIAPKLKRELEIIAEDG- 270

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 271 RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 330

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L
Sbjct: 331 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKEL 385

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +VI +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 386 DMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 440

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 441 QLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 500

Query: 285 QKQV 288
           + QV
Sbjct: 501 RSQV 504


>gi|302537370|ref|ZP_07289712.1| RNA polymerase, subunit sigma [Streptomyces sp. C]
 gi|302446265|gb|EFL18081.1| RNA polymerase, subunit sigma [Streptomyces sp. C]
          Length = 526

 Score =  255 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 75/304 (24%), Positives = 139/304 (45%), Gaps = 40/304 (13%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------------REHGD 46
             +  Y+ +I K+P+L  ++E  LAKR                             E G 
Sbjct: 228 DPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANSDKLAPKLKRELEIIAEDG- 286

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 287 RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 346

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L
Sbjct: 347 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKEL 401

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +VI +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 402 DMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 456

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 457 QLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 516

Query: 285 QKQV 288
           + QV
Sbjct: 517 RSQV 520


>gi|1072017|gb|AAA81640.1| sigma factor [Mycobacterium bovis]
 gi|1072019|gb|AAA81641.1| sigma factor [Mycobacterium bovis]
          Length = 528

 Score =  255 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 79/319 (24%), Positives = 148/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------REHGDL- 47
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+  
Sbjct: 215 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSERGEKL 273

Query: 48  ----------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 274 PAAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 333

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 334 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 391

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 392 REPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 443

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 444 AVVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 503

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 504 RQIESKTMSKLRHPSRSQV 522


>gi|119717187|ref|YP_924152.1| RNA polymerase sigma factor [Nocardioides sp. JS614]
 gi|119537848|gb|ABL82465.1| RNA polymerase, sigma 70 subunit, RpoD [Nocardioides sp. JS614]
          Length = 495

 Score =  255 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 75/317 (23%), Positives = 142/317 (44%), Gaps = 40/317 (12%)

Query: 2   NRKNMSIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKR------------------- 40
           +     ++V G     +  Y+ +I K+P+L  + E  LAKR                   
Sbjct: 183 DEPEQQVMVAGATADPVKDYLKQIGKVPLLNAEMEVELAKRIEAGLFSEEKLGKGGKLSA 242

Query: 41  -------YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
                  +       A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KF
Sbjct: 243 KVSEELEWIAEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 302

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  +       
Sbjct: 303 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGRE 360

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
             PE    +AK+L+++  +VI +        SL+  +   +   S++ D +    D +  
Sbjct: 361 PTPE---ELAKELDMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAI 412

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQ 271
           V  +       +  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQ
Sbjct: 413 VPADAVSFTLLQEQLHAVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQ 472

Query: 272 IEARAFKKVQESIQKQV 288
           IE++   K++   + QV
Sbjct: 473 IESKTMSKLRHPSRSQV 489


>gi|160915039|ref|ZP_02077252.1| hypothetical protein EUBDOL_01047 [Eubacterium dolichum DSM 3991]
 gi|158432838|gb|EDP11127.1| hypothetical protein EUBDOL_01047 [Eubacterium dolichum DSM 3991]
          Length = 398

 Score =  255 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 78/276 (28%), Positives = 141/276 (51%), Gaps = 12/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L+ +EE  +A+R +  GD  A  +L++++LRLVV IA  Y G G+
Sbjct: 124 DPVKMYLKEIGRVELLDPKEEPEIARRIQ-AGDEEAKKKLISANLRLVVSIAKKYVGRGM 182

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 183 LFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 241

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L      +   E++   AK  N+S  +V  +        SL   I   
Sbjct: 242 -TINKLTRIQRQLVQDLGRDPTAEEIA--AKMENISPEKVREIQKIALEPVSLETPI--G 296

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D +     E    +  ++ +   +  L  RE ++   R    +  
Sbjct: 297 EEDDSHLGDFI---EDKEALSPDEYANNQLLKDEINTVLQGLTEREEKVLRLRFGLYDGR 353

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 354 TRTLEEVGKEFNVTRERIRQIEAKALRKLKHPTRSK 389


>gi|269140667|ref|YP_003297368.1| RNA polymerase factor sigma-32 [Edwardsiella tarda EIB202]
 gi|267986328|gb|ACY86157.1| RNA polymerase factor sigma-32 [Edwardsiella tarda EIB202]
 gi|304560452|gb|ADM43116.1| RNA polymerase sigma factor RpoH [Edwardsiella tarda FL6-60]
          Length = 284

 Score =  255 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 103/289 (35%), Positives = 167/289 (57%), Gaps = 8/289 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  Y+      PML  +EE  L +R    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLTLVPQGSLEAYVRAANAYPMLTAEEERALGERLHYKGDLDAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEMGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VSE +V+ M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVELVARELGVSEKDVLEMESRM 175

Query: 181 -AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPR 238
            A D + +   +   + +       + D        IE +  ++   + L+ ++  L+ R
Sbjct: 176 AAQDMAFDLPGDDEQEGAPTAPVLFLQDKSSDFANEIEDDNWESHAADKLSVALEGLDER 235

Query: 239 ERRIFEARRLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + I  AR L  +N  TL+ L+  + VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 SQHIIRARWLDSDNKATLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 284


>gi|260906542|ref|ZP_05914864.1| RNA polymerase principal sigma factor [Brevibacterium linens BL2]
          Length = 473

 Score =  255 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 76/303 (25%), Positives = 138/303 (45%), Gaps = 38/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY------------------REHGDLS------- 48
             +  Y+ +I K+ +L   EE  LAKR                   RE  D         
Sbjct: 175 DPVKDYLKQIGKVALLNAAEEVDLAKRIEAGMYAEHLLDAGGITEPRESMDYKWIIHDGR 234

Query: 49  -AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ W
Sbjct: 235 IAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATW 294

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L+
Sbjct: 295 WIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPSPE---ELAKELD 349

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++   V+ +        SL+  +   +   S++ D +    D +  V  +       +  
Sbjct: 350 MTPERVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPSDSVSFTLLQEQ 404

Query: 228 LTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L   +  L+ RE  +   R    +  P TL+ +   + V+RER+RQIE++   K++   +
Sbjct: 405 LHSVLDTLSEREAGVVSMRFGLNDGQPKTLDEIGKVYGVTRERIRQIESKTMAKLRHPSR 464

Query: 286 KQV 288
            QV
Sbjct: 465 SQV 467


>gi|153306|gb|AAA26763.1| principal sigma-like factor [Streptomyces aureofaciens]
 gi|450078|prf||1920369B RNA polymerase:SUBUNIT=sigma
          Length = 525

 Score =  255 bits (653), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 75/304 (24%), Positives = 139/304 (45%), Gaps = 40/304 (13%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------------REHGD 46
             +  Y+ +I K+P+L  ++E  LAKR                             E G 
Sbjct: 227 DPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANSDKLAPKLKRELEIIAEDG- 285

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 286 RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 345

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L
Sbjct: 346 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKEL 400

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +VI +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 401 DMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 455

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 456 QLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 515

Query: 285 QKQV 288
           + QV
Sbjct: 516 RSQV 519


>gi|302670285|ref|YP_003830245.1| RNA polymerase sigma factor RpoD [Butyrivibrio proteoclasticus
           B316]
 gi|302394758|gb|ADL33663.1| RNA polymerase sigma factor RpoD [Butyrivibrio proteoclasticus
           B316]
          Length = 521

 Score =  255 bits (652), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 84/319 (26%), Positives = 140/319 (43%), Gaps = 43/319 (13%)

Query: 1   MNRKNMSII--VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD------------ 46
           M   ++S+   ++ E  +  Y+ EI K+P+L   +E  LA+      D            
Sbjct: 205 MENIDLSVPDGISIEDPVRMYLKEIGKVPLLTADQEIDLAQAMEAGADAEKELADDKDVN 264

Query: 47  -----------------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
                              A  RL  ++LRLVV IA  Y G G+   +++ EGN+GL++A
Sbjct: 265 KLSDARKKELNAIIYEGEEAKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKA 324

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V+KFD  +GF+ +TY+ WWI+ A+   I      ++I     +      L R+   L   
Sbjct: 325 VEKFDFRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE--TINKLIRVSRQLLQE 382

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
                 PE+V   AK++N+    V  +        SL   I   ++  S   D++  D  
Sbjct: 383 LGREPLPEEV---AKEMNMPVERVREILKISQEPVSLETPI--GEEEDSHLGDFIQDD-- 435

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRE 267
               V  +       +  L   +  L  RE+++   R   ++    TLE +  EF V+RE
Sbjct: 436 -NVPVPADAAAFTLLKEQLVEVLGTLTEREQKVLRLRFGLDDGRARTLEEVGKEFNVTRE 494

Query: 268 RVRQIEARAFKKVQESIQK 286
           R+RQIEA+A +K++   + 
Sbjct: 495 RIRQIEAKALRKLRHPSRS 513


>gi|37527948|ref|NP_931293.1| RNA polymerase factor sigma-32 [Photorhabdus luminescens subsp.
           laumondii TTO1]
 gi|36787384|emb|CAE16473.1| RNA polymerase sigma-32 factor [Photorhabdus luminescens subsp.
           laumondii TTO1]
          Length = 285

 Score =  255 bits (652), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 101/290 (34%), Positives = 164/290 (56%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  Y+      PML  +EE  LA+R    GDL AA +L+ SHLR 
Sbjct: 1   MAKEMQTLALVPQGSLEGYVRASNTYPMLTAEEEKELAERLHYQGDLDAAKKLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARSYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +AK+L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVEMVAKELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNP 237
           +  +    +    D    Q    ++Y  D        + E     +  + L+ ++  L+ 
Sbjct: 176 SAQDMAFDMSADDDSQEGQPVAPVLYLQDKASDFADGIEEDNWENHAADKLSVAIESLDE 235

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I   R L ++   TL+ L+ ++ VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQDIIRCRWLDDDNKSTLQELADKYGVSAERVRQLEKNAMKKLRVAIEA 285


>gi|254386999|ref|ZP_05002279.1| RNA polymerase sigma factor [Streptomyces sp. Mg1]
 gi|194345824|gb|EDX26790.1| RNA polymerase sigma factor [Streptomyces sp. Mg1]
          Length = 520

 Score =  255 bits (652), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 75/314 (23%), Positives = 143/314 (45%), Gaps = 40/314 (12%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------- 41
           + +++       +  Y+ +I K+P+L  ++E  LAKR                       
Sbjct: 212 QQVAVAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANSDKLAPKLKR 271

Query: 42  -----REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                 E G   A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  
Sbjct: 272 ELEIIAEDG-RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYT 330

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  +         P
Sbjct: 331 KGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTP 388

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           E    +AK+L+++  +VI +        SL+  +   +   S++ D +    D +  V  
Sbjct: 389 E---ELAKELDMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPA 440

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEA 274
           +       +  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE+
Sbjct: 441 DAVSFTLLQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIES 500

Query: 275 RAFKKVQESIQKQV 288
           +   K++   + QV
Sbjct: 501 KTMSKLRHPSRSQV 514


>gi|15609840|ref|NP_217219.1| RNA polymerase sigma factor [Mycobacterium tuberculosis H37Rv]
 gi|15842241|ref|NP_337278.1| RNA polymerase sigma factor [Mycobacterium tuberculosis CDC1551]
 gi|31793875|ref|NP_856368.1| RNA polymerase sigma factor [Mycobacterium bovis AF2122/97]
 gi|121638578|ref|YP_978802.1| RNA polymerase sigma factor [Mycobacterium bovis BCG str. Pasteur
           1173P2]
 gi|148662544|ref|YP_001284067.1| RNA polymerase sigma factor [Mycobacterium tuberculosis H37Ra]
 gi|148823893|ref|YP_001288647.1| RNA polymerase sigma factor [Mycobacterium tuberculosis F11]
 gi|167970074|ref|ZP_02552351.1| RNA polymerase sigma factor RpoD [Mycobacterium tuberculosis H37Ra]
 gi|218754439|ref|ZP_03533235.1| RNA polymerase sigma factor [Mycobacterium tuberculosis GM 1503]
 gi|224991070|ref|YP_002645759.1| RNA polymerase sigma factor [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|253798215|ref|YP_003031216.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis KZN
           1435]
 gi|254551759|ref|ZP_05142206.1| RNA polymerase sigma factor [Mycobacterium tuberculosis '98-R604
           INH-RIF-EM']
 gi|260187720|ref|ZP_05765194.1| RNA polymerase sigma factor [Mycobacterium tuberculosis CPHL_A]
 gi|289448358|ref|ZP_06438102.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           CPHL_A]
 gi|289553511|ref|ZP_06442721.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis KZN
           605]
 gi|289762874|ref|ZP_06522252.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis GM
           1503]
 gi|294994205|ref|ZP_06799896.1| RNA polymerase sigma factor [Mycobacterium tuberculosis 210]
 gi|297635311|ref|ZP_06953091.1| RNA polymerase sigma factor [Mycobacterium tuberculosis KZN 4207]
 gi|297732307|ref|ZP_06961425.1| RNA polymerase sigma factor [Mycobacterium tuberculosis KZN R506]
 gi|306780885|ref|ZP_07419222.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu002]
 gi|306790106|ref|ZP_07428428.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu004]
 gi|306798608|ref|ZP_07436910.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu006]
 gi|306804467|ref|ZP_07441135.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu008]
 gi|306807495|ref|ZP_07444163.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu007]
 gi|306968762|ref|ZP_07481423.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu009]
 gi|307080806|ref|ZP_07489976.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu011]
 gi|313659640|ref|ZP_07816520.1| RNA polymerase sigma factor [Mycobacterium tuberculosis KZN V2475]
 gi|61234251|sp|P0A602|RPOD_MYCTU RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A
 gi|61234258|sp|P0A603|RPOD_MYCBO RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A
 gi|1072023|gb|AAA81643.1| sigma factor [Mycobacterium bovis]
 gi|1072025|gb|AAA81644.1| sigma factor [Mycobacterium tuberculosis str. Erdman]
 gi|1171102|gb|AAA86043.1| sigma factor MysA [Mycobacterium tuberculosis H37Rv]
 gi|2181994|emb|CAB09463.1| RNA POLYMERASE SIGMA FACTOR SIGA (SIGMA-A) [Mycobacterium
           tuberculosis H37Rv]
 gi|13882532|gb|AAK47092.1| RNA polymerase principal sigma factor SigA [Mycobacterium
           tuberculosis CDC1551]
 gi|31619469|emb|CAD94907.1| RNA POLYMERASE SIGMA FACTOR SIGA (SIGMA-A) [Mycobacterium bovis
           AF2122/97]
 gi|121494226|emb|CAL72704.1| RNA polymerase sigma factor sigA [Mycobacterium bovis BCG str.
           Pasteur 1173P2]
 gi|148506696|gb|ABQ74505.1| RNA polymerase sigma factor [Mycobacterium tuberculosis H37Ra]
 gi|148722420|gb|ABR07045.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis F11]
 gi|224774185|dbj|BAH26991.1| RNA polymerase sigma factor [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|253319718|gb|ACT24321.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis KZN
           1435]
 gi|289421316|gb|EFD18517.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           CPHL_A]
 gi|289438143|gb|EFD20636.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis KZN
           605]
 gi|289710380|gb|EFD74396.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis GM
           1503]
 gi|308326286|gb|EFP15137.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu002]
 gi|308333457|gb|EFP22308.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu004]
 gi|308341125|gb|EFP29976.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu006]
 gi|308346090|gb|EFP34941.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu007]
 gi|308348951|gb|EFP37802.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu008]
 gi|308353649|gb|EFP42500.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu009]
 gi|308361450|gb|EFP50301.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu011]
 gi|326904319|gb|EGE51252.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis W-148]
 gi|328457987|gb|AEB03410.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis KZN
           4207]
          Length = 528

 Score =  255 bits (652), Expect = 5e-66,   Method: Composition-based stats.
 Identities = 79/319 (24%), Positives = 148/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------REHGDL- 47
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+  
Sbjct: 215 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSERGEKL 273

Query: 48  ----------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 274 PAAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 333

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 334 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 391

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 392 REPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 443

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 444 AVVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 503

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 504 RQIESKTMSKLRHPSRSQV 522


>gi|332977407|gb|EGK14184.1| DNA-directed RNA polymerase sigma subunit RpoH [Psychrobacter sp.
           1501(2011)]
          Length = 362

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 107/271 (39%), Positives = 165/271 (60%), Gaps = 5/271 (1%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           I L  Y++ + +IP+L  ++E  LA RY + GD+ AA  LV SHLR V+ IA  Y GYGL
Sbjct: 84  INLGAYMNSVHQIPILTTEQEQELAHRYYDEGDVEAARILVMSHLRFVIHIARSYSGYGL 143

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P ++++ EGN+GLM+AVK+FDP +G RL ++++ WIKA + E+++R+W +VK+ TT   +
Sbjct: 144 PQADLIQEGNLGLMKAVKRFDPNKGVRLVSFAVHWIKAEIHEFVIRNWRIVKVATTKAHR 203

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
           +LFFNLR LK      T+N L  E+  AIA  LNV+  +V+ M  RL   ++     +S 
Sbjct: 204 KLFFNLRSLKK-----TNNQLTLEEADAIAADLNVTRKQVLEMESRLTSYDASFEAQSSD 258

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D++        + D     +++ + +  +N  N L  +M  L+ R R I E R L E   
Sbjct: 259 DEDGHYAPQLFLEDGVDPAEMVEDADWEENNTNALMDAMDTLDDRSRDIVEQRWLSEQKS 318

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           TL  L++ + +S ERVRQIE  A  K++E++
Sbjct: 319 TLHELAAVYNISAERVRQIEKNAMDKIREAM 349


>gi|19862496|sp|Q04506|RPOD_LACLA RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-42
          Length = 386

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 81/279 (29%), Positives = 138/279 (49%), Gaps = 14/279 (5%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD--LSAAHRLVTSHLRLVVKIAMGYRG 70
           +  +  Y+ EI + P++   EE  LA+     G+    A   L  ++LRLVV IA  Y G
Sbjct: 112 DDPVRMYLKEIGRYPLISLDEETKLAEAIIAGGEGAEFAKQMLAEANLRLVVSIAKRYSG 171

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            G+   +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    
Sbjct: 172 RGMQFLDLIQEGNMGLMKAVDKFDHTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 231

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
            +      L R++ +L      +  PE    I K+L+++  +V  +        SL   I
Sbjct: 232 VE--TINKLIRVQRNLLQELGRDPSPE---EIGKELHMAPDKVREVLKIAQEPVSLETPI 286

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
              +++ S   D++  D     +  ++   R   R  L   M  L  RE  +   R   +
Sbjct: 287 --GEEDDSHLGDFIEDD---VIESPVDYTNRILLREQLDEVMDTLTDREENVLRMRFGLD 341

Query: 251 NP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +    TLE++  +F+V+RER+RQIEA+A KK++   + +
Sbjct: 342 DGRMHTLEDVGKQFKVTRERIRQIEAKAIKKLRHPRRSK 380


>gi|253991200|ref|YP_003042556.1| RNA polymerase factor sigma-32 [Photorhabdus asymbiotica subsp.
           asymbiotica ATCC 43949]
 gi|253782650|emb|CAQ85814.1| component of rna polymerase, sigma 32 factor [Photorhabdus
           asymbiotica]
          Length = 285

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 102/290 (35%), Positives = 164/290 (56%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  YI      PML  +EE  LA+R    GDL AA +L+ SHLR 
Sbjct: 1   MAKEMQTLALVPQGSLEGYIRASNAYPMLTAEEEKELAERLHYQGDLDAAKKLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARSYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +AK+L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVEMVAKELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNP 237
           +  +    +    D    Q    ++Y  D        + E     +  + L+ ++  L+ 
Sbjct: 176 SAQDMAFDMSADDDNQEGQSVAPVLYLQDKASDFAGGIEEDNWENHAADKLSVAIEGLDE 235

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I   R L ++   TL+ L+ ++ VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQDIIRCRWLDDDNKSTLQELADKYGVSAERVRQLEKNAMKKLRVAIEA 285


>gi|40353297|gb|AAR84412.1| essential primary sigma 70 factor [Frankia sp. EaI-12]
          Length = 409

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 81/314 (25%), Positives = 144/314 (45%), Gaps = 39/314 (12%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------------- 42
           ++ +++       +  Y+ EI K+P+L  +E+  LAKR                      
Sbjct: 99  KEELALKAPTSEPVRMYLKEIGKVPLLTAEEQVDLAKRIEAGLFASDKLAVATKKTSPQM 158

Query: 43  -------EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
                  E     A  +LV ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD 
Sbjct: 159 RRDLEAIERDGQIAKRKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDY 218

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            +G++ +TY+ WWI+ A+   I      ++I     +      L R++  L         
Sbjct: 219 TKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE--TINKLIRIQRQLLQDLGREPS 276

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
           PE    IAK+++++  +V  +        SL   I   ++  S   D++    D    V 
Sbjct: 277 PE---EIAKEMDLTPDKVREILKVSQEPVSLETPI--GEEEDSHLGDFI---EDCDAVVP 328

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIE 273
           ++       +  L   +  L+ RE+++ + R      +P TLE +  EF V+RER+RQIE
Sbjct: 329 VDAASFILLQEQLDSVLHTLSDREKKVIQLRFGLTDGHPRTLEEVGREFGVTRERIRQIE 388

Query: 274 ARAFKKVQESIQKQ 287
           ++   K++   + Q
Sbjct: 389 SKTLSKLRHPSRSQ 402


>gi|229820409|ref|YP_002881935.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Beutenbergia
           cavernae DSM 12333]
 gi|229566322|gb|ACQ80173.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Beutenbergia
           cavernae DSM 12333]
          Length = 499

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 71/303 (23%), Positives = 137/303 (45%), Gaps = 38/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR--------------------------YREHGDL 47
             +  Y+ +I K+ +L  ++E  LAKR                          +      
Sbjct: 201 DPVKDYLKQIGKVALLNAEQEVELAKRIEAGLFAEETLAAGGSMEFKLRRELEWIAADGR 260

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ W
Sbjct: 261 RAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATW 320

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L+
Sbjct: 321 WIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKELD 375

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++  +V+ +        SL+  +   +   S++ D +    D +  V  +       +  
Sbjct: 376 MTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQEQ 430

Query: 228 LTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   +
Sbjct: 431 LHAVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSR 490

Query: 286 KQV 288
            QV
Sbjct: 491 SQV 493


>gi|257126628|ref|YP_003164742.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Leptotrichia
           buccalis C-1013-b]
 gi|257050567|gb|ACV39751.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Leptotrichia
           buccalis C-1013-b]
          Length = 392

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 80/284 (28%), Positives = 143/284 (50%), Gaps = 13/284 (4%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M+  ++ +  +  Y+ EI +IP+L  +EE   A+R  + G+  A  +L+ S+LRLVV IA
Sbjct: 113 MAESMDVDEPIKMYLREIGQIPLLSYEEEIDYAQRVLD-GEEEAKQKLIESNLRLVVSIA 171

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             +   GL + +++ EGN+GLM+AV+KF+ E+GF+ +TY+ WWI+ A+   I      ++
Sbjct: 172 KKHTNRGLKMLDLIQEGNMGLMKAVEKFEYEKGFKFSTYATWWIRQAITRAIADQGRTIR 231

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           I        +   + ++K   + I     K      +A+KL +   +V S+        S
Sbjct: 232 IPVH-----MIETINKIKKESRIILQETGKEPTAEELAEKLELPVEKVKSILEMNQDPIS 286

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L   + S  +  S+  D++  D         +   R   +  L   +  LN RE  +   
Sbjct: 287 LETPVGS--EEDSELGDFVEDDKFAN---PYDATTRILLKEQLDEVLKTLNEREEMVLRY 341

Query: 246 RRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           R   ++    TLE +   F V+RER+RQIE +A +K++   +++
Sbjct: 342 RYGLDDGSQKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRRK 385


>gi|239982743|ref|ZP_04705267.1| RNA polymerase sigma factor [Streptomyces albus J1074]
          Length = 491

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 75/304 (24%), Positives = 139/304 (45%), Gaps = 40/304 (13%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------------REHGD 46
             +  Y+ +I K+P+L  ++E  LAKR                             E G 
Sbjct: 193 DPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANADKIAPKLKRELEIIAEDG- 251

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 252 RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 311

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L
Sbjct: 312 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKEL 366

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +VI +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 367 DMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 421

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 422 QLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 481

Query: 285 QKQV 288
           + QV
Sbjct: 482 RSQV 485


>gi|315651467|ref|ZP_07904490.1| DNA-directed RNA polymerase sigma subunit RpoD [Eubacterium
           saburreum DSM 3986]
 gi|315486287|gb|EFU76646.1| DNA-directed RNA polymerase sigma subunit RpoD [Eubacterium
           saburreum DSM 3986]
          Length = 389

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 80/287 (27%), Positives = 144/287 (50%), Gaps = 15/287 (5%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD---LSAAHRLVTSHLRL 60
           +++   +  E  +  Y+ EI KIP+L   EE  LAK+  +  +     A  ++  S+LRL
Sbjct: 104 EDLDDYIAIEDSIKMYLKEIGKIPLLSVDEEMNLAKKICDPDEAVRKEARKQMAESNLRL 163

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ WWI+ A+   I   
Sbjct: 164 VVSIAKRYMGRGMQFLDLIQEGNLGLLRAVEKFDYQKGFKFSTYATWWIRQAITRSIADQ 223

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L +++  L        +P++V   AK + +  S+V  +    
Sbjct: 224 ARTIRIPVHMVE--TINRLIKIQRKLVQEFGREPRPDEV---AKVMGIPVSKVREIMSFA 278

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               S+   I   D++ S   D+L    D   ++ +         + L   +  L  RE+
Sbjct: 279 LEPVSMETPI--GDEDDSHLGDFL---QDSNAKIPVNFAMDVLLHDQLMEVIKSLTEREQ 333

Query: 241 RIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           ++   R   E+  P TLE +   F ++RER+RQIEA++ +K++   +
Sbjct: 334 KVILLRFGLEDGKPRTLEEVGKVFGITRERIRQIEAKSLRKLRNPSK 380


>gi|294670676|ref|ZP_06735551.1| hypothetical protein NEIELOOT_02398 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
 gi|291307564|gb|EFE48807.1| hypothetical protein NEIELOOT_02398 [Neisseria elongata subsp.
           glycolytica ATCC 29315]
          Length = 287

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 114/282 (40%), Positives = 180/282 (63%), Gaps = 7/282 (2%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           + +G   L +YIH +  IP+L  +EE+ LA+R +  GD+ AA +L+ SHLR+VV IA GY
Sbjct: 11  VPSGHGSLDQYIHTVNSIPLLTPEEEHNLAER-KMRGDVEAAKQLILSHLRVVVSIARGY 69

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGL  ++++ EGNIGLM+AVK+++P+RG RL ++++ WIKA + E+ILR+W LV++ T
Sbjct: 70  DGYGLNQADLIQEGNIGLMKAVKRYEPDRGARLFSFAVHWIKAEIHEFILRNWRLVRVAT 129

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           T  Q++LFFNLR ++  L A++     P++  AIA  L V  SEV+ M  R+ G +    
Sbjct: 130 TKPQRKLFFNLRSMRKSLSALS-----PKEAQAIADDLGVKLSEVLEMEQRMTGKDVALL 184

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
             NS D ++    DWL    +   + +  K     +   L  +++ L+ R RRI E R L
Sbjct: 185 ADNSDDDDNFAPIDWLADHDNEPTRQIERKAHYTLQTEGLQNALAKLDDRSRRIVETRWL 244

Query: 249 QEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           Q++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 245 QDDGGLTLHELAAEYGVSAERIRQIEAKAMQKLRTFLAEETE 286


>gi|308051462|ref|YP_003915028.1| RNA polymerase, sigma 32 subunit, RpoH [Ferrimonas balearica DSM
           9799]
 gi|307633652|gb|ADN77954.1| RNA polymerase, sigma 32 subunit, RpoH [Ferrimonas balearica DSM
           9799]
          Length = 286

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 112/288 (38%), Positives = 173/288 (60%), Gaps = 10/288 (3%)

Query: 2   NRKNMSIIV--NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLR 59
            R NM+++V   G   L  YI  +  IPML  +EE  LA++  E GDL AA  L+ +HLR
Sbjct: 4   TRPNMALMVVPQGHGTLESYIQAVNAIPMLSAEEEQYLARQV-EQGDLDAAKHLIMAHLR 62

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
            VV +A  Y GYGLP ++++ EGNIGLM+AVK+FDP  G RL ++++ WIKA + EY+L+
Sbjct: 63  FVVHVARSYAGYGLPQADLIQEGNIGLMKAVKRFDPNIGVRLVSFAVHWIKAEIHEYVLK 122

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
           +W +VK+ TT  Q++LFFNLR+ K  L   +      E+V  +A +L VSESEV+ M  R
Sbjct: 123 NWRIVKVATTKAQRKLFFNLRKAKKRLGWFS-----AEEVSTVADELGVSESEVMEMEAR 177

Query: 180 LAG-DESLN-ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
           +A  D + + A     D+ +     +L        + L +++  +  +  L  +++ L+ 
Sbjct: 178 MAAVDAAFDIAPERDDDEGAFAPALFLEDKQSDHAEALEQEDWDRQSQQRLHAALNTLDE 237

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           R R I  AR L E   TL+ L+  ++VS ER+RQ+E  A KK++ +++
Sbjct: 238 RSRDILMARWLDEPKATLQELADRYQVSAERIRQLEKNAIKKLKSAME 285


>gi|295394756|ref|ZP_06804971.1| DNA-directed RNA polymerase sigma subunit RpoD [Brevibacterium
           mcbrellneri ATCC 49030]
 gi|294972352|gb|EFG48212.1| DNA-directed RNA polymerase sigma subunit RpoD [Brevibacterium
           mcbrellneri ATCC 49030]
          Length = 473

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 74/303 (24%), Positives = 136/303 (44%), Gaps = 38/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE--------------------------HGDL 47
             +  Y+ +I K+ +L   EE  LAKR                             H   
Sbjct: 175 DPVKDYLKQIGKVALLNAAEEVDLAKRIEAGMYAEHLVDEGKVTDARDLRDYKWIIHDGR 234

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ W
Sbjct: 235 IAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATW 294

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L+
Sbjct: 295 WIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKELD 349

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++   V+ +        SL+  +   +   S++ D +    D +  V  +       +  
Sbjct: 350 MTPERVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADSVSFTLLQEQ 404

Query: 228 LTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L   +  L+ RE  +   R    +  P TL+ +   + V+RER+RQIE++   K++   +
Sbjct: 405 LHSVLDTLSEREAGVVSMRFGLNDGQPKTLDEIGKVYGVTRERIRQIESKTMAKLRHPSR 464

Query: 286 KQV 288
            QV
Sbjct: 465 SQV 467


>gi|329120658|ref|ZP_08249321.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Neisseria
           bacilliformis ATCC BAA-1200]
 gi|327460882|gb|EGF07216.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Neisseria
           bacilliformis ATCC BAA-1200]
          Length = 287

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 116/288 (40%), Positives = 182/288 (63%), Gaps = 7/288 (2%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +     + +G   L +YIH +  IP+L  +EE+ LA+R +  GD+ AA RL+ SHLR+VV
Sbjct: 5   QTTTLPVPSGHGSLEQYIHTVNSIPLLTPEEEHNLAER-KMGGDVEAAKRLILSHLRVVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA GY GYGL  ++++ EGNIGLM+AVK+++P+RG RL ++++ WIKA + E+ILR+W 
Sbjct: 64  SIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPDRGARLFSFAVHWIKAEIHEFILRNWR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           LV++ TT  Q++LFFNLR ++  L A++     P++  AIA  L V  SEV+ M  R+ G
Sbjct: 124 LVRVATTKPQRKLFFNLRSMRKSLSALS-----PKEAQAIADDLGVKLSEVMEMEQRMTG 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
            +      NS D++S    DWL    +   + +  K     +   L  +++ L+ R RRI
Sbjct: 179 RDIALLADNSDDEDSFAPIDWLADHDNEPTRQIERKAHHALQTEGLQNALAKLDERSRRI 238

Query: 243 FEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
            E R LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 239 VETRWLQDDGGLTLHELAAEYGVSAERIRQIEAKAMQKLRGFLAEEAE 286


>gi|329910210|ref|ZP_08275256.1| RNA polymerase sigma factor RpoH [Oxalobacteraceae bacterium
           IMCC9480]
 gi|327546240|gb|EGF31276.1| RNA polymerase sigma factor RpoH [Oxalobacteraceae bacterium
           IMCC9480]
          Length = 298

 Score =  255 bits (652), Expect = 6e-66,   Method: Composition-based stats.
 Identities = 125/275 (45%), Positives = 176/275 (64%), Gaps = 10/275 (3%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  YI  + ++PML  +EE  LA+R R+  DL AA  +V SHLRLVV IA GY GYGL
Sbjct: 26  GNIDSYISAVNRLPMLTHEEEMSLARRLRDQNDLGAAQGMVLSHLRLVVSIARGYLGYGL 85

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P ++++ EGNIGLM+AVK+FDP++G RL +Y+M WIKA M EYIL++W LVK+ TT  Q+
Sbjct: 86  PHADLIQEGNIGLMKAVKRFDPDQGVRLVSYAMHWIKAEMHEYILKNWRLVKVATTKAQR 145

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINS 192
           +LFFNLR  K  L     +++ P QV A+A+ LNV   EVI M  RL+G D +L A  + 
Sbjct: 146 KLFFNLRSHKTGL-----DSMTPAQVEALAQTLNVKREEVIEMETRLSGRDIALEAPTDD 200

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            D   +    +L  D +    VL  ++  + + + L+++++ L+ R RRI EAR L  + 
Sbjct: 201 EDDKFA-PIAYLSSDRNEPTNVLEAQQYDRLQSDGLSQALNKLDERSRRIVEARWLANDD 259

Query: 253 ---VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
               TL  L+ EF VS ER+RQIEA A KK++ S+
Sbjct: 260 GSGATLHELAKEFGVSAERIRQIEAVALKKMKGSL 294


>gi|291458966|ref|ZP_06598356.1| RNA polymerase sigma factor RpoD [Oribacterium sp. oral taxon 078
           str. F0262]
 gi|291418220|gb|EFE91939.1| RNA polymerase sigma factor RpoD [Oribacterium sp. oral taxon 078
           str. F0262]
          Length = 388

 Score =  255 bits (651), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 84/280 (30%), Positives = 146/280 (52%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           +  E  +  Y+ EI  + +L  +EEY LA R ++ GD +A  RL+ ++LRLVV IA  Y 
Sbjct: 113 IGTEDPVRMYLKEIGTVSLLSAEEEYALAIR-KQQGDEAAKQRLIEANLRLVVSIAKRYT 171

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   ++V EGN+GL++ V+KFDPE+GF+L+TY+ WWI+ ++   +      +++   
Sbjct: 172 GRGMSFLDLVQEGNLGLIKGVEKFDPEKGFKLSTYATWWIRQSVTRALADQARTIRVPVH 231

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      + ++    + +T        V  +A+ L++SE +V  +        SL   
Sbjct: 232 MVE-----TINKMSKMQRKLTLELGYEPSVKELAEHLDMSEDKVQEIMQIAREPASLETP 286

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   +++ S   D++    D          E    R  +   +  L  RER++   R   
Sbjct: 287 I--GEEDDSNLGDFVA---DANVLTPESNVEAVMLREHIDSLLGDLKERERQVIVLRFGL 341

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+  P TLE +  EF V+RER+RQIEA+A +K++  ++ +
Sbjct: 342 EDGHPRTLEEVGKEFNVTRERIRQIEAKALRKLRNPVRSK 381


>gi|256823783|ref|YP_003147746.1| RNA polymerase sigma-32 subunit RpoH [Kangiella koreensis DSM
           16069]
 gi|256797322|gb|ACV27978.1| RNA polymerase, sigma 32 subunit, RpoH [Kangiella koreensis DSM
           16069]
          Length = 283

 Score =  255 bits (651), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 107/282 (37%), Positives = 170/282 (60%), Gaps = 8/282 (2%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +M++ V     +  Y+  +  IP+L  ++E  LA  + ++ DL AA +LV +HLR VV I
Sbjct: 7   SMALAVPT-GSIDGYVSTVSAIPVLSVEQEQKLAHEFHDNNDLEAARQLVMAHLRFVVYI 65

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y GYGLP ++++ EGNIGLM+AVK+FDP  G RL ++++ WIKA + EY+LR+W +V
Sbjct: 66  ARSYSGYGLPQADLIQEGNIGLMKAVKRFDPTVGVRLVSFAVHWIKAEIHEYVLRNWRIV 125

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGD 183
           KI TT  Q++LFFNLR  K  L  + +     ++V A+A+ L VSE EV  M  RL A D
Sbjct: 126 KIATTKAQRKLFFNLRSKKKTLNWLNN-----DEVNAVAQDLGVSEEEVRRMEGRLNAHD 180

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRI 242
            S +A   S D ++       +   +      IE+E+ +++R + L  ++  L+ R + I
Sbjct: 181 ASFDAPNASDDDDAVYAPIHYLESPNSDPAQAIEQEDWQDQREVRLMSALKTLDERSQDI 240

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + R L +   TL +L+ ++ +S ER+RQ+E  A  K++ +I
Sbjct: 241 LQQRWLSDQKATLHDLADKYGISAERIRQLEKNAMNKIKNAI 282


>gi|312898762|ref|ZP_07758151.1| RNA polymerase sigma factor RpoD [Megasphaera micronuciformis
           F0359]
 gi|310620193|gb|EFQ03764.1| RNA polymerase sigma factor RpoD [Megasphaera micronuciformis
           F0359]
          Length = 437

 Score =  255 bits (651), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 83/292 (28%), Positives = 134/292 (45%), Gaps = 25/292 (8%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS------------AAHRLVTSH 57
           VN +  +  Y+ EI ++P+L  +EE  LAKR  E G               A  +L  ++
Sbjct: 151 VNIDDPVRMYLKEIGRVPLLSAEEEITLAKRI-EAGSAEGATPEEVSAGNIAKKKLTDAN 209

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I
Sbjct: 210 LRLVVSIAKRYVGRGMLFLDLIQEGNLGLLKAVEKFDYSKGYKFSTYATWWIRQAITRAI 269

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
                 ++I     +      L R+   L         PE    IA+K+ V    V  + 
Sbjct: 270 ADQARTIRIPVHMVE--TINKLIRISRQLLQDKGREPLPE---EIAEKMGVPVERVREIM 324

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                  SL   I   ++  S   D++    D +     +       +  +    S L  
Sbjct: 325 KIAQEPVSLETPI--GEEEDSHLGDFI---EDQEAIAPDDAASFILLKEQIEDVFSCLTD 379

Query: 238 RERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           RER++   R       P TLE +   F V+RER+RQIE +A  K++   +++
Sbjct: 380 RERKVLYLRFGLKDGRPRTLEEVGQHFNVTRERIRQIEGKALSKLRNWGKRE 431


>gi|83746847|ref|ZP_00943894.1| RNA polymerase sigma-32 factor [Ralstonia solanacearum UW551]
 gi|207727816|ref|YP_002256210.1| rna polymerase sigma h (sigma-32) factor protein [Ralstonia
           solanacearum MolK2]
 gi|207742220|ref|YP_002258612.1| rna polymerase sigma h (sigma-32) factor protein [Ralstonia
           solanacearum IPO1609]
 gi|83726432|gb|EAP73563.1| RNA polymerase sigma-32 factor [Ralstonia solanacearum UW551]
 gi|206591057|emb|CAQ56669.1| rna polymerase sigma h (sigma-32) factor protein [Ralstonia
           solanacearum MolK2]
 gi|206593608|emb|CAQ60535.1| rna polymerase sigma h (sigma-32) factor protein [Ralstonia
           solanacearum IPO1609]
          Length = 306

 Score =  255 bits (651), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 119/287 (41%), Positives = 174/287 (60%), Gaps = 12/287 (4%)

Query: 7   SIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           ++   G +G L  YI  + ++PML  +EE  LA+ Y   G+L AA RLV SHLRLVV IA
Sbjct: 23  ALAFPGSLGNLDAYIQSVNRVPMLTAEEEQQLARDYHATGNLDAARRLVLSHLRLVVSIA 82

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGLP ++++ EGNIGLM+AVK+FDP++G RL +Y++ WIKA M EYIL++W +VK
Sbjct: 83  RQYLGYGLPHADLIQEGNIGLMKAVKRFDPDQGVRLVSYAIHWIKAEMHEYILKNWRMVK 142

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDE 184
           + TT  Q++LFFNLR  K             +++ A+A++LNV  +EV  M  RL  GD 
Sbjct: 143 VATTKAQRKLFFNLRSHK----QDAHATFTSDEIDAVAQELNVKGAEVREMETRLSGGDI 198

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           +L   I+  ++ S     +L   H+   +VL  +   + +   +  +++ L+ R RRI E
Sbjct: 199 ALEGQIDDGEE-SFAPIAYLADTHNEPTRVLETRGHDRLQSEGIETALAKLDDRSRRIIE 257

Query: 245 ARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           AR L          TL  L+ EF VS ER+RQIE+ A KK++ ++Q 
Sbjct: 258 ARWLNVNDDGSGGATLHELADEFGVSAERIRQIESAAMKKMKGALQA 304


>gi|58583919|ref|YP_202935.1| RNA polymerase factor sigma-32 [Xanthomonas oryzae pv. oryzae
           KACC10331]
 gi|58428513|gb|AAW77550.1| RNA polymerase sigma-32 factor [Xanthomonas oryzae pv. oryzae
           KACC10331]
          Length = 329

 Score =  255 bits (651), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 119/291 (40%), Positives = 173/291 (59%), Gaps = 15/291 (5%)

Query: 1   MNRKNMSIIV-------NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRL 53
           MN+   + +V       +    L  YI  + +IP+L   EE  LA+R+R+  DL AA  L
Sbjct: 39  MNQTTSTALVANNLPIPSALGSLDAYIGAVHQIPVLSVDEEQNLARRFRDELDLDAAREL 98

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V SHLR VV +A GY GYGLP+ +++ EGNIGLM+AVK+FDP+ G RL ++++ WI+A M
Sbjct: 99  VHSHLRFVVHVARGYNGYGLPLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAVHWIRAEM 158

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
            E+IL++W +VK+ TT  Q++LFFNLR+ K  L  +        +V A+AK LNVSE EV
Sbjct: 159 HEFILKNWRIVKVATTKAQRKLFFNLRKSKTRLGWLN-----ASEVTAVAKDLNVSEREV 213

Query: 174 ISMNCRLAG-DESLNA-LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           + M  RL+G D   +A      D        +LV + +   Q     +   N+  +L   
Sbjct: 214 MEMESRLSGRDIGFDASSDEDDDHGPPSPVSYLVANEEDPSQAYERHDSEDNQLQLLREG 273

Query: 232 MSVLNPRERRIFEARRLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           M+ L+ R R I + R L  ++ VTL+ L+ E+ VS ER+RQIEA A KK++
Sbjct: 274 MAGLDTRSRDIVKRRWLDSDSKVTLQELADEYGVSAERIRQIEANALKKMK 324


>gi|315604554|ref|ZP_07879617.1| DNA-directed RNA polymerase sigma subunit RpoD [Actinomyces sp.
           oral taxon 180 str. F0310]
 gi|315313566|gb|EFU61620.1| DNA-directed RNA polymerase sigma subunit RpoD [Actinomyces sp.
           oral taxon 180 str. F0310]
          Length = 516

 Score =  255 bits (651), Expect = 7e-66,   Method: Composition-based stats.
 Identities = 71/304 (23%), Positives = 139/304 (45%), Gaps = 39/304 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY----------REHGDL---------------- 47
             +  Y+ +I K+ +L  ++E  LA+R           +   D                 
Sbjct: 217 DPVKDYLKQIGKVSLLNAEQEVDLARRIEAGLYAEYKLKNQADEMTSRERRELHFLAQDG 276

Query: 48  -SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 277 QQAKNHLLEANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 336

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L
Sbjct: 337 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKEL 391

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +V+ +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 392 DMTAEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAIVPADAVSFTLLQE 446

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R    +  P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 447 QLHHVLDTLSEREAGVVSMRFGLGDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 506

Query: 285 QKQV 288
           + QV
Sbjct: 507 RSQV 510


>gi|254363063|ref|ZP_04979122.1| DNA-directed RNA polymerase sigma subunit RpoH [Mannheimia
           haemolytica PHL213]
 gi|261492837|ref|ZP_05989384.1| DNA-directed RNA polymerase sigma subunit RpoH [Mannheimia
           haemolytica serotype A2 str. BOVINE]
 gi|261494798|ref|ZP_05991276.1| DNA-directed RNA polymerase sigma subunit RpoH [Mannheimia
           haemolytica serotype A2 str. OVINE]
 gi|153094728|gb|EDN75518.1| DNA-directed RNA polymerase sigma subunit RpoH [Mannheimia
           haemolytica PHL213]
 gi|261309509|gb|EEY10734.1| DNA-directed RNA polymerase sigma subunit RpoH [Mannheimia
           haemolytica serotype A2 str. OVINE]
 gi|261311519|gb|EEY12675.1| DNA-directed RNA polymerase sigma subunit RpoH [Mannheimia
           haemolytica serotype A2 str. BOVINE]
          Length = 319

 Score =  255 bits (651), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 99/273 (36%), Positives = 161/273 (58%), Gaps = 6/273 (2%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  L  YI    + P+L  ++E  LA+RY    D+ AA +L+ SH+R V+ IA GY GYG
Sbjct: 48  QGNLDSYIRMANQYPILTAEQEKELAERYYYDEDVEAAKQLILSHMRFVIHIARGYLGYG 107

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP+++++ EGNIGLM+AVK+FDP  G RL ++++ W+KA + EY+L++W +VK+ TT  Q
Sbjct: 108 LPLADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWVKAEIHEYVLKNWRIVKVATTKAQ 167

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALIN 191
           ++LFFNLR+ K  L    +     E++  +A  L VS  EV  M  R+ G D   +    
Sbjct: 168 RKLFFNLRKNKNRLAWFNE-----EEIKKVADDLGVSVEEVREMESRMTGQDLGFDLPAG 222

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             D++S     ++          L +++        L  +++ L+ R + I + R L +N
Sbjct: 223 DDDEDSYAPSMYIEDSSSNFADDLEDEQHNGQATAQLAYALATLDERSQDIIKTRWLDDN 282

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL++L+ ++ +S ERVRQ+E  A KK++E+I
Sbjct: 283 KATLQDLADKYNISAERVRQLENAALKKIKEAI 315


>gi|75761907|ref|ZP_00741832.1| RNA polymerase sigma factor rpoD [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|74490615|gb|EAO53906.1| RNA polymerase sigma factor rpoD [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
          Length = 268

 Score =  255 bits (651), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 78/272 (28%), Positives = 134/272 (49%), Gaps = 13/272 (4%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
            Y+ EI ++ +L  +EE  LA R  E GD  A  RL  ++LRLVV IA  Y G G+   +
Sbjct: 1   MYLKEIGRVDLLSAEEEIRLATRI-EEGDEEAKRRLAEANLRLVVSIAKRYVGRGMLFLD 59

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     +     
Sbjct: 60  LIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE--TIN 117

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R++  L         PE    I ++++++  +V  +        SL   I   +++ 
Sbjct: 118 KLIRVQRQLLQDLGREPSPE---EIGEEMDLAPEKVREILKIAQEPVSLETPI--GEEDD 172

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTL 255
           S   D++    D +     +    +  +  L   +  L  RE  +   R   ++    TL
Sbjct: 173 SHLGDFI---EDQEATSPADHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTL 229

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +   F V+RER+RQIEA+A +K++   + +
Sbjct: 230 EEVGKVFGVTRERIRQIEAKALRKLRHPSRSK 261


>gi|312196071|ref|YP_004016132.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EuI1c]
 gi|311227407|gb|ADP80262.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EuI1c]
          Length = 393

 Score =  255 bits (651), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 83/314 (26%), Positives = 143/314 (45%), Gaps = 40/314 (12%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY--------------------- 41
            + ++        +  Y+ EI K+P+L   EE  LAKR                      
Sbjct: 84  EEALNAKAPTSDPVRMYLKEIGKVPLLTAAEEVDLAKRIEAGLFAAEKLGGGRRLTVALR 143

Query: 42  ------REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
                    GD+ A  +LV ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD 
Sbjct: 144 VDLEAVARDGDV-AKRKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDY 202

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            +G++ +TY+ WWI+ A+   I      ++I     +      L R++  L         
Sbjct: 203 TKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE--TINKLIRIQRQLLQDLGREPL 260

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
           PE    IAK+++++  +V  +        SL   I   ++  S   D++    D    V 
Sbjct: 261 PE---EIAKEMDLTPDKVREILKVAQEPVSLETPI--GEEEDSHLGDFI---EDSDAVVP 312

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIE 273
           ++       +  L   +  L+ RE+++ + R      +P TLE +  EF V+RER+RQIE
Sbjct: 313 VDAASFLLLQEQLDSVLHTLSDREKKVIQLRFGLTDGHPRTLEEVGREFGVTRERIRQIE 372

Query: 274 ARAFKKVQESIQKQ 287
           ++   K++   + Q
Sbjct: 373 SKTLSKLRHPSRSQ 386


>gi|293400669|ref|ZP_06644814.1| RNA polymerase sigma factor RpoD [Erysipelotrichaceae bacterium
           5_2_54FAA]
 gi|291305695|gb|EFE46939.1| RNA polymerase sigma factor RpoD [Erysipelotrichaceae bacterium
           5_2_54FAA]
          Length = 396

 Score =  255 bits (651), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 78/276 (28%), Positives = 141/276 (51%), Gaps = 12/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L+ +EE  +A+R +  GD  A  +L++++LRLVV IA  Y G G+
Sbjct: 122 DPVKMYLKEIGRVELLDPKEEPEIARRIQ-AGDEEAKKKLISANLRLVVSIAKKYVGRGM 180

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 181 LFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 239

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L      +   E++   AK  N+S  +V  +        SL   I   
Sbjct: 240 -TINKLTRIQRQLVQDLGRDPSAEEIA--AKMENISPEKVREIQKIALEPVSLETPI--G 294

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D +     E    +  ++ +   +  L  RE ++   R    +  
Sbjct: 295 EEDDSHLGDFI---EDKEALSPDEYANNQLLKDEINTVLQGLTEREEKVLRLRFGLYDGR 351

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 352 TRTLEEVGKEFNVTRERIRQIEAKALRKLKHPTRSK 387


>gi|41408918|ref|NP_961754.1| RNA polymerase sigma factor [Mycobacterium avium subsp.
           paratuberculosis K-10]
 gi|41397277|gb|AAS05137.1| SigA [Mycobacterium avium subsp. paratuberculosis K-10]
          Length = 509

 Score =  255 bits (651), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 77/312 (24%), Positives = 143/312 (45%), Gaps = 42/312 (13%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------REHGDL-------- 47
           +      +  Y+ +I K+ +L  +EE  LAKR               E G+         
Sbjct: 202 LTASADSVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMSEMAERGEKLPAAQRRD 261

Query: 48  ---------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
                     A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G
Sbjct: 262 MMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKG 321

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           ++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L         PE 
Sbjct: 322 YKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDPGREPTPE- 378

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +  V ++ 
Sbjct: 379 --ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSEAVVAVDA 431

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARA 276
                 ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++ 
Sbjct: 432 VSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKT 491

Query: 277 FKKVQESIQKQV 288
             K++   + QV
Sbjct: 492 MSKLRHPSRSQV 503


>gi|84393530|ref|ZP_00992284.1| RNA polymerase sigma factor [Vibrio splendidus 12B01]
 gi|84375809|gb|EAP92702.1| RNA polymerase sigma factor [Vibrio splendidus 12B01]
          Length = 291

 Score =  255 bits (651), Expect = 8e-66,   Method: Composition-based stats.
 Identities = 108/286 (37%), Positives = 163/286 (56%), Gaps = 8/286 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  +   + +  +  L  YI      PML  +EE  LA+R    G++ AA  L+ SHLR 
Sbjct: 1   MANQAYQMALVTQDSLDSYIRSANSYPMLTPEEERGLAERLHYKGEIDAAKGLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A GY GYGLP++++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VKI TT  Q++LFFNLR+ K  L    +      +V  +A++L V  SEV  M  RL
Sbjct: 121 WRIVKIATTKAQRKLFFNLRKSKKRLGWFNNG-----EVETVARELGVEPSEVREMESRL 175

Query: 181 -AGDESLNALINSSDKNS--SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
            A D +  A ++  D  S  +    +L        + +       +  N L  ++  L+ 
Sbjct: 176 AAQDATFEAPMDDDDGGSAYTAPVYYLEDKASDVAETVEAANWESHTNNRLGLALKSLDE 235

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           R + I  +R L +N  TL++L+  + +S ERVRQ+E  A KK++ S
Sbjct: 236 RSQHIVRSRWLDDNKSTLQDLADTYSISAERVRQLEKNAMKKLKAS 281


>gi|77359323|ref|YP_338898.1| RNA polymerase factor sigma-32 [Pseudoalteromonas haloplanktis
           TAC125]
 gi|76874234|emb|CAI85455.1| RNA polymerase sigma-32 factor (Heat shock regulatory protein
           F33.4) [Pseudoalteromonas haloplanktis TAC125]
          Length = 287

 Score =  255 bits (651), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 105/284 (36%), Positives = 167/284 (58%), Gaps = 10/284 (3%)

Query: 6   MSIIVNGE-IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           M++ V  +   +  Y+  +  IPML+ ++E  LA R +E GDLSAA +L+ SHLR V  I
Sbjct: 8   MALTVGQQSASMDGYLQAVSTIPMLKVEQEQELATRLQEEGDLSAAKQLIMSHLRFVAHI 67

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + E++L++W +V
Sbjct: 68  AKGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEFVLKNWRIV 127

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           K+ TT  Q++LFFNLR+ K  L           +V  +A +L VSE EV  M  R++G +
Sbjct: 128 KVATTKAQRKLFFNLRKNKKRLGWFNQ-----AEVSTVASELGVSEKEVREMESRMSGQD 182

Query: 185 SLNALINSSDKNSS----QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               L    D ++         +L          + +++ ++     L  ++  L+ R +
Sbjct: 183 MGFDLTGDDDDSAPSSTYSPVQYLTDGTADLADDIEQQQWQEQSHTRLFSALKTLDERSQ 242

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            I  AR L ++  TL+ L+ ++ VS ERVRQ+E  A KK+Q ++
Sbjct: 243 DIVSARWLTDDKATLQELAEKYSVSAERVRQLEKTAMKKLQAAM 286


>gi|296139587|ref|YP_003646830.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Tsukamurella
           paurometabola DSM 20162]
 gi|296027721|gb|ADG78491.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Tsukamurella
           paurometabola DSM 20162]
          Length = 483

 Score =  254 bits (650), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 79/319 (24%), Positives = 149/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-------------YREHGDL- 47
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR             + E G+  
Sbjct: 170 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLFAEQMINRWVERGEKP 228

Query: 48  ----------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 229 AIGIRRDMNWIARDGNRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 288

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 289 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 346

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 347 REPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 398

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 399 AVVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 458

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 459 RQIESKTMSKLRHPSRSQV 477


>gi|241889518|ref|ZP_04776817.1| RNA polymerase sigma factor RpoD [Gemella haemolysans ATCC 10379]
 gi|241863825|gb|EER68208.1| RNA polymerase sigma factor RpoD [Gemella haemolysans ATCC 10379]
          Length = 361

 Score =  254 bits (650), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 84/281 (29%), Positives = 138/281 (49%), Gaps = 15/281 (5%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR---EHGDLSAAHRLVTSHLRLVVKIAM 66
           +     +  Y+ EI K+P+L K++E  L+K      E     A   L  ++LRLVV IA 
Sbjct: 82  IRTNDPVRMYLKEIGKVPLLSKEKELELSKIIETGTEEEKEQAKKDLAEANLRLVVSIAK 141

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I
Sbjct: 142 RYVGRGMLFLDLIQEGNMGLIKAVEKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI 201

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
                +      L R++  L        KPE    IAKK+N++  +V  +        SL
Sbjct: 202 PVHMVE--TINRLIRIQRQLLQDLGREPKPE---EIAKKMNMTPEKVREILKIAQEPVSL 256

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              I   +++ S   D++    D + Q  +E    +  +  L   +  L  RE  + + R
Sbjct: 257 ETPI--GEEDDSHLGDFI---EDKEAQSPVEHAANELLKEQLEEILETLTDREENVLKLR 311

Query: 247 RL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
                    TLE + S F V+RER+RQIEA+A +K++   +
Sbjct: 312 FGLKDGKTHTLEEVGSAFGVTRERIRQIEAKAIRKLKHPSK 352


>gi|227495998|ref|ZP_03926309.1| RNA polymerase sigma factor [Actinomyces urogenitalis DSM 15434]
 gi|226834486|gb|EEH66869.1| RNA polymerase sigma factor [Actinomyces urogenitalis DSM 15434]
          Length = 541

 Score =  254 bits (650), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 73/304 (24%), Positives = 136/304 (44%), Gaps = 39/304 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR---------------------------YREHGD 46
             +  Y+ +I K+ +L   EE  LAKR                           +  +  
Sbjct: 242 DPVKDYLKQIGKVALLNAAEEVELAKRIEAGMYAEYLLGTEGNELDAKYRRELHWISNDG 301

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ 
Sbjct: 302 QRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYAT 361

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +A +L
Sbjct: 362 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAVEL 416

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +VI +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 417 DMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 471

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 472 QLHAVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 531

Query: 285 QKQV 288
           + QV
Sbjct: 532 RSQV 535


>gi|46143484|ref|ZP_00135165.2| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|126209296|ref|YP_001054521.1| RNA polymerase factor sigma-32 [Actinobacillus pleuropneumoniae
           L20]
 gi|126098088|gb|ABN74916.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 5b str. L20]
          Length = 316

 Score =  254 bits (650), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 98/273 (35%), Positives = 160/273 (58%), Gaps = 6/273 (2%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  L  YI    + P+L  ++E  LA+RY    D+ AA +L+ SH+R V+ IA GY GYG
Sbjct: 46  QGNLDSYIRMANQYPILTAEQEKELAERYYYDEDVEAAKQLILSHMRFVIHIARGYLGYG 105

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP+++++ EGNIGLM+AVK+FDP  G RL ++++ W+KA + EY+L++W +VK+ TT  Q
Sbjct: 106 LPLADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWVKAEIHEYVLKNWRIVKVATTKAQ 165

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALIN 191
           ++LFFNLR+ K  L    +     E++  +A+ L VS  EV  M  R+ G D   +  + 
Sbjct: 166 RKLFFNLRKNKNRLAWFNE-----EEIQKVAEDLGVSPEEVREMESRMTGQDLGFDLPVG 220

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             D        +L  +       L +++        L  +++ L+ R + I + R L E 
Sbjct: 221 EDDDEVYTPSMYLEDNSSNFADDLEDEQYNGQATAQLAYALATLDERSQDIIKTRWLDEE 280

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL++L+ ++ +S ERVRQ+E  A KK++++I
Sbjct: 281 KATLQDLAEKYGISAERVRQLENAALKKIKDAI 313


>gi|322834883|ref|YP_004214910.1| RNA polymerase, sigma 32 subunit, RpoH [Rahnella sp. Y9602]
 gi|321170084|gb|ADW75783.1| RNA polymerase, sigma 32 subunit, RpoH [Rahnella sp. Y9602]
          Length = 285

 Score =  254 bits (650), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 102/290 (35%), Positives = 166/290 (57%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  Y+      PML  +EE  LA+R   +GDL AA  L+ SHLR 
Sbjct: 1   MTKEMRTLALVPQGSLEAYVRAANAYPMLTAEEERALAERLHYNGDLEAAKELILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VAHIARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L   +      ++V  +A++L V+  +V+ M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKNKQRLGWFSH-----DEVEHVARELGVTSKDVLEMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQ---EQVLIEKEERKNRRNMLTRSMSVLNP 237
           A  +         +         ++Y  D      + + E    ++  + L+ +M  L+ 
Sbjct: 176 AAQDMTFDPTPDDEPRDGAAMAPMLYLQDKSSDFAETIEEDNWDQDATDKLSSAMEGLDE 235

Query: 238 RERRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L + N  TL+ L+ ++ VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQDIIRARWLDDENKSTLQELADKYGVSAERVRQLEKNAMKKLRMAIEA 285


>gi|118497682|ref|YP_898732.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           novicida U112]
 gi|194323654|ref|ZP_03057430.1| alternative sigma factor RpoH [Francisella tularensis subsp.
           novicida FTE]
 gi|254373048|ref|ZP_04988537.1| RNA polymerase sigma-32 factor [Francisella tularensis subsp.
           novicida GA99-3549]
 gi|254374500|ref|ZP_04989981.1| RNA polymerase sigma-32 factor [Francisella novicida GA99-3548]
 gi|118423588|gb|ABK89978.1| RNA polymerase sigma-32 factor [Francisella novicida U112]
 gi|151570775|gb|EDN36429.1| RNA polymerase sigma-32 factor [Francisella novicida GA99-3549]
 gi|151572219|gb|EDN37873.1| RNA polymerase sigma-32 factor [Francisella novicida GA99-3548]
 gi|194322018|gb|EDX19500.1| alternative sigma factor RpoH [Francisella tularensis subsp.
           novicida FTE]
 gi|332678395|gb|AEE87524.1| RNA polymerase sigma factor RpoH [Francisella cf. novicida Fx1]
          Length = 292

 Score =  254 bits (650), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 105/286 (36%), Positives = 174/286 (60%), Gaps = 7/286 (2%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
             K  ++ V  +  LS Y++ +  +P+L  ++E  LA+RY+   DL AA +LV SHLR V
Sbjct: 9   ATKTKTLPVVSDNNLSAYLNFVNTLPVLSLEQEQELARRYKYKKDLDAAQQLVLSHLRFV 68

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            KIA  + GYGL I++++ EGNIGLM+AV KFDP++G RL ++++ WIKA M +Y+L++W
Sbjct: 69  TKIARNFSGYGLSIADLIQEGNIGLMKAVSKFDPDQGVRLVSFAVHWIKAEMHDYVLKNW 128

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL- 180
            +VK+ TT  Q++LFFNLR  K  +  ++      E +  +A++L V E  VI M  R+ 
Sbjct: 129 KIVKVATTKAQRKLFFNLRSSKDKIGWLS-----SEDIKELAEELGVKEETVIEMEKRMC 183

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            GD SL+      D   +  Q   + D     E  +++++   N + ++   +S  + R 
Sbjct: 184 QGDASLDLPYTDDDGEQTSQQSLYLEDKSSNIEHQVVQQDYYDNFKAIVKDVLSGFDTRT 243

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + I  +R L +N  TL++L++++ +S ERVRQIE  A  K++++I+
Sbjct: 244 KDIIMSRYLLDNKATLQDLAAKYNISAERVRQIEEDALAKLKKAIK 289


>gi|148380889|ref|YP_001255430.1| RNA polymerase sigma factor RpoD [Clostridium botulinum A str. ATCC
           3502]
 gi|153931224|ref|YP_001385198.1| RNA polymerase sigma factor RpoD [Clostridium botulinum A str. ATCC
           19397]
 gi|153937635|ref|YP_001388667.1| RNA polymerase sigma factor RpoD [Clostridium botulinum A str.
           Hall]
 gi|153940633|ref|YP_001392215.1| RNA polymerase sigma factor RpoD [Clostridium botulinum F str.
           Langeland]
 gi|168179368|ref|ZP_02614032.1| RNA polymerase sigma factor RpoD [Clostridium botulinum NCTC 2916]
 gi|168181623|ref|ZP_02616287.1| RNA polymerase sigma factor RpoD [Clostridium botulinum Bf]
 gi|170757237|ref|YP_001782571.1| RNA polymerase sigma factor RpoD [Clostridium botulinum B1 str.
           Okra]
 gi|170761654|ref|YP_001788251.1| RNA polymerase sigma factor RpoD [Clostridium botulinum A3 str.
           Loch Maree]
 gi|187778482|ref|ZP_02994955.1| hypothetical protein CLOSPO_02076 [Clostridium sporogenes ATCC
           15579]
 gi|226950364|ref|YP_002805455.1| RNA polymerase sigma factor RpoD [Clostridium botulinum A2 str.
           Kyoto]
 gi|237796391|ref|YP_002863943.1| RNA polymerase sigma factor RpoD [Clostridium botulinum Ba4 str.
           657]
 gi|148290373|emb|CAL84500.1| RNA polymerase sigma factor (sigma-43) [Clostridium botulinum A
           str. ATCC 3502]
 gi|152927268|gb|ABS32768.1| RNA polymerase sigma factor RpoD [Clostridium botulinum A str. ATCC
           19397]
 gi|152933549|gb|ABS39048.1| RNA polymerase sigma factor RpoD [Clostridium botulinum A str.
           Hall]
 gi|152936529|gb|ABS42027.1| RNA polymerase sigma factor RpoD [Clostridium botulinum F str.
           Langeland]
 gi|169122449|gb|ACA46285.1| RNA polymerase sigma factor RpoD [Clostridium botulinum B1 str.
           Okra]
 gi|169408643|gb|ACA57054.1| RNA polymerase sigma factor RpoD [Clostridium botulinum A3 str.
           Loch Maree]
 gi|182669799|gb|EDT81775.1| RNA polymerase sigma factor RpoD [Clostridium botulinum NCTC 2916]
 gi|182675034|gb|EDT86995.1| RNA polymerase sigma factor RpoD [Clostridium botulinum Bf]
 gi|187772107|gb|EDU35909.1| hypothetical protein CLOSPO_02076 [Clostridium sporogenes ATCC
           15579]
 gi|226843729|gb|ACO86395.1| RNA polymerase sigma factor RpoD [Clostridium botulinum A2 str.
           Kyoto]
 gi|229260977|gb|ACQ52010.1| RNA polymerase sigma factor RpoD [Clostridium botulinum Ba4 str.
           657]
 gi|295320212|gb|ADG00590.1| RNA polymerase sigma factor RpoD [Clostridium botulinum F str.
           230613]
 gi|322807253|emb|CBZ04827.1| RNA polymerase sigma factor RpoD [Clostridium botulinum H04402 065]
          Length = 361

 Score =  254 bits (650), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 80/277 (28%), Positives = 136/277 (49%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI K+ +L  +EE  LA+R  E GD+ A  +L  ++LRLVV IA  Y G G
Sbjct: 89  DDPVRMYLKEIGKVALLTSEEEIELAQRI-EAGDMVAKKKLAEANLRLVVSIAKRYVGRG 147

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I     +
Sbjct: 148 MLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 207

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 L R+   L        +PE+V  I   + +   +V  +        SL   I  
Sbjct: 208 --TINKLIRVSRQLLQELGREPQPEEVAKI---MEMPVDKVREIMKIAQEPVSLETPI-- 260

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            ++  S   D++      +     E       +  L   +  L PRE ++   R   ++ 
Sbjct: 261 GEEEDSHLGDFIPD---DEAPAPAEAAAFTMLKEQLINVLDTLTPREEKVLRLRFGLDDG 317

Query: 253 --VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 318 RARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 354


>gi|188591091|ref|YP_001795691.1| RNA polymerase factor sigma-32 [Cupriavidus taiwanensis LMG 19424]
 gi|170937985|emb|CAP62969.1| RNA polymerase sigma H (sigma 32) factor; transcription of heat
           shock and stress proteins [Cupriavidus taiwanensis LMG
           19424]
          Length = 309

 Score =  254 bits (650), Expect = 9e-66,   Method: Composition-based stats.
 Identities = 121/292 (41%), Positives = 179/292 (61%), Gaps = 13/292 (4%)

Query: 2   NRKNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           N  + ++     +G L  YI  + +IP+L  +EE  LA+  R+H  + AA RLV SHLRL
Sbjct: 22  NTGSFALTFPATVGNLDSYIQAVHRIPLLTAEEEQRLARELRDHDSVEAARRLVMSHLRL 81

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y GYGLP ++++ EGNIGLM+AVK+FDP++G RL +Y+M WIKA + EY+L++
Sbjct: 82  VVSIARQYLGYGLPHADLIQEGNIGLMKAVKRFDPDQGVRLVSYAMHWIKAEIHEYVLKN 141

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR  K        +   PEQV A+A++LNV   EV+ M  RL
Sbjct: 142 WRMVKVATTKAQRKLFFNLRSHKQ-----GGHTFTPEQVEAVARELNVKPEEVMEMETRL 196

Query: 181 -AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
             GD +L   ++  ++  +    +L  +H+   +V+  K + + +   L  +++ L+ R 
Sbjct: 197 SGGDLALEGQVDDGEEEFA-PIAYLADNHNEPTRVMEAKRQDRMQVEGLEEALAKLDERS 255

Query: 240 RRIFEARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           RRI EAR L          TL  L+ EF VS ER+RQIEA A KK++ ++Q 
Sbjct: 256 RRIIEARWLNVEDDGSGGATLHELADEFGVSAERIRQIEAAAMKKMKGALQA 307


>gi|303229406|ref|ZP_07316196.1| RNA polymerase sigma factor RpoD [Veillonella atypica
           ACS-134-V-Col7a]
 gi|303230872|ref|ZP_07317619.1| RNA polymerase sigma factor RpoD [Veillonella atypica
           ACS-049-V-Sch6]
 gi|302514632|gb|EFL56627.1| RNA polymerase sigma factor RpoD [Veillonella atypica
           ACS-049-V-Sch6]
 gi|302515942|gb|EFL57894.1| RNA polymerase sigma factor RpoD [Veillonella atypica
           ACS-134-V-Col7a]
          Length = 388

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 78/296 (26%), Positives = 133/296 (44%), Gaps = 23/296 (7%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSA-----------AHRL 53
           ++   VN +  +  Y+ EI ++P+L   EE VLAK+     +  A             +L
Sbjct: 97  SVDASVNIDDPVRMYLKEIGRVPLLSADEEIVLAKQIEAGAEEDATYKEIQLSKKAKKKL 156

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V ++LRLVV IA  Y G G+   +++ EGN+GL++AV KFD  +G++ +TY+ WWI+ A+
Sbjct: 157 VDANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVDKFDYTKGYKFSTYATWWIRQAI 216

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
              I      ++I     +      L R+   L         PE    IA+ + ++   V
Sbjct: 217 TRAIADQARTIRIPVHMVE--TINKLIRISRQLLQDKGREPTPE---EIAEGMGITAERV 271

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             +        SL   I   ++  S   D++    D       +       +  +    +
Sbjct: 272 REIQKIAQEPVSLETPI--GEEEDSHLGDFI---EDQDAVAPDDAASYILLQEQIEDVFT 326

Query: 234 VLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            L  RE+++   R       P TLE +   F V+RER+RQIE +A  K++   ++ 
Sbjct: 327 CLTDREQQVLILRFGLKDGKPRTLEEVGQHFNVTRERIRQIEGKALTKLRNRGKRD 382


>gi|332980900|ref|YP_004462341.1| RNA polymerase sigma-70 subunit RpoD [Mahella australiensis 50-1
           BON]
 gi|332698578|gb|AEE95519.1| RNA polymerase, sigma 70 subunit, RpoD [Mahella australiensis 50-1
           BON]
          Length = 356

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 82/280 (29%), Positives = 138/280 (49%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           VN +  +  Y+ EI KIP+L   EE  LAKR  E GD  A  RL  ++LRLVV IA  Y 
Sbjct: 81  VNIDDPVRMYLKEIGKIPLLSSDEEIELAKRI-EQGDEEAKKRLAEANLRLVVSIAKRYV 139

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I   
Sbjct: 140 GRGMLFLDLIQEGNLGLLKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH 199

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      + +L    + +     +      +A+++ +S  +V  +        SL   
Sbjct: 200 MVE-----TINKLVRVSRQLMQELGREPAPEEVAEEMGISVDKVRDIMKIAQEPVSLETP 254

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++            E       +  L   +  L PRE ++   R   
Sbjct: 255 I--GEEEDSHLGDFIPD---DDAPAPAEAAAFTLLKEQLMDVLDTLTPREEKVLRLRFGL 309

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++    TLE +  EF+V+RER+RQIEA+A +K++   + +
Sbjct: 310 DDGRARTLEEVGKEFDVTRERIRQIEAKALRKLRHPSRSK 349


>gi|328907303|gb|EGG27069.1| RNA polymerase sigma factor RpoD [Propionibacterium sp. P08]
          Length = 506

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 76/318 (23%), Positives = 143/318 (44%), Gaps = 41/318 (12%)

Query: 2   NRKNMSIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRY------------------ 41
           +    +++V G     +  Y+ +I K+ +L   EE  LAKR                   
Sbjct: 193 DEPEQTVMVAGATADPVKDYLKQIGKVALLNAVEEVDLAKRIEAGLFAGEQLADPDAKIP 252

Query: 42  -REHGDLS--------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
            ++  D          A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 253 EKDREDYEWIAEDGKVAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEK 312

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWIK A+   +      ++I     +  +   L R++  +      
Sbjct: 313 FDYTKGYKFSTYATWWIKQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGR 370

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE    +A +L+++  +VI +        SL+  +   +   S++ D +    D + 
Sbjct: 371 EPTPE---ELANELDMTAEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEA 422

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVR 270
            V  +       +  L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 423 IVPADAVNFTLLQEQLHDVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIR 482

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 483 QIESKTMSKLRHPSRSQV 500


>gi|157364824|ref|YP_001471591.1| RpoD family RNA polymerase sigma factor [Thermotoga lettingae TMO]
 gi|157315428|gb|ABV34527.1| RNA polymerase, sigma 70 subunit, RpoD family [Thermotoga lettingae
           TMO]
          Length = 400

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 81/276 (29%), Positives = 138/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI KIP+L   +E  LA+R  + G+  A  +L+ S+LRLVV IA  Y G GL
Sbjct: 123 DPIKMYLREIGKIPLLTPSQERELARR-AQIGNKRAKEKLIESNLRLVVSIAKRYIGRGL 181

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P  +++ EGNIGL++AV+KFD ++G++ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 182 PFLDLIQEGNIGLLKAVEKFDWKKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 240

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                + +L    +     + +   +  +AK ++    +V  +        SL A +   
Sbjct: 241 ----TINKLNRITREYYQKHGEQPSLEELAKLMDKPVDKVEEILQASKETVSLEAPV--G 294

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQEN 251
           +   S   D++    D       ++  R   R  L + +  LNPRE  + + R   L   
Sbjct: 295 EDEDSTVGDFVA---DENITSPKKEAMRMLMREELEKVLKTLNPREAMVLKMRYGLLDGK 351

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIE +A +K++   + +
Sbjct: 352 AKTLEEVGQYFNVTRERIRQIEVKALRKLRHPSRSK 387


>gi|317046493|ref|YP_004114141.1| RNA polymerase,sigma 32 subunit,RpoH [Pantoea sp. At-9b]
 gi|316948110|gb|ADU67585.1| RNA polymerase, sigma 32 subunit, RpoH [Pantoea sp. At-9b]
          Length = 285

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 108/290 (37%), Positives = 164/290 (56%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +     L  YI      PML  +EE  LA+R    GDL AA  L+ SHLR 
Sbjct: 1   MTKEMQTLAIAPLGNLESYIRAANVWPMLSAEEEKALAERLHYQGDLDAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHIARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVEMVARELGVSSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNP 237
           A  +    +    +   S+    ++Y  D        + E     +  + LT +M  L+ 
Sbjct: 176 AAQDMTFDMSADDENGESKTMAPVLYLQDKTSDFADGIEEDNWDAHAADKLTDAMQGLDE 235

Query: 238 RERRIFEARRLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L  EN  TL+ L+ ++ VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQHIIRARWLDEENKTTLQELADQYGVSAERVRQLEKNAMKKLRMAIEA 285


>gi|161869654|ref|YP_001598821.1| RNA polymerase factor sigma-32 [Neisseria meningitidis 053442]
 gi|161595207|gb|ABX72867.1| RNA polymerase sigma-32 factor [Neisseria meningitidis 053442]
 gi|316983693|gb|EFV62674.1| alternative sigma factor RpoH [Neisseria meningitidis H44/76]
 gi|325140133|gb|EGC62662.1| alternative sigma factor RpoH [Neisseria meningitidis CU385]
 gi|325200603|gb|ADY96058.1| alternative sigma factor RpoH [Neisseria meningitidis H44/76]
          Length = 287

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 118/289 (40%), Positives = 185/289 (64%), Gaps = 7/289 (2%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N   +  I +G   L +YIH + +IPML ++EE  LA+R +  GDL+AA +L+ SHLR+V
Sbjct: 3   NAFALPAIQSGNGSLEQYIHTVNRIPMLTQEEETRLAER-QHKGDLNAAKQLILSHLRVV 61

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+ILR+W
Sbjct: 62  VSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILRNW 121

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            LV++ TT  Q++LFFNLR ++ +L A++     P++   IA  L V  SEV+ M  R+ 
Sbjct: 122 RLVRVATTKPQRKLFFNLRSMRKNLNALS-----PKEAQDIADDLGVKLSEVLEMEQRMT 176

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           G +      NS D++S    DWL        + L ++     +   L  +++ L+ R RR
Sbjct: 177 GHDIAIMADNSDDEDSFAPIDWLADHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRR 236

Query: 242 IFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           I E+R LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 237 IVESRWLQDDGGLTLHQLAAEYGVSAERIRQIEAKAMQKLRGFLTEEAE 285


>gi|307325028|ref|ZP_07604232.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306889174|gb|EFN20156.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 502

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 75/304 (24%), Positives = 139/304 (45%), Gaps = 40/304 (13%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------------REHGD 46
             +  Y+ +I K+P+L  ++E  LAKR                             E G 
Sbjct: 204 DPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANSDKLAPKLKRELEIIAEDG- 262

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 263 RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 322

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L
Sbjct: 323 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKEL 377

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +VI +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 378 DMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 432

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 433 QLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 492

Query: 285 QKQV 288
           + QV
Sbjct: 493 RSQV 496


>gi|320096194|ref|ZP_08027783.1| DNA-directed RNA polymerase sigma subunit RpoD [Actinomyces sp.
           oral taxon 178 str. F0338]
 gi|319976875|gb|EFW08629.1| DNA-directed RNA polymerase sigma subunit RpoD [Actinomyces sp.
           oral taxon 178 str. F0338]
          Length = 543

 Score =  254 bits (650), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 71/304 (23%), Positives = 138/304 (45%), Gaps = 39/304 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY----------REHGDL---------------- 47
             +  Y+ +I K+ +L   +E  LA+R           +   D                 
Sbjct: 244 DPVKDYLKQIGKVSLLNAAQEVDLARRIEAGLYAEYKLKNRADEMTSKERRELHFLAQDG 303

Query: 48  -SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 304 QQAKNHLLEANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 363

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L
Sbjct: 364 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKEL 418

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +V+ +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 419 DMTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAIVPADAVSFTLLQE 473

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R    +  P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 474 QLHHVLDTLSEREAGVVSMRFGLGDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 533

Query: 285 QKQV 288
           + QV
Sbjct: 534 RSQV 537


>gi|257063660|ref|YP_003143332.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Slackia
           heliotrinireducens DSM 20476]
 gi|256791313|gb|ACV21983.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Slackia
           heliotrinireducens DSM 20476]
          Length = 394

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 85/314 (27%), Positives = 141/314 (44%), Gaps = 42/314 (13%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHG------ 45
           + S+ +     +  Y+ EI K+P+L   EE  LA +               E G      
Sbjct: 82  DTSVTMLTGDPVRMYLKEIGKVPLLTPSEEVDLAMKIEAGVAATAELEKAEEEGVELDRR 141

Query: 46  -----------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                       L A  +L+ ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD
Sbjct: 142 ERRRLTRVEQVGLDAKDQLIEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFD 201

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +GF+ +TY+ WWI+ A+   I      ++I     +      L R++  L      + 
Sbjct: 202 YTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE--TINKLVRIQRQLLQELGRDP 259

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            PE    I +K+ +S   V  +        SL   I   ++  SQ  D++  D      V
Sbjct: 260 SPE---EIGEKMGLSAERVREIQKLSQEPVSLETPI--GEEEDSQLGDFIEDDS---AIV 311

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
            ++       +  L++ +  L  RER +   R   E+  P TLE +  EF V+RER+RQI
Sbjct: 312 PVDAASFAMMQEQLSKVLDTLGERERNVVIKRFGLEDGQPHTLEEVGREFGVTRERIRQI 371

Query: 273 EARAFKKVQESIQK 286
           E++   K++   + 
Sbjct: 372 ESKTLAKLRHPSRS 385


>gi|326571483|gb|EGE21498.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis BC7]
          Length = 371

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 107/272 (39%), Positives = 158/272 (58%), Gaps = 7/272 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + L  YI+ + +IP+L  +EE  LA+RY   GD+ AA  LV SHLR V+ IA  Y GYGL
Sbjct: 97  VNLGAYINTVHQIPILTPEEERALAERYYHDGDVEAARLLVMSHLRFVIHIARSYSGYGL 156

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
             ++++ EGN+GLM+AVK+FDP +G RL ++++ WIKA + E+++++W +VK+ TT   +
Sbjct: 157 SQADLIQEGNLGLMKAVKRFDPNKGVRLVSFAVHWIKAEIHEFVIKNWRIVKVATTKAHR 216

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINS 192
           +LFFNLR LK      + N L  ++  AIA  LNV+  +V+ M  RL   D S  A   S
Sbjct: 217 KLFFNLRSLKK-----SSNQLTLDEATAIANDLNVTVKQVLEMESRLTSYDASFEAQD-S 270

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            D          + D      V+ E +  +N    L  +M  L+ R R I   R L +  
Sbjct: 271 DDDEGRYAPQLFLEDAVNPADVVEEADWEENTTTALKDAMETLDERSRDIITQRWLADQK 330

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL  L++ + +S ERVRQIE  A  K++E+I
Sbjct: 331 STLHELAATYNISAERVRQIEKNAMNKIKEAI 362


>gi|317056182|ref|YP_004104649.1| RpoD subfamily RNA polymerase sigma-70 subunit [Ruminococcus albus
           7]
 gi|315448451|gb|ADU22015.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ruminococcus
           albus 7]
          Length = 366

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 77/279 (27%), Positives = 135/279 (48%), Gaps = 15/279 (5%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSA---AHRLVTSHLRLVVKIAMGYR 69
           +  +  Y+ EI ++P+L  +EE  LA+      D  A     RL  ++LRLVV IA  Y 
Sbjct: 90  DDPVKIYLKEIGRVPLLTSEEEIQLAEMMSGDNDREAVKARKRLAEANLRLVVSIAKRYV 149

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ WWI+ A+   I      ++I   
Sbjct: 150 GRGMSFLDLIQEGNMGLIKAVEKFDYKKGFKFSTYATWWIRQAITRAIADQARTIRIPVH 209

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      + ++K     +   N        IA++L++S   V  +        SL   
Sbjct: 210 MVE-----TITKVKKVSSQLLHKNGHDPSPEEIAEELDMSVERVREIMRIAQDPVSLETP 264

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++            E       +  + + +S L  RE ++   R   
Sbjct: 265 I--GEEEDSHLGDFIPD---DDAPAPAEAASLVLLKEQIDQVLSTLTEREEKVLRLRFGL 319

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ++    TLE +  EF+V+RER+RQIEA+A +K++   + 
Sbjct: 320 QDGRSRTLEEVGQEFKVTRERIRQIEAKALRKLRHPNRS 358


>gi|239616750|ref|YP_002940072.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Kosmotoga olearia
           TBF 19.5.1]
 gi|239505581|gb|ACR79068.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Kosmotoga olearia
           TBF 19.5.1]
          Length = 405

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 78/280 (27%), Positives = 140/280 (50%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ +  +  Y+ EI KIP+L   +E  LA+R ++ GD  A   L+T++LRLVV IA  Y 
Sbjct: 122 ISLKDPIKMYLKEIGKIPLLTPSKERELARRAQK-GDKKAREELITANLRLVVSIAKRYI 180

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G GL   +++ EGNIGL++AV+KFD ++G++ +TY+ WWI+ A+   I      +++   
Sbjct: 181 GRGLSFLDLIQEGNIGLIKAVEKFDWKKGYKFSTYATWWIRQAITRAIADQARTIRVPVH 240

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      + ++   ++     + +   V  + K    +  ++  +        SL + 
Sbjct: 241 MVE-----TINKVNKVIREHLQEHGEYPTVEELGKLTGKTPEKIEEILAASKETVSLESP 295

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-- 247
           I S D+ S+         HD   +   E   +   R  +   +  L+PRE  + + R   
Sbjct: 296 I-SGDEESTMGDFV----HDESIEKPEEAAIKMLLREQIDEVLDTLSPREAMVLKMRYGL 350

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L     TLE +   F V+RER+RQIE +A +K++   + +
Sbjct: 351 LDGKTKTLEEVGQFFNVTRERIRQIEVKALRKLRHPSRSK 390


>gi|302554625|ref|ZP_07306967.1| RNA polymerase sigma factor RpoS [Streptomyces viridochromogenes
           DSM 40736]
 gi|302472243|gb|EFL35336.1| RNA polymerase sigma factor RpoS [Streptomyces viridochromogenes
           DSM 40736]
          Length = 513

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 75/304 (24%), Positives = 139/304 (45%), Gaps = 40/304 (13%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------------REHGD 46
             +  Y+ +I K+P+L  ++E  LAKR                             E G 
Sbjct: 215 DPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANSDKLAPKLKRELEIIAEDG- 273

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 274 RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 333

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L
Sbjct: 334 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKEL 388

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +VI +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 389 DMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 443

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 444 QLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 503

Query: 285 QKQV 288
           + QV
Sbjct: 504 RSQV 507


>gi|325677627|ref|ZP_08157279.1| RNA polymerase sigma factor RpoD [Ruminococcus albus 8]
 gi|324110595|gb|EGC04759.1| RNA polymerase sigma factor RpoD [Ruminococcus albus 8]
          Length = 366

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 80/290 (27%), Positives = 141/290 (48%), Gaps = 18/290 (6%)

Query: 5   NMSIIVNG---EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSA---AHRLVTSHL 58
           ++S+  +G   +  +  Y+ EI ++P+L  +EE  LA+      D  A     RL  ++L
Sbjct: 79  DISLSTDGIAIDDPVKIYLKEIGRVPLLTSEEEIQLAEMMSGDNDRDASKARKRLAEANL 138

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV IA  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ WWI+ A+   I 
Sbjct: 139 RLVVSIAKRYVGRGMSFLDLIQEGNMGLIKAVEKFDYKKGFKFSTYATWWIRQAITRAIA 198

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
                ++I     +      + ++K     +   N        IA+ L++S  +V  +  
Sbjct: 199 DQARTIRIPVHMVE-----TITKVKKASSQLLHKNGHDPSPEEIAEDLDMSVEKVREIMR 253

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
                 SL   I   ++  S   D++            E       +  + + +S L  R
Sbjct: 254 IAQDPVSLETPI--GEEEDSHLGDFIPD---DDAPAPAEAASLVLLKEQIDQVLSTLTER 308

Query: 239 ERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E ++   R   E+    TLE +  EF+V+RER+RQIEA+A +K++   + 
Sbjct: 309 EEKVLRLRFGLEDGRSRTLEEVGQEFKVTRERIRQIEAKALRKLRHPNRS 358


>gi|19704653|ref|NP_604215.1| RNA polymerase sigma factor rpoD [Fusobacterium nucleatum subsp.
           nucleatum ATCC 25586]
 gi|19714957|gb|AAL95514.1| RNA polymerase sigma factor rpoD [Fusobacterium nucleatum subsp.
           nucleatum ATCC 25586]
          Length = 331

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 80/285 (28%), Positives = 144/285 (50%), Gaps = 13/285 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           N+      +  +  Y+ EI ++P+L  +EE   AK+  E GD  A+ +L+ S+LRLVV I
Sbjct: 50  NLGNSAKVDEPIKMYLREIGQVPLLTHEEEIDYAKKAYE-GDEEASKKLIESNLRLVVSI 108

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  +   GL + +++ EGNIGLM+AV+KF+  +G++ +TY+ WWI+ A+   I      +
Sbjct: 109 AKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTI 168

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I        +   + ++K   +       K      +A++L +   ++ ++        
Sbjct: 169 RIPVH-----MIETINKIKKESRIYLQETGKDASPEILAERLGMEVDKIKAIQEMNQEPI 223

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   + S  +  S+  D++    D +     E   R   R  L   +  L+PRE ++  
Sbjct: 224 SLETPVGS--EEDSELGDFV---EDQKTTSPYEATNRAILREELDAVLKTLSPREEKVLR 278

Query: 245 ARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R   ++  P TLE +   F V+RER+RQIE +A +K++   +K+
Sbjct: 279 YRYGLDDSSPKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRKK 323


>gi|15676610|ref|NP_273754.1| RNA polymerase factor sigma-32 [Neisseria meningitidis MC58]
 gi|7225940|gb|AAF41127.1| RNA polymerase sigma-32 factor [Neisseria meningitidis MC58]
          Length = 290

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 118/289 (40%), Positives = 185/289 (64%), Gaps = 7/289 (2%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N   +  I +G   L +YIH + +IPML ++EE  LA+R +  GDL+AA +L+ SHLR+V
Sbjct: 6   NAFALPAIQSGNGSLEQYIHTVNRIPMLTQEEETRLAER-QHKGDLNAAKQLILSHLRVV 64

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+ILR+W
Sbjct: 65  VSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILRNW 124

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            LV++ TT  Q++LFFNLR ++ +L A++     P++   IA  L V  SEV+ M  R+ 
Sbjct: 125 RLVRVATTKPQRKLFFNLRSMRKNLNALS-----PKEAQDIADDLGVKLSEVLEMEQRMT 179

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           G +      NS D++S    DWL        + L ++     +   L  +++ L+ R RR
Sbjct: 180 GHDIAIMADNSDDEDSFAPIDWLADHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRR 239

Query: 242 IFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           I E+R LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 240 IVESRWLQDDGGLTLHQLAAEYGVSAERIRQIEAKAMQKLRGFLTEEAE 288


>gi|271968332|ref|YP_003342528.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)-like
           protein [Streptosporangium roseum DSM 43021]
 gi|270511507|gb|ACZ89785.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)-like
           protein [Streptosporangium roseum DSM 43021]
          Length = 561

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 73/304 (24%), Positives = 140/304 (46%), Gaps = 39/304 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------HGDL---------------- 47
             +  Y+ +I K+P+L  ++E  LAKR              GD                 
Sbjct: 262 DPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEEQLGTDGDKLPVDVRAELEWIAEDG 321

Query: 48  -SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 322 RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 381

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +A++L
Sbjct: 382 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAREL 436

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +V+ +        SL+  +   ++  S++ D +    D +  V  +       + 
Sbjct: 437 DMTPEKVVEVQKYGREPISLHTPL--GEEGDSEFGDLI---EDSEAIVPADAVSFTLLQE 491

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 492 QLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 551

Query: 285 QKQV 288
           + QV
Sbjct: 552 RSQV 555


>gi|86747323|ref|YP_483819.1| sigma 32 (RpoH) [Rhodopseudomonas palustris HaA2]
 gi|86570351|gb|ABD04908.1| sigma 32 (RpoH) [Rhodopseudomonas palustris HaA2]
          Length = 329

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 118/270 (43%), Positives = 166/270 (61%), Gaps = 1/270 (0%)

Query: 17  SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
             Y+  I + P+LE  EE  L +R+ +H D +AA  L+TSHLRL  K+A  +R YG P+ 
Sbjct: 23  KSYMRAIGRYPVLEPDEEARLWQRWLQHRDKAAADALITSHLRLAAKLARDFRRYGFPLG 82

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           ++++E N+GLM A+ +FDPERG R +T ++WWI++A+ ++I+RSWSLV+IG T  QK+LF
Sbjct: 83  DLIAEANLGLMMALDRFDPERGARFSTCAVWWIRSAIYDHIIRSWSLVRIGRTPAQKKLF 142

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
           F LR     LQ      L  E    I+  L+V   EVI M  RL+GD SLN  ++  D+ 
Sbjct: 143 FRLRGEIRRLQPDHHGTLTKELAEQISATLDVPLREVIEMEQRLSGDRSLNTPLSDLDE- 201

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           S +WQD +  D    E VL   +E  ++R  L  ++  L+ RER IF AR L E P + E
Sbjct: 202 SGEWQDLIADDAPNAEAVLAGHDELDHQRRALQDALVQLDARERYIFSARHLGERPASFE 261

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +     +S ERVRQIEARAF KV  S ++
Sbjct: 262 TIGQSLSISAERVRQIEARAFAKVANSARR 291


>gi|209696299|ref|YP_002264230.1| RNA polymerase factor sigma-32 [Aliivibrio salmonicida LFI1238]
 gi|208010253|emb|CAQ80584.1| RNA polymerase sigma-32 factor [Aliivibrio salmonicida LFI1238]
          Length = 286

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 106/287 (36%), Positives = 169/287 (58%), Gaps = 8/287 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+++  S+ V  +  +  Y+  + + PML  ++E  LA+R     ++ AA  L+ SHLR 
Sbjct: 1   MSKEMYSMAVVSQDSIDSYLRSVNRYPMLTVEKERDLAERLHYKEEIEAAKELILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A GY GYGLP+++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARGYSGYGLPLADLIQEGNVGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L    +      +V A+AK L VS SEV  M  RL
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKNKKRLGWFNNG-----EVEAVAKDLGVSPSEVREMESRL 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNP 237
           A  +S        D     +   + Y  D Q  +   L E        N L  +++ L+ 
Sbjct: 176 AAQDSTFEAPTEDDDRDMAFTAPVYYLEDKQSDIAHSLEEDNWEDYTNNRLANAIATLDD 235

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R + I ++R L +   TL+ L++ + VS ER+RQ+E  A KK+++++
Sbjct: 236 RSQHIVQSRWLTDEKTTLQELANTYSVSAERIRQLEKNAMKKLKDAV 282


>gi|291522892|emb|CBK81185.1| RNA polymerase, sigma 70 subunit, RpoD [Coprococcus catus GD/7]
          Length = 366

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 80/279 (28%), Positives = 141/279 (50%), Gaps = 13/279 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V+ E  +  Y+ EI  + +L  +EE  L+KR  E GD  A  R++ ++LRLVV IA  Y 
Sbjct: 90  VSLEDPVRMYLKEIGSVKLLSPEEEVELSKR-AEAGDQKAKDRIIEANLRLVVSIAKKYV 148

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+P  +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ ++   I      +++   
Sbjct: 149 GRGIPFLDLIQEGNMGLIKAVEKFDYAKGFKFSTYATWWIRQSITRGIADKGKTIRVPVH 208

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +        R+  +L          E    IA++L  ++ +V           S+++ 
Sbjct: 209 MVE--TINKTLRMSRNLLQELGREPTSE---EIAERLGTTKQKVEEALEISRDPVSMDSP 263

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL- 248
           I   ++  S   D++    D       +  + +  +  L  ++  L  RER++ E R   
Sbjct: 264 I--GEEEDSSLGDFI---EDENMLSPSDSADYQMLKKELVNALDTLTDRERKVIELRFGL 318

Query: 249 -QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                 TLE +  EF+V+RER+RQIEA+A +K++   + 
Sbjct: 319 IDGQARTLEEVGKEFKVTRERIRQIEAKALRKLRHPSRS 357


>gi|165977273|ref|YP_001652866.1| RNA polymerase factor sigma-32 [Actinobacillus pleuropneumoniae
           serovar 3 str. JL03]
 gi|190151190|ref|YP_001969715.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 7 str. AP76]
 gi|303252711|ref|ZP_07338873.1| RNA polymerase factor sigma-32 [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|307248906|ref|ZP_07530917.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 2 str. S1536]
 gi|307262328|ref|ZP_07543976.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 12 str. 1096]
 gi|307264539|ref|ZP_07546123.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 13 str. N273]
 gi|165877374|gb|ABY70422.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 3 str. JL03]
 gi|189916321|gb|ACE62573.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 7 str. AP76]
 gi|302648450|gb|EFL78644.1| RNA polymerase factor sigma-32 [Actinobacillus pleuropneumoniae
           serovar 2 str. 4226]
 gi|306854601|gb|EFM86793.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 2 str. S1536]
 gi|306867991|gb|EFM99819.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 12 str. 1096]
 gi|306870138|gb|EFN01898.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 13 str. N273]
          Length = 316

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 98/273 (35%), Positives = 160/273 (58%), Gaps = 6/273 (2%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  L  YI    + P+L  ++E  LA+RY    D+ AA +L+ SH+R V+ IA GY GYG
Sbjct: 46  QGNLDSYIRMANQYPILTAEQEKELAERYYYDEDVEAAKQLILSHMRFVIHIARGYLGYG 105

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP+++++ EGNIGLM+AVK+FDP  G RL ++++ W+KA + EY+L++W +VK+ TT  Q
Sbjct: 106 LPLADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWVKAEIHEYVLKNWRIVKVATTKAQ 165

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALIN 191
           ++LFFNLR+ K  L    +     E++  +A+ L VS  EV  M  R+ G D   +  + 
Sbjct: 166 RKLFFNLRKNKNRLAWFNE-----EEIQKVAEDLGVSPEEVREMESRMTGQDLGFDLPVG 220

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             D        +L  +       L +++        L  +++ L+ R + I + R L E 
Sbjct: 221 EDDDEVYTPSMYLEDNSSNFADDLEDEQYNGQATAQLAYALATLDERSQDIIKTRWLDEE 280

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL++L+ ++ +S ERVRQ+E  A KK++++I
Sbjct: 281 KATLQDLAEKYGISAERVRQLENAALKKIKDAI 313


>gi|154509177|ref|ZP_02044819.1| hypothetical protein ACTODO_01698 [Actinomyces odontolyticus ATCC
           17982]
 gi|153798811|gb|EDN81231.1| hypothetical protein ACTODO_01698 [Actinomyces odontolyticus ATCC
           17982]
          Length = 561

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 71/304 (23%), Positives = 139/304 (45%), Gaps = 39/304 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY----------REHGDL---------------- 47
             +  Y+ +I K+ +L  ++E  LA+R           +   D                 
Sbjct: 262 DPVKDYLKQIGKVSLLNAEQEVDLARRIEAGLYAEYKLKNQADEMTSRERRELHFLAQDG 321

Query: 48  -SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 322 QQAKNHLLEANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 381

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L
Sbjct: 382 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKEL 436

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +V+ +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 437 DMTAEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAIVPADAVSFTLLQE 491

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R    +  P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 492 QLHHVLDTLSEREAGVVSMRFGLGDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 551

Query: 285 QKQV 288
           + QV
Sbjct: 552 RSQV 555


>gi|323492929|ref|ZP_08098069.1| RNA polymerase factor sigma-32 [Vibrio brasiliensis LMG 20546]
 gi|323312822|gb|EGA65946.1| RNA polymerase factor sigma-32 [Vibrio brasiliensis LMG 20546]
          Length = 285

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 109/287 (37%), Positives = 167/287 (58%), Gaps = 8/287 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  +   + V  +  L  YI  +   PML   EE  LA+R    G++ AA  L+ SHLR 
Sbjct: 1   MTNQAYPMAVVTQDSLDSYIRSVNSYPMLTADEERELAERLHYDGEIEAAKGLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A GY GYGLP++++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VKI TT  Q++LFFNLR+ K  L    +      +V  +A++L V  +EV  M  RL
Sbjct: 121 WRIVKIATTKAQRKLFFNLRKSKKRLGWFNNG-----EVETVARELGVEPAEVREMESRL 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE---ERKNRRNMLTRSMSVLNP 237
           A  ++   + +  D ++S +   +VY  D    V    E      +  N L+ ++  L+ 
Sbjct: 176 AAQDATFEMPSDDDDSASSYTAPMVYLEDKASDVADNVEAANWEAHTNNRLSLALKTLDD 235

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R + I  +R L +N  TL+ L+  + VS ER+RQ+E  A KK++ ++
Sbjct: 236 RSQHIVRSRWLDDNKSTLQELAETYSVSAERIRQLEKNAMKKLKAAV 282


>gi|332295554|ref|YP_004437477.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermodesulfobium
           narugense DSM 14796]
 gi|332178657|gb|AEE14346.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermodesulfobium
           narugense DSM 14796]
          Length = 356

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 80/276 (28%), Positives = 138/276 (50%), Gaps = 13/276 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E  + +Y+ EI KIP+L+  EE  LA+R   HGD +A  +L  ++LRLVV IA  Y   G
Sbjct: 84  EDPVRQYLKEIGKIPLLKHSEEKYLAERAF-HGDEAAKKKLAEANLRLVVSIAKKYTKRG 142

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I     +
Sbjct: 143 LLFLDLIQEGNMGLLRAVEKFDYRKGYKFSTYATWWIRQAVTRAIADQARTIRIPVHMVE 202

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 + + K  ++ ++    +      IA+K+ V+  ++  +        S+   I  
Sbjct: 203 -----TINKYKKTVRNLSQQLSRKPTDEEIAEKMEVNVEKIHEIKRISQEPISIETPI-- 255

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QE 250
                S   D++  +        +E    +  +  L   +  L PRER +   R      
Sbjct: 256 GKDEDSHLGDFIADESISS---PMEAVTYRLLKEDLEEVIKDLQPRERDVVRLRFGLVDG 312

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +  TLE +  EF V+RER+RQIEA+A +K++   + 
Sbjct: 313 HARTLEEVGKEFGVTRERIRQIEAKALRKLRHPSRS 348


>gi|145224520|ref|YP_001135198.1| RNA polymerase sigma factor [Mycobacterium gilvum PYR-GCK]
 gi|315444851|ref|YP_004077730.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Mycobacterium sp. Spyr1]
 gi|145217006|gb|ABP46410.1| RNA polymerase, sigma 70 subunit, RpoD family [Mycobacterium gilvum
           PYR-GCK]
 gi|315263154|gb|ADT99895.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Mycobacterium sp. Spyr1]
          Length = 488

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 79/319 (24%), Positives = 148/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------REHGDL- 47
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+  
Sbjct: 175 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYCTQLMAEFAEKGEKL 233

Query: 48  ----------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 234 TTAQRRDYMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 293

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 294 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 351

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 352 REPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 403

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 404 AVVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 463

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 464 RQIESKTMSKLRHPSRSQV 482


>gi|269125851|ref|YP_003299221.1| RpoD subfamily RNA polymerase sigma-70 subunit [Thermomonospora
           curvata DSM 43183]
 gi|268310809|gb|ACY97183.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermomonospora
           curvata DSM 43183]
          Length = 559

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 76/304 (25%), Positives = 138/304 (45%), Gaps = 39/304 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREH----------GD----------------- 46
             +  Y+ +I K+P+L  ++E  LAKR              GD                 
Sbjct: 260 DPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEERLATMGDQLSEEDKADLEWIAEDG 319

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ 
Sbjct: 320 RRAKAHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYAT 379

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L
Sbjct: 380 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKEL 434

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +VI +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 435 DMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAIVPADAVSFTLLQE 489

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 490 QLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 549

Query: 285 QKQV 288
           + QV
Sbjct: 550 RSQV 553


>gi|88705470|ref|ZP_01103181.1| RNA polymerase sigma-32 factor [Congregibacter litoralis KT71]
 gi|88700560|gb|EAQ97668.1| RNA polymerase sigma-32 factor [Congregibacter litoralis KT71]
          Length = 338

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 103/272 (37%), Positives = 162/272 (59%), Gaps = 7/272 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L+ Y+  + K+P+L    E+ LA++    GD+ AA  LV SHLR V  IA  YRGYGL 
Sbjct: 70  NLAAYVQAVAKVPVLSADREHELAEKLFYDGDVQAARELVMSHLRFVAHIARSYRGYGLA 129

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGN+GLM+AVK+FDP +G RL ++++ WIKA + EYILR+W +VKI TT  Q++
Sbjct: 130 EADLIQEGNVGLMKAVKRFDPTKGVRLVSFAVHWIKAEIHEYILRNWRIVKIATTKAQRK 189

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSS 193
           LFFNLR  K  L  ++      ++  A+A  L V   EV  M  RL+  D + +A + + 
Sbjct: 190 LFFNLRSAKKSLAWLS-----ADEAKAVADDLGVDVQEVHRMEGRLSSHDVAFDAPVGAD 244

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIE-KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
           D+   Q   + + D        +E  E + + +  L  +++ L+ R R I   R L ++ 
Sbjct: 245 DEEGWQAPQYYLEDQSVDPATNVENSEWQADSQAQLHAAIAELDERSRNILAQRWLTDDK 304

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL  L++E++VS ER+RQ+E  A KK+++ +
Sbjct: 305 ATLHELAAEYDVSAERIRQLEQAAMKKIRKVL 336


>gi|444799|prf||1908232B RNA polymerase:SUBUNIT=sigma factor
          Length = 340

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 81/279 (29%), Positives = 137/279 (49%), Gaps = 14/279 (5%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD--LSAAHRLVTSHLRLVVKIAMGYRG 70
           +  +  Y+ EI + P++   EE  LA+     G+    A   L  ++LRLVV IA  Y G
Sbjct: 66  DDPVRMYLKEIGRYPLISLDEETKLAEAIIAGGEGAEFAKQMLAEANLRLVVSIAKRYSG 125

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            G    +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    
Sbjct: 126 RGNQFLDLIQEGNMGLMKAVDKFDHTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 185

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
            +      L R++ +L      +  PE    I K+L+++  +V  +        SL   I
Sbjct: 186 VE--TINKLIRVQRNLLQELGRDPSPE---EIGKELHMAPDKVREVLKIAQEPVSLETPI 240

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
              +++ S   D++  D     +  ++   R   R  L   M  L  RE  +   R   +
Sbjct: 241 --GEEDDSHLGDFIEDD---VIESPVDYTNRILLREQLDEVMDTLTDREENVLRMRFGLD 295

Query: 251 NP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +    TLE++  +F+V+RER+RQIEA+A KK++   + +
Sbjct: 296 DGRMHTLEDVGKQFKVTRERIRQIEAKAIKKLRHPRRSK 334


>gi|25028360|ref|NP_738414.1| RNA polymerase sigma factor [Corynebacterium efficiens YS-314]
 gi|23493645|dbj|BAC18614.1| sigma factor SigA [Corynebacterium efficiens YS-314]
          Length = 506

 Score =  254 bits (649), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 78/325 (24%), Positives = 149/325 (45%), Gaps = 49/325 (15%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY----------------REHG 45
            RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR                    G
Sbjct: 187 ARKDAELTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYATHKMEEMEAAYAAG 245

Query: 46  DLSAA--------------------HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           D  A                     + L+ ++LRLVV +A  Y G G+   +++ EGN+G
Sbjct: 246 DKDAKLTPAVKRDLRAIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLG 305

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  
Sbjct: 306 LIRAVEKFDYSKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRE 363

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           L         P     ++K++++SE +V+ +        SL+  I   D+  SQ  D++ 
Sbjct: 364 LLQELGREPTP---QELSKEMDISEEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI- 417

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFE 263
              D +  V ++       ++ L   +  L+ RE  + + R    +  P TL+ +   + 
Sbjct: 418 --EDSEAVVAVDAVSFTLLQDQLQDVLETLSEREAGVVKLRFGLTDGMPRTLDEIGQVYG 475

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           V+RER+RQIE++   K++   + QV
Sbjct: 476 VTRERIRQIESKTMSKLRHPSRSQV 500


>gi|294788977|ref|ZP_06754217.1| alternative sigma factor RpoH [Simonsiella muelleri ATCC 29453]
 gi|294483079|gb|EFG30766.1| alternative sigma factor RpoH [Simonsiella muelleri ATCC 29453]
          Length = 289

 Score =  253 bits (648), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 116/291 (39%), Positives = 179/291 (61%), Gaps = 8/291 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M       I +G   L +YIH +  IPML  +EE  LA+R +  GD+ AA +L+ SHLR+
Sbjct: 1   MTNAFALPIPSGHGSLEQYIHTVNAIPMLSLEEETKLAER-QLRGDIEAAKQLILSHLRV 59

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA GY GYGL  ++++ EGNIGLM+AVK+F+P  G RL ++++ WIKA + E+ILR+
Sbjct: 60  VVSIARGYDGYGLNQADLIQEGNIGLMKAVKRFEPVHGARLFSFAVHWIKAEIHEFILRN 119

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W LV+I TT  Q++LFFNLR ++  L A++     P++   IA  L V  +EV+ M  R+
Sbjct: 120 WRLVRIATTKPQRKLFFNLRSMRKSLNALS-----PKEAQEIADDLGVKLTEVMEMEQRM 174

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            G D +L A  +  +++S    DWL  +     Q + ++     +   L  +++ L+ R 
Sbjct: 175 TGNDVALLAESDDDNEDSFAPIDWLADNDSEPSQQIAKQAHYALQTEGLQNALAQLDERS 234

Query: 240 RRIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           RRI E R L  +  +TL +L++E+ VS ER+RQIEA+A +K++  +  + E
Sbjct: 235 RRIVETRWLADDGGLTLHDLAAEYGVSAERIRQIEAKAMQKLRGFLASEAE 285


>gi|17545093|ref|NP_518495.1| RNA polymerase factor sigma-32 [Ralstonia solanacearum GMI1000]
 gi|17427383|emb|CAD13902.1| probable rna polymerase sigma h (sigma-32) factor transcription
           regulator protein [Ralstonia solanacearum GMI1000]
          Length = 306

 Score =  253 bits (648), Expect = 1e-65,   Method: Composition-based stats.
 Identities = 119/287 (41%), Positives = 174/287 (60%), Gaps = 12/287 (4%)

Query: 7   SIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           ++   G +G L  YI  + ++PML  +EE  LA+ Y   G+L AA RLV SHLRLVV IA
Sbjct: 23  ALAFPGSLGNLDAYIQSVNRVPMLTAEEEQQLARDYHATGNLDAARRLVLSHLRLVVSIA 82

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGLP ++++ EGN+GLM+AVK+FDP++G RL +Y++ WIKA M EYIL++W +VK
Sbjct: 83  RQYLGYGLPHADLIQEGNVGLMKAVKRFDPDQGVRLVSYAIHWIKAEMHEYILKNWRMVK 142

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDE 184
           + TT  Q++LFFNLR  K             ++V A+A++LNV  +EV  M  RL  GD 
Sbjct: 143 VATTKAQRKLFFNLRSHK----QDAHATFTSDEVDAVAQELNVKGAEVREMETRLSGGDI 198

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           +L   I+  ++ S     +L   H+   +VL  +   + +   +  +++ L+ R RRI E
Sbjct: 199 ALEGQIDDGEE-SFAPIAYLADTHNEPTRVLEGRGRDRLQSEGIETALAKLDDRSRRIIE 257

Query: 245 ARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           AR L          TL  L+ EF VS ER+RQIE+ A KK++ ++Q 
Sbjct: 258 ARWLHVNDDGSGGATLHELADEFGVSAERIRQIESAAMKKMKGALQS 304


>gi|300692652|ref|YP_003753647.1| RNA polymerase sigma H (sigma 32) factor; transcription of heat
           shock and stress proteins [Ralstonia solanacearum PSI07]
 gi|299079712|emb|CBJ52389.1| RNA polymerase sigma H (sigma 32) factor; transcription of heat
           shock and stress proteins [Ralstonia solanacearum PSI07]
          Length = 306

 Score =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 119/287 (41%), Positives = 174/287 (60%), Gaps = 12/287 (4%)

Query: 7   SIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           ++   G +G L  YI  + ++PML  +EE  LA+ Y   G+L AA RLV SHLRLVV IA
Sbjct: 23  ALAFPGSLGNLDAYIQSVNRVPMLTAEEEQQLARDYHATGNLDAARRLVLSHLRLVVSIA 82

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGLP ++++ EGNIGLM+AVK+FDP++G RL +Y++ WIKA M EYIL++W +VK
Sbjct: 83  RQYLGYGLPHADLIQEGNIGLMKAVKRFDPDQGVRLVSYAIHWIKAEMHEYILKNWRMVK 142

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDE 184
           + TT  Q++LFFNLR  K             +++ A+A++LNV  +EV  M  RL  GD 
Sbjct: 143 VATTKAQRKLFFNLRSHK----QDAHATFTSDEIDAVAQELNVKGTEVREMETRLSGGDI 198

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           +L   I+  ++ S     +L   H+   +VL  +   + +   +  +++ L+ R RRI E
Sbjct: 199 ALEGQIDDGEE-SFAPIAYLADAHNEPTRVLEARGHDRLQSEGIETALAKLDDRSRRIIE 257

Query: 245 ARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           AR L          TL  L+ EF VS ER+RQIE+ A KK++ ++Q 
Sbjct: 258 ARWLNVNDDGSGGATLHELADEFGVSAERIRQIESAAMKKMKGALQA 304


>gi|326332703|ref|ZP_08198965.1| RNA polymerase sigma (70) factor RpoD [Nocardioidaceae bacterium
           Broad-1]
 gi|325949484|gb|EGD41562.1| RNA polymerase sigma (70) factor RpoD [Nocardioidaceae bacterium
           Broad-1]
          Length = 530

 Score =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 75/317 (23%), Positives = 143/317 (45%), Gaps = 40/317 (12%)

Query: 2   NRKNMSIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKR------------------- 40
           +    +++V G     +  Y+ +I K+P+L  + E  LAKR                   
Sbjct: 218 DEPEQTVMVAGATADPVKDYLKQIGKVPLLNAEMEVELAKRIEAGLFAEEKLGKGGKITP 277

Query: 41  -------YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
                  +       A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KF
Sbjct: 278 KMLDELEWIAEDGKRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKF 337

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  +       
Sbjct: 338 DYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGRE 395

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
             PE    +AK+L+++  +VI +        SL+  +   +   S++ D +    D +  
Sbjct: 396 PTPE---ELAKELDMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAI 447

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQ 271
           V  +       +  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQ
Sbjct: 448 VPADAVSFTLLQEQLHAVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQ 507

Query: 272 IEARAFKKVQESIQKQV 288
           IE++   K++   + QV
Sbjct: 508 IESKTMSKLRHPSRSQV 524


>gi|309812669|ref|ZP_07706413.1| RNA polymerase sigma factor RpoD [Dermacoccus sp. Ellin185]
 gi|308433364|gb|EFP57252.1| RNA polymerase sigma factor RpoD [Dermacoccus sp. Ellin185]
          Length = 550

 Score =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 72/303 (23%), Positives = 138/303 (45%), Gaps = 38/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR--------------------------YREHGDL 47
             +  Y+ +I K+ +L  ++E  LAKR                          +      
Sbjct: 252 DPVKDYLKQIGKVALLNAEQEVELAKRIEAGLFAEQKLESGVKMDMKLKRELWWIASDGK 311

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ W
Sbjct: 312 NAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATW 371

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L+
Sbjct: 372 WIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKELD 426

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++  +VI +        SL+  +   +   S++ D +    D +  V  +       +  
Sbjct: 427 MTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQEQ 481

Query: 228 LTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   +
Sbjct: 482 LHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSR 541

Query: 286 KQV 288
            QV
Sbjct: 542 SQV 544


>gi|326569916|gb|EGE19966.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis BC8]
          Length = 371

 Score =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 106/272 (38%), Positives = 157/272 (57%), Gaps = 7/272 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + L  YI+ + +IP+L  +EE  LA+RY   GD+ A   LV SHLR V+ IA  Y GYGL
Sbjct: 97  VNLGAYINTVHQIPILTPEEERALAERYYHDGDVEATRLLVMSHLRFVIHIARSYSGYGL 156

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
             ++++ EGN+GLM+AVK+FDP +G RL ++++ WIKA + E+++++W +VK+ TT   +
Sbjct: 157 SQADLIQEGNLGLMKAVKRFDPNKGVRLVSFAVHWIKAEIHEFVIKNWRIVKVATTKAHR 216

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINS 192
           +LFFNLR LK      + N L  ++  AIA  LNV+  +V+ M  RL   D S  A   S
Sbjct: 217 KLFFNLRSLKK-----SSNQLTLDEATAIANDLNVTVKQVLEMESRLTSYDASFEAQD-S 270

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            D          + D      V+ E +  +N    L  +M  L+ R R I   R L +  
Sbjct: 271 DDDEGRYAPQLFLEDAVNPADVVEEADWEENTTTALKDAMETLDERSRDIITQRWLADQK 330

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL  L++ + +S ERVRQIE  A  K++E+I
Sbjct: 331 STLHELAATYNISAERVRQIEKNAMNKIKEAI 362


>gi|216733|dbj|BAA01038.1| RNA polymerase sigma factor [Lactococcus lactis]
          Length = 340

 Score =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 81/279 (29%), Positives = 138/279 (49%), Gaps = 14/279 (5%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD--LSAAHRLVTSHLRLVVKIAMGYRG 70
           +  +  Y+ EI + P++   EE  LA+     G+    A   L  ++LRLVV IA  Y G
Sbjct: 66  DDPVRMYLKEIGRYPLISLDEETKLAEAIIAGGEGAEFAKQMLAEANLRLVVSIAKRYSG 125

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            G+   +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    
Sbjct: 126 RGMQFLDLIQEGNMGLMKAVDKFDHTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 185

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
            +      L R++ +L      +  PE    I K+L+++  +V  +        SL   I
Sbjct: 186 VE--TINKLIRVQRNLLQELGRDPSPE---EIGKELHMAPDKVREVLKIAQEPVSLETPI 240

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
              +++ S   D++  D     +  ++   R   R  L   M  L  RE  +   R   +
Sbjct: 241 --GEEDDSHLGDFIEDD---VIESPVDYTNRILLREQLDEVMDTLTDREENVLRMRFGLD 295

Query: 251 NP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +    TLE++  +F+V+RER+RQIEA+A KK++   + +
Sbjct: 296 DGRMHTLEDVGKQFKVTRERIRQIEAKAIKKLRHPRRSK 334


>gi|313113550|ref|ZP_07799138.1| RNA polymerase sigma factor RpoD [Faecalibacterium cf. prausnitzii
           KLE1255]
 gi|310624065|gb|EFQ07432.1| RNA polymerase sigma factor RpoD [Faecalibacterium cf. prausnitzii
           KLE1255]
          Length = 377

 Score =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 86/277 (31%), Positives = 145/277 (52%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI ++P+L  ++E  LA R  + GD  A  +L  ++LRLVV +A  Y G G
Sbjct: 104 DDPVKAYLKEIGRVPLLTAEQETELA-RAAQAGDEDARRKLSEANLRLVVSVAKRYAGRG 162

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP  +++ EGN+GLM+A +KF+PERGF+ +TY+ WWI+ ++   I      ++I      
Sbjct: 163 LPFLDLIQEGNLGLMKAAEKFEPERGFKFSTYATWWIRQSITRAIADQGRTIRIPVH--- 219

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
             L  ++ R+K     +   N +      IA +L++    V  +        SL   +  
Sbjct: 220 --LVESINRVKKMTGDLLRKNGREPTAEEIAVQLDMEPDRVRELLQLAQDPISLETPV-- 275

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            ++  +  +D++  +  G   V +++  R+  R  L   +  L PRE R+   R   E+ 
Sbjct: 276 GEEEDAHLEDFIQDEDAG---VPVDEAGRQLLRRELFSVLKSLTPREERVIALRFGLEDG 332

Query: 253 --VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE L  EF V+RERVRQIEA+A +K++   + +
Sbjct: 333 RAHTLEELGKEFNVTRERVRQIEAKALRKLRHPSRAK 369


>gi|62258694|gb|AAX77814.1| unknown protein [synthetic construct]
          Length = 327

 Score =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 106/286 (37%), Positives = 175/286 (61%), Gaps = 7/286 (2%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
             K  ++ V  +  LS Y++ +  +P+L  ++E  LA+RY+   DL AA +LV SHLR V
Sbjct: 35  ATKTKTLPVVSDNNLSAYLNFVNTLPVLSLEQEQELARRYKYKKDLDAAQQLVLSHLRFV 94

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            KIA  + GYGL I++++ EGNIGLM+AV KFDP++G RL ++++ WIKA M +Y+L++W
Sbjct: 95  TKIARNFSGYGLSIADLIQEGNIGLMKAVSKFDPDQGVRLLSFAVHWIKAEMHDYVLKNW 154

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL- 180
            +VK+ TT  Q++LFFNLR  K  +  ++  N+K      +A++L V E  VI M  R+ 
Sbjct: 155 KIVKVATTKAQRKLFFNLRSSKDKIGWLSSENIK-----ELAEELGVKEETVIEMEKRMC 209

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            GD SL+      D   +  Q   + D     E  +++++   N + ++   +S  + R 
Sbjct: 210 QGDASLDLPYTDDDGEQTSQQSLYLEDKSSNIEHQVVQQDYYDNFKAIVKDVLSGFDTRT 269

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + I  +R L +N  TL++L++++ +S ERVRQIE  A  K++++I+
Sbjct: 270 KDIIMSRYLLDNKATLQDLAAKYNISAERVRQIEEDALAKLKKAIK 315


>gi|294138987|ref|YP_003554965.1| RNA polymerase sigma-32 factor [Shewanella violacea DSS12]
 gi|293325456|dbj|BAJ00187.1| RNA polymerase sigma-32 factor [Shewanella violacea DSS12]
          Length = 286

 Score =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 107/286 (37%), Positives = 175/286 (61%), Gaps = 8/286 (2%)

Query: 4   KNMSIIVN-GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           ++M+++V  G   L  Y+H    I MLE ++E+ LAKR +E GD+ AA +L+ SHLR VV
Sbjct: 6   QSMALVVPHGSGSLEAYVHSAHNISMLEAKQEHELAKRLQETGDIQAAKQLIMSHLRFVV 65

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A GY GYGLP ++++ EGNIGLM+AVK+FDP  G RL ++++ WIKA + EY+L++W 
Sbjct: 66  HVAKGYSGYGLPQADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWIKAEIHEYVLKNWR 125

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L   +D      +V  +A+ L VS+++V  M  R+A 
Sbjct: 126 IVKVATTKAQRKLFFNLRKSKKRLGWFSD-----AEVGMVAENLGVSKADVTEMESRMAA 180

Query: 183 DESLNALINSSDKN-SSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLNPRER 240
            +    L + +D +         + DH       +E +  + + +  L  ++  L+ R +
Sbjct: 181 QDPAFDLASDNDDDIQDYAPALYLEDHSSDLANQVETDNFEADNQTRLLAAIKTLDERSQ 240

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            I +AR L E+  TL+ L++ ++VS ER+RQ+E  A  K++  ++ 
Sbjct: 241 HILQARWLNEDKTTLQELAATYQVSAERIRQLEKNAMNKLKGRMEA 286


>gi|256832655|ref|YP_003161382.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Jonesia
           denitrificans DSM 20603]
 gi|256686186|gb|ACV09079.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Jonesia
           denitrificans DSM 20603]
          Length = 504

 Score =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 73/304 (24%), Positives = 139/304 (45%), Gaps = 39/304 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------HGDLS------------ 48
             +  Y+ +I K+ +L  ++E  LAKR                 GD              
Sbjct: 205 DPVKDYLKQIGKVALLNAEQEVELAKRIEAGLYAEERLAAGVAEGDRKLEREYRWIIQDG 264

Query: 49  --AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 265 KRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 324

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L
Sbjct: 325 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKEL 379

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +V+ +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 380 DMTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 434

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L + +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 435 QLHQVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 494

Query: 285 QKQV 288
           + QV
Sbjct: 495 RSQV 498


>gi|238921550|ref|YP_002935065.1| RNA polymerase factor sigma-32 [Edwardsiella ictaluri 93-146]
 gi|238871119|gb|ACR70830.1| alternative sigma factor RpoH, putative [Edwardsiella ictaluri
           93-146]
          Length = 284

 Score =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 103/289 (35%), Positives = 167/289 (57%), Gaps = 8/289 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  Y+      PML  +EE  L +R    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLTLVPQGSLEAYVRAANAYPMLTAEEERALGERLHYKGDLDAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEMGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VSE +V+ M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVELVARELGVSEKDVLEMESRM 175

Query: 181 -AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPR 238
            A D + +   +   + +       + D        IE +  ++   + L+ ++  L+ R
Sbjct: 176 AAQDMAFDLPGDDEQEGAPAAPVLFLQDKSSDFANEIEDDNWESHAADKLSVALEGLDER 235

Query: 239 ERRIFEARRLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + I  AR L  +N  TL+ L+  + VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 SQHIIRARWLDSDNKATLQELADRYGVSAERVRQLEKNAMKKLRMAIEA 284


>gi|293189827|ref|ZP_06608541.1| carbamoyl-phosphate synthase L chain, ATP-binding [Actinomyces
           odontolyticus F0309]
 gi|292821242|gb|EFF80187.1| carbamoyl-phosphate synthase L chain, ATP-binding [Actinomyces
           odontolyticus F0309]
          Length = 561

 Score =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 71/304 (23%), Positives = 139/304 (45%), Gaps = 39/304 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY----------REHGDL---------------- 47
             +  Y+ +I K+ +L  ++E  LA+R           +   D                 
Sbjct: 262 DPVKDYLKQIGKVSLLNAEQEVDLARRIEAGLYAEYKLKNQADEMTSRERRELHFLAQDG 321

Query: 48  -SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 322 QQAKNHLLEANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 381

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L
Sbjct: 382 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKEL 436

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +V+ +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 437 DMTAEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAIVPADAVSFTLLQE 491

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R    +  P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 492 QLHHVLDTLSEREAGVVSMRFGLGDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 551

Query: 285 QKQV 288
           + QV
Sbjct: 552 RSQV 555


>gi|290956933|ref|YP_003488115.1| major vegetative sigma factor HrdB [Streptomyces scabiei 87.22]
 gi|260646459|emb|CBG69556.1| major vegetative sigma factor HrdB [Streptomyces scabiei 87.22]
          Length = 516

 Score =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 75/304 (24%), Positives = 139/304 (45%), Gaps = 40/304 (13%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------------REHGD 46
             +  Y+ +I K+P+L  ++E  LAKR                             E G 
Sbjct: 218 DPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANADKLAPKLKRELEIIAEDG- 276

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 277 RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 336

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L
Sbjct: 337 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKEL 391

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +VI +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 392 DMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 446

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 447 QLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 506

Query: 285 QKQV 288
           + QV
Sbjct: 507 RSQV 510


>gi|18310989|ref|NP_562923.1| RNA polymerase sigma factor RpoD [Clostridium perfringens str. 13]
 gi|18145671|dbj|BAB81713.1| transcription initiation factor sigma A [Clostridium perfringens
           str. 13]
          Length = 373

 Score =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 78/277 (28%), Positives = 137/277 (49%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI K+P+L  ++E  LAK+  E G   A  +L  ++LRLVV IA  Y G G
Sbjct: 101 DDPVRMYLKEIGKVPLLSSEDEIELAKKI-EEGSNYAKKKLAEANLRLVVSIAKRYVGRG 159

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I     +
Sbjct: 160 MLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 219

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 L R++  L      +  PE    ++K++++   +V  +        SL   I  
Sbjct: 220 --TINKLIRIQRQLVQELGRDPLPE---ELSKQMDMPVDKVREILKIAQEPVSLETPI-- 272

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            ++  S   D++            E       +  L   +  L PRE ++   R   ++ 
Sbjct: 273 GEEEDSHLGDFIPD---DDAPAPAEAAAFTMLKEQLINVLDTLTPREEKVLRLRFGLDDG 329

Query: 253 --VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 330 RARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 366


>gi|254369205|ref|ZP_04985217.1| DNA-directed RNA polymerase [Francisella tularensis subsp.
           holarctica FSC022]
 gi|157122155|gb|EDO66295.1| DNA-directed RNA polymerase [Francisella tularensis subsp.
           holarctica FSC022]
          Length = 292

 Score =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 106/286 (37%), Positives = 176/286 (61%), Gaps = 7/286 (2%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           + K  ++ V  +  LS Y++ +  +P+L  ++E  LA+RY+   DL AA +LV SHLR V
Sbjct: 9   STKTKTLPVVSDNNLSAYLNFVNTLPVLSLEQEQELARRYKYKKDLDAAQQLVLSHLRFV 68

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            KIA  + GYGL I++++ EGNIGLM+AV KFDP++G RL ++++ WIKA M +Y+L++W
Sbjct: 69  TKIARNFSGYGLSIADLIQEGNIGLMKAVSKFDPDQGVRLLSFAVHWIKAEMHDYVLKNW 128

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL- 180
            +VK+ TT  Q++LFFNLR  K  +  ++  N+K      +A++L V E  VI M  R+ 
Sbjct: 129 KIVKVATTKAQRKLFFNLRSSKDKIGWLSSENIK-----ELAEELGVKEETVIEMEKRMC 183

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            GD SL+      D   +  Q   + D     E  +++++   N + ++   +S  + R 
Sbjct: 184 QGDASLDLPYTDDDGEQTSQQSLYLEDKSSNIEHQVVQQDYYDNFKAIVKDVLSGFDTRT 243

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + I  +R L +N  TL++L++++ +S ERVRQIE  A  K++++I+
Sbjct: 244 KDIIMSRYLLDNKATLQDLAAKYNISAERVRQIEEDALAKLKKAIK 289


>gi|328675965|gb|AEB28640.1| RNA polymerase sigma factor RpoH [Francisella cf. novicida 3523]
          Length = 292

 Score =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 106/286 (37%), Positives = 174/286 (60%), Gaps = 7/286 (2%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
             K  ++ V  +  LS Y++ +  +P+L  ++E  LA+RY+   DL AA +LV SHLR V
Sbjct: 9   ATKTKTLPVVSDNNLSAYLNFVNTLPVLSLEQEQELARRYKYKKDLDAAQQLVLSHLRFV 68

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            KIA  + GYGL I++++ EGNIGLM+AV KFDPE+G RL ++++ WIKA M +Y+L++W
Sbjct: 69  TKIARNFSGYGLSIADLIQEGNIGLMKAVSKFDPEQGVRLVSFAVHWIKAEMHDYVLKNW 128

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL- 180
            +VK+ TT  Q++LFFNLR  K  +  ++      E +  +A++L V E  VI M  R+ 
Sbjct: 129 KIVKVATTKAQRKLFFNLRSSKDKIGWLS-----SEDIKELAEELGVKEETVIEMEKRMC 183

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            GD SL+      D   +  Q   + D     E  +++++   N + ++   +S  + R 
Sbjct: 184 QGDASLDLPYTDDDGEQTSQQSLYLEDKSSNIEHQVVQQDYYDNFKAIVKDVLSGFDTRT 243

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + I  +R L +N  TL++L++++ +S ERVRQIE  A  K++++I+
Sbjct: 244 KDIIMSRYLLDNKATLQDLAAKYNISAERVRQIEEDALAKLKKAIK 289


>gi|302522320|ref|ZP_07274662.1| RNA polymerase sigma factor RpoS [Streptomyces sp. SPB78]
 gi|302431215|gb|EFL03031.1| RNA polymerase sigma factor RpoS [Streptomyces sp. SPB78]
          Length = 514

 Score =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 75/304 (24%), Positives = 139/304 (45%), Gaps = 40/304 (13%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------------REHGD 46
             +  Y+ +I K+P+L  ++E  LAKR                             E G 
Sbjct: 216 DPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANSDKLAPKLQRELEIIAEDG- 274

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 275 RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 334

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L
Sbjct: 335 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKEL 389

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +VI +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 390 DMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 444

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 445 QLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 504

Query: 285 QKQV 288
           + QV
Sbjct: 505 RSQV 508


>gi|169838629|ref|ZP_02871817.1| RNA polymerase sigma factor RpoD [candidate division TM7
           single-cell isolate TM7a]
          Length = 323

 Score =  253 bits (648), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 82/275 (29%), Positives = 144/275 (52%), Gaps = 12/275 (4%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
            +  +  Y+ EI KIP+L  +EE  LA R  + GD  A  ++  +++RLVV IA  Y G 
Sbjct: 47  SDDSVRLYLREIGKIPLLSAEEEMELAHRVVQ-GDKKAKDKMAEANMRLVVSIAKRYSGR 105

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL   +++ EGN GL++AV+KFDP++GF+ +TY+ WWI+ A+   I     +++I     
Sbjct: 106 GLDFLDLIQEGNTGLLRAVEKFDPDKGFKFSTYATWWIRQAITRAIADQARVIRIPVHMV 165

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI- 190
           +      + +L    + +T    +   +  ++K+L++   ++  +        SL+A + 
Sbjct: 166 E-----TINKLLRTQRRMTQELNREPTIEELSKELDMEPDKIEYVMKIKQDIHSLDAGVG 220

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
              D+  S   D++    D       E    +  +  +   +S L+ RE++I + R   E
Sbjct: 221 RDGDEEDSVLGDFI---EDEDTATPEESASSQLLKEQVQGILSSLSDREQKIIKMRFGLE 277

Query: 251 NP--VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           N    TLE +  EF V+RER+RQIEA+A  K+++ 
Sbjct: 278 NGKSHTLEEVGQEFAVTRERIRQIEAKALAKLRKH 312


>gi|56708190|ref|YP_170086.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           tularensis SCHU S4]
 gi|110670661|ref|YP_667218.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           tularensis FSC198]
 gi|134302102|ref|YP_001122071.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           tularensis WY96-3418]
 gi|187931929|ref|YP_001891914.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           mediasiatica FSC147]
 gi|224457293|ref|ZP_03665766.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|254370677|ref|ZP_04986682.1| RNA polymerase sigma-32 factor [Francisella tularensis subsp.
           tularensis FSC033]
 gi|254875002|ref|ZP_05247712.1| alternative sigma factor rpoH [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|56604682|emb|CAG45745.1| RNA polymerase sigma-32 factor [Francisella tularensis subsp.
           tularensis SCHU S4]
 gi|110320994|emb|CAL09128.1| RNA polymerase sigma-32 factor [Francisella tularensis subsp.
           tularensis FSC198]
 gi|134049879|gb|ABO46950.1| alternative sigma factor RpoH [Francisella tularensis subsp.
           tularensis WY96-3418]
 gi|151568920|gb|EDN34574.1| RNA polymerase sigma-32 factor [Francisella tularensis subsp.
           tularensis FSC033]
 gi|187712838|gb|ACD31135.1| RNA polymerase sigma-32 factor [Francisella tularensis subsp.
           mediasiatica FSC147]
 gi|254841001|gb|EET19437.1| alternative sigma factor rpoH [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|282159406|gb|ADA78797.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           tularensis NE061598]
          Length = 292

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 106/286 (37%), Positives = 175/286 (61%), Gaps = 7/286 (2%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
             K  ++ V  +  LS Y++ +  +P+L  ++E  LA+RY+   DL AA +LV SHLR V
Sbjct: 9   ATKTKTLPVVSDNNLSAYLNFVNTLPVLSLEQEQELARRYKYKKDLDAAQQLVLSHLRFV 68

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            KIA  + GYGL I++++ EGNIGLM+AV KFDP++G RL ++++ WIKA M +Y+L++W
Sbjct: 69  TKIARNFSGYGLSIADLIQEGNIGLMKAVSKFDPDQGVRLLSFAVHWIKAEMHDYVLKNW 128

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL- 180
            +VK+ TT  Q++LFFNLR  K  +  ++  N+K      +A++L V E  VI M  R+ 
Sbjct: 129 KIVKVATTKAQRKLFFNLRSSKDKIGWLSSENIK-----ELAEELGVKEETVIEMEKRMC 183

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            GD SL+      D   +  Q   + D     E  +++++   N + ++   +S  + R 
Sbjct: 184 QGDASLDLPYTDDDGEQTSQQSLYLEDKSSNIEHQVVQQDYYDNFKAIVKDVLSGFDTRT 243

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + I  +R L +N  TL++L++++ +S ERVRQIE  A  K++++I+
Sbjct: 244 KDIIMSRYLLDNKATLQDLAAKYNISAERVRQIEEDALAKLKKAIK 289


>gi|269956779|ref|YP_003326568.1| RpoD subfamily RNA polymerase sigma-70 subunit [Xylanimonas
           cellulosilytica DSM 15894]
 gi|269305460|gb|ACZ31010.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Xylanimonas
           cellulosilytica DSM 15894]
          Length = 549

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 72/312 (23%), Positives = 139/312 (44%), Gaps = 47/312 (15%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR--------------------------------- 40
             +  Y+ +I K+ +L  ++E  LAKR                                 
Sbjct: 242 DPVKDYLKQIGKVALLNAEQEVELAKRIEAGLFAEEKLSKDFADFDRTKADADTRRLVRD 301

Query: 41  --YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
             +  H    A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G
Sbjct: 302 LQWIAHDGKRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKG 361

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           ++ +TY+ WWI+ A+   +      ++I     +  +   L R++  +         PE 
Sbjct: 362 YKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE- 418

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              +AK+L+++  +V+ +        SL+  +   +   S++ D +    D +  V  + 
Sbjct: 419 --ELAKELDMTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADA 471

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARA 276
                 +  L + +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++ 
Sbjct: 472 VSFTLLQEQLHQVLDTLSEREAGVVSMRFGLQDGQPKTLDEIGKVYGVTRERIRQIESKT 531

Query: 277 FKKVQESIQKQV 288
             K++   + QV
Sbjct: 532 MSKLRHPSRSQV 543


>gi|85859725|ref|YP_461927.1| RNA polymerase sigma-B factor [Syntrophus aciditrophicus SB]
 gi|85722816|gb|ABC77759.1| RNA polymerase sigma-B factor [Syntrophus aciditrophicus SB]
          Length = 289

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 116/270 (42%), Positives = 177/270 (65%), Gaps = 6/270 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI EI + P+L  +EE+  A  ++++ ++ AA +LV S+LR VVKIA  YR YG+ +
Sbjct: 10  LEVYIAEINRFPILTAEEEFRYAIEWKKNQNMEAAEKLVVSNLRFVVKIAHEYRNYGVKL 69

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM AVKKFDP +G+RL +Y++WWI+A +Q YI+++WSLVKIGTT  Q++L
Sbjct: 70  ADLIQEGNIGLMHAVKKFDPYKGYRLISYAVWWIRAYIQNYIIKTWSLVKIGTTQAQRKL 129

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALINSSD 194
           FF L + K  +QA++   LK  +   IA+ L V E EV  M+ R++  D SL+  I   D
Sbjct: 130 FFKLNKTKKDIQALS---LKNPEFSEIAESLGVREGEVEEMDVRMSNRDLSLDMAI--GD 184

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
              S   D+L Y  + QE  LI KEE +  R  +T +++VLN +E  I   R + ++P T
Sbjct: 185 DGGSSHMDFLTYAGEDQETALIRKEEAELVRKNITGALAVLNEKEMYIIRNRVMADDPKT 244

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L+ +   + ++RER RQIE +A KK++ ++
Sbjct: 245 LQEIGDIYNITRERARQIEKQALKKLRLAL 274


>gi|254515828|ref|ZP_05127888.1| alternative sigma factor RpoH [gamma proteobacterium NOR5-3]
 gi|219675550|gb|EED31916.1| alternative sigma factor RpoH [gamma proteobacterium NOR5-3]
          Length = 303

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 103/272 (37%), Positives = 162/272 (59%), Gaps = 7/272 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L+ Y+  + ++P+L  + E++LA++    GD+ AA  LV SHLR V  IA  YRGYGL 
Sbjct: 35  NLAAYVQAVARVPVLSPEREHMLAEKLFYDGDVQAARELVMSHLRFVAHIARSYRGYGLS 94

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGN+GLM+AVK+FDP +G RL ++++ WIKA + EYILR+W +VKI TT  Q++
Sbjct: 95  EADLIQEGNVGLMKAVKRFDPTKGVRLVSFAVHWIKAEIHEYILRNWRIVKIATTKAQRK 154

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSS 193
           LFFNLR  K  L  ++      ++  A+A  L V   EV  M  RL+  D + +A   S 
Sbjct: 155 LFFNLRSAKKSLAWLS-----ADEAQAVANDLGVDVQEVHRMEGRLSSHDVAFDAPAGSD 209

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEK-EERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
           D    Q   + + D      + +E  E + + +  L  +++ L+ R R I   R L ++ 
Sbjct: 210 DDEGWQAPQYYLEDRSADPAIDVEDSEWQADSQAQLHAAIADLDERSRNILAQRWLTDDK 269

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL  L++E+ VS ER+RQ+E  A KK+++ +
Sbjct: 270 ATLHELAAEYGVSAERIRQLEQAAMKKIRQVL 301


>gi|220912379|ref|YP_002487688.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Arthrobacter
           chlorophenolicus A6]
 gi|219859257|gb|ACL39599.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Arthrobacter
           chlorophenolicus A6]
          Length = 433

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 71/304 (23%), Positives = 135/304 (44%), Gaps = 39/304 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------------HGD 46
             +  Y+ +I K+ +L  ++E  LA R                              H  
Sbjct: 134 DPVKDYLKQIGKVALLNAEQEVDLALRIEAGLFAEEKIAADDGSMEPKYKRELEFIIHDG 193

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ 
Sbjct: 194 KRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYAT 253

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +A +L
Sbjct: 254 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELALEL 308

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +V+ +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 309 DMTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 363

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 364 QLHSVLDTLSEREAGVVAMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 423

Query: 285 QKQV 288
           + QV
Sbjct: 424 RSQV 427


>gi|329769784|ref|ZP_08261185.1| RNA polymerase sigma factor rpoD [Gemella sanguinis M325]
 gi|328838146|gb|EGF87764.1| RNA polymerase sigma factor rpoD [Gemella sanguinis M325]
          Length = 362

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 85/281 (30%), Positives = 139/281 (49%), Gaps = 15/281 (5%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR---EHGDLSAAHRLVTSHLRLVVKIAM 66
           +     +  Y+ EI K+P+L K++E  L+K      E     A   L  ++LRLVV IA 
Sbjct: 83  IRTNDPVRMYLKEIGKVPLLSKEKELELSKIIENGTEEEKEQAKKDLAEANLRLVVSIAK 142

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y G G+   +++ EGN+GL++AV+KFD E+GF+ +TY+ WWI+ A+   I      ++I
Sbjct: 143 RYVGRGMLFLDLIQEGNMGLIKAVEKFDYEKGFKFSTYATWWIRQAITRAIADQARTIRI 202

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
                +      L R++  L        KPE    IAKK+N++  +V  +        SL
Sbjct: 203 PVHMVE--TINRLIRVQRQLLQDLGREPKPE---EIAKKMNMTPDKVREILKIAQEPVSL 257

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              I   +++ S   D++    D + Q  +E    +  +  L   +  L  RE  + + R
Sbjct: 258 ETPI--GEEDDSHLGDFI---EDKEAQSPVEHAANELLKEQLEEILETLTDREENVLKLR 312

Query: 247 RL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
                    TLE + S F V+RER+RQIEA+A +K++   +
Sbjct: 313 FGLKDGKTHTLEEVGSAFGVTRERIRQIEAKAIRKLKHPSK 353


>gi|85710830|ref|ZP_01041891.1| RNA polymerase sigma factor [Idiomarina baltica OS145]
 gi|85695234|gb|EAQ33171.1| RNA polymerase sigma factor [Idiomarina baltica OS145]
          Length = 286

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 117/285 (41%), Positives = 179/285 (62%), Gaps = 9/285 (3%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           K M++ V    GL  YI  + +IPML  ++E  LAKR +E  DL AA  L+ SHLR VV 
Sbjct: 6   KTMALSVPQGGGLDGYIQSVNRIPMLSAEKEKALAKRLQEDKDLDAAKELIMSHLRFVVH 65

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA GY GYGLP ++++ EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+W +
Sbjct: 66  IARGYSGYGLPQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRV 125

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VK+ TT  Q++LFFNLR++K  L          ++V  +AK+L VS  EV+ M  R++  
Sbjct: 126 VKVATTKAQRKLFFNLRKMKKRLGWFNQ-----DEVETVAKELGVSSKEVMEMEARMSAH 180

Query: 184 E---SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLNPRE 239
           +    L++  + S + S+      + D        IE E+ + + +  L  +MS L+ R 
Sbjct: 181 DQAFELSSDDDDSKEGSTYSPAMYLEDKRSDLAEEIETEDYEAHTQKKLFSAMSELDERS 240

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + I ++R L E+ VTL +L++++EVS ERVRQ+E  A KK++ ++
Sbjct: 241 QDIVQSRWLSESKVTLHDLAAKYEVSAERVRQLEQNAMKKLRAAM 285


>gi|282862331|ref|ZP_06271393.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces sp.
           ACTE]
 gi|282562670|gb|EFB68210.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces sp.
           ACTE]
          Length = 515

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 75/314 (23%), Positives = 143/314 (45%), Gaps = 40/314 (12%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------- 41
           + +++       +  Y+ +I K+P+L  ++E  LAKR                       
Sbjct: 207 QQVAVAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANSDKLAPKLKR 266

Query: 42  -----REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                 E G   A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  
Sbjct: 267 ELEIIAEDG-RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYT 325

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  +         P
Sbjct: 326 KGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTP 383

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           E    +AK+L+++  +VI +        SL+  +   +   S++ D +    D +  V  
Sbjct: 384 E---ELAKELDMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPA 435

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEA 274
           +       +  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE+
Sbjct: 436 DAVSFTLLQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIES 495

Query: 275 RAFKKVQESIQKQV 288
           +   K++   + QV
Sbjct: 496 KTMSKLRHPSRSQV 509


>gi|118465794|ref|YP_882772.1| RNA polymerase sigma factor [Mycobacterium avium 104]
 gi|254776035|ref|ZP_05217551.1| RNA polymerase sigma factor [Mycobacterium avium subsp. avium ATCC
           25291]
 gi|118167081|gb|ABK67978.1| sigma factor MysA [Mycobacterium avium 104]
          Length = 496

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 79/319 (24%), Positives = 148/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------REHGDL- 47
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+  
Sbjct: 183 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMSEMAERGEKL 241

Query: 48  ----------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 242 PAAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 301

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 302 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 359

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 360 REPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 411

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 412 AVVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 471

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 472 RQIESKTMSKLRHPSRSQV 490


>gi|403013|emb|CAA50594.1| major sigma factor [Lactococcus lactis]
          Length = 340

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 81/279 (29%), Positives = 138/279 (49%), Gaps = 14/279 (5%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD--LSAAHRLVTSHLRLVVKIAMGYRG 70
           +  +  Y+ EI + P++   EE  LA+     G+    A   L  ++LRLVV IA  Y G
Sbjct: 66  DDPVRMYLKEIGRYPLISLDEETKLAEAIIAGGEGAEFAKQMLAEANLRLVVSIAKRYSG 125

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            G+   +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    
Sbjct: 126 RGMQFLDLIQEGNMGLMKAVDKFDQTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 185

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
            +      L R++ +L      +  PE    I K+L+++  +V  +        SL   I
Sbjct: 186 VE--TINKLIRVQRNLLQELGRDPSPE---EIGKELHMAPDKVREVLKIAQEPVSLETPI 240

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
              +++ S   D++  D     +  ++   R   R  L   M  L  RE  +   R   +
Sbjct: 241 --GEEDDSHLGDFIEDD---VIESPVDYTNRILLREQLDEVMDTLTDREENVLRMRFGLD 295

Query: 251 NP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +    TLE++  +F+V+RER+RQIEA+A KK++   + +
Sbjct: 296 DGRMHTLEDVGKQFKVTRERIRQIEAKAIKKLRHPRRSK 334


>gi|326443878|ref|ZP_08218612.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 537

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 75/314 (23%), Positives = 143/314 (45%), Gaps = 40/314 (12%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------- 41
           + +++       +  Y+ +I K+P+L  ++E  LAKR                       
Sbjct: 229 QQVAVAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANADKLAPKLKR 288

Query: 42  -----REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                 E G   A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  
Sbjct: 289 ELEIIAEDG-RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYT 347

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  +         P
Sbjct: 348 KGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTP 405

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           E    +AK+L+++  +VI +        SL+  +   +   S++ D +    D +  V  
Sbjct: 406 E---ELAKELDMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPA 457

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEA 274
           +       +  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE+
Sbjct: 458 DAVSFTLLQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIES 517

Query: 275 RAFKKVQESIQKQV 288
           +   K++   + QV
Sbjct: 518 KTMSKLRHPSRSQV 531


>gi|225021265|ref|ZP_03710457.1| hypothetical protein CORMATOL_01277 [Corynebacterium matruchotii
           ATCC 33806]
 gi|224945998|gb|EEG27207.1| hypothetical protein CORMATOL_01277 [Corynebacterium matruchotii
           ATCC 33806]
          Length = 617

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 76/325 (23%), Positives = 150/325 (46%), Gaps = 49/325 (15%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY----------------REHG 45
            RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR                   +G
Sbjct: 298 ARKDAELTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYADYRMKQMEKAYSNG 356

Query: 46  DLSAA--------------------HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           D  A                     + L+ ++LRLVV +A  Y G G+   +++ EGN+G
Sbjct: 357 DKEAKLTPAVKRDLRAIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLG 416

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  
Sbjct: 417 LIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRE 474

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           L         P     ++K+++++E +V+ +        SL+  I   D+  SQ  D++ 
Sbjct: 475 LLQDLGREPTP---YELSKEMDITEDKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI- 528

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFE 263
              D +  + ++       ++ L   +  L+ RE  + + R    +  P TL+ +   + 
Sbjct: 529 --EDSEAVIAVDAVSFTLLQDQLQDVLHTLSEREAGVVKLRFGLTDGMPRTLDEIGQVYG 586

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           V+RER+RQIE++   K++   + QV
Sbjct: 587 VTRERIRQIESKTMSKLRHPSRSQV 611


>gi|294638156|ref|ZP_06716412.1| alternative sigma factor RpoH [Edwardsiella tarda ATCC 23685]
 gi|291088723|gb|EFE21284.1| alternative sigma factor RpoH [Edwardsiella tarda ATCC 23685]
          Length = 284

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 104/289 (35%), Positives = 168/289 (58%), Gaps = 8/289 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+++  ++ +  +  L  Y+      PML  +EE  L +R    GDL AA +L+ SHLR 
Sbjct: 1   MSKEMQTLTLVPQGSLEAYVRAANAYPMLTAEEERALGERLHYQGDLDAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEMGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VSE +V+ M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVELVARELGVSEKDVLEMESRM 175

Query: 181 -AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPR 238
            A D + +   +   + +       + D        IE +  ++   + L+ ++  L+ R
Sbjct: 176 AAQDMAFDLPNDDEQEGAPAAPVLFLQDKSSDFANEIEDDNWESHAADKLSVALEGLDER 235

Query: 239 ERRIFEARRLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + I  AR L  EN  TL+ L+  + VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 SQHIIRARWLDSENKATLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 284


>gi|241764416|ref|ZP_04762441.1| RNA polymerase, sigma 32 subunit, RpoH [Acidovorax delafieldii 2AN]
 gi|241366206|gb|EER60777.1| RNA polymerase, sigma 32 subunit, RpoH [Acidovorax delafieldii 2AN]
          Length = 312

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 114/289 (39%), Positives = 171/289 (59%), Gaps = 13/289 (4%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +V     L  YI  + ++P+L  +EE   A++ R+H D+ AA RLV SHLRLVV IA  Y
Sbjct: 20  LVPPLGNLDAYISAVNRLPLLTHEEEQTYARKLRDHNDVDAAGRLVMSHLRLVVSIARQY 79

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGLP  +++ EGN+GLM+AVK+FDP++G RL +Y+M WIKA + EYIL++W +VK+ T
Sbjct: 80  LGYGLPHGDLIQEGNVGLMKAVKRFDPDQGVRLVSYAMHWIKAEIHEYILKNWRMVKVAT 139

Query: 129 TANQKRLFFNLRRLKG------HLQAITDNN-LKPEQVVAIAKKLNVSESEVISMNCRLA 181
           T  Q++LFFNLR +K        + A T  + L  +++ A+A +LNV   EVI M  R+A
Sbjct: 140 TKAQRKLFFNLRSMKQGFKADAAVDAATHRDTLSEQEIDAVATQLNVKREEVIEMETRMA 199

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLNPRER 240
           G + L     S D   +      + D   +   +IE  +R     + +  +++ L+ R R
Sbjct: 200 GGDVLLDPAPSDDGEQAFGPIGYLADASHEPTAMIESRQRDALATDGIAMALARLDDRSR 259

Query: 241 RIFEARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           RI E R L         +TL  L++ + VS ER+RQIE  A KK++ ++
Sbjct: 260 RIVEERWLKVNDDGTGGMTLHELAAVYGVSAERIRQIEVAAMKKMKTAL 308


>gi|150015739|ref|YP_001307993.1| RNA polymerase sigma factor RpoD [Clostridium beijerinckii NCIMB
           8052]
 gi|149902204|gb|ABR33037.1| RNA polymerase, sigma 70 subunit, RpoD family [Clostridium
           beijerinckii NCIMB 8052]
          Length = 376

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 78/277 (28%), Positives = 135/277 (48%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI K+P+L  ++E   AK   E G+  A  +L  ++LRLVV IA  Y G G
Sbjct: 104 DDPVRMYLKEIGKVPLLSSEQEITYAKEI-EEGNQKAKKKLAEANLRLVVSIAKRYVGRG 162

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I     +
Sbjct: 163 MLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 222

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 L R++  L      +  PE    I+K + +   +V  +        SL   I  
Sbjct: 223 --TINKLIRVQRQLLQELGRDPFPE---EISKVMELPVDKVREIQKIAQEPVSLETPI-- 275

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            ++  S   D++      +     E       +  L   +  L PRE ++   R   ++ 
Sbjct: 276 GEEEDSHLGDFIPD---DEAPAPAEAAAFTMLKEQLINVLDTLTPREEKVLRLRFGLDDG 332

Query: 253 --VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 333 RARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 369


>gi|319949012|ref|ZP_08023109.1| RNA polymerase sigma factor [Dietzia cinnamea P4]
 gi|319437300|gb|EFV92323.1| RNA polymerase sigma factor [Dietzia cinnamea P4]
          Length = 460

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 78/319 (24%), Positives = 149/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR--------------------- 40
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR                     
Sbjct: 147 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATWYMAQVTERGEKL 205

Query: 41  ---------YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                    + E   + A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 206 TTAQRRDFKWIERDGVRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 265

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 266 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 323

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 324 REPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 375

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R    +  P TL+ +   + V+RER+
Sbjct: 376 AVVAVDAVSFTLLQDQLRSVLDTLSEREAGVVRLRFGLTDGLPRTLDEIGQVYGVTRERI 435

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 436 RQIESKTMSKLRHPSRSQV 454


>gi|307251409|ref|ZP_07533324.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 4 str. M62]
 gi|306856577|gb|EFM88718.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 4 str. M62]
          Length = 316

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 98/273 (35%), Positives = 160/273 (58%), Gaps = 6/273 (2%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  L  YI    + P+L  ++E  LA+RY    D+ AA +L+ SH+R V+ IA GY GYG
Sbjct: 46  QGNLDSYIRMANQYPILTAEQEKELAERYYYDEDVEAAKQLILSHMRFVIHIARGYLGYG 105

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP+++++ EGNIGLM+AVK+FDP  G RL ++++ W+KA + EY+L++W +VK+ TT  Q
Sbjct: 106 LPLADLIQEGNIGLMKAVKRFDPNVGVRLVSFAIHWVKAEIHEYVLKNWRIVKVATTKAQ 165

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALIN 191
           ++LFFNLR+ K  L    +     E++  +A+ L VS  EV  M  R+ G D   +  + 
Sbjct: 166 RKLFFNLRKNKNRLAWFNE-----EEIQKVAEDLGVSPEEVREMESRMTGQDLGFDLPVG 220

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             D        +L  +       L +++        L  +++ L+ R + I + R L E 
Sbjct: 221 EDDDEVYTPSMYLEDNSSNFADDLEDEQYNGQATAQLAYALATLDERSQDIIKTRWLDEE 280

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL++L+ ++ +S ERVRQ+E  A KK++++I
Sbjct: 281 KATLQDLAEKYGISAERVRQLENAALKKIKDAI 313


>gi|305681425|ref|ZP_07404232.1| RNA polymerase sigma factor RpoD [Corynebacterium matruchotii ATCC
           14266]
 gi|305659630|gb|EFM49130.1| RNA polymerase sigma factor RpoD [Corynebacterium matruchotii ATCC
           14266]
          Length = 608

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 76/325 (23%), Positives = 150/325 (46%), Gaps = 49/325 (15%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY----------------REHG 45
            RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR                   +G
Sbjct: 289 ARKDAELTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYADYRMKQMEKAYSNG 347

Query: 46  DLSAA--------------------HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           D  A                     + L+ ++LRLVV +A  Y G G+   +++ EGN+G
Sbjct: 348 DKEAKLTPAVKRDLRAIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLG 407

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  
Sbjct: 408 LIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRE 465

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           L         P     ++K+++++E +V+ +        SL+  I   D+  SQ  D++ 
Sbjct: 466 LLQDLGREPTP---YELSKEMDITEDKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI- 519

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFE 263
              D +  + ++       ++ L   +  L+ RE  + + R    +  P TL+ +   + 
Sbjct: 520 --EDSEAVIAVDAVSFTLLQDQLQDVLHTLSEREAGVVKLRFGLTDGMPRTLDEIGQVYG 577

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           V+RER+RQIE++   K++   + QV
Sbjct: 578 VTRERIRQIESKTMSKLRHPSRSQV 602


>gi|329940007|ref|ZP_08289289.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
 gi|329300833|gb|EGG44729.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
          Length = 512

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 75/304 (24%), Positives = 139/304 (45%), Gaps = 40/304 (13%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------------REHGD 46
             +  Y+ +I K+P+L  ++E  LAKR                             E G 
Sbjct: 214 DPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLASADKLAPKLKRELEIIAEDG- 272

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 273 RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 332

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L
Sbjct: 333 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKEL 387

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +VI +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 388 DMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 442

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 443 QLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 502

Query: 285 QKQV 288
           + QV
Sbjct: 503 RSQV 506


>gi|329946883|ref|ZP_08294295.1| RNA polymerase sigma factor RpoD [Actinomyces sp. oral taxon 170
           str. F0386]
 gi|328526694|gb|EGF53707.1| RNA polymerase sigma factor RpoD [Actinomyces sp. oral taxon 170
           str. F0386]
          Length = 543

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 73/304 (24%), Positives = 138/304 (45%), Gaps = 39/304 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY----------REHGD----------------- 46
             +  Y+ +I K+ +L  ++E  LAKR            E G+                 
Sbjct: 244 DPVKDYLKQIGKVALLNAEQEVELAKRIEAGLYAEHRLAEEGNDLPAKLRRELHWVAQDG 303

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ 
Sbjct: 304 QRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYAT 363

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +A +L
Sbjct: 364 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAVEL 418

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +V+ +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 419 DMTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 473

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 474 QLHAVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 533

Query: 285 QKQV 288
           + QV
Sbjct: 534 RSQV 537


>gi|1163231|gb|AAC45341.1| DNA polymerase sigma 32 subunit [Vibrio cholerae]
          Length = 286

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 107/289 (37%), Positives = 170/289 (58%), Gaps = 11/289 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  +   + +  +  L  YI  +   PML   EE  LA+R    GD+ AA  L+ SHLR 
Sbjct: 1   MTNQAYPMALVSQDSLDSYIRSVNGYPMLSADEERELAERLHYKGDIDAAKGLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A GY GYGLP++++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VKI TT  Q++LFFNLR+ K  L    +      +V  +A++L V  +EV  M  RL
Sbjct: 121 WRIVKIATTKAQRKLFFNLRKSKKRLGWFNNG-----EVETVARELGVEPAEVREMESRL 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR----NMLTRSMSVLN 236
           A  ++   +    D+N   +   ++Y  D     L +  E +N        L+ +++ L+
Sbjct: 176 AAQDAAFEMSAEDDENGMAYTAPVLYLEDKHSD-LADNLEAENWEAHTTQRLSMALASLD 234

Query: 237 PRERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              + I  AR L ++   TL++L++++ VS ER+RQ+E  A +K++E++
Sbjct: 235 DGSQHIVRARWLDDDNKTTLQDLAAKYGVSAERIRQLEKNAMRKLKEAV 283


>gi|114561466|ref|YP_748979.1| RNA polymerase factor sigma-32 [Shewanella frigidimarina NCIMB 400]
 gi|114332759|gb|ABI70141.1| RNA polymerase, sigma 32 subunit, RpoH [Shewanella frigidimarina
           NCIMB 400]
          Length = 285

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 109/290 (37%), Positives = 172/290 (59%), Gaps = 10/290 (3%)

Query: 1   MNRKNMSI---IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSH 57
           M  +  S+   + +    L  YI  +  I ML+   EY +AKR +E+GDL AA +L+ SH
Sbjct: 1   MTYQTQSMALAVPHNASSLEAYIQSVTSINMLDADTEYDIAKRLQENGDLQAAKQLIMSH 60

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LR VV +A GY GYGLP ++++ EGNIGLM+AVK+FDP+ G RL ++++ WIKA + EY+
Sbjct: 61  LRFVVHVAKGYSGYGLPQADLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYV 120

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           L++W +VK+ TT  Q++LFFN+R+ K  L   +D      +V  +A+ L VS+++V  M 
Sbjct: 121 LKNWRIVKVATTKAQRKLFFNIRKSKKRLGWFSD-----AEVTMVAENLGVSKADVTEME 175

Query: 178 CRLAGDESLNALINSSDKNSSQW-QDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVL 235
            R+A  +    L N SD +   +     + DH       +E    + + +  L  ++  L
Sbjct: 176 SRMAAQDPAFDLTNDSDDDHHDFAPALYLEDHSSDVADQVEHANWEADSQTRLLSAIKTL 235

Query: 236 NPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + R + I  AR L +  VTL+ L+S +EVS ER+RQ+E  A  K++  ++
Sbjct: 236 DERSQHILRARWLDDTKVTLQELASTYEVSAERIRQLEKNAMNKLKSCME 285


>gi|187927337|ref|YP_001897824.1| RNA polymerase factor sigma-32 [Ralstonia pickettii 12J]
 gi|309779962|ref|ZP_07674716.1| alternative sigma factor RpoH [Ralstonia sp. 5_7_47FAA]
 gi|187724227|gb|ACD25392.1| RNA polymerase, sigma 32 subunit, RpoH [Ralstonia pickettii 12J]
 gi|308921321|gb|EFP66964.1| alternative sigma factor RpoH [Ralstonia sp. 5_7_47FAA]
          Length = 309

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 118/286 (41%), Positives = 174/286 (60%), Gaps = 10/286 (3%)

Query: 7   SIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           ++   G +G +  YI  + ++PML  +EE  LA+ YR++ +L AA RLV SHLRLVV IA
Sbjct: 26  ALAFPGNLGNIDAYIQSVNRVPMLSAEEEQRLAREYRDNDNLDAARRLVLSHLRLVVSIA 85

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            GY GYGLP ++++ EGNIGLM+AVK+FDP++G RL +Y+M WIKA M EYIL++W +VK
Sbjct: 86  RGYLGYGLPHADLIQEGNIGLMKAVKRFDPDQGVRLVSYAMHWIKAEMHEYILKNWRMVK 145

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           + TT  Q++LFFNLR  K   QA        +++ A+A +LNV  +EV  M  RL+G + 
Sbjct: 146 VATTKAQRKLFFNLRSHKQDAQA----TFTSDEIDAVAAELNVKGTEVREMETRLSGGDI 201

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
                    + S     +L   H+   +V+  +   + +   +  +++ L+ R RRI EA
Sbjct: 202 ALEGQMDDGEESFAPIAYLADTHNEPTRVIEARSNDRMQSEGIEAALAKLDDRSRRIIEA 261

Query: 246 RRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R L          TL  L+ EF VS ER+RQIE+ A KK++ ++Q 
Sbjct: 262 RWLNVNDDGSGGSTLHELADEFGVSAERIRQIESAAMKKMKGALQA 307


>gi|325266382|ref|ZP_08133060.1| DNA-directed RNA polymerase sigma subunit RpoH [Kingella
           denitrificans ATCC 33394]
 gi|324982175|gb|EGC17809.1| DNA-directed RNA polymerase sigma subunit RpoH [Kingella
           denitrificans ATCC 33394]
          Length = 332

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 120/293 (40%), Positives = 178/293 (60%), Gaps = 10/293 (3%)

Query: 1   MNRKNMSIIV-NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLR 59
           M     ++ V +G   L +YIH +  IPML  +EE  LA+R +  GDL AA +L+ SHLR
Sbjct: 41  MTNHAFALPVPSGHGNLEQYIHTVNNIPMLSAEEETRLAER-QIKGDLEAAKQLILSHLR 99

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           +VV IA GY GYGL  ++++ EGNIGLM+AVK+F+P  G RL ++++ WIKA + E+ILR
Sbjct: 100 VVVSIARGYDGYGLNQADLIQEGNIGLMKAVKRFEPHHGARLFSFAVHWIKAEIHEFILR 159

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
           +W LV++ TT  Q++LFFNLR ++  L+A++     P++   IA  L V  SEV+ M  R
Sbjct: 160 NWRLVRVATTKPQRKLFFNLRSMRNSLKALS-----PKEAQDIADDLGVKVSEVMEMEQR 214

Query: 180 LAG-DESLNALINSSDKNSS-QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
           + G D  L A     D+N++    DWL          L +K     +   L  +++ L+ 
Sbjct: 215 MTGHDIGLLADNQDDDENNAFAPIDWLSDSQHEPSHQLAQKAHYALQTEGLQAALAQLDE 274

Query: 238 RERRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           R RRI E R L +    TL  L++EF VS ER+RQIEA+A +K++  ++ Q +
Sbjct: 275 RSRRIVETRWLHDGQAATLHELAAEFGVSAERIRQIEAKAIQKLRAIMENQAD 327


>gi|312139434|ref|YP_004006770.1| sigma-70 factor siga [Rhodococcus equi 103S]
 gi|325672677|ref|ZP_08152373.1| RNA polymerase principal sigma factor SigA [Rhodococcus equi ATCC
           33707]
 gi|311888773|emb|CBH48085.1| sigma-70 factor SigA [Rhodococcus equi 103S]
 gi|325556554|gb|EGD26220.1| RNA polymerase principal sigma factor SigA [Rhodococcus equi ATCC
           33707]
          Length = 459

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 79/319 (24%), Positives = 148/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------REHGDL- 47
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+  
Sbjct: 146 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLFATHKMNEMAEKGEKP 204

Query: 48  ----------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 205 SPTDRRNLNWITRDGNRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 264

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 265 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 322

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 323 REPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 374

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 375 AVVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 434

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 435 RQIESKTMSKLRHPSRSQV 453


>gi|298246437|ref|ZP_06970243.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297553918|gb|EFH87783.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 422

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 80/292 (27%), Positives = 136/292 (46%), Gaps = 29/292 (9%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAK----------------RYREHGDLSAAHRLVTS 56
           +  +  Y+ EI ++P+L   EE  LA+                RY   G   A  RL  +
Sbjct: 134 DDPVRMYLREIGRVPLLTAHEEIRLAQLMERGKAERLKPAPNYRYISEG-EEAQKRLTEA 192

Query: 57  HLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           +LRLVV +A  Y G G+ + +++ EGNIGL++AV+KFD  +GF+ +TY+ WWI+ A+   
Sbjct: 193 NLRLVVSVAKKYIGRGMNLLDLIQEGNIGLIRAVEKFDYNKGFKFSTYATWWIRQAITRA 252

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
           I      ++I     +      L R+   L          E    IA ++ +S  +V  +
Sbjct: 253 IADQARTIRIPVHMVE--TINRLIRISRRLLQDLGREPTSE---EIAAQMEISAEKVREI 307

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
                   SL   I   +++ S   D++    D       +    +  +  +   +  L 
Sbjct: 308 IKVSQEPVSLETPI--GEEDDSHLGDFI---EDHTALAPADAASHQLLKEQVEDVLDSLT 362

Query: 237 PRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            RER++ + R   ++    TLE +  EF V+RER+RQIEA+A +K++   + 
Sbjct: 363 ERERKVLQLRFGLDDGRSRTLEEVGKEFHVTRERIRQIEAKALRKLRHPSRS 414


>gi|296112758|ref|YP_003626696.1| RNA polymerase sigma factor 32 [Moraxella catarrhalis RH4]
 gi|295920452|gb|ADG60803.1| RNA polymerase sigma factor 32 [Moraxella catarrhalis RH4]
 gi|326561004|gb|EGE11369.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis 7169]
 gi|326566767|gb|EGE16906.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis 103P14B1]
 gi|326567391|gb|EGE17506.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis BC1]
 gi|326575234|gb|EGE25162.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis CO72]
 gi|326576679|gb|EGE26586.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis 101P30B1]
 gi|326577646|gb|EGE27523.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis O35E]
          Length = 371

 Score =  253 bits (647), Expect = 2e-65,   Method: Composition-based stats.
 Identities = 108/272 (39%), Positives = 161/272 (59%), Gaps = 7/272 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + L  YI+ + +IP+L  +EE  LA+RY   GD+ AA  LV SHLR V+ IA  Y GYGL
Sbjct: 97  VNLGAYINTVHQIPILTPEEERALAERYYHDGDVEAARLLVMSHLRFVIHIARSYSGYGL 156

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
             ++++ EGN+GLM+AVK+FDP +G RL ++++ WIKA + E+++++W +VK+ TT   +
Sbjct: 157 SQADLIQEGNLGLMKAVKRFDPNKGVRLVSFAVHWIKAEIHEFVIKNWRIVKVATTKAHR 216

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINS 192
           +LFFNLR LK      + N L  ++  AIA  LNV+  +V+ M  RL   D S  A  + 
Sbjct: 217 KLFFNLRSLKK-----SSNQLTLDEATAIANDLNVTVKQVLEMESRLTSYDASFEAQDSD 271

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            D+     Q +L  D      V+ E +  +N    L  +M  L+ R R I   R L +  
Sbjct: 272 DDEGRYAPQLFL-EDAVNPADVVEEADWEENTTTALKDAMETLDERSRDIITQRWLADQK 330

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL  L++ + +S ERVRQIE  A  K++E+I
Sbjct: 331 STLHELAATYNISAERVRQIEKNAMNKIKEAI 362


>gi|241661869|ref|YP_002980229.1| RNA polymerase factor sigma-32 [Ralstonia pickettii 12D]
 gi|240863896|gb|ACS61557.1| RNA polymerase, sigma 32 subunit, RpoH [Ralstonia pickettii 12D]
          Length = 309

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 118/286 (41%), Positives = 174/286 (60%), Gaps = 10/286 (3%)

Query: 7   SIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           ++   G +G +  YI  + ++PML  +EE  LA+ YR++ +L AA RLV SHLRLVV IA
Sbjct: 26  ALAFPGNLGNIDAYIQSVNRVPMLSAEEEQRLAREYRDNDNLDAARRLVLSHLRLVVSIA 85

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            GY GYGLP ++++ EGNIGLM+AVK+FDP++G RL +Y+M WIKA M EYIL++W +VK
Sbjct: 86  RGYLGYGLPHADLIQEGNIGLMKAVKRFDPDQGVRLVSYAMHWIKAEMHEYILKNWRMVK 145

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           + TT  Q++LFFNLR  K   QA        +++ A+A +LNV  +EV  M  RL+G + 
Sbjct: 146 VATTKAQRKLFFNLRSHKQDAQA----TFTSDEIDAVAAELNVKGTEVREMETRLSGGDI 201

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
                    + S     +L   H+   +V+  +   + +   +  +++ L+ R RRI EA
Sbjct: 202 ALEGQMDDGEESYAPIAYLADTHNEPTRVIEARSNDRMQSEGIEAALAKLDDRSRRIIEA 261

Query: 246 RRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R L          TL  L+ EF VS ER+RQIE+ A KK++ ++Q 
Sbjct: 262 RWLNVNDDGSGGSTLHELADEFGVSAERIRQIESAAMKKMKGALQA 307


>gi|325068636|ref|ZP_08127309.1| RNA polymerase, sigma 70 subunit, RpoD [Actinomyces oris K20]
          Length = 542

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 73/304 (24%), Positives = 138/304 (45%), Gaps = 39/304 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY----------REHGD----------------- 46
             +  Y+ +I K+ +L  ++E  LAKR            E G+                 
Sbjct: 243 DPVKDYLKQIGKVALLNAEQEVELAKRIEAGLYAEHRLAEEGNDLPAKLRRELHWVAQDG 302

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ 
Sbjct: 303 QRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYAT 362

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +A +L
Sbjct: 363 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAVEL 417

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +V+ +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 418 DMTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 472

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 473 QLHAVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 532

Query: 285 QKQV 288
           + QV
Sbjct: 533 RSQV 536


>gi|18202317|sp|P58290|RPOD_LACLC RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-42
          Length = 364

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 81/279 (29%), Positives = 138/279 (49%), Gaps = 14/279 (5%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD--LSAAHRLVTSHLRLVVKIAMGYRG 70
           +  +  Y+ EI + P++   EE  LA+     G+    A   L  ++LRLVV IA  Y G
Sbjct: 90  DDPVRMYLKEIGRYPLISLDEETKLAEAIIAGGEGAEFAKQMLAEANLRLVVSIAKRYSG 149

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            G+   +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I    
Sbjct: 150 RGMQFLDLIQEGNMGLMKAVDKFDQTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM 209

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
            +      L R++ +L      +  PE    I K+L+++  +V  +        SL   I
Sbjct: 210 VE--TINKLIRVQRNLLQELGRDPSPE---EIGKELHMAPDKVREVLKIAQEPVSLETPI 264

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
              +++ S   D++  D     +  ++   R   R  L   M  L  RE  +   R   +
Sbjct: 265 --GEEDDSHLGDFIEDD---VIESPVDYTNRILLREQLDEVMDTLTDREENVLRMRFGLD 319

Query: 251 NP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +    TLE++  +F+V+RER+RQIEA+A KK++   + +
Sbjct: 320 DGRMHTLEDVGKQFKVTRERIRQIEAKAIKKLRHPRRSK 358


>gi|153840380|ref|ZP_01993047.1| alternative sigma factor RpoH [Vibrio parahaemolyticus AQ3810]
 gi|149745954|gb|EDM57084.1| alternative sigma factor RpoH [Vibrio parahaemolyticus AQ3810]
          Length = 274

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 108/279 (38%), Positives = 162/279 (58%), Gaps = 9/279 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++   + +  +  L  YI  +   PML   EE  LA+R    G++ AA  L+ SHLR 
Sbjct: 1   MTKEAYPMALVTQDSLDSYIRSVNSYPMLTADEERELAERLHYKGEIEAAKGLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A GY GYGLP++++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VKI TT  Q++LFFNLR+ K  L    +      +V  +A++L V  SEV  M  RL
Sbjct: 121 WRIVKIATTKAQRKLFFNLRKSKKRLGWFNNG-----EVETVARELGVEPSEVREMESRL 175

Query: 181 AGDES-LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE---ERKNRRNMLTRSMSVLN 236
           A  +S  +   +  D  +S +   ++Y  D    V    E      +  N L  +++ L+
Sbjct: 176 AAVDSTFDMPTDDDDSATSSYTAPMLYLEDKSSDVADNIEAANWEMHTNNRLGHALASLD 235

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
            R +RI  +R L +   TL++L+ EF VS ER+RQ+E  
Sbjct: 236 ERSQRIVRSRWLDDEKATLQDLADEFGVSAERIRQLEKN 274


>gi|297202863|ref|ZP_06920260.1| RNA polymerase sigma factor RpoS [Streptomyces sviceus ATCC 29083]
 gi|297148238|gb|EDY59236.2| RNA polymerase sigma factor RpoS [Streptomyces sviceus ATCC 29083]
          Length = 512

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 75/314 (23%), Positives = 143/314 (45%), Gaps = 40/314 (12%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------- 41
           + +++       +  Y+ +I K+P+L  ++E  LAKR                       
Sbjct: 204 QQVAVAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANADKLAPKLKR 263

Query: 42  -----REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                 E G   A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  
Sbjct: 264 ELEIIAEDG-RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYT 322

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  +         P
Sbjct: 323 KGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTP 380

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           E    +AK+L+++  +VI +        SL+  +   +   S++ D +    D +  V  
Sbjct: 381 E---ELAKELDMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPA 432

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEA 274
           +       +  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE+
Sbjct: 433 DAVSFTLLQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIES 492

Query: 275 RAFKKVQESIQKQV 288
           +   K++   + QV
Sbjct: 493 KTMSKLRHPSRSQV 506


>gi|121999080|ref|YP_001003867.1| RNA polymerase sigma-32 subunit RpoH [Halorhodospira halophila SL1]
 gi|121590485|gb|ABM63065.1| RNA polymerase, sigma 32 subunit, RpoH [Halorhodospira halophila
           SL1]
          Length = 287

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 108/284 (38%), Positives = 172/284 (60%), Gaps = 10/284 (3%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           N+ +  + E     YI  + +IP+L+  EEY LA+R +  GDL AA +LV SHLR VV +
Sbjct: 12  NLPLPTSSEDA---YIQAVSQIPVLDADEEYELARRCQYEGDLDAARQLVLSHLRFVVHV 68

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A GYRGYGL + +++ EGNIGLM+AVK+FDP+ G RL ++++ WI+A + E+ILR+W +V
Sbjct: 69  ARGYRGYGLALGDLIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIRAEIHEFILRNWRIV 128

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-D 183
           K+ TT  Q++LFFNLR  K  L  +T      E+V A+A+ L V    V+ M  RL+G D
Sbjct: 129 KVATTKAQRKLFFNLRGAKKRLGWMT-----REEVNAVAEDLGVQPETVLEMESRLSGQD 183

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER-KNRRNMLTRSMSVLNPRERRI 242
              + L++  D+  ++     + D       ++E  +   ++ + L +++  L+ R + I
Sbjct: 184 LGFDPLVSEEDEEQARAPVAYLEDRRFDPAEVVESSDWGTHQDDSLHQALGQLDERSQNI 243

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             AR L+E   TL+ L+  + VS ER+RQ+E  A  K++ ++  
Sbjct: 244 LRARWLEEERQTLQELAERYGVSAERIRQLEKNAISKLRGAVSA 287


>gi|108799152|ref|YP_639349.1| RNA polymerase sigma factor [Mycobacterium sp. MCS]
 gi|119868267|ref|YP_938219.1| RNA polymerase sigma factor [Mycobacterium sp. KMS]
 gi|108769571|gb|ABG08293.1| RNA polymerase, sigma 28 subunit [Mycobacterium sp. MCS]
 gi|119694356|gb|ABL91429.1| RNA polymerase, sigma 70 subunit, RpoD family [Mycobacterium sp.
           KMS]
          Length = 480

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 78/319 (24%), Positives = 149/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------------- 41
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR                     
Sbjct: 167 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLFATQKLAELAEKGEKL 225

Query: 42  --REHGDLS--------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
             ++  D+         A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 226 PVQQRRDMQWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 285

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 286 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 343

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 344 REPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 395

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 396 AVVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 455

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 456 RQIESKTMSKLRHPSRSQV 474


>gi|167627742|ref|YP_001678242.1| RNA polymerase factor sigma-32 [Francisella philomiragia subsp.
           philomiragia ATCC 25017]
 gi|167597743|gb|ABZ87741.1| RNA polymerase sigma-32 factor [Francisella philomiragia subsp.
           philomiragia ATCC 25017]
          Length = 292

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 105/286 (36%), Positives = 175/286 (61%), Gaps = 7/286 (2%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           K  S+ V  +  L+ Y++ +  +P+L  +EE  LA+RY+   DL AA +LV SHLR V K
Sbjct: 11  KGKSLPVVSDNNLNSYLNFVNSLPILSVEEEQELARRYKYQKDLDAAQQLVLSHLRFVTK 70

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  + GYGL I++++ EGNIGLM+AV KFDP++G RL ++++ WIKA M +Y+L++W +
Sbjct: 71  IARNFSGYGLSIADLIQEGNIGLMKAVSKFDPDQGVRLVSFAVHWIKAEMHDYVLKNWKI 130

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AG 182
           VK+ TT  Q++LFFNLR  K  +  ++      E +  +A++L V E  VI M  R+  G
Sbjct: 131 VKVATTKAQRKLFFNLRSSKDKIGWLS-----SEDIKQLAEELGVKEETVIEMEKRMCQG 185

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           D SL+      +   S  Q + + D     E  +++++   N + ++   +S  + R + 
Sbjct: 186 DASLDLPYTDDEGGQSNQQSFYLEDKSSDIEHQIVQQDYYDNFKAIVKDVISGFDTRTKD 245

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           I  +R L +   TL++L++++ +S ERVRQIE  A  K++++I+ +
Sbjct: 246 IIMSRYLLDTKATLQDLAAKYNISAERVRQIEEEALVKLRKAIKNK 291


>gi|126434760|ref|YP_001070451.1| RNA polymerase sigma factor [Mycobacterium sp. JLS]
 gi|126234560|gb|ABN97960.1| RNA polymerase, sigma 70 subunit, RpoD family [Mycobacterium sp.
           JLS]
          Length = 480

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 78/319 (24%), Positives = 149/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------------- 41
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR                     
Sbjct: 167 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLFATQKLAELAEKGEKL 225

Query: 42  --REHGDLS--------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
             ++  D+         A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 226 PVQQRRDMQWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 285

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 286 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 343

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 344 REPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 395

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 396 AVVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 455

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 456 RQIESKTMSKLRHPSRSQV 474


>gi|284031355|ref|YP_003381286.1| RpoD subfamily RNA polymerase sigma-70 subunit [Kribbella flavida
           DSM 17836]
 gi|283810648|gb|ADB32487.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Kribbella flavida
           DSM 17836]
          Length = 442

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 78/318 (24%), Positives = 145/318 (45%), Gaps = 41/318 (12%)

Query: 2   NRKNMSIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRY------------------ 41
           +     ++V G     +  Y+ +I K+P+L  ++E  LAKR                   
Sbjct: 129 DEPEQQVMVAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEEQLSDESAKLK 188

Query: 42  ---REHGD------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
              R+  D        A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 189 DKVRDEYDWISEDGRRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEK 248

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  +      
Sbjct: 249 FDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGR 306

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE    +AK+L+++  +VI +        SL+  +   +   S++ D +    D + 
Sbjct: 307 EPTPE---ELAKELDMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEA 358

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVR 270
            V  E       +  L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 359 IVPAEAVSFTLLQEQLHAVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIR 418

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 419 QIESKTMSKLRHPSRSQV 436


>gi|285019635|ref|YP_003377346.1| RNA polymerase sigma-32 factor protein [Xanthomonas albilineans GPE
           PC73]
 gi|283474853|emb|CBA17352.1| probable rna polymerase sigma-32 factor protein [Xanthomonas
           albilineans]
          Length = 292

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 118/276 (42%), Positives = 171/276 (61%), Gaps = 8/276 (2%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           I +    L  YI  + +IP+L  +EE+ LA RYR+  DL AA  LV SHLR VV +A GY
Sbjct: 17  IPSPLGSLDAYIGAVHQIPVLTSEEEHALAVRYRDQEDLDAARELVHSHLRFVVHVARGY 76

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGLP+ ++V EGNIGLM+AVK+FDP+ G RL ++++ WI+A M EYIL++W +VK+ T
Sbjct: 77  NGYGLPLGDLVQEGNIGLMKAVKRFDPDMGVRLVSFAVHWIRAEMHEYILKNWRIVKVAT 136

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN 187
           T  Q++LFFNLR+ K  L       +   +V A+AK LNVSE EV+ M  RL+G D   +
Sbjct: 137 TKAQRKLFFNLRKSKTRLGW-----MNAAEVTAVAKDLNVSEREVLEMESRLSGRDIGFD 191

Query: 188 ALINSSDKN-SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           A  +  D +       +L+ + +   Q     +   N+  +L   ++ L+ R R I E R
Sbjct: 192 APSDEDDDHAPPSPAAYLMANEEDPSQAYERADSDDNQLQLLREGLAELDARSRDIIERR 251

Query: 247 RLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L  ++ +TL+ L+ E+ VS ER+RQIEA A KK++
Sbjct: 252 WLDADSKITLQELADEYGVSAERIRQIEANALKKMK 287


>gi|326384438|ref|ZP_08206118.1| RNA polymerase sigma factor [Gordonia neofelifaecis NRRL B-59395]
 gi|326196783|gb|EGD53977.1| RNA polymerase sigma factor [Gordonia neofelifaecis NRRL B-59395]
          Length = 466

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 79/319 (24%), Positives = 148/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGDL- 47
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+  
Sbjct: 153 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLFATERLRRVMESGEKL 211

Query: 48  ----------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 212 SVAQRRDLSWISRDGNRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 271

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 272 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 329

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 330 REPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 381

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 382 AVVAVDAVSFTLLQDQLQDVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 441

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 442 RQIESKTMSKLRHPSRSQV 460


>gi|188535384|ref|YP_001909181.1| RNA polymerase factor sigma-32 [Erwinia tasmaniensis Et1/99]
 gi|188030426|emb|CAO98320.1| RNA polymerase sigma-32 factor [Erwinia tasmaniensis Et1/99]
          Length = 284

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 104/289 (35%), Positives = 161/289 (55%), Gaps = 8/289 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +     L  YI      PML  +EE  LA+R    GDL AA  L+ SHLR 
Sbjct: 1   MTKEMQTLAIAPLGNLDSYIRAANARPMLTAEEEKALAERLHYQGDLEAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKAKQRLGWFNQ-----DEVEMVARELGVSSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNS-SQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPR 238
           A  +         +    S      + D        IE++  ++   + L  +M  L+ R
Sbjct: 176 AAQDMTFDPAPDDEGEGRSMAPMLYLQDKSSDFANGIEEDNWEDHAADKLNDAMQGLDER 235

Query: 239 ERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + I  AR L ++   TL+ L+  + VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 SQHIIRARWLDDDNKTTLQELADRYGVSAERVRQLEKNAMKKLRVAIEA 284


>gi|312195623|ref|YP_004015684.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EuI1c]
 gi|311226959|gb|ADP79814.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EuI1c]
          Length = 418

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 80/304 (26%), Positives = 140/304 (46%), Gaps = 38/304 (12%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKR--------------------------YREHG 45
               + +Y+ +I ++ +L  +EE  LAKR                          + E  
Sbjct: 118 SHDSVRQYLSQIGRVRLLTAEEEVDLAKRVEAGLFAAEKLAAENGLVGDLRRELVWVERD 177

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
              A  RLV ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+
Sbjct: 178 GEIAKSRLVEANLRLVVSIARRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYA 237

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
            WWI+ A+   I      ++I     +      L R++  L         PE    IAK+
Sbjct: 238 TWWIRQAITRAIADQARTIRIPVHMVE--TINKLIRIQRQLLQDLGREPTPE---EIAKE 292

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           ++++  +V  +        SL   I   ++  S   D++    D    V ++       +
Sbjct: 293 MDLTPDKVREIQKVAQEPISLETPI--GEEEDSHLGDFI---EDSDAVVPVDAASFLLLQ 347

Query: 226 NMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             L   +  L+ RE+++ + R      +P TLE +  EF V+RER+RQIE++   K++  
Sbjct: 348 EQLDSVLHTLSDREKKVIQLRFGLTDGHPRTLEEVGREFGVTRERIRQIESKTLSKLRHP 407

Query: 284 IQKQ 287
            + Q
Sbjct: 408 SRSQ 411


>gi|261377878|ref|ZP_05982451.1| alternative sigma factor RpoH [Neisseria cinerea ATCC 14685]
 gi|269145731|gb|EEZ72149.1| alternative sigma factor RpoH [Neisseria cinerea ATCC 14685]
          Length = 290

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 119/289 (41%), Positives = 183/289 (63%), Gaps = 7/289 (2%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N   +  I +G   L +YIH +  IPML   EE  LA+R R+ GDL+AA +L+ SHLR+V
Sbjct: 6   NAFALPAIQSGNGSLEQYIHTVNSIPMLTLDEETHLAERQRK-GDLNAAKQLILSHLRVV 64

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+ILR+W
Sbjct: 65  VSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILRNW 124

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            LV++ TT  Q++LFFNLR ++ +L A++     P++   IA  L V  SEV+ M  R+ 
Sbjct: 125 RLVRVATTKPQRKLFFNLRSMRKNLNALS-----PKEAQEIADDLGVKLSEVLEMEQRMT 179

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           G +      NS D++S    DWL        + L ++     +   L  +++ L+ R RR
Sbjct: 180 GHDIAIMADNSDDEDSFAPIDWLADHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRR 239

Query: 242 IFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           I E+R LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 240 IVESRWLQDDGGLTLHQLAAEYGVSAERIRQIEAKAMQKLRGFLAEEAE 288


>gi|5911381|gb|AAD55771.1|AF177466_1 sigma-32 factor RpoH [Methylovorus sp. SS1]
          Length = 284

 Score =  253 bits (646), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 118/288 (40%), Positives = 174/288 (60%), Gaps = 7/288 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M        V+    L +Y+  I+  P+L  +EEY LA R R+  D+ AA  L+ SHLRL
Sbjct: 1   MTNALTIPSVSSLDSLDQYLRTIKAFPVLSVEEEYDLATRLRKGTDIEAAKGLIVSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  IA GY GYGLP ++++ EGN+GLM+AV++FDP+RG RL +++M WIKA + EYI+R+
Sbjct: 61  VASIARGYSGYGLPQADLIQEGNVGLMKAVRRFDPDRGVRLVSFAMHWIKAEIHEYIVRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W LVK+ TT  Q++LFFNLR +K        + L P +V  IA++L V   EV+ M  R+
Sbjct: 121 WRLVKVATTKAQRKLFFNLRSMKK-----NSHTLSPAEVADIARELRVKPEEVVEMESRM 175

Query: 181 AGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            G E SL    +   +++     +L        ++L E+E   N+   L  ++  L+ R 
Sbjct: 176 GGHEISLEGNSDDDTEDNFSPIAYLEDQQPEPSELLAEREAEHNQTVGLAHALESLDERS 235

Query: 240 RRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           RRI +AR LQE N  TL +L++EF VS ER+RQIE +A +K++  +  
Sbjct: 236 RRIVQARWLQENNSATLHDLAAEFGVSAERIRQIEQKAMQKMKGMLSA 283


>gi|1072021|gb|AAA81642.1| sigma factor [Mycobacterium bovis]
          Length = 528

 Score =  252 bits (645), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 79/319 (24%), Positives = 147/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------REHGDL- 47
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+  
Sbjct: 215 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSERGEKL 273

Query: 48  ----------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 274 PAAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 333

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 334 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 391

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 392 REPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 443

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 444 AVVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 503

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K+    + QV
Sbjct: 504 RQIESKTMSKLHHPSRSQV 522


>gi|332995320|gb|AEF05375.1| RNA polymerase sigma factor [Alteromonas sp. SN2]
          Length = 284

 Score =  252 bits (645), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 109/282 (38%), Positives = 167/282 (59%), Gaps = 6/282 (2%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           +++++ V     +  Y+  + +I ML  +EE  LA R RE  DL AA +LV SHLR VV 
Sbjct: 6   QSLALSVPHSGSIEGYVQAVSRIDMLTAEEERALAVRLREDEDLEAARKLVMSHLRFVVH 65

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y GYGLP ++++ EGNIGLM+AVK+FDP  G RL ++++ WIKA + E++L++W +
Sbjct: 66  IAKSYSGYGLPQADLIQEGNIGLMKAVKRFDPTVGVRLVSFAVHWIKAEIHEFVLKNWRI 125

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VK+ TT  Q++LFFNLR+ K  L   T      E+V  +A +L VS  EV+ M  R++  
Sbjct: 126 VKVATTKAQRKLFFNLRKAKKRLGWFTH-----EEVQTVASELGVSTKEVLQMEARMSSQ 180

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
           +    L    D+  +      + D     E  +I  +   N    L  ++  L+ R + I
Sbjct: 181 DQAFDLSADEDETGNFAPVQFLEDKSTDVEMDVINNDWDTNASKRLYSAIKTLDDRSQDI 240

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            E R L ++ +TL++L+ ++EVS ERVRQIE  A KK+Q ++
Sbjct: 241 IETRWLADSKITLQDLADKYEVSAERVRQIEKNAMKKLQAAM 282


>gi|238021049|ref|ZP_04601475.1| hypothetical protein GCWU000324_00946 [Kingella oralis ATCC 51147]
 gi|237868029|gb|EEP69035.1| hypothetical protein GCWU000324_00946 [Kingella oralis ATCC 51147]
          Length = 290

 Score =  252 bits (645), Expect = 3e-65,   Method: Composition-based stats.
 Identities = 122/291 (41%), Positives = 180/291 (61%), Gaps = 8/291 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           MN      + +G   L +YIH +  IPML  +EE  LA+R +  GDL AA +L+ SHLR+
Sbjct: 1   MNNAFALSVPSGHGSLEQYIHTVNSIPMLTLEEETSLAQR-QLRGDLEAAKQLILSHLRV 59

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA GY GYGL  ++++ EGN+GLM+AVK+F+P  G RL ++++ WIKA + E+ILR+
Sbjct: 60  VVSIARGYDGYGLNQADLIQEGNVGLMKAVKRFEPTHGARLFSFAVHWIKAEIHEFILRN 119

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W LV+I TT  Q++LFFNLR ++  L A++     P++   IA  L V  S+V+ M  R+
Sbjct: 120 WRLVRIATTKPQRKLFFNLRSMRKSLSALS-----PKEAQDIADDLGVKLSDVLEMEQRM 174

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            G D +L A  +  D N+    DWL  D     Q L +K     +   L  ++S L+ R 
Sbjct: 175 TGNDVALLADNSDDDDNNFAPIDWLSDDSSEPSQQLAKKAHYALQTEGLRNALSQLDERS 234

Query: 240 RRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           RRI E R LQ++  +TL  L++EF VS ER+RQIEA+A +K++  + +  +
Sbjct: 235 RRIVETRWLQDDGGLTLHELAAEFGVSAERIRQIEAKAMQKLRALLAENAD 285


>gi|120403451|ref|YP_953280.1| RNA polymerase sigma factor [Mycobacterium vanbaalenii PYR-1]
 gi|119956269|gb|ABM13274.1| RNA polymerase, sigma 70 subunit, RpoD family [Mycobacterium
           vanbaalenii PYR-1]
          Length = 478

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 79/320 (24%), Positives = 147/320 (45%), Gaps = 45/320 (14%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------------------- 42
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR                     
Sbjct: 165 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMAELADKGEKL 223

Query: 43  ------------EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
                         GD  A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV
Sbjct: 224 PAAQRRDMMWICRDGDR-AKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAV 282

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L    
Sbjct: 283 EKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDL 340

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
                PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D 
Sbjct: 341 GREPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDS 392

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRER 268
           +  V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER
Sbjct: 393 EAVVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRER 452

Query: 269 VRQIEARAFKKVQESIQKQV 288
           +RQIE++   K++   + QV
Sbjct: 453 IRQIESKTMSKLRHPSRSQV 472


>gi|116670178|ref|YP_831111.1| RNA polymerase, sigma 28 subunit [Arthrobacter sp. FB24]
 gi|116610287|gb|ABK03011.1| RNA polymerase, sigma 70 subunit, RpoD [Arthrobacter sp. FB24]
          Length = 441

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 71/304 (23%), Positives = 135/304 (44%), Gaps = 39/304 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------------HGD 46
             +  Y+ +I K+ +L  ++E  LA R                              H  
Sbjct: 142 DPVKDYLKQIGKVALLNAEQEVDLALRIEAGLFAEEKIAADDGSMDPKLKRELEFVIHDG 201

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ 
Sbjct: 202 KRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYAT 261

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +A +L
Sbjct: 262 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELALEL 316

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +V+ +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 317 DMTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 371

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 372 QLHSVLDTLSEREAGVVAMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 431

Query: 285 QKQV 288
           + QV
Sbjct: 432 RSQV 435


>gi|261210147|ref|ZP_05924444.1| RNA polymerase sigma-32 factor [Vibrio sp. RC341]
 gi|260840687|gb|EEX67236.1| RNA polymerase sigma-32 factor [Vibrio sp. RC341]
          Length = 286

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 108/289 (37%), Positives = 168/289 (58%), Gaps = 11/289 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  +   + +  +  L  YI  +   PML   EE  LA+R     D+ AA  L+ SHLR 
Sbjct: 1   MTNQAYPMALVSQDSLDSYIRSVNGYPMLTADEERELAERLHYKEDIEAAKGLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A GY GYGLP++++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VKI TT  Q++LFFNLR+ K  L    +      +V  +A++L V  SEV  M  RL
Sbjct: 121 WRIVKIATTKAQRKLFFNLRKSKKRLGWFNNG-----EVETVARELGVEPSEVREMESRL 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR----NMLTRSMSVLN 236
           A  ++   +    D+N   +   ++Y  D     L +  E +N        L+ +++ L+
Sbjct: 176 AAQDAAFEMSAEDDENGMAYTAPVLYLEDKHSD-LADNLEAENWEAHTTQRLSMALASLD 234

Query: 237 PRERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            R + I  AR L ++   TL++L+  + VS ER+RQ+E  A +K++E++
Sbjct: 235 ERSQHIVRARWLDDDNKTTLQDLAEMYGVSAERIRQLEKNAMRKLKEAV 283


>gi|303251140|ref|ZP_07337324.1| RNA polymerase factor sigma-32 [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|307253519|ref|ZP_07535389.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|302649991|gb|EFL80163.1| RNA polymerase factor sigma-32 [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
 gi|306859020|gb|EFM91063.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 6 str. Femo]
          Length = 316

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 98/273 (35%), Positives = 160/273 (58%), Gaps = 6/273 (2%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  L  YI    + P+L  ++E  LA+RY    D+ AA +L+ SH+R V+ IA GY GYG
Sbjct: 46  QGNLDSYIRMANQYPILTAEQEKELAERYYYDEDVEAAKQLILSHMRFVIHIARGYLGYG 105

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP+++++ EGNIGLM+AVK+FDP  G RL ++++ W+KA + EY+L++W +VK+ TT  Q
Sbjct: 106 LPLADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWVKAEIHEYVLKNWRIVKVATTKAQ 165

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALIN 191
           ++LFFNLR+ K  L    +     E++  +A+ L VS  EV  M  R+ G D   +  + 
Sbjct: 166 RKLFFNLRKNKNRLAWFNE-----EEIQKVAEDLGVSPEEVREMESRMTGQDLGFDLPVG 220

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             D        +L  +       L +++        L  +++ L+ R + I + R L E 
Sbjct: 221 EDDDEVYTPSMYLEDNSSNFADDLEDEQYNGQATAQLAYALATLDKRSQDIIKTRWLDEE 280

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL++L+ ++ +S ERVRQ+E  A KK++++I
Sbjct: 281 KATLQDLAEKYGISAERVRQLENAALKKIKDAI 313


>gi|307246764|ref|ZP_07528832.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|307255748|ref|ZP_07537551.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 9 str. CVJ13261]
 gi|307257933|ref|ZP_07539687.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 10 str. D13039]
 gi|307260200|ref|ZP_07541909.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 11 str. 56153]
 gi|306852339|gb|EFM84576.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 1 str. 4074]
 gi|306861308|gb|EFM93299.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 9 str. CVJ13261]
 gi|306863580|gb|EFM95509.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 10 str. D13039]
 gi|306865745|gb|EFM97624.1| RNA polymerase sigma-32 factor [Actinobacillus pleuropneumoniae
           serovar 11 str. 56153]
          Length = 316

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 98/273 (35%), Positives = 160/273 (58%), Gaps = 6/273 (2%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  L  YI    + P+L  ++E  LA+RY    D+ AA +L+ SH+R V+ IA GY GYG
Sbjct: 46  QGNLDSYIRMANQYPILTAEQEKELAERYYYDEDVEAAKQLILSHMRFVIHIARGYLGYG 105

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP+++++ EGNIGLM+AVK+FDP  G RL ++++ W+KA + EY+L++W +VK+ TT  Q
Sbjct: 106 LPLADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWVKAEIHEYVLKNWRIVKVATTKAQ 165

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALIN 191
           ++LFFNLR+ K  L    +     E++  +A+ L VS  EV  M  R+ G D   +  + 
Sbjct: 166 RKLFFNLRKNKNRLAWFNE-----EEIQKVAEDLGVSLEEVREMESRMTGQDLGFDLPVG 220

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             D        +L  +       L +++        L  +++ L+ R + I + R L E 
Sbjct: 221 EDDDEVYTPSMYLEDNSSNFADDLEDEQYNGQATAQLAYALATLDERSQDIIKTRWLDEE 280

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL++L+ ++ +S ERVRQ+E  A KK++++I
Sbjct: 281 KATLQDLAEKYGISAERVRQLENAALKKIKDAI 313


>gi|262038195|ref|ZP_06011589.1| RNA polymerase sigma factor RpoD [Leptotrichia goodfellowii F0264]
 gi|261747776|gb|EEY35221.1| RNA polymerase sigma factor RpoD [Leptotrichia goodfellowii F0264]
          Length = 393

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 80/284 (28%), Positives = 143/284 (50%), Gaps = 13/284 (4%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M+  ++ +  +  Y+ EI +IP+L  +EE   A+R  + GD  A  +L+ S+LRLVV IA
Sbjct: 114 MAESMDVDEPIKMYLREIGQIPLLSYEEEIDYAQRVLK-GDEEAKQKLIESNLRLVVSIA 172

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             +   GL + +++ EGN+GLM+AV+KF+ E+GF+ +TY+ WWI+ A+   I      ++
Sbjct: 173 KKHTNRGLKMLDLIQEGNMGLMKAVEKFEYEKGFKFSTYATWWIRQAITRAIADQGRTIR 232

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           I        +   + ++K   + I     K      ++KKL +   +V ++        S
Sbjct: 233 IPVH-----MIETINKIKKESRIILQETGKEPTAEELSKKLEIPVDKVKNILEMNQDPIS 287

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L   + S  +  S+  D++  D         +   R   +  L   +  LN RE  +   
Sbjct: 288 LETPVGS--EEDSELGDFVEDDKFLN---PYDATTRVLLKEQLDEILKTLNEREEMVLRY 342

Query: 246 RRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           R   ++    TLE +   F V+RER+RQIE +A +K++   +++
Sbjct: 343 RYGLDDGSQKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRRK 386


>gi|110803528|ref|YP_699284.1| RNA polymerase sigma factor RpoD [Clostridium perfringens SM101]
 gi|169343561|ref|ZP_02864560.1| RNA polymerase sigma factor RpoD [Clostridium perfringens C str.
           JGS1495]
 gi|170763881|ref|ZP_02634334.2| RNA polymerase sigma factor RpoD [Clostridium perfringens B str.
           ATCC 3626]
 gi|170764050|ref|ZP_02630759.2| RNA polymerase sigma factor RpoD [Clostridium perfringens E str.
           JGS1987]
 gi|170764227|ref|ZP_02638581.2| RNA polymerase sigma factor RpoD [Clostridium perfringens CPE str.
           F4969]
 gi|182420445|ref|ZP_02641259.2| RNA polymerase sigma factor RpoD [Clostridium perfringens NCTC
           8239]
 gi|182624422|ref|ZP_02952206.1| RNA polymerase sigma factor RpoD [Clostridium perfringens D str.
           JGS1721]
 gi|110684029|gb|ABG87399.1| RNA polymerase sigma factor RpoD [Clostridium perfringens SM101]
 gi|169298121|gb|EDS80211.1| RNA polymerase sigma factor RpoD [Clostridium perfringens C str.
           JGS1495]
 gi|170663661|gb|EDT16344.1| RNA polymerase sigma factor RpoD [Clostridium perfringens E str.
           JGS1987]
 gi|170713105|gb|EDT25287.1| RNA polymerase sigma factor RpoD [Clostridium perfringens B str.
           ATCC 3626]
 gi|170715649|gb|EDT27831.1| RNA polymerase sigma factor RpoD [Clostridium perfringens CPE str.
           F4969]
 gi|177910425|gb|EDT72802.1| RNA polymerase sigma factor RpoD [Clostridium perfringens D str.
           JGS1721]
 gi|182382279|gb|EDT79758.1| RNA polymerase sigma factor RpoD [Clostridium perfringens NCTC
           8239]
          Length = 366

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 78/277 (28%), Positives = 137/277 (49%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI K+P+L  ++E  LAK+  E G   A  +L  ++LRLVV IA  Y G G
Sbjct: 94  DDPVRMYLKEIGKVPLLSSEDEIELAKKI-EEGSNYAKKKLAEANLRLVVSIAKRYVGRG 152

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I     +
Sbjct: 153 MLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 212

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 L R++  L      +  PE    ++K++++   +V  +        SL   I  
Sbjct: 213 --TINKLIRIQRQLVQELGRDPLPE---ELSKQMDMPVDKVREILKIAQEPVSLETPI-- 265

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            ++  S   D++            E       +  L   +  L PRE ++   R   ++ 
Sbjct: 266 GEEEDSHLGDFIPD---DDAPAPAEAAAFTMLKEQLINVLDTLTPREEKVLRLRFGLDDG 322

Query: 253 --VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 323 RARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 359


>gi|313201748|ref|YP_004040406.1| RNA polymerase sigma-32 subunit RpoH [Methylovorus sp. MP688]
 gi|312441064|gb|ADQ85170.1| RNA polymerase, sigma 32 subunit, RpoH [Methylovorus sp. MP688]
          Length = 290

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 119/288 (41%), Positives = 175/288 (60%), Gaps = 7/288 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M        V+    L +Y+  I+  P+L  +EEY LA R R+  D+ AA  L+ SHLRL
Sbjct: 7   MTNALTIPSVSSLDSLDQYLRTIKAFPVLSAEEEYDLATRLRKDNDIDAAKGLIVSHLRL 66

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  IA GY GYGLP ++++ EGN+GLM+AV++FDP+RG RL +++M WIKA + EYI+R+
Sbjct: 67  VASIARGYSGYGLPQADLIQEGNVGLMKAVRRFDPDRGVRLVSFAMHWIKAEIHEYIVRN 126

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W LVK+ TT  Q++LFFNLR +K        + L P++V  IA++L V   EV+ M  R+
Sbjct: 127 WRLVKVATTKAQRKLFFNLRSMKK-----NSHTLSPDEVADIARELKVKPEEVVEMESRM 181

Query: 181 AGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            G E SL    +   ++S     +L        ++L E+E   N+   L  ++  L+ R 
Sbjct: 182 GGHEISLEGNSDDDSEDSFSPIAYLEDQQPEPSELLAEREAEHNQTVGLAHALESLDDRS 241

Query: 240 RRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           RRI +AR LQE N  TL +L++EF VS ER+RQIE +A +K++  +  
Sbjct: 242 RRIVQARWLQENNSATLHDLAAEFGVSAERIRQIEQKAMQKMKGMLSA 289


>gi|172087778|ref|YP_205833.2| RNA polymerase, sigma-32 (sigma-H) factor [Vibrio fischeri ES114]
 gi|197336399|ref|YP_002157235.1| alternative sigma factor RpoH [Vibrio fischeri MJ11]
 gi|171902364|gb|AAW86945.2| RNA polymerase, sigma-32 (sigma-H) factor [Vibrio fischeri ES114]
 gi|197317889|gb|ACH67336.1| alternative sigma factor RpoH [Vibrio fischeri MJ11]
          Length = 286

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 107/287 (37%), Positives = 167/287 (58%), Gaps = 8/287 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+++  S+ V  +  +  Y+  +   PML   EE  LA+R     ++ AA  L+ SHLR 
Sbjct: 1   MSKEMYSMAVVSQDSIDSYLRSVNSYPMLTVAEERELAERLHYKEEIEAAKELILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A GY GYGLP+++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARGYSGYGLPLADLIQEGNVGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L    +      +V A+AK L V+ SEV  M  RL
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKNKKRLGWFNNG-----EVEAVAKDLGVAPSEVREMEARL 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNP 237
           A  +S        D     +   + Y  D Q  V   L E        N L  +++ L+ 
Sbjct: 176 AAQDSTFEAPAEDDDRDMAFTAPVYYLEDKQSDVAYSLEEDNWEDYTNNRLANAIATLDE 235

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R + I ++R L +   TL+ L+  ++VS ER+RQ+E  A KK+++++
Sbjct: 236 RSQHIVQSRWLADEKATLQELADTYQVSAERIRQLEKNAMKKLKDAV 282


>gi|119961685|ref|YP_947521.1| RNA polymerase sigma (70) factor RpoD [Arthrobacter aurescens TC1]
 gi|119948544|gb|ABM07455.1| RNA polymerase sigma (70) factor RpoD [Arthrobacter aurescens TC1]
          Length = 437

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 71/304 (23%), Positives = 135/304 (44%), Gaps = 39/304 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------------HGD 46
             +  Y+ +I K+ +L  ++E  LA R                              H  
Sbjct: 138 DPVKDYLKQIGKVALLNAEQEVDLALRIEAGLFAEEKINADDGSMDPKLKRELEFVIHDG 197

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ 
Sbjct: 198 KRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYAT 257

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +A +L
Sbjct: 258 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELALEL 312

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +V+ +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 313 DMTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 367

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 368 QLHSVLDTLSEREAGVVAMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 427

Query: 285 QKQV 288
           + QV
Sbjct: 428 RSQV 431


>gi|332670669|ref|YP_004453677.1| RpoD subfamily RNA polymerase sigma-70 subunit [Cellulomonas fimi
           ATCC 484]
 gi|332339707|gb|AEE46290.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cellulomonas fimi
           ATCC 484]
          Length = 538

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 73/303 (24%), Positives = 139/303 (45%), Gaps = 38/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------------HGD-L 47
             +  Y+ +I K+ +L  ++E  LAKR                             GD  
Sbjct: 240 DPVKDYLKQIGKVALLNAEQEVELAKRIEAGLFAEERLNAGVAMEPKLRRELEWIAGDGR 299

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ W
Sbjct: 300 RAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATW 359

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L+
Sbjct: 360 WIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKELD 414

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++  +V+ +        SL+  +   +   S++ D +    D +  V  +       +  
Sbjct: 415 MTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQEQ 469

Query: 228 LTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L + +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   +
Sbjct: 470 LHQVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSR 529

Query: 286 KQV 288
            QV
Sbjct: 530 SQV 532


>gi|325202493|gb|ADY97947.1| alternative sigma factor RpoH [Neisseria meningitidis M01-240149]
 gi|325207756|gb|ADZ03208.1| alternative sigma factor RpoH [Neisseria meningitidis NZ-05/33]
          Length = 287

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 119/289 (41%), Positives = 183/289 (63%), Gaps = 7/289 (2%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N   +  I +G   L +YIH +  IPML ++EE  LA+R R  GDL+AA +L+ SHLR+V
Sbjct: 3   NAFALPAIQSGNGSLEQYIHTVNSIPMLSQEEETRLAER-RIKGDLNAAKQLILSHLRVV 61

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA GY GYGL  ++++ EGNIGLM+AVK++ P RG RL ++++ WIKA + E+ILR+W
Sbjct: 62  VSIARGYDGYGLNQADLIQEGNIGLMKAVKRYKPGRGARLFSFAVHWIKAEIHEFILRNW 121

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            LV++ TT  Q++LFFNLR ++ +L A++     P++   IA  L V  SEV+ M  R+ 
Sbjct: 122 RLVRVATTKPQRKLFFNLRSMRKNLNALS-----PKEAQDIADDLGVKLSEVLEMEQRMT 176

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           G +      NS D++S    DWL        + L ++     +   L  +++ L+ R RR
Sbjct: 177 GHDIAIMADNSDDEDSFAPIDWLADHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRR 236

Query: 242 IFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           I E+R LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 237 IVESRWLQDDGGLTLHQLAAEYGVSAERIRQIEAKAMQKLRGFLTEEAE 285


>gi|34763652|ref|ZP_00144580.1| RNA polymerase sigma factor rpoD [Fusobacterium nucleatum subsp.
           vincentii ATCC 49256]
 gi|237742311|ref|ZP_04572792.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. 4_1_13]
 gi|27886661|gb|EAA23826.1| RNA polymerase sigma factor rpoD [Fusobacterium nucleatum subsp.
           vincentii ATCC 49256]
 gi|229429959|gb|EEO40171.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. 4_1_13]
          Length = 340

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 80/285 (28%), Positives = 143/285 (50%), Gaps = 13/285 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           N+      +  +  Y+ EI ++P+L   EE   AK+  E GD  A+ +L+ S+LRLVV I
Sbjct: 59  NLGNSAKVDEPIKMYLREIGQVPLLTHDEEIEYAKKAYE-GDEEASKKLIESNLRLVVSI 117

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  +   GL + +++ EGNIGLM+AV+KF+  +G++ +TY+ WWI+ A+   I      +
Sbjct: 118 AKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTI 177

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I        +   + ++K   +       K      +A++L +   ++ ++        
Sbjct: 178 RIPVH-----MIETINKIKKESRIYLQETGKDASPEILAERLGMEVDKIKAIQEMNQEPI 232

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   + S  +  S+  D++    D +     E   R   R  L   +  L+PRE ++  
Sbjct: 233 SLETPVGS--EEDSELGDFV---EDQKTTSPYEATNRAILREELDAVLKTLSPREEKVLR 287

Query: 245 ARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R   ++  P TLE +   F V+RER+RQIE +A +K++   +K+
Sbjct: 288 YRYGLDDSSPKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRKK 332


>gi|257095687|ref|YP_003169328.1| RNA polymerase sigma-32 subunit RpoH [Candidatus Accumulibacter
           phosphatis clade IIA str. UW-1]
 gi|257048211|gb|ACV37399.1| RNA polymerase, sigma 32 subunit, RpoH [Candidatus Accumulibacter
           phosphatis clade IIA str. UW-1]
          Length = 286

 Score =  252 bits (645), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 121/286 (42%), Positives = 177/286 (61%), Gaps = 9/286 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M        V+    +  YI   R+ PML ++EE+ LA R+R+  DL AA +LV SHLRL
Sbjct: 1   MTHALALPTVSAVGSIDAYIQAARQFPMLTQEEEFRLATRFRDDSDLDAARQLVLSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ IA GY GYGLP ++++ EGNIGLM+AVK+FDP  G RL ++++ WIKA + EY+L++
Sbjct: 61  VISIARGYLGYGLPHADLIQEGNIGLMKAVKRFDPAHGVRLVSFAIHWIKAEIHEYVLKN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR +K + +A++     P QV  IA +L+V   EV  M  RL
Sbjct: 121 WRMVKLATTKAQRKLFFNLRSMKANSEALS-----PGQVTDIAHRLSVKPEEVSEMEARL 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLNPRE 239
            G +   AL   SD +        + DH  +   ++E   R+      L  +++ L+PR 
Sbjct: 176 TGHDL--ALDGDSDDDEVFAPISYLADHSSEPVHVLEARARERLHNEGLQGALASLDPRS 233

Query: 240 RRIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           RRI EAR L  E+P TL  L++EF VS ER+RQ+E +A +K++ S+
Sbjct: 234 RRIVEARWLTDESPATLHELAAEFGVSAERIRQVEVKAMQKMRASL 279


>gi|85058065|ref|YP_453767.1| RNA polymerase factor sigma-32 [Sodalis glossinidius str.
           'morsitans']
 gi|84778585|dbj|BAE73362.1| RNA polymerase sigma-32 factor RpoH [Sodalis glossinidius str.
           'morsitans']
          Length = 285

 Score =  252 bits (644), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 103/290 (35%), Positives = 159/290 (54%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M +    +    +  L  Y+      PML  +EE  LA+R    GDL AA +L+ SHLR 
Sbjct: 1   MIKNMQVLAYVPQGSLEAYVRAANAYPMLTAEEERALAERLHYQGDLEAAKKLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHIARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +AK+L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVEMVAKELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNP 237
           A  +         +    Q    ++Y  D        + E     +  + L+ ++  L+ 
Sbjct: 176 AAQDMTFDPTPEDEAREGQPMAPMLYLQDKSSDFADGIEEDNWDDHAADKLSAALEGLDE 235

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L ++   TL+ L+  + VS ERVRQ+E  A KK++  I+ 
Sbjct: 236 RSQDIIRARWLDDDNKSTLQELADRYGVSAERVRQLEKNAMKKMRLVIEA 285


>gi|239991260|ref|ZP_04711924.1| RNA polymerase sigma factor [Streptomyces roseosporus NRRL 11379]
          Length = 515

 Score =  252 bits (644), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 75/314 (23%), Positives = 143/314 (45%), Gaps = 40/314 (12%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------- 41
           + +++       +  Y+ +I K+P+L  ++E  LAKR                       
Sbjct: 207 QQVAVAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANADKLAPKLKR 266

Query: 42  -----REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                 E G   A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  
Sbjct: 267 ELEIIAEDG-RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYT 325

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  +         P
Sbjct: 326 KGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTP 383

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           E    +AK+L+++  +VI +        SL+  +   +   S++ D +    D +  V  
Sbjct: 384 E---ELAKELDMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPA 435

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEA 274
           +       +  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE+
Sbjct: 436 DAVSFTLLQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIES 495

Query: 275 RAFKKVQESIQKQV 288
           +   K++   + QV
Sbjct: 496 KTMSKLRHPSRSQV 509


>gi|253999699|ref|YP_003051762.1| RNA polymerase sigma-32 subunit RpoH [Methylovorus sp. SIP3-4]
 gi|253986378|gb|ACT51235.1| RNA polymerase, sigma 32 subunit, RpoH [Methylovorus sp. SIP3-4]
          Length = 284

 Score =  252 bits (644), Expect = 4e-65,   Method: Composition-based stats.
 Identities = 119/288 (41%), Positives = 175/288 (60%), Gaps = 7/288 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M        V+    L +Y+  I+  P+L  +EEY LA R R+  D+ AA  L+ SHLRL
Sbjct: 1   MTNALTIPSVSSLDSLDQYLRTIKAFPVLSAEEEYDLATRLRKDNDIDAAKGLIVSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  IA GY GYGLP ++++ EGN+GLM+AV++FDP+RG RL +++M WIKA + EYI+R+
Sbjct: 61  VASIARGYSGYGLPQADLIQEGNVGLMKAVRRFDPDRGVRLVSFAMHWIKAEIHEYIVRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W LVK+ TT  Q++LFFNLR +K        + L P++V  IA++L V   EV+ M  R+
Sbjct: 121 WRLVKVATTKAQRKLFFNLRSMKK-----NSHTLSPDEVADIARELKVKPEEVVEMESRM 175

Query: 181 AGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            G E SL    +   ++S     +L        ++L E+E   N+   L  ++  L+ R 
Sbjct: 176 GGHEISLEGNSDDDSEDSFSPIAYLEDQQPEPSELLAEREAEHNQTVGLAHALESLDDRS 235

Query: 240 RRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           RRI +AR LQE N  TL +L++EF VS ER+RQIE +A +K++  +  
Sbjct: 236 RRIVQARWLQENNSATLHDLAAEFGVSAERIRQIEQKAMQKMKGMLSA 283


>gi|326204489|ref|ZP_08194346.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           papyrosolvens DSM 2782]
 gi|325985282|gb|EGD46121.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Clostridium
           papyrosolvens DSM 2782]
          Length = 359

 Score =  252 bits (644), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 82/280 (29%), Positives = 138/280 (49%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ +  +  Y+ EI K+P+L   EE  LA R  E+GD+ A  RL  ++LRLVV IA  Y 
Sbjct: 84  ISIDDPVRMYLKEIGKVPLLSADEEIDLAHRM-ENGDIEAKRRLAEANLRLVVSIAKRYV 142

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   +++ EGN+GL++AV+KFD  RGF+ +TY+ WWI+ A+   I      ++I   
Sbjct: 143 GRGMQFLDLIQEGNLGLIKAVEKFDYRRGFKFSTYATWWIRQAITRAIADQARTIRIPVH 202

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      + +L    + +     +  Q   IAK++ +S  +V  +        SL   
Sbjct: 203 MVE-----TINKLIRVSRQLLQELGREPQPDEIAKEIGMSVDKVREIMKISQEPVSLETP 257

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   ++  S   D++            E       +  L   +  L  RE ++   R   
Sbjct: 258 I--GEEEDSHLGDFIPD---DDAPAPAEAAAFTLLKEQLIDVLDTLTAREEKVLRLRFGL 312

Query: 250 ENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 313 DDGRARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 352


>gi|297250602|ref|ZP_06934149.1| alternative sigma factor RpoH [Neisseria polysaccharea ATCC 43768]
 gi|296838520|gb|EFH22458.1| alternative sigma factor RpoH [Neisseria polysaccharea ATCC 43768]
          Length = 290

 Score =  252 bits (644), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 119/289 (41%), Positives = 184/289 (63%), Gaps = 7/289 (2%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N   +  I +G   L +YIH +  IPML ++EE  LA+R R  GDL+AA +L+ SHLR+V
Sbjct: 6   NAFALPAIQSGNGSLEQYIHTVNSIPMLSQEEETRLAER-RIKGDLNAAKQLILSHLRVV 64

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+ILR+W
Sbjct: 65  VSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILRNW 124

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            LV++ TT  Q++LFFNLR ++ +L A++     P++   IA  L V  SEV+ M  R+ 
Sbjct: 125 RLVRVATTKPQRKLFFNLRSMRKNLNALS-----PKEAQEIADDLGVKLSEVLEMEQRMT 179

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           G +      NS D++S    DWL        + L ++     +   L  +++ L+ R RR
Sbjct: 180 GHDIAIMADNSDDEDSFAPIDWLADHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRR 239

Query: 242 IFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           I E+R LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 240 IVESRWLQDDGGLTLHQLAAEYGVSAERIRQIEAKAMQKLRGFLAEEAE 288


>gi|318059566|ref|ZP_07978289.1| RNA polymerase sigma factor [Streptomyces sp. SA3_actG]
 gi|318075441|ref|ZP_07982773.1| RNA polymerase sigma factor [Streptomyces sp. SA3_actF]
          Length = 446

 Score =  252 bits (644), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 75/304 (24%), Positives = 139/304 (45%), Gaps = 40/304 (13%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------------REHGD 46
             +  Y+ +I K+P+L  ++E  LAKR                             E G 
Sbjct: 148 DPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANSDKLAPKLQRELEIIAEDG- 206

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 207 RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 266

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L
Sbjct: 267 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKEL 321

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +VI +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 322 DMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 376

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 377 QLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 436

Query: 285 QKQV 288
           + QV
Sbjct: 437 RSQV 440


>gi|182418305|ref|ZP_02949600.1| RNA polymerase sigma factor RpoD [Clostridium butyricum 5521]
 gi|237666788|ref|ZP_04526773.1| RNA polymerase sigma factor RpoD [Clostridium butyricum E4 str.
           BoNT E BL5262]
 gi|182377687|gb|EDT75231.1| RNA polymerase sigma factor RpoD [Clostridium butyricum 5521]
 gi|237657987|gb|EEP55542.1| RNA polymerase sigma factor RpoD [Clostridium butyricum E4 str.
           BoNT E BL5262]
          Length = 369

 Score =  252 bits (644), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 77/277 (27%), Positives = 137/277 (49%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI K+P+L  ++E   A++  E G+  A  +L  ++LRLVV IA  Y G G
Sbjct: 97  DDPVRMYLKEIGKVPLLSSEQEIEYAQQI-EEGNQRAKKKLAEANLRLVVSIAKRYVGRG 155

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I     +
Sbjct: 156 MLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 215

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 L R++  L      +  PE    I+K +++   +V  +        SL   I  
Sbjct: 216 --TINKLIRVQRQLLQELGRDPFPE---EISKVMDLPVDKVREIQKIAQEPVSLETPI-- 268

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            ++  S   D++      +     E       +  L   +  L PRE ++   R   ++ 
Sbjct: 269 GEEEDSHLGDFIPD---DEAPAPAEAAAFTMLKEQLINVLDTLTPREEKVLRLRFGLDDG 325

Query: 253 --VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 326 RARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 362


>gi|307546422|ref|YP_003898901.1| RNA polymerase factor sigma-32 [Halomonas elongata DSM 2581]
 gi|307218446|emb|CBV43716.1| RNA polymerase factor sigma-32 [Halomonas elongata DSM 2581]
          Length = 288

 Score =  252 bits (644), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 110/271 (40%), Positives = 160/271 (59%), Gaps = 7/271 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ YI  +  IPML   EE  LA R  + GDL AA RLV SHLR VV IA  Y GYGL  
Sbjct: 17  LNGYIQAVNGIPMLTVDEERELAFRLHDEGDLEAARRLVMSHLRFVVHIARSYSGYGLAQ 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGN+GLM+AVK+FDP +G RL ++++ WIKA + E++LR+W +VK+ TT  Q++L
Sbjct: 77  ADLIQEGNVGLMKAVKRFDPNQGVRLVSFAVHWIKAEIHEFVLRNWRIVKVATTKAQRKL 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSSD 194
           FFNLR  K  L  +  N     +V AIAK L+V    V  M  RL A D   +A     +
Sbjct: 137 FFNLRGAKKRLAWLNSN-----EVEAIAKDLDVKPEVVREMEGRLSAHDAGFDAAPGEDE 191

Query: 195 KNSSQWQDWLVYDHDGQEQV-LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           +++ Q     + D        L + +  ++    L  ++S L+ R R I + R L ++  
Sbjct: 192 ESAYQAPVHYLDDASQDPATQLEDSDWEEDSTQRLQAALSELDERSRDILQRRWLSDDKS 251

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           TL +L+  + VS ER+RQ+E  A KK+++SI
Sbjct: 252 TLHDLADVYGVSAERIRQLEKNAMKKIRQSI 282


>gi|238924709|ref|YP_002938225.1| RNA polymerase sigma factor RpoD [Eubacterium rectale ATCC 33656]
 gi|238876384|gb|ACR76091.1| RNA polymerase sigma factor RpoD [Eubacterium rectale ATCC 33656]
          Length = 434

 Score =  252 bits (644), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 83/316 (26%), Positives = 135/316 (42%), Gaps = 49/316 (15%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------------- 43
           V+ E  +  Y+ EI K+P+L   EE  LA+   +                          
Sbjct: 121 VSVEDPVRMYLKEIGKVPLLSADEEIELAQNMEDGAVATEKINVLKGRIDGASEEEKAEI 180

Query: 44  -----------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  RL  ++LRLVV IA  Y G G+   +++ EGN+GL++AV+K
Sbjct: 181 KEEIKTLQRDVDKGADAKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEK 240

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD ++G++ +TY+ WWI+ A+   I      ++I     +      L R+   L      
Sbjct: 241 FDYKKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE--TINKLIRVSRQLLQELGR 298

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE    IAK++N+    V  +        SL   I   ++  S   D++  D     
Sbjct: 299 EPSPE---EIAKEMNMPVERVREILKISQEPVSLETPI--GEEEDSHLGDFIKDD---NV 350

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
            V  +       +  L   +  L  RE+++   R   E+    TLE +  EF V+RER+R
Sbjct: 351 PVPADAAAFTLLKEQLEEVLGTLTEREQKVLTLRFGLEDGRARTLEEVGKEFNVTRERIR 410

Query: 271 QIEARAFKKVQESIQK 286
           QIEA+A +K++   + 
Sbjct: 411 QIEAKALRKLRHPSRS 426


>gi|332653408|ref|ZP_08419153.1| RNA polymerase sigma factor RpoD [Ruminococcaceae bacterium D16]
 gi|332518554|gb|EGJ48157.1| RNA polymerase sigma factor RpoD [Ruminococcaceae bacterium D16]
          Length = 446

 Score =  252 bits (644), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 81/319 (25%), Positives = 143/319 (44%), Gaps = 42/319 (13%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------REHGDL 47
           ++  +M      +  +  Y+ EI K+ +L   EE  LA+               +E G+ 
Sbjct: 131 VDPNSMVDSFGTDDPVRMYLKEIGKVNLLSSDEEIELAQAMGAGAEAKEQLAELQESGEE 190

Query: 48  -----------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
                             A  RL  ++LRLVV IA  Y G G+   +++ EGN+GL++AV
Sbjct: 191 IPAEVLAELNKAIKRGERAKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNLGLIKAV 250

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +KFD  +G++ +TY+ WWI+ A+   I      ++I     +      + R+   L    
Sbjct: 251 EKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE--TINKVIRVSRQLLQEL 308

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
            ++  PE    IA+++++    V  +        SL   I   ++  S   D++  +   
Sbjct: 309 GHDPSPE---EIAEEMSMPVERVREILKIAQEPVSLETPI--GEEEDSHLGDFIPDEDAS 363

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRER 268
           +     E       +  L   +S L PRE ++ + R   E+    TLE +  EF V+RER
Sbjct: 364 E---PAEAASFTLLKEQLVEVLSTLTPREEKVLKLRFGIEDGRTRTLEEVGKEFNVTRER 420

Query: 269 VRQIEARAFKKVQESIQKQ 287
           +RQIEA+A +K++   + +
Sbjct: 421 IRQIEAKALRKLRHPSRSK 439


>gi|254490572|ref|ZP_05103758.1| alternative sigma factor RpoH [Methylophaga thiooxidans DMS010]
 gi|224464316|gb|EEF80579.1| alternative sigma factor RpoH [Methylophaga thiooxydans DMS010]
          Length = 287

 Score =  252 bits (644), Expect = 5e-65,   Method: Composition-based stats.
 Identities = 112/289 (38%), Positives = 177/289 (61%), Gaps = 12/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           + +  M++   G   L  Y   +  IP+L  +EEY LA R ++ GDL AA RLV SHLR 
Sbjct: 5   VAKYEMALAPIG--NLDAYTSLVHTIPVLTAEEEYDLATRLQQDGDLEAAQRLVLSHLRF 62

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV+IA GY GYGLP+++++ EGNIGLM+AVK+F+PE+G RL ++++ W++A + EY++R+
Sbjct: 63  VVRIAKGYSGYGLPVADLIQEGNIGLMKAVKRFNPEKGVRLVSFAVHWVRAEIHEYVIRN 122

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VKI TT  Q++LFFNLR  K  L  +       E+V A+A+ L V+ + V+ M  RL
Sbjct: 123 WRIVKIATTKAQRKLFFNLRSAKQRLGWLNQ-----EEVEAVAEDLGVTPANVMDMERRL 177

Query: 181 AG-DESLNALINSSDKNSSQ--WQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLN 236
           A  D S +   +S+D   +      +L    +      +E+E   + +   LT +++ L+
Sbjct: 178 AQPDASFDLPADSNDDEETHFSPVAYLAGPENSDPSQQLEQENYSDYQQQKLTNALATLD 237

Query: 237 PRERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            R R I   R L +++  TL  L+ +++VS ER+RQIE  A KK+++ +
Sbjct: 238 DRSRDIIMQRWLNEDDKATLHTLADQYQVSAERIRQIENNAMKKLKKMM 286


>gi|262273588|ref|ZP_06051402.1| RNA polymerase sigma-32 factor [Grimontia hollisae CIP 101886]
 gi|262222566|gb|EEY73877.1| RNA polymerase sigma-32 factor [Grimontia hollisae CIP 101886]
          Length = 287

 Score =  252 bits (643), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 109/288 (37%), Positives = 170/288 (59%), Gaps = 9/288 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  +  ++    +  L  Y+ ++   PML   EE  LA+R     DL AA  L+ SHLR 
Sbjct: 1   MTAEMYALAPISQDSLDSYLQQVNSYPMLTADEERELAERLHYEEDLDAAKSLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA GY GYGLPIS++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHIARGYSGYGLPISDLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          E+V  +A++L V  +EV  M  RL
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKSKKRLGWFN-----AEEVNMVAEQLGVDAAEVREMESRL 175

Query: 181 -AGDESLNALINSSD-KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN-MLTRSMSVLNP 237
            A D   +A +   + +  +    + + D        +E +  ++  N  L ++MS L+ 
Sbjct: 176 AAQDAGFDAGVGDDEREGGAVAPVFYLEDKSSDIATNLESQNWEDHTNRRLAQAMSGLDA 235

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R + I  +R L ++  VTL+ L+  ++VS ER+RQ+E  A +K+++++
Sbjct: 236 RSQHIIRSRWLDDDNKVTLQELADHYQVSAERIRQLEKNAMRKLKDAV 283


>gi|291619275|ref|YP_003522017.1| RpoH [Pantoea ananatis LMG 20103]
 gi|291154305|gb|ADD78889.1| RpoH [Pantoea ananatis LMG 20103]
 gi|327395604|dbj|BAK13026.1| RNA polymerase sigma-32 factor RpoH [Pantoea ananatis AJ13355]
          Length = 285

 Score =  252 bits (643), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 105/290 (36%), Positives = 162/290 (55%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +     L  Y+      PML  +EE  LA+R    GDL AA  L+ SHLR 
Sbjct: 1   MTKEMQTLAIAPLGNLESYVRAANTWPMLSAEEEKALAERLHYQGDLDAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHIARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVEMVARELGVSSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNP 237
           A  +    +    +    +    ++Y  D        + E     +  + LT +M  L+ 
Sbjct: 176 AAQDMTFDMSADDESGEGKSMAPVLYLQDKTSDFADGIEEDNWESHAADKLTYAMEGLDE 235

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L E+   TL+ L+  + VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQHIIRARWLDEDNKTTLQELADRYGVSAERVRQLEKNAMKKLRMAIEA 285


>gi|1582791|prf||2119302A sigma factor
          Length = 445

 Score =  252 bits (643), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 75/314 (23%), Positives = 143/314 (45%), Gaps = 40/314 (12%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------- 41
           + +++       +  Y+ +I K+P+L  ++E  LAKR                       
Sbjct: 137 QQVAVAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANADKLAPKLKR 196

Query: 42  -----REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                 E G   A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  
Sbjct: 197 ELEIIAEDG-RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYT 255

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  +         P
Sbjct: 256 KGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTP 313

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           E    +AK+L+++  +VI +        SL+  +   +   S++ D +    D +  V  
Sbjct: 314 E---ELAKELDMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPA 365

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEA 274
           +       +  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE+
Sbjct: 366 DAVSFTLLQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIES 425

Query: 275 RAFKKVQESIQKQV 288
           +   K++   + QV
Sbjct: 426 KTMSKLRHPSRSQV 439


>gi|333024008|ref|ZP_08452072.1| putative RNA polymerase sigma factor RpoS [Streptomyces sp. Tu6071]
 gi|332743860|gb|EGJ74301.1| putative RNA polymerase sigma factor RpoS [Streptomyces sp. Tu6071]
          Length = 493

 Score =  252 bits (643), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 75/304 (24%), Positives = 139/304 (45%), Gaps = 40/304 (13%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------------REHGD 46
             +  Y+ +I K+P+L  ++E  LAKR                             E G 
Sbjct: 195 DPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANSDKLAPKLQRELEIIAEDG- 253

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 254 RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 313

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L
Sbjct: 314 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKEL 368

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +VI +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 369 DMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 423

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 424 QLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 483

Query: 285 QKQV 288
           + QV
Sbjct: 484 RSQV 487


>gi|304387988|ref|ZP_07370160.1| DNA-directed RNA polymerase sigma subunit RpoH [Neisseria
           meningitidis ATCC 13091]
 gi|304337987|gb|EFM04125.1| DNA-directed RNA polymerase sigma subunit RpoH [Neisseria
           meningitidis ATCC 13091]
          Length = 290

 Score =  252 bits (643), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 119/289 (41%), Positives = 184/289 (63%), Gaps = 7/289 (2%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N   +  I +G   L +YIH +  IPML ++EE  LA+R R  GDL+AA +L+ SHLR+V
Sbjct: 6   NAFALPAIQSGNGSLEQYIHTVNSIPMLSQEEETRLAER-RIKGDLNAAKQLILSHLRVV 64

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+ILR+W
Sbjct: 65  VSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILRNW 124

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            LV++ TT  Q++LFFNLR ++ +L A++     P++   IA  L V  SEV+ M  R+ 
Sbjct: 125 RLVRVATTKPQRKLFFNLRSMRKNLNALS-----PKEAQDIADDLGVKLSEVLEMEQRMT 179

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           G +      NS D++S    DWL        + L ++     +   L  +++ L+ R RR
Sbjct: 180 GHDIAIMADNSDDEDSFAPIDWLADHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRR 239

Query: 242 IFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           I E+R LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 240 IVESRWLQDDGGLTLHQLAAEYGVSAERIRQIEAKAMQKLRGFLTEKAE 288


>gi|294631847|ref|ZP_06710407.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. e14]
 gi|292835180|gb|EFF93529.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. e14]
          Length = 515

 Score =  252 bits (643), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 75/304 (24%), Positives = 139/304 (45%), Gaps = 40/304 (13%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------------REHGD 46
             +  Y+ +I K+P+L  ++E  LAKR                             E G 
Sbjct: 217 DPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANSDKLAPKLKRELEIIAEDG- 275

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 276 RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 335

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L
Sbjct: 336 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKEL 390

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +VI +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 391 DMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 445

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 446 QLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 505

Query: 285 QKQV 288
           + QV
Sbjct: 506 RSQV 509


>gi|297562250|ref|YP_003681224.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
 gi|296846698|gb|ADH68718.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
          Length = 571

 Score =  252 bits (643), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 74/304 (24%), Positives = 137/304 (45%), Gaps = 39/304 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYR------------------EHGDL-------- 47
             +  Y+ +I K+P+L  ++E  LAKR                    E  D         
Sbjct: 272 DPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEEKLAEEAELLTVELRDELEWIAEDG 331

Query: 48  -SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ 
Sbjct: 332 GRAKKHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYAT 391

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +A++L
Sbjct: 392 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAREL 446

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +V+ +        SL+  +   +   S++ D +    D +     E       + 
Sbjct: 447 DMTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAIQPGEAVSFTLLQE 501

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 502 QLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 561

Query: 285 QKQV 288
           + QV
Sbjct: 562 RSQV 565


>gi|319778863|ref|YP_004129776.1| RNA polymerase sigma factor RpoH [Taylorella equigenitalis MCE9]
 gi|317108887|gb|ADU91633.1| RNA polymerase sigma factor RpoH [Taylorella equigenitalis MCE9]
          Length = 292

 Score =  252 bits (643), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 114/288 (39%), Positives = 173/288 (60%), Gaps = 6/288 (2%)

Query: 2   NRKNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
             K+M +I    +G +  YI E+ +IP+L  ++E   A+R ++ GDL AA  L+  HLRL
Sbjct: 10  THKSMDLINPSALGTIEAYIQEVNRIPILTAEQERDYAERLQKSGDLKAAQALILPHLRL 69

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y GYGLP ++++ EGNIGLM+AVK+FD  RG RL T++M WIKA + EY++R+
Sbjct: 70  VVSVARQYLGYGLPHADLIQEGNIGLMKAVKRFDVSRGVRLVTFAMHWIKAEIHEYVIRN 129

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W LVKI TT  Q++LFFNL  L+         +L  + +V IAKKLNV   +V+ M  R+
Sbjct: 130 WRLVKIATTKAQRKLFFNLNSLRPE-----GKSLDNDDIVGIAKKLNVRPEDVVEMEKRM 184

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +G +     +   D + +  Q     +    E V++ +E  K     L  ++  L+ R R
Sbjct: 185 SGHDIALDTLMDEDDDYAPIQYLADDEAYEPENVMLAQEHDKLENQGLKSALDQLDDRSR 244

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            I E+R L E+  TL +L++++ VS ER+RQIE  A KK++  ++  V
Sbjct: 245 HIIESRWLSEDKPTLHDLAAQYNVSAERIRQIENAAIKKMRSYLEDYV 292


>gi|121634509|ref|YP_974754.1| RNA polymerase factor sigma-32 [Neisseria meningitidis FAM18]
 gi|218767834|ref|YP_002342346.1| RNA polymerase factor sigma-32 [Neisseria meningitidis Z2491]
 gi|120866215|emb|CAM09955.1| putative RNA polymerase sigma-32 factor [Neisseria meningitidis
           FAM18]
 gi|121051842|emb|CAM08148.1| putative RNA polymerase sigma-32 factor [Neisseria meningitidis
           Z2491]
 gi|261392916|emb|CAX50501.1| RNA polymerase sigma factor RpoH (Sigma-32) [Neisseria meningitidis
           8013]
          Length = 290

 Score =  252 bits (643), Expect = 6e-65,   Method: Composition-based stats.
 Identities = 119/289 (41%), Positives = 184/289 (63%), Gaps = 7/289 (2%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N   +  I +G   L +YIH +  IPML ++EE  LA+R R  GDL+AA +L+ SHLR+V
Sbjct: 6   NAFALPAIQSGNGSLEQYIHTVNSIPMLSQEEETRLAER-RIKGDLNAAKQLILSHLRVV 64

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+ILR+W
Sbjct: 65  VSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILRNW 124

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            LV++ TT  Q++LFFNLR ++ +L A++     P++   IA  L V  SEV+ M  R+ 
Sbjct: 125 RLVRVATTKPQRKLFFNLRSMRKNLNALS-----PKEAQDIADDLGVKLSEVLEMEQRMT 179

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           G +      NS D++S    DWL        + L ++     +   L  +++ L+ R RR
Sbjct: 180 GHDIAIMADNSDDEDSFAPIDWLADHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRR 239

Query: 242 IFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           I E+R LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 240 IVESRWLQDDGGLTLHQLAAEYGVSAERIRQIEAKAMQKLRGFLTEEAE 288


>gi|283457795|ref|YP_003362387.1| DNA-directed RNA polymerase, sigma subunit [Rothia mucilaginosa
           DY-18]
 gi|283133802|dbj|BAI64567.1| DNA-directed RNA polymerase, sigma subunit [Rothia mucilaginosa
           DY-18]
          Length = 460

 Score =  252 bits (643), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 74/303 (24%), Positives = 136/303 (44%), Gaps = 38/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE--------------------------HGDL 47
             +  Y+ +I K+ +L  Q+E  LAKR                             H   
Sbjct: 162 DPVKDYLKQIGKVSLLNAQQEVDLAKRIEAGLYAEHKLAENPDMDKDLKKALRWVVHDGK 221

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ W
Sbjct: 222 RAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYSKGFKFSTYATW 281

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   +      ++I     +  +   L R++  +         PE    + K+L+
Sbjct: 282 WIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELGKELD 336

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++  +VI +        SL+  +   +   S++ D +    D +  V  +       +  
Sbjct: 337 MTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQEQ 391

Query: 228 LTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   +
Sbjct: 392 LHSVLDTLSEREAGVVAMRFGMTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSR 451

Query: 286 KQV 288
            QV
Sbjct: 452 SQV 454


>gi|169351085|ref|ZP_02868023.1| hypothetical protein CLOSPI_01864 [Clostridium spiroforme DSM 1552]
 gi|169292147|gb|EDS74280.1| hypothetical protein CLOSPI_01864 [Clostridium spiroforme DSM 1552]
          Length = 415

 Score =  252 bits (643), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 78/289 (26%), Positives = 137/289 (47%), Gaps = 12/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M++  +   V     +  Y+ EI ++ +L   +E  LAK+  E GD +A   L  ++LRL
Sbjct: 129 MDKNQLGSNVKINDPVKMYLKEIGRVELLSHDDEIKLAKKILE-GDEAAKKELAAANLRL 187

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 188 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYTKGFKFSTYATWWIRQAITRAIADQ 247

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L          E++        ++  +V  +    
Sbjct: 248 ARTIRIPVHMVE--TINKLTRIQRLLIQELGREPTAEEIAERID--GMTPEKVREIQKIS 303

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++  +           E  K+    L   +  L  RE 
Sbjct: 304 LEPVSLETPI--GEEDDSHLGDFIEDEGVMSPDDYAANELLKDE---LNEVLLELTDREE 358

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++   R   ++    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 359 KVLRLRFGLDDGRTRTLEEVGKEFSVTRERIRQIEAKALRKLKHPSRSK 407


>gi|182435494|ref|YP_001823213.1| RNA polymerase sigma factor [Streptomyces griseus subsp. griseus
           NBRC 13350]
 gi|326776131|ref|ZP_08235396.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces cf.
           griseus XylebKG-1]
 gi|11132962|sp|P77951|HRDB_STRGR RecName: Full=RNA polymerase principal sigma factor hrdB
 gi|1617256|gb|AAB16905.1| principal sigma factor [Streptomyces griseus]
 gi|178464010|dbj|BAG18530.1| RNA polymerase principal sigma factor hrdB [Streptomyces griseus
           subsp. griseus NBRC 13350]
 gi|326656464|gb|EGE41310.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces cf.
           griseus XylebKG-1]
          Length = 514

 Score =  252 bits (643), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 75/314 (23%), Positives = 143/314 (45%), Gaps = 40/314 (12%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------- 41
           + +++       +  Y+ +I K+P+L  ++E  LAKR                       
Sbjct: 206 QQVAVAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANADKLAPKLKR 265

Query: 42  -----REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                 E G   A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  
Sbjct: 266 ELEIIAEDG-RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYT 324

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  +         P
Sbjct: 325 KGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTP 382

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           E    +AK+L+++  +VI +        SL+  +   +   S++ D +    D +  V  
Sbjct: 383 E---ELAKELDMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPA 434

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEA 274
           +       +  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE+
Sbjct: 435 DAVSFTLLQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIES 494

Query: 275 RAFKKVQESIQKQV 288
           +   K++   + QV
Sbjct: 495 KTMSKLRHPSRSQV 508


>gi|254804595|ref|YP_003082816.1| RNA polymerase sigma subunit [Neisseria meningitidis alpha14]
 gi|254668137|emb|CBA04749.1| RNA polymerase sigma subunit [Neisseria meningitidis alpha14]
 gi|254669711|emb|CBA03845.1| RNA polymerase sigma-32 factor [Neisseria meningitidis alpha153]
 gi|308388900|gb|ADO31220.1| putative RNA polymerase sigma-32 factor [Neisseria meningitidis
           alpha710]
 gi|319410084|emb|CBY90418.1| RNA polymerase sigma factor RpoH (Sigma-32) [Neisseria meningitidis
           WUE 2594]
 gi|325127782|gb|EGC50690.1| alternative sigma factor RpoH [Neisseria meningitidis N1568]
 gi|325129864|gb|EGC52669.1| alternative sigma factor RpoH [Neisseria meningitidis OX99.30304]
 gi|325131835|gb|EGC54535.1| alternative sigma factor RpoH [Neisseria meningitidis M6190]
 gi|325133774|gb|EGC56430.1| alternative sigma factor RpoH [Neisseria meningitidis M13399]
 gi|325136066|gb|EGC58676.1| alternative sigma factor RpoH [Neisseria meningitidis M0579]
 gi|325137885|gb|EGC60460.1| alternative sigma factor RpoH [Neisseria meningitidis ES14902]
 gi|325141969|gb|EGC64407.1| alternative sigma factor RpoH [Neisseria meningitidis 961-5945]
 gi|325144085|gb|EGC66393.1| alternative sigma factor RpoH [Neisseria meningitidis M01-240013]
 gi|325197931|gb|ADY93387.1| alternative sigma factor RpoH [Neisseria meningitidis G2136]
 gi|325203799|gb|ADY99252.1| alternative sigma factor RpoH [Neisseria meningitidis M01-240355]
 gi|325206445|gb|ADZ01898.1| alternative sigma factor RpoH [Neisseria meningitidis M04-240196]
          Length = 287

 Score =  252 bits (643), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 119/289 (41%), Positives = 184/289 (63%), Gaps = 7/289 (2%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N   +  I +G   L +YIH +  IPML ++EE  LA+R R  GDL+AA +L+ SHLR+V
Sbjct: 3   NAFALPAIQSGNGSLEQYIHTVNSIPMLSQEEETRLAER-RIKGDLNAAKQLILSHLRVV 61

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+ILR+W
Sbjct: 62  VSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILRNW 121

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            LV++ TT  Q++LFFNLR ++ +L A++     P++   IA  L V  SEV+ M  R+ 
Sbjct: 122 RLVRVATTKPQRKLFFNLRSMRKNLNALS-----PKEAQDIADDLGVKLSEVLEMEQRMT 176

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           G +      NS D++S    DWL        + L ++     +   L  +++ L+ R RR
Sbjct: 177 GHDIAIMADNSDDEDSFAPIDWLADHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRR 236

Query: 242 IFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           I E+R LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 237 IVESRWLQDDGGLTLHQLAAEYGVSAERIRQIEAKAMQKLRGFLTEEAE 285


>gi|317495391|ref|ZP_07953760.1| RNA polymerase sigma factor RpoD [Gemella moribillum M424]
 gi|316914450|gb|EFV35927.1| RNA polymerase sigma factor RpoD [Gemella moribillum M424]
          Length = 361

 Score =  252 bits (643), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 84/281 (29%), Positives = 137/281 (48%), Gaps = 15/281 (5%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR---EHGDLSAAHRLVTSHLRLVVKIAM 66
           +     +  Y+ EI K+P+L K++E  L+K      E     A   L  ++LRLVV IA 
Sbjct: 82  IRTNDPVRMYLKEIGKVPLLSKEKELELSKIIESGTESEKEQAKKDLAEANLRLVVSIAK 141

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I
Sbjct: 142 RYVGRGMLFLDLIQEGNMGLIKAVEKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRI 201

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
                +      L R++  L        KPE    IAKK+N++  +V  +        SL
Sbjct: 202 PVHMVE--TINRLIRVQRQLLQDLGREPKPE---EIAKKMNMTPDKVREILKIAQEPVSL 256

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              I   +++ S   D++    D   Q  +E    +  +  L   +  L  RE  + + R
Sbjct: 257 ETPI--GEEDDSHLGDFI---EDKDAQSPVEHAANELLKEQLEEILETLTDREENVLKLR 311

Query: 247 RL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
                    TLE + S F V+RER+RQIEA+A +K++   +
Sbjct: 312 FGLKDGKTHTLEEVGSAFGVTRERIRQIEAKAIRKLKHPSK 352


>gi|311742667|ref|ZP_07716476.1| DNA-directed RNA polymerase sigma subunit RpoD [Aeromicrobium
           marinum DSM 15272]
 gi|311314295|gb|EFQ84203.1| DNA-directed RNA polymerase sigma subunit RpoD [Aeromicrobium
           marinum DSM 15272]
          Length = 464

 Score =  252 bits (643), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 75/303 (24%), Positives = 138/303 (45%), Gaps = 38/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY--------------------REHGD------L 47
             +  Y+ +I K+ +L   EE  LAKR                     RE  D       
Sbjct: 166 DPVKDYLKQIGKVSLLTAGEEVELAKRIEAGLFAEEKLAKGGRISPKMREELDWIVVDGR 225

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ W
Sbjct: 226 RAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATW 285

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   +      ++I     +  +   L R++  +         P+    +AK+L+
Sbjct: 286 WIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPD---ELAKELD 340

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++  +V+ +        SL+  +   +   S++ D +    D +  V  +       +  
Sbjct: 341 MTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAIVPADAVSFTLLQEQ 395

Query: 228 LTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   +
Sbjct: 396 LHAVLDTLSERESGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSR 455

Query: 286 KQV 288
            QV
Sbjct: 456 SQV 458


>gi|257068601|ref|YP_003154856.1| RNA polymerase, sigma 70 subunit, RpoD [Brachybacterium faecium DSM
           4810]
 gi|256559419|gb|ACU85266.1| RNA polymerase, sigma 70 subunit, RpoD [Brachybacterium faecium DSM
           4810]
          Length = 433

 Score =  252 bits (643), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 73/309 (23%), Positives = 140/309 (45%), Gaps = 44/309 (14%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY--------REHGD------------------- 46
             +  Y+ +I K+ +L   +E  LA+R         +  GD                   
Sbjct: 129 DPVKDYLKQIGKVALLNAAQEVELAERIEAGLYAEQKLKGDDSFRDKNGRLTKAGRELTM 188

Query: 47  -----LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
                 +A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ 
Sbjct: 189 IADDGRAAKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYAKGYKF 248

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY+ WWI+ A+   +      ++I     +  +   L R++  +         PE    
Sbjct: 249 STYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---E 303

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           +AK+L+++  +V+ +        SL+  +   +   S++ D +    D +  V  +    
Sbjct: 304 LAKELDMTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSF 358

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKK 279
              +  L   +  L+ RE  +   R   E+  P TL+ +   + V+RER+RQIE++   K
Sbjct: 359 TLLQEQLHSVLDTLSEREAGVVSMRFGLEDGQPKTLDEIGKVYGVTRERIRQIESKTMSK 418

Query: 280 VQESIQKQV 288
           ++   + QV
Sbjct: 419 LRHPSRSQV 427


>gi|326563747|gb|EGE13998.1| RNA polymerase factor sigma-32 [Moraxella catarrhalis 46P47B1]
          Length = 371

 Score =  252 bits (643), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 107/272 (39%), Positives = 159/272 (58%), Gaps = 7/272 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + L  YI+ + +IP+L  +EE  LA+RY   GD+ AA  LV SHLR V+ IA  Y GYGL
Sbjct: 97  VNLGAYINTVHQIPILTPEEERALAERYYHDGDVEAARLLVMSHLRFVIHIARSYSGYGL 156

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
             ++++ EGN+GLM+AVK+FDP +G RL ++++ WIKA + E+++++W +VK+ TT   +
Sbjct: 157 SQADLIQEGNLGLMKAVKRFDPNKGVRLVSFAVHWIKAEIHEFVIKNWRIVKVATTKAHR 216

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINS 192
           +LFFNLR LK      + N L  ++  AIA  LNV+  +V+ M  RL   D S  A   S
Sbjct: 217 KLFFNLRSLKK-----SSNQLTLDEATAIANDLNVTVKQVLEMESRLTSYDASFEAQD-S 270

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            D          + D      V+ E +  +N    L  +M +L+ R R I   R L +  
Sbjct: 271 DDDEGRYAPQLFLEDAVNPADVVEEADWEENTTTALKDAMEILDERSRDIITQRWLADQK 330

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL  L++ + +S ERVRQIE  A  K++E+I
Sbjct: 331 STLHELAATYNISAERVRQIEKNAMNKIKEAI 362


>gi|71064787|ref|YP_263514.1| RNA polymerase factor sigma-32 [Psychrobacter arcticus 273-4]
 gi|71037772|gb|AAZ18080.1| putative Sigma 32 (RpoH) [Psychrobacter arcticus 273-4]
          Length = 341

 Score =  252 bits (643), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 110/272 (40%), Positives = 164/272 (60%), Gaps = 7/272 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + L  YI+ + +IP+L   +E  LA RY + GD+ AA  LV SHLR V+ IA  Y GYGL
Sbjct: 64  VNLGAYINTVHQIPILTPTQEQELAHRYYDEGDVEAARLLVMSHLRFVIHIARSYSGYGL 123

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P ++++ EGN+GLM+AVK+FDP +G RL ++++ WIKA + E+++R+W +VK+ TT   +
Sbjct: 124 PQADLIQEGNLGLMKAVKRFDPNKGVRLVSFAVHWIKAEIHEFVIRNWRIVKVATTKAHR 183

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINS 192
           +LFFNLR LK      T+N L  E+  AIA  LNV+  +V+ M  RL   D S  A  +S
Sbjct: 184 KLFFNLRSLKK-----TNNQLTIEEADAIANDLNVTRKQVLEMESRLTSYDASFEAQ-SS 237

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            D +        + D     +++ E +  +N  + L  +M  L+ R R I E R L E  
Sbjct: 238 DDDDGRYAPQLFLEDGIDPAEIVEESDWEENNSSALIAAMETLDDRSRDIVEQRWLSEQK 297

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL  L++ + +S ERVRQIE  A  K++E++
Sbjct: 298 STLHELAAVYSISAERVRQIEKNAMDKIREAM 329


>gi|239817346|ref|YP_002946256.1| RNA polymerase, sigma 32 subunit, RpoH [Variovorax paradoxus S110]
 gi|239803923|gb|ACS20990.1| RNA polymerase, sigma 32 subunit, RpoH [Variovorax paradoxus S110]
          Length = 313

 Score =  252 bits (643), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 113/290 (38%), Positives = 171/290 (58%), Gaps = 14/290 (4%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +V     L  YI    ++PML  +EE   A+R R+H DL AA  L+ SHLRLVV I+  Y
Sbjct: 20  MVPPLGNLDAYISAANRLPMLTLEEEQGFARRLRDHNDLEAAGALILSHLRLVVSISRQY 79

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGLP  +++ EGN+GLM+AVK+FDP++G RL +Y+M WIKA + EYIL++W +VK+ T
Sbjct: 80  LGYGLPHGDLIQEGNVGLMKAVKRFDPDQGVRLVSYAMHWIKAEIHEYILKNWRMVKVAT 139

Query: 129 TANQKRLFFNLRRLKGHLQA--------ITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           T  Q++LFFNLR +K   +A           + L P++V  +A +LNV   EV+ M  RL
Sbjct: 140 TKAQRKLFFNLRSMKQGFKADSAAADNGTHRDTLSPDEVSQMATRLNVKPEEVLEMETRL 199

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLNPRE 239
           +G + L     S D + +      + D   +   L+E ++R     + +  ++  L+ R 
Sbjct: 200 SGGDVLLDPGPSDDGDEAFGPIAYLADATQEPTALLESQQRDRLSSDGIATALEALDDRS 259

Query: 240 RRIFEARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           RRI E R L         +TL +L++ + VS ER+RQIE  A KK+++++
Sbjct: 260 RRIVEERWLKVNDDGSGGMTLHDLAAVYGVSAERIRQIEVAAMKKMKKAL 309


>gi|169630092|ref|YP_001703741.1| RNA polymerase sigma factor [Mycobacterium abscessus ATCC 19977]
 gi|169242059|emb|CAM63087.1| Probable RNA polymerase sigma factor RpoD (Sigma-A) [Mycobacterium
           abscessus]
          Length = 467

 Score =  251 bits (642), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 79/319 (24%), Positives = 148/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGDL- 47
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+  
Sbjct: 154 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQIVTELTEKGEKL 212

Query: 48  ----------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 213 PAAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 272

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 273 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 330

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 331 REPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 382

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 383 AVVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 442

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 443 RQIESKTMSKLRHPSRSQV 461


>gi|332308280|ref|YP_004436131.1| RNA polymerase, sigma 32 subunit, RpoH [Glaciecola agarilytica
           4H-3-7+YE-5]
 gi|332175609|gb|AEE24863.1| RNA polymerase, sigma 32 subunit, RpoH [Glaciecola agarilytica
           4H-3-7+YE-5]
          Length = 283

 Score =  251 bits (642), Expect = 7e-65,   Method: Composition-based stats.
 Identities = 103/284 (36%), Positives = 165/284 (58%), Gaps = 6/284 (2%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           + + +++ V     +  Y+  +  I ML  +EE  LA+R ++  DL AA +L+ SHLR V
Sbjct: 4   DMRALTLTVPQTGSIETYVQAVSSIDMLSAEEEKGLAERLQQEDDLLAARKLIMSHLRFV 63

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA  Y GYGLP ++++ EGNIGLM+AV++FDP  G RL ++++ WIKA + E++LR+W
Sbjct: 64  VHIAKSYSGYGLPQADLIQEGNIGLMKAVRRFDPTVGVRLVSFAVHWIKAEIHEFVLRNW 123

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            +VK+ TT  Q++LFFNLR+ K  L   T       +V  +A  L VSE EV+ M  R++
Sbjct: 124 RIVKVATTKAQRKLFFNLRKNKKRLGWFTH-----AEVQKVASDLGVSEKEVLQMEARMS 178

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRER 240
             +    L    D++ S      + D     E  ++  +        L  ++  L+ R +
Sbjct: 179 SHDQAFDLSADDDESGSFAPVQFLEDKSPDVETEVVNADWDATASQKLYSAIKTLDERSQ 238

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            I + R L ++  TL++L+ +++VS ERVRQIE  A KK+Q ++
Sbjct: 239 HIIQTRWLSDDKTTLQDLADKYQVSAERVRQIEKNAMKKLQSAM 282


>gi|294815528|ref|ZP_06774171.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|294328127|gb|EFG09770.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 529

 Score =  251 bits (642), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 75/314 (23%), Positives = 143/314 (45%), Gaps = 40/314 (12%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------- 41
           + +++       +  Y+ +I K+P+L  ++E  LAKR                       
Sbjct: 221 QQVAVAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANADKLAPKLKR 280

Query: 42  -----REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                 E G   A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  
Sbjct: 281 ELEIIAEDG-RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYT 339

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  +         P
Sbjct: 340 KGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTP 397

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           E    +AK+L+++  +VI +        SL+  +   +   S++ D +    D +  V  
Sbjct: 398 E---ELAKELDMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPA 449

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEA 274
           +       +  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE+
Sbjct: 450 DAVSFTLLQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIES 509

Query: 275 RAFKKVQESIQKQV 288
           +   K++   + QV
Sbjct: 510 KTMSKLRHPSRSQV 523


>gi|262068176|ref|ZP_06027788.1| RNA polymerase sigma factor RpoD [Fusobacterium periodonticum ATCC
           33693]
 gi|291378119|gb|EFE85637.1| RNA polymerase sigma factor RpoD [Fusobacterium periodonticum ATCC
           33693]
          Length = 502

 Score =  251 bits (642), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 80/285 (28%), Positives = 143/285 (50%), Gaps = 13/285 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           N+      +  +  Y+ EI ++P+L   EE   AK+  E GD  A+ +L+ S+LRLVV I
Sbjct: 221 NLGNSAKVDEPIKMYLREIGQVPLLTHDEEIEYAKKAYE-GDEEASQKLIESNLRLVVSI 279

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  +   GL + +++ EGNIGLM+AV+KF+  +G++ +TY+ WWI+ A+   I      +
Sbjct: 280 AKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTI 339

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I        +   + ++K   +       K      +A++L +   ++ ++        
Sbjct: 340 RIPVH-----MIETINKIKKESRIYLQETGKDASPEILAERLGMEVEKIKAIQEMNQEPI 394

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   + S  +  S+  D++    D +     E   R   R  L   +  L+PRE ++  
Sbjct: 395 SLETPVGS--EEDSELGDFV---EDQKTTSPYEATNRAILREELDGVLKTLSPREEKVLR 449

Query: 245 ARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R   ++  P TLE +   F V+RER+RQIE +A +K++   +K+
Sbjct: 450 YRYGLDDSSPKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRKK 494


>gi|24114721|ref|NP_709231.1| RNA polymerase factor sigma-32 [Shigella flexneri 2a str. 301]
 gi|30065262|ref|NP_839433.1| RNA polymerase factor sigma-32 [Shigella flexneri 2a str. 2457T]
 gi|110807289|ref|YP_690809.1| RNA polymerase factor sigma-32 [Shigella flexneri 5 str. 8401]
 gi|24053937|gb|AAN44938.1| sigma(32) factor of RNA polymerase [Shigella flexneri 2a str. 301]
 gi|30043524|gb|AAP19244.1| sigma(32) factor of RNA polymerase [Shigella flexneri 2a str.
           2457T]
 gi|110616837|gb|ABF05504.1| RNA polymerase sigma factor [Shigella flexneri 5 str. 8401]
 gi|281602809|gb|ADA75793.1| Sigma(32) factor of RNA polymerase [Shigella flexneri 2002017]
 gi|313647240|gb|EFS11692.1| alternative sigma factor RpoH [Shigella flexneri 2a str. 2457T]
 gi|332749439|gb|EGJ79856.1| alternative sigma factor RpoH [Shigella flexneri K-671]
 gi|332750286|gb|EGJ80697.1| alternative sigma factor RpoH [Shigella flexneri 4343-70]
 gi|332751371|gb|EGJ81774.1| alternative sigma factor RpoH [Shigella flexneri 2747-71]
 gi|332996248|gb|EGK15875.1| alternative sigma factor RpoH [Shigella flexneri VA-6]
 gi|332996590|gb|EGK16215.1| alternative sigma factor RpoH [Shigella flexneri K-272]
 gi|332997356|gb|EGK16972.1| alternative sigma factor RpoH [Shigella flexneri K-218]
 gi|333012512|gb|EGK31893.1| alternative sigma factor RpoH [Shigella flexneri K-304]
 gi|333012998|gb|EGK32374.1| alternative sigma factor RpoH [Shigella flexneri K-227]
          Length = 284

 Score =  251 bits (642), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 109/289 (37%), Positives = 161/289 (55%), Gaps = 8/289 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  K  S+ +     L  YI      PML   EE  LA++   HGDL AA  L+ SHLR 
Sbjct: 1   MTDKMQSLALAPVGNLDSYIRAANAWPMLSADEERALAEKLHYHGDLEAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVEMVARELGVTSKDVREMESRM 175

Query: 181 -AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE-ERKNRRNMLTRSMSVLNPR 238
            A D + +   +    +        + D        IE +   +   N LT +M  L+ R
Sbjct: 176 AAQDMTFDLSSDDDSDSQPMAPVLYLQDKSSNFADGIEDDNWEEQAANRLTDAMHGLDER 235

Query: 239 ERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + I  AR L E+   TL+ L+  + VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 SQDIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 284


>gi|240013602|ref|ZP_04720515.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae DGI18]
 gi|240112396|ref|ZP_04726886.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae MS11]
 gi|240120672|ref|ZP_04733634.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID24-1]
 gi|268598456|ref|ZP_06132623.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae MS11]
 gi|268582587|gb|EEZ47263.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae MS11]
          Length = 290

 Score =  251 bits (642), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 120/289 (41%), Positives = 183/289 (63%), Gaps = 7/289 (2%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N   +  I +G   L +YIH +  IPML ++EE  LA+R R  GDL+AA +L+ SHLR+V
Sbjct: 6   NAFALPAIQSGNGSLEQYIHTVNSIPMLSQEEETRLAER-RIKGDLNAAKQLILSHLRVV 64

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+ILR+W
Sbjct: 65  VSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILRNW 124

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            LV++ TT  Q++LFFNLR ++ +L     N L P++   IA  L V  SEV+ M  R+ 
Sbjct: 125 RLVRVATTKPQRKLFFNLRSMRKNL-----NVLSPKEAQDIADDLGVKLSEVLEMEQRMT 179

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           G +      NS D++S    DWL        + L ++     +   L  +++ L+ R RR
Sbjct: 180 GHDIAIMTDNSDDEDSFAPIDWLADHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRR 239

Query: 242 IFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           I E+R LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 240 IVESRWLQDDGGLTLHQLAAEYGVSAERIRQIEAKAMQKLRGFLTEEAE 288


>gi|309389374|gb|ADO77254.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Halanaerobium
           praevalens DSM 2228]
          Length = 310

 Score =  251 bits (642), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 78/277 (28%), Positives = 145/277 (52%), Gaps = 11/277 (3%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ E+ K+ +L+K+EE  LAKR  E GD  A  +L  ++LRLVV IA  Y G G
Sbjct: 35  DDSVRVYLKEMGKVDLLDKEEEVELAKRI-EQGDQRAREQLTEANLRLVVSIAKKYIGQG 93

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +   +++ EGN GLM+AV+KFD  +G++ +TY+ WWI+ ++   +      ++I     +
Sbjct: 94  MSFLDLIQEGNKGLMKAVEKFDYTKGYKFSTYATWWIRQSITRALADQARTIRIPVHMVE 153

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 LRR++  L+   +       +  I +++N+   +V+ +       +  +     
Sbjct: 154 --TMNKLRRIEKRLKKDLERE---PTLEEIGEEMNMEPEKVLEIQKLAMNQQPTSLDTPI 208

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            ++  S  +D++        ++L   E  K+    L   +  L  RE+RI + R   E+ 
Sbjct: 209 GEEKDSHLKDFIEDQDAPAPEMLASSELLKD---QLETVLDTLTDREKRIIKLRFGLEDG 265

Query: 253 --VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TL+ + S+F V+RER+RQI+A+A +K++   + +
Sbjct: 266 RQRTLKEVGSQFGVTRERIRQIQAKALRKLRHPTRSK 302


>gi|163841160|ref|YP_001625565.1| RNA polymerase principal sigma factor [Renibacterium salmoninarum
           ATCC 33209]
 gi|1808669|emb|CAA71796.1| RNA polymerase [Renibacterium salmoninarum]
 gi|162954636|gb|ABY24151.1| RNA polymerase principal sigma factor [Renibacterium salmoninarum
           ATCC 33209]
          Length = 462

 Score =  251 bits (642), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 71/304 (23%), Positives = 135/304 (44%), Gaps = 39/304 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------------HGD 46
             +  Y+ +I K+ +L  ++E  LA R                              H  
Sbjct: 163 DPVKDYLKQIGKVALLNAEQEVDLALRIEAGLYAEEKLAADDGKITEKLNREYQWVIHDG 222

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ 
Sbjct: 223 KRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNMGLIRAVEKFDYTKGFKFSTYAT 282

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +A +L
Sbjct: 283 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELALEL 337

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +V+ +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 338 DMTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 392

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 393 QLHSVLDTLSEREAGVVAMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 452

Query: 285 QKQV 288
           + QV
Sbjct: 453 RSQV 456


>gi|29828986|ref|NP_823620.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29606091|dbj|BAC70155.1| RNA polymerase major sigma factor, sigma-70 family [Streptomyces
           avermitilis MA-4680]
          Length = 512

 Score =  251 bits (642), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 75/304 (24%), Positives = 139/304 (45%), Gaps = 40/304 (13%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------------REHGD 46
             +  Y+ +I K+P+L  ++E  LAKR                             E G 
Sbjct: 214 DPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANADKLAPKLKRELEIIAEDG- 272

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 273 RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 332

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L
Sbjct: 333 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKEL 387

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +VI +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 388 DMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 442

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 443 QLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 502

Query: 285 QKQV 288
           + QV
Sbjct: 503 RSQV 506


>gi|304397877|ref|ZP_07379753.1| RNA polymerase, sigma 32 subunit, RpoH [Pantoea sp. aB]
 gi|308188475|ref|YP_003932606.1| RNA polymerase sigma-32 factor [Pantoea vagans C9-1]
 gi|304354588|gb|EFM18959.1| RNA polymerase, sigma 32 subunit, RpoH [Pantoea sp. aB]
 gi|308058985|gb|ADO11157.1| RNA polymerase sigma-32 factor [Pantoea vagans C9-1]
          Length = 285

 Score =  251 bits (642), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 105/290 (36%), Positives = 164/290 (56%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +     L  Y+      PML  +EE  LA+R    GDL AA  L+ SHLR 
Sbjct: 1   MTKEMQTLAIAPLGNLESYVRAANTWPMLSAEEEKALAERLHYQGDLEAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y GYGLP +++V EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHIARNYSGYGLPQADLVQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVEMVARELGVSSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNP 237
           A  +    +    + +  +    ++Y  D        + E     +  + L+ +M  L+ 
Sbjct: 176 AAQDMTFDMSADDESSEGRSMAPVLYLQDKTSDFADGIEEDNWDAHAADKLSYAMEGLDE 235

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L E+   TL+ L+ ++ VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQHIIRARWLDEDNKTTLQELADQYGVSAERVRQLEKNAMKKLRMAIEA 285


>gi|289706929|ref|ZP_06503266.1| RNA polymerase sigma factor RpoD [Micrococcus luteus SK58]
 gi|289556364|gb|EFD49718.1| RNA polymerase sigma factor RpoD [Micrococcus luteus SK58]
          Length = 509

 Score =  251 bits (642), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 75/303 (24%), Positives = 139/303 (45%), Gaps = 38/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR------------------YREHGD--------L 47
             +  Y+ +I K+ +L  ++E  LA R                  YRE  D         
Sbjct: 211 DPVKDYLKQIGKVALLNAEQEVDLAMRIEAGLYAEHVVQHEASDDYRERRDIQLIIADGR 270

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ W
Sbjct: 271 KAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATW 330

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L+
Sbjct: 331 WIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKELD 385

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++  +V+ +        SL+  +   +   S++ D +    D +  V  +       +  
Sbjct: 386 MTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQEQ 440

Query: 228 LTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   +
Sbjct: 441 LHSVLDTLSEREAGVVAMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSR 500

Query: 286 KQV 288
            QV
Sbjct: 501 SQV 503


>gi|225388598|ref|ZP_03758322.1| hypothetical protein CLOSTASPAR_02334 [Clostridium asparagiforme
           DSM 15981]
 gi|225045346|gb|EEG55592.1| hypothetical protein CLOSTASPAR_02334 [Clostridium asparagiforme
           DSM 15981]
          Length = 405

 Score =  251 bits (642), Expect = 8e-65,   Method: Composition-based stats.
 Identities = 86/280 (30%), Positives = 146/280 (52%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V+    +  Y+ EI  I +L  +EE  LAKR  E GD  A  RLV ++LRLVV IA  Y 
Sbjct: 130 VSTGDPIREYLKEIGAIALLTPEEEAGLAKRCAE-GDEEAGKRLVEANLRLVVSIAKRYT 188

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   ++V EGNIGLM+AV+KFD E+G+RL+TY+ WW+K A+   +      +++   
Sbjct: 189 GRGMSFLDLVQEGNIGLMKAVEKFDYEKGYRLSTYATWWVKQAITRALADQARTIRLPVH 248

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      + +++   + ++    +      +A+ + ++E  V  +        SL   
Sbjct: 249 MVE-----AVNKIRRTQRDLSVQLGRDPSNRELAEAVGMTEKRVEELIQTSGDTVSLETP 303

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           +   D++ S   D++    D       ++ E    R  +   +  LN RER++ + R   
Sbjct: 304 V--GDEDGSSLGDFVA---DNAGDSTEDQAENVLLREEIDSMLQGLNERERQVIKLRFGL 358

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           EN  P+TLE +  +F V+RER+RQIE  A +K++  ++ +
Sbjct: 359 ENGRPLTLEEVGRQFNVTRERIRQIETAALRKLRNPVRSK 398


>gi|89256211|ref|YP_513573.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           holarctica LVS]
 gi|115314678|ref|YP_763401.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           holarctica OSU18]
 gi|156502270|ref|YP_001428335.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           holarctica FTNF002-00]
 gi|167009752|ref|ZP_02274683.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           holarctica FSC200]
 gi|254367537|ref|ZP_04983563.1| RNA polymerase sigma-32 factor [Francisella tularensis subsp.
           holarctica 257]
 gi|290952961|ref|ZP_06557582.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           holarctica URFT1]
 gi|295313833|ref|ZP_06804405.1| RNA polymerase factor sigma-32 [Francisella tularensis subsp.
           holarctica URFT1]
 gi|89144042|emb|CAJ79290.1| RNA polymerase sigma-32 factor [Francisella tularensis subsp.
           holarctica LVS]
 gi|115129577|gb|ABI82764.1| DNA-directed RNA polymerase [Francisella tularensis subsp.
           holarctica OSU18]
 gi|134253353|gb|EBA52447.1| RNA polymerase sigma-32 factor [Francisella tularensis subsp.
           holarctica 257]
 gi|156252873|gb|ABU61379.1| alternative sigma factor RpoH [Francisella tularensis subsp.
           holarctica FTNF002-00]
          Length = 292

 Score =  251 bits (642), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 106/286 (37%), Positives = 176/286 (61%), Gaps = 7/286 (2%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           + K  ++ V  +  LS Y++ +  +P+L  ++E  LA+RY+   DL AA +LV SHLR V
Sbjct: 9   STKTKTLPVVSDNNLSAYLNFVNTLPVLSLEQEQELARRYKYKKDLDAAQQLVLSHLRFV 68

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            KIA  + GYGL I++++ EGNIGLM+AV KFDP++G RL ++++ WIKA M +Y+L++W
Sbjct: 69  TKIARNFSGYGLSIADLIQEGNIGLMKAVSKFDPDQGVRLLSFAVHWIKAEMHDYVLKNW 128

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL- 180
            +VK+ TT  Q++LFFNLR  K  +  ++  N+K      +A++L V E  VI M  R+ 
Sbjct: 129 KIVKVATTKAQRKLFFNLRSSKDKIGWLSSENIK-----ELAEELGVKEETVIEMEKRMC 183

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            GD SL+      D   +  Q   + D     E  +++++   N + ++   +S  + R 
Sbjct: 184 QGDASLDLSYTDDDGEQTSQQSLYLEDKSSNIEHQVVQQDYYDNFKAIVKDVLSGFDTRT 243

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + I  +R L +N  TL++L++++ +S ERVRQIE  A  K++++I+
Sbjct: 244 KDIIMSRYLLDNKATLQDLAAKYNISAERVRQIEEDALAKLKKAIK 289


>gi|308177806|ref|YP_003917212.1| RNA polymerase sigma factor RpoD [Arthrobacter arilaitensis Re117]
 gi|307745269|emb|CBT76241.1| RNA polymerase sigma factor RpoD [Arthrobacter arilaitensis Re117]
          Length = 403

 Score =  251 bits (642), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 72/304 (23%), Positives = 139/304 (45%), Gaps = 39/304 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY-----------REHGDLS-------------- 48
             +  Y+ +I K+ +L  ++E  LA R            ++ G +               
Sbjct: 104 DPVKDYLKQIGKVALLNAEQEVDLALRIEAGLFATDKLEKDDGSMDQRLRWDYEQIIHDG 163

Query: 49  --AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ 
Sbjct: 164 KIAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYAT 223

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L
Sbjct: 224 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKEL 278

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +V+ +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 279 DMTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 333

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 334 QLHSVLDTLSEREAGVVAMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 393

Query: 285 QKQV 288
           + QV
Sbjct: 394 RSQV 397


>gi|302542036|ref|ZP_07294378.1| RNA polymerase sigma (70) factor RpoD [Streptomyces hygroscopicus
           ATCC 53653]
 gi|302459654|gb|EFL22747.1| RNA polymerase sigma (70) factor RpoD [Streptomyces himastatinicus
           ATCC 53653]
          Length = 502

 Score =  251 bits (642), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 75/304 (24%), Positives = 139/304 (45%), Gaps = 40/304 (13%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------------REHGD 46
             +  Y+ +I K+P+L  ++E  LAKR                             E G 
Sbjct: 204 DPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANSDKLAPKLKRELEIIAEDG- 262

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 263 RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 322

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L
Sbjct: 323 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKEL 377

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +VI +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 378 DMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 432

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 433 QLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 492

Query: 285 QKQV 288
           + QV
Sbjct: 493 RSQV 496


>gi|296270363|ref|YP_003652995.1| RpoD subfamily RNA polymerase sigma-70 [Thermobispora bispora DSM
           43833]
 gi|296093150|gb|ADG89102.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobispora
           bispora DSM 43833]
          Length = 555

 Score =  251 bits (642), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 74/304 (24%), Positives = 141/304 (46%), Gaps = 39/304 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY----------REHGDL---------------- 47
             +  Y+ +I K+P+L  ++E  LAKR            + GD                 
Sbjct: 256 DPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEEQLAKEGDKLPPDVKAELEWIAEDG 315

Query: 48  -SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 316 KRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 375

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +A++L
Sbjct: 376 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAREL 430

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +VI +        SL+  +   ++  S++ D +    D +  V  +       + 
Sbjct: 431 DMTPEKVIEVQKYGREPISLHTPL--GEEGDSEFGDLI---EDSEAVVPADAVSFTLLQE 485

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 486 QLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 545

Query: 285 QKQV 288
           + QV
Sbjct: 546 RSQV 549


>gi|291526136|emb|CBK91723.1| RNA polymerase, sigma 70 subunit, RpoD [Eubacterium rectale DSM
           17629]
 gi|291527130|emb|CBK92716.1| RNA polymerase, sigma 70 subunit, RpoD [Eubacterium rectale M104/1]
          Length = 418

 Score =  251 bits (642), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 83/316 (26%), Positives = 135/316 (42%), Gaps = 49/316 (15%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------------- 43
           V+ E  +  Y+ EI K+P+L   EE  LA+   +                          
Sbjct: 105 VSVEDPVRMYLKEIGKVPLLSADEEIELAQNMEDGAVATEKINVLKGRIDGASEEEKAEI 164

Query: 44  -----------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  RL  ++LRLVV IA  Y G G+   +++ EGN+GL++AV+K
Sbjct: 165 KEEIKTLQRDVDKGADAKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEK 224

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD ++G++ +TY+ WWI+ A+   I      ++I     +      L R+   L      
Sbjct: 225 FDYKKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE--TINKLIRVSRQLLQELGR 282

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE    IAK++N+    V  +        SL   I   ++  S   D++  D     
Sbjct: 283 EPSPE---EIAKEMNMPVERVREILKISQEPVSLETPI--GEEEDSHLGDFIKDD---NV 334

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
            V  +       +  L   +  L  RE+++   R   E+    TLE +  EF V+RER+R
Sbjct: 335 PVPADAAAFTLLKEQLEEVLGTLTEREQKVLTLRFGLEDGRARTLEEVGKEFNVTRERIR 394

Query: 271 QIEARAFKKVQESIQK 286
           QIEA+A +K++   + 
Sbjct: 395 QIEAKALRKLRHPSRS 410


>gi|15803973|ref|NP_290009.1| RNA polymerase factor sigma-32 [Escherichia coli O157:H7 EDL933]
 gi|15833564|ref|NP_312337.1| RNA polymerase factor sigma-32 [Escherichia coli O157:H7 str.
           Sakai]
 gi|16131333|ref|NP_417918.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli str.
           K-12 substr. MG1655]
 gi|26250076|ref|NP_756116.1| RNA polymerase factor sigma-32 [Escherichia coli CFT073]
 gi|74314061|ref|YP_312480.1| RNA polymerase factor sigma-32 [Shigella sonnei Ss046]
 gi|82545824|ref|YP_409771.1| RNA polymerase factor sigma-32 [Shigella boydii Sb227]
 gi|82778725|ref|YP_405074.1| RNA polymerase factor sigma-32 [Shigella dysenteriae Sd197]
 gi|89110551|ref|AP_004331.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli str.
           K-12 substr. W3110]
 gi|91212950|ref|YP_542936.1| RNA polymerase factor sigma-32 [Escherichia coli UTI89]
 gi|110643701|ref|YP_671431.1| RNA polymerase factor sigma-32 [Escherichia coli 536]
 gi|117625739|ref|YP_859062.1| RNA polymerase factor sigma-32 [Escherichia coli APEC O1]
 gi|157158396|ref|YP_001464926.1| RNA polymerase factor sigma-32 [Escherichia coli E24377A]
 gi|157162938|ref|YP_001460256.1| RNA polymerase factor sigma-32 [Escherichia coli HS]
 gi|168747045|ref|ZP_02772067.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4113]
 gi|168753229|ref|ZP_02778236.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4401]
 gi|168759499|ref|ZP_02784506.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4501]
 gi|168765824|ref|ZP_02790831.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4486]
 gi|168772630|ref|ZP_02797637.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4196]
 gi|168779560|ref|ZP_02804567.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4076]
 gi|168785282|ref|ZP_02810289.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str. EC869]
 gi|168797247|ref|ZP_02822254.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str. EC508]
 gi|170018307|ref|YP_001723261.1| RNA polymerase factor sigma-32 [Escherichia coli ATCC 8739]
 gi|170082975|ref|YP_001732295.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli str.
           K-12 substr. DH10B]
 gi|170683649|ref|YP_001745710.1| RNA polymerase factor sigma-32 [Escherichia coli SMS-3-5]
 gi|170766775|ref|ZP_02901228.1| alternative sigma factor RpoH [Escherichia albertii TW07627]
 gi|187730400|ref|YP_001882152.1| RNA polymerase factor sigma-32 [Shigella boydii CDC 3083-94]
 gi|188495507|ref|ZP_03002777.1| alternative sigma factor RpoH [Escherichia coli 53638]
 gi|191169502|ref|ZP_03031234.1| alternative sigma factor RpoH [Escherichia coli B7A]
 gi|191170346|ref|ZP_03031899.1| alternative sigma factor RpoH [Escherichia coli F11]
 gi|193061907|ref|ZP_03043004.1| alternative sigma factor RpoH [Escherichia coli E22]
 gi|193068783|ref|ZP_03049743.1| alternative sigma factor RpoH [Escherichia coli E110019]
 gi|194427076|ref|ZP_03059628.1| alternative sigma factor RpoH [Escherichia coli B171]
 gi|194431093|ref|ZP_03063386.1| alternative sigma factor RpoH [Shigella dysenteriae 1012]
 gi|194435828|ref|ZP_03067931.1| alternative sigma factor RpoH [Escherichia coli 101-1]
 gi|195934955|ref|ZP_03080337.1| RNA polymerase factor sigma-32 [Escherichia coli O157:H7 str.
           EC4024]
 gi|208806017|ref|ZP_03248354.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4206]
 gi|208814463|ref|ZP_03255792.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4045]
 gi|208821158|ref|ZP_03261478.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4042]
 gi|209398124|ref|YP_002272905.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4115]
 gi|209920920|ref|YP_002295004.1| RNA polymerase factor sigma-32 [Escherichia coli SE11]
 gi|215488736|ref|YP_002331167.1| RNA polymerase factor sigma-32 [Escherichia coli O127:H6 str.
           E2348/69]
 gi|217325718|ref|ZP_03441802.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           TW14588]
 gi|218550723|ref|YP_002384514.1| RNA polymerase factor sigma-32 [Escherichia fergusonii ATCC 35469]
 gi|218556012|ref|YP_002388925.1| RNA polymerase factor sigma-32 [Escherichia coli IAI1]
 gi|218560529|ref|YP_002393442.1| RNA polymerase factor sigma-32 [Escherichia coli S88]
 gi|218691746|ref|YP_002399958.1| RNA polymerase factor sigma-32 [Escherichia coli ED1a]
 gi|218697144|ref|YP_002404811.1| RNA polymerase factor sigma-32 [Escherichia coli 55989]
 gi|218702206|ref|YP_002409835.1| RNA polymerase factor sigma-32 [Escherichia coli IAI39]
 gi|218707055|ref|YP_002414574.1| RNA polymerase factor sigma-32 [Escherichia coli UMN026]
 gi|227883607|ref|ZP_04001412.1| RNA polymerase factor sigma-32 [Escherichia coli 83972]
 gi|237703208|ref|ZP_04533689.1| alternative sigma factor RpoH [Escherichia sp. 3_2_53FAA]
 gi|238902552|ref|YP_002928348.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli BW2952]
 gi|253771710|ref|YP_003034541.1| RNA polymerase factor sigma-32 [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254038629|ref|ZP_04872685.1| alternative sigma factor RpoH [Escherichia sp. 1_1_43]
 gi|254163385|ref|YP_003046493.1| RNA polymerase factor sigma-32 [Escherichia coli B str. REL606]
 gi|254795381|ref|YP_003080218.1| RNA polymerase factor sigma-32 [Escherichia coli O157:H7 str.
           TW14359]
 gi|256020809|ref|ZP_05434674.1| RNA polymerase factor sigma-32 [Shigella sp. D9]
 gi|256025815|ref|ZP_05439680.1| RNA polymerase factor sigma-32 [Escherichia sp. 4_1_40B]
 gi|260846245|ref|YP_003224023.1| RNA polymerase, sigma 32 factor [Escherichia coli O103:H2 str.
           12009]
 gi|260857567|ref|YP_003231458.1| RNA polymerase, sigma 32 factor [Escherichia coli O26:H11 str.
           11368]
 gi|260870186|ref|YP_003236588.1| RNA polymerase, sigma 32 factor [Escherichia coli O111:H- str.
           11128]
 gi|261224744|ref|ZP_05939025.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli O157:H7
           str. FRIK2000]
 gi|261254361|ref|ZP_05946894.1| RNA polymerase, sigma 32 factor [Escherichia coli O157:H7 str.
           FRIK966]
 gi|291284801|ref|YP_003501619.1| RNA polymerase sigma factor [Escherichia coli O55:H7 str. CB9615]
 gi|293407042|ref|ZP_06650966.1| RNA polymerase factor sigma-32 [Escherichia coli FVEC1412]
 gi|293412884|ref|ZP_06655552.1| alternative sigma factor RpoH [Escherichia coli B354]
 gi|293416865|ref|ZP_06659502.1| alternative sigma factor RpoH [Escherichia coli B185]
 gi|293453766|ref|ZP_06664185.1| alternative sigma factor RpoH [Escherichia coli B088]
 gi|297517521|ref|ZP_06935907.1| RNA polymerase factor sigma-32 [Escherichia coli OP50]
 gi|298382788|ref|ZP_06992383.1| RNA polymerase sigma-32 factor [Escherichia coli FVEC1302]
 gi|300815334|ref|ZP_07095559.1| alternative sigma factor RpoH [Escherichia coli MS 107-1]
 gi|300822733|ref|ZP_07102870.1| alternative sigma factor RpoH [Escherichia coli MS 119-7]
 gi|300898837|ref|ZP_07117141.1| alternative sigma factor RpoH [Escherichia coli MS 198-1]
 gi|300907388|ref|ZP_07125036.1| alternative sigma factor RpoH [Escherichia coli MS 84-1]
 gi|300917205|ref|ZP_07133887.1| alternative sigma factor RpoH [Escherichia coli MS 115-1]
 gi|300930998|ref|ZP_07146356.1| alternative sigma factor RpoH [Escherichia coli MS 187-1]
 gi|300936478|ref|ZP_07151398.1| alternative sigma factor RpoH [Escherichia coli MS 21-1]
 gi|300946790|ref|ZP_07161034.1| alternative sigma factor RpoH [Escherichia coli MS 116-1]
 gi|300956796|ref|ZP_07169063.1| alternative sigma factor RpoH [Escherichia coli MS 175-1]
 gi|300985247|ref|ZP_07177344.1| alternative sigma factor RpoH [Escherichia coli MS 45-1]
 gi|300987360|ref|ZP_07178168.1| alternative sigma factor RpoH [Escherichia coli MS 200-1]
 gi|301018548|ref|ZP_07182926.1| alternative sigma factor RpoH [Escherichia coli MS 69-1]
 gi|301021811|ref|ZP_07185775.1| alternative sigma factor RpoH [Escherichia coli MS 196-1]
 gi|301050314|ref|ZP_07197203.1| alternative sigma factor RpoH [Escherichia coli MS 185-1]
 gi|301302348|ref|ZP_07208480.1| alternative sigma factor RpoH [Escherichia coli MS 124-1]
 gi|301645904|ref|ZP_07245818.1| alternative sigma factor RpoH [Escherichia coli MS 146-1]
 gi|306816195|ref|ZP_07450333.1| RNA polymerase factor sigma-32 [Escherichia coli NC101]
 gi|307140144|ref|ZP_07499500.1| RNA polymerase factor sigma-32 [Escherichia coli H736]
 gi|307311872|ref|ZP_07591510.1| RNA polymerase, sigma 32 subunit, RpoH [Escherichia coli W]
 gi|309794740|ref|ZP_07689162.1| alternative sigma factor RpoH [Escherichia coli MS 145-7]
 gi|312968227|ref|ZP_07782437.1| alternative sigma factor RpoH [Escherichia coli 2362-75]
 gi|331644161|ref|ZP_08345290.1| alternative sigma factor RpoH [Escherichia coli H736]
 gi|331649268|ref|ZP_08350354.1| alternative sigma factor RpoH [Escherichia coli M605]
 gi|331655044|ref|ZP_08356043.1| alternative sigma factor RpoH [Escherichia coli M718]
 gi|331659757|ref|ZP_08360695.1| alternative sigma factor RpoH [Escherichia coli TA206]
 gi|331665070|ref|ZP_08365971.1| alternative sigma factor RpoH [Escherichia coli TA143]
 gi|331670287|ref|ZP_08371126.1| alternative sigma factor RpoH [Escherichia coli TA271]
 gi|331674946|ref|ZP_08375703.1| alternative sigma factor RpoH [Escherichia coli TA280]
 gi|331679529|ref|ZP_08380199.1| alternative sigma factor RpoH [Escherichia coli H591]
 gi|331685107|ref|ZP_08385693.1| alternative sigma factor RpoH [Escherichia coli H299]
 gi|332282016|ref|ZP_08394429.1| RNA polymerase sigma 32 (sigma H) factor [Shigella sp. D9]
 gi|84028120|sp|P0AGB5|RP32_ECO57 RecName: Full=RNA polymerase sigma-32 factor; AltName: Full=Heat
           shock regulatory protein F33.4
 gi|84028121|sp|P0AGB4|RP32_ECOL6 RecName: Full=RNA polymerase sigma-32 factor; AltName: Full=Heat
           shock regulatory protein F33.4
 gi|84028122|sp|P0AGB3|RP32_ECOLI RecName: Full=RNA polymerase sigma-32 factor; AltName: Full=Heat
           shock regulatory protein F33.4
 gi|12518117|gb|AAG58570.1|AE005569_10 RNA polymerase, sigma(32) factor; regulation of proteins induced at
           high temperatures [Escherichia coli O157:H7 str. EDL933]
 gi|26110505|gb|AAN82690.1|AE016768_108 RNA polymerase sigma-32 factor [Escherichia coli CFT073]
 gi|147732|gb|AAA24587.1| RNA polymerase sigma-32 subunit [Escherichia coli]
 gi|466597|gb|AAB18436.1| RNA polymerase sigma-32 subunit [Escherichia coli str. K-12 substr.
           MG1655]
 gi|1789871|gb|AAC76486.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli str.
           K-12 substr. MG1655]
 gi|13363784|dbj|BAB37733.1| RNA polymerase sigma32 factor [Escherichia coli O157:H7 str. Sakai]
 gi|73671328|gb|AAZ80075.1| RpoH [Escherichia coli LW1655F+]
 gi|73857538|gb|AAZ90245.1| RNA polymerase, sigma(32) factor [Shigella sonnei Ss046]
 gi|81242873|gb|ABB63583.1| RNA polymerase, sigma(32) factor [Shigella dysenteriae Sd197]
 gi|81247235|gb|ABB67943.1| RNA polymerase sigma(32) factor [Shigella boydii Sb227]
 gi|85676582|dbj|BAE77832.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli str.
           K12 substr. W3110]
 gi|91074524|gb|ABE09405.1| component of RNA polymerase, sigma 32 factor [Escherichia coli
           UTI89]
 gi|110345293|gb|ABG71530.1| RNA polymerase sigma-32 factor [Escherichia coli 536]
 gi|115514863|gb|ABJ02938.1| RNA polymerase sigma factor [Escherichia coli APEC O1]
 gi|157068618|gb|ABV07873.1| alternative sigma factor RpoH [Escherichia coli HS]
 gi|157080426|gb|ABV20134.1| alternative sigma factor RpoH [Escherichia coli E24377A]
 gi|169753235|gb|ACA75934.1| RNA polymerase, sigma 32 subunit, RpoH [Escherichia coli ATCC 8739]
 gi|169890810|gb|ACB04517.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli str.
           K-12 substr. DH10B]
 gi|170124213|gb|EDS93144.1| alternative sigma factor RpoH [Escherichia albertii TW07627]
 gi|170521367|gb|ACB19545.1| alternative sigma factor RpoH [Escherichia coli SMS-3-5]
 gi|187427392|gb|ACD06666.1| alternative sigma factor RpoH [Shigella boydii CDC 3083-94]
 gi|187771635|gb|EDU35479.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4196]
 gi|188018405|gb|EDU56527.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4113]
 gi|188490706|gb|EDU65809.1| alternative sigma factor RpoH [Escherichia coli 53638]
 gi|189002511|gb|EDU71497.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4076]
 gi|189359084|gb|EDU77503.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4401]
 gi|189364663|gb|EDU83082.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4486]
 gi|189369524|gb|EDU87940.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4501]
 gi|189374649|gb|EDU93065.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str. EC869]
 gi|189380077|gb|EDU98493.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str. EC508]
 gi|190900463|gb|EDV60280.1| alternative sigma factor RpoH [Escherichia coli B7A]
 gi|190909154|gb|EDV68740.1| alternative sigma factor RpoH [Escherichia coli F11]
 gi|192932697|gb|EDV85294.1| alternative sigma factor RpoH [Escherichia coli E22]
 gi|192957859|gb|EDV88302.1| alternative sigma factor RpoH [Escherichia coli E110019]
 gi|194415037|gb|EDX31307.1| alternative sigma factor RpoH [Escherichia coli B171]
 gi|194420548|gb|EDX36624.1| alternative sigma factor RpoH [Shigella dysenteriae 1012]
 gi|194425371|gb|EDX41355.1| alternative sigma factor RpoH [Escherichia coli 101-1]
 gi|208725818|gb|EDZ75419.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4206]
 gi|208735740|gb|EDZ84427.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4045]
 gi|208741281|gb|EDZ88963.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4042]
 gi|209159524|gb|ACI36957.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           EC4115]
 gi|209756038|gb|ACI76331.1| RNA polymerase sigma32 factor [Escherichia coli]
 gi|209756040|gb|ACI76332.1| RNA polymerase sigma32 factor [Escherichia coli]
 gi|209756042|gb|ACI76333.1| RNA polymerase sigma32 factor [Escherichia coli]
 gi|209756044|gb|ACI76334.1| RNA polymerase sigma32 factor [Escherichia coli]
 gi|209756046|gb|ACI76335.1| RNA polymerase sigma32 factor [Escherichia coli]
 gi|209914179|dbj|BAG79253.1| RNA polymerase sigma-32 factor [Escherichia coli SE11]
 gi|215266808|emb|CAS11249.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli O127:H6
           str. E2348/69]
 gi|217321939|gb|EEC30363.1| alternative sigma factor RpoH [Escherichia coli O157:H7 str.
           TW14588]
 gi|218353876|emb|CAV00268.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli 55989]
 gi|218358264|emb|CAQ90911.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia fergusonii
           ATCC 35469]
 gi|218362780|emb|CAR00406.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli IAI1]
 gi|218367298|emb|CAR05076.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli S88]
 gi|218372192|emb|CAR20054.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli IAI39]
 gi|218429310|emb|CAR10124.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli ED1a]
 gi|218434152|emb|CAR15069.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli UMN026]
 gi|222035167|emb|CAP77912.1| RNA polymerase sigma-32 factor [Escherichia coli LF82]
 gi|226839135|gb|EEH71158.1| alternative sigma factor RpoH [Escherichia sp. 1_1_43]
 gi|226902472|gb|EEH88731.1| alternative sigma factor RpoH [Escherichia sp. 3_2_53FAA]
 gi|227839486|gb|EEJ49952.1| RNA polymerase factor sigma-32 [Escherichia coli 83972]
 gi|238863499|gb|ACR65497.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli BW2952]
 gi|242378982|emb|CAQ33780.1| RNA polymerase, sigma 32 (sigma H) factor, subunit of RNA
           polymerase sigma 32 [Escherichia coli BL21(DE3)]
 gi|253322754|gb|ACT27356.1| RNA polymerase, sigma 32 subunit, RpoH [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|253975286|gb|ACT40957.1| RNA polymerase sigma factor [Escherichia coli B str. REL606]
 gi|253979442|gb|ACT45112.1| RNA polymerase sigma factor [Escherichia coli BL21(DE3)]
 gi|254594781|gb|ACT74142.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli O157:H7
           str. TW14359]
 gi|257756216|dbj|BAI27718.1| RNA polymerase, sigma 32 factor [Escherichia coli O26:H11 str.
           11368]
 gi|257761392|dbj|BAI32889.1| RNA polymerase, sigma 32 factor [Escherichia coli O103:H2 str.
           12009]
 gi|257766542|dbj|BAI38037.1| RNA polymerase, sigma 32 factor [Escherichia coli O111:H- str.
           11128]
 gi|260447523|gb|ACX37945.1| RNA polymerase, sigma 32 subunit, RpoH [Escherichia coli DH1]
 gi|281180490|dbj|BAI56820.1| RNA polymerase sigma-32 factor [Escherichia coli SE15]
 gi|284923451|emb|CBG36546.1| RNA polymerase sigma-32 factor [Escherichia coli 042]
 gi|290764674|gb|ADD58635.1| RNA polymerase sigma factor [Escherichia coli O55:H7 str. CB9615]
 gi|291321892|gb|EFE61323.1| alternative sigma factor RpoH [Escherichia coli B088]
 gi|291425853|gb|EFE98887.1| RNA polymerase factor sigma-32 [Escherichia coli FVEC1412]
 gi|291431441|gb|EFF04426.1| alternative sigma factor RpoH [Escherichia coli B185]
 gi|291468531|gb|EFF11024.1| alternative sigma factor RpoH [Escherichia coli B354]
 gi|294492777|gb|ADE91533.1| alternative sigma factor RpoH [Escherichia coli IHE3034]
 gi|298276624|gb|EFI18142.1| RNA polymerase sigma-32 factor [Escherichia coli FVEC1302]
 gi|299881444|gb|EFI89655.1| alternative sigma factor RpoH [Escherichia coli MS 196-1]
 gi|300297943|gb|EFJ54328.1| alternative sigma factor RpoH [Escherichia coli MS 185-1]
 gi|300306228|gb|EFJ60748.1| alternative sigma factor RpoH [Escherichia coli MS 200-1]
 gi|300316435|gb|EFJ66219.1| alternative sigma factor RpoH [Escherichia coli MS 175-1]
 gi|300357522|gb|EFJ73392.1| alternative sigma factor RpoH [Escherichia coli MS 198-1]
 gi|300399667|gb|EFJ83205.1| alternative sigma factor RpoH [Escherichia coli MS 69-1]
 gi|300400897|gb|EFJ84435.1| alternative sigma factor RpoH [Escherichia coli MS 84-1]
 gi|300408118|gb|EFJ91656.1| alternative sigma factor RpoH [Escherichia coli MS 45-1]
 gi|300415544|gb|EFJ98854.1| alternative sigma factor RpoH [Escherichia coli MS 115-1]
 gi|300453547|gb|EFK17167.1| alternative sigma factor RpoH [Escherichia coli MS 116-1]
 gi|300458400|gb|EFK21893.1| alternative sigma factor RpoH [Escherichia coli MS 21-1]
 gi|300461176|gb|EFK24669.1| alternative sigma factor RpoH [Escherichia coli MS 187-1]
 gi|300524733|gb|EFK45802.1| alternative sigma factor RpoH [Escherichia coli MS 119-7]
 gi|300532226|gb|EFK53288.1| alternative sigma factor RpoH [Escherichia coli MS 107-1]
 gi|300842511|gb|EFK70271.1| alternative sigma factor RpoH [Escherichia coli MS 124-1]
 gi|301075893|gb|EFK90699.1| alternative sigma factor RpoH [Escherichia coli MS 146-1]
 gi|305850591|gb|EFM51048.1| RNA polymerase factor sigma-32 [Escherichia coli NC101]
 gi|306908016|gb|EFN38516.1| RNA polymerase, sigma 32 subunit, RpoH [Escherichia coli W]
 gi|307555555|gb|ADN48330.1| component of RNA polymerase [Escherichia coli ABU 83972]
 gi|307628534|gb|ADN72838.1| RNA polymerase factor sigma-32 [Escherichia coli UM146]
 gi|308121790|gb|EFO59052.1| alternative sigma factor RpoH [Escherichia coli MS 145-7]
 gi|309703867|emb|CBJ03208.1| RNA polymerase sigma-32 factor [Escherichia coli ETEC H10407]
 gi|312287052|gb|EFR14962.1| alternative sigma factor RpoH [Escherichia coli 2362-75]
 gi|312948014|gb|ADR28841.1| RNA polymerase factor sigma-32 [Escherichia coli O83:H1 str. NRG
           857C]
 gi|315062740|gb|ADT77067.1| RNA polymerase, sigma 32 (sigma H) factor [Escherichia coli W]
 gi|315138035|dbj|BAJ45194.1| RNA polymerase sigma factor [Escherichia coli DH1]
 gi|315256058|gb|EFU36026.1| alternative sigma factor RpoH [Escherichia coli MS 85-1]
 gi|315286128|gb|EFU45566.1| alternative sigma factor RpoH [Escherichia coli MS 110-3]
 gi|315291684|gb|EFU51040.1| alternative sigma factor RpoH [Escherichia coli MS 153-1]
 gi|315295969|gb|EFU55278.1| alternative sigma factor RpoH [Escherichia coli MS 16-3]
 gi|320175708|gb|EFW50796.1| RNA polymerase sigma factor RpoH [Shigella dysenteriae CDC 74-1112]
 gi|320187771|gb|EFW62446.1| RNA polymerase sigma factor RpoH [Shigella flexneri CDC 796-83]
 gi|320191521|gb|EFW66171.1| RNA polymerase sigma factor RpoH [Escherichia coli O157:H7 str.
           EC1212]
 gi|320194037|gb|EFW68670.1| RNA polymerase sigma factor RpoH [Escherichia coli WV_060327]
 gi|320199638|gb|EFW74228.1| RNA polymerase sigma factor RpoH [Escherichia coli EC4100B]
 gi|320639745|gb|EFX09339.1| RNA polymerase factor sigma-32 [Escherichia coli O157:H7 str.
           G5101]
 gi|320645244|gb|EFX14260.1| RNA polymerase factor sigma-32 [Escherichia coli O157:H- str.
           493-89]
 gi|320650555|gb|EFX19021.1| RNA polymerase factor sigma-32 [Escherichia coli O157:H- str. H
           2687]
 gi|320655748|gb|EFX23671.1| RNA polymerase factor sigma-32 [Escherichia coli O55:H7 str.
           3256-97 TW 07815]
 gi|320661531|gb|EFX28946.1| RNA polymerase factor sigma-32 [Escherichia coli O55:H7 str. USDA
           5905]
 gi|320666554|gb|EFX33537.1| RNA polymerase factor sigma-32 [Escherichia coli O157:H7 str.
           LSU-61]
 gi|323154300|gb|EFZ40503.1| alternative sigma factor RpoH [Escherichia coli EPECa14]
 gi|323174100|gb|EFZ59728.1| alternative sigma factor RpoH [Escherichia coli LT-68]
 gi|323376672|gb|ADX48940.1| RNA polymerase, sigma 32 subunit, RpoH [Escherichia coli KO11]
 gi|323934553|gb|EGB30953.1| sigma protein RpoH [Escherichia coli E1520]
 gi|323939321|gb|EGB35532.1| sigma proteinRpoH [Escherichia coli E482]
 gi|323944315|gb|EGB40390.1| sigma protein RpoH [Escherichia coli H120]
 gi|323950129|gb|EGB46012.1| sigma proteinRpoH [Escherichia coli H252]
 gi|323954785|gb|EGB50566.1| sigma proteinRpoH [Escherichia coli H263]
 gi|323959687|gb|EGB55338.1| sigma proteinRpoH [Escherichia coli H489]
 gi|323966125|gb|EGB61562.1| sigma proteinRpoH [Escherichia coli M863]
 gi|323970059|gb|EGB65334.1| sigma proteinRpoH [Escherichia coli TA007]
 gi|323974898|gb|EGB70009.1| sigma proteinRpoH [Escherichia coli TW10509]
 gi|324009349|gb|EGB78568.1| alternative sigma factor RpoH [Escherichia coli MS 57-2]
 gi|324014559|gb|EGB83778.1| alternative sigma factor RpoH [Escherichia coli MS 60-1]
 gi|324018638|gb|EGB87857.1| alternative sigma factor RpoH [Escherichia coli MS 117-3]
 gi|324111782|gb|EGC05762.1| sigma proteinRpoH [Escherichia fergusonii B253]
 gi|324116341|gb|EGC10260.1| sigma proteinRpoH [Escherichia coli E1167]
 gi|325499010|gb|EGC96869.1| RNA polymerase factor sigma-32 [Escherichia fergusonii ECD227]
 gi|326337569|gb|EGD61404.1| RNA polymerase sigma factor RpoH [Escherichia coli O157:H7 str.
           1044]
 gi|326344680|gb|EGD68429.1| RNA polymerase sigma factor RpoH [Escherichia coli O157:H7 str.
           1125]
 gi|330909502|gb|EGH38016.1| RNA polymerase sigma factor RpoH [Escherichia coli AA86]
 gi|331036455|gb|EGI08681.1| alternative sigma factor RpoH [Escherichia coli H736]
 gi|331041766|gb|EGI13910.1| alternative sigma factor RpoH [Escherichia coli M605]
 gi|331047059|gb|EGI19137.1| alternative sigma factor RpoH [Escherichia coli M718]
 gi|331052972|gb|EGI25005.1| alternative sigma factor RpoH [Escherichia coli TA206]
 gi|331057580|gb|EGI29566.1| alternative sigma factor RpoH [Escherichia coli TA143]
 gi|331062349|gb|EGI34269.1| alternative sigma factor RpoH [Escherichia coli TA271]
 gi|331067855|gb|EGI39253.1| alternative sigma factor RpoH [Escherichia coli TA280]
 gi|331072701|gb|EGI44026.1| alternative sigma factor RpoH [Escherichia coli H591]
 gi|331077478|gb|EGI48690.1| alternative sigma factor RpoH [Escherichia coli H299]
 gi|332085344|gb|EGI90516.1| alternative sigma factor RpoH [Shigella boydii 5216-82]
 gi|332085690|gb|EGI90854.1| alternative sigma factor RpoH [Shigella dysenteriae 155-74]
 gi|332090225|gb|EGI95323.1| alternative sigma factor RpoH [Shigella boydii 3594-74]
 gi|332104368|gb|EGJ07714.1| RNA polymerase sigma 32 (sigma H) factor [Shigella sp. D9]
 gi|332345416|gb|AEE58750.1| alternative sigma factor RpoH [Escherichia coli UMNK88]
          Length = 284

 Score =  251 bits (642), Expect = 9e-65,   Method: Composition-based stats.
 Identities = 109/289 (37%), Positives = 161/289 (55%), Gaps = 8/289 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  K  S+ +     L  YI      PML   EE  LA++   HGDL AA  L+ SHLR 
Sbjct: 1   MTDKMQSLALAPVGNLDSYIRAANAWPMLSADEERALAEKLHYHGDLEAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVEMVARELGVTSKDVREMESRM 175

Query: 181 -AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE-ERKNRRNMLTRSMSVLNPR 238
            A D + +   +    +        + D        IE +   +   N LT +M  L+ R
Sbjct: 176 AAQDMTFDLSSDDDSDSQPMAPVLYLQDKSSNFADGIEDDNWEEQAANRLTDAMQGLDER 235

Query: 239 ERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + I  AR L E+   TL+ L+  + VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 SQDIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 284


>gi|139436983|ref|ZP_01771143.1| Hypothetical protein COLAER_00117 [Collinsella aerofaciens ATCC
           25986]
 gi|133776630|gb|EBA40450.1| Hypothetical protein COLAER_00117 [Collinsella aerofaciens ATCC
           25986]
          Length = 454

 Score =  251 bits (642), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 84/314 (26%), Positives = 144/314 (45%), Gaps = 42/314 (13%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR---------------------- 42
           + S ++     +  Y+ EI K+ +L   EE  LA +                        
Sbjct: 142 DASTVMLTGDPVRMYLKEIGKVDLLTASEEVDLAMKIEAGLEATEKLEAADAGELELTRA 201

Query: 43  --------EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                   E+  L A   L++++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD
Sbjct: 202 EIRRLTRIENVGLEAKQALISANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFD 261

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
            ++GF+ +TY+ WWI+ A+   I      ++I     +      L R++  L      + 
Sbjct: 262 YQKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE--TINKLVRVQRQLLQDLGRDP 319

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            PE++ A   ++++S   V  +        SL   I   ++  SQ  D++    D Q  V
Sbjct: 320 TPEEIGA---EMDMSADRVREIQKISQEPVSLETPI--GEEEDSQLGDFI---EDSQAIV 371

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQI 272
             +       +  LT+ +  L  RER++ E R      +P TLE +  EF V+RER+RQI
Sbjct: 372 PPDAASFSMLQEQLTQVLDSLADRERKVIELRFGLVDGHPRTLEEVGREFGVTRERIRQI 431

Query: 273 EARAFKKVQESIQK 286
           E++   K++   + 
Sbjct: 432 ESKTLAKLRHPSRS 445


>gi|152978131|ref|YP_001343760.1| RNA polymerase factor sigma-32 [Actinobacillus succinogenes 130Z]
 gi|150839854|gb|ABR73825.1| RNA polymerase, sigma 32 subunit, RpoH [Actinobacillus succinogenes
           130Z]
          Length = 281

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 103/285 (36%), Positives = 169/285 (59%), Gaps = 7/285 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           MN++   ++V  +  L  YI    + PML  ++E   A+R     DL AA  L+ SHLR 
Sbjct: 1   MNKEAQMMLVP-QGNLEGYIRAANEYPMLTAEQEKDYAERLYYQDDLDAAKALILSHLRF 59

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A GY GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+L++
Sbjct: 60  VIHVARGYAGYGLPQADLIQEGNIGLMKAVRRFNPEMGVRLVSFAVHWIKAEIHEYVLKN 119

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L   ++N     +V  +A +L VS+ +VI M  R+
Sbjct: 120 WRIVKVATTKAQRKLFFNLRKTKQRLGWFSEN-----EVDLVANELGVSKEDVIEMESRM 174

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            G D   +   + +++ +     +L          L  +       + LT +M  L+ R 
Sbjct: 175 TGADIGFDLPADDAEEETFAPSMYLEDKSSNFAAELENENFETQAVDQLTVAMETLDARS 234

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + I + R L EN  TL +L++++ +S ERVRQ+E+ A KK++ ++
Sbjct: 235 QDIIKTRWLDENKATLHDLAAKYNISAERVRQLESNALKKLKSAV 279


>gi|283787904|ref|YP_003367769.1| RNA polymerase sigma-32 factor [Citrobacter rodentium ICC168]
 gi|282951358|emb|CBG91057.1| RNA polymerase sigma-32 factor [Citrobacter rodentium ICC168]
          Length = 284

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 109/290 (37%), Positives = 165/290 (56%), Gaps = 10/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +     L  YI      PML   EE  LA+R    GDL AA  L+ SHLR 
Sbjct: 1   MTKEMQNLALAPVGNLESYIRAANAWPMLSADEERALAERLHYQGDLEAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVEMVARELGVSSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQ---EQVLIEKEERKNRRNMLTRSMSVLNP 237
           A  + +   ++  D++ SQ    ++Y  D        + E        + LT +M  L+ 
Sbjct: 176 AA-QDMTFDMSPDDESDSQPMAPVLYLQDKTSNFADGIEEDNWEDQAASKLTHAMEGLDE 234

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L E+   TL+ L+  + VS ERVRQ+E  A KK++ +I+ 
Sbjct: 235 RSQAIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 284


>gi|18477828|emb|CAC83737.1| RNA polymerase sigma 70 [Rhodococcus fascians]
          Length = 474

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 79/319 (24%), Positives = 148/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------REHGDL- 47
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+  
Sbjct: 161 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLFAVEKMRESAEKGEKL 219

Query: 48  ----------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 220 PVAQRRDMTWICRDGNRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 279

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 280 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 337

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 338 REPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 389

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 390 AVVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 449

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 450 RQIESKTMSKLRHPSRSQV 468


>gi|113866384|ref|YP_724873.1| RNA polymerase factor sigma-32 [Ralstonia eutropha H16]
 gi|113525160|emb|CAJ91505.1| DNA-directed RNA polymerase sigma subunit (RpoH) [Ralstonia
           eutropha H16]
          Length = 308

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 119/279 (42%), Positives = 171/279 (61%), Gaps = 12/279 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             L  YI  + +IP+L  +EE  LA+  R+H  + AA ++V SHLRLVV IA  Y GYGL
Sbjct: 34  GNLDSYIQAVHRIPLLTAEEEQRLARELRDHDSVDAARQMVMSHLRLVVSIARQYLGYGL 93

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P ++++ EGNIGLM+AVK+FDP++G RL +Y+M WIKA + EY+L++W +VK+ TT  Q+
Sbjct: 94  PHADLIQEGNIGLMKAVKRFDPDQGVRLVSYAMHWIKAEIHEYVLKNWRMVKVATTKAQR 153

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINS 192
           +LFFNLR  K        +   PEQV A+A++LNV   EV+ M  RL  GD +L   I+ 
Sbjct: 154 KLFFNLRSHKQ-----GAHTFTPEQVEAVARELNVKPEEVMEMETRLSGGDLALEGQIDD 208

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---- 248
            ++  +    +L  +H+   +VL  K   + +   L  ++  L+ R RRI EAR L    
Sbjct: 209 GEEEFA-PIAYLADNHNEPTRVLEAKRHDRMQVEGLEEALGKLDERSRRIIEARWLHVED 267

Query: 249 -QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                 TL  L+ EF VS ER+RQIEA A KK++ ++Q 
Sbjct: 268 DGSGGSTLHELADEFGVSAERIRQIEAAAMKKMKGALQA 306


>gi|121611388|ref|YP_999195.1| RNA polymerase sigma-32 subunit RpoH [Verminephrobacter eiseniae
           EF01-2]
 gi|121556028|gb|ABM60177.1| RNA polymerase, sigma 32 subunit, RpoH [Verminephrobacter eiseniae
           EF01-2]
          Length = 313

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 113/295 (38%), Positives = 174/295 (58%), Gaps = 14/295 (4%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
            +V     L  YI  + ++P+L  ++E   A++++EH DL AA RLV SHLRLVV IA  
Sbjct: 19  TLVPALGNLDAYIAAVNRLPLLTYEQEQSYARQFKEHNDLDAAGRLVLSHLRLVVSIARQ 78

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y GYGLP  +++ EGNIGLM+AVK+FDP++G RL +Y+M WIKA + EYIL++W +VK+ 
Sbjct: 79  YLGYGLPHGDLIQEGNIGLMKAVKRFDPDQGVRLVSYAMHWIKAEIHEYILKNWRMVKVA 138

Query: 128 TTANQKRLFFNLRRLKGHLQAIT--------DNNLKPEQVVAIAKKLNVSESEVISMNCR 179
           TT  Q++LFFNLR +K   +A           + L   ++ A+A +L+V   EVI M  R
Sbjct: 139 TTKAQRKLFFNLRSMKQGFKADAGATDAATYRDTLSEHEIDAVAAQLHVKREEVIEMETR 198

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLNPR 238
           ++G + L     S D   +      + D   +   LIE  +R     + + ++++ L+ R
Sbjct: 199 MSGGDVLLDPAPSDDGEQAFGPIAYLADASHEPTALIESRQRDALATDGIAKALASLDER 258

Query: 239 ERRIFEARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            RRI + R L         +TL +L++ + VS ER+RQIE  A KK+++++ K  
Sbjct: 259 SRRIVQERWLKVNDDGTGGMTLHDLAAIYGVSAERIRQIEVAAMKKMKQALVKYA 313


>gi|94309217|ref|YP_582427.1| RNA polymerase factor sigma-32 [Cupriavidus metallidurans CH34]
 gi|93353069|gb|ABF07158.1| RNA polymerase sigma 32 (sigma H) factor [Cupriavidus metallidurans
           CH34]
          Length = 311

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 122/286 (42%), Positives = 177/286 (61%), Gaps = 13/286 (4%)

Query: 6   MSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
            ++   G +G L  YI  + +IPML  +EE  LA+  R++  + AA R+V SHLRLVV I
Sbjct: 28  FALTFPGTLGNLDSYIQAVHRIPMLTPEEELSLARDLRDNDSVDAARRMVMSHLRLVVSI 87

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y GYGLP ++++ EGNIGLM+AVK+FDPE+G RL +Y+M WIKA + EY+L++W +V
Sbjct: 88  ARQYLGYGLPHADLIQEGNIGLMKAVKRFDPEQGVRLVSYAMHWIKAEIHEYVLKNWRMV 147

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGD 183
           K+ TT  Q++LFFNLR  K        +   PEQ+ A+A++LNV   EV+ M  R+  GD
Sbjct: 148 KVATTKAQRKLFFNLRSHKQ-----GSHTFTPEQIEAVARELNVKPEEVMEMETRMSGGD 202

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            +L   I   ++  +    +L  +H+   QVL  K   + +   L  +++ L+PR RRI 
Sbjct: 203 MALEGQIEDGEEEFA-PIAYLADNHNEPTQVLEAKRHDRLQVEGLEEALTKLDPRSRRII 261

Query: 244 EARRLQENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           EAR L  N       TL  L+ EF VS ER+RQIE+ A KK++ ++
Sbjct: 262 EARWLDVNDDGSGGATLHELADEFGVSAERIRQIESAAMKKMKGAL 307


>gi|118469122|ref|YP_887090.1| RNA polymerase sigma factor [Mycobacterium smegmatis str. MC2 155]
 gi|555680|gb|AAA85642.1| sigma factor MysA [Mycobacterium smegmatis]
 gi|118170409|gb|ABK71305.1| sigma factor MysA [Mycobacterium smegmatis str. MC2 155]
          Length = 466

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 78/319 (24%), Positives = 149/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------------- 41
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR                     
Sbjct: 153 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQKLAELAEKGEKL 211

Query: 42  --REHGDLS--------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
             ++  D+         A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 212 PVQQRRDMQWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 271

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 272 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 329

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 330 REPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 381

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 382 AVVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 441

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 442 RQIESKTMSKLRHPSRSQV 460


>gi|114570847|ref|YP_757527.1| RNA polymerase sigma 32 subunit RpoH [Maricaulis maris MCS10]
 gi|114341309|gb|ABI66589.1| RNA polymerase, sigma 32 subunit, RpoH [Maricaulis maris MCS10]
          Length = 305

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 113/287 (39%), Positives = 175/287 (60%), Gaps = 3/287 (1%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           + G  R++       +L +++E  LA+R+++  D  A H L  +H+RLV+ +A  ++ YG
Sbjct: 19  DAGEQRFVKSAMARDLLSREDEADLARRWKDDRDEKALHELTEAHMRLVIAVAAKFKRYG 78

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP S+++ EGNIGLM+A  +FDPER  R +TY  WWI++ +Q+Y+LR+WS+V+ GTT+ Q
Sbjct: 79  LPFSDLIQEGNIGLMKAADRFDPERDVRFSTYVTWWIRSCIQDYVLRNWSIVRTGTTSAQ 138

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALIN 191
           K LFFNLRR++ ++  +  +++ P+    IAK L V E +V +M  RL A D SLNA + 
Sbjct: 139 KSLFFNLRRIRANIGDLDGSSITPDNRQKIAKDLRVRERDVENMALRLSASDRSLNAPV- 197

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             D   SQWQD+LV D    E  ++ + + + R   L  ++  LN RE+ I   RRL+E+
Sbjct: 198 -GDAEDSQWQDFLVDDTAAPETEVMNRTDSERRSAWLGLALDGLNSREQFIIRERRLRED 256

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQ 298
             TL +L     +S+ERVRQIE  A  K+++ +   V       LL 
Sbjct: 257 GSTLASLGDSLGISKERVRQIENAALAKLRDHLTANVGDPHEAGLLP 303


>gi|307298746|ref|ZP_07578549.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermotogales
           bacterium mesG1.Ag.4.2]
 gi|306915911|gb|EFN46295.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermotogales
           bacterium mesG1.Ag.4.2]
          Length = 416

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 75/288 (26%), Positives = 142/288 (49%), Gaps = 13/288 (4%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
               M   ++ +  +  Y+ EI KI +L    E  LA+R ++ G+  A   L+T++LRLV
Sbjct: 125 TTPEMYDNISLKDPIKMYLKEIGKISLLTPSRERELARRAQK-GEPKAKEELITANLRLV 183

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA  Y G GL   +++ EGNIGL++AV+KFD ++G++ +TY+ WWI+ A+   I    
Sbjct: 184 VSIAKRYIGRGLTFLDLIQEGNIGLIKAVEKFDWKKGYKFSTYATWWIRQAITRAIADQA 243

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             +++     +      + +L   ++    ++ +   +  +      +  ++  +     
Sbjct: 244 RTIRVPVHMVE-----TINKLNKVIREHLQDHGEYPTIEELGNLTGKTPEKIEEILAASK 298

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              SL + I+  ++  S   D++   HD   +   E   +   R  + + +  L+PRE  
Sbjct: 299 ETVSLESPISGDEE--STMGDFI---HDDSMEQPEEAAMKMLLREQIDQILDTLSPREAM 353

Query: 242 IFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           + + R   L     TLE +   F V+RER+RQIE +A +K++   + +
Sbjct: 354 VLKMRYGLLDGKTKTLEEVGQFFNVTRERIRQIEVKALRKLRHPSRSK 401


>gi|254391058|ref|ZP_05006266.1| RNA polymerase principal sigma factor hrdB [Streptomyces
           clavuligerus ATCC 27064]
 gi|197704753|gb|EDY50565.1| RNA polymerase principal sigma factor hrdB [Streptomyces
           clavuligerus ATCC 27064]
          Length = 514

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 75/314 (23%), Positives = 143/314 (45%), Gaps = 40/314 (12%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------- 41
           + +++       +  Y+ +I K+P+L  ++E  LAKR                       
Sbjct: 206 QQVAVAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANADKLAPKLKR 265

Query: 42  -----REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                 E G   A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  
Sbjct: 266 ELEIIAEDG-RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYT 324

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  +         P
Sbjct: 325 KGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTP 382

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           E    +AK+L+++  +VI +        SL+  +   +   S++ D +    D +  V  
Sbjct: 383 E---ELAKELDMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPA 434

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEA 274
           +       +  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE+
Sbjct: 435 DAVSFTLLQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIES 494

Query: 275 RAFKKVQESIQKQV 288
           +   K++   + QV
Sbjct: 495 KTMSKLRHPSRSQV 508


>gi|325962990|ref|YP_004240896.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Arthrobacter
           phenanthrenivorans Sphe3]
 gi|323469077|gb|ADX72762.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Arthrobacter
           phenanthrenivorans Sphe3]
          Length = 437

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 71/304 (23%), Positives = 135/304 (44%), Gaps = 39/304 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------------HGD 46
             +  Y+ +I K+ +L  ++E  LA R                              H  
Sbjct: 138 DPVKDYLKQIGKVALLNAEQEVDLALRIEAGLFAEEKINADDGSMDPKYKRELEFIIHDG 197

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ 
Sbjct: 198 KRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYAT 257

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +A +L
Sbjct: 258 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELALEL 312

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +V+ +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 313 DMTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 367

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 368 QLHSVLDTLSEREAGVVAMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 427

Query: 285 QKQV 288
           + QV
Sbjct: 428 RSQV 431


>gi|291613119|ref|YP_003523276.1| RNA polymerase, sigma 32 subunit, RpoH [Sideroxydans lithotrophicus
           ES-1]
 gi|291583231|gb|ADE10889.1| RNA polymerase, sigma 32 subunit, RpoH [Sideroxydans lithotrophicus
           ES-1]
          Length = 289

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 119/288 (41%), Positives = 180/288 (62%), Gaps = 9/288 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           MN      I +    L  Y+  + + P+L  +EE  LA R++ H DL AA +LV SHLR+
Sbjct: 1   MNASMSLPIPSAVGSLESYVQAVNRFPVLSHEEELSLANRFKAHNDLDAARQLVLSHLRV 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A GY GYGLP ++++ EGNIGLM+AVK++D  RG RL ++++ WI+A + EY++R+
Sbjct: 61  VVSVARGYAGYGLPQADLIQEGNIGLMKAVKRYDATRGVRLVSFALHWIRAEIHEYVVRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W LVKI TT +Q++LFFNLR +K  L+      LKP+QV  IA++LNVSE +V+ M  R 
Sbjct: 121 WRLVKIATTKSQRKLFFNLRSMKQGLE-----PLKPQQVREIAQQLNVSERDVVEMEARF 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRE 239
           AG E     ++  +  S     +L  + + +   ++E  ER++     L ++++ L+ R 
Sbjct: 176 AGHEVALEPLSGEEDESYAPISYLADNAEHEPSYILEAAEREHLHTAGLAQALASLDERS 235

Query: 240 RRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           RRI EAR L++      TL  L+ EF+VS ER+RQIE +A  K+Q  +
Sbjct: 236 RRIVEARWLRDEEEHAATLHELADEFKVSAERIRQIEQKALSKMQALL 283


>gi|269798255|ref|YP_003312155.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Veillonella
           parvula DSM 2008]
 gi|282850493|ref|ZP_06259872.1| RNA polymerase sigma factor RpoD [Veillonella parvula ATCC 17745]
 gi|294792116|ref|ZP_06757264.1| RNA polymerase sigma factor RpoD [Veillonella sp. 6_1_27]
 gi|294793987|ref|ZP_06759124.1| RNA polymerase sigma factor RpoD [Veillonella sp. 3_1_44]
 gi|269094884|gb|ACZ24875.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Veillonella
           parvula DSM 2008]
 gi|282579986|gb|EFB85390.1| RNA polymerase sigma factor RpoD [Veillonella parvula ATCC 17745]
 gi|294455557|gb|EFG23929.1| RNA polymerase sigma factor RpoD [Veillonella sp. 3_1_44]
 gi|294457346|gb|EFG25708.1| RNA polymerase sigma factor RpoD [Veillonella sp. 6_1_27]
          Length = 386

 Score =  251 bits (641), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 78/291 (26%), Positives = 130/291 (44%), Gaps = 23/291 (7%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSA-----------AHRLVTSHL 58
           VN +  +  Y+ EI ++P+L   EE VLAK+        A             +LV ++L
Sbjct: 100 VNIDDPVRMYLKEIGRVPLLSADEEIVLAKQIEAGAQEDATYKDIQLSKKAKKKLVDANL 159

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV IA  Y G G+   +++ EGN+GL++AV KFD  +G++ +TY+ WWI+ A+   I 
Sbjct: 160 RLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVDKFDYTKGYKFSTYATWWIRQAITRAIA 219

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
                ++I     +      L R+   L         PE    IA+ + ++   V  +  
Sbjct: 220 DQARTIRIPVHMVE--TINKLIRISRQLLQDKGREPLPE---EIAEGMGITVERVREIQK 274

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
                 SL   I   ++  S   D++    D       +       +  +    + L  R
Sbjct: 275 IAQEPVSLETPI--GEEEDSHLGDFI---EDQDAIAPDDAASYILLQEQIEDVFTCLTDR 329

Query: 239 ERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+++   R       P TLE +   F V+RER+RQIE +A  K++   ++ 
Sbjct: 330 EQQVLILRFGLKDGKPRTLEEVGQHFNVTRERIRQIEGKALTKLRNRGKRD 380


>gi|241668310|ref|ZP_04755888.1| RNA polymerase factor sigma-32 [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
 gi|254876843|ref|ZP_05249553.1| RNA polymerase sigma-32 factor [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
 gi|254842864|gb|EET21278.1| RNA polymerase sigma-32 factor [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
          Length = 292

 Score =  250 bits (640), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 105/286 (36%), Positives = 174/286 (60%), Gaps = 7/286 (2%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           K  S+ V  +  L+ Y++ +  +P+L  +EE  LA+RY+   DL AA +LV SHLR V K
Sbjct: 11  KGKSLPVVSDNNLNSYLNFVNSLPILSVEEEQELARRYKYQKDLDAAQQLVLSHLRFVTK 70

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  + GYGL I++++ EGNIGLM+AV KFDP++G RL ++++ WIKA M +Y+L++W +
Sbjct: 71  IARNFSGYGLSIADLIQEGNIGLMKAVSKFDPDQGVRLVSFAVHWIKAEMHDYVLKNWKI 130

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AG 182
           VK+ TT  Q++LFFNLR  K  +  ++      E +  +A++L V E  VI M  R+  G
Sbjct: 131 VKVATTKAQRKLFFNLRSSKDKIGWLS-----SEDIKQLAEELGVKEETVIEMEKRMCQG 185

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           D SL+      +   S  Q   + D     E  +++++   N + ++   +S  + R + 
Sbjct: 186 DASLDLPYTDDEGGQSNQQSLYLEDKSSDIEHQIVQQDYYDNFKAIVKDVISGFDTRTKD 245

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           I  +R L +   TL++L++++ +S ERVRQIE  A  K++++I+ +
Sbjct: 246 IIMSRYLLDTKATLQDLATKYNISAERVRQIEEEALVKLRKAIKNK 291


>gi|258653895|ref|YP_003203051.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nakamurella
           multipartita DSM 44233]
 gi|258557120|gb|ACV80062.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nakamurella
           multipartita DSM 44233]
          Length = 448

 Score =  250 bits (640), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 77/319 (24%), Positives = 147/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAK---------------------- 39
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAK                      
Sbjct: 135 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVDLAKRIEAGLYSSERMRQFEEAGERL 193

Query: 40  --------RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                   R+ +     A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 194 PNQMRRDLRWIKRDGERAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 253

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 254 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 311

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 312 REPTPE---ELAKEMDITPDKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 363

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 364 AVVAVDAVSFTLLQDQLQAVLQTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 423

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 424 RQIESKTMSKLRHPSRSQV 442


>gi|300313436|ref|YP_003777528.1| RNA polymerase sigma-32 factor protein [Herbaspirillum seropedicae
           SmR1]
 gi|300076221|gb|ADJ65620.1| RNA polymerase sigma-32 factor protein [Herbaspirillum seropedicae
           SmR1]
          Length = 299

 Score =  250 bits (640), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 128/286 (44%), Positives = 180/286 (62%), Gaps = 11/286 (3%)

Query: 6   MSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +++  +G +G +  YI  + ++PML  +EE  LA+  RE  DL AA ++V SHLRLVV I
Sbjct: 18  LALGFSGSLGNIDAYISAVNRLPMLTHEEEVKLARDLREKNDLGAAQKMVLSHLRLVVSI 77

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A GY GYGLP ++++ EGNIGLM+AVK+FDP +  RL +Y+M WIKA + EYIL++W LV
Sbjct: 78  ARGYLGYGLPHADLIQEGNIGLMKAVKRFDPAQNVRLVSYAMHWIKAEIHEYILKNWRLV 137

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-D 183
           K+ TT  Q++LFFNLR  K  L A+T     P QV A+AK L+V   EVI M  RL+G D
Sbjct: 138 KVATTKAQRKLFFNLRSHKEGLDAMT-----PAQVEALAKTLDVKREEVIEMETRLSGRD 192

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            +L +  +  D   +    +L  D+    +V+  K+  + +   L  ++S L+ R RRI 
Sbjct: 193 IALESPTDDEDDKFA-PIAYLSSDNSEPTRVIEAKQYDRLQSEGLEAALSKLDERSRRIV 251

Query: 244 EARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           EAR L  +     TL  L+ EF VS ER+RQIEA A KK++ S+Q 
Sbjct: 252 EARWLANDDGSGATLHELADEFGVSAERIRQIEAVALKKMKTSLQA 297


>gi|320008126|gb|ADW02976.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 515

 Score =  250 bits (640), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 75/314 (23%), Positives = 143/314 (45%), Gaps = 40/314 (12%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------- 41
           + +++       +  Y+ +I K+P+L  ++E  LAKR                       
Sbjct: 207 QQVAVAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANSDKLAPKLKR 266

Query: 42  -----REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                 E G   A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  
Sbjct: 267 ELEIIAEDG-RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYT 325

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  +         P
Sbjct: 326 KGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTP 383

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           E    +AK+L+++  +VI +        SL+  +   +   S++ D +    D +  V  
Sbjct: 384 E---ELAKELDMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPA 435

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEA 274
           +       +  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE+
Sbjct: 436 DAVSFTLLQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIES 495

Query: 275 RAFKKVQESIQKQV 288
           +   K++   + QV
Sbjct: 496 KTMSKLRHPSRSQV 509


>gi|269127406|ref|YP_003300776.1| RpoD subfamily RNA polymerase sigma-70 subunit [Thermomonospora
           curvata DSM 43183]
 gi|268312364|gb|ACY98738.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermomonospora
           curvata DSM 43183]
          Length = 385

 Score =  250 bits (640), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 85/315 (26%), Positives = 142/315 (45%), Gaps = 39/315 (12%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY------------------RE 43
           +  ++   V     +  Y+ EI ++P+L  +EE  LAK                    RE
Sbjct: 76  DEDDLGKRVPTSDLVRIYLREIGRVPLLTAEEEVELAKTIEAGLFAEEKLARAAFISPRE 135

Query: 44  HGDLS--------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
             DL         A  RL+ ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD 
Sbjct: 136 RLDLELIAREGARAKQRLIEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDY 195

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            +GF+ +TY+ WWI+ A+   I      ++I     +      L R++  L         
Sbjct: 196 TKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE--TINKLVRVQRQLHQDLGREPT 253

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
           P     I  ++ +    V+ +        SL + I   D +     D++    D    V 
Sbjct: 254 P---AEIGAEMGLPAERVVEIQRIAQEPVSLQSPIGEEDSD---LGDFI---EDADAVVP 304

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIE 273
           +E       ++ L   +  L+ RE+RI + R      +P TLE +  EF V+RER+RQIE
Sbjct: 305 LEAAAFILLQDQLEDILCTLSEREQRIIQLRFGLTDGHPRTLEEVGREFGVTRERIRQIE 364

Query: 274 ARAFKKVQESIQKQV 288
           ++   K++   + Q+
Sbjct: 365 SKTLAKLRHPSRAQM 379


>gi|184201082|ref|YP_001855289.1| RNA polymerase sigma factor SigA [Kocuria rhizophila DC2201]
 gi|183581312|dbj|BAG29783.1| RNA polymerase sigma factor SigA [Kocuria rhizophila DC2201]
          Length = 572

 Score =  250 bits (640), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 71/304 (23%), Positives = 135/304 (44%), Gaps = 39/304 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------------HGD 46
             +  Y+ +I K+ +L  ++E  LA R                              H  
Sbjct: 273 DPVKDYLKQIGKVALLNAEQEVDLALRIEAGLYAEHKFADEADSMDANTRRAYRWVIHDG 332

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ 
Sbjct: 333 RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYAT 392

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +A +L
Sbjct: 393 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELANEL 447

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +V+ +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 448 DMTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 502

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 503 QLHSVLDTLSEREAGVVAMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 562

Query: 285 QKQV 288
           + QV
Sbjct: 563 RSQV 566


>gi|237740231|ref|ZP_04570712.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. 2_1_31]
 gi|229422248|gb|EEO37295.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. 2_1_31]
          Length = 269

 Score =  250 bits (640), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 80/272 (29%), Positives = 139/272 (51%), Gaps = 13/272 (4%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
            Y+ EI ++P+L   EE   AKR  E GD  A+ +L+ S+LRLVV IA  +   GL + +
Sbjct: 1   MYLREIGQVPLLTHDEEIEYAKRAYE-GDEEASQKLIESNLRLVVSIAKKHTNRGLKLLD 59

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV+KF+  +G++ +TY+ WWI+ A+   I      ++I        +  
Sbjct: 60  LIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPVH-----MIE 114

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + ++K   +       K      +A++L +   ++ ++        SL   + S  +  
Sbjct: 115 TINKIKKESRIYLQETGKDASPEILAERLGMEVEKIKAIQEMNQEPISLETPVGS--EED 172

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTL 255
           S+  D++    D +     E   R   R  L   +  L+PRE ++   R   ++  P TL
Sbjct: 173 SELGDFV---EDQKTTSPYEATNRAILREELDGVLKTLSPREEKVLRYRYGLDDSSPKTL 229

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +   F V+RER+RQIE +A +K++   +K+
Sbjct: 230 EEVGKIFNVTRERIRQIEVKALRKLRHPSRKK 261


>gi|237749576|ref|ZP_04580056.1| RNA polymerase sigma-32 factor [Oxalobacter formigenes OXCC13]
 gi|229380938|gb|EEO31029.1| RNA polymerase sigma-32 factor [Oxalobacter formigenes OXCC13]
          Length = 299

 Score =  250 bits (640), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 121/288 (42%), Positives = 183/288 (63%), Gaps = 9/288 (3%)

Query: 1   MNRKNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLR 59
           ++R  ++ ++ G +G +  YI EI ++PML ++ E  LA+RY E+ DL+AA  LV SHLR
Sbjct: 13  VSRHALAPVLTGSLGNIEAYIAEINRLPMLTQERETELAQRYHENNDLAAAQELVLSHLR 72

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           LV  IA  Y GYGLP ++++ EGNIGLM+AVK+FDP+ G RL +Y++ WIKA + EYILR
Sbjct: 73  LVASIARNYLGYGLPHADLIQEGNIGLMKAVKRFDPKMGVRLVSYAIHWIKAEIHEYILR 132

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
           +W +VK+ TT  Q++LFFNLR  K   +A+T      EQ+ ++A+KLNV + EV  M  R
Sbjct: 133 NWRMVKVATTKAQRKLFFNLRSHKSGNEAMT-----REQIRSLAEKLNVKDEEVSEMETR 187

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           L+G +      +  D ++     +L  +     +VL  K+  + +   L  ++  L+ R 
Sbjct: 188 LSGHDIALETQHDDDDDNFAPIAYLSSEQTEPTRVLEAKQHDRLQSEGLAEALDKLDDRS 247

Query: 240 RRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +RI EAR L+ +     TL +L+ EF VS ER+RQIEA A KK++ ++
Sbjct: 248 KRIIEARWLKNDDGSGATLHDLAEEFGVSAERIRQIEAAALKKMKNTL 295


>gi|91775055|ref|YP_544811.1| sigma 32 (RpoH) [Methylobacillus flagellatus KT]
 gi|91709042|gb|ABE48970.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacillus flagellatus
           KT]
          Length = 285

 Score =  250 bits (640), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 117/286 (40%), Positives = 176/286 (61%), Gaps = 6/286 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M        ++    L +Y+  I+  P+L  +EE  LA R +++ DL AA  LV SHLRL
Sbjct: 1   MTNSMTLPAISSFDSLDQYLRAIKSFPVLSAEEELKLATRLKKYNDLEAAKTLVVSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  IA  Y GYGLP ++++ EGNIGLM+AV++FDP+RG RL +++M WIKA + EYI+R+
Sbjct: 61  VASIARNYAGYGLPQADLIQEGNIGLMKAVRRFDPDRGVRLVSFAMHWIKAEIHEYIVRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W LVK+ TT  Q++LFFNLR +K    A    +L  ++V  IA++LNV   EV+ M  R+
Sbjct: 121 WRLVKVATTKAQRKLFFNLRSMKKGQTA----SLHSDEVAHIARELNVKPEEVLEMEARM 176

Query: 181 AGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G E SL    +  +++      +L   H    ++L  +E  +     L+ +++ L+ R 
Sbjct: 177 SGHEISLEGNADDDNEDMFSPISYLQASHAEPSEILEAQEADQLHTTGLSTALAKLDDRS 236

Query: 240 RRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           RRI EAR LQE +  TL +L+ EF VS ER+RQIE +A K+++  +
Sbjct: 237 RRIVEARWLQEGHNATLHDLAEEFGVSAERIRQIEQKAMKQMRGFL 282


>gi|59800736|ref|YP_207448.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae FA 1090]
 gi|194098013|ref|YP_002001061.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae NCCP11945]
 gi|239998477|ref|ZP_04718401.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae 35/02]
 gi|240016041|ref|ZP_04722581.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae FA6140]
 gi|240080183|ref|ZP_04724726.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae FA19]
 gi|240115137|ref|ZP_04729199.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID18]
 gi|240117420|ref|ZP_04731482.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID1]
 gi|240122976|ref|ZP_04735932.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID332]
 gi|240125228|ref|ZP_04738114.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae SK-92-679]
 gi|240127682|ref|ZP_04740343.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae SK-93-1035]
 gi|254493195|ref|ZP_05106366.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae 1291]
 gi|260441046|ref|ZP_05794862.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae DGI2]
 gi|268594335|ref|ZP_06128502.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae 35/02]
 gi|268596331|ref|ZP_06130498.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae FA19]
 gi|268600810|ref|ZP_06134977.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID18]
 gi|268603115|ref|ZP_06137282.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID1]
 gi|268681596|ref|ZP_06148458.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID332]
 gi|268683824|ref|ZP_06150686.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae SK-92-679]
 gi|268686066|ref|ZP_06152928.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae SK-93-1035]
 gi|291044379|ref|ZP_06570088.1| RNA polymerase sigma factor [Neisseria gonorrhoeae DGI2]
 gi|293399564|ref|ZP_06643717.1| alternative sigma factor RpoH [Neisseria gonorrhoeae F62]
 gi|59717631|gb|AAW89036.1| putative RNA polymerase sigma-32 [Neisseria gonorrhoeae FA 1090]
 gi|193933303|gb|ACF29127.1| RNA polymerase sigma factor [Neisseria gonorrhoeae NCCP11945]
 gi|226512235|gb|EEH61580.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae 1291]
 gi|268547724|gb|EEZ43142.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae 35/02]
 gi|268550119|gb|EEZ45138.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae FA19]
 gi|268584941|gb|EEZ49617.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID18]
 gi|268587246|gb|EEZ51922.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID1]
 gi|268621880|gb|EEZ54280.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae PID332]
 gi|268624108|gb|EEZ56508.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae SK-92-679]
 gi|268626350|gb|EEZ58750.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae SK-93-1035]
 gi|291011273|gb|EFE03269.1| RNA polymerase sigma factor [Neisseria gonorrhoeae DGI2]
 gi|291610133|gb|EFF39255.1| alternative sigma factor RpoH [Neisseria gonorrhoeae F62]
          Length = 290

 Score =  250 bits (640), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 120/289 (41%), Positives = 183/289 (63%), Gaps = 7/289 (2%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N   +  I +G   L +YIH +  IPML ++EE  LA+R R  GDL+AA +L+ SHLR+V
Sbjct: 6   NAFALPAIQSGNGSLEQYIHTVNSIPMLSQEEETRLAER-RIKGDLNAAKQLILSHLRVV 64

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+ILR+W
Sbjct: 65  VSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILRNW 124

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            LV++ TT  Q++LFFNLR ++ +L     N L P++   IA  L V  SEV+ M  R+ 
Sbjct: 125 RLVRVATTKPQRKLFFNLRSMRKNL-----NVLSPKEAQDIADDLGVKLSEVLEMEQRMT 179

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           G +      NS D++S    DWL        + L ++     +   L  +++ L+ R RR
Sbjct: 180 GHDIAIMADNSDDEDSFAPIDWLADHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRR 239

Query: 242 IFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           I E+R LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 240 IVESRWLQDDGGLTLHQLAAEYGVSAERIRQIEAKAMQKLRGFLTEEAE 288


>gi|317163755|gb|ADV07296.1| RNA polymerase factor sigma-32 [Neisseria gonorrhoeae TCDC-NG08107]
          Length = 287

 Score =  250 bits (640), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 120/289 (41%), Positives = 183/289 (63%), Gaps = 7/289 (2%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N   +  I +G   L +YIH +  IPML ++EE  LA+R R  GDL+AA +L+ SHLR+V
Sbjct: 3   NAFALPAIQSGNGSLEQYIHTVNSIPMLSQEEETRLAER-RIKGDLNAAKQLILSHLRVV 61

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+ILR+W
Sbjct: 62  VSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILRNW 121

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            LV++ TT  Q++LFFNLR ++ +L     N L P++   IA  L V  SEV+ M  R+ 
Sbjct: 122 RLVRVATTKPQRKLFFNLRSMRKNL-----NVLSPKEAQDIADDLGVKLSEVLEMEQRMT 176

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           G +      NS D++S    DWL        + L ++     +   L  +++ L+ R RR
Sbjct: 177 GHDIAIMADNSDDEDSFAPIDWLADHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRR 236

Query: 242 IFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           I E+R LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 237 IVESRWLQDDGGLTLHQLAAEYGVSAERIRQIEAKAMQKLRGFLTEEAE 285


>gi|239931428|ref|ZP_04688381.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 430

 Score =  250 bits (640), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 84/301 (27%), Positives = 137/301 (45%), Gaps = 38/301 (12%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKR----------YREHGDLS------------ 48
                  +Y+ EI +IP+L   EE  LA+R           R   DL             
Sbjct: 129 PSSDLFRQYLREIGRIPLLTAAEEVELARRVEAGLFAEEKLRLTPDLDSRLAHDLDRLVV 188

Query: 49  ----AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
               A  RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY
Sbjct: 189 MGRMAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTY 248

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + WWI+ AM   +      +++     +  L   + R++  +         PE+V A   
Sbjct: 249 ATWWIRQAMSRALADQARTIRVPVHVVE--LINRVVRVQRRMLQERGREPTPEEVAA--- 303

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            L++    V  +        SL+A +   +++     D +    DG     +E       
Sbjct: 304 HLDLPPERVGEVLRLAQEPVSLHAPV--GEEDDVALGDLI---EDGDAASPVESAAFLLL 358

Query: 225 RNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           R  L   +S L  RER++ + R       P TLE +   F V+RER+RQIE++   K+++
Sbjct: 359 REHLEAVLSTLGERERKVVQLRYGLVDGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRD 418

Query: 283 S 283
            
Sbjct: 419 H 419


>gi|239917829|ref|YP_002957387.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Micrococcus luteus NCTC
           2665]
 gi|281413678|ref|ZP_06245420.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family protein [Micrococcus
           luteus NCTC 2665]
 gi|239839036|gb|ACS30833.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Micrococcus luteus NCTC
           2665]
          Length = 497

 Score =  250 bits (640), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 75/303 (24%), Positives = 139/303 (45%), Gaps = 38/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR------------------YREHGD--------L 47
             +  Y+ +I K+ +L  ++E  LA R                  YRE  D         
Sbjct: 199 DPVKDYLKQIGKVALLNAEQEVDLAMRIEAGLYAEHVVQHEASDDYRERRDIQLIIADGR 258

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ W
Sbjct: 259 KAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATW 318

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L+
Sbjct: 319 WIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKELD 373

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++  +V+ +        SL+  +   +   S++ D +    D +  V  +       +  
Sbjct: 374 MTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQEQ 428

Query: 228 LTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   +
Sbjct: 429 LHSVLDTLSEREAGVVAMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSR 488

Query: 286 KQV 288
            QV
Sbjct: 489 SQV 491


>gi|302557983|ref|ZP_07310325.1| RNA polymerase sigma (70) factor RpoD [Streptomyces griseoflavus
           Tu4000]
 gi|302475601|gb|EFL38694.1| RNA polymerase sigma (70) factor RpoD [Streptomyces griseoflavus
           Tu4000]
          Length = 509

 Score =  250 bits (640), Expect = 1e-64,   Method: Composition-based stats.
 Identities = 75/304 (24%), Positives = 138/304 (45%), Gaps = 40/304 (13%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------------REHGD 46
             +  Y+ +I K+P+L  ++E  LAKR                             E G 
Sbjct: 211 DPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANSDKLAPKLKRELEIIAEDG- 269

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 270 RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 329

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI  A+   +      ++I     +  +   L R++  +         PE    +AK+L
Sbjct: 330 WWICQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKEL 384

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +VI +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 385 DMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 439

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 440 QLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 499

Query: 285 QKQV 288
           + QV
Sbjct: 500 RSQV 503


>gi|326318574|ref|YP_004236246.1| RNA polymerase sigma-32 subunit RpoH [Acidovorax avenae subsp.
           avenae ATCC 19860]
 gi|323375410|gb|ADX47679.1| RNA polymerase, sigma 32 subunit, RpoH [Acidovorax avenae subsp.
           avenae ATCC 19860]
          Length = 313

 Score =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 110/294 (37%), Positives = 171/294 (58%), Gaps = 14/294 (4%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           ++     L  YI  + ++PML  +EE   A+R +EH D+ AA R+V SHLRLVV IA  Y
Sbjct: 20  LIPPLGNLDAYISAVNRLPMLTAEEERTYARRLKEHNDVEAAGRMVMSHLRLVVSIARQY 79

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGLP  +++ EGN+GLM+AVK+FDP++  RL +Y+M WIKA + EYIL++W +VK+ T
Sbjct: 80  LGYGLPHGDLIQEGNVGLMKAVKRFDPDQNVRLVSYAMHWIKAEIHEYILKNWRMVKVAT 139

Query: 129 TANQKRLFFNLRRLKGHLQA--------ITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           T +Q++LFFNLR +K   +A             L  +++  +A++LNV   EVI M  RL
Sbjct: 140 TKSQRKLFFNLRSMKQGFKADSAAGNTGTHRETLSEQEIDVVAQQLNVKREEVIEMETRL 199

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLNPRE 239
           +G + +     S D   +      + D   +   +IE  +R     + +  +++ L+ R 
Sbjct: 200 SGGDVMLDPAPSDDGEQAYGPIAYLADGTHEPTAMIESRQRDVLATDGIANALATLDDRS 259

Query: 240 RRIFEARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RRI E R L         +TL  L++ + VS ER+RQIE  A KK+++++ +  
Sbjct: 260 RRIVEERWLKVNDDGSGGMTLHELAAVYGVSAERIRQIEVAAMKKMKKALAEYA 313


>gi|229815176|ref|ZP_04445512.1| hypothetical protein COLINT_02221 [Collinsella intestinalis DSM
           13280]
 gi|229809186|gb|EEP44952.1| hypothetical protein COLINT_02221 [Collinsella intestinalis DSM
           13280]
          Length = 448

 Score =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 86/314 (27%), Positives = 147/314 (46%), Gaps = 42/314 (13%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY------------REHGDLS---- 48
           + S ++     +  Y+ EI K+ +L   EE  LA +             +E G++     
Sbjct: 135 DASTVMLTGDPVRMYLKEIGKVDLLTAAEEVDLAMKIEAGLDAADKLEKQEAGEIELTRA 194

Query: 49  --------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                         A   L++++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD
Sbjct: 195 EMRRLMRVEQVGLDAKQALISANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFD 254

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
            E+GF+ +TY+ WWI+ A+   I      ++I     +      L R++  L      + 
Sbjct: 255 YEKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE--TINKLVRVQRQLLQDLGRDP 312

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            PE++ A   ++++S   V  +        SL   I   ++  SQ  D++    D Q  V
Sbjct: 313 TPEEIGA---EMDMSADRVREIQKISQEPVSLETPI--GEEEDSQLGDFI---EDAQAVV 364

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
             +       +  LT+ +  L  RER++ E R   E+  P TLE +  EF V+RER+RQI
Sbjct: 365 PADAASFSMLQEQLTQVLDGLAERERKVIELRFGLEDGHPRTLEEVGREFGVTRERIRQI 424

Query: 273 EARAFKKVQESIQK 286
           E++   K++   + 
Sbjct: 425 ESKTLAKLRHPSRS 438


>gi|109900247|ref|YP_663502.1| RNA polymerase, sigma 32 subunit, RpoH [Pseudoalteromonas atlantica
           T6c]
 gi|109702528|gb|ABG42448.1| RNA polymerase, sigma 32 subunit, RpoH [Pseudoalteromonas atlantica
           T6c]
          Length = 289

 Score =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 103/284 (36%), Positives = 165/284 (58%), Gaps = 6/284 (2%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           + + +++ V     +  Y+  +  I ML  +EE  LA+R ++  DL AA +L+ SHLR V
Sbjct: 10  DMRALTLTVPQTGSIETYVQAVSSINMLTAEEERGLAERLQQEDDLLAARKLIMSHLRFV 69

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA  Y GYGLP ++++ EGNIGLM+AV++FDP  G RL ++++ WIKA + E++LR+W
Sbjct: 70  VHIAKSYSGYGLPQADLIQEGNIGLMKAVRRFDPTVGVRLVSFAVHWIKAEIHEFVLRNW 129

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            +VK+ TT  Q++LFFNLR+ K  L   T       +V  +A  L VSE EV+ M  R++
Sbjct: 130 RIVKVATTKAQRKLFFNLRKNKKRLGWFTH-----AEVQKVASDLGVSEKEVLQMEARMS 184

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRER 240
             +    L    D++ S      + D     E  ++  +        L  ++  L+ R +
Sbjct: 185 SHDQAFDLSADDDESGSFAPVQFLEDKSADVETDVVNADWDATASQKLYSAIKTLDERSQ 244

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            I + R L ++  TL++L+ +++VS ERVRQIE  A KK+Q ++
Sbjct: 245 HIIQTRWLSDDKTTLQDLADKYQVSAERVRQIEKNAMKKLQSAM 288


>gi|270158013|ref|ZP_06186670.1| RNA polymerase sigma-32 factor RpoH [Legionella longbeachae D-4968]
 gi|289163720|ref|YP_003453858.1| RNA polymerase sigma-32 factor [Legionella longbeachae NSW150]
 gi|269990038|gb|EEZ96292.1| RNA polymerase sigma-32 factor RpoH [Legionella longbeachae D-4968]
 gi|288856893|emb|CBJ10704.1| RNA polymerase sigma-32 factor [Legionella longbeachae NSW150]
          Length = 284

 Score =  250 bits (640), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 108/275 (39%), Positives = 171/275 (62%), Gaps = 7/275 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  YIH + +IPML  +EE   A+R+   GDL AA RLV +HLR VV++A GY GYGL
Sbjct: 15  GSIDAYIHRVNQIPMLSLEEEIACAERFHSEGDLEAARRLVLAHLRYVVRVARGYLGYGL 74

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+++++ EGN+GLM+AVK+FDP+ G RL ++++ WIKA + E++LR+W +VKI TT  Q+
Sbjct: 75  PLNDLIQEGNVGLMKAVKRFDPKMGVRLVSFAVHWIKAEIHEFVLRNWRIVKIATTKAQR 134

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINS 192
           +LFFNLR++K  L  ++      E+V A+A  L VS  +V+ M  RL A D   +A    
Sbjct: 135 KLFFNLRQMKNRLGWMSH-----EEVSAVANDLGVSREDVLVMEQRLNAMDTPYDAPDAD 189

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPRERRIFEARRLQEN 251
                    +  +++ +    V++E +   ++ R  L  ++  L+ R + I + R L E 
Sbjct: 190 DHDEFYTAPERYLFNTNDDPSVMLENDSASDQGREKLMFALEQLDERSQDILQQRWLSEE 249

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +TL +L+ ++ VS ERVRQ+E  A KK+++ I+ 
Sbjct: 250 KLTLHDLAKKYGVSAERVRQLEKNAMKKLKQYIES 284


>gi|78049505|ref|YP_365680.1| RNA polymerase factor sigma-32 [Xanthomonas campestris pv.
           vesicatoria str. 85-10]
 gi|294626531|ref|ZP_06705130.1| RNA polymerase sigma factor [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 11122]
 gi|294665098|ref|ZP_06730402.1| RNA polymerase sigma factor [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 10535]
 gi|78037935|emb|CAJ25680.1| RNA polymerase sigma-32 factor [Xanthomonas campestris pv.
           vesicatoria str. 85-10]
 gi|292599221|gb|EFF43359.1| RNA polymerase sigma factor [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 11122]
 gi|292605140|gb|EFF48487.1| RNA polymerase sigma factor [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 10535]
          Length = 294

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 119/291 (40%), Positives = 173/291 (59%), Gaps = 15/291 (5%)

Query: 1   MNRKNMSIIV-------NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRL 53
           MN+   + +V       +    L  YI  + +IP+L   EE  LA+R+R+  DL AA  L
Sbjct: 4   MNQTTSTALVANNLPIPSALGSLDAYIGAVHQIPVLSVDEEQDLARRFRDELDLDAAREL 63

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V SHLR VV +A GY GYGLP+ +++ EGNIGLM+AVK+FDP+ G RL ++++ WI+A M
Sbjct: 64  VHSHLRFVVHVARGYNGYGLPLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAVHWIRAEM 123

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
            E+IL++W +VK+ TT  Q++LFFNLR+ K  L  +        +V A+AK LNVSE EV
Sbjct: 124 HEFILKNWRIVKVATTKAQRKLFFNLRKSKTRLGWLN-----ASEVTAVAKDLNVSEREV 178

Query: 174 ISMNCRLAG-DESLNA-LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           + M  RL+G D   +A      D        +LV + +   Q     +   N+  +L   
Sbjct: 179 MEMESRLSGRDIGFDASSDEDDDHGPPSPVSYLVANEEDPSQAYERHDSEDNQLQLLREG 238

Query: 232 MSVLNPRERRIFEARRLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           M+ L+ R R I + R L  ++ VTL+ L+ E+ VS ER+RQIEA A KK++
Sbjct: 239 MAGLDARSRDIVKRRWLDSDSKVTLQELADEYGVSAERIRQIEANALKKMK 289


>gi|146410|gb|AAA23991.1| heat shock regulatory protein [Escherichia coli]
          Length = 284

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 109/289 (37%), Positives = 162/289 (56%), Gaps = 8/289 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  K  S+ +     L  YI      PML   EE  LA++   HGDL AA  L+ SHLR 
Sbjct: 1   MTDKMQSLALAPVGNLDSYIRAANAWPMLSADEERALAEKLHYHGDLEAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVEMVARELGVTSKDVREMESRM 175

Query: 181 -AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE-ERKNRRNMLTRSMSVLNPR 238
            A D + +   +    + +      + D        IE +   +   N LT +M  L+ R
Sbjct: 176 AAQDMTFDLASDDDSDSHAMAPVLYLQDKSSNFADGIEDDNWEEQAANRLTDAMQGLDER 235

Query: 239 ERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + I  AR L E+   TL+ L+  + VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 SQDIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 284


>gi|297156708|gb|ADI06420.1| RNA polymerase sigma factor [Streptomyces bingchenggensis BCW-1]
          Length = 515

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 75/304 (24%), Positives = 139/304 (45%), Gaps = 40/304 (13%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------------REHGD 46
             +  Y+ +I K+P+L  ++E  LAKR                             E G 
Sbjct: 217 DPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANSDKLAPKLKRELEIIAEDG- 275

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 276 RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 335

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L
Sbjct: 336 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKEL 390

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +VI +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 391 DMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 445

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 446 QLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 505

Query: 285 QKQV 288
           + QV
Sbjct: 506 RSQV 509


>gi|210633964|ref|ZP_03297935.1| hypothetical protein COLSTE_01853 [Collinsella stercoris DSM 13279]
 gi|210159008|gb|EEA89979.1| hypothetical protein COLSTE_01853 [Collinsella stercoris DSM 13279]
          Length = 445

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 85/314 (27%), Positives = 146/314 (46%), Gaps = 42/314 (13%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY------------REHGDLS---- 48
           + S ++     +  Y+ EI K+ +L   EE  LA +             +E G++     
Sbjct: 132 DASTVMLTGDPVRMYLKEIGKVDLLTAAEEVDLAMKIEAGLDAADKLEKQEAGEIELTRA 191

Query: 49  --------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                         A   L++++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD
Sbjct: 192 EMRRLMRVEQVGLDAKQALISANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFD 251

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
            E+GF+ +TY+ WWI+ A+   I      ++I     +      L R++  L      + 
Sbjct: 252 YEKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE--TINKLVRVQRQLLQDLGRDP 309

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            PE++ A   ++++S   V  +        SL   I   ++  SQ  D++    D Q  V
Sbjct: 310 TPEEIGA---EMDMSADRVREIQKISQEPVSLETPI--GEEEDSQLGDFI---EDAQAVV 361

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQI 272
             +       +  LT+ +  L  RER++ E R      +P TLE +  EF V+RER+RQI
Sbjct: 362 PADAASFSMLQEQLTQVLDGLAERERKVIELRFGLVDGHPRTLEEVGREFGVTRERIRQI 421

Query: 273 EARAFKKVQESIQK 286
           E++   K++   + 
Sbjct: 422 ESKTLAKLRHPSRS 435


>gi|50726933|gb|AAT81163.1| principal sigma factor [Streptomyces ansochromogenes]
          Length = 440

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 74/304 (24%), Positives = 138/304 (45%), Gaps = 40/304 (13%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------------REHGD 46
             +  Y+ +I K+P+L  ++E  LAKR                             E G 
Sbjct: 142 DPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANSDKLAPKLKRELEIIAEDG- 200

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 201 RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 260

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L
Sbjct: 261 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKEL 315

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +VI +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 316 DMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 370

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 371 QPDSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 430

Query: 285 QKQV 288
           + QV
Sbjct: 431 RSQV 434


>gi|134098380|ref|YP_001104041.1| RNA polymerase sigma factor [Saccharopolyspora erythraea NRRL 2338]
 gi|291006918|ref|ZP_06564891.1| RNA polymerase sigma factor [Saccharopolyspora erythraea NRRL 2338]
 gi|133911003|emb|CAM01116.1| RNA polymerase major sigma factor [Saccharopolyspora erythraea NRRL
           2338]
          Length = 467

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 77/319 (24%), Positives = 146/319 (45%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------ 43
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR                     
Sbjct: 154 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYAAERLRQAEEAEERL 212

Query: 44  ------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 213 AMQMRRDLRWIVRDGERAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 272

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 273 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 330

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 331 REPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 382

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   ++ L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 383 AVVAVDAVSFTLLQDQLQSVLATLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 442

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 443 RQIESKTMSKLRHPSRSQV 461


>gi|33594607|ref|NP_882251.1| RNA polymerase factor sigma-32 [Bordetella pertussis Tohama I]
 gi|33598734|ref|NP_886377.1| RNA polymerase factor sigma-32 [Bordetella parapertussis 12822]
 gi|33603808|ref|NP_891368.1| RNA polymerase factor sigma-32 [Bordetella bronchiseptica RB50]
 gi|33564683|emb|CAE44005.1| RNA polymerase sigma-32 factor [Bordetella pertussis Tohama I]
 gi|33574864|emb|CAE39527.1| RNA polymerase sigma-32 factor [Bordetella parapertussis]
 gi|33577933|emb|CAE35198.1| RNA polymerase sigma-32 factor [Bordetella bronchiseptica RB50]
 gi|332384018|gb|AEE68865.1| RNA polymerase factor sigma-32 [Bordetella pertussis CS]
          Length = 307

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 119/286 (41%), Positives = 180/286 (62%), Gaps = 9/286 (3%)

Query: 2   NRKNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           N   +++   G +G +  YI  + ++P+L  ++E  LA+R R+ GDL AA  LV SHLRL
Sbjct: 25  NALALAVANPGALGTIDAYISAVNRLPILTAEQEGQLARRLRDEGDLEAARELVVSHLRL 84

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y GYGLP ++++ EGN+GLM+AVK+FDPERG RL ++++ WIKA + E+I+R+
Sbjct: 85  VVSVARQYLGYGLPHADLIQEGNVGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEFIIRN 144

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W LVK+ TT  Q++LFFNLR ++          L PEQV  IA++LNV   +V  M  RL
Sbjct: 145 WRLVKVATTKAQRKLFFNLRSMR-----PDGQTLDPEQVDHIARELNVRREDVSEMEVRL 199

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRE 239
           +G + L+      D +S     +L  +   +   ++++    + +   L R++  L+ R 
Sbjct: 200 SGRD-LSLESQDDDDDSFAPIAYLSDEGRQEPSRVLDRMAHDDLQGAGLGRALEALDARS 258

Query: 240 RRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           RRI EAR LQ++  +TL  L+ EF VS ERVRQIEA A KK++ ++
Sbjct: 259 RRIIEARWLQDDGGLTLHELAQEFGVSAERVRQIEAAALKKMRGAL 304


>gi|325518946|gb|EGC98485.1| RNA polymerase factor sigma-32 [Burkholderia sp. TJI49]
          Length = 311

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 119/290 (41%), Positives = 173/290 (59%), Gaps = 12/290 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
             +++      L  YI  + +IP+L  +EE   A ++RE  +L AA RLV SHLRLVV I
Sbjct: 28  TQAMLPGQLGNLDAYIQAVNRIPLLTAEEERQYATQFREDNNLDAARRLVLSHLRLVVSI 87

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y GYGLP  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W  V
Sbjct: 88  ARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRTV 147

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGD 183
           K+ TT  Q++LFFNLR  K  +QA+T     PE++  +AK+LNV   EV  M  RL  GD
Sbjct: 148 KVATTKAQRKLFFNLRSHKKGVQAMT-----PEEIDGLAKELNVKREEVTEMETRLSGGD 202

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            +L   +   ++ S     +L   H+    VL  ++    + + + +++  L+ R RRI 
Sbjct: 203 IALEGQVEDGEE-SYAPIAYLADSHNEPTAVLAARQRDMLQTDGIAQALDALDARSRRII 261

Query: 244 EARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           EAR L          TL +L++EF VS ER+RQIEA A KK++ ++ +  
Sbjct: 262 EARWLHVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRTALAEYA 311


>gi|297191610|ref|ZP_06909008.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
 gi|297151002|gb|EFH30922.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
          Length = 516

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 75/314 (23%), Positives = 143/314 (45%), Gaps = 40/314 (12%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------- 41
           + +++       +  Y+ +I K+P+L  ++E  LAKR                       
Sbjct: 208 QQVAVAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANSDKLAPKLKR 267

Query: 42  -----REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                 E G   A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  
Sbjct: 268 ELEIIAEDG-RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYT 326

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  +         P
Sbjct: 327 KGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTP 384

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           E    +AK+L+++  +VI +        SL+  +   +   S++ D +    D +  V  
Sbjct: 385 E---ELAKELDMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPA 436

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEA 274
           +       +  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE+
Sbjct: 437 DAVSFTLLQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIES 496

Query: 275 RAFKKVQESIQKQV 288
           +   K++   + QV
Sbjct: 497 KTMSKLRHPSRSQV 510


>gi|257438255|ref|ZP_05614010.1| RNA polymerase sigma factor RpoD [Faecalibacterium prausnitzii
           A2-165]
 gi|257199332|gb|EEU97616.1| RNA polymerase sigma factor RpoD [Faecalibacterium prausnitzii
           A2-165]
          Length = 359

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 85/277 (30%), Positives = 146/277 (52%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI ++P+L  ++E  LA R  + GD  A  +L  ++LRLVV +A  Y G G
Sbjct: 86  DDPVKAYLKEIGRVPLLTMEQELELA-RAAQAGDADARRKLSEANLRLVVSVAKRYAGRG 144

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP  +++ EGN+GLM+A +KF+P+RGFR +TY+ WWI+ ++   I     +++I      
Sbjct: 145 LPFLDLIQEGNLGLMKAAEKFEPDRGFRFSTYATWWIRQSITRAIADQGRVIRIPVH--- 201

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
             L  ++ R+K     +   N +      IA +L++    V  +        SL   +  
Sbjct: 202 --LVESINRVKKTAGELLRKNGREPTAEEIAVRLDMEPDRVRELLQLAQDPISLETPV-- 257

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            ++  +  +D++  +  G   V +++  R+  R  L   +  L PRE R+   R   E+ 
Sbjct: 258 GEEEDAHLEDFIQDEEAG---VPVDEAGRELLRRELANVLKSLTPREERVLTLRFGLEDG 314

Query: 253 --VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE L  EF V+RER+RQIEA+A +K++   + +
Sbjct: 315 QARTLEELGKEFNVTRERIRQIEAKALRKLRHPSRAK 351


>gi|226306303|ref|YP_002766263.1| RNA polymerase sigma factor SigA [Rhodococcus erythropolis PR4]
 gi|226185420|dbj|BAH33524.1| RNA polymerase sigma factor SigA [Rhodococcus erythropolis PR4]
          Length = 452

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 78/319 (24%), Positives = 148/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------------- 41
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR                     
Sbjct: 139 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYAVQIMQDLADKGEKL 197

Query: 42  --REHGDL--------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
              +  D+         A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 198 PAAQRRDMSWICRDGNRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 257

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 258 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 315

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 316 REPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 367

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 368 AVVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 427

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 428 RQIESKTMSKLRHPSRSQV 446


>gi|295836123|ref|ZP_06823056.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. SPB74]
 gi|295825874|gb|EDY42152.2| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. SPB74]
          Length = 493

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 75/304 (24%), Positives = 139/304 (45%), Gaps = 40/304 (13%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------------REHGD 46
             +  Y+ +I K+P+L  ++E  LAKR                             E G 
Sbjct: 195 DPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANSDKLAPKLQRELEIIAEDGG 254

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 255 R-AKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 313

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L
Sbjct: 314 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKEL 368

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +VI +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 369 DMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 423

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 424 QLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 483

Query: 285 QKQV 288
           + QV
Sbjct: 484 RSQV 487


>gi|331696864|ref|YP_004333103.1| RpoD subfamily RNA polymerase sigma-70 subunit [Pseudonocardia
           dioxanivorans CB1190]
 gi|326951553|gb|AEA25250.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pseudonocardia
           dioxanivorans CB1190]
          Length = 461

 Score =  250 bits (639), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 79/319 (24%), Positives = 149/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGD-- 46
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+  
Sbjct: 148 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYAAERLRRAIESGEKV 206

Query: 47  ---------------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 207 SPQLRRDLRWIVRDGERAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 266

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 267 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 324

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 325 REPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 376

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   ++ L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 377 AVVAVDAVSFTLLQDQLQSVLATLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 436

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 437 RQIESKTMSKLRHPSRSQV 455


>gi|315655467|ref|ZP_07908366.1| DNA-directed RNA polymerase sigma subunit RpoD [Mobiluncus curtisii
           ATCC 51333]
 gi|315490122|gb|EFU79748.1| DNA-directed RNA polymerase sigma subunit RpoD [Mobiluncus curtisii
           ATCC 51333]
          Length = 553

 Score =  250 bits (638), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 72/305 (23%), Positives = 138/305 (45%), Gaps = 39/305 (12%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREH---------------------- 44
               +  Y+ +I K+ +L  ++E  L+KR     Y EH                      
Sbjct: 252 TSDPVKDYLKQIGKVALLNAEQEVDLSKRIEAGLYAEHLLKTKQETMTPKQIRELHYVVQ 311

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
               A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY
Sbjct: 312 DGQMAKNHLLEANLRLVVALAKKYTGRGMLFLDLIQEGNLGLIRAVEKFDYSKGYKFSTY 371

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + WWI+ A+   +      ++I     +  +   L R++  +         P+    +A+
Sbjct: 372 ATWWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPD---ELAQ 426

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L ++  +V+ +        SL+  +   +   S++ D +    D +  V  +       
Sbjct: 427 ELEMTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFMML 481

Query: 225 RNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +  L R +  L+ RE  +   R       P TL+ +   + V+RER+RQIEA+   K++ 
Sbjct: 482 QEQLQRVLDTLSERESGVIAMRFGLKDGQPKTLDEIGRRYGVTRERIRQIEAKTMSKLRH 541

Query: 283 SIQKQ 287
             + Q
Sbjct: 542 PARSQ 546


>gi|254232809|ref|ZP_04926136.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis C]
 gi|124601868|gb|EAY60878.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis C]
          Length = 528

 Score =  250 bits (638), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 78/319 (24%), Positives = 147/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------REHGDL- 47
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+  
Sbjct: 215 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSERGEKL 273

Query: 48  ----------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+ L++AV+
Sbjct: 274 PAAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLRLIRAVE 333

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 334 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 391

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 392 REPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 443

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 444 AVVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 503

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 504 RQIESKTMSKLRHPSRSQV 522


>gi|21244548|ref|NP_644130.1| RNA polymerase factor sigma-32 [Xanthomonas axonopodis pv. citri
           str. 306]
 gi|21110222|gb|AAM38666.1| RNA polymerase sigma-32 factor [Xanthomonas axonopodis pv. citri
           str. 306]
          Length = 291

 Score =  250 bits (638), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 117/276 (42%), Positives = 168/276 (60%), Gaps = 8/276 (2%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           I +    L  YI  + +IP+L   EE  LA+R+R+  DL AA  LV SHLR VV +A GY
Sbjct: 16  IPSALGSLDAYIGAVHQIPVLSVDEEQDLARRFRDELDLDAARELVHSHLRFVVHVARGY 75

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGLP+ +++ EGNIGLM+AVK+FDP+ G RL ++++ WI+A M E+IL++W +VK+ T
Sbjct: 76  NGYGLPLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAVHWIRAEMHEFILKNWRIVKVAT 135

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN 187
           T  Q++LFFNLR+ K  L  +        +V A+AK LNVSE EV+ M  RL+G D   +
Sbjct: 136 TKAQRKLFFNLRKSKTRLGWLN-----ASEVTAVAKDLNVSEREVMEMESRLSGRDIGFD 190

Query: 188 A-LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           A      D        +LV + +   Q     +   N+  +L   M+ L+ R R I + R
Sbjct: 191 ASSDEDDDHGPPSPVSYLVANEEDPSQAYERHDSEDNQLQLLREGMAGLDARSRDIVKRR 250

Query: 247 RLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L  ++ VTL+ L+ E+ VS ER+RQIEA A KK++
Sbjct: 251 WLDSDSKVTLQELADEYGVSAERIRQIEANALKKMK 286


>gi|56459340|ref|YP_154621.1| RNA polymerase factor sigma-32 [Idiomarina loihiensis L2TR]
 gi|56178350|gb|AAV81072.1| DNA-directed RNA polymerase sigma 32 subunit [Idiomarina loihiensis
           L2TR]
          Length = 286

 Score =  250 bits (638), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 111/285 (38%), Positives = 171/285 (60%), Gaps = 9/285 (3%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
             M++ V    GL  YI  + +IPML  ++E  LA R  E+ DL AA  L+ SHLR VV 
Sbjct: 6   NTMALSVPQGAGLDGYIQSVNRIPMLTAEKEKALATRLYENSDLDAAKELIMSHLRFVVH 65

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           +A  Y GYGLP ++++ EGNIGLM+AVK+FDP  G RL ++++ WIKA + EY+LR+W +
Sbjct: 66  VARSYSGYGLPQADLIQEGNIGLMKAVKRFDPSVGVRLVSFAVHWIKAEIHEYVLRNWRV 125

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VK+ TT  Q++LFFNLR++K  L   +       +V  +A +L VS  EV+ M  R++  
Sbjct: 126 VKVATTKAQRKLFFNLRKMKKRLGWFSQK-----EVETVANELGVSTKEVLEMETRMSAH 180

Query: 184 E---SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRE 239
           +    L++  + S + S+      + D        IE ++ +N     L  +MS L+ R 
Sbjct: 181 DQAFELSSDDDDSKEGSAYSPAMYLEDKRSDLAAEIEAKDYENHTQQKLLGAMSHLDERS 240

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + I ++R L E+  TL +L+ ++EVS ERVRQ+E  A KK++ ++
Sbjct: 241 QDIVQSRWLSEDKTTLHDLAEKYEVSAERVRQLEQNAMKKLRLAM 285


>gi|258404985|ref|YP_003197727.1| putative RNA polymerase, sigma 70 family subunit [Desulfohalobium
           retbaense DSM 5692]
 gi|257797212|gb|ACV68149.1| putative RNA polymerase, sigma 70 family subunit [Desulfohalobium
           retbaense DSM 5692]
          Length = 350

 Score =  250 bits (638), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 112/286 (39%), Positives = 176/286 (61%), Gaps = 8/286 (2%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V  +  L  Y+ E+ + P+LE  EE  LA+R R+  D SAA RL++SHLRLVVKIAM ++
Sbjct: 65  VAIQDPLKLYLREVNRFPLLEPDEEVELARRVRDENDQSAAFRLISSHLRLVVKIAMEFQ 124

Query: 70  GYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
              +  + ++V EGN+GLM+AV+KFDPERG + + Y+ +WI+A + ++I+ +W +VK+GT
Sbjct: 125 RRWMKNVLDLVQEGNVGLMKAVQKFDPERGIKFSYYASFWIRAYILKFIMDNWRMVKLGT 184

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN 187
           T  Q++LF+NL R K  LQA             +++ L+VSE  V+ M  RL G D SL+
Sbjct: 185 TQAQRKLFYNLSREKQRLQA----QGFDPDASTLSENLDVSEESVVEMTQRLGGHDLSLD 240

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           A +   + +SS   D+L     G E+ L ++E     R  L   +  LN +E+ I E R 
Sbjct: 241 APL--GEDSSSSRMDFLPALGAGIEESLAQQEMGSALRQHLQTILPKLNDKEKEILEHRL 298

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           L ++PVTL  +  ++ ++RERVRQIE+R  +K++  +  +++  S 
Sbjct: 299 LTDSPVTLREIGEKYGITRERVRQIESRLLQKLKTHLSSEIQDFSE 344


>gi|254302832|ref|ZP_04970190.1| DNA-directed RNA polymerase sigma subunit RpoD [Fusobacterium
           nucleatum subsp. polymorphum ATCC 10953]
 gi|148323024|gb|EDK88274.1| DNA-directed RNA polymerase sigma subunit RpoD [Fusobacterium
           nucleatum subsp. polymorphum ATCC 10953]
          Length = 418

 Score =  250 bits (638), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 81/285 (28%), Positives = 143/285 (50%), Gaps = 13/285 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           N+      +  +  Y+ EI ++P+L   EE   AKR  E GD  A+ +L+ S+LRLVV I
Sbjct: 137 NLGNSAKVDEPIKMYLREIGQVPLLTHDEEIEYAKRAYE-GDEEASKKLIESNLRLVVSI 195

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  +   GL + +++ EGNIGLM+AV+KF+  +G++ +TY+ WWI+ A+   I      +
Sbjct: 196 AKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTI 255

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I        +   + ++K   +       K      +A++L +   ++ ++        
Sbjct: 256 RIPVH-----MIETINKIKKESRIYLQETGKDASPEILAERLGMEVEKIKAIQEMNQEPI 310

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   + S  +  S+  D++    D +     E   R   R  L   +  L+PRE ++  
Sbjct: 311 SLETPVGS--EEDSELGDFV---EDQKTTSPYEATNRAILREELDAVLKTLSPREEKVLR 365

Query: 245 ARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R   ++  P TLE +   F V+RER+RQIE +A +K++   +K+
Sbjct: 366 YRYGLDDSSPKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRKK 410


>gi|145300817|ref|YP_001143658.1| RNA polymerase sigma-32 factor [Aeromonas salmonicida subsp.
           salmonicida A449]
 gi|142853589|gb|ABO91910.1| RNA polymerase sigma-32 factor [Aeromonas salmonicida subsp.
           salmonicida A449]
          Length = 284

 Score =  250 bits (638), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 107/286 (37%), Positives = 169/286 (59%), Gaps = 9/286 (3%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           ++ M++I  G   L  YI  +  IP+L  +EE  LA+R ++ GDL AA +LV SHLR VV
Sbjct: 6   QRTMALIPQG--SLEGYIQAVNSIPVLTAEEERELAERLQQGGDLEAARQLVMSHLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y GYGLP +++V EGNIGLM+AVK+FDP  G RL ++++ WIKA + EY+LR+W 
Sbjct: 64  HVAKSYAGYGLPQADLVQEGNIGLMKAVKRFDPTVGVRLVSFAVHWIKAEIHEYVLRNWR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L   +      ++V A+A +L VS ++V  M  R++ 
Sbjct: 124 MVKVATTKAQRKLFFNLRKSKKRLGWFSH-----DEVQAVAAELGVSPTDVTEMEARMSN 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPRERR 241
            +    L+   +          + D        IE +   +     L+ +++ L+ R + 
Sbjct: 179 YDQAFDLVGDDEDEGGFAPVHYLEDKSSDLAATIENDNWDDHATRRLSSALATLDERSQH 238

Query: 242 IFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           I  AR L ++   TL+ L+  + VS ERVRQ+E  A KK++++++ 
Sbjct: 239 IIRARWLDDDSKTTLQELADTYGVSAERVRQLEKNALKKLKDAMEA 284


>gi|71909448|ref|YP_287035.1| RNA polymerase factor sigma-32 [Dechloromonas aromatica RCB]
 gi|71849069|gb|AAZ48565.1| RNA polymerase, sigma 32 subunit, RpoH [Dechloromonas aromatica
           RCB]
          Length = 286

 Score =  250 bits (638), Expect = 2e-64,   Method: Composition-based stats.
 Identities = 115/285 (40%), Positives = 166/285 (58%), Gaps = 3/285 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M       I +    +  YI    + PML + EE  LA+R    GD+ AA +LV SHLRL
Sbjct: 1   MTYALALPIPSSVGNIDAYIQAANRYPMLTEAEESRLAERLHNDGDVEAARQLVLSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ IA GY GYGLP ++++ EGNIGLM+AVK+FDP RG RL +++M WIKA + EYIL++
Sbjct: 61  VISIARGYLGYGLPHADLIQEGNIGLMKAVKRFDPSRGVRLVSFAMHWIKAEIHEYILKN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W LVK+ TT  Q++LFFNLR +K   + I   +    Q   +A +L V + EV+ M  RL
Sbjct: 121 WRLVKVATTKAQRKLFFNLRSMKSGYEGIDTLSGT--QAAEVAARLGVKQDEVVEMETRL 178

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +G +          + +    D+L        +VL  K   + +   L  ++  L+PR R
Sbjct: 179 SGRDIALDGNPDDGEEAFAPIDYLADSRYEPTRVLENKAIARLQDEGLHEALEALDPRSR 238

Query: 241 RIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           RI EAR L +    TL +L+ EF+VS ER+RQIE +A +K++  +
Sbjct: 239 RIIEARWLHDGETATLHDLADEFDVSAERIRQIEVKALQKMRGVL 283


>gi|48745|emb|CAA37175.1| unnamed protein product [Streptomyces coelicolor A3(2)]
          Length = 442

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 75/304 (24%), Positives = 139/304 (45%), Gaps = 40/304 (13%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------------REHGD 46
             +  Y+ +I K+P+L  ++E  LAKR                             E G 
Sbjct: 144 DPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANSDKLAPKLKRELEIIAEDG- 202

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 203 RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 262

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L
Sbjct: 263 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKEL 317

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +VI +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 318 DMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 372

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 373 QLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 432

Query: 285 QKQV 288
           + QV
Sbjct: 433 RSQV 436


>gi|153309|gb|AAA26764.1| principal sigma-like factor [Streptomyces aureofaciens]
          Length = 528

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 75/303 (24%), Positives = 139/303 (45%), Gaps = 38/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYR----------EHGD----------------L 47
             +  Y+  I K+P+L  ++E  LAKR            E  D                 
Sbjct: 230 DPVKDYLKLIGKVPLLNAEQEVELAKRIEAGLFSEYKLEEEEDHKPAFKRELEILVEDGR 289

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ W
Sbjct: 290 RAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNVGLIRAVEKFDYTKGFKFSTYATW 349

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   +      ++I     +  +   L R++  +         PE    + K+L+
Sbjct: 350 WIRQAITRAMADQSRTIRIPVHMVE--IINKLARVQRQMLQDLGREPTPE---ELGKELD 404

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++  +VI +        SL+  +   ++  S++ D +    D +  V  +       +  
Sbjct: 405 MTPEKVIEVQKYGREPISLHTPL--GEEGDSEFGDLI---EDSEAVVPADAVSFTFLQEQ 459

Query: 228 LTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L   +  L+ RE  +   R    +  P TL+ +   + V+RER+RQIE++   K++   +
Sbjct: 460 LQSILGTLSEREAGVVSMRYGLNDGQPKTLDEIGRVYGVTRERIRQIESKTMSKLRHPSR 519

Query: 286 KQV 288
            QV
Sbjct: 520 SQV 522


>gi|293609550|ref|ZP_06691852.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|292828002|gb|EFF86365.1| conserved hypothetical protein [Acinetobacter sp. SH024]
          Length = 288

 Score =  250 bits (638), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 110/283 (38%), Positives = 167/283 (59%), Gaps = 8/283 (2%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +S+   G + L  YI  + +IP+L  ++E  LA+RY    DL AA  LV SHLR VV IA
Sbjct: 11  LSLSAPG-VNLGAYISTVNQIPILTAEQEKELAERYYYDQDLDAAKMLVMSHLRFVVHIA 69

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGLP  +++ EGN+GLM+AVK+FDP  G RL ++++ WIKA + EY++R+W +VK
Sbjct: 70  RSYAGYGLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVK 129

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDE 184
           I TT  Q++LFFNLR LK   + +T      E+  +IA  LNV+  +V+ M  RL A D 
Sbjct: 130 IATTKAQRKLFFNLRSLKKSSKKLT-----LEEAQSIANDLNVTPEQVLEMEGRLTAYDA 184

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR-NMLTRSMSVLNPRERRIF 243
           +  A  +  D          + D+      L+E E+ + +  + L  +M  L+ R R I 
Sbjct: 185 AFEAQGDDDDDTPHTAPALYLEDNRYDPARLVENEDWEEQSTSALHDAMDQLDDRSRNIL 244

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           + R L ++  TL  L++E+ VS ER+RQ+E  A +K++ ++  
Sbjct: 245 QRRWLDDDKSTLHELAAEYNVSAERIRQLEKNAMEKIKTAMSA 287


>gi|72162538|ref|YP_290195.1| RNA polymerase sigma factor [Thermobifida fusca YX]
 gi|71916270|gb|AAZ56172.1| carbamoyl-phosphate synthase L chain, ATP-binding [Thermobifida
           fusca YX]
          Length = 616

 Score =  249 bits (637), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 72/304 (23%), Positives = 136/304 (44%), Gaps = 39/304 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR---------------------------YREHGD 46
             +  Y+ +I K+P+L  ++E  LAKR                           +     
Sbjct: 317 DPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEEKLSKKGHELTPEEREELEWIAEDG 376

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 377 KRAKKHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 436

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L
Sbjct: 437 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKEL 491

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +V+ +        SL+  +   +   S++ D +    D +     E       + 
Sbjct: 492 DMTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAIQPGEAVSFTLLQE 546

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 547 QLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 606

Query: 285 QKQV 288
           + QV
Sbjct: 607 RSQV 610


>gi|93005058|ref|YP_579495.1| RNA polymerase factor sigma-32 [Psychrobacter cryohalolentis K5]
 gi|92392736|gb|ABE74011.1| sigma 32 (RpoH) [Psychrobacter cryohalolentis K5]
          Length = 287

 Score =  249 bits (637), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 107/271 (39%), Positives = 163/271 (60%), Gaps = 5/271 (1%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + L  YI+ + +IP+L   +E  LA RY + GD+ AA  LV SHLR V+ IA  Y GYGL
Sbjct: 10  VNLGAYINTVHQIPILTPTQEQELAHRYYDEGDVEAARLLVMSHLRFVIHIARSYSGYGL 69

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P ++++ EGN+GLM+AVK+FDP +G RL ++++ WIKA + E+++R+W +VK+ TT   +
Sbjct: 70  PQADLIQEGNLGLMKAVKRFDPNKGVRLVSFAVHWIKAEIHEFVIRNWRIVKVATTKAHR 129

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
           +LFFNLR LK      T+N L  E+  AIA  LNV+  +V+ M  RL   ++     +S 
Sbjct: 130 KLFFNLRSLKK-----TNNQLTLEEADAIANDLNVTRKQVLEMESRLTSYDASFEAQSSD 184

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D +        + D     +++ E +  +N  + L  +M  L+ R R I E R L E   
Sbjct: 185 DDDGRYAPQLFLEDGIDPAEIVEESDWEENNSSALIAAMETLDDRSRDIVEQRWLSEQKS 244

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           TL  L++ + +S ERVRQIE  A  K++E++
Sbjct: 245 TLHELAAVYSISAERVRQIEKNAMDKIREAM 275


>gi|291436829|ref|ZP_06576219.1| RNA polymerase sigma factor RpoD [Streptomyces ghanaensis ATCC
           14672]
 gi|291339724|gb|EFE66680.1| RNA polymerase sigma factor RpoD [Streptomyces ghanaensis ATCC
           14672]
          Length = 509

 Score =  249 bits (637), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 75/304 (24%), Positives = 139/304 (45%), Gaps = 40/304 (13%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------------REHGD 46
             +  Y+ +I K+P+L  ++E  LAKR                             E G 
Sbjct: 211 DPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANSDKLAPKLKRELEIIAEDG- 269

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 270 RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 329

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L
Sbjct: 330 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKEL 384

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +VI +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 385 DMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 439

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 440 QLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 499

Query: 285 QKQV 288
           + QV
Sbjct: 500 RSQV 503


>gi|256390959|ref|YP_003112523.1| RNA polymerase sigma factor [Catenulispora acidiphila DSM 44928]
 gi|256357185|gb|ACU70682.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Catenulispora
           acidiphila DSM 44928]
          Length = 559

 Score =  249 bits (637), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 74/304 (24%), Positives = 139/304 (45%), Gaps = 40/304 (13%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------------REHGD 46
             +  Y+ +I K+P+L  ++E  LAKR                             E G 
Sbjct: 261 DPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEEKLNDGEPLTPEFRRELDIIAEDG- 319

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 320 RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 379

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L
Sbjct: 380 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKEL 434

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +V+ +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 435 DMTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 489

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 490 QLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 549

Query: 285 QKQV 288
           + QV
Sbjct: 550 RSQV 553


>gi|21224164|ref|NP_629943.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
 gi|289768642|ref|ZP_06528020.1| transcription initiation factor sigma [Streptomyces lividans TK24]
 gi|12644145|sp|P18183|HRDB_STRCO RecName: Full=RNA polymerase principal sigma factor hrdB
 gi|3036885|emb|CAA18518.1| major vegetative sigma factor [Streptomyces coelicolor A3(2)]
 gi|289698841|gb|EFD66270.1| transcription initiation factor sigma [Streptomyces lividans TK24]
          Length = 511

 Score =  249 bits (637), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 75/304 (24%), Positives = 139/304 (45%), Gaps = 40/304 (13%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------------REHGD 46
             +  Y+ +I K+P+L  ++E  LAKR                             E G 
Sbjct: 213 DPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANSDKLAPKLKRELEIIAEDG- 271

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 272 RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 331

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L
Sbjct: 332 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKEL 386

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +VI +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 387 DMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 441

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 442 QLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 501

Query: 285 QKQV 288
           + QV
Sbjct: 502 RSQV 505


>gi|300741779|ref|ZP_07071800.1| RNA polymerase sigma (70) factor RpoD [Rothia dentocariosa M567]
 gi|300380964|gb|EFJ77526.1| RNA polymerase sigma (70) factor RpoD [Rothia dentocariosa M567]
          Length = 468

 Score =  249 bits (637), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 73/303 (24%), Positives = 135/303 (44%), Gaps = 38/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE--------------------------HGDL 47
             +  Y+ +I K+ +L  Q+E  LA R                             H   
Sbjct: 170 DPVKDYLKQIGKVSLLNAQQEVDLAMRIEAGLYAEHKLADNPDMDPKLKKELRWVIHDGK 229

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ W
Sbjct: 230 RAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYSKGFKFSTYATW 289

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   +      ++I     +  +   L R++  +         PE    + K+L+
Sbjct: 290 WIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELGKELD 344

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++  +VI +        SL+  +   +   S++ D +    D +  V  +       +  
Sbjct: 345 MAPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQEQ 399

Query: 228 LTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   +
Sbjct: 400 LHSVLDTLSEREAGVVAMRFGMTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSR 459

Query: 286 KQV 288
            QV
Sbjct: 460 SQV 462


>gi|304311558|ref|YP_003811156.1| RNA polymerase sigma factor [gamma proteobacterium HdN1]
 gi|301797291|emb|CBL45511.1| RNA polymerase sigma factor [gamma proteobacterium HdN1]
          Length = 285

 Score =  249 bits (637), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 108/271 (39%), Positives = 172/271 (63%), Gaps = 7/271 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+RY+  +  + +L   EE  LA+RY  + D+ AA +LV +HLR VV +A GY GYGL +
Sbjct: 17  LNRYLSAVNSVAILSADEERALAERYYYNEDVDAARQLVLAHLRFVVHVARGYNGYGLQL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           S++V EGN+GLM+AVK+FDP  G RL ++++ WIKA + E+ILR+W +VKI TT +Q++L
Sbjct: 77  SDLVQEGNVGLMKAVKRFDPTMGVRLVSFAVHWIKAEIHEFILRNWRIVKIATTKSQRKL 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR  K  L  ++      ++V  IA +LNVS  +V  M  RLA  D + +A +++ D
Sbjct: 137 FFNLRSHKRRLGVLSG-----DEVNMIATELNVSPEDVREMEGRLAAHDTAFDAPVDADD 191

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEER-KNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           +++SQ   + + D        +E  +   N  + L  +M+ L+ R R I + R   ++  
Sbjct: 192 ESASQAPVYYLEDASMDPAHQLEDAQWTDNTTDRLQLAMNSLDERSRDILQQRWFNDDKA 251

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           TL +L++++ VS ER+RQ+EA A KK++ ++
Sbjct: 252 TLHDLAAQYSVSAERIRQLEANAMKKIKLAM 282


>gi|319795672|ref|YP_004157312.1| RNA polymerase, sigma 32 subunit, rpoh [Variovorax paradoxus EPS]
 gi|315598135|gb|ADU39201.1| RNA polymerase, sigma 32 subunit, RpoH [Variovorax paradoxus EPS]
          Length = 313

 Score =  249 bits (637), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 110/290 (37%), Positives = 169/290 (58%), Gaps = 14/290 (4%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +V     L  YI    ++P+L  +EE   A++ R+  DL AA  L+ SHLRLVV I+  Y
Sbjct: 20  MVPPLGNLDAYISAANRLPLLTLEEEQGFARKLRDQNDLDAAGALILSHLRLVVSISRQY 79

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGLP  +++ EGN+GLM+AVK+FDP++G RL +Y+M WIKA + EYIL++W +VK+ T
Sbjct: 80  LGYGLPHGDLIQEGNVGLMKAVKRFDPDQGVRLVSYAMHWIKAEIHEYILKNWRMVKVAT 139

Query: 129 TANQKRLFFNLRRLKGHLQA--------ITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           T  Q++LFFNLR +K   +A             L P++V  +A +LNV   EV+ M  RL
Sbjct: 140 TKAQRKLFFNLRSMKQGFKADSAASDNGTHRETLSPDEVSQMATRLNVKPEEVLEMETRL 199

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLNPRE 239
           +G + L     S D + +      + D   +   L+E ++R     + +  ++  L+ R 
Sbjct: 200 SGGDVLLDPGPSDDGDEAFGPIAYLADATQEPTALLESQQRDRLSSDGIATALEALDARS 259

Query: 240 RRIFEARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           RRI E R L         +TL +L++ + VS ER+RQIE  A KK+++++
Sbjct: 260 RRIVEERWLKVNDDGSGGMTLHDLAAVYGVSAERIRQIEVAAMKKMKKAL 309


>gi|217969486|ref|YP_002354720.1| RNA polymerase factor sigma-32 [Thauera sp. MZ1T]
 gi|217506813|gb|ACK53824.1| RNA polymerase, sigma 32 subunit, RpoH [Thauera sp. MZ1T]
          Length = 283

 Score =  249 bits (637), Expect = 3e-64,   Method: Composition-based stats.
 Identities = 116/283 (40%), Positives = 179/283 (63%), Gaps = 8/283 (2%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           + ++  V     L +YI  + ++PML +Q+E  LA R R+ GD+ AA +LV SHLR+VV 
Sbjct: 3   QALTFPVPAAGSLDQYIQSVNRMPMLSEQQEVELATRLRDEGDVDAARQLVMSHLRVVVA 62

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA GY GYGLP ++++ EGNIGLM+AVK+FDP RG RL ++++ WIKA + EYIL++W L
Sbjct: 63  IARGYLGYGLPHADLIQEGNIGLMKAVKRFDPTRGVRLVSFAIHWIKAEIHEYILKNWRL 122

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG- 182
           VKI TT  Q++LFFNLR +K        + L+P +V +IA +L V   EV+ M  RL+G 
Sbjct: 123 VKIATTKAQRKLFFNLRGMKQ-----DSSTLQPAEVRSIAAQLGVKPEEVVEMETRLSGR 177

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
           D  L+A  +  D+  +    +L   H    + + + +  + + + L  +++ L+ R R I
Sbjct: 178 DIPLDAGSDDEDERFA-PIAYLPDPHAEPSEQVEQAQLARLQDSGLRDALASLDERSRAI 236

Query: 243 FEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + R L E +  TL  L++E+ VS ER+RQIEA+A +K++  +
Sbjct: 237 VQRRWLAEGDSATLHELAAEYGVSAERIRQIEAKAMQKMRGML 279


>gi|94499830|ref|ZP_01306366.1| RNA polymerase sigma-32 factor RpoH [Oceanobacter sp. RED65]
 gi|94428031|gb|EAT13005.1| RNA polymerase sigma-32 factor RpoH [Oceanobacter sp. RED65]
          Length = 288

 Score =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 107/285 (37%), Positives = 162/285 (56%), Gaps = 8/285 (2%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           +N++ +  G   L  Y++ I  I +L  +EE  LA R     DL AA RLV SHLR VV 
Sbjct: 8   QNIASLSPGRD-LDGYLNAIGGIAVLSAEEERELADRLYYESDLEAARRLVLSHLRFVVH 66

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y GYGL  S+++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+IL++W +
Sbjct: 67  IAKSYNGYGLNQSDLIQEGNVGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEFILKNWRI 126

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VK+ TT  Q++LFFNLR  K       +  L   +   IA+ L VS  EV  M  RL+  
Sbjct: 127 VKVATTKAQRKLFFNLRSAKKR-----NGWLNEAEAHKIAEDLGVSAKEVYEMEGRLSSH 181

Query: 184 ES-LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLNPRERR 241
           +S  ++ +   + ++ Q     + DH     + +E E  + +    L  ++  L+ R + 
Sbjct: 182 DSTFDSPVADDEDSAYQAPANYLEDHSFDPALAVENENYEQDSTARLQDALVQLDDRSKD 241

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           I   R L E+  TL  L+ E+ VS ER+RQ+E  A KK++  I+ 
Sbjct: 242 ILMRRWLGEHKATLHELADEYGVSAERIRQLEKNAMKKIKGMIEA 286


>gi|311111671|ref|YP_003982893.1| DNA-directed RNA polymerase sigma subunit RpoD [Rothia dentocariosa
           ATCC 17931]
 gi|310943165|gb|ADP39459.1| DNA-directed RNA polymerase sigma subunit RpoD [Rothia dentocariosa
           ATCC 17931]
          Length = 468

 Score =  249 bits (637), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 73/303 (24%), Positives = 135/303 (44%), Gaps = 38/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE--------------------------HGDL 47
             +  Y+ +I K+ +L  Q+E  LA R                             H   
Sbjct: 170 DPVKDYLKQIGKVSLLNAQQEVDLAMRIEAGLYAEHKLADNPDMDPKLKKELRWVIHDGK 229

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ W
Sbjct: 230 RAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYSKGFKFSTYATW 289

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   +      ++I     +  +   L R++  +         PE    + K+L+
Sbjct: 290 WIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELGKELD 344

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++  +VI +        SL+  +   +   S++ D +    D +  V  +       +  
Sbjct: 345 MAPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQEQ 399

Query: 228 LTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   +
Sbjct: 400 LHSVLDTLSEREAGVVAMRFGMTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSR 459

Query: 286 KQV 288
            QV
Sbjct: 460 SQV 462


>gi|300926841|ref|ZP_07142609.1| alternative sigma factor RpoH [Escherichia coli MS 182-1]
 gi|301329786|ref|ZP_07222521.1| alternative sigma factor RpoH [Escherichia coli MS 78-1]
 gi|300417191|gb|EFK00502.1| alternative sigma factor RpoH [Escherichia coli MS 182-1]
 gi|300844135|gb|EFK71895.1| alternative sigma factor RpoH [Escherichia coli MS 78-1]
          Length = 284

 Score =  249 bits (636), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 109/289 (37%), Positives = 161/289 (55%), Gaps = 8/289 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  K  S+ +     L  YI      PML   EE  LA++   HGDL AA  L+ SHLR 
Sbjct: 1   MTDKMQSLALAPVGNLDSYIRAANAWPMLSADEERALAEKLHYHGDLEAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVEMVARELGVTSKDVREMESRM 175

Query: 181 -AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE-ERKNRRNMLTRSMSVLNPR 238
            A D + +   +    +        + D        IE +   +   N LT +M  L+ R
Sbjct: 176 AAQDMTFDQSSDDDSDSQPMAPVLYLQDKSSNFADGIEDDNWEEQAANRLTDAMQGLDER 235

Query: 239 ERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + I  AR L E+   TL+ L+  + VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 SQDIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 284


>gi|322513377|ref|ZP_08066496.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Actinobacillus
           ureae ATCC 25976]
 gi|322120867|gb|EFX92727.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Actinobacillus
           ureae ATCC 25976]
          Length = 318

 Score =  249 bits (636), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 98/273 (35%), Positives = 161/273 (58%), Gaps = 6/273 (2%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  L  YI    + P+L  ++E  LA+RY    DL AA +L+ SH+R V+ IA GY GYG
Sbjct: 48  QGNLDSYIRMANQYPILSAEQEKELAERYYYDEDLEAAKQLILSHMRFVIHIARGYLGYG 107

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP+++++ EGNIGLM+AVK+FDP  G RL ++++ W+KA + EY+L++W +VK+ TT  Q
Sbjct: 108 LPLADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWVKAEIHEYVLKNWRIVKVATTKAQ 167

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALIN 191
           ++LFFNLR+ K  L    +     +++  +A+ L VS  EV  M  R+ G D   +    
Sbjct: 168 RKLFFNLRKNKNRLAWFNE-----DEIKKVAEDLGVSVEEVREMESRMTGQDLGFDLPAG 222

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             D  +     ++  +       L ++E        L  +++ L+ R + I + R L E+
Sbjct: 223 EDDDEAYAPSMYIEDNSSNFADELEDEEHTGEATAQLAYALATLDERSQDIIKTRWLDED 282

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL++L+ ++ +S ERVRQ+E  A KK++++I
Sbjct: 283 KATLQDLADKYGISAERVRQLENAALKKIKDAI 315


>gi|299534115|ref|ZP_07047467.1| RNA polymerase, sigma 32 subunit, RpoH [Comamonas testosteroni S44]
 gi|298718024|gb|EFI59029.1| RNA polymerase, sigma 32 subunit, RpoH [Comamonas testosteroni S44]
          Length = 314

 Score =  249 bits (636), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 117/291 (40%), Positives = 170/291 (58%), Gaps = 15/291 (5%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +V     L  YI  + ++PML  +EE   A++ +EH DL AA RLV SHLRLVV I+  Y
Sbjct: 20  LVPPLGNLDAYISAVNRMPMLTLEEEQDYARKLKEHNDLDAAGRLVMSHLRLVVSISRQY 79

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGLP  +++ EGN+GLM+AVK+FDP++G RL +Y+M WIKA + EYIL++W +VK+ T
Sbjct: 80  LGYGLPHGDLIQEGNVGLMKAVKRFDPDQGVRLVSYAMHWIKAEIHEYILKNWRMVKVAT 139

Query: 129 TANQKRLFFNLRRLKGHL---------QAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
           T  Q++LFFNLR +K  L         +      L   ++ A+A KLNV   EVI M  R
Sbjct: 140 TKAQRKLFFNLRSMKHDLKSDAAMADEELALRETLTSNEIDAVAAKLNVKREEVIEMETR 199

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPR 238
           LAG + L     S D   +      + D   +   ++E  +R +   + L  ++  L+ R
Sbjct: 200 LAGGDVLLDPSPSDDGEQAFGPIAYLADASHEPTAMLESRQRDHLATDGLVMALEGLDDR 259

Query: 239 ERRIFEARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            RRI E R L         +TL  L++E+ VS ER+RQIE  A KK+++++
Sbjct: 260 SRRIVEERWLKVNDDGSGGMTLHELAAEYGVSAERIRQIEVAAMKKMKKAL 310


>gi|255327076|ref|ZP_05368152.1| RNA polymerase sigma factor SigA [Rothia mucilaginosa ATCC 25296]
 gi|255296293|gb|EET75634.1| RNA polymerase sigma factor SigA [Rothia mucilaginosa ATCC 25296]
          Length = 457

 Score =  249 bits (636), Expect = 4e-64,   Method: Composition-based stats.
 Identities = 73/303 (24%), Positives = 135/303 (44%), Gaps = 38/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE--------------------------HGDL 47
             +  Y+ +I K+ +L  Q+E  LA R                             H   
Sbjct: 159 DPVKDYLKQIGKVSLLNAQQEVDLAMRIEAGLYAEHKLAENPDMDKDLKKALRWVIHDGK 218

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ W
Sbjct: 219 RAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYSKGFKFSTYATW 278

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   +      ++I     +  +   L R++  +         PE    + K+L+
Sbjct: 279 WIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELGKELD 333

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++  +VI +        SL+  +   +   S++ D +    D +  V  +       +  
Sbjct: 334 MTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQEQ 388

Query: 228 LTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   +
Sbjct: 389 LHSVLDTLSEREAGVVAMRFGMTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSR 448

Query: 286 KQV 288
            QV
Sbjct: 449 SQV 451


>gi|110798581|ref|YP_696687.1| RNA polymerase sigma factor RpoD [Clostridium perfringens ATCC
           13124]
 gi|15186722|dbj|BAB62883.1| RNA polymerase major sigma factor [Clostridium perfringens]
 gi|110673228|gb|ABG82215.1| RNA polymerase sigma factor RpoD [Clostridium perfringens ATCC
           13124]
          Length = 366

 Score =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 77/277 (27%), Positives = 136/277 (49%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI K+ +L  ++E  LAK+  E G   A  +L  ++LRLVV IA  Y G G
Sbjct: 94  DDPVRMYLKEIGKVQLLSSEDEIELAKKI-EEGSNYAKKKLAEANLRLVVSIAKRYVGRG 152

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I     +
Sbjct: 153 MLFLDLIQEGNLGLIKAVEKFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 212

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 L R++  L      +  PE    ++K++++   +V  +        SL   I  
Sbjct: 213 --TINKLIRIQRQLVQELGRDPLPE---ELSKQMDMPVDKVREILKIAQEPVSLETPI-- 265

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            ++  S   D++            E       +  L   +  L PRE ++   R   ++ 
Sbjct: 266 GEEEDSHLGDFIPD---DDAPAPAEAAAFTMLKEQLINVLDTLTPREEKVLRLRFGLDDG 322

Query: 253 --VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 323 RARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 359


>gi|332286014|ref|YP_004417925.1| RNA polymerase sigma-32 factor [Pusillimonas sp. T7-7]
 gi|330429967|gb|AEC21301.1| RNA polymerase sigma-32 factor [Pusillimonas sp. T7-7]
          Length = 293

 Score =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 126/287 (43%), Positives = 180/287 (62%), Gaps = 12/287 (4%)

Query: 2   NRKNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           N+  M+I   G +G +  YI  + ++PML ++EE  L KR R+H DL AA +L+TSHLRL
Sbjct: 13  NQLAMAISNPGALGTIEAYISAVNRLPMLTQEEETSLGKRLRDHDDLDAARQLITSHLRL 72

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y GYGL  ++++ EGN+GLM+AVK+FDPERG RL ++++ WIKA + EYI+R+
Sbjct: 73  VVSIARQYLGYGLAHADLIQEGNVGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYIVRN 132

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W LVK+ TT  Q++LFFNLRR++          L  EQV  IA++LNV   +V  M  R+
Sbjct: 133 WRLVKVATTKAQRKLFFNLRRMR-----PDGQTLDTEQVNEIARELNVRPEDVSEMEVRM 187

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ--VLIEKEERKNRRNMLTRSMSVLNPR 238
           +G E     + S+D          + D   QE   VL  +     + + L  ++ VL+ R
Sbjct: 188 SGRE---FALESNDDEDGYAPIAYLSDEGQQEPSRVLERRAYDALQGSGLADALDVLDER 244

Query: 239 ERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            RRI +AR LQ+    TL  L++EF VS ER+RQIEA AFKK++ ++
Sbjct: 245 SRRIVQARWLQDEGGATLHELAAEFGVSAERIRQIEAAAFKKLRVAL 291


>gi|226366217|ref|YP_002784000.1| RNA polymerase sigma factor [Rhodococcus opacus B4]
 gi|226244707|dbj|BAH55055.1| RNA polymerase sigma factor SigA [Rhodococcus opacus B4]
 gi|254553058|dbj|BAH85841.1| RNA polymerase sigma A factor [Rhodococcus opacus]
          Length = 457

 Score =  249 bits (636), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 79/319 (24%), Positives = 149/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------------- 41
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR                     
Sbjct: 144 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQIMQELSDSGEKL 202

Query: 42  --REHGDLS--------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
              +  D+S        A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 203 PAAQRRDMSWICRDGNRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 262

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 263 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 320

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 321 REPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 372

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 373 AVVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 432

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 433 RQIESKTMSKLRHPSRSQV 451


>gi|84625707|ref|YP_453079.1| RNA polymerase factor sigma-32 [Xanthomonas oryzae pv. oryzae MAFF
           311018]
 gi|289664834|ref|ZP_06486415.1| RNA polymerase factor sigma-32 [Xanthomonas campestris pv.
           vasculorum NCPPB702]
 gi|289671390|ref|ZP_06492465.1| RNA polymerase factor sigma-32 [Xanthomonas campestris pv.
           musacearum NCPPB4381]
 gi|84369647|dbj|BAE70805.1| RNA polymerase sigma-32 factor [Xanthomonas oryzae pv. oryzae MAFF
           311018]
          Length = 291

 Score =  248 bits (635), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 119/291 (40%), Positives = 173/291 (59%), Gaps = 15/291 (5%)

Query: 1   MNRKNMSIIV-------NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRL 53
           MN+   + +V       +    L  YI  + +IP+L   EE  LA+R+R+  DL AA  L
Sbjct: 1   MNQTTSTALVANNLPIPSALGSLDAYIGAVHQIPVLSVDEEQNLARRFRDELDLDAAREL 60

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V SHLR VV +A GY GYGLP+ +++ EGNIGLM+AVK+FDP+ G RL ++++ WI+A M
Sbjct: 61  VHSHLRFVVHVARGYNGYGLPLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAVHWIRAEM 120

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
            E+IL++W +VK+ TT  Q++LFFNLR+ K  L  +        +V A+AK LNVSE EV
Sbjct: 121 HEFILKNWRIVKVATTKAQRKLFFNLRKSKTRLGWLN-----ASEVTAVAKDLNVSEREV 175

Query: 174 ISMNCRLAG-DESLNA-LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           + M  RL+G D   +A      D        +LV + +   Q     +   N+  +L   
Sbjct: 176 MEMESRLSGRDIGFDASSDEDDDHGPPSPVSYLVANEEDPSQAYERHDSEDNQLQLLREG 235

Query: 232 MSVLNPRERRIFEARRLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           M+ L+ R R I + R L  ++ VTL+ L+ E+ VS ER+RQIEA A KK++
Sbjct: 236 MAGLDTRSRDIVKRRWLDSDSKVTLQELADEYGVSAERIRQIEANALKKMK 286


>gi|302525743|ref|ZP_07278085.1| RNA polymerase sigma factor RpoS [Streptomyces sp. AA4]
 gi|302434638|gb|EFL06454.1| RNA polymerase sigma factor RpoS [Streptomyces sp. AA4]
          Length = 476

 Score =  248 bits (635), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 80/319 (25%), Positives = 148/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGD-- 46
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+  
Sbjct: 163 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYAAERVRTAEEEGEKL 221

Query: 47  ---------------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 222 VTQMRRDLKWIVRDGERAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 281

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 282 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 339

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK++++S  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 340 REPTPE---ELAKEMDISPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 391

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 392 AVVAVDAVSFTLLQDQLQSVLQTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 451

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 452 RQIESKTMSKLRHPSRSQV 470


>gi|225377779|ref|ZP_03755000.1| hypothetical protein ROSEINA2194_03430 [Roseburia inulinivorans DSM
           16841]
 gi|225210363|gb|EEG92717.1| hypothetical protein ROSEINA2194_03430 [Roseburia inulinivorans DSM
           16841]
          Length = 426

 Score =  248 bits (635), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 85/317 (26%), Positives = 136/317 (42%), Gaps = 51/317 (16%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR--------------------------- 42
           V+ E  +  Y+ EI K+P+L  +EE  LAK                              
Sbjct: 113 VSIEDPVRMYLKEIGKVPLLSAEEEIELAKNMEAGAVAKEKIAILKSREEKATEEELAEI 172

Query: 43  -----------EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                      + GD  A  RL  ++LRLVV IA  Y G G+   +++ EGN+GL++AV+
Sbjct: 173 KEEIKNLQKDLDAGD-EAKKRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVE 231

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   I      ++I     +      L R+   L     
Sbjct: 232 KFDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE--TINKLIRVSRQLLQELG 289

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    IA ++N+    V  +        SL   I   ++  S   D++  D    
Sbjct: 290 REPSPE---EIAAEMNMPVERVREILKISQEPVSLETPI--GEEEDSHLGDFIQDD---N 341

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERV 269
             V  +       +  L   +  L  RE+++   R   E+    TLE +  EF V+RER+
Sbjct: 342 VPVPADAAAFTLLKEQLEEVLGTLTEREQKVLTLRFGLEDGRARTLEEVGKEFNVTRERI 401

Query: 270 RQIEARAFKKVQESIQK 286
           RQIEA+A +K++   + 
Sbjct: 402 RQIEAKALRKLRHPSRS 418


>gi|223936758|ref|ZP_03628668.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [bacterium
           Ellin514]
 gi|223894609|gb|EEF61060.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [bacterium
           Ellin514]
          Length = 352

 Score =  248 bits (635), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 91/278 (32%), Positives = 147/278 (52%), Gaps = 13/278 (4%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           +G+  +  Y+ EI ++ +L  Q+E  LA R ++ GD  A   ++ ++LRLVVKIA  Y G
Sbjct: 80  DGDTAIKLYLREIGQVQLLTPQQEIELAARIKK-GDKKARELMIKANLRLVVKIARDYEG 138

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            GLP+ +++SEGNIGLM+AV++FDP +G +L+TY  WWIK +++  +      +++    
Sbjct: 139 IGLPLLDLISEGNIGLMKAVERFDPAKGGKLSTYGSWWIKQSIKRALANQSKTIRLPVH- 197

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
               L   + +++     + +   +      +A +LN+S   V  M        SL+A I
Sbjct: 198 ----LVDKISKMRRTALKLQEILGREPSDEELADELNISAMRVSQMRTAAIRPASLDAPI 253

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
              D N+     +     D       E+ E K    ML   +  L+PRE  I  AR   +
Sbjct: 254 GDEDSNN-----FAEVVQDENADTPYEQLEEKTVTKMLQELVKTLDPREATILRARFGLD 308

Query: 251 --NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             N  TLE +  +F V+RERVRQI+  A KK+++ I+K
Sbjct: 309 GGNQKTLEEVGQKFGVTRERVRQIQNIALKKLRKMIEK 346


>gi|294812504|ref|ZP_06771147.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|294325103|gb|EFG06746.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 436

 Score =  248 bits (635), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 84/302 (27%), Positives = 138/302 (45%), Gaps = 39/302 (12%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------------REHGDLS--- 48
                  +Y+ EI +IP+L   EE  LA+R                    R   DL    
Sbjct: 134 PSSDLFRQYLREIGRIPLLTAAEEVELARRVEAGLFAEEKLAATPDLNSSRLAADLDRLV 193

Query: 49  -----AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
                A  RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +T
Sbjct: 194 VMGRMAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYTRGYKFST 253

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI+ AM   +      +++     +  L   + R++  +     +   PE+V A  
Sbjct: 254 YATWWIRQAMSRALADQARTIRVPVHVVE--LINRVVRVQRRMLQEQGSEPTPEEVAA-- 309

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
            +L++    V  +        SL+A +   ++      D +    DG     +E      
Sbjct: 310 -QLDLPPERVSEVLRLAQEPVSLHAPV--GEEEDVALGDLI---EDGDAASPVESAAFLL 363

Query: 224 RRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R  L   +S L  RER++ + R       P TLE +   F V+RER+RQIE++   K++
Sbjct: 364 LREHLEAVLSTLGERERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLR 423

Query: 282 ES 283
           + 
Sbjct: 424 DH 425


>gi|317154823|ref|YP_004122871.1| sigma-70 family RNA polymerase sigma factor [Desulfovibrio
           aespoeensis Aspo-2]
 gi|316945074|gb|ADU64125.1| RNA polymerase sigma factor, sigma-70 family [Desulfovibrio
           aespoeensis Aspo-2]
          Length = 397

 Score =  248 bits (635), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 106/278 (38%), Positives = 171/278 (61%), Gaps = 8/278 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             L  Y+ EI + P+L+ +EEY LAKR ++  D  AA +LV+SHLRLVV+IAM ++   +
Sbjct: 115 DPLQLYLKEIARFPLLDPEEEYALAKRVQDENDQDAAFKLVSSHLRLVVRIAMDFQRRWM 174

Query: 74  -PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
               +++ EGN+GL++AV KFDPE+G + + Y+ +W+KA + +YI+ +W +VK+GTT  Q
Sbjct: 175 QNALDLIQEGNVGLLKAVTKFDPEKGIKFSYYAAFWVKAYILKYIMDNWRMVKVGTTQTQ 234

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALIN 191
           ++LF+NL + +  LQA+           A++K L VSE+E+  M+ RL+  D SLNA + 
Sbjct: 235 RKLFYNLNKERQRLQAM----GFDPTTEALSKSLGVSEAEIDEMDQRLSRNDMSLNAPL- 289

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             + + +   D+L     G E+ L   +  +     L      LN +E  I + R L ++
Sbjct: 290 -GEDSDATRMDFLPSLGPGIEESLASDQIVELLLENLKAIRPTLNDKELAILDHRLLSDD 348

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           P+TL  +   FEV+RERVRQIEAR   K++E + ++++
Sbjct: 349 PMTLREIGERFEVTRERVRQIEARLIAKIREHMTEKIK 386


>gi|217077377|ref|YP_002335095.1| RNA polymerase sigma factor RpoD [Thermosipho africanus TCF52B]
 gi|217037232|gb|ACJ75754.1| RNA polymerase sigma factor RpoD [Thermosipho africanus TCF52B]
          Length = 371

 Score =  248 bits (635), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 74/273 (27%), Positives = 137/273 (50%), Gaps = 13/273 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y+ +I KIP+L +  E  LA+R +  GD  A  +LV S+LRLVV IA  Y G GL  
Sbjct: 97  IKMYLKDIGKIPLLSQSMERELARRAQL-GDERAKQKLVESNLRLVVSIAKRYVGKGLSF 155

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GL++AV+KFD ++G++ +TY+ WWI+ A+   I      +++     +   
Sbjct: 156 LDLIQEGNVGLLKAVEKFDWKKGYKFSTYATWWIRQAITRAIADQARTIRVPVHMVE--- 212

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + +++  ++     +     +  +AK +     +V  +        SL A +   + 
Sbjct: 213 --TINKVQKIMREYYQEHGTEIPIEELAKLIGKPVEKVEEILQAAKETTSLEAPV--GED 268

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPV 253
           + S   D++  +     +   ++  R   R  + + +  LN RE+ + + R         
Sbjct: 269 DDSTVGDFIADETIASPK---KEAMRMLIREEVDKVLETLNDREKLVLKMRYGLIDGKAK 325

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TLE +   F V+RER+RQIE +A +K++   + 
Sbjct: 326 TLEEVGQYFNVTRERIRQIEVKALRKLRHPSRS 358


>gi|238018971|ref|ZP_04599397.1| hypothetical protein VEIDISOL_00831 [Veillonella dispar ATCC 17748]
 gi|237864455|gb|EEP65745.1| hypothetical protein VEIDISOL_00831 [Veillonella dispar ATCC 17748]
          Length = 387

 Score =  248 bits (635), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 78/291 (26%), Positives = 131/291 (45%), Gaps = 23/291 (7%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHR-----------LVTSHL 58
           VN +  +  Y+ EI ++P+L   EE VLAK+        A ++           LV ++L
Sbjct: 101 VNIDDPVRMYLKEIGRVPLLSADEEIVLAKQIEAGAAEDATYKDVQLAKKAKKKLVDANL 160

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV IA  Y G G+   +++ EGN+GL++AV KFD  +G++ +TY+ WWI+ A+   I 
Sbjct: 161 RLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVDKFDYTKGYKFSTYATWWIRQAITRAIA 220

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
                ++I     +      L R+   L         PE    IA+ + ++   V  +  
Sbjct: 221 DQARTIRIPVHMVE--TINKLIRISRQLLQDKGREPLPE---EIAEGMGITVERVREIQK 275

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
                 SL   I   ++  S   D++    D       +       +  +    + L  R
Sbjct: 276 IAQEPVSLETPI--GEEEDSHLGDFI---EDQDAIAPDDAASYILLQEQIEDVFTCLTDR 330

Query: 239 ERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+++   R       P TLE +   F V+RER+RQIE +A  K++   ++ 
Sbjct: 331 EQQVLILRFGLKDGKPRTLEEVGQHFNVTRERIRQIEGKALTKLRNRGKRD 381


>gi|78357159|ref|YP_388608.1| sigma 70 family protein [Desulfovibrio desulfuricans subsp.
           desulfuricans str. G20]
 gi|78219564|gb|ABB38913.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfovibrio desulfuricans
           subsp. desulfuricans str. G20]
          Length = 360

 Score =  248 bits (635), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 107/282 (37%), Positives = 172/282 (60%), Gaps = 7/282 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYG 72
             L  Y+ EI + PML+  EE+ LA+R + H D  AA RLV+SHLRLVVKIAM + R + 
Sbjct: 79  DSLHLYLREISRFPMLKPDEEFELARRVQLHNDSDAAFRLVSSHLRLVVKIAMDFQRRWM 138

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
             + +++ EGN+GLM+AV KFDP++G + + Y+ +WIKA + ++I+ +W LVKIGTT  Q
Sbjct: 139 QNVLDLIQEGNVGLMRAVNKFDPDKGIKFSYYAAFWIKAYILKFIMDNWRLVKIGTTQAQ 198

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALIN 191
           ++LF+NL + +  L A             ++++L+V+  +V+ M  RL A D SL+  + 
Sbjct: 199 RKLFYNLNKERQKLIA----QGYDPDAAMLSERLDVTTEQVVEMEQRLDASDMSLDVQVG 254

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             +  S+   D+L     G E  L   E     +  +   + +LN +E  I  +R L E+
Sbjct: 255 D-ENGSASRMDFLPALGPGIEDTLANNEIAAMVQERIRDIVPLLNDKELDILNSRLLSED 313

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           PVTL  +  +++++RERVRQIEAR  +K+++ + K+++  SS
Sbjct: 314 PVTLREIGEKYDITRERVRQIEARLLQKIRDHLFKEIKDFSS 355


>gi|213964575|ref|ZP_03392775.1| RNA polymerase sigma factor A [Corynebacterium amycolatum SK46]
 gi|213952768|gb|EEB64150.1| RNA polymerase sigma factor A [Corynebacterium amycolatum SK46]
          Length = 520

 Score =  248 bits (635), Expect = 5e-64,   Method: Composition-based stats.
 Identities = 78/319 (24%), Positives = 152/319 (47%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------REHGDL- 47
            RK+ ++  + +  +  Y+ +I K+ +L  +EE  LAKR              ++ G+  
Sbjct: 207 ARKDAALTASAD-SVRAYLKQIGKVALLTAEEEVSLAKRIEAGLYAQYKIDEAKQAGERI 265

Query: 48  ----------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 266 AYAQKRDLREISRDGQRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 325

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 326 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 383

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++E +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 384 REPTPE---ELAKEMDITEEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 435

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERV 269
             + ++       ++ L   +  L+ RE  +   R    +  P TL+ +   + V+RER+
Sbjct: 436 AVIAVDAVSFTLLQDQLGDVLETLSEREAGVVRLRFGLTDGMPRTLDEIGQVYGVTRERI 495

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 496 RQIESKTMSKLRHPSRSQV 514


>gi|324997280|ref|ZP_08118392.1| RNA polymerase sigma factor [Pseudonocardia sp. P1]
          Length = 469

 Score =  248 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 79/319 (24%), Positives = 148/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGD-- 46
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E  D  
Sbjct: 156 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYGAERIRKLFESNDKL 214

Query: 47  ---------------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 215 SPQMRRDLRWIVRDGERAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 274

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 275 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 332

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 333 REPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 384

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   ++ L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 385 AVVAVDAVSFTLLQDQLQSVLATLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 444

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 445 RQIESKTMSKLRHPSRSQV 463


>gi|269837239|ref|YP_003319467.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphaerobacter
           thermophilus DSM 20745]
 gi|269786502|gb|ACZ38645.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphaerobacter
           thermophilus DSM 20745]
          Length = 390

 Score =  248 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 83/310 (26%), Positives = 146/310 (47%), Gaps = 38/310 (12%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------HGD------ 46
            R++++  V+    +  Y+ EI +  +L  +EE  LAKR            +GD      
Sbjct: 80  TRQDVADAVSVSDSVRLYLQEIGETSLLTMEEEVWLAKRMERGKIAEERLANGDYASEAE 139

Query: 47  -----------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
                        A   L+ ++LRLVV +A  Y G GL   +++ EGNIGLM+A  KFD 
Sbjct: 140 RAELLADKEDGEKARAHLIQANLRLVVSVAKKYVGRGLSFLDLIQEGNIGLMKATDKFDY 199

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           +RGF+ +TY+ WWI+ A+   I      +++     +      + R+K   Q +     +
Sbjct: 200 KRGFKFSTYATWWIRQAITRAISDQSRTIRLPVHVGE-----TINRVKKTSQRLQQIFER 254

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
                 +A+ +++ E +V  +        SL A +    +  +   D++  D        
Sbjct: 255 EPTFEEVARAMDIPEEKVRQVLDASRHPVSLEAPV--GQEGDAFLGDFIEDD---TMPPP 309

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIE 273
           +E   ++  ++ ++ ++S L  RERRI   R   E+    TLE +  EF ++RER+RQIE
Sbjct: 310 LELASQELLKHQISDALSKLTERERRIIILRFGLEDGQFRTLEEVGREFGITRERIRQIE 369

Query: 274 ARAFKKVQES 283
           A+A +K++  
Sbjct: 370 AKALRKLRHP 379


>gi|256784755|ref|ZP_05523186.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
          Length = 492

 Score =  248 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 75/304 (24%), Positives = 139/304 (45%), Gaps = 40/304 (13%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------------REHGD 46
             +  Y+ +I K+P+L  ++E  LAKR                             E G 
Sbjct: 194 DPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANSDKLAPKLKRELEIIAEDG- 252

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 253 RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 312

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L
Sbjct: 313 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKEL 367

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +VI +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 368 DMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 422

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 423 QLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 482

Query: 285 QKQV 288
           + QV
Sbjct: 483 RSQV 486


>gi|239928504|ref|ZP_04685457.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 490

 Score =  248 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 75/304 (24%), Positives = 139/304 (45%), Gaps = 40/304 (13%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------------REHGD 46
             +  Y+ +I K+P+L  ++E  LAKR                             E G 
Sbjct: 192 DPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANSDKLAPKLKRELEIIAEDG- 250

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 251 RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 310

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L
Sbjct: 311 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKEL 365

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +VI +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 366 DMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFTLLQE 420

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 421 QLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 480

Query: 285 QKQV 288
           + QV
Sbjct: 481 RSQV 484


>gi|120612533|ref|YP_972211.1| RNA polymerase sigma-32 subunit RpoH [Acidovorax citrulli AAC00-1]
 gi|120590997|gb|ABM34437.1| RNA polymerase, sigma 32 subunit, RpoH [Acidovorax citrulli
           AAC00-1]
          Length = 313

 Score =  248 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 109/294 (37%), Positives = 169/294 (57%), Gaps = 14/294 (4%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           ++     L  YI  + ++PML  +EE   A+R +EH D+ AA R+V SHLRLVV IA  Y
Sbjct: 20  LIPPLGNLDAYISAVNRLPMLTAEEERTYARRLKEHNDVEAAGRMVMSHLRLVVSIARQY 79

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGLP  +++ EGN+GLM+AVK+FDP++  RL +Y+M WIKA + EYIL++W +VK+ T
Sbjct: 80  LGYGLPHGDLIQEGNVGLMKAVKRFDPDQNVRLVSYAMHWIKAEIHEYILKNWRMVKVAT 139

Query: 129 TANQKRLFFNLRRLKG--------HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           T +Q++LFFNLR +K                  L  +++  +A++LNV   EVI M  RL
Sbjct: 140 TKSQRKLFFNLRSMKQGFKADAAAGDAGTHRETLSEQEIDVVAQQLNVKREEVIEMETRL 199

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLNPRE 239
           +G + +     S D   +      + D   +   +IE  +R     + +  +++ L+ R 
Sbjct: 200 SGGDVMLDPAPSDDGEQAYGPIAYLADGMHEPTAMIESRQRDVLATDGIANALATLDDRS 259

Query: 240 RRIFEARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RRI E R L         +TL  L++ + VS ER+RQIE  A KK+++++ +  
Sbjct: 260 RRIVEERWLKVNDDGSGGMTLHELAAVYGVSAERIRQIEVAAMKKMKKALAEYA 313


>gi|160941150|ref|ZP_02088487.1| hypothetical protein CLOBOL_06043 [Clostridium bolteae ATCC
           BAA-613]
 gi|158435711|gb|EDP13478.1| hypothetical protein CLOBOL_06043 [Clostridium bolteae ATCC
           BAA-613]
          Length = 406

 Score =  248 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 82/280 (29%), Positives = 147/280 (52%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V+    +  Y+ EI  I +L  +EE  LA+R +  GD+ A  +LV ++LRLVV IA  Y 
Sbjct: 131 VSTADPIREYLKEIGSIALLTPEEESDLARR-KSEGDVEAGRKLVEANLRLVVSIAKRYT 189

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   ++V EGN+GLM+AV+KFD  +G+RL+TY+ WW+K ++   +      +++   
Sbjct: 190 GRGMSFLDLVQEGNLGLMKAVEKFDYAKGYRLSTYATWWVKQSITRSLADQSRTIRLPVH 249

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      + +++   ++++    +   +  +A+++N+S   V  +        SL   
Sbjct: 250 MVE-----AVNKIRRAQRSLSVKLGREPSMEEVAEEVNMSGKRVAELIQASGDTVSLETP 304

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           +   D+  S   D++  D +   +   +K E    R  +   +  LNPRER +   R   
Sbjct: 305 V--GDEEGSNLGDFVADDANASTE---DKAESFLLREEIDSMLQGLNPREREVIILRFGL 359

Query: 250 E--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E  +P+TLE +   F V+RER+RQIE  A +K++   + +
Sbjct: 360 ETGHPLTLEEVGKRFNVTRERIRQIETAALRKLRNPSKSK 399


>gi|260550924|ref|ZP_05825130.1| alternative sigma factor RpoH [Acinetobacter sp. RUH2624]
 gi|260406051|gb|EEW99537.1| alternative sigma factor RpoH [Acinetobacter sp. RUH2624]
          Length = 288

 Score =  248 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 110/283 (38%), Positives = 167/283 (59%), Gaps = 8/283 (2%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +S+   G + L  YI  + +IP+L  ++E  LA+RY    DL AA  LV SHLR VV IA
Sbjct: 11  LSLSAPG-VNLGAYISTVNQIPILTAEQEKELAERYYYDQDLDAAKMLVMSHLRFVVHIA 69

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGLP  +++ EGN+GLM+AVK+FDP  G RL ++++ WIKA + EY++R+W +VK
Sbjct: 70  RSYAGYGLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVK 129

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDE 184
           I TT  Q++LFFNLR LK   + +T      E+  +IA  LNV+  +V+ M  RL A D 
Sbjct: 130 IATTKAQRKLFFNLRSLKKSSKKLT-----LEEAQSIANDLNVTPEQVLEMEGRLTAYDA 184

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR-NMLTRSMSVLNPRERRIF 243
           +  A  +  D          + D+      L+E E+ + +  + L  +M  L+ R R I 
Sbjct: 185 AFEAQGDDDDDTPHTAPALYLEDNRYDPARLVENEDWEEQSTSALHDAMDQLDDRSRNIL 244

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           + R L ++  TL  L++E+ VS ER+RQ+E  A +K++ ++  
Sbjct: 245 QRRWLDDDKSTLHELAAEYNVSAERIRQLEKNAMEKIKVAMSA 287


>gi|297571337|ref|YP_003697111.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Arcanobacterium
           haemolyticum DSM 20595]
 gi|296931684|gb|ADH92492.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Arcanobacterium
           haemolyticum DSM 20595]
          Length = 510

 Score =  248 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 73/303 (24%), Positives = 141/303 (46%), Gaps = 38/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY------------------REHGDLS------- 48
             +  Y+ +I K+ +L  +EE  LAKR                   R+  +L        
Sbjct: 212 DPVKDYLKQIGKVALLNAEEEVELAKRIEAGLFAQHILETTTIDDPRKRRELEIISRDGH 271

Query: 49  -AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ W
Sbjct: 272 KAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLVRAVEKFDYAKGYKFSTYATW 331

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   +      ++I     +      + +L    + +  +  +   V  +A +L+
Sbjct: 332 WIRQAITRAMADQARTIRIPVHMVEV-----INKLARVQRQMLQDLGREPTVEELAHELD 386

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++E +VI +        SL+  +   +   S++ D +    D +  V  +       +  
Sbjct: 387 MTEEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVGFTLLQEQ 441

Query: 228 LTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L + +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++   K++   +
Sbjct: 442 LHQVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSR 501

Query: 286 KQV 288
            QV
Sbjct: 502 SQV 504


>gi|160897140|ref|YP_001562722.1| RNA polymerase sigma 32 subunit RpoH [Delftia acidovorans SPH-1]
 gi|160362724|gb|ABX34337.1| RNA polymerase, sigma 32 subunit, RpoH [Delftia acidovorans SPH-1]
          Length = 314

 Score =  248 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 115/291 (39%), Positives = 172/291 (59%), Gaps = 15/291 (5%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +V     L  YI  + ++PML  +EE   A++ +EH DL AA RLV SHLRLVV I+  Y
Sbjct: 20  LVPPLGNLDAYISAVNRLPMLTLEEEQDYARKLKEHSDLDAAGRLVMSHLRLVVSISRQY 79

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGLP  +++ EGN+GLM+AVK+FDP++  RL +Y+M WIKA + EYIL++W +VK+ T
Sbjct: 80  LGYGLPHGDLIQEGNVGLMKAVKRFDPDQNVRLVSYAMHWIKAEIHEYILKNWRMVKVAT 139

Query: 129 TANQKRLFFNLRRLKGHLQ---------AITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
           T  Q++LFFNLR +K  L+         A+  + L   ++ A+A+KLNV   EV+ M  R
Sbjct: 140 TKAQRKLFFNLRSMKQGLKSDAAMAEDGAMLRDTLTSGEIDAVAEKLNVKREEVMEMETR 199

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPR 238
           LAG + L     S D   +      + D   +   +IE  +R +   + +  ++  L+ R
Sbjct: 200 LAGGDVLLDPSPSDDGEQAFGPIAYLADGAHEPTAMIESRQRDHLATDGIAMALDSLDDR 259

Query: 239 ERRIFEARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            RRI E R L         +TL  L++ + VS ER+RQIE  A KK+++++
Sbjct: 260 SRRIVEERWLKVNDDGSGGMTLHELAAVYGVSAERIRQIEVAAMKKMKKAL 310


>gi|325924311|ref|ZP_08185855.1| RNA polymerase, sigma 32 subunit, RpoH [Xanthomonas gardneri ATCC
           19865]
 gi|325545176|gb|EGD16486.1| RNA polymerase, sigma 32 subunit, RpoH [Xanthomonas gardneri ATCC
           19865]
          Length = 291

 Score =  248 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 118/276 (42%), Positives = 168/276 (60%), Gaps = 8/276 (2%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           I +    L  YI  + +IP+L   EE  LA+R+R+  DL AA  LV SHLR VV +A GY
Sbjct: 16  IPSALGSLDAYIGAVHQIPVLSVDEEQNLARRFRDELDLDAARELVHSHLRFVVHVARGY 75

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGLP+ +++ EGNIGLM+AVK+FDPE G RL ++++ WI+A M E+IL++W +VK+ T
Sbjct: 76  NGYGLPLGDLIQEGNIGLMKAVKRFDPEMGVRLVSFAVHWIRAEMHEFILKNWRIVKVAT 135

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN 187
           T  Q++LFFNLR+ K  L  +        +V A+AK LNVSE EV+ M  RL+G D   +
Sbjct: 136 TKAQRKLFFNLRKSKTRLGWLN-----ASEVTAVAKDLNVSEREVMEMESRLSGRDIGFD 190

Query: 188 A-LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           A      D        +LV + +   Q     +   N+  +L   +S L+ R R I + R
Sbjct: 191 ASSDEDDDHGPPSPVSYLVANEEDPSQAYERHDSEDNQLQLLREGLSGLDTRSRDIVKRR 250

Query: 247 RLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L  ++ VTL+ L+ E+ VS ER+RQIEA A KK++
Sbjct: 251 WLDSDSKVTLQELADEYGVSAERIRQIEANALKKMK 286


>gi|261855188|ref|YP_003262471.1| RNA polymerase, sigma 32 subunit, RpoH [Halothiobacillus
           neapolitanus c2]
 gi|261835657|gb|ACX95424.1| RNA polymerase, sigma 32 subunit, RpoH [Halothiobacillus
           neapolitanus c2]
          Length = 291

 Score =  248 bits (635), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 115/274 (41%), Positives = 180/274 (65%), Gaps = 8/274 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             L +Y+ E+R+IP+L   EE  LA++ +  GD+ AA +L+ SHLR VV IA GYRGYGL
Sbjct: 18  DSLQQYLAEVRRIPLLTADEEQKLAEQLKSTGDIDAAQKLIMSHLRFVVHIARGYRGYGL 77

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+++++ EGNIGLM+AVK+F+PE+  RL T+++ WI+A + EYIL++W +VKI TT  Q+
Sbjct: 78  PLADLIQEGNIGLMKAVKRFEPEQKVRLVTFAVHWIRAEIHEYILKNWRIVKIATTKAQR 137

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINS 192
           +LFF +R++K  L  +T      ++  AIA +LNV E EV++M  RL + D +++A +  
Sbjct: 138 KLFFKMRQMKSGLGWLT-----ADETRAIAAELNVPEREVVTMESRLYSHDIAIDAPVYD 192

Query: 193 SDKNSS--QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           S++  S   ++  LV  H    + +  + +  +R   +T ++  L+ R R I E R LQE
Sbjct: 193 SEQEGSGPSYEQILVDQHQVSVEDMTAQRDEDDRVTAMTHALHDLDARSRDILERRWLQE 252

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              TL+ L+ E++VS ERVRQIE  A KK++ ++
Sbjct: 253 PKATLQTLADEYQVSAERVRQIENAALKKLRLAL 286


>gi|302877701|ref|YP_003846265.1| RNA polymerase, sigma 32 subunit, RpoH [Gallionella
           capsiferriformans ES-2]
 gi|302580490|gb|ADL54501.1| RNA polymerase, sigma 32 subunit, RpoH [Gallionella
           capsiferriformans ES-2]
          Length = 284

 Score =  248 bits (634), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 122/288 (42%), Positives = 182/288 (63%), Gaps = 7/288 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           MN  N   + +    L  YIH +R+  +L ++EE+ LA R+R   DL AA +LV SHLR+
Sbjct: 1   MNIANSLPMPSALGSLDSYIHLVRRYAVLSQEEEFDLATRFRNDNDLDAARQLVLSHLRV 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A GY GYGLP ++++ EGNIGLM+AVK +DPE G RL ++++ WI+A + E+++R+
Sbjct: 61  VVSVARGYAGYGLPQADLIQEGNIGLMKAVKHYDPEFGVRLVSFALHWIRAEINEFVVRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VKI TT  Q++LFFNLR LK  L+++     KP+Q+  IA++LNVSE +VI M  R 
Sbjct: 121 WRMVKIATTKAQRKLFFNLRSLKQGLESL-----KPKQISEIAEQLNVSEHDVIEMEARF 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRE 239
           AG E       S D ++     +L    + +   ++E  E  + R   L R+++ L+ R 
Sbjct: 176 AGHEVALDPAGSDDDDTYAPIQYLADSEEHEPSNILESSEGLSLRTQGLARALASLDDRS 235

Query: 240 RRIFEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           RRI EAR L E+   TL +L++EF+VS ER+RQIE +A  K+   +  
Sbjct: 236 RRIVEARWLSEDQNATLHDLAAEFKVSAERIRQIEQKAMSKMHTFLSA 283


>gi|237785650|ref|YP_002906355.1| RNA polymerase sigma factor [Corynebacterium kroppenstedtii DSM
           44385]
 gi|237758562|gb|ACR17812.1| RNA polymerase sigma factor A [Corynebacterium kroppenstedtii DSM
           44385]
          Length = 621

 Score =  248 bits (634), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 76/319 (23%), Positives = 147/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------ 43
            RK+  +  + +  +  Y+ +I K+ +L  ++E  LA+R                     
Sbjct: 308 ARKDAELTASAD-SVRAYLKQIGKVALLNAEQEVSLAQRIEAGLYANHKLEELKASNTKL 366

Query: 44  ------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                       H    A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 367 SPAQSRDLRSIAHDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 426

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 427 KFDYTKGYKFSTYATWWIRQAITRSMADQARTIRIPVHMVE--VINKLGRIQRELLQDLS 484

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +A++++++E +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 485 REPTPE---ELAREMDITEDKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 536

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L  RE  +   R    +  P TL+ +   + V+RER+
Sbjct: 537 AVVAVDAVSFTLLQDQLQDVLKTLTEREAGVVRLRFGLTDGMPRTLDEIGQVYGVTRERI 596

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 597 RQIESKTMSKLRHPSRSQV 615


>gi|169632997|ref|YP_001706733.1| RNA polymerase factor sigma-32 [Acinetobacter baumannii SDF]
 gi|169795347|ref|YP_001713140.1| RNA polymerase factor sigma-32 [Acinetobacter baumannii AYE]
 gi|184158784|ref|YP_001847123.1| RNA polymerase factor sigma-32 [Acinetobacter baumannii ACICU]
 gi|213158666|ref|YP_002319964.1| alternative sigma factor RpoH (EsvH) [Acinetobacter baumannii
           AB0057]
 gi|215482881|ref|YP_002325084.1| alternative sigma factor RpoH [Acinetobacter baumannii AB307-0294]
 gi|239502880|ref|ZP_04662190.1| RNA polymerase factor sigma-32 [Acinetobacter baumannii AB900]
 gi|301346949|ref|ZP_07227690.1| RNA polymerase factor sigma-32 [Acinetobacter baumannii AB056]
 gi|301513493|ref|ZP_07238730.1| RNA polymerase factor sigma-32 [Acinetobacter baumannii AB058]
 gi|301596794|ref|ZP_07241802.1| RNA polymerase factor sigma-32 [Acinetobacter baumannii AB059]
 gi|332850459|ref|ZP_08432779.1| alternative sigma factor RpoH [Acinetobacter baumannii 6013150]
 gi|332871911|ref|ZP_08440323.1| alternative sigma factor RpoH [Acinetobacter baumannii 6013113]
 gi|169148274|emb|CAM86139.1| sigma H (sigma 32) factor of RNA polymerase [Acinetobacter
           baumannii AYE]
 gi|169151789|emb|CAP00610.1| sigma H (sigma 32) factor of RNA polymerase [Acinetobacter
           baumannii]
 gi|183210378|gb|ACC57776.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Acinetobacter baumannii ACICU]
 gi|193077812|gb|ABO12685.2| EsvH [Acinetobacter baumannii ATCC 17978]
 gi|213057826|gb|ACJ42728.1| alternative sigma factor RpoH (EsvH) [Acinetobacter baumannii
           AB0057]
 gi|213986534|gb|ACJ56833.1| alternative sigma factor RpoH [Acinetobacter baumannii AB307-0294]
 gi|322507403|gb|ADX02857.1| rpoH [Acinetobacter baumannii 1656-2]
 gi|323518699|gb|ADX93080.1| RNA polymerase factor sigma-32 [Acinetobacter baumannii
           TCDC-AB0715]
 gi|332730730|gb|EGJ62041.1| alternative sigma factor RpoH [Acinetobacter baumannii 6013150]
 gi|332731125|gb|EGJ62426.1| alternative sigma factor RpoH [Acinetobacter baumannii 6013113]
          Length = 288

 Score =  248 bits (634), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 110/283 (38%), Positives = 168/283 (59%), Gaps = 8/283 (2%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +S+   G + L  YI  + +IP+L  ++E  LA+RY    DL AA  LV SHLR VV IA
Sbjct: 11  LSLSAPG-VNLGAYISTVNQIPILTAEQEKELAERYYYDQDLDAAKMLVMSHLRFVVHIA 69

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGLP  +++ EGN+GLM+AVK+FDP  G RL ++++ WIKA + EY++R+W +VK
Sbjct: 70  RSYAGYGLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVK 129

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDE 184
           I TT  Q++LFFNLR LK   + +T      E+  +IA  LNV+  +V+ M  RL A D 
Sbjct: 130 IATTKAQRKLFFNLRSLKKSSKKLT-----LEEAQSIANDLNVTPEQVLEMEGRLTAYDA 184

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR-NMLTRSMSVLNPRERRIF 243
           +  A  +  D          + D+      L+E E+ + +  + L  +M+ L+ R R I 
Sbjct: 185 AFEAQGDDDDDTPHTAPVLYLEDNRYDPARLVENEDWEEQSTSALHDAMNQLDDRSRNIL 244

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           + R L ++  TL  L++E+ VS ER+RQ+E  A +K++ ++  
Sbjct: 245 QRRWLDDDKSTLHELAAEYNVSAERIRQLEKNAMEKIKVAMSA 287


>gi|237736224|ref|ZP_04566705.1| RNA polymerase sigma factor rpoD [Fusobacterium mortiferum ATCC
           9817]
 gi|229421777|gb|EEO36824.1| RNA polymerase sigma factor rpoD [Fusobacterium mortiferum ATCC
           9817]
          Length = 351

 Score =  248 bits (634), Expect = 6e-64,   Method: Composition-based stats.
 Identities = 79/277 (28%), Positives = 142/277 (51%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI +IP+L   EE   AKR  E GD  A+ +L+ ++LRLVV IA  +   G
Sbjct: 79  DEPIKMYLREIGQIPLLSHDEELEYAKRALE-GDEWASQQLIEANLRLVVSIAKKHTNRG 137

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L + +++ EGNIGLM+AV+KF+  +G++ +TY+ WWI+ A+   I      ++I      
Sbjct: 138 LKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPVH--- 194

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
             +   + ++K   +       K      +A++L +   +V ++        SL   + S
Sbjct: 195 --MIETINKIKKEARIYLQETGKDATPEVLAERLGMEVEKVKAIQEMNQDPISLETPVGS 252

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN- 251
             +  S+  D++    D +     E   R   R  L   ++ L+ RE ++   R   ++ 
Sbjct: 253 --EEDSELGDFV---EDNKMLNPYELTNRSLLREQLDGVLNSLSSREEKVLRYRYGLDDG 307

Query: 252 -PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            P TLE +   F+V+RER+RQIE +A +K++   +++
Sbjct: 308 SPKTLEEVGKIFKVTRERIRQIEVKALRKLRHPSRRK 344


>gi|303248805|ref|ZP_07335056.1| RNA polymerase sigma factor, sigma-70 family [Desulfovibrio
           fructosovorans JJ]
 gi|302489817|gb|EFL49747.1| RNA polymerase sigma factor, sigma-70 family [Desulfovibrio
           fructosovorans JJ]
          Length = 344

 Score =  248 bits (634), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 109/292 (37%), Positives = 182/292 (62%), Gaps = 6/292 (2%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           R   S  ++    L  Y+ EI K PML+ +EE  LA+R R+ GD  AA RL++SHLRLVV
Sbjct: 51  RAGSSGSLSTRDPLQLYLREIGKFPMLKPEEEQELARRVRDSGDEKAAFRLISSHLRLVV 110

Query: 63  KIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           KIAM ++   +  + +++ EGN+GLM+AV KFDP++G + + Y+ +WIKA + +YI+ +W
Sbjct: 111 KIAMDFQRRWMQNVLDLIQEGNVGLMRAVTKFDPDKGIKFSYYAAYWIKAYILKYIMDNW 170

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            +VKIGTT  Q++LF+NL + +  LQ +            +++ LNV+ES+++ M+ RL+
Sbjct: 171 RMVKIGTTQAQRKLFYNLNKERNRLQTL----GFDPSASQLSEALNVTESDIVEMDQRLS 226

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           G++ L+  ++  + ++S   D+L     G E++L   E        +      LN +E  
Sbjct: 227 GND-LSLDVSLGEDSTSTRLDFLPALTPGIEEILAGDEISHQLEKHIQTIRPSLNEKELD 285

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           + + R L ++PVTL  + +++ ++RERVRQIEAR  +K++E + K++E  SS
Sbjct: 286 LLDNRILSDSPVTLREIGAKYGITRERVRQIEARLLEKLKEHLSKRIEDFSS 337


>gi|315656627|ref|ZP_07909514.1| DNA-directed RNA polymerase sigma subunit RpoD [Mobiluncus curtisii
           subsp. holmesii ATCC 35242]
 gi|315492582|gb|EFU82186.1| DNA-directed RNA polymerase sigma subunit RpoD [Mobiluncus curtisii
           subsp. holmesii ATCC 35242]
          Length = 564

 Score =  248 bits (634), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 72/305 (23%), Positives = 138/305 (45%), Gaps = 39/305 (12%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREH---------------------- 44
               +  Y+ +I K+ +L  ++E  L+KR     Y EH                      
Sbjct: 263 TSDPVKDYLKQIGKVALLNAEQEVDLSKRIEAGLYAEHLLKTKQETMTPKQIRELHYVVQ 322

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
               A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY
Sbjct: 323 DGQMAKNHLLEANLRLVVALAKKYTGRGMLFLDLIQEGNLGLIRAVEKFDYSKGYKFSTY 382

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + WWI+ A+   +      ++I     +  +   L R++  +         P+    +A+
Sbjct: 383 ATWWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPD---ELAQ 437

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L ++  +V+ +        SL+  +   +   S++ D +    D +  V  +       
Sbjct: 438 ELEMTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFMML 492

Query: 225 RNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +  L R +  L+ RE  +   R       P TL+ +   + V+RER+RQIEA+   K++ 
Sbjct: 493 QEQLQRVLDTLSERESGVIAMRFGLKDGQPKTLDEIGRRYGVTRERIRQIEAKTMSKLRH 552

Query: 283 SIQKQ 287
             + Q
Sbjct: 553 PARSQ 557


>gi|237744142|ref|ZP_04574623.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. 7_1]
 gi|229431371|gb|EEO41583.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. 7_1]
          Length = 417

 Score =  248 bits (634), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 81/285 (28%), Positives = 143/285 (50%), Gaps = 13/285 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           N+      +  +  Y+ EI ++P+L   EE   AKR  E GD  A+ +L+ S+LRLVV I
Sbjct: 136 NLGNSAKVDEPIKMYLREIGQVPLLTHDEEIEYAKRAYE-GDEEASKKLIESNLRLVVSI 194

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  +   GL + +++ EGNIGLM+AV+KF+  +G++ +TY+ WWI+ A+   I      +
Sbjct: 195 AKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTI 254

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I        +   + ++K   +       K      +A++L +   ++ ++        
Sbjct: 255 RIPVH-----MIETINKIKKESRIYLQETGKDASPEILAERLGMEVDKIKAIQEMNQEPI 309

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   + S  +  S+  D++    D +     E   R   R  L   +  L+PRE ++  
Sbjct: 310 SLETPVGS--EEDSELGDFV---EDQKTTSPYEATNRAILREELDAVLKTLSPREEKVLR 364

Query: 245 ARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R   ++  P TLE +   F V+RER+RQIE +A +K++   +K+
Sbjct: 365 YRYGLDDSSPKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRKK 409


>gi|226939164|ref|YP_002794235.1| RNA polymerase factor sigma-32 [Laribacter hongkongensis HLHK9]
 gi|226714088|gb|ACO73226.1| RpoH [Laribacter hongkongensis HLHK9]
          Length = 282

 Score =  248 bits (634), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 115/288 (39%), Positives = 177/288 (61%), Gaps = 7/288 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           MN      + +    L +YI  +  IPML + EE  LA+R ++  D+ AA +LV SHLR+
Sbjct: 1   MNVTMNLPVPSANGSLDQYIAAVNSIPMLSQDEEQALARRLQQDNDVEAARQLVMSHLRV 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA GY GYGLP ++++ EGNIGLM+AVK+F+PERG RL ++++ WIKA + E+ILR+
Sbjct: 61  VVSIARGYAGYGLPQADLIQEGNIGLMKAVKRFEPERGVRLFSFAIHWIKAEIHEFILRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W LV++ TT  Q++LFFNLR +K    A++D   +      IA  L V   EV  M  R+
Sbjct: 121 WRLVRVATTKPQRKLFFNLRSMKQGFSALSDTEAR-----QIADDLGVKPEEVREMETRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +G + ++ L   +++      DWL        + L  +   + +R  + +++  L+PR R
Sbjct: 176 SG-QDISLLAEDNEEEGFAPIDWLADTRSEPTKQLEMQAYERLQREGIEQALQALDPRSR 234

Query: 241 RIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           RI EAR L  +  +TL +L++EF VS ER+RQIE +A KK++ ++  +
Sbjct: 235 RIIEARWLADDGGLTLHDLAAEFGVSAERIRQIEVKALKKMKLTMIAE 282


>gi|304389369|ref|ZP_07371334.1| DNA-directed RNA polymerase sigma subunit RpoD [Mobiluncus curtisii
           subsp. curtisii ATCC 35241]
 gi|304327487|gb|EFL94720.1| DNA-directed RNA polymerase sigma subunit RpoD [Mobiluncus curtisii
           subsp. curtisii ATCC 35241]
          Length = 564

 Score =  248 bits (634), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 72/305 (23%), Positives = 138/305 (45%), Gaps = 39/305 (12%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREH---------------------- 44
               +  Y+ +I K+ +L  ++E  L+KR     Y EH                      
Sbjct: 263 TSDPVKDYLKQIGKVALLNAEQEVDLSKRIEAGLYAEHLLKTKQETMTPKQIRELHYVVQ 322

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
               A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY
Sbjct: 323 DGQMAKNHLLEANLRLVVALAKKYTGRGMLFLDLIQEGNLGLIRAVEKFDYSKGYKFSTY 382

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + WWI+ A+   +      ++I     +  +   L R++  +         P+    +A+
Sbjct: 383 ATWWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPD---ELAQ 437

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L ++  +V+ +        SL+  +   +   S++ D +    D +  V  +       
Sbjct: 438 ELEMTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFMML 492

Query: 225 RNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +  L R +  L+ RE  +   R       P TL+ +   + V+RER+RQIEA+   K++ 
Sbjct: 493 QEQLQRVLDTLSERESGVIAMRFGLKDGQPKTLDEIGRRYGVTRERIRQIEAKTMSKLRH 552

Query: 283 SIQKQ 287
             + Q
Sbjct: 553 PARSQ 557


>gi|111023781|ref|YP_706753.1| RNA polymerase sigma factor [Rhodococcus jostii RHA1]
 gi|110823311|gb|ABG98595.1| sigma factor, sigma 70 type, probable group 1 (principle sigma
           factor) [Rhodococcus jostii RHA1]
          Length = 457

 Score =  248 bits (634), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 79/319 (24%), Positives = 149/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------------- 41
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR                     
Sbjct: 144 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQIMQELSDSGEKL 202

Query: 42  --REHGDLS--------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
              +  D+S        A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 203 PAAQRRDMSWICRDGNRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 262

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 263 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 320

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 321 REPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 372

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 373 AVVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 432

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 433 RQIESKTMSKLRHPSRSQV 451


>gi|325928799|ref|ZP_08189966.1| RNA polymerase, sigma 32 subunit, RpoH [Xanthomonas perforans
           91-118]
 gi|325540772|gb|EGD12347.1| RNA polymerase, sigma 32 subunit, RpoH [Xanthomonas perforans
           91-118]
          Length = 282

 Score =  248 bits (634), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 118/282 (41%), Positives = 169/282 (59%), Gaps = 8/282 (2%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
             N   I +    L  YI  + +IP+L   EE  LA+R+R+  DL AA  LV SHLR VV
Sbjct: 1   MANNLPIPSALGSLDAYIGAVHQIPVLSVDEEQDLARRFRDELDLDAARELVHSHLRFVV 60

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A GY GYGLP+ +++ EGNIGLM+AVK+FDP+ G RL ++++ WI+A M E+IL++W 
Sbjct: 61  HVARGYNGYGLPLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAVHWIRAEMHEFILKNWR 120

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L  +        +V A+AK LNVSE EV+ M  RL+G
Sbjct: 121 IVKVATTKAQRKLFFNLRKSKTRLGWLN-----ASEVTAVAKDLNVSEREVMEMESRLSG 175

Query: 183 -DESLNA-LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            D   +A      D        +LV + +   Q     +   N+  +L   M+ L+ R R
Sbjct: 176 RDIGFDASSDEDDDHGPPSPVSYLVANEEDPSQAYERHDSEDNQLQLLREGMAGLDARSR 235

Query: 241 RIFEARRLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            I + R L  ++ VTL+ L+ E+ VS ER+RQIEA A KK++
Sbjct: 236 DIVKRRWLDSDSKVTLQELADEYGVSAERIRQIEANALKKMK 277


>gi|307943602|ref|ZP_07658946.1| RNA polymerase sigma-32 factor [Roseibium sp. TrichSKD4]
 gi|307773232|gb|EFO32449.1| RNA polymerase sigma-32 factor [Roseibium sp. TrichSKD4]
          Length = 291

 Score =  248 bits (634), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 112/266 (42%), Positives = 175/266 (65%), Gaps = 1/266 (0%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           + +  K P L ++EE+ LA R+R++ D  A  +L  SH RLV+ +A  +R +GLP+ +++
Sbjct: 12  VRKAMKAPYLTREEEHDLAVRWRDNRDEKALEKLSLSHTRLVISVASKFRNFGLPLGDLI 71

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EG++GL++A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT+++QK LFFNL
Sbjct: 72  QEGHVGLLEAAARFEPEREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSSQKALFFNL 131

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSS 198
           RRL+  L     N    E    IA  + V  ++V +MN RL+G D SLNA +  S+ +SS
Sbjct: 132 RRLRAKLSGNQQNLTDSELHQKIADAIGVKPADVATMNARLSGPDTSLNAPVTDSEGSSS 191

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
             QD+LV D    + ++ E  + + RR  L  +M+VL  RE +I   RRL E   TLE+L
Sbjct: 192 DRQDFLVSDAPQPDDIVSESIDTERRRKWLASAMTVLTDRELKIVRERRLTEEGATLESL 251

Query: 259 SSEFEVSRERVRQIEARAFKKVQESI 284
             +  +S+ERVRQIE+RA +K++ ++
Sbjct: 252 GQKLGISKERVRQIESRAMEKLKTAL 277


>gi|254251367|ref|ZP_04944685.1| hypothetical protein BDAG_00552 [Burkholderia dolosa AUO158]
 gi|124893976|gb|EAY67856.1| hypothetical protein BDAG_00552 [Burkholderia dolosa AUO158]
          Length = 311

 Score =  248 bits (634), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 118/289 (40%), Positives = 175/289 (60%), Gaps = 12/289 (4%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +S++      +  YI  + +IP+L  +EE   A  +RE+ +L AA RLV SHLRLVV IA
Sbjct: 29  LSMLPGQLGNIDAYIQAVNRIPLLTAEEERQYATEFRENNNLEAARRLVLSHLRLVVSIA 88

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGLP  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W +VK
Sbjct: 89  RNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVK 148

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDE 184
           + TT  Q++LFFNLR  K  +QA+T     PE++  +A++LNV   EV  M  RL  GD 
Sbjct: 149 VATTKAQRKLFFNLRSHKKSMQAMT-----PEEIDGLAQELNVKREEVAEMETRLSGGDV 203

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           +L   +   ++ S     +L   H+    VL  ++    + + + +++  L+ R RRI E
Sbjct: 204 ALEGQVEDGEE-SYAPIAYLADSHNEPTAVLAARQRDMLQTDGIAQALDALDARSRRIIE 262

Query: 245 ARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           AR L          TL +L++EF VS ER+RQIEA A KK++ ++ +  
Sbjct: 263 ARWLNVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRTALAEYA 311


>gi|153873537|ref|ZP_02002087.1| RNA polymerase sigma-32 factor [Beggiatoa sp. PS]
 gi|152069997|gb|EDN67913.1| RNA polymerase sigma-32 factor [Beggiatoa sp. PS]
          Length = 288

 Score =  248 bits (634), Expect = 7e-64,   Method: Composition-based stats.
 Identities = 109/283 (38%), Positives = 171/283 (60%), Gaps = 9/283 (3%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           N  + V G   +  Y   I+ IP+L  + E  LA+R+    D+ AA  LV SHLR V+ I
Sbjct: 8   NQQLAVPG-TSIEGYAQAIKAIPLLSIEAERKLAERFIGEDDIEAARTLVMSHLRFVMHI 66

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  YRGYGLP ++++ EGNIGLM+AVK+FDP  G RL ++++ WI+A + EYILR+W +V
Sbjct: 67  AHNYRGYGLPQADLIQEGNIGLMKAVKRFDPTVGVRLVSFAVHWIRAEIHEYILRNWRIV 126

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGD 183
           K+ TT +Q++LFFNLR  K  L  +T      ++V  +AK L VS  +V  M  RL + D
Sbjct: 127 KVATTKSQRKLFFNLRSAKKRLGWLTQ-----DEVETVAKDLGVSPKDVREMELRLNSYD 181

Query: 184 ESLNALINSSDKNSS--QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
            S +  +++ D N+       +L  +      ++ + E + +    L ++++ L+ R + 
Sbjct: 182 LSFDMPVDADDDNAEILSPVGYLEDNRYDPADLVEQSEWKTHGHRQLHQALAKLDVRSQD 241

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           I + R L EN  TL+ L++ ++VS ER+RQIE  A KK++++I
Sbjct: 242 ILQKRWLSENKTTLQELANHYKVSAERIRQIENNALKKLKKNI 284


>gi|239626174|ref|ZP_04669205.1| DNA-directed RNA polymerase sigma subunit [Clostridiales bacterium
           1_7_47_FAA]
 gi|239520404|gb|EEQ60270.1| DNA-directed RNA polymerase sigma subunit [Clostridiales bacterium
           1_7_47FAA]
          Length = 409

 Score =  248 bits (634), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 82/279 (29%), Positives = 143/279 (51%), Gaps = 13/279 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V+    +  Y+ EI  I +L  +EE  LA+R +  GD  A  +LV ++LRLVV IA  Y 
Sbjct: 133 VSTADPIREYLKEIGSISLLTPEEETDLARR-KSEGDAEAGRQLVEANLRLVVSIAKRYT 191

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+   ++V EGN+GLM+AV+KFD  +G+RL+TY+ WW+K ++   +      +++   
Sbjct: 192 GRGMGFLDLVQEGNLGLMKAVEKFDYSKGYRLSTYATWWVKQSITRSLADQSRTIRLPVH 251

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      + +++   ++++    +      IA+++ + E  V  +        SL   
Sbjct: 252 MVE-----AVNKIRRAQRSLSVRLGREPSTEEIAEEVGMPEKRVTELIQASGDTVSLETP 306

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           +   D+  S   D++  D +   +   +K E    R  +   +  LNPRER +   R   
Sbjct: 307 V--GDEEGSNLGDFVADDANASTE---DKAESFLLREEIDAMLQGLNPREREVIILRFGL 361

Query: 250 E--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E  +P+TLE +   F V+RER+RQIE  A +K++   + 
Sbjct: 362 ETGHPLTLEEVGRRFNVTRERIRQIETAALRKLRNPSKS 400


>gi|221065333|ref|ZP_03541438.1| RNA polymerase, sigma 32 subunit, RpoH [Comamonas testosteroni
           KF-1]
 gi|220710356|gb|EED65724.1| RNA polymerase, sigma 32 subunit, RpoH [Comamonas testosteroni
           KF-1]
          Length = 324

 Score =  248 bits (634), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 117/291 (40%), Positives = 170/291 (58%), Gaps = 15/291 (5%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +V     L  YI  + ++PML  +EE   A++ +EH DL AA RLV SHLRLVV I+  Y
Sbjct: 30  LVPPLGNLDAYISAVNRMPMLTLEEEQDYARKLKEHNDLDAAGRLVMSHLRLVVSISRQY 89

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGLP  +++ EGN+GLM+AVK+FDP++G RL +Y+M WIKA + EYIL++W +VK+ T
Sbjct: 90  LGYGLPHGDLIQEGNVGLMKAVKRFDPDQGVRLVSYAMHWIKAEIHEYILKNWRMVKVAT 149

Query: 129 TANQKRLFFNLRRLKGHL---------QAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
           T  Q++LFFNLR +K  L         +      L   ++ A+A KLNV   EVI M  R
Sbjct: 150 TKAQRKLFFNLRSMKHELKSDAAMADDELALRETLTSNEIDAVAAKLNVKREEVIEMETR 209

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPR 238
           LAG + L     S D   +      + D   +   ++E  +R +   + L  ++  L+ R
Sbjct: 210 LAGGDVLLDPSPSDDGEQAFGPIAYLADASHEPTAMLESRQRDHLATDGLVMALEGLDDR 269

Query: 239 ERRIFEARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            RRI E R L         +TL  L++E+ VS ER+RQIE  A KK+++++
Sbjct: 270 SRRIVEERWLKVNDDGSGGMTLHELAAEYGVSAERIRQIEVAAMKKMKKAL 320


>gi|56477835|ref|YP_159424.1| RNA polymerase factor sigma-32 [Aromatoleum aromaticum EbN1]
 gi|56313878|emb|CAI08523.1| Sigma-32 factor RpoH (RNA polymerase sigma factor) [Aromatoleum
           aromaticum EbN1]
          Length = 283

 Score =  248 bits (633), Expect = 8e-64,   Method: Composition-based stats.
 Identities = 117/285 (41%), Positives = 174/285 (61%), Gaps = 6/285 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M++     +      + +YI  + +IP+L +QEE  LA R R  GDL AA  LV SHLRL
Sbjct: 1   MSQALSFPVPFAVGSIDQYIQSVNRIPLLTEQEEVSLATRLRNEGDLEAARGLVMSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV I+ GY GYGLP ++++ EGNIGLM+AVK+FDP+RG RL ++++ WIKA + EYIL++
Sbjct: 61  VVAISRGYLGYGLPHADLIQEGNIGLMKAVKRFDPDRGVRLVSFAIHWIKAEIHEYILKN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W LVKI TT  Q++LFFNLR LK          L  ++VVA+AK+L V   EV+ M  RL
Sbjct: 121 WRLVKIATTKAQRKLFFNLRSLKQDT-----GTLNRDEVVAVAKQLGVKPEEVVEMETRL 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            G +         D++      +L   +    +VL + +  + +   L+ +++ L+ R R
Sbjct: 176 TGRDIQLEGGPDDDEHHFAPIAYLPDPNAEPSEVLEQAQLARLQDEGLSDALASLDDRSR 235

Query: 241 RIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            I + R L E +  TL  L++E+ VS ER+RQIEA+A +K++  +
Sbjct: 236 TIVKRRWLTEGDSATLHELAAEYGVSAERIRQIEAKAMQKMRGLL 280


>gi|296327931|ref|ZP_06870466.1| DNA-directed RNA polymerase sigma subunit RpoD [Fusobacterium
           nucleatum subsp. nucleatum ATCC 23726]
 gi|296154887|gb|EFG95669.1| DNA-directed RNA polymerase sigma subunit RpoD [Fusobacterium
           nucleatum subsp. nucleatum ATCC 23726]
          Length = 418

 Score =  248 bits (633), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 80/285 (28%), Positives = 144/285 (50%), Gaps = 13/285 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           N+      +  +  Y+ EI ++P+L  +EE   AK+  E GD  A+ +L+ S+LRLVV I
Sbjct: 137 NLGNSAKVDEPIKMYLREIGQVPLLTHEEEIDYAKKAYE-GDEEASKKLIESNLRLVVSI 195

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  +   GL + +++ EGNIGLM+AV+KF+  +G++ +TY+ WWI+ A+   I      +
Sbjct: 196 AKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTI 255

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I        +   + ++K   +       K      +A++L +   ++ ++        
Sbjct: 256 RIPVH-----MIETINKIKKESRIYLQETGKDASPEILAERLGMEVDKIKAIQEMNQEPI 310

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   + S  +  S+  D++    D +     E   R   R  L   +  L+PRE ++  
Sbjct: 311 SLETPVGS--EEDSELGDFV---EDQKTTSPYEATNRAILREELDAVLKTLSPREEKVLR 365

Query: 245 ARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R   ++  P TLE +   F V+RER+RQIE +A +K++   +K+
Sbjct: 366 YRYGLDDSSPKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRKK 410


>gi|268590799|ref|ZP_06125020.1| alternative sigma factor RpoH [Providencia rettgeri DSM 1131]
 gi|291313578|gb|EFE54031.1| alternative sigma factor RpoH [Providencia rettgeri DSM 1131]
          Length = 292

 Score =  248 bits (633), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 103/292 (35%), Positives = 168/292 (57%), Gaps = 10/292 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M +   S+ +  +  +  Y+      PML  +EE  LA+R   HGDL AA +L+ SHLR 
Sbjct: 1   MTKDMQSLALVPQGSIEAYVRAANSYPMLTAEEEKELAERLHYHGDLDAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VIHVARSYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT +Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+
Sbjct: 121 WRIVKVATTKSQRKLFFNLRKNKKRLGWFNQ-----DEVDMVAQELGVSTKDVREMESRM 175

Query: 181 AGD---ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLN 236
           A       ++   +SSD          + D        IE +  ++   + L  ++  L+
Sbjct: 176 AAQDMAFDMSDDDDSSDFGGPVAPVLYLQDKASDFAGSIEDDNWESHATDRLADALDSLD 235

Query: 237 PRERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R + I  AR L ++   TL+ L+ ++ VS ERVRQ+E  A KK++ ++++ 
Sbjct: 236 ERSQDIIRARWLDDDNKTTLQELADKYGVSAERVRQLEKNAMKKLRLAMEED 287


>gi|260554461|ref|ZP_05826682.1| alternative sigma factor RpoH [Acinetobacter baumannii ATCC 19606]
 gi|260411003|gb|EEX04300.1| alternative sigma factor RpoH [Acinetobacter baumannii ATCC 19606]
          Length = 288

 Score =  248 bits (633), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 110/283 (38%), Positives = 168/283 (59%), Gaps = 8/283 (2%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +S+   G + L  YI  + +IP+L  ++E  LA+RY    DL AA  LV SHLR VV IA
Sbjct: 11  LSLSAPG-VNLGAYISTVNQIPILTAEQEKELAERYYYDQDLDAAKMLVMSHLRFVVHIA 69

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGLP  +++ EGN+GLM+AVK+FDP  G RL ++++ WIKA + EY++R+W +VK
Sbjct: 70  RSYAGYGLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVK 129

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDE 184
           I TT  Q++LFFNLR LK   + +T      E+  +IA  LNV+  +V+ M  RL A D 
Sbjct: 130 IATTKAQRKLFFNLRSLKKSSKKLT-----LEEAQSIANDLNVTPEQVMEMEGRLTAYDA 184

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR-NMLTRSMSVLNPRERRIF 243
           +  A  +  D          + D+      L+E E+ + +  + L  +M+ L+ R R I 
Sbjct: 185 AFEAQGDDDDDTPHTAPVLYLEDNRYDPARLVENEDWEEQSTSALHDAMNQLDDRSRNIL 244

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           + R L ++  TL  L++E+ VS ER+RQ+E  A +K++ ++  
Sbjct: 245 QRRWLDDDKSTLHELAAEYNVSAERIRQLEKNAMEKIKVAMSA 287


>gi|256027745|ref|ZP_05441579.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. D11]
 gi|260494274|ref|ZP_05814405.1| RNA polymerase sigma factor RpoS [Fusobacterium sp. 3_1_33]
 gi|289765702|ref|ZP_06525080.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. D11]
 gi|260198420|gb|EEW95936.1| RNA polymerase sigma factor RpoS [Fusobacterium sp. 3_1_33]
 gi|289717257|gb|EFD81269.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. D11]
          Length = 416

 Score =  248 bits (633), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 81/285 (28%), Positives = 143/285 (50%), Gaps = 13/285 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           N+      +  +  Y+ EI ++P+L   EE   AKR  E GD  A+ +L+ S+LRLVV I
Sbjct: 135 NLGNSAKVDEPIKMYLREIGQVPLLTHDEEIEYAKRAYE-GDEEASKKLIESNLRLVVSI 193

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  +   GL + +++ EGNIGLM+AV+KF+  +G++ +TY+ WWI+ A+   I      +
Sbjct: 194 AKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTI 253

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I        +   + ++K   +       K      +A++L +   ++ ++        
Sbjct: 254 RIPVH-----MIETINKIKKESRIYLQETGKDASPEILAERLGMEVDKIKAIQEMNQEPI 308

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   + S  +  S+  D++    D +     E   R   R  L   +  L+PRE ++  
Sbjct: 309 SLETPVGS--EEDSELGDFV---EDQKTTSPYEATNRAILREELDAVLKTLSPREEKVLR 363

Query: 245 ARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R   ++  P TLE +   F V+RER+RQIE +A +K++   +K+
Sbjct: 364 YRYGLDDSSPKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRKK 408


>gi|166710450|ref|ZP_02241657.1| RNA polymerase factor sigma-32 [Xanthomonas oryzae pv. oryzicola
           BLS256]
          Length = 282

 Score =  248 bits (633), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 118/282 (41%), Positives = 168/282 (59%), Gaps = 8/282 (2%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
             N   I +    L  YI  + +IP+L   EE  LA+R+R+  DL AA  LV SHLR VV
Sbjct: 1   MANNLPIPSALGSLDAYIGAVHQIPVLSVDEEQNLARRFRDELDLDAARELVHSHLRFVV 60

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A GY GYGLP+ +++ EGNIGLM+AVK+FDP+ G RL ++++ WI+A M E+IL++W 
Sbjct: 61  HVARGYNGYGLPLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAVHWIRAEMHEFILKNWR 120

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L  +        +V A+AK LNVSE EV+ M  RL+G
Sbjct: 121 IVKVATTKAQRKLFFNLRKSKTRLGWLN-----ASEVTAVAKDLNVSEREVMEMESRLSG 175

Query: 183 -DESLNA-LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            D   +A      D        +LV + +   Q     +   N   +L   M+ L+ R R
Sbjct: 176 RDIGFDASSDEDDDHGPPSPVSYLVANEEDPSQAYERHDSEDNHLQLLREGMAGLDTRSR 235

Query: 241 RIFEARRLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            I + R L  ++ VTL+ L+ E+ VS ER+RQIEA A KK++
Sbjct: 236 DIVKRRWLDSDSKVTLQELADEYGVSAERIRQIEANALKKMK 277


>gi|72161271|ref|YP_288928.1| sigma-70 factor [Thermobifida fusca YX]
 gi|71915003|gb|AAZ54905.1| sigma-70 factor [Thermobifida fusca YX]
          Length = 388

 Score =  248 bits (633), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 80/307 (26%), Positives = 145/307 (47%), Gaps = 45/307 (14%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKR-----YREHGDLSAA-------------------- 50
           +  Y+ EI ++P+L  +EE  LAK      Y E    +A                     
Sbjct: 87  VHAYLREIGRVPLLTAEEEVELAKAIEIGLYAEQKLRAARTGPVPAQYSPEWFEDLNELV 146

Query: 51  -------HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
                   RL+ S+LRLVV +A  Y G GL + +++ EGN+GL++AV+KFD  RG++ +T
Sbjct: 147 REGKLAKRRLIESNLRLVVSVAKRYLGRGLALLDLIQEGNLGLIRAVEKFDYTRGYKFST 206

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI+ A+   I      +++     +      + RL    + +     +   +  ++
Sbjct: 207 YATWWIRQAITRAIADQARTIRVPVHMVES-----INRLARTRRRLHQELGREPTLHELS 261

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           ++LNV    V+ ++       SL+  I   D   S + D++    D      +E      
Sbjct: 262 RELNVDHDRVVEIHRVSQEPISLHTPIGEED---SAFGDFI---EDTDAVPPVEAAAFVM 315

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            ++ L + +  L+ RE+R+   R   E+  P TLE +  +F V+RER+RQIE++   K++
Sbjct: 316 LQDQLAQVLGGLSEREQRVITLRFGLEDGKPHTLEEVGRKFGVTRERIRQIESKTLAKLR 375

Query: 282 ESIQKQV 288
           +  + ++
Sbjct: 376 QPSRARI 382


>gi|325122820|gb|ADY82343.1| RNA polymerase factor sigma-32 [Acinetobacter calcoaceticus PHEA-2]
          Length = 276

 Score =  248 bits (633), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 108/275 (39%), Positives = 163/275 (59%), Gaps = 7/275 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + L  YI  + +IP+L  ++E  LA+RY    DL AA  LV SHLR VV IA  Y GYGL
Sbjct: 6   VNLGAYISTVNQIPILTAEQEKELAERYYYDQDLDAAKMLVMSHLRFVVHIARSYAGYGL 65

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P  +++ EGN+GLM+AVK+FDP  G RL ++++ WIKA + EY++R+W +VKI TT  Q+
Sbjct: 66  PQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVKIATTKAQR 125

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINS 192
           +LFFNLR LK   + +T      E+  +IA  LNV+  +V+ M  RL A D +  A  + 
Sbjct: 126 KLFFNLRSLKKSSKKLT-----LEEAQSIANDLNVTPEQVLEMEGRLTAYDAAFEAQGDD 180

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR-NMLTRSMSVLNPRERRIFEARRLQEN 251
            D          + D+      L+E E+ + +  + L  +M  L+ R R I + R L ++
Sbjct: 181 DDDTPHTAPALYLEDNRYDPARLVENEDWEEQSTSALHDAMDQLDDRSRNILQRRWLDDD 240

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             TL  L++E+ VS ER+RQ+E  A +K++ ++  
Sbjct: 241 KSTLHELAAEYNVSAERIRQLEKNAMEKIKTAMSA 275


>gi|226952985|ref|ZP_03823449.1| sigma H (sigma 32) factor of RNA polymerase [Acinetobacter sp. ATCC
           27244]
 gi|294650567|ref|ZP_06727924.1| RNA polymerase factor sigma-32 [Acinetobacter haemolyticus ATCC
           19194]
 gi|226836306|gb|EEH68689.1| sigma H (sigma 32) factor of RNA polymerase [Acinetobacter sp. ATCC
           27244]
 gi|292823564|gb|EFF82410.1| RNA polymerase factor sigma-32 [Acinetobacter haemolyticus ATCC
           19194]
          Length = 289

 Score =  248 bits (633), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 111/283 (39%), Positives = 165/283 (58%), Gaps = 8/283 (2%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +S+   G + L  YI  + +IP+L  ++E  LA+RY    DL AA  LV SHLR VV IA
Sbjct: 12  LSLSAPG-VNLGAYISTVNQIPILTAEQEKELAERYYYDQDLDAAKLLVMSHLRFVVHIA 70

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGLP  +++ EGN+GLM+AVK+FDP  G RL ++++ WIKA + EY++R+W +VK
Sbjct: 71  RSYAGYGLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVK 130

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDE 184
           I TT  Q++LFFNLR LK      +   L  E+  AIA  LNV+  +V+ M  RL A D 
Sbjct: 131 IATTKAQRKLFFNLRSLKK-----SSKRLTLEEAQAIANDLNVTAEQVLEMEGRLTAYDA 185

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLNPRERRIF 243
           +  A  +  D          + D+      L E+E+ +      L ++M  L+ R R I 
Sbjct: 186 AFEAQGDDDDDTPHTAPALYLEDNRYDPARLAEEEDYEAQSTAALHQAMDQLDDRSRNIL 245

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           + R L ++  TL  L++E+ VS ER+RQ+E  A +K++ ++  
Sbjct: 246 QRRWLDDDKSTLHELAAEYNVSAERIRQLEKNAMEKIKTAMSA 288


>gi|3219170|dbj|BAA28785.1| sigma-32 homolog [Hydrogenophilus thermoluteolus]
          Length = 309

 Score =  248 bits (633), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 113/274 (41%), Positives = 167/274 (60%), Gaps = 8/274 (2%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           RYI  + + P+L + EE+ LA+R+ E  DL AA +LV ++LR VV IA  Y GYGLP ++
Sbjct: 39  RYIQAVNRFPVLSEAEEHELARRFHETNDLDAARKLVLANLRYVVMIARQYFGYGLPEAD 98

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGN+GL++AV++FDP +G R  T++ +WIKA + +YILR+W LVKI TT  QK+LFF
Sbjct: 99  LIQEGNVGLLKAVRRFDPYKGVRFITFAAYWIKAEIHDYILRNWRLVKIATTKAQKKLFF 158

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALINSSDKN 196
           NLR+L      +    L   +  AIA+ L V   EV  M+ R A GD +L A I+S ++ 
Sbjct: 159 NLRKL------LGSEPLTRAKADAIAETLAVKPEEVAEMHARFAGGDVALEAPIDSDEEA 212

Query: 197 SSQWQDWLVYDHDGQE-QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
             +     + D  G   + + E E  +     L ++++ L+ R R I   R L E P TL
Sbjct: 213 DWRAPLAYLPDPSGTPEEAVAEAEAERLSHEGLQQALTQLDERSRAIVTRRWLTEKPATL 272

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
             L++E+ +S ERVRQIEA A KK++  +  Q +
Sbjct: 273 HELAAEYGISAERVRQIEAAALKKLRVWLSPQAD 306


>gi|73540031|ref|YP_294551.1| RNA polymerase factor sigma-32 [Ralstonia eutropha JMP134]
 gi|72117444|gb|AAZ59707.1| Sigma-70 region 2 [Ralstonia eutropha JMP134]
          Length = 309

 Score =  248 bits (633), Expect = 9e-64,   Method: Composition-based stats.
 Identities = 117/279 (41%), Positives = 169/279 (60%), Gaps = 12/279 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             L  YI  + +IPML  +EE  LA+  RE   + AA +LV SHLRLVV IA  Y GYGL
Sbjct: 35  GNLESYIQAVHRIPMLTAEEEQRLARELREDDSVDAARQLVMSHLRLVVSIARQYLGYGL 94

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P ++++ EGNIGLM+AVK+FDP +G RL +Y+M WIKA + EY+L++W +VK+ TT  Q+
Sbjct: 95  PHADLIQEGNIGLMKAVKRFDPNQGVRLVSYAMHWIKAEIHEYVLKNWRMVKVATTKAQR 154

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINS 192
           +LFFNLR  K        +   PEQ+ A+A+ LNV   EV+ M  R+  GD +L   ++ 
Sbjct: 155 KLFFNLRSHKQ-----GSHTFTPEQIEAVARDLNVKPEEVMEMETRMSGGDLALEGQVDD 209

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---- 248
            ++  +    +L  +H+   +VL  K + + +   L  +++ L+ R RRI EAR L    
Sbjct: 210 GEEEFA-PIAYLADNHNEPTRVLEAKRQDRMQVEGLEEALARLDERSRRIIEARWLNVED 268

Query: 249 -QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                 TL  L+ EF VS ER+RQIE  A KK++ ++Q 
Sbjct: 269 DGSGGATLHELADEFGVSAERIRQIEVAAMKKMKGALQA 307


>gi|330831381|ref|YP_004394333.1| RNA polymerase sigma factor [Aeromonas veronii B565]
 gi|328806517|gb|AEB51716.1| RNA polymerase sigma factor [Aeromonas veronii B565]
          Length = 284

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 109/286 (38%), Positives = 169/286 (59%), Gaps = 9/286 (3%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           ++ M++I  G   L  YI  +  IP+L  +EE  LA+R ++ GDL AA +LV SHLR VV
Sbjct: 6   QRTMALIPQG--SLEGYIQAVNSIPVLSAEEERELAERLQQDGDLEAARQLVMSHLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y GYGLP +++V EGNIGLM+AVK+FDP  G RL ++++ WIKA + EY+LR+W 
Sbjct: 64  HVAKSYAGYGLPQADLVQEGNIGLMKAVKRFDPTVGVRLVSFAVHWIKAEIHEYVLRNWR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L  +       E+V A+A  L VS ++V  M  R+A 
Sbjct: 124 MVKVATTKAQRKLFFNLRKSKKRLGWLNH-----EEVQAVAADLGVSAADVTEMEARMAN 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPRERR 241
            +    L+   ++         + D        IE +   +     L+ +++ L+ R + 
Sbjct: 179 YDQAFDLVGDDEEEGGFAPVHYLEDKSSDLAATIENDNWDDHATRRLSSALATLDERSQH 238

Query: 242 IFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           I  AR L ++   TL+ L+  + VS ERVRQ+E  A KK++++++ 
Sbjct: 239 IIRARWLDDDSKTTLQELADTYGVSAERVRQLEKNALKKLKDAMEA 284


>gi|294790965|ref|ZP_06756123.1| RNA polymerase sigma (70) factor RpoD [Scardovia inopinata F0304]
 gi|294458862|gb|EFG27215.1| RNA polymerase sigma (70) factor RpoD [Scardovia inopinata F0304]
          Length = 588

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 68/304 (22%), Positives = 139/304 (45%), Gaps = 40/304 (13%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR----------------------------YREHG 45
             +  Y+ +I ++ +L  Q+E  L++R                            +  + 
Sbjct: 286 DPVKDYLKQIGRVNLLNAQQEVDLSERIEAGLYAQHLLDTTDPDKLSFQRKRELKWAAND 345

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
              A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+
Sbjct: 346 GKKAKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYA 405

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
            WWI+ A+   +      +++     +  +   L R++  +         P+    +A++
Sbjct: 406 TWWIRQAITRAMADQARTIRVPVHMVE--VINKLSRVQRQMLQDLGREPTPD---ELARE 460

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           L++   +V  +        SL+  +   +   S++ D +    D       E       +
Sbjct: 461 LDMPVEKVQEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDTDAIAPSEAVAFSLLQ 515

Query: 226 NMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
              T+ +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++   K++  
Sbjct: 516 EQFTQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGHVYGVTRERIRQIESKTMSKLRHP 575

Query: 284 IQKQ 287
            + Q
Sbjct: 576 SRSQ 579


>gi|229491308|ref|ZP_04385134.1| RNA polymerase sigma factor RpoD [Rhodococcus erythropolis SK121]
 gi|229321847|gb|EEN87642.1| RNA polymerase sigma factor RpoD [Rhodococcus erythropolis SK121]
          Length = 430

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 79/319 (24%), Positives = 149/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------------- 41
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR                     
Sbjct: 117 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYAVQIMQDLADKGEKL 175

Query: 42  --REHGDLS--------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
              +  D+S        A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 176 PAAQRRDMSWICRDGNRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 235

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 236 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 293

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 294 REPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 345

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 346 AVVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 405

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 406 RQIESKTMSKLRHPSRSQV 424


>gi|315226631|ref|ZP_07868419.1| DNA-directed RNA polymerase sigma subunit RpoD [Parascardovia
           denticolens DSM 10105]
 gi|315120763|gb|EFT83895.1| DNA-directed RNA polymerase sigma subunit RpoD [Parascardovia
           denticolens DSM 10105]
          Length = 690

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 67/306 (21%), Positives = 138/306 (45%), Gaps = 40/306 (13%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKR----------------------------YRE 43
               +  Y+ +I ++ +L  Q+E  L++R                            +  
Sbjct: 386 TSDPVKDYLKQIGRVNLLNAQQEVDLSERIEAGLYAQHLLDTTPADQMTFQRKRELKWAA 445

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           +    A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +T
Sbjct: 446 NDGRKAKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFST 505

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI+ A+   +      +++     +  +   L R++  +         P+    +A
Sbjct: 506 YATWWIRQAITRAMADQARTIRVPVHMVE--VINKLSRVQRQMLQDLGREPTPD---ELA 560

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           ++L++   +V  +        SL+  +   +   S++ D +    D       E      
Sbjct: 561 RELDMPVEKVQEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDTDAIAPSEAVAFSL 615

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +    + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++   K++
Sbjct: 616 LQEQFKQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGHVYGVTRERIRQIESKTMSKLR 675

Query: 282 ESIQKQ 287
              + Q
Sbjct: 676 HPSRSQ 681


>gi|297539272|ref|YP_003675041.1| RNA polymerase sigma-32 subunit RpoH [Methylotenera sp. 301]
 gi|297258619|gb|ADI30464.1| RNA polymerase, sigma 32 subunit, RpoH [Methylotenera sp. 301]
          Length = 285

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 125/286 (43%), Positives = 171/286 (59%), Gaps = 7/286 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+      ++     L  Y   I+  P+L  +EEY LA ++R   DL AA +L+ SHLRL
Sbjct: 1   MSNALTLPVLTASDSLEHYSRVIKAYPVLSAEEEYSLAVKFRADNDLEAARQLIVSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  IA GY GYGLP S+++ EGNIGLM+AVK+FDPERG RL +++M WIKA M EYI+R+
Sbjct: 61  VASIARGYNGYGLPQSDLIQEGNIGLMKAVKRFDPERGVRLVSFAMHWIKAEMHEYIVRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VKI TT  Q++LFFNLR +K  L     N+L+P +V  IAK+LNV   EV+ M  RL
Sbjct: 121 WRMVKIATTKAQRKLFFNLRSMKTGL-----NSLQPAEVAHIAKELNVKPEEVLEMEARL 175

Query: 181 AGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            G E SL A I+           +L  +     + L  K+        L  ++  L+ R 
Sbjct: 176 NGHEISLEANIDDDSDEQYSPIAYLPDEGLEPLEALESKQIEIAETTGLANALQNLDDRS 235

Query: 240 RRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           RR+ EAR LQ+    TL  L+ EF VS ER+RQIE +A +K++  +
Sbjct: 236 RRVVEARWLQDQGGKTLHELADEFGVSAERIRQIEQKAMQKMKSLM 281


>gi|1143832|gb|AAA84899.1| RNA polymerase sigma C subunit [Stigmatella aurantiaca DW4/3-1]
          Length = 293

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 118/280 (42%), Positives = 174/280 (62%), Gaps = 4/280 (1%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M   +     LS Y+ EI + P+L +QEE  LA+ +R+ GDL A HRLVTS+LR VVK+A
Sbjct: 1   MQASLTSTDSLSTYLSEINQYPLLTQQEEQALARSFRQ-GDLQAGHRLVTSNLRFVVKVA 59

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             YR YGL +S+++ E NIGLM+AV+KFDP++G RL +Y++WWI A +Q Y+L++WSLVK
Sbjct: 60  YEYRSYGLRMSDLIQEANIGLMKAVQKFDPDKGIRLISYAVWWILAYIQGYVLKNWSLVK 119

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DE 184
           +GTT  Q+RLFF L R +  L+   + +        IA+KLNV  SEV  M  R+ G D 
Sbjct: 120 LGTTQAQRRLFFALARTRRELEKQGNTDGNIVNAEEIARKLNVKASEVREMEQRMGGRDL 179

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL+A +   +   +   D++  D   Q   + +++E    R  + +++  L+PRER I E
Sbjct: 180 SLDAPM--GEDGDATHMDFVASDSVSQADEVADRQEADLARTRIQQALQRLDPRERFIIE 237

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            R + ++ +TL  L   F  SRER RQ+E RA  K++  +
Sbjct: 238 KRVMSDSEMTLSELGEHFGFSRERARQLEIRAKDKLKAEL 277


>gi|332875153|ref|ZP_08442986.1| alternative sigma factor RpoH [Acinetobacter baumannii 6014059]
 gi|332736597|gb|EGJ67591.1| alternative sigma factor RpoH [Acinetobacter baumannii 6014059]
          Length = 280

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 110/283 (38%), Positives = 168/283 (59%), Gaps = 8/283 (2%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +S+   G + L  YI  + +IP+L  ++E  LA+RY    DL AA  LV SHLR VV IA
Sbjct: 3   LSLSAPG-VNLGAYISTVNQIPILTAEQEKELAERYYYDQDLDAAKMLVMSHLRFVVHIA 61

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGLP  +++ EGN+GLM+AVK+FDP  G RL ++++ WIKA + EY++R+W +VK
Sbjct: 62  RSYAGYGLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVK 121

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDE 184
           I TT  Q++LFFNLR LK   + +T      E+  +IA  LNV+  +V+ M  RL A D 
Sbjct: 122 IATTKAQRKLFFNLRSLKKSSKKLT-----LEEAQSIANDLNVTPEQVLEMEGRLTAYDA 176

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR-NMLTRSMSVLNPRERRIF 243
           +  A  +  D          + D+      L+E E+ + +  + L  +M+ L+ R R I 
Sbjct: 177 AFEAQGDDDDDTPHTAPVLYLEDNRYDPARLVENEDWEEQSTSALHDAMNQLDDRSRNIL 236

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           + R L ++  TL  L++E+ VS ER+RQ+E  A +K++ ++  
Sbjct: 237 QRRWLDDDKSTLHELAAEYNVSAERIRQLEKNAMEKIKVAMSA 279


>gi|183598031|ref|ZP_02959524.1| hypothetical protein PROSTU_01387 [Providencia stuartii ATCC 25827]
 gi|188022810|gb|EDU60850.1| hypothetical protein PROSTU_01387 [Providencia stuartii ATCC 25827]
          Length = 292

 Score =  248 bits (633), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 104/296 (35%), Positives = 166/296 (56%), Gaps = 10/296 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M +   S+ +  +  +  Y+      PML  +EE  LA+R   HGDL AA +L+ SHLR 
Sbjct: 1   MTKDMQSLALVPQGSIEAYMRAANAYPMLTAEEEKELAERLHYHGDLDAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VIHVARSYAGYGLPQADLIQEGNIGLMKAVRRFNPEIGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VKI TT +Q++LFFNLR+ K  L          ++V  +AK+L VS  +V  M  R+
Sbjct: 121 WRIVKIATTKSQRKLFFNLRKNKKRLGWFNQ-----DEVDMVAKELGVSTKDVREMESRM 175

Query: 181 AGDESLNALINSSD----KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
           A  +    + +  D            +L          + E     +  + L  ++  L+
Sbjct: 176 AAQDMAFDMSDDDDSGDLGQPIAPVLFLQDKSSDFAGSIEEDNWESHATDRLADALDSLD 235

Query: 237 PRERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
            R + I  AR L ++   TL+ L+ ++ VS ERVRQ+E  A KK++ ++++  E S
Sbjct: 236 ERSQDIIRARWLDDDNKTTLQELADKYGVSAERVRQLEKNAMKKLRAAMEEGEEES 291


>gi|197287411|ref|YP_002153283.1| RNA polymerase factor sigma-32 [Proteus mirabilis HI4320]
 gi|227358346|ref|ZP_03842687.1| RNA polymerase sigma-32 factor [Proteus mirabilis ATCC 29906]
 gi|194684898|emb|CAR47059.1| RNA polymerase sigma-32 factor [Proteus mirabilis HI4320]
 gi|227161682|gb|EEI46719.1| RNA polymerase sigma-32 factor [Proteus mirabilis ATCC 29906]
          Length = 284

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 110/288 (38%), Positives = 170/288 (59%), Gaps = 8/288 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  S+ +  +  +  YI      PML  +EE  LA+R    GDL AA  L+ SHLR 
Sbjct: 1   MTKEMQSLALVPQGSIEAYIRAANSYPMLTAEEEKELAERLHYEGDLEAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VIHVARSYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT +Q++LFFNLR+ K  L          ++V  +AK+L VSES+V  M  R+
Sbjct: 121 WRIVKVATTKSQRKLFFNLRKNKKRLGWFNQ-----DEVELVAKELGVSESDVREMESRM 175

Query: 181 -AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPR 238
            A D + +   + SD +        + D        IE++   N   + LT ++  L+ R
Sbjct: 176 SAQDMAFDMSADDSDDSHPVAPVLFLEDKSSDFADGIEEDNWDNHAADRLTLAIKTLDER 235

Query: 239 ERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            + I  AR L  +N  TL+ L+ ++ VS ERVRQ+E  A KK++ +I+
Sbjct: 236 SQDIIRARWLEDDNKSTLQELADKYGVSAERVRQLEKNAMKKLRLAIE 283


>gi|54025729|ref|YP_119971.1| RNA polymerase sigma factor [Nocardia farcinica IFM 10152]
 gi|54017237|dbj|BAD58607.1| putative principal sigma factor [Nocardia farcinica IFM 10152]
          Length = 454

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 79/319 (24%), Positives = 148/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------REHGDL- 47
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+  
Sbjct: 141 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYAAEKMREFAESGEKL 199

Query: 48  ----------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 200 PVAMRRDYNWIVRDGNRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 259

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 260 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 317

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 318 REPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 369

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 370 AVVAVDAVSFTLLQDQLQSVLETLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 429

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 430 RQIESKTMSKLRHPSRSQV 448


>gi|254382161|ref|ZP_04997522.1| sigma factor [Streptomyces sp. Mg1]
 gi|194341067|gb|EDX22033.1| sigma factor [Streptomyces sp. Mg1]
          Length = 416

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 75/303 (24%), Positives = 139/303 (45%), Gaps = 38/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYR----------EHGD----------------L 47
             +  Y+  I K+P+L  ++E  LAKR            E  D                 
Sbjct: 118 DPVKDYLKLIGKVPLLNAEQEVELAKRIEAGLFSEYKLEEEEDHKATFKRELEILVEDGR 177

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ W
Sbjct: 178 RAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNVGLIRAVEKFDYTKGFKFSTYATW 237

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   +      ++I     +  +   L R++  +         PE    + K+L+
Sbjct: 238 WIRQAITRAMADQSRTIRIPVHMVE--IINKLARVQRQMLQDLGREPTPE---ELGKELD 292

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++  +VI +        SL+  +   ++  S++ D +    D +  V  +       +  
Sbjct: 293 MTPEKVIEVQKYGREPISLHTPL--GEEGDSEFGDLI---EDSEAVVPADAVSFTFLQEQ 347

Query: 228 LTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L   +  L+ RE  +   R    +  P TL+ +   + V+RER+RQIE++   K++   +
Sbjct: 348 LQSILGTLSEREAGVVSMRYGLNDGQPKTLDEIGRVYGVTRERIRQIESKTMSKLRHPSR 407

Query: 286 KQV 288
            QV
Sbjct: 408 SQV 410


>gi|227488750|ref|ZP_03919066.1| RNA polymerase sigma factor A [Corynebacterium glucuronolyticum
           ATCC 51867]
 gi|227091172|gb|EEI26484.1| RNA polymerase sigma factor A [Corynebacterium glucuronolyticum
           ATCC 51867]
          Length = 599

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 77/324 (23%), Positives = 149/324 (45%), Gaps = 48/324 (14%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------------- 41
            RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR                     
Sbjct: 281 ARKDAELTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYATHLLNQFKDPEWLE 339

Query: 42  -------REHGD--------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
                   +  D          A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL
Sbjct: 340 SHEKPANSQKKDLRTVARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGL 399

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L
Sbjct: 400 IRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQREL 457

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    P     +AK+++++E +V+ +        SL+  I   D+  SQ  D++  
Sbjct: 458 LQDLGREPTP---QELAKEMDITEEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI-- 510

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEV 264
             D +  V ++       ++ L   +  L+ RE  + + R    +  P TL+ +   + V
Sbjct: 511 -EDSEAVVAVDAVSFTLLQDQLQDVLKTLSEREAGVVKLRFGLTDGMPRTLDEIGQVYGV 569

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           +RER+RQIE++   K++   + QV
Sbjct: 570 TRERIRQIESKTMSKLRHPSRSQV 593


>gi|257467207|ref|ZP_05631518.1| RNA polymerase sigma factor rpoD [Fusobacterium gonidiaformans ATCC
           25563]
 gi|315918337|ref|ZP_07914577.1| RNA polymerase sigma factor rpoD [Fusobacterium gonidiaformans ATCC
           25563]
 gi|313692212|gb|EFS29047.1| RNA polymerase sigma factor rpoD [Fusobacterium gonidiaformans ATCC
           25563]
          Length = 352

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 81/277 (29%), Positives = 142/277 (51%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI +IP+L  +EE  LAK+  E GD  A  RL+ ++LRLVV IA  +   G
Sbjct: 79  DEPIKMYLREIGQIPLLTHKEELELAKKALE-GDEFANKRLIEANLRLVVSIAKKHTNRG 137

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L + +++ EGNIGLM+AV+KF+  +G++ +TY+ WWI+ A+   I      ++I      
Sbjct: 138 LKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPVH--- 194

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
             +   + ++K   +       K      +A++L +   +V S+        SL   + S
Sbjct: 195 --MIETINKIKKEARIYLQETGKDATPEILAERLGMEVEKVKSIQEMNQDPISLETPVGS 252

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN- 251
             +  S+  D++    D +     E   R   R  L   +  L+ RE ++   R   ++ 
Sbjct: 253 --EEDSELGDFV---EDQKMLTPYELTNRSLLREQLDSVLGSLSSREEKVLRYRYGLDDG 307

Query: 252 -PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            P TLE +   F+V+RER+RQIE +A +K++   +++
Sbjct: 308 SPKTLEEVGKIFKVTRERIRQIEVKALRKLRHPSRRK 344


>gi|152972335|ref|YP_001337481.1| RNA polymerase factor sigma-32 [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|206580698|ref|YP_002236168.1| alternative sigma factor RpoH [Klebsiella pneumoniae 342]
 gi|238896924|ref|YP_002921669.1| RNA polymerase factor sigma-32 [Klebsiella pneumoniae NTUH-K2044]
 gi|262040527|ref|ZP_06013768.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Klebsiella
           pneumoniae subsp. rhinoscleromatis ATCC 13884]
 gi|288933158|ref|YP_003437217.1| RNA polymerase, sigma 32 subunit, RpoH [Klebsiella variicola At-22]
 gi|290511960|ref|ZP_06551328.1| alternative sigma factor RpoH [Klebsiella sp. 1_1_55]
 gi|329999131|ref|ZP_08303332.1| alternative sigma factor RpoH [Klebsiella sp. MS 92-3]
 gi|150957184|gb|ABR79214.1| RNA polymerase sigma factor [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|206569756|gb|ACI11532.1| alternative sigma factor RpoH [Klebsiella pneumoniae 342]
 gi|238549251|dbj|BAH65602.1| RNA polymerase sigma factor [Klebsiella pneumoniae subsp.
           pneumoniae NTUH-K2044]
 gi|259042120|gb|EEW43150.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Klebsiella
           pneumoniae subsp. rhinoscleromatis ATCC 13884]
 gi|288887887|gb|ADC56205.1| RNA polymerase, sigma 32 subunit, RpoH [Klebsiella variicola At-22]
 gi|289775750|gb|EFD83750.1| alternative sigma factor RpoH [Klebsiella sp. 1_1_55]
 gi|328538425|gb|EGF64546.1| alternative sigma factor RpoH [Klebsiella sp. MS 92-3]
          Length = 284

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 107/289 (37%), Positives = 162/289 (56%), Gaps = 8/289 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +     L  YI      PML   EE  LA++    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLALAPVGNLESYIRAANTWPMLSADEERELAEKLHYQGDLEAAKKLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHIARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVEMVARELGVSSKDVREMESRM 175

Query: 181 -AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE-ERKNRRNMLTRSMSVLNPR 238
            A D + +   +    +        + D        IE +   +   N LT +M  L+ R
Sbjct: 176 AAQDMTFDMSSDDESDSQPMAPVLYLQDKTSNFADGIEDDNWEEQAANKLTDAMQGLDER 235

Query: 239 ERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + I  AR L E+   TL+ L+  + VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 SQDIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 284


>gi|300858628|ref|YP_003783611.1| RNA polymerase sigma factor A [Corynebacterium pseudotuberculosis
           FRC41]
 gi|300686082|gb|ADK29004.1| RNA polymerase sigma factor A [Corynebacterium pseudotuberculosis
           FRC41]
 gi|302206337|gb|ADL10679.1| RNA polymerase sigma factor rpoD (Sigma-A) [Corynebacterium
           pseudotuberculosis C231]
 gi|302330894|gb|ADL21088.1| RNA polymerase sigma factor rpoD (Sigma-A) [Corynebacterium
           pseudotuberculosis 1002]
 gi|308276579|gb|ADO26478.1| RNA polymerase sigma factor rpoD (Sigma-A) [Corynebacterium
           pseudotuberculosis I19]
          Length = 517

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 77/325 (23%), Positives = 150/325 (46%), Gaps = 49/325 (15%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR----------------EHG 45
            RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR                   +G
Sbjct: 198 ARKDAELTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYATYRMEQMEEAFNNG 256

Query: 46  DLS--------------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           D                      A + L+ ++LRLVV +A  Y G G+   +++ EGN+G
Sbjct: 257 DKEAKLTPAVKRDLRAIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLG 316

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  
Sbjct: 317 LIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRE 374

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           L         P     +AK+++++E +V+ +        SL+  I   D+  SQ  D++ 
Sbjct: 375 LLQDLGREPTP---QELAKEMDITEEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI- 428

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFE 263
              D +  + ++       ++ L   +  L+ RE  + + R    +  P TL+ +   + 
Sbjct: 429 --EDSEAVIAVDAVSFTLLQDQLQDVLHTLSEREAGVVKLRFGLTDGMPRTLDEIGQVYG 486

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           V+RER+RQIE++   K++   + QV
Sbjct: 487 VTRERIRQIESKTMSKLRHPSRSQV 511


>gi|269215371|ref|ZP_06159225.1| RNA polymerase sigma factor RpoD [Slackia exigua ATCC 700122]
 gi|269131227|gb|EEZ62301.1| RNA polymerase sigma factor RpoD [Slackia exigua ATCC 700122]
          Length = 383

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 84/312 (26%), Positives = 140/312 (44%), Gaps = 42/312 (13%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------------------------ 42
           S ++     +  Y+ EI K+P+L   EE  LA +                          
Sbjct: 73  SAVMLTGDPVRMYLKEIGKVPLLTAAEEIDLAMKIEAGVAATAELERAEDEGIELNRRDK 132

Query: 43  ------EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                 E   L A  +L+ ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  
Sbjct: 133 RRLTRVEAVGLDAKQQLIEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYT 192

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +GF+ +TY+ WWI+ A+   I      ++I     +      L R++  L    + +  P
Sbjct: 193 KGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE--TINKLVRIQRQLLQDLNRDPTP 250

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           E    I +K+ +S   V  +        SL   I   ++  SQ  D++  D      V  
Sbjct: 251 E---EIGEKMGLSAERVREIQKISQEPVSLETPI--GEEEDSQLGDFIEDDS---AVVPP 302

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEA 274
           +       +  L++ +  L  RER++   R   E+  P TLE +  EF V+RER+RQIE+
Sbjct: 303 DAASFSMLQEQLSKVLDGLAERERKVISLRFGLEDGHPHTLEEVGREFGVTRERIRQIES 362

Query: 275 RAFKKVQESIQK 286
           +   K++   + 
Sbjct: 363 KTLAKLRHPSRS 374


>gi|323699411|ref|ZP_08111323.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio sp.
           ND132]
 gi|323459343|gb|EGB15208.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio
           desulfuricans ND132]
          Length = 375

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 113/281 (40%), Positives = 171/281 (60%), Gaps = 8/281 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYG 72
             L  Y+ EI + PMLE +EEY LAKR +E  D  AA +LV+SHLRLVVKIAM + R + 
Sbjct: 93  DPLQLYLKEIARFPMLEPEEEYALAKRVQEDNDQDAAFKLVSSHLRLVVKIAMDFQRRWM 152

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
               +++ EGN+GL++AV KFDPE+G + + Y+ +WIKA + +YI+ +W +VKIGTT  Q
Sbjct: 153 QNGLDLIQEGNVGLLKAVTKFDPEKGIKFSYYAAFWIKAYILKYIMDNWRMVKIGTTQTQ 212

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALIN 191
           ++LF+NL + +  LQ +           A++++L VSE+E+  M+ RL+  D SLN  + 
Sbjct: 213 RKLFYNLNKERQRLQTL----GFDPSTEALSERLGVSEAEIDEMDQRLSKNDMSLNTPL- 267

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             D + +   D+L     G E+ +   +      N +    + LN +E  I + R L ++
Sbjct: 268 -GDDSDTTRMDFLPSLAPGVEESIANDQIVDLLLNNIREIRASLNDKEVAILDRRLLSDD 326

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
           PVTL  +  EF V+RERVRQIEAR   K++E +  +V+  S
Sbjct: 327 PVTLREIGEEFGVTRERVRQIEARLMAKIREHLTDKVKDFS 367


>gi|317506483|ref|ZP_07964284.1| RNA polymerase sigma factor RpoD [Segniliparus rugosus ATCC
           BAA-974]
 gi|316255244|gb|EFV14513.1| RNA polymerase sigma factor RpoD [Segniliparus rugosus ATCC
           BAA-974]
          Length = 452

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 78/319 (24%), Positives = 146/319 (45%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGDL- 47
            RKN  +  + +  +  Y+ +I K+ +L  ++E  LAKR               E GD  
Sbjct: 139 ARKNAELTASAD-SVRAYLKQIGKVALLNAEQEVELAKRIEAGLYAQERLRIATEEGDRL 197

Query: 48  ----------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 198 PTTSRRDMNWVVRDGNRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 257

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 258 KFDYSKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 315

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    + +++++   +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 316 REPTPE---ELGREMDIPPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 367

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 368 AVVAVDAVSFTLLQDQLQAVLETLSEREAGVVRMRFGLTDGQPRTLDEIGQVYGVTRERI 427

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 428 RQIESKTMSKLRHPSRSQV 446


>gi|319764144|ref|YP_004128081.1| RNA polymerase sigma factor rpoh [Alicycliphilus denitrificans BC]
 gi|330826499|ref|YP_004389802.1| RNA polymerase sigma-32 subunit RpoH [Alicycliphilus denitrificans
           K601]
 gi|317118705|gb|ADV01194.1| RNA polymerase sigma factor RpoH [Alicycliphilus denitrificans BC]
 gi|329311871|gb|AEB86286.1| RNA polymerase, sigma 32 subunit, RpoH [Alicycliphilus
           denitrificans K601]
          Length = 311

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 115/288 (39%), Positives = 173/288 (60%), Gaps = 12/288 (4%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +V     L  YI  + ++P+L  +EE   A+++++  DL AA RLV SHLRLVV I+  Y
Sbjct: 20  LVPPLGNLDAYISAVNRLPLLTLEEEQRYAQQFKKDNDLEAAGRLVLSHLRLVVSISRQY 79

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGLP  +++ EGN+GLM+AVK+FDP++G RL +Y+M WIKA + EYIL++W +VK+ T
Sbjct: 80  LGYGLPHGDLIQEGNVGLMKAVKRFDPDQGVRLVSYAMHWIKAEIHEYILKNWRMVKVAT 139

Query: 129 TANQKRLFFNLRRLKGHLQA------ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           T  Q++LFFNLR +K   +A           L   ++  +A++LNV   EVI M  RLAG
Sbjct: 140 TKAQRKLFFNLRSMKQGFKADAIDADTHRETLSDHEIDMVAEQLNVKREEVIEMETRLAG 199

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLNPRERR 241
            + L     S D   +      + D   +   +IE  +R     + +T +++ L+ R RR
Sbjct: 200 GDVLLDPAPSDDGEQAFGPIAYLADTAHEPTAMIESRQRDALATDGITSALASLDARSRR 259

Query: 242 IFEARRLQENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           I E R LQ N      +TL  L++E+ VS ER+RQIE  A KK+++++
Sbjct: 260 IVEQRWLQVNDDGSGGMTLHELAAEYGVSAERIRQIEVAAMKKMKKAL 307


>gi|221199969|ref|ZP_03573012.1| alternative sigma factor RpoH [Burkholderia multivorans CGD2M]
 gi|221206876|ref|ZP_03579888.1| alternative sigma factor RpoH [Burkholderia multivorans CGD2]
 gi|221173531|gb|EEE05966.1| alternative sigma factor RpoH [Burkholderia multivorans CGD2]
 gi|221180208|gb|EEE12612.1| alternative sigma factor RpoH [Burkholderia multivorans CGD2M]
          Length = 311

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 119/288 (41%), Positives = 174/288 (60%), Gaps = 12/288 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S++      +  YI  + +IP+L  +EE   A  YRE+ +L AA RLV SHLRLVV IA 
Sbjct: 30  SMLPGQLGNIDAYIQAVNRIPLLTAEEERQYATEYRENNNLEAARRLVLSHLRLVVSIAR 89

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y GYGLP  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W +VK+
Sbjct: 90  NYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKV 149

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDES 185
            TT  Q++LFFNLR  K  +QA+T     PE++  +A++LNV   EV  M  RL  GD +
Sbjct: 150 ATTKAQRKLFFNLRSHKKGMQAMT-----PEEIDGLAQELNVKREEVTEMETRLSGGDIA 204

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L   +   ++ S     +L   H+    VL  ++    + + + +++  L+ R RRI EA
Sbjct: 205 LEGQVEDGEE-SYAPIAYLADSHNEPTAVLAARQRDMLQTDGIAQALDALDARSRRIIEA 263

Query: 246 RRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           R L          TL +L++EF VS ER+RQIEA A KK++ ++ +  
Sbjct: 264 RWLHVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRTALAEYA 311


>gi|161523666|ref|YP_001578678.1| RNA polymerase factor sigma-32 [Burkholderia multivorans ATCC
           17616]
 gi|189351565|ref|YP_001947193.1| RNA polymerase factor sigma-32 [Burkholderia multivorans ATCC
           17616]
 gi|160341095|gb|ABX14181.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia multivorans
           ATCC 17616]
 gi|189335587|dbj|BAG44657.1| RNA polymerase sigma-32 factor [Burkholderia multivorans ATCC
           17616]
          Length = 311

 Score =  247 bits (632), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 118/288 (40%), Positives = 174/288 (60%), Gaps = 12/288 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S++      +  YI  + +IP+L  +EE   A  YRE+ +L AA RLV SHLRLVV IA 
Sbjct: 30  SMLPGQLGNIDAYIQAVNRIPLLTAEEERQYATEYRENNNLEAARRLVLSHLRLVVSIAR 89

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y GYGLP  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W +VK+
Sbjct: 90  NYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKV 149

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDES 185
            TT  Q++LFFNLR  K  +QA+T     PE++  +A++LNV   +V  M  RL  GD +
Sbjct: 150 ATTKAQRKLFFNLRSHKKGMQAMT-----PEEIDGLAQELNVKREDVTEMETRLSGGDIA 204

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L   +   ++ S     +L   H+    VL  ++    + + + +++  L+ R RRI EA
Sbjct: 205 LEGQVEDGEE-SYAPIAYLADSHNEPTAVLAARQRDMLQTDGIAQALDALDARSRRIIEA 263

Query: 246 RRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           R L          TL +L++EF VS ER+RQIEA A KK++ ++ +  
Sbjct: 264 RWLHVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRTALAEYA 311


>gi|23502620|ref|NP_698747.1| RNA polymerase factor sigma-32 [Brucella suis 1330]
 gi|161619688|ref|YP_001593575.1| RNA polymerase factor sigma-32 [Brucella canis ATCC 23365]
 gi|254703536|ref|ZP_05165364.1| RNA polymerase factor sigma-32 [Brucella suis bv. 3 str. 686]
 gi|260568841|ref|ZP_05839309.1| sigma-70 factor family protein [Brucella suis bv. 4 str. 40]
 gi|23348625|gb|AAN30662.1| RNA polymerase sigma-70 factor family protein [Brucella suis 1330]
 gi|161336499|gb|ABX62804.1| RNA polymerase sigma factor, sigma-70 family [Brucella canis ATCC
           23365]
 gi|260154225|gb|EEW89307.1| sigma-70 factor family protein [Brucella suis bv. 4 str. 40]
          Length = 311

 Score =  247 bits (631), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 119/293 (40%), Positives = 185/293 (63%), Gaps = 4/293 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  ++          +   I      P LE++EE  LA R++E  D  A HR+ ++H+RL
Sbjct: 19  MAVRSFPAAAASSQSM---IRSAMSAPYLEREEERALAIRWKETKDQDALHRITSAHMRL 75

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A  +R + LP+S+++ EG +GL++A  +FDP+R  R +TY+ WWI+A+MQ+YILR+
Sbjct: 76  VISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRDVRFSTYASWWIRASMQDYILRN 135

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WS+V+ GT++ QK LFFNLRRL+  L    DN  K E    I+ +L VS S+V  M+ RL
Sbjct: 136 WSIVRGGTSSAQKALFFNLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRL 195

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D SL+A +N  +  +S+  D+LV DH  Q+++     + + R   LTR++  LN RE
Sbjct: 196 SGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIAESSIDMERRNCWLTRALDTLNERE 255

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
             I   RRL ++ VTLE L  +  +S+ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 256 LHIIRERRLDDDGVTLEALGEKLGISKERVRQIESRAMEKLKIALLSQHELAA 308


>gi|300784507|ref|YP_003764798.1| RNA polymerase primary sigma factor [Amycolatopsis mediterranei
           U32]
 gi|299794021|gb|ADJ44396.1| RNA polymerase primary sigma factor [Amycolatopsis mediterranei
           U32]
          Length = 467

 Score =  247 bits (631), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 80/319 (25%), Positives = 148/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGD-- 46
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+  
Sbjct: 154 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYAAERVRTAEEEGEKL 212

Query: 47  ---------------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 213 VTQMRRDLKWIVRDGERAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 272

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 273 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 330

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK++++S  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 331 REPTPE---ELAKEMDISPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 382

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 383 AVVAVDAVSFTLLQDQLQSVLQTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 442

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 443 RQIESKTMSKLRHPSRSQV 461


>gi|115372678|ref|ZP_01459985.1| alternative sigma factor RpoH [Stigmatella aurantiaca DW4/3-1]
 gi|310823838|ref|YP_003956196.1| RNA polymerase sigma-c factor [Stigmatella aurantiaca DW4/3-1]
 gi|115370399|gb|EAU69327.1| alternative sigma factor RpoH [Stigmatella aurantiaca DW4/3-1]
 gi|309396910|gb|ADO74369.1| RNA polymerase sigma-C factor [Stigmatella aurantiaca DW4/3-1]
          Length = 293

 Score =  247 bits (631), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 118/280 (42%), Positives = 175/280 (62%), Gaps = 4/280 (1%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M   +     LS Y+ EI + P+L +QEE  LA+ +R+ GDL A HRLVTS+LR VVK+A
Sbjct: 1   MQASLTSTDSLSTYLSEINQYPLLTQQEEQALARSFRQ-GDLQAGHRLVTSNLRFVVKVA 59

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             YR YGL +S+++ E NIGLM+AV+KFDP++G RL +Y++WWI+A +Q Y+L++WSLVK
Sbjct: 60  YEYRSYGLRMSDLIQEANIGLMKAVQKFDPDKGIRLISYAVWWIRAYIQGYVLKNWSLVK 119

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DE 184
           +GTT  Q+RLFF L R +  L+   + +        IA+KLNV  SEV  M  R+ G D 
Sbjct: 120 LGTTQAQRRLFFALARTRRELEKQGNTDGNIVNAEEIARKLNVKASEVREMEQRMGGRDL 179

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL+A +   +   +   D++  D   Q   + +++E    R  + +++  L+PRER I E
Sbjct: 180 SLDAPM--GEDGDATHMDFVASDSVSQADEVADRQEADLARTRIQQALQRLDPRERFIIE 237

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            R + ++ +TL  L   F  SRER RQ+E RA  K++  +
Sbjct: 238 KRVMSDSEMTLSELGEHFGFSRERARQLEIRAKDKLKAEL 277


>gi|164688461|ref|ZP_02212489.1| hypothetical protein CLOBAR_02106 [Clostridium bartlettii DSM
           16795]
 gi|164602874|gb|EDQ96339.1| hypothetical protein CLOBAR_02106 [Clostridium bartlettii DSM
           16795]
          Length = 306

 Score =  247 bits (631), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 82/284 (28%), Positives = 136/284 (47%), Gaps = 13/284 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           N + +VN +  +  Y+ EI KIP+L +QEE  +AKR  E GD  A   LV S+LRLVV I
Sbjct: 23  NSNNLVNLDDSMKIYLKEIGKIPLLSRQEELDIAKRICE-GDEVAKKILVESNLRLVVSI 81

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y    + + +++ EG +GL++A +KFD  +GF+ +TY+ WWIK  +   I      +
Sbjct: 82  ARKYARKEMAMLDLIQEGTLGLIRAAEKFDYTKGFKFSTYATWWIKQGITRAIADQSRTI 141

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           ++     +K     +  +   L        KPE    IAK+++V   +V+ +       +
Sbjct: 142 RVPVHMVEK--INKVSTISSQLAKELGREPKPE---EIAKRMHVPVEKVVQVIRISQRPQ 196

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           S+ + I   D    +         D +     E   R   ++ +   +  L+ RE+ + +
Sbjct: 197 SIESTIGQEDDTELEQVIP-----DKEAHSPEEIVTRSLLKDQIEYVLDTLSEREKGVIK 251

Query: 245 ARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R         TLE +   F V+RER RQIE +A +K+    + 
Sbjct: 252 LRFGLGDGEKKTLEEVGRAFNVTRERARQIEKKALRKLAHPSRS 295


>gi|189024846|ref|YP_001935614.1| RNA polymerase factor sigma-32 [Brucella abortus S19]
 gi|189020418|gb|ACD73140.1| Sigma-70 factor family [Brucella abortus S19]
          Length = 306

 Score =  247 bits (631), Expect = 1e-63,   Method: Composition-based stats.
 Identities = 119/293 (40%), Positives = 185/293 (63%), Gaps = 4/293 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  ++          +   I      P LE++EE  LA R++E  D  A HR+ ++H+RL
Sbjct: 14  MAVRSFPAAAASSQSM---IRSAMSAPYLEREEERALAIRWKETKDQDALHRITSAHMRL 70

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A  +R + LP+S+++ EG +GL++A  +FDP+R  R +TY+ WWI+A+MQ+YILR+
Sbjct: 71  VISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRDVRFSTYASWWIRASMQDYILRN 130

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WS+V+ GT++ QK LFFNLRRL+  L    DN  K E    I+ +L VS S+V  M+ RL
Sbjct: 131 WSIVRGGTSSAQKALFFNLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRL 190

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D SL+A +N  +  +S+  D+LV DH  Q+++     + + R   LTR++  LN RE
Sbjct: 191 SGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTRALDTLNERE 250

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
             I   RRL ++ VTLE L  +  +S+ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 251 LHIIRERRLDDDGVTLEALGEKLGISKERVRQIESRAMEKLKIALLSQHELAA 303


>gi|299769389|ref|YP_003731415.1| RNA polymerase factor sigma-32 [Acinetobacter sp. DR1]
 gi|298699477|gb|ADI90042.1| RNA polymerase factor sigma-32 [Acinetobacter sp. DR1]
          Length = 288

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 110/283 (38%), Positives = 167/283 (59%), Gaps = 8/283 (2%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +S+   G + L  YI  + +IP+L  ++E  LA+RY    DL AA  LV SHLR VV IA
Sbjct: 11  LSLSAPG-VNLGAYISTVNQIPILTAEQEKELAERYYYDQDLDAAKMLVMSHLRFVVHIA 69

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGLP  +++ EGN+GLM+AVK+FDP  G RL ++++ WIKA + EY++R+W +VK
Sbjct: 70  RSYAGYGLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVK 129

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDE 184
           I TT  Q++LFFNLR LK   + +T      E+  +IA  LNV+  +V+ M  RL A D 
Sbjct: 130 IATTKAQRKLFFNLRSLKKSSKKLT-----LEEAQSIANDLNVTAEQVLEMEGRLTAYDA 184

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR-NMLTRSMSVLNPRERRIF 243
           +  A  +  D          + D+      L+E E+ + +  + L  +M  L+ R R I 
Sbjct: 185 AFEAQGDDDDDTPHTAPALYLEDNRYDPARLVENEDWEEQSTSALHDAMDQLDDRSRNIL 244

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           + R L ++  TL  L++E+ VS ER+RQ+E  A +K++ ++  
Sbjct: 245 QRRWLDDDKSTLHELAAEYNVSAERIRQLEKNAMEKIKIAMSA 287


>gi|188574757|ref|YP_001911686.1| RNA polymerase factor sigma-32 [Xanthomonas oryzae pv. oryzae
           PXO99A]
 gi|188519209|gb|ACD57154.1| alternative sigma factor RpoH [Xanthomonas oryzae pv. oryzae
           PXO99A]
          Length = 282

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 118/282 (41%), Positives = 169/282 (59%), Gaps = 8/282 (2%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
             N   I +    L  YI  + +IP+L   EE  LA+R+R+  DL AA  LV SHLR VV
Sbjct: 1   MANNLPIPSALGSLDAYIGAVHQIPVLSVDEEQNLARRFRDELDLDAARELVHSHLRFVV 60

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A GY GYGLP+ +++ EGNIGLM+AVK+FDP+ G RL ++++ WI+A M E+IL++W 
Sbjct: 61  HVARGYNGYGLPLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAVHWIRAEMHEFILKNWR 120

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L  +        +V A+AK LNVSE EV+ M  RL+G
Sbjct: 121 IVKVATTKAQRKLFFNLRKSKTRLGWLN-----ASEVTAVAKDLNVSEREVMEMESRLSG 175

Query: 183 -DESLNA-LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            D   +A      D        +LV + +   Q     +   N+  +L   M+ L+ R R
Sbjct: 176 RDIGFDASSDEDDDHGPPSPVSYLVANEEDPSQAYERHDSEDNQLQLLREGMAGLDTRSR 235

Query: 241 RIFEARRLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            I + R L  ++ VTL+ L+ E+ VS ER+RQIEA A KK++
Sbjct: 236 DIVKRRWLDSDSKVTLQELADEYGVSAERIRQIEANALKKMK 277


>gi|332524130|ref|ZP_08400360.1| RNA polymerase sigma-32 factor [Rubrivivax benzoatilyticus JA2]
 gi|332107469|gb|EGJ08693.1| RNA polymerase sigma-32 factor [Rubrivivax benzoatilyticus JA2]
          Length = 306

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 117/282 (41%), Positives = 174/282 (61%), Gaps = 11/282 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI  + ++PML  QEE  L KR REHGDL AA RLV SHLRLVV ++  Y GYGLP 
Sbjct: 23  LDAYITAVNRLPMLSAQEEVALGKRLREHGDLEAAGRLVLSHLRLVVSVSRQYLGYGLPH 82

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM+AVK+FDP++G RL +Y++ WIKA + EYIL++W +VK+ TT  Q++L
Sbjct: 83  GDLIQEGNVGLMKAVKRFDPDQGVRLVSYALHWIKAEIHEYILKNWRMVKVATTKAQRKL 142

Query: 136 FFNLRRLKGHLQ------AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
           FFNLR +K  L+       +  + L P +V  +A++LNV   EV+ M  RLAG +     
Sbjct: 143 FFNLRSMKQGLKGEAAEADLHRSTLTPAEVETVARELNVKPDEVVEMETRLAGGDVALEP 202

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
                + S     +L  +     ++L  +       + + +++SVL+ R RRI E R L+
Sbjct: 203 QTDDSEESFAPIAYLADEASEPTRLLEARRRDWLSGDGIAQALSVLDARSRRIVEERWLK 262

Query: 250 ENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            N      +TL  L++E+ VS ER+RQIE  A KK++++++ 
Sbjct: 263 VNDDSSGGMTLHELAAEYGVSAERIRQIEVAAMKKMRKALEA 304


>gi|239906748|ref|YP_002953489.1| RNA polymerase sigma factor [Desulfovibrio magneticus RS-1]
 gi|239796614|dbj|BAH75603.1| RNA polymerase sigma factor [Desulfovibrio magneticus RS-1]
          Length = 348

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 105/286 (36%), Positives = 179/286 (62%), Gaps = 6/286 (2%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
            ++    L  Y+ EI K PML+ +EE  LA+R R+  D  AA RL++SHLRLVVKIAM +
Sbjct: 61  SLSTRDPLQLYLREIGKFPMLKPEEEQELARRVRDANDQKAAFRLISSHLRLVVKIAMDF 120

Query: 69  RGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           +   +  + +++ EGN+GLM+AV KFDP++G + + Y+ +WIKA + +YI+ +W +VKIG
Sbjct: 121 QRRWMQNVLDLIQEGNVGLMRAVTKFDPDKGIKFSYYAAYWIKAYILKYIMDNWRMVKIG 180

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
           TT  Q++LF+NL + +  LQ++            +++ LNV+ES+++ M+ RL+G++ L+
Sbjct: 181 TTQAQRKLFYNLNKERQRLQSL----GFDPSAAQLSQALNVTESDIVEMDQRLSGND-LS 235

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             ++  D  +S   D+L     G E++L   E        +      LN +E  + + R 
Sbjct: 236 LDVSLGDDTTSTRLDFLPALTPGIEEILAGDEISHQLDKHIQSIRPKLNEKEIELLDNRI 295

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           L ++PVTL  + +++ ++RERVRQIE+R  +K+++ + K++E  SS
Sbjct: 296 LSDSPVTLREIGAKYGITRERVRQIESRLLEKLKDHLSKRIEDFSS 341


>gi|332763556|gb|EGJ93795.1| alternative sigma factor RpoH [Shigella flexneri 2930-71]
          Length = 280

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 107/284 (37%), Positives = 159/284 (55%), Gaps = 8/284 (2%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
            S+ +     L  YI      PML   EE  LA++   HGDL AA  L+ SHLR VV IA
Sbjct: 2   QSLALAPVGNLDSYIRAANAWPMLSADEERALAEKLHYHGDLEAAKTLILSHLRFVVHIA 61

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+W +VK
Sbjct: 62  RNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVK 121

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDE 184
           + TT  Q++LFFNLR+ K  L          ++V  +A++L V+  +V  M  R+ A D 
Sbjct: 122 VATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVEMVARELGVTSKDVREMESRMAAQDM 176

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE-ERKNRRNMLTRSMSVLNPRERRIF 243
           + +   +    +        + D        IE +   +   N LT +M  L+ R + I 
Sbjct: 177 TFDLSSDDDSDSQPMAPVLYLQDKSSNFADGIEDDNWEEQAANRLTDAMHGLDERSQDII 236

Query: 244 EARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            AR L E+   TL+ L+  + VS ERVRQ+E  A KK++ +I+ 
Sbjct: 237 RARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 280


>gi|190576084|ref|YP_001973929.1| RNA polymerase factor sigma-32 [Stenotrophomonas maltophilia K279a]
 gi|190014006|emb|CAQ47646.1| putative RNA polymerase sigma-32 factor [Stenotrophomonas
           maltophilia K279a]
          Length = 291

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 112/276 (40%), Positives = 169/276 (61%), Gaps = 8/276 (2%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           I +    L  YI  + +IP+L   +E  LA+R+R+  DL AA  LV SHLR VV +A GY
Sbjct: 16  IPSALGSLDAYIGAVHQIPVLSVDDEQDLARRFRDGNDLDAARELVHSHLRFVVHVARGY 75

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGL + +++ EGNIGLM+AVK+FDP+ G RL ++++ WI+A M E+IL++W +VK+ T
Sbjct: 76  NGYGLALGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAVHWIRAEMHEFILKNWRIVKVAT 135

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN 187
           T  Q++LFFNLR+ K  L       +   +V A+AK LNVSE EV+ M  RL+G D   +
Sbjct: 136 TKAQRKLFFNLRKSKTRLGW-----MNAAEVSAVAKDLNVSEREVMEMESRLSGRDIGFD 190

Query: 188 ALINSSDKN-SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           A  +  +++       +LV D +        ++   N+  +L   ++ L+ R R I   R
Sbjct: 191 APTDEDNEHAPPSPAAFLVADDEDPSMAYEREDSEDNQMQLLREGLAELDARSRDIIRRR 250

Query: 247 RLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L  ++ VTL+ L+ E+ VS ER+RQ+EA A KK++
Sbjct: 251 WLDADSKVTLQELADEYGVSAERIRQVEANALKKMK 286


>gi|269219424|ref|ZP_06163278.1| carbamoyl-phosphate synthase L chain, ATP-binding [Actinomyces sp.
           oral taxon 848 str. F0332]
 gi|269211120|gb|EEZ77460.1| carbamoyl-phosphate synthase L chain, ATP-binding [Actinomyces sp.
           oral taxon 848 str. F0332]
          Length = 592

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 74/306 (24%), Positives = 141/306 (46%), Gaps = 41/306 (13%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYR---------EHGDLS---------------- 48
             +  Y+ +I K+P+L  +EE  LA+R           E G L                 
Sbjct: 291 DPVKDYLKQIGKVPLLNAEEEVELARRIEAGLYAQHILESGSLDKAKDRMYMRELKLISR 350

Query: 49  ----AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
               A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY
Sbjct: 351 DGQQAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLVRAVEKFDFTKGFKFSTY 410

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + WWI+ A+   +      ++I     +      + +L    + +  +  +    + +AK
Sbjct: 411 ATWWIRQAITRAMADQARTIRIPVHMVEV-----INKLARVQRQMLQDLGREPTTIELAK 465

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L+++E +VI +        SL+  +   +   S++ D +    D +  V  +       
Sbjct: 466 ELDMTEEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVGFTLL 520

Query: 225 RNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +  L + +  L+ RE  +   R         TL+ +   + V+RER+RQIE++   K++ 
Sbjct: 521 QEQLRQVLDTLSEREAGVVAMRFGLTDGQTKTLDEIGKVYGVTRERIRQIESKTMSKLRH 580

Query: 283 SIQKQV 288
             + QV
Sbjct: 581 PSRSQV 586


>gi|254428104|ref|ZP_05041811.1| alternative sigma factor RpoH [Alcanivorax sp. DG881]
 gi|196194273|gb|EDX89232.1| alternative sigma factor RpoH [Alcanivorax sp. DG881]
          Length = 287

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 105/283 (37%), Positives = 165/283 (58%), Gaps = 8/283 (2%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           + +++ V G   L  Y+  +  +P+L  +EE  L +R     DL AA  LV SHLR V  
Sbjct: 9   QALTLAVPGND-LDAYMRAVNAVPVLSAEEEQRLGERLYYDQDLDAARSLVLSHLRFVAH 67

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y GYGLP+ ++V EGN+GLM+AVK+FDP +G RL ++++ WIKA + EY++++W +
Sbjct: 68  IARSYTGYGLPLGDLVQEGNVGLMKAVKRFDPTKGVRLVSFAVHWIKAEIHEYVIKNWRI 127

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG- 182
           VK+ TT  Q++LFFNLR  K  L  +T      E+   +A  L V+ ++V  M  RL   
Sbjct: 128 VKVATTKAQRKLFFNLRGQKKRLGRLT-----MEEAQRVADDLGVTATQVKEMEGRLGAY 182

Query: 183 DESLNALINSSDKNS-SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           D S +   N  D ++      +L  D+     +L E+++++     L+ ++  L+ R R 
Sbjct: 183 DASFDGPTNDDDDSTVVSPAAYLHSDNSDPADLLAEQDKQQRESRQLSSALMALDERSRD 242

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           I E R L +   TL+ L+ E+ VS ER+RQ+E  A KK++ +I
Sbjct: 243 ILERRWLADQKSTLQELADEYGVSAERIRQLENNAIKKLRNAI 285


>gi|110835430|ref|YP_694289.1| RNA polymerase sigma-32 factor [Alcanivorax borkumensis SK2]
 gi|110648541|emb|CAL18017.1| RNA polymerase sigma-32 factor [Alcanivorax borkumensis SK2]
          Length = 289

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 105/283 (37%), Positives = 165/283 (58%), Gaps = 8/283 (2%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           + +++ V G   L  Y+  +  +P+L  +EE  L +R     DL AA  LV SHLR V  
Sbjct: 11  QALTLAVPGHD-LDAYMRAVNAVPVLSAEEEQRLGERLYYDQDLDAARSLVLSHLRFVAH 69

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y GYGLP+ ++V EGN+GLM+AVK+FDP +G RL ++++ WIKA + EY++++W +
Sbjct: 70  IARSYTGYGLPLGDLVQEGNVGLMKAVKRFDPTKGVRLVSFAVHWIKAEIHEYVIKNWRI 129

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG- 182
           VK+ TT  Q++LFFNLR  K  L  +T      E+   +A  L V+ ++V  M  RL   
Sbjct: 130 VKVATTKAQRKLFFNLRGQKKRLGRLT-----LEEAQRVADDLGVTAAQVKEMEGRLGAY 184

Query: 183 DESLNALINSSDKNS-SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           D S +   N  D ++      +L  D+     +L E+++++     L+ ++  L+ R R 
Sbjct: 185 DASFDGPTNDDDDSTVVSPAAYLHSDNSDPADLLAEQDQQQRESRQLSSALMALDERSRD 244

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           I E R L +   TL+ L+ E+ VS ER+RQ+E  A KK++ +I
Sbjct: 245 ILERRWLADQKSTLQELADEYSVSAERIRQLENNAIKKLRNAI 287


>gi|325913818|ref|ZP_08176177.1| RNA polymerase, sigma 32 subunit, RpoH [Xanthomonas vesicatoria
           ATCC 35937]
 gi|325539893|gb|EGD11530.1| RNA polymerase, sigma 32 subunit, RpoH [Xanthomonas vesicatoria
           ATCC 35937]
          Length = 291

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 119/276 (43%), Positives = 168/276 (60%), Gaps = 8/276 (2%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           I +    L  YI  + +IP+L   EE  LA+R+R+  DL AA  LV SHLR VV +A GY
Sbjct: 16  IPSALGSLDAYIGAVHQIPVLSVDEEQNLARRFRDELDLDAARELVHSHLRFVVHVARGY 75

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGLP+ +++ EGNIGLM+AVK+FDPE G RL ++++ WI+A M E+IL++W +VK+ T
Sbjct: 76  NGYGLPLGDLIQEGNIGLMKAVKRFDPEMGVRLVSFAVHWIRAEMHEFILKNWRIVKVAT 135

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN 187
           T  Q++LFFNLR+ K  L  +        +V A+AK LNVSE EV+ M  RL+G D   +
Sbjct: 136 TKAQRKLFFNLRKSKTRLGWLN-----ASEVTAVAKDLNVSEREVMEMESRLSGRDIGFD 190

Query: 188 A-LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           A      D        +LV + +   Q     +   N+  +L   M+ L+ R R I + R
Sbjct: 191 ASSDEDDDHGPPSPVSYLVANEEDPSQAYERHDSEDNQLQLLREGMAGLDTRSRDIVKRR 250

Query: 247 RLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L  E+ VTL+ L+ E+ VS ER+RQIEA A KK++
Sbjct: 251 WLDSESKVTLQELADEYGVSAERIRQIEANALKKMK 286


>gi|332703233|ref|ZP_08423321.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio
           africanus str. Walvis Bay]
 gi|332553382|gb|EGJ50426.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio
           africanus str. Walvis Bay]
          Length = 398

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 109/279 (39%), Positives = 172/279 (61%), Gaps = 8/279 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL-P 74
           L  Y+ EI + P+L+ +EE  LA+R R+ GD  AA RLVTSHLRLVVKIAM ++   +  
Sbjct: 118 LHMYMQEISRFPILKPEEEVELARRVRDTGDQDAAFRLVTSHLRLVVKIAMDFQRRWMQN 177

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++V EGN+GLM+AV+KFDPE+G + + Y+ +WIKA + ++I+ +W +VKIGTT  Q++
Sbjct: 178 VLDLVQEGNVGLMRAVQKFDPEKGIKFSYYAAFWIKAYILKFIMDNWRMVKIGTTQTQRK 237

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSS 193
           LF+NL + +  LQ+             ++K L VS  ++  M+ RL+  D SL+  I   
Sbjct: 238 LFYNLNKERQRLQS----QGFDPTSSTLSKSLGVSVEDIEEMDQRLSRSDMSLD--ITIG 291

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D  ++   D+L     G E+ L   E     R  L   + +L+ +E+ I + R L ++PV
Sbjct: 292 DDTTATRMDFLPALGPGIEETLANSEISALLREHLASIVPMLSDKEQDILQKRLLSDSPV 351

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
           TL  +  ++ ++RERVRQIEAR  +K++E +  ++E  S
Sbjct: 352 TLREIGDQYGITRERVRQIEARLLQKIREHLTDKIEDFS 390


>gi|323359909|ref|YP_004226305.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Microbacterium testaceum StLB037]
 gi|323276280|dbj|BAJ76425.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Microbacterium testaceum StLB037]
          Length = 436

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 73/313 (23%), Positives = 137/313 (43%), Gaps = 40/313 (12%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR------------------------ 40
           +  I       +  Y+ +I K+P+L   EE  LA R                        
Sbjct: 127 SAQITGATADPVKDYLKQIGKVPLLNAAEEVELAMRIEAGLFAEEKLSNMSAAEKTSQLG 186

Query: 41  ----YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
               +       A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  
Sbjct: 187 LDLQWVARDGQRAKSHLLGANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEKFDYT 246

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +GF+ +TY+ WWI+ A+   +      ++I     +  +   L R++  +         P
Sbjct: 247 KGFKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTP 304

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           E    ++++L+++  +VI +        SL+  +   +   S++ D +    D +  V  
Sbjct: 305 E---ELSRELDMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDTEAVVPA 356

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEA 274
           +       +  L   +  L+ RE  +   R    +  P TL+ +   F V+RER+RQIE+
Sbjct: 357 DAVGFTMLQRQLESLLDSLSEREAGVIRMRFGLGDGQPKTLDQIGDTFGVTRERIRQIES 416

Query: 275 RAFKKVQESIQKQ 287
           +   K++   + Q
Sbjct: 417 KTMAKLRHPSRSQ 429


>gi|319945291|ref|ZP_08019553.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Lautropia
           mirabilis ATCC 51599]
 gi|319741861|gb|EFV94286.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Lautropia
           mirabilis ATCC 51599]
          Length = 298

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 113/287 (39%), Positives = 177/287 (61%), Gaps = 10/287 (3%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           +  V     L  YI  + ++PML  +EE  LA+R++EH D+ AA  LVTSHLRLVV +A 
Sbjct: 17  APAVPSLGNLDAYISAVNRMPMLSAEEESSLARRFKEHQDVDAARTLVTSHLRLVVSVAR 76

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y GYGLP ++++ EGNIGLM+AVK+FDP+R  RL ++++ WIKA + EYIL++W LVK+
Sbjct: 77  QYLGYGLPHADLIQEGNIGLMKAVKRFDPDRSVRLVSFALHWIKAEIHEYILKNWRLVKV 136

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-S 185
            TT  Q++LFFNLR +K  L  +T     PE V  IA++LNV E +V  M  R+ G E +
Sbjct: 137 ATTKAQRKLFFNLRSMKKDLDTLT-----PEAVTDIAEQLNVREKDVTEMETRMTGHEIA 191

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L    +  +        +L        +++ +++    +   L+ +++ L+ R R I ++
Sbjct: 192 LEPQGDDEEGAGFGPAAYLAAPGSEPTEIIEDRQRDWLQTEGLSNALATLDERSRNIVQS 251

Query: 246 RRLQENP----VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           R L++       TL++L++E+ VS ER+RQIEA+A KK++ ++    
Sbjct: 252 RWLRDEDEGGSRTLQDLANEYGVSAERIRQIEAQAMKKMKAALASYA 298


>gi|227542254|ref|ZP_03972303.1| RNA polymerase sigma factor A [Corynebacterium glucuronolyticum
           ATCC 51866]
 gi|227182083|gb|EEI63055.1| RNA polymerase sigma factor A [Corynebacterium glucuronolyticum
           ATCC 51866]
          Length = 603

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 77/324 (23%), Positives = 149/324 (45%), Gaps = 48/324 (14%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------------- 41
            RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR                     
Sbjct: 285 ARKDAELTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYATHLLNQFKDPEWLE 343

Query: 42  -------REHGD--------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
                   +  D          A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL
Sbjct: 344 SHEKPANSQKKDLRTVARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGL 403

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L
Sbjct: 404 IRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQREL 461

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    P     +AK+++++E +V+ +        SL+  I   D+  SQ  D++  
Sbjct: 462 LQDLGREPTP---QELAKEMDITEEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI-- 514

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEV 264
             D +  V ++       ++ L   +  L+ RE  + + R    +  P TL+ +   + V
Sbjct: 515 -EDSEAVVAVDAVSFTLLQDQLQDVLKTLSEREAGVVKLRFGLTDGMPRTLDEIGQVYGV 573

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           +RER+RQIE++   K++   + QV
Sbjct: 574 TRERIRQIESKTMSKLRHPSRSQV 597


>gi|262278444|ref|ZP_06056229.1| EsvH [Acinetobacter calcoaceticus RUH2202]
 gi|262258795|gb|EEY77528.1| EsvH [Acinetobacter calcoaceticus RUH2202]
          Length = 288

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 110/283 (38%), Positives = 167/283 (59%), Gaps = 8/283 (2%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +S+   G + L  YI  + +IP+L  ++E  LA+RY    DL AA  LV SHLR VV IA
Sbjct: 11  LSLSAPG-VNLGAYISTVNQIPILTAEQEKELAERYYYDQDLDAAKMLVMSHLRFVVHIA 69

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGLP  +++ EGN+GLM+AVK+FDP  G RL ++++ WIKA + EY++R+W +VK
Sbjct: 70  RSYAGYGLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVK 129

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDE 184
           I TT  Q++LFFNLR LK   + +T      E+  +IA  LNV+  +V+ M  RL A D 
Sbjct: 130 IATTKAQRKLFFNLRSLKKSSKKLT-----LEEAQSIANDLNVTAEQVLEMEGRLTAYDA 184

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR-NMLTRSMSVLNPRERRIF 243
           +  A  +  D          + D+      L+E E+ + +  + L  +M  L+ R R I 
Sbjct: 185 AFEAQGDDDDDTPHTAPALYLEDNRYDPARLVENEDWEEQSTSALHNAMDQLDDRSRNIL 244

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           + R L ++  TL  L++E+ VS ER+RQ+E  A +K++ ++  
Sbjct: 245 QRRWLDDDKSTLHELAAEYNVSAERIRQLEKNAMEKIKIAMSA 287


>gi|319788352|ref|YP_004147827.1| RNA polymerase, sigma 32 subunit, RpoH [Pseudoxanthomonas
           suwonensis 11-1]
 gi|317466864|gb|ADV28596.1| RNA polymerase, sigma 32 subunit, RpoH [Pseudoxanthomonas
           suwonensis 11-1]
          Length = 292

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 112/279 (40%), Positives = 172/279 (61%), Gaps = 8/279 (2%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           + +    L  YI  + +IP+L  +EE  LA+RYR+  DL AA  LV SHLR VV +A GY
Sbjct: 17  VPSPLGSLEAYIGAVHQIPVLSVEEEQALARRYRDQEDLDAARELVHSHLRFVVHVARGY 76

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGL + +++ EGNIGLM+AVK+FDP+ G RL ++++ WI+A + E+IL++W +VK+ T
Sbjct: 77  NGYGLQLGDLIQEGNIGLMKAVKRFDPDLGVRLVSFAVHWIRAEIHEFILKNWRIVKVAT 136

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN 187
           T  Q++LFFNLR+ K  L       +   +V A+AK LNVSE EV+ M  RL+G D   +
Sbjct: 137 TKAQRKLFFNLRKAKTRLGW-----MNAAEVSAVAKDLNVSEREVLEMESRLSGRDIGFD 191

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR-NMLTRSMSVLNPRERRIFEAR 246
           A  +  ++++       +   D      +E+E+ +  + ++L   ++ L+ R R I   R
Sbjct: 192 APADEDEEHAPPSPAAYLVSMDEDPSQALEREDSEGHKLDLLRDGLASLDARSRDIIARR 251

Query: 247 RLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L +   VTL+ L+ E+ VS ER+RQIEA A KK++  +
Sbjct: 252 WLDDESKVTLQELADEYGVSAERIRQIEANAMKKMRALL 290


>gi|82703854|ref|YP_413420.1| RNA polymerase factor sigma-32 [Nitrosospira multiformis ATCC
           25196]
 gi|82411919|gb|ABB76028.1| RNA polymerase, sigma 32 subunit, RpoH [Nitrosospira multiformis
           ATCC 25196]
          Length = 281

 Score =  247 bits (631), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 117/282 (41%), Positives = 172/282 (60%), Gaps = 8/282 (2%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
             ++ V     L  YI  + +  +L ++EE  LA+  R+ G + AA +LV SHLRLVV I
Sbjct: 2   TFALTVPSAGSLENYIQSVNQFRILTQEEELQLARSLRDEGSIDAARQLVLSHLRLVVAI 61

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A GY+GYGLP ++++ EGNIGLM+AVK+FDPERG RL ++++ WIKA + E+ILR+W LV
Sbjct: 62  ARGYKGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEFILRNWRLV 121

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-D 183
           KI TT  Q++LFFNLR LK  L  ++       +V  +A++L V   EV+ M  R +G D
Sbjct: 122 KIATTKAQRKLFFNLRSLKQALDTMSQK-----EVAEVAEQLGVKPEEVVEMETRFSGRD 176

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SL   ++  D   +      + D      VL +++  + R   L +++  L+ R R I 
Sbjct: 177 ISLE-PLSEDDDEETFSPIAYLTDGSEPSHVLEDEQTMRLRGEGLEQALESLDARSRHII 235

Query: 244 EARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           EAR L+E +  TL  L+ E  VS ERVRQIEA+A +K++  +
Sbjct: 236 EARWLREKDTATLHELADELGVSAERVRQIEAKAMQKLRAVM 277


>gi|53718144|ref|YP_107130.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei K96243]
 gi|76812253|ref|YP_332145.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei 1710b]
 gi|126441976|ref|YP_001057600.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei 668]
 gi|126453430|ref|YP_001064846.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei 1106a]
 gi|134279764|ref|ZP_01766476.1| alternative sigma factor RpoH [Burkholderia pseudomallei 305]
 gi|167717993|ref|ZP_02401229.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei DM98]
 gi|167737009|ref|ZP_02409783.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei 14]
 gi|167814118|ref|ZP_02445798.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei 91]
 gi|167822644|ref|ZP_02454115.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei 9]
 gi|167844214|ref|ZP_02469722.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei B7210]
 gi|167892724|ref|ZP_02480126.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei 7894]
 gi|167901220|ref|ZP_02488425.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei NCTC
           13177]
 gi|167909437|ref|ZP_02496528.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei 112]
 gi|167917468|ref|ZP_02504559.1| RNA polymerase factor sigma-32 [Burkholderia pseudomallei BCC215]
 gi|217419877|ref|ZP_03451383.1| alternative sigma factor RpoH [Burkholderia pseudomallei 576]
 gi|226199497|ref|ZP_03795054.1| alternative sigma factor RpoH [Burkholderia pseudomallei Pakistan
           9]
 gi|237810751|ref|YP_002895202.1| alternative sigma factor RpoH [Burkholderia pseudomallei MSHR346]
 gi|242316271|ref|ZP_04815287.1| alternative sigma factor RpoH [Burkholderia pseudomallei 1106b]
 gi|254181885|ref|ZP_04888482.1| alternative sigma factor RpoH [Burkholderia pseudomallei 1655]
 gi|254187820|ref|ZP_04894332.1| alternative sigma factor RpoH [Burkholderia pseudomallei Pasteur
           52237]
 gi|254196825|ref|ZP_04903249.1| alternative sigma factor RpoH [Burkholderia pseudomallei S13]
 gi|254260127|ref|ZP_04951181.1| alternative sigma factor RpoH [Burkholderia pseudomallei 1710a]
 gi|254296064|ref|ZP_04963521.1| alternative sigma factor RpoH [Burkholderia pseudomallei 406e]
 gi|52208558|emb|CAH34494.1| RNA polymerase sigma-32 factor [Burkholderia pseudomallei K96243]
 gi|76581706|gb|ABA51181.1| alternative sigma factor RpoH [Burkholderia pseudomallei 1710b]
 gi|126221469|gb|ABN84975.1| alternative sigma factor RpoH [Burkholderia pseudomallei 668]
 gi|126227072|gb|ABN90612.1| alternative sigma factor RpoH [Burkholderia pseudomallei 1106a]
 gi|134248964|gb|EBA49046.1| alternative sigma factor RpoH [Burkholderia pseudomallei 305]
 gi|157805888|gb|EDO83058.1| alternative sigma factor RpoH [Burkholderia pseudomallei 406e]
 gi|157935500|gb|EDO91170.1| alternative sigma factor RpoH [Burkholderia pseudomallei Pasteur
           52237]
 gi|169653568|gb|EDS86261.1| alternative sigma factor RpoH [Burkholderia pseudomallei S13]
 gi|184212423|gb|EDU09466.1| alternative sigma factor RpoH [Burkholderia pseudomallei 1655]
 gi|217397181|gb|EEC37197.1| alternative sigma factor RpoH [Burkholderia pseudomallei 576]
 gi|225928378|gb|EEH24408.1| alternative sigma factor RpoH [Burkholderia pseudomallei Pakistan
           9]
 gi|237503746|gb|ACQ96064.1| alternative sigma factor RpoH [Burkholderia pseudomallei MSHR346]
 gi|242139510|gb|EES25912.1| alternative sigma factor RpoH [Burkholderia pseudomallei 1106b]
 gi|254218816|gb|EET08200.1| alternative sigma factor RpoH [Burkholderia pseudomallei 1710a]
          Length = 311

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 120/288 (41%), Positives = 171/288 (59%), Gaps = 12/288 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S++      +  YI  + +IP+L  +EE   A  YRE  +L AA RLV SHLRLVV +A 
Sbjct: 30  SMLPGHLGNIDAYIQAVNRIPLLSAEEERQYATEYREQNNLDAARRLVLSHLRLVVSVAR 89

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y GYGLP  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W +VK+
Sbjct: 90  NYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKV 149

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDES 185
            TT  Q++LFFNLR  K   QA T     PE++  +A++LNV   EV  M  RL  GD +
Sbjct: 150 ATTKAQRKLFFNLRSHKKGTQAFT-----PEEIDGLAQELNVKREEVAEMETRLSGGDIA 204

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L   I+  ++ S     +L   H+    VL  ++    + + + R++  L+ R RRI EA
Sbjct: 205 LEGQIDDGEE-SYAPIAYLADSHNEPTAVLAARQRDMLQTDGIARALESLDARSRRIIEA 263

Query: 246 RRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           R L          TL +L++EF VS ER+RQIEA A KK++ ++    
Sbjct: 264 RWLNVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRTALAAYA 311


>gi|163845340|ref|YP_001622995.1| RNA polymerase factor sigma-32 [Brucella suis ATCC 23445]
 gi|163676063|gb|ABY40173.1| RNA polymerase sigma factor, sigma-70 family [Brucella suis ATCC
           23445]
          Length = 311

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 118/293 (40%), Positives = 183/293 (62%), Gaps = 4/293 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  ++          +   I      P LE++EE  LA R++E  D  A HR+ ++H+RL
Sbjct: 19  MAVRSFPAAAASSQSM---IRSAMSAPYLEREEERALAIRWKETKDQDALHRITSAHMRL 75

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  +A  +R + LP+S+++ EG +GL++A  +FDP+R  R +TY+ WWI+A+MQ+YILR+
Sbjct: 76  VTSMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRDVRFSTYASWWIRASMQDYILRN 135

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WS+V+ GT++ QK LFFNL RL+  L    DN  K E    I+ +L VS S+V  M+ RL
Sbjct: 136 WSIVRGGTSSAQKALFFNLCRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRL 195

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D SL+A +N  +  +S+  D+LV DH  Q+++     + + R   LTR++  LN RE
Sbjct: 196 SGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIAESSIDMERRNCWLTRALDTLNERE 255

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
             I   RRL ++ VTLE L  +  +S+ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 256 LHIIRERRLDDDGVTLEALGEKLGISKERVRQIESRAMEKLKIALLSQHELAA 308


>gi|260578861|ref|ZP_05846767.1| RNA polymerase principal sigma factor SigA [Corynebacterium
           jeikeium ATCC 43734]
 gi|258603008|gb|EEW16279.1| RNA polymerase principal sigma factor SigA [Corynebacterium
           jeikeium ATCC 43734]
          Length = 552

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 77/319 (24%), Positives = 151/319 (47%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------REHGDL- 47
            RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR              +E G+  
Sbjct: 239 ARKDAELTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYAAYRLQEIKESGEKL 297

Query: 48  ----------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 298 SPMHRRDLREIDRDGRRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 357

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 358 KFDYVKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 415

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +A++++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 416 REPTPE---ELAREMDITVDKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 467

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  + + R    +  P TL+ +   + V+RER+
Sbjct: 468 AVVAVDAVSFTLLQDQLQDVLHTLSEREAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERI 527

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 528 RQIESKTMSKLRHPSRSQV 546


>gi|325983562|ref|YP_004295964.1| RNA polymerase, sigma 32 subunit, RpoH [Nitrosomonas sp. AL212]
 gi|325533081|gb|ADZ27802.1| RNA polymerase, sigma 32 subunit, RpoH [Nitrosomonas sp. AL212]
          Length = 281

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 118/285 (41%), Positives = 174/285 (61%), Gaps = 9/285 (3%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
             N   +      +  YI  +   P+L ++EE  LA+R    GD+ AA +L+ SHLR VV
Sbjct: 1   MTNALTLPTTGGSIESYIQSVNSFPILTQEEETSLARRLWNRGDIEAAQQLIMSHLRFVV 60

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA GY+GYGLP ++++ EGNIGLM+AVK+FDPERG RL ++++ WIKA + E+I+R+W 
Sbjct: 61  AIARGYKGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEFIMRNWR 120

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-A 181
           LVKI TT  Q++LFFNLR +K  L     + + P++V A+A +L V   EVI M  R   
Sbjct: 121 LVKIATTKQQRKLFFNLRSMKHGL-----DTMNPQEVDAMAAQLGVKAEEVIEMEKRFNG 175

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
            D SL  +  S D++ +      + D     Q+L +++    R   L +S+  L+ R R 
Sbjct: 176 SDISLEPV--SEDEDDTFSPINYLTDGTEPSQLLEKEQITHLREKGLQKSLDCLDKRSRH 233

Query: 242 IFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           I EAR L+E +  TL +L+ E  VS ERVRQIE +A +K++ +I+
Sbjct: 234 IIEARWLREKDTATLHDLADELGVSAERVRQIEVKALQKMRGAIK 278


>gi|288574317|ref|ZP_06392674.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dethiosulfovibrio
           peptidovorans DSM 11002]
 gi|288570058|gb|EFC91615.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dethiosulfovibrio
           peptidovorans DSM 11002]
          Length = 381

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 75/276 (27%), Positives = 134/276 (48%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI K+ +L+  EE  LAKR  E GD  A  +++ ++LRLVV IA  Y G G+
Sbjct: 110 DPVRMYLREIGKVDLLDASEEVELAKRV-EDGDQVAKQKIIDANLRLVVSIAKKYIGRGM 168

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 169 LFLDLIQEGNLGLIRAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 227

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                + ++    + +     +      I++ + +  ++V  +        SL   I   
Sbjct: 228 ----TINKMVRVSRQLVQRMGREPTDEEISEAMEIESTKVEEIRRIAQLPVSLETPI--G 281

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           ++  SQ  D++    D       +          +   +  L+ RER +   R   E+  
Sbjct: 282 EEEDSQLGDFI---EDRDMPSPEDAASCNLLHEQIEDMLDALSDREREVLRYRFGLEDGR 338

Query: 254 --TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 339 SYTLEEVGRRFGVTRERIRQIEAKALRKLRHPSRSK 374


>gi|254694416|ref|ZP_05156244.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 3 str. Tulya]
          Length = 311

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 119/293 (40%), Positives = 185/293 (63%), Gaps = 4/293 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  ++          +   I      P LE++EE  LA R++E  D  A HR+ ++H+RL
Sbjct: 19  MAVRSFPAAAASSQSM---IRSAMSAPYLEREEERALAIRWKETKDQDALHRITSAHMRL 75

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A  +R + LP+S+++ EG +GL++A  +FDP+R  R +TY+ WWI+A+MQ+YILR+
Sbjct: 76  VISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRDVRFSTYASWWIRASMQDYILRN 135

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WS+V+ GT++ QK LFFNLRRL+  L    DN  K E    I+ +L VS S+V  M+ RL
Sbjct: 136 WSIVRGGTSSAQKALFFNLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRL 195

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D SL+A +N  +  +S+  D+LV DH  Q+++     + + R   LTR++  LN RE
Sbjct: 196 SGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTRALDTLNERE 255

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
             I   RRL ++ VTLE L  +  +S+ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 256 LHIIRERRLDDDGVTLEALGEKLGISKERVRQIESRAMEKLKIALLSQHELAA 308


>gi|297160766|gb|ADI10478.1| RNA polymerase sigma factor [Streptomyces bingchenggensis BCW-1]
          Length = 453

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 83/301 (27%), Positives = 136/301 (45%), Gaps = 38/301 (12%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKR----------YREHGDLS------------ 48
                  +Y+ EI +IP+L   EE  LA+R               DL             
Sbjct: 152 PSSDLFRQYLREIGRIPLLSAAEEVELARRVEAGLFAEEKLSNTPDLDTQLAHDFDQLVV 211

Query: 49  ----AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
               A  RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY
Sbjct: 212 LGRMAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTY 271

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + WWI+ AM   +      +++     +  L   + R++  +         PE+V   A 
Sbjct: 272 ATWWIRQAMSRALADQARTIRVPVHVVE--LINRVVRVQRRMLQERGYEPTPEEV---AH 326

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            L++    V  +        SL+A +   +++     D +    DG     +E       
Sbjct: 327 HLDLLPERVSEVLRLAQEPVSLHAPV--GEEDDVALGDLI---EDGDAASPVESAAFLLL 381

Query: 225 RNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           R  L   +S L  RER++ + R       P TLE +   F V+RER+RQIE++   K+++
Sbjct: 382 REHLEAVLSTLGERERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRD 441

Query: 283 S 283
            
Sbjct: 442 H 442


>gi|71280363|ref|YP_266929.1| RNA polymerase factor sigma-32 [Colwellia psychrerythraea 34H]
 gi|71146103|gb|AAZ26576.1| RNA polymerase sigma-32 factor [Colwellia psychrerythraea 34H]
          Length = 285

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 101/285 (35%), Positives = 165/285 (57%), Gaps = 9/285 (3%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           + M + +     +  Y+     IPML  ++E+ LA R     DL AA  L+ SHLR V+ 
Sbjct: 3   EAMQLTLPKSGSIEAYMQSAYSIPMLTAEKEHDLATRLYNENDLQAAQELIMSHLRFVIH 62

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           +A GY GYGLP +++V EGN+GLM+AVK+F+PE G RL ++++ WIKA + E++L++W +
Sbjct: 63  VAKGYSGYGLPHADLVQEGNVGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEFVLKNWRI 122

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VK+ TT  Q++LFFNLR+ K  L   +      E+V  +A+ L V+  +V+ M  R++  
Sbjct: 123 VKVATTKAQRKLFFNLRKNKKRLGWFS-----TEEVNTVAENLGVTTKDVMEMESRMSSH 177

Query: 184 ESLNALINSSDKN---SSQWQDWLVYDHDGQEQVLIEKEERKNRRN-MLTRSMSVLNPRE 239
           +    L    D N   SS      + D      V +E +   N  N  L+ ++  L+ R 
Sbjct: 178 DQAFELSKDDDDNLGSSSFSPAQYLQDKQSDLAVEVENDNWDNHANKRLSTALVTLDERS 237

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + I + R L E+  TL+ L++++++S ERVRQ+E  A  K++ ++
Sbjct: 238 QDIIKTRWLTEDKTTLQELANKYQISAERVRQLEKNALSKLKNTM 282


>gi|264680055|ref|YP_003279964.1| RNA polymerase, sigma 32 subunit, RpoH [Comamonas testosteroni
           CNB-2]
 gi|262210570|gb|ACY34668.1| RNA polymerase, sigma 32 subunit, RpoH [Comamonas testosteroni
           CNB-2]
          Length = 324

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 117/291 (40%), Positives = 170/291 (58%), Gaps = 15/291 (5%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +V     L  YI  + ++PML  +EE   A++ +EH DL AA RLV SHLRLVV I+  Y
Sbjct: 30  LVPPLGNLDAYISAVNRMPMLTLEEEQDYARKLKEHNDLDAAGRLVMSHLRLVVSISRQY 89

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGLP  +++ EGN+GLM+AVK+FDP++G RL +Y+M WIKA + EYIL++W +VK+ T
Sbjct: 90  LGYGLPHGDLIQEGNVGLMKAVKRFDPDQGVRLVSYAMHWIKAEIHEYILKNWRMVKVAT 149

Query: 129 TANQKRLFFNLRRLKGHL---------QAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
           T  Q++LFFNLR +K  L         +      L   ++ A+A KLNV   EVI M  R
Sbjct: 150 TKAQRKLFFNLRSMKHDLKSDAAMADEELALRETLTSNEIDAVAAKLNVKREEVIEMETR 209

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPR 238
           LAG + L     S D   +      + D   +   ++E  +R +   + L  ++  L+ R
Sbjct: 210 LAGGDVLLDPSPSDDGEQAFGPIAYLADASHEPTAMLESRQRDHLATDGLVMALEGLDDR 269

Query: 239 ERRIFEARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            RRI E R L         +TL  L++E+ VS ER+RQIE  A KK+++++
Sbjct: 270 SRRIVEERWLKVNDDGSGGMTLHELAAEYGVSAERIRQIEVAAMKKMKKAL 320


>gi|91787153|ref|YP_548105.1| sigma 32 (RpoH) [Polaromonas sp. JS666]
 gi|91696378|gb|ABE43207.1| RNA polymerase, sigma 32 subunit, RpoH [Polaromonas sp. JS666]
          Length = 322

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 114/291 (39%), Positives = 172/291 (59%), Gaps = 11/291 (3%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +V     L  YI  + ++PML  ++E   AK+ +E+ DL +A +LV SHLRLVV I+  Y
Sbjct: 32  LVPPLGNLDAYISAVNRLPMLTLEQEQEFAKKLKENNDLDSAGKLVLSHLRLVVSISRKY 91

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGLP  +++ EGNIGLM+AVK+FDPE+  RL +Y+M WIKA + EYIL++W +VK+ T
Sbjct: 92  LGYGLPHGDLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHWIKAEIHEYILKNWRMVKVAT 151

Query: 129 TANQKRLFFNLRRLKGHLQAITD-----NNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           T  Q++LFFNLR +K   +   D     + L   Q+ ++AK LNV   EVI M  R++G 
Sbjct: 152 TKAQRKLFFNLRSMKQGFKDDADVATHRDTLTEGQIDSMAKTLNVKREEVIEMEQRMSGG 211

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRI 242
           + L     S D   +      + D   +   L+E  +R +   + ++ ++  L+PR RRI
Sbjct: 212 DVLLDPSPSDDGEDAFGPIAYLADATQEPTALMESRQRDSLASDGISAALQELDPRSRRI 271

Query: 243 FEARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            E R L         +TL +L+ E++VS ER+RQIE  A KK+++ +    
Sbjct: 272 VEERWLKVNDDGSGGMTLHDLADEYQVSAERIRQIEVSAMKKMKKVLAAYA 322


>gi|53724102|ref|YP_104622.1| RNA polymerase factor sigma-32 [Burkholderia mallei ATCC 23344]
 gi|121598782|ref|YP_991458.1| RNA polymerase factor sigma-32 [Burkholderia mallei SAVP1]
 gi|124383719|ref|YP_001027464.1| RNA polymerase factor sigma-32 [Burkholderia mallei NCTC 10229]
 gi|126449925|ref|YP_001082430.1| RNA polymerase factor sigma-32 [Burkholderia mallei NCTC 10247]
 gi|167001066|ref|ZP_02266867.1| alternative sigma factor RpoH [Burkholderia mallei PRL-20]
 gi|238561338|ref|ZP_00442201.2| alternative sigma factor RpoH [Burkholderia mallei GB8 horse 4]
 gi|254175044|ref|ZP_04881705.1| alternative sigma factor RpoH [Burkholderia mallei ATCC 10399]
 gi|254201710|ref|ZP_04908074.1| alternative sigma factor RpoH [Burkholderia mallei FMH]
 gi|254207043|ref|ZP_04913394.1| alternative sigma factor RpoH [Burkholderia mallei JHU]
 gi|254357524|ref|ZP_04973798.1| alternative sigma factor RpoH [Burkholderia mallei 2002721280]
 gi|52427525|gb|AAU48118.1| RNA polymerase sigma-32 factor [Burkholderia mallei ATCC 23344]
 gi|121227592|gb|ABM50110.1| alternative sigma factor RpoH [Burkholderia mallei SAVP1]
 gi|124291739|gb|ABN01008.1| RNA polymerase sigma-32 factor [Burkholderia mallei NCTC 10229]
 gi|126242795|gb|ABO05888.1| alternative sigma factor RpoH [Burkholderia mallei NCTC 10247]
 gi|147747604|gb|EDK54680.1| alternative sigma factor RpoH [Burkholderia mallei FMH]
 gi|147752585|gb|EDK59651.1| alternative sigma factor RpoH [Burkholderia mallei JHU]
 gi|148026588|gb|EDK84673.1| alternative sigma factor RpoH [Burkholderia mallei 2002721280]
 gi|160696089|gb|EDP86059.1| alternative sigma factor RpoH [Burkholderia mallei ATCC 10399]
 gi|238524810|gb|EEP88241.1| alternative sigma factor RpoH [Burkholderia mallei GB8 horse 4]
 gi|243063136|gb|EES45322.1| alternative sigma factor RpoH [Burkholderia mallei PRL-20]
          Length = 311

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 120/288 (41%), Positives = 171/288 (59%), Gaps = 12/288 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S++      +  YI  + +IP+L  +EE   A  YRE  +L AA RLV SHLRLVV +A 
Sbjct: 30  SMLPGHLGNIDAYIQAVNRIPLLSAEEERQYATEYREQNNLDAARRLVLSHLRLVVSVAR 89

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y GYGLP  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W +VK+
Sbjct: 90  NYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKV 149

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDES 185
            TT  Q++LFFNLR  K   QA T     PE++  +A++LNV   EV  M  RL  GD +
Sbjct: 150 ATTKAQRKLFFNLRSHKKGTQAFT-----PEEIDGLAQELNVKREEVAEMETRLSGGDIA 204

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L   I+  ++ S     +L   H+    VL  ++    + + + R++  L+ R RRI EA
Sbjct: 205 LEGQIDDGEE-SYAPIAYLADSHNEPTAVLAARQRDMLQTDGIARALESLDARSRRIIEA 263

Query: 246 RRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           R L          TL +L++EF VS ER+RQIEA A KK++ ++    
Sbjct: 264 RWLNVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRTALAAYA 311


>gi|257791063|ref|YP_003181669.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Eggerthella lenta
           DSM 2243]
 gi|317488219|ref|ZP_07946788.1| RNA polymerase sigma factor RpoD [Eggerthella sp. 1_3_56FAA]
 gi|325830757|ref|ZP_08164141.1| RNA polymerase sigma factor RpoD [Eggerthella sp. HGA1]
 gi|257474960|gb|ACV55280.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Eggerthella lenta
           DSM 2243]
 gi|316912661|gb|EFV34201.1| RNA polymerase sigma factor RpoD [Eggerthella sp. 1_3_56FAA]
 gi|325487164|gb|EGC89607.1| RNA polymerase sigma factor RpoD [Eggerthella sp. HGA1]
          Length = 409

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 82/314 (26%), Positives = 138/314 (43%), Gaps = 42/314 (13%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR---------------------- 42
           + S+ +     +  Y+ EI K+P+L   EE  LA +                        
Sbjct: 97  DASVTMLTGDPVRMYLKEIGKVPLLTAAEEIDLAMKIEAGVAAMEELEKAEDEGIELERR 156

Query: 43  --------EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                   E   + A  +L+ ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD
Sbjct: 157 EKRRLGRIEQVGIDAKQQLIEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFD 216

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +GF+ +TY+ WWI+ A+   I      ++I     +      L R++  L        
Sbjct: 217 YTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE--TINKLVRIQRQLLQELGREP 274

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            PE    I K++ +    V  +        SL   I   ++  SQ  D++  D      V
Sbjct: 275 SPE---EIGKEMGLPAERVREIQKISQEPVSLETPI--GEEEDSQLGDFIEDD---AAVV 326

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
             +       +  L++ +  L  RER++   R   E+  P TLE +  EF V+RER+RQI
Sbjct: 327 PPDAASFSMLQEQLSKVLDGLAERERKVISLRFGLEDGHPRTLEEVGREFGVTRERIRQI 386

Query: 273 EARAFKKVQESIQK 286
           E++   K++   + 
Sbjct: 387 ESKTLAKLRHPSRS 400


>gi|306844750|ref|ZP_07477335.1| RNA polymerase sigma factor, sigma-70 family [Brucella sp. BO1]
 gi|306274922|gb|EFM56692.1| RNA polymerase sigma factor, sigma-70 family [Brucella sp. BO1]
          Length = 311

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 119/293 (40%), Positives = 185/293 (63%), Gaps = 4/293 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  ++          +   I      P LE++EE  LA R++E  D  A HR+ ++H+RL
Sbjct: 19  MAVRSFPAAAASSQSM---IRSAMSAPYLEREEERALAIRWKETKDQDALHRITSAHMRL 75

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A  +R + LP+S+++ EG +GL++A  +FDP+R  R +TY+ WWI+A+MQ+YILR+
Sbjct: 76  VISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRDVRFSTYASWWIRASMQDYILRN 135

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WS+V+ GT++ QK LFFNLRRL+  L    DN  K E    I+ +L VS S+V  M+ RL
Sbjct: 136 WSIVRGGTSSAQKALFFNLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRL 195

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D SL+A +N  +  +S+  D+LV DH  Q+++     + + R   LTR++  LN RE
Sbjct: 196 SGPDSSLSAPMNGEESGASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTRALDTLNERE 255

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
             I   RRL ++ VTLE L  +  +S+ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 256 LHIIRERRLDDDGVTLEALGEKLGISKERVRQIESRAMEKLKIALLSQHELAA 308


>gi|21233199|ref|NP_639116.1| RNA polymerase factor sigma-32 [Xanthomonas campestris pv.
           campestris str. ATCC 33913]
 gi|66770141|ref|YP_244903.1| RNA polymerase factor sigma-32 [Xanthomonas campestris pv.
           campestris str. 8004]
 gi|188993348|ref|YP_001905358.1| RNA polymerase factor sigma-32 [Xanthomonas campestris pv.
           campestris str. B100]
 gi|3046929|gb|AAC38329.1| heat shock sigma factor 32 [Xanthomonas campestris pv. campestris]
 gi|21115547|gb|AAM43471.1| RNA polymerase sigma-32 factor [Xanthomonas campestris pv.
           campestris str. ATCC 33913]
 gi|66575473|gb|AAY50883.1| RNA polymerase sigma-32 factor [Xanthomonas campestris pv.
           campestris str. 8004]
 gi|167735108|emb|CAP53320.1| RNA polymerase sigma-32 factor [Xanthomonas campestris pv.
           campestris]
          Length = 291

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 119/276 (43%), Positives = 168/276 (60%), Gaps = 8/276 (2%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           I +    L  YI  + +IP+L   EE  LA+R+R+  DL AA  LV SHLR VV +A GY
Sbjct: 16  IPSALGSLDAYIGAVHQIPVLSVDEEQNLARRFRDELDLDAARELVHSHLRFVVHVARGY 75

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGLP+ +++ EGNIGLM+AVK+FDPE G RL ++++ WI+A M E+IL++W +VK+ T
Sbjct: 76  NGYGLPLGDLIQEGNIGLMKAVKRFDPEMGVRLVSFAVHWIRAEMHEFILKNWRIVKVAT 135

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN 187
           T  Q++LFFNLR+ K  L  +        +V A+AK LNVSE EV+ M  RL+G D   +
Sbjct: 136 TKAQRKLFFNLRKSKTRLGWLN-----ASEVTAVAKDLNVSEREVMEMESRLSGRDIGFD 190

Query: 188 A-LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           A      D        +LV + +   Q     +   N+  +L   M+ L+ R R I + R
Sbjct: 191 ASSDEDDDHGPPSPVSYLVANEEDPSQAYERHDSEDNQLQLLREGMAGLDTRSRDIVKRR 250

Query: 247 RLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L  E+ VTL+ L+ E+ VS ER+RQIEA A KK++
Sbjct: 251 WLDSESKVTLQELADEYGVSAERIRQIEANALKKMK 286


>gi|296393381|ref|YP_003658265.1| RpoD subfamily RNA polymerase sigma-70 factor [Segniliparus
           rotundus DSM 44985]
 gi|296180528|gb|ADG97434.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Segniliparus
           rotundus DSM 44985]
          Length = 441

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 78/319 (24%), Positives = 146/319 (45%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------REHGDL- 47
            RKN  +  + +  +  Y+ +I K+ +L  ++E  LAKR               E GD  
Sbjct: 128 ARKNAELTASAD-SVRAYLKQIGKVALLNAEQEVELAKRIEAGLYAQERLRIAAEEGDRL 186

Query: 48  ----------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 187 PTTSRRDLNWVVRDGNRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 246

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 247 KFDYSKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 304

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    + +++++   +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 305 REPTPE---ELGREMDIPPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 356

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 357 AVVAVDAVSFTLLQDQLQAVLETLSEREAGVVRMRFGLTDGQPRTLDEIGQVYGVTRERI 416

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 417 RQIESKTMSKLRHPSRSQV 435


>gi|291439801|ref|ZP_06579191.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291342696|gb|EFE69652.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 390

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 84/301 (27%), Positives = 137/301 (45%), Gaps = 38/301 (12%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKR----------YREHGDLS------------ 48
                  +Y+ EI +IP+L   EE  LA+R           R   DL             
Sbjct: 89  PSSDLFRQYLREIGRIPLLTAAEEVELARRVEAGLFAEEKLRLTPDLDSRLAHDLDRLVV 148

Query: 49  ----AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
               A  RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY
Sbjct: 149 MGRMAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTY 208

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + WWI+ AM   +      +++     +  L   + R++  +         PE+V A   
Sbjct: 209 ATWWIRQAMSRALADQARTIRVPVHVVE--LINRVVRVQRRMLQERGREPTPEEVAA--- 263

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            L++    V  +        SL+A +   +++     D +    DG     +E       
Sbjct: 264 HLDLPPERVGEVLRLAQEPVSLHAPV--GEEDDVALGDLI---EDGDAASPVESAAFLLL 318

Query: 225 RNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           R  L   +S L  RER++ + R       P TLE +   F V+RER+RQIE++   K+++
Sbjct: 319 REHLEAVLSTLGERERKVVQLRYGLVDGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRD 378

Query: 283 S 283
            
Sbjct: 379 H 379


>gi|298346920|ref|YP_003719607.1| RNA polymerase sigma factor SigA [Mobiluncus curtisii ATCC 43063]
 gi|298236981|gb|ADI68113.1| RNA polymerase sigma factor SigA [Mobiluncus curtisii ATCC 43063]
          Length = 563

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 72/305 (23%), Positives = 138/305 (45%), Gaps = 39/305 (12%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREH---------------------- 44
               +  Y+ +I K+ +L  ++E  L+KR     Y EH                      
Sbjct: 262 TSDPVKDYLKQIGKVALLNAEQEVDLSKRIEAGLYAEHLLKTKQETMTPKQIRELHYVVQ 321

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
               A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY
Sbjct: 322 DGQMAKNHLLEANLRLVVALAKKYTGRGMLFLDLIQEGNLGLIRAVEKFDYSKGYKFSTY 381

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + WWI+ A+   +      ++I     +  +   L R++  +         P+    +A+
Sbjct: 382 ATWWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPD---ELAQ 436

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L ++  +V+ +        SL+  +   +   S++ D +    D +  V  +       
Sbjct: 437 ELEMTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAVVPADAVSFMML 491

Query: 225 RNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +  L R +  L+ RE  +   R       P TL+ +   + V+RER+RQIEA+   K++ 
Sbjct: 492 QEQLQRVLDTLSERESGVIAMRFGLKDGQPKTLDEIGRRYGVTRERIRQIEAKTMSKLRH 551

Query: 283 SIQKQ 287
             + Q
Sbjct: 552 PARSQ 556


>gi|307728369|ref|YP_003905593.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. CCGE1003]
 gi|307582904|gb|ADN56302.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. CCGE1003]
          Length = 311

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 123/288 (42%), Positives = 170/288 (59%), Gaps = 12/288 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S++      +  YI  + +IPML   EE   A  +REH +L AA RLV SHLRLVV IA 
Sbjct: 30  SLLPGQLGNIDAYIQAVNRIPMLTPAEERQFATEFREHDNLEAARRLVLSHLRLVVSIAR 89

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y GYGLP ++++ EGNIGLM+AVK+FDPE+  RL +Y+M WIKA + EYILR+W +VK+
Sbjct: 90  NYLGYGLPHADLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHWIKAEIHEYILRNWRMVKV 149

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDES 185
            TT  Q++LFFNLR  K  L A T     P+++  +AK+LNV   EV  M  RL  GD +
Sbjct: 150 ATTKAQRKLFFNLRSHKQGLGAFT-----PDEIDGLAKELNVKREEVAEMETRLSGGDVA 204

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L   +   ++ S     +L   H     VL  ++  K + + +  ++  L+ R RRI EA
Sbjct: 205 LEGQVEDGEE-SYAPIAYLADSHSEPTAVLASRQRDKLQSDGIATALEALDARSRRIIEA 263

Query: 246 RRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           R L          TL  L+ EF VS ER+RQIEA A KK++ ++ +  
Sbjct: 264 RWLKVQDDGSGGSTLHELADEFGVSAERIRQIEASAMKKMRGALSEYA 311


>gi|119899581|ref|YP_934794.1| RNA polymerase factor sigma-32 [Azoarcus sp. BH72]
 gi|119671994|emb|CAL95908.1| RNA polymerase sigma-32 factor [Azoarcus sp. BH72]
          Length = 284

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 113/284 (39%), Positives = 177/284 (62%), Gaps = 10/284 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M++     + +    + +YI  + ++P+L +Q+E  LA R R+ GD+ AA +LV SHLR+
Sbjct: 1   MSQALSFPVPSVVGSIDQYIQAVNRVPLLTEQQEVELATRLRDDGDVDAARQLVMSHLRV 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA GY GYGLP ++++ EGNIGLM+AVK+FDP RG RL ++++ WIKA + EYIL++
Sbjct: 61  VVAIARGYLGYGLPHADLIQEGNIGLMKAVKRFDPTRGVRLVSFAIHWIKAEIHEYILKN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W LVKI TT  Q++LFFNLR LK          L  ++V A+A +L V   EV+ M  RL
Sbjct: 121 WRLVKIATTKAQRKLFFNLRSLKQDT-----GTLNRDEVEAVATQLGVKPEEVVEMETRL 175

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPR 238
           +G D  ++    + D++        +     +   ++E+ ER + ++  L +++  L+ R
Sbjct: 176 SGRDIPIDG--GNDDEDERFAPIAYLPAPAAEPSEVLERAERAHLQDTGLKQALGALDER 233

Query: 239 ERRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R I E R L + +  TL  L++E+ VS ER+RQIEA+A +K++
Sbjct: 234 SRTIVERRWLTDGDSATLHELAAEYGVSAERIRQIEAKAMQKMR 277


>gi|237728776|ref|ZP_04559257.1| RNA polymerase factor sigma-32 [Citrobacter sp. 30_2]
 gi|283835854|ref|ZP_06355595.1| alternative sigma factor RpoH [Citrobacter youngae ATCC 29220]
 gi|226909398|gb|EEH95316.1| RNA polymerase factor sigma-32 [Citrobacter sp. 30_2]
 gi|291068027|gb|EFE06136.1| alternative sigma factor RpoH [Citrobacter youngae ATCC 29220]
          Length = 284

 Score =  247 bits (630), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 106/289 (36%), Positives = 164/289 (56%), Gaps = 8/289 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +     L  YI      PML   EE  LA++    GDL AA  L+ SHLR 
Sbjct: 1   MTKEMQNLALAPVGNLESYIRAANAWPMLSADEERALAEKLHYQGDLEAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVEMVARELGVSSKDVREMESRM 175

Query: 181 -AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPR 238
            A D + +   +    +        + D        IE++  +++  N LT +M  L+ R
Sbjct: 176 AAQDMTFDMSSDDESDSQPMAPVLYLQDKSSNFADGIEEDNWEDQAANKLTHAMEGLDER 235

Query: 239 ERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + I  AR L E+   TL+ L+  + VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 SQDIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 284


>gi|150020921|ref|YP_001306275.1| RpoD family RNA polymerase sigma factor [Thermosipho melanesiensis
           BI429]
 gi|149793442|gb|ABR30890.1| RNA polymerase, sigma 70 subunit, RpoD family [Thermosipho
           melanesiensis BI429]
          Length = 370

 Score =  246 bits (629), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 74/273 (27%), Positives = 137/273 (50%), Gaps = 13/273 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y+ +I KIP+L +  E  LA+R ++ GD  A  +LV S+LRLVV IA  Y G GL  
Sbjct: 96  IKMYLKDIGKIPLLSQSMERELARRAQQ-GDERAKQKLVESNLRLVVSIAKRYVGKGLSF 154

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GL++AV+KFD ++G++ +TY+ WWI+ A+   I      +++     +   
Sbjct: 155 LDLIQEGNVGLLKAVEKFDWKKGYKFSTYATWWIRQAITRAIADQARTIRVPVHMVE--- 211

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + +++  ++     +     +  +AK +     +V  +        SL A +   + 
Sbjct: 212 --TINKVQKIMRDYYQQHGTEIPIEELAKIIGKPVEKVEEILQAAKETTSLEAPV--GED 267

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPV 253
             S   D++  +     +   ++  R   R  + + +  LN RE+ + + R         
Sbjct: 268 EDSTVGDFVADESIASPK---KEAMRMLIREEVEKVLETLNDREKLVLKMRYGLIDGKSK 324

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TLE +   F V+RER+RQIE +A +K++   + 
Sbjct: 325 TLEEVGQYFNVTRERIRQIEVKALRKLRHPSRS 357


>gi|62290634|ref|YP_222427.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 1 str. 9-941]
 gi|82700548|ref|YP_415122.1| RNA polymerase factor sigma-32 [Brucella melitensis biovar Abortus
           2308]
 gi|148559493|ref|YP_001259609.1| RNA polymerase factor sigma-32 [Brucella ovis ATCC 25840]
 gi|254689924|ref|ZP_05153178.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 6 str. 870]
 gi|254700417|ref|ZP_05162245.1| RNA polymerase factor sigma-32 [Brucella suis bv. 5 str. 513]
 gi|254719758|ref|ZP_05181569.1| RNA polymerase factor sigma-32 [Brucella sp. 83/13]
 gi|254730958|ref|ZP_05189536.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 4 str. 292]
 gi|256258178|ref|ZP_05463714.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 9 str. C68]
 gi|256370169|ref|YP_003107680.1| RNA polymerase factor sigma-32 [Brucella microti CCM 4915]
 gi|260547128|ref|ZP_05822866.1| sigma-70 factor family protein [Brucella abortus NCTC 8038]
 gi|297249027|ref|ZP_06932735.1| RNA polymerase sigma-32 factor [Brucella abortus bv. 5 str. B3196]
 gi|306839453|ref|ZP_07472261.1| RNA polymerase sigma factor, sigma-70 family [Brucella sp. NF 2653]
 gi|62196766|gb|AAX75066.1| RNA polymerase sigma-70 factor family protein [Brucella abortus bv.
           1 str. 9-941]
 gi|82616649|emb|CAJ11731.1| Sigma-70 factor family:Sigma-70 region 2:Sigma-70 region 4
           [Brucella melitensis biovar Abortus 2308]
 gi|148370750|gb|ABQ60729.1| RNA polymerase sigma-70 factor family protein [Brucella ovis ATCC
           25840]
 gi|256000332|gb|ACU48731.1| RNA polymerase factor sigma-32 [Brucella microti CCM 4915]
 gi|260095493|gb|EEW79371.1| sigma-70 factor family protein [Brucella abortus NCTC 8038]
 gi|297174160|gb|EFH33517.1| RNA polymerase sigma-32 factor [Brucella abortus bv. 5 str. B3196]
 gi|306405398|gb|EFM61669.1| RNA polymerase sigma factor, sigma-70 family [Brucella sp. NF 2653]
          Length = 311

 Score =  246 bits (629), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 119/293 (40%), Positives = 185/293 (63%), Gaps = 4/293 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  ++          +   I      P LE++EE  LA R++E  D  A HR+ ++H+RL
Sbjct: 19  MAVRSFPAAAASSQSM---IRSAMSAPYLEREEERALAIRWKETKDQDALHRITSAHMRL 75

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A  +R + LP+S+++ EG +GL++A  +FDP+R  R +TY+ WWI+A+MQ+YILR+
Sbjct: 76  VISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRDVRFSTYASWWIRASMQDYILRN 135

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WS+V+ GT++ QK LFFNLRRL+  L    DN  K E    I+ +L VS S+V  M+ RL
Sbjct: 136 WSIVRGGTSSAQKALFFNLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRL 195

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D SL+A +N  +  +S+  D+LV DH  Q+++     + + R   LTR++  LN RE
Sbjct: 196 SGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTRALDTLNERE 255

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
             I   RRL ++ VTLE L  +  +S+ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 256 LHIIRERRLDDDGVTLEALGEKLGISKERVRQIESRAMEKLKIALLSQHELAA 308


>gi|300812193|ref|ZP_07092635.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus PB2003/044-T3-4]
 gi|300496829|gb|EFK31909.1| RNA polymerase sigma factor RpoD [Lactobacillus delbrueckii subsp.
           bulgaricus PB2003/044-T3-4]
          Length = 378

 Score =  246 bits (629), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 88/274 (32%), Positives = 144/274 (52%), Gaps = 12/274 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY--RGY 71
             +  Y+ EI K+P+L + EE  +AKR  E+GD SA   L  ++LRLVV IA  Y     
Sbjct: 102 DSVRMYLKEIGKVPLLSRDEEVEVAKRI-ENGDESAKDELAAANLRLVVSIAKRYAKHNG 160

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
            + I +++ EGNIGLM+AV KFD  +GF+ +TY+ WWI+ A+   +     +++I     
Sbjct: 161 KMGILDLIQEGNIGLMKAVDKFDYSKGFKFSTYATWWIRQAITRALADQDRMIRIPVHVV 220

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
           +      + R++  LQ   D + KPE++ A   +      E+I++  +    +SL+  + 
Sbjct: 221 ES--INKMNRIQRTLQQDLDRDAKPEELAAEMNEPLQKVQEIITV-AKNQETDSLDKPV- 276

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             ++  SQ  D L  +     +     E  K++ +++      L  RE ++ + R   EN
Sbjct: 277 -GEEGDSQLGDLLEDNKAINPEEYTASEMLKDQLSIMMGEF--LTDREAKVLKLRFGLEN 333

Query: 252 --PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             P TLE +     V+RERVRQIEA+A KK++  
Sbjct: 334 DEPHTLEEVGRSLGVTRERVRQIEAKAVKKLKHH 367


>gi|117618742|ref|YP_854903.1| alternative sigma factor RpoH [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
 gi|117560149|gb|ABK37097.1| alternative sigma factor RpoH [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
          Length = 284

 Score =  246 bits (629), Expect = 2e-63,   Method: Composition-based stats.
 Identities = 108/286 (37%), Positives = 168/286 (58%), Gaps = 9/286 (3%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           ++ M++I  G   L  YI  +  IP+L  +EE  LA+R ++ GDL AA +LV SHLR VV
Sbjct: 6   QRTMALIPQG--SLEGYIQAVNSIPVLSAEEERELAERLQQGGDLEAARQLVMSHLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y GYGLP +++V EGNIGLM+AVK+FDP  G RL ++++ WIKA + EY+LR+W 
Sbjct: 64  HVAKSYAGYGLPQADLVQEGNIGLMKAVKRFDPSVGVRLVSFAVHWIKAEIHEYVLRNWR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L  +       E+V A+A  L VS ++V  M  R++ 
Sbjct: 124 MVKVATTKAQRKLFFNLRKSKKRLGWLNH-----EEVQAVAADLGVSAADVTEMEARMSN 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPRERR 241
            +    L+   ++         + D        IE +   +     L+ +++ L+ R + 
Sbjct: 179 YDQAFDLVGDDEEEGGFAPVHYLEDKSSDLAATIENDNWDDHATRRLSSALATLDERSQH 238

Query: 242 IFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           I  AR L +    TL+ L+  + VS ERVRQ+E  A KK++++++ 
Sbjct: 239 IIRARWLDDESKTTLQELADTYGVSAERVRQLEKNALKKLKDAMEA 284


>gi|291444398|ref|ZP_06583788.1| RNA polymerase principal sigma factor hrdA [Streptomyces
           roseosporus NRRL 15998]
 gi|291347345|gb|EFE74249.1| RNA polymerase principal sigma factor hrdA [Streptomyces
           roseosporus NRRL 15998]
          Length = 395

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 84/301 (27%), Positives = 141/301 (46%), Gaps = 38/301 (12%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY------------------REHGDLS---- 48
                  +Y+ EI +IP+L   EE  LA+R                   R  GDL     
Sbjct: 94  PTSDLFRQYLREIGRIPLLTAAEEVELARRVEAGLFAEERLTGTPDLDSRLAGDLDRLVV 153

Query: 49  ----AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
               A  RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY
Sbjct: 154 MGRTAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTY 213

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + WWI+ AM   +      +++     +  L   + R++  L          E    IA 
Sbjct: 214 ATWWIRQAMSRALADQARTIRVPVHVVE--LINRVVRVQRRLLQERGVEPTAED---IAV 268

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L+++   V  +        SL+A +   +++   + D +    DG     +E       
Sbjct: 269 ELDLTPERVTEVLRLAQEPVSLHAPV--GEEDDVSFGDLI---EDGDAASPVESAAFLLL 323

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           R  L   +S L  RER++ + R   ++  P TLE +   F V+RER+RQIE++   ++++
Sbjct: 324 RQHLEAVLSTLGERERKVVQLRYGLDDGRPRTLEEIGRIFGVTRERIRQIESKTLSRLRD 383

Query: 283 S 283
            
Sbjct: 384 H 384


>gi|192289929|ref|YP_001990534.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodopseudomonas palustris
           TIE-1]
 gi|192283678|gb|ACF00059.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodopseudomonas palustris
           TIE-1]
          Length = 326

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 116/268 (43%), Positives = 163/268 (60%), Gaps = 1/268 (0%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+  I + P+LE  EE  L +R+    D +AA  L+TSHLRL  K+A  YR YG PI ++
Sbjct: 25  YMRAIGRYPVLEPDEEARLWQRWHTARDKAAADVLITSHLRLAAKLARNYRRYGFPIGDL 84

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           ++E N+GLM A+ KFDP RG R AT ++WWI++A+ ++I+RSWSLV+IG T  QK+LFF 
Sbjct: 85  IAEANLGLMMALDKFDPTRGARFATCAVWWIRSAIYDHIVRSWSLVRIGRTPAQKKLFFR 144

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR     L+      L  +    I+  L+V   EVI M  RL+GD SLNA ++  D+ S 
Sbjct: 145 LRGEIRRLRPDHHGALTKDLAEQISTSLDVPLREVIEMEQRLSGDLSLNAPLSDLDE-SG 203

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           +WQD +  D    E +L   +E   +R  L  ++  L+ RER IF AR L + P + E +
Sbjct: 204 EWQDLIADDSPNAEAILAGHDELDRQRGALRDALVQLDARERYIFSARHLGDRPASFEAI 263

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQK 286
                +S ERVRQIEARAF KV  + ++
Sbjct: 264 GQSLSLSAERVRQIEARAFAKVATAARR 291


>gi|256845590|ref|ZP_05551048.1| RNA polymerase sigma factor RpoS [Fusobacterium sp. 3_1_36A2]
 gi|294785121|ref|ZP_06750409.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. 3_1_27]
 gi|256719149|gb|EEU32704.1| RNA polymerase sigma factor RpoS [Fusobacterium sp. 3_1_36A2]
 gi|294486835|gb|EFG34197.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. 3_1_27]
          Length = 418

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 80/285 (28%), Positives = 143/285 (50%), Gaps = 13/285 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           N+      +  +  Y+ EI ++P+L   EE   AK+  E GD  A+ +L+ S+LRLVV I
Sbjct: 137 NLGNSAKVDEPIKMYLREIGQVPLLTHDEEIEYAKKAYE-GDEEASKKLIESNLRLVVSI 195

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  +   GL + +++ EGNIGLM+AV+KF+  +G++ +TY+ WWI+ A+   I      +
Sbjct: 196 AKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTI 255

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I        +   + ++K   +       K      +A++L +   ++ ++        
Sbjct: 256 RIPVH-----MIETINKIKKESRIYLQETGKDASPEILAERLGMEVDKIKAIQEMNQEPI 310

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   + S  +  S+  D++    D +     E   R   R  L   +  L+PRE ++  
Sbjct: 311 SLETPVGS--EEDSELGDFV---EDQKTTSPYEATNRAILREELDAVLKTLSPREEKVLR 365

Query: 245 ARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R   ++  P TLE +   F V+RER+RQIE +A +K++   +K+
Sbjct: 366 YRYGLDDSSPKTLEEVGKIFNVTRERIRQIEVKALRKLRHPSRKK 410


>gi|212711019|ref|ZP_03319147.1| hypothetical protein PROVALCAL_02088 [Providencia alcalifaciens DSM
           30120]
 gi|212686187|gb|EEB45715.1| hypothetical protein PROVALCAL_02088 [Providencia alcalifaciens DSM
           30120]
          Length = 291

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 102/292 (34%), Positives = 168/292 (57%), Gaps = 10/292 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M +   S+ +  +  +  Y+      PML  +EE  LA+R    GDL AA +L+ SHLR 
Sbjct: 1   MTKDMQSLALVPQGSIEAYMRAANAYPMLTAEEEKELAERLHYDGDLEAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VIHIARSYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT +Q++LFFNLR+ K  L          ++V  +A++L VS  +V+ M  R+
Sbjct: 121 WRIVKVATTKSQRKLFFNLRKNKKRLGWFNQ-----DEVNMVAQELGVSTKDVLEMESRM 175

Query: 181 AGD---ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLN 236
           A       ++   +S D          + D        IE +  ++   + L  +++ L+
Sbjct: 176 AAQDMAFDMSDDDDSGDFGGPVAPVLYLQDKASDFANTIEDDNWESHATDRLADALASLD 235

Query: 237 PRERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R + I  AR L ++   TL+ L+ ++ VS ERVRQ+E  A KK++ +++ +
Sbjct: 236 ERSQDIIRARWLDDDNKTTLQELADKYGVSAERVRQLEKNAMKKLRLAMEDE 287


>gi|310777992|ref|YP_003966325.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ilyobacter
           polytropus DSM 2926]
 gi|309747315|gb|ADO81977.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ilyobacter
           polytropus DSM 2926]
          Length = 408

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 77/285 (27%), Positives = 145/285 (50%), Gaps = 13/285 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
            +S  V+ +  +  Y+ EI ++P+L  ++E   AK   E GD  A  +LV ++LRLVV I
Sbjct: 128 TISSGVDVDEPIKMYLREIGQVPLLTHKQEIEHAKNSAE-GDEWATQQLVEANLRLVVSI 186

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  +   GL + +++ EGNIGLM+AV+KF+  +G++ +TY+ WWI+ A+   I      +
Sbjct: 187 AKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTI 246

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I        +   + ++K   +       K      +A++L +   ++ ++        
Sbjct: 247 RIPVH-----MIETINKIKKESRIYLQETGKDATPEVLAERLGMESEKIKAILEMNQDPI 301

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   + S  +  S+  D++    D +     E+  R   +  L   +  L+ RE ++  
Sbjct: 302 SLETPVGS--EEDSELGDFV---EDNKMLSPYEQTNRNLLKEQLDDVLQSLSEREEKVLR 356

Query: 245 ARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R   ++  P TLE +   F+V+RER+RQIE +A +K++   +++
Sbjct: 357 FRYGLDDGCPRTLEEVGKIFKVTRERIRQIEVKALRKLRHPSRRK 401


>gi|262372449|ref|ZP_06065728.1| alternative sigma factor RpoH [Acinetobacter junii SH205]
 gi|262312474|gb|EEY93559.1| alternative sigma factor RpoH [Acinetobacter junii SH205]
          Length = 289

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 111/283 (39%), Positives = 167/283 (59%), Gaps = 8/283 (2%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +S+   G + L  YI  + +IP+L  ++E  LA+RY    DL AA  LV SHLR VV IA
Sbjct: 12  LSLSAPG-VNLGAYISTVNQIPILTAEQEKELAERYYYDQDLDAAKLLVMSHLRFVVHIA 70

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGLP  +++ EGN+GLM+AVK+FDP  G RL ++++ WIKA + EY++R+W +VK
Sbjct: 71  RSYAGYGLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVK 130

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDE 184
           I TT  Q++LFFNLR LK      +   L  E+  +IA  LNV+  +V+ M  RL A D 
Sbjct: 131 IATTKAQRKLFFNLRSLKK-----SSKRLTLEEAQSIANDLNVTPEQVLEMEGRLTAYDA 185

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR-NMLTRSMSVLNPRERRIF 243
           +  A  +  D          + D+      LIE+E+ + +  + L  +M  L+ R R I 
Sbjct: 186 AFEAQGDDDDDTPHTAPALYLEDNRYDPARLIEEEDYEEQSTSALHEAMDQLDDRSRNIL 245

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           + R L ++  TL  L++E+ VS ER+RQ+E  A +K++ ++  
Sbjct: 246 QRRWLDDDKSTLHELAAEYNVSAERIRQLEKNAMEKIKIAMSA 288


>gi|307824539|ref|ZP_07654764.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacter tundripaludum
           SV96]
 gi|307734523|gb|EFO05375.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacter tundripaludum
           SV96]
          Length = 285

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 104/283 (36%), Positives = 178/283 (62%), Gaps = 8/283 (2%)

Query: 6   MSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +++ +N  +G    Y++ +R++P L  ++E  LA ++R+ GDL AA  LV ++LR V+ +
Sbjct: 5   LALPINLSVGTFDAYLNVVRQMPKLTVEQERELALKFRDDGDLEAARELVMTNLRFVIHV 64

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A GY GYGL + +++ EGNIGLM+AVK+FDP+ G RL ++++ WIKA + EY++++W +V
Sbjct: 65  ARGYSGYGLSMPDIIQEGNIGLMKAVKRFDPDVGVRLVSFAVHWIKAEIHEYVIKNWGIV 124

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGD 183
           K+ TT  Q++LFFNLR+ K  L  +++     ++ VAIAK L+V  S V  M  RL + D
Sbjct: 125 KVATTKAQRKLFFNLRKSKQDLGWLSN-----DEAVAIAKDLDVDVSTVYEMEKRLGSRD 179

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLNPRERRI 242
            S +  ++ S + S       ++ H G   VL+E  + + + +++L  +M+ L+ R   I
Sbjct: 180 MSFDMPVDESTEESYVAPASYLHQHGGDPAVLLENSDWEGHEQDLLADAMAELDERSLDI 239

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             +R L +   TL  L+  + VS ER+RQ+E  A KK++ +++
Sbjct: 240 LSSRWLMDKKATLHELAERYNVSAERIRQLEQNAMKKLRAAVE 282


>gi|164687939|ref|ZP_02211967.1| hypothetical protein CLOBAR_01584 [Clostridium bartlettii DSM
           16795]
 gi|164602352|gb|EDQ95817.1| hypothetical protein CLOBAR_01584 [Clostridium bartlettii DSM
           16795]
          Length = 294

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 74/277 (26%), Positives = 142/277 (51%), Gaps = 11/277 (3%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
                +  Y+ EI +  ML   EE  LAK+  E     A    + ++ RLVV IA  YR 
Sbjct: 19  GSSNAMKMYLKEIEEYKMLSAVEEVELAKKVNEEI-PEAKEDFINANYRLVVSIAKKYRK 77

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
             + I +++  GNIGL++AV+K+D  +G++ +TY+ WWIK ++  YI    + ++I    
Sbjct: 78  ENVDILDLIQAGNIGLIKAVEKYDYTKGYKFSTYATWWIKQSITRYIDDCENTIRIPVHL 137

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
           +Q+     +  +K   Q +++   +   +  +A   ++   +VI +  R     SL+  I
Sbjct: 138 HQR-----INFVKRKKQELSNVLQREPSLEELADICDMDVDKVIEILKRDKNVVSLDTPI 192

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-- 248
              +   S   +++  D +    V++ + E+ N +  +   ++ L+ +E+++   R    
Sbjct: 193 K--EDEDSSLVEFIPSDANFS-DVVMHEVEQHNLKEKINELLTGLSEQEQKVLRMRFGLD 249

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            ++P TLE +   F V+RER+RQIEA+A +K++   +
Sbjct: 250 DDDPKTLEEIGKVFGVTRERIRQIEAKAIRKLRHPSR 286


>gi|298242664|ref|ZP_06966471.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297555718|gb|EFH89582.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 394

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 84/275 (30%), Positives = 149/275 (54%), Gaps = 13/275 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  + +Y+ EI + P+L  ++E  +A R   +GD+ A  RLV ++LRLVV IA  Y   G
Sbjct: 123 DNAIRQYLAEIGRFPLLTSEQELTIAWRVA-NGDMEAQKRLVEANLRLVVSIAKRYNNQG 181

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           + + +++ EGN+GL++AV+KFDP+RGFR +TY+ WWI+ A+   +      + +     +
Sbjct: 182 ISLLDLIQEGNLGLIRAVQKFDPQRGFRFSTYATWWIRQAISRAVAEHTRTIHVPVHVVE 241

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
             L + ++R+   L      +  PE    IA+ +N+++  V+ +        SL+A +  
Sbjct: 242 --LIYKMKRITRQLYQDLGRDPFPE---EIAQAINLTKERVVELQSIAEAPISLDAPLI- 295

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            +       D L    D       E    +  R+ ++R++  L+ RER++ E R    + 
Sbjct: 296 -EDEQYHLADML---EDTHAAAPAEVVTHQVLRDHISRALETLSQRERQVIELRYGLYDG 351

Query: 253 --VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              TLE LS+ F+++RER+RQIE +A + ++  IQ
Sbjct: 352 YCHTLEELSAYFKLTRERIRQIEVKALRTLRHPIQ 386


>gi|161505889|ref|YP_001573001.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. arizonae
           serovar 62:z4,z23:-- str. RSK2980]
 gi|160867236|gb|ABX23859.1| hypothetical protein SARI_04068 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 284

 Score =  246 bits (629), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 108/289 (37%), Positives = 161/289 (55%), Gaps = 8/289 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +     L  YI      PML   EE  LA+R    GDL AA  L+ SHLR 
Sbjct: 1   MTKEMQNLALAPVGNLESYIRAANAWPMLSADEERALAERLHYQGDLEAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKAKQRLGWFNQ-----DEVEMVARELGVSSKDVREMESRM 175

Query: 181 -AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE-ERKNRRNMLTRSMSVLNPR 238
            A D + +   +    +        + D        IE +   +   N LT +M  L+ R
Sbjct: 176 AAQDMTFDMSSDDESDSQPMAPVLYLQDKSSNFADGIEDDNWEEQAANRLTDAMQGLDER 235

Query: 239 ERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + I  AR L E+   TL+ L+  + VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 SQDIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 284


>gi|261344963|ref|ZP_05972607.1| alternative sigma factor RpoH [Providencia rustigianii DSM 4541]
 gi|282567106|gb|EFB72641.1| alternative sigma factor RpoH [Providencia rustigianii DSM 4541]
          Length = 291

 Score =  246 bits (628), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 103/291 (35%), Positives = 169/291 (58%), Gaps = 10/291 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M +   S+ +  +  +  YI      PML  +EE  LA+R    GDL AA +L+ SHLR 
Sbjct: 1   MTKDMQSLALVPQGSIEAYIRAANTYPMLSAEEEKELAERLHYDGDLEAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VIHIARSYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT +Q++LFFNLR+ K  L          ++V  +A++L VS  +V+ M  R+
Sbjct: 121 WRIVKVATTKSQRKLFFNLRKNKKRLGWFNQ-----DEVDMVAQELGVSTKDVLEMESRM 175

Query: 181 AGD---ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLN 236
           A       ++   +S D          + D        IE +  ++   + L+ +++ L+
Sbjct: 176 AAQDMAFDMSDDDDSGDFGGPIAPVLYLQDKSSDFAGSIEDDNWESHATDRLSDALASLD 235

Query: 237 PRERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R + I  AR L ++   TL+ L+ ++ VS ERVRQ+E  A KK++ ++++
Sbjct: 236 ERSQDIIRARWLDDDSKTTLQELADKYGVSAERVRQLEKNAMKKLRLAMEE 286


>gi|212703179|ref|ZP_03311307.1| hypothetical protein DESPIG_01221 [Desulfovibrio piger ATCC 29098]
 gi|212673445|gb|EEB33928.1| hypothetical protein DESPIG_01221 [Desulfovibrio piger ATCC 29098]
          Length = 364

 Score =  246 bits (628), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 109/287 (37%), Positives = 170/287 (59%), Gaps = 7/287 (2%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
              G   L  Y+ E+ + PML+ +EE+ LA R R+H D  AA RLV+SHLRLVV+IAM +
Sbjct: 79  STGGRDSLQLYLREVSRFPMLKPEEEHELAVRVRDHNDPDAAFRLVSSHLRLVVRIAMDF 138

Query: 69  RGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           +   +  + ++V EGN+GLM+AV KFDP++G + + Y+ +WIKA + ++I+ +W +VKIG
Sbjct: 139 QRRWMQNVLDLVQEGNVGLMRAVNKFDPDKGIKFSYYASFWIKAYILKFIMDNWRMVKIG 198

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESL 186
           TT  Q++LF+NL R +  L A             ++++L VSE ++  M+ RLA  D SL
Sbjct: 199 TTQVQRKLFYNLNRERQKLIA----QGFDPDAAMLSERLGVSEEQITEMDQRLAANDLSL 254

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           NA +   D   +   D+L     G E  L + E  +  R  L   +  LN +E  I + R
Sbjct: 255 NAQVG-EDAGGATRMDFLPALGPGIEDSLGDSEVAELLREKLKTILPKLNEKELYILQNR 313

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
            L ++PVTL  +   + V+RERVRQ+EAR  +K+++ +   ++  S 
Sbjct: 314 LLTDDPVTLREIGERYNVTRERVRQLEARLLEKIRQHLALDIKDFSD 360


>gi|254525091|ref|ZP_05137146.1| alternative sigma factor RpoH [Stenotrophomonas sp. SKA14]
 gi|219722682|gb|EED41207.1| alternative sigma factor RpoH [Stenotrophomonas sp. SKA14]
          Length = 291

 Score =  246 bits (628), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 111/276 (40%), Positives = 168/276 (60%), Gaps = 8/276 (2%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           I +    L  YI  + +IP+L   +E  LA+R+R+  DL AA  LV SHLR VV +A GY
Sbjct: 16  IPSALGSLDAYIGAVHQIPVLSVDDEQDLARRFRDGNDLDAARELVHSHLRFVVHVARGY 75

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGL + +++ EGNIGLM+AVK+FDP+ G RL ++++ WI+A M E+IL++W +VK+ T
Sbjct: 76  NGYGLALGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAVHWIRAEMHEFILKNWRIVKVAT 135

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN 187
           T  Q++LFFNLR+ K  L       +   +V A+AK LNVSE EV+ M  RL+G D   +
Sbjct: 136 TKAQRKLFFNLRKSKTRLGW-----MNAAEVSAVAKDLNVSEREVMEMESRLSGRDIGFD 190

Query: 188 ALINSSDKN-SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           A  +  +++       +LV + +         +   N+  +L   ++ L+ R R I   R
Sbjct: 191 APTDEDNEHAPPSPAAFLVANDEDPSMAYERADSEDNQMQLLREGLAELDARSRDIIRRR 250

Query: 247 RLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L  ++ VTL+ L+ E+ VS ER+RQ+EA A KK++
Sbjct: 251 WLDADSKVTLQELADEYGVSAERIRQVEANALKKMK 286


>gi|253997181|ref|YP_003049245.1| RNA polymerase sigma-32 subunit RpoH [Methylotenera mobilis JLW8]
 gi|253983860|gb|ACT48718.1| RNA polymerase, sigma 32 subunit, RpoH [Methylotenera mobilis JLW8]
          Length = 285

 Score =  246 bits (628), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 118/286 (41%), Positives = 171/286 (59%), Gaps = 7/286 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M       ++     L +Y   I+  P+L  +EE  LA R+++  DL AA +L+ SHLRL
Sbjct: 1   MTNALTVPVLTAADSLDQYTRAIKAYPILSAEEELTLANRFKKENDLEAARQLIVSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  IA GY GYGLP ++++ EGNIGLM+AVK+FDPERG RL +++M WIKA + EYI+R+
Sbjct: 61  VASIARGYMGYGLPQADLIQEGNIGLMKAVKRFDPERGVRLVSFAMHWIKAEIHEYIVRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W LVKI TT  Q++LFFNLR +K  +     N ++  ++  IA++LNV   EV+ M  RL
Sbjct: 121 WRLVKIATTKAQRKLFFNLRSMKTGI-----NTMQTSEIDHIARELNVKPEEVLEMESRL 175

Query: 181 AGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            G E SL + I+   +       +L  +     + L  K+        L  +++ L+ R 
Sbjct: 176 NGHEISLESNIDDDSEEHYSPIAYLQDESLTPPEALEAKQFEMAETTGLASALNHLDERS 235

Query: 240 RRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           RR+ EAR LQE+   TL  L+ EF VS ER+RQIE +A  K++  +
Sbjct: 236 RRVVEARWLQEDASKTLHELADEFGVSAERIRQIEQKAMLKMKTLM 281


>gi|50084493|ref|YP_046003.1| RNA polymerase factor sigma-32 [Acinetobacter sp. ADP1]
 gi|49530469|emb|CAG68181.1| sigma H (sigma 32) factor of RNA polymerase [Acinetobacter sp.
           ADP1]
          Length = 289

 Score =  246 bits (628), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 109/284 (38%), Positives = 167/284 (58%), Gaps = 9/284 (3%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +S+   G + L  YI  + +IP+L  ++E  LA+RY    DL AA  LV SHLR VV IA
Sbjct: 11  LSLSAPG-VNLGAYISTVNQIPILTAEQEKELAERYYYDQDLDAAKMLVMSHLRFVVHIA 69

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGLP  +++ EGN+GLM+AVK+FDP  G RL ++++ WIKA + EY++R+W +VK
Sbjct: 70  RSYAGYGLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVK 129

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           I TT  Q++LFFNLR LK   + +T      E+  +IA  LNV+  +V+ M  RL   ++
Sbjct: 130 IATTKAQRKLFFNLRSLKKSSKKLT-----LEEAQSIANDLNVTPEQVLEMEGRLTAYDA 184

Query: 186 LNALINSSDKNSSQWQDWLVYDHDG--QEQVLIEKEERKNRRN-MLTRSMSVLNPRERRI 242
                   D +SS      +Y  D       L E ++ + + +  L  +M+ L+ R R I
Sbjct: 185 AFETQGDDDDDSSTHVAPALYLEDNRYDPARLAENDDYEEQSSTALHEAMNQLDDRSRNI 244

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + R L ++  TL  L++E+ VS ER+RQ+E  A +K++ ++  
Sbjct: 245 LQRRWLDDDKSTLHELAAEYNVSAERIRQLEKNAMEKIKVAMSA 288


>gi|68536164|ref|YP_250869.1| RNA polymerase sigma factor [Corynebacterium jeikeium K411]
 gi|68263763|emb|CAI37251.1| RNA polymerase sigma factor A [Corynebacterium jeikeium K411]
          Length = 544

 Score =  246 bits (628), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 77/319 (24%), Positives = 151/319 (47%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------REHGDL- 47
            RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR              +E G+  
Sbjct: 231 ARKDAELTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYAAYRLQEIKESGEKL 289

Query: 48  ----------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 290 SPMHRRDLREIDRDGRRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 349

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 350 KFDYVKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 407

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +A++++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 408 REPTPE---ELAREMDITVDKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 459

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  + + R    +  P TL+ +   + V+RER+
Sbjct: 460 AVVAVDAVSFTLLQDQLQDVLHTLSEREAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERI 519

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 520 RQIESKTMSKLRHPSRSQV 538


>gi|237816135|ref|ZP_04595131.1| RNA polymerase sigma factor, sigma-70 family [Brucella abortus str.
           2308 A]
 gi|237788798|gb|EEP63010.1| RNA polymerase sigma factor, sigma-70 family [Brucella abortus str.
           2308 A]
          Length = 319

 Score =  246 bits (628), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 119/293 (40%), Positives = 185/293 (63%), Gaps = 4/293 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  ++          +   I      P LE++EE  LA R++E  D  A HR+ ++H+RL
Sbjct: 27  MAVRSFPAAAASSQSM---IRSAMSAPYLEREEERALAIRWKETKDQDALHRITSAHMRL 83

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A  +R + LP+S+++ EG +GL++A  +FDP+R  R +TY+ WWI+A+MQ+YILR+
Sbjct: 84  VISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRDVRFSTYASWWIRASMQDYILRN 143

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WS+V+ GT++ QK LFFNLRRL+  L    DN  K E    I+ +L VS S+V  M+ RL
Sbjct: 144 WSIVRGGTSSAQKALFFNLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRL 203

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D SL+A +N  +  +S+  D+LV DH  Q+++     + + R   LTR++  LN RE
Sbjct: 204 SGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTRALDTLNERE 263

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
             I   RRL ++ VTLE L  +  +S+ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 264 LHIIRERRLDDDGVTLEALGEKLGISKERVRQIESRAMEKLKIALLSQHELAA 316


>gi|78224050|ref|YP_385797.1| sigma 32 (RpoH) [Geobacter metallireducens GS-15]
 gi|78195305|gb|ABB33072.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter metallireducens
           GS-15]
          Length = 279

 Score =  246 bits (628), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 118/280 (42%), Positives = 179/280 (63%), Gaps = 7/280 (2%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
            M++ V  +   + Y+ EIRK P+L  +EE++ A ++ E  DL AAHRL+T++LR VVK+
Sbjct: 2   TMNLPVVAD-SFTLYLAEIRKFPVLTPEEEHLYAVKFYEEKDLEAAHRLITANLRFVVKV 60

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y+ YG+ + +++ EGNIGLM AV+KFDP +G RL +Y++WWI+A +Q YI+ +WSL+
Sbjct: 61  AAEYKSYGMKMLDLIQEGNIGLMMAVRKFDPHKGIRLISYAVWWIRAYIQNYIISAWSLL 120

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           KIGTT  QK+LFF L + K  ++ +T  +       A A  L+V ESEVI M+ R+ GD 
Sbjct: 121 KIGTTQAQKKLFFKLNQAKNAIRRLTGGD----DTEATALSLHVKESEVIEMDQRMRGDY 176

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL+A +   D       D LV +   QE+ L E++E       +T+++  LN +ER + E
Sbjct: 177 SLDAELV--DGEGLTMLDTLVDERQNQEEALAEQQEASRLHGQVTQALERLNEKERYVVE 234

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            R   + P+TL+ ++  F +SRERVRQIE  A KK++  +
Sbjct: 235 NRVTADEPLTLQEIADHFAISRERVRQIEEGALKKIKAYL 274


>gi|148272828|ref|YP_001222389.1| RNA polymerase sigma factor [Clavibacter michiganensis subsp.
           michiganensis NCPPB 382]
 gi|147830758|emb|CAN01698.1| RNA polymerase principal sigma factor [Clavibacter michiganensis
           subsp. michiganensis NCPPB 382]
          Length = 492

 Score =  246 bits (628), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 72/311 (23%), Positives = 137/311 (44%), Gaps = 38/311 (12%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR------------------------ 40
           + +I       +  Y+ +I K+ +L   EE  LA R                        
Sbjct: 185 STTITGATADPVKDYLKQIGKVALLNAAEEVELAMRIEAGLFAEDKLANTPGISRELERE 244

Query: 41  --YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
             +       A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G
Sbjct: 245 LRWVARDGQRAKSHLLGANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEKFDYTKG 304

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           F+ +TY+ WWI+ A+   +      ++I     +  +   L R++  +         PE 
Sbjct: 305 FKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE- 361

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              ++++L+++  +VI +        SL+  +   +   S++ D +    D +  V  + 
Sbjct: 362 --ELSRELDMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDTEAVVPADA 414

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARA 276
                 +  L   +  L+ RE  +   R    +  P TL+ +   F V+RER+RQIE++ 
Sbjct: 415 VGFTMLQKQLESLLDSLSEREAGVIRMRFGLGDGMPKTLDQIGDTFGVTRERIRQIESKT 474

Query: 277 FKKVQESIQKQ 287
             K++   + Q
Sbjct: 475 MAKLRHPSRSQ 485


>gi|90023234|ref|YP_529061.1| RNA polymerase factor sigma-32 [Saccharophagus degradans 2-40]
 gi|89952834|gb|ABD82849.1| CheW protein [Saccharophagus degradans 2-40]
          Length = 284

 Score =  246 bits (628), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 105/274 (38%), Positives = 164/274 (59%), Gaps = 7/274 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L+ YI  +  + +L  +EE  LA+      +L AA ++V +HLR VV IA  Y GYGL 
Sbjct: 16  NLNAYIQTVNGVAVLTAEEEKALAEDLYYRDNLDAARKMVMAHLRFVVHIAKSYSGYGLS 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            S+++ EGN+GLM+AVK+F+PE+G RL ++++ WIKA + E+ILR+W +VKI TT  Q++
Sbjct: 76  QSDLIQEGNVGLMKAVKRFNPEKGVRLVSFAVHWIKAEIHEFILRNWRIVKIATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSS 193
           LFFNLR  K  L  +T++     +  A+A+ LNV    V  M  RLA  D + +A  +  
Sbjct: 136 LFFNLRGQKKRLAWLTNS-----EAEAVAQDLNVDVKHVREMEGRLASFDATFDAGADED 190

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEER-KNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
           D  + Q     + D       L+E E+  +N  + LT ++  L+ R R I + R L ++ 
Sbjct: 191 DDTAYQAPANYLEDRRYDPSTLLEDEDWTENSVSGLTTALESLDDRSRDILQQRWLSDDK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            TL +L++++ VS ER+RQ+E  A KKV+  ++ 
Sbjct: 251 STLHDLAAQYGVSAERIRQLEKNAMKKVKTYLEA 284


>gi|116514228|ref|YP_813134.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Lactobacillus delbrueckii subsp. bulgaricus ATCC
           BAA-365]
 gi|116093543|gb|ABJ58696.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Lactobacillus delbrueckii subsp. bulgaricus ATCC
           BAA-365]
          Length = 378

 Score =  246 bits (628), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 89/275 (32%), Positives = 144/275 (52%), Gaps = 14/275 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY--RGY 71
             +  Y+ EI K+P+L + EE  +AKR + +GD SA   L  ++LRLVV IA  Y     
Sbjct: 102 DSVRMYLKEIGKVPLLSRDEEVEVAKRIK-NGDESAKDELAAANLRLVVSIAKRYAKHNG 160

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
            + I +++ EGNIGLM+AV KFD  +GF+ +TY+ WWI+ A+   +     +++I     
Sbjct: 161 KMGILDLIQEGNIGLMKAVDKFDYSKGFKFSTYATWWIRQAITRALADQDRMIRIPVHVV 220

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
           +      + R++  LQ   D N KPE++ A   +      E+I++  +    +SL+  + 
Sbjct: 221 ES--INKMNRIQRTLQQDLDRNAKPEELAAEMNEPLQKVQEIITV-AKNQETDSLDKSV- 276

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV-LNPRERRIFEARRLQE 250
             ++  SQ  D L    D +     E    +  ++ L+  M   L  RE ++ + R   E
Sbjct: 277 -GEEGDSQLGDLL---EDNKAINPEEYTAFEMLKDQLSGMMGEFLTDREAKVLKLRFGLE 332

Query: 251 N--PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           N  P TLE +     V+RERVRQIE +A KK+++ 
Sbjct: 333 NYEPHTLEEVGRSLGVTRERVRQIEDKAVKKLKQH 367


>gi|283852956|ref|ZP_06370215.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio sp.
           FW1012B]
 gi|283571646|gb|EFC19647.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio sp.
           FW1012B]
          Length = 342

 Score =  246 bits (628), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 108/287 (37%), Positives = 178/287 (62%), Gaps = 8/287 (2%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
            ++    L  Y+ EI K PML+ +EE  LA+R R+ GD  AA RL++SHLRLVVKIAM +
Sbjct: 55  SLSTRDPLHLYLREIGKFPMLKPEEEQELARRVRDLGDQKAAFRLISSHLRLVVKIAMDF 114

Query: 69  RGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           +   +  + +++ EGN+GLM+AV KFDP++G + + Y+ +WIKA + +YI+ +W +VKIG
Sbjct: 115 QRRWMQNVLDLIQEGNVGLMRAVTKFDPDKGIKFSYYAAYWIKAYILKYIMDNWRMVKIG 174

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESL 186
           TT  Q++LF+NL + +  LQ +            +++ LNV+ES+++ M+ RL+G D SL
Sbjct: 175 TTQAQRKLFYNLNKERHRLQTL----GFDPSASQLSQALNVTESDIVEMDQRLSGNDLSL 230

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           +  +   D ++S   D+L     G E++L   E        +      LN +E  + + R
Sbjct: 231 DMTL--GDDSTSTRLDFLPALTPGIEEILAGDEISHQLDKHIQTIRPKLNEKELDLLDNR 288

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
            L ++P TL  + +++ ++RERVRQIEAR  +K++E + +++E  SS
Sbjct: 289 ILSDSPATLREIGAKYGITRERVRQIEARLLEKLKEHLSRRIEDFSS 335


>gi|261754167|ref|ZP_05997876.1| RNA polymerase factor sigma-32 [Brucella suis bv. 3 str. 686]
 gi|261743920|gb|EEY31846.1| RNA polymerase factor sigma-32 [Brucella suis bv. 3 str. 686]
          Length = 293

 Score =  246 bits (628), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 119/293 (40%), Positives = 185/293 (63%), Gaps = 4/293 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  ++          +   I      P LE++EE  LA R++E  D  A HR+ ++H+RL
Sbjct: 1   MAVRSFPAAAASSQSM---IRSAMSAPYLEREEERALAIRWKETKDQDALHRITSAHMRL 57

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A  +R + LP+S+++ EG +GL++A  +FDP+R  R +TY+ WWI+A+MQ+YILR+
Sbjct: 58  VISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRDVRFSTYASWWIRASMQDYILRN 117

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WS+V+ GT++ QK LFFNLRRL+  L    DN  K E    I+ +L VS S+V  M+ RL
Sbjct: 118 WSIVRGGTSSAQKALFFNLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRL 177

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D SL+A +N  +  +S+  D+LV DH  Q+++     + + R   LTR++  LN RE
Sbjct: 178 SGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIAESSIDMERRNCWLTRALDTLNERE 237

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
             I   RRL ++ VTLE L  +  +S+ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 238 LHIIRERRLDDDGVTLEALGEKLGISKERVRQIESRAMEKLKIALLSQHELAA 290


>gi|227549126|ref|ZP_03979175.1| RNA polymerase major sigma subunit [Corynebacterium lipophiloflavum
           DSM 44291]
 gi|227078794|gb|EEI16757.1| RNA polymerase major sigma subunit [Corynebacterium lipophiloflavum
           DSM 44291]
          Length = 520

 Score =  246 bits (628), Expect = 3e-63,   Method: Composition-based stats.
 Identities = 78/325 (24%), Positives = 148/325 (45%), Gaps = 49/325 (15%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY----------------REHG 45
            RK+  +  + +  +  Y+ +I K+ +L+ + E  LAKR                    G
Sbjct: 201 ARKDAQLTASAD-SVRAYLKQIGKVALLDAELEVSLAKRIEAGLYAQHRLDEMERAAAEG 259

Query: 46  DLSAA--------------------HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           D  A                     + L+ ++LRLVV +A  Y G G+   +++ EGN+G
Sbjct: 260 DKEAKLTPAVKRDLRAVARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLG 319

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  
Sbjct: 320 LIRAVEKFDYSKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRE 377

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           L         P     +AK+++++E +V+ +        SL+  I   D+  SQ  D++ 
Sbjct: 378 LLQDLGREPTP---QELAKEMDITEEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI- 431

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFE 263
              D +  V ++       ++ L   +  L+ RE  +   R    +  P TL+ +   + 
Sbjct: 432 --EDSEAVVAVDAVSFTLLQDQLQDVLHTLSEREAGVVRLRFGLTDGMPRTLDEIGQVYG 489

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           V+RER+RQIE++   K++   + QV
Sbjct: 490 VTRERIRQIESKTMSKLRHPSRSQV 514


>gi|168235161|ref|ZP_02660219.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. SL480]
 gi|194737973|ref|YP_002116503.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. CVM19633]
 gi|194713475|gb|ACF92696.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. CVM19633]
 gi|197291332|gb|EDY30684.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Schwarzengrund str. SL480]
          Length = 284

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 108/289 (37%), Positives = 161/289 (55%), Gaps = 8/289 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +     L  YI      PML   EE  LA+R    GDL AA  L+ SHLR 
Sbjct: 1   MTKEMQNLALAPVGNLESYIRAANAWPMLSADEERALAERLHYQGDLEAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVEMVARELGVSSKDVREMESRM 175

Query: 181 -AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE-ERKNRRNMLTRSMSVLNPR 238
            A D + +   +    +        + D        IE +   +   N LT +M  L+ R
Sbjct: 176 AAQDMTFDMSSDDESDSQPMAPVLYLQDKSSNFADGIEDDNWEEQAANRLTDAMQGLDER 235

Query: 239 ERRIFEARRLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + I  AR L E+   TL+ L+  + VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 SQDIIRARWLDEDTKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 284


>gi|313837136|gb|EFS74850.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL037PA2]
 gi|314927842|gb|EFS91673.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL044PA1]
 gi|314971907|gb|EFT16005.1| RNA polymerase sigma factor RpoD [Propionibacterium acnes HL037PA3]
          Length = 370

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 76/318 (23%), Positives = 143/318 (44%), Gaps = 41/318 (12%)

Query: 2   NRKNMSIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRY------------------ 41
           +    +++V G     +  Y+ +I K+ +L   EE  LAKR                   
Sbjct: 57  DEPEQTVMVAGATADPVKDYLKQIGKVALLNAVEEVDLAKRIEAGLFAGEQLADPDAKIP 116

Query: 42  -REHGDLS--------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
            ++  D          A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 117 EKDREDYEWIAEDGKVAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEK 176

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWIK A+   +      ++I     +  +   L R++  +      
Sbjct: 177 FDYTKGYKFSTYATWWIKQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGR 234

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE    +A +L+++  +VI +        SL+  +   +   S++ D +    D + 
Sbjct: 235 EPTPE---ELANELDMTAEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEA 286

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVR 270
            V  +       +  L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 287 IVPADAVNFTLLQEQLHDVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIR 346

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 347 QIESKTMSKLRHPSRSQV 364


>gi|157149048|ref|YP_001456366.1| RNA polymerase factor sigma-32 [Citrobacter koseri ATCC BAA-895]
 gi|157086253|gb|ABV15931.1| hypothetical protein CKO_04887 [Citrobacter koseri ATCC BAA-895]
          Length = 284

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 105/289 (36%), Positives = 164/289 (56%), Gaps = 8/289 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +     L  YI      PML   EE  LA++    GDL AA  L+ SHLR 
Sbjct: 1   MTKEMQNLALAPVGNLESYIRAANAWPMLSADEERALAEKLHYQGDLEAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVEMVARELGVTSKDVREMESRM 175

Query: 181 -AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPR 238
            A D + +   +    +        + D        IE++  +++  N LT +M  L+ R
Sbjct: 176 AAQDMTFDMSSDDESDSQPMAPVLYLQDKTSNFADGIEEDNWEDQAANKLTHAMEGLDER 235

Query: 239 ERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + I  AR L E+   TL+ L+  + VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 SQDIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 284


>gi|74316363|ref|YP_314103.1| sigma-70 factor [Thiobacillus denitrificans ATCC 25259]
 gi|74055858|gb|AAZ96298.1| sigma-70 factor [Thiobacillus denitrificans ATCC 25259]
          Length = 281

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 115/282 (40%), Positives = 176/282 (62%), Gaps = 6/282 (2%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           + MS+ +     L  YI  +   PML  +EE  LA+ + +  DL AA RLV SHLR+VV 
Sbjct: 3   QTMSLPIPAAYSLDSYIQTVSHYPMLSLEEEQKLARAWHDEQDLEAARRLVLSHLRVVVS 62

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y GYGLP ++++ EGN+GLM+AVK+FDP+RG RL ++++ WI+A + EY+L+++ +
Sbjct: 63  IARHYLGYGLPHADLIQEGNVGLMKAVKRFDPDRGVRLVSFALHWIRAEIHEYVLKNYRM 122

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VK+ TT  Q++LFFNLR LK  L A+T      +Q  A+A++LNVS  +V+ M  RL+G 
Sbjct: 123 VKLATTKAQRKLFFNLRSLKQSLNALT-----VQQADAMAQELNVSRKDVLEMETRLSGH 177

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           +     +    ++      +L    +   Q L  ++  + R + LT ++  L+ R R I 
Sbjct: 178 DVSIDPMVDDGEDDYSPIAYLASAEENPAQRLEREQTERLRESGLTSALEELDERSRHII 237

Query: 244 EARRLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +AR L E  V TL  L++++ VS ER+RQIEARA +K++ SI
Sbjct: 238 QARWLSEGDVATLHELAAQYGVSAERIRQIEARALQKMRASI 279


>gi|308232215|ref|ZP_07415319.2| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu001]
 gi|308373480|ref|ZP_07667590.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu005]
 gi|308214639|gb|EFO74038.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu001]
 gi|308337452|gb|EFP26303.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           SUMu005]
          Length = 413

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 79/319 (24%), Positives = 148/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------REHGDL- 47
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+  
Sbjct: 100 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSERGEKL 158

Query: 48  ----------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 159 PAAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 218

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 219 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 276

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 277 REPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 328

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 329 AVVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 388

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 389 RQIESKTMSKLRHPSRSQV 407


>gi|107023748|ref|YP_622075.1| RNA polymerase factor sigma-32 [Burkholderia cenocepacia AU 1054]
 gi|116690835|ref|YP_836458.1| RNA polymerase factor sigma-32 [Burkholderia cenocepacia HI2424]
 gi|170734160|ref|YP_001766107.1| RNA polymerase factor sigma-32 [Burkholderia cenocepacia MC0-3]
 gi|254247164|ref|ZP_04940485.1| Sigma-70 region 2 [Burkholderia cenocepacia PC184]
 gi|105893937|gb|ABF77102.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia cenocepacia AU
           1054]
 gi|116648924|gb|ABK09565.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia cenocepacia
           HI2424]
 gi|124871940|gb|EAY63656.1| Sigma-70 region 2 [Burkholderia cenocepacia PC184]
 gi|169817402|gb|ACA91985.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia cenocepacia
           MC0-3]
          Length = 311

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 118/289 (40%), Positives = 173/289 (59%), Gaps = 12/289 (4%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
            S++      +  YI  + +IP+L  +EE   A  +RE  +L AA RLV SHLRLVV IA
Sbjct: 29  QSMLPGQLGNIDAYIQAVNRIPLLTAEEERRYATEFREDNNLDAARRLVLSHLRLVVSIA 88

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGLP  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W +VK
Sbjct: 89  RNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVK 148

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDE 184
           + TT  Q++LFFNLR  K  +QA+T     PE++  +A++LNV   EV  M  RL  GD 
Sbjct: 149 VATTKAQRKLFFNLRSHKKSMQAMT-----PEEIDGLAQELNVKREEVTEMETRLSGGDI 203

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           +L   +   ++ S     +L   H+    VL  ++    + + + +++  L+ R RRI E
Sbjct: 204 ALEGQVEDGEE-SYAPIAYLADSHNEPTAVLAARQRDMLQTDGIAQALDALDARSRRIIE 262

Query: 245 ARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           AR L          TL +L++EF VS ER+RQIEA A KK++ ++ +  
Sbjct: 263 ARWLHVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRTALAEYA 311


>gi|196232822|ref|ZP_03131672.1| RNA polymerase, sigma 70 subunit, RpoD family [Chthoniobacter
           flavus Ellin428]
 gi|196223021|gb|EDY17541.1| RNA polymerase, sigma 70 subunit, RpoD family [Chthoniobacter
           flavus Ellin428]
          Length = 296

 Score =  246 bits (628), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 85/289 (29%), Positives = 163/289 (56%), Gaps = 16/289 (5%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           MN K+     + + G+  Y+ EI +IP+L  ++E  LA + ++ GD +A   ++ S+LRL
Sbjct: 1   MNYKS---GEDSDSGIKIYLREIGQIPLLTPEQEIELAAKIKK-GDKAARSLMIRSNLRL 56

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VVKIA  Y   GLP+ +++SEGNIGLM+AV++FDP +G +L+TY+ WWIK +++  +   
Sbjct: 57  VVKIAHDYANLGLPLLDLISEGNIGLMKAVERFDPAKGGKLSTYAAWWIKQSIKRALANQ 116

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              +++        L   + +++     +++   +      +A+++ +S  ++  +    
Sbjct: 117 SKTIRLPVH-----LVDKISKMRRVALQMSEELGREPTDDELAEEVGLSSGKISQLKTVS 171

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL+A I  SD +S+++ + +    D +     E+   KN R+ +   + VL+ RE+
Sbjct: 172 IRPASLDAPI--SDDDSTEFGEIV---GDLEALTPFERLRDKNLRDEVGDLLEVLDEREK 226

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +I  +R   +     TLE +  +F V+RER+RQ++  A  K++ ++QK+
Sbjct: 227 KIIFSRFGLDGGKAKTLEEVGKKFGVTRERIRQLQNIALMKLRRALQKK 275


>gi|92115102|ref|YP_575030.1| RNA polymerase factor sigma-32 [Chromohalobacter salexigens DSM
           3043]
 gi|91798192|gb|ABE60331.1| RNA polymerase, sigma 32 subunit, RpoH [Chromohalobacter salexigens
           DSM 3043]
          Length = 288

 Score =  245 bits (627), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 107/271 (39%), Positives = 158/271 (58%), Gaps = 7/271 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ YI  + +I +L  +EE  L  R  E GDL AA RLV SHLR VV IA  Y GYGLP 
Sbjct: 17  LNGYIQAVNRIAVLSSEEERELGFRLYEQGDLEAARRLVMSHLRFVVHIARSYSGYGLPQ 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGN+GLM+AVK+FDP +G RL ++++ WIKA + EY+LR+W +VKI TT  Q++L
Sbjct: 77  ADLIQEGNVGLMKAVKRFDPTQGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKL 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR  K  L  + +     ++V AIAK L+V    V  M  RL+  D   +A  +  +
Sbjct: 137 FFNLRGAKKRLAWLNN-----DEVDAIAKDLDVKPQVVREMEGRLSAFDAGYDATPSEEE 191

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
               Q     + D        +E  +  ++  + L  ++  L+ R R I + R L E+  
Sbjct: 192 DQGYQAPAHYLDDERFDPAAQLEAADWEEDSTHRLQAALGELDERSRDILQRRWLAESKA 251

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           TL  L+  + VS ER+RQ+E  A KK+++ +
Sbjct: 252 TLHELADVYGVSAERIRQLEKNAMKKIKQQL 282


>gi|206559184|ref|YP_002229944.1| RNA polymerase factor sigma-32 [Burkholderia cenocepacia J2315]
 gi|198035221|emb|CAR51095.1| RNA polymerase sigma-32 factor [Burkholderia cenocepacia J2315]
          Length = 311

 Score =  245 bits (627), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 117/289 (40%), Positives = 173/289 (59%), Gaps = 12/289 (4%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
            S++      +  YI  + +IP+L  +EE   A  +R+  +L AA RLV SHLRLVV IA
Sbjct: 29  QSMLPGQLGNIDAYIQAVNRIPLLTAEEERRYATEFRDDNNLDAARRLVLSHLRLVVSIA 88

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGLP  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W +VK
Sbjct: 89  RNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVK 148

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDE 184
           + TT  Q++LFFNLR  K  +QA+T     PE++  +A++LNV   EV  M  RL  GD 
Sbjct: 149 VATTKAQRKLFFNLRSHKKSMQAMT-----PEEIDGLAQELNVKREEVTEMETRLSGGDI 203

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           +L   +   ++ S     +L   H+    VL  ++    + + + +++  L+ R RRI E
Sbjct: 204 ALEGQVEDGEE-SYAPIAYLADSHNEPTAVLAARQRDMLQTDGIAQALDALDARSRRIIE 262

Query: 245 ARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           AR L          TL +L++EF VS ER+RQIEA A KK++ ++ +  
Sbjct: 263 ARWLHVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRTALAEYA 311


>gi|154252145|ref|YP_001412969.1| RNA polymerase sigma-32 subunit RpoH [Parvibaculum lavamentivorans
           DS-1]
 gi|154156095|gb|ABS63312.1| RNA polymerase, sigma 32 subunit, RpoH [Parvibaculum
           lavamentivorans DS-1]
          Length = 298

 Score =  245 bits (627), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 119/283 (42%), Positives = 184/283 (65%), Gaps = 3/283 (1%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           RY+ +   +P+L++Q E+ LA+R+++HGD  A H L  +++RLV+ +A  +R YGLP  +
Sbjct: 15  RYMKQAMTVPLLDEQHEFDLARRWKDHGDEQALHELTCAYMRLVISLATRFRNYGLPYGD 74

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGN+GLMQA  +F+PERG R +TY+ WWI+AA+Q+YILR+WS+V+ GTTA  K LFF
Sbjct: 75  LIQEGNVGLMQAAARFEPERGVRFSTYASWWIRAAIQDYILRNWSIVRTGTTAAHKSLFF 134

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR-LAGDESLNALINS--SD 194
           NLRRL+  +   T  NL  +  + IAK+L V  S+V +++ R + GD SLNA ++   S 
Sbjct: 135 NLRRLRALIANGTRQNLTEDDRIFIAKRLGVGASDVATIDARLMTGDRSLNATVSDSTSS 194

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
           +N ++WQD L  +    E+ ++E  + K R   +  ++  LN RE  I   RRL+++  T
Sbjct: 195 ENLTEWQDLLPCERPLPEEEVMENHDSKQRSRWIEGALESLNERELTIIRERRLRDDVAT 254

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLL 297
           LE L     +S+ERVRQIE  A KK++ ++  +V    +  LL
Sbjct: 255 LETLGVRLGISKERVRQIEHMALKKLRTALLDKVPDPEAAGLL 297


>gi|16762736|ref|NP_458353.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. CT18]
 gi|16766854|ref|NP_462469.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhimurium str. LT2]
 gi|29144223|ref|NP_807565.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. Ty2]
 gi|62182067|ref|YP_218484.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Choleraesuis str. SC-B67]
 gi|161616616|ref|YP_001590580.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Paratyphi B str. SPB7]
 gi|167549215|ref|ZP_02342974.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA29]
 gi|167990783|ref|ZP_02571882.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar 4,[5],12:i:- str. CVM23701]
 gi|168232714|ref|ZP_02657772.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Kentucky str. CDC 191]
 gi|168241719|ref|ZP_02666651.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL486]
 gi|168260704|ref|ZP_02682677.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Hadar str. RI_05P066]
 gi|168465152|ref|ZP_02699044.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Newport str. SL317]
 gi|168818616|ref|ZP_02830616.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Weltevreden str. HI_N05-537]
 gi|194443524|ref|YP_002042813.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Newport str. SL254]
 gi|194449082|ref|YP_002047593.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL476]
 gi|194469731|ref|ZP_03075715.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Kentucky str. CVM29188]
 gi|197250526|ref|YP_002148491.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Agona str. SL483]
 gi|197265856|ref|ZP_03165930.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA23]
 gi|198244039|ref|YP_002217526.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Dublin str. CT_02021853]
 gi|200387614|ref|ZP_03214226.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Virchow str. SL491]
 gi|204928638|ref|ZP_03219837.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Javiana str. GA_MM04042433]
 gi|205354814|ref|YP_002228615.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 287/91]
 gi|207858806|ref|YP_002245457.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Enteritidis str. P125109]
 gi|213426834|ref|ZP_03359584.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. E02-1180]
 gi|213619347|ref|ZP_03373173.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-2068]
 gi|213649997|ref|ZP_03380050.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. J185]
 gi|213857359|ref|ZP_03384330.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. M223]
 gi|224585360|ref|YP_002639159.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
 gi|238910431|ref|ZP_04654268.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Tennessee str. CDC07-0191]
 gi|289829445|ref|ZP_06547057.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-3139]
 gi|25288476|pir||AB0992 RNA polymerase sigma-32 factor [imported] - Salmonella enterica
           subsp. enterica serovar Typhi (strain CT18)
 gi|16422128|gb|AAL22428.1| sigma H factor of RNA polymerase [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|16505042|emb|CAD08062.1| RNA polymerase sigma-32 factor [Salmonella enterica subsp. enterica
           serovar Typhi]
 gi|29139860|gb|AAO71425.1| RNA polymerase sigma-32 factor [Salmonella enterica subsp. enterica
           serovar Typhi str. Ty2]
 gi|62129700|gb|AAX67403.1| sigma H (sigma 32) factor of RNA polymerase; transcription of heat
           shock proteins induced by cytoplasmic stress [Salmonella
           enterica subsp. enterica serovar Choleraesuis str.
           SC-B67]
 gi|161365980|gb|ABX69748.1| hypothetical protein SPAB_04433 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|194402187|gb|ACF62409.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Newport str. SL254]
 gi|194407386|gb|ACF67605.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL476]
 gi|194456095|gb|EDX44934.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Kentucky str. CVM29188]
 gi|195632472|gb|EDX50956.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Newport str. SL317]
 gi|197214229|gb|ACH51626.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Agona str. SL483]
 gi|197244111|gb|EDY26731.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA23]
 gi|197938555|gb|ACH75888.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Dublin str. CT_02021853]
 gi|199604712|gb|EDZ03257.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Virchow str. SL491]
 gi|204322071|gb|EDZ07269.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Javiana str. GA_MM04042433]
 gi|205274595|emb|CAR39645.1| RNA polymerase sigma-32 factor [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 287/91]
 gi|205325609|gb|EDZ13448.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Saintpaul str. SARA29]
 gi|205330694|gb|EDZ17458.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar 4,[5],12:i:- str. CVM23701]
 gi|205333102|gb|EDZ19866.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Kentucky str. CDC 191]
 gi|205338892|gb|EDZ25656.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Heidelberg str. SL486]
 gi|205344405|gb|EDZ31169.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Weltevreden str. HI_N05-537]
 gi|205350317|gb|EDZ36948.1| alternative sigma factor RpoH [Salmonella enterica subsp. enterica
           serovar Hadar str. RI_05P066]
 gi|206710609|emb|CAR34967.1| RNA polymerase sigma-32 factor [Salmonella enterica subsp. enterica
           serovar Enteritidis str. P125109]
 gi|224469888|gb|ACN47718.1| RNA polymerase sigma factor [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
 gi|261248721|emb|CBG26559.1| RNA polymerase sigma-32 factor [Salmonella enterica subsp. enterica
           serovar Typhimurium str. D23580]
 gi|267995798|gb|ACY90683.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhimurium str. 14028S]
 gi|301160107|emb|CBW19627.1| RNA polymerase sigma-32 factor [Salmonella enterica subsp. enterica
           serovar Typhimurium str. SL1344]
 gi|312914591|dbj|BAJ38565.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhimurium str. T000240]
 gi|320087978|emb|CBY97740.1| RNA polymerase sigma-32 factor Heat shock regulatory protein F33.4
           [Salmonella enterica subsp. enterica serovar Weltevreden
           str. 2007-60-3289-1]
 gi|321226618|gb|EFX51668.1| RNA polymerase sigma factor RpoH [Salmonella enterica subsp.
           enterica serovar Typhimurium str. TN061786]
 gi|322614066|gb|EFY11002.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 315996572]
 gi|322617958|gb|EFY14851.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-1]
 gi|322625428|gb|EFY22254.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-3]
 gi|322629893|gb|EFY26666.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 495297-4]
 gi|322632218|gb|EFY28969.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 515920-1]
 gi|322636431|gb|EFY33138.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 515920-2]
 gi|322643092|gb|EFY39666.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 531954]
 gi|322644713|gb|EFY41249.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. NC_MB110209-0054]
 gi|322651265|gb|EFY47649.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. OH_2009072675]
 gi|322652822|gb|EFY49161.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. CASC_09SCPH15965]
 gi|322659124|gb|EFY55376.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 19N]
 gi|322663174|gb|EFY59378.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 81038-01]
 gi|322668661|gb|EFY64814.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. MD_MDA09249507]
 gi|322674536|gb|EFY70629.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 414877]
 gi|322678259|gb|EFY74320.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 366867]
 gi|322682485|gb|EFY78506.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 413180]
 gi|322684198|gb|EFY80204.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 446600]
 gi|322716555|gb|EFZ08126.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Choleraesuis str. A50]
 gi|323131927|gb|ADX19357.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhimurium str. 4/74]
 gi|323192247|gb|EFZ77479.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 609458-1]
 gi|323196326|gb|EFZ81478.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 556150-1]
 gi|323201872|gb|EFZ86935.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 609460]
 gi|323206415|gb|EFZ91376.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 507440-20]
 gi|323212008|gb|EFZ96835.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 556152]
 gi|323216913|gb|EGA01636.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB101509-0077]
 gi|323222313|gb|EGA06696.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB102109-0047]
 gi|323224327|gb|EGA08616.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB110209-0055]
 gi|323228255|gb|EGA12386.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. MB111609-0052]
 gi|323233477|gb|EGA17570.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 2009083312]
 gi|323237061|gb|EGA21128.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 2009085258]
 gi|323243724|gb|EGA27740.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. 315731156]
 gi|323246034|gb|EGA30021.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2009159199]
 gi|323250810|gb|EGA34688.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008282]
 gi|323255821|gb|EGA39571.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008283]
 gi|323261903|gb|EGA45470.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008284]
 gi|323267705|gb|EGA51187.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008285]
 gi|323268585|gb|EGA52052.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Montevideo str. IA_2010008287]
 gi|326625307|gb|EGE31652.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Dublin str. 3246]
 gi|326629958|gb|EGE36301.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Gallinarum str. 9]
 gi|332990419|gb|AEF09402.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhimurium str. UK-1]
          Length = 284

 Score =  245 bits (627), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 108/289 (37%), Positives = 161/289 (55%), Gaps = 8/289 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +     L  YI      PML   EE  LA+R    GDL AA  L+ SHLR 
Sbjct: 1   MTKEMQNLALAPVGNLESYIRAANAWPMLSADEERALAERLHYQGDLEAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVEMVARELGVSSKDVREMESRM 175

Query: 181 -AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE-ERKNRRNMLTRSMSVLNPR 238
            A D + +   +    +        + D        IE +   +   N LT +M  L+ R
Sbjct: 176 AAQDMTFDMSSDDESDSQPMAPVLYLQDKSSNFADGIEDDNWEEQAANRLTDAMQGLDER 235

Query: 239 ERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + I  AR L E+   TL+ L+  + VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 SQDIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 284


>gi|115352926|ref|YP_774765.1| RNA polymerase factor sigma-32 [Burkholderia ambifaria AMMD]
 gi|170701101|ref|ZP_02892077.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           IOP40-10]
 gi|172061774|ref|YP_001809426.1| RNA polymerase factor sigma-32 [Burkholderia ambifaria MC40-6]
 gi|115282914|gb|ABI88431.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           AMMD]
 gi|170134002|gb|EDT02354.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           IOP40-10]
 gi|171994291|gb|ACB65210.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           MC40-6]
          Length = 311

 Score =  245 bits (627), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 116/290 (40%), Positives = 174/290 (60%), Gaps = 12/290 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
             S++      +  YI  + +IP+L  +EE   A  +RE  +L +A RLV SHLRLVV I
Sbjct: 28  TQSMLPGQLGNIDAYIQAVNRIPLLTAEEERRYATEFREDNNLDSARRLVLSHLRLVVSI 87

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y GYGLP  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W +V
Sbjct: 88  ARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPTQNVRLVSYAIHWIKAEIHEYILRNWRMV 147

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGD 183
           K+ TT  Q++LFFNLR  K  +QA+T     PE++  +A++LNV   +V  M  RL  GD
Sbjct: 148 KVATTKAQRKLFFNLRSHKKSMQAMT-----PEEIDGLAQELNVKREDVTEMETRLSGGD 202

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            +L   ++  ++ S     +L   H+    VL  ++    + + + +++  L+ R RRI 
Sbjct: 203 IALEGQVDDGEE-SYAPIAYLADSHNEPSAVLAARQRDMLQTDGIAQALEALDARSRRII 261

Query: 244 EARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           EAR L          TL +L++EF VS ER+RQIEA A KK++ ++ +  
Sbjct: 262 EARWLNVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRTALAEYA 311


>gi|227495524|ref|ZP_03925840.1| sigma factor [Actinomyces coleocanis DSM 15436]
 gi|226831071|gb|EEH63454.1| sigma factor [Actinomyces coleocanis DSM 15436]
          Length = 505

 Score =  245 bits (627), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 71/304 (23%), Positives = 140/304 (46%), Gaps = 39/304 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY----------REHGDLS--------------- 48
             +  Y+ +I K+ +L   +E  LA+R           +  GD                 
Sbjct: 206 DPVKDYLKQIGKVSLLTAADEVDLARRIEAGLYAEHKIKTEGDELPSKLRRELQILVHDG 265

Query: 49  --AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             + + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 266 QLSKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYAT 325

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +  +   L R++  +         PE    +AK+L
Sbjct: 326 WWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKEL 380

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  +V+ +        SL+  +   +   S++ D +    D +  V  +       + 
Sbjct: 381 DMTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDSEAIVPTDAVSFTLLQE 435

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L + +  L+ RE  +   R    +  P TL+ +   + V+RER+RQIE++   K++   
Sbjct: 436 QLHKVLDTLSEREAGVVSMRFGLGDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPS 495

Query: 285 QKQV 288
           + QV
Sbjct: 496 RSQV 499


>gi|154498377|ref|ZP_02036755.1| hypothetical protein BACCAP_02366 [Bacteroides capillosus ATCC
           29799]
 gi|150272688|gb|EDM99866.1| hypothetical protein BACCAP_02366 [Bacteroides capillosus ATCC
           29799]
          Length = 441

 Score =  245 bits (627), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 80/324 (24%), Positives = 141/324 (43%), Gaps = 47/324 (14%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAK----------RYRE------- 43
           ++   +      +  +  Y+ EI K+ +L   EE  LA+          R  E       
Sbjct: 121 VDPNTLVDSFGIDDPVRMYLKEIGKVNLLNPDEEVQLAQDMGAGDAAKARMAEIEAAEKR 180

Query: 44  ------------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
                                 +A  RL  ++LRLVV IA  Y G G+   +++ EGN+G
Sbjct: 181 GEPIVLTPEEEKALKKDIRRGEAAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNLG 240

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I     +      + R+   
Sbjct: 241 LIKAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE--TINKVIRVSRQ 298

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           L     ++  PE    IA+++N+   +V  +        SL   I   ++  S   D++ 
Sbjct: 299 LLQELGHDPSPE---EIAEEMNMPVDKVREILKIAQEPVSLETPI--GEEEDSHLGDFIP 353

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFE 263
            +   +     E       +  L   +  L PRE ++ + R   E+    TLE +  EF 
Sbjct: 354 DEDASE---PSEAASFTLLKEQLVDVLGTLTPREEKVLKLRFGIEDGRTRTLEEVGKEFN 410

Query: 264 VSRERVRQIEARAFKKVQESIQKQ 287
           V+RER+RQIEA+A +K++   + +
Sbjct: 411 VTRERIRQIEAKALRKLRHPSRSK 434


>gi|300781032|ref|ZP_07090886.1| RNA polymerase sigma factor rpoD [Corynebacterium genitalium ATCC
           33030]
 gi|300532739|gb|EFK53800.1| RNA polymerase sigma factor rpoD [Corynebacterium genitalium ATCC
           33030]
          Length = 536

 Score =  245 bits (627), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 78/325 (24%), Positives = 150/325 (46%), Gaps = 49/325 (15%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY----------------REHG 45
            RK+  +  + +  +  Y+ +I K+ +L+ ++E  LAKR                  + G
Sbjct: 217 ARKDAQLTASAD-SVRAYLKQIGKVALLDAEQEVSLAKRIEAGLYAQHRLDEMQRAADEG 275

Query: 46  DLSAA--------------------HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           D  A                     + L+ ++LRLVV +A  Y G G+   +++ EGN+G
Sbjct: 276 DKDAKLTPAVKRDLRAVARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLG 335

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  
Sbjct: 336 LIRAVEKFDYSKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRE 393

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           L         P     +AK+++++E +V+ +        SL+  I   D+  SQ  D++ 
Sbjct: 394 LLQDLGREPTP---QELAKEMDITEEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI- 447

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFE 263
              D +  V ++       ++ L   +  L+ RE  +   R    +  P TL+ +   + 
Sbjct: 448 --EDSEAVVAVDAVSFTLLQDQLQDVLHTLSEREAGVVRLRFGLTDGMPRTLDEIGQVYG 505

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           V+RER+RQIE++   K++   + QV
Sbjct: 506 VTRERIRQIESKTMSKLRHPSRSQV 530


>gi|325686024|gb|EGD28082.1| DNA-directed RNA polymerase sigma subunit RpoD [Lactobacillus
           delbrueckii subsp. lactis DSM 20072]
          Length = 378

 Score =  245 bits (627), Expect = 4e-63,   Method: Composition-based stats.
 Identities = 90/275 (32%), Positives = 144/275 (52%), Gaps = 14/275 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY--RGY 71
             +  Y+ EI K+P+L + EE  +AKR  E+GD SA   L  ++LRLVV IA  Y     
Sbjct: 102 DSVRMYLKEIGKVPLLSRDEEVEVAKRI-ENGDESAKDELAAANLRLVVSIAKRYAKHNG 160

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
            + I +++ EGNIGLM+AV KFD  +GF+ +TY+ WWI+ A+   +     +++I     
Sbjct: 161 KMGILDLIQEGNIGLMKAVDKFDYSKGFKFSTYATWWIRQAITRALADQDRMIRIPVHVV 220

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
           +      + R++  LQ   D + KPE++ A   +      E+I++  +    +SL+  + 
Sbjct: 221 ES--INKMNRIQRILQQDLDRDAKPEELAAEMNEPLQKVQEIITV-AKNQETDSLDKPV- 276

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV-LNPRERRIFEARRLQE 250
             ++  SQ  D L    D +     E    +  ++ L+  M   L  RE ++ + R   E
Sbjct: 277 -GEEGDSQLGDLL---EDNKATNPEEYTAFEMLKDQLSSMMGEFLTNREAKVLKLRFGLE 332

Query: 251 N--PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           N  P TLE +     V+RERVRQIEA+A KK++  
Sbjct: 333 NDEPHTLEEVGRSLGVTRERVRQIEAKAVKKLKHH 367


>gi|253581343|ref|ZP_04858569.1| DNA-directed RNA polymerase sigma subunit RpoD [Fusobacterium
           varium ATCC 27725]
 gi|251836707|gb|EES65241.1| DNA-directed RNA polymerase sigma subunit RpoD [Fusobacterium
           varium ATCC 27725]
          Length = 414

 Score =  245 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 81/285 (28%), Positives = 145/285 (50%), Gaps = 13/285 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           N+S  +  +  +  Y+ EI +IP+L   EE   AKR  E GD  A+ +L+ ++LRLVV I
Sbjct: 134 NLSGDMKVDEPIKMYLREIGQIPLLSHDEELEYAKRALE-GDEWASKQLIEANLRLVVSI 192

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  +   GL + +++ EGNIGLM+AV+KF+  +G++ +TY+ WWI+ A+   I      +
Sbjct: 193 AKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYSKGYKFSTYATWWIRQAITRAIADQGRTI 252

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I        +   + ++K   +       K      + ++L +   +V ++        
Sbjct: 253 RIPVH-----MIETINKIKKEARIYLQETGKDATPEVLGERLGMEVDKVKAIQEMNQDPI 307

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   + S  +  S+  D++    D +     E   R   R  L   ++ L+ RE R+  
Sbjct: 308 SLETPVGS--EEDSELGDFV---EDHKMLNPYELTNRSLLREQLNGVLNTLSSREERVLR 362

Query: 245 ARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R   ++  P TLE +   F+V+RER+RQIE +A +K++   +++
Sbjct: 363 YRYGLDDGSPKTLEEVGKIFKVTRERIRQIEVKALRKLRHPSRRK 407


>gi|83718896|ref|YP_441014.1| RNA polymerase factor sigma-32 [Burkholderia thailandensis E264]
 gi|167579742|ref|ZP_02372616.1| RNA polymerase factor sigma-32 [Burkholderia thailandensis TXDOH]
 gi|167617818|ref|ZP_02386449.1| RNA polymerase factor sigma-32 [Burkholderia thailandensis Bt4]
 gi|257140333|ref|ZP_05588595.1| RNA polymerase factor sigma-32 [Burkholderia thailandensis E264]
 gi|83652721|gb|ABC36784.1| RNA polymerase sigma-32 factor [Burkholderia thailandensis E264]
          Length = 311

 Score =  245 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 121/288 (42%), Positives = 170/288 (59%), Gaps = 12/288 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S++      +  YI  + +IP+L  +EE   A  YRE   L AA RLV SHLRLVV IA 
Sbjct: 30  SMLPGQLGNIDAYIQAVNRIPLLTAEEERQYATEYREQNSLDAARRLVLSHLRLVVSIAR 89

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y GYGLP  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W +VK+
Sbjct: 90  NYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKV 149

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDES 185
            TT  Q++LFFNLR  K   QA T     PE++  +A++LNV   EV  M  RL  GD +
Sbjct: 150 ATTKAQRKLFFNLRSHKKGTQAFT-----PEEIDGLAQELNVKREEVAEMETRLSGGDIA 204

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L   I+  ++ S     +L   H+    VL  ++    + + + R++  L+ R RRI EA
Sbjct: 205 LEGQIDDGEE-SYAPIAYLADSHNEPTAVLAARQRDMLQTDGIARALDSLDARSRRIIEA 263

Query: 246 RRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           R L          TL +L++EF VS ER+RQIEA A KK++ ++    
Sbjct: 264 RWLNVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRTALAAYA 311


>gi|301644085|ref|ZP_07244098.1| alternative sigma factor RpoH [Escherichia coli MS 146-1]
 gi|301077566|gb|EFK92372.1| alternative sigma factor RpoH [Escherichia coli MS 146-1]
          Length = 283

 Score =  245 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 100/285 (35%), Positives = 160/285 (56%), Gaps = 10/285 (3%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           K MS++      L  YI      PML ++EE  LA   + H DL AA +L+ SHLR V+ 
Sbjct: 3   KEMSVLAP-VGNLDSYIRAAYACPMLSQEEEQQLASNLQIHDDLDAAKQLILSHLRFVIH 61

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y GYGLP ++++ EGNIGLM+AV++F+P+ G RL ++++ W+K+ + EY+LR+W +
Sbjct: 62  IARQYSGYGLPQADLIQEGNIGLMKAVRRFNPDVGVRLVSFAVHWVKSEIHEYVLRNWRI 121

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R++  
Sbjct: 122 VKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVDMVARELGVSVKDVREMESRMSAQ 176

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQ---VLIEKEERKNRRNMLTRSMSVLNPRER 240
           +    +    + ++       +Y  D       ++ E        + L  +M  L+PR +
Sbjct: 177 DMAYDIYPDDETDTHHPVSPSLYLQDKSSDFAGMIEEDNWDAQATDHLVAAMETLDPRSQ 236

Query: 241 RIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            I  AR L ++   TL  L+  + +S ERVRQ+E  A KK++ +I
Sbjct: 237 DIIRARWLDDDNKATLHELAERYGISAERVRQLENNAMKKLRSAI 281


>gi|223041647|ref|ZP_03611844.1| RNA polymerase sigma-32 factor [Actinobacillus minor 202]
 gi|223017511|gb|EEF15925.1| RNA polymerase sigma-32 factor [Actinobacillus minor 202]
          Length = 321

 Score =  245 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 104/281 (37%), Positives = 163/281 (58%), Gaps = 9/281 (3%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           NM +       L  YI    + P+L   +E  LA+RY    D+ AA +L+ SH+R V+ I
Sbjct: 45  NMPVTTG---NLESYIRMANQYPILTADQEKELAERYYYDEDVEAAKQLILSHMRFVIHI 101

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A GY GYGLP+++++ EGNIGLM+AVK+FDP  G RL ++++ W+KA + EY+LR+W +V
Sbjct: 102 ARGYLGYGLPLADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWVKAEIHEYVLRNWRIV 161

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-D 183
           K+ TT  Q++LFFNLR+ K  L    +     E++  +A  L VSE EV  M  R+ G D
Sbjct: 162 KVATTKAQRKLFFNLRKNKNRLAWFNE-----EEIKRVAHDLGVSEEEVREMESRMTGQD 216

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
              +      +  +     +L  +       L ++E        L  ++S L+ R + I 
Sbjct: 217 LGFDLPSGDDEDEAYTPSMYLEDNSSNFADELEDEEHTGEATAQLAYALSTLDERSQDII 276

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + R L EN +TL +L++++++S ERVRQ+E  A KK++ +I
Sbjct: 277 KTRWLDENKLTLHDLAAKYQISAERVRQLENAALKKIKNAI 317


>gi|256061796|ref|ZP_05451931.1| RNA polymerase factor sigma-32 [Brucella neotomae 5K33]
          Length = 311

 Score =  245 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 118/293 (40%), Positives = 185/293 (63%), Gaps = 4/293 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  ++          +   I      P LE++EE  LA R++E  D  A HR+ ++H+RL
Sbjct: 19  MAVRSFPAAAASSQSM---IRSAMSAPYLEREEERALAIRWKETKDQDALHRITSAHMRL 75

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A  +R + LP+S+++ EG +GL++A  +FDP+R  R +TY+ WWI+A+MQ+YILR+
Sbjct: 76  VISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRDVRFSTYAFWWIRASMQDYILRN 135

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WS+V+ GT++ QK LFFNLRRL+  L    DN  K E    I+ +L VS S++  M+ RL
Sbjct: 136 WSIVRGGTSSAQKALFFNLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDIEFMDSRL 195

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D SL+A +N  +  +S+  D+LV DH  Q+++     + + R   LTR++  LN RE
Sbjct: 196 SGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTRALDTLNERE 255

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
             I   RRL ++ VTLE L  +  +S+ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 256 LHIIRERRLDDDGVTLEALGEKLGISKERVRQIESRAMEKLKIALLSQHELAA 308


>gi|297559739|ref|YP_003678713.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
 gi|296844187|gb|ADH66207.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
          Length = 364

 Score =  245 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 78/301 (25%), Positives = 130/301 (43%), Gaps = 36/301 (11%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREH------------------GDL 47
           +G   +  Y+ EI ++P+L  ++E  LAK      Y +H                     
Sbjct: 65  SGSDLVRLYLREIGRVPLLSAEQEVELAKAVEVGLYAQHCAPVEGVRTAEELACLVEEGR 124

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   L+ ++LRLVV IA  Y G GL + ++V EGN+GL++AV+KFD  +GF+ +TY+ W
Sbjct: 125 RAKRSLIEANLRLVVSIAKRYMGRGLLLLDLVQEGNLGLIRAVEKFDYGKGFKFSTYATW 184

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I     +      + ++      +     +   V  I+    
Sbjct: 185 WIRQAITRAIADQARTIRIPVHMVE-----TINKVVRVQHQLHQQLGREPSVEEISSAAG 239

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
                V+ +        SL + I   + +   +        D      +E       +  
Sbjct: 240 FVGQRVVEIQRIAREPVSLQSPIGEEESDFGDFI------EDSDAVAPVEAAAFTVLQEQ 293

Query: 228 LTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L   +  L+ RERRI   R      +P TLE +  EF V+RER+RQIEA+   K++   +
Sbjct: 294 LGAILGGLSDRERRIIRLRFGMADGHPHTLEEVGREFGVTRERIRQIEAKTLAKLRHPSR 353

Query: 286 K 286
            
Sbjct: 354 A 354


>gi|167561467|ref|ZP_02354383.1| RNA polymerase factor sigma-32 [Burkholderia oklahomensis EO147]
 gi|167568698|ref|ZP_02361572.1| RNA polymerase factor sigma-32 [Burkholderia oklahomensis C6786]
          Length = 311

 Score =  245 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 119/289 (41%), Positives = 171/289 (59%), Gaps = 12/289 (4%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
            S++      +  YI  + +IP+L  +EE   A  YR+  +L AA +LV SHLRLVV IA
Sbjct: 29  QSMLPGQLGNIDAYIQAVNRIPLLTPEEERQYATEYRDGNNLDAARQLVLSHLRLVVSIA 88

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGLP  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W +VK
Sbjct: 89  RNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVK 148

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDE 184
           + TT  Q++LFFNLR  K   QA T     PE++  +A++LNV   EV  M  RL  GD 
Sbjct: 149 VATTKAQRKLFFNLRSHKKGTQAFT-----PEEIDGLAQELNVKREEVAEMETRLSGGDI 203

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           +L   I+  ++ S     +L   H+    VL  ++    + + + R++  L+ R RRI E
Sbjct: 204 ALEGQIDDGEE-SYAPIAYLADSHNEPTAVLAARQRDMLQTDGIARALESLDARSRRIIE 262

Query: 245 ARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           AR L          TL +L++EF VS ER+RQIEA A KK++ ++    
Sbjct: 263 ARWLNVGDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRTALAAYA 311


>gi|167835356|ref|ZP_02462239.1| RNA polymerase factor sigma-32 [Burkholderia thailandensis MSMB43]
          Length = 311

 Score =  245 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 118/289 (40%), Positives = 171/289 (59%), Gaps = 12/289 (4%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
            S++      +  YI  + ++P+L  +EE   A  YRE  +L AA +LV SHLRLVV +A
Sbjct: 29  YSMLPGQLGNIDAYIQAVNRVPLLTAEEERQYATEYREQNNLDAARQLVLSHLRLVVSVA 88

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGLP  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W +VK
Sbjct: 89  RNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVK 148

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDE 184
           + TT  Q++LFFNLR  K   QA T     PE++  +A++LNV   EV  M  RL  GD 
Sbjct: 149 VATTKAQRKLFFNLRSHKKGTQAFT-----PEEIDGLAQELNVKREEVAEMETRLSGGDI 203

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           +L   I+  ++ S     +L   H+    VL  ++    + + + R++  L+ R RRI E
Sbjct: 204 ALEGQIDDGEE-SYAPIAYLADSHNEPTAVLAARQRDMLQTDGIARALESLDARSRRIIE 262

Query: 245 ARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           AR L          TL +L++EF VS ER+RQIEA A KK++ ++    
Sbjct: 263 ARWLNVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRTALAAYA 311


>gi|167585406|ref|ZP_02377794.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ubonensis Bu]
          Length = 311

 Score =  245 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 118/288 (40%), Positives = 173/288 (60%), Gaps = 12/288 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S++      +  YI  + +IP+L  +EE   A  +RE  +L AA RLV SHLRLVV IA 
Sbjct: 30  SMLPGQLGNIDAYIQAVNRIPLLTAEEERRYATEFREQNNLDAARRLVLSHLRLVVSIAR 89

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y GYGLP  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W +VK+
Sbjct: 90  NYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKV 149

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDES 185
            TT  Q++LFFNLR  K  +QA+T     PE++  +A++LNV   EV  M  RL  GD +
Sbjct: 150 ATTKAQRKLFFNLRSHKKGMQAMT-----PEEIDGLAQELNVKREEVTEMETRLSGGDIA 204

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L   +   ++ S     +L   H+    VL  ++    + + + +++  L+ R RRI EA
Sbjct: 205 LEGQVEDGEE-SYAPIAYLADSHNEPTAVLAARQRDMLQTDGIAQALDALDARSRRIIEA 263

Query: 246 RRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           R L          TL +L++EF VS ER+RQIEA A KK++ ++ +  
Sbjct: 264 RWLHVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRTALAEYA 311


>gi|223937956|ref|ZP_03629855.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [bacterium
           Ellin514]
 gi|223893357|gb|EEF59819.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [bacterium
           Ellin514]
          Length = 353

 Score =  245 bits (627), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 88/278 (31%), Positives = 148/278 (53%), Gaps = 13/278 (4%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           +G    + Y+ E+ +  +L  QEE  LAKR ++ GD  A  +++ ++LRLVVKIA  Y  
Sbjct: 79  DGNTAFNLYLREVGQTKLLTPQEEVDLAKRIKK-GDKKAREQMIKANLRLVVKIAREYED 137

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
           YG+P+ ++++EGN+GLM+AV++FDP +G +L+TYS WWIK +++  +      +++    
Sbjct: 138 YGMPLLDLINEGNMGLMKAVERFDPAKGAKLSTYSAWWIKQSIKRALANQSKTIRLPVHV 197

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
             K   F++R+    LQ +       E    +  +L  S  +V  +        SL A +
Sbjct: 198 VDK--LFHMRQASVKLQEVLGREPTDE---ELGDELGFSAQKVAQLRTAAIRPASLEAPL 252

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
              D  +S+  D +    D       E+ E K   +ML   ++ L+PRE  I   R   +
Sbjct: 253 --GDDETSRIADVV---RDETADTPYEQLEEKTNTSMLRELVATLDPREAEILRYRFGLD 307

Query: 251 N--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                TLE +  +F V+RER+RQI+  A  K+++ I+K
Sbjct: 308 GDPERTLEEVGQKFGVTRERIRQIQNVALNKLRKQIEK 345


>gi|302551232|ref|ZP_07303574.1| RNA polymerase sigma factor RpoS [Streptomyces viridochromogenes
           DSM 40736]
 gi|302468850|gb|EFL31943.1| RNA polymerase sigma factor RpoS [Streptomyces viridochromogenes
           DSM 40736]
          Length = 438

 Score =  245 bits (626), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 83/301 (27%), Positives = 136/301 (45%), Gaps = 38/301 (12%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKR----------YREHGDLS------------ 48
                  +Y+ EI ++P+L   EE  LA+R           R   DL             
Sbjct: 137 PSSDLFRQYLREIGRVPLLTAAEEVELARRVEAGLFAEEKLRLAPDLDSQLAVDLDRLVV 196

Query: 49  ----AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
               A  RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY
Sbjct: 197 MGRMAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTY 256

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + WWI+ AM   +      +++     +  L   + R++  +         PE+V A   
Sbjct: 257 ATWWIRQAMSRALADQARTIRVPVHVVE--LINRVVRVQRRMLQERGYEPTPEEVAA--- 311

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            L +    V  +        SL+A +   +++     D +    DG     +E       
Sbjct: 312 HLELPPERVGEVLRLAQEPVSLHAPV--GEEDDVALGDLI---EDGDAASPVESAAFLLL 366

Query: 225 RNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           R  L   +S L  RER++ + R       P TLE +   F V+RER+RQIE++   K+++
Sbjct: 367 REHLEAVLSTLGERERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRD 426

Query: 283 S 283
            
Sbjct: 427 H 427


>gi|254708375|ref|ZP_05170203.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M163/99/10]
 gi|254708771|ref|ZP_05170582.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis B2/94]
 gi|254714614|ref|ZP_05176425.1| RNA polymerase factor sigma-32 [Brucella ceti M644/93/1]
 gi|254717512|ref|ZP_05179323.1| RNA polymerase factor sigma-32 [Brucella ceti M13/05/1]
 gi|256030297|ref|ZP_05443911.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M292/94/1]
 gi|256160470|ref|ZP_05458159.1| RNA polymerase factor sigma-32 [Brucella ceti M490/95/1]
 gi|256255677|ref|ZP_05461213.1| RNA polymerase factor sigma-32 [Brucella ceti B1/94]
 gi|260167971|ref|ZP_05754782.1| RNA polymerase factor sigma-32 [Brucella sp. F5/99]
 gi|261757411|ref|ZP_06001120.1| sigma-70 factor family [Brucella sp. F5/99]
 gi|261737395|gb|EEY25391.1| sigma-70 factor family [Brucella sp. F5/99]
          Length = 311

 Score =  245 bits (626), Expect = 5e-63,   Method: Composition-based stats.
 Identities = 118/293 (40%), Positives = 184/293 (62%), Gaps = 4/293 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  ++          +   I      P LE++EE  LA R++E  D  A HR+ ++H+RL
Sbjct: 19  MAVRSFPAAAASSQSM---IRSAMSAPYLEREEERALAIRWKETKDQDALHRITSAHMRL 75

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A  +R + LP+S+++ EG +GL++A  +FDP+R  R +TY+ WWI+A+MQ+YILR+
Sbjct: 76  VISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRDVRFSTYASWWIRASMQDYILRN 135

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WS+V+ GT++ QK LFFNLRRL+  L    DN  K E    I+ +L VS S+V  M+ RL
Sbjct: 136 WSIVRGGTSSAQKALFFNLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRL 195

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D SL+  +N  +  +S+  D+LV DH  Q+++     + + R   LTR++  LN RE
Sbjct: 196 SGPDSSLSVPMNGEETGASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTRALDTLNERE 255

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
             I   RRL ++ VTLE L  +  +S+ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 256 LHIIRERRLDDDGVTLEALGEKLGISKERVRQIESRAMEKLKIALLSQHELAA 308


>gi|167854819|ref|ZP_02477597.1| RNA polymerase factor sigma-32 [Haemophilus parasuis 29755]
 gi|219871694|ref|YP_002476069.1| RNA polymerase factor sigma-32 [Haemophilus parasuis SH0165]
 gi|167854117|gb|EDS25353.1| RNA polymerase factor sigma-32 [Haemophilus parasuis 29755]
 gi|219691898|gb|ACL33121.1| RNA polymerase factor sigma-32 [Haemophilus parasuis SH0165]
          Length = 315

 Score =  245 bits (626), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 103/279 (36%), Positives = 168/279 (60%), Gaps = 6/279 (2%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           +++V     L  YI    + P+L  ++E  LA+R+    DL AA +L+ SHLR VV IA 
Sbjct: 37  NMLVPQGATLDSYIRMANQYPVLTAEQEKELAERFYYDEDLDAAKQLIMSHLRFVVYIAR 96

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           GY GYGLP+++++ EGNIGLM+AVK+F+PE G RLA++++ W+KA + EY+L++W +VK+
Sbjct: 97  GYLGYGLPLADLIQEGNIGLMKAVKRFNPEIGVRLASFAVHWVKAEIHEYVLKNWRIVKV 156

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DES 185
            TT +Q++LFFNLR+ K  L    +     E++  +A++L VS  +V  M  R+ G D  
Sbjct: 157 ATTKSQRKLFFNLRKNKQRLAWFNE-----EEIRKVAEELGVSTDDVKEMESRMVGQDIG 211

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
            +  +   D ++     +L  +       L  +E        L  +++ L+ R + I + 
Sbjct: 212 FDTSVGDDDDDNYVPSMYLEDESSNFVDELEYEEYSGRATAQLAYALAQLDERSQNIIKT 271

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R L EN  TL  L++++ +S ERVRQ+E +A KK+++ I
Sbjct: 272 RWLDENKATLHELAAQYNISAERVRQLENQALKKIKDVI 310


>gi|38233991|ref|NP_939758.1| RNA polymerase sigma factor [Corynebacterium diphtheriae NCTC
           13129]
 gi|38200253|emb|CAE49937.1| RNA polymerase sigma factor [Corynebacterium diphtheriae]
          Length = 502

 Score =  245 bits (626), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 77/325 (23%), Positives = 150/325 (46%), Gaps = 49/325 (15%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR----------------EHG 45
            RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR                   +G
Sbjct: 183 ARKDAELSASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYATYRMEQMEEAFNNG 241

Query: 46  DLS--------------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           D                      A + L+ ++LRLVV +A  Y G G+   +++ EGN+G
Sbjct: 242 DKEAKLTPAVKRDLRAIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLG 301

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  
Sbjct: 302 LIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRE 359

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           L         P     +AK+++++E +V+ +        SL+  I   D+  SQ  D++ 
Sbjct: 360 LLQDLGREPTP---QELAKEMDITEEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI- 413

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFE 263
              D +  + ++       ++ L   +  L+ RE  + + R    +  P TL+ +   + 
Sbjct: 414 --EDSEAVIAVDAVSFTLLQDQLQDVLHTLSEREAGVVKLRFGLTDGMPRTLDEIGQVYG 471

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           V+RER+RQIE++   K++   + QV
Sbjct: 472 VTRERIRQIESKTMSKLRHPSRSQV 496


>gi|323524659|ref|YP_004226812.1| RNA polymerase sigma-32 subunit RpoH [Burkholderia sp. CCGE1001]
 gi|323381661|gb|ADX53752.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. CCGE1001]
          Length = 311

 Score =  245 bits (626), Expect = 6e-63,   Method: Composition-based stats.
 Identities = 123/284 (43%), Positives = 169/284 (59%), Gaps = 12/284 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S++      +  YI  + +IPML   EE   A  +REH +L AA RLV SHLRLVV IA 
Sbjct: 30  SLLPGQLGNIDAYIQAVNRIPMLTPAEERQFATEFREHDNLEAARRLVLSHLRLVVSIAR 89

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y GYGLP ++++ EGNIGLM+AVK+FDPE+  RL +Y+M WIKA + EYILR+W +VK+
Sbjct: 90  NYLGYGLPHADLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHWIKAEIHEYILRNWRMVKV 149

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDES 185
            TT  Q++LFFNLR  K  L A T     P+++  +AK+LNV   EV  M  RL  GD +
Sbjct: 150 ATTKAQRKLFFNLRSHKQGLGAFT-----PDEIDGLAKELNVKREEVAEMETRLSGGDIA 204

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L   +   ++ S     +L   H     VL  ++  K + + +  ++  L+ R RRI EA
Sbjct: 205 LEGQVEDGEE-SYAPIAYLADSHSEPTAVLASRQRDKLQSDGIATALEALDARSRRIIEA 263

Query: 246 RRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R L          TL  L+ EF VS ER+RQIEA A KK++ ++
Sbjct: 264 RWLKVQDDGSGGSTLHELADEFGVSAERIRQIEASAMKKMRGAL 307


>gi|260755457|ref|ZP_05867805.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 6 str. 870]
 gi|260758679|ref|ZP_05871027.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 4 str. 292]
 gi|260884475|ref|ZP_05896089.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 9 str. C68]
 gi|261214728|ref|ZP_05929009.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 3 str. Tulya]
 gi|261750913|ref|ZP_05994622.1| RNA polymerase factor sigma-32 [Brucella suis bv. 5 str. 513]
 gi|265984775|ref|ZP_06097510.1| RNA polymerase factor sigma-32 [Brucella sp. 83/13]
 gi|294851008|ref|ZP_06791684.1| RNA polymerase sigma-32 factor [Brucella sp. NVSL 07-0026]
 gi|260668997|gb|EEX55937.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 4 str. 292]
 gi|260675565|gb|EEX62386.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 6 str. 870]
 gi|260874003|gb|EEX81072.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 9 str. C68]
 gi|260916335|gb|EEX83196.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 3 str. Tulya]
 gi|261740666|gb|EEY28592.1| RNA polymerase factor sigma-32 [Brucella suis bv. 5 str. 513]
 gi|264663367|gb|EEZ33628.1| RNA polymerase factor sigma-32 [Brucella sp. 83/13]
 gi|294821651|gb|EFG38647.1| RNA polymerase sigma-32 factor [Brucella sp. NVSL 07-0026]
          Length = 293

 Score =  245 bits (626), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 119/293 (40%), Positives = 185/293 (63%), Gaps = 4/293 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  ++          +   I      P LE++EE  LA R++E  D  A HR+ ++H+RL
Sbjct: 1   MAVRSFPAAAASSQSM---IRSAMSAPYLEREEERALAIRWKETKDQDALHRITSAHMRL 57

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A  +R + LP+S+++ EG +GL++A  +FDP+R  R +TY+ WWI+A+MQ+YILR+
Sbjct: 58  VISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRDVRFSTYASWWIRASMQDYILRN 117

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WS+V+ GT++ QK LFFNLRRL+  L    DN  K E    I+ +L VS S+V  M+ RL
Sbjct: 118 WSIVRGGTSSAQKALFFNLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRL 177

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D SL+A +N  +  +S+  D+LV DH  Q+++     + + R   LTR++  LN RE
Sbjct: 178 SGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTRALDTLNERE 237

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
             I   RRL ++ VTLE L  +  +S+ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 238 LHIIRERRLDDDGVTLEALGEKLGISKERVRQIESRAMEKLKIALLSQHELAA 290


>gi|317061552|ref|ZP_07926037.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. D12]
 gi|313687228|gb|EFS24063.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. D12]
          Length = 363

 Score =  245 bits (625), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 81/277 (29%), Positives = 142/277 (51%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI +IP+L  +EE  LAK+  E GD  A  RL+ ++LRLVV IA  +   G
Sbjct: 90  DEPIKMYLREIGQIPLLTHKEELELAKKALE-GDEFANKRLIEANLRLVVSIAKKHTNRG 148

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L + +++ EGNIGLM+AV+KF+  +G++ +TY+ WWI+ A+   I      ++I      
Sbjct: 149 LKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPVH--- 205

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
             +   + ++K   +       K      +A++L +   +V S+        SL   + S
Sbjct: 206 --MIETINKIKKEARIYLQETGKDATPEILAERLGMEVEKVKSIQEMNQDPISLETPVGS 263

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN- 251
             +  S+  D++    D +     E   R   R  L   +  L+ RE ++   R   ++ 
Sbjct: 264 --EEDSELGDFV---EDQKMLTPYELTNRSLLREQLDSVLGSLSSREEKVLRYRYGLDDG 318

Query: 252 -PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            P TLE +   F+V+RER+RQIE +A +K++   +++
Sbjct: 319 SPKTLEEVGKIFKVTRERIRQIEVKALRKLRHPSRRK 355


>gi|30424475|dbj|BAC76410.1| heat shock sigma-32 factor [Colwellia maris]
          Length = 285

 Score =  245 bits (625), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 102/285 (35%), Positives = 166/285 (58%), Gaps = 9/285 (3%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           + M + +     +  Y+     IPML  ++E+ LA R     DLSAA  L+ SHLR V+ 
Sbjct: 3   QAMQLTLPQSGSIEAYMRSAYSIPMLTAEKEHNLATRLYNENDLSAAQELIMSHLRFVIH 62

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           +A GY GYGLP +++V EGN+GLM+AVK+F+PE G RL ++++ WIKA + EY+L++W +
Sbjct: 63  VAKGYSGYGLPHADLVQEGNVGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLKNWRI 122

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VK+ TT  Q++LFFNLR+ K  L   +      E+V  +A+ L V+  +V+ M  R++  
Sbjct: 123 VKVATTKAQRKLFFNLRKNKKRLGWFS-----TEEVNTVAENLGVTTKDVMEMESRMSSY 177

Query: 184 ESLNALINSSDKN---SSQWQDWLVYDHDGQEQVLIEKEERKNRRN-MLTRSMSVLNPRE 239
           +    L    D N   S+      + D      V +E +   N  N  L+ ++  L+ R 
Sbjct: 178 DQAFELSKDDDDNLGASNFSPAQYLQDKQSDLAVEVENDNWDNHANKRLSTALVTLDERS 237

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + I + R L E+  TL+ L++++++S ERVRQ+E  A  K++ ++
Sbjct: 238 QDIIKTRWLTEDKTTLQELANKYQISAERVRQLEKNALSKLKNTM 282


>gi|240948113|ref|ZP_04752523.1| RNA polymerase factor sigma-32 [Actinobacillus minor NM305]
 gi|240297593|gb|EER48085.1| RNA polymerase factor sigma-32 [Actinobacillus minor NM305]
          Length = 321

 Score =  245 bits (625), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 104/281 (37%), Positives = 163/281 (58%), Gaps = 9/281 (3%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           NM +       L  YI    + P+L   +E  LA+RY    D+ AA +L+ SH+R V+ I
Sbjct: 45  NMPVTTG---NLESYIRMANQYPILTADQEKELAERYYYDEDVEAAKQLILSHMRFVIHI 101

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A GY GYGLP+++++ EGNIGLM+AVK+FDP  G RL ++++ W+KA + EY+LR+W +V
Sbjct: 102 ARGYLGYGLPLADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWVKAEIHEYVLRNWRIV 161

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-D 183
           K+ TT  Q++LFFNLR+ K  L    +     E++  +A  L VSE EV  M  R+ G D
Sbjct: 162 KVATTKAQRKLFFNLRKNKNRLAWFNE-----EEIKRVAHDLGVSEEEVREMESRMTGQD 216

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
              +      +  +     +L  +       L ++E        L  ++S L+ R + I 
Sbjct: 217 LGFDLPSGDDEDEAYTPSMYLEDNSSNFADELEDEEHTGEATAQLAYALSTLDERSQDII 276

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + R L EN +TL +L++++++S ERVRQ+E  A KK++ +I
Sbjct: 277 KTRWLDENKLTLHDLAAKYQISAERVRQLENAALKKIKNAI 317


>gi|171320177|ref|ZP_02909239.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           MEX-5]
 gi|171094591|gb|EDT39643.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           MEX-5]
          Length = 311

 Score =  245 bits (625), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 116/288 (40%), Positives = 174/288 (60%), Gaps = 12/288 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S++      +  YI  + +IP+L  +EE   A  +RE  +L +A RLV SHLRLVV IA 
Sbjct: 30  SMLPGQLGNIDAYIQAVNRIPLLTAEEERRYATEFREDNNLDSARRLVLSHLRLVVSIAR 89

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y GYGLP  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W +VK+
Sbjct: 90  NYLGYGLPHGDLIQEGNIGLMKAVKRFDPTQNVRLVSYAIHWIKAEIHEYILRNWRMVKV 149

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDES 185
            TT  Q++LFFNLR  K  +QA+T     PE++  +A++LNV   +V  M  RL  GD +
Sbjct: 150 ATTKAQRKLFFNLRSHKKSMQAMT-----PEEIDGLAQELNVKREDVTEMETRLSGGDIA 204

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L   ++  ++ S     +L   H+    VL  ++    + + + +++  L+ R RRI EA
Sbjct: 205 LEGQVDDGEE-SYAPIAYLADSHNEPSAVLAARQRDMLQTDGIAQALEALDARSRRIIEA 263

Query: 246 RRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           R L          TL +L++EF VS ER+RQIEA A KK++ ++ +  
Sbjct: 264 RWLNVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRTALAEYA 311


>gi|328955627|ref|YP_004372960.1| RNA polymerase, sigma 70 subunit, RpoD [Coriobacterium glomerans
           PW2]
 gi|328455951|gb|AEB07145.1| RNA polymerase, sigma 70 subunit, RpoD [Coriobacterium glomerans
           PW2]
          Length = 442

 Score =  245 bits (625), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 83/314 (26%), Positives = 141/314 (44%), Gaps = 42/314 (13%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR---------------------- 42
           + S ++     +  Y+ EI K+ +L   +E  LA +                        
Sbjct: 130 DASTVMLTGDPVRMYLKEIGKVDLLTAADEVDLAMKIEAGLEAAEKLESSDRGEIALTRA 189

Query: 43  --------EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                   E   L A   L++++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD
Sbjct: 190 DMRRLSRIEQVGLEAKQALISANLRLVVSIAKRYVGRGMHFLDLIQEGNLGLIRAVEKFD 249

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
            E+GF+ +TY+ WWI+ A+   I      ++I     +      L R++  L      + 
Sbjct: 250 YEKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE--TINKLVRVQRQLLQELGRDP 307

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            PE++ A   ++ +S   V  +        SL   I   ++  SQ  D++    D Q  V
Sbjct: 308 TPEEIGA---EMEMSADRVREIQKISQEPVSLETPI--GEEEDSQLGDFI---EDAQAVV 359

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQI 272
             +       R  L + +  L  RER++ E R      +P TLE +  +F V+RER+RQI
Sbjct: 360 PPDAASFSMLREQLVQVLDSLADRERKVIELRFGLNDGHPRTLEEVGRDFGVTRERIRQI 419

Query: 273 EARAFKKVQESIQK 286
           E++   K++   + 
Sbjct: 420 ESKTLAKLRHPSRS 433


>gi|260771645|ref|ZP_05880565.1| RNA polymerase sigma-32 factor [Vibrio metschnikovii CIP 69.14]
 gi|260613422|gb|EEX38621.1| RNA polymerase sigma-32 factor [Vibrio metschnikovii CIP 69.14]
          Length = 285

 Score =  245 bits (625), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 113/288 (39%), Positives = 170/288 (59%), Gaps = 10/288 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  +   + +  +  L  YI  +   PML  +EE  LA+R    GD+ AA  L+ SHLR 
Sbjct: 1   MTNQAYPMALISQDSLDSYIRSVSSYPMLTAEEERELAERLHYSGDIEAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A GY GYGLPI+++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARGYSGYGLPIADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VKI TT  Q++LFFNLR+ K  L    +      +V  +A++L V  +EV  M  RL
Sbjct: 121 WRIVKIATTKAQRKLFFNLRKSKKRLGWFNNG-----EVETVARELGVEPAEVREMESRL 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM----LTRSMSVLN 236
           A  +S        D N + +   ++Y  D Q   L E  E +N  N     L+ +++ L+
Sbjct: 176 AALDSTFEFSAEDDDNPNAYTAPVLYLEDKQSD-LAENIEAQNWENHTNHRLSLALASLD 234

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            R + I  +R L +   TL+ L+  ++VS ER+RQ+E  A KK++E++
Sbjct: 235 ERSQHIVRSRWLDDQKATLQELADLYQVSAERIRQLEKNAMKKLKEAV 282


>gi|296135250|ref|YP_003642492.1| RNA polymerase, sigma 32 subunit, RpoH [Thiomonas intermedia K12]
 gi|294339349|emb|CAZ87705.1| RNA polymerase sigma-32 factor (Heat shock regulatory protein
           F33.4) [Thiomonas sp. 3As]
 gi|295795372|gb|ADG30162.1| RNA polymerase, sigma 32 subunit, RpoH [Thiomonas intermedia K12]
          Length = 302

 Score =  245 bits (625), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 112/284 (39%), Positives = 163/284 (57%), Gaps = 10/284 (3%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
             + +     L  YI  + ++PML  +EE  LA+ +RE GD  AA +LV SHLRLVV  A
Sbjct: 20  FPLALPSLGNLDAYISAVNRLPMLSAEEEARLARTWREQGDKDAAGKLVLSHLRLVVSTA 79

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGLP ++++ EGNIGLM+AVK+FDP  G RL +Y++ WIKA + EYILR+W LVK
Sbjct: 80  RQYLGYGLPHADLIQEGNIGLMKAVKRFDPAHGVRLVSYALHWIKAEIHEYILRNWRLVK 139

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           + TT +Q++LFFNLR +K       +  +   Q+  +A+ LNV   +VI M  R+ G + 
Sbjct: 140 VATTKSQRKLFFNLRSMKT-----ANAGMNEAQIDDMAQALNVKREDVIEMESRMGGADI 194

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
                    + S     +L  +      VL  +   + +   L  ++ +L+ R R I E 
Sbjct: 195 ALDPTVEDGEESYAPISYLADNTQEPMAVLEARSHDRLQVEGLENALELLDARSRAIVEQ 254

Query: 246 RRLQENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R LQ N       TL  L++E+ VS ER+RQIE  A KK+++S+
Sbjct: 255 RWLQVNDDGSGGKTLHELAAEYGVSAERIRQIEVAAMKKMRKSL 298


>gi|120556648|ref|YP_960999.1| RNA polymerase factor sigma-32 [Marinobacter aquaeolei VT8]
 gi|120326497|gb|ABM20812.1| RNA polymerase, sigma 32 subunit, RpoH [Marinobacter aquaeolei VT8]
          Length = 286

 Score =  245 bits (625), Expect = 7e-63,   Method: Composition-based stats.
 Identities = 105/269 (39%), Positives = 156/269 (57%), Gaps = 7/269 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  YI    +IP+L   EE  LA+R   HGD+ AA +LV SHLR V+ IA  Y GYGL 
Sbjct: 16  NLESYIQAASRIPVLSVDEERELAERLHYHGDVEAARQLVLSHLRFVIHIARSYAGYGLA 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++
Sbjct: 76  QADLIQEGNVGLMKAVKRFNPEYGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSS 193
           LFFNLR  K  L  +  + LK     A+A  L V    V  M  RLA  D + +  ++  
Sbjct: 136 LFFNLRSQKKKLAWLNHDELK-----AVANDLGVEPHVVREMEGRLASQDTAFDGPMDDD 190

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN-MLTRSMSVLNPRERRIFEARRLQENP 252
           + N+ Q   + + D      V +E  +     N  L +++  L+ R + I   R L E+ 
Sbjct: 191 EDNAYQAPAYYLEDRRSDPAVQLENADWSEDSNGRLMQALEQLDERSQDILRERWLSESK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TL  L+ ++ VS ER+RQ+E  A KK++
Sbjct: 251 STLHELADKYGVSAERIRQLEKNAMKKIR 279


>gi|149909450|ref|ZP_01898105.1| RNA polymerase sigma factor [Moritella sp. PE36]
 gi|149807560|gb|EDM67509.1| RNA polymerase sigma factor [Moritella sp. PE36]
          Length = 287

 Score =  245 bits (625), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 107/290 (36%), Positives = 170/290 (58%), Gaps = 11/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M++   S+ +  +  +  YI  +  IPML  ++E  L +R +  GD+ AA +L+ SHLR 
Sbjct: 1   MSKDMQSMALVPQGSIEAYIQGVNNIPMLTAEQEKELGERLQNEGDVDAARQLIMSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A GY GYGL  ++++ EGNIGLM+AVK+F+PE G RL ++++ W+KA + E++LR+
Sbjct: 61  VVHVARGYAGYGLAQADLIQEGNIGLMKAVKRFNPEVGVRLVSFAVHWVKAEIHEFVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L   T       +V  +A+ L VS  +V+ M  R+
Sbjct: 121 WRVVKVATTKAQRKLFFNLRKSKKRLGWFT-----SAEVKTVAETLGVSTKDVVEMESRM 175

Query: 181 AGDE---SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM---LTRSMSV 234
           +  +    L A  +S   + S       Y  D    V ++ E     ++    LT ++S 
Sbjct: 176 SYSDQAFDLYADDDSDKDSGSTSFSPAQYLEDNASDVALQVERENWDKSASLSLTNAISE 235

Query: 235 LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L+ R + I ++R L E+  TL+ L+  + VS ERVRQ+E  A KK++E I
Sbjct: 236 LDERSQDIVKSRWLAEDKATLQYLADRYGVSAERVRQLEKNAMKKLREFI 285


>gi|221195781|ref|ZP_03568834.1| RNA polymerase sigma factor RpoD [Atopobium rimae ATCC 49626]
 gi|221184255|gb|EEE16649.1| RNA polymerase sigma factor RpoD [Atopobium rimae ATCC 49626]
          Length = 455

 Score =  245 bits (625), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 82/314 (26%), Positives = 140/314 (44%), Gaps = 42/314 (13%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR---------------------- 42
           + S ++     +  Y+ EI K+ +L   EE  LA +                        
Sbjct: 143 DTSTVMLTGDPVRMYLKEIGKVDLLTASEEVNLAMKIEAGTEATQKLEDFEDEKIELSRA 202

Query: 43  --------EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                   E   L A  +L++++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD
Sbjct: 203 EQRRLMRIEQVGLDAKQQLISANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFD 262

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +GF+ +TY+ WWI+ A+   I      ++I     +      L R++  L      + 
Sbjct: 263 YTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE--TINKLIRVQRQLLQDLGRDP 320

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            PE++ A   ++ +S   V  +        SL   I   ++  SQ  D++    D     
Sbjct: 321 TPEEIGA---EMGMSPDRVREIQKISQEPVSLETPI--GEEEDSQLGDFI---EDSTAIA 372

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
             +       R  L + +  L  RER++ + R   E+  P TLE +  EF V+RER+RQI
Sbjct: 373 PPDAASDSMLREQLEQVLDGLADRERKVIKFRFGLEDGRPRTLEEVGREFGVTRERIRQI 432

Query: 273 EARAFKKVQESIQK 286
           E++   K++   + 
Sbjct: 433 ESKTLAKLRHPSRS 446


>gi|194367438|ref|YP_002030048.1| RNA polymerase factor sigma-32 [Stenotrophomonas maltophilia
           R551-3]
 gi|194350242|gb|ACF53365.1| RNA polymerase, sigma 32 subunit, RpoH [Stenotrophomonas
           maltophilia R551-3]
          Length = 291

 Score =  245 bits (625), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 111/276 (40%), Positives = 171/276 (61%), Gaps = 8/276 (2%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           I +    L  YI  + +IP+L   +E  LA+R+R+  DL AA  LV SHLR VV +A GY
Sbjct: 16  IPSALGSLDAYIGAVHQIPVLSVDDEQDLARRFRDGNDLDAARELVHSHLRFVVHVARGY 75

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGL + +++ EGNIGLM+AVK+FDPE G RL ++++ WI+A M E+IL++W +VK+ T
Sbjct: 76  NGYGLALGDLIQEGNIGLMKAVKRFDPEMGVRLVSFAVHWIRAEMHEFILKNWRIVKVAT 135

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN 187
           T  Q++LFFNLR+ K  L       +   +V A+AK LNVSE EV+ M  RL+G D   +
Sbjct: 136 TKAQRKLFFNLRKSKTRLGW-----MNAAEVSAVAKDLNVSEREVMEMESRLSGRDIGFD 190

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR-NMLTRSMSVLNPRERRIFEAR 246
           A  +  ++++       +  +D    +  E+ + ++ +  +L   ++ L+ R R I   R
Sbjct: 191 APTDEDNEHAPPSPAAYLVANDEDPSMAYERADSEDNQMQLLREGLAELDARSRDIIRRR 250

Query: 247 RLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L  ++ VTL+ L+ E+ VS ER+RQ+EA A KK++
Sbjct: 251 WLDADSKVTLQELADEYGVSAERIRQVEANALKKMK 286


>gi|291451171|ref|ZP_06590561.1| RNA polymerase sigma factor [Streptomyces albus J1074]
 gi|291354120|gb|EFE81022.1| RNA polymerase sigma factor [Streptomyces albus J1074]
          Length = 397

 Score =  245 bits (625), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 79/296 (26%), Positives = 136/296 (45%), Gaps = 39/296 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHG--------------------------DLSA 49
             +Y+ EI +IP+L   +E  LA+R  E G                             A
Sbjct: 102 FRQYLREIGRIPLLSAADEVELARRV-EAGVFAAAKLAGGCADAGLARDLRRLVVLGERA 160

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RGF+ +TY+ WWI
Sbjct: 161 KGRLIEANLRLVVSVAKRYTGRGLTMLDLVQEGNLGLIRAVEKFDYTRGFKFSTYATWWI 220

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + AM   +      +++     +      + R+    +A+     +      + ++L +S
Sbjct: 221 RQAMSRALADQARTIRVPVHVVEL-----INRVVRTQRALLQEAGREPAAEEVGERLGLS 275

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             +V  +        SL+A +    ++     D +    D       E       R  L 
Sbjct: 276 AEKVEEVLRLAHEPISLHAPV--GGEDDVFLGDLI---EDADAASPAESAALLLLRQHLD 330

Query: 230 RSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             ++ L  RER++ + R   ++  P TLE +   F V+RERVRQIE++  ++++E 
Sbjct: 331 AVLATLGDRERQVVQLRYGFDDGRPRTLEEIGRLFGVTRERVRQIESKTLRRLREH 386


>gi|88858433|ref|ZP_01133075.1| RNA polymerase sigma factor [Pseudoalteromonas tunicata D2]
 gi|88820050|gb|EAR29863.1| RNA polymerase sigma factor [Pseudoalteromonas tunicata D2]
          Length = 288

 Score =  245 bits (625), Expect = 8e-63,   Method: Composition-based stats.
 Identities = 102/286 (35%), Positives = 166/286 (58%), Gaps = 9/286 (3%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +  M  +      +  Y+  +  I ML  ++E  LA + ++ GDL AA +L+ SHLR V 
Sbjct: 6   QAMMLTVPQQSGSMEGYLQAVSGIAMLSAEDEQALAVKLQQDGDLDAARQLIMSHLRFVA 65

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA GY GYGLP ++++ EGNIGLM+AVK+FDP  G RL ++++ WIKA + EY+L++W 
Sbjct: 66  HIAKGYSGYGLPQADLIQEGNIGLMKAVKRFDPTVGVRLVSFAVHWIKAEIHEYVLKNWR 125

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR+ K  L         PE+V  +A +L V+E +V  M  R++ 
Sbjct: 126 IVKVATTKAQRKLFFNLRKNKKRLGWFN-----PEEVSTVANELGVTEKDVREMEARMSS 180

Query: 183 DESLNALINSSDKNSS----QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
            + +  L    D ++S        +L  +       + E++  +   N L  ++  L+ R
Sbjct: 181 QDMVFDLTTDDDDSTSATQYSPVQYLTDNSVDLADKIEEEQWEEQTHNRLFHALKSLDER 240

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + I + R L ++  TL++L+ +++VS ERVRQ+E  A KK+Q  +
Sbjct: 241 SQDIVQTRWLSDDKATLQDLAVKYDVSAERVRQLEKTAMKKLQHLL 286


>gi|313123887|ref|YP_004034146.1| RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           bulgaricus ND02]
 gi|312280450|gb|ADQ61169.1| RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           bulgaricus ND02]
          Length = 378

 Score =  245 bits (625), Expect = 9e-63,   Method: Composition-based stats.
 Identities = 89/275 (32%), Positives = 143/275 (52%), Gaps = 14/275 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY--RGY 71
             +  Y+ EI K+P+L + EE  +AKR  E+GD  A   L  ++LRLVV IA  Y     
Sbjct: 102 DSVRMYLKEIGKVPLLSRDEEVEVAKRI-ENGDELAKDELAAANLRLVVSIAKRYAKHNG 160

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
            + I +++ EGNIGLM+AV KFD  +GF+ +TY+ WWI+ A+   +     +++I     
Sbjct: 161 KMGILDLIQEGNIGLMKAVDKFDYSKGFKFSTYATWWIRQAITRALADQDRMIRIPVHVV 220

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
           +      + R++  LQ   D + KPE++ A   +      E+I++  +    +SL+  + 
Sbjct: 221 ES--INKMNRIQRILQQDLDRDAKPEELAAEMNEPLQKVQEIITV-AKNQETDSLDKPV- 276

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV-LNPRERRIFEARRLQE 250
             ++  SQ  D L    D +     E    +  ++ L+  M   L  RE ++ + R   E
Sbjct: 277 -GEEGDSQLGDLL---EDNKAINPEEYTASEMLKDQLSSMMGEFLTDREAKVLKLRFGLE 332

Query: 251 N--PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           N  P TLE +     V+RERVRQIEA+A KK++  
Sbjct: 333 NDEPHTLEEVGRSLGVTRERVRQIEAKAVKKLKHH 367


>gi|257453204|ref|ZP_05618503.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. 3_1_5R]
 gi|317059738|ref|ZP_07924223.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. 3_1_5R]
 gi|313685414|gb|EFS22249.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. 3_1_5R]
          Length = 436

 Score =  245 bits (625), Expect = 9e-63,   Method: Composition-based stats.
 Identities = 81/277 (29%), Positives = 142/277 (51%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI +IP+L  +EE  LAK+  E GD  A  RL+ ++LRLVV IA  +   G
Sbjct: 163 DEPIKMYLREIGQIPLLTHKEELELAKKALE-GDEFANKRLIEANLRLVVSIAKKHTNRG 221

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L + +++ EGNIGLM+AV+KF+  +G++ +TY+ WWI+ A+   I      ++I      
Sbjct: 222 LKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPVH--- 278

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
             +   + ++K   +       K      +A++L +   +V S+        SL   + S
Sbjct: 279 --MIETINKIKKEARIYLQETGKDATPEILAERLGMEVEKVKSIQEMNQDPISLETPVGS 336

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN- 251
             +  S+  D++    D +     E   R   R  L   +  L+ RE ++   R   ++ 
Sbjct: 337 --EEDSELGDFV---EDQKMLTPYELTNRSLLREQLDSVLGSLSSREEKVLRYRYGLDDG 391

Query: 252 -PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            P TLE +   F+V+RER+RQIE +A +K++   +++
Sbjct: 392 SPKTLEEVGKIFKVTRERIRQIEVKALRKLRHPSRRK 428


>gi|313893234|ref|ZP_07826811.1| RNA polymerase sigma factor RpoD [Veillonella sp. oral taxon 158
           str. F0412]
 gi|313442587|gb|EFR61002.1| RNA polymerase sigma factor RpoD [Veillonella sp. oral taxon 158
           str. F0412]
          Length = 386

 Score =  245 bits (625), Expect = 9e-63,   Method: Composition-based stats.
 Identities = 78/291 (26%), Positives = 131/291 (45%), Gaps = 23/291 (7%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHR-----------LVTSHL 58
           VN +  +  Y+ EI ++P+L   EE VLAK+        A ++           LV ++L
Sbjct: 100 VNIDDPVRMYLKEIGRVPLLSADEEIVLAKQIEAGAAEDATYKDIQLAKKAKKKLVDANL 159

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLVV IA  Y G G+   +++ EGN+GL++AV KFD  +G++ +TY+ WWI+ A+   I 
Sbjct: 160 RLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVDKFDYTKGYKFSTYATWWIRQAITRAIA 219

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
                ++I     +      L R+   L         PE    IA+ + ++   V  +  
Sbjct: 220 DQARTIRIPVHMVE--TINKLIRISRQLLQDKGREPLPE---EIAEGMGITVERVREIQK 274

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
                 SL   I   ++  S   D++    D       +       +  +    + L  R
Sbjct: 275 IAQEPVSLETPI--GEEEDSHLGDFI---EDQDAIAPDDAASYILLQEQIEDVFTCLTDR 329

Query: 239 ERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+++   R       P TLE +   F V+RER+RQIE +A  K++   ++ 
Sbjct: 330 EQQVLILRFGLKDGKPRTLEEVGQHFNVTRERIRQIEGKALTKLRNRGKRD 380


>gi|295675387|ref|YP_003603911.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. CCGE1002]
 gi|295435230|gb|ADG14400.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. CCGE1002]
          Length = 311

 Score =  244 bits (624), Expect = 9e-63,   Method: Composition-based stats.
 Identities = 123/284 (43%), Positives = 169/284 (59%), Gaps = 12/284 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S++      +  YI  + +IPML   EE   A   REH +L AA RLV SHLRLVV IA 
Sbjct: 30  SLLPGQLGNIDAYIQAVNRIPMLTPAEERKFATELREHDNLEAARRLVLSHLRLVVSIAR 89

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y GYGLP ++++ EGNIGLM+AVK+FDPE+  RL +Y+M WIKA + EYILR+W +VK+
Sbjct: 90  NYLGYGLPHADLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHWIKAEIHEYILRNWRMVKV 149

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDES 185
            TT  Q++LFFNLR  K  L A T     P+++  +AK+LNV   EV  M  RL  GD +
Sbjct: 150 ATTKAQRKLFFNLRSHKQGLGAFT-----PDEIEGLAKELNVKREEVAEMETRLSGGDIA 204

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L   +   ++ S     +L   H     VL  ++  + + + +  ++  L+PR RRI EA
Sbjct: 205 LEGQVEDGEE-SYAPIAYLADSHSEPTAVLASRQRDRLQSDGIASALDALDPRSRRIIEA 263

Query: 246 RRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R L          TL  L+ EF VS ER+RQIEA A KK++ ++
Sbjct: 264 RWLKVADDGSGGSTLHELADEFGVSAERIRQIEASAMKKMRGAL 307


>gi|257784627|ref|YP_003179844.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Atopobium
           parvulum DSM 20469]
 gi|257473134|gb|ACV51253.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Atopobium
           parvulum DSM 20469]
          Length = 455

 Score =  244 bits (624), Expect = 9e-63,   Method: Composition-based stats.
 Identities = 81/314 (25%), Positives = 138/314 (43%), Gaps = 42/314 (13%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR---------------------- 42
           + + ++     +  Y+ EI K+ +L   EE  LA +                        
Sbjct: 143 DTTTVMLTGDPVRMYLKEIGKVDLLTASEEVHLAMKIEAGTAASQKLEDFEDGLIELNRA 202

Query: 43  --------EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                   E   L A  +L++++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD
Sbjct: 203 EQRRLMRIESVGLDAKQQLISANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFD 262

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +GF+ +TY+ WWI+ A+   I      ++I     +      L R++  L      + 
Sbjct: 263 YTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE--TINKLIRVQRQLLQDFGRDP 320

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            PE    I  ++ +S   V  +        SL   I   ++  SQ  D++    D     
Sbjct: 321 TPE---EIGSEMGMSPDRVREIQKISQEPVSLETPI--GEEEDSQLGDFI---EDSTAVA 372

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
             +       R  L + +  L  RER++ + R   E+  P TLE +  EF V+RER+RQI
Sbjct: 373 PPDAASDSMLREQLEQVLDSLADRERKVIKFRFGLEDGHPRTLEEVGKEFGVTRERIRQI 432

Query: 273 EARAFKKVQESIQK 286
           E++   K++   + 
Sbjct: 433 ESKTLAKLRHPSRS 446


>gi|222112015|ref|YP_002554279.1| RNA polymerase sigma-32 subunit RpoH [Acidovorax ebreus TPSY]
 gi|221731459|gb|ACM34279.1| RNA polymerase, sigma 32 subunit, RpoH [Acidovorax ebreus TPSY]
          Length = 311

 Score =  244 bits (624), Expect = 9e-63,   Method: Composition-based stats.
 Identities = 114/292 (39%), Positives = 173/292 (59%), Gaps = 12/292 (4%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +V     L  YI  + +IP+L ++EE   A++ ++  ++ AA RLV SHLRLVV I+  Y
Sbjct: 20  LVPPLGNLDAYISAVNRIPLLTQEEEQRYARQLKDDNNVEAAGRLVLSHLRLVVSISRQY 79

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGLP  +++ EGN+GLM+AVK+FDP++G RL +Y+M WIKA + EYIL++W +VK+ T
Sbjct: 80  LGYGLPHGDLIQEGNVGLMKAVKRFDPDQGVRLVSYAMHWIKAEIHEYILKNWRMVKVAT 139

Query: 129 TANQKRLFFNLRRLKG-----HLQAITDNN-LKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           T  Q++LFFNLR +K       L A T    L   ++  +A++LNV   EVI M  RL+G
Sbjct: 140 TKAQRKLFFNLRSMKQGFKADALDADTHRETLSDHEIDLVAEQLNVKREEVIEMETRLSG 199

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLNPRERR 241
            + L     S D   +      + D   +   +IE  +R     + +  ++  L+ R RR
Sbjct: 200 GDVLLDPAPSDDGEQAFGPIAYLADAGHEPTAMIESRQRDALATDGIATALDSLDARSRR 259

Query: 242 IFEARRLQENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           I E R LQ N      +TL  L++E+ VS ER+RQIE  A KK+++++ +  
Sbjct: 260 IVEQRWLQVNDDGSGGMTLHELAAEYGVSAERIRQIEVAAMKKMKKALAEYA 311


>gi|269958772|ref|YP_003328559.1| RNA polymerase sigma-32 factor [Anaplasma centrale str. Israel]
 gi|269848601|gb|ACZ49245.1| RNA polymerase sigma-32 factor [Anaplasma centrale str. Israel]
          Length = 307

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 126/276 (45%), Positives = 186/276 (67%), Gaps = 4/276 (1%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           G   L  YI ++R  P+L ++EE  LA+ +   G ++ AH+LVTSHLRLVVK+AMG++ Y
Sbjct: 28  GSGDLVSYIAQVRTFPVLSEEEEKRLAENWYRRGSVADAHKLVTSHLRLVVKVAMGFKNY 87

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GLP+ E++ EGNIGLMQAVK+F+P+ G RLATY++WWIKA++++YILRSWS +++GTT  
Sbjct: 88  GLPLMELIMEGNIGLMQAVKRFNPDLGSRLATYAVWWIKASIKDYILRSWSCIRVGTTQA 147

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALI 190
           QK+LFF+LR++K  L      ++  ++V  IA++   SE EV  M+   A  D SLN  +
Sbjct: 148 QKKLFFSLRKIKKRLLGC-GTSMTQKEVKTIAEECATSEEEVERMDRFFASRDVSLNEPV 206

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           +   ++S + QD +      QE + +  EE   +++M   ++S L+ R R IF  RRLQE
Sbjct: 207 HG--ESSVELQDLVPSSLPSQEAMYLADEESAIKKSMFDAALSTLDHRHRDIFTRRRLQE 264

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            P TLE LS ++ VS+ERVRQIE +A  K++  I+ 
Sbjct: 265 RPDTLEKLSEKYGVSKERVRQIELQALCKIKTFIEA 300


>gi|89092456|ref|ZP_01165410.1| RNA polymerase sigma factor [Oceanospirillum sp. MED92]
 gi|89083544|gb|EAR62762.1| RNA polymerase sigma factor [Oceanospirillum sp. MED92]
          Length = 284

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 105/279 (37%), Positives = 166/279 (59%), Gaps = 7/279 (2%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++    L  Y+  +  IP+L  +EE  LA+R    GD+ AA +LV SHLR VV +A  Y 
Sbjct: 11  LSPGQNLDAYVQNVTAIPVLSVEEERSLAERLHFDGDVEAARQLVMSHLRFVVHVAKTYS 70

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYGLP+ +++ EGN+GLM+AVK+FDP  G RL ++++ W+KA M E+ILR+W +VK+ TT
Sbjct: 71  GYGLPLGDLIQEGNVGLMKAVKRFDPTMGVRLVSFAVHWVKAEMHEFILRNWRIVKVATT 130

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNA 188
             Q++LFFNLR  K  L  +T+     ++V AIA+ L V    V  M  R+A  D + +A
Sbjct: 131 KAQRKLFFNLRSKKKSLSWMTN-----DEVNAIAEDLGVEAKVVRQMEGRMASVDTAFDA 185

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKE-ERKNRRNMLTRSMSVLNPRERRIFEARR 247
              + D+ ++      + D      + +E+    ++ +  L  +MS L+ R + I   R 
Sbjct: 186 PEGADDEQAAWAPAHYLEDKSADPSMQLEEANWEQDSQRRLMSAMSELDERSKDILARRW 245

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           L ++  TL  L++E+ VS ER+RQ+E  A KK++ S++ 
Sbjct: 246 LTDDKATLHELAAEYGVSAERIRQLEKNAMKKIRVSMEA 284


>gi|121603798|ref|YP_981127.1| RNA polymerase sigma-32 subunit RpoH [Polaromonas naphthalenivorans
           CJ2]
 gi|120592767|gb|ABM36206.1| RNA polymerase, sigma 32 subunit, RpoH [Polaromonas
           naphthalenivorans CJ2]
          Length = 322

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 112/287 (39%), Positives = 174/287 (60%), Gaps = 11/287 (3%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +V     L  YI  + ++PML  ++E   +K+ +E+ DL +A +LV SHLRLVV I+  Y
Sbjct: 32  MVPPLGNLDAYISAVNRLPMLTLEQEQEFSKKLKENNDLDSAGKLVLSHLRLVVSISRKY 91

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGLP  +++ EGNIGLM+AVK+FDP++  RL +Y+M WIKA + EYIL++W +VK+ T
Sbjct: 92  LGYGLPHGDLIQEGNIGLMKAVKRFDPDQNVRLVSYAMHWIKAEIHEYILKNWRMVKVAT 151

Query: 129 TANQKRLFFNLRRLKGHLQAITD-----NNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           T  Q++LFFNLR +K   +   D     + L   Q+ ++A+ LNV   EVI M  R++G 
Sbjct: 152 TKAQRKLFFNLRSMKQGYKDDADVATHRDTLTESQIDSMARTLNVKREEVIEMEQRMSGG 211

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRI 242
           + L     + D + +      + D   +   L+E  ER +   + L+ ++  L+PR RRI
Sbjct: 212 DVLLDPSPNDDGDDAFGPIAYLADAAQEPTALMESRERDDLMTDGLSTALQELDPRARRI 271

Query: 243 FEARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            E R L         +TL +L++E++VS ER+RQIE  A KK+++ +
Sbjct: 272 VEERWLNVNDDGSGGMTLHDLAAEYKVSAERIRQIEVAAMKKMKKVL 318


>gi|156740438|ref|YP_001430567.1| RpoD family RNA polymerase sigma factor [Roseiflexus castenholzii
           DSM 13941]
 gi|156231766|gb|ABU56549.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus
           castenholzii DSM 13941]
          Length = 405

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 82/301 (27%), Positives = 141/301 (46%), Gaps = 37/301 (12%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR---------EHGD-------------- 46
           +  +  +  Y+ EI ++ +L  QEE +LA++           ++GD              
Sbjct: 104 IGVDDPVRVYLREIGRVNLLTAQEEIMLAQQVERGEQANERLQNGDYTPVERLQLHRWVQ 163

Query: 47  --LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
              +A  RL+ ++LRLVV IA  Y G G+ + +++ EGNIGLM+A +KFD  +G++ +TY
Sbjct: 164 EGQAARERLIQANLRLVVSIAKKYLGRGMSLLDLIQEGNIGLMRATEKFDYRKGYKFSTY 223

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + WWI+ A+   I      +++     +      + R    +Q  T  +  P+    IA 
Sbjct: 224 ATWWIRQAITRVIADQSRTIRLPVHVGE--TINRVMRTSNRIQQTTGRDPTPD---EIAL 278

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L +   +V  +        SL   I    +  S   D++    DG+    +E       
Sbjct: 279 ELGIPVEKVRRVLEAARQTISLETPI--GPEGDSVLADFI---EDGKGATPMESASSHIL 333

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQE 282
           R  +  ++  L  RERRI + R    +    TLE +  EF ++RER+RQIEAR  +K++ 
Sbjct: 334 REQIDSALEKLPERERRIIQLRYGLYDGHYRTLEEVGREFGITRERIRQIEARVLRKLRH 393

Query: 283 S 283
            
Sbjct: 394 P 394


>gi|238028681|ref|YP_002912912.1| RNA polymerase factor sigma-32 [Burkholderia glumae BGR1]
 gi|237877875|gb|ACR30208.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia glumae BGR1]
          Length = 311

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 116/288 (40%), Positives = 173/288 (60%), Gaps = 12/288 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S++      +  YI  + +IPML  +EE   A  +R+  +L +A RLV SHLRLVV IA 
Sbjct: 30  SMLPGQLGNIDAYIQAVNRIPMLTPEEERQYATEFRDQQNLESARRLVLSHLRLVVSIAR 89

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y GYGLP  +++ EGNIGLM+AVK+FDP++  RL +Y++ WIKA + EYILR+W +VK+
Sbjct: 90  NYLGYGLPHGDLIQEGNIGLMKAVKRFDPDQNVRLVSYAIHWIKAEIHEYILRNWRMVKV 149

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDES 185
            TT  Q++LFFNLR  K  +QA+T     PE++  +A++LNV   +V  M  RL  GD +
Sbjct: 150 ATTKAQRKLFFNLRSHKKGMQAMT-----PEEIDGLAQELNVKREDVAEMETRLSGGDIA 204

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L   +   ++ S     +L   H+    VL  ++  + +   ++ ++  L+ R RRI EA
Sbjct: 205 LEGQVEDGEE-SFAPIAYLADSHNEPTAVLASRQRDRLQTEGISEALDSLDTRSRRIIEA 263

Query: 246 RRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           R L          TL +L++EF VS ER+RQIEA A KK++ ++    
Sbjct: 264 RWLNVGDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRAALAAYA 311


>gi|39995761|ref|NP_951712.1| RNA polymerase sigma-32 factor [Geobacter sulfurreducens PCA]
 gi|39982525|gb|AAR33985.1| RNA polymerase sigma-32 factor [Geobacter sulfurreducens PCA]
 gi|298504771|gb|ADI83494.1| RNA polymerase sigma-32 factor RpoH [Geobacter sulfurreducens
           KN400]
          Length = 284

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 117/280 (41%), Positives = 177/280 (63%), Gaps = 7/280 (2%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +MS+ V  +  L+ Y+ EIRK P+L  +EEY  A ++ E  DL AAH L+TS+LR VVKI
Sbjct: 2   SMSLPVVAD-SLTVYLREIRKFPVLTPEEEYRFAVKFYEDKDLEAAHSLITSNLRFVVKI 60

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  YR YGL + +++ EGN+GLM AV+KF+P +G RL +Y++WWI+A +Q +I+ +WSL+
Sbjct: 61  AAEYRSYGLKMLDLIQEGNVGLMMAVRKFNPYKGIRLISYAVWWIRAYIQNHIISAWSLL 120

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           KIGTT  QK+LFF L + K  ++ +T      + + A A  L+V ESEV+ M+ R+ GD 
Sbjct: 121 KIGTTQAQKKLFFKLNQAKNAIKGLTG----TDDIEATATSLHVKESEVLEMDQRMRGDF 176

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
            L+A I + D       + L  +   QE  L E +E +  +  +  ++  LN +ER I E
Sbjct: 177 YLDAEIKNGDG--LTILETLADERQNQEDTLAELQESELLKQHIAGALGKLNEKERFIVE 234

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            R   + P+TL+ ++  F +SRERVRQIE  A +K++  +
Sbjct: 235 QRVTADTPLTLQEIADRFSISRERVRQIEEAALRKIKSYL 274


>gi|312797371|ref|YP_004030293.1| RNA polymerase sigma-32 factor [Burkholderia rhizoxinica HKI 454]
 gi|312169146|emb|CBW76149.1| RNA polymerase sigma-32 factor [Burkholderia rhizoxinica HKI 454]
          Length = 319

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 119/289 (41%), Positives = 166/289 (57%), Gaps = 10/289 (3%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           + S++      L  YI  + +IP+L + +E  LA  YRE   L AA +LV SHLRLVV I
Sbjct: 36  SKSMLPGTLGNLDAYIQAVNRIPLLSQADETRLAIEYREQNKLDAARQLVLSHLRLVVSI 95

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y GYGLP ++++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W +V
Sbjct: 96  ARNYLGYGLPHADLIQEGNIGLMKAVKRFDPRQNVRLVSYAIHWIKAEIHEYILRNWRMV 155

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           K+ TT  Q++LFFNLR  K  +QA T     P+++  +AK+LNV   EV  M  RLAG +
Sbjct: 156 KVATTKAQRKLFFNLRSHKQGMQAFT-----PDEIAGLAKELNVKREEVTEMETRLAGGD 210

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
                     + S     +L         VL  ++    +   L  ++  L+ R RRI E
Sbjct: 211 IALEGQFEDGEESFAPIAYLADSRTEPTTVLASRQRDLLQTEGLAEALESLDARSRRIIE 270

Query: 245 ARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           AR L          TL  L+ EF VS ER+RQIEA A KK++ ++Q+  
Sbjct: 271 ARWLQVQDDGSGGATLHELADEFGVSAERIRQIEASAMKKMRSALQQYA 319


>gi|104774138|ref|YP_619118.1| RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
 gi|103423219|emb|CAI98047.1| RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           bulgaricus ATCC 11842]
 gi|325125917|gb|ADY85247.1| RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           bulgaricus 2038]
          Length = 378

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 89/275 (32%), Positives = 144/275 (52%), Gaps = 14/275 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY--RGY 71
             +  Y+ EI K+P+L + EE  +AKR + +GD SA   L  ++LRLVV IA  Y     
Sbjct: 102 DSVRMYLKEIGKVPLLSRDEEVEVAKRIK-NGDESAKDELAAANLRLVVSIAKRYAKHNG 160

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
            + I +++ EGNIGLM+AV KFD  +GF+ +TY+ WWI+ A+   +     +++I     
Sbjct: 161 KMGILDLIQEGNIGLMKAVDKFDYSKGFKFSTYATWWIRQAITRALADQDRMIRIPVHVV 220

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
           +      + R++  LQ   D N KPE++ A   +      E+I++  +    +SL+  + 
Sbjct: 221 ES--INKMNRIQRTLQQDLDRNAKPEELAAEMNEPLQKVQEIITV-AKNQETDSLDKSV- 276

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV-LNPRERRIFEARRLQE 250
             ++  SQ  D L    D +     E    +  ++ L+  M   L  RE ++ + R   E
Sbjct: 277 -GEEGDSQLGDLL---EDNKAINPEEYTAFEMLKDQLSGMMGEFLTDREAKVLKLRFGLE 332

Query: 251 N--PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           N  P TLE +     V+RERVRQIE +A KK+++ 
Sbjct: 333 NYEPHTLEEVGRSLGVTRERVRQIEDKAVKKLKQH 367


>gi|170691517|ref|ZP_02882682.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia graminis
           C4D1M]
 gi|170143722|gb|EDT11885.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia graminis
           C4D1M]
          Length = 311

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 122/284 (42%), Positives = 169/284 (59%), Gaps = 12/284 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S++      +  YI  + +IPML   EE   A  +REH +L AA RLV SHLRLVV IA 
Sbjct: 30  SLLPGQLGNIDAYIQAVNRIPMLTPAEERQFATEFREHDNLEAARRLVLSHLRLVVSIAR 89

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y GYGLP ++++ EGNIGLM+AVK+FDPE+  RL +Y+M WIKA + EYILR+W +VK+
Sbjct: 90  NYLGYGLPHADLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHWIKAEIHEYILRNWRMVKV 149

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDES 185
            TT  Q++LFFNLR  K  L + T     P+++  +AK+LNV   EV  M  RL  GD +
Sbjct: 150 ATTKAQRKLFFNLRSHKQGLGSFT-----PDEIEGLAKELNVKREEVAEMETRLSGGDIA 204

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L   +   ++ S     +L   H     VL  ++  K + + +  ++  L+ R RRI EA
Sbjct: 205 LEGQVEDGEE-SYAPIAYLADSHSEPTAVLASRQRDKLQSDGIATALEALDARSRRIIEA 263

Query: 246 RRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R L          TL  L+ EF VS ER+RQIEA A KK++ ++
Sbjct: 264 RWLKVQDDGSGGSTLHELADEFGVSAERIRQIEASAMKKMRGAL 307


>gi|237747428|ref|ZP_04577908.1| RNA polymerase sigma-32 factor [Oxalobacter formigenes HOxBLS]
 gi|229378779|gb|EEO28870.1| RNA polymerase sigma-32 factor [Oxalobacter formigenes HOxBLS]
          Length = 299

 Score =  244 bits (624), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 121/283 (42%), Positives = 175/283 (61%), Gaps = 9/283 (3%)

Query: 6   MSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           ++    G +G +  YI E+ ++P+L  ++E  LA RYRE  DLSAA  LV SHLRLVV I
Sbjct: 18  LAPAFTGSLGNIEAYIAEVNRLPILTLEQETDLALRYRERNDLSAAQELVLSHLRLVVSI 77

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y GYGLP ++++ EGNIGLM+AVK+FDP  G RL +Y++ WIKA + EYILR+W +V
Sbjct: 78  ARNYLGYGLPHADLIQEGNIGLMKAVKRFDPGMGVRLVSYAIHWIKAEIHEYILRNWRMV 137

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           KI TT  Q++LFFNLR  K  L     +++   Q+ ++A+KLNV + EV  M  RL G +
Sbjct: 138 KIATTKAQRKLFFNLRSHKNGL-----DSMTRAQIRSLAEKLNVKDEEVAEMETRLNGHD 192

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
                 +  D ++     +L  +      +L  ++  + +   L  +++ L+PR RRI E
Sbjct: 193 IALETQHDDDDDNFAPIAYLSSEQTEPASILEARQNDRMQSEGLAEALAKLDPRSRRIVE 252

Query: 245 ARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           AR L     N  TL  L++EF VS ER+RQIEA A KK++ ++
Sbjct: 253 ARWLNSDDGNSATLHALAAEFGVSAERIRQIEAAALKKMKNTL 295


>gi|189218244|ref|YP_001938886.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Methylacidiphilum infernorum V4]
 gi|189185102|gb|ACD82287.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Methylacidiphilum infernorum V4]
          Length = 287

 Score =  244 bits (623), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 85/281 (30%), Positives = 154/281 (54%), Gaps = 12/281 (4%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           + N +  L  Y+ EI +IP+L K++E  LAKR ++ GD  A  +++ ++LRLVVKIA  Y
Sbjct: 1   MDNNDSALKLYLREISQIPLLTKEKEVELAKRIQQ-GDQEARRQMIQANLRLVVKIAHDY 59

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
              GLP+ +++SEGNIGLM+AV +FDP +G +L+TY+ WWIK +++  +      +++  
Sbjct: 60  ANSGLPLPDLISEGNIGLMKAVDRFDPSKGGKLSTYAAWWIKQSIKRALANQSKTIRLPV 119

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
                 L   + +++     +++   +      +A++L +S ++V  +        SL+A
Sbjct: 120 H-----LVDKIAKMRRVAMQLSEILGRDPTDEELAEELGMSTTKVAELRTIAIRPASLDA 174

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +   ++        LV D         +    +N +N +   +  L+ RER+I   R  
Sbjct: 175 TV--GEEEDGTALGELVKDESA--ASPDQSVLDQNLKNTIMELLPKLDERERKILSLRFG 230

Query: 249 QE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            E    +TLE +  EF V+RER+RQ++  A +K+++ ++KQ
Sbjct: 231 LEGNEQMTLEEIGKEFHVTRERIRQLQNIALRKIRKELEKQ 271


>gi|119944398|ref|YP_942078.1| RNA polymerase sigma-32 factor RpoH [Psychromonas ingrahamii 37]
 gi|119863002|gb|ABM02479.1| RNA polymerase sigma-32 factor RpoH [Psychromonas ingrahamii 37]
          Length = 283

 Score =  244 bits (623), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 108/285 (37%), Positives = 166/285 (58%), Gaps = 6/285 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M   N S+ +  +  +  Y+  + +  ML  + E  LA+R    GDL+AA +LV SHLR 
Sbjct: 1   MKNTNNSMSLVPQGSIGAYVQSVNQFSMLSAEAEKELAERLFHEGDLAAAKKLVMSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y GYGL  ++++ EGNIGLM+AVK+FDP  G RL ++++ WIKA + EY++R+
Sbjct: 61  VVYIAKSYAGYGLAQADLIQEGNIGLMKAVKRFDPSVGVRLVSFAVHWIKAEIHEYVIRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VKI TT  Q++LFFNLRR K  L   +      ++V  +A+ LNVS  +V+ M  RL
Sbjct: 121 WRMVKIATTKAQRKLFFNLRRAKKRLGWFSH-----DEVATVAENLNVSTKDVLEMESRL 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRE 239
              +    L +S D  S       + D      QV+  +  + + +N L  ++S L+ R 
Sbjct: 176 NAQDQSFDLSDSDDDESGFAPVQYLEDKSADVFQVVATENTQLHTKNKLYSALSTLDERS 235

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + I  +R L E   TL +L++ + +S ER+RQ+E  A KK+Q ++
Sbjct: 236 QDIVSSRWLSEPKATLHDLAARYGISAERIRQLEENAMKKLQSNM 280


>gi|302545597|ref|ZP_07297939.1| RNA polymerase sigma (70) factor RpoD [Streptomyces hygroscopicus
           ATCC 53653]
 gi|302463215|gb|EFL26308.1| RNA polymerase sigma (70) factor RpoD [Streptomyces himastatinicus
           ATCC 53653]
          Length = 443

 Score =  244 bits (623), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 83/301 (27%), Positives = 137/301 (45%), Gaps = 38/301 (12%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKR----------YREHGDLS------------ 48
                  +Y+ EI +IP+L   EE  LA+R               DL             
Sbjct: 142 PSSDLFRQYLREIGRIPLLSAAEEVELARRVEAGLFAEEKLASAPDLDSQLALDLDRLVV 201

Query: 49  ----AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
               A  RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY
Sbjct: 202 LGRMAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTY 261

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + WWI+ AM   +      +++     +  L   + R++  +         PE+V   A 
Sbjct: 262 ATWWIRQAMSRALADQARTIRVPVHVVE--LINRVVRVQRRMLQERGYEPTPEEV---AI 316

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            L+++   V  +        SL+A +   +++     D +    DG     +E       
Sbjct: 317 HLDLTPERVSEVLRLAQEPVSLHAPV--GEEDDVALGDLI---EDGDAASPVESAAFLLL 371

Query: 225 RNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           R  L   +S L  RER++ + R       P TLE +   F V+RER+RQIE++   K+++
Sbjct: 372 REHLEAVLSTLGERERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRD 431

Query: 283 S 283
            
Sbjct: 432 H 432


>gi|149925644|ref|ZP_01913908.1| RNA polymerase sigma factor [Limnobacter sp. MED105]
 gi|149825761|gb|EDM84969.1| RNA polymerase sigma factor [Limnobacter sp. MED105]
          Length = 308

 Score =  244 bits (623), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 118/288 (40%), Positives = 175/288 (60%), Gaps = 9/288 (3%)

Query: 3   RKNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           R   +++  G +G L  YI    +IPML  +EE  L +R +   DL AA RLV SHLRLV
Sbjct: 20  RDPWALVARGPLGNLDAYISATHQIPMLSPEEEVELGERLQRDNDLEAARRLVLSHLRLV 79

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V +A  Y GYGLP ++++ EGNIGLM+AVK+FDP RG RL ++++ WIKA + EYI+R+W
Sbjct: 80  VAVARQYLGYGLPHADLIQEGNIGLMKAVKRFDPTRGVRLVSFALHWIKAEIHEYIIRNW 139

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            +VK+ TT   ++LFFNL   K +        L P+Q+  +A +LNV   +V  M  R+A
Sbjct: 140 RMVKMITTKAHRKLFFNLNSFKKY-----GQTLSPDQINEVASELNVRPEDVYDMERRMA 194

Query: 182 GDE-SLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           G E SL+ +++  S++NS     +L  +     +VL      +     L  +++ L+ R 
Sbjct: 195 GHEFSLDPVVDVDSEENSYNPVRYLAAEGAEPTEVLEGANMERLHSEGLDMALASLDERS 254

Query: 240 RRIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +RI  +R L  EN  TL +L++E  VS ERVRQIE +A KK++ ++ K
Sbjct: 255 QRIISSRWLAGENAKTLHDLAAELGVSAERVRQIETQAMKKMKTALLK 302


>gi|145594022|ref|YP_001158319.1| RNA polymerase sigma factor [Salinispora tropica CNB-440]
 gi|145303359|gb|ABP53941.1| RNA polymerase sigma factor RpoD [Salinispora tropica CNB-440]
          Length = 542

 Score =  244 bits (623), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 78/312 (25%), Positives = 145/312 (46%), Gaps = 42/312 (13%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY------------REHGDLS-------- 48
           +      +  Y+ +I K+P+L  ++E  LAKR              E GD          
Sbjct: 235 LTASADSVRAYLKQIGKVPLLNAEQEVELAKRIEAGLYATEQLRAAEEGDEKFNRDMQRD 294

Query: 49  ----------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
                     A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G
Sbjct: 295 MMWISRDGERAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKG 354

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           ++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L         PE 
Sbjct: 355 YKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLGREPTPE- 411

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +  V ++ 
Sbjct: 412 --ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSEAVVAVDA 464

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARA 276
                 ++ L + +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++ 
Sbjct: 465 VSFSLLQDQLQQVLQTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKT 524

Query: 277 FKKVQESIQKQV 288
             K++   + QV
Sbjct: 525 MSKLRHPSRSQV 536


>gi|145295815|ref|YP_001138636.1| RNA polymerase sigma factor [Corynebacterium glutamicum R]
 gi|140845735|dbj|BAF54734.1| hypothetical protein [Corynebacterium glutamicum R]
          Length = 494

 Score =  244 bits (623), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 78/325 (24%), Positives = 149/325 (45%), Gaps = 49/325 (15%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR----------------EHG 45
            RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR                    G
Sbjct: 175 ARKDAELTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYATHRMEEMEEAFAAG 233

Query: 46  DLS--------------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           D                      A + L+ ++LRLVV +A  Y G G+   +++ EGN+G
Sbjct: 234 DKDAKLTPAVKRDLRAIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLG 293

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  
Sbjct: 294 LIRAVEKFDYSKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRE 351

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           L         P     ++K++++SE +V+ +        SL+  I   D+  SQ  D++ 
Sbjct: 352 LLQELGREPTP---QELSKEMDISEEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI- 405

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFE 263
              D +  V ++       ++ L   +  L+ RE  + + R    +  P TL+ +   + 
Sbjct: 406 --EDSEAVVAVDAVSFTLLQDQLQDVLETLSEREAGVVKLRFGLTDGMPRTLDEIGQVYG 463

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           V+RER+RQIE++   K++   + QV
Sbjct: 464 VTRERIRQIESKTMSKLRHPSRSQV 488


>gi|30248598|ref|NP_840668.1| RNA polymerase factor sigma-32 [Nitrosomonas europaea ATCC 19718]
 gi|30180193|emb|CAD84495.1| Sigma-70 factor family [Nitrosomonas europaea ATCC 19718]
          Length = 280

 Score =  244 bits (623), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 123/280 (43%), Positives = 175/280 (62%), Gaps = 7/280 (2%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M++ V     L  YI      P+L ++EE  LAKR RE GD++AAH+LV SHLR+VV IA
Sbjct: 5   MALPVMAGGDLDSYIRATSSFPVLSREEEASLAKRMREEGDVNAAHQLVLSHLRVVVTIA 64

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            GY GYGLP ++++ EGNIGLM+AV++FDPERG RL ++++ WI+A + E+I+R+W LVK
Sbjct: 65  RGYLGYGLPHADLIQEGNIGLMKAVRRFDPERGVRLISFAIHWIRAEIHEFIMRNWRLVK 124

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           I TT  Q++LFFNLR +K  L  ++       +V ++A++L V   EV+ M  R +G + 
Sbjct: 125 IATTKQQRKLFFNLRSMKKGLDTMSQ-----AEVASMAEQLGVKAEEVVEMETRFSGRDI 179

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
               +  SD++      WL    D   ++  E+ ER      L  S+  L+ R RRI EA
Sbjct: 180 SLEPVTDSDEDDFSPIAWLTDGSDPSRELEKEQLER-LTHARLKNSLDSLDERSRRIIEA 238

Query: 246 RRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R L+E+   TL  L+ E  VS ERVRQIEA+A KK++  I
Sbjct: 239 RWLREDKAATLHELADELGVSAERVRQIEAKAMKKMRAEI 278


>gi|261325797|ref|ZP_05964994.1| RNA polymerase factor sigma-32 [Brucella neotomae 5K33]
 gi|261301777|gb|EEY05274.1| RNA polymerase factor sigma-32 [Brucella neotomae 5K33]
          Length = 293

 Score =  244 bits (623), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 118/293 (40%), Positives = 185/293 (63%), Gaps = 4/293 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  ++          +   I      P LE++EE  LA R++E  D  A HR+ ++H+RL
Sbjct: 1   MAVRSFPAAAASSQSM---IRSAMSAPYLEREEERALAIRWKETKDQDALHRITSAHMRL 57

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A  +R + LP+S+++ EG +GL++A  +FDP+R  R +TY+ WWI+A+MQ+YILR+
Sbjct: 58  VISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRDVRFSTYAFWWIRASMQDYILRN 117

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WS+V+ GT++ QK LFFNLRRL+  L    DN  K E    I+ +L VS S++  M+ RL
Sbjct: 118 WSIVRGGTSSAQKALFFNLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDIEFMDSRL 177

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D SL+A +N  +  +S+  D+LV DH  Q+++     + + R   LTR++  LN RE
Sbjct: 178 SGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTRALDTLNERE 237

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
             I   RRL ++ VTLE L  +  +S+ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 238 LHIIRERRLDDDGVTLEALGEKLGISKERVRQIESRAMEKLKIALLSQHELAA 290


>gi|88658518|ref|YP_507464.1| RNA polymerase sigma-32 factor [Ehrlichia chaffeensis str.
           Arkansas]
 gi|88599975|gb|ABD45444.1| RNA polymerase sigma-32 factor [Ehrlichia chaffeensis str.
           Arkansas]
          Length = 297

 Score =  244 bits (623), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 134/285 (47%), Positives = 190/285 (66%), Gaps = 3/285 (1%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           SI    +  L  YI+E+   P+L  +EE  LA+ + E+G ++ AHRLVTSHLRLVVK+A+
Sbjct: 5   SIFSLTQDNLMSYINEVHAFPILSPEEEDRLARNWYENGIVADAHRLVTSHLRLVVKVAL 64

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            ++ Y LP+ E++ EGNIGLMQAVKKF+P  GFRL+TY++WWIKA +++YIL+SWS +KI
Sbjct: 65  SFKNYELPLIELIMEGNIGLMQAVKKFNPTLGFRLSTYAIWWIKAFIKDYILKSWSCIKI 124

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR-LAGDES 185
           GTT  Q++LFF+LR++K  L    ++N+  E +  IA K + SE EV  MN   L  D S
Sbjct: 125 GTTQAQRKLFFSLRKIKKKLFKY-NHNITKEDIKLIANKCSTSEQEVEQMNRYFLYRDRS 183

Query: 186 LNALINSSDK-NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           LN L+ S+D  N  + Q+ +  D   QE   +  EE   ++ ++++++S LN R R IF 
Sbjct: 184 LNELVFSNDNQNGVELQEIIKCDTPNQEDTYLLNEELNIKKALISQALSTLNERYRDIFI 243

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
            RRL E P TL+ LS E+ +S+ERVRQIE  AF KV+  I  + E
Sbjct: 244 RRRLIEEPDTLDKLSQEYNISKERVRQIEMHAFTKVKNFIISERE 288


>gi|302537866|ref|ZP_07290208.1| RNA polymerase sigma factor RpoS [Streptomyces sp. C]
 gi|302446761|gb|EFL18577.1| RNA polymerase sigma factor RpoS [Streptomyces sp. C]
          Length = 481

 Score =  244 bits (623), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 75/303 (24%), Positives = 139/303 (45%), Gaps = 38/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYR----------EHGD----------------L 47
             +  Y+  I K+P+L  ++E  LAKR            E  D                 
Sbjct: 183 DPVKDYLKLIGKVPLLNAEQEVELAKRIEAGLFSEYKLEEEEDHKPAFKRELEILVEDGR 242

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ W
Sbjct: 243 RAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNVGLIRAVEKFDYTKGFKFSTYATW 302

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   +      ++I     +  +   L R++  +         PE    + K+L+
Sbjct: 303 WIRQAITRAMADQSRTIRIPVHMVE--IINKLARVQRQMLQDLGREPTPE---ELGKELD 357

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++  +VI +        SL+  +   ++  S++ D +    D +  V  +       +  
Sbjct: 358 MTPEKVIEVQKYGREPISLHTPL--GEEGDSEFGDLI---EDSEAVVPADAVSFTFLQEQ 412

Query: 228 LTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L   +  L+ RE  +   R    +  P TL+ +   + V+RER+RQIE++   K++   +
Sbjct: 413 LQSILGTLSEREAGVVSMRYGLNDGQPKTLDEIGRVYGVTRERIRQIESKTMSKLRHPSR 472

Query: 286 KQV 288
            QV
Sbjct: 473 SQV 475


>gi|56415467|ref|YP_152542.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. ATCC 9150]
 gi|197364396|ref|YP_002144033.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. AKU_12601]
 gi|56129724|gb|AAV79230.1| RNA polymerase sigma-32 factor [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. ATCC 9150]
 gi|197095873|emb|CAR61447.1| RNA polymerase sigma-32 factor [Salmonella enterica subsp. enterica
           serovar Paratyphi A str. AKU_12601]
          Length = 284

 Score =  244 bits (623), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 108/289 (37%), Positives = 161/289 (55%), Gaps = 8/289 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +     L  YI      PML   EE  LA+R    GDL AA  L+ SHLR 
Sbjct: 1   MTKEMQNLALAPVGNLESYIRAANAWPMLSADEERALAERLHYQGDLEAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVEMVARELGVSSKDVREMESRM 175

Query: 181 -AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE-ERKNRRNMLTRSMSVLNPR 238
            A D + +   +    +        + D        IE +   +   N LT +M  L+ R
Sbjct: 176 AAQDMTFDMSSDDESDSQPMAPVLYLQDKSSNFADGIEDDNWEEQAANRLTDAMQGLDER 235

Query: 239 ERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + I  AR L E+   TL+ L+  + VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 SQDIIRARWLDEDNKSTLQELADRYGVSVERVRQLEKNAMKKLRAAIEA 284


>gi|94676476|ref|YP_588537.1| alternative sigma factor RpoH [Baumannia cicadellinicola str. Hc
           (Homalodisca coagulata)]
 gi|94219626|gb|ABF13785.1| alternative sigma factor RpoH [Baumannia cicadellinicola str. Hc
           (Homalodisca coagulata)]
          Length = 286

 Score =  244 bits (623), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 103/287 (35%), Positives = 166/287 (57%), Gaps = 8/287 (2%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           +++ +I++ +  L  Y+      PML  +EE  LA++    GD+ AA  L+ SHLR V+ 
Sbjct: 5   RSVLVIIDKKGSLEDYVKAANAYPMLTAEEELKLAEKLHYQGDIEAAKLLILSHLRFVIN 64

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y GY LP ++++ EGNIGLM+AV+KF+PE G RL ++++ WIKA + EY+LR+W +
Sbjct: 65  IARTYSGYNLPQADLIQEGNIGLMKAVRKFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRI 124

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VK+ TT  Q+RLFFNLR++K  L          E+V  +AK+L V+  +V  M  R+A  
Sbjct: 125 VKVATTKAQRRLFFNLRKIKQRLGWFNQ-----EEVEMVAKELGVTSKDVREMESRMAAQ 179

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK---NRRNMLTRSMSVLNPRER 240
           +     I + +         ++Y  D         EE+    +  + L  ++  L+ R +
Sbjct: 180 DIAFDPIPNDEVPDKLLMAPILYLQDKGSDFADRIEEQNWEYHAADKLNIALDKLDERSK 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            I  AR L     TL++L++++ VS ER+RQ+E  A KK++ +I+ Q
Sbjct: 240 NIIAARWLDNKKSTLQDLANKYGVSAERIRQLEKNAMKKIRMAIEAQ 286


>gi|134297011|ref|YP_001120746.1| RNA polymerase factor sigma-32 [Burkholderia vietnamiensis G4]
 gi|134140168|gb|ABO55911.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia vietnamiensis
           G4]
          Length = 331

 Score =  244 bits (623), Expect = 1e-62,   Method: Composition-based stats.
 Identities = 116/290 (40%), Positives = 173/290 (59%), Gaps = 12/290 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
             S++      +  YI  + +IP+L  +EE   A  +RE  +L AA +LV SHLRLVV I
Sbjct: 48  TQSLLPGQLGNIDAYIQAVNRIPLLSAEEERRYATEFREDNNLDAARKLVLSHLRLVVSI 107

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y GYGLP  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W +V
Sbjct: 108 ARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMV 167

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGD 183
           K+ TT  Q++LFFNLR  K  +QA+T     PE++  +A++LNV   EV  M  RL  GD
Sbjct: 168 KVATTKAQRKLFFNLRSHKKSMQAMT-----PEEIDGLAQELNVKREEVTEMETRLSGGD 222

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            +L   +   ++ +     +L   H+    VL  ++    + + + +++  L+ R RRI 
Sbjct: 223 IALEGQVEDGEE-AYAPIAYLADSHNEPTAVLAARQRDMLQTDGIAQALEALDARSRRII 281

Query: 244 EARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           EAR L          TL +L++EF VS ER+RQIEA A KK++ ++ +  
Sbjct: 282 EARWLNVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRTALAEYA 331


>gi|186475070|ref|YP_001856540.1| RNA polymerase factor sigma-32 [Burkholderia phymatum STM815]
 gi|184191529|gb|ACC69494.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia phymatum
           STM815]
          Length = 311

 Score =  243 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 120/288 (41%), Positives = 170/288 (59%), Gaps = 12/288 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S++      +  YI  + +IPML   EE   A  YRE  +L +A +LV SHLRLVV IA 
Sbjct: 30  SLLPGQLGNIDAYIQAVNRIPMLTPAEERQFATEYREQNNLESARKLVLSHLRLVVSIAR 89

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y GYGLP ++++ EGNIGLM+AVK+FDPE+  RL +Y+M WIKA + EYILR+W +VK+
Sbjct: 90  NYLGYGLPHADLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHWIKAEIHEYILRNWRMVKV 149

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDES 185
            TT  Q++LFFNLR  K  LQ+ T     P+++  +AK+LNV   EV  M  RL  GD +
Sbjct: 150 ATTKAQRKLFFNLRSHKQGLQSFT-----PDEIDGLAKELNVKREEVAEMETRLSGGDVA 204

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L   +   ++ +     +L   H     VL  ++  +   + +  ++  L+ R RRI EA
Sbjct: 205 LEGQVEDGEE-AFAPIAYLADSHSEPTAVLAARQRDRLHSDGIASALESLDSRSRRIIEA 263

Query: 246 RRLQENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           R LQ         TL  L+ EF VS ER+RQIEA A KK++ ++ +  
Sbjct: 264 RWLQVEDDGSGGSTLHELADEFGVSAERIRQIEASAMKKMRTALAEYA 311


>gi|261219345|ref|ZP_05933626.1| RNA polymerase factor sigma-32 [Brucella ceti M13/05/1]
 gi|261222881|ref|ZP_05937162.1| RNA polymerase factor sigma-32 [Brucella ceti B1/94]
 gi|261315875|ref|ZP_05955072.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M163/99/10]
 gi|261316262|ref|ZP_05955459.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis B2/94]
 gi|261322406|ref|ZP_05961603.1| RNA polymerase factor sigma-32 [Brucella ceti M644/93/1]
 gi|265987326|ref|ZP_06099883.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M292/94/1]
 gi|265998840|ref|ZP_06111397.1| RNA polymerase factor sigma-32 [Brucella ceti M490/95/1]
 gi|260921465|gb|EEX88118.1| RNA polymerase factor sigma-32 [Brucella ceti B1/94]
 gi|260924434|gb|EEX91002.1| RNA polymerase factor sigma-32 [Brucella ceti M13/05/1]
 gi|261295096|gb|EEX98592.1| RNA polymerase factor sigma-32 [Brucella ceti M644/93/1]
 gi|261295485|gb|EEX98981.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis B2/94]
 gi|261304901|gb|EEY08398.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M163/99/10]
 gi|262553529|gb|EEZ09298.1| RNA polymerase factor sigma-32 [Brucella ceti M490/95/1]
 gi|264659523|gb|EEZ29784.1| RNA polymerase factor sigma-32 [Brucella pinnipedialis M292/94/1]
          Length = 293

 Score =  243 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 118/293 (40%), Positives = 184/293 (62%), Gaps = 4/293 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  ++          +   I      P LE++EE  LA R++E  D  A HR+ ++H+RL
Sbjct: 1   MAVRSFPAAAASSQSM---IRSAMSAPYLEREEERALAIRWKETKDQDALHRITSAHMRL 57

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A  +R + LP+S+++ EG +GL++A  +FDP+R  R +TY+ WWI+A+MQ+YILR+
Sbjct: 58  VISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRDVRFSTYASWWIRASMQDYILRN 117

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WS+V+ GT++ QK LFFNLRRL+  L    DN  K E    I+ +L VS S+V  M+ RL
Sbjct: 118 WSIVRGGTSSAQKALFFNLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRL 177

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D SL+  +N  +  +S+  D+LV DH  Q+++     + + R   LTR++  LN RE
Sbjct: 178 SGPDSSLSVPMNGEETGASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTRALDTLNERE 237

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
             I   RRL ++ VTLE L  +  +S+ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 238 LHIIRERRLDDDGVTLEALGEKLGISKERVRQIESRAMEKLKIALLSQHELAA 290


>gi|160902123|ref|YP_001567704.1| RpoD family RNA polymerase sigma factor [Petrotoga mobilis SJ95]
 gi|160359767|gb|ABX31381.1| RNA polymerase, sigma 70 subunit, RpoD family [Petrotoga mobilis
           SJ95]
          Length = 418

 Score =  243 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 80/274 (29%), Positives = 135/274 (49%), Gaps = 14/274 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI K+ +L    E  LA+R ++ GD  A   L+ ++LRLV+ IA  Y G GL
Sbjct: 143 DPIKIYLKEISKVELLSPSRERQLARRAQK-GDQKARDELIKANLRLVISIAKRYTGRGL 201

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGNIGL++AV KFD  +GF+ +TY+ WWI+ A+   I      ++I       
Sbjct: 202 TFLDLIQEGNIGLIKAVDKFDWRKGFKFSTYATWWIRQAITRAIADQARTIRIPVH---- 257

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS- 192
            L   + R+   ++     N        +A+ L+  E ++  +        SLN+ I+S 
Sbjct: 258 -LVETINRMNKVIREYLQENGDYPSAQELAEILDKPEDKINEILMSAKDVLSLNSPISSG 316

Query: 193 -SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQ 249
             D   S+  D++      +E    E+ ++   +  L   +  LN +E  + + R   L 
Sbjct: 317 NGDDEESETGDFI----STEETTPEEEAQKMIMKERLEEVLDTLNSKEALVLKMRYGFLD 372

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               TLE +   F V+RER+RQIE +A +K++  
Sbjct: 373 GKQKTLEEVGQFFNVTRERIRQIETKALRKLRHP 406


>gi|3219168|dbj|BAA28784.1| sigma-32 homolog [Achromobacter xylosoxidans]
          Length = 306

 Score =  243 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 122/287 (42%), Positives = 178/287 (62%), Gaps = 11/287 (3%)

Query: 2   NRKNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           N   ++I   G +G +  YI  + ++P+L  + E  L +R R+  DL AA  L+ SHLRL
Sbjct: 25  NALALAIANPGALGTIDAYISAVNRLPVLSAERETELGRRLRDQEDLGAARELILSHLRL 84

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y GYGLP ++++ EGN+GLM+AVK+FDPERG RL ++++ WIKA + EYI+R+
Sbjct: 85  VVSVARQYLGYGLPHADLIQEGNVGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYIIRN 144

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W LVK+ TT  Q++LFFNLR ++          L PEQV  IA++LNV   +V  M  RL
Sbjct: 145 WRLVKVATTKAQRKLFFNLRSMR-----PDGQTLDPEQVEHIARELNVRREDVSEMEVRL 199

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR-NMLTRSMSVLNPR 238
           +G D SL       D +S     +L  D   +   ++E+  R   + + L+ ++  L+PR
Sbjct: 200 SGRDMSLEN--QDDDDDSYAPIAYLSDDGRQEPTRVLERAARDQLQGSGLSDALEALDPR 257

Query: 239 ERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            RRI EAR LQ++   TL  L+ EF VS ER+RQIEA A KK++ ++
Sbjct: 258 SRRIVEARWLQDDGGATLHELAQEFGVSAERIRQIEAAALKKMRGNL 304


>gi|62390750|ref|YP_226152.1| RNA polymerase sigma factor [Corynebacterium glutamicum ATCC 13032]
 gi|41326088|emb|CAF20251.1| RNA POLYMERASE SIGMA 70 FACTOR [Corynebacterium glutamicum ATCC
           13032]
          Length = 494

 Score =  243 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 78/325 (24%), Positives = 149/325 (45%), Gaps = 49/325 (15%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR----------------EHG 45
            RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR                    G
Sbjct: 175 ARKDAELTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYATHRMEEMEEAFAAG 233

Query: 46  DLS--------------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           D                      A + L+ ++LRLVV +A  Y G G+   +++ EGN+G
Sbjct: 234 DKDAKLTPAVKRDLRAIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLG 293

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  
Sbjct: 294 LIRAVEKFDYSKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRE 351

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           L         P     ++K++++SE +V+ +        SL+  I   D+  SQ  D++ 
Sbjct: 352 LLQELGREPTP---QELSKEMDISEEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI- 405

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFE 263
              D +  V ++       ++ L   +  L+ RE  + + R    +  P TL+ +   + 
Sbjct: 406 --EDSEAVVAVDAVSFTLLQDQLQDVLETLSEREAGVVKLRFGLTDGMPRTLDEIGQVYG 463

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           V+RER+RQIE++   K++   + QV
Sbjct: 464 VTRERIRQIESKTMSKLRHPSRSQV 488


>gi|330719751|gb|EGG98273.1| RNA polymerase sigma factor RpoH [gamma proteobacterium IMCC2047]
          Length = 283

 Score =  243 bits (622), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 112/284 (39%), Positives = 168/284 (59%), Gaps = 8/284 (2%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
            M  +V G+  L+ Y+  +  IP+L  ++E  LA+R     DL AA +L+ SHLR VV I
Sbjct: 6   TMDNMVPGQ-NLAAYVTSVSSIPVLTAEQEKELAERLYYQEDLEAARQLIMSHLRFVVHI 64

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y GYGLP  +++ EGN+GLM+AVK+FDPERG RL ++++ WIKA + EYILR+W +V
Sbjct: 65  AKSYSGYGLPQGDLIQEGNVGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYILRNWRIV 124

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGD 183
           K+ TT  Q++LFFNLR  K  L  +++     ++V AIA+ L V    V  M  RL A D
Sbjct: 125 KVATTKAQRKLFFNLRGAKKSLAWLSN-----DEVDAIAEDLGVDAKVVRQMEGRLSAHD 179

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRI 242
              +   +  D ++ Q     + D       L+E++  +   N  L  +M+ L+ R + I
Sbjct: 180 APFDMGADDDDDSAYQAPANYLEDKRCDPVDLLEQQNWQETSNRKLFEAMADLDERSKDI 239

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             AR L E   TL +L+ ++ VS ER+RQ+E  A KK++ ++Q 
Sbjct: 240 LNARWLSEQKSTLHDLADKYGVSAERIRQLEKNAMKKIKVAMQA 283


>gi|269925789|ref|YP_003322412.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
 gi|269789449|gb|ACZ41590.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
          Length = 363

 Score =  243 bits (621), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 90/284 (31%), Positives = 144/284 (50%), Gaps = 15/284 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE  LAKR  E GD  A  R V ++LRLVV IA  Y G GL
Sbjct: 90  DAVKIYLREIGSVPLLTPKEEVELAKRI-EKGDTEALQRFVLANLRLVVSIAKRYVGRGL 148

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGNIGLM+AV+KFD  +G R +TY+ WWI+ A+   I      +++    N++
Sbjct: 149 PLLDLIQEGNIGLMRAVQKFDWRKGHRFSTYATWWIRQAITRAIGDKSREIRLPAHINEE 208

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                + R++  L    +    PE    IA+K   S   V  +   L    SL+  +   
Sbjct: 209 --LNRINRIRQQLSQTVNREPTPE---EIAEKAGTSPERVRELLGYLQQPVSLDTPV--G 261

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           ++  S   +++       E+   ++  +     +L     VL PRE+R+ + R    +  
Sbjct: 262 EEADSTLGEFVPDVRANPEEEATDEVLKTEMDRVLDE---VLTPREKRVLQLRYGLGDGH 318

Query: 254 T--LENLSSEFEVSRERVRQIEARAFKKVQE--SIQKQVELSSS 293
           T  LE +  E  V+RERVRQ+E +A +K++   +I+K  E    
Sbjct: 319 TYSLEKVGRELGVTRERVRQLEKQALEKLRRGPAIRKLAEYMEE 362


>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 =  243 bits (621), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 76/273 (27%), Positives = 130/273 (47%), Gaps = 14/273 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +H+I K   L  ++   + KR    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 347 LHQIEKETGLTIEQIKNINKRMAIGEAKAKRAKKEMVEANLRLVISIAKKYTNRGLQFLD 406

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 407 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 464

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +   T     PE    +A+++ +SE ++  +        S+   I   D   
Sbjct: 465 KLNRVSRQILQETGCEPTPE---ELAERMFMSEDKIRKVLKIAKEPVSMETPI--GDDED 519

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D    + ++     N R      +S L PRE ++   R   +     TL
Sbjct: 520 SHLGDFI---EDTNLDLPLDSATSDNLRAATNDVLSGLTPREAKVLRMRFGIDMNTDHTL 576

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           E +  +F+V+RER+RQIEA+A +K++   + ++
Sbjct: 577 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEI 609


>gi|71737989|ref|YP_276878.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv.
           phaseolicola 1448A]
 gi|257482996|ref|ZP_05637037.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. tabaci
           ATCC 11528]
 gi|289624653|ref|ZP_06457607.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. aesculi
           str. NCPPB3681]
 gi|289648492|ref|ZP_06479835.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. aesculi
           str. 2250]
 gi|289672442|ref|ZP_06493332.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. syringae
           FF5]
 gi|298485264|ref|ZP_07003357.1| RNA polymerase sigma factor RpoH [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
 gi|302187226|ref|ZP_07263899.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. syringae
           642]
 gi|71558542|gb|AAZ37753.1| RNA polymerase sigma-32 factor [Pseudomonas syringae pv.
           phaseolicola 1448A]
 gi|298160252|gb|EFI01280.1| RNA polymerase sigma factor RpoH [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
 gi|320326376|gb|EFW82429.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. glycinea
           str. B076]
 gi|320331634|gb|EFW87572.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. glycinea
           str. race 4]
 gi|330871135|gb|EGH05844.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. aesculi
           str. 0893_23]
 gi|330872356|gb|EGH06505.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. glycinea
           str. race 4]
 gi|330891333|gb|EGH23994.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. mori str.
           301020]
 gi|330898959|gb|EGH30378.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. japonica
           str. M301072PT]
 gi|330954977|gb|EGH55237.1| RNA polymerase factor sigma-32 [Pseudomonas syringae Cit 7]
 gi|330982560|gb|EGH80663.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. aptata
           str. DSM 50252]
 gi|330985905|gb|EGH84008.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. lachrymans
           str. M301315]
 gi|331011765|gb|EGH91821.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. tabaci
           ATCC 11528]
          Length = 284

 Score =  243 bits (621), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 101/272 (37%), Positives = 156/272 (57%), Gaps = 7/272 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+H +  IP+L  ++E  LA+      DL AA ++V +HLR VV IA  Y GYGL 
Sbjct: 16  NLEAYVHTVNSIPLLTPEQERELAESLYYEQDLDAARQMVLAHLRFVVHIARSYSGYGLA 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++
Sbjct: 76  QADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           LFFNLR  K  L  + +     ++V  +A+ L V   EV  M  RL G +        +D
Sbjct: 136 LFFNLRSQKKRLAWLNN-----DEVHRVAESLGVEPREVREMESRLTGHDMAFDPAAEAD 190

Query: 195 KNSS--QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            +S+     ++L        + L + +   N    L +++ VL+ R R I   R L E  
Sbjct: 191 DDSAFQSPANYLEDHRYDPARQLEDSDWTDNSTANLHQALDVLDERSRDILYQRWLAEEK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL +L+ ++ VS ER+RQ+E  A  K++ SI
Sbjct: 251 ATLHDLAQKYNVSAERIRQLEKSAMNKLKTSI 282


>gi|306836272|ref|ZP_07469254.1| RNA polymerase sigma factor rpoD [Corynebacterium accolens ATCC
           49726]
 gi|304567864|gb|EFM43447.1| RNA polymerase sigma factor rpoD [Corynebacterium accolens ATCC
           49726]
          Length = 492

 Score =  243 bits (621), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 78/325 (24%), Positives = 150/325 (46%), Gaps = 49/325 (15%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY----------------REHG 45
            RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR                 R  G
Sbjct: 173 ARKDAQLTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYAQHRMDEMEKARAEG 231

Query: 46  DL--------------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           D                      A + L+ ++LRLVV +A  Y G G+   +++ EGN+G
Sbjct: 232 DKAAKLSPMEKRDLRSIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLG 291

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  
Sbjct: 292 LIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRE 349

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           L         P     +AK+++++E +V+ +        SL+  I   D+  SQ  D++ 
Sbjct: 350 LLQDLGREPTP---QELAKEMDITEEKVMEIQQYAREPISLDQTI--GDEGDSQLGDFI- 403

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFE 263
              D +  + ++       ++ L   ++ L+ RE  +   R    +  P TL+ +   + 
Sbjct: 404 --EDSEAVIAVDAVSFTLLQDQLQDVLTTLSEREAGVVRLRFGLTDGMPRTLDEIGQVYG 461

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           V+RER+RQIE++   K++   + QV
Sbjct: 462 VTRERIRQIESKTMSKLRHPSRSQV 486


>gi|197122293|ref|YP_002134244.1| RNA polymerase, sigma 70 family subunit [Anaeromyxobacter sp. K]
 gi|196172142|gb|ACG73115.1| putative RNA polymerase, sigma 70 family subunit [Anaeromyxobacter
           sp. K]
          Length = 307

 Score =  243 bits (621), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 114/284 (40%), Positives = 168/284 (59%), Gaps = 6/284 (2%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
             +      L  Y+ EI + P+L  ++E  LA++Y    D  AAHRLVT++LR VVK+A 
Sbjct: 4   QSVPGTASSLEVYLSEINRFPLLTVEDEQRLARQYCADRDTRAAHRLVTANLRFVVKVAY 63

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            YR YG  +++++ EGNIGLM+AV+KFDP++G RL +Y++WWI+A +Q YIL+SWSLVK+
Sbjct: 64  EYRSYGFRMADLIQEGNIGLMKAVQKFDPDKGIRLISYAVWWIRAYIQNYILKSWSLVKL 123

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKP---EQVVAIAKKLNVSESEVISMNCRLAG- 182
           GTT  Q++LFF+L R K  L   +  +           +AKKL V   EV  M  R+ G 
Sbjct: 124 GTTQAQRKLFFSLARTKRELDKRSQEHGADSDGHDANKVAKKLRVKPGEVREMEQRMEGR 183

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
           D SL+A +   D       D+L      Q+  L   +E+K     +  ++  L+ RER I
Sbjct: 184 DLSLDAPM--GDDGGYSHVDFLPSGTASQDDELSGVQEQKVVSGRVGEALGRLDQRERYI 241

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            E R + + P+TL+ L   F  SRER RQ+E RA +K++E ++ 
Sbjct: 242 IEMRVMSDRPLTLKELGEHFGFSRERARQLEIRAKEKLKEELRA 285


>gi|23308878|ref|NP_601117.2| RNA polymerase sigma factor [Corynebacterium glutamicum ATCC 13032]
 gi|21324681|dbj|BAB99304.1| DNA-directed RNA polymerase sigma subunits (sigma70/sigma32) (SigA)
           [Corynebacterium glutamicum ATCC 13032]
          Length = 498

 Score =  243 bits (621), Expect = 2e-62,   Method: Composition-based stats.
 Identities = 78/325 (24%), Positives = 149/325 (45%), Gaps = 49/325 (15%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR----------------EHG 45
            RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR                    G
Sbjct: 179 ARKDAELTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYATHRMEEMEEAFAAG 237

Query: 46  DLS--------------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           D                      A + L+ ++LRLVV +A  Y G G+   +++ EGN+G
Sbjct: 238 DKDAKLTPAVKRDLRAIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLG 297

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  
Sbjct: 298 LIRAVEKFDYSKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRE 355

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           L         P     ++K++++SE +V+ +        SL+  I   D+  SQ  D++ 
Sbjct: 356 LLQELGREPTP---QELSKEMDISEEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI- 409

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFE 263
              D +  V ++       ++ L   +  L+ RE  + + R    +  P TL+ +   + 
Sbjct: 410 --EDSEAVVAVDAVSFTLLQDQLQDVLETLSEREAGVVKLRFGLTDGMPRTLDEIGQVYG 467

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           V+RER+RQIE++   K++   + QV
Sbjct: 468 VTRERIRQIESKTMSKLRHPSRSQV 492


>gi|172040581|ref|YP_001800295.1| RNA polymerase sigma factor [Corynebacterium urealyticum DSM 7109]
 gi|171851885|emb|CAQ04861.1| RNA polymerase sigma factor A [Corynebacterium urealyticum DSM
           7109]
          Length = 545

 Score =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 75/319 (23%), Positives = 152/319 (47%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------REHGDL- 47
            R++ ++  + +  +  Y+ +I K+ +L  ++E  LAKR              +E G+  
Sbjct: 232 ARRDAALTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYANYRLKQIKESGERL 290

Query: 48  ----------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 291 SPMNRRDLREIDRDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 350

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 351 KFDYSKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 408

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +A++++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 409 REPTPE---ELAREMDITVDKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 460

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERV 269
             + ++       ++ L   +  L+ RE  + + R    +  P TL+ +   + V+RER+
Sbjct: 461 AVIAVDAVSFTLLQDQLQDVLHTLSEREAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERI 520

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 521 RQIESKTMSKLRHPSRSQV 539


>gi|257464031|ref|ZP_05628416.1| RNA polymerase sigma factor rpoD [Fusobacterium sp. D12]
          Length = 436

 Score =  243 bits (621), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 81/277 (29%), Positives = 142/277 (51%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI +IP+L  +EE  LAK+  E GD  A  RL+ ++LRLVV IA  +   G
Sbjct: 163 DEPIKMYLREIGQIPLLTHKEELELAKKALE-GDEFANKRLIEANLRLVVSIAKKHTNRG 221

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L + +++ EGNIGLM+AV+KF+  +G++ +TY+ WWI+ A+   I      ++I      
Sbjct: 222 LKLLDLIQEGNIGLMKAVEKFEYTKGYKFSTYATWWIRQAITRAIADQGRTIRIPVH--- 278

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
             +   + ++K   +       K      +A++L +   +V S+        SL   + S
Sbjct: 279 --MIETINKIKKEARIYLQETGKDATPEILAERLGMEVEKVKSIQEMNQDPISLETPVGS 336

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN- 251
             +  S+  D++    D +     E   R   R  L   +  L+ RE ++   R   ++ 
Sbjct: 337 --EEDSELGDFV---EDQKMLTPYELTNRSLLREQLDSVLGSLSSREEKVLRYRYGLDDG 391

Query: 252 -PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            P TLE +   F+V+RER+RQIE +A +K++   +++
Sbjct: 392 SPKTLEEVGKIFKVTRERIRQIEVKALRKLRHPSRRK 428


>gi|294102609|ref|YP_003554467.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Aminobacterium
           colombiense DSM 12261]
 gi|293617589|gb|ADE57743.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Aminobacterium
           colombiense DSM 12261]
          Length = 377

 Score =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 77/276 (27%), Positives = 136/276 (49%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI K+P+LE  +E  LAKR  E G+  A  +++ ++LRLVV IA  Y G G+
Sbjct: 106 DPVRMYLREIGKVPLLEPAQEVELAKRV-EAGEEEAKQQIIDANLRLVVSIAKKYIGRGM 164

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      +++     + 
Sbjct: 165 LFLDLIQEGNLGLIRAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRVPVHMVE- 223

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                + ++    + +     +      IA ++ +  S+V  +        SL   I   
Sbjct: 224 ----TINKMVRVSRQLVQKLGREPTDEEIAAEMEIEPSKVEEIRRIAQLPVSLETPI--G 277

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           ++  SQ  D++    D       E          +   +  L+ RER + + R   E+  
Sbjct: 278 EEEDSQLGDFI---EDRDLPSPEEAAASHLLHEQIDEMLEALSEREREVLQYRFGLEDGR 334

Query: 254 --TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 335 SYTLEEVGKRFGVTRERIRQIEAKALRKLRHPSRSK 370


>gi|171909626|ref|ZP_02925096.1| RNA polymerase sigma factor [Verrucomicrobium spinosum DSM 4136]
          Length = 298

 Score =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 83/277 (29%), Positives = 157/277 (56%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           + G+  Y+ EI K  +L  Q+E  LA+R ++ GD  A   ++ ++LRLVVKIA  Y  YG
Sbjct: 7   DGGIKIYLREIGKTDLLTPQQEVELAERIKK-GDPEARSHMIRANLRLVVKIAQDYANYG 65

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP+ +++SEGNIGLM+AV++FDP +G +L+TY+ WWIK +++  +      +++      
Sbjct: 66  LPLLDLISEGNIGLMKAVERFDPNKGGKLSTYAAWWIKQSIKRALANQSKTIRLPVH--- 122

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
             +   + +++    A+++   +      +++++ +   ++  +        SL+A I  
Sbjct: 123 --MVDKISKMRRVAMAMSEELGREPTDDELSEEIGIDRGKLSQLKVASMRPASLDAPI-- 178

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN- 251
           S+ +S+++ + +    D   Q   +    KN  + L   ++VL+ RER+I +AR      
Sbjct: 179 SEDDSTEFGEIV---GDENAQTPFDLLSHKNMHSQLDGLLTVLDERERKIIDARFGLNGQ 235

Query: 252 -PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE +  EF V+RER+RQ++  A +K++ ++QK+
Sbjct: 236 KARTLEEVGQEFGVTRERIRQLQNIALRKLRRALQKK 272


>gi|257470878|ref|ZP_05634968.1| RNA polymerase sigma factor rpoD [Fusobacterium ulcerans ATCC
           49185]
 gi|317065080|ref|ZP_07929565.1| RNA polymerase sigma factor rpoD [Fusobacterium ulcerans ATCC
           49185]
 gi|313690756|gb|EFS27591.1| RNA polymerase sigma factor rpoD [Fusobacterium ulcerans ATCC
           49185]
          Length = 418

 Score =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 81/285 (28%), Positives = 145/285 (50%), Gaps = 13/285 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           N+S  +  +  +  Y+ EI +IP+L   EE   AKR  E GD  A+ +L+ ++LRLVV I
Sbjct: 138 NLSGDMKVDEPIKMYLREIGQIPLLSHDEELEYAKRALE-GDDWASKQLIEANLRLVVSI 196

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  +   GL + +++ EGNIGLM+AV+KF+  +G++ +TY+ WWI+ A+   I      +
Sbjct: 197 AKKHTNRGLKLLDLIQEGNIGLMKAVEKFEYSKGYKFSTYATWWIRQAITRAIADQGRTI 256

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I        +   + ++K   +       K      + ++L +   +V ++        
Sbjct: 257 RIPVH-----MIETINKIKKEARIYLQETGKDATPEVLGERLGMEVDKVKAIQEMNQDPI 311

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   + S  +  S+  D++    D +     E   R   R  L   ++ L+ RE R+  
Sbjct: 312 SLETPVGS--EEDSELGDFV---EDHKMLNPYELTNRSLLREQLNGVLNTLSSREERVLR 366

Query: 245 ARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R   ++  P TLE +   F+V+RER+RQIE +A +K++   +++
Sbjct: 367 YRYGLDDGSPKTLEEVGKIFKVTRERIRQIEVKALRKLRHPSRRK 411


>gi|220917075|ref|YP_002492379.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter
           dehalogenans 2CP-1]
 gi|219954929|gb|ACL65313.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter
           dehalogenans 2CP-1]
          Length = 307

 Score =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 114/284 (40%), Positives = 168/284 (59%), Gaps = 6/284 (2%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
             +      L  Y+ EI + P+L  ++E  LA++Y    D  AAHRLVT++LR VVK+A 
Sbjct: 4   QSVPGTASSLEVYLSEINRFPLLTVEDEQRLARQYCADRDTRAAHRLVTANLRFVVKVAY 63

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            YR YG  +++++ EGNIGLM+AV+KFDP++G RL +Y++WWI+A +Q YIL+SWSLVK+
Sbjct: 64  EYRSYGFRMADLIQEGNIGLMKAVQKFDPDKGIRLISYAVWWIRAYIQNYILKSWSLVKL 123

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKP---EQVVAIAKKLNVSESEVISMNCRLAG- 182
           GTT  Q++LFF+L R K  L   +  +           +AKKL V   EV  M  R+ G 
Sbjct: 124 GTTQAQRKLFFSLARTKRELDKRSQEHGADSDGHDANKVAKKLRVKPGEVREMEQRMEGR 183

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
           D SL+A +   D       D+L      Q+  L   +E+K     +  ++  L+ RER I
Sbjct: 184 DLSLDAPM--GDDGGYSHVDFLPSGTASQDDELSGVQEQKVVSGRVVEALGRLDQRERYI 241

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            E R + + P+TL+ L   F  SRER RQ+E RA +K++E ++ 
Sbjct: 242 IEMRVMSDRPLTLKELGEHFGFSRERARQLEIRAKEKLKEELRA 285


>gi|256375646|ref|YP_003099306.1| RNA polymerase sigma factor [Actinosynnema mirum DSM 43827]
 gi|255919949|gb|ACU35460.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Actinosynnema
           mirum DSM 43827]
          Length = 435

 Score =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 77/319 (24%), Positives = 146/319 (45%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------ 43
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR                     
Sbjct: 122 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYAAERLRRAEDESEKL 180

Query: 44  ------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 181 TPQMRRDLRWIVRDGERAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 240

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 241 KFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 298

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 299 REPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 350

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   ++ L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 351 AVVAVDAVSFTLLQDQLQSVLATLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 410

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 411 RQIESKTMSKLRHPSRSQV 429


>gi|209519627|ref|ZP_03268417.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. H160]
 gi|209499913|gb|EDZ99978.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. H160]
          Length = 311

 Score =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 121/277 (43%), Positives = 165/277 (59%), Gaps = 12/277 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  YI  + +IPML   EE   A   REH +L AA RLV SHLRLVV IA  Y GYGL
Sbjct: 37  GNIDAYIQAVNRIPMLTPAEERQFATELREHDNLEAARRLVLSHLRLVVSIARNYLGYGL 96

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P ++++ EGNIGLM+AVK+FDPE+  RL +Y+M WIKA + EYILR+W +VK+ TT  Q+
Sbjct: 97  PHADLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHWIKAEIHEYILRNWRMVKVATTKAQR 156

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINS 192
           +LFFNLR  K  L A T     P+++  +A++LNV   EV  M  RL  GD +L   +  
Sbjct: 157 KLFFNLRSHKQGLGAFT-----PDEIDGLARELNVKREEVAEMETRLSGGDIALEGQVED 211

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---- 248
            ++ S     +L   H     VL  ++  +   + +  ++  L+PR RRI EAR L    
Sbjct: 212 GEE-SYAPIAYLADSHSEPTAVLASRQRDRLHSDGIASALDALDPRSRRIIEARWLKVAD 270

Query: 249 -QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                 TL  L+ EF VS ER+RQIEA A KK++ ++
Sbjct: 271 DGSGGSTLHELADEFGVSAERIRQIEASAMKKMRGAL 307


>gi|254975054|ref|ZP_05271526.1| RNA polymerase sigma factor rpoD [Clostridium difficile QCD-66c26]
 gi|255092443|ref|ZP_05321921.1| RNA polymerase sigma factor rpoD [Clostridium difficile CIP 107932]
 gi|255100524|ref|ZP_05329501.1| RNA polymerase sigma factor rpoD [Clostridium difficile QCD-63q42]
 gi|255308764|ref|ZP_05352935.1| RNA polymerase sigma factor rpoD [Clostridium difficile ATCC 43255]
 gi|255314181|ref|ZP_05355764.1| RNA polymerase sigma factor rpoD [Clostridium difficile QCD-76w55]
 gi|255516860|ref|ZP_05384536.1| RNA polymerase sigma factor rpoD [Clostridium difficile QCD-97b34]
 gi|255649961|ref|ZP_05396863.1| RNA polymerase sigma factor rpoD [Clostridium difficile QCD-37x79]
 gi|306520043|ref|ZP_07406390.1| RNA polymerase sigma factor rpoD [Clostridium difficile QCD-32g58]
          Length = 294

 Score =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 75/277 (27%), Positives = 143/277 (51%), Gaps = 11/277 (3%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           N    +  Y+ EI +  ML   EE  LAK       + A  + + S+ RLVV IA  Y+ 
Sbjct: 19  NVSNAMKMYLKEIEEYKMLSAGEEVELAKEIINSSSV-AKEKFINSNYRLVVSIAKRYKR 77

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
             + + +++  GNIGL++AV+K+D ++G++ +TY+ WWIK ++  YI    + ++I    
Sbjct: 78  DSIDMLDLIQAGNIGLIKAVEKYDYKKGYKFSTYATWWIKQSITRYIDDCENTIRIPIHL 137

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
           +Q+     +  +K   Q + +  L+   +  IA    +   +V+ +  R     SL+  +
Sbjct: 138 HQR-----INFVKKKKQELLNVLLREPTIDEIADACGLEVDKVLELLRRDKNVVSLDTPL 192

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-- 248
              +   S   +++  D D +  V+I + E+ N +  +   ++ L  +E+++   R    
Sbjct: 193 K--EDEDSSLVEFIPSDADFK-DVVIHEVEQHNLKEKIEELLTGLGEQEQQVLRMRFGID 249

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            ++P TLE +   F V+RER+RQIEA+A +K++   +
Sbjct: 250 DDDPKTLEQIGKVFGVTRERIRQIEAKAIRKLRHPSK 286


>gi|227503480|ref|ZP_03933529.1| RNA polymerase major sigma subunit [Corynebacterium accolens ATCC
           49725]
 gi|227075983|gb|EEI13946.1| RNA polymerase major sigma subunit [Corynebacterium accolens ATCC
           49725]
          Length = 493

 Score =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 78/325 (24%), Positives = 150/325 (46%), Gaps = 49/325 (15%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY----------------REHG 45
            RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR                 R  G
Sbjct: 174 ARKDAQLTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYAQHRMDEMEKARAEG 232

Query: 46  DL--------------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           D                      A + L+ ++LRLVV +A  Y G G+   +++ EGN+G
Sbjct: 233 DKAAKLSPMEKRDLRSIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLG 292

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  
Sbjct: 293 LIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRE 350

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           L         P     +AK+++++E +V+ +        SL+  I   D+  SQ  D++ 
Sbjct: 351 LLQDLGREPTP---QELAKEMDITEEKVMEIQQYAREPISLDQTI--GDEGDSQLGDFI- 404

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFE 263
              D +  + ++       ++ L   ++ L+ RE  +   R    +  P TL+ +   + 
Sbjct: 405 --EDSEAVIAVDAVSFTLLQDQLQDVLTTLSEREAGVVRLRFGLTDGMPRTLDEIGQVYG 462

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           V+RER+RQIE++   K++   + QV
Sbjct: 463 VTRERIRQIESKTMSKLRHPSRSQV 487


>gi|52842873|ref|YP_096672.1| RNA polymerase factor sigma-32 [Legionella pneumophila subsp.
           pneumophila str. Philadelphia 1]
 gi|52629984|gb|AAU28725.1| RNA polymerase sigma-32 factor RpoH [Legionella pneumophila subsp.
           pneumophila str. Philadelphia 1]
          Length = 292

 Score =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 110/274 (40%), Positives = 177/274 (64%), Gaps = 7/274 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             L  YIH + +IPML  +EE   A+R+   GD+ AA +LV +HLR VV++A GY GYGL
Sbjct: 23  GSLDSYIHRVNQIPMLTLEEEIAYAERFHSEGDIEAARQLVLAHLRYVVRVARGYLGYGL 82

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+S+++ EGN+GLM+AVK+FDP+ G RL ++++ WIKA + E++LR+W +VK+ TT  Q+
Sbjct: 83  PLSDLIQEGNVGLMKAVKRFDPKMGVRLVSFAVHWIKAEIHEFVLRNWRIVKVATTKAQR 142

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINS 192
           +LFFNLR++K  L   ++     E+V A+AK L VS  +V+ M  RL   D S +A    
Sbjct: 143 KLFFNLRQMKNRLGWFSN-----EEVDAVAKDLGVSREDVLLMEQRLNVMDSSYDAPDVD 197

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPRERRIFEARRLQEN 251
            + ++ +  +  +++ +    VL+E E+  ++ R  L  +M  L+ R + I + R L E 
Sbjct: 198 DNDDAYKAPERYLFNVNDDPAVLLENEDTGDQGREKLLFAMEQLDERSQDILQQRWLAEE 257

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            +TL +L+ ++ VS ERVRQ+E  A KK+++ ++
Sbjct: 258 KLTLHDLAEKYGVSAERVRQLEKNAMKKIRQYME 291


>gi|251771333|gb|EES51914.1| RNA polymerase, sigma 70 subunit, RpoD family [Leptospirillum
           ferrodiazotrophum]
          Length = 307

 Score =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 98/294 (33%), Positives = 158/294 (53%), Gaps = 15/294 (5%)

Query: 10  VNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           V+G+IG L+ Y+  +R  P+L   EE  LA+R    GD  A  R++ S+LRLVV IA  Y
Sbjct: 23  VSGDIGSLALYLRTLRDYPLLSASEEVDLARRIA-TGDAEARERMILSNLRLVVMIAKRY 81

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            G GLP  +++ EGN+GLM+AV ++DPE+GFR +TY+ WWI+ +++  ++    ++++  
Sbjct: 82  AGRGLPFPDLIEEGNLGLMKAVDRYDPEKGFRFSTYASWWIRQSIERAVINLGHMIRLPV 141

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
              +K     + R    ++ +     +P+   A A+K  ++  E  S+   +A   SL+A
Sbjct: 142 HMREK-----VNRYLAAVEQMVSTGREPDPSEA-ARKAGLTVEEFESLYPLIAATISLDA 195

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +   D+N+   +D L    D +    +E   R+     L  ++SVL PRER I   R  
Sbjct: 196 PVGEQDENT--LKDVL---GDPEADSPLEVVSRREEGRELEAALSVLRPRERDILFLRFG 250

Query: 249 --QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQKP 300
              E+P TL+ +     ++RERVRQIEA A  K++  I      +S    L  P
Sbjct: 251 LSGEDPKTLDEIGRRLGITRERVRQIEAVALSKMRAYIDDARPFASHHSPLPPP 304


>gi|238755238|ref|ZP_04616583.1| RNA polymerase sigma-32 factor [Yersinia ruckeri ATCC 29473]
 gi|238706579|gb|EEP98951.1| RNA polymerase sigma-32 factor [Yersinia ruckeri ATCC 29473]
          Length = 285

 Score =  243 bits (620), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 103/290 (35%), Positives = 163/290 (56%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  YI      PML  +EE  LA+R    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLALVPQGSLEAYIRAANAYPMLTAEEERELAERLHYQGDLGAAKKLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VAHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          E+V  +AK+L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----EEVELVAKELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNP 237
           +  +         D    Q    ++Y  D        + E     +  + L+ ++  L+ 
Sbjct: 176 SAQDMTFDPTPDDDVRDGQSMAPVLYLQDKTSDFADGIEEDNWESHAADKLSYALEGLDE 235

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L ++   TL+ L+ ++ VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQHIIRARWLDDDNKTTLQELADQYGVSAERVRQLEKNAMKKLRIAIEA 285


>gi|303256291|ref|ZP_07342307.1| alternative sigma factor RpoH [Burkholderiales bacterium 1_1_47]
 gi|330998988|ref|ZP_08322713.1| alternative sigma factor RpoH [Parasutterella excrementihominis YIT
           11859]
 gi|302861020|gb|EFL84095.1| alternative sigma factor RpoH [Burkholderiales bacterium 1_1_47]
 gi|329575730|gb|EGG57256.1| alternative sigma factor RpoH [Parasutterella excrementihominis YIT
           11859]
          Length = 306

 Score =  242 bits (619), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 113/288 (39%), Positives = 167/288 (57%), Gaps = 12/288 (4%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           ++I       L  YI    K P+L  + E+ LA R +EHGD+ AA  LV SHLRLV+ IA
Sbjct: 22  LAIPDASLGSLEEYIRAANKAPILSAEREHELAVRLQEHGDMEAAGELVMSHLRLVISIA 81

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y+GYGLP  +++ EGNIGLM+AVK+F+P  G RL T++M WIK+ +QEY+LR+W LVK
Sbjct: 82  RQYQGYGLPFGDLIQEGNIGLMKAVKRFNPNNGARLVTFAMTWIKSEIQEYVLRNWRLVK 141

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDE 184
           + TT +Q++LFFNLR+LK   + +        +   IA+ L+V  SEV  M  R+   D 
Sbjct: 142 VATTKSQRKLFFNLRKLKDDTKLLG-----TSEAEKIAETLDVKPSEVFEMEKRMLGSDV 196

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
            ++     +D+  +   +WL  + D  E  +          N L  ++  L+ R RRI E
Sbjct: 197 EIDEPSGGTDEGMA-PSEWLTDERDTPENTIARGAYENTIENRLPEAVKKLDDRSRRIIE 255

Query: 245 ARRLQEN-----PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           AR L  +       TL +L+ E  VS+ERVRQ+E +AF  ++  +++ 
Sbjct: 256 ARWLYNDQDGSKGATLADLAKEMGVSQERVRQLEKKAFATLKTYLKED 303


>gi|255325126|ref|ZP_05366232.1| RNA polymerase major sigma subunit [Corynebacterium
           tuberculostearicum SK141]
 gi|311739588|ref|ZP_07713423.1| RNA polymerase sigma factor rpoD [Corynebacterium pseudogenitalium
           ATCC 33035]
 gi|255297691|gb|EET77002.1| RNA polymerase major sigma subunit [Corynebacterium
           tuberculostearicum SK141]
 gi|311305404|gb|EFQ81472.1| RNA polymerase sigma factor rpoD [Corynebacterium pseudogenitalium
           ATCC 33035]
          Length = 490

 Score =  242 bits (619), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 78/325 (24%), Positives = 150/325 (46%), Gaps = 49/325 (15%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY----------------REHG 45
            RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR                 R  G
Sbjct: 171 ARKDAQLTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYAQHRMDEMEKARAEG 229

Query: 46  DL--------------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           D                      A + L+ ++LRLVV +A  Y G G+   +++ EGN+G
Sbjct: 230 DKAAKLSPMEKRDLRSIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLG 289

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  
Sbjct: 290 LIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRE 347

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           L         P     +AK+++++E +V+ +        SL+  I   D+  SQ  D++ 
Sbjct: 348 LLQDLGREPTP---QELAKEMDITEEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI- 401

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFE 263
              D +  + ++       ++ L   ++ L+ RE  +   R    +  P TL+ +   + 
Sbjct: 402 --EDSEAVIAVDAVSFTLLQDQLQDVLTTLSEREAGVVRLRFGLTDGMPRTLDEIGQVYG 459

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           V+RER+RQIE++   K++   + QV
Sbjct: 460 VTRERIRQIESKTMSKLRHPSRSQV 484


>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 =  242 bits (619), Expect = 3e-62,   Method: Composition-based stats.
 Identities = 74/276 (26%), Positives = 131/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +H+I K   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 342 LHQIEKETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 401

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 402 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 459

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +     +   PE    +A+++ +SE ++  +        S+   +   D   
Sbjct: 460 KLNRVSRQMLQEIGHEPTPE---ELAERMLMSEDKIRKVLKIAKEPISMETPV--GDDED 514

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D    + ++     N R      +S L PRE ++   R   +     TL
Sbjct: 515 SHLGDFI---EDTNHDLPLDSATSDNLRTATHDILSGLTPREAKVLRMRFGIDMNTDHTL 571

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + ++  S
Sbjct: 572 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEILRS 607


>gi|154249128|ref|YP_001409953.1| RpoD family RNA polymerase sigma factor [Fervidobacterium nodosum
           Rt17-B1]
 gi|154153064|gb|ABS60296.1| RNA polymerase, sigma 70 subunit, RpoD family [Fervidobacterium
           nodosum Rt17-B1]
          Length = 372

 Score =  242 bits (619), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 72/273 (26%), Positives = 141/273 (51%), Gaps = 13/273 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y+ +I KI +L   EE  LA+R  + GD  A   L+ S+LRLVV +A  Y G GL  
Sbjct: 98  IKMYLRDIGKIRLLTPSEEKRLAQR-AQMGDQRAKEELIISNLRLVVSMAKRYLGKGLSF 156

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EG++GL++AV+KFD  +G++ +TY+ WWI+ A+   I      +++     +   
Sbjct: 157 LDLIQEGSLGLIKAVEKFDWSKGYKFSTYATWWIRQAITRAIADQARTIRVPVHMVE--- 213

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + +++   +     + +   +  IA+++     ++  +        SL   +  +++
Sbjct: 214 --TINKIQKIKREYVQEHGEEPSIEYIAEQVGKPVDKIEEILQAAPETLSLETPV--NEE 269

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PV 253
           + S   D++  +  G  +   ++  R   R  + + +  LN RE+++ + R    N  P+
Sbjct: 270 DDSSMGDFIADESIGSPK---KEAIRTLMREEIDKLLETLNDREKKVLKMRYGLYNGKPM 326

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TLE +   F V+RER+RQIE +A +K++   + 
Sbjct: 327 TLEEVGQFFGVTRERIRQIEVKALRKLRHPSRS 359


>gi|12958492|gb|AAK09321.1|AF320817_2 sigma factor SigA [[Brevibacterium] flavum]
          Length = 498

 Score =  242 bits (619), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 78/325 (24%), Positives = 149/325 (45%), Gaps = 49/325 (15%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR----------------EHG 45
            RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR                    G
Sbjct: 179 ARKDAELTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYATHRMEEMEEAFAAG 237

Query: 46  DLS--------------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           D                      A + L+ ++LRLVV +A  Y G G+   +++ EGN+G
Sbjct: 238 DKDAKLTPAVRRDLRAIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLG 297

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  
Sbjct: 298 LIRAVEKFDYSKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRE 355

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           L         P     ++K++++SE +V+ +        SL+  I   D+  SQ  D++ 
Sbjct: 356 LLQELGREPTP---QELSKEMDISEEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI- 409

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFE 263
              D +  V ++       ++ L   +  L+ RE  + + R    +  P TL+ +   + 
Sbjct: 410 --EDSEAVVAVDAVSFTLLQDQLQDVLETLSEREAGVVKLRFGLTDGMPRTLDEIGQVYG 467

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           V+RER+RQIE++   K++   + QV
Sbjct: 468 VTRERIRQIESKTMSKLRHPSRSQV 492


>gi|126699102|ref|YP_001087999.1| RNA polymerase sigma factor rpoD [Clostridium difficile 630]
 gi|115250539|emb|CAJ68363.1| RNA polymerase sigma factor SigA2 (sigma-43) [Clostridium
           difficile]
          Length = 296

 Score =  242 bits (619), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 75/277 (27%), Positives = 143/277 (51%), Gaps = 11/277 (3%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           N    +  Y+ EI +  ML   EE  LAK       + A  + + S+ RLVV IA  Y+ 
Sbjct: 21  NVSNAMKMYLKEIEEYKMLSAGEEVELAKEIINSSSV-AKEKFINSNYRLVVSIAKRYKR 79

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
             + + +++  GNIGL++AV+K+D ++G++ +TY+ WWIK ++  YI    + ++I    
Sbjct: 80  DSIDMLDLIQAGNIGLIKAVEKYDYKKGYKFSTYATWWIKQSITRYIDDCENTIRIPIHL 139

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
           +Q+     +  +K   Q + +  L+   +  IA    +   +V+ +  R     SL+  +
Sbjct: 140 HQR-----INFVKKKKQELLNVLLREPTIDEIADACGLEVDKVLELLRRDKNVVSLDTPL 194

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-- 248
              +   S   +++  D D +  V+I + E+ N +  +   ++ L  +E+++   R    
Sbjct: 195 K--EDEDSSLVEFIPSDADFK-DVVIHEVEQHNLKEKIEELLTGLGEQEQQVLRMRFGID 251

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            ++P TLE +   F V+RER+RQIEA+A +K++   +
Sbjct: 252 DDDPKTLEQIGKVFGVTRERIRQIEAKAIRKLRHPSK 288


>gi|121595815|ref|YP_987711.1| RNA polymerase sigma-32 subunit RpoH [Acidovorax sp. JS42]
 gi|120607895|gb|ABM43635.1| RNA polymerase, sigma 32 subunit, RpoH [Acidovorax sp. JS42]
          Length = 321

 Score =  242 bits (619), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 114/292 (39%), Positives = 173/292 (59%), Gaps = 12/292 (4%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +V     L  YI  + ++P+L ++EE   A++ ++  ++ AA RLV SHLRLVV I+  Y
Sbjct: 30  LVPPLGNLDAYISAVNRLPLLTQEEEQRYARQLKDDNNVEAAGRLVLSHLRLVVSISRQY 89

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGLP  +++ EGN+GLM+AVK+FDP++G RL +Y+M WIKA + EYIL++W +VK+ T
Sbjct: 90  LGYGLPHGDLIQEGNVGLMKAVKRFDPDQGVRLVSYAMHWIKAEIHEYILKNWRMVKVAT 149

Query: 129 TANQKRLFFNLRRLKG-----HLQAITDNN-LKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           T  Q++LFFNLR +K       L A T    L   ++  +A++LNV   EVI M  RL+G
Sbjct: 150 TKAQRKLFFNLRSMKQGFKADALDADTHRETLSDHEIDLVAEQLNVKREEVIEMETRLSG 209

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLNPRERR 241
            + L     S D   +      + D   +   LIE  +R     + +  ++  L+ R RR
Sbjct: 210 GDVLLDPAPSDDGEQAFGPIAYLADAGHEPTALIESRQRDALATDGIATALDSLDARSRR 269

Query: 242 IFEARRLQENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           I E R LQ N      +TL  L++E+ VS ER+RQIE  A KK+++++ +  
Sbjct: 270 IVEQRWLQVNDDGSGGMTLHELATEYGVSAERIRQIEVAAMKKMKKALAEYA 321


>gi|133286|sp|P11539|RP32_CITFR RecName: Full=RNA polymerase sigma-32 factor; AltName: Full=Heat
           shock regulatory protein
 gi|40469|emb|CAA33083.1| unnamed protein product [Citrobacter freundii]
          Length = 284

 Score =  242 bits (619), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 105/289 (36%), Positives = 163/289 (56%), Gaps = 8/289 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +     L  YI      PML   EE  LA++    GDL AA  L+ SHLR 
Sbjct: 1   MTKEMQNLALAPVGNLESYIRAANAWPMLSADEERALAEKLHYQGDLEAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y GYGL  ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARNYAGYGLRQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVEMVARELGVSSKDVREMESRM 175

Query: 181 -AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPR 238
            A D + +   +    +        + D        IE++  +++  N LT +M  L+ R
Sbjct: 176 AAQDMTFDMSSDDESDSQPMAPVLYLQDKSSNFADGIEEDNWEDQAANKLTHAMEGLDER 235

Query: 239 ERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + I  AR L E+   TL+ L+  + VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 SQDIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 284


>gi|254430902|ref|ZP_05044605.1| DNA-directed RNA polymerase sigma subunit [Cyanobium sp. PCC 7001]
 gi|197625355|gb|EDY37914.1| DNA-directed RNA polymerase sigma subunit [Cyanobium sp. PCC 7001]
          Length = 503

 Score =  242 bits (619), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 78/313 (24%), Positives = 143/313 (45%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE--------------HG------------ 45
            E  +  Y+ EI +I +L   EE  LA++  +              HG            
Sbjct: 191 TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLQLEELAAQFEADHGHYPDNKEWAALV 250

Query: 46  -------------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 251 DMPLIKFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 310

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 311 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKTLSQE 365

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA+ + ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 366 FGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADIENPE 423

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
           Q + +   R++    L   ++ L+PRER +   R   ++    TLE +   F+V+RER+R
Sbjct: 424 QDVAKNLLRED----LEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIR 479

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 480 QIEAKALRKLRHP 492


>gi|73667010|ref|YP_303026.1| sigma-70 region 2:sigma-70 region 4 [Ehrlichia canis str. Jake]
 gi|72394151|gb|AAZ68428.1| RNA polymerase, sigma 32 subunit, RpoH [Ehrlichia canis str. Jake]
          Length = 300

 Score =  242 bits (619), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 134/286 (46%), Positives = 189/286 (66%), Gaps = 4/286 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N    SI    +  L  Y++E+   P+L  +EE  LAK + E+G +  AHRLVTSHLRL
Sbjct: 5   INMLTNSIFSLTQDNLMSYMNEVHTFPILSPEEEDRLAKNWYENGIVEDAHRLVTSHLRL 64

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VVKIA+ ++ YGLP+ E++ EGNIGLMQAVKKF+P  GFRL+TY++WWIKA++++YIL+S
Sbjct: 65  VVKIALSFKNYGLPLIELIMEGNIGLMQAVKKFNPTLGFRLSTYAIWWIKASIKDYILKS 124

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WS +KIGTT  Q++LFF+LR++K  L     NN+  + +  IA + + SE EV  MN   
Sbjct: 125 WSCIKIGTTQAQRKLFFSLRKIKQKLFKY--NNITQDDIKLIANECSTSEQEVEQMNRYF 182

Query: 181 A-GDESLNALINSSDKN-SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
              D SLN ++ S+D     + Q+ +  D   QE   +  EE   +  ++T+++S LN R
Sbjct: 183 TYRDRSLNEVVFSNDNQKGIELQEIIKCDTPNQEDTYLLNEEASLKETLITQALSTLNER 242

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            R IF  RRL ENP TL+ LS E+++S+ERVRQIE  AF KV+  I
Sbjct: 243 YRDIFIRRRLIENPDTLDTLSQEYKISKERVRQIEMHAFTKVKNFI 288


>gi|77919976|ref|YP_357791.1| RNA polymerase, sigma (32) factor [Pelobacter carbinolicus DSM
           2380]
 gi|77546059|gb|ABA89621.1| RNA polymerase, sigma 32 subunit, RpoH [Pelobacter carbinolicus DSM
           2380]
          Length = 286

 Score =  242 bits (619), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 122/283 (43%), Positives = 188/283 (66%), Gaps = 8/283 (2%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
             N+ + V+    LS YI +IR   +L K+EE+ L + Y  + ++ AA +L+ ++LR VV
Sbjct: 1   MNNLPLPVS-SDNLSLYIAQIRAFELLTKEEEFRLTQDYHRNQNIEAAQQLICANLRFVV 59

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           KIA  YRGYGL + +++ EGNIGLM+AVKKFDP+RG R  TY++WWI+A +  +I+R+WS
Sbjct: 60  KIAHEYRGYGLKLLDIIQEGNIGLMKAVKKFDPDRGLRFITYAVWWIRAYIHNFIIRNWS 119

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           LVKIGTT  QK+LFF L +++  +Q +T      E   AIA++LNV + EV  M  R+AG
Sbjct: 120 LVKIGTTQAQKKLFFKLNQVRSAIQRMTG----SEDTKAIARELNVRDDEVEDMARRMAG 175

Query: 183 -DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
            D SL+  +   +  +    D L  + + QE++LI+++E++   + +  ++  LN RERR
Sbjct: 176 RDTSLDMRLVEGEDFT--LLDSLADERESQEELLIKQQEKQITTSHIHGALQELNDRERR 233

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           I E R LQE P TL+ L+ +F +SRERVRQ+E  A +K+++++
Sbjct: 234 IVEERILQEEPRTLQALADDFGISRERVRQLEKNALEKIRKTL 276


>gi|270264290|ref|ZP_06192557.1| RNA polymerase sigma-32 factor [Serratia odorifera 4Rx13]
 gi|270041939|gb|EFA15036.1| RNA polymerase sigma-32 factor [Serratia odorifera 4Rx13]
          Length = 285

 Score =  242 bits (619), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 104/290 (35%), Positives = 162/290 (55%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  YI      PML  +EE  LA+R    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLALVPQGSLEAYIRAANTYPMLTAEEERELAERLHYQGDLEAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VAHIARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVELVARELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNP 237
           A  +         D    Q    ++Y  D        + E     N  + L  ++  L+ 
Sbjct: 176 AAQDMTFDPTPDDDARDGQSMAPVLYLQDKSSDFAEGIEEDNWESNAADKLAYALEGLDE 235

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L ++   TL+ L+ ++ VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQHIIRARWLDDDNKSTLQELADQYGVSAERVRQLEKNAMKKLKMAIEA 285


>gi|222053896|ref|YP_002536258.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter sp. FRC-32]
 gi|221563185|gb|ACM19157.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter sp. FRC-32]
          Length = 283

 Score =  242 bits (619), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 115/284 (40%), Positives = 184/284 (64%), Gaps = 9/284 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           MN  +M ++V+    LS Y+ EI++ P+L  +EE+  A R+ E  DL AAH+L+TS+LR 
Sbjct: 1   MNY-SMPVVVD---NLSLYLAEIKRFPVLSPEEEHECAVRFYEKKDLEAAHKLITSNLRF 56

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VVKIA  YR YG+ + +++ EGN+GLM AV+KF+P +GFRL +Y++WWI+A +Q +I+ +
Sbjct: 57  VVKIAGEYRAYGMKMLDLIQEGNVGLMMAVRKFNPHKGFRLISYAVWWIRAYIQNHIISA 116

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WSL+KIGTT  Q++LFF L + K  ++ +T      E   A A+ L+V E+EV  M+ R+
Sbjct: 117 WSLLKIGTTQAQRKLFFKLNQAKSAIRNMTGGG---EDFQATAEALDVKETEVAEMDQRM 173

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            GD  L+A + + +       + L  +   QE++L E +E       +  +++ LN +ER
Sbjct: 174 RGDFFLDAQVITGEG--LTMLESLPDERRNQEELLAEAQESALLEKQVASALTCLNEKER 231

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + E R   E+P+TL+ ++  F +SRERVRQIE  A KK+++++
Sbjct: 232 YVIEQRVSAESPLTLQEIADHFSISRERVRQIEEGALKKMKQAL 275


>gi|317403164|gb|EFV83689.1| RNA polymerase sigma factor [Achromobacter xylosoxidans C54]
          Length = 294

 Score =  242 bits (619), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 125/288 (43%), Positives = 177/288 (61%), Gaps = 13/288 (4%)

Query: 2   NRKNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           N   ++I   G +G +  YI  + ++P+L  + E  L +R R+  DL AA  LV SHLRL
Sbjct: 13  NALALAIANPGALGTIDAYISAVNRLPVLSAERETELGRRLRDSEDLGAARELVLSHLRL 72

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y GYGLP ++++ EGN+GLM+AVK+FDPERG RL ++++ WIKA + EYI+R+
Sbjct: 73  VVSVARQYLGYGLPHADLIQEGNVGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYIIRN 132

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W LVK+ TT  Q++LFFNLR ++          L PEQV  IA++LNV   +V  M  RL
Sbjct: 133 WRLVKVATTKAQRKLFFNLRSMR-----PDGQTLDPEQVDHIARELNVRREDVSEMEVRL 187

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQ--VLIEKEERKNRRNMLTRSMSVLNP 237
           +G D SL    N  D + S      + D   QE   VL      + + + L+ ++  L+P
Sbjct: 188 SGRDMSLE---NQDDDDDSYAPIAYLSDEGRQEPTRVLERAARDQLQSSGLSSALEALDP 244

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R RRI EAR LQ++   TL  L+ EF VS ER+RQIEA A KK++ ++
Sbjct: 245 RSRRIVEARWLQDDGGATLHELAQEFGVSAERIRQIEAAALKKMRGNL 292


>gi|330944706|gb|EGH46637.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. pisi str.
           1704B]
          Length = 284

 Score =  242 bits (619), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 101/272 (37%), Positives = 156/272 (57%), Gaps = 7/272 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+H +  IP+L  ++E  LA+      DL AA ++V +HLR VV IA  Y GYGL 
Sbjct: 16  NLEAYVHTVNSIPLLTPEQERELAESLYYEQDLDAARQMVLAHLRFVVHIARSYSGYGLA 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++
Sbjct: 76  QADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           LFFNLR  K  L  + +     ++V  +A+ L V   EV  M  RL G +        +D
Sbjct: 136 LFFNLRSQKKRLAWLNN-----DEVHRVAESLGVEPREVREMESRLTGHDMAFDPAAEAD 190

Query: 195 KNSS--QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            +S+     ++L        + L + +   N    L +++ VL+ R R I   R L E  
Sbjct: 191 DDSAFQSPANYLEDHRYDPARQLEDSDWTDNSPANLHQALDVLDERSRDILYQRWLAEEK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL +L+ ++ VS ER+RQ+E  A  K++ SI
Sbjct: 251 ATLHDLAQKYNVSAERIRQLEKSAMNKLKTSI 282


>gi|108805110|ref|YP_645047.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108766353|gb|ABG05235.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 366

 Score =  242 bits (619), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 83/284 (29%), Positives = 135/284 (47%), Gaps = 13/284 (4%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           ++  V     +  Y+ EI ++P+L   +E  LAK     G   +  +LV ++LRLVV IA
Sbjct: 87  LAHAVATGDSIRMYLAEIGRVPLLTHADEIRLAKAIS-RGCKRSKDKLVEANLRLVVSIA 145

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             YR  G+   +++ EGNIGL++A +KFD  +GF+ +TY+ WWI+ A+   I      ++
Sbjct: 146 KKYRNRGVSFLDLIQEGNIGLIRAAEKFDYRKGFKFSTYATWWIRQAITRAIADKGRTIR 205

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           I     +K       R +  +          E+V   A++L V   EV+ +        S
Sbjct: 206 IPVHMVEK--VNKYHRTQRRMTQALGREPTDEEV---AEELGVPVEEVLRLQEISQRSIS 260

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L   +   D  SS   D+L    D       +       +  L  ++  L  RER+I E 
Sbjct: 261 LETPV--GDDESSSLGDFL---EDASAVTPTDAVSESLLKLHLREALDELPERERQIIEM 315

Query: 246 RRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           R     + P TLE +  EF+++RERVRQI+ +    ++E  + Q
Sbjct: 316 RFGMKDDRPRTLEEVGREFDITRERVRQIQMKTLNLLREQRRTQ 359


>gi|51246044|ref|YP_065928.1| RNA polymerase sigma-B factor [Desulfotalea psychrophila LSv54]
 gi|50877081|emb|CAG36921.1| probable RNA polymerase sigma-B factor [Desulfotalea psychrophila
           LSv54]
          Length = 332

 Score =  242 bits (618), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 106/287 (36%), Positives = 173/287 (60%), Gaps = 8/287 (2%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
            N ++       L RY+ EI +  +L ++E   LA RY+E GD  AA+ LV+S+LRLVVK
Sbjct: 35  DNENLPAVSNPALHRYLQEISQYELLTREETDALATRYKESGDQDAAYTLVSSNLRLVVK 94

Query: 64  IAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           +AM ++ Y +    +++ EGN+GL+QA KKFDP RG + + Y+ +WI+A + ++I+ +W 
Sbjct: 95  VAMDFQKYWMQNFMDLIQEGNVGLVQATKKFDPYRGVKFSYYAAYWIRAYVLKFIMDNWR 154

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           LVKIGTT  Q++LFF+L + K     + ++     +   +A++LNV E EVI M  R+  
Sbjct: 155 LVKIGTTQAQRKLFFSLNKEKK----LLESQGFDPKPKLLAERLNVREKEVIEMGQRMDN 210

Query: 183 -DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
            D SL + + S   +  + + +L  +  G E V+  KE +     ++      LN +ER 
Sbjct: 211 WDVSLESPVRSDSDD--EQKSFLPSNGPGIESVVAGKEIKVKLTELIDVLKVNLNDKERM 268

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           I E R L + P+TL+N++ +F +SRERVRQIE    KK+++  + ++
Sbjct: 269 ILEKRLLTDEPLTLQNIADKFGISRERVRQIEVNLLKKMKKYFEAEM 315


>gi|302560773|ref|ZP_07313115.1| RNA polymerase sigma (70) factor RpoD [Streptomyces griseoflavus
           Tu4000]
 gi|302478391|gb|EFL41484.1| RNA polymerase sigma (70) factor RpoD [Streptomyces griseoflavus
           Tu4000]
          Length = 404

 Score =  242 bits (618), Expect = 4e-62,   Method: Composition-based stats.
 Identities = 83/301 (27%), Positives = 136/301 (45%), Gaps = 38/301 (12%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKR----------YREHGDLS------------ 48
                  +Y+ EI +IP+L   EE  LA+R           R   DL             
Sbjct: 103 PSSDLFRQYLREIGRIPLLTAAEEVELARRVEAGLFAEEKLRLTPDLDSGLALDLDRLVV 162

Query: 49  ----AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
               A  RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY
Sbjct: 163 MGRMAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTY 222

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + WWI+ AM   +      +++     +  L   + R++  +         P +V A   
Sbjct: 223 ATWWIRQAMSRALADQARTIRVPVHVVE--LINRVVRVQRRMLQERGYEPTPGEVAA--- 277

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            L++    V  +        SL+A +   +++     D +    DG     +E       
Sbjct: 278 HLDLPPERVGEVLRLAQEPVSLHAPV--GEEDDVALGDLI---EDGDAASPVESAAFLLL 332

Query: 225 RNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           R  L   +S L  RER++ + R       P TLE +   F V+RER+RQIE++   K+++
Sbjct: 333 REHLEAVLSTLGERERKVVQLRYGLVDGRPRTLEEIGRLFGVTRERIRQIESKTLNKLRD 392

Query: 283 S 283
            
Sbjct: 393 H 393


>gi|225630797|ref|YP_002727588.1| heat shock sigma factor RpoH [Wolbachia sp. wRi]
 gi|225592778|gb|ACN95797.1| heat shock sigma factor RpoH [Wolbachia sp. wRi]
          Length = 270

 Score =  242 bits (618), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 120/262 (45%), Positives = 183/262 (69%), Gaps = 2/262 (0%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           ML ++EE  LAK + ++ D+S+AH+L+TSHL LVVKIAM ++ YGL + ++V EGN+GLM
Sbjct: 1   MLSQEEEVRLAKNWNQYKDVSSAHKLITSHLNLVVKIAMKFKNYGLLLMDLVMEGNMGLM 60

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
            AVKKF+P+ GFR +TY++WWI+A+++++IL+SWS VKIGTT  Q+RLFF+LR++K  + 
Sbjct: 61  HAVKKFNPDLGFRFSTYAVWWIEASIKDFILKSWSFVKIGTTQAQRRLFFSLRKIKKRIL 120

Query: 148 AITDNN-LKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALINSSDKNSSQWQDWLV 205
             T+   L  E++ AI+ +L+VSE +V+ MN R+A  D+SLN  I   D +  + QD + 
Sbjct: 121 QYTNRETLNNEEIKAISNELSVSEGDVLQMNYRMACKDQSLNDCIKIGDDSKRELQDMIP 180

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            +   QE      EE++ +  +L  +++ LN R R IF +R L EN  TL+ LS ++ VS
Sbjct: 181 CNLVSQEVTYQNHEEKELKEAILNNALASLNERARDIFISRYLSENIQTLDELSKKYCVS 240

Query: 266 RERVRQIEARAFKKVQESIQKQ 287
           RER+RQ+  +A  KV++ IQ +
Sbjct: 241 RERIRQLAEQAMAKVKQYIQSE 262


>gi|225853213|ref|YP_002733446.1| RNA polymerase factor sigma-32 [Brucella melitensis ATCC 23457]
 gi|256263296|ref|ZP_05465828.1| sigma-70 factor [Brucella melitensis bv. 2 str. 63/9]
 gi|225641578|gb|ACO01492.1| RNA polymerase sigma factor, sigma-70 family protein [Brucella
           melitensis ATCC 23457]
 gi|263093265|gb|EEZ17362.1| sigma-70 factor [Brucella melitensis bv. 2 str. 63/9]
 gi|326409772|gb|ADZ66837.1| RNA polymerase factor sigma-32 [Brucella melitensis M28]
          Length = 311

 Score =  242 bits (618), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 117/274 (42%), Positives = 180/274 (65%), Gaps = 1/274 (0%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           I      P LE++EE  LA R++E  D  A HR+ ++H+RLV+ +A  +R + LP+S+++
Sbjct: 35  IRSAMSAPYLEREEERALAIRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLI 94

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EG +GL++   +FDP+R  R +TY+ WWI+A+MQ+YILR+WS+V+ GT++ QK LFFNL
Sbjct: 95  QEGYVGLLEEAARFDPDRDVRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKVLFFNL 154

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSS 198
           RRL+  L    DN  K E    I+ +L VS S+V  M+ RL+G D SL+A +N  +  +S
Sbjct: 155 RRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEETGAS 214

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           +  D+LV DH  Q+++     + + R   LTR++  LN RE  I   RRL ++ VTLE L
Sbjct: 215 RRMDFLVDDHPLQDEIAESSIDMERRNRWLTRALDTLNERELHIIRERRLDDDGVTLEAL 274

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
             +  +S+ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 275 GEKLGISKERVRQIESRAMEKLKIALLSQHELAA 308


>gi|116333403|ref|YP_794930.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Lactobacillus brevis ATCC 367]
 gi|116098750|gb|ABJ63899.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Lactobacillus brevis ATCC 367]
          Length = 368

 Score =  242 bits (618), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 67/254 (26%), Positives = 117/254 (46%), Gaps = 13/254 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L   EE  LA R  E+G+ +A   L  ++LRLVV IA  Y G G+
Sbjct: 103 DPVRMYLKEIGRVNLLTADEEVALALRI-ENGEEAAKQELAEANLRLVVSIAKRYVGRGM 161

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 162 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 220

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L         PE++ A   ++++   +V  +        SL   I   
Sbjct: 221 -TINKLIRIQRQLLQDLGREPTPEEIGA---EMDMPTEKVREILKIAQEPVSLETPI--G 274

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D       +    +  +  L   +  L  RE  +   R   ++  
Sbjct: 275 EEDDSHLGDFI---EDQDATSPADHAAYELLKEQLESVLDTLTDREENVLRLRFGLDDGR 331

Query: 253 -VTLENLSSEFEVS 265
             TLE +   F V+
Sbjct: 332 TRTLEEVGKVFGVT 345


>gi|13195265|gb|AAK15630.1|AF326348_2 RNA polymerase major sigma subunit [Corynebacterium ammoniagenes]
          Length = 467

 Score =  242 bits (618), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 76/325 (23%), Positives = 149/325 (45%), Gaps = 49/325 (15%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR----------------EHG 45
            RK+  +  + +  +  Y+ +I K+ +L  ++E  LA+R                    G
Sbjct: 148 ARKDAQLTASAD-SVRAYLKQIGKVALLNAEQEVSLAERIEAGLYAQHRLDEMERLIAEG 206

Query: 46  D--------------------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           D                      A + L+ ++LRLVV +A  Y G G+   +++ EGN+G
Sbjct: 207 DAAAKLSPAQKRDLRWIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLG 266

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  
Sbjct: 267 LIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRE 324

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           L         P     +AK+++++E +V+ +        SL+  I   D+  SQ  D++ 
Sbjct: 325 LLQDLGREPTP---QELAKEMDITEEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI- 378

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFE 263
              D +  + ++       ++ L   ++ L+ RE  +   R    +  P TL+ +   + 
Sbjct: 379 --EDSEAVIAVDAVSFTLLQDQLQDVLTTLSEREAGVVRLRFGLTDGMPRTLDEIGQVYG 436

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           V+RER+RQIE++   K++   + QV
Sbjct: 437 VTRERIRQIESKTMSKLRHPSRSQV 461


>gi|119475401|ref|ZP_01615754.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2143]
 gi|119451604|gb|EAW32837.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2143]
          Length = 282

 Score =  242 bits (618), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 104/287 (36%), Positives = 164/287 (57%), Gaps = 6/287 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+    ++ +     L+ Y+  +   P+L  + E+ LA+    H +L +A  LV +HLR 
Sbjct: 1   MSTALQTVNLVPGSNLNAYMQTVNNFPVLTAEREHELAEALYYHENLESARELVMAHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y GYGLP+++++ EGNIGLM+AVK+F+PE+G RL ++++ W+KA M EYILR+
Sbjct: 61  VVHIARSYNGYGLPLADLIQEGNIGLMKAVKRFNPEKGVRLVSFAVHWVKAEMHEYILRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR  K  L  + +      +  AIA+ LNV   EV  M  RL
Sbjct: 121 WRIVKVATTKAQRKLFFNLRGAKKKLAWLNEK-----EAHAIAEDLNVDVKEVRRMESRL 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRE 239
              +         + +        + DH     +L+E  + +   N  L  ++  L+ R 
Sbjct: 176 TASDLGFDAGADDEDDGFVAPAHYLEDHSANPAMLLEDADWEQNSNQHLQLALEQLDERS 235

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R I +AR L ++  TL +L+ ++ VS ERVRQ+E  A KKV+ +++ 
Sbjct: 236 RDIIQARWLSDSKSTLHDLAGKYGVSAERVRQLEKNAMKKVRATMEA 282


>gi|330812379|ref|YP_004356841.1| RNA polymerase sigma factor [Pseudomonas brassicacearum subsp.
           brassicacearum NFM421]
 gi|327380487|gb|AEA71837.1| RNA polymerase sigma factor [Pseudomonas brassicacearum subsp.
           brassicacearum NFM421]
          Length = 284

 Score =  242 bits (618), Expect = 5e-62,   Method: Composition-based stats.
 Identities = 104/272 (38%), Positives = 156/272 (57%), Gaps = 7/272 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+H +  IP+L  ++E  LA+      DL AA ++V +HLR VV IA  Y GYGL 
Sbjct: 16  NLEAYVHTVNSIPLLTPEQERELAESLYYEQDLEAARQMVLAHLRFVVHIARSYSGYGLA 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++
Sbjct: 76  QADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           LFFNLR  K  L  + +     E+V  +A+ L V   EV  M  RL G +        +D
Sbjct: 136 LFFNLRSQKKRLAWLNN-----EEVHRVAESLGVEPREVREMESRLTGHDMAFDPAAEAD 190

Query: 195 KNSS-QWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENP 252
            +S+ Q     + DH       +E  +  +  N  L  ++ VL+ R R I   R L E  
Sbjct: 191 DDSAFQSPANYLEDHRYDPARQLEDADWSDNSNTNLHEALEVLDERSRDILYQRWLAEEK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL +L+ ++ VS ER+RQ+E  A  K++ SI
Sbjct: 251 ATLHDLAQKYNVSAERIRQLEKSAMNKLKVSI 282


>gi|89900482|ref|YP_522953.1| sigma 32 (RpoH) [Rhodoferax ferrireducens T118]
 gi|89345219|gb|ABD69422.1| sigma 32 (RpoH) [Rhodoferax ferrireducens T118]
          Length = 313

 Score =  242 bits (618), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 107/294 (36%), Positives = 172/294 (58%), Gaps = 14/294 (4%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +V     L  YI    ++PML  +EE   ++++R+  DL+AA +LV SHLRLVV ++  Y
Sbjct: 20  MVPALGNLDAYISAANRLPMLTLEEEQEFSRKFRQDNDLAAAGKLVLSHLRLVVSVSRQY 79

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGLP  +++ EGN+GLM+AVK+FDP+ G RL +Y++ WIKA + EYIL++W +VK+ T
Sbjct: 80  LGYGLPHGDLIQEGNVGLMKAVKRFDPDHGVRLVSYALHWIKAEIHEYILKNWRMVKVAT 139

Query: 129 TANQKRLFFNLRRLKGHLQA--------ITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           T  Q++LFFNLR +K   ++           + L  +Q+ A+A +L V   EV+ M  RL
Sbjct: 140 TKAQRKLFFNLRSMKQRYKSDDAAADLGTHRDTLNEDQIDAMALELRVKREEVMEMETRL 199

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLNPRE 239
           +G + L     + D + +      + D   +   +IE  +R     + +  ++  L+ R 
Sbjct: 200 SGGDVLLDPSPTDDGDDAFGPIAYLTDTRHEPTEMIEAHQRDLLASDGIATALEALDERS 259

Query: 240 RRIFEARRLQENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RRI E R L+ N      +TL  L++ + VS ER+RQIE  A KK+++++ +  
Sbjct: 260 RRIVEERWLKVNDDNSGGMTLHELAAVYGVSAERIRQIEVAAMKKMKKTLAEYA 313


>gi|303233350|ref|ZP_07320019.1| RNA polymerase sigma factor RpoD [Atopobium vaginae PB189-T1-4]
 gi|302480479|gb|EFL43570.1| RNA polymerase sigma factor RpoD [Atopobium vaginae PB189-T1-4]
          Length = 441

 Score =  242 bits (618), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 80/314 (25%), Positives = 137/314 (43%), Gaps = 42/314 (13%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR---------------------- 42
           + S ++     +  Y+ EI K+ +L   +E  LA +                        
Sbjct: 129 DSSTVMLTGDPVRMYLKEIGKVDLLTADDEVHLAMKIEAGNKATEQLEKAEKGEIELSRS 188

Query: 43  --------EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                   E   L A   L +++LRL V IA  Y G G+   +++ EGN+GL++AV+KFD
Sbjct: 189 EMRRLMREEQVGLDAKQALTSANLRLTVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFD 248

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +GF+ +TY+ WWI+ A+   I      ++I     +      L R++  L      + 
Sbjct: 249 YTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE--TINKLVRIQRQLLQELGRDP 306

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            PE    I K++N+S  ++  +        SL   I   ++  S   D++    D     
Sbjct: 307 SPE---EIGKEMNMSPDKIREIQKISQEPVSLETPI--GEEEDSSLGDFI---EDSTAVA 358

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
             +       R  L + +  L  RER++ + R   E+  P TLE +  EF V+RER+RQI
Sbjct: 359 PPDAASDSMLREQLNQVLDSLADRERKVIKFRFGLEDGHPRTLEEVGREFGVTRERIRQI 418

Query: 273 EARAFKKVQESIQK 286
           E++   K++   + 
Sbjct: 419 ESKTLAKLRHPSRS 432


>gi|229593148|ref|YP_002875267.1| RNA polymerase factor sigma-32 [Pseudomonas fluorescens SBW25]
 gi|312963636|ref|ZP_07778117.1| RNA polymerase sigma-32 factor [Pseudomonas fluorescens WH6]
 gi|229365014|emb|CAY53168.1| RNA polymerase sigma-32 factor [Pseudomonas fluorescens SBW25]
 gi|311282145|gb|EFQ60745.1| RNA polymerase sigma-32 factor [Pseudomonas fluorescens WH6]
          Length = 284

 Score =  242 bits (617), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 104/272 (38%), Positives = 156/272 (57%), Gaps = 7/272 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+H +  IP+L  ++E  LA+      DL AA ++V +HLR VV IA  Y GYGL 
Sbjct: 16  NLEAYVHTVNSIPLLTPEQERELAESLYYEQDLGAARQMVLAHLRFVVHIARSYSGYGLA 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++
Sbjct: 76  QADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           LFFNLR  K  L  + +     E+V  +A+ L V   EV  M  RL G +        +D
Sbjct: 136 LFFNLRSQKKRLAWLNN-----EEVHRVAESLGVEPREVREMESRLTGHDMAFDPAAEAD 190

Query: 195 KNSS-QWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENP 252
            +S+ Q     + DH       +E  +  +  N  L  ++ VL+ R R I   R L E  
Sbjct: 191 DDSAFQSPANYLEDHRYDPARQLEDADWSDNSNHNLHEALEVLDDRSRDILYQRWLAEEK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL +L+ ++ VS ER+RQ+E  A  K++ SI
Sbjct: 251 ATLHDLAQKYNVSAERIRQLEKSAMNKLKLSI 282


>gi|296117756|ref|ZP_06836340.1| RNA polymerase sigma factor [Corynebacterium ammoniagenes DSM
           20306]
 gi|295969487|gb|EFG82728.1| RNA polymerase sigma factor [Corynebacterium ammoniagenes DSM
           20306]
          Length = 471

 Score =  242 bits (617), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 76/325 (23%), Positives = 149/325 (45%), Gaps = 49/325 (15%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR----------------EHG 45
            RK+  +  + +  +  Y+ +I K+ +L  ++E  LA+R                    G
Sbjct: 152 ARKDAQLTASAD-SVRAYLKQIGKVALLNAEQEVSLAERIEAGLYAQHRMDEMERLTAEG 210

Query: 46  D--------------------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           D                      A + L+ ++LRLVV +A  Y G G+   +++ EGN+G
Sbjct: 211 DAAAKLSPAQKRDLRWIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLG 270

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  
Sbjct: 271 LIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRE 328

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           L         P     +AK+++++E +V+ +        SL+  I   D+  SQ  D++ 
Sbjct: 329 LLQDLGREPTP---QELAKEMDITEEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI- 382

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFE 263
              D +  + ++       ++ L   ++ L+ RE  +   R    +  P TL+ +   + 
Sbjct: 383 --EDSEAVIAVDAVSFTLLQDQLQDVLTTLSEREAGVVRLRFGLTDGMPRTLDEIGQVYG 440

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           V+RER+RQIE++   K++   + QV
Sbjct: 441 VTRERIRQIESKTMSKLRHPSRSQV 465


>gi|294629207|ref|ZP_06707767.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. e14]
 gi|292832540|gb|EFF90889.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. e14]
          Length = 386

 Score =  242 bits (617), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 84/296 (28%), Positives = 139/296 (46%), Gaps = 38/296 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRY------------------REHGDLS--------A 49
             +Y+ EI +IP+L   EE  LA+R                   R  GDL         A
Sbjct: 90  FRQYLREIGRIPLLTAAEEVELARRVEAGLFAEEKLSSTPDLDSRLAGDLDRLVVSGRMA 149

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY+ WWI
Sbjct: 150 KRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWI 209

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + AM   +      +++     +  L   + R++  +         P +V A   +L+++
Sbjct: 210 RQAMSRALADQARTIRVPVHVVE--LINRVVRVQRRMLQERGYEPTPAEVAA---QLDLT 264

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
              V  +        SL+A +   +++     D +    DG     +E       R  L 
Sbjct: 265 PDRVGEVLRLAQEPVSLHAPV--GEEDDVALGDLI---EDGDAASPVESAAFLLLREHLE 319

Query: 230 RSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +S L  RER++ + R       P TLE +   F V+RER+RQIE++   K+++ 
Sbjct: 320 AVLSTLGERERKVVQLRYGLMDGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRDH 375


>gi|123440620|ref|YP_001004614.1| RNA polymerase factor sigma-32 [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|332159850|ref|YP_004296427.1| RNA polymerase factor sigma-32 [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|122087581|emb|CAL10362.1| RNA polymerase sigma-32 factor [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|318607604|emb|CBY29102.1| RNA polymerase sigma factor RpoH [Yersinia enterocolitica subsp.
           palearctica Y11]
 gi|325664080|gb|ADZ40724.1| RNA polymerase factor sigma-32 [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|330862604|emb|CBX72757.1| RNA polymerase sigma-32 factor [Yersinia enterocolitica W22703]
          Length = 285

 Score =  242 bits (617), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 102/290 (35%), Positives = 163/290 (56%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  YI      PML  +EE  LA+R    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLALVPQGSLEAYIRAANAYPMLTAEEERELAERLHYQGDLEAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VAHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +AK+L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVELVAKELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNP 237
           +  +         +    Q    ++Y  D        + E     +  + LT ++  L+ 
Sbjct: 176 SAQDMTFDPTPDDEVRDGQSMAPVLYLQDKTSDFADGIEEDNWDNHAADKLTYALEGLDE 235

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L ++   TL+ L+ ++ VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQHIIRARWLDDDNKSTLQELADQYGVSAERVRQLEKNAMKKLRMAIEA 285


>gi|78067614|ref|YP_370383.1| RNA polymerase factor sigma-32 [Burkholderia sp. 383]
 gi|77968359|gb|ABB09739.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. 383]
          Length = 311

 Score =  242 bits (617), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 117/289 (40%), Positives = 172/289 (59%), Gaps = 12/289 (4%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
            S++      +  YI  + +IP+L  +EE   A  +RE  +L +A RLV SHLRLVV I+
Sbjct: 29  QSMLPGQLGNIDAYIQAVNRIPLLTVEEERQYATEFREGNNLDSARRLVLSHLRLVVSIS 88

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGLP  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W  VK
Sbjct: 89  RNYLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRTVK 148

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDE 184
           + TT  Q++LFFNLR  K  LQA+T     PE++  +AK+LNV   +V  M  RL  GD 
Sbjct: 149 VATTKAQRKLFFNLRSHKKGLQAMT-----PEEIDGLAKELNVKREDVTEMETRLSGGDI 203

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           +L   +   ++ S     +L   H+    VL  ++    + + + +++  L+ R RRI E
Sbjct: 204 ALEGQVEDGEE-SYAPIAYLADSHNEPTAVLAARQRDTLQTDGIAQALDALDARSRRIIE 262

Query: 245 ARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           AR L          TL +L++EF VS ER+RQIEA A KK++ ++ +  
Sbjct: 263 ARWLHVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRTALAEYA 311


>gi|108762657|ref|YP_634340.1| RNA polymerase sigma-C factor [Myxococcus xanthus DK 1622]
 gi|585929|sp|Q07083|RPSC_MYXXA RecName: Full=RNA polymerase sigma-C factor
 gi|293866|gb|AAA25408.1| sigma factor [Myxococcus xanthus]
 gi|108466537|gb|ABF91722.1| RNA polymerase sigma-C factor [Myxococcus xanthus DK 1622]
          Length = 295

 Score =  242 bits (617), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 113/279 (40%), Positives = 175/279 (62%), Gaps = 4/279 (1%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S   +    LS Y+ EI + P+L + +E  L+KR+R  GDL+A H+LVT++LR VVK+A 
Sbjct: 4   SNSFSSPDSLSTYLSEINQYPLLTQPQEQELSKRFR-AGDLAAGHQLVTANLRFVVKVAY 62

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            YR YGL +S+++ E NIGLM+AV+KFDP++G RL +Y++WWI+A +Q  IL++WSLVK+
Sbjct: 63  EYRSYGLKMSDLIQEANIGLMKAVQKFDPDKGIRLISYAVWWIRAYIQNCILKNWSLVKL 122

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DES 185
           GTT  Q+RLFF+L R +  L+ +   +        IA+KLNV  SEV  M  R+ G D S
Sbjct: 123 GTTQAQRRLFFSLARTRRELEKMGAGDANVVNAEEIARKLNVKASEVREMEQRMGGRDLS 182

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L+A +   +   +   D++  +       + ++++    R ++ R++  L+PRER I E 
Sbjct: 183 LDAPM--GEDGDATHLDFVESESVSAVDEVADRQQANLTRELVQRALRRLDPRERFIIEQ 240

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R + +  +TL  L   F  SRER RQ+E RA  K++ ++
Sbjct: 241 RVMGDAEMTLSELGEHFGFSRERARQLEIRAKDKLKLAL 279


>gi|330818365|ref|YP_004362070.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia gladioli BSR3]
 gi|327370758|gb|AEA62114.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia gladioli BSR3]
          Length = 311

 Score =  242 bits (617), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 115/290 (39%), Positives = 175/290 (60%), Gaps = 12/290 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           + S++      +  YI  + +IPML  +EE   A  +R+  +L +A RLV SHLRLVV I
Sbjct: 28  SQSMLPGQLGNIDAYIQSVNRIPMLTLEEERQYATEFRDQNNLESARRLVLSHLRLVVSI 87

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y GYGLP  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W +V
Sbjct: 88  ARNYLGYGLPHGDLIQEGNIGLMKAVKRFDPNQNVRLVSYAIHWIKAEIHEYILRNWRMV 147

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGD 183
           K+ TT  Q++LFFNLR  K  +QA+T     PE++  +A++LNV   +V  M  RL  GD
Sbjct: 148 KVATTKAQRKLFFNLRSHKKGMQAMT-----PEEIDGLAQELNVKREDVAEMETRLSGGD 202

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            +L   ++  ++ S     +L   H+    V+  ++  + + + ++ ++  L+ R RRI 
Sbjct: 203 IALEGQVDDGEE-SFAPIAYLADSHNEPTAVIASRQRDRLQTDGISEALESLDARSRRII 261

Query: 244 EARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           EAR L          TL +L++EF VS ER+RQIEA A KK++ ++    
Sbjct: 262 EARWLNVEDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRAALAAYA 311


>gi|256114330|ref|ZP_05455068.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 3 str.
           Ether]
          Length = 311

 Score =  242 bits (617), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 118/293 (40%), Positives = 184/293 (62%), Gaps = 4/293 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  ++          +   I      P LE++EE  LA R++E  D  A HR+ ++H+RL
Sbjct: 19  MAVRSFPAAAASSQSM---IRSAMSAPYLEREEERALAIRWKETKDQDALHRITSAHMRL 75

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A  +R + LP+S+++ EG +GL++   +FDP+R  R +TY+ WWI+A+MQ+YILR+
Sbjct: 76  VISMAGRFRKFKLPMSDLIQEGYVGLLEEAARFDPDRDVRFSTYASWWIRASMQDYILRN 135

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WS+V+ GT++ QK LFFNLRRL+  L    DN  K E    I+ +L VS S+V  M+ RL
Sbjct: 136 WSIVRGGTSSAQKVLFFNLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRL 195

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D SL+A +N  +  +S+  D+LV DH  Q+++     + + R   LTR++  LN RE
Sbjct: 196 SGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTRALDTLNERE 255

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
             I   RRL ++ VTLE L  +  +S+ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 256 LHIIRERRLDDDGVTLEALGEKLGISKERVRQIESRAMEKLKIALLSQHELAA 308


>gi|311103433|ref|YP_003976286.1| alternative sigma factor RpoH [Achromobacter xylosoxidans A8]
 gi|310758122|gb|ADP13571.1| alternative sigma factor RpoH [Achromobacter xylosoxidans A8]
          Length = 294

 Score =  242 bits (617), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 124/288 (43%), Positives = 176/288 (61%), Gaps = 13/288 (4%)

Query: 2   NRKNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           N   ++I   G +G +  YI  + ++P+L  + E  L +R R+  DL AA  L+ SHLRL
Sbjct: 13  NALALAIANPGALGTIDAYISSVNRLPVLSAERETELGRRLRDQEDLGAARELILSHLRL 72

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y GYGLP ++++ EGN+GLM+AVK+FDPERG RL ++++ WIKA + EYI+R+
Sbjct: 73  VVSVARQYLGYGLPHADLIQEGNVGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYIIRN 132

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W LVK+ TT  Q++LFFNLR ++          L P+QV  IA++LNV   +V  M  RL
Sbjct: 133 WRLVKVATTKAQRKLFFNLRSMR-----PDGQTLDPDQVDHIARELNVRREDVSEMEVRL 187

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQ--VLIEKEERKNRRNMLTRSMSVLNP 237
           +G D SL    N  D + S      + D   QE   VL      + +   LT ++  L+P
Sbjct: 188 SGRDMSLE---NQDDDDDSYAPIAYLSDEGRQEPTRVLERAARDQLQSAGLTDALQALDP 244

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R RRI EAR LQ++   TL  L+ EF VS ER+RQIEA A KK++ ++
Sbjct: 245 RSRRIVEARWLQDDGGATLHELAQEFGVSAERIRQIEAAALKKMRGNL 292


>gi|259507416|ref|ZP_05750316.1| RNA polymerase principal sigma factor SigA [Corynebacterium
           efficiens YS-314]
 gi|259164981|gb|EEW49535.1| RNA polymerase principal sigma factor SigA [Corynebacterium
           efficiens YS-314]
          Length = 381

 Score =  242 bits (617), Expect = 6e-62,   Method: Composition-based stats.
 Identities = 78/325 (24%), Positives = 149/325 (45%), Gaps = 49/325 (15%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY----------------REHG 45
            RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR                    G
Sbjct: 62  ARKDAELTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYATHKMEEMEAAYAAG 120

Query: 46  DLSAA--------------------HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           D  A                     + L+ ++LRLVV +A  Y G G+   +++ EGN+G
Sbjct: 121 DKDAKLTPAVKRDLRAIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLG 180

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  
Sbjct: 181 LIRAVEKFDYSKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRE 238

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           L         P     ++K++++SE +V+ +        SL+  I   D+  SQ  D++ 
Sbjct: 239 LLQELGREPTP---QELSKEMDISEEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI- 292

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFE 263
              D +  V ++       ++ L   +  L+ RE  + + R    +  P TL+ +   + 
Sbjct: 293 --EDSEAVVAVDAVSFTLLQDQLQDVLETLSEREAGVVKLRFGLTDGMPRTLDEIGQVYG 350

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           V+RER+RQIE++   K++   + QV
Sbjct: 351 VTRERIRQIESKTMSKLRHPSRSQV 375


>gi|320353914|ref|YP_004195253.1| RNA polymerase sigma 32 subunit RpoH [Desulfobulbus propionicus DSM
           2032]
 gi|320122416|gb|ADW17962.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfobulbus propionicus
           DSM 2032]
          Length = 328

 Score =  242 bits (617), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 111/290 (38%), Positives = 184/290 (63%), Gaps = 8/290 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +   + ++       L RY+ EI +  +L ++E   LA R++E GD  AA+RLV+S+LRL
Sbjct: 22  LTSSDDNLPALSNPALHRYLQEISQYELLSREETEELAVRFQETGDPDAAYRLVSSNLRL 81

Query: 61  VVKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           VVK+AM ++ Y +    +++ EGN+GL+QA KKFDP RG + + Y+ +WI+A + ++I+ 
Sbjct: 82  VVKVAMDFQKYWMQNFMDLIQEGNVGLVQATKKFDPYRGVKFSYYAAYWIRAYILKFIMD 141

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
           +W LVKIGTT  Q++LFF+L + K  L++      KPE V  +A++LNV ESEVI M  R
Sbjct: 142 NWRLVKIGTTQAQRKLFFSLNKEKKLLES---QGFKPE-VKLLAERLNVKESEVIEMGQR 197

Query: 180 LAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           +   D SL A + S  ++  + +++L ++  G E+++  +E R+    +L    + LN +
Sbjct: 198 MDNWDVSLEAPVRSDSED--EQKNFLPHEGPGIEEMVASQEMRERLAGILADLSTRLNEK 255

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           E+ I   R L + P TL+ ++ EF +SRERVRQIE+   KK+++  +K++
Sbjct: 256 EQVILTTRLLSDEPKTLQTIADEFNISRERVRQIESNLLKKLRKQFEKEM 305


>gi|257056422|ref|YP_003134254.1| RNA polymerase, sigma 70 subunit, RpoD [Saccharomonospora viridis
           DSM 43017]
 gi|256586294|gb|ACU97427.1| RNA polymerase, sigma 70 subunit, RpoD [Saccharomonospora viridis
           DSM 43017]
          Length = 439

 Score =  242 bits (617), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 81/319 (25%), Positives = 147/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGD-- 46
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+  
Sbjct: 126 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYAAERLRIAEEEGEKL 184

Query: 47  ---------------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 185 STQMRRDLKWIVRDGERAKSHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 244

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +GF+ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 245 KFDYTKGFKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 302

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK++++S  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 303 REPTPE---ELAKEMDISPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 354

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 355 AVVAVDAVSFTLLQDQLQSVLQTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 414

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 415 RQIESKTMSKLRHPSRSQV 433


>gi|260683114|ref|YP_003214399.1| RNA polymerase sigma factor rpoD [Clostridium difficile CD196]
 gi|260686712|ref|YP_003217845.1| RNA polymerase sigma factor rpoD [Clostridium difficile R20291]
 gi|260209277|emb|CBA62619.1| RNA polymerase sigma factor rpoD [Clostridium difficile CD196]
 gi|260212728|emb|CBE03837.1| RNA polymerase sigma factor rpoD [Clostridium difficile R20291]
          Length = 301

 Score =  242 bits (617), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 75/277 (27%), Positives = 143/277 (51%), Gaps = 11/277 (3%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           N    +  Y+ EI +  ML   EE  LAK       + A  + + S+ RLVV IA  Y+ 
Sbjct: 26  NVSNAMKMYLKEIEEYKMLSAGEEVELAKEIINSSSV-AKEKFINSNYRLVVSIAKRYKR 84

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
             + + +++  GNIGL++AV+K+D ++G++ +TY+ WWIK ++  YI    + ++I    
Sbjct: 85  DSIDMLDLIQAGNIGLIKAVEKYDYKKGYKFSTYATWWIKQSITRYIDDCENTIRIPIHL 144

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
           +Q+     +  +K   Q + +  L+   +  IA    +   +V+ +  R     SL+  +
Sbjct: 145 HQR-----INFVKKKKQELLNVLLREPTIDEIADACGLEVDKVLELLRRDKNVVSLDTPL 199

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-- 248
              +   S   +++  D D +  V+I + E+ N +  +   ++ L  +E+++   R    
Sbjct: 200 K--EDEDSSLVEFIPSDADFK-DVVIHEVEQHNLKEKIEELLTGLGEQEQQVLRMRFGID 256

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            ++P TLE +   F V+RER+RQIEA+A +K++   +
Sbjct: 257 DDDPKTLEQIGKVFGVTRERIRQIEAKAIRKLRHPSK 293


>gi|291459241|ref|ZP_06598631.1| RNA polymerase sigma factor RpoD [Oribacterium sp. oral taxon 078
           str. F0262]
 gi|291418495|gb|EFE92214.1| RNA polymerase sigma factor RpoD [Oribacterium sp. oral taxon 078
           str. F0262]
          Length = 398

 Score =  242 bits (617), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 81/273 (29%), Positives = 136/273 (49%), Gaps = 13/273 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           +  +  +  Y+ EI  IP+L  +EE  LA+R +E GD  A  RLV ++LRLVV IA  Y 
Sbjct: 121 IETDDPVRFYLKEIGTIPLLSPEEEKELARRSKE-GDPLARQRLVEANLRLVVSIAKRYT 179

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G+ I +++ EGN+GLM+ V+KF+P++GF+L+TY+ WWI+  +   +      +++   
Sbjct: 180 GRGMSILDLIQEGNLGLMKGVEKFEPDKGFKLSTYATWWIRQGITRALADQSRTIRVPVH 239

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +      + ++    + +T           +A  LN++E ++  +        SL   
Sbjct: 240 MVES-----INKVTRTQRRLTLELGYEPSPKELAASLNMTEEKLKEILDVSKQPTSLETP 294

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL- 248
           +   D+  S   D++  +         +       R  + + +  L  RER +   R   
Sbjct: 295 V--GDEEDSNLSDFVADEK---MISPEQNAANVMLREEIDKLLENLKDRERDVLIHRFGL 349

Query: 249 -QENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             E   TLE +   F V+RERVRQIEA+A KK+
Sbjct: 350 HGEESHTLEEVGQMFGVTRERVRQIEAKALKKI 382


>gi|28210583|ref|NP_781527.1| RNA polymerase sigma factor rpoD [Clostridium tetani E88]
 gi|28203021|gb|AAO35464.1| RNA polymerase sigma factor rpoD [Clostridium tetani E88]
          Length = 282

 Score =  242 bits (617), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 88/276 (31%), Positives = 139/276 (50%), Gaps = 15/276 (5%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  ++ Y+ EI +  +L  +EE  LAKR  E GD  A   L+ S+LRLVV IA  Y G G
Sbjct: 10  DDYINMYLKEIGQSDLLTAEEEIDLAKRI-EKGDERAKSELIKSNLRLVVSIAKKYIGRG 68

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L   ++V EGN+GLM+AV K+D ++G+R +TY+ WWIK A+   I      ++I    N+
Sbjct: 69  LSFLDLVQEGNLGLMKAVDKYDYKKGYRFSTYATWWIKQAVTRSIADQSRTIRIPVHMNE 128

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
             +   + R K  L+   D          IA+   +S  ++  +        SL   +  
Sbjct: 129 --VISKMIRTKKKLEQELDRE---PTEEEIAETAEISIEKIKRIYNVSQDPVSLETPV-- 181

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR---LQ 249
            +   +  Q+++  D    E  + E+       + L+  +S L+PRE RI   R      
Sbjct: 182 GENEDTILQNFISDDRYLPEDKVTEQMLG----DTLSNVLSTLSPREERIVRLRYGLVGD 237

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
               TLE +  EF ++RER+RQIEARA +K++   +
Sbjct: 238 GESRTLEEIGREFNLTRERIRQIEARAIRKLRHPTR 273


>gi|323144379|ref|ZP_08078987.1| alternative sigma factor RpoH [Succinatimonas hippei YIT 12066]
 gi|322415832|gb|EFY06558.1| alternative sigma factor RpoH [Succinatimonas hippei YIT 12066]
          Length = 295

 Score =  242 bits (617), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 121/287 (42%), Positives = 172/287 (59%), Gaps = 11/287 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  N+   V     +  Y+  I K PMLE+++E  LAKR R++GDL AA +LV SHLRL
Sbjct: 8   LNPSNLPAPVG---NIDAYVKAINKFPMLEEEDERTLAKRLRDYGDLDAARKLVLSHLRL 64

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA GY GYGLPIS+++ EGNIGLM+AVK FDP+ G RLA +++ WIKA + +Y++++
Sbjct: 65  VVSIARGYLGYGLPISDLIQEGNIGLMKAVKHFDPDVGGRLAAFAVHWIKAEIHDYVIKN 124

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFF LR+ K  L   +D+         +A  L VS  +V  M  RL
Sbjct: 125 WRVVKVATTKAQRKLFFKLRQNKQRLGWFSDSERN-----KVADDLGVSADDVAEMETRL 179

Query: 181 AGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR-NMLTRSMSVLNP 237
           AG +        + SDK SS      + D +       E  + +N   + L +++  L+ 
Sbjct: 180 AGQDIGFDADSDDDSDKGSSFSPSAYLEDENSNFANTFENIDYENYELSSLRKALDSLDE 239

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R R I + R L EN  TL+ LS +  VS ERVRQIE +A KK++ +I
Sbjct: 240 RSRYIVQRRWLDENKATLQELSEKLNVSIERVRQIENQALKKIKSNI 286


>gi|77461555|ref|YP_351062.1| RNA polymerase factor sigma-32 [Pseudomonas fluorescens Pf0-1]
 gi|77385558|gb|ABA77071.1| RNA polymerase, sigma 32 subunit, RpoH [Pseudomonas fluorescens
           Pf0-1]
          Length = 284

 Score =  242 bits (617), Expect = 7e-62,   Method: Composition-based stats.
 Identities = 104/272 (38%), Positives = 156/272 (57%), Gaps = 7/272 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+H +  IP+L  ++E  LA+      DL AA ++V +HLR VV IA  Y GYGL 
Sbjct: 16  NLEAYVHTVNSIPLLTPEQERELAESLYYEQDLGAARQMVLAHLRFVVHIARSYSGYGLA 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++
Sbjct: 76  QADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           LFFNLR  K  L  + +     E+V  +A+ L V   EV  M  RL G +        +D
Sbjct: 136 LFFNLRSQKKRLAWLNN-----EEVHRVAESLGVEPREVREMESRLTGHDMAFDPAAEAD 190

Query: 195 KNSS-QWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENP 252
            +S+ Q     + DH       +E  +  +  N  L  ++ VL+ R R I   R L E  
Sbjct: 191 DDSAFQSPANYLEDHRYDPARQLEDADWSDNSNHNLHEALEVLDERSRDILYQRWLAEEK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL +L+ ++ VS ER+RQ+E  A  K++ SI
Sbjct: 251 ATLHDLAQKYNVSAERIRQLEKSAMNKLKLSI 282


>gi|258645217|ref|ZP_05732686.1| RNA polymerase sigma factor RpoD [Dialister invisus DSM 15470]
 gi|260402567|gb|EEW96114.1| RNA polymerase sigma factor RpoD [Dialister invisus DSM 15470]
          Length = 388

 Score =  242 bits (617), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 83/295 (28%), Positives = 133/295 (45%), Gaps = 23/295 (7%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREH-------GDL----SAAHRL 53
           N S  +N +  +  Y+ EI  I +L   +E  LAK   +         D      A   L
Sbjct: 100 NTSDSINIDDPVKMYLKEIGAIKLLTGSQEIELAKLVEKGSFDDATGRDKMAADEAKKAL 159

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
             ++LRLVV IA  Y G GL   +++ EGN+GL++AV KFD  +GF+ +TY+ WWI+ A+
Sbjct: 160 SDANLRLVVSIAKKYLGRGLQFLDLIQEGNLGLLKAVDKFDYTKGFKFSTYATWWIRQAI 219

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
              I      +++     +      L R+   L          E    +AK + VS +++
Sbjct: 220 TRAIADQARTIRVPVHMVE--TINKLNRISRQLLQEKGREATNE---ELAKAMGVSVAKI 274

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             +        SL   I   +K  S   D++    D +     +       R  +   + 
Sbjct: 275 REVKKIAQDPISLETPI--GEKEDSHLGDFI---EDHEAIAPDDAAGSILLREQIDELLR 329

Query: 234 VLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L  RER++ E R       P TLE +   F+V+RER+RQIE +A  K+++S + 
Sbjct: 330 ELTDRERQVLELRFGLKDGRPRTLEEVGKYFDVTRERIRQIEGKALTKLKKSAKS 384


>gi|255655509|ref|ZP_05400918.1| RNA polymerase sigma factor rpoD [Clostridium difficile QCD-23m63]
          Length = 294

 Score =  241 bits (616), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 74/277 (26%), Positives = 143/277 (51%), Gaps = 11/277 (3%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           N    +  Y+ EI +  ML   EE  LAK       + A  + + S+ RLVV IA  Y+ 
Sbjct: 19  NVSNAMKMYLKEIEEYKMLSAGEEVELAKEIINSSSV-AKEKFINSNYRLVVSIAKRYKR 77

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
             + + +++  GNIGL++AV+K+D ++G++ +TY+ WWIK ++  YI    + ++I    
Sbjct: 78  DSIDMLDLIQAGNIGLIKAVEKYDYKKGYKFSTYATWWIKQSITRYIDDCENTIRIPIHL 137

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
           +Q+     +  +K   Q + +  L+   +  IA    +   +V+ +  R     SL+  +
Sbjct: 138 HQR-----INFVKKKKQELLNVLLREPTIDEIADACGLEVDKVLELLRRDKNVVSLDTPL 192

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-- 248
              +   S   +++  D D +  V++ + E+ N +  +   ++ L  +E+++   R    
Sbjct: 193 K--EDEDSSLVEFIPSDADFK-DVVMHEVEQHNLKEKIEELLTGLGEQEQQVLRMRFGID 249

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            ++P TLE +   F V+RER+RQIEA+A +K++   +
Sbjct: 250 DDDPKTLEQIGRVFGVTRERIRQIEAKAIRKLRHPSK 286


>gi|221211178|ref|ZP_03584157.1| alternative sigma factor RpoH [Burkholderia multivorans CGD1]
 gi|221168539|gb|EEE01007.1| alternative sigma factor RpoH [Burkholderia multivorans CGD1]
          Length = 281

 Score =  241 bits (616), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 120/287 (41%), Positives = 177/287 (61%), Gaps = 13/287 (4%)

Query: 9   IVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++ G++G +  YI  + +IP+L  +EE   A  YRE+ +L AA RLV SHLRLVV IA  
Sbjct: 1   MLPGQLGNIDAYIQAVNRIPLLTAEEERQYATEYRENNNLEAARRLVLSHLRLVVSIARN 60

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y GYGLP  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W +VK+ 
Sbjct: 61  YLGYGLPHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKVA 120

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESL 186
           TT  Q++LFFNLR  K  +QA+T     PE++  +A++LNV   EV  M  RL  GD +L
Sbjct: 121 TTKAQRKLFFNLRSHKKGMQAMT-----PEEIDGLAQELNVKREEVTEMETRLSGGDIAL 175

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
              +   ++ S     +L   H+    VL  ++    + + + +++  L+ R RRI EAR
Sbjct: 176 EGQVEDGEE-SYAPIAYLADSHNEPTAVLAARQRDMLQTDGIAQALDALDARSRRIIEAR 234

Query: 247 RL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            L          TL +L++EF VS ER+RQIEA A KK++ ++ +  
Sbjct: 235 WLHVDDDGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRTALAEYA 281


>gi|307324812|ref|ZP_07604018.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306889694|gb|EFN20674.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 414

 Score =  241 bits (616), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 85/296 (28%), Positives = 137/296 (46%), Gaps = 38/296 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYR----------EHGDLS----------------A 49
             +Y+ EI +IP+L   EE  LA+R               DL                 A
Sbjct: 118 FRQYLREIGRIPLLSAVEEVELARRVEAGLFAEEKLGNTPDLDSQLAVDLDRLVVLGRVA 177

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY+ WWI
Sbjct: 178 KRRLIEANLRLVVSVAKRYIGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWI 237

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + AM   +      +++     +  L   + R++  +         PE+V A    L   
Sbjct: 238 RQAMSRALADQARTIRVPVHVVE--LINRVVRVQRRMLQERGYEPTPEEVAAHLDLLPER 295

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
            SEV+ +        SL+A +   +++     D +    DG     +E       R  L 
Sbjct: 296 VSEVLRL---AQEPVSLHAPV--GEEDDVALGDLI---EDGDAASPVESAAFLLLREHLE 347

Query: 230 RSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +S L  RER++ + R       P TLE +   F V+RER+RQIE++   K+++ 
Sbjct: 348 AVLSTLGERERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRDH 403


>gi|187479755|ref|YP_787780.1| RNA polymerase factor sigma-32 [Bordetella avium 197N]
 gi|115424342|emb|CAJ50895.1| RNA polymerase sigma-32 factor [Bordetella avium 197N]
          Length = 307

 Score =  241 bits (616), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 116/284 (40%), Positives = 179/284 (63%), Gaps = 11/284 (3%)

Query: 6   MSIIVNGEIGL---SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           ++++V     L     YI  + ++P+L  ++E  LA+R R+  DL +A  LV SHLRLVV
Sbjct: 27  LALVVANPGALGTIDAYITTVNRLPVLTAEQESTLARRLRDSDDLESARELVLSHLRLVV 86

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y GYGLP ++++ EGN+GLM+AVK+FDPERG RL ++++ WIKA + EYI+R+W 
Sbjct: 87  SVARQYLGYGLPHADLIQEGNVGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYIIRNWR 146

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           LVK+ TT  Q++LFFNLR ++        + L  EQV  IA++LNV   +V  M  RL+G
Sbjct: 147 LVKVATTKAQRKLFFNLRSMR-----PDGHTLDTEQVDHIARELNVRREDVSEMEVRLSG 201

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERR 241
            + L+      D +      +L  +   +   ++E++ R + +   L+ +++ L+PR RR
Sbjct: 202 RD-LSLENQDDDDDGYAPIAYLSDECREEPTRVLERKARDDLQGKGLSDAITALDPRSRR 260

Query: 242 IFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           I EAR LQ+    TL  L++EF VS ER+RQIEA A KK++ ++
Sbjct: 261 IVEARWLQDEGGATLHELAAEFGVSAERIRQIEAAALKKMRGAL 304


>gi|239940961|ref|ZP_04692898.1| putative RNA polymerase principal sigma factor [Streptomyces
           roseosporus NRRL 15998]
 gi|239987439|ref|ZP_04708103.1| putative RNA polymerase principal sigma factor [Streptomyces
           roseosporus NRRL 11379]
          Length = 363

 Score =  241 bits (616), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 84/301 (27%), Positives = 141/301 (46%), Gaps = 38/301 (12%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY------------------REHGDLS---- 48
                  +Y+ EI +IP+L   EE  LA+R                   R  GDL     
Sbjct: 62  PTSDLFRQYLREIGRIPLLTAAEEVELARRVEAGLFAEERLTGTPDLDSRLAGDLDRLVV 121

Query: 49  ----AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
               A  RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY
Sbjct: 122 MGRTAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTY 181

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + WWI+ AM   +      +++     +  L   + R++  L          E    IA 
Sbjct: 182 ATWWIRQAMSRALADQARTIRVPVHVVE--LINRVVRVQRRLLQERGVEPTAED---IAV 236

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L+++   V  +        SL+A +   +++   + D +    DG     +E       
Sbjct: 237 ELDLTPERVTEVLRLAQEPVSLHAPV--GEEDDVSFGDLI---EDGDAASPVESAAFLLL 291

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           R  L   +S L  RER++ + R   ++  P TLE +   F V+RER+RQIE++   ++++
Sbjct: 292 RQHLEAVLSTLGERERKVVQLRYGLDDGRPRTLEEIGRIFGVTRERIRQIESKTLSRLRD 351

Query: 283 S 283
            
Sbjct: 352 H 352


>gi|148358598|ref|YP_001249805.1| hypothetical protein LPC_0471 [Legionella pneumophila str. Corby]
 gi|148280371|gb|ABQ54459.1| hypothetical protein LPC_0471 [Legionella pneumophila str. Corby]
          Length = 284

 Score =  241 bits (616), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 110/275 (40%), Positives = 177/275 (64%), Gaps = 7/275 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             L  YIH + +IPML  +EE   A+R+   GD+ AA +LV +HLR VV++A GY GYGL
Sbjct: 15  GSLDSYIHRVNQIPMLTLEEEIAYAERFHSEGDIEAARQLVLAHLRYVVRVARGYLGYGL 74

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+S+++ EGN+GLM+AVK+FDP+ G RL ++++ WIKA + E++LR+W +VK+ TT  Q+
Sbjct: 75  PLSDLIQEGNVGLMKAVKRFDPKMGVRLVSFAVHWIKAEIHEFVLRNWRIVKVATTKAQR 134

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINS 192
           +LFFNLR++K  L   ++     E+V A+AK L VS  +V+ M  RL   D S +A    
Sbjct: 135 KLFFNLRQMKNRLGWFSN-----EEVDAVAKDLGVSREDVLLMEQRLNVMDSSYDAPDVD 189

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPRERRIFEARRLQEN 251
            + ++ +  +  +++ +    VL+E E+  ++ R  L  +M  L+ R + I + R L E 
Sbjct: 190 DNDDAYKAPERYLFNVNDDPAVLLENEDTGDQGREKLLFAMEQLDERSQDILQQRWLAEE 249

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +TL +L+ ++ VS ERVRQ+E  A KK+++ ++ 
Sbjct: 250 KLTLHDLAEKYGVSAERVRQLEKNAMKKIRQYMES 284


>gi|219847152|ref|YP_002461585.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus
           aggregans DSM 9485]
 gi|219541411|gb|ACL23149.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus
           aggregans DSM 9485]
          Length = 398

 Score =  241 bits (616), Expect = 8e-62,   Method: Composition-based stats.
 Identities = 80/299 (26%), Positives = 139/299 (46%), Gaps = 39/299 (13%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLA--------------------------KRYREHGD 46
              +  Y+ EI ++P+L  ++E  LA                          +R +E GD
Sbjct: 98  SDSVRLYLREIGQVPLLTAEQEKQLAQMIERGQAAERKLATLPPDSPEAAKLRRIKEQGD 157

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  ++  ++LRLVV IA  YR  GLP+ +++ EG++GL++A++KFD  +G++ +TY+ 
Sbjct: 158 -EARQKMAAANLRLVVSIAKRYRDRGLPLLDLIQEGSLGLLRAIEKFDHTKGYKFSTYAT 216

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWIK A+   +     LV++        L   L R++   + +T +  +      +A  L
Sbjct: 217 WWIKQALSRALADQSRLVRLPVH-----LGETLNRIQSARRQLTQSLGREPTDTELANHL 271

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +SE ++  +        SL   +   ++  S   D++   H                R 
Sbjct: 272 GMSEEKLRELRRTAQDPVSLATPV--GEEADSTLADFIPDPHALDADDAAAS---GMLRQ 326

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +  ++  L+ RERR+ E R       P TLE +   F V+RERVRQIE +A +K++  
Sbjct: 327 QIAAALDQLSERERRVLELRYGLADGQPRTLEEVGKAFGVTRERVRQIEVKALRKLRHP 385


>gi|312884403|ref|ZP_07744108.1| RNA polymerase factor sigma-32 [Vibrio caribbenthicus ATCC
           BAA-2122]
 gi|309367925|gb|EFP95472.1| RNA polymerase factor sigma-32 [Vibrio caribbenthicus ATCC
           BAA-2122]
          Length = 285

 Score =  241 bits (616), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 106/287 (36%), Positives = 166/287 (57%), Gaps = 8/287 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  +   +    +  L  Y+  +   PML  +EE  LA+R    G++ AA  L+ SHLR 
Sbjct: 1   MTTQAYPMTAVTQDSLDSYVRSVNSYPMLTAEEERELAERLHYDGEIDAAKGLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A GY GYGLP++++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VKI TT  Q++LFFNLR+ K  L           +V  +A++L V  SEV  M  RL
Sbjct: 121 WRIVKIATTKAQRKLFFNLRKSKKRLGWFNQG-----EVETVARELGVEPSEVREMESRL 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE---ERKNRRNMLTRSMSVLNP 237
           A  ++   + +  D   + +   +VY  D    +    E      +  N L+ ++  L+ 
Sbjct: 176 AAQDATFEVPSDDDDAHTSYVAPMVYLEDKASDIADNIEAANWEAHTNNRLSLALKSLDE 235

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R + I  +R L +N  TL+ L+  ++VS ER+RQ+E  A KK+++++
Sbjct: 236 RSQHIVRSRWLDDNKSTLQELAETYQVSAERIRQLEKNAMKKLKDAV 282


>gi|254389040|ref|ZP_05004270.1| RNA polymerase principal sigma factor hrdA [Streptomyces
           clavuligerus ATCC 27064]
 gi|326441042|ref|ZP_08215776.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|197702757|gb|EDY48569.1| RNA polymerase principal sigma factor hrdA [Streptomyces
           clavuligerus ATCC 27064]
          Length = 385

 Score =  241 bits (616), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 84/302 (27%), Positives = 138/302 (45%), Gaps = 39/302 (12%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------------REHGDLS--- 48
                  +Y+ EI +IP+L   EE  LA+R                    R   DL    
Sbjct: 83  PSSDLFRQYLREIGRIPLLTAAEEVELARRVEAGLFAEEKLAATPDLNSSRLAADLDRLV 142

Query: 49  -----AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
                A  RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +T
Sbjct: 143 VMGRMAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYTRGYKFST 202

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI+ AM   +      +++     +  L   + R++  +     +   PE+V A  
Sbjct: 203 YATWWIRQAMSRALADQARTIRVPVHVVE--LINRVVRVQRRMLQEQGSEPTPEEVAA-- 258

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
            +L++    V  +        SL+A +   ++      D +    DG     +E      
Sbjct: 259 -QLDLPPERVSEVLRLAQEPVSLHAPV--GEEEDVALGDLI---EDGDAASPVESAAFLL 312

Query: 224 RRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R  L   +S L  RER++ + R       P TLE +   F V+RER+RQIE++   K++
Sbjct: 313 LREHLEAVLSTLGERERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLR 372

Query: 282 ES 283
           + 
Sbjct: 373 DH 374


>gi|28867660|ref|NP_790279.1| RNA polymerase sigma-32 factor [Pseudomonas syringae pv. tomato
           str. DC3000]
 gi|213967796|ref|ZP_03395943.1| RNA polymerase sigma-32 factor [Pseudomonas syringae pv. tomato T1]
 gi|301382433|ref|ZP_07230851.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. tomato
           Max13]
 gi|302061175|ref|ZP_07252716.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. tomato
           K40]
 gi|302132032|ref|ZP_07258022.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. tomato
           NCPPB 1108]
 gi|28850895|gb|AAO53974.1| RNA polymerase sigma-32 factor [Pseudomonas syringae pv. tomato
           str. DC3000]
 gi|213927572|gb|EEB61120.1| RNA polymerase sigma-32 factor [Pseudomonas syringae pv. tomato T1]
 gi|330965442|gb|EGH65702.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. actinidiae
           str. M302091]
 gi|331014973|gb|EGH95029.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. lachrymans
           str. M302278PT]
          Length = 284

 Score =  241 bits (616), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 101/272 (37%), Positives = 155/272 (56%), Gaps = 7/272 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+H +  IP+L  + E  LA+      DL AA ++V +HLR VV IA  Y GYGL 
Sbjct: 16  NLEAYVHTVNSIPLLTPERERELAESLYYEQDLDAARQMVLAHLRFVVHIARSYSGYGLA 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++
Sbjct: 76  QADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           LFFNLR  K  L  + +     ++V  +A+ L V   EV  M  RL G +        +D
Sbjct: 136 LFFNLRSQKKRLAWLNN-----DEVHRVAESLGVEPREVREMESRLTGHDMAFDPAAEAD 190

Query: 195 KNSS--QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            +S+     ++L        + L + +   N    L +++ VL+ R R I   R L E  
Sbjct: 191 DDSAFQSPANYLEDHRYDPARQLEDADWTDNSTANLHQALDVLDERSRDILYQRWLAEEK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL +L+ ++ VS ER+RQ+E  A  K++ SI
Sbjct: 251 ATLHDLAQKYNVSAERIRQLEKSAMNKLKTSI 282


>gi|86158413|ref|YP_465198.1| RNA polymerase sigma factor RpoH [Anaeromyxobacter dehalogenans
           2CP-C]
 gi|85774924|gb|ABC81761.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter
           dehalogenans 2CP-C]
          Length = 307

 Score =  241 bits (616), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 114/284 (40%), Positives = 165/284 (58%), Gaps = 6/284 (2%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
             +      L  Y+ EI + P+L   EE  LA+++    D  AAHRLVT++LR VVK+A 
Sbjct: 4   QSVPGTASSLELYLSEINRFPLLTVDEEQRLARQFCADRDTRAAHRLVTANLRFVVKVAY 63

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            YR YG  +++++ EGNIGLM+AV+KFDP++G RL +Y++WWI+A +Q YIL+SWSLVK+
Sbjct: 64  EYRSYGFRMADLIQEGNIGLMKAVQKFDPDKGIRLISYAVWWIRAYIQNYILKSWSLVKL 123

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKP---EQVVAIAKKLNVSESEVISMNCRLAG- 182
           GTT  Q++LFF+L R K  L   +              +AKKL V   EV  M  R+ G 
Sbjct: 124 GTTQAQRKLFFSLARTKRELDKRSQEQGADSDGHDANKVAKKLRVKPGEVREMEQRMEGR 183

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
           D SL+A +   D       D+L      Q+  L   +E+K     +  ++  L+ RER I
Sbjct: 184 DLSLDAPM--GDDGGYSHVDFLASGSTSQDDELSGVQEQKVVSGRIVEALGRLDQRERYI 241

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            E R + + P+TL+ L   F  SRER RQ+E RA  K++E ++ 
Sbjct: 242 IEMRVMSDRPLTLKELGEHFGFSRERARQLEIRAKDKLKEELRA 285


>gi|254503566|ref|ZP_05115717.1| RNA polymerase sigma factor, sigma-70 family [Labrenzia alexandrii
           DFL-11]
 gi|222439637|gb|EEE46316.1| RNA polymerase sigma factor, sigma-70 family [Labrenzia alexandrii
           DFL-11]
          Length = 287

 Score =  241 bits (616), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 106/266 (39%), Positives = 174/266 (65%), Gaps = 1/266 (0%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           +    K P L ++EE  LA ++R++ D  A  +L  SH+RLV+ +A  ++ +GL I +++
Sbjct: 8   VKTAMKAPYLTREEELELAIQWRDNKDEKALEKLSLSHMRLVIAVASRFKNFGLNIGDLI 67

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EG++GL++A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT+++QK LFFNL
Sbjct: 68  QEGHVGLLEAAARFEPEREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSSQKALFFNL 127

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSS 198
           RRL+  L +        E    IA  + V +S+V  MN RL+G D SLNA +  ++ +S+
Sbjct: 128 RRLRAKLSSNQTPLTDSELHQKIADAIGVKQSDVAVMNARLSGPDTSLNAPVTDTEGSSA 187

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
             QD+LV D    ++++ E  + + R   L  ++ VL+ RE +I   RRL E+  TLE+L
Sbjct: 188 DRQDFLVSDAPQPDEIVTENIDAERRNTWLASALDVLSERELKIVRERRLSEDGATLESL 247

Query: 259 SSEFEVSRERVRQIEARAFKKVQESI 284
             +  +S+ERVRQIE+RA +K++ ++
Sbjct: 248 GKKLGISKERVRQIESRALQKLKSAL 273


>gi|114331030|ref|YP_747252.1| RNA polymerase factor sigma-32 [Nitrosomonas eutropha C91]
 gi|114308044|gb|ABI59287.1| RNA polymerase, sigma 32 subunit, RpoH [Nitrosomonas eutropha C91]
          Length = 280

 Score =  241 bits (616), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 121/281 (43%), Positives = 176/281 (62%), Gaps = 9/281 (3%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +++ V     L  YI      P+L ++EE  LAK+ +E+GD++AAH+LV SHLR VV IA
Sbjct: 5   LTLPVISGGNLESYIRAANSFPVLSREEEISLAKKMQENGDINAAHQLVLSHLRTVVMIA 64

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            GY GYGLP ++++ EGNIGLM+AV++FDPERG RL ++++ WIKA + E+I+R+W LVK
Sbjct: 65  RGYLGYGLPHADLIQEGNIGLMKAVRRFDPERGVRLISFAIHWIKAEIHEFIMRNWRLVK 124

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DE 184
           I TT  Q++LFFNLR +K  L  +        +V  +A++L V   EV+ M  R +G D 
Sbjct: 125 IATTKPQRKLFFNLRSMKEGLDTMNQ-----AEVATMAEQLGVKAEEVVEMETRFSGRDI 179

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL  L +S +++ S      + D     + L +++  +     L  S+  L+ R RRI E
Sbjct: 180 SLEPLTDSDEEDFS--PIAYLTDGSDPSRELEKEQLERLTHAKLKDSLDSLDERSRRIIE 237

Query: 245 ARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           AR L+E+   TL  L+ E  VS ERVRQIEA+A KK++  I
Sbjct: 238 ARWLREDKAATLHELAKELGVSAERVRQIEAKAMKKMRAEI 278


>gi|222475169|ref|YP_002563585.1| RNA polymerase sigma-32 factor (rpoH) [Anaplasma marginale str.
           Florida]
 gi|222419306|gb|ACM49329.1| RNA polymerase sigma-32 factor (rpoH) [Anaplasma marginale str.
           Florida]
          Length = 307

 Score =  241 bits (616), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 129/276 (46%), Positives = 190/276 (68%), Gaps = 4/276 (1%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           G   L  Y+ ++R  P+L ++EE  LA+ +   G ++ AHRLVTSHLRLVVKIAMG++ Y
Sbjct: 28  GSDDLVSYVAQVRTFPILSEEEEKRLAENWYRRGSVADAHRLVTSHLRLVVKIAMGFKSY 87

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GLPI E++ EGNIGLMQAVK+F+P+ GFRLATY++WWIKA++++YILRSWS +++GTT  
Sbjct: 88  GLPIMELIMEGNIGLMQAVKRFNPDLGFRLATYAVWWIKASIKDYILRSWSCIRVGTTQA 147

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALI 190
           QK+LFF+LR++K  L +   +++  +++ AIA++   SE EV  M+   A  D SLN  +
Sbjct: 148 QKKLFFSLRKIKKRLLSC-GSSMTKKEIKAIAEECATSEEEVERMDRFFANRDVSLNEQV 206

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           +   ++S + QD +      QE + +  EE   +++M   +++ L+ R R IF  RRLQE
Sbjct: 207 HG--ESSVELQDLVPSSLPSQEIMYLADEESAIKKSMFDSALATLDDRHRDIFTRRRLQE 264

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            P TLE LS E+ VS+ERVRQIE +A  K++  I+ 
Sbjct: 265 RPDTLEKLSEEYGVSKERVRQIELQALCKIKSFIEA 300


>gi|189424394|ref|YP_001951571.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter lovleyi SZ]
 gi|189420653|gb|ACD95051.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter lovleyi SZ]
          Length = 285

 Score =  241 bits (616), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 119/285 (41%), Positives = 182/285 (63%), Gaps = 4/285 (1%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
            + I       S+Y+ EI+  P+L++QEE+ LA R  E  DLSAA  L+TS+LR VVKIA
Sbjct: 2   YAAIPVTTDSFSKYLSEIKSFPLLDEQEEHRLAVRLFEENDLSAAQTLITSNLRFVVKIA 61

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             YR YGL + +++ EGNIGLM AV+KF+P RGFRL TY++WWI+A +Q YI+ SWSL+K
Sbjct: 62  AEYRNYGLKMLDLIQEGNIGLMLAVRKFNPYRGFRLITYAVWWIRAQIQSYIVSSWSLLK 121

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           IGTT  Q++LFF L++ K  +  ++ N      + A A  L+V E+EV  M  RL G+ S
Sbjct: 122 IGTTQAQRKLFFKLKQAKNAI--LSMNGGDEGDLPATALSLDVREAEVEEMELRLMGEVS 179

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L+A   + +  S    + LV D   QE  L + +E++  R ++  ++S L  +E+ + + 
Sbjct: 180 LDAEQVAGEGGS--LLETLVDDRPNQESQLADLQEQQALRVVVADAVSRLGEKEQFVVKQ 237

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
           R + ++P+TL+ ++  F +SRERVRQIE  A +K++  +   ++L
Sbjct: 238 RIVADDPMTLQEIADHFSISRERVRQIEENALRKIKGFLGASMQL 282


>gi|297199501|ref|ZP_06916898.1| RNA polymerase sigma factor RpoS [Streptomyces sviceus ATCC 29083]
 gi|297147415|gb|EDY56986.2| RNA polymerase sigma factor RpoS [Streptomyces sviceus ATCC 29083]
          Length = 428

 Score =  241 bits (616), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 82/301 (27%), Positives = 136/301 (45%), Gaps = 38/301 (12%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKR----------YREHGDLS------------ 48
                  +Y+ EI +IP+L   EE  LA+R               DL             
Sbjct: 127 PSSDLFRQYLREIGRIPLLTAVEEVELARRVEAGLFAEEKLSSTPDLDSQLALDLDRLVV 186

Query: 49  ----AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
               A  RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY
Sbjct: 187 LGRMAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTY 246

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + WWI+ AM   +      +++     +  L   + R++  +         PE+V A   
Sbjct: 247 ATWWIRQAMSRALADQARTIRVPVHVVE--LINRVVRVQRRMLQERGYEPTPEEVAA--- 301

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            L+++   V  +        SL+A +   +++     D +    DG     +E       
Sbjct: 302 HLDLAPERVSEVLRLAQEPVSLHAPV--GEEDDVALGDLI---EDGDAASPVESAAFLLL 356

Query: 225 RNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           R  L   +S L  RER++ + R         TLE +   F V+RER+RQIE++   K+++
Sbjct: 357 REHLEAVLSTLGERERKVVQLRYGLADGRARTLEEIGRIFGVTRERIRQIESKTLNKLRD 416

Query: 283 S 283
            
Sbjct: 417 H 417


>gi|22124334|ref|NP_667757.1| RNA polymerase factor sigma-32 [Yersinia pestis KIM 10]
 gi|45442990|ref|NP_994529.1| RNA polymerase factor sigma-32 [Yersinia pestis biovar Microtus
           str. 91001]
 gi|51594579|ref|YP_068770.1| RNA polymerase factor sigma-32 [Yersinia pseudotuberculosis IP
           32953]
 gi|108806209|ref|YP_650125.1| RNA polymerase factor sigma-32 [Yersinia pestis Antiqua]
 gi|108810319|ref|YP_646086.1| RNA polymerase factor sigma-32 [Yersinia pestis Nepal516]
 gi|145600678|ref|YP_001164754.1| RNA polymerase factor sigma-32 [Yersinia pestis Pestoides F]
 gi|153997132|ref|ZP_02022265.1| RNA polymerase sigma-32 factor [Yersinia pestis CA88-4125]
 gi|162418961|ref|YP_001605171.1| RNA polymerase factor sigma-32 [Yersinia pestis Angola]
 gi|165926363|ref|ZP_02222195.1| alternative sigma factor RpoH [Yersinia pestis biovar Orientalis
           str. F1991016]
 gi|165939186|ref|ZP_02227737.1| alternative sigma factor RpoH [Yersinia pestis biovar Orientalis
           str. IP275]
 gi|166011667|ref|ZP_02232565.1| alternative sigma factor RpoH [Yersinia pestis biovar Antiqua str.
           E1979001]
 gi|166213537|ref|ZP_02239572.1| alternative sigma factor RpoH [Yersinia pestis biovar Antiqua str.
           B42003004]
 gi|167401873|ref|ZP_02307361.1| alternative sigma factor RpoH [Yersinia pestis biovar Antiqua str.
           UG05-0454]
 gi|167420986|ref|ZP_02312739.1| alternative sigma factor RpoH [Yersinia pestis biovar Orientalis
           str. MG05-1020]
 gi|167426241|ref|ZP_02317994.1| alternative sigma factor RpoH [Yersinia pestis biovar Mediaevalis
           str. K1973002]
 gi|170026187|ref|YP_001722692.1| RNA polymerase factor sigma-32 [Yersinia pseudotuberculosis YPIII]
 gi|186893581|ref|YP_001870693.1| RNA polymerase factor sigma-32 [Yersinia pseudotuberculosis PB1/+]
 gi|218930813|ref|YP_002348688.1| RNA polymerase factor sigma-32 [Yersinia pestis CO92]
 gi|229837138|ref|ZP_04457303.1| RNA polymerase, sigma 32 (sigma H) factor [Yersinia pestis
           Pestoides A]
 gi|229839498|ref|ZP_04459657.1| RNA polymerase, sigma 32 (sigma H) factor [Yersinia pestis biovar
           Orientalis str. PEXU2]
 gi|229900061|ref|ZP_04515198.1| RNA polymerase, sigma 32 (sigma H) factor [Yersinia pestis biovar
           Orientalis str. India 195]
 gi|229900493|ref|ZP_04515622.1| RNA polymerase, sigma 32 (sigma H) factor [Yersinia pestis
           Nepal516]
 gi|270488848|ref|ZP_06205922.1| alternative sigma factor RpoH [Yersinia pestis KIM D27]
 gi|294505476|ref|YP_003569538.1| RNA polymerase sigma factor [Yersinia pestis Z176003]
 gi|21957109|gb|AAM84008.1|AE013642_9 RNA polymerase, sigma(32) factor [Yersinia pestis KIM 10]
 gi|45437857|gb|AAS63406.1| RNA polymerase sigma-32 factor [Yersinia pestis biovar Microtus
           str. 91001]
 gi|51587861|emb|CAH19464.1| RNA polymerase sigma-32 factor [Yersinia pseudotuberculosis IP
           32953]
 gi|108773967|gb|ABG16486.1| RNA polymerase sigma-32 factor [Yersinia pestis Nepal516]
 gi|108778122|gb|ABG12180.1| RNA polymerase sigma-32 factor [Yersinia pestis Antiqua]
 gi|115349424|emb|CAL22397.1| RNA polymerase sigma-32 factor [Yersinia pestis CO92]
 gi|145212374|gb|ABP41781.1| RNA polymerase sigma-32 factor [Yersinia pestis Pestoides F]
 gi|149289438|gb|EDM39516.1| RNA polymerase sigma-32 factor [Yersinia pestis CA88-4125]
 gi|162351776|gb|ABX85724.1| alternative sigma factor RpoH [Yersinia pestis Angola]
 gi|165912959|gb|EDR31585.1| alternative sigma factor RpoH [Yersinia pestis biovar Orientalis
           str. IP275]
 gi|165921887|gb|EDR39084.1| alternative sigma factor RpoH [Yersinia pestis biovar Orientalis
           str. F1991016]
 gi|165989436|gb|EDR41737.1| alternative sigma factor RpoH [Yersinia pestis biovar Antiqua str.
           E1979001]
 gi|166205210|gb|EDR49690.1| alternative sigma factor RpoH [Yersinia pestis biovar Antiqua str.
           B42003004]
 gi|166961115|gb|EDR57136.1| alternative sigma factor RpoH [Yersinia pestis biovar Orientalis
           str. MG05-1020]
 gi|167048766|gb|EDR60174.1| alternative sigma factor RpoH [Yersinia pestis biovar Antiqua str.
           UG05-0454]
 gi|167054760|gb|EDR64564.1| alternative sigma factor RpoH [Yersinia pestis biovar Mediaevalis
           str. K1973002]
 gi|169752721|gb|ACA70239.1| RNA polymerase, sigma 32 subunit, RpoH [Yersinia pseudotuberculosis
           YPIII]
 gi|186696607|gb|ACC87236.1| RNA polymerase, sigma 32 subunit, RpoH [Yersinia pseudotuberculosis
           PB1/+]
 gi|229682512|gb|EEO78599.1| RNA polymerase, sigma 32 (sigma H) factor [Yersinia pestis
           Nepal516]
 gi|229686841|gb|EEO78920.1| RNA polymerase, sigma 32 (sigma H) factor [Yersinia pestis biovar
           Orientalis str. India 195]
 gi|229695864|gb|EEO85911.1| RNA polymerase, sigma 32 (sigma H) factor [Yersinia pestis biovar
           Orientalis str. PEXU2]
 gi|229706081|gb|EEO92090.1| RNA polymerase, sigma 32 (sigma H) factor [Yersinia pestis
           Pestoides A]
 gi|262363541|gb|ACY60262.1| RNA polymerase sigma factor [Yersinia pestis D106004]
 gi|262367470|gb|ACY64027.1| RNA polymerase sigma factor [Yersinia pestis D182038]
 gi|270337352|gb|EFA48129.1| alternative sigma factor RpoH [Yersinia pestis KIM D27]
 gi|294355935|gb|ADE66276.1| RNA polymerase sigma factor [Yersinia pestis Z176003]
 gi|320013591|gb|ADV97162.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Medievalis
           str. Harbin 35]
          Length = 285

 Score =  241 bits (616), Expect = 9e-62,   Method: Composition-based stats.
 Identities = 102/290 (35%), Positives = 164/290 (56%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  YI      PML  +EE  LA+R    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLALVPQGSLEAYIRAANAYPMLTAEEERELAERLHYQGDLGAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VAHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +AK+L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVELVAKELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNP 237
           +  +         +    Q+   ++Y  D        + E     +  + L+ ++  L+ 
Sbjct: 176 SAQDMTFDPSPDDEARDGQFMAPVLYLQDKTSDFADGIEEDNWDSHAADKLSYALEGLDE 235

Query: 238 RERRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L + N  TL+ L+ ++ VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQHIIRARWLDDENKSTLQELADQYGVSAERVRQLEKNAMKKLRMAIEA 285


>gi|15894582|ref|NP_347931.1| RNA polymerase sigma factor RpoD [Clostridium acetobutylicum ATCC
           824]
 gi|464686|sp|P33656|RPOD_CLOAB RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A;
           AltName: Full=Major vegetative sigma factor
 gi|15024230|gb|AAK79271.1|AE007642_3 RNA polymerase sigma factor RPOD [Clostridium acetobutylicum ATCC
           824]
 gi|312373|emb|CAA80625.1| major vegetative sigma factor [Clostridium acetobutylicum ATCC 824]
 gi|325508714|gb|ADZ20350.1| major vegetative sigma factor [Clostridium acetobutylicum EA 2018]
          Length = 378

 Score =  241 bits (616), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 82/277 (29%), Positives = 143/277 (51%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI K+P+L  +EE  LA+R + +GD SA  +L  ++LRLVV IA  Y G G
Sbjct: 106 DDPVRMYLKEIGKVPLLSPEEEIDLAQRIK-NGDRSARKKLAEANLRLVVSIAKRYVGRG 164

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +   +++ EGN+GL++AV+KFD ++GF+ +TY+ WWI+ A+   I      ++I     +
Sbjct: 165 MLFLDLIQEGNLGLIKAVEKFDFKKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 224

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 L R+   L        +PE    IAK +++   +V  +        SL   I  
Sbjct: 225 --TINKLIRVSRQLLQELGREPQPE---EIAKIMDMPVDKVREIMKIAQEPVSLETPI-- 277

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            ++  S   D++      +     +    +  +  L + ++ L PRE ++   R   ++ 
Sbjct: 278 GEEEDSHLGDFIPD---DEAPAPADAAAFRMLKEQLLKILNTLTPREEKVLRLRFGLDDG 334

Query: 253 --VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 335 RARTLEEVGKEFNVTRERIRQIEAKALRKLRHPSRSK 371


>gi|294786990|ref|ZP_06752244.1| RNA polymerase sigma (70) factor RpoD [Parascardovia denticolens
           F0305]
 gi|294485823|gb|EFG33457.1| RNA polymerase sigma (70) factor RpoD [Parascardovia denticolens
           F0305]
          Length = 403

 Score =  241 bits (616), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 67/306 (21%), Positives = 138/306 (45%), Gaps = 40/306 (13%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKR----------------------------YRE 43
               +  Y+ +I ++ +L  Q+E  L++R                            +  
Sbjct: 99  TSDPVKDYLKQIGRVNLLNAQQEVDLSERIEAGLYAQHLLDTTPADQMTFQRKRELKWAA 158

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           +    A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +T
Sbjct: 159 NDGRKAKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFST 218

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI+ A+   +      +++     +  +   L R++  +         P+    +A
Sbjct: 219 YATWWIRQAITRAMADQARTIRVPVHMVE--VINKLSRVQRQMLQDLGREPTPD---ELA 273

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           ++L++   +V  +        SL+  +   +   S++ D +    D       E      
Sbjct: 274 RELDMPVEKVQEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDTDAIAPSEAVAFSL 328

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +    + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++   K++
Sbjct: 329 LQEQFKQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGHVYGVTRERIRQIESKTMSKLR 388

Query: 282 ESIQKQ 287
              + Q
Sbjct: 389 HPSRSQ 394


>gi|225628325|ref|ZP_03786359.1| RNA polymerase sigma factor, sigma-70 family protein [Brucella ceti
           str. Cudo]
 gi|225616171|gb|EEH13219.1| RNA polymerase sigma factor, sigma-70 family protein [Brucella ceti
           str. Cudo]
          Length = 278

 Score =  241 bits (616), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 117/274 (42%), Positives = 180/274 (65%), Gaps = 1/274 (0%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           I      P LE++EE  LA R++E  D  A HR+ ++H+RLV+ +A  +R + LP+S+++
Sbjct: 2   IRSAMSAPYLEREEERALAIRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLI 61

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EG +GL++A  +FDP+R  R +TY+ WWI+A+MQ+YILR+WS+V+ GT++ QK LFFNL
Sbjct: 62  QEGYVGLLEAAARFDPDRDVRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKALFFNL 121

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSS 198
           RRL+  L    DN  K E    I+ +L VS S+V  M+ RL+G D SL+  +N  +  +S
Sbjct: 122 RRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRLSGPDSSLSVPMNGEETGAS 181

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           +  D+LV DH  Q+++     + + R   LTR++  LN RE  I   RRL ++ VTLE L
Sbjct: 182 RRMDFLVDDHPLQDEIAESSIDMERRNRWLTRALDTLNERELHIIRERRLDDDGVTLEAL 241

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
             +  +S+ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 242 GEKLGISKERVRQIESRAMEKLKIALLSQHELAA 275


>gi|95929333|ref|ZP_01312076.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfuromonas acetoxidans
           DSM 684]
 gi|95134449|gb|EAT16105.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfuromonas acetoxidans
           DSM 684]
          Length = 282

 Score =  241 bits (616), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 118/286 (41%), Positives = 184/286 (64%), Gaps = 10/286 (3%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
             N+ ++++G      Y+ +I +   L+++ EY LA RYR++ DL AAH+LV ++LR VV
Sbjct: 1   MSNLPLVIDG---FDHYMAQISQFEPLDRETEYELANRYRKNNDLDAAHKLVCANLRFVV 57

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           KIA  Y+ YGL + ++V EGNIGLM+A+KKFDP+R  RL +Y++WWI+A +  YI+ +WS
Sbjct: 58  KIAYEYQAYGLKMIDLVQEGNIGLMKAIKKFDPDRNIRLISYAVWWIRAYIHNYIINAWS 117

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           LVKIGTT  +K+LFF L++ +  LQ +            IA++LNVS  EV  M+ RL G
Sbjct: 118 LVKIGTTQARKKLFFKLKQTRDALQKM----GNDADHAEIARQLNVSTDEVAEMSVRLGG 173

Query: 183 -DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
            D SL+  +     +++   D LV     QEQ LIE E      + + +++S LN RE+ 
Sbjct: 174 RDSSLDGQLTP--DSTTSHLDTLVDHDKDQEQRLIELEHESLTTHRVQQALSHLNEREQH 231

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           I  +R LQ++  TL++L+ ++ +S+ERVRQ+E RA +K++  + +Q
Sbjct: 232 IVHSRILQDDKATLQDLADQYGISKERVRQLEKRALEKLKNLLIEQ 277


>gi|159037077|ref|YP_001536330.1| RNA polymerase sigma factor [Salinispora arenicola CNS-205]
 gi|157915912|gb|ABV97339.1| RNA polymerase, sigma 70 subunit, RpoD family [Salinispora
           arenicola CNS-205]
          Length = 532

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 77/312 (24%), Positives = 145/312 (46%), Gaps = 42/312 (13%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------------EHGDLS-------- 48
           +      +  Y+ +I K+P+L  ++E  LAKR              E G+          
Sbjct: 225 LTASADSVRAYLKQIGKVPLLNAEQEVELAKRIEAGLYAAERLRATEEGEEKLNRDMQRD 284

Query: 49  ----------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
                     A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G
Sbjct: 285 LMWISRDGERAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKG 344

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           ++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L         PE 
Sbjct: 345 YKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLGREPTPE- 401

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +  V ++ 
Sbjct: 402 --ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSEAVVAVDA 454

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARA 276
                 ++ L + +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++ 
Sbjct: 455 VSFSLLQDQLQQVLQTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKT 514

Query: 277 FKKVQESIQKQV 288
             K++   + QV
Sbjct: 515 MSKLRHPSRSQV 526


>gi|329121328|ref|ZP_08249954.1| DNA-directed RNA polymerase sigma subunit RpoD [Dialister
           micraerophilus DSM 19965]
 gi|327469737|gb|EGF15203.1| DNA-directed RNA polymerase sigma subunit RpoD [Dialister
           micraerophilus DSM 19965]
          Length = 396

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 74/285 (25%), Positives = 132/285 (46%), Gaps = 23/285 (8%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREH-----------GDLSAAHRLVTSHLR 59
           N    +  Y+ E    P+L  +EE  LAK+  +                A   +  ++LR
Sbjct: 114 NVSDPVRLYLRECGATPLLSAEEEMTLAKQIEKGKMLDATEEDKLRAEDAKKEMANANLR 173

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           LVV IA  Y G G+P  +++ EGNIGL++AV KFD ++G++ +TY+ WWI+ A+   I  
Sbjct: 174 LVVSIAKKYPGRGMPFLDLIQEGNIGLLKAVDKFDYKKGYKFSTYATWWIRQAITRSIAD 233

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
               +++     +      + ++    +       +      +AK++ +S  ++      
Sbjct: 234 QARTIRVPVHMVE-----TINKMNRIGRKFLQEFGREASNEELAKEMGISVEKIREAKKA 288

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
                SL   I   +K  S   D++    D +     E+     RR  + + ++ L  RE
Sbjct: 289 AQDPISLETPI--GEKEDSHLGDFI---EDQKTSSPEEEAAATMRREQIYKLLNELTERE 343

Query: 240 RRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           + +   R   ++  P TLE +   F V+RER+RQIE +A KK+++
Sbjct: 344 KGVLALRFGMDDGTPRTLEEVGKYFGVTRERIRQIEGKALKKLRK 388


>gi|289523410|ref|ZP_06440264.1| RNA polymerase sigma factor RpoD [Anaerobaculum hydrogeniformans
           ATCC BAA-1850]
 gi|289503102|gb|EFD24266.1| RNA polymerase sigma factor RpoD [Anaerobaculum hydrogeniformans
           ATCC BAA-1850]
          Length = 412

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 83/281 (29%), Positives = 136/281 (48%), Gaps = 13/281 (4%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
            V+    +  Y+ EI KI +L  +EE  LAKR  E     A  +L+ ++LRLVV IA  Y
Sbjct: 136 SVSISDPVRMYLREIGKISLLTPEEEVELAKRVEEGE-EEAKKKLIEANLRLVVSIAKKY 194

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            G GL   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I  
Sbjct: 195 IGRGLSFLDLIQEGNLGLIRAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPV 254

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
              +      + +L    + +     +   +  IA+ L +   +V  +        SL  
Sbjct: 255 HMVE-----TINKLIRVSRQLVQQLGREPTIEEIAQSLGLPPEKVEDIQRIAQEPVSLET 309

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            I   ++  SQ  D+L    D +     +    +  R  L   +  L  RER +   R  
Sbjct: 310 PI--GEEEDSQLGDFL---EDKESPNPEDATAGQLLREQLEEMLGELTEREREVLRLRFG 364

Query: 249 QENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            E+    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 365 LEDGHAHTLEEVGKRFNVTRERIRQIEAKALRKLRHPSRSK 405


>gi|54298657|ref|YP_125026.1| RNA polymerase factor sigma-32 [Legionella pneumophila str. Paris]
 gi|296108313|ref|YP_003620014.1| RNA polymerase sigma-32 factor [Legionella pneumophila 2300/99
           Alcoy]
 gi|53752442|emb|CAH13874.1| RNA polymerase sigma-32 factor [Legionella pneumophila str. Paris]
 gi|295650215|gb|ADG26062.1| RNA polymerase sigma-32 factor [Legionella pneumophila 2300/99
           Alcoy]
          Length = 284

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 110/274 (40%), Positives = 177/274 (64%), Gaps = 7/274 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             L  YIH + +IPML  +EE   A+R+   GD+ AA +LV +HLR VV++A GY GYGL
Sbjct: 15  GSLDSYIHRVNQIPMLTLEEEIAYAERFHSEGDIEAARQLVLAHLRYVVRVARGYLGYGL 74

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+S+++ EGN+GLM+AVK+FDP+ G RL ++++ WIKA + E++LR+W +VK+ TT  Q+
Sbjct: 75  PLSDLIQEGNVGLMKAVKRFDPKMGVRLVSFAVHWIKAEIHEFVLRNWRIVKVATTKAQR 134

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINS 192
           +LFFNLR++K  L   ++     E+V A+AK L VS  +V+ M  RL   D S +A    
Sbjct: 135 KLFFNLRQMKNRLGWFSN-----EEVDAVAKDLGVSREDVLLMEQRLNVMDSSYDAPDVD 189

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPRERRIFEARRLQEN 251
            + ++ +  +  +++ +    VL+E E+  ++ R  L  +M  L+ R + I + R L E 
Sbjct: 190 DNDDAYKAPERYLFNVNDDPAVLLENEDTGDQGREKLLFAMEQLDERSQDILQQRWLAEE 249

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            +TL +L+ ++ VS ERVRQ+E  A KK+++ ++
Sbjct: 250 KLTLHDLAEKYGVSAERVRQLEKNAMKKIRQYME 283


>gi|297194519|ref|ZP_06911917.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
 gi|297152294|gb|EFH31643.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
          Length = 366

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 82/301 (27%), Positives = 137/301 (45%), Gaps = 38/301 (12%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKR----------YREHGDLS------------ 48
                  +Y+ EI +IP+L   EE  LA+R               D              
Sbjct: 65  PTSDLFRQYLREIGRIPLLTAAEEVELARRVEAGLFAEEKLANTPDPDSQLAVDLDRLVV 124

Query: 49  ----AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
               A  RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY
Sbjct: 125 MGRMAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTY 184

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + WWI+ AM   +      +++     +  L   + R++  +         PE+V   A 
Sbjct: 185 ATWWIRQAMSRALADQARTIRVPVHVVE--LINRVVRVQRRMLQERGYEPTPEEV---AT 239

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            L ++   V  +        SL+A +   +++     D +    DG     +E       
Sbjct: 240 HLELTSERVSEVLRLAQEPVSLHAPV--GEEDDVALGDLI---EDGDAASPVESAAFLLL 294

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           R  L   +S L  RER++ + R   ++  P TLE +   F V+RER+RQIE++   K+++
Sbjct: 295 REHLDAVLSTLGERERKVVQLRYGLDDGRPRTLEEIGRLFGVTRERIRQIESKTLNKLRD 354

Query: 283 S 283
            
Sbjct: 355 H 355


>gi|66047972|ref|YP_237813.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. syringae
           B728a]
 gi|237802354|ref|ZP_04590815.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. oryzae
           str. 1_6]
 gi|63258679|gb|AAY39775.1| Sigma-70 region 2:Sigma-70 region 4 [Pseudomonas syringae pv.
           syringae B728a]
 gi|330957082|gb|EGH57342.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. maculicola
           str. ES4326]
 gi|330970950|gb|EGH71016.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. aceris
           str. M302273PT]
 gi|331025211|gb|EGI05267.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. oryzae
           str. 1_6]
          Length = 284

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 100/272 (36%), Positives = 154/272 (56%), Gaps = 7/272 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+  +  IP+L  + E  LA+      DL AA ++V +HLR VV IA  Y GYGL 
Sbjct: 16  NLEAYVQTVNSIPLLTPERERELAESLYYEQDLDAARQMVLAHLRFVVHIARSYSGYGLA 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++
Sbjct: 76  QADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           LFFNLR  K  L  + +     ++V  +A+ L V   EV  M  RL G +        +D
Sbjct: 136 LFFNLRSQKKRLAWLNN-----DEVHRVAESLGVEPREVREMESRLTGHDMAFDPAAEAD 190

Query: 195 KNSS--QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            +S+     ++L        + L + +   N    L +++ VL+ R R I   R L E  
Sbjct: 191 DDSAFQSPANYLEDHRYDPARQLEDSDWTDNSTANLHQALDVLDERSRDILYQRWLAEEK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL +L+ ++ VS ER+RQ+E  A  K++ SI
Sbjct: 251 ATLHDLAQKYNVSAERIRQLEKSAMNKLKTSI 282


>gi|153947554|ref|YP_001399239.1| RNA polymerase factor sigma-32 [Yersinia pseudotuberculosis IP
           31758]
 gi|152959049|gb|ABS46510.1| alternative sigma factor RpoH [Yersinia pseudotuberculosis IP
           31758]
          Length = 285

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 102/290 (35%), Positives = 164/290 (56%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  YI      PML  +EE  LA+R    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLALVPQGSLEAYIRAANAYPMLTAEEERELAERLHYQGDLGAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VAHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +AK+L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVELVAKELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNP 237
           +  +         +    Q+   ++Y  D        + E     +  + L+ ++  L+ 
Sbjct: 176 SAQDMTFDPSPDDEARDGQFMAPVLYLQDKTSDFADGIEEDNWDTHAADKLSYALEGLDE 235

Query: 238 RERRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L + N  TL+ L+ ++ VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQHIIRARWLDDENKSTLQELADQYGVSAERVRQLEKNAMKKLRMAIEA 285


>gi|332529979|ref|ZP_08405929.1| RNA polymerase sigma-32 subunit RpoH [Hylemonella gracilis ATCC
           19624]
 gi|332040452|gb|EGI76828.1| RNA polymerase sigma-32 subunit RpoH [Hylemonella gracilis ATCC
           19624]
          Length = 326

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 112/301 (37%), Positives = 172/301 (57%), Gaps = 21/301 (6%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +V     L  YI  + ++PML  +EE   A+++R++ DL AA +LV SHLRLVV  A  Y
Sbjct: 26  LVPPLGNLDAYITAVNRMPMLTAEEEQEFARKFRDNNDLEAAGKLVLSHLRLVVATARQY 85

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGLP  +++ EGN+GLM+AVK+FDP++G RL +Y++ WIKA + EYIL++W +VK+ T
Sbjct: 86  MGYGLPHGDLIQEGNVGLMKAVKRFDPDQGVRLVSYALHWIKAEIHEYILKNWRMVKVAT 145

Query: 129 TANQKRLFFNLRRLKGHLQAIT---------------DNNLKPEQVVAIAKKLNVSESEV 173
           T  Q++LFFNLR  K   +A +                  L   ++  +A++LNV   EV
Sbjct: 146 TKAQRKLFFNLRSKKQGYKAASAADSSLHDGLDAATHRETLSEHEIDQMARELNVKREEV 205

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSM 232
           I M  RL+G + +       D   S      + D   +   +IE  +R     + + +++
Sbjct: 206 IEMETRLSGGDVMLDPGPGEDGEDSFGPIAYLTDAGHEPTAMIEARQRDRLATDGIAKAL 265

Query: 233 SVLNPRERRIFEARRLQENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             L+PR RRI E R L+ N      +TL  L++E+ VS ER+RQIE  A KK++ ++ + 
Sbjct: 266 DALDPRSRRIVEERWLKVNDDASGGMTLHELAAEYGVSAERIRQIEVAAMKKMKTALAEY 325

Query: 288 V 288
            
Sbjct: 326 A 326


>gi|54295507|ref|YP_127922.1| RNA polymerase factor sigma-32 [Legionella pneumophila str. Lens]
 gi|53755339|emb|CAH16835.1| RNA polymerase sigma-32 factor [Legionella pneumophila str. Lens]
          Length = 284

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 113/283 (39%), Positives = 181/283 (63%), Gaps = 10/283 (3%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           MS+ V     L  YIH + +IPML  +EE   A+R+   GD+ AA +LV +HLR VV++A
Sbjct: 10  MSLPVG---SLDSYIHRVNQIPMLTLEEEIAYAERFHSEGDIEAARQLVLAHLRYVVRVA 66

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            GY GYGLP+S+++ EGN+GLM+AVK+FDP+ G RL ++++ WIKA + E++LR+W +VK
Sbjct: 67  RGYLGYGLPLSDLIQEGNVGLMKAVKRFDPKMGVRLVSFAVHWIKAEIHEFVLRNWRIVK 126

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDE 184
           + TT  Q++LFFNLR++K  L   ++     E+V A+AK L VS  +V+ M  RL   D 
Sbjct: 127 VATTKAQRKLFFNLRQMKNRLGWFSN-----EEVDAVAKDLGVSREDVLLMEQRLNVMDS 181

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPRERRIF 243
           S +A     + ++ +  +  +++ +    VL+E E+  ++ R  L  +M  L+ R + I 
Sbjct: 182 SYDAPDVDDNDDAYKAPERYLFNVNDDPAVLLENEDTGDQGREKLLFAMEQLDERSQDIL 241

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           + R L E  +TL +L+ ++ VS ERVRQ+E  A KK+++ ++ 
Sbjct: 242 QQRWLAEEKLTLHDLAEKYGVSAERVRQLEKNAMKKIRQYMEA 284


>gi|50954703|ref|YP_061991.1| RNA polymerase sigma factor [Leifsonia xyli subsp. xyli str.
           CTCB07]
 gi|50951185|gb|AAT88886.1| RNA polymerase, sigma-70 family factor [Leifsonia xyli subsp. xyli
           str. CTCB07]
          Length = 440

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 73/311 (23%), Positives = 138/311 (44%), Gaps = 38/311 (12%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR------------------------ 40
           + +I       +  Y+ +I K+P+L   EE  LA R                        
Sbjct: 133 STTITGATADPVKDYLKQIGKVPLLNAAEEVELAMRIEAGLFAEDRLANTPNMPRELERE 192

Query: 41  --YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
             +       A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G
Sbjct: 193 LRWVARDGQRAKSHLLGANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEKFDYTKG 252

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           F+ +TY+ WWI+ A+   +      ++I     +  +   L R++  +         PE 
Sbjct: 253 FKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE- 309

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              ++K+L+++  +V+ +        SL+  +   +   S++ D +    D +  V  + 
Sbjct: 310 --ELSKELDMTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDIEAVVPADA 362

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARA 276
                 +  L   +  L+ RE  +   R    +  P TL+ +   F V+RER+RQIE++ 
Sbjct: 363 VGFTMLQKQLESLLDSLSEREAGVIRMRFGLGDGMPKTLDQIGDTFGVTRERIRQIESKT 422

Query: 277 FKKVQESIQKQ 287
             K++   + Q
Sbjct: 423 MAKLRHPSRSQ 433


>gi|70733139|ref|YP_262912.1| RNA polymerase factor sigma-32 [Pseudomonas fluorescens Pf-5]
 gi|68347438|gb|AAY95044.1| transcription initiation factor sigma 32 [Pseudomonas fluorescens
           Pf-5]
          Length = 284

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 103/272 (37%), Positives = 156/272 (57%), Gaps = 7/272 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+H +  IP+L  ++E  LA+      DL AA ++V +HLR VV IA  Y GYGL 
Sbjct: 16  NLEAYVHTVNSIPLLTPEQERELAESLYYEQDLEAARQMVLAHLRFVVHIARSYSGYGLA 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++
Sbjct: 76  QADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           LFFNLR  K  L  + +     E+V  +A+ L V   EV  M  RL G +        +D
Sbjct: 136 LFFNLRSQKKRLAWLNN-----EEVHRVAESLGVEPREVREMESRLTGQDMAFDPAAEAD 190

Query: 195 KNSS-QWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENP 252
            +S+ Q     + DH     + +E  +  +     L  ++ VL+ R R I   R L E  
Sbjct: 191 DDSAFQSPANYLEDHRYDPALQLEDADWSDNSTSNLHEALEVLDERSRDILYQRWLAEEK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL +L+ ++ VS ER+RQ+E  A  K++ SI
Sbjct: 251 ATLHDLAQKYNVSAERIRQLEKSAMNKLKLSI 282


>gi|187922577|ref|YP_001894219.1| RNA polymerase factor sigma-32 [Burkholderia phytofirmans PsJN]
 gi|187713771|gb|ACD14995.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia phytofirmans
           PsJN]
          Length = 311

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 121/284 (42%), Positives = 167/284 (58%), Gaps = 12/284 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S++      +  YI  + +IPML   EE   A  +RE  +L +A RLV SHLRLVV IA 
Sbjct: 30  SLLPGQLGNIDAYIQAVNRIPMLTPAEERQFATEFREQDNLESARRLVLSHLRLVVSIAR 89

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y GYGLP ++++ EGNIGLM+AVK+FDPE+  RL +Y+M WIKA + EYILR+W +VK+
Sbjct: 90  NYLGYGLPHADLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHWIKAEIHEYILRNWRMVKV 149

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDES 185
            TT  Q++LFFNLR  K  L A T     P+Q+  +AK+LNV   EV  M  RL  GD +
Sbjct: 150 ATTKAQRKLFFNLRSHKQGLGAFT-----PDQIDDLAKELNVKREEVSEMETRLSGGDIA 204

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L   +   ++ +     +L   H     VL  ++  K   + +  ++  L+ R RRI EA
Sbjct: 205 LEGQVEDGEE-AYAPIAYLADSHSEPTAVLASRQRDKLHSDGIASALDALDARSRRIIEA 263

Query: 246 RRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R L          TL  L+ EF VS ER+RQIEA A KK++ ++
Sbjct: 264 RWLKVEDDGSGGSTLHELADEFGVSAERIRQIEASAMKKMRGAL 307


>gi|307611543|emb|CBX01223.1| RNA polymerase sigma-32 factor [Legionella pneumophila 130b]
          Length = 284

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 110/275 (40%), Positives = 177/275 (64%), Gaps = 7/275 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             L  YIH + +IPML  +EE   A+R+   GD+ AA +LV +HLR VV++A GY GYGL
Sbjct: 15  GSLDSYIHRVNQIPMLTLEEEIAYAERFHSEGDIEAARQLVLAHLRYVVRVARGYLGYGL 74

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+S+++ EGN+GLM+AVK+FDP+ G RL ++++ WIKA + E++LR+W +VK+ TT  Q+
Sbjct: 75  PLSDLIQEGNVGLMKAVKRFDPKMGVRLVSFAVHWIKAEIHEFVLRNWRIVKVATTKAQR 134

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINS 192
           +LFFNLR++K  L   ++     E+V A+AK L VS  +V+ M  RL   D S +A    
Sbjct: 135 KLFFNLRQMKNRLGWFSN-----EEVDAVAKDLGVSREDVLLMEQRLNVMDSSYDAPDVD 189

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPRERRIFEARRLQEN 251
            + ++ +  +  +++ +    VL+E E+  ++ R  L  +M  L+ R + I + R L E 
Sbjct: 190 DNDDAYKAPERYLFNVNDDPAVLLENEDTGDQGREKLLFAMEQLDERSQDILQQRWLAEE 249

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +TL +L+ ++ VS ERVRQ+E  A KK+++ ++ 
Sbjct: 250 KLTLHDLAEKYGVSAERVRQLEKNAMKKIRQYMEA 284


>gi|308233952|ref|ZP_07664689.1| RNA polymerase, sigma 70 subunit, RpoD [Atopobium vaginae DSM
           15829]
 gi|328943964|ref|ZP_08241429.1| putative DNA-directed RNA polymerase sigma subunit RpoD [Atopobium
           vaginae DSM 15829]
 gi|327491933|gb|EGF23707.1| putative DNA-directed RNA polymerase sigma subunit RpoD [Atopobium
           vaginae DSM 15829]
          Length = 441

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 81/316 (25%), Positives = 136/316 (43%), Gaps = 42/316 (13%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD---------------- 46
           R + S ++     +  Y+ EI K+ +L   EE  LA + +   D                
Sbjct: 127 RIDSSAVMLTGDPVRMYLKEIGKVDLLNASEEVHLAMKIQAGTDASKKLEAAENGEIELT 186

Query: 47  --------------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                         L A   L +++LRL V IA  Y G G+   +++ EGN+GL++AV+K
Sbjct: 187 RAEQRRLMRIEQVGLDAKQALTSANLRLTVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEK 246

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +GF+ +TY+ WWI+ A+   I      ++I     +      L R++  L      
Sbjct: 247 FDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE--TINKLVRVQKELLQDLGR 304

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE    I +++ +S   V  +        SL   I   ++  S   D++    D   
Sbjct: 305 EPTPE---EIGEQMKMSADRVREIQKISQEPVSLETPI--GEEEDSSLGDFI---EDSTA 356

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVR 270
               +       R  L + +  L  RER++ + R   E+  P TLE +  EF V+RER+R
Sbjct: 357 VAPPDAASDSMLREQLNQVLDGLADRERKVIKFRFGLEDGHPRTLEEVGREFGVTRERIR 416

Query: 271 QIEARAFKKVQESIQK 286
           QIE++   K++   + 
Sbjct: 417 QIESKTLAKLRHPSRS 432


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

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 66/243 (27%), Positives = 112/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RGF+ +TY+ 
Sbjct: 617 RKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGFKFSTYAT 676

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A K+
Sbjct: 677 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGAEPDPAT---LAIKM 731

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R 
Sbjct: 732 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDNNTLAPADAALHASMRG 786

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 787 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 846

Query: 285 QKQ 287
           +  
Sbjct: 847 RSD 849


>gi|29832222|ref|NP_826856.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29609340|dbj|BAC73391.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 389

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 84/301 (27%), Positives = 136/301 (45%), Gaps = 38/301 (12%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKR----------YREHGDLS------------ 48
                  +Y+ EI +IP+L   EE  LA+R               DL             
Sbjct: 88  PSSDLFRQYLREIGRIPLLTAAEEVELARRVEAGLFAEEKLSSTPDLDSQLGLDLDKLVV 147

Query: 49  ----AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
               A  RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY
Sbjct: 148 MGRMAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTY 207

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + WWI+ AM   +      +++     +  L   + R++  +         PE+V A   
Sbjct: 208 ATWWIRQAMSRALADQARTIRVPVHVVE--LINRVVRVQRRMLQERGYEPTPEEVAAHLD 265

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
                 SEV+ +        SL+A +   +++     D +    DG     +E       
Sbjct: 266 LPGERVSEVLRL---AQEPVSLHAPV--GEEDDVALGDLI---EDGDATSPVESAAFLLL 317

Query: 225 RNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           R  L   +S L  RER++ + R       P TLE +   F V+RER+RQIE++   K+++
Sbjct: 318 REHLDAVLSTLGERERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRD 377

Query: 283 S 283
            
Sbjct: 378 H 378


>gi|157368473|ref|YP_001476462.1| RNA polymerase factor sigma-32 [Serratia proteamaculans 568]
 gi|157320237|gb|ABV39334.1| RNA polymerase, sigma 32 subunit, RpoH [Serratia proteamaculans
           568]
          Length = 285

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 105/290 (36%), Positives = 162/290 (55%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  YI      PML  +EE  LA+R    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLALVPQGSLEAYIRAANTYPMLTAEEERELAERLHYQGDLEAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VAHIARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVELVARELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNP 237
           A  +         D    Q    ++Y  D        + E     N  + L  +M  L+ 
Sbjct: 176 AAQDMTFDPTPDDDAREGQSMAPVLYLQDKSSDFAEGIEEDNWESNAADKLAYAMEGLDE 235

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L ++   TL+ L+ ++ VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQHIIRARWLDDDNKSTLQELADQYGVSAERVRQLEKNAMKKLKMAIEA 285


>gi|1710647|sp|P50510|RP32_SERMA RecName: Full=RNA polymerase sigma-32 factor
 gi|1143376|dbj|BAA09442.1| sigma-32 homolog [Serratia marcescens]
          Length = 285

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 103/290 (35%), Positives = 162/290 (55%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  YI      PML  +EE  LA+R    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLALVPQGSLEAYIRAANAYPMLTAEEERELAERLHYQGDLDAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VAHIARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVELVARELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNP 237
           A  +         +    Q    ++Y  D        + E     N  + L  ++  L+ 
Sbjct: 176 AAQDMTFDPTPDDEARDGQSMAPVLYLQDKSSDFAEGIEEDNWESNAADKLAYALEGLDE 235

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L ++   TL+ L+ ++ VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQHIIRARWLDDDNKSTLQELADQYGVSAERVRQLEKNAMKKLKMAIEA 285


>gi|326539488|gb|ADZ87703.1| RNA polymerase sigma factor, sigma-70 family protein [Brucella
           melitensis M5-90]
          Length = 293

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 117/274 (42%), Positives = 180/274 (65%), Gaps = 1/274 (0%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           I      P LE++EE  LA R++E  D  A HR+ ++H+RLV+ +A  +R + LP+S+++
Sbjct: 17  IRSAMSAPYLEREEERALAIRWKETKDQDALHRITSAHMRLVISMAGRFRKFKLPMSDLI 76

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EG +GL++   +FDP+R  R +TY+ WWI+A+MQ+YILR+WS+V+ GT++ QK LFFNL
Sbjct: 77  QEGYVGLLEEAARFDPDRDVRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKVLFFNL 136

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSS 198
           RRL+  L    DN  K E    I+ +L VS S+V  M+ RL+G D SL+A +N  +  +S
Sbjct: 137 RRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEETGAS 196

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           +  D+LV DH  Q+++     + + R   LTR++  LN RE  I   RRL ++ VTLE L
Sbjct: 197 RRMDFLVDDHPLQDEIAESSIDMERRNRWLTRALDTLNERELHIIRERRLDDDGVTLEAL 256

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
             +  +S+ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 257 GEKLGISKERVRQIESRAMEKLKIALLSQHELAA 290


>gi|296161515|ref|ZP_06844320.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. Ch1-1]
 gi|295888159|gb|EFG67972.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia sp. Ch1-1]
          Length = 311

 Score =  241 bits (615), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 121/284 (42%), Positives = 168/284 (59%), Gaps = 12/284 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S++      +  YI  + +IPML   EE   A  +RE  +L +A RLV SHLRLVV IA 
Sbjct: 30  SLLPGQLGNIDAYIQAVNRIPMLTPAEERQFATEFREQDNLESARRLVLSHLRLVVSIAR 89

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y GYGLP ++++ EGNIGLM+AVK+FDPE+  RL +Y+M WIKA + EYILR+W +VK+
Sbjct: 90  NYLGYGLPHADLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHWIKAEIHEYILRNWRMVKV 149

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDES 185
            TT  Q++LFFNLR  K  L A T     P+++  +AK+LNV   EV  M  RL  GD +
Sbjct: 150 ATTKAQRKLFFNLRSHKQGLGAFT-----PDEIEGLAKELNVKREEVSEMETRLSGGDIA 204

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L   +   ++ S     +L   H     VL  ++  K + + +  ++  L+ R RRI EA
Sbjct: 205 LEGQVEDGEE-SYAPIAYLADSHSEPTAVLASRQRDKLQSDGIASALDALDARSRRIIEA 263

Query: 246 RRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R L          TL  L+ EF VS ER+RQIEA A KK++ ++
Sbjct: 264 RWLKVEDDGSGGSTLHELADEFGVSAERIRQIEASAMKKMRGAL 307


>gi|238750715|ref|ZP_04612214.1| RNA polymerase sigma-32 factor [Yersinia rohdei ATCC 43380]
 gi|238711105|gb|EEQ03324.1| RNA polymerase sigma-32 factor [Yersinia rohdei ATCC 43380]
          Length = 285

 Score =  240 bits (614), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 101/290 (34%), Positives = 163/290 (56%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  YI      PML  +EE  LA+R    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLALVPQGSLEAYIRAANAYPMLTAEEERELAERLHYQGDLGAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VAHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +AK+L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVELVAKELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQ---EQVLIEKEERKNRRNMLTRSMSVLNP 237
           +  +         +    Q    ++Y  D        + E     +  + L+ ++  L+ 
Sbjct: 176 SAQDMTFDPSPDDEARDGQSMAPVLYLQDKTSDFADSIEEDNWDDHAADKLSYALEGLDE 235

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L ++   TL+ L+ ++ VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQHIIRARWLDDDNKSTLQELADQYGVSAERVRQLEKNAMKKLRMAIEA 285


>gi|313892356|ref|ZP_07825948.1| RNA polymerase sigma factor RpoD [Dialister microaerophilus UPII
           345-E]
 gi|313119215|gb|EFR42415.1| RNA polymerase sigma factor RpoD [Dialister microaerophilus UPII
           345-E]
          Length = 393

 Score =  240 bits (614), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 74/285 (25%), Positives = 132/285 (46%), Gaps = 23/285 (8%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREH-----------GDLSAAHRLVTSHLR 59
           N    +  Y+ E    P+L  +EE  LAK+  +                A   +  ++LR
Sbjct: 111 NVSDPVRLYLRECGATPLLSAEEEMTLAKQIEKGKMLDATEEDKLRAEDAKKEMANANLR 170

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           LVV IA  Y G G+P  +++ EGNIGL++AV KFD ++G++ +TY+ WWI+ A+   I  
Sbjct: 171 LVVSIAKKYPGRGMPFLDLIQEGNIGLLKAVDKFDYKKGYKFSTYATWWIRQAITRSIAD 230

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
               +++     +      + ++    +       +      +AK++ +S  ++      
Sbjct: 231 QARTIRVPVHMVE-----TINKMNRIGRKFLQEFGREASNEELAKEMGISVEKIREAKKA 285

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
                SL   I   +K  S   D++    D +     E+     RR  + + ++ L  RE
Sbjct: 286 AQDPISLETPI--GEKEDSHLGDFI---EDQKTSSPEEEAAATMRREQIYKLLNELTERE 340

Query: 240 RRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           + +   R   ++  P TLE +   F V+RER+RQIE +A KK+++
Sbjct: 341 KGVLALRFGMDDGTPRTLEEVGKYFGVTRERIRQIEGKALKKLRK 385


>gi|311064624|ref|YP_003971349.1| RNA polymerase principal sigma factor HrdB [Bifidobacterium bifidum
           PRL2010]
 gi|310866943|gb|ADP36312.1| RNA polymerase principal sigma factor HrdB [Bifidobacterium bifidum
           PRL2010]
          Length = 506

 Score =  240 bits (614), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 65/303 (21%), Positives = 138/303 (45%), Gaps = 39/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR---------------------------YREHGD 46
             +  Y+ +I ++ +L  ++E  L++R                           +  +  
Sbjct: 206 DPVKDYLKQIGRVSLLNAEQEVDLSERIEAGLYAQHLLDTESDGMDFKRKRELKWAANDG 265

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ 
Sbjct: 266 KKAKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYAT 325

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      +++     +  +   L R++  +         P+    +A++L
Sbjct: 326 WWIRQAITRAMADQARTIRVPVHMVE--VINKLSRVQRQMLQDLGREPTPD---ELAREL 380

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   +V  +        SL+  +   +   S++ D +    D       +       + 
Sbjct: 381 DMPVEKVQEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDTDAIAPSDAVAFSLLQE 435

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++   K++   
Sbjct: 436 QFKQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPS 495

Query: 285 QKQ 287
           + Q
Sbjct: 496 RSQ 498


>gi|224283384|ref|ZP_03646706.1| RNA polymerase sigma factor [Bifidobacterium bifidum NCIMB 41171]
          Length = 506

 Score =  240 bits (614), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 65/303 (21%), Positives = 138/303 (45%), Gaps = 39/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR---------------------------YREHGD 46
             +  Y+ +I ++ +L  ++E  L++R                           +  +  
Sbjct: 206 DPVKDYLKQIGRVSLLNAEQEVDLSERIEAGLYAQHLLDTESDGMDFKRKRELKWAANDG 265

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ 
Sbjct: 266 KKAKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYAT 325

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      +++     +  +   L R++  +         P+    +A++L
Sbjct: 326 WWIRQAITRAMADQARTIRVPVHMVE--VINKLSRVQRQMLQDLGREPTPD---ELAREL 380

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   +V  +        SL+  +   +   S++ D +    D       +       + 
Sbjct: 381 DMPVEKVQEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDTDAIAPSDAVAFSLLQE 435

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++   K++   
Sbjct: 436 QFKQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPS 495

Query: 285 QKQ 287
           + Q
Sbjct: 496 RSQ 498


>gi|146313497|ref|YP_001178571.1| RNA polymerase factor sigma-32 [Enterobacter sp. 638]
 gi|145320373|gb|ABP62520.1| RNA polymerase, sigma 32 subunit, RpoH [Enterobacter sp. 638]
          Length = 285

 Score =  240 bits (614), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 109/290 (37%), Positives = 163/290 (56%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +     L  YI      PML  +EE  LA++    GDL AA  L+ SHLR 
Sbjct: 1   MTKEMQTLALAPVGNLESYIRAANTWPMLTAEEEKELAEKLHYQGDLEAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          E+V  +A++L VS  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKAKQRLGWFNQ-----EEVEMVARELGVSSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQ---EQVLIEKEERKNRRNMLTRSMSVLNP 237
           A  +    + +  D   SQ    ++Y  D        + E        N LT +M  L+ 
Sbjct: 176 AAQDMTFDMSSDDDAQDSQPMAPVLYLQDKTSNFADGIEEDNWEDQAANKLTHAMEGLDE 235

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L E+   TL+ L+  + VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQAIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 285


>gi|119503515|ref|ZP_01625598.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2080]
 gi|119460577|gb|EAW41669.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2080]
          Length = 282

 Score =  240 bits (614), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 107/281 (38%), Positives = 159/281 (56%), Gaps = 9/281 (3%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           MS+       L  Y+  +  IP+L    E  LA++    G + +A  LV +HLR VV IA
Sbjct: 7   MSMTPGA--NLPAYVQAVSGIPILSVDREQALAEKLYYEGCVDSARELVLAHLRFVVHIA 64

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGL   +++ EGN+GLM+AVK+FDP +G RL ++++ WIKA M E+ILR+W +VK
Sbjct: 65  RSYSGYGLAEGDLIQEGNVGLMKAVKRFDPNKGVRLVSFAVHWIKAEMHEFILRNWRIVK 124

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDE 184
           + TT  Q++LFFNLR  K  L  +       E+  AIA  L V E+EV  M  RL + D 
Sbjct: 125 VATTKAQRKLFFNLRSAKKSLGWLN-----AEETQAIAADLGVDEAEVQRMEGRLSSRDI 179

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLNPRERRIF 243
           + +   ++ D+++ Q     + D        IE E+   +  N L  ++S L+ R R I 
Sbjct: 180 AFDLPTDADDEDAWQSPQAYLDDISTDPARCIEAEDSARDGENRLRAALSDLDERSRNIV 239

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             R L E   TL  L++E+ VS ER+RQ+E  A KK++ ++
Sbjct: 240 TQRWLAEQKATLHELAAEYGVSAERIRQLEVNAMKKLKNTL 280


>gi|311696378|gb|ADP99251.1| RNA polymerase, sigma 32 subunit, RpoH [marine bacterium HP15]
          Length = 286

 Score =  240 bits (614), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 103/269 (38%), Positives = 154/269 (57%), Gaps = 7/269 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  YI    +IP+L   EE  LA+R    GD+ AA +LV SHLR V+ IA  Y GYGL 
Sbjct: 16  NLESYIQAASRIPVLTVDEERELAERLHYEGDVEAARQLVMSHLRFVIHIARSYSGYGLA 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++
Sbjct: 76  QADLIQEGNVGLMKAVKRFNPEYGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSS 193
           LFFNLR  K  L  ++ + L      A+A+ L V    V  M  RLA  D + +   +  
Sbjct: 136 LFFNLRSQKKKLAWLSHDELN-----AVAEDLGVEPRVVREMEGRLASQDTAFDGPQDDD 190

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN-MLTRSMSVLNPRERRIFEARRLQENP 252
           D N+ Q   + + D        +E  +  +  N  L +++  L+ R + I   R L E+ 
Sbjct: 191 DDNAYQAPAYYLEDARSNPATQLENADWSDDSNGRLMQALGQLDERSQDILRERWLSESK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            TL  L+  + VS ER+RQ+E  A KK++
Sbjct: 251 STLHELADRYGVSAERIRQLEKNAMKKIR 279


>gi|238784413|ref|ZP_04628423.1| RNA polymerase sigma-32 factor [Yersinia bercovieri ATCC 43970]
 gi|238714705|gb|EEQ06707.1| RNA polymerase sigma-32 factor [Yersinia bercovieri ATCC 43970]
          Length = 285

 Score =  240 bits (614), Expect = 1e-61,   Method: Composition-based stats.
 Identities = 101/290 (34%), Positives = 162/290 (55%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  YI      PML  +EE  LA+R    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLALVPQGSLEAYIRAANAYPMLTAEEERELAERLHYQGDLGAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VAHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +AK+L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVELVAKELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNP 237
           +  +         +    Q    ++Y  D        + E     +  + L  ++  L+ 
Sbjct: 176 SAQDMTFDPSPDDEARDGQSMAPVLYLQDKTSDFADGIEEDNWDNHAADKLAYALEGLDE 235

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L ++   TL+ L+ ++ VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQHIIRARWLDDDNKSTLQELADQYGVSAERVRQLEKNAMKKLRMAIEA 285


>gi|153004710|ref|YP_001379035.1| RNA polymerase sigma factor RpoH [Anaeromyxobacter sp. Fw109-5]
 gi|152028283|gb|ABS26051.1| RNA polymerase sigma factor RpoH [Anaeromyxobacter sp. Fw109-5]
          Length = 307

 Score =  240 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 116/282 (41%), Positives = 174/282 (61%), Gaps = 6/282 (2%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           I      L  Y+ EI + P+L   EE  LA+ +R+ GD  AAHRLVT++LR VVK++  Y
Sbjct: 6   IPTTTSSLELYLSEINRFPLLTVDEEQRLARLFRDEGDTRAAHRLVTANLRFVVKVSYEY 65

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           R YG  +++++ EGNIGLM+AV+KFDP++G RL +Y++WWI+A +Q YIL+SWSLVK+GT
Sbjct: 66  RSYGFKMADLIQEGNIGLMKAVQKFDPDKGIRLISYAVWWIRAYIQNYILKSWSLVKLGT 125

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVV---AIAKKLNVSESEVISMNCRLAG-DE 184
           T  Q++LFF+L R K  L  ++  + +         IAKKL V  +EV  M  R+ G D 
Sbjct: 126 TQAQRKLFFSLARTKRELDKMSVEHGRDSDAQDKGKIAKKLRVKPAEVEEMEQRMDGRDL 185

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL+A +   D       D++      Q+  L + EE++     +T +++ L+ RER I E
Sbjct: 186 SLDAPM--GDDGGYSHIDFVAAKSAAQDDELSDAEEQQIVSAKVTAALARLDQRERYIIE 243

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R + + P+TL+ L   F  SRER RQ+E RA +K+++ +  
Sbjct: 244 QRVMSDRPLTLKELGEHFGFSRERARQLEIRAKEKLKQELHA 285


>gi|91781700|ref|YP_556906.1| RNA polymerase factor sigma-32 [Burkholderia xenovorans LB400]
 gi|91685654|gb|ABE28854.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia xenovorans
           LB400]
          Length = 307

 Score =  240 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 121/284 (42%), Positives = 168/284 (59%), Gaps = 12/284 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S++      +  YI  + +IPML   EE   A  +RE  +L +A RLV SHLRLVV IA 
Sbjct: 26  SLLPGQLGNIDAYIQAVNRIPMLTPAEERQFATEFREQDNLESARRLVLSHLRLVVSIAR 85

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y GYGLP ++++ EGNIGLM+AVK+FDPE+  RL +Y+M WIKA + EYILR+W +VK+
Sbjct: 86  NYLGYGLPHADLIQEGNIGLMKAVKRFDPEQNVRLVSYAMHWIKAEIHEYILRNWRMVKV 145

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDES 185
            TT  Q++LFFNLR  K  L A T     P+++  +AK+LNV   EV  M  RL  GD +
Sbjct: 146 ATTKAQRKLFFNLRSHKQGLGAFT-----PDEIEGLAKELNVKREEVSEMETRLSGGDIA 200

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L   +   ++ S     +L   H     VL  ++  K + + +  ++  L+ R RRI EA
Sbjct: 201 LEGQVEDGEE-SYAPIAYLADSHSEPTAVLASRQRDKLQSDGIASALDALDARSRRIIEA 259

Query: 246 RRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R L          TL  L+ EF VS ER+RQIEA A KK++ ++
Sbjct: 260 RWLKVEDDGSGGSTLHELADEFGVSAERIRQIEASAMKKMRGAL 303


>gi|328542017|ref|YP_004302126.1| RNA polymerase sigma factor [polymorphum gilvum SL003B-26A1]
 gi|326411767|gb|ADZ68830.1| RNA polymerase sigma factor [Polymorphum gilvum SL003B-26A1]
          Length = 289

 Score =  240 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 112/268 (41%), Positives = 178/268 (66%), Gaps = 1/268 (0%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           +      P L ++EE  LA R+R+  D++A  RL  +H+RLV+ +A  +R +GLP+++++
Sbjct: 12  VKAAMNAPYLTREEELELATRWRQDKDVAALERLSLAHMRLVIAVASRFRNFGLPMNDLI 71

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EG++GL++A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFFNL
Sbjct: 72  QEGHVGLLEAAARFEPEREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSTQKALFFNL 131

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSS 198
           RRL+  L +   +  + E    IA+ + V  ++V  MN RL+G D SLNA I  SD +S+
Sbjct: 132 RRLRAKLSSNRVDLPETELHRQIAEAIGVKTADVDLMNARLSGPDTSLNAPIIDSDGSSA 191

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
             QD+L+ D    ++ + E  + + +R  L  +M+VL  RER+I   RRL E   TLE L
Sbjct: 192 DRQDFLISDAPLPDETVSENIDSERQRRWLRSAMNVLTERERKIVSERRLTEEGATLEAL 251

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQK 286
            ++  +S+ERVRQIE RA +K++E++ K
Sbjct: 252 GAKMGISKERVRQIENRALEKLREALLK 279


>gi|227504950|ref|ZP_03934999.1| RNA polymerase major sigma subunit [Corynebacterium striatum ATCC
           6940]
 gi|227198459|gb|EEI78507.1| RNA polymerase major sigma subunit [Corynebacterium striatum ATCC
           6940]
          Length = 465

 Score =  240 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 78/325 (24%), Positives = 151/325 (46%), Gaps = 49/325 (15%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY----------------REHG 45
            RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR                 R  G
Sbjct: 146 ARKDAQLTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYAQYRMDEMEKARAEG 204

Query: 46  DL--------------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           D                      A + L+ ++LRLVV +A  Y G G+   +++ EGN+G
Sbjct: 205 DKAAKLSPMEKRDLRSIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLG 264

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  
Sbjct: 265 LIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRE 322

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           L         P   + +AK+++++E +V+ +        SL+  I   D+  SQ  D++ 
Sbjct: 323 LLQDLGREPTP---IELAKEMDITEEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI- 376

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFE 263
              D +  + ++       ++ L   ++ L+ RE  +   R    +  P TL+ +   + 
Sbjct: 377 --EDSEAVIAVDAVSFTLLQDQLQDVLTTLSEREAGVVRLRFGLTDGMPRTLDEIGQVYG 434

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           V+RER+RQIE++   K++   + QV
Sbjct: 435 VTRERIRQIESKTMSKLRHPSRSQV 459


>gi|238763647|ref|ZP_04624607.1| RNA polymerase sigma-32 factor [Yersinia kristensenii ATCC 33638]
 gi|238789414|ref|ZP_04633200.1| RNA polymerase sigma-32 factor [Yersinia frederiksenii ATCC 33641]
 gi|238793542|ref|ZP_04637166.1| RNA polymerase sigma-32 factor [Yersinia intermedia ATCC 29909]
 gi|238698125|gb|EEP90882.1| RNA polymerase sigma-32 factor [Yersinia kristensenii ATCC 33638]
 gi|238722557|gb|EEQ14211.1| RNA polymerase sigma-32 factor [Yersinia frederiksenii ATCC 33641]
 gi|238727132|gb|EEQ18662.1| RNA polymerase sigma-32 factor [Yersinia intermedia ATCC 29909]
          Length = 285

 Score =  240 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 101/290 (34%), Positives = 163/290 (56%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  YI      PML  +EE  LA+R    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLALVPQGSLEAYIRAANAYPMLTAEEERELAERLHYQGDLGAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VAHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +AK+L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVELVAKELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNP 237
           +  +         +    Q    ++Y  D        + E     +  + L+ ++  L+ 
Sbjct: 176 SAQDMTFDPSPDDEARDGQSMAPVLYLQDKTSDFADGIEEDNWDNHAADKLSYALEGLDE 235

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L ++   TL+ L+ ++ VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQHIIRARWLDDDNKSTLQELADQYGVSAERVRQLEKNAMKKLRMAIEA 285


>gi|238798006|ref|ZP_04641495.1| RNA polymerase sigma-32 factor [Yersinia mollaretii ATCC 43969]
 gi|238718109|gb|EEQ09936.1| RNA polymerase sigma-32 factor [Yersinia mollaretii ATCC 43969]
          Length = 285

 Score =  240 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 101/290 (34%), Positives = 162/290 (55%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  YI      PML  +EE  LA+R    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLALVPQGSLEAYIRAANAYPMLTAEEERELAERLHYQGDLGAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VAHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +AK+L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVELVAKELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQ---EQVLIEKEERKNRRNMLTRSMSVLNP 237
           +  +         +    Q    ++Y  D        + E     +  + L  ++  L+ 
Sbjct: 176 SAQDMTFDPSPDDEARDGQSMAPVLYLQDKTSDFADSIEEDNWDGHAADKLAYALEGLDE 235

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L ++   TL+ L+ ++ VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQHIIRARWLDDDNKSTLQELADQYGVSAERVRQLEKNAMKKLRMAIEA 285


>gi|293393954|ref|ZP_06638260.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Serratia
           odorifera DSM 4582]
 gi|291423514|gb|EFE96737.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Serratia
           odorifera DSM 4582]
          Length = 285

 Score =  240 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 103/290 (35%), Positives = 162/290 (55%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  YI      PML  +EE  LA+R    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLALVPQGSLEAYIRAANAYPMLTAEEERELAERLHYQGDLEAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VAHIARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVELVARELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNP 237
           A  +         +    Q    ++Y  D        + E     N  + L  ++  L+ 
Sbjct: 176 AAQDMTFDPTPDDEARDGQSMAPVLYLQDKTSDFAEGIEEDNWESNAADKLAYALEGLDE 235

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L ++   TL+ L+ ++ VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQHIIRARWLDDDNKSTLQELADQYGVSAERVRQLEKNAMKKLKMAIEA 285


>gi|238759635|ref|ZP_04620796.1| RNA polymerase sigma-32 factor [Yersinia aldovae ATCC 35236]
 gi|238702178|gb|EEP94734.1| RNA polymerase sigma-32 factor [Yersinia aldovae ATCC 35236]
          Length = 285

 Score =  240 bits (614), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 101/290 (34%), Positives = 162/290 (55%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  YI      PML  +EE  LA+R    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLALVPQGSLEAYIRAANAYPMLTAEEERELAERLHYQGDLGAAKQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VAHVARNYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +AK+L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVELVAKELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNP 237
           +  +         +         ++Y  D        + E     +  + L+ +M  L+ 
Sbjct: 176 SAQDMTFDPSPDDEARDGHSMAPVLYLQDKSSDFADGIEEDNWDSHAADKLSYAMEGLDE 235

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L ++   TL+ L+ ++ VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQHIIRARWLDDDNKSTLQELADQYGVSAERVRQLEKNAMKKLRMAIEA 285


>gi|265995632|ref|ZP_06108189.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 3 str.
           Ether]
 gi|262766916|gb|EEZ12534.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 3 str.
           Ether]
          Length = 293

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 118/293 (40%), Positives = 184/293 (62%), Gaps = 4/293 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  ++          +   I      P LE++EE  LA R++E  D  A HR+ ++H+RL
Sbjct: 1   MAVRSFPAAAASSQSM---IRSAMSAPYLEREEERALAIRWKETKDQDALHRITSAHMRL 57

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A  +R + LP+S+++ EG +GL++   +FDP+R  R +TY+ WWI+A+MQ+YILR+
Sbjct: 58  VISMAGRFRKFKLPMSDLIQEGYVGLLEEAARFDPDRDVRFSTYASWWIRASMQDYILRN 117

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WS+V+ GT++ QK LFFNLRRL+  L    DN  K E    I+ +L VS S+V  M+ RL
Sbjct: 118 WSIVRGGTSSAQKVLFFNLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRL 177

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D SL+A +N  +  +S+  D+LV DH  Q+++     + + R   LTR++  LN RE
Sbjct: 178 SGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTRALDTLNERE 237

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
             I   RRL ++ VTLE L  +  +S+ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 238 LHIIRERRLDDDGVTLEALGEKLGISKERVRQIESRAMEKLKIALLSQHELAA 290


>gi|114798150|ref|YP_762122.1| putative alternative sigma factor RpoH [Hyphomonas neptunium ATCC
           15444]
 gi|114738324|gb|ABI76449.1| putative alternative sigma factor RpoH [Hyphomonas neptunium ATCC
           15444]
          Length = 295

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 109/270 (40%), Positives = 171/270 (63%), Gaps = 3/270 (1%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +++    K P+L+   E  LA+R+RE  D +A H L T+++RLV+ +A  +R YGLP+++
Sbjct: 14  QFVKTAMKAPLLDPAHEASLARRWREAEDEAALHELTTAYMRLVISMAAKFRHYGLPMAD 73

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +VSEGN+GLMQA  +F+PER  R +TY+ WWI++++Q+Y+LR+WS+V+ GTT+ QK LFF
Sbjct: 74  LVSEGNVGLMQAAARFEPEREVRFSTYASWWIRSSIQDYVLRNWSIVRTGTTSAQKSLFF 133

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKN 196
           NLRRL+  +  + D  +  E    ++  L V   +V  M+ RL+G D SLNA +      
Sbjct: 134 NLRRLRARISDLGDGTMTRENKQWVSTHLGVPLRDVEIMSARLSGSDRSLNAPLTM--DG 191

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
            ++WQD +  +    E+ ++   +   R   ++ +M  L PRE  I   RRL E P TLE
Sbjct: 192 DAEWQDMIADEGAPPEEAVMRSHDTARRHEWISEAMEALTPRETYIITRRRLSEEPQTLE 251

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L  E  VS+ERVRQIE +A  K++ ++++
Sbjct: 252 ALGHELGVSKERVRQIEHQALSKLKRALEQ 281


>gi|88813090|ref|ZP_01128332.1| RpoH [Nitrococcus mobilis Nb-231]
 gi|88789723|gb|EAR20848.1| RpoH [Nitrococcus mobilis Nb-231]
          Length = 292

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 109/285 (38%), Positives = 162/285 (56%), Gaps = 8/285 (2%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           R ++S +         YI  + ++P L  +EEY LA+RYR+H DL AA  LV SHLR VV
Sbjct: 9   RSDLSTLPLKLGSEEHYIQAVNRLPTLSAEEEYQLARRYRDHNDLKAARGLVLSHLRFVV 68

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA GY+GYGLP+++++ EGNIGLM+AVK+FDP  G RL ++++ WI+A + E+ILR+W 
Sbjct: 69  HIARGYKGYGLPLTDLIQEGNIGLMKAVKRFDPAVGVRLVSFAVHWIRAEIHEFILRNWR 128

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR  K  L  +        +V A+A  L V    V  M  RL+G
Sbjct: 129 IVKVATTKAQRKLFFNLRGAKKRLGWLN-----RAEVDAVANDLGVKPETVQEMELRLSG 183

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK---NRRNMLTRSMSVLNPRE 239
            E        + ++    +    Y  D +     E E      ++   L  +++ L+ R 
Sbjct: 184 QEVSFDPGPDAAEDDDIVRAPAAYLRDQRPNPAEEIESHDWQTHQSESLATALAHLDERS 243

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R I   R L E   TL+ L+  + VS ER+RQ+E  A KK++ ++
Sbjct: 244 RAIVHERWLNEPKATLQELAERYAVSAERIRQLEKNALKKLRLAM 288


>gi|293602894|ref|ZP_06685333.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Achromobacter
           piechaudii ATCC 43553]
 gi|292818688|gb|EFF77730.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Achromobacter
           piechaudii ATCC 43553]
          Length = 294

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 119/286 (41%), Positives = 177/286 (61%), Gaps = 9/286 (3%)

Query: 2   NRKNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           N   ++I   G +G +  YI  + ++P+L  + E  L +R R+  DL AA  L+ SHLRL
Sbjct: 13  NALALAIANPGALGTIDAYISAVNRLPVLSAERETELGRRLRDQEDLGAARELILSHLRL 72

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y GYGLP ++++ EGN+GLM+AVK+FDPERG RL ++++ WIKA + EYI+R+
Sbjct: 73  VVSVARQYLGYGLPHADLIQEGNVGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEYIIRN 132

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W LVK+ TT  Q++LFFNLR ++          L P+QV  IA++LNV   +V  M  RL
Sbjct: 133 WRLVKVATTKAQRKLFFNLRSMR-----PDGQTLDPDQVDHIARELNVRREDVSEMEVRL 187

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRE 239
           +G E ++      D +S     +L  D   +   ++E+  R   ++  LT ++  L+ R 
Sbjct: 188 SGRE-MSLENQDDDDDSFAPIAYLSDDGRQEPTRVLERAARDELQSTGLTTALEALDARS 246

Query: 240 RRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           RRI EAR LQ++   TL  L+ EF VS ER+RQIEA A KK++ ++
Sbjct: 247 RRIVEARWLQDDGGATLHELAQEFGVSAERIRQIEAAALKKMRGNL 292


>gi|239979292|ref|ZP_04701816.1| RNA polymerase sigma factor [Streptomyces albus J1074]
          Length = 357

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 79/296 (26%), Positives = 136/296 (45%), Gaps = 39/296 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHG--------------------------DLSA 49
             +Y+ EI +IP+L   +E  LA+R  E G                             A
Sbjct: 62  FRQYLREIGRIPLLSAADEVELARRV-EAGVFAAAKLAGGCADAGLARDLRRLVVLGERA 120

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RGF+ +TY+ WWI
Sbjct: 121 KGRLIEANLRLVVSVAKRYTGRGLTMLDLVQEGNLGLIRAVEKFDYTRGFKFSTYATWWI 180

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + AM   +      +++     +      + R+    +A+     +      + ++L +S
Sbjct: 181 RQAMSRALADQARTIRVPVHVVEL-----INRVVRTQRALLQEAGREPAAEEVGERLGLS 235

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             +V  +        SL+A +    ++     D +    D       E       R  L 
Sbjct: 236 AEKVEEVLRLAHEPISLHAPV--GGEDDVFLGDLI---EDADAASPAESAALLLLRQHLD 290

Query: 230 RSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             ++ L  RER++ + R   ++  P TLE +   F V+RERVRQIE++  ++++E 
Sbjct: 291 AVLATLGDRERQVVQLRYGFDDGRPRTLEEIGRLFGVTRERVRQIESKTLRRLREH 346


>gi|309378784|emb|CBX22610.1| unnamed protein product [Neisseria lactamica Y92-1009]
          Length = 287

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 115/289 (39%), Positives = 183/289 (63%), Gaps = 7/289 (2%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N   +  I +G   L +YI  +  IPML ++EE  LA+R R  GDL+AA +L+ SHLR+V
Sbjct: 3   NTFALPAIQSGNGSLEQYIRTVNSIPMLSQEEETRLAER-RIKGDLNAAKQLILSHLRVV 61

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+IL++W
Sbjct: 62  VSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILKNW 121

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            LV++ TT  Q++LFFNLR ++ +L A++     P++  +IA  L V  SEV+ M  R+ 
Sbjct: 122 RLVRVATTKPQRKLFFNLRSMRKNLNALS-----PKEAQSIADDLGVKLSEVLEMEQRMT 176

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           G +      N+ D ++    DWL        + L ++     +   L  +++ L+ R RR
Sbjct: 177 GRDIAIMADNNDDDDNFAPIDWLADHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRR 236

Query: 242 IFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           I E+R LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 237 IVESRWLQDDGGLTLHQLAAEYGVSAERIRQIEAKAMQKLRGFLTEEAE 285


>gi|33151352|ref|NP_872705.1| RNA polymerase factor sigma-32 [Haemophilus ducreyi 35000HP]
 gi|33147572|gb|AAP95094.1| RNA polymerase sigma-32 factor [Haemophilus ducreyi 35000HP]
          Length = 319

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 99/273 (36%), Positives = 160/273 (58%), Gaps = 6/273 (2%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  L  YI    + P+L  ++E  LA+RY    D+ AA +L+ SH+R V+ IA GY GYG
Sbjct: 48  QGNLDSYIRMANQYPILTAEQEKTLAERYYYDEDVDAAKQLILSHMRFVIHIARGYMGYG 107

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP+++++ EGNIGLM+AVK+FDP  G RL ++++ W+KA + EY+L++W +VK+ TT  Q
Sbjct: 108 LPLADLIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWVKAEIHEYVLKNWRIVKVATTKAQ 167

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALIN 191
           ++LFFNLR+ K  L    +     +++  +A+ L VS  EV  M  R+ G D   +   N
Sbjct: 168 RKLFFNLRKNKHRLAWFNE-----DEIQQVAQDLGVSTEEVREMESRMTGQDVGFDISAN 222

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             +        +L  +       L E++        L  +++ L+ R + I + R L EN
Sbjct: 223 EDESEVYVPSMYLEDNSSNFADELEEEQHTGEATAKLAYALATLDERSQDIIKTRWLDEN 282

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL  L++++ +S ERVRQ+E  A KK++++I
Sbjct: 283 KATLHELAAKYSISAERVRQLENAALKKIKDTI 315


>gi|313140538|ref|ZP_07802731.1| RNA polymerase principal sigma factor [Bifidobacterium bifidum
           NCIMB 41171]
 gi|313133048|gb|EFR50665.1| RNA polymerase principal sigma factor [Bifidobacterium bifidum
           NCIMB 41171]
          Length = 500

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 65/303 (21%), Positives = 138/303 (45%), Gaps = 39/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR---------------------------YREHGD 46
             +  Y+ +I ++ +L  ++E  L++R                           +  +  
Sbjct: 200 DPVKDYLKQIGRVSLLNAEQEVDLSERIEAGLYAQHLLDTESDGMDFKRKRELKWAANDG 259

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ 
Sbjct: 260 KKAKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYAT 319

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      +++     +  +   L R++  +         P+    +A++L
Sbjct: 320 WWIRQAITRAMADQARTIRVPVHMVE--VINKLSRVQRQMLQDLGREPTPD---ELAREL 374

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   +V  +        SL+  +   +   S++ D +    D       +       + 
Sbjct: 375 DMPVEKVQEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDTDAIAPSDAVAFSLLQE 429

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++   K++   
Sbjct: 430 QFKQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPS 489

Query: 285 QKQ 287
           + Q
Sbjct: 490 RSQ 492


>gi|187929499|ref|YP_001899986.1| RNA polymerase sigma factor RpoD [Ralstonia pickettii 12J]
 gi|187726389|gb|ACD27554.1| RNA polymerase, sigma 70 subunit, RpoD [Ralstonia pickettii 12J]
          Length = 829

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 68/247 (27%), Positives = 115/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 584 ERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 643

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T N   P     +
Sbjct: 644 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGNEPDPAT---L 698

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+ + E ++  +        S+   I   D + S   D++    D       E     
Sbjct: 699 AEKMEMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTLAPAEAALHG 753

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 754 SMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKL 813

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 814 RHPSRSD 820


>gi|296451502|ref|ZP_06893237.1| RNA polymerase sigma factor rpoD [Clostridium difficile NAP08]
 gi|296880149|ref|ZP_06904116.1| RNA polymerase sigma factor rpoD [Clostridium difficile NAP07]
 gi|296259567|gb|EFH06427.1| RNA polymerase sigma factor rpoD [Clostridium difficile NAP08]
 gi|296428874|gb|EFH14754.1| RNA polymerase sigma factor rpoD [Clostridium difficile NAP07]
          Length = 301

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 74/277 (26%), Positives = 143/277 (51%), Gaps = 11/277 (3%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           N    +  Y+ EI +  ML   EE  LAK       + A  + + S+ RLVV IA  Y+ 
Sbjct: 26  NVSNAMKMYLKEIEEYKMLSAGEEVELAKEIINSSSV-AKEKFINSNYRLVVSIAKRYKR 84

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
             + + +++  GNIGL++AV+K+D ++G++ +TY+ WWIK ++  YI    + ++I    
Sbjct: 85  DSIDMLDLIQAGNIGLIKAVEKYDYKKGYKFSTYATWWIKQSITRYIDDCENTIRIPIHL 144

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
           +Q+     +  +K   Q + +  L+   +  IA    +   +V+ +  R     SL+  +
Sbjct: 145 HQR-----INFVKKKKQELLNVLLREPTIDEIADACGLEVDKVLELLRRDKNVVSLDTPL 199

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-- 248
              +   S   +++  D D +  V++ + E+ N +  +   ++ L  +E+++   R    
Sbjct: 200 K--EDEDSSLVEFIPSDADFK-DVVMHEVEQHNLKEKIEELLTGLGEQEQQVLRMRFGID 256

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            ++P TLE +   F V+RER+RQIEA+A +K++   +
Sbjct: 257 DDDPKTLEQIGRVFGVTRERIRQIEAKAIRKLRHPSK 293


>gi|227833276|ref|YP_002834983.1| RNA polymerase sigma factor A [Corynebacterium aurimucosum ATCC
           700975]
 gi|262184260|ref|ZP_06043681.1| RNA polymerase sigma factor [Corynebacterium aurimucosum ATCC
           700975]
 gi|227454292|gb|ACP33045.1| RNA polymerase sigma factor A [Corynebacterium aurimucosum ATCC
           700975]
          Length = 485

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 78/325 (24%), Positives = 151/325 (46%), Gaps = 49/325 (15%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY----------------REHG 45
            RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR                 R  G
Sbjct: 166 ARKDAELTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYAQYRMDEMEKARAEG 224

Query: 46  DL--------------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           D                      A + L+ ++LRLVV +A  Y G G+   +++ EGN+G
Sbjct: 225 DKAAKLSPMEKRDMRAIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLG 284

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  
Sbjct: 285 LIRAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRE 342

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           L         P   + +AK+++++E +V+ +        SL+  I   D+  SQ  D++ 
Sbjct: 343 LLQDLGREPTP---LELAKEMDITEEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI- 396

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFE 263
              D +  + ++       ++ L   ++ L+ RE  +   R    +  P TL+ +   + 
Sbjct: 397 --EDSEAVIAVDAVSFTLLQDQLQDVLTTLSEREAGVVRLRFGLTDGMPRTLDEIGQVYG 454

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           V+RER+RQIE++   K++   + QV
Sbjct: 455 VTRERIRQIESKTMSKLRHPSRSQV 479


>gi|300933014|ref|ZP_07148270.1| RNA polymerase sigma factor [Corynebacterium resistens DSM 45100]
          Length = 571

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 77/319 (24%), Positives = 151/319 (47%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------REHGDL- 47
            RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR              +E G+  
Sbjct: 258 ARKDAELTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYAAYRLQEIKESGEKL 316

Query: 48  ----------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 317 SPMHRRDLREIERDGRRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 376

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 377 KFDYVKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 434

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +A++++++  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 435 REPSPE---ELAREMDITVDKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 486

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERV 269
             V ++       ++ L   +  L+ RE  + + R    +  P TL+ +   + V+RER+
Sbjct: 487 AVVAVDAVSFTLLQDQLQDVLHTLSDREAGVVKLRFGLTDGMPRTLDEIGQVYGVTRERI 546

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 547 RQIESKTMSKLRHPSRSQV 565


>gi|302335781|ref|YP_003800988.1| RNA polymerase, sigma 70 subunit, RpoD [Olsenella uli DSM 7084]
 gi|301319621|gb|ADK68108.1| RNA polymerase, sigma 70 subunit, RpoD [Olsenella uli DSM 7084]
          Length = 453

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 81/317 (25%), Positives = 139/317 (43%), Gaps = 42/317 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------------------- 42
           ++ + S ++     +  Y+ EI K+ +L   EE  LA +                     
Sbjct: 138 HKLDSSAVMLTGDPVRMYLKEIGKVDLLTASEEVHLAMKIEAGTEATERLEAADRGEIEL 197

Query: 43  -----------EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                      E   L A   L++++LRL V IA  Y G G+   +++ EGN+GL++AV+
Sbjct: 198 TRAEQRRLMRIEQVGLEAKQALISANLRLTVSIAKRYVGRGMLFLDLIQEGNLGLIRAVE 257

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +GF+ +TY+ WWI+ A+   I      ++I     +      L R++  L     
Sbjct: 258 KFDYTKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE--TINKLVRVQRQLLQDLG 315

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
            +  PE++ A   ++ +S   V  +        SL   I   ++  S   D++    D  
Sbjct: 316 RDPTPEEIGA---EMGISADRVREIQKISQEPVSLETPI--GEEEDSSLGDFI---EDSS 367

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERV 269
                E       R  L + +  L  RER++ + R   E+  P TLE +  EF V+RER+
Sbjct: 368 AVAPPEAASDSMLREQLEQVLDSLADRERKVIKFRFGLEDGHPRTLEEVGREFGVTRERI 427

Query: 270 RQIEARAFKKVQESIQK 286
           RQIE++   K++   + 
Sbjct: 428 RQIESKTLAKLRHPSRS 444


>gi|153008471|ref|YP_001369686.1| RNA polymerase factor sigma-32 [Ochrobactrum anthropi ATCC 49188]
 gi|151560359|gb|ABS13857.1| RNA polymerase, sigma 32 subunit, RpoH [Ochrobactrum anthropi ATCC
           49188]
          Length = 311

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 116/293 (39%), Positives = 184/293 (62%), Gaps = 4/293 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  +++         +   I      P LE++EE  LA R++E  D  A HR+ ++H+RL
Sbjct: 19  MVARSLPATAASSQSM---IRSAMSAPYLEREEERALAIRWKELKDQDALHRITSAHMRL 75

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A  +R + LP+++++ EG +GL++A  +FDPER  R +TY+ WWI+A+MQ+YILR+
Sbjct: 76  VISMAGRFRKFKLPMNDLIQEGYVGLLEAAARFDPEREVRFSTYASWWIRASMQDYILRN 135

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WS+V+ GT++ QK LFFNLRRL+  L    DN  K E    I+ +L VS S+V  M+ RL
Sbjct: 136 WSIVRGGTSSAQKALFFNLRRLRSKLAQSDDNMTKAEMYREISDQLGVSTSDVEIMDSRL 195

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D SL+A +N+ +  + +  D+LV DH  Q+++     + + R   L  ++  LN RE
Sbjct: 196 SGPDSSLSAPVNNEESGAVRRMDFLVDDHPLQDEIAESSIDMERRNQWLNVALDTLNERE 255

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
             I   RRL ++ VTLE L  +  +S+ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 256 LHIIRERRLDDDGVTLEALGEKLGISKERVRQIESRAMEKLKIALLSQHELAA 308


>gi|189423258|ref|YP_001950435.1| RNA polymerase, sigma 70 family subunit [Geobacter lovleyi SZ]
 gi|189419517|gb|ACD93915.1| putative RNA polymerase, sigma 70 family subunit [Geobacter lovleyi
           SZ]
          Length = 280

 Score =  240 bits (613), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 113/276 (40%), Positives = 172/276 (62%), Gaps = 5/276 (1%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
              L+ Y+ EIRK  +L + EE   A ++ E  DL AAH L+TS+LR VVK+A  YR YG
Sbjct: 9   SDSLTLYLSEIRKFNLLTEDEERDYAVKFFEEKDLEAAHTLITSNLRYVVKVASEYRHYG 68

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L + +++ EGNIGLM AV+KF+P RG RL +Y++WWI+A +Q YI+ +WSLVKIGTT  Q
Sbjct: 69  LKMLDLIQEGNIGLMMAVRKFNPYRGVRLISYAVWWIRAYIQNYIVSAWSLVKIGTTQAQ 128

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
           ++LF+ LR+ K  L  +T  +        ++  L+V + EV+ M  RL G+ SLN  I  
Sbjct: 129 RKLFYGLRKTKEALLKLTGRD---SDAFEVSSMLHVPDHEVVEMEQRLKGEVSLNEEIIE 185

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            D       + +  D   QE++L E ++  + +  +  ++  LN +E+ I E R   ++P
Sbjct: 186 GDG--LTILETIADDRMNQEEMLGEYQQEHSLKKAIAHALQGLNEKEKYIVEHRITNDDP 243

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TL++++  F +SRERVRQIE RA  K++  +Q Q+
Sbjct: 244 LTLQDIADHFSISRERVRQIEERALVKLKNVLQPQL 279


>gi|289578595|ref|YP_003477222.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter italicus Ab9]
 gi|289528308|gb|ADD02660.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Thermoanaerobacter italicus Ab9]
          Length = 273

 Score =  240 bits (612), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 80/274 (29%), Positives = 138/274 (50%), Gaps = 14/274 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y+ EI  IP+L  +EE  L KR  E GD  A  R + S+LRLVV IA GY G G+  
Sbjct: 4   IGMYLREISHIPLLTPEEENELLKRI-EEGDEEAKKRFIESNLRLVVSIAKGYVGKGISF 62

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GL++AV++FD  +G++ +TY+ WWIK  +   I      ++I     +   
Sbjct: 63  PDLIQEGNLGLLKAVERFDYRKGYKFSTYATWWIKQTITRAIADQARTIRIPVHMVES-- 120

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + +L    +       +   +  IA+++N+SE +   +   + G  SL   +   + 
Sbjct: 121 ---VNKLLKIQKQFLQKLGREPSIEEIAEEMNISEKKAKVLLEIVQGIVSLEEPV--GED 175

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--V 253
            + +  D +    D +    +E+ E    +  +   +S L PRE ++   R   ++    
Sbjct: 176 ENGKLGDIIA---DKEAVDPVEELESMLLKEQVDEVLSTLAPREEKVLRLRFGLDDGKIR 232

Query: 254 TLENLSSEF-EVSRERVRQIEARAFKKVQESIQK 286
           TLE +  E   +SRERVRQIE +A K+++   + 
Sbjct: 233 TLEEVGKELGGISRERVRQIETKALKRLRHPNRS 266


>gi|171060212|ref|YP_001792561.1| RNA polymerase sigma-32 subunit RpoH [Leptothrix cholodnii SP-6]
 gi|170777657|gb|ACB35796.1| RNA polymerase, sigma 32 subunit, RpoH [Leptothrix cholodnii SP-6]
          Length = 313

 Score =  240 bits (612), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 111/287 (38%), Positives = 166/287 (57%), Gaps = 11/287 (3%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +V     L  YI  + ++P+L  +EE   A+R R+  D+ AA RLV SHLRLVV +A  Y
Sbjct: 23  LVPSLGNLDAYISAVNRLPLLTHEEEVSFARRLRDSQDVEAAGRLVLSHLRLVVSVARQY 82

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGLP  +++ EGN+GLM+AVK+FDPE+G RL +Y+M WIKA + EY+L++W +VK+ T
Sbjct: 83  LGYGLPHGDLIQEGNVGLMKAVKRFDPEQGVRLVSYAMHWIKAEIHEYVLKNWRVVKLAT 142

Query: 129 TANQKRLFFNLRRLKGHLQAITDNN------LKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           T  Q++LFFNLR +K  L+    +       L   ++  +A++LNV   EVI M  R AG
Sbjct: 143 TKAQRKLFFNLRSMKRQLKGEAADGDTHRSSLTEAEIDTVARELNVKREEVIEMEARFAG 202

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
            +      +  D  S     +L  +     + L      +     L R++  L+ R RRI
Sbjct: 203 GDVALEPGSDEDDESYTPIAYLADERQEPTRALEAAHRDELAGPGLLRALDALDARSRRI 262

Query: 243 FEARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            E R L         +TL +L++E+ VS ER+RQIE  A KK+++++
Sbjct: 263 VEERWLKVNDDGSGGLTLHDLAAEYGVSAERIRQIEVAAMKKMRKAL 309


>gi|238063497|ref|ZP_04608206.1| rpoD family RNA polymerase, sigma-70 subunit [Micromonospora sp.
           ATCC 39149]
 gi|237885308|gb|EEP74136.1| rpoD family RNA polymerase, sigma-70 subunit [Micromonospora sp.
           ATCC 39149]
          Length = 534

 Score =  240 bits (612), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 77/312 (24%), Positives = 145/312 (46%), Gaps = 42/312 (13%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY------------REHGDLS-------- 48
           +      +  Y+ +I K+P+L  ++E  LAKR              E G+          
Sbjct: 227 LTASADSVRAYLKQIGKVPLLNAEQEVELAKRIEAGLYAAERLRAAEEGEEKLVREMVRD 286

Query: 49  ----------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
                     A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G
Sbjct: 287 LGWISRDGERAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKG 346

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           ++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L         PE 
Sbjct: 347 YKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLGREPTPE- 403

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +  V ++ 
Sbjct: 404 --ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSEAVVAVDA 456

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARA 276
                 ++ L + +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++ 
Sbjct: 457 VSFSLLQDQLQQVLQTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKT 516

Query: 277 FKKVQESIQKQV 288
             K++   + QV
Sbjct: 517 MSKLRHPSRSQV 528


>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 =  240 bits (612), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 74/276 (26%), Positives = 131/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +++I K   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 350 LYQIEKETGLTIEQVKNINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 409

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 410 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 467

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +   T     PE    ++K++ +SE ++  +        S+   I   D   
Sbjct: 468 KLNRISRQILQETGCEPTPE---ELSKRMLISEDKIRKVLKIAKEPVSMETPI--GDDED 522

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D    + ++     N +      +S L PRE ++   R   +     TL
Sbjct: 523 SHLGDFI---EDTNLDLPLDSATSDNLKAATNDVLSGLTPREAKVLRMRFGIDMNTDHTL 579

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + ++  S
Sbjct: 580 EEVGRQFDVTRERIRQIEAKALRKLRHPSRSEILRS 615


>gi|261400394|ref|ZP_05986519.1| alternative sigma factor RpoH [Neisseria lactamica ATCC 23970]
 gi|313668808|ref|YP_004049092.1| RNA polymerase sigma-32 factor [Neisseria lactamica ST-640]
 gi|269209833|gb|EEZ76288.1| alternative sigma factor RpoH [Neisseria lactamica ATCC 23970]
 gi|313006270|emb|CBN87733.1| putative RNA polymerase sigma-32 factor [Neisseria lactamica
           020-06]
          Length = 290

 Score =  240 bits (612), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 115/289 (39%), Positives = 183/289 (63%), Gaps = 7/289 (2%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N   +  I +G   L +YI  +  IPML ++EE  LA+R R  GDL+AA +L+ SHLR+V
Sbjct: 6   NAFALPAIQSGNGSLEQYIRTVNSIPMLSQEEETRLAER-RIKGDLNAAKQLILSHLRVV 64

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+IL++W
Sbjct: 65  VSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILKNW 124

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            LV++ TT  Q++LFFNLR ++ +L A++     P++  +IA  L V  SEV+ M  R+ 
Sbjct: 125 RLVRVATTKPQRKLFFNLRSMRKNLNALS-----PKEAQSIADDLGVKLSEVLEMEQRMT 179

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           G +      N+ D ++    DWL        + L ++     +   L  +++ L+ R RR
Sbjct: 180 GRDIAIMADNNDDDDNFAPIDWLADHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRSRR 239

Query: 242 IFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           I E+R LQ++  +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 240 IVESRWLQDDGGLTLHQLAAEYGVSAERIRQIEAKAMQKLRGFLTEEAE 288


>gi|220904711|ref|YP_002480023.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio
           desulfuricans subsp. desulfuricans str. ATCC 27774]
 gi|219869010|gb|ACL49345.1| putative RNA polymerase, sigma 70 family subunit [Desulfovibrio
           desulfuricans subsp. desulfuricans str. ATCC 27774]
          Length = 433

 Score =  240 bits (612), Expect = 2e-61,   Method: Composition-based stats.
 Identities = 107/286 (37%), Positives = 167/286 (58%), Gaps = 7/286 (2%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V     L  Y+ E+ + PML+ +EE+ LA R R+H D  AA RLV+SHLRLVV+IAM ++
Sbjct: 148 VGTRDSLHLYLREVSRFPMLKPEEEHELAVRVRDHNDADAAFRLVSSHLRLVVRIAMDFQ 207

Query: 70  GYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
              +  + ++V EGN+GLM+AV KFDP++G + + Y+ +WIKA + ++I+ +W +VKIGT
Sbjct: 208 RRWMQNVLDLVQEGNVGLMRAVNKFDPDKGIKFSYYASFWIKAYILKFIMDNWRMVKIGT 267

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN 187
           T  Q++LF+NL R +  L               ++++L V+E ++  M+ RLA  D SLN
Sbjct: 268 TQVQRKLFYNLNRERQKLI----MQGYDPDAAMLSERLGVTEEQINEMDQRLASTDMSLN 323

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           A +   D   +   D+L     G E  L   E     R+ L   M  LN +E+ I   R 
Sbjct: 324 AQVG-EDSGGATRMDFLPALGPGIEDSLASTEIAGIVRSKLKTIMPKLNEKEQYILHNRL 382

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           L + P+TL  +   + ++RERVRQ+EAR  +K+ + ++  +E  S 
Sbjct: 383 LSDEPITLREIGERYNITRERVRQLEARLVEKIGQHMKNDIEDFSD 428


>gi|310287737|ref|YP_003938995.1| RNA polymerase sigma factor [Bifidobacterium bifidum S17]
 gi|309251673|gb|ADO53421.1| RNA polymerase sigma factor [Bifidobacterium bifidum S17]
          Length = 506

 Score =  240 bits (612), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 65/303 (21%), Positives = 138/303 (45%), Gaps = 39/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR---------------------------YREHGD 46
             +  Y+ +I ++ +L  ++E  L++R                           +  +  
Sbjct: 206 DPVKDYLKQIGRVSLLNAEQEVDLSERIEAGLYAQHLLDTESDGMDFKRKRELKWAANDG 265

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ 
Sbjct: 266 KKAKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYAT 325

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      +++     +  +   L R++  +         P+    +A++L
Sbjct: 326 WWIRQAITRAMADQARTIRVPVHMVE--VINKLSRVQRQMLQDLGREPTPD---ELAREL 380

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   +V  +        SL+  +   +   S++ D +    D       +       + 
Sbjct: 381 DMPVEKVQEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDTDAIAPSDAVAFSLLQE 435

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++   K++   
Sbjct: 436 QFKQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPS 495

Query: 285 QKQ 287
           + Q
Sbjct: 496 RSQ 498


>gi|269793869|ref|YP_003313324.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Sanguibacter keddieii DSM
           10542]
 gi|269096054|gb|ACZ20490.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Sanguibacter keddieii DSM
           10542]
          Length = 342

 Score =  239 bits (611), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 70/303 (23%), Positives = 138/303 (45%), Gaps = 38/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR---------YREHGD-----------------L 47
             +  Y+  I ++P+L  ++E  +A R         Y E G+                 +
Sbjct: 44  DPVKDYLKIIGRVPLLNAEQEIEIAMRIEAGMLAAHYLESGEYPKGATKRELEVITADGV 103

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   LV ++LRLVV IA  Y G GL   +++ EGN GL++AV+KFD  +GF+ +TY+ W
Sbjct: 104 RAKSHLVEANLRLVVSIAKKYTGRGLLFLDLIQEGNTGLIRAVEKFDYAKGFKFSTYATW 163

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   +      ++I     +      + ++    + +  +  +      +A +L+
Sbjct: 164 WIRQAITRGMADQARTIRIPVHMVEV-----INKVSRAQRQMLQDLGREPTPEELALELD 218

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++  +V+ +        SL+  +   ++  S++ D +    D +  V  +       +  
Sbjct: 219 MTPEKVLEVQKHGREPISLHTPL--GEEGGSEFGDLI---EDTEAVVPADAVNFSFLQQQ 273

Query: 228 LTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           +   +  L+ RE  +   R    +  P TL+ +   + V+RER+RQIE++   K++   +
Sbjct: 274 IHGILDTLSEREAGVITMRYGLTDGLPKTLDQIGHVYGVTRERIRQIESKTMSKLRHPSR 333

Query: 286 KQV 288
            QV
Sbjct: 334 SQV 336


>gi|170782020|ref|YP_001710352.1| putative RNA polymerase sigma factor [Clavibacter michiganensis
           subsp. sepedonicus]
 gi|169156588|emb|CAQ01739.1| putative RNA polymerase sigma factor [Clavibacter michiganensis
           subsp. sepedonicus]
          Length = 355

 Score =  239 bits (611), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 72/311 (23%), Positives = 137/311 (44%), Gaps = 38/311 (12%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR------------------------ 40
           + +I       +  Y+ +I K+ +L   EE  LA R                        
Sbjct: 48  STTITGATADPVKDYLKQIGKVALLNAAEEVELAMRIEAGLFAEDKLANTPGISRELERE 107

Query: 41  --YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
             +       A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G
Sbjct: 108 LRWVARDGQRAKSHLLGANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEKFDYTKG 167

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           F+ +TY+ WWI+ A+   +      ++I     +  +   L R++  +         PE 
Sbjct: 168 FKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE- 224

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              ++++L+++  +VI +        SL+  +   +   S++ D +    D +  V  + 
Sbjct: 225 --ELSRELDMTPEKVIEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDTEAVVPADA 277

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARA 276
                 +  L   +  L+ RE  +   R    +  P TL+ +   F V+RER+RQIE++ 
Sbjct: 278 VGFTMLQKQLESLLDSLSEREAGVIRMRFGLGDGMPKTLDQIGDTFGVTRERIRQIESKT 337

Query: 277 FKKVQESIQKQ 287
             K++   + Q
Sbjct: 338 MAKLRHPSRSQ 348


>gi|209965510|ref|YP_002298425.1| RNA polymerase sigma-32 factor [Rhodospirillum centenum SW]
 gi|209958976|gb|ACI99612.1| RNA polymerase sigma-32 factor [Rhodospirillum centenum SW]
          Length = 295

 Score =  239 bits (611), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 125/273 (45%), Positives = 180/273 (65%), Gaps = 4/273 (1%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           +I    K P+L +  E+ LAKR+RE GD +A H LV S+ RLVV  A  +R YGLP+ ++
Sbjct: 16  FIKASMKEPLLSRDHEFDLAKRWRERGDEAALHELVRSYTRLVVATAARFRNYGLPMGDL 75

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GLMQA  +F+P+R  R +TY+ WWI++AMQ+YILR+WS+V+ GTTA QK LFFN
Sbjct: 76  VQEGNVGLMQAAARFEPDREVRFSTYAAWWIRSAMQDYILRNWSIVRTGTTAAQKALFFN 135

Query: 139 LRRLKGHLQ-AITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSSDKN 196
           LRRL+  ++ + + + L P+    IA++LNV ES+V SM  RL A D+SLN+ +     +
Sbjct: 136 LRRLRAKIEDSPSASALSPDGRRRIAEELNVDESDVESMEMRLAAADQSLNSPVAEGGDD 195

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
             +WQD+L       E V+I   + + R   L  ++  L+PRER I   RRL+++  TLE
Sbjct: 196 --EWQDFLSDQRPSPEDVVIGMRDGRMRSRWLAEALGELSPRERTIIAQRRLRDDGATLE 253

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
            L     VS+ERVRQ+E RA  K++ S+ ++VE
Sbjct: 254 ELGRVLGVSKERVRQLEHRALMKLRASMIRRVE 286


>gi|255003152|ref|ZP_05278116.1| RNA polymerase sigma-32 factor (rpoH) [Anaplasma marginale str.
           Puerto Rico]
 gi|255004281|ref|ZP_05279082.1| RNA polymerase sigma-32 factor (rpoH) [Anaplasma marginale str.
           Virginia]
          Length = 296

 Score =  239 bits (611), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 129/276 (46%), Positives = 190/276 (68%), Gaps = 4/276 (1%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           G   L  Y+ ++R  P+L ++EE  LA+ +   G ++ AHRLVTSHLRLVVKIAMG++ Y
Sbjct: 17  GSDDLVSYVAQVRTFPILSEEEEKRLAENWYRRGSVADAHRLVTSHLRLVVKIAMGFKSY 76

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GLPI E++ EGNIGLMQAVK+F+P+ GFRLATY++WWIKA++++YILRSWS +++GTT  
Sbjct: 77  GLPIMELIMEGNIGLMQAVKRFNPDLGFRLATYAVWWIKASIKDYILRSWSCIRVGTTQA 136

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALI 190
           QK+LFF+LR++K  L +   +++  +++ AIA++   SE EV  M+   A  D SLN  +
Sbjct: 137 QKKLFFSLRKIKKRLLSC-GSSMTKKEIKAIAEECATSEEEVERMDRFFANRDVSLNEQV 195

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           +   ++S + QD +      QE + +  EE   +++M   +++ L+ R R IF  RRLQE
Sbjct: 196 HG--ESSVELQDLVPSSLPSQEIMYLADEESAIKKSMFDSALATLDDRHRDIFTRRRLQE 253

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            P TLE LS E+ VS+ERVRQIE +A  K++  I+ 
Sbjct: 254 RPDTLEKLSEEYGVSKERVRQIELQALCKIKSFIEA 289


>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 =  239 bits (611), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 68/247 (27%), Positives = 115/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 628 ERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 687

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T N   P     +
Sbjct: 688 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGNEPDPAT---L 742

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+ + E ++  +        S+   I   D + S   D++    D       E     
Sbjct: 743 AEKMEMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTLAPAEAALHG 797

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 798 SMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKL 857

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 858 RHPSRSD 864


>gi|148658692|ref|YP_001278897.1| RpoD family RNA polymerase sigma factor [Roseiflexus sp. RS-1]
 gi|148570802|gb|ABQ92947.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus sp.
           RS-1]
          Length = 401

 Score =  239 bits (611), Expect = 3e-61,   Method: Composition-based stats.
 Identities = 80/299 (26%), Positives = 139/299 (46%), Gaps = 39/299 (13%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAK--------------------------RYREHGD 46
           +  +  Y+ EI ++ +L  QEE +LA+                          R+ + G 
Sbjct: 103 DDPVRVYLREIGRVNLLTAQEEIMLAQQVERGEQASERLQKGDYAPSERLQLHRWVQEG- 161

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +A  RL+ ++LRLVV IA  Y G G+ + +++ EGNIGLM+A +KFD  +G++ +TY+ 
Sbjct: 162 QAARERLIQANLRLVVSIAKKYLGRGMSLLDLIQEGNIGLMRATEKFDYRKGYKFSTYAT 221

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      +++     +      + R    +Q  T  +  P+    IA +L
Sbjct: 222 WWIRQAITRVIADQSRTIRLPVHVGE--TINRVMRASNRIQQTTGRDPTPD---EIALEL 276

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I    +  +   D++    DG+    ++       R 
Sbjct: 277 GIPVEKVRRVLEAARQTISLETPI--GTEGDTVLADFI---EDGKGVTPMDSASHHILRE 331

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +  ++  L  RERRI + R    +    TLE +  EF ++RER+RQIEAR  +K++  
Sbjct: 332 QIDSALEKLPERERRIIQLRYGLYDGHYRTLEEVGREFGITRERIRQIEARVLRKLRHP 390


>gi|87302644|ref|ZP_01085461.1| RNA polymerase sigma factor [Synechococcus sp. WH 5701]
 gi|87282988|gb|EAQ74945.1| RNA polymerase sigma factor [Synechococcus sp. WH 5701]
          Length = 469

 Score =  239 bits (611), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 77/313 (24%), Positives = 144/313 (46%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRY--------------REHG------------ 45
            E  +  Y+ EI +I +L   EE  LA++               +++G            
Sbjct: 157 TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLLLEELAGQFEQDNGHYPDNKEWAVLV 216

Query: 46  -------------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 217 DMPPVKFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 276

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 277 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKVLSQE 331

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA+ + ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 332 FGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADIENPE 389

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
           Q + +   R++    L   ++ L+PRER +   R   ++    TLE +   F+V+RER+R
Sbjct: 390 QDVAKNLLRED----LEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIR 445

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 446 QIEAKALRKLRHP 458


>gi|330466485|ref|YP_004404228.1| RNA polymerase sigma factor [Verrucosispora maris AB-18-032]
 gi|328809456|gb|AEB43628.1| RNA polymerase sigma factor [Verrucosispora maris AB-18-032]
          Length = 535

 Score =  239 bits (610), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 77/312 (24%), Positives = 145/312 (46%), Gaps = 42/312 (13%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY------------REHGDLS-------- 48
           +      +  Y+ +I K+P+L  ++E  LAKR              E G+          
Sbjct: 228 LTASADSVRAYLKQIGKVPLLNAEQEVELAKRIEAGLYAAERLRAAEEGEEKLARDMQRD 287

Query: 49  ----------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
                     A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G
Sbjct: 288 LLWISRDGERAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKG 347

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           ++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L         PE 
Sbjct: 348 YKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLGREPTPE- 404

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +  V ++ 
Sbjct: 405 --ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSEAVVAVDA 457

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARA 276
                 ++ L + +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++ 
Sbjct: 458 VSFSLLQDQLQQVLQTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKT 517

Query: 277 FKKVQESIQKQV 288
             K++   + QV
Sbjct: 518 MSKLRHPSRSQV 529


>gi|290960625|ref|YP_003491807.1| Principal sigma factor HrdA [Streptomyces scabiei 87.22]
 gi|260650151|emb|CBG73267.1| Principal sigma factor HrdA [Streptomyces scabiei 87.22]
          Length = 387

 Score =  239 bits (610), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 83/301 (27%), Positives = 138/301 (45%), Gaps = 38/301 (12%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY------------------REHGDLS---- 48
                  +Y+ EI +IP+L   EE  LA+R                   R   DL     
Sbjct: 86  PSSDLFRQYLREIGRIPLLTAVEEVELARRVEAGLFAEERLGTASGLDTRLALDLDRLVV 145

Query: 49  ----AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
               A  RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY
Sbjct: 146 MGRMAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTY 205

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + WWI+ AM   +      +++     +  L   + R++  +         P++V A   
Sbjct: 206 ATWWIRQAMSRALADQARTIRVPVHVVE--LINRVVRVQRRMLQERGYEPTPDEVAA--- 260

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            L+++   V  +        SL+A +   +++     D +    DG     +E       
Sbjct: 261 HLDLAPERVSEVLRLAQEPVSLHAPV--GEEDDVALGDLI---EDGDAASPVESAAFLLL 315

Query: 225 RNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           R  L   +S L  RER++ + R       P TLE +   F V+RER+RQIE++   K+++
Sbjct: 316 REHLEAVLSTLGERERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRD 375

Query: 283 S 283
            
Sbjct: 376 H 376


>gi|182438860|ref|YP_001826579.1| putative RNA polymerase principal sigma factor [Streptomyces
           griseus subsp. griseus NBRC 13350]
 gi|326779516|ref|ZP_08238781.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces cf.
           griseus XylebKG-1]
 gi|178467376|dbj|BAG21896.1| putative RNA polymerase principal sigma factor [Streptomyces
           griseus subsp. griseus NBRC 13350]
 gi|326659849|gb|EGE44695.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces cf.
           griseus XylebKG-1]
          Length = 363

 Score =  239 bits (610), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 85/296 (28%), Positives = 140/296 (47%), Gaps = 38/296 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRY------------------REHGDLS--------A 49
             +Y+ EI +IP+L   EE  LA+R                   R  GDL         A
Sbjct: 67  FRQYLREIGRIPLLTAAEEVELARRVEAGLFAEERLAGTPDLDSRLAGDLDRLVVMGRTA 126

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY+ WWI
Sbjct: 127 KRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWI 186

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + AM   +      +++     +  L   + R++  L          E    IA  L+++
Sbjct: 187 RQAMSRALADQARTIRVPVHVVE--LINRVVRVQRRLLQERGVEPTAED---IAVDLDLT 241

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
              V  +        SL+A +   +++   + D +    DG     +E       R  L 
Sbjct: 242 PERVTDILRLAQEPVSLHAPV--GEEDDVSFGDLI---EDGDAASPVESAAFLLLREHLE 296

Query: 230 RSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +S L  RER++ + R   E+  P TLE +   F V+RER+RQIE++   ++++ 
Sbjct: 297 AVLSTLGERERKVVQLRYGLEDGRPRTLEEIGRIFGVTRERIRQIESKTLSRLRDH 352


>gi|289207353|ref|YP_003459419.1| RNA polymerase, sigma 32 subunit, RpoH [Thioalkalivibrio sp.
           K90mix]
 gi|288942984|gb|ADC70683.1| RNA polymerase, sigma 32 subunit, RpoH [Thioalkalivibrio sp.
           K90mix]
          Length = 289

 Score =  239 bits (610), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 97/275 (35%), Positives = 162/275 (58%), Gaps = 9/275 (3%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             L  Y+  + +I +L+ + E  LA+   E  DL AA +L+  +LR VV +A GY+GYGL
Sbjct: 18  GNLDHYMQAVSRIEVLDPEHERELARSLHERNDLDAARQLILHNLRFVVHVARGYQGYGL 77

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGN+GLM+AV++FDP +G RL ++++ WI+A + E+ILR+W +VK+ TT  Q+
Sbjct: 78  PLGDLIQEGNVGLMKAVRRFDPNQGVRLVSFAVHWIRAEIHEFILRNWRIVKVATTKAQR 137

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
           +LFFNLR  K  L  +++     ++V A+A+ L VSE++V  M  RL+  ++       S
Sbjct: 138 KLFFNLRSAKQRLGWMSN-----DEVSAVARDLGVSENDVWEMERRLSSQDASFDPAPDS 192

Query: 194 DKNSSQWQD----WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           D   +         +    D   QV  +++  ++ +  L  ++  L+ R R I   R + 
Sbjct: 193 DDEHTYLAPAQRLSIEDMSDDPAQVAEDEDWDRHYQERLASTLGELDERSRDILARRYMS 252

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           E   TL  L++E+ VS ER+RQIE  A K+++ + 
Sbjct: 253 EPKATLHELAAEYGVSAERIRQIENNAIKRIRTAF 287


>gi|94987055|ref|YP_594988.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Lawsonia intracellularis PHE/MN1-00]
 gi|94731304|emb|CAJ54667.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Lawsonia intracellularis PHE/MN1-00]
          Length = 385

 Score =  239 bits (610), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 102/294 (34%), Positives = 174/294 (59%), Gaps = 7/294 (2%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           ++  +S        L  Y+ E+ + PML+ +EE  LA+  ++ G   AA RL++SHLRLV
Sbjct: 92  SQVTLSTTTATRDSLQLYLREVSRFPMLKPEEELRLAQDVQKKGCSKAAFRLISSHLRLV 151

Query: 62  VKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VKIAM ++   +  + +++ EGN+GLM+AV KFDP++G + + Y+ +WI+A + ++I+ +
Sbjct: 152 VKIAMDFQRRWMQNVLDLIQEGNVGLMRAVNKFDPDKGIKFSYYAAFWIRAYILKFIMDN 211

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VKIGTT  Q++LF+NL R +  L A            ++A +L V E ++I M  RL
Sbjct: 212 WRMVKIGTTQAQRKLFYNLNRERQKLLA----EGFDPDTSSLALRLGVGEEQIIEMQQRL 267

Query: 181 -AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            A D SL+  +     N+S+  D+L   + G E+ L  +E     ++ +   + +L+ +E
Sbjct: 268 DASDMSLDVTVGEETGNASRI-DFLPAINPGIEESLAGQEIAILLQDRIKDILPLLSEKE 326

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
             I   R L ++PVTL  +  ++ V+RERVRQ+EAR  +K++  + +Q+   S 
Sbjct: 327 VYILHNRLLTDDPVTLREIGEKYSVTRERVRQLEARLLQKLRTHLSRQIGDFSE 380


>gi|292492240|ref|YP_003527679.1| RNA polymerase sigma factor RpoH [Nitrosococcus halophilus Nc4]
 gi|291580835|gb|ADE15292.1| RNA polymerase sigma factor RpoH [Nitrosococcus halophilus Nc4]
          Length = 287

 Score =  239 bits (610), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 106/279 (37%), Positives = 167/279 (59%), Gaps = 7/279 (2%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++      L  Y   +  IP+L   +E+ LA R R+H DL AA +LV SHLR VV+IA G
Sbjct: 12  LVPVAVGDLDTYCQTVHSIPILSADQEHNLALRLRDHHDLDAARQLVLSHLRFVVRIARG 71

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y GYGLP+++++ EGNIGLM+AVK+FDPE+G RL ++++ WI+A + E+ILR+W +VK+ 
Sbjct: 72  YSGYGLPLADLIQEGNIGLMKAVKRFDPEQGVRLVSFAVHWIRAEIHEFILRNWRIVKVA 131

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESL 186
           TT  Q++LFFNLR  K  L  +        +V  +A+ L VS  +V+ M  RL+  D   
Sbjct: 132 TTKAQRKLFFNLRSAKKRLGWLNRK-----EVDEVARDLGVSPKQVLEMEARLSSQDTPF 186

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEA 245
                 + ++        ++D        +E+ +++N     L +++  L+PR R I   
Sbjct: 187 EGPNAENSEDDIPAPIAYLFDPTTDPARQMERLDQENHYGQRLQQALEALDPRSRAIIHR 246

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R LQE+  TL  L++E+++S ER+RQ+E  A KK++  +
Sbjct: 247 RWLQESKSTLHELAAEYQISAERIRQLENNAIKKLRSML 285


>gi|160902085|ref|YP_001567666.1| RpoD family RNA polymerase sigma factor [Petrotoga mobilis SJ95]
 gi|160359729|gb|ABX31343.1| RNA polymerase, sigma 70 subunit, RpoD family [Petrotoga mobilis
           SJ95]
          Length = 424

 Score =  239 bits (610), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 78/286 (27%), Positives = 140/286 (48%), Gaps = 10/286 (3%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
            M   ++ +  +  Y+ EI K  +L    E  LA+R  + GD  A   L+ ++LRLV+ I
Sbjct: 139 EMCDNISLQDPIKIYLKEISKSKLLTPSRERKLARR-AQMGDKRAREELIKANLRLVISI 197

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y G+GL   +++ EGNIGLM+AV KFD ++G++ +TYS WWI+ A+   I      V
Sbjct: 198 AKRYVGHGLGFLDLIQEGNIGLMKAVAKFDWKKGYKFSTYSYWWIRQAITRAIADQGRTV 257

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I        L   + R+   +      N +   +  ++  ++    ++  +        
Sbjct: 258 RIPVH-----LVETINRMNRVVNKYIQENGEVPDLEELSVLMDKPVDKMKEVLISAKNIF 312

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SLNA I  S+   ++ +  ++   D       E+  +   R  +   +  L+P+E  I +
Sbjct: 313 SLNAPI--SNDVDAEGESEVLDFIDSDSPTPDEEGRKMIIRQKMEMIIDTLSPKEAMILK 370

Query: 245 ARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            R         TLE +   F V+RER+RQIE+++ +K++   +K++
Sbjct: 371 MRYGFVDGKQKTLEEVGEFFNVTRERIRQIESKSIRKLKHPARKKM 416


>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 =  239 bits (610), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 66/243 (27%), Positives = 112/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RGF+ +TY+ 
Sbjct: 585 RKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGFKFSTYAT 644

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A K+
Sbjct: 645 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGAEPDPAT---LAIKM 699

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R 
Sbjct: 700 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDNNTLAPADAALHASMRG 754

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 755 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 814

Query: 285 QKQ 287
           +  
Sbjct: 815 RSD 817


>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 =  239 bits (610), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 68/247 (27%), Positives = 115/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 576 ERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 635

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T N   P     +
Sbjct: 636 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGNEPDPAT---L 690

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+ + E ++  +        S+   I   D + S   D++    D       E     
Sbjct: 691 AEKMEMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTLAPAEAALHG 745

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 746 SMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKL 805

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 806 RHPSRSD 812


>gi|117925612|ref|YP_866229.1| RNA polymerase, sigma 32 subunit, RpoH [Magnetococcus sp. MC-1]
 gi|117609368|gb|ABK44823.1| RNA polymerase, sigma 32 subunit, RpoH [Magnetococcus sp. MC-1]
          Length = 290

 Score =  239 bits (610), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 126/285 (44%), Positives = 180/285 (63%), Gaps = 10/285 (3%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
            M +   GE  L+ Y+ ++   PML  +EE+ LA RYRE  DL AAH+LVTS+LR V  I
Sbjct: 4   TMLVPYKGENQLAGYMQQVDSYPMLSAEEEFELAVRYREQNDLEAAHKLVTSYLRYVASI 63

Query: 65  AMGYRGY-GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           A  Y+GY G+   ++V EG++GLMQAVK+FDP +GFRLATY+MWWIKA++QE++L  WSL
Sbjct: 64  AKEYQGYYGIKFMDLVQEGSVGLMQAVKRFDPHKGFRLATYAMWWIKASIQEFVLHHWSL 123

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG- 182
           VKIGTTA Q++LFFNLR+ K  L+ +        Q   + ++  VS   V+ M+ RL+G 
Sbjct: 124 VKIGTTAAQRKLFFNLRKSKDTLERL-----DATQAEEMGQRFGVSGEAVLEMDARLSGP 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
           D+SLN  +    +   + Q+ L      QE  L+  E  + ++ M+ +++S L+ RE+ I
Sbjct: 179 DDSLNRCLVEGGE---EIQNMLADSAPNQEMRLLASESERLQQQMIKQALSFLSEREQMI 235

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             AR +   PVTLE L     VSRER+RQ+E RA KK++   +  
Sbjct: 236 VRARIMCAEPVTLEVLGERLGVSRERIRQLETRALKKLRAFFEAD 280


>gi|115378280|ref|ZP_01465448.1| RNA polymerase sigma-B factor [Stigmatella aurantiaca DW4/3-1]
 gi|310821082|ref|YP_003953440.1| RNA polymerase sigma-b factor [Stigmatella aurantiaca DW4/3-1]
 gi|401024|sp|Q01624|RPSB_STIAD RecName: Full=RNA polymerase sigma-B factor
 gi|46680|emb|CAA78693.1| sigma factor (SigB) [Stigmatella aurantiaca DW4/3-1]
 gi|115364722|gb|EAU63789.1| RNA polymerase sigma-B factor [Stigmatella aurantiaca DW4/3-1]
 gi|309394154|gb|ADO71613.1| RNA polymerase sigma-B factor [Stigmatella aurantiaca DW4/3-1]
          Length = 296

 Score =  239 bits (610), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 117/265 (44%), Positives = 168/265 (63%), Gaps = 4/265 (1%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
              L+ Y+ EI +  +L  +EE  LA+++ + GDL+A HRLVTS+LR VVK++  YR YG
Sbjct: 11  SGSLTMYLSEINQYGLLSVEEEQALARKFVK-GDLAAGHRLVTSNLRFVVKVSYEYRSYG 69

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           + +S+++ EGNIGLM+AV+KFDP++G RL +Y++WWI+A +Q YIL+SWSLVK+GTT  Q
Sbjct: 70  IKMSDLIQEGNIGLMKAVQKFDPDKGIRLISYAVWWIRAYIQNYILKSWSLVKLGTTQAQ 129

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALIN 191
           ++LFF+L R +  L+     +     V  IA KLNV  SEV  M  R+ G D SL+A + 
Sbjct: 130 RKLFFSLARTRRELEKFGAGDGAVVNVDEIANKLNVKASEVREMEQRMGGRDLSLDAPMG 189

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
               NS    D++      Q+    +KEE     + +  ++  L+PRER I E R + E 
Sbjct: 190 EDGGNSH--VDFVASAAAPQDDEFADKEEAGLINSRVHMALMRLDPRERFIIEQRVMNER 247

Query: 252 PVTLENLSSEFEVSRERVRQIEARA 276
           P+TL+ L   F  SRER RQ+E RA
Sbjct: 248 PMTLKELGEHFGFSRERARQLEIRA 272


>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 =  239 bits (610), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 68/247 (27%), Positives = 115/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 576 ERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 635

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T N   P     +
Sbjct: 636 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGNEPDPAT---L 690

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+ + E ++  +        S+   I   D + S   D++    D       E     
Sbjct: 691 AEKMEMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTLAPAEAALHG 745

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 746 SMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKL 805

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 806 RHPSRSD 812


>gi|291301996|ref|YP_003513274.1| RpoD subfamily RNA polymerase sigma-70 subunit [Stackebrandtia
           nassauensis DSM 44728]
 gi|290571216|gb|ADD44181.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Stackebrandtia
           nassauensis DSM 44728]
          Length = 559

 Score =  239 bits (610), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 81/319 (25%), Positives = 149/319 (46%), Gaps = 43/319 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------REHGDL- 47
            RK+  +  + +  +  Y+ +I K+P+L   +E  LAKR              +E G+  
Sbjct: 246 ARKDAEMTASAD-SVRAYLKQIGKVPLLNAAQEVELAKRIEAGLYAVERLRQLKEAGEEI 304

Query: 48  ----------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 305 PTQVRRDLEWVTRDGDRAKNHLLAANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 364

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +GF+ +TY+ WWI+ A+   +      ++I     +  +   L R++  L     
Sbjct: 365 KFDYTKGFKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLG 422

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +AK++++S  +V+ +        SL+  I   D+  SQ  D++    D +
Sbjct: 423 REPAPE---ELAKEMDISPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSE 474

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
             V ++       +  L + +  L+ RE  +   R       P TL+ +   + V+RER+
Sbjct: 475 AVVAVDAVSFSLLQGQLQQVLQTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERI 534

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE++   K++   + QV
Sbjct: 535 RQIESKTMSKLRHPSRSQV 553


>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 =  239 bits (610), Expect = 4e-61,   Method: Composition-based stats.
 Identities = 68/247 (27%), Positives = 115/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 631 ERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 690

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T N   P     +
Sbjct: 691 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGNEPDPAT---L 745

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+ + E ++  +        S+   I   D + S   D++    D       E     
Sbjct: 746 AEKMEMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTLAPAEAALHG 800

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 801 SMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKL 860

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 861 RHPSRSD 867


>gi|149378434|ref|ZP_01896128.1| RNA polymerase sigma-32 factor RpoH [Marinobacter algicola DG893]
 gi|149357284|gb|EDM45812.1| RNA polymerase sigma-32 factor RpoH [Marinobacter algicola DG893]
          Length = 289

 Score =  239 bits (610), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 103/279 (36%), Positives = 158/279 (56%), Gaps = 7/279 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  YI    +IP+L  +EE  LA+R    GD+ AA  LV SHLR V+ IA  Y GYGL 
Sbjct: 16  NLESYIQAASRIPVLSVEEERKLAERLHYDGDVDAARELVLSHLRFVIHIARSYAGYGLS 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++
Sbjct: 76  QADLIQEGNVGLMKAVKRFNPEYGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSS 193
           LFFNLR  K  L  ++      ++V A+A  L V    V  M  RLA  D + +   +  
Sbjct: 136 LFFNLRSQKKRLAWLSH-----DEVNAVASDLGVEPRVVREMEGRLASHDTAFDGPQDDD 190

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN-MLTRSMSVLNPRERRIFEARRLQENP 252
           D N+ Q   + + D        +E+ +  +  N  L  ++  L+ R + I   R L ++ 
Sbjct: 191 DDNAYQAPAYYLEDKRSNPATQLEQSDWTDDSNGRLMAALEQLDERSQDILRERWLSDSK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
            TL  L+  + VS ER+RQ+E  A KK++  +  + E +
Sbjct: 251 STLHELADRYGVSAERIRQLEKNAMKKIRMHMTTEEEAA 289


>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 =  238 bits (609), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 112/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 586 RKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 645

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A K+
Sbjct: 646 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGAEPDPAT---LAIKM 700

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R 
Sbjct: 701 EMPEEKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDNNTLAPADAALHASMRG 755

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 756 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 815

Query: 285 QKQ 287
           +  
Sbjct: 816 RSD 818


>gi|90415296|ref|ZP_01223230.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2207]
 gi|90332619|gb|EAS47789.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2207]
          Length = 278

 Score =  238 bits (609), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 105/276 (38%), Positives = 163/276 (59%), Gaps = 8/276 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             L+ YI     +P+L   EE  L +      DL AA R+V +HLR VV IA  Y GYGL
Sbjct: 8   GNLNAYIQGTATVPILTIDEERALGESLYYQEDLDAARRMVMAHLRFVVHIARSYNGYGL 67

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+++++ EGN+GLM+AV++F+PE+G RL ++++ WIKA + E+ILR+W +VKI TT  Q+
Sbjct: 68  PLADLIQEGNVGLMKAVRRFNPEKGVRLVSFAVHWIKAEIHEFILRNWRIVKIATTKAQR 127

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINS 192
           +LFFNLR  K  LQ ++      ++  A+A  L V   +V+ M  RL + D + +A    
Sbjct: 128 KLFFNLRSAKKQLQWLS-----ADEAKAVADDLGVQVKDVMEMEMRLTSRDPAFDAPAGE 182

Query: 193 SDKNSS-QWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLNPRERRIFEARRLQE 250
            D++SS Q   + + D       L E ++ + +    L  ++S L+ R R I + R L +
Sbjct: 183 DDESSSFQAPVYFLEDKSMDPAQLAENDDWEVDNNTRLIAAVSDLDDRSRDILQRRWLND 242

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              TL  L++E+ VS ER+RQ+E  A KKV+  ++ 
Sbjct: 243 AKATLHELAAEYGVSAERIRQLEKNAMKKVRGLMEA 278


>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 =  238 bits (609), Expect = 5e-61,   Method: Composition-based stats.
 Identities = 68/247 (27%), Positives = 116/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 610 EKRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 669

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T N   P     +
Sbjct: 670 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGNEPDPAT---L 724

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+ + E ++  +        S+   I   D + S   D++    D       E     
Sbjct: 725 AEKMEMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTLAPAEAALDG 779

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 780 SMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKL 839

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 840 RHPSRSD 846


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

 Score =  238 bits (609), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 66/243 (27%), Positives = 112/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RGF+ +TY+ 
Sbjct: 559 RKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGFKFSTYAT 618

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A K+
Sbjct: 619 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGAEPDPAT---LAIKM 673

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R 
Sbjct: 674 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDNNTLAPADAALHASMRG 728

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 729 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 788

Query: 285 QKQ 287
           +  
Sbjct: 789 RSD 791


>gi|254995008|ref|ZP_05277198.1| RNA polymerase sigma-32 factor (rpoH) [Anaplasma marginale str.
           Mississippi]
          Length = 296

 Score =  238 bits (609), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 128/276 (46%), Positives = 190/276 (68%), Gaps = 4/276 (1%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           G   L  Y+ ++R  P+L ++EE  LA+ +   G ++ AHRLVTSHLRLVVKIAMG++ Y
Sbjct: 17  GSDDLVSYVAQVRTFPILSEEEEKRLAENWYRRGSVADAHRLVTSHLRLVVKIAMGFKSY 76

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GLPI E++ EGNIGLMQAVK+F+P+ GFRLATY++WWIKA++++YILRSWS +++GTT  
Sbjct: 77  GLPIMELIMEGNIGLMQAVKRFNPDLGFRLATYAVWWIKASIKDYILRSWSCIRVGTTQA 136

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALI 190
           QK+LFF+LR++K  L +   +++  +++ AIA++   SE EV  M+   A  D SLN  +
Sbjct: 137 QKKLFFSLRKIKKRLLSC-GSSMTKKEIKAIAEECATSEEEVERMDRFFANRDVSLNEQV 195

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           +   ++S + QD +      QE + +  EE   +++M   +++ L+ R R IF  RRL+E
Sbjct: 196 HG--ESSVELQDLVPSSLPSQEIMYLADEESAIKKSMFDSALATLDDRHRDIFTRRRLRE 253

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            P TLE LS E+ VS+ERVRQIE +A  K++  I+ 
Sbjct: 254 RPDTLEKLSEEYGVSKERVRQIELQALCKIKSFIEA 289


>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 =  238 bits (609), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 76/270 (28%), Positives = 128/270 (47%), Gaps = 14/270 (5%)

Query: 22  EIRKIPMLEKQE--EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           +I K+  L+ +E  E   A  Y E     A   +V ++LRLV+ IA  Y   GL   +++
Sbjct: 349 DIEKLTQLDLEELKEISRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 408

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L
Sbjct: 409 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKL 466

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
            R+   +         PE    +AK++++ E ++  +        S+   I   D   S 
Sbjct: 467 NRISRQMLQQYGREATPE---ELAKEMDMPEDKIRKVMKIAKEPISMETPI--GDDEDSH 521

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLEN 257
             D++    D   +  IE     N    +   ++ L PRE ++   R   +     TLE 
Sbjct: 522 LGDFI---EDTNVESPIENTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEE 578

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 579 VGKQFDVTRERIRQIEAKALRKLRHPSRSE 608


>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 =  238 bits (609), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 67/247 (27%), Positives = 114/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 655 EKRAREAKREMTVANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 714

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T +         +
Sbjct: 715 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGHE---PDAATL 769

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A K+ + E ++  +        S+   I   D   S   D++    DG      E     
Sbjct: 770 ALKMEIPEDKIRKIMKIAKEPVSMETPI--GDDEDSHLGDFI---EDGNTLAPAEAALHN 824

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 825 SMRDVVKDVLDSLTPREAKVLRMRFGVEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKM 884

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 885 RHPSRSD 891


>gi|170719544|ref|YP_001747232.1| RNA polymerase factor sigma-32 [Pseudomonas putida W619]
 gi|169757547|gb|ACA70863.1| RNA polymerase, sigma 32 subunit, RpoH [Pseudomonas putida W619]
          Length = 284

 Score =  238 bits (609), Expect = 6e-61,   Method: Composition-based stats.
 Identities = 103/272 (37%), Positives = 155/272 (56%), Gaps = 7/272 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+H +  IP+L  ++E  LA+R     DL AA ++V +HLR VV IA  Y GYGL 
Sbjct: 16  NLEAYVHTVNSIPLLTVEQERDLAERLYYEQDLEAARQMVMAHLRFVVHIARSYAGYGLA 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++
Sbjct: 76  QADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           LFFNLR  K  L  + +     ++V  +A+ L V   EV  M  RL+G +        +D
Sbjct: 136 LFFNLRSQKKRLAWLNN-----DEVHRVAESLGVEPREVREMESRLSGQDMAFDPAAEAD 190

Query: 195 KNSS-QWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENP 252
            +S+ Q     + DH     V +E  +  +     L  ++  L+ R R I   R L E  
Sbjct: 191 DDSAFQSPAHYLEDHRYDPAVQLEDADWSDNSTSNLHEALQGLDERSRDILYQRWLAEEK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL  L+ ++ VS ER+RQ+E  A  KV+  I
Sbjct: 251 ATLHELADKYSVSAERIRQLEKNAMNKVKALI 282


>gi|126664542|ref|ZP_01735526.1| RNA polymerase sigma factor [Marinobacter sp. ELB17]
 gi|126630868|gb|EBA01482.1| RNA polymerase sigma factor [Marinobacter sp. ELB17]
          Length = 286

 Score =  238 bits (608), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 103/274 (37%), Positives = 158/274 (57%), Gaps = 7/274 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  YI    +IP+L   EE  L++R    GD+ AA +L+ SHLR V+ IA  Y GYGL 
Sbjct: 16  NLESYIQAASRIPILTVDEERALSERLYYEGDVDAARQLILSHLRFVIHIARSYSGYGLN 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            S++V EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++
Sbjct: 76  QSDLVQEGNVGLMKAVKRFNPEYGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSS 193
           LFFNLR  K  L  ++ + L      A+A  L V    V  M  RL+  D + +  +N  
Sbjct: 136 LFFNLRGQKKKLAWLSHDELN-----AVAADLGVEARVVREMEGRLSSHDTAFDGPMNDD 190

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKE-ERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
           + ++ Q   + + DH       +E+    ++    L +++S L+ R + I   R L E  
Sbjct: 191 EDSAYQAPAYYLEDHRSNPATQLERSNWTEDSNGRLMQALSSLDDRSQDILRERWLSETK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            TL  L+  + VS ER+RQ+E  A KK++  +Q+
Sbjct: 251 STLHQLADRYGVSAERIRQLEKNAMKKIRLQMQE 284


>gi|145590108|ref|YP_001156705.1| RNA polymerase, sigma 32 subunit, RpoH [Polynucleobacter
           necessarius subsp. asymbioticus QLW-P1DMWA-1]
 gi|145048514|gb|ABP35141.1| RNA polymerase, sigma 32 subunit, RpoH [Polynucleobacter
           necessarius subsp. asymbioticus QLW-P1DMWA-1]
          Length = 309

 Score =  238 bits (608), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 112/286 (39%), Positives = 165/286 (57%), Gaps = 10/286 (3%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           +   G   L  YI  + ++PML   EE  LA+ +R   ++ AA  LV SHLRLVV +A  
Sbjct: 28  LPTLGVGTLDSYIAYVNRVPMLSAAEELHLAQEFRRTENVDAAKTLVLSHLRLVVSVARQ 87

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y GYG+P ++++ EGNIGLM+AVK++DP  G RL +Y++ WIKA + EYIL++W LVK  
Sbjct: 88  YLGYGIPHADLIQEGNIGLMKAVKRYDPNNGARLVSYAIHWIKAEIHEYILKNWRLVKTA 147

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
           TT  Q++LFFNLR  K  L A+T     P +V A+AK L+V  S+V  M  RLAG +   
Sbjct: 148 TTKAQRKLFFNLRSNKPTLSALT-----PSEVDALAKALDVKGSDVKEMEMRLAGGDIAL 202

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
              +S D+++     WL  +       +   E    +   L +++  L+ R R I ++R 
Sbjct: 203 EGDDSDDESAYAPIQWLADNTQEPTARIASAEADALQGPRLDQALMSLDERSRNIVQSRW 262

Query: 248 L-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           L          TL +L++E+ +S ERVRQIE  A KK++  ++ Q 
Sbjct: 263 LAMDAEGNGTKTLHDLAAEYGISAERVRQIETAALKKMRGLLEAQA 308


>gi|256396128|ref|YP_003117692.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Catenulispora
           acidiphila DSM 44928]
 gi|256362354|gb|ACU75851.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Catenulispora
           acidiphila DSM 44928]
          Length = 390

 Score =  238 bits (608), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 80/295 (27%), Positives = 132/295 (44%), Gaps = 40/295 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHG---------------------------DLS 48
             +Y+ EI ++P+L    E  LA+   E G                             +
Sbjct: 94  FRQYLREIGRVPLLNAVLEVELAQAV-EAGLFAEEKLTFQTHLKPQLRRELAILVLEGQA 152

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  RL+ ++LRLVV IA  Y G G+ I ++V EGN+GL++AV+KFD  RG++ +TY+ WW
Sbjct: 153 AKRRLIEANLRLVVSIAKRYLGRGMSILDLVQEGNLGLIRAVEKFDYTRGYKFSTYATWW 212

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ AM   +      +++     +  L   + RL+  L         P+ +  +   L V
Sbjct: 213 IRQAMSRALADQARTIRVPVHVVE--LMNRVVRLQRRLLQENGVEPTPDDIAEV---LGV 267

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +   V+ +        SL+A +   +++     D +    D       +       R  L
Sbjct: 268 AVERVVEVLRLAQEPVSLHAPV--GEEDDVALGDLI---EDADAVSPADSVAVVMLREHL 322

Query: 229 TRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +S L  RE+R+ + R       P TLE +   F V+RER+RQIEA+   K++
Sbjct: 323 DALLSTLGEREKRVVQLRYGLTDGQPHTLEEIGRTFGVTRERIRQIEAKTLAKLR 377


>gi|229817449|ref|ZP_04447731.1| hypothetical protein BIFANG_02712 [Bifidobacterium angulatum DSM
           20098]
 gi|229785238|gb|EEP21352.1| hypothetical protein BIFANG_02712 [Bifidobacterium angulatum DSM
           20098]
          Length = 482

 Score =  238 bits (608), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 65/303 (21%), Positives = 139/303 (45%), Gaps = 39/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR---------------------------YREHGD 46
             +  Y+ +I ++ +L  ++E  L++R                           +  +  
Sbjct: 182 DPVKDYLKQIGRVSLLNAEQEVDLSERIEAGLYAQHLLDTEGDTMDFKRKRELKWAANDG 241

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ 
Sbjct: 242 KKAKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYAT 301

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      +++     +  +   L R++  +         P+    +A++L
Sbjct: 302 WWIRQAITRAMADQARTIRVPVHMVE--VINKLSRVQRQMLQDLGREPTPD---ELAREL 356

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   +V  +        SL+  +   +   S++ D +    D       +       ++
Sbjct: 357 DMPVEKVQEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDTDAIAPSDAVAFSLLQD 411

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++   K++   
Sbjct: 412 QFKQVLETLSPRESGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPS 471

Query: 285 QKQ 287
           + Q
Sbjct: 472 RSQ 474


>gi|218282286|ref|ZP_03488585.1| hypothetical protein EUBIFOR_01167 [Eubacterium biforme DSM 3989]
 gi|218216721|gb|EEC90259.1| hypothetical protein EUBIFOR_01167 [Eubacterium biforme DSM 3989]
          Length = 409

 Score =  238 bits (608), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 77/297 (25%), Positives = 137/297 (46%), Gaps = 36/297 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------------HGDLS 48
             +  Y+ EI +IP+L+ +EE ++A++ +E                              
Sbjct: 111 DPVKMYLKEIGQIPLLDPKEEPIIARQIQEGEQAKEDIKNPDLSEEEKKKLAKIIADGEE 170

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L++S+LRLVV IA  Y G G+   +++ EGN GL++AV+KFD  +GF+ +TY+ WW
Sbjct: 171 AKQTLISSNLRLVVSIAKKYVGRGMLFLDLIQEGNCGLIKAVEKFDYTKGFKFSTYATWW 230

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ ++   I      ++I     +      L R++  L      +  PE++    +  N+
Sbjct: 231 IRQSITRAIADQARTIRIPVHMVE--TINKLTRIQRQLVQDLGRDPMPEEIAEKME--NI 286

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  +V  +        SL   I   +++ S   D++    D       +    +  ++ +
Sbjct: 287 SAEKVREIQKIALDPVSLETPI--GEEDDSHLGDFI---EDKDTLSPDDYTNNQLLKDEI 341

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
              +  L  RE ++   R   L     TLE +  EF V+RER+RQIEA+A +K++  
Sbjct: 342 NAVLQGLTEREEKVLRLRFGLLDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLKNP 398


>gi|284046131|ref|YP_003396471.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Conexibacter
           woesei DSM 14684]
 gi|283950352|gb|ADB53096.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Conexibacter
           woesei DSM 14684]
          Length = 367

 Score =  238 bits (608), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 85/276 (30%), Positives = 140/276 (50%), Gaps = 13/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             L  ++ +I K+ +L  QEE  LAKR  E GDL A  ++V S+LRLVV IA  YR  GL
Sbjct: 97  DSLQLFLKDIGKVRLLTAQEEVDLAKRI-ERGDLDAKQKMVESNLRLVVSIAKNYRNQGL 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P  +++ EG +GL++A +KFD  +GF+ +TY+ WWI+ A+   +      ++I     +K
Sbjct: 156 PFLDLIQEGTLGLVRAAEKFDYRKGFKFSTYATWWIRQAIARALADKARTIRIPVHVVEK 215

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L ++    + +     +      IA    +   EV S+        SL   +   
Sbjct: 216 -----LNKIGRAERKLVTELGREPTAEEIADVTGIDPEEVDSIKRSAQAPVSLEKPV--G 268

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQEN 251
           D+  S++  ++    D + +   E+      +  L  ++  L+ RERR+ E R     E+
Sbjct: 269 DEEESEFGQFIA---DERAESPYERAAEILTKEALREALENLSYRERRVLELRYGLGGEH 325

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           P TL+ +   F V+RER+RQIE ++ KK+Q   + Q
Sbjct: 326 PRTLDEVGRTFNVTRERIRQIENQSLKKLQSLAEAQ 361


>gi|220936149|ref|YP_002515048.1| RNA polymerase, sigma 32 subunit, RpoH [Thioalkalivibrio sp.
           HL-EbGR7]
 gi|219997459|gb|ACL74061.1| RNA polymerase, sigma 32 subunit, RpoH [Thioalkalivibrio sp.
           HL-EbGR7]
          Length = 281

 Score =  238 bits (608), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 109/273 (39%), Positives = 162/273 (59%), Gaps = 7/273 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             L  YI  I ++P+L+ +EE  LA+  R+  DL AA +LV  +LR VV IA GY GYGL
Sbjct: 12  GSLDGYIQAITRLPVLDAEEEQRLARDLRDRQDLEAARKLVMHNLRFVVHIARGYSGYGL 71

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++ EGNIGLM+AVK+FDPE G RL ++++ WI+A + E+ILR+W +VK+ TT  Q+
Sbjct: 72  GLGDLIQEGNIGLMKAVKRFDPEMGVRLISFAVHWIRAEIHEFILRNWRIVKVATTKAQR 131

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN-ALIN 191
           +LFFNLR  K  L          E+V A+A  L V+ ++V+ M  RLAG D S + A  +
Sbjct: 132 KLFFNLRSAKQRLGWFN-----SEEVNAVADDLGVTPAQVLEMESRLAGQDVSFDPAPAS 186

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             D  S    + L+ +     + L   +   +    L   +  L+PR R I   R L E 
Sbjct: 187 DEDGPSLSPAETLIDESGDPAERLEADDWAAHHETRLHSGLEALDPRSRDIVARRWLTEQ 246

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL  L++E+ +S ERVRQ+E+ A +K++ S+
Sbjct: 247 KATLHELAAEYGISAERVRQLESNAMRKLRASL 279


>gi|226226576|ref|YP_002760682.1| RNA polymerase sigma factor [Gemmatimonas aurantiaca T-27]
 gi|226089767|dbj|BAH38212.1| RNA polymerase sigma factor [Gemmatimonas aurantiaca T-27]
          Length = 286

 Score =  238 bits (608), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 75/277 (27%), Positives = 139/277 (50%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E  L +Y+ +I   P++ ++EE  LA+R R+ GD  A  +LV S+LR VV +A  Y+  G
Sbjct: 14  EGSLDQYLRDISAYPLISREEEAELARRIRQ-GDQEALDKLVRSNLRFVVSVAKKYQNQG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           + +S++++EGN+GL++A +KFD  +G +  +Y++WWI+ A+ + +     +V++      
Sbjct: 73  VSLSDLINEGNLGLIRAARKFDETKGIKFISYAVWWIRQAILQALAEQSRIVRVPLNRA- 131

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 L R+     A+     +      IA  ++++E EV           SL+A +  
Sbjct: 132 ----GTLHRIGKRANALLQELGREATHAEIAHGMDITEEEVAKTMSISQVHLSLDAPLTP 187

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE-- 250
            + N       L Y  D       ++   K     +  S+  L  RE +I       +  
Sbjct: 188 GEDN-----RLLDYLPDTVHPTPEDQTFDKALTEAIEESLGGLKEREAKILRLYFGIDGA 242

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +P+TLE + S+  ++RERVRQI+ +A  +++   + +
Sbjct: 243 DPMTLEEIGSQLGITRERVRQIKEKALSRLRHVSRSK 279


>gi|317403353|gb|EFV83866.1| RNA polymerase sigma-70 factor [Achromobacter xylosoxidans C54]
          Length = 813

 Score =  238 bits (608), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 116/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 568 EAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 627

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T     P     +
Sbjct: 628 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGAEPDPAT---L 682

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+++ E ++  +        S+   I   D + S   D++    D       +     
Sbjct: 683 AQKMDMPEDKIRKILKIAKEPISMETPI--GDDDDSHLGDFI---EDTSTLAPSDAALHG 737

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 738 SMRDVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKL 797

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 798 RHPSRAD 804


>gi|158522485|ref|YP_001530355.1| RNA polymerase sigma 70 family subunit [Desulfococcus oleovorans
           Hxd3]
 gi|158511311|gb|ABW68278.1| putative RNA polymerase, sigma 70 family subunit [Desulfococcus
           oleovorans Hxd3]
          Length = 321

 Score =  238 bits (608), Expect = 7e-61,   Method: Composition-based stats.
 Identities = 101/277 (36%), Positives = 169/277 (61%), Gaps = 7/277 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG-YG 72
             L RY+ E+ +  +L +++E  L KR +E GD  AA+ L TS+LRLVVKIA+ ++  + 
Sbjct: 39  DPLQRYLKEVSRYNLLTREQEIELGKRVQEEGDEEAAYILATSNLRLVVKIALEFQRVWM 98

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
             + +++ EGNIGLM AV+KFDP +  + + Y+ +WIKA + ++++ +W LVKIGTT NQ
Sbjct: 99  QNLLDLIQEGNIGLMHAVQKFDPYKNVKFSYYASFWIKAYILKFVMDNWRLVKIGTTQNQ 158

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALIN 191
           ++LFF   RLK   QA+ D   +P   + +A++L V + EVI+M  RL   D SL+  + 
Sbjct: 159 RKLFF---RLKKEKQALIDQGFEPRPKL-LAERLGVPQKEVINMEQRLDMWDLSLDEPV- 213

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           S D ++ +     + +    ++ + +K  R+     L      L PRER IF+ R   + 
Sbjct: 214 SHDSDTQKGDLLDINNTQPVDEQVGDKALRQLVGEHLVEFKKTLTPRERDIFKTRIYTDQ 273

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           P+TL+++   + +SRERVRQ+E    KK+++  ++++
Sbjct: 274 PMTLQDIGERYAISRERVRQLEVNIIKKMRDFFKEKI 310


>gi|119026029|ref|YP_909874.1| RNA polymerase sigma factor [Bifidobacterium adolescentis ATCC
           15703]
 gi|118765613|dbj|BAF39792.1| RNA polymerase principal sigma factor; sigma 70 [Bifidobacterium
           adolescentis ATCC 15703]
          Length = 479

 Score =  238 bits (608), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 65/303 (21%), Positives = 138/303 (45%), Gaps = 39/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR---------------------------YREHGD 46
             +  Y+ +I ++ +L  ++E  L++R                           +  +  
Sbjct: 179 DPVKDYLKQIGRVNLLNAEQEVDLSERIEAGLYAQHLLDTESDKMDFKRRRELKWAANDG 238

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ 
Sbjct: 239 KRAKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYAT 298

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      +++     +  +   L R++  +         P+    +A++L
Sbjct: 299 WWIRQAITRAMADQARTIRVPVHMVE--VINKLSRVQRQMLQDLGREPTPD---ELAREL 353

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   +V  +        SL+  +   +   S++ D +    D       +       + 
Sbjct: 354 DMPVEKVQEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDTDAIAPSDAVAFSLLQE 408

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++   K++   
Sbjct: 409 QFKQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPS 468

Query: 285 QKQ 287
           + Q
Sbjct: 469 RSQ 471


>gi|298529795|ref|ZP_07017198.1| putative RNA polymerase, sigma 70 family subunit
           [Desulfonatronospira thiodismutans ASO3-1]
 gi|298511231|gb|EFI35134.1| putative RNA polymerase, sigma 70 family subunit
           [Desulfonatronospira thiodismutans ASO3-1]
          Length = 336

 Score =  238 bits (608), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 97/281 (34%), Positives = 175/281 (62%), Gaps = 8/281 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG-YG 72
             L  Y+ ++   P +  +EE+ LA+++R+ G+  AA  L+TS+LRLVVKIAM ++  + 
Sbjct: 55  DALRIYLRQVGNFPTMSAEEEFELARKFRDEGNQDAAFMLITSNLRLVVKIAMEFQRKWM 114

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
             + +++ EGN+GLM+A+KKFDP++G + + Y+ +WI+A + ++I+ +W +VK+GTT  Q
Sbjct: 115 KNVLDLIQEGNVGLMKALKKFDPDKGIKFSYYASFWIRAYILKFIMDNWRMVKVGTTQAQ 174

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALIN 191
           ++LF+NL + K  L+++           AI++ L+VSE++V+ M  RL   D SL+    
Sbjct: 175 RKLFYNLSKEKQRLESM----GITADADAISQSLDVSETDVVEMGQRLGQHDLSLDMP-- 228

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
            ++ +     + +    DG E++L++ E  +  +  +   M  L+ +E+ I E R L E+
Sbjct: 229 YNEDSDVTPMNVIPALGDGAEEILLQGETAQLLQQNIKELMPKLSDKEKDIIEMRLLAES 288

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
           PVTL  +  ++ ++RERVRQIE+R   K++  IQ+ ++  S
Sbjct: 289 PVTLREIGEKYGITRERVRQIESRLLGKIKAHIQENIDDFS 329


>gi|297569322|ref|YP_003690666.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfurivibrio
           alkaliphilus AHT2]
 gi|296925237|gb|ADH86047.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfurivibrio
           alkaliphilus AHT2]
          Length = 363

 Score =  238 bits (608), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 109/287 (37%), Positives = 175/287 (60%), Gaps = 8/287 (2%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
            + ++ V G   L RY+ EI +  +L + E   LA+ ++E GD  AA++LVT++LRLVVK
Sbjct: 68  DSANLPVVGNAALHRYLQEISQYRLLSRAETDELARLFKETGDPEAAYKLVTANLRLVVK 127

Query: 64  IAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           +AM ++ Y +    +++ EGNIGL+QAVKKFDP R  + + Y+ +WI+A + ++I+ +W 
Sbjct: 128 VAMDFQKYWMQNFLDLIQEGNIGLVQAVKKFDPYRQVKFSYYAAYWIRAYILKFIMDNWR 187

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           LVKIGTT  Q++LFF+L + K  L++      KPE  + +A++LNV ESEVI M+ R+  
Sbjct: 188 LVKIGTTQAQRKLFFSLNKEKKLLES---QGFKPEPKL-LAQRLNVKESEVIEMSQRMDN 243

Query: 183 -DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
            D SL + +     +  + +D+L       E+ +   E R+    +L +    LN +E  
Sbjct: 244 WDMSLESPMREDSGD--ERKDFLPVAGPSVEERVAADEVREWMAGILDKMRRTLNEKELA 301

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           I   R L + P TL+ ++  F +SRERVRQIEA   KK++  ++ +V
Sbjct: 302 ILRERLLSDEPATLQEIADRFAISRERVRQIEANLLKKMRTYLENEV 348


>gi|77165402|ref|YP_343927.1| RpoH [Nitrosococcus oceani ATCC 19707]
 gi|254433859|ref|ZP_05047367.1| alternative sigma factor RpoH [Nitrosococcus oceani AFC27]
 gi|76883716|gb|ABA58397.1| RNA polymerase, sigma 32 subunit, RpoH [Nitrosococcus oceani ATCC
           19707]
 gi|207090192|gb|EDZ67463.1| alternative sigma factor RpoH [Nitrosococcus oceani AFC27]
          Length = 287

 Score =  238 bits (607), Expect = 8e-61,   Method: Composition-based stats.
 Identities = 108/284 (38%), Positives = 167/284 (58%), Gaps = 7/284 (2%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
             N +++      L+ Y      IP+L  ++E  LA R R+H DL AA +LV SHLR V+
Sbjct: 7   NDNGALVPVAVGNLNTYCQNAHSIPVLSAEQERSLALRLRQHNDLEAARQLVLSHLRFVI 66

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           +IA GY GYGLP+++++ EGNIGLM+AVK+FDPE+G RL ++++ WI+A + E+ILR+W 
Sbjct: 67  RIARGYNGYGLPLADLIQEGNIGLMKAVKRFDPEQGVRLVSFAVHWIRAEIHEFILRNWR 126

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR  K  L  +        +V  +A+ L VS  +V+ M  RL+ 
Sbjct: 127 IVKVATTKAQRKLFFNLRSAKKRLGWLNRK-----EVDEVAQDLGVSPKQVMEMEARLSS 181

Query: 183 -DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR-NMLTRSMSVLNPRER 240
            D   +       +N        + D        +E  +++N     L +++ VL+ R R
Sbjct: 182 QDAPFDGSNAEESENGIPAPMAYLADPSADPAQKMELLDQENYYGQRLQQALEVLDLRSR 241

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            I   R LQEN  TL  L++E+++S ER+RQ+E  A KK++  +
Sbjct: 242 TIINRRWLQENKSTLHELAAEYQISAERIRQLENNAIKKMRSVL 285


>gi|225159269|ref|ZP_03725570.1| RNA polymerase, sigma 70 subunit, RpoD family [Opitutaceae
           bacterium TAV2]
 gi|224802166|gb|EEG20437.1| RNA polymerase, sigma 70 subunit, RpoD family [Opitutaceae
           bacterium TAV2]
          Length = 373

 Score =  238 bits (607), Expect = 9e-61,   Method: Composition-based stats.
 Identities = 87/274 (31%), Positives = 150/274 (54%), Gaps = 12/274 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+ EI K P+L   EE  LA+R R  GD +A   +++++LRLVVKIAM Y+ +GLP
Sbjct: 60  NLQLYLQEIGKTPLLTLDEEVTLARRIR-RGDKAARDHMISANLRLVVKIAMDYKDFGLP 118

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++SEGNIGL++AV++FDP +G +L+TY+ WWIK +++  +      +++        
Sbjct: 119 LLDLISEGNIGLVKAVERFDPRKGGKLSTYAAWWIKQSIKRALANQSKTIRLPVH----- 173

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           L   + R++    A+T+   +      IA +L +  S+V  +        SL+A +   +
Sbjct: 174 LVDKIARMRRTAMALTEQLGREPSDEEIAMELQIPTSKVAHLKSVSVRPASLDAPV--GE 231

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NP 252
              S     LV D +       E  + ++R   L   +  L PRE  I   R   +  + 
Sbjct: 232 DGDSSTFGELVGDENAV--SPFESLKERSRNADLKEMVDSLEPREAEIIRYRFGLDGRDE 289

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +TLE +  +F+V+RERVRQ++  A  K+++++ +
Sbjct: 290 LTLEEVGQKFKVTRERVRQLQNLALSKMRKAMSR 323


>gi|71892394|ref|YP_278128.1| RNA polymerase factor sigma-32 [Candidatus Blochmannia
           pennsylvanicus str. BPEN]
 gi|71796500|gb|AAZ41251.1| RNA polymerase sigma-32 factor [Candidatus Blochmannia
           pennsylvanicus str. BPEN]
          Length = 282

 Score =  238 bits (607), Expect = 9e-61,   Method: Composition-based stats.
 Identities = 106/284 (37%), Positives = 165/284 (58%), Gaps = 9/284 (3%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +KN+++I  G   L  YI       ML  +EE  LAKR   +GDL AA +L+ SHLR VV
Sbjct: 6   QKNVTLIPQG--NLEAYIKVANAYTMLTAEEEKTLAKRLYYNGDLDAAKKLIVSHLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            ++  Y GYGLP ++++ EGNIGLM+AV++F+PE   RL ++++ WIK+ + EY+L++W 
Sbjct: 64  HVSRNYSGYGLPQADLIQEGNIGLMKAVRRFNPELDVRLVSFAVHWIKSEIHEYVLKNWR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VKI TT  Q++LFFNLR+ K  L           ++  +AK LNV+  +V  M  R++ 
Sbjct: 124 IVKIATTKAQRKLFFNLRKTKQRLGWFNAG-----EIEIVAKALNVTSKDVREMESRMSA 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
            + +    +S + N       ++Y  D       E+E      + L  ++  L+ R + I
Sbjct: 179 -QDMTFEQSSDEDNRGITIAPILYLQDKIVSSNEEEEWIDQVSDKLNAAIKTLDERSQHI 237

Query: 243 FEARRLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             AR L  +N  TL+ L++++ VS ERVRQ+E  A KK++  IQ
Sbjct: 238 IRARWLNVDNKSTLQELANQYGVSAERVRQLEKNAMKKMKLIIQ 281


>gi|300721688|ref|YP_003710964.1| sigma H (sigma 32) factor of RNA polymerase [Xenorhabdus
           nematophila ATCC 19061]
 gi|297628181|emb|CBJ88736.1| sigma H (sigma 32) factor of RNA polymerase; transcription of heat
           shock and stress proteins [Xenorhabdus nematophila ATCC
           19061]
          Length = 285

 Score =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 105/290 (36%), Positives = 167/290 (57%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  YI      PML  +EE  LA+R    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLALVPQGSLEGYIRASNTYPMLSAEEERELAERLHYQGDLDAAKKLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARSYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          +++  +AK+L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKAKQRLGWFNQ-----DEIELVAKELGVTSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNP 237
           +  +    +    D + SQ    ++Y  D        + E     +  + L+ +M  L+ 
Sbjct: 176 SAQDMAFDMSADDDNHDSQPVAPVLYLQDKASDFADGIEEDNWENHAADKLSVAMEGLDE 235

Query: 238 RERRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L + N  TL+ L+ ++ VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQDIIRARWLDDENKTTLQELADKYGVSAERVRQLEKNAMKKLRLAIEA 285


>gi|56416805|ref|YP_153879.1| RNA polymerase sigma-32 factor [Anaplasma marginale str. St.
           Maries]
 gi|56388037|gb|AAV86624.1| RNA polymerase sigma-32 factor [Anaplasma marginale str. St.
           Maries]
          Length = 290

 Score =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 129/276 (46%), Positives = 190/276 (68%), Gaps = 4/276 (1%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           G   L  Y+ ++R  P+L ++EE  LA+ +   G ++ AHRLVTSHLRLVVKIAMG++ Y
Sbjct: 11  GSDDLVSYVAQVRTFPILSEEEEKRLAENWYRRGSVADAHRLVTSHLRLVVKIAMGFKSY 70

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GLPI E++ EGNIGLMQAVK+F+P+ GFRLATY++WWIKA++++YILRSWS +++GTT  
Sbjct: 71  GLPIMELIMEGNIGLMQAVKRFNPDLGFRLATYAVWWIKASIKDYILRSWSCIRVGTTQA 130

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALI 190
           QK+LFF+LR++K  L +   +++  +++ AIA++   SE EV  M+   A  D SLN  +
Sbjct: 131 QKKLFFSLRKIKKRLLSC-GSSMTKKEIKAIAEECATSEEEVERMDRFFANRDVSLNEQV 189

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           +   ++S + QD +      QE + +  EE   +++M   +++ L+ R R IF  RRLQE
Sbjct: 190 HG--ESSVELQDLVPSSLPSQEIMYLADEESAIKKSMFDSALATLDDRHRDIFTRRRLQE 247

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            P TLE LS E+ VS+ERVRQIE +A  K++  I+ 
Sbjct: 248 RPDTLEKLSEEYGVSKERVRQIELQALCKIKSFIEA 283


>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 =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 75/270 (27%), Positives = 125/270 (46%), Gaps = 14/270 (5%)

Query: 22  EIRKIPMLEKQE--EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           E+ K   L   E  E   A  Y E     A   +V ++LRLV+ IA  Y   GL   +++
Sbjct: 356 EMEKASYLTLGEIKEISRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 415

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L
Sbjct: 416 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKL 473

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
            R+   +         PE    +AK++++ E ++  +        S+   I   D   S 
Sbjct: 474 NRISRQMLQQFGREATPE---ELAKEMDMPEDKIRKVMKIAKEPISMETPI--GDDEDSH 528

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLEN 257
             D++    D   +  I+     N    +   ++ L PRE ++   R   +     TLE 
Sbjct: 529 LGDFI---EDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEE 585

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 586 VGKQFDVTRERIRQIEAKALRKLRHPSRSE 615


>gi|28199909|ref|NP_780223.1| RNA polymerase factor sigma-32 [Xylella fastidiosa Temecula1]
 gi|28058040|gb|AAO29872.1| RNA polymerase sigma-32 factor [Xylella fastidiosa Temecula1]
          Length = 293

 Score =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 114/275 (41%), Positives = 168/275 (61%), Gaps = 9/275 (3%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           + N    L  YI  + +I +L   EE +LA+RYR+  DL AA  LV SHLR VV++A GY
Sbjct: 21  VPNALGSLEAYISAVHQISVLSVDEEQLLARRYRDQQDLDAARELVHSHLRFVVRVARGY 80

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGL + +++ EGNIGLM+AVK+FDP+ G RL +++M WI+A M E+IL++W +VK+ T
Sbjct: 81  SGYGLSLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAMHWIRAEMHEFILKNWRIVKVAT 140

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN 187
           T  Q++LFFNLR+ +  L       +  E+V A+A+ LNVSE EV+ M  RL+G D   +
Sbjct: 141 TKAQRKLFFNLRKSRTRLGW-----MNAEEVSAVARDLNVSEREVLEMESRLSGRDIGFD 195

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           A     D        +L+ +     Q        + +  +L   +SVL+ R R I + R 
Sbjct: 196 AP--EEDNAPPSPVGYLIANDGDPSQAYERGNSEETQLRLLQEGLSVLDTRSRDIIQRRW 253

Query: 248 LQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           L+ +  +TL+ L+ E+ VS ER+RQIEA A KK++
Sbjct: 254 LETDKKITLQELAEEYGVSAERIRQIEANALKKMK 288


>gi|87121174|ref|ZP_01077065.1| sigma factor RpoH [Marinomonas sp. MED121]
 gi|86163666|gb|EAQ64940.1| sigma factor RpoH [Marinomonas sp. MED121]
          Length = 291

 Score =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 104/272 (38%), Positives = 158/272 (58%), Gaps = 7/272 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  YI  +  IP+L  ++E  LA+R    GDL AA +LV SHLR VV IA  Y GYGL 
Sbjct: 16  NLESYIQAVSTIPILTAEDENKLAERLYYDGDLEAARQLVMSHLRFVVHIAKSYSGYGLN 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
             +++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+IL++W +VK+ TT  Q++
Sbjct: 76  QGDLIQEGNVGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEFILKNWRIVKVATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSS 193
           +FFNLR  K  L   ++     ++V ++A  L VS   V  M  R+ + D + +A  +  
Sbjct: 136 MFFNLRSAKKTLSWFSN-----DEVESVAGDLGVSPEVVRQMEGRMSSSDTTFDASSDDD 190

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEK-EERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
           D ++ Q     + DH      L E     ++    L  +MS L+ R R I   R L ++ 
Sbjct: 191 DDSAYQAPANYLEDHRYDPASLTENGNWEEDSNRRLQEAMSELDERSRNILVQRWLSDSK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL +L+ E+ VS ER+RQ+E  A  K++ S+
Sbjct: 251 STLHDLADEYGVSAERIRQLEKNAMAKIRTSM 282


>gi|289178873|gb|ADC86119.1| HrdB [Bifidobacterium animalis subsp. lactis BB-12]
          Length = 522

 Score =  238 bits (607), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 68/303 (22%), Positives = 138/303 (45%), Gaps = 39/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------HGD----------------- 46
             +  Y+ +I ++ +L  ++E  L++R              GD                 
Sbjct: 222 DPVKDYLKQIGRVSLLNAEQEVDLSERIEAGLYAQHLLDTEGDTMEFRRKRELKWAAADG 281

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ 
Sbjct: 282 KKAKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYAT 341

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      +++     +  +   L R++  +         P+    +A++L
Sbjct: 342 WWIRQAITRAMADQARTIRVPVHMVE--VINKLSRVQRQMLQDLGREPTPD---ELAREL 396

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   +V  +        SL+  +   +   S++ D +    D       E       + 
Sbjct: 397 DMPVEKVQEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDTDAIAPSEAVAFSLLQE 451

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++   K++   
Sbjct: 452 QFRQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPS 511

Query: 285 QKQ 287
           + Q
Sbjct: 512 RSQ 514


>gi|171742642|ref|ZP_02918449.1| hypothetical protein BIFDEN_01756 [Bifidobacterium dentium ATCC
           27678]
 gi|171278256|gb|EDT45917.1| hypothetical protein BIFDEN_01756 [Bifidobacterium dentium ATCC
           27678]
          Length = 461

 Score =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 65/303 (21%), Positives = 138/303 (45%), Gaps = 39/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR---------------------------YREHGD 46
             +  Y+ +I ++ +L  ++E  L++R                           +  +  
Sbjct: 161 DPVKDYLKQIGRVSLLNAEQEVDLSERIEAGLYAQHLLDTEASQMDFKRRRELKWAANDG 220

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ 
Sbjct: 221 KKAKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYAT 280

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      +++     +  +   L R++  +         P+    +A++L
Sbjct: 281 WWIRQAITRAMADQARTIRVPVHMVE--VINKLSRVQRQMLQDLGREPTPD---ELAREL 335

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   +V  +        SL+  +   +   S++ D +    D       +       + 
Sbjct: 336 DMPVEKVQEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDTDAIAPSDAVAFSLLQE 390

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++   K++   
Sbjct: 391 QFKQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPS 450

Query: 285 QKQ 287
           + Q
Sbjct: 451 RSQ 453


>gi|239621277|ref|ZP_04664308.1| RNA polymerase principal sigma factor [Bifidobacterium longum
           subsp. infantis CCUG 52486]
 gi|239515738|gb|EEQ55605.1| RNA polymerase principal sigma factor [Bifidobacterium longum
           subsp. infantis CCUG 52486]
          Length = 488

 Score =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 65/303 (21%), Positives = 137/303 (45%), Gaps = 39/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR---------------------------YREHGD 46
             +  Y+ +I ++ +L  ++E  L++R                           +     
Sbjct: 188 DPVKDYLKQIGRVSLLNAEQEVDLSERIEAGLYAQHLLDTESEGMEFKRKRELKWAAADG 247

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ 
Sbjct: 248 KKAKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYAT 307

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      +++     +  +   L R++  +         P+    +A++L
Sbjct: 308 WWIRQAITRAMADQARTIRVPVHMVE--VINKLSRVQRQMLQDLGREPTPD---ELAREL 362

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   +V  +        SL+  +   +   S++ D +    D       +       + 
Sbjct: 363 DMPVEKVQEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDTDAIAPSDAVAFSLLQE 417

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++   K++   
Sbjct: 418 QFKQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPS 477

Query: 285 QKQ 287
           + Q
Sbjct: 478 RSQ 480


>gi|295098975|emb|CBK88064.1| RNA polymerase, sigma 70 subunit, RpoD [Eubacterium cylindroides
           T2-87]
          Length = 368

 Score =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 76/301 (25%), Positives = 140/301 (46%), Gaps = 36/301 (11%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------------HGDLS 48
             +  Y+ EI +IP+L+ +EE ++AKR ++                              
Sbjct: 69  DPVKMYLKEIGQIPLLDPKEEPIIAKRIQDGEAAKKKLEEPDLDIEERKKLASVVADGEE 128

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L++S+LRLVV IA  Y G G+   +++ EGN GL++AV+KFD  +GF+ +TY+ WW
Sbjct: 129 AKQVLISSNLRLVVSIAKKYVGRGMLFLDLIQEGNCGLIKAVEKFDYTKGFKFSTYATWW 188

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ ++   I      ++I     +      L R++  L      +  PE++    +  N+
Sbjct: 189 IRQSITRAIADQARTIRIPVHMVE--TINKLTRIQRQLVQDLGRDPLPEEIAEKME--NI 244

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +  +V  +        SL   I   +++ S   D++    D +     +    +  ++ +
Sbjct: 245 TADKVREIQKIALDPVSLETPI--GEEDDSHLGDFI---EDKETLSPDDYTNNQLLKDEI 299

Query: 229 TRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +  L  RE ++   R    +    TLE +  EF V+RER+RQIEA+A +K++   + 
Sbjct: 300 NNVLQGLTEREEKVLRLRFGLMDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLKHPNRS 359

Query: 287 Q 287
           +
Sbjct: 360 K 360


>gi|33863540|ref|NP_895100.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str. MIT
           9313]
 gi|33640989|emb|CAE21447.1| Putative principal RNA polymerase sigma factor [Prochlorococcus
           marinus str. MIT 9313]
          Length = 461

 Score =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 79/313 (25%), Positives = 143/313 (45%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE--------------HG------------ 45
            E  +  Y+ EI +I +L   EE  LA++  +              HG            
Sbjct: 149 TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLHLEELAEQFNSDHGHYPNNKEWASLV 208

Query: 46  -------------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 209 EMPNIKFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 268

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 269 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKVLSQE 323

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA+ + ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 324 FGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIESDTENPE 381

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
           Q + +   R++    L   ++ L+PRER +   R   ++    TLE +   FEV+RER+R
Sbjct: 382 QDVAKNLLRED----LEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFEVTRERIR 437

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 438 QIEAKALRKLRHP 450


>gi|154488794|ref|ZP_02029643.1| hypothetical protein BIFADO_02101 [Bifidobacterium adolescentis
           L2-32]
 gi|154082931|gb|EDN81976.1| hypothetical protein BIFADO_02101 [Bifidobacterium adolescentis
           L2-32]
          Length = 478

 Score =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 65/303 (21%), Positives = 138/303 (45%), Gaps = 39/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR---------------------------YREHGD 46
             +  Y+ +I ++ +L  ++E  L++R                           +  +  
Sbjct: 178 DPVKDYLKQIGRVNLLNAEQEVDLSERIEAGLYAQHLLDTESDKMDFKRRRELKWAANDG 237

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ 
Sbjct: 238 KRAKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYAT 297

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      +++     +  +   L R++  +         P+    +A++L
Sbjct: 298 WWIRQAITRAMADQARTIRVPVHMVE--VINKLSRVQRQMLQDLGREPTPD---ELAREL 352

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   +V  +        SL+  +   +   S++ D +    D       +       + 
Sbjct: 353 DMPVEKVQEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDTDAIAPSDAVAFSLLQE 407

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++   K++   
Sbjct: 408 QFKQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPS 467

Query: 285 QKQ 287
           + Q
Sbjct: 468 RSQ 470


>gi|262369666|ref|ZP_06062994.1| RNA polymerase factor sigma-32 [Acinetobacter johnsonii SH046]
 gi|262315734|gb|EEY96773.1| RNA polymerase factor sigma-32 [Acinetobacter johnsonii SH046]
          Length = 289

 Score =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 109/284 (38%), Positives = 166/284 (58%), Gaps = 9/284 (3%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +S+   G + L  YI  + +IP+L  ++E  LA+RY    DL AA  LV SHLR VV IA
Sbjct: 11  LSLSAPG-VNLGAYISTVNQIPILTAEQEKELAERYYYDQDLDAAKLLVMSHLRFVVHIA 69

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGLP  +++ EGN+GLM+AVK+FDP  G RL ++++ WIKA + EY++R+W +VK
Sbjct: 70  RSYAGYGLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVK 129

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDE 184
           I TT  Q++LFFNLR         +   L  ++  +IA  LNV+  +V+ M  RL A D 
Sbjct: 130 IATTKAQRKLFFNLR-----SLKKSSKKLTLKEAQSIANDLNVTPEQVLEMEGRLTAYDA 184

Query: 185 SLNALINSSDKNSSQ-WQDWLVYDHDGQEQVLIEKEERKNRR-NMLTRSMSVLNPRERRI 242
           +  A  +  D+ S+       + D+      L E+E+ + +  N L  +M  L+ R R I
Sbjct: 185 AFEAQGDDDDEGSTHVAPALYLEDNRYDPARLAEEEDYEEQSTNALHDAMEQLDDRSRNI 244

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + R L +   TL  L++E+ VS ER+RQ+E  A +K++ ++  
Sbjct: 245 LQRRWLDDEKSTLHELAAEYNVSAERIRQLEKNAMEKIKVAMSS 288


>gi|221632805|ref|YP_002522027.1| sigma factor MysA [Thermomicrobium roseum DSM 5159]
 gi|221156346|gb|ACM05473.1| sigma factor MysA [Thermomicrobium roseum DSM 5159]
          Length = 369

 Score =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 84/302 (27%), Positives = 142/302 (47%), Gaps = 38/302 (12%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR---------EHGD-------------- 46
           ++    +  Y+ EI +  +L  QEE  LA+R           E GD              
Sbjct: 67  LSTSDTVRLYLQEIGETALLTPQEEVWLAQRIERGKIAKVRLERGDYKSEDERLALVADK 126

Query: 47  ---LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
                A   L+ ++LRLVV +A  Y G GL   +++ EGNIGLM+A +KFD +RG++ +T
Sbjct: 127 EDGERARAHLIQANLRLVVSVAKKYVGRGLSFLDLIQEGNIGLMKATEKFDYKRGYKFST 186

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI+ A+   I      +++     +      ++++   LQ I +        + +A
Sbjct: 187 YATWWIRQAITRAISDQSRTIRLPVHVGE--TINRIKKISHRLQQILEREPTQ---LEVA 241

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + L++ E ++  +        SL A I       +   D++    D  +   +E   ++ 
Sbjct: 242 RALDMPEEKIRQILEAARLPVSLEAPI--GQDGDAFLGDFI---EDETQPAPLEIASQQL 296

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R  L  ++S L  RERRI   R   E+    TLE +  EF ++RER+RQIEA+A +K++
Sbjct: 297 LRQQLEEALSRLTERERRIIILRYGLEDGQFRTLEEVGREFGITRERIRQIEAKALRKLR 356

Query: 282 ES 283
             
Sbjct: 357 HP 358


>gi|319407753|emb|CBI81400.1| RNA polymerase sigma-32 factor [Bartonella sp. 1-1C]
          Length = 303

 Score =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 107/276 (38%), Positives = 176/276 (63%), Gaps = 2/276 (0%)

Query: 11  NGEIGLSR-YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           N +  L R  +   ++ P LE+++E+ LA R++   D +A H++  +H+RLV+ IA  ++
Sbjct: 17  NTDTSLGRNMMRSAKQAPYLERKKEHDLALRWKNKRDDNAMHQIAAAHMRLVISIASRFK 76

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
            + +P+ ++V EG +GL++A  +FDP+RG R +TY+ WWI+A++Q+YILR+WS+V+ GT+
Sbjct: 77  RFKMPLGDLVQEGYVGLLEAAARFDPDRGVRFSTYATWWIRASIQDYILRNWSIVRGGTS 136

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNA 188
           ++QK LFFNLRRL+  L    +   K E   AI++KL VS ++V  M+ R +G D SL+ 
Sbjct: 137 SSQKALFFNLRRLRAKLAQDDNTLTKQEIFRAISEKLGVSVNDVEKMDFRFSGTDNSLSL 196

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            I+ + +      D L+ DH   + V+ +  + + R   L  ++ +LN RE  I   RRL
Sbjct: 197 SISENGETPIAKMDSLIDDHPLPDSVIEQAIDGQRRAQWLHEALQILNERELEIIRFRRL 256

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            E   TLE L  +  +S+ERVRQIEARA +K++ ++
Sbjct: 257 NEEGTTLEVLGEKLGISKERVRQIEARALQKLRCAL 292


>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 =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 66/241 (27%), Positives = 113/241 (46%), Gaps = 12/241 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 611 AKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 670

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I            + R+   +   T     P     +A K+ +
Sbjct: 671 IRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGAEPDPAT---LAIKMEM 725

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +        S+   I   D + S   D++    D       +     + RN++
Sbjct: 726 PEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDNNTLAPADAALHASMRNVV 780

Query: 229 TRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   + 
Sbjct: 781 KDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 840

Query: 287 Q 287
            
Sbjct: 841 D 841


>gi|104779584|ref|YP_606082.1| RNA polymerase factor sigma-32 [Pseudomonas entomophila L48]
 gi|95108571|emb|CAK13265.1| sigma H (sigma 32) factor of RNA polymerase RpoH [Pseudomonas
           entomophila L48]
          Length = 284

 Score =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 101/272 (37%), Positives = 156/272 (57%), Gaps = 7/272 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+H +  IP+L  ++E  L +R     DL AA ++V +HLR VV IA  Y GYGL 
Sbjct: 16  NLEAYVHTVNSIPLLTPEQERDLGERLYYEQDLEAARQMVMAHLRFVVHIARSYAGYGLA 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++
Sbjct: 76  QADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           LFFNLR  K  L  + +     ++V  +A+ L V   EV  M  RL+G +      + +D
Sbjct: 136 LFFNLRSQKKRLAWLNN-----DEVHRVAESLGVEPREVREMESRLSGQDMAFDPASEAD 190

Query: 195 KNSS-QWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENP 252
            +S+ Q     + DH     + +E  +  +  +  L  ++  L+ R R I   R L E  
Sbjct: 191 DDSAFQSPAHYLEDHRYDPALQLEDADWSDNSSSNLHEALQGLDDRSRDILYQRWLAEEK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL  L+ ++ VS ER+RQ+E  A  KV+  I
Sbjct: 251 ATLHELAEKYSVSAERIRQLEKNAMNKVKALI 282


>gi|15839280|ref|NP_299968.1| RNA polymerase factor sigma-32 [Xylella fastidiosa 9a5c]
 gi|9107932|gb|AAF85488.1|AE004075_3 RNA polymerase sigma-32 factor [Xylella fastidiosa 9a5c]
          Length = 293

 Score =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 114/275 (41%), Positives = 168/275 (61%), Gaps = 9/275 (3%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           + N    L  YI  + +I +L   EE +LA+RYR+  DL AA  LV SHLR VV++A GY
Sbjct: 21  VPNALGSLEAYISAVHQISVLSVDEEQLLARRYRDQQDLDAARELVHSHLRFVVRVARGY 80

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGL + +++ EGNIGLM+AVK+FDP+ G RL +++M WI+A M E+IL++W +VK+ T
Sbjct: 81  SGYGLSLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAMHWIRAEMHEFILKNWRIVKVAT 140

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN 187
           T  Q++LFFNLR+ +  L       +  E+V A+A+ LNVSE EV+ M  RL+G D   +
Sbjct: 141 TKAQRKLFFNLRKSRTRLGW-----MNAEEVSAVARDLNVSEREVLEMESRLSGRDIGFD 195

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           A     D        +L+ +     Q        + +  +L   +SVL+ R R I + R 
Sbjct: 196 AP--EEDNAPPSPVGYLIANDGDPSQAYERGNSEETKLRLLQEGLSVLDTRSRDIIQRRW 253

Query: 248 LQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           L+ +  +TL+ L+ E+ VS ER+RQIEA A KK++
Sbjct: 254 LETDKKITLQELAEEYGVSAERIRQIEANALKKMK 288


>gi|160871836|ref|ZP_02061968.1| alternative sigma factor RpoH [Rickettsiella grylli]
 gi|159120635|gb|EDP45973.1| alternative sigma factor RpoH [Rickettsiella grylli]
          Length = 290

 Score =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 109/278 (39%), Positives = 169/278 (60%), Gaps = 14/278 (5%)

Query: 17  SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
             YI  +++IP+L  +EE  LA+RY +H DL AA +L+ ++LR VV IA  Y GYGL ++
Sbjct: 18  DAYITRLKQIPVLSAEEEIELAERYYQHHDLDAAKKLIITNLRFVVHIAQTYMGYGLALA 77

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++ EGNIGLM+AVK+FDP+ G RL ++++ WIKA +QE+ILR+W +VKI TT  Q++LF
Sbjct: 78  DLIQEGNIGLMKAVKRFDPKVGVRLISFAVHWIKAEIQEFILRNWRIVKIATTKAQRKLF 137

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDK 195
           FNLR++K  L     N     ++ A+A  L V    V  M  RLA  D SL+  I+  D 
Sbjct: 138 FNLRKMKKRLGWFNQN-----EIEAVAHDLGVKPETVREMEFRLASNDMSLD--ISHDDP 190

Query: 196 NSS-----QWQDWLVYDHDGQEQVLIEKE-ERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           N +        D    D+      L+E     ++  + L ++++ L+ RE+ I   R L 
Sbjct: 191 NEAKSTRYPLLDIHFEDNRYDPARLLEASNSTESNHDNLYKALTQLDEREQNIIRDRWLM 250

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E  +TL+ L+  + VS ER+RQ+E +A K ++ ++ +Q
Sbjct: 251 EPKMTLQELAQRYHVSAERIRQLEQKAMKALRHTLLQQ 288


>gi|325275633|ref|ZP_08141532.1| RNA polymerase factor sigma-32 [Pseudomonas sp. TJI-51]
 gi|313501084|gb|ADR62450.1| RpoH [Pseudomonas putida BIRD-1]
 gi|324099220|gb|EGB97167.1| RNA polymerase factor sigma-32 [Pseudomonas sp. TJI-51]
          Length = 284

 Score =  237 bits (606), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 101/272 (37%), Positives = 154/272 (56%), Gaps = 7/272 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+H +  IP+L  ++E  L +R     D+ AA ++V +HLR VV IA  Y GYGL 
Sbjct: 16  NLEAYVHTVNSIPLLTVEQERDLGERLYYQQDVEAARQMVMAHLRFVVHIARSYAGYGLA 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++
Sbjct: 76  QADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           LFFNLR  K  L  + +     ++V  +A+ L V   EV  M  RL+G +        +D
Sbjct: 136 LFFNLRSQKKRLAWLNN-----DEVHRVAESLGVEPREVREMESRLSGQDMAFDPAAEAD 190

Query: 195 KNSS-QWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENP 252
            +S+ Q     + DH     V +E  +  +     L  ++  L+ R R I   R L E  
Sbjct: 191 DDSAFQSPAHYLEDHRYDPAVQLEDADWSDNSTSNLHEALQGLDERSRDILYQRWLAEEK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL  L+ ++ VS ER+RQ+E  A  KV+  I
Sbjct: 251 ATLHELADKYSVSAERIRQLEKNAMNKVKALI 282


>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 =  237 bits (605), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 75/270 (27%), Positives = 127/270 (47%), Gaps = 14/270 (5%)

Query: 22  EIRKIPMLEKQEEYVL--AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           +I K+  L+  +   L  A  Y E     A   +V ++LRLV+ IA  Y   GL   +++
Sbjct: 350 DIEKLTQLDLDDLKELSRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 409

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L
Sbjct: 410 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKL 467

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
            R+   +         PE    +AK++++ E ++  +        S+   I   D   S 
Sbjct: 468 NRISRQMLQQYGREATPE---ELAKEMDMPEDKIRKVMKIAKEPISMETPI--GDDEDSH 522

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLEN 257
             D++    D   +  IE     N    +   ++ L PRE ++   R   +     TLE 
Sbjct: 523 LGDFI---EDTNVESPIENTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEE 579

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 580 VGKQFDVTRERIRQIEAKALRKLRHPSRSE 609


>gi|124268355|ref|YP_001022359.1| RNA polymerase sigma-32 factor [Methylibium petroleiphilum PM1]
 gi|124261130|gb|ABM96124.1| RNA polymerase sigma-32 factor [Methylibium petroleiphilum PM1]
          Length = 319

 Score =  237 bits (605), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 109/291 (37%), Positives = 164/291 (56%), Gaps = 11/291 (3%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +V     L+ YI  + ++PML  +EE  L +R R+  DL AA RLV SHLRLVV ++  Y
Sbjct: 29  LVPSLGDLNAYIAAVNRLPMLTLEEEQSLGQRLRDEHDLEAAGRLVLSHLRLVVSVSRQY 88

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGLP  +++ EGN+GLM+AVK+FDP +G RL +Y++ WIKA + EY+LR+W +VK+ T
Sbjct: 89  LGYGLPHGDLIQEGNVGLMKAVKRFDPSQGVRLVSYALHWIKAEIHEYVLRNWRMVKLAT 148

Query: 129 TANQKRLFFNLRRLKGHLQ------AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           T  Q++LFFNLR +K   +       +  + L   ++  +A +L V   EVI M  RL+G
Sbjct: 149 TKAQRKLFFNLRSMKQGFKGDATDSDLHRSTLTDAEIDIVASELKVKREEVIEMETRLSG 208

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
            +            S     +L  D     +VL  +       + +  ++ VL+ R RRI
Sbjct: 209 GDVALDPQTDDGDESYAPIAYLADDRHEPTRVLDAQRRDALAGDGIGEALDVLDARSRRI 268

Query: 243 FEARRL-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            E R L         +TL  L++E+ VS ER+RQIE  A KK+++++    
Sbjct: 269 VEERWLKVNDNGSGGMTLHELAAEYGVSAERIRQIEVAAMKKMRKALAAYA 319


>gi|94265020|ref|ZP_01288789.1| Sigma-70 region 2 [delta proteobacterium MLMS-1]
 gi|94270029|ref|ZP_01291635.1| Sigma-70 region 2 [delta proteobacterium MLMS-1]
 gi|93450968|gb|EAT01953.1| Sigma-70 region 2 [delta proteobacterium MLMS-1]
 gi|93454509|gb|EAT04794.1| Sigma-70 region 2 [delta proteobacterium MLMS-1]
          Length = 337

 Score =  237 bits (605), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 115/284 (40%), Positives = 178/284 (62%), Gaps = 8/284 (2%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           ++ V G   L RY+ EI +  +L ++E   LA+R++E GD  AA++LVT++LRLVVK+AM
Sbjct: 41  NLPVVGNAALHRYLQEISQYRLLSREETDELARRFQESGDPDAAYQLVTANLRLVVKVAM 100

Query: 67  GYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            ++ Y +    +++ EGNIGL+QAVKKFDP R  + + Y+ +WI+A + ++I+ +W LVK
Sbjct: 101 DFQKYWMQNFLDLIQEGNIGLVQAVKKFDPYRQVKFSYYAAYWIRAYILKFIMDNWRLVK 160

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDE 184
           IGTT  Q++LFFNL + K  L+A         +   +A++LNV ESE+I M  RL  GD 
Sbjct: 161 IGTTQAQRKLFFNLNKEKKLLEA----QGFEPEPKLLAQRLNVKESEIIEMGQRLEHGDM 216

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL + +   + +  Q +D+L     G EQ + E E R+    ML +    LN +E  I +
Sbjct: 217 SLESPLR--EDSDEQRKDFLPMLGPGVEQRVAEDEIRQWMAAMLDKLRLTLNEKELAILD 274

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            R L ++P TL+ ++  F +SRERVRQIEA   KK++  ++ +V
Sbjct: 275 QRLLNDDPRTLQEIADRFTISRERVRQIEANLLKKMRLYLENEV 318


>gi|303327038|ref|ZP_07357480.1| deoxyuridine 5`-triphosphate nucleotidohydrolase [Desulfovibrio sp.
           3_1_syn3]
 gi|302863026|gb|EFL85958.1| deoxyuridine 5`-triphosphate nucleotidohydrolase [Desulfovibrio sp.
           3_1_syn3]
          Length = 352

 Score =  237 bits (605), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 106/281 (37%), Positives = 164/281 (58%), Gaps = 7/281 (2%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +         L  Y+ E+ + PML+ +EE+ LA R R+H D  AA RLV+SHLRLVV+IA
Sbjct: 63  LPSPAGARDSLHLYLREVSRFPMLKPEEEHELALRVRDHNDPDAAFRLVSSHLRLVVRIA 122

Query: 66  MGYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           M ++   +  + ++V EGN+GLM+AV KFDP++G + + Y+ +WIKA + ++I+ +W +V
Sbjct: 123 MDFQRRWMQNVLDLVQEGNVGLMRAVNKFDPDKGIKFSYYASFWIKAYILKFIMDNWRMV 182

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-D 183
           KIGTT  Q++LF+NL R +  L A             ++++L V+E ++  M+ RLA  D
Sbjct: 183 KIGTTQVQRKLFYNLNRERQKLIA----QGYDPDAAMLSERLGVTEDQINEMDQRLASTD 238

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SLN  +   D   +   D+L     G E  L   E     R+ L   M  LN +E  I 
Sbjct: 239 LSLNVQVG-EDSGGASRMDFLPALGPGIEDTLASDEIAGLVRSRLKTIMPKLNEKEVYIL 297

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + R L + PVTL  +   + V+RERVRQ+EAR  +K+++ +
Sbjct: 298 QNRLLTDEPVTLREIGERYNVTRERVRQLEARLLEKIRQHL 338


>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 =  237 bits (605), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 75/270 (27%), Positives = 125/270 (46%), Gaps = 14/270 (5%)

Query: 22  EIRKIPMLEKQE--EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           E+ K   L   E  E   A  Y E     A   +V ++LRLV+ IA  Y   GL   +++
Sbjct: 357 EMEKANYLTLGEIKEISRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 416

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L
Sbjct: 417 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKL 474

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
            R+   +         PE    +AK++++ E ++  +        S+   I   D   S 
Sbjct: 475 NRISRQMLQQFGREATPE---ELAKEMDMPEDKIRKVMKIAKEPISMETPI--GDDEDSH 529

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLEN 257
             D++    D   +  I+     N    +   ++ L PRE ++   R   +     TLE 
Sbjct: 530 LGDFI---EDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEE 586

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 587 VGKQFDVTRERIRQIEAKALRKLRHPSRSE 616


>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 =  237 bits (605), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 75/270 (27%), Positives = 125/270 (46%), Gaps = 14/270 (5%)

Query: 22  EIRKIPMLEKQE--EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           E+ K   L   E  E   A  Y E     A   +V ++LRLV+ IA  Y   GL   +++
Sbjct: 353 EMEKANYLTLGEIKEISRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 412

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L
Sbjct: 413 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKL 470

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
            R+   +         PE    +AK++++ E ++  +        S+   I   D   S 
Sbjct: 471 NRISRQMLQQFGREATPE---ELAKEMDMPEDKIRKVMKIAKEPISMETPI--GDDEDSH 525

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLEN 257
             D++    D   +  I+     N    +   ++ L PRE ++   R   +     TLE 
Sbjct: 526 LGDFI---EDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEE 582

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 583 VGKQFDVTRERIRQIEAKALRKLRHPSRSE 612


>gi|21244512|ref|NP_644094.1| RNA polymerase sigma factor RpoD [Xanthomonas axonopodis pv. citri
           str. 306]
 gi|32130007|sp|Q8PG33|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]
          Length = 625

 Score =  237 bits (605), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 75/270 (27%), Positives = 125/270 (46%), Gaps = 14/270 (5%)

Query: 22  EIRKIPMLEKQE--EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           E+ K   L   E  E   A  Y E     A   +V ++LRLV+ IA  Y   GL   +++
Sbjct: 357 EMEKANYLTLGEIKEISRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 416

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L
Sbjct: 417 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKL 474

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
            R+   +         PE    +AK++++ E ++  +        S+   I   D   S 
Sbjct: 475 NRISRQMLQQFGREATPE---ELAKEMDMPEDKIRKVMKIAKEPISMETPI--GDDEDSH 529

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLEN 257
             D++    D   +  I+     N    +   ++ L PRE ++   R   +     TLE 
Sbjct: 530 LGDFI---EDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEE 586

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 587 VGKQFDVTRERIRQIEAKALRKLRHPSRSE 616


>gi|58580221|ref|YP_199237.1| RNA polymerase sigma factor RpoD [Xanthomonas oryzae pv. oryzae
           KACC10331]
 gi|58424815|gb|AAW73852.1| RNA polymerase sigma-70 factor [Xanthomonas oryzae pv. oryzae
           KACC10331]
          Length = 629

 Score =  237 bits (605), Expect = 1e-60,   Method: Composition-based stats.
 Identities = 75/270 (27%), Positives = 125/270 (46%), Gaps = 14/270 (5%)

Query: 22  EIRKIPMLEKQE--EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           E+ K   L   E  E   A  Y E     A   +V ++LRLV+ IA  Y   GL   +++
Sbjct: 361 EMEKASYLTLGEIKEISRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 420

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L
Sbjct: 421 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKL 478

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
            R+   +         PE    +AK++++ E ++  +        S+   I   D   S 
Sbjct: 479 NRISRQMLQQFGREATPE---ELAKEMDMPEDKIRKVMKIAKEPISMETPI--GDDEDSH 533

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLEN 257
             D++    D   +  I+     N    +   ++ L PRE ++   R   +     TLE 
Sbjct: 534 LGDFI---EDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEE 590

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 591 VGKQFDVTRERIRQIEAKALRKLRHPSRSE 620


>gi|182682661|ref|YP_001830821.1| RNA polymerase factor sigma-32 [Xylella fastidiosa M23]
 gi|182632771|gb|ACB93547.1| RNA polymerase, sigma 32 subunit, RpoH [Xylella fastidiosa M23]
          Length = 288

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 114/275 (41%), Positives = 168/275 (61%), Gaps = 9/275 (3%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           + N    L  YI  + +I +L   EE +LA+RYR+  DL AA  LV SHLR VV++A GY
Sbjct: 16  VPNALGSLEAYISAVHQISVLSVDEEQLLARRYRDQQDLDAARELVHSHLRFVVRVARGY 75

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGL + +++ EGNIGLM+AVK+FDP+ G RL +++M WI+A M E+IL++W +VK+ T
Sbjct: 76  SGYGLSLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAMHWIRAEMHEFILKNWRIVKVAT 135

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN 187
           T  Q++LFFNLR+ +  L       +  E+V A+A+ LNVSE EV+ M  RL+G D   +
Sbjct: 136 TKAQRKLFFNLRKSRTRLGW-----MNAEEVSAVARDLNVSEREVLEMESRLSGRDIGFD 190

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           A     D        +L+ +     Q        + +  +L   +SVL+ R R I + R 
Sbjct: 191 AP--EEDNAPPSPVGYLIANDGDPSQAYERGNSEETQLRLLQEGLSVLDTRSRDIIQRRW 248

Query: 248 LQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           L+ +  +TL+ L+ E+ VS ER+RQIEA A KK++
Sbjct: 249 LETDKKITLQELAEEYGVSAERIRQIEANALKKMK 283


>gi|23295779|gb|AAN12882.1| principal sigma factor RpoD [Bifidobacterium animalis subsp.
           lactis]
          Length = 508

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 68/303 (22%), Positives = 138/303 (45%), Gaps = 39/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------HGD----------------- 46
             +  Y+ +I ++ +L  ++E  L++R              GD                 
Sbjct: 208 DPVKDYLKQIGRVSLLNAEQEVDLSERIEAGLYAQHLLDTEGDTMEFRRKRELKWAAADG 267

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ 
Sbjct: 268 KKAKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYAT 327

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      +++     +  +   L R++  +         P+    +A++L
Sbjct: 328 WWIRQAITRAMADQARTIRVPVHMVE--VINKLSRVQRQMLQDLGREPTPD---ELAREL 382

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   +V  +        SL+  +   +   S++ D +    D       E       + 
Sbjct: 383 DMPVEKVQEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDTDAIAPSEAVAFSLLQE 437

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++   K++   
Sbjct: 438 QFRQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPS 497

Query: 285 QKQ 287
           + Q
Sbjct: 498 RSQ 500


>gi|148550183|ref|YP_001270285.1| RNA polymerase factor sigma-32 [Pseudomonas putida F1]
 gi|148514241|gb|ABQ81101.1| RNA polymerase, sigma 32 subunit, RpoH [Pseudomonas putida F1]
          Length = 284

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 101/274 (36%), Positives = 154/274 (56%), Gaps = 7/274 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+H +  IP+L  ++E  L +R     D+ AA ++V +HLR VV IA  Y GYGL 
Sbjct: 16  NLEAYVHTVNSIPLLTVEQERDLGERLYYEQDVEAARQMVMAHLRFVVHIARSYAGYGLA 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++
Sbjct: 76  QADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           LFFNLR  K  L  + +     ++V  +A+ L V   EV  M  RL+G +        +D
Sbjct: 136 LFFNLRSQKKRLAWLNN-----DEVHRVAESLGVEPREVREMESRLSGQDMAFDPAAEAD 190

Query: 195 KNSS-QWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENP 252
            +S+ Q     + DH     V +E  +  +     L  ++  L+ R R I   R L E  
Sbjct: 191 DDSAFQSPAHYLEDHRYDPAVQLEDADWSDNSTSNLHEALQGLDERSRDILYQRWLAEEK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            TL  L+ ++ VS ER+RQ+E  A  KV+  I  
Sbjct: 251 ATLHELADKYSVSAERIRQLEKNAMNKVKALISA 284


>gi|213691851|ref|YP_002322437.1| RNA polymerase, sigma 70 subunit, RpoD family [Bifidobacterium
           longum subsp. infantis ATCC 15697]
 gi|213523312|gb|ACJ52059.1| RNA polymerase, sigma 70 subunit, RpoD family [Bifidobacterium
           longum subsp. infantis ATCC 15697]
 gi|320457946|dbj|BAJ68567.1| RNA polymerase sigma factor RpoD [Bifidobacterium longum subsp.
           infantis ATCC 15697]
          Length = 464

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 65/303 (21%), Positives = 137/303 (45%), Gaps = 39/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR---------------------------YREHGD 46
             +  Y+ +I ++ +L  ++E  L++R                           +     
Sbjct: 164 DPVKDYLKQIGRVSLLNAEQEVDLSERIEAGLYAQHLLDTESEGMEFKRKRELKWAAADG 223

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ 
Sbjct: 224 KKAKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYAT 283

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      +++     +  +   L R++  +         P+    +A++L
Sbjct: 284 WWIRQAITRAMADQARTIRVPVHMVE--VINKLSRVQRQMLQDLGREPTPD---ELAREL 338

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   +V  +        SL+  +   +   S++ D +    D       +       + 
Sbjct: 339 DMPVEKVQEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDTDAIAPSDAVAFSLLQE 393

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++   K++   
Sbjct: 394 QFKQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPS 453

Query: 285 QKQ 287
           + Q
Sbjct: 454 RSQ 456


>gi|171464209|ref|YP_001798322.1| RNA polymerase, sigma 32 subunit, RpoH [Polynucleobacter
           necessarius subsp. necessarius STIR1]
 gi|171193747|gb|ACB44708.1| RNA polymerase, sigma 32 subunit, RpoH [Polynucleobacter
           necessarius subsp. necessarius STIR1]
          Length = 307

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 112/284 (39%), Positives = 162/284 (57%), Gaps = 10/284 (3%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           +   G   L  YI  + ++PML   EE  LA+ +R   ++ AA  LV SHLRLVV +A  
Sbjct: 28  LPTLGVGTLDSYIAYVNRVPMLSAAEELHLAQEFRCTENVDAAKTLVLSHLRLVVSVARQ 87

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y GYG+P ++++ EGNIGLM+AVK++DP  G RLA+Y++ WIKA + EYIL++W LVK  
Sbjct: 88  YLGYGIPHADLIQEGNIGLMKAVKRYDPSNGARLASYAIHWIKAEIHEYILKNWRLVKTA 147

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
           TT  Q++LFFNLR  K  L A+T     P +V A+AK L+V  S+V  M  RLAG +   
Sbjct: 148 TTKAQRKLFFNLRSNKPTLSALT-----PNEVDALAKTLDVKGSDVKEMEMRLAGGDVAL 202

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
              +S + ++     WL          +   E    +   L +++  L+ R R I ++R 
Sbjct: 203 EGDDSDEDSAYAPIQWLADSSQEPTARIASAEANALQGPKLDQALMALDERSRNIVQSRW 262

Query: 248 L-----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           L          TL +L+ E+ +S ERVRQIE  A KK++  +Q 
Sbjct: 263 LAMDAEGNGTKTLHDLADEYGISAERVRQIETAALKKMRGLLQA 306


>gi|283783165|ref|YP_003373919.1| RNA polymerase sigma factor RpoD [Gardnerella vaginalis 409-05]
 gi|283441732|gb|ADB14198.1| RNA polymerase sigma factor RpoD [Gardnerella vaginalis 409-05]
          Length = 489

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 65/303 (21%), Positives = 136/303 (44%), Gaps = 39/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR---------------------------YREHGD 46
             +  Y+ +I ++ +L  ++E  L++R                           +     
Sbjct: 189 DPVKDYLKQIGRVSLLNAEQEVDLSERIEAGLYAQHLLDTQIDQMEFKRKRELKWAAADG 248

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ 
Sbjct: 249 KKAKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYAT 308

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      +++     +  +   L R++  +         P+    +A++L
Sbjct: 309 WWIRQAITRAMADQARTIRVPVHMVE--VINKLSRVQRQMLQDLGREPTPD---ELAREL 363

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   +V  +        SL+  +   +   S++ D +    D       +       + 
Sbjct: 364 DMPVEKVQEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDTDAIAPSDAVAFSLLQE 418

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              + +  L PRE  + + R   E+  P TL+++   + V+RER+RQIE++   K++   
Sbjct: 419 QFRQVLETLAPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPS 478

Query: 285 QKQ 287
           + Q
Sbjct: 479 RSQ 481


>gi|320010942|gb|ADW05792.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 358

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 82/299 (27%), Positives = 140/299 (46%), Gaps = 38/299 (12%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY--------REHGDLS-------------- 48
                  +Y+ EI +IP+L   +E  LA+R         R  G                 
Sbjct: 57  PTSDLFRQYLREIGRIPLLSAADEVELARRVEAGLFAEERLAGTPDPDSGLAVDLDRLVV 116

Query: 49  ----AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
               A  RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY
Sbjct: 117 MGRMAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTY 176

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + WWI+ AM   +      +++     +  L   + R++  +         PE+V A   
Sbjct: 177 ATWWIRQAMSRALADQARTIRVPVHVVE--LINRVVRVQRRMLQERGYEPAPEEVAA--- 231

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L+++   V  +        SL+A +   +++   + D +    DG     +E       
Sbjct: 232 QLDLTPERVSEVLRLAQEPVSLHAPV--GEEDDVAFGDLI---EDGDAASPVETAAFLLL 286

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R  L   +S L  RER++ + R   ++  P TLE +   F V+RER+RQIE++   K++
Sbjct: 287 REHLEVVLSTLGERERKVVQLRYGLDDGRPRTLEEIGRIFGVTRERIRQIESKTLDKLR 345


>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|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]
          Length = 625

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 75/270 (27%), Positives = 125/270 (46%), Gaps = 14/270 (5%)

Query: 22  EIRKIPMLEKQE--EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           E+ K   L   E  E   A  Y E     A   +V ++LRLV+ IA  Y   GL   +++
Sbjct: 357 EMEKANYLTLGEIKEISRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 416

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L
Sbjct: 417 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKL 474

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
            R+   +         PE    +AK++++ E ++  +        S+   I   D   S 
Sbjct: 475 NRISRQMLQQFGREATPE---ELAKEMDMPEDKIRKVMKIAKEPISMETPI--GDDEDSH 529

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLEN 257
             D++    D   +  I+     N    +   ++ L PRE ++   R   +     TLE 
Sbjct: 530 LGDFI---EDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEE 586

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 587 VGKQFDVTRERIRQIEAKALRKLRHPSRSE 616


>gi|163849112|ref|YP_001637156.1| RNA polymerase sigma factor RpoD [Chloroflexus aurantiacus J-10-fl]
 gi|222527085|ref|YP_002571556.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus sp.
           Y-400-fl]
 gi|163670401|gb|ABY36767.1| RNA polymerase sigma factor RpoD [Chloroflexus aurantiacus J-10-fl]
 gi|222450964|gb|ACM55230.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus sp.
           Y-400-fl]
          Length = 398

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 77/298 (25%), Positives = 136/298 (45%), Gaps = 37/298 (12%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------------HGDL 47
              +  Y+ EI ++P+L  ++E  LA+   +                             
Sbjct: 98  SDSVRLYLREIGQVPLLTAEQEKRLAQLIEQGQEAERKLATLPPDSPEAARLKQLKAKGE 157

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A  ++  ++LRLVV IA  YR  GLP+ +++ EG++GL++A++KFD  +G++ +TY+ W
Sbjct: 158 EARQQMAAANLRLVVSIAKRYRDRGLPLLDLIQEGSLGLLRAIEKFDYTKGYKFSTYATW 217

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WIK A+   +     LV++        L   L R++   + +T +  +      +A  L 
Sbjct: 218 WIKQALSRALADQSRLVRLPVH-----LGETLNRIQSARRQLTQSLGREPTDTELANHLG 272

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +SE ++  +        SL   +   ++  S   D++   H                R  
Sbjct: 273 MSEEKLRELRRTAQDPVSLATPV--GEEADSTLADFIPDPHALDADDAAAS---GMLRQQ 327

Query: 228 LTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +T ++  L+ RERR+ E R       P TLE +   F V+RERVRQIE +A +K++  
Sbjct: 328 ITAALDQLSERERRVLELRYGLVDGQPRTLEEVGKAFGVTRERVRQIEVKALRKLRHP 385


>gi|255319457|ref|ZP_05360671.1| alternative sigma factor RpoH [Acinetobacter radioresistens SK82]
 gi|262378519|ref|ZP_06071676.1| alternative sigma factor RpoH [Acinetobacter radioresistens SH164]
 gi|255303397|gb|EET82600.1| alternative sigma factor RpoH [Acinetobacter radioresistens SK82]
 gi|262299804|gb|EEY87716.1| alternative sigma factor RpoH [Acinetobacter radioresistens SH164]
          Length = 289

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 113/282 (40%), Positives = 169/282 (59%), Gaps = 9/282 (3%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +S+   G + L  YI  + +IP+L  ++E  LA+RY    DL AA  LV SHLR VV IA
Sbjct: 11  LSLSAPG-VNLGAYISTVNQIPILTAEQEKELAERYYYDQDLDAAKMLVMSHLRFVVHIA 69

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGLP  +++ EGN+GLM+AVK+FDP  G RL ++++ WIKA + EY++R+W +VK
Sbjct: 70  RSYAGYGLPQGDLIQEGNLGLMKAVKRFDPSMGVRLVSFAVHWIKAEIHEYVIRNWRIVK 129

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDE 184
           I TT  Q++LFFNLR LK   + +T      E+  +IA  LNV+  +V+ M  RL A D 
Sbjct: 130 IATTKAQRKLFFNLRSLKKSSKKLT-----LEEARSIANDLNVTPEQVLEMEGRLTAYDA 184

Query: 185 SLNALINSSDKNSSQ-WQDWLVYDHDGQEQVLIEKEERKNRRN-MLTRSMSVLNPRERRI 242
           +  A  +  D +SS       + D       L+E E+ + + N  L  +M  L+ R R I
Sbjct: 185 AFEAQGDDDDDSSSHVAPVLYLEDSRYDPARLVEDEDWEEQSNSALHNAMDQLDDRSRNI 244

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + R L ++  TL  L++E+ VS ER+RQ+E  A +K++ ++
Sbjct: 245 LQRRWLDDDKSTLHELAAEYNVSAERIRQLEKNAMEKIKVAM 286


>gi|88856913|ref|ZP_01131565.1| RNA polymerase sigma factor [marine actinobacterium PHSC20C1]
 gi|88813881|gb|EAR23751.1| RNA polymerase sigma factor [marine actinobacterium PHSC20C1]
          Length = 454

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 70/313 (22%), Positives = 137/313 (43%), Gaps = 40/313 (12%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR------------------------ 40
           + +I       +  Y+ +I K+ +L   +E  LA R                        
Sbjct: 145 SAAITGATADPVKDYLKQIGKVALLNAAQEVELAMRIEAGLFAEDKLAEMKPSEVRSTLG 204

Query: 41  ----YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
               +       A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  
Sbjct: 205 RELQWVAKDGQRAKSHLLGANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEKFDYT 264

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +GF+ +TY+ WWI+ A+   +      ++I     +  +   L R++  +         P
Sbjct: 265 KGFKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTP 322

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           E    ++++L+++  +V+ +        SL+  +   +   S++ D +    D +  V  
Sbjct: 323 E---ELSRELDMTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDTEAVVPA 374

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEA 274
           +       +  L   +  L+ RE  +   R    +  P TL+ +   F V+RER+RQIE+
Sbjct: 375 DAVGFTMLQKQLESLLDSLSEREAGVIRMRFGLGDGMPKTLDQIGDTFGVTRERIRQIES 434

Query: 275 RAFKKVQESIQKQ 287
           +   K++   + Q
Sbjct: 435 KTMAKLRHPSRSQ 447


>gi|327191758|gb|EGE58760.1| RNA polymerase factor sigma-32 [Rhizobium etli CNPAF512]
          Length = 319

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 110/268 (41%), Positives = 171/268 (63%), Gaps = 1/268 (0%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           R I      P L +QEE+ LA R+++H D  A +++  +H+RLV+ +A  +R +GLP+S+
Sbjct: 41  RMIKIAMAAPYLARQEEHDLATRWKDHDDRGARNQIAMAHMRLVISMAGKFRNFGLPMSD 100

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +V EG +GL++A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFF
Sbjct: 101 LVQEGYVGLLEAAARFEPERDVRFSTYASWWIRASIQDYILRNWSIVRGGTSSAQKALFF 160

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKN 196
           NLRRL+  L               IA  L VS ++V +M+ RL+G D SL A   S D  
Sbjct: 161 NLRRLRAKLAKGDTQLTLQSIHQEIAAALGVSLADVQTMDARLSGNDASLQAPSVSGDAE 220

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           S++  D+LV D    ++ +    + + RR  L  ++  LN RE +I  ARRL E+  TLE
Sbjct: 221 SAEKMDFLVSDDPLPDEQVSNMIDGERRRIWLASALKHLNEREMKIISARRLAEDGATLE 280

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
            L ++  +S+ERVRQIE+RA +K++ ++
Sbjct: 281 ELGADLGISKERVRQIESRAMEKLRTAL 308


>gi|254382896|ref|ZP_04998252.1| RNA polymerase sigma factor rpoD [Streptomyces sp. Mg1]
 gi|194341797|gb|EDX22763.1| RNA polymerase sigma factor rpoD [Streptomyces sp. Mg1]
          Length = 362

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 79/296 (26%), Positives = 132/296 (44%), Gaps = 38/296 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREH--------------------------GDLSA 49
             +Y+ EI +IP+L   EE  LA+R                                  A
Sbjct: 66  FRQYLREIGRIPLLTAAEEVELARRVEAGLFAEEKLAGHTDLDLQLTLDLDKLVVMGRMA 125

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             RL+ S+LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY+ WWI
Sbjct: 126 KRRLIESNLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWI 185

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + AM   +      +++     +      + R+    + +         V  +A  L ++
Sbjct: 186 RQAMSRALADQARTIRVPVHVVEL-----INRVVRVQRRMLQERGYEPTVEEVAVHLELT 240

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
              V+ +        SL+A +   +++     D +    DG     +E       R  L 
Sbjct: 241 PERVLEVLRLAQEPVSLHAPV--GEEDDVALGDLI---EDGDAASPVESAAFFLLREHLE 295

Query: 230 RSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +S L  RER++ + R       P TLE +   F V+RER+RQIE++   K+++ 
Sbjct: 296 AVLSTLGERERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRDH 351


>gi|21672345|ref|NP_660412.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. Sg
           (Schizaphis graminum)]
 gi|401010|sp|P32001|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 =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 73/276 (26%), Positives = 131/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I K   L  ++   + KR    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 348 LKQIEKETGLTIEQVKDINKRMSIGEAKAKRAKKEMVEANLRLVISIAKKYTNRGLQFLD 407

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 408 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 465

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +++K+ + E ++  +        S+   I   D + 
Sbjct: 466 KLNRISRQMLQEIGREPTPE---ELSEKMLIPEDKIRKVLKIAKEPISMETPI--GDDDD 520

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     +S L  RE ++   R   +     TL
Sbjct: 521 SHLGDFI---EDTTLELPLDSATSESLRSATHDVLSGLTAREAKVLRMRFGIDMNTDHTL 577

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 578 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 613


>gi|329934715|ref|ZP_08284756.1| RNA polymerase principal sigma factor HrdA [Streptomyces
           griseoaurantiacus M045]
 gi|329305537|gb|EGG49393.1| RNA polymerase principal sigma factor HrdA [Streptomyces
           griseoaurantiacus M045]
          Length = 363

 Score =  237 bits (605), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 83/296 (28%), Positives = 136/296 (45%), Gaps = 38/296 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYRE----------HGDLS----------------A 49
             +Y+ EI +IP+L   EE  LA+R               DL                 A
Sbjct: 67  FRQYLREIGRIPLLTAAEEVELARRVEAGLFAEEKLGSTPDLDSRLALDLDTLVVRGRMA 126

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY+ WWI
Sbjct: 127 KRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWI 186

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + AM   +      +++     +  L   + R++  +          E+V A   +L++S
Sbjct: 187 RQAMSRALADQARTIRVPVHVVE--LINRVVRVQRRMLQERGYEPSAEEVAA---QLDLS 241

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
              V  +        SL+A +   ++      D +    DG     +E       R  L 
Sbjct: 242 PERVGEVLRLAQEPVSLHAPV--GEEEDVALGDLI---EDGDATSPVESAAFLLLREHLD 296

Query: 230 RSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +S L  RER++ + R       P TLE +   F V+RER+RQIE++   K+++ 
Sbjct: 297 AVLSTLGERERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRDH 352


>gi|167036147|ref|YP_001671378.1| RNA polymerase factor sigma-32 [Pseudomonas putida GB-1]
 gi|166862635|gb|ABZ01043.1| RNA polymerase, sigma 32 subunit, RpoH [Pseudomonas putida GB-1]
          Length = 284

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 101/272 (37%), Positives = 154/272 (56%), Gaps = 7/272 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+H +  IP+L  ++E  L +R     D+ AA ++V +HLR VV IA  Y GYGL 
Sbjct: 16  NLEAYVHTVNSIPLLTVEQERDLGERLYYEQDVEAARQMVMAHLRFVVHIARSYAGYGLA 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++
Sbjct: 76  QADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           LFFNLR  K  L  + +     ++V  +A+ L V   EV  M  RL+G +        +D
Sbjct: 136 LFFNLRSQKKRLAWLNN-----DEVHRVAESLGVEPREVREMESRLSGQDMAFDPAAEAD 190

Query: 195 KNSS-QWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENP 252
            +S+ Q     + DH     V +E  +  +     L  ++  L+ R R I   R L E  
Sbjct: 191 DDSAFQSPAHYLEDHRYDPAVQLEDADWSDNSASNLHEALQGLDERSRDILYQRWLAEEK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL  L+ ++ VS ER+RQ+E  A  KV+  I
Sbjct: 251 ATLHELADKYSVSAERIRQLEKNAMNKVKALI 282


>gi|315502644|ref|YP_004081531.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Micromonospora
           sp. L5]
 gi|315409263|gb|ADU07380.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Micromonospora
           sp. L5]
          Length = 551

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 75/312 (24%), Positives = 143/312 (45%), Gaps = 42/312 (13%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR---------------------------- 40
           +      +  Y+ +I K+P+L  ++E  LAKR                            
Sbjct: 244 LTASADSVRAYLKQIGKVPLLNAEQEVELAKRIEAGLYAAERLRAADEGEEKLVRDLQRD 303

Query: 41  --YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
             +       A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G
Sbjct: 304 LMWISRDGERAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKG 363

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           ++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L         PE 
Sbjct: 364 YKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLGREPTPE- 420

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +  V ++ 
Sbjct: 421 --ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSEAVVAVDA 473

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARA 276
                 ++ L + +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++ 
Sbjct: 474 VSFSLLQDQLQQVLQTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKT 533

Query: 277 FKKVQESIQKQV 288
             K++   + QV
Sbjct: 534 MSKLRHPSRSQV 545


>gi|71275285|ref|ZP_00651572.1| Sigma-70 region 2:Sigma-70 region 4 [Xylella fastidiosa Dixon]
 gi|71902025|ref|ZP_00684069.1| Sigma-70 region 2:Sigma-70 region 4 [Xylella fastidiosa Ann-1]
 gi|71164094|gb|EAO13809.1| Sigma-70 region 2:Sigma-70 region 4 [Xylella fastidiosa Dixon]
 gi|71728204|gb|EAO30391.1| Sigma-70 region 2:Sigma-70 region 4 [Xylella fastidiosa Ann-1]
          Length = 288

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 114/275 (41%), Positives = 168/275 (61%), Gaps = 9/275 (3%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           + N    L  YI  + +I +L   EE +LA+RYR+  DL AA  LV SHLR VV++A GY
Sbjct: 16  VPNALGSLEAYISAVHQISVLSVDEEQLLARRYRDQQDLDAARELVHSHLRFVVRVARGY 75

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGL + +++ EGNIGLM+AVK+FDP+ G RL +++M WI+A M E+IL++W +VK+ T
Sbjct: 76  SGYGLSLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAMHWIRAEMHEFILKNWRIVKVAT 135

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN 187
           T  Q++LFFNLR+ +  L       +  E+V A+A+ LNVSE EV+ M  RL+G D   +
Sbjct: 136 TKAQRKLFFNLRKSRTRLGW-----MNAEEVSAVARDLNVSEREVLEMESRLSGRDIGFD 190

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           A     D        +L+ +     Q        + +  +L   +SVL+ R R I + R 
Sbjct: 191 AP--EEDNAPPSPVGYLIANDGDPSQAYERGNSEETQLRLLQEGLSVLDTRSRDIIQRRW 248

Query: 248 LQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           L+ +  +TL+ L+ E+ VS ER+RQIEA A KK++
Sbjct: 249 LETDKKITLQELAEEYGVSAERIRQIEANALKKMK 283


>gi|26991784|ref|NP_747209.1| RNA polymerase factor sigma-32 [Pseudomonas putida KT2440]
 gi|8885996|gb|AAF80334.1|AF157048_1 heat shock sigma factor RpoH [Pseudomonas putida]
 gi|24986895|gb|AAN70673.1|AE016711_1 RNA polymerase sigma-32 factor [Pseudomonas putida KT2440]
          Length = 284

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 101/272 (37%), Positives = 154/272 (56%), Gaps = 7/272 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+H +  IP+L  ++E  L +R     D+ AA ++V +HLR VV IA  Y GYGL 
Sbjct: 16  NLEAYVHTVNSIPLLTVEQERDLGERLYYEQDVEAARQMVMAHLRFVVHIARSYAGYGLA 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++
Sbjct: 76  QADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           LFFNLR  K  L  + +     ++V  +A+ L V   EV  M  RL+G +        +D
Sbjct: 136 LFFNLRSQKKRLAWLNN-----DEVHRVAESLGVEPREVREMESRLSGQDMAFDPAAEAD 190

Query: 195 KNSS-QWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENP 252
            +S+ Q     + DH     V +E  +  +     L  ++  L+ R R I   R L E  
Sbjct: 191 DDSAFQSPAHYLEDHRYDPAVQLEDADWSDNSTSNLHEALQGLDERSRDILYQRWLAEEK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL  L+ ++ VS ER+RQ+E  A  KV+  I
Sbjct: 251 ATLHELADKYSVSAERIRQLEKNAMNKVKALI 282


>gi|71901711|ref|ZP_00683785.1| Sigma-70 region 2:Sigma-70 region 4 [Xylella fastidiosa Ann-1]
 gi|71728528|gb|EAO30685.1| Sigma-70 region 2:Sigma-70 region 4 [Xylella fastidiosa Ann-1]
          Length = 288

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 114/275 (41%), Positives = 168/275 (61%), Gaps = 9/275 (3%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           + N    L  YI  + +I +L   EE +LA+RYR+  DL AA  LV SHLR VV++A GY
Sbjct: 16  VPNALGSLEAYISAVHQISVLSVDEEQLLARRYRDQQDLDAARELVHSHLRFVVRVARGY 75

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGL + +++ EGNIGLM+AVK+FDP+ G RL +++M WI+A M E+IL++W +VK+ T
Sbjct: 76  SGYGLSLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAMHWIRAEMHEFILKNWRIVKVAT 135

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN 187
           T  Q++LFFNLR+ +  L       +  E+V A+A+ LNVSE EV+ M  RL+G D   +
Sbjct: 136 TKAQRKLFFNLRKSRTRLGW-----MNAEEVSAVARDLNVSEREVLEMESRLSGRDIGFD 190

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           A     D        +L+ +     Q        + +  +L   +SVL+ R R I + R 
Sbjct: 191 AP--EEDNAPPSPVGYLIANDGDPSQAYERGNSEETQLRLLQEGLSVLDTRSRDIIQRRW 248

Query: 248 LQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           L+ +  +TL+ L+ E+ VS ER+RQIEA A KK++
Sbjct: 249 LETDKKITLQELAEEYGVSAERIRQIEANALKKMK 283


>gi|307578942|gb|ADN62911.1| RNA polymerase factor sigma-32 [Xylella fastidiosa subsp.
           fastidiosa GB514]
          Length = 282

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 114/275 (41%), Positives = 168/275 (61%), Gaps = 9/275 (3%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           + N    L  YI  + +I +L   EE +LA+RYR+  DL AA  LV SHLR VV++A GY
Sbjct: 10  VPNALGSLEAYISAVHQISVLSVDEEQLLARRYRDQQDLDAARELVHSHLRFVVRVARGY 69

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGL + +++ EGNIGLM+AVK+FDP+ G RL +++M WI+A M E+IL++W +VK+ T
Sbjct: 70  SGYGLSLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAMHWIRAEMHEFILKNWRIVKVAT 129

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN 187
           T  Q++LFFNLR+ +  L       +  E+V A+A+ LNVSE EV+ M  RL+G D   +
Sbjct: 130 TKAQRKLFFNLRKSRTRLGW-----MNAEEVSAVARDLNVSEREVLEMESRLSGRDIGFD 184

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           A     D        +L+ +     Q        + +  +L   +SVL+ R R I + R 
Sbjct: 185 AP--EEDNAPPSPVGYLIANDGDPSQAYERGNSEETQLRLLQEGLSVLDTRSRDIIQRRW 242

Query: 248 LQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           L+ +  +TL+ L+ E+ VS ER+RQIEA A KK++
Sbjct: 243 LETDKKITLQELAEEYGVSAERIRQIEANALKKMK 277


>gi|190575994|ref|YP_001973839.1| RNA polymerase sigma factor RpoD [Stenotrophomonas maltophilia
           K279a]
 gi|190013916|emb|CAQ47556.1| putative RNA polymerase sigma factor RpoD [Stenotrophomonas
           maltophilia K279a]
          Length = 617

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 75/270 (27%), Positives = 127/270 (47%), Gaps = 14/270 (5%)

Query: 22  EIRKIPMLEKQE--EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           +I  +  L+ +E  E   A  Y E     A   +V ++LRLV+ IA  Y   GL   +++
Sbjct: 349 DIETLTQLDLEELKEISRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 408

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L
Sbjct: 409 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKL 466

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
            R+   +         PE    +AK++++ E ++  +        S+   I   D   S 
Sbjct: 467 NRISRQMLQQYGREATPE---ELAKEMDMPEDKIRKVMKIAKEPISMETPI--GDDEDSH 521

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLEN 257
             D++    D   +  IE     N    +   ++ L PRE ++   R   +     TLE 
Sbjct: 522 LGDFI---EDTNVESPIENTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEE 578

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 579 VGKQFDVTRERIRQIEAKALRKLRHPSRSE 608


>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 =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 564 RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 623

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 624 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 678

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 679 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDNNTVAPADAALHASMRD 733

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 734 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 793

Query: 285 QKQ 287
           +  
Sbjct: 794 RSD 796


>gi|322421263|ref|YP_004200486.1| RNA polymerase sigma 32 subunit RpoH [Geobacter sp. M18]
 gi|320127650|gb|ADW15210.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter sp. M18]
          Length = 284

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 111/271 (40%), Positives = 167/271 (61%), Gaps = 6/271 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             L+ Y+ EI + P+L   EE  LA R+R+ GDL AAH+L+TS+LR VVKIA  YR YG+
Sbjct: 10  DSLTLYLTEINRFPLLSADEEMDLAYRFRDEGDLQAAHKLITSNLRFVVKIAGEYRSYGM 69

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++ EGNIGLM AV+KFDP +G RL +Y++WWI+A +Q +I+ +WSL+KIGTT  Q+
Sbjct: 70  KMLDLIQEGNIGLMMAVRKFDPAKGVRLISYAVWWIRAYIQNHIISAWSLLKIGTTQAQR 129

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
           +LFF L + K  +  +T        + A A  L+V ++E   M  RL G+ SL+  +   
Sbjct: 130 KLFFKLNQAKQAIINMTGEG----DLHAAAISLDVKDTEAREMEQRLRGELSLD--VEMF 183

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D     + + L      QE++L E++E       +  ++  LN +ER + E R   E P+
Sbjct: 184 DGEGGTFLETLPDLRQNQEEMLAERQETTILEQGVASALGHLNEKERFVIERRVAAEEPL 243

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           TL+ ++  F +SRERVRQIE  A KK++  +
Sbjct: 244 TLQEIADHFSISRERVRQIEEGALKKMKRFL 274


>gi|1149588|emb|CAA89984.1| SigA sigma factor [Corynebacterium glutamicum]
          Length = 497

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 78/325 (24%), Positives = 148/325 (45%), Gaps = 49/325 (15%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR----------------EHG 45
            RK+  +  + +  +  Y+ +I K+ +L  ++E  LAKR                    G
Sbjct: 178 ARKDAELTASAD-SVRAYLKQIGKVALLNAEQEVSLAKRIEAGLYATHRMEEMEEAFAAG 236

Query: 46  DLS--------------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           D                      A + L+ ++LRLVV +A  Y G G+   +++ EGN+G
Sbjct: 237 DKDAKLTPAVKRDLRAIARDGRKAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLG 296

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++AV+KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  
Sbjct: 297 LIRAVEKFDYSKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRE 354

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           L         P     ++K++++SE +V+ +        SL+  I   D+  SQ  D++ 
Sbjct: 355 LLQELGREPTP---QELSKEMDISEEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI- 408

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFE 263
              D +  V ++       ++ L   +  L+ RE  + + R    +  P TL+ +   + 
Sbjct: 409 --EDSEAVVAVDAVSFTLLQDQLQDVLETLSEREAGVVKLRFGLTDGMPRTLDEIGQVYG 466

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           V+RER+RQIE++   K +   + QV
Sbjct: 467 VTRERIRQIESKTMSKRRHPSRSQV 491


>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 =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 75/270 (27%), Positives = 125/270 (46%), Gaps = 14/270 (5%)

Query: 22  EIRKIPMLEKQE--EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           E+ K   L   E  E   A  Y E     A   +V ++LRLV+ IA  Y   GL   +++
Sbjct: 357 EMEKANYLTLGEIKEISRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 416

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L
Sbjct: 417 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKL 474

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
            R+   +         PE    +AK++++ E ++  +        S+   I   D   S 
Sbjct: 475 NRISRQMLQQFGREATPE---ELAKEMDMPEDKIRKVMKIAKEPISMETPI--GDDEDSH 529

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLEN 257
             D++    D   +  I+     N    +   ++ L PRE ++   R   +     TLE 
Sbjct: 530 LGDFI---EDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEE 586

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 587 VGKQFDVTRERIRQIEAKALRKLRHPSRSE 616


>gi|297243591|ref|ZP_06927522.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Gardnerella vaginalis AMD]
 gi|296888342|gb|EFH27083.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Gardnerella vaginalis AMD]
          Length = 489

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 65/303 (21%), Positives = 136/303 (44%), Gaps = 39/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR---------------------------YREHGD 46
             +  Y+ +I ++ +L  ++E  L++R                           +     
Sbjct: 189 DPVKDYLKQIGRVSLLNAEQEVDLSERIEAGLYAQHLLDTQIDQMEFKRKRELKWAAADG 248

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ 
Sbjct: 249 KKAKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYAT 308

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      +++     +  +   L R++  +         P+    +A++L
Sbjct: 309 WWIRQAITRAMADQARTIRVPVHMVE--VINKLSRVQRQMLQDLGREPTPD---ELAREL 363

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   +V  +        SL+  +   +   S++ D +    D       +       + 
Sbjct: 364 DMPVEKVQEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDTDAIAPSDAVAFSLLQE 418

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              + +  L PRE  + + R   E+  P TL+++   + V+RER+RQIE++   K++   
Sbjct: 419 QFRQVLETLAPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPS 478

Query: 285 QKQ 287
           + Q
Sbjct: 479 RSQ 481


>gi|241206826|ref|YP_002977922.1| RNA polymerase factor sigma-32 [Rhizobium leguminosarum bv.
           trifolii WSM1325]
 gi|86450985|gb|ABC96760.1| putative RNA polymerase sigma factor [Rhizobium leguminosarum bv.
           trifolii TA1]
 gi|240860716|gb|ACS58383.1| RNA polymerase, sigma 32 subunit, RpoH [Rhizobium leguminosarum bv.
           trifolii WSM1325]
          Length = 287

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 111/268 (41%), Positives = 171/268 (63%), Gaps = 1/268 (0%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           R I      P L +QEE+ LA R+++H D  A +++  +H+RLV+ +A  +R +GLP+S+
Sbjct: 9   RMIKIAMAAPYLARQEEHDLATRWKDHDDRGARNQIAMAHMRLVISMAGKFRNFGLPMSD 68

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +V EG +GL++A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFF
Sbjct: 69  LVQEGYVGLLEAAARFEPERDVRFSTYASWWIRASIQDYILRNWSIVRGGTSSAQKALFF 128

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKN 196
           NLRRL+  L               IA  L VS S+V +M+ RL+G D SL A   S D  
Sbjct: 129 NLRRLRAKLAKGDTQLTLQSIHQEIAAALGVSLSDVQTMDARLSGNDASLQAPSVSGDAE 188

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           S++  D+LV D    ++ +    + + RR  L  ++  LN RE +I  ARRL E+  TLE
Sbjct: 189 SAEKMDFLVSDDPLPDEQVSNMIDGERRRVWLASALKHLNEREMKIISARRLAEDGATLE 248

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
            L ++  +S+ERVRQIE+RA +K++ ++
Sbjct: 249 ELGADLGISKERVRQIESRAMEKLRSAL 276


>gi|256045366|ref|ZP_05448260.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|260565741|ref|ZP_05836224.1| sigma-70 factor family protein [Brucella melitensis bv. 1 str. 16M]
 gi|260151114|gb|EEW86209.1| sigma-70 factor family protein [Brucella melitensis bv. 1 str. 16M]
          Length = 311

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 117/293 (39%), Positives = 184/293 (62%), Gaps = 4/293 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  ++          +   I      P LE++EE  LA R++E  D  A HR+ ++H+RL
Sbjct: 19  MAVRSFPAAAASSQSM---IRSAMSAPYLEREEERALAIRWKETKDQDALHRITSAHMRL 75

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A  +R + LP+S+++ EG +GL++   +FDP+R  R +TY+ WWI+A+MQ+YILR+
Sbjct: 76  VISMAGRFRKFKLPMSDLIQEGYVGLLEEAARFDPDRDVRFSTYASWWIRASMQDYILRN 135

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WS+V+ GT++ QK LFFNLRRL+  L    DN  K E    I+ +L VS S+V  M+ RL
Sbjct: 136 WSIVRGGTSSAQKVLFFNLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRL 195

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D SL+A +N  +  +S+  D+LV DH  Q+++     + + R   LTR++  LN RE
Sbjct: 196 SGPDSSLSASMNGEETGASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTRALDTLNERE 255

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
             I   RRL ++ VTLE L  +  +S++RVRQIE+RA +K++ ++  Q EL++
Sbjct: 256 LHIIRERRLDDDGVTLEALGEKLGISKQRVRQIESRAMEKLKIALLSQHELAA 308


>gi|289667862|ref|ZP_06488937.1| RNA polymerase sigma factor RpoD [Xanthomonas campestris pv.
           musacearum NCPPB4381]
          Length = 624

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 75/270 (27%), Positives = 125/270 (46%), Gaps = 14/270 (5%)

Query: 22  EIRKIPMLEKQE--EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           E+ K   L   E  E   A  Y E     A   +V ++LRLV+ IA  Y   GL   +++
Sbjct: 356 EMEKSSYLTLGEIKEISRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 415

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L
Sbjct: 416 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKL 473

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
            R+   +         PE    +AK++++ E ++  +        S+   I   D   S 
Sbjct: 474 NRISRQMLQQFGREATPE---ELAKEMDMPEDKIRKVMKIAKEPISMETPI--GDDEDSH 528

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLEN 257
             D++    D   +  I+     N    +   ++ L PRE ++   R   +     TLE 
Sbjct: 529 LGDFI---EDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEE 585

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 586 VGKQFDVTRERIRQIEAKALRKLRHPSRSE 615


>gi|289664793|ref|ZP_06486374.1| RNA polymerase sigma factor RpoD [Xanthomonas campestris pv.
           vasculorum NCPPB702]
          Length = 624

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 75/270 (27%), Positives = 125/270 (46%), Gaps = 14/270 (5%)

Query: 22  EIRKIPMLEKQE--EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           E+ K   L   E  E   A  Y E     A   +V ++LRLV+ IA  Y   GL   +++
Sbjct: 356 EMEKSSYLTLGEIKEISRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 415

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L
Sbjct: 416 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKL 473

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
            R+   +         PE    +AK++++ E ++  +        S+   I   D   S 
Sbjct: 474 NRISRQMLQQFGREATPE---ELAKEMDMPEDKIRKVMKIAKEPISMETPI--GDDEDSH 528

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLEN 257
             D++    D   +  I+     N    +   ++ L PRE ++   R   +     TLE 
Sbjct: 529 LGDFI---EDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEE 585

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 586 VGKQFDVTRERIRQIEAKALRKLRHPSRSE 615


>gi|302866088|ref|YP_003834725.1| RNA polymerase sigma factor RpoD [Micromonospora aurantiaca ATCC
           27029]
 gi|302568947|gb|ADL45149.1| RNA polymerase sigma factor RpoD [Micromonospora aurantiaca ATCC
           27029]
          Length = 551

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 75/312 (24%), Positives = 143/312 (45%), Gaps = 42/312 (13%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR---------------------------- 40
           +      +  Y+ +I K+P+L  ++E  LAKR                            
Sbjct: 244 LTASADSVRAYLKQIGKVPLLNAEQEVELAKRIEAGLYAAERLRAADEGEEKLVRDLQRD 303

Query: 41  --YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
             +       A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G
Sbjct: 304 LMWISRDGERAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKG 363

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           ++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L         PE 
Sbjct: 364 YKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLGREPTPE- 420

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D +  V ++ 
Sbjct: 421 --ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSEAVVAVDA 473

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARA 276
                 ++ L + +  L+ RE  +   R       P TL+ +   + V+RER+RQIE++ 
Sbjct: 474 VSFSLLQDQLQQVLQTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKT 533

Query: 277 FKKVQESIQKQV 288
             K++   + QV
Sbjct: 534 MSKLRHPSRSQV 545


>gi|172062815|ref|YP_001810466.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia ambifaria
           MC40-6]
 gi|171995332|gb|ACB66250.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia ambifaria
           MC40-6]
          Length = 805

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 564 RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 623

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 624 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 678

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 679 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDNNTVAPADAALHASMRD 733

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 734 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 793

Query: 285 QKQ 287
           +  
Sbjct: 794 RSD 796


>gi|270263179|ref|ZP_06191449.1| RNA polymerase sigma factor RpoD [Serratia odorifera 4Rx13]
 gi|270042867|gb|EFA15961.1| RNA polymerase sigma factor RpoD [Serratia odorifera 4Rx13]
          Length = 648

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 379 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 438

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 439 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 496

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 497 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 551

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 552 SHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 608

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 609 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 644


>gi|166713725|ref|ZP_02244932.1| RNA polymerase sigma factor RpoD [Xanthomonas oryzae pv. oryzicola
           BLS256]
          Length = 624

 Score =  237 bits (604), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 75/270 (27%), Positives = 125/270 (46%), Gaps = 14/270 (5%)

Query: 22  EIRKIPMLEKQE--EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           E+ K   L   E  E   A  Y E     A   +V ++LRLV+ IA  Y   GL   +++
Sbjct: 356 EMEKASYLTLGEIKEISRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 415

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L
Sbjct: 416 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKL 473

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
            R+   +         PE    +AK++++ E ++  +        S+   I   D   S 
Sbjct: 474 NRISRQMLQQFGREATPE---ELAKEMDMPEDKIRKVMKIAKEPISMETPI--GDDEDSH 528

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLEN 257
             D++    D   +  I+     N    +   ++ L PRE ++   R   +     TLE 
Sbjct: 529 LGDFI---EDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEE 585

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 586 VGKQFDVTRERIRQIEAKALRKLRHPSRSE 615


>gi|298244288|ref|ZP_06968094.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297551769|gb|EFH85634.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 334

 Score =  236 bits (603), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 90/271 (33%), Positives = 145/271 (53%), Gaps = 13/271 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  + +Y+ EI   P+L  ++E  LA+R    GD  A  RL+ ++LRLVV IA  Y   G
Sbjct: 61  DDSVKQYLKEIGMYPLLTAEQELQLAERVA-RGDQYARQRLIEANLRLVVSIAKRYSNQG 119

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP+ +++ EGNIGLM+A +KFD +RGFR +TY+ WWI+ A+   I      + I     +
Sbjct: 120 LPLLDLIQEGNIGLMRATQKFDYKRGFRFSTYATWWIRQAISRAIAEHSRSIHIPVHVVE 179

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
             L + ++R+   L         PEQV A   +L +    V+ +        SL+A +  
Sbjct: 180 --LIYKIKRITRRLYQEQGVEPLPEQVAA---ELGLPRERVVELLNVSEQPISLDAPM-- 232

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QE 250
           +D       D L    D      I+   ++ +R  + ++M+VLNPRER I E R      
Sbjct: 233 ADDEEYHLSDML---EDTSMAPTIDVVSQQLQREHIEQAMTVLNPRERTIIEMRYGLKDG 289

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           + ++L+ +S  F ++RER+RQIE +A +K++
Sbjct: 290 HSLSLDEVSVLFHLTRERIRQIEVKALRKLR 320


>gi|190893879|ref|YP_001980421.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CIAT
           652]
 gi|190699158|gb|ACE93243.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CIAT
           652]
          Length = 287

 Score =  236 bits (603), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 110/268 (41%), Positives = 171/268 (63%), Gaps = 1/268 (0%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           R I      P L +QEE+ LA R+++H D  A +++  +H+RLV+ +A  +R +GLP+S+
Sbjct: 9   RMIKIAMAAPYLARQEEHDLATRWKDHDDRGARNQIAMAHMRLVISMAGKFRNFGLPMSD 68

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +V EG +GL++A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFF
Sbjct: 69  LVQEGYVGLLEAAARFEPERDVRFSTYASWWIRASIQDYILRNWSIVRGGTSSAQKALFF 128

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKN 196
           NLRRL+  L               IA  L VS ++V +M+ RL+G D SL A   S D  
Sbjct: 129 NLRRLRAKLAKGDTQLTLQSIHQEIAAALGVSLADVQTMDARLSGNDASLQAPSVSGDAE 188

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           S++  D+LV D    ++ +    + + RR  L  ++  LN RE +I  ARRL E+  TLE
Sbjct: 189 SAEKMDFLVSDDPLPDEQVSNMIDGERRRIWLASALKHLNEREMKIISARRLAEDGATLE 248

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
            L ++  +S+ERVRQIE+RA +K++ ++
Sbjct: 249 ELGADLGISKERVRQIESRAMEKLRTAL 276


>gi|302534283|ref|ZP_07286625.1| RNA polymerase sigma factor RpoS [Streptomyces sp. C]
 gi|302443178|gb|EFL14994.1| RNA polymerase sigma factor RpoS [Streptomyces sp. C]
          Length = 361

 Score =  236 bits (603), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 85/309 (27%), Positives = 140/309 (45%), Gaps = 38/309 (12%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY------------------REH 44
           R N +          +Y+ EI +IP+L   EE  LA+R                   +  
Sbjct: 52  RDNGAGTGPSADLFRQYLREIGRIPLLTAAEEVELARRVEAGLFAEEKLAGATDLDSQLA 111

Query: 45  GDLS--------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
            DL         A  RL+ S+LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  
Sbjct: 112 VDLDKLVVMGRMAKRRLIESNLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYA 171

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RG++ +TY+ WWI+ AM   +      +++     +  L   + R++  +          
Sbjct: 172 RGYKFSTYATWWIRQAMSRALADQARTIRVPVHVVE--LINRVVRVQRRMLQERGYEPTA 229

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           E+V A    L ++   V+ +        SL+A +   +++     D +    DG     +
Sbjct: 230 EEVAA---HLELTPERVLEVLRLAQEPVSLHAPV--GEEDDVALGDLI---EDGDAASPM 281

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEA 274
           E       R  L   +S L  RER++ + R       P TLE +   F V+RER+RQIE+
Sbjct: 282 ESAAFFLLREHLEAVLSTLGERERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIES 341

Query: 275 RAFKKVQES 283
           +   K+++ 
Sbjct: 342 KTLNKLRDH 350


>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 =  236 bits (603), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 378 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 437

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 438 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 495

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 496 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 550

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 551 SHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 607

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 608 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 643


>gi|1938356|gb|AAC45155.1| RpoD [Xanthomonas campestris pv. campestris]
          Length = 622

 Score =  236 bits (603), Expect = 2e-60,   Method: Composition-based stats.
 Identities = 74/270 (27%), Positives = 125/270 (46%), Gaps = 14/270 (5%)

Query: 22  EIRKIPMLEKQEEYVL--AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           E+ K   L   E   +  A  Y E     A   +V ++LRLV+ IA  Y   GL   +++
Sbjct: 354 EMEKANYLTLAEIKDISRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 413

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L
Sbjct: 414 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKL 471

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
            R+   +         PE    +AK++++ E ++  +        S+   I   D   S 
Sbjct: 472 NRISRQMLQQFGREPTPE---ELAKEMDMPEDKIRKVMKIAKEPISMETPI--GDDEDSH 526

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLEN 257
             D++    D   +  I+     N    +   ++ L PRE ++   R   +     TLE 
Sbjct: 527 LGDFI---EDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEE 583

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 584 VGKQFDVTRERIRQIEAKALRKLRHPSRSE 613


>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 =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 378 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 437

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 438 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 495

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 496 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 550

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 551 SHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 607

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 608 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 643


>gi|298253932|ref|ZP_06977519.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Gardnerella vaginalis 5-1]
 gi|297532075|gb|EFH71050.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Gardnerella vaginalis 5-1]
          Length = 489

 Score =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 65/303 (21%), Positives = 136/303 (44%), Gaps = 39/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR---------------------------YREHGD 46
             +  Y+ +I ++ +L  ++E  L++R                           +     
Sbjct: 189 DPVKDYLKQIGRVSLLNAEQEVDLSERIEAGLYAQHLLDTQIDQMEFKRKRELKWAAADG 248

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ 
Sbjct: 249 KKAKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYAT 308

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      +++     +  +   L R++  +         P+    +A++L
Sbjct: 309 WWIRQAITRAMADQARTIRVPVHMVE--VINKLSRVQRQMLQDLGREPTPD---ELAREL 363

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   +V  +        SL+  +   +   S++ D +    D       +       + 
Sbjct: 364 DMPVEKVQEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDTDAIAPSDAVAFSLLQE 418

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              + +  L PRE  + + R   E+  P TL+++   + V+RER+RQIE++   K++   
Sbjct: 419 QFRQVLETLAPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPS 478

Query: 285 QKQ 287
           + Q
Sbjct: 479 RSQ 481


>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 =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 75/270 (27%), Positives = 125/270 (46%), Gaps = 14/270 (5%)

Query: 22  EIRKIPMLEKQE--EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           E+ K   L   E  E   A  Y E     A   +V ++LRLV+ IA  Y   GL   +++
Sbjct: 356 EMEKANYLTLGEIKEISRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 415

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L
Sbjct: 416 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKL 473

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
            R+   +         PE    +AK++++ E ++  +        S+   I   D   S 
Sbjct: 474 NRISRQMLQQFGREATPE---ELAKEMDMPEDKIRKVMKIAKEPISMETPI--GDDEDSH 528

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLEN 257
             D++    D   +  I+     N    +   ++ L PRE ++   R   +     TLE 
Sbjct: 529 LGDFI---EDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEE 585

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 586 VGKQFDVTRERIRQIEAKALRKLRHPSRSE 615


>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 =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 75/270 (27%), Positives = 125/270 (46%), Gaps = 14/270 (5%)

Query: 22  EIRKIPMLEKQE--EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           E+ K   L   E  E   A  Y E     A   +V ++LRLV+ IA  Y   GL   +++
Sbjct: 356 EMEKANYLTLGEIKEISRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 415

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L
Sbjct: 416 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKL 473

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
            R+   +         PE    +AK++++ E ++  +        S+   I   D   S 
Sbjct: 474 NRISRQMLQQFGREATPE---ELAKEMDMPEDKIRKVMKIAKEPISMETPI--GDDEDSH 528

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLEN 257
             D++    D   +  I+     N    +   ++ L PRE ++   R   +     TLE 
Sbjct: 529 LGDFI---EDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEE 585

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 586 VGKQFDVTRERIRQIEAKALRKLRHPSRSE 615


>gi|158316157|ref|YP_001508665.1| RpoD family RNA polymerase sigma factor [Frankia sp. EAN1pec]
 gi|158111562|gb|ABW13759.1| RNA polymerase, sigma 70 subunit, RpoD family [Frankia sp. EAN1pec]
          Length = 400

 Score =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 76/312 (24%), Positives = 140/312 (44%), Gaps = 38/312 (12%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY------------------REHG 45
           + +++       +  Y+  I ++ +L  +EE  LAKR                   R   
Sbjct: 92  EELALTTPPSDPVRMYLKAIGRVRLLTAEEEVDLAKRIEAGLFASEKLAAIRRTSPRLRR 151

Query: 46  DLSA--------AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           DL A          +LV ++LRLVV IA  Y G G+ + +++ EGN+GL++AV+KFD  +
Sbjct: 152 DLEAIEQDGQIAKRKLVEANLRLVVSIAKRYVGRGMLLLDLIQEGNLGLIRAVEKFDYTK 211

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I     +      + ++    + +  +  +  
Sbjct: 212 GYKFSTYATWWIRQAVTRAIADQGRTIRIPVHMVE-----TINKVTRIQRQLLQDLGREP 266

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               IA +++++   V  +        +L   I   ++  SQ  D++    D    V  E
Sbjct: 267 SPEEIATQVDLAPHRVEEILKVGQTPVALETPI--GEEQDSQLGDFI---EDNDAIVPFE 321

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEAR 275
                  +  +   +  L+ RE+++ + R       P TLE +  EF V+RER+RQIE+R
Sbjct: 322 AASFVLLQEQIDSVLHTLSEREKKVIQLRFGLTDGQPRTLEQVGREFGVTRERIRQIESR 381

Query: 276 AFKKVQESIQKQ 287
              K+    + Q
Sbjct: 382 TLAKLSHPARSQ 393


>gi|259907100|ref|YP_002647456.1| RNA polymerase sigma factor RpoD [Erwinia pyrifoliae Ep1/96]
 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 =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 344 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 403

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 404 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 461

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 462 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 516

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 517 SHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 573

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 574 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 609


>gi|17986563|ref|NP_539197.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 1 str. 16M]
 gi|17982171|gb|AAL51461.1| RNA polymerase sigma-32 factor [Brucella melitensis bv. 1 str. 16M]
          Length = 319

 Score =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 117/293 (39%), Positives = 184/293 (62%), Gaps = 4/293 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  ++          +   I      P LE++EE  LA R++E  D  A HR+ ++H+RL
Sbjct: 27  MAVRSFPAAAASSQSM---IRSAMSAPYLEREEERALAIRWKETKDQDALHRITSAHMRL 83

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A  +R + LP+S+++ EG +GL++   +FDP+R  R +TY+ WWI+A+MQ+YILR+
Sbjct: 84  VISMAGRFRKFKLPMSDLIQEGYVGLLEEAARFDPDRDVRFSTYASWWIRASMQDYILRN 143

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WS+V+ GT++ QK LFFNLRRL+  L    DN  K E    I+ +L VS S+V  M+ RL
Sbjct: 144 WSIVRGGTSSAQKVLFFNLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRL 203

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D SL+A +N  +  +S+  D+LV DH  Q+++     + + R   LTR++  LN RE
Sbjct: 204 SGPDSSLSASMNGEETGASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTRALDTLNERE 263

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
             I   RRL ++ VTLE L  +  +S++RVRQIE+RA +K++ ++  Q EL++
Sbjct: 264 LHIIRERRLDDDGVTLEALGEKLGISKQRVRQIESRAMEKLKIALLSQHELAA 316


>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 =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 68/247 (27%), Positives = 116/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 582 ERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 641

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T N   P     +
Sbjct: 642 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGNEPDPAT---L 696

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+ + E ++  +        S+   I   D + S   D++    D       E     
Sbjct: 697 AEKMEMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTLAPAEAALHG 751

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 752 SMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKL 811

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 812 RHPSRSD 818


>gi|227547666|ref|ZP_03977715.1| RNA polymerase sigma factor [Bifidobacterium longum subsp. infantis
           ATCC 55813]
 gi|227211921|gb|EEI79817.1| RNA polymerase sigma factor [Bifidobacterium longum subsp. infantis
           ATCC 55813]
          Length = 464

 Score =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 65/303 (21%), Positives = 137/303 (45%), Gaps = 39/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR---------------------------YREHGD 46
             +  Y+ +I ++ +L  ++E  L++R                           +     
Sbjct: 164 DPVKDYLKQIGRVSLLNAEQEVDLSERIEAGLYAQHLLDTESEGMEFKRKRELKWAAADG 223

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ 
Sbjct: 224 KKAKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYAT 283

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      +++     +  +   L R++  +         P+    +A++L
Sbjct: 284 WWIRQAITRAMADQARTIRVPVHMVE--VINKLSRVQRQMLQDLGREPTPD---ELAREL 338

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   +V  +        SL+  +   +   S++ D +    D       +       + 
Sbjct: 339 DMPVEKVQEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDTDAIAPSDAVAFSLLQE 393

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++   K++   
Sbjct: 394 QFKQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPS 453

Query: 285 QKQ 287
           + Q
Sbjct: 454 RSQ 456


>gi|23465986|ref|NP_696589.1| RNA polymerase sigma factor [Bifidobacterium longum NCC2705]
 gi|46191322|ref|ZP_00206768.1| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Bifidobacterium longum DJO10A]
 gi|189439160|ref|YP_001954241.1| RNA polymerase sigma factor [Bifidobacterium longum DJO10A]
 gi|312132592|ref|YP_003999931.1| rpod [Bifidobacterium longum subsp. longum BBMN68]
 gi|317482450|ref|ZP_07941467.1| RNA polymerase sigma factor RpoD [Bifidobacterium sp. 12_1_47BFAA]
 gi|322689398|ref|YP_004209132.1| RNA polymerase sigma factor RpoD [Bifidobacterium longum subsp.
           infantis 157F]
 gi|322691364|ref|YP_004220934.1| RNA polymerase sigma factor RpoD [Bifidobacterium longum subsp.
           longum JCM 1217]
 gi|23326702|gb|AAN25225.1| RNA polymerase principal sigma factor; sigma 70 [Bifidobacterium
           longum NCC2705]
 gi|189427595|gb|ACD97743.1| DNA-directed RNA polymerase sigma subunit [Bifidobacterium longum
           DJO10A]
 gi|311773536|gb|ADQ03024.1| RpoD [Bifidobacterium longum subsp. longum BBMN68]
 gi|316916110|gb|EFV37515.1| RNA polymerase sigma factor RpoD [Bifidobacterium sp. 12_1_47BFAA]
 gi|320456220|dbj|BAJ66842.1| RNA polymerase sigma factor RpoD [Bifidobacterium longum subsp.
           longum JCM 1217]
 gi|320460734|dbj|BAJ71354.1| RNA polymerase sigma factor RpoD [Bifidobacterium longum subsp.
           infantis 157F]
          Length = 474

 Score =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 65/303 (21%), Positives = 137/303 (45%), Gaps = 39/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR---------------------------YREHGD 46
             +  Y+ +I ++ +L  ++E  L++R                           +     
Sbjct: 174 DPVKDYLKQIGRVSLLNAEQEVDLSERIEAGLYAQHLLDTESEGMEFKRKRELKWAAADG 233

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ 
Sbjct: 234 KKAKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYAT 293

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      +++     +  +   L R++  +         P+    +A++L
Sbjct: 294 WWIRQAITRAMADQARTIRVPVHMVE--VINKLSRVQRQMLQDLGREPTPD---ELAREL 348

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   +V  +        SL+  +   +   S++ D +    D       +       + 
Sbjct: 349 DMPVEKVQEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDTDAIAPSDAVAFSLLQE 403

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++   K++   
Sbjct: 404 QFKQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPS 463

Query: 285 QKQ 287
           + Q
Sbjct: 464 RSQ 466


>gi|21220928|ref|NP_626707.1| RNA polymerase principal sigma factor [Streptomyces coelicolor
           A3(2)]
 gi|289771799|ref|ZP_06531177.1| RNA polymerase principal sigma factor hrdA [Streptomyces lividans
           TK24]
 gi|19856645|sp|P18182|HRDA_STRCO RecName: Full=RNA polymerase principal sigma factor hrdA
 gi|6759560|emb|CAB69753.1| RNA polymerase principal sigma factor [Streptomyces coelicolor
           A3(2)]
 gi|289701998|gb|EFD69427.1| RNA polymerase principal sigma factor hrdA [Streptomyces lividans
           TK24]
          Length = 396

 Score =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 82/302 (27%), Positives = 137/302 (45%), Gaps = 40/302 (13%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG------------------------- 45
                  +Y+ EI +IP+L   EE  LA+R  E G                         
Sbjct: 95  PSSDLFRQYLREIGRIPLLSAAEEVDLARRV-EAGLFAEEKLRCSPGLDDRLALDLDRLV 153

Query: 46  --DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
                A  RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +T
Sbjct: 154 VLGRLAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFST 213

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI+ AM   +      +++     +  L   + R++  +         P++V A  
Sbjct: 214 YATWWIRQAMSRALADQARTIRVPVHVVE--LINRVVRVQRRMLQERGCEPTPQEVAA-- 269

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
             L+++   V  +        SL+A +   +++     D +    DG     +E      
Sbjct: 270 -HLDLAPERVGEVLRLAQEPVSLHAPV--GEEDDVALGDLI---EDGDAASPVESAAFLL 323

Query: 224 RRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R  L   +S L  RER++ + R       P TLE +   F V+RER+RQIE++   K++
Sbjct: 324 LRQHLEAVLSTLGERERKVVQLRYGLADGRPRTLEEIGRLFGVTRERIRQIESKTLSKLR 383

Query: 282 ES 283
           + 
Sbjct: 384 DH 385


>gi|153003975|ref|YP_001378300.1| RNA polymerase sigma-70 [Anaeromyxobacter sp. Fw109-5]
 gi|152027548|gb|ABS25316.1| RNA polymerase sigma-70 [Anaeromyxobacter sp. Fw109-5]
          Length = 299

 Score =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 117/284 (41%), Positives = 176/284 (61%), Gaps = 7/284 (2%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M+        L +Y+ EI K+ +L  +EE  LA+ +R+ G   AAH+LV ++LR VVK+A
Sbjct: 1   MNRSTGASSTLDQYLREINKVALLTVEEERRLAREFRDEGKTRAAHKLVEANLRFVVKVA 60

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             YR YGL +++++ EGNIGLM+AV+KFDP++  RL +Y++WWI+A +Q +IL+SWSLVK
Sbjct: 61  FEYRSYGLRMADLIQEGNIGLMKAVQKFDPDKEIRLISYAVWWIRAYIQNHILKSWSLVK 120

Query: 126 IGTTANQKRLFFNLRRLKGHLQAIT---DNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           IGTT  Q++LFF+L R +  ++ +T     + +   V  +AKKL V  S+V+ M  R+ G
Sbjct: 121 IGTTQAQRKLFFSLARTRHEIERVTPGAGLDSEGIDVNLVAKKLRVRASDVVEMQQRMEG 180

Query: 183 -DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
            D SL+A +      +S   ++   D D Q+  L   EE       +  +MS L+PRER 
Sbjct: 181 RDLSLDAPVADG---TSTHLEFTPSDADPQDDELARAEEDAIVNRRVNDAMSRLDPRERH 237

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           I EAR + +   TL +L   F  SRER RQ+E RA +K++  +Q
Sbjct: 238 IVEARIMGDGKETLRDLGQHFGFSRERARQLEIRALEKLRRELQ 281


>gi|160945279|ref|ZP_02092505.1| hypothetical protein FAEPRAM212_02798 [Faecalibacterium prausnitzii
           M21/2]
 gi|158443010|gb|EDP20015.1| hypothetical protein FAEPRAM212_02798 [Faecalibacterium prausnitzii
           M21/2]
 gi|295105509|emb|CBL03053.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii SL3/3]
          Length = 360

 Score =  236 bits (603), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 86/278 (30%), Positives = 143/278 (51%), Gaps = 13/278 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI ++P+L   +E  LAK  R      A   L  ++LRLVV +A  Y G G
Sbjct: 87  DDPVKTYLKEIGRVPLLTAGQEMALAKAARAGD-ADARRALSEANLRLVVSVAKRYAGRG 145

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP  +++ EGN+GLM+A +KF+PERGF+ +TY+ WWI+ ++   I      ++I      
Sbjct: 146 LPFLDLIQEGNLGLMKAAEKFEPERGFKFSTYATWWIRQSITRAIADQGRTIRIPVH--- 202

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
             L  ++ R+K     +   N +   V  IA  L++   +V  +        SL   +  
Sbjct: 203 --LVESINRVKKTAGDLLHKNGREPTVEEIAAALDMEPDKVRELLQLSQEPISLETPV-- 258

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            ++  +  +D++  +  G   V +++  R+  R  L   +  L PRE R+   R   E+ 
Sbjct: 259 GEEEDAHLEDFIQDEDAG---VPVDEAGRQLLRRELLHVLKSLTPREERVITLRFGLEDG 315

Query: 253 --VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
              TLE L  EF V+RERVRQIEA+A +K++   + ++
Sbjct: 316 RARTLEELGKEFNVTRERVRQIEAKALRKLRHPSRAKL 353


>gi|306822519|ref|ZP_07455897.1| DNA-directed RNA polymerase sigma subunit RpoD [Bifidobacterium
           dentium ATCC 27679]
 gi|304554064|gb|EFM41973.1| DNA-directed RNA polymerase sigma subunit RpoD [Bifidobacterium
           dentium ATCC 27679]
          Length = 472

 Score =  236 bits (602), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 65/303 (21%), Positives = 138/303 (45%), Gaps = 39/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR---------------------------YREHGD 46
             +  Y+ +I ++ +L  ++E  L++R                           +  +  
Sbjct: 172 DPVKDYLKQIGRVSLLNAEQEVDLSERIEAGLYAQHLLDTEASQMDFKRRRELKWAANDG 231

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ 
Sbjct: 232 KKAKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYAT 291

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      +++     +  +   L R++  +         P+    +A++L
Sbjct: 292 WWIRQAITRAMADQARTIRVPVHMVE--VINKLSRVQRQMLQDLGREPTPD---ELAREL 346

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   +V  +        SL+  +   +   S++ D +    D       +       + 
Sbjct: 347 DMPVEKVQEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDTDAIAPSDAVAFSLLQE 401

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++   K++   
Sbjct: 402 QFKQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPS 461

Query: 285 QKQ 287
           + Q
Sbjct: 462 RSQ 464


>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]
          Length = 620

 Score =  236 bits (602), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 73/261 (27%), Positives = 123/261 (47%), Gaps = 12/261 (4%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L + +E   A  Y E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+
Sbjct: 361 LTELKEISRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 420

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +  
Sbjct: 421 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQ 478

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                  PE    +AK++++ E ++  +        S+   I   D   S   D++    
Sbjct: 479 QYGREATPE---ELAKEMDMPEDKIRKVMKIAKEPISMETPI--GDDEDSHLGDFI---E 530

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSR 266
           D   +  IE     N    +   ++ L PRE ++   R   +     TLE +  +F+V+R
Sbjct: 531 DTNVESPIENTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTR 590

Query: 267 ERVRQIEARAFKKVQESIQKQ 287
           ER+RQIEA+A +K++   + +
Sbjct: 591 ERIRQIEAKALRKLRHPSRSE 611


>gi|256787912|ref|ZP_05526343.1| RNA polymerase principal sigma factor [Streptomyces lividans TK24]
          Length = 365

 Score =  236 bits (602), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 82/302 (27%), Positives = 137/302 (45%), Gaps = 40/302 (13%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG------------------------- 45
                  +Y+ EI +IP+L   EE  LA+R  E G                         
Sbjct: 64  PSSDLFRQYLREIGRIPLLSAAEEVDLARRV-EAGLFAEEKLRCSPGLDDRLALDLDRLV 122

Query: 46  --DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
                A  RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +T
Sbjct: 123 VLGRLAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFST 182

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI+ AM   +      +++     +  L   + R++  +         P++V A  
Sbjct: 183 YATWWIRQAMSRALADQARTIRVPVHVVE--LINRVVRVQRRMLQERGCEPTPQEVAA-- 238

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
             L+++   V  +        SL+A +   +++     D +    DG     +E      
Sbjct: 239 -HLDLAPERVGEVLRLAQEPVSLHAPV--GEEDDVALGDLI---EDGDAASPVESAAFLL 292

Query: 224 RRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R  L   +S L  RER++ + R       P TLE +   F V+RER+RQIE++   K++
Sbjct: 293 LRQHLEAVLSTLGERERKVVQLRYGLADGRPRTLEEIGRLFGVTRERIRQIESKTLSKLR 352

Query: 282 ES 283
           + 
Sbjct: 353 DH 354


>gi|153304|gb|AAA26762.1| principal sigma-like factor [Streptomyces aureofaciens]
 gi|450077|prf||1920369A RNA polymerase:SUBUNIT=sigma
          Length = 393

 Score =  236 bits (602), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 83/296 (28%), Positives = 136/296 (45%), Gaps = 38/296 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYRE----------HGDLS----------------A 49
             +Y+ EI +IP+L   EE  LA+R               DL                 A
Sbjct: 97  FRQYLREIGRIPLLTAAEEVDLARRVEAGLFAEEKLGGAADLDSQLAVDLDRLVVMGRMA 156

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             RL+ S+LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY+ WWI
Sbjct: 157 KRRLIESNLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWI 216

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + AM   +      +++     +  L   + R++  +          E+V   A  L ++
Sbjct: 217 RQAMSRALADQARTIRVPVHVVE--LINRVVRVQRRMLQERGYEPTAEEV---AVHLELT 271

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
              V+ +        SL+A +   +++     D +    DG     +E      R   L 
Sbjct: 272 PERVLEVLRLAQEPVSLHAPV--GEEDDVALGDLI---EDGDAASPVESAAFFLRCEHLE 326

Query: 230 RSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +S L  RER++ + R       P TLE +   F V+RER+RQIE++   K+++ 
Sbjct: 327 AVLSTLGERERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRDH 382


>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|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 =  236 bits (602), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 74/270 (27%), Positives = 125/270 (46%), Gaps = 14/270 (5%)

Query: 22  EIRKIPMLEKQEEYVL--AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           E+ K   L   E   +  A  Y E     A   +V ++LRLV+ IA  Y   GL   +++
Sbjct: 356 EMEKANYLTLAEIKDISRAMAYGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 415

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L
Sbjct: 416 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKL 473

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
            R+   +         PE    +AK++++ E ++  +        S+   I   D   S 
Sbjct: 474 NRISRQMLQQFGREATPE---ELAKEMDMPEDKIRKVMKIAKEPISMETPI--GDDEDSH 528

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLEN 257
             D++    D   +  I+     N    +   ++ L PRE ++   R   +     TLE 
Sbjct: 529 LGDFI---EDTNVESPIDNTTNINLSETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEE 585

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 586 VGKQFDVTRERIRQIEAKALRKLRHPSRSE 615


>gi|198284457|ref|YP_002220778.1| RNA polymerase sigma-32 subunit RpoH [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218667652|ref|YP_002427124.1| RNA polymerase sigma-32 factor [Acidithiobacillus ferrooxidans ATCC
           23270]
 gi|198248978|gb|ACH84571.1| RNA polymerase, sigma 32 subunit, RpoH [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218519865|gb|ACK80451.1| RNA polymerase sigma-32 factor [Acidithiobacillus ferrooxidans ATCC
           23270]
          Length = 286

 Score =  236 bits (602), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 106/272 (38%), Positives = 169/272 (62%), Gaps = 8/272 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
            GL+ Y+  +   P+L  +EE  LA+R R+HGD+ AA  LV SHLR VV++A GYRGYGL
Sbjct: 15  DGLAGYLRFVNAQPLLRPEEERDLARRLRDHGDVDAAKDLVLSHLRFVVRVARGYRGYGL 74

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
             ++++ EGNIGLM+AVK++DP+ G RL ++++ W+KA + E+ILR+W +VK+ TT  Q+
Sbjct: 75  QEADLIQEGNIGLMKAVKRYDPDHGVRLVSFAVHWVKAEIHEFILRNWRIVKVATTKAQR 134

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINS 192
           +LFFNLR  + H   ++      E+  A+A  L V++++V+ M  R++G D SLN  +  
Sbjct: 135 KLFFNLRSSRSHTGWMSG-----EESAAMADDLGVTQAQVLEMEGRMSGYDYSLN--LEP 187

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            ++        L        + L+E++  + +   L  ++S L  R+R I E R L ++P
Sbjct: 188 DEEREGGRAPDLADPTGSPIEQLVERDWDQQQHRALHTALSALPQRDRYIIENRWLSDDP 247

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL+ L  E  VS ERVRQ+E  +  K+++ +
Sbjct: 248 KTLQVLGDELGVSAERVRQLEKSSMGKLRQQM 279


>gi|195970121|ref|NP_387362.2| RNA polymerase factor sigma-32 [Sinorhizobium meliloti 1021]
 gi|307302477|ref|ZP_07582234.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium meliloti
           BL225C]
 gi|307316193|ref|ZP_07595637.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium meliloti
           AK83]
 gi|8131943|gb|AAF73147.1|AF149031_2 sigma factor RpoH2 [Sinorhizobium meliloti]
 gi|10129889|dbj|BAB13518.1| sigma factor [Sinorhizobium meliloti]
 gi|187904236|emb|CAC47835.2| RNA polymerase sigma factor (Sigma-32) [Sinorhizobium meliloti
           1021]
 gi|306898033|gb|EFN28775.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium meliloti
           AK83]
 gi|306903147|gb|EFN33737.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium meliloti
           BL225C]
          Length = 288

 Score =  236 bits (602), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 105/277 (37%), Positives = 168/277 (60%), Gaps = 1/277 (0%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           R I    + P LE+ EE+ LA+ +R   D  A +++  SH+RLV+ +A  +R +GLP+ +
Sbjct: 9   RMIKIAMEAPYLERDEEHALAQAWRNDNDQEARNKIAMSHMRLVISMAAKFRSFGLPMGD 68

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +V EG+IGL++A  +F+P R  R +TY+ WWI+A+MQ+Y+LR+WS+V+ GT++ QK LFF
Sbjct: 69  LVQEGHIGLLEAAARFEPSREVRFSTYATWWIRASMQDYVLRNWSIVRGGTSSAQKALFF 128

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKN 196
           NLRRL+  L               IA  L VS ++V +M+ RL+G D SL A I S D +
Sbjct: 129 NLRRLRARLAQGDRQLTSQAMHEEIAAALGVSLADVQTMDARLSGNDASLQAPIGSGDPD 188

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           +    D+L  +    ++ + +  + +  R  L  ++  L+ RE +I  ARRL E+  TLE
Sbjct: 189 AGARLDFLASEAPLPDEQVSDLIDGERARRWLQVALGELSEREMKIIRARRLTEDGATLE 248

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
            L     +S+ERVRQIE RA +K++ ++  +    ++
Sbjct: 249 ELGVALGISKERVRQIETRALEKLRAALTAKAPALTA 285


>gi|209551384|ref|YP_002283301.1| RNA polymerase factor sigma-32 [Rhizobium leguminosarum bv.
           trifolii WSM2304]
 gi|209537140|gb|ACI57075.1| RNA polymerase, sigma 32 subunit, RpoH [Rhizobium leguminosarum bv.
           trifolii WSM2304]
          Length = 287

 Score =  236 bits (602), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 110/268 (41%), Positives = 171/268 (63%), Gaps = 1/268 (0%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           R I      P L +QEE+ LA R+++H D  A +++  +H+RLV+ +A  +R +GLP+S+
Sbjct: 9   RMIKIAMAAPYLARQEEHDLAIRWKDHDDRGARNQIAMAHMRLVISMAGKFRNFGLPMSD 68

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +V EG +GL++A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFF
Sbjct: 69  LVQEGYVGLLEAAARFEPERDVRFSTYASWWIRASIQDYILRNWSIVRGGTSSAQKALFF 128

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKN 196
           NLRRL+  L               IA  L VS ++V +M+ RL+G D SL A   S D  
Sbjct: 129 NLRRLRAKLAKGDTQLTLQSIHQEIAAALGVSLADVQTMDARLSGNDASLQAPSVSGDAE 188

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           S++  D+LV D    ++ +    + + RR  L  ++  LN RE +I  ARRL E+  TLE
Sbjct: 189 SAEKMDFLVSDDPLPDEQVSNMIDGERRRVWLASALKHLNEREMKIISARRLAEDGATLE 248

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
            L ++  +S+ERVRQIE+RA +K++ ++
Sbjct: 249 ELGADLGISKERVRQIESRAMEKLRSAL 276


>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 =  236 bits (602), Expect = 3e-60,   Method: Composition-based stats.
 Identities = 66/243 (27%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  +HLRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 564 RQAKREMTEAHLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 623

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 624 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 678

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 679 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTVAPADAALHASMRD 733

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 734 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 793

Query: 285 QKQ 287
           +  
Sbjct: 794 RSD 796


>gi|159896548|ref|YP_001542795.1| RpoD family RNA polymerase sigma factor [Herpetosiphon aurantiacus
           ATCC 23779]
 gi|159889587|gb|ABX02667.1| RNA polymerase, sigma 70 subunit, RpoD family [Herpetosiphon
           aurantiacus ATCC 23779]
          Length = 400

 Score =  236 bits (602), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 78/304 (25%), Positives = 142/304 (46%), Gaps = 41/304 (13%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD----------------------- 46
           ++    +  Y+ EI  +P+L+ ++E  LA+   E GD                       
Sbjct: 97  ISVNDTVRLYLREIGLVPLLKGEQEVELARAM-EDGDKAQQELIENDHTLSDVERLALRR 155

Query: 47  -----LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
                  A   L T++LRLVV +A  Y G GL + +++ EGN+GL++AV+KF+  +GF+ 
Sbjct: 156 RIDRGEQAREHLTTANLRLVVSVAKKYIGRGLSLLDLIQEGNVGLIRAVEKFNYTKGFKF 215

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY+ WWI+ A+   I      ++I     +      + R+    + +T  N +      
Sbjct: 216 STYATWWIRQAITRAIADQARTIRIPVHMVE-----TINRMMRTARRLTQENGREPSDEE 270

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           +A+ L+++  +V S+        SL   +    +  SQ  D+L  +     +   +    
Sbjct: 271 LAQALDLTVEKVRSIRKTSMEPVSLETPV--GQEEDSQLGDFLPDEKL---EAPSDAASH 325

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKK 279
           +  R  + + +  L  RE+R+ + R   E+    TLE +  EF V+RER+RQIE +A +K
Sbjct: 326 QMLREQVAQVLDQLTEREKRVLKLRFGLEDGTQRTLEEVGKEFGVTRERIRQIEVKALRK 385

Query: 280 VQES 283
           ++  
Sbjct: 386 LRHP 389


>gi|116254340|ref|YP_770178.1| RNA polymerase factor sigma-32 [Rhizobium leguminosarum bv. viciae
           3841]
 gi|115258988|emb|CAK10097.1| putative rpoH sigma factor [Rhizobium leguminosarum bv. viciae
           3841]
          Length = 304

 Score =  236 bits (602), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 111/268 (41%), Positives = 171/268 (63%), Gaps = 1/268 (0%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           R I      P L +QEE+ LA R+++H D  A +++  +H+RLV+ +A  +R +GLP+S+
Sbjct: 26  RMIKIAMAAPYLARQEEHDLATRWKDHDDRGARNQIAMAHMRLVISMAGKFRNFGLPMSD 85

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +V EG +GL++A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFF
Sbjct: 86  LVQEGYVGLLEAAARFEPERDVRFSTYASWWIRASIQDYILRNWSIVRGGTSSAQKALFF 145

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKN 196
           NLRRL+  L               IA  L VS S+V +M+ RL+G D SL A   S D  
Sbjct: 146 NLRRLRAKLAKGDTQLTLQSIHQEIAAALGVSLSDVQTMDARLSGNDASLQAPSVSGDAE 205

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           S++  D+LV D    ++ +    + + RR  L  ++  LN RE +I  ARRL E+  TLE
Sbjct: 206 SAEKMDFLVSDDPLPDEQVSNMIDGERRRVWLASALKHLNEREMKIISARRLAEDGATLE 265

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
            L ++  +S+ERVRQIE+RA +K++ ++
Sbjct: 266 ELGADLGISKERVRQIESRAMEKLRSAL 293


>gi|212715646|ref|ZP_03323774.1| hypothetical protein BIFCAT_00546 [Bifidobacterium catenulatum DSM
           16992]
 gi|212661013|gb|EEB21588.1| hypothetical protein BIFCAT_00546 [Bifidobacterium catenulatum DSM
           16992]
          Length = 448

 Score =  236 bits (602), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 65/303 (21%), Positives = 138/303 (45%), Gaps = 39/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR---------------------------YREHGD 46
             +  Y+ +I ++ +L  ++E  L++R                           +  +  
Sbjct: 148 DPVKDYLKQIGRVSLLNAEQEVDLSERIEAGLYAQHLLDTESDQMDFKRKRELKWAANDG 207

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ 
Sbjct: 208 RRAKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYAT 267

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      +++     +  +   L R++  +         P+    +A++L
Sbjct: 268 WWIRQAITRAMADQARTIRVPVHMVE--VINKLSRVQRQMLQDLGREPTPD---ELAREL 322

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   +V  +        SL+  +   +   S++ D +    D       +       + 
Sbjct: 323 DMPVEKVQEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDTDAIAPSDAVAFSLLQE 377

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++   K++   
Sbjct: 378 QFRQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPS 437

Query: 285 QKQ 287
           + Q
Sbjct: 438 RSQ 440


>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 =  236 bits (602), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 68/247 (27%), Positives = 116/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 504 EAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 563

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T     P     +
Sbjct: 564 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRINRQILQETGAEPDPAT---L 618

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+++ E +V  +        S+   I   D + S   D++    D       E     
Sbjct: 619 AQKMDMPEDKVRKILKIAKEPISMETPI--GDDDDSHLGDFI---EDTGTLSPSEWALHG 673

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 674 SMRDVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKL 733

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 734 RHPSRAD 740


>gi|291457726|ref|ZP_06597116.1| RNA polymerase sigma factor RpoD [Bifidobacterium breve DSM 20213]
 gi|291380779|gb|EFE88297.1| RNA polymerase sigma factor RpoD [Bifidobacterium breve DSM 20213]
          Length = 472

 Score =  236 bits (602), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 65/303 (21%), Positives = 137/303 (45%), Gaps = 39/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR---------------------------YREHGD 46
             +  Y+ +I ++ +L  ++E  L++R                           +     
Sbjct: 172 DPVKDYLKQIGRVSLLNAEQEVDLSERIEAGLYAQHLLDTESEGMEFKRKRELKWAAADG 231

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ 
Sbjct: 232 KKAKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYAT 291

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      +++     +  +   L R++  +         P+    +A++L
Sbjct: 292 WWIRQAITRAMADQARTIRVPVHMVE--VINKLSRVQRQMLQDLGREPTPD---ELAREL 346

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   +V  +        SL+  +   +   S++ D +    D       +       + 
Sbjct: 347 DMPVEKVQEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDTDAIAPSDAVAFSLLQE 401

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++   K++   
Sbjct: 402 QFKQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPS 461

Query: 285 QKQ 287
           + Q
Sbjct: 462 RSQ 464


>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 =  236 bits (602), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 344 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 403

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 404 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 461

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 462 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 516

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 517 SHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 573

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 574 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 609


>gi|19910022|dbj|BAB87262.1| RNA polymerase sigma factor [Guillardia theta]
          Length = 490

 Score =  236 bits (602), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 80/333 (24%), Positives = 153/333 (45%), Gaps = 55/333 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------------- 43
            +  +  Y+  I ++ +L  +EE  LA+   +                            
Sbjct: 128 ADDSVRWYLQLIGRVRLLRPEEEIQLAREISQLLHWEHVKISLREKLQREPTSSEWTAAC 187

Query: 44  ------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                       H    A  R+V ++LRLVV IA  Y   G+ + +++ EG++GL++A +
Sbjct: 188 KVSDVKKFRSILHNARRAKERMVAANLRLVVSIAKRYVNRGMSLQDLIQEGSLGLIRAAE 247

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD E+GF+ +TY+ WW+K A+   I      +++        L+  +  ++   + +  
Sbjct: 248 KFDSEKGFKFSTYATWWVKQAVTRAIADHSRTIRLPVH-----LYDTISAIRKTTRTLNI 302

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +      IA+K+++S  ++ S+        SL   +  +D ++SQ  D++  D +  
Sbjct: 303 EIGRSPTEEEIAEKMDMSVEKLRSVLQSAQPTLSLERPLK-NDDDASQLSDFIEADQESP 361

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERV 269
           E    E  E+   R+ L   ++ L+PRER +   R   ++    TLE +   F V+RERV
Sbjct: 362 E----EHVEKSMLRDDLENVINSLSPRERDVVRMRYGLDDGRIKTLEEIGQIFSVTRERV 417

Query: 270 RQIEARAFKKVQESIQKQVE---LSSSPPLLQK 299
           RQIEA+A +K+++  +  +    + ++P  L +
Sbjct: 418 RQIEAKAIRKLRQPYRSSILRDYVLATPSNLDR 450


>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 =  236 bits (602), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 564 RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 623

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 624 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 678

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 679 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTVAPADAALHASMRD 733

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 734 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 793

Query: 285 QKQ 287
           +  
Sbjct: 794 RSD 796


>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 =  235 bits (601), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 568 RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 627

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 628 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 682

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 683 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDNNTVAPADAALHASMRD 737

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 738 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 797

Query: 285 QKQ 287
           +  
Sbjct: 798 RSD 800


>gi|296454312|ref|YP_003661455.1| RpoD family RNA polymerase sigma-70 factor [Bifidobacterium longum
           subsp. longum JDM301]
 gi|296183743|gb|ADH00625.1| RNA polymerase, sigma 70 subunit, RpoD family [Bifidobacterium
           longum subsp. longum JDM301]
          Length = 474

 Score =  235 bits (601), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 65/303 (21%), Positives = 137/303 (45%), Gaps = 39/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR---------------------------YREHGD 46
             +  Y+ +I ++ +L  ++E  L++R                           +     
Sbjct: 174 DPVKDYLKQIGRVSLLNAEQEVDLSERIEAGLYAQHLLDTESEGMEFKRKRELKWAAADG 233

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ 
Sbjct: 234 KKAKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYAT 293

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      +++     +  +   L R++  +         P+    +A++L
Sbjct: 294 WWIRQAITRAMADQARTIRVPVHMVE--VINKLSRVQRQMLQDLGREPTPD---ELAREL 348

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   +V  +        SL+  +   +   S++ D +    D       +       + 
Sbjct: 349 DMPVEKVQEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDTDAIAPSDAVAFSLLQE 403

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++   K++   
Sbjct: 404 QFKQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPS 463

Query: 285 QKQ 287
           + Q
Sbjct: 464 RSQ 466


>gi|239832848|ref|ZP_04681177.1| RNA polymerase sigma factor, sigma-70 family [Ochrobactrum
           intermedium LMG 3301]
 gi|239825115|gb|EEQ96683.1| RNA polymerase sigma factor, sigma-70 family [Ochrobactrum
           intermedium LMG 3301]
          Length = 278

 Score =  235 bits (601), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 117/274 (42%), Positives = 179/274 (65%), Gaps = 1/274 (0%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           I      P LE++EE  LA R+RE  D  A HR+ ++H+RLV+ +A  +R + LP+++++
Sbjct: 2   IRSAMSAPYLEREEERDLAIRWRELKDQEALHRITSAHMRLVISMAGRFRKFKLPMNDLI 61

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EG +GL++A  +FDPER  R +TY+ WWI+A+MQ+YILR+WS+V+ GT++ QK LFFNL
Sbjct: 62  QEGYVGLLEAAARFDPEREVRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKALFFNL 121

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSS 198
           RRL+  L    D   K E    I+ +L VS S+V  M+ RL+G D SL+A +NS +  +S
Sbjct: 122 RRLRSKLAQSDDTMSKAEIYREISDQLGVSTSDVEIMDSRLSGPDSSLSAPVNSEESGAS 181

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           +  D+LV DH  Q+++     + + R   L  ++  LN RE  I   RRL ++ VTLE L
Sbjct: 182 RRMDFLVDDHPLQDEIAESSIDMERRNQWLNVALDTLNERELHIIRERRLDDDGVTLEAL 241

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
             +  +S+ERVRQIE+RA +K++ ++  Q EL++
Sbjct: 242 GEKLGISKERVRQIESRAMEKLKIALLSQHELAA 275


>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 =  235 bits (601), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 116/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 561 EAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 620

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T     P     +
Sbjct: 621 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGAEPDPAT---L 675

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+++ E ++  +        S+   I   D + S   D++    D       +     
Sbjct: 676 AQKMDMPEDKIRKILKIAKEPISMETPI--GDDDDSHLGDFI---EDTSTLAPSDAALHG 730

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 731 SMRDVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKL 790

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 791 RHPSRAD 797


>gi|309801431|ref|ZP_07695558.1| RNA polymerase sigma factor RpoD [Bifidobacterium dentium
           JCVIHMP022]
 gi|308221946|gb|EFO78231.1| RNA polymerase sigma factor RpoD [Bifidobacterium dentium
           JCVIHMP022]
          Length = 461

 Score =  235 bits (601), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 65/303 (21%), Positives = 138/303 (45%), Gaps = 39/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR---------------------------YREHGD 46
             +  Y+ +I ++ +L  ++E  L++R                           +  +  
Sbjct: 161 DPVKDYLKQIGRVSLLNAEQEVDLSERIEAGLYAQHLLDTEASQMDFKRRRELKWAANDG 220

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ 
Sbjct: 221 KKAKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYAT 280

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      +++     +  +   L R++  +         P+    +A++L
Sbjct: 281 WWIRQAITRAMADQARTIRVPVHMVE--VINKLSRVQRQMLQDLGREPTPD---ELAREL 335

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   +V  +        SL+  +   +   S++ D +    D       +       + 
Sbjct: 336 DMPVEKVQEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDTDAIAPSDAVAFSLLQE 390

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++   K++   
Sbjct: 391 QFKQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPS 450

Query: 285 QKQ 287
           + Q
Sbjct: 451 RSQ 453


>gi|292486903|ref|YP_003529773.1| RNA polymerase sigma factor rpoD (Sigma-70) [Erwinia amylovora
           CFBP1430]
 gi|292900702|ref|YP_003540071.1| RNA polymerase sigma-70 factor [Erwinia amylovora ATCC 49946]
 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]
          Length = 614

 Score =  235 bits (601), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 345 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 404

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 405 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 462

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 463 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 517

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 518 SHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 574

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 575 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 610


>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 =  235 bits (601), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 343 LGQIEQETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 402

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 403 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 460

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 461 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 515

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 516 SHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 572

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 573 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 608


>gi|22127411|ref|NP_670834.1| RNA polymerase sigma factor RpoD [Yersinia pestis KIM 10]
 gi|21960500|gb|AAM87085.1|AE013956_10 RNA polymerase, sigma(70) factor [Yersinia pestis KIM 10]
          Length = 632

 Score =  235 bits (601), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 363 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 422

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 423 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 480

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 481 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 535

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 536 SHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 592

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 593 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 628


>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 =  235 bits (601), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 365 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 424

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 425 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 482

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 483 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 537

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 538 SHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 594

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 595 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 630


>gi|118578560|ref|YP_899810.1| RNA polymerase sigma-32 subunit RpoH [Pelobacter propionicus DSM
           2379]
 gi|118501270|gb|ABK97752.1| RNA polymerase, sigma 32 subunit, RpoH [Pelobacter propionicus DSM
           2379]
          Length = 292

 Score =  235 bits (601), Expect = 4e-60,   Method: Composition-based stats.
 Identities = 118/282 (41%), Positives = 177/282 (62%), Gaps = 5/282 (1%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             L+ Y+ EIRK  +L ++EE   A R+ E  DL AAH LVTS+LR VVKIA  YR YG+
Sbjct: 10  DSLTLYLAEIRKFNLLSEEEERSCAIRFYEEKDLEAAHTLVTSNLRYVVKIASEYRNYGM 69

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++ EGNIGLM AV+KF+P R  RL +Y++WWI+A +Q YI+ +WSL+KIGTT  Q+
Sbjct: 70  KMLDLIQEGNIGLMMAVRKFNPYRKIRLISYAVWWIRAYIQNYIVSAWSLIKIGTTQAQR 129

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
           +LF+ LR+ K  L  +T ++        IA  L V + EVI M  RL G+ SL+  I  S
Sbjct: 130 KLFYGLRKTKEALLRMTGSDN---DAAEIASMLQVPDHEVIDMEQRLKGEVSLDCQIVES 186

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D     + + +  D   QE++L E ++    +  + ++M  LN +ER I E R   + P+
Sbjct: 187 DG--LTFLETIADDRMNQEELLGENQQELQVKQRVIKAMEGLNEKERYIVEHRITSDEPL 244

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPP 295
           TL++++S F +SRERVRQ+E RA  K+++ ++  +E  +  P
Sbjct: 245 TLQDIASHFSISRERVRQLEERALAKLKKVLEPLMEKPADDP 286


>gi|268315720|ref|YP_003289439.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhodothermus
           marinus DSM 4252]
 gi|262333254|gb|ACY47051.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhodothermus
           marinus DSM 4252]
          Length = 279

 Score =  235 bits (601), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 82/274 (29%), Positives = 151/274 (55%), Gaps = 13/274 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI KIP+L  +EE  LA+R ++ GD  A H+L  ++LR VV +A  Y+G GL +
Sbjct: 10  LDQYLQEIGKIPLLTPEEEVELARRIKQ-GDEEALHKLTRANLRFVVSVAKKYQGQGLSL 68

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           +++++EGN GL++A ++FD  RGF+  +Y++WWI+ A+ + +     +V++    N+   
Sbjct: 69  ADLINEGNYGLIKAAQRFDETRGFKFISYAVWWIRQAILQALAEQSRVVRLP--LNRIGT 126

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              +R++   L    +     E    +A++LN+   ++           S++A     D 
Sbjct: 127 ISKIRKVSARLAQEHERAPSAE---ELAEELNIDVEKIREALQHTGRALSMDAPFTDDDD 183

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPV 253
           NS    D L  + D       E    ++ +  + R++S L+PRE  I        +E+P+
Sbjct: 184 NS--LLDVLPNEEDTSPD---EGLMEESLKIDIERALSTLHPREAEIIRLYFGIGREHPL 238

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           TLE +   F ++RERVRQI+ +A +K+++  +++
Sbjct: 239 TLEEIGQRFGLTRERVRQIKEKALRKLRQKHRRE 272


>gi|332969043|gb|EGK08083.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Kingella kingae
           ATCC 23330]
          Length = 287

 Score =  235 bits (601), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 117/283 (41%), Positives = 175/283 (61%), Gaps = 8/283 (2%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           I +G   L +YIH +  IPML  +EE  LA+R +  GDL AA +L+ SHLR+VV IA GY
Sbjct: 7   IPSGHGSLEQYIHTVNNIPMLSLEEEVGLAER-QIKGDLEAAKKLILSHLRVVVSIARGY 65

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGL  ++++ EGNIGLM+AVK+++P  G RL ++++ WIKA + E+ILR+W LV++ T
Sbjct: 66  DGYGLNQADLIQEGNIGLMKAVKRYEPNHGARLFSFAVHWIKAEIHEFILRNWRLVRVAT 125

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN 187
           T  Q++LFFNLR ++  L A++     P++  +IA  L V  SEV+ M  R+ G D  L 
Sbjct: 126 TKPQRKLFFNLRSMRSSLSALS-----PKEAQSIADDLGVKLSEVMEMEQRMTGRDIGLL 180

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           A  N  D  +    +WL        Q L  K     + + L  +++ L+ R RRI E R 
Sbjct: 181 ADNNDDDDAAFAPIEWLSDASHEPSQQLERKAHYALQTDGLQAALAQLDERSRRIVETRW 240

Query: 248 LQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           LQ+   +TL  L++E+ VS ER+RQIE +A +K++  + +Q +
Sbjct: 241 LQDEGALTLHELAAEYGVSAERIRQIEVKAMQKLKALLAEQAD 283


>gi|262195735|ref|YP_003266944.1| RNA polymerase, sigma 70 family subunit [Haliangium ochraceum DSM
           14365]
 gi|262079082|gb|ACY15051.1| putative RNA polymerase, sigma 70 family subunit [Haliangium
           ochraceum DSM 14365]
          Length = 389

 Score =  235 bits (601), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 101/279 (36%), Positives = 169/279 (60%), Gaps = 7/279 (2%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
              LS YI E ++ P+L ++EE+ LA +  E+ D  AA RL+ ++LRLVVKI+  YR   
Sbjct: 103 HDPLSAYIQETKRYPLLSREEEHDLAVKLVENEDADAARRLIEANLRLVVKISYEYRRAY 162

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
             + +++ EGNIGLMQAV+K+DP RG +L++Y+ WWI+A + ++IL +W LVKIGTT  Q
Sbjct: 163 RNLLDLIQEGNIGLMQAVRKYDPYRGVKLSSYAAWWIRAYILKFILNNWRLVKIGTTQAQ 222

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALIN 191
           ++LFFNLR+ +  L+ +            +A+ L+V+E EV+ M  RL+  D SL+A + 
Sbjct: 223 RKLFFNLRKERERLEQL----GFTPTPALLAENLDVTEKEVVEMEKRLSAPDASLDAPMQ 278

Query: 192 SSDKNSSQWQDWLV--YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
             +  + + +   +   + D  ++ + + + ++  R  L R    L  RE  IF  R L 
Sbjct: 279 GEEDGAPRTRMDYLPTEETDRPDRQVAQSQFQELLREKLERFAETLEGREETIFRERWLT 338

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           + P TL+ +  ++ VSRER RQ+E R   ++++ ++ ++
Sbjct: 339 DTPSTLQQIGDQYGVSRERARQLEKRLLGRLRKYLEAEL 377


>gi|117928920|ref|YP_873471.1| RNA polymerase, sigma 28 subunit [Acidothermus cellulolyticus 11B]
 gi|117649383|gb|ABK53485.1| RNA polymerase, sigma 28 subunit [Acidothermus cellulolyticus 11B]
          Length = 413

 Score =  235 bits (601), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 72/301 (23%), Positives = 135/301 (44%), Gaps = 39/301 (12%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------------EHGDLSA--- 49
               +  Y++EI + P+L+  +E  LAKR                     E  DL A   
Sbjct: 112 SHDPVRNYLNEIGRTPLLDAAQEVELAKRIEAGVYADVKLNDPTLQLTEEERRDLEAIRD 171

Query: 50  -----AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
                   ++ ++LRLVV +A  Y   G+   +V+ EGN+GL++AV+KFD  +G++ +TY
Sbjct: 172 DGARAKAHMLEANLRLVVSVAKRYSNRGMAFLDVIQEGNLGLIRAVEKFDYTKGYKFSTY 231

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +MWWI+ A+   +      +++     +      L +L    + +     +      +A 
Sbjct: 232 AMWWIRQAITRALADQARTIRLPVHVVE-----QLNKLTRLQRELHQQFGREPTAEELAA 286

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L+ +  ++  M        SL+  +   D   +   D +    D +     +  E +  
Sbjct: 287 ELDRTPEQIEEMLRNARQPVSLDNPV--GDDEDTLLGDLI---EDMEAPAASDALEYQAM 341

Query: 225 RNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            + + R+++ L+PRE R+   R       P TL+ +  +  ++RERVRQIE  A  K+++
Sbjct: 342 IDTVHRALAGLDPREARVIALRFGLVGGRPHTLDEIGRDVGLTRERVRQIEREALAKLRD 401

Query: 283 S 283
            
Sbjct: 402 P 402


>gi|300114350|ref|YP_003760925.1| RNA polymerase sigma 32 subunit RpoH [Nitrosococcus watsonii C-113]
 gi|299540287|gb|ADJ28604.1| RNA polymerase, sigma 32 subunit, RpoH [Nitrosococcus watsonii
           C-113]
          Length = 287

 Score =  235 bits (601), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 107/284 (37%), Positives = 167/284 (58%), Gaps = 7/284 (2%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
             N +++      L+ Y      IP+L   +E  LA R R++ DL AA +LV SHLR V+
Sbjct: 7   NDNWALVPLAVGNLNTYCQNAHSIPVLSADQERSLALRLRQYNDLEAARQLVLSHLRFVI 66

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           +IA GY GYGLP+++++ EGNIGLM+AVK+FDPE+G RL ++++ WI+A + E+ILR+W 
Sbjct: 67  RIARGYNGYGLPLADLIQEGNIGLMKAVKRFDPEQGVRLVSFAVHWIRAEIHEFILRNWR 126

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +VK+ TT  Q++LFFNLR  K  L  +        +V  +A+ L +S  +V+ M  RL+ 
Sbjct: 127 IVKVATTKAQRKLFFNLRSAKKRLGWLNRK-----EVNEVAQDLGISPKQVMEMEARLSS 181

Query: 183 -DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR-NMLTRSMSVLNPRER 240
            D   +       +NS       + D        +E  +++N     L +++ VL+ R R
Sbjct: 182 QDTPFDGTNTEESENSLPAPMAYLADPSADPAQKMELLDQENYYGQRLRQALEVLDLRSR 241

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            I   R LQEN  TL  L++E+++S ER+RQ+E  A KK++  +
Sbjct: 242 TIINRRWLQENKSTLHELAAEYQISAERIRQLENNAIKKMRSVL 285


>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 =  235 bits (601), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 70/267 (26%), Positives = 126/267 (47%), Gaps = 14/267 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           +  ++   + KR    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 341 ITIEQAKDINKRMSIGEAKAKRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 400

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 401 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 458

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    +++K+ + E ++  +        S+   I   D   S   D+L  
Sbjct: 459 LQEIGREPTPE---ELSEKMLIPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFL-- 511

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D    + ++    ++ R+     +S L  RE ++ + R   +     TLE +  +F+V
Sbjct: 512 -EDTSLDLPLDSATSESLRSATHDVLSGLTAREAKVLKMRFGIDMSTDHTLEEVGKQFDV 570

Query: 265 SRERVRQIEARAFKKVQESIQKQVELS 291
           +RER+RQIEA+A +K++   + ++  S
Sbjct: 571 TRERIRQIEAKALRKLRHPSRSEILRS 597


>gi|283456279|ref|YP_003360843.1| RNA polymerase principal sigma factor hrdB [Bifidobacterium dentium
           Bd1]
 gi|283102913|gb|ADB10019.1| RNA polymerase principal sigma factor hrdB [Bifidobacterium dentium
           Bd1]
          Length = 328

 Score =  235 bits (601), Expect = 5e-60,   Method: Composition-based stats.
 Identities = 65/303 (21%), Positives = 138/303 (45%), Gaps = 39/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR---------------------------YREHGD 46
             +  Y+ +I ++ +L  ++E  L++R                           +  +  
Sbjct: 28  DPVKDYLKQIGRVSLLNAEQEVDLSERIEAGLYAQHLLDTEASQMDFKRRRELKWAANDG 87

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ 
Sbjct: 88  KKAKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYAT 147

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      +++     +  +   L R++  +         P+    +A++L
Sbjct: 148 WWIRQAITRAMADQARTIRVPVHMVE--VINKLSRVQRQMLQDLGREPTPD---ELAREL 202

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   +V  +        SL+  +   +   S++ D +    D       +       + 
Sbjct: 203 DMPVEKVQEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDTDAIAPSDAVAFSLLQE 257

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++   K++   
Sbjct: 258 QFKQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPS 317

Query: 285 QKQ 287
           + Q
Sbjct: 318 RSQ 320


>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 =  235 bits (600), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 66/243 (27%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 586 RKAKKEMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 645

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A K+
Sbjct: 646 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGAEPDPAT---LAVKM 700

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++ E ++  +        S+   I   D + S   D++    D       +     + RN
Sbjct: 701 DMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDNNTLAPADAALHASMRN 755

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 756 VVKDVLDSLTPREAKVLRMRFGVEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 815

Query: 285 QKQ 287
           +  
Sbjct: 816 RSD 818


>gi|253699229|ref|YP_003020418.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter sp. M21]
 gi|251774079|gb|ACT16660.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter sp. M21]
          Length = 285

 Score =  235 bits (600), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 112/271 (41%), Positives = 167/271 (61%), Gaps = 5/271 (1%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             L+ Y+ EI + P+L   EE  LA R+R  GDL AAHRL+TS+LR VVKIA  YR YG+
Sbjct: 10  DNLTLYLTEINRFPLLTADEEMDLACRFRREGDLEAAHRLITSNLRFVVKIAGEYRSYGM 69

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++ EGNIGLM AV+KFDP++G RL +Y++WWI+A +Q +I+ +WSL+KIGTT  Q+
Sbjct: 70  KMLDLIQEGNIGLMMAVRKFDPDKGVRLISYAVWWIRAYIQNHIISAWSLLKIGTTQAQR 129

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
           +LFF L + K  +  +T        + A A  L+V + E   M  RL G+ SL+  +   
Sbjct: 130 KLFFKLNQAKQAIVNMTGEG----DLHAAAISLDVKDHEAQEMEQRLRGELSLDVEMFEG 185

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           +   +   + L      QE++L E++E       +  ++  LN +ER + E R   ENP+
Sbjct: 186 EGGGTFL-ESLPDLRQNQEEMLAERQETTILERNVASALEDLNEKERFVIEQRVAAENPM 244

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           TL+ ++  F +SRERVRQIE  A KK++  +
Sbjct: 245 TLQEIADHFSISRERVRQIEEGALKKMKRFL 275


>gi|265991792|ref|ZP_06104349.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|263002748|gb|EEZ15151.1| RNA polymerase factor sigma-32 [Brucella melitensis bv. 1 str.
           Rev.1]
          Length = 293

 Score =  235 bits (600), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 117/293 (39%), Positives = 184/293 (62%), Gaps = 4/293 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  ++          +   I      P LE++EE  LA R++E  D  A HR+ ++H+RL
Sbjct: 1   MAVRSFPAAAASSQSM---IRSAMSAPYLEREEERALAIRWKETKDQDALHRITSAHMRL 57

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A  +R + LP+S+++ EG +GL++   +FDP+R  R +TY+ WWI+A+MQ+YILR+
Sbjct: 58  VISMAGRFRKFKLPMSDLIQEGYVGLLEEAARFDPDRDVRFSTYASWWIRASMQDYILRN 117

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WS+V+ GT++ QK LFFNLRRL+  L    DN  K E    I+ +L VS S+V  M+ RL
Sbjct: 118 WSIVRGGTSSAQKVLFFNLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTSDVEFMDSRL 177

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +G D SL+A +N  +  +S+  D+LV DH  Q+++     + + R   LTR++  LN RE
Sbjct: 178 SGPDSSLSASMNGEETGASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTRALDTLNERE 237

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
             I   RRL ++ VTLE L  +  +S++RVRQIE+RA +K++ ++  Q EL++
Sbjct: 238 LHIIRERRLDDDGVTLEALGEKLGISKQRVRQIESRAMEKLKIALLSQHELAA 290


>gi|146284301|ref|YP_001174454.1| RNA polymerase factor sigma-32 [Pseudomonas stutzeri A1501]
 gi|145572506|gb|ABP81612.1| sigma factor RpoH [Pseudomonas stutzeri A1501]
 gi|327482685|gb|AEA85995.1| RNA polymerase factor sigma-32 [Pseudomonas stutzeri DSM 4166]
          Length = 284

 Score =  235 bits (600), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 102/274 (37%), Positives = 160/274 (58%), Gaps = 7/274 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+  +  +P+L  ++E  LA+R   H DL AA ++V +HLR VV IA  Y GYGL 
Sbjct: 16  NLEAYVQTVNSLPLLTVEQERELAERLFYHQDLEAARQMVLAHLRFVVHIARSYSGYGLA 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGN+GLM+AVK+F+PE G RL ++++ WI+A + E+ILR+W +VK+ TT  Q++
Sbjct: 76  QADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIRAEIHEFILRNWRIVKVATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           LFFNLR  K  L  + +     ++V A+A  L V   EV  M  RL G +        +D
Sbjct: 136 LFFNLRSQKKRLAWLNN-----DEVTAVADSLGVEPHEVREMESRLTGHDMAFDPAADAD 190

Query: 195 KNSS-QWQDWLVYDHDGQEQVLIEKEERKNRR-NMLTRSMSVLNPRERRIFEARRLQENP 252
            +S+ Q     + DH       +E  +  +   + L  ++  L+ R R I + R L E+ 
Sbjct: 191 DDSAYQSPAHYLEDHRYDPARQLEDADWSDSSTSSLHAALEGLDERSRDILQQRWLNEDK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            TL +L++++ VS ER+RQ+E  A  K++ SIQ 
Sbjct: 251 ATLHDLAAKYNVSAERIRQLEKNAMNKLKGSIQA 284


>gi|197121539|ref|YP_002133490.1| RNA polymerase, sigma 70 family subunit [Anaeromyxobacter sp. K]
 gi|196171388|gb|ACG72361.1| putative RNA polymerase, sigma 70 family subunit [Anaeromyxobacter
           sp. K]
          Length = 300

 Score =  235 bits (600), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 115/284 (40%), Positives = 178/284 (62%), Gaps = 7/284 (2%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M+        L +Y+ EI ++ +L  +EE  LA+++R+ G+  A HRLV ++LR VVK+A
Sbjct: 1   MNRPSTASSTLDQYLREINRVALLTVEEERRLARQFRDEGNTRAGHRLVEANLRFVVKVA 60

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             YR YGL +++++ EGNIGLM+AV+KFDP++  RL +Y++WWI+A +Q +IL+SWSLVK
Sbjct: 61  FEYRSYGLRMADLIQEGNIGLMKAVQKFDPDKEIRLISYAVWWIRAYIQNHILKSWSLVK 120

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ---VVAIAKKLNVSESEVISMNCRLAG 182
           IGTT  Q++LFF+L R +  ++ +T      E+   V  +AKKL V  S+V+ M  R+ G
Sbjct: 121 IGTTQAQRKLFFSLARTRHEIERLTPGAGLAEEGIDVALVAKKLRVRPSDVVEMTQRMEG 180

Query: 183 -DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
            D SL+A +      +S   ++   D + Q++ L   EE       ++ +M  L+PRER 
Sbjct: 181 RDLSLDAPVADG---TSTHLEFTPADGEPQDEELARAEEDALLARRVSEAMGRLDPRERH 237

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           I EAR + E   TL +L   F  SRER RQ+E RA +K++  ++
Sbjct: 238 IVEARIMGEGKETLRDLGHHFGFSRERARQLEIRALEKLRRDLE 281


>gi|312200424|ref|YP_004020485.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EuI1c]
 gi|311231760|gb|ADP84615.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EuI1c]
          Length = 403

 Score =  235 bits (600), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 83/307 (27%), Positives = 132/307 (42%), Gaps = 39/307 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYR---------------------------EHGD 46
             +  Y+  I K P+L  + E  LAKR                             E   
Sbjct: 104 DPVRMYLASIGKTPLLTAEGEVDLAKRIEAGLFAGHKLETAVEEMSPGQRLDLIAVERDG 163

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             AA +LV ++LRLVV IA  Y G G+   +VV EGN+GL++AV+KFD  +G++ +TY+ 
Sbjct: 164 QVAARQLVEANLRLVVSIAKRYAGRGMLFLDVVQEGNLGLIRAVEKFDYTKGYKFSTYAT 223

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WW++ A+   +      V++     +  L   L RL+  L          E    +A  L
Sbjct: 224 WWVRQAITRALADQSRTVRLPVHLVE--LLNQLVRLRRELLMELGREATRE---ELATAL 278

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            V+ + V  +        SL++ +   D   ++  D +    D      +E      R  
Sbjct: 279 GVTANRVDELQRISREPVSLDSPV--GDDADTELGDLI---EDTAAIEPVEAAMVSVRAA 333

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L+  +  L  RERR+ + R         TLE +  EF ++RER+RQIE R   K++   
Sbjct: 334 QLSAVLRALPDRERRVIQLRFGLADGQVHTLEEIGREFGLTRERIRQIEQRTLAKLRHPA 393

Query: 285 QKQVELS 291
           + +   S
Sbjct: 394 RSEALRS 400


>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 =  235 bits (600), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 563 RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 622

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 623 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 677

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 678 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTVAPADAALHASMRD 732

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 733 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 792

Query: 285 QKQ 287
           +  
Sbjct: 793 RSD 795


>gi|330040254|ref|XP_003239821.1| RNA-polymerase sigma factor [Cryptomonas paramecium]
 gi|327206746|gb|AEA38923.1| RNA-polymerase sigma factor [Cryptomonas paramecium]
          Length = 414

 Score =  235 bits (600), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 79/319 (24%), Positives = 147/319 (46%), Gaps = 52/319 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------------- 43
            +  +  Y+  I K+ +L+ +EE  LA+   +                            
Sbjct: 82  SDDSVRWYLQLIGKVKLLKPEEEIQLAREISQLLQWEHIKVFLKEKLGREPTALEWSAAC 141

Query: 44  ------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                       +    A  R++ ++LRLVV IA  Y   G+ + ++V EG++GL++A +
Sbjct: 142 KISDVQKFKTVLYNSRKAKERMIAANLRLVVSIAKRYSNRGMSLQDLVQEGSLGLIRATE 201

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD E+GF+ +TY+ WWIK ++   I      +++        L+  L  +K   + +T 
Sbjct: 202 KFDSEKGFKFSTYATWWIKQSVSRAIADHSRTIRLPVH-----LYDTLSAIKKTTRILTI 256

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +      IA K++V+  ++ S+        SL   I  +D +++Q  D++  D +  
Sbjct: 257 ELGRSPTEEEIACKMDVTVDKLRSVLQSAQPTLSLEKPIK-NDGDTAQLSDFIEADQESP 315

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERV 269
           +    E  E+   R+ L   ++ L+ RER +   R   ++    TLE +   F V+RERV
Sbjct: 316 D----EHVEKSMLRDDLRDVINSLSLRERDVIRMRYGLDDGKIRTLEEIGQIFSVTRERV 371

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIEA+A +K+++  +  +
Sbjct: 372 RQIEAKAIRKLRQPYRSSI 390


>gi|73666941|ref|YP_302957.1| RNA polymerase sigma factor rpoD [Ehrlichia canis str. Jake]
 gi|72394082|gb|AAZ68359.1| RNA polymerase, sigma 70 subunit, RpoD [Ehrlichia canis str. Jake]
          Length = 622

 Score =  235 bits (600), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 75/272 (27%), Positives = 133/272 (48%), Gaps = 19/272 (6%)

Query: 24  RKIPMLEKQ----EEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
            KI +L  +    E   L  + ++H   +  A   ++ ++LRLVV IA  Y   GL   +
Sbjct: 354 SKIKLLSGENNLTEFKALVTKIQKHERAANQAKQEMIKANLRLVVSIAKKYSNRGLQFLD 413

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +V EGNIGLM+AV KFD +RG++ +TY+ WW++ A+   I      ++I        +  
Sbjct: 414 LVQEGNIGLMKAVDKFDYKRGYKFSTYATWWVRQAITRAIADQARTIRIPVH-----MIE 468

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + ++   L+ +     +   +  ++ KLN++  ++  +   +    SL + I   D +S
Sbjct: 469 TVNKINRTLRQMLHEMGREPTLEELSAKLNINVDKIRKVMKIVKDPVSLESPI--GDDDS 526

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVT 254
           S + D +    D +     +     + R + T+ +S L P+E RI   R          T
Sbjct: 527 STFGDCI---EDKRAVKPEDAAVLADLREITTKVLSTLTPKEERILRMRFGIGKGGKDHT 583

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 584 LEEVGKLFNVTRERIRQIEAKALRKLRHPSRA 615


>gi|86359605|ref|YP_471497.1| RNA polymerase factor sigma-32 [Rhizobium etli CFN 42]
 gi|86283707|gb|ABC92770.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CFN
           42]
          Length = 287

 Score =  235 bits (600), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 110/268 (41%), Positives = 171/268 (63%), Gaps = 1/268 (0%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           R I      P L +QEE+ LA R+++H D  A +++  +H+RLV+ +A  +R +GLP+S+
Sbjct: 9   RMIKIAMAAPYLARQEEHDLATRWKDHDDRGARNQIAMAHMRLVISMAGKFRNFGLPMSD 68

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +V EG +GL++A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFF
Sbjct: 69  LVQEGYVGLLEAAARFEPERDVRFSTYASWWIRASIQDYILRNWSIVRGGTSSAQKALFF 128

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKN 196
           NLRRL+  L               IA  L VS ++V +M+ RL+G D SL A   S D  
Sbjct: 129 NLRRLRAKLARGDTQLTLQSIHQEIAAALGVSLADVQTMDARLSGNDASLQAPSVSGDAE 188

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           S++  D+LV D    ++ +    + + RR  L  ++  LN RE +I  ARRL E+  TLE
Sbjct: 189 SAEKMDFLVSDDPLPDEQVSNMIDGERRRVWLASALKHLNEREMKIISARRLAEDGATLE 248

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
            L ++  +S+ERVRQIE+RA +K++ ++
Sbjct: 249 ELGADLGISKERVRQIESRAMEKLRSAL 276


>gi|110635708|ref|YP_675916.1| RNA polymerase factor sigma-32 [Mesorhizobium sp. BNC1]
 gi|110286692|gb|ABG64751.1| RNA polymerase, sigma 32 subunit, RpoH [Chelativorans sp. BNC1]
          Length = 284

 Score =  235 bits (600), Expect = 6e-60,   Method: Composition-based stats.
 Identities = 110/268 (41%), Positives = 173/268 (64%), Gaps = 1/268 (0%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           I    K P L ++EE+ LA +++E  D  A HR++ +H+RLV+ +A  +R +GL +S+++
Sbjct: 10  IKAAMKAPYLGREEEHELALQWKERQDQQALHRMIMAHMRLVIAMAGKFRNFGLSMSDLI 69

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EG++GL++A  +FDPER  R +TY+ WWI+A+MQ+YILR+WS+V+ GT++ QK LFFNL
Sbjct: 70  QEGHVGLLEAAARFDPEREVRFSTYATWWIRASMQDYILRNWSIVRGGTSSAQKALFFNL 129

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSSDKNSS 198
           RRL+  LQ         +    +A+ L VSES+V  M+ RL A D SLNA + S    +S
Sbjct: 130 RRLRMKLQKAGGTTPSEDVYREVAQALRVSESDVAMMDSRLAAADASLNAPLRSDSDPTS 189

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           +  D+L+ D    ++++ E  + + +   L +++  LN RE  I   RRL E   TLE L
Sbjct: 190 ERIDFLICDKPQPDELVREAIDGERKAQWLHQALGTLNGRELTIVRERRLSEEGATLEAL 249

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQK 286
            +   +S+ERVRQIE+RA +K++ ++ K
Sbjct: 250 GASLGISKERVRQIESRALEKLRTALVK 277


>gi|170731288|ref|YP_001776721.1| RNA polymerase factor sigma-32 [Xylella fastidiosa M12]
 gi|167966081|gb|ACA13091.1| RNA polymerase sigma-32 factor [Xylella fastidiosa M12]
          Length = 288

 Score =  235 bits (600), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 114/275 (41%), Positives = 168/275 (61%), Gaps = 9/275 (3%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           + N    L  YI  + +I +L   EE +LA+RYR+  DL AA  LV SHLR VV++A GY
Sbjct: 16  VPNALGSLEAYISAVHQISVLSVDEEQLLARRYRDQQDLDAARELVHSHLRFVVRVARGY 75

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGL + +++ EGNIGLM+AVK+FDP+ G RL +++M WI+A M E+IL++W +VK+ T
Sbjct: 76  SGYGLSLGDLIQEGNIGLMKAVKRFDPDMGVRLVSFAMHWIRAEMHEFILKNWRIVKVAT 135

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN 187
           T  Q++LFFNLR+ +  L       +  E+V A+A+ LNVSE EV+ M  RL+G D   +
Sbjct: 136 TKAQRKLFFNLRKSRTRLGW-----MNAEEVSAVARDLNVSEREVLEMESRLSGRDIGFD 190

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           A     D        +L+ +     Q        + +  +L   +SVL+ R R I + R 
Sbjct: 191 AP--EEDNAPLSPVGYLIANDGDPSQAYERGNSEETQLRLLQEGLSVLDTRSRDIIQRRW 248

Query: 248 LQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           L+ +  +TL+ L+ E+ VS ER+RQIEA A KK++
Sbjct: 249 LETDKKITLQELAEEYGVSAERIRQIEANALKKMK 283


>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 =  235 bits (600), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 567 RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 626

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 627 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 681

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 682 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTVAPADAALHASMRD 736

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 737 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 796

Query: 285 QKQ 287
           +  
Sbjct: 797 RSD 799


>gi|183601374|ref|ZP_02962744.1| RNA polymerase sigma factor RpoD [Bifidobacterium animalis subsp.
           lactis HN019]
 gi|219683429|ref|YP_002469812.1| RNA polymerase sigma factor [Bifidobacterium animalis subsp. lactis
           AD011]
 gi|241191127|ref|YP_002968521.1| RNA polymerase sigma factor [Bifidobacterium animalis subsp. lactis
           Bl-04]
 gi|241196533|ref|YP_002970088.1| RNA polymerase sigma factor [Bifidobacterium animalis subsp. lactis
           DSM 10140]
 gi|183218980|gb|EDT89621.1| RNA polymerase sigma factor RpoD [Bifidobacterium animalis subsp.
           lactis HN019]
 gi|219621079|gb|ACL29236.1| principal sigma factor RpoD [Bifidobacterium animalis subsp. lactis
           AD011]
 gi|240249519|gb|ACS46459.1| DNA-directed RNA polymerase sigma subunit [Bifidobacterium animalis
           subsp. lactis Bl-04]
 gi|240251087|gb|ACS48026.1| DNA-directed RNA polymerase sigma subunit [Bifidobacterium animalis
           subsp. lactis DSM 10140]
 gi|295794116|gb|ADG33651.1| DNA-directed RNA polymerase sigma subunit [Bifidobacterium animalis
           subsp. lactis V9]
          Length = 488

 Score =  235 bits (600), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 68/303 (22%), Positives = 138/303 (45%), Gaps = 39/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------HGD----------------- 46
             +  Y+ +I ++ +L  ++E  L++R              GD                 
Sbjct: 188 DPVKDYLKQIGRVSLLNAEQEVDLSERIEAGLYAQHLLDTEGDTMEFRRKRELKWAAADG 247

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ 
Sbjct: 248 KKAKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYAT 307

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      +++     +  +   L R++  +         P+    +A++L
Sbjct: 308 WWIRQAITRAMADQARTIRVPVHMVE--VINKLSRVQRQMLQDLGREPTPD---ELAREL 362

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   +V  +        SL+  +   +   S++ D +    D       E       + 
Sbjct: 363 DMPVEKVQEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDTDAIAPSEAVAFSLLQE 417

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++   K++   
Sbjct: 418 QFRQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPS 477

Query: 285 QKQ 287
           + Q
Sbjct: 478 RSQ 480


>gi|222150148|ref|YP_002551105.1| RNA polymerase factor sigma-32 [Agrobacterium vitis S4]
 gi|221737130|gb|ACM38093.1| alternative sigma factor RpoH [Agrobacterium vitis S4]
          Length = 285

 Score =  235 bits (600), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 107/259 (41%), Positives = 167/259 (64%), Gaps = 1/259 (0%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE+QEE+ LA R++   D  A +++  +H+RLV+ +A  +RG+GLP+ +++ EG IGL
Sbjct: 18  PYLERQEEHDLAVRWKHGNDQVARNQIAHAHMRLVIAMASKFRGFGLPLGDLIQEGYIGL 77

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +F+P R  R +TY+ WWI+A+MQ+YILR+WS+V+ GT+++QK LFFNLRRL+  L
Sbjct: 78  LEAAARFEPTRDVRFSTYAGWWIRASMQDYILRNWSIVRGGTSSSQKALFFNLRRLRAKL 137

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLV 205
                          IA  L VS ++V SM+ RL+  D SL A I+++ +  ++  D L 
Sbjct: 138 AQGDQRLTDQAIHQEIATALGVSLADVQSMDARLSSNDTSLQAPISNNGEEGAERLDMLA 197

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            D    ++ + +  + + R + L  +M+ LN RE RI  ARRL E+  TLE L  E  +S
Sbjct: 198 SDEPTPDEQVTDMIDTERRLDWLRGAMAHLNEREMRIIRARRLSEDGATLEELGCELGIS 257

Query: 266 RERVRQIEARAFKKVQESI 284
           +ERVRQIE RA +K++ ++
Sbjct: 258 KERVRQIETRAMEKLKVAL 276


>gi|86157496|ref|YP_464281.1| RNA polymerase sigma-32 subunit RpoH [Anaeromyxobacter dehalogenans
           2CP-C]
 gi|85774007|gb|ABC80844.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter
           dehalogenans 2CP-C]
          Length = 300

 Score =  235 bits (599), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 118/289 (40%), Positives = 181/289 (62%), Gaps = 12/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           MNR + S        L +Y+ EI ++ +L  +EE  LA+++R+ G+  A HRLV ++LR 
Sbjct: 1   MNRPSTSSST-----LDQYLREINRVALLTVEEERRLARQFRDEGNTRAGHRLVEANLRF 55

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VVK+A  YR YGL +++++ EGNIGLM+AV+KFDP++  RL +Y++WWI+A +Q +IL+S
Sbjct: 56  VVKVAFEYRSYGLRMADLIQEGNIGLMKAVQKFDPDKEIRLISYAVWWIRAYIQNHILKS 115

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ---VVAIAKKLNVSESEVISMN 177
           WSLVKIGTT  Q++LFF+L R +  ++ +T      E+   V  +AKKL V  S+V+ M 
Sbjct: 116 WSLVKIGTTQAQRKLFFSLARTRHEIERLTPGAGLAEEGIDVALVAKKLRVRPSDVVEMT 175

Query: 178 CRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
            R+ G D SL+A +      +S   ++   D + Q++ L   EE       ++ +M  L+
Sbjct: 176 QRMEGRDLSLDAPVADG---TSTHLEFTPADGEPQDEELARAEEDALLARRVSEAMGRLD 232

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           PRER I EAR + E   TL +L   F  SRER RQ+E RA +K++  ++
Sbjct: 233 PRERHIVEARIMGEGKETLRDLGHHFGFSRERARQLEIRALEKLRRDLE 281


>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 =  235 bits (599), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 116/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 525 EAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 584

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T     P     +
Sbjct: 585 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGAEPDPAT---L 639

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+++ E ++  +        S+   I   D + S   D++    D       +     
Sbjct: 640 AQKMDMPEDKIRKILKIAKEPISMETPI--GDDDDSHLGDFI---EDTSTLAPSDAALHG 694

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 695 SMRDVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKL 754

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 755 RHPSRAD 761


>gi|1519642|gb|AAB07554.1| SigD [Chloroflexus aurantiacus J-10-fl]
          Length = 398

 Score =  235 bits (599), Expect = 7e-60,   Method: Composition-based stats.
 Identities = 78/298 (26%), Positives = 138/298 (46%), Gaps = 37/298 (12%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------------HGDL 47
              +  Y+ EI ++P+L  ++E  LA+   +                             
Sbjct: 98  SDSVRLYLREIGQVPLLTAEQEKRLAQLIEQGQEAERKLATLPPDSPEAARLKQLKAKGE 157

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A H +  ++LRLVV IA  YR  GLP+ +++ EG++GL++A++KFD  +G++ +TY+ W
Sbjct: 158 EARHEMAAANLRLVVSIAKRYRDRGLPLLDLIQEGSLGLLRAIEKFDYTKGYKFSTYATW 217

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WIK A+   +     LV++        L   L R++   + +T +  +      +A  L 
Sbjct: 218 WIKQALSRALADQSRLVRLPVH-----LGETLNRIQSARRQLTQSLGREPTDTELANHLG 272

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +SE ++ ++        SL   +   ++ +S   D++   H                R  
Sbjct: 273 MSEEKLATVRRTAQDPVSLATPV--GEEANSTLADFIPDPHALDADDAAAS---GIVRQQ 327

Query: 228 LTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +T ++  L+ RERR+ E R       P TLE +   F V+RERVRQIE +A +K++  
Sbjct: 328 ITAALDQLSERERRVLELRYGLVDGQPRTLEEVGKAFGVTRERVRQIEVKALRKLRHP 385


>gi|220916304|ref|YP_002491608.1| RNA polymerase, sigma 70 family subunit [Anaeromyxobacter
           dehalogenans 2CP-1]
 gi|219954158|gb|ACL64542.1| putative RNA polymerase, sigma 70 family subunit [Anaeromyxobacter
           dehalogenans 2CP-1]
          Length = 300

 Score =  235 bits (599), Expect = 8e-60,   Method: Composition-based stats.
 Identities = 115/284 (40%), Positives = 178/284 (62%), Gaps = 7/284 (2%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M+        L +Y+ EI ++ +L  +EE  LA+++R+ G+  A HRLV ++LR VVK+A
Sbjct: 1   MNRPSTASSTLDQYLREINRVALLTVEEERRLARQFRDEGNTRAGHRLVEANLRFVVKVA 60

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             YR YGL +++++ EGNIGLM+AV+KFDP++  RL +Y++WWI+A +Q +IL+SWSLVK
Sbjct: 61  FEYRSYGLRMADLIQEGNIGLMKAVQKFDPDKEIRLISYAVWWIRAYIQNHILKSWSLVK 120

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ---VVAIAKKLNVSESEVISMNCRLAG 182
           IGTT  Q++LFF+L R +  ++ +T      E+   V  +AKKL V  S+V+ M  R+ G
Sbjct: 121 IGTTQAQRKLFFSLARTRHEIERLTPGAGLAEEGIDVALVAKKLRVRPSDVVEMTQRMEG 180

Query: 183 -DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
            D SL+A +      +S   ++   D + Q++ L   EE       ++ +M  L+PRER 
Sbjct: 181 RDLSLDAPVADG---TSTHLEFTPADGEPQDEELARAEEDALLARRVSEAMGRLDPRERH 237

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           I EAR + E   TL +L   F  SRER RQ+E RA +K++  ++
Sbjct: 238 IVEARIMGEGKETLRDLGHHFGFSRERARQLEIRALEKLRRDLE 281


>gi|254468686|ref|ZP_05082092.1| alternative sigma factor RpoH [beta proteobacterium KB13]
 gi|207087496|gb|EDZ64779.1| alternative sigma factor RpoH [beta proteobacterium KB13]
          Length = 281

 Score =  235 bits (599), Expect = 8e-60,   Method: Composition-based stats.
 Identities = 119/286 (41%), Positives = 173/286 (60%), Gaps = 7/286 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           MN      +         Y  +++ IP+L + EE  LAK+  E  DL+AA +L+ SHLRL
Sbjct: 1   MNNALTIPLSPSLDSFDLYQQQVQAIPLLTEHEEMNLAKKLHEENDLNAARQLIMSHLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+KIA  Y GYGL  +++V EGNIGLM+AVK+FDP RG RL +++M+WIKA +QE+++R+
Sbjct: 61  VIKIARSYSGYGLNQADLVQEGNIGLMKAVKRFDPSRGVRLVSFAMYWIKAEIQEFVVRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W LVK  TT  Q++LFFNLR +K  LQ      LK E++  IAK+LNV ES+V  M  R 
Sbjct: 121 WRLVKTATTKAQRKLFFNLRSMKKTLQ-----PLKQEEIKEIAKELNVKESDVKEMEYRF 175

Query: 181 AGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            G+E +L+     ++    +   +L  ++    + LI KE   N  + L+ ++  ++ R 
Sbjct: 176 NGNEIALDYQDEDNEDEVFRPISYLQDENADPVKQLISKESESNNLSALSNAIKSIDERS 235

Query: 240 RRIFEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R I E+R L E    TL  L+ E  VS ER+RQIE  A KK++  +
Sbjct: 236 RYILESRWLNEEKSKTLHELADELGVSAERIRQIEQNALKKLKSLM 281


>gi|148265963|ref|YP_001232669.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter uraniireducens
           Rf4]
 gi|146399463|gb|ABQ28096.1| RNA polymerase, sigma 32 subunit, RpoH [Geobacter uraniireducens
           Rf4]
          Length = 280

 Score =  235 bits (599), Expect = 8e-60,   Method: Composition-based stats.
 Identities = 113/271 (41%), Positives = 174/271 (64%), Gaps = 5/271 (1%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             LS Y+ EIR+ P+L  +EE+ LA +  E  DL AAHRL+TS+LR VVKIA  YR YG+
Sbjct: 6   DNLSLYLAEIRRFPVLSAEEEHGLAVKLYEEKDLEAAHRLITSNLRFVVKIAGEYRSYGM 65

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++ EGNIGLM AV+KF+P +GFRL +Y++WWI+A +Q +I+ +WSL+KIGTT  Q+
Sbjct: 66  KMLDLIQEGNIGLMMAVRKFNPYKGFRLISYAVWWIRAYIQNHIVSTWSLLKIGTTQAQR 125

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
           +LFF L + K  ++++T      + + A A  L+V ESE   M+ R+ GD  L+A + + 
Sbjct: 126 KLFFKLNQAKSAIRSMTGGG---DDLQAAALSLDVKESEAQEMDQRMRGDYFLDAEVVTG 182

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           +       + L  +   QE++L E EE       +  +++ LN +ER + E R   + P+
Sbjct: 183 EG--LTMLESLPDERRNQEELLGEAEESAILEREVAAALTCLNEKERYVIEQRVSSDEPL 240

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           TL+ ++  F +SRERVRQIE  A KK++ ++
Sbjct: 241 TLQEIADHFSISRERVRQIEEGALKKMKRAL 271


>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 =  235 bits (599), Expect = 8e-60,   Method: Composition-based stats.
 Identities = 74/298 (24%), Positives = 140/298 (46%), Gaps = 17/298 (5%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPM---LEKQEEYVLAKRYR--EHGDLSAAHRLVT 55
           MN+     +   E  + R + ++R+I     L  ++   + +R    E     A   +V 
Sbjct: 325 MNKPWSDKLSEVEDDVMRSLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVE 384

Query: 56  SHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQE 115
           ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+  
Sbjct: 385 ANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 444

Query: 116 YILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
            I      ++I            L R+   +         PE    +A+++ + E ++  
Sbjct: 445 SIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPSPE---ELAERMLMPEDKIRK 499

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
           +        S+   +   D + S   D++    D   ++ ++    ++ R+     ++ L
Sbjct: 500 VLKIAKEPISMETPV--GDDDDSHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGL 554

Query: 236 NPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
             RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 555 TAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 612


>gi|90420276|ref|ZP_01228184.1| RNA polymerase major sigma-32 factor [Aurantimonas manganoxydans
           SI85-9A1]
 gi|90335610|gb|EAS49360.1| RNA polymerase major sigma-32 factor [Aurantimonas manganoxydans
           SI85-9A1]
          Length = 289

 Score =  235 bits (599), Expect = 9e-60,   Method: Composition-based stats.
 Identities = 106/267 (39%), Positives = 173/267 (64%), Gaps = 2/267 (0%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           I      P L+++EEY LA R++E  D  A H++ ++H+RLV+ +A  +R +GL +++++
Sbjct: 11  IRAAMSAPYLQREEEYELAVRWKEKRDQEALHKITSAHMRLVISMAAKFRHFGLAMNDLI 70

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EG++GL++A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFFNL
Sbjct: 71  QEGHVGLLEAAARFEPEREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKALFFNL 130

Query: 140 RRLKGHLQAITDNNLK-PEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           RRL+  L    D  +        IA  L VSE +V  M+ RL+G D SLNA +   +  S
Sbjct: 131 RRLRARLSQGADGGVTGSAMYKEIATALKVSEGDVALMDSRLSGPDSSLNAPLMEDESGS 190

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           +  QD+LV +    ++++    + + R   L  ++ VL+ RE +I   RRLQ++  TLE 
Sbjct: 191 ADRQDFLVSNSPLPDEMVSVSIDDERRVTWLHSALDVLSERELKIIRERRLQDDGATLEA 250

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESI 284
           L ++  +S+ERVRQIE RA +K++ ++
Sbjct: 251 LGTKLGISKERVRQIETRALEKLRAAL 277


>gi|225351336|ref|ZP_03742359.1| hypothetical protein BIFPSEUDO_02929 [Bifidobacterium
           pseudocatenulatum DSM 20438]
 gi|225157680|gb|EEG70963.1| hypothetical protein BIFPSEUDO_02929 [Bifidobacterium
           pseudocatenulatum DSM 20438]
          Length = 472

 Score =  235 bits (599), Expect = 9e-60,   Method: Composition-based stats.
 Identities = 65/303 (21%), Positives = 138/303 (45%), Gaps = 39/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR---------------------------YREHGD 46
             +  Y+ +I ++ +L  ++E  L++R                           +  +  
Sbjct: 172 DPVKDYLKQIGRVSLLNAEQEVDLSERIEAGLYAQHLLDTESDQMDFKRKRELKWAANDG 231

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ 
Sbjct: 232 RRAKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYAT 291

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      +++     +  +   L R++  +         P+    +A++L
Sbjct: 292 WWIRQAITRAMADQARTIRVPVHMVE--VINKLSRVQRQMLQDLGREPTPD---ELAREL 346

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   +V  +        SL+  +   +   S++ D +    D       +       + 
Sbjct: 347 DMPVEKVQEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDTDAIAPSDAVAFSLLQE 401

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++   K++   
Sbjct: 402 QFRQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPS 461

Query: 285 QKQ 287
           + Q
Sbjct: 462 RSQ 464


>gi|320334918|ref|YP_004171629.1| RpoD subfamily RNA polymerase sigma-70 factor [Deinococcus
           maricopensis DSM 21211]
 gi|319756207|gb|ADV67964.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Deinococcus
           maricopensis DSM 21211]
          Length = 525

 Score =  235 bits (599), Expect = 9e-60,   Method: Composition-based stats.
 Identities = 78/296 (26%), Positives = 130/296 (43%), Gaps = 36/296 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE--------------------------HGDL 47
             + +Y+HEI ++P+L  +EE  LA+R  E                              
Sbjct: 224 DPVRQYLHEIGRVPLLTLEEEISLARRIEEGEEARKVLDEQPELEDRQRRRLQRQVEDGA 283

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   L+ ++LRLVV IA  Y G GL   +++ EGN GL++AV+KF+  R ++ +TY+ W
Sbjct: 284 AARQGLIEANLRLVVSIAKKYTGRGLGFLDLIQEGNQGLIRAVEKFEYRRRYKFSTYATW 343

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I     +      L R    LQ         E++   A    
Sbjct: 344 WIRQAINRAIADQARTIRIPVHMVE--TINKLTRTARQLQQELSREPTYEEIAE-AMGPG 400

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
              ++V  +        SL   I   D+  S + D++    D      +E   +      
Sbjct: 401 WDAAKVEEVQKVSQEPVSLETPI--GDEKDSFYGDFIP---DENLDSPVENAAKTLLSEE 455

Query: 228 LTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           L +++S L  RE  + + R+        TLE +   F V+RER+RQIE +A +K++
Sbjct: 456 LEKALSKLTEREAMVLKFRKGLVDGREHTLEEVGQRFNVTRERIRQIENKALRKLK 511


>gi|298245985|ref|ZP_06969791.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297553466|gb|EFH87331.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 417

 Score =  235 bits (599), Expect = 9e-60,   Method: Composition-based stats.
 Identities = 79/291 (27%), Positives = 137/291 (47%), Gaps = 23/291 (7%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
              +  Y+ EI ++PM+  + E  LA+R  E GD  A  + + ++LRLVV IA  Y G G
Sbjct: 147 SDAVMTYLREIGRVPMITHEREIELAQRI-ESGDRDAMKQFILANLRLVVSIAKRYVGRG 205

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L + +++ EGNIGL++AV+++D  RG R +T++ WWI+ A+   +      +++    N 
Sbjct: 206 LTLLDLIQEGNIGLIRAVQRYDWRRGHRFSTHATWWIRQAISRAVADKGRTIRLPVYVN- 264

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 L R++   Q +     +      +A+   +    +I +        SL   +  
Sbjct: 265 ----TALNRIRRERQRLLQELGREPSEQELAEATGLDPVRMIELQAAPGAPVSLELPV-- 318

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            + +  +  D L        + L   +  K+    +    SVL PRE+ + + R    N 
Sbjct: 319 GEDDDQELGDVLPDTESASPEDLATTQTLKDEVQRVLE--SVLTPREQLVLQLRFGLGNG 376

Query: 253 --VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQKPR 301
               LE +  E  ++RERVRQIEA A  K+++           PP+L++ R
Sbjct: 377 QAHPLEQVGRELGITRERVRQIEAGALAKLRQ-----------PPVLERLR 416


>gi|88812406|ref|ZP_01127656.1| RNA polymerase sigma factor [Nitrococcus mobilis Nb-231]
 gi|88790413|gb|EAR21530.1| RNA polymerase sigma factor [Nitrococcus mobilis Nb-231]
          Length = 356

 Score =  235 bits (599), Expect = 9e-60,   Method: Composition-based stats.
 Identities = 82/270 (30%), Positives = 136/270 (50%), Gaps = 13/270 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A+R  + GD SA  R++ S+LRLVVKIA  Y   GL   ++
Sbjct: 88  YLNEIGYSPLLTAKEEVYYARR-AQGGDESARKRMIESNLRLVVKIARRYMNRGLAFLDL 146

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K +   
Sbjct: 147 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-IKEINQY 205

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +         +  IA  ++ S  +V  M     G  S++  I        
Sbjct: 206 LRVAR----QLVQRLDHEPTLEEIAIAMDRSIEDVRHMMGLNEGVTSVDIPI--GRDADR 259

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
              D +  + +      ++ E+  +    L   ++ L  ++R + E R         TLE
Sbjct: 260 VLLDAIPDEVNPDPFAALQDEDVVSH---LDAWLNELTEKQRAVVERRFGLHGHEKATLE 316

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  E  V+RERVRQI+  A KK++E +++
Sbjct: 317 EVGDEIGVTRERVRQIQIDALKKLREVMER 346


>gi|227329605|ref|ZP_03833629.1| RNA polymerase sigma factor RpoD [Pectobacterium carotovorum subsp.
           carotovorum WPP14]
          Length = 611

 Score =  235 bits (599), Expect = 9e-60,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 342 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 401

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 402 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 459

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 460 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 514

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 515 SHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 571

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 572 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 607


>gi|238024932|ref|YP_002909164.1| RNA polymerase, sigma 70 subunit, RpoD family protein [Burkholderia
           glumae BGR1]
 gi|237879597|gb|ACR31929.1| RNA polymerase, sigma 70 subunit, RpoD family protein [Burkholderia
           glumae BGR1]
          Length = 805

 Score =  234 bits (598), Expect = 9e-60,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 564 RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 623

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 624 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 678

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 679 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDSNTVAPADAALHASMRD 733

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 734 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 793

Query: 285 QKQ 287
           +  
Sbjct: 794 RSD 796


>gi|88807657|ref|ZP_01123169.1| RNA polymerase sigma factor [Synechococcus sp. WH 7805]
 gi|88788871|gb|EAR20026.1| RNA polymerase sigma factor [Synechococcus sp. WH 7805]
          Length = 447

 Score =  234 bits (598), Expect = 9e-60,   Method: Composition-based stats.
 Identities = 77/313 (24%), Positives = 143/313 (45%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE--------------HG------------ 45
            E  +  Y+ EI +I +L   EE  LA++  +              +G            
Sbjct: 135 TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLHLEELAAQFESDNGKLPDTKEWAALV 194

Query: 46  -------------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 195 EMPVIRFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 254

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 255 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKVLSQE 309

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA+ + ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 310 FGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADIENPE 367

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
           Q + +   R++    L   ++ L+PRER +   R   ++    TLE +   F+V+RER+R
Sbjct: 368 QDVAKNLLRED----LEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIR 423

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 424 QIEAKALRKLRHP 436


>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 =  234 bits (598), Expect = 9e-60,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 564 RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 623

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 624 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 678

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 679 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTVAPADAAPHASMRD 733

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 734 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 793

Query: 285 QKQ 287
           +  
Sbjct: 794 RSD 796


>gi|227113748|ref|ZP_03827404.1| RNA polymerase sigma factor RpoD [Pectobacterium carotovorum subsp.
           brasiliensis PBR1692]
          Length = 611

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 342 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 401

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 402 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 459

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 460 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 514

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 515 SHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 571

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 572 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 607


>gi|325103187|ref|YP_004272841.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pedobacter
           saltans DSM 12145]
 gi|324972035|gb|ADY51019.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pedobacter
           saltans DSM 12145]
          Length = 286

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 79/288 (27%), Positives = 153/288 (53%), Gaps = 14/288 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+HEI K+ ++  +EE +LA++ RE GD +A  RL  ++LR VV
Sbjct: 5   KITQSITNRESQSLDKYLHEIGKVDLITAEEEVILAQKIRE-GDQAALERLTKTNLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A K+FD  +GF+  +Y++WWI+ ++ + I     
Sbjct: 64  SVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETKGFKFISYAVWWIRQSILQAIAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    NQ      + +    L+   +    PE    +A  L  +  ++         
Sbjct: 124 IVRLP--LNQVGSLSKISKAFSKLEQEYEREPSPE---ELADILETTVDKISDTLSNSGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     ++N+    D L  D+   + +LI+    ++    + RS+S L  RER I
Sbjct: 179 HVSMDAPFVQGEENT--LLDVLENDNPNTDSMLID----ESLSEEIKRSLSTLTEREREI 232

Query: 243 FEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
                     +P++LE +  +F ++RERVRQI+ +A ++++ + + ++
Sbjct: 233 IVLFFGLGSNHPLSLEEIGEKFNLTRERVRQIKDKALQRLRHTSRSKI 280


>gi|73540591|ref|YP_295111.1| RNA polymerase sigma factor RpoD [Ralstonia eutropha JMP134]
 gi|72118004|gb|AAZ60267.1| Sigma-70 region 1.2 [Ralstonia eutropha JMP134]
          Length = 783

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 68/247 (27%), Positives = 116/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 538 EKRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 597

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T N   P     +
Sbjct: 598 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGNEPDPAT---L 652

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+ + E ++  +        S+   I   D + S   D++    D       E     
Sbjct: 653 AEKMEMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTLAPAEAALHG 707

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 708 SMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKL 767

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 768 RHPSRSD 774


>gi|28493466|ref|NP_787627.1| RNA polymerase sigma factor [Tropheryma whipplei str. Twist]
 gi|28476507|gb|AAO44596.1| RNA polymerase sigma factor [Tropheryma whipplei str. Twist]
          Length = 387

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 78/311 (25%), Positives = 142/311 (45%), Gaps = 40/311 (12%)

Query: 7   SIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRY----------REHGDLS------ 48
           S +++G     +  Y+ +I K+ +L   EE  LAKR            E GDL+      
Sbjct: 80  SPVISGATADPVKDYLKQIGKVSLLTADEEVSLAKRIEAGLFAEEKLSESGDLAPKLKRE 139

Query: 49  ----------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
                     A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G
Sbjct: 140 LRWVVRDGQRAKDHLLAANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEKFDYVKG 199

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           F+ +TY+ WWI+ A+   +      ++I     +  +   L R++  L         P+ 
Sbjct: 200 FKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLSRVQRQLLQDLGREPTPD- 256

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              + ++L++    V+ +        SL+  +   D+  S++ D +    D       + 
Sbjct: 257 --ELGRELDMPPERVVEVQKYGREPISLHTPL--GDEGDSEFGDLI---EDVDAVAPDDA 309

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARA 276
                 +  L   +  L+ RE  +   R   ++  P TL+ +   F+V+RER+RQIEA+ 
Sbjct: 310 VGFSMLQQQLRLLLDSLSEREAGVIRMRFGLDDDMPKTLDYVGEYFDVTRERIRQIEAKT 369

Query: 277 FKKVQESIQKQ 287
             K++   + Q
Sbjct: 370 MAKLRHPSRSQ 380


>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 =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 68/276 (24%), Positives = 132/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 362 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 421

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +  
Sbjct: 422 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIE 476

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + +L G  + +     +      +A+++ + E ++  +        S+   I   D   
Sbjct: 477 TINKLNGISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 534

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 535 SHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 591

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 592 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 627


>gi|116514979|ref|YP_802608.1| RNA polymerase major s factor [Buchnera aphidicola str. Cc (Cinara
           cedri)]
 gi|116256833|gb|ABJ90515.1| RNA polymerase major s factor [Buchnera aphidicola str. Cc (Cinara
           cedri)]
          Length = 613

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 65/248 (26%), Positives = 121/248 (48%), Gaps = 12/248 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 368 EEKAKRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 427

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            L R+   +         PE    +
Sbjct: 428 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEIGREPTPE---EL 482

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           ++K+ +SE ++  +        S+   I   + + +   D++    D   ++ +E    +
Sbjct: 483 SEKMLISEEKIRKVLKIAKEPISMETPI--GEDDDTHLGDFI---EDTNLELPLESATSE 537

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + + +    +S L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 538 SLKTITNDVLSGLTDREAKVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKALRKL 597

Query: 281 QESIQKQV 288
           +   + ++
Sbjct: 598 RHPSRSEI 605


>gi|254444043|ref|ZP_05057519.1| RNA polymerase sigma factor, sigma-70 family [Verrucomicrobiae
           bacterium DG1235]
 gi|198258351|gb|EDY82659.1| RNA polymerase sigma factor, sigma-70 family [Verrucomicrobiae
           bacterium DG1235]
          Length = 377

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 80/275 (29%), Positives = 147/275 (53%), Gaps = 12/275 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            +  Y+ EI +I +L   +E  LA+R +  G+  A   ++ S+LRLVVKIA  Y+ +GLP
Sbjct: 80  SIRTYLQEIGRIDLLTPAQEVTLARRIQ-AGEKEARDLMIKSNLRLVVKIAHDYKDFGLP 138

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++SEGNIGL++AV++FDP++G +L+TY+ WWIK +++  +      +++        
Sbjct: 139 VLDLISEGNIGLVKAVERFDPDKGGKLSTYAAWWIKQSIKRALANQSKTIRLPVH----- 193

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           L   + R++     +T+   +      +A+ L +  ++V  +        SLNA +   D
Sbjct: 194 LVDKISRMRKMALMLTEELGREPTDQELAEMLEMPVNKVSHLKSVSVRPTSLNAPVG-ED 252

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENP 252
            NS+++ + +  D         E    K+ R  L   +  L  RE  I   R     ++P
Sbjct: 253 GNSTEFGEIVGDD---NAPTPYENLHEKSLRGDLHEMIDGLEDREAEIIRLRFGLNGDSP 309

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +TLE +   F+++RERVRQ++  A  K+++ +  +
Sbjct: 310 LTLEEVGQVFDITRERVRQLQNIALSKMRKIMASK 344


>gi|282880271|ref|ZP_06288987.1| putative RNA polymerase sigma factor RpoD [Prevotella timonensis
           CRIS 5C-B1]
 gi|281305866|gb|EFA97910.1| putative RNA polymerase sigma factor RpoD [Prevotella timonensis
           CRIS 5C-B1]
          Length = 292

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 76/286 (26%), Positives = 147/286 (51%), Gaps = 12/286 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI +  +L  +EE  LA+R ++ GD  A  +L  ++LR VV
Sbjct: 10  KITKSITNRESAALDKYLQEIGREDLLSTEEEIELAQRIKK-GDRKALDKLTKANLRFVV 68

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + I     
Sbjct: 69  SVAKQYQNQGLSLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSR 128

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    NQ      + +L+   +   +   +      IA+++++ E +VI        
Sbjct: 129 IVRLP--LNQVGSVNKINQLQNKFEQEFE---RRPNSSEIAERIDIPEDKVIDAMKANGK 183

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A  +  D NS      +    D    +   +   ++ R  +  ++  LN RER +
Sbjct: 184 HVSVDAPFSDGDDNS-----LIDVLPDSDIPMADNELVMESLRKEIADALHTLNERERNV 238

Query: 243 FEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            E       P +TLE +   + ++RERVRQI  +A +K++++ + +
Sbjct: 239 IECFYGINQPEMTLEEIGDRYGLTRERVRQIREKALRKLRKNTKNK 284


>gi|197116970|ref|YP_002137397.1| RNA polymerase sigma-32 factor RpoH [Geobacter bemidjiensis Bem]
 gi|197086330|gb|ACH37601.1| RNA polymerase sigma-32 factor RpoH [Geobacter bemidjiensis Bem]
          Length = 285

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 110/280 (39%), Positives = 171/280 (61%), Gaps = 5/280 (1%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             L+ Y+ EI + P+L   EE  LA R+R  GDL AAHRL+T++LR VVKIA  YR YG+
Sbjct: 10  DNLTLYLAEINRFPLLTADEEMDLAGRFRREGDLEAAHRLITANLRFVVKIAGEYRSYGM 69

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++ EGNIGLM AV+KFDP++G RL +Y++WWI+A +Q +I+ +WSL+KIGTT  Q+
Sbjct: 70  KMLDLIQEGNIGLMMAVRKFDPDKGVRLISYAVWWIRAYIQNHIISAWSLLKIGTTQAQR 129

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
           +LFF L + K  +  +T        + A A  L+V ++E   M  RL G+ SL+  +   
Sbjct: 130 KLFFKLNQAKQAIVNMTGEG----DLHAAAISLDVKDNEAREMEQRLRGELSLDVEMFEG 185

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           +   +   + L      QE++L E++E       +  ++  LN +E+ + E R   E+P+
Sbjct: 186 EGGGTFL-ESLPDLRQNQEEMLAERQETTILERNVASALENLNEKEKFVIEQRVAAEDPM 244

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           TL+ ++  F +SRERVRQIE  A KK++  +   V  + +
Sbjct: 245 TLQEIADHFSISRERVRQIEEGALKKMKRFLAPLVMEAEA 284


>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 =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 71/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 343 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 402

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 403 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 460

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 461 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 515

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    +N R+     ++ L  RE ++   R   +     TL
Sbjct: 516 SHLGDFI---EDTTLELPLDSATSENLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 572

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 573 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 608


>gi|311086952|gb|ADP67032.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. JF99
           (Acyrthosiphon pisum)]
          Length = 612

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 71/267 (26%), Positives = 127/267 (47%), Gaps = 14/267 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L  ++   + KR    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 352 LTIEQVKDINKRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 411

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 412 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 469

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    +++K+ + E ++  +        S+   I   D + S   D++  
Sbjct: 470 LQEIGREPTPE---ELSEKMLIPEDKIRKVLKIAKEPISMETPI--GDDDDSHLGDFI-- 522

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   ++ ++    ++ R+     +S L  RE ++   R   +     TLE +  +F+V
Sbjct: 523 -EDTTLELPLDSATSESLRSATHDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 581

Query: 265 SRERVRQIEARAFKKVQESIQKQVELS 291
           +RER+RQIEA+A +K++   + +V  S
Sbjct: 582 TRERIRQIEAKALRKLRHPSRSEVLRS 608


>gi|328882302|emb|CCA55541.1| RNA polymerase principal sigma factor HrdA [Streptomyces venezuelae
           ATCC 10712]
          Length = 336

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 81/301 (26%), Positives = 139/301 (46%), Gaps = 38/301 (12%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKR----------YREHGDLS------------ 48
                  +Y+ EI +IP+L  +EE  LA+R               DL             
Sbjct: 35  PSSDLFRQYLREIGRIPLLTAEEEVDLARRVEAGLFAEEKLANTPDLDSRLASDLDRLVV 94

Query: 49  ----AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
               A  +L+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY
Sbjct: 95  LGRIAKRKLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTY 154

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + WWI+ AM   +      +++     +  L   + R++  +          E+V A   
Sbjct: 155 ATWWIRQAMSRALADQARTIRVPVHVVE--LINRVIRVQRRMLQERGYEPTAEEVAA--- 209

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L+++   V  +        SL+A +   ++      D +    DG     +E       
Sbjct: 210 QLDLAPERVGEVLRLAQEPVSLHAPV--GEEEDVALGDLI---EDGDAASPVESAAFLLL 264

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           R  L   +S L  RER++ + R   ++  P TLE +   F V+RER+RQIE++   K+++
Sbjct: 265 RRHLEDVLSTLGERERKVVQLRYGLDDGRPRTLEEIGRIFGVTRERIRQIESKTLGKLRD 324

Query: 283 S 283
            
Sbjct: 325 H 325


>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 =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 343 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 402

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 403 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 460

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 461 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 515

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 516 SHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 572

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 573 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 608


>gi|87123878|ref|ZP_01079728.1| Sigma-70 factor [Synechococcus sp. RS9917]
 gi|86168447|gb|EAQ69704.1| Sigma-70 factor [Synechococcus sp. RS9917]
          Length = 456

 Score =  234 bits (598), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 76/313 (24%), Positives = 141/313 (45%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG-------------------------- 45
            E  +  Y+ EI +I +L   EE  LA++  +                            
Sbjct: 144 TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLLLEELAAQFESDNGREPDTKEWAALV 203

Query: 46  -------------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 204 EMPVIKFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 263

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 264 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKVLSQE 318

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA+ + ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 319 FGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADIENPE 376

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
           Q + +   R++    L   ++ L+PRER +   R   ++    TLE +   F+V+RER+R
Sbjct: 377 QDVAKNLLRED----LEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIR 432

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 433 QIEAKALRKLRHP 445


>gi|325971114|ref|YP_004247305.1| RNA polymerase, sigma 70 family subunit [Spirochaeta sp. Buddy]
 gi|324026352|gb|ADY13111.1| putative RNA polymerase, sigma 70 family subunit [Spirochaeta sp.
           Buddy]
          Length = 293

 Score =  234 bits (597), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 83/290 (28%), Positives = 157/290 (54%), Gaps = 12/290 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  + S   +    LS Y+ EI +IP+L  QEE VLAKR ++ GD  A  R++ S+LR 
Sbjct: 8   LNHTDDSYAYDDANILSMYLKEINQIPLLTPQEELVLAKRAQK-GDEFARKRMIESNLRF 66

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y+  G+P+ ++++EGNIGLM A++KFDP++G+   +Y++WWI+ ++ + I   
Sbjct: 67  VVNVAKKYQNQGMPLVDLINEGNIGLMTALEKFDPDKGYHFISYAVWWIRQSIMKAINEK 126

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              V++       R    L+  K     + D +     +  I          V ++    
Sbjct: 127 SRAVRLPL----NRTNELLQMHKAQRSLMKDLSTDDPSMEEIGTLTGFDPKHVSNLLSIS 182

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL+A +  +D ++S   D++  +    EQ L++   +++ R++L    + L+ +ER
Sbjct: 183 RDLISLDAPVF-TDGSASNIGDFIEDESQNPEQSLLDASLKEDVRSLL----ATLSDKER 237

Query: 241 RIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            I E R   E   P++L+ +   + +++ER+RQIE +A ++++   + ++
Sbjct: 238 DIIELRFGLEGKTPMSLKEIGELYNLTKERIRQIEKKALERLRNPSKSKM 287


>gi|262376306|ref|ZP_06069536.1| alternative sigma factor RpoH [Acinetobacter lwoffii SH145]
 gi|262308907|gb|EEY90040.1| alternative sigma factor RpoH [Acinetobacter lwoffii SH145]
          Length = 289

 Score =  234 bits (597), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 106/284 (37%), Positives = 164/284 (57%), Gaps = 9/284 (3%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +S+   G + L  YI  + +IP+L  ++E  LA+RY    DL AA  LV SHLR VV IA
Sbjct: 11  LSLSAPG-VNLGAYISTVNQIPILTAEQEKELAERYYYDQDLDAAKMLVMSHLRFVVHIA 69

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y GYGLP  +++ EGN+GLM+AVK+FDP  G RL ++++ WIKA + EY++R+W +VK
Sbjct: 70  RSYAGYGLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAEIHEYVIRNWRIVK 129

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG--D 183
           I TT  Q++LFFNLR LK   + +T       +  +IA  LNV+  +V+ M  RL     
Sbjct: 130 IATTKAQRKLFFNLRSLKKSSKKLT-----LAEAQSIANDLNVTPEQVLEMEGRLTAYDA 184

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR-NMLTRSMSVLNPRERRI 242
               +  +  + ++       + D+      LIE E+ + +  + L  +M  L+ R R I
Sbjct: 185 AFDASSDDDDEGSTHVAPALYLEDNRYDPARLIENEDYEEQSTSALHEAMDQLDDRSRNI 244

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + R L +   TL  L++E+ VS ER+RQ+E  A +K++ ++  
Sbjct: 245 LQRRWLDDEKSTLHELAAEYNVSAERIRQLEKNAMEKIKVAMSS 288


>gi|118594538|ref|ZP_01551885.1| RNA polymerase sigma factor [Methylophilales bacterium HTCC2181]
 gi|118440316|gb|EAV46943.1| RNA polymerase sigma factor [Methylophilales bacterium HTCC2181]
          Length = 286

 Score =  234 bits (597), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 124/286 (43%), Positives = 180/286 (62%), Gaps = 8/286 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           MN   ++     +   + Y   IRKIP L  +EEY LA R +   DL AA +L+ SHL+L
Sbjct: 1   MNNLTLTTPFVSDD-FNIYQETIRKIPSLTAEEEYELASRLKRDNDLEAAKKLILSHLKL 59

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+KIA  Y GY LP +++V EGNIGLM+AVKKFDP+RG RL +Y+++WIKA +QEY++++
Sbjct: 60  VMKIARSYSGYNLPHADLVQEGNIGLMKAVKKFDPDRGVRLVSYAIYWIKAEIQEYVVKN 119

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W LVK  TT  Q++LFFNLR L+  LQ      LKPE++ +IA +LNV ESEV  M  RL
Sbjct: 120 WRLVKTATTKAQRKLFFNLRSLRKTLQ-----PLKPEEIKSIANELNVKESEVREMEFRL 174

Query: 181 AGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            G E +++   + S+++  +   +L  +     + +   +   N    L  ++S L+ R 
Sbjct: 175 NGKETTIDYSDDESEEDHFRPISYLEDETPSPLEKIEMDQAESNVSAELQHALSELDSRS 234

Query: 240 RRIFEARRLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R + EAR L +N   TL  L+S+F+VS ER+RQIE  AFKK++  +
Sbjct: 235 RSVVEARWLNDNKSETLNELASKFKVSAERIRQIEKNAFKKIRALM 280


>gi|12744861|gb|AAK06822.1|AF326688_1 RNA polymerase sigma-32 factor [Burkholderia pseudomallei]
          Length = 281

 Score =  234 bits (597), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 116/281 (41%), Positives = 164/281 (58%), Gaps = 12/281 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  YI  + +IP+L  +EE   A  YRE  +L AA RLV SHLRLVV +A  Y GYGL
Sbjct: 7   GNIDAYIQAVNRIPLLSAEEERQYATEYREQNNLDAARRLVLSHLRLVVSVARNYLGYGL 66

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P  +++ EGNIGLM+AVK+FDP +  RL +Y++ WIKA + EYILR+W +VK+G      
Sbjct: 67  PHGDLIQEGNIGLMKAVKRFDPAQNVRLVSYAIHWIKAEIHEYILRNWRMVKVGDDEGAA 126

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINS 192
           + FFNLR  K   QA T     PE++  +A++LNV   EV  M  RL  GD +L   I+ 
Sbjct: 127 QAFFNLRSHKKGTQAFT-----PEEIDGLAQELNVKREEVAEMETRLSGGDIALEGQIDD 181

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---- 248
            ++ S     +L   H+    VL  ++    + + + R++  L+ R RRI EAR L    
Sbjct: 182 GEE-SYAPIAYLADSHNEPTAVLAARQRDMLQTDGIARALESLDARSRRIIEARWLNVDD 240

Query: 249 -QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
                 TL +L++EF VS ER+RQIEA A KK++ ++    
Sbjct: 241 DGSGGSTLHDLAAEFGVSAERIRQIEASAMKKMRTALAAYA 281


>gi|27375413|ref|NP_766942.1| RNA polymerase subunit [Bradyrhizobium japonicum USDA 110]
 gi|1834377|emb|CAA70861.1| RNA polymerase subunit [Bradyrhizobium japonicum]
 gi|27348550|dbj|BAC45567.1| RNA polymerase subunit [Bradyrhizobium japonicum USDA 110]
          Length = 307

 Score =  234 bits (597), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 129/269 (47%), Positives = 175/269 (65%), Gaps = 1/269 (0%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           LS Y   IR+  +LE  +E  LA+R+ E  D  AA  LVTSHLRL  K+A GY+GYGLP+
Sbjct: 25  LSAYSAAIRRYELLEPGQEQQLARRWHETRDRGAADALVTSHLRLAAKLARGYKGYGLPM 84

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++++E N+GL+ A  +F+P RG R +TY++WWIKAA+ EYILRSWSLVKIGTTA QK+L
Sbjct: 85  VDLIAEANLGLVIAASRFEPGRGARFSTYAIWWIKAAIHEYILRSWSLVKIGTTAAQKKL 144

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           FF LR           + L P+    IA KL+V+  EVI M+ RL GD SLNA +   ++
Sbjct: 145 FFKLRSEIRKATGSVMSGLTPDVAELIAGKLDVTAREVIEMDARLNGDMSLNARVG-GEE 203

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
           + ++ +  LV      E +L + E+ + R   L  ++  L  RER +FEARRL E PVTL
Sbjct: 204 SGTELEALLVDGAVDAETMLADHEQTERRAKALRVALGGLAARERHVFEARRLTECPVTL 263

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + L+ E  +S ERVRQIE RAF KV+ ++
Sbjct: 264 DQLARELSISSERVRQIEIRAFAKVKRAV 292


>gi|88705821|ref|ZP_01103530.1| RNA polymerase sigma-38 subunit [Congregibacter litoralis KT71]
 gi|88699892|gb|EAQ97002.1| RNA polymerase sigma-38 subunit [Congregibacter litoralis KT71]
          Length = 331

 Score =  234 bits (597), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 84/283 (29%), Positives = 144/283 (50%), Gaps = 15/283 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI  +P+L   EE   A R  + GD +A  R++ S+LRLVVKIA  Y   G+ + ++
Sbjct: 62  YLNEIGFVPLLTADEEKHYA-RLTQKGDEAARKRMIESNLRLVVKIARRYLHRGMSLLDL 120

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 121 IEEGNLGLMRAVEKFDPERGFRFSTYATWWIRQTIERGIMNQARTIRLPIHVV-KDLNGC 179

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +T           IA + + S  EV  +        S++A +     + S
Sbjct: 180 LRAAR----ELTQQLDHEPTTQEIASRTHKSAKEVSRLMGLNERVSSVDAPLGP--DSDS 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              + +  DH        E+ +  +  + +   ++ L  ++R +   R   L     TLE
Sbjct: 234 SVVETIADDHLCD---PSEQLQNDDVHDSVADWLNELTDKQREVVMRRFGLLGHESSTLE 290

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQK 299
            +  E  ++RERVRQI+  A K+++  +++Q   + +  LLQ+
Sbjct: 291 EVGQEIGLTRERVRQIQVEALKRLRRILERQGLSADA--LLQR 331


>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 =  234 bits (597), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 118/247 (47%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E+    A   ++ ++LRLV+ IA  Y   GL   +++ EGN+GLM+AV KF+  RG++ +
Sbjct: 633 ENRARLAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNVGLMKAVDKFEYRRGYKFS 692

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T     P     +
Sbjct: 693 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGIEPDPAT---L 747

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+++ + E ++  +        S+   I   D + S   D++  +H    Q   +  +  
Sbjct: 748 AERMEMPEEKIRKILKIAKEPISMETPI--GDDDDSHLGDFIEDNHTLAPQ---DAAQYS 802

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R +    +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 803 SLRFVTKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKL 862

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 863 RHPSRSD 869


>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 =  234 bits (597), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 342 LKQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 401

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 402 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 459

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 460 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 514

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 515 SHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 571

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 572 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 607


>gi|116749546|ref|YP_846233.1| sigma-70 region 2 domain-containing protein [Syntrophobacter
           fumaroxidans MPOB]
 gi|116698610|gb|ABK17798.1| sigma-70 region 2 domain protein [Syntrophobacter fumaroxidans
           MPOB]
          Length = 326

 Score =  234 bits (597), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 107/278 (38%), Positives = 177/278 (63%), Gaps = 8/278 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
                Y+ EI++ P+L ++EE  LA RYRE GD+ A ++L+T++LRLVVKIAM ++ Y +
Sbjct: 43  DPFRIYLDEIKRYPLLSREEETDLAIRYREKGDIEAGYKLITANLRLVVKIAMDFQRYWM 102

Query: 74  -PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
             + +++ EGN+GLMQAVKKFDP RG++ + Y+ +WIKA + ++I+ +W LVKIGTT  Q
Sbjct: 103 QNLMDLIQEGNVGLMQAVKKFDPYRGYKFSYYASFWIKAYIIKFIMDNWKLVKIGTTQAQ 162

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALIN 191
           ++LFFNLR+ K  L+A             ++ +L+V ESE+I M+ RL + + SL++ + 
Sbjct: 163 RKLFFNLRKEKERLEA----QGIEASPKLLSHRLDVKESEIIEMDQRLNSWEISLDSPLK 218

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
              +++ +   +L  D    +  + ++E +    + L      L  +E  IF+ R L E 
Sbjct: 219 EDSEDTHK--SFLPSDDLPVDDQIADREAKAILHDKLLLFREQLKGKEAVIFDKRLLTEE 276

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           P+TL+ +   F +SRERVRQIE+R  KK++  +++++E
Sbjct: 277 PMTLQEIGDRFGISRERVRQIESRLKKKLKAYLEEEIE 314


>gi|308234847|ref|ZP_07665584.1| RNA polymerase sigma factor [Gardnerella vaginalis ATCC 14018]
 gi|311114490|ref|YP_003985711.1| DNA-directed RNA polymerase sigma subunit RpoD [Gardnerella
           vaginalis ATCC 14019]
 gi|310945984|gb|ADP38688.1| DNA-directed RNA polymerase sigma subunit RpoD [Gardnerella
           vaginalis ATCC 14019]
          Length = 434

 Score =  234 bits (597), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 65/303 (21%), Positives = 137/303 (45%), Gaps = 39/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR---------------------------YREHGD 46
             +  Y+ +I ++ +L  ++E  L++R                           +     
Sbjct: 134 DPVKDYLKQIGRVSLLNAEQEVDLSERIEAGLYAQHLLDTQIDQMEFKRKRELKWAAADG 193

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ 
Sbjct: 194 KKAKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYAT 253

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      +++     +  +   L R++  +         P+    +A++L
Sbjct: 254 WWIRQAITRAMADQARTIRVPVHMVE--VINKLSRVQRQMLQDLGREPTPD---ELAREL 308

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   +V  +        SL+  +   +   S++ D +    D       +       + 
Sbjct: 309 DMPVEKVQEVQKYGREPISLHTPL--GEDGDSEFGDLI---EDTDAIAPSDAVAFSLLQE 363

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++   K++   
Sbjct: 364 QFRQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPS 423

Query: 285 QKQ 287
           + Q
Sbjct: 424 RSQ 426


>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 [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|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 =  234 bits (597), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 71/267 (26%), Positives = 127/267 (47%), Gaps = 14/267 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L  ++   + KR    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 352 LTIEQVKDINKRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 411

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 412 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 469

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    +++K+ + E ++  +        S+   I   D + S   D++  
Sbjct: 470 LQEIGREPTPE---ELSEKMLIPEDKIRKVLKIAKEPISMETPI--GDDDDSHLGDFI-- 522

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   ++ ++    ++ R+     +S L  RE ++   R   +     TLE +  +F+V
Sbjct: 523 -EDTTLELPLDSATSESLRSATHDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 581

Query: 265 SRERVRQIEARAFKKVQESIQKQVELS 291
           +RER+RQIEA+A +K++   + +V  S
Sbjct: 582 TRERIRQIEAKALRKLRHPSRSEVLRS 608


>gi|219681993|ref|YP_002468377.1| RNA polymerase sigma factor [Buchnera aphidicola str. Tuc7
           (Acyrthosiphon pisum)]
 gi|219621726|gb|ACL29882.1| RNA polymerase sigma factor [Buchnera aphidicola str. Tuc7
           (Acyrthosiphon pisum)]
          Length = 612

 Score =  234 bits (597), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 71/267 (26%), Positives = 127/267 (47%), Gaps = 14/267 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L  ++   + KR    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 352 LTIEQVKDINKRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 411

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 412 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 469

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    +++K+ + E ++  +        S+   I   D + S   D++  
Sbjct: 470 LQEIGREPTPE---ELSEKMLIPEDKIRKVLKIAKEPISMETPI--GDDDDSHLGDFI-- 522

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   ++ ++    ++ R+     +S L  RE ++   R   +     TLE +  +F+V
Sbjct: 523 -EDTTLELPLDSATSESLRSATHDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 581

Query: 265 SRERVRQIEARAFKKVQESIQKQVELS 291
           +RER+RQIEA+A +K++   + +V  S
Sbjct: 582 TRERIRQIEAKALRKLRHPSRSEVLRS 608


>gi|47028349|gb|AAT09107.1| RpoH-like sigma factor [Rhizobium sp. TAL11145]
          Length = 289

 Score =  234 bits (597), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 113/285 (39%), Positives = 176/285 (61%), Gaps = 8/285 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+ KNMS          R I      P L + EE+ LA R+++H D  A +++ T+H+RL
Sbjct: 1   MHMKNMSAD-------RRMIKIAMAAPYLGRDEEHDLAIRWKDHDDRGARNKIATAHMRL 53

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A  +R +GLP+S++V EG +GL++A  +F+PER  R +TY+ WWI+A++Q+YILR+
Sbjct: 54  VISMAGKFRNFGLPMSDLVQEGYVGLLEAAARFEPEREVRFSTYASWWIRASIQDYILRN 113

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WS+V+ GT++ QK LFFNLRRL+  L               IA  L VS ++V +M+ RL
Sbjct: 114 WSIVRGGTSSAQKALFFNLRRLRAKLARGNTGVTVQSIHEEIAVALGVSLADVQTMDARL 173

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +  D SL A   S D  S++  D+L+ D    ++ +    + + RR  L  ++  LN RE
Sbjct: 174 SSNDASLQAPSISGDAESAERMDFLISDEPLPDEQVSNMIDGERRRVWLASALKHLNERE 233

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +I  ARRL E+  TLE L ++  +S+ERVRQIE+RA +K++ ++
Sbjct: 234 MKIIRARRLVEDGATLEELGADLGISKERVRQIESRAMEKLRSAL 278


>gi|182415180|ref|YP_001820246.1| RpoD family RNA polymerase sigma factor [Opitutus terrae PB90-1]
 gi|177842394|gb|ACB76646.1| RNA polymerase, sigma 70 subunit, RpoD family [Opitutus terrae
           PB90-1]
          Length = 353

 Score =  234 bits (597), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 86/291 (29%), Positives = 154/291 (52%), Gaps = 12/291 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           ++ +       L  Y+ EI K  +L   EE  LAKR R+ GD +A   ++ ++LRLVVKI
Sbjct: 40  DVPVAHGDRSNLQLYLQEIGKTALLTIDEEISLAKRIRK-GDKAARDHMIKANLRLVVKI 98

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           AM Y+ +GLP+ +++SEGNIGL++AV++FDP +G +L+TY+ WWIK +++  +      +
Sbjct: 99  AMDYKDFGLPLLDLISEGNIGLIKAVERFDPRKGGKLSTYAAWWIKQSIKRALANQSKTI 158

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           ++        L   + +++    A+T+   +      +A +L +  S+V  +        
Sbjct: 159 RLPVH-----LVDKISKMRRTAMALTEELGREPTDEELAIELQIPTSKVAHLKSVSVRPA 213

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL+A +   ++  S     +V D +       E    KN  + L   ++ L+ RE  I  
Sbjct: 214 SLDAPV--GEEGDSATFGEIVGDDNAV--SPFEGLREKNLNSDLHAMVASLDEREAEIIR 269

Query: 245 ARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
            R   +  + +TLE +   F V+RER+RQ+E  A  K+++++ K   + +S
Sbjct: 270 LRFGLDGKDELTLEEVGRRFHVTRERIRQLEYLALSKMRKAMAKHEAIRTS 320


>gi|256829638|ref|YP_003158366.1| RNA polymerase sigma-32 subunit RpoH [Desulfomicrobium baculatum
           DSM 4028]
 gi|256578814|gb|ACU89950.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfomicrobium baculatum
           DSM 4028]
          Length = 356

 Score =  234 bits (597), Expect = 1e-59,   Method: Composition-based stats.
 Identities = 103/282 (36%), Positives = 168/282 (59%), Gaps = 8/282 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             L  Y+ EI+K   LE+ EE+ LA+RYR+  +  AA  L+TS+LRLVVKIAM ++   +
Sbjct: 74  DPLHIYLQEIKKFKPLEQDEEFDLARRYRDEKEEQAAFILITSNLRLVVKIAMDFQRRWM 133

Query: 74  -PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
             + +++ EGN+GLM+AV+KFDP++G + + Y+ +WIKA + ++I+ +W +VKIGTT  Q
Sbjct: 134 KNVLDLIQEGNVGLMKAVQKFDPDKGIKFSYYASFWIKAYILKFIMDNWRMVKIGTTQAQ 193

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALIN 191
           ++LF+NL + +  LQA             ++K L VSE++++ M  RL   D SL+  I 
Sbjct: 194 RKLFYNLGKERQRLQA----QGFDPTTSTLSKNLQVSEADIVEMGQRLGQHDVSLDMKI- 248

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             D +S    D++     G E+ +   E      + +      LN +E  I E R L ++
Sbjct: 249 -GDDSSFTPMDFIPALEAGIEEQMAADEISVLIHDNIDAIRDGLNEKELDILEQRLLADS 307

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           P+TL  +  ++ ++RERVRQIEAR  +K++  +   ++  SS
Sbjct: 308 PITLREIGDKYGITRERVRQIEARLLQKIKAQMSSTIQDFSS 349


>gi|320161271|ref|YP_004174495.1| RNA polymerase sigma factor [Anaerolinea thermophila UNI-1]
 gi|319995124|dbj|BAJ63895.1| RNA polymerase sigma factor [Anaerolinea thermophila UNI-1]
          Length = 409

 Score =  234 bits (597), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 79/307 (25%), Positives = 139/307 (45%), Gaps = 38/307 (12%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------------H 44
           ++ +  +  Y+ E+ ++P+L  +EE  LA+R                             
Sbjct: 107 IDTDDTIGLYLKEVSRVPLLTAEEEVELAQRIERGRMAREELARGNVSPKRRQELRRLIE 166

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
              +A   L+T++ RLV+ +A  Y G G+P  +++ EGNIGL++A KKFD  RG + +TY
Sbjct: 167 DGWAAREHLITANSRLVISVAKKYMGRGVPFLDLIQEGNIGLIRATKKFDYRRGHKFSTY 226

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + WWI+ A+   I      +++        +   + +L      +T    +   V  +A+
Sbjct: 227 ATWWIRQAVTRAIADQGRTIRVPVH-----MGDQINKLLRVQHQLTQRLGREPSVEELAE 281

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            L+V   +V +M        SL       D+  S   D++  +         +       
Sbjct: 282 ALDVPPRKVENMIQVARRPLSLETPT--DDEEDSVLGDFIEDEEAPPPD---DTATYNLL 336

Query: 225 RNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           R  L   ++ L PRE RI + R   L     TLE +  +  V+RERVRQIEA+A  +++ 
Sbjct: 337 RQHLEEVLNTLPPREVRILQLRYGLLDGQAYTLEEVGRKMGVTRERVRQIEAQALSRLRH 396

Query: 283 -SIQKQV 288
            SI++++
Sbjct: 397 PSIRRKL 403


>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 =  234 bits (597), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 116/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGN+GLM+AV KF+  RG++ +
Sbjct: 533 EQAAREAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNVGLMKAVDKFEYRRGYKFS 592

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    +              +
Sbjct: 593 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKVNRISRQHLQETGTEPDAAVL 647

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+ + E +V  +        S+   I   D + S   D++    D       E   + 
Sbjct: 648 AEKMEMPEDKVRKILKIAREPISMETPI--GDDDDSHLGDFI---EDSGTLAPTEAAMQA 702

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             R+++   +  L PRE ++   R   E  N  TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 703 GLRDVVKEILDSLTPREAKVLRMRFGIEMANDHTLEEVGKQFDVTRERIRQIEAKALRKL 762

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 763 KHPTRSD 769


>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 =  234 bits (597), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 344 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 403

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 404 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 461

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 462 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 516

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 517 SHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 573

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 574 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 609


>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 =  233 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 71/267 (26%), Positives = 127/267 (47%), Gaps = 14/267 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L  ++   + KR    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 352 LTIEQVKDINKRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 411

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 412 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 469

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    +++K+ + E ++  +        S+   I   D + S   D++  
Sbjct: 470 LQEIGREPTPE---ELSEKMLIPEDKIRKVLKIAKEPISMETPI--GDDDDSHLGDFI-- 522

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   ++ ++    ++ R+     +S L  RE ++   R   +     TLE +  +F+V
Sbjct: 523 -EDTTLELPLDSATSESLRSATHDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 581

Query: 265 SRERVRQIEARAFKKVQESIQKQVELS 291
           +RER+RQIEA+A +K++   + +V  S
Sbjct: 582 TRERIRQIEAKALRKLRHPSRSEVLRS 608


>gi|309791990|ref|ZP_07686468.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Oscillochloris
           trichoides DG6]
 gi|308225984|gb|EFO79734.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Oscillochloris
           trichoides DG6]
          Length = 396

 Score =  233 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 76/297 (25%), Positives = 137/297 (46%), Gaps = 37/297 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAK-------------------------RYREHGDLS 48
             +  Y+ EI ++P+L  ++E  LA+                         R +      
Sbjct: 97  DSVRLYLREIGQVPLLTAEQEKRLAQTIERGQKAQVKIKDLDPTSAEAVELRRQIEKGND 156

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++  ++LRLVV IA  YR  GLP+ +++ EG++GL++A++KFD ++GF+ +TY+ WW
Sbjct: 157 ARQQMAAANLRLVVSIAKRYRDRGLPLLDLIQEGSLGLLRAIEKFDHDKGFKFSTYATWW 216

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           IK A+   +     LV++        L   L R++   + +T    +      +A +L++
Sbjct: 217 IKQALSRALADQSRLVRLPVH-----LGETLNRIQAARRQLTQRLGREPYDSELADELSM 271

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S+ ++  +        SL   +   ++  S   D++   H                R  +
Sbjct: 272 SQEKLRELRRTAQDPVSLATPV--GEEADSTLADFIPDPHALDADDAAAS---GMLRQQI 326

Query: 229 TRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             ++  L  RER++ E R       P TLE +   F V+RERVRQIE +A +K++  
Sbjct: 327 ATALDQLTERERKVLELRYGLTDGQPRTLEEVGKAFGVTRERVRQIEVKALRKLRHP 383


>gi|118591280|ref|ZP_01548678.1| RNA polymerase sigma factor [Stappia aggregata IAM 12614]
 gi|118435952|gb|EAV42595.1| RNA polymerase sigma factor [Stappia aggregata IAM 12614]
          Length = 287

 Score =  233 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 107/266 (40%), Positives = 173/266 (65%), Gaps = 1/266 (0%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           +    K P L ++EE  LA R+R+  D  A  +L  SH+RLV+ +A  +R +GL + +++
Sbjct: 10  VRAAMKAPYLTREEELELAIRWRQERDEKALEKLSLSHMRLVIAVASRFRNFGLSLGDLI 69

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EG++GL++A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT+++QK LFFNL
Sbjct: 70  QEGHVGLLEAAARFEPEREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSSQKALFFNL 129

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSS 198
           RRL+  L          E    IA  + V +S+V  MN RL+G D SLNA +  S+ +S+
Sbjct: 130 RRLRAKLSGNQTPLTDSELHQKIADAIGVKQSDVALMNARLSGPDTSLNAPVTDSEGSSA 189

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
             QD+LV D    ++++    + + R+  L+ ++ VL+ RE +I   RRL E+  TLE+L
Sbjct: 190 DRQDFLVSDAPLPDEIVTVSIDTERRQRWLSSALEVLSERELKIVRERRLSEDGATLESL 249

Query: 259 SSEFEVSRERVRQIEARAFKKVQESI 284
             +  +S+ERVRQIE+RA +K++ ++
Sbjct: 250 GVKLGISKERVRQIESRAMEKLKSAL 275


>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 =  233 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 346 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 405

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 406 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 463

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 464 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 518

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 519 SHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 575

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 576 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 611


>gi|222475070|ref|YP_002563485.1| RNA polymerase sigma factor (rpoD) [Anaplasma marginale str.
           Florida]
 gi|255003048|ref|ZP_05278012.1| RNA polymerase sigma factor (rpoD) [Anaplasma marginale str. Puerto
           Rico]
 gi|255004170|ref|ZP_05278971.1| RNA polymerase sigma factor (rpoD) [Anaplasma marginale str.
           Virginia]
 gi|222419206|gb|ACM49229.1| RNA polymerase sigma factor (rpoD) [Anaplasma marginale str.
           Florida]
          Length = 646

 Score =  233 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 71/272 (26%), Positives = 130/272 (47%), Gaps = 19/272 (6%)

Query: 24  RKIPMLEKQEE----YVLAKRYREHGDL--SAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
            K+ +L  ++       L  + ++H      A   ++ ++LRLVV IA  Y   GL   +
Sbjct: 378 NKVRLLSGEDSPGNFKALVAKIQKHERTANKAKQEMIKANLRLVVSIAKKYSNRGLQFLD 437

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +V EGNIGLM+AV KFD +RG++ +TY+ WW++ A+   I      ++I        +  
Sbjct: 438 LVQEGNIGLMKAVDKFDYKRGYKFSTYATWWVRQAITRAIADQARTIRIPVH-----MIE 492

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + ++   L+ +     +   +  ++ +L ++  ++  +   +    SL + I   D +S
Sbjct: 493 TVNKINRTLRQMLHEIGREPTLEELSTRLGMNVEKIRKVMKIVKDPVSLESPI--GDDDS 550

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVT 254
           S + D +    D +           + R + T+ +S L P+E RI   R          T
Sbjct: 551 STFGDCI---EDKRAVKPENAAVLADLREITTKVLSTLTPKEERILRMRFGIGKGGKDHT 607

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 608 LEEVGKLFNVTRERIRQIEAKALRKLRHPSRA 639


>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 =  233 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 342 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 401

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 402 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 459

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 460 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 514

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 515 SHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 571

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 572 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 607


>gi|253991033|ref|YP_003042389.1| RNA polymerase sigma factor RpoD [Photorhabdus asymbiotica subsp.
           asymbiotica ATCC 43949]
 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 =  233 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 75/298 (25%), Positives = 139/298 (46%), Gaps = 17/298 (5%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPM---LEKQEEYVLAKRYR--EHGDLSAAHRLVT 55
           MN+     ++  E  + R +  +R+I     L  ++   + +R    E     A   +V 
Sbjct: 360 MNKPWSEKLLEVEEEIQRSLQRLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVE 419

Query: 56  SHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQE 115
           ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+  
Sbjct: 420 ANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 479

Query: 116 YILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
            I      ++I            L R+   +         PE    +A+++ + E ++  
Sbjct: 480 SIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRK 534

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
           +        S+   I   D   S   D++    D   ++ ++    ++ R+     ++ L
Sbjct: 535 VLKIAKEPISMETPI--GDDEDSHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGL 589

Query: 236 NPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
             RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 590 TAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 647


>gi|295839080|ref|ZP_06826013.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. SPB74]
 gi|295827312|gb|EDY44634.2| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. SPB74]
          Length = 360

 Score =  233 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 81/298 (27%), Positives = 133/298 (44%), Gaps = 40/298 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHG---------------------------DLS 48
             +Y+ EI +IP+L   +E  LA+R  E G                             +
Sbjct: 64  FRQYLREIGRIPLLNAADEVELARRV-EAGLFAEEKLAGPGPLDTRLALDLDRLVVLGRA 122

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  RL+ S+LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RGF+ +TY+ WW
Sbjct: 123 AKRRLIESNLRLVVSVAKRYAGRGLTMLDLVQEGNLGLIRAVEKFDYTRGFKFSTYATWW 182

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ AM   +      +++     +      + R+    + +            +A  L +
Sbjct: 183 IRQAMSRALADQARTIRVPVHVVEL-----INRVVRARRTLLQERGHEPCDAEVAAVLGL 237

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +   V  +        SL+  +   D+      D +    DG      E       R  L
Sbjct: 238 TPERVGEVLRLAQEPVSLHTPVGGEDE--VALGDLI---EDGDAPSPPESAALLLLRRHL 292

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              +S L  RER++ + R   ++  P TLE + + F V+RER+RQIEA+   K++  +
Sbjct: 293 EDVLSTLGERERQVVQLRYGLDDGRPRTLEEIGTLFGVTRERIRQIEAKTLAKLRSHV 350


>gi|261820103|ref|YP_003258209.1| RNA polymerase sigma factor RpoD [Pectobacterium wasabiae WPP163]
 gi|261604116|gb|ACX86602.1| RNA polymerase, sigma 70 subunit, RpoD [Pectobacterium wasabiae
           WPP163]
          Length = 611

 Score =  233 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 342 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 401

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 402 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 459

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 460 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 514

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 515 SHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 571

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 572 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 607


>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 =  233 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 343 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 402

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 403 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 460

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 461 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 515

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 516 SHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 572

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 573 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 608


>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 =  233 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 562 RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 621

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 622 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 676

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 677 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTVAPADAALHASMRD 731

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 732 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 791

Query: 285 QKQ 287
           +  
Sbjct: 792 RSD 794


>gi|295132793|ref|YP_003583469.1| RNA polymerase sigma-70 factor [Zunongwangia profunda SM-A87]
 gi|294980808|gb|ADF51273.1| RNA polymerase sigma-70 factor [Zunongwangia profunda SM-A87]
          Length = 287

 Score =  233 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 145/276 (52%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI K+ ++   EE  LA+R +  GD  A  +L  ++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQEIGKVDLITADEEVELAQRIK-AGDNRALEKLTKANLRFVVSVAKQYQNQGLT 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + +     +V++        
Sbjct: 76  LPDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNK---- 131

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
              ++ ++      +  ++ +P     IAK+L+++ ++V           S++A +   +
Sbjct: 132 -IGSINKINKTFAFLEQSHERPPSAEEIAKELDMTINDVKESMKNSGRHVSMDAPLV--E 188

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
              S   D L     G+     +    ++ R  + R++  L PRE  +        +  P
Sbjct: 189 GEDSNLYDVL---RSGESPNPDKDLLHESLRTEIERALETLTPREADVIRLYFGLGDQHP 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 246 MTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|56459854|ref|YP_155135.1| DNA-directed RNA polymerase sigma 38 subunit [Idiomarina loihiensis
           L2TR]
 gi|56178864|gb|AAV81586.1| DNA-directed RNA polymerase sigma 38 subunit [Idiomarina loihiensis
           L2TR]
          Length = 322

 Score =  233 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 89/277 (32%), Positives = 143/277 (51%), Gaps = 13/277 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   ++R  + GD +A  R++ S+LRLVVKIA  Y   GLP+ ++
Sbjct: 52  YLGEIGFSPLLTAEEEVFYSRRALK-GDKAARRRMIESNLRLVVKIARRYSNRGLPLLDL 110

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 111 VEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 169

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            IAK LN    ++  M        S++  I     N  
Sbjct: 170 LRAAR----ELAHKLDHEPTAEDIAKSLNKPVGDITKMLRLNERIGSVDTPI--GGDNDK 223

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
              D L  D D   + +++ E   N +  +T  +  LN ++R +   R       P TLE
Sbjct: 224 ALLDILTDDADTGPEGVLQDE---NLKGNITEWLQSLNQKQREVLARRFGLMGYEPSTLE 280

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           ++  E  ++RERVRQI+  A +K+++S+++Q     S
Sbjct: 281 DVGREIGLTRERVRQIQVEALRKLRDSLKQQGLTLDS 317


>gi|311747140|ref|ZP_07720925.1| RNA polymerase sigma-70 factor [Algoriphagus sp. PR1]
 gi|126578848|gb|EAZ83012.1| RNA polymerase sigma-70 factor [Algoriphagus sp. PR1]
          Length = 287

 Score =  233 bits (596), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 77/287 (26%), Positives = 146/287 (50%), Gaps = 13/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           + +  I       L +Y+ EI K+ +L   EE VLAKR RE GD  A  +L  ++LR VV
Sbjct: 5   KISKQITNRESQSLDKYLQEIGKVDLLTADEEVVLAKRIRE-GDQLALEKLTKANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 64  SVAKQYQNQGLSLGDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++           +L ++      +     +      +A+ L V+ +EV+        
Sbjct: 124 IVRLPLNR-----VGSLNKISKTFSELEQRFEREPSPEELAEVLEVTANEVVDTMKISGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     ++NS    D L  D D   +   +     + R  + R++S L  RE  +
Sbjct: 179 HVSMDAPFVQGEENS--LLDVLENDGD---EKPDDGLMNDSLRKEVQRALSTLTQREADV 233

Query: 243 FEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
                    E+ +TLE +  +F ++RERVRQI+ +A ++++ + + +
Sbjct: 234 ITLYFGLNGEHAMTLEEIGEKFNLTRERVRQIKEKAIRRLRHTSRSK 280


>gi|270283843|ref|ZP_05965086.2| RNA polymerase principal sigma factor; sigma 70 [Bifidobacterium
           gallicum DSM 20093]
 gi|270277549|gb|EFA23403.1| RNA polymerase principal sigma factor; sigma 70 [Bifidobacterium
           gallicum DSM 20093]
          Length = 485

 Score =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 64/303 (21%), Positives = 137/303 (45%), Gaps = 39/303 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR---------------------------YREHGD 46
             +  Y+ +I ++ +L  ++E  L++R                           +  +  
Sbjct: 185 DPVKDYLKQIGRVSLLNAEQEVDLSERIEAGLYAQHLLDTESEGMSFARKRELKWAANDG 244

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD ++GF+ +TY+ 
Sbjct: 245 KKAKDHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDWKKGFKFSTYAT 304

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      +++     +  +   L R++  +         P+    +A++L
Sbjct: 305 WWIRQAITRAMADQARTIRVPVHMVE--VINKLSRVQRQMLQDLGREPTPD---ELAREL 359

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   +V  +        SL+  +   +    ++ D +    D       +       + 
Sbjct: 360 DMPVEKVQEVQKYGREPISLHTPL--GEDGDPEFGDLI---EDTDAIAPSDAVAFSLLQE 414

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              + +  L+PRE  + + R   E+  P TL+++   + V+RER+RQIE++   K++   
Sbjct: 415 QFKQVLETLSPREAGVIKMRYGLEDGQPKTLDDIGRVYGVTRERIRQIESKTMSKLRHPS 474

Query: 285 QKQ 287
           + Q
Sbjct: 475 RSQ 477


>gi|33593188|ref|NP_880832.1| RNA polymerase sigma factor RpoD [Bordetella pertussis Tohama I]
 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]
          Length = 760

 Score =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 116/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 515 EAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 574

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T     P     +
Sbjct: 575 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGAEPDPAT---L 629

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+++ E ++  +        S+   I   D + S   D++    D       +     
Sbjct: 630 AQKMDMPEDKIRKILKIAKEPISMETPI--GDDDDSHLGDFI---EDTATLAPSDAALHG 684

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 685 SMRDVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKL 744

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 745 RHPSRAD 751


>gi|299066184|emb|CBJ37368.1| RNA polymerase sigma70 factor [Ralstonia solanacearum CMR15]
          Length = 777

 Score =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 68/247 (27%), Positives = 115/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 532 ERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 591

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T N   P     +
Sbjct: 592 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGNEPDPAT---L 646

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+ + E ++  +        S+   I   D + S   D++    D       E     
Sbjct: 647 AEKMEMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTLAPAEAALHG 701

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 702 SMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKL 761

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 762 RHPSRSD 768


>gi|291618943|ref|YP_003521685.1| RpoD [Pantoea ananatis LMG 20103]
 gi|291153973|gb|ADD78557.1| RpoD [Pantoea ananatis LMG 20103]
 gi|327395293|dbj|BAK12715.1| RNA polymerase sigma factor RpoD [Pantoea ananatis AJ13355]
          Length = 614

 Score =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 73/298 (24%), Positives = 140/298 (46%), Gaps = 17/298 (5%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPM---LEKQEEYVLAKRYR--EHGDLSAAHRLVT 55
           MN+     +++ +  + R + ++ +I     L  ++   + +R    E     A   +V 
Sbjct: 323 MNKPWSEKLLDVQDDVMRSLQKLAQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVE 382

Query: 56  SHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQE 115
           ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+  
Sbjct: 383 ANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 442

Query: 116 YILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
            I      ++I            L R+   +         PE    +A+++ + E ++  
Sbjct: 443 SIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRK 497

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
           +        S+   I   D   S   D++    D   ++ ++    ++ R+     ++ L
Sbjct: 498 VLKIAKEPISMETPI--GDDEDSHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGL 552

Query: 236 NPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
             RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 553 TAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 610


>gi|254514875|ref|ZP_05126936.1| RNA polymerase sigma factor RpoS [gamma proteobacterium NOR5-3]
 gi|219677118|gb|EED33483.1| RNA polymerase sigma factor RpoS [gamma proteobacterium NOR5-3]
          Length = 367

 Score =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 78/277 (28%), Positives = 142/277 (51%), Gaps = 13/277 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI  +P+L   EE   A R  + GD +A  R++ S+LRLVV IA  Y   G+ + ++
Sbjct: 98  YLNEIGFVPLLSADEEKHYA-RLVQKGDEAARKRMIESNLRLVVNIARRYLHRGMSLLDL 156

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 157 IEEGNLGLMRAVEKFDPERGFRFSTYATWWIRQTIERGIMNQARTIRLPIHVV-KDLNGC 215

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +T           IA + + + +EV  +        S++A +  +  + S
Sbjct: 216 LRAAR----ELTQQLDHDPTTQEIASRTHKTATEVSRLMGLNERVSSMDAPLGPN--SDS 269

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              + +  +H        E+ +  +  + +   +  L+ ++R +   R   L  +  TLE
Sbjct: 270 SVAETIADEHGCD---PSEQIQDDDVHDSVAHWLDELSEKQREVVVRRFGLLGYDSCTLE 326

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
            +  E  ++RERVRQI+  A K+++  +++Q   + +
Sbjct: 327 EVGQEIGLTRERVRQIQVEALKRLRRILERQGLSADA 363


>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|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]
          Length = 612

 Score =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 343 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 402

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 403 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 460

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 461 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 515

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 516 SHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 572

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 573 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 608


>gi|58579073|ref|YP_197285.1| RNA polymerase sigma-32 factor [Ehrlichia ruminantium str.
           Welgevonden]
 gi|58417699|emb|CAI26903.1| RNA polymerase sigma-32 factor [Ehrlichia ruminantium str.
           Welgevonden]
          Length = 320

 Score =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 127/282 (45%), Positives = 186/282 (65%), Gaps = 3/282 (1%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
             SI+   +  L  YI+E++   +L  +EE  LAK + EHG ++ AH+LVTSHLRLVVK+
Sbjct: 27  TSSILSLTQDNLMSYINEVQSFQVLSLEEEEKLAKNWYEHGVIADAHKLVTSHLRLVVKV 86

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A+ ++ YGLP+ E++ EGNIGLMQAVKKF+P  GFRL+TY++WWIKA++++YIL+SWS +
Sbjct: 87  ALSFKNYGLPLIELIMEGNIGLMQAVKKFNPNLGFRLSTYAIWWIKASIKDYILKSWSCI 146

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GD 183
           KIGTT  Q++LFF+LR           NN+  E +  IA + + SE EV  MN      D
Sbjct: 147 KIGTTQAQRKLFFSLR-KIKKKLLKYHNNITKEDIKMIANECSTSEQEVEQMNKYFTYRD 205

Query: 184 ESLNALINS-SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
           +SLN ++ S   +N  Q QD +  +   QE   +  EE   +++++T++++ LN R R I
Sbjct: 206 KSLNDVVFSNGSQNGVQLQDMIKCEDPNQEDAYLLNEETDIKKSLITQALATLNERHRDI 265

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           F  R+L E P TLE LS ++ +S+ER+RQIE  AF KV+  +
Sbjct: 266 FIRRKLIEEPDTLEILSKKYNISKERIRQIETHAFLKVKNFV 307


>gi|58617131|ref|YP_196330.1| RNA polymerase sigma-32 factor [Ehrlichia ruminantium str. Gardel]
 gi|58416743|emb|CAI27856.1| RNA polymerase sigma-32 factor [Ehrlichia ruminantium str. Gardel]
          Length = 319

 Score =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 127/282 (45%), Positives = 186/282 (65%), Gaps = 3/282 (1%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
             SI+   +  L  YI+E++   +L  +EE  LAK + EHG ++ AH+LVTSHLRLVVK+
Sbjct: 27  TSSILSLTQDNLMSYINEVQSFQVLSLEEEEKLAKNWYEHGVIADAHKLVTSHLRLVVKV 86

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A+ ++ YGLP+ E++ EGNIGLMQAVKKF+P  GFRL+TY++WWIKA++++YIL+SWS +
Sbjct: 87  ALSFKNYGLPLIELIMEGNIGLMQAVKKFNPNLGFRLSTYAIWWIKASIKDYILKSWSCI 146

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GD 183
           KIGTT  Q++LFF+LR           NN+  E +  IA + + SE EV  MN      D
Sbjct: 147 KIGTTQAQRKLFFSLR-KIKKKLLKYHNNITKEDIKMIANECSTSEQEVEQMNKYFTYRD 205

Query: 184 ESLNALINS-SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
           +SLN ++ S   +N  Q QD +  +   QE   +  EE   +++++T++++ LN R R I
Sbjct: 206 KSLNDVVFSNGSQNGVQLQDMIKCEDPNQEDAYLLNEETDIKKSLITQALATLNERHRDI 265

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           F  R+L E P TLE LS ++ +S+ER+RQIE  AF KV+  +
Sbjct: 266 FIRRKLIEEPDTLEILSKKYNISKERIRQIETHAFLKVKNFV 307


>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 =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 116/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 505 EAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 564

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T     P     +
Sbjct: 565 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGAEPDPAT---L 619

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+++ E ++  +        S+   I   D + S   D++    D       +     
Sbjct: 620 AQKMDMPEDKIRKILKIAKEPISMETPI--GDDDDSHLGDFI---EDTSTLAPSDAALHG 674

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 675 SMRDVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKL 734

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 735 RHPSRAD 741


>gi|154707560|ref|YP_001423635.1| RNA polymerase factor sigma-32 [Coxiella burnetii Dugway 5J108-111]
 gi|154356846|gb|ABS78308.1| RNA polymerase sigma-32 factor [Coxiella burnetii Dugway 5J108-111]
          Length = 288

 Score =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 106/278 (38%), Positives = 168/278 (60%), Gaps = 9/278 (3%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  YI  + +IP+L  +EE+ LA ++R+  DL AA +LV SHLR VV+IA GY GYGL
Sbjct: 16  GSIGSYISWVNRIPLLSAEEEHDLANKFRQSNDLEAARKLVLSHLRFVVRIARGYSGYGL 75

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
             ++++ EGNIGLM+AVK+FDP+ G RLA++++ WI+A + E+IL++W +VKI TT  Q+
Sbjct: 76  SQADLIQEGNIGLMKAVKRFDPQVGVRLASFAVHWIRAEIHEFILKNWRIVKIATTKAQR 135

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINS 192
           +LFFNLR+        +D+     +  A+A++LNVS  +V  M  RL + DE+ +     
Sbjct: 136 KLFFNLRKHAKKRGWFSDH-----EAFALAEELNVSTKDVRQMEERLNSYDEAFDGADEE 190

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKE---ERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           SD  +  W     Y  D +    ++ E      ++ + L  +M  L+ R R I   R L 
Sbjct: 191 SDSGTPSWGAPAHYLEDKRYNPALQLERSNWADDQEHRLHNAMQSLDDRSRDILYQRWLS 250

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E   TL  L++++ VS ER+RQ+E  A +K++ ++  +
Sbjct: 251 EKKSTLHELAAQYAVSAERIRQLEKNAMQKIRTAMADE 288


>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 =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 116/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 515 EAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 574

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T     P     +
Sbjct: 575 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGAEPDPAT---L 629

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+++ E ++  +        S+   I   D + S   D++    D       +     
Sbjct: 630 AQKMDMPEDKIRKILKIAKEPISMETPI--GDDDDSHLGDFI---EDTATLAPSDAALHG 684

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 685 SMRDVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKL 744

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 745 RHPSRAD 751


>gi|124514327|gb|EAY55841.1| RNA polymerase, sigma 70 subunit, RpoD family [Leptospirillum
           rubarum]
          Length = 499

 Score =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 89/281 (31%), Positives = 147/281 (52%), Gaps = 17/281 (6%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+ +++K  +L  +EE  LAKR R  GD SA   ++ S+LRLVV IA  Y G GL 
Sbjct: 48  ALGSYLKKLQKSHLLTFEEEQDLAKRVR-AGDESARQAMIQSNLRLVVSIAKRYIGRGLL 106

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++ EGN+GLM+AV KFDP++GFR +TY+ WWI+ A++  I+    ++++     +K 
Sbjct: 107 LEDLIEEGNLGLMKAVSKFDPDKGFRFSTYASWWIRQAIERGIINQGHMIRLPVHMMEK- 165

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   L  ++  +      + +   +  +A+K  +   ++  +   L    SL+  I   D
Sbjct: 166 VNAYLNAIERQVA-----DGQQPDIETLARKNGLKVRDLQEIQALLKNTVSLDTPI--GD 218

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ----- 249
           +  S  +D LV   D      I   E +   + L  S+++L  +ERR+   R        
Sbjct: 219 REDSTLKDILV---DPTSFSPISTIESREEGDRLRESLALLKDKERRVIHLRFGLPGEGP 275

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
           E  +TLE +     V+RERVRQIEA A  K++  ++   E 
Sbjct: 276 EEGMTLEAIGQMLGVTRERVRQIEASAMAKLRAYMEDPSEF 316


>gi|326629245|gb|EGE35588.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 9]
          Length = 660

 Score =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 71/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 391 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 450

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 451 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 508

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+ A I   D   
Sbjct: 509 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMEAPI--GDDED 563

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 564 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 620

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 621 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 656


>gi|294055548|ref|YP_003549206.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Coraliomargarita
           akajimensis DSM 45221]
 gi|293614881|gb|ADE55036.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Coraliomargarita
           akajimensis DSM 45221]
          Length = 342

 Score =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 81/280 (28%), Positives = 151/280 (53%), Gaps = 13/280 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S+  +   GL  Y+ EI K  +L  QEE  LAKR ++ G+ +A   +++++LRLVVKIA 
Sbjct: 38  SMSYDERSGLRAYMQEIGKTALLTPQEEVELAKRIQK-GNKAARDHMISANLRLVVKIAH 96

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y  +GLP+ +++SEGNIGL++AV++FDP +G +L+TY+ WWIK +++  +      +++
Sbjct: 97  DYNNFGLPLMDLISEGNIGLVKAVERFDPSKGGKLSTYAAWWIKQSIKRALANQSKTIRL 156

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
                   L   +  ++     + D   +      IA  + +  ++V  +        SL
Sbjct: 157 PVH-----LVDKIAYMRKITAELADELDREPTDEEIAYTMGMPVNKVAHLKSVSVRPSSL 211

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           +A +   +   + + + +    D  +   +E  + K+  N +   +++L+ RE  I   R
Sbjct: 212 DAPV--GEDGDTSFGELV---GDENQATPLENLQEKSLSNDMHSMIALLDQREAEIIRLR 266

Query: 247 RL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                E+P+TLE +  +F+++RERVRQI+  A  K++  +
Sbjct: 267 FGLDGEHPLTLEEVGEQFKITRERVRQIQNIAIHKMRRLM 306


>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 =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 342 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 401

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 402 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 459

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 460 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 514

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 515 SHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 571

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 572 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 607


>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 =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 116/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 481 EAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 540

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T     P     +
Sbjct: 541 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGAEPDPAT---L 595

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+++ E ++  +        S+   I   D + S   D++    D       +     
Sbjct: 596 AQKMDMPEDKIRKILKIAKEPISMETPI--GDDDDSHLGDFI---EDTSTLAPSDAALHG 650

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 651 SMRDVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKL 710

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 711 RHPSRAD 717


>gi|53802588|ref|YP_112675.1| RNA polymerase factor sigma-32 [Methylococcus capsulatus str. Bath]
 gi|53756349|gb|AAU90640.1| RNA polymerase sigma-32 factor [Methylococcus capsulatus str. Bath]
          Length = 286

 Score =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 106/274 (38%), Positives = 167/274 (60%), Gaps = 8/274 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y   + ++P L+  EE  LA R+R+  DL AA RLV ++LR V  IA GY GYGL
Sbjct: 14  GSIDDYFAAVNRLPRLDADEERELAIRFRDEQDLEAARRLVLANLRFVAYIARGYLGYGL 73

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+++++ EGNIGLM+AVK++DP+ G RL ++++ WI+A + E+I+++W +VKI TT  Q+
Sbjct: 74  PLADLIQEGNIGLMKAVKRYDPDVGVRLVSFAVHWIRAEIHEFIIQNWRIVKIATTKAQR 133

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINS 192
           +LFFNLR++K  L  +T     PE+  A+A +L V   +V  M  RL   D +L A    
Sbjct: 134 KLFFNLRKMKNRLGWLT-----PEEAAAVAAELGVDVEDVYKMENRLNNPDMALEAHGED 188

Query: 193 S-DKNSSQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFEARRLQE 250
             D   S      +    G   +LIE  E +N ++  L  ++  L+ R R I  +R L E
Sbjct: 189 DGDDRESHAPIHYLQQEGGDPALLIEHSEWENRQQEKLQEAIGQLDERSRDIVASRWLSE 248

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + +TL +L++ + VS ER+RQ+E+ A KK++ ++
Sbjct: 249 DKLTLHDLAARYNVSAERIRQLESSAMKKLRNAL 282


>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 =  233 bits (595), Expect = 2e-59,   Method: Composition-based stats.
 Identities = 74/298 (24%), Positives = 141/298 (47%), Gaps = 17/298 (5%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPM---LEKQEEYVLAKRYR--EHGDLSAAHRLVT 55
           MN+   + ++  E  + R + ++R+I     L  ++   + +R    E     A   +V 
Sbjct: 325 MNKPWSNKLLEIEEEVMRSLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVE 384

Query: 56  SHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQE 115
           ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+  
Sbjct: 385 ANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 444

Query: 116 YILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
            I      ++I            L R+   +         PE    +A+++ + E ++  
Sbjct: 445 SIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPSPE---ELAERMMMPEDKIRK 499

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
           +        S+   +   D   S   D++    D   ++ ++    ++ R+     ++ L
Sbjct: 500 VLKIAKEPISMETPV--GDDEDSHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGL 554

Query: 236 NPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
             RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 555 TAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 612


>gi|254482649|ref|ZP_05095887.1| alternative sigma factor RpoH [marine gamma proteobacterium
           HTCC2148]
 gi|214037008|gb|EEB77677.1| alternative sigma factor RpoH [marine gamma proteobacterium
           HTCC2148]
          Length = 284

 Score =  233 bits (595), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 106/272 (38%), Positives = 165/272 (60%), Gaps = 7/272 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L+ Y+  +  IP+L  + E  LA+    + +L+AA  LV SHLR VV IA  Y GYGL 
Sbjct: 16  NLAAYVQAVGSIPVLSPERERELAEDLFYNDNLTAARELVMSHLRFVVHIARSYSGYGLA 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGN+GLM+A+K+FDPE+G RL ++++ WIKA M EYILR+W +VK+ TT  Q++
Sbjct: 76  EADLIQEGNVGLMKAIKRFDPEKGVRLVSFAVHWIKAEMHEYILRNWRIVKVATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSS 193
           LFFNLR  K  L  ++      ++  A+A+ L V   EV  M  RL + D + +   +S 
Sbjct: 136 LFFNLRSKKKSLSWLS-----ADEAKAVAEDLGVDVKEVHRMEGRLTSRDLAYDMSTDSD 190

Query: 194 DKNSSQWQDWLVYDHDGQE-QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
           D ++ Q   + + DH     Q + E + ++N +  L  +++ L+ R R I   R L E+ 
Sbjct: 191 DDDAWQAPQYYLEDHSSDPAQTVEEGDWKQNSQAQLHSALADLDERSRNILAQRWLAEDK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL  L+ ++ VS ER+RQ+EA A KK++ +I
Sbjct: 251 STLHELADQYGVSAERIRQLEANAMKKLKVAI 282


>gi|68171251|ref|ZP_00544654.1| 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 [Ehrlichia chaffeensis str. Sapulpa]
 gi|88657966|ref|YP_507558.1| RNA polymerase sigma factor RpoD [Ehrlichia chaffeensis str.
           Arkansas]
 gi|67999333|gb|EAM85979.1| 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 [Ehrlichia chaffeensis str. Sapulpa]
 gi|88599423|gb|ABD44892.1| RNA polymerase sigma factor RpoD [Ehrlichia chaffeensis str.
           Arkansas]
          Length = 622

 Score =  233 bits (595), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 74/272 (27%), Positives = 133/272 (48%), Gaps = 19/272 (6%)

Query: 24  RKIPMLEKQ----EEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
            KI +L  +    E   L  + ++H   +  A   ++ ++LRLVV IA  Y   GL   +
Sbjct: 354 SKIKLLSGENNLTEFKALVTKIQKHERAANQAKQEMIKANLRLVVSIAKKYSNRGLQFLD 413

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +V EGNIGLM+AV KFD +RG++ +TY+ WW++ A+   I      ++I        +  
Sbjct: 414 LVQEGNIGLMKAVDKFDYKRGYKFSTYATWWVRQAITRAIADQARTIRIPVH-----MIE 468

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + ++   L+ +     +   +  ++ +LN++  ++  +   +    SL + I   D +S
Sbjct: 469 TVNKINRTLRQMLHEMGREPTLEELSARLNINVDKIRKVMKIVKDPVSLESPI--GDDDS 526

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVT 254
           S + D +    D +     +     + R + T+ +S L P+E RI   R          T
Sbjct: 527 STFGDCI---EDKRAVKPEDAAVLADLREITTKVLSTLTPKEERILRMRFGIGKGGKDHT 583

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 584 LEEVGKLFNVTRERIRQIEAKALRKLRHPSRA 615


>gi|227823777|ref|YP_002827750.1| RNA polymerase factor sigma-32 [Sinorhizobium fredii NGR234]
 gi|227342779|gb|ACP26997.1| RNA polymerase sigma factor, sigma-70 family [Sinorhizobium fredii
           NGR234]
          Length = 288

 Score =  233 bits (595), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 101/268 (37%), Positives = 163/268 (60%), Gaps = 1/268 (0%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE+ EE+ LA+ +R   D  A +++  SH+RLV+ +A  +R +GLP+ ++V EG+IGL
Sbjct: 18  PYLERDEEHALAEAWRNDHDQEARNKIAMSHMRLVIAMAAKFRSFGLPMGDLVQEGHIGL 77

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +F+P R  R +TY+ WWI+A+MQ+++LR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 78  LEAAARFEPSREVRFSTYATWWIRASMQDFVLRNWSIVRGGTSSAQKALFFNLRRLRARL 137

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLV 205
                          IA  L VS ++V +M+ RL+G D SL A +   D +     D+L 
Sbjct: 138 AQGDRQLTSLAMHQEIAAALGVSLADVQTMDARLSGNDASLQAPVGHGDSDGGARLDFLP 197

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            D    ++ + +  + +  R  L  +++ L  RE +I  ARRL E+  TLE L     +S
Sbjct: 198 SDAPLPDEQVSDMIDGERARRWLQVALTQLTEREMKIIRARRLSEDGATLEELGLALGIS 257

Query: 266 RERVRQIEARAFKKVQESIQKQVELSSS 293
           +ERVRQIE RA +K++ ++  +    ++
Sbjct: 258 KERVRQIETRALEKLRTALASRAPALTA 285


>gi|123443868|ref|YP_001007839.1| RNA polymerase sigma factor RpoD [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|122090829|emb|CAL13711.1| RNA polymerase sigma factor RpoD [Yersinia enterocolitica subsp.
           enterocolitica 8081]
          Length = 612

 Score =  233 bits (595), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 343 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 402

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 403 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 460

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 461 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 515

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 516 SHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 572

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 573 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 608


>gi|304396867|ref|ZP_07378747.1| RNA polymerase, sigma 70 subunit, RpoD [Pantoea sp. aB]
 gi|304355663|gb|EFM20030.1| RNA polymerase, sigma 70 subunit, RpoD [Pantoea sp. aB]
          Length = 613

 Score =  233 bits (595), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 69/267 (25%), Positives = 126/267 (47%), Gaps = 14/267 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 353 LTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 412

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 413 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 470

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    +A+++ + E ++  +        S+   I   D   S   D++  
Sbjct: 471 LQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 523

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   ++ ++    ++ R+     ++ L  RE ++   R   +     TLE +  +F+V
Sbjct: 524 -EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 582

Query: 265 SRERVRQIEARAFKKVQESIQKQVELS 291
           +RER+RQIEA+A +K++   + +V  S
Sbjct: 583 TRERIRQIEAKALRKLRHPSRSEVLRS 609


>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 =  233 bits (595), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 129/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 362 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 421

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 422 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 479

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 480 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 534

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 535 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 591

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 592 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 627


>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 =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 129/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 345 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 404

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 405 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 462

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 463 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 517

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 518 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 574

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 575 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 610


>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 =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 69/267 (25%), Positives = 126/267 (47%), Gaps = 14/267 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 353 LTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 412

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 413 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 470

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    +A+++ + E ++  +        S+   I   D   S   D++  
Sbjct: 471 LQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 523

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   ++ ++    ++ R+     ++ L  RE ++   R   +     TLE +  +F+V
Sbjct: 524 -EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 582

Query: 265 SRERVRQIEARAFKKVQESIQKQVELS 291
           +RER+RQIEA+A +K++   + +V  S
Sbjct: 583 TRERIRQIEAKALRKLRHPSRSEVLRS 609


>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 =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 344 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 403

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 404 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 461

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 462 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 516

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 517 SHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 573

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 574 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 609


>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 =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 69/263 (26%), Positives = 121/263 (46%), Gaps = 14/263 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L   E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 363 LSIAEIKEINRRISIGEAKAARAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 422

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 423 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRVSRQM 480

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    + +++++ E +V  +        S+   I   D   S   D++  
Sbjct: 481 LQEMGREPTPE---ELGERMDMPEDKVRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 533

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q  ++    ++ R      ++ L  RE ++   R   +     TLE +  +F+V
Sbjct: 534 -EDTTMQSPVDAATAESLREATRDVLASLTAREAKVLAMRFGIDMNTDHTLEEVGKQFDV 592

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   + +
Sbjct: 593 TRERIRQIEAKALRKLRHPSRSE 615


>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 =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 343 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 402

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 403 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 460

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 461 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 515

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 516 SHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 572

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 573 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 608


>gi|192362020|ref|YP_001983950.1| RNA polymerase factor sigma-32 [Cellvibrio japonicus Ueda107]
 gi|190688185|gb|ACE85863.1| alternative sigma factor RpoH [Cellvibrio japonicus Ueda107]
          Length = 286

 Score =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 103/277 (37%), Positives = 161/277 (58%), Gaps = 6/277 (2%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           ++     L+ Y+  +    +L  +EE  LA+   ++G+L AA +LV +HLR VV IA  Y
Sbjct: 12  VLAPGANLNAYVQAVSSFAILSVEEEQQLARDLHDNGNLDAARKLVMAHLRFVVHIARSY 71

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGLP+ +++ EGN+GLM+AVK+FDP++G RL ++++ WIKA + E+ILR+W +VKI T
Sbjct: 72  NGYGLPLGDLIQEGNVGLMKAVKRFDPDKGVRLVSFAVHWIKAEIHEFILRNWRIVKIAT 131

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN 187
           T  Q++LFFNLR  K  L  +++     ++  A+A  L V   +V  M  RLA  D   +
Sbjct: 132 TKAQRKLFFNLRGAKKRLAWLSN-----DEAEAVALDLGVDVKQVREMEGRLASYDAGFD 186

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           A  +  D N     ++L  +       L E    +   N L  +M  L+ R R I + R 
Sbjct: 187 ASDDDEDDNYVAPANYLEDNRYDPAARLEEANWEEASVNGLEMAMEKLDDRSRVILQRRW 246

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L ++  TL +L++E+ VS ER+RQ+E  A  KV+  +
Sbjct: 247 LNDDKATLHDLAAEYGVSAERIRQLEKNAMNKVKAMM 283


>gi|165922507|ref|ZP_02219678.1| alternative sigma factor RpoH [Coxiella burnetii RSA 334]
 gi|212211687|ref|YP_002302623.1| RNA polymerase factor sigma-32 [Coxiella burnetii CbuG_Q212]
 gi|165916712|gb|EDR35316.1| alternative sigma factor RpoH [Coxiella burnetii RSA 334]
 gi|212010097|gb|ACJ17478.1| RNA polymerase sigma-32 factor [Coxiella burnetii CbuG_Q212]
          Length = 288

 Score =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 105/278 (37%), Positives = 167/278 (60%), Gaps = 9/278 (3%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  YI  + +IP+L  +EE+ LA ++R+  DL AA +LV SHLR VV+IA GY GYGL
Sbjct: 16  GSIGSYISWVNRIPLLSAEEEHDLANKFRQSNDLEAARKLVLSHLRFVVRIARGYSGYGL 75

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
             ++++ EGNIGLM+AVK+FDP+ G RL ++++ WI+A + E+IL++W +VKI TT  Q+
Sbjct: 76  SQADLIQEGNIGLMKAVKRFDPQVGVRLVSFAVHWIRAEIHEFILKNWRIVKIATTKAQR 135

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINS 192
           +LFFNLR+        +D+     +  A+A++LNVS  +V  M  RL + DE+ +     
Sbjct: 136 KLFFNLRKHAKKRGWFSDH-----EAFALAEELNVSTKDVRQMEERLNSYDEAFDGADEE 190

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKE---ERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           SD  +  W     Y  D +    ++ E      ++ + L  +M  L+ R R I   R L 
Sbjct: 191 SDSGTPSWGAPAHYLEDKRYNPALQLERSNWADDQEHRLHNAMQSLDDRSRDILYQRWLS 250

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E   TL  L++++ VS ER+RQ+E  A +K++ ++  +
Sbjct: 251 EKKSTLHELAAQYAVSAERIRQLEKNAMQKIRTAMADE 288


>gi|120434745|ref|YP_860432.1| RNA polymerase sigma-70 factor [Gramella forsetii KT0803]
 gi|117576895|emb|CAL65364.1| RNA polymerase sigma-70 factor [Gramella forsetii KT0803]
          Length = 287

 Score =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 146/276 (52%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI K+ ++   EE  LA+R +  GD  A  +L  ++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQEIGKVDLITADEEVELAQRIK-AGDDRALEKLTKANLRFVVSVAKQYQNQGLT 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + +     +V++        
Sbjct: 76  LPDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNK---- 131

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
              ++ ++      +  ++ +P     IAK+L+++ ++V           S++A +   +
Sbjct: 132 -IGSINKINKTFAFLEQSHERPPSAEEIAKELDMTINDVKESMKNSGRHVSMDAPLV--E 188

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
              S   D L     G+     ++   ++ R  + R++  L PRE  +        +  P
Sbjct: 189 GEDSNLYDVL---RSGESPNPDKELLHESLRTEIERALETLTPREADVIRLYFGLGDQHP 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 246 MTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|332163001|ref|YP_004299578.1| RNA polymerase sigma factor RpoD [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 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)]
          Length = 612

 Score =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 343 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 402

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 403 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 460

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 461 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 515

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 516 SHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 572

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 573 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 608


>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 =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 71/274 (25%), Positives = 128/274 (46%), Gaps = 14/274 (5%)

Query: 22  EIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           EI +   L  Q+   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++
Sbjct: 356 EIERQTNLTVQQIREVCERISAGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 415

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L
Sbjct: 416 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKL 473

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
            R+   +         PE    +A+++ + E ++  +        S+   I   D + S 
Sbjct: 474 NRISRQMLQEMGREASPE---ELAERMGMPEDKIRKVLKIAKEPISMETPI--GDDDDSH 528

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLEN 257
             D++    D   ++ ++    ++ +      +  L PRE ++   R   +     TLE 
Sbjct: 529 LGDFI---EDSTLELPLDSATAQSLKAATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEE 585

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           +  +F+V+RER+RQIEA+A +K++   + +   S
Sbjct: 586 VGKQFDVTRERIRQIEAKALRKLRHPSRSETLRS 619


>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 =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 343 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 402

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 403 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 460

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 461 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 515

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 516 SHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 572

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 573 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 608


>gi|206602787|gb|EDZ39268.1| RNA polymerase, RpoD-like sigma subunit [Leptospirillum sp. Group
           II '5-way CG']
          Length = 499

 Score =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 89/281 (31%), Positives = 147/281 (52%), Gaps = 17/281 (6%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+ +++K  +L  +EE  LAKR R  GD SA   ++ S+LRLVV IA  Y G GL 
Sbjct: 48  ALGSYLKKLQKSHLLTFEEEQDLAKRVR-AGDESARQAMIQSNLRLVVSIAKRYIGRGLL 106

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++ EGN+GLM+AV KFDP++GFR +TY+ WWI+ A++  I+    ++++     +K 
Sbjct: 107 LEDLIEEGNLGLMKAVSKFDPDKGFRFSTYASWWIRQAIERGIINQGHMIRLPVHMMEK- 165

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   L  ++  +      + +   +  +A+K  +   ++  +   L    SL+  I   D
Sbjct: 166 VNAYLNAIERQVA-----DGQQPDIENLARKNGLKVRDLQEIQALLKNTVSLDTPI--GD 218

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ----- 249
           +  S  +D LV   D      I   E +   + L  S+++L  +ERR+   R        
Sbjct: 219 REDSTLKDILV---DPTSFSPISTIESREEGDRLRESLALLKDKERRVIHLRFGLPGEGP 275

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
           E  +TLE +     V+RERVRQIEA A  K++  ++   E 
Sbjct: 276 EEGMTLEAIGQMLGVTRERVRQIEASAMAKLRAYMEDPSEF 316


>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 =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 68/247 (27%), Positives = 115/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 510 ERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 569

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T N   P     +
Sbjct: 570 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGNEPDPAT---L 624

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+ + E ++  +        S+   I   D + S   D++    D       E     
Sbjct: 625 AEKMEMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTLAPAEAALHG 679

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 680 SMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKL 739

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 740 RHPSRSD 746


>gi|156932573|ref|YP_001436489.1| RNA polymerase sigma factor RpoD [Cronobacter sakazakii ATCC
           BAA-894]
 gi|156530827|gb|ABU75653.1| hypothetical protein ESA_00355 [Cronobacter sakazakii ATCC BAA-894]
          Length = 614

 Score =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 129/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 345 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 404

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 405 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 462

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 463 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 517

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 518 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 574

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 575 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 610


>gi|62181728|ref|YP_218145.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 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. A50]
          Length = 658

 Score =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 129/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 389 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 448

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 449 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 506

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 507 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 561

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 562 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 618

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 619 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 654


>gi|330504211|ref|YP_004381080.1| RNA polymerase sigma factor RpoS [Pseudomonas mendocina NK-01]
 gi|328918497|gb|AEB59328.1| RNA polymerase sigma factor RpoS [Pseudomonas mendocina NK-01]
          Length = 335

 Score =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 82/277 (29%), Positives = 135/277 (48%), Gaps = 13/277 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLTPEEEVHFA-RLAQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +T           IA  L     EV  M        S++  ++    +  
Sbjct: 185 LRAAR----ELTQKLDHEPSAEEIANLLEKPVGEVKRMLGLNERVSSVD--VSLGPDSDK 238

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
              D L  D       L++ ++       + + +S L  ++R +   R         TLE
Sbjct: 239 TLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSDLTDKQREVVVRRFGLRGHESCTLE 295

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
            +  E  ++RERVRQI+  A K+++E ++K    S +
Sbjct: 296 EVGQEIGLTRERVRQIQVEALKRLREILEKNGLSSDA 332


>gi|322831339|ref|YP_004211366.1| RNA polymerase, sigma 70 subunit, RpoD [Rahnella sp. Y9602]
 gi|321166540|gb|ADW72239.1| RNA polymerase, sigma 70 subunit, RpoD [Rahnella sp. Y9602]
          Length = 612

 Score =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 343 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 402

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 403 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 460

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 461 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 515

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 516 SHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 572

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 573 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 608


>gi|152998320|ref|YP_001343155.1| RNA polymerase factor sigma-32 [Marinomonas sp. MWYL1]
 gi|150839244|gb|ABR73220.1| RNA polymerase, sigma 32 subunit, RpoH [Marinomonas sp. MWYL1]
          Length = 288

 Score =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 104/279 (37%), Positives = 161/279 (57%), Gaps = 8/279 (2%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           +++ G+  L  YI  + +IP+L   EE  LA+R     DL AA  LV SHLR VV IA  
Sbjct: 10  MMIPGQ-NLESYIQAVSRIPILTADEEKALAERLYYQEDLEAARTLVMSHLRFVVHIAKS 68

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y GYGL   +++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+IL++W +VK+ 
Sbjct: 69  YSGYGLAQGDLIQEGNVGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEFILKNWRIVKVA 128

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESL 186
           TT  Q+++FFNLR  K  L   +++     +V ++A  L V+   V  M  RL + D + 
Sbjct: 129 TTKAQRKMFFNLRSAKKSLSWFSNS-----EVESVASDLGVTPEVVRQMEGRLSSSDMAF 183

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEK-EERKNRRNMLTRSMSVLNPRERRIFEA 245
           +A  +  D ++ Q     + DH      L+E     ++    L  +M+ L+ R R I   
Sbjct: 184 DASADDDDDSAFQAPSQYLEDHRSDPATLLENGNWEEDSNQRLEVAMADLDERSRNILVQ 243

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R L +   TL  L+ E+ VS ER+RQ+E  A KK++ ++
Sbjct: 244 RWLSDAKSTLHELADEYGVSAERIRQLEKNAMKKIRLAM 282


>gi|269958878|ref|YP_003328667.1| RNA polymerase sigma factor [Anaplasma centrale str. Israel]
 gi|269848709|gb|ACZ49353.1| RNA polymerase sigma factor [Anaplasma centrale str. Israel]
          Length = 649

 Score =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 71/272 (26%), Positives = 130/272 (47%), Gaps = 19/272 (6%)

Query: 24  RKIPMLEKQEE----YVLAKRYREHGDL--SAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
            K+ +L  ++       L  + ++H      A   ++ ++LRLVV IA  Y   GL   +
Sbjct: 381 NKVRLLSGEDSPGSFKALVAKIQKHERTANKAKQEMIKANLRLVVSIAKKYSNRGLQFLD 440

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +V EGNIGLM+AV KFD +RG++ +TY+ WW++ A+   I      ++I        +  
Sbjct: 441 LVQEGNIGLMKAVDKFDYKRGYKFSTYATWWVRQAITRAIADQARTIRIPVH-----MIE 495

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + ++   L+ +     +   +  ++ +L ++  ++  +   +    SL + I   D +S
Sbjct: 496 TVNKINRTLRQMLHEIGREPTLEELSARLGMNVEKIRKVMKIVKDPVSLESPI--GDDDS 553

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVT 254
           S + D +    D +           + R + T+ +S L P+E RI   R          T
Sbjct: 554 STFGDCI---EDKRAVKPENAAVLADLREITTKVLSTLTPKEERILRMRFGIGKGGKDHT 610

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 611 LEEVGKLFNVTRERIRQIEAKALRKLRHPSRA 642


>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 =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 71/276 (25%), Positives = 131/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +H+I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 338 LHQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 397

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 398 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 455

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 456 KLNRISRQMLQEMGREPMPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 510

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 511 SHLGDFI---EDTTFELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 567

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 568 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 603


>gi|313672395|ref|YP_004050506.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Calditerrivibrio
           nitroreducens DSM 19672]
 gi|312939151|gb|ADR18343.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Calditerrivibrio
           nitroreducens DSM 19672]
          Length = 337

 Score =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 77/268 (28%), Positives = 135/268 (50%), Gaps = 13/268 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ E+ K P+L K+EE  LA+R  E GD  A   ++  +LRLVV IA  Y   G+P+
Sbjct: 67  LVFYLKELSKCPVLSKEEECELARRI-EEGDEKAKETMINCNLRLVVSIAKKYANKGVPL 125

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++SEGNIGL++AV+KFD  +GF+ +TY+ WWI+ A++  I+ +  +V++     +   
Sbjct: 126 EDLISEGNIGLIRAVEKFDYRKGFKFSTYATWWIRQAIERAIIANTKIVRVPVHVLE--Y 183

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + + K  LQ     N        ++    ++ S +      +  D S++A I+  ++
Sbjct: 184 IKKILKAKSELQETLGRN---PTYTELSTYTGITLSNIYKAVEAMRHDVSIDAPISEDEQ 240

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--V 253
            +           D       +     N + ++++ M  LN  E+ I   R   +     
Sbjct: 241 ENMHNLIP-----DNIHTDPFDHAFELNIQKLVSKWMGYLNETEKLIITLRYGLDGKRSR 295

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TL+ +  E  ++RER+RQIE R   K++
Sbjct: 296 TLDEVGKELNLTRERIRQIEKRVLNKLR 323


>gi|89092114|ref|ZP_01165069.1| RNA polymerase sigma factor RpoS [Oceanospirillum sp. MED92]
 gi|89083849|gb|EAR63066.1| RNA polymerase sigma factor RpoS [Oceanospirillum sp. MED92]
          Length = 339

 Score =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 82/288 (28%), Positives = 141/288 (48%), Gaps = 14/288 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  K++ +          Y++EI   P+L  +EE   + R    GD +A  R++ S+LRL
Sbjct: 53  MAHKDL-LNAKNLDATQLYLNEIGFSPLLSAEEEVYFS-RLALKGDEAARKRMIESNLRL 110

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+  
Sbjct: 111 VVKIARRYINRGLTLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQ 170

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              +++      K L   LR  +  L    D+   PE++  +  K   +   ++ +N R+
Sbjct: 171 TRTIRLPIHVV-KELNVYLRAAR-ELAQKLDHEPSPEEIAELVDKPVENVERMLGLNERV 228

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +   S++  +      S    D +          L++     N    L R +  L  +  
Sbjct: 229 S---SVDTPMGKDSDKS--LLDTIPDTVSSDPATLLQN---SNISGNLDRWLDALPEKHA 280

Query: 241 RIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +   R         TLE +  E  ++RERVRQI+  A +K+++ ++K
Sbjct: 281 EVLSRRFGLRGYEMSTLEEVGKEIGLTRERVRQIQVEALRKLRDIVEK 328


>gi|16761985|ref|NP_457602.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. CT18]
 gi|29143472|ref|NP_806814.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
 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 =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 129/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 391 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 450

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 451 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 508

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 509 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 563

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 564 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 620

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 621 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 656


>gi|33520062|ref|NP_878894.1| RNA polymerase factor sigma-32 [Candidatus Blochmannia floridanus]
 gi|33504408|emb|CAD83301.1| RNA polymerase sigma-32 factor [Candidatus Blochmannia floridanus]
          Length = 283

 Score =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 101/281 (35%), Positives = 164/281 (58%), Gaps = 10/281 (3%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           RKN+++   G   L  YI      PML  +EE  LAK    +GDL+AA +L+ SHLR V+
Sbjct: 6   RKNVTLASQG--TLEAYIRAANLYPMLTVEEEQKLAKNLYYNGDLNAAKKLIVSHLRFVI 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y GYGL  ++++ EGNIGLM+++++F+PE   RL ++++ WIK+ + EY+L++W 
Sbjct: 64  HVARNYSGYGLSQADLIQEGNIGLMKSIRRFNPELDVRLVSFAVHWIKSEIHEYVLKNWR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-A 181
           +VKI TT  Q++LFFNLR+ K  L    +      ++  +AK L+V+  +V  M  R+ A
Sbjct: 124 IVKIATTKAQRKLFFNLRKTKQRLGWFNEG-----EIEMVAKTLHVTCKDVREMESRMAA 178

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
            D +L       D  +      ++Y  D    +  E+E      N L  +++ L+ R + 
Sbjct: 179 QDMTLEQPYLDEDDKNI-LSIPMLYLQDKITIIDDEEEWIDQVSNKLNIALNTLDKRSQH 237

Query: 242 IFEARRLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           I  AR L  +N  TL+ L++++ +S ER+RQ+E  A KK++
Sbjct: 238 IIRARWLNADNKTTLQELANQYGISAERIRQLEKNAMKKMK 278


>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 =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 343 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 402

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 403 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 460

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 461 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 515

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 516 SHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 572

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 573 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 608


>gi|254495200|ref|ZP_05108124.1| RNA polymerase sigma-70 factor RpoD [Polaribacter sp. MED152]
 gi|85819552|gb|EAQ40709.1| RNA polymerase sigma-70 factor RpoD [Polaribacter sp. MED152]
          Length = 287

 Score =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 72/278 (25%), Positives = 145/278 (52%), Gaps = 13/278 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI K+ ++   EE  LA+  +  GD  A  +L  ++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQEIGKVDLITADEEVELAQLIK-AGDQRALEKLTKANLRFVVSVAKQYQNQGLT 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + +     +V++    N+  
Sbjct: 76  LPDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLP--LNKIG 133

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               + ++   L+   +    PE    IAKKL+++ ++V           S++A +   +
Sbjct: 134 SINKINKMYAFLEQENERPPSPE---EIAKKLDMTVNDVKESMKNSGRHVSMDAPLI--E 188

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
              S   D L          ++     ++ R  + R++  L PRE  + +         P
Sbjct: 189 GEDSNLYDVLNSGESPNPDRVL---LHESLRIEINRALETLTPREADVVKLYFGLGEHQP 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
           +TLE +   F+++RERVRQI+ +A ++++ + + ++ +
Sbjct: 246 MTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKILM 283


>gi|150398305|ref|YP_001328772.1| RNA polymerase factor sigma-32 [Sinorhizobium medicae WSM419]
 gi|150029820|gb|ABR61937.1| RNA polymerase, sigma 32 subunit, RpoH [Sinorhizobium medicae
           WSM419]
          Length = 288

 Score =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 103/277 (37%), Positives = 167/277 (60%), Gaps = 1/277 (0%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           R I    + P LE+ EE+ LA+ +R   D  A +++  SH+RLV+ +A  +R +GLP+ +
Sbjct: 9   RMIKIAMEAPYLERDEEHALAEAWRNDNDQEARNKIAMSHMRLVISMAAKFRSFGLPMGD 68

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +V EG+IGL++A  +F+P R  R +TY+ WWI+A+MQ+Y+LR+WS+V+ GT++ QK LFF
Sbjct: 69  LVQEGHIGLLEAAARFEPSREVRFSTYATWWIRASMQDYVLRNWSIVRGGTSSAQKALFF 128

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKN 196
           NLRRL+  L               IA  + VS ++V +M+ RL+G D SL A I   D +
Sbjct: 129 NLRRLRARLAQGDRQLTSQAVHEEIAAAIGVSLADVQTMDARLSGNDASLQAPIGGGDPD 188

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           +    D+L  +    ++ + +  + +  R  L  ++  L+ RE +I  ARRL E+  TLE
Sbjct: 189 AGARLDFLASEAPLPDEQVSDLIDGERARRWLHVALGELSEREMKIIRARRLSEDGATLE 248

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
            L     +S+ERVRQIE RA +K++ ++  +    ++
Sbjct: 249 ELGVALGISKERVRQIETRALEKLRAALTARAPALTA 285


>gi|94984583|ref|YP_603947.1| RNA polymerase, sigma 28 subunit [Deinococcus geothermalis DSM
           11300]
 gi|94554864|gb|ABF44778.1| RNA polymerase, sigma 28 subunit [Deinococcus geothermalis DSM
           11300]
          Length = 532

 Score =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 79/297 (26%), Positives = 132/297 (44%), Gaps = 37/297 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------HGDL---------------- 47
             + +Y+HEI ++P+L  +EE  LA+R  E           GD                 
Sbjct: 230 DPVRQYLHEIGRVPLLTLEEEIALARRIEEGEEARKMLEEAGDELDDRARRRLMRQMEDG 289

Query: 48  -SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +A   L+ ++LRLVV IA  Y G GL   +++ EGN GL++AV+KF+  R ++ +TY+ 
Sbjct: 290 AAARQGLIEANLRLVVSIAKKYTGRGLGFLDLIQEGNQGLIRAVEKFEYRRRYKFSTYAT 349

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I     +      L R    LQ         E++   A   
Sbjct: 350 WWIRQAINRAIADQARTIRIPVHMVE--TINKLTRTARQLQQELSREPTYEEIAE-AMGP 406

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
               ++V  +        SL   I   D+  S + D++    D      ++   +     
Sbjct: 407 GWDAAKVEEVQKVSQEPVSLETPI--GDEKDSFYGDFIP---DENLDSPVDNAAKTLLSE 461

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L +++S L  RE  + + R+        TLE +   F V+RER+RQIE +A +K++
Sbjct: 462 ELEKALSKLTEREALVLKFRKGLVDGREHTLEEVGQRFNVTRERIRQIENKALRKLK 518


>gi|77359643|ref|YP_339218.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Pseudoalteromonas haloplanktis
           TAC125]
 gi|76874554|emb|CAI85775.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Pseudoalteromonas haloplanktis
           TAC125]
          Length = 324

 Score =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 139/271 (51%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   +++    G  ++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 53  YLGEIGFSPLLSAEEEVFFSRK-SLKGCEASRKRMIESNLRLVVKIARRYNNRGLALLDL 111

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 112 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 170

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +T           IA  L+    +V  M        S++  I    +N +
Sbjct: 171 LRTAR----ELTQKLDHEPTAEEIAACLDKPVEDVTKMLRLNEKIASVDMPI--GGENDT 224

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D +  D++   +  ++     +    +   +  LNP++R +   R   L   P TLE
Sbjct: 225 ALLDIIADDNNVGPEGEVQN---NDMNKHIVDWLGELNPKQREVLARRFGLLGYEPSTLE 281

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+  A +++++ +Q++
Sbjct: 282 DVGREIGLTRERVRQIQVEALRRLKDILQQE 312


>gi|133468|sp|P27785|RPOD_STRAU RecName: Full=RNA polymerase sigma factor rpoD
          Length = 317

 Score =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 83/296 (28%), Positives = 136/296 (45%), Gaps = 38/296 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYRE----------HGDLS----------------A 49
             +Y+ EI +IP+L   EE  LA+R               DL                 A
Sbjct: 21  FRQYLREIGRIPLLTAAEEVDLARRVEAGLFAEEKLGGAADLDSQLAVDLDRLVVMGRMA 80

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             RL+ S+LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY+ WWI
Sbjct: 81  KRRLIESNLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFSTYATWWI 140

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + AM   +      +++     +  L   + R++  +          E+V   A  L ++
Sbjct: 141 RQAMSRALADQARTIRVPVHVVE--LINRVVRVQRRMLQERGYEPTAEEV---AVHLELT 195

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
              V+ +        SL+A +   +++     D +    DG     +E      R   L 
Sbjct: 196 PERVLEVLRLAQEPVSLHAPV--GEEDDVALGDLI---EDGDAASPVESAAFFLRCEHLE 250

Query: 230 RSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +S L  RER++ + R       P TLE +   F V+RER+RQIE++   K+++ 
Sbjct: 251 AVLSTLGERERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIESKTLNKLRDH 306


>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 =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 339 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 398

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 399 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 456

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 457 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 511

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 512 SHLGDFI---EDTTLKLPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 568

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 569 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 604


>gi|159899067|ref|YP_001545314.1| RpoD family RNA polymerase sigma factor [Herpetosiphon aurantiacus
           ATCC 23779]
 gi|159892106|gb|ABX05186.1| RNA polymerase, sigma 70 subunit, RpoD family [Herpetosiphon
           aurantiacus ATCC 23779]
          Length = 386

 Score =  233 bits (594), Expect = 3e-59,   Method: Composition-based stats.
 Identities = 82/300 (27%), Positives = 135/300 (45%), Gaps = 39/300 (13%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYR----------------EHGDL--------- 47
           +  +  Y+ EI ++P+L   EE  LAK+                  EH D          
Sbjct: 86  DDPVRMYLQEIGQVPLLTAAEEVDLAKKMEVAHAANDTLLQDDGMLEHSDRISLKRHIDT 145

Query: 48  --SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
             +A   L+ ++LRLVV IA  Y  YGL + ++V EGNIGLM+AV+KFD  +G + +TY+
Sbjct: 146 GRAARQHLIQANLRLVVSIAKKYTSYGLTMMDLVQEGNIGLMRAVEKFDYTKGHKFSTYA 205

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
            WWI+ A+   I      +++     +      ++R    LQ        PE    IA+ 
Sbjct: 206 TWWIRQAITRAIADQSRTIRLPVHMGE--AISQVKRTSHKLQQTMQREPTPE---EIAEA 260

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           + ++ S+V           SL   +    +   +  D++  D        ++       R
Sbjct: 261 MGITASKVRRTLEASMHPLSLEMPV--GQEGEGRMGDFIEDDRVS---TPVDAAAMTMLR 315

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +   +  L  RER+I + R   ++    TLE +  EF ++RER+RQIEA A +K++  
Sbjct: 316 EQIEEVLQKLPERERKIIQLRYGLKDGRYRTLEEVGLEFGITRERIRQIEAVALRKLRHP 375


>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 =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 129/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 389 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 448

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 449 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 506

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 507 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 561

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 562 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 618

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 619 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 654


>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|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. 4/74]
 gi|326624968|gb|EGE31313.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Dublin str. 3246]
 gi|332990077|gb|AEF09060.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhimurium str. UK-1]
          Length = 660

 Score =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 129/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 391 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 450

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 451 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 508

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 509 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 563

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 564 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 620

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 621 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 656


>gi|581612|emb|CAA37172.1| unnamed protein product [Streptomyces coelicolor A3(2)]
          Length = 396

 Score =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 81/302 (26%), Positives = 136/302 (45%), Gaps = 40/302 (13%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG------------------------- 45
                  +Y+ EI +IP+L   EE  LA+R  E G                         
Sbjct: 95  PSSDLFRQYLREIGRIPLLSAAEEVDLARRV-EAGLFAEEKLRCSPGLDDRLALDLDRLV 153

Query: 46  --DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
                A  RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +T
Sbjct: 154 VLGRLAKRRLIEANLRLVVSVAKRYVGRGLTMLDLVQEGNLGLIRAVEKFDYARGYKFST 213

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI+ AM   +      +++     +  L   + R++  +         P++V A  
Sbjct: 214 YATWWIRQAMSRALADQARTIRVPVHVVE--LINRVVRVQRRMLQERGCEPTPQEVAA-- 269

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
             L+++   V  +        SL+A +   +++     D +    DG     +E      
Sbjct: 270 -HLDLAPERVGEVLRLAQEPVSLHAPV--GEEDDVALGDLI---EDGDAASPVESAAFLL 323

Query: 224 RRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R  L   +S L  RER++ + R       P TLE +     V+RER+RQIE++   K++
Sbjct: 324 LRQHLEAVLSTLGERERKVVQLRYGLADGRPRTLEEIGRLGGVTRERIRQIESKTLSKLR 383

Query: 282 ES 283
           + 
Sbjct: 384 DH 385


>gi|266618720|pdb|3IYD|F Chain F, Three-Dimensional Em Structure Of An Intact Activator-
           Dependent Transcription Initiation Complex
          Length = 613

 Score =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 129/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 344 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 403

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 404 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 461

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 462 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 516

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 517 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 573

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 574 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 609


>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 =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 71/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +H+I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 345 LHQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 404

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 405 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 462

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 463 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 517

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 518 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 574

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 575 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 610


>gi|294340365|emb|CAZ88746.1| RNA polymerase sigma factor rpoD (Sigma-70) [Thiomonas sp. 3As]
          Length = 778

 Score =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 116/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGN+GLM+AV KF+  RG++ +
Sbjct: 533 EQAAREAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNVGLMKAVDKFEYRRGYKFS 592

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    +              +
Sbjct: 593 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKVNRISRQHLQETGTEPDAAVL 647

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+ + E +V  +        S+   I   D + S   D++    D       E   + 
Sbjct: 648 AEKMEMPEDKVRKILKIAREPISMETPI--GDDDDSHLGDFI---EDSGTLAPTEAAMQA 702

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             R+++   +  L PRE ++   R   E  N  TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 703 GLRDVVKEILDSLTPREAKVLRMRFGIEMANDHTLEEVGKQFDVTRERIRQIEAKALRKL 762

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 763 KHPTRSD 769


>gi|28572422|ref|NP_789202.1| RNA polymerase sigma factor [Tropheryma whipplei TW08/27]
 gi|28410553|emb|CAD66939.1| RNA polymerase principal sigma factor hrdb [Tropheryma whipplei
           TW08/27]
          Length = 387

 Score =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 78/311 (25%), Positives = 141/311 (45%), Gaps = 40/311 (12%)

Query: 7   SIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRY----------REHGDLS------ 48
           S +++G     +  Y+ +I K+ +L   EE  LAKR            E GDL+      
Sbjct: 80  SPVISGATADPVKDYLKQIGKVSLLTADEEVSLAKRIEAGLFAEEKLSESGDLAPKLKRE 139

Query: 49  ----------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
                     A   L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G
Sbjct: 140 LRWVVRDGQRAKDHLLAANLRLVVSLAKRYTGRGMQFLDLIQEGNLGLIRAVEKFDYVKG 199

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           F+ +TY+ WWI+ A+   +      ++I     +  +   L R++  L         P+ 
Sbjct: 200 FKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLSRVQRQLLQDLGREPTPD- 256

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              + ++L++    V+ +        SL+  +   D+  S++ D +    D       + 
Sbjct: 257 --ELGRELDMPPERVVEVQKYGREPISLHTPL--GDEGDSEFGDLI---EDVDAVAPDDA 309

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARA 276
                 +  L   +  L+ RE  +   R   +   P TL+ +   F+V+RER+RQIEA+ 
Sbjct: 310 VGFSMLQQQLRLLLDSLSEREAGVIRMRFGLDYDMPKTLDYVGEYFDVTRERIRQIEAKT 369

Query: 277 FKKVQESIQKQ 287
             K++   + Q
Sbjct: 370 MAKLRHPSRSQ 380


>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 =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 68/242 (28%), Positives = 115/242 (47%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 409 KKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 468

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            L R+   +         PE    +A+K+
Sbjct: 469 WWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEKGREPTPE---ELAEKM 523

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        SL   +   D + S   D++    D    V  E    ++ +N
Sbjct: 524 GLPEDKIRKVMKIAKEPISLETPV--GDDDDSHLGDFI---EDSSIVVPAEAATSESLKN 578

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +   +  + PRE ++   R     P   TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 579 AINNVLDEMPPREAQVLRMRFGIGMPSDHTLEEVGRQFGVTRERIRQIEAKALRKLRHPC 638

Query: 285 QK 286
           + 
Sbjct: 639 RS 640


>gi|39939114|ref|NP_950880.1| DNA-directed RNA polymerase sigma subunit [Onion yellows
           phytoplasma OY-M]
 gi|39722223|dbj|BAD04713.1| DNA-directed RNA polymerase sigma subunit [Onion yellows
           phytoplasma OY-M]
          Length = 460

 Score =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 80/307 (26%), Positives = 142/307 (46%), Gaps = 41/307 (13%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYV--------------LAK-----------RYREHGD- 46
           +  +  Y+ EI +IP+L   EE                LAK           + +E  D 
Sbjct: 151 DDSVRMYLKEIGQIPLLSLAEEQKKSILVFLGKQAKQKLAKHKTKEIELSEEQLQEAHDQ 210

Query: 47  ----LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
                 A   LV S+ RLVV IA  Y G G+   +++ EGN+GLM+AV KFD ++GF+ +
Sbjct: 211 IEQARRAKDILVESNYRLVVSIAKRYIGRGILFLDLIQEGNMGLMRAVDKFDYQKGFKFS 270

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I     +      + ++    + +T    K   V  +
Sbjct: 271 TYATWWIRQAITRAIADQARTIRIPVHIVE-----TINKMALCTRKLTQKLKKKPTVEEL 325

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A K+N+S  ++ S+        SL A    ++++ +   D++    D       E   ++
Sbjct: 326 ADKMNISAEKIRSIQYIEKKPISLEAPARENEEDETSLGDFI---SDPNILSPHEYMMKE 382

Query: 223 NRRNMLTRSMS-VLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
             + +L   +   L  RE ++ + R   L     TLE + + F V+RER+RQIE++A ++
Sbjct: 383 VTQKLLDEVLENTLTDREEKVLKMRYGLLDGKTHTLEEVGTLFGVTRERIRQIESKALRR 442

Query: 280 VQESIQK 286
           ++   ++
Sbjct: 443 LRTPAKQ 449


>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 =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 74/278 (26%), Positives = 126/278 (45%), Gaps = 14/278 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           +   + I +I K   L   E   ++KR    E     A   +V ++LRLV+ IA  Y   
Sbjct: 360 LAFQQKIADIEKELSLSVAEIKDISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNR 419

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I     
Sbjct: 420 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM- 478

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
                  + R+   L         PE    + ++L + E +V  +        S+   I 
Sbjct: 479 -IETINKINRVSRQLLQEMGREPTPE---ELGERLEMDEVKVRKVLKIAKEPISMETPI- 533

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             D   S   D++    D      I+    +  +      +  L  RE ++ + R   + 
Sbjct: 534 -GDDEDSHLGDFI---EDQNITSPIDAATSEGLKEATREVLENLTEREAKVLKMRFGIDM 589

Query: 252 P--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           P   TLE +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 590 PTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 627


>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 =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 129/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 344 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 403

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 404 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 461

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 462 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 516

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 517 SHLGDFI---EDPTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 573

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 574 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 609


>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 =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 342 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 401

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 402 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 459

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 460 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 514

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 515 SHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 571

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 572 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 607


>gi|161506225|ref|YP_001573337.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:-- str. RSK2980]
 gi|160867572|gb|ABX24195.1| hypothetical protein SARI_04418 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 660

 Score =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 129/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 391 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 450

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 451 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 508

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 509 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 563

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 564 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 620

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 621 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 656


>gi|332518972|ref|ZP_08395439.1| RNA polymerase sigma factor, sigma-70 family [Lacinutrix algicola
           5H-3-7-4]
 gi|332044820|gb|EGI81013.1| RNA polymerase sigma factor, sigma-70 family [Lacinutrix algicola
           5H-3-7-4]
          Length = 287

 Score =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 145/276 (52%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI K+ ++   EE  LA+R +  GD  A  +L  ++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQEIGKVDLITADEEVELAQRIK-AGDQVALEKLTKANLRFVVSVAKQYQNQGLT 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     +V++        
Sbjct: 76  LPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNK---- 131

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
              ++ ++      +   + +P     IAK+L+++ ++V           S++A +   +
Sbjct: 132 -IGSINKINKTFAFLEQAHERPPSAEEIAKELDMTINDVKESMKNSGRHVSMDAPLV--E 188

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
              S   D L   + G+      +   ++ R  + R++  L PRE  +        N  P
Sbjct: 189 GEDSNLYDVL---NSGESPNPDRELLHESLRTEIERALETLTPREADVIRLYFGLGNQHP 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 246 MTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|83648911|ref|YP_437346.1| RNA polymerase sigma-70 factor RpoD [Hahella chejuensis KCTC 2396]
 gi|83636954|gb|ABC32921.1| RNA polymerase sigma-70 factor RpoD [Hahella chejuensis KCTC 2396]
          Length = 639

 Score =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 71/249 (28%), Positives = 117/249 (46%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 393 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+  H+         PE   
Sbjct: 453 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRHMLQEMGREATPE--- 507

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +AKK+++ E +V  +        S+   I   D   S   D++    D   +  I+   
Sbjct: 508 ELAKKMDMPEDKVRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDSHAESPIDSAT 562

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            +  +    R ++ L  RE ++   R   E     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 563 TEGLKESTRRVLAGLTAREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALR 622

Query: 279 KVQESIQKQ 287
           K++   +  
Sbjct: 623 KLRHPSRSD 631


>gi|329298675|ref|ZP_08256011.1| RNA polymerase sigma factor RpoD [Plautia stali symbiont]
          Length = 610

 Score =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 69/267 (25%), Positives = 126/267 (47%), Gaps = 14/267 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 350 LTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 409

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 410 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 467

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    +A+++ + E ++  +        S+   I   D   S   D++  
Sbjct: 468 LQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 520

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   ++ ++    ++ R+     ++ L  RE ++   R   +     TLE +  +F+V
Sbjct: 521 -EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 579

Query: 265 SRERVRQIEARAFKKVQESIQKQVELS 291
           +RER+RQIEA+A +K++   + +V  S
Sbjct: 580 TRERIRQIEAKALRKLRHPSRSEVLRS 606


>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 =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 342 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 401

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 402 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 459

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 460 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 514

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 515 SHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 571

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 572 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 607


>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 =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 66/243 (27%), Positives = 113/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 578 RKAKKEMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 637

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A K+
Sbjct: 638 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGAEPDPAT---LAVKM 692

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + RN
Sbjct: 693 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDNNTLAPSDAALHASMRN 747

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 748 VVKDVLDSLTPREAKVLRMRFGVEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 807

Query: 285 QKQ 287
           +  
Sbjct: 808 RSD 810


>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 =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 129/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 391 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 450

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 451 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 508

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 509 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 563

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 564 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 620

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 621 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 656


>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|253772097|ref|YP_003034928.1| RNA polymerase sigma factor RpoD [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254038237|ref|ZP_04872295.1| RNA polymerase sigma factor RpoD [Escherichia sp. 1_1_43]
 gi|254163014|ref|YP_003046122.1| RNA polymerase sigma factor RpoD [Escherichia coli B str. REL606]
 gi|256024353|ref|ZP_05438218.1| RNA polymerase sigma factor RpoD [Escherichia sp. 4_1_40B]
 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|307139755|ref|ZP_07499111.1| RNA polymerase sigma factor RpoD [Escherichia coli H736]
 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|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]
          Length = 613

 Score =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 129/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 344 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 403

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 404 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 461

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 462 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 516

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 517 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 573

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 574 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 609


>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 =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 129/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 345 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 404

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 405 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 462

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 463 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 517

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 518 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 574

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 575 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 610


>gi|212711167|ref|ZP_03319295.1| hypothetical protein PROVALCAL_02239 [Providencia alcalifaciens DSM
           30120]
 gi|212686335|gb|EEB45863.1| hypothetical protein PROVALCAL_02239 [Providencia alcalifaciens DSM
           30120]
          Length = 615

 Score =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 346 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 405

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 406 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 463

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 464 KLNRISRQMLQEMGREPSPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 518

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 519 SHLGDFI---EDTTLELPLDSATSESLRSATHEVLAGLTAREAKVLRMRFGIDMNTDHTL 575

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 576 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 611


>gi|254424926|ref|ZP_05038644.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
 gi|196192415|gb|EDX87379.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
          Length = 404

 Score =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 79/313 (25%), Positives = 141/313 (45%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAK---------RYREHGD---------------- 46
            E  +  Y+ EI +I +L  +EE  LA+         R R+  D                
Sbjct: 92  TEDSIRLYLQEIGRIRLLRAEEEIELARKIADLLELERIRDEIDDQLDDEPTDADWANAV 151

Query: 47  --------------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 152 DMPLPAFRRRLYQGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 211

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 212 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKLLSQE 266

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA ++ ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 267 LGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIESDGETPE 324

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
               ++  +   R  L   +S L+PRER +   R   ++    TLE +   F V+RER+R
Sbjct: 325 ----DEVSKSLLREDLESVLSTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIR 380

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 381 QIEAKALRKLRHP 393


>gi|330821204|ref|YP_004350066.1| RNA polymerase, sigma 70 subunit, RpoD family protein [Burkholderia
           gladioli BSR3]
 gi|327373199|gb|AEA64554.1| RNA polymerase, sigma 70 subunit, RpoD family protein [Burkholderia
           gladioli BSR3]
          Length = 805

 Score =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 564 RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 623

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 624 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 678

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 679 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDSNTVAPADAALHASMRD 733

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 734 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 793

Query: 285 QKQ 287
           +  
Sbjct: 794 RSD 796


>gi|153209360|ref|ZP_01947367.1| alternative sigma factor RpoH [Coxiella burnetii 'MSU Goat Q177']
 gi|212217703|ref|YP_002304490.1| RNA polymerase factor sigma-32 [Coxiella burnetii CbuK_Q154]
 gi|120575393|gb|EAX32017.1| alternative sigma factor RpoH [Coxiella burnetii 'MSU Goat Q177']
 gi|212011965|gb|ACJ19345.1| RNA polymerase sigma-32 factor [Coxiella burnetii CbuK_Q154]
          Length = 288

 Score =  232 bits (593), Expect = 4e-59,   Method: Composition-based stats.
 Identities = 105/278 (37%), Positives = 167/278 (60%), Gaps = 9/278 (3%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  YI  + +IP+L  +EE+ LA ++R+  DL AA +LV SHLR VV+IA GY GYGL
Sbjct: 16  GSIGSYISLVNRIPLLSAEEEHDLANKFRQSNDLEAARKLVLSHLRFVVRIARGYSGYGL 75

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
             ++++ EGNIGLM+AVK+FDP+ G RL ++++ WI+A + E+IL++W +VKI TT  Q+
Sbjct: 76  SQADLIQEGNIGLMKAVKRFDPQVGVRLVSFAVHWIRAEIHEFILKNWRIVKIATTKAQR 135

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINS 192
           +LFFNLR+        +D+     +  A+A++LNVS  +V  M  RL + DE+ +     
Sbjct: 136 KLFFNLRKHAKKRGWFSDH-----EAFALAEELNVSTKDVRQMEERLNSYDEAFDGADEE 190

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKE---ERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           SD  +  W     Y  D +    ++ E      ++ + L  +M  L+ R R I   R L 
Sbjct: 191 SDSGTPSWGAPAHYLEDKRYNPALQLERSNWADDQEHRLHNAMQSLDDRSRDILYQRWLS 250

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E   TL  L++++ VS ER+RQ+E  A +K++ ++  +
Sbjct: 251 EKKSTLHELAAQYAVSAERIRQLEKNAMQKIRTAMADE 288


>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 =  232 bits (593), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 129/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 344 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 403

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 404 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 461

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 462 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 516

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 517 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 573

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 574 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 609


>gi|15803609|ref|NP_289642.1| RNA polymerase sigma factor RpoD [Escherichia coli O157:H7 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|256019017|ref|ZP_05432882.1| RNA polymerase sigma factor RpoD [Shigella sp. D9]
 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 70 factor [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|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 1180]
 gi|323183651|gb|EFZ69048.1| RNA polymerase sigma factor rpoD [Escherichia coli 1357]
 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 KO11]
 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]
          Length = 613

 Score =  232 bits (593), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 129/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 344 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 403

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 404 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 461

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 462 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 516

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 517 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 573

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 574 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 609


>gi|57239060|ref|YP_180196.1| RNA polymerase sigma factor rpoD [Ehrlichia ruminantium str.
           Welgevonden]
 gi|58579003|ref|YP_197215.1| RNA polymerase sigma factor rpoD [Ehrlichia ruminantium str.
           Welgevonden]
 gi|58617062|ref|YP_196261.1| RNA polymerase sigma factor rpoD [Ehrlichia ruminantium str.
           Gardel]
 gi|57161139|emb|CAH58052.1| RNA polymerase sigma-70 factor [Ehrlichia ruminantium str.
           Welgevonden]
 gi|58416674|emb|CAI27787.1| RNA polymerase sigma factor rpoD [Ehrlichia ruminantium str.
           Gardel]
 gi|58417629|emb|CAI26833.1| RNA polymerase sigma factor rpoD [Ehrlichia ruminantium str.
           Welgevonden]
          Length = 622

 Score =  232 bits (592), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 74/272 (27%), Positives = 133/272 (48%), Gaps = 19/272 (6%)

Query: 24  RKIPMLEKQ----EEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
            KI +L  +    E   L  + ++H   +  A   ++ ++LRLVV IA  Y   GL   +
Sbjct: 354 NKIKLLSGENSLAEFKSLVTKIQKHERAATQAKQEMIKANLRLVVSIAKKYSNRGLQFLD 413

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +V EGNIGLM+AV KFD +RG++ +TY+ WW++ A+   I      ++I        +  
Sbjct: 414 LVQEGNIGLMKAVDKFDYKRGYKFSTYATWWVRQAITRAIADQARTIRIPVH-----MIE 468

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + ++   L+ +     +   +  ++ +LN++  ++  +   +    SL + I   D +S
Sbjct: 469 TVNKINRTLRQMLHEIGREPTLEELSARLNINVDKIRKVMKIVKDPVSLESPI--GDDDS 526

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVT 254
           S + D +    D +     +     + R + T+ +S L P+E RI   R          T
Sbjct: 527 STFGDCI---EDKRAVRPEDAAVLADLREITTKVLSTLTPKEERILRMRFGIGKGGKDHT 583

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 584 LEEVGKLFNVTRERIRQIEAKALRKLRHPSRA 615


>gi|332666643|ref|YP_004449431.1| RpoD subfamily RNA polymerase sigma-70 subunit [Haliscomenobacter
           hydrossis DSM 1100]
 gi|332335457|gb|AEE52558.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Haliscomenobacter
           hydrossis DSM 1100]
          Length = 289

 Score =  232 bits (592), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 77/288 (26%), Positives = 152/288 (52%), Gaps = 12/288 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI K+ +L  +EE  LAKR ++ GD +A  +L  ++LR VV
Sbjct: 5   KITKSITNRESQSLEKYLQEIGKVDLLTPEEEVELAKRIKQ-GDQAALEKLTKANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL +S++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 64  SVAKQYQNQGLSLSDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    N+      + +    L+   +    PE    +A+ L +   EV +     A 
Sbjct: 124 IVRLP--LNKVGSLNKINKAFSELEQEFEREPSPE---ELAEMLEIPTEEVETTLGVAAR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     + NS       V +++         +  ++ R  + RS+S L  R+  +
Sbjct: 179 HVSMDAPFVEGEDNSLLD----VLENNTTPSTDAGLDYNESLRREIERSLSTLTDRQCDV 234

Query: 243 FEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +       E+P++LE++  +F ++RERVRQI+ +A  K++ + + ++
Sbjct: 235 IKLYFGIGVEHPMSLEDIGEKFGLTRERVRQIKDKAINKLRSANRSKL 282


>gi|326797246|ref|YP_004315066.1| RNA polymerase, sigma 32 subunit, RpoH [Marinomonas mediterranea
           MMB-1]
 gi|326548010|gb|ADZ93230.1| RNA polymerase, sigma 32 subunit, RpoH [Marinomonas mediterranea
           MMB-1]
          Length = 288

 Score =  232 bits (592), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 107/274 (39%), Positives = 161/274 (58%), Gaps = 7/274 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+  +  IP+L  +EE  LA+R    GDL AA  LV SHLR VV IA  Y GYGL  
Sbjct: 17  LESYVQGVSTIPILTAEEEQKLAERLYYDGDLEAARALVMSHLRFVVHIAKSYSGYGLSQ 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++V EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+IL++W +VK+ TT  Q+++
Sbjct: 77  GDLVQEGNVGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEFILKNWRIVKVATTKAQRKM 136

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR  K  L  + ++     +V A+A  L VS   V  M  R++  D + +A  +  D
Sbjct: 137 FFNLRSAKKTLSWLNNS-----EVDAVANDLGVSPDVVRQMEGRMSSTDMAFDATTDDDD 191

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEK-EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
            ++ Q     + D      +L+E      +    L ++MS L+ R R I   R L EN  
Sbjct: 192 DSAFQAPASYLEDGRYDPAMLLEDGNWEADSNRRLQQAMSDLDERSRNILVQRWLSENKS 251

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           TL +L+ E+ VS ER+RQ+E  A KK++ ++ ++
Sbjct: 252 TLHDLADEYGVSAERIRQLEKNAMKKIRVAMGEE 285


>gi|330836598|ref|YP_004411239.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           coccoides DSM 17374]
 gi|329748501|gb|AEC01857.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           coccoides DSM 17374]
          Length = 293

 Score =  232 bits (592), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 81/283 (28%), Positives = 154/283 (54%), Gaps = 13/283 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           N S +      LS Y+ EI +IPML  +EEY +AK   E G+  A +RLV S+LR VV I
Sbjct: 13  NQSDMHEDVNILSIYLKEINRIPMLTHEEEYKVAKLAAE-GNQKARNRLVESNLRFVVNI 71

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y+  GLP+ ++++EGNIGLM A++KFD ++G+   +Y++WWI+ A+ + I      V
Sbjct: 72  AKKYQNQGLPLGDLINEGNIGLMNAIEKFDVDKGYHFISYAVWWIRQAILKAISEKSRTV 131

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           ++            L +++   +++ + +     +  I +   +  S V  +        
Sbjct: 132 RLPLNRA-----NELMQIQKAQKSLMNESGAEPTMEEIGRLTQLDPSHVADLIAISKEMV 186

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL+A + +   NSS   D++    D  + V+I+   +++    + + ++ L+ +E  I E
Sbjct: 187 SLDAPVFTDSGNSS-VGDFIQDGADSPDDVIIDSALKED----INKVLATLSEKEMEILE 241

Query: 245 ARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            R     ++P++L+ +   + +++ER+RQIE +A +++Q+  +
Sbjct: 242 FRFGLNGQHPMSLKEIGELYNLTKERIRQIEKKAIERLQQPSR 284


>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|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]
          Length = 613

 Score =  232 bits (592), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 129/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 344 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 403

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 404 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 461

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 462 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 516

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 517 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 573

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 574 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 609


>gi|220921709|ref|YP_002497010.1| RNA polymerase factor sigma-32 [Methylobacterium nodulans ORS 2060]
 gi|219946315|gb|ACL56707.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium nodulans
           ORS 2060]
          Length = 293

 Score =  232 bits (592), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 111/259 (42%), Positives = 171/259 (66%), Gaps = 1/259 (0%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE++EE  LA R+++  D  A HRL+++H+RLV+ +A  +R YGLP++++V EG++GL
Sbjct: 19  PFLEREEERGLAVRWKDERDEQALHRLISAHMRLVIALAGRFRHYGLPMADLVQEGHVGL 78

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 79  MEAAARFEPERDVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRARL 138

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLV 205
              TD  +  E    IA  + VS  +V  M+ RL+G D SLNA I      S++  D+LV
Sbjct: 139 MQSTDERVGDEIHSRIATAIGVSREDVALMDARLSGPDMSLNAPITDEGDASAERVDFLV 198

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
                 ++ + +  + + R   L ++++VL+ RE RI   RRL E+  TLE L     +S
Sbjct: 199 DTSPLPDEAVSDAVDGERRLTWLRQALTVLSERELRILHERRLAEDQATLEALGHRLGIS 258

Query: 266 RERVRQIEARAFKKVQESI 284
           +ERVRQIE RA +K++ ++
Sbjct: 259 KERVRQIENRALEKLRRAL 277


>gi|319899398|ref|YP_004159495.1| RNA polymerase sigma-32 factor [Bartonella clarridgeiae 73]
 gi|319403366|emb|CBI76925.1| RNA polymerase sigma-32 factor [Bartonella clarridgeiae 73]
          Length = 303

 Score =  232 bits (592), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 104/266 (39%), Positives = 169/266 (63%), Gaps = 1/266 (0%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           +    + P LE+++E+ LA R+++  D +A H++  +H+RLV+ IA  ++ + +P+ ++V
Sbjct: 27  MRSAMQAPYLERKKEHDLALRWKDKRDDNAMHQIAAAHMRLVISIASRFKRFKMPLGDLV 86

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EG +GL++A  +FDP+R  R +TY+ WWI+A++Q+YILR+WS+V+ GT+++QK LFFNL
Sbjct: 87  QEGYVGLLEAAARFDPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSSQKALFFNL 146

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSSDKNSS 198
           RRL+  L        K E    I++KL VS S+V  M+ R  A D SL+  ++ + +N  
Sbjct: 147 RRLRAKLAQDDSTLTKQEIFRTISEKLGVSVSDVEKMDFRFSAADNSLSLSVSENGENPI 206

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
              D LV DH   + V+ +  + + R   L  ++ +LN RE  I   RRL E   TLE L
Sbjct: 207 AKMDSLVDDHPLPDAVIEQAIDGQRRTKWLYEALKILNERELEIIRFRRLNEEGATLEVL 266

Query: 259 SSEFEVSRERVRQIEARAFKKVQESI 284
             +  +S+ERVRQIEARA +K++ ++
Sbjct: 267 GQKLGISKERVRQIEARALQKLRCAL 292


>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 =  232 bits (592), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 74/277 (26%), Positives = 126/277 (45%), Gaps = 14/277 (5%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
              + I EI +   L  +E   +AKR    E     A   +V ++LRLV+ IA  Y   G
Sbjct: 354 AFQQKIAEIEQDLNLNVREIKEIAKRMAVGEAKARRAKKEMVEANLRLVISIAKKYTNRG 413

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I      
Sbjct: 414 LQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM-- 471

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 + R+   L         PE    + ++L + E +V  +        S+   I  
Sbjct: 472 IETINKINRVSRQLLQEMGREPTPE---ELGERLEMDEVKVRKVLKIAKEPISMETPI-- 526

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            D   S   D++    D      ++    +  +      +  L  RE ++ + R   + P
Sbjct: 527 GDDEDSHLGDFI---EDSNITSPVDAATSEGLKEATREVLENLTEREAKVLKMRFGIDMP 583

Query: 253 --VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 584 TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 620


>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 =  232 bits (592), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 69/273 (25%), Positives = 128/273 (46%), Gaps = 14/273 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 344 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 403

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 404 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 461

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 462 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 516

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 517 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 573

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           E +  +F+V+RER+RQIEA+A +K++   + +V
Sbjct: 574 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEV 606


>gi|88801442|ref|ZP_01116970.1| putative sigma factor A [Polaribacter irgensii 23-P]
 gi|88782100|gb|EAR13277.1| putative sigma factor A [Polaribacter irgensii 23-P]
          Length = 287

 Score =  232 bits (592), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 73/278 (26%), Positives = 147/278 (52%), Gaps = 13/278 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI K+ ++   EE  LA+  +  GD  A  +L  ++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQEIGKVDLITADEEVELAQLIK-AGDQRALEKLTKANLRFVVSVAKQYQNQGLT 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + +     +V++    N+  
Sbjct: 76  LPDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLP--LNKIG 133

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               + ++   L+   +   +P     IAKKL+++ ++V           S++A +   +
Sbjct: 134 SINKINKMYAFLEQENE---RPPSAEEIAKKLDMTVNDVKESMKNSGRHVSMDAPLI--E 188

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
              S   D L   + G+      K   ++ R  + R++  L PRE  + +         P
Sbjct: 189 GEDSNLYDVL---NSGESPNPDRKLLHESLRIEIDRALETLTPREADVVKLYFGLGEHQP 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
           +TLE +   F+++RERVRQI+ +A ++++ + + ++ +
Sbjct: 246 MTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKILM 283


>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 =  232 bits (592), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 129/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 345 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 404

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 405 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 462

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 463 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 517

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 518 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 574

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 575 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 610


>gi|110638185|ref|YP_678394.1| RNA polymerase sigma-70 factor [Cytophaga hutchinsonii ATCC 33406]
 gi|110280866|gb|ABG59052.1| RNA polymerase sigma-70 factor [Cytophaga hutchinsonii ATCC 33406]
          Length = 287

 Score =  232 bits (592), Expect = 5e-59,   Method: Composition-based stats.
 Identities = 75/288 (26%), Positives = 142/288 (49%), Gaps = 13/288 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           + +  I       L +Y+ EI K+ +L   EE  LAKR RE GD  A  +L  ++LR VV
Sbjct: 5   KISKQITNRESQSLDKYLQEIGKVDLLTPDEEVDLAKRIRE-GDQLALEKLTKANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 64  SVAKQYQNQGLSLGDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++           +L ++      +     +      +A+ L VS +EV+        
Sbjct: 124 IVRLPLNR-----VGSLNKISKTFSELEQKYEREPSPDELAEVLEVSTAEVVDTLKISGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     ++NS      L    +  E          + R  + R++S L  RE  +
Sbjct: 179 HVSMDAPFVQGEENS-----LLDVLENSSESAPDSSLMNDSLRREVQRALSTLTQREADV 233

Query: 243 FEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
                    E+ +TLE +  +F ++RERVRQI+ +A ++++ + + + 
Sbjct: 234 ISLYFGLNGEHSMTLEEIGEKFNLTRERVRQIKEKAIRRLRHTSRSKA 281


>gi|297184127|gb|ADI20246.1| hypothetical protein [uncultured Sphingobacterium sp. EB080_L08E11]
          Length = 287

 Score =  232 bits (592), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 74/276 (26%), Positives = 146/276 (52%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI K+ ++  +EE  LA+R +  GD  A  +L  ++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQEIGKVELITAEEEVELAQRIK-AGDQIALEKLTKANLRFVVSVAKQYQNQGLT 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     +V++    N+  
Sbjct: 76  LPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLP--LNKIG 133

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               + +   +L+   +   +P     I+K L +SES+V           S++A +   +
Sbjct: 134 SINKINKAYAYLEQEHE---RPPSAAEISKHLEMSESDVKESMRNSGRHVSMDAPLV--E 188

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NP 252
              S   D L   +        E     + R  + RS++ L PRE  +          +P
Sbjct: 189 GEDSNLYDVL---NSSDSPHPDEDLMMDSLRTEIERSLATLTPREGDVIRLYFGLGGQHP 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TLE +  +F+++RERVRQI+ +A ++++ + + ++
Sbjct: 246 MTLEEIGEKFDLTRERVRQIKEKAIRRMKHTSRSKI 281


>gi|27904539|ref|NP_777665.1| RNA polymerase factor sigma-32 [Buchnera aphidicola str. Bp
           (Baizongia pistaciae)]
 gi|31340406|sp|Q89B27|RP32_BUCBP RecName: Full=RNA polymerase sigma-32 factor
 gi|27903936|gb|AAO26770.1| RNA polymerase sigma-32 factor [Buchnera aphidicola str. Bp
           (Baizongia pistaciae)]
          Length = 287

 Score =  232 bits (592), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 100/287 (34%), Positives = 168/287 (58%), Gaps = 10/287 (3%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           +  ++       L  YI E    PML  QEE  L+++   HGDL+AA  L+ SHLR V+ 
Sbjct: 5   ETKTLPAISLGNLDSYIREANSWPMLSSQEEKYLSEKLFYHGDLNAAKTLILSHLRFVIH 64

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           ++  Y GYGL  ++++ EGNIGLM+AV++F+P+ G RL ++++ WIK+ + EY+LR+W +
Sbjct: 65  VSRNYSGYGLLQADLIQEGNIGLMKAVRRFNPKIGVRLVSFAVHWIKSEIHEYVLRNWRI 124

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AG 182
           VK+ TT +Q++LFFNLR+ K  L    D+ L       +A++L V   +V  M  R+ A 
Sbjct: 125 VKVATTKSQRKLFFNLRKTKQRLGWFNDHEL-----ELVAQELGVKREDVREMESRMSAQ 179

Query: 183 DESL-NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR-NMLTRSMSVLNPRER 240
           D +L +   N  ++ +  +    + D        +E++  +  + N L+ ++S L+ R R
Sbjct: 180 DIALHHVPDNFREEQNFSYTIPYLKDSLSDFANHVEEDNWEAHKTNKLSNALSSLDERSR 239

Query: 241 RIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            I  AR L   ++ +TL  ++  + +S ERVRQ+E  A KK++ +I+
Sbjct: 240 NIIHARWLDDSDHKMTLREIAHNYGISAERVRQLEKNAMKKLKVAIE 286


>gi|160331013|ref|XP_001712214.1| rpoD [Hemiselmis andersenii]
 gi|159765661|gb|ABW97889.1| rpoD [Hemiselmis andersenii]
          Length = 485

 Score =  232 bits (592), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 78/319 (24%), Positives = 147/319 (46%), Gaps = 52/319 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------------- 43
            +  +  Y+  I ++ +L  +EE  LA+   +                            
Sbjct: 128 ADDSVRWYLQLIGRVRLLRPEEEIQLAREISQLLHWEHVKISLREKLQREPTSSEWTAAC 187

Query: 44  ------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                       H    A  R+V ++LRLVV IA  Y   G+ + +++ EG++GL++A +
Sbjct: 188 KVSDVKKFRAILHNARRAKERMVAANLRLVVSIAKRYVNRGMSLQDLIQEGSLGLIRAAE 247

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD E+GF+ +TY+ WW+K A+   I      +++        L+  +  ++   + +  
Sbjct: 248 KFDSEKGFKFSTYATWWVKQAVTRAIADHSRTIRLPVH-----LYDTISAIRKTTRTLNI 302

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +      IA+K+++S  ++ S+        SL   +  +D ++SQ  D++  D +  
Sbjct: 303 EIGRSPTEEEIAEKMDMSVEKLRSVLQSAQPTLSLERPLK-NDDDASQLSDFIEADQESP 361

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERV 269
           E    E  E+   R+ L   ++ L+PRER +   R   ++    TLE +   F V+RERV
Sbjct: 362 E----EHVEKSMLRDDLENVINSLSPRERDVVRMRYGLDDGRIKTLEEIGQIFSVTRERV 417

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIEA+A +K+++  +  +
Sbjct: 418 RQIEAKAIRKLRQPYRSSI 436


>gi|124022438|ref|YP_001016745.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str. MIT
           9303]
 gi|123962724|gb|ABM77480.1| Putative principal RNA polymerase sigma factor [Prochlorococcus
           marinus str. MIT 9303]
          Length = 444

 Score =  232 bits (592), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 79/313 (25%), Positives = 143/313 (45%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE--------------HG------------ 45
            E  +  Y+ EI +I +L   EE  LA++  +              HG            
Sbjct: 132 TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLHLEELAEQFNSDHGHYPNNKEWAALV 191

Query: 46  -------------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 192 EMPNIKFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 251

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 252 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKVLSQE 306

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA+ + ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 307 FGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIESDTENPE 364

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
           Q + +   R++    L   ++ L+PRER +   R   ++    TLE +   FEV+RER+R
Sbjct: 365 QDVAKNLLRED----LEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFEVTRERIR 420

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 421 QIEAKALRKLRHP 433


>gi|85057387|ref|YP_456303.1| RNA polymerase sigma factor RpoD [Aster yellows witches'-broom
           phytoplasma AYWB]
 gi|84789492|gb|ABC65224.1| RNA polymerase sigma factor RpoD [Aster yellows witches'-broom
           phytoplasma AYWB]
          Length = 465

 Score =  232 bits (592), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 80/307 (26%), Positives = 142/307 (46%), Gaps = 41/307 (13%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYV--------------LAK-----------RYREHGD- 46
           +  +  Y+ EI +IP+L   EE                LAK           + +E  D 
Sbjct: 156 DDSVRMYLKEIGQIPLLSLAEEQKKSILVFLGKQAKQKLAKHKTKEIELSEDQLQEAHDQ 215

Query: 47  ----LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
                 A   LV S+ RLVV IA  Y G G+   +++ EGN+GLM+AV KFD ++GF+ +
Sbjct: 216 IKQARRAKDILVESNYRLVVSIAKRYIGRGILFLDLIQEGNMGLMRAVDKFDYQKGFKFS 275

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I     +      + ++    + +T    K   V  +
Sbjct: 276 TYATWWIRQAITRAIADQARTIRIPVHIVE-----TINKMALCTRKLTQKLKKKPTVEEL 330

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A K+N+S  ++ S+        SL A    ++++ +   D++    D       E   ++
Sbjct: 331 ADKMNISAEKIRSIQYIEKKPISLEAPARENEEDETSLGDFI---SDPNILSPHEYMMKE 387

Query: 223 NRRNMLTRSMS-VLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
             + +L   +   L  RE ++ + R   L     TLE + + F V+RER+RQIE++A ++
Sbjct: 388 VTQKLLDEVLENTLTEREEKVLKMRYGLLDGKTHTLEEVGTLFGVTRERIRQIESKALRR 447

Query: 280 VQESIQK 286
           ++   ++
Sbjct: 448 LRTPAKQ 454


>gi|114764201|ref|ZP_01443439.1| RNA polymerase sigma factor [Pelagibaca bermudensis HTCC2601]
 gi|114543353|gb|EAU46369.1| RNA polymerase sigma factor [Roseovarius sp. HTCC2601]
          Length = 292

 Score =  232 bits (592), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 104/272 (38%), Positives = 174/272 (63%), Gaps = 6/272 (2%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
            +  K  +L+ + E  LA  +R+H D +A HRL+ +++RL + +A  ++ YG P+ +++ 
Sbjct: 13  RKAMKAELLDAETELQLAYAWRDHRDEAALHRLINAYMRLAISMAAKFKRYGAPMGDLIQ 72

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           E  +GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFN+R
Sbjct: 73  EAGLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMR 132

Query: 141 RLKGHLQAITDNNLKPEQV----VAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDK 195
           R++  L+       +  +      AIAK++ V   +V  M+ RL+G D SLNA   S+D+
Sbjct: 133 RVQARLEREAAAEGRALERHSLHAAIAKEVGVPLHDVEMMDGRLSGSDFSLNA-TQSTDE 191

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
           +  +W D L  D +    ++  K +    R  L  +++ LN RER I   R+L++   TL
Sbjct: 192 DGREWIDTLEDDGEQSASLVEGKLDNDQLREWLVVALTGLNDRERFIVRERKLRDETRTL 251

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+L  E  +S+ERVRQ+EA AF K+++S++ Q
Sbjct: 252 ESLGQELGLSKERVRQLEAAAFVKMRKSLEAQ 283


>gi|1072030|gb|AAB60181.1| RNA polymerase sigma-subunit [Escherichia coli]
          Length = 603

 Score =  232 bits (592), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 129/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 334 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 393

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 394 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 451

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 452 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 506

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 507 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 563

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 564 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 599


>gi|57239125|ref|YP_180261.1| RNA polymerase sigma-32 factor [Ehrlichia ruminantium str.
           Welgevonden]
 gi|57161204|emb|CAH58118.1| RNA polymerase sigma-32 factor [Ehrlichia ruminantium str.
           Welgevonden]
          Length = 296

 Score =  232 bits (592), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 127/282 (45%), Positives = 186/282 (65%), Gaps = 3/282 (1%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
             SI+   +  L  YI+E++   +L  +EE  LAK + EHG ++ AH+LVTSHLRLVVK+
Sbjct: 3   TSSILSLTQDNLMSYINEVQSFQVLSLEEEEKLAKNWYEHGVIADAHKLVTSHLRLVVKV 62

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A+ ++ YGLP+ E++ EGNIGLMQAVKKF+P  GFRL+TY++WWIKA++++YIL+SWS +
Sbjct: 63  ALSFKNYGLPLIELIMEGNIGLMQAVKKFNPNLGFRLSTYAIWWIKASIKDYILKSWSCI 122

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GD 183
           KIGTT  Q++LFF+LR           NN+  E +  IA + + SE EV  MN      D
Sbjct: 123 KIGTTQAQRKLFFSLR-KIKKKLLKYHNNITKEDIKMIANECSTSEQEVEQMNKYFTYRD 181

Query: 184 ESLNALINS-SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
           +SLN ++ S   +N  Q QD +  +   QE   +  EE   +++++T++++ LN R R I
Sbjct: 182 KSLNDVVFSNGSQNGVQLQDMIKCEDPNQEDAYLLNEETDIKKSLITQALATLNERHRDI 241

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           F  R+L E P TLE LS ++ +S+ER+RQIE  AF KV+  +
Sbjct: 242 FIRRKLIEEPDTLEILSKKYNISKERIRQIETHAFLKVKNFV 283


>gi|324115354|gb|EGC09318.1| RNA polymerase sigma proteinRpoD [Escherichia fergusonii B253]
          Length = 613

 Score =  232 bits (592), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 71/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +H+I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 344 LHQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 403

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 404 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 461

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 462 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 516

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 517 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 573

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 574 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 609


>gi|319953761|ref|YP_004165028.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Cellulophaga
           algicola DSM 14237]
 gi|319422421|gb|ADV49530.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cellulophaga
           algicola DSM 14237]
          Length = 287

 Score =  232 bits (592), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 72/276 (26%), Positives = 146/276 (52%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI K+ ++   EE  LA+R ++ GD +A  +L  ++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQEIGKVDLITADEEVELAQRIKK-GDQAALEKLTKANLRFVVSVAKQYQNQGLT 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     +V++    N+  
Sbjct: 76  LPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLP--LNKIG 133

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               + +    L+   +    PE    IAK+L+++  +V           S++A +   D
Sbjct: 134 SINKINKTFAFLEQAHERQPSPE---EIAKELDMTVEDVKQSLKNSGRHVSMDAPLI--D 188

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENP 252
              S   D L     G+      +   ++ R  + R++  L PRE  +         ++ 
Sbjct: 189 GEDSNLYDVL---RSGESPNPDRELLHESLRTEIERALETLTPREADVIRLYFGLAGQHS 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 246 MTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|302343327|ref|YP_003807856.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfarculus baarsii DSM
           2075]
 gi|301639940|gb|ADK85262.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfarculus baarsii DSM
           2075]
          Length = 346

 Score =  232 bits (591), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 108/276 (39%), Positives = 165/276 (59%), Gaps = 8/276 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL- 73
            L RY+ E R+ P+L ++EE  LA+R+ E  D  AA  LVTS+LRLVVKIAM ++ Y + 
Sbjct: 63  ALQRYLWEARQYPLLSREEEDALARRFVEEQDPEAAAMLVTSNLRLVVKIAMEHQRYWMR 122

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++ EGN+GL+QAV+KFDP RG + + Y+ +WIKA + ++I+ +W LV++GTT  Q+
Sbjct: 123 NLLDLIQEGNMGLLQAVQKFDPFRGIKFSYYASFWIKAYILKFIMDNWRLVRVGTTQAQR 182

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINS 192
           +LF+ LRR K  LQA             + ++L VSE +V+ M  RL   E SL+A +  
Sbjct: 183 KLFYKLRREKEKLQA----QGVTPGPRLLGQRLGVSEKDVVDMEQRLDSWELSLDAPVR- 237

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            D +    ++ L       EQ L + E R+     L      L+ +E+ I + R L ENP
Sbjct: 238 -DDSDDTHKNLLPSPRPTAEQDLADSELRQLFHRKLMEFRQTLDDKEQDILDNRLLAENP 296

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            TL  +     VSRER+RQ++ R  +K+ E +Q+Q+
Sbjct: 297 QTLSEVGDRHGVSRERIRQLQVRLMEKLGEFMQEQI 332


>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 =  232 bits (591), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 129/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 346 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 405

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 406 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 463

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 464 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 518

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 519 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 575

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 576 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 611


>gi|147756|gb|AAA24601.1| RNA polymerase sigma-subunit [Escherichia coli]
          Length = 613

 Score =  232 bits (591), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 129/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 344 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 403

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 404 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 461

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 462 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 516

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 517 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTL 573

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 574 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 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 =  232 bits (591), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 347 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 406

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 407 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 464

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 465 KLNRISRQMLQEMGREPSPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 519

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 520 SHLGDFI---EDTTLELPLDSATSESLRSATHEVLAGLTAREAKVLRMRFGIDMNTDHTL 576

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 577 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 612


>gi|218550316|ref|YP_002384107.1| RNA polymerase sigma factor RpoD [Escherichia fergusonii ATCC
           35469]
 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 =  232 bits (591), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 71/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +H+I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 344 LHQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 403

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 404 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 461

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 462 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 516

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 517 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 573

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 574 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 609


>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 =  232 bits (591), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 71/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 346 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 405

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 406 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 463

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+ A I   D   
Sbjct: 464 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMEAPI--GDDED 518

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 519 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 575

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 576 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 611


>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 =  232 bits (591), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 559 RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 618

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 619 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 673

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 674 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTVAPADAALHASMRD 728

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 729 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 788

Query: 285 QKQ 287
           +  
Sbjct: 789 RSD 791


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

 Score =  232 bits (591), Expect = 6e-59,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 116/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 488 EAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 547

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T     P     +
Sbjct: 548 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGAEPDPAT---L 602

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+++ E ++  +        S+   I   D + S   D++    D       +     
Sbjct: 603 AQKMDMPEDKIRKILKIAKEPISMETPI--GDDDDSHLGDFI---EDTATLAPSDAALHG 657

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 658 SMRDVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKL 717

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 718 RHPSRAD 724


>gi|16130963|ref|NP_417539.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli str.
           K-12 substr. MG1655]
 gi|89109837|ref|AP_003617.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli str.
           K-12 substr. W3110]
 gi|170082610|ref|YP_001731930.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli str.
           K-12 substr. DH10B]
 gi|238902178|ref|YP_002927974.1| RNA polymerase, sigma 70 (sigma D) factor [Escherichia coli BW2952]
 gi|1710680|sp|P00579|RPOD_ECOLI RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 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]
          Length = 613

 Score =  232 bits (591), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 129/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 344 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 403

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 404 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 461

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 462 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 516

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 517 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTL 573

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 574 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 609


>gi|296104731|ref|YP_003614877.1| RNA polymerase sigma-70 factor [Enterobacter cloacae subsp. cloacae
           ATCC 13047]
 gi|295059190|gb|ADF63928.1| RNA polymerase sigma-70 factor [Enterobacter cloacae subsp. cloacae
           ATCC 13047]
          Length = 615

 Score =  232 bits (591), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 129/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 346 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 405

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 406 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 463

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 464 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 518

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 519 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 575

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 576 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 611


>gi|293610908|ref|ZP_06693207.1| conserved hypothetical protein [Acinetobacter sp. SH024]
 gi|292826560|gb|EFF84926.1| conserved hypothetical protein [Acinetobacter sp. SH024]
          Length = 628

 Score =  232 bits (591), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 74/278 (26%), Positives = 126/278 (45%), Gaps = 14/278 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           +   + I +I K   L   E   ++KR    E     A   +V ++LRLV+ IA  Y   
Sbjct: 352 LAFQQKIADIEKELSLSVAEIKDISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNR 411

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I     
Sbjct: 412 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM- 470

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
                  + R+   L         PE    + ++L + E +V  +        S+   I 
Sbjct: 471 -IETINKINRVSRQLLQEMGREPTPE---ELGERLEMDEVKVRKVLKIAKEPISMETPI- 525

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             D   S   D++    D      I+    +  +      +  L  RE ++ + R   + 
Sbjct: 526 -GDDEDSHLGDFI---EDQNITSPIDAATSEGLKEATREVLENLTEREAKVLKMRFGIDM 581

Query: 252 P--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           P   TLE +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 582 PTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 619


>gi|295097580|emb|CBK86670.1| RNA polymerase, sigma 70 subunit, RpoD [Enterobacter cloacae subsp.
           cloacae NCTC 9394]
          Length = 614

 Score =  232 bits (591), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 71/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +H+I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 345 LHQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 404

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 405 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 462

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 463 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 517

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 518 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 574

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 575 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 610


>gi|284046806|ref|YP_003397146.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Conexibacter
           woesei DSM 14684]
 gi|283951027|gb|ADB53771.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Conexibacter
           woesei DSM 14684]
          Length = 380

 Score =  232 bits (591), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 82/269 (30%), Positives = 135/269 (50%), Gaps = 13/269 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             L  Y+  I ++ +L  ++E  LA+R  E GD+ A  +++ ++LRLVV IA GY G GL
Sbjct: 110 DSLRLYLRSIGRVNLLTAEQEVHLAQRI-ERGDMRAKQQMIEANLRLVVSIAKGYLGRGL 168

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EG++GL++AV+KFD  RGF+ +TY+ WWI+ A+   I      ++I     +K
Sbjct: 169 TFLDLIQEGSLGLIRAVEKFDHRRGFKFSTYATWWIRQAVTRAIADKGRTIRIPVHMVEK 228

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L ++    + +  +  +      IA +L  +  EV  +        SL   I   
Sbjct: 229 -----LNKVVHVERQLVQSLGREPTPEEIAAELECTVREVRDILRMAQQPVSLEKPI--G 281

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-- 251
           ++  S+  D++    D   +   E      RR+ + R++  L  RER + E R       
Sbjct: 282 EEEESELGDFV---EDQTAESPFELASENLRRDNVRRALQALPQREREVIEMRFGLGGGR 338

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKV 280
           P TLE +   F V+RER+RQIE    KK+
Sbjct: 339 PRTLEEVGRAFNVTRERIRQIENHTLKKL 367


>gi|294676015|ref|YP_003576630.1| RNA polymerase sigma-32 factor [Rhodobacter capsulatus SB 1003]
 gi|294474835|gb|ADE84223.1| RNA polymerase sigma-32 factor-1 [Rhodobacter capsulatus SB 1003]
          Length = 292

 Score =  232 bits (591), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 104/274 (37%), Positives = 176/274 (64%), Gaps = 6/274 (2%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
            +  +   L+ + E  LA+ +R+H D +A HRLV++++RL + +A  +R YG P+++++ 
Sbjct: 13  RQAMRAEYLDAETEAALARAWRDHRDEAALHRLVSAYMRLAISMASKFRRYGAPMNDLIQ 72

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           E ++GLM+A  KFDP+RG R +TY++WWIKA++QE+++R+WS+V+ G+T++QK LFFNL+
Sbjct: 73  EASLGLMKAADKFDPDRGVRFSTYAVWWIKASIQEFVMRNWSMVRTGSTSSQKALFFNLK 132

Query: 141 RLKGHLQAITDNNL----KPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDK 195
           R++  +Q   +         +    +A  + VS ++V  M  RL+G D SLNA   S D+
Sbjct: 133 RVQAQIQREAEAEGVVLDGAQLREKVAISIGVSMADVEMMEGRLSGSDLSLNAP-QSHDE 191

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
           +  +W D L  +    E  + E  +    R+ L ++M  L+ RER I   RRL + P TL
Sbjct: 192 DGREWVDTLEDEGGSPETRVTEAHDGAKMRDWLGQAMGQLSARERYIVAQRRLIDEPRTL 251

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           E+L  E  +S+ER+RQ+EA+AF K+++S++ + E
Sbjct: 252 ESLGEELGLSKERIRQLEAQAFSKMRKSLESRSE 285


>gi|163787530|ref|ZP_02181977.1| RNA polymerase sigma-70 factor [Flavobacteriales bacterium ALC-1]
 gi|159877418|gb|EDP71475.1| RNA polymerase sigma-70 factor [Flavobacteriales bacterium ALC-1]
          Length = 287

 Score =  232 bits (591), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 144/276 (52%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI K+ ++   EE  LA+R +  GD  A  +L  ++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQEIGKVDLITADEEVELAQRIK-AGDQIALEKLTKANLRFVVSVAKQYQNQGLT 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     +V++        
Sbjct: 76  LPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNK---- 131

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
              ++ ++      +  ++ +P     IAK+L+++ ++V           S++A +   +
Sbjct: 132 -IGSINKINKTFAFLEQSHERPPSAEEIAKELDMTINDVKESMKNSGRHVSMDAPLV--E 188

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
              S   D L     G+          ++ R  + R++  L PRE  +        N  P
Sbjct: 189 GEDSNLYDVL---RSGESPNPDRDLLHESLRTEIERALETLTPREADVIRLYFGLGNQHP 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 246 MTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>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 =  232 bits (591), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 64/247 (25%), Positives = 115/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 539 ESNSRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 598

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    +              +
Sbjct: 599 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKMNRLSRQHLQEFGFEPDASIL 653

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A K+ + E ++  +        S+   I   D + S   D++    D      +E   + 
Sbjct: 654 AAKMEIPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDSANTAPLEAAMQA 708

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 709 GLRDVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKL 768

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 769 KHPSRSD 775


>gi|162605994|ref|XP_001713512.1| RNA-polymerase sigma factor [Guillardia theta]
 gi|13794432|gb|AAK39807.1|AF165818_15 RNA-polymerase sigma factor [Guillardia theta]
          Length = 460

 Score =  232 bits (591), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 78/322 (24%), Positives = 147/322 (45%), Gaps = 52/322 (16%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------------- 43
           I   +  +  Y+  I ++ +L   EE  LA+   +                         
Sbjct: 108 IQKADDSVRWYLQLIGRVRLLRPDEEIQLAREISQLLHWEHVKISLRDKLRREPTNSEWT 167

Query: 44  ---------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
                          H    A  R+V ++LRLVV IA  Y   G+ + +++ EG++GL++
Sbjct: 168 AACKVSDVRKFRSILHNARRAKERMVAANLRLVVSIAKRYVNRGMSLQDLIQEGSLGLIR 227

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A +KFD E+GF+ +TY+ WW+K A+   I      +++        L+  +  ++   + 
Sbjct: 228 AAEKFDSEKGFKFSTYATWWVKQAVTRAIADHSRTIRLPVH-----LYDTISAIRKTTRN 282

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           +     +      IAK++++S  ++ ++        SL   +  +D ++SQ  D++  D 
Sbjct: 283 LNIEIGRSPTEEEIAKRMDMSVEKLRNVLQSAQPTLSLERPLK-NDDDTSQLSDFIEADQ 341

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSR 266
           +  E    E  E+   R+ L   ++ L+PRER +   R   ++    TLE +   F V+R
Sbjct: 342 ESPE----EHVEKSMLRDDLENVINSLSPRERDVVRMRYGLDDGRIKTLEEIGQIFSVTR 397

Query: 267 ERVRQIEARAFKKVQESIQKQV 288
           ERVRQIEA+A +K+++  +  +
Sbjct: 398 ERVRQIEAKAIRKLRQPYRSSI 419


>gi|163759996|ref|ZP_02167080.1| RNA polymerase sigma-32 factor [Hoeflea phototrophica DFL-43]
 gi|162282954|gb|EDQ33241.1| RNA polymerase sigma-32 factor [Hoeflea phototrophica DFL-43]
          Length = 278

 Score =  232 bits (591), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 104/270 (38%), Positives = 162/270 (60%), Gaps = 2/270 (0%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           +      P LE+ EE+ LA  ++ + D  A H++  +H+RLV+ +A  +R +GLP+ ++V
Sbjct: 2   VRAAMAAPYLERDEEHDLAVAWKNNKDQDALHKITMAHMRLVISMAAKFRNFGLPMGDLV 61

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EG++GL++A  +FDPER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFFNL
Sbjct: 62  QEGHVGLLEAAARFDPEREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKALFFNL 121

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKN-S 197
           RRL+  L             + IA  L V   +V  M+ RL+G D SLNA ++  +   S
Sbjct: 122 RRLRARLAQDDPTLTDSAIHIQIADSLGVHVKDVAVMDARLSGPDSSLNAPMSDGESGAS 181

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           S   D+L  D    ++ +    + + R   L  +++ LNPRE  I   RRL E   TLE 
Sbjct: 182 SDRMDFLKSDEPLPDEQVSTIIDEERRNTWLGDALNTLNPRELLIIRKRRLAEEGATLEA 241

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L +   +S+ERVRQIE RA +K++  +  +
Sbjct: 242 LGATLGISKERVRQIENRALEKLRAVLSSE 271


>gi|308804840|ref|XP_003079732.1| SigA (ISS) [Ostreococcus tauri]
 gi|116058189|emb|CAL53378.1| SigA (ISS) [Ostreococcus tauri]
          Length = 525

 Score =  232 bits (591), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 77/337 (22%), Positives = 144/337 (42%), Gaps = 56/337 (16%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE--------------------------- 43
                +  Y+ +I  + +L   +E  LAKR ++                           
Sbjct: 198 PSTDSMRSYLKDIGSVTLLNAGQEVELAKRIQDLMHLESIRENLIEETGPGVELSESQWA 257

Query: 44  --------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
                         H   +A + ++ ++LRLVV IA  Y    +   +++ EG +GL++ 
Sbjct: 258 AAAGLNVSALRQRLHDGKAAKNEMIQANLRLVVSIAKKYANTNMSFQDLIQEGCVGLIRG 317

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
            +KFD +RG++ +TY+ WWI+ A+   I      +++        LF  + R+    Q  
Sbjct: 318 AEKFDFQRGYKFSTYAHWWIRQAVTRSISDQSRTIRLPVH-----LFEIISRISKMEQKF 372

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
              N +P  +  IA ++ +S  ++  +        SL A     +      +D L+   D
Sbjct: 373 ALYNGRPPTLEEIASEMEMSVEKITQIKKAAQAPVSL-AQTMGGENKGRTIEDTLI---D 428

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRE 267
              +   +   +   +  L   ++ LNPRER +   R   ++    TLE + + F V+RE
Sbjct: 429 ANAEGPEKVSGKSLLKEDLENVLNTLNPRERDVLRLRYGLDDGRVKTLEEIGTVFSVTRE 488

Query: 268 RVRQIEARAFKKVQESIQKQVE----LSSSPPLLQKP 300
           R+RQIEA+A +K+++  + QV     +  +PP   +P
Sbjct: 489 RIRQIEAKALRKLKQPSRNQVLQEYFVDDAPPNTHRP 525


>gi|317493716|ref|ZP_07952133.1| RNA polymerase sigma factor RpoD [Enterobacteriaceae bacterium
           9_2_54FAA]
 gi|316918043|gb|EFV39385.1| RNA polymerase sigma factor RpoD [Enterobacteriaceae bacterium
           9_2_54FAA]
          Length = 610

 Score =  232 bits (591), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 72/276 (26%), Positives = 131/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +H+I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 341 LHQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 400

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 401 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 458

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 459 KLNRISRQMLQEMGREPTPE---ELAERMMMPEDKIRKVLKIAKEPISMETPI--GDDED 513

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     +S L  RE ++   R   +     TL
Sbjct: 514 SHLGDFI---EDTTLELPLDSATSESLRSATRDVLSGLTAREAKVLRMRFGIDMNTDHTL 570

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 571 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 606


>gi|226946813|ref|YP_002801886.1| RNA polymerase factor sigma-32 [Azotobacter vinelandii DJ]
 gi|226721740|gb|ACO80911.1| RNA polymerase sigma-32 factor [Azotobacter vinelandii DJ]
          Length = 284

 Score =  232 bits (591), Expect = 7e-59,   Method: Composition-based stats.
 Identities = 104/272 (38%), Positives = 156/272 (57%), Gaps = 7/272 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+H +  IP+L  ++E  LA R     DL AA ++V +HLR VV IA  Y GYGL 
Sbjct: 16  NLEAYVHAVNSIPLLTAEQERELADRLYYQQDLDAARQMVLAHLRFVVHIARSYSGYGLA 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            S+++ EGN+GLM+AVK+F+PE G RL ++++ WI+A + E+ILR+W +VKI TT  Q++
Sbjct: 76  QSDLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIRAEIHEFILRNWRIVKIATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           LFFNLR  K  L  + +     E+V A+A+ L V   EV  M  RL+G +        +D
Sbjct: 136 LFFNLRSQKKRLAWLNN-----EEVDAVAESLGVEPHEVREMESRLSGQDMAFDPAADAD 190

Query: 195 KNSS--QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            +S       +L        + L E +   +    L  ++  L+ R R I   R L E  
Sbjct: 191 DDSVFQAPAHYLEDQRYDPARQLEEADWSDSAAANLHEALEGLDERSRDILYQRWLAEEK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL +L+++++VS ER+RQ+E  A  K++ SI
Sbjct: 251 ATLHDLAAKYKVSAERIRQLEKSALNKLKGSI 282


>gi|163754266|ref|ZP_02161389.1| RNA polymerase sigma-70 factor [Kordia algicida OT-1]
 gi|161326480|gb|EDP97806.1| RNA polymerase sigma-70 factor [Kordia algicida OT-1]
          Length = 287

 Score =  232 bits (591), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 68/276 (24%), Positives = 146/276 (52%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI K+ ++   EE  LA+R +  GD  A  +L  ++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQEIGKVDLITADEEVELAQRIK-AGDQIALEKLTKANLRFVVSVAKQYQNQGLT 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     +V++        
Sbjct: 76  LPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNK---- 131

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
              ++ ++      +  ++ +      IAK+L+++ ++V           S++A +   +
Sbjct: 132 -IGSINKINKTFAYLEQSHERIPSAEEIAKELDMTVNDVKESMKNSGRHVSMDAPLV--E 188

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
              S   D L   + G+     ++   ++ +  + R++  L PRE  +        N  P
Sbjct: 189 GEDSNLYDVL---NSGESPNPDKELLHESLKTEIERALETLTPREADVIRLYFGLGNQHP 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 246 MTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|183597880|ref|ZP_02959373.1| hypothetical protein PROSTU_01215 [Providencia stuartii ATCC 25827]
 gi|188022641|gb|EDU60681.1| hypothetical protein PROSTU_01215 [Providencia stuartii ATCC 25827]
          Length = 617

 Score =  232 bits (591), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 348 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 407

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 408 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 465

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 466 KLNRISRQMLQEMGREPSPE---ELAERMMMPEDKIRKVLKIAKEPISMETPI--GDDED 520

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 521 SHLGDFI---EDNTLELPLDSATSESLRSATHEVLAGLTAREAKVLRMRFGIDMNTDHTL 577

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 578 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 613


>gi|124006216|ref|ZP_01691051.1| RpoD [Microscilla marina ATCC 23134]
 gi|123988140|gb|EAY27798.1| RpoD [Microscilla marina ATCC 23134]
          Length = 287

 Score =  232 bits (591), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 75/288 (26%), Positives = 144/288 (50%), Gaps = 13/288 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           + +  I       L +Y+ EI K+ +L   EE  LAKR RE GD  A  +L  ++LR VV
Sbjct: 5   KISKQITNRESQSLDKYLQEIGKVDLLTPDEEVELAKRIRE-GDQVALEKLTKANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 64  SVAKQYQNQGLSLGDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++           +L ++      +     +      +A+ L+V+ SEV+        
Sbjct: 124 IVRLPLNR-----VGSLNKISKTFSELEQKYEREPSPDELAEVLDVTTSEVVDTLKISGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     ++NS      L    +  E     +    + R  + R++S L  RE  +
Sbjct: 179 HVSMDAPFVQGEENS-----LLDVLENESEVKPDSELMNDSLRKEVQRALSTLTQREADV 233

Query: 243 FEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
                    E+ +TLE +  +F ++RERVRQI+ +A ++++ + + + 
Sbjct: 234 ITLYFGLNGEHAMTLEEIGEKFNLTRERVRQIKEKAIRRLRHTSRSKA 281


>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 =  232 bits (591), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 75/298 (25%), Positives = 140/298 (46%), Gaps = 17/298 (5%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPM---LEKQEEYVLAKRYR--EHGDLSAAHRLVT 55
           MN+     ++  E  + R + ++R+I     L  ++   + +R    E     A   +V 
Sbjct: 323 MNKPWSEKLLEVEDEVQRSLQKLRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVE 382

Query: 56  SHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQE 115
           ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+  
Sbjct: 383 ANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 442

Query: 116 YILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
            I      ++I            L R+   +         PE    +A+++ + E ++  
Sbjct: 443 SIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRK 497

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
           +        S+   I   D   S   D++    D   ++ ++    ++ R+     ++ L
Sbjct: 498 VLKIAKEPISMETPI--GDDEDSHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGL 552

Query: 236 NPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
             RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 553 TAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 610


>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 =  232 bits (591), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 69/276 (25%), Positives = 126/276 (45%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + ++ +   L   +   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 348 LQQVEQETGLSIAQIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 407

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 408 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 465

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 466 KLNRISRQMLQEMGREPNPE---ELAERMGMPEDKIRKVLKIAKEPISMETPI--GDDED 520

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D    +  +    ++ +      +S L  RE ++   R   +     TL
Sbjct: 521 SHLGDFI---EDTTLALPADAATSESLKAATRDVLSGLTAREAKVLRMRFGIDMNTDHTL 577

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 578 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 613


>gi|297520936|ref|ZP_06939322.1| RNA polymerase sigma factor RpoD [Escherichia coli OP50]
          Length = 436

 Score =  232 bits (591), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 129/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 167 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 226

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 227 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 284

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 285 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 339

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 340 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 396

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 397 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 432


>gi|299131999|ref|ZP_07025194.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Afipia sp. 1NLS2]
 gi|298592136|gb|EFI52336.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Afipia sp. 1NLS2]
          Length = 709

 Score =  231 bits (590), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 76/273 (27%), Positives = 130/273 (47%), Gaps = 17/273 (6%)

Query: 21  HEIRKIPMLEKQE-----EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           HEI+++  L   E     + VL  +  E     A   +V ++LRLV+ IA  Y   GL  
Sbjct: 438 HEIQQLAALTGLEIGEFRKIVLGVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQF 497

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +
Sbjct: 498 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----M 552

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + ++    + + +   +      +A+KL +   +V  +        SL   +   D+
Sbjct: 553 IETINKIVRTSRQMLNEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPLSLETPV--GDE 610

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPV 253
             S   D++    D    + I+   + N R   TR ++ L PRE R+   R         
Sbjct: 611 EDSHLGDFI---EDKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDH 667

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 668 TLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 700


>gi|296105152|ref|YP_003615298.1| RNA polymerase factor sigma-32 [Enterobacter cloacae subsp. cloacae
           ATCC 13047]
 gi|295059611|gb|ADF64349.1| RNA polymerase factor sigma-32 [Enterobacter cloacae subsp. cloacae
           ATCC 13047]
          Length = 285

 Score =  231 bits (590), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 108/290 (37%), Positives = 165/290 (56%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +     L  YI      PML  +EE  LA++    GDL AA +L+ SHLR 
Sbjct: 1   MTKEMQTLALAPVGNLESYIRAANTWPMLTAEEEKELAEKLHYQGDLEAAKKLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVEMVARELGVSSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQ---EQVLIEKEERKNRRNMLTRSMSVLNP 237
           A  +    + +  D + SQ    ++Y  D        + E        N L+ +M  L+ 
Sbjct: 176 AAQDMTFDMSSDDDASDSQPMAPVLYLQDKTSNFADGIEEDNWEDQAANKLSYAMEGLDE 235

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L E+   TL+ L+  + VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQDIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 285


>gi|238896571|ref|YP_002921314.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae NTUH-K2044]
 gi|238548896|dbj|BAH65247.1| RNA polymerase sigma factor [Klebsiella pneumoniae subsp.
           pneumoniae NTUH-K2044]
          Length = 632

 Score =  231 bits (590), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 129/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 363 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 422

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 423 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 480

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 481 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 535

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 536 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 592

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 593 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 628


>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 =  231 bits (590), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 129/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 344 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 403

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 404 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 461

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 462 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 516

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 517 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 573

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 574 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 609


>gi|85712119|ref|ZP_01043172.1| DNA-directed RNA polymerase sigma 38 subunit [Idiomarina baltica
           OS145]
 gi|85694109|gb|EAQ32054.1| DNA-directed RNA polymerase sigma 38 subunit [Idiomarina baltica
           OS145]
          Length = 333

 Score =  231 bits (590), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 83/271 (30%), Positives = 141/271 (52%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   ++R  + GD++A  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 63  YLSEIGFSPLLTAEEEIFYSRRALK-GDIAARKRMIESNLRLVVKIARRYCNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 122 VEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 180

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            IA  LN    ++  M        S++  I     N  
Sbjct: 181 LRAAR----ELAHKLDHEPTAEDIAASLNKPVEDITKMLRLNERVTSVDTPI--GGDNDK 234

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  + D   + +++     + +  +T  +  LNP+++ +   R   L   P TLE
Sbjct: 235 ALLDILTDEADDGPEGVLQD---GDLKERITEWLDALNPKQKEVLARRFGLLGYEPSTLE 291

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+  A +K+++ +++Q
Sbjct: 292 DVGHEIGLTRERVRQIQVEALRKLRDFLRQQ 322


>gi|224369499|ref|YP_002603663.1| RpoH [Desulfobacterium autotrophicum HRM2]
 gi|223692216|gb|ACN15499.1| RpoH [Desulfobacterium autotrophicum HRM2]
          Length = 322

 Score =  231 bits (590), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 100/277 (36%), Positives = 165/277 (59%), Gaps = 8/277 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG-YG 72
             L  Y+ EI +  +L ++EE  L  + +E  D  AA+ +VTS+LRLVVKIA+ ++  + 
Sbjct: 41  DPLQSYLAEINRYRLLTREEEVNLGTKIQEENDSDAAYVMVTSNLRLVVKIALDFQRIWM 100

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
             + +++ EGNIGL++AVKKFDP +  + + Y+ +WIKA + ++I+ +W LVKIGTT  Q
Sbjct: 101 QNLLDLIQEGNIGLVKAVKKFDPYKNVKFSYYASFWIKAYILKFIMDNWRLVKIGTTQGQ 160

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALIN 191
           ++LFF   RLK   Q + D    P   + +++++ VSE E+I M+ RL G D SL+  + 
Sbjct: 161 RKLFF---RLKKEKQKLIDEGFDPGPKL-LSERMGVSEQEIIEMDQRLDGWDLSLDEPLR 216

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           +   + ++  +++  + D  E  +  KE        + +  + LNPRE  IF  R   + 
Sbjct: 217 N--DSDTERIEFINVESDSTEDRVARKEIEDILHVRVKKFTATLNPREMEIFSKRIFSDE 274

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           P TL+ +  E+ +SRERVRQIE    KK++E  + ++
Sbjct: 275 PRTLQEIGEEYNISRERVRQIENNIIKKMKEYFKNEM 311


>gi|296387874|ref|ZP_06877349.1| RNA polymerase sigma factor RpoS [Pseudomonas aeruginosa PAb1]
          Length = 334

 Score =  231 bits (590), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 83/278 (29%), Positives = 141/278 (50%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 66  YLNEIGFSPLLTPEEEVHFA-RLAQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 124

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 125 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 183

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++  + +K       ++ +N R+   D SL         + 
Sbjct: 184 LRAAR-ELTHKLDHEPSPEEIANLLEKPVAEVKRMLGLNERVTSVDVSL------GPDSD 236

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + ++ L  ++R +   R         TL
Sbjct: 237 KTLLDTLTDDRPTDPCELLQDDDLS---ESIDQWLTELTDKQREVVIRRFGLRGHESSTL 293

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E +  E  ++RERVRQI+  A K+++E ++K    S +
Sbjct: 294 EEVGQEIGLTRERVRQIQVEALKRLREILEKNGLSSDA 331


>gi|121730259|ref|ZP_01682638.1| RNA polymerase sigma-32 factor [Vibrio cholerae V52]
 gi|121627991|gb|EAX60548.1| RNA polymerase sigma-32 factor [Vibrio cholerae V52]
          Length = 259

 Score =  231 bits (590), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 103/262 (39%), Positives = 159/262 (60%), Gaps = 11/262 (4%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           ML   EE  LA+R    GD+ AA  L+ SHLR VV +A GY GYGLP++++V EGNIGLM
Sbjct: 1   MLSADEERELAERLHYKGDIDAAKGLILSHLRFVVHVARGYSGYGLPMADLVQEGNIGLM 60

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AVK+F+PE G RL ++++ WIKA + EY+LR+W +VKI TT  Q++LFFNLR+ K  L 
Sbjct: 61  KAVKRFNPEMGVRLVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKLFFNLRKSKKRLG 120

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
              +      +V  +A++L V  +EV  M  RLA  ++   +    D+N   +   ++Y 
Sbjct: 121 WFNNG-----EVETVARELGVEPAEVREMESRLAAQDAAFEMSAEDDENGMAYTAPVLYL 175

Query: 208 HDGQEQVLIEKEERKNRR----NMLTRSMSVLNPRERRIFEARRLQEN-PVTLENLSSEF 262
            D     L +  E +N        L+ +++ L+ R + I  AR L ++   TL++L+  +
Sbjct: 176 EDKHSD-LADNLEAENWEAHTTQRLSMALASLDERSQHIVRARWLDDDNKTTLQDLAEMY 234

Query: 263 EVSRERVRQIEARAFKKVQESI 284
            VS ER+RQ+E  A +K++E++
Sbjct: 235 GVSAERIRQLEKNAMRKLKEAV 256


>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 =  231 bits (590), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 69/263 (26%), Positives = 120/263 (45%), Gaps = 14/263 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L   E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 356 LTVAEIKEINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 415

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 416 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 473

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    + +++ + E ++  +        S+   I   D   S   D++  
Sbjct: 474 LQEMGREPTPE---ELGERMEMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 526

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q  I+    ++ +      +S L  RE ++   R   +     TLE +  +F+V
Sbjct: 527 -EDSTMQSPIDVATVESLKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 585

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   + +
Sbjct: 586 TRERIRQIEAKALRKLRHPTRSE 608


>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 =  231 bits (590), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 65/250 (26%), Positives = 119/250 (47%), Gaps = 12/250 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 368 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 427

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 428 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPSPE--- 482

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + E ++  +        S+   I   D   S   D++    D   ++ ++   
Sbjct: 483 ELAERMMMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDTTLELPLDSAT 537

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            ++ +N     ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 538 SESLKNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 597

Query: 279 KVQESIQKQV 288
           K++   + ++
Sbjct: 598 KLRHPSRSEI 607


>gi|56416704|ref|YP_153778.1| RNA polymerase sigma factor [Anaplasma marginale str. St. Maries]
 gi|56387936|gb|AAV86523.1| RNA polymerase sigma factor [Anaplasma marginale str. St. Maries]
          Length = 632

 Score =  231 bits (590), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 71/272 (26%), Positives = 130/272 (47%), Gaps = 19/272 (6%)

Query: 24  RKIPMLEKQEE----YVLAKRYREHGDL--SAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
            K+ +L  ++       L  + ++H      A   ++ ++LRLVV IA  Y   GL   +
Sbjct: 364 NKVRLLSGEDSPGNFKALVAKIQKHERTANKAKQEMIKANLRLVVSIAKKYSNRGLQFLD 423

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +V EGNIGLM+AV KFD +RG++ +TY+ WW++ A+   I      ++I        +  
Sbjct: 424 LVQEGNIGLMKAVDKFDYKRGYKFSTYATWWVRQAITRAIADQARTIRIPVH-----MIE 478

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + ++   L+ +     +   +  ++ +L ++  ++  +   +    SL + I   D +S
Sbjct: 479 TVNKINRTLRQMLHEIGREPTLEELSTRLGMNVEKIRKVMKIVKDPVSLESPI--GDDDS 536

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVT 254
           S + D +    D +           + R + T+ +S L P+E RI   R          T
Sbjct: 537 STFGDCI---EDKRAVKPENAAVLADLREITTKVLSTLTPKEERILRMRFGIGKGGKDHT 593

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 594 LEEVGKLFNVTRERIRQIEAKALRKLRHPSRA 625


>gi|5821404|dbj|BAA83808.1| sigma factor 32 [Pseudomonas putida]
          Length = 284

 Score =  231 bits (590), Expect = 8e-59,   Method: Composition-based stats.
 Identities = 101/272 (37%), Positives = 153/272 (56%), Gaps = 7/272 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+H +  IP+L  ++E  L +R     D+ AA ++V +HLR VV IA  Y GYGL 
Sbjct: 16  NLEAYVHTVNSIPLLTVEQERDLGERLYYEQDVEAARQMVMAHLRFVVHIARSYAGYGLA 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++
Sbjct: 76  QADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIPEFILRNWRIVKVATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           LFFNLR  K  L  + +     ++V  +A+ L V   EV  M  RL+G +        +D
Sbjct: 136 LFFNLRSQKKRLAWLNN-----DEVHRVAESLGVEPREVREMESRLSGQDMAFDPAAEAD 190

Query: 195 KNSS-QWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENP 252
            +S+ Q     + DH     V +E  +  +     L  ++   N R R I   R L E  
Sbjct: 191 DDSAFQSPAHYLEDHRYDPAVQLEDADWSDNSTSNLHEALQGWNERSRDILYQRWLAEEK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL  L+ ++ VS ER+RQ+E  A  KV+  I
Sbjct: 251 ATLHELADKYSVSAERIRQLEKNAMNKVKALI 282


>gi|170742915|ref|YP_001771570.1| RNA polymerase factor sigma-32 [Methylobacterium sp. 4-46]
 gi|168197189|gb|ACA19136.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium sp. 4-46]
          Length = 293

 Score =  231 bits (590), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 111/259 (42%), Positives = 171/259 (66%), Gaps = 1/259 (0%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE++EE  LA R+++  D  A HRL+++H+RLV+ +A  +R YGLP++++V EG++GL
Sbjct: 19  PFLEREEERGLAVRWKDKRDEQALHRLISAHMRLVIALAGRFRHYGLPMADLVQEGHVGL 78

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 79  MEAAARFEPERDVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRARL 138

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLV 205
              TD  +  E    IA  + VS  +V  M+ RL+G D SLNA I      S++  D+LV
Sbjct: 139 MQSTDERVGDEIHRRIATAIGVSREDVALMDARLSGPDMSLNAPITDEGDASAERVDFLV 198

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
                 ++ + +  + + R   L ++++VL+ RE RI   RRL E+  TLE L     +S
Sbjct: 199 DTSPLPDEAVSDAVDGERRLTWLRQALTVLSERELRILHERRLAEDQATLEALGHRLGIS 258

Query: 266 RERVRQIEARAFKKVQESI 284
           +ERVRQIE RA +K++ ++
Sbjct: 259 KERVRQIENRALEKLRRAL 277


>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|323208002|gb|EFZ92948.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Montevideo str. 507440-20]
 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]
          Length = 615

 Score =  231 bits (590), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 129/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 346 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 405

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 406 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 463

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 464 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 518

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 519 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 575

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 576 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 611


>gi|493078|gb|AAA92723.1| RpoH (sigma 32) [Pseudomonas aeruginosa]
          Length = 284

 Score =  231 bits (590), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 102/272 (37%), Positives = 155/272 (56%), Gaps = 7/272 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+H +  IP+L  ++E  LA+R     DL AA ++V +HLR VV IA  Y GYGL 
Sbjct: 16  NLEAYVHSVNSIPLLSPEQERELAERLFYQQDLEAARQMVLAHLRFVVHIAKSYSGYGLA 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++
Sbjct: 76  QADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           LFFNLR  K  L  + +     E+V  +A+ L V   EV  M  RL G +        +D
Sbjct: 136 LFFNLRSQKKRLAWLNN-----EEVHRVAESLGVEPREVREMESRLTGQDMAFDPAADAD 190

Query: 195 KNSS-QWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENP 252
             S+ Q     + DH       +E  +  +  +  L  ++  L+ R R I + R L E  
Sbjct: 191 DESAYQSPAHYLEDHRYDPARQLEDADWSDSSSANLHEALEGLDERSRDILQQRWLSEEK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL +L+ ++ VS ER+RQ+E  A  K++  I
Sbjct: 251 ATLHDLAEKYNVSAERIRQLEKNAMSKLKGRI 282


>gi|15598818|ref|NP_252312.1| RNA polymerase sigma factor RpoS [Pseudomonas aeruginosa PAO1]
 gi|116051619|ref|YP_789542.1| RNA polymerase sigma factor RpoS [Pseudomonas aeruginosa
           UCBPP-PA14]
 gi|218890153|ref|YP_002439017.1| RNA polymerase sigma factor RpoS [Pseudomonas aeruginosa LESB58]
 gi|254242320|ref|ZP_04935642.1| sigma factor RpoS [Pseudomonas aeruginosa 2192]
 gi|1173167|sp|P45684|RPOS_PSEAE RecName: Full=RNA polymerase sigma factor rpoS
 gi|9949780|gb|AAG07010.1|AE004782_8 sigma factor RpoS [Pseudomonas aeruginosa PAO1]
 gi|440378|dbj|BAA05131.1| RNA polymerase principal sigma factor [Pseudomonas aeruginosa]
 gi|52632371|gb|AAU85546.1| RNA polymerase sigma factor [Pseudomonas sp. M18]
 gi|115586840|gb|ABJ12855.1| sigma factor RpoS [Pseudomonas aeruginosa UCBPP-PA14]
 gi|126195698|gb|EAZ59761.1| sigma factor RpoS [Pseudomonas aeruginosa 2192]
 gi|218770376|emb|CAW26141.1| sigma factor RpoS [Pseudomonas aeruginosa LESB58]
          Length = 334

 Score =  231 bits (590), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 83/278 (29%), Positives = 141/278 (50%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 66  YLNEIGFSPLLTPEEEVHFA-RLAQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 124

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 125 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 183

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++  + +K       ++ +N R+   D SL         + 
Sbjct: 184 LRAAR-ELTHKLDHEPSPEEIANLLEKPVAEVKRMLGLNERVTSVDVSL------GPDSD 236

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + ++ L  ++R +   R         TL
Sbjct: 237 KTLLDTLTDDRPTDPCELLQDDDLS---ESIDQWLTELTDKQREVVIRRFGLRGHESSTL 293

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E +  E  ++RERVRQI+  A K+++E ++K    S +
Sbjct: 294 EEVGQEIGLTRERVRQIQVEALKRLREILEKNGLSSDA 331


>gi|332974186|gb|EGK11120.1| DNA-directed RNA polymerase sigma subunit RpoD [Psychrobacter sp.
           1501(2011)]
          Length = 624

 Score =  231 bits (590), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 71/259 (27%), Positives = 118/259 (45%), Gaps = 14/259 (5%)

Query: 33  EEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           E   +A+R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV
Sbjct: 367 EMKEVARRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 426

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
            KF+  RG++ +TY+ WWI+ A+   I      ++I            + R+   L    
Sbjct: 427 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKINRVSRQLLQEM 484

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
                PE    + ++L + E +V  +        S+   I   D   S   D++    D 
Sbjct: 485 GREPTPE---ELGERLEMDEVKVRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDQ 536

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRER 268
                +E       +      +S L  RE ++   R   + P   TLE +  +F+V+RER
Sbjct: 537 TISSPVEDATSAGLQEATRDVLSNLTEREAKVLRMRFGIDMPTDHTLEEVGKQFDVTRER 596

Query: 269 VRQIEARAFKKVQESIQKQ 287
           +RQIEA+A +K++   + +
Sbjct: 597 IRQIEAKALRKLRHPSRSE 615


>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 =  231 bits (590), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 69/267 (25%), Positives = 126/267 (47%), Gaps = 14/267 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 354 LTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 413

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 414 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 471

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    +A+++ + E ++  +        S+   I   D   S   D++  
Sbjct: 472 LQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 524

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   ++ ++    ++ R+     ++ L  RE ++   R   +     TLE +  +F+V
Sbjct: 525 -EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 583

Query: 265 SRERVRQIEARAFKKVQESIQKQVELS 291
           +RER+RQIEA+A +K++   + +V  S
Sbjct: 584 TRERIRQIEAKALRKLRHPSRSEVLRS 610


>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 =  231 bits (590), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 71/259 (27%), Positives = 118/259 (45%), Gaps = 14/259 (5%)

Query: 33  EEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           E   +A+R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV
Sbjct: 366 EMKEVARRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 425

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
            KF+  RG++ +TY+ WWI+ A+   I      ++I            + R+   L    
Sbjct: 426 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKINRVSRQLLQEM 483

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
                PE    + ++L + E +V  +        S+   I   D   S   D++    D 
Sbjct: 484 GREPTPE---ELGERLEMDEVKVRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDQ 535

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRER 268
                +E       +      +S L  RE ++   R   + P   TLE +  +F+V+RER
Sbjct: 536 TISSPVEDATSAGLQEATRDVLSNLTEREAKVLRMRFGIDMPTDHTLEEVGKQFDVTRER 595

Query: 269 VRQIEARAFKKVQESIQKQ 287
           +RQIEA+A +K++   + +
Sbjct: 596 IRQIEAKALRKLRHPSRSE 614


>gi|222087729|ref|YP_002546266.1| alternative sigma factor RpoH [Agrobacterium radiobacter K84]
 gi|221725177|gb|ACM28333.1| alternative sigma factor RpoH [Agrobacterium radiobacter K84]
          Length = 286

 Score =  231 bits (590), Expect = 9e-59,   Method: Composition-based stats.
 Identities = 109/268 (40%), Positives = 170/268 (63%), Gaps = 1/268 (0%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           R I      P L + EE+ LA R+++H D  A +++ T+H+RLV+ +A  +R +GLP+S+
Sbjct: 8   RMIKMAMAAPYLARDEEHDLAIRWKDHEDRGARNKIATAHMRLVISMAGKFRNFGLPMSD 67

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +V EG +GL++A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFF
Sbjct: 68  LVQEGYVGLLEAAARFEPEREVRFSTYASWWIRASIQDYILRNWSIVRGGTSSAQKALFF 127

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKN 196
           NLRRL+  L               IA  L VS S+V +M+ RL+  D SL A   S D  
Sbjct: 128 NLRRLRAKLARGNTGVTVQSIHEEIAVALGVSLSDVQTMDARLSSNDASLQAPSISGDAE 187

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           S++  D+L+ D    ++ +    + + RR  L  ++  LN RE +I  ARRL E+  TLE
Sbjct: 188 SAERMDFLISDEPLPDEQVSNMIDGERRRVWLASALKHLNEREMKIIRARRLVEDGATLE 247

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
            L ++  +S+ERVRQIE+RA +K++ ++
Sbjct: 248 ELGADLGISKERVRQIESRAMEKLRSAL 275


>gi|326800649|ref|YP_004318468.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphingobacterium
           sp. 21]
 gi|326551413|gb|ADZ79798.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphingobacterium
           sp. 21]
          Length = 286

 Score =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 77/288 (26%), Positives = 149/288 (51%), Gaps = 14/288 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+HEI K+ ++  +EE +LA++ RE GD +A  RL  ++LR VV
Sbjct: 5   KITQSITNRESQSLDKYLHEIGKVDLITAEEEVILAQKIRE-GDQAALERLTKTNLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A K+FD  +GF+  +Y++WWI+ ++ + I     
Sbjct: 64  SVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETKGFKFISYAVWWIRQSILQAIAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    NQ      + +    L+   +    PE    +A  L  +  ++         
Sbjct: 124 IVRLP--LNQVGSLSKISKAFSRLEQEYEREPSPE---ELADILETTVDKISDTLSNSGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     ++N+    D L       +  LI+    ++    + RS++ L  RER I
Sbjct: 179 HVSMDAPFVQGEENT--LLDVLENHDPNTDSNLID----ESLSEEIKRSLATLTEREREI 232

Query: 243 FEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
                     +P++LE +   F ++RERVRQI+ +A ++++ + + ++
Sbjct: 233 IVLFFGLGSNHPLSLEEIGETFNLTRERVRQIKDKALQRLRHTSRSKI 280


>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 =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 69/263 (26%), Positives = 120/263 (45%), Gaps = 14/263 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L   E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 356 LTVAEIKEINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 415

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 416 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 473

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    + +++ + E ++  +        S+   I   D   S   D++  
Sbjct: 474 LQEMGREPTPE---ELGERMEMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 526

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q  I+    ++ +      +S L  RE ++   R   +     TLE +  +F+V
Sbjct: 527 -EDSTMQSPIDVATVESLKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 585

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   + +
Sbjct: 586 TRERIRQIEAKALRKLRHPTRSE 608


>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 =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 65/250 (26%), Positives = 119/250 (47%), Gaps = 12/250 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 371 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 430

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 431 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPSPE--- 485

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + E ++  +        S+   I   D   S   D++    D   ++ ++   
Sbjct: 486 ELAERMMMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDTTLELPLDSAT 540

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            ++ +N     ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 541 SESLKNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 600

Query: 279 KVQESIQKQV 288
           K++   + ++
Sbjct: 601 KLRHPSRSEI 610


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

 Score =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 116/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 477 EAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 536

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T     P     +
Sbjct: 537 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGAEPDPAT---L 591

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+++ E ++  +        S+   I   D + S   D++    D       +     
Sbjct: 592 AQKMDMPEDKIRKILKIAKEPISMETPI--GDDDDSHLGDFI---EDTATLAPSDAALHG 646

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 647 SMRDVVKEVLDSLTPREAKVLRMRFGIEMSTDQTLEEVGKQFDVTRERIRQIEAKALRKL 706

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 707 RHPSRAD 713


>gi|15837951|ref|NP_298639.1| RNA polymerase sigma factor RpoD [Xylella fastidiosa 9a5c]
 gi|20140311|sp|Q9PDM9|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 =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 69/249 (27%), Positives = 118/249 (47%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RGF+
Sbjct: 371 YGEAKASKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVCKFEHRRGFK 430

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 431 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQQFGREATPE--- 485

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +AK++++ E ++  +        S+   I   D   S   D++    D   +  ++   
Sbjct: 486 ELAKEMDMPEDKIRKVMKIAKEPISMETPI--GDDEDSHLGDFI---EDPNVESPVDTTT 540

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
             N    +   ++ L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 541 NVNLSETVREVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 600

Query: 279 KVQESIQKQ 287
           K++   + +
Sbjct: 601 KLRHPSRSE 609


>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|61234163|sp|P0A2E3|RPOD_SALTY RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|61234169|sp|P0A2E4|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]
          Length = 615

 Score =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 129/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 346 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 405

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 406 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 463

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 464 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 518

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 519 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 575

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 576 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 611


>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 =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 114/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +  ++LRLV+ IA  Y   GL   +++ EGN+GLM+AV KF+  RG++ +
Sbjct: 566 EAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNVGLMKAVDKFEYRRGYKFS 625

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T     P     +
Sbjct: 626 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGVEPDP---AEL 680

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+++ E ++  +        S+   I   D   S   D+L    D       E  ++ 
Sbjct: 681 AEKMDMPEDKIRKILKIAKEPISMETPI--GDDEDSHLGDFL---EDFGTVAPAEAAQQS 735

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           +   +    +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 736 SLTEITKEVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGRQFDVTRERIRQIEAKALRKL 795

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 796 RHPSRSD 802


>gi|299768976|ref|YP_003731002.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter sp. DR1]
 gi|298699064|gb|ADI89629.1| RNA polymerase sigma factor rpoD (Sigma-70) [Acinetobacter sp. DR1]
          Length = 627

 Score =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 74/278 (26%), Positives = 126/278 (45%), Gaps = 14/278 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           +   + I +I K   L   E   ++KR    E     A   +V ++LRLV+ IA  Y   
Sbjct: 351 LAFQQKIADIEKELSLSVAEIKDISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNR 410

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I     
Sbjct: 411 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM- 469

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
                  + R+   L         PE    + ++L + E +V  +        S+   I 
Sbjct: 470 -IETINKINRVSRQLLQEMGREPTPE---ELGERLEMDEVKVRKVLKIAKEPISMETPI- 524

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             D   S   D++    D      I+    +  +      +  L  RE ++ + R   + 
Sbjct: 525 -GDDEDSHLGDFI---EDQNITSPIDAATSEGLKEATREVLENLTEREAKVLKMRFGIDM 580

Query: 252 P--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           P   TLE +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 581 PTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 618


>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 =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 69/263 (26%), Positives = 120/263 (45%), Gaps = 14/263 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L   E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 356 LTVAEIKEINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 415

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 416 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 473

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    + +++ + E ++  +        S+   I   D   S   D++  
Sbjct: 474 LQEMGREPTPE---ELGERMEMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 526

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q  I+    ++ +      +S L  RE ++   R   +     TLE +  +F+V
Sbjct: 527 -EDSTMQSPIDVATVESLKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 585

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   + +
Sbjct: 586 TRERIRQIEAKALRKLRHPTRSE 608


>gi|83859721|ref|ZP_00953241.1| RNA polymerase sigma factor [Oceanicaulis alexandrii HTCC2633]
 gi|83852080|gb|EAP89934.1| RNA polymerase sigma factor [Oceanicaulis alexandrii HTCC2633]
          Length = 301

 Score =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 113/262 (43%), Positives = 163/262 (62%), Gaps = 3/262 (1%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A  ++E GD  A H L T+++RLV+ IA  +R YGLP  ++VSEGNIGLMQA  +F+PER
Sbjct: 40  ATAWKEKGDEEALHALTTAYMRLVISIAAKFRHYGLPFPDLVSEGNIGLMQAAARFEPER 99

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
             R +TY+ WWI+A++Q+Y+LR+WS+V+ GTTA QK LFFNLRRL+  ++  +   L PE
Sbjct: 100 EVRFSTYATWWIRASIQDYVLRNWSIVRTGTTAAQKSLFFNLRRLRALIKDTSSGQLTPE 159

Query: 158 QVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
               +A+ L V E +V  M  RLA  D SLNA    S+    +WQD L  ++   E  ++
Sbjct: 160 NRAYVAQALRVGEDDVEKMASRLAAVDRSLNAPF--SEDGEGEWQDLLADENPDPETQVM 217

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           E  ++  R   L  ++S L+ RE+ I   RRL E+ VTLE L     +S+ERVRQ+E +A
Sbjct: 218 EDRDQAQRAQWLGEALSRLSEREQLIIRERRLGEDSVTLEKLGERLGISKERVRQVEHQA 277

Query: 277 FKKVQESIQKQVELSSSPPLLQ 298
             K+++ + + V       LL 
Sbjct: 278 LNKLKKYLTEVVGDPEEAGLLP 299


>gi|161829709|ref|YP_001597727.1| RNA polymerase factor sigma-32 [Coxiella burnetii RSA 331]
 gi|161761576|gb|ABX77218.1| alternative sigma factor RpoH [Coxiella burnetii RSA 331]
          Length = 288

 Score =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 104/278 (37%), Positives = 167/278 (60%), Gaps = 9/278 (3%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  YI  + +IP+L  +EE+ LA ++R+  DL AA +LV SHLR VV+IA GY GYGL
Sbjct: 16  GSIGSYISWVNRIPLLSAEEEHDLANKFRQSNDLEAARKLVLSHLRFVVRIARGYSGYGL 75

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
             ++++ EGNIGLM+AVK+FDP+ G RL ++++ WI+A + E+IL++W +VKI TT  Q+
Sbjct: 76  SQADLIQEGNIGLMKAVKRFDPQVGVRLVSFAVHWIRAEIHEFILKNWRIVKIATTKAQR 135

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINS 192
           +LFFNLR+        +D+     +  A+A++LNVS  +V  M  RL + DE+ +     
Sbjct: 136 KLFFNLRKHAKKRGWFSDH-----EAFALAEELNVSTKDVRQMEERLNSYDEAFDGADEE 190

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKE---ERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           SD  +  W     Y  D +    ++ E      ++ + L  +M  ++ R R I   R L 
Sbjct: 191 SDSGTPSWGAPAHYLEDKRYNPALQLERSNWADDQEHRLHNAMQSMDDRSRDILYQRWLS 250

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E   TL  L++++ VS ER+RQ+E  A +K++ ++  +
Sbjct: 251 EKKSTLHELAAQYSVSAERIRQLEKNAMQKIRTAMADE 288


>gi|326794473|ref|YP_004312293.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Marinomonas
           mediterranea MMB-1]
 gi|326545237|gb|ADZ90457.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Marinomonas
           mediterranea MMB-1]
          Length = 329

 Score =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 86/271 (31%), Positives = 142/271 (52%), Gaps = 12/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 57  YLSEIGFSPLLTAEEEVYFA-RLALKGDEAARKRMIESNLRLVVKISRRYLNRGLSLLDL 115

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 116 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 174

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +   Q + D+   PE    IA KL+    +V  M        S+++ +  S+ + S
Sbjct: 175 LRAARELTQQL-DHEPSPE---EIADKLDRPVEDVQKMLSLNERISSIDSPLGGSEGDKS 230

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
                +    D Q     ++ +  +  N +   +  LN ++R +   R       P TLE
Sbjct: 231 ----LVEVIPDTQHSNPEDERQEGDVLNSIDGWLDALNEKQREVIARRFGLRGYEPSTLE 286

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++ +E  ++RERVRQI+  A +K++  + KQ
Sbjct: 287 DVGAEIGLTRERVRQIQVEALRKLRLMLDKQ 317


>gi|156744261|ref|YP_001434390.1| RpoD family RNA polymerase sigma factor [Roseiflexus castenholzii
           DSM 13941]
 gi|156235589|gb|ABU60372.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus
           castenholzii DSM 13941]
          Length = 399

 Score =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 80/299 (26%), Positives = 132/299 (44%), Gaps = 38/299 (12%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRY--------------------------REHGD 46
           +  +  Y+ EI ++P+L  ++E +LAK                            +    
Sbjct: 100 DDPVRMYLQEIGQVPLLSAEQEVMLAKAMEAGHRARRALECEEYSSWQERMMYEQQVAQG 159

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV IA  Y  YGL + ++V EGNIGLM+AV+KFD  +G + +TY+ 
Sbjct: 160 NEARQHLIQANLRLVVSIAKKYTSYGLTMMDLVQEGNIGLMRAVEKFDYTKGHKFSTYAT 219

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      +++     +      ++R    LQ +      PE    IA  +
Sbjct: 220 WWIRQAITRAIADQSRTIRLPVHMGE--AISQVKRASHKLQQMMQREPTPE---EIADAM 274

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +S ++V           SL   +    +   +  D++  D         E       R 
Sbjct: 275 GISSTKVRRTLEASMHPLSLEMPV--GQEGEGRMGDFIEDDRIS---TPAEAAAASMLRE 329

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            L   +  L  RER+I + R   ++    TLE +  EF ++RER+RQIEA A +K++  
Sbjct: 330 QLEEVLQKLPERERKIIQLRYGLKDGRYRTLEEVGMEFGITRERIRQIEAVALRKLRHP 388


>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 =  231 bits (590), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 114/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +  ++LRLV+ IA  Y   GL   +++ EGN+GLM+AV KF+  RG++ +
Sbjct: 566 EAKARKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNVGLMKAVDKFEYRRGYKFS 625

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T     P     +
Sbjct: 626 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGVEPDP---AEL 680

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+++ E ++  +        S+   I   D   S   D+L    D       E  ++ 
Sbjct: 681 AEKMDMPEDKIRKILKIAKEPISMETPI--GDDEDSHLGDFL---EDFGTVAPAEAAQQS 735

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           +   +    +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 736 SLTEITKEVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGRQFDVTRERIRQIEAKALRKL 795

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 796 RHPSRSD 802


>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 =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 559 RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 618

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 619 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 673

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 674 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTVAPADAALHASMRD 728

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 729 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 788

Query: 285 QKQ 287
           +  
Sbjct: 789 RSD 791


>gi|146308041|ref|YP_001188506.1| RNA polymerase sigma factor RpoS [Pseudomonas mendocina ymp]
 gi|145576242|gb|ABP85774.1| RNA polymerase, sigma 38 subunit, RpoS [Pseudomonas mendocina ymp]
          Length = 335

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 82/277 (29%), Positives = 135/277 (48%), Gaps = 13/277 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLTPEEEVHFA-RLAQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +T           IA  L     EV  M        S++  ++    +  
Sbjct: 185 LRAAR----ELTQKLDHEPSAEEIANLLEKPVGEVKRMLGLNERVSSVD--VSLGPDSDK 238

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
              D L  D       L++ ++       + + +S L  ++R +   R         TLE
Sbjct: 239 TLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSDLTDKQREVVVRRFGLRGHESSTLE 295

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
            +  E  ++RERVRQI+  A K+++E ++K    S +
Sbjct: 296 EVGQEIGLTRERVRQIQVEALKRLREILEKNGLSSDA 332


>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 =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 70/269 (26%), Positives = 126/269 (46%), Gaps = 22/269 (8%)

Query: 32  QEEYVLA--------KRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           +EE  LA        +R    E     A   +V ++LRLV+ IA  Y   GL   +++ E
Sbjct: 362 EEETGLAISAIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 421

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           GNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R
Sbjct: 422 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNR 479

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           +   +         PE    +A+++ + E ++  +        S+   I   D   S   
Sbjct: 480 ISRQMLQEMGREPSPE---ELAERMMMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLG 534

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLS 259
           D++    D   ++ ++    ++ +N     ++ L  RE ++   R   +     TLE + 
Sbjct: 535 DFI---EDTTLELPLDSATSESLKNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVG 591

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +F+V+RER+RQIEA+A +K++   + ++
Sbjct: 592 KQFDVTRERIRQIEAKALRKLRHPSRSEI 620


>gi|86141299|ref|ZP_01059845.1| putative sigma factor A [Leeuwenhoekiella blandensis MED217]
 gi|85831858|gb|EAQ50313.1| putative sigma factor A [Leeuwenhoekiella blandensis MED217]
          Length = 287

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 143/276 (51%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI K+ ++   EE  LA+R +  GD  A  +L  ++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQEIGKVDLITADEEVELAQRIK-AGDQRALEKLTKANLRFVVSVAKQYQNQGLT 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     +V++        
Sbjct: 76  LPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNK---- 131

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
              ++ ++      +   N +P     IAK+L+++ +EV           S++A +   +
Sbjct: 132 -IGSINKINKTFAFLEQANERPPSPEEIAKELDMTVNEVKESLKNAGRHVSMDAPLI--E 188

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NP 252
              S   D L     G+      +   ++    + R++  L PRE  +          +P
Sbjct: 189 GEDSNLYDVL---RSGESPNPDRELLSESLSTEIERALETLTPREADVVRLYFGLGHQHP 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 246 MTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|209884282|ref|YP_002288139.1| RNA polymerase sigma factor RpoD [Oligotropha carboxidovorans OM5]
 gi|209872478|gb|ACI92274.1| RNA polymerase sigma factor RpoD [Oligotropha carboxidovorans OM5]
          Length = 708

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 75/273 (27%), Positives = 130/273 (47%), Gaps = 17/273 (6%)

Query: 21  HEIRKIPMLEKQE-----EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           HE++++  L   E     + VL  +  E     A   +V ++LRLV+ IA  Y   GL  
Sbjct: 437 HEVQQLAALTGLEIGEFRKIVLGVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQF 496

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +
Sbjct: 497 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----M 551

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + ++    + + +   +      +A+KL +   +V  +        SL   +   D+
Sbjct: 552 IETINKIVRTSRQMLNEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPLSLETPV--GDE 609

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPV 253
             S   D++    D    + I+   + N R   TR ++ L PRE R+   R         
Sbjct: 610 EDSHLGDFI---EDKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDH 666

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 667 TLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 699


>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 =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 129/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 345 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 404

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 405 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 462

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 463 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 517

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 518 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 574

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 575 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 610


>gi|149278388|ref|ZP_01884525.1| RNA polymerase sigma-70 factor [Pedobacter sp. BAL39]
 gi|255532892|ref|YP_003093264.1| sigma-70 family RNA polymerase sigma factor [Pedobacter heparinus
           DSM 2366]
 gi|149230758|gb|EDM36140.1| RNA polymerase sigma-70 factor [Pedobacter sp. BAL39]
 gi|255345876|gb|ACU05202.1| RNA polymerase sigma factor, sigma-70 family [Pedobacter heparinus
           DSM 2366]
          Length = 286

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 78/288 (27%), Positives = 149/288 (51%), Gaps = 14/288 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+HEI K+ ++  +EE +LA++ RE GD +A  RL  ++LR VV
Sbjct: 5   KITQSITNRESQSLDKYLHEIGKVDLITAEEEVILARKIRE-GDQAALERLTKTNLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A K+FD  +GF+  +Y++WWI+ ++ + I     
Sbjct: 64  SVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETKGFKFISYAVWWIRQSILQAIAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    NQ      + +    L+   +    PE    +A  L  +  ++         
Sbjct: 124 IVRLP--LNQVGSLSKISKAFSKLEQEYEREPSPE---ELADILETTVDKISDTLSNSGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     ++N+    D L       +  LI     ++    + RS+S L  RER I
Sbjct: 179 HVSMDAPFVQGEENT--LLDVLENHEPNTDSSLI----NESLSEEIKRSLSTLTEREREI 232

Query: 243 FEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
                     +P++LE +  +F ++RERVRQI+ +A ++++ + + ++
Sbjct: 233 IVLFFGLSTNHPLSLEEIGEKFNLTRERVRQIKDKALQRLRHTSRSKI 280


>gi|221633247|ref|YP_002522472.1| RNA polymerase sigma factor rpoD [Thermomicrobium roseum DSM 5159]
 gi|221156052|gb|ACM05179.1| RNA polymerase sigma factor rpoD [Thermomicrobium roseum DSM 5159]
          Length = 340

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 87/279 (31%), Positives = 137/279 (49%), Gaps = 13/279 (4%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
               L  Y+ +I + P+L  +EE  LAKR +E GD  A  R V S+LRLVV IA  Y G 
Sbjct: 66  ASDPLRLYLRDIAEAPLLTPEEEVELAKRIKE-GDTEALQRFVRSNLRLVVSIAKRYVGR 124

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL + +++ EGNIGLM+AV+KFD  RG+R +TY+ WWI+ A+   I      +++     
Sbjct: 125 GLSLLDLIQEGNIGLMRAVEKFDWRRGYRFSTYATWWIRQAITRAIADQGRTIRLPVHMT 184

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
                ++  R    L         PE    IA+ ++V   ++  +        SL+  + 
Sbjct: 185 DSITRYH--RTTTQLAQELGRQPTPE---EIAEAMSVQPEKIAQIVRAAQRAVSLDQPL- 238

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--Q 249
            S+++ +   D +    D   Q   E  E    R  +   + +L PRER + + R     
Sbjct: 239 -SEEDETSLGDLIA---DELAQSPEELAEESLMRRDIAEILEMLTPRERLVLQLRYGLSD 294

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
             P TL  +     +SRERVRQIE  A +K++   ++++
Sbjct: 295 GEPRTLAEVGDLLGISRERVRQIENEALRKLRRIARERL 333


>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 =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 67/251 (26%), Positives = 119/251 (47%), Gaps = 12/251 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 401 EQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 460

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            L R+   L         PE    +
Sbjct: 461 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQLLQEMGREATPE---EL 515

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+++ + E ++  +        S+   I   D + S   D++    D   ++ ++    +
Sbjct: 516 AERMGMPEDKIRKVLKIAKEPISMETPI--GDDDDSHLGDFI---EDSTLELPLDSATAQ 570

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + +      +  L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 571 SLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 630

Query: 281 QESIQKQVELS 291
           +   + +   S
Sbjct: 631 RHPSRSETLRS 641


>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 =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 67/251 (26%), Positives = 119/251 (47%), Gaps = 12/251 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 385 EQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 444

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            L R+   L         PE    +
Sbjct: 445 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQLLQEMGREATPE---EL 499

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+++ + E ++  +        S+   I   D + S   D++    D   ++ ++    +
Sbjct: 500 AERMGMPEDKIRKVLKIAKEPISMETPI--GDDDDSHLGDFI---EDSTLELPLDSATAQ 554

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + +      +  L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 555 SLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 614

Query: 281 QESIQKQVELS 291
           +   + +   S
Sbjct: 615 RHPSRSETLRS 625


>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 =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 67/251 (26%), Positives = 119/251 (47%), Gaps = 12/251 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 385 EQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 444

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            L R+   L         PE    +
Sbjct: 445 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQLLQEMGREATPE---EL 499

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+++ + E ++  +        S+   I   D + S   D++    D   ++ ++    +
Sbjct: 500 AERMGMPEDKIRKVLKIAKEPISMETPI--GDDDDSHLGDFI---EDSTLELPLDSATAQ 554

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + +      +  L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 555 SLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 614

Query: 281 QESIQKQVELS 291
           +   + +   S
Sbjct: 615 RHPSRSETLRS 625


>gi|197302434|ref|ZP_03167489.1| hypothetical protein RUMLAC_01162 [Ruminococcus lactaris ATCC
           29176]
 gi|197298332|gb|EDY32877.1| hypothetical protein RUMLAC_01162 [Ruminococcus lactaris ATCC
           29176]
          Length = 283

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 84/273 (30%), Positives = 141/273 (51%), Gaps = 12/273 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y++EI +IP+L+ +EE  L +R    GD  A  RL   +LRLVV IA  Y G G+P+
Sbjct: 21  LKIYLNEIGQIPLLDAEEEKELGRR-SVDGDEEARRRLEEGNLRLVVSIAKHYTGRGIPL 79

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AV+K+D  +  R +TY+ WWIK A+Q  I +    +++     +   
Sbjct: 80  MDLIQEGNIGLMRAVEKYDFTKENRFSTYASWWIKEAIQRAIDQQSREIRVPVHVAE--A 137

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              ++R+   LQ        PE++    K  + S  +V ++   L    SL   +   + 
Sbjct: 138 MKKVQRISKELQQSLGREATPEEIAE--KLGDKSTEDVKNILSYLQNPVSLETPV--GED 193

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--V 253
             +   D +    D       E      ++  ++  ++ LN RE+++   R   E+    
Sbjct: 194 GENNLGDMV---EDKASPTPEEAMNLLVQKEEVSELLNALNDREKQVIRLRYGLEDGKTH 250

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TLE +  E +V+RERVRQIE+RA +K++   ++
Sbjct: 251 TLEEIGEELKVTRERVRQIESRAMEKLRNKAER 283


>gi|255994475|ref|ZP_05427610.1| RNA polymerase sigma factor RpoD [Eubacterium saphenum ATCC 49989]
 gi|255993188|gb|EEU03277.1| RNA polymerase sigma factor RpoD [Eubacterium saphenum ATCC 49989]
          Length = 447

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 80/311 (25%), Positives = 142/311 (45%), Gaps = 45/311 (14%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLA-----------------KRYRE------- 43
             +  +  +  Y+ EI ++P+L ++EE +LA                 +R +E       
Sbjct: 136 TSIGIDDPVKMYLKEIGQVPLLTREEEKILATQVKHALAKQNEIRERLERLKEGSATYKK 195

Query: 44  ---------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                         A H+L  ++LRLVV IA  ++  G+   +++ EGN+GLM+AV KFD
Sbjct: 196 EMKLLDEYKQDYNKAMHQLCEANLRLVVSIAKNHKDRGMHFLDLIQEGNLGLMKAVDKFD 255

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
            +R F+ +TY+ WWI+ A+   I      ++I     +      L R+   L        
Sbjct: 256 VDRNFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE--TIHKLTRISRTLLQELGREP 313

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           KPE    IAK+++++  +V  +        SL   I   ++  S   D++    D +   
Sbjct: 314 KPE---EIAKEMDITTEKVRDILRISQEPVSLEKPI--GEEEDSHLGDFIP---DTEVPS 365

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQI 272
            ++       R+ L   ++ L  RER + + R         TLE +  +F+V+RER+RQI
Sbjct: 366 PLDVAFSSMLRDELLEVLNTLGERERNVLKLRFGLVDGKQRTLEEVGKQFDVTRERIRQI 425

Query: 273 EARAFKKVQES 283
           E++A +K++  
Sbjct: 426 ESKAIRKLKHP 436


>gi|254784503|ref|YP_003071931.1| RNA polymerase factor sigma-32 [Teredinibacter turnerae T7901]
 gi|237687248|gb|ACR14512.1| alternative sigma factor RpoH [Teredinibacter turnerae T7901]
          Length = 284

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 101/285 (35%), Positives = 163/285 (57%), Gaps = 8/285 (2%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           + + ++  G+  L+ Y+  +    +L  +EE  LA+      DL AA RLV +HLR VV 
Sbjct: 6   QALDVLAPGQ-NLNAYMQAVNNFAVLSAEEEKQLAEDLYYRQDLDAARRLVMAHLRFVVH 64

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y GYGL   +++ EGN+GLM+AVK+F+PE+G RL ++++ WIKA + E+ILR+W +
Sbjct: 65  IAKSYAGYGLAQGDLIQEGNVGLMKAVKRFNPEKGVRLVSFAVHWIKAEIHEFILRNWRI 124

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VK+ TT  Q++LFFNLR  K  L  +T+     ++  A+A+ LNV    V  M  RL+  
Sbjct: 125 VKVATTKAQRKLFFNLRGQKKRLAWLTN-----DEANAVAQDLNVDVKNVREMESRLSAY 179

Query: 184 ESLNALINSSDKNSS-QWQDWLVYDHDGQEQVLIEKEER-KNRRNMLTRSMSVLNPRERR 241
           ++        D  ++ Q     + D       ++E  +  +N    L R+M  L+ R R 
Sbjct: 180 DAAFDAGADDDDETAYQAPANYLEDRRYDPSTMLENADWTENSVAGLERAMDQLDDRSRD 239

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           I + R L ++  TL  L+ ++ VS ER+RQ+E  A KK++ +++ 
Sbjct: 240 ILQQRWLSDSKATLHELADKYGVSAERIRQLEKNAMKKMRVAMEA 284


>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 =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 129/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 344 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 403

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 404 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 461

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 462 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 516

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 517 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 573

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 574 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 609


>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|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]
          Length = 613

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 129/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 344 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 403

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 404 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 461

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 462 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 516

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 517 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 573

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 574 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 609


>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 =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 70/269 (26%), Positives = 126/269 (46%), Gaps = 22/269 (8%)

Query: 32  QEEYVLA--------KRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           +EE  LA        +R    E     A   +V ++LRLV+ IA  Y   GL   +++ E
Sbjct: 362 EEETGLAISAIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 421

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           GNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R
Sbjct: 422 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNR 479

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           +   +         PE    +A+++ + E ++  +        S+   I   D   S   
Sbjct: 480 ISRQMLQEMGREPSPE---ELAERMMMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLG 534

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLS 259
           D++    D   ++ ++    ++ +N     ++ L  RE ++   R   +     TLE + 
Sbjct: 535 DFI---EDTTLELPLDSATSESLKNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVG 591

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +F+V+RER+RQIEA+A +K++   + ++
Sbjct: 592 KQFDVTRERIRQIEAKALRKLRHPSRSEI 620


>gi|289827081|ref|ZP_06545870.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-3139]
          Length = 615

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 129/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 346 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 405

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 406 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 463

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 464 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 518

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 519 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 575

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 576 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 611


>gi|194477302|ref|YP_002049481.1| RNA polymerase sigma factor [Paulinella chromatophora]
 gi|171192309|gb|ACB43271.1| RNA polymerase sigma factor [Paulinella chromatophora]
          Length = 460

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 77/313 (24%), Positives = 142/313 (45%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-----------HG--------------- 45
            E  +  Y+ EI +I +L   EE  LA++  +            G               
Sbjct: 148 TEDSIRVYLQEIGRIRLLRPDEEIELARKISDLLYLEELAGQFEGRKGYYPDNKEWAALV 207

Query: 46  -------------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 208 EMSLIKFRRRLMLGRRAKAKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 267

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 268 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKVLSQE 322

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA+ + ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 323 FGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADIENPE 380

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
           Q + +   R++    L   ++ L+PRER +   R   ++    TLE +   F+V+RER+R
Sbjct: 381 QDVAKNLLRED----LEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIR 436

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 437 QIEAKALRKLRHP 449


>gi|253700182|ref|YP_003021371.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           M21]
 gi|251775032|gb|ACT17613.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           M21]
          Length = 333

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 71/276 (25%), Positives = 141/276 (51%), Gaps = 13/276 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI+K  +L   EE  LA R  + GD +A  R++ S+LRLVVKIA  Y   G
Sbjct: 53  DDAIKLYLREIQKTKLLTADEEKELAARI-DLGDKAARDRMIVSNLRLVVKIAKRYINRG 111

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP  +++ EGN+GL++AV++F   +  R +TY+ WWI+ +++  ++     +++    + 
Sbjct: 112 LPFLDLIEEGNMGLIKAVERFKLSKECRFSTYATWWIRQSIERALVNQSRTIRLPVHVSD 171

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                ++ ++    + +     +   +  +A  L V+ + V  +   L    S+   +  
Sbjct: 172 -----DINKMLRVTRELVQKMNREPTIKEVADTLEVNITYVRRLMVLLKKTYSIERPM-- 224

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE-- 250
            + N     D +         VL+E     N+  ++++    L+  E++I   R   +  
Sbjct: 225 GENNDYFLIDTIEDTSTISPAVLLEDL---NKYELVSKWFETLSDAEKKILTLRFGLDDK 281

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +P TL+ +   F V+RER+RQIEA++ +K+++ ++ 
Sbjct: 282 DPQTLDTIGRSFGVTRERIRQIEAKSLEKLRKIVEA 317


>gi|313109026|ref|ZP_07794999.1| sigma factor RpoS [Pseudomonas aeruginosa 39016]
 gi|310881501|gb|EFQ40095.1| sigma factor RpoS [Pseudomonas aeruginosa 39016]
          Length = 344

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 83/278 (29%), Positives = 141/278 (50%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 76  YLNEIGFSPLLTPEEEVHFA-RLAQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 134

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 135 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 193

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++  + +K       ++ +N R+   D SL         + 
Sbjct: 194 LRAAR-ELTHKLDHEPSPEEIANLLEKPVAEVKRMLGLNERVTSVDVSL------GPDSD 246

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + ++ L  ++R +   R         TL
Sbjct: 247 KTLLDTLTDDRPTDPCELLQDDDLS---ESIDQWLTELTDKQREVVIRRFGLRGHESSTL 303

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E +  E  ++RERVRQI+  A K+++E ++K    S +
Sbjct: 304 EEVGQEIGLTRERVRQIQVEALKRLREILEKNGLSSDA 341


>gi|313674339|ref|YP_004052335.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Marivirga
           tractuosa DSM 4126]
 gi|312941037|gb|ADR20227.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Marivirga
           tractuosa DSM 4126]
          Length = 287

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 73/288 (25%), Positives = 145/288 (50%), Gaps = 13/288 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           + +  I       L +Y+ EI K+ +L   EE  LA R ++ GD  A  +L  ++LR VV
Sbjct: 5   KISKQITNRESQSLDKYLQEIGKVDLLTPDEEVDLAVRIKQ-GDQLALEKLTKANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 64  SVAKQYQNQGLSLGDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++           +L ++      +     +      +A+ L V+ +EV+        
Sbjct: 124 IVRLPLNR-----VGSLNKISKTFSTLEQKFEREPSPDELAEVLEVTSNEVVDTMKISGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     ++NS    D L  D    E+   ++    + R  + R++S L  RE  +
Sbjct: 179 HVSMDAPFVQGEENS--LLDVLENDG---EESPDDELMNDSLRREVQRALSTLTQREADV 233

Query: 243 FEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
                    E+ +TLE +  +F ++RERVRQI+ +A ++++ + + + 
Sbjct: 234 ITLYFGLNGEHSMTLEEIGEKFNLTRERVRQIKEKAIRRLRHTSRSKA 281


>gi|301155442|emb|CBW14908.1| RNA polymerase, sigma 70 (sigma D) factor [Haemophilus
           parainfluenzae T3T1]
          Length = 629

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 127/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVL--AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +  I +   L  Q+   +  A    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 360 LANIEQHTNLTIQQMREICDAVSRGEQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 419

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 420 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 477

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D + 
Sbjct: 478 KLNRISRQMLQEMGREATPE---ELAERMGMPEDKIRKVLKIAKEPISMETPI--GDDDD 532

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ +      +  L PRE ++   R   +     TL
Sbjct: 533 SHLGDFI---EDSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTL 589

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +   S
Sbjct: 590 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRS 625


>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 =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 64/247 (25%), Positives = 117/247 (47%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E    +A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 539 EAASRAAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 598

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    +              +
Sbjct: 599 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKMNRISRQHLQEFGFEPDASLL 653

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+ + E ++  +        S+   I   D + S   D++    D      +E   + 
Sbjct: 654 AQKMEIPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTANTAPVEAAMQA 708

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             R ++   +  L PRE ++   R   E  +  TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 709 GLREVVKEILDGLTPREAKVLRMRFGIEMTSDHTLEEVGKQFDVTRERIRQIEAKALRKL 768

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 769 KHPSRSD 775


>gi|319406278|emb|CBI79915.1| RNA polymerase sigma-32 factor [Bartonella sp. AR 15-3]
          Length = 303

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 105/266 (39%), Positives = 171/266 (64%), Gaps = 1/266 (0%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           +    + P LE+++E+ LA R+++  D  A H++  +H+RLV+ IA  ++ + +P+ ++V
Sbjct: 27  MRSAMRAPYLERKKEHDLALRWKDKRDDDAMHQIAAAHMRLVISIASRFKRFKMPLGDLV 86

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EG +GL++A  +FDPER  R +TY+ WWI+A++Q+YILR+WS+V+ GT+++QK LFFNL
Sbjct: 87  QEGYVGLLEAAARFDPEREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSSQKALFFNL 146

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSS 198
           RRL+  L    +   K E   AI++KL VS ++V  M+ R +G D SL+  I+ S +   
Sbjct: 147 RRLRAKLAQDDNTLTKQEIFSAISEKLGVSVNDVEKMDFRFSGTDNSLSLSISESGETPI 206

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
              D L+ DH   + V+ +  + + R   L  ++ +LN RE  I   RRL+E   TLE L
Sbjct: 207 AKMDSLIDDHPLPDAVIEQVIDGQRRAQWLYEALQILNERELEIIRFRRLKEEGATLEVL 266

Query: 259 SSEFEVSRERVRQIEARAFKKVQESI 284
             +  +S+ERVRQIEARA +K++ ++
Sbjct: 267 GEKLGISKERVRQIEARALQKLRCAL 292


>gi|195940831|ref|ZP_03086213.1| RNA polymerase factor sigma-32 [Escherichia coli O157:H7 str.
           EC4024]
 gi|1710645|sp|P50508|RP32_ENTCL RecName: Full=RNA polymerase sigma-32 factor
 gi|1143326|dbj|BAA09440.1| sigma-32 homolog [Enterobacter cloacae]
 gi|295097059|emb|CBK86149.1| RNA polymerase, sigma 32 subunit, RpoH [Enterobacter cloacae subsp.
           cloacae NCTC 9394]
          Length = 285

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 108/290 (37%), Positives = 163/290 (56%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +     L  YI      PML  +EE  LA++    GDL AA  L+ SHLR 
Sbjct: 1   MTKEMQTLALAPVGNLESYIRAANTWPMLTAEEEKELAEKLHYQGDLEAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVEMVARELGVSSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQ---EQVLIEKEERKNRRNMLTRSMSVLNP 237
           A  +    +    D + SQ    ++Y  D        + E        N LT +M  L+ 
Sbjct: 176 AAQDMTFDMSADDDASDSQPMAPVLYLQDKTSNFADGIEEDNWEDQAANKLTFAMEGLDE 235

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L E+   TL+ L+  + VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQDIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 285


>gi|32130003|sp|Q87DT7|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 =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 69/249 (27%), Positives = 118/249 (47%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RGF+
Sbjct: 371 YGEAKASKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVCKFEHRRGFK 430

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 431 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQQFGREATPE--- 485

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +AK++++ E ++  +        S+   I   D   S   D++    D   +  ++   
Sbjct: 486 ELAKEMDMPEDKIRKVMKIAKEPISMETPI--GDDEDSHLGDFI---EDPNVESPVDTTT 540

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
             N    +   ++ L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 541 NVNLSETVREVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 600

Query: 279 KVQESIQKQ 287
           K++   + +
Sbjct: 601 KLRHPSRSE 609


>gi|15595573|ref|NP_249067.1| RNA polymerase factor sigma-32 [Pseudomonas aeruginosa PAO1]
 gi|116054106|ref|YP_788549.1| RNA polymerase factor sigma-32 [Pseudomonas aeruginosa UCBPP-PA14]
 gi|152989115|ref|YP_001345866.1| RNA polymerase factor sigma-32 [Pseudomonas aeruginosa PA7]
 gi|218889117|ref|YP_002437981.1| RNA polymerase factor sigma-32 [Pseudomonas aeruginosa LESB58]
 gi|254243475|ref|ZP_04936797.1| sigma factor RpoH [Pseudomonas aeruginosa 2192]
 gi|296386874|ref|ZP_06876373.1| RNA polymerase factor sigma-32 [Pseudomonas aeruginosa PAb1]
 gi|313112005|ref|ZP_07797792.1| RNA polymerase sigma-32 factor [Pseudomonas aeruginosa 39016]
 gi|2507390|sp|P42378|RP32_PSEAE RecName: Full=RNA polymerase sigma-32 factor
 gi|9946228|gb|AAG03765.1|AE004475_7 sigma factor RpoH [Pseudomonas aeruginosa PAO1]
 gi|765096|dbj|BAA08769.1| heat-shock sigma factor [Pseudomonas aeruginosa]
 gi|998760|gb|AAB33935.1| heat-shock sigma factor sigma 32 [Pseudomonas aeruginosa]
 gi|115589327|gb|ABJ15342.1| RNA polymerase sigma-32 factor [Pseudomonas aeruginosa UCBPP-PA14]
 gi|126196853|gb|EAZ60916.1| sigma factor RpoH [Pseudomonas aeruginosa 2192]
 gi|150964273|gb|ABR86298.1| alternative sigma factor RpoH [Pseudomonas aeruginosa PA7]
 gi|218769340|emb|CAW25100.1| sigma factor RpoH [Pseudomonas aeruginosa LESB58]
 gi|310884294|gb|EFQ42888.1| RNA polymerase sigma-32 factor [Pseudomonas aeruginosa 39016]
          Length = 284

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 102/272 (37%), Positives = 155/272 (56%), Gaps = 7/272 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+H +  IP+L  ++E  LA+R     DL AA ++V +HLR VV IA  Y GYGL 
Sbjct: 16  NLEAYVHSVNSIPLLSPEQERELAERLFYQQDLEAARQMVLAHLRFVVHIAKSYSGYGLA 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++
Sbjct: 76  QADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           LFFNLR  K  L  + +     E+V  +A+ L V   EV  M  RL G +        +D
Sbjct: 136 LFFNLRSQKKRLAWLNN-----EEVHRVAESLGVEPREVREMESRLTGQDMAFDPAADAD 190

Query: 195 KNSS-QWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENP 252
             S+ Q     + DH       +E  +  +  +  L  ++  L+ R R I + R L E  
Sbjct: 191 DESAYQSPAHYLEDHRYDPARQLEDADWSDSSSANLHEALEGLDERSRDILQQRWLSEEK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL +L+ ++ VS ER+RQ+E  A  K++  I
Sbjct: 251 ATLHDLAEKYNVSAERIRQLEKNAMSKLKGRI 282


>gi|315127432|ref|YP_004069435.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Pseudoalteromonas sp. SM9913]
 gi|315015946|gb|ADT69284.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Pseudoalteromonas sp. SM9913]
          Length = 323

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 80/271 (29%), Positives = 140/271 (51%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A++    G  ++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 52  YLGEIGFSPLLSAEEEVFFARK-SLKGCEASRKRMIESNLRLVVKIARRYNNRGLALLDL 110

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 111 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 169

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +T           IA+ L+    +V  M        S++  I S  +N S
Sbjct: 170 LRTAR----ELTQKLDHEPTAEEIAESLDRPVEDVTKMLRLNEKIASVDMPIGS--ENDS 223

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D +  + +   +  ++     +    +   +  LNP++R +   R   L   P TLE
Sbjct: 224 ALLDVIADEKNVGPEGEVQN---NDMNTHIIDWLGELNPKQREVLARRFGLLGYEPSTLE 280

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+  A +++++ +Q++
Sbjct: 281 DVGREIGLTRERVRQIQVEALRRLKDILQQE 311


>gi|260548994|ref|ZP_05823216.1| RNA polymerase sigma factor sigma-70 [Acinetobacter sp. RUH2624]
 gi|260408162|gb|EEX01633.1| RNA polymerase sigma factor sigma-70 [Acinetobacter sp. RUH2624]
          Length = 628

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 74/278 (26%), Positives = 126/278 (45%), Gaps = 14/278 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           +   + I +I K   L   E   ++KR    E     A   +V ++LRLV+ IA  Y   
Sbjct: 352 LAFQQKIADIEKELNLSVAEIKDISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNR 411

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I     
Sbjct: 412 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM- 470

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
                  + R+   L         PE    + ++L + E +V  +        S+   I 
Sbjct: 471 -IETINKINRVSRQLLQEMGREPTPE---ELGERLEMDEVKVRKVLKIAKEPISMETPI- 525

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             D   S   D++    D      I+    +  +      +  L  RE ++ + R   + 
Sbjct: 526 -GDDEDSHLGDFI---EDQNITSPIDAATSEGLKEATREVLENLTEREAKVLKMRFGIDM 581

Query: 252 P--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           P   TLE +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 582 PTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 619


>gi|112702894|emb|CAL34114.1| RNA polymerase sigma factor rpoD [Cronobacter sakazakii]
          Length = 359

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 129/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 90  LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 149

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 150 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 207

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 208 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 262

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 263 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 319

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 320 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 355


>gi|91204871|ref|YP_537226.1| RNA polymerase sigma factor RpoD [Rickettsia bellii RML369-C]
 gi|122426123|sp|Q1RKH7|RPOD_RICBR RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|91068415|gb|ABE04137.1| RNA polymerase sigma factor [Rickettsia bellii RML369-C]
          Length = 641

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 72/252 (28%), Positives = 123/252 (48%), Gaps = 11/252 (4%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A +  E   L A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 377 AIQKSERQTLQAKKDMIEANLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRR 436

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I        +   + ++    + + +      
Sbjct: 437 GYKFSTYATWWIRQAITRAIADQARTIRIPVH-----MIETINKIIRTSRQMLNELGYEP 491

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               IA +L++   +V  +        SL   +   D NS    D++    D      I+
Sbjct: 492 TPAEIAARLSMPIDKVRKVMKIAKEPISLENPVGDGDDNS-YLGDFI---EDKNAVAPID 547

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              + N R + TR ++ L PRE R+   R         TLE +  +F+V+RER+RQIE++
Sbjct: 548 AAIQSNLREVTTRVLATLTPREERVLRMRFGIGMNTDHTLEEVGQQFKVTRERIRQIESK 607

Query: 276 AFKKVQESIQKQ 287
           A +K+Q  I+ +
Sbjct: 608 ALRKLQHPIRSK 619


>gi|83643468|ref|YP_431903.1| RNA polymerase factor sigma-32 [Hahella chejuensis KCTC 2396]
 gi|83631511|gb|ABC27478.1| RNA polymerase sigma-32 factor RpoH [Hahella chejuensis KCTC 2396]
          Length = 284

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 110/280 (39%), Positives = 169/280 (60%), Gaps = 7/280 (2%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           ++     L  Y+H +  IP+L  +EE  LA+R+ ++ DL AA +LV +HLR VV IA  Y
Sbjct: 10  MLAPVGNLEGYVHAVNSIPVLSAEEERELAERFHQNEDLYAARQLVMAHLRFVVHIAKSY 69

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGL  +++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ T
Sbjct: 70  SGYGLSQADLVQEGNIGLMKAVKRFNPEFGVRLVSFAVHWIKAEIHEFILRNWRIVKVAT 129

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN 187
           T  Q++LFFNLR  K  L  +T++  K     A+A+ L V    V  M  RLAG D S +
Sbjct: 130 TKAQRKLFFNLRSAKKRLAWLTNDEAK-----AVAEDLGVDTHVVREMESRLAGQDTSFD 184

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE-ERKNRRNMLTRSMSVLNPRERRIFEAR 246
           A  +  D+ + +     + D      +++E E   ++  + L  +++ L+ R + I + R
Sbjct: 185 AGADEDDETAFKAPANYLEDRRYDPAMMLENENWEEDSNSRLHDALTQLDERSKDIIQKR 244

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L EN  TL  L+ E+ VS ER+RQ+E  A KKV+  ++ 
Sbjct: 245 WLAENKATLHELADEYGVSAERIRQLEKNAMKKVKLMLEA 284


>gi|71899844|ref|ZP_00681993.1| 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|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 =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 69/249 (27%), Positives = 118/249 (47%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RGF+
Sbjct: 376 YGEAKASKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVCKFEHRRGFK 435

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 436 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQQFGREATPE--- 490

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +AK++++ E ++  +        S+   I   D   S   D++    D   +  ++   
Sbjct: 491 ELAKEMDMPEDKIRKVMKIAKEPISMETPI--GDDEDSHLGDFI---EDPNVESPVDTTT 545

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
             N    +   ++ L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 546 NVNLSETVREVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 605

Query: 279 KVQESIQKQ 287
           K++   + +
Sbjct: 606 KLRHPSRSE 614


>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 =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 69/273 (25%), Positives = 128/273 (46%), Gaps = 14/273 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 341 LRQIEEETGLSIEQVKDINRRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 400

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 401 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 458

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D + 
Sbjct: 459 KLNRVSRQMLQEMGREPAPE---ELAERMLMPEEKIRKVLKIAKEPISMETPI--GDDDD 513

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 514 SHLGDFI---EDTTLELPLDSATSESLRLATNDVLAGLTAREAKVLRMRFGIDMNTDHTL 570

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           E +  +F+V+RER+RQIEA+A +K++   +  V
Sbjct: 571 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSDV 603


>gi|167754493|ref|ZP_02426620.1| hypothetical protein ALIPUT_02789 [Alistipes putredinis DSM 17216]
 gi|167659118|gb|EDS03248.1| hypothetical protein ALIPUT_02789 [Alistipes putredinis DSM 17216]
          Length = 286

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 75/287 (26%), Positives = 143/287 (49%), Gaps = 12/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI K  ++  +EE  LA+R ++ GD  A  +L  ++LR VV
Sbjct: 5   KITKSITNRESASLDKYLQEIGKEELITVEEEVELAQRIKK-GDQEALEKLTKANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 64  SVAKQYQNQGLSLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    NQ      + +     +   +    PE    +A +L + + +V         
Sbjct: 124 IVRLP--LNQVGSLNKINKAFARFEQEHERTPSPE---ELANELELPKEKVTDTLRVAGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     + NS    D LV          +  E        + R++  L  RER I
Sbjct: 179 HVSVDAPFADGEDNS--LLDVLVNPDSPNADRGLINESLSTE---VDRALETLTERERDI 233

Query: 243 FEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +       + +TLE +  +F+++RERVRQI+ +A ++++ S + ++
Sbjct: 234 IKYFFGIGCSEMTLEEIGEKFDLTRERVRQIKEKAIRRLRHSSRSKL 280


>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|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]
          Length = 616

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 69/263 (26%), Positives = 120/263 (45%), Gaps = 14/263 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L   E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 356 LTVAEIKEINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 415

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 416 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 473

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    + +++ + E ++  +        S+   I   D   S   D++  
Sbjct: 474 LQEMGREPTPE---ELGERMEMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 526

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q  I+    ++ +      +S L  RE ++   R   +     TLE +  +F+V
Sbjct: 527 -EDSTMQSPIDVATVESLKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 585

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   + +
Sbjct: 586 TRERIRQIEAKALRKLRHPTRSE 608


>gi|260767412|ref|ZP_05876349.1| RNA polymerase sigma factor RpoD [Vibrio furnissii CIP 102972]
 gi|260617524|gb|EEX42706.1| RNA polymerase sigma factor RpoD [Vibrio furnissii CIP 102972]
 gi|315181195|gb|ADT88109.1| RNA polymerase sigma factor RpoD [Vibrio furnissii NCTC 11218]
          Length = 628

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 69/276 (25%), Positives = 127/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +  I +   L  +    +++R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 359 LQIIEQETSLTVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 418

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 419 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 476

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 477 KLNRISRQMLQEMGREPLPE---ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDED 531

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++     + +      ++ L PRE ++   R   +     TL
Sbjct: 532 SHLGDFI---EDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTL 588

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +   S
Sbjct: 589 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRS 624


>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 =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 66/250 (26%), Positives = 119/250 (47%), Gaps = 12/250 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 363 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 422

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 423 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPTPE--- 477

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + E ++  +        S+   I   D   S   D++    D   ++ ++   
Sbjct: 478 ELAERMMMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDTTLELPLDSAT 532

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            ++ RN     ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 533 GESLRNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 592

Query: 279 KVQESIQKQV 288
           K++   + ++
Sbjct: 593 KLRHPSRSEI 602


>gi|325283594|ref|YP_004256135.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Deinococcus
           proteolyticus MRP]
 gi|324315403|gb|ADY26518.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Deinococcus
           proteolyticus MRP]
          Length = 487

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 80/308 (25%), Positives = 137/308 (44%), Gaps = 38/308 (12%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR----------EHGDL----- 47
             +M   V+ +  + +Y+HEI ++P+L  +EE  LA+R            E G+      
Sbjct: 175 YDDMPRAVSND-PVRQYLHEIGRVPLLTLEEEIALARRIEDGEFARVELEEKGEELDDRG 233

Query: 48  ------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
                       +A   L+ ++LRLVV IA  Y G GL   +++ EGN GL++AV+KF+ 
Sbjct: 234 RRALQRRMEDGAAARQGLIEANLRLVVSIAKKYTGRGLNFLDLIQEGNQGLIRAVEKFEY 293

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            R ++ +TY+ WWI+ A+   I      ++I     +      L R    LQ        
Sbjct: 294 RRRYKFSTYATWWIRQAINRAIADQARTIRIPVHMVE--TINKLTRTARQLQQELSREAL 351

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
           PE++   A       ++V  +        SL   I   D+  S + D++  D        
Sbjct: 352 PEEIAE-AMGPGWDANKVEEVQKVSQEPVSLETPI--GDEKDSFYGDFIPDD---NLDSP 405

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIE 273
           ++   +      L +++  L  RE  + + R+        TLE +   F V+RER+RQIE
Sbjct: 406 VDNAAKTLLSEELEKALGKLTEREAMVLKFRKGLVDGREHTLEEVGQRFNVTRERIRQIE 465

Query: 274 ARAFKKVQ 281
            +A +K++
Sbjct: 466 NKALRKLK 473


>gi|152985831|ref|YP_001346901.1| RNA polymerase sigma factor RpoS [Pseudomonas aeruginosa PA7]
 gi|150960989|gb|ABR83014.1| RNA polymerase sigma factor RpoS [Pseudomonas aeruginosa PA7]
          Length = 344

 Score =  231 bits (589), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 84/278 (30%), Positives = 141/278 (50%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 76  YLNEIGFSPLLTPEEEVHFA-RLAQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 134

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 135 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 193

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++  + +K       ++ +N R+   D SL         + 
Sbjct: 194 LRAAR-ELTHKLDHEPSPEEIANLLEKPVAEVKRMLGLNERVTSVDVSL------GPDSD 246

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + +S L  ++R +   R         TL
Sbjct: 247 KTLLDTLTDDRPTDPCELLQDDDLS---ESIDQWLSELTDKQREVVIRRFGLRGHESSTL 303

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E +  E  ++RERVRQI+  A K+++E ++K    S +
Sbjct: 304 EEVGQEIGLTRERVRQIQVEALKRLREILEKNGLSSDA 341


>gi|114570679|ref|YP_757359.1| RNA polymerase sigma factor RpoD [Maricaulis maris MCS10]
 gi|114341141|gb|ABI66421.1| RNA polymerase, sigma 70 subunit, RpoD [Maricaulis maris MCS10]
          Length = 710

 Score =  230 bits (588), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 71/252 (28%), Positives = 120/252 (47%), Gaps = 15/252 (5%)

Query: 40  RYREHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           R  + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  
Sbjct: 460 RTVQKGEREARVAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 519

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RG++ +TY+ WWI+ A+   I      ++I        +   + ++    + +     + 
Sbjct: 520 RGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGRE 574

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
                +A+KL +   +V  +        SL   I   D+  S   D++    D    + I
Sbjct: 575 PTPEELAEKLAMPLEKVRKVMKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAVLPI 629

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEA 274
           +   + N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA
Sbjct: 630 DAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEA 689

Query: 275 RAFKKVQESIQK 286
           +A +K++   + 
Sbjct: 690 KALRKLKHPSRS 701


>gi|318080032|ref|ZP_07987364.1| RNA polymerase sigma factor [Streptomyces sp. SA3_actF]
          Length = 340

 Score =  230 bits (588), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 81/295 (27%), Positives = 133/295 (45%), Gaps = 40/295 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHG---------------------------DLS 48
             +Y+ EI +IP+L   +E  LA+R  E G                             +
Sbjct: 44  FRQYLREIGRIPLLTAADEVDLARRV-EAGLFAEAKLAGPGPLDTRLALDLDRLVVLGRA 102

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  RL+ S+LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RGF+ +TY+ WW
Sbjct: 103 AKRRLIESNLRLVVSVAKRYAGRGLTMLDLVQEGNLGLIRAVEKFDYTRGFKFSTYATWW 162

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ AM   +      +++     +      + R+    + +            +A  L +
Sbjct: 163 IRQAMSRALADQARTIRVPVHVVEL-----INRVVRVQRGLLQERGHEPSHAEVAALLGL 217

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           ++  V  +        SL+  +   D+      D +    DG      E       R  L
Sbjct: 218 TKERVGEVLRLAQEPVSLHTPVGGEDE--VALGDLI---EDGDAPSPPESAALLLLRRHL 272

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +S L  RER++ + R   ++  P TLE + + F V+RER+RQIEA+   K++
Sbjct: 273 EDVLSTLGERERQVVQLRYGLDDGRPRTLEEIGTLFGVTRERIRQIEAKTLAKLR 327


>gi|260767191|ref|ZP_05876133.1| RNA polymerase sigma factor RpoS [Vibrio furnissii CIP 102972]
 gi|260617799|gb|EEX42976.1| RNA polymerase sigma factor RpoS [Vibrio furnissii CIP 102972]
 gi|315181178|gb|ADT88092.1| RNA polymerase sigma factor RpoS [Vibrio furnissii NCTC 11218]
          Length = 329

 Score =  230 bits (588), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 81/287 (28%), Positives = 140/287 (48%), Gaps = 13/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           R+              Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVV
Sbjct: 41  REEFDASTKSLDATQMYLSEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLVV 99

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           KI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++    
Sbjct: 100 KISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTR 159

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            +++      K L   LR  +     ++           IA +L+    +V  M      
Sbjct: 160 TIRLPIHVV-KELNIYLRTAR----ELSQKLDHEPTAEEIAVELDKPVDDVSKMLRLNER 214

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++  I           D +   ++   +V  + +   + R+ L   +  LNP+++ +
Sbjct: 215 ISSVDTPI--GGDGDKALLDIIPDINNSDPEVSTQDD---DIRDSLVAWLDELNPKQKEV 269

Query: 243 FEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 270 LARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILMKQ 316


>gi|153802558|ref|ZP_01957144.1| RNA polymerase sigma factor RpoS [Vibrio cholerae MZO-3]
 gi|124121921|gb|EAY40664.1| RNA polymerase sigma factor RpoS [Vibrio cholerae MZO-3]
          Length = 335

 Score =  230 bits (588), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 82/287 (28%), Positives = 138/287 (48%), Gaps = 13/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           R+              Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVV
Sbjct: 46  REEFDASAKSLDATQMYLSEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLVV 104

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           KI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++    
Sbjct: 105 KISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTR 164

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            +++      K L   LR  +     ++           IA +L+    +V  M      
Sbjct: 165 TIRLPIHVV-KELNIYLRTAR----ELSQRLDHEPTPEEIALELDRPVDDVTKMLRLNER 219

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++  I           D L   H+   +   + +   + R  L   +  LNP+++ +
Sbjct: 220 ISSVDTPI--GGDGDKALLDILPDSHNADPEFSTQDD---DIRESLLNWLDELNPKQKEV 274

Query: 243 FEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 275 LARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVKQ 321


>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 =  230 bits (588), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 69/263 (26%), Positives = 120/263 (45%), Gaps = 14/263 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L   E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 356 LTVAEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 415

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 416 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 473

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    + +++ + E ++  +        S+   I   D   S   D++  
Sbjct: 474 LQEMGREPTPE---ELGERMEMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 526

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q  I+    ++ +      +S L  RE ++   R   +     TLE +  +F+V
Sbjct: 527 -EDSTMQSPIDVATVESLKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 585

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   + +
Sbjct: 586 TRERIRQIEAKALRKLRHPTRSE 608


>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 =  230 bits (588), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 343 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 402

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 403 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 460

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 461 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 515

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 516 SHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 572

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 573 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 608


>gi|187764347|gb|ACD36026.1| RNA polymerase sigma factor [Pseudomonas fluorescens]
          Length = 322

 Score =  230 bits (588), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 82/271 (30%), Positives = 139/271 (51%), Gaps = 15/271 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 60  YLNEIGFSPLLTPEEEVHFA-RLAQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 118

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 119 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 177

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++  + +K       ++ +N R+   D SL         + 
Sbjct: 178 LRAAR-ELTHKLDHEPSPEEIANLLEKPVAEVKRMLGLNERVTSVDVSL------GPDSD 230

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + ++ L  ++R +   R         TL
Sbjct: 231 KTLLDTLTDDRPTDPCELLQDDDLS---ESIDQWLTELTDKQREVVIRRFGLRGHESSTL 287

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E +  E  ++RERVRQI+  A K+++E ++K
Sbjct: 288 EEVGQEIGLTRERVRQIQVEALKRLREILEK 318


>gi|318058872|ref|ZP_07977595.1| RNA polymerase principal sigma factor [Streptomyces sp. SA3_actG]
 gi|333027299|ref|ZP_08455363.1| putative RNA polymerase sigma (70) factor RpoD [Streptomyces sp.
           Tu6071]
 gi|332747151|gb|EGJ77592.1| putative RNA polymerase sigma (70) factor RpoD [Streptomyces sp.
           Tu6071]
          Length = 338

 Score =  230 bits (588), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 81/295 (27%), Positives = 133/295 (45%), Gaps = 40/295 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHG---------------------------DLS 48
             +Y+ EI +IP+L   +E  LA+R  E G                             +
Sbjct: 42  FRQYLREIGRIPLLTAADEVDLARRV-EAGLFAEAKLAGPGPLDTRLALDLDRLVVLGRA 100

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  RL+ S+LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RGF+ +TY+ WW
Sbjct: 101 AKRRLIESNLRLVVSVAKRYAGRGLTMLDLVQEGNLGLIRAVEKFDYTRGFKFSTYATWW 160

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ AM   +      +++     +      + R+    + +            +A  L +
Sbjct: 161 IRQAMSRALADQARTIRVPVHVVEL-----INRVVRVQRGLLQERGHEPSHAEVAALLGL 215

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           ++  V  +        SL+  +   D+      D +    DG      E       R  L
Sbjct: 216 TKERVGEVLRLAQEPVSLHTPVGGEDE--VALGDLI---EDGDAPSPPESAALLLLRRHL 270

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +S L  RER++ + R   ++  P TLE + + F V+RER+RQIEA+   K++
Sbjct: 271 EDVLSTLGERERQVVQLRYGLDDGRPRTLEEIGTLFGVTRERIRQIEAKTLAKLR 325


>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 =  230 bits (588), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 70/269 (26%), Positives = 126/269 (46%), Gaps = 22/269 (8%)

Query: 32  QEEYVLA--------KRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           +EE  LA        +R    E     A   +V ++LRLV+ IA  Y   GL   +++ E
Sbjct: 346 EEETGLAISAIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 405

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           GNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R
Sbjct: 406 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNR 463

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           +   +         PE    +A+++ + E ++  +        S+   I   D   S   
Sbjct: 464 ISRQMLQEMGREPSPE---ELAERMMMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLG 518

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLS 259
           D++    D   ++ ++    ++ +N     ++ L  RE ++   R   +     TLE + 
Sbjct: 519 DFI---EDTTLELPLDSATSESLKNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVG 575

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +F+V+RER+RQIEA+A +K++   + ++
Sbjct: 576 KQFDVTRERIRQIEAKALRKLRHPSRSEI 604


>gi|254283645|ref|ZP_04958613.1| alternative sigma factor RpoH [gamma proteobacterium NOR51-B]
 gi|219679848|gb|EED36197.1| alternative sigma factor RpoH [gamma proteobacterium NOR51-B]
          Length = 291

 Score =  230 bits (588), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 104/280 (37%), Positives = 161/280 (57%), Gaps = 7/280 (2%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           ++ +     L  YI  +  IPML  + E  LA++      +++A  LV +HLR VV IA 
Sbjct: 15  ALSMAPGANLPAYIQAVGTIPMLSAEREQALAEKLYYGECVASARELVLAHLRFVVHIAR 74

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y GYGL  ++++ EGN+GLM+AVK+FDP +G RL ++++ WIKA M E+ILR+W +VK+
Sbjct: 75  SYSGYGLAEADLIQEGNVGLMKAVKRFDPNKGVRLVSFAVHWIKAEMHEFILRNWRIVKV 134

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDES 185
            TT  Q++LFFNLR  K +L  +T +     +  AIA+ L V E+EV  M  RL+  D +
Sbjct: 135 ATTKAQRKLFFNLRSAKKNLSWLTHS-----ETQAIAEDLGVPEAEVQRMEGRLSCRDMA 189

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE-ERKNRRNMLTRSMSVLNPRERRIFE 244
            +A  ++ D ++ Q     + D      V +E      +    L  +++ L+ R + I  
Sbjct: 190 FDAPSDADDDDAWQAPQHYLQDLSSDPAVAVEAANSSADDETRLHAALAQLDARSQDILA 249

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            R L E   TL  L++E  VS ER+RQ+EA A KK++  +
Sbjct: 250 RRWLAEKKATLHELAAEHGVSAERIRQLEANAMKKLRTGL 289


>gi|269137812|ref|YP_003294512.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Edwardsiella tarda EIB202]
 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 =  230 bits (588), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 71/276 (25%), Positives = 131/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +H+I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 342 LHQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 401

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 402 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 459

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 460 KLNRISRQMLQEMGREPTPE---ELAERMMMPEDKIRKVLKIAKEPISMETPI--GDDED 514

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 515 SHLGDFI---EDTTLELPLDSATSESLRSATRDVLAGLTAREAKVLRMRFGIDMNTDHTL 571

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 572 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 607


>gi|262364690|gb|ACY61247.1| RNA polymerase sigma factor RpoD [Yersinia pestis D182038]
          Length = 352

 Score =  230 bits (588), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 83  LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 142

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 143 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 200

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 201 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 255

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 256 SHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 312

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 313 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 348


>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 =  230 bits (588), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 73/272 (26%), Positives = 124/272 (45%), Gaps = 14/272 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +  I K   L   E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 345 LRNISKDTGLTIVELKEINRRISIGETRARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 404

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 405 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 462

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A ++++ E ++  +        S+   I   D   
Sbjct: 463 KLNRISRQMLQEMGREATPE---ELAVRMDMPEDKIRKVLKIAKEPISMETPI--GDDED 517

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++  D     +  I+    +  R   T  +S L  RE ++   R   +     TL
Sbjct: 518 SHLGDFIEDDG---AESPIDTATIEGLREATTSVLSGLTAREAKVLRMRFGIDMNTDHTL 574

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 575 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 606


>gi|329896515|ref|ZP_08271573.1| RNA polymerase sigma factor RpoH [gamma proteobacterium IMCC3088]
 gi|328921732|gb|EGG29105.1| RNA polymerase sigma factor RpoH [gamma proteobacterium IMCC3088]
          Length = 286

 Score =  230 bits (588), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 101/271 (37%), Positives = 160/271 (59%), Gaps = 6/271 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L+ YI  +  IP+L  + E  LA+    + +L AA +LV SHLR VV IA  Y GYGL 
Sbjct: 16  NLAAYIQTVSSIPVLSVERERELAEDLYYNDNLEAARQLVMSHLRFVVHIARSYSGYGLA 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGN+GLM+AVK+F+PE+G RL ++++ WIKA M E+ILR+W +VK+ TT  Q++
Sbjct: 76  EADLIQEGNVGLMKAVKRFNPEKGVRLVSFAVHWIKAEMHEFILRNWRIVKVATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSS 193
           LFFNLR  K  L  ++      E+  A+A  L V   EV +M  R+ + D + +A  +S 
Sbjct: 136 LFFNLRSSKKALAWLS-----AEEAQAVADDLGVDVREVATMEARMSSRDVAFDAPSDSD 190

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D +    Q +L        Q +     +++  + L  ++  L+ R R I   R L +   
Sbjct: 191 DDDVYAPQYYLEDHRADPAQQVESTNWQEDSESRLHYALEQLDERSRDILAQRWLNDEKA 250

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           TL +L++++ VS ER+RQ+E  A +KV++ +
Sbjct: 251 TLHDLAAQYGVSAERIRQLEQNAMQKVRKLM 281


>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|71902125|ref|ZP_00684157.1| 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|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 =  230 bits (588), Expect = 1e-58,   Method: Composition-based stats.
 Identities = 69/249 (27%), Positives = 118/249 (47%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RGF+
Sbjct: 376 YGEAKASKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVCKFEHRRGFK 435

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 436 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQQFGREATPE--- 490

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +AK++++ E ++  +        S+   I   D   S   D++    D   +  ++   
Sbjct: 491 ELAKEMDMPEDKIRKVMKIAKEPISMETPI--GDDEDSHLGDFI---EDPNVESPVDTTT 545

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
             N    +   ++ L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 546 NVNLSETVREVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 605

Query: 279 KVQESIQKQ 287
           K++   + +
Sbjct: 606 KLRHPSRSE 614


>gi|269836760|ref|YP_003318988.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphaerobacter
           thermophilus DSM 20745]
 gi|269786023|gb|ACZ38166.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphaerobacter
           thermophilus DSM 20745]
          Length = 538

 Score =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 76/264 (28%), Positives = 129/264 (48%), Gaps = 16/264 (6%)

Query: 29  LEKQEEYVLAKRYRE---HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           L +++E  L  R+ E    GD+ A  +L  ++LRLVV +A  Y G G+ + ++V EGN+G
Sbjct: 279 LLRRDEAALQARWEEFVVRGDI-ARKKLTEANLRLVVSVAKKYGGRGMSMLDLVQEGNLG 337

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++AV+KF   +GF+ +TY+ WWI+ A+   I      ++I     ++     L R    
Sbjct: 338 LIRAVEKFQHHKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVEQ--INRLIRTSRR 395

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           LQ         E    IA ++ +   +V  +        SL   I   ++  S   D++ 
Sbjct: 396 LQQELGREPTSE---EIAAEMGLPPDKVREILKISQEPVSLEMPI--GEEEDSNLGDFI- 449

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFE 263
              D +     +    K  +  +   +  L  RERR+ E R   ++    TLE +  EF 
Sbjct: 450 --EDSKALAPSDAASLKLLKEQVDDVLGSLGDRERRVLELRFGLDDGRTRTLEEVGREFG 507

Query: 264 VSRERVRQIEARAFKKVQESIQKQ 287
           V+RER+RQIEA+A +K++   + +
Sbjct: 508 VTRERIRQIEAKALRKLRHPSRSK 531



 Score = 37.1 bits (85), Expect = 3.0,   Method: Composition-based stats.
 Identities = 11/37 (29%), Positives = 21/37 (56%), Gaps = 1/37 (2%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD 46
           V+ +  +  Y+ EI ++ +L  ++E  LA+   E GD
Sbjct: 122 VSLDDPVRIYLREIGRVQLLTGEQEVALAQAM-ERGD 157


>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 =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 72/282 (25%), Positives = 129/282 (45%), Gaps = 20/282 (7%)

Query: 20  IHEIRKIPMLEKQ------EEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           +  I K+  +E++      +   + +R    E     A   +V ++LRLV+ IA  Y   
Sbjct: 343 LRAIGKLQQIEEETGLSIAQIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNR 402

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I     
Sbjct: 403 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM- 461

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
                  L R+   +         PE    +A ++ + E ++  +        S+   I 
Sbjct: 462 -IETINKLNRISRQMLQEMGREPNPE---ELAMRMGMPEDKIRKVLKIAKEPISMETPI- 516

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE- 250
             D   S   D++    D    +  +    ++ RN     ++ L  RE ++   R   + 
Sbjct: 517 -GDDEDSHLGDFI---EDTTLALPADAATSESLRNATREVLAGLTAREAKVLRMRFGIDM 572

Query: 251 -NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
               TLE +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 573 NTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 614


>gi|222056415|ref|YP_002538777.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           FRC-32]
 gi|221565704|gb|ACM21676.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           FRC-32]
          Length = 358

 Score =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 140/276 (50%), Gaps = 13/276 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI+K  +L   EE  LA R  + GD +A  +++ S+LRLVVKIA  Y   G
Sbjct: 82  DDAIKLYLREIQKTKLLTADEEKELAARI-DRGDKAARDKMIESNLRLVVKIAKRYINRG 140

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP  +++ EGN+GL++AV++F   +  R +TY+ WWI+ +++  ++     +++    + 
Sbjct: 141 LPFLDLIEEGNMGLIKAVERFKLSKECRFSTYATWWIRQSIERALVNQSRTIRLPVHVSD 200

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                ++ ++    + +     +   +  +A  + V+ + +  +   L    S+   +  
Sbjct: 201 -----DINKMLRITRELLQKINREPSIKEVATAMEVNSAYIRRLMVLLKKTYSIERPM-- 253

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE-- 250
            + N     D +    D       E  E  NR  M+++    L+  E++I   R   +  
Sbjct: 254 GENNDYFLIDTI---EDTSTVSPAELLEDVNRYEMVSKWFDTLSDNEKKILTLRFGLDDK 310

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +P TL+ +   F V+RER+RQIEA++ +K+++ ++ 
Sbjct: 311 DPQTLDTIGRSFGVTRERIRQIEAKSLEKLRKIMEA 346


>gi|88607510|ref|YP_505167.1| RNA polymerase sigma factor RpoD [Anaplasma phagocytophilum HZ]
 gi|88598573|gb|ABD44043.1| RNA polymerase sigma factor RpoD [Anaplasma phagocytophilum HZ]
          Length = 627

 Score =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 71/272 (26%), Positives = 132/272 (48%), Gaps = 19/272 (6%)

Query: 24  RKIPMLEKQE----EYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
            ++ +L  ++       L  + ++H   +  A   ++ ++LRLVV IA  Y   GL   +
Sbjct: 359 NRVKLLSGEDCPGSFKALVAKIQKHERTANRAKQEMIKANLRLVVSIAKKYSNRGLQFLD 418

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +V EGNIGLM+AV KFD +RG++ +TY+ WW++ A+   I      ++I        +  
Sbjct: 419 LVQEGNIGLMKAVDKFDYKRGYKFSTYATWWVRQAITRAIADQARTIRIPVH-----MIE 473

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + ++   L+ +     +   +  ++ +LN++  ++  +   +    SL + I   D +S
Sbjct: 474 TVNKINRTLRQMLHEIGREPTLEELSARLNINVEKIRKVMKIVKDPVSLESPI--GDDDS 531

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVT 254
           S + D +    D +           + R + T+ +S L P+E RI   R          T
Sbjct: 532 STFGDCI---EDKRAVKPENAAVLADLREITTKVLSTLTPKEERILRMRFGIGKSGKDHT 588

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 589 LEEVGRLFNVTRERIRQIEAKALRKLRHPSRA 620


>gi|284008589|emb|CBA75169.1| RNA polymerase sigma-70 factor [Arsenophonus nasoniae]
          Length = 622

 Score =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 353 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 412

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 413 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 470

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 471 KLNRISRQMLQEMGREPSPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 525

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 526 SHLGDFI---EDTTLELPLDSATSESLRSATHEVLAGLTTREAKVLRMRFGIDMNTDHTL 582

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 583 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 618


>gi|238918478|ref|YP_002931992.1| RNA polymerase sigma factor RpoD [Edwardsiella ictaluri 93-146]
 gi|238868046|gb|ACR67757.1| RNA polymerase sigma factor RpoD, putative [Edwardsiella ictaluri
           93-146]
          Length = 611

 Score =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 71/276 (25%), Positives = 131/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +H+I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 342 LHQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 401

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 402 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 459

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 460 KLNRISRQMLQEMGREPTPE---ELAERMMMPEDKIRKVLKIAKEPISMETPI--GDDED 514

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 515 SHLGDFI---EDTTLELPLDSATSESLRSATRDVLAGLTAREAKVLRMRFGIDMNTDHTL 571

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 572 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 607


>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 =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 69/267 (25%), Positives = 125/267 (46%), Gaps = 14/267 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 353 LTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 412

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 413 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 470

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    +A+++ + E ++  +        S+   I   D   S   D++  
Sbjct: 471 LQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 523

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   ++ ++    ++ R      ++ L  RE ++   R   +     TLE +  +F+V
Sbjct: 524 -EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 582

Query: 265 SRERVRQIEARAFKKVQESIQKQVELS 291
           +RER+RQIEA+A +K++   + +V  S
Sbjct: 583 TRERIRQIEAKALRKLRHPSRSEVLRS 609


>gi|42526449|ref|NP_971547.1| RNA polymerase sigma-70 factor family protein [Treponema denticola
           ATCC 35405]
 gi|41816642|gb|AAS11428.1| RNA polymerase sigma-70 factor family protein [Treponema denticola
           ATCC 35405]
 gi|325473389|gb|EGC76584.1| RNA polymerase sigma factor [Treponema denticola F0402]
          Length = 286

 Score =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 80/289 (27%), Positives = 149/289 (51%), Gaps = 12/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  +  +        L+ Y+ EI +IP+L  +EE   AK   E GD  A + LV S+LR 
Sbjct: 1   MYNRTKNNYDAEMNSLATYLKEINQIPLLTAEEEIKYAK-LAEKGDEDAKNMLVNSNLRF 59

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y+  GLP+ +++SEGNIGLM A ++FD  +G++  +Y++WWIK ++ + I   
Sbjct: 60  VVNVAKKYQNQGLPLMDLISEGNIGLMNAAERFDVSKGYKFISYAVWWIKQSILKAICEK 119

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
             ++++            L +++   + I  +  + +++  IA  LN+  S V ++    
Sbjct: 120 SRMIRLPLNRA-----NELVQIEKAKKEIDFSGNETKELNEIAGILNMDNSMVHTIMNAA 174

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               S++A +   +  SS   D+L    D   Q+  +     + R+ +   +  L+ RE 
Sbjct: 175 REPISIDAPVFD-EPGSSSVNDFL---QDETHQMPEDYAMDMSLRDEVNELLKNLDDREA 230

Query: 241 RIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            I   R       P++L+ +   F +++ER+RQIE +A +++++  +KQ
Sbjct: 231 EIIRYRFGLGGYAPLSLKEVGLIFNLTKERIRQIEKKALQQLKKPAEKQ 279


>gi|219847900|ref|YP_002462333.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus
           aggregans DSM 9485]
 gi|219542159|gb|ACL23897.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus
           aggregans DSM 9485]
          Length = 381

 Score =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 83/299 (27%), Positives = 133/299 (44%), Gaps = 38/299 (12%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRY------REHGDLS------------------ 48
           +  +  Y+ EI ++P+L  ++E  LAK        R+  D                    
Sbjct: 82  DDPVRMYLQEIGQVPLLTAEQEVELAKAMEAGAIARQRLDREEYASARERFELERAVQQG 141

Query: 49  --AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A H L+ ++LRLVV IA  Y  YGL + ++V EGNIGLM+AV+KFD ++G + +TY+ 
Sbjct: 142 QDARHHLIQANLRLVVSIAKKYTSYGLTMMDLVQEGNIGLMRAVEKFDYKKGHKFSTYAT 201

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      +++     +      ++R    LQ        PE    IA  +
Sbjct: 202 WWIRQAITRAIADQSRTIRLPVHMGE--AISQVKRTSHRLQQTMQREPTPE---EIADAM 256

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +S  +V           SL   +    +   +  D++  D         E       R 
Sbjct: 257 GISAGKVRRTLEASMHPLSLEMPV--GQEGEGRMGDFIEDDRIS---TPAEAAAASLLRE 311

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            L   +  L  RER+I + R   ++    TLE +  EF ++RER+RQIEA A +K++  
Sbjct: 312 QLEEVLMKLPERERKIIQLRYGLKDGRYRTLEEVGIEFGITRERIRQIEAVALRKLRHP 370


>gi|114320976|ref|YP_742659.1| RNA polymerase, sigma 28 subunit [Alkalilimnicola ehrlichii MLHE-1]
 gi|114227370|gb|ABI57169.1| RNA polymerase, sigma 38 subunit, RpoS [Alkalilimnicola ehrlichii
           MLHE-1]
          Length = 342

 Score =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 136/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   ++R  + GD +A  R++ S+LRLVVKIA  Y   GL   ++
Sbjct: 74  YLNEIGYSPLLSAEEEVYFSRR-AQRGDAAARARMIESNLRLVVKIARRYMNRGLAFLDL 132

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K +   
Sbjct: 133 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV-IKEINQY 191

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +T        V  IA  +     +V  M     G  S++  I        
Sbjct: 192 LRAARK----LTQELDHEPSVEEIADHMGRDVEDVRRMRGLNEGTTSVDVPI--GRDADR 245

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
              D +  +++      +   +  +    L   +  L  ++R + E R      +  TLE
Sbjct: 246 VLLDAIPDENNVD---PVSALQDGDVFGNLEAWLGELTEKQRAVVERRFGLNGHDRATLE 302

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            + +E  V+RERVRQI+  A ++++E ++++
Sbjct: 303 QVGNEIGVTRERVRQIQIDALRRLREVMERE 333


>gi|262042263|ref|ZP_06015428.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|259040327|gb|EEW41433.1| RNA polymerase sigma factor RpoD [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
          Length = 611

 Score =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 129/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 342 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 401

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 402 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 459

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 460 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 514

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 515 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 571

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 572 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 607


>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 =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 72/282 (25%), Positives = 129/282 (45%), Gaps = 20/282 (7%)

Query: 20  IHEIRKIPMLEKQ------EEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           +  I K+  +E++      +   + +R    E     A   +V ++LRLV+ IA  Y   
Sbjct: 341 LRSIGKLQQIEEETGLSIAQIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNR 400

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I     
Sbjct: 401 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM- 459

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
                  L R+   +         PE    +A ++ + E ++  +        S+   I 
Sbjct: 460 -IETINKLNRISRQMLQEMGREPNPE---ELAMRMGMPEDKIRKVLKIAKEPISMETPI- 514

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE- 250
             D   S   D++    D    +  +    ++ RN     ++ L  RE ++   R   + 
Sbjct: 515 -GDDEDSHLGDFI---EDTTLALPADAATSESLRNATREVLAGLTAREAKVLRMRFGIDM 570

Query: 251 -NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
               TLE +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 571 NTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 612


>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|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]
          Length = 623

 Score =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 69/249 (27%), Positives = 118/249 (47%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RGF+
Sbjct: 376 YGEAKASKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVCKFEHRRGFK 435

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 436 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQQFGREATPE--- 490

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +AK++++ E ++  +        S+   I   D   S   D++    D   +  ++   
Sbjct: 491 ELAKEMDMPEDKIRKVMKIAKEPISMETPI--GDDEDSHLGDFI---EDPNVESPVDTTT 545

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
             N    +   ++ L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 546 NVNLSETVREVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 605

Query: 279 KVQESIQKQ 287
           K++   + +
Sbjct: 606 KLRHPSRSE 614


>gi|2618586|dbj|BAA23365.1| sigma factor [Vibrio cholerae]
          Length = 335

 Score =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 82/287 (28%), Positives = 138/287 (48%), Gaps = 13/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           R+              Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVV
Sbjct: 46  REEFDASAKSLDATQMYLSEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLVV 104

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           KI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++    
Sbjct: 105 KISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYTTWWIRQTIERALMNQTR 164

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            +++      K L   LR  +     ++           IA +L+    +V  M      
Sbjct: 165 TIRLPIHVV-KELNIYLRTAR----ELSQRLDHEPTPEEIALELDRPVDDVTKMLRLNER 219

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++  I           D L   H+   +   + +   + R  L   +  LNP+++ +
Sbjct: 220 ISSVDTPI--GGDGDKALLDILPDSHNADPEFSTQDD---DIRESLLNWLDELNPKQKEV 274

Query: 243 FEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 275 LARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVKQ 321


>gi|33239946|ref|NP_874888.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus subsp.
           marinus str. CCMP1375]
 gi|33237472|gb|AAP99540.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Prochlorococcus marinus subsp. marinus str. CCMP1375]
          Length = 438

 Score =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 78/313 (24%), Positives = 141/313 (45%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR--------------EHGD----------- 46
            E  +  Y+ EI +I +L   EE  LA++                EHG+           
Sbjct: 126 TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLHLEELAIQFESEHGNYPTKKEWAALV 185

Query: 47  --------------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 186 NMPMARFRRRLMLARRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 245

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 246 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKVLSQE 300

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA+ + ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 301 FGRKPSEEEIAESMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIESDSENPE 358

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
             +     +   R  L   ++ L+PRER +   R   ++    TLE +   F+V+RER+R
Sbjct: 359 LDVA----KTLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIR 414

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 415 QIEAKALRKLRHP 427


>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 =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 74/278 (26%), Positives = 126/278 (45%), Gaps = 14/278 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           +   + I +I K   L   E   ++KR    E     A   +V ++LRLV+ IA  Y   
Sbjct: 351 LAFQQKIADIEKELNLSVAEIKDISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNR 410

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I     
Sbjct: 411 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM- 469

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
                  + R+   L         PE    + ++L + E +V  +        S+   I 
Sbjct: 470 -IETINKINRVSRQLLQEMGREPTPE---ELGERLEMDEVKVRKVLKIAKEPISMETPI- 524

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             D   S   D++    D      I+    +  +      +  L  RE ++ + R   + 
Sbjct: 525 -GDDEDSHLGDFI---EDQNITSPIDAATSEGLKEATREVLENLTEREAKVLKMRFGIDM 580

Query: 252 P--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           P   TLE +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 581 PTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 618


>gi|261868195|ref|YP_003256117.1| RNA polymerase sigma factor RpoD [Aggregatibacter
           actinomycetemcomitans D11S-1]
 gi|261413527|gb|ACX82898.1| RNA polymerase sigma factor RpoD (Sigma-70) [Aggregatibacter
           actinomycetemcomitans D11S-1]
          Length = 616

 Score =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 118/247 (47%), Gaps = 12/247 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 376 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 435

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            L R+   +         PE    +A+++
Sbjct: 436 WWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREASPE---ELAERM 490

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D   ++ ++    ++ + 
Sbjct: 491 GMPEDKIRKVLKIAKEPISMETPI--GDDDDSHLGDFI---EDSTLELPLDSATVQSLKA 545

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                +  L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 546 ATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 605

Query: 285 QKQVELS 291
           + +   S
Sbjct: 606 RSETLRS 612


>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 =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 74/270 (27%), Positives = 124/270 (45%), Gaps = 24/270 (8%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           I EI +           LA  Y E     A   +V ++LRLV+ IA  Y   GL   +++
Sbjct: 362 IREIGR----------QLA--YGEAKARKAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 409

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L
Sbjct: 410 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKL 467

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
            R+   +         PE    +AK++++ E ++  +        S+   I   D   S 
Sbjct: 468 NRISRQMLQQYGREATPE---ELAKEMDMPEDKIRKVMKIAKEPISMETPI--GDDEDSH 522

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLEN 257
             D++    D   +  I+     N    +   ++ L PRE ++   R   +     TLE 
Sbjct: 523 LGDFI---EDTNVESPIDSTTNTNLMETVRDVLAGLTPREAKVLRMRFGIDMNTDHTLEE 579

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 580 VGKQFDVTRERIRQIEAKALRKLRHPSRSE 609


>gi|156563504|dbj|BAF76047.1| Sigma70 [Ralstonia solanacearum]
          Length = 755

 Score =  230 bits (588), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 68/247 (27%), Positives = 115/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 510 ERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 569

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T N   P     +
Sbjct: 570 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGNEPDPAT---L 624

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+ + E ++  +        S+   I   D + S   D++    D       E     
Sbjct: 625 AEKMEMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTLAPAEAALHG 679

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 680 SMRGVVKDVLDSLAPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKL 739

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 740 RHPSRSD 746


>gi|149924702|ref|ZP_01913051.1| sigma 32 (RpoH) [Plesiocystis pacifica SIR-1]
 gi|149814429|gb|EDM74021.1| sigma 32 (RpoH) [Plesiocystis pacifica SIR-1]
          Length = 371

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 112/277 (40%), Positives = 172/277 (62%), Gaps = 6/277 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             ++ Y+ E+R+ P+L +++E+ LA R+ EHGD  AA RLVTS+LRLVVKIA  YR    
Sbjct: 88  DPMAAYMAEVRRHPLLTREQEHELAVRWVEHGDQEAAKRLVTSNLRLVVKIANEYRRGYQ 147

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + ++V EGN+GL++AV+KFDP RG +L+TYS WWI+A + ++IL +W LVKIGTT NQ+
Sbjct: 148 NLLDLVQEGNVGLLKAVQKFDPYRGVKLSTYSGWWIRAYVLKHILNNWRLVKIGTTQNQR 207

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINS 192
           +LFFNLR+ +  L               IAK+L+VS  EV+ M  R+   D SLNA + S
Sbjct: 208 KLFFNLRKQREALI----RAGIDPTAENIAKELDVSTEEVVEMQKRMGAPDASLNAPLGS 263

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLNPRERRIFEARRLQEN 251
            ++  ++ +  ++ D     +  +  EE K    + L    + L+ RE  IF  R + + 
Sbjct: 264 GEEPGARTRLDMLEDETTDPEGEVSGEEFKRLLHDKLRTFGATLSGREAEIFGERLIADE 323

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           P+TL+ L   + VSRER RQ+E R   ++++ +Q ++
Sbjct: 324 PITLQALGERWGVSRERARQVEKRMVLRLRKYLQAEL 360


>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 =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 495 RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 554

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 555 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 609

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 610 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTVAPADAALHASMRD 664

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 665 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 724

Query: 285 QKQ 287
           +  
Sbjct: 725 RSD 727


>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|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 =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 67/251 (26%), Positives = 119/251 (47%), Gaps = 12/251 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 385 EQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 444

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            L R+   L         PE    +
Sbjct: 445 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQLLQEMGREATPE---EL 499

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+++ + E ++  +        S+   I   D + S   D++    D   ++ ++    +
Sbjct: 500 AERMGMPEDKIRKVLKIAKEPISMETPI--GDDDDSHLGDFI---EDSTLELPLDSATAQ 554

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + +      +  L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 555 SLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 614

Query: 281 QESIQKQVELS 291
           +   + +   S
Sbjct: 615 RHPSRSETLRS 625


>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 =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 67/251 (26%), Positives = 119/251 (47%), Gaps = 12/251 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 385 EQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 444

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            L R+   L         PE    +
Sbjct: 445 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQLLQEMGREATPE---EL 499

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+++ + E ++  +        S+   I   D + S   D++    D   ++ ++    +
Sbjct: 500 AERMGMPEDKIRKVLKIAKEPISMETPI--GDDDDSHLGDFI---EDSTLELPLDSATAQ 554

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + +      +  L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 555 SLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 614

Query: 281 QESIQKQVELS 291
           +   + +   S
Sbjct: 615 RHPSRSETLRS 625


>gi|269925486|ref|YP_003322109.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
 gi|269789146|gb|ACZ41287.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
          Length = 338

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 70/309 (22%), Positives = 137/309 (44%), Gaps = 37/309 (11%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR----------------EHG 45
           +++   +  + +  +  Y+ EI  +P+L  ++E  LAK+                  E  
Sbjct: 29  DKQEEDLSEDLDDSVRMYLREIGLVPLLTAEQEVELAKKMERGKKAQSVLDSGKYEPEQR 88

Query: 46  D---------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           D           A   L+ ++LRLVV +A  +   GL + +++ EGNIGLM+A  KFD  
Sbjct: 89  DKLLAEVDEGERARRHLIEANLRLVVSVAKKHMNRGLSLLDLIEEGNIGLMRATDKFDYR 148

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +GF+ +TY+ WWI+ A+   I      +++     +      +  L    + ++    + 
Sbjct: 149 KGFKFSTYATWWIRQAVTRAIADQARTIRLPVHITE-----TMNHLYKASRKLSQELGRE 203

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
                +A+ + ++  +V  +        SL   +       S    ++    D   +  +
Sbjct: 204 PTCEELAEYMGMNPEKVRLIMRASRHPLSLEGPV--GTDGDSSLGQFIP---DSTTETPV 258

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEA 274
           +    +  +  L++ ++ L  +ER++   R   E   P TLE +     V+RERVRQIEA
Sbjct: 259 DLAIGEVLKRELSKVLNSLTEKERKVMVLRYGLEGSSPHTLEEVGHRLGVTRERVRQIEA 318

Query: 275 RAFKKVQES 283
           +A +K+++ 
Sbjct: 319 KALEKLRKP 327


>gi|260063687|ref|YP_003196767.1| putative sigma factor A [Robiginitalea biformata HTCC2501]
 gi|88783132|gb|EAR14305.1| putative sigma factor A [Robiginitalea biformata HTCC2501]
          Length = 287

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 68/276 (24%), Positives = 144/276 (52%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI K+ ++   EE  LA+R +  GD +A  +L  ++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQEIGKVDLITADEEVELAQRIK-AGDQAALEKLTKANLRFVVSVAKQYQNQGLT 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     +V++        
Sbjct: 76  LPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNK---- 131

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
              ++ ++      +   + +      IAK+L+++  +V           S++A +   D
Sbjct: 132 -IGSINKINKTFAFLEQAHERVPSAEEIAKELDMTVEDVKQSLKNSGRHVSMDAPLI--D 188

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENP 252
              S   D L     G+     ++   ++ R  + R++  L PRE  +         ++ 
Sbjct: 189 GEDSNLYDVL---RSGESPNPDKELLHESLRTEIERALETLTPREADVIRLYFGLAGQHS 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 246 MTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|269468904|gb|EEZ80491.1| DNA-directed RNA polymerase, sigma subunit [uncultured SUP05
           cluster bacterium]
          Length = 603

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 71/271 (26%), Positives = 128/271 (47%), Gaps = 22/271 (8%)

Query: 28  MLEKQEEYVL-------AKRYREHGDLSAAH---RLVTSHLRLVVKIAMGYRGYGLPISE 77
           +LE +EE  L         +    GD  A     +++ ++LRLV+ IA  Y   GL   +
Sbjct: 335 LLEFEEEMQLTVPELKALNKLYRRGDRRAKKAKSQMIEANLRLVISIAKKYANRGLQFLD 394

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGN+GLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 395 LIQEGNVGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 452

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R++  L         PE    +A ++ + E ++  +        S+   +   D   
Sbjct: 453 KLNRVRRQLLQKFGREATPE---ELAVEMELPEYKINKILKIAKEPLSMETPV--GDDED 507

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D      +E   R++ +      ++ L+PRE ++ + R   +     TL
Sbjct: 508 SNIGDFI---EDTNLSSPVEITTRESLKETTGELLANLSPREAKVLKMRFGIDMNTDHTL 564

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E +  +F+V+RER+RQIEA+A +K++   + 
Sbjct: 565 EEVGRQFDVTRERIRQIEAKALRKLRHPSRA 595


>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|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 =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 67/251 (26%), Positives = 119/251 (47%), Gaps = 12/251 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 385 EQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 444

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            L R+   L         PE    +
Sbjct: 445 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQLLQEMGREATPE---EL 499

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+++ + E ++  +        S+   I   D + S   D++    D   ++ ++    +
Sbjct: 500 AERMGMPEDKIRKVLKIAKEPISMETPI--GDDDDSHLGDFI---EDSTLELPLDSATAQ 554

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + +      +  L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 555 SLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 614

Query: 281 QESIQKQVELS 291
           +   + +   S
Sbjct: 615 RHPSRSETLRS 625


>gi|291550766|emb|CBL27028.1| RNA polymerase, sigma 70 subunit, RpoD [Ruminococcus torques L2-14]
          Length = 280

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 83/288 (28%), Positives = 139/288 (48%), Gaps = 14/288 (4%)

Query: 3   RKNMSIIVNGEI--GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
            K++++    E+   L  Y++EI +IP+L ++EE  L  +    GD  A  +L   +LRL
Sbjct: 2   EKDLNLPEGTEVTEPLKIYLNEIGQIPLLSEEEERDLGCK-SASGDEDARRKLEEGNLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y G G+ + +++ EGNIGLM A +K+D  +  R +TY+ WWIK AMQ  I + 
Sbjct: 61  VVSLAKHYTGRGITLMDLIQEGNIGLMHAAEKYDYTKENRFSTYASWWIKEAMQRAIDQQ 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              +++     +      ++++   LQ        PE++    K  + S   V  +   L
Sbjct: 121 SREIRVPVHVAEN--MKKVQKISKDLQQKFGREATPEEIAEEMK--DKSPEFVKEILSYL 176

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   +   +   +   D +    D       +   +  ++  +   +  LN RER
Sbjct: 177 QNPVSLETPV--GEDGENNLGDMV---EDKDATTPEDAMNQLVQKEEVQELLESLNDRER 231

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ++   R   E+    TLE +  E  V+RERVRQIEARA +K++    K
Sbjct: 232 QVIRLRFGLEDGKTHTLEEIGDELNVTRERVRQIEARAMEKLRSKATK 279


>gi|297181479|gb|ADI17666.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [uncultured gamma proteobacterium HF0130_23I23]
          Length = 602

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 73/256 (28%), Positives = 121/256 (47%), Gaps = 14/256 (5%)

Query: 37  LAKRY--REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           L KR      G L A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+
Sbjct: 350 LNKRINKAYRGLLRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 409

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             RG++ +TY+ WWI+ A+   I      ++I            L RL   +        
Sbjct: 410 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRLSRQMMQEIGREP 467

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            PE    ++K+L++ E ++  +        S+   I   D   S   D+L    D     
Sbjct: 468 TPE---EMSKRLDIPEDKMRKVMKIAKEPISMETPI--GDDEDSNLGDFL---EDSSINS 519

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQI 272
            I+    ++ ++     ++ L  RE ++   R      N  TLE +  +F+V+RER+RQI
Sbjct: 520 PIDDASIRSLKDSTDEILASLTAREAKVLRMRFGIGMNNDHTLEEVGKQFDVTRERIRQI 579

Query: 273 EARAFKKVQESIQKQV 288
           EA+A +K++   +  V
Sbjct: 580 EAKALRKLRHPSRSDV 595


>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 =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 66/249 (26%), Positives = 118/249 (47%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 369 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 428

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 429 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRVSRQMLQEMGREPTPE--- 483

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + E ++  +        S+   I   D   S   D++    DG  ++ ++   
Sbjct: 484 ELAERMVMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDGSGELPVDSAT 538

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            +N +      ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 539 SENLKGATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 598

Query: 279 KVQESIQKQ 287
           K++   + +
Sbjct: 599 KLRHPSRSE 607


>gi|261341953|ref|ZP_05969811.1| alternative sigma factor RpoH [Enterobacter cancerogenus ATCC
           35316]
 gi|288315861|gb|EFC54799.1| alternative sigma factor RpoH [Enterobacter cancerogenus ATCC
           35316]
          Length = 285

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 107/290 (36%), Positives = 164/290 (56%), Gaps = 9/290 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +     L  YI      PML  +EE  LA++    GDL AA  L+ SHLR 
Sbjct: 1   MTKEMQTLALAPVGNLESYIRAANTWPMLTAEEEKELAEKLHYQGDLEAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVEMVARELGVSSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQ---EQVLIEKEERKNRRNMLTRSMSVLNP 237
           A  +    + +  D + SQ    ++Y  D        + E        N L+ +M  L+ 
Sbjct: 176 AAQDMTFDMSSDDDASDSQPMAPVLYLQDKTSNFADGIEEDNWEDQAANKLSFAMEGLDE 235

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R + I  AR L E+   TL+ L+  + VS ERVRQ+E  A KK++ +I+ 
Sbjct: 236 RSQDIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 285


>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 =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 64/241 (26%), Positives = 116/241 (48%), Gaps = 12/241 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 360 AKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 419

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I            L R+   +         P+    +A ++++
Sbjct: 420 IRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPTPD---ELAARMDM 474

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E +V  +        S+   I   D + S   D++    D +    +E     + R   
Sbjct: 475 PEDKVRKVMKIAKEPISMETPI--GDDDDSHLGDFI---EDSRVLSPVEHATVASLRETT 529

Query: 229 TRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   + 
Sbjct: 530 QQVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRS 589

Query: 287 Q 287
           +
Sbjct: 590 E 590


>gi|309785782|ref|ZP_07680413.1| alternative sigma factor RpoH [Shigella dysenteriae 1617]
 gi|308926902|gb|EFP72378.1| alternative sigma factor RpoH [Shigella dysenteriae 1617]
 gi|315614730|gb|EFU95370.1| alternative sigma factor RpoH [Escherichia coli 3431]
 gi|323162701|gb|EFZ48540.1| alternative sigma factor RpoH [Escherichia coli E128010]
 gi|323164790|gb|EFZ50582.1| alternative sigma factor RpoH [Shigella sonnei 53G]
 gi|323179012|gb|EFZ64586.1| alternative sigma factor RpoH [Escherichia coli 1180]
 gi|323182926|gb|EFZ68327.1| alternative sigma factor RpoH [Escherichia coli 1357]
 gi|323188948|gb|EFZ74232.1| alternative sigma factor RpoH [Escherichia coli RN587/1]
 gi|327251097|gb|EGE62790.1| alternative sigma factor RpoH [Escherichia coli STEC_7v]
          Length = 257

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 102/262 (38%), Positives = 152/262 (58%), Gaps = 8/262 (3%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           ML   EE  LA++   HGDL AA  L+ SHLR VV IA  Y GYGLP ++++ EGNIGLM
Sbjct: 1   MLSADEERALAEKLHYHGDLEAAKTLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLM 60

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV++F+PE G RL ++++ WIKA + EY+LR+W +VK+ TT  Q++LFFNLR+ K  L 
Sbjct: 61  KAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLG 120

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSSDKNSSQWQDWLVY 206
                    ++V  +A++L V+  +V  M  R+ A D + +   +    +        + 
Sbjct: 121 WFNQ-----DEVEMVARELGVTSKDVREMESRMAAQDMTFDLSSDDDSDSQPMAPVLYLQ 175

Query: 207 DHDGQEQVLIEKE-ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-PVTLENLSSEFEV 264
           D        IE +   +   N LT +M  L+ R + I  AR L E+   TL+ L+  + V
Sbjct: 176 DKSSNFADGIEDDNWEEQAANRLTDAMQGLDERSQDIIRARWLDEDNKSTLQELADRYGV 235

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S ERVRQ+E  A KK++ +I+ 
Sbjct: 236 SAERVRQLEKNAMKKLRAAIEA 257


>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]
          Length = 628

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 70/257 (27%), Positives = 118/257 (45%), Gaps = 14/257 (5%)

Query: 35  YVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
             +AKR    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV K
Sbjct: 373 KDIAKRMAVGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 432

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+  RG++ +TY+ WWI+ A+   I      ++I            + R+   L      
Sbjct: 433 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKINRVSRQLLQEMGR 490

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE    + ++L + E +V  +        S+   I   D   S   D++    D   
Sbjct: 491 EPTPE---ELGERLEMDEVKVRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDSNI 542

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
              I+    +  +      +  L  RE ++ + R   + P   TLE +  +F+V+RER+R
Sbjct: 543 TSPIDAATSEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIR 602

Query: 271 QIEARAFKKVQESIQKQ 287
           QIEA+A +K++   + +
Sbjct: 603 QIEAKALRKLRHPSRSE 619


>gi|148827724|ref|YP_001292477.1| DNA primase [Haemophilus influenzae PittGG]
 gi|148718966|gb|ABR00094.1| DNA primase [Haemophilus influenzae PittGG]
          Length = 629

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 67/251 (26%), Positives = 119/251 (47%), Gaps = 12/251 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 385 EQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 444

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            L R+   L         PE    +
Sbjct: 445 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQLLQEMGREATPE---EL 499

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+++ + E ++  +        S+   I   D + S   D++    D   ++ ++    +
Sbjct: 500 AERMGMPEDKIRKVLKIAKEPISMETPI--GDDDDSHLGDFI---EDSTLELPLDSATAQ 554

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + +      +  L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 555 SLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 614

Query: 281 QESIQKQVELS 291
           +   + +   S
Sbjct: 615 RHPSRSETLRS 625


>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 =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 495 RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 554

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 555 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 609

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 610 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTVAPADAALHASMRD 664

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 665 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 724

Query: 285 QKQ 287
           +  
Sbjct: 725 RSD 727


>gi|327480191|gb|AEA83501.1| RNA polymerase sigma factor RpoS [Pseudomonas stutzeri DSM 4166]
          Length = 332

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 84/278 (30%), Positives = 141/278 (50%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 64  YLNEIGFSPLLTPEEEVHFA-RLAQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 122

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 123 VEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 181

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++  + +K       ++ +N R+   D SL           
Sbjct: 182 LRAAR-ELTQKLDHEPSPEEIANLLEKPVGEVKRMLGLNERVTSVDVSL------GPDTD 234

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L+  ++  N  ++    +S L+ ++R +   R         TL
Sbjct: 235 KTLLDTLTDDRPTDPCELLLDDDLSNSIDL---WLSDLSEKQREVVIRRFGLRGHEASTL 291

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E +  E  ++RERVRQI+  A ++++E +++    S +
Sbjct: 292 EEVGQEIGLTRERVRQIQVEALRRLREILERNGLSSDA 329


>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 =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 68/247 (27%), Positives = 116/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 438 ERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 497

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T N   P     +
Sbjct: 498 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGNEPDPAT---L 552

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+ + E ++  +        S+   I   D + S   D++    D       E     
Sbjct: 553 AEKMEMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTLAPAEAALHG 607

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 608 SMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKL 667

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 668 RHPSRSD 674


>gi|29655194|ref|NP_820886.1| RNA polymerase factor sigma-32 [Coxiella burnetii RSA 493]
 gi|6716381|gb|AAF26609.1|AF120928_1 heat-shock sigma factor [Coxiella burnetii]
 gi|29542466|gb|AAO91400.1| RNA polymerase sigma-32 factor [Coxiella burnetii RSA 493]
          Length = 288

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 104/278 (37%), Positives = 167/278 (60%), Gaps = 9/278 (3%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  YI  + +IP+L  +EE+ LA ++R+  DL AA +LV SHLR VV+IA GY GYGL
Sbjct: 16  GSIGSYISWVNRIPLLSAEEEHDLANKFRQSNDLEAARKLVLSHLRFVVRIARGYSGYGL 75

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
             ++++ EGNIGLM+AVK+FDP+ G RL ++++ WI+A + E+IL++W +VKI TT  Q+
Sbjct: 76  SQADLIQEGNIGLMKAVKRFDPQVGVRLVSFAVHWIRAEIHEFILKNWRIVKIATTKAQR 135

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINS 192
           +LFFNLR+        +D+     +  A+A++LNVS  +V  M  RL + DE+ +     
Sbjct: 136 KLFFNLRKHAKKRGWFSDH-----EAFALAEELNVSTKDVRQMEERLNSYDEAFDGADEE 190

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKE---ERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           SD  +  W     Y  D +    ++ E      ++ + L  +M  ++ R R I   R L 
Sbjct: 191 SDSGTPSWGAPAHYLEDKRYNPALQLERSNWADDQEHRLHNAMQSMDDRSRDILYQRWLS 250

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E   TL  L++++ VS ER+RQ+E  A +K++ ++  +
Sbjct: 251 EKKSTLHELAAQYAVSAERIRQLEKNAMQKIRTAMADE 288


>gi|296112900|ref|YP_003626838.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis RH4]
 gi|295920594|gb|ADG60945.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis RH4]
 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 =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 69/249 (27%), Positives = 116/249 (46%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 379 IGEAKARRAKKDMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 438

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            + R+   L         PE   
Sbjct: 439 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKINRVSRQLLQEMGREPTPE--- 493

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + ++L++ E++V  +        S+   I   D   S   D++    D      IE   
Sbjct: 494 ELGERLDMDEAKVRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDNTISSPIENAT 548

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFK 278
            +  R      +  L  RE ++ + R   + P   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 549 AEGLREATREVLDNLTEREAKVLKMRFGIDMPSDHTLEEVGKQFDVTRERIRQIEAKALR 608

Query: 279 KVQESIQKQ 287
           K++   + +
Sbjct: 609 KLRHPSRSE 617


>gi|325280261|ref|YP_004252803.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Odoribacter
           splanchnicus DSM 20712]
 gi|324312070|gb|ADY32623.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Odoribacter
           splanchnicus DSM 20712]
          Length = 286

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 78/287 (27%), Positives = 142/287 (49%), Gaps = 12/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI K  ++  +EE  LA+R R+ GD  A  +L  ++LR VV
Sbjct: 5   KITKSITNRESASLDKYLQEIGKEDLITVEEEVELAQRIRK-GDQKALEKLTRANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 64  SVAKQYQNQGLSLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    NQ      + +     +   +    PE    +A  L++   +V         
Sbjct: 124 IVRLP--LNQVGSLNKINKAFSRFEQENERRPSPE---ELADSLDLPAEKVADTLRVSGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     + NS    D LV D        +  E        + R++S L  RER I
Sbjct: 179 HISVDAPFVEGEDNS--LLDVLVNDDSPIADRTLINESLSTE---VERALSTLTERERDI 233

Query: 243 FEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +         +TLE +  +F ++RERVRQI+ +A ++++ S + ++
Sbjct: 234 IKLFFGINTQEMTLEEIGEKFGLTRERVRQIKEKAIRRLRHSSRSKL 280


>gi|323495851|ref|ZP_08100919.1| RNA polymerase sigma factor RpoS [Vibrio sinaloensis DSM 21326]
 gi|323319067|gb|EGA72010.1| RNA polymerase sigma factor RpoS [Vibrio sinaloensis DSM 21326]
          Length = 331

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 81/287 (28%), Positives = 141/287 (49%), Gaps = 13/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +++             Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVV
Sbjct: 43  KEDFDASAKSLDATQLYLGEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLVV 101

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           KI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++    
Sbjct: 102 KISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTR 161

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            +++      K L   LR  +     ++           IA KL+    +V  M      
Sbjct: 162 TIRLPIHVV-KELNIYLRTAR----ELSQKLDHEPTAEEIATKLDKPVDDVSKMLRLNER 216

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++  I           D +   ++   +V  + +   + +N L   +  LNP+++ +
Sbjct: 217 ISSVDTPI--GGDGEKALLDIIPDVNNSDPEVSTQDD---DIKNSLIHWLDELNPKQKEV 271

Query: 243 FEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 272 LARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILIKQ 318


>gi|258546170|ref|ZP_05706404.1| deoxyuridine 5`-triphosphate nucleotidohydrolase [Cardiobacterium
           hominis ATCC 15826]
 gi|258518595|gb|EEV87454.1| deoxyuridine 5`-triphosphate nucleotidohydrolase [Cardiobacterium
           hominis ATCC 15826]
          Length = 287

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 108/279 (38%), Positives = 166/279 (59%), Gaps = 7/279 (2%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           +     + +YI +IR+IP L+ +EE  LA   +E  D++AA  L+  HL+ VV IA G+ 
Sbjct: 14  LTPSTDIDQYIAKIRQIPALDAEEERKLAIALQETNDINAAQTLIVHHLKFVVHIARGFT 73

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYGLP+ +++ EGN+GLM+AVK+F+P+RG RL ++++ WIK+ + EYI+R+W +VKI TT
Sbjct: 74  GYGLPLGDLIQEGNVGLMKAVKRFEPQRGVRLVSFAVHWIKSEIHEYIIRNWRMVKIATT 133

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNA 188
             Q++LFFNLR +K  L  + +   K     AIA +LNVS  +V  M  R+ G D +   
Sbjct: 134 KAQRKLFFNLRSMKKSLNWLNEAEAK-----AIADELNVSTKDVFEMESRIHGQDIAFEL 188

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
             +  D +      WL  D     +     E     +  L + +  L+PR R I +AR L
Sbjct: 189 NDDDEDNDHFSPSQWLADDSIDPAEHTEHAEHENLMQRKLAKGLQALDPRSRAIVQARWL 248

Query: 249 QEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            E+   TL+ L+SE+ VS ER+RQIE +A  +++  I+ 
Sbjct: 249 NEDSKATLQTLASEYNVSAERIRQIEQQAMHQLRAHIEA 287


>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 =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 67/251 (26%), Positives = 119/251 (47%), Gaps = 12/251 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 385 EQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 444

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            L R+   L         PE    +
Sbjct: 445 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQLLQEMGREATPE---EL 499

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+++ + E ++  +        S+   I   D + S   D++    D   ++ ++    +
Sbjct: 500 AERMGMPEDKIRKVLKIAKEPISMETPI--GDDDDSHLGDFI---EDSTLELPLDSATAQ 554

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + +      +  L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 555 SLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 614

Query: 281 QESIQKQVELS 291
           +   + +   S
Sbjct: 615 RHPSRSETLRS 625


>gi|229512804|ref|ZP_04402271.1| RNA polymerase sigma factor RpoS [Vibrio cholerae TMA 21]
 gi|229350053|gb|EEO15006.1| RNA polymerase sigma factor RpoS [Vibrio cholerae TMA 21]
 gi|327483355|gb|AEA77762.1| RNA polymerase sigma factor RpoS [Vibrio cholerae LMA3894-4]
          Length = 335

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 82/287 (28%), Positives = 138/287 (48%), Gaps = 13/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           R+              Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVV
Sbjct: 46  REEFDASAKSLDATQMYLSEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLVV 104

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           KI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++    
Sbjct: 105 KISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTR 164

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            +++      K L   LR  +     ++           IA +L+    +V  M      
Sbjct: 165 TIRLPIHVV-KELNIYLRTAR----ELSQRLDHEPTPEEIALELDRPVDDVTKMLRLNER 219

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++  I           D L   H+   +   + +   + R  L   +  LNP+++ +
Sbjct: 220 ISSVDTPI--GGDGDKALLDILPDSHNADPEFSTQDD---DIRESLLNWLDELNPKQKEV 274

Query: 243 FEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 275 LARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVKQ 321


>gi|15640556|ref|NP_230185.1| RNA polymerase sigma-38 factor [Vibrio cholerae O1 biovar El Tor
           str. N16961]
 gi|121590676|ref|ZP_01678009.1| RNA polymerase sigma factor RpoS [Vibrio cholerae 2740-80]
 gi|121728563|ref|ZP_01681585.1| RNA polymerase sigma factor RpoS [Vibrio cholerae V52]
 gi|153819103|ref|ZP_01971770.1| RNA polymerase sigma factor RpoS [Vibrio cholerae NCTC 8457]
 gi|153823615|ref|ZP_01976282.1| RNA polymerase sigma factor RpoS [Vibrio cholerae B33]
 gi|227080717|ref|YP_002809268.1| RNA polymerase sigma factor RpoS [Vibrio cholerae M66-2]
 gi|229507145|ref|ZP_04396651.1| RNA polymerase sigma factor RpoS [Vibrio cholerae BX 330286]
 gi|229508992|ref|ZP_04398480.1| RNA polymerase sigma factor RpoS [Vibrio cholerae B33]
 gi|229519660|ref|ZP_04409103.1| RNA polymerase sigma factor RpoS [Vibrio cholerae RC9]
 gi|229606176|ref|YP_002876824.1| RNA polymerase sigma factor RpoS [Vibrio cholerae MJ-1236]
 gi|254850774|ref|ZP_05240124.1| RNA polymerase sigma factor rpoS [Vibrio cholerae MO10]
 gi|255744238|ref|ZP_05418191.1| RNA polymerase sigma factor RpoS [Vibrio cholera CIRS 101]
 gi|262149032|ref|ZP_06028176.1| RNA polymerase sigma factor RpoS [Vibrio cholerae INDRE 91/1]
 gi|6094129|sp|O51804|RPOS_VIBCH RecName: Full=RNA polymerase sigma factor rpoS; AltName:
           Full=Sigma-38 factor
 gi|2897902|gb|AAC38175.1| sigma S [Vibrio cholerae]
 gi|9654961|gb|AAF93702.1| RNA polymerase sigma-38 factor [Vibrio cholerae O1 biovar El Tor
           str. N16961]
 gi|121547462|gb|EAX57570.1| RNA polymerase sigma factor RpoS [Vibrio cholerae 2740-80]
 gi|121629175|gb|EAX61616.1| RNA polymerase sigma factor RpoS [Vibrio cholerae V52]
 gi|126510335|gb|EAZ72929.1| RNA polymerase sigma factor RpoS [Vibrio cholerae NCTC 8457]
 gi|126518864|gb|EAZ76087.1| RNA polymerase sigma factor RpoS [Vibrio cholerae B33]
 gi|227008605|gb|ACP04817.1| RNA polymerase sigma factor RpoS [Vibrio cholerae M66-2]
 gi|229344349|gb|EEO09324.1| RNA polymerase sigma factor RpoS [Vibrio cholerae RC9]
 gi|229353917|gb|EEO18851.1| RNA polymerase sigma factor RpoS [Vibrio cholerae B33]
 gi|229355890|gb|EEO20810.1| RNA polymerase sigma factor RpoS [Vibrio cholerae BX 330286]
 gi|229368831|gb|ACQ59254.1| RNA polymerase sigma factor RpoS [Vibrio cholerae MJ-1236]
 gi|254846479|gb|EET24893.1| RNA polymerase sigma factor rpoS [Vibrio cholerae MO10]
 gi|255738178|gb|EET93570.1| RNA polymerase sigma factor RpoS [Vibrio cholera CIRS 101]
 gi|262031177|gb|EEY49797.1| RNA polymerase sigma factor RpoS [Vibrio cholerae INDRE 91/1]
          Length = 335

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 82/287 (28%), Positives = 138/287 (48%), Gaps = 13/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           R+              Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVV
Sbjct: 46  REEFDASAKSLDATQMYLSEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLVV 104

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           KI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++    
Sbjct: 105 KISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTR 164

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            +++      K L   LR  +     ++           IA +L+    +V  M      
Sbjct: 165 TIRLPIHVV-KELNIYLRTAR----ELSQRLDHEPTPEEIALELDRPVDDVTKMLRLNER 219

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++  I           D L   H+   +   + +   + R  L   +  LNP+++ +
Sbjct: 220 ISSVDTPI--GGDGDKALLDILPDSHNADPEFSTQDD---DIRESLLNWLDELNPKQKEV 274

Query: 243 FEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 275 LARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVKQ 321


>gi|222034799|emb|CAP77541.1| RNA polymerase sigma factor rpoD [Escherichia coli LF82]
          Length = 613

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 129/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 344 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 403

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 404 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIAVQARTIRIPVHM--IETIN 461

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 462 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 516

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 517 SHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 573

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 574 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 609


>gi|269123266|ref|YP_003305843.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptobacillus
           moniliformis DSM 12112]
 gi|268314592|gb|ACZ00966.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptobacillus
           moniliformis DSM 12112]
          Length = 379

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 81/276 (29%), Positives = 139/276 (50%), Gaps = 14/276 (5%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
             +S   + +  +  Y+ EI +IP+L+ +EE+ LA+R  E GD  A  +L+ S+LRLVV 
Sbjct: 97  TTVSESSDVDEPIKMYLREIGQIPLLKSEEEFELARRIGE-GDERAKQQLMESNLRLVVS 155

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  +   GL + +++ EGNIGLM+AV+KF+ ++GF+ +TY+ WWI+ A+   I      
Sbjct: 156 IAKKHTNRGLKLLDLIQEGNIGLMKAVEKFESDKGFKFSTYATWWIRQAITRAIADQGRT 215

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           ++I        +   + ++K   +       K      +A+ + +   +V ++       
Sbjct: 216 IRIPVH-----MIETINKIKKASRIHLQETGKEPTDDYLAEIVEMPVEKVKNILEMNQDP 270

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM-SVLNPRERRI 242
            SL   + S D   S+  D++  D         E   R   +  L   +   LN RE ++
Sbjct: 271 ISLETPVGSEDD--SELGDFVEDDKFLN---PHEATVRSVLKEKLNDVLRKELNEREEQV 325

Query: 243 FEARRLQEN--PVTLENLSSEFEVSRERVRQIEARA 276
              R   ++  P TLE +   F+V+RER+RQIE +A
Sbjct: 326 LRLRYGLDDGAPKTLEEVGKIFDVTRERIRQIEVKA 361


>gi|148654372|ref|YP_001274577.1| RpoD family RNA polymerase sigma factor [Roseiflexus sp. RS-1]
 gi|148566482|gb|ABQ88627.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus sp.
           RS-1]
          Length = 402

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 80/299 (26%), Positives = 131/299 (43%), Gaps = 38/299 (12%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRY--------------------------REHGD 46
           +  +  Y+ EI ++P+L  ++E +LAK                            +    
Sbjct: 103 DDPVRMYLQEIGQVPLLSAEQEVMLAKAMEAGHRARRALEREEYSSWQERVMYEQQVAQG 162

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV IA  Y  YGL + ++V EGNIGLM+AV+KFD  +G + +TY+ 
Sbjct: 163 NEARQHLIQANLRLVVSIAKKYTSYGLTMMDLVQEGNIGLMRAVEKFDYTKGHKFSTYAT 222

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      +++     +      ++R    LQ        PE    IA  +
Sbjct: 223 WWIRQAITRAIADQSRTIRLPVHMGE--AISQVKRTSHKLQQTMQREPTPE---EIADAM 277

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +S ++V           SL   +    +   +  D++  D         E       R 
Sbjct: 278 GISSTKVRRTLEASMHPLSLEMPV--GQEGEGRMGDFIEDDRIS---TPAEAAAASMLRE 332

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            L   +  L  RER+I + R   ++    TLE +  EF ++RER+RQIEA A +K++  
Sbjct: 333 QLEEVLQKLPERERKIIQLRYGLKDGRYRTLEEVGMEFGITRERIRQIEAVALRKLRHP 391


>gi|318041167|ref|ZP_07973123.1| RNA polymerase sigma factor RpoD [Synechococcus sp. CB0101]
          Length = 464

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 78/313 (24%), Positives = 143/313 (45%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE--------------HG------------ 45
            E  +  Y+ EI +I +L   EE  LA++  +              HG            
Sbjct: 152 TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLQLEELAAQFETDHGHYPDTKEWAALV 211

Query: 46  -------------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 212 DMPLIKFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 271

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 272 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKTLSQE 326

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA+ + ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 327 FGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADIENPE 384

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
           Q + +   R++    L   ++ L+PRER +   R   ++    TLE +   F+V+RER+R
Sbjct: 385 QDVAKNLLRED----LEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIR 440

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 441 QIEAKALRKLRHP 453


>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 =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 72/272 (26%), Positives = 127/272 (46%), Gaps = 14/272 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           ++EI K   L   +   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 342 LNEIEKETGLTIAKVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 401

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 402 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 459

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 460 KLNRISRQMLQEMGREPLPE---ELAERMAMPEDKIRKVLKIAKEPISMETPI--GDDED 514

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D    + I+    ++ RN +   +  L  RE ++   R   +     TL
Sbjct: 515 SHLGDFI---EDNTLDLPIDSATSESLRNSVRDVLGGLTAREAKVLRMRFGIDMNTDHTL 571

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 572 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 603


>gi|118579103|ref|YP_900353.1| RNA polymerase sigma-32 subunit RpoH [Pelobacter propionicus DSM
           2379]
 gi|118501813|gb|ABK98295.1| RNA polymerase, sigma 32 subunit, RpoH [Pelobacter propionicus DSM
           2379]
          Length = 282

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 113/271 (41%), Positives = 176/271 (64%), Gaps = 5/271 (1%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             L+ Y+ EIRK  +L ++EE+  A  + E  DL AAH L+TS+LR VV++A  YR YGL
Sbjct: 10  DSLALYLAEIRKFTLLSEEEEHRTAIAFYEKKDLRAAHTLITSNLRFVVRVAYEYRHYGL 69

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++ EGNIGLM AVKK++P +G RL +Y++WWI+A +Q +++ +WSL+KIGTT  Q+
Sbjct: 70  KMLDLIQEGNIGLMMAVKKYNPFKGVRLISYAVWWIRAYIQNHVISAWSLLKIGTTQAQR 129

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
           +LFF LR  +  ++ +       + + + A+ LNVS+SEV+ M  RL G+ SL+A +   
Sbjct: 130 KLFFKLREARNAIRHLNGGE---DDLQSTARSLNVSDSEVVEMEQRLRGECSLDAELPGG 186

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           +       D LV D   QE++L E + ++  R  +  ++S LN +ER + E R   + P+
Sbjct: 187 EG--VTGLDGLVDDRMNQEELLSECQLQRKLRTDVATAVSALNEKERFVIEHRVSADTPL 244

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           TL+ ++S F +SRERVRQIE  A KK++ S+
Sbjct: 245 TLQEIASRFSISRERVRQIEEAALKKLKLSL 275


>gi|95930284|ref|ZP_01313022.1| RNA polymerase, sigma 28 subunit [Desulfuromonas acetoxidans DSM
           684]
 gi|95133747|gb|EAT15408.1| RNA polymerase, sigma 28 subunit [Desulfuromonas acetoxidans DSM
           684]
          Length = 296

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 73/282 (25%), Positives = 140/282 (49%), Gaps = 13/282 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
            +G+  +  Y+H+I+K  +L  +EE  LA +  E GD  A  +++ S+LRLVVKIA  Y 
Sbjct: 23  TSGDDAIKYYLHDIQKSKLLTAEEERALATKV-EAGDEQARAKMIESNLRLVVKIAKRYM 81

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
             GLP  +++ EGN+GL++AV++F   +  R +TY+ WWI+ +++  ++     +++   
Sbjct: 82  NRGLPFLDLIEEGNMGLIKAVERFQVAKECRFSTYATWWIRQSIERALVNQSRTIRLPVH 141

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
            +      N+ R+    + +            IA+ +     EV  +   +    S+   
Sbjct: 142 VSD-----NVNRMLKATKEVLKKLNHEPSEAQIAEAMGAPVEEVRRLQQLVKKTYSIEHP 196

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           +  +D  S      +    D       E  E +++ + + + +S L   ER I   R   
Sbjct: 197 LGDNDNYS-----LMDTLEDSSVINPAELLENQDQYDFVNKWLSSLKENERDILMLRFGL 251

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
            +  P TL+ +   + V+RER+RQIEA++  K++  ++++ E
Sbjct: 252 NDCEPETLDTIGKRYGVTRERIRQIEAKSLDKLRRMMREEAE 293


>gi|226356403|ref|YP_002786143.1| RNA polymerase sigma factor, sigma-70 family [Deinococcus deserti
           VCD115]
 gi|226318393|gb|ACO46389.1| putative RNA polymerase sigma factor, sigma-70 family [Deinococcus
           deserti VCD115]
          Length = 547

 Score =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 77/296 (26%), Positives = 129/296 (43%), Gaps = 36/296 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS------------------------- 48
             + +Y+HEI ++ +L  +EE  LA+R  E  +                           
Sbjct: 246 DPVRQYLHEIGRVSLLTLEEEIALARRIEEGEEARKLLEEDVELDDRGRRRLMRQMEDGA 305

Query: 49  -AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   L+ ++LRLVV IA  Y G GL   +++ EGN GL++AV+KF+  R ++ +TY+ W
Sbjct: 306 NARQGLIEANLRLVVSIAKKYTGRGLGFLDLIQEGNQGLIRAVEKFEYRRRYKFSTYATW 365

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I     +      L R    LQ         E++   A    
Sbjct: 366 WIRQAINRAIADQARTIRIPVHMVE--TINKLTRTARQLQQELSREATHEEIAE-AMGPG 422

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
              ++V  +        SL   I   D+  S + D++    D      +E   +      
Sbjct: 423 WDAAKVEEVQKVSQEPVSLETPI--GDEKDSFYGDFIP---DENLDSPVENAAKTLLSEE 477

Query: 228 LTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           L +++S L  RE  + + R+        TLE +   F V+RER+RQIE +A +K++
Sbjct: 478 LEKALSKLTEREAMVLKFRKGLVDGREHTLEEVGQRFSVTRERIRQIENKALRKLK 533


>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 =  230 bits (587), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 67/251 (26%), Positives = 119/251 (47%), Gaps = 12/251 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 379 EQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 438

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            L R+   L         PE    +
Sbjct: 439 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQLLQEMGREATPE---EL 493

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+++ + E ++  +        S+   I   D + S   D++    D   ++ ++    +
Sbjct: 494 AERMGMPEDKIRKVLKIAKEPISMETPI--GDDDDSHLGDFI---EDSTLELPLDSATAQ 548

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + +      +  L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 549 SLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 608

Query: 281 QESIQKQVELS 291
           +   + +   S
Sbjct: 609 RHPSRSETLRS 619


>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 =  230 bits (586), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 118/247 (47%), Gaps = 12/247 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 384 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 443

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            L R+   +         PE    +A+++
Sbjct: 444 WWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREASPE---ELAERM 498

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D   ++ ++    ++ + 
Sbjct: 499 GMPEDKIRKVLKIAKEPISMETPI--GDDDDSHLGDFI---EDNTLELPLDSATAQSLKV 553

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                +  L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 554 ATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 613

Query: 285 QKQVELS 291
           + +   S
Sbjct: 614 RSETLRS 620


>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 =  230 bits (586), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 70/267 (26%), Positives = 126/267 (47%), Gaps = 14/267 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L  +    +++R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 355 LSVERVKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 414

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 415 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 472

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    +A+++ + E ++  +        S+   I   D   S   D++  
Sbjct: 473 LQEMGREPLPE---ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 525

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   ++ ++     N +   +  ++ L PRE ++   R   +     TLE +  +F+V
Sbjct: 526 -EDTTLELPMDSATMNNLKMATSEVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDV 584

Query: 265 SRERVRQIEARAFKKVQESIQKQVELS 291
           +RER+RQIEA+A +K++   + +V  S
Sbjct: 585 TRERIRQIEAKALRKLRHPSRSEVLRS 611


>gi|121998209|ref|YP_001002996.1| RpoD family RNA polymerase sigma factor [Halorhodospira halophila
           SL1]
 gi|121589614|gb|ABM62194.1| RNA polymerase, sigma 38 subunit, RpoS [Halorhodospira halophila
           SL1]
          Length = 336

 Score =  230 bits (586), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 80/271 (29%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI    +L  +EE  LA+R ++ GD +A  R++ S+LRLVVKIA  Y   GL   ++
Sbjct: 68  YLNEIGHASLLTAEEEVALARRVQQ-GDAAARARMIESNLRLVVKIARRYMNRGLAFLDL 126

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++       +    
Sbjct: 127 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERGIMNQTRTIRLPIHV--IKEINQ 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
             R +  L    D+      V  IA  +  S  +V  M     G  S++  I     +  
Sbjct: 185 YLRTQRRLTQTLDHE---PTVDEIADAMGRSPEDVRRMRGLNEGTTSVDVPI--GKDSDR 239

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
              D +  +  G  + ++E +   +    L   +  L  ++R + E R         TLE
Sbjct: 240 VLLDAIPDETQGMPENVLEDD---DVVRHLQDWLGFLTDKQRAVLERRFGLNGHERYTLE 296

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            + ++  V+RERVRQI+  A ++++E +++ 
Sbjct: 297 QVGTQVGVTRERVRQIQIDALRRLRELMERD 327


>gi|312888769|ref|ZP_07748333.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Mucilaginibacter
           paludis DSM 18603]
 gi|311298769|gb|EFQ75874.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Mucilaginibacter
           paludis DSM 18603]
          Length = 286

 Score =  230 bits (586), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 77/288 (26%), Positives = 147/288 (51%), Gaps = 14/288 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+HEI K+ ++  +EE +LA++ RE GD +A  RL  ++LR VV
Sbjct: 5   KITQSITNRESQSLDKYLHEIGKVDLITAEEEVILAQKIRE-GDQAALERLTKTNLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A K+FD  +GF+  +Y++WWI+ ++ + I     
Sbjct: 64  SVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETKGFKFISYAVWWIRQSILQAIAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    NQ      + +    L+   +    PE    +A  L  +  ++         
Sbjct: 124 IVRLP--LNQVGSLSKISKAFSKLEQEYEREPSPE---ELADILETTVDKISDTLSNSGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     ++N+      L+   D  E         ++    + RS+S L  RER I
Sbjct: 179 HVSMDAPFVQGEENT------LLDVLDNHEPNTDFHLINESLAEEIKRSLSTLTEREREI 232

Query: 243 FEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
                     +P +LE +  +F ++RERVRQI+ +A ++++ + + ++
Sbjct: 233 VVLFFGLGSNSPFSLEEIGEKFNLTRERVRQIKDKALQRLRHTSRSKI 280


>gi|12958587|gb|AAK09363.1|AF321124_1 RpoS [Vibrio harveyi]
          Length = 327

 Score =  230 bits (586), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 80/288 (27%), Positives = 141/288 (48%), Gaps = 13/288 (4%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
            R+              Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLV
Sbjct: 38  AREEFDASSKSLDATQLYLGEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLV 96

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           VKI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++   
Sbjct: 97  VKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQT 156

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             +++      K L   LR  +     ++           IA +L++   +V  M     
Sbjct: 157 RTIRLPIHVV-KELNIYLRTAR----ELSQKLDHEPTAEEIAAQLDIPVEDVSKMLRLNE 211

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              S++  I           D +   ++   +V  + +   + ++ L   +  LNP+++ 
Sbjct: 212 RISSVDTPI--GGDGEKALLDIIPDANNSDPEVSTQDD---DIKSSLIHWLEELNPKQKE 266

Query: 242 IFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +   R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 267 VLARRFGLLGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLREILIKQ 314


>gi|330466466|ref|YP_004404209.1| RNA polymerase sigma factor SigB [Verrucosispora maris AB-18-032]
 gi|328809437|gb|AEB43609.1| RNA polymerase sigma factor SigB [Verrucosispora maris AB-18-032]
          Length = 335

 Score =  230 bits (586), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 72/300 (24%), Positives = 138/300 (46%), Gaps = 38/300 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYRE--------------------------HGDLSA 49
           +  Y++ I +  +L   +E  LAKR                                 +A
Sbjct: 39  VRAYLNGIGRTKLLTAAQEVELAKRIEAGLFAEEKLTTCTPVSAQLQADLTLIAQEGQAA 98

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            + L+ ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI
Sbjct: 99  KNHLLEANLRLVVSIAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWI 158

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + A+   +      ++I     +      + R+    + ++ +  +   V  IA+ L+V 
Sbjct: 159 RQAITRAMADQARTIRIPVHMVE-----QVNRMVRARRELSVSLGREPSVAEIARALDVP 213

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E +VI +        SL+  +   +   S   D++          +++  +R   RN ++
Sbjct: 214 EFQVIELISYDREPVSLDQTV--GEDGESALGDFVAA---VDPSSMVDDADRGELRNEVS 268

Query: 230 RSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             ++ L+ RE+ +   R   ++    TL+ +  EF +SRER+RQIE     K++   + Q
Sbjct: 269 IVLATLSQREQAVIRLRFGLDDGRQRTLDEVGREFGLSRERIRQIEKVTLLKLRAPERAQ 328


>gi|147674644|ref|YP_001216035.1| RNA polymerase sigma factor RpoS [Vibrio cholerae O395]
 gi|262169845|ref|ZP_06037535.1| RNA polymerase sigma factor RpoS [Vibrio cholerae RC27]
 gi|146316527|gb|ABQ21066.1| RNA polymerase sigma factor RpoS [Vibrio cholerae O395]
 gi|227012360|gb|ACP08570.1| RNA polymerase sigma factor RpoS [Vibrio cholerae O395]
 gi|262021579|gb|EEY40290.1| RNA polymerase sigma factor RpoS [Vibrio cholerae RC27]
          Length = 335

 Score =  230 bits (586), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 82/287 (28%), Positives = 138/287 (48%), Gaps = 13/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           R+              Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVV
Sbjct: 46  REEFDASAKSLDATQMYLSEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLVV 104

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           KI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++    
Sbjct: 105 KISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTR 164

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            +++      K L   LR  +     ++           IA +L+    +V  M      
Sbjct: 165 TIRLPIHVV-KELNIYLRTAR----ELSQRLDHEPTPEEIALELDRPVDDVTKMLRLNER 219

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++  I           D L   H+   +   + +   + R  L   +  LNP+++ +
Sbjct: 220 ISSVDTPI--GGDGDKALLDILPDSHNADPEFSTQDD---DIRESLLNWLDELNPKQKEV 274

Query: 243 FEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 275 LARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVKQ 321


>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 =  230 bits (586), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 130/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 348 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 407

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 408 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 465

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 466 KLNRISRQMLQEMGREPSPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 520

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 521 SHLGDFI---EDTTLELPLDSATSESLRSATHEVLAGLTAREAKVLRMRFGIDMNTDHTL 577

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 578 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 613


>gi|187736115|ref|YP_001878227.1| RNA polymerase, sigma 70 subunit, RpoD family [Akkermansia
           muciniphila ATCC BAA-835]
 gi|187426167|gb|ACD05446.1| RNA polymerase, sigma 70 subunit, RpoD family [Akkermansia
           muciniphila ATCC BAA-835]
          Length = 688

 Score =  230 bits (586), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 74/262 (28%), Positives = 124/262 (47%), Gaps = 18/262 (6%)

Query: 30  EKQEE----YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
              E       L K  RE     A   +V ++LRLV+ IA  Y   GL   +++ EGN+G
Sbjct: 426 TADEMGDAYQELRKWLREA--RRAKDEMVEANLRLVISIAKKYTNRGLSFLDLIQEGNMG 483

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           LM+AV+KF+  RG++ +TY+ WWI+ A+   I      ++I            L R++  
Sbjct: 484 LMKAVEKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLMRVQKQ 541

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           L         PE    IA+++++    V S+        SL A +   D + + + D++ 
Sbjct: 542 LVQEYGREPTPE---EIAEEIHLPVERVRSVLKMAQQPISLQAPV--GDSDDTSFGDFI- 595

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFE 263
              D   +  +E+      +  +   +  L  RER + E R      +P TLE +  +F 
Sbjct: 596 --EDKAAENPMEEASFSFLKEKIKDVLDTLTDREREVIEQRFGLRDGSPRTLEEVGRQFS 653

Query: 264 VSRERVRQIEARAFKKVQESIQ 285
           V+RER+RQIEA+A +K++   +
Sbjct: 654 VTRERIRQIEAKALRKLRHPTR 675


>gi|34581080|ref|ZP_00142560.1| RNA polymerase sigma factor [Rickettsia sibirica 246]
 gi|229587226|ref|YP_002845727.1| RNA polymerase sigma factor RpoD [Rickettsia africae ESF-5]
 gi|28262465|gb|EAA25969.1| RNA polymerase sigma factor [Rickettsia sibirica 246]
 gi|228022276|gb|ACP53984.1| RNA polymerase sigma factor [Rickettsia africae ESF-5]
          Length = 634

 Score =  230 bits (586), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 70/247 (28%), Positives = 121/247 (48%), Gaps = 11/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E   L A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 375 ERQTLQAKKDMIEANLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 434

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    + + +          I
Sbjct: 435 TYATWWIRQAITRAIADQARTIRIPVH-----MIETINKILRTSRQMLNELGYEPTATEI 489

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A +L++   +V  +        SL   +   D +  Q  D++    D      I+   + 
Sbjct: 490 ANRLSMPLDKVRKVMKIAKEPISLENPVGD-DSDGGQLGDFI---EDKNAVAPIDAAIQS 545

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R + TR ++ L PRE R+   R         TLE +  +F+V+RER+RQIE++A +K+
Sbjct: 546 NLREVTTRVLATLTPREERVLRMRFGIGMNTDHTLEEVGQQFKVTRERIRQIESKALRKL 605

Query: 281 QESIQKQ 287
           Q  I+ +
Sbjct: 606 QHPIRSK 612


>gi|294634612|ref|ZP_06713146.1| RNA polymerase sigma factor RpoD [Edwardsiella tarda ATCC 23685]
 gi|291091942|gb|EFE24503.1| RNA polymerase sigma factor RpoD [Edwardsiella tarda ATCC 23685]
          Length = 613

 Score =  230 bits (586), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 71/276 (25%), Positives = 131/276 (47%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +H+I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 344 LHQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 403

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 404 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 461

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 462 KLNRISRQMLQEMGREPTPE---ELAERMMMPEDKIRKVLKIAKEPISMETPI--GDDED 516

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 517 SHLGDFI---EDTTLELPLDSATSESLRSATRDVLAGLTAREAKVLRMRFGIDMNTDHTL 573

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 574 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 609


>gi|313159603|gb|EFR58965.1| putative RNA polymerase sigma factor RpoD [Alistipes sp. HGB5]
          Length = 286

 Score =  230 bits (586), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 75/287 (26%), Positives = 142/287 (49%), Gaps = 12/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI K  ++  +EE  LA+R ++ GD  A  +L  ++LR VV
Sbjct: 5   KITKSITNRESASLDKYLQEIGKEELITVEEEVELAQRIKK-GDQEALEKLTKANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 64  SVAKQYQNQGLSLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    NQ      + +     +   +    PE    +A +L + + +V         
Sbjct: 124 IVRLP--LNQVGSLNKINKAFARFEQEHERTPSPE---ELATELELPKEKVTDTLRVAGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     + NS    D LV          +  E        + R++  L  RER I
Sbjct: 179 HVSVDAPFADGEDNS--LLDVLVNPDSPNADRGLINESLSTE---VDRALETLTDRERDI 233

Query: 243 FEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +         +TLE +  +F+++RERVRQI+ +A ++++ S + ++
Sbjct: 234 IKYFFGIGTSEMTLEEIGEKFDLTRERVRQIKEKAIRRLRHSSRSKL 280


>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 =  230 bits (586), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 65/250 (26%), Positives = 119/250 (47%), Gaps = 12/250 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 369 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 428

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 429 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPSPE--- 483

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + E ++  +        S+   I   D   S   D++    D   ++ ++   
Sbjct: 484 ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDTTLELPLDSAT 538

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            ++ +N     ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 539 GESLKNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 598

Query: 279 KVQESIQKQV 288
           K++   + ++
Sbjct: 599 KLRHPSRSEI 608


>gi|86608944|ref|YP_477706.1| sigma-70 family RNA polymerase sigma factor [Synechococcus sp.
           JA-2-3B'a(2-13)]
 gi|86557486|gb|ABD02443.1| RNA polymerase sigma-70 factor family [Synechococcus sp.
           JA-2-3B'a(2-13)]
          Length = 320

 Score =  230 bits (586), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 77/292 (26%), Positives = 143/292 (48%), Gaps = 15/292 (5%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLR 59
           NR   + +   E  +  ++ E+ + P+L  ++E  L +   E G     A   LV ++LR
Sbjct: 31  NRATQASL--SEDSVGVFLREMARYPLLNAEQEVKLGRLIAEGGAAGERAKRELVRANLR 88

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           LVV IA  Y   G+P  +++ EG IGL++A +KF+ ERG++ +TY+ WWI+  +   +  
Sbjct: 89  LVVSIAKKYLNRGVPFLDLIQEGTIGLIRAAEKFEYERGYKFSTYAYWWIRQGITRAVAN 148

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
              LV+I     +K     L ++K   + +T+   +      IA+ L +S  ++ ++   
Sbjct: 149 QGRLVRIPVHMVEK-----LNQVKRIRRELTETLNRRPTQAEIAEALEISPDKLDALLTL 203

Query: 180 L-AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           L AG ++L+       +   +    +    D        + +       L   +  L+PR
Sbjct: 204 LEAGRQTLSLHTPVGKEEDRELMQLI---EDANSLTPESQMDLHLLSAQLEEMLEQLSPR 260

Query: 239 ERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           E+ I + R   ++    TL  +   F +SRERVRQI+ARA +K++   ++++
Sbjct: 261 EQEILKLRYGLKDGHLHTLSEIGQLFGLSRERVRQIQARAMRKLRHPRRQEI 312


>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 =  230 bits (586), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 67/251 (26%), Positives = 119/251 (47%), Gaps = 12/251 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 379 EQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 438

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            L R+   L         PE    +
Sbjct: 439 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQLLQEMGREATPE---EL 493

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+++ + E ++  +        S+   I   D + S   D++    D   ++ ++    +
Sbjct: 494 AERMGMPEDKIRKVLKIAKEPISMETPI--GDDDDSHLGDFI---EDSTLELPLDSATAQ 548

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + +      +  L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 549 SLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 608

Query: 281 QESIQKQVELS 291
           +   + +   S
Sbjct: 609 RHPSRSETLRS 619


>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 =  230 bits (586), Expect = 2e-58,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 380 RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 439

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 440 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 494

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 495 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTVAPADAALHASMRD 549

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 550 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 609

Query: 285 QKQ 287
           +  
Sbjct: 610 RSD 612


>gi|126728120|ref|ZP_01743936.1| RNA polymerase sigma-32 factor [Sagittula stellata E-37]
 gi|126711085|gb|EBA10135.1| RNA polymerase sigma-32 factor [Sagittula stellata E-37]
          Length = 277

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 100/269 (37%), Positives = 169/269 (62%), Gaps = 6/269 (2%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K  +L+ + E  LA  +R+  D +A HRL+ +++RL + +A  ++ YG P+++++ E  
Sbjct: 1   MKAELLDAETELRLAYAWRDEKDEAALHRLIQAYMRLAISMAAKFKRYGAPMNDLIQEAG 60

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           +GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFN+RR++
Sbjct: 61  LGLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKALFFNMRRVQ 120

Query: 144 GHLQAITD----NNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSS 198
             L+             +    IA ++ V   +V  M  RL+G D SLNA   S +    
Sbjct: 121 ARLEREAQAIGAQLDSHQLRHMIASEIGVPLRDVEMMEGRLSGSDFSLNA-TQSVEDEGR 179

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           +W D L  D     +++    + +  R+ L ++M  LN RER I   R+L++ P TLE+L
Sbjct: 180 EWIDTLEDDSAHGAEIVENSHDTECLRDWLVQAMGSLNERERFIVRERKLRDEPRTLESL 239

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +E  +S+ERVRQ+EA AF K++++++ Q
Sbjct: 240 GNELGLSKERVRQLEAAAFGKMRKALEAQ 268


>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 =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 70/274 (25%), Positives = 127/274 (46%), Gaps = 14/274 (5%)

Query: 22  EIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           EI +   L   +   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++
Sbjct: 355 EIERQTNLTVSQIREVCERISAGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLI 414

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L
Sbjct: 415 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKL 472

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
            R+   +         PE    +A+++ + E ++  +        S+   I   D + S 
Sbjct: 473 NRISRQMLQEMGREASPE---ELAERMGMPEDKIRKVLKIAKEPISMETPI--GDDDDSH 527

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLEN 257
             D++    D   ++ ++    ++ +      +  L PRE ++   R   +     TLE 
Sbjct: 528 LGDFI---EDSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEE 584

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           +  +F+V+RER+RQIEA+A +K++   + +   S
Sbjct: 585 VGKQFDVTRERIRQIEAKALRKLRHPSRSETLRS 618


>gi|325478784|gb|EGC81895.1| RNA polymerase sigma factor RpoD [Anaerococcus prevotii
           ACS-065-V-Col13]
          Length = 604

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 72/244 (29%), Positives = 120/244 (49%), Gaps = 12/244 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +A  +L  ++LRLVV IA  Y G G+   +++ EGN+GLM+AV K+D  RGF+ +TY+ 
Sbjct: 366 KAAKQKLAETNLRLVVSIAKKYVGRGMSFLDLIQEGNMGLMKAVDKYDYNRGFKFSTYAT 425

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I     +      L R++  L      +   E    IA+++
Sbjct: 426 WWIRQAITRAIADQARTIRIPVHMVE--TINKLVRIQRQLVQDLGRDPSNE---EIAEQM 480

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   +++ S   D++  D         E       R 
Sbjct: 481 GIEVEKVQEIRKISQEPVSLETPI--GEEDDSHLGDFIEDD---TAIDPGEAANYTMLRE 535

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +S L  RE+R+ + R       P TLE +  EF+V+RER+RQIEA+A +K++   
Sbjct: 536 QLNDVLSCLGAREKRVLQLRFGLIDGTPRTLEEVGKEFDVTRERIRQIEAKALRKLKSPN 595

Query: 285 QKQV 288
           + ++
Sbjct: 596 KSEL 599



 Score = 41.3 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 14/41 (34%), Positives = 24/41 (58%), Gaps = 2/41 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRL 53
           +  +  Y+ EI K+ +L   EE +LA+R  E G++ A  +L
Sbjct: 118 DDPVKMYLKEIGKVSLLTATEEIILARRM-EMGEI-ARKKL 156


>gi|291515538|emb|CBK64748.1| RNA polymerase sigma factor, sigma-70 family [Alistipes shahii WAL
           8301]
          Length = 286

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 75/287 (26%), Positives = 142/287 (49%), Gaps = 12/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI K  ++  +EE  LA+R ++ GD  A  +L  ++LR VV
Sbjct: 5   KITKSITNRESASLDKYLQEIGKEELITVEEEVELAQRIKK-GDQEALEKLTKANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 64  SVAKQYQNQGLSLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    NQ      + +     +   +    PE    +A +L + + +V         
Sbjct: 124 IVRLP--LNQVGSLNKINKAFARFEQEHERTPSPE---ELATELELPKEKVTDTLRVAGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     + NS    D LV          +  E        + R++  L  RER I
Sbjct: 179 HVSVDAPFADGEDNS--LLDVLVNPDSPNADRGLINESLSTE---VDRALETLTERERDI 233

Query: 243 FEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +         +TLE +  +F+++RERVRQI+ +A ++++ S + ++
Sbjct: 234 IKYFFGIGTSEMTLEEIGEKFDLTRERVRQIKEKAIRRLRHSSRSKL 280


>gi|304409306|ref|ZP_07390926.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica OS183]
 gi|307303664|ref|ZP_07583417.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica BA175]
 gi|304351824|gb|EFM16222.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica OS183]
 gi|306912562|gb|EFN42985.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica BA175]
 gi|315266575|gb|ADT93428.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella baltica OS678]
          Length = 611

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 70/269 (26%), Positives = 126/269 (46%), Gaps = 22/269 (8%)

Query: 32  QEEYVLA--------KRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           +EE  LA        +R    E     A   +V ++LRLV+ IA  Y   GL   +++ E
Sbjct: 346 EEETGLAISAIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 405

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           GNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R
Sbjct: 406 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNR 463

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           +   +         PE    +A+++ + E ++  +        S+   I   D   S   
Sbjct: 464 ISRQMLQEMGREPSPE---ELAERMMMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLG 518

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLS 259
           D++    D   ++ ++    ++ +N     ++ L  RE ++   R   +     TLE + 
Sbjct: 519 DFI---EDTTLELPLDSATSESLKNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVG 575

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +F+V+RER+RQIEA+A +K++   + ++
Sbjct: 576 KQFDVTRERIRQIEAKALRKLRHPSRSEI 604


>gi|229520830|ref|ZP_04410252.1| RNA polymerase sigma factor RpoS [Vibrio cholerae TM 11079-80]
 gi|229342063|gb|EEO07059.1| RNA polymerase sigma factor RpoS [Vibrio cholerae TM 11079-80]
          Length = 335

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 83/288 (28%), Positives = 138/288 (47%), Gaps = 13/288 (4%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
            R+              Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLV
Sbjct: 45  AREEFDASAKSLDATQMYLSEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLV 103

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           VKI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++   
Sbjct: 104 VKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQT 163

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             +++       +      R    L    D+   PE    IA +L+    +V  M     
Sbjct: 164 RTIRLPIHV--VKELNIYVRTARELSQRLDHEPTPE---EIALELDRPVDDVTKMLRLNE 218

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              S++  I           D L   H+   +   + +   + R  L   +  LNP+++ 
Sbjct: 219 RISSVDTPI--GGDGDKALLDILPDSHNADPEFSTQDD---DIRESLLNWLDELNPKQKE 273

Query: 242 IFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +   R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 274 VLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVKQ 321


>gi|146281946|ref|YP_001172099.1| RNA polymerase sigma factor RpoS [Pseudomonas stutzeri A1501]
 gi|145570151|gb|ABP79257.1| sigma factor RpoS [Pseudomonas stutzeri A1501]
          Length = 332

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 83/278 (29%), Positives = 140/278 (50%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 64  YLNEIGFSPLLTPEEEVHFA-RLAQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 122

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 123 VEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 181

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++  + +K       ++ +N R+   D SL           
Sbjct: 182 LRAAR-ELTQKLDHEPSPEEIANLLEKPVGEVKRMLGLNERVTSVDVSL------GPDTD 234

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L+  ++       + + +S L+ ++R +   R         TL
Sbjct: 235 KTLLDTLTDDRPTDPCELLLDDDLS---ASIDQWLSDLSEKQREVVIRRFGLRGHEASTL 291

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E +  E  ++RERVRQI+  A ++++E +++    S +
Sbjct: 292 EEVGQEIGLTRERVRQIQVEALRRLREILERNGLSSDA 329


>gi|153214922|ref|ZP_01949705.1| RNA polymerase sigma factor RpoS [Vibrio cholerae 1587]
 gi|153826929|ref|ZP_01979596.1| RNA polymerase sigma factor RpoS [Vibrio cholerae MZO-2]
 gi|153829928|ref|ZP_01982595.1| RNA polymerase sigma factor RpoS [Vibrio cholerae 623-39]
 gi|229530348|ref|ZP_04419736.1| RNA polymerase sigma factor RpoS [Vibrio cholerae 12129(1)]
 gi|254226840|ref|ZP_04920411.1| RNA polymerase sigma factor RpoS [Vibrio cholerae V51]
 gi|254291219|ref|ZP_04962015.1| RNA polymerase sigma factor RpoS [Vibrio cholerae AM-19226]
 gi|262190768|ref|ZP_06048995.1| RNA polymerase sigma factor RpoS [Vibrio cholerae CT 5369-93]
 gi|124114995|gb|EAY33815.1| RNA polymerase sigma factor RpoS [Vibrio cholerae 1587]
 gi|125620637|gb|EAZ49000.1| RNA polymerase sigma factor RpoS [Vibrio cholerae V51]
 gi|148874616|gb|EDL72751.1| RNA polymerase sigma factor RpoS [Vibrio cholerae 623-39]
 gi|149739232|gb|EDM53500.1| RNA polymerase sigma factor RpoS [Vibrio cholerae MZO-2]
 gi|150422913|gb|EDN14864.1| RNA polymerase sigma factor RpoS [Vibrio cholerae AM-19226]
 gi|229332121|gb|EEN97609.1| RNA polymerase sigma factor RpoS [Vibrio cholerae 12129(1)]
 gi|262033353|gb|EEY51864.1| RNA polymerase sigma factor RpoS [Vibrio cholerae CT 5369-93]
          Length = 335

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 82/287 (28%), Positives = 138/287 (48%), Gaps = 13/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           R+              Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVV
Sbjct: 46  REEFDASAKSLDATQMYLSEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLVV 104

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           KI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++    
Sbjct: 105 KISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTR 164

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            +++      K L   LR  +     ++           IA +L+    +V  M      
Sbjct: 165 TIRLPIHVV-KELNIYLRTAR----ELSQRLDHEPTPEEIALELDRPVDDVTKMLRLNER 219

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++  I           D L   H+   +   + +   + R  L   +  LNP+++ +
Sbjct: 220 ISSVDTPI--GGDGDKALLDILPDSHNADPEFSTQDD---DIRESLLNWLDELNPKQKEV 274

Query: 243 FEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 275 LARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVKQ 321


>gi|298247391|ref|ZP_06971196.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297550050|gb|EFH83916.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 385

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 81/293 (27%), Positives = 133/293 (45%), Gaps = 34/293 (11%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS---------------------AAHR 52
             L  Y+ E+ ++P+L  ++E  LA++  E G L                      A  R
Sbjct: 93  DTLETYLREMGRVPLLTSEQEVQLAQQI-ERGKLEQERARLLKVPPEHAIMDSAQNARDR 151

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L  ++LRLVV IA  Y G G+ +++++ EGN GLM AV+KFD  RGF+ +TY+ WWI+ A
Sbjct: 152 LTEANLRLVVSIARKYMGRGMALADLIQEGNAGLMLAVEKFDYTRGFKFSTYATWWIRQA 211

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   I      +++    ++      + RL      +     +      IA+++++S   
Sbjct: 212 INRAIANQARTIRLPVHFHE-----AVNRLHRTSSQLFQELGREPSAEEIAERMHISVDT 266

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           V  +        SL + +   D   S   D++    D       +   R   R  +   +
Sbjct: 267 VYDILEAGKQPISLESPV--GDDGDSSLGDFV---EDQVTASPADITTRNILREQIAHVL 321

Query: 233 SVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             LN RER I +     L     TL  +     +SRERVRQIEA+A +K+++S
Sbjct: 322 DELNERERHIIQYHFGFLDGKEHTLAEIGENLHLSRERVRQIEAKALRKLRQS 374


>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 =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 442 RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 501

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 502 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 556

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 557 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDNNTVAPADAALHASMRD 611

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 612 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 671

Query: 285 QKQ 287
           +  
Sbjct: 672 RSD 674


>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 =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 67/251 (26%), Positives = 119/251 (47%), Gaps = 12/251 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 384 EQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 443

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            L R+   L         PE    +
Sbjct: 444 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQLLQEMGREATPE---EL 498

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+++ + E ++  +        S+   I   D + S   D++    D   ++ ++    +
Sbjct: 499 AERMGMPEDKIRKVLKIAKEPISMETPI--GDDDDSHLGDFI---EDSTLELPLDSATAQ 553

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + +      +  L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 554 SLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 613

Query: 281 QESIQKQVELS 291
           +   + +   S
Sbjct: 614 RHPSRSETLRS 624


>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 =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 67/251 (26%), Positives = 119/251 (47%), Gaps = 12/251 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 385 EQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 444

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            L R+   L         PE    +
Sbjct: 445 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQLLQEMGREATPE---EL 499

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+++ + E ++  +        S+   I   D + S   D++    D   ++ ++    +
Sbjct: 500 AERMGMPEDKIRKVLKIAKEPISMETPI--GDDDDSHLGDFI---EDSTLELPLDSATAQ 554

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + +      +  L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 555 SLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 614

Query: 281 QESIQKQVELS 291
           +   + +   S
Sbjct: 615 RHPSRSETLRS 625


>gi|15604688|ref|NP_221206.1| RNA polymerase sigma factor RpoD [Rickettsia prowazekii str. Madrid
           E]
 gi|464670|sp|P33451|RPOD_RICPR RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|434681|gb|AAB81404.1| major sigma factor of RNA polymerase [Rickettsia prowazekii]
 gi|3861383|emb|CAA15282.1| RNA POLYMERASE SIGMA FACTOR RPOD (rpoD) [Rickettsia prowazekii]
 gi|292572521|gb|ADE30436.1| RNA polymerase sigma factor [Rickettsia prowazekii Rp22]
          Length = 635

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 70/247 (28%), Positives = 121/247 (48%), Gaps = 11/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E   L A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 376 ERQTLQAKKDMIEANLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 435

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    + + +          I
Sbjct: 436 TYATWWIRQAITRAIADQARTIRIPVH-----MIETINKILRTSRQMLNELGYEPTATEI 490

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A +L++   +V  +        SL   +   D +  Q  D++    D      I+   + 
Sbjct: 491 ANRLSMPLDKVRKVMKIAKEPISLENPVGD-DSDGGQLGDFI---EDKNAVAPIDAAIQS 546

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R + TR ++ L PRE R+   R         TLE +  +F+V+RER+RQIE++A +K+
Sbjct: 547 NLREVTTRVLATLTPREERVLRMRFGIGMNTDHTLEEVGQQFKVTRERIRQIESKALRKL 606

Query: 281 QESIQKQ 287
           Q  I+ +
Sbjct: 607 QHPIRSK 613


>gi|259416055|ref|ZP_05739975.1| RNA polymerase sigma-32 factor [Silicibacter sp. TrichCH4B]
 gi|259347494|gb|EEW59271.1| RNA polymerase sigma-32 factor [Silicibacter sp. TrichCH4B]
          Length = 292

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 106/272 (38%), Positives = 181/272 (66%), Gaps = 6/272 (2%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
               K  +L+ + E  LA  +R+H D+ A HRL+T+++RL V +A  +R YG P+++++ 
Sbjct: 13  KRAMKAELLDAETELALAYAWRDHQDVQALHRLITAYMRLAVSMASKFRRYGAPMNDLIQ 72

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           E  +GLM+A +KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFN+R
Sbjct: 73  EAGLGLMKAAEKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMR 132

Query: 141 RLKGHLQAITDNNL----KPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDK 195
           R++  L+   +++     + +    +A+++ V   +V  M+ RLAG D SLNA + S+D+
Sbjct: 133 RVQAQLEREAESDGVELDRHKLHQMVAEEIGVPLRDVEMMDGRLAGADFSLNA-VQSADE 191

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
           +  +W D L  D +   + +    +R+  R  L  +++ LN RER I   R+L+E   TL
Sbjct: 192 DGREWIDALEDDSEQAAERVAADHDRRQLREWLVTALNGLNERERFIVRERKLREESRTL 251

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+L +E  +S+ERVRQ+EA AF K+++S++ Q
Sbjct: 252 ESLGNELGLSKERVRQLEAAAFLKMRKSLEGQ 283


>gi|227536516|ref|ZP_03966565.1| RNA polymerase sigma-70 factor [Sphingobacterium spiritivorum ATCC
           33300]
 gi|300773589|ref|ZP_07083458.1| DNA-directed RNA polymerase sigma subunit RpoD [Sphingobacterium
           spiritivorum ATCC 33861]
 gi|227243593|gb|EEI93608.1| RNA polymerase sigma-70 factor [Sphingobacterium spiritivorum ATCC
           33300]
 gi|300759760|gb|EFK56587.1| DNA-directed RNA polymerase sigma subunit RpoD [Sphingobacterium
           spiritivorum ATCC 33861]
          Length = 286

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 77/288 (26%), Positives = 148/288 (51%), Gaps = 14/288 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+HEI K+ ++  +EE +LA+R RE GD  A  +L  ++LR VV
Sbjct: 5   KITQSITNRESQSLDKYLHEIGKVDLITAEEEVILAQRIRE-GDQVALEKLTKTNLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A K+FD  +GF+  +Y++WWI+ ++ + I     
Sbjct: 64  SVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETKGFKFISYAVWWIRQSILQAIAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    NQ      + +    L+   +    PE    +A  L  +  +V         
Sbjct: 124 IVRLP--LNQVGSLSKISKAFSKLEQEYEREPSPE---ELADILETTVDKVSDTLSNSGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     ++N+    D L       +  LI+    ++    + RS++ L  RER I
Sbjct: 179 HVSMDAPFVQGEENT--LLDVLENHDPDTDSSLID----ESLSEEIKRSLATLTEREREI 232

Query: 243 FEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
                     + ++LE +  +F ++RERVRQI+ +A ++++ + + ++
Sbjct: 233 IVLFFGLGSNHQLSLEEIGEKFNLTRERVRQIKDKALQRLRHTSRSKI 280


>gi|27904560|ref|NP_777686.1| RNA polymerase sigma factor RpoD [Buchnera aphidicola str. Bp
           (Baizongia pistaciae)]
 gi|31340403|sp|Q89B10|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 =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 69/267 (25%), Positives = 125/267 (46%), Gaps = 14/267 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L   +   + KR    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 349 LTIHQVKNINKRISLGEAKAKRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 408

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 409 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQI 466

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    +++++ + E ++  +        S+   I   + + S   D+L  
Sbjct: 467 LQEIGREPTPE---ELSERMLIPEDKIRKVLKIAKEPISMETPI--GEDDDSHLGDFL-- 519

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   ++ ++     + R+     +S L  RE ++   R   +     TLE +  +F+V
Sbjct: 520 -EDTNIELPLDSATSASLRSATKNVLSGLTTREAKVLRMRFGIDMNTDHTLEEVGKQFDV 578

Query: 265 SRERVRQIEARAFKKVQESIQKQVELS 291
           +RER+RQIEA+A +K++   + ++  S
Sbjct: 579 TRERIRQIEAKALRKLRHPSRSEILRS 605


>gi|115374575|ref|ZP_01461855.1| sigma-E factor [Stigmatella aurantiaca DW4/3-1]
 gi|310823765|ref|YP_003956123.1| RNA polymerase sigma factor [Stigmatella aurantiaca DW4/3-1]
 gi|115368445|gb|EAU67400.1| sigma-E factor [Stigmatella aurantiaca DW4/3-1]
 gi|309396837|gb|ADO74296.1| RNA polymerase sigma factor [Stigmatella aurantiaca DW4/3-1]
          Length = 366

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 111/276 (40%), Positives = 177/276 (64%), Gaps = 6/276 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             L  Y+ E+ + P+L+++EEY LAK+Y++ GD+ AA+RLV S+LRLVVK+A  Y    L
Sbjct: 85  DPLQAYMAEVTRHPLLKREEEYALAKQYQQTGDVRAAYRLVASNLRLVVKLAHEYHRNPL 144

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + ++V EGNIGLMQAVKK+DPERG +L++Y+ WWI+A +  YI+ +W +VK+GTT  Q+
Sbjct: 145 SLLDLVQEGNIGLMQAVKKYDPERGVKLSSYAAWWIRAYILRYIMDNWKMVKLGTTEAQR 204

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINS 192
           +LFF LR+ +  L A             +A++LNV+E +V+ M+ RL  DE S++A +  
Sbjct: 205 KLFFKLRQEQDKLIA----QGFEPNPKLLAERLNVTEQDVVEMDQRLGHDEVSIDAPVGD 260

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            +  +S+    L     G E+ L  +E ++  R  L      L  +ER IFE+R   + P
Sbjct: 261 -ESRASRADRLLPSSAVGAEERLGNEELKELFREKLAEFAQTLEGKERFIFESRLTADEP 319

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TL+++  ++ VSRER RQIEA    +++E +++++
Sbjct: 320 LTLQDIGDKYGVSRERARQIEAALINRMREFMRERI 355


>gi|297180571|gb|ADI16783.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [uncultured gamma proteobacterium HF0010_11B23]
          Length = 605

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 73/256 (28%), Positives = 120/256 (46%), Gaps = 14/256 (5%)

Query: 37  LAKRY--REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           L KR      G L A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+
Sbjct: 353 LNKRINKAYRGLLRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFE 412

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             RG++ +TY+ WWI+ A+   I      ++I            L RL   +        
Sbjct: 413 YRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRLSRQMMQEIGREP 470

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            PE    ++K+L++ E ++  +        S+   I   D   S   D+L    D     
Sbjct: 471 TPE---EMSKRLDIPEDKMRKVMKIAKEPISMETPI--GDDEDSNLGDFL---EDTSINS 522

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQI 272
            I+    +  ++     ++ L  RE ++   R      N  TLE +  +F+V+RER+RQI
Sbjct: 523 PIDDASIRGLKDATDEILASLTAREAKVLRMRFGIGMNNDHTLEEVGKQFDVTRERIRQI 582

Query: 273 EARAFKKVQESIQKQV 288
           EA+A +K++   +  V
Sbjct: 583 EAKALRKLRHPTRSDV 598


>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 =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 127/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVL--AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +  I +   L  Q+   +  A    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 360 LANIEQHTNLTIQQMREICDAVSRGEQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 419

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 420 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 477

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D + 
Sbjct: 478 KLNRISRQMLQEMGREATPE---ELAERMGMPEDKIRKVLKIAKEPISMETPI--GDDDD 532

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ +      +  L PRE ++   R   +     TL
Sbjct: 533 SHLGDFI---EDSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTL 589

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +   S
Sbjct: 590 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRS 625


>gi|293391709|ref|ZP_06636043.1| DNA-directed RNA polymerase sigma subunit RpoD [Aggregatibacter
           actinomycetemcomitans D7S-1]
 gi|290952243|gb|EFE02362.1| DNA-directed RNA polymerase sigma subunit RpoD [Aggregatibacter
           actinomycetemcomitans D7S-1]
          Length = 616

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 118/247 (47%), Gaps = 12/247 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 376 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 435

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            L R+   +         PE    +A+++
Sbjct: 436 WWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREASPE---ELAERM 490

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D   ++ ++    ++ + 
Sbjct: 491 GMPEDKIRKVLKIAKEPISMETPI--GDDDDSHLGDFI---EDSTLELPLDSATVQSLKA 545

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                +  L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 546 ATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 605

Query: 285 QKQVELS 291
           + +   S
Sbjct: 606 RSETLRS 612


>gi|167583913|ref|ZP_02376301.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia ubonensis Bu]
          Length = 681

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 440 RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 499

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 500 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 554

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 555 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDNNTVAPADAALHASMRD 609

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 610 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 669

Query: 285 QKQ 287
           +  
Sbjct: 670 RSD 672


>gi|157829159|ref|YP_001495401.1| RNA polymerase sigma factor RpoD [Rickettsia rickettsii str.
           'Sheila Smith']
 gi|165933888|ref|YP_001650677.1| RNA polymerase sigma factor RpoD [Rickettsia rickettsii str. Iowa]
 gi|157801640|gb|ABV76893.1| RNA polymerase sigma factor RpoD [Rickettsia rickettsii str.
           'Sheila Smith']
 gi|165908975|gb|ABY73271.1| RNA polymerase sigma factor [Rickettsia rickettsii str. Iowa]
          Length = 634

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 70/247 (28%), Positives = 121/247 (48%), Gaps = 11/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E   L A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 375 ERQTLQAKKDMIEANLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 434

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    + + +          I
Sbjct: 435 TYATWWIRQAITRAIADQARTIRIPVH-----MIETINKILRTSRQMLNELGYEPTATEI 489

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A +L++   +V  +        SL   +   D +  Q  D++    D      I+   + 
Sbjct: 490 ANRLSMPLDKVRKVMKIAKEPISLENPVGD-DSDGGQLGDFI---EDKNAVAPIDAAIQS 545

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R + TR ++ L PRE R+   R         TLE +  +F+V+RER+RQIE++A +K+
Sbjct: 546 NLREVTTRVLATLTPREERVLRMRFGIGMNTDHTLEEVGQQFKVTRERIRQIESKALRKL 605

Query: 281 QESIQKQ 287
           Q  I+ +
Sbjct: 606 QHPIRSK 612


>gi|261210105|ref|ZP_05924403.1| RNA polymerase sigma factor RpoS [Vibrio sp. RC341]
 gi|260840870|gb|EEX67412.1| RNA polymerase sigma factor RpoS [Vibrio sp. RC341]
          Length = 336

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 81/288 (28%), Positives = 138/288 (47%), Gaps = 13/288 (4%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
            R+              Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLV
Sbjct: 45  AREEFDASAKSLDATQMYLSEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLV 103

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           VKI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++   
Sbjct: 104 VKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQT 163

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             +++      K L   LR  +     ++           IA +L+    +V  M     
Sbjct: 164 RTIRLPIHVV-KELNIYLRTAR----ELSQRLDHEPTPEEIALELDRPVDDVTKMLRLNE 218

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              S++  I           D L   ++   +   + +   + R  L   +  LNP+++ 
Sbjct: 219 RISSVDTPI--GGDGDKALLDILPDSNNADPEFSTQDD---DIRESLLNWLDELNPKQKE 273

Query: 242 IFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +   R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 274 VLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVKQ 321


>gi|227486750|ref|ZP_03917066.1| DNA-directed RNA polymerase sigma subunit RpoD [Anaerococcus
           lactolyticus ATCC 51172]
 gi|227235220|gb|EEI85235.1| DNA-directed RNA polymerase sigma subunit RpoD [Anaerococcus
           lactolyticus ATCC 51172]
          Length = 601

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 82/293 (27%), Positives = 137/293 (46%), Gaps = 19/293 (6%)

Query: 4   KNMSIIVNGEIGLSRYI--HEIRKIPMLEKQE--EYVLAKRYREH--GDLSAAHRLVTSH 57
           +N  I+ + E     YI       + ML ++E  E  L K+ +        A  +L  ++
Sbjct: 315 RNRKILSDDEASYLSYIIDQRNMSLKMLNREEFNEDEL-KKLKVDVLKSQRAKEKLAETN 373

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVV IA  Y G G+   +++ EGN+GLM+AV K+D  RGF+ +TY+ WWI+ A+   I
Sbjct: 374 LRLVVSIAKKYVGRGMSFLDLIQEGNMGLMKAVDKYDYNRGFKFSTYATWWIRQAITRAI 433

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
                 ++I     +      L R++  L      +   E++  I   + +   +V  + 
Sbjct: 434 ADQARTIRIPVHMVE--TINKLVRIQRQLVQDLGRDPSNEEIADI---MGIEVEKVSEIR 488

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                  SL   I   +++ S   D++  D         E       R  L   +S L  
Sbjct: 489 KIAQEPVSLETPI--GEEDDSHLGDFIEDD---TAIDPGEAANYTMLREQLNDVLSCLGA 543

Query: 238 RERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           RE+R+ + R       P TLE +  EF+V+RER+RQIEA+A +K++   + ++
Sbjct: 544 REKRVLQLRFGLIDGTPRTLEEVGKEFDVTRERIRQIEAKALRKLKSPNKSEL 596



 Score = 40.2 bits (93), Expect = 0.39,   Method: Composition-based stats.
 Identities = 12/38 (31%), Positives = 22/38 (57%), Gaps = 1/38 (2%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAA 50
           +  +  Y+ EI K+ +L   EE +LA+R  E G+++  
Sbjct: 115 DDPVKMYLKEIGKVDLLTATEEIILARRM-ETGEIAHK 151


>gi|221212356|ref|ZP_03585333.1| RNA polymerase sigma factor RpoD [Burkholderia multivorans CGD1]
 gi|221167455|gb|EED99924.1| RNA polymerase sigma factor RpoD [Burkholderia multivorans CGD1]
          Length = 682

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 441 RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 500

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 501 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 555

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 556 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTVAPADAALHASMRD 610

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 611 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 670

Query: 285 QKQ 287
           +  
Sbjct: 671 RSD 673


>gi|83746506|ref|ZP_00943557.1| RpoD [Ralstonia solanacearum UW551]
 gi|83726837|gb|EAP73964.1| RpoD [Ralstonia solanacearum UW551]
          Length = 391

 Score =  230 bits (586), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 68/247 (27%), Positives = 115/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 146 ERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 205

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T N   P     +
Sbjct: 206 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGNEPDPAT---L 260

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+ + E ++  +        S+   I   D + S   D++    D       E     
Sbjct: 261 AEKMEMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTLAPAEAALHG 315

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 316 SMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKL 375

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 376 RHPSRSD 382


>gi|325287834|ref|YP_004263624.1| RpoD subfamily RNA polymerase sigma 70 subunit [Cellulophaga lytica
           DSM 7489]
 gi|324323288|gb|ADY30753.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cellulophaga
           lytica DSM 7489]
          Length = 287

 Score =  229 bits (585), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 74/276 (26%), Positives = 143/276 (51%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ +I KI ++   EE  LA++ R  GD +A  +L  ++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQDISKIDLITANEEVELAQKIR-AGDEAALEKLTNANLRFVVSVAKQYQNQGLK 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + +     +V++        
Sbjct: 76  LPDLINEGNVGLVKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNK---- 131

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
              ++ ++K     +   + +P     IAK+L +S SEV           S++A     +
Sbjct: 132 -IGSINKIKKAFSYLEQTHERPPSAEEIAKELELSVSEVKQSMKNSGRHVSMDAPFK--E 188

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP-- 252
              S   D + Y          EK   ++    + R++  L+PRE  + +      +   
Sbjct: 189 GEDSNLYDVIKYGESPNPD---EKLMHQSLNTEINRALETLSPREADVVKLYYGIGDKHS 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TLE +   F+++RERVRQI  +A +K++ + + ++
Sbjct: 246 MTLEEIGQIFDLTRERVRQIREKAIRKLKHNSRSKI 281


>gi|301169248|emb|CBW28845.1| RNA polymerase, sigma 70 (sigma D) factor [Haemophilus influenzae
           10810]
          Length = 629

 Score =  229 bits (585), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 67/251 (26%), Positives = 119/251 (47%), Gaps = 12/251 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 385 EQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 444

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            L R+   L         PE    +
Sbjct: 445 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQLLQEMGREATPE---EL 499

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+++ + E ++  +        S+   I   D + S   D++    D   ++ ++    +
Sbjct: 500 AERMGMPEDKIRKVLKIAKEPISMETPI--GDDDDSHLGDFI---EDSTLELPLDSATAQ 554

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + +      +  L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 555 SLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 614

Query: 281 QESIQKQVELS 291
           +   + +   S
Sbjct: 615 RHPSRSETLRS 625


>gi|327404710|ref|YP_004345548.1| RpoD subfamily RNA polymerase sigma-70 subunit [Fluviicola
           taffensis DSM 16823]
 gi|327320218|gb|AEA44710.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Fluviicola
           taffensis DSM 16823]
          Length = 289

 Score =  229 bits (585), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 76/276 (27%), Positives = 145/276 (52%), Gaps = 11/276 (3%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI ++ ++  +EE  LAKR +  GD  A  RL  ++LR VV ++  Y+  GL 
Sbjct: 17  SLDKYLQEIGRVELITAEEEVELAKRIK-AGDKRALERLTKANLRFVVSVSKQYQNQGLS 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     +V++    N+  
Sbjct: 76  LPDLINEGNLGLIKAAERFDETRGFKFISYAVWWIRQSILQALAEQARIVRLP--LNKIG 133

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               + R    L+ + +   +P     +A+ L  S  +V       A   S++A +   D
Sbjct: 134 TINKINRAYSELEQVYE---RPPSADELAEFLECSVEDVRQSLANTARHLSMDAPLVDGD 190

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV- 253
           ++SS   D L  D     +  + KE     R  + RS+S L+ RE  +            
Sbjct: 191 ESSSSMYDVLPNDALPSPENELNKESL---RKEIERSLSSLSGREGDVVRLYYGLNGKHA 247

Query: 254 -TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 248 LTLEEIGDLFDLTRERVRQIKEKAIRRLKHTSRSRM 283


>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|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]
          Length = 682

 Score =  229 bits (585), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 441 RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 500

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 501 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 555

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 556 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTVAPADAALHASMRD 610

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 611 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 670

Query: 285 QKQ 287
           +  
Sbjct: 671 RSD 673


>gi|16127277|ref|NP_421841.1| RNA polymerase sigma factor RpoD [Caulobacter crescentus CB15]
 gi|1710678|sp|P52324|RPOD_CAUCR RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|1079588|gb|AAA82054.1| RNA polymerase principal sigma factor [Caulobacter crescentus CB15]
 gi|13424691|gb|AAK25009.1| RNA polymerase sigma factor RpoD [Caulobacter crescentus CB15]
 gi|1585612|prf||2201399A sigma73 factor
          Length = 652

 Score =  229 bits (585), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 70/246 (28%), Positives = 117/246 (47%), Gaps = 12/246 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 408 EREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 467

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    + +     +      +
Sbjct: 468 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREPTPEEL 522

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+KL +   +V  +        SL   I   D+  S   D++    D    + I+   + 
Sbjct: 523 AEKLAMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAILPIDAAIQS 577

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 578 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKL 637

Query: 281 QESIQK 286
           +   + 
Sbjct: 638 KHPSRS 643


>gi|325518128|gb|EGC97914.1| RNA polymerase sigma factor RpoD [Burkholderia sp. TJI49]
          Length = 682

 Score =  229 bits (585), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 441 RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 500

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 501 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 555

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 556 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDNNTVAPADAALHASMRD 610

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 611 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 670

Query: 285 QKQ 287
           +  
Sbjct: 671 RSD 673


>gi|27382460|ref|NP_773989.1| RNA polymerase sigma factor RpoD [Bradyrhizobium japonicum USDA
           110]
 gi|1742976|emb|CAA67902.1| primary sigma factor [Bradyrhizobium japonicum]
 gi|27355631|dbj|BAC52614.1| primary sigma factor [Bradyrhizobium japonicum USDA 110]
          Length = 719

 Score =  229 bits (585), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 74/273 (27%), Positives = 128/273 (46%), Gaps = 17/273 (6%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAH---RLVTSHLRLVVKIAMGYRGYGLPI 75
           HE+ ++  L   E     K     + G+  A      +V ++LRLV+ IA  Y   GL  
Sbjct: 448 HEVHQLAALTGLEIVEFRKIVHSVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQF 507

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +
Sbjct: 508 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----M 562

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + ++    + + +   +      +A+KL +   +V  +        SL   +   D+
Sbjct: 563 IETINKIVRTSRQMLNEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPLSLETPV--GDE 620

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPV 253
             S   D++    D    + I+   + N R   TR ++ L PRE R+   R         
Sbjct: 621 EDSHLGDFI---EDKNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDH 677

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 678 TLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 710


>gi|308048570|ref|YP_003912136.1| RNA polymerase, sigma 38 subunit, RpoS [Ferrimonas balearica DSM
           9799]
 gi|307630760|gb|ADN75062.1| RNA polymerase, sigma 38 subunit, RpoS [Ferrimonas balearica DSM
           9799]
          Length = 328

 Score =  229 bits (585), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 81/271 (29%), Positives = 134/271 (49%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R +      + +R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 59  YLSEIGFSPLLTAEEEVYYARRAQRD-CAKSRNRMIESNLRLVVKIARRYNNRGLALLDL 117

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 118 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 176

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            IA KL+    +V  M        S++  I     +  
Sbjct: 177 LRTAR----ELAHTLDHEPTAEEIAMKLDKPVEDVSRMLKLNEKISSVDTPI--GGDSDK 230

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D +  D     +V   + +  +    + R +  LN ++R +   R   L   P TLE
Sbjct: 231 ALLDVIADDDRVCPEV---QAQDDDINGSVVRWLGELNSKQREVLARRFGLLGYEPSTLE 287

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+  A ++++E I  Q
Sbjct: 288 DVGREIGLTRERVRQIQVEALRRLRELIGAQ 318


>gi|170736023|ref|YP_001777283.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia cenocepacia
           MC0-3]
 gi|169818211|gb|ACA92793.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia cenocepacia
           MC0-3]
          Length = 683

 Score =  229 bits (585), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 442 RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 501

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 502 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 556

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 557 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTVAPADAALHASMRD 611

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 612 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 671

Query: 285 QKQ 287
           +  
Sbjct: 672 RSD 674


>gi|51474026|ref|YP_067783.1| RNA polymerase sigma factor RpoD [Rickettsia typhi str. Wilmington]
 gi|81389911|sp|Q68VQ5|RPOD_RICTY RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|51460338|gb|AAU04301.1| RNA polymerase sigma factor RpoD [Rickettsia typhi str. Wilmington]
          Length = 635

 Score =  229 bits (585), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 70/247 (28%), Positives = 121/247 (48%), Gaps = 11/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E   L A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 376 ERQTLQAKKDMIEANLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 435

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    + + +          I
Sbjct: 436 TYATWWIRQAITRAIADQARTIRIPVH-----MIETINKILRTSRQMLNELGYEPTATEI 490

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A +L++   +V  +        SL   +   D +  Q  D++    D      I+   + 
Sbjct: 491 ANRLSMPLDKVRKVMKIAKEPISLENPVGD-DSDGGQLGDFI---EDKNAVAPIDAAIQS 546

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R + TR ++ L PRE R+   R         TLE +  +F+V+RER+RQIE++A +K+
Sbjct: 547 NLREVTTRVLATLTPREERVLRMRFGIGMNTDHTLEEVGQQFKVTRERIRQIESKALRKL 606

Query: 281 QESIQKQ 287
           Q  I+ +
Sbjct: 607 QHPIRSK 613


>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 =  229 bits (585), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 64/249 (25%), Positives = 115/249 (46%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 363 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 422

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 423 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREATPE--- 477

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + E  +  +        S+   I   D   S   D++    D    + ++   
Sbjct: 478 ELAERMMMPEDRIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDTTLSLPVDAAT 532

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
           + + +      ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 533 KDSLKGATDDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 592

Query: 279 KVQESIQKQ 287
           K++   + +
Sbjct: 593 KLRHPSRSE 601


>gi|294139649|ref|YP_003555627.1| RNA polymerase sigma-70 factor [Shewanella violacea DSS12]
 gi|7388082|sp|O24744|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 =  229 bits (585), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 66/250 (26%), Positives = 119/250 (47%), Gaps = 12/250 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 368 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 427

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 428 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPTPE--- 482

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + E ++  +        S+   I   D   S   D++    D   ++ ++   
Sbjct: 483 ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDTTLELPLDSAT 537

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            ++ RN     ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 538 GESLRNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 597

Query: 279 KVQESIQKQV 288
           K++   + ++
Sbjct: 598 KLRHPSRSEI 607


>gi|157804249|ref|YP_001492798.1| RNA polymerase sigma factor RpoD [Rickettsia canadensis str.
           McKiel]
 gi|157785512|gb|ABV74013.1| RNA polymerase sigma factor RpoD [Rickettsia canadensis str.
           McKiel]
          Length = 635

 Score =  229 bits (585), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 70/247 (28%), Positives = 121/247 (48%), Gaps = 11/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E   L A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 376 ERQTLQAKKDMIEANLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 435

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    + + +          I
Sbjct: 436 TYATWWIRQAITRAIADQARTIRIPVH-----MIETINKILRTSRQMLNELGYEPTATEI 490

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A +L++   +V  +        SL   +   D +  Q  D++    D      I+   + 
Sbjct: 491 ANRLSMPLDKVRKVMKIAKEPISLENPVGD-DSDGGQLGDFI---EDKNAVAPIDAAIQS 546

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R + TR ++ L PRE R+   R         TLE +  +F+V+RER+RQIE++A +K+
Sbjct: 547 NLREVTTRVLATLTPREERVLRMRFGIGMNTDHTLEEVGQQFKVTRERIRQIESKALRKL 606

Query: 281 QESIQKQ 287
           Q  I+ +
Sbjct: 607 QHPIRSK 613


>gi|67459749|ref|YP_247373.1| RNA polymerase sigma factor RpoD [Rickettsia felis URRWXCal2]
 gi|75535861|sp|Q4UJT1|RPOD_RICFE RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|67005282|gb|AAY62208.1| RNA polymerase sigma factor [Rickettsia felis URRWXCal2]
          Length = 635

 Score =  229 bits (585), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 70/247 (28%), Positives = 121/247 (48%), Gaps = 11/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E   L A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 376 ERQTLQAKKDMIEANLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 435

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    + + +          I
Sbjct: 436 TYATWWIRQAITRAIADQARTIRIPVH-----MIETINKILRTSRQMLNELGYEPTATEI 490

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A +L++   +V  +        SL   +   D +  Q  D++    D      I+   + 
Sbjct: 491 ANRLSMPLDKVRKVMKIAKEPISLENPVGD-DSDGGQLGDFI---EDKNAVAPIDAAIQS 546

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R + TR ++ L PRE R+   R         TLE +  +F+V+RER+RQIE++A +K+
Sbjct: 547 NLREVTTRVLATLTPREERVLRMRFGIGMNTDHTLEEVGQQFKVTRERIRQIESKALRKL 606

Query: 281 QESIQKQ 287
           Q  I+ +
Sbjct: 607 QHPIRSK 613


>gi|220936192|ref|YP_002515091.1| RNA polymerase, sigma 70 subunit, RpoD [Thioalkalivibrio sp.
           HL-EbGR7]
 gi|219997502|gb|ACL74104.1| RNA polymerase, sigma 70 subunit, RpoD [Thioalkalivibrio sp.
           HL-EbGR7]
          Length = 619

 Score =  229 bits (585), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 72/267 (26%), Positives = 122/267 (45%), Gaps = 14/267 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L   E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 358 LTISEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 417

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 418 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 475

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    +++++ + E +V  +        S+   I   D   S   D++  
Sbjct: 476 LQEMGREATPE---ELSERMEMPEDKVRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 528

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D      IE   R+         ++ L PRE ++   R   +     TLE +  +F+V
Sbjct: 529 -EDVNVMSPIEAATREGLSEATRDVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDV 587

Query: 265 SRERVRQIEARAFKKVQESIQKQVELS 291
           +RER+RQIEA+A +K++   + ++  S
Sbjct: 588 TRERIRQIEAKALRKLRHPSRSEMLRS 614


>gi|15893252|ref|NP_360966.1| RNA polymerase sigma factor RpoD [Rickettsia conorii str. Malish 7]
 gi|47606046|sp|Q92FZ8|RPOD_RICCN RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|15620471|gb|AAL03867.1| RNA polymerase sigma factor [Rickettsia conorii str. Malish 7]
          Length = 634

 Score =  229 bits (585), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 70/247 (28%), Positives = 121/247 (48%), Gaps = 11/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E   L A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 375 ERQTLQAKKDMIEANLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 434

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    + + +          I
Sbjct: 435 TYATWWIRQAITRAIADQARTIRIPVH-----MIETINKILRTSRQMLNELGYEPTATEI 489

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A +L++   +V  +        SL   +   D +  Q  D++    D      I+   + 
Sbjct: 490 ANRLSMPLDKVRKVMKIAKEPISLENPVGD-DSDGGQLGDFI---EDKNAVAPIDAAIQS 545

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R + TR ++ L PRE R+   R         TLE +  +F+V+RER+RQIE++A +K+
Sbjct: 546 NLREVTTRVLATLTPREERVLRMRFGIGMNTDHTLEEVGQQFKVTRERIRQIESKALRKL 605

Query: 281 QESIQKQ 287
           Q  I+ +
Sbjct: 606 QHPIRSK 612


>gi|197119058|ref|YP_002139485.1| RNA polymerase sigma-38 factor, stationary phase [Geobacter
           bemidjiensis Bem]
 gi|197088418|gb|ACH39689.1| RNA polymerase sigma-38 factor, stationary phase [Geobacter
           bemidjiensis Bem]
          Length = 333

 Score =  229 bits (585), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 71/275 (25%), Positives = 141/275 (51%), Gaps = 13/275 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI+K  +L   EE  LA R  + GD +A  R++ S+LRLVVKIA  Y   G
Sbjct: 53  DDAIKLYLREIQKTKLLTADEEKELAARI-DLGDKAARDRMIVSNLRLVVKIAKRYINRG 111

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP  +++ EGN+GL++AV++F   +  R +TY+ WWI+ +++  ++     +++    + 
Sbjct: 112 LPFLDLIEEGNMGLIKAVERFKLSKECRFSTYATWWIRQSIERALVNQSRTIRLPVHVSD 171

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                ++ ++    + +     +   +  +A  L V+ + V  +   L    S+   +  
Sbjct: 172 -----DINKMLRVTRELVQKMNREPSIKEVADTLEVNVTYVRRLMVLLKKTYSIERPM-- 224

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE-- 250
            + N     D +         VL+E     N+  ++++    L+  E++I   R   +  
Sbjct: 225 GENNDYFLIDTIEDTSTISPAVLLEDL---NKYELVSKWFETLSDAEKKILTLRFGLDDK 281

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           +P TL+ +   F V+RER+RQIEA++ +K+++ ++
Sbjct: 282 DPQTLDTIGRSFGVTRERIRQIEAKSLEKLRKIVE 316


>gi|148238947|ref|YP_001224334.1| RNA polymerase sigma factor RpoD [Synechococcus sp. WH 7803]
 gi|147847486|emb|CAK23037.1| RNA polymerase sigma factor RpoD, sigma-70 family [Synechococcus
           sp. WH 7803]
          Length = 450

 Score =  229 bits (585), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 77/313 (24%), Positives = 143/313 (45%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE--------------HG------------ 45
            E  +  Y+ EI +I +L   EE  LA++  +              +G            
Sbjct: 138 TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLHLEELAAQFESDNGKLPDTKEWAALV 197

Query: 46  -------------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 198 EMPVIRFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 257

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 258 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKVLSQE 312

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA+ + ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 313 FGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADIENPE 370

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
           Q + +   R++    L   ++ L+PRER +   R   ++    TLE +   F+V+RER+R
Sbjct: 371 QDVAKNLLRED----LEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIR 426

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 427 QIEAKALRKLRHP 439


>gi|4128212|gb|AAD03549.1| principal sigma factor [Burkholderia cepacia]
          Length = 621

 Score =  229 bits (585), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 380 RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 439

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 440 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 494

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 495 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDNNTVAPADAALHASMRD 549

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 550 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 609

Query: 285 QKQ 287
           +  
Sbjct: 610 RSD 612


>gi|332532870|ref|ZP_08408743.1| RNA polymerase sigma factor RpoS [Pseudoalteromonas haloplanktis
           ANT/505]
 gi|332037716|gb|EGI74167.1| RNA polymerase sigma factor RpoS [Pseudoalteromonas haloplanktis
           ANT/505]
          Length = 324

 Score =  229 bits (585), Expect = 3e-58,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   +++    G  ++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 53  YLGEIGFSPLLSAEEEVFFSRK-SLRGCEASRKRMIESNLRLVVKIARRYNNRGLALLDL 111

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 112 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 170

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +T           IA  L+    +V  M        S++  I    +N S
Sbjct: 171 LRTAR----ELTQKLDHEPTADEIAACLDRPVEDVTKMLRLNERIASVDMPI--GGENDS 224

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D +  +     +  ++     +    +   +  LNP++R +   R   L   P TLE
Sbjct: 225 VLLDIIPDEKSAGPEGEVQN---NDINKHIVDWLGELNPKQREVLARRFGLLGYEPSTLE 281

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+  A +++++ +Q++
Sbjct: 282 DVGREIGLTRERVRQIQVEALRRLKDILQQE 312


>gi|303279757|ref|XP_003059171.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226459007|gb|EEH56303.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 587

 Score =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 69/339 (20%), Positives = 145/339 (42%), Gaps = 56/339 (16%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------ 43
            +++ S        +  Y+ +I  + +L  ++E  LA R ++                  
Sbjct: 242 TKRDPSTSRRQTDSMKTYLKDIGSVSLLTGEQEVELAMRIQDLVYLEGVREQLEEEAKRR 301

Query: 44  --------------------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
                                          A ++++ ++LRLVV IA  Y    +   +
Sbjct: 302 KQTSEVSNFDWAIAANVTERELKERLDAGKRAKNQMIQANLRLVVSIAKRYANKSMSFQD 361

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EG +GL++  +KFD +RG++ +TY+ WWI+ A+   I      +++        LF 
Sbjct: 362 LIQEGCVGLIRGAEKFDFKRGYKFSTYAHWWIRQAVTRSISDQSRTIRLPVH-----LFE 416

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + R+    + +     +      IA+ ++++  ++  +        SL+  +  +D +S
Sbjct: 417 IISRMSKVERQLVMKYGRDPTTEEIAEVMDMTVEKINQIQKASLVPISLSQSV--NDDDS 474

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TL 255
              ++ LV DH    +   +   +   +  L   ++ L+PRER +   R   ++    TL
Sbjct: 475 RTVEETLVDDH---AEHPDDATGKVLLKEDLENVLNTLSPRERDVLRLRYGMDDGRVKTL 531

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSP 294
           E + + F V+RER+RQIEA+A +K+++  +  +     P
Sbjct: 532 EEIGNVFSVTRERIRQIEAKALRKLRQPSRNGILREYLP 570


>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 =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 62/243 (25%), Positives = 117/243 (48%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 542 RAAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 601

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + ++    +              +A+++
Sbjct: 602 WWIRQAITRSIADQARTIRIPVH-----MIETINKMNRISRQHLQEFGFEPDASVLAERM 656

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D      +E   +   R+
Sbjct: 657 EIPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDAANTAPMEAAMQAGLRD 711

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E  +  TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 712 VVKDILDSLTPREAKVLRMRFGIEMTSDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPS 771

Query: 285 QKQ 287
           +  
Sbjct: 772 RSD 774


>gi|288923254|ref|ZP_06417393.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EUN1f]
 gi|288345398|gb|EFC79788.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EUN1f]
          Length = 400

 Score =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 73/309 (23%), Positives = 131/309 (42%), Gaps = 38/309 (12%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------------------------ 42
           +  +     +  Y+  I ++ +L   EE  LAKR                          
Sbjct: 95  ASAMPTSDPVRMYLKTIGRVRLLTAAEEVDLAKRIEAGLFASEKLAATRKISPQLRQDLQ 154

Query: 43  --EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A  +LV ++LRLVV IA  Y G G+ + +++ EGN+GL++AV+KFD  +G++
Sbjct: 155 AVEQDGQIAKRKLVEANLRLVVSIAKRYVGRGMLLLDLIQEGNLGLIRAVEKFDYTKGYK 214

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   +      ++I     +      + R++  L         PE   
Sbjct: 215 FSTYATWWIRQAVTRALADQGRTIRIPVHMAE--TVNKVTRIQRQLLQELGREPSPE--- 269

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I  +++++  +V  +        +L   I    +  SQ  D++  D         E   
Sbjct: 270 EIGTQIDLTAHKVEEILKIAQTPVALETPI--GAEQDSQLGDFIEDDD---AIAPFEAAS 324

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFK 278
               +  +   +  L  RE+++ + R       P TLE +  EF + +ER+RQIE+R   
Sbjct: 325 SVLLQKHIESVLHTLPAREKKVIQLRFGLTDGQPRTLEQIGREFGIPQERIRQIESRTLA 384

Query: 279 KVQESIQKQ 287
           K+    + Q
Sbjct: 385 KLSHPARSQ 393


>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 =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 71/275 (25%), Positives = 121/275 (44%), Gaps = 14/275 (5%)

Query: 17  SRYIHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            R I +I +   L   E   + +R    E     A   +V ++LRLV+ IA  Y   GL 
Sbjct: 333 QRQIGQIEEATGLTVTEIKEINRRMSMGEARARRAKKEMVEANLRLVISIAKKYTNRGLQ 392

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
             +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        
Sbjct: 393 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IE 450

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               L R+   +         PE    + +++ + E +V  +        S+   I   D
Sbjct: 451 TINKLNRISRQMLQEMGREPTPE---ELGERMEMPEDKVRKVLKIAKEPISMETPI--GD 505

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NP 252
              S   D++    D      I+    +  +      +  L  RE ++   R   +    
Sbjct: 506 DEDSHLGDFI---EDQTIHSPIDSATGQGLQEATKDVLGGLTAREAKVLRMRFGIDMNTD 562

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            TLE +  +F+V+RER+RQIEA+A +K++   +  
Sbjct: 563 HTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSD 597


>gi|256545301|ref|ZP_05472665.1| RNA polymerase sigma factor RpoD [Anaerococcus vaginalis ATCC
           51170]
 gi|256398982|gb|EEU12595.1| RNA polymerase sigma factor RpoD [Anaerococcus vaginalis ATCC
           51170]
          Length = 614

 Score =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 72/261 (27%), Positives = 124/261 (47%), Gaps = 14/261 (5%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           +  +   L +   +     A  +L  ++LRLVV IA  Y G G+   +++ EGN+GLM+A
Sbjct: 361 DADDVKRLNRAIFDAN--RAKQKLAETNLRLVVSIAKKYVGRGMSFLDLIQEGNMGLMKA 418

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V K+D  RGF+ +TY+ WWI+ A+   I      ++I     +      L R++  L   
Sbjct: 419 VDKYDYNRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE--TINKLVRIQRQLVQD 476

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
              +   E    IA+++ +   +V  +        SL   I   ++  S   D++  D  
Sbjct: 477 LGRDPSNE---EIAEQMGIEVEKVQEIRKIAQEPVSLETPI--GEEEDSHLGDFIEDDTA 531

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRE 267
                  +       R+ L   +S L  RE+R+ + R       P TLE +  EF+V+RE
Sbjct: 532 INPD---DAANYSMLRDQLNDVLSCLGAREKRVLQLRFGLIDGTPRTLEEVGKEFDVTRE 588

Query: 268 RVRQIEARAFKKVQESIQKQV 288
           R+RQIEA+A +K++   + ++
Sbjct: 589 RIRQIEAKALRKLKSPNKSEL 609



 Score = 39.0 bits (90), Expect = 0.89,   Method: Composition-based stats.
 Identities = 13/40 (32%), Positives = 23/40 (57%), Gaps = 1/40 (2%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHR 52
           +  +  Y+ EI K+ +L+  EE  LAK+  E GD++   +
Sbjct: 128 DDPVKMYLKEIGKVKLLDAHEEIFLAKKM-ELGDIAFRSK 166


>gi|84515923|ref|ZP_01003284.1| RNA polymerase sigma factor [Loktanella vestfoldensis SKA53]
 gi|84510365|gb|EAQ06821.1| RNA polymerase sigma factor [Loktanella vestfoldensis SKA53]
          Length = 277

 Score =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 101/269 (37%), Positives = 169/269 (62%), Gaps = 6/269 (2%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            +  +L+ + E  LA  +R+  D  A HRL+T+++RL + +A  ++ YG P+++++ E +
Sbjct: 1   MRAELLDAETELRLAYAWRDQRDEEALHRLITAYMRLAISMASKFKRYGAPMNDLIQEAS 60

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           +GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFN+RR++
Sbjct: 61  VGLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQ 120

Query: 144 GHLQAITDNNL----KPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSS 198
             L+             E    IA ++ V   +V  M+ RL+G D SLNA   S +    
Sbjct: 121 ARLEREAAAEGLHLETHELHEKIAIEVGVPLHDVQMMDGRLSGSDFSLNA-TQSMEDEGR 179

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           +W D L  D     + +    +    R  L  +++ LN RE+ I   R+L+++P TLE+L
Sbjct: 180 EWIDALEDDAPQAAEKVENSHDTDTLRQWLVTALTALNDREQFIVRERKLRDDPRTLESL 239

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            SE  +S+ERVRQ+EA AF K+++S++ Q
Sbjct: 240 GSELGLSKERVRQLEAAAFGKMRKSLEAQ 268


>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 =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 70/246 (28%), Positives = 117/246 (47%), Gaps = 12/246 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 409 EREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 468

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    + +     +      +
Sbjct: 469 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREPTPEEL 523

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+KL +   +V  +        SL   I   D+  S   D++    D    + I+   + 
Sbjct: 524 AEKLAMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAILPIDAAIQS 578

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 579 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKL 638

Query: 281 QESIQK 286
           +   + 
Sbjct: 639 KHPSRS 644


>gi|124025264|ref|YP_001014380.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str.
           NATL1A]
 gi|123960332|gb|ABM75115.1| Putative principal RNA polymerase sigma factor [Prochlorococcus
           marinus str. NATL1A]
          Length = 420

 Score =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 78/313 (24%), Positives = 141/313 (45%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR--------------EHG------------ 45
            E  +  Y+ EI +I +L   EE  LA++                E+G            
Sbjct: 106 TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLQLEEEAAQFESENGHFPSVKEWAVLA 165

Query: 46  -------------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 166 DMPLTRFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 225

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 226 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKVLSQE 280

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA+ + ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 281 FGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADIENPE 338

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
           Q +     +   R  L   ++ L+PRER +   R   ++    TLE +   F+V+RER+R
Sbjct: 339 QDVA----KTLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIR 394

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 395 QIEAKALRKLRHP 407


>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 =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 439 RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 498

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 499 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 553

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 554 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTVAPADAALHASMRD 608

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 609 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 668

Query: 285 QKQ 287
           +  
Sbjct: 669 RSD 671


>gi|126734879|ref|ZP_01750625.1| RNA polymerase sigma-32 factor [Roseobacter sp. CCS2]
 gi|126715434|gb|EBA12299.1| RNA polymerase sigma-32 factor [Roseobacter sp. CCS2]
          Length = 277

 Score =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 103/269 (38%), Positives = 169/269 (62%), Gaps = 6/269 (2%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K  +L+ + E  LA  +R+  D  A HRL+T+++RL + +A  ++ YG P+++++ E +
Sbjct: 1   MKAELLDAETELALAYAWRDERDEKALHRLITAYMRLAISMASKFKRYGAPMNDLIQEAS 60

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           +GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFN+RR++
Sbjct: 61  VGLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQ 120

Query: 144 GHLQAITDNNLK----PEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSS 198
             L+       +     E    IA ++ V   +V  M  RL+G D SLNA   S +    
Sbjct: 121 ARLEREAAAEGRVMDKQEMRELIAIEVGVPLHDVEMMEGRLSGSDFSLNA-TQSVEDEGR 179

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           +W D L  D     + +    +    R  L  ++S LN RE+ I   R+L+E+P TLE+L
Sbjct: 180 EWIDALEDDGPQAAETVEHTHDNDTLRQWLLTALSNLNDREQFIVRERKLREDPRTLESL 239

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +E  +S+ERVRQ+EA AF K+++S++ Q
Sbjct: 240 GTELGLSKERVRQLEAAAFGKMRKSLESQ 268


>gi|258623793|ref|ZP_05718750.1| RNA polymerase sigma-38 factor [Vibrio mimicus VM603]
 gi|258583916|gb|EEW08708.1| RNA polymerase sigma-38 factor [Vibrio mimicus VM603]
          Length = 336

 Score =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 81/287 (28%), Positives = 138/287 (48%), Gaps = 13/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           R+              Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVV
Sbjct: 46  REEFDASAKSLDATQMYLSEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLVV 104

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           KI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++    
Sbjct: 105 KISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTR 164

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            +++      K L   LR  +     ++           IA +L+    +V  M      
Sbjct: 165 TIRLPIHVV-KELNIYLRTAR----ELSQRLDHEPTPEEIALELDKPVDDVTKMLRLNER 219

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++  I           D L   ++   +   + +   + R  L   +  LNP+++ +
Sbjct: 220 ISSVDTPI--GGDGDKALLDILPDSNNADPEFSTQDD---DIRESLLNWLDELNPKQKEV 274

Query: 243 FEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 275 LARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVKQ 321


>gi|254786794|ref|YP_003074223.1| RNA polymerase sigma factor RpoS [Teredinibacter turnerae T7901]
 gi|237685659|gb|ACR12923.1| RNA polymerase sigma factor RpoS [Teredinibacter turnerae T7901]
          Length = 337

 Score =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 78/277 (28%), Positives = 142/277 (51%), Gaps = 13/277 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L   EE   A+R  + GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSADEEVYFARRALK-GDEAARKRMIESNLRLVVKISRRYVNRGLALLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++       +    
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV--VKELNV 183

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
             R    L    D+    E++  + +K       ++++N R+    S++A I  + + + 
Sbjct: 184 YLRAARELSQKLDHEPSAEEIAELLEKPVEDVERMLALNERVT---SMDAPIGPASEKTV 240

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
                     D Q    +E  E  +    L   +  L+ ++R +   R         TLE
Sbjct: 241 VDTVP-----DQQVSDPVELLEDSDLSTSLNSWLDELSEKQREVVARRFGLRGHETSTLE 295

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
            +  E  ++RERVRQI+  A +++++ ++KQ   +++
Sbjct: 296 EVGREIGLTRERVRQIQVEALRRLRDILEKQGLDATA 332


>gi|162447798|ref|YP_001620930.1| DNA-directed RNA polymerase subunit D [Acholeplasma laidlawii
           PG-8A]
 gi|161985905|gb|ABX81554.1| DNA-directed RNA polymerase subunit D [Acholeplasma laidlawii
           PG-8A]
          Length = 419

 Score =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 75/317 (23%), Positives = 138/317 (43%), Gaps = 42/317 (13%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG---------------- 45
           N   +   +  +  +  Y+ EI +IP+L   +E   A    +                  
Sbjct: 102 NIDAIPSSIKVDDPVRMYLKEIGQIPLLNIDDERKYAIMVYQGRVALEQLEAVRNGEVDL 161

Query: 46  -DLS-------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            D               A  +LV ++ RLVV IA  Y   GL   +++ EGN+GLM+AV 
Sbjct: 162 SDEDVQSLEDTIRKGHYAKEKLVEANYRLVVSIAKKYTQRGLLFLDLIQEGNMGLMRAVD 221

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD E+GF+ +TY+ WWI+ A+   +      ++I     +      + ++    + +  
Sbjct: 222 KFDYEKGFKFSTYATWWIRQAITRAVADQARTIRIPVHMVE-----TINKMIRIQRQLVQ 276

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +   +  IA+K++++  +V ++        SL A +   ++  S   D++    D  
Sbjct: 277 ELGRDATIEEIAEKMDITPEKVQNIQRIAKEPISLEAPV--GEEEDSSLGDFI---SDPN 331

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERV 269
                +   ++  +  L   +  L  RE ++   R   L     TLE +  EF V+RER+
Sbjct: 332 ALNPHDYMMQEMVKKTLDEVLETLTDREEKVLRLRYGLLDGKTHTLEEVGREFGVTRERI 391

Query: 270 RQIEARAFKKVQESIQK 286
           RQIEA+A +K++   ++
Sbjct: 392 RQIEAKALRKLRSPQRQ 408


>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 =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 70/272 (25%), Positives = 126/272 (46%), Gaps = 22/272 (8%)

Query: 32  QEEYVL-AKRYREHGDL---------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           ++E  L  ++ R  GD           A   +V ++LRLV+ IA  Y   GL   +++ E
Sbjct: 358 EQEAHLTIEQIRNIGDRISQGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 417

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           GNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R
Sbjct: 418 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNR 475

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           +             PE    +A+++ + E ++  +        S+   I   D + S   
Sbjct: 476 ISRQCLQEMGREATPE---ELAERMGMPEDKIRKVLKIAKEPISMETPI--GDDDDSHLG 530

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLS 259
           D++    D   ++ ++    ++ +      +  L PRE ++   R   +     TLE + 
Sbjct: 531 DFI---EDSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVG 587

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
            +F+V+RER+RQIEA+A +K++   + +   S
Sbjct: 588 KQFDVTRERIRQIEAKALRKLRHPSRSETLRS 619


>gi|317050370|ref|YP_004111486.1| RNA polymerase sigma factor RpoD [Desulfurispirillum indicum S5]
 gi|316945454|gb|ADU64930.1| RNA polymerase sigma factor RpoD [Desulfurispirillum indicum S5]
          Length = 627

 Score =  229 bits (585), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 74/273 (27%), Positives = 129/273 (47%), Gaps = 14/273 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDL--SAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + EI +   ++  E   + ++ RE  +   +A  +L+ ++LRLVV IA  Y   GL   +
Sbjct: 358 LREIEESTGVDANELMSIVQQVREGEEESKAAKMQLIEANLRLVVSIAKKYTNRGLQFLD 417

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 418 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRAIADQARTIRIPVHM--IETIN 475

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R   +L         PE    IA K+++   +V  +        SL   I   ++  
Sbjct: 476 KLVRTSRNLVQELGREPTPE---EIADKMDLPVEKVRKVLKIAKEPISLETPI--GEEED 530

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
           S   D++    D       E     N +  +   +  L+ RE  + + R     ++  TL
Sbjct: 531 SSLGDFI---EDKNTVSPAEAVISFNLKEQVRSVLHTLSAREAEVLKLRFGIDTDSDHTL 587

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           E +  +F V+RER+RQIEA+A +K++   + ++
Sbjct: 588 EEVGKKFNVTRERIRQIEAKALRKLRHPTRSKI 620


>gi|258623525|ref|ZP_05718526.1| RNA polymerase sigma-38 factor [Vibrio mimicus VM573]
 gi|262172378|ref|ZP_06040056.1| RNA polymerase sigma factor RpoS [Vibrio mimicus MB-451]
 gi|258584187|gb|EEW08935.1| RNA polymerase sigma-38 factor [Vibrio mimicus VM573]
 gi|261893454|gb|EEY39440.1| RNA polymerase sigma factor RpoS [Vibrio mimicus MB-451]
          Length = 336

 Score =  229 bits (584), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 81/287 (28%), Positives = 138/287 (48%), Gaps = 13/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           R+              Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVV
Sbjct: 46  REEFDASAKSLDATQMYLSEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLVV 104

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           KI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++    
Sbjct: 105 KISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTR 164

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            +++      K L   LR  +     ++           IA +L+    +V  M      
Sbjct: 165 TIRLPIHVV-KELNIYLRTAR----ELSQRLDHEPTPEEIALELDKPVDDVTKMLRLNER 219

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++  I           D L   ++   +   + +   + R  L   +  LNP+++ +
Sbjct: 220 ISSVDTPI--GGDGDKALLDILPDSNNADPEFSTQDD---DIRESLLNWLDELNPKQKEV 274

Query: 243 FEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 275 LARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVKQ 321


>gi|157826344|ref|YP_001494064.1| RNA polymerase sigma factor RpoD [Rickettsia akari str. Hartford]
 gi|157800302|gb|ABV75556.1| RNA polymerase sigma factor RpoD [Rickettsia akari str. Hartford]
          Length = 635

 Score =  229 bits (584), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 70/247 (28%), Positives = 121/247 (48%), Gaps = 11/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E   L A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 376 ERQTLQAKKDMIEANLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 435

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    + + +          I
Sbjct: 436 TYATWWIRQAITRAIADQARTIRIPVH-----MIETINKILRTSRQMLNELGYEPTATEI 490

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A +L++   +V  +        SL   +   D +  Q  D++    D      I+   + 
Sbjct: 491 ANRLSMPLDKVRKVMKIAKEPISLENPVGD-DSDGGQLGDFI---EDKNAIAPIDAAIQS 546

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R + TR ++ L PRE R+   R         TLE +  +F+V+RER+RQIE++A +K+
Sbjct: 547 NLREVTTRVLATLTPREERVLRMRFGIGMNTDHTLEEVGQQFKVTRERIRQIESKALRKL 606

Query: 281 QESIQKQ 287
           Q  I+ +
Sbjct: 607 QHPIRSK 613


>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|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]
          Length = 618

 Score =  229 bits (584), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 74/298 (24%), Positives = 139/298 (46%), Gaps = 17/298 (5%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPM---LEKQEEYVLAKRYR--EHGDLSAAHRLVT 55
           MN+     +   E  + R + ++++I +   L  ++   + +R    E     A   +V 
Sbjct: 327 MNKPWSEKLAGIEEEVQRSLQKLQQIEVETGLTIEQVKDINRRMSIGEAKARRAKKEMVE 386

Query: 56  SHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQE 115
           ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+  
Sbjct: 387 ANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 446

Query: 116 YILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
            I      ++I            L R+   +         PE    +A+++ + E ++  
Sbjct: 447 SIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPSPE---ELAERMLMPEDKIRK 501

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
           +        S+   I   D   S   D++    D   ++ ++    ++ R+     +  L
Sbjct: 502 VLKIAKEPISMETPI--GDDEDSHLGDFI---EDTTLELPLDSATSESLRSATHEVLGGL 556

Query: 236 NPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
             RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 557 TLREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 614


>gi|78185245|ref|YP_377680.1| RNA polymerase sigma factor RpoD [Synechococcus sp. CC9902]
 gi|78169539|gb|ABB26636.1| Sigma-70 factor [Synechococcus sp. CC9902]
          Length = 451

 Score =  229 bits (584), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 77/313 (24%), Positives = 142/313 (45%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-----------------HGDLS------ 48
            E  +  Y+ EI +I +L   EE  LA++  +                   D        
Sbjct: 139 TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLYLEELAAQFESDNGREPDKKEWAALV 198

Query: 49  ----------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 199 EMPLIRFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 258

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 259 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKVLSQE 313

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA+ + ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 314 FGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADIENPE 371

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
           Q + +   R++    L   ++ L+PRER +   R   ++    TLE +   F+V+RER+R
Sbjct: 372 QDVAKNLLRED----LEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIR 427

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 428 QIEAKALRKLRHP 440


>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 =  229 bits (584), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 71/272 (26%), Positives = 124/272 (45%), Gaps = 14/272 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +  + K   L   E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 343 LRAVSKETGLTIAELKEINRRISIGETRARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 402

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 403 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 460

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A ++++ E ++  +        S+   I   D   
Sbjct: 461 KLNRISRQMLQEMGREATPE---ELAARMDMPEDKIRKVLKIAKEPISMETPI--GDDED 515

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++  D     +  I+    +  R   T  ++ L  RE ++   R   +     TL
Sbjct: 516 SHLGDFIEDDG---AESPIDIATIEGLRESTTMVLAGLTAREAKVLRMRFGIDMNTDHTL 572

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 573 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 604


>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 =  229 bits (584), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 128/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +  I +   L  +    +++R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 373 LQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 432

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 433 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 490

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 491 KLNRISRQMLQEMGREPLPE---ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDED 545

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++     + +      ++ L PRE ++   R   +     TL
Sbjct: 546 SHLGDFI---EDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTL 602

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 603 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 638


>gi|260902364|ref|ZP_05910759.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus AQ4037]
 gi|308110564|gb|EFO48104.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus AQ4037]
          Length = 329

 Score =  229 bits (584), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 80/287 (27%), Positives = 141/287 (49%), Gaps = 13/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           R+              Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVV
Sbjct: 41  REEFDASSKSLDATQLYLGEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLVV 99

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           KI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++    
Sbjct: 100 KISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTR 159

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            +++      K L   LR  +     ++           IA +L++   +V  M      
Sbjct: 160 TIRLPIHVV-KELNIYLRTAR----ELSQKLDHEPTAEEIAAQLDIPVEDVSKMLRLNER 214

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++  I           D +   ++   +V  + +   + ++ L   +  LNP+++ +
Sbjct: 215 ISSVDTPI--GGDGEKALLDIIPDANNSDPEVSTQDD---DIKSSLIHWLEELNPKQKEV 269

Query: 243 FEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 270 LARRFGLLGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLREILIKQ 316


>gi|323493642|ref|ZP_08098763.1| RNA polymerase sigma factor RpoS [Vibrio brasiliensis LMG 20546]
 gi|323312165|gb|EGA65308.1| RNA polymerase sigma factor RpoS [Vibrio brasiliensis LMG 20546]
          Length = 326

 Score =  229 bits (584), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 80/287 (27%), Positives = 140/287 (48%), Gaps = 13/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           ++              Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVV
Sbjct: 38  KEEFDASTKSLDATQLYLGEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLVV 96

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           KI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++    
Sbjct: 97  KISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTR 156

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            +++      K L   LR  +     ++           IA +L+    +V  M      
Sbjct: 157 TIRLPIHVV-KELNIYLRTAR----ELSQKLDHEPTAEEIATQLDKPVDDVSKMLRLNER 211

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++  I           D +   ++   +V  + +   + +N L   +  LNP+++ +
Sbjct: 212 ISSVDTPI--GGDGEKALLDIIPDINNSDPEVSTQDD---DIKNSLIHWLDELNPKQKEV 266

Query: 243 FEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 267 LARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILIKQ 313


>gi|262401766|ref|ZP_06078332.1| RNA polymerase sigma factor RpoS [Vibrio sp. RC586]
 gi|262352183|gb|EEZ01313.1| RNA polymerase sigma factor RpoS [Vibrio sp. RC586]
          Length = 336

 Score =  229 bits (584), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 83/287 (28%), Positives = 138/287 (48%), Gaps = 13/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           R+              Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVV
Sbjct: 46  REEFDASAKSLDATQMYLSEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLVV 104

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           KI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++    
Sbjct: 105 KISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTR 164

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            +++      K L   LR  +     ++           IA +L+    +V  M      
Sbjct: 165 TIRLPIHVV-KELNIYLRTAR----ELSQRLDHEPTPEEIALELDRPVDDVTKMLRLNER 219

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++  I           D L   H+   +   + +   + R  L   M  LNP+++ +
Sbjct: 220 ISSVDTPI--GGDGDKALLDILPDSHNADPEFSTQDD---DIRESLLGWMDELNPKQKEV 274

Query: 243 FEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 275 LARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVKQ 321


>gi|212633971|ref|YP_002310496.1| RNA polymerase sigma factor [Shewanella piezotolerans WP3]
 gi|212555455|gb|ACJ27909.1| RNA polymerase sigma factor [Shewanella piezotolerans WP3]
          Length = 612

 Score =  229 bits (584), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 66/250 (26%), Positives = 119/250 (47%), Gaps = 12/250 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 366 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 425

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 426 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPSPE--- 480

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + E ++  +        S+   I   D   S   D++    D   ++ ++   
Sbjct: 481 ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDTTLELPLDSAT 535

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            ++ RN     ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 536 GESLRNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 595

Query: 279 KVQESIQKQV 288
           K++   + ++
Sbjct: 596 KLRHPSRSEI 605


>gi|254230502|ref|ZP_04923875.1| RNA polymerase sigma factor RpoS [Vibrio sp. Ex25]
 gi|262393289|ref|YP_003285143.1| RNA polymerase sigma factor RpoS [Vibrio sp. Ex25]
 gi|151936974|gb|EDN55859.1| RNA polymerase sigma factor RpoS [Vibrio sp. Ex25]
 gi|262336883|gb|ACY50678.1| RNA polymerase sigma factor RpoS [Vibrio sp. Ex25]
          Length = 328

 Score =  229 bits (584), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 80/288 (27%), Positives = 141/288 (48%), Gaps = 13/288 (4%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
            R+              Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLV
Sbjct: 39  AREEFDASSKSLDATQLYLGEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLV 97

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           VKI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++   
Sbjct: 98  VKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQT 157

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             +++      K L   LR  +     ++           IA +L++   +V  M     
Sbjct: 158 RTIRLPIHVV-KELNIYLRTAR----ELSQKLDHEPTAEEIAAQLDIPVEDVSKMLRLNE 212

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              S++  I           D +   ++   +V  + +   + ++ L   +  LNP+++ 
Sbjct: 213 RISSVDTPI--GGDGEKALLDIIPDANNSDPEVSTQDD---DIKSSLIHWLEELNPKQKE 267

Query: 242 IFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +   R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 268 VLARRFGLLGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLREVLIKQ 315


>gi|99080297|ref|YP_612451.1| RNA polymerase factor sigma-32 [Ruegeria sp. TM1040]
 gi|99036577|gb|ABF63189.1| RNA polymerase, sigma 32 subunit, RpoH [Ruegeria sp. TM1040]
          Length = 292

 Score =  229 bits (584), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 105/272 (38%), Positives = 178/272 (65%), Gaps = 6/272 (2%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
            +  K  +L+ + E  LA  +R+  D+ A HRL+T+++RL V +A  +R YG P+++++ 
Sbjct: 13  KQAMKAELLDAETELALAYAWRDEKDVQALHRLITAYMRLAVSMASKFRRYGAPMNDLIQ 72

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           E  +GLM+A +KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFN+R
Sbjct: 73  EAGLGLMKAAEKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMR 132

Query: 141 RLKGHLQAITDNNL----KPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDK 195
           R++  L+           + + +  +A+++ V   +V  M+ RLAG D SLNA + S+D+
Sbjct: 133 RVQAQLEREAAGEGVELDRHKLMQMVAEEIGVPLRDVEMMDGRLAGADFSLNA-VQSADE 191

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
           +  +W D L  D +     +    +R+  R  L  +++ LN RER I   R+L+E   TL
Sbjct: 192 DGREWIDALEDDSEQAADRVEADHDRRQLREWLLSALNGLNERERFIVRERKLREEARTL 251

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+L +E  +S+ERVRQ+EA AF K+++S++ Q
Sbjct: 252 ESLGNELGLSKERVRQLEAAAFSKMRKSLEGQ 283


>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 =  229 bits (584), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 439 RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 498

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 499 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 553

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 554 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTVAPADAALHASMRD 608

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 609 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 668

Query: 285 QKQ 287
           +  
Sbjct: 669 RSD 671


>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 =  229 bits (584), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 71/273 (26%), Positives = 126/273 (46%), Gaps = 14/273 (5%)

Query: 23  IRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           I +   L  Q    +++R    E     A   +V ++LRLV+ IA  Y   GL   +++ 
Sbjct: 348 IERETSLTVQSIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 407

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L 
Sbjct: 408 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLN 465

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
           R+   +         PE    +A+++ + E ++  +        S+   I   D   S  
Sbjct: 466 RISRQMLQEMGREPLPE---ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDEDSHL 520

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENL 258
            D++    D   ++ ++     + R      ++ L PRE ++   R   +     TLE +
Sbjct: 521 GDFI---EDTTLELPLDSATATSLRGATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEV 577

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
             +F+V+RER+RQIEA+A +K++   + +   S
Sbjct: 578 GKQFDVTRERIRQIEAKALRKLRHPSRSETLRS 610


>gi|167842198|ref|ZP_02468882.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis
           MSMB43]
          Length = 680

 Score =  229 bits (584), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 439 RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 498

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 499 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 553

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 554 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDSNTVAPADAALHASMRD 608

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 609 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 668

Query: 285 QKQ 287
           +  
Sbjct: 669 RSD 671


>gi|224024118|ref|ZP_03642484.1| hypothetical protein BACCOPRO_00840 [Bacteroides coprophilus DSM
           18228]
 gi|224017340|gb|EEF75352.1| hypothetical protein BACCOPRO_00840 [Bacteroides coprophilus DSM
           18228]
          Length = 317

 Score =  229 bits (584), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 74/287 (25%), Positives = 143/287 (49%), Gaps = 12/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI +  ++  +EE  LA+R R+ GD  A  +L  ++LR VV
Sbjct: 36  KITKSITNRESASLDKYLQEIGREDLITVEEEVELAQRIRK-GDRVALEKLTRANLRFVV 94

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 95  SVAKQYQNQGLSLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSR 154

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    NQ      + +     +   +    PE    +A +L +   ++         
Sbjct: 155 IVRLP--LNQVGSLNKISKAFSKFEQENERRPSPE---ELADELEIPVDKISDTLKVSGR 209

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     + NS    D LV D        +  E        + R++S L  RE+ I
Sbjct: 210 HISVDAPFVEGEDNS--LLDVLVNDDSPMADRSLVNESLS---REIDRALSTLTEREKDI 264

Query: 243 FEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +         +TLE +  +F ++RERVRQI+ +A ++++++ + ++
Sbjct: 265 IQMFFGINTQEMTLEEIGDKFGLTRERVRQIKEKAIRRLRQNSRSKL 311


>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 =  229 bits (584), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 72/276 (26%), Positives = 127/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +  I K   L  Q    +++R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 345 LDMIEKETSLTVQSIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 404

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 405 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 462

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 463 KLNRISRQMLQEMGREPLPE---ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDED 517

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++     + R      ++ L PRE ++   R   +     TL
Sbjct: 518 SHLGDFI---EDTTLELPLDSATATSLRGATKDVLAGLTPREAKVLRMRFGIDMNTDHTL 574

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +   S
Sbjct: 575 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRS 610


>gi|282861771|ref|ZP_06270835.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces sp.
           ACTE]
 gi|282563587|gb|EFB69125.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces sp.
           ACTE]
          Length = 355

 Score =  229 bits (584), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 82/301 (27%), Positives = 143/301 (47%), Gaps = 38/301 (12%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY------------------REHGDLS---- 48
                  +Y+ EI +IP+L   +E  LA+R                   R   DL     
Sbjct: 54  PSSDLFRQYLREIGRIPLLGAADEVELARRVEAGLFAEERLAATPGPDTRLAQDLGRLVV 113

Query: 49  ----AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
               A  RL+ ++LRLVV +A  Y G GL + ++V EGN+GL++AV+KFD  RG++ +TY
Sbjct: 114 QGRMAERRLIEANLRLVVSVAKRYAGRGLTMLDLVQEGNLGLIRAVEKFDYTRGYKFSTY 173

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + WWI+ AM   +      +++     +  L   + R++  L     +    E+V A   
Sbjct: 174 ATWWIRQAMSRALADQARTIRVPVHVVE--LINRVVRVQRRLLQERGHEPSAEEVAA--- 228

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L+++   V ++        SL+A +   +++   + D +    DG     +E       
Sbjct: 229 QLDLTPERVETILRLAQEPVSLHAPV--GEEDDVAFGDLI---EDGDAPSPVESAAFLLL 283

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           R  L   +S L  RER++ + R   ++  P TLE +   F V+RER+RQIE++   ++++
Sbjct: 284 REHLEAVLSTLGERERKVVQLRYGLDDGRPRTLEEIGRLFGVTRERIRQIESKTLARLRD 343

Query: 283 S 283
            
Sbjct: 344 H 344


>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 =  229 bits (584), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 73/278 (26%), Positives = 127/278 (45%), Gaps = 14/278 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           +   + I +I K   L  +E   ++KR    E     A   +V ++LRLV+ IA  Y   
Sbjct: 351 LAFQQKIADIEKELDLNVKEIKDISKRMAVGEAKARRAKKEMVEANLRLVISIAKKYTNR 410

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I     
Sbjct: 411 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM- 469

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
                  + R+   L         PE    + ++L + E +V  +        S+   I 
Sbjct: 470 -IETINKINRVSRQLLQEMGREPTPE---ELGERLEMDEVKVRKVLKIAKEPISMETPI- 524

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             D   S   D++    D      ++    +  +      +  L  RE ++ + R   + 
Sbjct: 525 -GDDEDSHLGDFI---EDSNITSPVDAATSEGLKEATREVLENLTEREAKVLKMRFGIDM 580

Query: 252 P--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           P   TLE +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 581 PTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 618


>gi|262164038|ref|ZP_06031777.1| RNA polymerase sigma factor RpoS [Vibrio mimicus VM223]
 gi|262027566|gb|EEY46232.1| RNA polymerase sigma factor RpoS [Vibrio mimicus VM223]
          Length = 336

 Score =  229 bits (584), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 81/287 (28%), Positives = 138/287 (48%), Gaps = 13/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           R+              Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVV
Sbjct: 46  REEFDASAKSLDATQMYLSEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLVV 104

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           KI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++    
Sbjct: 105 KISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTR 164

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            +++      K L   LR  +     ++           IA +L+    +V  M      
Sbjct: 165 TIRLPIHVV-KELNIYLRTAR----ELSQRLDHEPTPEEIALELDKPVDDVTKMLRLNER 219

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++  I           D L   ++   +   + +   + R  L   +  LNP+++ +
Sbjct: 220 ISSVDTPI--GGDGDKALLDILPDSNNADPEFSTQDD---DIRESLLNWLDELNPKQKEV 274

Query: 243 FEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 275 LARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREVLVKQ 321


>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|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]
          Length = 680

 Score =  229 bits (584), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 439 RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 498

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 499 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 553

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 554 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTVAPADAALHASMRD 608

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 609 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 668

Query: 285 QKQ 287
           +  
Sbjct: 669 RSD 671


>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 =  229 bits (584), Expect = 4e-58,   Method: Composition-based stats.
 Identities = 65/249 (26%), Positives = 113/249 (45%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 385 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 444

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            + R++  +         PE   
Sbjct: 445 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKINRVQRQMLQEMGREPTPE--- 499

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +  +L + E +V  +        S+   I   D   S   D++    DG  +  ++   
Sbjct: 500 ELGVRLEMPEDKVRKVLKIAKEPISMETPI--GDDEDSSLGDFI---EDGNMESPVDSAT 554

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
                      ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 555 SLGLEEATRDVLANLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 614

Query: 279 KVQESIQKQ 287
           K++   + +
Sbjct: 615 KLRHPSRSE 623


>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 =  229 bits (584), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 65/250 (26%), Positives = 119/250 (47%), Gaps = 12/250 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 370 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 430 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPSPE--- 484

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + E ++  +        S+   I   D   S   D++    D   ++ ++   
Sbjct: 485 ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDTTLELPLDSAT 539

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            ++ +N     ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 540 GESLKNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 279 KVQESIQKQV 288
           K++   + ++
Sbjct: 600 KLRHPSRSEI 609


>gi|126727888|ref|ZP_01743716.1| RNA polymerase sigma factor [Rhodobacterales bacterium HTCC2150]
 gi|126702829|gb|EBA01934.1| RNA polymerase sigma factor [Rhodobacterales bacterium HTCC2150]
          Length = 661

 Score =  229 bits (584), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 70/242 (28%), Positives = 119/242 (49%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 421 RAAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 480

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +AKKL
Sbjct: 481 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAKKL 535

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++N + 
Sbjct: 536 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAVLPLDSAIQENLKE 590

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 591 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 650

Query: 285 QK 286
           + 
Sbjct: 651 RS 652


>gi|293376344|ref|ZP_06622581.1| RNA polymerase sigma factor RpoD [Turicibacter sanguinis PC909]
 gi|325843397|ref|ZP_08167955.1| RNA polymerase sigma factor RpoD [Turicibacter sp. HGF1]
 gi|292645033|gb|EFF63106.1| RNA polymerase sigma factor RpoD [Turicibacter sanguinis PC909]
 gi|325489319|gb|EGC91693.1| RNA polymerase sigma factor RpoD [Turicibacter sp. HGF1]
          Length = 456

 Score =  229 bits (584), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 75/260 (28%), Positives = 127/260 (48%), Gaps = 17/260 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L  +E    A+R  + G   A  RLV ++LRLVV IA  + G G+   +++ EGN+GL++
Sbjct: 203 LSDEE----ARRVIQEG-EYAKKRLVEANLRLVVSIAKRHVGRGMLFLDLIQEGNMGLIK 257

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     +      L R++  L  
Sbjct: 258 AVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE--TINKLVRIQRQLVQ 315

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                  PE    I++K+ ++  +V  +        SL + +   +++ S   D++    
Sbjct: 316 ELGREPLPE---EISEKMGIAPEKVREILKISQEPVSLESPV--GEEDDSHLGDFIP--- 367

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSR 266
           D       E    +  +  L   +  L  RE R+   R   E+    TLE +  EF V+R
Sbjct: 368 DADALSPSEFASNEMLKKELDDVLETLTDREERVLRLRFGLEDGRTRTLEEVGKEFGVTR 427

Query: 267 ERVRQIEARAFKKVQESIQK 286
           ER+RQIEA+A +K++   + 
Sbjct: 428 ERIRQIEAKALRKLRHPSRS 447


>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 =  229 bits (584), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 73/286 (25%), Positives = 127/286 (44%), Gaps = 24/286 (8%)

Query: 16  LSRYIHEIRKIPM----------LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVK 63
           L +Y  EI +             L  QE   + +R    E     A   ++ ++LRLV+ 
Sbjct: 413 LEKYSKEIYRAQRNLAQLEEQNNLNIQEIKEINRRVAIGEAKSRRAKKEMIEANLRLVIS 472

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      
Sbjct: 473 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 532

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           ++I            L R+   +   T     PE    + +++++ E +V  +       
Sbjct: 533 IRIPVHM--IETINKLNRISRQILQETGIEATPE---ELGRRMDMPEEKVRKVLKIAKEP 587

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            S+   I   +   S   D++    D   +  ++              +S L PRE ++ 
Sbjct: 588 ISMETPI--GEDEDSNLGDFI---EDINMESPVDFATSAGLMEATREILSTLTPREAKVL 642

Query: 244 EARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             R   +     TLE +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 643 RMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRAE 688


>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 =  229 bits (584), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 73/277 (26%), Positives = 127/277 (45%), Gaps = 14/277 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           L + + EI     L   E   + +R    E     A   +V ++LRLV+ IA  Y   GL
Sbjct: 355 LQKKLAEIEHEASLNISEIKEINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGL 414

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I       
Sbjct: 415 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--I 472

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R+   +         PE    +A+++ + E ++  +        S+   I   
Sbjct: 473 ETINKLNRVSRQMLQEMGREATPE---ELAERMEMPEDKIRKVLKISKEPISMETPI--G 527

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--N 251
           D   S   D++    D +     +   R++        +S L PRE ++   R   +   
Sbjct: 528 DDEDSHLGDFI---EDEKVASPSDSAARESLSEATREILSTLTPREAKVLRMRFGIDMNT 584

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
             TLE +  +F+V+RER+RQIEA+A +K++   + ++
Sbjct: 585 DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRAEL 621


>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 =  229 bits (584), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 70/246 (28%), Positives = 117/246 (47%), Gaps = 12/246 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 405 EREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 464

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    + +     +      +
Sbjct: 465 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREPTPEEL 519

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+KL +   +V  +        SL   I   D+  S   D++    D    + I+   + 
Sbjct: 520 AEKLAMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAILPIDAAIQS 574

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 575 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKL 634

Query: 281 QESIQK 286
           +   + 
Sbjct: 635 KHPSRS 640


>gi|88797598|ref|ZP_01113187.1| RNA polymerase sigma factor [Reinekea sp. MED297]
 gi|88779770|gb|EAR10956.1| RNA polymerase sigma factor [Reinekea sp. MED297]
          Length = 290

 Score =  229 bits (584), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 99/278 (35%), Positives = 151/278 (54%), Gaps = 7/278 (2%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
            ++    L  YI  +    +L  +EE  LA+R   H DL +A RLV SHLR VV IA  Y
Sbjct: 14  TLSPGQNLEAYITTVNGFELLSAEEEKDLAERLYYHDDLESARRLVMSHLRFVVHIAKSY 73

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGL   +++ EGN+GLM+A+++F+PE G RL ++++ WIKA + EYIL++W +VKI T
Sbjct: 74  SGYGLNQGDLIQEGNVGLMKAIRRFNPEVGVRLVSFAVHWIKAEIHEYILKNWRIVKIAT 133

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES--L 186
           T  Q++LFFNLR  K  L  + +      +  AIA  L V +  V  M  RL   ++   
Sbjct: 134 TKAQRKLFFNLRSSKKRLGWLNER-----EAQAIADDLGVEKKIVYDMEGRLTASDAAFD 188

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
               +  D  +    D+L+ + D     + +     +    L  ++  L+ R R I + R
Sbjct: 189 GFNDDDDDGAAFHPSDYLMNEADDPAAAVEQANYTDDAHGQLFSALEDLDDRSRDIIQQR 248

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L E   TL  L+ ++ VS ER+RQ+E  A  KV++ +
Sbjct: 249 WLNEEKATLHELADKYGVSAERIRQLEKNAMNKVKKVM 286


>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 =  229 bits (584), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 127/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +  I +   L  Q    +++R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 349 LKTIEEETSLTVQSIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 408

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 409 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 466

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 467 KLNRISRQMLQEMGREPLPE---ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDED 521

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++     + +      ++ L PRE ++   R   +     TL
Sbjct: 522 SHLGDFI---EDTTLELPLDSATAGSLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTL 578

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +   S
Sbjct: 579 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRS 614


>gi|167745452|ref|ZP_02417579.1| hypothetical protein ANACAC_00143 [Anaerostipes caccae DSM 14662]
 gi|317472996|ref|ZP_07932299.1| sigma-70 family RNA polymerase sigma factor [Anaerostipes sp.
           3_2_56FAA]
 gi|167655173|gb|EDR99302.1| hypothetical protein ANACAC_00143 [Anaerostipes caccae DSM 14662]
 gi|316899541|gb|EFV21552.1| sigma-70 family RNA polymerase sigma factor [Anaerostipes sp.
           3_2_56FAA]
          Length = 347

 Score =  229 bits (584), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 82/285 (28%), Positives = 143/285 (50%), Gaps = 19/285 (6%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR-GY 71
           E  +  Y+H I +IP+L K +E  LAK   E G  SA  +++ S+LRLVV +A  Y  G 
Sbjct: 73  EDSVKAYLHRIGRIPLLSKDQEERLAKEI-EAGSQSAKDKMINSNLRLVVSVAKRYAAGS 131

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           G+ + +++ EGNIGLM+AV KFD  RG++ +TY+MWWI+ ++   I      ++I     
Sbjct: 132 GMALLDLIQEGNIGLMKAVDKFDYRRGYKFSTYAMWWIRQSVTRAIADQARTIRIPVHMK 191

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
           +K     + ++ G  +   + N +      +A+ + +S  ++  +    +   SL++ + 
Sbjct: 192 EK-----MGKVSGAARKFLEENGREPNADELAELMEISRDQMDEIMRLYSDTVSLDSPVG 246

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             +          V D    EQ   +  E+      +   +S L  RE+ I   R     
Sbjct: 247 EEED---AMLMNFVADESMPEQY--QTAEQGILSEQINEILSELTEREQTILRLRFGFVE 301

Query: 252 PV--TLENLSSEFEVSRERVRQIEARAFKKVQ-----ESIQKQVE 289
               TLE +  E+ V+RER+RQIE +A +K++     +S++  +E
Sbjct: 302 NRIWTLEEVGREYHVTRERIRQIEGKALRKLKMKKETKSLRAYIE 346


>gi|157965030|ref|YP_001499854.1| RNA polymerase sigma factor RpoD [Rickettsia massiliae MTU5]
 gi|157844806|gb|ABV85307.1| RNA polymerase sigma factor [Rickettsia massiliae MTU5]
          Length = 633

 Score =  229 bits (584), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 70/247 (28%), Positives = 121/247 (48%), Gaps = 11/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E   L A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 374 ERQTLQAKKDMIEANLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 433

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    + + +          I
Sbjct: 434 TYATWWIRQAITRAIADQARTIRIPVH-----MIETINKILRTSRQMLNELGYEPTATEI 488

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A +L++   +V  +        SL   +   D +  Q  D++    D      I+   + 
Sbjct: 489 ANRLSMPLDKVRKVMKIAKEPISLENPVGD-DSDGGQLGDFI---EDKNAVAPIDAAIQS 544

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R + TR ++ L PRE R+   R         TLE +  +F+V+RER+RQIE++A +K+
Sbjct: 545 NLREVTTRVLATLTPREERVLRMRFGIGMNTDHTLEEVGQQFKVTRERIRQIESKALRKL 604

Query: 281 QESIQKQ 287
           Q  I+ +
Sbjct: 605 QHPIRSK 611


>gi|330831100|ref|YP_004394052.1| RNA polymerase sigma factor [Aeromonas veronii B565]
 gi|328806236|gb|AEB51435.1| RNA polymerase sigma factor [Aeromonas veronii B565]
          Length = 618

 Score =  229 bits (584), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 71/276 (25%), Positives = 126/276 (45%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L   +   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 349 LQQIEEETGLSIAQIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 408

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 409 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 466

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A ++ + E ++  +        S+   I   D   
Sbjct: 467 KLNRISRQMLQEMGREPNPE---ELAMRMGMPEDKIRKVLKIAKEPISMETPI--GDDED 521

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D    +  +    ++ RN     ++ L  RE ++   R   +     TL
Sbjct: 522 SHLGDFI---EDTTLALPADAATSESLRNATREVLAGLTAREAKVLRMRFGIDMNTDHTL 578

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 579 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 614


>gi|126663248|ref|ZP_01734246.1| RNA polymerase sigma-70 factor [Flavobacteria bacterium BAL38]
 gi|126624906|gb|EAZ95596.1| RNA polymerase sigma-70 factor [Flavobacteria bacterium BAL38]
          Length = 287

 Score =  229 bits (584), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 146/276 (52%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI K+ ++   EE  LA+R +  GD  A  +L  ++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQEIGKVDLITADEEVELAQRIK-AGDQRALEKLTKANLRFVVSVAKQYQNQGLT 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     +V++    N+  
Sbjct: 76  LPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLP--LNKIG 133

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               + ++   L+   +   +P     IAK+L+++ ++V           S++A +   +
Sbjct: 134 SINKINKMYALLEQSNE---RPPSAEEIAKELDMTVNDVKESMKNSGRHLSMDAPLV--E 188

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
              S   D L     G+      +   ++ +  + R++  L PRE  +        +  P
Sbjct: 189 GEDSNLYDVL---RSGESPNPDRELIHESLQTEIERALETLTPREADVVRLYFGLGDQHP 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 246 MTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>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 =  229 bits (584), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 128/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +  I +   L  +    +++R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 358 LQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 417

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 418 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 475

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 476 KLNRISRQMLQEMGREPLPE---ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDED 530

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++     + +      ++ L PRE ++   R   +     TL
Sbjct: 531 SHLGDFI---EDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTL 587

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 588 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 623


>gi|226945910|ref|YP_002800983.1| RNA polymerase sigma factor RpoS [Azotobacter vinelandii DJ]
 gi|16226165|gb|AAL16091.1|AF421351_3 stationary phase sigma factor [Azotobacter vinelandii]
 gi|226720837|gb|ACO80008.1| RNA polymerase sigma factor [Azotobacter vinelandii DJ]
          Length = 334

 Score =  229 bits (584), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 81/277 (29%), Positives = 134/277 (48%), Gaps = 13/277 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L   EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 66  YLNEIGFSPLLTPAEEVHFA-RLAQRGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 124

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 125 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 183

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +T           IA  L    +EV  M        S++  ++    +  
Sbjct: 184 LRAAR----ELTQKLDHEPSAEEIANLLEKPVAEVKRMLGLNERVTSVD--VSLGPDSDK 237

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
              D L  D       L++ ++       + + +  L  ++R +   R         TLE
Sbjct: 238 TLLDVLTDDRPSDPCDLLQDDDLSQS---IDQWLFDLTEKQREVVVRRFGLRGHESCTLE 294

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
            +  E  ++RERVRQI+  A K+++E ++K    S +
Sbjct: 295 EVGQEIGLTRERVRQIQVEALKRLREILEKNGLSSDA 331


>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 =  228 bits (583), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 117/247 (47%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 509 EASSREAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 568

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    +             ++
Sbjct: 569 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKMNRLSRQHLQEFGFEPDAPSL 623

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+ + E ++  +        S+   I   D + S   D++    D      IE   + 
Sbjct: 624 AEKMEMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNNTAPIEAAMQS 678

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 679 GLRDVVRDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKAIRKL 738

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 739 KHPSRSD 745


>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 =  228 bits (583), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 73/286 (25%), Positives = 127/286 (44%), Gaps = 24/286 (8%)

Query: 16  LSRYIHEIRKIPM----------LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVK 63
           L +Y  EI +             L  QE   + +R    E     A   ++ ++LRLV+ 
Sbjct: 413 LEKYSKEIYRAQRNLAQLEEQNNLNIQEIKEINRRVAIGEAKSRRAKKEMIEANLRLVIS 472

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      
Sbjct: 473 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 532

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           ++I            L R+   +   T     PE    + +++++ E +V  +       
Sbjct: 533 IRIPVHM--IETINKLNRISRQILQETGIEATPE---ELGRRMDMPEEKVRKVLKIAKEP 587

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            S+   I   +   S   D++    D   +  ++              +S L PRE ++ 
Sbjct: 588 ISMETPI--GEDEDSNLGDFI---EDINMESPVDFATSAGLMEATREILSTLTPREAKVL 642

Query: 244 EARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             R   +     TLE +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 643 RMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRAE 688


>gi|78222633|ref|YP_384380.1| sigma 28 (flagella/sporulation) [Geobacter metallireducens GS-15]
 gi|78193888|gb|ABB31655.1| RNA polymerase, sigma 38 subunit, RpoS [Geobacter metallireducens
           GS-15]
          Length = 326

 Score =  228 bits (583), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 71/274 (25%), Positives = 145/274 (52%), Gaps = 13/274 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI++  +L   EE VLA R  + GD +A  +++ S+LRLVVKIA  Y   G
Sbjct: 55  DDAIKLYLREIQRTTLLTADEEKVLASRIAK-GDKAARDKMIESNLRLVVKIAKRYINRG 113

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP  +++ EGN+GL++AV++F   +  R +TY+ WWI+ +++  ++     +++    + 
Sbjct: 114 LPFLDLIEEGNMGLIKAVERFKLSKECRFSTYATWWIRQSIERALVNQSRTIRLPVHVSD 173

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                ++ ++    + + +   +   V  +A ++NV+ + +  +   L    S+   +  
Sbjct: 174 -----DINKMLKITRELVNRFNREPTVKEVATEMNVNSAYIRRLMVLLKKTYSIERPM-- 226

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN- 251
            + +     D +         VL+E     N+  ++++  + L+  E++I   R   E+ 
Sbjct: 227 GENSDYFLIDTIEDTSSVSPAVLLEDL---NKYEIVSKWFASLSENEQKILTLRFGLEDK 283

Query: 252 -PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            P TL+ +   F V+RER+RQIEA++ +K+++ I
Sbjct: 284 EPQTLDTIGRSFGVTRERIRQIEAKSLEKLRKYI 317


>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|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 =  228 bits (583), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 73/286 (25%), Positives = 127/286 (44%), Gaps = 24/286 (8%)

Query: 16  LSRYIHEIRKIPM----------LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVK 63
           L +Y  EI +             L  QE   + +R    E     A   ++ ++LRLV+ 
Sbjct: 413 LEKYSKEIYRAQRNLAQLEEQNNLNIQEIKEINRRVAIGEAKSRRAKKEMIEANLRLVIS 472

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      
Sbjct: 473 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 532

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           ++I            L R+   +   T     PE    + +++++ E +V  +       
Sbjct: 533 IRIPVHM--IETINKLNRISRQILQETGIEATPE---ELGRRMDMPEEKVRKVLKIAKEP 587

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            S+   I   +   S   D++    D   +  ++              +S L PRE ++ 
Sbjct: 588 ISMETPI--GEDEDSNLGDFI---EDINMESPVDFATSAGLMEATREILSTLTPREAKVL 642

Query: 244 EARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             R   +     TLE +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 643 RMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRAE 688


>gi|72383665|ref|YP_293020.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str.
           NATL2A]
 gi|72003515|gb|AAZ59317.1| sigma-70 factor [Prochlorococcus marinus str. NATL2A]
          Length = 420

 Score =  228 bits (583), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 78/313 (24%), Positives = 141/313 (45%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR--------------EHG------------ 45
            E  +  Y+ EI +I +L   EE  LA++                E+G            
Sbjct: 106 TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLQLEEEAAQFESENGHFPSVKEWAVLA 165

Query: 46  -------------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 166 DMPLARFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 225

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 226 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKVLSQE 280

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA+ + ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 281 FGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADIENPE 338

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
           Q +     +   R  L   ++ L+PRER +   R   ++    TLE +   F+V+RER+R
Sbjct: 339 QDVA----KTLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIR 394

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 395 QIEAKALRKLRHP 407


>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 =  228 bits (583), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 70/246 (28%), Positives = 117/246 (47%), Gaps = 12/246 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 408 EREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 467

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    + +     +      +
Sbjct: 468 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREPTPEEL 522

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+KL +   +V  +        SL   I   D+  S   D++    D    + I+   + 
Sbjct: 523 AEKLAMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAVLPIDAAIQS 577

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 578 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKL 637

Query: 281 QESIQK 286
           +   + 
Sbjct: 638 KHPSRS 643


>gi|149190125|ref|ZP_01868401.1| RNA polymerase sigma-38 factor [Vibrio shilonii AK1]
 gi|148836014|gb|EDL52975.1| RNA polymerase sigma-38 factor [Vibrio shilonii AK1]
          Length = 325

 Score =  228 bits (583), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 80/288 (27%), Positives = 140/288 (48%), Gaps = 13/288 (4%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           ++               Y+ EI   P+L  +EE + A+R  + GD +A  R++ S+LRLV
Sbjct: 36  DKDMYDASAKSLDATQLYLGEIGFSPLLTAEEEVLYARRALK-GDEAARKRMIESNLRLV 94

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           VKI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++   
Sbjct: 95  VKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQT 154

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             +++      K L   LR  +     ++           IA+KL+   S+V  M     
Sbjct: 155 RTIRLPIHVV-KELNIYLRTAR----ELSQKLDHEPTAEEIAQKLDKPVSDVSKMLRLNE 209

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              S++  I    + +      L    D          +  + ++ L   +  LNP+++ 
Sbjct: 210 RISSVDTPIGGDGEKA-----LLDIIPDSTHSDPEVSTQDDDIKSSLIHWLDELNPKQKE 264

Query: 242 IFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +   R   L   P TLE +  E  ++RERVRQI+    +++++ + KQ
Sbjct: 265 VLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLRDILIKQ 312


>gi|238651104|ref|YP_002916962.1| RNA polymerase sigma factor RpoD [Rickettsia peacockii str. Rustic]
 gi|238625202|gb|ACR47908.1| RNA polymerase sigma factor RpoD [Rickettsia peacockii str. Rustic]
          Length = 634

 Score =  228 bits (583), Expect = 5e-58,   Method: Composition-based stats.
 Identities = 69/247 (27%), Positives = 120/247 (48%), Gaps = 11/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E   L A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 375 ERQTLQAKKDMIEANLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 434

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    + + +          I
Sbjct: 435 TYATWWIRQAITRAIADQARTIRIPVH-----MIETINKILRTSRQMLNELGYEPTATEI 489

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A +L++   +V  +        SL   +   D +  Q  D++    D      I+   + 
Sbjct: 490 ANRLSMPLDKVRKVMKIAKEPISLENPVGD-DSDGGQLGDFI---EDKNAVAPIDAAIQS 545

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R +  R ++ L PRE R+   R         TLE +  +F+V+RER+RQIE++A +K+
Sbjct: 546 NLREVTIRVLATLTPREERVLRMRFGIGMNTDHTLEEVGQQFKVTRERIRQIESKALRKL 605

Query: 281 QESIQKQ 287
           Q  I+ +
Sbjct: 606 QHPIRSK 612


>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 =  228 bits (583), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 67/267 (25%), Positives = 124/267 (46%), Gaps = 14/267 (5%)

Query: 29  LEKQEEYVLAKRYREH--GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L  Q+   + +R  +       A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 363 LTIQQIREICERIAQGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 422

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 423 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 480

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    +A+++ + E ++  +        S+   I   D + S   D++  
Sbjct: 481 LQEMGREASPE---ELAERMGMPEDKIRKVLKIAKEPISMETPI--GDDDDSHLGDFI-- 533

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   ++ ++    ++ +      +  L  RE ++   R   +     TLE +  +F+V
Sbjct: 534 -EDSTLELPLDSATAQSLKAATHEVLEGLTSREAKVLRMRFGIDMNTDHTLEEVGKQFDV 592

Query: 265 SRERVRQIEARAFKKVQESIQKQVELS 291
           +RER+RQIEA+A +K++   + +   S
Sbjct: 593 TRERIRQIEAKALRKLRHPSRSETLRS 619


>gi|116075287|ref|ZP_01472547.1| RNA polymerase sigma factor [Synechococcus sp. RS9916]
 gi|116067484|gb|EAU73238.1| RNA polymerase sigma factor [Synechococcus sp. RS9916]
          Length = 479

 Score =  228 bits (583), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 76/313 (24%), Positives = 141/313 (45%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG-------------------------- 45
            E  +  Y+ EI +I +L   EE  LA++  +                            
Sbjct: 167 TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLLLEELAAQFESDNGREPDTKEWAALV 226

Query: 46  -------------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 227 EMPLIKFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 286

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 287 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKVLSQE 341

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA+ + ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 342 FGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADIENPE 399

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
           Q + +   R++    L   ++ L+PRER +   R   ++    TLE +   F+V+RER+R
Sbjct: 400 QDVAKNLLRED----LEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIR 455

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 456 QIEAKALRKLRHP 468


>gi|93005952|ref|YP_580389.1| sigma 70 (RpoD) [Psychrobacter cryohalolentis K5]
 gi|92393630|gb|ABE74905.1| sigma 70 (RpoD) [Psychrobacter cryohalolentis K5]
          Length = 648

 Score =  228 bits (583), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 71/259 (27%), Positives = 120/259 (46%), Gaps = 14/259 (5%)

Query: 33  EEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           +   +A+R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV
Sbjct: 391 DMKDVARRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 450

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
            KF+  RG++ +TY+ WWI+ A+   I      ++I            + R+   L    
Sbjct: 451 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKINRVSRQLLQEM 508

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
                PE    + ++L + E++V  +        S+   I   D   S   D++    DG
Sbjct: 509 GREPTPE---ELGERLEMDEAKVRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDG 560

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRER 268
                ++       R      +  L  RE R+ + R   + P   TLE +  +F+V+RER
Sbjct: 561 TISSPVDDATAAGLREATRDVLGNLTEREARVLKMRFGIDMPTDHTLEEVGKQFDVTRER 620

Query: 269 VRQIEARAFKKVQESIQKQ 287
           +RQIEA+A +K++   + +
Sbjct: 621 IRQIEAKALRKLRHPSRSE 639


>gi|158522162|ref|YP_001530032.1| RpoD family RNA polymerase sigma factor [Desulfococcus oleovorans
           Hxd3]
 gi|158510988|gb|ABW67955.1| RNA polymerase, sigma 70 subunit, RpoD family [Desulfococcus
           oleovorans Hxd3]
          Length = 738

 Score =  228 bits (583), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 68/244 (27%), Positives = 115/244 (47%), Gaps = 12/244 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            ++   L+ ++LRLVV IA  Y   GL   +++ EGN+GLM+AV KF+  RG++ +TY+ 
Sbjct: 498 KASKSELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNVGLMKAVDKFEYRRGYKFSTYAT 557

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            L R   +L         PE    IA+K+
Sbjct: 558 WWIRQAITRAIADQARTIRIPVHM--IETINKLIRTSRYLVQERGYEPSPE---EIAEKM 612

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   ++  S   D++    D +  +  E     N   
Sbjct: 613 EIPLEKVRRVLKIAREPISLETPI--GEEEDSHLGDFI---EDKKFMIPSEAAVSMNLSE 667

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              + ++ L PRE ++   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 668 QTRKVLATLTPREEKVLRMRFGIGEKADHTLEEVGRDFAVTRERIRQIEAKALRKLRHPT 727

Query: 285 QKQV 288
           + ++
Sbjct: 728 RSKM 731


>gi|107099361|ref|ZP_01363279.1| hypothetical protein PaerPA_01000373 [Pseudomonas aeruginosa PACS2]
          Length = 274

 Score =  228 bits (583), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 102/272 (37%), Positives = 155/272 (56%), Gaps = 7/272 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+H +  IP+L  ++E  LA+R     DL AA ++V +HLR VV IA  Y GYGL 
Sbjct: 6   NLEAYVHSVNSIPLLSPEQERELAERLFYQQDLEAARQMVLAHLRFVVHIAKSYSGYGLA 65

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++
Sbjct: 66  QADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRK 125

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           LFFNLR  K  L  + +     E+V  +A+ L V   EV  M  RL G +        +D
Sbjct: 126 LFFNLRSQKKRLAWLNN-----EEVHRVAESLGVEPREVREMESRLTGQDMAFDPAADAD 180

Query: 195 KNSS-QWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENP 252
             S+ Q     + DH       +E  +  +  +  L  ++  L+ R R I + R L E  
Sbjct: 181 DESAYQSPAHYLEDHRYDPARQLEDADWSDSSSANLHEALEGLDERSRDILQQRWLSEEK 240

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL +L+ ++ VS ER+RQ+E  A  K++  I
Sbjct: 241 ATLHDLAEKYNVSAERIRQLEKNAMSKLKGRI 272


>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 =  228 bits (583), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 72/267 (26%), Positives = 124/267 (46%), Gaps = 14/267 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L  +    +++R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 352 LSIERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 411

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 412 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 469

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    +A+++ + E ++  +        S+   I   D   S   D++  
Sbjct: 470 LQEMGREPIPE---ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 522

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q+ ++     N R      ++ L PRE ++   R   +     TLE +  +F+V
Sbjct: 523 -EDNTLQLPMDAATATNLRAATNDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDV 581

Query: 265 SRERVRQIEARAFKKVQESIQKQVELS 291
           +RER+RQIEA+A +K++   +  V  S
Sbjct: 582 TRERIRQIEAKALRKLRHPSRSDVLRS 608


>gi|92118365|ref|YP_578094.1| RNA polymerase sigma factor RpoD [Nitrobacter hamburgensis X14]
 gi|91801259|gb|ABE63634.1| RNA polymerase, sigma 70 subunit, RpoD [Nitrobacter hamburgensis
           X14]
          Length = 717

 Score =  228 bits (583), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 74/273 (27%), Positives = 128/273 (46%), Gaps = 17/273 (6%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAH---RLVTSHLRLVVKIAMGYRGYGLPI 75
            EI+++  L   E     K     + G+  A      +V ++LRLV+ IA  Y   GL  
Sbjct: 446 GEIQQLAALTGLEIGEFRKIVHSVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQF 505

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +
Sbjct: 506 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----M 560

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + ++    + + +   +      +A+KL +   +V  +        SL   +   D+
Sbjct: 561 IETINKIVRTSRQMLNEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPLSLETPV--GDE 618

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPV 253
             S   D++    D    + I+   + N R   TR ++ L PRE R+   R         
Sbjct: 619 EDSHLGDFI---EDKNAVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDH 675

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 676 TLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 708


>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 =  228 bits (583), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 72/261 (27%), Positives = 122/261 (46%), Gaps = 18/261 (6%)

Query: 34  EYVLAKRYR---EHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           E    +R     + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM
Sbjct: 403 EITEFRRIVAMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 462

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +   + ++    +
Sbjct: 463 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSR 517

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
            +     +      +A+KL +   +V  +        SL   I   D+  S   D++   
Sbjct: 518 QMLHEIGREPTPEELAEKLQMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI--- 572

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVS 265
            D    + I+   + N R   TR ++ L PRE R+   R         TLE +  +F V+
Sbjct: 573 EDKNAVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVT 632

Query: 266 RERVRQIEARAFKKVQESIQK 286
           RER+RQIEA+A +K++   + 
Sbjct: 633 RERIRQIEAKALRKLKHPSRS 653


>gi|108803721|ref|YP_643658.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108764964|gb|ABG03846.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 365

 Score =  228 bits (583), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 79/272 (29%), Positives = 134/272 (49%), Gaps = 13/272 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI K P+L K +E  LAKR  E GD  A   L  ++LRLVV IA  Y G G+
Sbjct: 94  DAVQMYLDEIGKTPLLSKAQEVYLAKRI-ERGDRRAKAHLTRANLRLVVSIAKKYAGRGV 152

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++ EGNIGLM+AV+KFD  +G++ +TY+ WWI+ A+   I      +++     +K
Sbjct: 153 SLLDLIQEGNIGLMRAVEKFDYRKGYKFSTYATWWIRQAVTRAIADKGRTIRVPVHMVEK 212

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                  R++  L +  + +   E+V             +  ++ R     S++      
Sbjct: 213 --INKYYRVQRTLASELNRDPTDEEVAREMGVEVEEVERIRQVSRR-----SISLETPVG 265

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QEN 251
           + +SS+  D++  +       L +       +  +  +++ L  RER + E R       
Sbjct: 266 EDHSSELGDFIADEESESPHDLAKS---SLLKARMREALNGLPERERMVLEYRFGLTGGQ 322

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           P TLE +   F+V+RER+RQI+  A  K++ S
Sbjct: 323 PKTLEEVGERFDVTRERIRQIQLTALAKIKSS 354


>gi|295101750|emb|CBK99295.1| RNA polymerase sigma factor RpoD, C-terminal domain/RNA polymerase
           sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii L2-6]
          Length = 359

 Score =  228 bits (583), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 85/277 (30%), Positives = 142/277 (51%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI ++P+L  +EE     R  + GD  A  RL  ++LRLVV +A  Y G G
Sbjct: 86  DDPVKTYLKEIGRVPLLSAEEEAA-LARAAQAGDEDARRRLSEANLRLVVSVAKRYAGRG 144

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP  +++ EGN+GLM+A +KF+P+RGF+ +TY+ WWI+ ++   I      ++I      
Sbjct: 145 LPFLDLIQEGNLGLMKAAEKFEPDRGFKFSTYATWWIRQSITRAIADQGRTIRIPVH--- 201

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
             L  ++ R+K     +     +      IA +L++  + V  +        SL   +  
Sbjct: 202 --LVESINRVKKTAGELLRRTGREPTAEEIAAQLDMEPARVRELIQLAQDPISLETPV-- 257

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            ++  +  +D++  D  G   V  ++  R+  R  L   +  L PRE R+   R   E+ 
Sbjct: 258 GEEEDAHLEDFIQDDEAG---VPADEAGRQLLRRELMNVLKSLTPREERVIALRFGLEDG 314

Query: 253 --VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE L  EF V+RERVRQIEA+A +K++   + +
Sbjct: 315 RARTLEELGREFNVTRERVRQIEAKALRKLRHPSRAK 351


>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 =  228 bits (583), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 72/246 (29%), Positives = 115/246 (46%), Gaps = 12/246 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 427 ERDSARAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 486

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            L R    +         PE    +
Sbjct: 487 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKLVRTSRQMLHEIGREPAPE---EL 541

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+KL +   +V  +        SL   I   D+  S   D++    D    + ++   + 
Sbjct: 542 AEKLGMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDKTAIIPLDAAIQT 596

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 597 NLREATTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTRERIRQIEAKALRKL 656

Query: 281 QESIQK 286
           +   + 
Sbjct: 657 KHPSRS 662


>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 =  228 bits (583), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 72/296 (24%), Positives = 133/296 (44%), Gaps = 24/296 (8%)

Query: 6   MSIIVNGEIGLSRYIHEIRK----------IPMLEKQEEYVLAKRYR--EHGDLSAAHRL 53
           MS+       + RY H IR+            ML  +E   ++++    E     A   +
Sbjct: 351 MSLGKAFASAIERYQHAIREKQSNLIALQDSSMLPIRELKEISRQMATGEAKARKAKREM 410

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           + ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+
Sbjct: 411 IEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAI 470

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
              I      ++I        +   + ++    + I            +A+++++ E ++
Sbjct: 471 TRSIADQARTIRIPVH-----MIETINKMNRISRQILQETGAEPDPAELARRMDMPEDKI 525

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             +        S+   I   D + S   D++    D       +     + +      + 
Sbjct: 526 RKIMKISKEPISMETPI--GDDDDSHLGDFI---EDLATMAPSDAAMYASLKEATKEVLD 580

Query: 234 VLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 581 SLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSE 636


>gi|87118598|ref|ZP_01074497.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Marinomonas sp. MED121]
 gi|86166232|gb|EAQ67498.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Marinomonas sp. MED121]
          Length = 330

 Score =  228 bits (583), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 81/273 (29%), Positives = 140/273 (51%), Gaps = 12/273 (4%)

Query: 17  SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
             Y+ EI   P+L  +EE   A++    GD S+  R++ S+LRLVVKI+  Y   GL + 
Sbjct: 56  QMYLSEIGFSPLLSAEEEVYYARK-SLKGDESSRKRMIESNLRLVVKISRRYLNRGLSLL 114

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L 
Sbjct: 115 DLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELN 173

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
             LR  +     +T           IA  L+    +V  M        S+++ +   D +
Sbjct: 174 VYLRAAR----ELTQKLDHEPSAEDIADMLDRPVEDVQKMLSLNERISSIDSPVGGMDTD 229

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVT 254
            S  +      H G E    ++ +  +  + +   ++ LN ++R +   R       P T
Sbjct: 230 KSLVEIIADEQHAGPE----DERQFSDVVHNIDHWLNDLNEKQREVIARRFGLRGYEPST 285

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           LE++ +E  ++RERVRQI+  A +K++  ++KQ
Sbjct: 286 LEDVGAEIGLTRERVRQIQVEALRKLKLMMEKQ 318


>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 =  228 bits (583), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 118/247 (47%), Gaps = 12/247 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 381 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 440

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            L R+   +         PE    +A+++
Sbjct: 441 WWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREATPE---ELAERM 495

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D   ++ ++    ++ + 
Sbjct: 496 GMPEDKIRKVLKIAKEPISMETPI--GDDDDSHLGDFI---EDSTLELPLDSATAQSLKA 550

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                +  L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 551 ATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 610

Query: 285 QKQVELS 291
           + +   S
Sbjct: 611 RSETLRS 617


>gi|227499774|ref|ZP_03929874.1| DNA-directed RNA polymerase sigma subunit RpoD [Anaerococcus
           tetradius ATCC 35098]
 gi|227218160|gb|EEI83426.1| DNA-directed RNA polymerase sigma subunit RpoD [Anaerococcus
           tetradius ATCC 35098]
          Length = 606

 Score =  228 bits (583), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 72/244 (29%), Positives = 119/244 (48%), Gaps = 12/244 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  +L  ++LRLVV IA  Y G G+   +++ EGN+GLM+AV K+D  RGF+ +TY+ 
Sbjct: 368 KRAKQKLAETNLRLVVSIAKKYVGRGMSFLDLIQEGNMGLMKAVDKYDYNRGFKFSTYAT 427

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I     +      L R++  L      +   E    IA+++
Sbjct: 428 WWIRQAITRAIADQARTIRIPVHMVE--TINKLVRIQRQLVQDLGRDPSNE---EIAEQM 482

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   +++ S   D++  D         E       R 
Sbjct: 483 GIEVDKVQEIRKISQEPVSLETPI--GEEDDSHLGDFIEDD---TAVDPGEAANYTMLRE 537

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +S L  RE+R+ + R       P TLE +  EF+V+RER+RQIEA+A +K++   
Sbjct: 538 QLNDVLSCLGAREKRVLQLRFGLIDGTPRTLEEVGKEFDVTRERIRQIEAKALRKLKSPN 597

Query: 285 QKQV 288
           + ++
Sbjct: 598 KSEL 601



 Score = 40.6 bits (94), Expect = 0.31,   Method: Composition-based stats.
 Identities = 14/41 (34%), Positives = 24/41 (58%), Gaps = 2/41 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRL 53
           +  +  Y+ EI K+ +L   EE +LA+R  E G++ A  +L
Sbjct: 120 DDPVKMYLKEIGKVSLLTATEEIILARRM-EMGEI-AKKKL 158


>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 =  228 bits (583), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 439 RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 498

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 499 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 553

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 554 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTVAPADAALHASMRD 608

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 609 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 668

Query: 285 QKQ 287
           +  
Sbjct: 669 RSD 671


>gi|153840560|ref|ZP_01993227.1| RpoS [Vibrio parahaemolyticus AQ3810]
 gi|149745777|gb|EDM56907.1| RpoS [Vibrio parahaemolyticus AQ3810]
          Length = 415

 Score =  228 bits (583), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 78/272 (28%), Positives = 138/272 (50%), Gaps = 13/272 (4%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
            Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + +
Sbjct: 1   MYLGEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLVVKISRRYSNRGLALLD 59

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++      ++      K L  
Sbjct: 60  LIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTTRLPIHVV-KELNI 118

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            LR  +     ++           IA +L++   +V  M        S++  I       
Sbjct: 119 YLRTAR----ELSQKLDHEPTAEEIAAQLDIPVEDVSKMLRLNERISSVDTPI--GGDGE 172

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTL 255
               D +   ++   +V  + +   + ++ L   +  LNP+++ +   R   L   P TL
Sbjct: 173 KALLDIIPDANNSDPEVSTQDD---DIKSSLIHWLEELNPKQKEVLARRFGLLGYEPSTL 229

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +  E  ++RERVRQI+    ++++E  +K+
Sbjct: 230 EEVGREIGLTRERVRQIQVEGLRRLREMKEKK 261


>gi|15616654|ref|NP_239866.1| RNA polymerase factor sigma-32 [Buchnera aphidicola str. APS
           (Acyrthosiphon pisum)]
 gi|219681412|ref|YP_002467797.1| RNA polymerase sigma factor [Buchnera aphidicola str. 5A
           (Acyrthosiphon pisum)]
 gi|219681968|ref|YP_002468352.1| RNA polymerase sigma factor [Buchnera aphidicola str. Tuc7
           (Acyrthosiphon pisum)]
 gi|257471086|ref|ZP_05635085.1| RNA polymerase factor sigma-32 [Buchnera aphidicola str. LSR1
           (Acyrthosiphon pisum)]
 gi|7994684|sp|O05385|RP32_BUCAI RecName: Full=RNA polymerase sigma-32 factor
 gi|25288470|pir||H84932 DNA-directed RNA polymerase (EC 2.7.7.6) sigma-32 factor [imported]
           - Buchnera sp. (strain APS)
 gi|1929472|gb|AAB51433.1| heat shock sigma factor 32 [Buchnera aphidicola]
 gi|10038717|dbj|BAB12752.1| RNA polymerase sigma-32 factor [Buchnera aphidicola str. APS
           (Acyrthosiphon pisum)]
 gi|219621701|gb|ACL29857.1| RNA polymerase sigma factor [Buchnera aphidicola str. Tuc7
           (Acyrthosiphon pisum)]
 gi|219624255|gb|ACL30410.1| RNA polymerase sigma factor [Buchnera aphidicola str. 5A
           (Acyrthosiphon pisum)]
 gi|311085774|gb|ADP65856.1| RNA polymerase factor sigma-32 [Buchnera aphidicola str. LL01
           (Acyrthosiphon pisum)]
 gi|311086927|gb|ADP67007.1| RNA polymerase factor sigma-32 [Buchnera aphidicola str. JF99
           (Acyrthosiphon pisum)]
          Length = 284

 Score =  228 bits (583), Expect = 6e-58,   Method: Composition-based stats.
 Identities = 106/289 (36%), Positives = 165/289 (57%), Gaps = 8/289 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  K   + V     L  YI      PML  +EE  L KR R +GDL AA  L+ SHLR 
Sbjct: 1   MINKVQILSVTPPGNLDAYIRIANLWPMLSIEEEKKLTKRLRYNGDLDAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ I+  Y GYGL  S+++ EGNIGLM+AV++F+PE G RL ++++ WIK+ + EY+LR+
Sbjct: 61  VIHISRNYSGYGLLQSDLIQEGNIGLMKAVRRFNPEIGVRLVSFAVHWIKSEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT +Q++LFFNLR+ K  L    +     E++  +A++L VS  +V  M  R+
Sbjct: 121 WRIVKVATTKSQRKLFFNLRKTKKRLGWFNE-----EEIQIVARELGVSSRDVREMESRM 175

Query: 181 -AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPR 238
            A D + N        + +      + D        +E++  +    N L+ ++  L+ R
Sbjct: 176 SAQDVAFNPSPEEHCDSKTNSSIQYLQDKTSNFANGVEQDNWEEHAANKLSSALLRLDER 235

Query: 239 ERRIFEARRLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R I  AR L +N   TL+N+++ + +S ERVRQ+E  A KK++ +I+ 
Sbjct: 236 SRHIIHARWLDKNKKNTLQNIANNYGISAERVRQLEKNAMKKLKLAIEA 284


>gi|146329254|ref|YP_001209773.1| RNA polymerase sigma-32 factor [Dichelobacter nodosus VCS1703A]
 gi|146232724|gb|ABQ13702.1| RNA polymerase sigma-32 factor [Dichelobacter nodosus VCS1703A]
          Length = 297

 Score =  228 bits (583), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 104/271 (38%), Positives = 174/271 (64%), Gaps = 7/271 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           + +YI ++R+IP+L+  EE+ LA   +++  L+AA  L+  HL+ VV IA G+ GYGLP+
Sbjct: 27  IDQYIAKVRQIPILDADEEFRLATELQQNHSLAAAQTLIVHHLKFVVHIARGFLGYGLPL 86

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AVK+F+P+RG RL ++++ WIK+ + EY++R+W LVKI TT  Q++L
Sbjct: 87  GDLIQEGNIGLMKAVKRFEPQRGVRLVSFAVHWIKSEIHEYVIRNWRLVKIATTKAQRKL 146

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR +K ++  ++D      +   IA+ LNVS  +V+ M  R+ G D + + L  + D
Sbjct: 147 FFNLRSMKKNMHWLSD-----AEAQTIAEDLNVSVKDVLEMESRIHGQDIAFDPLDENDD 201

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE-NPV 253
           + +     WL  +           E++   ++ LT+ ++ L+ R R I E+R L E   V
Sbjct: 202 EENVAPAAWLTDESVDPALSTEHHEQKHLLQHQLTQGLNQLDARSREIIESRWLNEHEKV 261

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           TL+ L+S++ +S ER+RQIE +A  +++ S+
Sbjct: 262 TLQTLASKYHISAERIRQIEQQALLQLKNSM 292


>gi|325297456|ref|YP_004257373.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacteroides
           salanitronis DSM 18170]
 gi|324317009|gb|ADY34900.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacteroides
           salanitronis DSM 18170]
          Length = 286

 Score =  228 bits (582), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 74/287 (25%), Positives = 145/287 (50%), Gaps = 12/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI +  ++  +EE  LA+R R+ GD +A  +L  ++LR VV
Sbjct: 5   KITKSITNRESASLDKYLQEIGREDLITVEEEVELAQRIRK-GDRAALEKLTRANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 64  SVAKQYQNQGLSLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQAR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    NQ      + +     +   +    PE    +A +L++   ++         
Sbjct: 124 IVRLP--LNQVGSLNKISKAFSKFEQENERRPSPE---ELADELDIPVDKISDTLKVSGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     + NS    D LV D        +  E        + R++S L  RE+ I
Sbjct: 179 HISVDAPFVEGEDNS--LLDVLVNDDSPMADRSLVNESLS---REIDRALSTLTDREKEI 233

Query: 243 FEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +         +TLE +  +F ++RERVRQI+ +A ++++++ + ++
Sbjct: 234 IQMFFGIGTQEMTLEEIGDKFGLTRERVRQIKEKAIRRLRQNSRSKL 280


>gi|258542087|ref|YP_003187520.1| RNA polymerase sigma factor RpoD [Acetobacter pasteurianus IFO
           3283-01]
 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 =  228 bits (582), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 72/246 (29%), Positives = 115/246 (46%), Gaps = 12/246 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 427 ERDSARAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 486

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            L R    +         PE    +
Sbjct: 487 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKLVRTSRQMLHEIGREPAPE---EL 541

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+KL +   +V  +        SL   I   D+  S   D++    D    + ++   + 
Sbjct: 542 AEKLGMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDKTAIIPLDAAIQT 596

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 597 NLREATTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTRERIRQIEAKALRKL 656

Query: 281 QESIQK 286
           +   + 
Sbjct: 657 KHPSRS 662


>gi|145284374|gb|ABP51953.1| RpoS [Vibrio alginolyticus]
          Length = 328

 Score =  228 bits (582), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 80/288 (27%), Positives = 141/288 (48%), Gaps = 13/288 (4%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
            R+              Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLV
Sbjct: 39  AREKFDASSKSLDATQLYLGEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLV 97

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           VKI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++   
Sbjct: 98  VKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQT 157

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             +++      K L   LR  +     ++           IA +L++   +V  M     
Sbjct: 158 RTIRLPIHVV-KELNIYLRTAR----ELSQKLDHEPTAEEIAAQLDIPVEDVSKMLRLNE 212

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              S++  I           D +   ++   +V  + +   + ++ L   +  LNP+++ 
Sbjct: 213 RISSVDTPI--GGDGEKALLDIIPDANNSDPEVSTQDD---DIKSSLIHWLEELNPKQKE 267

Query: 242 IFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +   R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 268 VLARRFGLLGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLREVLIKQ 315


>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 =  228 bits (582), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 73/283 (25%), Positives = 130/283 (45%), Gaps = 24/283 (8%)

Query: 21  HEIRKIPMLEKQEEYVL--------AKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
             I K+ M+  +EE  L        ++R    E     A   +V ++LRLV+ IA  Y  
Sbjct: 365 RSIAKLKMI--EEETSLNVQNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTN 422

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I    
Sbjct: 423 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 482

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
                   L R+   +         PE    +A+++ + E ++  +        S+   I
Sbjct: 483 --IETINKLNRISRQMLQEMGREPLPE---ELAERMQMPEDKIRKVLKIAKEPISMETPI 537

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
              D   S   D++    D   ++ ++     + +      ++ L PRE ++   R   +
Sbjct: 538 --GDDEDSHLGDFI---EDTTLELPLDSATATSLKVATKDVLAGLTPREAKVLRMRFGID 592

Query: 251 --NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
                TLE +  +F+V+RER+RQIEA+A +K++   + +   S
Sbjct: 593 MNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRS 635


>gi|189424151|ref|YP_001951328.1| RNA polymerase, sigma 70 subunit, RpoD family [Geobacter lovleyi
           SZ]
 gi|189420410|gb|ACD94808.1| RNA polymerase, sigma 70 subunit, RpoD family [Geobacter lovleyi
           SZ]
          Length = 320

 Score =  228 bits (582), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 139/276 (50%), Gaps = 13/276 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ +I++ P+L  + E  LA+R  E GD +A ++++ ++LRLVVKIA  Y   G
Sbjct: 54  DDPVKIYLRDIQRTPLLNAEAEKELARRV-EQGDKAARNQMIEANLRLVVKIAKRYLNRG 112

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP  +++ EGN+GLM+AV++F  E+  R +TY+ WWI+ +++  ++     +++    + 
Sbjct: 113 LPFLDLIEEGNLGLMKAVERFSLEKECRFSTYATWWIRQSIERALVNQSRTIRLPVHVSD 172

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                ++ R+    + ++    +   V  +A  + +    +  +   L    S++  I  
Sbjct: 173 -----DISRMLKVSRQLSQELHREPSVQELADAMQIKPLHIRKLMILLRRTCSMDVPI-- 225

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE-- 250
            + N     D +    D       +  E  +R  ++      L+  ER I   R   +  
Sbjct: 226 GEGNDFFLVDTI---EDTNAVSPADLLENIDRYELIAEHFDQLSENERTILGLRFGLDDR 282

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +P TL+ +   F V+RER+RQIEA++ +K++   + 
Sbjct: 283 DPQTLDTIGQSFGVTRERIRQIEAKSLEKLKALAKS 318


>gi|91227834|ref|ZP_01262007.1| DNA-directed RNA polymerase, sigma subunit [Vibrio alginolyticus
           12G01]
 gi|269965239|ref|ZP_06179373.1| RNA polymerase sigma-38 factor [Vibrio alginolyticus 40B]
 gi|91188344|gb|EAS74640.1| DNA-directed RNA polymerase, sigma subunit [Vibrio alginolyticus
           12G01]
 gi|269830225|gb|EEZ84452.1| RNA polymerase sigma-38 factor [Vibrio alginolyticus 40B]
          Length = 328

 Score =  228 bits (582), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 80/288 (27%), Positives = 141/288 (48%), Gaps = 13/288 (4%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
            R+              Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLV
Sbjct: 39  AREEFDASSKSLDATQLYLGEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLV 97

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           VKI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++   
Sbjct: 98  VKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQT 157

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             +++      K L   LR  +     ++           IA +L++   +V  M     
Sbjct: 158 RTIRLPIHVV-KELNIYLRTAR----ELSQKLDHEPTAEEIAAQLDIPVEDVSKMLRLNE 212

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              S++  I           D +   ++   +V  + +   + ++ L   +  LNP+++ 
Sbjct: 213 RISSVDTPI--GGDGEKALLDIIPDANNSDPEVSTQDD---DIKSSLIHWLEELNPKQKE 267

Query: 242 IFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +   R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 268 VLARRFGLLGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLREVLIKQ 315


>gi|298293645|ref|YP_003695584.1| RNA polymerase, sigma 32 subunit, RpoH [Starkeya novella DSM 506]
 gi|296930156|gb|ADH90965.1| RNA polymerase, sigma 32 subunit, RpoH [Starkeya novella DSM 506]
          Length = 293

 Score =  228 bits (582), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 110/270 (40%), Positives = 170/270 (62%), Gaps = 4/270 (1%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
                 P+L++ EEY LA+R+ E  D  A H L+ +H+RL + IA  +R YGLP+ +++ 
Sbjct: 13  RAAMAAPLLDRTEEYELARRWAEQHDEKALHALIHAHMRLAIAIARRFRNYGLPMPDLIQ 72

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           EG+IGLM+A  +F+     R ATY+ WWI+AA+Q+Y+LR+WS+V+ GT++ QK LFFNLR
Sbjct: 73  EGHIGLMEAASRFETTHEVRFATYASWWIRAAIQDYVLRNWSIVRGGTSSGQKALFFNLR 132

Query: 141 RLKGHLQAI---TDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSSDKN 196
           R++  L+          + E   +IA+KL VSE EV  M+ RL   D SLNA ++  +++
Sbjct: 133 RVRARLERANGGAGETTREEMHRSIAEKLGVSEIEVARMDARLNVPDLSLNAPLSFGEED 192

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
            ++  D LV      ++ +  + + + RR  L  ++  LN RE RI EARRL E+  TLE
Sbjct: 193 GAERMDQLVAADPLPDEQVSMEIDGERRRRWLQGALRGLNEREFRIIEARRLTEDSETLE 252

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L     +S+ERVRQIE+RA +K++ ++ +
Sbjct: 253 VLGERLGISKERVRQIESRAIEKLRIALTR 282


>gi|162457339|ref|YP_001619706.1| RNA polymerase sigma factor rpoD [Sorangium cellulosum 'So ce 56']
 gi|161167921|emb|CAN99226.1| RNA polymerase sigma factor rpoD [Sorangium cellulosum 'So ce 56']
          Length = 443

 Score =  228 bits (582), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 106/282 (37%), Positives = 168/282 (59%), Gaps = 5/282 (1%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           + ++    L  Y+ E+++  +L   EE  L  +Y +  D++ A RLVT++LRLVVK+A  
Sbjct: 159 VALSRTDPLQAYLREVQRHALLTPDEEKELTIKYTKTQDVATAARLVTANLRLVVKLAYE 218

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           YR     I +++ EGNIGLMQAVK++DP RG +L++Y+ WWI+A +  +IL +W LVK+G
Sbjct: 219 YRRAYKNIMDLIQEGNIGLMQAVKRYDPYRGVKLSSYAAWWIRAYILRFILNNWRLVKLG 278

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESL 186
           TT  Q++LFFNL + K  L A+            IAK+L+V E EV+ M+ RLA G+ SL
Sbjct: 279 TTQAQRKLFFNLNKEKAKLSAM----GIEPTAAEIAKRLSVEEKEVVDMDRRLASGEASL 334

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           +A +   +  +    + LV      +      E      + L++    L  ++  IF+ R
Sbjct: 335 DAPVGDLEGRTIPRVELLVSSGASPDTAFEASEMGMLVHDRLSKFRETLKGKDVIIFDKR 394

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
              E+P+TL+ L +EF +SRERVRQ+EAR   K++  +Q+++
Sbjct: 395 MAAEDPLTLQELGNEFGISRERVRQLEARLQSKLRTYLQEEL 436


>gi|163802977|ref|ZP_02196864.1| protein-L-isoaspartate O-methyltransferase [Vibrio sp. AND4]
 gi|159173267|gb|EDP58095.1| protein-L-isoaspartate O-methyltransferase [Vibrio sp. AND4]
          Length = 328

 Score =  228 bits (582), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 80/288 (27%), Positives = 141/288 (48%), Gaps = 13/288 (4%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
            R+              Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLV
Sbjct: 39  TREEFDASSKSLDATQLYLGEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLV 97

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           VKI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++   
Sbjct: 98  VKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQT 157

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             +++      K L   LR  +     ++           IA +L++   +V  M     
Sbjct: 158 RTIRLPIHVV-KELNIYLRTAR----ELSQKLDHEPTAEEIAAQLDIPVEDVSKMLRLNE 212

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              S++  I           D +   ++   +V  + +   + ++ L   +  LNP+++ 
Sbjct: 213 RISSVDTPI--GGDGEKALLDIIPDANNSDPEVSTQDD---DIKSSLILWLEELNPKQKE 267

Query: 242 IFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +   R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 268 VLARRFGLLGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLREILIKQ 315


>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 =  228 bits (582), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 115/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 533 ESSSRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 592

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    +              +
Sbjct: 593 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKMNRISRQHLQEFGFEPDAGIL 647

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A K+ + E ++  +        S+   I   D + S   D++    D      IE   + 
Sbjct: 648 AAKMEIPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDSSNTAPIEAAMQA 702

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 703 GLRDVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKL 762

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 763 KHPSRSD 769


>gi|238899138|ref|YP_002924820.1| sigma H (sigma 32) factor of RNA polymerase; transcription of heat
           shock and stress proteins [Candidatus Hamiltonella
           defensa 5AT (Acyrthosiphon pisum)]
 gi|229466898|gb|ACQ68672.1| sigma H (sigma 32) factor of RNA polymerase; transcription of heat
           shock and stress proteins [Candidatus Hamiltonella
           defensa 5AT (Acyrthosiphon pisum)]
          Length = 285

 Score =  228 bits (582), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 102/288 (35%), Positives = 163/288 (56%), Gaps = 9/288 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +  +  L  Y+       ML ++EE  LA+R   HGDL+AA +L+ SHLR 
Sbjct: 1   MMKEMPTLALMPQGSLEAYLRVSNSYAMLTEEEERALAERLHSHGDLNAARQLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  IA  Y GYGLP ++++ EGNIGLM+AV++F+P  G RL ++++ WIKA + EY+LR+
Sbjct: 61  VAHIARHYSGYGLPQADLIQEGNIGLMKAVRRFNPNMGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L   + N     +V  +AK+L V+  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKAKQRLGWFSQN-----EVDMVAKELGVTSKDVREMESRM 175

Query: 181 -AGDESLNALINSS--DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
            A D +    +     +  S     +L   +      + +     +  + L  ++  L+ 
Sbjct: 176 SAQDMAFELPLEDESREGQSPAPVMYLEDKNSDFADNIEKNNWGDHAADSLWVALKGLDE 235

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R + I  AR L ++   TL+ L+  + VS ERVRQ+E  A KK++ SI
Sbjct: 236 RSQDIIRARWLDDDNKSTLQELADRYGVSAERVRQLEKNAMKKLRLSI 283


>gi|197294657|ref|YP_001799198.1| RNA polymerase sigma factor [Candidatus Phytoplasma australiense]
 gi|171853984|emb|CAM11947.1| RNA polymerase sigma factor [Candidatus Phytoplasma australiense]
          Length = 476

 Score =  228 bits (582), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 75/318 (23%), Positives = 142/318 (44%), Gaps = 41/318 (12%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYV------LAKRYREH----------- 44
           N   ++  +  +  +  Y+ EI +IP+L K+EE        L K  ++            
Sbjct: 158 NITKINSDIKIDDSVRMYLKEIGRIPLLSKEEEQKKTFAVFLGKEAKKKLTKFRNQEIDL 217

Query: 45  GDLS-------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            D               A   LV S+ RLVV IA  Y G G+   +++ EGN+GLM+AV 
Sbjct: 218 SDQEVKQLESQIIQANQAKDVLVESNYRLVVSIAKRYIGRGVLFLDLIQEGNMGLMRAVD 277

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD ++G RL+TY+ +W+   +   I      ++I     +      + ++    + +T 
Sbjct: 278 KFDYQKGLRLSTYATYWVIQGVTRAIADQARTIRIPVHIVE-----TINKMSLCTRKLTQ 332

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              K   +  +A+K+N+   ++ S+        SL      + ++ +   D++    D  
Sbjct: 333 ELKKKPTIEELAEKMNIPADKLRSIQYIEKKPISLEVPPAENKEDETSLGDFI---SDPN 389

Query: 212 EQVLIEKEERKNRRNMLTRSMS-VLNPRERRIFEARR--LQENPVTLENLSSEFEVSRER 268
                E   ++  + +L   +   L  RE ++ + R   L     TLE + + F V+RER
Sbjct: 390 VLSPHEYMMKEVTQKLLDEVLENTLTEREEKVLKMRYGFLDGKVYTLEEIGNLFGVTRER 449

Query: 269 VRQIEARAFKKVQESIQK 286
           +RQIE++A ++++   ++
Sbjct: 450 IRQIESKALRRLRTPAKQ 467


>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 =  228 bits (582), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 116/243 (47%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 547 RDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 606

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + ++    +              +A K+
Sbjct: 607 WWIRQAITRSIADQARTIRIPVH-----MIETINKMNRISRQHLQEFGFEPDASILAAKM 661

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    DG     IE   +   R+
Sbjct: 662 EIPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDGANTAPIEAAMQAGLRD 716

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E  +  TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 717 VVKDILDGLTPREAKVLRMRFGIEMTSDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPS 776

Query: 285 QKQ 287
           +  
Sbjct: 777 RSD 779


>gi|146299193|ref|YP_001193784.1| RpoD family RNA polymerase sigma factor [Flavobacterium johnsoniae
           UW101]
 gi|57471283|gb|AAW50927.1| RpoD [Flavobacterium johnsoniae]
 gi|146153611|gb|ABQ04465.1| RNA polymerase, sigma 70 subunit, RpoD family [Flavobacterium
           johnsoniae UW101]
          Length = 287

 Score =  228 bits (582), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 72/276 (26%), Positives = 146/276 (52%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI K+ ++   EE  LA+R +  GD  A  +L  ++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQEIGKVDLITADEEVELAQRIK-AGDQRALEKLTKANLRFVVSVAKQYQNQGLT 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     +V++    N+  
Sbjct: 76  LPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLP--LNKIG 133

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               + ++   L+   +   +P     IAK+L+++ ++V           S++A +   +
Sbjct: 134 SINKINKMYALLEQSNE---RPPSAEEIAKELDMTVNDVKESMKNSGRHLSMDAPLV--E 188

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
              S   D L     G+      +   ++ R  + RS+  L PRE  +        +  P
Sbjct: 189 GEDSNLYDVL---RSGESPNPDRELIHESLRTEIERSLETLTPREADVVRLYFGLGDQHP 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 246 MTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>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 =  228 bits (582), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 128/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +  I +   L  +    +++R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 373 LQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 432

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 433 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 490

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 491 KLNRISRQMLQEMGREPLPE---ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDED 545

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++     + +      ++ L PRE ++   R   +     TL
Sbjct: 546 SHLGDFI---EDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTL 602

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 603 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 638


>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 =  228 bits (582), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 72/267 (26%), Positives = 124/267 (46%), Gaps = 14/267 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L  +    +++R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 352 LSIERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 411

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 412 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 469

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    +A+++ + E ++  +        S+   I   D   S   D++  
Sbjct: 470 LQEMGREPIPE---ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 522

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q+ ++     N R      ++ L PRE ++   R   +     TLE +  +F+V
Sbjct: 523 -EDNTLQLPMDAATATNLRAATNDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDV 581

Query: 265 SRERVRQIEARAFKKVQESIQKQVELS 291
           +RER+RQIEA+A +K++   +  V  S
Sbjct: 582 TRERIRQIEAKALRKLRHPSRSDVLRS 608


>gi|126175320|ref|YP_001051469.1| RpoD family RNA polymerase sigma factor [Shewanella baltica OS155]
 gi|125998525|gb|ABN62600.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella baltica
           OS155]
          Length = 326

 Score =  228 bits (582), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 82/271 (30%), Positives = 141/271 (52%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   +++  + G   + +R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 57  YLGEIGFSPLLSAEEEVYFSRKALK-GCAKSRNRMIESNLRLVVKIARRYNNRGLALLDL 115

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 116 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 174

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            IA+KL VS ++V  M        S++  +     N  
Sbjct: 175 LRTAR----ELAQKLDHEPTAEEIAEKLQVSSADVSRMLKLNEKITSVDTPLWG--DNDK 228

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  D +      ++ E+  N    + + ++ LN ++R +   R   L   P TLE
Sbjct: 229 ALLDILADDDNVGPDYKVQDEDISNS---VVKWLNELNTKQREVLARRFGLLGYEPSTLE 285

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++ +E  ++RERVRQI+  A K++++ +  Q
Sbjct: 286 DVGAEIGLTRERVRQIQVEALKRLRDLLGSQ 316


>gi|317969651|ref|ZP_07971041.1| RNA polymerase sigma factor RpoD [Synechococcus sp. CB0205]
          Length = 470

 Score =  228 bits (582), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 77/313 (24%), Positives = 143/313 (45%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE--------------HG------------ 45
            E  +  Y+ EI +I +L   EE  LA++  +              +G            
Sbjct: 158 TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLQLEELANQFEADNGHYPDTKEWATLV 217

Query: 46  -------------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 218 EMPLVKFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 277

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 278 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKTLSQE 332

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA+ + ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 333 FGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADIENPE 390

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
           Q + +   R++    L   ++ L+PRER +   R   ++    TLE +   F+V+RER+R
Sbjct: 391 QDVAKNLLRED----LEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIR 446

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 447 QIEAKALRKLRHP 459


>gi|225011103|ref|ZP_03701566.1| RNA polymerase, sigma 70 subunit, RpoD family [Flavobacteria
           bacterium MS024-3C]
 gi|225004737|gb|EEG42696.1| RNA polymerase, sigma 70 subunit, RpoD family [Flavobacteria
           bacterium MS024-3C]
          Length = 287

 Score =  228 bits (582), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 82/276 (29%), Positives = 147/276 (53%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ +I KI ++  QEE  LA+R +  GD  A  RL T++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQDISKIDLINAQEEVELAQRIK-AGDAVALERLTTANLRFVVSVAKQYQNQGLT 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ A+ + +     +V++    N+  
Sbjct: 76  LPDLINEGNVGLVKAAKRFDETRGFKFISYAVWWIRQAILQALAEQARIVRLP--LNKIG 133

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               + +   +L+        PE    IAK+L ++ S+V           S++A +   +
Sbjct: 134 SINKINKAFSYLEQAHQRPPSPE---EIAKELEMTVSDVKQSLKNSGRHVSMDAPLIDGE 190

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
            NSS +      D    +Q LI+          +TR++  L+PRE  + +         P
Sbjct: 191 -NSSLYDVLDYGDSPRPDQALIQSSLHTE----ITRALDTLSPREADVIKLFYGIGEQPP 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TL  +   F+++RERVRQI  +A +K++ S + ++
Sbjct: 246 MTLAEIGLTFDLTRERVRQIREKAIRKLRHSSKNKL 281


>gi|206895369|ref|YP_002247042.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Coprothermobacter proteolyticus DSM 5265]
 gi|206737986|gb|ACI17064.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Coprothermobacter proteolyticus DSM 5265]
          Length = 360

 Score =  228 bits (582), Expect = 7e-58,   Method: Composition-based stats.
 Identities = 83/270 (30%), Positives = 143/270 (52%), Gaps = 14/270 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+H++ +  +L  ++E +LA+R  E  D +A   L+  +LRLV+ IA  Y   GL   E+
Sbjct: 91  YLHDVGQYDLLTAEQERILAQRI-EKNDAAAREELIKRNLRLVISIAKKYTNKGLSFMEL 149

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGL++AV+KFD  +G++ +TY+ WWIK A+   +     L++      +      
Sbjct: 150 IQEGNIGLIKAVEKFDWRKGYKFSTYATWWIKQAITRALADQSRLIRRPVHMVE-----A 204

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM-NCRLAGDESLNALINSSDKNS 197
             + +  L  + +   +   V  +A+ L  SE +V+++        +SL+A I   D++ 
Sbjct: 205 YHQFQKKLNELYNQLGREPTVQELAEALGFSEDKVLALKQMSNPEPQSLDATI--GDQDD 262

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTL 255
           S+ QD++    +G       +EER+         +S LN RER I E R    +    TL
Sbjct: 263 SRVQDFVPDTGEGAADKYFWEEERRRVL---EEVLSTLNKREREIIEMRYGLVDGVEHTL 319

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           E + + F ++RERVRQIE +A +K++   +
Sbjct: 320 EEVGASFNITRERVRQIETKALRKLRHPTR 349


>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|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]
          Length = 625

 Score =  228 bits (582), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 128/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +  I +   L  +    +++R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 356 LQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 415

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 416 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 473

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 474 KLNRISRQMLQEMGREPLPE---ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDED 528

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++     + +      ++ L PRE ++   R   +     TL
Sbjct: 529 SHLGDFI---EDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTL 585

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 586 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 621


>gi|239995277|ref|ZP_04715801.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Alteromonas macleodii ATCC
           27126]
          Length = 330

 Score =  228 bits (582), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 79/271 (29%), Positives = 135/271 (49%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    G  ++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 59  YLGEIGFSPLLTAEEEVYFARR-SLKGCEASRKRMIVSNLRLVVKIARRYNNRGLALLDL 117

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++       +    
Sbjct: 118 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV--VKELNV 175

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
             R    L    D+    E    IA  L+    +V  M        S++  I    +N  
Sbjct: 176 YLRASRELSQKLDHEPTAE---EIALALDKPVEDVTKMLRLNERITSVDTPI--GGENDK 230

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
              D +  +    E    E  +  + ++ +   +  LNP++R +   R       P TLE
Sbjct: 231 ALLDIIADEK---EFSPEESLQDSDIKSNIVTWLEELNPKQREVLARRFGLMGYEPSTLE 287

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++ +E  ++RERVRQI+  A +++++ +  Q
Sbjct: 288 DVGAEIGLTRERVRQIQVEALRRLRDMLGHQ 318


>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]
 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|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]
 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]
          Length = 628

 Score =  228 bits (582), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 74/278 (26%), Positives = 126/278 (45%), Gaps = 14/278 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           +   + I +I K   L   E   ++KR    E     A   +V ++LRLV+ IA  Y   
Sbjct: 352 LAFQQKIADIEKELGLNVSEIKDISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNR 411

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I     
Sbjct: 412 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM- 470

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
                  + R+   L         PE    + ++L + E +V  +        S+   I 
Sbjct: 471 -IETINKINRVSRQLLQEMGREPTPE---ELGERLEMDEVKVRKVLKIAKEPISMETPI- 525

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             D   S   D++    D      I+    +  +      +  L  RE ++ + R   + 
Sbjct: 526 -GDDEDSHLGDFI---EDQNITSPIDAATSEGLKEATREVLENLTEREAKVLKMRFGIDM 581

Query: 252 P--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           P   TLE +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 582 PTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 619


>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 =  228 bits (582), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 65/241 (26%), Positives = 115/241 (47%), Gaps = 12/241 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV+KF+  RG++ +TY+ WW
Sbjct: 357 AKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVEKFEYRRGYKFSTYATWW 416

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I            L R++  L         PE    +A+++ +
Sbjct: 417 IRQAITRSIADQARTIRIPVHM--IETINKLNRIQRQLLQKMGREPTPE---ELAEEMEM 471

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E +V  +        S+   +   D   S   D++    D       +  + +     +
Sbjct: 472 PEDKVRKVMKIAKEPISMETPV--GDDEDSSLGDFI---EDSNILSPQDSADLEGMGETV 526

Query: 229 TRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +S L PRE ++   R         TLE +  +F+V+RER+RQIEA+A +K++   + 
Sbjct: 527 REMLSTLTPREAKVLRMRFGLGMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRA 586

Query: 287 Q 287
           +
Sbjct: 587 E 587


>gi|239931595|ref|ZP_04688548.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291439967|ref|ZP_06579357.1| transcription initiation factor sigma [Streptomyces ghanaensis ATCC
           14672]
 gi|291342862|gb|EFE69818.1| transcription initiation factor sigma [Streptomyces ghanaensis ATCC
           14672]
          Length = 335

 Score =  228 bits (582), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 79/311 (25%), Positives = 139/311 (44%), Gaps = 38/311 (12%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------REH 44
           +S  +     +  Y+  I ++ +L  ++E  LAKR                      RE 
Sbjct: 27  LSSDLGTADQVKDYLRLISRVRLLTAEQEVELAKRIEAGLYAERLLAEEPVLEPRYRREL 86

Query: 45  G-----DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           G        A + L  ++LRLVV +A  Y G GL   +++ EGN GL++AV+KFD  +GF
Sbjct: 87  GLLAEDGRRAKNHLTEANLRLVVSVAKRYTGRGLQFMDLIQEGNAGLIRAVEKFDYTKGF 146

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWIK  +   +      ++I   A +  +   + R++  L   T     PE V
Sbjct: 147 KFSTYATWWIKQGITRAMADQSRTIRIPVHAVE--VINRVARVRRELIRATGTEPTPEDV 204

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
              A   ++S  ++  ++       SL+  +  S++   ++ D +V   D       E  
Sbjct: 205 AERA---SISVEKLAELDAYAREPVSLDLPL--SEEGGGEFGDLIV---DSDSPSPWEVV 256

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAF 277
              + +  +   ++ L+PRE  I   R     E P TLE +   + V+RER+RQIE++  
Sbjct: 257 AFGHLQRAVRSVLADLSPREAGIISLRYGLFGERPRTLEEIGQVYGVTRERIRQIESKTM 316

Query: 278 KKVQESIQKQV 288
            K++   +   
Sbjct: 317 SKLRHPARSHA 327


>gi|32490821|ref|NP_871075.1| RNA polymerase factor sigma-32 [Wigglesworthia glossinidia
           endosymbiont of Glossina brevipalpis]
 gi|25166027|dbj|BAC24218.1| rpoH [Wigglesworthia glossinidia endosymbiont of Glossina
           brevipalpis]
          Length = 281

 Score =  228 bits (582), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 99/287 (34%), Positives = 164/287 (57%), Gaps = 7/287 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M + N+   VN +  L  YI +     ML  +EE +L +R   +GDL AA +L+ SHLR 
Sbjct: 1   MKKINILTCVN-QSSLESYIKKANSYSMLSIEEEKILTERLHYNGDLLAAKKLILSHLRF 59

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV I+  Y GYGL  ++++ EGN+GLM+AVK+F+P  G RL ++++ WIKA + EY+LR+
Sbjct: 60  VVHISRNYSGYGLQRADLIQEGNVGLMKAVKRFNPAIGVRLVSFAVHWIKAEIHEYVLRN 119

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L           +V  +AK L V+  +V  M  R+
Sbjct: 120 WRIVKVATTKAQRKLFFNLRKAKKKLGWFNQY-----EVDMLAKSLGVTSKDVREMESRM 174

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +  +      +  DK+ +    +L          + E     +  + L+ ++S L+ R +
Sbjct: 175 SAKDMAFDFNSEEDKHKNNAILYLKDKTSDFADTIEEDNWDIHATDKLSAALSNLDLRSQ 234

Query: 241 RIFEARRLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            I  +R L+ +N  TL+ L+ ++ +S ER+RQ+E  A KK++ +++ 
Sbjct: 235 EIIRSRWLRYDNKSTLKELAKKYGISAERIRQLEKNAMKKIRFAVES 281


>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 =  228 bits (582), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 71/275 (25%), Positives = 120/275 (43%), Gaps = 14/275 (5%)

Query: 17  SRYIHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            R I +I     L   E   + +R    E     A   +V ++LRLV+ IA  Y   GL 
Sbjct: 333 QRQIGQIEAATGLTVTEIKEINRRMSMGEARARRAKKEMVEANLRLVISIAKKYTNRGLQ 392

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
             +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        
Sbjct: 393 FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IE 450

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               L R+   +         PE    + +++ + E +V  +        S+   I   D
Sbjct: 451 TINKLNRISRQMLQEMGREPTPE---ELGERMEMPEDKVRKVLKIAKEPISMETPI--GD 505

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NP 252
              S   D++    D      I+    +         ++ L  RE ++   R   +    
Sbjct: 506 DEDSHLGDFI---EDQTINSPIDAATGQGLMEATKDVLAGLTAREAKVLRMRFGIDMNTD 562

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            TLE +  +F+V+RER+RQIEA+A +K++   +  
Sbjct: 563 HTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSD 597


>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 =  228 bits (582), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 72/267 (26%), Positives = 125/267 (46%), Gaps = 14/267 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L  +    +++R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 359 LSIERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 418

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 419 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 476

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    +A+++ + E ++  +        S+   I   D   S   D++  
Sbjct: 477 LQEMGREPLPE---ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 529

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q+ ++   + N R      ++ L PRE ++   R   +     TLE +  +F+V
Sbjct: 530 -EDTTLQLPMDAATQTNLRAATNEVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDV 588

Query: 265 SRERVRQIEARAFKKVQESIQKQVELS 291
           +RER+RQIEA+A +K++   +  V  S
Sbjct: 589 TRERIRQIEAKALRKLRHPSRSDVLRS 615


>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 =  228 bits (582), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 73/246 (29%), Positives = 115/246 (46%), Gaps = 12/246 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 414 ERDSARAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 473

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            L R    +         PE    +
Sbjct: 474 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKLVRTSRQMLHEIGREPAPE---EL 528

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+KL +   +V  +        SL   I   D+  S   D++    D    + ++   + 
Sbjct: 529 AEKLGMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDKAAVIPLDAAIQT 583

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R   TR +S L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 584 NLREATTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTRERIRQIEAKALRKL 643

Query: 281 QESIQK 286
           +   + 
Sbjct: 644 KHPSRS 649


>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 =  228 bits (582), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 75/278 (26%), Positives = 126/278 (45%), Gaps = 14/278 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           +   + I +I K   L   E   ++KR    E     A   +V ++LRLV+ IA  Y   
Sbjct: 354 LAFQQKIADIEKELGLNVSEIKDISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNR 413

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I     
Sbjct: 414 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM- 472

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
                  + R+   L         PE    + ++L + E +V  +        S+   I 
Sbjct: 473 -IETINKINRVSRQLLQEMGREPTPE---ELGERLEMDEVKVRKVLKIAKEPISMETPI- 527

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             D   S   D++    D      I+    K  +      +  L  RE ++ + R   + 
Sbjct: 528 -GDDEDSHLGDFI---EDQNITSPIDAATSKGLKEATREVLENLTEREAKVLKMRFGIDM 583

Query: 252 P--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           P   TLE +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 584 PTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 621


>gi|260878982|ref|ZP_05891337.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus AN-5034]
 gi|260895455|ref|ZP_05903951.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus Peru-466]
 gi|157674653|gb|ABV60415.1| RpoS [Vibrio parahaemolyticus]
 gi|308088215|gb|EFO37910.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus Peru-466]
 gi|308090442|gb|EFO40137.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus AN-5034]
 gi|328474140|gb|EGF44945.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus 10329]
          Length = 329

 Score =  228 bits (582), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 80/287 (27%), Positives = 141/287 (49%), Gaps = 13/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           R+              Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVV
Sbjct: 41  REEFDASSKSLDATQLYLGEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLVV 99

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           KI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++    
Sbjct: 100 KISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTR 159

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            +++      K L   LR  +     ++           IA +L++   +V  M      
Sbjct: 160 TIRLPIHVV-KELNIYLRTAR----ELSQKLDHEPTAEEIAAQLDIPVEDVSKMLRLNER 214

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++  I           D +   ++   +V  + +   + ++ L   +  LNP+++ +
Sbjct: 215 ISSVDTPI--GGDGEKALLDIIPDANNSDPEVSTQDD---DIKSSLIHWLEELNPKQKEV 269

Query: 243 FEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 270 LARRFGLLGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLREILIKQ 316


>gi|188579854|ref|YP_001923299.1| RNA polymerase sigma factor RpoD [Methylobacterium populi BJ001]
 gi|179343352|gb|ACB78764.1| RNA polymerase, sigma 70 subunit, RpoD [Methylobacterium populi
           BJ001]
          Length = 667

 Score =  228 bits (582), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 71/258 (27%), Positives = 121/258 (46%), Gaps = 15/258 (5%)

Query: 34  EYVLAKRYREHGDLSAAH---RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           EY       + G+  A      ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV
Sbjct: 411 EYRKIVAMVQKGEREARQAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 470

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
            KF+  RG++ +TY+ WWI+ A+   I      ++I        +   + ++    + + 
Sbjct: 471 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQML 525

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
               +      +A+KL +   +V  +        SL   I   D+  S   D++    D 
Sbjct: 526 HEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDK 580

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRER 268
              + I+   + N R   TR ++ L PRE R+   R         TLE +  +F V+RER
Sbjct: 581 NVVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRER 640

Query: 269 VRQIEARAFKKVQESIQK 286
           +RQIEA+A +K++   + 
Sbjct: 641 IRQIEAKALRKLKHPSRS 658


>gi|328952031|ref|YP_004369365.1| putative RNA polymerase, sigma 70 family subunit [Desulfobacca
           acetoxidans DSM 11109]
 gi|328452355|gb|AEB08184.1| putative RNA polymerase, sigma 70 family subunit [Desulfobacca
           acetoxidans DSM 11109]
          Length = 328

 Score =  228 bits (582), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 109/282 (38%), Positives = 168/282 (59%), Gaps = 8/282 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG-YG 72
             L RY+ EI + P+L+ +EE  LA  Y E  D  AA+ L+TS+LRLVVKIA+ ++  + 
Sbjct: 44  DALQRYMGEINRYPLLQPEEEKRLATLYHETADQDAAYTLITSNLRLVVKIALDFQKFWM 103

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
             + +++ EGNIGLMQA+KKFDP RG +L+ Y+ +WIKA + ++I+ +W LVKIGTT  Q
Sbjct: 104 RNLLDLIQEGNIGLMQAIKKFDPYRGIKLSYYASFWIKAYILKFIMDNWKLVKIGTTQAQ 163

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALIN 191
           ++LFF+L++ K  L+A             I+ +LNV E+EVI M+ RL   E SL+A + 
Sbjct: 164 RKLFFSLKKEKERLRA----QGYEADPKLISTRLNVKEAEVIEMDQRLGSWEFSLDAPLK 219

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           S  +      ++L       ++ L  +E +      L    + L   ER I + R L E+
Sbjct: 220 SDSEE--LHINFLTSGETAADEHLAREEMKDIFLMRLAEFRNTLKDNERDILDLRLLAEH 277

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           P+TL+ + +   +SRERVRQIE R  KK+++ +  ++    S
Sbjct: 278 PLTLQEIGARHNISRERVRQIEERLLKKLRQFMHNEIPDFQS 319


>gi|254559198|ref|YP_003066293.1| sigma D factor of RNA polymerase [Methylobacterium extorquens DM4]
 gi|254266476|emb|CAX22240.1| sigma D (sigma 70) factor of RNA polymerase [Methylobacterium
           extorquens DM4]
          Length = 666

 Score =  228 bits (582), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 71/258 (27%), Positives = 121/258 (46%), Gaps = 15/258 (5%)

Query: 34  EYVLAKRYREHGDLSAAH---RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           EY       + G+  A      ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV
Sbjct: 410 EYRKIVAMVQKGEREARQAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 469

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
            KF+  RG++ +TY+ WWI+ A+   I      ++I        +   + ++    + + 
Sbjct: 470 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQML 524

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
               +      +A+KL +   +V  +        SL   I   D+  S   D++    D 
Sbjct: 525 HEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDK 579

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRER 268
              + I+   + N R   TR ++ L PRE R+   R         TLE +  +F V+RER
Sbjct: 580 NVVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRER 639

Query: 269 VRQIEARAFKKVQESIQK 286
           +RQIEA+A +K++   + 
Sbjct: 640 IRQIEAKALRKLKHPSRS 657


>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 =  228 bits (582), Expect = 8e-58,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 129/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 343 LRQIEEETGLSIEQIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 402

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 403 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 460

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 461 KLNRISRQMLQEIGREPTPE---ELAERMFMPEDKIRKVLKIAKEPLSMETPI--GDDED 515

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           +   D++    D   ++ +E    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 516 THLGDFI---EDTTLELPLESATSESLRSATHEILAGLTAREAKVLRMRFGIDMNTDHTL 572

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F V+RER+RQIEA+A +K++   + +V  S
Sbjct: 573 EEVGKQFAVTRERIRQIEAKALRKLRHPSRSEVLRS 608


>gi|153835750|ref|ZP_01988417.1| RNA polymerase sigma factor RpoS [Vibrio harveyi HY01]
 gi|156975773|ref|YP_001446680.1| hypothetical protein VIBHAR_03517 [Vibrio harveyi ATCC BAA-1116]
 gi|148867581|gb|EDL66895.1| RNA polymerase sigma factor RpoS [Vibrio harveyi HY01]
 gi|156527367|gb|ABU72453.1| hypothetical protein VIBHAR_03517 [Vibrio harveyi ATCC BAA-1116]
          Length = 328

 Score =  228 bits (582), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 80/288 (27%), Positives = 141/288 (48%), Gaps = 13/288 (4%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
            R+              Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLV
Sbjct: 39  AREEFDASSKSLDATQLYLGEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLV 97

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           VKI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++   
Sbjct: 98  VKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQT 157

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             +++      K L   LR  +     ++           IA +L++   +V  M     
Sbjct: 158 RTIRLPIHVV-KELNIYLRTAR----ELSQKLDHEPTAEEIAAQLDIPVEDVSKMLRLNE 212

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              S++  I           D +   ++   +V  + +   + ++ L   +  LNP+++ 
Sbjct: 213 RISSVDTPI--GGDGEKALLDIIPDANNSDPEVSTQDD---DIKSSLIHWLEELNPKQKE 267

Query: 242 IFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +   R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 268 VLARRFGLLGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLREILIKQ 315


>gi|88607306|ref|YP_505338.1| RNA polymerase sigma-32 factor [Anaplasma phagocytophilum HZ]
 gi|88598369|gb|ABD43839.1| RNA polymerase sigma-32 factor [Anaplasma phagocytophilum HZ]
          Length = 289

 Score =  228 bits (581), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 123/271 (45%), Positives = 185/271 (68%), Gaps = 4/271 (1%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           G   L  Y+ ++R  PML ++EE   A+ + ++  ++ AH+LVTSHLRLVVK+AMG+R Y
Sbjct: 10  GADDLLAYMEQVRAFPMLTEREEKECAENWHKNRSVADAHKLVTSHLRLVVKVAMGFRSY 69

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GLP+ E++ EGNIGLMQAVKKF+PE GFRL+TY++WWIKA++++YILRSWS ++IGTT  
Sbjct: 70  GLPLMELIMEGNIGLMQAVKKFNPELGFRLSTYAIWWIKASIKDYILRSWSCMRIGTTQA 129

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALI 190
           QK+LFF+LR++K  +   +  +     + AIA++   SE EV SM+   +  D SL+  +
Sbjct: 130 QKKLFFSLRKIKRRILGCS-ASASQSDIRAIAEECGTSEKEVESMDRFFSNRDISLSDKV 188

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
               ++ ++ QD +      QE + +  EE   +  M+  ++S L+ R R IF  R+L+E
Sbjct: 189 C--CESGTELQDLIPCSSPNQEVMYLSHEESVMKDQMVKEALSTLDERHRDIFSRRKLKE 246

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +P TLE LS E+ VS+ER+RQIE ++F KV+
Sbjct: 247 HPDTLETLSEEYGVSKERIRQIELQSFSKVR 277


>gi|71065817|ref|YP_264544.1| putative sigma-70 factor (RpoD) [Psychrobacter arcticus 273-4]
 gi|71038802|gb|AAZ19110.1| putative sigma-70 factor (RpoD) [Psychrobacter arcticus 273-4]
          Length = 647

 Score =  228 bits (581), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 71/259 (27%), Positives = 119/259 (45%), Gaps = 14/259 (5%)

Query: 33  EEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           +   +A+R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV
Sbjct: 390 DMKDVARRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 449

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
            KF+  RG++ +TY+ WWI+ A+   I      ++I            + R+   L    
Sbjct: 450 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKINRVSRQLLQEM 507

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
                PE    + ++L + E +V  +        S+   I   D   S   D++    DG
Sbjct: 508 GREPTPE---ELGERLEMDEVKVRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDG 559

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRER 268
                ++       R      +  L  RE R+ + R   + P   TLE +  +F+V+RER
Sbjct: 560 TISSPVDDATAAGLREATRDVLGNLTEREARVLKMRFGIDMPTDHTLEEVGKQFDVTRER 619

Query: 269 VRQIEARAFKKVQESIQKQ 287
           +RQIEA+A +K++   + +
Sbjct: 620 IRQIEAKALRKLRHPSRSE 638


>gi|254510133|ref|ZP_05122200.1| RNA polymerase sigma-32 factor [Rhodobacteraceae bacterium KLH11]
 gi|221533844|gb|EEE36832.1| RNA polymerase sigma-32 factor [Rhodobacteraceae bacterium KLH11]
          Length = 292

 Score =  228 bits (581), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 103/272 (37%), Positives = 173/272 (63%), Gaps = 6/272 (2%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
            +  K  +L+ + E  LA  +R++ D  A HRL+T+++RL + +A  ++ YG P+++++ 
Sbjct: 13  RQAMKAELLDAETELQLAYAWRDNRDEQALHRLITAYMRLAISMAAKFKRYGAPMNDLIQ 72

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           E  +GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFN+R
Sbjct: 73  EAGLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMR 132

Query: 141 RLKGHLQAITDNNL----KPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDK 195
           R++  L+           + +    IA ++ V   +V  M  RLAG D SLNA + S+D+
Sbjct: 133 RVQARLEREAATEGLDLDRHQLHQMIAAEIGVPLRDVEMMEGRLAGSDFSLNA-VQSADE 191

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
           +  +W D L  D +   + +    + +  R+ L  +M  LN RER I   R+L+E   TL
Sbjct: 192 DGREWIDALEDDREQAAESVEHSHDTQQLRDWLVTAMQALNDRERFIVRERKLREPARTL 251

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+L  E  +S+ERVRQ+EA AF K++++++ Q
Sbjct: 252 ESLGQELGLSKERVRQLEAAAFTKMRKNLEAQ 283


>gi|192289891|ref|YP_001990496.1| RNA polymerase sigma factor RpoD [Rhodopseudomonas palustris TIE-1]
 gi|192283640|gb|ACF00021.1| RNA polymerase, sigma 70 subunit, RpoD family [Rhodopseudomonas
           palustris TIE-1]
          Length = 698

 Score =  228 bits (581), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 69/246 (28%), Positives = 118/246 (47%), Gaps = 12/246 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 454 EREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 513

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    + + +   +      +
Sbjct: 514 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLNEIGREPTPEEL 568

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+KL +   +V  +        SL   +   D+  S   D++    D    + I+   + 
Sbjct: 569 AEKLGMPLEKVRKVLKIAKEPLSLETPV--GDEEDSHLGDFI---EDKNAVLPIDAAIQS 623

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 624 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKL 683

Query: 281 QESIQK 286
           +   + 
Sbjct: 684 KHPSRS 689


>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 =  228 bits (581), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 73/286 (25%), Positives = 127/286 (44%), Gaps = 24/286 (8%)

Query: 16  LSRYIHEIRKIPM----------LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVK 63
           L +Y  EI +             L  QE   + +R    E     A   ++ ++LRLV+ 
Sbjct: 413 LEKYSKEIYRAQRNLAQLEEQNNLNIQEIKEINRRVAIGEAKSRRAKKEMIEANLRLVIS 472

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      
Sbjct: 473 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 532

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           ++I            L R+   +   T     PE    + +++++ E +V  +       
Sbjct: 533 IRIPVHM--IETINKLNRISRQILQETGIEATPE---ELGRRIDMPEEKVRKVLKIAKEP 587

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            S+   I   +   S   D++    D   +  ++              +S L PRE ++ 
Sbjct: 588 ISMETPI--GEDEDSNLGDFI---EDINMESPVDFATSAGLMEATREILSTLTPREAKVL 642

Query: 244 EARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             R   +     TLE +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 643 RMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRAE 688


>gi|91978433|ref|YP_571092.1| RNA polymerase sigma factor RpoD [Rhodopseudomonas palustris BisB5]
 gi|91684889|gb|ABE41191.1| RNA polymerase sigma factor RpoD-like [Rhodopseudomonas palustris
           BisB5]
          Length = 711

 Score =  228 bits (581), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 69/246 (28%), Positives = 118/246 (47%), Gaps = 12/246 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 467 EREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 526

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    + + +   +      +
Sbjct: 527 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLNEIGREPTPEEL 581

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+KL +   +V  +        SL   +   D+  S   D++    D    + I+   + 
Sbjct: 582 AEKLGMPLEKVRKVLKIAKEPLSLETPV--GDEEDSHLGDFI---EDKNAVLPIDAAIQS 636

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 637 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKL 696

Query: 281 QESIQK 286
           +   + 
Sbjct: 697 KHPSRS 702


>gi|296159636|ref|ZP_06842459.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. Ch1-1]
 gi|295890080|gb|EFG69875.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. Ch1-1]
          Length = 680

 Score =  228 bits (581), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 439 RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 498

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 499 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 553

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 554 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDNNTVAPADAALHASMRD 608

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 609 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 668

Query: 285 QKQ 287
           +  
Sbjct: 669 RSD 671


>gi|254470295|ref|ZP_05083699.1| sigma 70 [Pseudovibrio sp. JE062]
 gi|211960606|gb|EEA95802.1| sigma 70 [Pseudovibrio sp. JE062]
          Length = 701

 Score =  228 bits (581), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 69/251 (27%), Positives = 119/251 (47%), Gaps = 15/251 (5%)

Query: 41  YREHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
             + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 452 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 511

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I        +   + ++    + +     +  
Sbjct: 512 GYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREP 566

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +++KL +   +V  +        SL   I   D+  S   D++    D    + I+
Sbjct: 567 TPEELSEKLQMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAILPID 621

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              + N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+
Sbjct: 622 AAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 681

Query: 276 AFKKVQESIQK 286
           A +K++   + 
Sbjct: 682 ALRKLKHPSRS 692


>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 =  228 bits (581), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 440 RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 499

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 500 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 554

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 555 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTVAPADAALHASMRD 609

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 610 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 669

Query: 285 QKQ 287
           +  
Sbjct: 670 RSD 672


>gi|146309186|ref|YP_001189651.1| RNA polymerase factor sigma-32 [Pseudomonas mendocina ymp]
 gi|145577387|gb|ABP86919.1| RNA polymerase, sigma 32 subunit, RpoH [Pseudomonas mendocina ymp]
          Length = 284

 Score =  228 bits (581), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 100/272 (36%), Positives = 159/272 (58%), Gaps = 7/272 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+H +  IP+L  ++E  LA+      DL AA ++V +HLR VV IA  Y GYGL 
Sbjct: 16  NLEAYVHAVNSIPLLTPEQERELAESLYYQQDLEAARQMVLAHLRFVVHIARSYSGYGLA 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGN+GLM+AVK+F+PE G RL ++++ WI+A + E+IL++W +VK+ TT  Q++
Sbjct: 76  QADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIRAEIHEFILKNWRIVKVATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSS 193
           LFFNLR  K  L  + +     ++V A+A+ L V   EV  M  RL G D + +   ++ 
Sbjct: 136 LFFNLRSQKKRLAWLNN-----DEVTAVAESLGVEPHEVREMESRLTGQDMAFDPASDAD 190

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENP 252
           D ++ Q     + DH       +E  +  +  +  L  ++  L+ R R I   R L E  
Sbjct: 191 DDSAFQSPAHYLEDHRYDPARQLEDADWSDSSSSNLHEALESLDERSRDILYQRWLAEEK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL +L++++ VS ER+RQ+E  A  K++ SI
Sbjct: 251 ATLHDLAAKYNVSAERIRQLEKNAMNKLKGSI 282


>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 =  228 bits (581), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 439 RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 498

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 499 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 553

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 554 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDNNTVAPADAALHASMRD 608

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 609 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 668

Query: 285 QKQ 287
           +  
Sbjct: 669 RSD 671


>gi|298241844|ref|ZP_06965651.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297554898|gb|EFH88762.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 366

 Score =  228 bits (581), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 84/280 (30%), Positives = 129/280 (46%), Gaps = 13/280 (4%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
             E     Y+ +IR   +L   EE  LA+R    GD  A  +LV S+LRLV+ IA  Y  
Sbjct: 93  GSEDAFQSYLRDIRGYGLLTHAEEIDLAQRAA-AGDTIARRKLVESNLRLVISIARRYTS 151

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            G+P+ +++ EGN+GLM+A +KFD +RG    TY+ WWI+ A+         ++ +    
Sbjct: 152 TGVPLIDLIQEGNLGLMRAAEKFDHQRGCHFGTYATWWIRQAVSRAAGEQSRMIHLPEHV 211

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
           + +     +RR+   L      +  PEQ   IA+  +    EV ++   +    SL+  +
Sbjct: 212 STR--LRKVRRISAQLSQENGLDPMPEQ---IAEACHFEVDEVKNLLGVIEQPVSLDTPV 266

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
              D+      D L  D         E   R      L R+++VL PRER +   R    
Sbjct: 267 --DDETRYSLGDTLEDD---TTPAPAETASRHLLGEELHRALAVLTPRERSVVMLRYGIG 321

Query: 251 NP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +    TL  +  E  +SRERVRQ+E  A  K++     Q 
Sbjct: 322 DGRSRTLLEVGKELGISRERVRQLEVVALMKLRSVTNAQA 361


>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 =  228 bits (581), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 66/253 (26%), Positives = 118/253 (46%), Gaps = 12/253 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 393 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 452

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 453 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPLPE--- 507

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + E ++  +        S+   I   D   S   D++    D   ++ ++   
Sbjct: 508 ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDTTLELPLDSAT 562

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 563 ATSLKMATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 622

Query: 279 KVQESIQKQVELS 291
           K++   + +   S
Sbjct: 623 KLRHPSRSETLRS 635


>gi|332994558|gb|AEF04613.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Alteromonas sp. SN2]
          Length = 330

 Score =  228 bits (581), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 79/271 (29%), Positives = 136/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A++    G  ++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 59  YLGEIGFSPLLSAEEEVFFARK-ALRGCEASRKRMIVSNLRLVVKIARRYNNRGLALLDL 117

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 118 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 176

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA  L+    +V  M        S++  I    +N  
Sbjct: 177 LRAAR----ELSQKLDHEPTAEEIALALDKPVEDVTKMLRLNERITSVDTPI--GGENDK 230

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
              D L  +    E    E  +  + ++ +   +  LNP++R +   R       P TLE
Sbjct: 231 ALLDILADEK---EFGPEENLQDSDIKSNIVGWLEELNPKQREVLARRFGLMGYEPSTLE 287

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++ +E  ++RERVRQI+  A +++++ +  Q
Sbjct: 288 DVGAEIGLTRERVRQIQVEALRRLRDILGHQ 318


>gi|209965454|ref|YP_002298369.1| RNA polymerase sigma-32 factor [Rhodospirillum centenum SW]
 gi|209958920|gb|ACI99556.1| RNA polymerase sigma-32 factor [Rhodospirillum centenum SW]
          Length = 307

 Score =  228 bits (581), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 122/292 (41%), Positives = 176/292 (60%), Gaps = 4/292 (1%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           MS+       L  Y  +  + PML+  EE +LA+ + E  D  A  RLV SH+RL VKIA
Sbjct: 4   MSVFSESIDVLRAYTAQANRHPMLDPAEEQMLARAWAERQDRKAFDRLVRSHMRLAVKIA 63

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y   GLP+ +++SE NIGL++AV++FDP+RGFRLATY++WWI+A +Q Y+L +WS++K
Sbjct: 64  SKYARSGLPMGDLISEANIGLVKAVQRFDPDRGFRLATYALWWIRAEVQTYVLHNWSMLK 123

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE- 184
            G TA  KRLFFNLR+ +  L  I D  +  E+   +A +L  S  EV  M  R A    
Sbjct: 124 GGNTAALKRLFFNLRQTQRRLG-IQDRIMSDEEADRVADELGASVDEVREMEHRFATPVT 182

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SLN  +   +    +  D L  + +  E  L EK E   R+ ++  ++  L  RER IF 
Sbjct: 183 SLNVPV--GEDGDHEALDLLADETETVEVRLAEKSELAVRKALMVDALGALGDRERHIFV 240

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPL 296
           +R L + PVTLE L+ ++ VS+ER+RQIE+ A+KKV   ++   E S++P L
Sbjct: 241 SRNLTDQPVTLETLAQQYGVSKERIRQIESGAYKKVARRVRGAAEASAAPIL 292


>gi|77919031|ref|YP_356846.1| DNA-directed RNA polymerase, sigma 70/sigma 32 subunit [Pelobacter
           carbinolicus DSM 2380]
 gi|77545114|gb|ABA88676.1| RNA polymerase, sigma 38 subunit, RpoS [Pelobacter carbinolicus DSM
           2380]
          Length = 347

 Score =  228 bits (581), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 66/279 (23%), Positives = 139/279 (49%), Gaps = 13/279 (4%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
             +  +  Y+ EI+K  +L  ++E +LA+R  + GD++A  R++ S+LRLVVKIA  Y  
Sbjct: 64  PSDDAIKLYLKEIQKTKLLTAEDERMLARRISQ-GDMAARDRMIESNLRLVVKIAKRYMN 122

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            GLP  +++ EGN+GL++AV++F   +  R +TY+ WWI+ +++  ++     +++    
Sbjct: 123 RGLPFLDLIEEGNMGLIKAVERFKLSKECRFSTYATWWIRQSIERALVNQSRTIRLPVHV 182

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
           +      ++ +     + +     +  +V  IA+ + V  + +  +   +    S+   +
Sbjct: 183 SD-----DINKFIKISRELVHQYNREPKVEEIAEYMGVEPAYIRRLMVLVKKTYSIEHPM 237

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
              +       D +           ++  ++      +      L+  ER I   R   +
Sbjct: 238 --GENRDYSLIDTIEDPKADNPSTFVDDIDK---YAHVCNWFETLSENEREILMLRFGLD 292

Query: 251 N--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +  P TL+ +   F V+RER+RQIEA++ +K++  +++Q
Sbjct: 293 DQEPQTLDTIGRRFGVTRERIRQIEAKSLQKLRNLMEEQ 331


>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 =  228 bits (581), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 127/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +  I +   L  Q    +++R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 351 LKMIEEETSLTVQSIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 410

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 411 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 468

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 469 KLNRISRQMLQEMGREPLPE---ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDED 523

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++     + +      ++ L PRE ++   R   +     TL
Sbjct: 524 SHLGDFI---EDTTLELPLDSATATSLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTL 580

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +   S
Sbjct: 581 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRS 616


>gi|297614550|gb|ADI48581.1| putative DNA-directed RNA polymerase sigma 38 subunit [uncultured
           bacterium fss6]
          Length = 322

 Score =  228 bits (581), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 88/271 (32%), Positives = 147/271 (54%), Gaps = 12/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   ++  R+ GD  A  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 51  YLSEIGYSPLLSAEEEVHFSRLARK-GDAKARARMIESNLRLVVKIARRYTNRGLALLDL 109

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 110 VEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNSY 168

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            IA+KL+VS ++V  M        S++  +  SD N  
Sbjct: 169 LRAAR----ELAHTLDHEPTAEDIAEKLDVSVADVSRMLRLNERVTSVDTPMGGSD-NDK 223

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  D+D   +  +++E   + R+ +   +  LN ++R +   R   L   P TLE
Sbjct: 224 TLVDMLTDDNDYGPEGDMQEE---DVRDHIMTWLENLNEKQREVLARRFGLLGYEPATLE 280

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+  A +++++ +++Q
Sbjct: 281 DVGREIGLTRERVRQIQVEALRRLRDMLRQQ 311


>gi|254509205|ref|ZP_05121302.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus 16]
 gi|219547863|gb|EED24891.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus 16]
          Length = 331

 Score =  228 bits (581), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 79/287 (27%), Positives = 140/287 (48%), Gaps = 13/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           ++              Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVV
Sbjct: 43  KEEFDASAKSLDATQLYLGEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLVV 101

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           KI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++    
Sbjct: 102 KISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTR 161

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            +++      K L   LR  +     ++           IA +L+    +V  M      
Sbjct: 162 TIRLPIHVV-KELNIYLRTAR----ELSQKLDHEPTAEEIATQLDKPVDDVSKMLRLNER 216

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++  I           D +   ++   +V  + +   + ++ L   +  LNP+++ +
Sbjct: 217 ISSVDTPI--GGDGEKALLDIIPDVNNSDPEVSTQDD---DIKSSLVHWLDELNPKQKEV 271

Query: 243 FEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 272 LARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILIKQ 318


>gi|116072877|ref|ZP_01470142.1| RNA polymerase sigma factor [Synechococcus sp. BL107]
 gi|116064403|gb|EAU70164.1| RNA polymerase sigma factor [Synechococcus sp. BL107]
          Length = 451

 Score =  228 bits (581), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 77/313 (24%), Positives = 142/313 (45%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-----------------HGDLS------ 48
            E  +  Y+ EI +I +L   EE  LA++  +                   D        
Sbjct: 139 TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLYLEELAAQFESDNGREPDKKEWAALV 198

Query: 49  ----------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 199 EMPLIRFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 258

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 259 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKVLSQE 313

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA+ + ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 314 FGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADIENPE 371

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
           Q + +   R++    L   ++ L+PRER +   R   ++    TLE +   F+V+RER+R
Sbjct: 372 QDVAKNLLRED----LEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIR 427

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 428 QIEAKALRKLRHP 440


>gi|239948365|ref|ZP_04700118.1| RNA polymerase sigma factor, sigma-70 family [Rickettsia
           endosymbiont of Ixodes scapularis]
 gi|239922641|gb|EER22665.1| RNA polymerase sigma factor, sigma-70 family [Rickettsia
           endosymbiont of Ixodes scapularis]
          Length = 635

 Score =  228 bits (581), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 70/247 (28%), Positives = 121/247 (48%), Gaps = 11/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E   L A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 376 ERQTLQAKKDMIEANLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 435

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    + + +          I
Sbjct: 436 TYATWWIRQAITRAIADQARTIRIPVH-----MIETINKILRISRQMLNELGYEPTATEI 490

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A +L++   +V  +        SL   +   D +  Q  D++    D      I+   + 
Sbjct: 491 ANRLSMPLDKVCKVMKIAKEPISLENPVGD-DIDGGQLGDFI---EDKNAVAPIDAAIQS 546

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R + TR ++ L PRE R+   R         TLE +  +F+V+RER+RQIE++A +K+
Sbjct: 547 NLREVTTRVLATLTPREERVLRMRFGIGMNTDHTLEEVGQQFKVTRERIRQIESKALRKL 606

Query: 281 QESIQKQ 287
           Q  I+ +
Sbjct: 607 QHPIRSK 613


>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 =  228 bits (581), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 128/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +  I +   L  +    +++R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 359 LQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 418

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 419 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 476

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 477 KLNRISRQMLQEMGREPLPE---ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDED 531

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++     + +      ++ L PRE ++   R   +     TL
Sbjct: 532 SHLGDFI---EDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTL 588

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 589 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 624


>gi|159903037|ref|YP_001550381.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str. MIT
           9211]
 gi|159888213|gb|ABX08427.1| Putative principal RNA polymerase sigma factor [Prochlorococcus
           marinus str. MIT 9211]
          Length = 425

 Score =  228 bits (581), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 77/313 (24%), Positives = 140/313 (44%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR--------------EHG------------ 45
            E  +  Y+ EI +I +L   EE  LA++                E+G            
Sbjct: 113 TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLNLEEIAIQFESENGHYPSKKEWAALV 172

Query: 46  -------------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 173 EMPVIRFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 232

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 233 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKVLSQE 287

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA+ + ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 288 FGRKPSEEEIAESMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIESDSENPE 345

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
             +     +   R  L   ++ L+PRER +   R   ++    TLE +   F+V+RER+R
Sbjct: 346 LDVA----KTLLREDLEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIR 401

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 402 QIEAKALRKLRHP 414


>gi|148257986|ref|YP_001242571.1| RNA polymerase sigma factor RpoD [Bradyrhizobium sp. BTAi1]
 gi|146410159|gb|ABQ38665.1| RNA polymerase, sigma 70 subunit, RpoD [Bradyrhizobium sp. BTAi1]
          Length = 702

 Score =  228 bits (581), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 69/246 (28%), Positives = 118/246 (47%), Gaps = 12/246 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 458 EREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 517

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    + + +   +      +
Sbjct: 518 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLNEIGREPTPEEL 572

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+KL +   +V  +        SL   +   D+  S   D++    D    + I+   + 
Sbjct: 573 AEKLGMPLEKVRKVLKIAKEPLSLETPV--GDEEDSHLGDFI---EDKNAILPIDAAIQS 627

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 628 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKL 687

Query: 281 QESIQK 286
           +   + 
Sbjct: 688 KHPSRS 693


>gi|118581147|ref|YP_902397.1| RpoD family RNA polymerase sigma factor [Pelobacter propionicus DSM
           2379]
 gi|118503857|gb|ABL00340.1| RNA polymerase, sigma 70 subunit, RpoD family [Pelobacter
           propionicus DSM 2379]
          Length = 323

 Score =  228 bits (581), Expect = 9e-58,   Method: Composition-based stats.
 Identities = 70/270 (25%), Positives = 141/270 (52%), Gaps = 13/270 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ +I++ P+L  ++E  +A++  E GD++A ++++ S+LRLVVKIA  Y   G
Sbjct: 58  DDAIKIYLRDIQRTPLLTAEQEKEVARQI-EKGDMAARNKMIESNLRLVVKIAKRYINRG 116

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP  +++ EGN+GL++AV++F+  +  R +TY+ WWI+ A+   ++     +++    + 
Sbjct: 117 LPFLDLIEEGNLGLIKAVERFNLAKECRFSTYATWWIRQAIDRALVNQSRTIRLPVHVSD 176

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                ++ R+    + ++    +      IA+++NV  + V  +   L    S+   I  
Sbjct: 177 -----DINRMAKVTRRLSQTLQREPHAHEIAEEMNVKLAYVRRLMTLLRRTCSMETPI-- 229

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN- 251
            D +     D +          L+E  +R      ++     L+  E++I   R   ++ 
Sbjct: 230 GDGSDYFLIDTIEDTSMVAPSDLLENIDR---YEQISEHFKELSESEQKILALRFGLDDK 286

Query: 252 -PVTLENLSSEFEVSRERVRQIEARAFKKV 280
            P TL+ +   F V+RER+RQIEA++ +K+
Sbjct: 287 EPQTLDTIGRSFGVTRERIRQIEAKSLEKL 316


>gi|312972274|ref|ZP_07786448.1| alternative sigma factor RpoH [Escherichia coli 1827-70]
 gi|310334651|gb|EFQ00856.1| alternative sigma factor RpoH [Escherichia coli 1827-70]
          Length = 257

 Score =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 103/262 (39%), Positives = 152/262 (58%), Gaps = 8/262 (3%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           ML   EE  LA++   HGDL AA  L+ SHLR VV IA  Y GYGLP ++++ EGNIGLM
Sbjct: 1   MLSADEERALAEKLHYHGDLEAAKTLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLM 60

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV++F+PE G RL ++++ WIKA + EY+LR+W +VK+ TT  Q++LFFNLR+ K  L 
Sbjct: 61  KAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLG 120

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSSDKNSSQWQDWLVY 206
                    ++V  +A++L V+  +V  M  R+ A D + +   N    +        + 
Sbjct: 121 WFNQ-----DEVEMVARELGVTSKDVREMESRMAAQDMTFDLSSNDDSDSQPMAPVLYLQ 175

Query: 207 DHDGQEQVLIEKE-ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-PVTLENLSSEFEV 264
           D        IE +   +   N LT +M  L+ R + I  AR L E+   TL+ L+  + V
Sbjct: 176 DKSSNFADGIEDDNWEEQAANRLTDAMQGLDERSQDIIRARWLDEDNKSTLQELADRYGV 235

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S ERVRQ+E  A KK++ +I+ 
Sbjct: 236 SAERVRQLEKNAMKKLRAAIEA 257


>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 =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 128/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +  I +   L  +    +++R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 326 LQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 385

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 386 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 443

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 444 KLNRISRQMLQEMGREPLPE---ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDED 498

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++     + +      ++ L PRE ++   R   +     TL
Sbjct: 499 SHLGDFI---EDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTL 555

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 556 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 591


>gi|260425737|ref|ZP_05779717.1| RNA polymerase sigma-32 factor [Citreicella sp. SE45]
 gi|260423677|gb|EEX16927.1| RNA polymerase sigma-32 factor [Citreicella sp. SE45]
          Length = 292

 Score =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 107/272 (39%), Positives = 172/272 (63%), Gaps = 6/272 (2%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
               K  +L+ + E  LA  +R+  D ++ HRL+ +++RL + +A  ++ YG P+ ++V 
Sbjct: 13  RRAMKAELLDAETELRLAYAWRDQRDEASLHRLINAYMRLAISMASKFKRYGAPMGDLVQ 72

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           E  +GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFN+R
Sbjct: 73  EAGLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMR 132

Query: 141 RLKGHLQAITDNNLKPEQV----VAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDK 195
           R++  L+       K  +      AIA+++ V  S+V  M  RL+G D SLNA   SSD+
Sbjct: 133 RVQARLEREAAAEGKTLERHMLHAAIAQEIGVPLSDVEMMEGRLSGSDFSLNA-TQSSDE 191

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
           +  +W D L  D +    V+  + +    R  L  +MS LN RER I   R+L++   TL
Sbjct: 192 DGREWIDTLEDDGEQGSSVVEGRLDNAQLREWLVVAMSALNDRERFIVRERKLRDETRTL 251

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+L  E  +S+ERVRQ+EA AF K+++S++ Q
Sbjct: 252 ESLGQELGLSKERVRQLEAAAFAKMRKSLEAQ 283


>gi|84499725|ref|ZP_00998013.1| RNA polymerase sigma factor [Oceanicola batsensis HTCC2597]
 gi|84392869|gb|EAQ05080.1| RNA polymerase sigma factor [Oceanicola batsensis HTCC2597]
          Length = 292

 Score =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 110/287 (38%), Positives = 177/287 (61%), Gaps = 9/287 (3%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M++  + +  LSR      K  +L+ + E  LA  +R+  D  A HRLVT+++RL + +A
Sbjct: 1   MALDHSTDTSLSR---RAMKAELLDAETELSLAYSWRDDRDERALHRLVTAYMRLAISMA 57

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             YR YG P+++++ E  +GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+
Sbjct: 58  SKYRRYGAPMNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVR 117

Query: 126 IGTTANQKRLFFNLRRLKGHLQAIT----DNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            G+T++QK LFFN+RR++  L+       +   K +    +A ++ V   +V  M+ RL+
Sbjct: 118 TGSTSSQKSLFFNMRRVQAKLEREALGRGETLDKHQLHQLVAMEVGVPLRDVQMMDGRLS 177

Query: 182 G-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           G D SLNA   S D+   +W D +  D     + +    +R+  R  L  +MS LN RE 
Sbjct: 178 GSDFSLNA-TQSVDEEGREWIDTIEDDGVQAAEAVEADHDRETLRLWLAEAMSDLNDRET 236

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            I   R+L++ P TLE+L  E  +S+ERVRQ+EA AFKK++  ++ Q
Sbjct: 237 LIVTERKLRDAPRTLESLGQELGLSKERVRQLEAAAFKKMRRHLESQ 283


>gi|218528655|ref|YP_002419471.1| RNA polymerase sigma factor RpoD [Methylobacterium chloromethanicum
           CM4]
 gi|240137186|ref|YP_002961655.1| sigma D (sigma 70) factor of RNA polymerase [Methylobacterium
           extorquens AM1]
 gi|218520958|gb|ACK81543.1| RNA polymerase, sigma 70 subunit, RpoD [Methylobacterium
           chloromethanicum CM4]
 gi|240007152|gb|ACS38378.1| sigma D (sigma 70) factor of RNA polymerase [Methylobacterium
           extorquens AM1]
          Length = 666

 Score =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 71/258 (27%), Positives = 121/258 (46%), Gaps = 15/258 (5%)

Query: 34  EYVLAKRYREHGDLSAAH---RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           EY       + G+  A      ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV
Sbjct: 410 EYRKIVAMVQKGEREARQAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 469

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
            KF+  RG++ +TY+ WWI+ A+   I      ++I        +   + ++    + + 
Sbjct: 470 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQML 524

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
               +      +A+KL +   +V  +        SL   I   D+  S   D++    D 
Sbjct: 525 HEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDK 579

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRER 268
              + I+   + N R   TR ++ L PRE R+   R         TLE +  +F V+RER
Sbjct: 580 NVVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRER 639

Query: 269 VRQIEARAFKKVQESIQK 286
           +RQIEA+A +K++   + 
Sbjct: 640 IRQIEAKALRKLKHPSRS 657


>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 =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 62/247 (25%), Positives = 117/247 (47%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A H ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 595 EAKAKKAKHEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 654

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I     +++I        +   + ++    + I            +
Sbjct: 655 TYATWWIRQAITRSIADQARIIRIPVH-----MIETINKINRITRQILQETGVEPDSAML 709

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+++   ++  +        S+   I   D + S   D++    D       E   ++
Sbjct: 710 AEKMDMPIEKIRKILKISKDPISMETPI--GDDDDSHLGDFI---EDTSTLSPEEAALQR 764

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           +   +    ++ L  RE ++   R      +  TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 765 SMSEVFDEVINSLTQREGKVLRMRFGIGMSSDQTLEEVGKQFDVTRERIRQIEAKALRKL 824

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 825 RHPSRAD 831


>gi|313891780|ref|ZP_07825385.1| RNA polymerase sigma factor RpoD [Dialister microaerophilus UPII
           345-E]
 gi|329121139|ref|ZP_08249770.1| DNA-directed RNA polymerase sigma subunit RpoD [Dialister
           micraerophilus DSM 19965]
 gi|313119774|gb|EFR42961.1| RNA polymerase sigma factor RpoD [Dialister microaerophilus UPII
           345-E]
 gi|327471301|gb|EGF16755.1| DNA-directed RNA polymerase sigma subunit RpoD [Dialister
           micraerophilus DSM 19965]
          Length = 374

 Score =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 74/274 (27%), Positives = 122/274 (44%), Gaps = 23/274 (8%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREH-----------GDLSAAHRLVTSHLRLV 61
           +  +  Y+ EI  + +L  +EE  LAK   +                A   L  ++LRLV
Sbjct: 96  DDPVKMYLKEIGTVDLLTAEEEVTLAKAVEKGLLLGATEEEKINADKAKKALSDANLRLV 155

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA  Y G GL   +++ EGN+GL++AV KFD  +G++ +TY+ WWI+ ++   I    
Sbjct: 156 VSIAKKYLGRGLQFLDLIQEGNLGLLKAVDKFDYTKGYKFSTYATWWIRQSITRAIADQA 215

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             +++     +      L R+   L               IAK ++VS  +V  +     
Sbjct: 216 RTIRVPVHMVE--TINKLNRISRQLLQEKGREPTE---YEIAKAMDVSVGKVREVKKIAQ 270

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              SL   I   +K  S   D++    D       +  +    +  +   ++ L  RER+
Sbjct: 271 DPISLETPI--GEKEDSHLGDFI---EDQDAIAPDDATDSILLKEQIEELLTNLTDRERQ 325

Query: 242 IFEARRL--QENPVTLENLSSEFEVSRERVRQIE 273
           + E R       P TLE + + F+V+RER+RQIE
Sbjct: 326 VLELRFGLKDGRPRTLEEVGNNFDVTRERIRQIE 359


>gi|254497834|ref|ZP_05110600.1| RNA polymerase sigma 70 factor (RpoD) [Legionella drancourtii
           LLAP12]
 gi|254352912|gb|EET11681.1| RNA polymerase sigma 70 factor (RpoD) [Legionella drancourtii
           LLAP12]
          Length = 628

 Score =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 70/249 (28%), Positives = 118/249 (47%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 379 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 438

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +   T     PE   
Sbjct: 439 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQILQETGREATPE--- 493

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+K+ +SE ++  +        S+   +   D + S   D++    D   +  I+   
Sbjct: 494 ELAEKMELSEDKIRKVLKIAKEPISMETPV--GDDDDSHLGDFI---EDNNIESPIDMAT 548

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            +  R      +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 549 AEGLREATLEILETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALR 608

Query: 279 KVQESIQKQ 287
           K++   + +
Sbjct: 609 KLRHPSRSE 617


>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 =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 68/257 (26%), Positives = 118/257 (45%), Gaps = 14/257 (5%)

Query: 35  YVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
             ++KR    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV K
Sbjct: 373 KEISKRMAVGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 432

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+  RG++ +TY+ WWI+ A+   I      ++I            + R+   L      
Sbjct: 433 FEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKINRVSRQLLQEMGR 490

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              PE    + ++L + E +V  +        S+   I   D   S   D++    D   
Sbjct: 491 EPTPE---ELGERLEMDEVKVRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDSNI 542

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
              ++    +  +      +  L  RE ++ + R   + P   TLE +  +F+V+RER+R
Sbjct: 543 TSPVDAATSEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIR 602

Query: 271 QIEARAFKKVQESIQKQ 287
           QIEA+A +K++   + +
Sbjct: 603 QIEAKALRKLRHPSRSE 619


>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 =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 115/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 509 ESSSRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 568

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    +              +
Sbjct: 569 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKMNRISRQHLQEFGFEPDAGIL 623

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A K+ + E ++  +        S+   I   D + S   D++    D      IE   + 
Sbjct: 624 AAKMEIPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDSSNTAPIEAAMQA 678

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 679 GLRDVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKL 738

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 739 KHPSRSD 745


>gi|213963182|ref|ZP_03391440.1| RNA polymerase sigma factor RpoD [Capnocytophaga sputigena Capno]
 gi|213954266|gb|EEB65590.1| RNA polymerase sigma factor RpoD [Capnocytophaga sputigena Capno]
          Length = 287

 Score =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 66/276 (23%), Positives = 145/276 (52%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI ++ ++   EE  LA+R +  GD++A  +L  ++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQEIGRVDLITADEEVELAQRIK-AGDVAALEKLTKANLRFVVSVAKQYQNQGLT 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     +V++    N+  
Sbjct: 76  LPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLP--LNKIG 133

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               + ++  +L+   +   +      IA++L++S ++V           S++A +   +
Sbjct: 134 SINKINKMYAYLEQANE---RVPSAEEIARELDMSVNDVKESMKNAGRHISMDAPLV--E 188

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
              S   D +  +         +     + R  + R++  L PRE  +        +   
Sbjct: 189 GEDSNLYDVIRSNESPNPD---KSLILDSLRTEIERALETLTPREADVIRLYFGLGDQHA 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 246 MTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|225011624|ref|ZP_03702062.1| RNA polymerase, sigma 70 subunit, RpoD family [Flavobacteria
           bacterium MS024-2A]
 gi|225004127|gb|EEG42099.1| RNA polymerase, sigma 70 subunit, RpoD family [Flavobacteria
           bacterium MS024-2A]
          Length = 287

 Score =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 69/276 (25%), Positives = 143/276 (51%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI K+ ++  +EE  LA+R +  GD  A  +L  ++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQEIGKVDLITAEEEVELAQRIK-AGDQIALEKLTKANLRFVVSVAKQYQNQGLT 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     +V++    N+  
Sbjct: 76  LPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLP--LNKIG 133

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               + +    L+   +     E    IAK+L+++ ++V           S++A +   +
Sbjct: 134 SINKINKTYAFLEQAHERAPSAE---EIAKELDMTINDVKESLKNSGRHVSMDAPLV--E 188

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
              S   D L          ++     ++ R  + R++  L PRE  +        +   
Sbjct: 189 GEDSNLYDVLNSGESPNPDRVL---LHESLRTEIERALETLTPREADVVRLYFGLGDQHA 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 246 MTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|296272949|ref|YP_003655580.1| RpoD subfamily RNA polymerase sigma-70 factor subunit [Arcobacter
           nitrofigilis DSM 7299]
 gi|296097123|gb|ADG93073.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Arcobacter
           nitrofigilis DSM 7299]
          Length = 626

 Score =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 74/260 (28%), Positives = 130/260 (50%), Gaps = 15/260 (5%)

Query: 29  LEKQEEYVLAKRYREHGDL--SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           LE +E   + ++ +    +   A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGL
Sbjct: 365 LEPEELIDVLEQIKRGKKITDEAKTRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGL 424

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+ ++G++ +TY+ WWI+ A+   I      ++I        +   + R+   +
Sbjct: 425 MKAVDKFEYKKGYKFSTYATWWIRQAISRAIADQARTIRIPIH-----MIETINRINKII 479

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +     N K   V  IAK++ +   +V  +        SL A I S +    ++ D++  
Sbjct: 480 RKGIQENGKEPNVDEIAKEVGLPVDKVKQVIKITKEPVSLEAPIGSDED--GKFGDFVPD 537

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN---PVTLENLSSEFE 263
           D        ++   +++ +N + + ++ LN RE+ +   R    +     TLE +  E  
Sbjct: 538 DK---APTPVDNIMKEDLQNQIDQILAQLNEREQAVVRMRFGLMDDASDRTLEEIGKELS 594

Query: 264 VSRERVRQIEARAFKKVQES 283
           V+RERVRQIE+ A KK++  
Sbjct: 595 VTRERVRQIESSAIKKLKHP 614



 Score = 40.2 bits (93), Expect = 0.41,   Method: Composition-based stats.
 Identities = 10/36 (27%), Positives = 21/36 (58%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+ +IP+L K+EE  ++K+     D+
Sbjct: 102 SDSPVRMYLREMGQIPLLTKEEEIEISKKIEMGEDI 137


>gi|119774181|ref|YP_926921.1| RNA polymerase sigma-38 factor [Shewanella amazonensis SB2B]
 gi|119766681|gb|ABL99251.1| RNA polymerase sigma-38 factor [Shewanella amazonensis SB2B]
          Length = 327

 Score =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 82/271 (30%), Positives = 136/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   +++    G   + +R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 58  YLSEIGFSPLLTAEEEVYYSRK-ALRGCEKSRNRMIESNLRLVVKIARRYNNRGLALLDL 116

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 117 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 175

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            IA KLN+   EV  M        S++  +     N  
Sbjct: 176 LRTAR----ELAHKLDHEPTAEEIAAKLNLPSVEVSRMLKLNEKITSVDVPL--GGDNDK 229

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  D        ++ E+  N    +   ++ LN ++R +   R   L   P TLE
Sbjct: 230 ALLDVLPDDDSVGPDYKVQDEDISNS---VVNWLNELNTKQREVLARRFGLLGYEPSTLE 286

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++ +E  ++RERVRQI+  A K++++ +  Q
Sbjct: 287 DVGAEIGLTRERVRQIQVEALKRLRDILSAQ 317


>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|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]
          Length = 620

 Score =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 73/283 (25%), Positives = 130/283 (45%), Gaps = 24/283 (8%)

Query: 21  HEIRKIPMLEKQEEYVL--------AKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
             I K+ M+  +EE  L        ++R    E     A   +V ++LRLV+ IA  Y  
Sbjct: 346 RSIAKLKMI--EEETSLNVQNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTN 403

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I    
Sbjct: 404 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 463

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
                   L R+   +         PE    +A+++ + E ++  +        S+   I
Sbjct: 464 --IETINKLNRISRQMLQEMGREPLPE---ELAERMQMPEDKIRKVLKIAKEPISMETPI 518

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
              D   S   D++    D   ++ ++     + +      ++ L PRE ++   R   +
Sbjct: 519 --GDDEDSHLGDFI---EDTTLELPLDSATATSLKMATKDVLAGLTPREAKVLRMRFGID 573

Query: 251 --NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
                TLE +  +F+V+RER+RQIEA+A +K++   + +   S
Sbjct: 574 MNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRS 616


>gi|84394590|ref|ZP_00993293.1| RNA polymerase sigma factor [Vibrio splendidus 12B01]
 gi|84374781|gb|EAP91725.1| RNA polymerase sigma factor [Vibrio splendidus 12B01]
          Length = 573

 Score =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 71/273 (26%), Positives = 126/273 (46%), Gaps = 14/273 (5%)

Query: 23  IRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           I +   L  Q    +++R    E     A   +V ++LRLV+ IA  Y   GL   +++ 
Sbjct: 307 IERETSLTVQSIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 366

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L 
Sbjct: 367 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLN 424

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
           R+   +         PE    +A+++ + E ++  +        S+   I   D   S  
Sbjct: 425 RISRQMLQEMGREPLPE---ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDEDSHL 479

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENL 258
            D++    D   ++ ++     + R      ++ L PRE ++   R   +     TLE +
Sbjct: 480 GDFI---EDTTLELPLDSATATSLRGATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEV 536

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
             +F+V+RER+RQIEA+A +K++   + +   S
Sbjct: 537 GKQFDVTRERIRQIEAKALRKLRHPSRSETLRS 569


>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 =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 114/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 381 EAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 440

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   L         PE    +
Sbjct: 441 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKINRVSRQLLQEMGREPTPE---EL 495

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
            ++L + E +V  +        S+   I   D   S   D++    D      ++    +
Sbjct: 496 GERLEMDEVKVRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDSNITSPVDAATSE 550

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKV 280
             +      +  L  RE ++ + R   + P   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 551 GLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKL 610

Query: 281 QESIQKQ 287
           +   + +
Sbjct: 611 RHPSRSE 617


>gi|332292552|ref|YP_004431161.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Krokinobacter
           diaphorus 4H-3-7-5]
 gi|332170638|gb|AEE19893.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Krokinobacter
           diaphorus 4H-3-7-5]
          Length = 287

 Score =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 69/276 (25%), Positives = 145/276 (52%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI K+ ++   EE  LA+R +  GD  A  +L  ++LR VV ++  Y+  GL 
Sbjct: 17  SLDKYLQEIGKVDLITADEEVELAQRIK-AGDHRALEKLTKANLRFVVSVSKQYQNQGLT 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     +V++        
Sbjct: 76  LPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNK---- 131

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
              ++ ++      +   N +P     IAK+L++S ++V           S++A +   +
Sbjct: 132 -IGSINKINKTFAFLEQANERPPSPEEIAKELDMSINDVKESLKNSGRHISMDAPLV--E 188

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
              S   D L   + G+      +   ++ +  + R++  L PRE  +        +  P
Sbjct: 189 GEDSNLYDVL---NSGESPNPDRELLHESLKTEIERALETLTPREADVVRLYFGLGDQQP 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 246 MTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>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|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 =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 114/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 381 EAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 440

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   L         PE    +
Sbjct: 441 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKINRVSRQLLQEMGREPTPE---EL 495

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
            ++L + E +V  +        S+   I   D   S   D++    D      ++    +
Sbjct: 496 GERLEMDEVKVRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDSNITSPVDAATSE 550

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKV 280
             +      +  L  RE ++ + R   + P   TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 551 GLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALRKL 610

Query: 281 QESIQKQ 287
           +   + +
Sbjct: 611 RHPSRSE 617


>gi|254498663|ref|ZP_05111381.1| RNA polymerase factor sigma-32 [Legionella drancourtii LLAP12]
 gi|254352111|gb|EET10928.1| RNA polymerase factor sigma-32 [Legionella drancourtii LLAP12]
          Length = 280

 Score =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 113/288 (39%), Positives = 181/288 (62%), Gaps = 10/288 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M    M++ V     L  YIH + +IPML  +EE   A+R+   GD+ AA RLV +HLR 
Sbjct: 1   MQLAAMNLPVG---SLDAYIHRVNQIPMLTMEEEIACAERFHSEGDIEAARRLVLAHLRY 57

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV++A GY GYGLP+++++ EGN+GLM+AVK+FDP+ G RL ++++ WIKA + E++LR+
Sbjct: 58  VVRVARGYLGYGLPLNDLIQEGNVGLMKAVKRFDPKMGVRLVSFAVHWIKAEIHEFVLRN 117

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VKI TT  Q++LFFNLR++K  L   ++     E+V A+AK L VS  EV+ M  RL
Sbjct: 118 WRIVKIATTKAQRKLFFNLRQMKNRLGWFSN-----EEVAAVAKDLGVSTDEVLVMEQRL 172

Query: 181 -AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPR 238
            A D   +A     + +     +  +++ +    +++EKE   +R R  L  ++  L+ R
Sbjct: 173 NAMDAPYDAPDADDNDDFHMAPERYLFNVNDDPALVLEKESTGDRGREQLLLALEQLDER 232

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + I + R L ++ +TL +L+ ++ +S ERVRQ+E  A KK+++ I+ 
Sbjct: 233 SQDILQQRWLADDKLTLHDLAEKYAISAERVRQLEKNAMKKLRQFIEA 280


>gi|153001641|ref|YP_001367322.1| RpoD family RNA polymerase sigma factor [Shewanella baltica OS185]
 gi|160876377|ref|YP_001555693.1| RpoD family RNA polymerase sigma factor [Shewanella baltica OS195]
 gi|217972427|ref|YP_002357178.1| RNA polymerase sigma 70 subunit RpoD subfamily [Shewanella baltica
           OS223]
 gi|151366259|gb|ABS09259.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella baltica
           OS185]
 gi|160861899|gb|ABX50433.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella baltica
           OS195]
 gi|217497562|gb|ACK45755.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Shewanella
           baltica OS223]
 gi|315268567|gb|ADT95420.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Shewanella
           baltica OS678]
          Length = 326

 Score =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 82/271 (30%), Positives = 141/271 (52%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   +++  + G   + +R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 57  YLGEIGFSPLLSAEEEVYFSRKALK-GCAKSRNRMIESNLRLVVKIARRYNNRGLALLDL 115

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 116 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 174

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            IA+KL VS ++V  M        S++  +     N  
Sbjct: 175 LRTAR----ELAQKLDHEPTAEEIAEKLQVSSADVSRMLKLNEKITSVDTPL--GGDNDK 228

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  D +      ++ E+  N    + + ++ LN ++R +   R   L   P TLE
Sbjct: 229 ALLDILADDDNVGPDYKVQDEDISNS---VVKWLNELNTKQREVLARRFGLLGYEPSTLE 285

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++ +E  ++RERVRQI+  A K++++ +  Q
Sbjct: 286 DVGAEIGLTRERVRQIQVEALKRLRDLLGSQ 316


>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 =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 116/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 536 ESASRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 595

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    +              +
Sbjct: 596 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKMNRISRQHLQEFGFEPDASIL 650

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A K+ + E ++  +        S+   I   D + S   D++    DG     I+   + 
Sbjct: 651 AAKMEIPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDGANTAPIDAAMQA 705

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 706 GLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKL 765

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 766 KHPSRSD 772


>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 =  228 bits (581), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 69/263 (26%), Positives = 120/263 (45%), Gaps = 14/263 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L   E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 355 LTIAEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 414

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 415 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 472

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    + +++ + E ++  +        S+   I   D   S   D++  
Sbjct: 473 LQEMGREPTPE---ELGERMEMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 525

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q  I+    ++ +      +S L  RE ++   R   +     TLE +  +F+V
Sbjct: 526 -EDSTMQSPIDVATVESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 584

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   + +
Sbjct: 585 TRERIRQIEAKALRKLRHPTRSE 607


>gi|146338438|ref|YP_001203486.1| RNA polymerase sigma factor RpoD [Bradyrhizobium sp. ORS278]
 gi|146191244|emb|CAL75249.1| sigma D (sigma 70) factor of RNA polymerase [Bradyrhizobium sp.
           ORS278]
          Length = 703

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 69/246 (28%), Positives = 118/246 (47%), Gaps = 12/246 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 459 EREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 518

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    + + +   +      +
Sbjct: 519 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLNEIGREPTPEEL 573

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+KL +   +V  +        SL   +   D+  S   D++    D    + I+   + 
Sbjct: 574 AEKLGMPLEKVRKVLKIAKEPLSLETPV--GDEEDSHLGDFI---EDKNAILPIDAAIQS 628

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 629 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKL 688

Query: 281 QESIQK 286
           +   + 
Sbjct: 689 KHPSRS 694


>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 =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 62/247 (25%), Positives = 117/247 (47%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 394 ESKARRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 453

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    + I   + +      +
Sbjct: 454 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKMNRISRQILQESGREPDPAEL 508

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+ + E ++  +        S+   I   D + S   D++    D       +     
Sbjct: 509 AEKMEMPEEKIRKIMKISKEPISMETPI--GDDDDSHLGDFI---EDQNNLAPSDAAMYS 563

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + ++     +  L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 564 SLKDATKEVLDTLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 623

Query: 281 QESIQKQ 287
           +   + +
Sbjct: 624 RHPTRSE 630


>gi|28200488|gb|AAO31615.1| RNA polymerase subunit sigma factor S [Vibrio vulnificus]
          Length = 343

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 82/287 (28%), Positives = 140/287 (48%), Gaps = 13/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           R+              Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVV
Sbjct: 42  REEFDASNKSLDATQLYLGEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLVV 100

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           KI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++    
Sbjct: 101 KISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTR 160

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            +++      K L   LR  +     ++           IA +L++   +V  M      
Sbjct: 161 TIRLPIHVV-KELNIYLRTAR----ELSQKLDHEPTAEEIAAQLDIPVDDVSKMLRLNER 215

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++  I           D +   ++   +V  + E   + R  L   +  LNP+++ +
Sbjct: 216 ISSVDTPI--GGDGEKALLDIIPDANNSDPEVSTQDE---DMRVSLIHWLEELNPKQKEV 270

Query: 243 FEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 271 LARRFGLLGYEPSTLEEVGQEIGLTRERVRQIQVEGLRRLREVLIKQ 317


>gi|78778882|ref|YP_396994.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str. MIT
           9312]
 gi|78712381|gb|ABB49558.1| Sigma-70 factor [Prochlorococcus marinus str. MIT 9312]
          Length = 393

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 76/313 (24%), Positives = 139/313 (44%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------------- 43
            E  +  Y+ EI +I +L   EE  LA++  +                            
Sbjct: 81  TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLQLEELATQYESEKGHFPSVREWAELI 140

Query: 44  -----------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 141 DMPLSKFRRRLLLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 200

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 201 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKVLSQE 255

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA+ + ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 256 FGRKPSEEEIAESMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADIENPE 313

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
           Q +     +   R  L   ++ L+PRER +   R   ++    TLE +   F+V+RER+R
Sbjct: 314 QDV----SKTLLREDLEGVLATLSPRERDVLRLRYGIDDGRMKTLEEIGQIFDVTRERIR 369

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 370 QIEAKALRKLRHP 382


>gi|254481825|ref|ZP_05095068.1| RNA polymerase sigma factor RpoS [marine gamma proteobacterium
           HTCC2148]
 gi|214037954|gb|EEB78618.1| RNA polymerase sigma factor RpoS [marine gamma proteobacterium
           HTCC2148]
          Length = 353

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 77/271 (28%), Positives = 132/271 (48%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L   EE   A R    GD S   R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 85  YLNEIGYSPLLTADEEKYYA-RLAIKGDESGRKRMIESNLRLVVKISRRYINRGLTLLDL 143

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 144 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERGIMNQTRTIRLPIHVV-KELNVY 202

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +T           IA  L+   ++V  M        S++  +      + 
Sbjct: 203 LRAAR----ELTQKLDHEPTAEEIADMLDRPAADVKRMLGLNERVTSMDTPVGPDSDKAV 258

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
              D +   H+     L++     + ++ +   +  L+ ++R +   R         TLE
Sbjct: 259 --VDTIADTHESDPSQLLQD---SDIKDSIGSWLDELSEKQREVVARRFGLRGYESSTLE 313

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +  E  ++RERVRQI+  A K+++  ++ Q
Sbjct: 314 EVGREIGLTRERVRQIQVEALKRLRGIMETQ 344


>gi|104783164|ref|YP_609662.1| RNA polymerase sigma factor RpoS [Pseudomonas entomophila L48]
 gi|95112151|emb|CAK16878.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Pseudomonas entomophila L48]
          Length = 335

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 83/278 (29%), Positives = 142/278 (51%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++ ++ +K       ++ +N R++  D SL         + 
Sbjct: 185 LRAAR-ELTQKLDHEPSPEEIASLLEKPVAEVKRMLGLNERVSSVDVSL------GPDSD 237

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + +  L  ++R +   R         TL
Sbjct: 238 KTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLGELTDKQREVVVRRFGLRGHESSTL 294

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 295 EDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSSES 332


>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 =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 73/246 (29%), Positives = 115/246 (46%), Gaps = 12/246 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 414 ERDSARAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 473

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            L R    +         PE    +
Sbjct: 474 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKLVRTSRQMLHEIGREPAPE---EL 528

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+KL +   +V  +        SL   I   D+  S   D++    D    + ++   + 
Sbjct: 529 AEKLGMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDKTAVIPLDAAIQT 583

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R   TR +S L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 584 NLREATTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTRERIRQIEAKALRKL 643

Query: 281 QESIQK 286
           +   + 
Sbjct: 644 KHPSRS 649


>gi|254504180|ref|ZP_05116331.1| Sigma-70 region 3 family [Labrenzia alexandrii DFL-11]
 gi|222440251|gb|EEE46930.1| Sigma-70 region 3 family [Labrenzia alexandrii DFL-11]
          Length = 671

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 72/261 (27%), Positives = 122/261 (46%), Gaps = 18/261 (6%)

Query: 34  EYVLAKRYR---EHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           E    +R     + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM
Sbjct: 412 EITEFRRIVAMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 471

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +   + ++    +
Sbjct: 472 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSR 526

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
            +     +      +A+KL +   +V  +        SL   I   D+  S   D++   
Sbjct: 527 QMLHEIGREPTPEELAEKLQMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI--- 581

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVS 265
            D    + I+   + N R   TR ++ L PRE R+   R         TLE +  +F V+
Sbjct: 582 EDKNAVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVT 641

Query: 266 RERVRQIEARAFKKVQESIQK 286
           RER+RQIEA+A +K++   + 
Sbjct: 642 RERIRQIEAKALRKLKHPSRS 662


>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 =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 64/249 (25%), Positives = 117/249 (46%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 364 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 423

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +      +  P+   
Sbjct: 424 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGRDPHPD--- 478

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + E ++  +        S+   I   D   S   D++    D    + ++   
Sbjct: 479 ELAERMMMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDTTIALPVDCAT 533

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            ++ +N     +  L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 534 SESLKNATNEVLEGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 593

Query: 279 KVQESIQKQ 287
           K++   + +
Sbjct: 594 KLRHPSRSE 602


>gi|163848612|ref|YP_001636656.1| sigma-70 family RNA polymerase sigma factor [Chloroflexus
           aurantiacus J-10-fl]
 gi|222526547|ref|YP_002571018.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus sp.
           Y-400-fl]
 gi|163669901|gb|ABY36267.1| RNA polymerase sigma factor, sigma-70 family [Chloroflexus
           aurantiacus J-10-fl]
 gi|222450426|gb|ACM54692.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus sp.
           Y-400-fl]
          Length = 381

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 81/300 (27%), Positives = 132/300 (44%), Gaps = 40/300 (13%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVL---------------------------AKRYREHG 45
           +  +  Y+ EI ++P+L  ++E  L                            +R  + G
Sbjct: 82  DDPVRMYLQEIGQVPLLTAEQEVELAKAMEAGAAARQRLDREEYTSARERFELERAVQQG 141

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
              A H L+ ++LRLVV IA  Y  YGL + ++V EGNIGLM+AV+KFD ++G + +TY+
Sbjct: 142 -QDARHHLIQANLRLVVSIAKKYTSYGLTMMDLVQEGNIGLMRAVEKFDYKKGHKFSTYA 200

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
            WWI+ A+   I      +++     +      ++R    LQ        PE    IA  
Sbjct: 201 TWWIRQAITRAIADQSRTIRLPVHMGE--AISQVKRTSHRLQQTMQREPTPE---EIADA 255

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           + +S  +V           SL   +    +   +  D++  D         E       R
Sbjct: 256 MGISAGKVRRTLEASMHPLSLEMPV--GQEGEGRMGDFIEDDRIS---TPAEAAAASLLR 310

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             L   +  L  RER+I + R   ++    TLE +  EF ++RER+RQIEA A +K++  
Sbjct: 311 EQLEEVLMKLPERERKIIQLRYGLKDGRYRTLEEVGIEFGITRERIRQIEAVALRKLRHP 370


>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 =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 72/267 (26%), Positives = 124/267 (46%), Gaps = 14/267 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L  +    +++R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 356 LSIERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 415

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 416 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 473

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    +A+++ + E ++  +        S+   I   D   S   D++  
Sbjct: 474 LQEMGREPLPE---ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 526

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q+ ++     N R      ++ L PRE ++   R   +     TLE +  +F+V
Sbjct: 527 -EDTTLQLPMDAATATNLRAATNDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDV 585

Query: 265 SRERVRQIEARAFKKVQESIQKQVELS 291
           +RER+RQIEA+A +K++   +  V  S
Sbjct: 586 TRERIRQIEAKALRKLRHPSRSDVLRS 612


>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 =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 537 RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 596

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 597 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 651

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 652 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDNNTVAPADAALHASMRD 706

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 707 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 766

Query: 285 QKQ 287
           +  
Sbjct: 767 RSD 769


>gi|332878128|ref|ZP_08445857.1| putative RNA polymerase sigma factor RpoD [Capnocytophaga sp. oral
           taxon 329 str. F0087]
 gi|332683866|gb|EGJ56734.1| putative RNA polymerase sigma factor RpoD [Capnocytophaga sp. oral
           taxon 329 str. F0087]
          Length = 287

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 67/276 (24%), Positives = 147/276 (53%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI ++ ++   EE  LA+R +E GD++A  +L  ++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQEIGRVDLITADEEVELAQRIKE-GDVAALEKLTKANLRFVVSVAKQYQNQGLT 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     +V++    N+  
Sbjct: 76  LPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLP--LNKIG 133

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               + ++  +L+   +   +      IA++L++S ++V           S++A +   +
Sbjct: 134 SINKINKMYAYLEQANE---RVPSAEEIARELDMSVNDVKESMKNSGRHISMDAPLV--E 188

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
              S   D +  +         ++    + R  + R++  L PRE  +        +   
Sbjct: 189 GEDSNLYDVIRSNESPNPD---KELILASLRTEIERALETLTPREADVIRLYFGLGDQHA 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 246 MTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|312113102|ref|YP_004010698.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhodomicrobium
           vannielii ATCC 17100]
 gi|311218231|gb|ADP69599.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhodomicrobium
           vannielii ATCC 17100]
          Length = 697

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 73/252 (28%), Positives = 119/252 (47%), Gaps = 15/252 (5%)

Query: 40  RYREHGDLSAAH---RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           +  + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  
Sbjct: 447 KIVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 506

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RG++ +TY+ WWI+ A+   I      ++I            + R    +         P
Sbjct: 507 RGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKIVRTSRQMMHEIGREPTP 564

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           E    +A+KL++   +V  +        SL   I   D+  S   D++    D    + I
Sbjct: 565 E---ELAEKLSMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAILPI 616

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEA 274
           +   + N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA
Sbjct: 617 DAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEA 676

Query: 275 RAFKKVQESIQK 286
           +A +K++   + 
Sbjct: 677 KALRKLKHPSRS 688


>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 =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 116/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 535 ESASRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 594

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    +              +
Sbjct: 595 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKMNRISRQHLQEFGFEPDASIL 649

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A K+ + E ++  +        S+   I   D + S   D++    DG     I+   + 
Sbjct: 650 AAKMEIPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDGANTAPIDAAMQA 704

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 705 GLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKL 764

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 765 KHPSRSD 771


>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 =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 440 RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 499

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 500 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 554

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 555 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDNNTVAPADAALHASMRD 609

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 610 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 669

Query: 285 QKQ 287
           +  
Sbjct: 670 RSD 672


>gi|262340892|ref|YP_003283747.1| RNA polymerase sigma-70 factor [Blattabacterium sp. (Blattella
           germanica) str. Bge]
 gi|262272229|gb|ACY40137.1| RNA polymerase sigma-70 factor [Blattabacterium sp. (Blattella
           germanica) str. Bge]
          Length = 287

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 82/288 (28%), Positives = 146/288 (50%), Gaps = 13/288 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +    +       L +Y+HEI KIP+L  +EE   A+R RE GD SA  +LV ++LR VV
Sbjct: 5   KITKQVTNRESESLDKYLHEIGKIPLLTPEEEVEYARRARE-GDASAIDKLVNANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++ + +FD  RGF+  +Y +WWI+ A+ + I     
Sbjct: 64  SVAKQYQNQGLSLCDLINEGNLGLIKGILRFDETRGFKCISYVVWWIRQAILQAIAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            ++  T          L ++   L  +     +      IA+ L+++E +V         
Sbjct: 124 SIRQPTNK-----LALLNKILKTLAQLEQELQRTPSAREIAEYLDMNEKDVEESIKNSGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A +   +   S   D +  D   +     E  E+++ R  + R +  L+ RERR+
Sbjct: 179 HVSMDAPLI--EGEDSNLYDLVRSDESPRPD---EHLEKESLRKDIKRILETLSERERRV 233

Query: 243 FEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
                      P+TLE +    +++RERVRQIE+ A K+++ S + ++
Sbjct: 234 IILHFGLNGSPPMTLEEVGQSCDLTRERVRQIESIALKRLKHSSRSKI 281


>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 =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 66/253 (26%), Positives = 118/253 (46%), Gaps = 12/253 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 374 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 433

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 434 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPLPE--- 488

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + E ++  +        S+   I   D   S   D++    D   ++ ++   
Sbjct: 489 ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDTTLELPLDSAT 543

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 544 AGSLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 603

Query: 279 KVQESIQKQVELS 291
           K++   + +   S
Sbjct: 604 KLRHPSRSETLRS 616


>gi|94498543|ref|ZP_01305098.1| sigma 70 (RpoD) [Sphingomonas sp. SKA58]
 gi|94421986|gb|EAT07032.1| sigma 70 (RpoD) [Sphingomonas sp. SKA58]
          Length = 682

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 68/251 (27%), Positives = 120/251 (47%), Gaps = 15/251 (5%)

Query: 41  YREHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
             + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 433 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 492

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I        +   + +L    +       +  
Sbjct: 493 GYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTSRQFLHEQGREP 547

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A++L++   +V  +        SL   I   D+  S   D++    D    + ++
Sbjct: 548 TPEEMAERLSMPLEKVRKVMKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAIIPVD 602

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              + N +  +TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+
Sbjct: 603 AAIQANLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 662

Query: 276 AFKKVQESIQK 286
           A +K++   + 
Sbjct: 663 ALRKLKHPSRS 673


>gi|319425507|gb|ADV53581.1| RNA polymerase, sigma 70 subunit, RpoD [Shewanella putrefaciens
           200]
          Length = 613

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 69/269 (25%), Positives = 126/269 (46%), Gaps = 22/269 (8%)

Query: 32  QEEYVLA--------KRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           +EE  LA        +R    E     A   +V ++LRLV+ IA  Y   GL   +++ E
Sbjct: 348 EEETGLAISAIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 407

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           GNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R
Sbjct: 408 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNR 465

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           +   +         PE    +A+++ + E ++  +        S+   I   D   S   
Sbjct: 466 ISRQMLQEMGREPSPE---ELAERMMMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLG 520

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLS 259
           D++    D   ++ ++    ++ ++     ++ L  RE ++   R   +     TLE + 
Sbjct: 521 DFI---EDTTLELPLDSATSESLKSATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVG 577

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +F+V+RER+RQIEA+A +K++   + ++
Sbjct: 578 KQFDVTRERIRQIEAKALRKLRHPSRSEI 606


>gi|149370109|ref|ZP_01889960.1| RNA polymerase sigma-70 factor [unidentified eubacterium SCB49]
 gi|149356600|gb|EDM45156.1| RNA polymerase sigma-70 factor [unidentified eubacterium SCB49]
          Length = 287

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 71/276 (25%), Positives = 145/276 (52%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ E+ KI ++  +EE  LA++ +  GD  A  +L  ++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQEVGKIDLITAEEEVELAQKIK-AGDQRALEKLTNANLRFVVSVAKQYQNQGLT 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A  +FD  RGF+  +Y++WWI+ A+ + +     +V++    N+  
Sbjct: 76  LPDLINEGNVGLIKAASRFDETRGFKFISYAVWWIRQAILQALAEQSRIVRLP--LNKIG 133

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               + +   HL+        PE    IAK+L+++ ++V           S++A +   +
Sbjct: 134 SINKINKAFTHLEQAHQRPPSPE---EIAKELDMTINDVKESIKNSGRSISMDAPLTEGE 190

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
                  +     + G+     +    ++ R  + R++  L PRE  + +      +  P
Sbjct: 191 D-----YNLYDVLNTGESPNPDQALLLESLRTEIERALETLTPRESDVIKLYFGLSDQRP 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TLE + S F+++RERVRQI+ +A ++++ + +  +
Sbjct: 246 MTLEEIGSTFDLTRERVRQIKEKAVRRLKHTSRSTI 281


>gi|22298160|ref|NP_681407.1| RNA polymerase sigma factor RpoD [Thermosynechococcus elongatus
           BP-1]
 gi|22294339|dbj|BAC08169.1| principal RNA polymerase sigma factor [Thermosynechococcus
           elongatus BP-1]
          Length = 418

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 76/318 (23%), Positives = 139/318 (43%), Gaps = 57/318 (17%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRY--------------REHGD----------- 46
            E  +  Y+ EI +I +L   EE  LA++               +E G            
Sbjct: 101 TEDSIRLYLQEIGRIRLLRADEEIELARKIADLLEMERVRDRLCQELGCTAEELERNPEP 160

Query: 47  -------------------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
                                A  ++V S+LRLVV IA  Y   GL   +++ EG++GL+
Sbjct: 161 WAKELGMTVPAFRHRLFVGRKAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLI 220

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +A +KFD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   +
Sbjct: 221 RAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTK 275

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
            ++    +      IA ++ ++  ++  +        SL   I    +  S+  D++  D
Sbjct: 276 LLSQEMGRKPTEEEIADRMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIESD 333

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVS 265
                +   ++  +   R  L   +  L+PRER + + R   ++    TLE +   F V+
Sbjct: 334 G----ETPEDQVSKHLLREDLETVLCTLSPRERDVLKLRYGLDDGRMKTLEEIGQLFNVT 389

Query: 266 RERVRQIEARAFKKVQES 283
           RER+RQIEA+A +K++  
Sbjct: 390 RERIRQIEAKALRKLRHP 407


>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 =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 68/263 (25%), Positives = 121/263 (46%), Gaps = 14/263 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L   E   + ++    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 360 LTIAEIKDINRQMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 419

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 420 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 477

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    + +++++ E ++  +        S+   I   D   S   D++  
Sbjct: 478 LQEMGREPTPE---ELGERMDMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 530

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q  IE    ++ +      ++ L  RE ++   R   +     TLE +  +F+V
Sbjct: 531 -EDSTMQSPIEVATVESLKEATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 589

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   + +
Sbjct: 590 TRERIRQIEAKALRKLRHPSRSE 612


>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 =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 439 RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 498

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 499 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 553

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 554 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTVAPADAALHASMRD 608

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 609 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 668

Query: 285 QKQ 287
           +  
Sbjct: 669 RSD 671


>gi|157412913|ref|YP_001483779.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str. MIT
           9215]
 gi|157387488|gb|ABV50193.1| Putative principal RNA polymerase sigma factor [Prochlorococcus
           marinus str. MIT 9215]
          Length = 393

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 76/313 (24%), Positives = 139/313 (44%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------------- 43
            E  +  Y+ EI +I +L   EE  LA++  +                            
Sbjct: 81  TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLQLEELATQYESEKGHFPSVREWAELI 140

Query: 44  -----------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 141 DMPLSKFRRRLLLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 200

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 201 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKVLSQE 255

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA+ + ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 256 FGRKPSEEEIAESMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADIENPE 313

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
           Q +     +   R  L   ++ L+PRER +   R   ++    TLE +   F+V+RER+R
Sbjct: 314 QDV----SKTLLREDLEGVLATLSPRERDVLRLRYGIDDGRMKTLEEIGQIFDVTRERIR 369

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 370 QIEAKALRKLRHP 382


>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 =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 66/253 (26%), Positives = 118/253 (46%), Gaps = 12/253 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 397 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 456

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 457 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPLPE--- 511

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + E ++  +        S+   I   D   S   D++    D   ++ ++   
Sbjct: 512 ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDTTLELPLDSAT 566

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 567 ATSLKAATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 626

Query: 279 KVQESIQKQVELS 291
           K++   + +   S
Sbjct: 627 KLRHPSRSETLRS 639


>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 =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 70/263 (26%), Positives = 120/263 (45%), Gaps = 14/263 (5%)

Query: 29  LEKQE--EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L   E  E   A    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 357 LTVAEIKEINRAMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 416

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 417 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 474

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    + +++++ E ++  +        S+   I   D   S   D++  
Sbjct: 475 LQEMGREPTPE---ELGERMDMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 527

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q  IE    ++ +      ++ L  RE ++   R   +     TLE +  +F+V
Sbjct: 528 -EDSTMQSPIEMATSESLKESTREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 586

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   + +
Sbjct: 587 TRERIRQIEAKALRKLRHPSRSE 609


>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 =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 69/269 (25%), Positives = 126/269 (46%), Gaps = 22/269 (8%)

Query: 32  QEEYVLA--------KRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           +EE  LA        +R    E     A   +V ++LRLV+ IA  Y   GL   +++ E
Sbjct: 351 EEETGLAISAIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 410

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           GNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R
Sbjct: 411 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNR 468

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           +   +         PE    +A+++ + E ++  +        S+   I   D   S   
Sbjct: 469 ISRQMLQEMGREPSPE---ELAERMMMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLG 523

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLS 259
           D++    D   ++ ++    ++ ++     ++ L  RE ++   R   +     TLE + 
Sbjct: 524 DFI---EDTTLELPLDSATSESLKSATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVG 580

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +F+V+RER+RQIEA+A +K++   + ++
Sbjct: 581 KQFDVTRERIRQIEAKALRKLRHPSRSEI 609


>gi|115523078|ref|YP_779989.1| RNA polymerase sigma factor RpoD [Rhodopseudomonas palustris
           BisA53]
 gi|115517025|gb|ABJ05009.1| RNA polymerase, sigma 70 subunit, RpoD [Rhodopseudomonas palustris
           BisA53]
          Length = 704

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 74/273 (27%), Positives = 127/273 (46%), Gaps = 17/273 (6%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAH---RLVTSHLRLVVKIAMGYRGYGLPI 75
            EI+ +  L   E     K     + G+  A      +V ++LRLV+ IA  Y   GL  
Sbjct: 433 QEIQSLAALTGLEIGEFRKIVHSVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQF 492

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +
Sbjct: 493 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----M 547

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + ++    + + +   +      +A+KL +   +V  +        SL   +   D+
Sbjct: 548 IETINKIVRTSRQMLNEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPLSLETPV--GDE 605

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPV 253
             S   D++    D    + I+   + N R   TR ++ L PRE R+   R         
Sbjct: 606 EDSHLGDFI---EDKNAVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDH 662

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 663 TLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 695


>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 =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 66/253 (26%), Positives = 118/253 (46%), Gaps = 12/253 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 371 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 430

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 431 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPLPE--- 485

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + E ++  +        S+   I   D   S   D++    D   ++ ++   
Sbjct: 486 ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDTTLELPLDSAT 540

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 541 ATSLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 600

Query: 279 KVQESIQKQVELS 291
           K++   + +   S
Sbjct: 601 KLRHPSRSETLRS 613


>gi|260424772|ref|ZP_05733235.2| RNA polymerase sigma-43 factor [Dialister invisus DSM 15470]
 gi|260403136|gb|EEW96683.1| RNA polymerase sigma-43 factor [Dialister invisus DSM 15470]
          Length = 394

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 67/273 (24%), Positives = 122/273 (44%), Gaps = 23/273 (8%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAK-----RYREHGDL------SAAHRLVTSHLRLVV 62
             +  Y+ E    P+L  ++E  LA+     +  E  D        A   +  ++LRLVV
Sbjct: 115 DPVRLYLRECGTTPLLTSEQEMKLAQTIEIGKMPEATDEQKRMAAEAKKEMANANLRLVV 174

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA  Y G G+P  +++ EGN+GL++AV KFD  +G++ +TY+ WWI+ A+   I     
Sbjct: 175 SIAKKYPGRGMPFLDLIQEGNMGLLKAVDKFDYTKGYKFSTYATWWIRQAITRSIADQAR 234

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            +++     +      + ++    +     + +      +AK++  S  ++         
Sbjct: 235 TIRVPVHMVE-----TINKMNRVGRHFLQEHGREATNEELAKEMETSVEKIREAKKAAQD 289

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             SL   I   +K  S   D++    D +     ++     RR  + + +  L  RE+ +
Sbjct: 290 PISLETPI--GEKEDSHLGDFI---EDQKTASPEDEAAATMRREQIHQLLETLTEREKGV 344

Query: 243 FEARRLQENP--VTLENLSSEFEVSRERVRQIE 273
              R   ++    TLE +   F V+RER+RQIE
Sbjct: 345 IALRYGIDDGTQRTLEEVGKYFGVTRERIRQIE 377


>gi|229588834|ref|YP_002870953.1| RNA polymerase sigma factor RpoS [Pseudomonas fluorescens SBW25]
 gi|229360700|emb|CAY47558.1| RNA polymerase sigma factor [Pseudomonas fluorescens SBW25]
          Length = 334

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 84/278 (30%), Positives = 142/278 (51%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 66  YLNEIGFSPLLTPEEEVHFA-RLSQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 124

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 125 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 183

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++  + +K       ++ +N R++  D SL         + 
Sbjct: 184 LRAAR-ELTQKLDHEPSPEEIANLLEKPVAEVKRMLGLNERVSSVDVSL------GPDSD 236

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + +S L  ++R +   R         TL
Sbjct: 237 KTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTDKQREVVIRRFGLRGHESSTL 293

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 294 EDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSSES 331


>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 =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 67/247 (27%), Positives = 115/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 408 EAKARRAKRDMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 467

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T           +
Sbjct: 468 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGME---ADAATL 522

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A K+ + E ++  +        S+   +   D + S   D++    D      IE     
Sbjct: 523 AIKMEMPEDKIRKILKIAKEPISMETPV--GDDDDSHLGDFI---EDANSLAPIEAAVYD 577

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + RN+    +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 578 SLRNVTKDILDSLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 637

Query: 281 QESIQKQ 287
           +   + +
Sbjct: 638 RHPSRSE 644


>gi|170723213|ref|YP_001750901.1| RNA polymerase sigma factor RpoS [Pseudomonas putida W619]
 gi|169761216|gb|ACA74532.1| RNA polymerase, sigma 70 subunit, RpoD family [Pseudomonas putida
           W619]
          Length = 335

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 83/278 (29%), Positives = 141/278 (50%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++  + +K       ++ +N R++  D SL         + 
Sbjct: 185 LRAAR-ELTQKLDHEPSPEEIATLLEKPVAEVKRMLGLNERVSSVDVSL------GPDSD 237

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + +  L  ++R +   R         TL
Sbjct: 238 KTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLGELTDKQREVVVRRFGLRGHESSTL 294

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 295 EDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSSES 332


>gi|5305130|emb|CAB46191.1| RNA polymerase sigma factor [Pseudomonas putida]
          Length = 335

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 83/278 (29%), Positives = 141/278 (50%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++  + +K       ++ +N R++  D SL         + 
Sbjct: 185 LRAAR-ELTQKLDHEPSPEEIATLLEKPVAEVKRMLGLNERVSSVDVSL------GPDSD 237

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + +  L  ++R +   R         TL
Sbjct: 238 KTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLGELTDKQREVVVRRFGLRGHESSTL 294

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 295 EDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSSES 332


>gi|39934363|ref|NP_946639.1| RNA polymerase sigma factor RpoD [Rhodopseudomonas palustris
           CGA009]
 gi|39648212|emb|CAE26731.1| RNA polymerase sigma 70 subunit, RpoD [Rhodopseudomonas palustris
           CGA009]
          Length = 698

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 69/246 (28%), Positives = 118/246 (47%), Gaps = 12/246 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 454 EREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 513

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    + + +   +      +
Sbjct: 514 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLNEIGREPTPEEL 568

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+KL +   +V  +        SL   +   D+  S   D++    D    + I+   + 
Sbjct: 569 AEKLGMPLEKVRKVLKIAKEPLSLETPV--GDEEDSHLGDFI---EDKNAVLPIDAAIQS 623

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 624 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKL 683

Query: 281 QESIQK 286
           +   + 
Sbjct: 684 KHPSRS 689


>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 =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 72/267 (26%), Positives = 124/267 (46%), Gaps = 14/267 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L  +    +++R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 356 LSIERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 415

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 416 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 473

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    +A+++ + E ++  +        S+   I   D   S   D++  
Sbjct: 474 LQEMGREPLPE---ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 526

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q+ ++     N R      ++ L PRE ++   R   +     TLE +  +F+V
Sbjct: 527 -EDTTLQLPMDAATATNLRAATNDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDV 585

Query: 265 SRERVRQIEARAFKKVQESIQKQVELS 291
           +RER+RQIEA+A +K++   +  V  S
Sbjct: 586 TRERIRQIEAKALRKLRHPSRSDVLRS 612


>gi|186702713|gb|ACC91623.1| RNA polymerase sigma factor [Pseudomonas sp. CT07]
          Length = 336

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 84/278 (30%), Positives = 142/278 (51%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 68  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 126

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 127 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 185

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++  + +K       ++ +N R++  D SL         + 
Sbjct: 186 LRAAR-ELTQKLDHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSL------GPDSD 238

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + +S L  ++R +   R         TL
Sbjct: 239 KTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTDKQREVVVRRFGLRGHESSTL 295

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 296 EDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSSES 333


>gi|309791233|ref|ZP_07685765.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Oscillochloris
           trichoides DG6]
 gi|308226795|gb|EFO80491.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Oscillochloris
           trichoides DG6]
          Length = 391

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 81/300 (27%), Positives = 133/300 (44%), Gaps = 40/300 (13%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL------------------------- 47
           +  +  Y+ EI ++P+L  ++E  LAK   E GD+                         
Sbjct: 92  DDPVRMYLQEIGQVPLLTAEKEVELAKSM-EAGDIARQRIDREEYTSGRERMELERAYAL 150

Query: 48  --SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
              +   L+ ++LRLVV IA  Y  YGL + ++V EGNIGLM+AV+KFD  +G + +TY+
Sbjct: 151 GCESRQHLIQANLRLVVSIAKKYTSYGLTMMDLVQEGNIGLMRAVEKFDYTKGHKFSTYA 210

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
            WWI+ A+   I      +++     +      ++R    LQ        PE    IA+ 
Sbjct: 211 TWWIRQAITRAIADQSRTIRLPVHMGE--AISQVKRTSHKLQQSMQREPTPE---EIAEA 265

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           + +S  +V           SL   +    +   +  D++  D         E       R
Sbjct: 266 MGISAGKVRRTLEASMHPLSLEMPV--GQEGEGRMGDFIEDDRIS---TPSEAAAAAMLR 320

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +   +  L  RER+I + R   ++    TLE +  EF ++RER+RQIEA A +K++  
Sbjct: 321 EQIEEVLQKLPERERKIIQLRYGLKDGRYRTLEEVGVEFGITRERIRQIEAVALRKLRHP 380


>gi|73541439|ref|YP_295959.1| sigma-70 region 1.2 [Ralstonia eutropha JMP134]
 gi|72118852|gb|AAZ61115.1| Sigma-70 region 1.2 [Ralstonia eutropha JMP134]
          Length = 653

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 63/248 (25%), Positives = 118/248 (47%), Gaps = 12/248 (4%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            E     A H +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ 
Sbjct: 407 AERQMRQAKHEMTQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGWKF 466

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY+ WW++ A+   I      +++     ++     L RL   L   T     P     
Sbjct: 467 STYATWWVRQAVTRAIADQARTIRVPVHMIEQ--INKLNRLSRELMQQTGKEPDP---AV 521

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           +A+++++ E +V ++        S+   +   +   +   D +    D       +   +
Sbjct: 522 LAERMDMPEEKVRAIMKIAREPVSMETPV--GEDGDTSLGDMIA---DSDTATPADAALQ 576

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKK 279
            + R ++   +  L PRE ++   R   +     TLE +  +F+V+RER+RQIE++A +K
Sbjct: 577 ASLREVVREMLDELTPREAKVLRMRFGIDMATDYTLEEVGKQFDVTRERIRQIESKAMRK 636

Query: 280 VQESIQKQ 287
           ++   +  
Sbjct: 637 LRHPSRAD 644


>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 =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 67/250 (26%), Positives = 115/250 (46%), Gaps = 12/250 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 368 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 427

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 428 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPNPE--- 482

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + E +V  +        S+   I   D   S   D++    D      I+   
Sbjct: 483 ELAERMMMPEDKVRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDTTIDSPIDSAT 537

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            ++ R      ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 538 MESLRGATNDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 597

Query: 279 KVQESIQKQV 288
           K++   +  +
Sbjct: 598 KLRHPSRSDL 607


>gi|296932701|gb|ADH93504.1| RNA polymerase sigma factor RpoD [Pseudomonas sp. In5]
          Length = 616

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 69/263 (26%), Positives = 120/263 (45%), Gaps = 14/263 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L   E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 356 LTIAEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 415

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 416 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 473

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    + +++ + E ++  +        S+   I   D   S   D++  
Sbjct: 474 LQEMGREPTPE---ELGERMEMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 526

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q  I+    ++ +      +S L  RE ++   R   +     TLE +  +F+V
Sbjct: 527 -EDSTMQSPIDVATVESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 585

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   + +
Sbjct: 586 TRERIRQIEAKALRKLRHPTRSE 608


>gi|218710550|ref|YP_002418171.1| RNA polymerase sigma factor RpoS [Vibrio splendidus LGP32]
 gi|218323569|emb|CAV19793.1| RNA polymerase sigma factor rpoS (Sigma-38 factor) [Vibrio
           splendidus LGP32]
          Length = 335

 Score =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 81/271 (29%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 63  YLGEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHVV-KELNIY 180

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA KL+    +V  M        S++  I        
Sbjct: 181 LRTAR----ELSQKLDHEPTAEEIASKLDKPVGDVSKMLRLNERVSSVDTPI--GGDGEK 234

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D +   ++   +V     +  + +N L   +  LNP+++ +   R   L   P TLE
Sbjct: 235 ALLDIIPDINNSDPEV---STQDSDIKNSLIFWLDELNPKQKEVLARRFGLLGYEPSTLE 291

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 292 EVGREISLTRERVRQIQVEGLRRLREILIKQ 322


>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 =  227 bits (580), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 65/250 (26%), Positives = 119/250 (47%), Gaps = 12/250 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 366 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 425

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 426 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPSPE--- 480

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + E ++  +        S+   I   D   S   D++    D   ++ ++   
Sbjct: 481 ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDTTLELPLDSAT 535

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            ++ +N     ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 536 GESLKNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 595

Query: 279 KVQESIQKQV 288
           K++   + ++
Sbjct: 596 KLRHPSRSEI 605


>gi|325277035|ref|ZP_08142696.1| RNA polymerase sigma factor RpoS [Pseudomonas sp. TJI-51]
 gi|324097832|gb|EGB96017.1| RNA polymerase sigma factor RpoS [Pseudomonas sp. TJI-51]
          Length = 335

 Score =  227 bits (579), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 83/278 (29%), Positives = 141/278 (50%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++  + +K       ++ +N R++  D SL         + 
Sbjct: 185 LRAAR-ELTQKLDHEPSPEEIATLLEKPVAEVKRMLGLNERVSSVDVSL------GPDSD 237

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + +  L  ++R +   R         TL
Sbjct: 238 KTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLGELTDKQREVVVRRFGLRGHESSTL 294

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 295 EDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSSES 332


>gi|159901184|ref|YP_001547431.1| RpoD family RNA polymerase sigma factor [Herpetosiphon aurantiacus
           ATCC 23779]
 gi|159894223|gb|ABX07303.1| RNA polymerase, sigma 70 subunit, RpoD family [Herpetosiphon
           aurantiacus ATCC 23779]
          Length = 375

 Score =  227 bits (579), Expect = 1e-57,   Method: Composition-based stats.
 Identities = 78/302 (25%), Positives = 135/302 (44%), Gaps = 39/302 (12%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD----------------------- 46
           V+ +  +  Y+ EI ++ +L   EE +LAK+  E G+                       
Sbjct: 73  VSLDDPVRMYLREIGQVHLLTAHEETMLAKQL-ERGERAMIRLARHEYLLEEKARLQQQV 131

Query: 47  ---LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
               +A   L+ ++LRLVV IA  Y G G+   +++ EGNIGLM+A +KFD  +GF+ +T
Sbjct: 132 LESEAARQHLIQANLRLVVSIAKKYVGRGMSFLDLIQEGNIGLMRATEKFDYHKGFKFST 191

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI+ A+   I      +++     +      + R+K     +     +      I 
Sbjct: 192 YATWWIRQAITRSISDHSRTIRLPVHVGE-----TINRVKRTAHKLQQALEREPSAEEIG 246

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + L +   +V  +        SL   +   ++  S   D++  D   +    ++      
Sbjct: 247 EALGLPADKVRRVLEVARQPVSLETPV--GNEGDSVLGDFIEDDRSSE---PLDHATEHL 301

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R  L   +  L+ RERRI E R    +    TLE +  EF ++RER+RQIEA+  +K++
Sbjct: 302 LREQLDEVLCKLDERERRIIELRYGLVDGKYRTLEEVGREFGITRERIRQIEAKVLRKLR 361

Query: 282 ES 283
             
Sbjct: 362 HP 363


>gi|71736784|ref|YP_275947.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv.
           phaseolicola 1448A]
 gi|71557337|gb|AAZ36548.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv.
           phaseolicola 1448A]
          Length = 335

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 84/278 (30%), Positives = 142/278 (51%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++  + +K       ++ +N R++  D SL         + 
Sbjct: 185 LRAAR-ELTQKLDHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSL------GPDSD 237

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + +S L  ++R +   R         TL
Sbjct: 238 KTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTEKQREVVIRRFGLRGYESSTL 294

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 295 EDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSSES 332


>gi|77457359|ref|YP_346864.1| RNA polymerase sigma factor RpoS [Pseudomonas fluorescens Pf0-1]
 gi|77381362|gb|ABA72875.1| RNA polymerase, sigma 38 subunit, RpoS [Pseudomonas fluorescens
           Pf0-1]
          Length = 335

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 84/278 (30%), Positives = 142/278 (51%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++  + +K       ++ +N R++  D SL         + 
Sbjct: 185 LRAAR-ELTQKLDHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSL------GPDSD 237

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + +S L  ++R +   R         TL
Sbjct: 238 KTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTDKQREVVVRRFGLRGHESSTL 294

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 295 EDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSSES 332


>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 =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 68/260 (26%), Positives = 121/260 (46%), Gaps = 14/260 (5%)

Query: 32  QEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           +E   + KR    E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+A
Sbjct: 557 EELKHINKRMNSGERASRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 616

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V KF+  RG++ +TY+ WWI+ A+   I      ++I        +   + ++    +  
Sbjct: 617 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKMNRISRQH 671

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
                       +A K+ + E ++  +        S+   I   D + S   D++    D
Sbjct: 672 LQEFGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---ED 726

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRE 267
           G     I+   +   R+++   +  L PRE ++   R   E     TLE +  +F+V+RE
Sbjct: 727 GNNTAPIDAAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRE 786

Query: 268 RVRQIEARAFKKVQESIQKQ 287
           R+RQIEA+A +K++   +  
Sbjct: 787 RIRQIEAKALRKLKHPSRSD 806


>gi|83941156|ref|ZP_00953618.1| RNA polymerase sigma factor [Sulfitobacter sp. EE-36]
 gi|83955715|ref|ZP_00964295.1| RNA polymerase sigma factor [Sulfitobacter sp. NAS-14.1]
 gi|83840009|gb|EAP79185.1| RNA polymerase sigma factor [Sulfitobacter sp. NAS-14.1]
 gi|83846976|gb|EAP84851.1| RNA polymerase sigma factor [Sulfitobacter sp. EE-36]
          Length = 660

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 420 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 479

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A+KL
Sbjct: 480 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAEKL 534

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++N + 
Sbjct: 535 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAVLPLDSAIQENLKE 589

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 590 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 649

Query: 285 QK 286
           + 
Sbjct: 650 RS 651


>gi|298488362|ref|ZP_07006394.1| RNA polymerase sigma factor RpoS [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
 gi|298157184|gb|EFH98272.1| RNA polymerase sigma factor RpoS [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
          Length = 335

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 84/278 (30%), Positives = 143/278 (51%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++  + +K       ++ +N R++  D SL         + 
Sbjct: 185 LRAAR-ELTQKLDHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSL------GPDSD 237

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++  +    + + +S L  ++R +   R         TL
Sbjct: 238 KTLLDTLTDDRPTDPCELLQDDDLSHS---IDQWLSELTEKQREVVIRRFGLRGHESSTL 294

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 295 EDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSSES 332


>gi|296161119|ref|ZP_06843929.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. Ch1-1]
 gi|295888642|gb|EFG68450.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. Ch1-1]
          Length = 705

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 72/262 (27%), Positives = 127/262 (48%), Gaps = 12/262 (4%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L++  E   A    E   L A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM
Sbjct: 445 PLDEFREVCRALSASEAKTLRAKGEMIEANLRLVISIAKRYTNRGLLFLDLIQEGNIGLM 504

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV KF+  RG++ +TY+ WWI+ A+   I      +++        +  +L +LK   +
Sbjct: 505 RAVDKFEYRRGYKFSTYATWWIRQAVSRSIADQARTIRVPVH-----MIESLNKLKRISR 559

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
            I            +A+++ + E +V +M   +    SL+A +  +D  S          
Sbjct: 560 QILQETGSEPDAALLAQRMEMQEQKVRAMLRIVREPVSLDASVGENDDTSIGDLI----- 614

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVS 265
            D    +  +     + R+ ++ ++  L PRE +I   R   E     TLE L  +FE++
Sbjct: 615 EDSTAILPDDAALHASMRDAISEALMTLTPREAKILRLRFGIESGRDHTLEELGEQFELT 674

Query: 266 RERVRQIEARAFKKVQESIQKQ 287
           RER+RQIE +A +K++   + +
Sbjct: 675 RERIRQIEVKALRKLRHPARSE 696


>gi|90580773|ref|ZP_01236576.1| RNA polymerase sigma factor [Vibrio angustum S14]
 gi|90438041|gb|EAS63229.1| RNA polymerase sigma factor [Vibrio angustum S14]
          Length = 616

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 72/267 (26%), Positives = 124/267 (46%), Gaps = 14/267 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L  +    +++R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 356 LSIERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 415

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 416 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 473

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    +A+++ + E ++  +        S+   I   D   S   D++  
Sbjct: 474 LQEMGREPLPE---ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 526

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q+ ++     N R      ++ L PRE ++   R   +     TLE +  +F+V
Sbjct: 527 -EDTTLQLPMDAATATNLRAATNDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDV 585

Query: 265 SRERVRQIEARAFKKVQESIQKQVELS 291
           +RER+RQIEA+A +K++   +  V  S
Sbjct: 586 TRERIRQIEAKALRKLRHPSRSDVLRS 612


>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 =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 64/247 (25%), Positives = 115/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 557 EANSRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 616

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    +              +
Sbjct: 617 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKMNRISRQHLQEFGFEPDASIL 671

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A K+ + E ++  +        S+   I   D + S   D++    D      I+   + 
Sbjct: 672 AAKMEIPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDSNNTAPIDAAMQA 726

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 727 GLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKL 786

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 787 KHPSRSD 793


>gi|322420057|ref|YP_004199280.1| RpoD subfamily RNA polymerase sigma-70 factor [Geobacter sp. M18]
 gi|320126444|gb|ADW14004.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           M18]
          Length = 330

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 72/276 (26%), Positives = 141/276 (51%), Gaps = 13/276 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI+K  +L   EE  LA R  + GD +A  R++ S+LRLVVKIA  Y   G
Sbjct: 54  DDAIKLYLREIQKTKLLTADEEKELAARI-DLGDKAARDRMIVSNLRLVVKIAKRYINRG 112

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP  +++ EGN+GL++AV++F   +  R +TY+ WWI+ +++  ++     +++    + 
Sbjct: 113 LPFLDLIEEGNMGLIKAVERFKLSKECRFSTYATWWIRQSIERALVNQSRTIRLPVHVSD 172

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                ++ ++    + +     +   +  +A  L V+ + V  +   L    S+   +  
Sbjct: 173 -----DINKMLRVTRELVQKMNREPTIKEVADTLEVNVTYVRRLMVLLKKTYSIERPM-- 225

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE-- 250
            + N     D +         VL+E     N+  ++++    L+  E++I   R   E  
Sbjct: 226 GENNDYFLIDTIEDTSTISPAVLLEDL---NKYELVSKWFETLSDAEKKILTLRFGLEDK 282

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +P TL+ +   F V+RER+RQIEA++ +K+++ ++ 
Sbjct: 283 DPQTLDTIGRSFGVTRERIRQIEAKSLEKLRKILEA 318


>gi|237800176|ref|ZP_04588637.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. oryzae
           str. 1_6]
 gi|331023033|gb|EGI03090.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. oryzae
           str. 1_6]
          Length = 335

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 84/278 (30%), Positives = 142/278 (51%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVYFA-RLSQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++  + +K       ++ +N R++  D SL         + 
Sbjct: 185 LRAAR-ELTQKLDHEPTPEEIANLLEKPVGEVKRMLGLNERVSSVDVSL------GPDSD 237

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + +S L  ++R +   R         TL
Sbjct: 238 KTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTEKQREVVIRRFGLRGHESSTL 294

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 295 EDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSSES 332


>gi|319409355|emb|CBI82999.1| RNA polymerase sigma-32 factor [Bartonella schoenbuchensis R1]
          Length = 303

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 103/266 (38%), Positives = 171/266 (64%), Gaps = 1/266 (0%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           +    + P LEK++E+ LA R+++  D  A H++  +H+RLV+ IA  ++ + +P+S++V
Sbjct: 27  MRSAMQAPYLEKKKEHDLALRWKDKRDDKAMHQIAAAHMRLVISIASRFKRFKMPLSDLV 86

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EG +GL++A  +F+P+R  R +TY+ WWI+A++Q+YILR+WS+V+ GT+++QK LFFNL
Sbjct: 87  QEGYVGLLEAAARFEPDRDVRFSTYATWWIRASIQDYILRNWSIVRGGTSSSQKALFFNL 146

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSS 198
           RRL+  L        K +    I++KL VS S+V +M+ R +G D SL+  ++ +D NS 
Sbjct: 147 RRLRAQLVQDDSTMSKQDIFRVISEKLGVSVSDVETMDFRFSGTDNSLSMSVSENDDNSV 206

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
              D LV +    + ++ +  + + R   L  ++ +LN RE  I   RRL E   TLE L
Sbjct: 207 TKLDTLVDEKPLPDSLIEKVIDGQRRTQWLYDALQILNERELEIIRFRRLNEESATLEFL 266

Query: 259 SSEFEVSRERVRQIEARAFKKVQESI 284
             +  +S+ERVRQIEARA +K++ ++
Sbjct: 267 GEKLGISKERVRQIEARALQKLRCAL 292


>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 =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 67/253 (26%), Positives = 118/253 (46%), Gaps = 12/253 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 370 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 430 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPLPE--- 484

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + E ++  +        S+   I   D   S   D++    D   ++ ++   
Sbjct: 485 ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDTTLELPVDSAT 539

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
             + R      ++ L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 540 MTSLRVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 279 KVQESIQKQVELS 291
           K++   + +   S
Sbjct: 600 KLRHPSRSETLRS 612


>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 =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 117/247 (47%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 491 ESNSRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 550

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    +              +
Sbjct: 551 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKMNRLSRQHLQEFGFEPDASIL 605

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+ + E ++  +        S+   I   D + S   D++    DG     +E   + 
Sbjct: 606 AEKMEIPEEKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDGANTAPLEAAMQA 660

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 661 GLRDVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKL 720

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 721 KHPSRSD 727


>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 =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 69/273 (25%), Positives = 123/273 (45%), Gaps = 14/273 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +  I +   L  +    + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 346 LSVIEQTTGLSIERIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 405

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 406 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 463

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 464 KLNRISRQMLQEMGREPNPE---ELAERMMMPEDKIRKVLKIAKEPISMETPI--GDDED 518

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D      I+    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 519 SHLGDFI---EDTTIDSPIDSATMESLRGATNDVLAGLTAREAKVLRMRFGIDMNTDHTL 575

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           E +  +F+V+RER+RQIEA+A +K++   +  +
Sbjct: 576 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSDL 608


>gi|323138995|ref|ZP_08074055.1| RNA polymerase, sigma 32 subunit, RpoH [Methylocystis sp. ATCC
           49242]
 gi|322395749|gb|EFX98290.1| RNA polymerase, sigma 32 subunit, RpoH [Methylocystis sp. ATCC
           49242]
          Length = 294

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 116/269 (43%), Positives = 178/269 (66%), Gaps = 2/269 (0%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           +    + P LE+ EE  LA  +R+HGD  A H+L  +H+RLV+ +A  +R YGLPI+++V
Sbjct: 12  MKAAAEAPFLERDEEKALAVAWRDHGDRRALHKLTAAHMRLVIALAAKFRHYGLPIADLV 71

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EG++GL++A  +F PER  R +TY+ WWI+A++Q+Y+LR+WS+V+ GT+++QK LFFNL
Sbjct: 72  QEGHVGLLEAAARFAPERDVRFSTYATWWIRASIQDYVLRNWSIVRGGTSSSQKALFFNL 131

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD-KNS 197
           RRL+  L    D     +   AIAK L VS ++V  M+ RL+G D SLNA +   D   S
Sbjct: 132 RRLRARLARDPDAYGSGDAYQAIAKALGVSRADVEMMDSRLSGSDVSLNAQLVDDDSSGS 191

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           +Q  D+LV DH   ++ + E  +   R   L  ++++L+ RE RI + RRL +N VTLE 
Sbjct: 192 AQRMDFLVDDHPLPDEAVQETMDSDRRARWLKDALAILSERELRIVQERRLTDNLVTLET 251

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQK 286
           L  +  +S+ERVRQIE+RA  K+++++ +
Sbjct: 252 LGDKLGISKERVRQIESRALIKLRKALSR 280


>gi|33861053|ref|NP_892614.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus subsp.
           pastoris str. CCMP1986]
 gi|33639785|emb|CAE18955.1| Putative principal RNA polymerase sigma factor [Prochlorococcus
           marinus subsp. pastoris str. CCMP1986]
          Length = 396

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 76/313 (24%), Positives = 139/313 (44%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------------- 43
            E  +  Y+ EI +I +L   EE  LA++  +                            
Sbjct: 84  TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLQLEELATQYESEKGHFPSVREWAELT 143

Query: 44  -----------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 144 DMPLSKFRRRLLLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 203

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 204 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKVLSQE 258

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA+ + ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 259 FGRKPSEEEIAESMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADIENPE 316

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
           Q +     +   R  L   ++ L+PRER +   R   ++    TLE +   F+V+RER+R
Sbjct: 317 QDV----SKTLLREDLEGVLATLSPRERDVLRLRYGIDDGRMKTLEEIGQIFDVTRERIR 372

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 373 QIEAKALRKLRHP 385


>gi|304410159|ref|ZP_07391778.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Shewanella
           baltica OS183]
 gi|307302130|ref|ZP_07581888.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Shewanella
           baltica BA175]
 gi|304351568|gb|EFM15967.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Shewanella
           baltica OS183]
 gi|306914168|gb|EFN44589.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Shewanella
           baltica BA175]
          Length = 326

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 82/271 (30%), Positives = 141/271 (52%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   +++  + G   + +R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 57  YLGEIGFSPLLSAEEEVYFSRKALK-GCAKSRNRMIESNLRLVVKIARRYNNRGLALLDL 115

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 116 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 174

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            IA+KL VS ++V  M        S++  +     N  
Sbjct: 175 LRTAR----ELAQKLDHEPTAEEIAEKLQVSSADVSRMLKLNEKITSVDMPL--GGDNDK 228

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  D +      ++ E+  N    + + ++ LN ++R +   R   L   P TLE
Sbjct: 229 ALLDILADDDNVGPDYKVQDEDISNS---VVKWLNELNTKQREVLARRFGLLGYEPSTLE 285

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++ +E  ++RERVRQI+  A K++++ +  Q
Sbjct: 286 DVGAEIGLTRERVRQIQVEALKRLRDLLGSQ 316


>gi|119944095|ref|YP_941775.1| RNA polymerase sigma-70 factor RpoD [Psychromonas ingrahamii 37]
 gi|119862699|gb|ABM02176.1| RNA polymerase sigma-70 factor RpoD [Psychromonas ingrahamii 37]
          Length = 617

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 66/249 (26%), Positives = 115/249 (46%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 371 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 430

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +        +PE   
Sbjct: 431 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRVSRQMLQEMGREPQPE--- 485

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + E +V  +        S+   I   D   S   D++    D    +      
Sbjct: 486 ELAERMMMPEDKVRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDTTIALPANCAT 540

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            ++ +N     +  L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 541 SESLKNATNDVLEGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 600

Query: 279 KVQESIQKQ 287
           K++   + +
Sbjct: 601 KLRHPSRSE 609


>gi|26988355|ref|NP_743780.1| RNA polymerase sigma factor RpoS [Pseudomonas putida KT2440]
 gi|148549360|ref|YP_001269462.1| RNA polymerase sigma factor RpoS [Pseudomonas putida F1]
 gi|167032190|ref|YP_001667421.1| RNA polymerase sigma factor RpoS [Pseudomonas putida GB-1]
 gi|24983106|gb|AAN67244.1|AE016351_6 RNA polymerase sigma factor RpoS [Pseudomonas putida KT2440]
 gi|148513418|gb|ABQ80278.1| RNA polymerase, sigma 70 subunit, RpoD family [Pseudomonas putida
           F1]
 gi|166858678|gb|ABY97085.1| RNA polymerase, sigma 70 subunit, RpoD family [Pseudomonas putida
           GB-1]
 gi|313500209|gb|ADR61575.1| RpoS [Pseudomonas putida BIRD-1]
          Length = 335

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 83/278 (29%), Positives = 141/278 (50%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++  + +K       ++ +N R++  D SL         + 
Sbjct: 185 LRAAR-ELTQKLDHEPSPEEIATLLEKPVAEVKRMLGLNERVSSVDVSL------GPDSD 237

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + +  L  ++R +   R         TL
Sbjct: 238 KTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLGELTDKQREVVVRRFGLRGHESSTL 294

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 295 EDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSSES 332


>gi|260361829|ref|ZP_05774845.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus K5030]
 gi|308114475|gb|EFO52015.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus K5030]
          Length = 329

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 80/287 (27%), Positives = 140/287 (48%), Gaps = 13/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           R+              Y+ EI   P+L  +EE + A+R    GD +A  R+  S+LRLVV
Sbjct: 41  REEFDASSKSLDATQLYLGEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMFESNLRLVV 99

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           KI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++    
Sbjct: 100 KISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTR 159

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            +++      K L   LR  +     ++           IA +L++   +V  M      
Sbjct: 160 TIRLPIHVV-KELNIYLRTAR----ELSQKLDHEPTAEEIAAQLDIPVEDVSKMLRLNER 214

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++  I           D +   ++   +V  + +   + ++ L   +  LNP+++ +
Sbjct: 215 ISSVDTPI--GGDGEKALLDIIPDANNSDPEVSTQDD---DIKSSLIHWLEELNPKQKEV 269

Query: 243 FEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 270 LARRFGLLGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLREILIKQ 316


>gi|86751238|ref|YP_487734.1| RNA polymerase sigma factor RpoD [Rhodopseudomonas palustris HaA2]
 gi|86574266|gb|ABD08823.1| sigma 70 (RpoD) [Rhodopseudomonas palustris HaA2]
          Length = 714

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 69/246 (28%), Positives = 118/246 (47%), Gaps = 12/246 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 470 EREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 529

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    + + +   +      +
Sbjct: 530 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLNEIGREPTPEEL 584

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+KL +   +V  +        SL   +   D+  S   D++    D    + I+   + 
Sbjct: 585 AEKLGMPLEKVRKVLKIAKEPLSLETPV--GDEEDSHLGDFI---EDKNAVLPIDAAIQS 639

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 640 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKL 699

Query: 281 QESIQK 286
           +   + 
Sbjct: 700 KHPSRS 705


>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 =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 64/247 (25%), Positives = 115/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 557 EANSRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 616

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    +              +
Sbjct: 617 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKMNRISRQHLQEFGFEPDASIL 671

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A K+ + E ++  +        S+   I   D + S   D++    D      I+   + 
Sbjct: 672 AAKMEIPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDSNNTAPIDAAMQA 726

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 727 GLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKL 786

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 787 KHPSRSD 793


>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 =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 68/267 (25%), Positives = 125/267 (46%), Gaps = 14/267 (5%)

Query: 29  LEKQEEYVLAKRYREH--GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L  Q+   + +R  +       A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 368 LTVQQIRDIGERIAQGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 427

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 428 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 485

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    +A+++ + E ++  +        S+   I   D + S   D++  
Sbjct: 486 LQEMGREASPE---ELAERMGMPEDKIRKVLKIAKEPISMETPI--GDDDDSHLGDFI-- 538

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   ++ ++    ++ +      +  L PRE ++   R   +     TLE +  +F+V
Sbjct: 539 -EDSTLELPLDSATAQSLKVATHEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDV 597

Query: 265 SRERVRQIEARAFKKVQESIQKQVELS 291
           +RER+RQIEA+A +K++   + +   S
Sbjct: 598 TRERIRQIEAKALRKLRHPSRSETLRS 624


>gi|90422490|ref|YP_530860.1| RNA polymerase sigma factor RpoD [Rhodopseudomonas palustris
           BisB18]
 gi|90104504|gb|ABD86541.1| sigma 70 (RpoD) [Rhodopseudomonas palustris BisB18]
          Length = 702

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 69/246 (28%), Positives = 118/246 (47%), Gaps = 12/246 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 458 EREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 517

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    + + +   +      +
Sbjct: 518 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLNEIGREPTPEEL 572

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+KL +   +V  +        SL   +   D+  S   D++    D    + I+   + 
Sbjct: 573 AEKLGMPLEKVRKVLKIAKEPLSLETPV--GDEEDSHLGDFI---EDKNAILPIDAAIQS 627

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 628 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKL 687

Query: 281 QESIQK 286
           +   + 
Sbjct: 688 KHPSRS 693


>gi|301059188|ref|ZP_07200126.1| putative alternative sigma factor RpoH [delta proteobacterium
           NaphS2]
 gi|300446678|gb|EFK10505.1| putative alternative sigma factor RpoH [delta proteobacterium
           NaphS2]
          Length = 329

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 105/277 (37%), Positives = 172/277 (62%), Gaps = 8/277 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG- 72
             L  Y+ EI++  +L ++EE  LA R +E+ D  AA RLVTS+LRLVVKIAM +  Y  
Sbjct: 47  DPLQIYLLEIKQYHLLTREEEIELATRIQENNDDDAAFRLVTSNLRLVVKIAMDFHRYWT 106

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
             + +++ EGN+GL+QAV+KFDP RG + + Y+ +WIKA + ++I+ +W +VKIGTT +Q
Sbjct: 107 KNLLDLIQEGNLGLLQAVRKFDPYRGIKFSYYASFWIKAYILKFIMDNWKMVKIGTTQSQ 166

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALIN 191
           ++LFFNL + +  L A       PE  + +A+KL+V ESEV+ M  RL G E SL+A + 
Sbjct: 167 RKLFFNLAKERDKLIA---QGFTPEPRL-LAEKLDVKESEVVEMTQRLGGWEISLSAPV- 221

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             + +   +  +L       + +L   E +      L      L+ +E  IF+ R L E 
Sbjct: 222 -GEDSRESYGSFLPDPAMAADDLLSNDESKNVLTKSLQEFRKTLSGKEADIFDNRILAEK 280

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           P+TL++L  ++++SRER+RQI+ +  K +++ +++++
Sbjct: 281 PLTLQDLGDKYKISRERIRQIQEKIIKNIRKWLKEKI 317


>gi|218780916|ref|YP_002432234.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfatibacillum
           alkenivorans AK-01]
 gi|218762300|gb|ACL04766.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfatibacillum
           alkenivorans AK-01]
          Length = 595

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 71/243 (29%), Positives = 112/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 355 KDAKAELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 414

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            L R   +L         PE    IA+K+
Sbjct: 415 WWIRQAITRAIADQARTIRIPVHM--IETINKLIRTSRYLVQELGREPTPE---EIAQKM 469

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
                +V  +        SL   I   ++  S   D++    D +  +  E     N   
Sbjct: 470 EFPLEKVRRVLKIAKEPISLETPI--GEEEDSHLGDFI---EDKKFMLPSEAAISLNLAE 524

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              + ++ L PRE ++   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 525 QTRKVLATLTPREEKVLRMRFGIGEKADHTLEEVGKDFSVTRERIRQIEAKALRKLRHPS 584

Query: 285 QKQ 287
           + Q
Sbjct: 585 RSQ 587


>gi|228472793|ref|ZP_04057551.1| RNA polymerase sigma factor RpoD [Capnocytophaga gingivalis ATCC
           33624]
 gi|228275844|gb|EEK14610.1| RNA polymerase sigma factor RpoD [Capnocytophaga gingivalis ATCC
           33624]
          Length = 287

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 72/276 (26%), Positives = 146/276 (52%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI K+ ++   EE  LA+R +  GD  A  RL  ++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQEIGKVDLISADEEVELAQRIK-AGDKIALERLTKANLRFVVSVAKQYQNQGLT 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     +V++    N+  
Sbjct: 76  LPDLINEGNMGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLP--LNKIG 133

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               + ++  +L+   +   +      IAK+L++S ++V           S++A +   +
Sbjct: 134 SINKINKMYAYLEQTHE---RVPSAEEIAKELDMSVNDVKESMKNSGRHISMDAPLV--E 188

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
              S   D L     G+     ++   ++ +  + R++  L PRE  +           P
Sbjct: 189 GEDSNLYDVL---RSGESPNPDKELMHESLKTEIERALETLTPREADVIRLYFGLGENYP 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TLE +   FE++RERVRQI+ +A ++++ + + ++
Sbjct: 246 MTLEEIGETFELTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|254525463|ref|ZP_05137515.1| sigma-70 factor [Prochlorococcus marinus str. MIT 9202]
 gi|221536887|gb|EEE39340.1| sigma-70 factor [Prochlorococcus marinus str. MIT 9202]
          Length = 393

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 76/313 (24%), Positives = 139/313 (44%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------------- 43
            E  +  Y+ EI +I +L   EE  LA++  +                            
Sbjct: 81  TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLQLEELATQYESEKGHFPSVREWAELI 140

Query: 44  -----------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 141 DMPLSKFRRRLLLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 200

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 201 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKVLSQE 255

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA+ + ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 256 FGRKPSEEEIAESMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADIENPE 313

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
           Q +     +   R  L   ++ L+PRER +   R   ++    TLE +   F+V+RER+R
Sbjct: 314 QDV----SKTLLREDLEGVLATLSPRERDVLRLRYGIDDGRMKTLEEIGQIFDVTRERIR 369

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 370 QIEAKALRKLRHP 382


>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|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]
          Length = 625

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 128/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +  I +   L  +    +++R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 356 LQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 415

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 416 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 473

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 474 KLNRISRQMLQEMGREPLPE---ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDED 528

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++     + +      ++ L PRE ++   R   +     TL
Sbjct: 529 SHLGDFI---EDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTL 585

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 586 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 621


>gi|323142246|ref|ZP_08077080.1| RNA polymerase sigma factor RpoD [Phascolarctobacterium sp. YIT
           12067]
 gi|322413309|gb|EFY04194.1| RNA polymerase sigma factor RpoD [Phascolarctobacterium sp. YIT
           12067]
          Length = 546

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 76/258 (29%), Positives = 119/258 (46%), Gaps = 13/258 (5%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           ++   L K     GD  A   L  ++LRLVV IA  Y G G+   +++ EGN+GL++AV 
Sbjct: 293 EDFEKLLKAVAHQGD-EAKQCLSEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVD 351

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +GF+ +TY+ WWI+ A+   I      ++I     +      L R+   L     
Sbjct: 352 KFDYNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE--TINKLIRVSRQLLQELG 409

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    IAK+++ S   V  +        SL   I   ++  S   D++    D  
Sbjct: 410 REPLPE---EIAKEMDTSVDRVREIMKIAQEPVSLETPI--GEEEDSHLGDFI---EDHD 461

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERV 269
                +       R  L   +  L  RE+R+ E R   E+    TLE +   F V+RER+
Sbjct: 462 APAPADAASFTLLREQLEEVLETLTIREKRVLELRFGLEDGRSRTLEEVGQHFGVTRERI 521

Query: 270 RQIEARAFKKVQESIQKQ 287
           RQIEA+A +K++   + +
Sbjct: 522 RQIEAKALRKLRHPSRSK 539



 Score = 39.4 bits (91), Expect = 0.67,   Method: Composition-based stats.
 Identities = 13/40 (32%), Positives = 25/40 (62%), Gaps = 2/40 (5%)

Query: 4   KNMSII--VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY 41
           +NMS+   ++ +  +  Y+ EI ++P+L  ++E  LAKR 
Sbjct: 102 ENMSVPEGISIDDPVRMYLKEIGRVPLLIGEDEVKLAKRM 141


>gi|254488657|ref|ZP_05101862.1| Sigma-70, region 3 family [Roseobacter sp. GAI101]
 gi|214045526|gb|EEB86164.1| Sigma-70, region 3 family [Roseobacter sp. GAI101]
          Length = 671

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 431 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 490

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A+KL
Sbjct: 491 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAEKL 545

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++N + 
Sbjct: 546 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAVLPLDSAIQENLKE 600

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 601 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 660

Query: 285 QK 286
           + 
Sbjct: 661 RS 662


>gi|262392398|ref|YP_003284252.1| RNA polymerase sigma factor RpoD [Vibrio sp. Ex25]
 gi|262335992|gb|ACY49787.1| RNA polymerase sigma factor RpoD [Vibrio sp. Ex25]
          Length = 620

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 73/283 (25%), Positives = 130/283 (45%), Gaps = 24/283 (8%)

Query: 21  HEIRKIPMLEKQEEYVL--------AKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
             I K+ M+  +EE  L        ++R    E     A   +V ++LRLV+ IA  Y  
Sbjct: 346 RSIAKLKMI--EEETSLNVQNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTN 403

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I    
Sbjct: 404 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 463

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
                   L R+   +         PE    +A+++ + E ++  +        S+   I
Sbjct: 464 --IETINKLNRISRQMLQEMGREPLPE---ELAERMQMPEDKIRKVLKIAKEPISMETPI 518

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
              D   S   D++    D   ++ ++     + +      ++ L PRE ++   R   +
Sbjct: 519 --GDDEDSHLGDFI---EDTTLELPLDSATATSLKVATKDVLAGLTPREAKVLRMRFGID 573

Query: 251 --NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
                TLE +  +F+V+RER+RQIEA+A +K++   + +   S
Sbjct: 574 MNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRS 616


>gi|56267933|gb|AAV85439.1| RpoS [Listonella anguillarum]
 gi|56267935|gb|AAV85440.1| RpoS [Listonella anguillarum]
 gi|167987243|gb|ACA13292.1| RpoS [Listonella anguillarum]
 gi|222101826|gb|ACM44037.1| RNA polymerase sigma factor [Listonella anguillarum]
          Length = 333

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 80/288 (27%), Positives = 139/288 (48%), Gaps = 13/288 (4%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
            ++              Y+ EI   P+L  QEE + A+R    GD +A  R++ S+LRLV
Sbjct: 44  AKEGFDASTKSLDATQMYLSEIGFSPLLTAQEEVLYARR-SLRGDEAARKRMIESNLRLV 102

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           VKI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++   
Sbjct: 103 VKISRRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQT 162

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             +++      K L   LR  +     ++           IA +L+    +V  M     
Sbjct: 163 RTIRLPIHVV-KELNIYLRTAR----ELSQKLDHEPTAEEIAFQLDKPVEDVSKMLRLNE 217

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              S++  I           D +   ++   ++  + +   + R  L   +  LNP+++ 
Sbjct: 218 RISSVDTPI--GGDGDKALLDIIPDTNNSDPEISTQDD---DIRESLLNWLDELNPKQKE 272

Query: 242 IFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +   R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 273 VLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVKQ 320


>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 =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 119/247 (48%), Gaps = 12/247 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 388 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 447

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            L  +   +   T     PE    +++++
Sbjct: 448 WWIRQAITRSIADQARTIRIPVHM--IETINKLNHISRQILQETGREPSPE---ELSERM 502

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D   S   D++    D   ++ +E    ++ R+
Sbjct: 503 LIPEEKIRKVLKIAREPISMETPI--GDDEDSHLGDFI---EDTTLELPLESATSESLRS 557

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                +S L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 558 ATNEVLSGLTTREAKVLRMRFGIDMHTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 617

Query: 285 QKQVELS 291
           + ++  S
Sbjct: 618 RSELLRS 624


>gi|300777898|ref|ZP_07087756.1| DNA-directed RNA polymerase sigma subunit RpoD [Chryseobacterium
           gleum ATCC 35910]
 gi|57471279|gb|AAW50925.1| RpoD [Chryseobacterium indologenes]
 gi|300503408|gb|EFK34548.1| DNA-directed RNA polymerase sigma subunit RpoD [Chryseobacterium
           gleum ATCC 35910]
          Length = 288

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 72/276 (26%), Positives = 148/276 (53%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI K+ ++   EE  LA+R R  GD +A  +L+ ++LR VV ++  Y+  GL 
Sbjct: 17  SLDKYLQEIGKVELITADEEVELAQRIR-AGDRAALEKLIKANLRFVVSVSKQYQNQGLS 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GLM+A K++D  RGF+  +Y++WWI+ ++ + +     +V++    N+  
Sbjct: 76  LPDLINEGNLGLMKAAKRYDETRGFKFISYAVWWIRQSILQALAEQSRIVRLP--LNKIG 133

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               + +   HL+   +    PE++  +   L++SE ++           S++A +   +
Sbjct: 134 SINKINKAYAHLEQENERPPSPEELAEV---LDMSEEDIKESMKNSGRHLSMDAPLV--E 188

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NP 252
              S   D L     G+     +    ++ +  + R+++ L PRE  +          +P
Sbjct: 189 GEDSNLYDVL---RSGESPSPDKDLMLESLQIEIERALNTLTPREADLVRLYFGLNGKHP 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TLE +   F+++RERVRQI+ +A K+++ + + ++
Sbjct: 246 MTLEEIGETFDLTRERVRQIKEKAIKRLKHNTRSKI 281


>gi|330807812|ref|YP_004352274.1| RNA polymerase sigma factor [Pseudomonas brassicacearum subsp.
           brassicacearum NFM421]
 gi|327375920|gb|AEA67270.1| RNA polymerase sigma factor [Pseudomonas brassicacearum subsp.
           brassicacearum NFM421]
          Length = 335

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 84/278 (30%), Positives = 142/278 (51%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++  + +K       ++ +N R++  D SL         + 
Sbjct: 185 LRAAR-ELTQKLDHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSL------GPDSD 237

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + +S L  ++R +   R         TL
Sbjct: 238 KTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTDKQREVVIRRFGLRGHESSTL 294

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 295 EDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSSES 332


>gi|264677331|ref|YP_003277237.1| RNA polymerase, sigma 70 subunit, RpoD [Comamonas testosteroni
           CNB-2]
 gi|262207843|gb|ACY31941.1| RNA polymerase, sigma 70 subunit, RpoD [Comamonas testosteroni
           CNB-2]
          Length = 815

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 68/260 (26%), Positives = 121/260 (46%), Gaps = 14/260 (5%)

Query: 32  QEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           +E   + KR    E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+A
Sbjct: 557 EELKHINKRMNSGERASRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 616

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V KF+  RG++ +TY+ WWI+ A+   I      ++I        +   + ++    +  
Sbjct: 617 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKMNRISRQH 671

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
                       +A K+ + E ++  +        S+   I   D + S   D++    D
Sbjct: 672 LQEFGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---ED 726

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRE 267
           G     I+   +   R+++   +  L PRE ++   R   E     TLE +  +F+V+RE
Sbjct: 727 GNNTAPIDAAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRE 786

Query: 268 RVRQIEARAFKKVQESIQKQ 287
           R+RQIEA+A +K++   +  
Sbjct: 787 RIRQIEAKALRKLKHPSRSD 806


>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 =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 65/249 (26%), Positives = 112/249 (44%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 387 IGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 446

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 447 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRVSRQMLQEMGREPTPE--- 501

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + +++++ E +V  +        S+   I   D   S   D++    D      +E   
Sbjct: 502 ELGERMDMPEDKVRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDTTIISPVESAT 556

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            +         ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 557 MEGLMEATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 616

Query: 279 KVQESIQKQ 287
           K++   +  
Sbjct: 617 KLRHPSRSD 625


>gi|120598086|ref|YP_962660.1| RpoD family RNA polymerase sigma factor [Shewanella sp. W3-18-1]
 gi|146293843|ref|YP_001184267.1| RpoD family RNA polymerase sigma factor [Shewanella putrefaciens
           CN-32]
 gi|120558179|gb|ABM24106.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella sp.
           W3-18-1]
 gi|145565533|gb|ABP76468.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella
           putrefaciens CN-32]
          Length = 326

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 81/271 (29%), Positives = 139/271 (51%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   +++  + G   + +R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 57  YLGEIGFSPLLSAEEEVYFSRKALK-GCEKSRNRMIESNLRLVVKIARRYNNRGLALLDL 115

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 116 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 174

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            IA+KL V  ++V  M        S++  +     N  
Sbjct: 175 LRTAR----ELAQKLDHEPTAEEIAEKLQVPSADVSRMLKLNEKITSVDTPL--GGDNDK 228

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  D        ++ E+  N    + + ++ LN ++R +   R   L   P TLE
Sbjct: 229 ALIDILADDDSVGPDYKVQDEDISNS---VVKWLNELNTKQREVLARRFGLLGYEPSTLE 285

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++ +E  ++RERVRQI+  A K++++ +  Q
Sbjct: 286 DVGAEIGLTRERVRQIQVEALKRLRDLLGSQ 316


>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 =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 128/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +  I +   L  +    +++R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 352 LQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 411

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 412 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 469

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 470 KLNRISRQMLQEMGREPLPE---ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDED 524

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++     + +      ++ L PRE ++   R   +     TL
Sbjct: 525 SHLGDFI---EDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTL 581

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 582 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 617


>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 =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 69/272 (25%), Positives = 124/272 (45%), Gaps = 14/272 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +  I K   L   +   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 341 LRAISKDTGLSIAQLKEINRRISIGETRARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 400

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 401 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 458

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A ++++ E ++  +        S+   I   D   
Sbjct: 459 KLNRISRQMLQEMGREATPE---ELAVRMDMPEDKIRKVLKIAKEPISMETPI--GDDED 513

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++  D     +  ++    +  +   T  ++ L  RE ++   R   +     TL
Sbjct: 514 SHLGDFIEDDG---AESPVDTATIEGLKESTTTVLAGLTAREAKVLRMRFGIDMNTDHTL 570

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 571 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 602


>gi|197335189|ref|YP_002157048.1| RNA polymerase sigma factor RpoD (Sigma-70) [Vibrio fischeri MJ11]
 gi|197316679|gb|ACH66126.1| RNA polymerase sigma factor RpoD (Sigma-70) [Vibrio fischeri MJ11]
          Length = 613

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 67/253 (26%), Positives = 119/253 (47%), Gaps = 12/253 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 367 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 426

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 427 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPLPE--- 481

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + E ++  +        S+   I   D   S   D++    D   ++ ++   
Sbjct: 482 ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDNTLELPVDSAT 536

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 537 STSLKFATNDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 596

Query: 279 KVQESIQKQVELS 291
           K++   + +V  S
Sbjct: 597 KLRHPSRSEVLRS 609


>gi|316935466|ref|YP_004110448.1| RpoD subfamily RNA polymerase sigma 70 subunit [Rhodopseudomonas
           palustris DX-1]
 gi|315603180|gb|ADU45715.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhodopseudomonas
           palustris DX-1]
          Length = 698

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 69/246 (28%), Positives = 118/246 (47%), Gaps = 12/246 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 454 EREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 513

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    + + +   +      +
Sbjct: 514 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLNEIGREPTPEEL 568

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+KL +   +V  +        SL   +   D+  S   D++    D    + I+   + 
Sbjct: 569 AEKLGMPLEKVRKVLKIAKEPLSLETPV--GDEEDSHLGDFI---EDKNAVLPIDAAIQS 623

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 624 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKL 683

Query: 281 QESIQK 286
           +   + 
Sbjct: 684 KHPSRS 689


>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 =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 66/253 (26%), Positives = 118/253 (46%), Gaps = 12/253 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 371 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 430

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 431 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPLPE--- 485

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + E ++  +        S+   I   D   S   D++    D   ++ ++   
Sbjct: 486 ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDTTLELPLDSAT 540

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 541 STSLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 600

Query: 279 KVQESIQKQVELS 291
           K++   + +   S
Sbjct: 601 KLRHPSRSETLRS 613


>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 =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 67/253 (26%), Positives = 119/253 (47%), Gaps = 12/253 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 364 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 423

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 424 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPLPE--- 478

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + E ++  +        S+   I   D   S   D++    D   ++ ++   
Sbjct: 479 ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDNTLELPVDSAT 533

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 534 STSLKFATNDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 593

Query: 279 KVQESIQKQVELS 291
           K++   + +V  S
Sbjct: 594 KLRHPSRSEVLRS 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 =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 128/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +  I +   L  +    +++R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 356 LQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 415

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 416 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 473

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 474 KLNRISRQMLQEMGREPLPE---ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDED 528

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++     + +      ++ L PRE ++   R   +     TL
Sbjct: 529 SHLGDFI---EDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTL 585

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 586 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 621


>gi|114771658|ref|ZP_01449062.1| RNA polymerase sigma factor [alpha proteobacterium HTCC2255]
 gi|114547730|gb|EAU50620.1| RNA polymerase sigma factor [alpha proteobacterium HTCC2255]
          Length = 656

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 71/242 (29%), Positives = 117/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            SA   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 416 RSAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 475

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A KL
Sbjct: 476 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELASKL 530

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + +E   + N + 
Sbjct: 531 QMPLDKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAILPLESAIQGNLKE 585

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 586 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 645

Query: 285 QK 286
           + 
Sbjct: 646 RS 647


>gi|37680992|ref|NP_935601.1| DNA-directed RNA polymerase, sigma subunit [Vibrio vulnificus
           YJ016]
 gi|37199742|dbj|BAC95572.1| DNA-directed RNA polymerase, sigma subunit [Vibrio vulnificus
           YJ016]
          Length = 330

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 82/287 (28%), Positives = 140/287 (48%), Gaps = 13/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           R+              Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVV
Sbjct: 42  REEFDASNKSLDATQLYLGEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLVV 100

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           KI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++    
Sbjct: 101 KISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTR 160

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            +++      K L   LR  +     ++           IA +L++   +V  M      
Sbjct: 161 TIRLPIHVV-KELNIYLRTAR----ELSQKLDHEPTAEEIAAQLDIPVDDVSKMLRLNER 215

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++  I           D +   ++   +V  + E   + R  L   +  LNP+++ +
Sbjct: 216 ISSVDTPI--GGDGEKALLDIIPDANNSDPEVSTQDE---DMRVSLIHWLEELNPKQKEV 270

Query: 243 FEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 271 LARRFGLLGYEPSTLEEVGQEIGLTRERVRQIQVEGLRRLREVLIKQ 317


>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 =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 74/289 (25%), Positives = 131/289 (45%), Gaps = 25/289 (8%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRL 60
           R+   ++++ E  +   I EI             + +R    E     A   +V ++LRL
Sbjct: 323 RRAQQVLIDAERKVGMTIGEI-----------KDINRRMSIGEAKARRAKKEMVEANLRL 371

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I   
Sbjct: 372 VISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQ 431

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I            L R+   +         P+    +A+++ + E +V  +    
Sbjct: 432 ARTIRIPVHM--IETINKLNRVSRQMLQEMGREPSPD---ELAERMEMPEDKVRKVLKIA 486

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               S+   I   D   S   D++    D      ++   R+  R  +   +S L PRE 
Sbjct: 487 KEPISMETPI--GDDEDSHLGDFI---EDINAMSPVDSATREGLRESVKGVLSGLTPREA 541

Query: 241 RIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 542 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSE 590


>gi|160872453|ref|ZP_02062585.1| RNA polymerase sigma factor RpoS [Rickettsiella grylli]
 gi|159121252|gb|EDP46590.1| RNA polymerase sigma factor RpoS [Rickettsiella grylli]
          Length = 330

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 86/271 (31%), Positives = 133/271 (49%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A+   + GD  A  R++ S+LRLVVKIA  Y   GL   ++
Sbjct: 62  YLNEIGFSPLLSAEEEVYYARLIAK-GDQDARKRMIESNLRLVVKIARHYNNRGLQFLDL 120

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM AV+KFDPERGFR +TY+ WW++ A++  I+     V++      K L   
Sbjct: 121 IEEGNLGLMHAVEKFDPERGFRFSTYATWWVRQAIERAIMNQARTVRLPIHVV-KELNVY 179

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L+  +     +T           IAK L+    EV  M        S++A  +S      
Sbjct: 180 LQAAR----ELTQKLDHKPTSDEIAKWLDRPFEEVERMLGLNEHITSVDAPASSEADKP- 234

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E       E +N R  L   +  L+  +R +   R   L  + +TLE
Sbjct: 235 ----LLETLSDNRENDPEHILEGENLRKRLEGWLKQLSTNQREVIARRYGLLGCDRMTLE 290

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +     ++RERVRQI+    K +++ ++KQ
Sbjct: 291 EVGEVIGLTRERVRQIQVEGLKTLRKIMEKQ 321


>gi|157169065|ref|YP_258338.2| RNA polymerase sigma factor RpoS [Pseudomonas fluorescens Pf-5]
 gi|1000294|gb|AAB02846.1| RpoS [Pseudomonas fluorescens Pf-5]
 gi|157061761|gb|AAY90494.2| RNA polymerase sigma factor RpoS [Pseudomonas fluorescens Pf-5]
          Length = 335

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 84/278 (30%), Positives = 142/278 (51%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++  + +K       ++ +N R++  D SL         + 
Sbjct: 185 LRAAR-ELTQKLDHEPSPEEIANLLEKPVAEVKRMLGLNERVSSVDVSL------GPDSD 237

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + +S L  ++R +   R         TL
Sbjct: 238 KTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTEKQREVVVRRFGLRGHESSTL 294

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 295 EDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSSES 332


>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 =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 112/247 (45%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 409 EAKARRAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 468

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T     P     +
Sbjct: 469 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGIEPDPAT---L 523

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A K+ + E ++  +        S+   I   D   S   D++    D       +     
Sbjct: 524 AIKMEMPEDKIRKIMKIAKEPISMETPI--GDDEDSHLGDFI---EDASTLSPDDSAIYA 578

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R+     +  L  RE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 579 NLRDATREVLDSLTSREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 638

Query: 281 QESIQKQ 287
           +   + +
Sbjct: 639 RHPTRSE 645


>gi|170727680|ref|YP_001761706.1| RpoD family RNA polymerase sigma factor [Shewanella woodyi ATCC
           51908]
 gi|169813027|gb|ACA87611.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella woodyi
           ATCC 51908]
          Length = 322

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 80/271 (29%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   +++  + G   + +R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 53  YLSEIGFSPLLSAEEEVYFSRKALK-GCDKSRNRMIESNLRLVVKIARRYNNRGLALLDL 111

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 112 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 170

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            IA+KL++  ++V  M        S++  +     N  
Sbjct: 171 LRTAR----ELAHKLDHEPTAEEIAEKLDLPSADVSRMLKLNERITSVDTPL--GGDNDK 224

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  D +      ++ E+       + + +  LN ++R +   R   L   P TLE
Sbjct: 225 ALLDVLADDDNVGPDYKVQDEDMS---KSVVKWLDELNTKQREVLARRFGLLGYEPSTLE 281

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           N+  E  ++RERVRQI+  A K++++ +  Q
Sbjct: 282 NVGKEIGLTRERVRQIQVEALKRLKDLLSAQ 312


>gi|33150232|gb|AAP97086.1| RNA polymerase sigma factor [Pseudomonas chlororaphis]
 gi|103488976|gb|ABF71881.1| RpoS [Pseudomonas chlororaphis]
          Length = 334

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 84/278 (30%), Positives = 142/278 (51%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 66  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 124

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 125 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 183

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++  + +K       ++ +N R++  D SL         + 
Sbjct: 184 LRAAR-ELTQKLDHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSL------GPDSD 236

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + +S L  ++R +   R         TL
Sbjct: 237 KTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTDKQREVVVRRFGLRGHESSTL 293

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 294 EDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSSES 331


>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 =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 67/253 (26%), Positives = 119/253 (47%), Gaps = 12/253 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 367 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 426

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 427 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPLPE--- 481

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + E ++  +        S+   I   D   S   D++    D   ++ ++   
Sbjct: 482 ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDNTLELPVDSAT 536

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 537 STSLKFATNDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 596

Query: 279 KVQESIQKQVELS 291
           K++   + +V  S
Sbjct: 597 KLRHPSRSEVLRS 609


>gi|256377300|ref|YP_003100960.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Actinosynnema
           mirum DSM 43827]
 gi|255921603|gb|ACU37114.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Actinosynnema
           mirum DSM 43827]
          Length = 349

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 74/306 (24%), Positives = 128/306 (41%), Gaps = 39/306 (12%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREH-------------------- 44
            N       Y+  I ++ +L   +E  LA+R     Y EH                    
Sbjct: 46  ANAADSTRAYLKAIGRVRLLTADQEVELARRVEAGLYAEHLLDLPPAARGSRRPIELRRV 105

Query: 45  --GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
                 A   L+ ++LRLVV IA  Y G G+ + +V+ EGN+GL++AV+KFD  +GF+ +
Sbjct: 106 VRDGQRAKDHLLEANLRLVVSIAKRYTGKGMALLDVIQEGNLGLVRAVEKFDYAKGFKFS 165

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   +      +++     +        +L    + +   N +      +
Sbjct: 166 TYATWWIRQAITRALADQSRTIRLPVHMVEVVT-----KLARVERDLLHRNGREATAEEV 220

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A +L+V+  +V+ +        SL+  I    +  +   D +    D      +E     
Sbjct: 221 AVELDVTPEKVVELRQHARTPVSLDQTI--GAEADTSIGDLIA---DENAVAPLEAVSSA 275

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKV 280
                L   +  L PRE  +   R    +    TLE +   + V+RER+RQIE+R   K+
Sbjct: 276 LLSADLRAVLDTLTPREAGVVRMRYGFPDGVLHTLEEVGRVYGVTRERIRQIESRTMAKL 335

Query: 281 QESIQK 286
           Q   + 
Sbjct: 336 QHPARS 341


>gi|42524684|ref|NP_970064.1| RNA polymerase sigma-32 factor [Bdellovibrio bacteriovorus HD100]
 gi|39576894|emb|CAE78123.1| RNA polymerase sigma-32 factor [Bdellovibrio bacteriovorus HD100]
          Length = 373

 Score =  227 bits (579), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 97/286 (33%), Positives = 169/286 (59%), Gaps = 8/286 (2%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           + S  +     L  Y++EIR+  +L ++EE  LAK+Y E  D  AA  LV ++LR VVK+
Sbjct: 92  DTSKALTSADPLVMYLNEIRRYKVLTREEEMALAKKYFESKDPEAAQALVKANLRFVVKV 151

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y  +G  + +++ EGN+GLM AV++F+P +G RL TY++WWI+  +QE+++R +S+V
Sbjct: 152 AAEYSKFGSKMIDLIQEGNVGLMHAVREFNPYKGARLITYAVWWIRGYIQEFLMRQYSMV 211

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-D 183
           +IGTT NQ++LF+ L++ K  L A+         +  I+ +L + E EV  M  R++G D
Sbjct: 212 RIGTTQNQRKLFYQLQKEKEALDAM----GIEPNIGLISSRLGIPEDEVRDMTMRMSGRD 267

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
            SL+  +   D++ +   D      D   ++ L   E+ +  +  +      L+ RE+ I
Sbjct: 268 VSLDRPV--DDESGTTLGDLQRGPSDQPLDEALAHNEQLEILKQKIEEIRPELSEREKII 325

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            + R L ++P+TL+ +  +  ++RE VRQ+EAR  KK++  +++  
Sbjct: 326 LDERILNDDPLTLQEIGEKHGITREAVRQMEARLMKKIKAKMEEDA 371


>gi|186472768|ref|YP_001860110.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia phymatum
           STM815]
 gi|184195100|gb|ACC73064.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia phymatum
           STM815]
          Length = 685

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 444 RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 503

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 504 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 558

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 559 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTVAPSDAALHASMRD 613

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 614 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 673

Query: 285 QKQ 287
           +  
Sbjct: 674 RSD 676


>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 =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 74/278 (26%), Positives = 126/278 (45%), Gaps = 14/278 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           +   + I +I K   L   E   ++KR    E     A   +V ++LRLV+ IA  Y   
Sbjct: 304 LAFQQKIADIEKELGLNVSEIKDISKRMAIGEAKARRAKKEMVEANLRLVISIAKKYTNR 363

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I     
Sbjct: 364 GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM- 422

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
                  + R+   L         PE    + ++L + E +V  +        S+   I 
Sbjct: 423 -IETINKINRVSRQLLQEMGREPTPE---ELGERLEMDEVKVRKVLKIAKEPISMETPI- 477

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             D   S   D++    D      I+    +  +      +  L  RE ++ + R   + 
Sbjct: 478 -GDDEDSHLGDFI---EDQNITSPIDAATSEGLKEATREVLENLTEREAKVLKMRFGIDM 533

Query: 252 P--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           P   TLE +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 534 PTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 571


>gi|119468990|ref|ZP_01612015.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Alteromonadales bacterium TW-7]
 gi|119447642|gb|EAW28909.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Alteromonadales bacterium TW-7]
          Length = 324

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 80/271 (29%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A++    G  ++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 53  YLGEIGFSPLLSAEEEVFFARK-SLKGCEASRKRMIESNLRLVVKIARRYNNRGLALLDL 111

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 112 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 170

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +T           IA+ L+    +V  M        S++  I    +N S
Sbjct: 171 LRTAR----ELTQKLDHEPTAEEIAECLDKPVEDVTKMLRLNEKIASVDMPI--GGENDS 224

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  +     +  ++  E       +   +  LN ++R +   R   L   P TLE
Sbjct: 225 VLLDILPDEKGNGPEGEVQDTEINKH---IVDWLGELNLKQREVLARRFGLLGYEPSTLE 281

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+  A +++++ +Q++
Sbjct: 282 DVGREIGLTRERVRQIQVEALRRLKDILQQE 312


>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 =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 67/253 (26%), Positives = 119/253 (47%), Gaps = 12/253 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 377 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 436

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 437 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPLPE--- 491

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + E ++  +        S+   I   D   S   D++    D   ++ ++   
Sbjct: 492 ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDTTLELPLDSAT 546

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
             + R     +++ L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 547 ATSLRAATRDALAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 606

Query: 279 KVQESIQKQVELS 291
           K++   + +   S
Sbjct: 607 KLRHPSRSETLRS 619


>gi|257487049|ref|ZP_05641090.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. tabaci
           ATCC 11528]
 gi|320323089|gb|EFW79178.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. glycinea
           str. B076]
 gi|320329639|gb|EFW85628.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. glycinea
           str. race 4]
 gi|330878042|gb|EGH12191.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. glycinea
           str. race 4]
 gi|330985141|gb|EGH83244.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv.
           lachrymans str. M301315]
 gi|331009312|gb|EGH89368.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. tabaci
           ATCC 11528]
          Length = 335

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 84/278 (30%), Positives = 142/278 (51%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++  + +K       ++ +N R++  D SL         + 
Sbjct: 185 LRAAR-ELTQKLDHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSL------GPDSD 237

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + +S L  ++R +   R         TL
Sbjct: 238 KTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTEKQREVVIRRFGLRGHESSTL 294

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 295 EDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSSES 332


>gi|116668483|gb|ABK15514.1| sigma factor [Pseudomonas alkylphenolia]
          Length = 335

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 84/278 (30%), Positives = 143/278 (51%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++ ++ +K       ++ +N R++  D SL         + 
Sbjct: 185 LRAAR-ELTQKLDHEPSPEEIASLLEKPVGEVKRMLGLNERVSSVDVSL------GPDSD 237

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + +S L  ++R +   R         TL
Sbjct: 238 KTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTDKQREVVIRRFGLRGHESSTL 294

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 295 EDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSSES 332


>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 =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 64/243 (26%), Positives = 115/243 (47%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   ++ ++LRLV+ IA  Y   G+   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 437 RQAKREMIEANLRLVISIAKKYVNRGMQFLDLIQEGNIGLMKAVDKFEYRRGWKFSTYAT 496

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WW++ A+   +      +++            L R+   +   T     P     +AK++
Sbjct: 497 WWVRQAVTRALADQARTIRVPVHM--IETINKLNRISREILQQTGQEAHP---AVLAKRM 551

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +SE +V S+        SL   +   D   +   D +    D       E     N R 
Sbjct: 552 EMSEEKVRSILKIAKQPVSLETPV--GDDADATLGDMI---EDVSASSPAEAAIHANMRA 606

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  +++ L+PRE ++   R   +     TLE +  +F+V+RER+RQIE++A +K+    
Sbjct: 607 AIDEALNGLSPREAKVLRMRFGLDTNSDHTLEEVGKQFDVTRERIRQIESKAMRKLMHPS 666

Query: 285 QKQ 287
           +  
Sbjct: 667 RAD 669


>gi|167584375|ref|ZP_02376763.1| sigma 70 (RpoD) [Burkholderia ubonensis Bu]
          Length = 611

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 65/248 (26%), Positives = 116/248 (46%), Gaps = 12/248 (4%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            E     A  +++ ++LRLV+ IA  Y   G+   +++ EGNIGLM+AV KF+  RG++ 
Sbjct: 366 AESKMRQAKRQMIEANLRLVISIAKKYVNRGMQFLDLIQEGNIGLMKAVDKFEYRRGWKF 425

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY+ WW++ A+   +      +++            L R+   +   T     P     
Sbjct: 426 STYATWWVRQAVTRALADQARTIRVPVHM--IETINKLNRISREILQQTGQEAHP---AV 480

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           +AK++ +SE +V S+        SL   +   D   +   D +    D       E    
Sbjct: 481 LAKRMEMSEEKVRSILKIAKQPVSLETPV--GDDADATLGDMI---EDVSASSPAEAAIH 535

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKK 279
            N R  +  ++  L+PRE ++   R   +     TLE +  +F+V+RER+RQIE++A +K
Sbjct: 536 ANMRAAIDEALDGLSPREAKVLRMRFGLDTTSDHTLEEVGKQFDVTRERIRQIESKAMRK 595

Query: 280 VQESIQKQ 287
           +    +  
Sbjct: 596 LMHPSRAD 603


>gi|24374942|ref|NP_718985.1| RNA polymerase sigma-38 factor [Shewanella oneidensis MR-1]
 gi|24349657|gb|AAN56429.1|AE015779_6 RNA polymerase sigma-38 factor [Shewanella oneidensis MR-1]
          Length = 326

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 82/271 (30%), Positives = 140/271 (51%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   +++  + G   + +R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 57  YLGEIGFSPLLSAEEEVYFSRKALK-GCEKSRNRMIESNLRLVVKIARRYNNRGLALLDL 115

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 116 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 174

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            IA+KL VS  +V  M        S++  +     N  
Sbjct: 175 LRTAR----ELAQKLDHEPTAEEIAEKLQVSSVDVSRMLKLNEKITSVDVPL--GGDNDK 228

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  D +      ++ E+  N    + + ++ LN ++R +   R   L   P TLE
Sbjct: 229 ALLDVLADDDNVGPDYKVQDEDISNS---VVKWLNELNTKQREVLARRFGLLGYEPSTLE 285

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++ +E  ++RERVRQI+  A K++++ +  Q
Sbjct: 286 DVGAEIGLTRERVRQIQVEALKRLRDLLGAQ 316


>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 =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 128/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +  I +   L  +    +++R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 356 LQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 415

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 416 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 473

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 474 KLNRISRQMLQEMGREPLPE---ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDED 528

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++     + +      ++ L PRE ++   R   +     TL
Sbjct: 529 SHLGDFI---EDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTL 585

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 586 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 621


>gi|94985446|ref|YP_604810.1| RNA polymerase, sigma 28 subunit [Deinococcus geothermalis DSM
           11300]
 gi|94555727|gb|ABF45641.1| RNA polymerase, sigma 28 subunit [Deinococcus geothermalis DSM
           11300]
          Length = 403

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 79/303 (26%), Positives = 133/303 (43%), Gaps = 36/303 (11%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------------------- 43
           S  ++    L +Y+HEI ++P+L   EE  LA+RY E                       
Sbjct: 95  SPALSQGDSLRQYLHEIGRVPLLTVAEEMDLARRYEEGEAARQALDSNPDLDDRTRRQLQ 154

Query: 44  ---HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
                  +A   L+ ++LRLVV IA  Y   GL + +++ EGN GL++AV+KF+  RG++
Sbjct: 155 RQVEDGAAAKQALIEANLRLVVSIAKRYTNRGLGLLDLIQEGNQGLIRAVEKFEYRRGYK 214

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ ++   I      +++     +      L R+   L+        P ++ 
Sbjct: 215 FSTYATWWIRQSLTRAIADKSRTIRVPVHMVE--TINRLSRMTRQLEMELSREPLPAEIA 272

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
             A       ++V           SL   I   ++  S + D+L  D   +    I+   
Sbjct: 273 E-AMGPGWDAAKVEETQKVGWEPMSLEMPI--GEEGDSTYGDFLPDD---RFASPIQNAS 326

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           +      L R+   LN RE  +   R   +  +  TLE +     V+RERVRQIE +A +
Sbjct: 327 QALLSEALERAFGTLNEREALVLRLRHGFVDGHEHTLEEVGQLLSVTRERVRQIENKALR 386

Query: 279 KVQ 281
           K++
Sbjct: 387 KLK 389


>gi|224823888|ref|ZP_03696997.1| RNA polymerase, sigma 70 subunit, RpoD [Lutiella nitroferrum 2002]
 gi|224604343|gb|EEG10517.1| RNA polymerase, sigma 70 subunit, RpoD [Lutiella nitroferrum 2002]
          Length = 640

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 66/272 (24%), Positives = 127/272 (46%), Gaps = 14/272 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + E++   ML  ++   + ++    E     A   ++ ++LRLV+ IA  Y   GL   +
Sbjct: 366 LAELQDRAMLSIKDLKEINRQMSAGESKARRAKKEMIEANLRLVISIAKKYTNRGLQFLD 425

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 426 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 483

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + R+   +   T +   P     +A+++ + E ++  +        S+   I   D + 
Sbjct: 484 KMNRISRQILQETGHEPDP---AELAERMEMPEDKIRKIMKISKEPISMETPI--GDDDD 538

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D       +     + ++     +  L PRE ++   R   +     TL
Sbjct: 539 SHLGDFI---EDQNNLAPSDAAMYSSLKDATKEVLETLTPREAKVLRMRFGIDMNTDHTL 595

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 596 EEVGKQFDVTRERIRQIEAKALRKLRHPTRSE 627


>gi|157688389|gb|ABV64841.1| RpoS [Pseudomonas sp. 122]
          Length = 334

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 84/278 (30%), Positives = 142/278 (51%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 66  YLNEIGFSPLLTPEEEVHFA-RLSQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 124

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 125 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 183

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++  + +K       ++ +N R++  D SL         + 
Sbjct: 184 LRAAR-ELTQKLDHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSL------GPDSD 236

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + +S L  ++R +   R         TL
Sbjct: 237 KTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTDKQREVVIRRFGLRGHESSTL 293

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 294 EDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSSES 331


>gi|261749591|ref|YP_003257277.1| RNA polymerase sigma factor rpoD [Blattabacterium sp. (Periplaneta
           americana) str. BPLAN]
 gi|261497684|gb|ACX84134.1| RNA polymerase sigma factor rpoD [Blattabacterium sp. (Periplaneta
           americana) str. BPLAN]
          Length = 287

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 83/288 (28%), Positives = 146/288 (50%), Gaps = 13/288 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +    +       L +Y+HEI KIP+L  +EE   A+R RE GD SA  +LV ++LR VV
Sbjct: 5   KITKQVTNRESESLDKYLHEIGKIPLLTPEEEVEYARRARE-GDSSAIEKLVNANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++ + +FD  RGF+  +Y +WWI+ A+ + I     
Sbjct: 64  SVAKQYQNQGLSLCDLINEGNLGLIKGILRFDETRGFKCISYVVWWIRQAILQAIAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            ++  T          L ++   L  +     +      IA+ L+++E +V         
Sbjct: 124 SIRQPTNK-----LALLNKILKTLAQLEQELQRTPSAREIAEHLDMNEKDVEESIKNSGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A +   +   S   D +  D   +     E  ER++ R  + R +  L+ RERR+
Sbjct: 179 HVSMDAPLI--EGEDSNLYDLVRSDESPRPD---EHLERESLRKDIKRILETLSERERRV 233

Query: 243 FEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
                      P+TLE +    +++RERVRQIE+ A K+++ S + ++
Sbjct: 234 IILHFGLNGSPPMTLEEVGQSCDLTRERVRQIESIALKRLKHSSRSKI 281


>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 =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 64/250 (25%), Positives = 118/250 (47%), Gaps = 12/250 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 374 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 433

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 434 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPSPE--- 488

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + E ++  +        S+   I   D   S   D++    D   ++ ++   
Sbjct: 489 ELAERMAMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDTTLELPLDSAT 543

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            ++ +      ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 544 SESLKQATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 603

Query: 279 KVQESIQKQV 288
           K++   + ++
Sbjct: 604 KLRHPSRSEI 613


>gi|48727551|gb|AAT46075.1| RNA polymerase sigma factor [Pseudomonas chlororaphis]
          Length = 334

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 84/278 (30%), Positives = 142/278 (51%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 66  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 124

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 125 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 183

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++  + +K       ++ +N R++  D SL         + 
Sbjct: 184 LRAAR-ELTQKLDHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSL------GPDSD 236

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + +S L  ++R +   R         TL
Sbjct: 237 KTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTDKQREVVVRRFGLRGHESSTL 293

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 294 EDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSSES 331


>gi|297539657|ref|YP_003675426.1| RNA polymerase sigma-70 subunit RpoD [Methylotenera sp. 301]
 gi|297259004|gb|ADI30849.1| RNA polymerase, sigma 70 subunit, RpoD [Methylotenera sp. 301]
          Length = 645

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 69/247 (27%), Positives = 118/247 (47%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RGF+ +
Sbjct: 398 EARARRAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGFKFS 457

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T     P     +
Sbjct: 458 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGVEPDP---ALL 512

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+ + E ++  +        S+   I   D   S   D++    DGQ    ++     
Sbjct: 513 AEKMEMPEDKIRKILKISKEPISMETPI--GDDEDSHLGDFI---EDGQTLAPVDAAIYA 567

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R+  +  +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 568 SLRDATSEVLESLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 627

Query: 281 QESIQKQ 287
           +   + +
Sbjct: 628 RHPTRSE 634


>gi|192358973|ref|YP_001982681.1| RNA polymerase sigma factor RpoS [Cellvibrio japonicus Ueda107]
 gi|190685138|gb|ACE82816.1| RNA polymerase sigma factor RpoS [Cellvibrio japonicus Ueda107]
          Length = 335

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 84/277 (30%), Positives = 145/277 (52%), Gaps = 13/277 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L   EE   A++  + GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 66  YLNEIGFSPLLLSAEEVFFARKALK-GDEAARKRMIESNLRLVVKISRRYVNRGLALLDL 124

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 125 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 183

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +  L    D+   PE++  + +K       ++S+N R+    S++A I +S   + 
Sbjct: 184 LRAAR-ELSQKLDHEPTPEEIANLLEKPVADVEHMLSLNERVT---SIDAPIGASSDRTV 239

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
              D +   H      L++  +       L   +  L  ++R +   R         TLE
Sbjct: 240 --ADTIADTHVSDPAALLQDSDLT---ASLDHWLEELTEKQREVLARRFGLRGYEVSTLE 294

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
            +  E  ++RERVRQI+  A K++++ ++KQ   S +
Sbjct: 295 EVGHEIGLTRERVRQIQVEALKRLRDIMEKQGLDSEA 331


>gi|153828433|ref|ZP_01981100.1| RNA polymerase sigma factor RpoD [Vibrio cholerae 623-39]
 gi|148876142|gb|EDL74277.1| RNA polymerase sigma factor RpoD [Vibrio cholerae 623-39]
          Length = 572

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 128/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +  I +   L  +    +++R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 303 LQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 362

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 363 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 420

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 421 KLNRISRQMLQEMGREPLPE---ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDED 475

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++     + +      ++ L PRE ++   R   +     TL
Sbjct: 476 SHLGDFI---EDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTL 532

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 533 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 568


>gi|66044622|ref|YP_234463.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. syringae
           B728a]
 gi|289675304|ref|ZP_06496194.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. syringae
           FF5]
 gi|6644290|gb|AAF20993.1|AF208000_1 RpoS [Pseudomonas syringae pv. syringae]
 gi|24415296|gb|AAN59882.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. aptata]
 gi|24415299|gb|AAN59884.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. aptata]
 gi|63255329|gb|AAY36425.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Pseudomonas syringae pv. syringae B728a]
 gi|330896091|gb|EGH28312.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. japonica
           str. M301072PT]
          Length = 335

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 84/278 (30%), Positives = 142/278 (51%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++  + +K       ++ +N R++  D SL         + 
Sbjct: 185 LRAAR-ELTQKLDHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSL------GPDSD 237

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + +S L  ++R +   R         TL
Sbjct: 238 KTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTEKQREVVIRRFGLRGHESSTL 294

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 295 EDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSSES 332


>gi|307944279|ref|ZP_07659620.1| RNA polymerase sigma factor RpoD [Roseibium sp. TrichSKD4]
 gi|307772625|gb|EFO31845.1| RNA polymerase sigma factor RpoD [Roseibium sp. TrichSKD4]
          Length = 669

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 72/261 (27%), Positives = 122/261 (46%), Gaps = 18/261 (6%)

Query: 34  EYVLAKRYR---EHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           E    +R     + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM
Sbjct: 410 EITEFRRIVAMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLM 469

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +   + ++    +
Sbjct: 470 KAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSR 524

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
            +     +      +A+KL +   +V  +        SL   I   D+  S   D++   
Sbjct: 525 QMLHEIGREPTPEELAEKLQMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI--- 579

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVS 265
            D    + I+   + N R   TR ++ L PRE R+   R         TLE +  +F V+
Sbjct: 580 EDKNAVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVT 639

Query: 266 RERVRQIEARAFKKVQESIQK 286
           RER+RQIEA+A +K++   + 
Sbjct: 640 RERIRQIEAKALRKLKHPSRS 660


>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 =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 70/247 (28%), Positives = 118/247 (47%), Gaps = 11/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 396 ETKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 455

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            L R+   +   T     PE    +
Sbjct: 456 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQILQATGKEPSPED---L 510

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           +KK+ + E ++  +        S+   I   D + S   D++    D      I+    +
Sbjct: 511 SKKMGLPEDKIRKILKIAKEPISMETPIGDEDGD-SHLGDFI---EDAAALSPIDAATIE 566

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             R    R ++ L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 567 GLRETAQRVLASLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 626

Query: 281 QESIQKQ 287
           +   + +
Sbjct: 627 RHPTRSE 633


>gi|107099562|ref|ZP_01363480.1| hypothetical protein PaerPA_01000575 [Pseudomonas aeruginosa PACS2]
          Length = 604

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 70/263 (26%), Positives = 120/263 (45%), Gaps = 14/263 (5%)

Query: 29  LEKQE--EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L   E  E   A    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 344 LTVAEIKEINRAMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 403

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 404 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 461

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    + +++++ E ++  +        S+   I   D   S   D++  
Sbjct: 462 LQEMGREPTPE---ELGERMDMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 514

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q  IE    ++ +      ++ L  RE ++   R   +     TLE +  +F+V
Sbjct: 515 -EDSTMQSPIEMATSESLKESTREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 573

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   + +
Sbjct: 574 TRERIRQIEAKALRKLRHPSRSE 596


>gi|289626003|ref|ZP_06458957.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. aesculi
           str. NCPPB3681]
 gi|289651481|ref|ZP_06482824.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. aesculi
           str. 2250]
 gi|330868573|gb|EGH03282.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. aesculi
           str. 0893_23]
          Length = 335

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 84/278 (30%), Positives = 142/278 (51%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++  + +K       ++ +N R++  D SL         + 
Sbjct: 185 LRAAR-ELTQKLDHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSL------GPDSD 237

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + +S L  ++R +   R         TL
Sbjct: 238 KTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTEKQREVVIRRFGLRGHESSTL 294

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 295 EDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSSES 332


>gi|25991936|gb|AAN76995.1|AF481769_1 primary sigma 70 transcriptional factor [Frankia sp. ACN14a]
          Length = 385

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 68/296 (22%), Positives = 132/296 (44%), Gaps = 38/296 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKR-----YREHG---------------------DLSA 49
           +  Y+ EI K+P+L   +E  L+KR     + EH                        +A
Sbjct: 89  VRMYLREIGKVPLLNAAQEVELSKRVEAGLFAEHKLESDPDLPADLRRDLGLLVKDGHAA 148

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             +LV+++LRLVV +A  Y G G+ + ++V EGN+GL++AV+KFD  +G++ +TY+ WWI
Sbjct: 149 KQQLVSANLRLVVSVAKKYSGRGMTLLDLVQEGNLGLIRAVEKFDYAKGYKFSTYATWWI 208

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + A+   +      ++I     +      + ++    + +     +      +A +L++ 
Sbjct: 209 RQAIGRALADQARTIRIPVHVVE-----QINKITRLQRQLVSTLGREPTDEELALELDMP 263

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             +V+ +        SL   +   D   S   D++    D       +       ++ + 
Sbjct: 264 IEQVVELRRYAQDTVSLETSV--GDDGDSVLGDFI---EDSDATSPADAASYGAMQDEIE 318

Query: 230 RSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +  LNPRER +   R         TL  + +   ++RER+RQIE    +++++ 
Sbjct: 319 NVLGGLNPREREVMRLRFGLADGKQHTLAEVGNRLGLTRERIRQIERDTLRELRKP 374


>gi|85715949|ref|ZP_01046926.1| RNA polymerase sigma factor [Nitrobacter sp. Nb-311A]
 gi|85697147|gb|EAQ35028.1| RNA polymerase sigma factor [Nitrobacter sp. Nb-311A]
          Length = 716

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 74/273 (27%), Positives = 129/273 (47%), Gaps = 17/273 (6%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAH---RLVTSHLRLVVKIAMGYRGYGLPI 75
            EI+++  L   E     K  +  + G+  A      +V ++LRLV+ IA  Y   GL  
Sbjct: 445 GEIQQLAALTGLEIGEFRKIVQGVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQF 504

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +
Sbjct: 505 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----M 559

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + ++    + + +   +      +A+KL +   +V  +        SL   +   D+
Sbjct: 560 IETINKIVRTSRQMLNEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPLSLETPV--GDE 617

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPV 253
             S   D++    D    + I+   + N R   TR ++ L PRE R+   R         
Sbjct: 618 EDSHLGDFI---EDKNAVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDH 674

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 675 TLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 707


>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 =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 64/243 (26%), Positives = 113/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 439 RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 498

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 499 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 553

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 554 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTVAPADAALHASMRD 608

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+  +K++   
Sbjct: 609 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKTLRKLRHPS 668

Query: 285 QKQ 287
           +  
Sbjct: 669 RSD 671


>gi|315224630|ref|ZP_07866455.1| DNA-directed RNA polymerase sigma subunit RpoD [Capnocytophaga
           ochracea F0287]
 gi|314945415|gb|EFS97439.1| DNA-directed RNA polymerase sigma subunit RpoD [Capnocytophaga
           ochracea F0287]
          Length = 287

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 66/276 (23%), Positives = 146/276 (52%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI ++ ++   EE  LA+R +  GD++A  +L  ++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQEIGRVDLITADEEVELAQRIK-AGDVAALEKLTKANLRFVVSVAKQYQNQGLT 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     +V++    N+  
Sbjct: 76  LPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLP--LNKIG 133

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               + ++  +L+   +   +      IA++L++S ++V           S++A +   +
Sbjct: 134 SINKINKMYAYLEQANE---RVPSAEEIARELDMSVNDVKESMKNAGRHISMDAPLV--E 188

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENP 252
              S   D +  +        +      + R  + R++  L PRE  +         ++ 
Sbjct: 189 GEDSNLYDVIRSNESPNPDKAL---ILDSLRTEIERALETLTPREADVVRLYFGLSDQHA 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 246 MTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|261250212|ref|ZP_05942788.1| RNA polymerase sigma factor RpoD [Vibrio orientalis CIP 102891]
 gi|260939328|gb|EEX95314.1| RNA polymerase sigma factor RpoD [Vibrio orientalis CIP 102891]
          Length = 618

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 66/253 (26%), Positives = 118/253 (46%), Gaps = 12/253 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 372 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 431

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 432 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPLPE--- 486

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + E ++  +        S+   I   D   S   D++    D   ++ ++   
Sbjct: 487 ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDTTLELPLDSAT 541

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 542 AGSLKVATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 601

Query: 279 KVQESIQKQVELS 291
           K++   + +   S
Sbjct: 602 KLRHPSRSETLRS 614


>gi|156973168|ref|YP_001444075.1| RNA polymerase sigma factor RpoD [Vibrio harveyi ATCC BAA-1116]
 gi|156524762|gb|ABU69848.1| hypothetical protein VIBHAR_00848 [Vibrio harveyi ATCC BAA-1116]
          Length = 620

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 73/283 (25%), Positives = 130/283 (45%), Gaps = 24/283 (8%)

Query: 21  HEIRKIPMLEKQEEYVL--------AKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
             I K+ M+  +EE  L        ++R    E     A   +V ++LRLV+ IA  Y  
Sbjct: 346 RSIAKLKMI--EEETSLNVQNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTN 403

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I    
Sbjct: 404 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 463

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
                   L R+   +         PE    +A+++ + E ++  +        S+   I
Sbjct: 464 --IETINKLNRISRQMLQEMGREPLPE---ELAERMQMPEDKIRKVLKIAKEPISMETPI 518

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
              D   S   D++    D   ++ ++     + +      ++ L PRE ++   R   +
Sbjct: 519 --GDDEDSHLGDFI---EDTTLELPLDSATATSLKMATKDVLAGLTPREAKVLRMRFGID 573

Query: 251 --NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
                TLE +  +F+V+RER+RQIEA+A +K++   + +   S
Sbjct: 574 MNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRS 616


>gi|154245186|ref|YP_001416144.1| RNA polymerase sigma factor RpoD [Xanthobacter autotrophicus Py2]
 gi|154159271|gb|ABS66487.1| RNA polymerase, sigma 70 subunit, RpoD [Xanthobacter autotrophicus
           Py2]
          Length = 666

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 71/258 (27%), Positives = 122/258 (47%), Gaps = 15/258 (5%)

Query: 34  EYVLAKRYREHGDLSAAH---RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           E+    +  + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV
Sbjct: 410 EFRKIVQMVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 469

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
            KF+  RG++ +TY+ WWI+ A+   I      ++I        +   + ++    + + 
Sbjct: 470 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQML 524

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
               +      +A+KL +   +V  +        SL   I   D+  S   D++    D 
Sbjct: 525 HEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDK 579

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRER 268
              + I+   + N R   TR ++ L PRE R+   R         TLE +  +F V+RER
Sbjct: 580 NAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRER 639

Query: 269 VRQIEARAFKKVQESIQK 286
           +RQIEA+A +K++   + 
Sbjct: 640 IRQIEAKALRKLKHPSRS 657


>gi|302187929|ref|ZP_07264602.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. syringae
           642]
          Length = 335

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 84/278 (30%), Positives = 142/278 (51%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++  + +K       ++ +N R++  D SL         + 
Sbjct: 185 LRAAR-ELTQKLDHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSL------GPDSD 237

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + +S L  ++R +   R         TL
Sbjct: 238 KTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTEKQREVVIRRFGLRGHESSTL 294

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 295 EDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSSES 332


>gi|298491609|ref|YP_003721786.1| RpoD subfamily RNA polymerase sigma 70 subunit ['Nostoc azollae'
           0708]
 gi|298233527|gb|ADI64663.1| RNA polymerase, sigma 70 subunit, RpoD subfamily ['Nostoc azollae'
           0708]
          Length = 390

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 79/313 (25%), Positives = 140/313 (44%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAK-------------------------------- 39
            E  +  Y+ EI +I +L   EE  LA+                                
Sbjct: 78  TEDSIRLYLQEIGRIRLLRADEEIELARKIADLLELERVRDRLYEQLEREPQFKEWAEAV 137

Query: 40  -------RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                  RYR H    A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 138 QLPLPTFRYRLHVGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 197

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 198 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKLLSQE 252

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA ++ ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 253 MGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIESDGETPE 310

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
               ++  +   R  L + +  L+PRER +   R   ++    TLE +   F V+RER+R
Sbjct: 311 ----DQVSKNLLREDLEKVLDSLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIR 366

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 367 QIEAKALRKLRHP 379


>gi|298292324|ref|YP_003694263.1| RNA polymerase, sigma 70 subunit, RpoD [Starkeya novella DSM 506]
 gi|296928835|gb|ADH89644.1| RNA polymerase, sigma 70 subunit, RpoD [Starkeya novella DSM 506]
          Length = 666

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 71/259 (27%), Positives = 123/259 (47%), Gaps = 15/259 (5%)

Query: 33  EEYVLAKRYREHGDLSAAH---RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           +E+    +  + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+A
Sbjct: 409 QEFRKIVQMVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 468

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V KF+  RG++ +TY+ WWI+ A+   I      ++I        +   + ++    + +
Sbjct: 469 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQM 523

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
                +      +A+KL +   +V  +        SL   I   D+  S   D++    D
Sbjct: 524 LHEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---ED 578

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRE 267
               + I+   + N R   TR ++ L PRE R+   R         TLE +  +F V+RE
Sbjct: 579 KNAILPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRE 638

Query: 268 RVRQIEARAFKKVQESIQK 286
           R+RQIEA+A +K++   + 
Sbjct: 639 RIRQIEAKALRKLKHPSRS 657


>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 =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 128/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +  I +   L  +    +++R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 334 LQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 393

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 394 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 451

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 452 KLNRISRQMLQEMGREPLPE---ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDED 506

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++     + +      ++ L PRE ++   R   +     TL
Sbjct: 507 SHLGDFI---EDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTL 563

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 564 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 599


>gi|288957081|ref|YP_003447422.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
 gi|288909389|dbj|BAI70878.1| RNA polymerase sigma-32 factor [Azospirillum sp. B510]
          Length = 298

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 123/281 (43%), Positives = 174/281 (61%), Gaps = 7/281 (2%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
            +I    + P+L +  E+ LA+++RE  D  A H+LV ++ RLVV  A  +R YGLP+ +
Sbjct: 15  SFIKASMREPLLSRDHEFDLARKWREGSDERALHQLVRAYTRLVVATASRFRNYGLPMGD 74

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +V EGN+GLMQA  +F+P+R  R +TY+ WWI++AMQ+YILR+WS+V+ GTTA QK LFF
Sbjct: 75  LVQEGNVGLMQAASRFEPDREVRFSTYAAWWIRSAMQDYILRNWSIVRTGTTAAQKSLFF 134

Query: 138 NLRRLKGHLQAITDNN----LKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINS 192
           NLRRL+  + + T N     L  E    IA +L V  +EV +M  RL+G D+SLN  +  
Sbjct: 135 NLRRLRAKIDSATQNGSGAPLTKEGREWIAGELRVEVAEVEAMEMRLSGADQSLNTPVAD 194

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
              +   WQD+L       E V+I   +   R   L  ++  L+PRER I   RRL+E  
Sbjct: 195 GSDDD--WQDFLADQRPSPEDVVIGMRDANTRSQWLAEALGELSPRERTIIRERRLREEG 252

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
            TLE L  E  VS+ERVRQ+E RA  K+++S+ K+VE S  
Sbjct: 253 ATLEELGRELGVSKERVRQLEHRALLKLRQSMLKRVEDSDD 293


>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 =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 66/249 (26%), Positives = 114/249 (45%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 368 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 427

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 428 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPTPE--- 482

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + +++++ E ++  +        S+   I   D   S   D++    D Q    ++   
Sbjct: 483 ELGERMDMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDIQALSPVDSAT 537

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            +  R      ++ L  RE ++   R   E     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 538 AEGLREATRSVLAGLTARESKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALR 597

Query: 279 KVQESIQKQ 287
           K++   +  
Sbjct: 598 KLRHPSRSD 606


>gi|308270755|emb|CBX27365.1| RNA polymerase sigma factor rpoD [uncultured Desulfobacterium sp.]
          Length = 568

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 69/240 (28%), Positives = 113/240 (47%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L  ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 330 AKSELTRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 389

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I            L R   +L         PE    IA+K+ +
Sbjct: 390 IRQAITRAIADQARTIRIPVHM--IETINKLIRTSRYLVQEQGREPSPE---EIAEKMEI 444

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   I   ++  S   D++    D +  +  +    +N     
Sbjct: 445 PLEKVRKVLKIAREPISLETPI--GEEEDSHLGDFI---EDKKFMLPSDAAINQNLAEQT 499

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + ++ L PRE ++   R         TLE +  +F+V+RER+RQIEA+A +K++   + 
Sbjct: 500 RKVLATLTPREEKVLRMRFGIGERADHTLEEVGQDFQVTRERIRQIEAKALRKLRHPTRS 559


>gi|254461643|ref|ZP_05075059.1| RNA polymerase sigma-70 factor RpoD [Rhodobacterales bacterium
           HTCC2083]
 gi|206678232|gb|EDZ42719.1| RNA polymerase sigma-70 factor RpoD [Rhodobacteraceae bacterium
           HTCC2083]
          Length = 660

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 70/242 (28%), Positives = 117/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 420 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 479

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A KL
Sbjct: 480 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAAKL 534

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++N + 
Sbjct: 535 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAVLPLDSAIQENLKE 589

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR +S L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 590 TTTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 649

Query: 285 QK 286
           + 
Sbjct: 650 RS 651


>gi|27364956|ref|NP_760484.1| RNA polymerase sigma factor RpoS [Vibrio vulnificus CMCP6]
 gi|320155343|ref|YP_004187722.1| RNA polymerase sigma factor RpoS [Vibrio vulnificus MO6-24/O]
 gi|27361102|gb|AAO10011.1| RNA polymerase sigma factor RpoS [Vibrio vulnificus CMCP6]
 gi|319930655|gb|ADV85519.1| RNA polymerase sigma factor RpoS [Vibrio vulnificus MO6-24/O]
          Length = 330

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 82/287 (28%), Positives = 140/287 (48%), Gaps = 13/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           R+              Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVV
Sbjct: 42  REEFDASNKSLDATQLYLGEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLVV 100

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           KI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++    
Sbjct: 101 KISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTR 160

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            +++      K L   LR  +     ++           IA +L++   +V  M      
Sbjct: 161 TIRLPIHVV-KELNIYLRTAR----ELSQKLDHEPTAEEIAAQLDIPVDDVSKMLRLNER 215

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++  I           D +   ++   +V  + E   + R  L   +  LNP+++ +
Sbjct: 216 ISSVDTPI--GGDGEKALLDIIPDANNSDPEVSTQDE---DMRVSLIHWLEELNPKQKEV 270

Query: 243 FEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 271 LARRFGLLGYEPSTLEEVGQEIGLTRERVRQIQVEGLRRLREVLIKQ 317


>gi|148264661|ref|YP_001231367.1| RpoD family RNA polymerase sigma factor [Geobacter uraniireducens
           Rf4]
 gi|146398161|gb|ABQ26794.1| RNA polymerase, sigma 38 subunit, RpoS [Geobacter uraniireducens
           Rf4]
          Length = 336

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 141/276 (51%), Gaps = 13/276 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI+K  +L   EE  LA R  + G+ +A  +++ S+LRLVVKIA  Y   G
Sbjct: 60  DDAIKLYLREIQKTKLLTADEEKELAARI-DKGEKAARDKMIESNLRLVVKIAKRYINRG 118

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP  +++ EGN+GL++AV++F   +  R +TY+ WWI+ +++  ++     +++    + 
Sbjct: 119 LPFLDLIEEGNMGLIKAVERFKLSKECRFSTYATWWIRQSIERALVNQSRTIRLPVHVSD 178

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                ++ ++    + +     +   +  +A  ++V+ + +  +   L    S+   +  
Sbjct: 179 -----DINKMLRITRELVQKVNREPSIKEVATAMDVNSAYIRRLMVLLKKTYSIERPM-- 231

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE-- 250
            + N     D +    D       E  E  NR  M+++    L+  E+RI   R   +  
Sbjct: 232 GENNDYFLIDTI---EDTSTVSPAELLEDVNRYEMVSKWFETLSDSEKRILTLRFGLDDK 288

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +P TL+ +   F V+RER+RQIEA++ +K+++ ++ 
Sbjct: 289 DPQTLDTIGRSFGVTRERIRQIEAKSLEKLRKILEA 324


>gi|302382122|ref|YP_003817945.1| RNA polymerase, sigma 70 subunit, RpoD [Brevundimonas subvibrioides
           ATCC 15264]
 gi|302192750|gb|ADL00322.1| RNA polymerase, sigma 70 subunit, RpoD [Brevundimonas subvibrioides
           ATCC 15264]
          Length = 652

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 70/246 (28%), Positives = 117/246 (47%), Gaps = 12/246 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 408 EREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 467

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    + +     +      +
Sbjct: 468 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREPTPEEL 522

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+KL +   +V  +        SL   I   D+  S   D++    D    + I+   + 
Sbjct: 523 AEKLAMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAILPIDAAIQS 577

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 578 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKL 637

Query: 281 QESIQK 286
           +   + 
Sbjct: 638 KHPSRS 643


>gi|3646419|emb|CAA07705.1| sigma-70 factor [Pseudomonas tolaasii]
          Length = 616

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 69/263 (26%), Positives = 120/263 (45%), Gaps = 14/263 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L   E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 356 LTIAEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 415

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 416 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 473

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    + +++ + E ++  +        S+   I   D   S   D++  
Sbjct: 474 LQEMGREPTPE---ELGERMEMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 526

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q  I+    ++ +      +S L  RE ++   R   +     TLE +  +F+V
Sbjct: 527 -EDSTMQSPIDVATVESLKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 585

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   + +
Sbjct: 586 TRERIRQIEAKALRKLRHPTRSE 608


>gi|288942274|ref|YP_003444514.1| RNA polymerase sigma-32 subunit RpoH [Allochromatium vinosum DSM
           180]
 gi|288897646|gb|ADC63482.1| RNA polymerase, sigma 32 subunit, RpoH [Allochromatium vinosum DSM
           180]
          Length = 279

 Score =  227 bits (578), Expect = 2e-57,   Method: Composition-based stats.
 Identities = 110/283 (38%), Positives = 169/283 (59%), Gaps = 8/283 (2%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           K+ SI+  G I    YI+   +IP+L  +EE  LA R R+  D+ AA RLVTSHLR V++
Sbjct: 3   KDFSILPTGTI--EAYINSAYQIPVLTLEEERSLAVRLRDQNDMEAAKRLVTSHLRFVIR 60

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA GY GYGLP+ +++ EG +GLM+AV++F+P+ G RL ++++ WI+A + EYILR+W +
Sbjct: 61  IARGYLGYGLPLPDLIQEGTVGLMKAVRRFEPDMGVRLVSFAVHWIRAEIHEYILRNWRI 120

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-G 182
           VK+ TT  Q++LFFNLR  K  L  +T       +V  +A  L V    V+ M  RL+  
Sbjct: 121 VKVATTKAQRKLFFNLRSSKKRLGWLTKQ-----EVDEVAADLGVKPEVVLQMESRLSNQ 175

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
           D S + L +  D + +    +L        ++L  ++  +++R  L  +++ L+ R + I
Sbjct: 176 DLSFDGLEDDDDDSPAAPSTYLPDVRMEPSRLLEHEDTDRDQRERLYAALADLDERSKTI 235

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              R L E   TL  L+ +F VS ER+RQIE  A KKV+  ++
Sbjct: 236 LFERWLSEKKQTLHELAEKFGVSAERIRQIEKNAMKKVRLQLE 278


>gi|256420372|ref|YP_003121025.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chitinophaga
           pinensis DSM 2588]
 gi|256035280|gb|ACU58824.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chitinophaga
           pinensis DSM 2588]
          Length = 291

 Score =  227 bits (578), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 77/288 (26%), Positives = 151/288 (52%), Gaps = 12/288 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI K+ ++  +EE  LA R ++ GD  A  +L  ++LR VV
Sbjct: 7   KITKSITNRESQSLEKYLQEIGKVDLITPEEEVNLAIRIKQ-GDQRALEKLTKANLRFVV 65

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL +S++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 66  SVAKQYQNQGLSLSDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSR 125

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    N+  L   + +    L+   +    P+++  I   L ++  EV +     A 
Sbjct: 126 IVRLP--LNKVGLSNKISKAYSQLEQEFEREPSPDELATI---LEINTEEVEATLGVAAR 180

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     + NS    D L   +        E +   + R  + RS+S L  R++ +
Sbjct: 181 HVSMDAPFIDGEDNS--LLDVLANPNAVNAD--EELDHHDSLRREIERSLSTLTDRQKDV 236

Query: 243 FEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
                    E+P++LE++  +F ++RERVRQI+ +A  K++ + + ++
Sbjct: 237 IILYFGIAVEHPMSLEDIGEKFGLTRERVRQIKDKAITKLRTTSRSKL 284


>gi|123965795|ref|YP_001010876.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str. MIT
           9515]
 gi|123200161|gb|ABM71769.1| Putative principal RNA polymerase sigma factor [Prochlorococcus
           marinus str. MIT 9515]
          Length = 397

 Score =  227 bits (578), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 76/313 (24%), Positives = 139/313 (44%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------------- 43
            E  +  Y+ EI +I +L   EE  LA++  +                            
Sbjct: 85  TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLQLEELATQFESEKGHFPSVREWAELI 144

Query: 44  -----------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 145 DMPLSKFRRRLLLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 204

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 205 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKVLSQE 259

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA+ + ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 260 FGRKPSEEEIAESMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADIENPE 317

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
           Q +     +   R  L   ++ L+PRER +   R   ++    TLE +   F+V+RER+R
Sbjct: 318 QDV----SKTLLREDLEGVLATLSPRERDVLRLRYGIDDGRMKTLEEIGQIFDVTRERIR 373

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 374 QIEAKALRKLRHP 386


>gi|119473196|ref|ZP_01614893.1| RNA polymerase sigma factor rpoD (Sigma-70) [Alteromonadales
           bacterium TW-7]
 gi|119444560|gb|EAW25875.1| RNA polymerase sigma factor rpoD (Sigma-70) [Alteromonadales
           bacterium TW-7]
          Length = 614

 Score =  227 bits (578), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 69/273 (25%), Positives = 123/273 (45%), Gaps = 14/273 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +  I +   L  +    + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 344 LSIIEQTTGLSIERIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 403

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 404 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 461

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 462 KLNRISRQMLQEMGREPNPE---ELAERMMMPEDKIRKVLKIAKEPISMETPI--GDDED 516

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D      I+    ++ R      ++ L  RE ++   R   +     TL
Sbjct: 517 SHLGDFI---EDTTIDSPIDSATMESLRGATNDVLAGLTAREAKVLRMRFGIDMNTDHTL 573

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           E +  +F+V+RER+RQIEA+A +K++   +  +
Sbjct: 574 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSDL 606


>gi|148553355|ref|YP_001260937.1| RNA polymerase sigma factor RpoD [Sphingomonas wittichii RW1]
 gi|148498545|gb|ABQ66799.1| RNA polymerase, sigma 70 subunit, RpoD [Sphingomonas wittichii RW1]
          Length = 674

 Score =  227 bits (578), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 76/293 (25%), Positives = 136/293 (46%), Gaps = 17/293 (5%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLE--KQEEYVLAKRYREHGDLSAA---HRLVT 55
           +++K  +   N    + R  +EI +I         E+       + G+  A      +V 
Sbjct: 383 IDKKWANFAANEADAVDRIRNEIGEIAQATGMALSEFRRIVNMVQKGEREARIAKKEMVE 442

Query: 56  SHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQE 115
           ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+  
Sbjct: 443 ANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITR 502

Query: 116 YILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
            I      ++I        +   + +L    + I     +      +A++L++   +V  
Sbjct: 503 SIADQARTIRIPVH-----MIETINKLVRTSRQILHEIGREPTPEELAERLSMPLEKVRK 557

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
           +        SL   I   D+  S   D++    D    + ++   + N +  +TR ++ L
Sbjct: 558 VMKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAIIPVDAAIQSNLKETVTRVLASL 612

Query: 236 NPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 613 TPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 665


>gi|330894625|gb|EGH27286.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. mori
           str. 301020]
          Length = 335

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 84/278 (30%), Positives = 142/278 (51%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++  + +K       ++ +N R++  D SL         + 
Sbjct: 185 LRAAR-ELTQKLDHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSL------GPDSD 237

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + +S L  ++R +   R         TL
Sbjct: 238 KTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTEKQREVVIRRFGLRGHESSTL 294

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 295 EDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSSES 332


>gi|254476970|ref|ZP_05090356.1| Sigma-70, region 3 family [Ruegeria sp. R11]
 gi|214031213|gb|EEB72048.1| Sigma-70, region 3 family [Ruegeria sp. R11]
          Length = 661

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 421 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 480

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A+KL
Sbjct: 481 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAEKL 535

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++N + 
Sbjct: 536 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAVLPLDSAIQENLKE 590

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 591 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 650

Query: 285 QK 286
           + 
Sbjct: 651 RS 652


>gi|150005266|ref|YP_001300010.1| RNA polymerase sigma factor rpoD [Bacteroides vulgatus ATCC 8482]
 gi|212694793|ref|ZP_03302921.1| hypothetical protein BACDOR_04327 [Bacteroides dorei DSM 17855]
 gi|237710938|ref|ZP_04541419.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 9_1_42FAA]
 gi|237727237|ref|ZP_04557718.1| RNA polymerase sigma factor rpoD [Bacteroides sp. D4]
 gi|254883735|ref|ZP_05256445.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 4_3_47FAA]
 gi|265750524|ref|ZP_06086587.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 3_1_33FAA]
 gi|294777100|ref|ZP_06742557.1| putative RNA polymerase sigma factor RpoD [Bacteroides vulgatus
           PC510]
 gi|319643459|ref|ZP_07998082.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 3_1_40A]
 gi|149933690|gb|ABR40388.1| RNA polymerase sigma factor rpoD [Bacteroides vulgatus ATCC 8482]
 gi|212662647|gb|EEB23221.1| hypothetical protein BACDOR_04327 [Bacteroides dorei DSM 17855]
 gi|229434093|gb|EEO44170.1| RNA polymerase sigma factor rpoD [Bacteroides dorei 5_1_36/D4]
 gi|229454782|gb|EEO60503.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 9_1_42FAA]
 gi|254836528|gb|EET16837.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 4_3_47FAA]
 gi|263237420|gb|EEZ22870.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 3_1_33FAA]
 gi|294448969|gb|EFG17512.1| putative RNA polymerase sigma factor RpoD [Bacteroides vulgatus
           PC510]
 gi|317384864|gb|EFV65820.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 3_1_40A]
          Length = 286

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 74/287 (25%), Positives = 143/287 (49%), Gaps = 12/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI +  ++  +EE  LA+R R+ GD  A  +L  ++LR VV
Sbjct: 5   KITKSITNRESASLDKYLQEIGREDLITVEEEVELAQRIRK-GDRVALEKLTRANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 64  SVAKQYQNQGLSLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    NQ      + +     +   +    PE    +A +L +   ++         
Sbjct: 124 IVRLP--LNQVGSLNKISKAFSKFEQENERRPSPE---ELADELEIPVDKISDTLKVSGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     + NS    D LV D        +  E        + R++S L  RE+ I
Sbjct: 179 HISVDAPFVEGEDNS--LLDVLVNDDSPMADRSLVNESLA---REIDRALSTLTEREKDI 233

Query: 243 FEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +         +TLE +  +F ++RERVRQI+ +A ++++++ + ++
Sbjct: 234 IQMFFGINTQEMTLEEIGDKFGLTRERVRQIKEKAIRRLRQNSRSKL 280


>gi|330505413|ref|YP_004382282.1| RNA polymerase factor sigma-32 [Pseudomonas mendocina NK-01]
 gi|328919699|gb|AEB60530.1| RNA polymerase factor sigma-32 [Pseudomonas mendocina NK-01]
          Length = 284

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 99/272 (36%), Positives = 156/272 (57%), Gaps = 7/272 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+H +  IP+L  ++E  LA+      DL AA ++V +HLR VV IA  Y GYGL 
Sbjct: 16  NLEAYVHAVNSIPLLTPEQERELAENLFYQQDLEAARQMVLAHLRFVVHIARSYSGYGLA 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGN+GLM+AVK+F+PE G RL ++++ WI+A + E+IL++W +VK+ TT  Q++
Sbjct: 76  QADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIRAEIHEFILKNWRIVKVATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           LFFNLR  K  L  + +     ++V A+A+ L V   EV  M  RL G +        +D
Sbjct: 136 LFFNLRSQKKRLAWLNN-----DEVTAVAESLGVEPHEVREMESRLTGQDMAFDPAADAD 190

Query: 195 KNSS-QWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENP 252
            +S+ Q     + DH       +E  +  +  +  L  ++  L+ R R I   R L E  
Sbjct: 191 DDSAFQSPAHYLEDHRYDPARQLEDADWSDSSSSNLHEALESLDERSRDILYQRWLAEEK 250

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL +L++++ VS ER+RQ+E  A  K++  I
Sbjct: 251 ATLHDLAAKYNVSAERIRQLEKNAMNKLKGCI 282


>gi|325294741|ref|YP_004281255.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Desulfurobacterium thermolithotrophum DSM 11699]
 gi|325065189|gb|ADY73196.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Desulfurobacterium thermolithotrophum DSM 11699]
          Length = 322

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 77/285 (27%), Positives = 149/285 (52%), Gaps = 14/285 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V  +  L  ++  I KIP+L ++EE   AKR +  GD  A  +LV S+LR VV +A  Y 
Sbjct: 47  VPDKDSLDAFLKSISKIPLLSREEEIEYAKRAK-AGDKEALKKLVESNLRFVVSVAKKYL 105

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G GLP+ ++++EG +GL++A ++FDP++G +  +Y++WWI+ ++ + + +    VKI   
Sbjct: 106 GCGLPLHDLIAEGILGLIEAARRFDPDKGVKFISYAVWWIRQSIMQALAQQTGAVKIPVK 165

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
                    + ++      +     +      +A+ + +   E+  +        SL+  
Sbjct: 166 QA-----VLVNKITRSYGELLKKLGREPTTEELAEYVGMEPKEIERLLTVCQVPLSLDTP 220

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   D+  + ++D+L  +   + +  + +EE K     +   +  L P+E++I   R   
Sbjct: 221 I--GDEEDTTFKDFLKGEGTAEVEEKVVQEELKQS---IQEMLEQLTPQEKKIIIMRFGL 275

Query: 250 E--NPVTLENLSSEFEVSRERVRQIEARAFKKVQE-SIQKQVELS 291
           +   P TL  +  +  +SRERVRQ+E RA KK++E +++K++ + 
Sbjct: 276 DGNEPKTLREIGEKLGISRERVRQLETRAKKKMKEYALRKKLNVF 320


>gi|153814577|ref|ZP_01967245.1| hypothetical protein RUMTOR_00791 [Ruminococcus torques ATCC 27756]
 gi|317501262|ref|ZP_07959466.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|331089991|ref|ZP_08338881.1| hypothetical protein HMPREF1025_02464 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|145848071|gb|EDK24989.1| hypothetical protein RUMTOR_00791 [Ruminococcus torques ATCC 27756]
 gi|316897329|gb|EFV19396.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|330402905|gb|EGG82471.1| hypothetical protein HMPREF1025_02464 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 273

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 83/276 (30%), Positives = 143/276 (51%), Gaps = 14/276 (5%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           +     L  Y++EI +IP+L++ EE  L +R  + GD SA  RL   +LRLVV IA  Y 
Sbjct: 6   IQESEPLRIYLNEIGEIPLLDETEEKELGRRISD-GDESARARLEEGNLRLVVSIAKHYT 64

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G GLP+ +++ EGNIGLM A +K+D  +  R +TY+ WWIK A+   I +    +++   
Sbjct: 65  GRGLPLMDLIQEGNIGLMHAAEKYDYTKDNRFSTYASWWIKEAITRAIDQQSREIRVPVH 124

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL-NVSESEVISMNCRLAGDESLNA 188
             +     N++R++   + +     +  +   IAKKL + +E EV ++   +    SL  
Sbjct: 125 VAE-----NIKRVQKAAKELQQEFGREAEPGEIAKKLGDRTEEEVKNILSYIRNPVSLET 179

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +    ++S    D++    D  E    +  +   R+  +   +  LN RE+ +   R  
Sbjct: 180 PVGEDGEDS--LGDFV---EDRSETTPEDAMDVLVRKEEVQELLETLNDREKEVISLRFG 234

Query: 249 Q--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              +   TLE +     ++RERVRQIE++A +K+++
Sbjct: 235 LGKDRTYTLEEIGESLGITRERVRQIESKAMEKLRK 270


>gi|282899714|ref|ZP_06307678.1| sigA (Sigma 28 (Flagella/Sporulation)) [Cylindrospermopsis
           raciborskii CS-505]
 gi|281195593|gb|EFA70526.1| sigA (Sigma 28 (Flagella/Sporulation)) [Cylindrospermopsis
           raciborskii CS-505]
          Length = 390

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 81/313 (25%), Positives = 139/313 (44%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAK-------------------------------- 39
            E  +  Y+ EI +I +L   EE  LA+                                
Sbjct: 78  TEDSIRLYLQEIGRIRLLRADEEIELARKIADLLELERVRDDLYEQLEREPEFREWAEAV 137

Query: 40  -------RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                  RYR H    A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 138 KLPLPTFRYRLHVGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 197

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 198 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKLLSQE 252

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA ++ ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 253 MGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIESDGETPE 310

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
               ++  +   R  L R +  L PRER +   R   +N    TLE +   F V+RER+R
Sbjct: 311 ----DQVSKSLLREDLERVLDSLGPRERDVLRLRYGLDNGRMKTLEEIGQIFNVTRERIR 366

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 367 QIEAKALRKLRHP 379


>gi|148241988|ref|YP_001227145.1| RNA polymerase sigma factor RpoD [Synechococcus sp. RCC307]
 gi|147850298|emb|CAK27792.1| RNA polymerase sigma factor RpoD, sigma-70 family [Synechococcus
           sp. RCC307]
          Length = 401

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 77/313 (24%), Positives = 142/313 (45%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE--------------HG------------ 45
            E  +  Y+ EI +I +L   EE  LA++  +              HG            
Sbjct: 89  TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLHLEELADQYEEDHGKYPDNREWAVLV 148

Query: 46  -------------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 149 DMPPIKFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 208

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 209 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKVLSQE 263

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA+ + ++  ++  +        SL   I    +  S+  D++  D +  +
Sbjct: 264 FGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADIENPD 321

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
           Q + +   R++    L   ++ L+PRER +   R   ++    TLE +   F+V+RER+R
Sbjct: 322 QDVAKNLLRED----LEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIR 377

Query: 271 QIEARAFKKVQES 283
           QIEA+A  K++  
Sbjct: 378 QIEAKALLKLRHP 390


>gi|6175878|gb|AAF05319.1|AF178851_2 sigma factor 38 [Pseudomonas putida]
          Length = 335

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 80/278 (28%), Positives = 137/278 (49%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     + +       +    
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIPLPIHV--VKELNV 183

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
             R    L    D+   PE++  + +K       ++ +N R++  D SL         + 
Sbjct: 184 YSRAARELTQKLDHEPSPEEIATLLEKPVAEVKRMLGLNERVSSVDVSL------GPDSD 237

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + +  L  ++R +   R         TL
Sbjct: 238 KTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLGELTDKQREVVVRRFGLRGHESSTL 294

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 295 EDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSSES 332


>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 =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 69/263 (26%), Positives = 120/263 (45%), Gaps = 14/263 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L   E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 356 LTIAEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 415

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 416 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 473

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    + +++ + E ++  +        S+   I   D   S   D++  
Sbjct: 474 LQEMGREPTPE---ELGERMEMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 526

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q  I+    ++ +      +S L  RE ++   R   +     TLE +  +F+V
Sbjct: 527 -EDSTMQSPIDVATVESLKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 585

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   + +
Sbjct: 586 TRERIRQIEAKALRKLRHPTRSE 608


>gi|256819198|ref|YP_003140477.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Capnocytophaga
           ochracea DSM 7271]
 gi|256580781|gb|ACU91916.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Capnocytophaga
           ochracea DSM 7271]
          Length = 287

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 66/276 (23%), Positives = 146/276 (52%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI ++ ++   EE  LA+R +  GD++A  +L  ++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQEIGRVDLITADEEVELAQRIK-AGDVAALEKLTKANLRFVVSVAKQYQNQGLT 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     +V++    N+  
Sbjct: 76  LPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLP--LNKIG 133

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               + ++  +L+   +   +      IA++L++S ++V           S++A +   +
Sbjct: 134 SINKINKMYAYLEQANE---RVPSAEEIARELDMSVNDVKESMKNAGRHISMDAPLV--E 188

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENP 252
              S   D +  +         +     + R  + R++  L PRE  +         ++ 
Sbjct: 189 GEDSNLYDVIRSNESPNPD---KSLILDSLRTEIERALETLTPREADVVRLYFGLSDQHA 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 246 MTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|88798840|ref|ZP_01114422.1| RNA polymerase sigma factor [Reinekea sp. MED297]
 gi|88778320|gb|EAR09513.1| RNA polymerase sigma factor [Reinekea sp. MED297]
          Length = 614

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 71/272 (26%), Positives = 123/272 (45%), Gaps = 14/272 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +  I+K   +   E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 345 LRNIQKNTGITLAEVKDIHRRISIGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 404

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 405 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 462

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++++ E ++  +        SL   I   D   
Sbjct: 463 KLNRISRQMLQEMGREPTPE---ELAERMDMPEDKIRKVLKISKEPISLETPI--GDDED 517

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
           S   D++    D    + +        R+  T  ++ L  RE ++   R         TL
Sbjct: 518 SSLGDFI---EDNTMILPVNSATSTGLRDATTEVLAGLTAREAKVLRMRFGINMNTDHTL 574

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +  +F+V+RER+RQIEA+A +K++   +  
Sbjct: 575 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSD 606


>gi|284036901|ref|YP_003386831.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirosoma
           linguale DSM 74]
 gi|283816194|gb|ADB38032.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirosoma
           linguale DSM 74]
          Length = 287

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 77/288 (26%), Positives = 147/288 (51%), Gaps = 13/288 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           + +  I       L +Y+ EI K+ +L   EE  LA++ RE GD  +  RL  ++LR VV
Sbjct: 5   KISKQITNRESQSLDKYLQEIGKVDLLTPDEEVTLAQKIRE-GDQLSLERLTKANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 64  SVAKQYQNQGLSLGDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    N+      + +    L+   +    PE++ A+   L +S +EV+        
Sbjct: 124 IVRLP--LNRVGSLNKISKTFSDLEQKFEREPSPEELAAV---LEISAAEVVDTLKISGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     ++NS    D L  D    E          + R  + R++S L  RE  +
Sbjct: 179 HVSMDAPFVQGEENS--LLDVLENDG---EDKPDSGLINDSLRKEVQRALSTLTQREADV 233

Query: 243 FEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
                    E+ +TLE +  +F ++RERVRQI+ +A ++++ + + + 
Sbjct: 234 ITLYFGLNGEHAMTLEEIGEKFNLTRERVRQIKEKAIRRLRHTSRSKA 281


>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 =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 67/243 (27%), Positives = 113/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 362 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 421

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            L R+   +         PE    +A+++
Sbjct: 422 WWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREATPE---ELAERM 476

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E +V  +        S+   +   D   S   D+L    D   +  IE    +    
Sbjct: 477 EMPEDKVRKVLKIAKEPISMETPV--GDDEDSSLGDFL---QDVNAESPIEAAVGEGLSE 531

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                ++ L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 532 STRDILAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPT 591

Query: 285 QKQ 287
           +  
Sbjct: 592 RSD 594


>gi|157374437|ref|YP_001473037.1| RpoD family RNA polymerase sigma factor [Shewanella sediminis
           HAW-EB3]
 gi|157316811|gb|ABV35909.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella sediminis
           HAW-EB3]
          Length = 323

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 80/271 (29%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   +++  + G   + +R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 54  YLSEIGFSPLLSAEEEVYFSRKALK-GCGKSRNRMIESNLRLVVKIARRYNNRGLALLDL 112

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 113 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 171

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            IA+KL++  ++V  M        S++  +     N  
Sbjct: 172 LRTAR----ELAHKLDHEPTAEEIAEKLDLPSADVSRMLKLNERITSVDTPL--GGDNDK 225

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  D        ++ E+       + + +  LN ++R +   R   L   P TLE
Sbjct: 226 ALLDVLADDDSVGPDYKVQDEDMS---KSVVKWLDELNTKQREVLARRFGLLGYEPSTLE 282

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           N+  E  ++RERVRQI+  A K++++ +  Q
Sbjct: 283 NVGKEIGLTRERVRQIQVEALKRLKDLLGSQ 313


>gi|33340521|gb|AAQ14856.1| RpoD [Pseudomonas fluorescens]
          Length = 616

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 69/263 (26%), Positives = 120/263 (45%), Gaps = 14/263 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L   E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 356 LTIAEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 415

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 416 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 473

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    + +++ + E ++  +        S+   I   D   S   D++  
Sbjct: 474 LQEMGREPTPE---ELGERMEMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 526

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q  I+    ++ +      +S L  RE ++   R   +     TLE +  +F+V
Sbjct: 527 -EDSTMQSPIDVATVESLKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 585

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   + +
Sbjct: 586 TRERIRQIEAKALRKLRHPTRSE 608


>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|133310|sp|P26480|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]
          Length = 617

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 70/263 (26%), Positives = 120/263 (45%), Gaps = 14/263 (5%)

Query: 29  LEKQE--EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L   E  E   A    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 357 LTVAEIKEINRAMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 416

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 417 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 474

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    + +++++ E ++  +        S+   I   D   S   D++  
Sbjct: 475 LQEMGREPTPE---ELGERMDMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 527

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q  IE    ++ +      ++ L  RE ++   R   +     TLE +  +F+V
Sbjct: 528 -EDSTMQSPIEMATSESLKESTREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 586

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   + +
Sbjct: 587 TRERIRQIEAKALRKLRHPSRSE 609


>gi|307824736|ref|ZP_07654959.1| RNA polymerase, sigma 70 subunit, RpoD [Methylobacter tundripaludum
           SV96]
 gi|307734094|gb|EFO04948.1| RNA polymerase, sigma 70 subunit, RpoD [Methylobacter tundripaludum
           SV96]
          Length = 602

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 71/300 (23%), Positives = 127/300 (42%), Gaps = 38/300 (12%)

Query: 16  LSRYIHEIRKI--PMLEKQEEYVLAKRYR------------------------EHGDLSA 49
             +Y++   K    + E+++E   A++                          E     A
Sbjct: 304 FDQYLNAGSKYSETLKEREKEVRKAQKILADIEAEYGLTISGLKDINRRMSIGEAKARRA 363

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI
Sbjct: 364 KKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWI 423

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + A+   I      ++I            L R+   +         PE    +A+++ + 
Sbjct: 424 RQAITRSIADQARTIRIPVHM--IETINKLNRISRQILQELGREATPE---ELAERMEMP 478

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E +V  +        S+   I   D   S   D++    D +    +E       R    
Sbjct: 479 EDKVRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDAKVLSPVEAATIAGLRESTQ 533

Query: 230 RSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             ++ L  RE ++   R         TLE +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 534 NVLAGLTAREAKVLRMRFGINMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 593


>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 =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 66/253 (26%), Positives = 118/253 (46%), Gaps = 12/253 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 374 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 433

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 434 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPLPE--- 488

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + E ++  +        S+   I   D   S   D++    D   ++ ++   
Sbjct: 489 ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDTTLELPLDSAT 543

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 544 ATSLKMATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 603

Query: 279 KVQESIQKQVELS 291
           K++   + +   S
Sbjct: 604 KLRHPSRSETLRS 616


>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 =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 64/250 (25%), Positives = 119/250 (47%), Gaps = 12/250 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 373 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 432

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 433 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPSPE--- 487

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + E ++  +        S+   I   D   S   D++    D   ++ ++   
Sbjct: 488 ELAERMMMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDTTLELPLDSAT 542

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            ++ ++     ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 543 SESLKSATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 602

Query: 279 KVQESIQKQV 288
           K++   + ++
Sbjct: 603 KLRHPSRSEI 612


>gi|282896628|ref|ZP_06304643.1| sigA (Sigma 28 (Flagella/Sporulation)) [Raphidiopsis brookii D9]
 gi|281198498|gb|EFA73384.1| sigA (Sigma 28 (Flagella/Sporulation)) [Raphidiopsis brookii D9]
          Length = 390

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 80/313 (25%), Positives = 139/313 (44%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAK-------------------------------- 39
            E  +  Y+ EI +I +L   EE  LA+                                
Sbjct: 78  TEDSIRLYLQEIGRIRLLRADEEIELARKIADLLELERVRDDLYEQLEREPEFREWAEAV 137

Query: 40  -------RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                  RYR H    A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 138 KLPLPTFRYRLHVGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 197

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 198 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKLLSQE 252

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA ++ ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 253 MGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIESDGETPE 310

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
               ++  +   R  L R +  L PRER +   R   ++    TLE +   F V+RER+R
Sbjct: 311 ----DQVSKSLLREDLERVLDSLGPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIR 366

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 367 QIEAKALRKLRHP 379


>gi|28868771|ref|NP_791390.1| RNA polymerase sigma-38 factor [Pseudomonas syringae pv. tomato
           str. DC3000]
 gi|301383956|ref|ZP_07232374.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. tomato
           Max13]
 gi|302064158|ref|ZP_07255699.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. tomato
           K40]
 gi|302134085|ref|ZP_07260075.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. tomato
           NCPPB 1108]
 gi|3132688|gb|AAC16326.1| sigma factor [Pseudomonas syringae pv. tomato]
 gi|28852010|gb|AAO55085.1| RNA polymerase sigma-38 factor [Pseudomonas syringae pv. tomato
           str. DC3000]
 gi|331016398|gb|EGH96454.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv.
           lachrymans str. M302278PT]
          Length = 335

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 84/278 (30%), Positives = 142/278 (51%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++  + +K       ++ +N R++  D SL         + 
Sbjct: 185 LRAAR-ELTQKLDHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSL------GPDSD 237

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + +S L  ++R +   R         TL
Sbjct: 238 KTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTEKQREVVIRRFGLRGHESSTL 294

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 295 EDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSSES 332


>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 =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 63/247 (25%), Positives = 115/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 563 ERASRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 622

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    +              +
Sbjct: 623 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKMNRISRQHLQEFGFEPDASIL 677

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A K+ + E ++  +        S+   I   D + S   D++    D      ++   + 
Sbjct: 678 AAKMEIPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNNTAPVDAAMQA 732

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 733 GLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKL 792

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 793 KHPSRSD 799


>gi|94500747|ref|ZP_01307276.1| nonessential primary sigma factor [Oceanobacter sp. RED65]
 gi|94427069|gb|EAT12050.1| nonessential primary sigma factor [Oceanobacter sp. RED65]
          Length = 331

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 80/277 (28%), Positives = 135/277 (48%), Gaps = 13/277 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  QEE   A+  R+ GD     R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 58  YLNEIGFSPLLTPQEEVHFARLARK-GDEKGRKRMIESNLRLVVKIARRYVNRGLTLLDL 116

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 117 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 175

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +T           IA  L     +V  M        S++  +     +  
Sbjct: 176 LRAAR----ELTQKLDHEPTAEEIADLLEKPVDDVKRMLGLNERVTSVDTPL--GYNSDK 229

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
              D +  +       +++ ++  +    L   +  L  ++R +   R         TLE
Sbjct: 230 AILDTIADEAVSDPCQVLQDDDISSS---LDGWLDELTEKQREVIARRFGLRGYEISTLE 286

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
            +  E  ++RERVRQI+  A K+++E ++KQ   ++S
Sbjct: 287 EVGFEIGLTRERVRQIQVEALKRLREIMEKQGLNATS 323


>gi|91792562|ref|YP_562213.1| RNA polymerase sigma factor RpoS [Shewanella denitrificans OS217]
 gi|91714564|gb|ABE54490.1| RNA polymerase sigma factor RpoS [Shewanella denitrificans OS217]
          Length = 327

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 83/271 (30%), Positives = 139/271 (51%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   +++  + G   + +R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 58  YLGEIGFSPLLSAEEEVFFSRKALK-GCEKSRNRMIESNLRLVVKIARRYNNRGLALLDL 116

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 117 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 175

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            IA KL+VS S+V  M        S++  +     N  
Sbjct: 176 LRTAR----QLAQKLDHEPTAEEIAAKLDVSTSDVSRMLKLNEKITSVDTPL--GGDNEK 229

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D +  D        ++ E+  N    +   ++ LN ++R +   R   L   P TLE
Sbjct: 230 ALLDVIADDDSVGPDYQVQDEDLSNS---IVGWLNELNTKQREVLARRFGLLGYEPSTLE 286

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           N+ +E  ++RERVRQI+  A K++++ +  Q
Sbjct: 287 NVGAEIGLTRERVRQIQVEALKRLKDLLSSQ 317


>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 =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 68/264 (25%), Positives = 120/264 (45%), Gaps = 14/264 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L  +    + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 353 LSIERIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 412

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 413 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 470

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    +A+++ + E ++  +        S+   I   D   S   D++  
Sbjct: 471 LQEMGREPNPE---ELAERMMMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 523

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D      I+    ++ R      ++ L  RE ++   R   +     TLE +  +F+V
Sbjct: 524 -EDTTIDSPIDSATMESLRGATNDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 582

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           +RER+RQIEA+A +K++   +  +
Sbjct: 583 TRERIRQIEAKALRKLRHPSRSDL 606


>gi|294085800|ref|YP_003552560.1| sigma-70 factor RpoD [Candidatus Puniceispirillum marinum IMCC1322]
 gi|292665375|gb|ADE40476.1| Sigma 70 (RpoD) [Candidatus Puniceispirillum marinum IMCC1322]
          Length = 674

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 71/241 (29%), Positives = 112/241 (46%), Gaps = 12/241 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 435 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 494

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I            L R    +         PE    +A+KL+
Sbjct: 495 WIRQAITRSIADQARTIRIPVHM--IETINKLVRTSRQMLHEIGREPTPE---ELAEKLS 549

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +   +V  +        SL   I   D+  S   D++    D      ++     N R  
Sbjct: 550 MPIDKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAVQPLDAAIHANLRET 604

Query: 228 LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            TR ++ L  RE R+   R         TLE +  +F V+RER+RQIEA+A +K++   +
Sbjct: 605 TTRVLASLTAREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSR 664

Query: 286 K 286
            
Sbjct: 665 S 665


>gi|150026087|ref|YP_001296913.1| RNA polymerase sigma-70 factor RpoD [Flavobacterium psychrophilum
           JIP02/86]
 gi|149772628|emb|CAL44111.1| RNA polymerase sigma-70 factor RpoD [Flavobacterium psychrophilum
           JIP02/86]
          Length = 287

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 72/276 (26%), Positives = 147/276 (53%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI K+ ++   EE  LA+R +  GD  A  +L  ++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQEIGKVDLITADEEVELAQRIK-AGDQRALEKLTKANLRFVVSVAKQYQNQGLT 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     +V++    N+  
Sbjct: 76  LPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLP--LNKIG 133

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               + ++   L+   +   +P     IAK+L+++ ++V           S++A +   +
Sbjct: 134 SINKINKMYALLEQSNE---RPPSAEEIAKELDMTVNDVKESMKNSGRHLSMDAPLV--E 188

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENP 252
              S   D L     G+      +   ++ R  + RS+  L PRE  +         ++P
Sbjct: 189 GEDSNLYDVL---RSGESPNPDRELIIESLRTEIERSLETLTPREADVVRLYFGLADQHP 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 246 MTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|113969467|ref|YP_733260.1| RNA polymerase, sigma 28 subunit [Shewanella sp. MR-4]
 gi|114046700|ref|YP_737250.1| RNA polymerase, sigma 28 subunit [Shewanella sp. MR-7]
 gi|117919573|ref|YP_868765.1| RNA polymerase, sigma 38 subunit, RpoS [Shewanella sp. ANA-3]
 gi|113884151|gb|ABI38203.1| RNA polymerase, sigma 28 subunit [Shewanella sp. MR-4]
 gi|113888142|gb|ABI42193.1| RNA polymerase, sigma 28 subunit [Shewanella sp. MR-7]
 gi|117611905|gb|ABK47359.1| RNA polymerase, sigma 38 subunit, RpoS [Shewanella sp. ANA-3]
          Length = 326

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 82/271 (30%), Positives = 140/271 (51%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   +++  + G   + +R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 57  YLGEIGFSPLLSAEEEVYFSRKALK-GCEKSRNRMIESNLRLVVKIARRYNNRGLALLDL 115

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 116 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 174

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            IA+KL VS  +V  M        S++  +     N  
Sbjct: 175 LRTAR----ELAQKLDHEPTAEEIAEKLQVSSVDVSRMLKLNEKITSVDIPL--GGDNDK 228

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  D +      ++ E+  N    + + ++ LN ++R +   R   L   P TLE
Sbjct: 229 ALLDVLADDDNVGPDYKVQDEDISNS---VVKWLNELNTKQREVLARRFGLLGYEPSTLE 285

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++ +E  ++RERVRQI+  A K++++ +  Q
Sbjct: 286 DVGAEIGLTRERVRQIQVEALKRLRDLLGAQ 316


>gi|330813718|ref|YP_004357957.1| RNA polymerase sigma factor RpoD [Candidatus Pelagibacter sp.
           IMCC9063]
 gi|327486813|gb|AEA81218.1| RNA polymerase sigma factor RpoD [Candidatus Pelagibacter sp.
           IMCC9063]
          Length = 621

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 67/240 (27%), Positives = 116/240 (48%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 383 AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 442

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I            + R    + +       PE    ++KKL +
Sbjct: 443 IRQAITRSIADQARTIRIPVHM--IETINKIVRTSRQMMSEYGREPTPE---ELSKKLAM 497

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   +   D++ S   D++    D    + ++   +   +N  
Sbjct: 498 PLEKVRKVLKIAKEPISLETPV--GDEDDSSLGDFI---EDTNALIPVDAAIQTGLKNST 552

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           T+ ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 553 TKVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 612


>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 =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 67/247 (27%), Positives = 113/247 (45%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 416 EAKMRRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 475

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T     P     +
Sbjct: 476 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGAEPDPAT---L 530

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+ + E ++  +        S+   I   D + S   D++    D       E     
Sbjct: 531 AEKMEMPEEKIRKIMKISKEPISMETPI--GDDDDSHLGDFI---EDTATLAPAEAAMYS 585

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             R+     +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 586 GLRDATAEVLDSLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 645

Query: 281 QESIQKQ 287
           +   + +
Sbjct: 646 RHPSRSE 652


>gi|326335966|ref|ZP_08202143.1| RNA polymerase sigma-70 factor [Capnocytophaga sp. oral taxon 338
           str. F0234]
 gi|325691930|gb|EGD33892.1| RNA polymerase sigma-70 factor [Capnocytophaga sp. oral taxon 338
           str. F0234]
          Length = 287

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 73/276 (26%), Positives = 146/276 (52%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI K+ ++   EE  LA+R +  GD  A  RL  ++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQEIGKVDLISADEEVELAQRIK-AGDKVALERLTKANLRFVVSVAKQYQNQGLT 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     +V++    N+  
Sbjct: 76  LPDLINEGNMGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLP--LNKIG 133

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               + ++  +L+   +     E    IA++L++S S+V           S++A +   +
Sbjct: 134 SINKINKMYAYLEQTHERIPSAE---EIARELDMSVSDVKESMKNSGRHISMDAPLV--E 188

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
              S   D L     G+     ++   ++ +  + R++  L PRE  +           P
Sbjct: 189 GEDSNLYDVL---RSGESPNPDKELMHESLKTEIERALETLTPREADVIRLYFGLGENYP 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TLE +   FE++RERVRQI+ +A ++++ + + ++
Sbjct: 246 MTLEEIGETFELTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|254419911|ref|ZP_05033635.1| Sigma-70 region 3 family [Brevundimonas sp. BAL3]
 gi|196186088|gb|EDX81064.1| Sigma-70 region 3 family [Brevundimonas sp. BAL3]
          Length = 648

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 70/246 (28%), Positives = 117/246 (47%), Gaps = 12/246 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 404 EREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 463

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    + +     +      +
Sbjct: 464 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREPTPEEL 518

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+KL +   +V  +        SL   I   D+  S   D++    D    + I+   + 
Sbjct: 519 AEKLAMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAVLPIDAAIQS 573

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 574 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKL 633

Query: 281 QESIQK 286
           +   + 
Sbjct: 634 KHPSRS 639


>gi|312959424|ref|ZP_07773941.1| sigma-28 (flagella/sporulation) [Pseudomonas fluorescens WH6]
 gi|311286141|gb|EFQ64705.1| sigma-28 (flagella/sporulation) [Pseudomonas fluorescens WH6]
          Length = 335

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 84/278 (30%), Positives = 142/278 (51%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLTPEEEVHFA-RLSQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++  + +K       ++ +N R++  D SL         + 
Sbjct: 185 LRAAR-ELTQKLDHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSL------GPDSD 237

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + +S L  ++R +   R         TL
Sbjct: 238 KTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTDKQREVVIRRFGLRGHESSTL 294

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 295 EDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSSES 332


>gi|163850052|ref|YP_001638095.1| RNA polymerase sigma factor RpoD [Methylobacterium extorquens PA1]
 gi|163661657|gb|ABY29024.1| RNA polymerase sigma factor RpoD [Methylobacterium extorquens PA1]
          Length = 718

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 71/258 (27%), Positives = 121/258 (46%), Gaps = 15/258 (5%)

Query: 34  EYVLAKRYREHGDLSAAH---RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           EY       + G+  A      ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV
Sbjct: 462 EYRKIVAMVQKGEREARQAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 521

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
            KF+  RG++ +TY+ WWI+ A+   I      ++I        +   + ++    + + 
Sbjct: 522 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQML 576

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
               +      +A+KL +   +V  +        SL   I   D+  S   D++    D 
Sbjct: 577 HEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDK 631

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRER 268
              + I+   + N R   TR ++ L PRE R+   R         TLE +  +F V+RER
Sbjct: 632 NVVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRER 691

Query: 269 VRQIEARAFKKVQESIQK 286
           +RQIEA+A +K++   + 
Sbjct: 692 IRQIEAKALRKLKHPSRS 709


>gi|53714034|ref|YP_100026.1| RNA polymerase sigma factor RpoD [Bacteroides fragilis YCH46]
 gi|60682231|ref|YP_212375.1| putative sigma factor A [Bacteroides fragilis NCTC 9343]
 gi|253564677|ref|ZP_04842133.1| RpoD [Bacteroides sp. 3_2_5]
 gi|255010339|ref|ZP_05282465.1| putative sigma factor A [Bacteroides fragilis 3_1_12]
 gi|265766346|ref|ZP_06094387.1| RNA polymerase sigma factor RpoS [Bacteroides sp. 2_1_16]
 gi|313148138|ref|ZP_07810331.1| RNA polymerase sigma factor rpoD [Bacteroides fragilis 3_1_12]
 gi|52216899|dbj|BAD49492.1| RNA polymerase sigma factor RpoD [Bacteroides fragilis YCH46]
 gi|57471281|gb|AAW50926.1| RpoD [Bacteroides fragilis]
 gi|60493665|emb|CAH08454.1| putative sigma factor A [Bacteroides fragilis NCTC 9343]
 gi|251946142|gb|EES86519.1| RpoD [Bacteroides sp. 3_2_5]
 gi|263254014|gb|EEZ25479.1| RNA polymerase sigma factor RpoS [Bacteroides sp. 2_1_16]
 gi|301163709|emb|CBW23263.1| putative sigma factor A [Bacteroides fragilis 638R]
 gi|313136905|gb|EFR54265.1| RNA polymerase sigma factor rpoD [Bacteroides fragilis 3_1_12]
          Length = 286

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 75/287 (26%), Positives = 145/287 (50%), Gaps = 12/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI +  ++  +EE  LA+R R+ GD  A  +L  ++LR VV
Sbjct: 5   KITKSITNRESASLDKYLQEIGREDLITVEEEVELAQRIRK-GDRVALEKLTRANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 64  SVAKQYQNQGLSLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    NQ      + +     +   +    PE    +A +L++   ++         
Sbjct: 124 IVRLP--LNQVGSLNKISKAFSKFEQENERRPSPE---ELAGELDIPVDKISDTLKVSGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     + NS    D LV D        +  E        + R++S L  RE+ I
Sbjct: 179 HISVDAPFVEGEDNS--LLDVLVNDDSPMADRSLVNESLA---REIDRALSTLTDREKEI 233

Query: 243 FEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +      +  +TLE +  +F ++RERVRQI+ +A +++++S + ++
Sbjct: 234 IQMFFGIGQQEMTLEEIGDKFGLTRERVRQIKEKAIRRLRQSNRSKL 280


>gi|312883942|ref|ZP_07743659.1| hypothetical protein VIBC2010_01628 [Vibrio caribbenthicus ATCC
           BAA-2122]
 gi|309368400|gb|EFP95935.1| hypothetical protein VIBC2010_01628 [Vibrio caribbenthicus ATCC
           BAA-2122]
          Length = 325

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 79/288 (27%), Positives = 140/288 (48%), Gaps = 13/288 (4%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
            ++              Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLV
Sbjct: 36  AKEEFDASTKSLDATQLYLGEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLV 94

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           VKI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++   
Sbjct: 95  VKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQT 154

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             +++      K L   LR  +     ++           IA +L+    +V  M     
Sbjct: 155 RTIRLPIHVV-KELNIYLRTAR----ELSQKLDHEPTAEEIALQLDKPVDDVSKMLRLNE 209

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              S++  I           D +   ++   +V  + +   + ++ L   +  LNP+++ 
Sbjct: 210 RISSVDTPI--GGDGEKALLDIIPDVNNSDPEVSTQDD---DIKSSLIDWLDELNPKQKE 264

Query: 242 IFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +   R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 265 VLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVKQ 312


>gi|330812146|ref|YP_004356608.1| RNA polymerase sigma factor (sigma-70) [Pseudomonas brassicacearum
           subsp. brassicacearum NFM421]
 gi|327380254|gb|AEA71604.1| RNA polymerase sigma factor (sigma-70) [Pseudomonas brassicacearum
           subsp. brassicacearum NFM421]
          Length = 615

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 69/263 (26%), Positives = 120/263 (45%), Gaps = 14/263 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L   E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 355 LSIAEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 414

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 415 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 472

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    + +++ + E ++  +        S+   I   D   S   D++  
Sbjct: 473 LQEMGREPTPE---ELGERMEMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 525

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q  I+    ++ +      +S L  RE ++   R   +     TLE +  +F+V
Sbjct: 526 -EDSTMQSPIDVATVESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 584

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   + +
Sbjct: 585 TRERIRQIEAKALRKLRHPTRSE 607


>gi|311693206|gb|ADP96079.1| RNA polymerase, sigma 70 subunit, RpoD [marine bacterium HP15]
          Length = 615

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 66/249 (26%), Positives = 113/249 (45%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 364 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 423

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 424 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPTPE--- 478

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + +++ + E ++  +        S+   I   D   S   D++    D Q    ++   
Sbjct: 479 ELGERMEMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDIQALSPVDSAT 533

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            +  R      ++ L  RE ++   R   E     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 534 AEGLREATRSVLAGLTARESKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALR 593

Query: 279 KVQESIQKQ 287
           K++   +  
Sbjct: 594 KLRHPSRSD 602


>gi|331007677|ref|ZP_08330813.1| RNA polymerase sigma factor RpoH [gamma proteobacterium IMCC1989]
 gi|330418520|gb|EGG93050.1| RNA polymerase sigma factor RpoH [gamma proteobacterium IMCC1989]
          Length = 288

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 103/283 (36%), Positives = 162/283 (57%), Gaps = 8/283 (2%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +++    ++ Y+  +    +L  +EE  L +R   H DL AA  LV +HLR VV IA  Y
Sbjct: 10  MLSPGANINAYMQAVNSFAVLTVEEEKDLGERLYYHEDLDAARGLVMAHLRFVVHIAKSY 69

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGL  S+++ EGN+GLM+AVK+F+PE+G RL ++++ WIKA M E+ILR+W +VK+ T
Sbjct: 70  AGYGLSQSDLIQEGNVGLMKAVKRFNPEKGVRLVSFAVHWIKAEMHEFILRNWRIVKVAT 129

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           T  Q++LFFNLR  K  L  ++      ++  A+A  LNV    V  M  RL+  ++   
Sbjct: 130 TKAQRKLFFNLRGQKKRLGWLS-----YDEATAVAADLNVEVKHVHEMESRLSAYDASFD 184

Query: 189 LINSSDKNSSQ--WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
             N  D  S+     ++L        Q L   +   +  + L  +++ L+ R + I + R
Sbjct: 185 ADNDDDDESAYKAPANYLEDHRYNPAQELEASDWSDDNASRLRTALATLDERSQVIIQRR 244

Query: 247 RL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            L  +N  TL  L++EF VS ER+RQ+E  A KKV+ +++ +V
Sbjct: 245 WLNDDNKSTLHELAAEFGVSAERIRQLEKNAMKKVKTAMETEV 287


>gi|197103189|ref|YP_002128567.1| RNA polymerase sigma 32 subunit(heat shock sigma factor)
           [Phenylobacterium zucineum HLK1]
 gi|196480465|gb|ACG79992.1| RNA polymerase sigma 32 subunit(heat shock sigma factor)
           [Phenylobacterium zucineum HLK1]
          Length = 310

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 126/274 (45%), Positives = 179/274 (65%), Gaps = 2/274 (0%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+  +R+ P+L + EEY LA+R R+  DL+AAHRL+TSHLRL  KIA GYRGYGLP
Sbjct: 18  SLRQYLSAVRRYPVLTRDEEYALARRVRDEVDLAAAHRLMTSHLRLAAKIACGYRGYGLP 77

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++SE N+GL+ A+ KFD ER  RL+TY+ WWI+AA+Q+YILR WS+VK+GT+A QKR
Sbjct: 78  LEDMISEANVGLLHAIYKFDLERDCRLSTYAAWWIRAALQDYILRHWSIVKLGTSATQKR 137

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALINSS 193
           LFF  RR +  ++A     L  + +  +A+  +V   ++  M  RL   D SL+AL +  
Sbjct: 138 LFFGFRRARARVEACPSELLAGDSIAKMAELFHVPPGDITGMEARLGWRDLSLSAL-HGD 196

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           +    + +     +    E  L E +ER  R  +LT+++S L  RE RIF ARRL++ P 
Sbjct: 197 EGEPDRLERLADENAQDPETALSEADERDYRTRLLTQALSPLGSREHRIFVARRLRDPPA 256

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            L  L+ E+ VS ER+RQIE RAF+KVQ  +  Q
Sbjct: 257 PLAELAQEYGVSCERIRQIEMRAFEKVQRFVTDQ 290


>gi|33241312|ref|NP_876254.1| DNA-directed RNA polymerase sigma subunit [Prochlorococcus marinus
           subsp. marinus str. CCMP1375]
 gi|33238842|gb|AAQ00907.1| DNA-directed RNA polymerase sigma subunit [Prochlorococcus marinus
           subsp. marinus str. CCMP1375]
          Length = 339

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 79/292 (27%), Positives = 141/292 (48%), Gaps = 31/292 (10%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLA--------------------KRYREHGDLSAAH 51
           G   +  Y+  I ++P+L   EE  LA                    +R++      A  
Sbjct: 48  GTDSIGFYLSSIGRVPLLTPAEEIELAHHVQKMKGLLDIPKENINTRQRHQIRMGKRARD 107

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ ++LRLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+ 
Sbjct: 108 RMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQ 167

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            M   I  S   +++    ++K     L +++   + ++ N  +    V +A +L +   
Sbjct: 168 GMTRAIDNSARTIRLPIHISEK-----LSKMRRISRELSHNLGRQPNRVELANELGMEPK 222

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           ++  +  + A   SL++     +  S+  +       D      +E  +R  ++  L+  
Sbjct: 223 DLEDLMAQSAPCASLDSHARGEEDRSTLGELI----PDPNYDEPMECMDRNMQKEHLSGW 278

Query: 232 MSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +S LN RE++I   R     E P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 279 LSQLNEREQKIMRLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 330


>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 =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 73/246 (29%), Positives = 115/246 (46%), Gaps = 12/246 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 405 ERDSARAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 464

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            L R    +         PE    +
Sbjct: 465 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKLVRTSRQMLHEIGREPAPE---EL 519

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+KL +   +V  +        SL   I   D+  S   D++    D    + ++   + 
Sbjct: 520 AEKLGMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDKTAVIPLDAAIQT 574

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R   TR +S L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 575 NLREATTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTRERIRQIEAKALRKL 634

Query: 281 QESIQK 286
           +   + 
Sbjct: 635 KHPSRS 640


>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 =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 65/249 (26%), Positives = 113/249 (45%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 385 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 444

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            + R++  +         PE   
Sbjct: 445 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKINRVQRQMLQEMGREPTPE--- 499

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +  +L + E +V  +        S+   I   D   S   D++    DG  +  ++   
Sbjct: 500 ELGVRLEMPEDKVRKVLKIAKEPISMETPI--GDDEDSSLGDFI---EDGNMESPVDSAT 554

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
                      ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 555 SLGLEEATRDVLANLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 614

Query: 279 KVQESIQKQ 287
           K++   + +
Sbjct: 615 KLRHPSRSE 623


>gi|120553862|ref|YP_958213.1| RpoD family RNA polymerase sigma factor [Marinobacter aquaeolei
           VT8]
 gi|120323711|gb|ABM18026.1| RNA polymerase, sigma 38 subunit, RpoS [Marinobacter aquaeolei VT8]
          Length = 332

 Score =  226 bits (577), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A+  R+ G+ S   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 64  YLNEIGFSPLLTPEEEVYFARLARK-GEESGRKRMIESNLRLVVKIARRYVNRGLTLLDL 122

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 123 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNLY 181

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +T           IA+ ++    +V  M        S++  I +    S 
Sbjct: 182 LRAAR----ELTQKLDHEPTAEEIARMVDKPVDDVKRMLGLNERVASMDTPIGAGSDKS- 236

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
              D +  +       L++     N  + L + +  L+ +++ +   R         TLE
Sbjct: 237 -LMDTVADEGASDPADLLQD---NNMCSCLEKWIDQLSDKQQEVLSRRFGLRGYPISTLE 292

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +  E  ++RERVRQI+  A ++++E ++K+
Sbjct: 293 EVGQEIGLTRERVRQIQVEALRRLREILEKE 323


>gi|327405377|ref|YP_004346215.1| RpoD subfamily RNA polymerase sigma-70 subunit [Fluviicola
           taffensis DSM 16823]
 gi|327320885|gb|AEA45377.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Fluviicola
           taffensis DSM 16823]
          Length = 288

 Score =  226 bits (576), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 73/288 (25%), Positives = 149/288 (51%), Gaps = 12/288 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ +I K  ++  +EE  LA++ ++ GD  A  +L  ++LR VV
Sbjct: 5   KITKSITNRESQSLDKYLQDIGKEELITAEEEVELARKIKQ-GDQRALEKLTRANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 64  SVAKQYQNQGLTLPDLINEGNLGLIKAAQKFDETRGFKFISYAVWWIRQSILQALAEQAR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    NQ      + +    L+   +   +P     +A+ L V E ++         
Sbjct: 124 IVRLP--LNQVGSLNKINKAFSRLEQEFE---RPPSAEELAEALEVPEDKIKESLNVSGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A ++SS+   +        D    +  L+ +  +K     + RS+S L  +ER I
Sbjct: 179 HVSMDAPLSSSEDGGTLMDVMANADSPKADHALMAESLQKE----IERSLSTLTDKEREI 234

Query: 243 FEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
                     + +TLE + ++F ++RERVRQI+ +A ++++ + + ++
Sbjct: 235 IRLFFGIGMNHGLTLEEIGAKFNLTRERVRQIKEKAIRRLRHTSRNKL 282


>gi|148469868|gb|ABQ65863.1| stationary sigma factor [Pseudomonas fluorescens]
          Length = 335

 Score =  226 bits (576), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 83/278 (29%), Positives = 141/278 (50%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPE GFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPEHGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++  + +K       ++ +N R++  D SL         + 
Sbjct: 185 LRAAR-ELTQKLDHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSL------GPDSD 237

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + +S L  ++R +   R         TL
Sbjct: 238 KTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTDKQREVVIRRFGLRGHESSTL 294

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 295 EDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSSES 332


>gi|23428541|gb|AAL11450.1| RNA polymerase sigma-70 subunit [Serratia plymuthica]
          Length = 612

 Score =  226 bits (576), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 69/276 (25%), Positives = 129/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 343 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 402

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ +GNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 403 LIRKGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 460

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 461 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 515

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +     TL
Sbjct: 516 SHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMNTDHTL 572

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V RER+RQIEA+A +K++   + +V  S
Sbjct: 573 EEVGKQFDVIRERIRQIEAKALRKLRHPSRSEVLRS 608


>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 =  226 bits (576), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGN+GLM+AV KF+  RGF+ +TY+ 
Sbjct: 544 RKAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNVGLMKAVDKFEFRRGFKFSTYAT 603

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 604 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGVEPDPAT---LAEKM 658

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++ E ++  +        S+   I   D + S   D++    D       +     + R 
Sbjct: 659 DMPEDKIRKILKIAKEPISMETPI--GDDDDSHLGDFI---EDTTTLAPSDAALHDSMRE 713

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 714 VVKEVLDSLTPREAKVLRMRFGVEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 773

Query: 285 QKQ 287
           +  
Sbjct: 774 RAD 776


>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 =  226 bits (576), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 68/260 (26%), Positives = 121/260 (46%), Gaps = 14/260 (5%)

Query: 32  QEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           +E   + KR    E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+A
Sbjct: 557 EELKHINKRMNSGERASRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 616

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V KF+  RG++ +TY+ WWI+ A+   I      ++I        +   + ++    +  
Sbjct: 617 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKMNRISRQH 671

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
                       +A K+ + E ++  +        S+   I   D + S   D++    D
Sbjct: 672 LQEFGFEPDASILAAKMEIPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---ED 726

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRE 267
           G     I+   +   R+++   +  L PRE ++   R   E     TLE +  +F+V+RE
Sbjct: 727 GNNTAPIDAAMQAGLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRE 786

Query: 268 RVRQIEARAFKKVQESIQKQ 287
           R+RQIEA+A +K++   +  
Sbjct: 787 RIRQIEAKALRKLKHPSRSD 806


>gi|32423705|gb|AAP81248.1| sigma-32 subunit of RNA polymerase [Candidatus Portiera
           aleyrodidarum]
          Length = 280

 Score =  226 bits (576), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 108/273 (39%), Positives = 158/273 (57%), Gaps = 6/273 (2%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E  +  YI  +   P++  Q+EY LA+R R  GDL AA  LV S+LR V+ IA  Y GYG
Sbjct: 7   ETNIEGYIKTVLGFPIISAQDEYDLARRLRNKGDLDAARCLVISNLRFVIHIARSYSGYG 66

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L  S+++ EGN+GLM+AVK+FDP  G RL ++++ WIKA + EY+LR+W +VKI TT +Q
Sbjct: 67  LQNSDIIQEGNVGLMKAVKRFDPAHGVRLVSFAIHWIKAEIHEYVLRNWRIVKIATTKSQ 126

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
           ++LFF+LR  K  L     N L  E++ +IAK LNV  + V  M CRL+  +        
Sbjct: 127 RKLFFSLRCAKTSL-----NWLNREEIKSIAKDLNVKPTVVREMECRLSSTDYGFDNKQK 181

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPRERRIFEARRLQEN 251
            +KN+ +     + D      +  E  + +      L  +++ L+ R R I + R L E 
Sbjct: 182 EEKNNYKNPSNYLEDSRFDPALQFENFDFERYSYRRLYVALNKLDERVRDILKQRWLNEP 241

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL  L+  + VS ER+RQ+E RA KK++  I
Sbjct: 242 KATLHELADIYGVSAERIRQLEQRAIKKIKNYI 274


>gi|144900406|emb|CAM77270.1| RNA polymerase sigma factor rpod [Magnetospirillum gryphiswaldense
           MSR-1]
          Length = 664

 Score =  226 bits (576), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 71/241 (29%), Positives = 115/241 (47%), Gaps = 12/241 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 425 KAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 484

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I            L R    +         PE    +A+KL+
Sbjct: 485 WIRQAITRSIADQARTIRIPVHM--IETINKLVRTSRQMLHEIGREPTPE---ELAEKLS 539

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +   +V  +        SL   I   D+  S   D++    D    + ++   + N R  
Sbjct: 540 MPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAVLPLDAAIQANLRET 594

Query: 228 LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   +
Sbjct: 595 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSR 654

Query: 286 K 286
            
Sbjct: 655 S 655


>gi|84687692|ref|ZP_01015565.1| RNA polymerase sigma factor [Maritimibacter alkaliphilus HTCC2654]
 gi|84664275|gb|EAQ10766.1| RNA polymerase sigma factor [Rhodobacterales bacterium HTCC2654]
          Length = 670

 Score =  226 bits (576), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 430 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 489

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A+KL
Sbjct: 490 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAEKL 544

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++N + 
Sbjct: 545 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAVLPLDSAIQENLKE 599

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 600 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 659

Query: 285 QK 286
           + 
Sbjct: 660 RS 661


>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 =  226 bits (576), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 71/258 (27%), Positives = 121/258 (46%), Gaps = 15/258 (5%)

Query: 34  EYVLAKRYREHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           E+       + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV
Sbjct: 410 EFRKIVAMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 469

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
            KF+  RG++ +TY+ WWI+ A+   I      ++I        +   + ++    + + 
Sbjct: 470 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQML 524

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
               +      +A+KL +   +V  +        SL   I   D+  S   D++    D 
Sbjct: 525 HEIGREPTPEELAEKLQMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDK 579

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRER 268
              + I+   + N R   TR ++ L PRE R+   R         TLE +  +F V+RER
Sbjct: 580 NAVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRER 639

Query: 269 VRQIEARAFKKVQESIQK 286
           +RQIEA+A +K++   + 
Sbjct: 640 IRQIEAKALRKLKHPSRS 657


>gi|114704974|ref|ZP_01437882.1| RNA polymerase sigma factor protein (sigma-70) [Fulvimarina pelagi
           HTCC2506]
 gi|114539759|gb|EAU42879.1| RNA polymerase sigma factor protein (sigma-70) [Fulvimarina pelagi
           HTCC2506]
          Length = 682

 Score =  226 bits (576), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 69/246 (28%), Positives = 117/246 (47%), Gaps = 12/246 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 438 EREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 497

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    + +     +      +
Sbjct: 498 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREPTPEEL 552

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+KL +   +V  +        SL   +   D+  S   D++    D    + I+   + 
Sbjct: 553 AEKLAMPLEKVRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKNAVLPIDAAIQG 607

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 608 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKL 667

Query: 281 QESIQK 286
           +   + 
Sbjct: 668 KHPSRS 673


>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 =  226 bits (576), Expect = 3e-57,   Method: Composition-based stats.
 Identities = 64/250 (25%), Positives = 119/250 (47%), Gaps = 12/250 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 373 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 432

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 433 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPSPE--- 487

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + E ++  +        S+   I   D   S   D++    D   ++ ++   
Sbjct: 488 ELAERMMMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDTTLELPLDSAT 542

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            ++ ++     ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 543 SESLKSATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 602

Query: 279 KVQESIQKQV 288
           K++   + ++
Sbjct: 603 KLRHPSRSEI 612


>gi|254476880|ref|ZP_05090266.1| RNA polymerase, sigma 32 subunit, RpoH [Ruegeria sp. R11]
 gi|214031123|gb|EEB71958.1| RNA polymerase, sigma 32 subunit, RpoH [Ruegeria sp. R11]
          Length = 292

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 101/270 (37%), Positives = 172/270 (63%), Gaps = 6/270 (2%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
               K  +L+ + E  LA  +R+  D+ A HRL+ +++RL + +A  +R YG P+++++ 
Sbjct: 13  KRAMKAELLDAETELKLAYAWRDERDVQALHRLINAYMRLAISMASKFRRYGAPMNDLIQ 72

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           E  +GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFN+R
Sbjct: 73  EAGLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMR 132

Query: 141 RLKGHLQAIT----DNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDK 195
           R++  L+       +   + +    IA ++ V   +V  M+ RL+G D SLNA + S++ 
Sbjct: 133 RVQAQLEREAAASGEQLDQHQLHQKIATEIGVPLRDVQMMDGRLSGADFSLNA-VQSAED 191

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
              +W + L  D     +++ E  + +  R  L  +M  LN RER I   R+L++ P TL
Sbjct: 192 EGREWIEALEDDSAQAAELVEESHDTRQLRTWLVEAMQALNDRERFIITERKLRDKPRTL 251

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           E+L  E  +S+ERVRQ+EA AF+K+++S++
Sbjct: 252 ESLGDELGLSKERVRQLEAAAFQKMRKSLE 281


>gi|86132636|ref|ZP_01051229.1| RNA polymerase sigma-70 factor RpoD [Dokdonia donghaensis MED134]
 gi|85816878|gb|EAQ38063.1| RNA polymerase sigma-70 factor RpoD [Dokdonia donghaensis MED134]
          Length = 287

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 67/276 (24%), Positives = 144/276 (52%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI K+ ++  +EE  LA+R +  GD  A  +L  ++LR VV ++  Y+  GL 
Sbjct: 17  SLDKYLQEIGKVDLITAEEEVELAQRIK-AGDHRALEQLTKANLRFVVSVSKQYQNQGLT 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     +V++        
Sbjct: 76  LPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLPLNK---- 131

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
              ++ ++      +   N +P     IAK+L+++  +V           S++A +   +
Sbjct: 132 -IGSINKINKTFAFLEQANERPPSPEEIAKELDMTIKDVKESLKNSGRHISMDAPLV--E 188

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
              S   D L   + G+          ++ +  + R++  L PRE  +        +  P
Sbjct: 189 GEDSNLYDVL---NSGESPNPDRALLHESLKTEIERALETLTPREADVVRLYFGLGDQRP 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           ++LE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 246 MSLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>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 =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 73/272 (26%), Positives = 123/272 (45%), Gaps = 14/272 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + EI     L   E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 333 LKEIADKNGLSVAEIKEINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 392

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 393 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 450

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E +V  +        S+   I   D   
Sbjct: 451 KLNRVSRQMLQEMGREATPE---ELAERMEMPEDKVRKVLKIAKEPISMETPI--GDDED 505

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D      ++    +  R  +   +S L PRE ++   R   +     TL
Sbjct: 506 SHLGDFI---EDTSVTSPVDSATSEGLRESVREVLSGLTPREAKVLRMRFGIDMNTDHTL 562

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +  +F+V+RER+RQIEA+A +K++   +  
Sbjct: 563 EEVGKQFDVTRERIRQIEAKALRKLRHPTRSD 594


>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 =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 71/246 (28%), Positives = 118/246 (47%), Gaps = 12/246 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 410 ERDSARAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 469

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + +L    + +     +  Q   +
Sbjct: 470 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTSRQMLHEIGREPQPEEL 524

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+KL +   +V  +        SL   I   D+  S   D++    D    + ++   + 
Sbjct: 525 AEKLGMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDKAAIIPLDAAIQA 579

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R   TR +S L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 580 NLREATTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTRERIRQIEAKALRKL 639

Query: 281 QESIQK 286
           +   + 
Sbjct: 640 KHPSRS 645


>gi|189461487|ref|ZP_03010272.1| hypothetical protein BACCOP_02146 [Bacteroides coprocola DSM 17136]
 gi|198275894|ref|ZP_03208425.1| hypothetical protein BACPLE_02077 [Bacteroides plebeius DSM 17135]
 gi|189431821|gb|EDV00806.1| hypothetical protein BACCOP_02146 [Bacteroides coprocola DSM 17136]
 gi|198271523|gb|EDY95793.1| hypothetical protein BACPLE_02077 [Bacteroides plebeius DSM 17135]
          Length = 286

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 74/287 (25%), Positives = 143/287 (49%), Gaps = 12/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI +  ++  +EE  LA+R R+ GD  A  +L  ++LR VV
Sbjct: 5   KITKSITNRESASLDKYLQEIGREDLITVEEEVELAQRIRK-GDRIALEKLTRANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 64  SVAKQYQNQGLSLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    NQ      + +     +   +    PE    +A +L +   ++         
Sbjct: 124 IVRLP--LNQVGSLNKISKAFSKFEQENERRPSPE---ELADELEIPVDKISDTLKVSGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     + NS    D LV D        +  E        + R++S L  RE+ I
Sbjct: 179 HISVDAPFVEGEDNS--LLDVLVNDDSPMADRSLVNESLS---REIDRALSTLTEREKDI 233

Query: 243 FEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +         +TLE +  +F ++RERVRQI+ +A ++++++ + ++
Sbjct: 234 IQMFFGINTQEMTLEEIGDKFGLTRERVRQIKEKAIRRLRQNSRSKL 280


>gi|126667564|ref|ZP_01738534.1| nonessential primary sigma factor [Marinobacter sp. ELB17]
 gi|126627990|gb|EAZ98617.1| nonessential primary sigma factor [Marinobacter sp. ELB17]
          Length = 333

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 79/271 (29%), Positives = 136/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A+  R+ G+ S   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 65  YLNEIGFSPLLTPEEEVYFARLARK-GEESGRKRMIESNLRLVVKIARRYVNRGLTLLDL 123

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 124 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERGIMNQTRTIRLPIHVV-KELNLY 182

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +T           IA+K++    +V  M        S++  I +  + S 
Sbjct: 183 LRAAR----ELTQQLDHEPTAEEIARKVDKPVKDVKRMLGLNERVASMDTPIGAGGEKS- 237

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
                L    D       +  +  N    L + +  L+ +++ +   R         TLE
Sbjct: 238 ----LLDTVADEGASDPADVLQDNNISVCLQQWIDQLSEKQQEVLARRFGLRGYPVSTLE 293

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +  E  ++RERVRQI+  A ++++E ++K+
Sbjct: 294 EVGQEIGLTRERVRQIQVEALRRLREILEKE 324


>gi|193884351|dbj|BAG54997.1| Sigma70 [Ralstonia solanacearum]
          Length = 758

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 113/240 (47%), Gaps = 12/240 (5%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 510 ERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 569

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T N   P     +
Sbjct: 570 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGNEPDPAT---L 624

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+ + E ++  +        S+   I   D + S   D++    D       E     
Sbjct: 625 AEKMEMPEDKIRKIRKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTLAPAEAALHG 679

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 680 SMRGVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKL 739


>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 =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 74/249 (29%), Positives = 117/249 (46%), Gaps = 15/249 (6%)

Query: 43  EHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG+
Sbjct: 409 QKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 468

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWI+ A+   I      ++I            L R    +         PE  
Sbjct: 469 KFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLVRTSRQMLHEIGREPTPE-- 524

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +A+KL +   +V  +        SL   I   D+  S   D++    D    + I+  
Sbjct: 525 -ELAEKLGMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAILPIDAA 578

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAF 277
            + N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A 
Sbjct: 579 IQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKAL 638

Query: 278 KKVQESIQK 286
           +K++   + 
Sbjct: 639 RKLKHPSRS 647


>gi|330964173|gb|EGH64433.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv.
           actinidiae str. M302091]
          Length = 335

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 84/278 (30%), Positives = 141/278 (50%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE +  + +K       ++ +N R++  D SL         + 
Sbjct: 185 LRAAR-ELTQKLDHEPSPEDIANLLEKPVGEVKRMLGLNERVSSVDVSL------GPDSD 237

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + +S L  ++R +   R         TL
Sbjct: 238 KTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTEKQREVVIRRFGLRGHESSTL 294

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 295 EDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSSES 332


>gi|260431476|ref|ZP_05785447.1| RNA polymerase sigma-32 factor [Silicibacter lacuscaerulensis
           ITI-1157]
 gi|260415304|gb|EEX08563.1| RNA polymerase sigma-32 factor [Silicibacter lacuscaerulensis
           ITI-1157]
          Length = 292

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 106/287 (36%), Positives = 181/287 (63%), Gaps = 9/287 (3%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M++    +  +SR   +  K  +L+ + E  LA  +R+  D  A HRL+T+++RL + +A
Sbjct: 1   MALDNPNDFSMSR---QAMKAELLDAETELRLAYAWRDERDEQALHRLITAYMRLAISMA 57

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             ++ YG P+++++ E  +GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+
Sbjct: 58  AKFKRYGAPMNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVR 117

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNL----KPEQVVAIAKKLNVSESEVISMNCRLA 181
            G+T++QK LFFN+RR++  L+    ++     + +    IA ++ V   +V  M+ RLA
Sbjct: 118 TGSTSSQKSLFFNMRRVQARLEREAASDGVELDRHQLHQMIAAEIGVPLRDVEMMHGRLA 177

Query: 182 G-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           G D SLNA + S+D++  +W D L  D     +++    + +  R  L  +M  LN RER
Sbjct: 178 GSDFSLNA-VQSADEDGREWIDALEDDSAQAAELVEHGHDTRQLREWLITAMQALNERER 236

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            I   R+L++   TLE+L  E  +S+ERVRQ+EA AF K+++S++ Q
Sbjct: 237 FIVRERKLRDPARTLESLGQELGLSKERVRQLEAAAFAKMRKSLEGQ 283


>gi|163733984|ref|ZP_02141425.1| RNA polymerase sigma-70 factor RpoD [Roseobacter litoralis Och 149]
 gi|161392520|gb|EDQ16848.1| RNA polymerase sigma-70 factor RpoD [Roseobacter litoralis Och 149]
          Length = 660

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 420 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 479

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A+KL
Sbjct: 480 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAEKL 534

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++N + 
Sbjct: 535 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAVLPLDSAIQENLKE 589

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 590 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 649

Query: 285 QK 286
           + 
Sbjct: 650 RS 651


>gi|39996625|ref|NP_952576.1| RNA polymerase sigma-70 factor family [Geobacter sulfurreducens
           PCA]
 gi|39983506|gb|AAR34899.1| RNA polymerase sigma-70 factor family [Geobacter sulfurreducens
           PCA]
 gi|298505638|gb|ADI84361.1| RNA polymerase sigma-38 factor, stationary phase [Geobacter
           sulfurreducens KN400]
          Length = 328

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 143/276 (51%), Gaps = 13/276 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI++  +L   EE  LA R  + GD +A  +++ S+LRLVVKIA  Y   G
Sbjct: 57  DDAIKLYLREIQRTRLLTADEEKELAGRIAK-GDKAARDKMIESNLRLVVKIAKRYINRG 115

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP  +++ EGN+GL++AV++F   +  R +TY+ WWI+ +++  ++     +++    + 
Sbjct: 116 LPFLDLIEEGNMGLIKAVERFKLSKECRFSTYATWWIRQSIERALVNQSRTIRLPVHVSD 175

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                ++ ++    + +     +   V  +A ++ V+ + V  +   L    S+   +  
Sbjct: 176 -----DINKMLKITRELVQRLNREPSVKEVATEMKVNSAYVRRLMVLLKKTYSIERPM-- 228

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN- 251
            + +     D +         VL+E     N+  ++++  + L+  E+ I   R   E+ 
Sbjct: 229 GENSDYFLIDTIEDTSTVSPAVLLEDL---NKYEIVSKWFASLSENEQTILTLRFGLEDK 285

Query: 252 -PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            P TL+ +   F V+RER+RQIEA++ +K+++ I++
Sbjct: 286 EPQTLDTIGRSFGVTRERIRQIEAKSLEKLRKYIEE 321


>gi|121602584|ref|YP_988464.1| RNA polymerase factor sigma-32 [Bartonella bacilliformis KC583]
 gi|120614761|gb|ABM45362.1| RNA polymerase sigma-32 factor [Bartonella bacilliformis KC583]
          Length = 303

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 104/284 (36%), Positives = 178/284 (62%), Gaps = 3/284 (1%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N KN +   +G +G    +    + P LE+++EY LA R+++  D  A H++  +H+RLV
Sbjct: 11  NNKNYNDT-DGSLGRDM-VRSAMQAPYLERKKEYDLALRWKDKRDDEAMHQIAAAHMRLV 68

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           + IA  ++ + +P+ ++V EG +GL++A  +F+P+R  R +TY+ WWI+A++Q+YILR+W
Sbjct: 69  ISIASRFKRFKMPLGDLVQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNW 128

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
           S+V+ GT+++QK LFFNLRRL+  L        K +   +IA+KL+V  S+V  M+ R +
Sbjct: 129 SIVRGGTSSSQKALFFNLRRLRAQLVQEDSTLTKQDIFRSIAEKLSVPVSDVERMDFRFS 188

Query: 182 G-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           G D SL+  I+ ++++     D LV +H   + ++ +  + + R   L  ++ +LN RE 
Sbjct: 189 GADNSLSVSISENEESPVTKIDNLVDEHPLPDILIEKAIDGQRRTQWLYDALQILNEREM 248

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            I   RRL +   TLE+L     +S+ERVRQIE RA +K++ ++
Sbjct: 249 EIIRFRRLNDESATLESLGERLGISKERVRQIEVRALQKLRRAL 292


>gi|148259873|ref|YP_001234000.1| RNA polymerase sigma factor RpoD [Acidiphilium cryptum JF-5]
 gi|326403199|ref|YP_004283280.1| RNA polymerase sigma factor RpoD [Acidiphilium multivorum AIU301]
 gi|146401554|gb|ABQ30081.1| RNA polymerase, sigma 70 subunit, RpoD [Acidiphilium cryptum JF-5]
 gi|325050060|dbj|BAJ80398.1| RNA polymerase sigma factor RpoD [Acidiphilium multivorum AIU301]
          Length = 638

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 73/246 (29%), Positives = 114/246 (46%), Gaps = 12/246 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 394 ERDSTRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 453

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            L R    +         PE    +
Sbjct: 454 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKLVRTSRQMLHEIGREPTPE---EL 508

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+KL +   +V  +        SL   I   D+  S   D++    D    + ++     
Sbjct: 509 AEKLGMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAIIPLDAAVHA 563

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R   TR +S L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 564 NLREAATRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTRERIRQIEAKALRKL 623

Query: 281 QESIQK 286
           +   + 
Sbjct: 624 KHPSRS 629


>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 =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 73/246 (29%), Positives = 115/246 (46%), Gaps = 12/246 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 411 ERDSARAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 470

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            L R    +         PE    +
Sbjct: 471 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKLVRTSRQMLHEIGREPAPE---EL 525

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+KL +   +V  +        SL   I   D+  S   D++    D    + ++   + 
Sbjct: 526 AEKLGMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDKTAVIPLDAAIQT 580

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R   TR +S L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 581 NLREATTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTRERIRQIEAKALRKL 640

Query: 281 QESIQK 286
           +   + 
Sbjct: 641 KHPSRS 646


>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 =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 64/250 (25%), Positives = 119/250 (47%), Gaps = 12/250 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 373 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 432

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 433 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPSPE--- 487

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + E ++  +        S+   I   D   S   D++    D   ++ ++   
Sbjct: 488 ELAERMMMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDTTLELPLDSAT 542

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            ++ ++     ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 543 SESLKSATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 602

Query: 279 KVQESIQKQV 288
           K++   + ++
Sbjct: 603 KLRHPSRSEI 612


>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 =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 69/263 (26%), Positives = 122/263 (46%), Gaps = 14/263 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L   +   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 349 LTIGKVKEINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 408

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 409 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 466

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    +A+++ + E ++  +        S+   I   D   S   D++  
Sbjct: 467 LQEMGREPLPE---ELAERMMMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 519

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D    + I+    ++ RN +   +  L  RE ++   R   +     TLE +  +F+V
Sbjct: 520 -EDNTLDLPIDSATSESLRNSVRDVLGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 578

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   + +
Sbjct: 579 TRERIRQIEAKALRKLRHPSRSE 601


>gi|330959229|gb|EGH59489.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv.
           maculicola str. ES4326]
          Length = 336

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 83/278 (29%), Positives = 142/278 (51%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 68  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 126

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 127 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 185

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++  + ++       ++ +N R++  D SL         + 
Sbjct: 186 LRAAR-ELTQKLDHEPSPEEIANLLERPVGEVKRMLGLNERVSSVDVSL------GPDSD 238

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + +S L  ++R +   R         TL
Sbjct: 239 KTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTEKQREVVIRRFGLRGHESSTL 295

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 296 EDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSSES 333


>gi|110679091|ref|YP_682098.1| RNA polymerase sigma factor RpoD [Roseobacter denitrificans OCh
           114]
 gi|109455207|gb|ABG31412.1| RNA polymerase sigma-70 factor RpoD [Roseobacter denitrificans OCh
           114]
          Length = 661

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 421 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 480

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A+KL
Sbjct: 481 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAEKL 535

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++N + 
Sbjct: 536 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAVLPLDSAIQENLKE 590

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 591 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 650

Query: 285 QK 286
           + 
Sbjct: 651 RS 652


>gi|331006084|ref|ZP_08329420.1| RNA polymerase sigma factor RpoS [gamma proteobacterium IMCC1989]
 gi|330420121|gb|EGG94451.1| RNA polymerase sigma factor RpoS [gamma proteobacterium IMCC1989]
          Length = 342

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 77/277 (27%), Positives = 136/277 (49%), Gaps = 13/277 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A++    G+ +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 71  YLNEIGFSPLLSAEEEVFFARK-SLKGEEAARKRMIESNLRLVVKISRRYVNRGLALLDL 129

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 130 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 188

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA  L+   ++V  M        S++  +N   +   
Sbjct: 189 LRAAR----ELSQKLDHEPSAEEIANLLDKPVADVEKMLGLNERVNSID--VNIGPQGDK 242

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
              D +   H      L++     +    +   ++ L  ++R +   R         TLE
Sbjct: 243 TLSDTIPDQHVSDPVSLLQD---SDMSASIDGWLTELTEKQREVLCRRFGLRGYETSTLE 299

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
            +  E  ++RERVRQI+  A K++++ ++ Q   S S
Sbjct: 300 EVGREIGLTRERVRQIQVEALKRLKDIMELQGLDSES 336


>gi|319940794|ref|ZP_08015133.1| RNA polymerase sigma factor [Sutterella wadsworthensis 3_1_45B]
 gi|319805676|gb|EFW02457.1| RNA polymerase sigma factor [Sutterella wadsworthensis 3_1_45B]
          Length = 281

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 118/279 (42%), Positives = 173/279 (62%), Gaps = 11/279 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  ++    + PML  +EE  LA + R+  DL AA +LV SHLRLV+ IA G+ GYGLP 
Sbjct: 4   LDAFLRAAERAPMLTAEEEKTLALKLRDQNDLEAAQKLVLSHLRLVISIARGFLGYGLPY 63

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++ EGNIGLM+A++++DP+RG RL T+++ WI++ +QEYI+R+W +VK+ TT NQ++L
Sbjct: 64  ADLIQEGNIGLMKAIRRYDPDRGARLMTFAVHWIRSEIQEYIIRNWRIVKLATTKNQRKL 123

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
           FFNLR+LK   QA     L  ++   IA  L+V   EV+ M  R+ G E S++   +S D
Sbjct: 124 FFNLRQLKEDSQAA----LTNQEAQRIALTLDVKPKEVLDMEERMYGQETSIDGPADSDD 179

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--- 251
            +     DWL    D  E +L  ++ +      L  +++ L+PR RR+ EAR L  +   
Sbjct: 180 DDRFSPSDWLTRTSDQPEAILEAEDRQHLEGEGLQTALAALDPRSRRVIEARYLTVDADG 239

Query: 252 ---PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              PVTL+ L+ E  VS ERVRQIE  A KK+ E +  Q
Sbjct: 240 TAKPVTLQALAHELGVSAERVRQIEKLAIKKMGEKLAGQ 278


>gi|238063483|ref|ZP_04608192.1| sigma-70 region 2 domain-containing protein [Micromonospora sp.
           ATCC 39149]
 gi|237885294|gb|EEP74122.1| sigma-70 region 2 domain-containing protein [Micromonospora sp.
           ATCC 39149]
          Length = 334

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 73/300 (24%), Positives = 132/300 (44%), Gaps = 37/300 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------HGDLS--------A 49
           +  Y++ I +  +L  ++E  LAKR                       DL         A
Sbjct: 37  VRAYLNGIGRTKLLTAEQEVELAKRIEAGLFAEEKLATCTPVSTVLRADLEIIVAEGRTA 96

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+ ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI
Sbjct: 97  KDHLLEANLRLVVSIAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWI 156

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + A+   +      ++I     +      + R+    + +     +   V  +A+ ++V 
Sbjct: 157 RQAITRAMADQARTIRIPVHMVE-----QVNRMVRARRELAVTLGREPTVAEVARAMDVP 211

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E +VI +        SL+  +   +   S   D++       E            RN + 
Sbjct: 212 EFQVIELISYDREPVSLDQAV--GEDGESALGDFVAAVDPAAE--PGATAVDGELRNEVR 267

Query: 230 RSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             ++ L+ RE+ +   R   ++    TL+ +  EF +SRER+RQIE     K++   + Q
Sbjct: 268 IVLATLSQREQAVIRLRFGLDDGRQRTLDEVGREFGLSRERIRQIEKVTLLKLRAPERAQ 327


>gi|332140079|ref|YP_004425817.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Alteromonas macleodii str.
           'Deep ecotype']
 gi|332143123|ref|YP_004428861.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Alteromonas macleodii str.
           'Deep ecotype']
 gi|327550101|gb|AEA96819.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Alteromonas macleodii str.
           'Deep ecotype']
 gi|327553145|gb|AEA99863.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Alteromonas macleodii str.
           'Deep ecotype']
          Length = 330

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 79/271 (29%), Positives = 135/271 (49%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    G  ++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 59  YLGEIGFSPLLTAEEEVYFARR-SLKGCEASRKRMIVSNLRLVVKIARRYNNRGLALLDL 117

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++       +    
Sbjct: 118 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV--VKELNV 175

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
             R    L    D+    E    IA  L+    +V  M        S++  I    +N  
Sbjct: 176 YLRASRELSQKLDHEPTAE---EIAAALDKPVEDVTKMLRLNERITSVDTPI--GGENDK 230

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
              D +  +    E    E  +  + ++ +   +  LNP++R +   R       P TLE
Sbjct: 231 ALLDIIADEK---EFSPEESLQDSDIKSNIITWLEELNPKQREVLARRFGLMGYEPSTLE 287

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++ +E  ++RERVRQI+  A +++++ +  Q
Sbjct: 288 DVGAEIGLTRERVRQIQVEALRRLRDMLGHQ 318


>gi|124267677|ref|YP_001021681.1| putative 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 =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 116/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 501 EKASRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 560

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    +              +
Sbjct: 561 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKMNRLSRQHLQEFGFEPDAPTL 615

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+ + E ++  +        S+   I   D + S   D++    D      IE   + 
Sbjct: 616 AEKMEMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNNTAPIEAAMQA 670

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 671 GLRDVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKAIRKL 730

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 731 KHPSRSD 737


>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 =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 66/253 (26%), Positives = 118/253 (46%), Gaps = 12/253 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 378 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 437

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 438 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPLPE--- 492

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + E ++  +        S+   I   D   S   D++    D   ++ ++   
Sbjct: 493 ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDTTLELPLDSAT 547

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
             + +      ++ L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 548 ATSLKAATKDVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 607

Query: 279 KVQESIQKQVELS 291
           K++   + +   S
Sbjct: 608 KLRHPSRSETLRS 620


>gi|319790059|ref|YP_004151692.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermovibrio
           ammonificans HB-1]
 gi|317114561|gb|ADU97051.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermovibrio
           ammonificans HB-1]
          Length = 318

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 79/285 (27%), Positives = 150/285 (52%), Gaps = 14/285 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V  +  L  ++  I KIP+L ++EE  LAKR +  GD  A  +LV S+LR VV +A  Y 
Sbjct: 43  VPDKDSLDAFLKSISKIPLLSREEEIELAKRAK-AGDKEALKKLVESNLRFVVSVAKKYL 101

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G GLP+ ++++EG +GL++A ++FDP++G +  +Y++WWI+ ++ + + +    VKI   
Sbjct: 102 GCGLPLHDLIAEGILGLIEAARRFDPDKGVKFISYAVWWIRQSIMQALAQQTGAVKIPVK 161

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
                    + ++      +     +   +  +A  + +   EV  +        SL+  
Sbjct: 162 QA-----VLVNKITRSYGELLKKLGREPTIEELADYVGMEPKEVERLLSICQVPLSLDTP 216

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   D+  + ++D+L  +   + +  + +EE K     +   +  L P+E++I   R   
Sbjct: 217 I--GDEEDTTFKDFLKGEGTAEVEEKVVQEELKQS---IQEMLEQLTPQEKKIIIMRFGL 271

Query: 250 E--NPVTLENLSSEFEVSRERVRQIEARAFKKVQE-SIQKQVELS 291
           +   P TL  +  +  +SRERVRQ+E RA KK++E +++K++ + 
Sbjct: 272 DGNEPKTLREIGEKLGISRERVRQLETRAKKKMKEYALRKKLNVF 316


>gi|327313374|ref|YP_004328811.1| putative RNA polymerase sigma factor RpoD [Prevotella denticola
           F0289]
 gi|326944913|gb|AEA20798.1| putative RNA polymerase sigma factor RpoD [Prevotella denticola
           F0289]
          Length = 327

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 78/287 (27%), Positives = 147/287 (51%), Gaps = 12/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI    M+  +EE  LA+R R+ GD  A  RL  ++LR VV
Sbjct: 45  KITKSITNRESASLDKYLQEIGHEEMISIEEEVELAQRIRK-GDRKALERLTKANLRFVV 103

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + I     
Sbjct: 104 SVAKQYQNQGLSLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSR 163

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           ++++    NQ      + ++   L      N +   +  IA+  ++ E ++       + 
Sbjct: 164 IIRLP--LNQVSSVNKINKI---LNQFEQENERRPSIGEIAQSTDIPEEKIADAIKVSSR 218

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     D + S   D +  D+       + +E     R  + R + VL  RE+++
Sbjct: 219 HVSVDAPFY--DDDQSSLLDVIPNDNVPSTDRGLVEESL---REEIGRVLQVLEDREKKV 273

Query: 243 FEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            EA        +TLE + S++ ++RERVRQI+ +A +++++    +V
Sbjct: 274 VEAYFGINQREMTLEEIGSKYNLTRERVRQIKEKAIRRLRQQTNSKV 320


>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 =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 73/283 (25%), Positives = 130/283 (45%), Gaps = 24/283 (8%)

Query: 21  HEIRKIPMLEKQEEYVL--------AKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
             I K+ M+  +EE  L        ++R    E     A   +V ++LRLV+ IA  Y  
Sbjct: 300 RSIAKLKMI--EEETSLNVQNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTN 357

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I    
Sbjct: 358 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 417

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
                   L R+   +         PE    +A+++ + E ++  +        S+   I
Sbjct: 418 --IETINKLNRISRQMLQEMGREPLPE---ELAERMQMPEDKIRKVLKIAKEPISMETPI 472

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
              D   S   D++    D   ++ ++     + +      ++ L PRE ++   R   +
Sbjct: 473 --GDDEDSHLGDFI---EDTTLELPLDSATATSLKVATKDVLAGLTPREAKVLRMRFGID 527

Query: 251 --NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
                TLE +  +F+V+RER+RQIEA+A +K++   + +   S
Sbjct: 528 MNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRS 570


>gi|88798286|ref|ZP_01113872.1| RNA polymerase sigma factor RpoS [Reinekea sp. MED297]
 gi|88779062|gb|EAR10251.1| RNA polymerase sigma factor RpoS [Reinekea sp. MED297]
          Length = 344

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 80/277 (28%), Positives = 148/277 (53%), Gaps = 13/277 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A+  R+ G+ +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 75  YLNEIGFSPLLSPEEEVYFARLARK-GEPAGRKRMIESNLRLVVKIARRYLNRGLTLLDL 133

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 134 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 192

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +  L    D+   PE +  + +K      +++++N R+    S++  I  S + S 
Sbjct: 193 LRAAR-ELAQKLDHEPTPEDIAQLLEKPVEDVKKMLALNERVT---SIDTPIGPSSEKS- 247

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
                L    D +     +  +  + +  + R +  L+ ++R +   R         TLE
Sbjct: 248 ----LLETISDDRASDPSDTLQDDDLKASIDRWLDELSEKQREVVARRFGLRGYETSTLE 303

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           ++  E  ++RERVRQI+  + +++++ ++KQ   S++
Sbjct: 304 DVGREIGLTRERVRQIQVESLRRLRDIMEKQGLTSTA 340


>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|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]
          Length = 595

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 128/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +  I +   L  +    +++R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 326 LQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 385

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 386 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 443

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 444 KLNRISRQMLQEMGREPLPE---ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDED 498

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++     + +      ++ L PRE ++   R   +     TL
Sbjct: 499 SHLGDFI---EDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTL 555

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 556 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 591


>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 =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 68/263 (25%), Positives = 120/263 (45%), Gaps = 14/263 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L   E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 355 LSLAEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 414

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 415 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 472

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    + +++ + E ++  +        S+   I   D   S   D++  
Sbjct: 473 LQEMGREPTPE---ELGERMEMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 525

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q  I+    ++ +      ++ L  RE ++   R   +     TLE +  +F+V
Sbjct: 526 -EDSTMQSPIDVATVESLKEATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 584

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   + +
Sbjct: 585 TRERIRQIEAKALRKLRHPTRSE 607


>gi|50262051|gb|AAT72766.1| putative sigma factor 32 [Dichelobacter nodosus]
          Length = 283

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 104/271 (38%), Positives = 174/271 (64%), Gaps = 7/271 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           + +YI ++R+IP+L+  EE+ LA   +++  L+AA  L+  HL+ VV IA G+ GYGLP+
Sbjct: 13  IDQYIAKVRQIPILDADEEFRLATELQQNHSLAAAQTLIVHHLKFVVHIARGFLGYGLPL 72

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AVK+F+P+RG RL ++++ WIK+ + EY++R+W LVKI TT  Q++L
Sbjct: 73  GDLIQEGNIGLMKAVKRFEPQRGVRLVSFAVHWIKSEIHEYVIRNWRLVKIATTKAQRKL 132

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR +K ++  ++D      +   IA+ LNVS  +V+ M  R+ G D + + L  + D
Sbjct: 133 FFNLRSMKKNMHWLSD-----AEAQTIAEDLNVSVKDVLEMESRIHGQDIAFDPLDENDD 187

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE-NPV 253
           + +     WL  +           E++   ++ LT+ ++ L+ R R I E+R L E   V
Sbjct: 188 EENVAPAAWLTDESVDPALSTEHHEQKHLLQHQLTQGLNQLDARSREIIESRWLNEHEKV 247

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           TL+ L+S++ +S ER+RQIE +A  +++ S+
Sbjct: 248 TLQTLASKYHISAERIRQIEQQALLQLKNSM 278


>gi|329848685|ref|ZP_08263713.1| RNA polymerase sigma factor rpoD [Asticcacaulis biprosthecum C19]
 gi|328843748|gb|EGF93317.1| RNA polymerase sigma factor rpoD [Asticcacaulis biprosthecum C19]
          Length = 699

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 70/249 (28%), Positives = 119/249 (47%), Gaps = 15/249 (6%)

Query: 43  EHGDLSAAH---RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG+
Sbjct: 452 QKGEREARQAKTEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 511

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWI+ A+   I      ++I        +   + ++    + +     +    
Sbjct: 512 KFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREPTP 566

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +A+KL +   +V  +        SL   I   D+  S   D++    D    + I+  
Sbjct: 567 EELAEKLAMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAVLPIDAA 621

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAF 277
            + N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A 
Sbjct: 622 IQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKAL 681

Query: 278 KKVQESIQK 286
           +K++   + 
Sbjct: 682 RKLKHPSRS 690


>gi|284049111|ref|YP_003399450.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidaminococcus
           fermentans DSM 20731]
 gi|283953332|gb|ADB48135.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidaminococcus
           fermentans DSM 20731]
          Length = 589

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 76/255 (29%), Positives = 122/255 (47%), Gaps = 14/255 (5%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L  R    GD +A   L  ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD 
Sbjct: 339 RLLHRMEFCGD-NAKKCLSEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDY 397

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            +GF+ +TY+ WWI+ A+   I      ++I     +      L R+   L         
Sbjct: 398 NKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE--TINKLVRVSRQLLQELGREPT 455

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
           PE    IAK+++VS   V  +        SL   I   ++  S   D++    D +    
Sbjct: 456 PE---EIAKEMDVSVERVREIQKIAQEPVSLETPI--GEEEDSHLGDFI---EDQEAPSP 507

Query: 216 IEKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQI 272
            +       +  L + +   L+ RERR+ E R    +    TLE +   F V+RER+RQI
Sbjct: 508 ADAASYTLLQEQLGKVLQEHLSARERRVLELRFGLMDGRTRTLEEVGQYFGVTRERIRQI 567

Query: 273 EARAFKKVQESIQKQ 287
           EA+A +K++   + +
Sbjct: 568 EAKALRKLRSPKRSK 582



 Score = 37.1 bits (85), Expect = 3.0,   Method: Composition-based stats.
 Identities = 11/37 (29%), Positives = 19/37 (51%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSA 49
           +  +  Y+ EI ++P+L   +E  LAKR  +     A
Sbjct: 157 DDPVRMYLKEIGRVPLLAGDDEIKLAKRADKGNQAKA 193


>gi|24372864|ref|NP_716906.1| RNA polymerase sigma-70 factor [Shewanella oneidensis MR-1]
 gi|24346976|gb|AAN54351.1|AE015572_6 RNA polymerase sigma-70 factor [Shewanella oneidensis MR-1]
          Length = 616

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 64/250 (25%), Positives = 119/250 (47%), Gaps = 12/250 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 370 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 430 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPSPE--- 484

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + E ++  +        S+   I   D   S   D++    D   ++ ++   
Sbjct: 485 ELAERMMMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDTTLELPLDSAT 539

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            ++ ++     ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 540 SESLKSATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 279 KVQESIQKQV 288
           K++   + ++
Sbjct: 600 KLRHPSRSEI 609


>gi|260435157|ref|ZP_05789127.1| RNA polymerase sigma factor RpoD [Synechococcus sp. WH 8109]
 gi|260413031|gb|EEX06327.1| RNA polymerase sigma factor RpoD [Synechococcus sp. WH 8109]
          Length = 458

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 77/313 (24%), Positives = 143/313 (45%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE--------------HG------------ 45
            E  +  Y+ EI +I +L   EE  LA++  +              +G            
Sbjct: 146 TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLYLEELAAQFESDNGREPDNKEWAALV 205

Query: 46  -------------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 206 EMPLIRFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 265

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 266 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKVLSQE 320

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA+ + ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 321 FGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADIENPE 378

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
           Q + +   R++    L   ++ L+PRER +   R   ++    TLE +   F+V+RER+R
Sbjct: 379 QDVAKNLLRED----LEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIR 434

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 435 QIEAKALRKLRHP 447


>gi|333030005|ref|ZP_08458066.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacteroides
           coprosuis DSM 18011]
 gi|332740602|gb|EGJ71084.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacteroides
           coprosuis DSM 18011]
          Length = 286

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 73/287 (25%), Positives = 143/287 (49%), Gaps = 12/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI +  ++  +EE  LA+R ++ GD  A  +L  ++LR VV
Sbjct: 5   KITKSITNRESASLDKYLQEIGREDLITVEEEVELAQRIKK-GDRVALEKLTKANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 64  SVAKQYQNQGLSLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    NQ      + +     +   +    P     +A +L +   +V         
Sbjct: 124 IVRLP--LNQVGSLNKISKAFAKFEQEYERRPSP---QELADELEMPVDKVTDTLKVSGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     + NS    D LV D        +  E        + R++S L  RE++I
Sbjct: 179 HISVDAPFVEGEDNS--LLDVLVNDDSPMADRSLVNESLS---EEIDRALSTLEDREKQI 233

Query: 243 FEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +         +TLE +  +F ++RERVRQI+ +A ++++++ + ++
Sbjct: 234 IKMFFGIGCQEMTLEEIGDKFGLTRERVRQIKEKAIRRLRQNNRSKL 280


>gi|297170837|gb|ADI21856.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [uncultured verrucomicrobium HF0130_25O04]
          Length = 303

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 72/278 (25%), Positives = 143/278 (51%), Gaps = 13/278 (4%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           + +  L  Y+ +I  +P+L  +EE  LA R + +GD  A   ++T++LRLVVKIA  Y  
Sbjct: 4   DEQESLDIYLRQISTVPLLTVEEEIELASRIK-NGDEKARETMITANLRLVVKIAKEYSN 62

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            GL + ++++EGNIGLM+AV++FDP +G +L+TY  WWIK A++  +      +++    
Sbjct: 63  IGLSLLDLINEGNIGLMKAVERFDPSKGGKLSTYGAWWIKQAIKRALANQSKTIRLPVHM 122

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
             +       +++     + +   +      +A ++N+  + +  +        SL++ +
Sbjct: 123 VDRVT-----QIRRTSVQLAEKLGREPTDEELAAEMNLPVARITLLKSVSRKPASLDSPL 177

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
              + + S   + +  +         E  + K+    +   ++ L PRE  I   R   E
Sbjct: 178 --GENDGSTLGEMVADEKSAN---PYEHLQSKSLVGDVNSVLAQLEPREADIIRLRFGLE 232

Query: 251 --NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              P+TLE +  +  V+RERVRQ++ +A +++++++  
Sbjct: 233 GLEPLTLEEVGEKIGVTRERVRQLQEQALRQLRKNMAS 270


>gi|127512145|ref|YP_001093342.1| RpoD family RNA polymerase sigma factor [Shewanella loihica PV-4]
 gi|126637440|gb|ABO23083.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella loihica
           PV-4]
          Length = 324

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 80/271 (29%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   +++  + G   + +R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 55  YLSEIGFSPLLSAEEEVYFSRKALK-GCEKSRNRMIESNLRLVVKIARRYNNRGLALLDL 113

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 114 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 172

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            IA++L++  S+V  M        S++  +     N  
Sbjct: 173 LRTAR----ELAHKLDHEPTAEEIAEQLDLPSSDVSKMLKLNERITSVDTPL--GGDNDK 226

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  D        ++ ++       + R +  LN ++R +   R   L   P TLE
Sbjct: 227 ALLDVLADDDCVGPDYKVQDDDMS---KSVVRWLDELNSKQREVLARRFGLLGYEPSTLE 283

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           N+  E  ++RERVRQI+  A K++++ +  Q
Sbjct: 284 NVGKEIGLTRERVRQIQVEALKRLRDLLSAQ 314


>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 =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 72/269 (26%), Positives = 121/269 (44%), Gaps = 23/269 (8%)

Query: 32  QEEYVLA---------KRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           +EE VL          +R    E     A   +V ++LRLV+ IA  Y   GL   +++ 
Sbjct: 348 EEEMVLLPVSHIKEVNRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 407

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L 
Sbjct: 408 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLN 465

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
           R+   +         PE    + ++L + E +V  +        S+   I   D + S  
Sbjct: 466 RVSRQMLQEMGREPTPE---ELGERLEMPEDKVRKVLKIAKEPISMETPI--GDDDDSHL 520

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENL 258
            D++    DG   + I+    +         +  L  RE ++   R   +     TLE +
Sbjct: 521 GDFI---EDGTMLLPIDSATGEGLIEATRNVLGGLTAREAKVLRMRFGIDMNTDHTLEEV 577

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             +F+V+RER+RQIEA+A +K++   + +
Sbjct: 578 GKQFDVTRERIRQIEAKALRKLRHPSRSE 606


>gi|305664513|ref|YP_003860800.1| putative sigma factor A [Maribacter sp. HTCC2170]
 gi|88708530|gb|EAR00766.1| putative sigma factor A [Maribacter sp. HTCC2170]
          Length = 287

 Score =  226 bits (576), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 144/276 (52%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI K+ ++   EE  LA+R +  GD  A  +L  ++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQEIGKVDLITADEEVELAQRIK-AGDQIALEKLTKANLRFVVSVAKQYQNQGLT 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     +V++    N+  
Sbjct: 76  LPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLP--LNKIG 133

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               + +    L+   +     E    IAK+L+++  +V           S++A + + +
Sbjct: 134 SINKINKTFAFLEQAHERMPSAE---EIAKELDMTVEDVKQSLKNSGRHVSMDAPLIAGE 190

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENP 252
              S   D L     G+      +   ++ R  + R++  L PRE  +         ++ 
Sbjct: 191 D--SNLYDVL---RSGESPNPDRELLHESLRTEIERALETLTPREADVIRLYFGLAGQHS 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 246 MTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|297180174|gb|ADI16396.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [uncultured bacterium HF130_12L15]
          Length = 288

 Score =  225 bits (575), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 115/278 (41%), Positives = 181/278 (65%), Gaps = 1/278 (0%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           +N E   S  I   RK P L++ EE+ LA R+R+  D  A HR+  +H+RLV+ +A  +R
Sbjct: 1   MNAEPAGSSMISAARKAPYLDRVEEHDLAVRWRDDRDQEALHRITMAHMRLVISMAGKFR 60

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
            +GLP+S++V EG++GL++A  +F+PER  R +TY+ WWI+A+MQ++ILR+WS+V+ GT+
Sbjct: 61  YFGLPMSDLVQEGHVGLLEAAARFEPERDVRFSTYATWWIRASMQDHILRNWSIVRGGTS 120

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNA 188
           + QK LFFNLRRL+  L   T+          IA  + VS ++V  M+ RL+G D SLNA
Sbjct: 121 SAQKALFFNLRRLRARLAQGTEPLKGAAVYQEIADAIGVSVADVALMDSRLSGPDSSLNA 180

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +    +++S+  D+LV +    ++V+    + + R   L R++ VLN RE RI   RRL
Sbjct: 181 PVADGGESTSERMDFLVSEDPTPDEVVSASIDDERRTMWLNRALGVLNDRELRIIRERRL 240

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ++   TLE+L ++  +S+ERVRQIE RA +K++ ++ K
Sbjct: 241 RDEGATLESLGAKLGISKERVRQIENRALEKLRSALLK 278


>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 =  225 bits (575), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 72/263 (27%), Positives = 123/263 (46%), Gaps = 14/263 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L   E   + ++    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 359 LSISEIKEINRKMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 418

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 419 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQI 476

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
              T     PE    +A+K+ +SE ++  +        S+   +   D + S   D++  
Sbjct: 477 LQETGREATPE---ELAEKMELSEDKIRKVLKIAKEPISMETPV--GDDDDSHLGDFI-- 529

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   +  I+    +  R      +  L PRE ++   R   E     TLE +  +F+V
Sbjct: 530 -EDNNIESPIDMATAEGLREATLEILETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDV 588

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   + +
Sbjct: 589 TRERIRQIEAKALRKLRHPSRSE 611


>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 =  225 bits (575), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 70/263 (26%), Positives = 120/263 (45%), Gaps = 14/263 (5%)

Query: 29  LEKQE--EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L   E  E   A    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 357 LTVAEIKEINRAMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 416

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 417 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 474

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    + +++++ E ++  +        S+   I   D   S   D++  
Sbjct: 475 LQEMGREPNPE---ELGERMDMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 527

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q  IE    ++ +      ++ L  RE ++   R   +     TLE +  +F+V
Sbjct: 528 -EDSTMQSPIEMATSESLKESTREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 586

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   + +
Sbjct: 587 TRERIRQIEAKALRKLRHPSRSE 609


>gi|330968927|gb|EGH68993.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. aceris
           str. M302273PT]
          Length = 335

 Score =  225 bits (575), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 84/278 (30%), Positives = 143/278 (51%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + +K       ++ +N R++  D SL         + 
Sbjct: 185 LRAARELTQKL-DHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSL------GPDSD 237

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + +S L  ++R +   R         TL
Sbjct: 238 KTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTEKQREVVIRRFGLRGHESSTL 294

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 295 EDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSSES 332


>gi|318040855|ref|ZP_07972811.1| RNA polymerase sigma factor, sigma-70 family protein [Synechococcus
           sp. CB0101]
          Length = 321

 Score =  225 bits (575), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 81/290 (27%), Positives = 142/290 (48%), Gaps = 31/290 (10%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLA--------------------KRYREHGDLSAAHRL 53
             +  Y+  I ++P+L   EE  LA                    ++++      A  R+
Sbjct: 32  DSIGWYLSNIGRVPLLTAAEEIELAHHVQLMKQLQELPSDQLTPRQKHQIRMGCRARDRM 91

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           + ++LRLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+  M
Sbjct: 92  MAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGM 151

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
              I  S   +++    ++K     L +++   + ++    +    + +A  + +   E+
Sbjct: 152 TRAIDNSARTIRLPIHVSEK-----LSKMRRITRELSHRFGRQPNRLELAHAMGMQPEEL 206

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             +  + A   SL+A     D  S+  +  L+ D +  E   ++  +R  ++  L   +S
Sbjct: 207 EDLISQSAPCASLDAHARGDDDRSTLGE--LIADPNSNES--MDSMDRNLQKEHLGTWLS 262

Query: 234 VLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            LN RERRI E R   E   P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 263 QLNERERRIIELRFGLEGQEPLTLAEIGRQINVSRERVRQLEAKAILKLR 312


>gi|255034849|ref|YP_003085470.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dyadobacter
           fermentans DSM 18053]
 gi|254947605|gb|ACT92305.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dyadobacter
           fermentans DSM 18053]
          Length = 287

 Score =  225 bits (575), Expect = 4e-57,   Method: Composition-based stats.
 Identities = 74/288 (25%), Positives = 143/288 (49%), Gaps = 13/288 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           + +  I       L +Y+ EI K+ +L   EE  LA++ R+ GD  A  RL  ++LR VV
Sbjct: 5   KISKQITNRESQSLDKYLQEIGKVDLLTPDEEVTLAQKIRD-GDQLALERLTKANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 64  SVAKQYQNQGLSLGDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++           +L ++      +     +      +A+ L +S SEV+        
Sbjct: 124 IVRLPLNR-----VGSLNKISKTFSELEQRFEREPSPEELAEVLEISSSEVVDTMKISGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     ++NS    D L  D + +    +  E     R  + R++  L  RE  +
Sbjct: 179 HVSMDAPFVQGEENS--LLDVLENDLEDKPDSGLVNESL---RKEVQRALCTLTQREADV 233

Query: 243 FEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
                    E+ +TLE +  +F ++RERVRQI+ +A ++++   + + 
Sbjct: 234 IALYFGLNGEHAMTLEEIGEKFNLTRERVRQIKEKAIRRLRHVSRSKA 281


>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 =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 69/272 (25%), Positives = 128/272 (47%), Gaps = 14/272 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +  I++   L   E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 339 LAAIQEATGLAVSEVKEINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 398

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +  
Sbjct: 399 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIE 453

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + +L    + +     +  Q   +A+++ + E +V  +        S+   I   D   
Sbjct: 454 TINKLNRTSRQMLQEMGREPQPDELAERMEMPEDKVRKVLKIAKEPISMETPI--GDDED 511

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D      ++   R+  +  +   ++ L PRE ++   R   +     TL
Sbjct: 512 SHLGDFI---EDAAVMSPVDSATREGLKESVREVLAGLTPREAKVLRMRFGIDMNTDHTL 568

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 569 EEVGKQFDVTRERIRQIEAKALRKLRHPTRSE 600


>gi|325849230|ref|ZP_08170681.1| RNA polymerase sigma factor RpoD [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
 gi|325480230|gb|EGC83297.1| RNA polymerase sigma factor RpoD [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
          Length = 612

 Score =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 72/261 (27%), Positives = 124/261 (47%), Gaps = 14/261 (5%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           +  +   L +   +     A  +L  ++LRLVV IA  Y G G+   +++ EGN+GLM+A
Sbjct: 359 DADDVKRLNRAIFDAN--RAKQKLAETNLRLVVSIAKKYVGRGMSFLDLIQEGNMGLMKA 416

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V K+D  RGF+ +TY+ WWI+ A+   I      ++I     +      L R++  L   
Sbjct: 417 VDKYDYNRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE--TINKLVRIQRQLVQD 474

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
              +   E    IA+++ +   +V  +        SL   I   ++  S   D++  D  
Sbjct: 475 LGRDPSNE---EIAEQMGIEVEKVQEIRKIAQEPVSLETPI--GEEEDSHLGDFIEDDTA 529

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRE 267
                  +       R+ L   +S L  RE+R+ + R       P TLE +  EF+V+RE
Sbjct: 530 INPD---DAANYSMLRDQLNDVLSCLGAREKRVLQLRFGLIDGTPRTLEEVGKEFDVTRE 586

Query: 268 RVRQIEARAFKKVQESIQKQV 288
           R+RQIEA+A +K++   + ++
Sbjct: 587 RIRQIEAKALRKLKSPNKSEL 607



 Score = 39.8 bits (92), Expect = 0.46,   Method: Composition-based stats.
 Identities = 13/40 (32%), Positives = 23/40 (57%), Gaps = 1/40 (2%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHR 52
           +  +  Y+ EI K+ +L+  EE  LAK+  E GD++   +
Sbjct: 126 DDPVKMYLKEIGKVKLLDAHEEIFLAKKM-ELGDIALRSK 164


>gi|147674012|ref|YP_001216017.1| 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 =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 127/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +  I +   L  +    ++ R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 352 LQMIEQETSLSVERIKDISHRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 411

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 412 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 469

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 470 KLNRISRQMLQEMGREPLPE---ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDED 524

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++     + +      ++ L PRE ++   R   +     TL
Sbjct: 525 SHLGDFI---EDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTL 581

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 582 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 617


>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 =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 63/247 (25%), Positives = 115/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 556 EASSRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 615

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    +              +
Sbjct: 616 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKMNRISRQHLQEFGFEPDASIL 670

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A K+ + E ++  +        S+   I   D + S   D++    D      ++   + 
Sbjct: 671 AAKMEIPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDSSNTAPVDAAMQA 725

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 726 GLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKL 785

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 786 KHPSRSD 792


>gi|72383848|ref|YP_293202.1| sigma-70 region 1.2 [Ralstonia eutropha JMP134]
 gi|72123191|gb|AAZ65345.1| Sigma-70 region 1.2 [Ralstonia eutropha JMP134]
          Length = 624

 Score =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 64/243 (26%), Positives = 117/243 (48%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLV+ IA  Y   G+   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 384 RQAKRELIEANLRLVISIAKKYVNRGMHFLDLIQEGNIGLMKAVDKFEYRRGWKFSTYAT 443

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WW++ A+   +      +++     +  +   L R+    +  T     P     +A+++
Sbjct: 444 WWVRQAVTRALADQARTIRVPVHMVE--MINKLNRISRDFRQQTGREAHP---AVLAERM 498

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +SE +V S+        SL   +   D   +   D +    D       E     + R 
Sbjct: 499 EMSEEKVRSILRSARQPVSLETPV--GDDADATLGDMI---EDVSASSPAEAAIHADMRA 553

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  ++  L+PRE ++   R   +     TLE +S +F+V+RER+RQIE++A +K+    
Sbjct: 554 AIDEALDGLSPREAKVLRMRFGLDTTSDRTLEEVSKQFDVTRERIRQIESQAMRKLLHPS 613

Query: 285 QKQ 287
           +  
Sbjct: 614 RAD 616


>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 =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 69/263 (26%), Positives = 122/263 (46%), Gaps = 14/263 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           +  +E   + K+    E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 383 ISAKELKEINKQMTTGEARARRAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 442

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RGF+ +TY+ WWI+ A+   I      ++I            + R+   +
Sbjct: 443 MKAVDKFEYRRGFKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQI 500

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
              T     P     +A+K+ + E ++  +        S+   I   D   S   D++  
Sbjct: 501 LQETGIEPDP---ALLAEKMEMPEDKIRKILKISKEPISMETPI--GDDEDSHLGDFI-- 553

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D      ++     + R+  +  +  L PRE ++   R   E     TLE +  +F+V
Sbjct: 554 -EDSTTLAPVDAAVYASLRDATSEVLESLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDV 612

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   + +
Sbjct: 613 TRERIRQIEAKALRKLRHPTRSE 635


>gi|126695861|ref|YP_001090747.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str. MIT
           9301]
 gi|126542904|gb|ABO17146.1| Putative principal RNA polymerase sigma factor [Prochlorococcus
           marinus str. MIT 9301]
          Length = 394

 Score =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 76/313 (24%), Positives = 139/313 (44%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------------- 43
            E  +  Y+ EI +I +L   EE  LA++  +                            
Sbjct: 82  TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLQLEELATQYESEKGHFPSVREWAELI 141

Query: 44  -----------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 142 DMPLPKFRRRLLLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 201

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 202 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKVLSQE 256

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA+ + ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 257 FGRKPSEEEIAESMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADIENPE 314

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
           Q +     +   R  L   ++ L+PRER +   R   ++    TLE +   F+V+RER+R
Sbjct: 315 QDV----SKTLLREDLEGVLATLSPRERDVLRLRYGIDDGRMKTLEEIGQIFDVTRERIR 370

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 371 QIEAKALRKLRHP 383


>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 =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 63/247 (25%), Positives = 115/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 552 EASSRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 611

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    +              +
Sbjct: 612 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKMNRISRQHLQEFGFEPDASIL 666

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A K+ + E ++  +        S+   I   D + S   D++    D      ++   + 
Sbjct: 667 AAKMEIPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDSNNTAPVDAAMQA 721

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 722 GLRDVVKDILDGLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKL 781

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 782 KHPSRSD 788


>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 =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 115/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 389 EAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 448

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   L         PE    +
Sbjct: 449 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKINRVSRQLLQEMGREPTPE---EL 503

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
            ++L + E +V  +        S+   I   D   S   D++    D      +++   +
Sbjct: 504 GERLEMDEVKVRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDSSISSPVDEATAQ 558

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             +      ++ L  RE ++ + R   +     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 559 GLKEATREVLANLTEREAKVLKMRFGIDMSTDHTLEEVGKQFDVTRERIRQIEAKALRKL 618

Query: 281 QESIQKQ 287
           +   + +
Sbjct: 619 RHPSRSE 625


>gi|21672319|ref|NP_660386.1| RNA polymerase factor sigma-32 [Buchnera aphidicola str. Sg
           (Schizaphis graminum)]
 gi|25091196|sp|Q8KA76|RP32_BUCAP RecName: Full=RNA polymerase sigma-32 factor
 gi|21622919|gb|AAM67597.1| RNA polymerase sigma-32 factor [Buchnera aphidicola str. Sg
           (Schizaphis graminum)]
          Length = 285

 Score =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 101/289 (34%), Positives = 160/289 (55%), Gaps = 9/289 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  K   + V     L  YI      PML  +EE +L KR R H DL AA  L+ SHLR 
Sbjct: 1   MTNKVQILSVTALGNLDAYIRIANLWPMLSIKEEKLLTKRLRYHDDLDAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ I+  Y GYGL  ++++ EGNIGLM+AV++F+P+ G RL ++++ WIK+ + EY+LR+
Sbjct: 61  VIHISRNYSGYGLLQADLIQEGNIGLMKAVRRFNPDIGVRLVSFAVHWIKSEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT +Q++LFFNLR+ K  L          E++  +A++L VS  +V  M  R+
Sbjct: 121 WRIVKVATTKSQRKLFFNLRKNKKRLGWFNQ-----EEIEIVARELGVSSEDVREMESRM 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEERKNRRNMLTRSMSVLNP 237
           +  +         D    +    + Y  D        L +    K+  + L+ ++  L+ 
Sbjct: 176 SAQDITFNPFPEEDLKDGKINGNMFYLQDKTSNFANGLEQDNWNKHTTSKLSNALLRLDE 235

Query: 238 RERRIFEARRLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           R R I  AR L +    TL+ +++ + +S ERVRQ+E  A KK++ +I+
Sbjct: 236 RSRNIIRARWLDKKEKNTLQKIANNYGISAERVRQLEKNAMKKLKIAIE 284


>gi|291279867|ref|YP_003496702.1| DNA-directed RNA polymerase sigma 70 factor [Deferribacter
           desulfuricans SSM1]
 gi|290754569|dbj|BAI80946.1| DNA-directed RNA polymerase sigma 70 factor [Deferribacter
           desulfuricans SSM1]
          Length = 598

 Score =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 62/244 (25%), Positives = 117/244 (47%), Gaps = 12/244 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV+KF+  RG++ +TY+ 
Sbjct: 359 EKAKSELIEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVEKFEYRRGYKFSTYAT 418

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ ++   I      ++I        +   + ++   ++ +     K      IA+++
Sbjct: 419 WWIRQSITRAIADQARTIRIPVH-----MIETINKMIRTIRQLQIELGKEPTPEEIAERM 473

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   +V  +        SL   I   +   S   D++    D   +  +++   +  + 
Sbjct: 474 DIPVEKVKKVLKIAKEPVSLETPI--GEDEDSSLGDFI---EDQSAKNPLDEVVYEKLKE 528

Query: 227 MLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                +  L PRE  +   R     ++  TLE +   F V+RER+RQIEA+A +K++   
Sbjct: 529 HTRAILDTLTPREASVLRLRFGIDCDSDHTLEEVGRRFNVTRERIRQIEAKALRKLRHPT 588

Query: 285 QKQV 288
           + ++
Sbjct: 589 RSRI 592



 Score = 42.5 bits (99), Expect = 0.084,   Method: Composition-based stats.
 Identities = 17/74 (22%), Positives = 33/74 (44%), Gaps = 1/74 (1%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVT-SHLRLVVKIAMGY 68
           +  +  +  Y+ E+  IP+L ++EE  +AKR  E         L+  S    ++ +A   
Sbjct: 93  IGVDDPVRLYLREMGNIPLLSREEEVEVAKRIEEGQKKVIRSVLLFPSTASEIMSLAEKI 152

Query: 69  RGYGLPISEVVSEG 82
               L I +++  G
Sbjct: 153 NEGTLRIKDIIDIG 166


>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 =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 67/273 (24%), Positives = 124/273 (45%), Gaps = 14/273 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +  + +   L  +    + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 345 LRNMEQTTGLSVERIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 404

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 405 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 462

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 463 KLNRISRQMLQEMGREPNPE---ELAERMMMPEDKIRKVLKIAKEPISMETPI--GDDED 517

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   +  I+    ++ +      ++ L  RE ++   R   +     TL
Sbjct: 518 SHLGDFI---EDSTIESPIDSATMESLKGATHEVLAGLTAREAKVLRMRFGIDMNTDHTL 574

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           E +  +F+V+RER+RQIEA+A +K++   +  +
Sbjct: 575 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSDL 607


>gi|256830224|ref|YP_003158952.1| RpoD subfamily RNA polymerase sigma-70 subunit [Desulfomicrobium
           baculatum DSM 4028]
 gi|256579400|gb|ACU90536.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfomicrobium
           baculatum DSM 4028]
          Length = 588

 Score =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 74/257 (28%), Positives = 120/257 (46%), Gaps = 12/257 (4%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE +   R      L A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV K
Sbjct: 334 EEILWRIRKGNTDALDAKQELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 393

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RG++ +TY+ WWI+ A+   I      ++I            L R   +L      
Sbjct: 394 FEYQRGYKFSTYATWWIRQAITRAIADQARTIRIPVHM--IETINKLVRTSRYLVQELGR 451

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +  PE    IA++++    +V  +        SL   I   D+  S   D++    D + 
Sbjct: 452 DPSPE---EIAERMDYPLEKVKKVLKIAKEPISLETPI--GDEEDSSLGDFI---EDKKA 503

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
               ++         + + +S L PRE ++   R         TLE +   F V+RER+R
Sbjct: 504 VAPADEVVNTKLAEQIAQVLSDLTPREEQVLRKRFGIGEKSDHTLEEVGKLFNVTRERIR 563

Query: 271 QIEARAFKKVQESIQKQ 287
           QIEA+A +K++  ++ Q
Sbjct: 564 QIEAKALRKLRHPVRSQ 580


>gi|182680201|ref|YP_001834347.1| RNA polymerase sigma factor RpoD [Beijerinckia indica subsp. indica
           ATCC 9039]
 gi|182636084|gb|ACB96858.1| RNA polymerase, sigma 70 subunit, RpoD family [Beijerinckia indica
           subsp. indica ATCC 9039]
          Length = 685

 Score =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 70/246 (28%), Positives = 117/246 (47%), Gaps = 12/246 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 441 EREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 500

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    + +     +      +
Sbjct: 501 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREPTPEEL 555

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+KL +   +V  +        SL   I   D+  S   D++    D    + I+   + 
Sbjct: 556 AEKLAMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAILPIDAAIQS 610

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 611 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKL 670

Query: 281 QESIQK 286
           +   + 
Sbjct: 671 KHPSRS 676


>gi|163747450|ref|ZP_02154802.1| RNA polymerase sigma factor RpoD [Oceanibulbus indolifex HEL-45]
 gi|161379303|gb|EDQ03720.1| RNA polymerase sigma factor RpoD [Oceanibulbus indolifex HEL-45]
          Length = 671

 Score =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 70/242 (28%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 431 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 490

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A+KL
Sbjct: 491 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAEKL 545

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++N + 
Sbjct: 546 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAVLPLDSAIQENLKE 600

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR +S L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 601 TTTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 660

Query: 285 QK 286
           + 
Sbjct: 661 RS 662


>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 =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 68/263 (25%), Positives = 120/263 (45%), Gaps = 14/263 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L   E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 355 LSLAEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 414

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 415 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 472

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    + +++ + E ++  +        S+   I   D   S   D++  
Sbjct: 473 LQEMGREPTPE---ELGERMEMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 525

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q  I+    ++ +      ++ L  RE ++   R   +     TLE +  +F+V
Sbjct: 526 -EDSTMQSPIDVATVESLKEATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 584

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   + +
Sbjct: 585 TRERIRQIEAKALRKLRHPTRSE 607


>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 =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 97  RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 156

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 157 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 211

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 212 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDNNTVAPADAALHASMRD 266

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 267 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 326

Query: 285 QKQ 287
           +  
Sbjct: 327 RSD 329


>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 =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 67/249 (26%), Positives = 113/249 (45%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 366 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 425

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 426 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPTPE--- 480

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + +++ + E ++  +        S+   I   D   S   D++    D Q    ++   
Sbjct: 481 ELGERMEMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDIQALSPVDSAT 535

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            +  R      +S L  RE ++   R   E     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 536 AEGLREATRSVLSGLTARESKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALR 595

Query: 279 KVQESIQKQ 287
           K++   +  
Sbjct: 596 KLRHPSRSD 604


>gi|84390122|ref|ZP_00991384.1| DNA-directed RNA polymerase, sigma subunit [Vibrio splendidus
           12B01]
 gi|84376776|gb|EAP93651.1| DNA-directed RNA polymerase, sigma subunit [Vibrio splendidus
           12B01]
          Length = 326

 Score =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 81/288 (28%), Positives = 141/288 (48%), Gaps = 13/288 (4%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
            ++ + +          Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLV
Sbjct: 37  AKEEVEVTSKSLDATQLYLGEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLV 95

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           VKI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++   
Sbjct: 96  VKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQT 155

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             +++      K L   LR  +     ++           IA KL+    +V  M     
Sbjct: 156 RTIRLPIHVV-KELNIYLRTAR----ELSQKLDHEPTAEEIASKLDKPVGDVSKMLRLNE 210

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              S++  I           D +   ++   +V     +  + +N L   +  LNP+++ 
Sbjct: 211 RVSSVDTPI--GGDGEKALLDIIPDINNSDPEV---STQDSDIKNSLIFWLDELNPKQKE 265

Query: 242 IFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +   R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 266 VLARRFGLLGYEPSTLEEVGREISLTRERVRQIQVEGLRRLREILIKQ 313


>gi|313206169|ref|YP_004045346.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Riemerella
           anatipestifer DSM 15868]
 gi|312445485|gb|ADQ81840.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Riemerella
           anatipestifer DSM 15868]
 gi|315023147|gb|EFT36160.1| RNA polymerase sigma factor RpoD [Riemerella anatipestifer RA-YM]
 gi|325336386|gb|ADZ12660.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Riemerella anatipestifer RA-GD]
          Length = 288

 Score =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 71/276 (25%), Positives = 147/276 (53%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI K+ ++   EE  LA++ R  GD  A  +L+ ++LR VV ++  Y+  GL 
Sbjct: 17  SLDKYLQEIGKVDLITADEEVELAQKIR-AGDKVALEKLIKANLRFVVSVSKQYQNQGLS 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GLM+A K++D  RGF+  +Y++WWI+ ++ + +     +V++    N+  
Sbjct: 76  LPDLINEGNLGLMKAAKRYDETRGFKFISYAVWWIRQSILQALAEQSRIVRLP--LNKIG 133

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               + +   HL+   +    PE++  +   L++SE ++           S++A +   +
Sbjct: 134 SINKINKAYAHLEQENERPPSPEELAEV---LDMSEEDIKESMKNSGRHLSMDAPLV--E 188

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NP 252
              S   D L     G+     ++   ++ +  + R++  L PRE  +          +P
Sbjct: 189 GEDSNLYDVL---RSGESPSPDKELMLESLQIEIERALQTLTPREADLVRLYFGLNGKHP 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TLE +   F+++RERVRQI+ +A K+++ + + ++
Sbjct: 246 MTLEEIGETFDLTRERVRQIKEKAIKRLKHNSRSKI 281


>gi|257066626|ref|YP_003152882.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Anaerococcus
           prevotii DSM 20548]
 gi|256798506|gb|ACV29161.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Anaerococcus
           prevotii DSM 20548]
          Length = 602

 Score =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 74/262 (28%), Positives = 124/262 (47%), Gaps = 14/262 (5%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L  ++   L +         A  +L  ++LRLVV IA  Y G G+   +++ EGN+GLM+
Sbjct: 348 LSDEDILDLRRAVLNS--KRAKKKLAETNLRLVVSIAKKYVGRGMSFLDLIQEGNMGLMK 405

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           AV K+D  RGF+ +TY+ WWI+ A+   I      ++I     +      L R++  L  
Sbjct: 406 AVDKYDYNRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE--TINKLVRIQRQLVQ 463

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
               +   E    IA+++ +   +V  +        SL   I   +++ S   D++  D 
Sbjct: 464 DLGRDPSNE---EIAEQMGLEVEKVQEIRKISQEPVSLETPI--GEEDDSHLGDFIEDDS 518

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSR 266
                   E       R  L   +S L  RE+R+ + R       P TLE +  EF+V+R
Sbjct: 519 ---AIDPGEAANYTMLREQLNDVLSCLGAREKRVLQLRFGLIDGTPRTLEEVGKEFDVTR 575

Query: 267 ERVRQIEARAFKKVQESIQKQV 288
           ER+RQIEA+A +K++   + ++
Sbjct: 576 ERIRQIEAKALRKLKSPNKSEL 597



 Score = 41.0 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 14/41 (34%), Positives = 24/41 (58%), Gaps = 2/41 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRL 53
           +  +  Y+ EI K+ +L   EE +LA+R  E G++ A  +L
Sbjct: 116 DDPVKMYLKEIGKVDLLTATEEIILARRM-EMGEI-ARKKL 154


>gi|13473307|ref|NP_104874.1| RNA polymerase factor sigma-32 [Mesorhizobium loti MAFF303099]
 gi|14024055|dbj|BAB50660.1| RpoH-like sigma factor C [Mesorhizobium loti MAFF303099]
          Length = 287

 Score =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 107/269 (39%), Positives = 169/269 (62%), Gaps = 2/269 (0%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           +    K P LE+ EE+ LA  +++  D +A H +  +H+RLV+ +A  +R YGLP+ +++
Sbjct: 11  VRAAMKAPYLERDEEHRLALLWKQDNDQNALHSITVAHMRLVISMASKFRHYGLPLGDLI 70

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EG++GL++A  +F+PER  R +TY+ WWI+A+MQ+YILR+WS+V+ GT++ QK LFFNL
Sbjct: 71  QEGHVGLLEAAARFEPEREVRFSTYATWWIRASMQDYILRNWSIVRGGTSSAQKALFFNL 130

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSS 198
           RRL+  L    +          ++  L VSE++V  M+ RL+  D SLN  +   D  ++
Sbjct: 131 RRLRARLANGAEPLSNTTLYREVSVALGVSEADVAMMDSRLSAPDSSLNMPLAD-DAGAT 189

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           +  D+LV D    ++++ +K +   R   L  ++  LN RE RI E RRL +   TLE L
Sbjct: 190 ERMDFLVSDDPLPDEIVGDKIDVARRSLWLKEALHALNARELRIIEERRLNDEGATLEAL 249

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQ 287
                +S+ERVRQIEARA +K++ ++ KQ
Sbjct: 250 GETLGISKERVRQIEARAMEKLKVALVKQ 278


>gi|325857152|ref|ZP_08172442.1| putative RNA polymerase sigma factor RpoD [Prevotella denticola
           CRIS 18C-A]
 gi|325483215|gb|EGC86193.1| putative RNA polymerase sigma factor RpoD [Prevotella denticola
           CRIS 18C-A]
          Length = 327

 Score =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 78/287 (27%), Positives = 147/287 (51%), Gaps = 12/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI    M+  +EE  LA+R R+ GD  A  RL  ++LR VV
Sbjct: 45  KITKSITNRESASLDKYLQEIGHEEMISIEEEVELAQRIRK-GDRKALERLTKANLRFVV 103

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + I     
Sbjct: 104 SVAKQYQNQGLSLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSR 163

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           ++++    NQ      + ++   L      N +   +  IA+  ++ E ++       + 
Sbjct: 164 IIRLP--LNQVSSVNKINKI---LNQFEQENERRPSIGEIAQSTDIPEEKIADAIKVSSR 218

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     D + S   D +  D+       + +E     R  + R + VL  RE+++
Sbjct: 219 HVSVDAPFY--DDDQSSLLDVIPNDNVPSTDRGLVEESL---REEIGRVLQVLEDREKKV 273

Query: 243 FEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            EA        +TLE + S++ ++RERVRQI+ +A +++++    +V
Sbjct: 274 VEAYFGINQREMTLEEIGSKYNLTRERVRQIKEKAIRRLRQQTNSKV 320


>gi|255535549|ref|YP_003095920.1| RNA polymerase sigma factor RpoD [Flavobacteriaceae bacterium
           3519-10]
 gi|255341745|gb|ACU07858.1| RNA polymerase sigma factor RpoD [Flavobacteriaceae bacterium
           3519-10]
          Length = 294

 Score =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 71/276 (25%), Positives = 147/276 (53%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI K+ ++   EE  LA++ R  GD  A  +L+ ++LR VV ++  Y+  GL 
Sbjct: 23  SLDKYLQEIGKVDLITADEEVDLAQKIR-AGDRVALEKLIKANLRFVVSVSKQYQNQGLS 81

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GLM+A K++D  RGF+  +Y++WWI+ ++ + +     +V++    N+  
Sbjct: 82  LPDLINEGNLGLMKAAKRYDETRGFKFISYAVWWIRQSILQALAEQSRIVRLP--LNKIG 139

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               + +   HL+   +    PE++  +   L++SE ++           S++A +   +
Sbjct: 140 SINKINKAYAHLEQENERPPSPEELAEV---LDMSEDDIKESMKNSGRHLSMDAPLV--E 194

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NP 252
              S   D L     G+     ++   ++ +  + R++  L PRE  +          +P
Sbjct: 195 GEDSNLYDVL---RSGESPSPDKELMLESLQIEIERALQTLTPREADLVRLYFGLNGKHP 251

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TLE +   F+++RERVRQI+ +A K+++ + + ++
Sbjct: 252 MTLEEIGETFDLTRERVRQIKEKAIKRLKHNTRSKI 287


>gi|157961021|ref|YP_001501055.1| RpoD family RNA polymerase sigma factor [Shewanella pealeana ATCC
           700345]
 gi|157846021|gb|ABV86520.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella pealeana
           ATCC 700345]
          Length = 322

 Score =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 79/271 (29%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   +++    G   + +R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 53  YLGEIGFSPLLSAEEEVYFSRK-SLKGCEKSRNRMIESNLRLVVKIARRYNNRGLALLDL 111

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 112 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 170

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            IA KL++  ++V  M        S++  +    ++  
Sbjct: 171 LRTAR----ELAHKLDHEPTAEEIADKLDLPSADVSRMLKLNERITSVDTPL--GGESDK 224

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  D +      ++ E+       + + +  LN ++R +   R   L   P TLE
Sbjct: 225 ALLDVLADDDNVGPDYKVQDEDMS---KSVVKWLDELNTKQREVLARRFGLLGYEPSTLE 281

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           N+  E  ++RERVRQI+  A K++++ +  Q
Sbjct: 282 NVGKEIGLTRERVRQIQVEALKRLKDLLGAQ 312


>gi|111225055|ref|YP_715849.1| alternative primary sigma 70 transcriptional factor [Frankia alni
           ACN14a]
 gi|111152587|emb|CAJ64329.1| Alternative primary sigma 70 transcriptional factor [Frankia alni
           ACN14a]
          Length = 373

 Score =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 68/296 (22%), Positives = 132/296 (44%), Gaps = 38/296 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKR-----YREHG---------------------DLSA 49
           +  Y+ EI K+P+L   +E  L+KR     + EH                        +A
Sbjct: 77  VRMYLREIGKVPLLNAAQEVELSKRVEAGLFAEHKLESDPDLPADLRRDLGLLVKDGHAA 136

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             +LV+++LRLVV +A  Y G G+ + ++V EGN+GL++AV+KFD  +G++ +TY+ WWI
Sbjct: 137 KQQLVSANLRLVVSVAKKYSGRGMTLLDLVQEGNLGLIRAVEKFDYAKGYKFSTYATWWI 196

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + A+   +      ++I     +      + ++    + +     +      +A +L++ 
Sbjct: 197 RQAIGRALADQARTIRIPVHVVE-----QINKITRLQRQLVSTLGREPTDEELALELDMP 251

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             +V+ +        SL   +   D   S   D++    D       +       ++ + 
Sbjct: 252 IEQVVELRRYAQDTVSLETSV--GDDGDSVLGDFI---EDSDATSPADAASYGAMQDEIE 306

Query: 230 RSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +  LNPRER +   R         TL  + +   ++RER+RQIE    +++++ 
Sbjct: 307 NVLGGLNPREREVMRLRFGLADGKQHTLAEVGNRLGLTRERIRQIERDTLRELRKP 362


>gi|304312494|ref|YP_003812092.1| RNA sigma factor RpoS [gamma proteobacterium HdN1]
 gi|301798227|emb|CBL46449.1| RNA sigma factor RpoS [gamma proteobacterium HdN1]
          Length = 342

 Score =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 82/271 (30%), Positives = 143/271 (52%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A+R    G+  A  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 73  YLNEIGFSPLLTPEEEVYYARR-ALRGNADARKRMIESNLRLVVKIARRYVNRGLSLLDL 131

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 132 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 190

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +   Q + D+   PE++ A+  K       ++ +N R++   S+++ +      S 
Sbjct: 191 LRAARELTQKL-DHEPTPEEISALLDKPLEDVKRMLGLNERIS---SVDSPVGFDSDKS- 245

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
              D +    +     L++  + KN    +   +  L  ++R +   R         TLE
Sbjct: 246 -LLDTIADTKNTDPAELLQDADLKNS---IDYWLDQLPGKQREVIARRFGLRGFEMSTLE 301

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +  E  ++RERVRQI+  A K++++ ++KQ
Sbjct: 302 EVGREIGLTRERVRQIQVEALKRLRDLLEKQ 332


>gi|282877766|ref|ZP_06286579.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           buccalis ATCC 35310]
 gi|281300082|gb|EFA92438.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           buccalis ATCC 35310]
          Length = 298

 Score =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 76/286 (26%), Positives = 146/286 (51%), Gaps = 12/286 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI    ++  +EE  LA+R ++ GD  A  +L  ++LR VV
Sbjct: 16  KITKSITNRESAALDKYLQEIGHEDLISIEEEIELAQRIKK-GDRKALEKLTKANLRFVV 74

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + I     
Sbjct: 75  SVAKQYQNQGLSLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSR 134

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    NQ      + R+   L      + +   V  IA ++++ E +++        
Sbjct: 135 IVRLP--LNQVGSVNKINRI---LNKFEQEHERRPNVDEIADQIDLPEDKIVEAMKVNGK 189

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A I   +   S   D L             +   ++ R  +  +++VLN RER I
Sbjct: 190 HISVDAPIM--EGADSSLLDVLPNTESPMAD---NELVMESLREEVASALNVLNERERNI 244

Query: 243 FEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            E         +TLE +  +F ++RERVRQI+ +A ++++++ + +
Sbjct: 245 IECFYGINQREMTLEEIGDKFGLTRERVRQIKEKALRRLRQNTKSK 290


>gi|217977790|ref|YP_002361937.1| RNA polymerase sigma factor RpoD [Methylocella silvestris BL2]
 gi|217503166|gb|ACK50575.1| RNA polymerase, sigma 70 subunit, RpoD [Methylocella silvestris
           BL2]
          Length = 683

 Score =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 70/246 (28%), Positives = 117/246 (47%), Gaps = 12/246 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 439 EREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 498

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    + +     +      +
Sbjct: 499 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREPTPEEL 553

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+KL +   +V  +        SL   I   D+  S   D++    D    + I+   + 
Sbjct: 554 AEKLAMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAILPIDAAIQS 608

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 609 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKL 668

Query: 281 QESIQK 286
           +   + 
Sbjct: 669 KHPSRS 674


>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 =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 65/250 (26%), Positives = 119/250 (47%), Gaps = 12/250 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 365 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 424

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 425 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPSPE--- 479

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + E ++  +        S+   I   D   S   D++    D   ++ ++   
Sbjct: 480 ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDTTLELPLDSAT 534

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            ++ +N     ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 535 GESLKNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 594

Query: 279 KVQESIQKQV 288
           K++   + ++
Sbjct: 595 KLRHPSRSEI 604


>gi|315499353|ref|YP_004088157.1| RNA polymerase, sigma 70 subunit, rpod [Asticcacaulis excentricus
           CB 48]
 gi|315417365|gb|ADU14006.1| RNA polymerase, sigma 70 subunit, RpoD [Asticcacaulis excentricus
           CB 48]
          Length = 696

 Score =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 70/249 (28%), Positives = 119/249 (47%), Gaps = 15/249 (6%)

Query: 43  EHGDLSAAH---RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG+
Sbjct: 449 QKGEREARQAKTEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 508

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWI+ A+   I      ++I        +   + ++    + +     +    
Sbjct: 509 KFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREPTP 563

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +A+KL +   +V  +        SL   I   D+  S   D++    D    + I+  
Sbjct: 564 EELAEKLAMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAVLPIDAA 618

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAF 277
            + N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A 
Sbjct: 619 IQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKAL 678

Query: 278 KKVQESIQK 286
           +K++   + 
Sbjct: 679 RKLKHPSRS 687


>gi|75676624|ref|YP_319045.1| RNA polymerase sigma factor RpoD [Nitrobacter winogradskyi Nb-255]
 gi|74421494|gb|ABA05693.1| RNA polymerase, sigma 70 subunit, RpoD [Nitrobacter winogradskyi
           Nb-255]
          Length = 717

 Score =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 74/273 (27%), Positives = 129/273 (47%), Gaps = 17/273 (6%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAH---RLVTSHLRLVVKIAMGYRGYGLPI 75
            EI+++  L   E     K  +  + G+  A      +V ++LRLV+ IA  Y   GL  
Sbjct: 446 GEIQQLAALTGLEIGEFRKIVQGVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQF 505

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +
Sbjct: 506 LDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----M 560

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + ++    + + +   +      +A+KL +   +V  +        SL   +   D+
Sbjct: 561 IETINKIVRTSRQMLNEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPLSLETPV--GDE 618

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPV 253
             S   D++    D    + I+   + N R   TR ++ L PRE R+   R         
Sbjct: 619 EDSHLGDFI---EDKNAVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDH 675

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 676 TLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 708


>gi|330950646|gb|EGH50906.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae Cit 7]
          Length = 335

 Score =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 83/278 (29%), Positives = 143/278 (51%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + ++       ++ +N R++  D SL         + 
Sbjct: 185 LRAARELTQKL-DHEPSPEEIANLLERPVGEVKRMLGLNERVSSVDVSL------GPDSD 237

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + +S L  ++R +   R         TL
Sbjct: 238 KTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTEKQREVVIRRFGLRGHESSTL 294

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 295 EDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSSES 332


>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 =  225 bits (575), Expect = 5e-57,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 114/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 433 EKRAREAKREMTVANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 492

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    + I            +
Sbjct: 493 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKMNRISRQILQETGHEPDAATL 547

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A K+ + E ++  +        S+   I   D   S   D++    DG      E     
Sbjct: 548 ALKMEIPEDKIRKIMKIAKEPISMETPI--GDDEDSHLGDFI---EDGNTLAPAEAALHD 602

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R+++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 603 SMRDVVKDVLDSLTPREAKVLRMRFGVEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKM 662

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 663 RHPSRSD 669


>gi|83594214|ref|YP_427966.1| RNA polymerase sigma factor RpoD [Rhodospirillum rubrum ATCC 11170]
 gi|83577128|gb|ABC23679.1| Sigma 70 (RpoD) [Rhodospirillum rubrum ATCC 11170]
          Length = 696

 Score =  225 bits (575), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 71/241 (29%), Positives = 112/241 (46%), Gaps = 12/241 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 457 RAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 516

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I            L R    +         PE    +A+KL 
Sbjct: 517 WIRQAITRSIADQARTIRIPVHM--IETINKLVRTSRQMLHEIGREPTPE---ELAEKLQ 571

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +   +V  +        SL   I   D+  S   D++    D      ++     N R  
Sbjct: 572 MPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAVQPLDAAINSNLRET 626

Query: 228 LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   +
Sbjct: 627 CTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSR 686

Query: 286 K 286
            
Sbjct: 687 S 687


>gi|330872696|gb|EGH06845.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv.
           morsprunorum str. M302280PT]
          Length = 335

 Score =  225 bits (574), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 84/278 (30%), Positives = 142/278 (51%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTVERAIMNQTRTIRLPIHVV-KELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++  + +K       ++ +N R++  D SL         + 
Sbjct: 185 LRAAR-ELTQKLDHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSL------GPDSD 237

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + +S L  ++R +   R         TL
Sbjct: 238 KTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTEKQREVVIRRFGLRGHESSTL 294

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 295 EDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSSES 332


>gi|123968088|ref|YP_001008946.1| RNA polymerase sigma factor RpoD [Prochlorococcus marinus str.
           AS9601]
 gi|123198198|gb|ABM69839.1| Putative principal RNA polymerase sigma factor [Prochlorococcus
           marinus str. AS9601]
          Length = 394

 Score =  225 bits (574), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 76/313 (24%), Positives = 139/313 (44%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------------- 43
            E  +  Y+ EI +I +L   EE  LA++  +                            
Sbjct: 82  TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLQLEELATQYESEKGHFPSVREWAELI 141

Query: 44  -----------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 142 DMPLAKFRRRLLLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 201

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 202 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKVLSQE 256

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA+ + ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 257 FGRKPSEEEIAESMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADIENPE 314

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
           Q +     +   R  L   ++ L+PRER +   R   ++    TLE +   F+V+RER+R
Sbjct: 315 QDV----SKTLLREDLEGVLATLSPRERDVLRLRYGIDDGRMKTLEEIGQIFDVTRERIR 370

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 371 QIEAKALRKLRHP 383


>gi|260775503|ref|ZP_05884400.1| RNA polymerase sigma factor RpoS [Vibrio coralliilyticus ATCC
           BAA-450]
 gi|260608684|gb|EEX34849.1| RNA polymerase sigma factor RpoS [Vibrio coralliilyticus ATCC
           BAA-450]
          Length = 327

 Score =  225 bits (574), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 79/288 (27%), Positives = 140/288 (48%), Gaps = 13/288 (4%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
            ++              Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLV
Sbjct: 38  AKEEFDASTKSLDATQLYLGEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLV 96

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           VKI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++   
Sbjct: 97  VKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQT 156

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             +++      K L   LR  +     ++           IA +L+    +V  M     
Sbjct: 157 RTIRLPIHVV-KELNIYLRTAR----ELSQKLDHEPTAEEIATQLDKPVDDVSKMLRLNE 211

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              S++  I           D +   ++   +V  + +   + ++ L   +  LNP+++ 
Sbjct: 212 RISSVDTPI--GGDGEKALLDIIPDVNNSDPEVSTQDD---DIKSSLIHWLDELNPKQKE 266

Query: 242 IFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +   R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 267 VLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILIKQ 314


>gi|329890710|ref|ZP_08269053.1| RNA polymerase sigma factor rpoD [Brevundimonas diminuta ATCC
           11568]
 gi|328846011|gb|EGF95575.1| RNA polymerase sigma factor rpoD [Brevundimonas diminuta ATCC
           11568]
          Length = 640

 Score =  225 bits (574), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 69/252 (27%), Positives = 120/252 (47%), Gaps = 15/252 (5%)

Query: 40  RYREHGDLSAAH---RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           +  + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  
Sbjct: 390 QMVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 449

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RG++ +TY+ WWI+ A+   I      ++I        +   + ++    + +     + 
Sbjct: 450 RGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTQRQMLHEIGRE 504

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
                +A++L +   +V  +        SL   I   D+  S   D++    D    + I
Sbjct: 505 ATPEELAERLAMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAVLPI 559

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEA 274
           +   + N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA
Sbjct: 560 DAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEA 619

Query: 275 RAFKKVQESIQK 286
           +A +K++   + 
Sbjct: 620 KALRKLKHPSRS 631


>gi|2289784|dbj|BAA21674.1| rpoS sigma factor [Pseudomonas tolaasii]
          Length = 336

 Score =  225 bits (574), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 84/278 (30%), Positives = 143/278 (51%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 68  YLNEIGFSPLLTPEEEVHFA-RLSQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 126

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 127 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 185

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + +K       ++ +N R++  D SL         + 
Sbjct: 186 LRAARELTQKL-DHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSL------GPDSD 238

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + +S L  ++R +   R         TL
Sbjct: 239 KTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTDKQREVVIRRFGLRGHESSTL 295

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 296 EDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSSES 333


>gi|145594010|ref|YP_001158307.1| RNA polymerase sigma factor SigB [Salinispora tropica CNB-440]
 gi|145303347|gb|ABP53929.1| sigma-70 region 2 domain protein [Salinispora tropica CNB-440]
          Length = 332

 Score =  225 bits (574), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 67/300 (22%), Positives = 131/300 (43%), Gaps = 37/300 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYR--------------------------EHGDLSA 49
           +  Y+  I +  +L   +E  L++R                                 +A
Sbjct: 35  VRAYLQGIGRTKLLTAAQEVELSRRIEAGLFAATKLATCTPVSVALRADLELVAAEGRAA 94

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+ ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI
Sbjct: 95  KDHLLEANLRLVVSIAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWI 154

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + A+   +      ++I     +      + R+    + ++ +  +   V  +A+ L++ 
Sbjct: 155 RQAITRAMADQARTIRIPVHMVE-----QVNRMVRTRRELSVSLGREPTVAEVARTLDIP 209

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E +VI +        SL+  +    ++        V    G +  +   E R+       
Sbjct: 210 EIQVIELISYDREPVSLDQTVGEDGESPLGDFVAAVDSTAGTDDTVSGGELRQEMCG--- 266

Query: 230 RSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             ++ L+ RE+ +   R   ++    TL+ +  EF +SRER+RQIE     K++   + Q
Sbjct: 267 -VLATLSQREQAVIRLRFGLDDGRQRTLDEVGREFGLSRERIRQIEKGTLHKLRAPERAQ 325


>gi|94986960|ref|YP_594893.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Lawsonia intracellularis PHE/MN1-00]
 gi|94731209|emb|CAJ54571.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Lawsonia intracellularis PHE/MN1-00]
          Length = 590

 Score =  225 bits (574), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 75/261 (28%), Positives = 122/261 (46%), Gaps = 12/261 (4%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE +   +   +  + A   L+ S+LRLVV IA  Y   GL   +++ EGNIGLM+AV K
Sbjct: 336 EEVLWRIKRGNNAAMRAKQELIRSNLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 395

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RG++ +TY+ WWI+ A+   I      ++I            L R   +L      
Sbjct: 396 FEYQRGYKFSTYATWWIRQAITRAIADQARTIRIPVHM--IETINKLIRTSRYLVQEFGR 453

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +  PE    IA++++    +V  +        SL   I   D+  S   D++    D + 
Sbjct: 454 DPTPE---EIAERMDYPLDKVKKVLKIAKEPISLETPI--GDEEDSSLGDFI---EDKKA 505

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
               E+         +   ++ L PRE ++   R         TLE +   F V+RER+R
Sbjct: 506 VAPSEEVVNTKLSEQIASVLADLTPREEQVLRKRFGIGEKSDHTLEEVGKLFNVTRERIR 565

Query: 271 QIEARAFKKVQESIQKQVELS 291
           QIEA+A +K++  ++ QV  S
Sbjct: 566 QIEAKALRKLRHPVRSQVLRS 586


>gi|259416365|ref|ZP_05740285.1| RNA polymerase sigma factor RpoD [Silicibacter sp. TrichCH4B]
 gi|259347804|gb|EEW59581.1| RNA polymerase sigma factor RpoD [Silicibacter sp. TrichCH4B]
          Length = 664

 Score =  225 bits (574), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 424 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 483

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A+KL
Sbjct: 484 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAEKL 538

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++N + 
Sbjct: 539 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAVLPLDSAIQENLKE 593

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 594 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 653

Query: 285 QK 286
           + 
Sbjct: 654 RS 655


>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 =  225 bits (574), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 64/248 (25%), Positives = 118/248 (47%), Gaps = 12/248 (4%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            E     A H +  ++LRLV+ IA  Y   G+   +++ EGNIGLM+AV KF+  RG++ 
Sbjct: 410 AERQMRQAKHEMTQANLRLVISIAKKYTNRGMLFLDLIQEGNIGLMKAVDKFEYRRGWKF 469

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY+ WW++ A+   I      +++     ++     L RL   +   T     P     
Sbjct: 470 STYATWWVRQAVTRAIADQARTIRVPVHMIEQ--INKLNRLSREIMQQTGKEPDP---AV 524

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           +A++L+++E +V S+        S+   +   +   +   D +    D       +   +
Sbjct: 525 LAERLDMTEDKVRSIMKIAKEPVSMETPV--GEDGDTSLGDMIA---DSDTATPADAALQ 579

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKK 279
              R ++   +  L PRE ++   R   +     TLE +  +F+V+RER+RQIE++A KK
Sbjct: 580 AGLRAVVREMLDELTPREAKVLRMRFGIDMSTDYTLEEVGKQFDVTRERIRQIESKAMKK 639

Query: 280 VQESIQKQ 287
           ++   +  
Sbjct: 640 LRHPSRAD 647


>gi|90418027|ref|ZP_01225939.1| DNA-directed RNA polymerase major sigma factor [Aurantimonas
           manganoxydans SI85-9A1]
 gi|90337699|gb|EAS51350.1| DNA-directed RNA polymerase major sigma factor [Aurantimonas
           manganoxydans SI85-9A1]
          Length = 668

 Score =  225 bits (574), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 69/246 (28%), Positives = 117/246 (47%), Gaps = 12/246 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 424 EREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 483

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    + +     +      +
Sbjct: 484 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREPTPEEL 538

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+KL +   +V  +        SL   +   D+  S   D++    D    + I+   + 
Sbjct: 539 AEKLAMPLEKVRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKNAILPIDAAIQG 593

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 594 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKL 653

Query: 281 QESIQK 286
           +   + 
Sbjct: 654 KHPSRS 659


>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 =  225 bits (574), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 71/276 (25%), Positives = 128/276 (46%), Gaps = 22/276 (7%)

Query: 28  MLEKQEEYVL-AKRYREHGDL---------SAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +L+ ++E  L   + RE  D           A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 352 LLKIEQETNLTISQIREICDKVAQGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 411

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 412 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 469

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +          E    +A+++ + E ++  +        S+   I   D + 
Sbjct: 470 KLNRISRQMLQKMGREATSE---ELAERMGMPEDKIRKVLKIAKEPISMETPI--GDDDD 524

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      +  L PRE ++   R   +     TL
Sbjct: 525 SHLGDFI---EDNTLELPLDSATAQSLRAATHEVLEGLTPREAKVLRMRFGIDMNTDHTL 581

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +   S
Sbjct: 582 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRS 617


>gi|158334991|ref|YP_001516163.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158305232|gb|ABW26849.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 371

 Score =  225 bits (574), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 77/313 (24%), Positives = 139/313 (44%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAK-------------------------------- 39
            E  +  Y+ EI +I +L   EE  LA+                                
Sbjct: 59  TEDSIRLYLQEIGRIRLLRADEEIELARKIADLLELERIYDDLFDRLEREPQLQEWALEV 118

Query: 40  -------RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                  R+R H    A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 119 DMPLNRFRHRLHAGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 178

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 179 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKLLSQE 233

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA ++ ++  ++  +        SL   I    +  S+  D++  D     
Sbjct: 234 MGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIESDG---- 287

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
           +   ++  +   R  L   +  L+PRER + + R   ++    TLE +   F V+RER+R
Sbjct: 288 ETPEDQVSKSLLREDLETVLDTLSPRERDVLKLRYGLDDGRMKTLEEIGQIFNVTRERIR 347

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 348 QIEAKALRKLRHP 360


>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 =  225 bits (574), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 71/276 (25%), Positives = 128/276 (46%), Gaps = 22/276 (7%)

Query: 28  MLEKQEEYVL-AKRYREHGDL---------SAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +L+ ++E  L   + RE  D           A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 326 LLKIEQETNLTISQIREICDKVAQGELKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 385

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 386 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 443

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +          E    +A+++ + E ++  +        S+   I   D + 
Sbjct: 444 KLNRISRQMLQKMGREATSE---ELAERMGMPEDKIRKVLKIAKEPISMETPI--GDDDD 498

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++    ++ R      +  L PRE ++   R   +     TL
Sbjct: 499 SHLGDFI---EDNTLELPLDSATAQSLRAATHEVLEGLTPREAKVLRMRFGIDMNTDHTL 555

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +   S
Sbjct: 556 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSETLRS 591


>gi|29346721|ref|NP_810224.1| RNA polymerase sigma factor rpoD (sigma-A) [Bacteroides
           thetaiotaomicron VPI-5482]
 gi|153808302|ref|ZP_01960970.1| hypothetical protein BACCAC_02591 [Bacteroides caccae ATCC 43185]
 gi|160882661|ref|ZP_02063664.1| hypothetical protein BACOVA_00615 [Bacteroides ovatus ATCC 8483]
 gi|160891864|ref|ZP_02072867.1| hypothetical protein BACUNI_04321 [Bacteroides uniformis ATCC 8492]
 gi|167762326|ref|ZP_02434453.1| hypothetical protein BACSTE_00679 [Bacteroides stercoris ATCC
           43183]
 gi|218130148|ref|ZP_03458952.1| hypothetical protein BACEGG_01736 [Bacteroides eggerthii DSM 20697]
 gi|237712837|ref|ZP_04543318.1| conserved hypothetical protein [Bacteroides sp. D1]
 gi|237718434|ref|ZP_04548915.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 2_2_4]
 gi|255693898|ref|ZP_05417573.1| RNA polymerase sigma-70 factor [Bacteroides finegoldii DSM 17565]
 gi|260173882|ref|ZP_05760294.1| RNA polymerase sigma factor rpoD (sigma-A) [Bacteroides sp. D2]
 gi|262408807|ref|ZP_06085352.1| RNA polymerase sigma factor RpoS [Bacteroides sp. 2_1_22]
 gi|270296469|ref|ZP_06202669.1| conserved hypothetical protein [Bacteroides sp. D20]
 gi|293371428|ref|ZP_06617859.1| putative RNA polymerase sigma factor RpoD [Bacteroides ovatus SD
           CMC 3f]
 gi|294648199|ref|ZP_06725739.1| putative RNA polymerase sigma factor RpoD [Bacteroides ovatus SD CC
           2a]
 gi|294810777|ref|ZP_06769425.1| putative RNA polymerase sigma factor RpoD [Bacteroides
           xylanisolvens SD CC 1b]
 gi|298484065|ref|ZP_07002233.1| RNA polymerase sigma-70 factor [Bacteroides sp. D22]
 gi|299149080|ref|ZP_07042142.1| RNA polymerase sigma-70 factor [Bacteroides sp. 3_1_23]
 gi|315922146|ref|ZP_07918386.1| RNA polymerase sigma factor rpoD [Bacteroides sp. D2]
 gi|317476641|ref|ZP_07935886.1| sigma-70 family RNA polymerase sigma factor [Bacteroides eggerthii
           1_2_48FAA]
 gi|317480344|ref|ZP_07939445.1| sigma-70 family RNA polymerase sigma factor [Bacteroides sp.
           4_1_36]
 gi|329955895|ref|ZP_08296698.1| putative RNA polymerase sigma factor RpoD [Bacteroides clarus YIT
           12056]
 gi|29338618|gb|AAO76418.1| RNA polymerase sigma factor rpoD (Sigma-A) [Bacteroides
           thetaiotaomicron VPI-5482]
 gi|149129205|gb|EDM20421.1| hypothetical protein BACCAC_02591 [Bacteroides caccae ATCC 43185]
 gi|156111976|gb|EDO13721.1| hypothetical protein BACOVA_00615 [Bacteroides ovatus ATCC 8483]
 gi|156858342|gb|EDO51773.1| hypothetical protein BACUNI_04321 [Bacteroides uniformis ATCC 8492]
 gi|167699969|gb|EDS16548.1| hypothetical protein BACSTE_00679 [Bacteroides stercoris ATCC
           43183]
 gi|217987652|gb|EEC53980.1| hypothetical protein BACEGG_01736 [Bacteroides eggerthii DSM 20697]
 gi|229447165|gb|EEO52956.1| conserved hypothetical protein [Bacteroides sp. D1]
 gi|229452367|gb|EEO58158.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 2_2_4]
 gi|260620263|gb|EEX43134.1| RNA polymerase sigma-70 factor [Bacteroides finegoldii DSM 17565]
 gi|262353018|gb|EEZ02113.1| RNA polymerase sigma factor RpoS [Bacteroides sp. 2_1_22]
 gi|270273873|gb|EFA19735.1| conserved hypothetical protein [Bacteroides sp. D20]
 gi|292633625|gb|EFF52183.1| putative RNA polymerase sigma factor RpoD [Bacteroides ovatus SD
           CMC 3f]
 gi|292636474|gb|EFF54952.1| putative RNA polymerase sigma factor RpoD [Bacteroides ovatus SD CC
           2a]
 gi|294442110|gb|EFG10929.1| putative RNA polymerase sigma factor RpoD [Bacteroides
           xylanisolvens SD CC 1b]
 gi|298269746|gb|EFI11339.1| RNA polymerase sigma-70 factor [Bacteroides sp. D22]
 gi|298513841|gb|EFI37728.1| RNA polymerase sigma-70 factor [Bacteroides sp. 3_1_23]
 gi|313696021|gb|EFS32856.1| RNA polymerase sigma factor rpoD [Bacteroides sp. D2]
 gi|316903519|gb|EFV25372.1| sigma-70 family RNA polymerase sigma factor [Bacteroides sp.
           4_1_36]
 gi|316907237|gb|EFV28946.1| sigma-70 family RNA polymerase sigma factor [Bacteroides eggerthii
           1_2_48FAA]
 gi|328525275|gb|EGF52325.1| putative RNA polymerase sigma factor RpoD [Bacteroides clarus YIT
           12056]
          Length = 286

 Score =  225 bits (574), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 75/287 (26%), Positives = 144/287 (50%), Gaps = 12/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI +  ++  +EE  LA+R R+ GD  A  +L  ++LR VV
Sbjct: 5   KITKSITNRESASLDKYLQEIGREDLITVEEEVELAQRIRK-GDRVALEKLTRANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 64  SVAKQYQNQGLSLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    NQ      + +     +   +    PE    +A +L +   ++         
Sbjct: 124 IVRLP--LNQVGSLNKISKAFSKFEQENERRPSPE---ELADELEIPVDKISDTLKVSGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     + NS    D LV D        +  E        + R++S L  RE+ I
Sbjct: 179 HISVDAPFVEGEDNS--LLDVLVNDDSPMADRSLVNESLA---REIDRALSTLTDREKEI 233

Query: 243 FEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +      +  +TLE +  +F ++RERVRQI+ +A +++++S + ++
Sbjct: 234 IQMFFGIGQQEMTLEEIGDKFGLTRERVRQIKEKAIRRLRQSNRSKL 280


>gi|86146341|ref|ZP_01064665.1| DNA-directed RNA polymerase, sigma subunit [Vibrio sp. MED222]
 gi|85835820|gb|EAQ53954.1| DNA-directed RNA polymerase, sigma subunit [Vibrio sp. MED222]
          Length = 326

 Score =  225 bits (574), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 81/271 (29%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 54  YLGEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 112

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 113 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHVV-KELNIY 171

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA KL+    +V  M        S++  I        
Sbjct: 172 LRTAR----ELSQKLDHEPTAEEIASKLDKPVGDVSKMLRLNERVSSVDTPI--GGDGEK 225

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D +   ++   +V     +  + +N L   +  LNP+++ +   R   L   P TLE
Sbjct: 226 ALLDIIPDINNSDPEV---STQDSDIKNSLIFWLDELNPKQKEVLARRFGLLGYEPSTLE 282

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 283 EVGREISLTRERVRQIQVEGLRRLREILIKQ 313


>gi|84515379|ref|ZP_01002741.1| RNA polymerase sigma factor [Loktanella vestfoldensis SKA53]
 gi|84510662|gb|EAQ07117.1| RNA polymerase sigma factor [Loktanella vestfoldensis SKA53]
          Length = 659

 Score =  225 bits (574), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 419 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 478

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A+KL
Sbjct: 479 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAEKL 533

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++N + 
Sbjct: 534 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAILPLDSAIQENLKE 588

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 589 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 648

Query: 285 QK 286
           + 
Sbjct: 649 RS 650


>gi|288920765|ref|ZP_06415065.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EUN1f]
 gi|288347841|gb|EFC82118.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EUN1f]
          Length = 425

 Score =  225 bits (574), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 68/296 (22%), Positives = 132/296 (44%), Gaps = 38/296 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKR-----YREHG---------------------DLSA 49
           +  Y+ EI K+P+L   +E  L+KR     + EH                        +A
Sbjct: 129 VRMYLREIGKVPLLNAAQEVELSKRVEAGLFAEHKLETDEGLAEDLRRDLGLLVTDGQAA 188

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             +LV+++LRLVV +A  Y G G+ + ++V EGN+GL++AV+KFD  +G++ +TY+ WWI
Sbjct: 189 KQQLVSANLRLVVSVAKKYSGRGMTLLDLVQEGNLGLIRAVEKFDYAKGYKFSTYATWWI 248

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + A+   +      ++I     +      + ++    + +     +      +A +L++ 
Sbjct: 249 RQAIGRALADQARTIRIPVHVVE-----QINKITRLQRQLVSTLGREPTDEELAFELDMP 303

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             +V+ +        SL   +   D   S   D++    D       +       ++ + 
Sbjct: 304 IEQVVELRRYAQDTVSLETSV--GDDGDSVLGDFI---EDSDATSPADAASYGAMQDEID 358

Query: 230 RSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +  LNPRER +   R         TL  + +   ++RER+RQIE    +++++ 
Sbjct: 359 NVLGALNPREREVMRLRFGLADGKQHTLAEVGNRLGLTRERIRQIERDTLRELRKP 414


>gi|159896899|ref|YP_001543146.1| RpoD family RNA polymerase sigma factor [Herpetosiphon aurantiacus
           ATCC 23779]
 gi|159889938|gb|ABX03018.1| RNA polymerase, sigma 70 subunit, RpoD family [Herpetosiphon
           aurantiacus ATCC 23779]
          Length = 391

 Score =  225 bits (574), Expect = 6e-57,   Method: Composition-based stats.
 Identities = 82/300 (27%), Positives = 135/300 (45%), Gaps = 40/300 (13%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL------------------------- 47
           E  +  Y+ EI ++ +L  +EE  LAK+  E G                           
Sbjct: 92  EDSVQMYLREIGEVELLTAEEEITLAKQI-ETGRKAEHQLQTEQYATWDERTALERRVDF 150

Query: 48  --SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
                 +L  ++LRLVV +A  Y G  +   +++ EGNIGLM+AV+KFD  +G R +TY+
Sbjct: 151 GNEGRRKLTQANLRLVVSVAKKYIGNHMSFMDLIQEGNIGLMRAVEKFDYRKGNRFSTYA 210

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
            WWI+ A+   I      +++    ++      +RR+   L+        P+    +A  
Sbjct: 211 TWWIRQAVTRAIAEQSRTIRLPVHLSES--IAQMRRVAYQLEQALQREATPD---ELADA 265

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           L VS  +V  M        SL   I    +   +  ++L  D D   +  +E+  R   +
Sbjct: 266 LGVSLRKVKRMLNASVQPVSLEQPI--GKEGQGRVGEFLADDTD---EAPLEQATRMMLQ 320

Query: 226 NMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           + L  ++S L  RER+I   R         TLE + +EF ++RER RQIEA A + +++ 
Sbjct: 321 DELADALSQLPDRERQILLLRYGLADGKRRTLEEVGAEFGITRERTRQIEAEAMRHLRQP 380


>gi|312963434|ref|ZP_07777916.1| sigma-70 [Pseudomonas fluorescens WH6]
 gi|311282240|gb|EFQ60839.1| sigma-70 [Pseudomonas fluorescens WH6]
          Length = 616

 Score =  225 bits (574), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 69/263 (26%), Positives = 120/263 (45%), Gaps = 14/263 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L   E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 356 LTIAEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 415

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 416 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 473

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    + +++ + E ++  +        S+   I   D   S   D++  
Sbjct: 474 LQEMGREPTPE---ELGERMEMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 526

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q  I+    ++ +      +S L  RE ++   R   +     TLE +  +F+V
Sbjct: 527 -EDSTMQSPIDVATVESLKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 585

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   + +
Sbjct: 586 TRERIRQIEAKALRKLRHPTRSE 608


>gi|271966792|ref|YP_003340988.1| RNA polymerase sigma factor RpoD [Streptosporangium roseum DSM
           43021]
 gi|270509967|gb|ACZ88245.1| RNA polymerase sigma factor RpoD [Streptosporangium roseum DSM
           43021]
          Length = 331

 Score =  225 bits (574), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 66/302 (21%), Positives = 133/302 (44%), Gaps = 39/302 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKR---------------------------YREHGDLS 48
           +  Y+  I K+ +L  ++E  LA+R                           +     L 
Sbjct: 34  VKDYLRRIGKVALLSAEQEVELARRIEAGLFAAECLGTQAQAPSTVVRAELEWLAEDGLR 93

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A + L+ ++LRLVV IA  + G G+  ++++ EGN+GL++A +KFD  +GF+ +TY+ WW
Sbjct: 94  AKNHLLEANLRLVVSIAKRHTGRGMAFADLIQEGNLGLIRAAEKFDYTKGFKFSTYATWW 153

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           IK A+   +      ++I     +  +   + R++  +         P     +A +L++
Sbjct: 154 IKQAVTRALADQGRTIRIPVHMVE--VINKVARVQRQMMVTLGREPSP---QELAVELDM 208

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +  ++  +        SL+  +    +  +++ D +    D +  +  E       +  L
Sbjct: 209 TVEKITEVQKYGREPISLHTPL--GAEGDAEFGDVI---EDSEAILPEEAVTFILLQRQL 263

Query: 229 TRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +  L+ RE  +   R       P TL+ +   F V+RER+RQIE++   K++   + 
Sbjct: 264 HAVLEALSEREAGVMRLRFGLADGQPKTLDEIGKVFGVTRERIRQIESKTMSKLRHPARA 323

Query: 287 QV 288
           + 
Sbjct: 324 RA 325


>gi|193089925|gb|ACF15191.1| RpoS [Pseudomonas sp. DF41]
          Length = 335

 Score =  225 bits (574), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 82/278 (29%), Positives = 140/278 (50%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERG R +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGSRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++  + +K       ++ +N R++  D SL         + 
Sbjct: 185 LRAAR-ELTQKLDHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSL------GPDSD 237

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + +S L  ++  +   R         TL
Sbjct: 238 KTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTDKQWEVVIRRFGLRGHESSTL 294

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 295 EDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSSES 332


>gi|332185826|ref|ZP_08387573.1| RNA polymerase sigma factor RpoD [Sphingomonas sp. S17]
 gi|332014184|gb|EGI56242.1| RNA polymerase sigma factor RpoD [Sphingomonas sp. S17]
          Length = 671

 Score =  225 bits (574), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 68/251 (27%), Positives = 120/251 (47%), Gaps = 15/251 (5%)

Query: 41  YREHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
             + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 422 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 481

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I        +   + +L    +       +  
Sbjct: 482 GYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTSRQFLHEQGREP 536

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A++L++   +V  +        SL   I   D+  S   D++    D    + ++
Sbjct: 537 TPEEMAERLSMPLEKVRKVMKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAVIPVD 591

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              + N +  +TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+
Sbjct: 592 AAIQANLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 651

Query: 276 AFKKVQESIQK 286
           A +K++   + 
Sbjct: 652 ALRKLKHPSRS 662


>gi|163738642|ref|ZP_02146056.1| RNA polymerase, sigma 38 subunit, RpoS [Phaeobacter gallaeciensis
           BS107]
 gi|161387970|gb|EDQ12325.1| RNA polymerase, sigma 38 subunit, RpoS [Phaeobacter gallaeciensis
           BS107]
          Length = 662

 Score =  225 bits (574), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 422 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 481

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A+KL
Sbjct: 482 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAEKL 536

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++N + 
Sbjct: 537 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAVLPLDSAIQENLKE 591

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 592 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 651

Query: 285 QK 286
           + 
Sbjct: 652 RS 653


>gi|83859451|ref|ZP_00952972.1| RNA polymerase sigma factor [Oceanicaulis alexandrii HTCC2633]
 gi|83852898|gb|EAP90751.1| RNA polymerase sigma factor [Oceanicaulis alexandrii HTCC2633]
          Length = 678

 Score =  225 bits (574), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 115/240 (47%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 440 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 499

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + +     +      +A+KL++
Sbjct: 500 IRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREPTPEELAEKLSM 554

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   I   D+  S   D++    D    + I+     N R   
Sbjct: 555 PLEKVRKVMKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAVLPIDAAIHSNLRETT 609

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           T  ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 610 TLVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 669


>gi|89070863|ref|ZP_01158102.1| RNA polymerase sigma factor [Oceanicola granulosus HTCC2516]
 gi|89043551|gb|EAR49761.1| RNA polymerase sigma factor [Oceanicola granulosus HTCC2516]
          Length = 657

 Score =  225 bits (574), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 417 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 476

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A+KL
Sbjct: 477 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAEKL 531

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++N + 
Sbjct: 532 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAVLPLDSAIQENLKE 586

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 587 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 646

Query: 285 QK 286
           + 
Sbjct: 647 RS 648


>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 =  225 bits (574), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 112/247 (45%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 420 EAKMRRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 479

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T     P     +
Sbjct: 480 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGQEPDPAT---L 534

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+ + E ++  +        S+   I   D + S   D++    D       E     
Sbjct: 535 AEKMEMPEEKIRKIMKISKEPISMETPI--GDDDDSHLGDFI---EDTATLAPAEAAMYS 589

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             R+     +  L  RE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 590 GLRDATCEVLDSLTQREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 649

Query: 281 QESIQKQ 287
           +   + +
Sbjct: 650 RHPSRSE 656


>gi|253573078|ref|ZP_04850470.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 1_1_6]
 gi|251837335|gb|EES65434.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 1_1_6]
          Length = 286

 Score =  225 bits (574), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 75/287 (26%), Positives = 144/287 (50%), Gaps = 12/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI +  ++  +EE  LA+R R+ GD  A  +L  ++LR VV
Sbjct: 5   KITKSITNRESASLDKYLQEIGREDLITVEEEVELAQRIRK-GDRVALEKLTRANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 64  SVAKQYQNQGLSLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    NQ      + +     +   +    PE    +A +L +   ++         
Sbjct: 124 IVRLP--LNQVGSLNKISKAFSKFEQENERRPSPE---ELADELEIPVDKISDTLKVSGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     + NS    D LV D        +  E        + R++S L  RE+ I
Sbjct: 179 HISVDAPFVEGEDNS--LLDVLVNDDSPMADRSLVNESLA---REIDRALSTLTEREKEI 233

Query: 243 FEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +      +  +TLE +  +F ++RERVRQI+ +A +++++S + ++
Sbjct: 234 IQMFFGIGQQEMTLEEIGDKFGLTRERVRQIKEKAIRRLRQSNRSKL 280


>gi|271962349|ref|YP_003336545.1| RNA polymerase sigma factor RpoD [Streptosporangium roseum DSM
           43021]
 gi|270505524|gb|ACZ83802.1| RNA polymerase sigma factor RpoD [Streptosporangium roseum DSM
           43021]
          Length = 324

 Score =  225 bits (574), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 71/301 (23%), Positives = 131/301 (43%), Gaps = 37/301 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------------HGDLS 48
             +  Y+ +I +IP+L   +E  LA+R                                 
Sbjct: 27  DPVRDYLRQIARIPLLTAGQEVELARRVEAGLFARERLGAEGLPAALRAELECVADDGRR 86

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R V ++LRLVV IA  + G G+P+ +++ EGN+GL++AV+KFD   GF+ +TY+ WW
Sbjct: 87  AKDRFVEANLRLVVSIAKRHAGRGVPLLDLIQEGNLGLIRAVEKFDHRLGFKFSTYATWW 146

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           IK A+   +      V++     +  +   + R++  L         PE    IA +L++
Sbjct: 147 IKQAITRAMADQARTVRVPVHMVE--MINKVARVERQLLCDLGREPTPE---EIAAELDL 201

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +  +V  +        SL+  +   D+  S+  D +    D +             +  +
Sbjct: 202 TPEKVTEIKGHGREPISLHTPL--GDEGDSELGDLI---EDAEAVTPEAAVAFTLLQEQV 256

Query: 229 TRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              ++ L  RE  +   R       P TL+ +   + ++RER+RQIE++   +++   + 
Sbjct: 257 RALLATLTGREAGVISMRFGFADGRPWTLDEIGRVYGLTRERIRQIESKTMSRLRHPSRS 316

Query: 287 Q 287
           Q
Sbjct: 317 Q 317


>gi|218885598|ref|YP_002434919.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           vulgaris str. 'Miyazaki F']
 gi|218756552|gb|ACL07451.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           vulgaris str. 'Miyazaki F']
          Length = 590

 Score =  225 bits (574), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 74/261 (28%), Positives = 121/261 (46%), Gaps = 12/261 (4%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE +   +      + A   L+ S+LRLVV IA  Y   GL   +++ EGNIGLM+AV K
Sbjct: 336 EEVLWRIKRGNTHAMRAKQELIRSNLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 395

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RG++ +TY+ WWI+ A+   I      ++I            L R   +L      
Sbjct: 396 FEYQRGYKFSTYATWWIRQAITRAIADQARTIRIPVHM--IETINKLIRTSRYLVQELGR 453

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +  PE    IA++++    +V  +        SL   I   D+  S   D++    D + 
Sbjct: 454 DPTPE---EIAERMDYPIDKVKKVLKIAKEPISLETPI--GDEEDSSLGDFI---EDKKA 505

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
               E+         +   ++ L PRE ++   R         TLE +   F V+RER+R
Sbjct: 506 VAPAEEVVNTKLSEQIASVLADLTPREEQVLRKRFGIGEKSDHTLEEVGKLFNVTRERIR 565

Query: 271 QIEARAFKKVQESIQKQVELS 291
           QIEA+A +K++  ++ Q+  S
Sbjct: 566 QIEAKALRKLRHPVRSQMLRS 586


>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 =  225 bits (574), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 67/249 (26%), Positives = 114/249 (45%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 369 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 428

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 429 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRVSRQMLQEMGREPTPE--- 483

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + ++L + E +V  +        S+   I   D + S   D++    DG   + I+   
Sbjct: 484 ELGERLEMPEDKVRKVLKIAKEPISMETPI--GDDDDSHLGDFI---EDGTMVLPIDSAT 538

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            +         +  L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 539 GEGLIEATRNVLGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 598

Query: 279 KVQESIQKQ 287
           K++   + +
Sbjct: 599 KLRHPSRSE 607


>gi|260434101|ref|ZP_05788072.1| RNA polymerase sigma factor RpoD [Silicibacter lacuscaerulensis
           ITI-1157]
 gi|260417929|gb|EEX11188.1| RNA polymerase sigma factor RpoD [Silicibacter lacuscaerulensis
           ITI-1157]
          Length = 662

 Score =  225 bits (574), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 73/271 (26%), Positives = 130/271 (47%), Gaps = 14/271 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L+  E   + ++ +  E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 393 MAQIGQYVGLDISEFRRIVQQVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLD 452

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +  
Sbjct: 453 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIE 507

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + +L    + +     +      +A+KL +   +V  +        SL   I   D+  
Sbjct: 508 TINKLVRTGRQMLHEIGREPTPEELAEKLQMPLEKVRKVMKIAKEPISLETPI--GDEED 565

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTL 255
           SQ  D++    D    + ++   ++N +   TR ++ L PRE R+   R         TL
Sbjct: 566 SQLGDFI---EDKNAVLPLDSAIQENLKETTTRVLASLTPREERVLRMRFGIGMNTDHTL 622

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 623 EEVGQQFSVTRERIRQIEAKALRKLKHPSRS 653


>gi|258406014|ref|YP_003198756.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfohalobium
           retbaense DSM 5692]
 gi|257798241|gb|ACV69178.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfohalobium
           retbaense DSM 5692]
          Length = 587

 Score =  225 bits (573), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 77/257 (29%), Positives = 124/257 (48%), Gaps = 13/257 (5%)

Query: 34  EYVLAKRYREHGD-LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           E +L +  R + D L A   L+ S+LRLVV IA  Y   GL   +++ EGNIGLM+AV K
Sbjct: 333 EEILWRINRGNYDALRAKQELIRSNLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 392

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RG++ +TY+ WWI+ A+   I      ++I            L R   +L      
Sbjct: 393 FEYQRGYKFSTYATWWIRQAITRAIADQARTIRIPVHM--IETINKLIRTSRYLVQELGR 450

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           + +PE    IA++++    +V  +        SL   I   D+  S   D++    D + 
Sbjct: 451 DPQPE---EIAERMDYPVEKVKKVLKIAKEPISLETPI--GDEEDSSLGDFI---EDKKA 502

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
               E+         ++  +S L PRE ++   R         TLE +   F V+RER+R
Sbjct: 503 VAPAEEAVNSKLAEQISTVLSELTPREEQVLRKRFGIGEKSDHTLEEVGKLFNVTRERIR 562

Query: 271 QIEARAFKKVQESIQKQ 287
           QIEA+A +K++  ++ Q
Sbjct: 563 QIEAKALRKLRHPVRSQ 579



 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 11/44 (25%), Positives = 24/44 (54%), Gaps = 1/44 (2%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVT 55
               +  Y+ E+  +P+L+++ E  +AK+  E G+L   + L+ 
Sbjct: 95  SSDPVRMYLREMGIVPLLDREGEVEIAKKI-EDGELEVLYALIE 137


>gi|150007022|ref|YP_001301765.1| RNA polymerase sigma factor rpoD [Parabacteroides distasonis ATCC
           8503]
 gi|154495210|ref|ZP_02034215.1| hypothetical protein PARMER_04266 [Parabacteroides merdae ATCC
           43184]
 gi|218256952|ref|ZP_03474423.1| hypothetical protein PRABACTJOHN_00076 [Parabacteroides johnsonii
           DSM 18315]
 gi|255015941|ref|ZP_05288067.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 2_1_7]
 gi|256841904|ref|ZP_05547409.1| RNA polymerase sigma factor RpoS [Parabacteroides sp. D13]
 gi|262384222|ref|ZP_06077357.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 2_1_33B]
 gi|298377447|ref|ZP_06987400.1| RNA polymerase sigma-70 factor [Bacteroides sp. 3_1_19]
 gi|301308863|ref|ZP_07214815.1| RNA polymerase sigma-70 factor [Bacteroides sp. 20_3]
 gi|149935446|gb|ABR42143.1| RNA polymerase sigma factor rpoD [Parabacteroides distasonis ATCC
           8503]
 gi|154085357|gb|EDN84402.1| hypothetical protein PARMER_04266 [Parabacteroides merdae ATCC
           43184]
 gi|218225859|gb|EEC98509.1| hypothetical protein PRABACTJOHN_00076 [Parabacteroides johnsonii
           DSM 18315]
 gi|256736220|gb|EEU49549.1| RNA polymerase sigma factor RpoS [Parabacteroides sp. D13]
 gi|262293925|gb|EEY81858.1| RNA polymerase sigma factor rpoD [Bacteroides sp. 2_1_33B]
 gi|298265861|gb|EFI07521.1| RNA polymerase sigma-70 factor [Bacteroides sp. 3_1_19]
 gi|300833387|gb|EFK64005.1| RNA polymerase sigma-70 factor [Bacteroides sp. 20_3]
          Length = 286

 Score =  225 bits (573), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 71/287 (24%), Positives = 140/287 (48%), Gaps = 12/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI +  ++  +EE  LA+  +  GD  A  +L  ++LR VV
Sbjct: 5   KITKSITNRESASLDKYLQEIGREDLITVEEEVELAQAIK-RGDRRALEKLTRANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 64  SVAKQYQNQGLSLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    NQ      + +     +   +    PE    +A +L++   ++         
Sbjct: 124 IVRLP--LNQVGSLNKISKAFSKFEQENERRPSPE---ELADELDIPVDKISDTLKVSGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     + NS    D LV D        +  E        + R+++ L  RE  I
Sbjct: 179 HISVDAPFVEGEDNS--LLDVLVNDDAPIADRSLMNESLA---KEIDRALATLTERECEI 233

Query: 243 FEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +         +TLE +  +F ++RERVRQI+ +A +++++  + ++
Sbjct: 234 IKMFFGIGCQEMTLEEIGDKFGLTRERVRQIKEKAIRRLRQGTRSKL 280


>gi|212697198|ref|ZP_03305326.1| hypothetical protein ANHYDRO_01765 [Anaerococcus hydrogenalis DSM
           7454]
 gi|212675973|gb|EEB35580.1| hypothetical protein ANHYDRO_01765 [Anaerococcus hydrogenalis DSM
           7454]
          Length = 617

 Score =  225 bits (573), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 72/261 (27%), Positives = 124/261 (47%), Gaps = 14/261 (5%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           +  +   L +   +     A  +L  ++LRLVV IA  Y G G+   +++ EGN+GLM+A
Sbjct: 364 DADDVKRLNRAIFDAN--RAKQKLAETNLRLVVSIAKKYVGRGMSFLDLIQEGNMGLMKA 421

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V K+D  RGF+ +TY+ WWI+ A+   I      ++I     +      L R++  L   
Sbjct: 422 VDKYDYNRGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE--TINKLVRIQRQLVQD 479

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
              +   E    IA+++ +   +V  +        SL   I   ++  S   D++  D  
Sbjct: 480 LGRDPSNE---EIAEQMGIEVEKVQEIRKIAQEPVSLETPI--GEEEDSHLGDFIEDDTA 534

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRE 267
                  +       R+ L   +S L  RE+R+ + R       P TLE +  EF+V+RE
Sbjct: 535 INPD---DAANYSMLRDQLNDVLSCLGAREKRVLQLRFGLIDGTPRTLEEVGKEFDVTRE 591

Query: 268 RVRQIEARAFKKVQESIQKQV 288
           R+RQIEA+A +K++   + ++
Sbjct: 592 RIRQIEAKALRKLKSPNKSEL 612



 Score = 39.8 bits (92), Expect = 0.51,   Method: Composition-based stats.
 Identities = 13/40 (32%), Positives = 23/40 (57%), Gaps = 1/40 (2%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHR 52
           +  +  Y+ EI K+ +L+  EE  LAK+  E GD++   +
Sbjct: 131 DDPVKMYLKEIGKVKLLDAHEEIFLAKKM-ELGDIALRSK 169


>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 =  225 bits (573), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 71/258 (27%), Positives = 121/258 (46%), Gaps = 15/258 (5%)

Query: 34  EYVLAKRYREHGDLSAAH---RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           EY       + G+  A      ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV
Sbjct: 403 EYRRIVNMVQKGEREARQAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 462

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
            KF+  RG++ +TY+ WWI+ A+   I      ++I        +   + ++    + + 
Sbjct: 463 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQML 517

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
               +      +A+KL +   +V  +        SL   I   D+  S   D++    D 
Sbjct: 518 HEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDK 572

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRER 268
              + I+   + N R   TR ++ L PRE R+   R         TLE +  +F V+RER
Sbjct: 573 NVVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRER 632

Query: 269 VRQIEARAFKKVQESIQK 286
           +RQIEA+A +K++   + 
Sbjct: 633 IRQIEAKALRKLKHPSRS 650


>gi|85708548|ref|ZP_01039614.1| RNA polymerase sigma factor [Erythrobacter sp. NAP1]
 gi|85690082|gb|EAQ30085.1| RNA polymerase sigma factor [Erythrobacter sp. NAP1]
          Length = 674

 Score =  225 bits (573), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 68/251 (27%), Positives = 119/251 (47%), Gaps = 15/251 (5%)

Query: 41  YREHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
             + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 425 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 484

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I        +   + +L    +       +  
Sbjct: 485 GYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTSRQFLHEEGREP 539

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A +L++   +V  +        SL   I   D+  S   D++    D    + ++
Sbjct: 540 TPEEMAARLSMPLEKVRKVMKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAVIPVD 594

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              + N +  +TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+
Sbjct: 595 AAIQANLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 654

Query: 276 AFKKVQESIQK 286
           A +K++   + 
Sbjct: 655 ALRKLKHPSRS 665


>gi|158313089|ref|YP_001505597.1| RpoD family RNA polymerase sigma factor [Frankia sp. EAN1pec]
 gi|158108494|gb|ABW10691.1| RNA polymerase, sigma 70 subunit, RpoD family [Frankia sp. EAN1pec]
          Length = 423

 Score =  225 bits (573), Expect = 7e-57,   Method: Composition-based stats.
 Identities = 68/296 (22%), Positives = 132/296 (44%), Gaps = 38/296 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKR-----YREHG---------------------DLSA 49
           +  Y+ EI K+P+L   +E  L+KR     + EH                        +A
Sbjct: 127 VRMYLREIGKVPLLNAAQEVELSKRVEAGLFAEHKLDTDQDLADDLRRDLGVLVTDGQAA 186

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             +LV+++LRLVV +A  Y G G+ + ++V EGN+GL++AV+KFD  +G++ +TY+ WWI
Sbjct: 187 KQQLVSANLRLVVSVAKKYSGRGMTLLDLVQEGNLGLIRAVEKFDYAKGYKFSTYATWWI 246

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + A+   +      ++I     +      + ++    + +     +      +A +L++ 
Sbjct: 247 RQAIGRALADQARTIRIPVHVVE-----QINKITRLQRQLVSTLGREPTDEELALELDMP 301

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             +V+ +        SL   +   D   S   D++    D       +       ++ + 
Sbjct: 302 IEQVVELRRYAQDTVSLETSV--GDDGDSVLGDFI---EDSDATSPADAASYGAMQDEID 356

Query: 230 RSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +  LNPRER +   R         TL  + +   ++RER+RQIE    +++++ 
Sbjct: 357 NVLGALNPREREVMRLRFGLADGKQHTLAEVGNRLGLTRERIRQIERDTLRELRKP 412


>gi|254465185|ref|ZP_05078596.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacterales bacterium
           Y4I]
 gi|206686093|gb|EDZ46575.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacterales bacterium
           Y4I]
          Length = 292

 Score =  225 bits (573), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 104/272 (38%), Positives = 177/272 (65%), Gaps = 6/272 (2%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
            +  K  +L+   E  LA  +R+  D+ + HRL+ +++RL + +A  ++ YG P+++++ 
Sbjct: 13  RQAMKAELLDADTERRLAYAWRDDRDVESLHRLINAYMRLAISMAAKFKRYGAPMNDLIQ 72

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           E  +GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFN+R
Sbjct: 73  EAGLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMR 132

Query: 141 RLKGHLQAITDNNLKP----EQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDK 195
           R++  L+    ++  P    +    IA ++ V   +V  M  RL+G D SLNA + S+D+
Sbjct: 133 RVQAQLEREARSSGVPLDQHQLHQKIATEIGVPLRDVEMMEGRLSGADFSLNA-VQSTDE 191

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
              +W D L  D    E ++ E+ +R+  R  L  ++  LN RER I   R+L++ P TL
Sbjct: 192 EGREWIDALEDDASQAEDLVQERHDRRQLRKWLVTALQALNDRERFIITERKLRDRPRTL 251

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+L +E  +S+ERVRQ+EA AF+K+++S++ Q
Sbjct: 252 ESLGTELGLSKERVRQLEAGAFQKMRKSLESQ 283


>gi|323342093|ref|ZP_08082326.1| DNA-directed RNA polymerase sigma subunit RpoD [Erysipelothrix
           rhusiopathiae ATCC 19414]
 gi|322464518|gb|EFY09711.1| DNA-directed RNA polymerase sigma subunit RpoD [Erysipelothrix
           rhusiopathiae ATCC 19414]
          Length = 459

 Score =  225 bits (573), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 80/352 (22%), Positives = 143/352 (40%), Gaps = 75/352 (21%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEE--------------------------- 34
           N    + +V     +  Y+ EI ++ +L+ ++E                           
Sbjct: 108 NELTSANMVRINDPVKMYLKEIGRVNLLDAKDEPEIARRLQEGEQAKEFIINKYKEIVDP 167

Query: 35  ----YVLAKRYREH----------------GDLS-----------------AAHRLVTSH 57
                 LA+R  E+                GD                   A   L++++
Sbjct: 168 AITDEELAERLTENQIGYFFDDFEAYLTENGDEENLAFLTNWVATYYDGLEARRILISAN 227

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I
Sbjct: 228 LRLVVSIAKKYVGRGMLFLDLIQEGNMGLVKAVEKFDYTKGFKFSTYATWWIRQAITRAI 287

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
                 ++I     +      L R++  L          E++ A  +  N++  +V  + 
Sbjct: 288 ADQARTIRIPVHMVE--TINKLTRIQRSLVQTLGREPTAEEIAAEME--NITPEKVREIQ 343

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                  SL   I   +++ S   D++    D       E    +  +  +   +  L  
Sbjct: 344 KIALDPVSLETPI--GEEDDSHLGDFI---EDKDALSPDEYANNQLLKEEIKMVLEGLTE 398

Query: 238 RERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           RE ++   R   E+    TLE +  EF V+RER+RQIEA+A +K++   + +
Sbjct: 399 REEKVLRLRFGLEDGRTRTLEEVGKEFNVTRERIRQIEAKALRKLKHPTRSK 450


>gi|167724581|ref|ZP_02407817.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei DM98]
          Length = 680

 Score =  225 bits (573), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 64/243 (26%), Positives = 113/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 439 RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 498

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 499 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 553

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 554 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTVAPADAALHASMRD 608

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L P E ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 609 VVKDVLDSLTPSEAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 668

Query: 285 QKQ 287
           +  
Sbjct: 669 RSD 671


>gi|113954073|ref|YP_731235.1| RNA polymerase sigma factor RpoD [Synechococcus sp. CC9311]
 gi|113881424|gb|ABI46382.1| RNA polymerase sigma factor RpoD [Synechococcus sp. CC9311]
          Length = 440

 Score =  225 bits (573), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 77/313 (24%), Positives = 143/313 (45%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE--------------HG------------ 45
            E  +  Y+ EI +I +L   EE  LA++  +              +G            
Sbjct: 128 TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLHLEELAAQFESDNGKLPETKEWAALV 187

Query: 46  -------------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 188 EMPVIRFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 247

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 248 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKVLSQE 302

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA+ + ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 303 FGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADIENPE 360

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
           Q + +   R++    L   ++ L+PRER +   R   ++    TLE +   F+V+RER+R
Sbjct: 361 QDVAKNLLRED----LEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIR 416

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 417 QIEAKALRKLRHP 429


>gi|52842571|ref|YP_096370.1| RNA polymerase sigma 70 factor (RpoD) [Legionella pneumophila
           subsp. pneumophila str. Philadelphia 1]
 gi|52629682|gb|AAU28423.1| RNA polymerase sigma 70 factor (RpoD) [Legionella pneumophila
           subsp. pneumophila str. Philadelphia 1]
          Length = 623

 Score =  225 bits (573), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 70/249 (28%), Positives = 118/249 (47%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 374 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 433

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +   T     PE   
Sbjct: 434 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQILQETGREATPE--- 488

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+K+ +SE ++  +        S+   +   D + S   D++    D   +  I+   
Sbjct: 489 ELAEKMELSEDKIRKVLKIAKEPISMETPV--GDDDDSHLGDFI---EDNNIESPIDMAT 543

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            +  R      +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 544 AEGLREATLEILETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALR 603

Query: 279 KVQESIQKQ 287
           K++   + +
Sbjct: 604 KLRHPSRSE 612


>gi|145347899|ref|XP_001418397.1| predicted protein [Ostreococcus lucimarinus CCE9901]
 gi|144578626|gb|ABO96690.1| predicted protein [Ostreococcus lucimarinus CCE9901]
          Length = 344

 Score =  225 bits (573), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 77/336 (22%), Positives = 140/336 (41%), Gaps = 56/336 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------------- 43
               +  Y+ +I  + +L   +E  LAKR ++                            
Sbjct: 13  ATDSMRSYLKDIGSVTLLNAGQEVELAKRIQDLMHLESIRENLVEETGPGAEVTDYQWAS 72

Query: 44  -------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
                            SA + ++ ++LRLVV IA  Y    +   +++ EG +GL++  
Sbjct: 73  AAGLNVQALHQRLRDGKSAKNEMIQANLRLVVSIAKKYANSNMSFQDLIQEGCVGLIRGA 132

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +KFD +RG++ +TY+ WWI+ A+   I      +++        LF  + R+    Q   
Sbjct: 133 EKFDFQRGYKFSTYAHWWIRQAVTRSISDQSRTIRLPVH-----LFEIISRISKMEQKFA 187

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
            +N +      IA ++++S  ++  +        SL A     D      +D LV   D 
Sbjct: 188 LHNGRNPTTEEIAAEMDMSAEKITQIKKAAQAPVSL-AQTMGGDNKGRTVEDTLV---DV 243

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRER 268
             +   +   +   +  L   ++ LNPRER +   R   ++    TLE + + F V+RER
Sbjct: 244 TAEGPEKVSGKSLLKEDLENVLNTLNPRERDVLRLRYGLDDGRVKTLEEIGTVFSVTRER 303

Query: 269 VRQIEARAFKKVQESIQKQVE----LSSSPPLLQKP 300
           +RQIEA+A +K+++  +  +       S    L KP
Sbjct: 304 IRQIEAKALRKLKQPSRNSILQEYFADSDASSLPKP 339


>gi|302036606|ref|YP_003796928.1| RNA polymerase, sigma S (sigma 38) factor [Candidatus Nitrospira
           defluvii]
 gi|300604670|emb|CBK41002.1| RNA polymerase, sigma S (sigma 38) factor [Candidatus Nitrospira
           defluvii]
          Length = 332

 Score =  225 bits (573), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 87/290 (30%), Positives = 145/290 (50%), Gaps = 13/290 (4%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           NR   S    G   +  Y+ E+RK  +L  +EE  L KR    GD +A   ++ ++LRLV
Sbjct: 48  NRPAESGRAEGLDTIKSYLREVRKSTLLNFKEEQALGKRVM-AGDEAARQEMIEANLRLV 106

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           + I   Y   G P +++V EGN+GL++AV+KF+ +RGFR +TY+ WWI+  ++  I+   
Sbjct: 107 ISIGKRYMNRGFPFADIVEEGNLGLIKAVEKFNYKRGFRFSTYASWWIRQFIERAIINQG 166

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            LV++     ++     L R  G ++ +     +  +   +A KL  S +EV  +   + 
Sbjct: 167 KLVRLPVHVVER-----LNRYLGKVEQLVHELGREPRADEVAAKLKTSVAEVDDLKQLVR 221

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              SL++ I  SD+  +  +D +    D       E  E   RR  L   +  L  +ER 
Sbjct: 222 TTCSLDSPI--SDRQDTFLRDVI---EDPLCLTPAETTEGVMRRAELMAWVKELPEKERT 276

Query: 242 IFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           +  AR   +     TLE +  E  ++RERVRQIE  A  +++  I+++  
Sbjct: 277 VILARFGLDGAESRTLEEIGQEMGLTRERVRQIETAALARLRGIIERKTM 326


>gi|158425267|ref|YP_001526559.1| RNA polymerase sigma factor RpoD [Azorhizobium caulinodans ORS 571]
 gi|158332156|dbj|BAF89641.1| sigma-70 [Azorhizobium caulinodans ORS 571]
          Length = 690

 Score =  225 bits (573), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 71/258 (27%), Positives = 122/258 (47%), Gaps = 15/258 (5%)

Query: 34  EYVLAKRYREHGDLSAAH---RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           E+    +  + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV
Sbjct: 434 EFRKIVQMVQKGEKEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 493

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
            KF+  RG++ +TY+ WWI+ A+   I      ++I        +   + ++    + + 
Sbjct: 494 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQML 548

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
               +      +A+KL +   +V  +        SL   I   D+  S   D++    D 
Sbjct: 549 HEIGREPTPEELAEKLGMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDK 603

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRER 268
              + I+   + N R   TR ++ L PRE R+   R         TLE +  +F V+RER
Sbjct: 604 NAVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRER 663

Query: 269 VRQIEARAFKKVQESIQK 286
           +RQIEA+A +K++   + 
Sbjct: 664 IRQIEAKALRKLKHPSRS 681


>gi|258653916|ref|YP_003203072.1| RNA polymerase sigma factor SigB [Nakamurella multipartita DSM
           44233]
 gi|258557141|gb|ACV80083.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nakamurella
           multipartita DSM 44233]
          Length = 334

 Score =  225 bits (573), Expect = 8e-57,   Method: Composition-based stats.
 Identities = 73/301 (24%), Positives = 138/301 (45%), Gaps = 38/301 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRY------------------REHGDLS--------AAHR 52
           Y++ I K  +L  ++E  LAKR                   +   DL         A + 
Sbjct: 41  YLNGIGKTALLTAEQEVELAKRIEAGVFAAHVLESDVEMSPQRRKDLRMVVRDGGRARNH 100

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 101 LLVANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQA 160

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +      +++     ++     L RLK  L      +     +  +A +  + E +
Sbjct: 161 ISRGMADQGRTIRLPVHLVEQ--VNKLSRLKRELHQQLGRD---ATLAELAHESGIPEEK 215

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           +  +        SL+  + S ++  +   D++        +  +         + + R +
Sbjct: 216 IADLLDHARDPVSLDMPVGSDEE--APLGDFIEDSESTSAEAAVVA---GFMHDDINRVL 270

Query: 233 SVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
             L+ RE+ +   R   ++  P TL+ +   F +SRERVRQIE  +  K++   + +V  
Sbjct: 271 RTLDDREQTVVRLRYGLDDGRPRTLDEIGRHFGISRERVRQIERDSMAKLRVGDRSEVLR 330

Query: 291 S 291
           S
Sbjct: 331 S 331


>gi|70732951|ref|YP_262722.1| RNA polymerase sigma factor RpoD [Pseudomonas fluorescens Pf-5]
 gi|1710687|sp|P52326|RPOD_PSEFL RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|929808|emb|CAA59134.1| sigma 70 [Pseudomonas fluorescens]
 gi|68347250|gb|AAY94856.1| RNA polymerase sigma factor RpoD [Pseudomonas fluorescens Pf-5]
          Length = 615

 Score =  225 bits (573), Expect = 9e-57,   Method: Composition-based stats.
 Identities = 69/263 (26%), Positives = 121/263 (46%), Gaps = 14/263 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L+  E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 355 LKIAEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 414

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 415 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 472

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    + +++ + E ++  +        S+   I   D   S   D++  
Sbjct: 473 LQEMGREPTPE---ELGERMEMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 525

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q  I+    ++ +      +S L  RE ++   R   +     TLE +  +F+V
Sbjct: 526 -EDSTMQSPIDVATVESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 584

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   + +
Sbjct: 585 TRERIRQIEAKALRKLRHPTRSE 607


>gi|261250229|ref|ZP_05942805.1| RNA polymerase sigma factor RpoS [Vibrio orientalis CIP 102891]
 gi|260939345|gb|EEX95331.1| RNA polymerase sigma factor RpoS [Vibrio orientalis CIP 102891]
          Length = 323

 Score =  225 bits (573), Expect = 9e-57,   Method: Composition-based stats.
 Identities = 79/288 (27%), Positives = 140/288 (48%), Gaps = 13/288 (4%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
            ++              Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLV
Sbjct: 34  AKEEFDASTKSLDATQLYLGEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLV 92

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           VKI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++   
Sbjct: 93  VKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQT 152

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             +++      K L   LR  +     ++           IA +L+    +V  M     
Sbjct: 153 RTIRLPIHVV-KELNIYLRTAR----ELSQKLDHEPTAEEIATQLDKPVDDVSKMLRLNE 207

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              S++  I           D +   ++   +V  + +   + ++ L   +  LNP+++ 
Sbjct: 208 RISSVDTPI--GGDGEKALLDIIPDINNSDPEVSTQDD---DIKSSLIHWLDELNPKQKE 262

Query: 242 IFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +   R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 263 VLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILIKQ 310


>gi|269837876|ref|YP_003320104.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphaerobacter
           thermophilus DSM 20745]
 gi|269787139|gb|ACZ39282.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphaerobacter
           thermophilus DSM 20745]
          Length = 341

 Score =  225 bits (573), Expect = 9e-57,   Method: Composition-based stats.
 Identities = 80/270 (29%), Positives = 133/270 (49%), Gaps = 13/270 (4%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
               +  Y+ +I + P+L  +EE  LAKR  E GD+ A  R V S+LRLVV IA  Y G 
Sbjct: 68  ATDPIRLYLRDIAQAPLLTAEEEVELAKRI-EEGDVEALQRFVRSNLRLVVSIAKRYVGR 126

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL + +++ EGN+GL++AV+K+D  RG+R +TY+ WWI+ A+   I      +++     
Sbjct: 127 GLSLLDLIQEGNLGLIRAVQKYDWRRGYRFSTYATWWIRQAITRAIADQGRTIRLPVH-- 184

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
              +  ++ R +  +  +T    +P +   +A+ ++V   +V           SL   I 
Sbjct: 185 ---MIDSITRYRRTVMQLTQELGRPPRAEEVAEAMSVPPEKVEQFIRAAQRTISLEKPI- 240

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             +       D +    D   +   E+      +  +   +  L PRER + + R    N
Sbjct: 241 -GEDEEGTLADLIA---DEVARSPEEEAVETLLQRDVAEVLEELTPRERLVLQLRFGLGN 296

Query: 252 --PVTLENLSSEFEVSRERVRQIEARAFKK 279
             P TL  +  + ++SRERVRQIE+ A +K
Sbjct: 297 GSPHTLSEVGQQLDISRERVRQIESEALRK 326


>gi|99081981|ref|YP_614135.1| RNA polymerase sigma factor RpoD [Ruegeria sp. TM1040]
 gi|99038261|gb|ABF64873.1| RNA polymerase, sigma 38 subunit, RpoS [Ruegeria sp. TM1040]
          Length = 664

 Score =  225 bits (573), Expect = 9e-57,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 424 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 483

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A+KL
Sbjct: 484 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAEKL 538

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++N + 
Sbjct: 539 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAVLPLDSAIQENLKE 593

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 594 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 653

Query: 285 QK 286
           + 
Sbjct: 654 RS 655


>gi|163736875|ref|ZP_02144293.1| RNA polymerase, sigma 32 subunit, RpoH [Phaeobacter gallaeciensis
           BS107]
 gi|161389479|gb|EDQ13830.1| RNA polymerase, sigma 32 subunit, RpoH [Phaeobacter gallaeciensis
           BS107]
          Length = 292

 Score =  225 bits (573), Expect = 9e-57,   Method: Composition-based stats.
 Identities = 105/270 (38%), Positives = 174/270 (64%), Gaps = 6/270 (2%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
               K  +L+ + E  LA  +R+  D+ A HRL+ +++RL + +A  +R YG P+++++ 
Sbjct: 13  KRAMKAELLDAETELQLAYAWRDERDVQALHRLINAYMRLAISMASKFRRYGAPMNDLIQ 72

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           E  +GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFN+R
Sbjct: 73  EAGLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMR 132

Query: 141 RLKGHLQAITD----NNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDK 195
           R++  L+           K +    IA ++ V   +V  M+ RLAG D SLNA + SS+ 
Sbjct: 133 RVQAQLERQAQSDGARLDKHQLHQQIATEIGVPLRDVQMMDGRLAGSDFSLNA-VQSSED 191

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
              +W + L  D     +++ E  + +  R+ L  +M  LN RER I   R+L+E P TL
Sbjct: 192 EGREWIEALEDDSAQAAELVEESHDTRQLRDWLVEAMQALNERERFIITERKLREKPRTL 251

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           E+L +E ++S+ERVRQ+EA AF+K+++S++
Sbjct: 252 ESLGNELDLSKERVRQLEAGAFQKMRKSLE 281


>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 =  225 bits (573), Expect = 9e-57,   Method: Composition-based stats.
 Identities = 70/249 (28%), Positives = 118/249 (47%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 372 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 431

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +   T     PE   
Sbjct: 432 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQILQETGREATPE--- 486

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+K+ +SE ++  +        S+   +   D + S   D++    D   +  I+   
Sbjct: 487 ELAEKMELSEDKIRKVLKIAKEPISMETPV--GDDDDSHLGDFI---EDNNIESPIDMAT 541

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            +  R      +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 542 AEGLREATLEILETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALR 601

Query: 279 KVQESIQKQ 287
           K++   + +
Sbjct: 602 KLRHPSRSE 610


>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 =  225 bits (573), Expect = 9e-57,   Method: Composition-based stats.
 Identities = 70/246 (28%), Positives = 117/246 (47%), Gaps = 12/246 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 394 EREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 453

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    + +     +      +
Sbjct: 454 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREPTPEEL 508

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+KL +   +V  +        SL   I   D+  S   D++    D    + I+   + 
Sbjct: 509 AEKLAMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAVLPIDAAIQS 563

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 564 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKL 623

Query: 281 QESIQK 286
           +   + 
Sbjct: 624 KHPSRS 629


>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 =  225 bits (573), Expect = 9e-57,   Method: Composition-based stats.
 Identities = 70/249 (28%), Positives = 118/249 (47%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 372 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 431

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +   T     PE   
Sbjct: 432 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQILQETGREATPE--- 486

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+K+ +SE ++  +        S+   +   D + S   D++    D   +  I+   
Sbjct: 487 ELAEKMELSEDKIRKVLKIAKEPISMETPV--GDDDDSHLGDFI---EDNNIESPIDMAT 541

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            +  R      +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 542 AEGLREATLEILETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALR 601

Query: 279 KVQESIQKQ 287
           K++   + +
Sbjct: 602 KLRHPSRSE 610


>gi|149202416|ref|ZP_01879389.1| RNA polymerase sigma-32 factor [Roseovarius sp. TM1035]
 gi|149144514|gb|EDM32545.1| RNA polymerase sigma-32 factor [Roseovarius sp. TM1035]
          Length = 277

 Score =  225 bits (573), Expect = 9e-57,   Method: Composition-based stats.
 Identities = 105/268 (39%), Positives = 170/268 (63%), Gaps = 6/268 (2%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K  ML+ + E  LA  +R+  D  A HRL+ +++RL + +A  +R YG P+++++ E  
Sbjct: 1   MKAEMLDAETELALAYAWRDQRDEEALHRLINAYMRLAISMASKFRRYGAPMNDLIQEAG 60

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           +GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFN+RR++
Sbjct: 61  LGLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQ 120

Query: 144 GHLQAITDNNLKP----EQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSS 198
             L+     N +     +    IA ++ V   +V  M  RL+G D SLNA   SS+    
Sbjct: 121 ARLEREALANGEQLDGYQLREMIAHEVGVPLRDVEMMEGRLSGSDFSLNA-TQSSEDEGR 179

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           QW D L  D    ++++    +    R  L  ++S LN RER I   R+L+++P TLE+L
Sbjct: 180 QWIDTLEDDGARGDEIVERDHDMHALRTWLADALSRLNDRERFIVRERKLRDDPRTLESL 239

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQK 286
             E  +S+ERVRQ+EA AF+K+++ ++K
Sbjct: 240 GEELNLSKERVRQLEAAAFQKMRKHLEK 267


>gi|126739146|ref|ZP_01754840.1| RNA polymerase sigma-32 factor [Roseobacter sp. SK209-2-6]
 gi|126719763|gb|EBA16471.1| RNA polymerase sigma-32 factor [Roseobacter sp. SK209-2-6]
          Length = 292

 Score =  225 bits (573), Expect = 9e-57,   Method: Composition-based stats.
 Identities = 103/273 (37%), Positives = 167/273 (61%), Gaps = 6/273 (2%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
            +  K  +L+ + E  LA  +R+  D+ A HRL  +++RL + +A  +  YG P+++++ 
Sbjct: 13  RKAMKAELLDAETERALAYAWRDQRDVKALHRLTNAYMRLAISMAAKFNRYGAPMNDLIQ 72

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           E  +GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFNLR
Sbjct: 73  EAGLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKTLFFNLR 132

Query: 141 RLKGHLQAIT----DNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDK 195
           R++  L+           + +    IA ++ V   +V  M+ RL+G D SLNA   +SD 
Sbjct: 133 RVQAQLERRAYADGHRLDRHQLHQKIASEIGVPLRDVEMMDGRLSGSDFSLNAN-QASDN 191

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
           +  +W D L  +H    + +    +R+  R  L  +M  L  RER I  AR+LQE   TL
Sbjct: 192 DGREWIDALEDEHAEGAEQVEGTHDRRQLRQWLVEAMQSLTERERFIIVARKLQEPFRTL 251

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           E+L  E  +S+ERVRQ+EA A KK+++++    
Sbjct: 252 EDLGQELNLSKERVRQLEAAALKKMRKALASHA 284


>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 =  225 bits (573), Expect = 9e-57,   Method: Composition-based stats.
 Identities = 64/243 (26%), Positives = 115/243 (47%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 394 RDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 453

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + ++    +              +A K+
Sbjct: 454 WWIRQAITRSIADQARTIRIPVH-----MIETINKMNRISRQHLQEFGFEPDASLLAAKM 508

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D      IE   +   R+
Sbjct: 509 EIPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDASNTAPIEAAMQAGLRD 563

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E  +  TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 564 VVKDILDGLTPREAKVLRMRFGIEMTSDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPS 623

Query: 285 QKQ 287
           +  
Sbjct: 624 RSD 626


>gi|1575485|gb|AAB09543.1| LprpoD [Legionella pneumophila]
          Length = 620

 Score =  225 bits (573), Expect = 9e-57,   Method: Composition-based stats.
 Identities = 73/258 (28%), Positives = 122/258 (47%), Gaps = 14/258 (5%)

Query: 34  EYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           E     R    GD +  A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV 
Sbjct: 362 EIKDINRKMSIGDEARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVD 421

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +   T 
Sbjct: 422 KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQILQETG 479

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
               PE    +A+K+ +SE ++  +        S+   +   D + S   D++    D  
Sbjct: 480 REATPE---ELAEKMELSEDKIRKVLKIAKEPISMETPV--GDDDDSHLGDFI---EDNN 531

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERV 269
            +  I+    +  R      +  L PRE ++   R   E     TLE +  +F+V+RER+
Sbjct: 532 IESPIDMATAEGLREATLEILETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERI 591

Query: 270 RQIEARAFKKVQESIQKQ 287
           RQIEA+A +K++   + +
Sbjct: 592 RQIEAKALRKLRHPSRSE 609


>gi|295087657|emb|CBK69180.1| RNA polymerase sigma factor, sigma-70 family [Bacteroides
           xylanisolvens XB1A]
          Length = 286

 Score =  225 bits (573), Expect = 9e-57,   Method: Composition-based stats.
 Identities = 75/287 (26%), Positives = 144/287 (50%), Gaps = 12/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI +  ++  +EE  LA+R R+ GD  A  +L  ++LR VV
Sbjct: 5   KITKSITNRESASLDKYLQEIGREDLITVEEEVELAQRIRK-GDRVALEKLTRANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 64  SVAKQYQNQGLSLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    NQ      + +     +   +    PE    +A +L +   ++         
Sbjct: 124 IVRLP--LNQVGSLNKISKAFSKFEQENERRPSPE---ELAVELEIPVDKISDTLKVSGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     + NS    D LV D        +  E        + R++S L  RE+ I
Sbjct: 179 HISVDAPFVEGEDNS--LLDVLVNDDSPMADRSLVNESLA---REIDRALSTLTDREKEI 233

Query: 243 FEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +      +  +TLE +  +F ++RERVRQI+ +A +++++S + ++
Sbjct: 234 IQMFFGIGQQEMTLEEIGDKFGLTRERVRQIKEKAIRRLRQSNRSKL 280


>gi|296532787|ref|ZP_06895466.1| RNA polymerase sigma factor RpoD [Roseomonas cervicalis ATCC 49957]
 gi|296266895|gb|EFH12841.1| RNA polymerase sigma factor RpoD [Roseomonas cervicalis ATCC 49957]
          Length = 639

 Score =  225 bits (573), Expect = 9e-57,   Method: Composition-based stats.
 Identities = 69/241 (28%), Positives = 117/241 (48%), Gaps = 12/241 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 400 QAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 459

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I        +   + +L    + +     +  Q   +A+KL 
Sbjct: 460 WIRQAITRSIADQARTIRIPVH-----MIETINKLVRTSRQMLHEIGREPQPEELAEKLG 514

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +   +V  +        SL   I   D+  S   D++    D    + ++   + N R  
Sbjct: 515 MPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDKAAIIPLDAAIQSNLREA 569

Query: 228 LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   +
Sbjct: 570 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTRERIRQIEAKALRKLKHPSR 629

Query: 286 K 286
            
Sbjct: 630 S 630


>gi|307611207|emb|CBX00855.1| RNA polymerase sigma factor rpoD [Legionella pneumophila 130b]
          Length = 619

 Score =  225 bits (573), Expect = 9e-57,   Method: Composition-based stats.
 Identities = 70/249 (28%), Positives = 118/249 (47%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 370 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +   T     PE   
Sbjct: 430 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQILQETGREATPE--- 484

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+K+ +SE ++  +        S+   +   D + S   D++    D   +  I+   
Sbjct: 485 ELAEKMELSEDKIRKVLKIAKEPISMETPV--GDDDDSHLGDFI---EDNNIESPIDMAT 539

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            +  R      +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 540 AEGLREATLEILETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 279 KVQESIQKQ 287
           K++   + +
Sbjct: 600 KLRHPSRSE 608


>gi|262378901|ref|ZP_06072058.1| RNA polymerase sigma factor sigma-70 [Acinetobacter radioresistens
           SH164]
 gi|262300186|gb|EEY88098.1| RNA polymerase sigma factor sigma-70 [Acinetobacter radioresistens
           SH164]
          Length = 629

 Score =  225 bits (573), Expect = 9e-57,   Method: Composition-based stats.
 Identities = 66/249 (26%), Positives = 114/249 (45%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 382 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 441

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            + R+   L         PE   
Sbjct: 442 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKINRVSRQLLQEMGREPTPE--- 496

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + ++L + E +V  +        S+   I   D   S   D++    D      ++   
Sbjct: 497 ELGERLEMDEVKVRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDQNITSPVDAAT 551

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFK 278
            +  +      +  L  RE ++ + R   + P   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 552 SEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALR 611

Query: 279 KVQESIQKQ 287
           K++   + +
Sbjct: 612 KLRHPSRSE 620


>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 =  225 bits (573), Expect = 9e-57,   Method: Composition-based stats.
 Identities = 70/249 (28%), Positives = 118/249 (47%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 370 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +   T     PE   
Sbjct: 430 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQILQETGREATPE--- 484

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+K+ +SE ++  +        S+   +   D + S   D++    D   +  I+   
Sbjct: 485 ELAEKMELSEDKIRKVLKIAKEPISMETPV--GDDDDSHLGDFI---EDNNIESPIDMAT 539

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            +  R      +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 540 AEGLREATLEILETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 279 KVQESIQKQ 287
           K++   + +
Sbjct: 600 KLRHPSRSE 608


>gi|332704204|ref|ZP_08424292.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           africanus str. Walvis Bay]
 gi|332554353|gb|EGJ51397.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           africanus str. Walvis Bay]
          Length = 594

 Score =  225 bits (573), Expect = 9e-57,   Method: Composition-based stats.
 Identities = 75/261 (28%), Positives = 121/261 (46%), Gaps = 12/261 (4%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE +   R        A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV K
Sbjct: 340 EEVLWRIRRGNENASRAKRELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 399

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RG++ +TY+ WWI+ A+   I      ++I            L R   +L      
Sbjct: 400 FEYQRGYKFSTYATWWIRQAITRAIADQARTIRIPVHM--IETINKLIRTSRYLVQELGR 457

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +  PE    IA++++    +V  +        SL   I   D+  S   D++    D + 
Sbjct: 458 DPTPE---EIAERMDYPIEKVKKVLKIAKEPISLETPI--GDEEDSSLGDFI---EDKKA 509

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
               E+         + + +S L PRE ++   R         TLE +   F V+RER+R
Sbjct: 510 VAPAEEVVNTKLSEQIGKVLSDLTPREEQVLRKRFGIGEKSDHTLEEVGKLFNVTRERIR 569

Query: 271 QIEARAFKKVQESIQKQVELS 291
           QIEA+A +K++  ++ Q+  S
Sbjct: 570 QIEAKALRKLRHPVRSQILRS 590



 Score = 35.9 bits (82), Expect = 7.1,   Method: Composition-based stats.
 Identities = 13/42 (30%), Positives = 25/42 (59%), Gaps = 1/42 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVT 55
             +  Y+ E+  +P+L+++ E V+AK+  E G+L   + LV 
Sbjct: 104 DPVRMYLREMGSVPLLDREGEVVIAKKI-ESGELDVLYALVE 144


>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 =  225 bits (573), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 66/249 (26%), Positives = 114/249 (45%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 379 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 438

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            + R+   L         PE   
Sbjct: 439 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKINRVSRQLLQEMGREPTPE--- 493

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + ++L + E +V  +        S+   I   D   S   D++    D      ++   
Sbjct: 494 ELGERLEMDEVKVRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDQNITSPVDAAT 548

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFK 278
            +  +      +  L  RE ++ + R   + P   TLE +  +F+V+RER+RQIEA+A +
Sbjct: 549 SEGLKEATREVLENLTEREAKVLKMRFGIDMPTDHTLEEVGKQFDVTRERIRQIEAKALR 608

Query: 279 KVQESIQKQ 287
           K++   + +
Sbjct: 609 KLRHPSRSE 617


>gi|291278687|ref|YP_003495522.1| DNA-directed RNA polymerase sigma 70 factor [Deferribacter
           desulfuricans SSM1]
 gi|290753389|dbj|BAI79766.1| DNA-directed RNA polymerase sigma 70 factor [Deferribacter
           desulfuricans SSM1]
          Length = 298

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 76/275 (27%), Positives = 145/275 (52%), Gaps = 12/275 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            ++ Y++EI K P L K+EE  L+KR  E GD  A + ++  +L+LVV IA  Y   GL 
Sbjct: 26  SITIYLNEIIKYPTLSKEEEIELSKRI-EQGDEEAKNLMINCNLKLVVSIAKKYNNRGLQ 84

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGNIGL++AV+KFD  +GF+ +TY+ WWI+ A++  ++    +V+I    N+  
Sbjct: 85  LIDLINEGNIGLIKAVEKFDYRKGFKFSTYATWWIRQAIERALVNQTKMVRIPVHMNE-- 142

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
              N+ ++K   + +     +   +  ++ + N+S   +      +  + S++  I  ++
Sbjct: 143 ---NINKVKKATEKLRRKLKREPTLFELSTECNMSLLTIQKTIDAMQQNISIDGTI--NE 197

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NP 252
            ++S   D L       +    +K  ++  R ++   +  LN  E+ +   R   +   P
Sbjct: 198 DDNSTLHDILPDPESKAD--PFKKIVQEKNRELIMNWIECLNENEKELIIKRFGLDGKEP 255

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            TL+ +     V+RERVRQIE R   K++  ++ +
Sbjct: 256 ETLDKIGKRLGVTRERVRQIEKRILTKLRNHLKTK 290


>gi|54298252|ref|YP_124621.1| RNA polymerase sigma factor rpoD (sigma-70) [Legionella pneumophila
           str. Paris]
 gi|53752037|emb|CAH13463.1| RNA polymerase sigma factor rpoD (Sigma-70) [Legionella pneumophila
           str. Paris]
          Length = 621

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 70/249 (28%), Positives = 118/249 (47%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 372 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 431

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +   T     PE   
Sbjct: 432 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQILQETGREATPE--- 486

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+K+ +SE ++  +        S+   +   D + S   D++    D   +  I+   
Sbjct: 487 ELAEKMELSEDKIRKVLKIAKEPISMETPV--GDDDDSHLGDFI---EDNNIESPIDMAT 541

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            +  R      +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 542 AEGLREATLEILETLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALR 601

Query: 279 KVQESIQKQ 287
           K++   + +
Sbjct: 602 KLRHPSRSE 610


>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 =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 67/247 (27%), Positives = 114/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E    SA   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 502 EAKARSAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 561

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T    +P     +
Sbjct: 562 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGQEPEP---AVL 616

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+ ++E ++  +        S+   I   D   S   D++    D       +     
Sbjct: 617 AEKMEMTEEKIRKILKISKEPISMETPI--GDDEDSHLGDFI---EDVSTMEPADAAIYA 671

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             R +    +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 672 GLRTVTKDVLDSLTPREAKVLRMRFGIEMNTDHTLEEVGRQFDVTRERIRQIEAKALRKL 731

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 732 RHPARSD 738


>gi|42521092|ref|NP_967007.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of
           Drosophila melanogaster]
 gi|42410833|gb|AAS14941.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of
           Drosophila melanogaster]
          Length = 642

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 72/260 (27%), Positives = 124/260 (47%), Gaps = 15/260 (5%)

Query: 32  QEEYVLAKRYREHGDL--SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           QE   L KR ++H      A   ++ ++LRLVV IA  Y   GL + +++ EGNIGLM+A
Sbjct: 386 QEFKELIKRIQKHEREVSEAKQEMIKANLRLVVSIAKKYSKRGLDLLDLIQEGNIGLMKA 445

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V KFD +RG++ +TY  WW++ ++   I     +V+I     +      + ++   L+ +
Sbjct: 446 VDKFDYKRGYKFSTYGTWWVRQSITRAIPEQSKVVRIPVHMVEI-----ISKINRALRKM 500

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
           T    +   +  ++ +L +    +  +        SL A     D  SS + D +    D
Sbjct: 501 THEMGREPTLEELSVELTMPLERIRKVMKIARDPVSLEAPTGKDD--SSTFGDCI---ED 555

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSR 266
            +     +     + R + T  ++ L P+E RI   R          TLE +   F V+R
Sbjct: 556 KRVSRPEDAAILADLRGITTNVLATLTPKEERILRMRFGLGKDGKEHTLEEVGKIFNVTR 615

Query: 267 ERVRQIEARAFKKVQESIQK 286
           ER+RQIEA+A +K++   + 
Sbjct: 616 ERIRQIEAKALRKLKHPSRA 635


>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 =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 66/249 (26%), Positives = 115/249 (46%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 323 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 382

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 383 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPTPE--- 437

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + +++ + E ++  +        S+   I   D   S   D++    D   Q  I+   
Sbjct: 438 ELGERMEMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDSAMQSPIDVAT 492

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            ++ +      +S L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 493 VESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 552

Query: 279 KVQESIQKQ 287
           K++   + +
Sbjct: 553 KLRHPTRSE 561


>gi|254362696|ref|ZP_04978782.1| DNA-directed RNA polymerase sigma subunit RpoD [Mannheimia
           haemolytica PHL213]
 gi|153094317|gb|EDN75178.1| DNA-directed RNA polymerase sigma subunit RpoD [Mannheimia
           haemolytica PHL213]
          Length = 623

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 117/247 (47%), Gaps = 12/247 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 383 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 442

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            L R+             PE    +A+++
Sbjct: 443 WWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQCLQEMGREATPE---ELAERM 497

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D   ++ ++    ++ R 
Sbjct: 498 GMPEDKIRKVLKIAKEPISMETPI--GDDDDSHLGDFI---QDESLELPLDSATAESLRM 552

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                +  L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 553 ATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 612

Query: 285 QKQVELS 291
           + +   S
Sbjct: 613 RSETLRS 619


>gi|329960773|ref|ZP_08299079.1| putative RNA polymerase sigma factor RpoD [Bacteroides fluxus YIT
           12057]
 gi|328532374|gb|EGF59175.1| putative RNA polymerase sigma factor RpoD [Bacteroides fluxus YIT
           12057]
          Length = 286

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 75/287 (26%), Positives = 144/287 (50%), Gaps = 12/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI +  ++  +EE  LA+R R+ GD  A  +L  ++LR VV
Sbjct: 5   KITKSITNRESASLDKYLQEIGREDLITVEEEVELAQRIRK-GDRIALEKLTRANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 64  SVAKQYQNQGLSLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    NQ      + +     +   +    PE    +A +L +   ++         
Sbjct: 124 IVRLP--LNQVGSLNKISKAFSKFEQENERRPSPE---ELADELEIPVDKISDTLKVSGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     + NS    D LV D        +  E        + R++S L  RE+ I
Sbjct: 179 HISVDAPFVEGEDNS--LLDVLVNDDSPMADRSLVNESLA---REIDRALSTLTEREKEI 233

Query: 243 FEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +      +  +TLE +  +F ++RERVRQI+ +A +++++S + ++
Sbjct: 234 IQMFFGIGQQEMTLEEIGDKFGLTRERVRQIKEKAIRRLRQSNRSKL 280


>gi|189467039|ref|ZP_03015824.1| hypothetical protein BACINT_03421 [Bacteroides intestinalis DSM
           17393]
 gi|224535443|ref|ZP_03675982.1| hypothetical protein BACCELL_00305 [Bacteroides cellulosilyticus
           DSM 14838]
 gi|319901765|ref|YP_004161493.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacteroides
           helcogenes P 36-108]
 gi|189435303|gb|EDV04288.1| hypothetical protein BACINT_03421 [Bacteroides intestinalis DSM
           17393]
 gi|224522909|gb|EEF92014.1| hypothetical protein BACCELL_00305 [Bacteroides cellulosilyticus
           DSM 14838]
 gi|319416796|gb|ADV43907.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Bacteroides
           helcogenes P 36-108]
          Length = 286

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 75/287 (26%), Positives = 144/287 (50%), Gaps = 12/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI +  ++  +EE  LA+R R+ GD  A  +L  ++LR VV
Sbjct: 5   KITKSITNRESASLDKYLQEIGREDLITVEEEVELAQRIRK-GDRIALEKLTRANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 64  SVAKQYQNQGLSLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    NQ      + +     +   +    PE    +A +L +   ++         
Sbjct: 124 IVRLP--LNQVGSLNKISKAFSKFEQENERRPSPE---ELADELEIPVDKISDTLKVSGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     + NS    D LV D        +  E        + R++S L  RE+ I
Sbjct: 179 HISVDAPFVEGEDNS--LLDVLVNDDSPMADRSLVNESLA---REIDRALSTLTDREKEI 233

Query: 243 FEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +      +  +TLE +  +F ++RERVRQI+ +A +++++S + ++
Sbjct: 234 IQMFFGIGQQEMTLEEIGDKFGLTRERVRQIKEKAIRRLRQSNRSKL 280


>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 =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 117/247 (47%), Gaps = 12/247 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 383 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 442

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            L R+             PE    +A+++
Sbjct: 443 WWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQCLQEMGREATPE---ELAERM 497

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D   ++ ++    ++ R 
Sbjct: 498 GMPEDKIRKVLKIAKEPISMETPI--GDDDDSHLGDFI---QDESLELPLDSATAESLRM 552

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                +  L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 553 ATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 612

Query: 285 QKQVELS 291
           + +   S
Sbjct: 613 RSETLRS 619


>gi|254293486|ref|YP_003059509.1| RNA polymerase sigma factor RpoD [Hirschia baltica ATCC 49814]
 gi|254042017|gb|ACT58812.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Hirschia baltica
           ATCC 49814]
          Length = 683

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 68/249 (27%), Positives = 118/249 (47%), Gaps = 15/249 (6%)

Query: 43  EHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG+
Sbjct: 436 QKGEREARVAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 495

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWI+ A+   I      ++I        +   + ++    + +     +    
Sbjct: 496 KFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTQRQMLHEIGREPTP 550

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +A+KL +   ++  +        SL   I   D   S   D++    D    + ++  
Sbjct: 551 EELAEKLGLPLEKIRKVLKIAKEPISLETPI--GDDEDSNLGDFI---EDKMALLPVDAA 605

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAF 277
            + N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A 
Sbjct: 606 IQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKAL 665

Query: 278 KKVQESIQK 286
           +K++   + 
Sbjct: 666 RKLKHPSRS 674


>gi|186686393|ref|YP_001869589.1| RNA polymerase sigma factor RpoD [Nostoc punctiforme PCC 73102]
 gi|8118663|gb|AAF73062.1|AF265349_1 primary vegetative sigma factor [Nostoc punctiforme]
 gi|186468845|gb|ACC84646.1| RNA polymerase, sigma 70 subunit, RpoD family [Nostoc punctiforme
           PCC 73102]
          Length = 389

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 79/313 (25%), Positives = 140/313 (44%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAK-------------------------------- 39
            E  +  Y+ EI +I +L   EE  LA+                                
Sbjct: 77  TEDSIRLYLQEIGRIRLLRADEEIELARKIADLLELERVRERLSEQLDRDPRDSEWAEAV 136

Query: 40  -------RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                  RYR H    A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 137 QLPLPAFRYRLHVGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 196

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 197 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKLLSQE 251

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA ++ ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 252 MGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIESDGETPE 309

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
               ++  +   R  L + +  L+PRER +   R   ++    TLE +   F V+RER+R
Sbjct: 310 ----DQVSKNLLREDLEKVLDSLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIR 365

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 366 QIEAKALRKLRHP 378


>gi|114776318|ref|ZP_01451363.1| RpoS [Mariprofundus ferrooxydans PV-1]
 gi|114553148|gb|EAU55546.1| RpoS [Mariprofundus ferrooxydans PV-1]
          Length = 282

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 80/287 (27%), Positives = 143/287 (49%), Gaps = 18/287 (6%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           MS    G   ++ Y+ EI +  +L   EE  LAKR    GD  A H +V ++LRLVVKI+
Sbjct: 1   MSSNSGGLEPMAIYMREISRYELLTAAEEIALAKRIG-AGDKEAHHYMVQANLRLVVKIS 59

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y   G+ +++++ EGN+GL++AV+KFD   G R +TY+ WWI+ A++  I+     ++
Sbjct: 60  RRYMNRGVALADLIEEGNLGLIRAVEKFDVTHGCRFSTYATWWIRQAVERAIMNQSRTIR 119

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           +     +      L  L  H   +     +    V IA+ + VS   +  +       +S
Sbjct: 120 VPVHVGK-----ELYALTKHTNRLRSELERDPTDVEIAEAMGVSVQRIQELMGAAVRTDS 174

Query: 186 LNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            + +++          D+ +YD   D   +   ++ +   R  +L   MS L  +ER + 
Sbjct: 175 ADDMLHDD-------SDFTLYDVTADEAAESPGDQMQTVLRNEILQVWMSKLEKKEREVV 227

Query: 244 EARRLQE---NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             R   +   +P TLE +  +  V+RER+RQI+ +A +K++  + ++
Sbjct: 228 RLRYGLDDAGDPWTLEMIGEQLGVTRERIRQIQVQALQKLRRIVSQE 274


>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 =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 112/247 (45%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 504 EAKARRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 563

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T    +P     +
Sbjct: 564 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGQEPEP---AVL 618

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+ + E ++  +        S+   I   D   S   D++    D       +     
Sbjct: 619 AEKMEMPEEKIRKILKISKEPISMETPI--GDDEDSHLGDFI---EDASTMEPADAAVYA 673

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             R +    +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 674 GLRTVTKDVLDSLTPREAKVLRMRFGIEMNTDHTLEEVGRQFDVTRERIRQIEAKALRKL 733

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 734 RHPARSD 740


>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 =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 70/272 (25%), Positives = 123/272 (45%), Gaps = 14/272 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKR--YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + EI +   L   E   +A++    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 338 LAEISEDRGLSISEIKEIARQMSISEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 397

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+ +RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 398 LIQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 455

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         P+    +A+++ + E +V  +        S+   I   D   
Sbjct: 456 KLNRVARQMLQEMGREPTPD---ELAERVEMPEDKVRKVLKISKEPISMETPI--GDDED 510

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D       +    +  R      ++ L  RE ++   R   +     TL
Sbjct: 511 SHLGDFV---EDVNVISPSDSAIIEGLREATQGVLNGLTEREAKVLRMRFGIDMNTDHTL 567

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +  +F+V+RER+RQIEA+A +K++   +  
Sbjct: 568 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSD 599


>gi|134098366|ref|YP_001104027.1| RNA polymerase sigma factor SigB [Saccharopolyspora erythraea NRRL
           2338]
 gi|291006932|ref|ZP_06564905.1| RNA polymerase sigma factor SigB [Saccharopolyspora erythraea NRRL
           2338]
 gi|133910989|emb|CAM01102.1| RNA polymerase sigma factor [Saccharopolyspora erythraea NRRL 2338]
          Length = 324

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 73/297 (24%), Positives = 132/297 (44%), Gaps = 38/297 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRY------------------REHGDLS--------AAHR 52
           Y++ I +  +L  QEE  LAKR                       DL         A + 
Sbjct: 31  YLNGIGRTALLTAQEEVDLAKRIEAGVFANHVLETSGKLSPERRSDLKAVVRDGVLAKNH 90

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 91  LMEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQA 150

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +      +++     ++     + R+K  L          E    +A +  ++  +
Sbjct: 151 ITRGMADQSRTIRLPVHLVEQ--VNKIARIKRDLHQKLGREATDE---ELANEAGLTVEK 205

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           V  +        SL+  +    +  +   D++    D +             ++ L R +
Sbjct: 206 VADLLDHSRDPVSLDMPV--GAEEDAPLGDFI---EDAESADAENAVISGFLQDDLRRVL 260

Query: 233 SVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           S L  RE+ +   R   ++  P TL+ +   F +SRERVRQIE     K+++  +  
Sbjct: 261 STLEEREQAVIRMRYGLDDGQPRTLDQIGKAFGLSRERVRQIEREVMSKLRQGDRAD 317


>gi|83309796|ref|YP_420060.1| RNA polymerase sigma factor RpoD [Magnetospirillum magneticum
           AMB-1]
 gi|82944637|dbj|BAE49501.1| DNA-directed RNA polymerase [Magnetospirillum magneticum AMB-1]
          Length = 679

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 71/241 (29%), Positives = 115/241 (47%), Gaps = 12/241 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 440 RAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 499

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I            L R    +         PE    +A+KL+
Sbjct: 500 WIRQAITRSIADQARTIRIPVHM--IETINKLVRTSRQMLHEIGREPTPE---ELAEKLS 554

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +   +V  +        SL   I   D+  S   D++    D    + ++   + N R  
Sbjct: 555 MPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAVLPLDAAIQANLRET 609

Query: 228 LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   +
Sbjct: 610 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSR 669

Query: 286 K 286
            
Sbjct: 670 S 670


>gi|1710688|sp|P52327|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 =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 69/263 (26%), Positives = 120/263 (45%), Gaps = 14/263 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L   E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 354 LTVAEIKEINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 413

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 414 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 471

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    + +++ + E ++  +        S+   I   D   S   D++  
Sbjct: 472 LQEMGREPTPE---ELGERMEMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 524

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q  I     ++ +      +S L  RE ++   R   +     TLE +  +F+V
Sbjct: 525 -EDSTMQSPIYVATVESLKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 583

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A++K++   + +
Sbjct: 584 TRERIRQIEAKAWRKLRHPTRSE 606


>gi|149184445|ref|ZP_01862763.1| RNA polymerase sigma factor RpoD [Erythrobacter sp. SD-21]
 gi|148831765|gb|EDL50198.1| RNA polymerase sigma factor RpoD [Erythrobacter sp. SD-21]
          Length = 668

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 69/251 (27%), Positives = 121/251 (48%), Gaps = 15/251 (5%)

Query: 41  YREHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
             + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 419 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 478

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I        +   + +L    +    +  +  
Sbjct: 479 GYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKLVRCSRQFLHDQGREP 533

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A+KL++   +V  +        SL   I   D+  S   D++    D    + ++
Sbjct: 534 TPEEMAEKLSMPLEKVRKVMKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAIIPVD 588

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              + N +  +TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+
Sbjct: 589 AAIQANLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 648

Query: 276 AFKKVQESIQK 286
           A +K++   + 
Sbjct: 649 ALRKLKHPSRS 659


>gi|109900163|ref|YP_663418.1| RNA polymerase, sigma 28 subunit [Pseudoalteromonas atlantica T6c]
 gi|109702444|gb|ABG42364.1| RNA polymerase, sigma 38 subunit, RpoS [Pseudoalteromonas atlantica
           T6c]
          Length = 327

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 81/268 (30%), Positives = 144/268 (53%), Gaps = 13/268 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   ++R  + GD ++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 56  YLGEIGFSPLLSAEEEVYFSRRALK-GDEASRQRMIVSNLRLVVKIARRYNNRGLALLDL 114

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++       +    
Sbjct: 115 VEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV--VKELNV 172

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
             R    L    D+    E++    +K     ++++ +N R+    S++  I S  +N +
Sbjct: 173 YLRTSRELAQKLDHEPTAEEIAEAVQKPVADVTKMLRLNERIT---SVDTPIGS--ENDN 227

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D +  D+    +   E  + KN +  +   +  LNP++R +   R   L   P TLE
Sbjct: 228 VLLDIIADDNGHDPE---EDLQDKNVKLSIVGWLEDLNPKQREVLARRFGLLGYEPSTLE 284

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++  E  ++RERVRQI+  A +++++ +
Sbjct: 285 DVGVEIGLTRERVRQIQVEALRRLKDML 312


>gi|332880149|ref|ZP_08447831.1| putative RNA polymerase sigma factor RpoD [Capnocytophaga sp. oral
           taxon 329 str. F0087]
 gi|332681908|gb|EGJ54823.1| putative RNA polymerase sigma factor RpoD [Capnocytophaga sp. oral
           taxon 329 str. F0087]
          Length = 286

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 74/287 (25%), Positives = 145/287 (50%), Gaps = 12/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI +  ++  +EE  LA+R R+ GD  A  +L  ++LR VV
Sbjct: 5   KITKSITNRESASLDKYLQEIGREDLITVEEEVELAQRIRK-GDRVALEKLTRANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 64  SVAKQYQNQGLSLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    NQ      + +     +   +    PE    +A +L +   ++         
Sbjct: 124 IVRLP--LNQVGSLNKISKAFSKFEQENERRPSPE---ELADELEIPVDKISDTLKVSGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     + NS    D LV D        +  E        + R++S L+ RE+ I
Sbjct: 179 HISVDAPFVEGEDNS--LLDVLVNDDSPMADRTLVNESLS---REIDRALSTLSEREKEI 233

Query: 243 FEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +      +  +TLE +  +F ++RERVRQI+ +A ++++++ + ++
Sbjct: 234 IQMFFGINHQEMTLEEIGDKFNLTRERVRQIKEKAIRRLRQNTKSKL 280


>gi|294011419|ref|YP_003544879.1| RNA polymerase primary sigma factor [Sphingobium japonicum UT26S]
 gi|292674749|dbj|BAI96267.1| RNA polymerase primary sigma factor [Sphingobium japonicum UT26S]
          Length = 681

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 68/251 (27%), Positives = 120/251 (47%), Gaps = 15/251 (5%)

Query: 41  YREHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
             + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 432 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 491

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I        +   + +L    +       +  
Sbjct: 492 GYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTSRQFLHEQGREP 546

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A++L++   +V  +        SL   I   D+  S   D++    D    + ++
Sbjct: 547 TPEEMAERLSMPLEKVRKVMKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAIIPVD 601

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              + N +  +TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+
Sbjct: 602 AAIQANLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 661

Query: 276 AFKKVQESIQK 286
           A +K++   + 
Sbjct: 662 ALRKLKHPSRS 672


>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 =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 69/263 (26%), Positives = 121/263 (46%), Gaps = 14/263 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L+  E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 356 LKIAEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 415

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 416 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 473

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    + +++ + E ++  +        S+   I   D   S   D++  
Sbjct: 474 LQEMGREPTPE---ELGERMEMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 526

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q  I+    ++ +      +S L  RE ++   R   +     TLE +  +F+V
Sbjct: 527 -EDSTMQSPIDVATVESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 585

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   + +
Sbjct: 586 TRERIRQIEAKALRKLRHPTRSE 608


>gi|225630998|ref|YP_002727789.1| RNA polymerase sigma 70 subunit, RpoD [Wolbachia sp. wRi]
 gi|225592979|gb|ACN95998.1| RNA polymerase sigma 70 subunit, RpoD [Wolbachia sp. wRi]
          Length = 650

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 72/260 (27%), Positives = 124/260 (47%), Gaps = 15/260 (5%)

Query: 32  QEEYVLAKRYREHGDL--SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           QE   L KR ++H      A   ++ ++LRLVV IA  Y   GL + +++ EGNIGLM+A
Sbjct: 394 QEFKELIKRIQKHEREVSEAKQEMIKANLRLVVSIAKKYSKRGLDLLDLIQEGNIGLMKA 453

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V KFD +RG++ +TY  WW++ ++   I     +V+I     +      + ++   L+ +
Sbjct: 454 VDKFDYKRGYKFSTYGTWWVRQSITRAIPEQSKVVRIPVHMVEI-----ISKINRALRKM 508

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
           T    +   +  ++ +L +    +  +        SL A     D  SS + D +    D
Sbjct: 509 THEMGREPTLEELSVELTMPLERIRKVMKIARDPVSLEAPTGKDD--SSTFGDCI---ED 563

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSR 266
            +     +     + R + T  ++ L P+E RI   R          TLE +   F V+R
Sbjct: 564 KRVSRPEDAAILADLRGITTNVLATLTPKEERILRMRFGLGKDGKEHTLEEVGKIFNVTR 623

Query: 267 ERVRQIEARAFKKVQESIQK 286
           ER+RQIEA+A +K++   + 
Sbjct: 624 ERIRQIEAKALRKLKHPSRA 643


>gi|297570260|ref|YP_003691604.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfurivibrio
           alkaliphilus AHT2]
 gi|296926175|gb|ADH86985.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfurivibrio
           alkaliphilus AHT2]
          Length = 555

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 79/264 (29%), Positives = 130/264 (49%), Gaps = 14/264 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L++QE   L  +    E     A +RLV S+LRLVV +A  Y G GL + ++V EGNIGL
Sbjct: 294 LDRQELSALLAQISLGEEISREAKNRLVQSNLRLVVSVAKKYAGRGLQLLDLVQEGNIGL 353

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV+KF+  RG++ +TY+ WWI+ A+   I      ++I        +   + R+    
Sbjct: 354 MKAVEKFEYRRGYKFSTYATWWIRQAVTRAIADQGRTIRIPVH-----MIDTINRMLKGA 408

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +     + +      +A+ L V  ++V S+        SL+  + S +   S   D++  
Sbjct: 409 KEYQRQHGREPTPEEMAEHLGVDIAKVKSILKIAKEPLSLDTPVGSGED--SFLSDFI-- 464

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D       E     + ++ L R +  L PRE  +   R   +    +TLE +   F V
Sbjct: 465 -EDADSTSPDEATIYDSLQDNLARVLKTLTPREEMVLRLRFGIDTATDLTLEEVGENFSV 523

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           +RER+RQIEA+A KK++   +K +
Sbjct: 524 TRERIRQIEAKALKKLKHPTRKSI 547



 Score = 39.4 bits (91), Expect = 0.62,   Method: Composition-based stats.
 Identities = 16/69 (23%), Positives = 32/69 (46%), Gaps = 3/69 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTS--HLRLVVKIAMGYRGY 71
             +  Y+ E+  + +L  +EE  +AK   E G+ +    LV +   L  + +IA   +  
Sbjct: 108 DPVKVYLQEMGAVALLSSEEEVAVAKEI-ERGERTIQDALVIAPPALAYLDEIAKKIQHG 166

Query: 72  GLPISEVVS 80
              +S++V 
Sbjct: 167 NRMLSDIVR 175


>gi|294678570|ref|YP_003579185.1| RNA polymerase sigma factor RpoD [Rhodobacter capsulatus SB 1003]
 gi|1173126|sp|P46400|RPOD_RHOCA RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|881516|gb|AAA70413.1| RpoD [Rhodobacter capsulatus SB 1003]
 gi|294477390|gb|ADE86778.1| RNA polymerase sigma factor RpoD [Rhodobacter capsulatus SB 1003]
          Length = 674

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 434 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 493

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A+KL
Sbjct: 494 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAEKL 548

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++N + 
Sbjct: 549 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAILPLDSAIQENLKE 603

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 604 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 663

Query: 285 QK 286
           + 
Sbjct: 664 RS 665


>gi|163742972|ref|ZP_02150355.1| RNA polymerase sigma factor [Phaeobacter gallaeciensis 2.10]
 gi|161383655|gb|EDQ08041.1| RNA polymerase sigma factor [Phaeobacter gallaeciensis 2.10]
          Length = 662

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 422 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 481

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A+KL
Sbjct: 482 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAEKL 536

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++N + 
Sbjct: 537 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAVLPLDSAIQENLKE 591

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 592 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 651

Query: 285 QK 286
           + 
Sbjct: 652 RS 653


>gi|83644704|ref|YP_433139.1| nonessential primary sigma factor [Hahella chejuensis KCTC 2396]
 gi|83632747|gb|ABC28714.1| nonessential primary sigma factor [Hahella chejuensis KCTC 2396]
          Length = 332

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 80/271 (29%), Positives = 142/271 (52%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R    GD     R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 64  YLNEIGFSPLLTPEEEVHFA-RMARRGDEKGRKRMIESNLRLVVKIARRYVNRGLSLLDL 122

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++       +    
Sbjct: 123 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV--VKELNV 180

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
             R    L    D+    E++  + +K       ++ +N R+    S+++ I  + + S 
Sbjct: 181 YLRASRELTQKLDHEPSAEEIADLLEKPVKDVKRMLGLNERIT---SVDSPIGGNAEKS- 236

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPV-TLE 256
              D +  +       L++  + K     L R +  L+ +++ +   R  L+  P+ TLE
Sbjct: 237 -LLDTVADEASNDPAELLQDSDLKGC---LDRWLDQLSDKQQEVIARRFGLRGYPMSTLE 292

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +  E  ++RERVRQI+  A K+++E ++K+
Sbjct: 293 EVGQEIGLTRERVRQIQVEALKRMRELLEKE 323


>gi|330995823|ref|ZP_08319720.1| putative RNA polymerase sigma factor RpoD [Paraprevotella
           xylaniphila YIT 11841]
 gi|329574553|gb|EGG56118.1| putative RNA polymerase sigma factor RpoD [Paraprevotella
           xylaniphila YIT 11841]
          Length = 286

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 74/287 (25%), Positives = 145/287 (50%), Gaps = 12/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI +  ++  +EE  LA+R R+ GD  A  +L  ++LR VV
Sbjct: 5   KITKSITNRESASLDKYLQEIGREDLITVEEEVELAQRIRK-GDRVALEKLTRANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 64  SVAKQYQNQGLSLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    NQ      + +     +   +    PE    +A +L +   ++         
Sbjct: 124 IVRLP--LNQVGSLNKISKAFSKFEQENERRPSPE---ELADELEIPVDKISDTLKVSGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     + NS    D LV D        +  E        + R++S L+ RE+ I
Sbjct: 179 HISVDAPFVEGEDNS--LLDVLVNDDSPMADRTLVNESLA---REIDRALSTLSEREKEI 233

Query: 243 FEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +      +  +TLE +  +F ++RERVRQI+ +A ++++++ + ++
Sbjct: 234 IQMFFGINHQEMTLEEIGDKFNLTRERVRQIKEKAIRRLRQNTKSKL 280


>gi|159045518|ref|YP_001534312.1| RNA polymerase factor sigma-32 [Dinoroseobacter shibae DFL 12]
 gi|157913278|gb|ABV94711.1| RNA polymerase sigma 32 factor [Dinoroseobacter shibae DFL 12]
          Length = 293

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 106/282 (37%), Positives = 176/282 (62%), Gaps = 9/282 (3%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           +GE+ LSR      +  +L+ + E  LA  +R+  D  A HRL+T+++RL + +A  ++ 
Sbjct: 7   SGEMSLSR---RAMQAELLDAETELRLAYAWRDQRDEEALHRLITAYMRLAISMAAKFKR 63

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
           YG P+++++ E  +GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T+
Sbjct: 64  YGAPMNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTS 123

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKP----EQVVAIAKKLNVSESEVISMNCRLAG-DES 185
           +QK LFFN+RR++  L+    +  +P    +    IA ++ V   +V  M  RLAG D S
Sbjct: 124 SQKSLFFNMRRVQARLEREAASAGEPLDRHQLRQMIATEVGVPLHDVEMMEGRLAGSDYS 183

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           LNA   S++    +W D L        +++ +  + +  R  L  +M  LN RER I   
Sbjct: 184 LNA-TQSTEDEGREWIDTLEDTGAQAAELVEQDHDIETLRGWLITAMDALNERERFIVRE 242

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           R+L++ P TLE+L  E  +S+ERVRQ+EA AF K+++++  Q
Sbjct: 243 RKLRDQPRTLESLGQELGLSKERVRQLEAAAFGKMRKNLMNQ 284


>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 =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 69/272 (25%), Positives = 123/272 (45%), Gaps = 14/272 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +  +L   E   + ++    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 353 LQDIERENILTIGEIKEVNRKMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 412

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 413 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 470

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A ++++ E +V  +        S+   I   D   
Sbjct: 471 KLNRISRQMIQEMGREATPE---ELAARMDMPEDKVRKVLKIAKEPISMETPI--GDDED 525

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D      ++    +  R      ++ L  RE ++   R   +     TL
Sbjct: 526 SHLGDFI---EDSGVISPLDSATAEGLREATQNMLASLTSREAKVLRMRFGIDMNTDHTL 582

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +  +F+V+RER+RQIEA+A +K++   +  
Sbjct: 583 EEVGKQFDVTRERIRQIEAKALRKLRHPTRSD 614


>gi|254511749|ref|ZP_05123816.1| Sigma-70, region 3 family [Rhodobacteraceae bacterium KLH11]
 gi|221535460|gb|EEE38448.1| Sigma-70, region 3 family [Rhodobacteraceae bacterium KLH11]
          Length = 662

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 422 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 481

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A+KL
Sbjct: 482 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAEKL 536

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++N + 
Sbjct: 537 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAVLPLDSAIQENLKE 591

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 592 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 651

Query: 285 QK 286
           + 
Sbjct: 652 RS 653


>gi|94311053|ref|YP_584263.1| RNA polymerase sigma factor RpoS [Cupriavidus metallidurans CH34]
 gi|93354905|gb|ABF08994.1| RNA polymerase sigma 38 (sigma S) factor [Cupriavidus metallidurans
           CH34]
          Length = 386

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 81/278 (29%), Positives = 133/278 (47%), Gaps = 11/278 (3%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
               +  Y++ I   P+L   EE   +    + GD SA   ++  +LRLVV IA GY   
Sbjct: 110 AADTVQHYLNRISIKPLLSAPEELHFST-LAKGGDFSARQVMIERNLRLVVSIAKGYLNR 168

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           G+P+ +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++     
Sbjct: 169 GVPLLDLIEEGNLGLMHAIEKFDPSRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV- 227

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
             R    + R K HL+     + +   +  IA  L  +  EV  +        SL+    
Sbjct: 228 -IRELNQVLRAKRHLEK-GGTDGRDASLEDIAHLLGKTPDEVQDVLALNEHTTSLDTPF- 284

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE- 250
                 S   D+L  +H+      +   E +N   ++   ++ L+ + R + E R     
Sbjct: 285 -DLDPGSSLLDFLSDEHNAAPDQEVAHRELEN---LMKLWLARLSEKHRYVVERRFGLNH 340

Query: 251 -NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             P TLE L+ E  ++RERVRQI+  A  K++     Q
Sbjct: 341 IEPATLEELAEEMGLTRERVRQIQQEALVKLKRHFASQ 378


>gi|260425299|ref|ZP_05779279.1| RNA polymerase sigma factor RpoD [Citreicella sp. SE45]
 gi|260423239|gb|EEX16489.1| RNA polymerase sigma factor RpoD [Citreicella sp. SE45]
          Length = 665

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 70/242 (28%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 425 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 484

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A+KL
Sbjct: 485 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAEKL 539

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++N + 
Sbjct: 540 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAILPLDSAIQENLKE 594

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR +S L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 595 TTTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 654

Query: 285 QK 286
           + 
Sbjct: 655 RS 656


>gi|114764808|ref|ZP_01443990.1| RNA polymerase sigma factor [Pelagibaca bermudensis HTCC2601]
 gi|114542694|gb|EAU45717.1| RNA polymerase sigma factor [Roseovarius sp. HTCC2601]
          Length = 661

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 70/242 (28%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 421 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 480

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A+KL
Sbjct: 481 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAEKL 535

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++N + 
Sbjct: 536 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAILPLDSAIQENLKE 590

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR +S L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 591 TTTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 650

Query: 285 QK 286
           + 
Sbjct: 651 RS 652


>gi|148978207|ref|ZP_01814737.1| DNA-directed RNA polymerase, sigma subunit [Vibrionales bacterium
           SWAT-3]
 gi|145962629|gb|EDK27905.1| DNA-directed RNA polymerase, sigma subunit [Vibrionales bacterium
           SWAT-3]
          Length = 326

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 81/271 (29%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 54  YLGEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 112

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 113 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHVV-KELNIY 171

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA KL+    +V  M        S++  I        
Sbjct: 172 LRTAR----ELSQKLDHEPTAEEIASKLDKPVGDVSKMLRLNERVSSVDTPI--GGDGEK 225

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D +   ++   +V     +  + +N L   +  LNP+++ +   R   L   P TLE
Sbjct: 226 ALLDIIPDINNSDPEV---STQDSDIKNSLIFWLDELNPKQKEVLARRFGLLGYEPSTLE 282

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 283 EVGREISLTRERVRQIQVEGLRRLREILIKQ 313


>gi|33866315|ref|NP_897874.1| RNA polymerase sigma factor RpoD [Synechococcus sp. WH 8102]
 gi|33639290|emb|CAE08298.1| Putative principal RNA polymerase sigma factor [Synechococcus sp.
           WH 8102]
          Length = 471

 Score =  224 bits (572), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 77/313 (24%), Positives = 142/313 (45%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-----------------HGDLS------ 48
            E  +  Y+ EI +I +L   EE  LA++  +                   D        
Sbjct: 159 TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLHLEELAAQFESDNGREPDKKEWAALV 218

Query: 49  ----------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 219 EMPLIRFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 278

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 279 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKVLSQE 333

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA+ + ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 334 FGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADIENPE 391

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
           Q + +   R++    L   ++ L+PRER +   R   ++    TLE +   F+V+RER+R
Sbjct: 392 QDVAKNLLRED----LEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIR 447

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 448 QIEAKALRKLRHP 460


>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 =  224 bits (571), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 63/247 (25%), Positives = 115/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 489 EKASRDAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 548

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    +              +
Sbjct: 549 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKMNRISRQHLQEFGFEPDAPTL 603

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+ + E ++  +        S+   I   D + S   D++    D      ++   + 
Sbjct: 604 AEKMEIPEDKIRKIMMIAKEPISMETPI--GDDDDSHLGDFI---EDTNNVAPVDAAMQA 658

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             R ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 659 GLREVVKDILDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKAIRKL 718

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 719 KHPSRSD 725


>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 =  224 bits (571), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 120/247 (48%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 409 EARSHRAKRDMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 468

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    + I     +      +
Sbjct: 469 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKMNRISRQILQETGQEADAATL 523

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+ ++E ++  +        S+   +   D + S   D++    D    V IE    +
Sbjct: 524 AEKMEMTEDKIHKILKIAKEPISMETPV--GDDDDSHLGDFI---EDSNTTVPIEAAVYE 578

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R+  +  +  L  RE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 579 SLRSATSDILDSLTQREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 638

Query: 281 QESIQKQ 287
           +   + +
Sbjct: 639 RHPSRSE 645


>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 =  224 bits (571), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 64/249 (25%), Positives = 112/249 (44%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 354 IGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 413

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 414 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPTPE--- 468

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + +++++ E +V  +        S+   I   D   S   D++    D      ++   
Sbjct: 469 ELGERMDMPEDKVRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDNTIAQPVDSAT 523

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            +  +      +  L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 524 GQGLQEATKDVLGGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 583

Query: 279 KVQESIQKQ 287
           K++   +  
Sbjct: 584 KLRHPSRSD 592


>gi|90020900|ref|YP_526727.1| RNA polymerase sigma factor RpoS [Saccharophagus degradans 2-40]
 gi|89950500|gb|ABD80515.1| RNA polymerase sigma factor RpoS [Saccharophagus degradans 2-40]
          Length = 333

 Score =  224 bits (571), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 76/277 (27%), Positives = 141/277 (50%), Gaps = 13/277 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A++  + G  ++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 63  YLNEIGFSPLLSAEEEVFFARKALK-GCEASRKRMIESNLRLVVKIARRYVNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++       +    
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV--VKELNV 179

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
             R    L    D+   PE++  + +K       ++++N R+    S++  I  S + + 
Sbjct: 180 YLRAARELSQKLDHEPSPEEIATLLEKPLEDVERMLALNERVT---SMDVPIGPSSEKTV 236

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
                     D      +E  +  +    L   +  L+ ++R +   R         TLE
Sbjct: 237 VDTVA-----DQDVSDPVELLQESDLSQSLDGWLDELSEKQREVVARRFGLRGHETSTLE 291

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
            +  E  ++RERVRQI+  A +++++ ++KQ   ++S
Sbjct: 292 EVGKEIGLTRERVRQIQVEALRRLRDILEKQGLDAAS 328


>gi|332308186|ref|YP_004436037.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Glaciecola
           agarilytica 4H-3-7+YE-5]
 gi|332175515|gb|AEE24769.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Glaciecola
           agarilytica 4H-3-7+YE-5]
          Length = 327

 Score =  224 bits (571), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 80/268 (29%), Positives = 143/268 (53%), Gaps = 13/268 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   ++R  + GD ++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 56  YLGEIGFSPLLSAEEEVYFSRRALK-GDEASRQRMIVSNLRLVVKIARRYNNRGLALLDL 114

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++       +    
Sbjct: 115 VEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV--VKELNV 172

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
             R    L    D+    E++    ++     ++++ +N R+    S++  I S   N +
Sbjct: 173 YLRTSRELAQKLDHEPTAEEIAEAVQRPVADVTKMLRLNERIT---SVDTPIGS--DNDN 227

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D +  D+    +   E  + KN +  +   +  LNP++R +   R   L   P TLE
Sbjct: 228 VLLDIIADDNGHDPE---EDLQDKNVKLSIVGWLEDLNPKQREVLARRFGLLGYEPSTLE 284

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++  E  ++RERVRQI+  A +++++ +
Sbjct: 285 DVGVEIGLTRERVRQIQVEALRRLKDML 312


>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 =  224 bits (571), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 65/250 (26%), Positives = 116/250 (46%), Gaps = 12/250 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 364 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 423

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 424 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPTPE--- 478

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + E ++  +        S+   I   D   S   D++    D      ++   
Sbjct: 479 ELAERMMMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDTTLAQPVDSAT 533

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            ++ +      ++ L  RE ++   R   E     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 534 AESLKAATAEVLAGLTAREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALR 593

Query: 279 KVQESIQKQV 288
           K++   + ++
Sbjct: 594 KLRHPSRSEI 603


>gi|254464472|ref|ZP_05077883.1| Sigma-70 region 3 family [Rhodobacterales bacterium Y4I]
 gi|206685380|gb|EDZ45862.1| Sigma-70 region 3 family [Rhodobacterales bacterium Y4I]
          Length = 662

 Score =  224 bits (571), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 117/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 422 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 481

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A KL
Sbjct: 482 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELADKL 536

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++N + 
Sbjct: 537 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAVLPLDSAIQENLKE 591

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 592 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 651

Query: 285 QK 286
           + 
Sbjct: 652 RS 653


>gi|83951483|ref|ZP_00960215.1| RNA polymerase sigma factor [Roseovarius nubinhibens ISM]
 gi|83836489|gb|EAP75786.1| RNA polymerase sigma factor [Roseovarius nubinhibens ISM]
          Length = 660

 Score =  224 bits (571), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 71/246 (28%), Positives = 118/246 (47%), Gaps = 12/246 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 416 EQEARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 475

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + +L    + +     +      +
Sbjct: 476 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEEL 530

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+KL +   +V  +        SL   I   D+  SQ  D++    D    + ++   + 
Sbjct: 531 AEKLQMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAVLPLDSAIQD 585

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N +   TR +S L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 586 NLKETTTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKL 645

Query: 281 QESIQK 286
           +   + 
Sbjct: 646 KHPSRS 651


>gi|325954752|ref|YP_004238412.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Weeksella virosa
           DSM 16922]
 gi|323437370|gb|ADX67834.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Weeksella virosa
           DSM 16922]
          Length = 288

 Score =  224 bits (571), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 144/276 (52%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI K+ ++  +EE  LA+R +  GD  A  +L  ++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQEIGKVDLITAEEEVELAQRIK-AGDRVALEKLTKANLRFVVSVAKQYQNQGLS 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     +V++    N+  
Sbjct: 76  LPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLP--LNKIG 133

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               + +    L+   +     E++  +   L++SE +V           S++A +   +
Sbjct: 134 SINKINKAYALLEQEHERAPSAEEISEV---LDMSEGDVKESLKNSGRHVSMDAPLV--E 188

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NP 252
              S   D L   + G+          ++ R  + R++  L PRE  +          +P
Sbjct: 189 GEDSNLYDVL---NIGESPSPDNTLMIESLRVEIERALQTLTPREADLIRLYFGLNGAHP 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 246 MTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>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 =  224 bits (571), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 68/263 (25%), Positives = 119/263 (45%), Gaps = 14/263 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L   E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 340 LSVSEIKEINRRMSMGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 399

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 400 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 457

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    + +++++ E +V  +        S+   I   D   S   D++  
Sbjct: 458 LQEMGREPTPE---ELGERMDMPEDKVRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 510

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D      ++    +  +   T  ++ L  RE ++   R   +     TLE +  +F+V
Sbjct: 511 -EDVTIASPVDSATGQGLQEATTEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 569

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   +  
Sbjct: 570 TRERIRQIEAKALRKLRHPTRSD 592


>gi|300704422|ref|YP_003746025.1| RNA polymerase sigma factor rpos [Ralstonia solanacearum CFBP2957]
 gi|299072086|emb|CBJ43418.1| RNA polymerase sigma factor rpoS [Ralstonia solanacearum CFBP2957]
          Length = 376

 Score =  224 bits (571), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 78/278 (28%), Positives = 135/278 (48%), Gaps = 11/278 (3%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
               +  Y++ I   P+L   EE   + R +  G+ +A   ++  +LRLVV IA GY   
Sbjct: 100 AADTVQHYLNRISIKPLLTPAEELHFSTRAK-AGEFAARQVMIERNLRLVVSIAKGYLNR 158

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           G+P+ +++ EGN+GLM A++KFDPERGFR +TY+ WWI+ +++  I+     V++     
Sbjct: 159 GVPLLDLIEEGNLGLMHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV- 217

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
             R    + R K HL+  +  + +   +  IA  L  +  EV  +        SL+    
Sbjct: 218 -IRELNQVLRAKRHLEK-SGIDGRDASIEDIAHLLGKTTDEVQDVLSLNEHTTSLDTPF- 274

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE- 250
                 +   D+L  +H        ++   +    ++   ++ L+ + R + E R     
Sbjct: 275 -DLDPGTSLLDFLSDEHGASPD---QEVAHRELSQLMKSWLARLSDKHRYVVERRFGLNH 330

Query: 251 -NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             P TLE L++E  ++RERVRQI+  A  K++     Q
Sbjct: 331 IEPATLEELAAEMGLTRERVRQIQQEALVKLKRHFASQ 368


>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 =  224 bits (571), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 67/272 (24%), Positives = 122/272 (44%), Gaps = 14/272 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + E+ K   +  +E   + K  +  E     A   ++ ++LRLV+ IA  Y   GL   +
Sbjct: 223 LAEMEKTAQISIEELKEINKNMQSSERETARAKEEMIQANLRLVISIAKKYTNRGLQFLD 282

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 283 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 340

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + R+       T  +        +A+ + + E ++  +        S+   I   D + 
Sbjct: 341 KMNRISRQYLQETGED---PDSAKLAELMEMPEDKIRKIMKIAKEPISMETPI--GDDDD 395

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D       +     + R +    +  L PRE ++   R   +     TL
Sbjct: 396 SHLGDFI---EDVNNVAPADAAMYSSLREVTADVLESLTPREAKVLRMRFGIDMNTDHTL 452

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +  +F+V+RER+RQIEA+A +K++   +  
Sbjct: 453 EEVGKQFDVTRERIRQIEAKALRKLRHPTRSD 484


>gi|332994458|gb|AEF04513.1| RNA polymerase sigma factor [Alteromonas sp. SN2]
          Length = 608

 Score =  224 bits (571), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 63/249 (25%), Positives = 115/249 (46%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 362 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 421

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 422 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPTPE--- 476

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +++++ + E ++  +        S+   I   D   S   D++    D      ++   
Sbjct: 477 ELSERMLMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDSTIIQPLDSAT 531

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
             + ++     ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 532 GGSLKDATQEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 591

Query: 279 KVQESIQKQ 287
           K++   + +
Sbjct: 592 KLRHPSRSE 600


>gi|91216377|ref|ZP_01253344.1| RNA polymerase sigma factor rpoD (Sigma-A) [Psychroflexus torquis
           ATCC 700755]
 gi|91185515|gb|EAS71891.1| RNA polymerase sigma factor rpoD (Sigma-A) [Psychroflexus torquis
           ATCC 700755]
          Length = 287

 Score =  224 bits (571), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 66/276 (23%), Positives = 139/276 (50%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI K+ ++  +EE  LA++ +  GD  A  +L  ++LR VV ++  Y+  GL 
Sbjct: 17  SLDKYLQEIGKVDLITAEEEVELAQKIK-AGDDLALEKLTKANLRFVVSVSKQYQNQGLT 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++   +     +V++        
Sbjct: 76  LPDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILSALAEQSRVVRLPLNK---- 131

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
              ++ ++      +   + +P     IAK+L ++ ++V           S++A +   +
Sbjct: 132 -IGSINKINKTFAILEQRHQRPPSPDEIAKELEMTVNDVKESLKNSGRHLSMDAPLI--E 188

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
              S   D L +   G+          ++ +  + R++  L  RE  +        N  P
Sbjct: 189 GEDSNLYDVLKF---GESPNPENDLLHESLQTEIERALETLTTREADVIRLYFGLGNQQP 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TLE +   F ++RERVRQI+ +  ++++ + +  +
Sbjct: 246 MTLEEIGETFGLTRERVRQIKEKGVRRLKHTSRSTI 281


>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 =  224 bits (571), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 65/250 (26%), Positives = 119/250 (47%), Gaps = 12/250 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 370 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 430 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPSPE--- 484

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + E ++  +        S+   I   D   S   D++    D   ++ ++   
Sbjct: 485 ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDTTLELPLDSAT 539

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            ++ +N     ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 540 GESLKNATHEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 279 KVQESIQKQV 288
           K++   + ++
Sbjct: 600 KLRHPSRSEI 609


>gi|163740703|ref|ZP_02148097.1| RNA polymerase sigma factor [Phaeobacter gallaeciensis 2.10]
 gi|161386561|gb|EDQ10936.1| RNA polymerase sigma factor [Phaeobacter gallaeciensis 2.10]
          Length = 292

 Score =  224 bits (571), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 103/270 (38%), Positives = 173/270 (64%), Gaps = 6/270 (2%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
               K  +L+ + E  LA  +R+  D+ A HRL+ +++RL + +A  +R YG P+++++ 
Sbjct: 13  KRAMKAELLDAETELQLAYAWRDERDVQALHRLINAYMRLAISMASKFRRYGAPMNDLIQ 72

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           E  +GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFN+R
Sbjct: 73  EAGLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMR 132

Query: 141 RLKGHLQAITDNNLKP----EQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDK 195
           R++  L+    +        +    IA ++ V   +V  M+ RLAG D SLNA + S+++
Sbjct: 133 RVQAQLERQAQSEGTRLDQHQLHQQIATEIGVPLRDVQMMDGRLAGADFSLNA-VQSAEE 191

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
              +W + L  D     +++ E  + +  R  L  +M  LN RER I   R+L+E P TL
Sbjct: 192 EGREWIEALEDDSAQAAELVEESHDTRQLRTWLVEAMQALNDRERFIITERKLREKPRTL 251

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           E+L +E  +S+ERVRQ+EA AF+K+++S++
Sbjct: 252 ESLGTELGLSKERVRQLEAGAFQKMRKSLE 281


>gi|260222953|emb|CBA33035.1| RNA polymerase sigma factor rpoD [Curvibacter putative symbiont of
           Hydra magnipapillata]
          Length = 519

 Score =  224 bits (571), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 63/243 (25%), Positives = 117/243 (48%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 278 RAAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 337

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + ++    +              +A+K+
Sbjct: 338 WWIRQAITRSIADQARTIRIPVH-----MIETINKMNRISRQHLQEFGFEPDASVLAEKM 392

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D      +E   +   R+
Sbjct: 393 EIPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDSANTAPMEAAMQAGLRD 447

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E  +  TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 448 VVKDILDSLTPREAKVLRMRFGIEMTSDHTLEEVGKQFDVTRERIRQIEAKALRKLKHPS 507

Query: 285 QKQ 287
           +  
Sbjct: 508 RSD 510


>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 =  224 bits (571), Expect = 1e-56,   Method: Composition-based stats.
 Identities = 66/249 (26%), Positives = 113/249 (45%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 366 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 425

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 426 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPTPE--- 480

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + +++ + E ++  +        S+   I   D   S   D++    D Q    ++   
Sbjct: 481 ELGERMEMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDIQALSPVDSAT 535

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            +  R      ++ L  RE ++   R   E     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 536 AEGLREATRSVLAGLTARESKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALR 595

Query: 279 KVQESIQKQ 287
           K++   +  
Sbjct: 596 KLRHPSRSD 604


>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 =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 128/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +  I +   L  +    +++R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 253 LQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 312

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 313 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 370

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 371 KLNRISRQMLQEMGREPLPE---ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDED 425

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++     + +      ++ L PRE ++   R   +     TL
Sbjct: 426 SHLGDFI---EDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTL 482

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 483 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 518


>gi|182416400|ref|YP_001821466.1| RpoD family RNA polymerase sigma factor [Opitutus terrae PB90-1]
 gi|177843614|gb|ACB77866.1| RNA polymerase, sigma 70 subunit, RpoD family [Opitutus terrae
           PB90-1]
          Length = 640

 Score =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 70/270 (25%), Positives = 126/270 (46%), Gaps = 14/270 (5%)

Query: 20  IHEIRKIPMLEKQE--EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I  I  ++  E  + V   R        A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 306 LKQIETIHRIDPAELLKVVTQTRVHVREAHQAKTEMVEANLRLVISIAKKYTNRGLSFLD 365

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGN+GLM+AV+KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 366 LIQEGNMGLMKAVEKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETLN 423

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + +++  L     +   PE+V   A ++N+    V  +        SL + +   D + 
Sbjct: 424 KVMQVQKQLLQEYGHEPTPEEV---ADEMNLPVERVQQIMKMAQQPISLQSPV--GDGDD 478

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
           + + D++    D   +   +       R  +   +  L  RERR+   R         TL
Sbjct: 479 TSFGDFI---EDKSAENPYDMTAFSLLREKIIDVLDSLTERERRVLSLRFGLIDGYSRTL 535

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           E +  +F+V+RER+RQIEA+A +K++   +
Sbjct: 536 EEVGKQFKVTRERIRQIEAKALRKMRHPTR 565



 Score = 41.7 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 10/44 (22%), Positives = 26/44 (59%), Gaps = 1/44 (2%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTS 56
           +  +  Y+ ++ ++P+L +++E  ++KR  E+ +L A   L  +
Sbjct: 122 DDPVRMYLKQMGQVPLLTREQEVEISKRI-ENAELKAQEALFQA 164


>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 =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 66/248 (26%), Positives = 117/248 (47%), Gaps = 13/248 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 380 RKAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 439

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            L R+             PE    +A+K+
Sbjct: 440 WWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQCLQEMGREATPE---ELAEKM 494

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   +   D + S   D++    D   ++ ++    ++ R 
Sbjct: 495 GMPEDKIRKVLKIAKEPISMETPV--GDDDDSHLGDFI---EDSSLELPLDSATAESLRI 549

Query: 227 MLTRSMSV-LNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
                +   L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++  
Sbjct: 550 ATNAVLEEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 609

Query: 284 IQKQVELS 291
            + +   S
Sbjct: 610 SRSETLRS 617


>gi|126733203|ref|ZP_01748950.1| RNA polymerase sigma-70 factor RpoD [Roseobacter sp. CCS2]
 gi|126716069|gb|EBA12933.1| RNA polymerase sigma-70 factor RpoD [Roseobacter sp. CCS2]
          Length = 660

 Score =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 420 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 479

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A+KL
Sbjct: 480 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAEKL 534

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++N + 
Sbjct: 535 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAILPLDSAIQENLKE 589

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 590 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 649

Query: 285 QK 286
           + 
Sbjct: 650 RS 651


>gi|209695924|ref|YP_002263854.1| RNA polymerase sigma subunit RpoS (sigma-38) [Aliivibrio
           salmonicida LFI1238]
 gi|208009877|emb|CAQ80190.1| RNA polymerase sigma subunit RpoS (sigma-38) [Aliivibrio
           salmonicida LFI1238]
          Length = 321

 Score =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 82/271 (30%), Positives = 139/271 (51%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   + R    GD++A  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 49  YLSEIGFSPLLTAEEEVYFS-RLALKGDVAARSRMIESNLRLVVKIARRYNHRGLALLDL 107

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 108 VEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 166

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +  L    D+   PE++     K     S ++ +N R+A  +S+      +  +  
Sbjct: 167 LRAAR-ELSQKLDHEPTPEEIAEKLDKPVSDVSRMLRLNERVASVDSM-----VAGDSDK 220

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D +    D +      + +  +    L   +  LNP+++ +   R   L     TLE
Sbjct: 221 ALLDIIP---DTKHADPESETQTNDINESLVGWLGQLNPKQKEVVARRFGLLGYEASTLE 277

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +  E  ++RERVRQI+    ++++E + +Q
Sbjct: 278 QVGREIGLTRERVRQIQVEGLRRLREIMTQQ 308


>gi|163868737|ref|YP_001609951.1| RNA polymerase sigma factor RpoD [Bartonella tribocorum CIP 105476]
 gi|161018398|emb|CAK01956.1| RNA polymerase sigma factor [Bartonella tribocorum CIP 105476]
          Length = 671

 Score =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 69/240 (28%), Positives = 118/240 (49%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V S+LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 433 AKKEMVESNLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 492

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + I     +      ++ KL++
Sbjct: 493 IRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQILHEIGREPTPEELSSKLSM 547

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   +   D++ S   D++    D    + I+   + N R+  
Sbjct: 548 PLEKVRKVLKIAKEPISLETPV--GDEDDSHLGDFI---EDRNALLPIDAAIQANLRDTT 602

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 603 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 662


>gi|225677095|ref|ZP_03788097.1| RNA polymerase sigma 70 subunit, RpoD [Wolbachia endosymbiont of
           Muscidifurax uniraptor]
 gi|225590854|gb|EEH12079.1| RNA polymerase sigma 70 subunit, RpoD [Wolbachia endosymbiont of
           Muscidifurax uniraptor]
          Length = 669

 Score =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 72/260 (27%), Positives = 124/260 (47%), Gaps = 15/260 (5%)

Query: 32  QEEYVLAKRYREHGDL--SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           QE   L KR ++H      A   ++ ++LRLVV IA  Y   GL + +++ EGNIGLM+A
Sbjct: 413 QEFKELIKRIQKHEREVSEAKQEMIKANLRLVVSIAKKYSKRGLDLLDLIQEGNIGLMKA 472

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V KFD +RG++ +TY  WW++ ++   I     +V+I     +      + ++   L+ +
Sbjct: 473 VDKFDYKRGYKFSTYGTWWVRQSITRAIPEQSKVVRIPVHMVEI-----ISKINRALRKM 527

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
           T    +   +  ++ +L +    +  +        SL A     D  SS + D +    D
Sbjct: 528 THEMGREPTLEELSVELTMPLERIRKVMKIARDPVSLEAPTGKDD--SSTFGDCI---ED 582

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSR 266
            +     +     + R + T  ++ L P+E RI   R          TLE +   F V+R
Sbjct: 583 KRVSRPEDAAILADLRGITTNVLATLTPKEERILRMRFGLGKDGKEHTLEEVGKIFNVTR 642

Query: 267 ERVRQIEARAFKKVQESIQK 286
           ER+RQIEA+A +K++   + 
Sbjct: 643 ERIRQIEAKALRKLKHPSRA 662


>gi|242279084|ref|YP_002991213.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           salexigens DSM 2638]
 gi|242121978|gb|ACS79674.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           salexigens DSM 2638]
          Length = 585

 Score =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 72/256 (28%), Positives = 119/256 (46%), Gaps = 12/256 (4%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE +   ++     + A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV K
Sbjct: 331 EEVLWRIKHGNRSAMRAKQELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 390

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RG++ +TY+ WWI+ A+   I      ++I            L R   +L      
Sbjct: 391 FEYQRGYKFSTYATWWIRQAITRAIADQARTIRIPVHM--IETINKLIRTSRYLVQELGR 448

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +  PE    IA++++    +V  +        SL   I   D+  S   D++    D + 
Sbjct: 449 DPSPE---EIAERMDYPLEKVKKVLKIAKEPISLETPI--GDEEDSSLGDFI---EDKKA 500

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
               E+         +   +S L PRE ++   R         TLE +   F V+RER+R
Sbjct: 501 AAPAEEVVSTKLGEQIATVLSDLTPREEQVLRKRFGIGEKSDHTLEEVGKLFNVTRERIR 560

Query: 271 QIEARAFKKVQESIQK 286
           QIEA+A +K++  ++ 
Sbjct: 561 QIEAKALRKLRHPVRS 576


>gi|254439883|ref|ZP_05053377.1| RNA polymerase sigma factor, sigma-70 family [Octadecabacter
           antarcticus 307]
 gi|198255329|gb|EDY79643.1| RNA polymerase sigma factor, sigma-70 family [Octadecabacter
           antarcticus 307]
          Length = 292

 Score =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 101/272 (37%), Positives = 172/272 (63%), Gaps = 6/272 (2%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
            +  K  +L+ + E  LA  +R+  D  A HRL+T+++RL + +A  +R YG P+++++ 
Sbjct: 13  RKAMKAELLDAETELALAYAWRDERDEQALHRLITAYMRLAISMASKFRRYGAPMNDLIQ 72

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           E ++GLM+A  KFDP+RG R +TY++WWIKA++Q++++R+WS+V+ G+T++QK LFFNLR
Sbjct: 73  EASLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDHVMRNWSMVRTGSTSSQKSLFFNLR 132

Query: 141 RLKGHLQAIT----DNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDK 195
           R++  L+       +   + +    IA ++ V   +V  M  RL+G D SLNA   SS+ 
Sbjct: 133 RVQARLEREAMKRGETLDRHDMRQMIATEVGVPLRDVEMMEGRLSGSDFSLNA-TQSSED 191

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
              +W D L  D +   + +    +    R  L  +++ L+ RE+ I   R+L++ P TL
Sbjct: 192 EGREWIDALEDDGEQAAETVQNSHDTDTLRQWLLTALTALSDREQFIVRERKLRDAPRTL 251

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+L +E  +S+ERVRQ+EA AF K+++S++ Q
Sbjct: 252 ESLGTELGLSKERVRQLEAAAFGKMRKSLEGQ 283


>gi|86137897|ref|ZP_01056473.1| RNA polymerase sigma-70 factor RpoD [Roseobacter sp. MED193]
 gi|85825489|gb|EAQ45688.1| RNA polymerase sigma-70 factor RpoD [Roseobacter sp. MED193]
          Length = 663

 Score =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 423 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 482

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A+KL
Sbjct: 483 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAEKL 537

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++N + 
Sbjct: 538 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAVLPLDSAIQENLKE 592

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 593 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 652

Query: 285 QK 286
           + 
Sbjct: 653 RS 654


>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 =  224 bits (571), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 61/248 (24%), Positives = 114/248 (45%), Gaps = 12/248 (4%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            E     A   ++ ++LRLV+ IA  Y   G+   +++ EGNIGLM+AV KF+  RG++ 
Sbjct: 420 AESKMRKAKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEGNIGLMKAVDKFEYRRGWKF 479

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY+ WW++ A+   +      +++            L R+   +   T     P     
Sbjct: 480 STYATWWVRQAVTRSLADQARTIRVPVHM--IETINKLNRISREILQQTGQEAHP---AV 534

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           +A+++ +SE +V  +        SL   +   D   +   D +    D       +   +
Sbjct: 535 LAERMELSEEKVRGILKIAKQPVSLETPV--GDDGDATLGDMI---EDAAVSSPADAAMQ 589

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKK 279
            + R  +  ++  L+PRE ++   R         TLE +  +F+V+RER+RQIE++A +K
Sbjct: 590 ADLRAAIDDALDSLSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIRQIESKAMRK 649

Query: 280 VQESIQKQ 287
           +    +  
Sbjct: 650 LMHPSRAD 657


>gi|315636974|ref|ZP_07892198.1| DNA-directed RNA polymerase sigma subunit RpoD [Arcobacter butzleri
           JV22]
 gi|315478804|gb|EFU69513.1| DNA-directed RNA polymerase sigma subunit RpoD [Arcobacter butzleri
           JV22]
          Length = 626

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 71/260 (27%), Positives = 128/260 (49%), Gaps = 15/260 (5%)

Query: 29  LEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L  +E   + ++ +    ++  +  R+  S+LRLVV IA  Y   GLP  +++ EGNIGL
Sbjct: 365 LTPEELKAVLEQIKRGKQITDTSKTRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGL 424

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+ ++G++ +TY+ WWI+ A+   I      ++I        +   + R+   +
Sbjct: 425 MKAVDKFEYKKGYKFSTYATWWIRQAISRAIADQARTIRIPIH-----MIETINRINKII 479

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +     N K   +  IAK++ +   +V  +        SL A I S +    ++ D++  
Sbjct: 480 RKGVQENGKEPDIEEIAKEVGLPVDKVKQVIKITKEPVSLEAPIGSDED--GKFGDFVPD 537

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN---PVTLENLSSEFE 263
           +        I+   +++ +  + + +S LN RE+ +   R          TLE +  E  
Sbjct: 538 EK---APTPIDNIMKEDLQGQIDQILSQLNEREQAVIRMRFGLMEDASDRTLEEIGKELN 594

Query: 264 VSRERVRQIEARAFKKVQES 283
           V+RERVRQIE+ A KK++  
Sbjct: 595 VTRERVRQIESSAIKKLKHP 614



 Score = 41.0 bits (95), Expect = 0.24,   Method: Composition-based stats.
 Identities = 10/36 (27%), Positives = 21/36 (58%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+ +IP+L K+EE  ++K+     D+
Sbjct: 101 SDSPVRMYLREMGQIPLLTKEEEVEISKKIETGEDI 136


>gi|149911458|ref|ZP_01900075.1| sigma S (sigma 38) factor of RNA polymerase, major
           sigmafactorduring stationary phase [Moritella sp. PE36]
 gi|149805489|gb|EDM65496.1| sigma S (sigma 38) factor of RNA polymerase, major
           sigmafactorduring stationary phase [Moritella sp. PE36]
          Length = 319

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 86/289 (29%), Positives = 146/289 (50%), Gaps = 16/289 (5%)

Query: 4   KNMSIIVNGEIGLSR---YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           ++  +I N    L     Y+ EI   P+L  +EE   A+R    GD S+  R++ S+LRL
Sbjct: 32  EDEHLIPNDAKSLDATQLYLGEIGFSPLLTAEEEVFYARR-ALRGDASSRKRMIESNLRL 90

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+  
Sbjct: 91  VVKIARRYNNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQ 150

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              +++      K L   LR  +     +            IA KL+   ++V  M    
Sbjct: 151 TRTIRLPIHVV-KELNVYLRAAR----ELAHELDHEPTAEDIADKLDKPVADVSKMLRLN 205

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               S++  I     +S +    ++ D  G       + +  + +  + R +  LNP++R
Sbjct: 206 ERISSVDTPIG---GDSEKALLDIISDEKG--DGPESRTQNDDIKFSIIRWLEELNPKQR 260

Query: 241 RIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   L  +  TLE++  E  ++RERVRQI+  A ++++E + +Q
Sbjct: 261 EVLARRFGLLGYDASTLEDVGREIGLTRERVRQIQVEALRRLREVLAQQ 309


>gi|226355184|ref|YP_002784924.1| RNA polymerase sigma factor, sigma-70 family [Deinococcus deserti
           VCD115]
 gi|226317174|gb|ACO45170.1| putative RNA polymerase sigma factor, sigma-70 family [Deinococcus
           deserti VCD115]
          Length = 399

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 79/296 (26%), Positives = 129/296 (43%), Gaps = 36/296 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE--------------------------HGDL 47
             L +Y+HEI +I +L   EE  LA+RY E                              
Sbjct: 98  DSLRQYLHEIGQIELLSAVEEMDLARRYEEGEAARNELESNPDLDDRHRRHLQRLVEDGE 157

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   L  ++LRLVV IA  Y   GL + +++ EGN GL++AV+KF+  RG++ +TY+ W
Sbjct: 158 AAKKSLTEANLRLVVSIAKKYANRGLNLLDLIQEGNQGLIRAVEKFEYRRGYKFSTYATW 217

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++     +      L R+   L+         E++   A    
Sbjct: 218 WIRQALTRAIADKSRTIRVPVHMVE--TINKLSRISRQLEMELSREPLAEEMAE-AMGPG 274

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
               +V           SL   I   D+  S + D+L  +  G     ++   +      
Sbjct: 275 WDAEKVTDTQKVGHEPISLETPI--GDEGDSFYGDFLPDERFGS---PVQNASQTLLSEA 329

Query: 228 LTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           L R++S L  RE  + + R   +     TLE +     V+RERVRQIE++A +K++
Sbjct: 330 LERALSSLGEREALVLKLRNGFVDGREHTLEEVGQLLSVTRERVRQIESKALRKLK 385


>gi|221134905|ref|ZP_03561208.1| RNA polymerase, sigma 70 subunit, RpoD [Glaciecola sp. HTCC2999]
          Length = 607

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 63/249 (25%), Positives = 115/249 (46%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 361 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 420

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 421 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPTPE--- 475

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +++++ + E ++  +        S+   I   D   S   D++    D      ++   
Sbjct: 476 ELSERMIMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDNTIIQPLDSAT 530

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
             + ++     ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 531 GGSLKDATQDVLAGLTQREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 590

Query: 279 KVQESIQKQ 287
           K++   + +
Sbjct: 591 KLRHPSRSE 599


>gi|294141938|ref|YP_003557916.1| RNA polymerase sigma-38 factor [Shewanella violacea DSS12]
 gi|293328407|dbj|BAJ03138.1| RNA polymerase sigma-38 factor [Shewanella violacea DSS12]
          Length = 328

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 81/271 (29%), Positives = 135/271 (49%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   +++    G   + +R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 59  YLGEIGFSPLLSAEEEVYFSRK-SLKGCGKSRNRMIESNLRLVVKIARRYNNRGLALLDL 117

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 118 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 176

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            IA KL++  S+V  M        S++  +     N  
Sbjct: 177 LRTAR----ELAHKLDHEPTAEEIAAKLDLPSSDVSRMLKLNERITSVDTPL--GGDNDK 230

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  D        ++ E+       + + +  LN ++R +   R   L   P TLE
Sbjct: 231 ALLDVLAADDSVGPDYKVQDEDMS---KSVVKWLDELNTKQREVLARRFGLLGYEPSTLE 287

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           N+  E  ++RERVRQI+  A K++++ +  Q
Sbjct: 288 NVGKEIGLTRERVRQIQVEALKRLKDLLGAQ 318


>gi|56696627|ref|YP_166988.1| RNA polymerase sigma factor RpoD [Ruegeria pomeroyi DSS-3]
 gi|56678364|gb|AAV95030.1| RNA polymerase sigma-70 factor RpoD [Ruegeria pomeroyi DSS-3]
          Length = 660

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 420 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 479

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A+KL
Sbjct: 480 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAEKL 534

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++N + 
Sbjct: 535 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAVLPLDSAIQENLKE 589

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 590 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 649

Query: 285 QK 286
           + 
Sbjct: 650 RS 651


>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 =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 113/247 (45%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 410 EAKARRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 469

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T     P     +
Sbjct: 470 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGAEPDPAT---L 524

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           AKK+++ E ++  +        S+   I   D + S   D++    D       +     
Sbjct: 525 AKKMDMPEDKIRKIMKISKEPISMETPI--GDDDDSHLGDFI---EDSGTLAPADAAMYS 579

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R +    +  L  RE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 580 SLRGVTKEILDTLTTREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 639

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 640 RHPTRSD 646


>gi|163749990|ref|ZP_02157234.1| RNA polymerase sigma-38 factor [Shewanella benthica KT99]
 gi|161330264|gb|EDQ01245.1| RNA polymerase sigma-38 factor [Shewanella benthica KT99]
          Length = 323

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 81/271 (29%), Positives = 136/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   +++    G   + +R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 54  YLGEIGFSPLLSAEEEVYFSRK-SLKGCGKSRNRMIESNLRLVVKIARRYNNRGLALLDL 112

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 113 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 171

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            IA KL++  S+V  M        S++  +     N  
Sbjct: 172 LRTAR----ELAHKLDHEPTAEEIAAKLDLPCSDVSRMLKLNERITSVDTPL--GGDNDK 225

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  D +      ++ E+       + + +  LN ++R +   R   L   P TLE
Sbjct: 226 ALLDVLAADDNVGPDYKVQNEDMS---KSVVKWLDELNTKQREVLARRFGLLGYEPSTLE 282

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           N+  E  ++RERVRQI+  A K++++ +  Q
Sbjct: 283 NVGKEIGLTRERVRQIQVEALKRLKDLLGAQ 313


>gi|2792523|gb|AAC38577.1| alternative RNA sigma factor RpoS [Ralstonia solanacearum]
          Length = 376

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 78/278 (28%), Positives = 135/278 (48%), Gaps = 11/278 (3%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
               +  Y++ I   P+L   EE   + R +  G+ +A   ++  +LRLVV IA GY   
Sbjct: 100 AADTVQHYLNRISIKPLLTPAEELHFSTRAK-AGEFAARQVMIERNLRLVVSIAKGYLNR 158

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           G+P+ +++ EGN+GLM A++KFDPERGFR +TY+ WWI+ +++  I+     V++     
Sbjct: 159 GVPLLDLIEEGNLGLMHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV- 217

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
             R    + R K HL+  +  + +   +  IA  L  +  EV  +        SL+    
Sbjct: 218 -IRELNQVLRAKRHLEK-SGIDGRDASIEDIAHLLGKTTEEVQDVLSLNEHTTSLDTPF- 274

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE- 250
                 +   D+L  +H        ++   +    ++   ++ L+ + R + E R     
Sbjct: 275 -DLDPGTSLLDFLSDEHGASPD---QEVAHRELSQLMKSWLARLSDKHRYVVERRFGLNH 330

Query: 251 -NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             P TLE L++E  ++RERVRQI+  A  K++     Q
Sbjct: 331 IEPATLEELAAEMGLTRERVRQIQQEALVKLKRHFASQ 368


>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 =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 70/246 (28%), Positives = 117/246 (47%), Gaps = 12/246 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 426 EREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 485

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    + +     +      +
Sbjct: 486 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREPTPEEL 540

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           ++KL +   +V  +        SL   I   D+  S   D++    D    + IE   + 
Sbjct: 541 SEKLAMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAVLPIEAAIQS 595

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 596 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKL 655

Query: 281 QESIQK 286
           +   + 
Sbjct: 656 KHPSRS 661


>gi|302185957|ref|ZP_07262630.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. syringae
           642]
          Length = 616

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 69/263 (26%), Positives = 121/263 (46%), Gaps = 14/263 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L+  E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 356 LKIAEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 415

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 416 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 473

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    + +++ + E ++  +        S+   I   D   S   D++  
Sbjct: 474 LQEMGREPTPE---ELGERMEMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 526

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q  I+    ++ +      +S L  RE ++   R   +     TLE +  +F+V
Sbjct: 527 -EDSTMQSPIDVATVESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 585

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   + +
Sbjct: 586 TRERIRQIEAKALRKLRHPTRSE 608


>gi|327479259|gb|AEA82569.1| RNA polymerase sigma factor RpoD [Pseudomonas stutzeri DSM 4166]
          Length = 617

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 66/249 (26%), Positives = 115/249 (46%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 371 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 430

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 431 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPTPE--- 485

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + +++ + E ++  +        S+   I   D   S   D++    D   Q  I+   
Sbjct: 486 ELGERMEMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDSAMQSPIDVAT 540

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            ++ +      +S L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 541 VESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 600

Query: 279 KVQESIQKQ 287
           K++   + +
Sbjct: 601 KLRHPTRSE 609


>gi|1519636|gb|AAB07551.1| SigA [Chloroflexus aurantiacus J-10-fl]
          Length = 343

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 81/300 (27%), Positives = 133/300 (44%), Gaps = 40/300 (13%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVL---------------------------AKRYREHG 45
           +  +  Y+ EI ++P+L  ++E  L                            +R  + G
Sbjct: 44  DDPVRMYLQEIGQVPLLTAEQEVELAKAMEAGAAARQRLDREDTPRPRARFELERAVQQG 103

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
              A H L+ ++LRLVV IA  Y  YGL + ++V EGNIGLM+AV+KFD ++G + +TY+
Sbjct: 104 -QDARHHLIQANLRLVVSIAKKYTSYGLTMMDLVQEGNIGLMRAVEKFDYKKGHKFSTYA 162

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
            WWI+ A+   I      +++     +      ++R    LQ     +  PE    IA  
Sbjct: 163 TWWIRQAITRAIADQSRTIRLPVHMGE--AISQVKRTSHRLQQTMQRDATPE---EIADA 217

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           + +S  +V           SL   +    +   +  D++  D         E       R
Sbjct: 218 MGISAGKVRRTLEASMHPLSLEMPV--GQEGEGRMGDFIEDDRIS---TPAEAPAASLLR 272

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             L   +  L  RER+I + R   ++    TLE +  EF ++RER+RQIEA A +K++  
Sbjct: 273 EQLEEVLMKLPERERKIIQLRYGLKDGRYRTLEEVGIEFGITRERIRQIEAVALRKLRHP 332


>gi|323697926|ref|ZP_08109838.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio sp.
           ND132]
 gi|323457858|gb|EGB13723.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           desulfuricans ND132]
          Length = 583

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 72/256 (28%), Positives = 118/256 (46%), Gaps = 12/256 (4%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE +   +      + A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV K
Sbjct: 329 EEVLWRIKSGNQTAMQAKQELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 388

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RG++ +TY+ WWI+ A+   I      ++I            L R   +L      
Sbjct: 389 FEYQRGYKFSTYATWWIRQAITRAIADQARTIRIPVHM--IETINKLIRTSRYLVQELGR 446

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +  PE    IA++++    +V  +        SL   I   D+  S   D++    D + 
Sbjct: 447 DPSPE---EIAERMDYPLEKVKKVLKIAKEPISLETPI--GDEEDSSLGDFI---EDKKA 498

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
               E+         +   +S L PRE ++   R         TLE +   F V+RER+R
Sbjct: 499 TAPAEEVVSTKLSEQIASVLSDLTPREEQVLRKRFGIGEKSDHTLEEVGKLFNVTRERIR 558

Query: 271 QIEARAFKKVQESIQK 286
           QIEA+A +K++  ++ 
Sbjct: 559 QIEAKALRKLRHPVRS 574



 Score = 36.3 bits (83), Expect = 6.2,   Method: Composition-based stats.
 Identities = 12/42 (28%), Positives = 26/42 (61%), Gaps = 1/42 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVT 55
             +  Y+ E+  +P+L+++ E V+AK+  E+G++   + LV 
Sbjct: 93  DPVRMYLREMGAVPLLDREGEVVIAKKI-ENGEMDVLYSLVE 133


>gi|94263094|ref|ZP_01286913.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
 gi|93456637|gb|EAT06745.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
          Length = 540

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 72/242 (29%), Positives = 124/242 (51%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A +RLV ++LRLVV +A  Y G GL + +++ EGNIGLM+AV+KF+  RG++ +TY+ 
Sbjct: 300 QEAKNRLVQANLRLVVSVAKKYAGRGLQLLDLIQEGNIGLMKAVEKFEYRRGYKFSTYAT 359

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + R+    +     + +      +A+ L
Sbjct: 360 WWIRQAVTRAIADQGRTIRIPVH-----MIDTINRMLKGAKEFQRQHGREPTPDEMAQHL 414

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            V  ++V S+        SL+  +   + N S   D++    D +     E    +N ++
Sbjct: 415 GVEVAKVKSVLKIAKEPLSLDTPV--GNSNDSFLADFI---EDTEAASPDEATIYENLQS 469

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L R +  L+PRE  +   R   +  +  TLE +   F V+RER+RQIEA+A KK++   
Sbjct: 470 NLRRVLKTLSPREEMVLRLRFGLDTAMDLTLEEVGENFAVTRERIRQIEAKALKKLKHPA 529

Query: 285 QK 286
           ++
Sbjct: 530 RR 531



 Score = 36.3 bits (83), Expect = 5.7,   Method: Composition-based stats.
 Identities = 12/43 (27%), Positives = 23/43 (53%), Gaps = 1/43 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTS 56
             +  Y+ E+  +P+L  +EE  +A+   E G+L     L+T+
Sbjct: 98  DPVKVYLQEMGSVPLLSTEEEIAVAREI-EAGELLIQQALLTA 139


>gi|56695321|ref|YP_165669.1| RNA polymerase factor sigma-32 [Ruegeria pomeroyi DSS-3]
 gi|56677058|gb|AAV93724.1| RNA polymerase sigma-32 factor [Ruegeria pomeroyi DSS-3]
          Length = 292

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 101/271 (37%), Positives = 175/271 (64%), Gaps = 6/271 (2%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
            +  K  +L+ + E  LA  +R+H D +A HRL+T+++RL + +A  ++ YG P+++++ 
Sbjct: 13  RQAMKAELLDAETELALAYAWRDHRDEAALHRLITAYMRLAISMAAKFKRYGAPMNDLIQ 72

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           E  +GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFN+R
Sbjct: 73  EAGLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMR 132

Query: 141 RLKGHLQAITDNNL----KPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDK 195
           R++  L+     +     + +    IA ++ V   +V  M  RL+G D SLNA   +SD+
Sbjct: 133 RVQARLEREAATDGLALDRHQLHQMIASEIGVPLRDVEMMEGRLSGSDFSLNA-TQASDE 191

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
              +W + L  + +   +++  + + +  R+ L  +M  LN RER I   R+L++ P TL
Sbjct: 192 EGREWIEALEDESEQAAELVAHRHDTEQLRDWLIEAMQALNERERFIVRERKLRDEPRTL 251

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E+L  E  +S+ERVRQ+EA AF K+++S++ 
Sbjct: 252 ESLGDELGLSKERVRQLEAAAFAKMRKSLEA 282


>gi|319781051|ref|YP_004140527.1| RNA polymerase sigma factor, sigma-70 family [Mesorhizobium ciceri
           biovar biserrulae WSM1271]
 gi|317166939|gb|ADV10477.1| RNA polymerase sigma factor, sigma-70 family [Mesorhizobium ciceri
           biovar biserrulae WSM1271]
          Length = 287

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 109/269 (40%), Positives = 170/269 (63%), Gaps = 2/269 (0%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           +    K P LE+ EE+ LA  ++E  D +A H +  +H+RLV+ +A  +R YGLP+ ++V
Sbjct: 11  VRAAMKAPYLERDEEHRLALLWKEDNDQNALHSITVAHMRLVISMASKFRHYGLPLGDLV 70

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EG++GL++A  +F+PER  R +TY+ WWI+A+MQ+YILR+WS+V+ GT++ QK LFFNL
Sbjct: 71  QEGHVGLLEAAARFEPEREVRFSTYATWWIRASMQDYILRNWSIVRGGTSSAQKALFFNL 130

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSS 198
           RRL+  L    +          +++ L VSE++V  M+ RL+  D SLN  +   D  S+
Sbjct: 131 RRLRARLANGAEPLSNATLYREVSEALGVSEADVAMMDSRLSAPDSSLNMPVAD-DAGST 189

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           +  ++LV D    ++++ +K +   R   L  ++  LN RE RI E RRL +   TLE L
Sbjct: 190 ERMEFLVSDDPLPDEIVGDKIDVARRSLWLREALRALNARELRIIEERRLNDEGATLEAL 249

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQ 287
                +S+ERVRQIEARA +K++ ++ KQ
Sbjct: 250 GETLGISKERVRQIEARAMEKLKVALVKQ 278


>gi|126730240|ref|ZP_01746051.1| RNA polymerase sigma factor RpoD [Sagittula stellata E-37]
 gi|126708973|gb|EBA08028.1| RNA polymerase sigma factor RpoD [Sagittula stellata E-37]
          Length = 667

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 70/242 (28%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 427 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 486

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A+KL
Sbjct: 487 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAEKL 541

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++N + 
Sbjct: 542 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAILPLDSAIQENLKE 596

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR +S L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 597 TTTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 656

Query: 285 QK 286
           + 
Sbjct: 657 RS 658


>gi|25900789|emb|CAD57977.1| RNA polymerase sigma factor [Pseudomonas oleovorans]
          Length = 335

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 82/278 (29%), Positives = 141/278 (50%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQKGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMSQTRTIRLPFHVV-KELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++  + +K       ++ +N R++  D SL         + 
Sbjct: 185 LRAAR-ELTQKLDHEPSPEEIATLLEKPVAEVKRMLGLNERVSSVDVSL------GPDSD 237

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + +  L  ++R +   R         TL
Sbjct: 238 KTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLGELTDKQREVVVRRFGLRGHESSTL 294

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E++  E  ++RERVRQI+    ++++E ++K    S S
Sbjct: 295 EDVGLEIGLTRERVRQIQVEGLERLREILEKNGLSSES 332


>gi|325285575|ref|YP_004261365.1| RpoD subfamily RNA polymerase sigma 70 subunit [Cellulophaga lytica
           DSM 7489]
 gi|324321029|gb|ADY28494.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cellulophaga
           lytica DSM 7489]
          Length = 287

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 71/276 (25%), Positives = 143/276 (51%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI K+ ++   EE  LA+R +  GD  A  +L  ++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQEIGKVDLITADEEVELAQRIK-AGDQVALEKLTKANLRFVVSVAKQYQNQGLT 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     +V++    N+  
Sbjct: 76  LPDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLP--LNKIG 133

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               + +    L+   +     E    IAK+L+++  +V           S++A +   D
Sbjct: 134 SINKINKTFAFLEQAHERKPSAE---EIAKELDMTIEDVKQSLKNSGRHVSMDAPLI--D 188

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENP 252
              S   D L     G+      +   ++ R  + R++  L PRE  +         ++ 
Sbjct: 189 GEDSNLYDVL---RSGESPNPDRELLIESLRTEIERALETLTPREADVIRLYFGLAEQHS 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TLE +   F+++RERVRQI+ +A ++++ + + ++
Sbjct: 246 MTLEEIGETFDLTRERVRQIKEKAIRRLKHTSRSKI 281


>gi|23008120|ref|ZP_00049697.1| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Magnetospirillum magnetotacticum
           MS-1]
          Length = 307

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 71/258 (27%), Positives = 121/258 (46%), Gaps = 15/258 (5%)

Query: 34  EYVLAKRYREHGDLSAAH---RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           EY       + G+  A      ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV
Sbjct: 51  EYRKIVAMVQKGEREARQAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 110

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
            KF+  RG++ +TY+ WWI+ A+   I      ++I        +   + ++    + + 
Sbjct: 111 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQML 165

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
               +      +A+KL +   +V  +        SL   I   D+  S   D++    D 
Sbjct: 166 HEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDK 220

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRER 268
              + I+   + N R   TR ++ L PRE R+   R         TLE +  +F V+RER
Sbjct: 221 NVVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRER 280

Query: 269 VRQIEARAFKKVQESIQK 286
           +RQIEA+A +K++   + 
Sbjct: 281 IRQIEAKALRKLKHPSRS 298


>gi|260767580|ref|ZP_05876516.1| RNA polymerase sigma-32 factor [Vibrio furnissii CIP 102972]
 gi|260617480|gb|EEX42663.1| RNA polymerase sigma-32 factor [Vibrio furnissii CIP 102972]
 gi|315178774|gb|ADT85688.1| RNA polymerase sigma-32 factor [Vibrio furnissii NCTC 11218]
          Length = 258

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 100/248 (40%), Positives = 150/248 (60%), Gaps = 10/248 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
               GD+ AA  L+ SHLR VV +A GY GYGLP++++V EGNIGLM+AVK+F+PE G R
Sbjct: 14  LHYSGDIEAAKGLILSHLRFVVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVR 73

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
           L ++++ WIKA + EY+LR+W +VKI TT  Q++LFFNLR+ K  L    +      +V 
Sbjct: 74  LVSFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKLFFNLRKSKKRLGWFNNG-----EVE 128

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A++L V  SEV  M  RLA  ++   + N  D N + +   ++Y  D Q   L E  E
Sbjct: 129 TVARELGVEPSEVREMESRLAAQDATFEMSNDDDDNPNAYTAPVLYLEDKQSD-LAENVE 187

Query: 221 RKNRR----NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
            +N        L  ++S L+ R + I  +R L +   TL+ L+  + VS ER+RQ+E  A
Sbjct: 188 AQNWEAHTNQRLALALSSLDERSQHIVRSRWLDDQKATLQELAEMYNVSAERIRQLEKNA 247

Query: 277 FKKVQESI 284
            KK+++++
Sbjct: 248 MKKLKDAV 255


>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 =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 66/272 (24%), Positives = 124/272 (45%), Gaps = 14/272 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + E+ K   +  +E   + K  +  E     A   ++ ++LRLV+ IA  Y   GL   +
Sbjct: 376 VAEMEKSAQISIEELKEINKNMQNSERETARAKEEMIQANLRLVISIAKKYTNRGLQFLD 435

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +  
Sbjct: 436 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIE 490

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + ++    +     + +      +A+ + + E ++  +        S+   I   D + 
Sbjct: 491 TINKMNRISRQYLQEHGEDPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPI--GDDDD 548

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D       E     + R +    +  L PRE ++   R   +     TL
Sbjct: 549 SHLGDFI---EDVNNVAPAEAAMYSSLREVTADVLESLTPREAKVLRMRFGIDMNTDHTL 605

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +  +F+V+RER+RQIEA+A +K++   +  
Sbjct: 606 EEVGKQFDVTRERIRQIEAKALRKLRHPTRSD 637


>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 =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 67/247 (27%), Positives = 118/247 (47%), Gaps = 12/247 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 381 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 440

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            L R+             PE    +A+++
Sbjct: 441 WWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQCLQEMGREATPE---ELAERM 495

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           N+ E ++  +        S+   I   D + S   D++    D   ++ ++    ++ R 
Sbjct: 496 NMPEDKIRKVLKIAKEPISMETPI--GDDDDSHLGDFI---QDESLELPLDSATAESLRI 550

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                +  L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 551 ATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 610

Query: 285 QKQVELS 291
           + +   S
Sbjct: 611 RSETLRS 617


>gi|239906706|ref|YP_002953447.1| RNA polymerase sigma factor SigA [Desulfovibrio magneticus RS-1]
 gi|239796572|dbj|BAH75561.1| RNA polymerase sigma factor SigA [Desulfovibrio magneticus RS-1]
          Length = 588

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 73/257 (28%), Positives = 120/257 (46%), Gaps = 12/257 (4%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE +   +   +    A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV K
Sbjct: 334 EEVLWRIKRGNNAAQRAKQELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 393

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RG++ +TY+ WWI+ A+   I      ++I            L R   +L      
Sbjct: 394 FEYQRGYKFSTYATWWIRQAITRAIADQARTIRIPVHM--IETINKLIRTSRYLVQELGR 451

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +  PE    IA++++    +V  +        SL   I   D+  S   D++    D + 
Sbjct: 452 DPTPE---EIAERMDYPLEKVKKVLKIAKEPISLETPI--GDEEDSSLGDFI---EDKKA 503

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
               E+         + + +S L PRE ++   R         TLE +   F V+RER+R
Sbjct: 504 LAPAEEVVNTKLGEQIGKVLSDLTPREEQVLRKRFGLGEKSDHTLEEVGKLFNVTRERIR 563

Query: 271 QIEARAFKKVQESIQKQ 287
           QIEA+A +K++  ++ Q
Sbjct: 564 QIEAKALRKLRHPVRSQ 580



 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 12/54 (22%), Positives = 29/54 (53%), Gaps = 1/54 (1%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVT 55
           +  ++         +  Y+ E+  +P+L+++ E V+AK+  E+G++   + LV 
Sbjct: 86  SEDSLDYSSRSTDPVRMYLREMGAVPLLDREGEVVIAKKI-ENGEMEVLYALVE 138


>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 =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 67/249 (26%), Positives = 111/249 (44%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 355 IGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 414

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 415 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPTPE--- 469

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + +++ + E +V  +        S+   I   D   S   D++    DG     +E   
Sbjct: 470 ELGERMEMPEEKVRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDGTITSPVESAT 524

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
                      +S L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 525 DVGLTESTRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 584

Query: 279 KVQESIQKQ 287
           K++   +  
Sbjct: 585 KLRHPSRSD 593


>gi|297163178|gb|ADI12890.1| RNA polymerase sigma factor [Streptomyces bingchenggensis BCW-1]
          Length = 336

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 80/311 (25%), Positives = 134/311 (43%), Gaps = 38/311 (12%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY------------------REHGDL 47
           +   V     +  Y+  I ++ +L  ++E  LAKR                      G+L
Sbjct: 29  LDTPVGSTDPVKDYLKLIARVRLLTAEQEVDLAKRIEAGLYAERLLRERPGLDRHSRGEL 88

Query: 48  --------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                    A   LV ++LRLVV +A  Y G GL   +++ EGN GL++A +KFD  +GF
Sbjct: 89  GALAEDGHRAKTHLVEANLRLVVSVAKRYTGRGLAFLDLIQEGNTGLIRAAEKFDYAKGF 148

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWIK A+   +      +++     +  L   + R++  L   T     PEQV
Sbjct: 149 KFSTYATWWIKQAVSRALADQSRTIRVPVHTVE--LINRIARVRRELILDTGAEPTPEQV 206

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
              A+   V    +  ++       SL+  +  SD+  S++ D +V   D       +  
Sbjct: 207 AEKAE---VPVGRLAELDGYTKEPVSLH--VALSDEGDSEFGDLIV---DSDTPSPWDMV 258

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAF 277
                +  L   ++ + PRE  I   R         TLE +   + V+RER+RQIE+R  
Sbjct: 259 TFSLLQQALRTLLAEMTPREAGIISLRYGLFGGRARTLEEIGQVYGVTRERIRQIESRTM 318

Query: 278 KKVQESIQKQV 288
            K++   + Q 
Sbjct: 319 SKLRHPSRSQA 329


>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 =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 71/251 (28%), Positives = 119/251 (47%), Gaps = 15/251 (5%)

Query: 41  YREHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
             + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 420 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 479

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I            L R        +     PE
Sbjct: 480 GYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLVRCSRQFLHESGREPTPE 537

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A++L++   +V  +        SL   I   D+  S   D++    D    + ++
Sbjct: 538 ---EMAERLSMPLEKVRKVMKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAVIPVD 589

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              + N +  +TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+
Sbjct: 590 AAVQSNLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 649

Query: 276 AFKKVQESIQK 286
           A +K++   + 
Sbjct: 650 ALRKLKHPSRS 660


>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 =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 67/263 (25%), Positives = 119/263 (45%), Gaps = 14/263 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L+  E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 345 LQISEIKEINRRMSMGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 404

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 405 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 462

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    + +++++ E +V  +        S+   I   D   S   D++  
Sbjct: 463 LQEMGREPTPE---ELGERMDMPEDKVRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 515

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D      ++    +  +      ++ L  RE ++   R   +     TLE +  +F+V
Sbjct: 516 -EDSTISSPVDSATGQGLQEATKDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 574

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   +  
Sbjct: 575 TRERIRQIEAKALRKLRHPTRSD 597


>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 =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 67/247 (27%), Positives = 118/247 (47%), Gaps = 12/247 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 381 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 440

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            L R+             PE    +A+++
Sbjct: 441 WWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQCLQEMGREATPE---ELAERM 495

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           N+ E ++  +        S+   I   D + S   D++    D   ++ ++    ++ R 
Sbjct: 496 NMPEDKIRKVLKIAKEPISMETPI--GDDDDSHLGDFI---QDESLELPLDSATAESLRI 550

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                +  L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 551 ATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 610

Query: 285 QKQVELS 291
           + +   S
Sbjct: 611 RSETLRS 617


>gi|157737257|ref|YP_001489940.1| RNA polymerase sigma factor RpoD [Arcobacter butzleri RM4018]
 gi|157699111|gb|ABV67271.1| RNA polymerase sigma 70 factor [Arcobacter butzleri RM4018]
          Length = 626

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 71/260 (27%), Positives = 128/260 (49%), Gaps = 15/260 (5%)

Query: 29  LEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L  +E   + ++ +    ++  +  R+  S+LRLVV IA  Y   GLP  +++ EGNIGL
Sbjct: 365 LTPEELKAVLEQIKRGKQITDTSKTRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGL 424

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+ ++G++ +TY+ WWI+ A+   I      ++I        +   + R+   +
Sbjct: 425 MKAVDKFEYKKGYKFSTYATWWIRQAISRAIADQARTIRIPIH-----MIETINRINKII 479

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +     N K   +  IAK++ +   +V  +        SL A I S +    ++ D++  
Sbjct: 480 RKGVQENGKEPDIEEIAKEVGLPVDKVKQVIKITKEPVSLEAPIGSDED--GKFGDFVPD 537

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN---PVTLENLSSEFE 263
           +        I+   +++ +  + + +S LN RE+ +   R          TLE +  E  
Sbjct: 538 EK---APTPIDNIMKEDLQGQIDQILSQLNEREQAVIRMRFGLMEDASDRTLEEIGKELN 594

Query: 264 VSRERVRQIEARAFKKVQES 283
           V+RERVRQIE+ A KK++  
Sbjct: 595 VTRERVRQIESSAIKKLKHP 614



 Score = 41.0 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 10/36 (27%), Positives = 21/36 (58%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+ +IP+L K+EE  ++K+     D+
Sbjct: 101 SDSPVRMYLREMGQIPLLTKEEEVEISKKIETGEDI 136


>gi|298209056|ref|YP_003717235.1| RNA polymerase sigma factor rpoD (Sigma-A) [Croceibacter atlanticus
           HTCC2559]
 gi|83848983|gb|EAP86852.1| RNA polymerase sigma factor rpoD (Sigma-A) [Croceibacter atlanticus
           HTCC2559]
          Length = 287

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 72/276 (26%), Positives = 147/276 (53%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI K+ ++  +EE  LA+R R  GD  A  +L  ++LR VV ++  Y+  GL 
Sbjct: 17  SLDKYLQEIGKVDLITAEEEVELAQRIR-AGDNRALEKLTKANLRFVVSVSKQYQNQGLT 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + +     +V++    N+  
Sbjct: 76  LPDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLP--LNKIG 133

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               + ++  +L+        PE    IA++L ++ SEV           S++A +   +
Sbjct: 134 SINKINKMYAYLEQSNQRPPTPE---EIAQELEMTISEVKESLKNSGRHLSMDAPLVDGE 190

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NP 252
            ++           + ++ +L+E  + +     + R++  L PRE  +           P
Sbjct: 191 DSNLYDVLKFGESPNPEKDLLVESLQTE-----IDRALETLTPREADVIRLYFGLGQQQP 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TLE +   FE++RERVRQI+ +A ++++ + + ++
Sbjct: 246 LTLEEIGETFELTRERVRQIKEKATRRLKHTSRSKI 281


>gi|260574108|ref|ZP_05842113.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacter sp. SW2]
 gi|259023574|gb|EEW26865.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacter sp. SW2]
          Length = 292

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 104/272 (38%), Positives = 172/272 (63%), Gaps = 6/272 (2%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
            +  K  +L+ + E  LA  +R+  D +A HRL+T+++RL + +A  +R YG P+++++ 
Sbjct: 13  RQAMKAELLDAETELRLAYAWRDQRDEAALHRLITAYMRLAISMAAKFRRYGAPMNDLIQ 72

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           E ++GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFNL+
Sbjct: 73  EASLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNLK 132

Query: 141 RLKGHLQAITDNNLKP----EQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDK 195
           R++  L+       +     +    +A+++ V  ++V  M  RLAG D SLNA   SS+ 
Sbjct: 133 RVQAKLEREAAQRGESLDGHQLREMVAREVGVPLADVEMMEGRLAGSDFSLNA-TQSSED 191

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
              +W D L  D     + +    +    R  L  +M+ LNPRER I   R+L+ +  TL
Sbjct: 192 EGREWIDALEDDGVQAAEAVEGAHDAARLRGWLVVAMAALNPRERFIVTERKLRGDGRTL 251

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+L +E  +S+ERVRQ+EA AF K++ S++ Q
Sbjct: 252 ESLGAELGLSKERVRQLEAAAFAKLRRSLEGQ 283


>gi|257483092|ref|ZP_05637133.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. tabaci
           ATCC 11528]
 gi|289627702|ref|ZP_06460656.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. aesculi
           str. NCPPB3681]
 gi|289649021|ref|ZP_06480364.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. aesculi
           str. 2250]
 gi|298485287|ref|ZP_07003379.1| RNA polymerase sigma factor RpoD [Pseudomonas savastanoi pv.
           savastanoi NCPPB 3335]
 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
           ATCC 11528]
          Length = 616

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 69/263 (26%), Positives = 121/263 (46%), Gaps = 14/263 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L+  E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 356 LKIAEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 415

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 416 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 473

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    + +++ + E ++  +        S+   I   D   S   D++  
Sbjct: 474 LQEMGREPTPE---ELGERMEMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 526

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q  I+    ++ +      +S L  RE ++   R   +     TLE +  +F+V
Sbjct: 527 -EDSTMQSPIDVATVESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 585

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   + +
Sbjct: 586 TRERIRQIEAKALRKLRHPTRSE 608


>gi|134094484|ref|YP_001099559.1| RNA polymerase sigma factor RpoS [Herminiimonas arsenicoxydans]
 gi|133738387|emb|CAL61432.1| RNA polymerase sigma factor rpoS (Sigma-38) [Herminiimonas
           arsenicoxydans]
          Length = 344

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 83/272 (30%), Positives = 138/272 (50%), Gaps = 11/272 (4%)

Query: 17  SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
             Y+++I   P+L   EE   A    + G+ +A  +++  +LRLVV IA  Y   G+ + 
Sbjct: 73  QHYLNQIGARPLLTVPEEVHFAT-LAKQGNFAARQKMIEHNLRLVVSIAKHYINRGVVLL 131

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++ EGN+GLM+A+ KF+PERGFR +TY+ WWI+ +++  I+     V++       R  
Sbjct: 132 DLIEEGNLGLMRAIDKFEPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV--VREL 189

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
               R K HL+A   ++ K      IA  +  S  +V  +        SL+A +      
Sbjct: 190 NQTLRAKFHLEA-QHHDGKDATAEDIAHLVERSVEDVQDILALSEHASSLDAPL--DGDP 246

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVT 254
            S   D L  DH     VL E +E      ++   +  L+ ++R +   R     ++P T
Sbjct: 247 QSSLMDLLQGDHANDPDVLAEHQEMIV---LVRDWLDKLSDKQRLVITRRFGLDNDDPAT 303

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE L++E  V+RERVRQI+  A  K++ S+ +
Sbjct: 304 LEELATEMHVTRERVRQIQQEALVKLKRSLAR 335


>gi|257064907|ref|YP_003144579.1| RNA polymerase sigma factor, sigma-70 family [Slackia
           heliotrinireducens DSM 20476]
 gi|256792560|gb|ACV23230.1| RNA polymerase sigma factor, sigma-70 family [Slackia
           heliotrinireducens DSM 20476]
          Length = 314

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 83/296 (28%), Positives = 138/296 (46%), Gaps = 42/296 (14%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYR------------------------------E 43
             +  Y+ +I K+ +L   EE  LAK+Y+                              +
Sbjct: 15  DSIRMYLRDIGKVDLLTPAEEVELAKKYQTGLAAEAALAQMNEGSVEVDRRECRKLLRVQ 74

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
                A  +LV ++LRLVV IA  YRG GLP+ ++V EGN+GL++AV+KFD  +GF+L+T
Sbjct: 75  RAGQEAKDKLVAANLRLVVSIAKKYRGRGLPLLDLVQEGNLGLIRAVEKFDYTKGFKLST 134

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI+ A+   I      +++        L   + R++  L    + +  P     IA
Sbjct: 135 YATWWIRQAVTRAIADKARTIRLPVHV--VGLMNKVVRVQHELADELERDPSP---AEIA 189

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
            +L +SE  V+ +    +   SL   +   D  +S+  D++    D   +   +      
Sbjct: 190 DRLGISEQCVVELLKLGSEPLSLETPV--GDDKTSEIGDFI---EDRNSEDAFDAAAEAM 244

Query: 224 RRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAF 277
            R+ +  ++S L  RER+I E R       P TL  +  +  V+RER+RQIE++  
Sbjct: 245 LRDDVASALSRLPERERKIIELRFGIVDGEPRTLAQIGDQLGVTRERIRQIESKTL 300


>gi|291287657|ref|YP_003504473.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Denitrovibrio
           acetiphilus DSM 12809]
 gi|290884817|gb|ADD68517.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Denitrovibrio
           acetiphilus DSM 12809]
          Length = 626

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 66/248 (26%), Positives = 120/248 (48%), Gaps = 12/248 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E+    A  +L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV+KF+ +RG++ +
Sbjct: 383 ENETEKAKSKLIEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVEKFEYKRGYKFS 442

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + ++   LQ        PE    I
Sbjct: 443 TYATWWIRQAITRAIADQARTIRIPVHM--IETINKMMKITRQLQQDMGREPTPE---EI 497

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           + K+++   ++  +        SL   I   +   S   D++    D   +   E+    
Sbjct: 498 SSKMDIPVEKIKKVMKIAKEPVSLETPI--GEDEDSSLGDFI---EDKSAKNPSEEVTYL 552

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             +    + +  L+ RE  + + R     ++  TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 553 KLKEHTKQILETLSHREASVLKLRFGIECDSDHTLEEVGKQFNVTRERIRQIEAKALRKL 612

Query: 281 QESIQKQV 288
           +   + ++
Sbjct: 613 RHPTRSRI 620



 Score = 36.7 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 13/63 (20%), Positives = 28/63 (44%), Gaps = 1/63 (1%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL-VVKIAMG 67
            ++ +  +  Y+ E+  I +L ++EE  +AK   E         L+  +  + ++ IA  
Sbjct: 90  SISTDDPVRLYLKEMGNIALLNREEEIEVAKEIEEGQRKVVRAVLLYPNTAMKIMDIARN 149

Query: 68  YRG 70
            R 
Sbjct: 150 IRN 152


>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|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. M302280PT]
          Length = 616

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 69/263 (26%), Positives = 121/263 (46%), Gaps = 14/263 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L+  E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 356 LKIAEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 415

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 416 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 473

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    + +++ + E ++  +        S+   I   D   S   D++  
Sbjct: 474 LQEMGREPTPE---ELGERMEMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 526

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q  I+    ++ +      +S L  RE ++   R   +     TLE +  +F+V
Sbjct: 527 -EDSTMQSPIDVATVESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 585

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   + +
Sbjct: 586 TRERIRQIEAKALRKLRHPTRSE 608


>gi|307295455|ref|ZP_07575291.1| RNA polymerase, sigma 70 subunit, RpoD [Sphingobium
           chlorophenolicum L-1]
 gi|306878494|gb|EFN09714.1| RNA polymerase, sigma 70 subunit, RpoD [Sphingobium
           chlorophenolicum L-1]
          Length = 681

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 68/251 (27%), Positives = 120/251 (47%), Gaps = 15/251 (5%)

Query: 41  YREHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
             + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 432 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 491

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I        +   + +L    +       +  
Sbjct: 492 GYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTSRQFLHEQGREP 546

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A++L++   +V  +        SL   I   D+  S   D++    D    + ++
Sbjct: 547 TPEEMAERLSMPLEKVRKVMKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAIIPVD 601

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              + N +  +TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+
Sbjct: 602 AAIQANLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 661

Query: 276 AFKKVQESIQK 286
           A +K++   + 
Sbjct: 662 ALRKLKHPSRS 672


>gi|83747939|ref|ZP_00944970.1| RpoS [Ralstonia solanacearum UW551]
 gi|83725357|gb|EAP72504.1| RpoS [Ralstonia solanacearum UW551]
          Length = 381

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 78/278 (28%), Positives = 136/278 (48%), Gaps = 11/278 (3%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
               +  Y++ I   P+L   EE   + R +  G+ +A   ++  +LRLVV IA GY   
Sbjct: 105 AADTVQHYLNRISIKPLLTPAEELHFSTRAK-AGEFAARQVMIERNLRLVVSIAKGYLNR 163

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           G+P+ +++ EGN+GLM A++KFDPERGFR +TY+ WWI+ +++  I+     V++     
Sbjct: 164 GVPLLDLIEEGNLGLMHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV- 222

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
             R    + R K HL+  +  + +   +  IA  L  +  EV  +        SL+    
Sbjct: 223 -IRELNQVLRAKRHLEK-SGIDGRDASIEDIAHLLGKTTEEVQDVLSLNEHTTSLDTPF- 279

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE- 250
               + +   D+L  +H        ++   +    ++   ++ L+ + R + E R     
Sbjct: 280 -DLDSGTSLLDFLSDEHGASPD---QEVAHRELSQLMKSWLARLSDKHRYVVERRFGLNH 335

Query: 251 -NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             P TLE L++E  ++RERVRQI+  A  K++     Q
Sbjct: 336 IEPATLEELAAEMGLTRERVRQIQQEALVKLKRHFASQ 373


>gi|303327390|ref|ZP_07357831.1| RNA polymerase sigma-70 factor [Desulfovibrio sp. 3_1_syn3]
 gi|302862330|gb|EFL85263.1| RNA polymerase sigma-70 factor [Desulfovibrio sp. 3_1_syn3]
          Length = 589

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 74/257 (28%), Positives = 118/257 (45%), Gaps = 12/257 (4%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE +   +      + A   L+ S+LRLVV IA  Y   GL   +++ EGNIGLM+AV K
Sbjct: 335 EEVLWRIKRGNTAAMRAKQELIRSNLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 394

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RG++ +TY+ WWI+ A+   I      ++I            L R   +L      
Sbjct: 395 FEYQRGYKFSTYATWWIRQAITRAIADQARTIRIPVHM--IETINKLIRTSRYLVQELGR 452

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +  PE    IA+++     +V  +        SL   I   D+  S   D++    D + 
Sbjct: 453 DPTPE---EIAERMEYPVEKVKKVLKIAKEPISLETPI--GDEEDSSLGDFI---EDKKA 504

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
               E+         L   ++ L PRE ++   R         TLE +   F V+RER+R
Sbjct: 505 VAPAEEVINTKLSEQLAAVLADLTPREEQVLRKRFGIAEKSDHTLEEVGKLFNVTRERIR 564

Query: 271 QIEARAFKKVQESIQKQ 287
           QIEA+A +K++  ++ Q
Sbjct: 565 QIEAKALRKLRHPVRSQ 581


>gi|260576520|ref|ZP_05844509.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhodobacter sp.
           SW2]
 gi|259021243|gb|EEW24550.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhodobacter sp.
           SW2]
          Length = 668

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 428 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 487

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A+KL
Sbjct: 488 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAEKL 542

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++N + 
Sbjct: 543 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAILPLDSAIQENLKE 597

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 598 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 657

Query: 285 QK 286
           + 
Sbjct: 658 RS 659


>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 =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 69/244 (28%), Positives = 115/244 (47%), Gaps = 12/244 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RGF+ +TY+ 
Sbjct: 383 KRAKEEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGFKFSTYAT 442

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            L R+   LQ     +  PE    ++  +
Sbjct: 443 WWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRMLQQKNGRDPTPE---ELSVAM 497

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++ E ++  +        S+   I   D   S   D+L    D      +E    +    
Sbjct: 498 DMPEDKIRKVWKIAKEPISMETPI--GDDEDSHLGDFL---EDSNVISPLEAATTRGLSE 552

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                ++ L PRE R+   R   +     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 553 ATNEVLASLTPREERVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKALRKLRHPN 612

Query: 285 QKQV 288
           + ++
Sbjct: 613 RSEL 616


>gi|41855|emb|CAA78689.1| KatF [Escherichia coli]
          Length = 377

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 79/278 (28%), Positives = 140/278 (50%), Gaps = 13/278 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 73  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 131

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 132 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 190

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    +   
Sbjct: 191 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE--- 243

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
             +  L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 244 --KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 301

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSP 294
           ++  E  ++RERVRQI+    ++++E +Q Q     +P
Sbjct: 302 DVGREIGLTRERVRQIQVEGLRRLREILQTQGLNIEAP 339


>gi|227499199|ref|ZP_03929334.1| RNA polymerase [Acidaminococcus sp. D21]
 gi|226904646|gb|EEH90564.1| RNA polymerase [Acidaminococcus sp. D21]
          Length = 582

 Score =  223 bits (570), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 73/244 (29%), Positives = 117/244 (47%), Gaps = 13/244 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L  ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ 
Sbjct: 342 EKAKKALSEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIKAVEKFDYNKGFKFSTYAT 401

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I     +      L R+   L         PE    IA+++
Sbjct: 402 WWIRQAITRAIADQARTIRIPVHMVE--TINKLVRVSRQLLQELGREPTPE---EIAQEM 456

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +V    V  +        SL   I   ++  S   D++    D +     E       + 
Sbjct: 457 DVPVERVREIQKIAQEPVSLETPI--GEEEDSHLGDFI---EDQEAPSPAEAASYTLLQE 511

Query: 227 MLTRSM-SVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            L + +   L+PRERR+ E R   L     TLE +   F V+RER+RQIEA+A +K++  
Sbjct: 512 QLGKVLQEHLSPRERRVLELRFGLLDGRTRTLEEVGQYFGVTRERIRQIEAKALRKLRSP 571

Query: 284 IQKQ 287
            + +
Sbjct: 572 KRSK 575



 Score = 36.7 bits (84), Expect = 4.0,   Method: Composition-based stats.
 Identities = 12/37 (32%), Positives = 22/37 (59%), Gaps = 1/37 (2%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSA 49
           +  +  Y+ EI ++P+L   +E  LAKR  + G+ +A
Sbjct: 151 DDPVRMYLKEIGRVPLLSGNDEIKLAKR-TDKGNQAA 186


>gi|299140647|ref|ZP_07033785.1| RNA polymerase sigma-70 factor [Prevotella oris C735]
 gi|298577613|gb|EFI49481.1| RNA polymerase sigma-70 factor [Prevotella oris C735]
          Length = 287

 Score =  223 bits (569), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 76/286 (26%), Positives = 149/286 (52%), Gaps = 12/286 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI    ++  +EE  LA++ +  GD  A  +L  ++LR VV
Sbjct: 5   KITKSITNRESASLDKYLQEIGHEDLISVEEEVELAQKIK-RGDRRALEKLTRANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + I     
Sbjct: 64  SVAKQYQNQGLSLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++           ++ ++K  L  +   N +   +  IA K+++ E +V         
Sbjct: 124 IVRLPLNQ-----VGSVNKIKRVLNKLEQENEQFPTIEEIAAKVDIPEDKVADAIKSNGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A +   ++NS    D L  ++      ++ +E     R+ +  ++  LN RER I
Sbjct: 179 HVSVDAPLAEGEENS--LLDILPNNNAQMADSMLVQESL---RDEVANALQSLNERERNI 233

Query: 243 FEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            EA        +TLE +  +F ++RERVRQI+ +A ++++ + + +
Sbjct: 234 IEAFFGINQSEMTLEEIGDKFGLTRERVRQIKEKAIRRLRHNTKNK 279


>gi|302336705|ref|YP_003801911.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           smaragdinae DSM 11293]
 gi|301633890|gb|ADK79317.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           smaragdinae DSM 11293]
          Length = 322

 Score =  223 bits (569), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 74/309 (23%), Positives = 137/309 (44%), Gaps = 42/309 (13%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD------------------ 46
           +  +  N    LS Y+ +I   P+L K+EE ++ +  +E                     
Sbjct: 12  DSDVDFNDSDPLSLYLKQISAYPLLTKEEELMIGREIQERKQELLELEELLGKEEIERSA 71

Query: 47  ------------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                         +  R++TS+LRLVV IA  Y+  GL   +++ EGNIGL++AV++FD
Sbjct: 72  YLFRKRTIEAVLRKSRDRMITSNLRLVVSIAKKYQHRGLSFLDLIDEGNIGLIEAVERFD 131

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +  + +TY  WWI+ ++ + +      ++I            +R+L    + +T    
Sbjct: 132 YTKRCKFSTYGTWWIQQSVIKALADKGRTIRIPIHV-----LNIIRKLFSVTKHLTQELG 186

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +      IA  +++    V S+        SL+  +   D+N +   D +  D       
Sbjct: 187 RDPSSAEIAAYMDLPVERVESILQYSGETASLD--VTVDDENITSLSDLVFSDD---YIE 241

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
             E       +++L   +  L+ RE+ I + R    +  P+TLE + S   ++RERVRQI
Sbjct: 242 PFESVFHVTLKDLLDTILGQLSEREQTIIKLRFGLADRTPLTLEEIGSILGITRERVRQI 301

Query: 273 EARAFKKVQ 281
           + +A +K++
Sbjct: 302 QNKAIEKLR 310


>gi|256375630|ref|YP_003099290.1| RNA polymerase sigma factor SigB [Actinosynnema mirum DSM 43827]
 gi|255919933|gb|ACU35444.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Actinosynnema
           mirum DSM 43827]
          Length = 330

 Score =  223 bits (569), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 72/292 (24%), Positives = 131/292 (44%), Gaps = 38/292 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYRE--------------------------HGDLSAAHR 52
           Y++ I K  +L   +E  LAKR                                L A + 
Sbjct: 37  YLNGIGKTALLTAAQEVELAKRIEAGVFAHHVLETTTALNAGRADELRALVRDGLRAKNH 96

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 97  LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQA 156

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +      +++     ++     L R+K  L          E    +A +  +S ++
Sbjct: 157 ITRGMADQGRTIRLPVHLVEQ--VNKLARIKRDLHQQLGREATNE---ELAAESGLSPTK 211

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           V  +        SL+  +    +  +   D++        +  +        ++ L R +
Sbjct: 212 VSDLLDHARDPVSLDMPV--GAEEDAPLGDFIEDSDATDAESAV---ISGLLQDDLRRVL 266

Query: 233 SVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           + L  RE+ +   R   E+  P TL+ +  +F +SRERVRQIE     K+++
Sbjct: 267 ATLEQREQAVIRLRYGLEDGQPRTLDQIGKQFGLSRERVRQIEREVMSKLRQ 318


>gi|220904357|ref|YP_002479669.1| RpoD subfamily RNA polymerase sigma-70 subunit [Desulfovibrio
           desulfuricans subsp. desulfuricans str. ATCC 27774]
 gi|219868656|gb|ACL48991.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           desulfuricans subsp. desulfuricans str. ATCC 27774]
          Length = 589

 Score =  223 bits (569), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 74/257 (28%), Positives = 118/257 (45%), Gaps = 12/257 (4%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE +   +      + A   L+ S+LRLVV IA  Y   GL   +++ EGNIGLM+AV K
Sbjct: 335 EEVLWRIKRGNTAAMRAKQELIRSNLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 394

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RG++ +TY+ WWI+ A+   I      ++I            L R   +L      
Sbjct: 395 FEYQRGYKFSTYATWWIRQAITRAIADQARTIRIPVHM--IETINKLIRTSRYLVQELGR 452

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +  PE    IA+++     +V  +        SL   I   D+  S   D++    D + 
Sbjct: 453 DPTPE---EIAERMEYPVEKVKKVLKIAKEPISLETPI--GDEEDSSLGDFI---EDKKA 504

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
               E+         L   ++ L PRE ++   R         TLE +   F V+RER+R
Sbjct: 505 VAPAEEVINTKLSEQLAAVLADLTPREEQVLRKRFGIAEKSDHTLEEVGKLFNVTRERIR 564

Query: 271 QIEARAFKKVQESIQKQ 287
           QIEA+A +K++  ++ Q
Sbjct: 565 QIEAKALRKLRHPVRSQ 581


>gi|108757418|ref|YP_634007.1| RNA polymerase sigma-E factor [Myxococcus xanthus DK 1622]
 gi|108461298|gb|ABF86483.1| RNA polymerase sigma-E factor [Myxococcus xanthus DK 1622]
          Length = 278

 Score =  223 bits (569), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 106/271 (39%), Positives = 177/271 (65%), Gaps = 6/271 (2%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           + E+++ P+L ++EE  LA+ Y+E GD++AA+RLV S+LRLVVK+A  Y    L + ++V
Sbjct: 1   MAEVQRHPLLTREEELQLARHYKESGDVNAAYRLVASNLRLVVKLAHEYHRNPLSLLDLV 60

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EGNIGLMQAVKK+DPERG +L++Y+ WWI+A +  YI+ +W +VK+GTT  Q++LFF L
Sbjct: 61  QEGNIGLMQAVKKYDPERGVKLSSYAAWWIRAYILRYIMDNWKMVKLGTTEAQRKLFFKL 120

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNSS 198
           R+ +  L A             +A++LNV+E +V+ M+ RL  DE S++A + + D + +
Sbjct: 121 RQEQEKLIA----QGFEASPKLLAERLNVTEQDVVEMDQRLGHDEMSIDAPLGNDDDSRT 176

Query: 199 QWQD-WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
              D +L  +    ++ L  ++ +   R  L+     L  +ER IFE+R + + P+TL++
Sbjct: 177 TRADRYLPSNSMPADERLGAEQLKALFREKLSEFARTLEGKERFIFESRLVSDEPLTLQD 236

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +  ++ VSRER RQIEA    ++++ +++Q+
Sbjct: 237 IGDKYGVSRERARQIEAALINRMRDFMREQI 267


>gi|254000081|ref|YP_003052144.1| RNA polymerase sigma-70 subunit RpoD [Methylovorus sp. 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 sp. SIP3-4]
 gi|312441356|gb|ADQ85462.1| RNA polymerase, sigma 70 subunit, RpoD [Methylovorus sp. MP688]
          Length = 638

 Score =  223 bits (569), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 114/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 391 EARARRAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 450

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T     P     +
Sbjct: 451 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---L 505

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+ + E ++  +        S+   I   D + S   D++    D      ++     
Sbjct: 506 AEKMEMPEDKIRKILKISKEPISMETPI--GDDDDSHLGDFI---EDMTTLAPVDAAVYA 560

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R      +  L  RE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 561 SLREATKEVLESLTAREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 620

Query: 281 QESIQKQ 287
           +   + +
Sbjct: 621 RHPTRSE 627


>gi|212702263|ref|ZP_03310391.1| hypothetical protein DESPIG_00274 [Desulfovibrio piger ATCC 29098]
 gi|212674326|gb|EEB34809.1| hypothetical protein DESPIG_00274 [Desulfovibrio piger ATCC 29098]
          Length = 589

 Score =  223 bits (569), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 80/278 (28%), Positives = 126/278 (45%), Gaps = 23/278 (8%)

Query: 23  IRKIPMLEKQEEY----------VLAKRYR-EHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           I KI +L + +E           VL +  R     + A   L+ S+LRLVV IA  Y   
Sbjct: 314 IGKIEILSRLQEKCCHNVNDLEEVLWRIKRGNTAAMRAKQELIRSNLRLVVSIAKKYTNR 373

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ WWI+ A+   I      ++I     
Sbjct: 374 GLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQAITRAIADQARTIRIPVHM- 432

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
                  L R   +L      +  PE    IA+++     +V  +        SL   I 
Sbjct: 433 -IETINKLIRTSRYLVQELGRDPTPE---EIAERMEYPVEKVKKVLKIAKEPISLETPI- 487

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             D+  S   D++    D +     E+         L   ++ L PRE ++   R     
Sbjct: 488 -GDEEDSSLGDFI---EDKKAVAPAEEVINTKLSEQLAAVLADLTPREEQVLRKRFGIAE 543

Query: 252 P--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
               TLE +   F V+RER+RQIEA+A +K++  ++ Q
Sbjct: 544 KSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPVRSQ 581


>gi|56552519|ref|YP_163358.1| RNA polymerase sigma factor RpoD [Zymomonas mobilis subsp. mobilis
           ZM4]
 gi|241762241|ref|ZP_04760323.1| 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|241373288|gb|EER62907.1| RNA polymerase, sigma 70 subunit, RpoD [Zymomonas mobilis subsp.
           mobilis ATCC 10988]
          Length = 671

 Score =  223 bits (569), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 69/251 (27%), Positives = 121/251 (48%), Gaps = 15/251 (5%)

Query: 41  YREHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
             + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 422 MVQKGEREARIAKTEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 481

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I        +   + +L    + I     +  
Sbjct: 482 GYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTSRQILHEIGREP 536

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A++L++   +V  +        SL   I   D+  S   D++    D    + ++
Sbjct: 537 TPEELAERLSMPLEKVRKVMKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAIIPVD 591

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              + N +  +TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+
Sbjct: 592 AAIQANLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 651

Query: 276 AFKKVQESIQK 286
           A +K++   + 
Sbjct: 652 ALRKLKHPSRS 662


>gi|262276866|ref|ZP_06054659.1| RNA polymerase sigma factor RpoD [alpha proteobacterium HIMB114]
 gi|262223969|gb|EEY74428.1| RNA polymerase sigma factor RpoD [alpha proteobacterium HIMB114]
          Length = 613

 Score =  223 bits (569), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 64/240 (26%), Positives = 116/240 (48%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 375 AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 434

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + +     +      ++KKL +
Sbjct: 435 IRQAITRSIADQARTIRIPVH-----MIETINKIVRTQRQMMSEFGREPTPEELSKKLAM 489

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   +   D+  S   D++    D    + ++   +   +N  
Sbjct: 490 PLEKVRKVLKIAKEPVSLETPV--GDEEDSTLGDFI---EDSNALIPVDAAVQTALKNTT 544

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           T+ ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 545 TKVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 604


>gi|158969744|gb|ABW86844.1| RpoS [Vibrio alginolyticus]
          Length = 330

 Score =  223 bits (569), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 80/290 (27%), Positives = 141/290 (48%), Gaps = 15/290 (5%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPML--EKQEEYVLAKRYREHGDLSAAHRLVTSHLR 59
            R+              Y+ EI   P+L    +EE + A+R    GD +A  R++ S+LR
Sbjct: 39  AREEFDASSKSLDATQLYLGEIGFSPLLILTAEEEVLYARR-ALRGDEAARKRMIESNLR 97

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           LVVKI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++ 
Sbjct: 98  LVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMN 157

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
               +++      K L   LR  +     ++           IA +L++   +V  M   
Sbjct: 158 QTRTIRLPIHVV-KELNIYLRTAR----ELSQKLDHEPTAEEIAAQLDIPVEDVSKMLRL 212

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
                S++  I           D +   ++   +V  + +   + ++ L   +  LNP++
Sbjct: 213 NERISSVDTPI--GGDGEKALLDIIPDANNSDPEVSTQDD---DIKSSLIHWLEELNPKQ 267

Query: 240 RRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           + +   R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 268 KEVLARRFGLLGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLREVLIKQ 317


>gi|319408880|emb|CBI82537.1| RNA polymerase sigma factor [Bartonella schoenbuchensis R1]
          Length = 667

 Score =  223 bits (569), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 118/240 (49%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 429 AKKEMVEANLRLVISIAKRYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 488

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + I     +      ++ KL++
Sbjct: 489 IRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQILHEIGREPTPEELSSKLSM 543

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   +   D++ S   D++    D    + I+   + N R+  
Sbjct: 544 PLEKVRKVLKIAKEPISLETPV--GDEDDSHLGDFI---EDRNALLPIDAAIQANLRDTT 598

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 599 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 658


>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 =  223 bits (569), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 71/258 (27%), Positives = 122/258 (47%), Gaps = 15/258 (5%)

Query: 34  EYVLAKRYREHGDLSAAH---RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           E+    +  + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV
Sbjct: 413 EFRKIVQMVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 472

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
            KF+  RG++ +TY+ WWI+ A+   I      ++I        +   + ++    + + 
Sbjct: 473 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQML 527

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
               +      +++KL +   +V  +        SL   I   D+  S   D++    D 
Sbjct: 528 HEIGREPTPEELSEKLAMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDK 582

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRER 268
              + IE   + N R   TR ++ L PRE R+   R         TLE +  +F V+RER
Sbjct: 583 NAILPIEAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRER 642

Query: 269 VRQIEARAFKKVQESIQK 286
           +RQIEA+A +K++   + 
Sbjct: 643 IRQIEAKALRKLKHPSRS 660


>gi|86742187|ref|YP_482587.1| sigma 38 [Frankia sp. CcI3]
 gi|86569049|gb|ABD12858.1| sigma 38 [Frankia sp. CcI3]
          Length = 422

 Score =  223 bits (569), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 67/296 (22%), Positives = 131/296 (44%), Gaps = 38/296 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------HGDL--------SA 49
           +  Y+ EI K+P+L   +E  L+KR                       DL        +A
Sbjct: 126 VRMYLREIGKVPLLNAAQEVELSKRVEAGLFAEYKLESVPDLPADLRRDLGLLVKDGHAA 185

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             +LV+++LRLVV +A  Y G G+ + ++V EGN+GL++AV+KFD  +G++ +TY+ WWI
Sbjct: 186 KQQLVSANLRLVVSVAKKYSGRGMTLLDLVQEGNLGLIRAVEKFDYAKGYKFSTYATWWI 245

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + A+   +      ++I     +      + ++    + +     +      +A +L++ 
Sbjct: 246 RQAIGRALADQARTIRIPVHVVE-----QINKITRLQRQLVSTLGREPTDEELALELDMP 300

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             +V+ +        SL   +   D   S   D++    D       +       ++ + 
Sbjct: 301 IEQVVELRRYAQDTVSLETSV--GDDGDSVLGDFI---EDSDATSPADAASYGAMQDEIE 355

Query: 230 RSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +  L+PRER +   R         TL  + +   ++RER+RQIE    +++++ 
Sbjct: 356 NVLGGLSPREREVMRLRFGLADGKQHTLAEVGNRLGLTRERIRQIERDTLRELRKP 411


>gi|330963831|gb|EGH64091.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv.
           actinidiae str. M302091]
          Length = 616

 Score =  223 bits (569), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 69/263 (26%), Positives = 121/263 (46%), Gaps = 14/263 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L+  E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 356 LKIAEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 415

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 416 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 473

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    + +++ + E ++  +        S+   I   D   S   D++  
Sbjct: 474 LQEMGREPTPE---ELGERMEMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 526

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q  I+    ++ +      +S L  RE ++   R   +     TLE +  +F+V
Sbjct: 527 -EDSTMQSPIDVATVESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 585

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   + +
Sbjct: 586 TRERIRQIEAKALRKLRHPTRSE 608


>gi|281425773|ref|ZP_06256686.1| RNA polymerase sigma-70 factor [Prevotella oris F0302]
 gi|281400034|gb|EFB30865.1| RNA polymerase sigma-70 factor [Prevotella oris F0302]
          Length = 287

 Score =  223 bits (569), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 76/286 (26%), Positives = 149/286 (52%), Gaps = 12/286 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI    ++  +EE  LA++ +  GD  A  +L  ++LR VV
Sbjct: 5   KITKSITNRESASLDKYLQEIGHEDLISVEEEVELAQKIK-RGDRRALEKLTRANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + I     
Sbjct: 64  SVAKQYQNQGLSLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++           ++ ++K  L  +   N +   +  IA K+++ E +V         
Sbjct: 124 IVRLPLNQ-----VGSVNKIKRVLNKLEQENEQFPTIEEIAAKVDIPEDKVADAIKSNGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A +   ++NS    D L  ++      ++ +E     R+ +  ++  LN RER I
Sbjct: 179 HVSVDAPLAEGEENS--LLDILPNNNAQMADSVLVQESL---RDEVANALQSLNERERNI 233

Query: 243 FEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            EA        +TLE +  +F ++RERVRQI+ +A ++++ + + +
Sbjct: 234 VEAFFGINQSEMTLEEIGDKFGLTRERVRQIKEKAIRRLRHNTKNK 279


>gi|325280730|ref|YP_004253272.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Odoribacter
           splanchnicus DSM 20712]
 gi|324312539|gb|ADY33092.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Odoribacter
           splanchnicus DSM 20712]
          Length = 289

 Score =  223 bits (569), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 72/270 (26%), Positives = 143/270 (52%), Gaps = 10/270 (3%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            + +Y+ EI KI +L  +EE  LAK+ R  GD +A  +LV S+LR VV +A  Y+ +GL 
Sbjct: 17  SIEKYLQEIGKIHVLSPEEEADLAKKIR-SGDRAAREKLVLSNLRFVVSVAKQYQNHGLT 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A + FD  +GF+  +Y++WWI+ ++ + I  +  L+++    N+  
Sbjct: 76  LGDLINEGNVGLIKAAECFDETKGFKFISYAVWWIRQSILQAIAENARLIRLP--LNKIS 133

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               + R    L+         E    IA+K++++  EV           S++A + + +
Sbjct: 134 TINKVNRCYTLLEQEFQREPTEE---EIAEKMDMTPEEVKENMKIATKPVSMDAPLTTDE 190

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
           ++ S +  ++    D   Q       + + +  + RS + L+ RE  I            
Sbjct: 191 ESISLYDVYIA--PDPSIQAPESSLNQDSLKTDIERSFAALSVREATILSMYYGLNGYSS 248

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           ++LE + ++  ++ ERVRQ++ +A +K++E
Sbjct: 249 MSLEEIGTKLGLTSERVRQVKTKAIRKLKE 278


>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 =  223 bits (569), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 70/267 (26%), Positives = 124/267 (46%), Gaps = 22/267 (8%)

Query: 32  QEEYVL-------AKRYREHGDLSAAH---RLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           +EE  L         +    GD  A     +++ ++LRLV+ IA  Y   GL   +++ E
Sbjct: 339 EEEMQLTIVELKKLNKMYRRGDRRAKKAKSQMIEANLRLVISIAKKYANRGLQFLDLIQE 398

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           GN+GLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R
Sbjct: 399 GNVGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNR 456

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           ++  L          E    +A ++ + E ++I +        S+   +   D   S   
Sbjct: 457 VRRQLLQKFGREASSE---ELATEMELPEYKIIKILKIAKEPLSMETPV--GDDEDSNIG 511

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLS 259
           D++    D      +E   +++ R      +S L+PRE ++ + R         TLE + 
Sbjct: 512 DFI---EDTNLSSPVEITTKESLRETTGDLLSNLSPREAKVLKMRFGINMNTDHTLEEVG 568

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQK 286
            +F+V+RER+RQIEA+A +K++   + 
Sbjct: 569 RQFDVTRERIRQIEAKALRKLRHPSRA 595


>gi|15606649|ref|NP_214029.1| RNA polymerase sigma factor RpoD [Aquifex aeolicus VF5]
 gi|2983864|gb|AAC07417.1| RNA polymerase sigma factor RpoD [Aquifex aeolicus VF5]
          Length = 575

 Score =  223 bits (569), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 72/262 (27%), Positives = 122/262 (46%), Gaps = 15/262 (5%)

Query: 31  KQEEYVLAKRYREHGDLS---AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            +EE     +  E G      A   ++ S+LRLVV IA  Y   GL   +++ EGNIGLM
Sbjct: 317 PEEELPKVMKIIEQGRKKVVQAKQVMIQSNLRLVVSIAKKYVNRGLHFLDLIQEGNIGLM 376

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV K+D  +G++ +TY+ WWI+ A+   I      ++I        +   + ++    +
Sbjct: 377 KAVDKYDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVH-----MIETINKIIKASK 431

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
            +   N +      IA+ L++   +V  +        SL   I   D + +  +D++   
Sbjct: 432 KLFQENGREPTPEEIAEYLDIPVEKVKKVMKFSQEPISLETPI--GDDDDTFLKDFI--- 486

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVS 265
            D       E+  RK  R  L + +S L+ +ER I   R         TLE +   F V+
Sbjct: 487 EDKSIPNPEEQVTRKLLREQLQKVLSTLSEKEREILMYRYGLVDGTEYTLEQVGKMFNVT 546

Query: 266 RERVRQIEARAFKKVQESIQKQ 287
           RER+RQIE +A +K++   + +
Sbjct: 547 RERIRQIENKALRKLRHPARAK 568



 Score = 37.5 bits (86), Expect = 2.2,   Method: Composition-based stats.
 Identities = 9/37 (24%), Positives = 21/37 (56%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY 41
           +++        +  Y+ E+ KIP+L+++EE   A++ 
Sbjct: 79  SLTSSSRDGDPVKLYLREMGKIPLLKREEEIYYARQI 115


>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 =  223 bits (569), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 71/267 (26%), Positives = 127/267 (47%), Gaps = 22/267 (8%)

Query: 32  QEEYVL-------AKRYREHGDLSAAH---RLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           +EE  L         +    GD  A     +++ ++LRLV+ IA  Y   GL   +++ E
Sbjct: 336 EEEMQLTITELKTLNKMYRRGDRRAKKAKSQMIEANLRLVISIAKKYANRGLQFLDLIQE 395

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           GN+GLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R
Sbjct: 396 GNVGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNR 453

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           ++  L         PE    +A ++ + E ++I +        S+   +   D   S   
Sbjct: 454 VRRQLLQKFGREASPE---ELATEMELPEYKIIKILKISKEPLSMETPV--GDDEDSNIG 508

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLS 259
           D++    D      +E   +++ R   +  +S L+PRE ++ + R   +     TLE + 
Sbjct: 509 DFI---EDTNLSSPVEITTKESLRETTSELLSNLSPREAKVLKMRFGIDMNTDHTLEEVG 565

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQK 286
            +F+V+RER+RQIEA+A +K++   + 
Sbjct: 566 RQFDVTRERIRQIEAKALRKLRHPSRA 592


>gi|254441274|ref|ZP_05054767.1| Sigma-70 region 3 family [Octadecabacter antarcticus 307]
 gi|198251352|gb|EDY75667.1| Sigma-70 region 3 family [Octadecabacter antarcticus 307]
          Length = 655

 Score =  223 bits (569), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 117/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 415 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 474

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A KL
Sbjct: 475 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAAKL 529

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++N + 
Sbjct: 530 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAVLPLDSAIQENLKE 584

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 585 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 644

Query: 285 QK 286
           + 
Sbjct: 645 RS 646


>gi|296284010|ref|ZP_06862008.1| RNA polymerase sigma factor RpoD [Citromicrobium bathyomarinum
           JL354]
          Length = 667

 Score =  223 bits (569), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 70/259 (27%), Positives = 123/259 (47%), Gaps = 15/259 (5%)

Query: 33  EEYVLAKRYREHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           EE+       + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+A
Sbjct: 410 EEFRRIVNMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 469

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V KF+  RG++ +TY+ WWI+ A+   I      ++I        +   + +L    +  
Sbjct: 470 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTSRQF 524

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
                +      +A++L++   +V  +        SL   I   D+  S   D++    D
Sbjct: 525 LHEQGREPTPEEMAERLSMPLEKVRKVMKIAKEPISLETPI--GDEEDSHLGDFI---ED 579

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRE 267
               + ++   + N +  +TR ++ L PRE R+   R         TLE +  +F V+RE
Sbjct: 580 KNAIIPVDAAIQSNLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRE 639

Query: 268 RVRQIEARAFKKVQESIQK 286
           R+RQIEA+A +K++   + 
Sbjct: 640 RIRQIEAKALRKLKHPSRS 658


>gi|37522577|ref|NP_925954.1| group 2 sigma 70-type sigma factor [Gloeobacter violaceus PCC 7421]
 gi|35213578|dbj|BAC90949.1| group 2 sigma 70-type sigma factor [Gloeobacter violaceus PCC 7421]
          Length = 305

 Score =  223 bits (569), Expect = 2e-56,   Method: Composition-based stats.
 Identities = 79/284 (27%), Positives = 139/284 (48%), Gaps = 15/284 (5%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRG 70
           E  + +++ E+ + P+L  ++E  LA+     G  +  A  RLV ++LRLVV IA  Y  
Sbjct: 29  EDSVGQFLREMSRYPLLTSEQEVELAQVIATGGSEAEAAKRRLVRANLRLVVSIAKKYLN 88

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            G+P  +++ EG IGLM+A +KFD ERGF+ +TY+ WWI+  +   I      V++    
Sbjct: 89  RGVPFLDLIQEGAIGLMRAAEKFDFERGFKFSTYAYWWIRQGITRAIASQSRTVRLPVHM 148

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
            +K     L ++K   + +T    +      +A+ L +   ++  +    AG  +L+  +
Sbjct: 149 VEK-----LNQVKRVRRQLTQELARKPTKPEMAEALELDIDKLDEILD--AGRRTLSLHV 201

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-- 248
               +  ++    +    D       E  +       +   + +L PRER I E R    
Sbjct: 202 KVGKEEDTELLQLI---EDSDTISPSEVLDHNLLVEQIESLLHLLTPRERDIIELRFGLA 258

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
             N  TL ++   + +SRERVRQI+A+A +K++   ++QV L  
Sbjct: 259 DGNSYTLADIGEMYNLSRERVRQIQAKAMRKLRHP-RRQVLLRD 301


>gi|303245332|ref|ZP_07331616.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           fructosovorans JJ]
 gi|302493181|gb|EFL53043.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           fructosovorans JJ]
          Length = 588

 Score =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 73/257 (28%), Positives = 119/257 (46%), Gaps = 12/257 (4%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE +   +        A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV K
Sbjct: 334 EEVLWRIKRGNTAAQRAKQELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 393

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RG++ +TY+ WWI+ A+   I      ++I            L R   +L      
Sbjct: 394 FEYQRGYKFSTYATWWIRQAITRAIADQARTIRIPVHM--IETINKLIRTSRYLVQELGR 451

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +  PE    IA++++    +V  +        SL   I   D+  S   D++    D + 
Sbjct: 452 DPTPE---EIAERMDYPLEKVKKVLKIAKEPISLETPI--GDEEDSSLGDFI---EDKKA 503

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
               E+         + + +S L PRE ++   R         TLE +   F V+RER+R
Sbjct: 504 LAPAEEVVNTKLGEQIGKVLSDLTPREEQVLRKRFGLGEKSDHTLEEVGKLFNVTRERIR 563

Query: 271 QIEARAFKKVQESIQKQ 287
           QIEA+A +K++  ++ Q
Sbjct: 564 QIEAKALRKLRHPVRSQ 580



 Score = 36.7 bits (84), Expect = 3.9,   Method: Composition-based stats.
 Identities = 12/54 (22%), Positives = 28/54 (51%), Gaps = 1/54 (1%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVT 55
           +   +         +  Y+ E+  +P+L+++ E V+AK+  E+G++   + LV 
Sbjct: 86  SEDTLDYSSRSTDPVRMYLREMGAVPLLDREGEVVIAKKI-ENGEMDVLYALVE 138


>gi|117924113|ref|YP_864730.1| RpoD family RNA polymerase sigma factor [Magnetococcus sp. MC-1]
 gi|117607869|gb|ABK43324.1| RNA polymerase, sigma 70 subunit, RpoD [Magnetococcus sp. MC-1]
          Length = 683

 Score =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 71/246 (28%), Positives = 112/246 (45%), Gaps = 12/246 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 439 ERRANQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEWRRGYKFS 498

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            L R    +         PE    I
Sbjct: 499 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKLVRTSRQMVQEMGREPTPE---EI 553

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+++++S  +V  +        SL   +   D+  S   D++    D       E     
Sbjct: 554 AERMSMSLEKVRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKSMLSPSEHAIMS 608

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R+   R +  L  RE  +   R     P   TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 609 NLRDTTGRVLQTLTSREEHVLRMRFGIGLPTDHTLEEVGKQFNVTRERIRQIEAKALRKL 668

Query: 281 QESIQK 286
           +   + 
Sbjct: 669 RHPTRS 674


>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 =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 61/248 (24%), Positives = 114/248 (45%), Gaps = 12/248 (4%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            E     A   ++ ++LRLV+ IA  Y   G+   +++ EGNIGLM+AV KF+  RG++ 
Sbjct: 420 AESKMRKAKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEGNIGLMKAVDKFEYRRGWKF 479

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY+ WW++ A+   +      +++            L R+   +   T     P     
Sbjct: 480 STYATWWVRQAVTRSLADQARTIRVPVHM--IETINKLNRISREILQQTGQEAHP---AV 534

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           +A+++ +SE +V  +        SL   +   D   +   D +    D       +   +
Sbjct: 535 LAERMELSEEKVRGILKIAKQPVSLETPV--GDDGDATLGDMI---EDAAVSSPADAAMQ 589

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKK 279
            + R  +  ++  L+PRE ++   R         TLE +  +F+V+RER+RQIE++A +K
Sbjct: 590 ADLRAAIDDALDSLSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIRQIESKAMRK 649

Query: 280 VQESIQKQ 287
           +    +  
Sbjct: 650 LMHPSRAD 657


>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 =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 69/251 (27%), Positives = 121/251 (48%), Gaps = 15/251 (5%)

Query: 41  YREHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
             + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 422 MVQKGEREARIAKTEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 481

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I        +   + +L    + I     +  
Sbjct: 482 GYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTSRQILHEIGREP 536

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A++L++   +V  +        SL   I   D+  S   D++    D    + ++
Sbjct: 537 TPEELAERLSMPLEKVRKVMKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAIIPVD 591

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              + N +  +TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+
Sbjct: 592 AAIQANLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 651

Query: 276 AFKKVQESIQK 286
           A +K++   + 
Sbjct: 652 ALRKLKHPSRS 662


>gi|119512308|ref|ZP_01631394.1| RNA polymerase sigma factor [Nodularia spumigena CCY9414]
 gi|119463021|gb|EAW43972.1| RNA polymerase sigma factor [Nodularia spumigena CCY9414]
          Length = 391

 Score =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 79/313 (25%), Positives = 140/313 (44%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAK-------------------------------- 39
            E  +  Y+ EI +I +L   EE  LA+                                
Sbjct: 79  TEDSIRLYLQEIGRIRLLRADEEIELARKIADLLELERVRDRLQEQLEREPEYREWAEAV 138

Query: 40  -------RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                  RYR H    A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 139 QIPLPAFRYRLHIGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 198

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 199 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKLLSQE 253

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA ++ ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 254 MGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIESDGETPE 311

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
               ++  +   R  L + +  L+PRER +   R   ++    TLE +   F V+RER+R
Sbjct: 312 ----DQVSKNLLREDLEKVLDSLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIR 367

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 368 QIEAKALRKLRHP 380


>gi|212634213|ref|YP_002310738.1| RNA polymerase sigma-38 factor [Shewanella piezotolerans WP3]
 gi|212555697|gb|ACJ28151.1| RNA polymerase sigma-38 factor [Shewanella piezotolerans WP3]
          Length = 322

 Score =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 81/271 (29%), Positives = 139/271 (51%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   +++    G   + +R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 53  YLGEIGFSPLLSAEEEVFFSRK-SLKGCEKSRNRMIESNLRLVVKIARRYNNRGLALLDL 111

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 112 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 170

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            IA+KL++S S+V  M        S++  +    ++  
Sbjct: 171 LRTAR----ELAHKLDHEPTAEEIAEKLDLSSSDVSRMLKLNERITSVDTPL--GGESDK 224

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  D +      ++ E+       + + +  LN ++R +   R   L   P TLE
Sbjct: 225 ALLDVLADDDNVGPDYKVQDEDMS---KSVVKWLDELNTKQREVLARRFGLLGYEPSTLE 281

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           N+  E  ++RERVRQI+  A K++++ +  Q
Sbjct: 282 NVGKEIGLTRERVRQIQVEALKRLKDLLGAQ 312


>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 =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 61/248 (24%), Positives = 119/248 (47%), Gaps = 12/248 (4%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            E     A   ++ ++LRLV+ IA  Y   G+   +++ EGNIGLM+AV KF+  RG++ 
Sbjct: 418 AESKMRQAKREMIEANLRLVISIAKKYVNRGMHFLDLIQEGNIGLMKAVDKFEYRRGWKF 477

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY+ WW++ A+   I      +++     +      L R++  +   T     P     
Sbjct: 478 STYATWWVRQAITRAIADQARTIRVPVHMIES--INKLNRIQREIVQQTGQEPHP---SV 532

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           +A+++++ E+++ S+        SL++ +   +   +   D +    D       +    
Sbjct: 533 LAERMDMPEAKIRSILKIAKNPASLDSPV--GEDADTTLGDMI---EDTSATSPADAAVH 587

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKK 279
            N R  +  ++  L PRE ++   R   +    +TLE +  +F+V+RER+RQIE +A +K
Sbjct: 588 ANMRRAIDEALDALTPREAKVLRMRYGIDTASELTLEEVGRQFDVTRERIRQIEGKAIRK 647

Query: 280 VQESIQKQ 287
           +    +  
Sbjct: 648 LNHPSRAD 655


>gi|1514627|emb|CAA62840.1| starvation sigma factor [Pseudomonas putida]
          Length = 335

 Score =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 82/278 (29%), Positives = 142/278 (51%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A   ++ GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFAPLVQK-GDPAGRKRMMQSNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + +K       ++ +N R++  D SL         + 
Sbjct: 185 LRAARELTQKL-DHEPSPEEIATLLEKPVAEVKRMLGLNERVSSVDVSL------GPDSD 237

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + +  L  ++R +   R         TL
Sbjct: 238 KTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLGELTDKQREVVVRRFGLRGHESSTL 294

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 295 EDVGLEIGLTRERVRQIQVEGLKRLREILEKNGHTSES 332


>gi|217140|dbj|BAA01749.1| principal sigma factor [Synechococcus elongatus PCC 7942]
          Length = 384

 Score =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 78/313 (24%), Positives = 140/313 (44%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGDL----------- 47
            E  +  Y+ EI +I +L   EE  LA++               E  D            
Sbjct: 72  TEDSIRLYLQEIGRIRLLRADEEIELARQIADLLALERIRDELLEQLDRLPSDAEWAAAV 131

Query: 48  ---------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 132 DSPLDEFRRRLFRGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 191

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 192 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKLLSQE 246

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA ++ ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 247 MGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADGETPE 304

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
             + +   R++    L   +S L+PRER +   R   ++    TLE +   F V+RER+R
Sbjct: 305 DEVAKNLLRED----LEGVLSTLSPRERDVLRLRYGLDDGRMKTLEEIGQLFNVTRERIR 360

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 361 QIEAKALRKLRHP 373


>gi|78779769|ref|YP_397881.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9312]
 gi|78713268|gb|ABB50445.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9312]
          Length = 313

 Score =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 79/302 (26%), Positives = 146/302 (48%), Gaps = 36/302 (11%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------EHG-------------------D 46
           G   +S Y+  I ++P+L   EE  L  + +      E G                    
Sbjct: 16  GNDPISWYLQNIGRVPLLTPAEEIELGNQVQKMMILTEDGQLNEKIKEFTTQQKRIIKIG 75

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  R++ ++LRLVV +A  Y+G GL + ++V EG++GL +AV+KFDP RG++ +TY+ 
Sbjct: 76  RRAKERMMKANLRLVVSVAKKYQGKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAF 135

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ +M   I      +++    +++     L  ++   + +          + IA+ +
Sbjct: 136 WWIRQSMTRAIACQSRTIRLPVHLSER-----LAAIRKVSRELAHKLGAMPSRIEIAEAM 190

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   E+ S+  +     SL+A +N  D   S   D +    D   +  ++K E+K  + 
Sbjct: 191 DIDVEELDSVLRQALSTSSLDAPVN-GDDGRSFLGDLIA---DSNTEEPLDKVEQKMHQE 246

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L + +S L+ +E+ + + R   +     TL  +    EVSRERVRQ+E +A +K++   
Sbjct: 247 QLGKWLSHLSEQEQHVLKLRFGLDGNERHTLAEIGRLLEVSRERVRQVELKALRKLRNLT 306

Query: 285 QK 286
           +K
Sbjct: 307 RK 308


>gi|124266448|ref|YP_001020452.1| RNA polymerase sigma S (sigma-38) factor transcription regulator
           protein [Methylibium petroleiphilum PM1]
 gi|124259223|gb|ABM94217.1| RNA polymerase sigma S (sigma-38) factor transcription regulator
           protein [Methylibium petroleiphilum PM1]
          Length = 343

 Score =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 85/279 (30%), Positives = 141/279 (50%), Gaps = 7/279 (2%)

Query: 12  GEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           GE+G  L  Y+ EIR+ P+    EE+ +A R R  GD +A  +++  +LRLVV IA  Y 
Sbjct: 59  GEVGNTLQTYLREIRRAPLFTPDEEFAMATRAR-AGDFAARQQMIERNLRLVVSIAKSYL 117

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
             GLP+++++ EGN+GLM A+ KF+PERGFR +TY+ WWI+ +++  I+    LV++   
Sbjct: 118 SRGLPMTDLIEEGNLGLMHAIGKFEPERGFRFSTYASWWIRQSIERAIMHQARLVRLPVH 177

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             ++       R     +A    + +  +V  IA  L    +EV  +        SL+A 
Sbjct: 178 VVRELNQVLKARRALEGEAAASADGRTVRVDEIAAALGRPVTEVSELLRFAEQPTSLDAP 237

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           +     N ++    +V D   Q    +          +L   +  L+ RER +   R   
Sbjct: 238 LERQAGNGAETLGDMVADE--QATDPLGHTLNHELDVLLEHGLGELSEREREVLAGRYGL 295

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  P TLE L+    ++RER+RQI+  A  K++  + +
Sbjct: 296 HDREPETLEVLAERLGLTRERIRQIQQEALLKLKRRMAR 334


>gi|331017645|gb|EGH97701.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv.
           lachrymans str. M302278PT]
          Length = 616

 Score =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 69/263 (26%), Positives = 121/263 (46%), Gaps = 14/263 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L+  E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 356 LKIAEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 415

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 416 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 473

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    + +++ + E ++  +        S+   I   D   S   D++  
Sbjct: 474 LQEMGREPTPE---ELGERMEMPEDKIRKVLKITKEPISMETPI--GDDEDSHLGDFI-- 526

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q  I+    ++ +      +S L  RE ++   R   +     TLE +  +F+V
Sbjct: 527 -EDSTMQSPIDVATVESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 585

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   + +
Sbjct: 586 TRERIRQIEAKALRKLRHPTRSE 608


>gi|313203522|ref|YP_004042179.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Paludibacter
           propionicigenes WB4]
 gi|312442838|gb|ADQ79194.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Paludibacter
           propionicigenes WB4]
          Length = 287

 Score =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 76/287 (26%), Positives = 142/287 (49%), Gaps = 11/287 (3%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI +  ++  +EE  LA+R R  GD  A  +L  ++LR VV
Sbjct: 5   KITKSITNRESASLDKYLQEIGREDLITVEEEVELAQRIR-AGDRIALEKLTRANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 64  SVAKQYQNQGLSLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    NQ      + +     +   +    PE    +A  L++   ++         
Sbjct: 124 IVRLP--LNQVGSLNKINKAFSKFEQENERKPSPE---ELADVLDIPVDKIADTMKVSGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     + N S     +  D    ++VLI +   K    +L      L+ RER I
Sbjct: 179 HISVDAPFVEGEDN-SLLDVMINDDSPNADRVLINESLSKEIERVLAF---TLSDRERDI 234

Query: 243 FEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +         +TLE +  EF ++RERVRQI+ +A +K++ + + ++
Sbjct: 235 VKKFFGIGVAEMTLEEIGDEFGLTRERVRQIKEKAIRKLRPNAKSKL 281


>gi|300023333|ref|YP_003755944.1| RNA polymerase, sigma 70 subunit, RpoD [Hyphomicrobium
           denitrificans ATCC 51888]
 gi|299525154|gb|ADJ23623.1| RNA polymerase, sigma 70 subunit, RpoD [Hyphomicrobium
           denitrificans ATCC 51888]
          Length = 666

 Score =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 73/258 (28%), Positives = 123/258 (47%), Gaps = 15/258 (5%)

Query: 34  EYVLAKRYREHGDLSAAH---RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           EY    +  + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV
Sbjct: 410 EYRRIVKAVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 469

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
            KF+  RG++ +TY+ WWI+ A+   I      ++I        +   + ++    + + 
Sbjct: 470 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQML 524

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
               +      +A+KL +   +V  +        SL   I   D+  S   D++    D 
Sbjct: 525 HEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDR 579

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRER 268
              + IE   + N R+  TR ++ L PRE R+   R         TLE +  +F V+RER
Sbjct: 580 NAVLPIEAAIQSNLRDTTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRER 639

Query: 269 VRQIEARAFKKVQESIQK 286
           +RQIEA+A +K++   + 
Sbjct: 640 IRQIEAKALRKLKHPSRS 657


>gi|56750888|ref|YP_171589.1| RNA polymerase sigma factor RpoD [Synechococcus elongatus PCC 6301]
 gi|56685847|dbj|BAD79069.1| principal RNA polymerase sigma factor RpoD1 [Synechococcus
           elongatus PCC 6301]
          Length = 399

 Score =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 76/313 (24%), Positives = 139/313 (44%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------------- 43
            E  +  Y+ EI +I +L   EE  LA++  +                            
Sbjct: 87  TEDSIRLYLQEIGRIRLLRADEEIELARQIADLLALERIRDELLEQLDRLPSDAEWAAAV 146

Query: 44  -----------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 147 DSPLDEFRRRLFRGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 206

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 207 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKLLSQE 261

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA ++ ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 262 MGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADGETPE 319

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
             + +   R++    L   +S L+PRER +   R   ++    TLE +   F V+RER+R
Sbjct: 320 DEVAKNLLRED----LEGVLSTLSPRERDVLRLRYGLDDGRMKTLEEIGQLFNVTRERIR 375

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 376 QIEAKALRKLRHP 388


>gi|163781693|ref|ZP_02176693.1| RNA polymerase sigma factor RpoD [Hydrogenivirga sp. 128-5-R1-1]
 gi|159882913|gb|EDP76417.1| RNA polymerase sigma factor RpoD [Hydrogenivirga sp. 128-5-R1-1]
          Length = 571

 Score =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 79/272 (29%), Positives = 120/272 (44%), Gaps = 20/272 (7%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLS---AAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +EI  IP     EE        E G      A   ++ S+LRLVV IA  Y   GL   +
Sbjct: 308 NEIGVIP-----EEIKRVMGIIEQGRKKVVKAKQVMIQSNLRLVVSIAKKYVNRGLHFLD 362

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV K+D  +G++ +TY+ WWI+ A+   I      ++I           
Sbjct: 363 LIQEGNIGLMKAVDKYDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHM--IETIN 420

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + +    L         PE    IAK L ++  +V  +        SL   I   D   
Sbjct: 421 RIIKASKRLFQELGREPTPE---EIAKHLGMTPDKVRKVLRSAQEPISLETPI--GDDED 475

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
           +  +D++    D       E   RK  R  L R +  L+ +ER I   R         TL
Sbjct: 476 TFLKDFI---EDKSVPNPEEYVSRKLLREQLERVLETLSDKEREILRYRYGLVDGTEYTL 532

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +   F V+RER+RQIE++A +K++   + +
Sbjct: 533 EQVGKMFNVTRERIRQIESKAIRKLRHPSRAK 564



 Score = 37.1 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 10/41 (24%), Positives = 24/41 (58%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY 41
           ++ ++ +++      +  Y+ E+ KIP+L +Q+E   AK+ 
Sbjct: 71  VSTESFTVMGRDGDPVKLYLKEMGKIPLLTRQQEIHYAKQI 111


>gi|1588486|prf||2208419B RNA polymerase sigma factor
          Length = 391

 Score =  223 bits (569), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 75/313 (23%), Positives = 140/313 (44%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS----------------------- 48
            E  +  Y+ EI +I +L  +EE  LA++  +  +L                        
Sbjct: 79  TEDSIRIYLQEIGRIRLLRAEEEIELARKIADLLELERMREQLTEHESRVPTDKEWAEAA 138

Query: 49  ----------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 139 GMPLKDFRRRLFHGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 198

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 199 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKILSQE 253

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA+++ ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 254 LGRKPTEEEIAERMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADGETPE 311

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
               ++  +   R  L   +  L+ RER +   R   ++    TLE +   F V+RER+R
Sbjct: 312 ----DQVSKSLLREDLENVLDTLSARERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIR 367

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 368 QIEAKALRKLRHP 380


>gi|33864510|ref|NP_896070.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9313]
 gi|33641290|emb|CAE22420.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9313]
          Length = 344

 Score =  223 bits (568), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 81/292 (27%), Positives = 144/292 (49%), Gaps = 31/292 (10%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLA--------------------KRYREHGDLSAAH 51
           G   +  Y+  I ++P+L   EE  LA                    +R++      A  
Sbjct: 53  GTDAIGFYLSSIGRVPLLTAAEEIELAHHVQAMKELLELPEQDQTPRQRHKIRMGKRARD 112

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R+++++LRLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+ 
Sbjct: 113 RMMSANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQ 172

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            M   I  S   +++    ++K     L +++   + ++    +    + +A  + +   
Sbjct: 173 GMTRAIDNSARTIRLPIHISEK-----LSKMRRISRELSHRFGRQPNRLELAHAMGIQPQ 227

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           ++  +  + A   SL+A     +  S+  +  L+ D DG E   +E  +R  ++  L   
Sbjct: 228 DLEDLIAQSAPCASLDAHARGEEDRSTLGE--LIPDPDGAE--PMEGLDRSIQKEHLGGW 283

Query: 232 MSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +S LN RE++I   R     E P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 284 LSQLNEREQKILRLRFGLDGEEPLTLAEIGRQISVSRERVRQLEAKAILKLR 335


>gi|153005405|ref|YP_001379730.1| RNA polymerase sigma-70 [Anaeromyxobacter sp. Fw109-5]
 gi|152028978|gb|ABS26746.1| RNA polymerase sigma-70 [Anaeromyxobacter sp. Fw109-5]
          Length = 357

 Score =  223 bits (568), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 110/291 (37%), Positives = 174/291 (59%), Gaps = 14/291 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             L  Y+ EI + P+L ++EE+ LA RYRE GD+ AA+RLV S+LRLVVKIA  YR    
Sbjct: 69  DPLRAYMAEIARHPLLSREEEHELAVRYRETGDVDAAYRLVASNLRLVVKIAHEYRRTAF 128

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + ++V EGN+GLMQAVKK+DP +G +L++Y+ WWI+A +  +I+ +W +VK+GTT  Q+
Sbjct: 129 QLLDLVQEGNMGLMQAVKKYDPWKGVKLSSYAAWWIRAYIIRFIMENWRMVKLGTTQAQR 188

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINS 192
           +LFFNL + +  L A             +AK L+V E +V  M  R+AG D SL+A +  
Sbjct: 189 KLFFNLAKEREKLLA----RGIEPTPRLLAKNLDVEEKDVEEMTARMAGEDLSLDAPLRG 244

Query: 193 SDKNS--SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL-NPRERRIFEARRL- 248
            +  S  ++         D  ++ L +++ R+  R  L      + + +ER IF+ R L 
Sbjct: 245 DEDGSRQTRLDRVAGDGADAPDERLGDEQLRRLFREKLETFSKTIRDEKERYIFDKRLLP 304

Query: 249 --QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV---ELSSSP 294
              E P+TL+ +   F+++RER RQIEA+   ++++ ++ ++   EL   P
Sbjct: 305 AGGEAPLTLQEIGDRFKLTRERARQIEAKLTARLRDYLRAEIPDFELLGPP 355


>gi|221134005|ref|ZP_03560310.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Glaciecola sp. HTCC2999]
          Length = 326

 Score =  223 bits (568), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 86/268 (32%), Positives = 144/268 (53%), Gaps = 12/268 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE +  ++  + GD  A  R++ S+LRLVVKIA  Y+  GL + ++
Sbjct: 53  YLNEIGFSPLLSAEEEVLHGRKALK-GDKDARERMIVSNLRLVVKIARRYKDRGLALLDL 111

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     V++      K L   
Sbjct: 112 VEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTVRLPIHVV-KELNIY 170

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            IA KL+VS  +V  M       +S+++ ++     +S
Sbjct: 171 LRTARN----LAQELDHEPTAEEIADKLDVSTEDVNKMLRLNERIKSVDSYLSHESDGNS 226

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLE 256
                   +H G E    EK +  + +N +   +  LNP++R +   R       P TLE
Sbjct: 227 LLDILPDSNHSGPE----EKNQEDDIKNNIVMWLQELNPKQREVLSRRFGLMGFEPDTLE 282

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
           N+ +E  ++RERVRQI+  A +++++ +
Sbjct: 283 NVGAEIGLTRERVRQIQVEALRRLKDML 310


>gi|198282770|ref|YP_002219091.1| RpoD family RNA polymerase sigma-70 subunit [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218666687|ref|YP_002424966.1| RNA polymerase sigma-38 factor [Acidithiobacillus ferrooxidans ATCC
           23270]
 gi|198247291|gb|ACH82884.1| RNA polymerase, sigma 70 subunit, RpoD family [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218518900|gb|ACK79486.1| RNA polymerase sigma-38 factor [Acidithiobacillus ferrooxidans ATCC
           23270]
          Length = 317

 Score =  223 bits (568), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 73/271 (26%), Positives = 134/271 (49%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  ++E  L  R  + GD +A   ++ S+LRLVVK+A  Y   GLP+ ++
Sbjct: 49  YLREIGHRPLLTAEQEVTLG-RMVQTGDQAARCTMIESNLRLVVKVARHYLNRGLPLLDL 107

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++       +    
Sbjct: 108 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQNIERALMNQTRTIRLPIHV--MKELSA 165

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           + R    L      +  PE+V     +   +  + + M+ R+    SL+         S 
Sbjct: 166 VLRATRCLAQTLQRDPTPEEVAEALDRSVDAVRDCLEMDGRVT---SLDMPYGKGSDRS- 221

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLE 256
              D +    D     + ++ E +N    + + ++ +  + R +   R   +  +  TLE
Sbjct: 222 -LADLVA---DTNAPGVEQRLENQNLSRQVHQWIATMTEKHRLVLLWRFGLDGTDGATLE 277

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            + S   ++RERVRQI+  A   ++  I+ +
Sbjct: 278 EVGSRLGITRERVRQIQVEALLVLRHRIEAE 308


>gi|42521867|ref|NP_967247.1| RNA polymerase sigma factor RpoD [Bdellovibrio bacteriovorus HD100]
 gi|39574397|emb|CAE77901.1| RNA polymerase sigma factor RpoD [Bdellovibrio bacteriovorus HD100]
          Length = 609

 Score =  223 bits (568), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 73/241 (30%), Positives = 115/241 (47%), Gaps = 12/241 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 370 AAKSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 429

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I            L R   +L         PE    IA K++
Sbjct: 430 WIRQAITRAIADQARTIRIPVHM--IETINKLVRTSRYLIQELGREPTPE---EIADKMD 484

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +   +V  +        SL   +   ++  S   D++    D +     E     N    
Sbjct: 485 MPVDKVRKVLKIAKEPISLETPV--GEEEDSHLGDFI---EDKKVINPAEAIVNLNLAEQ 539

Query: 228 LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             R +S L PRE ++   R    +E+  TLE +  +F V+RER+RQIEA+A +K++   +
Sbjct: 540 TRRVLSTLTPREEKVLRMRFGIGEESDHTLEEVGQDFNVTRERIRQIEAKALRKLRHPSR 599

Query: 286 K 286
            
Sbjct: 600 S 600


>gi|66047868|ref|YP_237709.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. syringae
           B728a]
 gi|63258575|gb|AAY39671.1| 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 [Pseudomonas syringae pv. syringae B728a]
          Length = 616

 Score =  223 bits (568), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 69/263 (26%), Positives = 121/263 (46%), Gaps = 14/263 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L+  E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 356 LKIAEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 415

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 416 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 473

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    + +++ + E ++  +        S+   I   D   S   D++  
Sbjct: 474 LQEMGREPTPE---ELGERMEMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 526

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q  I+    ++ +      +S L  RE ++   R   +     TLE +  +F+V
Sbjct: 527 -EDSTMQSPIDVATVESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 585

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   + +
Sbjct: 586 TRERIRQIEAKALRKLRHPTRSE 608


>gi|159037062|ref|YP_001536315.1| RNA polymerase sigma factor SigB [Salinispora arenicola CNS-205]
 gi|157915897|gb|ABV97324.1| RNA polymerase, sigma 70 subunit, RpoD family [Salinispora
           arenicola CNS-205]
          Length = 328

 Score =  223 bits (568), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 71/301 (23%), Positives = 135/301 (44%), Gaps = 39/301 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHG---------------------------DLS 48
           +  Y++ I K  +L   +E  L++R  E G                             +
Sbjct: 31  VRAYLYGIGKTKLLTAAQEVELSRRI-EAGLFAEAKLAACTPVSATLRADLELVAVEGRA 89

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WW
Sbjct: 90  AKDHLLEANLRLVVSIAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWW 149

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   +      ++I     +      + R+    + ++ +  +   V  +A+ L+V
Sbjct: 150 IRQAITRAMADQSRTIRIPVHMVE-----QVNRMVRTRRDLSVSLGREPTVTEVARALDV 204

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++I +        SL+  +   +   S   D++               ER   R  +
Sbjct: 205 PEVQIIELISYDREPVSLDQAV--GEDGESPLGDFVAV--VNATAAPDNTAERGELRQEV 260

Query: 229 TRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              ++ L+ RE+ +   R   ++    TL+ +  EF +SRER+RQIE    +K++   + 
Sbjct: 261 RGVLATLSQREQAVIRLRFGLDDGRQRTLDEVGREFGLSRERIRQIEKGTLRKLRAPERA 320

Query: 287 Q 287
           Q
Sbjct: 321 Q 321


>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 =  223 bits (568), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 117/247 (47%), Gaps = 12/247 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 379 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 438

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            L R+             PE    +A+++
Sbjct: 439 WWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQCLQEMGREATPE---ELAERM 493

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D   ++ ++    ++ R 
Sbjct: 494 GMPEDKIRKVLKIAKEPISMETPI--GDDDDSHLGDFI---QDESLELPLDSATAESLRL 548

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                +  L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 549 ATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 608

Query: 285 QKQVELS 291
           + +   S
Sbjct: 609 RSETLRS 615


>gi|330898880|gb|EGH30299.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. japonica
           str. M301072PT]
 gi|330980978|gb|EGH79081.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. aptata
           str. DSM 50252]
          Length = 616

 Score =  223 bits (568), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 69/263 (26%), Positives = 121/263 (46%), Gaps = 14/263 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L+  E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 356 LKIAEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 415

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 416 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 473

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    + +++ + E ++  +        S+   I   D   S   D++  
Sbjct: 474 LQEMGREPTPE---ELGERMEMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 526

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q  I+    ++ +      +S L  RE ++   R   +     TLE +  +F+V
Sbjct: 527 -EDSTMQSPIDVATVESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 585

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   + +
Sbjct: 586 TRERIRQIEAKALRKLRHPTRSE 608


>gi|254452739|ref|ZP_05066176.1| RNA polymerase sigma-70 factor RpoD [Octadecabacter antarcticus
           238]
 gi|198267145|gb|EDY91415.1| RNA polymerase sigma-70 factor RpoD [Octadecabacter antarcticus
           238]
          Length = 637

 Score =  223 bits (568), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 117/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 397 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 456

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A KL
Sbjct: 457 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAAKL 511

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++N + 
Sbjct: 512 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAVLPLDSAIQENLKE 566

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 567 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 626

Query: 285 QK 286
           + 
Sbjct: 627 RS 628


>gi|260911780|ref|ZP_05918352.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella sp. oral
           taxon 472 str. F0295]
 gi|260634106|gb|EEX52224.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella sp. oral
           taxon 472 str. F0295]
          Length = 287

 Score =  223 bits (568), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 74/287 (25%), Positives = 146/287 (50%), Gaps = 12/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI    ++  +EE  LA+R R+ GD  A  +L  ++LR VV
Sbjct: 5   KITKSITNRESDSLDKYLQEIGHEELISVEEEVELAQRIRK-GDRKALEKLTKANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + I     
Sbjct: 64  SVAKQYQNQGLSLQDLINEGNVGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    NQ      + ++   L      N +   +  IA+K ++ E ++         
Sbjct: 124 IVRLPV--NQVGSVNKINKI---LNKFEQENERRPSINEIAEKTDLPEDKIEDAIKVTGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     + NS      L    +     +  +  +++ R  +  ++  LN RER +
Sbjct: 179 HISVDAPFVDGEDNS-----LLDLLTNSDMPTVDNELVKESLRAEIAEALQFLNERERNV 233

Query: 243 FEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            EA        +TLE +  ++ ++RERVRQI+ +A ++++ + + ++
Sbjct: 234 IEAFFGINQMEMTLEEIGDKYGLTRERVRQIKEKAIRRLRNNTKNKM 280


>gi|196229539|ref|ZP_03128404.1| RNA polymerase, sigma 70 subunit, RpoD family [Chthoniobacter
           flavus Ellin428]
 gi|196226771|gb|EDY21276.1| RNA polymerase, sigma 70 subunit, RpoD family [Chthoniobacter
           flavus Ellin428]
          Length = 671

 Score =  223 bits (568), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 74/266 (27%), Positives = 127/266 (47%), Gaps = 15/266 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L  +E     K  +      L A   +V ++LRLV+ IA  Y   GL   +++ EGN+GL
Sbjct: 408 LSPEEFQEEYKELKVWLKKALKAKTEMVEANLRLVISIAKKYTNRGLSFLDLIQEGNMGL 467

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV+KF+  RG++ +TY+ WWI+ A+   I      ++I            L R++  L
Sbjct: 468 MKAVEKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLMRVQKQL 525

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE+V   A ++ +    V ++        SL + +  SD  S  + D++  
Sbjct: 526 VQDYGREPTPEEV---ADEIQLPVERVRAVLKMAQQPISLQSPVGESDDTS--FGDFI-- 578

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
             D   + L +       +  +   +  L  RER++ E R         TLE +  +F+V
Sbjct: 579 -EDKGAENLSDMTAIVLLKEKIKDVLETLTERERQVLEQRFGLVDGYSRTLEEVGRQFKV 637

Query: 265 SRERVRQIEARAFKKVQESIQ-KQVE 289
           +RER+RQIEA+A +K++   + +Q+E
Sbjct: 638 TRERIRQIEAKALRKMRHPTRIRQLE 663



 Score = 39.4 bits (91), Expect = 0.69,   Method: Composition-based stats.
 Identities = 13/65 (20%), Positives = 28/65 (43%), Gaps = 6/65 (9%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ ++ ++P+L +++E  ++KR         A   V  H+     IA  Y    
Sbjct: 214 DDPVRMYLKQMGQVPLLTREQEVEISKRI------EDAELNVQKHINRFGFIARAYLDLA 267

Query: 73  LPISE 77
             + E
Sbjct: 268 HKLQE 272


>gi|58257340|gb|AAK30051.2| RpoS sigma factor [Pseudomonas fluorescens]
          Length = 335

 Score =  223 bits (568), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 82/278 (29%), Positives = 143/278 (51%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 184

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           L   +  L    D+   PE++  + +K       ++ +N R++  D SL+        + 
Sbjct: 185 LGAAR-ELTQKLDHEPSPEEIANMLEKPVTEVKRMLGLNERVSSVDVSLDP------DSD 237

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       ++++++       + + +S L  ++R +   R         TL
Sbjct: 238 KTVLDTLTDDRPTDRCEVLQEDDLSQG---IDQWLSELTEKQREVVVRRFGLRGHESSTL 294

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 295 EDVGLEIGLTRERVRQIQIEGLKRLREILEKNGLSSES 332


>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 =  223 bits (568), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 117/247 (47%), Gaps = 12/247 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 378 RRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 437

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            L R+             PE    +A+++
Sbjct: 438 WWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQCLQEMGREATPE---ELAERM 492

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D   ++ ++    ++ R 
Sbjct: 493 GMPEDKIRKVLKIAKEPISMETPI--GDDDDSHLGDFI---QDESLELPLDSATAESLRI 547

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                +  L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 548 ATNEVLEGLTPREEKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 607

Query: 285 QKQVELS 291
           + +   S
Sbjct: 608 RSETLRS 614


>gi|85705219|ref|ZP_01036318.1| RNA polymerase sigma factor [Roseovarius sp. 217]
 gi|85670092|gb|EAQ24954.1| RNA polymerase sigma factor [Roseovarius sp. 217]
          Length = 661

 Score =  223 bits (568), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 70/242 (28%), Positives = 117/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 421 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 480

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A+KL
Sbjct: 481 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAEKL 535

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   + N + 
Sbjct: 536 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNVILPLDSAIQDNLKE 590

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR +S L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 591 TTTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 650

Query: 285 QK 286
           + 
Sbjct: 651 RS 652


>gi|21449377|gb|AAM54109.1|AF453501_35 RNA polymerase sigma factor [Actinosynnema pretiosum subsp.
           auranticum]
          Length = 348

 Score =  223 bits (568), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 75/306 (24%), Positives = 130/306 (42%), Gaps = 39/306 (12%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREH-------------------- 44
            N       Y+  I ++ +L   +E  LA+R     Y EH                    
Sbjct: 45  ANAADSTRAYLKAIGRVRLLTADQEVELARRVEAGLYAEHLLDLPPAARGSRRPVELRRV 104

Query: 45  --GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
                 A   L+ ++LRLVV IA  Y G G+ + +V+ EGN+GL++AV+KFD  +GF+ +
Sbjct: 105 VRDGQRAKDHLLEANLRLVVSIAKRYTGKGMALLDVIQEGNLGLVRAVEKFDYAKGFKFS 164

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   +      +++     +  +   L R++  L      N +      +
Sbjct: 165 TYATWWIRQAITRALADQSRTIRLPVHMVE--VVTKLARIERDL---LHRNGREATAEEV 219

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A +L+V+  +V+ +        SL+  I    +  +   D +    D      +E     
Sbjct: 220 AVELDVTPEKVVELRQHARTPVSLDQTI--GAEADTSIGDLIA---DENAVAPLEAVSSA 274

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKV 280
                L   +  L PRE  +   R    +    TL+ +   + V+RER+RQIE+R   K+
Sbjct: 275 LLSADLRAVLETLTPREAGVVRMRYGFPDGVLHTLDEVGRVYGVTRERIRQIESRTMAKL 334

Query: 281 QESIQK 286
           Q   + 
Sbjct: 335 QHPARS 340


>gi|283851053|ref|ZP_06368337.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio sp.
           FW1012B]
 gi|283573449|gb|EFC21425.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio sp.
           FW1012B]
          Length = 588

 Score =  223 bits (568), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 73/257 (28%), Positives = 119/257 (46%), Gaps = 12/257 (4%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE +   +        A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV K
Sbjct: 334 EEVLWRIKRGNTAAQRAKQELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 393

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RG++ +TY+ WWI+ A+   I      ++I            L R   +L      
Sbjct: 394 FEYQRGYKFSTYATWWIRQAITRAIADQARTIRIPVHM--IETINKLIRTSRYLVQELGR 451

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +  PE    IA++++    +V  +        SL   I   D+  S   D++    D + 
Sbjct: 452 DPTPE---EIAERMDYPLEKVKKVLKIAKEPISLETPI--GDEEDSSLGDFI---EDKKA 503

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
               E+         + + +S L PRE ++   R         TLE +   F V+RER+R
Sbjct: 504 LAPAEEVVNTKLGEQIGKVLSDLTPREEQVLRKRFGLGEKSDHTLEEVGKLFNVTRERIR 563

Query: 271 QIEARAFKKVQESIQKQ 287
           QIEA+A +K++  ++ Q
Sbjct: 564 QIEAKALRKLRHPVRSQ 580



 Score = 36.7 bits (84), Expect = 4.1,   Method: Composition-based stats.
 Identities = 12/54 (22%), Positives = 28/54 (51%), Gaps = 1/54 (1%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVT 55
           +   +         +  Y+ E+  +P+L+++ E V+AK+  E+G++   + LV 
Sbjct: 86  SEDTLDYSSRSTDPVRMYLREMGAVPLLDREGEVVIAKKI-ENGEMDVLYALVE 138


>gi|124024683|ref|YP_001018990.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Prochlorococcus marinus str. MIT 9303]
 gi|123964969|gb|ABM79725.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Prochlorococcus marinus str. MIT 9303]
          Length = 344

 Score =  223 bits (568), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 80/292 (27%), Positives = 144/292 (49%), Gaps = 31/292 (10%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLA--------------------KRYREHGDLSAAH 51
           G   +  Y+  I ++P+L   EE  LA                    +R++      A  
Sbjct: 53  GTDAIGFYLSSIGRVPLLTAAEEIELAHHVQAMKELLELPEQDHTPRQRHKIRMGKRARD 112

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R+++++LRLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+ 
Sbjct: 113 RMMSANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQ 172

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            M   I  S   +++    ++K     L +++   + ++    +    + +A  + +   
Sbjct: 173 GMTRAIDNSARTIRLPIHISEK-----LSKMRRISRELSHRFGRQPNRLELAHAMGIQPQ 227

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           ++  +  + A   SL+A     +  S+  +  L+ D +G E   +E  +R  ++  L   
Sbjct: 228 DLEDLIAQSAPCASLDAHARGEEDRSTLGE--LIPDPNGAE--PMEGLDRSIQKEHLGGW 283

Query: 232 MSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +S LN RE++I   R     E P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 284 LSQLNEREQKILRLRFGLDGEEPLTLAEIGRQISVSRERVRQLEAKAILKLR 335


>gi|317502748|ref|ZP_07960858.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella salivae
           DSM 15606]
 gi|315666141|gb|EFV05698.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella salivae
           DSM 15606]
          Length = 287

 Score =  223 bits (568), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 73/274 (26%), Positives = 144/274 (52%), Gaps = 12/274 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ EI    ++  +EE  LA++ +  GD  A  +L  ++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQEIGHEDLISVEEEVELAQKIK-RGDRRALEKLTRANLRFVVSVAKQYQNQGLS 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V++        
Sbjct: 76  LPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLPLNQ---- 131

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
              ++ ++K  L  +   N     +  IA K+++ E +V           S++A     +
Sbjct: 132 -VGSVNKIKRVLNKLEQENEHFPTIEEIAAKVDIPEEKVADAIKSNGRHVSVDAPFAEGE 190

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-PV 253
           +NS      L    +   Q+      +++ R+ ++ ++  LN RER I EA        +
Sbjct: 191 ENS-----LLDVLPNSNAQMADNVLVQESLRDEISSALKSLNERERNIIEAFFGINQAEM 245

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           TLE +  +F ++RERVRQI+ +A ++++ + + +
Sbjct: 246 TLEEIGDKFGLTRERVRQIKEKAIRRLRNNSKNK 279


>gi|218777994|ref|YP_002429312.1| RNA polymerase, sigma 70 family subunit [Desulfatibacillum
           alkenivorans AK-01]
 gi|218759378|gb|ACL01844.1| putative RNA polymerase, sigma 70 family subunit [Desulfatibacillum
           alkenivorans AK-01]
          Length = 328

 Score =  223 bits (568), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 103/281 (36%), Positives = 162/281 (57%), Gaps = 8/281 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG-YG 72
             L RY+ EI K P+L ++EE  LA R +E  D  AA+RLVT++LRLVVKIA+ ++  + 
Sbjct: 40  DPLQRYLSEISKYPLLTREEERELAVRVQEFDDPDAAYRLVTANLRLVVKIALEFQRVWM 99

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
             + +++ EGNIGLMQA +KFDP +  + + YS +WIKA + ++I+ +W LVKIGTT  Q
Sbjct: 100 QNLLDLIQEGNIGLMQAARKFDPYKNVKFSYYSSFWIKAYILKFIMDNWRLVKIGTTQAQ 159

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALIN 191
           ++LFF         +          +   +++KL VSE ++I M+ RL   D SL+A + 
Sbjct: 160 RKLFFK----LKKEKQKLLEEGFDPKPKLLSEKLGVSERDIIDMDQRLNNWDLSLDAPVK 215

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             D + S+  ++L    +  E  +  KE     R  +      L  RE  IF+ R   ++
Sbjct: 216 --DDSDSERIEFLSTPSESAEDQVARKEMETILREKIDIFRKTLKERELEIFDERVFSDS 273

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
           PVTL+ +     +SRERVRQ+E+   KK++  ++K++   S
Sbjct: 274 PVTLQQIGDRHGISRERVRQVESGVVKKLKAFLEKEIPDFS 314


>gi|85373960|ref|YP_458022.1| RNA polymerase sigma factor RpoD [Erythrobacter litoralis HTCC2594]
 gi|84787043|gb|ABC63225.1| RNA polymerase sigma-70 factor [Erythrobacter litoralis HTCC2594]
          Length = 675

 Score =  223 bits (568), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 68/251 (27%), Positives = 120/251 (47%), Gaps = 15/251 (5%)

Query: 41  YREHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
             + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 426 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 485

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I        +   + +L    +       +  
Sbjct: 486 GYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTSRQFLHEQGREP 540

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A++L++   +V  +        SL   I   D+  S   D++    D    + ++
Sbjct: 541 TPEEMAERLSMPLEKVRKVMKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAIIPVD 595

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              + N +  +TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+
Sbjct: 596 AAIQANLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 655

Query: 276 AFKKVQESIQK 286
           A +K++   + 
Sbjct: 656 ALRKLKHPSRS 666


>gi|326387391|ref|ZP_08209000.1| RNA polymerase sigma factor RpoD [Novosphingobium nitrogenifigens
           DSM 19370]
 gi|326208047|gb|EGD58855.1| RNA polymerase sigma factor RpoD [Novosphingobium nitrogenifigens
           DSM 19370]
          Length = 667

 Score =  223 bits (568), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 68/251 (27%), Positives = 120/251 (47%), Gaps = 15/251 (5%)

Query: 41  YREHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
             + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 418 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 477

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I        +   + +L    +       +  
Sbjct: 478 GYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTSRQFLHEQGREP 532

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A++L++   +V  +        SL   I   D+  S   D++    D    + ++
Sbjct: 533 TPEEMAERLSMPLEKVRKVMKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAIIPVD 587

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              + N +  +TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+
Sbjct: 588 AAIQSNLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 647

Query: 276 AFKKVQESIQK 286
           A +K++   + 
Sbjct: 648 ALRKLKHPSRS 658


>gi|311895920|dbj|BAJ28328.1| putative RNA polymerase sigma factor [Kitasatospora setae KM-6054]
          Length = 389

 Score =  223 bits (568), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 75/302 (24%), Positives = 130/302 (43%), Gaps = 44/302 (14%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRY------------------------REHGDLS--- 48
           L +Y+ EI ++ +L   EE  LA+                          R  GDL    
Sbjct: 87  LRQYLREIGRVRLLTAVEEVELARAIEAGLFAEEALDRVPPAAERRPADERLLGDLDRLV 146

Query: 49  -----AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
                A  RL+ ++LRLVV +A  Y G GL + +++ EGN+GL++AV+KFD  RG++ +T
Sbjct: 147 VLGRIAKRRLIEANLRLVVSVAKRYVGRGLTLLDLIQEGNVGLIRAVEKFDYARGYKFST 206

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI+ AM   +      +++     +      + R+    + +            + 
Sbjct: 207 YATWWIRQAMSRALADQARTIRVPVHVVEL-----INRVLRVQRGLLQERGVEPTAAEVG 261

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
             L +    V  +        SL+  +   +++     D +    D       E      
Sbjct: 262 AVLQLPPERVREVLKLAQEPVSLHTPV--GEEDDVALGDLI---EDADAASPPESAAFLL 316

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R  L   ++ L  RER++ + R   ++  P TLE +   F V+RER+RQIEA+   K++
Sbjct: 317 LREHLEAVLATLGERERQVVQLRYGLDDGRPRTLEEIGHLFGVTRERIRQIEAKTLGKLR 376

Query: 282 ES 283
           + 
Sbjct: 377 DH 378


>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 =  223 bits (568), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 117/247 (47%), Gaps = 12/247 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 379 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 438

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            L R+             PE    +A+++
Sbjct: 439 WWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQCLQEMGREATPE---ELAERM 493

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D   ++ ++    ++ R 
Sbjct: 494 GMPEDKIRKVLKIAKEPISMETPI--GDDDDSHLGDFI---QDESLELPLDSATAESLRL 548

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                +  L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 549 ATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 608

Query: 285 QKQVELS 291
           + +   S
Sbjct: 609 RSETLRS 615


>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 =  223 bits (568), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 72/246 (29%), Positives = 115/246 (46%), Gaps = 12/246 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 407 ERDSTRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 466

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            L R    +         PE    +
Sbjct: 467 TYATWWIRQAITRSIADQAKTIRIPVHM--IETINKLVRTSRQMLHEIGREPAPE---EL 521

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+KL +   +V  +        SL   I   D+  S   D++    D    + ++   + 
Sbjct: 522 AEKLGMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDKTAVIPLDAAIQT 576

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 577 NLREATTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTRERIRQIEAKALRKL 636

Query: 281 QESIQK 286
           +   + 
Sbjct: 637 KHPSRS 642


>gi|26554290|ref|NP_758224.1| RNA polymerase sigma factor [Mycoplasma penetrans HF-2]
 gi|26454299|dbj|BAC44628.1| RNA polymerase sigma factor [Mycoplasma penetrans HF-2]
          Length = 427

 Score =  223 bits (568), Expect = 3e-56,   Method: Composition-based stats.
 Identities = 69/285 (24%), Positives = 136/285 (47%), Gaps = 16/285 (5%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAH----RLVTSHLRLVVKIAMGY 68
           + G+  +++ +    ML  QEE  + K   +  D +       +L+TS+LRLV  IA  Y
Sbjct: 140 DDGIKSFLNVLGSSKMLTSQEEQEIGK-MLDSEDKTIREYAINQLMTSNLRLVTSIAKKY 198

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
              GL + +++ EG++GLM+A+ KFD + G + +TY+ WWI+ A+   I      ++I  
Sbjct: 199 LNRGLDLEDLLQEGSLGLMKAITKFDYKLGNKFSTYATWWIRQAITRAIADQARTIRIPV 258

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL--NVSESEVISMNCRLAGDESL 186
              +      L + +  L      +  PE++           +  +++++        SL
Sbjct: 259 HMVE--TINKLSKAERQLMQEYGRDPTPEELADAMDGTAAGFTAKKILNIKKLNIDPVSL 316

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           +  +   ++  S++ D++  D +   +   EKE      + + +    L  +E  I   R
Sbjct: 317 DKPVGKDEE--SKFVDFVKDDDNLNPEQFTEKELMGEHIDDILKKF--LQEKEEDIIRMR 372

Query: 247 RLQ---ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
                  +P+TLE +  ++ ++RERVRQIEA+A +K++   +  +
Sbjct: 373 YGLPPYSHPMTLEEVGEKYGITRERVRQIEAKALRKIKHPSKSGI 417


>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 =  223 bits (568), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 64/249 (25%), Positives = 117/249 (46%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 370 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 429

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +        +PE   
Sbjct: 430 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPQPE--- 484

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + E ++  +        S+   I   D   S   D++    D      ++   
Sbjct: 485 ELAERMEMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDSTIDSPVDAAT 539

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            ++ + +    ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 540 GESLKEVTDEILAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 599

Query: 279 KVQESIQKQ 287
           K++   + +
Sbjct: 600 KLRHPSRSE 608


>gi|332999494|gb|EGK19079.1| RNA polymerase sigma factor RpoS [Shigella flexneri VA-6]
          Length = 359

 Score =  223 bits (568), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 81/280 (28%), Positives = 142/280 (50%), Gaps = 14/280 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    +   
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE--- 231

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
             +  L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 232 --KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ-VELSSSPP 295
           ++  E  ++RERVRQI+    ++++E +Q Q  E  S+ P
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQTQGAEYRSAVP 329


>gi|72383143|ref|YP_292498.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. NATL2A]
 gi|72002993|gb|AAZ58795.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. NATL2A]
          Length = 340

 Score =  223 bits (568), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 76/292 (26%), Positives = 136/292 (46%), Gaps = 31/292 (10%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD--------------------LSAAH 51
               +  Y+  I ++P+L   EE  LA   ++  D                      A  
Sbjct: 49  ATDAIGFYLTSIGRVPLLTPAEEIELAHHVQQMKDLLNLPLEERSTRQKHKIKMGKRARD 108

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ ++LRLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+ 
Sbjct: 109 RMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQ 168

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            M   I  S   +++    ++K     L +++   + ++    +    + +A  + +   
Sbjct: 169 GMTRAIDNSARTIRLPIHISEK-----LSKMRRISRELSHRFGRQPNRLELANAMGIEPQ 223

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           ++  +  + A   SL+A     +  S+  +       D      +E  +R  ++  L   
Sbjct: 224 DLEDLVSQSAPCASLDAHARGEEDRSTLGELI----PDPNSDEPMEGMDRSIQKEHLGGW 279

Query: 232 MSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +S LN RE++I   R     E P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 280 LSQLNEREQKIMRLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 331


>gi|262202171|ref|YP_003273379.1| sigma-70 family RNA polymerase sigma factor [Gordonia bronchialis
           DSM 43247]
 gi|262085518|gb|ACY21486.1| RNA polymerase sigma factor, sigma-70 family [Gordonia bronchialis
           DSM 43247]
          Length = 337

 Score =  223 bits (568), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 66/315 (20%), Positives = 136/315 (43%), Gaps = 38/315 (12%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------------- 43
           M  +++         +  Y++ I +  +L  ++E  LAK+                    
Sbjct: 26  MTEQDLDAQSPAADLVRVYLNGIGRTALLNAEQEVELAKQIEAGLYAKHVLATKKRLSAA 85

Query: 44  ---------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                        +A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD
Sbjct: 86  KKRDLAIVVREGEAARAHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFD 145

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +GF+ +TY+ WWI+ A+   +      +++     ++     L R+K  L        
Sbjct: 146 YAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLARIKRELHQQLGREA 203

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
             E    +A +  +   ++  +        SL+  + S ++  +   D++    D +   
Sbjct: 204 TDE---ELANESGIPAEKIADLLDHSRDPVSLDMPVGSDEE--APLGDFI---EDAEATS 255

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
                        +   ++ L+ RE+++   R   ++  P TL+ +   F +SRERVRQI
Sbjct: 256 AESAVIAGLMHTDVRAVLATLDEREQQVIRMRYGLDDGQPRTLDQIGRMFGLSRERVRQI 315

Query: 273 EARAFKKVQESIQKQ 287
           E     K+++  + +
Sbjct: 316 EREVMGKLRQGDRAE 330


>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 =  223 bits (568), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 117/247 (47%), Gaps = 12/247 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 379 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 438

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            L R+             PE    +A+++
Sbjct: 439 WWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQCLQEMGREATPE---ELAERM 493

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D   ++ ++    ++ R 
Sbjct: 494 GMPEDKIRKVLKIAKEPISMETPI--GDDDDSHLGDFI---QDESLELPLDSATAESLRL 548

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                +  L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 549 ATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 608

Query: 285 QKQVELS 291
           + +   S
Sbjct: 609 RSETLRS 615


>gi|149378178|ref|ZP_01895895.1| nonessential primary sigma factor [Marinobacter algicola DG893]
 gi|149357540|gb|EDM46045.1| nonessential primary sigma factor [Marinobacter algicola DG893]
          Length = 333

 Score =  223 bits (568), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 77/271 (28%), Positives = 139/271 (51%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A+  R+ G+ S   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 65  YLNEIGFSPLLTPEEEVYFARLARK-GEESGRKRMIESNLRLVVKIARRYVNRGLTLLDL 123

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 124 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNLY 182

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +T           IA+ ++   ++V  M        S++  I +  + S 
Sbjct: 183 LRAAR----ELTQKLDHEPSAEEIARMVDKPVADVKRMLGLNERVASMDTPIGTGGEKS- 237

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
              D +  +       L++     N  + + + +  L+ +++ +   R         TLE
Sbjct: 238 -LLDTVADEGASDPADLLQD---NNMCSCVEKWIDQLSDKQQEVLSRRFGLRGYPISTLE 293

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +  E  ++RERVRQI+  A ++++E ++K+
Sbjct: 294 EVGQEIGLTRERVRQIQVEALRRLREILEKE 324


>gi|307152414|ref|YP_003887798.1| RpoD subfamily RNA polymerase sigma-70 factor [Cyanothece sp. PCC
           7822]
 gi|306982642|gb|ADN14523.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7822]
          Length = 377

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 76/313 (24%), Positives = 140/313 (44%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS----------------------- 48
            E  +  Y+ EI +I +L  +EE  LA++  +  +L                        
Sbjct: 65  TEDSIRIYLQEIGRIRLLRAEEEIELARKIADLLELERLREKLRRNLGRYPSDKEWAQQV 124

Query: 49  ----------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 125 GMELPAFQRRLYLGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 184

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 185 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKILSQE 239

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA ++ ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 240 MRRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADGETPE 297

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
               ++  +   R  L   +  L+PRER +   R   ++    TLE +   F V+RER+R
Sbjct: 298 ----DEVSKNLLREDLENVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIR 353

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 354 QIEAKALRKLRHP 366


>gi|113954631|ref|YP_732094.1| RNA polymerase sigma factor [Synechococcus sp. CC9311]
 gi|113881982|gb|ABI46940.1| RNA polymerase sigma factor [Synechococcus sp. CC9311]
          Length = 340

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 82/301 (27%), Positives = 145/301 (48%), Gaps = 31/301 (10%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLA--------------------KRYR 42
           R N S        +  Y+  I ++P+L   EE  LA                    +R+R
Sbjct: 40  RGNRSSGRLATDSIGHYLSSIGRVPLLTAAEEIELAHHVQAMKELLDIQEEERTPKQRHR 99

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
                 A  R++ ++LRLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +
Sbjct: 100 IRMGKRARDRMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFS 159

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+  M   I  S   +++    ++K     L +++   + ++    +    + +
Sbjct: 160 TYAYWWIRQGMTRAIDNSARTIRLPIHISEK-----LSKMRKITRELSHRFGRQPNRLEL 214

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A  + +   ++  +  + A   SL+A     +  S+  +  L+ D +G E   +E  +R 
Sbjct: 215 AHAMGIEPRDLEELIAQSAPCASLDAHARGEEDRSTLGE--LIPDPNGDE--PMEGMDRS 270

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            ++  L   +S LN RE++I   R     E P+TL  +  +  VSRERVRQ+E++A  K+
Sbjct: 271 IQKEHLGGWLSQLNEREQKILRLRFGLGGEEPLTLAEIGRQINVSRERVRQLESKAILKL 330

Query: 281 Q 281
           +
Sbjct: 331 R 331


>gi|209965297|ref|YP_002298212.1| RNA polymerase sigma factor RpoD [Rhodospirillum centenum SW]
 gi|209958763|gb|ACI99399.1| DNA-directed RNA polymerase, sigma subunit RpoD [Rhodospirillum
           centenum SW]
          Length = 648

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 71/241 (29%), Positives = 114/241 (47%), Gaps = 12/241 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 409 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 468

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I            L R    +         PE    +A++L 
Sbjct: 469 WIRQAITRSIADQARTIRIPVHM--IETINKLVRTSRQMLHEIGREPTPE---ELAERLM 523

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +   +V  +        SL   I   D+  S   D++    D    + ++   + N R  
Sbjct: 524 MPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAVLPLDAAIQANLRET 578

Query: 228 LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   +
Sbjct: 579 TTRILATLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSR 638

Query: 286 K 286
            
Sbjct: 639 S 639


>gi|163854463|ref|YP_001628761.1| RNA polymerase factor sigma-32 [Bordetella petrii DSM 12804]
 gi|163258191|emb|CAP40490.1| RNA polymerase sigma-32 factor [Bordetella petrii]
          Length = 295

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 120/288 (41%), Positives = 176/288 (61%), Gaps = 13/288 (4%)

Query: 2   NRKNMSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           N   ++I   G +G +  YI  + ++P+L  + E  L +R R+  DL AA  LV SHLRL
Sbjct: 13  NALALAIANPGSLGTIEAYISAVNRLPVLTAERETELGRRLRDRDDLDAARELVLSHLRL 72

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y GYGLP ++++ EGN+GLM+AVK+FDPERG RL ++++ WIKA + E+I+R+
Sbjct: 73  VVSVARQYLGYGLPHADLIQEGNVGLMKAVKRFDPERGVRLVSFAVHWIKAEIHEFIIRN 132

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR ++          L PEQV  IA++LNV   +V  M  RL
Sbjct: 133 WRMVKVATTKAQRKLFFNLRSMR-----PDGQTLDPEQVDRIAQELNVRREDVSEMEVRL 187

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQ--VLIEKEERKNRRNMLTRSMSVLNP 237
           +G D SL       D   +      + D   QE   VL  ++  + +   L  ++  L+ 
Sbjct: 188 SGRDLSLE---KQDDDEEAFAPISYLSDEGRQEPTRVLDRRDHDELQGAGLAHALQALDA 244

Query: 238 RERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R RRI EAR LQ++  VTL+ L+ EF VS ER+RQIE+ A KK++ ++
Sbjct: 245 RSRRIIEARWLQDDGGVTLQELAQEFGVSAERIRQIESAALKKMRGAL 292


>gi|213018850|ref|ZP_03334658.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of Culex
           quinquefasciatus JHB]
 gi|212995801|gb|EEB56441.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of Culex
           quinquefasciatus JHB]
          Length = 632

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 72/261 (27%), Positives = 125/261 (47%), Gaps = 15/261 (5%)

Query: 32  QEEYVLAKRYREHGDL--SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           QE   + KR ++H      A   ++ ++LRLVV IA  Y   GL + +++ EGNIGLM+A
Sbjct: 376 QEFKKVIKRIQKHEQEVSQAKQEMIKANLRLVVSIAKKYSKRGLDLLDLIQEGNIGLMKA 435

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V KFD +RG++ +TY  WW+K ++   I     +V+I     +      + ++   L+ +
Sbjct: 436 VDKFDYKRGYKFSTYGTWWVKQSITRAIPEQSKVVRIPVHMVEI-----ISKINKALRKM 490

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
           T    +   +  ++ +L +    +  +        SL A     D  SS + D +    D
Sbjct: 491 THEMGREPTLEELSIELAMPLERIRKVMKIARDPVSLEAPTGKDD--SSTFGDCI---ED 545

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSR 266
            +     +     + R + T  ++ L P+E RI   R          TLE +   F V+R
Sbjct: 546 KRVSKPEDAAILADLRGITTNVLATLTPKEERILRMRFGLGKDGKEHTLEEVGKIFNVTR 605

Query: 267 ERVRQIEARAFKKVQESIQKQ 287
           ER+RQIEA+A +K++   + +
Sbjct: 606 ERIRQIEAKALRKLKHPSRAK 626


>gi|320159820|ref|YP_004173044.1| RNA polymerase sigma factor [Anaerolinea thermophila UNI-1]
 gi|319993673|dbj|BAJ62444.1| RNA polymerase sigma factor [Anaerolinea thermophila UNI-1]
          Length = 396

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 77/295 (26%), Positives = 132/295 (44%), Gaps = 38/295 (12%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------------REHGDLSA- 49
           ++ +  +  Y+ E+ ++P+L  +EE  LAKR                    +  G+L A 
Sbjct: 93  ISSDDTVGLYLKEMSRVPLLSSEEEVELAKRIERGRAAKKELTRNSARLSPQRRGELEAQ 152

Query: 50  -------AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
                     L+ ++ RLVV IA  Y G G+P  +++ EGN+GLM+AV+K++ +RGFR +
Sbjct: 153 IQDGESAREHLIKANTRLVVSIAKRYIGRGVPFLDLIQEGNLGLMKAVEKYEYQRGFRFS 212

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+  +   I      +++      +     +RRL      +     +      +
Sbjct: 213 TYATWWIRQTITRSIADQGRTIRVPVHMVDR-----IRRLYRTTHEMEQKLGRTPTNEEL 267

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A  + +  S+V  M        SL + IN  D+  S+   ++    D      ++     
Sbjct: 268 ADAIGIKASKVDWMMRVSWLPLSLESPIN-EDEEDSELGQFI---EDQVTPSPMQTTYSN 323

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEAR 275
             R  +   +  L  RE RI   R   EN    TLE +  +F ++RER+RQIE +
Sbjct: 324 LLREKIQEVLDTLPAREARILRLRFGLENGRTYTLEEVGQKFGLTRERIRQIENK 378


>gi|312195044|ref|YP_004015105.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EuI1c]
 gi|311226380|gb|ADP79235.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia sp.
           EuI1c]
          Length = 424

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 66/296 (22%), Positives = 131/296 (44%), Gaps = 38/296 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------HGD--------LSA 49
           +  Y+ EI ++P+L   +E  L+KR                     H D         +A
Sbjct: 128 VRMYLREIGRVPLLNAAQEVELSKRVEAGLFAEHKLATAADLEPELHRDLKLLVRDGEAA 187

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             +LV+++LRLVV +A  Y G G+ + ++V EGN+GL++AV+KFD  +G++ +TY+ WWI
Sbjct: 188 KQQLVSANLRLVVSVAKKYSGRGMTLLDLVQEGNLGLIRAVEKFDYAKGYKFSTYATWWI 247

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + A+   +      ++I     +      + ++    + +     +      +A +L++ 
Sbjct: 248 RQAIGRALADQARTIRIPVHVVE-----QINKITRLQRQLVSTLGREPTDEELALELDMP 302

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             +V+ +        SL   +   D   S   D++    D       +       ++ + 
Sbjct: 303 LEQVVELRRYAQDTVSLETTV--GDDGDSVLGDFI---EDSDATSPADAASYGAMQDEID 357

Query: 230 RSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +  L+PRER +   R         TL  + +   ++RER+RQIE    +++++ 
Sbjct: 358 HVLGNLSPREREVMRLRFGLADGKQHTLAEVGNRLGLTRERIRQIERDTLRELRKP 413


>gi|254487022|ref|ZP_05100227.1| RNA polymerase sigma-32 factor [Roseobacter sp. GAI101]
 gi|214043891|gb|EEB84529.1| RNA polymerase sigma-32 factor [Roseobacter sp. GAI101]
          Length = 277

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 105/269 (39%), Positives = 171/269 (63%), Gaps = 6/269 (2%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K  +L+ + E  LA  +R+  D  A HRL+T+++RL + +A  ++ YG P+++++ E  
Sbjct: 1   MKAELLDAETELKLAYAWRDERDEEALHRLITAYMRLAISMAGKFKRYGAPMNDLIQEAG 60

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           +GLM+A  KFDP+RG R +TY++WWIKA++Q++++R+WS+V+ G+T++QK LFFN+RR++
Sbjct: 61  LGLMKAADKFDPDRGVRFSTYAVWWIKASIQDHVMRNWSMVRTGSTSSQKSLFFNMRRVQ 120

Query: 144 GHL----QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSS 198
             L    QA  +   K +    I+ ++ V   +V  M  RL+G D SLNA   SS+    
Sbjct: 121 ARLEREAQAAGETLDKHQLRQMISTEIGVPMHDVEMMEGRLSGSDYSLNA-TQSSEDEGR 179

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           +W D LV D     + + E  +    RN L  +M  LN RE+ I   R+L++ P TLE+L
Sbjct: 180 EWIDALVDDTAQAAERVEESHDIVTLRNWLLGAMQALNDREQFIVRERKLRDQPRTLESL 239

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             E  +S+ERVRQ+EA AF K++++++ Q
Sbjct: 240 GQELNLSKERVRQLEAAAFAKMRKTLETQ 268


>gi|288957899|ref|YP_003448240.1| RNA polymerase primary sigma factor [Azospirillum sp. B510]
 gi|288910207|dbj|BAI71696.1| RNA polymerase primary sigma factor [Azospirillum sp. B510]
          Length = 670

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 71/241 (29%), Positives = 114/241 (47%), Gaps = 12/241 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 431 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 490

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I            L R    +         PE    +A++L 
Sbjct: 491 WIRQAITRSIADQARTIRIPVHM--IETINKLVRTSRQMLHEIGREPTPE---ELAERLM 545

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +   +V  +        SL   I   D+  S   D++    D    + ++   + N R  
Sbjct: 546 MPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAVLPLDAAIQANLRET 600

Query: 228 LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   +
Sbjct: 601 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFNVTRERIRQIEAKALRKLKHPSR 660

Query: 286 K 286
            
Sbjct: 661 S 661


>gi|269925873|ref|YP_003322496.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
 gi|269789533|gb|ACZ41674.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
          Length = 326

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 81/303 (26%), Positives = 131/303 (43%), Gaps = 38/303 (12%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------------------REHG 45
             E  +S Y+ +I  IP+L   EE  LAK                           +E G
Sbjct: 29  GSEDSVSVYLRDIGAIPLLTPMEEIALAKAIEKGRQATRKLHQDLSPEEREAALRDKERG 88

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           ++ A  R++  +LRLVV IA  Y G GLP+S+++ EGN+GLM+A  KFD  RG+R +TY+
Sbjct: 89  EM-ARRRMIECNLRLVVSIARRYAGRGLPLSDLIEEGNLGLMRAADKFDYRRGYRFSTYA 147

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
            WWI+ A+   +     +V++     +  L  N+ ++   L          E    IA +
Sbjct: 148 TWWIRQAVTRALASQSRVVRLPVHVTE--LMHNITKVSHRLSQELGREPTSE---EIAAE 202

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           LN++   V  +        SL          + +         D   +   ++  R   R
Sbjct: 203 LNITPERVREVVKASQYPMSLEQPYGEDGDGTVEEII-----EDPNIESPADQVSRDILR 257

Query: 226 NMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +   +  L  RER++ + R      +  TLE +     V+RER+RQIE  A  K++  
Sbjct: 258 EQILALLDDLTDRERQVLDLRYGLTGNHSYTLEEVGKVLGVTRERIRQIEKEALSKLRPH 317

Query: 284 IQK 286
            + 
Sbjct: 318 AES 320


>gi|78357095|ref|YP_388544.1| sigma-70 factor [Desulfovibrio desulfuricans subsp. desulfuricans
           str. G20]
 gi|78219500|gb|ABB38849.1| RNA polymerase, sigma 70 subunit, RpoD [Desulfovibrio desulfuricans
           subsp. desulfuricans str. G20]
          Length = 589

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 74/261 (28%), Positives = 120/261 (45%), Gaps = 12/261 (4%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE +   +      + A   L+ S+LRLVV IA  Y   GL   +++ EGNIGLM+AV K
Sbjct: 335 EEVLWRIKRGNSHAMRAKQELIRSNLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 394

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RG++ +TY+ WWI+ A+   I      ++I            L R   +L      
Sbjct: 395 FEYQRGYKFSTYATWWIRQAITRAIADQARTIRIPVHM--IETINKLIRTSRYLVQELGR 452

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +  PE    IA++++    +V  +        SL   I   D+  S   D++    D + 
Sbjct: 453 DPTPE---EIAERMDYPIDKVKKVLKIAKEPISLETPI--GDEEDSSLGDFI---EDKKA 504

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
               E+         +   ++ L PRE ++   R         TLE +   F V+RER+R
Sbjct: 505 VAPAEEVVNTKLSEQIAAVLADLTPREEQVLRKRFGINEKSDHTLEEVGKLFNVTRERIR 564

Query: 271 QIEARAFKKVQESIQKQVELS 291
           QIEA+A +K++  ++ Q   S
Sbjct: 565 QIEAKALRKLRHPVRSQTLRS 585


>gi|89075068|ref|ZP_01161509.1| putative RNA polymerase sigma-38 factor [Photobacterium sp. SKA34]
 gi|89049155|gb|EAR54720.1| putative RNA polymerase sigma-38 factor [Photobacterium sp. SKA34]
          Length = 337

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 79/271 (29%), Positives = 135/271 (49%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD  A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 66  YLGEIGYSPLLTAEEEVLYARR-ALRGDEVARKRMIESNLRLVVKISRRYSNRGLALLDL 124

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 125 VEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 183

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            IA++L     +V  M        S++  I     +  
Sbjct: 184 LRTAR----ELAQKLDHEPTAEDIAQQLEKPVDDVNRMLRLNERVSSVDNPI--GGDSEK 237

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D +  +  G  +   + +   + +N +   +  LNP++R +   R   L     TLE
Sbjct: 238 ALLDIIPDEKGGSPESSTQDD---DIKNSIVHWLQELNPKQREVLARRFGLLGYEASTLE 294

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    +++++ +  Q
Sbjct: 295 DVGREIGLTRERVRQIQVEGLRRLRDMLTHQ 325


>gi|190571452|ref|YP_001975810.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of Culex
           quinquefasciatus Pel]
 gi|190357724|emb|CAQ55173.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of Culex
           quinquefasciatus Pel]
          Length = 633

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 72/261 (27%), Positives = 125/261 (47%), Gaps = 15/261 (5%)

Query: 32  QEEYVLAKRYREHGDL--SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           QE   + KR ++H      A   ++ ++LRLVV IA  Y   GL + +++ EGNIGLM+A
Sbjct: 377 QEFKKVIKRIQKHEQEVSQAKQEMIKANLRLVVSIAKKYSKRGLDLLDLIQEGNIGLMKA 436

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V KFD +RG++ +TY  WW+K ++   I     +V+I     +      + ++   L+ +
Sbjct: 437 VDKFDYKRGYKFSTYGTWWVKQSITRAIPEQSKVVRIPVHMVEI-----ISKINKALRKM 491

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
           T    +   +  ++ +L +    +  +        SL A     D  SS + D +    D
Sbjct: 492 THEMGREPTLEELSIELAMPLERIRKVMKIARDPVSLEAPTGKDD--SSTFGDCI---ED 546

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSR 266
            +     +     + R + T  ++ L P+E RI   R          TLE +   F V+R
Sbjct: 547 KRVSKPEDAAILADLRGITTNVLATLTPKEERILRMRFGLGKDGKEHTLEEVGKIFNVTR 606

Query: 267 ERVRQIEARAFKKVQESIQKQ 287
           ER+RQIEA+A +K++   + +
Sbjct: 607 ERIRQIEAKALRKLKHPSRAK 627


>gi|159044804|ref|YP_001533598.1| RNA polymerase sigma factor RpoD [Dinoroseobacter shibae DFL 12]
 gi|157912564|gb|ABV93997.1| RNA polymerase sigma factor [Dinoroseobacter shibae DFL 12]
          Length = 664

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 424 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 483

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A+KL
Sbjct: 484 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAEKL 538

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++N + 
Sbjct: 539 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAVLPLDSAIQENLKE 593

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 594 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 653

Query: 285 QK 286
           + 
Sbjct: 654 RS 655


>gi|81299460|ref|YP_399668.1| RNA polymerase sigma factor RpoD [Synechococcus elongatus PCC 7942]
 gi|93141306|sp|P38023|RPOD1_SYNE7 RecName: Full=RNA polymerase sigma factor rpoD1
 gi|81168341|gb|ABB56681.1| Sigma-70 factor [Synechococcus elongatus PCC 7942]
          Length = 399

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 76/313 (24%), Positives = 139/313 (44%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------------- 43
            E  +  Y+ EI +I +L   EE  LA++  +                            
Sbjct: 87  TEDSIRLYLQEIGRIRLLRADEEIELARQIADLLALERIRDELLEQLDRLPSDAEWAAAV 146

Query: 44  -----------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 147 DSPLDEFRRRLFRGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 206

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 207 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKLLSQE 261

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA ++ ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 262 MGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADGETPE 319

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
             + +   R++    L   +S L+PRER +   R   ++    TLE +   F V+RER+R
Sbjct: 320 DEVAKNLLRED----LEGVLSTLSPRERDVLRLRYGLDDGRMKTLEEIGQLFNVTRERIR 375

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 376 QIEAKALRKLRHP 388


>gi|167623164|ref|YP_001673458.1| RpoD family RNA polymerase sigma factor [Shewanella halifaxensis
           HAW-EB4]
 gi|167353186|gb|ABZ75799.1| RNA polymerase, sigma 70 subunit, RpoD family [Shewanella
           halifaxensis HAW-EB4]
          Length = 321

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 80/271 (29%), Positives = 139/271 (51%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   +++    G   + +R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 52  YLGEIGFSPLLSAEEEVYFSRK-SLKGCEKSRNRMIESNLRLVVKIARRYNNRGLALLDL 110

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 111 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 169

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            IA++L++S S+V  M        S++  +    ++  
Sbjct: 170 LRTAR----ELAHKLDHEPTAEEIAEQLDLSSSDVSRMLKLNERITSVDTPL--GGESDK 223

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  D +      ++ E+       + + +  LN ++R +   R   L   P TLE
Sbjct: 224 ALLDVLADDDNVGPDYKVQDEDIS---KSVVKWLDELNTKQREVLARRFGLLGYEPSTLE 280

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           N+  E  ++RERVRQI+  A K++++ +  Q
Sbjct: 281 NVGKEIGLTRERVRQIQVEALKRLKDLLGAQ 311


>gi|46580198|ref|YP_011006.1| RNA polymerase sigma-70 factor [Desulfovibrio vulgaris str.
           Hildenborough]
 gi|120602415|ref|YP_966815.1| RpoD family RNA polymerase sigma factor [Desulfovibrio vulgaris
           DP4]
 gi|46449615|gb|AAS96265.1| RNA polymerase sigma-70 factor [Desulfovibrio vulgaris str.
           Hildenborough]
 gi|120562644|gb|ABM28388.1| RNA polymerase, sigma 70 subunit, RpoD [Desulfovibrio vulgaris DP4]
 gi|311233814|gb|ADP86668.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfovibrio
           vulgaris RCH1]
          Length = 590

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 74/261 (28%), Positives = 120/261 (45%), Gaps = 12/261 (4%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE +   +      + A   L+ S+LRLVV IA  Y   GL   +++ EGNIGLM+AV K
Sbjct: 336 EEVLWRIKRGNSIAMRAKQELIRSNLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 395

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RG++ +TY+ WWI+ A+   I      ++I            L R   +L      
Sbjct: 396 FEYQRGYKFSTYATWWIRQAITRAIADQARTIRIPVHM--IETINKLIRTSRYLVQELGR 453

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +  PE    IA++++    +V  +        SL   I   D+  S   D++    D + 
Sbjct: 454 DPTPE---EIAERMDYPIDKVKKVLKIAKEPISLETPI--GDEEDSSLGDFI---EDKKA 505

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
               E+         +   ++ L PRE ++   R         TLE +   F V+RER+R
Sbjct: 506 VAPAEEVVNTKLGEQIASVLADLTPREEQVLRKRFGIGEKSDHTLEEVGKLFNVTRERIR 565

Query: 271 QIEARAFKKVQESIQKQVELS 291
           QIEA+A +K++  ++ Q   S
Sbjct: 566 QIEAKALRKLRHPVRSQTLRS 586


>gi|317484461|ref|ZP_07943373.1| RNA polymerase sigma factor RpoD [Bilophila wadsworthia 3_1_6]
 gi|316924285|gb|EFV45459.1| RNA polymerase sigma factor RpoD [Bilophila wadsworthia 3_1_6]
          Length = 590

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 75/261 (28%), Positives = 120/261 (45%), Gaps = 12/261 (4%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE +   +   +  + A   L+ S+LRLVV IA  Y   GL   +++ EGNIGLM+AV K
Sbjct: 336 EEVLWRIKRGNNAAMRAKQELIRSNLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 395

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RG++ +TY+ WWI+ A+   I      ++I            L R   +L      
Sbjct: 396 FEYQRGYKFSTYATWWIRQAITRAIADQARTIRIPVHM--IETINKLIRTSRYLVQELGR 453

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +  PE    IA ++     +V  +        SL   I   D+  S   D++    D + 
Sbjct: 454 DPTPE---EIADRMEYPVDKVKKVLKIAKEPISLETPI--GDEEDSSLGDFI---EDKKA 505

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
               E+         +   ++ L PRE ++   R         TLE +   F V+RER+R
Sbjct: 506 VAPAEEVVNTKLSEQIASVLADLTPREEQVLRKRFGIGEKSDHTLEEVGKLFNVTRERIR 565

Query: 271 QIEARAFKKVQESIQKQVELS 291
           QIEA+A +K++  ++ QV  S
Sbjct: 566 QIEAKALRKLRHPVRSQVLRS 586


>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 =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 115/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 397 EARARRAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 456

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T     P     +
Sbjct: 457 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---L 511

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+ + E ++  +        S+   I   D + S   D++    D      ++     
Sbjct: 512 AEKMEMPEDKIRKILKISKEPISMETPI--GDDDDSHLGDFI---EDVATLAPVDAAVYA 566

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R+     +  L  RE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 567 SLRDATKEVLESLTAREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 626

Query: 281 QESIQKQ 287
           +   + +
Sbjct: 627 RHPTRSE 633


>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 =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 63/247 (25%), Positives = 117/247 (47%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E    +A   +  ++LRLV+ IA  Y   GL   +++ EGN+GLM+AV KF+  RG++ +
Sbjct: 670 ESKARNAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNVGLMKAVDKFEYRRGYKFS 729

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + R+    +              +
Sbjct: 730 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINRMNRITRQELQETGVEPDSRRL 784

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+ + + E +++ +        S+   I   D + S   D+L    D Q     E  +  
Sbjct: 785 AELMEMPEDKILKIMKIAKEPISMETPI--GDDDDSHLGDFL---EDTQTVAPAEAVQNA 839

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           +  + + + +  L+PRE ++   R   E  +  TLE +  +F+V+RER+RQIE +A +K+
Sbjct: 840 SLSDTVKQVLDSLSPREAKVLRMRFGIEMQSDHTLEEVGKQFDVTRERIRQIETKALRKL 899

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 900 RHPSRAD 906


>gi|167829080|ref|ZP_02460551.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia pseudomallei
           9]
          Length = 285

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 65/243 (26%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 44  RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 103

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 104 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 158

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D       +     + R+
Sbjct: 159 EMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDTNTVAPADAALHASMRD 213

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 214 VVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 273

Query: 285 QKQ 287
           +  
Sbjct: 274 RSD 276


>gi|126738765|ref|ZP_01754461.1| RNA polymerase sigma factor RpoD [Roseobacter sp. SK209-2-6]
 gi|126719946|gb|EBA16653.1| RNA polymerase sigma factor RpoD [Roseobacter sp. SK209-2-6]
          Length = 663

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 423 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 482

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A+KL
Sbjct: 483 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAEKL 537

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++N + 
Sbjct: 538 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAVLPLDSAIQENLKE 592

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 593 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 652

Query: 285 QK 286
           + 
Sbjct: 653 RS 654


>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 =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 121/276 (43%), Gaps = 14/276 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + R I E+ +   L   E   + +R    E     A   +V ++LRLV+ IA  Y   GL
Sbjct: 333 MQRRISEVEQATGLSVAEIKEINRRMSMGEARARRAKKEMVEANLRLVISIAKKYTNRGL 392

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I       
Sbjct: 393 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--I 450

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R+   +         PE    + +++ + E +V  +        S+   I   
Sbjct: 451 ETINKLNRISRQMLQEMGREPTPE---ELGERMEMPEDKVRKVLKIAKEPISMETPI--G 505

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQEN 251
           D   S   D++    D      ++    +         ++ L  RE ++   R       
Sbjct: 506 DDEDSHLGDFI---EDVTISSPVDSATEEGLTEATQDVLAGLTAREAKVLRMRFGIGMNT 562

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +  +F+V+RER+RQIEA+A +K++   +  
Sbjct: 563 DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSD 598


>gi|110678526|ref|YP_681533.1| RNA polymerase factor sigma-32 [Roseobacter denitrificans OCh 114]
 gi|109454642|gb|ABG30847.1| RNA polymerase sigma-32 factor [Roseobacter denitrificans OCh 114]
          Length = 292

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 104/287 (36%), Positives = 180/287 (62%), Gaps = 9/287 (3%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M++    ++ LSR   +  K  +L+ + E  LA  +R+     + HRL+T+++RL + +A
Sbjct: 1   MALDSTRDMALSR---KAMKAELLDAETELELAYAWRDERCEKSLHRLITAYMRLAISMA 57

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             ++ YG P+++++ E  +GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+
Sbjct: 58  SKFKRYGAPMNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVR 117

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKP----EQVVAIAKKLNVSESEVISMNCRLA 181
            G+T++QK LFFN+RR++  L+  +  + +P    +    I+ ++ V   +V  M  RL+
Sbjct: 118 TGSTSSQKSLFFNMRRVQARLERESAASGEPLDRHQLRQMISTEIGVPLHDVEMMEGRLS 177

Query: 182 G-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           G D SLNA   S++    +W D L  D     + +    + +  R  L ++M+ LN RER
Sbjct: 178 GSDYSLNA-TQSTEDEGREWIDALEDDSAQAAETVEHHHDTEQLRAWLLQAMNDLNERER 236

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            I   R+L++ P TLE+L  E  +S+ERVRQ+EA AF K+++S++ Q
Sbjct: 237 FIVRERKLRDAPRTLESLGQELNLSKERVRQLEAAAFGKMRKSLENQ 283


>gi|146276891|ref|YP_001167050.1| RNA polymerase sigma factor RpoD [Rhodobacter sphaeroides ATCC
           17025]
 gi|145555132|gb|ABP69745.1| RNA polymerase, sigma 70 subunit, RpoD [Rhodobacter sphaeroides
           ATCC 17025]
          Length = 667

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 427 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 486

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A+KL
Sbjct: 487 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAEKL 541

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++N + 
Sbjct: 542 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAILPLDSAIQENLKE 596

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 597 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 656

Query: 285 QK 286
           + 
Sbjct: 657 RS 658


>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 =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 68/244 (27%), Positives = 114/244 (46%), Gaps = 12/244 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RGF+ +TY+ 
Sbjct: 377 KRAKEEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGFKFSTYAT 436

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            L R+   L         PE    +A+ +
Sbjct: 437 WWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRTLVQKNGREPTPE---ELAEAM 491

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++ E ++  +        S+   I   D   S   D++    D      +E    +    
Sbjct: 492 DMPEEKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDSNVMSPLEAATTRGLSE 546

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                ++ L PRE R+   R   +     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 547 ATNEVLASLTPREERVLRMRFGIDMNTDHTLEEVGRQFDVTRERIRQIEAKALRKLRHPN 606

Query: 285 QKQV 288
           + ++
Sbjct: 607 RSEL 610


>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 =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 64/248 (25%), Positives = 119/248 (47%), Gaps = 12/248 (4%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            E     A H +  ++LRLV+ IA  Y   G+   +++ EGNIGLM+AV KF+  RG++ 
Sbjct: 409 AERQMRQAKHEMTQANLRLVISIAKKYTNRGMQFLDLIQEGNIGLMKAVDKFEYRRGWKF 468

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY+ WW++ A+   I      +++     ++     L RL   +   T     P     
Sbjct: 469 STYATWWVRQAVTRAIADQARTIRVPVHMIEQ--INKLNRLSREIMQQTGKEPDP---AV 523

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           +A++L+++E +V S+        S+   +   +   +   D +    D       +   +
Sbjct: 524 LAERLDMTEDKVRSIMKIAKEPVSMETPV--GEDGDTSLGDMIA---DSDTATPADAALQ 578

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKK 279
              R ++   +  L+PRE ++   R   +     TLE +  +F+V+RER+RQIE++A KK
Sbjct: 579 AGLRAVVREMLDELSPREAKVLRMRFGIDMSTDYTLEEVGKQFDVTRERIRQIESKAMKK 638

Query: 280 VQESIQKQ 287
           ++   +  
Sbjct: 639 LRHPSRAD 646


>gi|34540402|ref|NP_904881.1| RNA polymerase sigma-70 factor [Porphyromonas gingivalis W83]
 gi|34396715|gb|AAQ65780.1| RNA polymerase sigma-70 factor [Porphyromonas gingivalis W83]
          Length = 287

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 73/283 (25%), Positives = 140/283 (49%), Gaps = 13/283 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           + + SI       L +Y+ EI +  ++  +EE  LA+  +  GD  A  +L  ++LR VV
Sbjct: 5   KISKSITNRESASLDKYLQEIGREDLISVEEEVELAQAIK-RGDRKALEKLTRANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 64  SVAKQYQNQGLSLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++            L ++    Q     N +      +AK+L+++E ++         
Sbjct: 124 IVRLPLNQ-----VGTLNKIIKAQQKFEQENERRPSSAELAKELDIAEDKIADTMKVSGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     + NS    D LV +        +  E        + R++S L  RE  I
Sbjct: 179 HISVDAPFVEGEDNS--LLDVLVNEDTPNTDKSLINESLAVE---IERALSTLTEREAEI 233

Query: 243 FEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +          +TLE +  +F ++RERVRQI+ +A +++++S
Sbjct: 234 VKLFFGIAGCQEMTLEEIGDKFGLTRERVRQIKEKAIRRLRQS 276


>gi|255261823|ref|ZP_05341165.1| RNA polymerase sigma factor RpoD (Sigma-A) [Thalassiobium sp.
           R2A62]
 gi|255104158|gb|EET46832.1| RNA polymerase sigma factor RpoD (Sigma-A) [Thalassiobium sp.
           R2A62]
          Length = 658

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 418 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 477

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A+KL
Sbjct: 478 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAEKL 532

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++N + 
Sbjct: 533 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAVLPLDSAIQENLKE 587

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 588 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 647

Query: 285 QK 286
           + 
Sbjct: 648 RS 649


>gi|89055941|ref|YP_511392.1| RNA polymerase sigma factor RpoD [Jannaschia sp. CCS1]
 gi|88865490|gb|ABD56367.1| RNA polymerase, sigma 70 subunit, RpoD [Jannaschia sp. CCS1]
          Length = 668

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 428 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 487

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A+KL
Sbjct: 488 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAEKL 542

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++N + 
Sbjct: 543 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAVLPLDSAIQENLKE 597

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 598 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 657

Query: 285 QK 286
           + 
Sbjct: 658 RS 659


>gi|124026883|ref|YP_001015998.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. NATL1A]
 gi|123961951|gb|ABM76734.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. NATL1A]
          Length = 340

 Score =  222 bits (567), Expect = 4e-56,   Method: Composition-based stats.
 Identities = 76/292 (26%), Positives = 136/292 (46%), Gaps = 31/292 (10%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD--------------------LSAAH 51
               +  Y+  I ++P+L   EE  LA   ++  D                      A  
Sbjct: 49  ATDAIGFYLTSIGRVPLLTPAEEIELAHHVQQMKDLLNLPLEERSTRQKHKIKMGKRARD 108

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ ++LRLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+ 
Sbjct: 109 RMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQ 168

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            M   I  S   +++    ++K     L +++   + ++    +    + +A  + +   
Sbjct: 169 GMTRAIDNSARTIRLPIHISEK-----LSKMRRISRELSHRFGRQPNRLELANAMGIEPQ 223

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           ++  +  + A   SL+A     +  S+  +       D      +E  +R  ++  L   
Sbjct: 224 DLEDLVSQSAPCASLDAHARGEEDRSTLGELI----PDPNSDEPMEGMDRSIQKEHLGGW 279

Query: 232 MSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +S LN RE++I   R     E P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 280 LSQLNEREQKIMRLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 331


>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 =  222 bits (567), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 71/259 (27%), Positives = 122/259 (47%), Gaps = 15/259 (5%)

Query: 33  EEYVLAKRYREHGDLSAAH---RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           +EY       + G+  A      ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+A
Sbjct: 409 QEYRKIVHMVQKGEREARQAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 468

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V KF+  RG++ +TY+ WWI+ A+   I      ++I        +   + ++    + +
Sbjct: 469 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQM 523

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
                +      +A+KL +   +V  +        SL   I   D+  S   D++    D
Sbjct: 524 LHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---ED 578

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRE 267
               + I+   + N R   TR ++ L PRE R+   R         TLE +  +F V+RE
Sbjct: 579 KNVVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRE 638

Query: 268 RVRQIEARAFKKVQESIQK 286
           R+RQIEA+A +K++   + 
Sbjct: 639 RIRQIEAKALRKLKHPSRS 657


>gi|319955596|ref|YP_004166863.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Cellulophaga
           algicola DSM 14237]
 gi|319424256|gb|ADV51365.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cellulophaga
           algicola DSM 14237]
          Length = 287

 Score =  222 bits (567), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 72/276 (26%), Positives = 146/276 (52%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ +I KI ++   EE  LA+R RE GD  A  +L T++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQDISKIDLITANEEVDLAQRIRE-GDQLALEKLTTANLRFVVSVAKQYQNQGLT 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ A+ + +     +V++        
Sbjct: 76  LPDLINEGNVGLVKAAKRFDETRGFKFISYAVWWIRQAILQALAEQSRIVRLPLNK---- 131

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
              ++ ++K     +   + +P     IAK+L ++ SEV           S++A +   +
Sbjct: 132 -IGSINKIKKAFSYLEQAHERPPSAEEIAKELEMTVSEVQQSLKNTGRHVSMDAPLKEGE 190

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENP 252
            ++            G+     ++  +++    + R++  L+ RE  + +       ++ 
Sbjct: 191 DSN-----LYNVIGSGESPNPDKQLLQQSLNIEINRALETLSQREADVVKLYYGIGDQHS 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TLE +   F+++RERVRQI  +A +K++ + + ++
Sbjct: 246 MTLEEIGQTFDLTRERVRQIREKAIRKLKHNSRSKI 281


>gi|255076341|ref|XP_002501845.1| predicted protein [Micromonas sp. RCC299]
 gi|226517109|gb|ACO63103.1| predicted protein [Micromonas sp. RCC299]
          Length = 595

 Score =  222 bits (567), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 69/323 (21%), Positives = 138/323 (42%), Gaps = 49/323 (15%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYR--------------EHGDLS----------- 48
             +  Y+ +I  + +L   EE  LAKR +              E+G              
Sbjct: 270 DSMKTYLKDIGTVSLLTGAEEVELAKRIQDLMYLNSVCERLEEENGGKEPTRFMWAIECN 329

Query: 49  ---------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
                          A + ++ ++LRLVV IA  Y    +   +++ EG +GL++  +KF
Sbjct: 330 ITEQELERRLEEGKRAKNAMIQANLRLVVSIAKRYANKSMSFQDLIQEGCVGLIRGAEKF 389

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D +RG++ +TY+ WWI+ A+   I      +++        LF  + R+    + +    
Sbjct: 390 DFKRGYKFSTYAHWWIRQAVTRSISDQSRTIRLPVH-----LFEIISRMSKVERQMVLKL 444

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            +      +A  + ++  ++  +        SL+  +N+S+    +  +  + D     +
Sbjct: 445 GRDPTHEELADAMEMTVEKIKQIKKASLVPISLSQTVNNSNGEDKRTVEDTLIDD--YTE 502

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQ 271
               +  +   +  L   ++ LNPRER +   R   ++    TLE + + F V+RER+RQ
Sbjct: 503 HPEGETGKVLLKEDLENVLNTLNPRERDVLRLRYGLDDGRVKTLEEIGNVFSVTRERIRQ 562

Query: 272 IEARAFKKVQESIQKQVELSSSP 294
           IEA+A +K+++  +  +     P
Sbjct: 563 IEAKALRKLRQPSRNGILREYLP 585


>gi|89053397|ref|YP_508848.1| RNA polymerase factor sigma-32 [Jannaschia sp. CCS1]
 gi|88862946|gb|ABD53823.1| RNA polymerase, sigma 32 subunit, RpoH [Jannaschia sp. CCS1]
          Length = 292

 Score =  222 bits (567), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 109/281 (38%), Positives = 177/281 (62%), Gaps = 9/281 (3%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           G+  LSR      K  +L+ + E  LA  +R+     + HRLVT+++RL + +A  ++ Y
Sbjct: 6   GDQSLSR---RAMKAELLDAETELRLAYAWRDDRCEESLHRLVTAYMRLAISMAAKFKRY 62

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           G P+++++ E  +GLM+A  KFDP+RG R +TY++WWIKA++Q++++R+WS+V+ G+T++
Sbjct: 63  GAPMNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDHVMRNWSMVRTGSTSS 122

Query: 132 QKRLFFNLRRLKGHLQAIT----DNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESL 186
           QK LFFN+RR++  L+       D   K +    IA ++ V   +V  M  RLAG D SL
Sbjct: 123 QKSLFFNMRRVQARLEREAMKSGDTLDKHQLRQMIATEVGVPLHDVEMMEGRLAGSDYSL 182

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           NA   S++    +W D L  D +  E ++    +    R+ L  SM+ LN RER I   R
Sbjct: 183 NA-TQSAEDEGREWIDTLEDDGEQAEHIVEHFHDTAQLRDWLIASMNALNDRERFIVRER 241

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +L+E+P TLE+L +E  +S+ERVRQ+EA AF K++++++ Q
Sbjct: 242 KLREDPRTLESLGTELGLSKERVRQLEAAAFGKMRKTLEAQ 282


>gi|114705882|ref|ZP_01438785.1| RNA polymerase sigma factor [Fulvimarina pelagi HTCC2506]
 gi|114538728|gb|EAU41849.1| RNA polymerase sigma factor [Fulvimarina pelagi HTCC2506]
          Length = 300

 Score =  222 bits (567), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 101/248 (40%), Positives = 164/248 (66%), Gaps = 1/248 (0%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A R++E+ D  A H++ ++H+RLV+ +A  +R +GL +++++ EG++GL++A  +F+PER
Sbjct: 42  AVRWKENRDQEALHKITSAHMRLVISMASKFRHFGLAMNDLIQEGHVGLLEAAARFEPER 101

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
             R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFFNLRRL+  L    +      
Sbjct: 102 EVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRARLSQGAEPISGNA 161

Query: 158 QVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
               IA  L VSES+V  M+ RL+G D SLNA +   +  S+  QD+LV D    ++ + 
Sbjct: 162 MYREIAGALKVSESDVALMDSRLSGPDSSLNAPLLDDESGSADRQDFLVADDPLPDETVS 221

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
              + + R   LT ++ VL+ RE +I   RRLQ++  TLE L ++  +S+ERVRQIE RA
Sbjct: 222 VSIDDERRVTWLTSALDVLSERELKIIRERRLQDDGATLEALGTKLGISKERVRQIETRA 281

Query: 277 FKKVQESI 284
            +K++ ++
Sbjct: 282 LEKLRSAL 289


>gi|17232755|ref|NP_489303.1| RNA polymerase sigma factor RpoD [Nostoc sp. PCC 7120]
 gi|75907632|ref|YP_321928.1| RNA polymerase sigma factor RpoD [Anabaena variabilis ATCC 29413]
 gi|133465|sp|P26683|RPOD_ANASP RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A
 gi|142108|gb|AAA22043.1| RNA polymerase sigma-subunit [Nostoc sp. PCC 7120]
 gi|17134402|dbj|BAB76962.1| transcription initiation factor sigma [Nostoc sp. PCC 7120]
 gi|75701357|gb|ABA21033.1| Sigma 28 (Flagella/Sporulation) [Anabaena variabilis ATCC 29413]
          Length = 390

 Score =  222 bits (567), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 78/313 (24%), Positives = 139/313 (44%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAK-------------------------------- 39
            E  +  Y+ EI +I +L   EE  LA+                                
Sbjct: 78  TEDSIRLYLQEIGRIRLLRADEEIELARKIADLLELERVRERLSEKLERDPRDSEWAEAV 137

Query: 40  -------RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                  RYR H    A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 138 QLPLPAFRYRLHIGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 197

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 198 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKLLSQE 252

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA ++ ++  ++  +        SL   I    +  S+  D++  D     
Sbjct: 253 MGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIESDG---- 306

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
           +   ++  +   R  L + +  L+PRER +   R   ++    TLE +   F V+RER+R
Sbjct: 307 ETPEDQVSKNLLREDLEKVLDSLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIR 366

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 367 QIEAKALRKLRHP 379


>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 =  222 bits (567), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 117/247 (47%), Gaps = 12/247 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 379 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 438

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            L R+             PE    +A+++
Sbjct: 439 WWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQCLQEMGREATPE---ELAERM 493

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D   ++ ++    ++ R 
Sbjct: 494 GMPEDKIRKVLKIAKEPISMETPI--GDDDDSHLGDFI---QDESLELPLDSATAESLRL 548

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                +  L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 549 ATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 608

Query: 285 QKQVELS 291
           + +   S
Sbjct: 609 RSETLRS 615


>gi|300867798|ref|ZP_07112441.1| RNA polymerase sigma factor RpoD [Oscillatoria sp. PCC 6506]
 gi|300334215|emb|CBN57613.1| RNA polymerase sigma factor RpoD [Oscillatoria sp. PCC 6506]
          Length = 391

 Score =  222 bits (567), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 78/313 (24%), Positives = 139/313 (44%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAK-------------------------------- 39
            E  +  Y+ EI +I +L   EE  LA+                                
Sbjct: 79  TEDSIRLYLQEIGRIRLLRADEEIELARKIADLLELERIREQLCEELERDPKDNEWANAV 138

Query: 40  -------RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                  R+R H    A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 139 GMPLPAFRHRLHLGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 198

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 199 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKLLSQE 253

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA ++ ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 254 MGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIESDGETPE 311

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
               ++  +   R  L   +  L+PRER +   R   ++    TLE +   F V+RER+R
Sbjct: 312 ----DQVSKNLLREDLESVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIR 367

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 368 QIEAKALRKLRHP 380


>gi|41853|emb|CAA34435.1| katF [Escherichia coli K-12]
          Length = 362

 Score =  222 bits (567), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 79/271 (29%), Positives = 139/271 (51%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 73  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 131

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 132 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 190

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++         V IA++L+    +V  M        S++  +    +   
Sbjct: 191 LRTAR----ELSHKLDHEPSAVEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE--- 243

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
             +  L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 244 --KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 301

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 302 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 332


>gi|10197699|gb|AAG14981.1|AF242209_6 alternative sigma factor [Escherichia coli]
          Length = 360

 Score =  222 bits (567), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    +   
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE--- 231

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
             +  L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 232 --KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>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
           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 =  222 bits (567), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 117/247 (47%), Gaps = 12/247 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 379 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 438

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            L R+             PE    +A+++
Sbjct: 439 WWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQCLQEMGREATPE---ELAERM 493

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D   ++ ++    ++ R 
Sbjct: 494 GMPEDKIRKVLKIAKEPISMETPI--GDDDDSHLGDFI---QDESLELPLDSATAESLRL 548

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                +  L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 549 ATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 608

Query: 285 QKQVELS 291
           + +   S
Sbjct: 609 RSETLRS 615


>gi|281357500|ref|ZP_06243988.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Victivallis
           vadensis ATCC BAA-548]
 gi|281316103|gb|EFB00129.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Victivallis
           vadensis ATCC BAA-548]
          Length = 432

 Score =  222 bits (566), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 86/285 (30%), Positives = 144/285 (50%), Gaps = 15/285 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYR---EHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
             +  Y+ EI +IP++ K+EE  LA       E     A   L+ ++LRLVVKIA  ++G
Sbjct: 158 DTMKVYMGEIARIPLVNKKEEAELADAIHGDNEDRHEDARSTLIKANLRLVVKIAHDFKG 217

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            GLP+ +++SEGNIGLM+AV+KFDP +G + ++Y+ WWIK +M+  +      ++I   +
Sbjct: 218 LGLPLLDLISEGNIGLMRAVEKFDPAKGAKFSSYAAWWIKQSMRRALANQSRTIRIPVQS 277

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
                   + ++K     + +   +      IA+ L+ SE  V  +        SL+  I
Sbjct: 278 A-----GKINKIKSVRMKLAEELGREPSDAEIAEHLDFSERTVAGLRLADLRTFSLHDPI 332

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-- 248
              ++   ++QD +   H      ++   E   R   L   +  L  RERRI E R    
Sbjct: 333 QQGEE--GEFQDIIPDRHAMTPDQILGDVESVFR---LMDLLEKLEERERRILEMRFGLR 387

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
              P+TLE +S E   +RERVRQI+ +A  K+++ +  +   ++ 
Sbjct: 388 GNRPLTLEEVSQEIGRTRERVRQIQNQALAKLKQLLVDEAGFAAD 432


>gi|149202116|ref|ZP_01879089.1| RNA polymerase sigma factor RpoD [Roseovarius sp. TM1035]
 gi|149144214|gb|EDM32245.1| RNA polymerase sigma factor RpoD [Roseovarius sp. TM1035]
          Length = 661

 Score =  222 bits (566), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 70/242 (28%), Positives = 117/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 421 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 480

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A+KL
Sbjct: 481 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAEKL 535

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   + N + 
Sbjct: 536 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNVILPLDSAIQDNLKE 590

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR +S L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 591 TTTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 650

Query: 285 QK 286
           + 
Sbjct: 651 RS 652


>gi|91217671|ref|ZP_01254628.1| putative sigma factor A [Psychroflexus torquis ATCC 700755]
 gi|91184175|gb|EAS70561.1| putative sigma factor A [Psychroflexus torquis ATCC 700755]
          Length = 288

 Score =  222 bits (566), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 74/276 (26%), Positives = 148/276 (53%), Gaps = 12/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ +I K+ ++  +EE  LA+R RE GD +A  +L  ++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQDISKVDLITAEEEVELAQRIRE-GDQAALEKLTNANLRFVVSVAKQYQNQGLK 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + +     +V++    N+  
Sbjct: 76  LPDLINEGNVGLVKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRVVRLP--LNKIG 133

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   + +   HL+ + +   +P   + IAK+L++SE++V           S++A     +
Sbjct: 134 VINKINKTFSHLEQVNE---RPPSAIEIAKELDMSEAQVKVALKNSGRHLSMDAPFKEGE 190

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
            N S   D L      +     ++  R +    + R++  L+ RE  +        N   
Sbjct: 191 -NDSNLYDVL---SSAESPTPDDQLMRDSLSIEINRALETLSQREADVIRLNYGIGNQPA 246

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TL+ +   F++SRERVRQI  +  ++++   + ++
Sbjct: 247 MTLQEIGDTFDLSRERVRQIREKGIRRLKHQSKNKM 282


>gi|330970856|gb|EGH70922.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. aceris
           str. M302273PT]
          Length = 616

 Score =  222 bits (566), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 69/263 (26%), Positives = 121/263 (46%), Gaps = 14/263 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L+  E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 356 LKIAEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 415

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 416 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 473

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    + +++ + E ++  +        S+   I   D   S   D++  
Sbjct: 474 LQEMGREPTPE---ELGERMEMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 526

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q  I+    ++ +      +S L  RE ++   R   +     TLE +  +F+V
Sbjct: 527 -EDSTMQSPIDVATVESLKEATREVLSGLTAREAKVLRMRFGIDMNTNHTLEEVGKQFDV 585

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   + +
Sbjct: 586 TRERIRQIEAKALRKLRHPTRSE 608


>gi|240850913|ref|YP_002972313.1| RNA polymerase sigma factor RpoD [Bartonella grahamii as4aup]
 gi|240268036|gb|ACS51624.1| RNA polymerase sigma factor RpoD [Bartonella grahamii as4aup]
          Length = 671

 Score =  222 bits (566), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 69/240 (28%), Positives = 118/240 (49%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V S+LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 433 AKKEMVESNLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 492

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + I     +      ++ KL++
Sbjct: 493 IRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQILHEIGREPTPEELSSKLSM 547

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   +   D++ S   D++    D    + I+   + N R+  
Sbjct: 548 PLEKVRKVLKIAKEPISLETPV--GDEDDSHLGDFI---EDRNALLPIDAAIQANLRDTT 602

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 603 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 662


>gi|110633818|ref|YP_674026.1| RNA polymerase sigma factor RpoD [Mesorhizobium sp. BNC1]
 gi|110284802|gb|ABG62861.1| RNA polymerase, sigma 38 subunit, RpoS [Chelativorans sp. BNC1]
          Length = 668

 Score =  222 bits (566), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 116/240 (48%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 430 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 489

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + +     +      +A+KL +
Sbjct: 490 IRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREPTPEELAEKLAM 544

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   +   D+  S   D++    D    + I+   + N R   
Sbjct: 545 PLEKVRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKSAILPIDAAIQANLRETT 599

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 600 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 659


>gi|78212231|ref|YP_381010.1| RNA polymerase sigma factor RpoD [Synechococcus sp. CC9605]
 gi|78196690|gb|ABB34455.1| Sigma-70 factor [Synechococcus sp. CC9605]
          Length = 435

 Score =  222 bits (566), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 77/313 (24%), Positives = 143/313 (45%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE--------------HG------------ 45
            E  +  Y+ EI +I +L   EE  LA++  +              +G            
Sbjct: 123 TEDSIRVYLQEIGRIRLLRPDEEIELARKIADLLYLEELAAQFESDNGREPDNKEWAALV 182

Query: 46  -------------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 183 EMPLIRFRRRLMLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 242

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 243 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKVLSQE 297

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA+ + ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 298 FGRKPTEEEIAESMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADIENPE 355

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
           Q + +   R++    L   ++ L+PRER +   R   ++    TLE +   F+V+RER+R
Sbjct: 356 QDVAKNLLRED----LEGVLATLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVTRERIR 411

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 412 QIEAKALRKLRHP 424


>gi|332829288|gb|EGK01942.1| hypothetical protein HMPREF9455_00064 [Dysgonomonas gadei ATCC
           BAA-286]
          Length = 286

 Score =  222 bits (566), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 71/287 (24%), Positives = 144/287 (50%), Gaps = 12/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI +  ++  +EE  LA+  ++ GD +A  +L  ++LR VV
Sbjct: 5   KITKSITNRESASLDKYLQEIGREDLITVEEEVELAQAIKK-GDRAALEKLTRANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 64  SVAKQYQNQGLSLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++           +L ++          N +      +A++L++   ++         
Sbjct: 124 IVRLPLNQ-----VGSLNKISKAFSKFEQENERKPSAEELAEQLDIPVDKIADSLKVSGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     + NS    D LV D        +  E  +     + R++S L  RE  I
Sbjct: 179 HISMDAPFVEGEDNS--LLDVLVNDDAPIADRTLINESLQQE---IERALSTLTERESEI 233

Query: 243 FEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +         +TLE +  +F+++RERVRQI+ +A K+++++ + ++
Sbjct: 234 IKMFFGIGYQEMTLEEIGDKFQLTRERVRQIKEKAIKRLRQNSRSKL 280


>gi|87200249|ref|YP_497506.1| RNA polymerase sigma factor RpoD [Novosphingobium aromaticivorans
           DSM 12444]
 gi|87135930|gb|ABD26672.1| RNA polymerase, sigma 70 subunit, RpoD [Novosphingobium
           aromaticivorans DSM 12444]
          Length = 667

 Score =  222 bits (566), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 68/251 (27%), Positives = 120/251 (47%), Gaps = 15/251 (5%)

Query: 41  YREHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
             + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 418 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 477

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I        +   + +L    +       +  
Sbjct: 478 GYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTSRQFLHEQGREP 532

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A++L++   +V  +        SL   I   D+  S   D++    D    + ++
Sbjct: 533 TPEEMAERLSMPLEKVRKVMKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAIIPVD 587

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              + N +  +TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+
Sbjct: 588 AAIQANLKETVTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 647

Query: 276 AFKKVQESIQK 286
           A +K++   + 
Sbjct: 648 ALRKLKHPSRS 658


>gi|269101863|ref|ZP_06154560.1| RNA polymerase sigma factor RpoS [Photobacterium damselae subsp.
           damselae CIP 102761]
 gi|268161761|gb|EEZ40257.1| RNA polymerase sigma factor RpoS [Photobacterium damselae subsp.
           damselae CIP 102761]
          Length = 333

 Score =  222 bits (566), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 79/271 (29%), Positives = 134/271 (49%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD  A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 61  YLGEIGFSPLLTAEEEVLYARR-ALRGDDVARKRMIESNLRLVVKISRRYSNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 VEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            IA +L     +V  M        S++  I  S     
Sbjct: 179 LRTAR----ELAQKLDHEPTAEDIAIQLEKPVDDVNRMLRLNERVSSVDNPI--SGDADK 232

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D +  +  G  +V     +  + ++ +   +  LNP++R +   R   L     TLE
Sbjct: 233 ALLDIIPDEKGGTPEV---STQTDDIKSSIVDWLDELNPKQREVLARRFGLLGYEASTLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    +++++ +  +
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLRDMLTHE 320


>gi|328954514|ref|YP_004371848.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfobacca
           acetoxidans DSM 11109]
 gi|328454838|gb|AEB10667.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfobacca
           acetoxidans DSM 11109]
          Length = 577

 Score =  222 bits (566), Expect = 5e-56,   Method: Composition-based stats.
 Identities = 79/271 (29%), Positives = 127/271 (46%), Gaps = 16/271 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSA---AHRLVTSHLRLVVKIAMGYRGYGLPIS 76
           + +I     L  ++   + KR +  GD  A      LV ++LRLVV IA  Y   GL   
Sbjct: 308 LQKIESETGLSAEKLLEIQKRVQ-RGDRQASRAKSELVEANLRLVVSIAKKYTNRGLQFL 366

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++ EGNIGLM+AV+KF+ ERG++ +TY+ WWI+ A+   I      ++I          
Sbjct: 367 DLIQEGNIGLMKAVEKFEYERGYKFSTYATWWIRQAITRAIADQARTIRIPVHM--IETI 424

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
             L R   +L         PE    +A+K+     +V  +        SL   I   ++ 
Sbjct: 425 NKLLRTSRYLVQEIGREPTPE---ELAEKMEYPLEKVRKVLKIAKEPISLETPI--GEEE 479

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VT 254
            S   D++    D +     E  E  N   +  + +S L PRE ++   R         T
Sbjct: 480 DSYLADFI---EDKKISSPTEAVENLNLAEITRKVLSTLTPREEKVIRLRFGIGEKTDHT 536

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           LE +  +F V+RER+RQIEA+A +K++ + +
Sbjct: 537 LEEVGKKFMVTRERIRQIEAKALRKLRHASR 567


>gi|332707223|ref|ZP_08427276.1| RNA polymerase sigma factor RpoD-like protein [Lyngbya majuscula
           3L]
 gi|332353957|gb|EGJ33444.1| RNA polymerase sigma factor RpoD-like protein [Lyngbya majuscula
           3L]
          Length = 373

 Score =  222 bits (566), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 79/313 (25%), Positives = 140/313 (44%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRY------------------REHGDLS----- 48
            E  +  Y+ EI +I +L   EE  LA++                   RE GD       
Sbjct: 61  TEDSIRLYLQEIGRIRLLRADEEIELARKIADLLELERVRERLSEQLEREPGDREWATEV 120

Query: 49  ----------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 121 DMELPAFRYRLHVGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 180

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 181 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKLLSQE 235

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA ++ ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 236 MGRKPTEEEIADRMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADGETPE 293

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
               ++  +   R  L   +  L+PRER +   R   ++    TLE +   F V+RER+R
Sbjct: 294 ----DQVSKNLLREDLESVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIR 349

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 350 QIEAKALRKLRHP 362


>gi|170078618|ref|YP_001735256.1| RNA polymerase sigma factor [Synechococcus sp. PCC 7002]
 gi|558881|gb|AAB41506.1| SigA [Synechococcus sp. PCC 7002]
 gi|169886287|gb|ACB00001.1| RNA polymerase sigma factor [Synechococcus sp. PCC 7002]
          Length = 375

 Score =  222 bits (566), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 75/313 (23%), Positives = 140/313 (44%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS----------------------- 48
            E  +  Y+ EI +I +L  +EE  LA++  +  +L                        
Sbjct: 63  TEDSIRIYLQEIGRIRLLRAEEEIELARKIADLLELERMREQLTEHESRVPTDKEWAEAA 122

Query: 49  ----------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 123 GMPLKDFRRRLFHGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 182

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 183 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKILSQE 237

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA+++ ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 238 LGRKPTEEEIAERMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADGETPE 295

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
               ++  +   R  L   +  L+ RER +   R   ++    TLE +   F V+RER+R
Sbjct: 296 ----DQVSKSLLREDLENVLDTLSARERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIR 351

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 352 QIEAKALRKLRHP 364


>gi|119386779|ref|YP_917834.1| RNA polymerase sigma factor RpoD [Paracoccus denitrificans PD1222]
 gi|119377374|gb|ABL72138.1| RNA polymerase, sigma 70 subunit, RpoD [Paracoccus denitrificans
           PD1222]
          Length = 664

 Score =  222 bits (566), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 70/246 (28%), Positives = 119/246 (48%), Gaps = 12/246 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 420 EKESRQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 479

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + +L    + +     +      +
Sbjct: 480 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEEL 534

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+KL +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++
Sbjct: 535 AEKLQMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAVLPLDSAIQE 589

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N +   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 590 NLKETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKL 649

Query: 281 QESIQK 286
           +   + 
Sbjct: 650 KHPSRS 655


>gi|332885662|gb|EGK05908.1| hypothetical protein HMPREF9456_02172 [Dysgonomonas mossii DSM
           22836]
          Length = 286

 Score =  222 bits (566), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 71/287 (24%), Positives = 146/287 (50%), Gaps = 12/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI +  ++  +EE  LA+  ++ GD +A  +L  ++LR VV
Sbjct: 5   KITKSITNRESASLDKYLQEIGREDLITVEEEVELAQAIKK-GDRAALEKLTRANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 64  SVAKQYQNQGLSLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++           +L ++          N +      +A++L++   ++         
Sbjct: 124 IVRLPLNQ-----VGSLNKISKAFSKFEQENERKPSAEELAEQLDIPVDKIADSLKVSGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     + NS    D LV D      +   K   ++ +  + R++S L  RE  I
Sbjct: 179 HISMDAPFVEGEDNS--LLDVLVNDD---APIADRKLINESLQQEIERALSTLTERESEI 233

Query: 243 FEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +         +TLE +  +F+++RERVRQI+ +A K+++++ + ++
Sbjct: 234 IKMFFGIGYQEMTLEEIGDKFQLTRERVRQIKEKAIKRLRQNSRSKL 280


>gi|166078602|gb|ABY81278.1| alternative sigma factor S [Listonella anguillarum]
          Length = 332

 Score =  222 bits (566), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 81/288 (28%), Positives = 140/288 (48%), Gaps = 14/288 (4%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
            ++              Y+ EI   P+L  QEE + A+R    GD +A  R++ S+LRLV
Sbjct: 44  AKEGFDASTKSLDATQMYLSEIGFSPLLTAQEEVLYARR-SLRGDEAARKRMIESNLRLV 102

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           VKI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++   
Sbjct: 103 VKISRRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQT 162

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             +++      K L   LR  +     ++           IA +L+  E +V  M     
Sbjct: 163 RTIRLPIHVV-KELNIYLRTAR----ELSQKLDHEPTAEEIAFQLDKPE-DVSKMLRLNE 216

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              S++  I           D +   ++   ++  + +   + R  L   +  LNP+++ 
Sbjct: 217 RISSVDTPI--GGDGDKALLDIIPDTNNSDPEISTQDD---DIRESLLNWLDELNPKQKE 271

Query: 242 IFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +   R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 272 VLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVKQ 319


>gi|289642419|ref|ZP_06474565.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia symbiont
           of Datisca glomerata]
 gi|289507764|gb|EFD28717.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Frankia symbiont
           of Datisca glomerata]
          Length = 425

 Score =  222 bits (566), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 67/296 (22%), Positives = 131/296 (44%), Gaps = 38/296 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKR--------YREHGDLS------------------A 49
           +  Y+ EI K+P+L   +E  L+KR        Y+   D                    A
Sbjct: 129 VRMYLREIGKVPLLNAAQEVELSKRVEAGLFAEYKLDTDTDLAPELRRDLQTLVRDGHAA 188

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             +LV+++LRLVV +A  Y G G+ + ++V EGN+GL++AV+KFD  +G++ +TY+ WWI
Sbjct: 189 KQQLVSANLRLVVSVAKKYSGRGMTLLDLVQEGNLGLIRAVEKFDYAKGYKFSTYATWWI 248

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + A+   +      ++I     +      + ++    + +     +      +A +L++ 
Sbjct: 249 RQAIGRALADQARTIRIPVHVVE-----QINKITRLQRQLVSTLGREPTDEELALELDMP 303

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             +V+ +        SL   +   D   S   D++    D       +       ++ + 
Sbjct: 304 IEQVVELRRYAQDTVSLETAV--GDDGDSVLGDFI---EDADATSPADAASYGAMQDEIE 358

Query: 230 RSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             ++ L PRER +   R         TL  + +   ++RER+RQIE    +++++ 
Sbjct: 359 GVLNSLTPREREVMRLRFGLADGKQHTLAEVGNRLGLTRERIRQIERDTLRELRKP 414


>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 =  222 bits (566), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 71/259 (27%), Positives = 122/259 (47%), Gaps = 15/259 (5%)

Query: 33  EEYVLAKRYREHGDLSAAH---RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           +EY       + G+  A      ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+A
Sbjct: 408 QEYRKIVHMVQKGEREARQAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKA 467

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V KF+  RG++ +TY+ WWI+ A+   I      ++I        +   + ++    + +
Sbjct: 468 VDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQM 522

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
                +      +A+KL +   +V  +        SL   I   D+  S   D++    D
Sbjct: 523 LHEIGREPTPEELAEKLAMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---ED 577

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRE 267
               + I+   + N R   TR ++ L PRE R+   R         TLE +  +F V+RE
Sbjct: 578 KNVVLPIDAAIQSNLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRE 637

Query: 268 RVRQIEARAFKKVQESIQK 286
           R+RQIEA+A +K++   + 
Sbjct: 638 RIRQIEAKALRKLKHPSRS 656


>gi|254526617|ref|ZP_05138669.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9202]
 gi|221538041|gb|EEE40494.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9202]
          Length = 339

 Score =  222 bits (566), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 76/292 (26%), Positives = 139/292 (47%), Gaps = 31/292 (10%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLA--------------------KRYREHGDLSAAH 51
               +  Y+  I ++P+L   EE  LA                      Y+      A  
Sbjct: 48  ASDSIGYYLSSIGRVPLLTPAEEIELAHHVQNMKKLLQIPETERTQRNLYQIKIGKRARD 107

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ ++LRLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+ 
Sbjct: 108 RMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQ 167

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            M   I  S   +++    ++K     L +++   + ++    +    + +A ++ + + 
Sbjct: 168 GMTRAIDNSARTIRLPIHISEK-----LSKMRRVSRELSHKFGRQPTRLEMATEMGIDQK 222

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           ++  +  + A   SL+A     +  S+  +       D   +  +E  +R  ++  L   
Sbjct: 223 DLEDLISQSAPCASLDAHARGEEDRSTLGELI----PDPNCEEPMEGMDRTIQKEHLGTW 278

Query: 232 MSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +S LN RE++I + R     E P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 279 LSQLNEREQKIMKLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 330


>gi|288927719|ref|ZP_06421566.1| RNA polymerase sigma-70 factor [Prevotella sp. oral taxon 317 str.
           F0108]
 gi|288330553|gb|EFC69137.1| RNA polymerase sigma-70 factor [Prevotella sp. oral taxon 317 str.
           F0108]
          Length = 287

 Score =  222 bits (566), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 73/287 (25%), Positives = 146/287 (50%), Gaps = 12/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI    ++  +EE  LA+R ++ GD  A  +L  ++LR VV
Sbjct: 5   KITKSITNRESDSLDKYLQEIGHEELISVEEEVELAQRIKK-GDRKALEKLTKANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + I     
Sbjct: 64  SVAKQYQNQGLSLQDLINEGNVGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    NQ      + ++   L      N +   +  IA+K ++ E ++         
Sbjct: 124 IVRLP--LNQVGSVNKINKI---LSKFEQENERRPSINEIAEKTDLPEDKIEDAIKVTGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     + NS      L    +     +  +  +++ R  +  ++  LN RER +
Sbjct: 179 HISVDAPFVDGEDNS-----LLDLLANTDTPTVDNELVKESLRAEIADALQYLNERERNV 233

Query: 243 FEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            EA        +TLE +  ++ ++RERVRQI+ +A ++++ + + ++
Sbjct: 234 IEAFFGINQMEMTLEEIGDKYGLTRERVRQIKEKAIRRLRNNTKNKM 280


>gi|148240837|ref|YP_001226224.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp. WH
           7803]
 gi|147849376|emb|CAK24927.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 7803]
          Length = 339

 Score =  222 bits (566), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 80/296 (27%), Positives = 144/296 (48%), Gaps = 31/296 (10%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLA--------------------KRYREHGDLSAAHRL 53
             +  Y+  I ++P+L   EE  LA                    +R+R      A  R+
Sbjct: 50  DSIGYYLSSIGRVPLLTAAEEIELAHHVQAMKELLDVPEGERTPRQRHRIRMGKRARDRM 109

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           + ++LRLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+  M
Sbjct: 110 MAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGM 169

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
              I  S   +++    ++K     L +++   + ++    +    + +A  + +   ++
Sbjct: 170 TRAIDNSARTIRLPIHISEK-----LSKMRRITRELSHRFGRQPNRLELANAMGIEPRDL 224

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             +  + A   SL+A     +  S+  +  L+ D +G E   +E  +R  ++  L   +S
Sbjct: 225 EELISQSAPCASLDAHARGEEDRSTLGE--LIPDPNGDE--PMEGMDRSIQKEHLGGWLS 280

Query: 234 VLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            LN RE++I   R   +   P+TL  +  +  VSRERVRQ+EA+A  K++    +Q
Sbjct: 281 QLNDREQKILRLRFGLDGAEPLTLAEIGRQINVSRERVRQLEAKAILKLRSMTDQQ 336


>gi|90580346|ref|ZP_01236153.1| putative RNA polymerase sigma-38 factor [Vibrio angustum S14]
 gi|90438648|gb|EAS63832.1| putative RNA polymerase sigma-38 factor [Vibrio angustum S14]
          Length = 337

 Score =  222 bits (566), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 79/271 (29%), Positives = 135/271 (49%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD  A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 66  YLGEIGYSPLLTAEEEVLYARR-ALRGDEVARKRMIESNLRLVVKISRRYSNRGLALLDL 124

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 125 VEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 183

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            IA++L     +V  M        S++  I     +  
Sbjct: 184 LRTAR----ELAQKLDHEPTAEDIAQQLEKPVDDVNRMLRLNERVSSVDNPI--GGDSEK 237

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D +  +  G  +   + +   + +N +   +  LNP++R +   R   L     TLE
Sbjct: 238 ALLDIIPDEKGGSPESSTQDD---DIKNSIVHWLQELNPKQREVLARRFGLLGYEASTLE 294

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    +++++ +  Q
Sbjct: 295 DVGREIGLTRERVRQIQVEGLRRLRDMLTHQ 325


>gi|304391338|ref|ZP_07373282.1| RNA polymerase sigma factor RpoD [Ahrensia sp. R2A130]
 gi|303296694|gb|EFL91050.1| RNA polymerase sigma factor RpoD [Ahrensia sp. R2A130]
          Length = 692

 Score =  222 bits (566), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 115/240 (47%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 454 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 513

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + +     +      ++ KL +
Sbjct: 514 IRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREPTPEELSTKLAM 568

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   I   D+  S   D++    D    + I+   + N R   
Sbjct: 569 PLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAILPIDAAIQSNLRETT 623

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 624 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 683


>gi|188994502|ref|YP_001928754.1| RNA polymerase sigma factor RpoD [Porphyromonas gingivalis ATCC
           33277]
 gi|188594182|dbj|BAG33157.1| RNA polymerase sigma factor RpoD [Porphyromonas gingivalis ATCC
           33277]
          Length = 287

 Score =  222 bits (566), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 73/283 (25%), Positives = 140/283 (49%), Gaps = 13/283 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           + + SI       L +Y+ EI +  ++  +EE  LA+  +  GD  A  +L  ++LR VV
Sbjct: 5   KISKSITNRESASLDKYLQEIGREDLISVEEEVELAQAIK-RGDRKALEKLTRANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 64  SVAKQYQNQGLSLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++            L ++    Q     N +      +AK+L+++E ++         
Sbjct: 124 IVRLPLNQ-----VGTLNKIIKAQQKFEQENERRPSSAELAKELDIAEDKIADTMKVSGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     + NS    D LV +        +  E        + R++S L  RE  I
Sbjct: 179 HISVDAPFVEGEDNS--LLDVLVNEDTPNTDKSLINESLAVE---IERALSTLTEREAEI 233

Query: 243 FEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +          +TLE +  +F ++RERVRQI+ +A +++++S
Sbjct: 234 VKLFFGIAGCQEMTLEEIGDKFGLTRERVRQIKEKAIRRLRQS 276


>gi|85704163|ref|ZP_01035266.1| RNA polymerase sigma-32 factor [Roseovarius sp. 217]
 gi|85671483|gb|EAQ26341.1| RNA polymerase sigma-32 factor [Roseovarius sp. 217]
          Length = 277

 Score =  222 bits (566), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 101/268 (37%), Positives = 171/268 (63%), Gaps = 6/268 (2%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K  ML+ + E  LA  +R+  D  A HRL+ +++RL + +A  +R YG P+++++ E  
Sbjct: 1   MKAEMLDAETELALAYAWRDQRDEEALHRLINAYMRLAISMASKFRRYGAPMNDLIQEAG 60

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           +GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFN+RR++
Sbjct: 61  LGLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMRRVQ 120

Query: 144 GHLQAITDNNLKP----EQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSS 198
             L+     N +     +    IA ++ V   +V  M  RL+G D SLNA   S++    
Sbjct: 121 ARLEREAMANGQQLDGYQLREMIAHEVGVPLRDVEMMEGRLSGSDFSLNA-TQSAEDEGR 179

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           +W D L  +    ++++    +    R+ L  +++ LN RER I   R+L+++P TLE+L
Sbjct: 180 EWIDTLEDEGARGDEIVERHHDMHALRDWLADALARLNERERFIVRERKLRDDPRTLESL 239

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQK 286
             E  +S+ERVRQ+EA AF+K+++ ++K
Sbjct: 240 GEELNLSKERVRQLEAAAFQKMRKHLEK 267


>gi|149914287|ref|ZP_01902818.1| RNA polymerase sigma factor RpoD [Roseobacter sp. AzwK-3b]
 gi|149811806|gb|EDM71639.1| RNA polymerase sigma factor RpoD [Roseobacter sp. AzwK-3b]
          Length = 662

 Score =  222 bits (566), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 72/249 (28%), Positives = 120/249 (48%), Gaps = 15/249 (6%)

Query: 43  EHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG+
Sbjct: 415 QKGEKEARLAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGY 474

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWI+ A+   I      ++I        +   + +L    + +     +    
Sbjct: 475 KFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTP 529

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +A+KL +   +V  +        SL   I   D+  SQ  D++    D    + ++  
Sbjct: 530 EELAEKLQMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNVVLPLDSA 584

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAF 277
            + N R   TR +S L PRE R+   R         TLE +  +F V+RER+RQIEA+A 
Sbjct: 585 IQDNLRETTTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKAL 644

Query: 278 KKVQESIQK 286
           +K++   + 
Sbjct: 645 RKLKHPSRS 653


>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 =  222 bits (566), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 69/263 (26%), Positives = 121/263 (46%), Gaps = 14/263 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L+  E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 355 LKIAEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 414

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 415 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 472

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    + +++ + E ++  +        S+   I   D   S   D++  
Sbjct: 473 LQEMGREPTPE---ELGERMEMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 525

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q  I+    ++ +      +S L  RE ++   R   +     TLE +  +F+V
Sbjct: 526 -EDSTMQSPIDVATVESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 584

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   + +
Sbjct: 585 TRERIRQIEAKALRKLRHPTRSE 607


>gi|163761137|ref|ZP_02168214.1| RNA polymerase sigma factor protein (sigma-70) [Hoeflea
           phototrophica DFL-43]
 gi|162281688|gb|EDQ31982.1| RNA polymerase sigma factor protein (sigma-70) [Hoeflea
           phototrophica DFL-43]
          Length = 680

 Score =  222 bits (566), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 69/252 (27%), Positives = 120/252 (47%), Gaps = 15/252 (5%)

Query: 40  RYREHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           +  + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  
Sbjct: 430 QMVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR 489

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RG++ +TY+ WWI+ A+   I      ++I        +   + ++    + +     + 
Sbjct: 490 RGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGRE 544

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
                +A+KL +   +V  +        SL   +   D+  S   D++    D    + I
Sbjct: 545 PTPEELAEKLAMPLEKVRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKNAILPI 599

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEA 274
           +   + N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA
Sbjct: 600 DAAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEA 659

Query: 275 RAFKKVQESIQK 286
           +A +K++   + 
Sbjct: 660 KALRKLKHPSRS 671


>gi|1350861|sp|P47765|RPOS_YEREN RecName: Full=RNA polymerase sigma factor rpoS
 gi|687583|gb|AAC43391.1| RpoS [Yersinia enterocolitica]
          Length = 331

 Score =  222 bits (566), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 79/281 (28%), Positives = 139/281 (49%), Gaps = 13/281 (4%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           + +G      Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y
Sbjct: 52  VTSGADATQLYLGEIGYSPLLTAEEEVYFARR-ALRGDVPSRRRMIESNLRLVVKIARRY 110

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
              GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++  
Sbjct: 111 SNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPI 170

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
               K L   LR  +     ++           IA++L+    +V  M        S++ 
Sbjct: 171 HIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDT 225

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR- 247
            +    + +      L    D  E    +  +  + +  + + +  LN ++R +   R  
Sbjct: 226 PLGGDSEKA-----LLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFG 280

Query: 248 -LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            L     TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 281 LLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQAQ 321


>gi|218245044|ref|YP_002370415.1| RNA polymerase sigma-70 subunit RpoD subfamily [Cyanothece sp. PCC
           8801]
 gi|257058068|ref|YP_003135956.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8802]
 gi|218165522|gb|ACK64259.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8801]
 gi|256588234|gb|ACU99120.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8802]
          Length = 379

 Score =  221 bits (565), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 76/313 (24%), Positives = 140/313 (44%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS----------------------- 48
            E  +  Y+ EI +I +L  +EE  LA++  +  +L                        
Sbjct: 67  TEDSIRIYLQEIGRIRLLRAEEEIELARKIADLLELERIREKMTEHMGRFPTDLEWSQAI 126

Query: 49  ----------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 127 NMEWHAFQRRLYLGRKAKDKMVHSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 186

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 187 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKILSQE 241

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA ++ ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 242 MRRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADGENPE 299

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
               ++  +   R  L   +  L+PRER +   R   ++    TLE +   F V+RER+R
Sbjct: 300 ----DEVSKNLLREDLENVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIR 355

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 356 QIEAKALRKLRHP 368


>gi|78780175|ref|YP_398287.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9312]
 gi|123969439|ref|YP_001010297.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. AS9601]
 gi|126697226|ref|YP_001092112.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9301]
 gi|78713674|gb|ABB50851.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9312]
 gi|123199549|gb|ABM71190.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. AS9601]
 gi|126544269|gb|ABO18511.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9301]
          Length = 339

 Score =  221 bits (565), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 76/292 (26%), Positives = 139/292 (47%), Gaps = 31/292 (10%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLA--------------------KRYREHGDLSAAH 51
               +  Y+  I ++P+L   EE  LA                      Y+      A  
Sbjct: 48  ASDSIGYYLSSIGRVPLLTPAEEIELAHHVQNMKKLLQIPETDRTQRNLYQIKIGKRARD 107

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ ++LRLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+ 
Sbjct: 108 RMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQ 167

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            M   I  S   +++    ++K     L +++   + ++    +    + +A ++ + + 
Sbjct: 168 GMTRAIDNSARTIRLPIHISEK-----LSKMRRVSRELSHKFGRQPTRLEMATEMGIDQK 222

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           ++  +  + A   SL+A     +  S+  +       D   +  +E  +R  ++  L   
Sbjct: 223 DLEDLISQSAPCASLDAHARGEEDRSTLGELI----PDPNCEEPMEGMDRTIQKEHLGTW 278

Query: 232 MSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +S LN RE++I + R     E P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 279 LSQLNEREQKIMKLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 330


>gi|257892237|ref|ZP_05671890.1| LOW QUALITY PROTEIN: RNA polymerase sigma factor RpoD [Enterococcus
           faecium 1,231,408]
 gi|257828616|gb|EEV55223.1| LOW QUALITY PROTEIN: RNA polymerase sigma factor RpoD [Enterococcus
           faecium 1,231,408]
          Length = 332

 Score =  221 bits (565), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 67/246 (27%), Positives = 114/246 (46%), Gaps = 13/246 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI ++ +L  +EE  LA +  E GD  A  RL  ++LRLVV IA  Y G G+
Sbjct: 98  DPVRMYLKEIGRVSLLTAEEEVALALKI-EEGDQEAKQRLAEANLRLVVSIAKRYVGRGM 156

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 157 QFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 215

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R++  L         PE++ A   ++++   +V  +        SL   I   
Sbjct: 216 -TINKLIRIQRQLLQDLGREPTPEEIGA---EMDLPTEKVREILKIAQEPVSLETPI--G 269

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +++ S   D++    D +     E    +  +  L   +  L  RE  +   R   ++  
Sbjct: 270 EEDDSHLGDFI---EDQEATSPAEHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGR 326

Query: 253 -VTLEN 257
             TLE 
Sbjct: 327 TRTLEE 332


>gi|73748391|ref|YP_307630.1| RNA polymerase, sigma factor [Dehalococcoides sp. CBDB1]
 gi|147669171|ref|YP_001213989.1| RpoD family RNA polymerase sigma factor [Dehalococcoides sp. BAV1]
 gi|289432439|ref|YP_003462312.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dehalococcoides
           sp. GT]
 gi|73660107|emb|CAI82714.1| RNA polymerase, sigma factor [Dehalococcoides sp. CBDB1]
 gi|146270119|gb|ABQ17111.1| RNA polymerase, sigma 70 subunit, RpoD family [Dehalococcoides sp.
           BAV1]
 gi|288946159|gb|ADC73856.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dehalococcoides
           sp. GT]
          Length = 520

 Score =  221 bits (565), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 70/242 (28%), Positives = 120/242 (49%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV +A  + G G+P+ +++ EGNIGL++AV+KFD  RGF+ +TY+ 
Sbjct: 281 KRAERHLIQANLRLVVSVAKKHIGRGMPLLDLIQEGNIGLIRAVEKFDFHRGFKFSTYAT 340

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I     +      L  +   L         P+    IA ++
Sbjct: 341 WWIRQAITRAIADQARTIRIPVHMVE--TINKLLSISRQLSQKLGREPTPD---EIALEM 395

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   +V  +        SL + I   ++  S   D++    D       +   R+  + 
Sbjct: 396 DLPPEKVREIAKVSQLPVSLESPI--GEEEDSHLGDFI---EDQNALAPPDAASRQLLKE 450

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +   +  L PRERR+ + R   E+    TLE +  EF V+RER+RQIEA+A +K++   
Sbjct: 451 QIDTVLGSLTPRERRVLQLRFGLEDGRSRTLEEVGKEFNVTRERIRQIEAKALRKLRHPS 510

Query: 285 QK 286
           + 
Sbjct: 511 RS 512



 Score = 42.5 bits (99), Expect = 0.077,   Method: Composition-based stats.
 Identities = 11/31 (35%), Positives = 20/31 (64%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE 43
           +  +  Y+HEI ++P+L  ++E  LAK+  E
Sbjct: 98  DDPVRMYLHEIGRVPLLSAEDEKTLAKKMEE 128


>gi|218438948|ref|YP_002377277.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
 gi|218171676|gb|ACK70409.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
          Length = 376

 Score =  221 bits (565), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 76/313 (24%), Positives = 140/313 (44%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS----------------------- 48
            E  +  Y+ EI +I +L  +EE  LA++  +  +L                        
Sbjct: 64  TEDSIRIYLQEIGRIRLLRAEEEIELARKIADLLELERLREKLRRSLGRYPSDKEWAEQV 123

Query: 49  ----------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 124 GMELPAFQRRLYLGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 183

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 184 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKILSQE 238

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA ++ ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 239 MRRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADGETPE 296

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
               ++  +   R  L   +  L+PRER +   R   ++    TLE +   F V+RER+R
Sbjct: 297 ----DEVSKNLLREDLENVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIR 352

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 353 QIEAKALRKLRHP 365


>gi|12483895|gb|AAG53883.1|AF275947_2 sigma factor RpoS [Escherichia coli]
          Length = 366

 Score =  221 bits (565), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 73  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 131

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 132 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 190

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    +   
Sbjct: 191 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE--- 243

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
             +  L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 244 --KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 301

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 302 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 332


>gi|297180868|gb|ADI17073.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [uncultured alpha proteobacterium HF0010_30A23]
          Length = 668

 Score =  221 bits (565), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 70/246 (28%), Positives = 115/246 (46%), Gaps = 12/246 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 424 ERDSNRAKAEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 483

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + +L    + +     +      +
Sbjct: 484 TYATWWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREATPEEL 538

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A +L +   +V  +        SL   I   D+  S   D++    D    + +E     
Sbjct: 539 AARLGMPLEKVRKVMKIAKEPISLETPI--GDEEDSHLGDFI---KDENAIIPVEAAINN 593

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R   TR +S L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 594 NLRESTTRVLSSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKL 653

Query: 281 QESIQK 286
           +   + 
Sbjct: 654 KHPSRS 659


>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 =  221 bits (565), Expect = 6e-56,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 113/247 (45%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 417 EAKMRRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 476

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T     P     +
Sbjct: 477 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGQEPDPAT---L 531

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+ + E ++  +        S+   I   D + S   D++    D       +     
Sbjct: 532 AEKMEMPEEKIRKIMKISKEPISMETPI--GDDDDSHLGDFI---EDQATLAPADAAMYS 586

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R+     +  L  RE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 587 SLRDATGEVLDSLTAREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 646

Query: 281 QESIQKQ 287
           +   + +
Sbjct: 647 RHPSRSE 653


>gi|311694174|gb|ADP97047.1| RNA polymerase, sigma 70 subunit, RpoD family [marine bacterium
           HP15]
          Length = 331

 Score =  221 bits (565), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 139/271 (51%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A+  R+ G+ S   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 63  YLNEIGFSPLLTPEEEVYFARLARK-GEESGRKRMIESNLRLVVKIARRYVNRGLTLLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNLY 180

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +T           IA+ ++   ++V  M        S++  I +  + S 
Sbjct: 181 LRAAR----ELTQKLDHEPSAEEIARMVDKPVADVKRMLGLNERVASMDTPIGAGGEKS- 235

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
              D +  +       L++     N  + L + +  L+ +++ +   R         TLE
Sbjct: 236 -LLDTVADEGASDPADLLQD---NNMCSCLEKWIDQLSDKQQEVLSRRFGLRGYPVSTLE 291

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +  E  ++RERVRQI+  A ++++E ++K+
Sbjct: 292 EVGQEIGLTRERVRQIQVEALRRLREILEKE 322


>gi|257438148|ref|ZP_05613903.1| RNA polymerase sigma factor RpoD [Faecalibacterium prausnitzii
           A2-165]
 gi|257199479|gb|EEU97763.1| RNA polymerase sigma factor RpoD [Faecalibacterium prausnitzii
           A2-165]
          Length = 461

 Score =  221 bits (565), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 73/255 (28%), Positives = 126/255 (49%), Gaps = 14/255 (5%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L ++    L K  R  G L+A   L  ++LRLVV IA  + G+ L   +++ EGNIGL+
Sbjct: 205 PLTEERRQELLK-IRRDG-LNARRSLSEANLRLVVSIAKKHVGHNLAFLDLIQEGNIGLI 262

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +A +KFD +RGFR +TY+ WWI+ A+   I      ++I     +      + R++    
Sbjct: 263 KAAEKFDCDRGFRFSTYATWWIRQAITRAIADQARTIRIPVHMVE-----TINRMRQATN 317

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
            +   N        +AK +++S   V  +        SL + +   ++  S   D++   
Sbjct: 318 QLVYQNGHEPTPEELAKAMDMSVERVREIQRMAQEPASLESPV--GEEEDSSLGDFVA-- 373

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVS 265
            D   +   +  +R      + +++  L PRE ++   R   ++  P TLE +  +F V+
Sbjct: 374 -DENAEAPGKAADRAMVAQQINQALKSLTPREEKVIRLRFGLDDGRPRTLEEVGRDFGVT 432

Query: 266 RERVRQIEARAFKKV 280
           RERVRQIEA+A +K+
Sbjct: 433 RERVRQIEAKAIRKL 447



 Score = 40.6 bits (94), Expect = 0.30,   Method: Composition-based stats.
 Identities = 14/41 (34%), Positives = 23/41 (56%), Gaps = 2/41 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRL 53
           +  +  Y+ +I +IP+L  ++E  L+KR   H    AAH L
Sbjct: 103 DDPVKNYLKQIGQIPLLSAEQEVDLSKRI--HAGAEAAHIL 141


>gi|300724640|ref|YP_003713965.1| sigma S (sigma 38) factor of RNA polymerase [Xenorhabdus
           nematophila ATCC 19061]
 gi|6643920|gb|AAF20816.1|AF198628_2 RpoS [Xenorhabdus nematophila]
 gi|297631182|emb|CBJ91877.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Xenorhabdus nematophila ATCC
           19061]
          Length = 331

 Score =  221 bits (565), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 79/271 (29%), Positives = 141/271 (52%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD++A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 62  YLGEIGFSPLLTAEEEVLFARR-ALRGDIAARQRMIESNLRLVVKISRRYSNRGLALLDL 120

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 121 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 179

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +         V  IA++L+    ++  M        S++  I  S  +  
Sbjct: 180 LRTAR----ELAHKLDHEPTVEEIAERLDKPVEDISRMMRLNERITSVDTPI--SGDSDK 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  ++D   +  I+ +   + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ALLDILSDENDSGPETTIQDD---DMKQSIVKWLFELNAKQREVLARRFGLLGYEAETLE 290

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    +++++ +  Q
Sbjct: 291 DVGREIGLTRERVRQIQVEGLRRLRDILHTQ 321


>gi|1237088|emb|CAA92648.1| major sigma factor [Rhodobacter capsulatus]
          Length = 674

 Score =  221 bits (565), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 68/242 (28%), Positives = 116/242 (47%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 434 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 493

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A+KL
Sbjct: 494 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAEKL 548

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I    +  SQ  D++    D    + ++   ++N + 
Sbjct: 549 QMPLEKVRKVMKIAKEPISLETPI--GHEEDSQLGDFI---EDKNAILPLDSAIQENLKE 603

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR +  L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 604 TTTRVLPSLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 663

Query: 285 QK 286
           + 
Sbjct: 664 RS 665


>gi|49475878|ref|YP_033919.1| RNA polymerase sigma factor RpoD [Bartonella henselae str.
           Houston-1]
 gi|49238686|emb|CAF27936.1| RNA polymerase sigma factor rpod [Bartonella henselae str.
           Houston-1]
          Length = 667

 Score =  221 bits (565), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 118/240 (49%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 429 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 488

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + I     +      ++ KL++
Sbjct: 489 IRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQILHEIGRDPTPEELSSKLSM 543

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   +   D++ S   D++    D    + I+   + N R+  
Sbjct: 544 PLEKVRKVLKIAKEPISLETPV--GDEDDSHLGDFI---EDRNALLPIDAAIQANLRDTT 598

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 599 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 658


>gi|219847826|ref|YP_002462259.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus
           aggregans DSM 9485]
 gi|219542085|gb|ACL23823.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus
           aggregans DSM 9485]
          Length = 361

 Score =  221 bits (565), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 84/299 (28%), Positives = 138/299 (46%), Gaps = 38/299 (12%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYR--------------------------EHGD 46
           E  +  Y+ EI ++P+L  +EE  LA++YR                          +   
Sbjct: 62  EDSVQLYLQEIGQVPLLTAEEEVELARQYRRGKEARQRLQNEDYANDRERMRLEIEQARG 121

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  RL+ ++LRLVV +A  Y G  +   ++V EGNIGLM+AV+KFD  +G R +TY+ 
Sbjct: 122 EEARRRLIQANLRLVVSVAKKYIGSPMAFMDLVQEGNIGLMRAVEKFDYTKGNRFSTYAT 181

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I     L+++    ++     +LRR    L+   +    PE    +A  L
Sbjct: 182 WWIRQAVTRAIAEQSRLIRLPVHLSES--IVHLRRAIYRLEQELEREPTPE---ELAHAL 236

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           N+S  +V  +        SL   +N+  +             D      +E  E+   + 
Sbjct: 237 NMSLRKVKRLLRASTQPISLEQPLNADQEGRVS-----ETLADETAASPMEIAEQNMLQA 291

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            L  +++ L  RER+I + R   L     TLE + + F ++RER RQIEA A ++++  
Sbjct: 292 ELNAALNELPERERKILQLRYGLLDGQRRTLEEVGATFGITRERTRQIEAEALRRLRHP 350


>gi|84502758|ref|ZP_01000877.1| RNA polymerase sigma factor [Oceanicola batsensis HTCC2597]
 gi|84389153|gb|EAQ01951.1| RNA polymerase sigma factor [Oceanicola batsensis HTCC2597]
          Length = 663

 Score =  221 bits (565), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 423 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 482

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A+KL
Sbjct: 483 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAEKL 537

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++N + 
Sbjct: 538 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAILPLDSAIQENLKE 592

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 593 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 652

Query: 285 QK 286
           + 
Sbjct: 653 RS 654


>gi|260062909|ref|YP_003195989.1| putative sigma factor A [Robiginitalea biformata HTCC2501]
 gi|88784477|gb|EAR15647.1| putative sigma factor A [Robiginitalea biformata HTCC2501]
          Length = 287

 Score =  221 bits (565), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 71/276 (25%), Positives = 143/276 (51%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ +I KI ++   EE  LA+R ++ GD  A  +L  ++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQDISKIDLITANEEVELAQRIKQ-GDQLALEKLTKANLRFVVSVAKQYQNQGLK 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + +     +V++        
Sbjct: 76  LPDLINEGNVGLVKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRVVRLPLNK---- 131

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
              ++ ++K     +   + +P     IAK+L+++ SEV           S++A +   +
Sbjct: 132 -IGSINKIKKTFSYLEQAHERPPSAEEIAKELDMTVSEVKQSIKNSGRHVSMDAPLR--E 188

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
              S   D L     G+     +    ++    + R++  L+PRE  + +      +   
Sbjct: 189 GEDSNLYDVL---RSGESPKPDKSLMLQSLNTEINRALETLSPREADVVKLYYGIGDQQS 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TL  +   F+++RERVRQI  +A +K++   + ++
Sbjct: 246 MTLAEIGQTFDLTRERVRQIREKAIRKLRHHSRSKL 281


>gi|301166786|emb|CBW26363.1| RNA polymerase sigma-32 factor [Bacteriovorax marinus SJ]
          Length = 350

 Score =  221 bits (565), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 99/276 (35%), Positives = 156/276 (56%), Gaps = 7/276 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             L+ Y+ EI K  +L  +EE  L ++  E GD+  A +LV ++LRLVVKIAM YR    
Sbjct: 76  DPLTAYLREISKYELLTIEEERELTQKLVETGDIEVAKKLVAANLRLVVKIAMEYRSSFQ 135

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++ EGNIGLM+AV K+DP++G +L+ Y+ WWIK+ + +YIL ++ LVKIGTT  QK
Sbjct: 136 NVMDLIQEGNIGLMKAVSKYDPDKGAKLSYYASWWIKSYILKYILDNFRLVKIGTTNEQK 195

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL---AGDESLNALI 190
           +LF+NL + K  L               +++ L VSE  V  M+ R+    G+ SL   +
Sbjct: 196 KLFYNLMKEKDRLAK----QGIEPDHKLLSENLGVSEKAVALMDGRMSSSGGELSLETPL 251

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
                +       +  D     + + + +  +  +  L   +S L  R+R IF+ R L E
Sbjct: 252 GHDSGSGVLSDILVDQDESDISEKIADAQGLEILQENLRDFVSGLKERDRDIFKKRLLSE 311

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            P +L+N++ E+ VSRER+RQIE R  K ++  + +
Sbjct: 312 VPPSLQNIADEYGVSRERIRQIEERLLKNLKVYMSE 347


>gi|300691814|ref|YP_003752809.1| RNA polymerase sigma factor rpoS [Ralstonia solanacearum PSI07]
 gi|299078874|emb|CBJ51535.1| RNA polymerase sigma factor rpoS [Ralstonia solanacearum PSI07]
          Length = 377

 Score =  221 bits (565), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 77/278 (27%), Positives = 134/278 (48%), Gaps = 11/278 (3%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
               +  Y++ I   P+L   EE   +    + G+ +A   ++  +LRLVV IA GY   
Sbjct: 101 AADTVQHYLNRISIKPLLTPAEELHFST-LAKAGEFAARQVMIERNLRLVVSIAKGYLNR 159

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           G+P+ +++ EGN+GLM A++KFDPERGFR +TY+ WWI+ +++  I+     V++     
Sbjct: 160 GVPLLDLIEEGNLGLMHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV- 218

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
             R    + R K HL+  +  + +   +  IA  L  +  EV  +        SL+    
Sbjct: 219 -IRELNQVLRAKRHLEK-SGIDGRDASIEDIAHLLGKTTDEVQDVLSLNEHTTSLDTPF- 275

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE- 250
                 +   D+L  +H        ++   +    ++   ++ L+ + R + E R     
Sbjct: 276 -DLDPGTSLLDFLSDEHGASPD---QEVAHRELSQLMKSWLARLSDKHRYVVERRFGLNH 331

Query: 251 -NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             P TLE L++E  ++RERVRQI+  A  K++     Q
Sbjct: 332 IEPATLEELAAEMGLTRERVRQIQQEALVKLKRHFASQ 369


>gi|99035119|ref|ZP_01314904.1| hypothetical protein Wendoof_01000264 [Wolbachia endosymbiont of
           Drosophila willistoni TSC#14030-0811.24]
          Length = 502

 Score =  221 bits (565), Expect = 7e-56,   Method: Composition-based stats.
 Identities = 72/260 (27%), Positives = 124/260 (47%), Gaps = 15/260 (5%)

Query: 32  QEEYVLAKRYREHGDL--SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           QE   L KR ++H      A   ++ ++LRLVV IA  Y   GL + +++ EGNIGLM+A
Sbjct: 246 QEFKELIKRIQKHEREVSEAKQEMIKANLRLVVSIAKKYSKRGLDLLDLIQEGNIGLMKA 305

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V KFD +RG++ +TY  WW++ ++   I     +V+I     +      + ++   L+ +
Sbjct: 306 VDKFDYKRGYKFSTYGTWWVRQSITRAIPEQSKVVRIPVHMVEI-----ISKINRALRKM 360

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
           T    +   +  ++ +L +    +  +        SL A     D  SS + D +    D
Sbjct: 361 THEMGREPTLEELSVELTMPLERIRKVMKIARDPVSLEAPTGKDD--SSTFGDCI---ED 415

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSR 266
            +     +     + R + T  ++ L P+E RI   R          TLE +   F V+R
Sbjct: 416 KRVSRPEDAAILADLRGITTNVLATLTPKEERILRMRFGLGKDGKEHTLEEVGKIFNVTR 475

Query: 267 ERVRQIEARAFKKVQESIQK 286
           ER+RQIEA+A +K++   + 
Sbjct: 476 ERIRQIEAKALRKLKHPSRA 495


>gi|154506043|ref|ZP_02042781.1| hypothetical protein RUMGNA_03585 [Ruminococcus gnavus ATCC 29149]
 gi|153793542|gb|EDN75962.1| hypothetical protein RUMGNA_03585 [Ruminococcus gnavus ATCC 29149]
          Length = 297

 Score =  221 bits (565), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 81/270 (30%), Positives = 141/270 (52%), Gaps = 13/270 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ EI +IP+L  +EE  L ++  E GD  A  ++  ++LRLVV +A  Y G G+  
Sbjct: 34  LKIYLKEIGRIPLLTAEEELELGRQIAE-GDTEARRKMEEANLRLVVAVAKHYAGKGMQF 92

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AV+KFD  +G + +TY++WWIK A+   +      +++     Q   
Sbjct: 93  MDLIQEGNIGLMRAVEKFDYTKGSKFSTYAVWWIKEAILRALDSQSREIRVPVRVAQ--- 149

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
             N+ ++    + +     +      IAK+L+++  EV  M   +    SL   +   D+
Sbjct: 150 --NMNKISKTERKMEQTLGREVAAEEIAKELHMTTEEVERMQSYIKNPVSLETPV--GDE 205

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--V 253
            +S  +D++    D QE    E      ++  +   +S L  +E++I   R   E+    
Sbjct: 206 ENSNLEDFI---EDTQEPTPEEAVAALVQKEEVQEMLSTLTEKEQKILRLRYGLEDGNVH 262

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQES 283
           TLE       V+RER+RQ+E+RA +K+++S
Sbjct: 263 TLEETGQILGVTRERIRQLESRALEKLRKS 292


>gi|15889446|ref|NP_355127.1| RNA polymerase sigma factor RpoD [Agrobacterium tumefaciens str.
           C58]
 gi|20141718|sp|P33452|RPOD_AGRT5 RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A;
           AltName: Full=Major vegetative sigma factor
 gi|15157308|gb|AAK87912.1| RNA polymerase sigma factor RpoD [Agrobacterium tumefaciens str.
           C58]
          Length = 684

 Score =  221 bits (565), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 69/251 (27%), Positives = 119/251 (47%), Gaps = 15/251 (5%)

Query: 41  YREHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
             + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 435 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 494

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I        +   + ++    + +     +  
Sbjct: 495 GYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREP 549

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A+KL +   +V  +        SL   +   D+  S   D++    D    + I+
Sbjct: 550 TPEELAEKLAMPLEKVRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKNALLPID 604

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              + N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+
Sbjct: 605 AAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 664

Query: 276 AFKKVQESIQK 286
           A +K++   + 
Sbjct: 665 ALRKLKHPSRS 675


>gi|89094383|ref|ZP_01167323.1| RNA polymerase sigma factor [Oceanospirillum sp. MED92]
 gi|89081275|gb|EAR60507.1| RNA polymerase sigma factor [Oceanospirillum sp. MED92]
          Length = 616

 Score =  221 bits (565), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 67/249 (26%), Positives = 114/249 (45%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 369 IGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 428

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 429 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREATPE--- 483

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + E +V  +        S+   I   D   S   D++    D      ++   
Sbjct: 484 ELAERMEMPEDKVRKVLKIAKEPISMETPI--GDDEDSSLGDFI---EDTTISSPVDSAT 538

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            +  R      ++ L  RE ++   R   E     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 539 GEGLREATREVLAGLTVRESKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALR 598

Query: 279 KVQESIQKQ 287
           K++   + +
Sbjct: 599 KLRHPSRSE 607


>gi|290476558|ref|YP_003469463.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Xenorhabdus bovienii SS-2004]
 gi|289175896|emb|CBJ82699.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Xenorhabdus bovienii SS-2004]
          Length = 331

 Score =  221 bits (565), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 81/271 (29%), Positives = 141/271 (52%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD++A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 62  YLGEIGFSPLLTAEEEVLFARR-ALRGDIAARQRMIESNLRLVVKISRRYSNRGLALLDL 120

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 121 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 179

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +         V  IA+KL+    +V  M        S++  I  S  +  
Sbjct: 180 LRTAR----ELAHKLDHEPSVEEIAEKLDRPIDDVSRMMRLNERITSVDTPI--SGDSDK 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  ++D   +  I+ +   + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ALLDILSDENDSGPETTIQDD---DMKQSIVKWLFELNAKQREVLARRFGLLGYEAETLE 290

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    +++++ +  Q
Sbjct: 291 DVGREIGLTRERVRQIQVEGLRRLRDILHTQ 321


>gi|49474476|ref|YP_032518.1| RNA polymerase sigma factor RpoD [Bartonella quintana str.
           Toulouse]
 gi|49239980|emb|CAF26393.1| RNA polymerase sigma factor rpod [Bartonella quintana str.
           Toulouse]
          Length = 670

 Score =  221 bits (565), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 118/240 (49%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 432 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 491

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + I     +      ++ KL++
Sbjct: 492 IRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQILHEIGREPTPEELSSKLSM 546

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   +   D++ S   D++    D    + I+   + N R+  
Sbjct: 547 PLEKVRKVLKIAKEPISLETPV--GDEDDSHLGDFI---EDRNALLPIDAAIQANLRDTT 601

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 602 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 661


>gi|54310169|ref|YP_131189.1| putative RNA polymerase sigma-38 factor [Photobacterium profundum
           SS9]
 gi|46914610|emb|CAG21387.1| putative RNA polymerase sigma-38 factor [Photobacterium profundum
           SS9]
          Length = 342

 Score =  221 bits (564), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 80/271 (29%), Positives = 134/271 (49%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD  A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 70  YLGEIGFSPLLTAEEEVLYARR-ALRGDEIARKRMIESNLRLVVKISRRYSNRGLALLDL 128

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 129 VEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 187

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            IA KL     +V  M        S++  I     +  
Sbjct: 188 LRTAR----ELAQKLDHEPTAEDIALKLEKPVDDVNRMLRLNERVSSVDNPI--GGDSEK 241

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D +  +  G  +   + +   + +N +   +  LNP++R +   R   L     TLE
Sbjct: 242 ALLDIIPDEKGGSPESSTQDD---DIKNSIVHWLQELNPKQREVLARRFGLLGYEASTLE 298

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    +++++ +  Q
Sbjct: 299 DVGREIGLTRERVRQIQVEGLRRLRDMLTHQ 329


>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 =  221 bits (564), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 61/242 (25%), Positives = 115/242 (47%), Gaps = 12/242 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  +++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 428 AAKQKMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 487

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I        +   + ++    +       +      +A+ ++
Sbjct: 488 WIRQAITRSIADQARTIRIPVH-----MIETINKMNRISRQYLQETGEEPDSAKLAELMD 542

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + E ++  +        S+   I   D + S   D++    D       E     + R +
Sbjct: 543 MPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDVNNVAPAEAAMYSSLREV 597

Query: 228 LTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
               +  L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   +
Sbjct: 598 TADVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTR 657

Query: 286 KQ 287
             
Sbjct: 658 SD 659


>gi|94499953|ref|ZP_01306488.1| RNA polymerase sigma factor [Oceanobacter sp. RED65]
 gi|94427811|gb|EAT12786.1| RNA polymerase sigma factor [Oceanobacter sp. RED65]
          Length = 606

 Score =  221 bits (564), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 66/249 (26%), Positives = 113/249 (45%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 360 IGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 419

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 420 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRVSRQMLQEMGREATPE--- 474

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++++ E ++  +        S+   I   D   S   D++    D      I+   
Sbjct: 475 ELAERMDMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDVNGHSPIDTAT 529

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
                +     +S L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 530 ETGLTDATRSVLSGLTARESKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 589

Query: 279 KVQESIQKQ 287
           K++   +  
Sbjct: 590 KLRHPSRSD 598


>gi|121601699|ref|YP_989245.1| RNA polymerase sigma factor RpoD [Bartonella bacilliformis KC583]
 gi|120613876|gb|ABM44477.1| RNA polymerase sigma factor RpoD [Bartonella bacilliformis KC583]
          Length = 666

 Score =  221 bits (564), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 118/240 (49%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 428 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 487

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + I     +      ++ KL++
Sbjct: 488 IRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQILHEIGREPTPEELSSKLSM 542

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   +   D++ S   D++    D    + I+   + N R+  
Sbjct: 543 PLEKVQKVLKIAKEPISLETPV--GDEDDSHLGDFI---EDRNALLPIDAAIQANLRDTT 597

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 598 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 657


>gi|298244164|ref|ZP_06967970.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297551645|gb|EFH85510.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 316

 Score =  221 bits (564), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 85/288 (29%), Positives = 151/288 (52%), Gaps = 13/288 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           ++     +     L  Y+ EI +IP+L    E  LA+R  E+G+  A + L+ ++LRLVV
Sbjct: 34  QETELSSLAQSDSLRLYLREISRIPLLSAVSESRLAER-AENGEKEARNHLIEANLRLVV 92

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA  Y G GL + +++ EGNIGL++AV KFD  +GFR +TY+ WWIK A+   IL    
Sbjct: 93  SIAKKYVGQGLSLEDLIGEGNIGLIRAVTKFDYRKGFRFSTYATWWIKQAITRAILEGTR 152

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++        +   + R+K   + +     +      I ++L ++   V  +      
Sbjct: 153 VVRLPVY-----IMEEVMRVKRTTRQLYQELGREPTPEIIGERLGMTAERVSELLIWAEK 207

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             SL+A ++  ++N+    D +    D +E+  +E  +++  R  + + +  L  RER++
Sbjct: 208 VFSLDAPLSEEEENT--LGDII---EDVRERGPMEITDQQLLREEIRKVLGQLTVRERQV 262

Query: 243 FEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            E R     ++  TLE +  + +V+RERVRQIE RA +K++     ++
Sbjct: 263 IELRFGLIDDHDHTLEEVGKKLKVTRERVRQIEERAIRKLRHPQASRI 310


>gi|262199546|ref|YP_003270755.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Haliangium
           ochraceum DSM 14365]
 gi|262082893|gb|ACY18862.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Haliangium
           ochraceum DSM 14365]
          Length = 697

 Score =  221 bits (564), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 83/297 (27%), Positives = 135/297 (45%), Gaps = 25/297 (8%)

Query: 4   KNMSIIVNGEIGLSRYIHEI-RKIPMLEKQ-----EEYVLAKRYREHGD-----LSAAHR 52
           K  ++ V+        I    +KI +LE++     EE  L + +RE  D       A   
Sbjct: 405 KRFALTVDDFDAFEAAIKNAQKKIKVLEEECRSSVEE--LRQTFREMSDGERMAERAKSE 462

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ WWI+ A
Sbjct: 463 LVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWWIRQA 522

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   I      ++I            L R   +L         PE    IA+++ +   +
Sbjct: 523 ITRAIADQARTIRIPVHM--IETINKLVRTSRYLVQELGREPTPE---EIAERMELPLDK 577

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           V  +        SL   I   ++  S   D++    D       +     N      + +
Sbjct: 578 VRKVLKIAKEPISLETPI--GEEEDSHLGDFI---EDKSVTSPSDAVISVNLAEQTRKVL 632

Query: 233 SVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           + L PRE ++   R         TLE +  +FEV+RER+RQIEA+A +K++   + +
Sbjct: 633 ATLTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLRHPSRSK 689


>gi|88858314|ref|ZP_01132956.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Pseudoalteromonas tunicata D2]
 gi|88819931|gb|EAR29744.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Pseudoalteromonas tunicata D2]
          Length = 339

 Score =  221 bits (564), Expect = 8e-56,   Method: Composition-based stats.
 Identities = 84/281 (29%), Positives = 139/281 (49%), Gaps = 13/281 (4%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           IV        Y+ EI   P+L  +EE   +++    G  ++  R++ S+LRLVVKIA  Y
Sbjct: 61  IVKNLDATQIYLGEIGFSPLLSAEEEVYFSRK-SLKGCEASRKRMIESNLRLVVKIARRY 119

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
              GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++  
Sbjct: 120 NNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPI 179

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
               K L   LR  +     +T           IA+KL+    +V  M        S++ 
Sbjct: 180 HVV-KELNVYLRTAR----ELTQKLDHEPTAEEIAEKLDRPVEDVTKMLRLNEKITSVDT 234

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR- 247
            I     +     D L  +  G  +  I+ E   + R  +   +  LN ++R +   R  
Sbjct: 235 PI--GGDSEKALLDILADEKGGGPESCIQDE---DIRENIVHWLEELNAKQREVLARRFG 289

Query: 248 -LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            L   P TLE++  E  ++RERVRQI+  A ++++E +  Q
Sbjct: 290 LLGYEPSTLEDVGKEIGLTRERVRQIQVEALRRLKEILMHQ 330


>gi|312134852|ref|YP_004002190.1| RNA polymerase, sigma 70 subunit, rpod subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|311774903|gb|ADQ04390.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Caldicellulosiruptor owensensis OL]
          Length = 273

 Score =  221 bits (564), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 76/270 (28%), Positives = 135/270 (50%), Gaps = 13/270 (4%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           +    +  +L  +EE  LAKR  E GD  A  +L  ++ RLV  IA  YRG+GL   +++
Sbjct: 9   LQAASEYELLTPEEEIELAKRI-EQGDEKAKEKLFRANKRLVANIAKRYRGFGLDYEDLM 67

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EG IGLM AV K+D  +G+R ATY+ WWI+ A+ + I  +   +++    ++      +
Sbjct: 68  QEGFIGLMNAVNKYDYRQGYRFATYATWWIRQAITKAIYNTGRNIRVPIHLHE-----QM 122

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
            +++   + +   N +   +  IAK++N S  +V  M        SL+  I   +   + 
Sbjct: 123 FKIRKVYRKLLQENNREPTIREIAKEMNWSTKKVQKMLDLFNEIVSLDTPI--GEDGLAT 180

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLEN 257
             D+++ D         E  E++     LT+    L+ +E+R+   R         TLE 
Sbjct: 181 IGDFMIDDK---AFSYFENVEKQLLVEQLTKYFDKLSEKEKRVIVLRYGLADGKGRTLEE 237

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           + +   ++RER+RQIE +A +K++ ++ K 
Sbjct: 238 VGNALNLTRERIRQIEIKALRKIRYNLLKD 267


>gi|294673737|ref|YP_003574353.1| RNA polymerase sigma factor RpoD [Prevotella ruminicola 23]
 gi|294473567|gb|ADE82956.1| putative RNA polymerase sigma factor RpoD [Prevotella ruminicola
           23]
          Length = 286

 Score =  221 bits (564), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 81/282 (28%), Positives = 148/282 (52%), Gaps = 12/282 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI K  M+  +EE  LA+R ++ GD  A  RL  ++LR VV
Sbjct: 5   KITKSITNRESAALEKYLQEISKETMISAEEEVELAQRIKK-GDTKALERLTKANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + I     
Sbjct: 64  SVAKQYQNQGLSLPDLINEGNLGLLKAAERFDETRGFKFISYAVWWIRQSILQAISEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    NQ      + R     + + +   +   V  IA+K+++ + ++         
Sbjct: 124 IVRLP--LNQVGSVNKINREINRFEQLNE---RRPSVDEIAEKVDLPQEKIDEAMAINGH 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     + N S        D    +  L+E+  +   +N    ++S LN RER +
Sbjct: 179 QISVDAPFVEGEDN-SLLDVMANSDAPLADNQLVEESLKSEIQN----ALSALNERERNV 233

Query: 243 FEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            EA      P +TLE + ++F ++RERVRQI+ +A +K++ S
Sbjct: 234 VEASYGINQPELTLEEIGTKFGLTRERVRQIKEKAIRKLRNS 275


>gi|254469018|ref|ZP_05082424.1| sigma 70 [beta proteobacterium KB13]
 gi|207087828|gb|EDZ65111.1| sigma 70 [beta proteobacterium KB13]
          Length = 658

 Score =  221 bits (564), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 67/247 (27%), Positives = 115/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 412 ESRARRAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 471

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T    +P     +
Sbjct: 472 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQATGQEPEP---AVL 526

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+ + E ++  +        S+   I   D   S   D++    D       +     
Sbjct: 527 AEKMEMPEDKIRKILKISKEPISMETPI--GDDEDSHLGDFI---EDLGTLTPDDAAVYS 581

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + RN+    +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 582 SLRNVTNEILEGLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 641

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 642 RHPTRSD 648


>gi|1519638|gb|AAB07552.1| SigB [Chloroflexus aurantiacus J-10-fl]
          Length = 346

 Score =  221 bits (564), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 83/300 (27%), Positives = 135/300 (45%), Gaps = 41/300 (13%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRL------------------- 53
           E  +  Y+ EI ++P+L  +EE  LA++Y       A  RL                   
Sbjct: 48  EDSVQLYLQEIGQVPLLTAEEEVELARQY--SRGKEARQRLRNEDSPTTANGCGWRWKWL 105

Query: 54  --------VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
                   + ++LRLVV +A  Y G  +   ++V EGNIGLM+AV+KFD  +G R +TY+
Sbjct: 106 AVKRRGGRIQANLRLVVSVAKKYIGSPMAFMDLVQEGNIGLMRAVEKFDYTKGNRFSTYA 165

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
            WWI+ A+   I     L+++    ++     +LRR    L+   +     E    +A  
Sbjct: 166 TWWIRQAVTRAIAEQSRLIRLPVHLSES--IVHLRRAIYRLEQELEREPTAE---ELAHA 220

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           LN+S  +V  +        SL   +N+  +             D      +E  E+K   
Sbjct: 221 LNMSVRKVKRLIRASTQPISLEQPLNNEQEGRVS-----ETLADETVASPMEIAEQKMLH 275

Query: 226 NMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             LT +++ L  RER+I + R         TLE + + F ++RER RQIEA A ++++  
Sbjct: 276 AELTAALNELPERERKILQLRYGLIDGQRRTLEEVGATFGITRERTRQIEAEALRRLRHP 335


>gi|289676145|ref|ZP_06497035.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. syringae
           FF5]
          Length = 438

 Score =  221 bits (564), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 69/263 (26%), Positives = 121/263 (46%), Gaps = 14/263 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L+  E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 178 LKIAEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 237

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 238 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 295

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    + +++ + E ++  +        S+   I   D   S   D++  
Sbjct: 296 LQEMGREPTPE---ELGERMEMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 348

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   Q  I+    ++ +      +S L  RE ++   R   +     TLE +  +F+V
Sbjct: 349 -EDSTMQSPIDVATVESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 407

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   + +
Sbjct: 408 TRERIRQIEAKALRKLRHPTRSE 430


>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 =  221 bits (564), Expect = 9e-56,   Method: Composition-based stats.
 Identities = 68/261 (26%), Positives = 114/261 (43%), Gaps = 12/261 (4%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L   +E        E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+
Sbjct: 361 LTAIKEINRRMSIGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMK 420

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +  
Sbjct: 421 AVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQ 478

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                  PE    + +++ + E +V  +        S+   I   D   S   D++    
Sbjct: 479 EMGREPTPE---ELGERMEMPEDKVRKVLKIAKEPISMETPI--GDDEDSHLGDFI---E 530

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSR 266
           D      +E    +         ++ L  RE ++   R   E     TLE +  +F+V+R
Sbjct: 531 DTTITSPVESATSQGLMEATKAVLAGLTAREAKVLRMRFGIEMNTDHTLEEVGKQFDVTR 590

Query: 267 ERVRQIEARAFKKVQESIQKQ 287
           ER+RQIEA+A +K++   +  
Sbjct: 591 ERIRQIEAKALRKLRHPSRSD 611


>gi|260599105|ref|YP_003211676.1| RNA polymerase sigma factor RpoS [Cronobacter turicensis z3032]
 gi|260218282|emb|CBA33240.1| RNA polymerase sigma factor rpoS [Cronobacter turicensis z3032]
          Length = 351

 Score =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 82  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYSNRGLALLDL 140

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 141 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 199

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +     +  
Sbjct: 200 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPL--GGDSEK 253

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  + D   +   +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 254 ALLDILADEKDNGPE---DTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 310

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 311 DVGREIGLTRERVRQIQVEGLRRLREILQGQ 341


>gi|71082746|ref|YP_265465.1| RNA polymerase sigma factor RpoD [Candidatus Pelagibacter ubique
           HTCC1062]
 gi|71061859|gb|AAZ20862.1| RNA polymerase sigma factor [Candidatus Pelagibacter ubique
           HTCC1062]
          Length = 595

 Score =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 68/241 (28%), Positives = 117/241 (48%), Gaps = 12/241 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 357 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 416

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + I     +      +A+KL +
Sbjct: 417 IRQAITRSIADQARTIRIPVH-----MIETINKIVRTQRLILSEFGREATPEELAQKLRM 471

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   +   D+  S   D++    D +    +E+  + N     
Sbjct: 472 PLDKVRKVLKISKEPVSLEKPV--GDEEDSSLGDFI---EDTKALAPLEQAIKSNLSEAT 526

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           T+ +S L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 527 TKILSTLTPREERVLRMRFGVGMNTDHTLEEVGLQFSVTRERIRQIEAKALRKLKHPSRS 586

Query: 287 Q 287
           +
Sbjct: 587 K 587


>gi|17545926|ref|NP_519328.1| RNA polymerase sigma factor RpoS [Ralstonia solanacearum GMI1000]
 gi|17428221|emb|CAD14909.1| rna polymerase sigma s (sigma-38) factor transcription regulator
           protein [Ralstonia solanacearum GMI1000]
          Length = 377

 Score =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 77/278 (27%), Positives = 134/278 (48%), Gaps = 11/278 (3%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
               +  Y++ I   P+L   EE   +    + G+ +A   ++  +LRLVV IA GY   
Sbjct: 101 AADTVQHYLNRISIKPLLTPAEELHFST-LAKAGEFAARQVMIERNLRLVVSIAKGYLNR 159

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           G+P+ +++ EGN+GLM A++KFDPERGFR +TY+ WWI+ +++  I+     V++     
Sbjct: 160 GVPLLDLIEEGNLGLMHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV- 218

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
             R    + R K HL+  +  + +   +  IA  L  +  EV  +        SL+    
Sbjct: 219 -IRELNQVLRAKRHLEK-SGIDGRDASIEDIAHLLGKTTEEVQDVLSLNEHTTSLDTPF- 275

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE- 250
                 +   D+L  +H        ++   +    ++   ++ L+ + R + E R     
Sbjct: 276 -DLDPGTSLLDFLSDEHGASPD---QEVAHRELSQLMKSWLARLSDKHRYVVERRFGLNH 331

Query: 251 -NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             P TLE L++E  ++RERVRQI+  A  K++     Q
Sbjct: 332 IEPATLEELAAEMGLTRERVRQIQQEALVKLKRHFASQ 369


>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 =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 64/249 (25%), Positives = 115/249 (46%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 367 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 426

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 427 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPTPE--- 481

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +++++ + E ++  +        S+   I   D   S   D++    D      ++   
Sbjct: 482 ELSERMLMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDSTIVQPLDSAT 536

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
             + +N     ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 537 GGSLKNATQEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 596

Query: 279 KVQESIQKQ 287
           K++   + +
Sbjct: 597 KLRHPSRSE 605


>gi|312129690|ref|YP_003997030.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Leadbetterella
           byssophila DSM 17132]
 gi|311906236|gb|ADQ16677.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Leadbetterella
           byssophila DSM 17132]
          Length = 287

 Score =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 71/288 (24%), Positives = 145/288 (50%), Gaps = 13/288 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           + +  I       L +Y+ EI K+ +L   EE +LA++ R+ GD  +  RL  ++LR VV
Sbjct: 5   KISKQITNRESQSLDKYLQEIGKVDLLTPDEEVILAQKIRD-GDQLSLERLTKANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A ++FD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 64  SVAKQYQNQGLSLGDLINEGNLGLIKAAQRFDETRGFKFISYAVWWIRQSILQALAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++           +L ++      +     +      +A+ L +S +EV+        
Sbjct: 124 IVRLPLNR-----VGSLNKISKTFSELEQRFEREPSPEELAEVLEISANEVVDTMKISGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     ++NS      L    +  E    ++    + R  + R++S L  RE  +
Sbjct: 179 HVSVDAPFVQGEENS-----LLDVLENDTEIRPDQELMNDSLRREVLRALSTLTQREAEV 233

Query: 243 FEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
                    E  +TLE +  +F ++RERVRQI+ +A ++++++ + + 
Sbjct: 234 IMFYFGLNGEQAMTLEEIGEKFNLTRERVRQIKEKAIRRLRQTSRSKA 281


>gi|190892699|ref|YP_001979241.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CIAT
           652]
 gi|190697978|gb|ACE92063.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CIAT
           652]
 gi|327189666|gb|EGE56814.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli
           CNPAF512]
          Length = 685

 Score =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 69/251 (27%), Positives = 119/251 (47%), Gaps = 15/251 (5%)

Query: 41  YREHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
             + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 436 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 495

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I        +   + ++    + +     +  
Sbjct: 496 GYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREP 550

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A+KL +   +V  +        SL   +   D+  S   D++    D    + I+
Sbjct: 551 TPEELAEKLAMPLEKVRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKNALLPID 605

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              + N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+
Sbjct: 606 AAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 665

Query: 276 AFKKVQESIQK 286
           A +K++   + 
Sbjct: 666 ALRKLKHPSRS 676


>gi|269104472|ref|ZP_06157168.1| RNA polymerase sigma factor RpoS [Photobacterium damselae subsp.
           damselae CIP 102761]
 gi|268161112|gb|EEZ39609.1| RNA polymerase sigma factor RpoS [Photobacterium damselae subsp.
           damselae CIP 102761]
          Length = 294

 Score =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 78/274 (28%), Positives = 141/274 (51%), Gaps = 11/274 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y+ +I   P+L K EE + +++    GD  +   ++ S+LRLVV IA  YRG G+ +
Sbjct: 18  IQLYLKDIALKPLLTKDEEILYSRK-ALVGDAKSKKVMIESNLRLVVSIAKKYRGSGMQL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           S+++ EGNIGL+ AV+KFDPERGFR +TY+ WWIK  ++  I      +++    ++   
Sbjct: 77  SDMIDEGNIGLITAVEKFDPERGFRFSTYATWWIKQTIERAIHNQARTIRLPVHVSK--- 133

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              +  +    + +   N        +A +L+ S  ++ ++    A   S +  I+S D 
Sbjct: 134 --EINTILRTHKQLMKTNNSEPTHEEVADELDKSVEDISALLSYDAPVMSFDQTISSEDS 191

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPV 253
           NS     ++  D D      I+K    + + +    +  LNPR+R I   R         
Sbjct: 192 NSQTMASFISDDSDNGPDAQIDK---NDIQKLTLTMLEGLNPRDREILCRRFGLMGYEAQ 248

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           TL+ ++ E  ++RER+RQ++  +  K++  +Q++
Sbjct: 249 TLQQVAEEVGLTRERIRQLQVSSLNKLKNVLQRE 282


>gi|270307915|ref|YP_003329973.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Dehalococcoides sp. VS]
 gi|270153807|gb|ACZ61645.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Dehalococcoides sp. VS]
          Length = 520

 Score =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 68/242 (28%), Positives = 122/242 (50%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV +A  + G G+P+ +++ EGNIGL++AV+KFD  RGF+ +TY+ 
Sbjct: 281 KRAERHLIQANLRLVVSVAKKHIGRGMPLLDLIQEGNIGLIRAVEKFDFHRGFKFSTYAT 340

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I     +      + +L    + ++    +      IA ++
Sbjct: 341 WWIRQAITRAIADQARTIRIPVHMVE-----TINKLLSISRQLSQKLGREPTPDEIALEM 395

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   +V  +        SL + I   ++  S   D++    D       +   R+  + 
Sbjct: 396 DLPPEKVREIAKVSQLPVSLESPI--GEEEDSHLGDFI---EDQNALAPPDAASRQLLKE 450

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +   +  L PRERR+ + R   E+    TLE +  EF V+RER+RQIEA+A +K++   
Sbjct: 451 QIDTVLGSLTPRERRVLQLRFGLEDGRSRTLEEVGKEFNVTRERIRQIEAKALRKLRHPS 510

Query: 285 QK 286
           + 
Sbjct: 511 RS 512



 Score = 42.5 bits (99), Expect = 0.083,   Method: Composition-based stats.
 Identities = 11/31 (35%), Positives = 20/31 (64%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE 43
           +  +  Y+HEI ++P+L  ++E  LAK+  E
Sbjct: 98  DDPVRMYLHEIGRVPLLSAEDEKTLAKKMEE 128


>gi|153839213|ref|ZP_01991880.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus AQ3810]
 gi|149747278|gb|EDM58264.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus AQ3810]
          Length = 274

 Score =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 79/272 (29%), Positives = 138/272 (50%), Gaps = 13/272 (4%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
            Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + +
Sbjct: 1   MYLGEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLVVKISRRYSNRGLALLD 59

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++      ++      K L  
Sbjct: 60  LIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTTRLPIHVV-KELNI 118

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            LR  +     ++           IA +L++   +V  M        S++  I       
Sbjct: 119 YLRTAR----ELSQKLDHEPTAEEIAAQLDIPVEDVSKMLRLNERISSVDTPI--GGDGE 172

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTL 255
               D +   ++   +V  + +   + ++ L   +  LNP+++ +   R   L   P TL
Sbjct: 173 KALLDIIPDANNSDPEVSTQDD---DIKSSLIHWLEELNPKQKEVLARRFGLLGYEPSTL 229

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 230 EEVGREIGLTRERVRQIQVEGLRRLREILIKQ 261


>gi|294787697|ref|ZP_06752941.1| 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 =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 63/263 (23%), Positives = 119/263 (45%), Gaps = 14/263 (5%)

Query: 29  LEKQEEYVLAKRY--REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           +  +E   ++K     E    +A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 388 ISIEELKEISKNMVVSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 447

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +   + ++    
Sbjct: 448 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKMNRIS 502

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +       +      +A+ + + E ++  +        S+   I   D   S   D++  
Sbjct: 503 RQYLQETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPI--GDDEDSHLGDFI-- 558

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D       +     + R +    +  L PRE ++   R   +     TLE +  +F+V
Sbjct: 559 -EDANNVAPSDAAMYSSLREVTKDVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDV 617

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   +  
Sbjct: 618 TRERIRQIEAKALRKLRHPTRSD 640


>gi|157414303|ref|YP_001485169.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9215]
 gi|157388878|gb|ABV51583.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9215]
          Length = 339

 Score =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 76/292 (26%), Positives = 139/292 (47%), Gaps = 31/292 (10%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLA--------------------KRYREHGDLSAAH 51
               +  Y+  I ++P+L   EE  LA                      Y+      A  
Sbjct: 48  ASDSIGYYLSSIGRVPLLTPAEEIELAHHVQNMKKLLQIPETERTQRNLYQIKIGKRARD 107

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ ++LRLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+ 
Sbjct: 108 RMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQ 167

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            M   I  S   +++    ++K     L +++   + ++    +    + +A ++ + + 
Sbjct: 168 GMTRAIDNSARTIRLPIHISEK-----LSKMRRVSRELSHKFGRQPTRLEMATEMGIDQK 222

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           ++  +  + A   SL+A     +  S+  +       D   +  +E  +R  ++  L   
Sbjct: 223 DLEDLISQSAPCASLDAHARGEEDRSTLGELI----PDPNCEEPMEGMDRTIQKEHLGTW 278

Query: 232 MSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +S LN RE++I + R     E P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 279 LSQLNEREQKIMKLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 330


>gi|310816221|ref|YP_003964185.1| RNA polymerase sigma factor [Ketogulonicigenium vulgare Y25]
 gi|308754956|gb|ADO42885.1| RNA polymerase sigma factor [Ketogulonicigenium vulgare Y25]
          Length = 658

 Score =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 72/242 (29%), Positives = 116/242 (47%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 418 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 477

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            L R    +         PE    +A+KL
Sbjct: 478 WWIRQAITRSIADQARTIRIPVHM--IETINKLVRTSRQMLHEIGREPTPE---ELAEKL 532

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++N + 
Sbjct: 533 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAILPLDSAIQENLKE 587

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 588 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 647

Query: 285 QK 286
           + 
Sbjct: 648 RS 649


>gi|254453216|ref|ZP_05066653.1| sigma 32 [Octadecabacter antarcticus 238]
 gi|198267622|gb|EDY91892.1| sigma 32 [Octadecabacter antarcticus 238]
          Length = 292

 Score =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 101/272 (37%), Positives = 171/272 (62%), Gaps = 6/272 (2%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
            +  K  +L+ + E  LA  +R+  D  A HRL+T+++RL + +A  +R YG P+++++ 
Sbjct: 13  RKAMKAELLDAETELALAYAWRDERDEQALHRLITAYMRLAISMASKFRRYGAPMNDLIQ 72

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           E ++GLM+A  KFDP+RG R +TY++WWIKA++Q++++R+WS+V+ G+T++QK LFFNLR
Sbjct: 73  EASLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDHVMRNWSMVRTGSTSSQKSLFFNLR 132

Query: 141 RLKGHLQAIT----DNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDK 195
           R++  L+       +   + +    IA ++ V   +V  M  RL+G D SLNA   SS+ 
Sbjct: 133 RVQARLEREAMKRGETLDRHDMRQMIATEVGVPLRDVEMMEGRLSGSDFSLNA-TQSSED 191

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
              +W D L  D +     +    +    R  L  +++ L+ RE+ I   R+L++ P TL
Sbjct: 192 EGREWIDALEDDGEQAADAVQNSHDTDTLRQWLLTALTALSDREQFIVRERKLRDAPRTL 251

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+L +E  +S+ERVRQ+EA AF K+++S++ Q
Sbjct: 252 ESLGTELSLSKERVRQLEAAAFGKMRKSLEGQ 283


>gi|118602568|ref|YP_903783.1| RNA polymerase, sigma 32 subunit, RpoH [Candidatus Ruthia magnifica
           str. Cm (Calyptogena magnifica)]
 gi|118567507|gb|ABL02312.1| RNA polymerase, sigma 32 subunit, RpoH [Candidatus Ruthia magnifica
           str. Cm (Calyptogena magnifica)]
          Length = 280

 Score =  221 bits (564), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 100/269 (37%), Positives = 170/269 (63%), Gaps = 10/269 (3%)

Query: 22  EIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           E++K P  L  ++E+ LA +  E+ DLSAA +LV SH+R V  IA GY+GYGL  +++V 
Sbjct: 17  EVQKYPPILNSEQEHELAVKLYENHDLSAARKLVLSHMRFVAFIAHGYKGYGLEQADLVQ 76

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           EG IGLM+AVK+F+P R  RLA+++++WI+A + E+I ++W +VK+ TT  Q++LFF L+
Sbjct: 77  EGTIGLMKAVKRFNPNRNVRLASFAVYWIRAEIHEFIFKNWKIVKVATTKAQRKLFFKLK 136

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
           + K H+ +    +L  EQ   IA  L V   +V+ M  RL  +   +     SD   S  
Sbjct: 137 QAKAHIYS----SLNEEQADKIANDLGVRRKDVLEMESRLQFN---DVTFEVSDDEDSLA 189

Query: 201 QDWLVYDHD--GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
            +  + + +    EQ+L+  + ++N++  L +++S L+ R   I ++R L+E   TL  L
Sbjct: 190 PEQYLTNENVQTPEQLLLINDSKQNQQQQLYKALSSLDERSLDILQSRYLKEEKTTLHTL 249

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           + ++ +S+ERVRQ+E +A +K++ ++Q+Q
Sbjct: 250 ADKYGISKERVRQLETKAMQKLKSNLQEQ 278


>gi|330721841|gb|EGG99811.1| RNA polymerase sigma factor RpoD [gamma proteobacterium IMCC2047]
          Length = 614

 Score =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 66/249 (26%), Positives = 112/249 (44%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 368 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 427

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 428 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRVSRQMLQEMGREPTPE--- 482

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + +++++ E +V  +        S+   I   D   S   D++    D      I+   
Sbjct: 483 ELGERMDMPEDKVRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDVNIDSPIDSAT 537

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            +         +S L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 538 AEGLSEATRGVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 597

Query: 279 KVQESIQKQ 287
           K++   +  
Sbjct: 598 KLRHPSRSD 606


>gi|88809396|ref|ZP_01124904.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 7805]
 gi|88786615|gb|EAR17774.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 7805]
          Length = 339

 Score =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 81/308 (26%), Positives = 149/308 (48%), Gaps = 31/308 (10%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLA--------------------KRY 41
           NR +  +       +  Y+  I ++P+L   EE  LA                    +R+
Sbjct: 38  NRSSRQVGRLSTDSIGYYLSTIGRVPLLTAAEEIELAHHVQAMKELLDVPEDERTPRQRH 97

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
           R      A  R++ ++LRLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ 
Sbjct: 98  RIRMGKRARDRMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKF 157

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY+ WWI+  M   I  S   +++    ++K     L +++   + ++    +    + 
Sbjct: 158 STYAYWWIRQGMTRAIDNSARTIRLPIHISEK-----LSKMRRITRELSHRFGRQPNRLE 212

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           ++  + ++  ++  +  + A   SL+A     +  S+  +  L+ D +G E   +E  +R
Sbjct: 213 LSNAMGIAPRDLEELIAQSAPCASLDAHARGEEDRSTLGE--LIPDPNGDE--PMEGMDR 268

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKK 279
             ++  L   +S LN RE++I   R   +   P+TL  +  +  VSRERVRQ+EA+A  K
Sbjct: 269 SIQKEHLGGWLSQLNEREQKILRLRFGLDGAEPLTLAEIGRQINVSRERVRQLEAKAILK 328

Query: 280 VQESIQKQ 287
           ++    +Q
Sbjct: 329 LRTMTDQQ 336


>gi|227822807|ref|YP_002826779.1| RNA polymerase sigma factor RpoD [Sinorhizobium fredii NGR234]
 gi|227341808|gb|ACP26026.1| RNA polymerase sigma factor RpoD [Sinorhizobium fredii NGR234]
          Length = 684

 Score =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 69/251 (27%), Positives = 119/251 (47%), Gaps = 15/251 (5%)

Query: 41  YREHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
             + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 435 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 494

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I        +   + ++    + +     +  
Sbjct: 495 GYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREP 549

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A+KL +   +V  +        SL   +   D+  S   D++    D    + I+
Sbjct: 550 TPEELAEKLAMPLEKVRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKNALLPID 604

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              + N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+
Sbjct: 605 AAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 664

Query: 276 AFKKVQESIQK 286
           A +K++   + 
Sbjct: 665 ALRKLKHPSRS 675


>gi|222086540|ref|YP_002545074.1| RNA polymerase sigma factor protein (sigma-70) [Agrobacterium
           radiobacter K84]
 gi|221723988|gb|ACM27144.1| RNA polymerase sigma factor protein (sigma-70) [Agrobacterium
           radiobacter K84]
          Length = 687

 Score =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 69/251 (27%), Positives = 119/251 (47%), Gaps = 15/251 (5%)

Query: 41  YREHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
             + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 438 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 497

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I        +   + ++    + +     +  
Sbjct: 498 GYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREP 552

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A+KL +   +V  +        SL   +   D+  S   D++    D    + I+
Sbjct: 553 TPEELAEKLAMPLEKVRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKNALLPID 607

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              + N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+
Sbjct: 608 AAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 667

Query: 276 AFKKVQESIQK 286
           A +K++   + 
Sbjct: 668 ALRKLKHPSRS 678


>gi|33861845|ref|NP_893406.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus subsp. pastoris str. CCMP1986]
 gi|33640213|emb|CAE19748.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus subsp. pastoris str. CCMP1986]
          Length = 313

 Score =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 78/302 (25%), Positives = 145/302 (48%), Gaps = 36/302 (11%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------EHG-------------------D 46
           G   +S Y+  I ++P+L   EE  L  + +      E G                    
Sbjct: 16  GNDPISWYLSNIGRVPLLTPAEEIELGNQVQKMMVLTEDGQLNEKTKEFTPQDKRTIKIG 75

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  R++ ++LRLVV +A  Y+G GL + ++V EG++GL +AV+KFDP RG++ +TY+ 
Sbjct: 76  RRAKERMMKANLRLVVSVAKKYQGKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAF 135

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ +M   I      +++    +++     L  ++   + +          + IA+ +
Sbjct: 136 WWIRQSMTRAIACQSRTIRLPVHLSER-----LATIRKISRELAHKLGAMPSRIEIAEAM 190

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   E+ S+  +     SL+A +N  D   S   D +    D   +  +++ E+K  + 
Sbjct: 191 EIDVEELDSVLRQALSTSSLDAPVN-GDDGRSFLGDLIA---DSNNEEPLDQVEQKMHQE 246

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L + +S L+ +E+ + + R   +     TL  +    EVSRERVRQ+E +A +K++   
Sbjct: 247 QLGKWLSHLSEQEQHVLKLRFGLDGNERHTLAEIGRLLEVSRERVRQVELKALRKLRNLT 306

Query: 285 QK 286
           +K
Sbjct: 307 RK 308


>gi|257056437|ref|YP_003134269.1| RNA polymerase sigma factor SigB [Saccharomonospora viridis DSM
           43017]
 gi|256586309|gb|ACU97442.1| RNA polymerase sigma factor, sigma-70 family [Saccharomonospora
           viridis DSM 43017]
          Length = 342

 Score =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 72/297 (24%), Positives = 129/297 (43%), Gaps = 38/297 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYRE--------------------------HGDLSAAHR 52
           Y++ I K  +L  +EE  LAKR                                  A + 
Sbjct: 49  YLNGIGKTALLTAEEEVDLAKRIEAGVFAQHVLDTSDDLSEERKAELSEVVRDGEEAKNH 108

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 109 LLQANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQA 168

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +      +++     ++     L R+K  L          E    +A +  ++E +
Sbjct: 169 ITRGMADQGRTIRLPVHLVEQ--VNKLARIKRDLHQRLGREATHE---ELAAESGIAEKK 223

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           V  +        SL+  +       +   D++    D +             ++ L R +
Sbjct: 224 VADLLDHARDPVSLDMPV--GADEDAPLGDFI---EDSEAANAENSVISTLLQDDLRRVL 278

Query: 233 SVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           + L+ RE  +   R   ++  P TL+ +   F +SRERVRQIE     K++   +  
Sbjct: 279 ATLDDREEHVIRLRYGLDDGQPRTLDQIGKHFSLSRERVRQIEREVMAKLRHGERAD 335


>gi|325293528|ref|YP_004279392.1| RNA polymerase sigma factor RpoD [Agrobacterium sp. H13-3]
 gi|325061381|gb|ADY65072.1| RNA polymerase sigma factor RpoD [Agrobacterium sp. H13-3]
          Length = 684

 Score =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 69/251 (27%), Positives = 119/251 (47%), Gaps = 15/251 (5%)

Query: 41  YREHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
             + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 435 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 494

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I        +   + ++    + +     +  
Sbjct: 495 GYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREP 549

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A+KL +   +V  +        SL   +   D+  S   D++    D    + I+
Sbjct: 550 TPEELAEKLAMPLEKVRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKNALLPID 604

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              + N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+
Sbjct: 605 AAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 664

Query: 276 AFKKVQESIQK 286
           A +K++   + 
Sbjct: 665 ALRKLKHPSRS 675


>gi|319898528|ref|YP_004158621.1| RNA polymerase sigma factor [Bartonella clarridgeiae 73]
 gi|319402492|emb|CBI76035.1| RNA polymerase sigma factor [Bartonella clarridgeiae 73]
          Length = 669

 Score =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 119/240 (49%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 431 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 490

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + I     +      ++ KL++
Sbjct: 491 IRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQILHEIGREPTPEELSSKLSM 545

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   +   D+++S   D++    D    + I+   + N R+  
Sbjct: 546 PLEKVRKVLKIAKEPISLETPV--GDEDASHLGDFI---EDRNALLPIDAAIQANLRDTT 600

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 601 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 660


>gi|323345452|ref|ZP_08085675.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella oralis
           ATCC 33269]
 gi|323093566|gb|EFZ36144.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella oralis
           ATCC 33269]
          Length = 295

 Score =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 76/285 (26%), Positives = 147/285 (51%), Gaps = 12/285 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI    ++  +EE  LA+R R+ GD  A  +L  ++LR VV
Sbjct: 14  KITKSITNRESASLDKYLQEIGHEELISVEEEVELAQRIRK-GDRKALEKLTKANLRFVV 72

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + I     
Sbjct: 73  SVAKQYQNQGLSLPDLINEGNVGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSR 132

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++           ++ ++   L      N +   +  IA ++++ E ++I        
Sbjct: 133 IVRLPLNQ-----VGSVNKINRALNKFEQENERHPSIEEIADRIDLPEEKIIDAMKINGK 187

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     + NS      L    + +     E+   ++ R+ ++R + +LN RER I
Sbjct: 188 HISVDAPFAEGEDNS-----LLDIMPNTESPTADERLVSESLRDEISRVLLLLNERERMI 242

Query: 243 FEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            EA        +TLE +  +F ++RERVRQI+ +A ++++ + + 
Sbjct: 243 IEAFFGINQQDMTLEEIGDKFGLTRERVRQIKEKAIRRLRNNTKS 287


>gi|304322159|ref|YP_003855802.1| RNA polymerase sigma factor [Parvularcula bermudensis HTCC2503]
 gi|303301061|gb|ADM10660.1| RNA polymerase sigma factor [Parvularcula bermudensis HTCC2503]
          Length = 650

 Score =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 69/240 (28%), Positives = 117/240 (48%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 412 AKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 471

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + I +   +      +A KL++
Sbjct: 472 IRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQILNEIGREPTPEELAAKLSM 526

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   I   D+  S   D++    D    + I+   + N R   
Sbjct: 527 PLEKVRKVMKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAILPIDAAIQSNLRETT 581

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 582 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 641


>gi|284052417|ref|ZP_06382627.1| RNA polymerase sigma factor RpoD [Arthrospira platensis str.
           Paraca]
 gi|291570496|dbj|BAI92768.1| principal RNA polymerase sigma factor SigA [Arthrospira platensis
           NIES-39]
          Length = 387

 Score =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 76/313 (24%), Positives = 139/313 (44%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS----------------------- 48
            E  +  Y+ EI +I +L   EE  LA++  +  +L                        
Sbjct: 75  TEDSIRLYLQEIGRIRLLRADEEIELARKIADLLELERIREKLIEHYHREPNEKEWANAV 134

Query: 49  ----------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 135 DMRLPEFRRRLFLGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 194

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 195 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKLLSQE 249

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA ++ ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 250 MGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIESDGETPE 307

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
               ++  +   R  L   +  L+PRER +   R   ++    TLE +   F V+RER+R
Sbjct: 308 ----DQVSKNLLREDLESVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIR 363

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 364 QIEAKALRKLRHP 376


>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 =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 68/247 (27%), Positives = 113/247 (45%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 401 EAKARRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 460

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T     P     +
Sbjct: 461 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEADPAT---L 515

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           AKK+ + E ++  +        S+   I   D + S   D++    D       E     
Sbjct: 516 AKKMEMPEEKIRKILKISKEPISMETPI--GDDDDSHLGDFI---EDHATLAPTEAALYS 570

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R +    +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 571 SLRFITKDVLDTLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 630

Query: 281 QESIQKQ 287
           +   +  
Sbjct: 631 RHPSRSD 637


>gi|91070600|gb|ABE11500.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [uncultured Prochlorococcus marinus clone HOT0M-8F9]
          Length = 340

 Score =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 75/292 (25%), Positives = 139/292 (47%), Gaps = 31/292 (10%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLA--------------------KRYREHGDLSAAH 51
               +  Y+  I ++P+L   EE  LA                      Y+      +  
Sbjct: 49  ASDSIGYYLSSIGRVPLLTPAEEIELAHHVQNMKKLLQIPETDRTQRNLYQIKIGKKSRD 108

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ ++LRLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+ 
Sbjct: 109 RMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQ 168

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            M   I  S   +++    ++K     L +++   + ++    +    + +A ++ + + 
Sbjct: 169 GMTRAIDNSARTIRLPIHISEK-----LSKMRRVSRELSHKFGRQPTRLEMATEMGIDQK 223

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           ++  +  + A   SL+A     +  S+  +       D   +  +E  +R  ++  L   
Sbjct: 224 DLEDLISQSAPCASLDAHARGEEDRSTLGELI----PDPNCEEPMEGMDRTIQKEHLGTW 279

Query: 232 MSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +S LN RE++I + R     E P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 280 LSQLNEREQKIMKLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 331


>gi|254459542|ref|ZP_05072958.1| sigma 32 [Rhodobacterales bacterium HTCC2083]
 gi|206676131|gb|EDZ40618.1| sigma 32 [Rhodobacteraceae bacterium HTCC2083]
          Length = 292

 Score =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 101/286 (35%), Positives = 177/286 (61%), Gaps = 9/286 (3%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M++   G+   SR      K  ML+ + E  LA  +R+    ++ HRL+ +++RL + +A
Sbjct: 1   MALDNAGDARFSR---RAMKAEMLDAETELKLAYAWRDERCEASLHRLINAYMRLAISMA 57

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             +R YG P+++++ E  +GLM+A  KFDP+RG R +TY++WWIKA++Q++++R+WS+V+
Sbjct: 58  SKFRRYGAPLNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDHVMRNWSMVR 117

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNL----KPEQVVAIAKKLNVSESEVISMNCRLA 181
            G+T++QK LFFN+RR++  L+           + +    I+ ++ V  ++V  M+ RL+
Sbjct: 118 TGSTSSQKSLFFNMRRVQARLEREAQQRGEALDRHQLHQMISTEIGVPLNDVEMMHGRLS 177

Query: 182 G-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           G D SLNA   S +    +W D L  D    E+++  + +    R  L  +M+ LN RER
Sbjct: 178 GSDFSLNA-TQSVEDEGREWIDALEDDGAQAEEIVENEHDTAQMREWLLGAMNALNERER 236

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            I   R+L + P TLE+L +E  +S+ER+RQ+EA AF+K++++++ 
Sbjct: 237 FIVRERKLLDEPRTLESLGNELGLSKERIRQLEAAAFQKMRKTLEA 282


>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 =  221 bits (563), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 65/276 (23%), Positives = 127/276 (46%), Gaps = 14/276 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           L + ++ + +   L   +   + +     E     A   ++ ++LRLV+ IA  Y   GL
Sbjct: 332 LQKRLNTVARDSKLTVAQTREVHRLITLGEAKARRAKKEMIEANLRLVISIAKKYTNRGL 391

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I       
Sbjct: 392 QFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--I 449

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R+   +         PE    +A+++++ E ++  +        S+   I   
Sbjct: 450 ETINKLNRISRQMLQEMGREATPE---ELAERMDLPEDKIRKVLKIAKEPISMETPI--G 504

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQEN 251
           + + S   D++    D      ++     +   ++   ++ L PRE ++   R       
Sbjct: 505 EDDDSNLGDFI---EDQSAISPMDSATNASLSEIVREILASLTPREAKVLMMRFGIGMNT 561

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 562 DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 597


>gi|330446961|ref|ZP_08310612.1| RNA polymerase sigma factor RpoS [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
 gi|328491152|dbj|GAA05109.1| RNA polymerase sigma factor RpoS [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
          Length = 333

 Score =  220 bits (562), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 79/271 (29%), Positives = 135/271 (49%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD  A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 62  YLGEIGYSPLLTAEEEVLYARR-ALRGDEVARKRMIESNLRLVVKISRRYSNRGLALLDL 120

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 121 VEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 179

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            IA++L     +V  M        S++  I     +  
Sbjct: 180 LRTAR----ELAQKLDHEPTAEDIAQQLEKPVDDVNRMLRLNERVSSVDNPI--GGDSEK 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D +  +  G  +   + +   + +N +   +  LNP++R +   R   L     TLE
Sbjct: 234 ALLDIIPDEKGGSPESSTQDD---DIKNSIVHWLQELNPKQREVLARRFGLLGYEASTLE 290

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    +++++ +  Q
Sbjct: 291 DVGREIGLTRERVRQIQVEGLRRLRDMLTHQ 321


>gi|220906934|ref|YP_002482245.1| RNA polymerase sigma-70 subunit RpoD subfamily [Cyanothece sp. PCC
           7425]
 gi|219863545|gb|ACL43884.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7425]
          Length = 378

 Score =  220 bits (562), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 78/313 (24%), Positives = 140/313 (44%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAK-------------------------------- 39
            E  +  Y+ EI +I +L   EE  LA+                                
Sbjct: 66  TEDSIRLYLQEIGRIRLLRADEEIELARKIADLLELERIREQLYDKLDREPQDQEWAGEV 125

Query: 40  -------RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                  R+R H    A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 126 DMPLQSFRHRLHIGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 185

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 186 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKLLSQE 240

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA ++ ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 241 MGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIESDGETPE 298

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
               ++  +   R  L   +  L+PRER + + R   ++    TLE +   F V+RER+R
Sbjct: 299 ----DQVSKNLLREDLETVLCTLSPRERDVLKLRYGLDDGRMKTLEEIGQLFNVTRERIR 354

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 355 QIEAKALRKLRHP 367


>gi|149915381|ref|ZP_01903908.1| RNA polymerase sigma factor [Roseobacter sp. AzwK-3b]
 gi|149810670|gb|EDM70511.1| RNA polymerase sigma factor [Roseobacter sp. AzwK-3b]
          Length = 292

 Score =  220 bits (562), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 99/271 (36%), Positives = 169/271 (62%), Gaps = 6/271 (2%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
               +  +L+ + E  LA  +R+  D  A HRL+T+++RL + +A  +R YG P+++++ 
Sbjct: 13  RTAMRAELLDAETELKLAYAWRDQRDEEALHRLITAYMRLAISMASKFRRYGAPMNDLIQ 72

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           E  +GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFN+R
Sbjct: 73  EAGLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMR 132

Query: 141 RLKGHLQAIT----DNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDK 195
           R++  ++       +     +    IA ++ V   +V  M  RL+G D SLNA   S + 
Sbjct: 133 RVQARIEREAMAKGEQLDGHQLREMIAHEVGVPLRDVEMMEGRLSGTDFSLNA-TQSVED 191

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
              +W D +  +    +Q++ +  +    R  L  +MS LN RER I   R+L++ P TL
Sbjct: 192 EGREWIDTIEDEGPRGDQLVEQDHDLMALREWLGDAMSKLNDRERFIVRERKLRDVPRTL 251

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E+L  E  +S+ERVRQ+EA AF+K+++ +++
Sbjct: 252 ESLGEELNLSKERVRQLEAAAFQKMRKHLER 282


>gi|114770145|ref|ZP_01447683.1| RNA polymerase sigma factor [alpha proteobacterium HTCC2255]
 gi|114548982|gb|EAU51865.1| RNA polymerase sigma factor [alpha proteobacterium HTCC2255]
          Length = 294

 Score =  220 bits (562), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 96/277 (34%), Positives = 173/277 (62%), Gaps = 6/277 (2%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
               K  ML+   EY LA  +R+H D  A HRL+ +++RL + +A  +R YG+   +++ 
Sbjct: 13  KTAMKAEMLDVDTEYKLAIAWRDHKDEDALHRLINAYMRLAISMASKFRRYGVSQQDLIQ 72

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           E  +GLM+A  KFDP++G R +TY+ WW+KA++Q++++R++S+V+ G+T NQK LFFN++
Sbjct: 73  EAGMGLMKAADKFDPDKGVRFSTYAQWWVKASIQDFVMRNYSMVRTGSTTNQKSLFFNIK 132

Query: 141 RLKGHLQAIT---DNNLKPEQVVA-IAKKLNVSESEVISMNCRL-AGDESLNALINSSDK 195
           R+K  L+      +  + P Q++  ++ +L V   +V+ MN R+  GD SLNA I S+D 
Sbjct: 133 RVKAQLERDAVQNNQTVTPAQILEQVSTELGVPMRDVMMMNGRMSGGDMSLNA-IQSNDD 191

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
              +W + L  +  G  +++ +  + +  +  + +SM VLN RE+ I   R++ ++P TL
Sbjct: 192 EGREWIETLADEAPGGAEIVEQSFDEEKLKIWIGQSMEVLNEREKYIVIQRKMIDSPRTL 251

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
           E++  E ++S+ER+RQIE  A +K+++ +      ++
Sbjct: 252 ESIGVELKLSKERIRQIENAALEKLKKRMGSDGHHAA 288


>gi|150397423|ref|YP_001327890.1| RNA polymerase sigma factor RpoD [Sinorhizobium medicae WSM419]
 gi|150028938|gb|ABR61055.1| RNA polymerase, sigma 70 subunit, RpoD [Sinorhizobium medicae
           WSM419]
          Length = 684

 Score =  220 bits (562), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 69/251 (27%), Positives = 119/251 (47%), Gaps = 15/251 (5%)

Query: 41  YREHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
             + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 435 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 494

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I        +   + ++    + +     +  
Sbjct: 495 GYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREP 549

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A+KL +   +V  +        SL   +   D+  S   D++    D    + I+
Sbjct: 550 TPEELAEKLAMPLEKVRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKNALLPID 604

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              + N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+
Sbjct: 605 AAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 664

Query: 276 AFKKVQESIQK 286
           A +K++   + 
Sbjct: 665 ALRKLKHPSRS 675


>gi|73541783|ref|YP_296303.1| RNA polymerase sigma factor RpoS [Ralstonia eutropha JMP134]
 gi|72119196|gb|AAZ61459.1| Sigma-70 region 1.2 [Ralstonia eutropha JMP134]
          Length = 391

 Score =  220 bits (562), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 79/278 (28%), Positives = 132/278 (47%), Gaps = 11/278 (3%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
               +  Y++ I   P+L   EE   +    + GD SA   ++  +LRLVV IA GY   
Sbjct: 115 AADTVQHYLNRISIKPLLSAPEELHFST-LAKDGDFSARQVMIERNLRLVVSIAKGYLNR 173

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           G+P+ +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++     
Sbjct: 174 GVPLLDLIEEGNLGLMHAIEKFDPSRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV- 232

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
             R    + R K HL+     + +   +  IA  L  +  EV  +        SL+    
Sbjct: 233 -IRELNQVLRAKRHLEK-GGTDGRDASLEDIAHLLGKTPDEVQDVLALNEHTTSLDTPF- 289

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE- 250
                 S   D+L  +H+       ++   +    ++   ++ L+ + R + E R     
Sbjct: 290 -DLDPGSSLLDFLSDEHNAAPD---QEVAHRELEGLMKLWLARLSEKHRYVVERRFGLNH 345

Query: 251 -NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             P TLE L+ E  ++RERVRQI+  A  K++     Q
Sbjct: 346 IEPATLEELAEEMGLTRERVRQIQQEALVKLKRHFASQ 383


>gi|86143196|ref|ZP_01061598.1| putative sigma factor A [Leeuwenhoekiella blandensis MED217]
 gi|85830101|gb|EAQ48561.1| putative sigma factor A [Leeuwenhoekiella blandensis MED217]
          Length = 288

 Score =  220 bits (562), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 73/276 (26%), Positives = 146/276 (52%), Gaps = 12/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L+ Y+ ++ K+ M+   EE  LA+R RE GD  A  RL  ++LR VV +A  Y+  GL 
Sbjct: 17  SLNTYLQDVSKLDMITADEEVELAQRIRE-GDQVALERLTKANLRFVVSVAKQYQNQGLK 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + I      V++    N+  
Sbjct: 76  LPDLINEGNVGLVKAAKRFDETRGFKFISYAVWWIRQSILQAISEHSRTVRLP--LNKIG 133

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               + +   +L+   +   +P     IAK+L+++ ++V         + S++A     +
Sbjct: 134 TISKINKAFSYLEQSLE---RPPSAEEIAKELDMTVAKVKLAMKNSGRNLSMDAPFKEGE 190

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENP 252
            +S+ +      +    +  L+++         + R++  L+PRE  + +       E P
Sbjct: 191 NDSNLYDVLKSGESPNPDADLMQESLGTE----IERALETLSPRESDVIKLNYGLGGEQP 246

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            TL+ +   F++SRERVRQI  +  ++++ + + +V
Sbjct: 247 HTLQEIGEMFDLSRERVRQIREKGIRRLRHTSRSKV 282


>gi|312891071|ref|ZP_07750594.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Mucilaginibacter
           paludis DSM 18603]
 gi|311296379|gb|EFQ73525.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Mucilaginibacter
           paludis DSM 18603]
          Length = 285

 Score =  220 bits (562), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 74/288 (25%), Positives = 147/288 (51%), Gaps = 14/288 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           + + SI       L +Y+ EI K+ ++   EE +LA++ RE GD +A  RL  ++LR VV
Sbjct: 5   KISQSITNRESQSLDKYLTEIGKVDLITADEEVILAQKIRE-GDQAALERLTKTNLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A K+FD  +GF+  +Y++WWI+ ++   +     
Sbjct: 64  SVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETKGFKFISYAVWWIRQSILSAVAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    NQ      +R+    L+   +          +A  L  +E ++         
Sbjct: 124 IVRLP--LNQIGSLNKIRQAFSKLEQQYERE---PSQAELADILETTEDKICDSLSNSGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     ++N+    D L  +    +  L+E+   +     + RS+  L  RER +
Sbjct: 179 HVSMDAPFVQGEENT--LLDVLQNNEPTTDDYLMEESLSQE----IMRSLVTLAEREREV 232

Query: 243 FEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
                   N  P++LE +  ++ ++RERVRQI+ +A ++++ + +  +
Sbjct: 233 IVLFFGLGNNYPLSLEEIGEKYNLTRERVRQIKDKALQRLRHTSRSNL 280


>gi|254416030|ref|ZP_05029786.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
 gi|196177205|gb|EDX72213.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
          Length = 380

 Score =  220 bits (562), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 76/313 (24%), Positives = 139/313 (44%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS----------------------- 48
            E  +  Y+ EI +I +L   EE  LA++  +  +L                        
Sbjct: 68  TEDSIRLYLQEIGRIRLLRADEEIELARKIADLLELERIRDRLYDQLEREPKEGEWAKEV 127

Query: 49  ----------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 128 EMELPAFRQRLFLGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 187

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 188 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKILSQE 242

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA ++ ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 243 LGRKPTEEEIADRMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADGETPE 300

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
               ++  +   R  L   +  L+PRER +   R   ++    TLE +   F V+RER+R
Sbjct: 301 ----DQVSKNLLREDLESVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIR 356

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 357 QIEAKALRKLRHP 369


>gi|115375627|ref|ZP_01462884.1| sigma factor [Stigmatella aurantiaca DW4/3-1]
 gi|310823184|ref|YP_003955542.1| RNA polymerase sigma factor rpod [Stigmatella aurantiaca DW4/3-1]
 gi|115367403|gb|EAU66381.1| sigma factor [Stigmatella aurantiaca DW4/3-1]
 gi|309396256|gb|ADO73715.1| RNA polymerase sigma factor RpoD [Stigmatella aurantiaca DW4/3-1]
          Length = 706

 Score =  220 bits (562), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 77/268 (28%), Positives = 120/268 (44%), Gaps = 22/268 (8%)

Query: 32  QEEYVL----------AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           +EE  L          A R  E     A   LV ++LRLVV IA  Y   GL   +++ E
Sbjct: 441 EEEANLPVDALRRNYDAIRLGERRAERAKSELVEANLRLVVSIAKKYTNRGLQFLDLIQE 500

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           GNIGLM+AV KF+ +RG++ +TY+ WWI+ A+   I      ++I            L R
Sbjct: 501 GNIGLMKAVDKFEYKRGYKFSTYATWWIRQAITRAIADQARTIRIPVHM--IETINKLIR 558

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
              +L         PE    IA+K+ +   +V  +        SL   I   ++  S   
Sbjct: 559 TSRYLVQEIGREPTPE---EIAEKMELPLDKVRKVLKIAKEPISLETPI--GEEEDSHLG 613

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLS 259
           D++    D       +     N      + ++ L PRE ++   R         TLE + 
Sbjct: 614 DFI---EDKSLVSPADAVINMNLAEQTRKVLATLTPREEKVLRMRFGIGEKSDHTLEEVG 670

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +FEV+RER+RQIEA+A +K++   + +
Sbjct: 671 QDFEVTRERIRQIEAKALRKLRHPSRSK 698


>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 =  220 bits (562), Expect = 1e-55,   Method: Composition-based stats.
 Identities = 68/259 (26%), Positives = 119/259 (45%), Gaps = 14/259 (5%)

Query: 33  EEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           E   + +R    E     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV
Sbjct: 449 ELKEINRRMSTGEAKARRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 508

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
            KF+  RG++ +TY+ WWI+ A+   I      ++I            + R+   +   T
Sbjct: 509 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQET 566

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
               +P     +A+K+ + E ++  +        S+   I   D   S   D++    D 
Sbjct: 567 GQEPEP---AVLAQKMEMPEEKIRKILKISKEPISMETPI--GDDEDSHLGDFI---EDS 618

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRER 268
                 +     + R++    +  L PRE ++   R   E     TLE +  +F+V+RER
Sbjct: 619 ATMAPADAAVYASLRDVTKDILDSLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRER 678

Query: 269 VRQIEARAFKKVQESIQKQ 287
           +RQIEA+A +K++   + +
Sbjct: 679 IRQIEAKALRKLRHPSRSE 697


>gi|123966683|ref|YP_001011764.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9515]
 gi|123201049|gb|ABM72657.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9515]
          Length = 313

 Score =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 77/302 (25%), Positives = 145/302 (48%), Gaps = 36/302 (11%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------EHG-------------------D 46
           G   +S Y+  I ++P+L   EE  L  + +      E G                    
Sbjct: 16  GNDPISWYLSNIGRVPLLTPAEEIELGNQVQKMMTLTEDGQLNEKTKEFTPQQKRTIKIG 75

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  R++ ++LRLVV +A  Y+G GL + ++V EG++GL +AV+KFDP RG++ +TY+ 
Sbjct: 76  RRAKERMMKANLRLVVSVAKKYQGKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAF 135

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ +M   I      +++    +++     L  ++   + +          + IA+ +
Sbjct: 136 WWIRQSMTRAIACQSRTIRLPVHLSER-----LATIRKVSRELAHKLGAMPSRIEIAEAM 190

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   E+ S+  +     SL+A +N  D   S   D +    D   +  +++ E+K  + 
Sbjct: 191 EIDVEELDSVLRQALSTSSLDAPVN-GDDGRSFLGDLIA---DSNNEEPLDQVEQKMHQE 246

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L + ++ L+ +E+ + + R   +     TL  +    EVSRERVRQ+E +A +K++   
Sbjct: 247 QLGKWLTHLSEQEQHVLKLRFGLDGNERHTLAEIGRLLEVSRERVRQVELKALRKLRNLT 306

Query: 285 QK 286
           +K
Sbjct: 307 RK 308


>gi|114562238|ref|YP_749751.1| RNA polymerase, sigma 28 subunit [Shewanella frigidimarina NCIMB
           400]
 gi|114333531|gb|ABI70913.1| RNA polymerase, sigma 28 subunit [Shewanella frigidimarina NCIMB
           400]
          Length = 323

 Score =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 82/271 (30%), Positives = 140/271 (51%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   +++    G   + +R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 54  YLGEIGFSPLLTAEEEVFFSRK-SLKGCEKSRNRMIESNLRLVVKISRRYNNRGLALLDL 112

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 113 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 171

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            IA+KL+VS  +V  M        S+++ +  S  N  
Sbjct: 172 LRTAR----QLAQKLDHEPTAEEIAEKLDVSTGDVSRMLKLNERITSVDSPL--SGDNEK 225

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D +  D        ++ E+  N    +   ++ LN ++R +   R   L   P TLE
Sbjct: 226 ALLDVIADDDSVGPDYRVQNEDLSNS---IVGWLNELNTKQREVLARRFGLLGYEPSTLE 282

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           N+ +E  ++RERVRQI+  A K++++ +  Q
Sbjct: 283 NVGAEIGLTRERVRQIQVEALKRLKDLLGSQ 313


>gi|239996603|ref|ZP_04717127.1| RNA polymerase sigma factor [Alteromonas macleodii ATCC 27126]
          Length = 382

 Score =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 63/249 (25%), Positives = 115/249 (46%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 136 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 195

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 196 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPTPE--- 250

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +++++ + E ++  +        S+   I   D   S   D++    D      ++   
Sbjct: 251 ELSERMLMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDSTIIQPLDSAT 305

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
             + ++     ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 306 GGSLKDATQEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 365

Query: 279 KVQESIQKQ 287
           K++   + +
Sbjct: 366 KLRHPSRSE 374


>gi|57234646|ref|YP_181295.1| RNA polymerase sigma factor RpoD [Dehalococcoides ethenogenes 195]
 gi|57225094|gb|AAW40151.1| RNA polymerase sigma factor RpoD [Dehalococcoides ethenogenes 195]
          Length = 520

 Score =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 68/242 (28%), Positives = 122/242 (50%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV +A  + G G+P+ +++ EGNIGL++AV+KFD  RGF+ +TY+ 
Sbjct: 281 KRAERHLIQANLRLVVSVAKKHIGRGMPLLDLIQEGNIGLIRAVEKFDFHRGFKFSTYAT 340

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I     +      + +L    + ++    +      IA ++
Sbjct: 341 WWIRQAITRAIADQARTIRIPVHMVE-----TINKLLSISRQLSQKLGREPTPDEIAVEM 395

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   +V  +        SL + I   ++  S   D++    D       +   R+  + 
Sbjct: 396 DLPPEKVREIAKVSQLPVSLESPI--GEEEDSHLGDFI---EDQNALAPPDAASRQLLKE 450

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +   +  L PRERR+ + R   E+    TLE +  EF V+RER+RQIEA+A +K++   
Sbjct: 451 QIDTVLGSLTPRERRVLQLRFGLEDGRSRTLEEVGKEFNVTRERIRQIEAKALRKLRHPS 510

Query: 285 QK 286
           + 
Sbjct: 511 RS 512



 Score = 42.5 bits (99), Expect = 0.084,   Method: Composition-based stats.
 Identities = 11/31 (35%), Positives = 20/31 (64%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE 43
           +  +  Y+HEI ++P+L  ++E  LAK+  E
Sbjct: 98  DDPVRMYLHEIGRVPLLSAEDEKTLAKKMEE 128


>gi|189183187|ref|YP_001936972.1| RNA polymerase sigma factor RpoD [Orientia tsutsugamushi str.
           Ikeda]
 gi|189179958|dbj|BAG39738.1| RNA polymerase sigma factor RpoD [Orientia tsutsugamushi str.
           Ikeda]
          Length = 615

 Score =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 72/273 (26%), Positives = 132/273 (48%), Gaps = 14/273 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
           Y  EI +  +L  +    + +  +  E     A  ++V S+ RLVV +A  Y   GLP  
Sbjct: 334 YFSEIEQAMLLPLKRFKEIIQAIQNGERKVRVAKKKMVESNTRLVVHVAKPYVNRGLPFL 393

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++ EGNIGLM+AV K++   G++ +T + WW++ ++   +      ++I          
Sbjct: 394 DLIQEGNIGLMKAVDKYNYLLGYKFSTCATWWVRQSISRAVADQARTIRIPVHMAD---- 449

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
             + ++    + + +          IA+KL++   +V  +        SL   I   +++
Sbjct: 450 -TISKIVRVSKQMHNELGYEPTASEIAEKLSMPIDKVKKVMRIAKEPVSLENPI--GEED 506

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VT 254
            S   D++    D    + IE+  + + R   TR++S L  RE R+   R     P   T
Sbjct: 507 GSCLSDFI---EDKNAILPIEEAIKFSLRETTTRALSTLTAREERVLRLRFGIGLPTDYT 563

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           LE +  EF+V+RERVRQIEA+A +K++  ++ +
Sbjct: 564 LEEVGGEFKVTRERVRQIEAKALRKLKHPVRSK 596


>gi|116253144|ref|YP_768982.1| RNA polymerase sigma factor RpoD [Rhizobium leguminosarum bv.
           viciae 3841]
 gi|115257792|emb|CAK08890.1| putative RNA polymerase sigma factor RpoD [Rhizobium leguminosarum
           bv. viciae 3841]
          Length = 685

 Score =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 69/251 (27%), Positives = 119/251 (47%), Gaps = 15/251 (5%)

Query: 41  YREHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
             + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 436 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 495

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I        +   + ++    + +     +  
Sbjct: 496 GYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREP 550

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A+KL +   +V  +        SL   +   D+  S   D++    D    + I+
Sbjct: 551 TPEELAEKLAMPLEKVRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKNALLPID 605

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              + N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+
Sbjct: 606 AAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 665

Query: 276 AFKKVQESIQK 286
           A +K++   + 
Sbjct: 666 ALRKLKHPSRS 676


>gi|15966067|ref|NP_386420.1| RNA polymerase sigma factor RpoD [Sinorhizobium meliloti 1021]
 gi|307305622|ref|ZP_07585369.1| RNA polymerase, sigma 70 subunit, RpoD [Sinorhizobium meliloti
           BL225C]
 gi|307317625|ref|ZP_07597064.1| RNA polymerase, sigma 70 subunit, RpoD [Sinorhizobium meliloti
           AK83]
 gi|7388096|sp|Q59753|RPOD_RHIME RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A;
           AltName: Full=Major vegetative sigma factor
 gi|1050336|gb|AAA88524.1| sigma factor [Sinorhizobium meliloti]
 gi|15075337|emb|CAC46893.1| RNA polymerase sigma factor transcription regulation protein
           [Sinorhizobium meliloti 1021]
 gi|306896783|gb|EFN27530.1| RNA polymerase, sigma 70 subunit, RpoD [Sinorhizobium meliloti
           AK83]
 gi|306902325|gb|EFN32921.1| RNA polymerase, sigma 70 subunit, RpoD [Sinorhizobium meliloti
           BL225C]
          Length = 684

 Score =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 69/251 (27%), Positives = 119/251 (47%), Gaps = 15/251 (5%)

Query: 41  YREHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
             + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 435 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 494

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I        +   + ++    + +     +  
Sbjct: 495 GYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREP 549

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A+KL +   +V  +        SL   +   D+  S   D++    D    + I+
Sbjct: 550 TPEELAEKLAMPLEKVRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKNALLPID 604

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              + N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+
Sbjct: 605 AAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 664

Query: 276 AFKKVQESIQK 286
           A +K++   + 
Sbjct: 665 ALRKLKHPSRS 675


>gi|221639823|ref|YP_002526085.1| RNA polymerase sigma factor RpoD [Rhodobacter sphaeroides KD131]
 gi|332558839|ref|ZP_08413161.1| RNA polymerase sigma factor RpoD [Rhodobacter sphaeroides WS8N]
 gi|221160604|gb|ACM01584.1| RNA polymerase sigma factor [Rhodobacter sphaeroides KD131]
 gi|332276551|gb|EGJ21866.1| RNA polymerase sigma factor RpoD [Rhodobacter sphaeroides WS8N]
          Length = 668

 Score =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 428 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 487

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A+KL
Sbjct: 488 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAEKL 542

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++N + 
Sbjct: 543 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAILPLDSAIQENLKE 597

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 598 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 657

Query: 285 QK 286
           + 
Sbjct: 658 RS 659


>gi|91762832|ref|ZP_01264797.1| RNA polymerase sigma factor [Candidatus Pelagibacter ubique
           HTCC1002]
 gi|91718634|gb|EAS85284.1| RNA polymerase sigma factor [Candidatus Pelagibacter ubique
           HTCC1002]
          Length = 607

 Score =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 68/241 (28%), Positives = 117/241 (48%), Gaps = 12/241 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 369 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 428

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + I     +      +A+KL +
Sbjct: 429 IRQAITRSIADQARTIRIPVH-----MIETINKIVRTQRLILSEFGREATPEELAQKLRM 483

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   +   D+  S   D++    D +    +E+  + N     
Sbjct: 484 PLDKVRKVLKISKEPVSLEKPV--GDEEDSSLGDFI---EDTKALAPLEQAIKSNLSEAT 538

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           T+ +S L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 539 TKILSTLTPREERVLRMRFGVGMNTDHTLEEVGLQFSVTRERIRQIEAKALRKLKHPSRS 598

Query: 287 Q 287
           +
Sbjct: 599 K 599


>gi|189424079|ref|YP_001951256.1| RNA polymerase, sigma 70 subunit, RpoD family [Geobacter lovleyi
           SZ]
 gi|189420338|gb|ACD94736.1| RNA polymerase, sigma 70 subunit, RpoD family [Geobacter lovleyi
           SZ]
          Length = 586

 Score =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 73/252 (28%), Positives = 121/252 (48%), Gaps = 12/252 (4%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A R  EH    A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +R
Sbjct: 338 AIREGEHKARIAKSELIEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQR 397

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I        +   + +L    + +   N +  
Sbjct: 398 GYKFSTYATWWIRQAITRAIADQARTIRIPVH-----MIETINKLIRTSRQLVQENGREP 452

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               IA ++ +   +V  +        SL   I   ++  S   D++    D      +E
Sbjct: 453 SPEEIADRMQLPLDKVRKVLKIAKEPISLETPI--GEEEDSHLGDFI---EDKGVVNPLE 507

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEAR 275
              + N     +R +S L PRE ++   R         TLE +  +FEV+RER+RQIEA+
Sbjct: 508 AVIKANLSEQTSRVLSTLTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAK 567

Query: 276 AFKKVQESIQKQ 287
           A +K++   + +
Sbjct: 568 ALRKLRHPSRSK 579


>gi|152995337|ref|YP_001340172.1| RpoD family RNA polymerase sigma factor [Marinomonas sp. MWYL1]
 gi|150836261|gb|ABR70237.1| RNA polymerase, sigma 70 subunit, RpoD family [Marinomonas sp.
           MWYL1]
          Length = 338

 Score =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 79/271 (29%), Positives = 131/271 (48%), Gaps = 12/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   + R    GD  A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 66  YLSEIGFSPLLTAEEEVYFS-RLSLKGDQKARTRMIESNLRLVVKISRRYLNRGLSLLDL 124

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 125 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 183

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +T           IA+ L+    +V  M        S++A     D N  
Sbjct: 184 LRAAR----ELTQKLDHEPSAEEIAEMLDCPVEDVQKMLGLNEKVSSIDA-TFGGDNNDK 238

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
              + L    D   Q      +  +  N +   +  L+ ++  +   R         TLE
Sbjct: 239 SLVEILA---DTLHQGPEADRQDGDVLNSIELWLDELSEKQCEVITRRFGLRGHEASTLE 295

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++ +E  ++RERVRQI+  A +K++  + K+
Sbjct: 296 HVGAEIGLTRERVRQIQVEALRKLRLIMDKE 326


>gi|90407885|ref|ZP_01216060.1| putative RNA polymerase sigma-38 factor [Psychromonas sp. CNPT3]
 gi|90310976|gb|EAS39086.1| putative RNA polymerase sigma-38 factor [Psychromonas sp. CNPT3]
          Length = 313

 Score =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 83/271 (30%), Positives = 141/271 (52%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  QEE   A+R    GD  A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 44  YLGEIGFSPLLTAQEEVYYARR-SLRGDDVARKRMIESNLRLVVKISRRYTNRGLSLLDL 102

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPE+GFR +TY+ WWI+  ++  I+     +++      K+L   
Sbjct: 103 VEEGNLGLIRAVEKFDPEKGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KKLNVY 161

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++ +         IA  L++   +V  +        S++  I ++     
Sbjct: 162 LRTAR----ELSHSLTHEPTAEDIALALDIPAKDVSKILKLNERISSVDIPIGNNSD--- 214

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
             ++ L    D +E +   + E ++ +  +   +  LNP++R +   R   L     TLE
Sbjct: 215 --KELLDIIPDRKEIIPENELENEDMKLRIVEWLEDLNPKQREVLARRFGLLGYEAATLE 272

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           N+  E  ++RERVRQI+  A K ++E + +Q
Sbjct: 273 NVGKEIGLTRERVRQIQVEALKCLREVLSQQ 303


>gi|391964|gb|AAA03294.1| RNA polymerase sigma factor [Shigella flexneri]
          Length = 362

 Score =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 141/271 (52%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ +I   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 73  YLGKIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 131

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 132 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 190

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR ++     ++         V IA++L+    +V  M        S++  +    +   
Sbjct: 191 LRTVR----ELSHKLDYEPSAVEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE--- 243

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
             +  L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 244 --KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVIARRFGLLGYEAATLE 301

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+ +  ++++E +Q Q
Sbjct: 302 DVGREIGLTRERVRQIQVQGLRRLREILQTQ 332


>gi|77463967|ref|YP_353471.1| RNA polymerase sigma factor RpoD [Rhodobacter sphaeroides 2.4.1]
 gi|126462810|ref|YP_001043924.1| RNA polymerase sigma factor RpoD [Rhodobacter sphaeroides ATCC
           17029]
 gi|77388385|gb|ABA79570.1| RNA polymerase sigma factor RpoD [Rhodobacter sphaeroides 2.4.1]
 gi|126104474|gb|ABN77152.1| RNA polymerase, sigma 70 subunit, RpoD family [Rhodobacter
           sphaeroides ATCC 17029]
          Length = 668

 Score =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 428 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 487

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A+KL
Sbjct: 488 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAEKL 542

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++N + 
Sbjct: 543 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAILPLDSAIQENLKE 597

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 598 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPS 657

Query: 285 QK 286
           + 
Sbjct: 658 RS 659


>gi|319406862|emb|CBI80497.1| RNA polymerase sigma factor [Bartonella sp. 1-1C]
          Length = 669

 Score =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 119/240 (49%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 431 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 490

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + I     +      ++ KL++
Sbjct: 491 IRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQILHEIGREPTPEELSSKLSM 545

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   +   D+++S   D++    D    + I+   + N R+  
Sbjct: 546 PLEKVRKVLKIAKEPISLETPV--GDEDASHLGDFI---EDRNALLPIDAAIQANLRDTT 600

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 601 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 660


>gi|221633686|ref|YP_002522912.1| RNA polymerase sigma 70 subunit, RpoD [Thermomicrobium roseum DSM
           5159]
 gi|221156620|gb|ACM05747.1| RNA polymerase sigma 70 subunit, RpoD [Thermomicrobium roseum DSM
           5159]
          Length = 509

 Score =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 71/253 (28%), Positives = 121/253 (47%), Gaps = 13/253 (5%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
            +R R  G  +A  +L  ++LRLVV IA  Y G GL + +++ EGN+GLM+AV KF   +
Sbjct: 262 WQRLRRDG-EAARRKLTEANLRLVVSIAKRYTGRGLTLLDLIQEGNLGLMRAVDKFQTHK 320

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           GF+ +TY+ WWI+ A+   +      +++        L   L R+    + +T    +  
Sbjct: 321 GFKFSTYATWWIRQAITRALADHARTIRLPVH-----LVETLNRVSRVARQLTQELGREP 375

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A  +N+    +  +        SL A +   ++  S   D+L    D +    ++
Sbjct: 376 TTSELAAAVNMPLDRLRELLQAAQDPVSLEAPVGQEEE--STLGDFL---EDERAVAPLD 430

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEAR 275
                  R  +   ++ L  RERR+   R   E+    TLE +   F V+RERVRQIEA+
Sbjct: 431 AAALSLLREQVQSLLATLTERERRVLAMRFGLEDGQTYTLEEVGRAFGVTRERVRQIEAK 490

Query: 276 AFKKVQESIQKQV 288
           A +K++   + + 
Sbjct: 491 ALRKLRHPQRARA 503



 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 8/27 (29%), Positives = 16/27 (59%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAK 39
           E  +  Y+ EI ++P+L  ++E  L +
Sbjct: 104 EDPVRLYLAEIGRVPLLTAEQEVELGR 130


>gi|86358552|ref|YP_470444.1| RNA polymerase sigma factor RpoD [Rhizobium etli CFN 42]
 gi|86282654|gb|ABC91717.1| RNA polymerase sigma factor protein (sigma-70) [Rhizobium etli CFN
           42]
          Length = 685

 Score =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 69/251 (27%), Positives = 119/251 (47%), Gaps = 15/251 (5%)

Query: 41  YREHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
             + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 436 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 495

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I        +   + ++    + +     +  
Sbjct: 496 GYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREP 550

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A+KL +   +V  +        SL   +   D+  S   D++    D    + I+
Sbjct: 551 TPEELAEKLAMPLEKVRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKNALLPID 605

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              + N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+
Sbjct: 606 AAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 665

Query: 276 AFKKVQESIQK 286
           A +K++   + 
Sbjct: 666 ALRKLKHPSRS 676


>gi|89068061|ref|ZP_01155478.1| RNA polymerase sigma factor [Oceanicola granulosus HTCC2516]
 gi|89046300|gb|EAR52357.1| RNA polymerase sigma factor [Oceanicola granulosus HTCC2516]
          Length = 281

 Score =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 101/272 (37%), Positives = 172/272 (63%), Gaps = 6/272 (2%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
            +  +  +L+ + E  LA  +R+  D  A HRL+T+++RL + +A  +R YG P+++++ 
Sbjct: 3   RKAMQAELLDAETELRLAYAWRDQRDERALHRLITAYMRLAISMAAKFRRYGAPMNDLIQ 62

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           E ++GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFNLR
Sbjct: 63  EASLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNLR 122

Query: 141 RLKGHLQAITDNNLKP----EQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDK 195
           R++  L+     +  P    +    IA ++ V   +V  M  RL+G D SLNA   S++ 
Sbjct: 123 RVQARLEREAAASGAPIDRQKMREMIAAEVGVPLHDVEMMEGRLSGSDYSLNA-TQSAED 181

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
              +W + L  D     + +    +    R+ L  ++S LN RER I + R+L+++P TL
Sbjct: 182 EGREWIEALEDDGMQAAEKVENSHDIDTLRHWLLNALSQLNERERFIVKERKLRDDPRTL 241

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+L  E  +S+ERVRQ+EA AF K+++ ++ +
Sbjct: 242 ESLGDELGLSKERVRQLEAAAFGKMRKMLETE 273


>gi|171914125|ref|ZP_02929595.1| RNA polymerase sigma factor RpoD [Verrucomicrobium spinosum DSM
           4136]
          Length = 576

 Score =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 120/240 (50%), Gaps = 11/240 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   +V ++LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+ +RG++ +TY+ W
Sbjct: 335 KAKTEMVEANLRLVISIAKKYTNRGLSFLDLIQEGNMGLMRAVEKFEYKRGYKFSTYATW 394

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I            L R++  L      +  P+    IA++++
Sbjct: 395 WIRQAITRSIADQARTIRIPVHM--IDTINKLLRVQKQLVQELGRDPTPD---EIAEEIH 449

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +    V ++        SL   +  SD + +++ D++    D      +E       R+ 
Sbjct: 450 LPVERVNAVLRMSQQPVSLQTKVGDSDGD-TEFGDFI---EDNTSVSPMELTAMNLLRDK 505

Query: 228 LTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L   +  L  RER + E R      +  TLE +  +F V+RER+RQIEA+A +K++   +
Sbjct: 506 LKDVLDSLTDRERAVLEQRFGLVDGSGRTLEEVGRQFHVTRERIRQIEAKALRKLRHPTR 565


>gi|113868347|ref|YP_726836.1| RNA polymerase sigma factor RpoS [Ralstonia eutropha H16]
 gi|113527123|emb|CAJ93468.1| DNA-directed RNA polymerase sigma subunit (sigma38) [Ralstonia
           eutropha H16]
          Length = 392

 Score =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 78/278 (28%), Positives = 132/278 (47%), Gaps = 11/278 (3%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
               +  Y++ I   P+L   EE   +    + GD +A   ++  +LRLVV IA GY   
Sbjct: 116 AADTVQHYLNRISIKPLLSAPEELHFST-LAKDGDFAARQVMIERNLRLVVSIAKGYLNR 174

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           G+P+ +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++     
Sbjct: 175 GVPLLDLIEEGNLGLMHAIEKFDPSRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV- 233

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
             R    + R K HL+     + +   +  IA  L  +  EV  +        SL+    
Sbjct: 234 -IRELNQVLRAKRHLEK-GGTDGRDASLEDIAHLLGKTPDEVQDVLALNEHTTSLDTPF- 290

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE- 250
                 S   D+L  +H+       ++   +    ++   ++ L+ + R + E R     
Sbjct: 291 -DLDPGSSLLDFLSDEHNAAPD---QEVAHRELEGLMKLWLARLSEKHRYVVERRFGLNH 346

Query: 251 -NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             P TLE L+ E  ++RERVRQI+  A  K++     Q
Sbjct: 347 IEPATLEELAEEMGLTRERVRQIQQEALVKLKRHFASQ 384


>gi|108804647|ref|YP_644584.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108765890|gb|ABG04772.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 304

 Score =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 82/273 (30%), Positives = 145/273 (53%), Gaps = 12/273 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+  I +  +L +  E  L++R ++ GD  A  +L+  +LRLVV +A  YRGYGLP 
Sbjct: 35  LAGYLDRIGRWRLLTRDGEIELSRRAKK-GDRKARQKLIEKNLRLVVSVAKKYRGYGLPF 93

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AV+KFDPERGFR +TY+ WWI+ A+Q  +      +++     +K  
Sbjct: 94  EDLIQEGNIGLMKAVEKFDPERGFRFSTYATWWIRQAVQRAVADKGRTIRVPVHMTEK-- 151

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              +R++      ++    +      IA++L     +V      +    SL+  + SS++
Sbjct: 152 ---IRKVSRTFNELSLELEREPTDEEIARRLEWDVEDVRLTISAMPDATSLDQPV-SSEE 207

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PV 253
           ++S+  D++  +        + KE   +    L  ++  L  R R +   R   ++  P 
Sbjct: 208 SASELGDFIEDERTSDTPDTVLKELESS---QLKEAIERLPERARYVLVRRYGLDDREPA 264

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TL  L  E ++SRERVRQ++  A + ++  I++
Sbjct: 265 TLAELGDELKISRERVRQLQREAERLLKAGIRR 297


>gi|317153216|ref|YP_004121264.1| RNA polymerase sigma factor RpoD [Desulfovibrio aespoeensis Aspo-2]
 gi|316943467|gb|ADU62518.1| RNA polymerase sigma factor RpoD [Desulfovibrio aespoeensis Aspo-2]
          Length = 581

 Score =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 70/242 (28%), Positives = 114/242 (47%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           + A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ 
Sbjct: 341 MRAKQELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYAT 400

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            L R   +L      +  PE    IA+++
Sbjct: 401 WWIRQAITRAIADQARTIRIPVHM--IETINKLIRTSRYLVQELGRDPSPE---EIAERM 455

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +    +V  +        SL   I   D+  S   D++    D +     E+        
Sbjct: 456 DYPLEKVKKVLKIAKEPISLETPI--GDEEDSSLGDFI---EDKKATAPAEEVVSTKLGE 510

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +   +S L PRE ++   R         TLE +   F V+RER+RQIEA+A +K++  +
Sbjct: 511 QIASVLSDLTPREEQVLRKRFGIGEKSDHTLEEVGKLFNVTRERIRQIEAKALRKLRHPV 570

Query: 285 QK 286
           + 
Sbjct: 571 RS 572



 Score = 36.3 bits (83), Expect = 4.8,   Method: Composition-based stats.
 Identities = 12/42 (28%), Positives = 26/42 (61%), Gaps = 1/42 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVT 55
             +  Y+ E+  +P+L+++ E V+AK+  E+G+L   + L+ 
Sbjct: 91  DPVRMYLREMGAVPLLDREGEVVIAKKI-ENGELEVLYSLIE 131


>gi|298208827|ref|YP_003717006.1| putative sigma factor A [Croceibacter atlanticus HTCC2559]
 gi|83848754|gb|EAP86623.1| putative sigma factor A [Croceibacter atlanticus HTCC2559]
          Length = 288

 Score =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 68/276 (24%), Positives = 143/276 (51%), Gaps = 12/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L+ Y+ ++ K+ ++  +EE  LA+R RE GD  A  +L  ++LR VV +A  Y+  GL 
Sbjct: 17  SLNNYLQDVSKLDLITAEEEVELAQRIRE-GDQIALEKLTKANLRFVVSVAKQYQNQGLR 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + +     +V++    N+  
Sbjct: 76  LPDLINEGNVGLVKAAKRFDETRGFKFISYAVWWIRQSILQALAEHSRVVRLP--LNKIG 133

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   + +   +L+   +   +P     IAK+L++  S+V +         S++A     +
Sbjct: 134 VINKINKTFSYLEQAYE---RPPSAAEIAKELDMPVSKVKTAMKNSGRSLSMDAPFQEGE 190

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NP 252
            +S+ +      +    +  L++          + R++  L  RE  +           P
Sbjct: 191 NDSNLYDVLKSGESPSPDNNLMQDSLSVE----IERALDTLTEREADVIRLNYGLGGQQP 246

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TL+ +   F++SRERVRQI  +  ++++   + ++
Sbjct: 247 LTLQEIGETFDLSRERVRQIREKGIRRLRHESKSKI 282


>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 =  220 bits (562), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 72/241 (29%), Positives = 112/241 (46%), Gaps = 12/241 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 400 RAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 459

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I            L R    +         PE    +A+KL 
Sbjct: 460 WIRQAITRSIADQARTIRIPVHM--IETINKLVRTSRQMLHEIGREPTPE---ELAEKLV 514

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +   +V  +        SL   I   D+  S   D++    D      ++     N R  
Sbjct: 515 MPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAVQPLDAAIHANLRET 569

Query: 228 LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   +
Sbjct: 570 TTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSR 629

Query: 286 K 286
            
Sbjct: 630 S 630


>gi|254673642|emb|CBA09200.1| RNA polymerase sigma-32 factor [Neisseria meningitidis alpha275]
          Length = 268

 Score =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 110/267 (41%), Positives = 167/267 (62%), Gaps = 8/267 (2%)

Query: 1   MNRK-NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLR 59
           MN    +  I +G   L +YIH +  IPML ++EE  LA+R R  GDL+AA +L+ SHLR
Sbjct: 1   MNNAFALPAIQSGNGSLEQYIHTVNSIPMLSQEEETRLAER-RIKGDLNAAKQLILSHLR 59

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           +VV IA GY GYGL  ++++ EGNIGLM+AVK+++P RG RL ++++ WIKA + E+ILR
Sbjct: 60  VVVSIARGYDGYGLNQADLIQEGNIGLMKAVKRYEPGRGARLFSFAVHWIKAEIHEFILR 119

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
           +W LV++ TT  Q++LFFNLR ++ +L A++     P++   IA  L V  SEV+ M  R
Sbjct: 120 NWRLVRVATTKPQRKLFFNLRSMRKNLNALS-----PKEAQDIADDLGVKLSEVLEMEQR 174

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           + G +      NS D++S    DWL        + L ++     +   L  +++ L+ R 
Sbjct: 175 MTGHDIAIMADNSDDEDSFAPIDWLADHDSEPSRQLSKQAHYALQTEGLQNALAQLDDRS 234

Query: 240 RRIFEARRLQEN-PVTLENLSSEFEVS 265
           RRI E+R LQ++  +TL  L++E+ VS
Sbjct: 235 RRIVESRWLQDDGGLTLHQLAAEYGVS 261


>gi|209550278|ref|YP_002282195.1| RNA polymerase sigma factor RpoD [Rhizobium leguminosarum bv.
           trifolii WSM2304]
 gi|209536034|gb|ACI55969.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhizobium
           leguminosarum bv. trifolii WSM2304]
          Length = 685

 Score =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 69/251 (27%), Positives = 119/251 (47%), Gaps = 15/251 (5%)

Query: 41  YREHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
             + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 436 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 495

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I        +   + ++    + +     +  
Sbjct: 496 GYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREP 550

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A+KL +   +V  +        SL   +   D+  S   D++    D    + I+
Sbjct: 551 TPEELAEKLAMPLEKVRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKNALLPID 605

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              + N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+
Sbjct: 606 AAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 665

Query: 276 AFKKVQESIQK 286
           A +K++   + 
Sbjct: 666 ALRKLKHPSRS 676


>gi|26249652|ref|NP_755692.1| RpoD protein [Escherichia coli CFT073]
 gi|26110080|gb|AAN82266.1|AE016767_26 RpoD protein [Escherichia coli CFT073]
          Length = 246

 Score =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 118/247 (47%), Gaps = 12/247 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 6   RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 65

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            L R+   +         PE    +A+++
Sbjct: 66  WWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPTPE---ELAERM 120

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D   S   D++    D   ++ ++    ++ R 
Sbjct: 121 LMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDTTLELPLDSATTESLRA 175

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 176 ATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 235

Query: 285 QKQVELS 291
           + +V  S
Sbjct: 236 RSEVLRS 242


>gi|86607034|ref|YP_475797.1| RNA polymerase sigma factor RpoD [Synechococcus sp. JA-3-3Ab]
 gi|86555576|gb|ABD00534.1| RNA polymerase sigma factor RpoD [Synechococcus sp. JA-3-3Ab]
          Length = 404

 Score =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 74/318 (23%), Positives = 138/318 (43%), Gaps = 57/318 (17%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS----------------------- 48
            +  +  Y+ EI +I +L   EE  LA++  +  +L                        
Sbjct: 87  TDDSIRVYLQEIGRIRLLRADEEIELARKIADLLELERAREAVFQRMGLWSDPEEVPETL 146

Query: 49  ---------------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
                                A  ++V S+LRLVV IA  Y   GL   +++ EG++GL+
Sbjct: 147 WAEEVKMSLPEFRRRLHRGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLI 206

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +A +KFD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   +
Sbjct: 207 RAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKVTK 261

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
            ++    +      IA ++ ++  ++  +        SL   I    +  S+  D++  +
Sbjct: 262 QLSQELGRRPTEEEIATRMEITIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIESE 319

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVS 265
                +   E+  +   R  L   +  L PRER + + R   ++    TLE +   F V+
Sbjct: 320 G----ETPEERVAKVLLREDLESVLETLTPRERDVLKLRYGLDDGRMKTLEEIGQIFNVT 375

Query: 266 RERVRQIEARAFKKVQES 283
           RER+RQIEA+A +K++  
Sbjct: 376 RERIRQIEAKALRKLRHP 393


>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 =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 64/249 (25%), Positives = 111/249 (44%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 367 IGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 426

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 427 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPTPE--- 481

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + +++ + E +V  +        S+   I   D   S   D++    D      ++   
Sbjct: 482 ELGERMEMPEDKVRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDTTIDSPVDSAT 536

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
            +         ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 537 IQGLTEATRSVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 596

Query: 279 KVQESIQKQ 287
           K++   +  
Sbjct: 597 KLRHPSRSD 605


>gi|332307721|ref|YP_004435572.1| RNA polymerase, sigma 70 subunit, RpoD [Glaciecola agarilytica
           4H-3-7+YE-5]
 gi|332175050|gb|AEE24304.1| RNA polymerase, sigma 70 subunit, RpoD [Glaciecola agarilytica
           4H-3-7+YE-5]
          Length = 613

 Score =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 64/249 (25%), Positives = 115/249 (46%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 367 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 426

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE   
Sbjct: 427 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPTPE--- 481

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +++++ + E ++  +        S+   I   D   S   D++    D      ++   
Sbjct: 482 ELSERMLMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDSTIVQPLDSAT 536

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
             + +N     ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 537 GGSLKNATQEVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 596

Query: 279 KVQESIQKQ 287
           K++   + +
Sbjct: 597 KLRHPSRSE 605


>gi|290511076|ref|ZP_06550445.1| RNA polymerase sigma factor RpoS [Klebsiella sp. 1_1_55]
 gi|289776069|gb|EFD84068.1| RNA polymerase sigma factor RpoS [Klebsiella sp. 1_1_55]
          Length = 347

 Score =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 78  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYSNRGLALLDL 136

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 137 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 195

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 196 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 250

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 251 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 306

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 307 DVGREIGLTRERVRQIQVEGLRRLREILQGQ 337


>gi|213969149|ref|ZP_03397288.1| RNA polymerase sigma-38 factor [Pseudomonas syringae pv. tomato T1]
 gi|213926147|gb|EEB59703.1| RNA polymerase sigma-38 factor [Pseudomonas syringae pv. tomato T1]
          Length = 334

 Score =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 82/278 (29%), Positives = 141/278 (50%), Gaps = 16/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +E +    R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEVH--FARLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 124

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 125 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 183

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++  + +K       ++ +N R++  D SL         + 
Sbjct: 184 LRAAR-ELTQKLDHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSL------GPDSD 236

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + +S L  ++R +   R         TL
Sbjct: 237 KTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTEKQREVVIRRFGLRGHESSTL 293

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 294 EDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSSES 331


>gi|114797662|ref|YP_761566.1| RNA polymerase sigma factor RpoD [Hyphomonas neptunium ATCC 15444]
 gi|114737836|gb|ABI75961.1| RNA polymerase sigma factor RpoD [Hyphomonas neptunium ATCC 15444]
          Length = 666

 Score =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 67/240 (27%), Positives = 115/240 (47%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 428 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 487

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + +     +      +A+KL +
Sbjct: 488 IRQAITRSIADQARTIRIPVH-----MIETINKIIRTQRQMLHEIGREPTPEELAEKLGL 542

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              ++  +        SL   I   D   S   D++    D    + ++   + N R   
Sbjct: 543 PLEKIRKVLKIAKEPISLETPI--GDDEDSNLGDFI---EDKMALLPVDAAIQSNLRETT 597

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 598 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 657


>gi|159904372|ref|YP_001551716.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9211]
 gi|159889548|gb|ABX09762.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9211]
          Length = 338

 Score =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 76/292 (26%), Positives = 137/292 (46%), Gaps = 31/292 (10%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLA--------------------KRYREHGDLSAAH 51
               +  Y+  I ++P+L   EE  LA                    +R++      A  
Sbjct: 47  ATDSIGFYLSSIGRVPLLTPAEEIELAHHVQKMKELLDIEKEKLSARQRHQIRMGKRARD 106

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ ++LRLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+ 
Sbjct: 107 RMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQ 166

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            M   I  S   +++    ++K     L +++   + ++    +    V +A  + +   
Sbjct: 167 GMTRAIDNSARTIRLPIHISEK-----LSKMRRISRELSHRFGRQPNRVELANAMGIEPQ 221

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           ++  +  + A   SL++     +  S+  +       D      +   +RK ++  L   
Sbjct: 222 DLEDLVAQSAPCASLDSHARGEEDRSTLGELI----PDPNYDEPMAGMDRKMQKEHLGGW 277

Query: 232 MSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +S LN RE++I   R     E P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 278 LSQLNEREQKIMRLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 329


>gi|117617733|ref|YP_855373.1| RNA polymerase sigma factor RpoS [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
 gi|117559140|gb|ABK36088.1| RNA polymerase sigma factor RpoS [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
          Length = 327

 Score =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 82/271 (30%), Positives = 136/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD +A  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 57  YLGEIGFSPLLTAEEEVYYARR-ALRGDKAARKRMIESNLRLVVKIARRYNNRGLVLLDL 115

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 116 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 174

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA  L+ S  +V  M        S++  I        
Sbjct: 175 LRTAR----ELSHRLDHEPTAEDIAFALDRSVDDVNRMLKLNEKITSVDTPI--GGDRDK 228

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  +     ++   + +  + R  +   +  LNP++R +   R   L   P TLE
Sbjct: 229 ALLDVLSDERGMGPEL---ESQDDDMRASIVHWLEELNPKQREVLARRFGLLGYEPATLE 285

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++ +E  ++RERVRQI+    ++++E +  Q
Sbjct: 286 DVGAEIGLTRERVRQIQVEGLRRLREILLGQ 316


>gi|86609652|ref|YP_478414.1| RNA polymerase sigma factor RpoD [Synechococcus sp.
           JA-2-3B'a(2-13)]
 gi|86558194|gb|ABD03151.1| RNA polymerase sigma factor RpoD [Synechococcus sp.
           JA-2-3B'a(2-13)]
          Length = 403

 Score =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 74/318 (23%), Positives = 137/318 (43%), Gaps = 57/318 (17%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS----------------------- 48
            +  +  Y+ EI +I +L   EE  LA++  +  +L                        
Sbjct: 86  TDDSIRVYLQEIGRIRLLRADEEIELARKIADLLELERAREAVFQRMGLWSDPEEVPDTL 145

Query: 49  ---------------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
                                A  ++V S+LRLVV IA  Y   GL   +++ EG++GL+
Sbjct: 146 WAEEVKMSLPEFRRRLHRGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLI 205

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +A +KFD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   +
Sbjct: 206 RAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKVTK 260

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
            ++    +      IA ++ ++  ++  +        SL   I    +  S+  D++  D
Sbjct: 261 LLSQELGRKPTEEEIATRMEITIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIESD 318

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVS 265
            +  E  +     +   R  L   +  L  RER + + R   ++    TLE +   F V+
Sbjct: 319 GETPEDRVA----KVLLREDLESVLETLTARERDVLKLRYGLDDGRMKTLEEIGQIFNVT 374

Query: 266 RERVRQIEARAFKKVQES 283
           RER+RQIEA+A +K++  
Sbjct: 375 RERIRQIEAKALRKLRHP 392


>gi|1765926|emb|CAA70052.1| RNA polymerase sigma-70 subunit [Rhizobium etli]
          Length = 685

 Score =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 69/251 (27%), Positives = 119/251 (47%), Gaps = 15/251 (5%)

Query: 41  YREHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
             + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 436 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 495

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I        +   + ++    + +     +  
Sbjct: 496 GYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREP 550

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A+KL +   +V  +        SL   +   D+  S   D++    D    + I+
Sbjct: 551 TPEELAEKLAMPLEKVRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKNALLPID 605

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              + N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+
Sbjct: 606 AAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 665

Query: 276 AFKKVQESIQK 286
           A +K++   + 
Sbjct: 666 ALRKLKHPSRS 676


>gi|254455607|ref|ZP_05069036.1| RNA polymerase sigma factor [Candidatus Pelagibacter sp. HTCC7211]
 gi|207082609|gb|EDZ60035.1| RNA polymerase sigma factor [Candidatus Pelagibacter sp. HTCC7211]
          Length = 608

 Score =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 68/241 (28%), Positives = 117/241 (48%), Gaps = 12/241 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 370 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 429

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + I     +      +A+KL +
Sbjct: 430 IRQAITRSIADQARTIRIPVH-----MIETINKIVRTQRLILSEFGREATPEELAQKLRM 484

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   +   D+  S   D++    D +    +E+  + N     
Sbjct: 485 PLDKVRKVLKISKEPVSLEKPV--GDEEDSSLGDFI---EDTKALAPLEQAIKSNLGEAT 539

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           T+ +S L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 540 TKILSTLTPREERVLRMRFGVGMNTDHTLEEVGLQFSVTRERIRQIEAKALRKLKHPSRS 599

Query: 287 Q 287
           +
Sbjct: 600 K 600


>gi|148654464|ref|YP_001274669.1| RpoD family RNA polymerase sigma factor [Roseiflexus sp. RS-1]
 gi|148566574|gb|ABQ88719.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus sp.
           RS-1]
          Length = 541

 Score =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 68/251 (27%), Positives = 122/251 (48%), Gaps = 14/251 (5%)

Query: 37  LAKRYREHGD--LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           L + +    D   +A   L  ++LRLVV +A  Y G GL + +++ EGN+GL++AV+KFD
Sbjct: 290 LWRDWNLAIDQGKTAREDLTQANLRLVVSVAKKYIGRGLQLLDLIQEGNVGLIRAVEKFD 349

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +GF+ +TY+ WWI+ A+   I      ++I     +      + RL    + +     
Sbjct: 350 YRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE-----TINRLMRESRRMLQELG 404

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +      +++ L +   +V S+        SL   +    +  SQ  D++    D +   
Sbjct: 405 REPTDEELSRALGIPVDKVRSIRKTSLEPVSLETPV--GQEEDSQLGDFI---EDSKVLA 459

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQI 272
             +    +  R  + + ++ L  RERR+ + R   E+    TLE +  EF V+RER+RQI
Sbjct: 460 PSDAASHQMLREQVEQVLNQLTERERRVLQLRFGLEDGHSRTLEEVGKEFGVTRERIRQI 519

Query: 273 EARAFKKVQES 283
           E +A +K++  
Sbjct: 520 EVKALRKLRHP 530



 Score = 36.3 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 8/32 (25%), Positives = 20/32 (62%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY 41
           ++    +  Y+ EI ++P+L  ++E +LA++ 
Sbjct: 114 ISVNDTVRMYLREIGRVPLLNARQEILLAQKI 145


>gi|90416198|ref|ZP_01224130.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2207]
 gi|90331923|gb|EAS47137.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2207]
          Length = 306

 Score =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 76/272 (27%), Positives = 138/272 (50%), Gaps = 14/272 (5%)

Query: 17  SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
           S Y+ EI   P+L   EE   A++  + GD SA  R++ S+LRLVVKIA  Y   GL + 
Sbjct: 32  SLYLKEIGYAPLLTAAEEVFYARKLLK-GDESARKRMIESNLRLVVKIARRYVNRGLELL 90

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++ EGNIGLM+AV+KFDPE G+R +TY+ WWI+  ++  ++     +++       +  
Sbjct: 91  DLIEEGNIGLMRAVEKFDPELGYRFSTYATWWIRQTIERGLMNQTRTIRLPVHI--VKEL 148

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
               R    L    D+   PE++     K      ++ S++ R++   S++  +  ++K+
Sbjct: 149 NVYVRASRKLAQRLDHTPTPEEIAEEVDKPVEDVLKIFSLSERIS---SIDIPVAENEKS 205

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVT 254
                  +             + E +N   +L + ++ L  ++R +   R         T
Sbjct: 206 ------LIETISAEGASSPERQVEGENLSEVLNKWLAQLPEKQREVLVRRFGLLHHQEET 259

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE +  E  ++RERVRQI+  A +++++ ++K
Sbjct: 260 LEQVGREIGLTRERVRQIQVDALRRLRDVLRK 291


>gi|152980760|ref|YP_001353824.1| RNA polymerase sigma factor RpoS [Janthinobacterium sp. Marseille]
 gi|151280837|gb|ABR89247.1| RNA polymerase nonessential primary-like sigma factor
           [Janthinobacterium sp. Marseille]
          Length = 345

 Score =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 82/272 (30%), Positives = 136/272 (50%), Gaps = 11/272 (4%)

Query: 17  SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
             Y+++I   P+L   EE   A    + G+ +A  +++  +LRLVV IA  Y   G+ + 
Sbjct: 74  QHYLNQIGTRPLLTVPEEVHFAT-LAKQGNFAARQKMIEHNLRLVVSIAKHYINRGVILL 132

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++ EGN+GLM+A+ KF+PERGFR +TY+ WWI+ +++  I+     V++       R  
Sbjct: 133 DLIEEGNLGLMRAIDKFEPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV--VREL 190

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
               R K HL+A   ++ K      IA  ++ S  +V  +        SL+A +      
Sbjct: 191 NQTLRAKFHLEA-QHHDGKDATAEDIAHLVDRSVEDVQDILALSEHATSLDAPL--DGDP 247

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVT 254
            S   D L  DH      L E  E      ++   +  L  ++R +   R     ++P T
Sbjct: 248 QSSLMDLLQGDHANDPDALAEHNEMTV---LVHDWLEKLPDKQRLVITRRFGLDNDDPAT 304

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE L++E  V+RERVRQI+  A  K++ S+ +
Sbjct: 305 LEALAAEMHVTRERVRQIQQEALVKLKRSLMR 336


>gi|322421611|ref|YP_004200834.1| RpoD subfamily RNA polymerase sigma-70 factor [Geobacter sp. M18]
 gi|320127998|gb|ADW15558.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           M18]
          Length = 583

 Score =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 77/253 (30%), Positives = 119/253 (47%), Gaps = 12/253 (4%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           LA    EH    A   LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +
Sbjct: 334 LAIEEGEHKAKLAKSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQ 393

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RG++ +TY+ WWI+ A+   I      ++I            L R    L         P
Sbjct: 394 RGYKFSTYATWWIRQAITRAIADQARTIRIPVHM--IETINKLIRTSRQLVQEIGREPSP 451

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           E    IA+++ +   +V  +        SL   I   ++  S   D++    D      +
Sbjct: 452 E---EIAERMALPLDKVRKVLKIAKEPISLETPI--GEEEDSHLGDFI---EDKGVVSPL 503

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEA 274
           E   + N     +R +S L PRE ++   R         TLE +  +FEV+RER+RQIEA
Sbjct: 504 EAVIKANLSEQTSRVLSTLTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEA 563

Query: 275 RAFKKVQESIQKQ 287
           +A +K++   + +
Sbjct: 564 KALRKLRHPSRAK 576


>gi|108763751|ref|YP_633357.1| RNA polymerase sigma factor RpoD [Myxococcus xanthus DK 1622]
 gi|133312|sp|P17531|RPOD_MYXXA RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-80
 gi|150118|gb|AAA25404.1| sigma factor (rpoD) [Myxococcus xanthus]
 gi|710343|gb|AAB60208.1| major sigma factor [Myxococcus xanthus]
 gi|108467631|gb|ABF92816.1| RNA polymerase sigma factor RpoD [Myxococcus xanthus DK 1622]
 gi|1586812|prf||2204381D sigma factor
          Length = 708

 Score =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 77/268 (28%), Positives = 120/268 (44%), Gaps = 22/268 (8%)

Query: 32  QEEYVL----------AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           +EE  L          A R  E     A   LV ++LRLVV IA  Y   GL   +++ E
Sbjct: 443 EEEANLPVESLRRNYDAIRLGERRAERAKSELVEANLRLVVSIAKKYTNRGLQFLDLIQE 502

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           GNIGLM+AV KF+ +RG++ +TY+ WWI+ A+   I      ++I            L R
Sbjct: 503 GNIGLMKAVDKFEYKRGYKFSTYATWWIRQAITRAIADQARTIRIPVHM--IETINKLIR 560

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
              +L         PE    IA+K+ +   +V  +        SL   I   ++  S   
Sbjct: 561 TSRYLVQEIGREPTPE---EIAEKMELPLDKVRKVLKIAKEPISLETPI--GEEEDSHLG 615

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLS 259
           D++    D       +     N      + ++ L PRE ++   R         TLE + 
Sbjct: 616 DFI---EDKSLVSPADAVINMNLAEQTRKVLATLTPREEKVLRMRFGIGEKSDHTLEEVG 672

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +FEV+RER+RQIEA+A +K++   + +
Sbjct: 673 QDFEVTRERIRQIEAKALRKLRHPSRSK 700


>gi|241205658|ref|YP_002976754.1| RNA polymerase sigma factor RpoD [Rhizobium leguminosarum bv.
           trifolii WSM1325]
 gi|240859548|gb|ACS57215.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhizobium
           leguminosarum bv. trifolii WSM1325]
          Length = 685

 Score =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 69/251 (27%), Positives = 119/251 (47%), Gaps = 15/251 (5%)

Query: 41  YREHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
             + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 436 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 495

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I        +   + ++    + +     +  
Sbjct: 496 GYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREP 550

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A+KL +   +V  +        SL   +   D+  S   D++    D    + I+
Sbjct: 551 TPEELAEKLAMPLEKVRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKNALLPID 605

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              + N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+
Sbjct: 606 AAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 665

Query: 276 AFKKVQESIQK 286
           A +K++   + 
Sbjct: 666 ALRKLKHPSRS 676


>gi|23013315|ref|ZP_00053224.1| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Magnetospirillum magnetotacticum
           MS-1]
          Length = 333

 Score =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 72/246 (29%), Positives = 116/246 (47%), Gaps = 12/246 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 89  ERESSRAKKEMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 148

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            L R    +         PE    +
Sbjct: 149 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKLVRTSRQMLHEIGREPTPE---EL 203

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+KL++   +V  +        SL   I   D+  S   D++    D    + ++   + 
Sbjct: 204 AEKLSMPLEKVRKVLKIAKEPISLETPI--GDEEDSHLGDFI---EDKNAVLPLDAAIQA 258

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 259 NLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKL 318

Query: 281 QESIQK 286
           +   + 
Sbjct: 319 KHPSRS 324


>gi|300727119|ref|ZP_07060538.1| RNA polymerase sigma-70 factor [Prevotella bryantii B14]
 gi|299775663|gb|EFI72254.1| RNA polymerase sigma-70 factor [Prevotella bryantii B14]
          Length = 295

 Score =  220 bits (561), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 77/286 (26%), Positives = 141/286 (49%), Gaps = 12/286 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L RY+ EI    ++   EE  LA+R ++ GD  A  RL  ++LR VV
Sbjct: 13  KITKSITNRESAALDRYLQEIGHEDLISVDEEVELAQRIKK-GDKRALERLTKANLRFVV 71

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A KKFD  RGF+  +Y++WWI+ ++ + I     
Sbjct: 72  SVAKQYQNQGLSLPDLINEGNLGLIKAAKKFDETRGFKFISYAVWWIRQSILQAIAEQSR 131

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    NQ      + RL    +   +   +   V  IA  +++ E ++         
Sbjct: 132 IVRLP--LNQVGSVNKINRLVNSFEQENE---RRPSVDEIADNIDLPEDKIADALNVNTH 186

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     + NS      L    +        +   ++ R  + R +  LN RER +
Sbjct: 187 HVSVDAPFQEGEDNS-----LLDVLPNTDIPSADSELVHESLREEIARVLETLNQRERNV 241

Query: 243 FEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            EA        +TLE +  ++ ++RERVRQI+ +A ++++ + + +
Sbjct: 242 VEAFFGIGQAEMTLEEIGDKYGLTRERVRQIKEKAIRRLRHNTKNK 287


>gi|238896221|ref|YP_002920957.1| RNA polymerase sigma factor RpoS [Klebsiella pneumoniae NTUH-K2044]
 gi|238548539|dbj|BAH64890.1| RNA polymerase sigma factor [Klebsiella pneumoniae subsp.
           pneumoniae NTUH-K2044]
          Length = 366

 Score =  220 bits (560), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 97  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYSNRGLALLDL 155

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 156 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 214

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 215 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 269

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 270 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 325

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 326 DVGREIGLTRERVRQIQVEGLRRLREILQGQ 356


>gi|119944449|ref|YP_942129.1| RNA polymerase sigma-38 factor RpoS [Psychromonas ingrahamii 37]
 gi|119863053|gb|ABM02530.1| RNA polymerase sigma-38 factor RpoS [Psychromonas ingrahamii 37]
          Length = 322

 Score =  220 bits (560), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 84/280 (30%), Positives = 141/280 (50%), Gaps = 13/280 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           V        Y+ EI   P+L  +EE   A+R    GD  +  R++ S+LRLVVKI+  Y 
Sbjct: 44  VKSMDATQLYLGEIGFSPLLTAEEEVYYARRLL-RGDQVSRKRMIESNLRLVVKISRRYN 102

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
             GL + ++V EGN+GL++AV+KFDPE+GFR +TY+ WWI+  ++  I+     +++   
Sbjct: 103 NRGLSLLDLVEEGNLGLIRAVEKFDPEKGFRFSTYATWWIRQTIERAIMNQTRTIRLPIH 162

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
              K+L   LR  +     +T           IA+ L VS  EV  +        S++  
Sbjct: 163 IV-KKLNVYLRTAR----ELTHTLTHEPTAEEIAEVLGVSAKEVSKILKLNERISSVDIP 217

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-- 247
           I ++       ++ L    D +E     + +  + +  + + +  LNP++R +   R   
Sbjct: 218 IGNNSD-----KELLDIIPDRKEASPENELQEADMKLRIVKWLEDLNPKQREVLARRFGL 272

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L     TLEN+  E  ++RERVRQI+  A K +++ + +Q
Sbjct: 273 LGYEAATLENVGKEIGLTRERVRQIQVEALKYLRDVLSEQ 312


>gi|170750108|ref|YP_001756368.1| RNA polymerase factor sigma-32 [Methylobacterium radiotolerans JCM
           2831]
 gi|170656630|gb|ACB25685.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium
           radiotolerans JCM 2831]
          Length = 291

 Score =  220 bits (560), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 112/279 (40%), Positives = 180/279 (64%), Gaps = 1/279 (0%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           ++I    + P L ++EE  LA R+++  D  A HRL+++H+RLV+ +A  +R YGLP+++
Sbjct: 10  QFIRTAMEAPFLAREEERGLAVRWKDERDERALHRLISAHMRLVIALAGRFRHYGLPMAD 69

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +V EG++GLM+A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFF
Sbjct: 70  LVQEGHVGLMEAAARFEPERDVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKALFF 129

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKN 196
           NLRRL+  L   T+ ++  E    IA  + VS  +V  M+ RL+G D SLNA +      
Sbjct: 130 NLRRLRARLMQSTEEHVGDEIHRRIASAIGVSRDDVALMDARLSGPDMSLNAPVGEDSDA 189

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           SS+  D+LV   D  ++ +    + + R + L ++++VL+ RE RI   RRL E+  TLE
Sbjct: 190 SSERMDFLVDGADLPDETVSATVDGERRLSWLQQALTVLSERELRILRERRLAEDQATLE 249

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPP 295
            L     +S+ERVRQIE RA +K++ ++  +   ++  P
Sbjct: 250 ALGQRLGISKERVRQIENRALEKLRRALADRFPAATGSP 288


>gi|87301519|ref|ZP_01084359.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
 gi|87283736|gb|EAQ75690.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
          Length = 322

 Score =  220 bits (560), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 76/290 (26%), Positives = 139/290 (47%), Gaps = 31/290 (10%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLA--------------------KRYREHGDLSAAHRL 53
             +  Y+  I ++P+L   EE  LA                    +R++      A  R+
Sbjct: 33  DSIGWYLSNIGRVPLLTAAEEIELAHHVQAMKLLLELPDASLTPRQRHQIRMGGRARDRM 92

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           + ++LRLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+  M
Sbjct: 93  MAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGM 152

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
              I  S   +++    ++K     L +++   + ++    +    + ++  + +   ++
Sbjct: 153 TRAIDNSARTIRLPIHVSEK-----LSKMRRITRELSHRFGRQPNRLELSHAMGMDIKDL 207

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             +  + A   SL+A     +  S+  +  L+ D    E   ++  +R  ++  L   +S
Sbjct: 208 EDLISQSAPCASLDAHARGEEDRSTLGE--LIADPASTE--PMDHMDRSIQKEHLGTWLS 263

Query: 234 VLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            LN RE+ I   R   E   P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 264 QLNEREQEILRLRFGLEGKEPLTLAEIGRKINVSRERVRQLEAKAIMKLR 313


>gi|328474970|gb|EGF45764.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes 220]
          Length = 346

 Score =  220 bits (560), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 69/253 (27%), Positives = 118/253 (46%), Gaps = 13/253 (5%)

Query: 4   KNMSIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
            +MS+    +I   +  Y+ EI ++ +L   EE  LAKR  E GD+ A  RL  ++LRLV
Sbjct: 91  TDMSVPPGVKINDPVRMYLKEIGRVDLLTADEEIALAKRI-EAGDIEAKGRLAEANLRLV 149

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA  Y G G+   +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I    
Sbjct: 150 VSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQA 209

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             ++I     +      L R++  L      +  PE    I +++++   +V  +     
Sbjct: 210 RTIRIPVHMVE--TINKLIRVQRSLLQDLGRDPSPE---EIGEEMDLPTEKVREILKIAQ 264

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              SL   I   +++ S   D++    D       +    +  +  L   +  L  RE  
Sbjct: 265 EPVSLETPI--GEEDDSHLGDFI---EDQDATSPSDHAAYELLKEQLEDVLDTLTDREEN 319

Query: 242 IFEARRLQENPVT 254
           +   R   ++  T
Sbjct: 320 VLRLRFGLDDGRT 332


>gi|119489756|ref|ZP_01622514.1| RNA polymerase sigma factor [Lyngbya sp. PCC 8106]
 gi|119454330|gb|EAW35480.1| RNA polymerase sigma factor [Lyngbya sp. PCC 8106]
          Length = 391

 Score =  220 bits (560), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 76/313 (24%), Positives = 138/313 (44%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS----------------------- 48
            E  +  Y+ EI +I +L   EE  LA+R  +  +L                        
Sbjct: 79  TEDSIRLYLQEIGRIRLLRADEEIELARRIADLLELERIREKLVEHNHCEPEDREWASAV 138

Query: 49  ----------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 139 DMALPEFRRRLYLGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 198

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 199 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKLLSQE 253

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA ++ ++  ++  +        SL   I    +  S+  D++  D     
Sbjct: 254 MGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIESDG---- 307

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
           +   ++  +   R  L   +  L+PRER +   R   ++    TLE +   F V+RER+R
Sbjct: 308 ETPEDQVSKNLLREDLESVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIR 367

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 368 QIEAKALRKLRHP 380


>gi|83950005|ref|ZP_00958738.1| RNA polymerase sigma factor [Roseovarius nubinhibens ISM]
 gi|83837904|gb|EAP77200.1| RNA polymerase sigma factor [Roseovarius nubinhibens ISM]
          Length = 277

 Score =  220 bits (560), Expect = 2e-55,   Method: Composition-based stats.
 Identities = 99/269 (36%), Positives = 168/269 (62%), Gaps = 6/269 (2%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            +  +L+ + E  LA  +R+  D  A HRL+ +++RL + +A  YR YG P+++++ E  
Sbjct: 1   MRAELLDAETELALAYAWRDQRDEEALHRLINAYMRLAISMASKYRRYGAPLNDLIQEAG 60

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           +GLM+A  KFDP+RG R +TY++WWIKA +Q+Y++R+WS+V+ G+T++QK LFFN+RR++
Sbjct: 61  LGLMKAADKFDPDRGVRFSTYAVWWIKAGIQDYVMRNWSMVRTGSTSSQKALFFNMRRVR 120

Query: 144 GHLQAITDNNLKP----EQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSS 198
             ++   + +       +    IA ++ V   +V  M  RL+G D SLNA   S++    
Sbjct: 121 AQIEREAEASGTRLDGHQLREMIATEVGVPLRDVEMMEGRLSGSDLSLNA-TQSTEDEGR 179

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           +W D L  D    E+++ E  +++  R  L  +++ LN RER I   R+L E   TLE+L
Sbjct: 180 EWIDALEDDGPRAEEMVEEDHDQRVLRLWLRDALAALNDRERFILRHRKLSEEVRTLESL 239

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             E  +S+ERVRQ+EA A  K+++ ++++
Sbjct: 240 GEELGLSKERVRQLEAAALVKMRKRLERE 268


>gi|310766652|gb|ADP11602.1| RNA polymerase sigma factor RpoS [Erwinia sp. Ejp617]
          Length = 330

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 79/271 (29%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVFFARR-ALRGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA+KL+    +V  M        S++  +     +  
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAQKLDKPVDDVSRMLRLNERITSVDTPL--GGDSEK 232

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  + D   +   +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 233 ALLDILADEKDNGPE---DTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQGQ 320


>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 =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 65/270 (24%), Positives = 121/270 (44%), Gaps = 24/270 (8%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           + EI K  +L ++E              +A   ++ ++LRLV+ IA  Y   GL   +++
Sbjct: 390 LKEINKNMVLSEKET------------SAAKQEMIQANLRLVISIAKKYTNRGLQFLDLI 437

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +   +
Sbjct: 438 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETI 492

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
            ++    +       +      +A+ + + E ++  +        S+   I   D + S 
Sbjct: 493 NKMNRISRQYLQETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPI--GDDDDSH 550

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLEN 257
             D++    D       E     +   +    +  L PRE ++   R   +     TLE 
Sbjct: 551 LGDFI---EDANNVAPAEAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEE 607

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +  +F+V+RER+RQIEA+A +K++   +  
Sbjct: 608 VGKQFDVTRERIRQIEAKALRKLRHPTRSD 637


>gi|188534815|ref|YP_001908612.1| RNA polymerase sigma factor RpoS [Erwinia tasmaniensis Et1/99]
 gi|188029857|emb|CAO97741.1| RNA polymerase sigma factor RpoS [Erwinia tasmaniensis Et1/99]
          Length = 330

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 79/271 (29%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVFFARR-ALRGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA+KL+    +V  M        S++  +     +  
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEKLDKPVDDVSRMLRLNERITSVDTPL--GGDSEK 232

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  + D   +   +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 233 ALLDILADEKDNGPE---DTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQGQ 320


>gi|113478384|ref|YP_724445.1| RNA polymerase sigma factor RpoD [Trichodesmium erythraeum IMS101]
 gi|110169432|gb|ABG53972.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
          Length = 386

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 77/313 (24%), Positives = 139/313 (44%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------HGDLS---------- 48
            E  +  Y+ EI +I +L   EE  LA++  +             H D            
Sbjct: 74  TEDSIRLYLQEIGRIRLLRADEEIELARKIADLLELERIREELIYHLDREPQVSEWANAV 133

Query: 49  ----------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 134 DMELPKFKRRLILGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 193

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 194 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKLLSQE 248

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA  + ++  ++  +        SL   I    +  S+  D++  D +  E
Sbjct: 249 MGRKPTEEEIATSMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIESDGETPE 306

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
               ++  +   R  L   ++ L+PRER +   R   ++    TLE +   F V+RER+R
Sbjct: 307 ----DEVSKNLLREDLESVLNSLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIR 362

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 363 QIEAKALRKLRHP 375


>gi|297625160|ref|YP_003706594.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Truepera
           radiovictrix DSM 17093]
 gi|297166340|gb|ADI16051.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Truepera
           radiovictrix DSM 17093]
          Length = 446

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 79/301 (26%), Positives = 134/301 (44%), Gaps = 37/301 (12%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------HGD------------- 46
           ++    + +Y+HEI ++ +L  +EE  LA+R  E           GD             
Sbjct: 140 LSTNDPVRQYLHEIGRVSLLTLEEEISLARRIEEGEAAQKRLDEEGDSLPEREQRALKRI 199

Query: 47  ----LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
                 A   L+ ++LRLVV IA  Y G GL   +++ EGN GL++AV+KF+  R ++ +
Sbjct: 200 VEDGEMARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYRRRYKFS 259

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I     +      L R    LQ         E+V   
Sbjct: 260 TYATWWIRQAINRAIADQARTIRIPVHMVE--TINKLTRTARQLQQELSREPSYEEVAE- 316

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A     S  +V  +        SL   I   D+  S + D++  D     +  +++  + 
Sbjct: 317 AMGPGWSAEKVEEVFKVSQEPVSLETPI--GDEKDSFYGDFIPDD---NVESPVDQASKT 371

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                L +++  L  RE  + + R+        TLE + + F V+RER+RQIE +A +K+
Sbjct: 372 LLSEELEKALDKLTERESMVLKFRKGLVDGREHTLEEVGAHFGVTRERIRQIENKALRKL 431

Query: 281 Q 281
           +
Sbjct: 432 K 432


>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 =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 112/247 (45%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV+KF+  RG++ +
Sbjct: 405 EAKMRQAKREMIEANLRLVISIAKKYTNRGLGFLDLIQEGNIGLMKAVEKFEWRRGYKFS 464

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +         PE    +
Sbjct: 465 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMMRVSRQIAQEIGREPTPE---EL 519

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+ L +   +V+ +        SL   I   D   SQ  D++  D     +  ++     
Sbjct: 520 AEHLELPVEKVLQILEVAKEPVSLETPI--GDDEDSQLGDFVEDD---NAENPLDSTIGA 574

Query: 223 NRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                    +  L  RE+++   R         TLE +  +F V+RER+RQIEA+A +K+
Sbjct: 575 ALAEATLEVLENLTDREQKVLRMRFGIGMNTDHTLEEVGKQFGVTRERIRQIEAKALRKL 634

Query: 281 QESIQKQ 287
           +   + Q
Sbjct: 635 RHPSRSQ 641


>gi|302866072|ref|YP_003834709.1| sigma-70 family RNA polymerase [Micromonospora aurantiaca ATCC
           27029]
 gi|315502628|ref|YP_004081515.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Micromonospora
           sp. L5]
 gi|302568931|gb|ADL45133.1| RNA polymerase sigma factor, sigma-70 family [Micromonospora
           aurantiaca ATCC 27029]
 gi|315409247|gb|ADU07364.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Micromonospora
           sp. L5]
          Length = 328

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 70/296 (23%), Positives = 131/296 (44%), Gaps = 37/296 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------HGD--------LSA 49
           +  Y++ I +  +L   +E  L+KR                     H D         +A
Sbjct: 31  VRAYLNGIGRTKLLTAAQEVELSKRIEAGLFAEEKLATCTPVSAELHADLALIAAEGRAA 90

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+ ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI
Sbjct: 91  KDHLLEANLRLVVSIAKRYTGRGMAFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWI 150

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + A+   +      ++I     +      + R+    + ++    +   V  +A  L + 
Sbjct: 151 RQAITRAMADQARTIRIPVHMVE-----QVNRMVRVRRELSVTLGREPTVSEVATALEIP 205

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E +VI +        SL+  +   +   S   D++       E    +       RN + 
Sbjct: 206 EFQVIELISYDREPVSLDQAV--GEDGESALGDFVAAVDPRTE--PGDAATNGELRNEVR 261

Query: 230 RSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             ++ L+ RE+ +   R   ++    TL+ +  EF +SRER+RQIE     K+++ 
Sbjct: 262 IVLATLSQREQAVIRLRFGLDDGRQRTLDEVGREFGLSRERIRQIEKVTLLKLRDP 317


>gi|197335185|ref|YP_002156867.1| RNA polymerase sigma factor RpoS [Vibrio fischeri MJ11]
 gi|197316675|gb|ACH66122.1| RNA polymerase sigma factor RpoS [Vibrio fischeri MJ11]
          Length = 321

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 83/271 (30%), Positives = 139/271 (51%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   + R    GD +A  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 49  YLGEIGFSPLLTAEEEVYFS-RLALKGDEAARARMIESNLRLVVKIARRYNHRGLALLDL 107

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 108 VEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 166

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +  L    D+   PE++     K     S ++ +N R+A  +S+      + ++  
Sbjct: 167 LRAAR-ELSQKLDHEPTPEEIAEKLDKPVSDVSRMLRLNERVASVDSM-----VAGESDK 220

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L    +   +   +K+   +    L   +  LNP+++ +   R   L     TLE
Sbjct: 221 ALLDILPDTKNSDPESETQKD---DINTSLVGWLGQLNPKQKEVVARRFGLLGYEAATLE 277

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +  E  ++RERVRQI+    ++++E +  Q
Sbjct: 278 QVGVEIGLTRERVRQIQVEGLRRLREIMTNQ 308


>gi|145300341|ref|YP_001143182.1| RNA polymerase, sigma factor RpoS [Aeromonas salmonicida subsp.
           salmonicida A449]
 gi|142853113|gb|ABO91434.1| RNA polymerase, sigma factor RpoS [Aeromonas salmonicida subsp.
           salmonicida A449]
          Length = 327

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 83/271 (30%), Positives = 136/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD +A  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 57  YLGEIGFSPLLTAEEEVYYARR-ALRGDKAARKRMIESNLRLVVKIACRYNNRGLVLLDL 115

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 116 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 174

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA  L+ S  +V  M        S++  I        
Sbjct: 175 LRTAR----ELSHRLDHEPTAEDIAFALDRSVDDVNRMLKLNEKITSVDTPI--GGDRDK 228

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  +     ++   + +  + R  +   +  LNP++R +   R   L   P TLE
Sbjct: 229 ALLDVLSDERGMGPEL---ESQDDDMRASIVHWLEELNPKQREVLARRFGLLGYEPATLE 285

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++ SE  ++RERVRQI+    ++++E +  Q
Sbjct: 286 DVGSEIGLTRERVRQIQVEGLRRLREILLGQ 316


>gi|77464172|ref|YP_353676.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides 2.4.1]
 gi|126463015|ref|YP_001044129.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides ATCC 17029]
 gi|221640041|ref|YP_002526303.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides KD131]
 gi|332559048|ref|ZP_08413370.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides WS8N]
 gi|77388590|gb|ABA79775.1| sigma factor RpoH2 (Sigma-32 group [Rhodobacter sphaeroides 2.4.1]
 gi|126104679|gb|ABN77357.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacter sphaeroides
           ATCC 17029]
 gi|221160822|gb|ACM01802.1| RNA polymerase, sigma 32 subunit, RpoH precursor [Rhodobacter
           sphaeroides KD131]
 gi|332276760|gb|EGJ22075.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides WS8N]
          Length = 292

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 106/272 (38%), Positives = 169/272 (62%), Gaps = 6/272 (2%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
            +  +  +L+ + E  LA  +R+  D  A HRL+T+++RL + +A  YR YG P+++++ 
Sbjct: 13  RQAMRAELLDAETELRLAYAWRDQRDERALHRLITAYMRLAISMASKYRRYGAPMNDLIQ 72

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           E ++GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WSLV+ G+T++QK LFFN+R
Sbjct: 73  EASLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSLVRTGSTSSQKALFFNMR 132

Query: 141 RLKGHLQAITDNNLKP----EQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDK 195
           R++  L+       +     +    +A  + V  S+V  M  RL+G D SLNA   S+D 
Sbjct: 133 RVQARLEREASQRGEALDAHQLREMVAHDVGVPLSDVEMMEGRLSGSDFSLNA-TQSADD 191

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
              +W D L  D     +V+    +    R  L  +M  LN RER I   R+L++ P TL
Sbjct: 192 EGREWIDALEDDSAQAAEVVEGSLDAARLRGWLVSAMQQLNARERFIVTERKLRDVPRTL 251

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+L  E ++S+ERVRQ+EA AF K++ S++ Q
Sbjct: 252 ESLGEELKLSKERVRQLEAAAFAKMRRSLEAQ 283


>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 =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 62/242 (25%), Positives = 111/242 (45%), Gaps = 12/242 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 404 AAKREMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 463

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I            + R+       T  +        +A+ + 
Sbjct: 464 WIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQYLQETGED---PDAAKLAELME 518

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + E ++  +        S+   I   D + S   D++    D       +     + R  
Sbjct: 519 MPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDVNNIAPADAAMYSSLREA 573

Query: 228 LTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
               +  L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   +
Sbjct: 574 TKDVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTR 633

Query: 286 KQ 287
             
Sbjct: 634 SD 635


>gi|163786482|ref|ZP_02180930.1| RNA polymerase sigma-70 factor [Flavobacteriales bacterium ALC-1]
 gi|159878342|gb|EDP72398.1| RNA polymerase sigma-70 factor [Flavobacteriales bacterium ALC-1]
          Length = 287

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 71/288 (24%), Positives = 145/288 (50%), Gaps = 13/288 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +    +    +  L +Y+ +I KIP++  +EE  LA+  ++ GD  A  +L T++LR VV
Sbjct: 5   KITKQVTNREDKSLDKYLQDISKIPLITAEEEVELAQLIKK-GDQVALDKLTTANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN GL++A K+FD  RGF+  +Y++WWI+ A+ + +     
Sbjct: 64  SVAKQYQNQGLKLPDLINEGNAGLVKAAKRFDETRGFKFISYAVWWIRQAILQALAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    N+      + +   HL+ +     +P     IA++L++S  EV         
Sbjct: 124 IVRLP--LNKIGTINKINKAFSHLEQLHQ---RPPNAEEIARELDISAREVKQSMKNSGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A +   +  S    D +      +    + KE        + R++  L  +E  +
Sbjct: 179 HLSMDAPLKDGETFS--LYDVVSATESPRPDKNLMKESLNLE---VERALETLTQKESDV 233

Query: 243 FEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
                   +  P+TLE +   ++++RERVRQI  +  ++++ + + ++
Sbjct: 234 IRLNFGIGDQPPMTLEEIGGIYDLTRERVRQIREKGIRRLRHASKSKI 281


>gi|95928999|ref|ZP_01311744.1| RNA polymerase, sigma 38 subunit, RpoS [Desulfuromonas acetoxidans
           DSM 684]
 gi|95134900|gb|EAT16554.1| RNA polymerase, sigma 38 subunit, RpoS [Desulfuromonas acetoxidans
           DSM 684]
          Length = 583

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 74/262 (28%), Positives = 120/262 (45%), Gaps = 14/262 (5%)

Query: 30  EKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
             +E     K     E    +A   LV ++LRLVV IA  Y   GL   +++ EGNIGLM
Sbjct: 323 SPEELVDSLKEVHRGEWRAKAAKTELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLM 382

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV KF+ +RG++ +TY+ WWI+ A+   I      ++I            L R    L 
Sbjct: 383 KAVDKFEYQRGYKFSTYATWWIRQAITRAIADQARTIRIPVHM--IETINKLIRTSRQLV 440

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                   PE    IA+++++   +V  +        SL   I   ++  S   D++   
Sbjct: 441 QELGREPIPE---EIAERMDLPLEKVRRVLKIAKEPISLETPI--GEEEDSSLGDFI--- 492

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVS 265
            D      +E   + N  +     +S L+PRE ++   R         TLE +  +F V+
Sbjct: 493 EDKGAVSPLEAVIKGNLSDQTAEVLSTLSPREEKVLRMRFGIGERSDHTLEEVGQDFNVT 552

Query: 266 RERVRQIEARAFKKVQESIQKQ 287
           RER+RQIEA+A +K++   + +
Sbjct: 553 RERIRQIEAKALRKLRHPSRAK 574


>gi|304413872|ref|ZP_07395289.1| RNA polymerase sigma S (sigma 38) factor [Candidatus Regiella
           insecticola LSR1]
 gi|304283592|gb|EFL91987.1| RNA polymerase sigma S (sigma 38) factor [Candidatus Regiella
           insecticola LSR1]
          Length = 332

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 80/271 (29%), Positives = 136/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD  +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 63  YLGEIGYSPLLTAEEEVYFARR-ALCGDQQSRRRMIESNLRLVVKIARRYGNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 180

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            IA++L+    +V  M        S+++ +     +  
Sbjct: 181 LRTAR----ELAHKLDHEPSAEEIAEQLDRPVDDVSRMLRLNERITSVDSPL--GGDSEK 234

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  D    E    +  +  + ++ + + +  LN ++R +   R   L     TLE
Sbjct: 235 ALLDILSDDS---ENGPEDTTQNDDMKHSIVKWLFELNAKQREVLARRFGLLGYEAATLE 291

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           N+  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 292 NVGKEIGLTRERVRQIQVEGLRRLREILQTQ 322


>gi|299067258|emb|CBJ38455.1| RNA polymerase sigma factor rpoS [Ralstonia solanacearum CMR15]
          Length = 376

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 77/278 (27%), Positives = 133/278 (47%), Gaps = 11/278 (3%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
               +  Y++ I   P+L   EE   +    + G+  A   ++  +LRLVV IA GY   
Sbjct: 100 AADTVQHYLNRISIKPLLTPAEELHFST-LAKAGEFPARQVMIERNLRLVVSIAKGYLNR 158

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           G+P+ +++ EGN+GLM A++KFDPERGFR +TY+ WWI+ +++  I+     V++     
Sbjct: 159 GVPLLDLIEEGNLGLMHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV- 217

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
             R    + R K HL+  +  + +   +  IA  L  +  EV  +        SL+    
Sbjct: 218 -IRELNQVLRAKRHLEK-SGIDGRDASIEDIAHLLGKTTDEVQDVLSLNEHTTSLDTPF- 274

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE- 250
                 +   D+L  +H        ++   +    ++   ++ L+ + R + E R     
Sbjct: 275 -DLDPGTSLLDFLSDEHGASPD---QEVAHRELSQLMKSWLARLSDKHRYVVERRFGLNH 330

Query: 251 -NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             P TLE L++E  ++RERVRQI+  A  K++     Q
Sbjct: 331 IEPATLEELAAEMGLTRERVRQIQQEALVKLKRHFASQ 368


>gi|237809473|ref|YP_002893913.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Tolumonas auensis
           DSM 9187]
 gi|237501734|gb|ACQ94327.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Tolumonas auensis
           DSM 9187]
          Length = 324

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 84/271 (30%), Positives = 135/271 (49%), Gaps = 14/271 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L   EE   A+R    GD +A +R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 55  YLGEIGFSPLLTA-EEVYFARR-ALRGDDAARNRMIESNLRLVVKIARRYNNRGLALLDL 112

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 113 VEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTVERAIMNQTRTIRLPIHVV-KELNVY 171

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            IA  L+    EV  M        S++  I      S 
Sbjct: 172 LRTAR----ELAQRLDHEPTAEDIASLLDKPVEEVSRMLKLNERICSVDTPIAGDGDKS- 226

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  D     +   ++ +  + ++ +   +  LNP++R +   R   L   P TLE
Sbjct: 227 -LIDILTDDRINCPE---DQTQDDDMQHSIVIWLEQLNPKQREVLARRFGLLGYEPATLE 282

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +  E  ++RERVRQI+    ++++E + +Q
Sbjct: 283 EVGEEIGLTRERVRQIQVEGLRRMKEMLTQQ 313


>gi|58584650|ref|YP_198223.1| DNA-directed RNA polymerase sigma 70 subunit, RpoD [Wolbachia
           endosymbiont strain TRS of Brugia malayi]
 gi|58418966|gb|AAW70981.1| DNA-directed RNA polymerase sigma 70 subunit, RpoD [Wolbachia
           endosymbiont strain TRS of Brugia malayi]
          Length = 649

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 70/260 (26%), Positives = 126/260 (48%), Gaps = 15/260 (5%)

Query: 32  QEEYVLAKRYREHGDL--SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           QE   L KR ++H      A   ++ ++LRLVV IA  Y   GL + +++ EGNIGLM+A
Sbjct: 393 QEFKELIKRTQKHEREVSEAKQGMIKANLRLVVSIAKKYSNRGLALLDLIQEGNIGLMKA 452

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V KFD +RG++ +TY  WW++ ++   I     +V+I     +      + ++   L+ +
Sbjct: 453 VDKFDYKRGYKFSTYGTWWVRQSITRAIPEQSKVVRIPVHMVEI-----ISKINRALRKL 507

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
           T    +   +  ++ +L +    +  +        SL+A     D  SS + D +    D
Sbjct: 508 THEMGREPTLEELSMELGMPLERIRKVMKIARDPVSLDAPTGKDD--SSTFGDCI---ED 562

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE---NPVTLENLSSEFEVSR 266
            +     +     + R + T  ++ L P+E RI   R          TLE +   F+V+R
Sbjct: 563 KRVSKPEDAAILTDLRCITTNLLATLTPKEERIIRMRFGLGKDCKEHTLEEIGCIFKVTR 622

Query: 267 ERVRQIEARAFKKVQESIQK 286
           ER+RQ+E++A +K++   + 
Sbjct: 623 ERIRQVESKALRKLKHPCRA 642


>gi|222149282|ref|YP_002550239.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis S4]
 gi|221736266|gb|ACM37229.1| RNA polymerase sigma factor RpoD [Agrobacterium vitis S4]
          Length = 681

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 69/251 (27%), Positives = 119/251 (47%), Gaps = 15/251 (5%)

Query: 41  YREHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
             + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 432 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 491

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I        +   + ++    + +     +  
Sbjct: 492 GYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREP 546

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A+KL +   +V  +        SL   +   D+  S   D++    D    + I+
Sbjct: 547 TPEELAEKLAMPLEKVRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKNALLPID 601

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              + N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+
Sbjct: 602 AAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 661

Query: 276 AFKKVQESIQK 286
           A +K++   + 
Sbjct: 662 ALRKLKHPSRS 672


>gi|34558185|ref|NP_908000.1| RNA polymerase sigma factor RpoD [Wolinella succinogenes DSM 1740]
 gi|34483904|emb|CAE10900.1| RNA POLYMERASE SIGMA FACTOR [Wolinella succinogenes]
          Length = 620

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 77/298 (25%), Positives = 145/298 (48%), Gaps = 26/298 (8%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPM----------LEKQEEYVLAKRYREHGDL--S 48
           M++ +++  V     +S Y+ EI+K+            LE ++   + ++ +   D+   
Sbjct: 322 MSKNDIASAVPEATMVSTYM-EIKKLFQTKQASEESFDLEPEKLKEILEQIKRGKDIADK 380

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ ++G++ +TY+ WW
Sbjct: 381 AKTKMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKKGYKFSTYATWW 440

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + R+   ++       K   V  I++++ +
Sbjct: 441 IRQAISRAIADQARTIRIPIH-----MIETINRINKIIRKYLQEEGKEPDVETISEEVGL 495

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V ++        SL A I S +    ++ D++    D      ++   +++ +  +
Sbjct: 496 PVDKVKNVIKITKEPISLEAPIGSDED--GKFGDFV---EDKSSVGPMDHILKEDLKTQI 550

Query: 229 TRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
              +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++  
Sbjct: 551 DEVLDQLNEREKAVIRMRFGLLEDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHP 608



 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 11/41 (26%), Positives = 20/41 (48%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY 41
           M  + +      +  +  Y+ E+ +IP+L K EE  L+K  
Sbjct: 91  MKERELLEWSRSDSPVRMYLREMGQIPLLTKDEEIELSKNI 131


>gi|209523577|ref|ZP_03272131.1| RNA polymerase, sigma 70 subunit, RpoD family [Arthrospira maxima
           CS-328]
 gi|209495982|gb|EDZ96283.1| RNA polymerase, sigma 70 subunit, RpoD family [Arthrospira maxima
           CS-328]
          Length = 387

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 75/313 (23%), Positives = 138/313 (44%), Gaps = 52/313 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS----------------------- 48
            E  +  Y+ EI +I +L   EE  LA++  +  +L                        
Sbjct: 75  TEDSIRLYLQEIGRIRLLRADEEIELARKIADLLELERIREKLIEHYHREPNEKEWANAV 134

Query: 49  ----------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +K
Sbjct: 135 DMRLPEFRRRLFLGRRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEK 194

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + ++  
Sbjct: 195 FDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKLLSQE 249

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA ++ ++  ++  +        SL   I    +  S+  D++  D     
Sbjct: 250 MGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIESDG---- 303

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
           +   ++  +   R  L   +  L+PRER +   R   ++    TLE +   F V+RER+R
Sbjct: 304 ETPEDQVSKNLLREDLESVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIR 363

Query: 271 QIEARAFKKVQES 283
           QIEA+A +K++  
Sbjct: 364 QIEAKALRKLRHP 376


>gi|146344240|ref|YP_001202096.1| putative RNA polymerase sigma-32 factor [Pseudomonas fluorescens
           SBW25]
 gi|146188052|emb|CAM96382.1| putative RNA polymerase sigma-32 factor [Pseudomonas fluorescens
           SBW25]
          Length = 291

 Score =  220 bits (560), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 105/281 (37%), Positives = 157/281 (55%), Gaps = 13/281 (4%)

Query: 1   MNRKNMSIIVNGEI------GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLV 54
           MN   +S     +I       L  Y+  I  IP +  +EE  L++R  EH D+ AA  LV
Sbjct: 1   MNTSTLSTKAAAQIPMVPGSNLDAYLTVIHSIPNMSAEEERRLSERLVEHNDMDAARELV 60

Query: 55  TSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114
           TS LR VV IA  Y GYGLP+S+++ EGNIGL++AVK+F+P    RL T+ + WI+A + 
Sbjct: 61  TSQLRFVVHIARSYSGYGLPLSDLIQEGNIGLIKAVKRFNPAAQVRLITFGVHWIRAEIN 120

Query: 115 EYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVI 174
           E+I+R+  +V++ TT  Q++LFFNLR+        + N L  ++   IA  LNVS  +V 
Sbjct: 121 EFIIRNGRMVRLATTKAQRKLFFNLRKQPR-----SRNWLTADETRHIADTLNVSVLDVK 175

Query: 175 SMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSM 232
            M  R+AG D S +   ++ D+++       + DH        E E       + L  ++
Sbjct: 176 EMETRMAGNDTSFDPAADADDESAYITPSHQIGDHRYDPAYQYETEADAGTSTDDLHAAL 235

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
           + L+ R R I   R L E+  TL +L+S++ VS ER+RQIE
Sbjct: 236 NNLDERSRDILAQRFLSESKATLNDLASKYNVSAERIRQIE 276


>gi|315122849|ref|YP_004063338.1| RNA polymerase sigma factor RpoD [Candidatus Liberibacter
           solanacearum CLso-ZC1]
 gi|313496251|gb|ADR52850.1| RNA polymerase sigma factor RpoD [Candidatus Liberibacter
           solanacearum CLso-ZC1]
          Length = 683

 Score =  219 bits (559), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 70/241 (29%), Positives = 119/241 (49%), Gaps = 12/241 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ +A  Y   GL   +++ EGNIGLM+AV+KFD   G++ +TY MWW
Sbjct: 445 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAVEKFDWCLGYKFSTYGMWW 504

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           +K A+   I      ++I        +   + ++    + +++   +      IAKKL +
Sbjct: 505 VKQAVTRSIADQSRTIRIPVH-----MIETINKVVRTARRMSNTIKREPTPDEIAKKLAM 559

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
               V  +        SL   I   D+++S   D++    D      ++   + N R   
Sbjct: 560 PLERVQKVLKITKEPISLETPI--GDEDTSHLGDFI---EDKNAVSPVDSAIQANLRENT 614

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 615 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 674

Query: 287 Q 287
           +
Sbjct: 675 K 675


>gi|220917834|ref|YP_002493138.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter
           dehalogenans 2CP-1]
 gi|219955688|gb|ACL66072.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter
           dehalogenans 2CP-1]
          Length = 322

 Score =  219 bits (559), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 110/291 (37%), Positives = 172/291 (59%), Gaps = 14/291 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             L  Y+ E+ + P+L + EE+ LA +YRE GD+ AA+RLV S+LRLVVKIA  YR    
Sbjct: 34  DPLRAYMAEVARHPVLSRDEEHALAVQYRETGDVDAAYRLVASNLRLVVKIAHEYRRTAF 93

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + ++V EGN+GLMQAVKK+DP +G +L++Y+ WWI+A +  +I+ +W LVK+GTT  Q+
Sbjct: 94  QLLDLVQEGNLGLMQAVKKYDPWKGVKLSSYAAWWIRAYIIRFIMENWRLVKLGTTQAQR 153

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINS 192
           +LFFNL + +  L A             +AK L V E +V  M+ R+A D+ SL+A + +
Sbjct: 154 KLFFNLSKEREKLLA----RGIEPTPRLLAKNLQVEEKDVEEMSARMAADDLSLDAPVGT 209

Query: 193 SDKNSSQWQDWLVYDH--DGQEQVLIEKEERKNRRNMLTRSMSVL-NPRERRIFEARRLQ 249
              +  Q +   + D      +  L +++ R+  R  L      L + +ER IFE R L 
Sbjct: 210 EGDDGRQNRLDRLADDGGPSPDAALGDEQLRRIFREKLDAFSGTLTDEKERYIFEHRLLP 269

Query: 250 EN---PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV---ELSSSP 294
            +   P+TL+ +   F ++RER RQIEA+   +++E ++ ++   EL   P
Sbjct: 270 PDGTPPLTLQEVGDHFRLTRERARQIEAKLTGRLREFLRAEIPDFELLGPP 320


>gi|302525710|ref|ZP_07278052.1| RNA polymerase sigma factor RpoS [Streptomyces sp. AA4]
 gi|302434605|gb|EFL06421.1| RNA polymerase sigma factor RpoS [Streptomyces sp. AA4]
          Length = 317

 Score =  219 bits (559), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 68/315 (21%), Positives = 139/315 (44%), Gaps = 38/315 (12%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY------------------R 42
           +   ++         +  Y++ I K  +L   +E  LAKR                   +
Sbjct: 6   LTDADLDAQSPAADLVRVYLNGIGKTALLTAADEVELAKRIEAGVFAQHMLDTAEDLTPQ 65

Query: 43  EHGDLS--------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
              +L         A + L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++AV+KFD
Sbjct: 66  RRKELRALVRDGHVAKNHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAVEKFD 125

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +GF+ +TY+ WWI+ A+   +      +++     ++     L R++  L      + 
Sbjct: 126 YSKGFKFSTYATWWIRQAITRGMADQGRTIRLPVHLVEQ--VNKLARIRRDLHQQLGRDA 183

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
             E++ A   +  +   ++  +  +     SL+  +    +  +   D++        + 
Sbjct: 184 THEELSA---ESGIPVHKISDLLDQSRDPVSLDMPV--GTEEDAPLGDFIEDSEATDAES 238

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
            +        ++ L R ++ L+ RE+ +   R   ++  P TL+ +   F +SRERVRQI
Sbjct: 239 AV---ISGLLQDDLRRVLATLDDREQHVIRLRYGLDDGQPRTLDQIGKHFGLSRERVRQI 295

Query: 273 EARAFKKVQESIQKQ 287
           E     K+++  +  
Sbjct: 296 EREVMAKLRQGERAD 310


>gi|197123044|ref|YP_002134995.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter sp. K]
 gi|196172893|gb|ACG73866.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter sp. K]
          Length = 322

 Score =  219 bits (559), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 110/291 (37%), Positives = 172/291 (59%), Gaps = 14/291 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             L  Y+ E+ + P+L + EE+ LA +YRE GD+ AA+RLV S+LRLVVKIA  YR    
Sbjct: 34  DPLRAYMAEVARHPVLSRDEEHALAVQYRETGDVDAAYRLVASNLRLVVKIAHEYRRTAF 93

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + ++V EGN+GLMQAVKK+DP +G +L++Y+ WWI+A +  +I+ +W LVK+GTT  Q+
Sbjct: 94  QLLDLVQEGNLGLMQAVKKYDPWKGVKLSSYAAWWIRAYIIRFIMENWRLVKLGTTQAQR 153

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINS 192
           +LFFNL + +  L A             +AK L V E +V  M+ R+A D+ SL+A + +
Sbjct: 154 KLFFNLSKEREKLLA----RGIEPTPRLLAKNLQVEEKDVEEMSARMAADDLSLDAPVGT 209

Query: 193 SDKNSSQWQDWLVYDH--DGQEQVLIEKEERKNRRNMLTRSMSVL-NPRERRIFEARRLQ 249
              +  Q +   + D      +  L +++ R+  R  L      L + +ER IFE R L 
Sbjct: 210 EGDDGRQNRLDRLADDGGPSPDAALGDEQLRRIFREKLDAFSGTLTDEKERYIFEHRLLP 269

Query: 250 EN---PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV---ELSSSP 294
            +   P+TL+ +   F ++RER RQIEA+   +++E ++ ++   EL   P
Sbjct: 270 PDGTPPLTLQEVGDHFRLTRERARQIEAKLTGRLREFLRAEIPDFELLGPP 320


>gi|37519772|ref|NP_923149.1| group 2 sigma 70-type sigma factor [Gloeobacter violaceus PCC 7421]
 gi|35210763|dbj|BAC88144.1| group 2 sigma 70-type sigma factor [Gloeobacter violaceus PCC 7421]
          Length = 356

 Score =  219 bits (559), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 80/281 (28%), Positives = 139/281 (49%), Gaps = 15/281 (5%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLR 59
            RK           +  Y+ EI +IP+L+ +EE +LA+   + G     A  +LV ++LR
Sbjct: 68  ARKTRQSASFERDSVGLYLQEIGRIPLLKPEEEVMLARAIAQGGPKGEWAKRKLVQANLR 127

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           LVV IA  Y   G+P  +++ EG++GL++A +KF+ ERG++ +TY+ WWI+ A+   +  
Sbjct: 128 LVVSIAKKYLNRGVPFLDLIQEGSMGLIRAAEKFEHERGYKFSTYAYWWIRQAITRAVAS 187

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
               V++        L   + R+K   + +     +      +A+ L ++E ++  +   
Sbjct: 188 QARTVRLPVH-----LVEKINRVKKVRRTLAQELGRTPSQGELAEALELAEEDLEHILRA 242

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE-ERKNRRNMLTRSMSVLNPR 238
                SLN  I    +  ++    +      Q  V I++E  R    ++L R    L PR
Sbjct: 243 ARRTVSLN--ITVGKEEDTELIHLIEDSQTDQPDVHIDRESMRVEVSDLLDR---HLTPR 297

Query: 239 ERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAF 277
           ER I + R         TL+ +   F++SRER+RQI+A+AF
Sbjct: 298 ERDILQLRFGLRDGQQRTLDQVGRMFDLSRERIRQIQAKAF 338


>gi|284009102|emb|CBA76093.1| RNA polymerase sigma factor RpoS [Arsenophonus nasoniae]
          Length = 329

 Score =  219 bits (559), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 135/271 (49%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD ++  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 60  YLGEIGYSPLLTAEEEVFYARR-ALRGDAASLQRMIESNLRLVVKISRRYSNRGLALLDL 118

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPE+GFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 119 IEEGNLGLIRAVEKFDPEKGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 177

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            IA++L+    +V  M        S++  I     +  
Sbjct: 178 LRIAR----ELAQKLDHEPSAEEIAERLDKPVDDVSRMLRLNERISSVDTPI--GGDSDK 231

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  D+D   +  I+     N +  + + +  LN ++R +   R   L     TLE
Sbjct: 232 ALLDVLSDDNDSGPEGTIQA---NNMKESIVKWLFELNAKQREVLARRFGLLGYESETLE 288

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +  E  ++RERVRQI+    +++++ +  Q
Sbjct: 289 EVGREIGLTRERVRQIQVEGLRRLKDILHNQ 319


>gi|319405291|emb|CBI78905.1| RNA polymerase sigma factor [Bartonella sp. AR 15-3]
          Length = 669

 Score =  219 bits (559), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 119/240 (49%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 431 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 490

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + I     +      ++ KL++
Sbjct: 491 IRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQILHEIGREPTPEELSSKLSM 545

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   +   D+++S   D++    D    + I+   + N R+  
Sbjct: 546 PLEKVRKVLKIAKEPISLETPV--GDEDASHLGDFI---EDRNALLPIDAAIQANLRDTT 600

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 601 TRILASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 660


>gi|298373668|ref|ZP_06983657.1| RNA polymerase sigma-70 factor [Bacteroidetes oral taxon 274 str.
           F0058]
 gi|298274720|gb|EFI16272.1| RNA polymerase sigma-70 factor [Bacteroidetes oral taxon 274 str.
           F0058]
          Length = 287

 Score =  219 bits (559), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 73/284 (25%), Positives = 143/284 (50%), Gaps = 13/284 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           SI       L +Y+ EI +  ++  ++E  LA+R R+ GD +A  +LV ++LR VV +A 
Sbjct: 9   SITNRESDSLDKYLQEIGREELITIEQEVELAQRIRK-GDHAALDKLVRANLRFVVSVAK 67

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y+  GL + +++ EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     +V++
Sbjct: 68  QYQNQGLSLPDLIDEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSRIVRL 127

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
               NQ      + +     +   +       V  IA  L +S  ++           S+
Sbjct: 128 P--LNQVGALNKINKAFQRFEQEHERL---PSVEEIATDLEISLDKITDTMKVSGRHISV 182

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS-VLNPRERRIFEA 245
           +A     + N+    D L+ D         +K   ++    + R++  +L  RER I + 
Sbjct: 183 DAPFVDGEDNT--LLDVLMNDSSPATD---QKLMSESLLTEIERALDALLQERERDIVKM 237

Query: 246 RRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
                   +TLE +  +F ++RERVRQI+ +A ++++ + + ++
Sbjct: 238 FFGIGCAEMTLEEIGDQFGLTRERVRQIKEKAIRRLRGNSKNKL 281


>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 =  219 bits (559), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 68/263 (25%), Positives = 117/263 (44%), Gaps = 14/263 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L   E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 343 LTVAEIKEINRRMSMGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 402

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 403 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 460

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    + +++ + E +V  +        S+   I   D   S   D++  
Sbjct: 461 LQEMGREPTPE---ELGERMEMPEDKVRKVLKIAKEPISMETPI--GDDEDSSLGDFI-- 513

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D      ++    +      T  ++ L  RE ++   R   +     TLE +  +F+V
Sbjct: 514 -EDVTIASPVDSATEEGLTEATTDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 572

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   +  
Sbjct: 573 TRERIRQIEAKALRKLRHPTRSD 595


>gi|254449272|ref|ZP_05062719.1| RNA polymerase sigma factor RpoS [gamma proteobacterium HTCC5015]
 gi|198261127|gb|EDY85425.1| RNA polymerase sigma factor RpoS [gamma proteobacterium HTCC5015]
          Length = 308

 Score =  219 bits (559), Expect = 3e-55,   Method: Composition-based stats.
 Identities = 77/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  ++E    +  +E GD +A  +++ S+LRLVVKI+  Y   GLP+ ++
Sbjct: 40  YLKEIEFSPLLTAEQEIHYGRLVQE-GDEAARRKMIESNLRLVVKISRRYMNRGLPLLDL 98

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPE+GFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 99  IEEGNLGLIRAVEKFDPEKGFRFSTYATWWIRQTIERGLMNQTRTIRLPIHV-IKELNVY 157

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +   Q       +      +AK L+    +V  M        S++  I    +  S
Sbjct: 158 LRAARAMQQEFA----REPTPEEVAKHLDKPVDDVCRMYGLNERVASVDVPI--GKEGDS 211

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
              D +  D       L++ EE       +   +  L+ +++ + E R     ++  TLE
Sbjct: 212 LLLDLIADDSVPDPTALLQSEEVAAY---VDHWLEELDAKQKAVVERRFGLHGQDYATLE 268

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +  E  V+RERVRQI+  + KK+++ ++ +
Sbjct: 269 VIGHELGVTRERVRQIQMESLKKLRKILEAE 299


>gi|292487251|ref|YP_003530123.1| RNA polymerase sigma factor rpoS [Erwinia amylovora CFBP1430]
 gi|292900377|ref|YP_003539746.1| RNA polymerase sigma subunit RpoS (sigma-38) [Erwinia amylovora
           ATCC 49946]
 gi|3183703|emb|CAA10959.1| RpoS [Erwinia amylovora]
 gi|291200225|emb|CBJ47353.1| RNA polymerase sigma subunit RpoS (sigma-38) [Erwinia amylovora
           ATCC 49946]
 gi|291552670|emb|CBA19715.1| RNA polymerase sigma factor rpoS [Erwinia amylovora CFBP1430]
          Length = 330

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 79/271 (29%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVFFARR-ALRGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA+KL+    +V  M        S++  +     +  
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEKLDKPVDDVSRMLRLNERITSVDTPL--GGDSEK 232

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  + D   +   +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 233 ALLDILADEKDNGPE---DTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQGQ 320


>gi|241662747|ref|YP_002981107.1| RNA polymerase sigma factor RpoS [Ralstonia pickettii 12D]
 gi|240864774|gb|ACS62435.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ralstonia
           pickettii 12D]
          Length = 378

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 77/278 (27%), Positives = 134/278 (48%), Gaps = 11/278 (3%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
               +  Y++ I   P+L   EE   +    + G+ +A   ++  +LRLVV IA GY   
Sbjct: 102 AADTVQHYLNRISIKPLLTPAEELHFST-LAKAGEFAARQVMIERNLRLVVSIAKGYLNR 160

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           G+P+ +++ EGN+GLM A++KFDPERGFR +TY+ WWI+ +++  I+     V++     
Sbjct: 161 GVPLLDLIEEGNLGLMHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV- 219

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
             R    + R K HL+  +  + +   +  IA  L  +  EV  +        SL+    
Sbjct: 220 -IRELNQVLRAKRHLEK-SGVDGRDASLEDIAHLLGKTTEEVQDVLSLNEHTTSLDTPF- 276

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE- 250
                 +   D+L  +H        ++   +    ++   ++ L+ + R + E R     
Sbjct: 277 -DLDPGTSLLDFLSDEHGASPD---QEVAHRELSQLMKSWLARLSDKHRYVVERRFGLNY 332

Query: 251 -NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             P TLE L++E  ++RERVRQI+  A  K++     Q
Sbjct: 333 IEPATLEELAAEMGLTRERVRQIQQEALVKLKRHFASQ 370


>gi|90412104|ref|ZP_01220111.1| putative RNA polymerase sigma-38 factor [Photobacterium profundum
           3TCK]
 gi|90327082|gb|EAS43461.1| putative RNA polymerase sigma-38 factor [Photobacterium profundum
           3TCK]
          Length = 334

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 79/271 (29%), Positives = 134/271 (49%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD  A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 62  YLGEIGFSPLLTAEEEVLYARR-ALRGDEIARKRMIESNLRLVVKISRRYSNRGLALLDL 120

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 121 VEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 179

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            IA +L     +V  M        S++  I     +  
Sbjct: 180 LRTAR----ELAQKLDHEPTAEDIALQLEKPVDDVNRMLRLNERVSSVDNPI--GGDSEK 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D +  +  G  +   + +   + +N +   +  LNP++R +   R   L     TLE
Sbjct: 234 ALLDIIPDEKGGSPESSTQDD---DIKNSIVHWLQELNPKQREVLARRFGLLGYEASTLE 290

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    +++++ +  Q
Sbjct: 291 DVGREIGLTRERVRQIQVEGLRRLRDMLTHQ 321


>gi|269126637|ref|YP_003300007.1| RpoD subfamily RNA polymerase sigma-70 subunit [Thermomonospora
           curvata DSM 43183]
 gi|268311595|gb|ACY97969.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermomonospora
           curvata DSM 43183]
          Length = 444

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 76/298 (25%), Positives = 136/298 (45%), Gaps = 38/298 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR--------------------------YREHGDL 47
             +  Y+  I +  +L  ++E  LAKR                          +      
Sbjct: 146 DSVHTYLKSIGRRQLLTAEQEVELAKRIEAGLYAEYKLENEPDLPPELREELEWVAADGR 205

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   ++ ++LRLVV +A  Y   GL + +VV EGN+GL++AV+KFD  +GF+ +TY+MW
Sbjct: 206 EAKSHMLEANLRLVVSVAKKYSDRGLSLLDVVQEGNLGLIRAVEKFDYTKGFKFSTYAMW 265

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+Q     S   +++     +  +   L R++  +         PE    +A +L+
Sbjct: 266 WIRQAIQRGFADSARTIRLPVHVLE--MLSKLSRVERDMHQRLGREPTPE---ELAAELD 320

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
            S ++V  +        SL++ I   +   ++  D +    D       E  +R+   + 
Sbjct: 321 KSPAQVRELLRTSRQPISLDSTI--GEDGETRIGDLI---EDIDSPEASEMVDRQLMADQ 375

Query: 228 LTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           L RS+S+L+PRE  I   R    +  P TL+ +     ++RER+RQ+E  +  K++  
Sbjct: 376 LRRSLSILSPREEMIMSMRFGLYDGTPRTLDEIGKHLGLTRERIRQLEKESLSKLRHP 433


>gi|291286384|ref|YP_003503200.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Denitrovibrio
           acetiphilus DSM 12809]
 gi|290883544|gb|ADD67244.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Denitrovibrio
           acetiphilus DSM 12809]
          Length = 322

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 71/268 (26%), Positives = 140/268 (52%), Gaps = 12/268 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI K P+L +++E  L++   E G   +   ++  +LRLVV IA  Y   G+ + ++
Sbjct: 54  YLNEISKYPVLTREQEGELSQGI-EKGCNDSKETMIKCNLRLVVSIAKKYINRGMNLVDL 112

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGNIGL++AV+KFD  +GF+ +TY+ WWI+ A++  I+    +V+I    ++     N
Sbjct: 113 VEEGNIGLLKAVEKFDYTKGFKFSTYATWWIRQAIERAIINQCRMVRIPVHMSE-----N 167

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           + ++      +     +   +  ++    +  S +  +   +  D SL+  +      SS
Sbjct: 168 ISKVMKTQNELQQKLGREPTIHELSTACKMPLSTLKKVFDAIKQDTSLDMPV--GGDESS 225

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
              +++  D    +  L  K E  +++ ++ + ++ L+  E+ I   R      +P TLE
Sbjct: 226 TLHEFIADDEKYLDPYL--KIENTSKKEIIFKWLTFLSDNEKTIIIRRYGLTGNDPETLE 283

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++ ++  ++RERVRQIE R   K++  +
Sbjct: 284 SIGNDLGITRERVRQIEKRVLSKMRNLL 311


>gi|300718097|ref|YP_003742900.1| RNA polymerase sigma factor [Erwinia billingiae Eb661]
 gi|299063933|emb|CAX61053.1| RNA polymerase sigma factor [Erwinia billingiae Eb661]
          Length = 330

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 79/271 (29%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVFFARR-ALRGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +T           IA++L+    +V  M        S++  +     +  
Sbjct: 179 LRTAR----ELTHKLDHEPSAEEIAEQLDKPVEDVSRMLRLNERITSVDTPL--GGDSEK 232

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  + D   +   +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 233 ALLDILADEKDNGPE---DTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQAQ 320


>gi|309782329|ref|ZP_07677056.1| RNA polymerase sigma factor RpoS [Ralstonia sp. 5_7_47FAA]
 gi|308918947|gb|EFP64617.1| RNA polymerase sigma factor RpoS [Ralstonia sp. 5_7_47FAA]
          Length = 378

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 77/278 (27%), Positives = 134/278 (48%), Gaps = 11/278 (3%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
               +  Y++ I   P+L   EE   +    + G+ +A   ++  +LRLVV IA GY   
Sbjct: 102 AADTVQHYLNRISIKPLLTPAEELHFST-LAKAGEFAARQVMIERNLRLVVSIAKGYLNR 160

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           G+P+ +++ EGN+GLM A++KFDPERGFR +TY+ WWI+ +++  I+     V++     
Sbjct: 161 GVPLLDLIEEGNLGLMHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV- 219

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
             R    + R K HL+  +  + +   +  IA  L  +  EV  +        SL+    
Sbjct: 220 -IRELNQVLRAKRHLEK-SGVDGRDASLEDIAHLLGKTTEEVQDVLSLNEHTTSLDTPF- 276

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE- 250
                 +   D+L  +H        ++   +    ++   ++ L+ + R + E R     
Sbjct: 277 -DLDPGTSLLDFLSDEHGASPD---QEVAHRELSQLMKSWLARLSDKHRYVVERRFGLNY 332

Query: 251 -NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             P TLE L++E  ++RERVRQI+  A  K++     Q
Sbjct: 333 IEPATLEELAAEMGLTRERVRQIQQEALVKLKRHFASQ 370


>gi|302036356|ref|YP_003796678.1| RNA polymerase sigma factor RpoD (Sigma-70) [Candidatus Nitrospira
           defluvii]
 gi|300604420|emb|CBK40752.1| RNA polymerase sigma factor RpoD (Sigma-70) [Candidatus Nitrospira
           defluvii]
          Length = 601

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 77/275 (28%), Positives = 128/275 (46%), Gaps = 21/275 (7%)

Query: 24  RKIPMLEKQEEYVLAKRYR---------EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            +I  LE +E  + A+  +         E         LV ++LRLVV IA  Y   GL 
Sbjct: 328 GRIRQLETEEALISAEEIKDAVKHLDVAEEKVKRGKAELVEANLRLVVSIAKKYTNRGLQ 387

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
             +++ EGNIGLM+AV KF+ +RG++ +TY+ WWI+ A+   I      ++I        
Sbjct: 388 FLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWWIRQAITRAIADQARTIRIPVHM--IE 445

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               L R   HL         PE    IA+++++   +V  +        SL   I   +
Sbjct: 446 TINKLIRTSRHLVQKLGREPTPE---EIAERMDLPLDKVRKILKIAREPISLETPI--GE 500

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
           +  S   D++    D +    +E   R + +  +  ++  L PRE ++   R        
Sbjct: 501 EEDSHLGDFI---EDKKAVSPLEAAIRYDLQRQINGALETLTPREEKVLRKRFGIGEATD 557

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            TLE +  +FEV+RER+RQIEA+A +K++   + +
Sbjct: 558 HTLEEVGQDFEVTRERIRQIEAKALRKLRHPSRSK 592


>gi|297561520|ref|YP_003680494.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
 gi|296845968|gb|ADH67988.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
          Length = 468

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 75/311 (24%), Positives = 137/311 (44%), Gaps = 44/311 (14%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------HGD----------------- 46
             +  Y+  I +  +L  ++E  LAKR             HG+                 
Sbjct: 164 DSVHTYLKAIGRRQLLTAEQEVDLAKRVEAGLYAEYRLGLHGEVDGSAPLAEAEVEELEW 223

Query: 47  -----LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
                  A   ++ ++LRLVV +A  Y   G+ + +VV EGN+GL++AV+KFD  +GF+ 
Sbjct: 224 VAEDGRKAKSHMLEANLRLVVSVAKKYSDRGMSLLDVVQEGNLGLIRAVEKFDYTKGFKF 283

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY+MWWI+ A+Q     S   +++     +  L   + RL+  +         PE    
Sbjct: 284 STYAMWWIRQAIQRGFADSARTIRLPVHVLE--LLSKVSRLERDMHQALGREPTPE---E 338

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           +  +L+ + +++  +        SL++ I   +   ++  D +    D       E  +R
Sbjct: 339 LGLELDKTPAQIEELLRVTRQPISLDSTI--GEDGETRIGDLI---EDVDASEASEVVDR 393

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           +   + L  ++S L PRE  I   R       P TL+ +     ++RER+RQ+E ++  K
Sbjct: 394 QLMADQLRNALSDLEPREATIMSLRFGLMDGRPRTLDEIGKHLGLTRERIRQLEKQSLSK 453

Query: 280 VQESIQKQVEL 290
           ++   + Q  L
Sbjct: 454 LRHPSRAQQLL 464


>gi|293375429|ref|ZP_06621710.1| RNA polymerase sigma factor RpoD [Turicibacter sanguinis PC909]
 gi|325844412|ref|ZP_08168139.1| RNA polymerase sigma factor RpoD [Turicibacter sp. HGF1]
 gi|292645982|gb|EFF64011.1| RNA polymerase sigma factor RpoD [Turicibacter sanguinis PC909]
 gi|325489086|gb|EGC91470.1| RNA polymerase sigma factor RpoD [Turicibacter sp. HGF1]
          Length = 464

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 76/260 (29%), Positives = 123/260 (47%), Gaps = 17/260 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L ++E    A R   H    A  RLV S+LRLVV IA  + G G+   +++ EGN+GL++
Sbjct: 211 LTEEE----ADRVL-HEAEYAKKRLVESNLRLVVSIARRHIGRGMLFLDLIQEGNMGLIK 265

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           AV+KFD  +GF+ +TY+ WWI+ A+   I      ++I            L R++  L  
Sbjct: 266 AVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPVHM--IETINKLVRIQRQLVQ 323

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                  PE    IA+K+ ++  +   +        SL + +   D+  S   D++    
Sbjct: 324 ELGREPLPE---EIAEKMEITPEKAREILKISQEPISLESPV--GDEADSSLGDFIP--- 375

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSR 266
           D       +    +  +  L   +  L  RE R+   R   E+    TLE +  EF V+R
Sbjct: 376 DADALSPSDFTSNEMLKKELAEVLETLTDREERVLRLRFGLEDGHTRTLEEVGKEFGVTR 435

Query: 267 ERVRQIEARAFKKVQESIQK 286
           ER+RQIEA+A +K++   + 
Sbjct: 436 ERIRQIEAKALRKLRHPSRS 455



 Score = 36.7 bits (84), Expect = 3.8,   Method: Composition-based stats.
 Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 1/35 (2%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
              +  Y+ EI ++ +L  QEE   AK+  E GD+
Sbjct: 133 SDPVHMYLKEIGRVELLSSQEEIKFAKKI-ERGDI 166


>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 =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 65/270 (24%), Positives = 121/270 (44%), Gaps = 24/270 (8%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           + EI K  +L ++E              +A   ++ ++LRLV+ IA  Y   GL   +++
Sbjct: 390 LKEINKNMVLSEKET------------SAAKQEMIQANLRLVISIAKKYTNRGLQFLDLI 437

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +   +
Sbjct: 438 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETI 492

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
            ++    +       +      +A+ + + E ++  +        S+   I   D + S 
Sbjct: 493 NKMNRISRQYLQETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPI--GDDDDSH 550

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLEN 257
             D++    D       E     +   +    +  L PRE ++   R   +     TLE 
Sbjct: 551 LGDFI---EDANNVAPAEAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEE 607

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +  +F+V+RER+RQIEA+A +K++   +  
Sbjct: 608 VGKQFDVTRERIRQIEAKALRKLRHPTRSD 637


>gi|152993293|ref|YP_001359014.1| RNA polymerase sigma factor RpoD [Sulfurovum sp. NBC37-1]
 gi|151425154|dbj|BAF72657.1| RNA polymerase sigma 70 factor [Sulfurovum sp. NBC37-1]
          Length = 612

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 71/260 (27%), Positives = 127/260 (48%), Gaps = 15/260 (5%)

Query: 29  LEKQEEYVLAKRYRE--HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L +++   + ++ R+       A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGL
Sbjct: 351 LSEEKLQAILEQIRQGKAKSEVAKTRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGL 410

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+ E+G++ +TY+ WWI+ A+   I      ++I        +   + R+   +
Sbjct: 411 MKAVDKFEYEKGYKFSTYATWWIRQAISRAIADQARTIRIPIH-----MIETINRINKII 465

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +       K   +  IAK++ ++  +V ++        SL   +   D++  ++ D++  
Sbjct: 466 RKHLQETGKEPDLETIAKEVGLTVDKVKNVIKITKEPVSLETPV--GDEDDGRFGDFI-- 521

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFE 263
             D       +   + +  N +   +  LN RE+ +   R      E+  TLE +  E  
Sbjct: 522 -EDKTTLSPTDAVLKDDLNNQIDEVLDQLNEREKAVIRMRFGLLEDESDRTLEEIGKELN 580

Query: 264 VSRERVRQIEARAFKKVQES 283
           V+RERVRQIE+ A KK++  
Sbjct: 581 VTRERVRQIESSAIKKLKHP 600



 Score = 45.2 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 14/36 (38%), Positives = 22/36 (61%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+ KIP+L K+EE  L+KR  E  D+
Sbjct: 101 SDSPVRMYLREMGKIPLLTKEEEVDLSKRIEEGEDI 136


>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 =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 116/247 (46%), Gaps = 13/247 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 374 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 433

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            L R+             PE    +A+++
Sbjct: 434 WWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQCLQEMGREATPE---ELAERM 488

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D   S   D++    D   ++ ++    ++ R 
Sbjct: 489 GMPEDKIRKVLKIAKEPISMETPIGDDD---SHLGDFI---QDENLELPLDSATAESLRL 542

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                +  L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 543 ATNEVLEGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 602

Query: 285 QKQVELS 291
           + +   S
Sbjct: 603 RSETLRS 609


>gi|1405331|dbj|BAA11832.1| chloroplast RNA polymerase sigma subunit [Cyanidium caldarium]
          Length = 591

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 80/324 (24%), Positives = 139/324 (42%), Gaps = 53/324 (16%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY--------------REHG----- 45
           ++S +   +  +  Y+ EI +  +L   EE  L+K+                EHG     
Sbjct: 267 DLSTVEAKDDTIRSYLREIGRYQLLHPGEEIELSKQVCILMDLEQFQRSFREEHGKSPTE 326

Query: 46  ----------------------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
                                    A  R+VT++LRLVV IA  Y   G+ + +++ EG+
Sbjct: 327 SEWAQGCGYGDDVEKLREHIRDGRKAKERMVTANLRLVVSIAKRYSNRGVALQDLIQEGS 386

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++ V+KFD ERGFR +TY+ WWI+ ++   I  S   +++    +       +  ++
Sbjct: 387 IGLIRGVEKFDAERGFRFSTYATWWIRQSITRAISDSSRSIRLPVHVHD-----TISLIR 441

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
              +A+     +P     I + + +  ++   +        SL   + S D        +
Sbjct: 442 KQTKALQVELGRPPSEEEICESVGIDRAKYRLVMECSRNIVSLETPLRSGDD-----VHF 496

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSE 261
           L       E+   E   R   R  + + +  L+ RER +   R       P TLE + S 
Sbjct: 497 LGESLIAPEERAEENCSRDTLRESIEKVLHCLSTREREVIRMRFGLTDGRPRTLEEVGSR 556

Query: 262 FEVSRERVRQIEARAFKKVQESIQ 285
           F V+RER+RQIE++A KK++   +
Sbjct: 557 FNVTRERIRQIESKALKKLRTPAE 580


>gi|194290015|ref|YP_002005922.1| RNA polymerase sigma factor rpos [Cupriavidus taiwanensis LMG
           19424]
 gi|193223850|emb|CAQ69859.1| RNA polymerase sigma factor rpoS [Cupriavidus taiwanensis LMG
           19424]
          Length = 395

 Score =  219 bits (559), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 78/278 (28%), Positives = 132/278 (47%), Gaps = 11/278 (3%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
               +  Y++ I   P+L   EE   +    + GD +A   ++  +LRLVV IA GY   
Sbjct: 119 AADTVQHYLNRISIKPLLSAPEELHFST-LAKDGDFAARQVMIERNLRLVVSIAKGYLNR 177

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           G+P+ +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++     
Sbjct: 178 GVPLLDLIEEGNLGLMHAIEKFDPSRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV- 236

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
             R    + R K HL+     + +   +  IA  L  +  EV  +        SL+    
Sbjct: 237 -IRELNQVLRAKRHLEK-GGTDGRDASLEDIAHLLGKTPDEVQDVLALNEHTTSLDTPF- 293

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE- 250
                 S   D+L  +H+       ++   +    ++   ++ L+ + R + E R     
Sbjct: 294 -DLDPGSSLLDFLSDEHNAAPD---QEVAHRELEGLMKLWLARLSEKHRYVVERRFGLNH 349

Query: 251 -NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             P TLE L+ E  ++RERVRQI+  A  K++     Q
Sbjct: 350 IEPATLEELAEEMGLTRERVRQIQQEALVKLKRHFASQ 387


>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 =  219 bits (558), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 65/247 (26%), Positives = 116/247 (46%), Gaps = 12/247 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 379 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 438

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            L R+             PE    +A+++
Sbjct: 439 WWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQCLQEMGREATPE---ELAERM 493

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D + S   D++    D   ++ ++    ++ R 
Sbjct: 494 GMPEDKIRKVLKIAKEPISMETPI--GDDDDSHLGDFI---QDESLELPLDSATAESLRL 548

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                +  L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 549 ATNEVLEGLTLREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPS 608

Query: 285 QKQVELS 291
           + +   S
Sbjct: 609 RSETLRS 615


>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 =  219 bits (558), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 117/247 (47%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 408 EARAKRAKREMIEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 467

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T    +P     +
Sbjct: 468 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQSTGQEPEP---SEL 522

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+ + E ++  +        S+   I   D   S   D++    D       +     
Sbjct: 523 AEKMEMPEEKIRKILKISKEPISMETPI--GDDEDSHLGDFI---EDVGTLTPDDAAVYG 577

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R++ +  +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 578 SLRSVTSEILEGLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 637

Query: 281 QESIQKQ 287
           +   + +
Sbjct: 638 RHPTRSE 644


>gi|91779751|ref|YP_554959.1| sigma 70 (RpoD) [Burkholderia xenovorans LB400]
 gi|91692411|gb|ABE35609.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia xenovorans
           LB400]
          Length = 647

 Score =  219 bits (558), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 72/261 (27%), Positives = 124/261 (47%), Gaps = 12/261 (4%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L++  E   A    E   L A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM
Sbjct: 387 PLDEFREVCRALSASEAKTLRAKGEMIEANLRLVISIAKRYTNRGLLFLDLIQEGNIGLM 446

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV KF+  RG++ +TY+ WWI+ A+   I      +++        +  +L +LK   +
Sbjct: 447 RAVDKFEYRRGYKFSTYATWWIRQAVSRSIADQARTIRVPVH-----MIESLNKLKRISR 501

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
            I            +A+ + + E +V +M   +    SL+A +  +D  S          
Sbjct: 502 KILQETGNEPDAALLAQLMEMQEQKVRAMLRIVKEPVSLDASVGENDDTSIGDLI----- 556

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVS 265
            D    +  +       R+ ++ ++  L PRE +I   R   E     TLE L  +FE++
Sbjct: 557 EDSAAILPDDAALHAGMRDAISEALMTLTPREAKILRLRFGIESSRDHTLEELGEQFELT 616

Query: 266 RERVRQIEARAFKKVQESIQK 286
           RER+RQIE +A +K++   + 
Sbjct: 617 RERIRQIEVKALRKLRHPARS 637


>gi|237751866|ref|ZP_04582346.1| LOW QUALITY PROTEIN: RNA polymerase sigma factor RpoD [Helicobacter
           winghamensis ATCC BAA-430]
 gi|229376742|gb|EEO26833.1| LOW QUALITY PROTEIN: RNA polymerase sigma factor RpoD [Helicobacter
           winghamensis ATCC BAA-430]
          Length = 615

 Score =  219 bits (558), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 78/298 (26%), Positives = 145/298 (48%), Gaps = 26/298 (8%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPM----------LEKQEEYVLAKRYREHGDL--S 48
           MN+  ++  V     +S Y+ EI+K+            LE ++   + ++ +   D+   
Sbjct: 320 MNKTEITAAVPEATMVSTYM-EIKKLFQTKAASEGSFDLEPEKLKQILEQIKRGKDIADK 378

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ ++G+R +TY+ WW
Sbjct: 379 AKTKMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKKGYRFSTYATWW 438

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + R+   ++       K   +  IA+++ +
Sbjct: 439 IRQAISRAIADQARTIRIPIH-----MIETINRINKIMRKCLQEEGKEPDLEKIAEEVGL 493

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V ++        SL A I + +    ++ D++    D      ++   +++ ++ +
Sbjct: 494 PLDKVKNVIKITKEPISLEAPIGNGED--GKFGDFV---EDKSAVGPMDHILKEDLKSQI 548

Query: 229 TRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
              +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++  
Sbjct: 549 DDVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHP 606



 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 10/41 (24%), Positives = 20/41 (48%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY 41
           M  + +      +  +  Y+ E+ +IP+L + EE  L+K  
Sbjct: 90  MKERELLEWSRSDSPVRMYLREMGQIPLLTRDEEIELSKNI 130


>gi|92114749|ref|YP_574677.1| sigma 28 (flagella/sporulation) [Chromohalobacter salexigens DSM
           3043]
 gi|91797839|gb|ABE59978.1| RNA polymerase, sigma 38 subunit, RpoS [Chromohalobacter salexigens
           DSM 3043]
          Length = 325

 Score =  219 bits (558), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 76/271 (28%), Positives = 133/271 (49%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE     R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 57  YLNEIGFSPLLTPEEEVHYG-RLAQKGDPAGRQRMIESNLRLVVKIARRYLNRGLSLLDL 115

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 116 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHVV-KELNIY 174

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +T           IA+ L+     V  M        S++  +    ++  
Sbjct: 175 LRAAR----ELTQRLDHEATAEEIAEFLDKPVGTVKKMLGLNERVSSVDYPM--GGESDK 228

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
              D L  +++   + L+      + +  +   ++ L  ++  +   R         TLE
Sbjct: 229 PLIDTLADENEAGPESLLVG---NDVKQHVDDWLAELTDKQMEVVVRRFGLRGHEAATLE 285

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +  E  ++RERVRQI+  A KK++  ++KQ
Sbjct: 286 EVGEEIGLTRERVRQIQVEALKKLRRVLEKQ 316


>gi|295102137|emb|CBK99682.1| RNA polymerase sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii L2-6]
          Length = 461

 Score =  219 bits (558), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 72/255 (28%), Positives = 126/255 (49%), Gaps = 14/255 (5%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L ++    L K  R+   L+A   L  ++LRLVV IA  + G+ L   +++ EGNIGL+
Sbjct: 205 PLTEERRQELLKTRRDG--LNARRSLSEANLRLVVSIAKKHVGHNLAFLDLIQEGNIGLI 262

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +A +KFD +RGFR +TY+ WWI+ A+   I      ++I     +      + R++    
Sbjct: 263 KAAEKFDCDRGFRFSTYATWWIRQAITRAIADQARTIRIPVHMVE-----TINRMRQATN 317

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
            +   N        +AK +++S   V  +        SL + +   ++  S   D++   
Sbjct: 318 QLVYQNGHEPTPEELAKAMDMSVERVREIQRMAQEPASLESPV--GEEEDSSLGDFVA-- 373

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVS 265
            D   +   +  +R      + +++  L PRE ++   R   ++  P TLE +  +F V+
Sbjct: 374 -DENAEAPGKAADRAMVAQQINQALKSLTPREEKVIRLRFGLDDGRPRTLEEVGRDFGVT 432

Query: 266 RERVRQIEARAFKKV 280
           RERVRQIEA+A +K+
Sbjct: 433 RERVRQIEAKAIRKL 447



 Score = 40.2 bits (93), Expect = 0.35,   Method: Composition-based stats.
 Identities = 14/41 (34%), Positives = 23/41 (56%), Gaps = 2/41 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRL 53
           +  +  Y+ +I +IP+L  ++E  L+KR   H    AAH L
Sbjct: 103 DDPVKNYLKQIGQIPLLSAEQEVDLSKRI--HAGAEAAHIL 141


>gi|312171353|emb|CBX79612.1| RNA polymerase sigma factor rpoS [Erwinia amylovora ATCC BAA-2158]
          Length = 330

 Score =  219 bits (558), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 79/271 (29%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVFFARR-ALRGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA+KL+    +V  M        S++  +     +  
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEKLDKPVDDVSRMLRLNERITSVDTPL--GGDSEK 232

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  + D   +   +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 233 ALLDILADEKDNGPE---DTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQGQ 320


>gi|319403851|emb|CBI77437.1| RNA polymerase sigma factor [Bartonella rochalimae ATCC BAA-1498]
          Length = 669

 Score =  219 bits (558), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 119/240 (49%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 431 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 490

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + I     +      ++ KL++
Sbjct: 491 IRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQILHEIGREPTPEELSSKLSM 545

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   +   D+++S   D++    D    + I+   + N R+  
Sbjct: 546 PLEKVRKVLKIAKEPISLETPV--GDEDASHLGDFI---EDRNALLPIDAAIQANLRDTT 600

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 601 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 660


>gi|271965471|ref|YP_003339667.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)-like
           protein [Streptosporangium roseum DSM 43021]
 gi|270508646|gb|ACZ86924.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)-like
           protein [Streptosporangium roseum DSM 43021]
          Length = 452

 Score =  219 bits (558), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 74/298 (24%), Positives = 131/298 (43%), Gaps = 38/298 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR--------------------------YREHGDL 47
             +  Y+  I +  +L   +E  LAKR                          +      
Sbjct: 154 DSVHTYLKSIGRRTLLTAAQEVELAKRIEAGLYAESKLEAEPGLSAAARDDLEWVAEDGR 213

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   ++ ++LRLVV +A  Y   G+ + +VV EGN+GL++AV+KFD  +G++ +TY+MW
Sbjct: 214 RAKDHMLEANLRLVVSVAKKYTDRGMALLDVVQEGNLGLIRAVEKFDYTKGYKFSTYAMW 273

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+Q     S   +++     +  +   L R++  +         PE    +A +L+
Sbjct: 274 WIRQAIQRGFADSARTIRLPVHVLE--MLSKLSRVERDMHQRLGREPTPE---ELAVELD 328

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
            +  ++  +        SLNA I   +   +   D L+ D D  E    E  +R+     
Sbjct: 329 KTPDQIEELLRTSRQPISLNATI--GEDGETTIGD-LIEDVDSPEAS--EVVDRQLLGEQ 383

Query: 228 LTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           L   +  L+PRE +I   R       P TL+ +     ++RER+RQ+E  +  K++  
Sbjct: 384 LRGVLGNLSPREAKIMALRFGLVDGKPHTLDEIGKHLGLTRERIRQLEKESLSKLRHP 441


>gi|78185860|ref|YP_378294.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CC9902]
 gi|78170154|gb|ABB27251.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. CC9902]
          Length = 328

 Score =  219 bits (558), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 79/292 (27%), Positives = 143/292 (48%), Gaps = 31/292 (10%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLA--------------------KRYREHGDLSAAH 51
               +  Y+  I ++P+L   EE  LA                    ++++      A  
Sbjct: 37  ATDSIGFYLSSIGRVPLLTAAEEIELAHHVQDMKQLKELPQEELTSRQKHKIRMGKRARD 96

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ ++LRLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+ 
Sbjct: 97  RMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQ 156

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            M   I  S   +++    ++K     L +++   + ++    +    + +A  + +   
Sbjct: 157 GMTRAIDNSARTIRLPIHISEK-----LSKMRRISRELSHRFGRQPNRLELASAMGIEPR 211

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           E+  +  + A   SL+A     +  S+  +  L+ D +G+E   +E  +R  ++  L   
Sbjct: 212 ELEDLITQSAPCASLDAHARGEEDRSTLGE--LIPDPNGEE--PMEGMDRSIQKEHLGGW 267

Query: 232 MSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +S LN RE++I   R     E P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 268 LSQLNEREQKILRLRFGLGGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 319


>gi|300871651|ref|YP_003786524.1| RNA polymerase sigma-70 factor RpoD [Brachyspira pilosicoli
           95/1000]
 gi|300689352|gb|ADK32023.1| RNA polymerase sigma factor rpoD (Sigma-70) [Brachyspira pilosicoli
           95/1000]
          Length = 568

 Score =  219 bits (558), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 66/242 (27%), Positives = 121/242 (50%), Gaps = 12/242 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   +V ++LRLV+ IA  Y   GL   ++V EGNIGL++AV KF+ ++G++ +TY+ W
Sbjct: 329 QAKDHIVKANLRLVISIAKKYTNRGLHFFDLVQEGNIGLIKAVDKFEYKKGYKFSTYATW 388

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++        +   + ++   L+       +   +  IA+ L+
Sbjct: 389 WIRQAITRSISDQARTIRVPVH-----MIEQINKVTRVLRQYMQQYGREPSIQEIARALS 443

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
             ES V S+        SLNA I   D+  +   + +    D + +        K  R  
Sbjct: 444 WPESRVKSVRNVAKDPVSLNAPI--GDEEDTILGELI---EDKEFESPQNITTFKILRKH 498

Query: 228 LTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           +   +  L  RE+++   R   ++    TLE +   F+V+RER+RQIEA+A ++++ + +
Sbjct: 499 IDSLLDNLPEREQKVIRMRYGLDDGYNHTLEEVGYVFKVTRERIRQIEAKAIRRLRATSK 558

Query: 286 KQ 287
           K+
Sbjct: 559 KK 560



 Score = 37.1 bits (85), Expect = 2.9,   Method: Composition-based stats.
 Identities = 31/170 (18%), Positives = 67/170 (39%), Gaps = 7/170 (4%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHL--RLVVKIAMGY 68
           N +  +  Y+ EI K+ +L   +E   +K+  E G+      ++ +HL    V+      
Sbjct: 74  NNDDPIRLYLKEIGKVDLLTHDDEVEYSKKI-ELGESEIESIILNTHLVVGEVLNTIKCV 132

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
               + I E++    I  +   +K   ER ++   +   ++  A ++Y+     + K  T
Sbjct: 133 HSGKVSIHEILEPPRIYNVSTQEKRKLERKYK--NFEKEYVDLA-EKYLALDKRIKKATT 189

Query: 129 TANQKRLFFNLRRLKGHLQAITDN-NLKPEQVVAIAKKLNVSESEVISMN 177
               K L      +K ++  +     L   ++  IA+KL      +  + 
Sbjct: 190 QKTIKNLTNEQNEIKENIVKLLSKVKLNRMEIDRIAEKLKFYLHRINQIE 239


>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 =  219 bits (558), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 60/249 (24%), Positives = 113/249 (45%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E    +A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 397 ISEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 456

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I        +   + ++    +       +     
Sbjct: 457 FSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKMNRISRQYLQETGEEPDSA 511

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+ + + E ++  +        S+   I   D + S   D++    D       +   
Sbjct: 512 KLAELMEMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDINNVAPADAAM 566

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
             +   +    +  L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 567 YSSLHEVTKEVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 626

Query: 279 KVQESIQKQ 287
           K++   +  
Sbjct: 627 KLRHPTRSD 635


>gi|255262130|ref|ZP_05341472.1| RNA polymerase sigma-32 factor [Thalassiobium sp. R2A62]
 gi|255104465|gb|EET47139.1| RNA polymerase sigma-32 factor [Thalassiobium sp. R2A62]
          Length = 292

 Score =  219 bits (558), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 97/272 (35%), Positives = 170/272 (62%), Gaps = 6/272 (2%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
               +  +L+ + E  LA  +R+     + HRL+T+++RL + +A  ++ YG P+++++ 
Sbjct: 13  RRAMRAELLDAETELKLAYAWRDERCEQSLHRLITAYMRLAISMASKFKRYGAPMNDLIQ 72

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           E ++GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFNLR
Sbjct: 73  EASLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNLR 132

Query: 141 RLKGHLQAIT----DNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDK 195
           R++  L+       +   + +    IA ++ V   +V  M  RL+G D SLNA   SS+ 
Sbjct: 133 RVQARLEREAATAGEELDRHQMRQMIATEVGVPLHDVEMMEGRLSGSDYSLNA-TQSSED 191

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
              +W D L  D D   + +    + +  R+ L  ++S L+ RE+ I   R++++   TL
Sbjct: 192 EGREWIDALEDDSDQAAENVENDHDTETLRSWLVTALSALSHREQYIVTERKIKDQTRTL 251

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+L  E  +S+ER+RQ+EA AF K+++S++ Q
Sbjct: 252 ESLGHELGLSKERIRQLEAAAFIKMRKSLEGQ 283


>gi|56750024|ref|YP_170725.1| group2 RNA polymerase sigma factor RpoD6 [Synechococcus elongatus
           PCC 6301]
 gi|56684983|dbj|BAD78205.1| group2 RNA polymerase sigma factor RpoD6 [Synechococcus elongatus
           PCC 6301]
          Length = 316

 Score =  219 bits (558), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 73/297 (24%), Positives = 143/297 (48%), Gaps = 33/297 (11%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL----------------------SAAH 51
             +S Y+  I +IP+L   +E  L ++ +   +L                       A  
Sbjct: 24  DNVSWYLSSIGRIPLLTADQEIELGQKVQVMMNLLEETSSDRTFTEAETAAIQLGQRAKE 83

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ ++LRLVV +A  Y+G GL   +++ EG +GL +AV+KFDP +G++ +TY+ WWI+ 
Sbjct: 84  RMIKANLRLVVSVAKKYQGKGLEFLDLIQEGALGLERAVEKFDPSKGYKFSTYAFWWIRQ 143

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           +M   I      +++     ++     L +++   + +     +      IA+ + +  +
Sbjct: 144 SMTRAIACQSRTIRLPVHLTER-----LSQIRKVTRELAHELGRLPSRQEIAEAVQLPLN 198

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           ++ ++  +     SL+A ++  D  S  +   L+ D +G E   ++  E   +R  L   
Sbjct: 199 DLETILRQSRQCTSLDAPVSGEDGKS--FLGELIADPNGNE--PMDIMENAMQREQLDAW 254

Query: 232 MSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +  L P+ER++   R    +    TL  +    EVSRERVRQ+E +A +K++   ++
Sbjct: 255 LEHLTPQERQVLYLRFGLGDGERHTLAEIGRMMEVSRERVRQVEVKALRKLRNLTKR 311


>gi|22124745|ref|NP_668168.1| RNA polymerase sigma factor RpoS [Yersinia pestis KIM 10]
 gi|45440189|ref|NP_991728.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Microtus
           str. 91001]
 gi|108808779|ref|YP_652695.1| RNA polymerase sigma factor RpoS [Yersinia pestis Antiqua]
 gi|108810903|ref|YP_646670.1| RNA polymerase sigma factor RpoS [Yersinia pestis Nepal516]
 gi|145600262|ref|YP_001164338.1| RNA polymerase sigma factor RpoS [Yersinia pestis Pestoides F]
 gi|153997601|ref|ZP_02022701.1| RNA polymerase sigma factor RpoS [Yersinia pestis CA88-4125]
 gi|162420853|ref|YP_001605522.1| RNA polymerase sigma factor RpoS [Yersinia pestis Angola]
 gi|165925871|ref|ZP_02221703.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Orientalis
           str. F1991016]
 gi|165936700|ref|ZP_02225267.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Orientalis
           str. IP275]
 gi|166010016|ref|ZP_02230914.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Antiqua
           str. E1979001]
 gi|166212931|ref|ZP_02238966.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Antiqua
           str. B42003004]
 gi|167398742|ref|ZP_02304266.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Antiqua
           str. UG05-0454]
 gi|167421704|ref|ZP_02313457.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Orientalis
           str. MG05-1020]
 gi|167423190|ref|ZP_02314943.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar
           Mediaevalis str. K1973002]
 gi|218930373|ref|YP_002348248.1| RNA polymerase sigma factor RpoS [Yersinia pestis CO92]
 gi|229838982|ref|ZP_04459141.1| RNA polymerase, sigma S (sigma 38) factor [Yersinia pestis biovar
           Orientalis str. PEXU2]
 gi|229896462|ref|ZP_04511630.1| RNA polymerase, sigma S (sigma 38) factor [Yersinia pestis
           Pestoides A]
 gi|229899549|ref|ZP_04514690.1| RNA polymerase, sigma S (sigma 38) factor [Yersinia pestis biovar
           Orientalis str. India 195]
 gi|229901116|ref|ZP_04516239.1| RNA polymerase, sigma S (sigma 38) factor [Yersinia pestis
           Nepal516]
 gi|270489294|ref|ZP_06206368.1| RNA polymerase sigma factor RpoS [Yersinia pestis KIM D27]
 gi|294505063|ref|YP_003569125.1| RNA polymerase sigma factor [Yersinia pestis Z176003]
 gi|21957564|gb|AAM84419.1|AE013686_2 RNA polymerase, sigma S (sigma38) factor [Yersinia pestis KIM 10]
 gi|45435045|gb|AAS60605.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Microtus
           str. 91001]
 gi|108774551|gb|ABG17070.1| RNA polymerase sigma factor RpoS [Yersinia pestis Nepal516]
 gi|108780692|gb|ABG14750.1| RNA polymerase sigma factor RpoS [Yersinia pestis Antiqua]
 gi|115348984|emb|CAL21944.1| RNA polymerase sigma factor RpoS [Yersinia pestis CO92]
 gi|145211958|gb|ABP41365.1| RNA polymerase sigma factor RpoS [Yersinia pestis Pestoides F]
 gi|149289238|gb|EDM39318.1| RNA polymerase sigma factor RpoS [Yersinia pestis CA88-4125]
 gi|162353668|gb|ABX87616.1| RNA polymerase sigma factor RpoS [Yersinia pestis Angola]
 gi|165915349|gb|EDR33959.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Orientalis
           str. IP275]
 gi|165922483|gb|EDR39660.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Orientalis
           str. F1991016]
 gi|165990923|gb|EDR43224.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Antiqua
           str. E1979001]
 gi|166205718|gb|EDR50198.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Antiqua
           str. B42003004]
 gi|166960623|gb|EDR56644.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Orientalis
           str. MG05-1020]
 gi|167051246|gb|EDR62654.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar Antiqua
           str. UG05-0454]
 gi|167057360|gb|EDR67106.1| RNA polymerase sigma factor RpoS [Yersinia pestis biovar
           Mediaevalis str. K1973002]
 gi|224483372|gb|ACN50513.1| RpoS [Yersinia pestis]
 gi|229681841|gb|EEO77934.1| RNA polymerase, sigma S (sigma 38) factor [Yersinia pestis
           Nepal516]
 gi|229687041|gb|EEO79116.1| RNA polymerase, sigma S (sigma 38) factor [Yersinia pestis biovar
           Orientalis str. India 195]
 gi|229695348|gb|EEO85395.1| RNA polymerase, sigma S (sigma 38) factor [Yersinia pestis biovar
           Orientalis str. PEXU2]
 gi|229700536|gb|EEO88567.1| RNA polymerase, sigma S (sigma 38) factor [Yersinia pestis
           Pestoides A]
 gi|262363123|gb|ACY59844.1| RNA polymerase sigma factor [Yersinia pestis D106004]
 gi|262367053|gb|ACY63610.1| RNA polymerase sigma factor [Yersinia pestis D182038]
 gi|270337798|gb|EFA48575.1| RNA polymerase sigma factor RpoS [Yersinia pestis KIM D27]
 gi|294355522|gb|ADE65863.1| RNA polymerase sigma factor [Yersinia pestis Z176003]
 gi|320016550|gb|ADW00122.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Medievalis
           str. Harbin 35]
          Length = 332

 Score =  219 bits (558), Expect = 4e-55,   Method: Composition-based stats.
 Identities = 79/271 (29%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+S+  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 63  YLGEIGYSPLLTAEEEVYFARR-ALRGDVSSRRRMIESNLRLVVKIARRYSNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 180

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 181 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 235

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D  E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 236 ----LLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 291

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 292 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 322


>gi|225851205|ref|YP_002731439.1| RNA polymerase sigma factor RpoD (Sigma-70) [Persephonella marina
           EX-H1]
 gi|225645895|gb|ACO04081.1| RNA polymerase sigma factor RpoD (Sigma-70) [Persephonella marina
           EX-H1]
          Length = 577

 Score =  219 bits (558), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 81/285 (28%), Positives = 127/285 (44%), Gaps = 29/285 (10%)

Query: 22  EIRKIPMLEKQEEYVLAKR--------------YREHGDLSA---AHRLVTSHLRLVVKI 64
           EI +   L+ QEE    K                 + G         ++V S+LRLVV I
Sbjct: 295 EILRTETLKLQEEIEELKEMIGTVPTEFDHVINIIQEGRKEVNETKQKIVQSNLRLVVSI 354

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y   GL   +++ EGNIGLM+AV KFD ++G++ +TY+ WWI+ A+   I      +
Sbjct: 355 AKKYTNRGLQFLDLIQEGNIGLMKAVDKFDYKKGYKFSTYATWWIRQAITRAIADQARTI 414

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I            L R+   +         PE    IAKK+ +   +V  +        
Sbjct: 415 RIPVHM--IETINKLVRVARSMVQELGREPTPE---EIAKKVGMPPEKVRKILRTSQEPI 469

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   I   D + S   D++    D       +   R+  R  L   +S L+ RE ++  
Sbjct: 470 SLETPI--GDDDESHLGDFI---EDKTVMSPEQHVLRQALRQQLEEVLSTLSEREEQVLR 524

Query: 245 ARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R   E+    TLE +  +F V+RER+RQIEA+A +K++   + +
Sbjct: 525 YRFGLEDDTEYTLEQVGKKFGVTRERIRQIEAKALRKLRHPHRAK 569



 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 40/211 (18%), Positives = 75/211 (35%), Gaps = 20/211 (9%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHL--RLVVKIAMGYR 69
            +  +  Y+ E+ KIP+L + EE  LAK             L TS L  RL+ + A    
Sbjct: 82  TDDPVKLYLKEMGKIPLLTRDEEIKLAKDIERGRKKVFRGLLRTSFLAERLLDEWAKVAD 141

Query: 70  GYG-------------LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           G                   E   E  +  M A+ K   ++G  LA    +     +++ 
Sbjct: 142 GRMKVKDIINIDSNEYDTEDESYDEAEV--MDAITKDFIQKGLTLAHM--YRELRDLEQA 197

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
           I+ +   V++     +K    N R +K      T  +   +++  +  KL   E ++   
Sbjct: 198 IIENPDDVELKKEFIEKHAKVN-RFIKSLNIKFTKLDKIADELKELYMKLKRKEKDLNKR 256

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
             RL   +     +   D +  +    +  +
Sbjct: 257 IKRLQKIDPDVEKLLKGDYDDPEILKKIEEN 287


>gi|62290370|ref|YP_222163.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 1 str.
           9-941]
 gi|254708148|ref|ZP_05169976.1| RNA polymerase sigma factor RpoD [Brucella pinnipedialis
           M163/99/10]
 gi|261315652|ref|ZP_05954849.1| RNA polymerase sigma factor RpoD [Brucella pinnipedialis
           M163/99/10]
 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]
          Length = 672

 Score =  219 bits (558), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 117/240 (48%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 434 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 493

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + +     +      +A+KL +
Sbjct: 494 IRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREPTPEELAEKLAM 548

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   +   D+  S   D++    D    + I+   + N R+  
Sbjct: 549 PLEKVRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKNALLPIDAAIQANLRDTT 603

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 604 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 663


>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 =  219 bits (558), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 117/240 (48%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 434 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 493

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + +     +      +A+KL +
Sbjct: 494 IRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREPTPEELAEKLTM 548

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   +   D+  S   D++    D    + I+   + N R+  
Sbjct: 549 PLEKVRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKNALLPIDAAIQANLRDTT 603

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 604 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 663


>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 =  219 bits (558), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 65/270 (24%), Positives = 121/270 (44%), Gaps = 24/270 (8%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           + EI K  +L ++E              +A   ++ ++LRLV+ IA  Y   GL   +++
Sbjct: 390 LKEINKNMVLSEKET------------SAAKQEMIQANLRLVISIAKKYTNRGLQFLDLI 437

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +   +
Sbjct: 438 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETI 492

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
            ++    +       +      +A+ + + E ++  +        S+   I   D + S 
Sbjct: 493 NKMNRISRQYLQETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPI--GDDDDSH 550

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLEN 257
             D++    D       E     +   +    +  L PRE ++   R   +     TLE 
Sbjct: 551 LGDFI---EDANNVAPAEAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEE 607

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +  +F+V+RER+RQIEA+A +K++   +  
Sbjct: 608 VGKQFDVTRERIRQIEAKALRKLRHPTRSD 637


>gi|315185379|gb|EFU19152.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           thermophila DSM 6578]
          Length = 292

 Score =  219 bits (558), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 75/275 (27%), Positives = 152/275 (55%), Gaps = 12/275 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           LS Y+ EI +IP+L ++EE   A R    GD  A  +LVT++LR VV +A  Y+  GLP+
Sbjct: 21  LSLYLKEINRIPLLSREEEDHYA-RLAAQGDQDAKEKLVTANLRFVVNVAKKYQNQGLPL 79

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++SEGNIGL+ A+++FDP++G+   +Y++WWI+ A+ + I     ++++         
Sbjct: 80  ADLISEGNIGLLNAIERFDPDKGYHFISYAVWWIRQAILKAISEKSRMIRLPLNRA---- 135

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              L +++   + +   + +  ++  +A+ L+  E  V ++        SL+  +   D+
Sbjct: 136 -NELVQIEKARKLVQTESGEHNEIKKVAETLDYDEDHVANLLNLSKEYVSLDTPVY-EDR 193

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPV 253
           +S+   D+L  +     + ++     K  +  +   ++ L  +E  I + R      +P+
Sbjct: 194 DSAMLGDYLKDEASRPPEDVV---LEKTLQEEIQEVLATLTEKEAEIIQYRFGLNGRHPM 250

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +L+ +   + +++ER+RQIE +A KK+Q+S + +V
Sbjct: 251 SLKEIGDMYNLTKERIRQIEKKALKKIQQSEKAKV 285


>gi|187928144|ref|YP_001898631.1| RNA polymerase sigma factor RpoS [Ralstonia pickettii 12J]
 gi|187725034|gb|ACD26199.1| RNA polymerase, sigma 70 subunit, RpoD family [Ralstonia pickettii
           12J]
          Length = 378

 Score =  219 bits (558), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 77/278 (27%), Positives = 134/278 (48%), Gaps = 11/278 (3%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
               +  Y++ I   P+L   EE   +    + G+ +A   ++  +LRLVV IA GY   
Sbjct: 102 AADTVQHYLNRISIKPLLTPAEELHFST-LAKAGEFAARQVMIERNLRLVVSIAKGYLNR 160

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           G+P+ +++ EGN+GLM A++KFDPERGFR +TY+ WWI+ +++  I+     V++     
Sbjct: 161 GVPLLDLIEEGNLGLMHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV- 219

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
             R    + R K HL+  +  + +   +  IA  L  +  EV  +        SL+    
Sbjct: 220 -IRELNQVLRAKRHLEK-SGVDGRDASLEDIAHLLGKTTEEVQDVLSLNEHTTSLDTPF- 276

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE- 250
                 +   D+L  +H        ++   +    ++   ++ L+ + R + E R     
Sbjct: 277 -DLDPGTSLLDFLSDEHGASPD---QEVAHRELSQLMKSWLARLSDKHRYVVERRFGLNY 332

Query: 251 -NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             P TLE L++E  ++RERVRQI+  A  K++     Q
Sbjct: 333 IEPATLEELAAEMGLTRERVRQIQQEALVKLKRHFASQ 370


>gi|156742920|ref|YP_001433049.1| RpoD family RNA polymerase sigma factor [Roseiflexus castenholzii
           DSM 13941]
 gi|156234248|gb|ABU59031.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus
           castenholzii DSM 13941]
          Length = 348

 Score =  219 bits (558), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 79/298 (26%), Positives = 126/298 (42%), Gaps = 38/298 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE--------------------------HGDL 47
             +  Y+ EI ++P+L   EE  LA+R                                 
Sbjct: 50  DSIQHYLQEIGRVPLLTAAEEIELAERMERGAAAERRLASGEDLSPQLRQALLADVAAAQ 109

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   L+ ++LRLVV IA  Y G GL + +++ EGNIGLM+AV+KFD  +G R +TY+ W
Sbjct: 110 EARRHLIQANLRLVVSIAKKYVGRGLSLLDLIQEGNIGLMRAVEKFDYHKGNRFSTYATW 169

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++    ++      ++R    L    +    PE    IA  L 
Sbjct: 170 WIRQAVTRAIAEQGRTIRLPVHMSES--VGQVKRTADRLAQALERQPTPE---EIATALG 224

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
                +  +        SL   +   +       D+L    D +    +E   ++  R  
Sbjct: 225 QPTERIERVLEASRRPVSLETPV--GEDGEHTLGDFL---QDSELPTPVEAASQQLLRRD 279

Query: 228 LTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           L  ++  LN RERRI + R         TLE +     ++RER RQIEA A ++++  
Sbjct: 280 LAAALDRLNERERRIIDLRYGLVDGQRRTLEEVGRVLGMTRERARQIEAEALRRLRAP 337


>gi|2624188|emb|CAA05499.1| rpoS gene [Kluyvera cryocrescens]
          Length = 345

 Score =  219 bits (558), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 76  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 134

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 135 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 193

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 194 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 248

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D  E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 249 ----LLDILADENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 304

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 305 DVGREIGLTRERVRQIQVEGLRRLREILQGQ 335


>gi|81300366|ref|YP_400574.1| principal RNA polymerase sigma factor SigA [Synechococcus elongatus
           PCC 7942]
 gi|81169247|gb|ABB57587.1| principal RNA polymerase sigma factor SigA [Synechococcus elongatus
           PCC 7942]
          Length = 310

 Score =  219 bits (558), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 73/297 (24%), Positives = 143/297 (48%), Gaps = 33/297 (11%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL----------------------SAAH 51
             +S Y+  I +IP+L   +E  L ++ +   +L                       A  
Sbjct: 18  DNVSWYLSSIGRIPLLTADQEIELGQKVQVMMNLLEETSSDRTFTEAETAAIQLGQRAKE 77

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ ++LRLVV +A  Y+G GL   +++ EG +GL +AV+KFDP +G++ +TY+ WWI+ 
Sbjct: 78  RMIKANLRLVVSVAKKYQGKGLEFLDLIQEGALGLERAVEKFDPSKGYKFSTYAFWWIRQ 137

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           +M   I      +++     ++     L +++   + +     +      IA+ + +  +
Sbjct: 138 SMTRAIACQSRTIRLPVHLTER-----LSQIRKVTRELAHELGRLPSRQEIAEAVQLPLN 192

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           ++ ++  +     SL+A ++  D  S  +   L+ D +G E   ++  E   +R  L   
Sbjct: 193 DLETILRQSRQCTSLDAPVSGEDGKS--FLGELIADPNGNE--PMDIMENAMQREQLDAW 248

Query: 232 MSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +  L P+ER++   R    +    TL  +    EVSRERVRQ+E +A +K++   ++
Sbjct: 249 LEHLTPQERQVLYLRFGLGDGERHTLAEIGRMMEVSRERVRQVEVKALRKLRNLTKR 305


>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 =  219 bits (558), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 66/247 (26%), Positives = 114/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 493 EAKARRAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 552

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T    +P     +
Sbjct: 553 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGQEPEP---AVL 607

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+ + E ++  +        S+   I   D   S   D++    D       +     
Sbjct: 608 AQKMEMPEEKIRKILKISKEPISMETPI--GDDEDSHLGDFI---EDAATMAPADAAVYA 662

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + R +    +  L PRE ++   R   E     TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 663 SLRGVTKDILDSLTPREAKVLRMRFGIEMNTDHTLEEVGKQFDVTRERIRQIEAKALRKL 722

Query: 281 QESIQKQ 287
           +   + +
Sbjct: 723 RHPARSE 729


>gi|194098357|ref|YP_002001415.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae NCCP11945]
 gi|239998768|ref|ZP_04718692.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae 35/02]
 gi|240112698|ref|ZP_04727188.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae MS11]
 gi|240117739|ref|ZP_04731801.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae PID1]
 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|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 =  219 bits (558), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 63/272 (23%), Positives = 122/272 (44%), Gaps = 14/272 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRY--REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + ++ K   +  +E   + K     E    +A   ++ ++LRLV+ IA  Y   GL   +
Sbjct: 368 LADMEKETRISIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLD 427

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +  
Sbjct: 428 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIE 482

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + ++    +       +      +A+ + + E ++  +        S+   I   D + 
Sbjct: 483 TINKMNRISRQHLQETGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPI--GDDDD 540

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D       +     +   +    +  L PRE ++   R   +     TL
Sbjct: 541 SHLGDFI---EDANNVAPADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTL 597

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +  +F+V+RER+RQIEA+A +K++   +  
Sbjct: 598 EEVGRQFDVTRERIRQIEAKALRKLRHPTRSD 629


>gi|149923522|ref|ZP_01911923.1| RNA polymerase sigma factor RpoD [Plesiocystis pacifica SIR-1]
 gi|149815591|gb|EDM75122.1| RNA polymerase sigma factor RpoD [Plesiocystis pacifica SIR-1]
          Length = 589

 Score =  219 bits (558), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 72/242 (29%), Positives = 112/242 (46%), Gaps = 12/242 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ W
Sbjct: 349 RAKAELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATW 408

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I            L R    L         PE    IA+K+ 
Sbjct: 409 WIRQAITRAIADQARTIRIPVHM--IETINKLIRTSRSLVQELGREPTPE---EIAEKME 463

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +   +V  +        SL   I   ++  S   D++    D       E     N  + 
Sbjct: 464 LPLDKVRKVLKIAKEPISLETPI--GEEEDSHLGDFI---EDKNAVSPAEVVININLADQ 518

Query: 228 LTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             R ++ L PRE ++   R         TLE +  +F V+RER+RQIEA+A +K++   +
Sbjct: 519 TRRVLATLTPREEKVLRMRFGIGETSDHTLEEVGQDFSVTRERIRQIEAKALRKLRHPSR 578

Query: 286 KQ 287
            +
Sbjct: 579 SK 580


>gi|330828425|ref|YP_004391377.1| RNA polymerase sigma factor [Aeromonas veronii B565]
 gi|328803561|gb|AEB48760.1| RNA polymerase sigma factor [Aeromonas veronii B565]
          Length = 327

 Score =  219 bits (558), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 82/271 (30%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD +A  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 57  YLGEIGFSPLLTAEEEVYYARR-ALRGDKAARKRMIESNLRLVVKIARRYNNRGLVLLDL 115

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 116 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 174

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA  L+ S  +V  M        S++  I        
Sbjct: 175 LRTAR----ELSHRLDHEPTAEDIAFALDRSVDDVNRMLKLNEKITSVDTPI--GGDRDK 228

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  +     ++   + +  + R+ +   +  LNP++R +   R   L   P TLE
Sbjct: 229 ALLDVLSDERGMGPEL---ESQEDDMRSSIVHWLEELNPKQREVLARRFGLLGYEPATLE 285

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++ +E  ++RERVRQI+    ++++E +  Q
Sbjct: 286 DVGAEIGLTRERVRQIQVEGLRRLREILLSQ 316


>gi|188996275|ref|YP_001930526.1| RNA polymerase, sigma 70 subunit, RpoD family [Sulfurihydrogenibium
           sp. YO3AOP1]
 gi|188931342|gb|ACD65972.1| RNA polymerase, sigma 70 subunit, RpoD family [Sulfurihydrogenibium
           sp. YO3AOP1]
          Length = 590

 Score =  219 bits (558), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 73/240 (30%), Positives = 114/240 (47%), Gaps = 12/240 (5%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV K+D ++GF+ +TY+ WWI
Sbjct: 352 KQVLVKANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKYDYKKGFKFSTYATWWI 411

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + A+   I      ++I            L R+   L         PE    IAKK  + 
Sbjct: 412 RQAITRAIADQARTIRIPVHM--IETINKLLRISRTLVQELGREPTPE---EIAKKAGMP 466

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             +V  +        SL   I S ++  S   D++    D       +   ++  R  L 
Sbjct: 467 ADKVRKILRTSQDPVSLETPIGSDEE--SHLGDFI---EDKTVLSPEQHMLKQALRLQLD 521

Query: 230 RSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             +S L+ RE ++   R   E+    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 522 EVLSTLSEREEQVLRYRFGLEDDTEHTLEQVGKRFGVTRERIRQIEAKALRKLRHPHRAK 581


>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 =  219 bits (558), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 65/270 (24%), Positives = 121/270 (44%), Gaps = 24/270 (8%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           + EI K  +L ++E              +A   ++ ++LRLV+ IA  Y   GL   +++
Sbjct: 390 LKEINKNMVLSEKET------------SAAKQEMIQANLRLVISIAKKYTNRGLQFLDLI 437

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +   +
Sbjct: 438 QEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETI 492

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
            ++    +       +      +A+ + + E ++  +        S+   I   D + S 
Sbjct: 493 NKMNRISRQYLQETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPI--GDDDDSH 550

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLEN 257
             D++    D       E     +   +    +  L PRE ++   R   +     TLE 
Sbjct: 551 LGDFI---EDANNVAPAEAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTLEE 607

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +  +F+V+RER+RQIEA+A +K++   +  
Sbjct: 608 VGKQFDVTRERIRQIEAKALRKLRHPTRSD 637


>gi|59712674|ref|YP_205450.1| RNA polymerase, sigma-S (sigma-38) factor [Vibrio fischeri ES114]
 gi|59480775|gb|AAW86562.1| RNA polymerase, sigma-S (sigma-38) factor [Vibrio fischeri ES114]
          Length = 321

 Score =  219 bits (558), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 83/271 (30%), Positives = 139/271 (51%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   + R    GD +A  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 49  YLGEIGFSPLLTAEEEVYFS-RLALKGDEAARARMIESNLRLVVKIARRYNHRGLALLDL 107

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 108 VEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 166

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +  L    D+   PE++     K     S ++ +N R+A  +S+      + ++  
Sbjct: 167 LRAAR-ELSQKLDHEPTPEEIAEKLDKPVSDVSRMLRLNERVASVDSM-----VAGESDK 220

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L    +   +   +K+   +    L   +  LNP+++ +   R   L     TLE
Sbjct: 221 ALLDILPDTKNSDPESETQKD---DINTSLVGWLGQLNPKQKEVVARRFGLLGYEAATLE 277

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +  E  ++RERVRQI+    ++++E +  Q
Sbjct: 278 QVGIEIGLTRERVRQIQVEGLRRLREIMTNQ 308


>gi|240127996|ref|ZP_04740657.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae SK-93-1035]
 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 =  219 bits (558), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 63/272 (23%), Positives = 122/272 (44%), Gaps = 14/272 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRY--REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + ++ K   +  +E   + K     E    +A   ++ ++LRLV+ IA  Y   GL   +
Sbjct: 368 LADMEKETRISIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLD 427

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +  
Sbjct: 428 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIE 482

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + ++    +       +      +A+ + + E ++  +        S+   I   D + 
Sbjct: 483 TINKMNRISRQHLQETGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPI--GDDDD 540

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D       +     +   +    +  L PRE ++   R   +     TL
Sbjct: 541 SHLGDFI---EDANNVAPADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTL 597

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +  +F+V+RER+RQIEA+A +K++   +  
Sbjct: 598 EEVGRQFDVTRERIRQIEAKALRKLRHPTRSD 629


>gi|240115443|ref|ZP_04729505.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae PID18]
 gi|260440745|ref|ZP_05794561.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae DGI2]
 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 =  219 bits (558), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 63/272 (23%), Positives = 122/272 (44%), Gaps = 14/272 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRY--REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + ++ K   +  +E   + K     E    +A   ++ ++LRLV+ IA  Y   GL   +
Sbjct: 368 LADMEKETRISIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLD 427

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +  
Sbjct: 428 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIE 482

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + ++    +       +      +A+ + + E ++  +        S+   I   D + 
Sbjct: 483 TINKMNRISRQHLQETGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPI--GDDDD 540

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D       +     +   +    +  L PRE ++   R   +     TL
Sbjct: 541 SHLGDFI---EDANNVAPADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTL 597

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +  +F+V+RER+RQIEA+A +K++   +  
Sbjct: 598 EEVGRQFDVTRERIRQIEAKALRKLRHPTRSD 629


>gi|298529696|ref|ZP_07017099.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Desulfonatronospira thiodismutans ASO3-1]
 gi|298511132|gb|EFI35035.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Desulfonatronospira thiodismutans ASO3-1]
          Length = 588

 Score =  219 bits (558), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 71/256 (27%), Positives = 123/256 (48%), Gaps = 13/256 (5%)

Query: 34  EYVLAKRYREHGD-LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           E +L +  + + + L A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV K
Sbjct: 334 EEILWRINKGNEEALRAKQELIRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDK 393

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RG++ +TY+ WWI+ A+   I      ++I            L R   +L      
Sbjct: 394 FEYQRGYKFSTYATWWIRQAITRAIADQARTIRIPVHM--IETINKLVRTSRYLVQELGR 451

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +  PE    IA++++    +V  +        SL   I   D+  S   D++    D + 
Sbjct: 452 DPSPE---EIAERMDYPLEKVKKVLKIAKEPISLETPI--GDEEDSSLGDFI---EDKKA 503

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
               ++         +++ ++ L PRE ++   R         TLE +   F V+RER+R
Sbjct: 504 VAPADEVVNSKLSEQISKVLAELTPREEQVLRKRFGIGEKSDHTLEEVGKLFNVTRERIR 563

Query: 271 QIEARAFKKVQESIQK 286
           QIEA+A +K++  ++ 
Sbjct: 564 QIEAKALRKLRHPVRS 579


>gi|152656|gb|AAA26473.1| sigma factor [Stigmatella aurantiaca]
          Length = 706

 Score =  219 bits (558), Expect = 5e-55,   Method: Composition-based stats.
 Identities = 77/268 (28%), Positives = 120/268 (44%), Gaps = 22/268 (8%)

Query: 32  QEEYVL----------AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           +EE  L          A R  E     A   LV ++LRLVV IA  Y   GL   +++ E
Sbjct: 441 EEEANLPVDALRRNYDAIRLGERRAERAKSELVEANLRLVVSIAKKYTNRGLQFLDLIQE 500

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           GNIGLM+AV KF+ +RG++ +TY+ WWI+ A+   I      ++I            L R
Sbjct: 501 GNIGLMKAVDKFEYKRGYKFSTYATWWIRQAITRAIADQARTIRIPVHM--IETINKLIR 558

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
              +L         PE    IA+K+ +   +V  +        SL   I   ++  S   
Sbjct: 559 TSRYLVQEIGREPTPE---EIAEKMELPLDKVRKVLKIAKEPISLETPI--GEEEDSHLG 613

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLS 259
           D++    D       +     N      + ++ L PRE ++   R         TLE + 
Sbjct: 614 DFI---EDKSLVSPADAVINMNLAARTRKVLATLTPREEKVLRMRFGIGEKSDHTLEEVG 670

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +FEV+RER+RQIEA+A +K++   + +
Sbjct: 671 QDFEVTRERIRQIEAKALRKLRHPSRSK 698


>gi|269120610|ref|YP_003308787.1| RNA polymerase, sigma 32 subunit, RpoH [Sebaldella termitidis ATCC
           33386]
 gi|268614488|gb|ACZ08856.1| RNA polymerase, sigma 32 subunit, RpoH [Sebaldella termitidis ATCC
           33386]
          Length = 270

 Score =  218 bits (557), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 82/273 (30%), Positives = 150/273 (54%), Gaps = 15/273 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y+ +I+K  +L ++EEY L +R +E     A H L+ S+LRLV+ IA    G GLP+
Sbjct: 8   IDLYLKDIQKYELLNREEEYELFRRIKEDDSQDARHELILSNLRLVISIAKKSLGNGLPL 67

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++SEGNIGL++A+ KFD  +G R +TY++WWIK ++++ I+     ++I +       
Sbjct: 68  IDLISEGNIGLIKAINKFDYTKGHRFSTYAVWWIKQSIKKAIINKGRDIRIPSYK----- 122

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           +  L ++   +    +++ +   V  IA++L + E +V  +        SLN +I  +  
Sbjct: 123 YEQLAKVNKVMVNYINDHGETPSVAYIAEQLEIKEYKVSLLINEFQDIISLNDVIGDN-- 180

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--V 253
               + + ++ + D  E+ +I+ ++    R +L    ++L+ RER I E R    N    
Sbjct: 181 ---IFLEDVIGNEDNIEEKIIKNDQINKMRELLD---NILSEREREIIELRYGLYNNKMH 234

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TL+ +  E  ++RERVRQIE +A  K++    +
Sbjct: 235 TLKEIGDELNITRERVRQIEKKAITKLKSHFHE 267


>gi|13472238|ref|NP_103805.1| RNA polymerase sigma factor RpoD [Mesorhizobium loti MAFF303099]
 gi|14022983|dbj|BAB49591.1| RNA polymerase sigma subunit [Mesorhizobium loti MAFF303099]
          Length = 674

 Score =  218 bits (557), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 116/240 (48%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 436 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 495

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + +     +      +A+KL +
Sbjct: 496 IRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREPTPEELAEKLAM 550

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   +   D+  S   D++    D    + I+   + N R   
Sbjct: 551 PLEKVRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKMAILPIDAAIQANLRETT 605

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 606 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 665


>gi|319782038|ref|YP_004141514.1| RNA polymerase sigma factor RpoD [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
 gi|317167926|gb|ADV11464.1| RNA polymerase sigma factor RpoD [Mesorhizobium ciceri biovar
           biserrulae WSM1271]
          Length = 673

 Score =  218 bits (557), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 116/240 (48%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 435 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 494

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + +     +      +A+KL +
Sbjct: 495 IRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREPTPEELAEKLAM 549

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   +   D+  S   D++    D    + I+   + N R   
Sbjct: 550 PLEKVRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKMAILPIDAAIQANLRETT 604

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 605 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 664


>gi|158340411|ref|YP_001521767.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158310652|gb|ABW32266.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 268

 Score =  218 bits (557), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 71/279 (25%), Positives = 138/279 (49%), Gaps = 15/279 (5%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           ++        Y+ EI + P+L  +EE  LA++ +  G+L A  R++  +LRLVV IA  +
Sbjct: 1   MITTPDSTQSYLQEIGRYPLLSPEEEINLARQVK-AGNLRAKQRMIECNLRLVVSIAKKH 59

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           +  GLP+ +++ EGNIGL +AV+KFD  +G R +TY+ WWI   +   +     ++++  
Sbjct: 60  QNRGLPLLDLIQEGNIGLSRAVEKFDLNQGCRFSTYAYWWIWQGITRALHNKTKMIRLPI 119

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
             NQ        ++K     +     +   +  +A  +++  + +           SL+ 
Sbjct: 120 HLNQLH-----SKIKRTYFQLNQEYGRQPSLDEVAYAMDIDPTHIQEQLQLSQEVISLDK 174

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +  S+       + +  DH  Q+       E    ++ L++ M  L+ R++ I   R  
Sbjct: 175 FV--SENQGDTLGELVAKDHSSQKYF-----ENLMNKDELSKLMGHLSERQQFIIGQRFG 227

Query: 249 QEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            E+  P TL  ++   ++SRE +R+IE +AF+++++  Q
Sbjct: 228 LEDGQPKTLVEIAKLLDMSREGIRRIEKKAFQQLKKYAQ 266


>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|240123293|ref|ZP_04736249.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae PID332]
 gi|240125543|ref|ZP_04738429.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae SK-92-679]
 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 =  218 bits (557), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 63/272 (23%), Positives = 122/272 (44%), Gaps = 14/272 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRY--REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + ++ K   +  +E   + K     E    +A   ++ ++LRLV+ IA  Y   GL   +
Sbjct: 368 LADMEKETRISIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLD 427

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +  
Sbjct: 428 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIE 482

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + ++    +       +      +A+ + + E ++  +        S+   I   D + 
Sbjct: 483 TINKMNRISRQHLQETGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPI--GDDDD 540

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D       +     +   +    +  L PRE ++   R   +     TL
Sbjct: 541 SHLGDFI---EDANNVAPADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTL 597

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +  +F+V+RER+RQIEA+A +K++   +  
Sbjct: 598 EEVGRQFDVTRERIRQIEAKALRKLRHPTRSD 629


>gi|1519634|gb|AAC44891.1| sigma 70-type sigma factor SigA [Rhodobacter sphaeroides]
          Length = 666

 Score =  218 bits (557), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 426 RQAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 485

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      +A+KL
Sbjct: 486 WWIRQAITRSIADQARTIRIPVH-----MIETINKLVRTGRQMLHEIGREPTPEELAEKL 540

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   D+  SQ  D++    D    + ++   ++N + 
Sbjct: 541 QMPLEKVRKVMKIAKEPISLETPI--GDEEDSQLGDFI---EDKNAILPLDSAIQENLKE 595

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 596 TTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERLRQIEAKALRKLKHPS 655

Query: 285 QK 286
           + 
Sbjct: 656 RS 657


>gi|118581452|ref|YP_902702.1| RpoD family RNA polymerase sigma factor [Pelobacter propionicus DSM
           2379]
 gi|118504162|gb|ABL00645.1| RNA polymerase, sigma 70 subunit, RpoD [Pelobacter propionicus DSM
           2379]
          Length = 582

 Score =  218 bits (557), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 73/259 (28%), Positives = 123/259 (47%), Gaps = 15/259 (5%)

Query: 34  EYVLAKRYREHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           E   A +  E G+  A      L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV
Sbjct: 327 ELSAALQAIEEGECKARIAKSELIEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAV 386

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
            KF+ +RG++ +TY+ WWI+ A+   I      ++I        +   + +L    + + 
Sbjct: 387 DKFEYQRGYKFSTYATWWIRQAITRAIADQARTIRIPVH-----MIETINKLIRTSRQLV 441

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
             N +      IA+++ +   +V  +        SL   I   ++  S   D++    D 
Sbjct: 442 QENGREPAPEEIAERMQLPLDKVRKVLKIAKEPISLETPI--GEEEDSHLGDFI---EDK 496

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRER 268
                IE   + N     +R +S L PRE ++   R         TLE +  +F V+RER
Sbjct: 497 AVISPIEAVIKANLSEQTSRVLSTLTPREEKVLRMRFGIGEKSDHTLEEVGQDFAVTRER 556

Query: 269 VRQIEARAFKKVQESIQKQ 287
           +RQIEA+A +K++   + +
Sbjct: 557 IRQIEAKALRKLRHPSRSK 575


>gi|224418172|ref|ZP_03656178.1| RNA polymerase sigma factor RpoD [Helicobacter canadensis MIT
           98-5491]
 gi|253827499|ref|ZP_04870384.1| RNA polymerase sigma factor RpoD [Helicobacter canadensis MIT
           98-5491]
 gi|313141707|ref|ZP_07803900.1| RNA polymerase sigma factor RpoD [Helicobacter canadensis MIT
           98-5491]
 gi|253510905|gb|EES89564.1| RNA polymerase sigma factor RpoD [Helicobacter canadensis MIT
           98-5491]
 gi|313130738|gb|EFR48355.1| RNA polymerase sigma factor RpoD [Helicobacter canadensis MIT
           98-5491]
          Length = 616

 Score =  218 bits (557), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 78/298 (26%), Positives = 146/298 (48%), Gaps = 26/298 (8%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKI---PM-------LEKQEEYVLAKRYREHGDLS-- 48
           MN+ ++   V     +S Y+ EI+K+    +       LE ++   + ++ +   D++  
Sbjct: 318 MNKSDIIAAVPEATMVSTYM-EIKKLFQTKLASEGSFDLEPEKLKQILEQIKRGKDIADR 376

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ ++G++ +TY+ WW
Sbjct: 377 AKTKMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKKGYKFSTYATWW 436

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + R+   ++       K   +  IA+++ +
Sbjct: 437 IRQAISRAIADQARTIRIPIH-----MIETINRINKIMRKYLQEEGKEPDIDKIAEEVGL 491

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V ++        SL A I + +    ++ D++    D      +E   +++ +  +
Sbjct: 492 PVDKVKNVIKITKEPISLEAPIGNGED--GKFGDFV---EDKGSVGPMESILKEDLKEQI 546

Query: 229 TRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
              +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++  
Sbjct: 547 DDVLDQLNEREKAVIRMRFGLLEDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHP 604



 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 9/41 (21%), Positives = 21/41 (51%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY 41
           M  + +      +  +  Y+ E+ +IP+L +++E  L+K  
Sbjct: 90  MKERELLEWSRSDSPVRMYLREMGQIPLLTREDEVELSKNI 130


>gi|18477825|emb|CAC83730.1| sigma factor [Rhodococcus fascians]
          Length = 323

 Score =  218 bits (557), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 66/311 (21%), Positives = 135/311 (43%), Gaps = 38/311 (12%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE--------------------- 43
           ++         +  Y++ I +  +L  +EE  LAKR                        
Sbjct: 16  DLDAQSPAADLVRVYLNGIGRTALLTAEEEVDLAKRIEAGLYAKQVLENTKRLSAVKKRN 75

Query: 44  -----HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
                    +A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +G
Sbjct: 76  LAIIVRDGSAARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYAKG 135

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           F+ +TY+ WWI+ A+   +      +++     ++     L R+K  L          E 
Sbjct: 136 FKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLARIKRELHQQLGREATDE- 192

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              ++ +  ++  ++  +        SL+  + S ++  +   D++    D +       
Sbjct: 193 --ELSSESGIAVEKIADLLDHSRDPVSLDMPVGSDEE--APLGDFI---EDSEATSAENA 245

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARA 276
                  + +   +  L+ RE+++   R   ++  P TL+ +   F +SRERVRQIE   
Sbjct: 246 VIAGLLHSDVRVVLGTLDEREQQVIRLRYGLDDGQPRTLDQIGKLFGLSRERVRQIEREV 305

Query: 277 FKKVQESIQKQ 287
             K+++  + +
Sbjct: 306 MVKLRQGDRAE 316


>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 =  218 bits (557), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 65/249 (26%), Positives = 116/249 (46%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 353 IGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 412

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         P+   
Sbjct: 413 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRVSRQMLQEMGREPTPD--- 467

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++++ + +V  +        S+   I   D   S   D++    D +     +   
Sbjct: 468 ELAERVDMPKDKVRKVLKIAKEPISMETPI--GDDEDSHLGDFV---EDAEVVSPPDAAI 522

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
               R    + ++ L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 523 FSGLRETTQQILAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 582

Query: 279 KVQESIQKQ 287
           K++   + +
Sbjct: 583 KLRHPSRSE 591


>gi|2961260|emb|CAA73683.1| rpoS [Enterobacter cloacae]
          Length = 346

 Score =  218 bits (557), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 77  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 135

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 136 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 194

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +     +  
Sbjct: 195 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPL--GGDSEK 248

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  + D   +   +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 249 ALLDILADEKDNGPE---DTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 305

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 306 DVGREIGLTRERVRQIQVEGLRRLREILQGQ 336


>gi|108804071|ref|YP_644008.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108765314|gb|ABG04196.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 294

 Score =  218 bits (557), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 83/268 (30%), Positives = 144/268 (53%), Gaps = 12/268 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L++Y+  I +  +L  QEE  L++R ++ GD  A  +L+  +LRLVV +A  YRGYGLP 
Sbjct: 24  LAKYLAHIGQGELLTHQEEIELSRRAKK-GDRKARQKLIEKNLRLVVSVAKKYRGYGLPF 82

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLM+AV+KFDPERGFR +TY+ WWI+ A+Q  +      +++     +K  
Sbjct: 83  EDLIQEGNIGLMKAVEKFDPERGFRFSTYATWWIRQAVQRAVADKGRTIRVPVHMTEK-- 140

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              +R++      ++    +      IA++L     +V      +    SL+  + SS++
Sbjct: 141 ---IRKVSRTFNELSLELEREPTDEEIARRLEWDVEDVRLTISAMPDATSLDQPV-SSEE 196

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PV 253
           ++S+  D++  +        + KE   +    L  ++  L  R R +   R   ++  P 
Sbjct: 197 SASELGDFIEDERTSDTPDTVLKELESS---QLKEAIERLPERARYVLVRRYGLDDREPA 253

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TL  L  E ++SRERVRQ++  A + ++
Sbjct: 254 TLAELGDELKISRERVRQLQREAERILK 281


>gi|225163701|ref|ZP_03726004.1| RNA polymerase, sigma 70 subunit, RpoD family [Opitutaceae
           bacterium TAV2]
 gi|224801692|gb|EEG19985.1| RNA polymerase, sigma 70 subunit, RpoD family [Opitutaceae
           bacterium TAV2]
          Length = 631

 Score =  218 bits (557), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 67/275 (24%), Positives = 126/275 (45%), Gaps = 14/275 (5%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKR--YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
            +   + EI     +E  +   + ++          A   +V ++LRLV+ IA  Y   G
Sbjct: 296 AIHARLREIEVEQRIEPAQLIEVVRKTNVHIREAHQAKTEMVEANLRLVISIAKKYTNRG 355

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L   +++ EGN+GLM+AV+KF+  RG++ +TY+ WWI+ A+   I      ++I      
Sbjct: 356 LSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM-- 413

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 + +++  L     +   PE+V   A ++N+    V  +        SL + +  
Sbjct: 414 IETLNKVMQVQKQLLQEFGHEPTPEEV---ADEMNLPVERVQQIMKMAQQPISLQSPV-- 468

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QE 250
            D + + + D++    D   +   +       R  +   +  L  RER++   R      
Sbjct: 469 GDGDDTSFGDFI---EDKSAENPYDMTAYSLLREKIIDVLDSLTERERKVLSLRFGLVDG 525

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              TLE +  +F+V+RER+RQIEA+A +K++   +
Sbjct: 526 YSRTLEEVGKQFKVTRERIRQIEAKALRKMRHPTR 560



 Score = 41.0 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 9/44 (20%), Positives = 24/44 (54%), Gaps = 1/44 (2%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTS 56
           +  +  Y+ ++ ++P+L +++E  ++KR  E  +  A   L  +
Sbjct: 117 DDPVRMYLKQMGQVPLLTREQEVEISKRI-ETAESKAQEALFEA 159


>gi|148284623|ref|YP_001248713.1| RNA polymerase sigma factor [Orientia tsutsugamushi str. Boryong]
 gi|146740062|emb|CAM80186.1| RNA polymerase sigma factor [Orientia tsutsugamushi str. Boryong]
          Length = 614

 Score =  218 bits (557), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 71/271 (26%), Positives = 131/271 (48%), Gaps = 14/271 (5%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
            EI +  +L  +    + +  +  E     A  ++V S+ RLVV +A  Y   GLP  ++
Sbjct: 335 GEIEQAMLLPLKRFKEIIQAIQNGERKVRVAKKKMVESNTRLVVHVAKPYVNRGLPFLDL 394

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM+AV K++   G++ +T + WW++ ++   +      ++I            
Sbjct: 395 IQEGNIGLMKAVDKYNYLLGYKFSTCATWWVRQSISRAVADQARTIRIPVHMAD-----T 449

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           + ++    + + +          IA+KL++   +V  +        SL   I   +++ S
Sbjct: 450 ISKIVRVSKQMHNELGYEPTASEIAEKLSMPIDKVKKVMRIAKEPVSLENPI--GEEDGS 507

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLE 256
              D++    D    + IE+  + + R   TR++S L  RE R+   R     P   TLE
Sbjct: 508 CLSDFI---EDKNAVLPIEEAIKFSLRETTTRALSTLTAREERVLRLRFGIGLPTDYTLE 564

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +  EF+V+RERVRQIEA+A +K++  ++ +
Sbjct: 565 EVGGEFKVTRERVRQIEAKALRKLKHPVRSK 595


>gi|146312853|ref|YP_001177927.1| RNA polymerase sigma factor RpoS [Enterobacter sp. 638]
 gi|145319729|gb|ABP61876.1| RNA polymerase, sigma 38 subunit, RpoS [Enterobacter sp. 638]
          Length = 330

 Score =  218 bits (557), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYSNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +     +  
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPL--GGDSEK 232

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  + D   +   +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 233 ALLDILADEKDNGPE---DTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQGQ 320


>gi|306844486|ref|ZP_07477075.1| RNA polymerase sigma factor RpoD [Brucella sp. BO1]
 gi|306275097|gb|EFM56853.1| RNA polymerase sigma factor RpoD [Brucella sp. BO1]
          Length = 672

 Score =  218 bits (557), Expect = 6e-55,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 117/240 (48%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 434 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 493

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + +     +      +A+KL +
Sbjct: 494 IRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREPTPEELAEKLAM 548

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   +   D+  S   D++    D    + I+   + N R+  
Sbjct: 549 PLEKVRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKNALLPIDAAIQANLRDTT 603

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 604 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 663


>gi|83944334|ref|ZP_00956789.1| RNA polymerase sigma factor [Sulfitobacter sp. EE-36]
 gi|83844878|gb|EAP82760.1| RNA polymerase sigma factor [Sulfitobacter sp. EE-36]
          Length = 295

 Score =  218 bits (557), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 106/287 (36%), Positives = 179/287 (62%), Gaps = 9/287 (3%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M++  + E  L+R      K  +L+ + E  LA  +R+  D  A HRL+T+++RL + +A
Sbjct: 4   MTLAQSREFSLTR---TAMKAELLDAETELKLAYAWRDERDEEALHRLITAYMRLAISMA 60

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             ++ YG  +++++ E  +GLM+A  KFDP+RG R +TY++WWIKA++Q++++R+WS+V+
Sbjct: 61  GKFKRYGASMNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDHVMRNWSMVR 120

Query: 126 IGTTANQKRLFFNLRRLKGHL----QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            G+T++QK LFFN+RR++  L    QA  +   K +    I+ ++ V   +V  M  RL+
Sbjct: 121 TGSTSSQKSLFFNMRRVQARLEREAQAAGETLDKHQLRQMISTEIGVPMHDVEMMEGRLS 180

Query: 182 G-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           G D SLNA   S++    +W D LV D     + + E  +    R+ L  +M  LN RE+
Sbjct: 181 GSDFSLNA-TQSAEDEGREWIDALVDDSAQAAERVEESHDTLTLRSWLLSAMQALNEREQ 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            I   R+L++ P TLE+L +E  +S+ERVRQ+EA AF K++++++ Q
Sbjct: 240 FIVRERKLRDQPRTLESLGAELSLSKERVRQLEAAAFGKMRKTLETQ 286


>gi|325971191|ref|YP_004247382.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta sp.
           Buddy]
 gi|324026429|gb|ADY13188.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta sp.
           Buddy]
          Length = 685

 Score =  218 bits (557), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 65/249 (26%), Positives = 125/249 (50%), Gaps = 12/249 (4%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           +Y +     A  RL+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+KF+  +GF
Sbjct: 440 KYGQKMMKDAKDRLIRANLRLVVSIAKKYTNRGLHFFDLVQEGNIGLIKAVEKFEYRKGF 499

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWI+ A+   I      +++        +   + ++    + +  +  +    
Sbjct: 500 KFSTYATWWIRQAITRSISDQARTIRVPVH-----MIEQINKVVRESRMLMQSLGREPTD 554

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +A+KL  +ES+V ++        SL   +   ++  S   D++    D + +    + 
Sbjct: 555 EEVAEKLGWTESKVKAVKNVAREPISLETPV--GEEEDSLLSDFI---EDKEVENPATQT 609

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAF 277
                +  L   ++ L  RE+ + + R   E+   +TLE +   FE++RER+RQIEA+A 
Sbjct: 610 AYSLLQEQLKDVLATLPAREQEVLKMRFGLEDGYSLTLEEVGLYFELTRERIRQIEAKAL 669

Query: 278 KKVQESIQK 286
           ++++   + 
Sbjct: 670 RRLRHPKRS 678



 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 9/33 (27%), Positives = 18/33 (54%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE 43
           +G+  +  Y+ EI K  +L   +E  L+K+  +
Sbjct: 198 SGDDPIRLYLREIGKENLLTADQEVELSKKMED 230


>gi|148657222|ref|YP_001277427.1| RpoD family RNA polymerase sigma factor [Roseiflexus sp. RS-1]
 gi|148569332|gb|ABQ91477.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus sp.
           RS-1]
          Length = 349

 Score =  218 bits (557), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 79/298 (26%), Positives = 127/298 (42%), Gaps = 38/298 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAK--------------------RYREH------GDL 47
             +  Y+ EI ++P+L   EE  LA+                    + R+          
Sbjct: 51  DSIQHYLQEIGRVPLLTAAEEVELAERMERGAAAARRLASAEDLSPQLRQALLDDVAAGQ 110

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   L+ ++LRLVV IA  Y G GL + +++ EGNIGLM+AV+KFD  +G R +TY+ W
Sbjct: 111 EARRHLIQANLRLVVSIAKKYVGRGLSLLDLIQEGNIGLMRAVEKFDHRKGNRFSTYATW 170

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++    ++      ++R    L  + +    PE    IA  L 
Sbjct: 171 WIRQAVTRAIAEQGRTIRLPVHMSES--VGQVKRAADRLAQVLERQPTPE---EIATALG 225

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
                +  +        SL   +   +       D+L    D      +E    +  R  
Sbjct: 226 QPTERIERVLEASRRPVSLEMPV--GEDGEHTLGDFL---QDSDLPTPVEAASHQLLRRD 280

Query: 228 LTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           L  ++  LN RERRI + R         TLE +     ++RER RQIEA A ++++  
Sbjct: 281 LAAALDRLNERERRIIDLRYGLVDGQRRTLEEVGRVLGMTRERARQIEAEALRRLRAP 338


>gi|77165179|ref|YP_343704.1| RpoS [Nitrosococcus oceani ATCC 19707]
 gi|254434741|ref|ZP_05048249.1| RNA polymerase sigma factor, sigma-70 family [Nitrosococcus oceani
           AFC27]
 gi|76883493|gb|ABA58174.1| RNA polymerase, sigma 38 subunit, RpoS [Nitrosococcus oceani ATCC
           19707]
 gi|207091074|gb|EDZ68345.1| RNA polymerase sigma factor, sigma-70 family [Nitrosococcus oceani
           AFC27]
          Length = 303

 Score =  218 bits (557), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 71/271 (26%), Positives = 136/271 (50%), Gaps = 14/271 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ E  K+P+L  +EE   A R  + GD  A + ++ S+LR+V+++A  +   GLP+ ++
Sbjct: 42  YMREAGKVPLLSAEEERHYA-RLAQQGDREARNHIIESNLRIVIRMATRHINRGLPLMDL 100

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL+ AV+KF+PE GFR +TY+ WWI+ A++  ++     +++         F  
Sbjct: 101 IEEGNLGLIDAVEKFNPELGFRFSTYASWWIRQAIERALMNQTRTIRVPIHV-----FKK 155

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           +R  +   +           +  IAK L+     +       A + SL+  +  S+    
Sbjct: 156 IRCYQKEARYFRQRYNIEPHLGEIAKLLHEPLERIQRYLSLQAPEISLDDPL--SEDTDD 213

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLE 256
              D L  + +    +     E  +++  +   +S L  R++ I + R   +     TLE
Sbjct: 214 CLVDLLPDERNNPAILW----EIFDKKASIHNQLSQLPERQQEIIKCRYGLDGYEVTTLE 269

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +  +  ++RERVRQI+  A K++++ I+ +
Sbjct: 270 EIGQKLGITRERVRQIQQTAIKRLRKIIESE 300


>gi|78221616|ref|YP_383363.1| RNA polymerase sigma factor RpoD-like [Geobacter metallireducens
           GS-15]
 gi|78192871|gb|ABB30638.1| RNA polymerase, sigma 70 subunit, RpoD [Geobacter metallireducens
           GS-15]
          Length = 579

 Score =  218 bits (557), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 74/241 (30%), Positives = 116/241 (48%), Gaps = 12/241 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ WW
Sbjct: 342 AKSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWW 401

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I            L R    L         PE    IA+++N+
Sbjct: 402 IRQAITRAIADQARTIRIPVHM--IETINKLIRTSRQLVQEIGREPSPE---EIAERMNL 456

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   I   ++  S   D++    D      +E   + N     
Sbjct: 457 PLDKVRKVLKIAKEPISLETPI--GEEEDSHLGDFI---EDKGVVSPLEAVIKANLSEQT 511

Query: 229 TRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +R +S L PRE ++   R         TLE +  +FEV+RER+RQIEA+A +K++   + 
Sbjct: 512 SRVLSTLTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLRHPSRA 571

Query: 287 Q 287
           +
Sbjct: 572 K 572


>gi|123969020|ref|YP_001009878.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. AS9601]
 gi|123199130|gb|ABM70771.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. AS9601]
          Length = 313

 Score =  218 bits (557), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 77/310 (24%), Positives = 146/310 (47%), Gaps = 36/310 (11%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------EHG------------ 45
           ++          +S Y+  I ++P+L   EE  L  + +      E G            
Sbjct: 8   QSEPPKRRSNDPISWYLQNIGRVPLLTPAEEIELGNQVQKMMILTEDGQLNEKVNEFTTQ 67

Query: 46  -------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
                     A  R++ ++LRLVV +A  Y+G GL + ++V EG++GL +AV+KFDP RG
Sbjct: 68  QKRTIKIGRRAKERMMKANLRLVVSVAKKYQGKGLELLDLVQEGSLGLERAVEKFDPTRG 127

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           ++ +TY+ WWI+ +M   I      +++    +++     L  ++   + +         
Sbjct: 128 YKFSTYAFWWIRQSMTRAIACQSRTIRLPVHLSER-----LASIRKVSRDLAHKLGAMPS 182

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            + IA+ + +   E+ S+  +     SL+A +N  D   S   D +    D   +  +++
Sbjct: 183 RIEIAEAMEIDVEELDSVLRQALSTSSLDAPVN-GDDGRSFLGDLIA---DSNNEEPLDQ 238

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARA 276
            E+K  +  L + +S L+ +E+ + + R   +     TL  +    EVSRERVRQ+E +A
Sbjct: 239 VEQKMHQEQLGKWLSHLSEQEQHVLKLRFGLDANERHTLAEIGRLLEVSRERVRQVELKA 298

Query: 277 FKKVQESIQK 286
            +K++   +K
Sbjct: 299 LRKLRNLTRK 308


>gi|300784474|ref|YP_003764765.1| RNA polymerase primary-like sigma factor [Amycolatopsis
           mediterranei U32]
 gi|299793988|gb|ADJ44363.1| RNA polymerase primary-like sigma factor [Amycolatopsis
           mediterranei U32]
          Length = 343

 Score =  218 bits (557), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 68/315 (21%), Positives = 134/315 (42%), Gaps = 38/315 (12%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------------- 43
           +   ++         +  Y++ I K  +L   +E  LAKR                    
Sbjct: 32  LTDADLDAQSPAADLVRVYLNGIGKTALLSAADEVELAKRIEAGVFAQHMLDTGENLTTK 91

Query: 44  ---------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                         A + L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++AV+KFD
Sbjct: 92  RRTELAALVRDGHVAKNHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAVEKFD 151

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +GF+ +TY+ WWI+ A+   +      +++     ++     L R+K  L      + 
Sbjct: 152 YSKGFKFSTYATWWIRQAITRGMADQGRTIRLPVHLVEQ--VNKLARIKRDLHQQLGRDA 209

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
             E    +A +  +   ++  +        SL+  +    +  +   D++        + 
Sbjct: 210 THE---ELAAESGIPAHKISDLLDHSRDPVSLDMPV--GTEEDAPLGDFIEDSEATDAES 264

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
            +        ++ L R ++ L+ RE+ +   R   ++  P TL+ +   F +SRERVRQI
Sbjct: 265 AV---ISGLLQDDLRRVLATLDDREQHVIRLRYGLDDGQPRTLDQIGKHFGLSRERVRQI 321

Query: 273 EARAFKKVQESIQKQ 287
           E     K+++  +  
Sbjct: 322 EREVMSKLRQGERAD 336


>gi|225627926|ref|ZP_03785962.1| RNA polymerase sigma factor RpoD [Brucella ceti str. Cudo]
 gi|256160209|ref|ZP_05457903.1| RNA polymerase sigma factor RpoD [Brucella ceti M490/95/1]
 gi|256255415|ref|ZP_05460951.1| RNA polymerase sigma factor RpoD [Brucella ceti B1/94]
 gi|260169148|ref|ZP_05755959.1| RNA polymerase sigma factor RpoD [Brucella sp. F5/99]
 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 =  218 bits (556), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 117/240 (48%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 434 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 493

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + +     +      +A+KL +
Sbjct: 494 IRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREPTPEELAEKLAM 548

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   +   D+  S   D++    D    + I+   + N R+  
Sbjct: 549 PLEKVRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKNALLPIDAAIQANLRDTT 603

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 604 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 663


>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 =  218 bits (556), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 69/260 (26%), Positives = 116/260 (44%), Gaps = 16/260 (6%)

Query: 34  EYVLAKRYREHGDLSAAH---RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           E   A R    G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV
Sbjct: 362 EIKEASRLMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 421

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
            KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +    
Sbjct: 422 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEM 479

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
                PE    +A ++ + E ++  +        S+   I   D   S   D++    D 
Sbjct: 480 GREPTPE---ELAARMEMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDR 531

Query: 211 QEQVLIEKEERKNRRNMLTRSMSV-LNPRERRIFEARR--LQENPVTLENLSSEFEVSRE 267
                 +       R ++   +   L PRE ++   R         TLE +  +F+V+RE
Sbjct: 532 NVAAPTDAAVNAAIREVVEELLDTGLTPREAKVLRMRFGIGMNTDHTLEEVGKQFDVTRE 591

Query: 268 RVRQIEARAFKKVQESIQKQ 287
           R+RQIEA+A +K++   + +
Sbjct: 592 RIRQIEAKALRKLRHPSRSE 611


>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|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]
          Length = 672

 Score =  218 bits (556), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 117/240 (48%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 434 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 493

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + +     +      +A+KL +
Sbjct: 494 IRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREPTPEELAEKLAM 548

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   +   D+  S   D++    D    + I+   + N R+  
Sbjct: 549 PLEKVRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKNALLPIDAAIQANLRDTT 603

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 604 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 663


>gi|1710686|sp|P52325|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 =  218 bits (556), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 63/272 (23%), Positives = 122/272 (44%), Gaps = 14/272 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRY--REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + ++ K   +  +E   + K     E    +A   ++ ++LRLV+ IA  Y   GL   +
Sbjct: 368 LADMEKETRISIEELKEINKNMVSSEKVSAAAKQEMIQANLRLVISIAKKYTNRGLQFLD 427

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +  
Sbjct: 428 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIE 482

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + ++    +       +      +A+ + + E ++  +        S+   I   D + 
Sbjct: 483 TINKMNRISRQHLQETGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPI--GDDDD 540

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D       +     +   +    +  L PRE ++   R   +     TL
Sbjct: 541 SHLGDFI---EDANNVAPADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTL 597

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +  +F+V+RER+RQIEA+A +K++   +  
Sbjct: 598 EEVGRQFDVTRERIRQIEAKALRKLRHPTRSD 629


>gi|254496518|ref|ZP_05109389.1| stationary phase specific sigma factor RpoS [Legionella drancourtii
           LLAP12]
 gi|254354257|gb|EET12921.1| stationary phase specific sigma factor RpoS [Legionella drancourtii
           LLAP12]
          Length = 342

 Score =  218 bits (556), Expect = 7e-55,   Method: Composition-based stats.
 Identities = 79/270 (29%), Positives = 141/270 (52%), Gaps = 13/270 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A      GD++A  +++ S+LRLVVKI+  Y   GLP+ ++
Sbjct: 75  YLSEIGFSPLLSAEEEVHYAT-LALKGDVAARKKMIESNLRLVVKISRRYLNRGLPLLDL 133

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM++V+KFDP RGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 134 IEEGNLGLMKSVEKFDPNRGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 192

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +   Q + D+   PE++  +  K      +++ +N ++A   S++  I   +  S 
Sbjct: 193 LRAARQLTQKL-DHEPSPEEIAEMVDKPLEDVQKLLGLNDKVA---SVDTPIGFDENKS- 247

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
              D +  ++      L+  E   N R  +   +  L   ++++   R         TLE
Sbjct: 248 -LLDTIADENSVNPAELLTNE---NLRLHIESLLDKLTENQQQVIARRFGLRGFEKATLE 303

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ++  E +++RERVRQI+  A K ++  ++K
Sbjct: 304 DVGKEIDLTRERVRQIQVEALKTLRGLLEK 333


>gi|149370424|ref|ZP_01890113.1| RNA polymerase sigma-70 factor [unidentified eubacterium SCB49]
 gi|149355975|gb|EDM44532.1| RNA polymerase sigma-70 factor [unidentified eubacterium SCB49]
          Length = 288

 Score =  218 bits (556), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 72/278 (25%), Positives = 147/278 (52%), Gaps = 12/278 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L+ Y+ ++ KI M+  +EE  LA+R RE GD  A  +L  ++LR V+ +A  Y+  GL 
Sbjct: 17  SLNSYLQDVSKIDMITAEEEVELAQRIRE-GDKRALDKLTRANLRFVISVAKQYQNQGLS 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + I     +V++    N+  
Sbjct: 76  LPDLINEGNVGLVKAAKRFDETRGFKFISYAVWWIRQSILQAIAEQSRIVRLP--LNKIG 133

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               +++   HLQ + +   +      IA +L+++ S V S         S++A     +
Sbjct: 134 DINKVKKASIHLQQVYE---RVPTAQEIANELDITVSSVKSSMKNSNRSISMDAPFQEGE 190

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ-ENP- 252
            +++ +         G+         +++ +  + R++  L+ RE  + +       NP 
Sbjct: 191 NDNNLYDVI----SSGESPNPDNGLMQESLKTEIDRALDTLSQREADVVKLNFGLSGNPV 246

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
           +TL+ +   F++SRERVRQI  +A ++++   +  + +
Sbjct: 247 MTLQEIGDTFDLSRERVRQIREKAIRRLRHESKSHILM 284


>gi|33867026|ref|NP_898585.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. WH 8102]
 gi|33639627|emb|CAE09011.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 8102]
          Length = 328

 Score =  218 bits (556), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 81/292 (27%), Positives = 142/292 (48%), Gaps = 31/292 (10%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAK--------------------RYREHGDLSAAH 51
               +  Y+  I +IP+L   EE  LA                     R++      A  
Sbjct: 37  ATDSIGFYLSSIGRIPLLTAAEEIELAHHVQEMKQLQELPEEELTSRHRHKIRMGKRARD 96

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ ++LRLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+ 
Sbjct: 97  RMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQ 156

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            M   I  S   +++    ++K     L +++   + ++    +    + +A  + +   
Sbjct: 157 GMTRAIDNSARTIRLPIHISEK-----LSKMRRISRELSHRFGRQPNRLELASAMGIEPR 211

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           E+  +  + A   SL+A     +  S+  +  L+ D +G+E   +E  +R  ++  L   
Sbjct: 212 ELEDLISQSAPCASLDAHARGEEDRSTLGE--LIPDPNGEE--PMEGMDRSIQKEHLGGW 267

Query: 232 MSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +S LN RE++I   R     E P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 268 LSQLNEREQKILRLRFGLGGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 319


>gi|332667453|ref|YP_004450241.1| RpoD subfamily RNA polymerase sigma-70 subunit [Haliscomenobacter
           hydrossis DSM 1100]
 gi|332336267|gb|AEE53368.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Haliscomenobacter
           hydrossis DSM 1100]
          Length = 288

 Score =  218 bits (556), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 78/278 (28%), Positives = 150/278 (53%), Gaps = 12/278 (4%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           I     + L +Y+++I KIPML   +E  LA+R R+ GD  A  +L  ++LR VV +A  
Sbjct: 10  ITARESLALDKYLNDIGKIPMLTADDEAELARRIRQ-GDDDAMAKLTRANLRFVVSVAKQ 68

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y+  GL +S++++EGN+GLM+A K+FD  +GF+  +Y++WWI+ ++ + I+    +V++ 
Sbjct: 69  YQNQGLSLSDLINEGNVGLMKAAKRFDETKGFKFISYAVWWIRQSILQAIVEYSRIVRLP 128

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
                     +  ++     A      +      + + L ++  EV +M        S++
Sbjct: 129 LNK-----VGSYNKVNEAYLAFIQQFEREPSNEELGELLEMNPREVGNMLKGNGRHVSVD 183

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           A ++  + +S+        D  G +  L+E    ++ ++ + + +S+LN RE  +  A  
Sbjct: 184 APLSGEEGDSTMLDVITDEDDMGPDFRLME----QSLKDEVKQGLSILNIREVEVLSAYY 239

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             E   P+TLE +   + ++RERVRQI+ RA +++++S
Sbjct: 240 GLEGQKPLTLEEIGEMYGLTRERVRQIKERAIRRLRKS 277


>gi|197120055|ref|YP_002140482.1| RNA polymerase sigma-70 factor RpoD [Geobacter bemidjiensis Bem]
 gi|197089415|gb|ACH40686.1| RNA polymerase sigma-70 factor RpoD [Geobacter bemidjiensis Bem]
          Length = 584

 Score =  218 bits (556), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 77/253 (30%), Positives = 119/253 (47%), Gaps = 12/253 (4%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           LA    EH    A   LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +
Sbjct: 335 LAIEEGEHKAKLAKSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQ 394

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RG++ +TY+ WWI+ A+   I      ++I            L R    L         P
Sbjct: 395 RGYKFSTYATWWIRQAITRAIADQARTIRIPVHM--IETINKLIRTSRQLVQEIGREPSP 452

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           E    IA+++ +   +V  +        SL   I   ++  S   D++    D      +
Sbjct: 453 E---EIAERMALPLDKVRKVLKIAKEPISLETPI--GEEEDSHLGDFI---EDKGVVSPL 504

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEA 274
           E   + N     +R +S L PRE ++   R         TLE +  +FEV+RER+RQIEA
Sbjct: 505 EAVIKANLSEQTSRVLSTLTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEA 564

Query: 275 RAFKKVQESIQKQ 287
           +A +K++   + +
Sbjct: 565 KALRKLRHPSRAK 577


>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|254689668|ref|ZP_05152922.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 6 str. 870]
 gi|254694158|ref|ZP_05155986.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 3 str.
           Tulya]
 gi|254697811|ref|ZP_05159639.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 2 str.
           86/8/59]
 gi|254702196|ref|ZP_05164024.1| RNA polymerase sigma factor RpoD [Brucella suis bv. 5 str. 513]
 gi|254714701|ref|ZP_05176512.1| RNA polymerase sigma factor RpoD [Brucella ceti M644/93/1]
 gi|254717762|ref|ZP_05179573.1| RNA polymerase sigma factor RpoD [Brucella ceti M13/05/1]
 gi|254730700|ref|ZP_05189278.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 4 str. 292]
 gi|256045103|ref|ZP_05448004.1| RNA polymerase sigma factor RpoD [Brucella melitensis bv. 1 str.
           Rev.1]
 gi|256114033|ref|ZP_05454810.1| RNA polymerase sigma factor RpoD [Brucella melitensis bv. 3 str.
           Ether]
 gi|256257919|ref|ZP_05463455.1| RNA polymerase sigma factor RpoD [Brucella abortus bv. 9 str. C68]
 gi|256369896|ref|YP_003107407.1| RNA polymerase sigma factor [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|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]
          Length = 672

 Score =  218 bits (556), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 117/240 (48%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 434 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 493

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + +     +      +A+KL +
Sbjct: 494 IRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREPTPEELAEKLAM 548

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   +   D+  S   D++    D    + I+   + N R+  
Sbjct: 549 PLEKVRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKNALLPIDAAIQANLRDTT 603

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 604 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 663


>gi|89073765|ref|ZP_01160279.1| hypothetical DNA-directed RNA polymerase, sigma subunit
           [Photobacterium sp. SKA34]
 gi|89050540|gb|EAR56032.1| hypothetical DNA-directed RNA polymerase, sigma subunit
           [Photobacterium sp. SKA34]
          Length = 291

 Score =  218 bits (556), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 83/289 (28%), Positives = 146/289 (50%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           MN+K       G+I +  Y+ +I + P+L K +E + +++    GD  + + L+ S+LRL
Sbjct: 3   MNKKEEQFSHGGDI-VHLYLKDISEKPLLTKDDEILYSRK-SLSGDAYSKNVLIESNLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  YRG  + IS+++ EGNIGLM AV+KFDPE+GFR +TY+ WWIK  ++  I   
Sbjct: 61  VVSIAKKYRGSSIHISDLIDEGNIGLMTAVEKFDPEKGFRFSTYATWWIKQTIERAIHNQ 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              +++    +  +    + R    L    +     E V  +  K     S  +S +  +
Sbjct: 121 GRTIRLPVHVS--KEINTIIRTHKQLVKKNNQEPSTELVAEVLNKTLDDISTTLSYDTPI 178

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               S +  I S  + SSQ    L+ D +  +    +  +    + + T  ++ LN R++
Sbjct: 179 ---VSYDQSITS--EASSQSIAVLIADENSAK--PDDLVDDLAIQKITTNVLNCLNNRDK 231

Query: 241 RIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            I   R   L     TL+ ++ E  ++RER+RQ++  +  K++ S+ + 
Sbjct: 232 EIICRRFGLLGYEAQTLQEVADEVGLTRERIRQLQVTSLAKLKNSLSRD 280


>gi|51595126|ref|YP_069317.1| RNA polymerase sigma factor RpoS [Yersinia pseudotuberculosis IP
           32953]
 gi|153948385|ref|YP_001402250.1| RNA polymerase sigma factor RpoS [Yersinia pseudotuberculosis IP
           31758]
 gi|170025640|ref|YP_001722145.1| RNA polymerase sigma factor RpoS [Yersinia pseudotuberculosis
           YPIII]
 gi|186894139|ref|YP_001871251.1| RNA polymerase sigma factor RpoS [Yersinia pseudotuberculosis
           PB1/+]
 gi|51588408|emb|CAH20016.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Yersinia pseudotuberculosis IP
           32953]
 gi|152959880|gb|ABS47341.1| RNA polymerase sigma factor RpoS [Yersinia pseudotuberculosis IP
           31758]
 gi|169752174|gb|ACA69692.1| RNA polymerase, sigma 70 subunit, RpoD family [Yersinia
           pseudotuberculosis YPIII]
 gi|186697165|gb|ACC87794.1| RNA polymerase, sigma 70 subunit, RpoD family [Yersinia
           pseudotuberculosis PB1/+]
          Length = 332

 Score =  218 bits (556), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 136/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 63  YLGEIGYSPLLTAEEEVYFARR-ALRGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 180

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 181 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 235

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D  E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 236 ----LLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 291

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 292 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 322


>gi|153207564|ref|ZP_01946247.1| RNA polymerase sigma factor RpoS [Coxiella burnetii 'MSU Goat
           Q177']
 gi|161829847|ref|YP_001597499.1| RNA polymerase sigma factor RpoS [Coxiella burnetii RSA 331]
 gi|165918356|ref|ZP_02218442.1| RNA polymerase sigma factor RpoS [Coxiella burnetii RSA 334]
 gi|212211994|ref|YP_002302930.1| RNA polymerase sigma factor [Coxiella burnetii CbuG_Q212]
 gi|212218001|ref|YP_002304788.1| RNA polymerase sigma factor [Coxiella burnetii CbuK_Q154]
 gi|120576532|gb|EAX33156.1| RNA polymerase sigma factor RpoS [Coxiella burnetii 'MSU Goat
           Q177']
 gi|161761714|gb|ABX77356.1| RNA polymerase sigma factor RpoS [Coxiella burnetii RSA 331]
 gi|165918006|gb|EDR36610.1| RNA polymerase sigma factor RpoS [Coxiella burnetii RSA 334]
 gi|212010404|gb|ACJ17785.1| RNA polymerase sigma factor [Coxiella burnetii CbuG_Q212]
 gi|212012263|gb|ACJ19643.1| RNA polymerase sigma factor [Coxiella burnetii CbuK_Q154]
          Length = 352

 Score =  218 bits (556), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 83/269 (30%), Positives = 138/269 (51%), Gaps = 13/269 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ E+   P+L  +EE  +A+R  + GD  A  +++ ++LRLVVKIA  Y   GLP  ++
Sbjct: 84  YLRELGFQPLLNAKEELKIARRVHK-GDPKARKQMIEANLRLVVKIARHYVNRGLPFLDL 142

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM AV+KFDPERGFR +TY+ WWI+  ++  I+     V++      K L   
Sbjct: 143 IEEGNLGLMTAVEKFDPERGFRFSTYATWWIRQTIERAIMNQSRTVRLPIHV-IKELNVY 201

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  K   Q + D+   PE V   A  ++    E+  +        S++  I  S+    
Sbjct: 202 LRTAKKLTQEV-DHEATPEDV---AHLIDKPVQEIRRIMDLAPSATSIDVPI--SEDGQK 255

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLE 256
              D L  D++     LI+  + ++    + R ++ L+ R R +   R         TLE
Sbjct: 256 SLVDTLADDNNIDPARLIQNVDLQDH---IERWLAQLDERHREVVILRFGLHENEKGTLE 312

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            +     ++RERVRQI+  A ++++  ++
Sbjct: 313 AVGKAVGLTRERVRQIQIDALQQLRHILE 341


>gi|1519382|gb|AAC46141.1| RNA polymerase subunit sigma 38 [Pectobacterium carotovorum]
          Length = 330

 Score =  218 bits (556), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVPSRRRMIESNLRLVVKIARRYNNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +     +  
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVNRMLALNERITSVDTPL--GGDSEK 232

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  + D   +   +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 233 ALLDILADEKDNGPE---DTTQDNDMKQNIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQVQ 320


>gi|254719520|ref|ZP_05181331.1| RNA polymerase sigma factor RpoD [Brucella sp. 83/13]
 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 =  218 bits (556), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 117/240 (48%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 434 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 493

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + +     +      +A+KL +
Sbjct: 494 IRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREPTPEELAEKLAM 548

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   +   D+  S   D++    D    + I+   + N R+  
Sbjct: 549 PLEKVRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKNALLPIDAAIQANLRDTT 603

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 604 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 663


>gi|225874024|ref|YP_002755483.1| RNA polymerase sigma factor rpoD [Acidobacterium capsulatum ATCC
           51196]
 gi|83356350|gb|ABC16653.1| major sigma factor RpoD [Acidobacterium capsulatum]
 gi|225793569|gb|ACO33659.1| RNA polymerase sigma factor rpoD [Acidobacterium capsulatum ATCC
           51196]
          Length = 597

 Score =  218 bits (556), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 68/242 (28%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 353 EQAKRELIEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 412

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      IA+++
Sbjct: 413 WWIRQAITRAIADQARTIRIPVH-----MIETINKLIRTSRQLVQELGREPTSEEIARRM 467

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++  ++V  +        SL   I   ++  S   D++    D Q     E     N + 
Sbjct: 468 DIPVAKVRKVLKIAQEPISLETPI--GEEEDSHLGDFI---EDSQAVSPSEAVISVNLKE 522

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             ++ +  L PRE R+ + R   E+    TLE +   F+V+RER+RQIEA+A +K++   
Sbjct: 523 YTSQVLRTLTPREERVIKMRFGLEDGSEHTLEEVGQSFQVTRERIRQIEAKALRKLRHPS 582

Query: 285 QK 286
           + 
Sbjct: 583 RS 584


>gi|227488742|ref|ZP_03919058.1| RNA polymerase sigma factor SigB [Corynebacterium glucuronolyticum
           ATCC 51867]
 gi|227542262|ref|ZP_03972311.1| RNA polymerase sigma factor SigB [Corynebacterium glucuronolyticum
           ATCC 51866]
 gi|227091164|gb|EEI26476.1| RNA polymerase sigma factor SigB [Corynebacterium glucuronolyticum
           ATCC 51867]
 gi|227182091|gb|EEI63063.1| RNA polymerase sigma factor SigB [Corynebacterium glucuronolyticum
           ATCC 51866]
          Length = 327

 Score =  218 bits (556), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 72/316 (22%), Positives = 144/316 (45%), Gaps = 41/316 (12%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLA----------------------- 38
           NR++ +        +  Y++ I K P+L  +EE  LA                       
Sbjct: 16  NRRHQTNDNPAADLVRVYLNGIGKTPLLSAEEEVELAKTVEVGLYARHLLNDPEYKPTRA 75

Query: 39  -----KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
                K     GD  A + ++ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KF
Sbjct: 76  MKRDLKELAREGDK-ARNHMLEANLRLVVSLAKRYSGRGMPLLDLIQEGNLGLIRAMEKF 134

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D  +GF+ +TY+ WWI+ A+   +      +++     ++     L R+K  +       
Sbjct: 135 DYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLSRIKREMYQQFGRE 192

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
           +  E    +A++  + E+++  +  +     SL+  + + ++  +   D++    D +  
Sbjct: 193 VTNE---ELAEESGIDENKIEMLFRQSRDPVSLDMPVGADEE--APLGDFI---EDSEAT 244

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQ 271
              E      R + +   +  L  RE+ +   R   ++  P TL+ +   + +SRERVRQ
Sbjct: 245 DAEEAVVVSLRHSDIRAVIDTLEGREQDVIRMRYGLDDGVPRTLDQIGRRYGLSRERVRQ 304

Query: 272 IEARAFKKVQESIQKQ 287
           IE     K++E  + +
Sbjct: 305 IEREVMAKLREGSRAE 320


>gi|256061534|ref|ZP_05451676.1| RNA polymerase sigma factor RpoD [Brucella neotomae 5K33]
 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 =  218 bits (556), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 117/240 (48%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 434 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 493

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + +     +      +A+KL +
Sbjct: 494 IRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREPTPEELAEKLAM 548

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   +   D+  S   D++    D    + I+   + N R+  
Sbjct: 549 PLEKVRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKNALLPIDAAIQANLRDTT 603

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 604 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 663


>gi|206603677|gb|EDZ40157.1| RNA polymerase, sigma 38 subunit, RpoS [Leptospirillum sp. Group II
           '5-way CG']
          Length = 598

 Score =  218 bits (556), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 72/247 (29%), Positives = 118/247 (47%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RGF+ +
Sbjct: 354 EQKVREAKAELIKANLRLVVSIAKRYTNRGLQFLDLIQEGNIGLMKAVDKFEYKRGFKFS 413

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            L R   HL         PE    +
Sbjct: 414 TYATWWIRQAITRAIADQARTIRIPVHM--IETINKLIRTTRHLVQELGREPLPE---EL 468

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           AK++ +   +V  +        SL   I   ++  S   D++    D +    I+   R 
Sbjct: 469 AKEMQMPVEKVRRVLKIAREPISLETPI--GEEEDSHLGDFI---EDKKSISPIDSAVRY 523

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
           +    + +++S L  RE ++   R         TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 524 DLVRKIGKALSSLTEREEKVIRLRFGVGESTDHTLEEVGQDFDVTRERIRQIEAKALRKL 583

Query: 281 QESIQKQ 287
           +   + +
Sbjct: 584 RHPSRSK 590


>gi|222053802|ref|YP_002536164.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           FRC-32]
 gi|221563091|gb|ACM19063.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           FRC-32]
          Length = 586

 Score =  218 bits (556), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 75/247 (30%), Positives = 118/247 (47%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           EH    A   LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +
Sbjct: 343 EHKAKLAKSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFS 402

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            L R    L         PE    I
Sbjct: 403 TYATWWIRQAITRAIADQARTIRIPVHM--IETINKLIRTSRQLVQEIGREPSPE---EI 457

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+++++   +V  +        SL   I   ++  S   D++    D      +E   + 
Sbjct: 458 AERMSLPLDKVRKVLKIAKEPISLETPI--GEEEDSHLGDFI---EDKGVVSPLEAVIKA 512

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKV 280
           N     +R +S L PRE ++   R         TLE +  +FEV+RER+RQIEA+A +K+
Sbjct: 513 NLSEQTSRVLSTLTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKL 572

Query: 281 QESIQKQ 287
           +   + +
Sbjct: 573 RHPSRAK 579


>gi|24114036|ref|NP_708546.1| RNA polymerase sigma factor RpoS [Shigella flexneri 2a str. 301]
 gi|24053158|gb|AAN44253.1| similar to sigmaD(70) factor of RNA polymerase [Shigella flexneri
           2a str. 301]
 gi|281602111|gb|ADA75095.1| RNA polymerase sigma factor [Shigella flexneri 2002017]
          Length = 342

 Score =  218 bits (556), Expect = 8e-55,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 73  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 131

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 132 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 190

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 191 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 245

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 246 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 301

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 302 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 332


>gi|254704732|ref|ZP_05166560.1| RNA polymerase sigma factor RpoD [Brucella suis bv. 3 str. 686]
          Length = 257

 Score =  218 bits (556), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 117/240 (48%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 19  AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 78

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + +     +      +A+KL +
Sbjct: 79  IRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREPTPEELAEKLAM 133

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   +   D+  S   D++    D    + I+   + N R+  
Sbjct: 134 PLEKVRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKNALLPIDAAIQANLRDTT 188

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 189 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 248


>gi|238761664|ref|ZP_04622639.1| RNA polymerase sigma factor rpoS [Yersinia kristensenii ATCC 33638]
 gi|238700178|gb|EEP92920.1| RNA polymerase sigma factor rpoS [Yersinia kristensenii ATCC 33638]
          Length = 332

 Score =  218 bits (556), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 79/271 (29%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+S+  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 63  YLGEIGYSPLLTAEEEVYFARR-ALRGDVSSRRRMIESNLRLVVKIARRYSNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 180

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    +   
Sbjct: 181 LRTAR----ELSHKLDHEPSAEEIAEQLDRPVDDVSRMLRLNERITSVDTPLGGDSE--- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
             +  L    D  E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 --KALLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 291

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 292 DVGREIGLTRERVRQIQVEGLRRLREILQAQ 322


>gi|4100838|gb|AAD01001.1| RpoS [Escherichia coli]
 gi|4100840|gb|AAD01002.1| RpoS [Escherichia coli]
 gi|4100842|gb|AAD01003.1| RpoS [Escherichia coli]
          Length = 328

 Score =  218 bits (556), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|56750962|ref|YP_171663.1| group2 RNA polymerase sigma factor RpoD4 [Synechococcus elongatus
           PCC 6301]
 gi|81299380|ref|YP_399588.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)-like
           [Synechococcus elongatus PCC 7942]
 gi|123769297|sp|Q31QR8|RPOD4_SYNE7 RecName: Full=RNA polymerase sigma factor rpoD4
 gi|56685921|dbj|BAD79143.1| group2 RNA polymerase sigma factor RpoD4 [Synechococcus elongatus
           PCC 6301]
 gi|81168261|gb|ABB56601.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)-like
           [Synechococcus elongatus PCC 7942]
          Length = 311

 Score =  218 bits (556), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 76/303 (25%), Positives = 146/303 (48%), Gaps = 33/303 (10%)

Query: 3   RKNMSIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYR------EHGDLS------ 48
           R+N++  V       +S Y+  I +IP+L  +EE  L+++ +      E+ D        
Sbjct: 6   RRNLNAAVERHTSDHVSWYLSSIGRIPLLTAEEEVELSRKVQLMMALLENPDAESNSENQ 65

Query: 49  --------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
                   A  +++ ++LRLVV +A  Y+  GL + +++ EG++GL +AV+KFDP  G++
Sbjct: 66  AVLQAGQRAKTKMLKANLRLVVSVAKKYQNQGLELLDLIQEGSLGLERAVEKFDPALGYK 125

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ +M   I      +++    ++K     + R+K   + +T    +     
Sbjct: 126 FSTYAYWWIRQSMTRAIDNHARTIRLPIHVSEK-----ISRIKKMTRELTHQLKRLPSRA 180

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            IA+ L +   +V  +  +     SL+A     D   S   D +    D +    ++  +
Sbjct: 181 EIAEALKLPLQDVEMLLSQSTPCTSLDAQAR-GDDGRSFLGDLIP---DPKSLEPMDAMD 236

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFK 278
           R  +   ++  ++ L  RE+++ + R         TL  +     VSRER+RQ+EARA +
Sbjct: 237 RHIQHEQISTWLAHLTEREQQVLQLRFGLHDGEQHTLAEIGRRLNVSRERIRQVEARALQ 296

Query: 279 KVQ 281
           K++
Sbjct: 297 KLR 299


>gi|302338230|ref|YP_003803436.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           smaragdinae DSM 11293]
 gi|301635415|gb|ADK80842.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           smaragdinae DSM 11293]
          Length = 291

 Score =  218 bits (556), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 75/288 (26%), Positives = 150/288 (52%), Gaps = 12/288 (4%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           N  + S     E  +S Y+ EI K+P+L +++E   A R    GD  A   L+ S+LR V
Sbjct: 6   NINSRSGDFGNENVISIYLKEINKVPLLSREDEDRYA-RLAADGDEHAKEMLIKSNLRFV 64

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V +A  Y+  GLP++++++EGNIGLM A++++D ++G+   +Y++WWI+ A+ + I    
Sbjct: 65  VNVAKKYQNQGLPLADLINEGNIGLMNAIERYDVDKGYHFISYAVWWIRQAILKAISEKA 124

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            ++++    N+      + + K  LQ       +      IA+ + +    V S+     
Sbjct: 125 RMIRLP--LNRANELVQIEKAKKGLQLEGKEEPE---FEEIARVVGMDAEHVASLVNISR 179

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              SL + I  +D++ S+  D++    D   +   E    ++ +  + + +  L+ +E  
Sbjct: 180 DLVSLESPIY-TDRSQSELGDFI---EDVDYKSPDETLMEQSLKEDIAKVLDTLSEKEAD 235

Query: 242 IFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           I   R   +   P++L+++   + +++ER+RQIE +A K++Q   ++Q
Sbjct: 236 IIRHRFGLDGRAPLSLKDIGDRYNLTKERIRQIEKKAIKRLQHPSRRQ 283


>gi|224370025|ref|YP_002604189.1| RpoD [Desulfobacterium autotrophicum HRM2]
 gi|223692742|gb|ACN16025.1| RpoD [Desulfobacterium autotrophicum HRM2]
          Length = 618

 Score =  218 bits (556), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 71/242 (29%), Positives = 112/242 (46%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 378 KYAKSELVRANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 437

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            L R   +L         PE    IA+K+
Sbjct: 438 WWIRQAITRAIADQARTIRIPVHM--IETINKLIRTSRYLVQEMGKEPSPE---EIAEKM 492

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   ++  S   D++    D +  +  E     N   
Sbjct: 493 EIPLDKVRRVLKIAREPISLETPI--GEEEDSHLGDFI---EDKKFSLPSEAAINLNLAE 547

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              + ++ L PRE ++   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 548 QTRKVLATLTPREEKVLRMRFGIGEKADHTLEEVGRDFTVTRERIRQIEAKALRKLRHPT 607

Query: 285 QK 286
           + 
Sbjct: 608 RS 609


>gi|163848723|ref|YP_001636767.1| sigma-70 family RNA polymerase sigma factor [Chloroflexus
           aurantiacus J-10-fl]
 gi|222526666|ref|YP_002571137.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus sp.
           Y-400-fl]
 gi|163670012|gb|ABY36378.1| RNA polymerase sigma factor, sigma-70 family [Chloroflexus
           aurantiacus J-10-fl]
 gi|222450545|gb|ACM54811.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus sp.
           Y-400-fl]
          Length = 360

 Score =  218 bits (556), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 83/299 (27%), Positives = 136/299 (45%), Gaps = 38/299 (12%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD-------------------------- 46
           E  +  Y+ EI ++P+L  +EE  LA++Y    +                          
Sbjct: 61  EDSVQLYLQEIGQVPLLTAEEEVELARQYSRGKEARQRLRNEDFANDRERMRLEMEMARG 120

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  RL+ ++LRLVV +A  Y G  +   ++V EGNIGLM+AV+KFD  +G R +TY+ 
Sbjct: 121 EEARRRLIQANLRLVVSVAKKYIGSPMAFMDLVQEGNIGLMRAVEKFDYTKGNRFSTYAT 180

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I     L+++    ++     +LRR    L+   +     E    +A  L
Sbjct: 181 WWIRQAVTRAIAEQSRLIRLPVHLSES--IVHLRRAIYRLEQELEREPTAE---ELAHAL 235

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           N+S  +V  +        SL   +N+  +             D      +E  E+K    
Sbjct: 236 NMSVRKVKRLIRASTQPISLEQPLNNEQEGRVS-----ETLADETVASPMEIAEQKMLHA 290

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            LT +++ L  RER+I + R         TLE + + F ++RER RQIEA A ++++  
Sbjct: 291 ELTAALNELPERERKILQLRYGLIDGQRRTLEEVGATFGITRERTRQIEAEALRRLRHP 349


>gi|283786707|ref|YP_003366572.1| RNA polymerase sigma factor (sigma-38) [Citrobacter rodentium
           ICC168]
 gi|282950161|emb|CBG89797.1| RNA polymerase sigma factor (sigma-38) [Citrobacter rodentium
           ICC168]
          Length = 330

 Score =  218 bits (556), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +     +  
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPL--GGDSEK 232

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  + D   +   +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 233 ALLDILADEKDNGPE---DTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|242238323|ref|YP_002986504.1| RNA polymerase sigma factor RpoS [Dickeya dadantii Ech703]
 gi|242130380|gb|ACS84682.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dickeya dadantii
           Ech703]
          Length = 330

 Score =  218 bits (556), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 79/271 (29%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+S+  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVSSRRRMIESNLRLVVKIARRYNNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +     +  
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAERLDRPVDDVNRMLRLNERITSVDTPL--GGDSDK 232

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  + D   +   +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 233 ALLDILADEKDNGPE---DTTQNNDMKQNIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|268591356|ref|ZP_06125577.1| RNA polymerase sigma factor RpoS [Providencia rettgeri DSM 1131]
 gi|291313333|gb|EFE53786.1| RNA polymerase sigma factor RpoS [Providencia rettgeri DSM 1131]
          Length = 328

 Score =  218 bits (555), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 82/271 (30%), Positives = 142/271 (52%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 59  YLSEIGFSPLLTAEEEVFYARR-ALRGDIASRQRMIESNLRLVVKISRRYNNRGLALLDL 117

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPE+GFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 118 IEEGNLGLIRAVEKFDPEKGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNIY 176

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +  L    D+   PE    IA++L+    +V  M        S++  I    + S 
Sbjct: 177 LRTAR-ELAQKLDHEPSPE---EIAEQLDKPVEDVSRMLRLNERITSVDTPIAGDSEKS- 231

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              + L  D+D   +  I+     + +  + + +  LNP++R +   R   L     TLE
Sbjct: 232 -LLEVLSDDNDSGPENTIQD---NDLKENIVKWLYELNPKQREVLARRFGLLGYEAETLE 287

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +  E  ++RERVRQI+    K++++ +  +
Sbjct: 288 EVGREIGLTRERVRQIQVEGLKRLKDILHGE 318


>gi|83953376|ref|ZP_00962098.1| RNA polymerase sigma factor [Sulfitobacter sp. NAS-14.1]
 gi|83842344|gb|EAP81512.1| RNA polymerase sigma factor [Sulfitobacter sp. NAS-14.1]
          Length = 295

 Score =  218 bits (555), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 106/287 (36%), Positives = 179/287 (62%), Gaps = 9/287 (3%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M++  + E  L+R      K  +L+ + E  LA  +R+  D  A HRL+T+++RL + +A
Sbjct: 4   MTLAQSREFSLTR---TAMKAELLDAETELKLAYAWRDERDEEALHRLITAYMRLAISMA 60

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             ++ YG  +++++ E  +GLM+A  KFDP+RG R +TY++WWIKA++Q++++R+WS+V+
Sbjct: 61  GKFKRYGASMNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDHVMRNWSMVR 120

Query: 126 IGTTANQKRLFFNLRRLKGHL----QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            G+T++QK LFFN+RR++  L    QA  +   K +    I+ ++ V   +V  M  RL+
Sbjct: 121 TGSTSSQKSLFFNMRRVQARLEREAQAAGETLDKHQLRQMISTEIGVPMHDVEMMEGRLS 180

Query: 182 G-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           G D SLNA   S++    +W D LV D     + + E  +    R+ L  +M  LN RE+
Sbjct: 181 GSDFSLNA-TQSAEDEGREWIDALVDDSAQAAERIEESHDTLTLRSWLLSAMQALNEREQ 239

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            I   R+L++ P TLE+L +E  +S+ERVRQ+EA AF K++++++ Q
Sbjct: 240 FIVRERKLRDQPRTLESLGAELSLSKERVRQLEAAAFGKMRKTLETQ 286


>gi|330959691|gb|EGH59951.1| putative RNA polymerase sigma-32 factor [Pseudomonas syringae pv.
           maculicola str. ES4326]
          Length = 291

 Score =  218 bits (555), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 108/292 (36%), Positives = 164/292 (56%), Gaps = 13/292 (4%)

Query: 1   MNRKNMSIIVNGEI------GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLV 54
           MN   +S     +I       L  Y+  I  +P +  +EE  L++R+ EH D+ AA +LV
Sbjct: 1   MNTPTLSTKAAAQIPMAPGSNLDAYLTVIHSLPKMSAEEERRLSERHFEHNDMDAARQLV 60

Query: 55  TSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114
           TS LR VV IA  Y GYGLP+S+++ EGNIGL++AVK+F+P    RL T+++  IKA + 
Sbjct: 61  TSQLRFVVHIARRYSGYGLPLSDLIQEGNIGLIKAVKRFNPAAQVRLITFAVHGIKAEIN 120

Query: 115 EYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVI 174
           EYILR+  +V++ TT  Q++L FNLR+        +   L  ++   IA  LNVS  +V 
Sbjct: 121 EYILRNCRMVRMATTKAQRKLLFNLRKQPR-----SRTWLTADETKHIADILNVSVRDVK 175

Query: 175 SMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN-MLTRSM 232
            M  R+AG D S +   ++ D ++       + DH      L E E   +  +  L  ++
Sbjct: 176 EMETRMAGNDTSFDPAADADDDSALLTPAHQLGDHRYDPAHLYETENDADTSSYDLHTAL 235

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + L+ R R I   R L E   TL +L+++++VS ER+RQIE  A  K++ SI
Sbjct: 236 NSLDERSRDILAQRFLSERKATLHDLATKYKVSAERIRQIEKLALAKLKVSI 287


>gi|307718169|ref|YP_003873701.1| RNA polymerase sigma-70 factor family protein [Spirochaeta
           thermophila DSM 6192]
 gi|306531894|gb|ADN01428.1| RNA polymerase sigma-70 factor family protein [Spirochaeta
           thermophila DSM 6192]
          Length = 303

 Score =  218 bits (555), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 74/275 (26%), Positives = 152/275 (55%), Gaps = 12/275 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           LS Y+ EI +IP+L ++EE   A R    GD  A  +LVT++LR VV +A  Y+  GLP+
Sbjct: 32  LSLYLKEINRIPLLTREEEDHYA-RLAAQGDQHAKEKLVTANLRFVVNVAKKYQNQGLPL 90

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           ++++SEGNIGL+ A+++FDP++G+   +Y++WWI+ A+ + I     ++++         
Sbjct: 91  ADLISEGNIGLLNAIERFDPDKGYHFISYAVWWIRQAILKAISEKSRMIRLPLNRA---- 146

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              L +++   + +   + +  ++  +A+ L+  E  V ++        SL+  +   D+
Sbjct: 147 -NELVQIEKARKLVQTESGEHNEIKKVAETLDYDEDHVANLLNLSKEYVSLDTPVY-EDR 204

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPV 253
           +S+   D+L  +     + ++     K  +  +   ++ L  +E  I + R      +P+
Sbjct: 205 DSAMLGDYLKDEASRPPEDVV---LEKTLQEEIQEVLATLTEKEAEIIQYRFGLNGRHPM 261

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +L+ +   + +++ER+RQIE +A KK+Q+S + ++
Sbjct: 262 SLKEIGDLYNLTKERIRQIEKKALKKIQQSEKAKI 296


>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 =  218 bits (555), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 63/242 (26%), Positives = 114/242 (47%), Gaps = 12/242 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  +++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 411 AAKQKMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 470

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I            + R+       T  +        +A+ + 
Sbjct: 471 WIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQYLQETGED---PDSAKLAELME 525

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + E ++  +        S+ + I   D + S   D++    D       E     + R +
Sbjct: 526 MPEDKIRKIMKIAKEPISMESPI--GDDDDSHLGDFI---EDVNNVAPAEAAMYSSLREV 580

Query: 228 LTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
               +  L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   +
Sbjct: 581 TAGVLESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTR 640

Query: 286 KQ 287
             
Sbjct: 641 SD 642


>gi|154706690|ref|YP_001423754.1| RNA polymerase sigma factor [Coxiella burnetii Dugway 5J108-111]
 gi|154355976|gb|ABS77438.1| RNA polymerase sigma factor [Coxiella burnetii Dugway 5J108-111]
          Length = 352

 Score =  218 bits (555), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 83/269 (30%), Positives = 138/269 (51%), Gaps = 13/269 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ E+   P+L  +EE  +A+R  + GD  A  +++ ++LRLVVKIA  Y   GLP  ++
Sbjct: 84  YLRELGFQPLLNAKEELKIARRVHK-GDPKARKQMIEANLRLVVKIARHYVNRGLPFLDL 142

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM AV+KFDPERGFR +TY+ WWI+  ++  I+     V++      K L   
Sbjct: 143 IEEGNLGLMSAVEKFDPERGFRFSTYATWWIRQTIERAIMNQSRTVRLPIHV-IKELNVY 201

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  K   Q + D+   PE V   A  ++    E+  +        S++  I  S+    
Sbjct: 202 LRTAKKLTQEV-DHEATPEDV---AHLIDKPVQEIRRIMDLAPSATSIDVPI--SEDGQK 255

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLE 256
              D L  D++     LI+  + ++    + R ++ L+ R R +   R         TLE
Sbjct: 256 SLVDTLADDNNIDPARLIQNVDLQDH---IERWLAQLDERHREVVILRFGLHENEKGTLE 312

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            +     ++RERVRQI+  A ++++  ++
Sbjct: 313 AVGKAVGLTRERVRQIQIDALQQLRHILE 341


>gi|163735266|ref|ZP_02142701.1| RNA polymerase sigma-32 factor [Roseobacter litoralis Och 149]
 gi|161391480|gb|EDQ15814.1| RNA polymerase sigma-32 factor [Roseobacter litoralis Och 149]
          Length = 284

 Score =  218 bits (555), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 99/272 (36%), Positives = 172/272 (63%), Gaps = 6/272 (2%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
            +  K  +L+ + E  LA  +R+     + HRL+T+++RL + +A  ++ YG P+++++ 
Sbjct: 5   RKAMKAELLDAETELRLAYAWRDERCEKSLHRLITAYMRLAISMASKFKRYGAPMNDLIQ 64

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           E  +GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+ G+T++QK LFFN+R
Sbjct: 65  EAGLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSMVRTGSTSSQKSLFFNMR 124

Query: 141 RLKGHLQAITDNNLKP----EQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDK 195
           R++  L+  +  + +P    +    I+ ++ V   +V  M  RL+G D SLNA   S++ 
Sbjct: 125 RVQARLERESAASGEPLDRHQLRQMISTEIGVPLHDVEMMEGRLSGSDYSLNA-TQSTED 183

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
              +W D L  D     + +    + +  R  L ++M+ LN RER I   R+L++ P TL
Sbjct: 184 EGREWIDALEDDSAQAAETVEHHHDTEQLRAWLLQAMNDLNERERFIVRERKLRDAPRTL 243

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+L  E  +S+ERVRQ+EA AF K++++++ Q
Sbjct: 244 ESLGQELSLSKERVRQLEAAAFGKMRKNLENQ 275


>gi|126696812|ref|YP_001091698.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9301]
 gi|126543855|gb|ABO18097.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9301]
          Length = 313

 Score =  218 bits (555), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 77/300 (25%), Positives = 144/300 (48%), Gaps = 36/300 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYR------EHG-------------------DLS 48
             +S Y+  I ++P+L   EE  L  + +      E G                      
Sbjct: 18  DPISWYLQNIGRVPLLTPAEEIELGNQVQKMMILTEDGQLNEKTNEFTTQQKRTIKIGRR 77

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R++ ++LRLVV +A  Y+G GL + ++V EG++GL +AV+KFDP RG++ +TY+ WW
Sbjct: 78  AKERMMKANLRLVVSVAKKYQGKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAFWW 137

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ +M   I      +++    +++     L  ++   + +          + IA+ + +
Sbjct: 138 IRQSMTRAIACQSRTIRLPVHLSER-----LASIRKVSRDLAHKLGAMPSRIEIAEAMEI 192

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              E+ S+  +     SL+A +N  D   S   D +    D   +  +++ E+K  +  L
Sbjct: 193 DVEELDSVLRQALSTSSLDAPVN-GDDGRSFLGDLIA---DSNNEEPLDQVEQKMHQEQL 248

Query: 229 TRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + +S L+ +E+ + + R   +     TL  +    EVSRERVRQ+E +A +K++   +K
Sbjct: 249 GKWLSHLSEQEQHVLKLRFGLDANERHTLAEIGRLLEVSRERVRQVELKALRKLRNLTRK 308


>gi|33862253|ref|NP_893814.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus subsp. pastoris str. CCMP1986]
 gi|33634471|emb|CAE20156.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus subsp. pastoris str. CCMP1986]
          Length = 339

 Score =  218 bits (555), Expect = 9e-55,   Method: Composition-based stats.
 Identities = 79/292 (27%), Positives = 148/292 (50%), Gaps = 31/292 (10%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLA------KRYREHGDLS--------------AAH 51
               +  Y+  I ++P+L   EE  LA      K+  E  ++               A  
Sbjct: 48  ASDSIGYYLSSIGRVPLLTAAEEIELAHHVQNMKKMLEIPEIERSSKHLRLIKIGKRARD 107

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R+++++LRLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+ 
Sbjct: 108 RMMSANLRLVVSVAKKYQNQGLDLLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQ 167

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            M   I  S   +++    ++K     L +++   + ++  + +    + +A  + + + 
Sbjct: 168 GMTRAIDNSARTIRLPIHISEK-----LSKMRRVSRELSQKSGRQPTRLEMATAMGIEQK 222

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           ++  +  + A   SL+A     +  S+  +  L+ D +G+E   +E  +R  ++  L   
Sbjct: 223 DLEDLISQSAPCASLDAHARGEEDRSTLGE--LIPDPNGEE--PMEGMDRTIQKEHLGTW 278

Query: 232 MSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++ LN RE++I + R     E P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 279 LTQLNEREQKIMKLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 330


>gi|320173409|gb|EFW48608.1| RNA polymerase sigma factor RpoS [Shigella dysenteriae CDC 74-1112]
          Length = 342

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 73  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 131

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 132 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 190

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 191 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 245

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 246 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 301

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 302 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 332


>gi|240080942|ref|ZP_04725485.1| RNA polymerase sigma factor RpoD [Neisseria gonorrhoeae FA19]
 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 =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 63/272 (23%), Positives = 122/272 (44%), Gaps = 14/272 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRY--REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + ++ K   +  +E   + K     E    +A   ++ ++LRLV+ IA  Y   GL   +
Sbjct: 368 LADMEKETRISIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLD 427

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +  
Sbjct: 428 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIE 482

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + ++    +       +      +A+ + + E ++  +        S+   I   D + 
Sbjct: 483 TINKMNRISRQHLQETGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPI--GDDDD 540

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D       +     +   +    +  L PRE ++   R   +     TL
Sbjct: 541 SHLGDFI---EDANNVAPADVAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTL 597

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +  +F+V+RER+RQIEA+A +K++   +  
Sbjct: 598 EEVGRQFDVTRERIRQIEAKALRKLRHPTRSD 629


>gi|145224529|ref|YP_001135207.1| RNA polymerase sigma factor SigB [Mycobacterium gilvum PYR-GCK]
 gi|145217015|gb|ABP46419.1| RNA polymerase, sigma 70 subunit, RpoD family [Mycobacterium gilvum
           PYR-GCK]
          Length = 329

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 66/312 (21%), Positives = 135/312 (43%), Gaps = 38/312 (12%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------- 43
           +++         +  Y++ I K  +L   +E  LAKR                       
Sbjct: 21  QDLDAQSPAADLVRVYLNGIGKTALLTAADEVELAKRIEAGLYAQHLLATRKRLGENRKR 80

Query: 44  ------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
                     +A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +
Sbjct: 81  DLAAVVRDGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYAK 140

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           GF+ +TY+ WWI+ A+   +      +++     ++     L R+K  +     N  +  
Sbjct: 141 GFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLARIKREMHQ---NLGREA 195

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A++  +   ++  +        SL+  + S ++  +   D++    D +      
Sbjct: 196 TDEELAEESGIPVEKINDLLEHSRDPVSLDMPVGSDEE--APLGDFI---EDAEAMSAEN 250

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
               +     +   ++ L+ RE+++   R   ++  P TL+ +   F +SRERVRQIE  
Sbjct: 251 AVISELLHTDIRYVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERE 310

Query: 276 AFKKVQESIQKQ 287
              K++   +  
Sbjct: 311 VMAKLRNGDRAD 322


>gi|305666839|ref|YP_003863126.1| RNA polymerase sigma factor rpoD (Sigma-A) [Maribacter sp.
           HTCC2170]
 gi|88709063|gb|EAR01297.1| RNA polymerase sigma factor rpoD (Sigma-A) [Maribacter sp.
           HTCC2170]
          Length = 287

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 72/276 (26%), Positives = 145/276 (52%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ +I KI ++  QEE  LA+R R  GD  A  +L T++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQDISKIELINAQEEVELAQRIR-AGDQVALEKLTTANLRFVVSVAKQYQNQGLK 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + +     +V++        
Sbjct: 76  LPDLINEGNLGLVKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRVVRLPLNK---- 131

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
              ++ ++K     +   + +P     IAK+L ++ +EV           S++A +   +
Sbjct: 132 -IGSINKIKKTFSYLEQAHERPPSAEEIAKELEMTVTEVKQSLKNTGRHVSMDAPLRQGE 190

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
              S   D L      +   ++    +++    + R++  L+PRE  + +      +   
Sbjct: 191 D--SNLYDVLRSGESPRPDKIL---LQQSLNTEINRALETLSPREADVVKLYYGIGDQQS 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +TL  +   F+++RERVRQI  +A +K++ + + ++
Sbjct: 246 MTLAEIGQTFDLTRERVRQIREKAIRKLRHNSRSKL 281


>gi|260591639|ref|ZP_05857097.1| RNA polymerase sigma-70 factor [Prevotella veroralis F0319]
 gi|260536439|gb|EEX19056.1| RNA polymerase sigma-70 factor [Prevotella veroralis F0319]
          Length = 287

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 77/287 (26%), Positives = 147/287 (51%), Gaps = 12/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI    M+  +EE  LA++ R+ GD  A  RL  ++LR VV
Sbjct: 5   KITKSITNRESASLDKYLQEIGHEEMISIEEEVELAQQIRK-GDRKALERLTKANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL +S++++EGN GL++A +KFD  RGF+  +Y++WWI+ ++ + I     
Sbjct: 64  SVAKQYQNQGLSLSDLINEGNFGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           ++++    NQ      + ++   L      N +   +  IA+  ++ E ++I        
Sbjct: 124 IIRLP--LNQVSSVNKINKV---LNKFEQENERRPSIDEIAQDTDIPEEKIIEAFKINTH 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A  +  D+  S   D +  D        + +E     R  + R + +L  RE+++
Sbjct: 179 HISVDAPFHDDDE--SSLLDVIPNDAIPSTDKSLVEESL---RAEIGRVLDILEDREKKV 233

Query: 243 FEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            EA        +TLE + S++ ++RERVRQI+ +A +++++    ++
Sbjct: 234 IEAYFGINQREMTLEEIGSKYGLTRERVRQIKEKAIRRLRQQTNSKI 280


>gi|253702377|ref|YP_003023566.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           M21]
 gi|251777227|gb|ACT19808.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           M21]
          Length = 584

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 77/253 (30%), Positives = 119/253 (47%), Gaps = 12/253 (4%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           LA    EH    A   LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +
Sbjct: 335 LAIEEGEHKAKLAKSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQ 394

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RG++ +TY+ WWI+ A+   I      ++I            L R    L         P
Sbjct: 395 RGYKFSTYATWWIRQAITRAIADQARTIRIPVHM--IETINKLIRTSRQLVQEIGREPSP 452

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           E    IA+++ +   +V  +        SL   I   ++  S   D++    D      +
Sbjct: 453 E---EIAERMALPLDKVRKVLKIAKEPISLETPI--GEEEDSHLGDFI---EDKGVVSPL 504

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEA 274
           E   + N     +R +S L PRE ++   R         TLE +  +FEV+RER+RQIEA
Sbjct: 505 EAVIKANLSEQTSRVLSTLTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEA 564

Query: 275 RAFKKVQESIQKQ 287
           +A +K++   + +
Sbjct: 565 KALRKLRHPSRAK 577


>gi|253689710|ref|YP_003018900.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pectobacterium
           carotovorum subsp. carotovorum PC1]
 gi|251756288|gb|ACT14364.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pectobacterium
           carotovorum subsp. carotovorum PC1]
          Length = 330

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVPSRRRMIESNLRLVVKIARRYNNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +     +  
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVNRMLRLNERITSVDTPL--GGDSEK 232

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  + D   +   +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 233 ALLDILADEKDNGPE---DTTQDNDMKQNIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQVQ 320


>gi|156740279|ref|YP_001430408.1| RpoD family RNA polymerase sigma factor [Roseiflexus castenholzii
           DSM 13941]
 gi|156231607|gb|ABU56390.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus
           castenholzii DSM 13941]
          Length = 541

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 66/239 (27%), Positives = 118/239 (49%), Gaps = 12/239 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +A   L  ++LRLVV +A  Y G GL + +++ EGN+GL++AV+KFD  +GF+ +TY+ 
Sbjct: 302 KTAREDLTQANLRLVVSVAKKYIGRGLQLLDLIQEGNVGLIRAVEKFDYRKGFKFSTYAT 361

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I     +      + RL    + +     +      +++ L
Sbjct: 362 WWIRQAITRAIADQARTIRIPVHMVE-----TINRLMRESRRMLQELGREPTDEELSRAL 416

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V S+        SL   +    +  SQ  D++    D +     +    +  R 
Sbjct: 417 GIPVDKVRSIRKTSLEPVSLETPV--GQEEDSQLGDFI---EDSKVLAPSDAASHQMLRE 471

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQES 283
            + + ++ L  RERR+ + R   E+    TLE +  EF V+RER+RQIE +A +K++  
Sbjct: 472 QVEQVLNQLTERERRVLQLRFGLEDGHSRTLEEVGKEFGVTRERIRQIEVKALRKLRHP 530



 Score = 37.1 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 8/32 (25%), Positives = 20/32 (62%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY 41
           ++    +  Y+ EI ++P+L  ++E +LA++ 
Sbjct: 114 ISINDTVRMYLREIGRVPLLTARQETLLAQKI 145


>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 =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 117/240 (48%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 428 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 487

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + +     +      +A+KL +
Sbjct: 488 IRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREPTPEELAEKLAM 542

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   +   D+  S   D++    D    + I+   + N R+  
Sbjct: 543 PLEKVRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKNALLPIDAAIQANLRDTT 597

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 598 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 657


>gi|23306702|gb|AAN15269.1| RNA polymerase sigma factor S variant [Escherichia coli]
          Length = 330

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|254527154|ref|ZP_05139206.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9202]
 gi|221538578|gb|EEE41031.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9202]
          Length = 313

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 77/300 (25%), Positives = 144/300 (48%), Gaps = 36/300 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYR------EHG-------------------DLS 48
             +S Y+  I ++P+L   EE  L  + +      E G                      
Sbjct: 18  DPISWYLQNIGRVPLLTPAEEIELGNQVQKMMILTEDGQLNEKINEFTTQQKRTIKIGRR 77

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R++ ++LRLVV +A  Y+G GL + ++V EG++GL +AV+KFDP RG++ +TY+ WW
Sbjct: 78  AKERMMKANLRLVVSVAKKYQGKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAFWW 137

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ +M   I      +++    +++     L  ++   + +          + IA+ + +
Sbjct: 138 IRQSMTRAIACQSRTIRLPVHLSER-----LASIRKVSRDLAHKLGAMPSRIEIAEAMEI 192

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              E+ S+  +     SL+A +N  D   S   D +    D   +  +++ E+K  +  L
Sbjct: 193 DVEELDSVLRQALSTSSLDAPVN-GDDGRSFLGDLIA---DSNNEEPLDQVEQKMHQEQL 248

Query: 229 TRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + +S L+ +E+ + + R   +     TL  +    EVSRERVRQ+E +A +K++   +K
Sbjct: 249 GKWLSHLSEQEQHVLKLRFGLDANERHTLAEIGRLLEVSRERVRQVELKALRKLRNLTRK 308


>gi|301165749|emb|CBW25321.1| RNA polymerase sigma-70 factor [Bacteriovorax marinus SJ]
          Length = 582

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 64/242 (26%), Positives = 112/242 (46%), Gaps = 12/242 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 343 AKSQLVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 402

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + +     +      IA+++ +
Sbjct: 403 IRQAITRAIADQARTIRIPVH-----MIETINKMVRTSRQLIQELGREPTPEEIAERMEL 457

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   I   ++  S   D++  D         +           
Sbjct: 458 PVDKVKKVQKISKEPISLETPI--GEEEDSSLGDFIEDDK---IISPADAVMSVTLSEQT 512

Query: 229 TRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +S L PRE ++   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 513 RSVLSTLTPREEKVLRMRFGIGEKSDHTLEEVGQDFFVTRERIRQIEAKALRKLRHPSRA 572

Query: 287 QV 288
           ++
Sbjct: 573 KM 574


>gi|239832356|ref|ZP_04680685.1| RNA polymerase sigma factor RpoD [Ochrobactrum intermedium LMG
           3301]
 gi|239824623|gb|EEQ96191.1| RNA polymerase sigma factor RpoD [Ochrobactrum intermedium LMG
           3301]
          Length = 672

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 117/240 (48%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 434 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 493

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + +     +      +A+KL +
Sbjct: 494 IRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREPTPEELAEKLAM 548

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   +   D+  S   D++    D    + I+   + N R+  
Sbjct: 549 PLEKVRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKNALLPIDAAIQANLRDTT 603

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 604 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 663


>gi|54025745|ref|YP_119987.1| RNA polymerase sigma factor SigB [Nocardia farcinica IFM 10152]
 gi|54017253|dbj|BAD58623.1| putative principal sigma factor [Nocardia farcinica IFM 10152]
          Length = 322

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 65/312 (20%), Positives = 133/312 (42%), Gaps = 38/312 (12%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------- 43
            ++         +  Y++ I +  +L   +E  LAKR                       
Sbjct: 14  SDLDAQSPAADLVRVYLNGIGRTALLTAADEVELAKRIEAGLYAQHLLETSKRLSAAKKK 73

Query: 44  ------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
                     +A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +
Sbjct: 74  DLAMIVRDGQAARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTK 133

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           GF+ +TY+ WWI+ A+   +      +++     ++     L R+K  L          E
Sbjct: 134 GFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLARIKRELHQQLGREATDE 191

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A +  +   ++  +        SL+  + + ++  +   D++    D +      
Sbjct: 192 ---ELAAESGIPVEKIADLLDHSRDPVSLDMPVGNDEE--APLGDFI---EDSEATSAES 243

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
                   + +   ++ L+ RE+++   R   ++  P TL+ +   F +SRERVRQIE  
Sbjct: 244 AVIAGLLHHDVRSVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERE 303

Query: 276 AFKKVQESIQKQ 287
              K+++  +  
Sbjct: 304 VMAKLRKGERAD 315


>gi|238791265|ref|ZP_04634904.1| RNA polymerase sigma factor rpoS [Yersinia intermedia ATCC 29909]
 gi|238729398|gb|EEQ20913.1| RNA polymerase sigma factor rpoS [Yersinia intermedia ATCC 29909]
          Length = 332

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 136/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 63  YLGEIGYSPLLTAEEEVYFARR-ALRGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 180

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 181 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 235

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D  E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 236 ----LLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 291

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 292 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 322


>gi|268680166|ref|YP_003304597.1| RNA polymerase sigma factor RpoD [Sulfurospirillum deleyianum DSM
           6946]
 gi|268618197|gb|ACZ12562.1| RNA polymerase sigma factor RpoD [Sulfurospirillum deleyianum DSM
           6946]
          Length = 617

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 76/298 (25%), Positives = 146/298 (48%), Gaps = 26/298 (8%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPM----------LEKQEEYVLAKRYREHGDL--S 48
           +N+++++ +V     +S Y+ EI+K+            L+ ++   + ++ +    +   
Sbjct: 319 LNKEDIATMVPEATMVSTYM-EIKKLFQTKEASKQGFDLDPEKLKEILEQIKRGKKIADE 377

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           +  R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ ++G++ +TY+ WW
Sbjct: 378 SKTRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKKGYKFSTYATWW 437

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + R+   ++       K   +  IA ++ +
Sbjct: 438 IRQAISRAIADQARTIRIPIH-----MIETINRINKIIRKHLQEEGKEPDIETIALEVGL 492

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  +V ++        SL A I   +++  ++ D++    D      +E   + + +  +
Sbjct: 493 SADKVKNVIKITKEPISLEAPI--GNEDDGKFGDFV---EDKTSIAPLEHILKSDLKEQI 547

Query: 229 TRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
              +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++  
Sbjct: 548 DDVLDQLNDREKAVIRMRFGLMHDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHP 605


>gi|254780289|ref|YP_003064702.1| RNA polymerase sigma factor RpoD [Candidatus Liberibacter asiaticus
           str. psy62]
 gi|254039966|gb|ACT56762.1| RNA polymerase sigma factor RpoD [Candidatus Liberibacter asiaticus
           str. psy62]
          Length = 682

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 73/241 (30%), Positives = 116/241 (48%), Gaps = 12/241 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ +A  Y   GL   +++ EGNIGLM+A +KFD   G++ +TY+MWW
Sbjct: 444 AKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWW 503

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           +K A+   I      ++I      K     + R    +         PE    IAKKL +
Sbjct: 504 VKQAITRSIADQSCTIRIPVHMRDK--IHKVVRTARRMSNKIKREPTPE---EIAKKLAM 558

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
               V  +        SL   I   D+++S   D++    D      ++   + N R   
Sbjct: 559 PVEGVRKVLKITKEPISLETPI--GDEDTSHLGDFI---EDKNAVSPLDSAIQANLRETT 613

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 614 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKLKHPSRS 673

Query: 287 Q 287
           +
Sbjct: 674 K 674


>gi|91212108|ref|YP_542094.1| RNA polymerase sigma factor RpoS [Escherichia coli UTI89]
 gi|117624976|ref|YP_853964.1| RNA polymerase sigma factor RpoS [Escherichia coli APEC O1]
 gi|227888284|ref|ZP_04006089.1| RNA polymerase sigma factor RpoS [Escherichia coli 83972]
 gi|237706630|ref|ZP_04537111.1| sigma factor RpoS [Escherichia sp. 3_2_53FAA]
 gi|254037782|ref|ZP_04871840.1| sigma factor RpoS [Escherichia sp. 1_1_43]
 gi|300815849|ref|ZP_07096073.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 107-1]
 gi|300820522|ref|ZP_07100673.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 119-7]
 gi|300906754|ref|ZP_07124436.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 84-1]
 gi|300919222|ref|ZP_07135745.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 115-1]
 gi|300922264|ref|ZP_07138390.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 182-1]
 gi|300930600|ref|ZP_07145992.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 187-1]
 gi|300941124|ref|ZP_07155636.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 21-1]
 gi|300946980|ref|ZP_07161206.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 116-1]
 gi|300954984|ref|ZP_07167395.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 175-1]
 gi|300976231|ref|ZP_07173328.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 200-1]
 gi|300976795|ref|ZP_07173612.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 45-1]
 gi|301027157|ref|ZP_07190526.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 69-1]
 gi|301306156|ref|ZP_07212232.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 124-1]
 gi|301326219|ref|ZP_07219602.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 78-1]
 gi|301645276|ref|ZP_07245227.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 146-1]
 gi|309795208|ref|ZP_07689627.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 145-7]
 gi|331643427|ref|ZP_08344558.1| RNA polymerase sigma factor RpoS [Escherichia coli H736]
 gi|331648464|ref|ZP_08349552.1| RNA polymerase sigma factor RpoS [Escherichia coli M605]
 gi|331654219|ref|ZP_08355219.1| RNA polymerase sigma factor RpoS [Escherichia coli M718]
 gi|331674247|ref|ZP_08375007.1| RNA polymerase sigma factor RpoS [Escherichia coli TA280]
 gi|331678721|ref|ZP_08379395.1| RNA polymerase sigma factor RpoS [Escherichia coli H591]
 gi|332280596|ref|ZP_08393009.1| sigma factor RpoS [Shigella sp. D9]
 gi|11036547|gb|AAG27177.1|AF270497_2 RpoS [Escherichia coli]
 gi|91073682|gb|ABE08563.1| sigma factor RpoS [Escherichia coli UTI89]
 gi|115514100|gb|ABJ02175.1| sigma factor RpoS [Escherichia coli APEC O1]
 gi|120538764|emb|CAM07120.1| sigma factor S [Escherichia coli]
 gi|226839406|gb|EEH71427.1| sigma factor RpoS [Escherichia sp. 1_1_43]
 gi|226899670|gb|EEH85929.1| sigma factor RpoS [Escherichia sp. 3_2_53FAA]
 gi|227834553|gb|EEJ45019.1| RNA polymerase sigma factor RpoS [Escherichia coli 83972]
 gi|300308576|gb|EFJ63096.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 200-1]
 gi|300318076|gb|EFJ67860.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 175-1]
 gi|300395189|gb|EFJ78727.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 69-1]
 gi|300401448|gb|EFJ84986.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 84-1]
 gi|300409981|gb|EFJ93519.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 45-1]
 gi|300413667|gb|EFJ96977.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 115-1]
 gi|300421394|gb|EFK04705.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 182-1]
 gi|300453367|gb|EFK16987.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 116-1]
 gi|300454167|gb|EFK17660.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 21-1]
 gi|300461542|gb|EFK25035.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 187-1]
 gi|300526786|gb|EFK47855.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 119-7]
 gi|300531778|gb|EFK52840.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 107-1]
 gi|300838588|gb|EFK66348.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 124-1]
 gi|300847064|gb|EFK74824.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 78-1]
 gi|301076441|gb|EFK91247.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 146-1]
 gi|308121179|gb|EFO58441.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 145-7]
 gi|315254525|gb|EFU34493.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 85-1]
 gi|315289257|gb|EFU48652.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 110-3]
 gi|315293697|gb|EFU53049.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 153-1]
 gi|315298766|gb|EFU58020.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 16-3]
 gi|323377395|gb|ADX49663.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Escherichia coli
           KO11]
 gi|324005707|gb|EGB74926.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 57-2]
 gi|324015519|gb|EGB84738.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 60-1]
 gi|324017012|gb|EGB86231.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 117-3]
 gi|331036898|gb|EGI09122.1| RNA polymerase sigma factor RpoS [Escherichia coli H736]
 gi|331042211|gb|EGI14353.1| RNA polymerase sigma factor RpoS [Escherichia coli M605]
 gi|331047601|gb|EGI19678.1| RNA polymerase sigma factor RpoS [Escherichia coli M718]
 gi|331068341|gb|EGI39736.1| RNA polymerase sigma factor RpoS [Escherichia coli TA280]
 gi|331073551|gb|EGI44872.1| RNA polymerase sigma factor RpoS [Escherichia coli H591]
 gi|332102948|gb|EGJ06294.1| sigma factor RpoS [Shigella sp. D9]
          Length = 342

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 73  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 131

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 132 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 190

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 191 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 245

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 246 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 301

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 302 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 332


>gi|313673328|ref|YP_004051439.1| RNA polymerase, sigma 70 subunit, rpod [Calditerrivibrio
           nitroreducens DSM 19672]
 gi|312940084|gb|ADR19276.1| RNA polymerase, sigma 70 subunit, RpoD [Calditerrivibrio
           nitroreducens DSM 19672]
          Length = 601

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 68/241 (28%), Positives = 119/241 (49%), Gaps = 12/241 (4%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             +L+ S+LRLVV IA  Y   GL   +++ EGNIGLM+AV+KF+ +RG++ +TY+ WWI
Sbjct: 365 KTKLIQSNLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVEKFEYQRGYKFSTYATWWI 424

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + A+   I      ++I            + ++   LQ        PE    IA+K++V 
Sbjct: 425 RQAITRAIADQARTIRIPVHM--IETINKMMKISRQLQVDLGREPTPE---EIAEKMDVP 479

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             +V  +        SL   I   +   S   D++    D + +  +++           
Sbjct: 480 VEKVKKVLRIAKEPVSLETPI--GEDEDSSLGDFI---EDKKSKNPLDEVVYLKLSEHTK 534

Query: 230 RSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           + +  L+PRE  +   R   +  +  TLE +  +F V+RER+RQIEA+A +K++   + +
Sbjct: 535 QILDTLSPREASVLRLRFGIDCSSDHTLEEVGKKFNVTRERIRQIEAKALRKLRHPTRSR 594

Query: 288 V 288
           +
Sbjct: 595 I 595



 Score = 35.9 bits (82), Expect = 7.5,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 20/36 (55%), Gaps = 1/36 (2%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS 48
           +  +  Y+ E+  IP+L ++EE  +AK   E+G   
Sbjct: 100 DDPVKLYLREMGNIPLLSREEETEVAKEI-ENGQRE 134


>gi|170765845|ref|ZP_02900656.1| RNA polymerase sigma factor RpoS [Escherichia albertii TW07627]
 gi|170124991|gb|EDS93922.1| RNA polymerase sigma factor RpoS [Escherichia albertii TW07627]
          Length = 434

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 165 YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 223

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 224 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 282

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 283 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 337

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 338 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 393

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 394 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 424



 Score =  128 bits (323), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 46/105 (43%), Positives = 70/105 (66%), Gaps = 1/105 (0%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRT 164


>gi|37524720|ref|NP_928064.1| RNA polymerase sigma factor RpoS [Photorhabdus luminescens subsp.
           laumondii TTO1]
 gi|36784145|emb|CAE13014.1| RNA polymerase sigma factor (sigma-38) [Photorhabdus luminescens
           subsp. laumondii TTO1]
          Length = 332

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 81/271 (29%), Positives = 139/271 (51%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 63  YLGEIGFSPLLTAEEEVFFARR-ALRGDVLARQRMIESNLRLVVKISRRYSNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 180

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +  L    D+   PE++     K     S ++ +N R+    S++  I+       
Sbjct: 181 LRTAR-ELAHKLDHEPSPEEIAEQLDKPVDDVSRMLRLNERI---ISVDTPISGDSD--- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
             +  L    D  E       +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 --KALLDVLSDENETGPEGTTQEDDMKKSIVKWLFELNSKQREVLARRFGLLGYEAETLE 291

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    +++++ +Q Q
Sbjct: 292 DVGKEIGLTRERVRQIQVEGLRRLKDIMQTQ 322


>gi|146276534|ref|YP_001166693.1| RNA polymerase factor sigma-32 [Rhodobacter sphaeroides ATCC 17025]
 gi|145554775|gb|ABP69388.1| RNA polymerase, sigma 32 subunit, RpoH [Rhodobacter sphaeroides
           ATCC 17025]
          Length = 292

 Score =  218 bits (555), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 107/272 (39%), Positives = 170/272 (62%), Gaps = 6/272 (2%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
            +  +  +L+ Q E  LA  +R+  D  A HRL+T+++RL + +A  YR YG P+++++ 
Sbjct: 13  RQAMRAELLDAQTELRLAYAWRDQRDERALHRLITAYMRLAISMASKYRRYGAPMNDLIQ 72

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           E ++GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WSLV+ G+T++QK LFFN+R
Sbjct: 73  EASLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDYVMRNWSLVRTGSTSSQKALFFNMR 132

Query: 141 RLKGHLQAIT----DNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDK 195
           R++  L+       +     +    +A  + V  S+V  M  RL+G D SLNA   S+D 
Sbjct: 133 RVQARLEREASQRGEQLDAHQLRELVAHDVGVPLSDVEMMEGRLSGSDFSLNA-TQSADD 191

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
              +W D L  D     +V+    + +  R  L  +M  LN RER I   R+L++ P TL
Sbjct: 192 EGREWIDALEDDSAQASEVVEGSLDAERLRGWLVVAMQQLNARERFIVTERKLRDVPRTL 251

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+L  E ++S+ERVRQ+EA AF K++ S++ Q
Sbjct: 252 ESLGEELKLSKERVRQLEAAAFAKMRRSLEAQ 283


>gi|307546200|ref|YP_003898679.1| RNA polymerase sigma factor RpoS [Halomonas elongata DSM 2581]
 gi|307218224|emb|CBV43494.1| RNA polymerase sigma factor RpoS [Halomonas elongata DSM 2581]
          Length = 330

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 81/278 (29%), Positives = 137/278 (49%), Gaps = 15/278 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE    +  R+ GD     R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 62  YLNEIGFSPLLTPEEEVHYGRLARQ-GDPQGRSRMIESNLRLVVKIARRYLNRGLTLLDL 120

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 121 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHVV-KELNIY 179

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +T           IA  L+   + V  M        S++  + S  ++  
Sbjct: 180 LRAAR----ELTQKLDHEATAEEIADHLDKPVASVKRMMGLNERVSSVDYPVGS--ESDK 233

Query: 199 QWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
              + L  D+D G E  L++     + +  +   ++ L  ++R +   R         TL
Sbjct: 234 PLIETLTDDNDLGPESTLVDG----DVKQHVDDWLAELTDKQREVVVRRFGLRGHEASTL 289

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E +  E  ++RERVRQI+  A KK++  + KQ     +
Sbjct: 290 EQVGEEIGLTRERVRQIQVEALKKLRRMLDKQGLDLDA 327


>gi|153826548|ref|ZP_01979215.1| RNA polymerase sigma factor RpoD [Vibrio cholerae MZO-2]
 gi|149739640|gb|EDM53854.1| RNA polymerase sigma factor RpoD [Vibrio cholerae MZO-2]
          Length = 302

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 70/276 (25%), Positives = 128/276 (46%), Gaps = 14/276 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +  I +   L  +    +++R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 33  LQMIEQETSLSVERIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 92

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 93  LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 150

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 151 KLNRISRQMLQEMGREPLPE---ELAERMQMPEDKIRKVLKIAKEPISMETPI--GDDED 205

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D   ++ ++     + +      ++ L PRE ++   R   +     TL
Sbjct: 206 SHLGDFI---EDTTLELPLDSATATSLKAATRDVLAGLTPREAKVLRMRFGIDMNTDHTL 262

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           E +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 263 EEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 298


>gi|168012500|ref|XP_001758940.1| plastid sigma facor SIG2 [Physcomitrella patens subsp. patens]
 gi|12697780|dbj|BAB21618.1| PpSIG2 [Physcomitrella patens]
 gi|14669832|dbj|BAB62008.1| PpSIG2 [Physcomitrella patens]
 gi|162690077|gb|EDQ76446.1| plastid sigma facor SIG2 [Physcomitrella patens subsp. patens]
          Length = 579

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 70/323 (21%), Positives = 143/323 (44%), Gaps = 51/323 (15%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------------------- 43
            +  +    +  Y+ +I +  +L  +EE  L+ + ++                       
Sbjct: 255 QLAADPSDPVRAYLRDIGRTKLLTAREEVDLSHQIQDLLKLENIKSNLEREIGRNATIGE 314

Query: 44  ----------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
                                A  ++V S+LRLVV IA  Y+G G+ + +++ EG++GL+
Sbjct: 315 WSRAVGMEQNAFEARLKKGRFAKDKMVNSNLRLVVSIAKNYQGRGMTLQDLIQEGSMGLV 374

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +  +KFDP +GF+ +TY+ WWI+ A+   I      +++     +  +   + + K  L 
Sbjct: 375 RGAEKFDPTKGFKFSTYAHWWIRQAVTRSIADQSRTIRLPIHLYE--VISRINKAKRMLV 432

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                  + E+V  +   + ++  ++ S+        S+   I   D +++  +     D
Sbjct: 433 QEHGREARNEEVAEL---VGLTVEKLKSVVKSAKAPGSMERPIGK-DGDTTLGELVADTD 488

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVS 265
            D  E  ++    ++  R  +   +  LNPRER +   R   ++    TLE +   F+V+
Sbjct: 489 VDSPEDAIV----KQLMRQDIEGVLRTLNPREREVLRLRFGLDDGRSKTLEEIGQIFKVT 544

Query: 266 RERVRQIEARAFKKVQESIQKQV 288
           RER+RQIEA+A +K+++  +  +
Sbjct: 545 RERIRQIEAKAMRKLRQPSRNSI 567


>gi|260464077|ref|ZP_05812272.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Mesorhizobium
           opportunistum WSM2075]
 gi|259030248|gb|EEW31529.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Mesorhizobium
           opportunistum WSM2075]
          Length = 674

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 116/240 (48%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 436 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 495

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + +     +      +A+KL +
Sbjct: 496 IRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREPTPEELAEKLAM 550

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   +   D+  S   D++    D    + I+   + N R   
Sbjct: 551 PLEKVRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKMAILPIDAAIQANLRETT 605

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 606 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 665


>gi|229496411|ref|ZP_04390127.1| RNA polymerase sigma-70 factor [Porphyromonas endodontalis ATCC
           35406]
 gi|229316639|gb|EEN82556.1| RNA polymerase sigma-70 factor [Porphyromonas endodontalis ATCC
           35406]
          Length = 287

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 73/281 (25%), Positives = 136/281 (48%), Gaps = 13/281 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI +  +++  EE  LA+  R  G+  A  +L  ++LR VV
Sbjct: 5   KITKSITNRESASLDKYLQEIGREELIDVDEEVRLAQEIR-RGNRRAQDKLTRANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + +++ EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 64  SVAKQYQNQGLSLPDLIDEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++              ++K  ++     N +   +  +A  L+ SE +V       + 
Sbjct: 124 IVRLPLNQ-----VGAQAKIKKAIEQFEQENERRPSIAELAIILDQSEEKVAVTLKSFSK 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     + NS    D LV +             R +    + R +S L+ RE  I
Sbjct: 179 HVSIDAPFVDGEDNS--LLDVLVNEDAPSTD---RSLMRDSLNTEIDRVLSTLSEREAEI 233

Query: 243 FEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +          +TLE +  +F ++RERVRQI+ +A +K++
Sbjct: 234 IKLFFGIGPNPEMTLEEIGDKFGLTRERVRQIKEKAIRKLR 274


>gi|212711364|ref|ZP_03319492.1| hypothetical protein PROVALCAL_02436 [Providencia alcalifaciens DSM
           30120]
 gi|212686093|gb|EEB45621.1| hypothetical protein PROVALCAL_02436 [Providencia alcalifaciens DSM
           30120]
          Length = 328

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 82/271 (30%), Positives = 139/271 (51%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 59  YLSEIGFSPLLTAEEEVFYARR-ALRGDVASRQRMIESNLRLVVKISRRYNNRGLALLDL 117

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPE+GFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 118 IEEGNLGLIRAVEKFDPEKGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNIY 176

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +  L    D+   PE    IA++L+    +V  M        S++  I    + S 
Sbjct: 177 LRTAR-ELAQKLDHEPSPE---EIAERLDKPVEDVSRMLRLNERITSVDTPIAGDSEKS- 231

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D  E       +  N +  + + +  LNP++R +   R   L     TLE
Sbjct: 232 ----LLEVLSDDNESGPENTIQDNNLKENIVKWLYELNPKQREVLARRFGLLGYEAETLE 287

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +  E  ++RERVRQI+    +++++ +Q +
Sbjct: 288 EVGREIGLTRERVRQIQVEGLRRLKDILQGE 318


>gi|217967697|ref|YP_002353203.1| putative RNA polymerase, sigma 70 family subunit [Dictyoglomus
           turgidum DSM 6724]
 gi|217336796|gb|ACK42589.1| putative RNA polymerase, sigma 70 family subunit [Dictyoglomus
           turgidum DSM 6724]
          Length = 413

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 80/340 (23%), Positives = 145/340 (42%), Gaps = 68/340 (20%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI KIP+L  +EE  LAKR  E GD  A  RL+ ++LRLVV +A  Y G G
Sbjct: 69  DDPVKMYLKEIGKIPLLTPEEEIELAKRV-EQGDEDAKKRLIEANLRLVVSVAKRYIGRG 127

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I     +
Sbjct: 128 LSFLDLIQEGNLGLIKAVEKFDWRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 187

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAI-----------------------------A 163
                 + ++   L          E +                                 
Sbjct: 188 --TMNKIHKITRLLTQSLGRKPTEEDIAKFLVIQQKLQEFEVYQESGEKISDDEIVEISM 245

Query: 164 KKLNVSESEVISMNCRLAGDESLNA--------------------------LINSSDKNS 197
             L+    +++ ++ +  G + L                             I+   +  
Sbjct: 246 LSLDEIAKKLVELHLKTKGKKELTKEKINEEAKELRHVLEEEIKQQTEKVREISMMGQEP 305

Query: 198 SQWQDWLVYDHDGQEQVLIEKEE--------RKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
              +  +  D D +    +E ++        +K+ +  +   ++ L+ RER I + R   
Sbjct: 306 LSLEMPVGEDEDNRLADFVENKDLSPADIAVQKSLKKDIEELLNELSEREREILKLRFGL 365

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E+  P TLE +   F V+RER+RQIEA+A ++++   + +
Sbjct: 366 EDNQPRTLEEVGKLFNVTRERIRQIEAKALRRLRHPSRSK 405


>gi|116074244|ref|ZP_01471506.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9916]
 gi|116069549|gb|EAU75301.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9916]
          Length = 341

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 79/290 (27%), Positives = 144/290 (49%), Gaps = 31/290 (10%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLA--------------------KRYREHGDLSAAHRL 53
             +  Y+  I +IP+L   EE  LA                    +R++      A  R+
Sbjct: 52  DSIGYYLSSIGRIPLLTPAEEIELAHHVQAMKQLLETPEDERTPRERHKIRMGKRARDRM 111

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           + ++LRLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+  M
Sbjct: 112 MAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGM 171

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
              I  S   +++    ++K     L +++   + ++    +    + +A  + +   ++
Sbjct: 172 TRAIDNSARTIRLPIHISEK-----LSKMRRISRELSHRFGRQPNRLELAHAMGIEPRDL 226

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             +  + A   SL+A     +  S+  +  L+ D +G++   +E  +R  ++  L   +S
Sbjct: 227 EDLISQSAPCASLDAHARGEEDRSTLGE--LIPDPNGEDS--MEGMDRSIQKEHLGGWLS 282

Query: 234 VLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            LN RE++I + R     E P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 283 QLNEREQKILKLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 332


>gi|73671310|gb|AAZ80066.1| RpoS variant [Escherichia coli LW1655F+]
          Length = 330

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|86157650|ref|YP_464435.1| sigma 32 (RpoH) [Anaeromyxobacter dehalogenans 2CP-C]
 gi|85774161|gb|ABC80998.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter
           dehalogenans 2CP-C]
          Length = 322

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 111/291 (38%), Positives = 174/291 (59%), Gaps = 14/291 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             L  Y+ E+ + P+L + EE+ LA +YRE GD+ AA++LV S+LRLVVKIA  YR    
Sbjct: 34  DPLRAYMAEVARHPVLSRDEEHALAVQYRETGDVDAAYKLVASNLRLVVKIAHEYRRTAF 93

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + ++V EGN+GLMQAVKK+DP +G +L++Y+ WWI+A +  +I+ +W LVK+GTT  Q+
Sbjct: 94  QLLDLVQEGNLGLMQAVKKYDPWKGVKLSSYAAWWIRAYIIRFIMENWRLVKLGTTQAQR 153

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINS 192
           +LFFNL + +  L A             +AK L V E +V  M+ R+A D+ SL+A + +
Sbjct: 154 KLFFNLSKEREKLLA----RGIEPTPRLLAKNLQVEEKDVEEMSARMAADDLSLDAPVGT 209

Query: 193 SDKNSSQWQDWLVYDHDGQ--EQVLIEKEERKNRRNMLTRSMSVL-NPRERRIFEARRLQ 249
              +  Q +   + D  GQ  +  L +++ R+  R  L      L + +ER IFE R L 
Sbjct: 210 EGDDGRQNRLDRLADDGGQAPDAALGDEQLRRIFREKLDAFSGTLTDEKERYIFEHRLLP 269

Query: 250 EN---PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV---ELSSSP 294
            +   P+TL+ +   F ++RER RQIEA+   +++E ++ ++   EL   P
Sbjct: 270 PDGTPPLTLQEVGDHFRLTRERARQIEAKLTGRLREFLRAEIPDFELLGPP 320


>gi|226306291|ref|YP_002766251.1| RNA polymerase sigma factor SigB [Rhodococcus erythropolis PR4]
 gi|229491301|ref|ZP_04385127.1| RNA polymerase sigma factor RpoD [Rhodococcus erythropolis SK121]
 gi|226185408|dbj|BAH33512.1| RNA polymerase sigma factor SigB [Rhodococcus erythropolis PR4]
 gi|229321840|gb|EEN87635.1| RNA polymerase sigma factor RpoD [Rhodococcus erythropolis SK121]
          Length = 323

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 66/305 (21%), Positives = 134/305 (43%), Gaps = 38/305 (12%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY------------------REHGD 46
           ++         +  Y++ I +  +L   +E  LAKR                    +  D
Sbjct: 16  DLDAQSPAADLVRVYLNGIGRTALLTAADEVELAKRIEAGLYASHVLATGKRLTVAKKRD 75

Query: 47  LS--------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           L+        A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +G
Sbjct: 76  LATIVREGQSARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYAKG 135

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           F+ +TY+ WWI+ A+   +      +++     ++     L R+K  L        +   
Sbjct: 136 FKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLARIKRELHQ---QLGREAT 190

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              +A++  +   ++  +        SL+  + + ++  +   D++    D +       
Sbjct: 191 DDELAEESGIPAHKIADLLDHSRDPVSLDMPVGNDEE--APLGDFI---EDSEATSAENA 245

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARA 276
                  + +   +  L+ RE+++   R   ++  P TL+ +   F +SRERVRQIE   
Sbjct: 246 VIAGLLHSDVRSVLGTLDEREQQVIRLRYGLDDGQPRTLDQIGKLFGLSRERVRQIEREV 305

Query: 277 FKKVQ 281
             K++
Sbjct: 306 MGKLR 310


>gi|88608622|ref|YP_506230.1| RNA polymerase sigma-32 factor [Neorickettsia sennetsu str.
           Miyayama]
 gi|88600791|gb|ABD46259.1| RNA polymerase sigma-32 factor [Neorickettsia sennetsu str.
           Miyayama]
          Length = 288

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 123/272 (45%), Positives = 177/272 (65%), Gaps = 5/272 (1%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
              Y  +I  IP+L+++EE  L  R+  H D+SAA RLV ++LRLVVK+ + +R YG P+
Sbjct: 13  FDAYARKILAIPILQEEEERELIDRWFVHRDISAAQRLVEAYLRLVVKVTVRFRNYGFPL 72

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++ SEGNIGLM+A+K F+P  G  +ATY++WWIKAA+ EY++RSWS+VKIGTTA Q+RL
Sbjct: 73  MDLASEGNIGLMKAIKNFNPTLGHGIATYAIWWIKAAINEYVIRSWSMVKIGTTAAQRRL 132

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSSD 194
           FFNLR+LK        +  +   V  I++ L VS+++V  M   L A D SLN  +   +
Sbjct: 133 FFNLRKLKNSGSVAGLDENQV--VKRISEILAVSKNDVEEMERILNARDVSLNMQL--GE 188

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
            +SS+  D + +    QE VL+E +ER+ +  +L  ++  L  R + IF AR L   P T
Sbjct: 189 DDSSEVHDLVPFPEANQEAVLLETQERQMKSQLLYEAVEALEARHKEIFVARSLSAVPRT 248

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           L+ L  +F +S+ERVRQI ARA KKV E ++K
Sbjct: 249 LKELGEKFSISQERVRQIHARAMKKVTEYVEK 280


>gi|39998179|ref|NP_954130.1| RNA polymerase sigma factor RpoD [Geobacter sulfurreducens PCA]
 gi|39985125|gb|AAR36480.1| RNA polymerase sigma factor RpoD [Geobacter sulfurreducens PCA]
 gi|298507117|gb|ADI85840.1| RNA polymerase sigma-70 factor RpoD [Geobacter sulfurreducens
           KN400]
          Length = 577

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 74/247 (29%), Positives = 116/247 (46%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +
Sbjct: 334 EAKSKLAKSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFS 393

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            L R    L         PE    I
Sbjct: 394 TYATWWIRQAITRAIADQARTIRIPVHM--IETINKLIRTSRQLVQEIGREPSPE---EI 448

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+++N+   +V  +        SL   I   ++  S   D++    D      +E   + 
Sbjct: 449 AERMNLPLDKVRKVLKIAKEPISLETPI--GEEEDSHLGDFI---EDKGVVSPLEAVIKA 503

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKV 280
           N      R ++ L PRE ++   R         TLE +  +FEV+RER+RQIEA+A +K+
Sbjct: 504 NLSEQTARVLATLTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKL 563

Query: 281 QESIQKQ 287
           +   + +
Sbjct: 564 RHPSRAK 570


>gi|296104425|ref|YP_003614571.1| RNA polymerase nonessential primary-like sigma factor [Enterobacter
           cloacae subsp. cloacae ATCC 13047]
 gi|295058884|gb|ADF63622.1| RNA polymerase nonessential primary-like sigma factor [Enterobacter
           cloacae subsp. cloacae ATCC 13047]
 gi|295097322|emb|CBK86412.1| RNA polymerase sigma factor RpoS [Enterobacter cloacae subsp.
           cloacae NCTC 9394]
          Length = 330

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +     +  
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPL--GGDSEK 232

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  + D   +   +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 233 ALLDILADEKDNGPE---DTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQGQ 320


>gi|15807631|ref|NP_294640.1| RNA polymerase sigma-A factor [Deinococcus radiodurans R1]
          Length = 360

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 75/296 (25%), Positives = 128/296 (43%), Gaps = 36/296 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE--------------------------HGDL 47
             + +Y+HEI ++ +L  +EE  LA+R  E                              
Sbjct: 59  DPVRQYLHEIGRVSLLTLEEEIALARRIEEGEEARKQLEEDESLDDRSRRRLMRQMEDGA 118

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   L+ ++LRLVV IA  Y G GL   +++ EGN GL++AV+KF+  R ++ +TY+ W
Sbjct: 119 AARQGLIEANLRLVVSIAKKYTGRGLGFLDLIQEGNQGLIRAVEKFEYRRRYKFSTYATW 178

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I     +      L R    LQ         E++   A    
Sbjct: 179 WIRQAINRAIADQARTIRIPVHMVE--TINKLTRTARQLQQELSREATHEEIAE-AMGPG 235

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
              ++V  +        SL   I   D+  S + D++    D      ++   +      
Sbjct: 236 WDAAKVEEVQKVSQEPVSLETPI--GDEKDSFYGDFIP---DENLDSPVDNAAKTLLSEE 290

Query: 228 LTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           L +++  L  RE  + + R+        TLE +   F V+RER+RQIE +A +K++
Sbjct: 291 LEKALGKLTEREAMVLKFRKGLVDGREHTLEEVGQRFSVTRERIRQIENKALRKLK 346


>gi|123441128|ref|YP_001005116.1| RNA polymerase sigma factor RpoS [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|332160357|ref|YP_004296934.1| RNA polymerase sigma factor RpoS [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|122088089|emb|CAL10877.1| RNA polymerase sigma factor RpoS [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|318604409|emb|CBY25907.1| RNA polymerase sigma factor RpoS [Yersinia enterocolitica subsp.
           palearctica Y11]
 gi|325664587|gb|ADZ41231.1| RNA polymerase sigma factor RpoS [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|330859888|emb|CBX70219.1| RNA polymerase sigma factor rpoS [Yersinia enterocolitica W22703]
          Length = 332

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 136/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 63  YLGEIGYSPLLTAEEEVYFARR-ALRGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 180

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 181 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 235

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D  E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 236 ----LLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 291

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 292 DVGREIGLTRERVRQIQVEGLRRLREILQAQ 322


>gi|261345855|ref|ZP_05973499.1| RNA polymerase sigma factor RpoS [Providencia rustigianii DSM 4541]
 gi|282566345|gb|EFB71880.1| RNA polymerase sigma factor RpoS [Providencia rustigianii DSM 4541]
          Length = 328

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 82/271 (30%), Positives = 143/271 (52%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 59  YLSEIGFSPLLTAEEEVFYARR-ALRGDIASRQRMIESNLRLVVKISRRYNNRGLALLDL 117

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPE+GFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 118 IEEGNLGLIRAVEKFDPEKGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNIY 176

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +  L    D+   PE    IA++L+    +V  M        S++  I    + S 
Sbjct: 177 LRTAR-ELAQKLDHEPSPE---EIAEQLDKPVEDVSRMLRLNERITSVDTPIAGDSEKS- 231

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              + L  D+D   +  I+     + +  + + +  LNP++R +   R   L     TLE
Sbjct: 232 -LLEVLSDDNDSGPENTIQD---NDLKENIVKWLYELNPKQREVLARRFGLLGYEAETLE 287

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +  E  ++RERVRQI+    +++++ +Q +
Sbjct: 288 EVGREIGLTRERVRQIQVEGLRRLKDILQGE 318


>gi|78214165|ref|YP_382944.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CC9605]
 gi|78198624|gb|ABB36389.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. CC9605]
          Length = 328

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 81/292 (27%), Positives = 143/292 (48%), Gaps = 31/292 (10%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAK--------------------RYREHGDLSAAH 51
               +  Y+  I +IP+L   EE  LA                     R++      A  
Sbjct: 37  ATDSIGFYLSSIGRIPLLTAAEEIELAHHVQAMKQLQELPEEELTSRHRHKIRMGKRARD 96

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ ++LRLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+ 
Sbjct: 97  RMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQ 156

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            M   I  S   +++    ++K     L +++   + ++    +    + +A  + +   
Sbjct: 157 GMTRAIDNSARTIRLPIHISEK-----LSKMRRISRELSHRFGRQPNRLELASAMGIEPR 211

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           E+  +  + A   SL+A     +  S+  +  L+ D +G+E   +E  +R  ++  L   
Sbjct: 212 ELEDLISQSAPCASLDAHARGEEDRSTLGE--LIPDPNGEE--PMEGMDRSIQKEHLGGW 267

Query: 232 MSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +S LN RE++I + R     E P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 268 LSQLNEREQKILKLRFGLGGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 319


>gi|41861|emb|CAA78692.1| KatF [Escherichia coli]
          Length = 342

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 73  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 131

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 132 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 190

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 191 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 245

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 246 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 301

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 302 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 332


>gi|52841515|ref|YP_095314.1| stationary phase specific sigma factor RpoS [Legionella pneumophila
           subsp. pneumophila str. Philadelphia 1]
 gi|52628626|gb|AAU27367.1| stationary phase specific sigma factor RpoS [Legionella pneumophila
           subsp. pneumophila str. Philadelphia 1]
          Length = 359

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 79/270 (29%), Positives = 141/270 (52%), Gaps = 13/270 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A      GD+ A  +++ S+LRLVVKIA  Y   GLP+ ++
Sbjct: 92  YLGEIGFSPLLTAEEEIHYAT-LALKGDMEARKKMIESNLRLVVKIARRYLNRGLPLLDL 150

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM++V+KFDP+RGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 151 IEEGNLGLMKSVEKFDPKRGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 209

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +   Q + D+   PE++  +  K      +++ +N ++A   S++  I   +  S 
Sbjct: 210 LRAARQLTQKL-DHEPSPEEIAEMVDKPLEDVQKLLGLNDKVA---SVDTPIGFDETKS- 264

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
              D +  ++      L+  E   N R  +   +  L   ++++   R         TLE
Sbjct: 265 -LLDTIADENSLNPAELLTNE---NLRQHIESLLDKLTENQQQVIARRFGLRGFEKATLE 320

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ++  E +++RERVRQI+  A K ++  +++
Sbjct: 321 DVGKEIDLTRERVRQIQVEALKTLRTLLER 350


>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 =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 64/243 (26%), Positives = 112/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLVV IA  Y   G+   +++ EGNIGL++AV KF+  RG++ +TY+ 
Sbjct: 211 RQAKRDMTEANLRLVVSIAKKYINRGMQFLDLIQEGNIGLLKAVDKFEYRRGYKFSTYAT 270

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      +++     +      L R+   +   T           +A  +
Sbjct: 271 WWIRQAVSRAIADQARTIRVPVHMLE--TVNKLNRIARRILQETGVEADLPT---LALHM 325

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++E +V  +        S+ + +   D   SQ  D++    D      +E     + R 
Sbjct: 326 ELTEQKVREIMKIAREPISMESPV--GDDGDSQLGDFI---QDSTTTAPLEAAVDASMRT 380

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +   +  L PRE +I   R   +     TLE +  +FEV+RER+RQIE++A  K++   
Sbjct: 381 AIKEVLDALPPREAKILRMRYGLDTQSDHTLEEVGKQFEVTRERIRQIESKALVKLRHPS 440

Query: 285 QKQ 287
           +  
Sbjct: 441 RAD 443


>gi|311278284|ref|YP_003940515.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Enterobacter
           cloacae SCF1]
 gi|308747479|gb|ADO47231.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Enterobacter
           cloacae SCF1]
          Length = 330

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYSNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +     +  
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPL--GGDSEK 232

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  + D   +   +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 233 ALLDILADEKDNGPE---DTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQGQ 320


>gi|254710518|ref|ZP_05172329.1| RNA polymerase sigma factor RpoD [Brucella pinnipedialis B2/94]
 gi|256032011|ref|ZP_05445625.1| RNA polymerase sigma factor RpoD [Brucella pinnipedialis M292/94/1]
 gi|261318089|ref|ZP_05957286.1| RNA polymerase sigma factor RpoD [Brucella pinnipedialis B2/94]
 gi|265989123|ref|ZP_06101680.1| RNA polymerase sigma factor RpoD [Brucella pinnipedialis M292/94/1]
 gi|261297312|gb|EEY00809.1| RNA polymerase sigma factor RpoD [Brucella pinnipedialis B2/94]
 gi|264661320|gb|EEZ31581.1| RNA polymerase sigma factor RpoD [Brucella pinnipedialis M292/94/1]
          Length = 672

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 117/240 (48%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 434 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 493

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + +     +      +A+KL +
Sbjct: 494 IRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREPTPEELAEKLAM 548

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   +   D+  S   D++    D    + I+   + N R+  
Sbjct: 549 PLEKVRKVLKIAKEPISLETPV--GDEEDSLLGDFI---EDKNALLPIDAAIQANLRDTT 603

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 604 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 663


>gi|289805538|ref|ZP_06536167.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. AG3]
          Length = 321

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|157413850|ref|YP_001484716.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9215]
 gi|157388425|gb|ABV51130.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9215]
          Length = 313

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 77/300 (25%), Positives = 144/300 (48%), Gaps = 36/300 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYR------EHG-------------------DLS 48
             +S Y+  I ++P+L   EE  L  + +      E G                      
Sbjct: 18  DPISWYLQNIGRVPLLTPAEEIELGNQVQKMMILTEDGQLNEKIKEFTTQQKRTIKIGRR 77

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R++ ++LRLVV +A  Y+G GL + ++V EG++GL +AV+KFDP RG++ +TY+ WW
Sbjct: 78  AKERMMKANLRLVVSVAKKYQGKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAFWW 137

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ +M   I      +++    +++     L  ++   + +          + IA+ + +
Sbjct: 138 IRQSMTRAIACQSRTIRLPVHLSER-----LASIRKVSRDLAHKLGAMPSRIEIAEAMEI 192

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              E+ S+  +     SL+A +N  D   S   D +    D   +  +++ E+K  +  L
Sbjct: 193 DVEELDSVLRQALSTSSLDAPVN-GDDGRSFLGDLIA---DSNNEEPLDQVEQKMHQEQL 248

Query: 229 TRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + +S L+ +E+ + + R   +     TL  +    EVSRERVRQ+E +A +K++   +K
Sbjct: 249 GKWLSHLSEQEQHVLKLRFGLDANERHTLAEIGRLLEVSRERVRQVELKALRKLRNLTRK 308


>gi|148358826|ref|YP_001250033.1| stationary phase specific sigma factor RpoS [Legionella pneumophila
           str. Corby]
 gi|296106871|ref|YP_003618571.1| stationary phase specific sigma factor RpoS [Legionella pneumophila
           2300/99 Alcoy]
 gi|148280599|gb|ABQ54687.1| stationary phase specific sigma factor RpoS [Legionella pneumophila
           str. Corby]
 gi|295648772|gb|ADG24619.1| stationary phase specific sigma factor RpoS [Legionella pneumophila
           2300/99 Alcoy]
          Length = 341

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 79/270 (29%), Positives = 141/270 (52%), Gaps = 13/270 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A      GD+ A  +++ S+LRLVVKIA  Y   GLP+ ++
Sbjct: 74  YLGEIGFSPLLTAEEEIHYAT-LALKGDMEARKKMIESNLRLVVKIARRYLNRGLPLLDL 132

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM++V+KFDP+RGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 133 IEEGNLGLMKSVEKFDPKRGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 191

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +   Q + D+   PE++  +  K      +++ +N ++A   S++  I   +  S 
Sbjct: 192 LRAARQLTQKL-DHEPSPEEIAEMVDKPLEDVQKLLGLNDKVA---SVDTPIGFDETKS- 246

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
              D +  ++      L+  E   N R  +   +  L   ++++   R         TLE
Sbjct: 247 -LLDTIADENSLNPAELLTNE---NLRQHIESLLDKLTENQQQVIARRFGLRGFEKATLE 302

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ++  E +++RERVRQI+  A K ++  +++
Sbjct: 303 DVGKEIDLTRERVRQIQVEALKTLRTLLER 332


>gi|124515193|gb|EAY56704.1| RNA polymerase, sigma 70 subunit, RpoD [Leptospirillum rubarum]
          Length = 598

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 72/247 (29%), Positives = 118/247 (47%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RGF+ +
Sbjct: 354 EQKVREAKAELIKANLRLVVSIAKRYTNRGLQFLDLIQEGNIGLMKAVDKFEYKRGFKFS 413

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            L R   HL         PE    +
Sbjct: 414 TYATWWIRQAITRAIADQARTIRIPVHM--IETINKLIRTTRHLVQELGREPLPE---EL 468

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           AK++ +   +V  +        SL   I   ++  S   D++    D +    I+   R 
Sbjct: 469 AKEMQMPVEKVRRVLKIAREPISLETPI--GEEEDSHLGDFI---EDKKSISPIDSAVRY 523

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
           +    + +++S L  RE ++   R         TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 524 DLVRKIGKALSSLTEREEKVIRLRFGVGESTDHTLEEVGQDFDVTRERIRQIEAKALRKL 583

Query: 281 QESIQKQ 287
           +   + +
Sbjct: 584 RHPSRSK 590


>gi|27735253|sp|P35540|RPOS_SHIFL RecName: Full=RNA polymerase sigma factor rpoS
 gi|332753598|gb|EGJ83977.1| RNA polymerase sigma factor RpoS [Shigella flexneri K-671]
 gi|333000355|gb|EGK19938.1| RNA polymerase sigma factor RpoS [Shigella flexneri K-218]
 gi|333015759|gb|EGK35097.1| RNA polymerase sigma factor RpoS [Shigella flexneri K-304]
          Length = 330

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|308273291|emb|CBX29894.1| RNA polymerase sigma-32 factor [uncultured Desulfobacterium sp.]
          Length = 298

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 102/277 (36%), Positives = 171/277 (61%), Gaps = 8/277 (2%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG-YG 72
             L RY+ E+    +L ++ EY LA +  +H D  AA+ +VTS+LRLVVKIA+ ++  + 
Sbjct: 20  DPLQRYMMEVSNHNLLSREREYALAVKVFDHDDKDAAYEIVTSNLRLVVKIALEFQRIWM 79

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
             + +++ EGNIGLMQAV+KFDP +  + + Y+ +WIKA + ++I+ +W LVKIGTT  Q
Sbjct: 80  QNLLDLIQEGNIGLMQAVRKFDPYKNVKFSYYASFWIKAYILKFIMDNWRLVKIGTTQGQ 139

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALIN 191
           ++LFF    LK   Q + D    P+  + ++++L V+E E++ M+ RL G D SLN  + 
Sbjct: 140 RKLFFK---LKKEKQDLIDQGFDPKPKL-LSERLGVTEKEIVDMDQRLDGWDVSLNTPL- 194

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
            SD + S+  +++ YD D  E+ + +K+      + +     ++  RE  IF+ R   +N
Sbjct: 195 -SDDSDSEKIEFISYDSDSAEEQVAKKQMDNLIYSKIDEFRKLMTKRENEIFDLRIFSDN 253

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           PVTL+ +   + +SRERVRQ+E     K++E I++++
Sbjct: 254 PVTLQEIGDRYGISRERVRQLEKNIITKMREFIKEEL 290


>gi|238786006|ref|ZP_04629967.1| RNA polymerase sigma factor rpoS [Yersinia bercovieri ATCC 43970]
 gi|238713067|gb|EEQ05118.1| RNA polymerase sigma factor rpoS [Yersinia bercovieri ATCC 43970]
          Length = 332

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 136/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 63  YLGEIGYSPLLTAEEEVYFARR-ALRGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 180

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 181 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 235

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D  E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 236 ----LLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 291

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 292 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 322


>gi|16130648|ref|NP_417221.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli str.
           K-12 substr. MG1655]
 gi|170082316|ref|YP_001731636.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli str.
           K-12 substr. DH10B]
 gi|238901878|ref|YP_002927674.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli BW2952]
 gi|1710676|sp|P13445|RPOS_ECOLI RecName: Full=RNA polymerase sigma factor rpoS; AltName:
           Full=Sigma-38
 gi|882634|gb|AAA69251.1| RNA polymerase sigma subunit RpoS (sigma-38) [Escherichia coli str.
           K-12 substr. MG1655]
 gi|1789098|gb|AAC75783.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli str.
           K-12 substr. MG1655]
 gi|23306700|gb|AAN15267.1| RNA polymerase sigma factor S [Escherichia coli]
 gi|23306712|gb|AAN15273.1| RNA polymerase sigma factor S [Escherichia coli]
 gi|169890151|gb|ACB03858.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli str.
           K-12 substr. DH10B]
 gi|238863502|gb|ACR65500.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli BW2952]
          Length = 330

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|216659|dbj|BAA02747.1| RNA polymerase sigma subunit, sigma-38 [Escherichia coli]
 gi|23306698|gb|AAN15268.1| RNA polymerase sigma factor S variant [Escherichia coli]
 gi|260448208|gb|ACX38630.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Escherichia coli
           DH1]
          Length = 330

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|238797130|ref|ZP_04640632.1| RNA polymerase sigma factor rpoS [Yersinia mollaretii ATCC 43969]
 gi|238718977|gb|EEQ10791.1| RNA polymerase sigma factor rpoS [Yersinia mollaretii ATCC 43969]
          Length = 332

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 136/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 63  YLGEIGYSPLLTAEEEVYFARR-ALRGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 180

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 181 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 235

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D  E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 236 ----LLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 291

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 292 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 322


>gi|153009018|ref|YP_001370233.1| RNA polymerase sigma factor RpoD [Ochrobactrum anthropi ATCC 49188]
 gi|151560906|gb|ABS14404.1| RNA polymerase, sigma 70 subunit, RpoD [Ochrobactrum anthropi ATCC
           49188]
          Length = 671

 Score =  217 bits (554), Expect = 1e-54,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 117/240 (48%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 433 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 492

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + +     +      +A+KL +
Sbjct: 493 IRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREPTPEELAEKLAM 547

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   +   D+  S   D++    D    + I+   + N R+  
Sbjct: 548 PLEKVRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKNALLPIDAAIQANLRDTT 602

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 603 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 662


>gi|238754524|ref|ZP_04615879.1| RNA polymerase sigma factor rpoS [Yersinia ruckeri ATCC 29473]
 gi|238707353|gb|EEP99715.1| RNA polymerase sigma factor rpoS [Yersinia ruckeri ATCC 29473]
          Length = 332

 Score =  217 bits (554), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 136/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 63  YLGEIGYSPLLTAEEEVYFARR-ALRGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 180

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 181 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 235

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D  E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 236 ----LLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 291

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 292 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 322


>gi|308187918|ref|YP_003932049.1| RNA polymerase sigma factor rpoD [Pantoea vagans C9-1]
 gi|308058428|gb|ADO10600.1| RNA polymerase sigma factor rpoD [Pantoea vagans C9-1]
          Length = 330

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVFFARR-ALRGDIPSRRRMIESNLRLVVKIARRYSNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +     +  
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPL--GGDSEK 232

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  + D   +   +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 233 ALLDILADEKDNGPE---DTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQAQ 320


>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 =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 63/272 (23%), Positives = 122/272 (44%), Gaps = 14/272 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRY--REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + ++ K   +  +E   + K     E    +A   ++ ++LRLV+ IA  Y   GL   +
Sbjct: 368 LADMEKETRISIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLD 427

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +  
Sbjct: 428 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIE 482

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + ++    +       +      +A+ + + E ++  +        S+   I   D + 
Sbjct: 483 TINKMNRISRQHLQETGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPI--GDDDD 540

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D       +     +   +    +  L PRE ++   R   +     TL
Sbjct: 541 SHLGDFI---EDANNVAPADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTL 597

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +  +F+V+RER+RQIEA+A +K++   +  
Sbjct: 598 EEVGRQFDVTRERIRQIEAKALRKLRHPTRSD 629


>gi|288940519|ref|YP_003442759.1| RNA polymerase sigma-70 subunit RpoD subfamily [Allochromatium
           vinosum DSM 180]
 gi|288895891|gb|ADC61727.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Allochromatium
           vinosum DSM 180]
          Length = 338

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 76/271 (28%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI +  +L  +EE   A R  + GD +A  R++  +LRLVVKIA  Y   GLP+ ++
Sbjct: 70  YLNEIGESRLLTAEEEIRFA-RLAQAGDNAARQRMIVCNLRLVVKIARRYLNRGLPLLDL 128

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     V++       +    
Sbjct: 129 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTVRLPIHV--VKEINI 186

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
             +    L    D++   E +  +  +       ++ +N R+    S++     S     
Sbjct: 187 YLKASRQLAQSLDHDPTSEDIAQLLDRPINEVKRMLGLNERIT---SVDTP--YSKDADK 241

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
              D L  D         E+ +  +    +   + +LN ++R + E R         TLE
Sbjct: 242 PLVDMLQDDGSSD---PTERIQDDDIHVNIEHWLGLLNDKQREVVERRFGLHGHENSTLE 298

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +++ E  V+RERVRQI+  A +++++ ++ +
Sbjct: 299 SVARELGVTRERVRQIQMDALRRLRDILESE 329


>gi|50122451|ref|YP_051618.1| RNA polymerase sigma factor RpoS [Pectobacterium atrosepticum
           SCRI1043]
 gi|227114060|ref|ZP_03827716.1| RNA polymerase sigma factor RpoS [Pectobacterium carotovorum subsp.
           brasiliensis PBR1692]
 gi|227327750|ref|ZP_03831774.1| RNA polymerase sigma factor RpoS [Pectobacterium carotovorum subsp.
           carotovorum WPP14]
 gi|49612977|emb|CAG76428.1| RNA polymerase sigma factor [Pectobacterium atrosepticum SCRI1043]
          Length = 330

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVPSRRRMIESNLRLVVKIARRYNNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +     +  
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVNRMLRLNERITSVDTPL--GGDSEK 232

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  + D   +   +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 233 ALLDILADEKDNGPE---DTTQDNDMKQNIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQVQ 320


>gi|6010728|gb|AAF01230.1|AF184099_1 mutant RpoS [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
          Length = 330

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|16752284|ref|NP_445653.1| RNA polymerase sigma factor [Chlamydophila pneumoniae AR39]
 gi|7190028|gb|AAF38883.1| RNA polymerase sigma factor, sigma-70 family [Chlamydophila
           pneumoniae AR39]
          Length = 591

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 69/255 (27%), Positives = 123/255 (48%), Gaps = 13/255 (5%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             + +R+ +     A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+
Sbjct: 323 VRMLQRWMDK-SQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFE 381

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             RG++ +TY+ WWI+ A+   I      ++I        +   + ++    + +     
Sbjct: 382 YRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVH-----MIETINKVLRGAKKLMMETG 436

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           K      +A++L ++   V  +        SL A +   + + S + D+L    D   + 
Sbjct: 437 KEPTPEELAEELGLTPDRVREIYKIAQHPISLQAEV--GEGSESSFGDFL---EDTAVES 491

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQI 272
             E       ++ +   +  L  RER +   R   L   P TLE + S F V+RER+RQI
Sbjct: 492 PAEATGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGKPKTLEEVGSAFNVTRERIRQI 551

Query: 273 EARAFKKVQESIQKQ 287
           EA+A +K++  I+ +
Sbjct: 552 EAKALRKMRHPIRSK 566



 Score = 38.6 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 8/32 (25%), Positives = 19/32 (59%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREH 44
           +  +  Y+ E+  +P+L ++EE  ++KR  + 
Sbjct: 119 DDPVRMYLKEMGTVPLLTREEEVEISKRIEKA 150


>gi|322831414|ref|YP_004211441.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rahnella sp.
           Y9602]
 gi|321166615|gb|ADW72314.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rahnella sp.
           Y9602]
          Length = 328

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 136/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 59  YLGEIGYSPLLTAEEEVYFARR-ALRGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 117

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 118 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 176

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            IA++L+    +V  M        S++  +     +  
Sbjct: 177 LRTAR----ELAHKLDHEPSAEEIAEQLDKPVHDVSRMLRLNERITSVDTPL--GGDSEK 230

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  + D   +   +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 231 ALLDILADEKDNGPE---DTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 287

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 288 DVGREIGLTRERVRQIQVEGLRRLREILQGQ 318


>gi|302345330|ref|YP_003813683.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           melaninogenica ATCC 25845]
 gi|302149662|gb|ADK95924.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           melaninogenica ATCC 25845]
          Length = 284

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 76/287 (26%), Positives = 150/287 (52%), Gaps = 12/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI    M+  +EE  LA++ R +GD  A  RL  ++LR VV
Sbjct: 2   KITKSITNRESASLDKYLQEIGHEEMISIEEEVELAQKIR-NGDRKALERLTKANLRFVV 60

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + I     
Sbjct: 61  SVAKQYQNQGLSLPDLINEGNVGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSR 120

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           ++++    NQ      + ++   L      N +   +  IA+  ++ E +++      + 
Sbjct: 121 IIRLP--LNQVSSVNKINKI---LTQFEQENERRPSIDEIAQNTDIPEDKIVDAMKVNSR 175

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     D+ SS        +    ++ L+E    ++ R  + R++ +L  RE+ +
Sbjct: 176 HVSVDAPFYD-DEQSSLLDVIPNDNTPSTDKELVE----ESLREEIGRALQILEDREKVV 230

Query: 243 FEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            EA        +TLE + S++ ++RERVRQI+ +A +++++    +V
Sbjct: 231 IEAYFGINQREMTLEEIGSKYNLTRERVRQIKEKAIRRLRQLSNSKV 277


>gi|255325135|ref|ZP_05366241.1| RNA polymerase sigma factor RpoD [Corynebacterium
           tuberculostearicum SK141]
 gi|255297700|gb|EET77011.1| RNA polymerase sigma factor RpoD [Corynebacterium
           tuberculostearicum SK141]
          Length = 365

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 67/309 (21%), Positives = 138/309 (44%), Gaps = 38/309 (12%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY------------------RE 43
           +R+N +        +  Y++ I K  +L  ++E  LA+                     E
Sbjct: 55  SRRNQTNDNPSADLVRVYLNGIGKTALLSAEDEVELAQAIEVGLYAEYKLNNAEKLTRAE 114

Query: 44  HGD--------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
             D          A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD 
Sbjct: 115 KRDLKILAREGKKARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDY 174

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            +GF+ +TY+ WWI+ A+   +      +++     ++     L R+K  +         
Sbjct: 175 AKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLSRIKREMYQSLGREAT 232

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
            E    ++++  + E+++  +  +     SL+  + + ++  +   D++        +  
Sbjct: 233 NE---ELSEESGIDENKIEMLLRQSRDPVSLDMPVGTDEE--APLGDFIEDAEATDAETA 287

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIE 273
           +    R    + +   +  L  RE+ +   R   ++  P TL+ +   F +SRERVRQIE
Sbjct: 288 VVASMR---HSDIRGVIDTLEKREQDVIRLRYGLDDGVPRTLDQIGRRFGLSRERVRQIE 344

Query: 274 ARAFKKVQE 282
                K+++
Sbjct: 345 REVMAKLRD 353


>gi|329902595|ref|ZP_08273157.1| RNA polymerase sigma factor RpoS [Oxalobacteraceae bacterium
           IMCC9480]
 gi|327548742|gb|EGF33384.1| RNA polymerase sigma factor RpoS [Oxalobacteraceae bacterium
           IMCC9480]
          Length = 334

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 78/268 (29%), Positives = 135/268 (50%), Gaps = 11/268 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+++I    +L   +E   A    + GD  A   ++  +LRLVV IA  Y   G+ + ++
Sbjct: 65  YLNQIGARALLTVAQEVHYAT-LAKAGDFPARQVMIEHNLRLVVSIAKHYINRGVVLLDL 123

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+A+ KF+PERGFR +TY+ WWI+ +++  I+     V++       R    
Sbjct: 124 IEEGNLGLMRAIDKFEPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV--IRELNQ 181

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           + R K HL+A+  ++ K   +  IA     S  +V  +        SL+A +       S
Sbjct: 182 VLRAKYHLEAL-HHDGKDASIDDIAHLTGRSAEDVQDILALSDHPASLDAPL--DADPGS 238

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
              D L  D     +   E+ E      ++   ++ L+ ++R I   R     ++P TLE
Sbjct: 239 SLMDLLPGDPGDGPEARAEQHETAL---LVRDWLARLSDKQRLIITRRFGLEDDDPATLE 295

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
            L++E  V+RERVRQ++  A  K++ ++
Sbjct: 296 ALAAEIGVTRERVRQVQQEALIKLKRAL 323


>gi|257126034|ref|YP_003164148.1| RNA polymerase, sigma 32 subunit, RpoH [Leptotrichia buccalis
           C-1013-b]
 gi|257049973|gb|ACV39157.1| RNA polymerase, sigma 32 subunit, RpoH [Leptotrichia buccalis
           C-1013-b]
          Length = 273

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 89/273 (32%), Positives = 156/273 (57%), Gaps = 15/273 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +S Y+ +I+K  +L K+EEY L +R RE  D  A   L+ S+LRLV+  A    G GLP+
Sbjct: 9   MSLYLSDIQKFDLLSKEEEYELLRRIREDNDEQARQLLILSNLRLVISTAKKSLGNGLPL 68

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++SEGNIGL++A+ KFD E+G R +TY++WWIK A+++ I+     ++I +       
Sbjct: 69  IDLISEGNIGLIKAINKFDYEKGHRFSTYAVWWIKQAIKKAIINIGRDIRIPSYK----- 123

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           +  L ++   ++  T  + +      IAKK+++ ES++I +        SLN  I  +  
Sbjct: 124 YEQLSKVNKAIKDYTAIHGEAPSTEYIAKKVDLKESKIILLLGEFQDIMSLNETIGDN-- 181

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--V 253
               + + ++  +D  E  +I++++    R +L R   +LN RER+I E R    +    
Sbjct: 182 ---IYLEDVIGKNDDVEDKIIKEDQLLEMRELLER---ILNERERKILEYRYGLYDNKIH 235

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TL+ +  +  ++RERVRQIE +A  K++E +++
Sbjct: 236 TLKEIGEQMGITRERVRQIEKKAITKLKEHLEE 268


>gi|89890814|ref|ZP_01202323.1| DNA-directed RNA polymerase major sigma-43 factor (sigma-A) rpoD
           [Flavobacteria bacterium BBFL7]
 gi|89516959|gb|EAS19617.1| DNA-directed RNA polymerase major sigma-43 factor (sigma-A) rpoD
           [Flavobacteria bacterium BBFL7]
          Length = 287

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 71/276 (25%), Positives = 146/276 (52%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y+ +I KI ++  +EE  LA+  ++ GD  A  +L T++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLQDISKIDLITAEEEVELAQLIKK-GDQRALEKLTTANLRFVVSVAKQYQNQGLK 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN GL++A K+FD  RGF+  +Y++WWI+ ++ + +     +V++    N+  
Sbjct: 76  LPDLINEGNAGLVKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLP--LNKIG 133

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               + +   HL+ + +    PE    +AK+L+++ S+V           S++A +   +
Sbjct: 134 SINKINKAFSHLEQLHERPPSPE---ELAKELDMTVSDVKQSLKNAGRHVSMDAPLK--E 188

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
             +S   D +           +  E        +TR++  L+ +E  +        N  P
Sbjct: 189 GETSNLYDVVRSGESPNPDRELMHESLTLE---ITRALETLSQKEADVISLYFGIGNQQP 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           ++LE +   F+++RERVRQI+ +  K+++++ + ++
Sbjct: 246 MSLEEIGETFDLTRERVRQIKEKGIKRLRQNSRSKI 281


>gi|225021249|ref|ZP_03710441.1| hypothetical protein CORMATOL_01261 [Corynebacterium matruchotii
           ATCC 33806]
 gi|224945982|gb|EEG27191.1| hypothetical protein CORMATOL_01261 [Corynebacterium matruchotii
           ATCC 33806]
          Length = 391

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 67/315 (21%), Positives = 142/315 (45%), Gaps = 39/315 (12%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAK--------------------RY 41
           +R+  +        +  Y++ I K  +L  ++E  LA+                    R 
Sbjct: 80  SRRGQNNDNPSADLVRVYLNGIGKTALLTAEDEVHLAQTIEVGLYAEYLLTDSDEPLTRA 139

Query: 42  REHG-------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           ++            A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD
Sbjct: 140 KKRDLKVLVKEGRKARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFD 199

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +GF+ +TY+ WWI+ A+   +      +++     ++     L R+K  +        
Sbjct: 200 YAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLSRIKREMYQQLGREA 257

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
             E    +A++  + ES++  +  +     SL+  + + ++  +   D++        + 
Sbjct: 258 TNE---ELAEESGIDESKIELLLRQSRDPVSLDMPVGADEE--APLGDFIEDSEAADAES 312

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
            +    R    + +   +  L  RE+ +   R   ++  P TL+ +  +F +SRERVRQI
Sbjct: 313 AVVASLR---HSDIRDVIGTLEDREQDVIRMRYGLDDGVPRTLDQIGRQFGLSRERVRQI 369

Query: 273 EARAFKKVQESIQKQ 287
           E    +K+++  + +
Sbjct: 370 EREVMRKLRDGQRAE 384


>gi|72161811|ref|YP_289468.1| RNA polymerase sigma factor [Thermobifida fusca YX]
 gi|71915543|gb|AAZ55445.1| RNA polymerase sigma factor [Thermobifida fusca YX]
          Length = 438

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 73/311 (23%), Positives = 137/311 (44%), Gaps = 44/311 (14%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR--------------------------------Y 41
             +  Y+  I +  +L  ++E  LAKR                                +
Sbjct: 134 DSVHTYLKAIGRRELLTAEQEVELAKRIEAGLYAEYKLGWLEESPGPQEMSETEREELEW 193

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
                  A   ++ ++LRLVV +A  Y   G+P+ +VV EGN+GL++AV+KFD  +G++ 
Sbjct: 194 IAEDGRRAKAHMLEANLRLVVSVAKKYSDRGMPLLDVVQEGNLGLIRAVEKFDYAKGYKF 253

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY+MWWI+ A+Q     S   +++     +  L   L RL+  +         P+    
Sbjct: 254 STYAMWWIRQAIQRGFADSARTIRLPVHVLE--LLSKLSRLERDMHQTLGREPTPD---E 308

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           +A++L  + +++  +        SL++ I   +   ++  D +    D       E  +R
Sbjct: 309 LAQELGKTPAQIEELLRITRQPISLDSTI--GEDGETRIGDLI---EDVDASEASEVVDR 363

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           +   + L R++  L PRE  I   R       P TL+ +     ++RER+RQ+E ++  K
Sbjct: 364 QLMADQLRRALDDLEPREATIMSLRFGLFDGRPRTLDEIGKHLGLTRERIRQLEKQSLSK 423

Query: 280 VQESIQKQVEL 290
           ++   + +  L
Sbjct: 424 LRHPSRARQLL 434


>gi|317049278|ref|YP_004116926.1| RpoD subfamily RNA polymerase sigma-70 factor [Pantoea sp. At-9b]
 gi|316950895|gb|ADU70370.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pantoea sp.
           At-9b]
          Length = 330

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVFFARR-ALRGDIPSRRRMIESNLRLVVKIARRYSNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +     +  
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPL--GGDSEK 232

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  + D   +   +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 233 ALLDILADEKDNGPE---DTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|255066480|ref|ZP_05318335.1| RNA polymerase sigma factor RpoD [Neisseria sicca ATCC 29256]
 gi|255049360|gb|EET44824.1| RNA polymerase sigma factor RpoD [Neisseria sicca ATCC 29256]
          Length = 649

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 63/272 (23%), Positives = 121/272 (44%), Gaps = 14/272 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRY--REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +  + K   +  +E   + K     E    +A   ++ ++LRLV+ IA  Y   GL   +
Sbjct: 375 LANMEKETRISIEELKDINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLD 434

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +  
Sbjct: 435 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIE 489

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + ++    +       +      +A+ + + E ++  +        S+   I   D + 
Sbjct: 490 TINKMNRISRQYLQETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPI--GDDDD 547

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D       +     +   +    +  L PRE ++   R   +     TL
Sbjct: 548 SHLGDFI---EDANNVAPADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTL 604

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +  +F+V+RER+RQIEA+A +K++   +  
Sbjct: 605 EEVGKQFDVTRERIRQIEAKALRKLRHPTRSD 636


>gi|71278347|ref|YP_267823.1| RNA polymerase sigma factor RpoS [Colwellia psychrerythraea 34H]
 gi|71144087|gb|AAZ24560.1| RNA polymerase sigma factor RpoS [Colwellia psychrerythraea 34H]
          Length = 296

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 80/271 (29%), Positives = 139/271 (51%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   + R    GD  +  R++ S+LRLVVKIA  Y   GLP+ ++
Sbjct: 27  YLSEIGFSPLLTAEEEVYFS-RLALKGDEPSRKRMIESNLRLVVKIARRYNNRGLPLLDL 85

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 86  IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNIY 144

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +  +Q +            IA+ L+   ++V  M        S++     + ++  
Sbjct: 145 LRASRELIQKLDHE----PTAEDIAQHLDRPVADVNKMLRLNERIASVDTPF--AGESDK 198

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D +  +     +  ++ E+  N    +   ++ LN ++R +   R   L     TLE
Sbjct: 199 ALLDVIADEKSTGPESDLQSEDMSNN---IIHWLNELNTKQREVLARRFGLLGYEASTLE 255

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           N+  E  ++RERVRQI+  A K++++ + +Q
Sbjct: 256 NVGREIGLTRERVRQIQVEALKRLRDILSQQ 286


>gi|49476176|ref|YP_034217.1| RNA polymerase factor sigma-32 [Bartonella henselae str. Houston-1]
 gi|49238984|emb|CAF28284.1| RNA polymerase sigma-32 factor [Bartonella henselae str. Houston-1]
          Length = 303

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 102/284 (35%), Positives = 171/284 (60%), Gaps = 2/284 (0%)

Query: 3   RKNMSIIVNGEIGLSR-YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
            KN     + +  L R  +    + P LE+Q+E+ LA R+++  D  A H++  +H+RLV
Sbjct: 9   YKNSKNYSDADKSLGRNMMRSAMQAPYLERQKEHDLALRWKDKRDDEAMHQIAAAHMRLV 68

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           + IA  ++ + +P+ ++V EG +GL++A  +F+P+R  R +TY+ WWI+A++Q+YILR+W
Sbjct: 69  IAIANRFKRFKMPLGDLVQEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNW 128

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
           S+V+ GT+++QK LFFNLRRL+  L        K +   +IA+KL VS  +V +M+ R +
Sbjct: 129 SIVRGGTSSSQKALFFNLRRLRAKLVQDDSALSKQDIFRSIAEKLGVSVRDVETMDFRFS 188

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR-NMLTRSMSVLNPRER 240
             ++  ++  S + ++   +   + D       LIE+     RR   L  ++ +LN RE 
Sbjct: 189 SSDNSLSVSVSENSDNPVAKMDALVDDSPLPDALIEQVIDGQRRTQWLYDALQILNEREL 248

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            I   RRL E   TLE L  +  +S+ERVRQIEARA +K++ ++
Sbjct: 249 EIIRFRRLNEEGATLEVLGEKLGISKERVRQIEARALQKLRSAL 292


>gi|37520903|ref|NP_924280.1| RNA polymerase sigma factor RpoD [Gloeobacter violaceus PCC 7421]
 gi|35211898|dbj|BAC89275.1| group2 RNA polymerase sigma factor [Gloeobacter violaceus PCC 7421]
          Length = 350

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 71/313 (22%), Positives = 133/313 (42%), Gaps = 47/313 (15%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE--------------------------- 43
           + +  +  Y+ EI ++ +L+  EE  LA+R                              
Sbjct: 37  STDDLVRLYLQEIGRVALLKPAEEIELARRIATWLSLEEKRSKFQAVAAESWLESANLTP 96

Query: 44  -------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                       A   LV ++LRLVV +A  Y+G GL + +++ EG +GL++A +KFD  
Sbjct: 97  QQWSTIVREGERAKAHLVKANLRLVVSVAKKYQGRGLHLLDLIQEGTLGLIRAAEKFDYT 156

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RGF+ +TY+ WWI+  +   I      +++     +K     + R+K   + ++    + 
Sbjct: 157 RGFKFSTYATWWIRQGITRAIAMQARTIRLPVHIVEK-----VNRIKKATRQLSQQLGRS 211

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
                IA+ + +   ++  +   +    SL   +    +  +   D +    +  E  ++
Sbjct: 212 PSEDEIAQAVEMDADQLRFVRKAIQLPVSLETPV--GREEDTALGDLIQAKGNEPEHGVV 269

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEA 274
               R      L   +  L PRER +   R         TL+ +  +F ++RER+RQIEA
Sbjct: 270 ----RDLMNQDLESLLQTLTPRERDVLRLRYGLIDGRSRTLDEVGQQFGLTRERIRQIEA 325

Query: 275 RAFKKVQESIQKQ 287
           RA +K++   + Q
Sbjct: 326 RALRKLRHPQRLQ 338


>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 =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 63/272 (23%), Positives = 121/272 (44%), Gaps = 14/272 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRY--REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +  + K   +  +E   + K     E    +A   ++ ++LRLV+ IA  Y   GL   +
Sbjct: 375 LANMEKETRISIEELKDINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLD 434

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +  
Sbjct: 435 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIE 489

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + ++    +       +      +A+ + + E ++  +        S+   I   D + 
Sbjct: 490 TINKMNRISRQYLQETGEEPDSAKLAELMEMPEDKIRKIMKIAKEPISMETPI--GDDDD 547

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D       +     +   +    +  L PRE ++   R   +     TL
Sbjct: 548 SHLGDFI---EDANNVAPADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTL 604

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +  +F+V+RER+RQIEA+A +K++   +  
Sbjct: 605 EEVGKQFDVTRERIRQIEAKALRKLRHPTRSD 636


>gi|167469361|ref|ZP_02334065.1| RNA polymerase sigma factor RpoS [Yersinia pestis FV-1]
          Length = 277

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 79/271 (29%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+S+  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 8   YLGEIGYSPLLSAEEEVYFARR-ALRGDVSSRRRMIESNLRLVVKIARRYSNRGLALLDL 66

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 67  IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 125

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    +   
Sbjct: 126 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE--- 178

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
             +  L    D  E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 179 --KALLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 236

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 237 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 267


>gi|320640384|gb|EFX09923.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           G5101]
          Length = 330

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHQLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|309378741|emb|CBX22691.1| unnamed protein product [Neisseria lactamica Y92-1009]
          Length = 642

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 62/272 (22%), Positives = 122/272 (44%), Gaps = 14/272 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRY--REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + ++ +   +  +E   + K     E    +A   ++ ++LRLV+ IA  Y   GL   +
Sbjct: 368 LADMERETRISIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLD 427

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +  
Sbjct: 428 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIE 482

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + ++    +       +      +A+ + + E ++  +        S+   I   D + 
Sbjct: 483 TINKMNRISRQHLQETGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPI--GDDDD 540

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D       +     +   +    +  L PRE ++   R   +     TL
Sbjct: 541 SHLGDFI---EDANNVAPADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTL 597

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +  +F+V+RER+RQIEA+A +K++   +  
Sbjct: 598 EEVGRQFDVTRERIRQIEAKALRKLRHPTRSD 629


>gi|253988173|ref|YP_003039529.1| RNA polymerase sigma factor RpoS [Photorhabdus asymbiotica subsp.
           asymbiotica ATCC 43949]
 gi|253779623|emb|CAQ82784.1| rna polymerase sigma factor (sigma-38) [Photorhabdus asymbiotica]
          Length = 332

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 82/271 (30%), Positives = 140/271 (51%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 63  YLGEIGFSPLLTAEEEVFFARR-ALRGDVLARRRMIESNLRLVVKISRRYSNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 180

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +  L    D+   PE++     K     S ++ +N R+    S++  I+S      
Sbjct: 181 LRTAR-ELAHKLDHEPSPEEIAEQLDKPVDDVSRMLRLNERI---ISVDTPISSDSD--- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
             +  L    D  E       +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 --KALLDVLSDENETGPEGTTQEDDMKKSIVKWLFELNSKQREVLARRFGLLGYEAETLE 291

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    +++++ +Q Q
Sbjct: 292 DVGKEIGLTRERVRQIQVEGLRRLKDIMQTQ 322


>gi|251771800|gb|EES52375.1| RNA polymerase, sigma 70 subunit, RpoD [Leptospirillum
           ferrodiazotrophum]
          Length = 590

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 74/246 (30%), Positives = 117/246 (47%), Gaps = 12/246 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RGF+ +
Sbjct: 346 EEKVREAKSELIKANLRLVVSIAKRYTNRGLQFLDLIQEGNIGLMKAVDKFEYKRGFKFS 405

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            L R   HL         PE    +
Sbjct: 406 TYATWWIRQAITRAIADQARTIRIPVHM--IETINKLIRTSRHLVQELGREPLPE---EL 460

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           AK++ +   +V  +        SL   I   ++  S   D++    D +    IE   R 
Sbjct: 461 AKEMQMPVDKVRRVLKIAREPISLETPI--GEEEDSHLGDFI---EDKKTISPIEAAVRY 515

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
           +    + +S+S L  RE ++   R         TLE +  +F+V+RER+RQIEA+A +K+
Sbjct: 516 DLVRKIGQSLSTLTDREEKVIRLRFGIGELTDHTLEEVGQDFDVTRERIRQIEAKALRKL 575

Query: 281 QESIQK 286
           +   + 
Sbjct: 576 RHPSRS 581


>gi|333001093|gb|EGK20663.1| RNA polymerase sigma factor RpoS [Shigella flexneri K-272]
 gi|333015402|gb|EGK34741.1| RNA polymerase sigma factor RpoS [Shigella flexneri K-227]
          Length = 330

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 139/271 (51%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR ++     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTVR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|313668077|ref|YP_004048361.1| RNA polymerase sigma factor [Neisseria lactamica ST-640]
 gi|313005539|emb|CBN86975.1| RNA polymerase sigma factor [Neisseria lactamica 020-06]
          Length = 642

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 63/272 (23%), Positives = 122/272 (44%), Gaps = 14/272 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRY--REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + ++ K   +  +E   + K     E    +A   ++ ++LRLV+ IA  Y   GL   +
Sbjct: 368 LADMEKETRISIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLD 427

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +  
Sbjct: 428 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIE 482

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + ++    +       +      +A+ + + E ++  +        S+   I   D + 
Sbjct: 483 TINKMNRISRQHLQETGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPI--GDDDD 540

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D       +     +   +    +  L PRE ++   R   +     TL
Sbjct: 541 SHLGDFI---EDANNVAPADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTL 597

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +  +F+V+RER+RQIEA+A +K++   +  
Sbjct: 598 EEVGRQFDVTRERIRQIEAKALRKLRHPTRSD 629


>gi|282858973|ref|ZP_06268111.1| sigma-70 region 2 [Prevotella bivia JCVIHMP010]
 gi|282588253|gb|EFB93420.1| sigma-70 region 2 [Prevotella bivia JCVIHMP010]
          Length = 286

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 73/282 (25%), Positives = 151/282 (53%), Gaps = 12/282 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI     + L +Y+ EI    +L  +EE  LA+R R+ GD  A  RL  ++LR VV
Sbjct: 5   KITKSITNRESMSLDKYLQEIGNEELLTPEEEVELAQRIRK-GDKKALERLTRANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  G+ + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + I     
Sbjct: 64  SVAKQYQTQGIDLPDLINEGNMGLIKAAKRFDETRGFKFISYAVWWIRQSILQAIAAQGR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           L+++   ANQ  +   + R+   L      N +   +  +A+++++SE  +         
Sbjct: 124 LIRLP--ANQIGVVNKITRI---LNKFEQENERIPNIDELAREVDLSEEHIEDALSLSFR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S+++     D+  S        +    ++ L++    ++ +  ++R++ +L+ RE+++
Sbjct: 179 QVSMDSPFKD-DEGVSLLDVMPSTNVPSTDKSLVD----ESLKEEISRALKILSEREQKV 233

Query: 243 FEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             A        ++LE +  +F +SRERVRQI+ +A + ++++
Sbjct: 234 LCAYYGIGQLEMSLEEIGDKFGLSRERVRQIKEKAIRNLRKA 275


>gi|261822742|ref|YP_003260848.1| RNA polymerase sigma factor RpoS [Pectobacterium wasabiae WPP163]
 gi|5912456|emb|CAB56153.1| RpoS protein [Pectobacterium carotovorum]
 gi|261606755|gb|ACX89241.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pectobacterium
           wasabiae WPP163]
          Length = 330

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDIPSRRRMIESNLRLVVKIARRYNNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +     +  
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVNRMLRLNERITSVDTPL--GGDSEK 232

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  + D   +   +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 233 ALLDILADEKDNGPE---DTTQDNDMKQNIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQVQ 320


>gi|320662323|gb|EFX29720.1| RNA polymerase sigma factor RpoS [Escherichia coli O55:H7 str. USDA
           5905]
          Length = 330

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|94266972|ref|ZP_01290621.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
 gi|93452327|gb|EAT02958.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
          Length = 353

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 73/242 (30%), Positives = 125/242 (51%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A +RLV ++LRLVV +A  Y G GL + +++ EGNIGLM+AV+KF+  RG++ +TY+ 
Sbjct: 113 QEAKNRLVQANLRLVVSVAKKYAGRGLQLLDLIQEGNIGLMKAVEKFEYRRGYKFSTYAT 172

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + R+    +     + +      +A+ L
Sbjct: 173 WWIRQAVTRAIADQGRTIRIPVH-----MIDTINRMLKGAKEFQRQHGREPTPDEMAQHL 227

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            V  ++V S+        SL+  + +S  N S   D++    D +     E    +N ++
Sbjct: 228 GVEVAKVKSVLKIAKEPLSLDTPVGNS--NDSFLADFI---EDTEAASPDEATIYENLQS 282

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L R +  L+PRE  +   R   +  +  TLE +   F V+RER+RQIEA+A KK++   
Sbjct: 283 NLRRVLKTLSPREEMVLRLRFGLDTAMDLTLEEVGENFAVTRERIRQIEAKALKKLKHPA 342

Query: 285 QK 286
           ++
Sbjct: 343 RR 344


>gi|123967121|ref|YP_001012202.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9515]
 gi|123201487|gb|ABM73095.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9515]
          Length = 339

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 77/292 (26%), Positives = 144/292 (49%), Gaps = 31/292 (10%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--------------------DLSAAH 51
               +  Y+  I ++P+L   EE  LA   +                          A  
Sbjct: 48  ASDSIGYYLSSIGRVPLLTAAEEIELAHHVQNMKKMLKIPEIERSSRNRHLIKVGKRARD 107

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R+++++LRLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+ 
Sbjct: 108 RMMSANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQ 167

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            M   I  S   +++    ++K     L +++   + ++  + +    + +A  + + + 
Sbjct: 168 GMTRAIDNSARTIRLPIHISEK-----LSKMRRVSRELSQKSGRQPTRLEMATAMGIDQK 222

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           ++  +  + A   SL+A     +  S+  +  L+ D +G+E   +E  +R  ++  L   
Sbjct: 223 DLEDLISQSAPCASLDAHARGEEDRSTLGE--LIPDPNGEE--PMEGMDRTIQKEHLGTW 278

Query: 232 MSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++ LN RE++I + R     E P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 279 LTQLNEREQKIMKLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 330


>gi|238758207|ref|ZP_04619386.1| RNA polymerase sigma factor rpoS [Yersinia aldovae ATCC 35236]
 gi|238703537|gb|EEP96075.1| RNA polymerase sigma factor rpoS [Yersinia aldovae ATCC 35236]
          Length = 332

 Score =  217 bits (553), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 136/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 63  YLGEIGYSPLLTAEEEVYFARR-ALRGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 180

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 181 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 235

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D  E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 236 ----LLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 291

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 292 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 322


>gi|302342714|ref|YP_003807243.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfarculus
           baarsii DSM 2075]
 gi|301639327|gb|ADK84649.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfarculus
           baarsii DSM 2075]
          Length = 590

 Score =  216 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 70/243 (28%), Positives = 114/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ 
Sbjct: 350 QDAKQELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYAT 409

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            L R   +L         PE    IA+K+
Sbjct: 410 WWIRQAITRAIADQARTIRIPVHM--IETINKLIRTSRYLVQEFGREPTPE---EIAEKM 464

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +    +V  +        SL   I   ++  S   D++    D +     +     N   
Sbjct: 465 DFPLEKVRKVLKIAKEPISLETPI--GEEEDSHLGDFI---EDKKVINPADAVISLNLCE 519

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              + ++ L PRE ++   R         TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 520 QTRKVLATLTPREEKVLRMRFGIGQKSDHTLEEVGRDFDVTRERIRQIEAKALRKLRHPS 579

Query: 285 QKQ 287
           + +
Sbjct: 580 RAK 582



 Score = 36.7 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 11/46 (23%), Positives = 22/46 (47%), Gaps = 1/46 (2%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHL 58
              +  Y+ E+ ++ +L ++ E  +AKR  E G+      L+   L
Sbjct: 98  SDPVKMYLREMGQVSLLTREGEVEIAKRI-EKGERQCIDALLECSL 142


>gi|282891123|ref|ZP_06299627.1| hypothetical protein pah_c047o017 [Parachlamydia acanthamoebae str.
           Hall's coccus]
 gi|281498940|gb|EFB41255.1| hypothetical protein pah_c047o017 [Parachlamydia acanthamoebae str.
           Hall's coccus]
          Length = 546

 Score =  216 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 74/255 (29%), Positives = 121/255 (47%), Gaps = 13/255 (5%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             + +R+ +     A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+
Sbjct: 291 VRMLQRWMDK-SQEAKREMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFE 349

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             RG++ +TY+ WWI+ A+   I      ++I            + R    L   T    
Sbjct: 350 YRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVHM--IETINKVLRGAKKLMMETGREP 407

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            PE    +A +L ++   V  +        SL A +   D   SQ+ D+L    D     
Sbjct: 408 SPE---ELANELGITAERVREIYKIAQHPISLQAEV--GDGGESQFGDFL---EDTGADS 459

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQI 272
             E       ++ +   ++ L  RER++   R   L   P TLE +  EF V+RER+RQI
Sbjct: 460 PAEATGYSILKDKMNEVLATLTDRERKVLIQRFGLLDGKPKTLEEVGVEFNVTRERIRQI 519

Query: 273 EARAFKKVQESIQKQ 287
           EA+A +K++   + +
Sbjct: 520 EAKALRKMRHPTRSK 534



 Score = 39.0 bits (90), Expect = 0.95,   Method: Composition-based stats.
 Identities = 8/34 (23%), Positives = 20/34 (58%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREH 44
           + +  +  Y+ E+  +P+L ++EE  ++KR  + 
Sbjct: 93  SPDDPVRMYLKEMGSVPLLSREEEVEISKRIEKA 126


>gi|254672481|emb|CBA05947.1| RNA polymerase sigma factor 70 [Neisseria meningitidis alpha275]
          Length = 642

 Score =  216 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 63/272 (23%), Positives = 122/272 (44%), Gaps = 14/272 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRY--REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + ++ K   +  +E   + K     E    +A   ++ ++LRLV+ IA  Y   GL   +
Sbjct: 368 LADMEKETRISIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLD 427

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +  
Sbjct: 428 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIE 482

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + ++    +       +      +A+ + + E ++  +        S+   I   D + 
Sbjct: 483 TINKMNRISRQHLQETGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPI--GDDDD 540

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D       +     +   +    +  L PRE ++   R   +     TL
Sbjct: 541 SHLGDFI---EDANNVAPADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTL 597

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +  +F+V+RER+RQIEA+A +K++   +  
Sbjct: 598 EEVGRQFDVTRERIRQIEAKALRKLRHPTRSD 629


>gi|329296050|ref|ZP_08253386.1| RNA polymerase sigma factor RpoS [Plautia stali symbiont]
          Length = 330

 Score =  216 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVFFARR-ALRGDIPSRRRMIESNLRLVVKIARRYSNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +     +  
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPL--GGDSEK 232

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  + D   +   +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 233 ALLDILADEKDNGPE---DTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|183600216|ref|ZP_02961709.1| hypothetical protein PROSTU_03759 [Providencia stuartii ATCC 25827]
 gi|188022512|gb|EDU60552.1| hypothetical protein PROSTU_03759 [Providencia stuartii ATCC 25827]
          Length = 328

 Score =  216 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 135/271 (49%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 59  YLSEIGFSPLLTAEEEVFYARR-ALRGDVASRQRMIESNLRLVVKISRRYNNRGLALLDL 117

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPE+GFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 118 IEEGNLGLIRAVEKFDPEKGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNIY 176

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            IA++L+    +V  M        S++  I    + S 
Sbjct: 177 LRTAR----ELAQKLDHEPSAEEIAEQLDKPVEDVSRMLRLNERITSVDTPIAGDSEKS- 231

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D  E       +  N +  + + +  LNP++R +   R   L     TLE
Sbjct: 232 ----LLEVLSDENESGPEHTIQDNNLKENIVKWLFELNPKQREVLARRFGLLGYEAETLE 287

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +  E  ++RERVRQI+    +++++ +Q +
Sbjct: 288 EVGREIGLTRERVRQIQVEGLRRLKDILQGE 318


>gi|149188695|ref|ZP_01866986.1| RNA polymerase sigma factor RpoS [Vibrio shilonii AK1]
 gi|148837356|gb|EDL54302.1| RNA polymerase sigma factor RpoS [Vibrio shilonii AK1]
          Length = 296

 Score =  216 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 74/271 (27%), Positives = 129/271 (47%), Gaps = 11/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y  E+    +L  ++E  +A++ R  GD  A   L+ S+LRLV++ A  Y   GL   ++
Sbjct: 27  YFKEVAGHDLLSAEDERHIARKAR-AGDTLARQHLINSNLRLVIRTAKRYSNRGLDFYDL 85

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           ++EGNIGL+QAV KFDPE G+R +TY++WWI+ A+   I+     +++     +      
Sbjct: 86  INEGNIGLIQAVDKFDPELGYRFSTYAVWWIQQAIDRAIMNQGRTIRVPVHVTK-----Q 140

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           +R        +            IA++   +  EV  +        SL+   N  D+   
Sbjct: 141 IRECSKAAHELRKEGNHEPTSSEIAERTGRAPEEVSKLLKLSEQSLSLD---NGWDEEGD 197

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
           +       D D   ++  +    +N    L   +  L  ++R I   R   L ++P TLE
Sbjct: 198 KKDHLQTIDDDDVFELPEQDIVTQNLNKALIDLVDSLPDKQRVILHHRFGLLDDDPKTLE 257

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +     V+RERVRQI+  A + +++ +++Q
Sbjct: 258 QVGEIVGVTRERVRQIQKSAMETLRDKLKRQ 288


>gi|15832849|ref|NP_311622.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           Sakai]
 gi|74313307|ref|YP_311726.1| RNA polymerase sigma factor RpoS [Shigella sonnei Ss046]
 gi|110642882|ref|YP_670612.1| RNA polymerase sigma factor RpoS [Escherichia coli 536]
 gi|110806628|ref|YP_690148.1| RNA polymerase sigma factor RpoS [Shigella flexneri 5 str. 8401]
 gi|157157336|ref|YP_001464064.1| RNA polymerase sigma factor RpoS [Escherichia coli E24377A]
 gi|157162189|ref|YP_001459507.1| RNA polymerase sigma factor RpoS [Escherichia coli HS]
 gi|168749933|ref|ZP_02774955.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4113]
 gi|168755487|ref|ZP_02780494.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4401]
 gi|168778725|ref|ZP_02803732.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4076]
 gi|168787997|ref|ZP_02813004.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC869]
 gi|170019013|ref|YP_001723967.1| RNA polymerase sigma factor RpoS [Escherichia coli ATCC 8739]
 gi|170684160|ref|YP_001744890.1| RNA polymerase sigma factor RpoS [Escherichia coli SMS-3-5]
 gi|191166775|ref|ZP_03028601.1| RNA polymerase sigma factor RpoS [Escherichia coli B7A]
 gi|191171134|ref|ZP_03032684.1| RNA polymerase sigma factor RpoS [Escherichia coli F11]
 gi|193065048|ref|ZP_03046123.1| RNA polymerase sigma factor RpoS [Escherichia coli E22]
 gi|193069671|ref|ZP_03050623.1| RNA polymerase sigma factor RpoS [Escherichia coli E110019]
 gi|194431745|ref|ZP_03064036.1| RNA polymerase sigma factor RpoS [Shigella dysenteriae 1012]
 gi|194438995|ref|ZP_03071079.1| RNA polymerase sigma factor RpoS [Escherichia coli 101-1]
 gi|208812039|ref|ZP_03253368.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4045]
 gi|209395891|ref|YP_002272204.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4115]
 gi|209920184|ref|YP_002294268.1| RNA polymerase sigma factor RpoS [Escherichia coli SE11]
 gi|217326648|ref|ZP_03442731.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           TW14588]
 gi|218559734|ref|YP_002392647.1| RNA polymerase sigma factor RpoS [Escherichia coli S88]
 gi|218696339|ref|YP_002404006.1| RNA polymerase sigma factor RpoS [Escherichia coli 55989]
 gi|218706235|ref|YP_002413754.1| RNA polymerase sigma factor RpoS [Escherichia coli UMN026]
 gi|253772403|ref|YP_003035234.1| RNA polymerase sigma factor RpoS [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254162672|ref|YP_003045780.1| RNA polymerase sigma factor RpoS [Escherichia coli B str. REL606]
 gi|256019474|ref|ZP_05433339.1| RNA polymerase sigma factor RpoS [Shigella sp. D9]
 gi|256024751|ref|ZP_05438616.1| RNA polymerase sigma factor RpoS [Escherichia sp. 4_1_40B]
 gi|260845388|ref|YP_003223166.1| RNA polymerase, sigma S factor [Escherichia coli O103:H2 str.
           12009]
 gi|260869420|ref|YP_003235822.1| RNA polymerase, sigma S factor [Escherichia coli O111:H- str.
           11128]
 gi|261226035|ref|ZP_05940316.1| RNA polymerase sigma factor [Escherichia coli O157:H7 str.
           FRIK2000]
 gi|261256708|ref|ZP_05949241.1| RNA polymerase, sigma S factor [Escherichia coli O157:H7 str.
           FRIK966]
 gi|291284068|ref|YP_003500886.1| RNA polymerase sigma factor [Escherichia coli O55:H7 str. CB9615]
 gi|293406233|ref|ZP_06650159.1| RNA polymerase sigma factor RpoS [Escherichia coli FVEC1412]
 gi|293412096|ref|ZP_06654819.1| RNA polymerase sigma factor RpoS [Escherichia coli B354]
 gi|293415987|ref|ZP_06658627.1| RNA polymerase sigma factor RpoS [Escherichia coli B185]
 gi|293449062|ref|ZP_06663483.1| RNA polymerase sigma factor RpoS [Escherichia coli B088]
 gi|298381970|ref|ZP_06991567.1| RNA polymerase sigma factor rpoS [Escherichia coli FVEC1302]
 gi|300899982|ref|ZP_07118185.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 198-1]
 gi|301027336|ref|ZP_07190677.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 196-1]
 gi|306812377|ref|ZP_07446575.1| RNA polymerase sigma factor RpoS [Escherichia coli NC101]
 gi|307139429|ref|ZP_07498785.1| RNA polymerase sigma factor RpoS [Escherichia coli H736]
 gi|307312831|ref|ZP_07592461.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Escherichia coli
           W]
 gi|312973048|ref|ZP_07787221.1| RNA polymerase sigma factor RpoS [Escherichia coli 1827-70]
 gi|331658855|ref|ZP_08359797.1| RNA polymerase sigma factor RpoS [Escherichia coli TA206]
 gi|331664297|ref|ZP_08365203.1| RNA polymerase sigma factor RpoS [Escherichia coli TA143]
 gi|331669480|ref|ZP_08370326.1| RNA polymerase sigma factor RpoS [Escherichia coli TA271]
 gi|331684360|ref|ZP_08384952.1| RNA polymerase sigma factor RpoS [Escherichia coli H299]
 gi|10197692|gb|AAG14975.1|AF242208_8 alternative sigma factor [Escherichia coli]
 gi|10197707|gb|AAG14988.1|AF242210_7 alternative sigma factor [Escherichia coli]
 gi|10197712|gb|AAG14992.1|AF242211_4 alternative sigma factor [Escherichia coli]
 gi|15529697|gb|AAL01412.1|AF410776_1 RpoS [Escherichia coli]
 gi|15529700|gb|AAL01414.1|AF410777_1 RpoS [Escherichia coli]
 gi|4887559|emb|CAB43502.1| alternative sigma factor, sigma 38 [Escherichia coli]
 gi|13363066|dbj|BAB37018.1| sigma factor RpoS [Escherichia coli O157:H7 str. Sakai]
 gi|37924617|gb|AAP59881.1| sigma S [Shigella boydii]
 gi|73856784|gb|AAZ89491.1| RNA polymerase, sigma S (sigma38) factor [Shigella sonnei Ss046]
 gi|83272618|gb|ABC00794.1| RpoS [Escherichia coli]
 gi|83272620|gb|ABC00795.1| RpoS [Escherichia coli]
 gi|83272622|gb|ABC00796.1| RpoS [Escherichia coli]
 gi|83272626|gb|ABC00798.1| RpoS [Escherichia coli]
 gi|110344474|gb|ABG70711.1| RNA polymerase sigma factor RpoS [Escherichia coli 536]
 gi|110616176|gb|ABF04843.1| RNA polymerase sigma factor [Shigella flexneri 5 str. 8401]
 gi|134036992|gb|ABO47833.1| sigma 38 factor [Escherichia coli]
 gi|134037004|gb|ABO47841.1| sigma 38 factor [Escherichia coli]
 gi|134037007|gb|ABO47843.1| sigma 38 factor [Escherichia coli]
 gi|134037010|gb|ABO47845.1| sigma 38 factor [Escherichia coli]
 gi|134037013|gb|ABO47847.1| sigma 38 factor [Escherichia coli]
 gi|157067869|gb|ABV07124.1| RNA polymerase sigma factor RpoS [Escherichia coli HS]
 gi|157079366|gb|ABV19074.1| RNA polymerase sigma factor RpoS [Escherichia coli E24377A]
 gi|169753941|gb|ACA76640.1| RNA polymerase, sigma 70 subunit, RpoD family [Escherichia coli
           ATCC 8739]
 gi|170521878|gb|ACB20056.1| RNA polymerase sigma factor RpoS [Escherichia coli SMS-3-5]
 gi|188015788|gb|EDU53910.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4113]
 gi|189003307|gb|EDU72293.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4076]
 gi|189357252|gb|EDU75671.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4401]
 gi|189372241|gb|EDU90657.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC869]
 gi|190903146|gb|EDV62869.1| RNA polymerase sigma factor RpoS [Escherichia coli B7A]
 gi|190908434|gb|EDV68023.1| RNA polymerase sigma factor RpoS [Escherichia coli F11]
 gi|192927345|gb|EDV81964.1| RNA polymerase sigma factor RpoS [Escherichia coli E22]
 gi|192957034|gb|EDV87485.1| RNA polymerase sigma factor RpoS [Escherichia coli E110019]
 gi|194420101|gb|EDX36179.1| RNA polymerase sigma factor RpoS [Shigella dysenteriae 1012]
 gi|194422116|gb|EDX38119.1| RNA polymerase sigma factor RpoS [Escherichia coli 101-1]
 gi|208733316|gb|EDZ82003.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4045]
 gi|209157291|gb|ACI34724.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4115]
 gi|209747660|gb|ACI72137.1| sigma factor RpoS [Escherichia coli]
 gi|209747662|gb|ACI72138.1| sigma factor RpoS [Escherichia coli]
 gi|209747664|gb|ACI72139.1| sigma factor RpoS [Escherichia coli]
 gi|209913443|dbj|BAG78517.1| RNA polymerase sigma factor S RpoS [Escherichia coli SE11]
 gi|217319015|gb|EEC27440.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           TW14588]
 gi|218353071|emb|CAU98896.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli 55989]
 gi|218366503|emb|CAR04255.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli S88]
 gi|218433332|emb|CAR14232.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli UMN026]
 gi|222034438|emb|CAP77180.1| RNA polymerase sigma factor rpoS [Escherichia coli LF82]
 gi|242378296|emb|CAQ33073.1| RNA polymerase, sigma S (sigma 38) factor, subunit of RNA
           polymerase sigma 38 [Escherichia coli BL21(DE3)]
 gi|253323447|gb|ACT28049.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|253974573|gb|ACT40244.1| RNA polymerase sigma factor [Escherichia coli B str. REL606]
 gi|253978740|gb|ACT44410.1| RNA polymerase sigma factor [Escherichia coli BL21(DE3)]
 gi|257760535|dbj|BAI32032.1| RNA polymerase, sigma S factor [Escherichia coli O103:H2 str.
           12009]
 gi|257765776|dbj|BAI37271.1| RNA polymerase, sigma S factor [Escherichia coli O111:H- str.
           11128]
 gi|281179747|dbj|BAI56077.1| RNA polymerase sigma factor S RpoS [Escherichia coli SE15]
 gi|290763941|gb|ADD57902.1| RNA polymerase sigma factor [Escherichia coli O55:H7 str. CB9615]
 gi|291322152|gb|EFE61581.1| RNA polymerase sigma factor RpoS [Escherichia coli B088]
 gi|291426239|gb|EFE99271.1| RNA polymerase sigma factor RpoS [Escherichia coli FVEC1412]
 gi|291432176|gb|EFF05158.1| RNA polymerase sigma factor RpoS [Escherichia coli B185]
 gi|291468867|gb|EFF11358.1| RNA polymerase sigma factor RpoS [Escherichia coli B354]
 gi|298277110|gb|EFI18626.1| RNA polymerase sigma factor rpoS [Escherichia coli FVEC1302]
 gi|299879329|gb|EFI87540.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 196-1]
 gi|300356491|gb|EFJ72361.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 198-1]
 gi|305854415|gb|EFM54853.1| RNA polymerase sigma factor RpoS [Escherichia coli NC101]
 gi|306907266|gb|EFN37772.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Escherichia coli
           W]
 gi|307554720|gb|ADN47495.1| sigma factor RpoS [Escherichia coli ABU 83972]
 gi|307625683|gb|ADN69987.1| RNA polymerase sigma factor RpoS [Escherichia coli UM146]
 gi|309703100|emb|CBJ02432.1| RNA polymerase sigma factor (sigma-38) [Escherichia coli ETEC
           H10407]
 gi|310332990|gb|EFQ00204.1| RNA polymerase sigma factor RpoS [Escherichia coli 1827-70]
 gi|312947273|gb|ADR28100.1| RNA polymerase sigma factor RpoS [Escherichia coli O83:H1 str. NRG
           857C]
 gi|315062022|gb|ADT76349.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli W]
 gi|315615130|gb|EFU95767.1| RNA polymerase sigma factor RpoS [Escherichia coli 3431]
 gi|320186525|gb|EFW61253.1| RNA polymerase sigma factor RpoS [Shigella flexneri CDC 796-83]
 gi|320189070|gb|EFW63729.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC1212]
 gi|320194880|gb|EFW69509.1| RNA polymerase sigma factor RpoS [Escherichia coli WV_060327]
 gi|320202392|gb|EFW76962.1| RNA polymerase sigma factor RpoS [Escherichia coli EC4100B]
 gi|320651231|gb|EFX19666.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H- str. H
           2687]
 gi|320656781|gb|EFX24669.1| RNA polymerase sigma factor RpoS [Escherichia coli O55:H7 str.
           3256-97 TW 07815]
 gi|320667375|gb|EFX34333.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           LSU-61]
 gi|323159951|gb|EFZ45921.1| RNA polymerase sigma factor RpoS [Escherichia coli E128010]
 gi|323167243|gb|EFZ52960.1| RNA polymerase sigma factor RpoS [Shigella sonnei 53G]
 gi|323172966|gb|EFZ58597.1| RNA polymerase sigma factor RpoS [Escherichia coli LT-68]
 gi|323180167|gb|EFZ65719.1| RNA polymerase sigma factor RpoS [Escherichia coli 1180]
 gi|323183273|gb|EFZ68670.1| RNA polymerase sigma factor RpoS [Escherichia coli 1357]
 gi|323188842|gb|EFZ74127.1| RNA polymerase sigma factor RpoS [Escherichia coli RN587/1]
 gi|323935702|gb|EGB32016.1| RNA polymerase sigma protein RpoS [Escherichia coli E1520]
 gi|323941428|gb|EGB37611.1| RNA polymerase sigma proteinRpoS [Escherichia coli E482]
 gi|323946373|gb|EGB42401.1| RNA polymerase sigma protein RpoS [Escherichia coli H120]
 gi|323951037|gb|EGB46913.1| RNA polymerase sigma proteinRpoS [Escherichia coli H252]
 gi|323957044|gb|EGB52769.1| RNA polymerase sigma proteinRpoS [Escherichia coli H263]
 gi|323960599|gb|EGB56225.1| RNA polymerase sigma proteinRpoS [Escherichia coli H489]
 gi|323966893|gb|EGB62322.1| RNA polymerase sigma proteinRpoS [Escherichia coli M863]
 gi|323971530|gb|EGB66763.1| RNA polymerase sigma proteinRpoS [Escherichia coli TA007]
 gi|323978651|gb|EGB73733.1| RNA polymerase sigma proteinRpoS [Escherichia coli TW10509]
 gi|324111374|gb|EGC05356.1| RNA polymerase sigma proteinRpoS [Escherichia fergusonii B253]
 gi|324119995|gb|EGC13873.1| RNA polymerase sigma proteinRpoS [Escherichia coli E1167]
 gi|325496210|gb|EGC94069.1| sigma factor RpoS [Escherichia fergusonii ECD227]
 gi|326339191|gb|EGD63006.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           1044]
 gi|326342926|gb|EGD66694.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           1125]
 gi|330908777|gb|EGH37291.1| RNA polymerase sigma factor RpoS [Escherichia coli AA86]
 gi|331053437|gb|EGI25466.1| RNA polymerase sigma factor RpoS [Escherichia coli TA206]
 gi|331058228|gb|EGI30209.1| RNA polymerase sigma factor RpoS [Escherichia coli TA143]
 gi|331063148|gb|EGI35061.1| RNA polymerase sigma factor RpoS [Escherichia coli TA271]
 gi|331077975|gb|EGI49181.1| RNA polymerase sigma factor RpoS [Escherichia coli H299]
 gi|332344623|gb|AEE57957.1| RNA polymerase sigma factor RpoS [Escherichia coli UMNK88]
          Length = 330

 Score =  216 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|29654959|ref|NP_820651.1| RNA polymerase sigma factor [Coxiella burnetii RSA 493]
 gi|81788312|sp|Q9KI19|RPOS_COXBU RecName: Full=RNA polymerase sigma factor rpoS
 gi|7340285|gb|AAF61172.1|AF244357_1 stress response sigma factor RpoS [Coxiella burnetii]
 gi|29542228|gb|AAO91165.1| RNA polymerase sigma factor [Coxiella burnetii RSA 493]
          Length = 352

 Score =  216 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 82/269 (30%), Positives = 138/269 (51%), Gaps = 13/269 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ E+   P+L  +EE  +A+R  + GD  A  +++ ++LRLVVKIA  Y   GLP  ++
Sbjct: 84  YLRELGFQPLLNAKEELKIARRVHK-GDPKARKQMIEANLRLVVKIARHYVNRGLPFLDL 142

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL+ AV+KFDPERGFR +TY+ WWI+  ++  I+     V++      K L   
Sbjct: 143 IEEGNLGLLTAVEKFDPERGFRFSTYATWWIRQTIERAIMNQSRTVRLPIHV-IKELNVY 201

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  K   Q + D+   PE V   A  ++    E+  +        S++  I  S+    
Sbjct: 202 LRTAKKLTQEV-DHEATPEDV---AHLIDKPVQEIRRIMDLAPSATSIDVPI--SEDGQK 255

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLE 256
              D L  D++     LI+  + ++    + R ++ L+ R R +   R         TLE
Sbjct: 256 SLVDTLADDNNIDPARLIQNVDLQDH---IERWLAQLDERHREVVILRFGLHENEKGTLE 312

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            +     ++RERVRQI+  A ++++  ++
Sbjct: 313 AVGKAVGLTRERVRQIQIDALQQLRHILE 341


>gi|251788478|ref|YP_003003199.1| RNA polymerase sigma factor RpoS [Dickeya zeae Ech1591]
 gi|247537099|gb|ACT05720.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dickeya zeae
           Ech1591]
          Length = 330

 Score =  216 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 80/271 (29%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GDLS+  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDLSSRRRMIESNLRLVVKIARRYNNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +     +  
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAERLDKPVDDVNRMLRLNERITSVDTPL--GGDSEK 232

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  + D   +   +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 233 ALLDILADEKDNGPE---DTTQDNDMKQNIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQVQ 320


>gi|317493947|ref|ZP_07952364.1| RNA polymerase sigma factor RpoS [Enterobacteriaceae bacterium
           9_2_54FAA]
 gi|316918274|gb|EFV39616.1| RNA polymerase sigma factor RpoS [Enterobacteriaceae bacterium
           9_2_54FAA]
          Length = 328

 Score =  216 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD ++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 59  YLGEIGYSPLLTAEEEVFFARR-ALRGDDASRRRMIESNLRLVVKIARRYSNRGLALLDL 117

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 118 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 176

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+   ++V  M        S++  +    + + 
Sbjct: 177 LRTAR----ELSHKLDHEPSAEEIAEQLDRPVTDVSRMLRLNERITSVDTPLGGDSEKA- 231

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D  E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 232 ----LLDILTDENESGPEDTTQSDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 287

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 288 DVGREIGLTRERVRQIQVEGLRRLREILQAQ 318


>gi|152971625|ref|YP_001336734.1| RNA polymerase sigma factor RpoS [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|206580660|ref|YP_002236889.1| RNA polymerase sigma factor RpoS [Klebsiella pneumoniae 342]
 gi|262041489|ref|ZP_06014687.1| RNA polymerase sigma factor [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|288933843|ref|YP_003437902.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Klebsiella
           variicola At-22]
 gi|330008320|ref|ZP_08306195.1| RNA polymerase sigma factor RpoS [Klebsiella sp. MS 92-3]
 gi|150956474|gb|ABR78504.1| RNA polymerase sigma factor [Klebsiella pneumoniae subsp.
           pneumoniae MGH 78578]
 gi|206569718|gb|ACI11494.1| RNA polymerase sigma factor RpoS [Klebsiella pneumoniae 342]
 gi|259041148|gb|EEW42221.1| RNA polymerase sigma factor [Klebsiella pneumoniae subsp.
           rhinoscleromatis ATCC 13884]
 gi|288888572|gb|ADC56890.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Klebsiella
           variicola At-22]
 gi|328535178|gb|EGF61679.1| RNA polymerase sigma factor RpoS [Klebsiella sp. MS 92-3]
          Length = 330

 Score =  216 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYSNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQGQ 320


>gi|238898782|ref|YP_002924464.1| RNA polymerase, sigma S (sigma 38) factor [Candidatus Hamiltonella
           defensa 5AT (Acyrthosiphon pisum)]
 gi|229466542|gb|ACQ68316.1| RNA polymerase, sigma S (sigma 38) factor [Candidatus Hamiltonella
           defensa 5AT (Acyrthosiphon pisum)]
          Length = 335

 Score =  216 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 82/271 (30%), Positives = 143/271 (52%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L   EE   A+R    GD S+  R++ S+LRLVVKI+  Y   GLP+ ++
Sbjct: 70  YLGEIGYSPLLTAAEEIYFARRVL-CGDESSRRRMIESNLRLVVKISRRYINRGLPLLDL 128

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 129 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 187

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +  L    D++  PE++     K     S ++ +N R++   S++    ++ +   
Sbjct: 188 LRAAR-ELSHKLDHDPSPEEIAEQLNKPVDYVSRMLRLNERIS---SVDTSFGNAAEKG- 242

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  + D   +   + +   + +  + + +  L+ ++R +   R   L   P TLE
Sbjct: 243 -LLDVLSDETDNDPENTTQND---DMKKSVVKWLFELSTKQREVLARRFGLLGYEPATLE 298

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +  E  ++RERVRQI+     +++E +Q Q
Sbjct: 299 EVGCEIGLTRERVRQIQVEGLLRLKEMLQTQ 329


>gi|295698248|ref|YP_003602903.1| alternative sigma factor RpoH [Candidatus Riesia pediculicola USDA]
 gi|295698251|ref|YP_003602906.1| alternative sigma factor RpoH [Candidatus Riesia pediculicola USDA]
 gi|291157186|gb|ADD79631.1| alternative sigma factor RpoH [Candidatus Riesia pediculicola USDA]
 gi|291157289|gb|ADD79734.1| alternative sigma factor RpoH [Candidatus Riesia pediculicola USDA]
          Length = 286

 Score =  216 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 101/288 (35%), Positives = 161/288 (55%), Gaps = 10/288 (3%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           KN S  +     LS YI      P+L  +EE      +  H DL AA +L+ SHLR V+ 
Sbjct: 3   KNKSFSLAISNNLSAYIKTAYSYPVLTMEEEKKYINLFYHHQDLRAAKKLILSHLRFVIH 62

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           I+  Y GYGL  ++++ EGN+GLM+AV+KF+P    RL ++++ WIKA + EYILR+W +
Sbjct: 63  ISKNYSGYGLLQADLIQEGNVGLMKAVQKFNPNASVRLVSFAIHWIKAEIHEYILRNWRI 122

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           VK+ TT  Q++LFFNLRR K  +           ++ ++AKKL VS+ +V  M  R+   
Sbjct: 123 VKVATTKAQRKLFFNLRRNKKKIGWFDQT-----EIDSVAKKLGVSKKDVREMESRMVAK 177

Query: 184 E---SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR-NMLTRSMSVLNPRE 239
           +    +N   N    +        + D        +EK+  +N     LT+++S L+ R 
Sbjct: 178 DMVFDINEEENRMKDDFFLIPALYLEDKSSTFFESLEKDNWENHTIKRLTQALSKLDKRS 237

Query: 240 RRIFEARRLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           + I + R L ++   TL++L+ +++VS ER+RQ+E  A KK++  I+ 
Sbjct: 238 QEIIKKRWLNQSGRETLQDLAKQYKVSAERIRQLEKNAMKKIRSLIES 285


>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 [Neisseria meningitidis alpha14]
 gi|304387052|ref|ZP_07369304.1| DNA-directed RNA polymerase sigma subunit RpoD [Neisseria
           meningitidis ATCC 13091]
 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]
          Length = 642

 Score =  216 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 63/272 (23%), Positives = 122/272 (44%), Gaps = 14/272 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRY--REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + ++ K   +  +E   + K     E    +A   ++ ++LRLV+ IA  Y   GL   +
Sbjct: 368 LADMEKETRISIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLD 427

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +  
Sbjct: 428 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIE 482

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + ++    +       +      +A+ + + E ++  +        S+   I   D + 
Sbjct: 483 TINKMNRISRQHLQETGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPI--GDDDD 540

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D       +     +   +    +  L PRE ++   R   +     TL
Sbjct: 541 SHLGDFI---EDANNVAPADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTL 597

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +  +F+V+RER+RQIEA+A +K++   +  
Sbjct: 598 EEVGRQFDVTRERIRQIEAKALRKLRHPTRSD 629


>gi|269302545|gb|ACZ32645.1| RNA polymerase sigma factor RpoD [Chlamydophila pneumoniae LPCoLN]
          Length = 570

 Score =  216 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 69/255 (27%), Positives = 122/255 (47%), Gaps = 13/255 (5%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             + +R+ +     A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+
Sbjct: 302 VRMLQRWMDK-SQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFE 360

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             RG++ +TY+ WWI+ A+   I      ++I        +   + ++    + +     
Sbjct: 361 YRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVH-----MIETINKVLRGAKKLMMETG 415

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           K      +A++L ++   V  +        SL A +   +   S + D+L    D   + 
Sbjct: 416 KEPTPEELAEELGLTPDRVREIYKIAQHPISLQAEV--GEGGESSFGDFL---EDTAVES 470

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQI 272
             E       ++ +   +  L  RER +   R   L   P TLE + S F V+RER+RQI
Sbjct: 471 PAEATGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGKPKTLEEVGSAFNVTRERIRQI 530

Query: 273 EARAFKKVQESIQKQ 287
           EA+A +K++  I+ +
Sbjct: 531 EAKALRKMRHPIRSK 545



 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 8/32 (25%), Positives = 19/32 (59%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREH 44
           +  +  Y+ E+  +P+L ++EE  ++KR  + 
Sbjct: 98  DDPVRMYLKEMGTVPLLTREEEVEISKRIEKA 129


>gi|242310656|ref|ZP_04809811.1| RNA polymerase sigma factor [Helicobacter pullorum MIT 98-5489]
 gi|239523054|gb|EEQ62920.1| RNA polymerase sigma factor [Helicobacter pullorum MIT 98-5489]
          Length = 615

 Score =  216 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 69/260 (26%), Positives = 130/260 (50%), Gaps = 15/260 (5%)

Query: 29  LEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           LE ++   + ++ +   D++  A  ++  S+LRLVV IA  Y   GLP  +++ EGNIGL
Sbjct: 354 LEPEKLKQILEQIKRGKDIADRAKTKMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGL 413

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+ ++G++ +TY+ WWI+ A+   I      ++I        +   + R+   +
Sbjct: 414 MKAVDKFEYKKGYKFSTYATWWIRQAISRAIADQARTIRIPIH-----MIETINRINKIM 468

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +       K   +  IA+++ +   +V ++        SL A I + +    ++ D++  
Sbjct: 469 RKYLQEEGKEPDIEKIAEEVGLPVDKVKNVIKITKEPISLEAPIGNGED--GKFGDFV-- 524

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFE 263
             D      ++   +++ +  +   +  LN RE+ +   R      E+  TLE +  E  
Sbjct: 525 -EDKASLGPMDSILKEDLKAQIDDVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELN 583

Query: 264 VSRERVRQIEARAFKKVQES 283
           V+RERVRQIE+ A KK++  
Sbjct: 584 VTRERVRQIESSAIKKLKHP 603



 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 9/41 (21%), Positives = 21/41 (51%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY 41
           M  + +      +  +  Y+ E+ +IP+L +++E  L+K  
Sbjct: 90  MKERELLEWSRSDSPVRMYLREMGQIPLLTREDEVELSKNI 130


>gi|218674803|ref|ZP_03524472.1| RNA polymerase sigma factor RpoD [Rhizobium etli GR56]
          Length = 254

 Score =  216 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 116/240 (48%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 16  AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 75

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + +     +      +A+KL +
Sbjct: 76  IRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREPTPEELAEKLAM 130

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   +   D+  S   D++    D    + I+   + N R   
Sbjct: 131 PLEKVRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKNALLPIDAAIQANLRETT 185

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 186 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 245


>gi|15618665|ref|NP_224951.1| RNA polymerase sigma factor [Chlamydophila pneumoniae CWL029]
 gi|15836289|ref|NP_300813.1| RNA polymerase sigma factor [Chlamydophila pneumoniae J138]
 gi|33242115|ref|NP_877056.1| RNA polymerase sigma factor [Chlamydophila pneumoniae TW-183]
 gi|6831651|sp|Q9Z7F0|RPOD_CHLPN RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A;
           AltName: Full=Sigma-66; AltName: Full=Sigma-70
 gi|4377063|gb|AAD18894.1| RNA Polymerase Sigma-66 [Chlamydophila pneumoniae CWL029]
 gi|8979129|dbj|BAA98964.1| RNA polymerase sigma-66 [Chlamydophila pneumoniae J138]
 gi|33236625|gb|AAP98713.1| sigma factor 70 [Chlamydophila pneumoniae TW-183]
          Length = 572

 Score =  216 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 69/255 (27%), Positives = 123/255 (48%), Gaps = 13/255 (5%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             + +R+ +     A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+
Sbjct: 304 VRMLQRWMDK-SQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFE 362

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             RG++ +TY+ WWI+ A+   I      ++I        +   + ++    + +     
Sbjct: 363 YRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVH-----MIETINKVLRGAKKLMMETG 417

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           K      +A++L ++   V  +        SL A +   + + S + D+L    D   + 
Sbjct: 418 KEPTPEELAEELGLTPDRVREIYKIAQHPISLQAEV--GEGSESSFGDFL---EDTAVES 472

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQI 272
             E       ++ +   +  L  RER +   R   L   P TLE + S F V+RER+RQI
Sbjct: 473 PAEATGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGKPKTLEEVGSAFNVTRERIRQI 532

Query: 273 EARAFKKVQESIQKQ 287
           EA+A +K++  I+ +
Sbjct: 533 EAKALRKMRHPIRSK 547



 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 8/32 (25%), Positives = 19/32 (59%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREH 44
           +  +  Y+ E+  +P+L ++EE  ++KR  + 
Sbjct: 100 DDPVRMYLKEMGTVPLLTREEEVEISKRIEKA 131


>gi|144899360|emb|CAM76224.1| Sigma-70 region 2:Sigma-70 region 4:Sigma-70 region 1.2
           [Magnetospirillum gryphiswaldense MSR-1]
          Length = 291

 Score =  216 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 104/282 (36%), Positives = 165/282 (58%), Gaps = 4/282 (1%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           MSI+       S Y   +R+  +L  ++E  L +R+++ GD  A  RL+++HLRLVVK A
Sbjct: 1   MSILRPASDTASAYYKAMRETALLSGEDEAELIRRWKDEGDEKARTRLLSAHLRLVVKTA 60

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             ++GYGL  +++V+EGN+GL++A++ FDP R  R +TY+ WW++AAM EY+L+  + V 
Sbjct: 61  GQFKGYGLSGADLVAEGNLGLVRALESFDPGRNLRFSTYAQWWVRAAMFEYVLKFSTPVN 120

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDE 184
            G +A +K+LFF LR +K  L   + N L   +   +A +L V +  V  M   L     
Sbjct: 121 FGLSAERKKLFFKLRGIKARLTGPSGNALSVAETAQVADELGVRDQRVAEMERLLTQSPR 180

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL+A +    ++   + + L  D    E+ L E++E   RR +L  +   L  RER I  
Sbjct: 181 SLDAPVG---ESGIPFGELLADDRPSVEETLGERQELMYRRELLKHAWEGLTERERDIVA 237

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R L+ENP+ LE+L+  + +SRERVRQIE  A  K++  ++ 
Sbjct: 238 QRTLRENPLRLEDLAQRYSISRERVRQIEGSALTKLKALVRA 279


>gi|148266058|ref|YP_001232764.1| RpoD family RNA polymerase sigma factor [Geobacter uraniireducens
           Rf4]
 gi|146399558|gb|ABQ28191.1| RNA polymerase, sigma 70 subunit, RpoD [Geobacter uraniireducens
           Rf4]
          Length = 586

 Score =  216 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 76/253 (30%), Positives = 119/253 (47%), Gaps = 12/253 (4%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           LA    E     A   LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +
Sbjct: 337 LAIEEGERKAKLAKSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQ 396

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RG++ +TY+ WWI+ A+   I      ++I            L R    L         P
Sbjct: 397 RGYKFSTYATWWIRQAITRAIADQARTIRIPVHM--IETINKLIRTSRQLVQEIGREPSP 454

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           E    IA+++++   +V  +        SL   I   ++  S   D++    D      +
Sbjct: 455 E---EIAERMSLPLDKVRKVLKIAKEPISLETPI--GEEEDSHLGDFI---EDKGVVSPL 506

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEA 274
           E   + N     +R +S L PRE ++   R         TLE +  +FEV+RER+RQIEA
Sbjct: 507 EAVIKANLSEQTSRVLSTLTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEA 566

Query: 275 RAFKKVQESIQKQ 287
           +A +K++   + +
Sbjct: 567 KALRKLRHPSRAK 579


>gi|315444860|ref|YP_004077739.1| RNA polymerase sigma factor, sigma-70 family [Mycobacterium sp.
           Spyr1]
 gi|315263163|gb|ADT99904.1| RNA polymerase sigma factor, sigma-70 family [Mycobacterium sp.
           Spyr1]
          Length = 319

 Score =  216 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 66/312 (21%), Positives = 135/312 (43%), Gaps = 38/312 (12%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------- 43
           +++         +  Y++ I K  +L   +E  LAKR                       
Sbjct: 11  QDLDAQSPAADLVRVYLNGIGKTALLTAADEVELAKRIEAGLYAQHLLATRKRLGENRKR 70

Query: 44  ------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
                     +A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +
Sbjct: 71  DLAAVVRDGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYAK 130

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           GF+ +TY+ WWI+ A+   +      +++     ++     L R+K  +     N  +  
Sbjct: 131 GFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLARIKREMHQ---NLGREA 185

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A++  +   ++  +        SL+  + S ++  +   D++    D +      
Sbjct: 186 TDEELAEESGIPVEKINDLLEHSRDPVSLDMPVGSDEE--APLGDFI---EDAEAMSAEN 240

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
               +     +   ++ L+ RE+++   R   ++  P TL+ +   F +SRERVRQIE  
Sbjct: 241 AVISELLHTDIRYVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERE 300

Query: 276 AFKKVQESIQKQ 287
              K++   +  
Sbjct: 301 VMAKLRNGDRAD 312


>gi|16761696|ref|NP_457313.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. CT18]
 gi|16766230|ref|NP_461845.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|56414872|ref|YP_151947.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. ATCC 9150]
 gi|62181426|ref|YP_217843.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|157148284|ref|YP_001455603.1| RNA polymerase sigma factor RpoS [Citrobacter koseri ATCC BAA-895]
 gi|167550225|ref|ZP_02343982.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Saintpaul str. SARA29]
 gi|168230998|ref|ZP_02656056.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Kentucky str. CDC 191]
 gi|168235962|ref|ZP_02661020.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. SL480]
 gi|168242664|ref|ZP_02667596.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL486]
 gi|168261948|ref|ZP_02683921.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Hadar str. RI_05P066]
 gi|168463936|ref|ZP_02697853.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Newport str. SL317]
 gi|168820376|ref|ZP_02832376.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Weltevreden str. HI_N05-537]
 gi|194442500|ref|YP_002042165.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Newport str. SL254]
 gi|194451079|ref|YP_002046882.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL476]
 gi|194470798|ref|ZP_03076782.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Kentucky str. CVM29188]
 gi|194738113|ref|YP_002115873.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. CVM19633]
 gi|197263839|ref|ZP_03163913.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Saintpaul str. SARA23]
 gi|197363800|ref|YP_002143437.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. AKU_12601]
 gi|198243199|ref|YP_002216890.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Dublin str. CT_02021853]
 gi|200388856|ref|ZP_03215468.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Virchow str. SL491]
 gi|204928102|ref|ZP_03219302.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Javiana str. GA_MM04042433]
 gi|207858184|ref|YP_002244835.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Enteritidis str. P125109]
 gi|213052392|ref|ZP_03345270.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. E00-7866]
 gi|213648321|ref|ZP_03378374.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. J185]
 gi|224584701|ref|YP_002638499.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Paratyphi C strain RKS4594]
 gi|237729723|ref|ZP_04560204.1| RNA polymerase sigma factor RpoS [Citrobacter sp. 30_2]
 gi|238909692|ref|ZP_04653529.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Tennessee str. CDC07-0191]
 gi|283835495|ref|ZP_06355236.1| RNA polymerase sigma factor RpoS [Citrobacter youngae ATCC 29220]
 gi|61236740|sp|P0A2E5|RPOS_SALTY RecName: Full=RNA polymerase sigma factor rpoS; AltName:
           Full=Sigma-38
 gi|61236751|sp|P0A2E6|RPOS_SALTI RecName: Full=RNA polymerase sigma factor rpoS; AltName:
           Full=Sigma-38
 gi|61236761|sp|P0A2E7|RPOS_SALDU RecName: Full=RNA polymerase sigma factor rpoS; AltName:
           Full=Sigma-38
 gi|1073666|pir||S49471 transcription initiation factor sigma kaltF - Salmonella
           choleraesuis
 gi|6010738|gb|AAF01235.1|AF184104_1 mutant RpoS [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
 gi|558645|emb|CAA57640.1| katF (rpoS) [Salmonella enterica]
 gi|602087|emb|CAA54798.1| KatF [Salmonella enterica subsp. enterica serovar Typhimurium]
 gi|16421473|gb|AAL21804.1| sigma S (sigma 38) factor of RNA polymerase [Salmonella enterica
           subsp. enterica serovar Typhimurium str. LT2]
 gi|16503997|emb|CAD06030.1| RNA polymerase sigma subunit RpoS (sigma-38) [Salmonella enterica
           subsp. enterica serovar Typhi]
 gi|56129129|gb|AAV78635.1| RNA polymerase sigma subunit RpoS (sigma-38) [Salmonella enterica
           subsp. enterica serovar Paratyphi A str. ATCC 9150]
 gi|62129059|gb|AAX66762.1| sigma S (sigma 38) factor of RNA polymerase, major sigmafactor
           during stationary phase [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|157085489|gb|ABV15167.1| hypothetical protein CKO_04101 [Citrobacter koseri ATCC BAA-895]
 gi|194401163|gb|ACF61385.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Newport str. SL254]
 gi|194409383|gb|ACF69602.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL476]
 gi|194457162|gb|EDX46001.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Kentucky str. CVM29188]
 gi|194713615|gb|ACF92836.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. CVM19633]
 gi|195633598|gb|EDX52012.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Newport str. SL317]
 gi|197095277|emb|CAR60830.1| RNA polymerase sigma subunit RpoS (sigma-38) [Salmonella enterica
           subsp. enterica serovar Paratyphi A str. AKU_12601]
 gi|197242094|gb|EDY24714.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Saintpaul str. SARA23]
 gi|197290706|gb|EDY30060.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. SL480]
 gi|197937715|gb|ACH75048.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Dublin str. CT_02021853]
 gi|199605954|gb|EDZ04499.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Virchow str. SL491]
 gi|204322424|gb|EDZ07621.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Javiana str. GA_MM04042433]
 gi|205324779|gb|EDZ12618.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Saintpaul str. SARA29]
 gi|205334505|gb|EDZ21269.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Kentucky str. CDC 191]
 gi|205338030|gb|EDZ24794.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL486]
 gi|205342988|gb|EDZ29752.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Weltevreden str. HI_N05-537]
 gi|205349304|gb|EDZ35935.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Hadar str. RI_05P066]
 gi|206709987|emb|CAR34342.1| RNA polymerase sigma subunit RpoS (sigma-38) [Salmonella enterica
           subsp. enterica serovar Enteritidis str. P125109]
 gi|224469228|gb|ACN47058.1| RNA polymerase sigma factor [Salmonella enterica subsp. enterica
           serovar Paratyphi C strain RKS4594]
 gi|226908329|gb|EEH94247.1| RNA polymerase sigma factor RpoS [Citrobacter sp. 30_2]
 gi|261248060|emb|CBG25894.1| RNA polymerase sigma subunit RpoS (sigma-38) [Salmonella enterica
           subsp. enterica serovar Typhimurium str. D23580]
 gi|267995054|gb|ACY89939.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 14028S]
 gi|291068697|gb|EFE06806.1| RNA polymerase sigma factor RpoS [Citrobacter youngae ATCC 29220]
 gi|301159483|emb|CBW19002.1| RNA polymerase sigma subunit RpoS (sigma-38) [Salmonella enterica
           subsp. enterica serovar Typhimurium str. SL1344]
 gi|312913942|dbj|BAJ37916.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhimurium str. T000240]
 gi|320087327|emb|CBY97092.1| RNA polymerase sigma factor rpoS [Salmonella enterica subsp.
           enterica serovar Weltevreden str. 2007-60-3289-1]
 gi|321225598|gb|EFX50652.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhimurium str. TN061786]
 gi|322614255|gb|EFY11186.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315996572]
 gi|322621681|gb|EFY18534.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-1]
 gi|322624542|gb|EFY21375.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-3]
 gi|322628873|gb|EFY25656.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-4]
 gi|322633400|gb|EFY30142.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-1]
 gi|322636024|gb|EFY32732.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-2]
 gi|322639617|gb|EFY36303.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 531954]
 gi|322646916|gb|EFY43419.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. NC_MB110209-0054]
 gi|322652217|gb|EFY48576.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. OH_2009072675]
 gi|322654704|gb|EFY51023.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. CASC_09SCPH15965]
 gi|322658925|gb|EFY55178.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 19N]
 gi|322664508|gb|EFY60702.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 81038-01]
 gi|322668243|gb|EFY64400.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. MD_MDA09249507]
 gi|322673777|gb|EFY69878.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 414877]
 gi|322677838|gb|EFY73901.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 366867]
 gi|322681332|gb|EFY77364.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 413180]
 gi|322683734|gb|EFY79744.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 446600]
 gi|322715910|gb|EFZ07481.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. A50]
 gi|323131276|gb|ADX18706.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 4/74]
 gi|323193878|gb|EFZ79081.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609458-1]
 gi|323200347|gb|EFZ85429.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556150-1]
 gi|323202369|gb|EFZ87413.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609460]
 gi|323205603|gb|EFZ90568.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 507440-20]
 gi|323210115|gb|EFZ95018.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556152]
 gi|323216417|gb|EGA01144.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB101509-0077]
 gi|323220766|gb|EGA05207.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB102109-0047]
 gi|323226390|gb|EGA10598.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB110209-0055]
 gi|323230730|gb|EGA14848.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB111609-0052]
 gi|323234919|gb|EGA19005.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009083312]
 gi|323238958|gb|EGA23008.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009085258]
 gi|323241658|gb|EGA25689.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315731156]
 gi|323248195|gb|EGA32131.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2009159199]
 gi|323251221|gb|EGA35094.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008282]
 gi|323257395|gb|EGA41091.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008283]
 gi|323263241|gb|EGA46779.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008284]
 gi|323264257|gb|EGA47763.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008285]
 gi|323271083|gb|EGA54511.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008287]
 gi|326624653|gb|EGE30998.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Dublin str. 3246]
 gi|332989795|gb|AEF08778.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhimurium str. UK-1]
          Length = 330

 Score =  216 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|555686|gb|AAA85644.1| sigma factor MysB [Mycobacterium smegmatis str. MC2 155]
          Length = 319

 Score =  216 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 65/312 (20%), Positives = 134/312 (42%), Gaps = 38/312 (12%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------- 43
            ++         +  Y++ I K  +L   +E  LAKR                       
Sbjct: 11  TDLDAQSPAADLVRVYLNGIGKTALLNAADEVELAKRIEAGLYAQHLLDTKKRLGEARKR 70

Query: 44  ------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
                     +A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +
Sbjct: 71  DLQAVVRDGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTK 130

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           GF+ +TY+ WWI+ A+   +      +++     ++     L R+K  +     N  +  
Sbjct: 131 GFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLARIKREMHQ---NLGREA 185

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A++  +   ++  +        SL+  + + ++  +   D++    D +      
Sbjct: 186 TDEELAEESGIPVEKINDLLEHSRDPVSLDMPVGTDEE--APLGDFI---EDSEAMSAEN 240

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
               +     +   ++ L+ RE+++   R   ++  P TL+ +   F +SRERVRQIE  
Sbjct: 241 AVISELLHTDIRYVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERE 300

Query: 276 AFKKVQESIQKQ 287
              K++   +  
Sbjct: 301 VMAKLRNGERAD 312


>gi|319760734|ref|YP_004124672.1| RNA polymerase sigma-32 factor [Candidatus Blochmannia vafer str.
           BVAF]
 gi|318039448|gb|ADV33998.1| RNA polymerase sigma-32 factor [Candidatus Blochmannia vafer str.
           BVAF]
          Length = 284

 Score =  216 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 106/289 (36%), Positives = 169/289 (58%), Gaps = 10/289 (3%)

Query: 1   MNRKNM--SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHL 58
           M  +NM  +I +  +  L  YI      PML  +EE  LA+R   + DL+AA +L+ SHL
Sbjct: 1   MTAENMYKNISLVPQGTLEAYIRATNLYPMLTAEEERELAERLYYNSDLNAAKKLIVSHL 60

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           R VV IA  Y GYGL  ++++ EGNIGLM++V++F+PE   RL ++++ WIK+ + EY+L
Sbjct: 61  RFVVHIARNYSGYGLAQADLIQEGNIGLMKSVRRFNPELDVRLVSFAVHWIKSEIHEYVL 120

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
           ++W +VKI TT  Q++LFFNLR+ K  L    +     E++  +AK L+V+  +V  M  
Sbjct: 121 KNWRIVKIATTKAQRKLFFNLRKTKQRLGWFNE-----EEIEMVAKTLHVTCKDVREMES 175

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           R+A  + +    +S D   +     ++Y  D    +  E+E      N L  +++ L+ R
Sbjct: 176 RMAA-QDMTFEQSSDDDEKNILSIPMLYLQDKVTMIDEEEEWINQVSNKLNIALNSLDKR 234

Query: 239 ERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            + I  AR L   +N  TL+ L++++ VS ER+RQ+E  A KK++  IQ
Sbjct: 235 SQHIIRARWLNTNDNKTTLQELANQYGVSAERIRQLEKNAMKKMKLIIQ 283


>gi|49474699|ref|YP_032741.1| RNA polymerase factor sigma-32 [Bartonella quintana str. Toulouse]
 gi|49240203|emb|CAF26671.1| RNA polymerase sigma-32 factor [Bartonella quintana str. Toulouse]
          Length = 303

 Score =  216 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 97/266 (36%), Positives = 164/266 (61%), Gaps = 1/266 (0%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           +    + P LE+Q+E+ LA R+++  D  A H++  +H+RLV+ IA  ++ + +P+ ++V
Sbjct: 27  MRSAMQAPYLERQKEHDLALRWKDKRDDDAMHQIAAAHMRLVIAIANRFKRFKMPLGDLV 86

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EG +GL++A  +F+P+R  R +TY+ WWI+A++Q+YILR+WS+V+ GT+++QK LFFNL
Sbjct: 87  QEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSSQKALFFNL 146

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
           RRL+  L    +   K +    IA++L VS  +V +M+ R +  ++  ++  S + ++  
Sbjct: 147 RRLRAKLVQDDNALTKQDIFRTIAERLGVSVRDVETMDFRFSSSDNSLSVSVSENSDNPI 206

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRR-NMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
            +   + D       LIE+     RR   L  ++  LN RE  I   RRL E   TLE L
Sbjct: 207 AKMDALVDDSPLPDALIEQVIDSQRRTQWLHDALQSLNERELEIIRFRRLNEEGATLEVL 266

Query: 259 SSEFEVSRERVRQIEARAFKKVQESI 284
             +  +S+ERVRQIEARA +K++ ++
Sbjct: 267 GEKLGISKERVRQIEARALQKLRSAL 292


>gi|320180825|gb|EFW55748.1| RNA polymerase sigma factor RpoS [Shigella boydii ATCC 9905]
          Length = 330

 Score =  216 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|318042101|ref|ZP_07974057.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CB0101]
          Length = 309

 Score =  216 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 77/298 (25%), Positives = 143/298 (47%), Gaps = 32/298 (10%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR----------EHG-----------DLSAA 50
           G   +S Y+  I ++P+L   EE  L  + +          E+G              + 
Sbjct: 16  GSDPISWYLSTIGRVPLLTPAEEIELGNQVQAMMRLTEEEPENGYTDQQKKTIRVGRRSK 75

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            R++ ++LRLVV +A  Y+G GL + +++ EG++GL +AV+KFDP RG++ +TY+ WWI+
Sbjct: 76  ERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWWIR 135

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            +M   I      +++    +++     L  ++     +            IA+ +++  
Sbjct: 136 QSMTRAIACQSRTIRLPVHLSER-----LTAIRKVSLDLAHKLGAMPSRKEIAEAMDMPI 190

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            E+ S+  +     SL+A +N  ++  S   D +    D      +++ ER      L R
Sbjct: 191 DELDSLLRQALTTSSLDAPVN-GEEGRSFLGDLIA---DNSHVEPLDQVERGMHHEQLGR 246

Query: 231 SMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +S L  +ER++ E R     E   TL  +    +VSRERVRQ+E +A +K++   ++
Sbjct: 247 WLSHLTEQERQVLELRFGLEGEERHTLAEIGRMLDVSRERVRQVELKALRKLRHLTRR 304


>gi|163869170|ref|YP_001610422.1| RNA polymerase factor sigma-32 [Bartonella tribocorum CIP 105476]
 gi|161018869|emb|CAK02427.1| RNA polymerase sigma-32 factor [Bartonella tribocorum CIP 105476]
          Length = 303

 Score =  216 bits (552), Expect = 2e-54,   Method: Composition-based stats.
 Identities = 100/266 (37%), Positives = 165/266 (62%), Gaps = 1/266 (0%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           +    K P LE+Q+E+ LA R+++  D  A H++  +H+RLV+ IA  ++ + +P+ ++V
Sbjct: 27  MRSAMKAPYLERQKEHDLALRWKDKRDDDAMHQIAAAHMRLVIAIANRFKRFKMPLGDLV 86

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EG +GL++A  +F+P+R  R +TY+ WWI+A++Q+YILR+WS+V+ GT+++QK LFFNL
Sbjct: 87  QEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSSQKALFFNL 146

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
           RRL+  L        K +    IA+KL VS  +V +M+ R +  ++  ++  S + +S  
Sbjct: 147 RRLRAKLVQDDSALSKQDIFRTIAEKLGVSVRDVETMDFRFSSSDNSLSVSVSENSDSPV 206

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRR-NMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
            +  ++ D       LIE+     RR   L  ++ +LN RE  I   RRL E   TLE L
Sbjct: 207 AKMDVLVDESPLPDALIEQVIDGQRRTQWLYDALQILNERELEIIRFRRLNEEGATLEVL 266

Query: 259 SSEFEVSRERVRQIEARAFKKVQESI 284
             +  +S+ERVRQIEARA +K++ ++
Sbjct: 267 GEKLGISKERVRQIEARALQKLRSAL 292


>gi|188997117|ref|YP_001931368.1| RNA polymerase, sigma 70 subunit, RpoD family [Sulfurihydrogenibium
           sp. YO3AOP1]
 gi|188932184|gb|ACD66814.1| RNA polymerase, sigma 70 subunit, RpoD family [Sulfurihydrogenibium
           sp. YO3AOP1]
          Length = 281

 Score =  216 bits (552), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 79/262 (30%), Positives = 136/262 (51%), Gaps = 11/262 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ ++ K PML  +EE  LA R ++ GD  A  +LV  +LR VV IA  + G+G+P+
Sbjct: 10  LQLYMQQMGKHPMLSPEEEKELAIRAKQ-GDKEALKKLVEGNLRFVVSIAKNFMGWGVPL 68

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           +++++ GN+GL++A K+FDP++  +  +Y++WWI+ A+ + I +    V+I       + 
Sbjct: 69  TDLIAAGNLGLIEAAKRFDPDKNVKFISYAVWWIRQAIMQTIFQQTGAVRIPV-----KE 123

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + ++K   + + +   +      IAK+LN S  +V +    +    SL+  +    +
Sbjct: 124 SLFIAKVKETYEKLKEELGREPTEEEIAKRLNTSVKKVKNALSIVRLPISLDMPLGEGGE 183

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPV 253
                 D L     G E +  E  E    +  L   + VL+ RE+ I + R     E P 
Sbjct: 184 EDFTLLDVLS--KKGTEDIEKELIEETIHKE-LESMLDVLDEREKEIIKMRYGLDGEEPK 240

Query: 254 TLENLSSEFEVSRERVRQIEAR 275
           TLE +  +  +SRERVRQ+E R
Sbjct: 241 TLEEVGEKLGISRERVRQLEQR 262


>gi|15677390|ref|NP_274545.1| RNA polymerase sigma factor RpoD [Neisseria meningitidis MC58]
 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]
          Length = 642

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 63/272 (23%), Positives = 122/272 (44%), Gaps = 14/272 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRY--REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + ++ K   +  +E   + K     E    +A   ++ ++LRLV+ IA  Y   GL   +
Sbjct: 368 LADMEKETRISIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLD 427

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +  
Sbjct: 428 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIE 482

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + ++    +       +      +A+ + + E ++  +        S+   I   D + 
Sbjct: 483 TINKMNRISRQHLQETGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPI--GDDDD 540

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D       +     +   +    +  L PRE ++   R   +     TL
Sbjct: 541 SHLGDFI---EDANNVAPADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTL 597

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +  +F+V+RER+RQIEA+A +K++   +  
Sbjct: 598 EEVGRQFDVTRERIRQIEAKALRKLRHPTRSD 629


>gi|4103482|gb|AAD01786.1| sigma-E factor [Myxococcus xanthus]
          Length = 280

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 105/273 (38%), Positives = 176/273 (64%), Gaps = 8/273 (2%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           + E+++ P+L ++EE  LA+ Y+E GD++AA+RLV  +LRLVVK+A  Y    L + ++V
Sbjct: 1   MAEVQRHPLLTREEELQLARHYKESGDVNAAYRLVAWNLRLVVKLAHEYHRNPLSLLDLV 60

Query: 80  --SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
              EGNIGLMQAVKK+DPERG +L++Y+ WWI+A +  YI+ +W +VK+GTT  Q++LFF
Sbjct: 61  LVQEGNIGLMQAVKKYDPERGVKLSSYAAWWIRAYILRYIMDNWKMVKLGTTEAQRKLFF 120

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKN 196
            LR+ +  L A             +A++LNV+E +V+ M+ RL  DE S++A + + D +
Sbjct: 121 KLRQEQEKLIA----QGFEASPKLLAERLNVTEQDVVEMDQRLGHDEMSIDAPLGNDDDS 176

Query: 197 SSQWQD-WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
            +   D +L  +    ++ L  ++ +   R  L+     L  +ER IFE+R + + P+TL
Sbjct: 177 RTTRADRYLPSNSMPADERLGAEQLKALFREKLSEFARTLEGKERFIFESRLVSDEPLTL 236

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +++  ++ VSRER RQIEA    ++++ +++Q+
Sbjct: 237 QDIGDKYGVSRERARQIEAALINRMRDFMREQI 269


>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]
          Length = 642

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 63/272 (23%), Positives = 122/272 (44%), Gaps = 14/272 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRY--REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + ++ K   +  +E   + K     E    +A   ++ ++LRLV+ IA  Y   GL   +
Sbjct: 368 LADMEKETRISIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLD 427

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +  
Sbjct: 428 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIE 482

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + ++    +       +      +A+ + + E ++  +        S+   I   D + 
Sbjct: 483 TINKMNRISRQHLQETGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPI--GDDDD 540

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D       +     +   +    +  L PRE ++   R   +     TL
Sbjct: 541 SHLGDFI---EDANNVAPADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTL 597

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +  +F+V+RER+RQIEA+A +K++   +  
Sbjct: 598 EEVGRQFDVTRERIRQIEAKALRKLRHPTRSD 629


>gi|292492664|ref|YP_003528103.1| RNA polymerase sigma factor RpoS [Nitrosococcus halophilus Nc4]
 gi|291581259|gb|ADE15716.1| RNA polymerase sigma factor RpoS [Nitrosococcus halophilus Nc4]
          Length = 325

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 57  YLSEIGFAPLLTAEEEVYHA-RLAQRGDPAGRKRMIESNLRLVVKIARRYMNRGLALLDL 115

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL+ AV+KFDPE GFR +TY+ WWI+  ++  ++     V++       +   +
Sbjct: 116 IEEGNLGLIHAVEKFDPEMGFRFSTYATWWIRQTIERALMNQTRTVRLPVHV--VKEIKS 173

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
            +R+   L    +++   E    +A++L+ S  E+  M        S++    S  + + 
Sbjct: 174 YQRVASKLAQELEHDPTFE---ELAQQLDKSVEEIKRMWSLKDNIASMDTGYRSDQEKT- 229

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
              D L  +       L++ ++ ++R  +    +S LN ++R +   R         TLE
Sbjct: 230 -LLDTLPDEGTPDPTTLLQNDDMQSRLEL---WLSQLNNKQREVVIRRFGLQGYESQTLE 285

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +     V+RERVRQI+  A K+++  + K+
Sbjct: 286 QVGQAIGVTRERVRQIQLEALKRLRRIMAKE 316


>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 =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 62/272 (22%), Positives = 121/272 (44%), Gaps = 14/272 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRY--REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +  + +   +  +E   + K     E    +A   ++ ++LRLV+ IA  Y   GL   +
Sbjct: 368 LANMERETRISIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLD 427

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +  
Sbjct: 428 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIE 482

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + ++    +       +      +A+ + + E ++  +        S+   I   D + 
Sbjct: 483 TINKMNRISRQHLQETGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPI--GDDDD 540

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D       +     +   +    +  L PRE ++   R   +     TL
Sbjct: 541 SHLGDFI---EDSNNIAPADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTL 597

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +  +F+V+RER+RQIEA+A +K++   +  
Sbjct: 598 EEVGKQFDVTRERIRQIEAKALRKLRHPTRSD 629


>gi|330836587|ref|YP_004411228.1| RNA polymerase, sigma 70 subunit, RpoD [Spirochaeta coccoides DSM
           17374]
 gi|329748490|gb|AEC01846.1| RNA polymerase, sigma 70 subunit, RpoD [Spirochaeta coccoides DSM
           17374]
          Length = 685

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 66/241 (27%), Positives = 122/241 (50%), Gaps = 12/241 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  RL  ++LRLVV IA  Y   GLP +++V EGNIGL++AV+KF+  + F+ +TY+ W
Sbjct: 448 AAKDRLTQANLRLVVSIAKKYTNRGLPFNDLVQEGNIGLIKAVEKFEFRKNFKFSTYATW 507

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++        +   + ++K    A+  +  +      IAKKL 
Sbjct: 508 WIRQAITRAISDQGRTIRVPVH-----MIEQINKVKKEENALIQSLGRNPTDEEIAKKLG 562

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
             E +V  +        SL   +   ++  S   D++    D   +    +      +  
Sbjct: 563 WPEEKVKGVKNVAREPISLETPV--GEEEDSLLSDFI---EDKDAENPASQTSYMLLQEQ 617

Query: 228 LTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L + ++ L PRE+ + + R   ++   +TLE +   F+V+RER+RQIEA++ ++++   +
Sbjct: 618 LQKELATLPPREKDVLKMRFGLDDGFALTLEEVGLSFKVTRERIRQIEAKSLRRMRHPKR 677

Query: 286 K 286
            
Sbjct: 678 S 678



 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 8/31 (25%), Positives = 17/31 (54%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE 43
           +  +  Y+ +I K  +L  ++E  LA++  E
Sbjct: 195 DDPIRLYLRDIGKESLLTAEQERELAQKMEE 225


>gi|292491540|ref|YP_003526979.1| RNA polymerase sigma factor, sigma-70 family [Nitrosococcus
           halophilus Nc4]
 gi|291580135|gb|ADE14592.1| RNA polymerase sigma factor, sigma-70 family [Nitrosococcus
           halophilus Nc4]
          Length = 311

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 74/271 (27%), Positives = 137/271 (50%), Gaps = 14/271 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ +  K P+L  +EE   A R  + GD  A  R++ S+LR+V+K+A  +   GLP+ ++
Sbjct: 42  YMRDAGKAPLLSAEEEKHYA-RLAQQGDRKARDRMIESNLRMVIKMATRHVNRGLPLMDL 100

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL+ AV+KFDPE GFR +TY+ WWI+ A++  ++     V+I            
Sbjct: 101 IEEGNLGLIHAVEKFDPELGFRFSTYASWWIEQAIERALMNQVRTVRIPVHV-----LKT 155

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           +RR +   + +   +    ++  IAK LN    ++         + SLN  ++  +++  
Sbjct: 156 IRRYQREAKRLGQTHNTEPRLEEIAKALNEPLEKIQRYLSFQIPETSLNDPLSEDNEDC- 214

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLE 256
                L+ D      +L E  ++      +   +S L  R++ + + R   +     TLE
Sbjct: 215 --LADLLPDERNNPAILWEIFDKNIT---INHQLSQLTDRQQEVLKRRYGLDGYEATTLE 269

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +     ++RERVRQI+  A K+++  ++ +
Sbjct: 270 EVGQTIGITRERVRQIQQTAIKRLRAIVESE 300


>gi|261755428|ref|ZP_05999137.1| RNA polymerase sigma factor RpoD [Brucella suis bv. 3 str. 686]
 gi|261745181|gb|EEY33107.1| RNA polymerase sigma factor RpoD [Brucella suis bv. 3 str. 686]
          Length = 235

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 67/236 (28%), Positives = 116/236 (49%), Gaps = 12/236 (5%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A
Sbjct: 1   MVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQA 60

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   I      ++I        +   + ++    + +     +      +A+KL +   +
Sbjct: 61  ITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREPTPEELAEKLAMPLEK 115

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           V  +        SL   +   D+  S   D++    D    + I+   + N R+  TR +
Sbjct: 116 VRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKNALLPIDAAIQANLRDTTTRVL 170

Query: 233 SVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           + L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 171 ASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 226


>gi|320105405|ref|YP_004180995.1| RpoD subfamily RNA polymerase sigma-70 factor [Terriglobus
           saanensis SP1PR4]
 gi|319923926|gb|ADV81001.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Terriglobus
           saanensis SP1PR4]
          Length = 567

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 66/242 (27%), Positives = 117/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 323 EKAKRELIEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 382

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      IA+++
Sbjct: 383 WWIRQAITRAIADQARTIRIPVH-----MIETINKLIRTSRQLVQELGREASSEEIARRM 437

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++  ++V  +        SL   I   ++  S   D++    D       +     N + 
Sbjct: 438 DIPVAKVRKVLKIAQEPISLETPI--GEEEDSHLGDFI---EDRMAVSPSDAVISVNLKE 492

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             ++ +  L PRE R+ + R   E+    TLE +   F+V+RER+RQIEA+A +K++   
Sbjct: 493 YTSQVLRTLTPREERVIKMRFGLEDGSEHTLEEVGQSFQVTRERIRQIEAKALRKLRHPS 552

Query: 285 QK 286
           + 
Sbjct: 553 RS 554


>gi|257092978|ref|YP_003166619.1| RNA polymerase sigma factor RpoS [Candidatus Accumulibacter
           phosphatis clade IIA str. UW-1]
 gi|257045502|gb|ACV34690.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Candidatus
           Accumulibacter phosphatis clade IIA str. UW-1]
          Length = 319

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 74/272 (27%), Positives = 139/272 (51%), Gaps = 13/272 (4%)

Query: 17  SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
             Y++ I   P+L   EE   A+R R  G+  A  +++  +LRLVV IA  Y   G+P+ 
Sbjct: 50  QHYLNAIGAKPLLSPAEEVNWARRAR-AGEFPARQKMIEHNLRLVVNIAKHYLNRGIPLL 108

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++ EGN+GL+ A++K+DPERGFR +TY+ WWI+ +++  I+     +++       +  
Sbjct: 109 DLIEEGNLGLIHAIEKYDPERGFRFSTYATWWIRQSIERAIMNQSRTIRLPVHV--VKDI 166

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
             + R   HL++ +   + P+++  +  +       V+++N R+A   SL+A +      
Sbjct: 167 NLVLRAIRHLESASGREICPDRIAHLIDRPVEDVRRVMALNERIA---SLDAPLQV--DP 221

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVT 254
           S    D +  +       L++  E      +L   +  L  + R++ E R       P T
Sbjct: 222 SQTVGDLIADESLLDPDELLQSNELG---ELLRNWLGQLAGKHRQVLERRYGLGGSEPST 278

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE ++ +  ++RERVRQI+  A   ++  I++
Sbjct: 279 LEEIAFDLNLTRERVRQIQIEALDHLRRIIRR 310


>gi|313112817|ref|ZP_07798464.1| putative RNA polymerase sigma factor RpoD [Faecalibacterium cf.
           prausnitzii KLE1255]
 gi|310624887|gb|EFQ08195.1| putative RNA polymerase sigma factor RpoD [Faecalibacterium cf.
           prausnitzii KLE1255]
          Length = 458

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 72/255 (28%), Positives = 125/255 (49%), Gaps = 14/255 (5%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L  ++   L K  R+   L+A   L  ++LRLVV IA  + G+ L   +++ EGNIGL+
Sbjct: 202 PLSDEKRAELLKTRRDG--LNARRSLSEANLRLVVSIAKKHVGHNLAFLDLIQEGNIGLI 259

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +A +KFD +RGFR +TY+ WWI+ A+   I      ++I     +      + R++    
Sbjct: 260 KAAEKFDCDRGFRFSTYATWWIRQAITRAIADQARTIRIPVHMVE-----TINRMRQATN 314

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
            +   N        +AK +++S   V  +        SL + +   ++  S   D++   
Sbjct: 315 QLVYQNGHEPTPEELAKAMDMSVERVREIQRMAQEPASLESPV--GEEEDSSLGDFVA-- 370

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVS 265
            D   +   +  +R      +  ++  L PRE ++   R   ++  P TLE +  +F V+
Sbjct: 371 -DENAEAPGKAADRAMVAQQINLALKSLTPREEKVIRLRFGLDDGRPRTLEEVGRDFGVT 429

Query: 266 RERVRQIEARAFKKV 280
           RERVRQIEA+A +K+
Sbjct: 430 RERVRQIEAKAIRKL 444



 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 13/41 (31%), Positives = 23/41 (56%), Gaps = 2/41 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRL 53
           +  +  Y+ +I +IP+L  ++E  L++R   H    AAH L
Sbjct: 100 DDPVKNYLKQIGQIPLLSAEQEVELSRRI--HAGAEAAHIL 138


>gi|271501815|ref|YP_003334841.1| RpoD subfamily RNA polymerase sigma-70 subunit [Dickeya dadantii
           Ech586]
 gi|270345370|gb|ACZ78135.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dickeya dadantii
           Ech586]
          Length = 330

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 79/271 (29%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+S+  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVSSRRRMIESNLRLVVKIARRYNNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +     +  
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAERLDKPVDDVNRMLRLNERITSVDTPL--GGDSEK 232

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  + D   +   +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 233 ALLDILADEKDNGPE---DTTQDNDMKQNIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQVQ 320


>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 =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 63/272 (23%), Positives = 122/272 (44%), Gaps = 14/272 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRY--REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + ++ K   +  +E   + K     E    +A   ++ ++LRLV+ IA  Y   GL   +
Sbjct: 384 LADMEKETRISIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLD 443

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +  
Sbjct: 444 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIE 498

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + ++    +       +      +A+ + + E ++  +        S+   I   D + 
Sbjct: 499 TINKMNRISRQHLQETGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPI--GDDDD 556

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D       +     +   +    +  L PRE ++   R   +     TL
Sbjct: 557 SHLGDFI---EDANNVAPADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTL 613

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +  +F+V+RER+RQIEA+A +K++   +  
Sbjct: 614 EEVGRQFDVTRERIRQIEAKALRKLRHPTRSD 645


>gi|5771430|gb|AAD51396.1|AF117715_5 stationary phase specific sigma factor homolog [Legionella
           pneumophila]
          Length = 341

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 79/270 (29%), Positives = 141/270 (52%), Gaps = 13/270 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A      GD+ A  +++ S+LRLVVKIA  Y   GLP+ ++
Sbjct: 74  YLGEIGFSPLLTAEEEIHYAT-LALKGDMEARKKMIESNLRLVVKIARRYLNRGLPLLDL 132

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM++V+KFDP+RGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 133 IEEGNLGLMKSVEKFDPKRGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 191

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +   Q + D+   PE++  +  K      +++ +N ++A   S++  I   +  S 
Sbjct: 192 LRAARQLTQKL-DHEPSPEEIAEMVDKPLEDVQKLLGLNDKVA---SVDTPIGFDETKS- 246

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
              D +  ++      L+  E   N R  +   +  L   ++++   R         TLE
Sbjct: 247 -LLDTIADENSLNPAELLTNE---NLRQHIESLLDKLTENQQQVIARRFGLRGFEKATLE 302

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ++  E +++RERVRQI+  A K ++  +++
Sbjct: 303 DVGKEIDLTRERVRQIQVEALKTLRTLLER 332


>gi|90577776|ref|ZP_01233587.1| hypothetical DNA-directed RNA polymerase, sigma subunit [Vibrio
           angustum S14]
 gi|90440862|gb|EAS66042.1| hypothetical DNA-directed RNA polymerase, sigma subunit [Vibrio
           angustum S14]
          Length = 291

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 82/289 (28%), Positives = 145/289 (50%), Gaps = 13/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N+K       G+I +  Y+ EI + P+L K++E + +++    GD  + + L+ S+LRL
Sbjct: 3   INKKEEQFSHGGDI-VHLYLKEISEKPLLTKEDEILYSRK-SLCGDACSKNVLIESNLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  YRG  + IS+++ EGNIGLM AV+KFDPE+GFR +TY+ WWIK  ++  I   
Sbjct: 61  VVSIAKKYRGSSIHISDLIDEGNIGLMTAVEKFDPEKGFRFSTYATWWIKQTIERAIHNQ 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              +++    +  +    + R    L    +     E V  +  K     S  +S +  +
Sbjct: 121 GRTIRLPVHVS--KEINTIIRTHKQLVKKNNQEPSTELVAEVLNKTLDDVSTTLSYDTPI 178

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               S +  I S  + +SQ    L+ D +  +    E  +    + +    +  LN R++
Sbjct: 179 ---VSYDQSITS--EATSQSIAVLIADENSAK--PDELVDDLAIQKITANVLKCLNNRDK 231

Query: 241 RIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            I   R   L     TL+ ++ E  ++RER+RQ++  +  K++ S+ + 
Sbjct: 232 EIICRRFGLLGYEAQTLQEVAEEVGLTRERIRQLQVTSLAKLKNSLSRD 280


>gi|332297439|ref|YP_004439361.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           brennaborense DSM 12168]
 gi|332180542|gb|AEE16230.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           brennaborense DSM 12168]
          Length = 287

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 72/280 (25%), Positives = 148/280 (52%), Gaps = 11/280 (3%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
            + + +  L+ Y+ EI KIP+L ++EE  LA +       +A  R+V ++LR VV +A  
Sbjct: 8   TMASDDNVLALYLKEINKIPLLSREEETDLAVKAAAGD-KAAKDRIVNANLRFVVNVAKK 66

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y+ +GL + +++SEGNIGLM A+++FD  +G+   +Y++WWI+ ++ + I     ++++ 
Sbjct: 67  YQNHGLDLVDLISEGNIGLMTAIERFDVSKGYHFISYAVWWIRQSILKAICEKSRMIRLP 126

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
                      L +++   + +  +  + E++  +A  LN+  S V  M        SL+
Sbjct: 127 LNRA-----NELVQIEHARKLVAQDKTEEEEITEVADMLNMDVSHVREMLNISRDMISLD 181

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           A I SSD++S+   ++L    D + +   +     + ++ +   +  L  +E  +   R 
Sbjct: 182 ASIRSSDQDSASIGEFL---EDSRYEDPADTVLNASMQDDIDGVLGTLTDKEADVLRYRF 238

Query: 248 L--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
                  ++L+ +  +F +++ER+RQIE +A K++Q   +
Sbjct: 239 GLNGNKSMSLKEVGDKFNLTKERIRQIEKKAIKRLQHPAR 278


>gi|260889708|ref|ZP_05900971.1| RNA polymerase sigma factor RpoD [Leptotrichia hofstadii F0254]
 gi|260860314|gb|EEX74814.1| RNA polymerase sigma factor RpoD [Leptotrichia hofstadii F0254]
          Length = 273

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 89/273 (32%), Positives = 156/273 (57%), Gaps = 15/273 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +S Y+ +I+K  +L K+EEY L KR RE  D  A   L+ S+LRLV+  A    G GLP+
Sbjct: 9   MSLYLSDIQKFDLLSKEEEYELLKRIREDDDEQARQLLILSNLRLVISTAKKSLGNGLPL 68

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++SEGNIGL++A+ KFD E+G R +TY++WWIK ++++ I+     ++I +       
Sbjct: 69  IDLISEGNIGLIKAINKFDYEKGHRFSTYAVWWIKQSIKKAIINIGRDIRIPSYK----- 123

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           +  L ++   ++  T  + +      IAK++++ ES+VI +        SLN  I  +  
Sbjct: 124 YEQLSKVNKVIKDYTAIHGEAPSTEYIAKEVDLKESKVILLLGEFQDIMSLNETIGDN-- 181

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--V 253
               + + ++  +D  E  +I++++    +++L R   VLN RER I E R    +    
Sbjct: 182 ---IYLEDIIGKNDDVEDKIIKEDQLIEMKDLLER---VLNERERAILEYRYGLYDNKIH 235

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TL+ +  +  ++RERVRQIE +A  K++E +++
Sbjct: 236 TLKEIGEQMGITRERVRQIEKKAITKLKEHLEE 268


>gi|332975259|gb|EGK12159.1| DNA-directed RNA polymerase sigma subunit RpoD [Kingella kingae
           ATCC 23330]
          Length = 654

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 60/242 (24%), Positives = 115/242 (47%), Gaps = 12/242 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  +++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ W
Sbjct: 411 AAKQKMIQANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATW 470

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I        +   + ++    +       +      +A+ + 
Sbjct: 471 WIRQAITRSIADQARTIRIPVH-----MIETINKMNRISRQYLQETGEEPDSAKLAELME 525

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + E ++  +        S+   I   D + S   D++    D       +     + R +
Sbjct: 526 MPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI---EDVNNVAPADAAMYSSLREV 580

Query: 228 LTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            +  +  L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   +
Sbjct: 581 TSDILESLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTR 640

Query: 286 KQ 287
             
Sbjct: 641 SD 642


>gi|299135760|ref|ZP_07028944.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidobacterium
           sp. MP5ACTX8]
 gi|298601884|gb|EFI58038.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidobacterium
           sp. MP5ACTX8]
          Length = 573

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 67/242 (27%), Positives = 117/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 329 EKAKRELIEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 388

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      IAK++
Sbjct: 389 WWIRQAITRAIADQARTIRIPVH-----MIETINKLIRTSRQLVQELGREASSEEIAKRM 443

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++  ++V  +        SL   I   ++  S   D++    D       +     N + 
Sbjct: 444 DIPVAKVRKVLKIAQEPISLETPI--GEEEDSHLGDFI---EDRMAVSPSDAVISVNLKE 498

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             ++ +  L PRE R+ + R   E+    TLE +   F+V+RER+RQIEA+A +K++   
Sbjct: 499 YTSQVLRTLTPREERVIKMRFGLEDGSEHTLEEVGQSFQVTRERIRQIEAKALRKLRHPS 558

Query: 285 QK 286
           + 
Sbjct: 559 RS 560


>gi|197286082|ref|YP_002151954.1| RNA polymerase sigma factor RpoS [Proteus mirabilis HI4320]
 gi|227356592|ref|ZP_03840979.1| RNA polymerase sigma factor RpoS [Proteus mirabilis ATCC 29906]
 gi|194683569|emb|CAR44440.1| RNA polymerase sigma factor RpoS [Proteus mirabilis HI4320]
 gi|227163348|gb|EEI48275.1| RNA polymerase sigma factor RpoS [Proteus mirabilis ATCC 29906]
          Length = 329

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 79/271 (29%), Positives = 135/271 (49%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 59  YLGEIGYSPLLSAEEEVFFARR-ALRGDIPSRQRMIESNLRLVVKISRRYTNRGLALLDL 117

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPE+GFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 118 IEEGNLGLIRAVEKFDPEKGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 176

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +         V  IA+ L+    +V  M        S++  I      + 
Sbjct: 177 LRTAR----ELAHKLDHEPSVEEIAQTLDKPVDDVSKMLRLNERISSVDTPIGGDSDKA- 231

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D  E+      +  N +  + + +  LNP++R +   R   L     TLE
Sbjct: 232 ----LLDIISDENEEGPEATIQNNNLKENIVKWLFELNPKQREVLARRFGLLGYEAETLE 287

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    +++++ +Q Q
Sbjct: 288 DVGREIGLTRERVRQIQVEGLRRLKDILQGQ 318


>gi|90416498|ref|ZP_01224429.1| RNA polymerase sigma factor RpoD [marine gamma proteobacterium
           HTCC2207]
 gi|90331697|gb|EAS46925.1| RNA polymerase sigma factor RpoD [marine gamma proteobacterium
           HTCC2207]
          Length = 612

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 63/243 (25%), Positives = 113/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 372 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 431

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            L R+   +         PE    +A+++
Sbjct: 432 WWIRQAITRSIADQARTIRIPVHM--IETINKLNRVSRQMLQEMGREPSPE---ELAERM 486

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   +   +   D +    D    + +++  + N   
Sbjct: 487 EMPEDKIRKVLKIAKEPISMETPI--GEDEDASIGDLI---EDTTIALPLDEATKNNLTE 541

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                +S L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 542 STRGVLSSLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPT 601

Query: 285 QKQ 287
           +  
Sbjct: 602 RSD 604


>gi|254796721|ref|YP_003081557.1| RNA polymerase sigma-32 factor (RpoH) [Neorickettsia risticii str.
           Illinois]
 gi|254589969|gb|ACT69331.1| RNA polymerase sigma-32 factor (RpoH) [Neorickettsia risticii str.
           Illinois]
          Length = 288

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 125/286 (43%), Positives = 180/286 (62%), Gaps = 8/286 (2%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
            + +S+ V+       Y  +I  IP+L+++EE  L  R+  H D+SAA RLV ++LRLVV
Sbjct: 1   MRELSLPVDNS-EFDAYARKILAIPILQEEEERDLIDRWFLHRDISAAQRLVEAYLRLVV 59

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           K+ + +R YG P+ ++ SEGNIGLM+A+K F+P  G  +ATY++WWIKAA+ EY++RSWS
Sbjct: 60  KVTVRFRNYGFPLMDLASEGNIGLMKAIKNFNPTLGHGIATYAIWWIKAAINEYVIRSWS 119

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-AIAKKLNVSESEVISMNCRL- 180
           +VKIGTTA Q++LFFNLR+LK          L   QVV  I++ L VS+++V  M   L 
Sbjct: 120 IVKIGTTAAQRKLFFNLRKLKNSGSVA---GLDEHQVVGKISEMLEVSKNDVEEMERILN 176

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
             D SLN  +   +  SS+  D + +    QE VL E  ER+ +  +L  ++  L  R +
Sbjct: 177 VRDVSLNMQL--GEDGSSEVHDLIPFPEANQEAVLSETRERQMKNRLLYEAVESLEARHK 234

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            IF AR L   P TL+ L  +F +S+ERVRQI ARA KKV E +++
Sbjct: 235 EIFVARSLSAVPRTLKELGEKFSISQERVRQIHARAMKKVAEYVEE 280


>gi|15803258|ref|NP_289290.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 EDL933]
 gi|12517195|gb|AAG57848.1|AE005502_2 RNA polymerase, sigma S (sigma38) factor; synthesis of many growth
           phase related proteins [Escherichia coli O157:H7 str.
           EDL933]
          Length = 330

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|257458803|ref|ZP_05623926.1| RNA polymerase sigma factor RpoD [Campylobacter gracilis RM3268]
 gi|257443791|gb|EEV18911.1| RNA polymerase sigma factor RpoD [Campylobacter gracilis RM3268]
          Length = 626

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 73/260 (28%), Positives = 127/260 (48%), Gaps = 15/260 (5%)

Query: 29  LEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           LE +    + ++ +       +A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGL
Sbjct: 365 LEPERLKEILEQIKRGKRISDNAKARMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGL 424

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+ +RG++ +TY+ WWI+ A+   I      ++I        +   + R+    
Sbjct: 425 MKAVDKFEYKRGYKFSTYATWWIRQAISRAIADQARTIRIPIH-----MIETINRINKIT 479

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +       K   +  IA+++ +S  +V  +        SL A I   +++  ++ D++  
Sbjct: 480 RKYMQEGGKEPDINVIAQEVGLSVDKVKQVIKITKEPISLEAPI--GNEDDGKFGDFV-- 535

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFE 263
             D      IE+  + + +  +   +  LN RER +   R      E+  TLE +  E  
Sbjct: 536 -EDKSSVSPIEQILKSDLKEQIDDILEQLNDRERTVIRMRFGLLDDESDRTLEEIGKELN 594

Query: 264 VSRERVRQIEARAFKKVQES 283
           ++RERVRQIE+ A KK++  
Sbjct: 595 ITRERVRQIESSAIKKLKHP 614



 Score = 39.4 bits (91), Expect = 0.71,   Method: Composition-based stats.
 Identities = 10/36 (27%), Positives = 21/36 (58%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+ +IP+L K+EE  ++K+     D+
Sbjct: 103 SDSPVRMYLREMGQIPLLTKEEEIEISKKIELGEDI 138


>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 =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 67/267 (25%), Positives = 119/267 (44%), Gaps = 18/267 (6%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 356 LTVEQIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 415

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 416 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRVARQM 473

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                + E ++  +        S+   I   D   S   D++  
Sbjct: 474 LQ-------EXXXXXXXXXXXMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 522

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   ++ +     ++ R+     ++ L PRE ++   R   +     TLE +  +F+V
Sbjct: 523 -EDTTLELPLGSATSESLRSATHEVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDV 581

Query: 265 SRERVRQIEARAFKKVQESIQKQVELS 291
           +RER+RQIEA+A +K++   + +V  S
Sbjct: 582 TRERIRQIEAKALRKLRHPSRSEVLRS 608


>gi|307132339|ref|YP_003884355.1| RNA polymerase sigma-S (sigma 38) factor [Dickeya dadantii 3937]
 gi|306529868|gb|ADM99798.1| RNA polymerase, sigma S (sigma 38) factor [Dickeya dadantii 3937]
          Length = 330

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 79/271 (29%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+S+  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVSSRRRMIESNLRLVVKIARRYNNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +     +  
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAERLDKPVDDVNRMLRLNERITSVDTPL--GGDSEK 232

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  + D   +   +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 233 ALLDILADEKDNGPE---DTTQDNDMKQNIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQVQ 320


>gi|218701232|ref|YP_002408861.1| RNA polymerase sigma factor RpoS [Escherichia coli IAI39]
 gi|218371218|emb|CAR19049.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli IAI39]
 gi|327251469|gb|EGE63155.1| RNA polymerase sigma factor RpoS [Escherichia coli STEC_7v]
          Length = 330

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 77/271 (28%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGF  +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFSFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|152990473|ref|YP_001356195.1| RNA polymerase sigma factor RpoD [Nitratiruptor sp. SB155-2]
 gi|151422334|dbj|BAF69838.1| RNA polymerase sigma 70 factor [Nitratiruptor sp. SB155-2]
          Length = 608

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 70/260 (26%), Positives = 128/260 (49%), Gaps = 15/260 (5%)

Query: 29  LEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L+ ++   + ++ +        A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGL
Sbjct: 347 LDPEQLAEILEQIKRGKKISEEAKTRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGL 406

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+ ++G++ +TY+ WWI+ A+   I      ++I        +   + R+   +
Sbjct: 407 MKAVDKFEYKKGYKFSTYATWWIRQAISRAIADQARTIRIPIH-----MIETINRINKIV 461

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +       K   V  IA+++ +   +V ++        SL A I   ++   ++ D++  
Sbjct: 462 RKHLQETGKEPDVETIAEEVGMPVEKVKNVIKITKEPVSLEAPI--GNEEDGKFGDFI-- 517

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFE 263
             D      +E   +++ ++ +   +  LN RE+ +   R      E+  TLE +  E  
Sbjct: 518 -EDKNAPNPLEVIMKEDMKSKIEEILENLNEREKAVVRMRFGLMPDESDRTLEEIGKELN 576

Query: 264 VSRERVRQIEARAFKKVQES 283
           V+RERVRQIE+ A KK++  
Sbjct: 577 VTRERVRQIESSAIKKLKHP 596



 Score = 40.2 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 10/30 (33%), Positives = 19/30 (63%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRY 41
            +  +  Y+ E+ +IP+L K+EE  L+K+ 
Sbjct: 102 SDSPVRMYLREMGQIPLLTKEEEIELSKKI 131


>gi|238750591|ref|ZP_04612091.1| RNA polymerase sigma factor rpoS [Yersinia rohdei ATCC 43380]
 gi|238711239|gb|EEQ03457.1| RNA polymerase sigma factor rpoS [Yersinia rohdei ATCC 43380]
          Length = 332

 Score =  216 bits (551), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 136/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 63  YLGEIGYSPLLTAEEEVYFARR-ALRGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 180

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    +   
Sbjct: 181 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE--- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
             +  L    D  E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 --KALLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 291

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 292 DVGREIGLTRERVRQIQVEGLRRLREILQGQ 322


>gi|291618595|ref|YP_003521337.1| RpoS [Pantoea ananatis LMG 20103]
 gi|291153625|gb|ADD78209.1| RpoS [Pantoea ananatis LMG 20103]
 gi|327394975|dbj|BAK12397.1| RNA polymerase sigma factor RpoS [Pantoea ananatis AJ13355]
          Length = 330

 Score =  216 bits (550), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVLFARR-ALRGDIPSRRRMIESNLRLVVKIARRYSNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +     +  
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPL--GGDSEK 232

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  + D   +   +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 233 ALLDILADEKDNGPE---DTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQGQ 320


>gi|225849654|ref|YP_002729888.1| RNA polymerase sigma-70 factor [Persephonella marina EX-H1]
 gi|225646208|gb|ACO04394.1| RNA polymerase sigma-70 factor [Persephonella marina EX-H1]
          Length = 281

 Score =  216 bits (550), Expect = 3e-54,   Method: Composition-based stats.
 Identities = 83/278 (29%), Positives = 146/278 (52%), Gaps = 12/278 (4%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M+     +  L+ YI ++ + P+L  +EE  LAKR ++ GD  A  +LV  +LR VV +A
Sbjct: 1   MADTEKEQTTLNLYIQKMAEHPLLTPEEEKELAKRAKK-GDKEALKKLVEGNLRFVVNVA 59

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             + G+G+P++++++ GN+GL++A K+FDPER  +  +Y++WWI+ A+ + I +    V+
Sbjct: 60  KNFMGWGVPLTDLIAAGNLGLIEAAKRFDPERDVKFISYAVWWIRQAIMQTIFQQTGAVR 119

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           I       +    + ++K   + + +   +   +  IA+K+  S  +V +    +    S
Sbjct: 120 IPV-----KESLFISKVKETYEKLKEELKREPTIEEIAEKVGASPKKVKNALQVVRMPYS 174

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L+  +    ++ +      V    G E V  E  E    +  L   ++VL+ RER I E 
Sbjct: 175 LDKPLGEEGEDLTLLD---VLSKKGTEDVEKEIVEESLHKE-LNTLLNVLDERERAIIEH 230

Query: 246 RRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R     E P TL  +     +SRERVRQ+E RA KK++
Sbjct: 231 RFGLNGEEPKTLTEVGEILGISRERVRQLEQRALKKLR 268


>gi|288803307|ref|ZP_06408740.1| RNA polymerase sigma-70 factor [Prevotella melaninogenica D18]
 gi|288334127|gb|EFC72569.1| RNA polymerase sigma-70 factor [Prevotella melaninogenica D18]
          Length = 287

 Score =  216 bits (550), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 76/287 (26%), Positives = 150/287 (52%), Gaps = 12/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI    M+  +EE  LA++ R +GD  A  RL  ++LR VV
Sbjct: 5   KITKSITNRESASLDKYLQEIGHEEMISIEEEVELAQKIR-NGDRKALERLTKANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + I     
Sbjct: 64  SVAKQYQNQGLSLPDLINEGNVGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           ++++    NQ      + ++   L      N +   +  IA+  ++ E +++      + 
Sbjct: 124 IIRLP--LNQVSSVNKINKI---LTQFEQENERRPSIDEIAQNTDIPEDKIVDAMKVNSR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     D+ SS        +    ++ L+E    ++ R  + R++ +L  RE+ +
Sbjct: 179 HVSVDAPFYD-DEQSSLLDVIPNDNTPSTDKELVE----ESLREEIGRALQILEDREKVV 233

Query: 243 FEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            EA        +TLE + S++ ++RERVRQI+ +A +++++    +V
Sbjct: 234 IEAYFGINQREMTLEEIGSKYNLTRERVRQIKEKAIRRLRQLSNSKV 280


>gi|148243603|ref|YP_001228760.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp.
           RCC307]
 gi|147851913|emb|CAK29407.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. RCC307]
          Length = 323

 Score =  216 bits (550), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 79/290 (27%), Positives = 142/290 (48%), Gaps = 31/290 (10%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--------------------AAHRL 53
             +  Y+  I ++P+L   EE  LA + ++   LS                    A  R+
Sbjct: 34  DSIGWYLSNIGRVPLLTAAEEIELAHQVQQMKQLSEIPAEERTPKQRQQVRMGCRARDRM 93

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           + ++LRLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+  M
Sbjct: 94  MAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGM 153

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
              I  S   +++    ++K     L +++   + +T    +    + +A  + +   E+
Sbjct: 154 TRAIDNSARTIRLPIHISEK-----LSKMRRITRELTHRFGRQPNRLELAHAMGMEPDEL 208

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             +  + A   SL+A     +  S+  +  L+ D    +   +E  +R+ ++  L   ++
Sbjct: 209 EELLSQSAPCASLDAHARGEEDRSTLGE--LIPDPSCNDS--MESMDRRIQKEHLGTWIT 264

Query: 234 VLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            LN RE++I + R   E   P TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 265 QLNEREQKILKLRFGLEGAEPQTLAEIGRQINVSRERVRQLEAKAILKLR 314


>gi|205353865|ref|YP_002227666.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 287/91]
 gi|205273646|emb|CAR38635.1| RNA polymerase sigma subunit RpoS (sigma-38) [Salmonella enterica
           subsp. enterica serovar Gallinarum str. 287/91]
 gi|326628975|gb|EGE35318.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 9]
          Length = 330

 Score =  216 bits (550), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>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 =  216 bits (550), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 60/248 (24%), Positives = 115/248 (46%), Gaps = 12/248 (4%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            E     A   ++ ++LRLV+ IA  Y   G+   +++ EGNIGLM+AV KF+  RG++ 
Sbjct: 419 AESKMRKAKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEGNIGLMKAVDKFEYRRGWKF 478

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY+ WW++ A+   +      +++            L R+   +   T     P     
Sbjct: 479 STYATWWVRQAVTRSLADQARTIRVPVHM--IETINKLNRISREILQQTGQEAHP---SV 533

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           +A+++++SE +V  +        S+   +   D   +   D +    D       +   +
Sbjct: 534 LAERMDLSEEKVRGILKIAKQPVSMETPV--GDDGDATLGDMI---EDSAASSPADAAMQ 588

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKK 279
            + R  +  ++  L+PRE ++   R         TLE +  +F+V+RER+RQIE++A +K
Sbjct: 589 ADLRAAIDDALDSLSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIRQIESKAMRK 648

Query: 280 VQESIQKQ 287
           +    +  
Sbjct: 649 LMHPSRAD 656


>gi|254445278|ref|ZP_05058754.1| Sigma-70 region 3 family [Verrucomicrobiae bacterium DG1235]
 gi|198259586|gb|EDY83894.1| Sigma-70 region 3 family [Verrucomicrobiae bacterium DG1235]
          Length = 576

 Score =  216 bits (550), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 69/261 (26%), Positives = 125/261 (47%), Gaps = 14/261 (5%)

Query: 29  LEKQEEYVLAKRYREHGDL--SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           LE ++   L    R H      A   +V ++LRLV+ IA  Y   GL   +++ EGN+GL
Sbjct: 294 LEPEKLLSLIAEVRRHLKAAHKAKTEMVEANLRLVISIAKKYTNRGLSFLDLIQEGNMGL 353

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV+KF+  RG++ +TY+ WWI+ A+   I      ++I            + +++  L
Sbjct: 354 MKAVEKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETLNKVMQVQKQL 411

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                +   PE+V   A+++ +    V ++        SL + +   D + + + D++  
Sbjct: 412 LQEYGHEPTPEEV---AEEMALPVERVQTIMKMAQQPISLQSPV--GDGDDTNFGDFI-- 464

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
             D   +   ++      R  +   +  L  RERR+   R         TLE +  +F+V
Sbjct: 465 -EDKSAENPYDQTAFSLLREKIIDVLDSLTERERRVLSLRFGLVDGYSRTLEEVGKQFKV 523

Query: 265 SRERVRQIEARAFKKVQESIQ 285
           +RER+RQIEA+A +K++   +
Sbjct: 524 TRERIRQIEAKALRKMRHPTR 544



 Score = 39.8 bits (92), Expect = 0.51,   Method: Composition-based stats.
 Identities = 9/42 (21%), Positives = 24/42 (57%), Gaps = 1/42 (2%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLV 54
           +  +  Y+ ++ ++P+L +++E  ++KR  E+ +  A   L 
Sbjct: 100 DDPVRMYLKQMGQVPLLTREQEVEISKRI-ENAEQKAQEELF 140


>gi|94971322|ref|YP_593370.1| sigma 38, RpoS [Candidatus Koribacter versatilis Ellin345]
 gi|94553372|gb|ABF43296.1| RNA polymerase, sigma 70 subunit, RpoD [Candidatus Koribacter
           versatilis Ellin345]
          Length = 574

 Score =  216 bits (550), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 66/242 (27%), Positives = 115/242 (47%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 331 EQAKKELIEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 390

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      IAK++
Sbjct: 391 WWIRQAITRAIADQARTIRIPVH-----MIETINKLIRTSRQLVQELGREPSSEEIAKRM 445

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++  ++V  +        SL   I   ++  S   D++    D       E     N ++
Sbjct: 446 DIPVAKVRKVLKIAQEPISLETPI--GEEEDSHLGDFI---EDRSMVSPAEAVINVNLKD 500

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              + +  L  RE ++ + R   E+    TLE +   F V+RER+RQIEA+A +K++   
Sbjct: 501 QTAQVLRTLTAREEKVIKMRFGLEDGSEHTLEEVGQSFAVTRERIRQIEAKALRKLRHPS 560

Query: 285 QK 286
           + 
Sbjct: 561 RS 562


>gi|296139548|ref|YP_003646791.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Tsukamurella
           paurometabola DSM 20162]
 gi|296027682|gb|ADG78452.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Tsukamurella
           paurometabola DSM 20162]
          Length = 330

 Score =  216 bits (550), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 63/315 (20%), Positives = 133/315 (42%), Gaps = 38/315 (12%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------------- 43
           +   ++         +  Y++ I +  +L  ++E  LAKR                    
Sbjct: 19  LTEADLDAQSPAADLVRVYLNGIGRTALLTAEDEVELAKRIEAGLYAQHLLDTKKRLSAS 78

Query: 44  ---------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                        +A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD
Sbjct: 79  KKRDLAFIVRDGQAARQHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFD 138

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +GF+ +TY+ WWI+ A+   +      +++        L   + +L    + +     
Sbjct: 139 YAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVH-----LVEQVNKLARIRRELHQQLG 193

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +      +A +  +   ++  +        SL+  + S ++  +   D++    D +   
Sbjct: 194 REATDAELAAESGIPAEKIADLMDHSRDPVSLDMPVGSDEE--APLGDFI---EDAEAAS 248

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
                      + +   ++ L+ RE+++   R   ++  P TL+ +   F +SRERVRQI
Sbjct: 249 AESAVISTLMHSDVRSVLATLDEREQQVIRLRYGLDDGQPRTLDQIGKLFGLSRERVRQI 308

Query: 273 EARAFKKVQESIQKQ 287
           E     K++   +  
Sbjct: 309 EREVMSKLRNGERAD 323


>gi|260436326|ref|ZP_05790296.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 8109]
 gi|260414200|gb|EEX07496.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 8109]
          Length = 308

 Score =  216 bits (550), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 81/292 (27%), Positives = 143/292 (48%), Gaps = 31/292 (10%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAK--------------------RYREHGDLSAAH 51
               +  Y+  I +IP+L   EE  LA                     R++      A  
Sbjct: 17  ATDSIGFYLSSIGRIPLLTAAEEIELAHHVQAMKQLQELPEEELTSRHRHKIRMGKRARD 76

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ ++LRLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+ 
Sbjct: 77  RMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQ 136

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            M   I  S   +++    ++K     L +++   + ++    +    + +A  + +   
Sbjct: 137 GMTRAIDNSARTIRLPIHISEK-----LSKMRRISRELSHRFGRQPNRLELASAMGIEPR 191

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           E+  +  + A   SL+A     +  S+  +  L+ D +G+E   +E  +R  ++  L   
Sbjct: 192 ELEDLISQSAPCASLDAHARGEEDRSTLGE--LIPDPNGEE--PMEGMDRSIQKEHLGGW 247

Query: 232 MSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +S LN RE++I + R     E P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 248 LSQLNEREQKILKLRFGLGGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 299


>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 =  216 bits (550), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 60/248 (24%), Positives = 115/248 (46%), Gaps = 12/248 (4%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            E     A   ++ ++LRLV+ IA  Y   G+   +++ EGNIGLM+AV KF+  RG++ 
Sbjct: 419 AESKMRKAKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEGNIGLMKAVDKFEYRRGWKF 478

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY+ WW++ A+   +      +++            L R+   +   T     P     
Sbjct: 479 STYATWWVRQAVTRSLADQARTIRVPVHM--IETINKLNRISREILQQTGQEAHP---SV 533

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           +A+++++SE +V  +        S+   +   D   +   D +    D       +   +
Sbjct: 534 LAERMDLSEEKVRGILKIAKQPVSMETPV--GDDGDATLGDMI---EDSAASSPADAAMQ 588

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKK 279
            + R  +  ++  L+PRE ++   R         TLE +  +F+V+RER+RQIE++A +K
Sbjct: 589 ADLRAAIDDALDSLSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIRQIESKAMRK 648

Query: 280 VQESIQKQ 287
           +    +  
Sbjct: 649 LMHPSRAD 656


>gi|259909441|ref|YP_002649797.1| RNA polymerase sigma factor [Erwinia pyrifoliae Ep1/96]
 gi|224965063|emb|CAX56595.1| RNA polymerase sigma factor [Erwinia pyrifoliae Ep1/96]
          Length = 277

 Score =  216 bits (550), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 79/271 (29%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 8   YLGEIGYSPLLTAEEEVFFARR-ALRGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 66

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 67  IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 125

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA+KL+    +V  M        S++  +     +  
Sbjct: 126 LRTAR----ELSHKLDHEPSAEEIAQKLDKPVDDVSRMLRLNERITSVDTPL--GGDSEK 179

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  + D   +   +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 180 ALLDILADEKDNGPE---DTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 236

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 237 DVGREIGLTRERVRQIQVEGLRRLREILQGQ 267


>gi|258593489|emb|CBE69828.1| RNA polymerase sigma factor rpoD (Sigma-80) [NC10 bacterium 'Dutch
           sediment']
          Length = 654

 Score =  216 bits (550), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 69/240 (28%), Positives = 115/240 (47%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ WW
Sbjct: 416 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMRAVDKFEYQRGYKFSTYATWW 475

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           ++ A+   I      ++I            L R   +L         PE    IA+K+++
Sbjct: 476 VRQAITRAIADQARTIRIPVHM--IETINKLTRASRYLVQEFGREPTPE---EIAQKIDL 530

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   I   ++  S   D++    D      IE     N     
Sbjct: 531 PVDKVRKVLKIAQEPISLETPI--GEEEGSHLGDFI---EDKGVISPIEAVIGMNLSGQT 585

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + +  L  RE++I + R    +    TLE +  +F+V+RER+RQIEA+A +K++   + 
Sbjct: 586 EQVLETLTEREQKILKLRFGLGDGRDHTLEEVGQQFDVTRERIRQIEAKALRKLRHPTRS 645



 Score = 37.5 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 24/50 (48%), Gaps = 1/50 (2%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTS 56
           S +   +  +  Y+ E+ K P+L ++ E  +AKR  E G    A  +  +
Sbjct: 154 SSVGRTDDPVRMYLREMGKTPLLTREGEIQIAKRI-EDGHKEVAEAVCQA 202


>gi|332765694|gb|EGJ95907.1| RNA polymerase sigma factor RpoS [Shigella flexneri 2930-71]
          Length = 330

 Score =  216 bits (550), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 77/271 (28%), Positives = 139/271 (51%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EG++GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGDLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E++Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLRETLQTQ 320


>gi|326324968|dbj|BAJ84180.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Oranienburg]
          Length = 330

 Score =  216 bits (550), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL +  +
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLNL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|118475308|ref|YP_891711.1| RNA polymerase sigma factor RpoD [Campylobacter fetus subsp. fetus
           82-40]
 gi|118414534|gb|ABK82954.1| RNA polymerase sigma factor [Campylobacter fetus subsp. fetus
           82-40]
          Length = 623

 Score =  216 bits (550), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 72/239 (30%), Positives = 118/239 (49%), Gaps = 13/239 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ ++G++ +TY+ W
Sbjct: 382 DAKARMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKKGYKFSTYATW 441

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I        +   + R+    +       K   V  IA+++ 
Sbjct: 442 WIRQAISRAIADQARTIRIPIH-----MIETINRINKINRKYLQEEGKEPDVSIIAREVG 496

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V  +        SL A I S D    ++ D++    D      +E+  + + +  
Sbjct: 497 LSIDKVKQVIKITKEPISLEAPIGSEDD--GKYGDFV---EDKTTLSPMEQILKGDLKEQ 551

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++  
Sbjct: 552 IDEVLDQLNDREKAVIRMRFGLLEDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHP 610



 Score = 36.3 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 9/36 (25%), Positives = 20/36 (55%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+ +I +L K+EE  ++K+     D+
Sbjct: 103 SDSPVRMYLREMGQISLLTKEEEVEISKKIELGEDI 138


>gi|161502017|ref|YP_001569129.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:-- str. RSK2980]
 gi|160863364|gb|ABX19987.1| hypothetical protein SARI_00033 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 330

 Score =  216 bits (550), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 77/271 (28%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGF  +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFSFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|148271746|ref|YP_001221307.1| putative RNA polymerase sigma 70 factor [Clavibacter michiganensis
           subsp. michiganensis NCPPB 382]
 gi|147829676|emb|CAN00592.1| putative RNA polymerase sigma 70 factor [Clavibacter michiganensis
           subsp. michiganensis NCPPB 382]
          Length = 347

 Score =  216 bits (550), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 73/305 (23%), Positives = 136/305 (44%), Gaps = 37/305 (12%)

Query: 7   SIIVNGE--IGLSRYIHEIRKIPMLEKQEEYVLAKRYR---------------------- 42
           S++  G     +  Y+ +I ++P+L  ++E  +A+R                        
Sbjct: 40  SLVTPGASTDAVKDYLRQIGRVPLLTAEQEVTVARRIEVGVLSQEVLDTRTDLTPAERRE 99

Query: 43  ----EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
                   + A   LV ++LRLVV IA  Y G GLP  +++ EGN+GL++AV+KFD + G
Sbjct: 100 YQTLAQDGMRAKQHLVNANLRLVVSIAKRYTGRGLPFLDLIQEGNMGLVRAVEKFDYQAG 159

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           F+ +TY+ WWIK ++   +  +   ++I           ++ R+    + +     +   
Sbjct: 160 FKFSTYASWWIKQSITRGMADTSRTIRIPVH-----TVEHINRINAVQRELAVELGRDPS 214

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           +  IA++ +   ++V  +  R     SL  L+  S  +       L+ D D  +   I+ 
Sbjct: 215 MEEIARESDTPVTKVRYLLDRAQEPMSLQVLVGGSGGDGDTEMADLIEDADVTQ--PIDV 272

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARA 276
             ++     + R +  L  R+  +   R       P +L  +S +  V+RERVRQIE + 
Sbjct: 273 VTQQLMAAHVMRLIDGLAERDAEVVRMRFGLAGLEPRSLAFVSQQLGVTRERVRQIEKKV 332

Query: 277 FKKVQ 281
             K++
Sbjct: 333 LAKLR 337


>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 =  216 bits (550), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 65/249 (26%), Positives = 113/249 (45%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 352 IGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 411

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         P+   
Sbjct: 412 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRVSRQMLQEMGREPTPD--- 466

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + + +V  +        S+   I   D   S   D++    D       +   
Sbjct: 467 ELAERVEMPKDKVRKVLKIAREPISMETPI--GDDEDSHLGDFV---EDAAVISPPDSAI 521

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
               R      ++ L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 522 FSGLRETTQLILAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 581

Query: 279 KVQESIQKQ 287
           K++   + +
Sbjct: 582 KLRHPSRSE 590


>gi|54294183|ref|YP_126598.1| RNA polymerase sigma factor RpoS [Legionella pneumophila str. Lens]
 gi|54297202|ref|YP_123571.1| RNA polymerase sigma factor RpoS [Legionella pneumophila str.
           Paris]
 gi|53750987|emb|CAH12398.1| RNA polymerase sigma factor RpoS [Legionella pneumophila str.
           Paris]
 gi|53754015|emb|CAH15486.1| RNA polymerase sigma factor RpoS [Legionella pneumophila str. Lens]
 gi|307609996|emb|CBW99528.1| RNA polymerase sigma factor RpoS [Legionella pneumophila 130b]
          Length = 341

 Score =  216 bits (550), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 79/270 (29%), Positives = 141/270 (52%), Gaps = 13/270 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A      GD+ A  +++ S+LRLVVKIA  Y   GLP+ ++
Sbjct: 74  YLGEIGFSPLLTAEEEIHYAT-LALKGDMEARKKMIESNLRLVVKIARRYLNRGLPLLDL 132

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM++V+KFDP+RGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 133 IEEGNLGLMKSVEKFDPKRGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 191

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +   Q + D+   PE++  +  K      +++ +N ++A   S++  I   +  S 
Sbjct: 192 LRAARQLTQKL-DHEPSPEEIAEMVDKPLEDVQKLLGLNDKVA---SVDTPIGFDETKS- 246

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
              D +  ++      L+  E   N R  +   +  L   ++++   R         TLE
Sbjct: 247 -LLDTIADENSLNPAELLTNE---NLRQHIESLLDKLTENQQQVIARRFGLRGFEKATLE 302

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ++  E +++RERVRQI+  A K ++  +++
Sbjct: 303 DVGKEIDLTRERVRQIQVEALKTLRTLLER 332


>gi|189501483|ref|YP_001957200.1| RNA polymerase sigma factor [Candidatus Amoebophilus asiaticus 5a2]
 gi|189496924|gb|ACE05471.1| RNA polymerase sigma factor, sigma-70 family [Candidatus
           Amoebophilus asiaticus 5a2]
          Length = 287

 Score =  216 bits (550), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 71/287 (24%), Positives = 142/287 (49%), Gaps = 13/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           + +  I       L +Y+ EI ++ +L  +EE  LAKR +  GD  A  +L  ++LR VV
Sbjct: 5   KISKQITNRESQSLDKYLQEIGRVDLLTPEEEVELAKRIK-SGDKIALEQLTKANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL +S++++EGN+GL+++ ++FD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 64  SVAKQYQNQGLSLSDLINEGNLGLIKSAQRFDETRGFKFISYAVWWIRQSILQALAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++            L +L      +     +      +A++L V+  E+         
Sbjct: 124 IVRLPLNR-----VGTLNKLSRTFSQLEQKYKREPTAEELAEELEVTPGEISDTMKISGR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     +++S         +    + ++ E   +      + R++S+L  RE  +
Sbjct: 179 HVSMDAPFVQGEEHSLLDVLEDDDEDKPDDTLIDESLCKD-----IERALSLLTEREAGV 233

Query: 243 FEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
                  +  NP+TLE + + F ++RERVRQI+ +A KK++     +
Sbjct: 234 ISYYFGLKGTNPMTLEEIGTRFNLTRERVRQIKEKAIKKLRHVASSK 280


>gi|301049496|ref|ZP_07196454.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 185-1]
 gi|300298727|gb|EFJ55112.1| RNA polymerase sigma factor RpoS [Escherichia coli MS 185-1]
          Length = 342

 Score =  216 bits (550), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 73  YLGEIGYSPLLTAKEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 131

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 132 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 190

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 191 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 245

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 246 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 301

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 302 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 332


>gi|260219679|emb|CBA26524.1| RNA polymerase sigma factor rpoS [Curvibacter putative symbiont of
           Hydra magnipapillata]
          Length = 340

 Score =  216 bits (550), Expect = 4e-54,   Method: Composition-based stats.
 Identities = 86/289 (29%), Positives = 145/289 (50%), Gaps = 8/289 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +  ++ S +  G   LS Y+  +R+ P+   ++E+ +A R R  GD +A   ++  +LRL
Sbjct: 48  IAEEDPSTLEQGPDALSVYLRGVRRTPLFTPEQEFEVATRAR-AGDFAARQSMIEHNLRL 106

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ IA GY G G+P+S+++ EGN+GLM A+ KF+PERGFR +TY+ WWI+ ++   ++  
Sbjct: 107 VISIAKGYAGRGVPMSDLIEEGNLGLMHAIDKFEPERGFRFSTYATWWIRQSVDRALMYQ 166

Query: 121 WSLVKIGTT-ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
              V++      + +     RRL  +   +     +  +V  IA  L     +V  +   
Sbjct: 167 GRAVRLPVNVVREVQQVLRARRLLENDAVLLAQRPEGIRVEDIAALLGRDAVDVTDLLAM 226

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
                SL+A  N +  +     D L               E      +L + ++ LNPRE
Sbjct: 227 AEAPRSLDAR-NDAGGDEHSLGDSLADTLAAAPDSTALAHEVD---ALLEQWIATLNPRE 282

Query: 240 RRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           + + EAR      +P TLE LS    ++RERVRQI+  A  K++  + +
Sbjct: 283 QEVLEARFGLHDRDPETLETLSERLGLTRERVRQIQNEALFKLKRYLAR 331


>gi|315137348|dbj|BAJ44507.1| RNA polymerase sigma factor RpoS [Escherichia coli DH1]
          Length = 330

 Score =  215 bits (549), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL +AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLTRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|305681000|ref|ZP_07403807.1| RNA polymerase sigma factor SigB [Corynebacterium matruchotii ATCC
           14266]
 gi|305659205|gb|EFM48705.1| RNA polymerase sigma factor SigB [Corynebacterium matruchotii ATCC
           14266]
          Length = 365

 Score =  215 bits (549), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 67/315 (21%), Positives = 142/315 (45%), Gaps = 39/315 (12%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAK--------------------RY 41
           +R+  +        +  Y++ I K  +L  ++E  LA+                    R 
Sbjct: 54  SRRGQNNDNPSADLVRVYLNGIGKTALLTAEDEVHLAQTIEVGLYAEYLLTDSDEPLTRA 113

Query: 42  REHG-------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           ++            A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD
Sbjct: 114 KKRDLKVLVKEGRKARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFD 173

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +GF+ +TY+ WWI+ A+   +      +++     ++     L R+K  +        
Sbjct: 174 YAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLSRIKREMYQQLGREA 231

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
             E    +A++  + ES++  +  +     SL+  + + ++  +   D++        + 
Sbjct: 232 TNE---ELAEESGIDESKIELLLRQSRDPVSLDMPVGADEE--APLGDFIEDSEAADAES 286

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
            +    R    + +   +  L  RE+ +   R   ++  P TL+ +  +F +SRERVRQI
Sbjct: 287 AVVASLR---HSDIRDVIGTLEDREQDVIRMRYGLDDGVPRTLDQIGRQFGLSRERVRQI 343

Query: 273 EARAFKKVQESIQKQ 287
           E    +K+++  + +
Sbjct: 344 EREVMRKLRDGQRAE 358


>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 =  215 bits (549), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 65/244 (26%), Positives = 117/244 (47%), Gaps = 12/244 (4%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            E   L A   ++ ++LRLV+ IA  Y   G+   +++ EGNIGLM+AV KF+  RG++ 
Sbjct: 418 AESKMLQAKREMIEANLRLVISIAKKYVNRGMHFLDLIQEGNIGLMKAVDKFEYRRGWKF 477

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY+ WW++ A+   +      ++I     +      L R+   +   T     P     
Sbjct: 478 STYATWWVRQAVTRSLADQARTIRIPVHMMES--INKLNRISREILQQTGREAHP---AV 532

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           +A+++ V E +V +M        SL   +   D+  +   D +    D       +   +
Sbjct: 533 LAQRMEVPEEKVRAMLKIGRQPLSLETPV--GDEADTTLSDVI---EDPMATSPADAAVQ 587

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKK 279
            N R  +  ++  L+PRE ++   R   +     TLE L  +F+++RER+RQIE++A +K
Sbjct: 588 ANLRAAINTALDALSPREAKVLRMRFGIDTASDCTLEELGKQFDLTRERIRQIESKAMRK 647

Query: 280 VQES 283
           +   
Sbjct: 648 LMHP 651


>gi|6463986|dbj|BAA86958.1| group 2 sigma factor RpoD4 [Synechococcus sp. PCC 7942]
          Length = 311

 Score =  215 bits (549), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 75/303 (24%), Positives = 145/303 (47%), Gaps = 33/303 (10%)

Query: 3   RKNMSIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYR------EHGDLS------ 48
           R+N++  V       +S Y+  I +IP+L  +EE  L+++ +      E+ D        
Sbjct: 6   RRNLNAAVERHTSDHVSWYLSSIGRIPLLTAEEEVELSRKVQLMMALLENPDAESNSENQ 65

Query: 49  --------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
                   A  +++ ++LRLVV +A   +  GL + +++ EG++GL +AV+KFDP  G++
Sbjct: 66  AVLQAGQRAKTKMLKANLRLVVSVAKKCQNQGLELLDLIQEGSLGLERAVEKFDPALGYK 125

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ +M   I      +++    ++K     + R+K   + +T    +     
Sbjct: 126 FSTYAYWWIRQSMTRAIDNHARTIRLPIHVSEK-----ISRIKKMTRELTHQLKRLPSRA 180

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            IA+ L +   +V  +  +     SL+A     D   S   D +    D +    ++  +
Sbjct: 181 EIAEALKLPLQDVEMLLSQSTPCTSLDAQAR-GDDGRSFLGDLIP---DPKSLEPMDAMD 236

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFK 278
           R  +   ++  ++ L  RE+++ + R         TL  +     VSRER+RQ+EARA +
Sbjct: 237 RHIQHEQISTWLAHLTEREQQVLQLRFGLHDGEQHTLAEIGRRLNVSRERIRQVEARALQ 296

Query: 279 KVQ 281
           K++
Sbjct: 297 KLR 299


>gi|108799144|ref|YP_639341.1| RNA polymerase sigma factor SigB [Mycobacterium sp. MCS]
 gi|119868259|ref|YP_938211.1| RNA polymerase sigma factor SigB [Mycobacterium sp. KMS]
 gi|126434752|ref|YP_001070443.1| RNA polymerase sigma factor SigB [Mycobacterium sp. JLS]
 gi|108769563|gb|ABG08285.1| RNA polymerase, sigma 28 subunit [Mycobacterium sp. MCS]
 gi|119694348|gb|ABL91421.1| RNA polymerase, sigma 70 subunit, RpoD family [Mycobacterium sp.
           KMS]
 gi|126234552|gb|ABN97952.1| RNA polymerase, sigma 70 subunit, RpoD family [Mycobacterium sp.
           JLS]
          Length = 319

 Score =  215 bits (549), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 66/312 (21%), Positives = 134/312 (42%), Gaps = 38/312 (12%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------- 43
            ++         +  Y++ I K  +L   +E  LAKR                       
Sbjct: 11  SDLDAQSPAADLVRVYLNGIGKTALLNAADEVELAKRIEAGLYAQHLLNTKKRLGESRKR 70

Query: 44  ------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
                     +A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +
Sbjct: 71  DLAAVVRDGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTK 130

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           GF+ +TY+ WWI+ A+   +      +++     ++     L R+K  +     N  +  
Sbjct: 131 GFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLARIKREMHQ---NLGREA 185

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A++  +   ++  +        SL+  + S ++  +   D++    D +      
Sbjct: 186 TDEELAEESGIPAEKIADLLEHSRDPVSLDMPVGSDEE--APLGDFI---EDAEAMSAEN 240

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
               +     +   ++ L+ RE+++   R   ++  P TL+ +   F +SRERVRQIE  
Sbjct: 241 AVISELLHTDIRHVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERE 300

Query: 276 AFKKVQESIQKQ 287
              K++   +  
Sbjct: 301 VMAKLRNGERAD 312


>gi|284104060|ref|ZP_06386126.1| RNA polymerase, sigma 70 subunit, RpoD family [Candidatus
           Poribacteria sp. WGA-A3]
 gi|283830219|gb|EFC34468.1| RNA polymerase, sigma 70 subunit, RpoD family [Candidatus
           Poribacteria sp. WGA-A3]
          Length = 271

 Score =  215 bits (549), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 81/274 (29%), Positives = 147/274 (53%), Gaps = 13/274 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI +I ++   EE  LA+R ++ GD  A  +L  ++LR VV +A  ++G GL +
Sbjct: 2   LDQYLKEIGQIDLVTPAEEAELARRIKQ-GDEEALLKLTRANLRFVVSVAKKFQGQGLHL 60

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           +++++EGN GL++A K+FD  RGF+  +Y++WWI+ ++ + +     +V++    NQ   
Sbjct: 61  TDLINEGNYGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQGRVVRLP--LNQIGT 118

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              +R+    L    + +   E    +A  L +   +V S   R A   S++A  N  D+
Sbjct: 119 ISKIRKSSARLAQEHERDPNLE---ELATDLQIDIEKVRSAMQRTARHLSMDAPFNEEDE 175

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPV 253
           NS    D L  +        +  E  K    +   ++S L PRE  I        +E+P+
Sbjct: 176 NS--LLDVLPSNEIAPPDEPLRGESLKIDIEV---ALSSLCPREAEITRLYFGVGREHPL 230

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           TLE +   F+++RERVRQI+ +A +K+++  +++
Sbjct: 231 TLEEIGLRFDLTRERVRQIKEKALRKLRQKHRRE 264


>gi|6010726|gb|AAF01229.1|AF184098_1 mutant RpoS [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
          Length = 330

 Score =  215 bits (549), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVQKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|24214932|ref|NP_712413.1| RNA polymerase sigma-70 factor [Leptospira interrogans serovar Lai
           str. 56601]
 gi|45657567|ref|YP_001653.1| RNA polymerase sigma-70 factor [Leptospira interrogans serovar
           Copenhageni str. Fiocruz L1-130]
 gi|26399555|sp|P59117|RPOD_LEPIN RecName: Full=RNA polymerase sigma factor rpoD
 gi|47605974|sp|P61540|RPOD_LEPIC RecName: Full=RNA polymerase sigma factor rpoD
 gi|24195965|gb|AAN49431.1|AE011394_5 RNA polymerase sigma-70 factor [Leptospira interrogans serovar Lai
           str. 56601]
 gi|45600806|gb|AAS70290.1| RNA polymerase sigma-70 factor [Leptospira interrogans serovar
           Copenhageni str. Fiocruz L1-130]
          Length = 585

 Score =  215 bits (549), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 59/242 (24%), Positives = 117/242 (48%), Gaps = 12/242 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   LV ++LRLVV IA  Y   G+   +++ EGNIGL++AV KF+ ++G++ +TY+ W
Sbjct: 346 QAKKELVKANLRLVVSIAKRYANRGMHFFDLIQEGNIGLIKAVDKFEYKKGYKFSTYATW 405

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++        +   + ++    +       +      IA++L 
Sbjct: 406 WIRQAITRAISDQARTIRVPVH-----MIEQVNKVIRETRLFIQEFGRDPNNEEIAERLG 460

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
               +V  +        SL   + S  +  S+  D++    D + +  +           
Sbjct: 461 WPVQKVKMVKNVAREPISLEIPVGS--EEDSELGDFIP---DTEVETPVNAAASSILAEQ 515

Query: 228 LTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + + +  L  RE+++   R   ++  P TLE +  +F+V+RER+RQIEA+A ++++   +
Sbjct: 516 IRQVLHTLPAREQKVIRMRFGLDDGYPQTLEEVGYQFKVTRERIRQIEAKALRRLRHPSR 575

Query: 286 KQ 287
            +
Sbjct: 576 SK 577



 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 14/62 (22%), Positives = 29/62 (46%), Gaps = 1/62 (1%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +++ +     E  +  Y+ EI K+ ++  + E  LAKR  E G+      +++S +    
Sbjct: 84  KESSASTSGSEDPIKLYLREIGKVSLISGETEVFLAKRI-EKGEKIIEETILSSSILRAN 142

Query: 63  KI 64
            I
Sbjct: 143 YI 144


>gi|83272624|gb|ABC00797.1| RpoS [Escherichia coli]
          Length = 330

 Score =  215 bits (549), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNPTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|441116|gb|AAA61628.1| RNA polymerase sigma factor [Salmonella enterica subsp. enterica
           serovar Typhimurium]
 gi|1090521|prf||2019251A RNA polymerase sigma factor
          Length = 330

 Score =  215 bits (549), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-DLRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|330721381|gb|EGG99448.1| RNA polymerase sigma factor RpoS [gamma proteobacterium IMCC2047]
          Length = 321

 Score =  215 bits (549), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 81/271 (29%), Positives = 132/271 (48%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R    GD +   R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 52  YLNEIGFSPLLSAEEEVYYA-RLALKGDEAGRKRMIESNLRLVVKISRRYVNRGLTLLDL 110

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 111 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHVV-KELNVY 169

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +T           IA+ L+     V  M        S++A +    + S 
Sbjct: 170 LRAAR----ELTQKLDHEPSAEEIAEMLDRPVENVKRMLKLNERVTSIDAPMGGDSERSM 225

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                     D       E  +  N    LT  +  L+ ++R +   R   L     TLE
Sbjct: 226 AENITGENVDD-----PSELLQNDNLHGNLTHWLGELSEKQREVIARRFGLLGYEMSTLE 280

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            + SE  ++RERVRQI+  A K+++  ++K+
Sbjct: 281 QVGSEIGLTRERVRQIQVEALKRLRAVMEKE 311


>gi|312139424|ref|YP_004006760.1| sigma-70 factor sigb [Rhodococcus equi 103S]
 gi|325672687|ref|ZP_08152383.1| RNA polymerase principal sigma factor SigB [Rhodococcus equi ATCC
           33707]
 gi|311888763|emb|CBH48075.1| sigma-70 factor SigB [Rhodococcus equi 103S]
 gi|325556564|gb|EGD26230.1| RNA polymerase principal sigma factor SigB [Rhodococcus equi ATCC
           33707]
          Length = 322

 Score =  215 bits (549), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 64/297 (21%), Positives = 132/297 (44%), Gaps = 38/297 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYRE--------------------------HGDLSAAHR 52
           Y++ I +  +L   +E  LA+R                                 +A   
Sbjct: 29  YLNGIGRTALLTAADEVDLARRIEAGLYAAHVLATKKRLTAAKKRDLATIVRDGEAARRH 88

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A
Sbjct: 89  LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTYATWWIRQA 148

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +      +++     ++     L R+K  L          E    ++++  + E +
Sbjct: 149 ITRGMADQSRTIRLPVHLVEQ--VNKLARIKRELHQQLGREATDE---ELSQESGIPEHK 203

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           +  +        SL+  + + ++  +   D++    D +              + +   +
Sbjct: 204 IADLLDHSRDPVSLDMPVGNDEE--APLGDFI---EDSEATSAENAVIAGLLHSDVRSVL 258

Query: 233 SVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           + L+ RE+++   R   ++  P TL+ +   F +SRERVRQIE     K+++  +  
Sbjct: 259 ATLDEREQQVIRLRYGLDDGQPRTLDQIGKLFGLSRERVRQIEREVMGKLRQGERAD 315


>gi|295103972|emb|CBL01516.1| RNA polymerase sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii SL3/3]
          Length = 457

 Score =  215 bits (549), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 72/255 (28%), Positives = 125/255 (49%), Gaps = 14/255 (5%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L ++    L K  R+   L+A   L  ++LRLVV IA  + G+ L   +++ EGNIGL+
Sbjct: 201 PLSEERRQELLKTRRDG--LNARRSLSEANLRLVVSIAKKHVGHNLAFLDLIQEGNIGLI 258

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +A +KFD +RGFR +TY+ WWI+ A+   I      ++I     +      + R++    
Sbjct: 259 KAAEKFDCDRGFRFSTYATWWIRQAITRAIADQARTIRIPVHMVE-----TINRMRQATN 313

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
            +   N        +AK +++S   V  +        SL + +   ++  S   D++   
Sbjct: 314 QLVYQNGHEPTPEELAKAMDMSVERVREIQRMAQEPASLESPV--GEEEDSSLGDFVA-- 369

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVS 265
            D   +   +  +R      +  ++  L PRE ++   R   ++  P TLE +  +F V+
Sbjct: 370 -DENAEAPGKAADRAMVAQQINLALKSLTPREEKVIRLRFGLDDGRPRTLEEVGRDFGVT 428

Query: 266 RERVRQIEARAFKKV 280
           RERVRQIEA+A +K+
Sbjct: 429 RERVRQIEAKAIRKL 443



 Score = 41.0 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 13/41 (31%), Positives = 23/41 (56%), Gaps = 2/41 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRL 53
           +  +  Y+ +I +IP+L  ++E  L++R   H    AAH L
Sbjct: 100 DDPVKNYLKQIGQIPLLSAEQEVELSRRI--HAGAEAAHIL 138


>gi|108803849|ref|YP_643786.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108765092|gb|ABG03974.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 289

 Score =  215 bits (549), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 88/267 (32%), Positives = 143/267 (53%), Gaps = 12/267 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y   I K  +L  QEE  L++R ++ GD  A  +L+  +LRLVV +A  YRGYGLP  ++
Sbjct: 22  YFARIDKGELLTHQEEIELSRRAKK-GDRKARQKLIEKNLRLVVSVAKKYRGYGLPFEDL 80

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM+AV+KFDPERGFR +TY+ WWI+ A+Q  +      +++     +K     
Sbjct: 81  IQEGNIGLMKAVEKFDPERGFRFSTYATWWIRQAVQRAVADKGRTIRVPVHMTEK----- 135

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           +R++      ++    +      +A+ L  +  EV  +   +    SLN  + SSD++SS
Sbjct: 136 IRKMARTYNELSAQLEREPTDEEVAEALGWTPEEVREVKGAMPDATSLNQPL-SSDEDSS 194

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLE 256
           +  +++  +        + ++        L +++  L  R R +   R   ++  P TL 
Sbjct: 195 EIGEFVEDERASDTAGAVARDIEN---AALRKAIERLPERNRHVLVRRYGLDDREPATLA 251

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQES 283
            LS E  VSRERVRQ++  A + +QES
Sbjct: 252 ELSEELGVSRERVRQLQREAERMIQES 278


>gi|111023771|ref|YP_706743.1| RNA polymerase sigma factor SigB [Rhodococcus jostii RHA1]
 gi|110823301|gb|ABG98585.1| sigma factor, sigma 70 type, group 2 (proven non-essential)
           [Rhodococcus jostii RHA1]
          Length = 323

 Score =  215 bits (549), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 66/311 (21%), Positives = 137/311 (44%), Gaps = 38/311 (12%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR---------EHG---------- 45
           ++         +  Y++ I +  +L   +E  L+KR           E G          
Sbjct: 16  DLDAQSPAADLVRVYLNGIGRTALLTAADEVELSKRIEAGLYAAHILETGKRLSPAKKRD 75

Query: 46  -------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
                    SA   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +G
Sbjct: 76  LATVVREGQSARAHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYAKG 135

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           F+ +TY+ WWI+ A+   +      +++     ++     L R+K  L        +   
Sbjct: 136 FKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLARIKRELHQ---QLGREAT 190

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              +A++  +   ++  +        SL+  + + ++  +   D++    D +       
Sbjct: 191 DDELAEESGIPAHKIADLLDHSRDPVSLDMPVGNDEE--APLGDFI---EDSEATSAENA 245

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARA 276
                  + +   ++ L+ RE+++   R   ++  P TL+ +   F +SRERVRQIE   
Sbjct: 246 VIAGLLHSDVRSVLATLDEREQQVIRLRYGLDDGQPRTLDQIGKLFGLSRERVRQIEREV 305

Query: 277 FKKVQESIQKQ 287
             K+++  + +
Sbjct: 306 MGKLRQGDRAE 316


>gi|269123355|ref|YP_003305932.1| RNA polymerase, sigma 32 subunit, RpoH [Streptobacillus
           moniliformis DSM 12112]
 gi|268314681|gb|ACZ01055.1| RNA polymerase, sigma 32 subunit, RpoH [Streptobacillus
           moniliformis DSM 12112]
          Length = 280

 Score =  215 bits (549), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 81/288 (28%), Positives = 147/288 (51%), Gaps = 15/288 (5%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M     +   N    +S YI +++   +L  +EE  L KR RE  D  A H L+ S+LRL
Sbjct: 1   MKNDKTNSSDNNINLISLYISDLQNHELLTSEEEVELFKRVREENDEQAKHLLILSNLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV  A    G G+P+ +++SEGN+GL++++ KFD  +G R +TY++WWIK  +++ I+  
Sbjct: 61  VVSEAKKLLGNGMPLIDLISEGNLGLIKSIDKFDYTKGLRFSTYAVWWIKQTIKKSIVNL 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I +       +  L ++   +++  +          IA+ L +  S+V+ +    
Sbjct: 121 GRDIRIPSYK-----YEQLSKVNKVIESYQNEFGDIPTAEYIAEVLGMKPSKVVLLQNEF 175

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SLN  I  +      + + ++   D  E  +I  ++     N+  +    LNPRE+
Sbjct: 176 QEIISLNDAIGDN-----IFLEDVIGQSDNVEDDIIRNDQLSEMYNLFDK---TLNPREK 227

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            I E R    N    TL+ +  +  ++RERVRQIE +A  K+++++++
Sbjct: 228 EILELRYGLANNKIHTLKEIGEKLSITRERVRQIEKKAITKLKKNLEE 275


>gi|309792450|ref|ZP_07686915.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Oscillochloris
           trichoides DG6]
 gi|308225522|gb|EFO79285.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Oscillochloris
           trichoides DG6]
          Length = 311

 Score =  215 bits (549), Expect = 5e-54,   Method: Composition-based stats.
 Identities = 85/311 (27%), Positives = 143/311 (45%), Gaps = 39/311 (12%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLA---------------------- 38
           M     +  +  E  +  Y++EI   P+L   +E  LA                      
Sbjct: 1   MTTSAFATPLPTE-SIILYLNEIGDEPLLTFDQEQHLAAQIEAGREAARRLADEHPFTPS 59

Query: 39  KRYRE----HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           +R+R     H   +A  +L+ S+LRLVV IA  Y+G+GL + +++ EG++GLM+AV KFD
Sbjct: 60  ERWRLEQQVHAGANARAQLINSNLRLVVSIARRYQGHGLSLLDLIQEGSLGLMRAVDKFD 119

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P RG + +TY+ +WI+ ++   I      V++     ++     L R +  L    D + 
Sbjct: 120 PSRGLKFSTYATYWIRQSVGRAIADHGRTVRLPVHLGER--LSRLARARQRLTQRLDRDP 177

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            PE+V   A +L ++  +V           SL+     SD  +    + +    D  E  
Sbjct: 178 TPEEV---ADELGITTDQVTRAEQAALTPASLDET--HSDDGTGALAEVI---SDPLEPT 229

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQI 272
            ++       R+ L  +MS L  RER I   R   E    +TLE +     ++RERVRQ+
Sbjct: 230 PLDHVAHGLLRDDLCEAMSHLTQRERSILNLRYGLEGETALTLEQIGQRLSLTRERVRQL 289

Query: 273 EARAFKKVQES 283
           E+ A +K+++ 
Sbjct: 290 ESEALRKLRDP 300


>gi|23428544|gb|AAL11451.1| RNA polymerase sigma-38 subunit [Serratia plymuthica]
          Length = 331

 Score =  215 bits (549), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 62  YLGEIGYSPLLTAEEEVYFARR-ALRGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 120

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 121 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 179

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +     +  
Sbjct: 180 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPL--GGDSEK 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  + D   +   +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ALLDILADEKDNGPE---DTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 290

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 291 DVGREIGLTRERVRQIQVEGLRRLREILQLQ 321


>gi|298248273|ref|ZP_06972078.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
            racemifer DSM 44963]
 gi|297550932|gb|EFH84798.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
            racemifer DSM 44963]
          Length = 1341

 Score =  215 bits (549), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 68/292 (23%), Positives = 132/292 (45%), Gaps = 35/292 (11%)

Query: 14   IGLSRYIHEIRKIPMLEKQEEYVLAKRYR----------EHGDLS------------AAH 51
              L +Y  EI + P+L  ++E  LA + +          + G+ S            A  
Sbjct: 1047 DSLRQYFREITQFPLLNAEQEKKLAHQIKFGQQAKEELEKRGEASSYIHVRIQQGKIARE 1106

Query: 52   RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            +L+  +LRLV+ +A  Y   G  + +++ EGN+GL++A +KFD ++G+R +TY+ WWI+ 
Sbjct: 1107 KLIEHNLRLVISVAKKYARVGRQLEDLIQEGNLGLIRACEKFDTDKGYRFSTYATWWIRQ 1166

Query: 112  AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            A+   +      +++        L   L +L    + +     +   +  +AK  N+   
Sbjct: 1167 AITRSLAEQSRTIRLPVY-----LVEKLHQLHRGQRDLELQLGREPTLEELAKHQNLDID 1221

Query: 172  EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
            +V           SL+A I    +  +   + +       ++ +    +    +  +++ 
Sbjct: 1222 KVQEYLVLRQQILSLDAPI--GAEQETTLGEMIEQPRSDPQENINNYAD----KEAVSQL 1275

Query: 232  MSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            M  L  R+RR+   R   E+     LE + S   V+RERVRQIE +A ++++
Sbjct: 1276 MQNLTERQRRVISLRFGLEDGKIHKLEEIGSMLNVTRERVRQIEEKALRQLK 1327


>gi|29840756|ref|NP_829862.1| RNA polymerase sigma factor [Chlamydophila caviae GPIC]
 gi|29835106|gb|AAP05740.1| RNA polymerase sigma factor, sigma-70 family [Chlamydophila caviae
           GPIC]
          Length = 572

 Score =  215 bits (549), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 69/255 (27%), Positives = 122/255 (47%), Gaps = 13/255 (5%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             + +R+ +     A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+
Sbjct: 304 VRMLQRWMDK-SQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFE 362

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             RG++ +TY+ WWI+ A+   I      ++I        +   + ++    + +     
Sbjct: 363 YRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVH-----MIETINKVLRGAKKLMMETG 417

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           K      +A++L ++   V  +        SL A +   +   S + D+L    D   + 
Sbjct: 418 KEPTPEELAEELGLTPDRVREIYKIAQHPISLQAEV--GEGGESSFGDFL---EDTGVES 472

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQI 272
             E       ++ +   +  L  RER +   R   L   P TLE + S F V+RER+RQI
Sbjct: 473 PAEATGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGKPKTLEEVGSAFNVTRERIRQI 532

Query: 273 EARAFKKVQESIQKQ 287
           EA+A +K++  I+ +
Sbjct: 533 EAKALRKMRHPIRSK 547



 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 8/32 (25%), Positives = 19/32 (59%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREH 44
           +  +  Y+ E+  +P+L ++EE  ++KR  + 
Sbjct: 100 DDPVRMYLKEMGTVPLLTREEEVEISKRIEKA 131


>gi|58698250|ref|ZP_00373169.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of
           Drosophila ananassae]
 gi|58535222|gb|EAL59302.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of
           Drosophila ananassae]
          Length = 270

 Score =  215 bits (549), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 72/260 (27%), Positives = 124/260 (47%), Gaps = 15/260 (5%)

Query: 32  QEEYVLAKRYREHGDL--SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           QE   L KR ++H      A   ++ ++LRLVV IA  Y   GL + +++ EGNIGLM+A
Sbjct: 14  QEFKELIKRIQKHEREVSEAKQEMIKANLRLVVSIAKKYSKRGLDLLDLIQEGNIGLMKA 73

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V KFD +RG++ +TY  WW++ ++   I     +V+I     +      + ++   L+ +
Sbjct: 74  VDKFDYKRGYKFSTYGTWWVRQSITRAIPEQSKVVRIPVHMVEI-----ISKINRALRKM 128

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
           T    +   +  ++ +L +    +  +        SL A     D  SS + D +    D
Sbjct: 129 THEMGREPTLEELSVELTMPLERIRKVMKIARDPVSLEAPTGKDD--SSTFGDCI---ED 183

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSR 266
            +     +     + R + T  ++ L P+E RI   R          TLE +   F V+R
Sbjct: 184 KRVSRPEDAAILADLRGITTNVLATLTPKEERILRMRFGLGKDGKEHTLEEVGKIFNVTR 243

Query: 267 ERVRQIEARAFKKVQESIQK 286
           ER+RQIEA+A +K++   + 
Sbjct: 244 ERIRQIEAKALRKLKHPSRA 263


>gi|82545186|ref|YP_409133.1| RNA polymerase sigma factor RpoS [Shigella boydii Sb227]
 gi|81246597|gb|ABB67305.1| RNA polymerase sigma S factor [Shigella boydii Sb227]
 gi|332092174|gb|EGI97252.1| RNA polymerase sigma factor RpoS [Shigella boydii 3594-74]
          Length = 331

 Score =  215 bits (549), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 137/271 (50%), Gaps = 12/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE V   R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEEVYFARRALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 120

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 121 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 179

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 180 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 234

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 235 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 290

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 291 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 321


>gi|169630111|ref|YP_001703760.1| RNA polymerase sigma factor SigB [Mycobacterium abscessus ATCC
           19977]
 gi|169242078|emb|CAM63106.1| RNA polymerase sigma factor [Mycobacterium abscessus]
          Length = 323

 Score =  215 bits (549), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 64/312 (20%), Positives = 136/312 (43%), Gaps = 38/312 (12%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------- 43
           +++         +  Y++ I K  +L  ++E  LAKR                       
Sbjct: 15  EDLDAQSPAADLVRVYLNGIGKTALLTAEDEVELAKRIEAGLYAQHLLDTKKRLGEARKK 74

Query: 44  ------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
                     +A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +
Sbjct: 75  DLAVIVREGNAARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYAK 134

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           GF+ +TY+ WWI+ A+   +      +++     ++     L R+K  L        +  
Sbjct: 135 GFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLARIKRELHQ---RLGREA 189

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A++  +   ++  +        SL+  + + ++  +   D++    D +      
Sbjct: 190 SDEELAEESGIPVEKIGDLLDHSRDPVSLDMPVGTDEE--APLGDFI---EDTEAMSAEN 244

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEAR 275
               +   + +   ++ L+ RE+++   R   ++    TL+ +   F +SRERVRQIE  
Sbjct: 245 AVIAELLHSDVRSVLATLDEREQQVIRLRYGLDDGQARTLDQIGKLFGLSRERVRQIERE 304

Query: 276 AFKKVQESIQKQ 287
              K++   + +
Sbjct: 305 VMAKLRHGDRAE 316


>gi|87123382|ref|ZP_01079233.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9917]
 gi|86169102|gb|EAQ70358.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9917]
          Length = 293

 Score =  215 bits (548), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 78/290 (26%), Positives = 142/290 (48%), Gaps = 31/290 (10%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLA--------------------KRYREHGDLSAAHRL 53
             +  Y+  I ++P+L   EE  LA                    +R++      A  R+
Sbjct: 4   DSIGYYLSSIGRVPLLTAAEEIELAHHVQAMKQLLELPEAERTPRQRHQIRMGKRARDRM 63

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           + ++LRLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+  M
Sbjct: 64  MAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGM 123

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
              I  S   +++    ++K     L +++   + ++    +    + +A  + +   ++
Sbjct: 124 TRAIDNSARTIRLPIHISEK-----LSKMRRISRELSHRFGRQPNRLELAHAMGIEPKDL 178

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             +  + A   SL+A     +  S+  +  L+ D +G E   +E  +R  ++  L   ++
Sbjct: 179 EDLISQSAPCASLDAHARGEEDRSTLGE--LIPDPNGAE--PMEGMDRSIQKEHLGGWLA 234

Query: 234 VLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            LN RE++I   R     E P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 235 QLNDREQKILRLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 284


>gi|319441590|ref|ZP_07990746.1| RNA polymerase sigma factor SigB [Corynebacterium variabile DSM
           44702]
          Length = 397

 Score =  215 bits (548), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 69/297 (23%), Positives = 138/297 (46%), Gaps = 38/297 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR---------EHGDL-----------------SAAHR 52
           Y++ I K  +L   +E  L++R           E G+                  +A   
Sbjct: 104 YLNGIGKTALLTAADEVELSQRIEAGLYAEHLLETGEKLTRARKRDLKILAREGRAARTH 163

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A
Sbjct: 164 LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTYATWWIRQA 223

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +      +++     ++     L R+K  +          E    +A++  + ES+
Sbjct: 224 ITRGMADQSRTIRLPVHLVEQ--VNKLSRIKREMYQHLGREATNE---ELAEESGIDESK 278

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           + ++  +     SL+  + S ++  +   D++        +  +    R    + +   +
Sbjct: 279 IETLLKQSRDPVSLDMPVGSDEE--APLGDFIEDSDSTDAEAAVVASLR---HSDVRAVL 333

Query: 233 SVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             L  RE+ + + R   ++  P TL+ +   F +SRERVRQIE     K++E  + +
Sbjct: 334 DTLEEREQDVIKLRYGLDDGMPRTLDQIGRSFGLSRERVRQIEREVMAKLREGERAE 390


>gi|226366207|ref|YP_002783990.1| RNA polymerase sigma factor SigB [Rhodococcus opacus B4]
 gi|226244697|dbj|BAH55045.1| RNA polymerase sigma factor SigB [Rhodococcus opacus B4]
 gi|254553060|dbj|BAH85842.1| RNA polymerase sigma B factor [Rhodococcus opacus]
          Length = 323

 Score =  215 bits (548), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 66/311 (21%), Positives = 137/311 (44%), Gaps = 38/311 (12%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR---------EHG---------- 45
           ++         +  Y++ I +  +L   +E  L+KR           E G          
Sbjct: 16  DLDAQSPAADLVRVYLNGIGRTALLTAADEVELSKRIEAGLYAAHILETGKRLSPAKKRD 75

Query: 46  -------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
                    SA   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +G
Sbjct: 76  LATVVREGQSARAHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYAKG 135

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           F+ +TY+ WWI+ A+   +      +++     ++     L R+K  L        +   
Sbjct: 136 FKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLARIKRELHQ---QLGREAT 190

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              +A++  +   ++  +        SL+  + + ++  +   D++    D +       
Sbjct: 191 DDELAEESGIPAHKIADLLDHSRDPVSLDMPVGNDEE--APLGDFI---EDSEATSAENA 245

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARA 276
                  + +   ++ L+ RE+++   R   ++  P TL+ +   F +SRERVRQIE   
Sbjct: 246 VIAGLLHSDVRTVLATLDEREQQVIRLRYGLDDGQPRTLDQIGKLFGLSRERVRQIEREV 305

Query: 277 FKKVQESIQKQ 287
             K+++  + +
Sbjct: 306 MGKLRQGDRAE 316


>gi|160942567|ref|ZP_02089814.1| hypothetical protein FAEPRAM212_00042 [Faecalibacterium prausnitzii
           M21/2]
 gi|158446151|gb|EDP23154.1| hypothetical protein FAEPRAM212_00042 [Faecalibacterium prausnitzii
           M21/2]
          Length = 457

 Score =  215 bits (548), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 72/255 (28%), Positives = 125/255 (49%), Gaps = 14/255 (5%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L ++    L K  R+   L+A   L  ++LRLVV IA  + G+ L   +++ EGNIGL+
Sbjct: 201 PLSEERRQELLKTRRDG--LNARRSLSEANLRLVVSIAKKHVGHNLAFLDLIQEGNIGLI 258

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +A +KFD +RGFR +TY+ WWI+ A+   I      ++I     +      + R++    
Sbjct: 259 KAAEKFDCDRGFRFSTYATWWIRQAITRAIADQARTIRIPVHMVE-----TINRMRQATN 313

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
            +   N        +AK +++S   V  +        SL + +   ++  S   D++   
Sbjct: 314 QLVYQNGHEPTPEELAKAMDMSVERVREIQRMAQEPASLESPV--GEEEDSSLGDFVA-- 369

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVS 265
            D   +   +  +R      +  ++  L PRE ++   R   ++  P TLE +  +F V+
Sbjct: 370 -DENAEAPGKAADRAMVAQQINLALKSLTPREEKVIRLRFGLDDGRPRTLEEVGRDFGVT 428

Query: 266 RERVRQIEARAFKKV 280
           RERVRQIEA+A +K+
Sbjct: 429 RERVRQIEAKAIRKL 443



 Score = 41.0 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 13/41 (31%), Positives = 23/41 (56%), Gaps = 2/41 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRL 53
           +  +  Y+ +I +IP+L  ++E  L++R   H    AAH L
Sbjct: 100 DDPVKNYLKQIGQIPLLSAEQEVELSRRI--HAGAEAAHIL 138


>gi|158340427|ref|YP_001521783.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158310668|gb|ABW32282.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 273

 Score =  215 bits (548), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 74/282 (26%), Positives = 144/282 (51%), Gaps = 15/282 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
                Y+ EI + P+L  +EE  LA++ +  G+L A  R++  +LRLVV IA  ++  GL
Sbjct: 5   DSTGAYLKEIGRYPLLSHEEEIQLARQAK-AGNLRAKQRMIECNLRLVVSIAKKHQNRGL 63

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P  +++ EG+IGL +AV+KF+PE+G+R +TY+ WWI+  +   I  +  ++++     Q 
Sbjct: 64  PFMDLIQEGSIGLSRAVEKFEPEQGYRFSTYAYWWIRQGITRSIQNNSRVIRLPVWHWQ- 122

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                  ++K   + ++    +   +  +A+ + +   ++      L    SL+  +   
Sbjct: 123 ----TGNQIKQTQRQLSQEFGREPTLAELAEAMEIDLDKLKQNMHHLQDVLSLDMQVGKE 178

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
                  QD  + +    EQ      E  N+   ++  +S+L+ R+R +   R   E+  
Sbjct: 179 -------QDTTLGELIEAEQSTPTHLELLNQSEEVSSYLSLLDERQRYVIVQRYGLEDGE 231

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
             T++++  +  VSRER+RQI  +A KK+Q++     E+ ++
Sbjct: 232 AKTMQDIGQQLGVSRERIRQIINKAMKKLQKNSDLATEIKTA 273


>gi|313886597|ref|ZP_07820310.1| putative RNA polymerase sigma factor RpoD [Porphyromonas
           asaccharolytica PR426713P-I]
 gi|332300881|ref|YP_004442802.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Porphyromonas
           asaccharolytica DSM 20707]
 gi|312923953|gb|EFR34749.1| putative RNA polymerase sigma factor RpoD [Porphyromonas
           asaccharolytica PR426713P-I]
 gi|332177944|gb|AEE13634.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Porphyromonas
           asaccharolytica DSM 20707]
          Length = 286

 Score =  215 bits (548), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 74/282 (26%), Positives = 138/282 (48%), Gaps = 12/282 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           + N SI       L RY+ EI +  ++  +EE  LA+     G+  A ++LV ++LR VV
Sbjct: 5   KINQSITNRESASLDRYLQEIGRTSLISPEEEVELAREIH-RGNRRALNKLVEANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGNIG+++A +KFD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 64  SVAKQYQNQGLSLPDLINEGNIGMIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    NQ  L   + +     + +      P     IA +L + E ++         
Sbjct: 124 IVRLP--LNQVGLQQKMNKAIVKFEQLNGRRPSP---QEIAAELELPEDKIREALKVQGK 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
            +SL+A     + N+      +  D    +  LI +         + R +  L  RE  +
Sbjct: 179 HQSLDAPFVEGEDNNM-LDVLVNEDTPSTDSSLINESLSAE----IDRILDQLGDREAEV 233

Query: 243 FEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
                    P +TLE +    ++SRERVRQI+ +A +++++S
Sbjct: 234 LRCFFGIGCPEMTLEEIGERTKLSRERVRQIKEKAIRRLKQS 275


>gi|86610159|ref|YP_478921.1| RNA polymerase sigma factor SigC [Synechococcus sp.
           JA-2-3B'a(2-13)]
 gi|86558701|gb|ABD03658.1| RNA polymerase sigma-70 factor family [Synechococcus sp.
           JA-2-3B'a(2-13)]
          Length = 366

 Score =  215 bits (548), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 72/316 (22%), Positives = 142/316 (44%), Gaps = 59/316 (18%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHG--------------------------------- 45
           Y+ EI ++P+L + EE  LA++ +++                                  
Sbjct: 51  YLQEIGRVPLLGRDEEVALAQKVQDYMKLLDLRLRLQKELGRDPTLAEWVAKANQYPEWA 110

Query: 46  -------------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A   ++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV+K
Sbjct: 111 QLTPEKLQQIQRIGKRAKEHMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEK 170

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FDP++G+R +TY+ WWI+  +   I      +++     +K     L ++K   + ++  
Sbjct: 171 FDPKKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEK-----LNKIKKAQRKLSQE 225

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +   +  IA +L ++  +V  +  R+    SL   +       ++  D L  D    E
Sbjct: 226 KGRTPTIEDIASELEMTPPQVRELLVRVPRSVSLETKV--GKDKDTELGDLLETDDISPE 283

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT--LENLSSEFEVSRERVR 270
           + ++ +   ++    L + +S L  RER +   R    +  T  L  +    ++SRERVR
Sbjct: 284 ETMMREALHRD----LQQLLSDLTSRERDVIRMRFGLGDGRTYSLAEIGRALDLSRERVR 339

Query: 271 QIEARAFKKVQESIQK 286
           QIEA+A +K+++  ++
Sbjct: 340 QIEAKALQKLRQPKRR 355


>gi|213859421|ref|ZP_03385125.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. M223]
          Length = 319

 Score =  215 bits (548), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 77/269 (28%), Positives = 137/269 (50%), Gaps = 13/269 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           ++  E  ++RERVRQI+    ++++E +Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQ 318


>gi|254430144|ref|ZP_05043847.1| RNA polymerase sigma factor [Cyanobium sp. PCC 7001]
 gi|197624597|gb|EDY37156.1| RNA polymerase sigma factor [Cyanobium sp. PCC 7001]
          Length = 318

 Score =  215 bits (548), Expect = 6e-54,   Method: Composition-based stats.
 Identities = 79/290 (27%), Positives = 140/290 (48%), Gaps = 31/290 (10%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLA------KRYRE--------------HGDLSAAHRL 53
             +  Y+  I ++P+L   EE  LA      KR +E                   A  R+
Sbjct: 29  DSIGWYLSNIGRVPLLTPAEEIELAHHVQAGKRLQEVPLEELTPKQKRQIRMAQRARDRM 88

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           + ++LRLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+  M
Sbjct: 89  MAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGM 148

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
              I  S   +++    ++K     L +++   + ++    +    + ++  +++   E+
Sbjct: 149 TRAIDNSARTIRLPIHISEK-----LSKMRRITRELSHRLGRQPNRLELSHAMDMRPEEL 203

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             +  + A   SL+A     +  S+  +  L+ D    E    +  +R  ++  L   +S
Sbjct: 204 EELMAQSAPCASLDAHARGDEDRSTLGE--LIADPASNEHF--DSMDRHIQKEHLGAWLS 259

Query: 234 VLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            LN RE++I + R   E   P+TL  +     VSRERVRQ+EA+A  K++
Sbjct: 260 QLNEREQKIIKLRFGLEGSEPLTLAEIGRLINVSRERVRQLEAKAIMKLR 309


>gi|208821597|ref|ZP_03261917.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4042]
 gi|218690868|ref|YP_002399080.1| RNA polymerase sigma factor RpoS [Escherichia coli ED1a]
 gi|260856852|ref|YP_003230743.1| RNA polymerase, sigma S factor [Escherichia coli O26:H11 str.
           11368]
 gi|208741720|gb|EDZ89402.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4042]
 gi|218428432|emb|CAR09358.2| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli ED1a]
 gi|257755501|dbj|BAI27003.1| RNA polymerase, sigma S factor [Escherichia coli O26:H11 str.
           11368]
 gi|284922677|emb|CBG35765.1| RNA polymerase sigma factor (sigma-38) [Escherichia coli 042]
          Length = 330

 Score =  215 bits (548), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 77/271 (28%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++            A++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEESAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|23306706|gb|AAN15274.1| N-terminal truncated RNA polymerase sigma factor S [Escherichia
           coli]
 gi|23306708|gb|AAN15270.1| N-terminal truncated RNA polymerase sigma factor S [Escherichia
           coli]
 gi|23306710|gb|AAN15272.1| N-terminal truncated RNA polymerase sigma factor S [Escherichia
           coli]
          Length = 277

 Score =  215 bits (548), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 8   YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 66

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 67  IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 125

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    +   
Sbjct: 126 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE--- 178

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
             +  L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 179 --KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 236

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 237 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 267


>gi|296127158|ref|YP_003634410.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Brachyspira
           murdochii DSM 12563]
 gi|296018974|gb|ADG72211.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Brachyspira
           murdochii DSM 12563]
          Length = 587

 Score =  215 bits (548), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 67/242 (27%), Positives = 119/242 (49%), Gaps = 12/242 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   +V ++LRLV+ IA  Y   GL   ++V EGNIGL++AV KF+ ++G++ +TY+ W
Sbjct: 348 QAKDHIVKANLRLVIAIAKKYVNRGLHFFDLVQEGNIGLIKAVDKFEYKKGYKFSTYATW 407

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++        +   + +++  L+     + +   +  IAK L 
Sbjct: 408 WIRQAITRSISDQARTIRVPVH-----MIEQINKVQRVLRQYMQQHGREPSIQEIAKALG 462

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
             ES V S+        SLNA I   D+  +   + +    D + +        K  R  
Sbjct: 463 WPESRVKSVRNVAKDPVSLNAPI--GDEEDTILGELI---EDKEFESPQNITTFKILRKQ 517

Query: 228 LTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           +   +  L  RE+++   R         TLE +   F+V+RER+RQIEA+A ++++   +
Sbjct: 518 IDSILDSLPDREQKVIRMRFGLVDGYSHTLEEVGYVFKVTRERIRQIEAKAIRRLRAQSK 577

Query: 286 KQ 287
           K+
Sbjct: 578 KK 579



 Score = 37.5 bits (86), Expect = 2.2,   Method: Composition-based stats.
 Identities = 12/48 (25%), Positives = 25/48 (52%), Gaps = 1/48 (2%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHL 58
           N +  +  Y+ EI K+ +L   +E   +K+  E G+    + ++ +HL
Sbjct: 93  NNDDPIRLYLKEIGKVSLLTHDDEVDYSKKI-ESGESEIENIILNTHL 139


>gi|322433717|ref|YP_004215929.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidobacterium
           sp. MP5ACTX9]
 gi|321161444|gb|ADW67149.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidobacterium
           sp. MP5ACTX9]
          Length = 566

 Score =  215 bits (548), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 66/242 (27%), Positives = 117/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 322 EKAKRELIEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 381

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   + +L    + +     +      IA+++
Sbjct: 382 WWIRQAITRAIADQARTIRIPVH-----MIETINKLIRTSRQLVQELGREASSEEIARRM 436

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++  ++V  +        SL   I   ++  S   D++    D       +     N + 
Sbjct: 437 DIPVAKVRKVLKIAQEPISLETPI--GEEEDSHLGDFI---EDRMAVSPADAVISVNLKE 491

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             ++ +  L PRE R+ + R   E+    TLE +   F+V+RER+RQIEA+A +K++   
Sbjct: 492 YTSQVLRTLTPREERVIKMRFGLEDGSEHTLEEVGQSFQVTRERIRQIEAKALRKLRHPS 551

Query: 285 QK 286
           + 
Sbjct: 552 RS 553


>gi|296448000|ref|ZP_06889906.1| RNA polymerase, sigma 32 subunit, RpoH [Methylosinus trichosporium
           OB3b]
 gi|296254510|gb|EFH01631.1| RNA polymerase, sigma 32 subunit, RpoH [Methylosinus trichosporium
           OB3b]
          Length = 289

 Score =  215 bits (548), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 108/268 (40%), Positives = 177/268 (66%), Gaps = 3/268 (1%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           +    + P LE++EE  LA  +++  D  A H+L ++H+RLV+ +A+ +R YGLP++++V
Sbjct: 12  VKAAMEAPFLEREEEKQLAIAWKDRRDGVALHKLASAHMRLVIALAVRFRHYGLPVADLV 71

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EG++GL++A  +F PER  R +TY+ WWI+A++Q+Y+LR+WS+V+ GT+++QK LFFNL
Sbjct: 72  QEGHVGLLEAAARFAPERDVRFSTYATWWIRASIQDYVLRNWSIVRGGTSSSQKALFFNL 131

Query: 140 RRLKGHLQAITDNNLKP-EQVVAIAKKLNVSESEVISMNCRLAG-DESLNA-LINSSDKN 196
           RRL+  L        +  +   AIA  + VS ++V  MN RLAG D SLN+ LI     +
Sbjct: 132 RRLRAKLAHAPQTAAESGDAFDAIAGAIGVSRADVELMNSRLAGSDVSLNSQLIEDDSAS 191

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           S++  D+LV D    ++++ ++ +   R   L  ++ +L+ RE RI + RRL E+ VTLE
Sbjct: 192 SAERMDFLVDDRPLPDEIVEDRLDSDRRARWLADALKLLSERELRIVQERRLSESLVTLE 251

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
           +L     +S+ERVRQIE RA  K+++++
Sbjct: 252 SLGDRLGISKERVRQIENRALCKLRKAL 279


>gi|297250830|ref|ZP_06934304.1| RNA polymerase sigma factor RpoD [Neisseria polysaccharea ATCC
           43768]
 gi|296837936|gb|EFH21874.1| RNA polymerase sigma factor RpoD [Neisseria polysaccharea ATCC
           43768]
          Length = 322

 Score =  215 bits (548), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 63/272 (23%), Positives = 122/272 (44%), Gaps = 14/272 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRY--REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + ++ K   +  +E   + K     E    +A   ++ ++LRLV+ IA  Y   GL   +
Sbjct: 48  LADMEKETRISIEELKEINKNMVSSEKETAAAKQEMIQANLRLVISIAKKYTNRGLQFLD 107

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +  
Sbjct: 108 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIE 162

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + ++    +       +      +A+ + + E ++  +        S+   I   D + 
Sbjct: 163 TINKMNRISRQHLQETGEEPDSAKLAELMQMPEDKIRKIMKIAKEPISMETPI--GDDDD 220

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
           S   D++    D       +     +   +    +  L PRE ++   R   +     TL
Sbjct: 221 SHLGDFI---EDANNIAPADAAMYTSLHEVTKEILESLTPREAKVLRMRFGIDMNTDHTL 277

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +  +F+V+RER+RQIEA+A +K++   +  
Sbjct: 278 EEVGRQFDVTRERIRQIEAKALRKLRHPTRSD 309


>gi|163744692|ref|ZP_02152052.1| RNA polymerase sigma-32 factor [Oceanibulbus indolifex HEL-45]
 gi|161381510|gb|EDQ05919.1| RNA polymerase sigma-32 factor [Oceanibulbus indolifex HEL-45]
          Length = 292

 Score =  215 bits (548), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 103/287 (35%), Positives = 176/287 (61%), Gaps = 9/287 (3%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           MS+    E  L+R      K  +L+   E  LA  +R+  D +A HRL+T+++RL + +A
Sbjct: 1   MSLQTAREFSLTR---TAMKAELLDADTELKLAYAWRDQRDEAALHRLITAYMRLAISMA 57

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             ++ YG P+++++ E  +GLM+A  KFDP+RG R +TY++WWIKA++Q++++R+WS+V+
Sbjct: 58  GKFKRYGAPMNDLIQEAGLGLMKAADKFDPDRGVRFSTYAVWWIKASIQDHVMRNWSMVR 117

Query: 126 IGTTANQKRLFFNLRRLKGHLQAIT----DNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            G+T++QK LFFN+RR++  L+       +   K +    I+ ++ V   +V  M  RL+
Sbjct: 118 TGSTSSQKSLFFNMRRVQARLEREASAVGETLDKHQLRQMISTEIGVPLHDVEMMEGRLS 177

Query: 182 G-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           G D SLNA   S++    +W + L  +     + + E+ +    RN L  +M  L+ RE+
Sbjct: 178 GSDYSLNA-TQSAEDEGREWIEALADESAQAAERVEEQHDTAQLRNWLLTAMQGLSDREQ 236

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            I   R+L++   TLE+L  E  +S+ERVRQ+EA AF K+++S++ Q
Sbjct: 237 FIVRERKLRDPSRTLESLGDELSLSKERVRQLEAAAFGKMRKSLEMQ 283


>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 =  215 bits (548), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 65/249 (26%), Positives = 113/249 (45%), Gaps = 12/249 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 352 IGEARARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 411

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         P+   
Sbjct: 412 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRVSRQMLQEMGREPTPD--- 466

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+++ + + +V  +        S+   I   D   S   D++    D       +   
Sbjct: 467 ELAERVEMPKDKVRKVLKIAREPISMETPI--GDDEDSHLGDFV---EDAAVISPPDSAI 521

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
               R      ++ L PRE ++   R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 522 FSGLRETTQLILAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 581

Query: 279 KVQESIQKQ 287
           K++   + +
Sbjct: 582 KLRHPSRSE 590


>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 =  215 bits (548), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 68/260 (26%), Positives = 116/260 (44%), Gaps = 16/260 (6%)

Query: 34  EYVLAKRYREHGDLSAAH---RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           E   A R    G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV
Sbjct: 368 EIKEASRLMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 427

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
            KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +    
Sbjct: 428 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEM 485

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
                PE    +A+++ + E ++  +        S+   I   D   S   D++    D 
Sbjct: 486 GREPSPE---ELAERMEMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDR 537

Query: 211 QEQVLIEKEERKNRRNMLTRSMSV-LNPRERRIFEARR--LQENPVTLENLSSEFEVSRE 267
                 +       R ++   +   L  RE ++   R         TLE +  +F+V+RE
Sbjct: 538 NVTAPADSAVNAAIREVVEELLDNGLTAREAKVLRMRFGIGMNTDHTLEEVGKQFDVTRE 597

Query: 268 RVRQIEARAFKKVQESIQKQ 287
           R+RQIEA+A +K++   + +
Sbjct: 598 RIRQIEAKALRKLRHPSRSE 617


>gi|82778108|ref|YP_404457.1| RNA polymerase sigma factor RpoS [Shigella dysenteriae Sd197]
 gi|81242256|gb|ABB62966.1| RNA polymerase, sigma S factor [Shigella dysenteriae Sd197]
          Length = 330

 Score =  215 bits (548), Expect = 7e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 139/271 (51%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E +++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIDLTRERVRQIQVEGLRRLREILQTQ 320


>gi|270264030|ref|ZP_06192298.1| RNA polymerase sigma factor RpoS [Serratia odorifera 4Rx13]
 gi|270042223|gb|EFA15319.1| RNA polymerase sigma factor RpoS [Serratia odorifera 4Rx13]
          Length = 332

 Score =  215 bits (548), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 63  YLGEIGYSPLLTAEEEVYFARR-ALRGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 180

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +     +  
Sbjct: 181 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPL--GGDSEK 234

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  + D   +   +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 235 ALLDILADEKDNGPE---DTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 291

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 292 DVGREIGLTRERVRQIQVEGLRRLREILQLQ 322


>gi|157369077|ref|YP_001477066.1| RNA polymerase sigma factor RpoS [Serratia proteamaculans 568]
 gi|157320841|gb|ABV39938.1| RNA polymerase, sigma 70 subunit, RpoD family [Serratia
           proteamaculans 568]
          Length = 332

 Score =  215 bits (548), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 63  YLGEIGYSPLLTAEEEVYFARR-ALRGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 180

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +     +  
Sbjct: 181 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPL--GGDSEK 234

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  + D   +   +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 235 ALLDILADEKDNGPE---DTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 291

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 292 DVGREIGLTRERVRQIQVEGLRRLREILQMQ 322


>gi|116328273|ref|YP_797993.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Leptospira borgpetersenii serovar Hardjo-bovis L550]
 gi|116330997|ref|YP_800715.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Leptospira borgpetersenii serovar Hardjo-bovis JB197]
 gi|116121017|gb|ABJ79060.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Leptospira borgpetersenii serovar Hardjo-bovis L550]
 gi|116124686|gb|ABJ75957.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Leptospira borgpetersenii serovar Hardjo-bovis JB197]
          Length = 585

 Score =  215 bits (548), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 59/242 (24%), Positives = 117/242 (48%), Gaps = 12/242 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   LV ++LRLVV IA  Y   G+   +++ EGNIGL++AV KF+ ++G++ +TY+ W
Sbjct: 346 QAKKELVKANLRLVVSIAKRYANRGMHFFDLIQEGNIGLIKAVDKFEYKKGYKFSTYATW 405

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++        +   + ++    +       +      IA++L 
Sbjct: 406 WIRQAITRAISDQARTIRVPVH-----MIEQVNKVIRETRLFIQEFGRDPNNEEIAERLG 460

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
               +V  +        SL   + S  +  S+  D++    D + +  +           
Sbjct: 461 WPVQKVKMVKNVAREPISLEIPVGS--EEDSELGDFIP---DTEVETPVNTAASSILAEQ 515

Query: 228 LTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + + +  L  RE+++   R   ++  P TLE +  +F+V+RER+RQIEA+A ++++   +
Sbjct: 516 IRQVLHTLPAREQKVIRMRFGLDDGYPQTLEEVGYQFKVTRERIRQIEAKALRRLRHPSR 575

Query: 286 KQ 287
            +
Sbjct: 576 SK 577


>gi|226328647|ref|ZP_03804165.1| hypothetical protein PROPEN_02542 [Proteus penneri ATCC 35198]
 gi|225203380|gb|EEG85734.1| hypothetical protein PROPEN_02542 [Proteus penneri ATCC 35198]
          Length = 327

 Score =  215 bits (547), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 79/271 (29%), Positives = 135/271 (49%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 58  YLGEIGYSPLLTAEEEVFFARR-ALRGDIPSRQRMIESNLRLVVKISRRYTNRGLALLDL 116

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPE+GFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 117 IEEGNLGLIRAVEKFDPEKGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 175

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +         V  IA+ L+    +V  M        S++  I      + 
Sbjct: 176 LRTAR----ELAHKLDHEPSVEEIAESLDKPVEDVSKMLRLNERITSVDTPIGGDSDKA- 230

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D  E+      +  N +  + + +  LNP++R +   R   L     TLE
Sbjct: 231 ----LLDIISDENEEGPEATIQNNNLKENIIKWLFELNPKQREVLARRFGLLGYEAETLE 286

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    +++++ +Q Q
Sbjct: 287 DVGREIGLTRERVRQIQVEGLRRLKDILQSQ 317


>gi|162452723|ref|YP_001615090.1| RNA polymerase sigma factor RpoD [Sorangium cellulosum 'So ce 56']
 gi|161163305|emb|CAN94610.1| RNA polymerase sigma factor RpoD [Sorangium cellulosum 'So ce 56']
          Length = 639

 Score =  215 bits (547), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 73/247 (29%), Positives = 113/247 (45%), Gaps = 12/247 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +
Sbjct: 395 ERMAERAKAELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYKRGYKFS 454

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            L R   +L         PE    I
Sbjct: 455 TYATWWIRQAITRAIADQARTIRIPVHM--IETINKLIRTSRYLVQEYGREPTPE---EI 509

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+K+ +   +V  +        SL   I   ++  S   D++    D       E     
Sbjct: 510 AEKMELPLDKVRKVLKIAKEPISLETPI--GEEEDSHLGDFI---EDKSVISPAEAVINM 564

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKV 280
           N      + +  L PRE ++   R         TLE +  +FEV+RER+RQIEA+A +K+
Sbjct: 565 NLAEQTRKVLKTLTPREEKVLRMRFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKL 624

Query: 281 QESIQKQ 287
           +   + +
Sbjct: 625 RHPSRSK 631


>gi|324999213|ref|ZP_08120325.1| RNA polymerase sigma factor SigB [Pseudonocardia sp. P1]
          Length = 380

 Score =  215 bits (547), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 71/312 (22%), Positives = 137/312 (43%), Gaps = 44/312 (14%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------- 41
           +++         +  Y++ I +  +L   EE  LAKR                       
Sbjct: 66  EDLDAQSPAADLVRVYLNGIGRTALLTAAEEVDLAKRIEAGIFAQHRLDTATAEGTLESL 125

Query: 42  --REHGDLS--------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
             +   DL         A + L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++AV+
Sbjct: 126 DPQYRRDLRAVVRDGALAKNHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAVE 185

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +GF+ +TY+ WWI+ A+   +      +++     ++     L R+K  +     
Sbjct: 186 KFDYTKGFKFSTYATWWIRQAITRGMADQARTIRLPVHLVEQ--VNKLARIKRDMHQ--- 240

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +      +A++  + E ++  +        SL+  + S ++  +   D++    D +
Sbjct: 241 RQGREPSEAELAQESGIPEHKISDLLDHARDPVSLDMPVGSEEE--APLGDFI---EDAE 295

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERV 269
                         + L R ++ L  RE+++   R   ++  P TL+ +   F +SRERV
Sbjct: 296 ATDAENTVISSLLSDDLRRVLATLEDREQKVIRMRFGLDDGQPRTLDQIGRAFTLSRERV 355

Query: 270 RQIEARAFKKVQ 281
           RQIE     K++
Sbjct: 356 RQIEREVMAKLR 367


>gi|116620135|ref|YP_822291.1| RpoD family RNA polymerase sigma factor [Candidatus Solibacter
           usitatus Ellin6076]
 gi|116223297|gb|ABJ82006.1| RNA polymerase, sigma 70 subunit, RpoD family [Candidatus
           Solibacter usitatus Ellin6076]
          Length = 563

 Score =  215 bits (547), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 116/242 (47%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 318 ETAKKELIEANLRLVVSIAKRYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 377

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WW++ A+   I      ++I        +   + +L    + +     +      +AK+L
Sbjct: 378 WWVRQAITRAIADQARTIRIPVH-----MIETINKLIRTSRQMVQELGREPSNEELAKRL 432

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +  S+V  +        SL   I   ++  S   D++V   D       +     N R 
Sbjct: 433 QLPVSKVRKVLRVAQEPISLETPI--GEEEESHLGDFIV---DQNGISPSDAVINLNLRE 487

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              + +  L PRE +I + R   E+    TLE +   F V+RER+RQIEA+A +K++   
Sbjct: 488 QTAQVLKTLTPREEKIIKMRFGLEDGSEHTLEEVGQNFAVTRERIRQIEAKALRKLRHPS 547

Query: 285 QK 286
           + 
Sbjct: 548 RS 549


>gi|226357433|ref|YP_002787172.1| RNA polymerase sigma factor, sigma-70 family [Deinococcus deserti
           VCD115]
 gi|226319423|gb|ACO47418.1| putative RNA polymerase sigma factor, sigma-70 family [Deinococcus
           deserti VCD115]
          Length = 363

 Score =  215 bits (547), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 78/301 (25%), Positives = 129/301 (42%), Gaps = 36/301 (11%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------REHGDLS------- 48
           ++     + +Y+HEI ++P+L   EE  LA+R               E G+         
Sbjct: 56  VIVSNDPVRQYLHEIGRVPLLTVTEEIDLARRMEAGQEARTQLETEHELGERERRRLQRT 115

Query: 49  ------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
                 A  +L+ ++LRLVV IA  Y   G+ + +++ EGN GL++  +KF+  RGF+ +
Sbjct: 116 VEDGEHAKQQLIEANLRLVVSIAKKYANRGMGLLDLIQEGNQGLIRGAEKFEYRRGFKFS 175

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I     +      L R    LQ          +    
Sbjct: 176 TYATWWIRQAVNRAIADQARNIRIPVHMVE--TINKLNRTTRQLQMELSREPSHAETAE- 232

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A      E +V           SL   +   D+  S   D+L  D     +  + +    
Sbjct: 233 AMGPGWDEVKVEETLRLTRDTISLATPV--GDEGDSSIADFLPDDRR---ESPLSRVSSV 287

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
                L R+++ L PRE  +   R   E+    TLE +   F V+RER+RQIE +A +K+
Sbjct: 288 LMSEALDRTLATLEPREALVIRLRNGLEDGREHTLEEVGKHFGVTRERIRQIENKALRKI 347

Query: 281 Q 281
           +
Sbjct: 348 K 348


>gi|319789700|ref|YP_004151333.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermovibrio
           ammonificans HB-1]
 gi|317114202|gb|ADU96692.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermovibrio
           ammonificans HB-1]
          Length = 563

 Score =  215 bits (547), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 74/253 (29%), Positives = 127/253 (50%), Gaps = 14/253 (5%)

Query: 35  YVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           Y LA++    +     A   LV S+LRLVV IA  Y   GL   +++ EGNIGLM+AV K
Sbjct: 309 YELAEKIYFYKKDSQEAKQILVRSNLRLVVSIAKKYINRGLHFLDLIQEGNIGLMKAVDK 368

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+  RG++ +TY+ WWI+ A+   I      ++I            + ++   +      
Sbjct: 369 FEYRRGYKFSTYATWWIRQAITRAIADQARTIRIPVHM--IETINKVIKISRQMFQEMGR 426

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             KPE    IA++L +  S+V S+        SL   I   D   S   +++    D + 
Sbjct: 427 EPKPE---EIAERLKMPASKVRSILQLAQEPVSLETPI--GDDEDSTLGNFI---EDTKS 478

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVR 270
            +  ++  +K+ +  +++ +S L+ RE  + + R   +     TLE +  E +V+RER+R
Sbjct: 479 PIPEQEVIKKDLQEKVSQLLSQLSEREALVLKLRFGLDGYPEHTLEQVGKELKVTRERIR 538

Query: 271 QIEARAFKKVQES 283
           QIE++A +K++ S
Sbjct: 539 QIESKALRKLRNS 551


>gi|331696792|ref|YP_004333031.1| RpoD subfamily RNA polymerase sigma-70 subunit [Pseudonocardia
           dioxanivorans CB1190]
 gi|326951481|gb|AEA25178.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pseudonocardia
           dioxanivorans CB1190]
          Length = 348

 Score =  215 bits (547), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 69/295 (23%), Positives = 130/295 (44%), Gaps = 42/295 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR------------------------------EHGDLS 48
           Y++ I K  +L   +E  LAKR                                      
Sbjct: 51  YLNGIGKTALLTAAQEVDLAKRIEAGVFARHVLDTAAAEGRELDPDYARDLRAVARDGAR 110

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A + L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++AV+KFD  +GF+ +TY+ WW
Sbjct: 111 ARNHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAVEKFDYAKGFKFSTYATWW 170

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   +      +++     ++     L R+K  +        +      +A++  +
Sbjct: 171 IRQAITRGMADQARTIRLPVHLVEQ--VNKLARIKRDMHQ---RLGREATHAELAEESGL 225

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E ++  +        SL+  + S ++  +   D++    D +              + L
Sbjct: 226 PEEKIADLLDHARDPVSLDMPVGSEEE--APLGDFI---EDAEAADAENTVISHLLHDDL 280

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R ++ L+ RE+ +   R   ++  P TL+ +   F +SRERVRQIE     K++
Sbjct: 281 RRVLATLDEREQNVIRMRYGLDDGQPCTLDQIGRRFGLSRERVRQIEREVMAKLR 335


>gi|225848787|ref|YP_002728951.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Sulfurihydrogenibium azorense Az-Fu1]
 gi|225643846|gb|ACN98896.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Sulfurihydrogenibium azorense Az-Fu1]
          Length = 282

 Score =  215 bits (547), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 80/277 (28%), Positives = 140/277 (50%), Gaps = 16/277 (5%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  ++  +       L  Y+ ++ K PML  +EE  LA R ++ GD  A  +LV  +LR 
Sbjct: 1   MANQDQELTT-----LQLYMQQMGKYPMLTPEEERELAIRAKK-GDKEALKKLVEGNLRF 54

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  + G+G+P++++++ GN+GL++A K+FDP++  +  +Y++WWI+ A+ + I + 
Sbjct: 55  VVNIAKNFMGWGVPLTDLIAAGNLGLIEAAKRFDPDKNVKFISYAVWWIRQAIMQTIFQQ 114

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              V+I       +    + ++K   + + ++  +      IAK+L  S  +V +    +
Sbjct: 115 TGAVRIPI-----KESLFISKVKNAYEKLKESLGREPTEEEIAKELKTSVKKVKNALAIV 169

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL+  +    +      D L     G E V  +  E    +    R ++VL+ RER
Sbjct: 170 RQPISLDMPLGEGGEEDFTLLDILS--KKGTEDVEKDLVESTL-KEEFERLLNVLDERER 226

Query: 241 RIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEAR 275
            I + R   E   P TLE +     +SRERVRQ+E R
Sbjct: 227 EIIKLRYGLEGLEPKTLEEVGEMLGISRERVRQLEQR 263


>gi|223936990|ref|ZP_03628898.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [bacterium
           Ellin514]
 gi|223894271|gb|EEF60724.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [bacterium
           Ellin514]
          Length = 614

 Score =  215 bits (547), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 66/240 (27%), Positives = 116/240 (48%), Gaps = 12/240 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   +  ++LRLV+ I   Y   GL   +++ EGN+GLM+ V+KF+  RG++ +TY+ W
Sbjct: 371 QAKTEMAEANLRLVISIGKKYTNRGLAFLDIIQEGNMGLMKGVEKFEYRRGYKFSTYATW 430

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I        +   L R +  L         PE    IA ++ 
Sbjct: 431 WIRQAITRAIADQARTIRIPVHM--IEIIGKLMRAQKQLLQEFGREATPE---EIADEMQ 485

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S   V S+        S+ A +   D + + + D++    D   +   +       ++ 
Sbjct: 486 ISVERVKSILKMAQQPISMQASV--GDSDDATFGDFI---EDKSAENPSDMTSYSLLKDK 540

Query: 228 LTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L   ++ L  RERRI E R    +    TLE +  +++V+RER+RQIEA+A +K++   +
Sbjct: 541 LNDVLATLTERERRIVELRFGLVDGYARTLEEVGKQYKVTRERIRQIEAKALRKLRHPTR 600



 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 8/38 (21%), Positives = 20/38 (52%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAA 50
           +  +  Y+ ++ K+P+L +++E  + KR  E  +    
Sbjct: 156 DDPVRMYLRQMGKVPLLTREQEVAICKRIEEAENEQRR 193


>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 =  215 bits (547), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 68/260 (26%), Positives = 116/260 (44%), Gaps = 16/260 (6%)

Query: 34  EYVLAKRYREHGDLSAAH---RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           E   A R    G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV
Sbjct: 361 EIKEASRLMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV 420

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
            KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +    
Sbjct: 421 DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEM 478

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
                PE    +A+++ + E ++  +        S+   I   D   S   D++    D 
Sbjct: 479 GREPSPE---ELAERMEMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDR 530

Query: 211 QEQVLIEKEERKNRRNMLTRSMSV-LNPRERRIFEARR--LQENPVTLENLSSEFEVSRE 267
                 +       R ++   +   L  RE ++   R         TLE +  +F+V+RE
Sbjct: 531 NVTAPADSAVNAAIREVVEELLDNGLTAREAKVLRMRFGIGMNTDHTLEEVGKQFDVTRE 590

Query: 268 RVRQIEARAFKKVQESIQKQ 287
           R+RQIEA+A +K++   + +
Sbjct: 591 RIRQIEAKALRKLRHPSRSE 610


>gi|296532040|ref|ZP_06894819.1| DNA-directed RNA polymerase sigma subunit RpoD [Roseomonas
           cervicalis ATCC 49957]
 gi|296267655|gb|EFH13501.1| DNA-directed RNA polymerase sigma subunit RpoD [Roseomonas
           cervicalis ATCC 49957]
          Length = 640

 Score =  215 bits (547), Expect = 8e-54,   Method: Composition-based stats.
 Identities = 76/237 (32%), Positives = 114/237 (48%), Gaps = 12/237 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L  ++LRLVV IA  YR  GL   +++ EGNIGLM+AV KFD  RGF+ ATY+ 
Sbjct: 401 RKAKEELTRANLRLVVHIAKRYRNRGLMFGDLIQEGNIGLMRAVDKFDWRRGFKFATYAT 460

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WW++ A+   +      +++     +      + R+             PE    +A +L
Sbjct: 461 WWVRQAITRSLADQARTIRVPVHMTE--TVGKVARMSRRFAQKAGREPTPE---ELAGEL 515

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +S  +V ++        SL   I   + +  +  D++    D    +  +   R   R+
Sbjct: 516 GMSVDKVRAVQRLAREPVSLENPI--GEDDDGRLGDFI---EDENAVMPFDAASRSAMRD 570

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              R +S L PRE RI   R     EN  TLE +   F V+RER+RQIEA+A KK+Q
Sbjct: 571 ATMRILSDLTPREERILRMRFGIGGENDHTLEEVGKTFNVTRERIRQIEAKALKKLQ 627



 Score = 36.3 bits (83), Expect = 6.3,   Method: Composition-based stats.
 Identities = 9/42 (21%), Positives = 20/42 (47%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD 46
           N + +   +  +  ++ E+    +L ++EE  LA+R     D
Sbjct: 130 NEASLARSDDPVRMFLREMSGTDLLSREEEIALAQRIEAGRD 171


>gi|228471226|ref|ZP_04056039.1| RNA polymerase sigma-70 factor [Porphyromonas uenonis 60-3]
 gi|228307041|gb|EEK16123.1| RNA polymerase sigma-70 factor [Porphyromonas uenonis 60-3]
          Length = 286

 Score =  215 bits (547), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 74/282 (26%), Positives = 138/282 (48%), Gaps = 12/282 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           + N SI       L RY+ EI +  ++  +EE  LA+     G+  A ++LV ++LR VV
Sbjct: 5   KINQSITNRESASLDRYLQEIGRTSLISPEEEVELAREIH-RGNRRALNKLVEANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGNIG+++A +KFD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 64  SVAKQYQNQGLSLPDLINEGNIGMIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    NQ  L   + +     + +      P     IA +L + E ++         
Sbjct: 124 IVRLP--LNQVGLQQKMNKAIVKFEQLNGRRPSP---QEIADELELPEDKIREALKVQGK 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
            +SL+A     + N+      +  D    +  LI +         + R +  L  RE  +
Sbjct: 179 HQSLDAPFVEGEDNNM-LDVLVNEDTPSTDSSLINESLSAE----IDRILEQLGDREAEV 233

Query: 243 FEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
                    P +TLE +    ++SRERVRQI+ +A +++++S
Sbjct: 234 LRCFFGIGCPEMTLEEIGERTKLSRERVRQIKEKAIRRLKQS 275


>gi|18073320|emb|CAC81021.1| mutant RpoS sigma factor [Escherichia coli]
          Length = 302

 Score =  215 bits (547), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 33  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 91

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 92  IEEGNQGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 150

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 151 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 205

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 206 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 261

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 262 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 292


>gi|91779694|ref|YP_554902.1| sigma 70 (RpoD) [Burkholderia xenovorans LB400]
 gi|91692354|gb|ABE35552.1| Sigma 70 (RpoD) [Burkholderia xenovorans LB400]
          Length = 628

 Score =  215 bits (547), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 66/239 (27%), Positives = 123/239 (51%), Gaps = 12/239 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   ++ ++LRLVV +A  Y   G+P+ ++V EGNIGLM+AV +F+  RGF+ +TY+ 
Sbjct: 388 QDARRAMIEANLRLVVSVAKKYVQSGMPLLDLVQEGNIGLMKAVDRFEYRRGFKFSTYAT 447

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ ++   I      +++            + R+K     +     +P +   +A +L
Sbjct: 448 WWIRQSVSRAIADYGRTIRVPVHMAD-----AMHRVKRVAGEMRQETGRPARSSELAARL 502

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +SE +V S+        SL+  I   ++  +   + +    D      ++   + + R 
Sbjct: 503 GMSEEKVRSVQRVTRQPVSLDVPI--GEEADTTLGEMV---EDSSTLAPLDALLQADLRV 557

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +  ++ VL PRE ++ + R   +  +  TLE L  +F+V+RERVRQI+ +A +K++ S
Sbjct: 558 AIDAALGVLTPREAKVIKLRFGVDAVSEHTLEELGDQFDVTRERVRQIQNKALQKLRHS 616


>gi|327398426|ref|YP_004339295.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Hippea maritima
           DSM 10411]
 gi|327181055|gb|AEA33236.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Hippea maritima
           DSM 10411]
          Length = 491

 Score =  215 bits (547), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 67/243 (27%), Positives = 122/243 (50%), Gaps = 12/243 (4%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            R++ ++LRLVV IA  +   GL   +++ EGNIGLM++V KFD ++GF+ +TY+ WWI+
Sbjct: 256 QRMIKANLRLVVSIAKKHLNRGLSFLDLIQEGNIGLMKSVDKFDYKKGFKFSTYATWWIR 315

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            ++   I      ++I        +   + ++    + +   N K      +A+ L + E
Sbjct: 316 QSISRAIADQARTIRIPVH-----MIETINKIVRASKLLIQENGKEPTAQELAEYLGMDE 370

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            ++ S+        SL   I   D N +  +D++    D + +  ++   + N +  +  
Sbjct: 371 EKIKSIIKIAKEPISLETPI--GDDNDTHLEDFI---EDTKSESPLDYVIKSNLKEKVEE 425

Query: 231 SMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +S L  RER++   R    +    TLE +     V+RERVRQIEA+A +K++   + +V
Sbjct: 426 VLSTLTDRERKVLMMRYGIGDGFDHTLEEVGKVLGVTRERVRQIEAKALRKLRHPKRSRV 485

Query: 289 ELS 291
             S
Sbjct: 486 LAS 488



 Score = 43.3 bits (101), Expect = 0.049,   Method: Composition-based stats.
 Identities = 12/41 (29%), Positives = 23/41 (56%), Gaps = 1/41 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVT 55
            +  Y+ E+  IP+L ++EE  +AK+  EH +     +L+ 
Sbjct: 81  AIRMYLREMGNIPLLSREEEIEIAKKIEEHKNNLTR-KLIE 120


>gi|37523331|ref|NP_926708.1| RNA polymerase sigma factor SigC [Gloeobacter violaceus PCC 7421]
 gi|35214335|dbj|BAC91703.1| group2 RNA polymerase sigma factor [Gloeobacter violaceus PCC 7421]
          Length = 362

 Score =  215 bits (547), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 73/309 (23%), Positives = 137/309 (44%), Gaps = 52/309 (16%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR------------------EHGDLS------------ 48
           Y+ EI ++P+L + EE  LA++ +                  E+ D              
Sbjct: 54  YLQEIGRVPLLGRDEEVELAQQVQKLMKLTALKESLQTSLGSEYSDEQWAEAAKVGLFEL 113

Query: 49  ---------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                    A  +++ ++LRLVV +A  Y+  GL + ++V EG +GL +AV+KFDP +G+
Sbjct: 114 KRQVLAGSRAKKKMIEANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGY 173

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           R +TY+ WWI+  +   I      +++     +K     L R+K   + ++ N  +   +
Sbjct: 174 RFSTYAYWWIRQGITRAIATQSRTIRLPVHITEK-----LNRIKKTQRKLSQNLGRTPTI 228

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IA++L +  + V  +  R+    SL   +                    +E    E  
Sbjct: 229 SEIAEELEMEPAHVRELMSRVPRSVSLETRVGKDKDTELGELLE------AEEVSPEESA 282

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT--LENLSSEFEVSRERVRQIEARAF 277
            +++ R  +   +  L  RER +   R    +  T  L  +    ++SRERVRQIE++A 
Sbjct: 283 VQESLRRDVKELLDDLTLRERDVITMRYGLLDGRTYSLSEIGRALDLSRERVRQIESKAL 342

Query: 278 KKVQESIQK 286
           +K+++  ++
Sbjct: 343 QKLRQPRRR 351


>gi|297518365|ref|ZP_06936751.1| RNA polymerase sigma factor RpoS [Escherichia coli OP50]
          Length = 327

 Score =  215 bits (547), Expect = 9e-54,   Method: Composition-based stats.
 Identities = 79/271 (29%), Positives = 142/271 (52%), Gaps = 16/271 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++D+    E++     K     S ++ +N R+    S++  +    + + 
Sbjct: 179 LRTAR----ELSDHEPSAEEIAEQLDKPVDDVSRMLRLNERIT---SVDTPLGGDSEKA- 230

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 231 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 286

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 287 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 317


>gi|224438138|ref|ZP_03659073.1| RNA polymerase sigma factor RpoD [Helicobacter cinaedi CCUG 18818]
 gi|313144578|ref|ZP_07806771.1| RNA polymerase sigma factor RpoD [Helicobacter cinaedi CCUG 18818]
 gi|313129609|gb|EFR47226.1| RNA polymerase sigma factor RpoD [Helicobacter cinaedi CCUG 18818]
          Length = 623

 Score =  215 bits (547), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 72/260 (27%), Positives = 129/260 (49%), Gaps = 15/260 (5%)

Query: 29  LEKQEEYVLAKRYREHGDL--SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           LE ++   + ++ +    +   A  ++  S+LRLVV IA  Y   GLP  +++ EGNIGL
Sbjct: 362 LEPEKLKEILEQIKRGKSISDKAKAKMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGL 421

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+ ++GF+ +TY+ WWI+ A+   I      ++I        +   + R+   +
Sbjct: 422 MKAVDKFEYKKGFKFSTYATWWIRQAISRAIADQARTIRIPIH-----MIETINRIHKIM 476

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +       K   +  IAK++ +   +V ++        SL+A I S D    ++ D++  
Sbjct: 477 RKHIQETGKEPDIEYIAKEVGLPIDKVKNVIKITKEPVSLDAPIGSDDD--GKFGDFV-- 532

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFE 263
             D      ++   +++ +  +   +  LN RE+ +   R      E+  TLE +  E  
Sbjct: 533 -EDKSSVGPMDYILKEDLKVQIDDVLEQLNDREKAVIRMRFGLLDDESDRTLEEIGKELN 591

Query: 264 VSRERVRQIEARAFKKVQES 283
           V+RERVRQIE+ A KK++  
Sbjct: 592 VTRERVRQIESSAIKKLKHP 611



 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 12/41 (29%), Positives = 21/41 (51%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY 41
           M  K +      +  +  Y+ E+ +IP+L K+EE  L+K  
Sbjct: 100 MKDKELLEWSRSDSPVRMYLREMGQIPLLTKEEEVSLSKNI 140


>gi|319957164|ref|YP_004168427.1| RNA polymerase, sigma 70 subunit, rpod [Nitratifractor salsuginis
           DSM 16511]
 gi|319419568|gb|ADV46678.1| RNA polymerase, sigma 70 subunit, RpoD [Nitratifractor salsuginis
           DSM 16511]
          Length = 618

 Score =  215 bits (547), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 70/254 (27%), Positives = 120/254 (47%), Gaps = 13/254 (5%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE +   R  +     A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV K
Sbjct: 363 EEILEQIRIGKAKSEKAKTRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDK 422

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ ++G++ +TY+ WWI+ A+   I      ++I        +   + R+   ++     
Sbjct: 423 FEYQKGYKFSTYATWWIRQAISRAIADQARTIRIPIH-----MIETINRINKIIRKHLQE 477

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             K   +  IA+++ +S  +V ++        SL   +   D++  ++ D++    D   
Sbjct: 478 TGKEPDLETIAEEVGLSVDKVKNVIKITKEPVSLETPV--GDEDDGRFGDFI---EDKNS 532

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV---TLENLSSEFEVSRERV 269
               E     +    +   +  LN RE+ +   R      +   TLE +  E  V+RERV
Sbjct: 533 ISPTEAVLNDDLNQQIDEVLGQLNEREQAVIRMRFGLLEDMSDRTLEEIGKELNVTRERV 592

Query: 270 RQIEARAFKKVQES 283
           RQIE+ A KK++  
Sbjct: 593 RQIESSAIKKLKHP 606



 Score = 43.3 bits (101), Expect = 0.044,   Method: Composition-based stats.
 Identities = 13/36 (36%), Positives = 22/36 (61%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+ KIP+L K+EE  L+K+  E  D+
Sbjct: 108 SDSPVRMYLREMGKIPLLTKEEEIELSKQIEEGEDI 143


>gi|307721137|ref|YP_003892277.1| RNA polymerase, sigma 70 subunit, RpoD [Sulfurimonas autotrophica
           DSM 16294]
 gi|306979230|gb|ADN09265.1| RNA polymerase, sigma 70 subunit, RpoD [Sulfurimonas autotrophica
           DSM 16294]
          Length = 615

 Score =  215 bits (547), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 80/298 (26%), Positives = 149/298 (50%), Gaps = 26/298 (8%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPM----------LEKQEEYVLAKRYREHGDLS-- 48
           + +++++ +V     +S Y+ EI+K+            +E ++   + ++ +   ++S  
Sbjct: 317 LTKEDIANMVPEATMVSTYM-EIKKLVQTKEASKNSFDMEPEKLADILEQIKRGKNISEI 375

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           +  ++  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ ++G++ +TY+ WW
Sbjct: 376 SKTKMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYQKGYKFSTYATWW 435

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + R+   ++     N K   V  IAK++ +
Sbjct: 436 IRQAISRAIADQARTIRIPIH-----MIETINRINKIMRKHLQENGKEPDVDTIAKEVGL 490

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  +V ++        SL A I S D    ++ D++    D       +   + + R  +
Sbjct: 491 SVEKVKNVIKITKEPISLEAPIGSEDD--GRFGDFI---EDKTSLSPSDAILKDDLRIQI 545

Query: 229 TRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            + +  LN RE+ + + R      E+  TLE +  E  V+RERVRQIE+ A KK++  
Sbjct: 546 EQVLEQLNEREKAVIKLRFGIMDDESDRTLEEIGKELSVTRERVRQIESSAIKKLKHP 603



 Score = 39.0 bits (90), Expect = 0.82,   Method: Composition-based stats.
 Identities = 9/30 (30%), Positives = 19/30 (63%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRY 41
            +  +  Y+ E+ +IP+L K+EE  ++K+ 
Sbjct: 103 SDSPVRMYLREMGQIPLLTKEEEIEISKKI 132


>gi|302867958|ref|YP_003836595.1| sigma-70 family RNA polymerase [Micromonospora aurantiaca ATCC
           27029]
 gi|302570817|gb|ADL47019.1| RNA polymerase sigma factor, sigma-70 family [Micromonospora
           aurantiaca ATCC 27029]
          Length = 314

 Score =  215 bits (547), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 72/305 (23%), Positives = 136/305 (44%), Gaps = 40/305 (13%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLA----------KRYREHGDL---------------- 47
             ++ Y+  I + P+L  ++E  L           +R  + GD                 
Sbjct: 14  DAVAAYLRTIGRTPLLTAEQETRLGARIEAGALAQRRLDDDGDRVGAAEQDRLRRLVADG 73

Query: 48  -SAAHRLVTSHLRLVVKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
             A H ++ ++LRLVV +A  Y   G  P+ +++ EG IGLM+AV+KFD  RG + +TY+
Sbjct: 74  RRARHHMIEANLRLVVSVAKRYALAGRLPLLDLIQEGTIGLMRAVEKFDHRRGLKFSTYA 133

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
            WWIK A+   +      +++     +      L R+    + +     +      +A +
Sbjct: 134 TWWIKQAIGRALTDQSRTIRLPAHLVEV-----LNRVNRTRRTLAGELDREPTPAEVAAR 188

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           + V   +V  +        SL+  + +    +++  D L  +  G   V++       RR
Sbjct: 189 VEVPAEKVELLLRHDREPVSLHTPV-AGAAGTTELGDLLPDEAPGPAGVVV----SSWRR 243

Query: 226 NMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             L   +  L+ RE  +   R   ++  P TL+ + +   ++RERVRQIE++A +K++  
Sbjct: 244 RYLDEVLGTLSEREAAVICQRYGLDDDRPSTLDEIGTRIGLTRERVRQIESQALRKLRHP 303

Query: 284 IQKQV 288
            + +V
Sbjct: 304 TRARV 308


>gi|240851254|ref|YP_002972657.1| RNA polymerase sigma-32 factor [Bartonella grahamii as4aup]
 gi|240268377|gb|ACS51965.1| RNA polymerase sigma-32 factor [Bartonella grahamii as4aup]
          Length = 303

 Score =  215 bits (547), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 98/266 (36%), Positives = 165/266 (62%), Gaps = 1/266 (0%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           +    + P LE+Q+E+ LA R+++  D  A H++  +H+RLV+ IA  ++ + +P+ ++V
Sbjct: 27  MRSAMQAPYLERQKEHDLALRWKDKRDDDAMHQIAAAHMRLVIAIANRFKRFKMPLGDLV 86

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EG +GL++A  +F+P+R  R +TY+ WWI+A++Q+YILR+WS+V+ GT+++QK LFFNL
Sbjct: 87  QEGYVGLLEAAARFEPDREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSSQKALFFNL 146

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
           RRL+  L        K +    IA+KL VS  +V +M+ R +  ++  ++  S + ++  
Sbjct: 147 RRLRAKLIQDDSALSKQDIFRTIAEKLGVSVRDVETMDFRFSSSDNSLSVSVSENSDNPI 206

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRR-NMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
            +  ++ D       LIE+     RR   L  ++ +LN RE  I   RRL E   TLE L
Sbjct: 207 AKMDVLVDDSPLPDALIEQVIDGQRRTQWLYDALQILNERELEIIRFRRLNEEGATLEVL 266

Query: 259 SSEFEVSRERVRQIEARAFKKVQESI 284
             +  +S+ERVRQIEARA +K++ ++
Sbjct: 267 GEKLGISKERVRQIEARALQKLRSAL 292


>gi|229526927|ref|ZP_04416329.1| RNA polymerase sigma factor RpoD [Vibrio cholerae bv. albensis
           VL426]
 gi|229336054|gb|EEO01074.1| RNA polymerase sigma factor RpoD [Vibrio cholerae bv. albensis
           VL426]
          Length = 547

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 117/240 (48%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WW
Sbjct: 309 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW 368

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + ++    + +     +      +A+KL +
Sbjct: 369 IRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREPTPEELAEKLAM 423

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   +   D+  S   D++    D    + I+   + N R+  
Sbjct: 424 PLEKVRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKNALLPIDAAIQANLRDTT 478

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+A +K++   + 
Sbjct: 479 TRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAKALRKLKHPSRS 538


>gi|89109528|ref|AP_003308.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli str.
           K-12 substr. W3110]
 gi|218547743|ref|YP_002381534.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia fergusonii
           ATCC 35469]
 gi|85675562|dbj|BAE76818.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli str.
           K12 substr. W3110]
 gi|218355284|emb|CAQ87891.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia fergusonii
           ATCC 35469]
 gi|320645931|gb|EFX14912.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H- str.
           493-89]
          Length = 291

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 22  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 80

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 81  IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 139

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    +   
Sbjct: 140 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE--- 192

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
             +  L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 193 --KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 250

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 251 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 281


>gi|160902263|ref|YP_001567844.1| RpoD family RNA polymerase sigma factor [Petrotoga mobilis SJ95]
 gi|160359907|gb|ABX31521.1| RNA polymerase, sigma 70 subunit, RpoD family [Petrotoga mobilis
           SJ95]
          Length = 414

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 75/273 (27%), Positives = 133/273 (48%), Gaps = 11/273 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y+ EI  I +L    E  LA R ++    +    LV ++LRLV+ IA  Y G GL  
Sbjct: 136 IKIYLREIGGIKLLTPSRERQLAIRAKKGDKKAKDE-LVKANLRLVISIAKRYTGRGLTF 194

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGL++AV+KFD +RGF+ +TY+ WW++ A+   I      ++I        L
Sbjct: 195 LDLIQEGNIGLIRAVEKFDWKRGFKFSTYATWWVRQAITRAIADQARTIRIPVH-----L 249

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
             ++ R+   ++       +      +A+ L+    ++  +        S++A I+ SD 
Sbjct: 250 VESINRMNIVIRKHLQETGEYPSTEKLAELLDKPLEKMDEILLATKEIISVDAPISGSDD 309

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPV 253
             +   D+L    D +     E   R   +  + + +  L P+E  + + R   L     
Sbjct: 310 EEAYIGDFL---EDSEADQPEEIAVRMILKEEIEKVLESLRPKEATVLKMRYGLLDGKMK 366

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TLE + + F V+RER+RQIE +A +K++   + 
Sbjct: 367 TLEEVGNFFNVTRERIRQIEVKALRKLRHPSRS 399


>gi|220934609|ref|YP_002513508.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thioalkalivibrio
           sp. HL-EbGR7]
 gi|219995919|gb|ACL72521.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thioalkalivibrio
           sp. HL-EbGR7]
          Length = 344

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 73/270 (27%), Positives = 131/270 (48%), Gaps = 13/270 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A R  + GD +   +++  +LRLVVKIA  Y   GL + ++
Sbjct: 75  YLSEIEFSPLLTPEEEVHYA-RLAQKGDEAGRRKMIECNLRLVVKIARRYMNRGLALLDL 133

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 134 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHV-IKELNVY 192

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            +A+ L+    +V  +        S++  I        
Sbjct: 193 LRTARK----LAQELDHEPTAEEVARHLDRPVGDVKRILALSERVTSVDLPI--GKDGER 246

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
              D +  +   +  +LI+ E+       +   +  L+ ++R +   R         TLE
Sbjct: 247 ALLDVIPDEQTPEPSILIQDEDVVQF---VDEWLQELDEKQREVIVRRFGLHGYERSTLE 303

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + +E  V+RERVRQI+  A K++++ ++ 
Sbjct: 304 QVGAELGVTRERVRQIQMDALKRLRKILES 333


>gi|195938492|ref|ZP_03083874.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4024]
          Length = 279

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 79/278 (28%), Positives = 140/278 (50%), Gaps = 13/278 (4%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           G +    Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   
Sbjct: 3   GSLRTQLYLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNR 61

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++     
Sbjct: 62  GLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV 121

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
            K L   LR  +     ++           IA++L+    +V  M        S++  + 
Sbjct: 122 -KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLG 176

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQ 249
              +     +  L    D +E    +  +  + +  + + +  LN ++R +   R   L 
Sbjct: 177 GDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLG 231

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
               TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 232 YEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 269


>gi|32266044|ref|NP_860076.1| RNA polymerase sigma factor RpoD [Helicobacter hepaticus ATCC
           51449]
 gi|32262093|gb|AAP77142.1| RNA polymerase sigma 70 factor [Helicobacter hepaticus ATCC 51449]
          Length = 623

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 72/260 (27%), Positives = 129/260 (49%), Gaps = 15/260 (5%)

Query: 29  LEKQEEYVLAKRYREHGDL--SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           LE ++   + ++ +    +   A  ++  S+LRLVV IA  Y   GLP  +++ EGNIGL
Sbjct: 362 LEPEKLKEILEQIKRGKSISDKAKAKMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGL 421

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+ ++GF+ +TY+ WWI+ A+   I      ++I        +   + R+   +
Sbjct: 422 MKAVDKFEYKKGFKFSTYATWWIRQAISRAIADQARTIRIPIH-----MIETINRIHKIM 476

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +       K   +  IAK++ +   +V ++        SL+A I S D    ++ D++  
Sbjct: 477 RKHVQETGKEPDIDFIAKEVGLPIDKVKNVIKITKEPVSLDAPIGSDDD--GKFGDFV-- 532

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFE 263
             D      ++   +++ +  +   +  LN RE+ +   R      E+  TLE +  E  
Sbjct: 533 -EDKSSVGPMDYILKEDLKVQIDEVLEQLNDREKAVIRMRFGLLDDESDRTLEEIGKELN 591

Query: 264 VSRERVRQIEARAFKKVQES 283
           V+RERVRQIE+ A KK++  
Sbjct: 592 VTRERVRQIESSAIKKLKHP 611



 Score = 36.7 bits (84), Expect = 3.8,   Method: Composition-based stats.
 Identities = 11/41 (26%), Positives = 21/41 (51%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY 41
           M  K +      +  +  Y+ E+ +I +L K+EE  L+K+ 
Sbjct: 100 MKDKELLEWSRSDSPVRMYLREMGQISLLTKEEEISLSKKI 140


>gi|300087894|ref|YP_003758416.1| RNA polymerase sigma 70 subunit RpoD subfamily [Dehalogenimonas
           lykanthroporepellens BL-DC-9]
 gi|299527627|gb|ADJ26095.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Dehalogenimonas
           lykanthroporepellens BL-DC-9]
          Length = 502

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 69/241 (28%), Positives = 119/241 (49%), Gaps = 12/241 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   L+ ++LRLVV +A  + G G+P+ +++ EGNIGL++AV+KFD  RGF+ +TY+ W
Sbjct: 264 KAERHLIQANLRLVVSVAKKHIGRGMPLLDLIQEGNIGLIRAVEKFDFHRGFKFSTYATW 323

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I     +      L  +   +         P+    IA ++ 
Sbjct: 324 WIRQAITRAIADQARTIRIPVHMVE--TINKLLSISRSMSQKLGREPTPD---EIAAEME 378

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +   +V  +        SL + I   ++  S   D++    D       +   R+  +  
Sbjct: 379 LPPEKVREIAKVSQLPVSLESPI--GEEEDSHLGDFI---EDQNALPPPDAASRQLLKEQ 433

Query: 228 LTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           +   +  L PRERR+ + R   E+    TLE +  EF V+RER+RQIEA+A +K++   +
Sbjct: 434 IDNVLDSLTPRERRVLQLRFGLEDGRSRTLEEVGKEFNVTRERIRQIEAKALRKLRHPTR 493

Query: 286 K 286
            
Sbjct: 494 S 494



 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 10/29 (34%), Positives = 19/29 (65%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRY 41
           +  +  Y+HEI ++P+L  + E +LAK+ 
Sbjct: 80  DDPVRMYLHEIGRVPLLNAETEKMLAKKM 108


>gi|19910026|dbj|BAB87264.1| RNA polymerase sigma factor [Cyanophora paradoxa]
          Length = 427

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 75/321 (23%), Positives = 138/321 (42%), Gaps = 49/321 (15%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREH-------------------------- 44
                 + +I E+    +L  +EE  L+++ R+                           
Sbjct: 100 GSSDSFNSFIKEVGSFELLSAEEEIELSRQIRDLVQLETVKKRLAARIGREPREDEWAMA 159

Query: 45  --------------GDLSAAHRLVTSHLRLVVKIAMGYRG-YGLPISEVVSEGNIGLMQA 89
                             A  RLV S+LR VV IA  Y   + +P+ +++ EG+IGLM+A
Sbjct: 160 AGTQPGPAFQSRILKGRRARARLVQSNLRWVVSIAKKYANKHTMPLQDLIQEGSIGLMKA 219

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
            ++FD ++GF+  TY+ WWI+ A+   +      +++    +       L  +K   Q +
Sbjct: 220 AERFDLDKGFKFLTYATWWIRQAIFRSLQDQGRTIRLPVHVHDS-----LYLIKKTRQQL 274

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
                +      +A +LN+  S +  +    +   SL + I SS+ +S++ ++ L    +
Sbjct: 275 ASRLGRIPTPEELADELNIPVSRLAFITQAASLPISLESPI-SSETSSTKARNNLGDFIE 333

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRE 267
            +     E+ ER   R  L   ++ L  RER I   R      +P TL+ +     ++RE
Sbjct: 334 SECLQPDEQLERTMLREDLENVLATLKARERDIIRMRYGLVDGSPKTLDEIGEIVGLTRE 393

Query: 268 RVRQIEARAFKKVQESIQKQV 288
           R+RQIE  A +K++   +K +
Sbjct: 394 RIRQIEQSAMRKLKAPYRKAI 414


>gi|86130344|ref|ZP_01048944.1| RNA polymerase sigma factor RpoD [Dokdonia donghaensis MED134]
 gi|332293359|ref|YP_004431968.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Krokinobacter
           diaphorus 4H-3-7-5]
 gi|85819019|gb|EAQ40178.1| RNA polymerase sigma factor RpoD [Dokdonia donghaensis MED134]
 gi|332171445|gb|AEE20700.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Krokinobacter
           diaphorus 4H-3-7-5]
          Length = 288

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 69/278 (24%), Positives = 147/278 (52%), Gaps = 12/278 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L+ Y+ ++ KI ++  +EE  LA+R ++ GD  A   L  ++LR V+ +A  Y+  GL 
Sbjct: 17  SLNNYLQDVSKIDLITAEEEVELAQRIQK-GDERALDALTRANLRFVISVAKQYQNQGLS 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           +S++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + I      V++    N+  
Sbjct: 76  LSDLINEGNVGLVKAAKRFDETRGFKFISYAVWWIRQSILQAIAEHARTVRLP--LNKIG 133

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               + +   +LQ + +          IAK L++SE +V      ++   S++A     +
Sbjct: 134 EISKINKAMVYLQQVHERK---PTSGEIAKYLDISEEKVKISLKNVSRSLSMDAPFAEGE 190

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
            +++ +      +    ++ L++    ++    + R++  L  +E  +        N   
Sbjct: 191 NDNNLYDVLSSSESPRPDRELMQ----ESLSIEINRALDTLTEKEAEVVRLNYGLGNQPA 246

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
           +TL+ +   F++SRERVRQI  +A K+++ + + ++ +
Sbjct: 247 MTLQEIGDIFDLSRERVRQIREKAIKRLRHTSKSKILM 284


>gi|118472772|ref|YP_887083.1| RNA polymerase sigma factor SigB [Mycobacterium smegmatis str. MC2
           155]
 gi|118174059|gb|ABK74955.1| sigma factor SigB [Mycobacterium smegmatis str. MC2 155]
          Length = 319

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 65/312 (20%), Positives = 134/312 (42%), Gaps = 38/312 (12%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------- 43
            ++         +  Y++ I K  +L   +E  LAKR                       
Sbjct: 11  TDLDAQSPAADLVRVYLNGIGKTALLNAADEVELAKRIEAGLYAQHLLDTKKRLGEARKR 70

Query: 44  ------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
                     +A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +
Sbjct: 71  DLQAVVRDGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTK 130

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           GF+ +TY+ WWI+ A+   +      +++     ++     L R+K  +     N  +  
Sbjct: 131 GFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLARIKREMHQ---NLGREA 185

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A++  +   ++  +        SL+  + + ++  +   D++    D +      
Sbjct: 186 TDEELAEESGIPVEKINDLLEHSRDPVSLDMPVGTDEE--APLGDFI---EDSEAMSAEN 240

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
               +     +   ++ L+ RE+++   R   ++  P TL+ +   F +SRERVRQIE  
Sbjct: 241 AVISELLHTDIRYVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERE 300

Query: 276 AFKKVQESIQKQ 287
              K++   +  
Sbjct: 301 VMAKLRNGERAD 312


>gi|270157097|ref|ZP_06185754.1| RNA polymerase sigma factor RpoS [Legionella longbeachae D-4968]
 gi|289164492|ref|YP_003454630.1| RNA polymerase sigma factor RpoS [Legionella longbeachae NSW150]
 gi|269989122|gb|EEZ95376.1| RNA polymerase sigma factor RpoS [Legionella longbeachae D-4968]
 gi|288857665|emb|CBJ11508.1| RNA polymerase sigma factor RpoS [Legionella longbeachae NSW150]
          Length = 341

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 78/270 (28%), Positives = 138/270 (51%), Gaps = 13/270 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A      GD++A  +++ S+LRLVVKI+  Y   GLP+ ++
Sbjct: 74  YLSEIGFSPLLSAEEEVHYAT-LALKGDVAARKKMIESNLRLVVKISRRYLNRGLPLLDL 132

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM++V+KFDP+RGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 133 IEEGNLGLMKSVEKFDPKRGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 191

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +   Q + D+   PE++  +  K      +++ +N ++    S++  I   +  S 
Sbjct: 192 LRAARQLTQKL-DHEPSPEEIAEMVDKPLEDVQKLLGLNDKVT---SVDTPIGFDENKS- 246

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
                L    D       E    +N R  +   +  L   ++++   R         TLE
Sbjct: 247 ----LLDTIPDENSVNPAELLTNENLRLHIESLLDKLTENQQQVIARRFGLRGFEKATLE 302

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ++  E +++RERVRQI+  A K ++  ++K
Sbjct: 303 DVGKEIDLTRERVRQIQVEALKTLRSLLEK 332


>gi|218962087|ref|YP_001741862.1| RNA polymerase sigma factor [Candidatus Cloacamonas
           acidaminovorans]
 gi|167730744|emb|CAO81656.1| RNA polymerase sigma factor [Candidatus Cloacamonas
           acidaminovorans]
          Length = 579

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 69/275 (25%), Positives = 125/275 (45%), Gaps = 16/275 (5%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYRE-----HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
            +IR++ +  K     L    RE          A + ++ +++RLV+ IA  Y   GL  
Sbjct: 303 RKIRRVELETKMTGNKLIFLLREIDRAERNKERAQNEMIEANVRLVISIAKHYNNRGLEF 362

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN GLM+AV+K+D  +G++ +TY+ WWI+ A+   I      ++I     +   
Sbjct: 363 LDLIQEGNTGLMRAVEKYDYRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMIES-- 420

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + R    L         PE++  +   L++   ++ ++        SL+  I   D 
Sbjct: 421 INKINRTSRRLMQKLGREPYPEEISEV---LDIPVEKIKNIMSISKEPVSLDKPIGH-DS 476

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--V 253
             S   D++    D          ER   +  +   +  L PRE R+   R   ++    
Sbjct: 477 EDSILGDFI---EDRTIISPERLAERSLLKKQVDEVLKTLTPREERVIRLRFGIDDGYHR 533

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           TLE + + F+V+RER+RQIE +A KK++   +  +
Sbjct: 534 TLEEVGNIFQVTRERIRQIEDKALKKLRHPSRAAI 568


>gi|332087476|gb|EGI92604.1| RNA polymerase sigma factor RpoS [Shigella boydii 5216-82]
          Length = 330

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNSKQREVPARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|167993163|ref|ZP_02574258.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar 4,[5],12:i:- str. CVM23701]
 gi|205328726|gb|EDZ15490.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar 4,[5],12:i:- str. CVM23701]
          Length = 330

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    + ++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRPLREILQTQ 320


>gi|46445811|ref|YP_007176.1| RNA polymerase sigma factor [Candidatus Protochlamydia amoebophila
           UWE25]
 gi|46399452|emb|CAF22901.1| probable transcription initiation factor sigma 70 [Candidatus
           Protochlamydia amoebophila UWE25]
          Length = 554

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 77/255 (30%), Positives = 124/255 (48%), Gaps = 13/255 (5%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             + +R+ +     A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+
Sbjct: 299 VKMLQRWMDK-SQEAKREMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFE 357

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             RG++ +TY+ WWI+ A+   I      ++I            + R    L   T    
Sbjct: 358 YRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVHM--IETINKVLRGAKKLMMETGREP 415

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            PE    +AK+L ++   V  +        SL A +   D   SQ+ D+L    D     
Sbjct: 416 SPE---ELAKELGITAERVREIYKIAQHPISLQAEV--GDGGESQFGDFL---EDTGADS 467

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQI 272
             E       ++ +   +S L+ RER++   R   L   P TLE +  EF V+RER+RQI
Sbjct: 468 PAEATGYSILKDKMGEVLSTLSDRERKVLIQRFGLLDGKPKTLEEVGVEFNVTRERIRQI 527

Query: 273 EARAFKKVQESIQKQ 287
           EA+A +K++  I+ +
Sbjct: 528 EAKALRKMRHPIRSK 542



 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 8/34 (23%), Positives = 20/34 (58%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREH 44
           + +  +  Y+ E+  +P+L ++EE  ++KR  + 
Sbjct: 93  SPDDPVRMYLKEMGSVPLLSREEEVEISKRIEKA 126


>gi|225619915|ref|YP_002721172.1| RNA polymerase sigma factor RpoD [Brachyspira hyodysenteriae WA1]
 gi|225214734|gb|ACN83468.1| RNA polymerase sigma factor RpoD [Brachyspira hyodysenteriae WA1]
          Length = 587

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 67/242 (27%), Positives = 120/242 (49%), Gaps = 12/242 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   +V ++LRLV+ IA  Y   GL   ++V EGNIGL++AV KF+ ++G++ +TY+ W
Sbjct: 348 QAKDHIVKANLRLVIAIAKKYVNRGLHFFDLVQEGNIGLIKAVDKFEYKKGYKFSTYATW 407

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++        +   + +++  L+     + +   +  IAK L+
Sbjct: 408 WIRQAITRSISDQARTIRVPVH-----MIEQINKVQRVLRQYMQQHGREPSIQEIAKALS 462

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
             ES V S+        SLNA I   D+  +   + +    D + +        K  R  
Sbjct: 463 WPESRVKSVRNVAKDPVSLNAPI--GDEEDTILGELI---EDKEFESPQNITTFKILRKQ 517

Query: 228 LTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           +   +  L  RE+++   R         TLE +   F+V+RER+RQIEA+A ++++   +
Sbjct: 518 IDSILDSLPDREQKVIRMRFGLVDGYSHTLEEVGYVFKVTRERIRQIEAKAIRRLRAQSK 577

Query: 286 KQ 287
           K+
Sbjct: 578 KK 579



 Score = 37.5 bits (86), Expect = 2.2,   Method: Composition-based stats.
 Identities = 12/48 (25%), Positives = 25/48 (52%), Gaps = 1/48 (2%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHL 58
           N +  +  Y+ EI K+ +L   +E   +K+  E G+    + ++ +HL
Sbjct: 93  NNDDPIRLYLKEIGKVSLLTHDDEVDYSKKI-ESGESEIENIILNTHL 139


>gi|119357820|ref|YP_912464.1| RNA polymerase, sigma 32 subunit, RpoH [Chlorobium phaeobacteroides
           DSM 266]
 gi|119355169|gb|ABL66040.1| RNA polymerase, sigma 32 subunit, RpoH [Chlorobium phaeobacteroides
           DSM 266]
          Length = 299

 Score =  214 bits (546), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 75/302 (24%), Positives = 141/302 (46%), Gaps = 30/302 (9%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD-----------LSAAH 51
           + +  I     + L RY+ EI K  +L  ++E  L K  +E  D             A  
Sbjct: 5   KISKQITNRESLSLDRYLQEIGKYDLLTAEDEVKLTKAIKEGYDTPVDTVEYRRAKRALD 64

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +L+  +LR VV +A  Y+  GL + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ 
Sbjct: 65  KLIKGNLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQ 124

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ + +     +V++            L ++      +     +      +A  L++   
Sbjct: 125 SILQALAEQSRIVRLPLNR-----VGTLNKISKAYSQLEQEFERDPNTRELANLLDMDSQ 179

Query: 172 EVISMNCRLAGDESLNALINSSDKN---SSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +V           S++A     D N        D  + DH   +  L  + ER       
Sbjct: 180 DVADTLKIAGRHVSVDAPFAQGDDNRLLDVLQNDGHLPDHGLNKDSLTLEVERS------ 233

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +SVL PRE  +  +      +NP+TLE +  +F+++RERVRQI+ +A +++++S   
Sbjct: 234 ---LSVLAPREADVIRSYFGIGMDNPLTLEEIGEKFKLTRERVRQIKEKAIRRLRQSAYS 290

Query: 287 QV 288
           ++
Sbjct: 291 KI 292


>gi|237785656|ref|YP_002906361.1| RNA polymerase sigma factor SigB [Corynebacterium kroppenstedtii
           DSM 44385]
 gi|237758568|gb|ACR17818.1| RNA polymerase sigma factor B [Corynebacterium kroppenstedtii DSM
           44385]
          Length = 326

 Score =  214 bits (545), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 68/297 (22%), Positives = 136/297 (45%), Gaps = 38/297 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYRE--------------------------HGDLSAAHR 52
           Y++ I +  +L  ++E  L++R                                 +A   
Sbjct: 34  YLNGIGRTALLNAEDEVELSQRIEAGLYAQHLLESDEQFTPSKKRDLKAVAKDGRAARAH 93

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A
Sbjct: 94  LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAVEKFDYTKGFKFSTYATWWIRQA 153

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +      +++     ++     L R+K  +          E    +A++  + ES+
Sbjct: 154 ITRGMADQSRTIRLPVHLVEQ--VNKLSRIKREMYQHLGREATNE---ELAEESGIDESK 208

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           +  +  +     SL+  + + ++  +   D++    D +     E      R + +   +
Sbjct: 209 IDLLLKQSRDPVSLDMPVGTDEE--APLGDFI---EDSEATDAEEAVVASLRHSDIRTVL 263

Query: 233 SVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           + L  RE+ +   R   ++  P TL+ +  EF +SRERVRQIE     K+++  +  
Sbjct: 264 ATLEKREQDVIRLRFGLDDGVPRTLDQIGREFGLSRERVRQIEREVMAKLRKGERAD 320


>gi|329943340|ref|ZP_08292114.1| RNA polymerase sigma factor rpoD [Chlamydophila psittaci Cal10]
 gi|332287916|ref|YP_004422817.1| RNA polymerase sigma factor [Chlamydophila psittaci 6BC]
 gi|313848489|emb|CBY17493.1| major sigma factor [Chlamydophila psittaci RD1]
 gi|325507028|gb|ADZ18666.1| RNA polymerase sigma factor [Chlamydophila psittaci 6BC]
 gi|328814887|gb|EGF84877.1| RNA polymerase sigma factor rpoD [Chlamydophila psittaci Cal10]
          Length = 571

 Score =  214 bits (545), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 69/255 (27%), Positives = 122/255 (47%), Gaps = 13/255 (5%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             + +R+ +     A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+
Sbjct: 304 VRMLQRWMDK-SQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFE 362

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             RG++ +TY+ WWI+ A+   I      ++I        +   + ++    + +     
Sbjct: 363 YRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVH-----MIETINKVLRGAKKLMMETG 417

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           K      +A++L ++   V  +        SL A +   +   S + D+L    D   + 
Sbjct: 418 KEPTPEELAEELGLTPDRVREIYKIAQHPISLQAEV--GEGGESSFGDFL---EDTGVES 472

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQI 272
             E       ++ +   +  L  RER +   R   L   P TLE + S F V+RER+RQI
Sbjct: 473 PAEATGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGKPKTLEEVGSAFNVTRERIRQI 532

Query: 273 EARAFKKVQESIQKQ 287
           EA+A +K++  I+ +
Sbjct: 533 EAKALRKMRHPIRSK 547



 Score = 38.3 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 8/32 (25%), Positives = 19/32 (59%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREH 44
           +  +  Y+ E+  +P+L ++EE  ++KR  + 
Sbjct: 100 DDPVRMYLKEMGTVPLLTREEEVEISKRIEKA 131


>gi|169883526|gb|ACA97858.1| RNA polymerase sigma factor [Microcystis aeruginosa PCC 7820]
          Length = 416

 Score =  214 bits (545), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 71/257 (27%), Positives = 129/257 (50%), Gaps = 13/257 (5%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K +EY+ A + R +    A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++
Sbjct: 160 LAKSKEYLSAFKRRLYHGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIR 219

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A +KFD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + 
Sbjct: 220 AAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKI 274

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           ++    +      IA K+ ++  ++  +        SL   I    +  S+  D++  D 
Sbjct: 275 LSQEMRRKPTEEEIATKMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADG 332

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSR 266
               +   ++  +   R  L   +  L+PRER +   R   ++    TLE +   F V+R
Sbjct: 333 ----ETPEDEVSKNLLREDLENVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTR 388

Query: 267 ERVRQIEARAFKKVQES 283
           ER+RQIEA+A +K++  
Sbjct: 389 ERIRQIEAKALRKLRHP 405



 Score = 39.4 bits (91), Expect = 0.61,   Method: Composition-based stats.
 Identities = 10/32 (31%), Positives = 18/32 (56%)

Query: 12 GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE 43
           E  +  Y+ EI +I +L  +EE  LA++  +
Sbjct: 65 TEDSIRIYLQEIGRIRLLRAEEEIELARKIAD 96


>gi|159026614|emb|CAO86546.1| rpoD1 [Microcystis aeruginosa PCC 7806]
          Length = 416

 Score =  214 bits (545), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 71/257 (27%), Positives = 129/257 (50%), Gaps = 13/257 (5%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K +EY+ A + R +    A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++
Sbjct: 160 LAKSKEYLSAFKRRLYHGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIR 219

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A +KFD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + 
Sbjct: 220 AAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKI 274

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           ++    +      IA K+ ++  ++  +        SL   I    +  S+  D++  D 
Sbjct: 275 LSQEMRRKPTEEEIATKMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADG 332

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSR 266
               +   ++  +   R  L   +  L+PRER +   R   ++    TLE +   F V+R
Sbjct: 333 ----ETPEDEVSKNLLREDLENVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTR 388

Query: 267 ERVRQIEARAFKKVQES 283
           ER+RQIEA+A +K++  
Sbjct: 389 ERIRQIEAKALRKLRHP 405



 Score = 39.4 bits (91), Expect = 0.61,   Method: Composition-based stats.
 Identities = 10/32 (31%), Positives = 18/32 (56%)

Query: 12 GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE 43
           E  +  Y+ EI +I +L  +EE  LA++  +
Sbjct: 65 TEDSIRIYLQEIGRIRLLRAEEEIELARKIAD 96


>gi|1710685|sp|P52322|RPOD_MICAE RecName: Full=RNA polymerase sigma factor rpoD1
 gi|786173|dbj|BAA08853.1| sigma factor [Microcystis aeruginosa]
 gi|1783286|dbj|BAA12850.1| principal sigma factor [Microcystis aeruginosa]
          Length = 416

 Score =  214 bits (545), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 71/257 (27%), Positives = 129/257 (50%), Gaps = 13/257 (5%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K +EY+ A + R +    A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++
Sbjct: 160 LAKSKEYLSAFKRRLYHGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIR 219

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A +KFD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + 
Sbjct: 220 AAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKI 274

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           ++    +      IA K+ ++  ++  +        SL   I    +  S+  D++  D 
Sbjct: 275 LSQEMRRKPTEEEIATKMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADG 332

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSR 266
               +   ++  +   R  L   +  L+PRER +   R   ++    TLE +   F V+R
Sbjct: 333 ----ETPEDEVSKNLLREDLENVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTR 388

Query: 267 ERVRQIEARAFKKVQES 283
           ER+RQIEA+A +K++  
Sbjct: 389 ERIRQIEAKALRKLRHP 405



 Score = 39.4 bits (91), Expect = 0.61,   Method: Composition-based stats.
 Identities = 10/32 (31%), Positives = 18/32 (56%)

Query: 12 GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE 43
           E  +  Y+ EI +I +L  +EE  LA++  +
Sbjct: 65 TEDSIRIYLQEIGRIRLLRAEEEIELARKIAD 96


>gi|120403441|ref|YP_953270.1| RNA polymerase sigma factor SigB [Mycobacterium vanbaalenii PYR-1]
 gi|119956259|gb|ABM13264.1| RNA polymerase, sigma 70 subunit, RpoD family [Mycobacterium
           vanbaalenii PYR-1]
          Length = 329

 Score =  214 bits (545), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 66/312 (21%), Positives = 134/312 (42%), Gaps = 38/312 (12%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------- 43
           +++         +  Y++ I K  +L   +E  LAKR                       
Sbjct: 21  QDLDAQSPAADLVRVYLNGIGKTALLNAADEVELAKRIEAGLYAQHLLDTRKRLGENRKR 80

Query: 44  ------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
                     +A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +
Sbjct: 81  DLAAVVRDGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYAK 140

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           GF+ +TY+ WWI+ A+   +      +++     ++     L R+K  +     N  +  
Sbjct: 141 GFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLARIKREMHQ---NLGREA 195

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A +  +   ++  +        SL+  + S ++  +   D++    D +      
Sbjct: 196 TDEELAAESGIPVEKITDLLEHSRDPVSLDMPVGSDEE--APLGDFI---EDAEAMSAEN 250

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
               +     +   ++ L+ RE+++   R   ++  P TL+ +   F +SRERVRQIE  
Sbjct: 251 AVISELLHTDIRYVLATLDEREQQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERE 310

Query: 276 AFKKVQESIQKQ 287
              K++   +  
Sbjct: 311 VMAKLRNGERAD 322


>gi|254794681|ref|YP_003079518.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           TW14359]
 gi|254594081|gb|ACT73442.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O157:H7
           str. TW14359]
          Length = 330

 Score =  214 bits (545), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + +    LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWPFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 320


>gi|29143180|ref|NP_806522.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
 gi|695759|emb|CAA57298.1| sigma S [Salmonella enterica subsp. enterica serovar Typhi]
 gi|3820469|emb|CAA76807.1| RNA polymerase sigma subunit [Salmonella enterica subsp. enterica
           serovar Typhi str. Ty2]
 gi|29138813|gb|AAO70382.1| RNA polymerase sigma subunit RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
          Length = 384

 Score =  214 bits (545), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 75/262 (28%), Positives = 131/262 (50%), Gaps = 13/262 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    +   
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE--- 231

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
             +  L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 232 --KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFK 278
           ++  E  ++RERVRQI+    +
Sbjct: 290 DVGREIGLTRERVRQIQVEGLR 311


>gi|57168867|ref|ZP_00367997.1| RNA polymerase sigma factor RpoD [Campylobacter coli RM2228]
 gi|305431982|ref|ZP_07401149.1| DNA-directed RNA polymerase sigma subunit RpoD [Campylobacter coli
           JV20]
 gi|57019703|gb|EAL56389.1| RNA polymerase sigma factor RpoD [Campylobacter coli RM2228]
 gi|304445066|gb|EFM37712.1| DNA-directed RNA polymerase sigma subunit RpoD [Campylobacter coli
           JV20]
          Length = 621

 Score =  214 bits (545), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 75/260 (28%), Positives = 128/260 (49%), Gaps = 15/260 (5%)

Query: 29  LEKQEEYVLAKRYREHGDL--SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           LEK+    + ++ +    +   A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGL
Sbjct: 358 LEKERLKEILEQIKRGKKISDEAKTRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGL 417

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+ +RG++ +TY+ WWI+ A+   I      ++I        +   + ++   +
Sbjct: 418 MKAVDKFEYKRGYKFSTYATWWIRQAISRAIADQARTIRIPIH-----MIETINQINKII 472

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +     + K   V  IAK++ +S  +V  +        SL A I S D    ++ D++  
Sbjct: 473 REHLQKDGKEPDVSVIAKEVGLSVDKVKQVIKITKEPISLEAPIGSEDD--GKFGDFV-- 528

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFE 263
             D      ++   + + +  +   +  LN RE+ +   R      E+  TLE +  E  
Sbjct: 529 -EDRNSLSPMDHILKDDLKEQIDEVLDQLNDREKAVIRMRFGLMDDESDRTLEEIGKELN 587

Query: 264 VSRERVRQIEARAFKKVQES 283
           V+RERVRQIE+ A KK++  
Sbjct: 588 VTRERVRQIESSAIKKLKHP 607


>gi|320538977|ref|ZP_08038652.1| RNA polymerase, sigma S (sigma 38) factor [Serratia symbiotica str.
           Tucson]
 gi|320030910|gb|EFW12914.1| RNA polymerase, sigma S (sigma 38) factor [Serratia symbiotica str.
           Tucson]
          Length = 332

 Score =  214 bits (545), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA+ Y   GL + ++
Sbjct: 63  YLGEIGYSPLLTAEEEVYFARR-ALRGDVLSRRRMIESNLRLVVKIALRYSNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 180

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +     +  
Sbjct: 181 LRTAR----ELSHRLDHEPSAEEIAEQLDKPVGDVSHMLRLNERITSVDTPL--GGDSEK 234

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  + D   +   + +   + +  + + +  LN ++R +   R   L     TLE
Sbjct: 235 ALLDILADEKDNGPEGTTQDD---DMKQSIVKWLFELNAKQREVLARRFGLLGYESATLE 291

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 292 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 322


>gi|520418|gb|AAA50747.1| major sigma factor [Chlamydophila psittaci]
          Length = 571

 Score =  214 bits (545), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 69/255 (27%), Positives = 122/255 (47%), Gaps = 13/255 (5%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             + +R+ +     A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+
Sbjct: 304 VRMLQRWMDK-SQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFE 362

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             RG++ +TY+ WWI+ A+   I      ++I        +   + ++    + +     
Sbjct: 363 YRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVH-----MIETINKVLRGAKKLMMETG 417

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           K      +A++L ++   V  +        SL A +   +   S + D+L    D   + 
Sbjct: 418 KEPTPEELAEELGLTPDRVREIYKIAQHPISLQAEV--GEGGESSFGDFL---EDTGVES 472

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQI 272
             E       ++ +   +  L  RER +   R   L   P TLE + S F V+RER+RQI
Sbjct: 473 PAEATGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGKPKTLEEVGSAFNVTRERIRQI 532

Query: 273 EARAFKKVQESIQKQ 287
           EA+A +K++  I+ +
Sbjct: 533 EAKALRKMRHPIRSK 547



 Score = 38.3 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 8/32 (25%), Positives = 19/32 (59%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREH 44
           +  +  Y+ E+  +P+L ++EE  ++KR  + 
Sbjct: 100 DDPVRMYLKEMGTVPLLTREEEVEISKRIEKA 131


>gi|15606622|ref|NP_214002.1| RNA polymerase sigma factor RpoS [Aquifex aeolicus VF5]
 gi|2983844|gb|AAC07398.1| RNA polymerase sigma factor RpoS [Aquifex aeolicus VF5]
          Length = 310

 Score =  214 bits (545), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 84/296 (28%), Positives = 146/296 (49%), Gaps = 38/296 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +++Y+ +I KIP+L  +EE  LA+R ++ GD  A  +LV S+LR VV +A  Y GYGLP 
Sbjct: 10  INQYLKKISKIPLLTPEEEKELARRAKQ-GDKEALKKLVESNLRFVVSVAKQYIGYGLPF 68

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           SE+++ GN+GL++A K+FDP+RG +  +Y++WWI+ A+ + + +    V+I     Q  +
Sbjct: 69  SELIAAGNLGLLEAAKRFDPDRGVKFISYAVWWIRQAIMQALSQQTGAVRIP--LKQSHI 126

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVA------IAKKLN---------------------- 167
              +  + G L    +    PE++        IAK+L                       
Sbjct: 127 INKISHIYGELSKKLEREPSPEEIAEELSKQMIAKELEKELGREPTEEEIEERFKKEGYK 186

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++  EV           SL+A +  ++        ++ +        + EK  ++  +  
Sbjct: 187 ITPEEVEKYLQVCRVPLSLDAPVGENEDT-----FFIDFLSKHGTAEVEEKVIQEVIQKE 241

Query: 228 LTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +S L  +ER++ E R       P TL  +     +SRERVRQ+E RA +K++
Sbjct: 242 IDDLLSKLTDKERKVIELRFGLKGNEPKTLREIGEILGLSRERVRQLETRALRKLR 297


>gi|116748652|ref|YP_845339.1| RpoD family RNA polymerase sigma factor [Syntrophobacter
           fumaroxidans MPOB]
 gi|116697716|gb|ABK16904.1| RNA polymerase, sigma 70 subunit, RpoD family [Syntrophobacter
           fumaroxidans MPOB]
          Length = 599

 Score =  214 bits (545), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 69/241 (28%), Positives = 115/241 (47%), Gaps = 12/241 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ WW
Sbjct: 361 AKSELIEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWW 420

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I            L R   +L         PE    IA+K+  
Sbjct: 421 IRQAITRAIADQARTIRIPVHM--IETINKLIRTSRYLVQELGREPTPE---EIAEKMEF 475

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +        SL   I   ++  S   D++    D +    ++     N     
Sbjct: 476 PVEKVRKVLKIAKEPISLETPI--GEEEDSHLGDFI---EDKRVASPVDAVINLNLSEQT 530

Query: 229 TRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            ++++ L PRE ++   R         TLE +  +F V+RER+RQIEA+A +K++   ++
Sbjct: 531 RKALATLTPREEKVLRMRFGIGEKADHTLEEVGQDFAVTRERIRQIEAKALRKLRHPSRR 590

Query: 287 Q 287
           +
Sbjct: 591 K 591


>gi|257457314|ref|ZP_05622485.1| RNA polymerase sigma factor RpoD [Treponema vincentii ATCC 35580]
 gi|257445236|gb|EEV20308.1| RNA polymerase sigma factor RpoD [Treponema vincentii ATCC 35580]
          Length = 286

 Score =  214 bits (545), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 79/280 (28%), Positives = 145/280 (51%), Gaps = 13/280 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
            + Y+ EI KIP+L  ++E   AK     GD  A   L+ S+LR VV +A  Y+   +PI
Sbjct: 14  FATYLREINKIPLLSVEDEVKYAKAAA-AGDEKAKKILIESNLRFVVNVAKKYQNKNIPI 72

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG-TTANQKR 134
            +++SEGNIGLM A  +FDP++G++  +Y++WWI+ A+ + I     ++++    AN+  
Sbjct: 73  MDLISEGNIGLMNAADRFDPDKGYKFISYAVWWIRQAILKAICEKSRMIRLPLNRANELV 132

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
                R+L G     T    + +++ AIA+ L +    V ++        SL+A    +D
Sbjct: 133 QIEKARKLTGK----TGTEPEDKELTAIAQDLRIEPEMVRTIMNAARDPVSLDAP-QFND 187

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENP 252
            +++   D++      Q +      +    R  +   ++ L+ RE  I   R        
Sbjct: 188 NSAASTGDFIEDTRYMQPESYALDIDL---RENVDALLASLSEREAEILRYRFGLNGYEQ 244

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
           ++L+ + + F +++ER+RQIE +A +++ +S+  Q EL S
Sbjct: 245 LSLKEVGTRFNLTKERIRQIEKKALERL-QSVGHQHELES 283


>gi|296161690|ref|ZP_06844493.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. Ch1-1]
 gi|295888004|gb|EFG67819.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. Ch1-1]
          Length = 628

 Score =  214 bits (545), Expect = 1e-53,   Method: Composition-based stats.
 Identities = 69/259 (26%), Positives = 131/259 (50%), Gaps = 14/259 (5%)

Query: 29  LEKQEEYVLAKRY--REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L  QE   ++++    +     A   ++ ++LRLVV +A  Y   G+P+ ++V EGNIGL
Sbjct: 368 LSLQELKRISRKMNVADRELQDARRAMIEANLRLVVSVAKKYVQSGMPLLDLVQEGNIGL 427

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV +F+  RGF+ +TY+ WWI+ ++   I      +++            ++R+ G +
Sbjct: 428 MKAVDRFEYRRGFKFSTYATWWIRQSVSRAIADYGRTIRVPVHMAD--AMHRVKRVAGEM 485

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +  T    +      +A +L +SE +V S+        SL+  I   +   +   + +  
Sbjct: 486 RQETGRQARS---SELAARLGMSEEKVRSVQRVTRQPVSLDVPI--GEDADTTLGEMV-- 538

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D      ++   + + R  +  ++ VL PRE ++ + R   +  +  TLE L  +F+V
Sbjct: 539 -EDPSALAPLDALLQADLRVAIDAALGVLTPREAKVIKLRFGVDAVSEHTLEELGDQFDV 597

Query: 265 SRERVRQIEARAFKKVQES 283
           +RERVRQI+ +A +K++ S
Sbjct: 598 TRERVRQIQNKALQKLRHS 616


>gi|86139299|ref|ZP_01057869.1| RNA polymerase sigma factor [Roseobacter sp. MED193]
 gi|85824143|gb|EAQ44348.1| RNA polymerase sigma factor [Roseobacter sp. MED193]
          Length = 292

 Score =  214 bits (545), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 105/284 (36%), Positives = 175/284 (61%), Gaps = 9/284 (3%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M++  + E  L        K  ML+ + E  LA  +R+H D+ A HRL  +++RL + +A
Sbjct: 1   MTLDHSTENPLP---KTAMKAEMLDAETEKRLAYAWRDHRDVEALHRLTNAYMRLAISMA 57

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
           + ++ YG P+++++ E  +GLM+A  KFDP+RG R +TY++WWIKA++Q+Y++R+WS+V+
Sbjct: 58  VKFKRYGAPMNDLIQEAGLGLMKAADKFDPDRGVRFSTYAIWWIKASVQDYVMRNWSMVR 117

Query: 126 IGTTANQKRLFFNLRRLKGHLQ----AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            G+T++QK LFFN+RR++  L+    A      K +    IA ++ V   +V  M+ RL+
Sbjct: 118 TGSTSSQKSLFFNMRRVQTQLERQANAQGQRLDKHQLHQQIASEIGVPIRDVEMMDGRLS 177

Query: 182 G-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           G D SLNA   S++    +W + L  D     +++    + +  R  L  +M  L+ RE+
Sbjct: 178 GADFSLNA-ARSTEAEGQEWIEILEDDSAQAAELVERSHDHRKLRKWLVEAMQGLSGREQ 236

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           RI  AR+L   P TLE L  E  +S+ERVRQ+EA AF+K+++++
Sbjct: 237 RIVVARKLSNPPRTLEALGRELSLSKERVRQLEAGAFQKMRKTL 280


>gi|15605346|ref|NP_220132.1| RNA polymerase sigma factor [Chlamydia trachomatis D/UW-3/CX]
 gi|76789354|ref|YP_328440.1| RNA polymerase sigma factor [Chlamydia trachomatis A/HAR-13]
 gi|166154830|ref|YP_001654948.1| RNA polymerase sigma factor [Chlamydia trachomatis 434/Bu]
 gi|166155705|ref|YP_001653960.1| RNA polymerase sigma factor [Chlamydia trachomatis
           L2b/UCH-1/proctitis]
 gi|255311437|ref|ZP_05354007.1| RNA polymerase sigma factor [Chlamydia trachomatis 6276]
 gi|255317738|ref|ZP_05358984.1| RNA polymerase sigma factor [Chlamydia trachomatis 6276s]
 gi|255348997|ref|ZP_05381004.1| RNA polymerase sigma factor [Chlamydia trachomatis 70]
 gi|255503536|ref|ZP_05381926.1| RNA polymerase sigma factor [Chlamydia trachomatis 70s]
 gi|255507214|ref|ZP_05382853.1| RNA polymerase sigma factor [Chlamydia trachomatis D(s)2923]
 gi|301336109|ref|ZP_07224353.1| RNA polymerase sigma factor [Chlamydia trachomatis L2tet1]
 gi|1710679|sp|P18333|RPOD_CHLTR RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A;
           AltName: Full=Sigma-66; AltName: Full=Sigma-70
 gi|144609|gb|AAA23165.1| RNA polymerase sigma-subunit [Chlamydia trachomatis]
 gi|3329060|gb|AAC68218.1| RNA Polymerase Sigma-66 [Chlamydia trachomatis D/UW-3/CX]
 gi|76167884|gb|AAX50892.1| RpoD [Chlamydia trachomatis A/HAR-13]
 gi|165930818|emb|CAP04316.1| RNA polymerase sigma factor [Chlamydia trachomatis 434/Bu]
 gi|165931693|emb|CAP07270.1| RNA polymerase sigma factor [Chlamydia trachomatis
           L2b/UCH-1/proctitis]
 gi|289525658|emb|CBJ15139.1| RNA polymerase sigma factor [Chlamydia trachomatis Sweden2]
 gi|296435222|gb|ADH17400.1| RNA polymerase sigma factor [Chlamydia trachomatis E/150]
 gi|296436151|gb|ADH18325.1| RNA polymerase sigma factor [Chlamydia trachomatis G/9768]
 gi|296438011|gb|ADH20172.1| RNA polymerase sigma factor [Chlamydia trachomatis G/11074]
 gi|296438941|gb|ADH21094.1| RNA polymerase sigma factor [Chlamydia trachomatis E/11023]
 gi|297140513|gb|ADH97271.1| RNA polymerase sigma factor [Chlamydia trachomatis G/9301]
 gi|297748745|gb|ADI51291.1| RpoD [Chlamydia trachomatis D-EC]
 gi|297749625|gb|ADI52303.1| RpoD [Chlamydia trachomatis D-LC]
          Length = 571

 Score =  214 bits (545), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 69/255 (27%), Positives = 120/255 (47%), Gaps = 13/255 (5%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             + +R+ +     A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+
Sbjct: 304 VRMLQRWMDK-SQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFE 362

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             RG++ +TY+ WWI+ A+   I      ++I        +   + ++    + +     
Sbjct: 363 YRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVH-----MIETINKVLRGAKKLMMETG 417

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           K      + ++L  +   V  +        SL A +   D   S + D+L    D   + 
Sbjct: 418 KEPTPEELGEELGFTPDRVREIYKIAQHPISLQAEV--GDGGESSFGDFL---EDTAVES 472

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQI 272
             E       ++ +   +  L  RER +   R   L   P TLE + S F V+RER+RQI
Sbjct: 473 PAEATGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGRPKTLEEVGSAFNVTRERIRQI 532

Query: 273 EARAFKKVQESIQKQ 287
           EA+A +K++  I+ +
Sbjct: 533 EAKALRKMRHPIRSK 547



 Score = 38.3 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 8/32 (25%), Positives = 19/32 (59%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREH 44
           +  +  Y+ E+  +P+L ++EE  ++KR  + 
Sbjct: 100 DDPVRMYLKEMGTVPLLTREEEVEISKRIEKA 131


>gi|62185569|ref|YP_220354.1| RNA polymerase sigma factor [Chlamydophila abortus S26/3]
 gi|62148636|emb|CAH64409.1| major sigma factor [Chlamydophila abortus S26/3]
          Length = 571

 Score =  214 bits (545), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 69/255 (27%), Positives = 122/255 (47%), Gaps = 13/255 (5%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             + +R+ +     A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+
Sbjct: 304 VRMLQRWMDK-SQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFE 362

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             RG++ +TY+ WWI+ A+   I      ++I        +   + ++    + +     
Sbjct: 363 YRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVH-----MIETINKVLRGAKKLMMETG 417

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           K      +A++L ++   V  +        SL A +   +   S + D+L    D   + 
Sbjct: 418 KEPTPEELAEELGLTPDRVREIYKIAQHPISLQAEV--GEGGESSFGDFL---EDTGVES 472

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQI 272
             E       ++ +   +  L  RER +   R   L   P TLE + S F V+RER+RQI
Sbjct: 473 PAEATGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGKPKTLEEVGSAFNVTRERIRQI 532

Query: 273 EARAFKKVQESIQKQ 287
           EA+A +K++  I+ +
Sbjct: 533 EAKALRKMRHPIRSK 547



 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 8/32 (25%), Positives = 19/32 (59%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREH 44
           +  +  Y+ E+  +P+L ++EE  ++KR  + 
Sbjct: 100 DDPVRMYLKEMGTVPLLTREEEVEISKRIEKA 131


>gi|189500956|ref|YP_001960426.1| RNA polymerase, sigma 70 subunit, RpoD family [Chlorobium
           phaeobacteroides BS1]
 gi|189496397|gb|ACE04945.1| RNA polymerase, sigma 70 subunit, RpoD family [Chlorobium
           phaeobacteroides BS1]
          Length = 299

 Score =  214 bits (545), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 78/299 (26%), Positives = 145/299 (48%), Gaps = 24/299 (8%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD-----------LSAAH 51
           + +  I     + L RY+ EI K  +L  ++E  L K  +   D             A  
Sbjct: 5   KISKQITNRESLSLDRYLQEIGKYELLTAEDEVKLTKAIKAGYDMPVDTTEYKRAKRALD 64

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +L+  +LR VV +A  Y+  GL + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ 
Sbjct: 65  KLIKGNLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQ 124

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ + +     +V++    N+      + +    L+   + +        +A  L++   
Sbjct: 125 SILQALAEQSRIVRLP--LNRVGTLNKISKAYSQLEQEYERD---PNTKELANLLDMDSQ 179

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           +V           S++A     D N  +  D L  D    +  L     R +    + RS
Sbjct: 180 DVADTLKIAGRHVSVDAPFAQGDDN--RLLDVLQNDGHKPDHGLT----RDSLNLEVERS 233

Query: 232 MSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +SVL PRE  +  +      +NP+TLE +  +F+++RERVRQI+ +A K++++S   +V
Sbjct: 234 LSVLAPREADVIRSYFGIGMDNPLTLEEIGEKFKLTRERVRQIKEKAIKRLRQSAYSKV 292


>gi|6010736|gb|AAF01234.1|AF184103_1 mutant RpoS [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
          Length = 330

 Score =  214 bits (545), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 77/271 (28%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++ ERVRQI+    ++++E +Q Q
Sbjct: 290 DVGREIGLTCERVRQIQVEGLRRLREILQTQ 320


>gi|166368188|ref|YP_001660461.1| RNA polymerase sigma factor RpoD [Microcystis aeruginosa NIES-843]
 gi|166090561|dbj|BAG05269.1| principal RNA polymerase sigma factor [Microcystis aeruginosa
           NIES-843]
          Length = 416

 Score =  214 bits (545), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 71/257 (27%), Positives = 129/257 (50%), Gaps = 13/257 (5%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K +EY+ A + R +    A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++
Sbjct: 160 LAKSKEYLSAFKRRLYHGRRAKEKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIR 219

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A +KFD E+G++ +TY+ WWI+ A+   I      +++        L+  + R+K   + 
Sbjct: 220 AAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKI 274

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           ++    +      IA K+ ++  ++  +        SL   I    +  S+  D++  D 
Sbjct: 275 LSQEMRRKPTEEEIATKMEMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADG 332

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSR 266
               +   ++  +   R  L   +  L+PRER +   R   ++    TLE +   F V+R
Sbjct: 333 ----ETPEDEVSKNLLREDLENVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTR 388

Query: 267 ERVRQIEARAFKKVQES 283
           ER+RQIEA+A +K++  
Sbjct: 389 ERIRQIEAKALRKLRHP 405


>gi|89897819|ref|YP_514929.1| RNA polymerase sigma factor [Chlamydophila felis Fe/C-56]
 gi|89331191|dbj|BAE80784.1| DNA-directed RNA polymerase sigma 70 [Chlamydophila felis Fe/C-56]
          Length = 570

 Score =  213 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 69/255 (27%), Positives = 122/255 (47%), Gaps = 13/255 (5%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             + +R+ +     A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+
Sbjct: 302 VRMLQRWMDK-SQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFE 360

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             RG++ +TY+ WWI+ A+   I      ++I        +   + ++    + +     
Sbjct: 361 YRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVH-----MIETINKVLRGAKKLMMETG 415

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           K      +A++L ++   V  +        SL A +   +   S + D+L    D   + 
Sbjct: 416 KEPTPEELAEELGLTPDRVREIYKIAQHPISLQAEV--GEGGESSFGDFL---EDTGVES 470

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQI 272
             E       ++ +   +  L  RER +   R   L   P TLE + S F V+RER+RQI
Sbjct: 471 PAEATGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGKPKTLEEVGSAFNVTRERIRQI 530

Query: 273 EARAFKKVQESIQKQ 287
           EA+A +K++  I+ +
Sbjct: 531 EAKALRKMRHPIRSK 545



 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 8/32 (25%), Positives = 19/32 (59%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREH 44
           +  +  Y+ E+  +P+L ++EE  ++KR  + 
Sbjct: 98  DDPVRMYLKEMGTVPLLTREEEVEISKRIEKA 129


>gi|302392313|ref|YP_003828133.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acetohalobium
           arabaticum DSM 5501]
 gi|302204390|gb|ADL13068.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acetohalobium
           arabaticum DSM 5501]
          Length = 275

 Score =  213 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 77/275 (28%), Positives = 138/275 (50%), Gaps = 16/275 (5%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            +++Y  +I    +L K+EE  LA++  + GD  A  +L+  +LRLVV IA  ++G GL 
Sbjct: 4   SINQYYQDIS-HDLLTKEEEISLARK-AQAGDSEAKDKLIRHNLRLVVSIANKHQGKGLD 61

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++V EGNIGL+ AV+KFDP++G+R +TY+ WWIK  +   I      ++I     QK 
Sbjct: 62  LQDLVQEGNIGLITAVEKFDPDKGYRFSTYASWWIKQRVTRAIANQGKTIRIPVHVWQKT 121

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD--ESLNALINS 192
               + ++K  LQ         E    IA++ ++S  ++  +   +      SLN  +  
Sbjct: 122 --NKIFKVKDDLQTELGREPTAE---EIAEETDISLEKIKEVMRVITDQNLASLNQFV-- 174

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN- 251
            D   ++    +     G     +E   ++  +  L   ++ L+ RE  +   R    + 
Sbjct: 175 GDDRDTELGQLVP---SGSADDPVEGTSQQLLKEDLEELLTELSDREAEVIRLRFGLRDS 231

Query: 252 -PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            P TL+ +  E  V+RER+RQI+ +A  +++   +
Sbjct: 232 RPRTLKEVGEELGVTRERIRQIQLKALNRLKHPTR 266


>gi|254432880|ref|ZP_05046583.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Cyanobium sp. PCC 7001]
 gi|197627333|gb|EDY39892.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Cyanobium sp. PCC 7001]
          Length = 331

 Score =  213 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 73/295 (24%), Positives = 140/295 (47%), Gaps = 31/295 (10%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--------------------DLSAAHRL 53
             +S Y+  I + P+L   EE  L  + +                          +  R+
Sbjct: 41  DPISWYLASIGREPLLTPAEEIELGNQVQAMMQLLEAAKPSYSDHEKKLLRIGKRSKQRM 100

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           + ++LRLVV +A  Y+G GL + +++ EG++GL +AV+KFDP RG++ +TY+ WWI+ +M
Sbjct: 101 MKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWWIRQSM 160

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
              I      +++    +++     L  ++     +            IA+ +++   E+
Sbjct: 161 TRAIACQSRTIRLPVHLSER-----LSAIRKVSLDLAHKLGAMPSRHEIAEAMDMPLDEL 215

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             +  +     SL+A +N  D+  S   D +    D  E+  +++ ER      L   M+
Sbjct: 216 DGLLRQALTTSSLDAPVN-GDEGRSFLGDLIA---DSSEEEPLDRVERGLNHEQLDHWMN 271

Query: 234 VLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L+ +ER + + R   E  +  TL  +  + +VSRERVRQ+E +A +K++   ++
Sbjct: 272 HLSEQERHVLQLRFGLEGRDRHTLAEIGRQLDVSRERVRQVELKALRKLRNLTRR 326


>gi|193212077|ref|YP_001998030.1| RNA polymerase sigma 32 subunit RpoH [Chlorobaculum parvum NCIB
           8327]
 gi|193085554|gb|ACF10830.1| RNA polymerase, sigma 32 subunit, RpoH [Chlorobaculum parvum NCIB
           8327]
          Length = 299

 Score =  213 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 79/299 (26%), Positives = 146/299 (48%), Gaps = 24/299 (8%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD-----------LSAAH 51
           + +  I     + L RY+ EI K  +L  ++E  L    +E  D             A  
Sbjct: 5   KISKQITNRESLSLDRYLQEIGKYDLLTAEDEVKLTMAIKEGYDMPVDTVEYKRAKRALD 64

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +L+  +LR VV +A  Y+  GL + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ 
Sbjct: 65  KLIKGNLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQ 124

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ + +     +V++    N+      + +    L+   + +        +A  L++   
Sbjct: 125 SILQALAEQSRIVRLP--LNRVGTLNKISKAYSQLEQEYERD---PNTKELANLLDMDSQ 179

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           +V           S++A     D N  +  D L  D    +  L     R +    + RS
Sbjct: 180 DVADTLKIAGRHVSVDAPFAQGDDN--RLLDVLQNDGHMPDHTL----NRDSLTLEVERS 233

Query: 232 MSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +SVL PRE  +  +      ENP+TLE +  +F+++RERVRQI+ +A +++++S  K+V
Sbjct: 234 LSVLAPREADVIRSYFGIGMENPLTLEEIGEKFKLTRERVRQIKEKAIRRLRQSAYKEV 292


>gi|237804965|ref|YP_002889119.1| RNA polymerase sigma factor [Chlamydia trachomatis B/TZ1A828/OT]
 gi|231273265|emb|CAX10180.1| RNA polymerase sigma factor [Chlamydia trachomatis B/TZ1A828/OT]
          Length = 571

 Score =  213 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 69/255 (27%), Positives = 120/255 (47%), Gaps = 13/255 (5%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             + +R+ +     A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+
Sbjct: 304 VRMLQRWMDK-SQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFE 362

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             RG++ +TY+ WWI+ A+   I      ++I        +   + ++    + +     
Sbjct: 363 YRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVH-----MIETINKVLRGAKKLMMETG 417

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           K      + ++L  +   V  +        SL A +   D   S + D+L    D   + 
Sbjct: 418 KEPTPEELGEELGFTPDRVREIYKIAQHPISLQAEV--GDGGESSFGDFL---EDTAVES 472

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQI 272
             E       ++ +   +  L  RER +   R   L   P TLE + S F V+RER+RQI
Sbjct: 473 PAEATGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGRPKTLEEVGSAFNVTRERIRQI 532

Query: 273 EARAFKKVQESIQKQ 287
           EA+A +K++  I+ +
Sbjct: 533 EAKALRKMRHPIRSK 547



 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 8/32 (25%), Positives = 19/32 (59%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREH 44
           +  +  Y+ E+  +P+L ++EE  ++KR  + 
Sbjct: 100 DDPVRMYLKEMGTVPLLTREEEVEISKRIEKA 131


>gi|300933022|ref|ZP_07148278.1| RNA polymerase sigma factor SigB [Corynebacterium resistens DSM
           45100]
          Length = 337

 Score =  213 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 70/297 (23%), Positives = 137/297 (46%), Gaps = 38/297 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH---------------------GDLSAAHR 52
           Y++ I K  +L  ++E  L++R     Y EH                        +A   
Sbjct: 44  YLNGIGKTALLTAEDEVELSQRIEVGLYAEHLLKNSTDLTRARKRDLKILAREGKAARSH 103

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A
Sbjct: 104 LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQA 163

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +      +++     ++     L R+K  +          E    +A++  + ES+
Sbjct: 164 ITRGMADQSRTIRLPVHLVEQ--VNKLSRIKREMYQHLGREATNE---ELAEESGIEESK 218

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           +  +  +     SL+  + S ++  +   D++        +  +    R    + +   +
Sbjct: 219 IELLLKQSRDPVSLDMPVGSDEE--APLGDFIEDSDATDAEAAVVASLR---HSDVRAVL 273

Query: 233 SVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             L  RE+ + + R   ++  P TL+ +   F +SRERVRQIE     K++E  +  
Sbjct: 274 GTLEEREQDVIKLRYGLDDGMPRTLDQIGRRFGLSRERVRQIEREVMAKLREGHRAD 330


>gi|296437079|gb|ADH19249.1| RNA polymerase sigma factor [Chlamydia trachomatis G/11222]
          Length = 571

 Score =  213 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 69/255 (27%), Positives = 120/255 (47%), Gaps = 13/255 (5%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             + +R+ +     A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+
Sbjct: 304 VRMLQRWMDK-SQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFE 362

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             RG++ +TY+ WWI+ A+   I      ++I        +   + ++    + +     
Sbjct: 363 YRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVH-----MIETINKVLRGAKKLMMETG 417

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           K      + ++L  +   V  +        SL A +   D   S + D+L    D   + 
Sbjct: 418 KEPTPEELGEELGFTPDRVREIYKIAQHPISLQAEV--GDGGESSFGDFL---EDTAVES 472

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQI 272
             E       ++ +   +  L  RER +   R   L   P TLE + S F V+RER+RQI
Sbjct: 473 PAEATGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGRPKTLEEVGSAFNVTRERIRQI 532

Query: 273 EARAFKKVQESIQKQ 287
           EA+A +K++  I+ +
Sbjct: 533 EAKALRKMRHPIRSK 547



 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 8/32 (25%), Positives = 19/32 (59%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREH 44
           +  +  Y+ E+  +P+L ++EE  ++KR  + 
Sbjct: 100 DDPVRMYLKEMGTVPLLTREEEVEISKRIEKA 131


>gi|153003633|ref|YP_001377958.1| RNA polymerase sigma-70 subunit RpoD [Anaeromyxobacter sp. Fw109-5]
 gi|152027206|gb|ABS24974.1| RNA polymerase, sigma 70 subunit, RpoD [Anaeromyxobacter sp.
           Fw109-5]
          Length = 819

 Score =  213 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 81/272 (29%), Positives = 124/272 (45%), Gaps = 22/272 (8%)

Query: 28  MLEKQEEYV-----LAKRYR-----EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           ML  QEE       L + YR     EH    A   LV ++LRLVV IA  Y   GL   +
Sbjct: 550 MLRVQEEAEVPVDELRRTYRTISDGEHKAERAKTELVEANLRLVVSIAKKYTNRGLQFLD 609

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+ +RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 610 LIQEGNIGLMKAVDKFEYKRGYKFSTYATWWIRQAITRAIADQARTIRIPVHM--IETIN 667

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R   +L         PE    IA+K+ +   +V  +        SL   I   ++  
Sbjct: 668 KLIRTSRYLVQELGREPTPE---EIAEKMELPLDKVRKVLKIAKEPISLETPI--GEEED 722

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTL 255
           S   D++    D       +     N      + ++ L PRE ++   R         TL
Sbjct: 723 SHLGDFI---EDKSLVSPSDAVINMNLAEQTRKVLATLTPREEKVLRMRFGIGEKSDHTL 779

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +  +FEV+RER+RQIEA+A +K++   + +
Sbjct: 780 EEVGQDFEVTRERIRQIEAKALRKLRHPSRSK 811


>gi|157164653|ref|YP_001467098.1| RNA polymerase sigma factor RpoD [Campylobacter concisus 13826]
 gi|112799942|gb|EAT97286.1| RNA polymerase sigma factor RpoD (Sigma-A) (Major vegetative
           sigmafactor) [Campylobacter concisus 13826]
          Length = 617

 Score =  213 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 76/254 (29%), Positives = 123/254 (48%), Gaps = 14/254 (5%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           E     KR ++  D  A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV K
Sbjct: 363 EILEQIKRGKKISD-EAKARMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDK 421

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+  +G++ +TY+ WWI+ A+   I      ++I        +   + R+    +     
Sbjct: 422 FEYRKGYKFSTYATWWIRQAISRAIADQARTIRIPIH-----MIETINRINKINRKYLQE 476

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             K   V  IAK++ +S  +V  +        SL A I +  +   ++ D++    D   
Sbjct: 477 EGKEPDVSVIAKEVGLSVDKVKQVIKITKEPISLEAPIAN--EEDGKFGDFV---EDKTS 531

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERV 269
              I++  + + R  +   +S LN RE+ +   R      E+  TLE +     V+RERV
Sbjct: 532 LSPIDQILKSDLREQIDDVLSQLNEREKAVISMRFGLLEDESDRTLEEIGKALNVTRERV 591

Query: 270 RQIEARAFKKVQES 283
           RQIE+ A KK++  
Sbjct: 592 RQIESSAIKKLKHP 605



 Score = 36.3 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 10/36 (27%), Positives = 19/36 (52%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+ +I +L K EE  ++KR     D+
Sbjct: 102 SDSPVRMYLREMGQIALLTKDEEVEISKRIELGEDI 137


>gi|19553123|ref|NP_601125.1| RNA polymerase sigma factor SigB [Corynebacterium glutamicum ATCC
           13032]
 gi|62390759|ref|YP_226161.1| RNA polymerase sigma factor SigB [Corynebacterium glutamicum ATCC
           13032]
 gi|1149591|emb|CAA89988.1| SigB sigma factor [Corynebacterium glutamicum]
 gi|21324689|dbj|BAB99312.1| DNA-directed RNA polymerase sigma subunits (sigma70/sigma32) (SigB)
           [Corynebacterium glutamicum ATCC 13032]
 gi|41326097|emb|CAF20260.1| RNA POLYMERASE SIGMA FACTOR [Corynebacterium glutamicum ATCC 13032]
          Length = 331

 Score =  213 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 71/310 (22%), Positives = 141/310 (45%), Gaps = 39/310 (12%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAK-----RYREH------------ 44
           +R+  +     +  +  Y++ I K  +L  ++E  LA+      Y EH            
Sbjct: 20  SRRGQTNDNPSQDLVRVYLNGIGKTALLTAEDEVELAQTIEVGLYAEHLLKNSEEPLTRA 79

Query: 45  ----------GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                         A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD
Sbjct: 80  MKRDLKVLAKDGKKARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFD 139

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +GF+ +TY+ WWI+ A+   +      +++     ++     L R+K  L        
Sbjct: 140 YSKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLSRIKRELYQHLGREA 197

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
             E    +A++  + ES++  +  +     SL+  + + ++  +   D++        + 
Sbjct: 198 TNE---ELAEESGIEESKIEMLLRQSRDPVSLDMPVGADEE--APLGDFIEDSEATDAES 252

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
            +    R    + +   ++ L PRE+ +   R   ++  P TL+ +   F +SRERVRQI
Sbjct: 253 AVVASMR---HSDIRAVLNTLEPREQDVIRLRYGLDDGVPRTLDQIGRRFGLSRERVRQI 309

Query: 273 EARAFKKVQE 282
           E     K+++
Sbjct: 310 EREVMSKLRD 319


>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 =  213 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 60/248 (24%), Positives = 114/248 (45%), Gaps = 12/248 (4%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            E     A   ++ ++LRLV+ IA  Y   G+   +++ EGNIGLM+AV KF+  RG++ 
Sbjct: 420 AESKMRKAKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEGNIGLMKAVDKFEYRRGWKF 479

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY+ WW++ A+   +      +++            L R+   +   T     P     
Sbjct: 480 STYATWWVRQAVTRSLADQARTIRVPVHM--IETINKLNRISREILQQTGQEAHP---SV 534

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           +A+++ +SE +V  +        S+   +   D   +   D +    D       +   +
Sbjct: 535 LAERMELSEEKVRGILKIAKQPVSMETPV--GDDGDATLGDMI---EDSAASSPADAAMQ 589

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKK 279
            + R  +  ++  L+PRE ++   R         TLE +  +F+V+RER+RQIE++A +K
Sbjct: 590 ADLRAAIDDALDSLSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIRQIESKAMRK 649

Query: 280 VQESIQKQ 287
           +    +  
Sbjct: 650 LMHPSRAD 657


>gi|116514965|ref|YP_802594.1| RNA polymerase sigma-32 factor [Buchnera aphidicola str. Cc (Cinara
           cedri)]
 gi|116256819|gb|ABJ90501.1| RNA polymerase sigma-32 factor [Buchnera aphidicola str. Cc (Cinara
           cedri)]
          Length = 291

 Score =  213 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 92/280 (32%), Positives = 160/280 (57%), Gaps = 12/280 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             L  YI       +L  ++E  LAK+   + D+ +A  L+ S+LR V+ +A  Y GYGL
Sbjct: 17  GSLEAYIRLANSFSILTSEKEKSLAKKLFFYSDIESAKLLILSNLRFVIHVAKNYSGYGL 76

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P ++++ EGNIGLM+A+++F+P    RL ++++ WIK+ + EY+LR+W +VKI TT  Q+
Sbjct: 77  PQADLIQEGNIGLMKAIRRFNPNINVRLVSFAVHWIKSEIHEYVLRNWRIVKIATTKAQR 136

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINS 192
           +LFFNLR+ K  L     +     ++  ++++L VS  EV  M  R+ A D + +     
Sbjct: 137 KLFFNLRKSKKRLGWFNRH-----EIDTVSQELGVSTQEVKEMEARMSAQDITFDLSAKD 191

Query: 193 SDKNSSQ---WQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPRERRIFEARRL 248
           S  +S        + + D      + IEK+       N LT ++ +L+ R ++I + R L
Sbjct: 192 SHLDSITNNLRTSFHLEDKKSNFSIKIEKDNWALHATNKLTNALLILDKRSQQIIKRRWL 251

Query: 249 QEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            ++   +TL+ ++ ++ +S ERVRQ+E  A KK++ +I+ 
Sbjct: 252 DDDKPKITLQAIARDYGISAERVRQLEKNAMKKLKIAIEA 291


>gi|222824021|ref|YP_002575595.1| RNA polymerase sigma 70 factor [Campylobacter lari RM2100]
 gi|222539243|gb|ACM64344.1| RNA polymerase sigma 70 factor [Campylobacter lari RM2100]
          Length = 625

 Score =  213 bits (544), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 74/260 (28%), Positives = 129/260 (49%), Gaps = 15/260 (5%)

Query: 29  LEKQEEYVLAKRYREHGDL--SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           LEK +   + ++ +    +   A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGL
Sbjct: 362 LEKDQLKEILEQIKRGKKISDEAKTRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGL 421

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+ +RG++ +TY+ WWI+ A+   I      ++I        +   + ++   +
Sbjct: 422 MKAVDKFEYKRGYKFSTYATWWIRQAISRAIADQARTIRIPIH-----MIETINQINKII 476

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +       K   V  IAK++ +S  +V  +        SL A I  S+++  ++ D++  
Sbjct: 477 REYLQKEGKEPDVSIIAKEVGLSVDKVKQVIKITKEPISLEAPI--SNEDDGKFGDFV-- 532

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFE 263
             D      ++   + + +  +   +  LN RE+ +   R      E+  TLE +  E  
Sbjct: 533 -EDRTSISPMDHILKDDLKEQIDEVLDQLNDREKAVIRMRFGLMDDESDRTLEEIGKELN 591

Query: 264 VSRERVRQIEARAFKKVQES 283
           V+RERVRQIE+ A KK++  
Sbjct: 592 VTRERVRQIESSAIKKLKHP 611


>gi|91777566|ref|YP_552774.1| sigma 70 (RpoD) [Burkholderia xenovorans LB400]
 gi|91690226|gb|ABE33424.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia xenovorans
           LB400]
          Length = 665

 Score =  213 bits (543), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 60/248 (24%), Positives = 114/248 (45%), Gaps = 12/248 (4%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            E     A   ++ ++LRLV+ IA  Y   G+   +++ EGNIGLM+AV KF+  RG++ 
Sbjct: 420 AESKMRKAKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEGNIGLMKAVDKFEYRRGWKF 479

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY+ WW++ A+   +      +++            L R+   +   T     P     
Sbjct: 480 STYATWWVRQAVTRSLADQARTIRVPVHM--IETINKLNRISREILQQTGQEAHP---SV 534

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           +A+++ +SE +V  +        S+   +   D   +   D +    D       +   +
Sbjct: 535 LAERMELSEEKVRGILKIAKQPVSMETPV--GDDGDATLGDMI---EDSAASSPADAAMQ 589

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKK 279
            + R  +  ++  L+PRE ++   R         TLE +  +F+V+RER+RQIE++A +K
Sbjct: 590 ADLRAAIDDALDSLSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIRQIESKAMRK 649

Query: 280 VQESIQKQ 287
           +    +  
Sbjct: 650 LMHPSRAD 657


>gi|144616|gb|AAA23168.1| sigma-A protein (sigA) [Chlamydia muridarum]
          Length = 571

 Score =  213 bits (543), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 69/255 (27%), Positives = 121/255 (47%), Gaps = 13/255 (5%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             + +R+ +     A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+
Sbjct: 304 VRMLQRWMDK-SQEAKQEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFE 362

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             RG++ +TY+ WWI+ A+   I      ++I        +   + ++    + +     
Sbjct: 363 YRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVH-----MIETINKVLRGAKKLMMETG 417

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           K      + ++L  +   V  +        SL A +   D   S + D+L    D   + 
Sbjct: 418 KEPTPEELGEELGFTPDRVREIYKIAQHPISLQAEV--GDSGESSFGDFL---EDTAVES 472

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQI 272
             E       ++ + + +  L  RER +   R   L   P TLE + S F V+RER+RQI
Sbjct: 473 PAEATGYSMLKDKMKKVLKTLTDRERFVLIHRFGLLDGRPKTLEEVGSAFNVTRERIRQI 532

Query: 273 EARAFKKVQESIQKQ 287
           EA+A +K++  I+ +
Sbjct: 533 EAKALRKMRHPIRSK 547



 Score = 38.3 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 8/32 (25%), Positives = 19/32 (59%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREH 44
           +  +  Y+ E+  +P+L ++EE  ++KR  + 
Sbjct: 100 DDPVRMYLKEMGTVPLLTREEEVEISKRIEKA 131


>gi|170782897|ref|YP_001711231.1| RNA polymerase principal sigma factor HrdD [Clavibacter
           michiganensis subsp. sepedonicus]
 gi|169157467|emb|CAQ02657.1| RNA polymerase principal sigma factor HrdD [Clavibacter
           michiganensis subsp. sepedonicus]
          Length = 347

 Score =  213 bits (543), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 75/305 (24%), Positives = 137/305 (44%), Gaps = 37/305 (12%)

Query: 7   SIIVNGE--IGLSRYIHEIRKIPMLEKQEEYVLAKRYR---------------------- 42
           S++  G     +  Y+ +I ++P+L  + E  +A+R                        
Sbjct: 40  SLVTPGASTDAVKDYLRQIGRVPLLTAELEVSVARRIEVGVLSQEVLDTRTDLTPAERRE 99

Query: 43  ----EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
                   + A   LV ++LRLVV IA  Y G GLP  +++ EGN+GL++AV+KFD + G
Sbjct: 100 YQTLAQDGMRAKQHLVNANLRLVVSIAKRYTGRGLPFLDLIQEGNMGLVRAVEKFDYQAG 159

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           F+ +TY+ WWIK ++   +  +   ++I           ++ R+    + + D   +   
Sbjct: 160 FKFSTYASWWIKQSITRGMADTSRTIRIPVH-----TVEHINRINAVQRELGDELGRDPS 214

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           +  IA++ +   ++V  +  R     SL  L+  S  +       L+ D D  +   I+ 
Sbjct: 215 MEEIARESDTPVTKVRYLLDRAQEPMSLQVLVGGSGGDGDTEMADLIEDADVTQ--PIDV 272

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARA 276
             ++     +TR +  L  R+  +   R       P +L  +S +  V+RERVRQIE + 
Sbjct: 273 VTQQLMAAHVTRLIDGLAERDAEVVRMRFGLAGLEPRSLAFVSQQLGVTRERVRQIEKKV 332

Query: 277 FKKVQ 281
             K++
Sbjct: 333 LAKLR 337


>gi|15835519|ref|NP_297278.1| RNA polymerase sigma factor [Chlamydia muridarum Nigg]
 gi|270285702|ref|ZP_06195096.1| RNA polymerase sigma factor [Chlamydia muridarum Nigg]
 gi|270289710|ref|ZP_06196012.1| RNA polymerase sigma factor [Chlamydia muridarum Weiss]
 gi|301337097|ref|ZP_07225299.1| RNA polymerase sigma factor [Chlamydia muridarum MopnTet14]
 gi|7388084|sp|P56835|RPOD_CHLMU RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A;
           AltName: Full=Sigma-66; AltName: Full=Sigma-70
 gi|7190932|gb|AAF39698.1| RNA polymerase sigma factor RpoD [Chlamydia muridarum Nigg]
          Length = 571

 Score =  213 bits (543), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 69/255 (27%), Positives = 120/255 (47%), Gaps = 13/255 (5%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             + +R+ +     A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+
Sbjct: 304 VRMLQRWMDK-SQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFE 362

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             RG++ +TY+ WWI+ A+   I      ++I        +   + ++    + +     
Sbjct: 363 YRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVH-----MIETINKVLRGAKKLMMETG 417

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           K      + ++L  +   V  +        SL A +   D   S + D+L    D   + 
Sbjct: 418 KEPTPEELGEELGFTPDRVREIYKIAQHPISLQAEV--GDSGESSFGDFL---EDTAVES 472

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQI 272
             E       ++ +   +  L  RER +   R   L   P TLE + S F V+RER+RQI
Sbjct: 473 PAEATGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGRPKTLEEVGSAFNVTRERIRQI 532

Query: 273 EARAFKKVQESIQKQ 287
           EA+A +K++  I+ +
Sbjct: 533 EAKALRKMRHPIRSK 547



 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 8/32 (25%), Positives = 19/32 (59%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREH 44
           +  +  Y+ E+  +P+L ++EE  ++KR  + 
Sbjct: 100 DDPVRMYLKEMGTVPLLTREEEVEISKRIEKA 131


>gi|163847594|ref|YP_001635638.1| sigma-70 family RNA polymerase sigma factor [Chloroflexus
           aurantiacus J-10-fl]
 gi|222525449|ref|YP_002569920.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus sp.
           Y-400-fl]
 gi|163668883|gb|ABY35249.1| RNA polymerase sigma factor, sigma-70 family [Chloroflexus
           aurantiacus J-10-fl]
 gi|222449328|gb|ACM53594.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus sp.
           Y-400-fl]
          Length = 345

 Score =  213 bits (543), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 76/296 (25%), Positives = 126/296 (42%), Gaps = 38/296 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD--------------------------L 47
             +  Y+ EI ++ +L   EE  LA+R     +                           
Sbjct: 47  DAVQHYLQEIGRVSLLTAAEEIELAERIERGNEAEAQLATATDLTPRERYELLQAVQQGE 106

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   L+ ++LRLVV IA  Y G GL + +++ EGNIGLM+AV+KFD  +G R +TY+ W
Sbjct: 107 EARRHLIQANLRLVVSIAKKYVGRGLALLDLIQEGNIGLMRAVEKFDYHKGNRFSTYATW 166

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++    ++      + ++K   + +  +  +      IA  L 
Sbjct: 167 WIRQAVTRAIAEQGRTIRLPVHMSES-----VGQVKRIAERLAQSLERQPTAEEIAMALG 221

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
                +  +        SL   +   D+      D+L  +         E   +K  R  
Sbjct: 222 QPVERIQRILEAARRPVSLETPV--GDEGEHTLGDFLTDEEL---PTPGEMAAQKLLRRD 276

Query: 228 LTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           L  ++  LN RERRI + R         TLE +     ++RER RQIEA A ++++
Sbjct: 277 LCAALDRLNDRERRIIDLRYGLVDGRRRTLEEVGRVLGMTRERARQIEAEALRRLR 332


>gi|312796084|ref|YP_004029006.1| RNA polymerase sigma factor rpoS [Burkholderia rhizoxinica HKI 454]
 gi|312167859|emb|CBW74862.1| RNA polymerase sigma factor rpoS [Burkholderia rhizoxinica HKI 454]
          Length = 358

 Score =  213 bits (543), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 81/281 (28%), Positives = 133/281 (47%), Gaps = 16/281 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+
Sbjct: 77  DTIQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFDARQMMIERNLRLVVSIAKGYLNRGV 135

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++       
Sbjct: 136 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV--I 193

Query: 134 RLFFNLRRLKGHLQAITD------NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
           R    + R K HL+          +  +   V  IA  +  +  EV  +        SL+
Sbjct: 194 RELNQVLRAKRHLERNASAPASGADEHRDASVDDIAYLIGKTPEEVADILALNEHTASLD 253

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           A +      +S   D L    D Q Q    + + +    +    +S L  + R + E R 
Sbjct: 254 APLEL--DPASSLLDLL---SDEQSQSPDAEAQHRELETLTRVWLSRLPDKHRHVIERRF 308

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              N  P TLE L+ E  ++RERVRQI+  A  +++     
Sbjct: 309 GLNNIEPATLEELADEMGLTRERVRQIQQEALARLKRYFAS 349


>gi|219849486|ref|YP_002463919.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus
           aggregans DSM 9485]
 gi|219543745|gb|ACL25483.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus
           aggregans DSM 9485]
          Length = 345

 Score =  213 bits (543), Expect = 2e-53,   Method: Composition-based stats.
 Identities = 76/296 (25%), Positives = 126/296 (42%), Gaps = 38/296 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE--------------------------HGDL 47
             +  Y+ EI ++ +L   EE  LA+R                                 
Sbjct: 47  DAVQHYLQEIGRVALLTAVEEVELAERIERGNAAEQRLATATDLTPRERCELLKAVQEGE 106

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   L+ ++LRLVV IA  Y G GL + +++ EGNIGLM+AV+KFD  +G R +TY+ W
Sbjct: 107 EARRHLIQANLRLVVSIAKKYVGRGLSLLDLIQEGNIGLMRAVEKFDHHKGNRFSTYATW 166

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   +      +++    ++      ++R+   L    +    PE    IA  L 
Sbjct: 167 WIRQAVTRALAEQGRTIRLPVHMSES--VAQVKRIADRLAQSLERQPTPE---EIAMALG 221

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
                +  +        SL   +   D+      D++  +         E   +K     
Sbjct: 222 QPVERIQRILEAARCPVSLETPV--GDEGEHTLGDFITDEEL---PAPGEIAAQKLLHRD 276

Query: 228 LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           L  +++ L+ RERRI + R   L     TLE +     ++RER RQIEA A ++++
Sbjct: 277 LCAALNQLSDRERRIIDLRYGLLDGRRRTLEEVGRVLGMTRERARQIEAEALRRLR 332


>gi|269926188|ref|YP_003322811.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
 gi|269789848|gb|ACZ41989.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
          Length = 463

 Score =  213 bits (543), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 68/247 (27%), Positives = 117/247 (47%), Gaps = 13/247 (5%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
             + R+ G   A  +L+ ++ RLVV IA  Y G GL + +++ EGNIGLM+A  KFD  R
Sbjct: 215 WNKVRKEG-EGAKCKLIEANTRLVVSIAKKYLGRGLSLLDLIQEGNIGLMRAADKFDYTR 273

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      +++            + ++    Q +        
Sbjct: 274 GYKFSTYATWWIRQAVTRAIADQSRTIRLPVHV-----CETVSKIHKTSQKLQQELGHEP 328

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
            +  ++ +L +   +V+ +        SL A I   +   S   D+L   H       ++
Sbjct: 329 TIEQLSSELGMPMKKVVQIQQASKFPVSLEAPI--GEDGDSMLGDFLEDVHVLN---PVQ 383

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEAR 275
           K      R  +   +  L P+ER++ E R         TLE + +EF ++RERVRQIE  
Sbjct: 384 KAANDILREQINSVLQNLPPKERKVLELRFGLVDGKCRTLEEVGNEFAITRERVRQIECT 443

Query: 276 AFKKVQE 282
           A ++++E
Sbjct: 444 ALRRLRE 450



 Score = 43.6 bits (102), Expect = 0.031,   Method: Composition-based stats.
 Identities = 9/29 (31%), Positives = 19/29 (65%)

Query: 13 EIGLSRYIHEIRKIPMLEKQEEYVLAKRY 41
          +  +  Y+ EI K+P+L  ++E +LA++ 
Sbjct: 69 DEPVQMYLREIGKVPLLTAEQEVILARKI 97


>gi|78777303|ref|YP_393618.1| RNA polymerase sigma factor RpoD [Sulfurimonas denitrificans DSM
           1251]
 gi|78497843|gb|ABB44383.1| sigma 28 (Flagella/Sporulation) [Sulfurimonas denitrificans DSM
           1251]
          Length = 623

 Score =  213 bits (543), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 77/298 (25%), Positives = 147/298 (49%), Gaps = 26/298 (8%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPM----------LEKQEEYVLAKRYREHGDLS-- 48
           + +++++ +V     +S Y+ EI+K+            ++ ++   + ++ +   ++S  
Sbjct: 325 LTKEDIATMVPEATMVSTYM-EIKKLVQTKEASKNSFDMDPEKLADILEQIKRGKNISEI 383

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           +  ++  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ ++G++ +TY+ WW
Sbjct: 384 SKTKMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYQKGYKFSTYATWW 443

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + R+   ++     + K   V  IA ++ +
Sbjct: 444 IRQAISRAIADQARTIRIPIH-----MIETINRINKIMRKHLQEHGKEPDVEVIALEVGL 498

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  +V ++        SL A I S D    ++ D++    D       +   + + R  +
Sbjct: 499 SVEKVKNVIKITKEPISLEAPIGSEDD--GRFGDFI---EDKTSLSPSDAILKDDLRVQI 553

Query: 229 TRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
              +  LN RE+ + + R      E+  TLE +  E  V+RERVRQIE+ A KK++  
Sbjct: 554 ESVLEQLNEREKAVIKLRFGIMDDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHP 611



 Score = 39.0 bits (90), Expect = 0.84,   Method: Composition-based stats.
 Identities = 9/30 (30%), Positives = 19/30 (63%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRY 41
            +  +  Y+ E+ +IP+L K+EE  ++K+ 
Sbjct: 103 SDSPVRMYLREMGQIPLLTKEEEIEISKKI 132


>gi|227504896|ref|ZP_03934945.1| RNA polymerase sigma factor SigB [Corynebacterium striatum ATCC
           6940]
 gi|227198489|gb|EEI78537.1| RNA polymerase sigma factor SigB [Corynebacterium striatum ATCC
           6940]
          Length = 337

 Score =  213 bits (543), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 70/309 (22%), Positives = 140/309 (45%), Gaps = 38/309 (12%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY------------------RE 43
           +R+N +        +  Y++ I K  +L  ++E  LA+R                    E
Sbjct: 27  SRRNQTNDNPSADLVRVYLNGIGKTALLSAEDEVELAQRIEVGLYAEYKLANAEKITRAE 86

Query: 44  HGD--------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
             D          A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD 
Sbjct: 87  KRDLKILVREGKKARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDY 146

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            +GF+ +TY+ WWI+ A+   +      +++     ++     L R+K  +         
Sbjct: 147 AKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLSRIKREMYQSLGREAT 204

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
            E    +A++  + ES++  +  +     SL+  + + ++  +   D++        +  
Sbjct: 205 NE---ELAEESGIEESKIEMLLRQSRDPVSLDMPVGTDEE--APLGDFIEDAEATDAETA 259

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIE 273
           +    R    + +   +  L  RE+ +   R   ++  P TL+ +  +F +SRERVRQIE
Sbjct: 260 VVAAMR---HSDIRGVIETLEEREQDVIRLRYGLDDGVPRTLDQIGRKFGLSRERVRQIE 316

Query: 274 ARAFKKVQE 282
                K+++
Sbjct: 317 REVMAKLRD 325


>gi|86606677|ref|YP_475440.1| RNA polymerase sigma factor SigC [Synechococcus sp. JA-3-3Ab]
 gi|86555219|gb|ABD00177.1| RNA polymerase sigma-70 factor family [Synechococcus sp. JA-3-3Ab]
          Length = 364

 Score =  213 bits (543), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 72/316 (22%), Positives = 142/316 (44%), Gaps = 59/316 (18%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHG--------------------------------- 45
           Y+ EI ++P+L + EE  LA+R +++                                  
Sbjct: 49  YLQEIGRVPLLGRDEEVALAQRVQDYMKLLDVRLRLQKELGREPTLAEWAARANQYPEWA 108

Query: 46  -------------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A   ++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV+K
Sbjct: 109 NLTPEKLQQIQRIGKRAKEHMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEK 168

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FDP++G+R +TY+ WWI+  +   I      +++     +K     L ++K   + ++  
Sbjct: 169 FDPKKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEK-----LNKIKKAQRKLSQE 223

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +   +  IA +L ++  +V  +  R+    SL   +       ++  D L  D    E
Sbjct: 224 KGRTPTIEDIASELEMTVPQVRELLVRVPRSVSLETKV--GKDKDTELGDLLETDDISPE 281

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT--LENLSSEFEVSRERVR 270
           + ++ +   ++    L + ++ L  RER +   R    +  T  L  +    ++SRERVR
Sbjct: 282 ETMMREALHRD----LQQLLADLTSRERDVIRMRFGLGDGRTYSLAEIGRALDLSRERVR 337

Query: 271 QIEARAFKKVQESIQK 286
           QIEA+A +K+++  ++
Sbjct: 338 QIEAKALQKLRQPKRR 353


>gi|294634769|ref|ZP_06713298.1| RNA polymerase sigma factor RpoS [Edwardsiella tarda ATCC 23685]
 gi|291091828|gb|EFE24389.1| RNA polymerase sigma factor RpoS [Edwardsiella tarda ATCC 23685]
          Length = 328

 Score =  213 bits (543), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 77/271 (28%), Positives = 135/271 (49%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD ++  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 60  YLGEIGYAPLLTAEEEVFFARR-ALRGDEASRKRMIESNLRLVVKISRRYSNRGLALLDL 118

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 119 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 177

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L     +V  M        S++  +    + + 
Sbjct: 178 LRTAR----ELSHKLDHEPSAEEIAEQLEKPVHDVSRMLRLNERITSVDTPLGGDSEKA- 232

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D  E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 233 ----LLDILTDENESGPEDCTQNDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 288

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 289 DVGREIGLTRERVRQIQVEGLRRLREILQGQ 319


>gi|77163721|ref|YP_342246.1| RpoS [Nitrosococcus oceani ATCC 19707]
 gi|254436220|ref|ZP_05049727.1| RNA polymerase sigma factor RpoS [Nitrosococcus oceani AFC27]
 gi|76882035|gb|ABA56716.1| RNA polymerase, sigma 38 subunit, RpoS [Nitrosococcus oceani ATCC
           19707]
 gi|207089331|gb|EDZ66603.1| RNA polymerase sigma factor RpoS [Nitrosococcus oceani AFC27]
          Length = 321

 Score =  213 bits (543), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 77/288 (26%), Positives = 144/288 (50%), Gaps = 13/288 (4%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
            R++  +  +       Y+ EI   P+L  +EE   A R  + G+ +   R++ S+LRLV
Sbjct: 36  TRESQPLGDHEFDATHLYLSEIGCAPLLTAEEEVYHA-RLAKKGNPAGRKRMIESNLRLV 94

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           VKI+  Y   GL + +++ EGN+GL+ AV+KFDPE GFR +TY+ WWI+  ++  ++   
Sbjct: 95  VKISRRYMNRGLALLDLIEEGNLGLIHAVEKFDPEMGFRFSTYATWWIRQTIERALMNQT 154

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             V++       +   + +R+   L    +++   E    +A++LN    E+  +     
Sbjct: 155 RTVRLPVHV--VKEIKSYQRVANKLAQELEHDPSFE---ELAQQLNKPVEEIKRVWSLKD 209

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              S++    ++ + +    D L  +      VL++ ++ ++R   L   +S LN ++R 
Sbjct: 210 NTASMDTGYRNNQEKT--LLDALPDEDAPDPTVLLQNDDMQSR---LKLWLSQLNDKQRE 264

Query: 242 IFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +   R       P TLE +     V+RERVRQI+    K+++  + K+
Sbjct: 265 VVIRRFGLQGYEPQTLEQVGQAIGVTRERVRQIQLETLKRLRRILTKE 312


>gi|237803044|ref|YP_002888238.1| RNA polymerase sigma factor [Chlamydia trachomatis B/Jali20/OT]
 gi|231274278|emb|CAX11073.1| RNA polymerase sigma factor [Chlamydia trachomatis B/Jali20/OT]
          Length = 571

 Score =  213 bits (543), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 69/255 (27%), Positives = 120/255 (47%), Gaps = 13/255 (5%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             + +R+ +     A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+
Sbjct: 304 VRMLQRWMDK-SQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFE 362

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             RG++ +TY+ WWI+ A+   I      ++I        +   + ++    + +     
Sbjct: 363 YRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVH-----MIETINKVLRGAKKLMMETG 417

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           K      + ++L  +   V  +        SL A +   D   S + D+L    D   + 
Sbjct: 418 KEPTPEELGEELGFTPDRVREIYKIAQHPISLQAEV--GDGGESSFGDFL---EDTAVES 472

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQI 272
             E       ++ +   +  L  RER +   R   L   P TLE + S F V+RER+RQI
Sbjct: 473 PAEVTGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGRPKTLEEVGSAFNVTRERIRQI 532

Query: 273 EARAFKKVQESIQKQ 287
           EA+A +K++  I+ +
Sbjct: 533 EAKALRKMRHPIRSK 547



 Score = 38.3 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 8/32 (25%), Positives = 19/32 (59%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREH 44
           +  +  Y+ E+  +P+L ++EE  ++KR  + 
Sbjct: 100 DDPVRMYLKEMGTVPLLTREEEVEISKRIEKA 131


>gi|325269188|ref|ZP_08135807.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           multiformis DSM 16608]
 gi|324988417|gb|EGC20381.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           multiformis DSM 16608]
          Length = 287

 Score =  213 bits (542), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 75/287 (26%), Positives = 145/287 (50%), Gaps = 12/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI    M+  +EE  LA+R R+ GD  A  RL  ++LR VV
Sbjct: 5   KITKSITNRESASLDKYLQEIGHEEMISIEEEVELAQRIRK-GDRKALERLTKANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + I     
Sbjct: 64  SVAKQYQNQGLSLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           ++++    NQ      + ++    +   +   +   +  IA+  ++ E ++       + 
Sbjct: 124 IIRLP--LNQVSSVNKINKILNRFEQENE---RRPSIDEIAQSTDLPEDKIADAMKANSR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     D   S   D +  D+       + +E     R  + R + +L  RE+ +
Sbjct: 179 HVSVDAPFY--DDEQSSLLDVIPNDNAPSTDRGLVEESL---REEIGRVLQILEDREKMV 233

Query: 243 FEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            EA        +TLE + S++ ++RERVRQI+ +A +++++    +V
Sbjct: 234 VEAYFGINQREMTLEEIGSKYNLTRERVRQIKEKAIRRLRQQTNSKV 280


>gi|148240072|ref|YP_001225459.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp. WH
           7803]
 gi|147848611|emb|CAK24162.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 7803]
          Length = 313

 Score =  213 bits (542), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 75/302 (24%), Positives = 142/302 (47%), Gaps = 36/302 (11%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------EHG-------------------D 46
               +S Y+  I +IP+L   EE  L  + +      E G                    
Sbjct: 16  SSDPISWYLATIGRIPLLTPAEEIELGNQVQQLMQLTEDGSIAADSDQFDGKQRRLIRVG 75

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  R++ ++LRLVV +A  Y+G GL + +++ EG++GL +AV+KFDP RG++ +TY+ 
Sbjct: 76  QRAKQRMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAF 135

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ +M   I      +++    +++     L  ++     +          + IA+ +
Sbjct: 136 WWIRQSMTRAIACQSRTIRLPVHLSER-----LTTIRKVSLDLAHKLGAMPSRLEIAEAM 190

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   E+ S+  +     SL+A +N  ++  S   D +    D   +  +++ E++    
Sbjct: 191 DMPVEELDSLLRQALTTSSLDAPVN-GEEGRSFLGDLIA---DSSLEEPLDRVEQRMHHE 246

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L R MS L+ +E+ +   R         TL  +    +VSRERVRQ+E +A +K++   
Sbjct: 247 QLGRWMSHLSDQEQHVLTLRFGLNGNERHTLAEIGRLLDVSRERVRQVELKALRKLRNLT 306

Query: 285 QK 286
           ++
Sbjct: 307 RR 308


>gi|296269678|ref|YP_003652310.1| RpoD subfamily RNA polymerase sigma-70 [Thermobispora bispora DSM
           43833]
 gi|296092465|gb|ADG88417.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobispora
           bispora DSM 43833]
          Length = 478

 Score =  213 bits (542), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 73/302 (24%), Positives = 132/302 (43%), Gaps = 42/302 (13%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGDL------------- 47
             +  Y+  I +  +L   +E  LAKR               E G+              
Sbjct: 176 DSVHTYLKSIGRRTLLTAAQEVELAKRIEAGLYAEYKLKQALESGEKLPPGFREDLEWVI 235

Query: 48  ----SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
                A   ++ ++LRLVV +A  Y   G+ + +VV EGN+GL++AV+KFD  +G++ +T
Sbjct: 236 EDGKRAKDHMLEANLRLVVSVAKKYTDRGMSLLDVVQEGNLGLIRAVEKFDYTKGYKFST 295

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+MWWI+ A+Q     S   +++     +  +   L R++  +         PE    +A
Sbjct: 296 YAMWWIRQAIQRGFADSARTIRLPVHVLE--MLSKLSRVERDMHQRLGREPTPE---ELA 350

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
            +L+ +  ++  +        SL++ I    ++       L+ D D  E    E  +R+ 
Sbjct: 351 VELDKTPDQIEELLRTSRQPISLDSTIG---EDGETCIGDLIEDVDSLEAS--EIVDRQL 405

Query: 224 RRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
               L   +  L+PRE +I   R       P TL+ +     ++RER+RQ+E  +  K++
Sbjct: 406 LAEQLKGMLDNLSPREAKIMSLRFGLVDGKPHTLDEIGKRLGLTRERIRQLEKESLSKLR 465

Query: 282 ES 283
             
Sbjct: 466 HP 467


>gi|288800917|ref|ZP_06406374.1| RNA polymerase sigma-70 factor [Prevotella sp. oral taxon 299 str.
           F0039]
 gi|288332378|gb|EFC70859.1| RNA polymerase sigma-70 factor [Prevotella sp. oral taxon 299 str.
           F0039]
          Length = 287

 Score =  213 bits (542), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 75/287 (26%), Positives = 150/287 (52%), Gaps = 12/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           + + SI    +  L +Y+ EI +  +L  +EE  LA++ +E GD  A  +L  ++LR VV
Sbjct: 5   KISKSITNREDSTLDKYLQEITQEKLLTTEEEITLARKIKE-GDKDALQKLTRANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 64  SVAKQYQHQGLSLPDLINEGNIGLIKAAEKFDDTRGFKFISYAVWWIRQSIMQALADQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           LV++    NQ      + ++    +   +       +  IA+++N+ +  V         
Sbjct: 124 LVRLP--LNQVGSVNKINKISHKFEQEFERK---PSIAEIAEEINLPQERVSDAIKGNNR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A +  +D N +   D L  +              ++ R  L  ++++L+ RER +
Sbjct: 179 HVSMDAPL--TDGNDNGLADLLQGNEGPDIDT---HLLLESLREELKLALNILDERERFV 233

Query: 243 FEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            EA      P +TL+ + ++  ++RER RQI  +A +K++++ Q ++
Sbjct: 234 IEAFYGINQPEMTLQEIGAKKGLTRERARQIREKAIRKLRKNTQNKL 280


>gi|260461453|ref|ZP_05809700.1| RNA polymerase, sigma 32 subunit, RpoH [Mesorhizobium opportunistum
           WSM2075]
 gi|259032523|gb|EEW33787.1| RNA polymerase, sigma 32 subunit, RpoH [Mesorhizobium opportunistum
           WSM2075]
          Length = 287

 Score =  213 bits (542), Expect = 3e-53,   Method: Composition-based stats.
 Identities = 108/269 (40%), Positives = 170/269 (63%), Gaps = 2/269 (0%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           +    K P LE+ EE+ LA  ++E  D +A H +  +H+RLV+ +A  +R YGLP+ +++
Sbjct: 11  VRAAMKAPYLERDEEHRLALLWKEDNDQNALHSITVAHMRLVISMASKFRHYGLPLGDLI 70

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EG++GL++A  +F+PER  R +TY+ WWI+A+MQ+YILR+WS+V+ GT++ QK LFFNL
Sbjct: 71  QEGHVGLLEAAARFEPERDVRFSTYATWWIRASMQDYILRNWSIVRGGTSSAQKALFFNL 130

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSS 198
           RRL+  L    +          ++  L VSE++V  M+ RL+  D SLN  +   D  ++
Sbjct: 131 RRLRARLANGAEPLSNETLYREVSVALGVSEADVAMMDSRLSAPDSSLNVPLAD-DAGAT 189

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           +  D+LV D    ++V+ ++ +   R   L  +++ LN RE RI E RRL +   TLE L
Sbjct: 190 ERMDFLVSDDPLPDEVVSDRIDVARRSVWLKAALAALNARELRIIEERRLSDEGATLEAL 249

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQ 287
                +S+ERVRQIEARA +K++ ++ KQ
Sbjct: 250 GETLGISKERVRQIEARAMEKLKVALVKQ 278


>gi|145295824|ref|YP_001138645.1| RNA polymerase sigma factor SigB [Corynebacterium glutamicum R]
 gi|12958494|gb|AAK09322.1|AF320818_1 sigma factor SigB [[Brevibacterium] flavum]
 gi|140845744|dbj|BAF54743.1| hypothetical protein [Corynebacterium glutamicum R]
          Length = 331

 Score =  213 bits (542), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 70/310 (22%), Positives = 141/310 (45%), Gaps = 39/310 (12%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAK-----RYREH------------ 44
           +R+  +     +  +  Y++ I K  +L  ++E  LA+      Y EH            
Sbjct: 20  SRRGQTNDNPSQDLVRVYLNGIGKTALLTAEDEVELAQTIEVGLYAEHLLKNSEEPLTRA 79

Query: 45  ----------GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                         A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD
Sbjct: 80  MKRDLKVLAKDGKKARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFD 139

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +GF+ +TY+ WWI+ A+   +      +++     ++     L R+K  +        
Sbjct: 140 YSKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLSRIKREMYQHLGREA 197

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
             E    +A++  + ES++  +  +     SL+  + + ++  +   D++        + 
Sbjct: 198 TNE---ELAEESGIEESKIEMLLRQSRDPVSLDMPVGADEE--APLGDFIEDSEATDAES 252

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
            +    R    + +   ++ L PRE+ +   R   ++  P TL+ +   F +SRERVRQI
Sbjct: 253 AVVASMR---HSDIRAVLNTLEPREQDVIRLRYGLDDGVPRTLDQIGRRFGLSRERVRQI 309

Query: 273 EARAFKKVQE 282
           E     K+++
Sbjct: 310 EREVMSKLRD 319


>gi|256425191|ref|YP_003125844.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chitinophaga
           pinensis DSM 2588]
 gi|256040099|gb|ACU63643.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chitinophaga
           pinensis DSM 2588]
          Length = 285

 Score =  213 bits (542), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 80/279 (28%), Positives = 149/279 (53%), Gaps = 15/279 (5%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
            I       + +Y+ EI KIP+L  +EE VLA+R +  GD  A  RL T +LR VV +A 
Sbjct: 9   QITNRDSQAVEKYLQEISKIPLLTPEEETVLAQRIK-MGDQKALERLTTGNLRFVVSVAK 67

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y+  GL +S++++EGN+GL++A ++FD  +GF+  +Y++WWI+ ++ + +     LV++
Sbjct: 68  QYQHQGLSLSDLINEGNLGLIKAAQRFDETKGFKFISYAVWWIRQSILQALAEQGRLVRL 127

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
               N+   +    +     +   +     E++  I   L +SESE+ ++        SL
Sbjct: 128 P--QNKIGTYNKANKAYMAFEQENEREPSTEELAEI---LEMSESEINNIFQSNTRHMSL 182

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           +A ++       + +D  + D      +  +   R + R  + R +  L+PRE  I  A 
Sbjct: 183 DAPVH-------EAEDVAMGDLLEGGDITDDDVMRDSLREEIRRVLKSLSPREAEIVNAY 235

Query: 247 RL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
                EN  T+E +  ++++++ER+RQI+ RA K++Q++
Sbjct: 236 FGLDGENGATIEQIGQKYDLTKERIRQIKERAIKRLQKA 274


>gi|300112902|ref|YP_003759477.1| RpoD subfamily RNA polymerase sigma 70 subunit [Nitrosococcus
           watsonii C-113]
 gi|299538839|gb|ADJ27156.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nitrosococcus
           watsonii C-113]
          Length = 310

 Score =  213 bits (542), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 76/288 (26%), Positives = 143/288 (49%), Gaps = 13/288 (4%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
            R++ S+  +       Y+ EI   P+L  +EE   A R  + G+ +   R++ S+LRLV
Sbjct: 25  TRESQSLNDHEFDATHLYLSEIGFAPLLTAEEEVYYA-RLAKKGNSAGRKRMIESNLRLV 83

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           VKI+  Y   GL + +++ EGN+GL+ AV+KFDPE GFR +TY+ WWI+  ++  ++   
Sbjct: 84  VKISRRYMNRGLALLDLIEEGNLGLIHAVEKFDPEMGFRFSTYATWWIRQTIERALMNQT 143

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             V++       +   + +R+   L    +++   E    +A++L+    E+  +     
Sbjct: 144 RTVRLPVHV--VKEIKSYQRVANKLAQELEHDPSFE---ELAQQLDKPVEEIKRVWSLKD 198

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              S++    ++ + +    D L  +      VL++ +   + +  L   +S LN ++R 
Sbjct: 199 NTASMDTGYRNNQEKT--LLDALPDEGAPDPTVLLQND---DMQARLELWLSQLNDKQRE 253

Query: 242 IFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +   R       P TLE +     V+RERVRQI+    K+++  + K+
Sbjct: 254 VVIRRFGLQGYEPQTLEQVGQAIGVTRERVRQIQLETLKRLRRILAKE 301


>gi|325295045|ref|YP_004281559.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Desulfurobacterium thermolithotrophum DSM 11699]
 gi|325065493|gb|ADY73500.1| RNA polymerase, sigma 70 subunit, RpoD subfamily
           [Desulfurobacterium thermolithotrophum DSM 11699]
          Length = 563

 Score =  213 bits (542), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 73/252 (28%), Positives = 124/252 (49%), Gaps = 14/252 (5%)

Query: 35  YVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           Y LA+R    +     A   LV S+LRLVV IA  Y   GL   +++ EGNIGLM+AV K
Sbjct: 309 YKLAERIYFYKKDSQEAKQILVRSNLRLVVSIAKKYINRGLHFLDLIQEGNIGLMKAVDK 368

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+  RG++ +TY+ WWI+ A+   I      ++I            + +    +      
Sbjct: 369 FEYRRGYKFSTYATWWIRQAITRAIADQARTIRIPVHM--IETINKVIKASRQMFLEKGR 426

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +PE    IA++L +  S+V S+        SL   I   D   S   +++    D + 
Sbjct: 427 EPRPE---EIAERLRMPASKVRSIIQLAQEPVSLETPI--GDDEDSTLGNFI---EDSKS 478

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVR 270
            +   +  +K+ +  +++ +S L+ RE  + + R   +     TLE +  E +V+RER+R
Sbjct: 479 PIPEHEVIKKDLQEKVSQLLSTLSEREALVLKLRFGLDGYPEHTLEQVGRELKVTRERIR 538

Query: 271 QIEARAFKKVQE 282
           QIE++A +K++ 
Sbjct: 539 QIESKALRKLKN 550


>gi|118618673|ref|YP_907005.1| RNA polymerase sigma factor SigB [Mycobacterium ulcerans Agy99]
 gi|118570783|gb|ABL05534.1| RNA polymerase sigma factor SigB [Mycobacterium ulcerans Agy99]
          Length = 323

 Score =  213 bits (542), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 72/312 (23%), Positives = 137/312 (43%), Gaps = 38/312 (12%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREH--------GD---- 46
            ++         +  Y++ I K  +L  + E  LAKR     Y EH        GD    
Sbjct: 15  SDLDAQSPAADLVRVYLNGIGKTALLNAEGEVELAKRIEAGLYAEHLLATRKRLGDNRKR 74

Query: 47  ---------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
                      A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +
Sbjct: 75  ELAAVVRDGAEARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTK 134

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           GF+ +TY+ WWI+ A+   +      +++     ++     L R+K   + I  N  +  
Sbjct: 135 GFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLARIK---REIHQNLGREA 189

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A +  +   ++  +        SL+  + S ++  +   D++    D +      
Sbjct: 190 TDEELAAESGIPVEKINDLLEHSRDPVSLDMPVGSDEE--APLGDFI---EDAEAMSAEN 244

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
               +     +   ++ L+ RE ++   R   ++  P TL+ +   F +SRERVRQIE  
Sbjct: 245 AVIAELLHTDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERD 304

Query: 276 AFKKVQESIQKQ 287
              K++   +  
Sbjct: 305 VMCKLRHGERAD 316


>gi|72382695|ref|YP_292050.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Prochlorococcus marinus str. NATL2A]
 gi|124026414|ref|YP_001015529.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. NATL1A]
 gi|72002545|gb|AAZ58347.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Prochlorococcus marinus str. NATL2A]
 gi|123961482|gb|ABM76265.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. NATL1A]
          Length = 313

 Score =  212 bits (541), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 80/302 (26%), Positives = 144/302 (47%), Gaps = 36/302 (11%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------EHG-------------------D 46
               +S Y+  I ++P+L   EE  L  + +      E G                    
Sbjct: 16  SSDPISWYLSSIGRVPLLTPAEEIELGNQVQTLMSLTEDGQIKEQSKEFTSHQRRLIRIG 75

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  R++ ++LRLVV +A  Y+G GL + ++V EG++GL +AV+KFDP RG++ +TY+ 
Sbjct: 76  RRAKERMMKANLRLVVSVAKKYQGKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAF 135

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ +M   I      +++    +++     L  ++     +          + IA+ +
Sbjct: 136 WWIRQSMTRAIACQSRTIRLPVHLSER-----LATIRKVSLDLAHKLGAMPSRIEIAEAM 190

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   E+ S+  +     SL+A +N  D+  S   D +    DG  +  ++K E+K  + 
Sbjct: 191 EIELEELDSILRQALTTSSLDAPVN-GDEGRSFLGDLIA---DGSGEEPLDKVEQKIHQE 246

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L R +S L+ +E+ +   R   E     TL  +    +VSRERVRQ+E +A +K++   
Sbjct: 247 QLGRWLSHLSEQEQHVIRLRFGLEGNERHTLAEIGRLLQVSRERVRQVELKALRKLRNLT 306

Query: 285 QK 286
           +K
Sbjct: 307 RK 308


>gi|297622151|ref|YP_003710288.1| RNA polymerase sigma factor rpoD [Waddlia chondrophila WSU 86-1044]
 gi|297377452|gb|ADI39282.1| RNA polymerase sigma factor rpoD [Waddlia chondrophila WSU 86-1044]
          Length = 555

 Score =  212 bits (541), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 73/255 (28%), Positives = 120/255 (47%), Gaps = 13/255 (5%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             + +R+ +     A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+
Sbjct: 300 VRMLQRWMDK-SQEAKREMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFE 358

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             RG++ +TY+ WWI+ A+   I      ++I            + R    L   T    
Sbjct: 359 YRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVHM--IETINKVLRGAKKLMMETGREP 416

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            PE    +A +L +S   +  +        SL A +   D   SQ+ D+L    D     
Sbjct: 417 TPE---ELANELGLSAERIREIYKIAQHPISLQAEV--GDGGESQFGDFL---EDTGADS 468

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
             E       ++ +   +  L  RER++   R    +  P TLE +  EF V+RER+RQI
Sbjct: 469 PAEATGYSILKDKMNEVLLTLTDRERKVLIQRFGLNDGKPKTLEEVGVEFNVTRERIRQI 528

Query: 273 EARAFKKVQESIQKQ 287
           EA+A +K++   + +
Sbjct: 529 EAKALRKMRHPTRSK 543



 Score = 39.4 bits (91), Expect = 0.60,   Method: Composition-based stats.
 Identities = 13/59 (22%), Positives = 27/59 (45%), Gaps = 13/59 (22%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           +  +  Y+ E+  +P+L ++EE  ++KR        A H+        + +I M +R  
Sbjct: 96  DDPVRMYLKEMGSVPLLTREEEVEISKRI-----EKAQHQ--------IERIIMRFRNS 141


>gi|289548873|ref|YP_003473861.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermocrinis
           albus DSM 14484]
 gi|289182490|gb|ADC89734.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermocrinis
           albus DSM 14484]
          Length = 568

 Score =  212 bits (541), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 75/286 (26%), Positives = 128/286 (44%), Gaps = 14/286 (4%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL--SAAHRLVTSHLRLVVK 63
             I+ N  + L + + E+R+   +  +E   + +  +E       A   +V  +LRLVV 
Sbjct: 286 FQILRNEYLALRKEVEELRREMGILPEEIGRVIQIIKEGRTKVTQAKQVMVKCNLRLVVS 345

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y   GL   +++ EGNIGLM+AV K+D  +G++ +TY+ WWI+ A+   I      
Sbjct: 346 IAKKYVNRGLHFLDLIQEGNIGLMKAVDKYDYRKGYKFSTYATWWIRQAITRAIADQART 405

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           ++I        +   +  +    + +T    +      IAK L +   +   +       
Sbjct: 406 IRIPVH-----MIETINDITKAHKKLTQELGREPTAEEIAKYLGIPVDKARKVMRMAQEP 460

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SL   I   D   +  +D++    D       E+  RK  R  L + +S L  +ER I 
Sbjct: 461 ISLETPI--GDDEDAHLKDFI---EDKSVPSPEEQVTRKLLREQLIKVLSTLGEKEREIL 515

Query: 244 EARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             R         TLE +   F V+RER+RQIE +A +K++   + +
Sbjct: 516 MYRYGLVDGTEYTLEQIGRMFNVTRERIRQIETKAIRKLRHPARSK 561



 Score = 36.7 bits (84), Expect = 3.8,   Method: Composition-based stats.
 Identities = 42/264 (15%), Positives = 90/264 (34%), Gaps = 31/264 (11%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG--- 70
             +  Y+ E+ KIP+L ++EE   AK+  E G       L+ +   L+ ++   +     
Sbjct: 81  DPVRLYMREMGKIPLLTREEEIKYAKQI-EMGRKIMRRGLLRTSF-LIDRVLKDWANVCN 138

Query: 71  ---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
                  I + V +      + V++++         +    ++ A        W  + + 
Sbjct: 139 GKLRVQDIVDTVDDS-----RTVEEYEESHEQLERYFMQKGLELAKAYKEALQWRDLYLQ 193

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL----NVSESEVISMNCRLAGD 183
              ++ +    L+R     + + D  LK  +   IA +L    N     +  +  R +  
Sbjct: 194 YGLSEYK-KEYLKRHARMNRVLKDMKLKYSRFEKIADELLNLYNRYSKRIKELEQRKSKL 252

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           ES++  I    +      D L    +         +  +N    L + +  L  RE  I 
Sbjct: 253 ESIHPNIEELIREYDLRPD-LQEKAEKAGYGFARFQILRNEYLALRKEVEELR-REMGIL 310

Query: 244 EARRLQENPVTLENLSSEFEVSRE 267
                       E +    ++ +E
Sbjct: 311 P-----------EEIGRVIQIIKE 323


>gi|110596913|ref|ZP_01385203.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4 [Chlorobium
           ferrooxidans DSM 13031]
 gi|110341600|gb|EAT60060.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4 [Chlorobium
           ferrooxidans DSM 13031]
          Length = 299

 Score =  212 bits (541), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 76/299 (25%), Positives = 145/299 (48%), Gaps = 24/299 (8%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD-----------LSAAH 51
           + +  I     + L RY+ EI K  +L  ++E  L K  ++  D             A  
Sbjct: 5   KISKQITNRESLSLDRYLQEIGKYDLLTAEDEVKLTKAIKDGFDMPVDTTEYKRAKRALD 64

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +L+  +LR VV +A  Y+  GL + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ 
Sbjct: 65  KLIKGNLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQ 124

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ + +     +V++    N+      + +    L+   + +        +A  L++   
Sbjct: 125 SILQALAEQSRIVRLP--LNRVGTLNKISKAYSQLEQEFERD---PNTRELATLLDMDSQ 179

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           +V           S++A     D N  +  D L  D      +      R +    + RS
Sbjct: 180 DVADTLKIAGRHVSVDAPFAQGDDN--RLLDVLQNDG----HLPDYGLNRDSLTLEVERS 233

Query: 232 MSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +SVL PRE  +  +      +NP+TLE +  +F+++RERVRQI+ +A +++++S   +V
Sbjct: 234 LSVLAPREADVIRSYFGIGMDNPLTLEEIGEKFKLTRERVRQIKEKAIRRLRQSAYSKV 292


>gi|213964561|ref|ZP_03392761.1| RNA polymerase sigma factor RpoD [Corynebacterium amycolatum SK46]
 gi|213952754|gb|EEB64136.1| RNA polymerase sigma factor RpoD [Corynebacterium amycolatum SK46]
          Length = 329

 Score =  212 bits (541), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 72/297 (24%), Positives = 139/297 (46%), Gaps = 38/297 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH---------------------GDLSAAHR 52
           Y++ I K  +L  +EE  L+KR     Y EH                        +A   
Sbjct: 36  YLNGIGKTALLSAEEEVELSKRIEAGVYAEHLLQTGAKMTRAKKRDVKILAKEGKAARAH 95

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y   G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A
Sbjct: 96  LLEANLRLVVSLAKRYTNRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQA 155

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +      +++     ++     + R+K  L          E    +A++  + E++
Sbjct: 156 ITRGMADQSRTIRLPVHLVEQ--VNKISRIKRELYQQLGREATNE---ELAEESGIPEAK 210

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           +  +  +     SL+  + + ++  +   D++    D +     E      R + + + +
Sbjct: 211 IEMLLRQSRDPVSLDMPVGTDEE--APLGDFI---EDSEATDAEEAVVASLRHHDVRKVL 265

Query: 233 SVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           S L  RE+ + + R   ++  P TL+ +   F +SRERVRQIE     K++E  +  
Sbjct: 266 STLEIREQEVIKLRYGLDDGLPRTLDQIGRHFGLSRERVRQIEREVMSKLREGDRAD 322


>gi|296159716|ref|ZP_06842538.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. Ch1-1]
 gi|295889930|gb|EFG69726.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia sp. Ch1-1]
          Length = 665

 Score =  212 bits (541), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 60/248 (24%), Positives = 114/248 (45%), Gaps = 12/248 (4%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            E     A   ++ ++LRLV+ IA  Y   G+   +++ EGNIGLM+AV KF+  RG++ 
Sbjct: 420 AESKMRKAKSEMIEANLRLVISIAKKYVNRGMLFLDLIQEGNIGLMKAVDKFEYRRGWKF 479

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY+ WW++ A+   +      +++            L R+   +   T     P     
Sbjct: 480 STYATWWVRQAVTRSLADQARTIRVPVHM--IETINKLNRISREILQQTGQEAHP---SV 534

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           +A+++ +SE +V  +        S+   +   D   +   D +    D       +   +
Sbjct: 535 LAERMELSEEKVRGILKIAKQPVSMETPV--GDDGDATLGDMI---EDSAASSPADAAMQ 589

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKK 279
            + R  +  ++  L+PRE ++   R         TLE +  +F+V+RER+RQIE++A +K
Sbjct: 590 ADLRAAIDDALDSLSPREAKVLRMRYGINTKSDHTLEEVGKQFDVTRERIRQIESKAMRK 649

Query: 280 VQESIQKQ 287
           +    +  
Sbjct: 650 LMHPSRAD 657


>gi|126659335|ref|ZP_01730471.1| RNA polymerase sigma factor SigD [Cyanothece sp. CCY0110]
 gi|126619417|gb|EAZ90150.1| RNA polymerase sigma factor SigD [Cyanothece sp. CCY0110]
          Length = 318

 Score =  212 bits (541), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 78/318 (24%), Positives = 141/318 (44%), Gaps = 52/318 (16%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR--------------EHG------ 45
           M +  +    +  Y+ EI ++P+L  +EE + AKR +              E G      
Sbjct: 1   MKLTKSNPDPVRAYLKEIGRVPLLTHEEEILYAKRVQRLVNLEKLRDDIIEETGQEPTEI 60

Query: 46  -------------------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
                                +A  ++V ++LRLVV +A  Y    L + +++ EG IG+
Sbjct: 61  QWAKTAKISRKELQSIIEIGEAAKRKMVEANLRLVVSVAKKYLKRNLDLLDLIQEGTIGM 120

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
            + V+KFDP +G+R +TY+ WWI+ A+   I      +++     +K     L ++K   
Sbjct: 121 QRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEK-----LNKIKKAQ 175

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           + ++    +   VV +A++L+++  +V     R     SL+  +   D   ++  D L  
Sbjct: 176 RELSQQKGRAATVVELAEELDLTPKQVREYLERARQPLSLD--LRVGDNQDTELGDLLED 233

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEV 264
           D     Q   +     + +  L R M  L  +++ +   R   L   P+TL  + S   +
Sbjct: 234 DG----QSPEDFATHSSLQFDLERLMEDLTSQQKEVIALRFGLLDGQPLTLAKIGSRLNI 289

Query: 265 SRERVRQIEARAFKKVQE 282
           SRERVRQIE  A  K+++
Sbjct: 290 SRERVRQIEREALSKLRK 307


>gi|328915181|gb|AEB56014.1| transcription initiation factor sigma 70 [Chlamydophila psittaci
           6BC]
          Length = 561

 Score =  212 bits (541), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 69/255 (27%), Positives = 122/255 (47%), Gaps = 13/255 (5%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             + +R+ +     A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+
Sbjct: 294 VRMLQRWMDK-SQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFE 352

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             RG++ +TY+ WWI+ A+   I      ++I        +   + ++    + +     
Sbjct: 353 YRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVH-----MIETINKVLRGAKKLMMETG 407

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           K      +A++L ++   V  +        SL A +   +   S + D+L    D   + 
Sbjct: 408 KEPTPEELAEELGLTPDRVREIYKIAQHPISLQAEV--GEGGESSFGDFL---EDTGVES 462

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQI 272
             E       ++ +   +  L  RER +   R   L   P TLE + S F V+RER+RQI
Sbjct: 463 PAEATGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGKPKTLEEVGSAFNVTRERIRQI 522

Query: 273 EARAFKKVQESIQKQ 287
           EA+A +K++  I+ +
Sbjct: 523 EAKALRKMRHPIRSK 537



 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 8/32 (25%), Positives = 19/32 (59%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREH 44
           +  +  Y+ E+  +P+L ++EE  ++KR  + 
Sbjct: 90  DDPVRMYLKEMGTVPLLTREEEVEISKRIEKA 121


>gi|254457867|ref|ZP_05071294.1| sigma 28 [Campylobacterales bacterium GD 1]
 gi|207085260|gb|EDZ62545.1| sigma 28 [Campylobacterales bacterium GD 1]
          Length = 623

 Score =  212 bits (541), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 77/298 (25%), Positives = 148/298 (49%), Gaps = 26/298 (8%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPM----------LEKQEEYVLAKRYREHGDLS-- 48
           + ++++S +V     +S Y+ EI+K+            +E ++   + ++ +   ++S  
Sbjct: 325 LTKEDISSMVPEATMVSTYM-EIKKLVQTKEASKNSFDMEPEKLLDILEQIKRGKNISEI 383

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           +  ++  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ ++G++ +TY+ WW
Sbjct: 384 SKTKMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYQKGYKFSTYATWW 443

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I        +   + R+   ++     + K   V  IA ++ +
Sbjct: 444 IRQAISRAIADQARTIRIPIH-----MIETINRINKIMRKHLQEHGKEPDVEVIALEVGL 498

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  +V ++        SL A I   +++  ++ D++    D       +   + + R  +
Sbjct: 499 SVEKVKNVIKITKEPISLEAPI--GNEDDGRFGDFI---EDKSSISPSDAILKDDLRVQI 553

Query: 229 TRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
              +  LN RE+ + + R      E+  TLE +  E  V+RERVRQIE+ A KK++  
Sbjct: 554 EGVLEQLNEREKAVIKLRFGIMDDESDRTLEEIGRELNVTRERVRQIESSAIKKLKHP 611



 Score = 39.0 bits (90), Expect = 0.88,   Method: Composition-based stats.
 Identities = 9/30 (30%), Positives = 19/30 (63%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRY 41
            +  +  Y+ E+ +IP+L K+EE  ++K+ 
Sbjct: 103 SDSPVRMYLREMGQIPLLTKEEEIEISKKI 132


>gi|253701007|ref|YP_003022196.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           M21]
 gi|251775857|gb|ACT18438.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geobacter sp.
           M21]
          Length = 325

 Score =  212 bits (541), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 75/285 (26%), Positives = 141/285 (49%), Gaps = 13/285 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EIRK  +L+  +E  LA +  + GD  A  R++ S+LRLVVKIA  YR  G
Sbjct: 48  DDAIKLYLIEIRKHALLDAVQEKELALKISQ-GDGDARKRMILSNLRLVVKIAKRYRNRG 106

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +P+ +++ EGNIGL++AV++F   +  R +TY+ WWI+ +++  ++     +++    + 
Sbjct: 107 MPLLDIIEEGNIGLIKAVERFKLSKECRFSTYATWWIRQSIERALINQVRTIRLPVHVSD 166

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 + R+    + +     +      +A  L ++   +  +   L    S+   +  
Sbjct: 167 -----EINRMFRENRVLELKLNREPTAKEVADNLGITVQRLRELMVVLKKTFSIEQPM-- 219

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN- 251
            ++      D +    D    +  E  E +NR  +++  +  L+  ER+I   R   E+ 
Sbjct: 220 GERGDFCLTDTI---QDTSTVLPTELLENQNRYELISNLLEFLSETERKILTLRFGLEDK 276

Query: 252 -PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPP 295
            P TL+ +   F V+RER+RQIE +A +K++  I    +L   P 
Sbjct: 277 APQTLDTIGQGFGVTRERIRQIEVKALEKLRLMIASFEDLERLPG 321


>gi|313682108|ref|YP_004059846.1| RNA polymerase, sigma 70 subunit, rpod [Sulfuricurvum kujiense DSM
           16994]
 gi|313154968|gb|ADR33646.1| RNA polymerase, sigma 70 subunit, RpoD [Sulfuricurvum kujiense DSM
           16994]
          Length = 620

 Score =  212 bits (541), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 68/237 (28%), Positives = 119/237 (50%), Gaps = 13/237 (5%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ ++G++ +TY+ WWI
Sbjct: 382 KTRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYQKGYKFSTYATWWI 441

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + A+   I      ++I        +   + R+   ++     + K   V  IA+++ +S
Sbjct: 442 RQAISRAIADQARTIRIPIH-----MIETINRINKIMRKHLQEHGKEPDVETIAEEVGLS 496

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             +V ++        SL A I   ++   ++ D++    D       +   + + +  + 
Sbjct: 497 VEKVKNVIKITKEPISLEAPI--GNEEDGRFGDFI---EDKMSLSPSDAILKDDLKVQIE 551

Query: 230 RSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +  LN RE+ + + R      E+  TLE +  E  V+RERVRQIE+ A KK++  
Sbjct: 552 SVLEQLNEREKAVIKMRFGIMDDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHP 608



 Score = 40.2 bits (93), Expect = 0.36,   Method: Composition-based stats.
 Identities = 10/30 (33%), Positives = 19/30 (63%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRY 41
            +  +  Y+ E+ +IP+L K+EE  ++KR 
Sbjct: 103 SDSPVRMYLREMGQIPLLTKEEEVEISKRM 132


>gi|315638945|ref|ZP_07894116.1| DNA-directed RNA polymerase sigma subunit RpoD [Campylobacter
           upsaliensis JV21]
 gi|315480974|gb|EFU71607.1| DNA-directed RNA polymerase sigma subunit RpoD [Campylobacter
           upsaliensis JV21]
          Length = 657

 Score =  212 bits (541), Expect = 4e-53,   Method: Composition-based stats.
 Identities = 76/249 (30%), Positives = 124/249 (49%), Gaps = 14/249 (5%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
            KR ++  D  A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ +R
Sbjct: 406 IKRGKKISD-EAKGRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKR 464

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I        +   + ++   ++     N K  
Sbjct: 465 GYKFSTYATWWIRQAISRAIADQARTIRIPIH-----MIETINQINKIIREHLQKNGKEP 519

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
            V  IAK++ +S  +V  +        SL A I S D    ++ D++    D      ++
Sbjct: 520 DVNDIAKEVGLSVDKVKQVIKITKEPISLEAPIGSEDD--GKFGDFV---EDKNSLSPMD 574

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEA 274
              + + +  +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+
Sbjct: 575 NILKDDLKEQIDEVLDQLNDREKAVIRMRFGLLEDESDRTLEEIGKELNVTRERVRQIES 634

Query: 275 RAFKKVQES 283
            A KK++  
Sbjct: 635 SAIKKLKHP 643


>gi|189219555|ref|YP_001940196.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Methylacidiphilum infernorum V4]
 gi|189186413|gb|ACD83598.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Methylacidiphilum infernorum V4]
          Length = 623

 Score =  212 bits (541), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 72/263 (27%), Positives = 126/263 (47%), Gaps = 13/263 (4%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           ++P+   +E++   K++     + A   +V ++LRLV+ IA  Y   GL   +++ EGN+
Sbjct: 358 QLPLPVFKEKHQELKQWLNEA-IKAKSEMVEANLRLVISIAKKYSNRGLSFLDLIQEGNM 416

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+AV+KF+  RG++ +TY+ WWI+ A+   I      ++I            L R++ 
Sbjct: 417 GLMKAVEKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLMRVQK 474

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L         PE    IA +  +S   + ++        SL A +   +   + + D++
Sbjct: 475 QLIQELGREPTPE---EIADETQMSVDRIRTIIKMAQHPISLQAQV--GESEDTTFGDFI 529

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEF 262
               D   +   E       R  +   +  L  RER + E R   L   P TLE +  +F
Sbjct: 530 ---EDKAAENPSEMTGYSLLREKIKDVLGTLTERERTVIEQRFGLLDGYPRTLEEVGKQF 586

Query: 263 EVSRERVRQIEARAFKKVQESIQ 285
            V+RER+RQIEA+A +K++   +
Sbjct: 587 RVTRERIRQIEAKALRKMRHPTR 609



 Score = 42.9 bits (100), Expect = 0.065,   Method: Composition-based stats.
 Identities = 12/58 (20%), Positives = 27/58 (46%), Gaps = 6/58 (10%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           +  +  Y+ ++ ++P+L +++E  ++KR  +         +V S L     IA  Y  
Sbjct: 164 DDPVRMYLKQMGQVPLLTREQEVEISKRIEQS------EAMVKSCLHSFHFIAKEYLN 215


>gi|194334634|ref|YP_002016494.1| RNA polymerase sigma-32 subunit RpoH [Prosthecochloris aestuarii
           DSM 271]
 gi|194312452|gb|ACF46847.1| RNA polymerase, sigma 32 subunit, RpoH [Prosthecochloris aestuarii
           DSM 271]
          Length = 299

 Score =  212 bits (541), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 77/299 (25%), Positives = 143/299 (47%), Gaps = 24/299 (8%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD-----------LSAAH 51
           + +  I     + L RY+ EI K  +L  ++E  L    +E  D             A  
Sbjct: 5   KISKQITNRESLSLDRYLQEIGKYELLTAEDEVKLTMAIKEGYDMPVDTPEYKRAKRALD 64

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +L+  +LR VV +A  Y+  GL + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ 
Sbjct: 65  KLIKGNLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQ 124

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ + +     +V++            L ++      +     +      +A  L++   
Sbjct: 125 SILQALAEQSRIVRLPLNR-----VGTLNKISKAYSQLEQEFERDPNTKELATVLDMDSQ 179

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           +V           S++A     D N  +  D L +D    +  L     R +    + RS
Sbjct: 180 DVADTLKIAGRHVSVDAPFAQGDDN--RLLDVLQHDGQKPDHGLT----RDSLTLEVERS 233

Query: 232 MSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +SVL PRE  +  +      ENP+TLE +  +F+++RERVRQI+ +A +++++S   +V
Sbjct: 234 LSVLAPREADVIRSYFGIGMENPLTLEEIGEKFKLTRERVRQIKEKAIRRLRQSAYSKV 292


>gi|218441429|ref|YP_002379758.1| RNA polymerase sigma factor SigD [Cyanothece sp. PCC 7424]
 gi|218174157|gb|ACK72890.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
          Length = 318

 Score =  212 bits (541), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 74/318 (23%), Positives = 135/318 (42%), Gaps = 52/318 (16%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------- 43
           M    N    +  Y+ EI ++P+L  +EE VLAKR +                       
Sbjct: 1   MKTAKNPTDPVRAYLREIGRVPLLTHEEEIVLAKRVQRFMALQDIKDALTQTLKREPQDS 60

Query: 44  -----------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
                                +A  ++V ++LRLVV +A  Y    L + +++ EG IG+
Sbjct: 61  EWASAAKITEEELHRAIAAGKAAKEKMVEANLRLVVSVAKKYLKRNLDLLDLIQEGTIGM 120

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
            + V+KFDP +G+R +TY+ WWI+ A+   I      +++     +K     L ++K   
Sbjct: 121 QRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEK-----LNKIKKAQ 175

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           + ++    +   +  +A++L ++  +V     R     SL+  +   D   ++  + L  
Sbjct: 176 RQLSQAKGRAATISELAEELELTPRQVRDYLERARQPLSLDLKV--GDNQDTELGELLED 233

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
                E        + +    L + MS L P+++ +   R       P+TL  +     +
Sbjct: 234 TGTSPEDYATHSSLQVD----LEKLMSDLTPQQKEVLALRFGLVDGQPLTLAKIGVRLNI 289

Query: 265 SRERVRQIEARAFKKVQE 282
           SRERVRQIE  A  K+++
Sbjct: 290 SRERVRQIEREALSKLRK 307


>gi|319404792|emb|CBI78393.1| RNA polymerase sigma-32 factor [Bartonella rochalimae ATCC
           BAA-1498]
          Length = 247

 Score =  212 bits (541), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 94/235 (40%), Positives = 152/235 (64%), Gaps = 1/235 (0%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           H++  +H+RLV+ IA  ++ + +P+ ++V EG +GL++A  +FDP+RG R +TY+ WWI+
Sbjct: 2   HQIAAAHMRLVISIASRFKRFKMPLGDLVQEGYVGLLEAAARFDPDRGVRFSTYATWWIR 61

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
           A++Q+YILR+WS+V+ GT+++QK LFFNLRRL+  L    +   K E   AI++KL VS 
Sbjct: 62  ASIQDYILRNWSIVRGGTSSSQKALFFNLRRLRAKLAQDDNTLTKQEIFRAISEKLGVSV 121

Query: 171 SEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           ++V  M+ R +G D SL+  I+ + +      D L+ DH   + V+ +  + + R   L 
Sbjct: 122 NDVEKMDFRFSGTDNSLSLSISENGETPIAKMDSLIDDHPLPDSVIEQAIDGQRRAQWLH 181

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            ++ +LN RE  I   RRL E   TLE L  +  +S+ERVRQIE RA +K++ ++
Sbjct: 182 EALQILNERELEIIRFRRLNEEGTTLEVLGEKLGISKERVRQIEVRALQKLRCAL 236


>gi|38233998|ref|NP_939765.1| RNA polymerase sigma factor SigB [Corynebacterium diphtheriae NCTC
           13129]
 gi|38605711|sp|P33118|RPSB_CORDI RecName: Full=RNA polymerase sigma factor sigB
 gi|38200260|emb|CAE49944.1| RNA polymerase sigma factor [Corynebacterium diphtheriae]
          Length = 329

 Score =  212 bits (541), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 67/315 (21%), Positives = 140/315 (44%), Gaps = 39/315 (12%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAK---------------------- 39
           +R+N +        +  Y++ I K  +L  ++E  LA+                      
Sbjct: 18  SRRNQTNDNPSADLVRVYLNGIGKTALLNAEDEVELAQTIEVGLYAEYLLENSQEPLTRA 77

Query: 40  -----RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                +        A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD
Sbjct: 78  MKRDLKVLVKEGRKARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFD 137

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +GF+ +TY+ WWI+ A+   +      +++     ++     L R+K  +        
Sbjct: 138 YSKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLSRIKREMYQQLGREA 195

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
             E    +A++  + ES++  +  +     SL+  + + ++  +   D++        + 
Sbjct: 196 TNE---ELAEESGIEESKIEMLLRQSRDPVSLDMPVGADEE--APLGDFIEDSEATDAES 250

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
            +    R    + +   +  L  RE+ +   R   ++  P TL+ +  +F +SRERVRQI
Sbjct: 251 AVVASLR---HSDIRTVLDTLEQREQDVIRLRYGLDDGVPRTLDQIGRQFGLSRERVRQI 307

Query: 273 EARAFKKVQESIQKQ 287
           E     K+++  + +
Sbjct: 308 EREVMSKLRDGARAE 322


>gi|291277050|ref|YP_003516822.1| RNA polymerase sigma-70 factor [Helicobacter mustelae 12198]
 gi|290964244|emb|CBG40093.1| RNA polymerase sigma factor (sigma-70) [Helicobacter mustelae
           12198]
          Length = 614

 Score =  212 bits (541), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 74/260 (28%), Positives = 128/260 (49%), Gaps = 15/260 (5%)

Query: 29  LEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L+ ++   + ++ +        A +++  S+LRLVV IA  Y   GLP  +++ EGNIGL
Sbjct: 353 LDPEKLKEILEQIKRGKIISDKAKNKMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGL 412

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KFD +R F+ +TY+ WWI+ A+   I      ++I        +   + R+   +
Sbjct: 413 MKAVDKFDYKRNFKFSTYATWWIRQAISRAIADQARTIRIPIH-----MIETINRIHKIM 467

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +       K   V  IA+K+ +S  +V  +        SL A I S +    ++ D++  
Sbjct: 468 RKYIQETGKEPDVEIIAEKVGLSVDKVKHVIKITKEPVSLEAPIGSDED--GKFGDFV-- 523

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFE 263
             D      +++  +++ R  +   +  LN RE+ +   R      E+  TLE +  E  
Sbjct: 524 -EDKNSTNTMDQIMKEDLRAQIFEVLDQLNEREQAVIRMRFGLLDDESDRTLEEIGKELN 582

Query: 264 VSRERVRQIEARAFKKVQES 283
           V+RERVRQIE+ A KK++  
Sbjct: 583 VTRERVRQIESSAIKKLKHP 602



 Score = 37.9 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 8/42 (19%), Positives = 23/42 (54%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR 42
           M  +++      +  +  Y+ E+ +I +L K++E  L+++ +
Sbjct: 91  MKERDLLEWSRSDSPVRMYLREMGQIELLTKEDEVELSRQIK 132


>gi|86157148|ref|YP_463933.1| sigma 70 (RpoD) [Anaeromyxobacter dehalogenans 2CP-C]
 gi|85773659|gb|ABC80496.1| RNA polymerase, sigma 70 subunit, RpoD [Anaeromyxobacter
           dehalogenans 2CP-C]
          Length = 805

 Score =  212 bits (541), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 82/284 (28%), Positives = 128/284 (45%), Gaps = 23/284 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYV-----LAKRYREHGD-----LSAAHRLVTSHLRLVVKIA 65
           L R +    +  +L  QEE       L + YR  GD       A   LV ++LRLVV IA
Sbjct: 525 LDRTLRSAGR-KILRVQEEAEVPVDELRRTYRMIGDGERKAERAKTELVEANLRLVVSIA 583

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ WWI+ A+   I      ++
Sbjct: 584 KKYTNRGLQFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWWIRQAITRAIADQARTIR 643

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           I            L R   +L         PE    IA+K+ +   +V  +        S
Sbjct: 644 IPVHM--IETINKLIRTSRYLVQELGREPTPE---EIAEKMELPLDKVRKVLKIAKEPIS 698

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L   I   ++  S   D++    D       +     N      + ++ L PRE ++   
Sbjct: 699 LETPI--GEEEDSHLGDFI---EDKSLVSPSDAVINMNLAEQTRKVLATLTPREEKVLRM 753

Query: 246 RRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           R         TLE +  +FEV+RER+RQIEA+A +K++   + +
Sbjct: 754 RFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLRHPSRSK 797


>gi|145219258|ref|YP_001129967.1| RNA polymerase, sigma 32 subunit, RpoH [Prosthecochloris
           vibrioformis DSM 265]
 gi|145205422|gb|ABP36465.1| RNA polymerase, sigma 32 subunit, RpoH [Chlorobium phaeovibrioides
           DSM 265]
          Length = 299

 Score =  212 bits (540), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 77/299 (25%), Positives = 145/299 (48%), Gaps = 24/299 (8%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD-----------LSAAH 51
           + +  I     + L RY+ EI K  +L   +E  L K  +E  D             A  
Sbjct: 5   KISKQITNRESLSLDRYLQEIGKYDLLTADDEVRLTKAIKEGFDMPLDTTEYKRAKRALD 64

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +L+  +LR VV +A  Y+  GL + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ 
Sbjct: 65  KLIKGNLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQ 124

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ + +     +V++    N+      + +    L+   + +        +A  L++   
Sbjct: 125 SILQALAEQSRIVRLP--LNRVGTLNKISKAYSQLEQEYERD---PNTKELANLLDMDSQ 179

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           +V           S++A     D N  +  D L  D      +      R +    + RS
Sbjct: 180 DVADTLKIAGRHVSVDAPFAQGDDN--RLLDVLQNDG----HLPDHGLNRDSLTLEVERS 233

Query: 232 MSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +SVL PRE  + ++      +NP+TLE +  +F+++RERVRQI+ +A +++++S   +V
Sbjct: 234 LSVLAPREADVIKSYFGIGMDNPLTLEEIGEKFKLTRERVRQIKEKAIRRLRQSAYSKV 292


>gi|77920269|ref|YP_358084.1| RNA polymerase, sigma(70) factor [Pelobacter carbinolicus DSM 2380]
 gi|77546352|gb|ABA89914.1| RNA polymerase, sigma 70 subunit, RpoD [Pelobacter carbinolicus DSM
           2380]
          Length = 588

 Score =  212 bits (540), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 71/242 (29%), Positives = 115/242 (47%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +A   LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ 
Sbjct: 347 KAAKSELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYAT 406

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            L R    L         PE    IA+++
Sbjct: 407 WWIRQAITRAIADQARTIRIPVHM--IETINKLIRTSRQLVQEMGREPVPE---EIAERM 461

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +        SL   I   ++  S   D++    D      +E   + N  +
Sbjct: 462 ELPLEKVRRVLKIAKEPISLETPI--GEEEDSSLGDFI---EDKGVVSPLEAVIKGNLSD 516

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             +R ++ L PRE ++   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 517 QTSRVLASLTPREEKVLRMRFGIGEKSDHTLEEVGQDFAVTRERIRQIEAKALRKLRHPS 576

Query: 285 QK 286
           + 
Sbjct: 577 RA 578


>gi|167627930|ref|YP_001678430.1| RNA polymerase sigma-70 factor [Francisella philomiragia subsp.
           philomiragia ATCC 25017]
 gi|167597931|gb|ABZ87929.1| RNA polymerase sigma-70 factor [Francisella philomiragia subsp.
           philomiragia ATCC 25017]
          Length = 578

 Score =  212 bits (540), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 64/242 (26%), Positives = 111/242 (45%), Gaps = 12/242 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   ++ ++LRLVV  A  Y   GL   +++ EGNIGLM+AV KFD  +GF+ +TY+ W
Sbjct: 339 QAKKEMIEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKGFKFSTYATW 398

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++            + R+K  +          E+++      N
Sbjct: 399 WIRQAITRSIADQARTIRVPVHM--IETINKVNRIKRQILQEKGREATEEEIIEYT--PN 454

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +++ ++  +        S+ + I   D   S   D++    D      IE    +N R  
Sbjct: 455 MTKDKLKKILNISHTPISMESPI--GDDEDSTVGDFI---EDKNNYSPIEAANLENLREA 509

Query: 228 LTRSMSV-LNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +   +   L  RE ++   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 510 IKELIDTGLTEREAKVLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIEAKALRKLKHPS 569

Query: 285 QK 286
           + 
Sbjct: 570 RS 571


>gi|330444010|ref|YP_004376996.1| RNA polymerase sigma factor, sigma-70 family [Chlamydophila pecorum
           E58]
 gi|328807120|gb|AEB41293.1| RNA polymerase sigma factor, sigma-70 family [Chlamydophila pecorum
           E58]
          Length = 562

 Score =  212 bits (540), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 69/255 (27%), Positives = 122/255 (47%), Gaps = 13/255 (5%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             + +R+ +     A   +V S+LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+
Sbjct: 294 VRMLQRWMDK-SQEAKKEMVESNLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFE 352

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             RG++ +TY+ WWI+ A+   I      ++I        +   + ++    + +     
Sbjct: 353 YRRGYKFSTYATWWIRQAVTRAIADQARTIRIPVH-----MIETINKVLRGAKKLMMETG 407

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           K      +A++L ++   V  +        SL A +   +   S + D+L    D   + 
Sbjct: 408 KEPSPEELAEELGLTPDRVREIYKIAQHPISLQAEV--GEGGESAFGDFL---EDTAVES 462

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQI 272
             E       ++ +   +  L  RER +   R   L   P TLE + S F V+RER+RQI
Sbjct: 463 PAEATGYSMLKDKMKEVLKTLTDRERFVLIHRFGLLDGKPKTLEEVGSAFNVTRERIRQI 522

Query: 273 EARAFKKVQESIQKQ 287
           EA+A +K++  I+ +
Sbjct: 523 EAKALRKMRHPIRSK 537



 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 8/32 (25%), Positives = 19/32 (59%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREH 44
           +  +  Y+ E+  +P+L ++EE  ++KR  + 
Sbjct: 90  DDPVRMYLKEMGTVPLLTREEEVEISKRIEKA 121


>gi|294660419|ref|NP_853171.2| RNA polymerase sigma factor RpoD [Mycoplasma gallisepticum str.
           R(low)]
 gi|284812078|gb|AAP56739.2| RNA polymerase sigma factor RpoD (Sigma-A) [Mycoplasma
           gallisepticum str. R(low)]
 gi|284930653|gb|ADC30592.1| RNA polymerase sigma factor RpoD (Sigma-A) [Mycoplasma
           gallisepticum str. R(high)]
          Length = 643

 Score =  212 bits (540), Expect = 5e-53,   Method: Composition-based stats.
 Identities = 70/285 (24%), Positives = 127/285 (44%), Gaps = 22/285 (7%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAH----RLVTSHLRLVVKIAMGY 68
           E  +  ++  +    +L   EE  +AK      D         +LVTS+LRLV  IA  Y
Sbjct: 355 EDNVKAFLGTLGSSKILNFGEEIQIAKLLGST-DPETREYAINQLVTSNLRLVTSIAKKY 413

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
              GL   +++ EG+IGLM+A+ KF+ + G + +TY+ WWI+ A+   I      V+I  
Sbjct: 414 LNRGLDFVDLIQEGSIGLMKAISKFNYKLGNKFSTYATWWIRQAITRAIADQARTVRIPV 473

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL-----NVSESEVISMNCRLAGD 183
              +      + +L    + +T    +   +  + + +       +  +V  +       
Sbjct: 474 HMVE-----TINKLIKTERMLTQQLGRDPTLEELTEAMGGQVNGFTPKKVADIKKLNQEP 528

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SL+  I   ++  SQ+ D++      +     EK       N L   ++ L  +E +I 
Sbjct: 529 VSLDKPIGHDEE--SQFVDFVKDRDILKPDEYTEKLIVTEHINEL--FINTLTKKEEQII 584

Query: 244 EARRLQ---ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             R         +TLE +  +F V+RER+RQIE++A +K++   +
Sbjct: 585 RMRYGLHPWHQQMTLEEVGQKFNVTRERIRQIESKALRKLKHPSK 629


>gi|225848841|ref|YP_002729005.1| RNA polymerase sigma factor RpoD (Sigma-A) (Major vegetative
           sigmafactor) [Sulfurihydrogenibium azorense Az-Fu1]
 gi|225644391|gb|ACN99441.1| RNA polymerase sigma factor RpoD (Sigma-A) (Major vegetative
           sigmafactor) [Sulfurihydrogenibium azorense Az-Fu1]
          Length = 586

 Score =  212 bits (540), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 71/240 (29%), Positives = 113/240 (47%), Gaps = 12/240 (5%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV K+D +RGF+ +TY+ WWI
Sbjct: 348 KQILVKANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKYDYKRGFKFSTYATWWI 407

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + A+   I      ++I            L R+   +         PE    IAKK+ + 
Sbjct: 408 RQAITRAIADQARTIRIPVHM--IETINKLIRVARSMVQELGREPTPE---EIAKKVGMP 462

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             +V  +        SL   I + ++  +   D++    D           +   R  L 
Sbjct: 463 AEKVKKILRTSQEPISLETPIGTDEE--THLGDFI---EDKSVLSPEAHMLKNALRMQLD 517

Query: 230 RSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             +S L+ RE ++   R   E+    TLE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 518 EVLSTLSEREEQVLRYRFGLEDDTEHTLEQVGKRFGVTRERIRQIEAKALRKLRHPHRAK 577


>gi|269140216|ref|YP_003296917.1| RNA polymerase sigma factor [Edwardsiella tarda EIB202]
 gi|228204742|gb|ACP74149.1| RNA polymerase sigma factor [Edwardsiella tarda]
 gi|267985877|gb|ACY85706.1| RNA polymerase sigma factor [Edwardsiella tarda EIB202]
 gi|304560047|gb|ADM42711.1| RNA polymerase sigma factor RpoS [Edwardsiella tarda FL6-60]
          Length = 328

 Score =  212 bits (540), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 77/271 (28%), Positives = 135/271 (49%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD ++  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 60  YLGEIGYAPLLTAEEEVFFARR-ALRGDEASRKRMIESNLRLVVKISRRYSNRGLALLDL 118

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 119 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 177

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L     +V  M        S++  +    + + 
Sbjct: 178 LRTAR----ELSHKLDHEPSAEEIAERLEKPVHDVSRMLRLNERITSVDTPLGGDSEKA- 232

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D  E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 233 ----LLDILTDENESGPEDCTQNDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 288

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 289 DVGREIGLTRERVRQIQVEGLRRLREILQMQ 319


>gi|241668482|ref|ZP_04756060.1| RNA polymerase sigma-70 factor [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
 gi|254877016|ref|ZP_05249726.1| RNA polymerase sigma-70 factor [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
 gi|254843037|gb|EET21451.1| RNA polymerase sigma-70 factor [Francisella philomiragia subsp.
           philomiragia ATCC 25015]
          Length = 578

 Score =  212 bits (540), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 64/242 (26%), Positives = 111/242 (45%), Gaps = 12/242 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   ++ ++LRLVV  A  Y   GL   +++ EGNIGLM+AV KFD  +GF+ +TY+ W
Sbjct: 339 QAKKEMIEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKGFKFSTYATW 398

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++            + R+K  +          E+++      N
Sbjct: 399 WIRQAITRSIADQARTIRVPVHM--IETINKVNRIKRQILQEKGREATEEEIIEYT--PN 454

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +++ ++  +        S+ + I   D   S   D++    D      IE    +N R  
Sbjct: 455 MTKDKLKKILNISHTPISMESPI--GDDEDSTVGDFI---EDKNNYSPIEAANLENLREA 509

Query: 228 LTRSMSV-LNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +   +   L  RE ++   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 510 IKELIDTGLTEREAKVLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIEAKALRKLKHPS 569

Query: 285 QK 286
           + 
Sbjct: 570 RS 571


>gi|224533326|ref|ZP_03673920.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi CA-11.2a]
 gi|224513491|gb|EEF83848.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi CA-11.2a]
          Length = 255

 Score =  212 bits (540), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 67/257 (26%), Positives = 122/257 (47%), Gaps = 16/257 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 3   EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 58

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RGF+ +TY+ WWI+ A+   I      +++        +   + RL    + +   
Sbjct: 59  FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVH-----MIEQINRLNRETRYLIQV 113

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             K      ++ +L     +V ++        SL   I   ++  S   D++    D   
Sbjct: 114 LGKDPTDEELSDRLGWELKKVKTVKSVSREPVSLETPI--GEEEDSVLSDFI---EDKAI 168

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +           ++ +   +  L  RE+ + + R   E+   +TLE +   F V+RER+R
Sbjct: 169 KNPANHTSFVVLQDQIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIR 228

Query: 271 QIEARAFKKVQESIQKQ 287
           QIE++A ++++   + Q
Sbjct: 229 QIESKALRRLKNPKKTQ 245


>gi|149188355|ref|ZP_01866649.1| RNA polymerase sigma factor [Vibrio shilonii AK1]
 gi|148837944|gb|EDL54887.1| RNA polymerase sigma factor [Vibrio shilonii AK1]
          Length = 290

 Score =  212 bits (540), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 89/286 (31%), Positives = 151/286 (52%), Gaps = 7/286 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+  +       +  LS Y+  I K P+L +++E  LA +        + + L+  HLR 
Sbjct: 1   MSASSYFTNAESKDSLSHYLGSISKYPLLSEEKERTLANKVVTENCSQSLNELILPHLRY 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  IA  + GYG+   +++  GN+GL++A+KKF+P RG RL ++++ WIK+ + EYI+++
Sbjct: 61  VAYIAKNFVGYGMSTLDIIQAGNVGLIKAIKKFNPARGIRLVSFAIHWIKSEINEYIIKN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WS+VK+ TT  Q++LFFNLR+ K     +++     EQ   IAK L V   +V  M+ RL
Sbjct: 121 WSMVKVATTKEQRKLFFNLRKHKNDSGWVSE-----EQAKDIAKNLKVRVRDVFVMDGRL 175

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPR 238
           +  D+ L +     + +    +D    +H        E+E   N   + L  ++  L+ R
Sbjct: 176 SNKDKQLESHNYDEEFHCPYTEDNYFREHRDDFADNHEEENWSNHLSSELKIAIQKLDER 235

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + I   R L     TL  L+ + ++S ER+RQIE     K++  +
Sbjct: 236 SKDIIFHRWLTNEKATLSELADKHQLSAERIRQIEVATLAKLKNLM 281


>gi|237738339|ref|ZP_04568820.1| RNA polymerase [Fusobacterium mortiferum ATCC 9817]
 gi|229420219|gb|EEO35266.1| RNA polymerase [Fusobacterium mortiferum ATCC 9817]
          Length = 273

 Score =  212 bits (540), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 82/273 (30%), Positives = 147/273 (53%), Gaps = 15/273 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +S Y+ +IRK  +LEK EE  L K+ +  GD+ A ++L+  +LRLVV IA  Y   GL +
Sbjct: 8   ISYYLEDIRKYKVLEKDEETELLKKAK-AGDIEAKNKLILCNLRLVVNIAKNYVNRGLSL 66

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++SEGN GL+ A++KFD ++GFR +TY++WWIK ++ + I+     ++I +       
Sbjct: 67  IDLISEGNFGLIYAIEKFDMKKGFRFSTYAVWWIKQSITKAIICKGRGIRIPSYK----- 121

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           +  L ++  ++            V  I++ LNV++ ++  +        SL+A I     
Sbjct: 122 YDLLSKVNRYVLNRVREEGIYPTVEEISEDLNVNKEKIEEIMVAFQDPMSLSASI----G 177

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--V 253
           +  Q +D +    +  E  + +    +  R  + + + VL+ RE++I + R   +     
Sbjct: 178 DDIQLEDIIA---NNSETSIEDDIIEEMGREQVRQIVKVLDEREKQILKLRFGLDGEEIH 234

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TLE +   F ++RERVRQIE +  KK++   +K
Sbjct: 235 TLEEIGQTFNITRERVRQIEKKTLKKLKMQCEK 267


>gi|188583534|ref|YP_001926979.1| RNA polymerase factor sigma-32 [Methylobacterium populi BJ001]
 gi|179347032|gb|ACB82444.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium populi
           BJ001]
          Length = 290

 Score =  212 bits (540), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 110/271 (40%), Positives = 176/271 (64%), Gaps = 1/271 (0%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           ++I    + P L ++EE  LA  ++E  D  A HRL+++H+RLV+ +A  +R YGLP+++
Sbjct: 10  QFIRTAMEAPFLAREEERGLAVAWKEARDERALHRLISAHMRLVIALAGRFRHYGLPMAD 69

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +V EG++GLM+A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFF
Sbjct: 70  LVQEGHVGLMEAAARFEPERDVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKALFF 129

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKN 196
           NLRRL+  L   T+  +  E    IA  + VS  +V  M+ RL+G D SLNA +    + 
Sbjct: 130 NLRRLRARLMQSTEEQVGSEIHGRIASAIGVSREDVALMDARLSGPDMSLNAPVGEESEA 189

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           SS+  D+LV +    ++ +    + + R   L ++++VL+ RE RI   RRL E+  TLE
Sbjct: 190 SSERMDFLVDNAALPDETVSALVDGERRLVWLRQALTVLSERELRILRERRLAEDQATLE 249

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            L     +S+ERVRQIE RA +K++ ++ ++
Sbjct: 250 ALGHRLGISKERVRQIENRALEKLRRALAEK 280


>gi|218247827|ref|YP_002373198.1| RNA polymerase sigma factor SigD [Cyanothece sp. PCC 8801]
 gi|257060853|ref|YP_003138741.1| RNA polymerase sigma factor SigD [Cyanothece sp. PCC 8802]
 gi|218168305|gb|ACK67042.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8801]
 gi|256591019|gb|ACV01906.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8802]
          Length = 318

 Score =  212 bits (540), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 73/318 (22%), Positives = 136/318 (42%), Gaps = 52/318 (16%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------- 43
           M++  +    +  Y+ EI ++P+L  +EE + AKR +                       
Sbjct: 1   MNVSKSSPDPVRAYLREIGRVPLLTHEEEILYAKRVQRFVALETLKESLTEELGQEPTIA 60

Query: 44  -----------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
                                +A  ++V ++LRLVV +A  Y    L + +++ EG IG+
Sbjct: 61  QWAKAAKMTQKELRSAIEAGEAAKRKMVEANLRLVVSVAKKYLKRNLDLLDLIQEGTIGM 120

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
            + V+KFDP +G+R +TY+ WWI+ A+   I      +++     +K     L ++K   
Sbjct: 121 QRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEK-----LNKIKKAQ 175

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           + ++    +   +  +A++L ++  +V     R     SL+  +   D   ++  D L  
Sbjct: 176 RQLSQEKGRAATIAELAEELELTPRQVREYLERARQPLSLD--LRVGDNQDTELGDLLED 233

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
                E        + +    L R M  L P+++ +   R       P+TL  + S   +
Sbjct: 234 TGQSPEDYATHSSLQLD----LDRLMEELTPQQKEVLALRFGLSDGKPLTLAKIGSILNI 289

Query: 265 SRERVRQIEARAFKKVQE 282
           SRERVRQIE  A  K+++
Sbjct: 290 SRERVRQIEREALAKLRK 307


>gi|37523928|ref|NP_927305.1| group2 RNA polymerase sigma factor [Gloeobacter violaceus PCC 7421]
 gi|35214934|dbj|BAC92300.1| group2 RNA polymerase sigma factor [Gloeobacter violaceus PCC 7421]
          Length = 344

 Score =  212 bits (540), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 79/319 (24%), Positives = 148/319 (46%), Gaps = 51/319 (15%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE--------------------------- 43
             +  +  Y++EI +IP +  +EE  LA+R +                            
Sbjct: 29  GSDDLVDLYLNEIGRIPRVTPEEEIHLARRIQAKLAIDGAREELAMRLGRPSPEEDVAAF 88

Query: 44  ------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                          L A  +L+ ++LRLVV IA  Y G  +P  +++ EGNIGLM+A +
Sbjct: 89  MGRDPKALIEATRQGLWAQRKLINANLRLVVSIAKKYIGRNVPFLDLIQEGNIGLMRATE 148

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFDPE+G+R +TY+ WWI+ ++   I      +++     +K     +R+++  ++  T 
Sbjct: 149 KFDPEKGYRFSTYATWWIRQSITRAIANQARTIRLPIHMVEK-----VRKVRREMRMATL 203

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +      +A +L +   ++ ++        SL+  + S  +      + +    DG 
Sbjct: 204 ELGRRPSEDELASRLAIKVKKLRTIQEVSRQPVSLDMPVGS--EGDISLGEMI---EDGT 258

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
            +   ++  +K   + L  +M+VL P ER +   R     E  +TL  +   F+++RER+
Sbjct: 259 AERPFDELVQKALASELYAAMNVLKPVEREVLALRFGLKGEEGLTLREVGERFDLTRERI 318

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQIE+ A +K++ S +KQ+
Sbjct: 319 RQIESEALRKLRRSKRKQI 337


>gi|226226116|ref|YP_002760222.1| RNA polymerase sigma factor [Gemmatimonas aurantiaca T-27]
 gi|226089307|dbj|BAH37752.1| RNA polymerase sigma factor [Gemmatimonas aurantiaca T-27]
          Length = 295

 Score =  212 bits (540), Expect = 6e-53,   Method: Composition-based stats.
 Identities = 76/269 (28%), Positives = 136/269 (50%), Gaps = 13/269 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y++E+   P+L+  EE  LAK+ R  GD  A   LV  +LR V+ +A  Y+  GLP+
Sbjct: 26  LDQYLYEVSTYPLLKAAEEIELAKKIR-AGDQDALQELVKRNLRFVISVAKKYQNRGLPL 84

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GL+ A +KFDP++G +  +Y++WWI+ A+   + R    V++         
Sbjct: 85  IDLIGEGNVGLLTAARKFDPDQGVKFISYAVWWIRQAILSSLARQGRTVRVPLNRT---- 140

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
             +L R+    + +     +      +A+   +S   V S+     GD  L+A     D 
Sbjct: 141 -ADLSRIIKASEILRQKLRREPSPEELAQVTGLSVDVVQSLAALNTGDVRLDAP-MDPDG 198

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PV 253
           + S  + ++  +    E    E+   +   + + +++S L PR+ ++       E     
Sbjct: 199 DRSLIERFVADEMPDTE----EEAMNRFLTDEIEQALSTLPPRDAKVLRLYFGLEGGREH 254

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQE 282
           TLE + S   V+RERVRQ+  RA K+++E
Sbjct: 255 TLEEIGSMLGVTRERVRQLRDRALKRLRE 283


>gi|189345950|ref|YP_001942479.1| RNA polymerase, sigma 32 subunit, RpoH [Chlorobium limicola DSM
           245]
 gi|189340097|gb|ACD89500.1| RNA polymerase, sigma 32 subunit, RpoH [Chlorobium limicola DSM
           245]
          Length = 299

 Score =  211 bits (539), Expect = 7e-53,   Method: Composition-based stats.
 Identities = 76/302 (25%), Positives = 142/302 (47%), Gaps = 30/302 (9%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD-----------LSAAH 51
           + +  I     + L RY+ EI K  +L   +E  L    +E  D             A  
Sbjct: 5   KISKQITNRESLSLDRYLQEIGKYDLLTADDEVKLTMAIKEGYDMPVDTVEYKRAKRALD 64

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +L+  +LR VV +A  Y+  GL + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ 
Sbjct: 65  KLIKGNLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQ 124

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ + +     +V++    N+      + +    L+   + +        +A  L++   
Sbjct: 125 SILQALAEQSRIVRLP--LNRVGTLNKISKAYSQLEQEFERD---PNTRELANLLDMDSQ 179

Query: 172 EVISMNCRLAGDESLNALINSSDKN---SSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +V           S++A     D N        D  + DH   +  L  + ER       
Sbjct: 180 DVADTLKIAGRHVSVDAPFAQGDDNRLLDVLQNDGHLPDHGLNKDSLTLEVERS------ 233

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +SVL PRE  +  +      +NP+TLE +  +F+++RERVRQI+ +A +++++S   
Sbjct: 234 ---LSVLAPREADVIRSYFGIGMDNPLTLEEIGEKFKLTRERVRQIKEKAIRRLRQSAYS 290

Query: 287 QV 288
           +V
Sbjct: 291 KV 292


>gi|284991968|ref|YP_003410522.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geodermatophilus
           obscurus DSM 43160]
 gi|284065213|gb|ADB76151.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Geodermatophilus
           obscurus DSM 43160]
          Length = 327

 Score =  211 bits (539), Expect = 7e-53,   Method: Composition-based stats.
 Identities = 67/297 (22%), Positives = 132/297 (44%), Gaps = 37/297 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYRE-------------------------HGDLSAAHRL 53
           Y++ I K  +L  ++E  L+KR                                +A   L
Sbjct: 35  YLNTIGKTALLTAEQEVELSKRIEAGLYAERLLTERQLTPALQRDYKALAADGKAAKRHL 94

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           + ++LRLVV +A  Y G+G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+
Sbjct: 95  LEANLRLVVSVAKRYTGHGMTFLDLIQEGNVGLIRAVEKFDYTKGFKFSTYATWWIRQAI 154

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
              +  S   +++     ++     + R +  +    +     E    +  +L+++   +
Sbjct: 155 TRAMADSGRTIRLPVHLAEQ--VNKVVRTRRRIHQELEREPTAE---ELGLELDMTPERI 209

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             +        SL+  + + ++  S+  D++         V  +    +  +  +   +S
Sbjct: 210 TELLEYSRDLVSLDQTVGADEE--SRLGDFIED---ADAAVAEDAVAFQMMKGDVRNVLS 264

Query: 234 VLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            L  RER +   R   +   P TLE +  +F +SRERVRQIE     K+++  +   
Sbjct: 265 TLEERERDVVVLRFGLDGGQPRTLEQIGKQFGLSRERVRQIERETMAKLRDPQRADA 321


>gi|154173683|ref|YP_001408074.1| RNA polymerase sigma factor RpoD [Campylobacter curvus 525.92]
 gi|112802903|gb|EAU00247.1| RNA polymerase sigma factor RpoD (Sigma-A) (Major vegetative
           sigmafactor) [Campylobacter curvus 525.92]
          Length = 614

 Score =  211 bits (539), Expect = 7e-53,   Method: Composition-based stats.
 Identities = 76/249 (30%), Positives = 122/249 (48%), Gaps = 14/249 (5%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
            KR ++  D  A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+  +
Sbjct: 365 IKRGKKISD-EAKARMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYRK 423

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I        +   + R+    +       K  
Sbjct: 424 GYKFSTYATWWIRQAISRAIADQARTIRIPIH-----MIETINRINKINRKYLQEEGKEP 478

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
            V  IAK++ +S  +V  +        SL A I +  +   ++ D++    D      IE
Sbjct: 479 DVSVIAKEVGLSVDKVKQVIKITKEPISLEAPIAN--EEDGKFGDFV---EDKSSLSPIE 533

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEA 274
           +  + + R  +   +S LN RE+ +   R      E+  TLE +     V+RERVRQIE+
Sbjct: 534 QILKGDLREQIDDVLSQLNDREKAVICMRFGLLEDESDRTLEEIGKALNVTRERVRQIES 593

Query: 275 RAFKKVQES 283
            A KK++  
Sbjct: 594 SAIKKLKHP 602


>gi|330982601|gb|EGH80704.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. aptata
           str. DSM 50252]
          Length = 459

 Score =  211 bits (539), Expect = 7e-53,   Method: Composition-based stats.
 Identities = 75/253 (29%), Positives = 128/253 (50%), Gaps = 15/253 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 20  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 78

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 79  IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 137

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +   Q + D+   PE++  + +K       ++ +N R++  D SL         + 
Sbjct: 138 LRAARELTQKL-DHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSL------GPDSD 190

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D       L++ ++       + + +S L  ++R +   R         TL
Sbjct: 191 KTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTEKQREVVIRRFGLRGHESSTL 247

Query: 256 ENLSSEFEVSRER 268
           E++  E  ++RER
Sbjct: 248 EDVGLEIGLTRER 260


>gi|309790033|ref|ZP_07684607.1| sigma-70 family RNA polymerase sigma factor [Oscillochloris
           trichoides DG6]
 gi|308227888|gb|EFO81542.1| sigma-70 family RNA polymerase sigma factor [Oscillochloris
           trichoides DG6]
          Length = 358

 Score =  211 bits (539), Expect = 7e-53,   Method: Composition-based stats.
 Identities = 75/299 (25%), Positives = 132/299 (44%), Gaps = 38/299 (12%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL------------------------- 47
           E  +  Y+HEI ++ +L  +EE  LA + R   +                          
Sbjct: 59  EDSIQIYLHEIGQVALLSAEEERDLAMQIRAGKEAQMQLDTERFANGAARAQLELTVARG 118

Query: 48  -SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  RL+ ++LRLVV +A  Y    +   ++V EGNIGLM+AV+KFD  +G R +TY+ 
Sbjct: 119 HEARRRLIQANLRLVVSVAKKYINSPMAFMDLVQEGNIGLMRAVEKFDHTKGNRFSTYAT 178

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I     ++++    ++      L +++  +  +     +      IA  +
Sbjct: 179 WWIRQAVSRSIAEQSRVIRLPVHLSES-----LVQMRRAIYKLEQQFEREPTAQEIAHSM 233

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +S  +V  +    A   SL   +     N+ Q         D   +  ++   +K    
Sbjct: 234 GLSLRKVKRLLQASAQPVSLEQPL-----NNEQEGRVGEVLADENVETPMDLATQKMFHQ 288

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            L  +++ L  RER+I + R         TLE +   F ++RER RQIEA A +++++ 
Sbjct: 289 ELYAALNDLPDRERKILQLRYGLFDGQRRTLEEVGMAFGITRERTRQIEAEAMRRLRQP 347


>gi|84872788|gb|ABC67485.1| RpoH2 [Sinorhizobium sp. BL3]
          Length = 286

 Score =  211 bits (539), Expect = 7e-53,   Method: Composition-based stats.
 Identities = 99/245 (40%), Positives = 149/245 (60%), Gaps = 1/245 (0%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE+ EE+ LA+ +R   D  A +++  SH+RLVV +A  +R +GLP+ ++V EG+IGL
Sbjct: 18  PYLERDEEHALAEAWRYDHDQEARNKIAMSHMRLVVAMAAKFRSFGLPMGDLVQEGHIGL 77

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +F+P R  R +TY+ WWI+A+MQ+Y+LR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 78  LEAAARFEPSREVRFSTYATWWIRASMQDYVLRNWSIVRGGTSSAQKALFFNLRRLRARL 137

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLV 205
                          IA  L VS ++V +M+ RL+G D SL A +   D  S    D+L 
Sbjct: 138 AQGDRQLTSQAMHEEIAAALGVSLADVQTMDARLSGNDASLQAPVGHGDAESGARLDFLP 197

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            D    ++ + E  + +  R  L  ++  L+ RE +I  ARRL E+  TLE L     +S
Sbjct: 198 SDAPLPDEQVSEMIDGERARRWLHSALRELSEREMKIIRARRLSEDGATLEELGVALGIS 257

Query: 266 RERVR 270
           +ERVR
Sbjct: 258 KERVR 262


>gi|68536171|ref|YP_250876.1| RNA polymerase sigma factor SigB [Corynebacterium jeikeium K411]
 gi|260578869|ref|ZP_05846775.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           jeikeium ATCC 43734]
 gi|68263770|emb|CAI37258.1| RNA polymerase sigma factor B [Corynebacterium jeikeium K411]
 gi|258603016|gb|EEW16287.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           jeikeium ATCC 43734]
          Length = 343

 Score =  211 bits (539), Expect = 8e-53,   Method: Composition-based stats.
 Identities = 67/297 (22%), Positives = 134/297 (45%), Gaps = 38/297 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR--------------------------EHGDLSAAHR 52
           Y++ I K  +L  ++E  L+KR                                 +A   
Sbjct: 50  YLNGIGKTALLTAEDEVELSKRIEVGLYSEYLLSNAEKLTRAKKRDLKVLAREGKAARSH 109

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A
Sbjct: 110 LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKGFKFSTYATWWIRQA 169

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +      +++     ++     L R+K  +          E    ++++  + ES+
Sbjct: 170 ITRGMADQSRTIRLPVHLVEQ--VNKLSRIKREMYQQLGREATNE---ELSEESGIEESK 224

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           +  +  +     SL+  + S ++  +   D++        +  +    R    + +   +
Sbjct: 225 IEMLLKQSRDPVSLDMPVGSDEE--APLGDFIEDSDATDAETAVVASLR---HSDVRAVL 279

Query: 233 SVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             L  RE+ + + R   ++  P TL+ +   F +SRERVRQIE     K++E  +  
Sbjct: 280 GTLEEREQDVIKLRYGLDDGMPRTLDQIGRRFGLSRERVRQIEREVMAKLREGDRAD 336


>gi|148244663|ref|YP_001219357.1| DNA-directed RNA polymerase sigma-32 factor [Candidatus
           Vesicomyosocius okutanii HA]
 gi|146326490|dbj|BAF61633.1| DNA-directed RNA polymerase sigma-32 factor [Candidatus
           Vesicomyosocius okutanii HA]
          Length = 277

 Score =  211 bits (539), Expect = 8e-53,   Method: Composition-based stats.
 Identities = 99/268 (36%), Positives = 167/268 (62%), Gaps = 10/268 (3%)

Query: 22  EIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           E++K P  L  +EE+ LA +  E+ +LSAA +LV SH+R V  IA  Y+GYGL  +++V 
Sbjct: 17  EVQKYPPILSSEEEHELAVQLYENHNLSAARKLVLSHMRFVAFIAHSYKGYGLEQADLVQ 76

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           EG IGLM+AVK+F+P R  RLA+++++WI+A + E+I ++W +VK+ TT  Q++LFF L+
Sbjct: 77  EGTIGLMKAVKRFNPHRNVRLASFAVYWIRAEIHEFIFKNWKIVKVATTKAQRKLFFKLK 136

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
           + K H+     N+L  EQ   IAK L V   +V+ M  RL      +      D+  S  
Sbjct: 137 QAKAHIY----NSLNEEQADKIAKDLGVRRKDVLEMESRLQFS---DVTFEVFDEEDSHA 189

Query: 201 QDWLVYDHD--GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
            +  + + +    EQ+L+  + +K ++  L +++S L+ R   I ++R L+E   TL  L
Sbjct: 190 PEQYLTNENIQTPEQLLLTDDSKKTQQQRLYKALSSLDERSLDILQSRYLKEEKTTLYTL 249

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQK 286
           + ++ +S+ERVRQ+E +A +K++ ++Q+
Sbjct: 250 ADKYSISKERVRQLETKAMQKLKSNLQE 277


>gi|154148465|ref|YP_001406295.1| RNA polymerase sigma factor RpoD [Campylobacter hominis ATCC
           BAA-381]
 gi|153804474|gb|ABS51481.1| RNA polymerase sigma factor RpoD (Sigma-A) (Major vegetative
           sigmafactor) [Campylobacter hominis ATCC BAA-381]
          Length = 624

 Score =  211 bits (539), Expect = 8e-53,   Method: Composition-based stats.
 Identities = 74/260 (28%), Positives = 129/260 (49%), Gaps = 19/260 (7%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
            KR ++  D  A   +  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+  +
Sbjct: 375 IKRGKKISD-EAKSLMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYRK 433

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I        +   + R+    +     N K  
Sbjct: 434 GYKFSTYATWWIRQAISRAIADQARTIRIPIH-----MIETINRINKINRKYVQENGKEP 488

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
            +  +AK++ +S  ++  +        SL A +   +++  ++ D++    D      I+
Sbjct: 489 DITILAKEVGLSIDKIKQVIKITKEPISLEAPV--GNEDDGKFGDFV---EDKGTISPID 543

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEA 274
           +  + + +  + + +  LN RER +   R      E+  TLE +  E  V+RERVRQIEA
Sbjct: 544 QILKNDLKEQIDKVLDQLNERERAVIRMRFGLLDDESDRTLEEIGKELSVTRERVRQIEA 603

Query: 275 RAFKKVQES-----IQKQVE 289
            A KK++       ++K +E
Sbjct: 604 SAIKKLKHPKVGRDLKKYIE 623


>gi|332297995|ref|YP_004439917.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           brennaborense DSM 12168]
 gi|332181098|gb|AEE16786.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           brennaborense DSM 12168]
          Length = 599

 Score =  211 bits (539), Expect = 8e-53,   Method: Composition-based stats.
 Identities = 66/260 (25%), Positives = 123/260 (47%), Gaps = 16/260 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L   +E    +R        A +RL+ ++LRLVV IA  Y   GL   ++V EGNIGL++
Sbjct: 346 LSMAKEIDRGRRMM----KEAKNRLINANLRLVVSIAKKYTNRGLQFFDLVQEGNIGLIK 401

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           AV+KF+  +G++ +TY+ WWI+ A+   I      +++        +   + ++    + 
Sbjct: 402 AVEKFEYRKGYKFSTYATWWIRQAITRSISDQARTIRVPVH-----MIEQINKVVRESRQ 456

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           +     +      IA +L    + V  +        SL   I   ++  S   D++    
Sbjct: 457 LMQRFGREPTDEEIAAQLGWPVNRVKQVKSVAREPISLETPI--GEEEDSLLGDFI---E 511

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSR 266
           D + +    K      ++ L   ++ L PRE+ + + R   ++   +TLE +   F V+R
Sbjct: 512 DKEVENPAAKTAYTMLQDHLRSILATLPPREQEVLKMRFGLDDGFSLTLEEVGLYFNVTR 571

Query: 267 ERVRQIEARAFKKVQESIQK 286
           ER+RQIEA+A ++++   + 
Sbjct: 572 ERIRQIEAKALRRLRHPRRS 591



 Score = 35.9 bits (82), Expect = 7.8,   Method: Composition-based stats.
 Identities = 9/33 (27%), Positives = 19/33 (57%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE 43
           +G+  +  Y+ EI K  +L  ++E  L+K+  +
Sbjct: 109 SGDDPVRLYLREIGKEHLLTAEQEVFLSKKMED 141


>gi|320449783|ref|YP_004201879.1| RNA polymerase sigma factor RpoD [Thermus scotoductus SA-01]
 gi|320149952|gb|ADW21330.1| RNA polymerase sigma factor RpoD [Thermus scotoductus SA-01]
          Length = 494

 Score =  211 bits (539), Expect = 8e-53,   Method: Composition-based stats.
 Identities = 66/237 (27%), Positives = 110/237 (46%), Gaps = 10/237 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +A   L+ ++LRLVV IA  Y G GL   +++ EGN GL++AV+KF+ +R F+ +TY+ 
Sbjct: 252 EAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYAT 311

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I     +      L R    LQ         E++   A   
Sbjct: 312 WWIRQAINRAIADQARTIRIPVHMVE--TINKLSRTARSLQQELGREPTYEEIAE-AMGP 368

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
                 V           SL   I   D+  S + D++    D      ++   +     
Sbjct: 369 GWDAKRVEETLKIAQEPVSLETPI--GDEKDSFYGDFIP---DENLPSPVDAAAQSLLAE 423

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L +++S L+ RE  + + R+        TLE + + F V+RER+RQIE +A +K++
Sbjct: 424 ELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLK 480


>gi|4929285|gb|AAD33933.1|AF144608_2 RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus]
          Length = 321

 Score =  211 bits (538), Expect = 8e-53,   Method: Composition-based stats.
 Identities = 78/287 (27%), Positives = 137/287 (47%), Gaps = 21/287 (7%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           R+              Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVV
Sbjct: 41  REEFDASSKSLDATQLYLGEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLVV 99

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           KI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++    
Sbjct: 100 KISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTR 159

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            +++      K L   LR  +     ++           IA +L++   +V  M      
Sbjct: 160 TIRLPIHVV-KELNIYLRTAR----ELSQKLDHEPTAEEIAAQLDIPVEDVSKMLRLNER 214

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++  I           D +   ++   +V  + +   + ++ L   +  LNP+++ +
Sbjct: 215 ISSVDTPI--GGDGEKALLDIIPDANNSDPEVSTQDD---DIKSSLIHWLEELNPKQKEV 269

Query: 243 FEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              R   L   P TLE +  E  ++RERVR        +++E + KQ
Sbjct: 270 LARRFGLLGYEPSTLEEVGREIGLTRERVR--------RLREILIKQ 308


>gi|51244645|ref|YP_064529.1| RNA polymerase sigma factor (RpoD) [Desulfotalea psychrophila
           LSv54]
 gi|50875682|emb|CAG35522.1| probable RNA polymerase sigma factor (RpoD) [Desulfotalea
           psychrophila LSv54]
          Length = 534

 Score =  211 bits (538), Expect = 9e-53,   Method: Composition-based stats.
 Identities = 68/254 (26%), Positives = 117/254 (46%), Gaps = 14/254 (5%)

Query: 36  VLAKRYREHG--DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
            L K   E       A   LV ++LRLV+ ++  +   GL  S+++ EGNIGLM+AV+KF
Sbjct: 281 ELLKEVEEGRFISKEAKEALVRANLRLVISVSKRFVNRGLQFSDLIQEGNIGLMKAVEKF 340

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D  RGF+ +TY+ WWI+ ++   I      +++        +   + R+    +      
Sbjct: 341 DYRRGFKFSTYATWWIRQSITRGIADQGRTIRLPVH-----MIETINRMLRVSKDFYLEE 395

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            +   V  +A +L     +V S         SL+  +   D   +   D++V   D    
Sbjct: 396 HREPSVEEVAGQLGTEVDKVKSALKIAKDAISLDTPV--GDDGETYLGDFIV---DKNCL 450

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQ 271
                    + +  L++ +S L+PRE ++ + R         TLE +   F V+RER+RQ
Sbjct: 451 GPDGFAMVASLKECLSQVLSSLSPREEKVLKMRYGILEKREYTLEEVGRCFNVTRERIRQ 510

Query: 272 IEARAFKKVQESIQ 285
           IEA+A  K++   +
Sbjct: 511 IEAQAISKLKHPSR 524


>gi|238921111|ref|YP_002934626.1| RNA polymerase sigma factor RpoS [Edwardsiella ictaluri 93-146]
 gi|238870680|gb|ACR70391.1| RNA polymerase sigma factor RpoS, putative [Edwardsiella ictaluri
           93-146]
          Length = 328

 Score =  211 bits (538), Expect = 9e-53,   Method: Composition-based stats.
 Identities = 77/271 (28%), Positives = 133/271 (49%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD ++  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 60  YLSEIGYAPLLTAEEEVFFARR-ALRGDEASRKRMIESNLRLVVKISRRYSNRGLALLDL 118

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 119 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 177

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            IA++L     +V  M        S++  +    +   
Sbjct: 178 LRTAR----ELAHKLDHEPSAEEIAERLEKPVHDVSRMLRLNERITSVDTPLGGDSE--- 230

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
             +  L    D  E    +  +  + +  +   +  LN ++R +   R   L     TLE
Sbjct: 231 --KALLDILTDENESGPEDCTQNDDMKQSIVNWLFELNAKQREVLARRFGLLGYEAATLE 288

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 289 DVGREIGLTRERVRQIQVEGLRRLREILQMQ 319


>gi|88809137|ref|ZP_01124646.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 7805]
 gi|88787079|gb|EAR18237.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 7805]
          Length = 313

 Score =  211 bits (538), Expect = 9e-53,   Method: Composition-based stats.
 Identities = 75/302 (24%), Positives = 142/302 (47%), Gaps = 36/302 (11%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------EHG-------------------D 46
               +S Y+  I +IP+L   EE  L  + +      E G                    
Sbjct: 16  SSDPISWYLATIGRIPLLTPAEEIELGNQVQKLMQLTEDGSIAADSELFDSKQRRLIRVG 75

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  R++ ++LRLVV +A  Y+G GL + +++ EG++GL +AV+KFDP RG++ +TY+ 
Sbjct: 76  QRAKQRMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAF 135

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ +M   I      +++    +++     L  ++     +          + IA+ +
Sbjct: 136 WWIRQSMTRAIACQSRTIRLPVHLSER-----LTSIRKVSLDLAHKLGAMPSRLEIAEAM 190

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   E+ S+  +     SL+A +N  ++  S   D +    D   +  +++ E++    
Sbjct: 191 DMPVEELDSLLRQALTTSSLDAPVN-GEEGRSFLGDLIA---DSSLEEPLDRVEQRIHHE 246

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L R MS L+ +E+ +   R         TL  +    +VSRERVRQ+E +A +K++   
Sbjct: 247 QLGRWMSHLSDQEQHVLTLRFGLNGNERHTLAEIGRLLDVSRERVRQVELKALRKLRNLT 306

Query: 285 QK 286
           ++
Sbjct: 307 RR 308


>gi|207093142|ref|ZP_03240929.1| RNA polymerase sigma factor RpoD [Helicobacter pylori
           HPKX_438_AG0C1]
          Length = 319

 Score =  211 bits (538), Expect = 9e-53,   Method: Composition-based stats.
 Identities = 70/237 (29%), Positives = 121/237 (51%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ W
Sbjct: 79  RAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATW 138

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WIK A+   I      ++I        +   + R+   ++     N K   +  +A+++ 
Sbjct: 139 WIKQAISRAIADQARTIRIPIH-----MIDTINRINKVMRKHIQENGKEPDLEVVAEEVG 193

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  
Sbjct: 194 LSLDKVKNVIKVTKEPISLETPVGNDDD--GKFGDFV---EDKNIVSSIDHIMREDLKVQ 248

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 249 IESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 305


>gi|297566693|ref|YP_003685665.1| RpoD subfamily RNA polymerase sigma-70 subunit [Meiothermus
           silvanus DSM 9946]
 gi|296851142|gb|ADH64157.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Meiothermus
           silvanus DSM 9946]
          Length = 483

 Score =  211 bits (538), Expect = 9e-53,   Method: Composition-based stats.
 Identities = 63/235 (26%), Positives = 110/235 (46%), Gaps = 10/235 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV IA  Y G GL   +++ EGN GL++AV+KF+ +R ++ +TY+ WW
Sbjct: 243 ARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRYKFSTYATWW 302

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I     +      L R    +Q         E++   A     
Sbjct: 303 IRQAINRAIADQARTIRIPVHMVE--TINKLTRTARQMQQELGREPTYEEISE-AMGPGW 359

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V           SL   I   D+  S + D++  +H       ++   +      L
Sbjct: 360 DAKKVEETFKIAQEPVSLETPI--GDEKDSFYGDFIPDEH---MASPVDSAAQSMLSEEL 414

Query: 229 TRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +++  L+ RE  + + R+        TLE + + F V+RER+RQIE +A +K++
Sbjct: 415 EKALGKLSDREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLK 469


>gi|294055048|ref|YP_003548706.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Coraliomargarita
           akajimensis DSM 45221]
 gi|293614381|gb|ADE54536.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Coraliomargarita
           akajimensis DSM 45221]
          Length = 639

 Score =  211 bits (538), Expect = 9e-53,   Method: Composition-based stats.
 Identities = 64/240 (26%), Positives = 115/240 (47%), Gaps = 12/240 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   +V ++LRLV+ IA  Y   GL   +++ EGN+GLM+AV+KF+  RG++ +TY+ W
Sbjct: 380 KAKTEMVEANLRLVISIAKKYTNRGLSFLDLIQEGNMGLMKAVEKFEYRRGYKFSTYATW 439

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I        +   L ++    + +            +A ++N
Sbjct: 440 WIRQAITRSIADQARTIRIPVH-----MIETLNKVMQVQKQLLQELGHEPTAEEVADEMN 494

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +    V S+        SL + +   D + + + D++    D   +   +       R  
Sbjct: 495 LPIERVQSIMKMAQQPISLQSPV--GDSDDTNFGDFI---EDKGAENPYDMTAYSLLREK 549

Query: 228 LTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           +T  +  L  RERR+   R         TLE +  +F+V+RER+RQIEA+A +K++   +
Sbjct: 550 ITDVLDSLTERERRVLSLRFGLADGYSRTLEEVGRQFKVTRERIRQIEAKALRKMRHPTR 609



 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 13/48 (27%), Positives = 28/48 (58%), Gaps = 1/48 (2%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +  +  Y+ ++ ++P+L ++EE  ++KR  E  +L A   L ++ L L
Sbjct: 163 DDPVRMYLKQMGQVPLLTREEEVAISKRI-EKAELRAQDALFSTALTL 209


>gi|227833285|ref|YP_002834992.1| RNA polymerase sigma factor B [Corynebacterium aurimucosum ATCC
           700975]
 gi|262184270|ref|ZP_06043691.1| RNA polymerase sigma factor SigB [Corynebacterium aurimucosum ATCC
           700975]
 gi|227454301|gb|ACP33054.1| RNA polymerase sigma factor B [Corynebacterium aurimucosum ATCC
           700975]
          Length = 331

 Score =  211 bits (538), Expect = 9e-53,   Method: Composition-based stats.
 Identities = 68/309 (22%), Positives = 138/309 (44%), Gaps = 38/309 (12%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAK---------------------- 39
           +R+N +        +  Y++ I K  +L  ++E  LA+                      
Sbjct: 21  SRRNQTNDNPSADLVRVYLNGIGKTALLSAEDEVELAQTIEVGLYAEYKLANAEKLTRAE 80

Query: 40  ----RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
               +        A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD 
Sbjct: 81  KRDLKILAREGKKARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDY 140

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            +GF+ +TY+ WWI+ A+   +      +++     ++     L R+K  +         
Sbjct: 141 AKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLSRIKREMYQSLGREAT 198

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
            E    +A++  + ES++  +  +     SL+  + + ++  +   D++        +  
Sbjct: 199 NE---ELAEESGIEESKIEMLLRQSRDPVSLDMPVGTDEE--APLGDFIEDAEATDAETA 253

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIE 273
           +    R    + +   +  L  RE+ +   R   ++  P TL+ +  +F +SRERVRQIE
Sbjct: 254 VVASMR---HSDIRSVIGSLEEREQDVIRLRYGLDDGVPRTLDQIGRKFGLSRERVRQIE 310

Query: 274 ARAFKKVQE 282
                K++E
Sbjct: 311 REVMAKLRE 319


>gi|197121174|ref|YP_002133125.1| RNA polymerase, sigma 70 subunit, RpoD family [Anaeromyxobacter sp.
           K]
 gi|196171023|gb|ACG71996.1| RNA polymerase, sigma 70 subunit, RpoD family [Anaeromyxobacter sp.
           K]
          Length = 805

 Score =  211 bits (538), Expect = 9e-53,   Method: Composition-based stats.
 Identities = 82/284 (28%), Positives = 128/284 (45%), Gaps = 23/284 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYV-----LAKRYREHGD-----LSAAHRLVTSHLRLVVKIA 65
           L R +    +  +L  QEE       L + YR  GD       A   LV ++LRLVV IA
Sbjct: 525 LDRTLRSAGR-KILRVQEEAEVPVEELRRTYRMIGDGERKAERAKTELVEANLRLVVSIA 583

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ WWI+ A+   I      ++
Sbjct: 584 KKYTNRGLQFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWWIRQAITRAIADQARTIR 643

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           I            L R   +L         PE    IA+K+ +   +V  +        S
Sbjct: 644 IPVHM--IETINKLIRTSRYLVQELGREPTPE---EIAEKMELPLDKVRKVLKIAKEPIS 698

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L   I   ++  S   D++    D       +     N      + ++ L PRE ++   
Sbjct: 699 LETPI--GEEEDSHLGDFI---EDKSLVSPSDAVINMNLAEQTRKVLATLTPREEKVLRM 753

Query: 246 RRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           R         TLE +  +FEV+RER+RQIEA+A +K++   + +
Sbjct: 754 RFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLRHPSRSK 797


>gi|261856530|ref|YP_003263813.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Halothiobacillus
           neapolitanus c2]
 gi|261836999|gb|ACX96766.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Halothiobacillus
           neapolitanus c2]
          Length = 343

 Score =  211 bits (538), Expect = 9e-53,   Method: Composition-based stats.
 Identities = 75/292 (25%), Positives = 138/292 (47%), Gaps = 18/292 (6%)

Query: 2   NRKNMSIIVNGEIG-----LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTS 56
           N + ++   +         +  Y+ ++    +L  +EE + ++R  + GD SA  +++  
Sbjct: 52  NEEELTTTFSASDSESVDPVRLYLRDVETERLLTAEEEVIYSRR-AQSGDESARQKMIVC 110

Query: 57  HLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           +LRLV+KIA  Y   GL + +++ EGNIGLM+AV+KFDPERGFR +TY+ WWI+  ++  
Sbjct: 111 NLRLVIKIARRYMNRGLDLLDLIEEGNIGLMRAVEKFDPERGFRFSTYATWWIRQTIERG 170

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
           ++     V++     ++   FN        + I  N         IA  L+   +EV+ +
Sbjct: 171 LMNQSRTVRLPVHVVKEVHTFN-----RAARKIAQNQNAEVTAEQIADHLDRPVNEVLKI 225

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
                   S ++ +    + S    D +      Q   L++          L + ++ L 
Sbjct: 226 MAFNERQSSFDSPLKGDGEFS--LLDLIPDQESNQPDELLQDA---GVHGFLDQLIAQLE 280

Query: 237 PRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            ++R +   R         TLE + +   V+RERVRQI+  A ++++   +K
Sbjct: 281 SKQREVLVRRYGLRGYETHTLEEVGNHLGVTRERVRQIQLEAVRRLKSLAKK 332


>gi|54302639|ref|YP_132632.1| DNA-directed RNA polymerase sigma factor [Photobacterium profundum
           SS9]
 gi|90412658|ref|ZP_01220660.1| hypothetical DNA-directed RNA polymerase, sigma subunit
           [Photobacterium profundum 3TCK]
 gi|46916063|emb|CAG22832.1| hypothetical DNA-directed RNA polymerase, sigma subunit
           [Photobacterium profundum SS9]
 gi|90326466|gb|EAS42878.1| hypothetical DNA-directed RNA polymerase, sigma subunit
           [Photobacterium profundum 3TCK]
          Length = 291

 Score =  211 bits (538), Expect = 9e-53,   Method: Composition-based stats.
 Identities = 79/274 (28%), Positives = 145/274 (52%), Gaps = 12/274 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y+ EI   P+L K EE + +++    GD  A   ++ S+LRLVV IA  YRG G+ +
Sbjct: 16  IQLYLREIALKPLLTKHEEILYSRK-SLTGDKEAKKVMIESNLRLVVSIAKKYRGSGMQL 74

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           S+++ EGNIGL+ +V+KFDPERGFR +TY+ WWIK  ++  I      +++    ++   
Sbjct: 75  SDLIDEGNIGLITSVEKFDPERGFRFSTYATWWIKQTIERCIHNQARTIRLPVHVSK--- 131

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              +  +    + +   N +      +A+KL  S  ++ S+    A   S +  IN  D 
Sbjct: 132 --EINTIIRTHKQLMKKNNQEPTREEVAEKLERSVDDISSVLAYDAPIVSFDQTIND-DA 188

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPV 253
           NS     ++  D   + +  ++K+   + + +    +  LN R+R I   R   L     
Sbjct: 189 NSQSISVFIADDSSDKPESQVDKD---DIKGLALAMLENLNQRDREILCRRFGLLGYEVQ 245

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           TL+ +++E  ++RER+RQ++  + KK++ ++++ 
Sbjct: 246 TLQQVANEVGLTRERIRQLQVSSLKKLKNTLERD 279


>gi|255322395|ref|ZP_05363541.1| RNA polymerase sigma factor RpoD [Campylobacter showae RM3277]
 gi|255300768|gb|EET80039.1| RNA polymerase sigma factor RpoD [Campylobacter showae RM3277]
          Length = 627

 Score =  211 bits (538), Expect = 9e-53,   Method: Composition-based stats.
 Identities = 70/249 (28%), Positives = 122/249 (48%), Gaps = 14/249 (5%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
            KR ++  D  A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ ++
Sbjct: 378 IKRGKKISD-EAKARMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKK 436

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I        +   + R+    +       K  
Sbjct: 437 GYKFSTYATWWIRQAISRAIADQARTIRIPIH-----MIETINRINKINRKYLQEEGKEP 491

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
            +  IA ++ +S  ++  +        SL A I   +++  ++ D++    D      ++
Sbjct: 492 DINVIAAEVGLSADKIKQVIKITKEPISLEAPI--GNEDDGKFGDFV---EDRSSLSPMD 546

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEA 274
              + + +  +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+
Sbjct: 547 HILKNDLKEQIDEVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIES 606

Query: 275 RAFKKVQES 283
            A KK++  
Sbjct: 607 SAIKKLKHP 615



 Score = 36.3 bits (83), Expect = 6.1,   Method: Composition-based stats.
 Identities = 9/36 (25%), Positives = 20/36 (55%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+ +I +L K+EE  ++K+     D+
Sbjct: 104 SDSPVRMYLREMGQIALLTKEEEVEISKKIELGEDI 139


>gi|195953901|ref|YP_002122191.1| RNA polymerase, sigma 70 subunit, RpoD family [Hydrogenobaculum sp.
           Y04AAS1]
 gi|195933513|gb|ACG58213.1| RNA polymerase, sigma 70 subunit, RpoD family [Hydrogenobaculum sp.
           Y04AAS1]
          Length = 578

 Score =  211 bits (538), Expect = 9e-53,   Method: Composition-based stats.
 Identities = 81/293 (27%), Positives = 136/293 (46%), Gaps = 18/293 (6%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEI-RKIPMLEKQEEYVLAKRYREHGDL---SAAHRLVTS 56
           M      I  +  + L R I +I R++ +L   EE        E G      +   +V S
Sbjct: 290 MPFHTFEISRSNYLALQREIEDIERRLGVLP--EELNKIINIIEQGRKRVKESKDMMVKS 347

Query: 57  HLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           +LRLVV IA  Y   GL   +++ EGN+GLM+AV K+D ++GF+ +TY+ WWIK A+   
Sbjct: 348 NLRLVVSIAKKYINRGLHFLDLIQEGNMGLMKAVDKYDYKKGFKFSTYATWWIKQAITRA 407

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
           I      ++I            + ++   L         PE    IAK LN+S  +V  +
Sbjct: 408 IADQAKTIRIPVHM--IETINKISKVSKKLFQEYGREPSPE---EIAKALNMSPEKVRKI 462

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
              +    SL   I   D   +  +D++    D       E   R+  R  + + ++ L+
Sbjct: 463 LKSIQEPISLETPI--GDDEDTHLKDFI---EDSSISNPEEATARRLLREQIEKIINTLS 517

Query: 237 PRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +ER +   R    +    TLE + + F ++RER+RQIE++A +K++   + +
Sbjct: 518 DKEREVIMYRFGLVDGIEHTLEQVGTMFNLTRERIRQIESKAIRKIRHPSRAK 570


>gi|309790481|ref|ZP_07685041.1| sigma-70 family RNA polymerase sigma factor [Oscillochloris
           trichoides DG6]
 gi|308227468|gb|EFO81136.1| sigma-70 family RNA polymerase sigma factor [Oscillochloris
           trichoides DG6]
          Length = 346

 Score =  211 bits (538), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 78/300 (26%), Positives = 129/300 (43%), Gaps = 40/300 (13%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL----------------------- 47
                +  Y+ EI ++ +L   EE  L++R  E GD                        
Sbjct: 45  PTPDAVQHYLQEIGRVSLLTANEEVELSERI-ERGDEAEERLATEDQLSGTQRRNLEHEV 103

Query: 48  ----SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
                A   L+ ++LRLVV IA  Y G GL + +++ EGNIGLM+AV+KFD  +G R +T
Sbjct: 104 ERGNDARRHLIQANLRLVVSIAKKYVGRGLSLLDLIQEGNIGLMRAVEKFDHRKGNRFST 163

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI+ A+   I      +++    ++      + ++K   + ++ +  +      IA
Sbjct: 164 YATWWIRQAVTRSIAEQGRTIRLPVHMSES-----VSQVKRTSERLSQSLERQPSAEEIA 218

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
             L      +  +        SL   +   D+      D+L  D         +    + 
Sbjct: 219 IALGQPTERIERVLEAARRPVSLETPV--GDEGEHTLGDFLPDDDL---PTPGDFASAQL 273

Query: 224 RRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R  L  ++  LN RERRI + R   L     TLE +     ++RER RQIEA A ++++
Sbjct: 274 LRQDLCAALDHLNERERRIIDLRYGLLDGRRRTLEEVGRTLGMTRERARQIEAEALRRLR 333


>gi|7416823|dbj|BAA94072.1| rpoS [Rubrivivax gelatinosus]
          Length = 322

 Score =  211 bits (538), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 81/271 (29%), Positives = 137/271 (50%), Gaps = 9/271 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ +IR+ P++  +EE+  A R R  GD +A   ++  +LRLVV IA  Y G G+P+
Sbjct: 48  LQSYLRDIRRAPLMSAEEEHATAVRAR-AGDFAARQAMIERNLRLVVSIAKHYVGRGMPM 106

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A  KF+PERGFR +TY+ WWI+ +++  I+    L+++      + L
Sbjct: 107 IDLIEEGNLGLMHATGKFEPERGFRFSTYASWWIRQSIERAIMHQARLIRLPVHVV-REL 165

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              L+  +    A      +P  V  +A  L     EV  +        SL+  +   ++
Sbjct: 166 NQVLKARRALESARRGEAERPVSVDEVAAALQRPVEEVAELLKLAEQPTSLDMPL---ER 222

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPV 253
            S +     V D D  +   +     +   ++L   ++ LN RER +   R       P 
Sbjct: 223 ESGESMLDTVADEDAID--PLGLTLSREAVHLLDNGLAELNEREREVLAGRFGLRDREPE 280

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           TLE L++   ++RER+RQI+  A  K++  +
Sbjct: 281 TLEELAARLGLTRERIRQIQQEALLKLKRRM 311


>gi|209524631|ref|ZP_03273179.1| RNA polymerase, sigma 70 subunit, RpoD family [Arthrospira maxima
           CS-328]
 gi|209495089|gb|EDZ95396.1| RNA polymerase, sigma 70 subunit, RpoD family [Arthrospira maxima
           CS-328]
          Length = 331

 Score =  211 bits (538), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 67/314 (21%), Positives = 135/314 (42%), Gaps = 52/314 (16%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------------- 43
            +    +  Y+ EI ++P+L  ++E V  K+ ++                          
Sbjct: 18  TSDTDSVRAYLREIGRVPLLTHEQEIVYGKQVQQATLLQEKRNELAKQLGYEPTEAQWAE 77

Query: 44  -------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
                        H    A  ++V ++LRLVV +A  Y    + + +++ EG IG+ + V
Sbjct: 78  LVNLSVAQLQHILHQGQLAKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGTIGMQRGV 137

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +KFDP +G+R +TY+ WWI+ A+   I      +++     +K     L ++K   + + 
Sbjct: 138 EKFDPTKGYRFSTYAYWWIRQAITRAIAEKGRTIRLPIHITEK-----LNKIKKAQRQLA 192

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
               +   +  +A +L+++  ++     +     SL+  +   D   ++  D L    + 
Sbjct: 193 QQLGRAATMNELAAELDLTPKQIREYLEKSRLPLSLD--LRVGDNQDTELVDLLEDTSNS 250

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRER 268
            EQ  +    R +    L   M+ L  ++R++   R   ++   +TL  +     +SRER
Sbjct: 251 PEQFALNSSLRSD----LESLMTDLTDQQRQVLALRFGLDDGQTLTLAKIGDRLNISRER 306

Query: 269 VRQIEARAFKKVQE 282
           VRQIE  A  K+++
Sbjct: 307 VRQIEREALTKLRK 320


>gi|220915874|ref|YP_002491178.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Anaeromyxobacter
           dehalogenans 2CP-1]
 gi|219953728|gb|ACL64112.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Anaeromyxobacter
           dehalogenans 2CP-1]
          Length = 802

 Score =  211 bits (538), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 82/284 (28%), Positives = 128/284 (45%), Gaps = 23/284 (8%)

Query: 16  LSRYIHEIRKIPMLEKQEEYV-----LAKRYREHGD-----LSAAHRLVTSHLRLVVKIA 65
           L R +    +  +L  QEE       L + YR  GD       A   LV ++LRLVV IA
Sbjct: 522 LDRTLRSAGR-KILRVQEEAEVPVEELRRTYRMIGDGERKAERAKTELVEANLRLVVSIA 580

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ WWI+ A+   I      ++
Sbjct: 581 KKYTNRGLQFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATWWIRQAITRAIADQARTIR 640

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           I            L R   +L         PE    IA+K+ +   +V  +        S
Sbjct: 641 IPVHM--IETINKLIRTSRYLVQELGREPTPE---EIAEKMELPLDKVRKVLKIAKEPIS 695

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L   I   ++  S   D++    D       +     N      + ++ L PRE ++   
Sbjct: 696 LETPI--GEEEDSHLGDFI---EDKSLVSPSDAVINMNLAEQTRKVLATLTPREEKVLRM 750

Query: 246 RRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           R         TLE +  +FEV+RER+RQIEA+A +K++   + +
Sbjct: 751 RFGIGEKSDHTLEEVGQDFEVTRERIRQIEAKALRKLRHPSRSK 794


>gi|82701632|ref|YP_411198.1| RNA polymerase sigma factor RpoS [Nitrosospira multiformis ATCC
           25196]
 gi|82409697|gb|ABB73806.1| RNA polymerase, sigma 38 subunit, RpoS [Nitrosospira multiformis
           ATCC 25196]
          Length = 317

 Score =  211 bits (538), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 78/269 (28%), Positives = 137/269 (50%), Gaps = 13/269 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y +EI    +L  +EE  L +R R++ D +A  +++  +LRLVV IA  Y  +G+ + ++
Sbjct: 50  YFNEIGHNALLTPKEEAELTRRVRQN-DFAARQKMIECNLRLVVNIAKHYTNHGVALLDL 108

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+G+M A+ KFDPERGFR +TY+ WWI+  ++  I+     +++       +    
Sbjct: 109 IEEGNMGMMHALDKFDPERGFRFSTYATWWIRQNIERCIMNQSRTIRLPVHV--IKDLNI 166

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           + +   HL+A T  + K E V   A  L  +  EV  M        SL+A ++       
Sbjct: 167 ILQAARHLEAHTGKDPKAEDV---AHLLGRTVKEVQRMLSLNQSMMSLDAPLDV--DPLL 221

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
              D +  D      ++ E+ E    +  +   ++ LN ++R I E R         TLE
Sbjct: 222 SIGDAIADDQSPGPDLMWEQSE---IKGRVQDWLNRLNDKQRYIIEQRYGLNGYETQTLE 278

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            L++  +++RERVRQI+  A + ++  ++
Sbjct: 279 QLAASLDLTRERVRQIQLEALQTLRMILR 307


>gi|14970557|emb|CAC44359.1| RpoS protein [Erwinia chrysanthemi]
          Length = 332

 Score =  211 bits (538), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 79/273 (28%), Positives = 138/273 (50%), Gaps = 15/273 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+S+  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVSSRRRMIESNLRLVVKIARRYNNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +     +  
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAERLDKPVDDVNRMLRLNERITSVDTPL--GGDSEK 232

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  + D   +   +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 233 ALLDILADEKDNGPE---DTTQDNDMKQNIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQI--EARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI  +    ++++E +Q Q
Sbjct: 290 DVGREIGLTRERVRQIQVQVEGLRRLREILQVQ 322


>gi|227503471|ref|ZP_03933520.1| RNA polymerase sigma factor SigB [Corynebacterium accolens ATCC
           49725]
 gi|306836281|ref|ZP_07469263.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           accolens ATCC 49726]
 gi|227075974|gb|EEI13937.1| RNA polymerase sigma factor SigB [Corynebacterium accolens ATCC
           49725]
 gi|304567873|gb|EFM43456.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           accolens ATCC 49726]
          Length = 337

 Score =  211 bits (538), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 65/309 (21%), Positives = 137/309 (44%), Gaps = 38/309 (12%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAK---------------------- 39
           +R+N +        +  Y++ I K  +L  ++E  LA+                      
Sbjct: 27  SRRNQTNDNPSADLVRVYLNGIGKTDLLSAEDEVELAQTIEVGLYAEYKLNNAEKLTRAE 86

Query: 40  ----RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
               +        A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD 
Sbjct: 87  KRDLKILAREGKKARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDY 146

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            +GF+ +TY+ WWI+ A+   +      +++     ++     L R+K  +         
Sbjct: 147 AKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLSRIKREMYQSLGREAT 204

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
            E    ++++  + E+++  +  +     SL+  + + ++  +   D++        +  
Sbjct: 205 NE---ELSEESGIDENKIEMLLRQSRDPVSLDMPVGTDEE--APLGDFIEDAEATDAETA 259

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIE 273
           +    R    + +   +  L  RE+ +   R   ++  P TL+ +   F +SRERVRQIE
Sbjct: 260 VVASMR---HSDIRGVIDTLEKREQDVIRLRYGLDDGVPRTLDQIGRRFGLSRERVRQIE 316

Query: 274 ARAFKKVQE 282
                K+++
Sbjct: 317 REVMAKLRD 325


>gi|300114080|ref|YP_003760655.1| RpoD subfamily RNA polymerase sigma 70 subunit [Nitrosococcus
           watsonii C-113]
 gi|299540017|gb|ADJ28334.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Nitrosococcus
           watsonii C-113]
          Length = 303

 Score =  211 bits (538), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 75/271 (27%), Positives = 136/271 (50%), Gaps = 14/271 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ E  K+P+L  +EE   A R    GD  A +R++ S+LR+V+K+A  +   GLP+ ++
Sbjct: 42  YMREAGKVPLLNAEEERYYA-RLALQGDREARNRIIESNLRIVIKVASRHVNRGLPLMDL 100

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL+ AV+KF+PE GFR +TY+ WWI+ A++  ++     +++         F  
Sbjct: 101 IEEGNLGLINAVEKFNPELGFRFSTYASWWIRQAIERALMNQTRTIRLPVHV-----FKK 155

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           +R  +  +           +   IAK L+     V       A + SL+  +N   ++  
Sbjct: 156 IRSYQKEVILFRQRYNIEPRSGEIAKLLHEPLERVQRYLSLQALETSLDDPLNEDTEDC- 214

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLE 256
                L+ D      +L E  ++   +  +   +S L  R++ I + R   +     TLE
Sbjct: 215 --LADLLPDERNNPALLWEIFDK---KASIYNQLSQLPERQQEILKRRYGLDGYEVTTLE 269

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +     ++RERVRQI+  A K++++ I+ +
Sbjct: 270 EIGHNLGITRERVRQIQQAAIKRLRKIIESE 300


>gi|172038507|ref|YP_001805008.1| RNA polymerase sigma factor SigD [Cyanothece sp. ATCC 51142]
 gi|171699961|gb|ACB52942.1| group 2 sigma-70 RNA polymerase sigma factor D [Cyanothece sp. ATCC
           51142]
          Length = 318

 Score =  211 bits (538), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 77/318 (24%), Positives = 140/318 (44%), Gaps = 52/318 (16%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR--------------EHG------ 45
           M +  +    +  Y+ EI ++P+L  +EE + AKR +              E G      
Sbjct: 1   MKLTKSNPDPVRAYLKEIGRVPLLTHEEEILYAKRVQRLVNLEKLREEIIEETGQEPTES 60

Query: 46  -------------------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
                                +A  ++V ++LRLVV +A  Y    L + +++ EG IG+
Sbjct: 61  QWAKAAKLSKREFRSIVESGEAAKRKMVEANLRLVVSVAKKYLKRNLDLLDLIQEGTIGM 120

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
            + V+KFDP +G+R +TY+ WWI+ A+   I      +++     +K     L ++K   
Sbjct: 121 QRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEK-----LNKIKKAQ 175

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           + ++    +   V  +A++L+++  +V     R     SL+  +   D   ++  D L  
Sbjct: 176 RELSQQKGRAATVTELAEELDLTPKQVREYLERARQPLSLD--LRVGDNQDTELGDLLED 233

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEV 264
           D     Q   +     + +  L R M  L  +++ +   R   L   P+TL  + S   +
Sbjct: 234 DG----QSPEDFATHSSLQFDLERLMEDLTSQQKEVIALRFGLLDGQPLTLAKIGSRLNI 289

Query: 265 SRERVRQIEARAFKKVQE 282
           SRERVRQIE  A  K+++
Sbjct: 290 SRERVRQIEREALSKLRK 307


>gi|78486471|ref|YP_392396.1| sigma 32 (RpoH) [Thiomicrospira crunogena XCL-2]
 gi|78364757|gb|ABB42722.1| sigma 32 (RpoH) [Thiomicrospira crunogena XCL-2]
          Length = 283

 Score =  211 bits (538), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 95/270 (35%), Positives = 154/270 (57%), Gaps = 5/270 (1%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            +  Y+  ++ +P L   EE  LA++     DL+AA +L+ S LR VV IA  Y GYGLP
Sbjct: 17  NIESYLRTVQTLPQLSADEERELAEKLYHDKDLNAARQLILSSLRYVVPIARSYNGYGLP 76

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           +++++ EGNIGLM+AVK+F+P    RL T+++ W++A + EY++++W +VK  TT  Q++
Sbjct: 77  LNDLIQEGNIGLMKAVKRFNPAEKVRLMTFAVHWVRAEINEYVIKNWRIVKTATTKAQRK 136

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           LFF LR  K  L+ + D +        IAK+L V+  +V+ M  RL G +    L    +
Sbjct: 137 LFFKLRSTKKSLEWLGDKDADT-----IAKELGVTRKDVLEMETRLYGQDMSVDLSPDEE 191

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
           + +S+    LV      E  L    +  +    + +++  L+ R R I + R L E+   
Sbjct: 192 EANSKTYPVLVSQELDPETQLANDSQSDHELGKMHQALKQLDQRSRDILQQRWLSEDKTG 251

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L+ LS ++ VS ER+RQIE +A K +  S+
Sbjct: 252 LKALSEKYGVSMERIRQIEQQAIKTLHASM 281


>gi|16330303|ref|NP_441031.1| RNA polymerase sigma factor SigD [Synechocystis sp. PCC 6803]
 gi|1652792|dbj|BAA17711.1| RNA polymerase sigma factor [Synechocystis sp. PCC 6803]
          Length = 318

 Score =  211 bits (538), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 73/311 (23%), Positives = 134/311 (43%), Gaps = 53/311 (17%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------------------ 43
             +  Y+ EI ++P+L  +EE V AK+ ++                              
Sbjct: 8   DSVRAYLREIGRVPLLTHEEEIVYAKQIQQVVSLNEIKKSLAEGKDGEPVSPSEWAKAAD 67

Query: 44  ----------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
                          A  ++V ++LRLVV +A  Y    L + +++ EG IG+ + V+KF
Sbjct: 68  LSIRELEKAIKEGERAKRKMVEANLRLVVSVAKKYLKRNLDLLDLIQEGTIGMQRGVEKF 127

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           DP +G+R +TY+ WWI+ A+   I      +++     +K     L ++K   + ++   
Sbjct: 128 DPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEK-----LNKIKKAQRQLSQEK 182

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            +   +  +A+ L ++  +V     R     SL+  +   D   ++  D L  D    E 
Sbjct: 183 GRAASIAELAEHLELTPKQVREYLERSRHPLSLD--LRVGDNQDTELGDLLEDDGPLPED 240

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQ 271
                  + +    L   M+ L P++R +   R    +  P+TL ++ S   +SRERVRQ
Sbjct: 241 FATYASLQLD----LDSLMAELTPQQREVLILRFGLNDGQPLTLASIGSMLSISRERVRQ 296

Query: 272 IEARAFKKVQE 282
           IE  A  K+++
Sbjct: 297 IEREALNKLRK 307


>gi|326384463|ref|ZP_08206143.1| RNA polymerase sigma factor SigB [Gordonia neofelifaecis NRRL
           B-59395]
 gi|326196808|gb|EGD54002.1| RNA polymerase sigma factor SigB [Gordonia neofelifaecis NRRL
           B-59395]
          Length = 332

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 62/315 (19%), Positives = 135/315 (42%), Gaps = 38/315 (12%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------------- 43
           +  +++         +  Y++ I +  +L  ++E  L+K                     
Sbjct: 21  LTEQDLDAQSPSADLVRVYLNGIGRTALLNAEQEVDLSKAIEAGLYAKHLLATKKRLTPA 80

Query: 44  ---------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                         A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++AV+KFD
Sbjct: 81  KKRDYAILVREGEQARAHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAVEKFD 140

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +G++ +TY+ WWI+ A+   +      +++     ++     L R++  L        
Sbjct: 141 YAKGYKFSTYATWWIRQAISRGMADQSRTIRLPVHLVEQ--VNKLARIRRELHQQLGREA 198

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
             E    +A +  +   ++  +        SL+  + + ++  +   D++        + 
Sbjct: 199 TDE---ELALESGIPAEKIADLMDHSRDPVSLDMPVGNDEE--APLGDFIEDAEATSAET 253

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
           ++         + +   +S L+ RE ++   R   ++  P TL+ +   F +SRERVRQI
Sbjct: 254 VV---IANLLHSDIRSVLSTLDEREMQVITMRYGLDDGQPRTLDQIGRAFGLSRERVRQI 310

Query: 273 EARAFKKVQESIQKQ 287
           E     K+++  + +
Sbjct: 311 EREVMGKLRQGDRAE 325


>gi|158335266|ref|YP_001516438.1| RNA polymerase sigma factor SigC [Acaryochloris marina MBIC11017]
 gi|158305507|gb|ABW27124.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 423

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 62/242 (25%), Positives = 129/242 (53%), Gaps = 13/242 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           + A   ++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV+KFDP +G+R +TY+ 
Sbjct: 182 IKAKEHMIQANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTKGYRFSTYAY 241

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   I      +++     +K     L ++K   + ++ +  +   +  IA+++
Sbjct: 242 WWIRQGITRAIATQSRTIRLPVHITEK-----LNKIKKAQRKLSQSKGRTASIEDIAQEM 296

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  ++  +  R+    SL   I       ++  D L  D    E++++    R++ + 
Sbjct: 297 DMTPEQIRELLVRVPRSVSLE--IKVGKDKDTELGDLLETDDISPEELIM----RESLQQ 350

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVT--LENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L + ++ L PRER +   R    +  T  L  +    ++SRERVRQIE++A +K+++  
Sbjct: 351 ELKQLLADLTPRERDVITMRFGLNDGKTHSLAQIGKSLDLSRERVRQIESKALQKLRQPK 410

Query: 285 QK 286
           ++
Sbjct: 411 RR 412


>gi|78186275|ref|YP_374318.1| RNA polymerase sigma-70 factor [Chlorobium luteolum DSM 273]
 gi|78166177|gb|ABB23275.1| RNA polymerase sigma-70 factor [Chlorobium luteolum DSM 273]
          Length = 299

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 76/294 (25%), Positives = 142/294 (48%), Gaps = 24/294 (8%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD-----------LSAAH 51
           + +  I     + L RY+ EI K  +L   +E  L K  +E  D             A  
Sbjct: 5   KISKQITNRESLSLDRYLQEIGKYDLLTADDEVRLTKAIKEGFDMPVDTTEYKRAKRALD 64

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +L+  +LR VV +A  Y+  GL + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ 
Sbjct: 65  KLIKGNLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQ 124

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ + +     +V++    N+      + +    L+   + +        +A  L++   
Sbjct: 125 SILQALAEQSRIVRLP--LNRVGTLNKISKAYSQLEQEFERD---PNTKELANLLDMDSQ 179

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           +V           S++A     D N  +  D L  D      +      R +    + RS
Sbjct: 180 DVADTLKIAGRHVSVDAPFAQGDDN--RLLDVLQNDG----HLPDHGLNRDSLTLEVERS 233

Query: 232 MSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +SVL PRE  + ++      +NP+TLE +  +F+++RERVRQI+ +A ++++ S
Sbjct: 234 LSVLAPREADVIKSYFGIGMDNPLTLEEIGEKFKLTRERVRQIKEKAIRRLRTS 287


>gi|153875311|ref|ZP_02003170.1| RNA polymerase subunit sigma-38 [Beggiatoa sp. PS]
 gi|152068225|gb|EDN66830.1| RNA polymerase subunit sigma-38 [Beggiatoa sp. PS]
          Length = 314

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 77/271 (28%), Positives = 145/271 (53%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI K  +L  +EE   A+R ++ G+ +A +R++  +LRLVVKIA  Y   GL + ++
Sbjct: 45  YLNEIGKSKLLTAEEEIKYARRAQQ-GNEAARNRMIEGNLRLVVKIARNYMNRGLALLDL 103

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM+AV KFDPE+GFR +TY+ WWI+  ++  I+     +++       +    
Sbjct: 104 IEEGNLGLMRAVNKFDPEKGFRFSTYATWWIRQTIERAIMNQNRTIRLPIHV--LKEINQ 161

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
             R    L    D+    E++    KK      +++ +N R     S+++   +  + S 
Sbjct: 162 CLRTNHVLSQTLDHEPTSEEIAKTLKKSKQEVEKLLEVNERA---ISMDSPWMNYSEKS- 217

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D +  + +   ++++E  +       L   +S L  ++R + E R      +  TLE
Sbjct: 218 -LIDNIPDELNPDPRLILEDADIIKC---LHLWLSQLTDKQRLVVERRFGIGNGDEATLE 273

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            + +E E++RERVRQI+  A ++++E ++++
Sbjct: 274 EIGAELELTRERVRQIQITATERLKEILERE 304


>gi|78185087|ref|YP_377522.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CC9902]
 gi|116072338|ref|ZP_01469605.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. BL107]
 gi|78169381|gb|ABB26478.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. CC9902]
 gi|116064860|gb|EAU70619.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. BL107]
          Length = 313

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 76/302 (25%), Positives = 141/302 (46%), Gaps = 36/302 (11%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------EHGDLS----------------- 48
               +S Y+  I +IP+L   EE  L  + +      E G                    
Sbjct: 16  SSDPVSWYLSTIGRIPLLTAAEEIELGNQVQAMMAFTEDGSKDFKVEDLTTKQRRMLRIG 75

Query: 49  --AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  R++ ++LRLVV +A  Y+G GL + +++ EG++GL +AV+KFDP RG++ +TY+ 
Sbjct: 76  RRAKERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAF 135

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ +M   I      +++    +++     L  ++     +          + IA+ +
Sbjct: 136 WWIRQSMTRAIACQSRTIRLPVHLSER-----LTTIRKVSLDLAHKLGAMPNRLEIAEAM 190

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   E+ S+  +     SL+A +N  ++  S   D +    D      ++  E++    
Sbjct: 191 DIPVEELDSLLRQALTTSSLDAPVN-GEEGRSFLGDLIA---DSSADEPLDIVEQRIHHE 246

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L R +S L+ +E+ +   R   E     TL  +    EVSRERVRQ+E +A +K++   
Sbjct: 247 QLGRWLSHLSEQEQNVLRLRFGLEGNERHTLAEIGRMMEVSRERVRQVELKALRKLRNLT 306

Query: 285 QK 286
           ++
Sbjct: 307 RR 308


>gi|284931435|gb|ADC31373.1| RNA polymerase sigma factor RpoD (Sigma-A) [Mycoplasma
           gallisepticum str. F]
          Length = 646

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 70/285 (24%), Positives = 127/285 (44%), Gaps = 22/285 (7%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAH----RLVTSHLRLVVKIAMGY 68
           E  +  ++  +    +L   EE  +AK      D         +LVTS+LRLV  IA  Y
Sbjct: 358 EDNVKAFLGTLGSSKILNFGEEIQIAKLLGST-DPETREYAINQLVTSNLRLVTSIAKKY 416

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
              GL   +++ EG+IGLM+A+ KF+ + G + +TY+ WWI+ A+   I      V+I  
Sbjct: 417 LNRGLDFVDLIQEGSIGLMKAISKFNYKLGNKFSTYATWWIRQAITRAIADQARTVRIPV 476

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL-----NVSESEVISMNCRLAGD 183
              +      + +L    + +T    +   +  + + +       +  +V  +       
Sbjct: 477 HMVE-----TINKLIKTERMLTQQLGRDPTLEELTEAMGGQVNGFTPKKVADIKKLNQEP 531

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SL+  I   ++  SQ+ D++      +     EK       N L   ++ L  +E +I 
Sbjct: 532 VSLDKPIGHDEE--SQFVDFVKDRDILKPDEYTEKLIVTEHINEL--FVNTLTKKEEQII 587

Query: 244 EARRLQ---ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             R         +TLE +  +F V+RER+RQIE++A +K++   +
Sbjct: 588 RMRYGLHPWHQQMTLEEVGQKFNVTRERIRQIESKALRKLKHPSK 632


>gi|218438398|ref|YP_002376727.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
 gi|218171126|gb|ACK69859.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
          Length = 295

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 72/288 (25%), Positives = 136/288 (47%), Gaps = 30/288 (10%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------HGDLSAAHRLVT 55
             +  Y+ EI + P+L  Q+E  LA + +                        A  ++++
Sbjct: 7   DNVKAYLQEIGRTPLLSSQQEVELATQVQNMMALLDKENLTPEEIKIIQQGKRAKRKMIS 66

Query: 56  SHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQE 115
           ++LRLVV IA  Y+  GL   +++ EG+IGL++ V+KFDP +G++ +TY+ WWI+ AM  
Sbjct: 67  ANLRLVVSIAKKYQRRGLSFLDLIQEGSIGLIRGVEKFDPSKGYKFSTYAYWWIRQAMTR 126

Query: 116 YILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
            I      +++ +   +      L +LK   + +T    +      IA +L +S +E+ +
Sbjct: 127 AIADQSRTIRLPSHLTES-----LNKLKRITRQLTGELGRRPTEEEIATELEISMNELRT 181

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
           +        S  +L    D   ++  + L  D     + + + E       M+ + +  L
Sbjct: 182 IRQADHRTRS-YSLNMKMDDEQTELAELLADDSANPNEFVAQIELSS----MVEQLLETL 236

Query: 236 NPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            PR++ I   R   +N   ++LE +     +SRERVRQ++ RA + ++
Sbjct: 237 PPRQQEIIALRYGLKNGKQMSLEEVGHHCNLSRERVRQLQNRAMRTLK 284


>gi|158338579|ref|YP_001519756.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158308820|gb|ABW30437.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 268

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 69/274 (25%), Positives = 134/274 (48%), Gaps = 15/274 (5%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +      L  Y+ EI + P+L  +EE  LA++ +  G+  A  +++ ++LRLVV IA  +
Sbjct: 1   MATQHDSLHYYLKEIGRFPLLTHEEEITLARQVQ-AGNPRAKRKMIEANLRLVVSIAKKH 59

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           +  GLP+ +++ EGN+GL  AV KF+PE+G R +TY+ WWI   +   +     +V++  
Sbjct: 60  QNRGLPLLDLIQEGNLGLSIAVDKFEPEQGNRFSTYAYWWILQGVTRSLQNKGRVVRLPV 119

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
              Q        ++K     ++    +   VV IA  + +  + +      L    SL+ 
Sbjct: 120 KHWQVG-----NQIKRTRHQLSQELGREPTVVEIADAMEMDLTRLKKYLHSLQETVSLDK 174

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            + S  +  +   D +  +   Q  + +  ++ +         +++L+ R+R +   R  
Sbjct: 175 FVGS--EQDTTLGDLIEGNDSTQSYLDLLLQDEELSGY-----LALLDDRQRFVISERYG 227

Query: 249 QEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
            E+  P ++E +  +  +SRERVRQI  +A + +
Sbjct: 228 LEDGKPKSMEKIGQKLGISRERVRQIIKKAMQTL 261


>gi|6175918|gb|AAF05334.1|AF182102_2 RNA polymerase sigma subunit [Escherichia coli]
 gi|6175933|gb|AAF05344.1|AF182107_2 RNA polymerase sigma subunit [Escherichia coli]
          Length = 313

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 75/264 (28%), Positives = 133/264 (50%), Gaps = 13/264 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKV 280
           ++  E  ++RERVRQI+    +++
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRL 313


>gi|283956399|ref|ZP_06373879.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 1336]
 gi|283792119|gb|EFC30908.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 1336]
          Length = 622

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 74/254 (29%), Positives = 126/254 (49%), Gaps = 14/254 (5%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           E     KR ++  D  A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV K
Sbjct: 366 EILEQIKRGKKISD-EAKGRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDK 424

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RG++ +TY+ WWI+ A+   I      ++I        +   + ++   ++     
Sbjct: 425 FEYKRGYKFSTYATWWIRQAISRAIADQARTIRIPIH-----MIETINQINKIIREHLQK 479

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           + K   V  IAK++ +S  +V  +        SL A I   +++  ++ D++    D   
Sbjct: 480 DGKEPDVSVIAKEVGLSVDKVKQVIKITKEPISLEAPI--GNEDDGKFGDFV---EDRNS 534

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERV 269
              ++   + + +  +   +  LN RE+ +   R      E+  TLE +  E  V+RERV
Sbjct: 535 LSPMDHILKDDLKEQIDEVLDQLNDREKAVIRMRFGLMDDESDRTLEEIGKELNVTRERV 594

Query: 270 RQIEARAFKKVQES 283
           RQIE+ A KK++  
Sbjct: 595 RQIESSAIKKLKHP 608


>gi|33240812|ref|NP_875754.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Prochlorococcus marinus subsp. marinus str. CCMP1375]
 gi|33238341|gb|AAQ00407.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Prochlorococcus marinus subsp. marinus str. CCMP1375]
          Length = 313

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 77/300 (25%), Positives = 145/300 (48%), Gaps = 36/300 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYR------EHG-------------------DLS 48
             +S Y+  I ++P+L   EE  L  + +      E G                      
Sbjct: 18  DPISWYLATIGRVPLLTPAEEIELGNQVQVMMNLTEDGMVNEKTKKFTSHERRSIRIGRR 77

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R++ ++LRLVV +A  Y+G GL + ++V EG++GL +AV+KFDP RG++ +TY+ WW
Sbjct: 78  AKERMMKANLRLVVSVAKKYQGKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAFWW 137

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ +M   I      +++    +++     L  ++     +          + IA+++++
Sbjct: 138 IRQSMTRAIACQSRTIRLPVHLSER-----LATIRKVSLDLAHKLGAMPNRLEIAEEMDI 192

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              E+ S+  +     SL+A +N  D   S   D +    D   +  ++K E+   +  L
Sbjct: 193 EVEELDSILRQALTTSSLDAPVN-GDDGRSFLGDLIA---DSSVEEPLDKVEQSIHQEQL 248

Query: 229 TRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R ++ L+ +E+ + + R   E  +  TL  +    EVSRERVRQ+E ++ +K++   +K
Sbjct: 249 GRWLTHLSEQEQHVLKLRFGLEGNDRHTLAEIGRLLEVSRERVRQVELKSLRKLRNLTRK 308


>gi|57505389|ref|ZP_00371317.1| RNA polymerase sigma factor RpoD [Campylobacter upsaliensis RM3195]
 gi|57016214|gb|EAL53000.1| RNA polymerase sigma factor RpoD [Campylobacter upsaliensis RM3195]
          Length = 619

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 76/254 (29%), Positives = 125/254 (49%), Gaps = 14/254 (5%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           E     KR ++  D  A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV K
Sbjct: 363 EILEQIKRGKKISD-EAKGRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDK 421

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RG++ +TY+ WWI+ A+   I      ++I        +   + ++   ++     
Sbjct: 422 FEYKRGYKFSTYATWWIRQAISRAIADQARTIRIPIH-----MIETINQINKIIREHLQK 476

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           N K   V  IAK++ +S  +V  +        SL A I S  +   ++ D++    D   
Sbjct: 477 NGKEPDVNDIAKEVGLSVDKVKQVIKITKEPISLEAPIGS--EEDGKFGDFV---EDKNS 531

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERV 269
              ++   + + +  +   +  LN RE+ +   R      E+  TLE +  E  V+RERV
Sbjct: 532 LSPMDNILKDDLKEQIDEVLDQLNDREKAVIRMRFGLLEDESDRTLEEIGKELNVTRERV 591

Query: 270 RQIEARAFKKVQES 283
           RQIE+ A KK++  
Sbjct: 592 RQIESSAIKKLKHP 605


>gi|255020521|ref|ZP_05292585.1| RNA polymerase sigma factor RpoS [Acidithiobacillus caldus ATCC
           51756]
 gi|254970041|gb|EET27539.1| RNA polymerase sigma factor RpoS [Acidithiobacillus caldus ATCC
           51756]
          Length = 316

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 77/286 (26%), Positives = 134/286 (46%), Gaps = 18/286 (6%)

Query: 9   IVNGEIGLSR-----YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           +  GE  L       Y+ EI   P+L  +EE     R  + GD+ A  R++  +LRLVV+
Sbjct: 33  VAPGEADLDWDATRIYLQEIGHNPLLTAEEEIYYG-RLVQQGDVRARTRMIECNLRLVVR 91

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           +A  Y   G+P+ +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     
Sbjct: 92  VARRYLHRGMPLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQNIERALMNQTRT 151

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           +++      K L   LR  +   Q +     +   V  +A  L+    +V          
Sbjct: 152 IRLPVHV-MKELAVVLRAARCLEQEL----RREPSVDEVAAALDRPVDQVRGCLEMDGRV 206

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SL+     +     Q +D      D + Q        +N    L   ++ L+ + R + 
Sbjct: 207 TSLD-----NSGQRDQGRDLNEVLSDAEAQGPEAMVAAQNLAVRLQSWLAGLSEKHRLVL 261

Query: 244 EARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             R   +  +  TLE + +   ++RERVRQI+  A   ++  I+ +
Sbjct: 262 SWRFGLDGGDGATLEEVGTRLGITRERVRQIQVEALLILRRRIEAE 307


>gi|296393377|ref|YP_003658261.1| RpoD subfamily RNA polymerase sigma-70 factor [Segniliparus
           rotundus DSM 44985]
 gi|296180524|gb|ADG97430.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Segniliparus
           rotundus DSM 44985]
          Length = 377

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 67/311 (21%), Positives = 134/311 (43%), Gaps = 38/311 (12%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAK-----RYREH--------------- 44
           ++         +  Y++ I +  +L   +E  LAK      Y EH               
Sbjct: 70  DLDTQSPAADLVRVYLNGIGRTALLTAADEVELAKSIEAGLYAEHLLKTSDNLTPQRRRE 129

Query: 45  ------GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
                    +A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +G
Sbjct: 130 LKTVARDGQAARTHLLEANLRLVVSLAKRYTGRGIPLLDLIQEGNLGLIRAMEKFDYAKG 189

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           F+ +TY+ WWI+ A+   +      +++     ++     L R+K  L          E 
Sbjct: 190 FKFSTYATWWIRQAITRGVADQSRTIRLPVHLVEQ--VNKLSRIKRELHQQLGREATSE- 246

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              ++++  + E  +  +        SL+  + + ++  +   D++    D +       
Sbjct: 247 --ELSRETGIPEHRIADLLDHSRDPVSLDMPVGADEE--APLGDFI---EDSEGASAENA 299

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARA 276
                    +   ++ LN  E+++   R   ++  P TL+ +   F +SRERVRQIE   
Sbjct: 300 VIAGFLHRDVRTVLATLNEVEQQVIRLRYGLDDGQPRTLDQIGKVFSLSRERVRQIEREV 359

Query: 277 FKKVQESIQKQ 287
             K++   + +
Sbjct: 360 MVKLRNGDRAE 370


>gi|193216316|ref|YP_001997515.1| RpoD family RNA polymerase, sigma 70 subunit [Chloroherpeton
           thalassium ATCC 35110]
 gi|193089793|gb|ACF15068.1| RNA polymerase, sigma 70 subunit, RpoD family [Chloroherpeton
           thalassium ATCC 35110]
          Length = 299

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 80/295 (27%), Positives = 150/295 (50%), Gaps = 26/295 (8%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD------------LSAA 50
           + +  I       L RY+ EI K  +L  QEE  L ++ ++ GD              A 
Sbjct: 5   KISKQITNRESQSLDRYLQEIGKFDLLTAQEEIELTRQIKK-GDGQPIDSKEYREARRAL 63

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            +L+ ++LR VV +A  Y+  GL + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+
Sbjct: 64  EKLIKANLRFVVSVAKQYQNQGLSLGDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIR 123

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            ++ + +     +V++    N+      + +    L+   + +   E    +A  L+++ 
Sbjct: 124 QSILQALAEQSRIVRLP--LNRVGTLNKIGKAFSQLEQEYERDPSTE---ELAHLLDMNS 178

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           SE+           S++A     D N  +  D L  D    +  L++    ++ R  + R
Sbjct: 179 SEITDTLKIAGRHISVDAPFAQGDDN--RLLDVLQNDSQRPDHGLLQ----ESLRLEVER 232

Query: 231 SMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           S+S L+PRE  +  +      ENP+TLE +   F+++RERVRQI+ +A ++++ S
Sbjct: 233 SLSALSPREADVIRSYFGIGMENPLTLEEIGERFKLTRERVRQIKEKAIRRLRHS 287


>gi|153876074|ref|ZP_02003579.1| RNA polymerase sigma-32 factor [Beggiatoa sp. PS]
 gi|152067462|gb|EDN66421.1| RNA polymerase sigma-32 factor [Beggiatoa sp. PS]
          Length = 242

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 91/236 (38%), Positives = 151/236 (63%), Gaps = 7/236 (2%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            +LV SHLR V+ IA GYRGYGLP+++++ EGNIGLM+AVK+F+P  G RL ++++ WI+
Sbjct: 8   KKLVISHLRFVLYIAHGYRGYGLPLADLIQEGNIGLMKAVKRFNPNVGVRLVSFAVHWIR 67

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
           A + E+ILR+W +VK+ TT  Q++LFFNLR +K  L  ++       +V  +A+ L VS 
Sbjct: 68  AEIHEFILRNWRIVKVVTTKAQRKLFFNLRSMKKRLGWLSQ-----AEVDKVAQDLGVSS 122

Query: 171 SEVISMNCRLA-GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNML 228
            +V+ M  RL+  D + +A ++S D +        + D+      L+E++E + +    L
Sbjct: 123 KDVLEMEKRLSMQDVAFDAPVDSDDDDEVFAPAAYLEDNRYDPAALVEQDEWEAHGHKQL 182

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             +   L+ R + I + R L E+  TL+ L++ ++VS ER+RQIE+ A KK+++++
Sbjct: 183 LHAFKKLDVRSQDILQQRWLSEDKATLQELANHYKVSAERIRQIESNALKKLKKNM 238


>gi|2764713|emb|CAA05353.1| sigma 70 [Campylobacter jejuni]
          Length = 622

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 74/254 (29%), Positives = 126/254 (49%), Gaps = 14/254 (5%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           E     KR ++  D  A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV K
Sbjct: 366 EILEQIKRGKKISD-EAKGRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDK 424

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RG++ +TY+ WWI+ A+   I      ++I        +   + ++   ++     
Sbjct: 425 FEYKRGYKFSTYATWWIRQAISRAIADQARTIRIPIH-----MIETINQINKIIREHLQK 479

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           + K   V  IAK++ +S  +V  +        SL A I   +++  ++ D++    D   
Sbjct: 480 DGKEPDVSVIAKEVGLSVDKVKQVIKITKEPISLEAPI--GNEDDGKFGDFV---EDRNS 534

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERV 269
              ++   + + +  +   +  LN RE+ +   R      E+  TLE +  E  V+RERV
Sbjct: 535 LSPMDHILKDDLKEQIDEVLDQLNDREKAVIRMRFGLMDDESDRTLEEIGKELNVTRERV 594

Query: 270 RQIEARAFKKVQES 283
           RQIE+ A KK++  
Sbjct: 595 RQIESSAIKKLKHP 608


>gi|257457793|ref|ZP_05622954.1| RNA polymerase sigma factor RpoD [Treponema vincentii ATCC 35580]
 gi|257444843|gb|EEV19925.1| RNA polymerase sigma factor RpoD [Treponema vincentii ATCC 35580]
          Length = 607

 Score =  211 bits (537), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 69/260 (26%), Positives = 121/260 (46%), Gaps = 16/260 (6%)

Query: 32  QEEYVLAKRYREHGD---LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           ++   LAK  R HG      A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++
Sbjct: 350 EDIIALAKEIR-HGHAMLKKAKDKLINANLRLVVSIAKKYTNRGLHFFDLVQEGNIGLIK 408

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           AV+KF+  +G++ +TY+ WWI+ A+   I      +++        +   + ++    + 
Sbjct: 409 AVEKFEYRKGYKFSTYATWWIRQAITRSISDQARTIRVPVH-----MIEQINKVTRESRQ 463

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           +     +      IA +L  +   V  +        SL   I   ++  S   D++    
Sbjct: 464 LMQKFGREPTDEEIAVQLGWNVERVKQVKNVAREPISLETPI--GEEEDSSLGDFI---E 518

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSR 266
           D   +      E    +  L   +S L  RE+ + + R   +    +TLE +   F V+R
Sbjct: 519 DKDVENPSNLTEYILLQEQLRSVLSCLPLREQEVLKMRFGLDEGYALTLEEVGLYFNVTR 578

Query: 267 ERVRQIEARAFKKVQESIQK 286
           ER+RQIEA+A ++++   Q 
Sbjct: 579 ERIRQIEAKALRRLRHPKQS 598


>gi|168768834|ref|ZP_02793841.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4486]
 gi|189362139|gb|EDU80558.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4486]
          Length = 329

 Score =  210 bits (536), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 135/271 (49%), Gaps = 14/271 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +   D   +
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLG-GDSEKA 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                     +G E    + + +++    L       N ++R +   R   L     TLE
Sbjct: 234 LLDILADEKENGPEDTTQDDDMKQSIVKWLFE-----NAKQREVLARRFGLLGYEAATLE 288

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 289 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 319


>gi|25028367|ref|NP_738421.1| RNA polymerase sigma factor SigB [Corynebacterium efficiens YS-314]
 gi|259507424|ref|ZP_05750324.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           efficiens YS-314]
 gi|23493652|dbj|BAC18621.1| sigma factor SigB [Corynebacterium efficiens YS-314]
 gi|259164989|gb|EEW49543.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           efficiens YS-314]
          Length = 333

 Score =  210 bits (536), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 68/310 (21%), Positives = 138/310 (44%), Gaps = 39/310 (12%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAK---------------------- 39
           +R+  +     +  +  Y++ I K  +L  ++E  LA+                      
Sbjct: 22  SRRGQTNDNPSQDLVRVYLNGIGKTALLTAEDEVELAQTIEVGLYAEYKLKHSDEPLTRA 81

Query: 40  -----RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                +        A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD
Sbjct: 82  MKRDLKVLAKEGKKARAHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFD 141

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +GF+ +TY+ WWI+ A+   +      +++     ++     L R+K  +        
Sbjct: 142 YTKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLSRIKREMYQHLGREA 199

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
             E    +A++  + ES++  +  +     SL+  + + ++  +   D++        + 
Sbjct: 200 TNE---ELAEESGIEESKIEMLLRQSRDPVSLDMPVGADEE--APLGDFIEDSEATDAET 254

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
            +    R    + +   +S L  RE+ +   R   E+  P TL+ +   F +SRERVRQI
Sbjct: 255 AVVASMR---HSDIRSVLSTLEQREQDVIRLRYGLEDGVPRTLDQIGRRFGLSRERVRQI 311

Query: 273 EARAFKKVQE 282
           E     K+++
Sbjct: 312 EREVMSKLRD 321


>gi|86150479|ref|ZP_01068704.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni CF93-6]
 gi|88596833|ref|ZP_01100070.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 84-25]
 gi|148926089|ref|ZP_01809775.1| RNA polymerase sigma factor (sigma-70) [Campylobacter jejuni subsp.
           jejuni CG8486]
 gi|218562617|ref|YP_002344396.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni NCTC 11168]
 gi|85839074|gb|EAQ56338.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni CF93-6]
 gi|88191674|gb|EAQ95646.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 84-25]
 gi|112360323|emb|CAL35119.1| RNA polymerase sigma factor (sigma-70) [Campylobacter jejuni subsp.
           jejuni NCTC 11168]
 gi|145845568|gb|EDK22660.1| RNA polymerase sigma factor (sigma-70) [Campylobacter jejuni subsp.
           jejuni CG8486]
 gi|284926231|gb|ADC28583.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni IA3902]
 gi|315058444|gb|ADT72773.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni S3]
 gi|315928360|gb|EFV07675.1| RNA polymerase sigma factor rpoD [Campylobacter jejuni subsp.
           jejuni DFVF1099]
          Length = 622

 Score =  210 bits (536), Expect = 1e-52,   Method: Composition-based stats.
 Identities = 74/254 (29%), Positives = 126/254 (49%), Gaps = 14/254 (5%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           E     KR ++  D  A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV K
Sbjct: 366 EILEQIKRGKKISD-EAKGRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDK 424

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RG++ +TY+ WWI+ A+   I      ++I        +   + ++   ++     
Sbjct: 425 FEYKRGYKFSTYATWWIRQAISRAIADQARTIRIPIH-----MIETINQINKIIREHLQK 479

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           + K   V  IAK++ +S  +V  +        SL A I   +++  ++ D++    D   
Sbjct: 480 DGKEPDVSVIAKEVGLSVDKVKQVIKITKEPISLEAPI--GNEDDGKFGDFV---EDRNS 534

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERV 269
              ++   + + +  +   +  LN RE+ +   R      E+  TLE +  E  V+RERV
Sbjct: 535 LSPMDHILKDDLKEQIDEVLDQLNDREKAVIRMRFGLMDDESDRTLEEIGKELNVTRERV 594

Query: 270 RQIEARAFKKVQES 283
           RQIE+ A KK++  
Sbjct: 595 RQIESSAIKKLKHP 608


>gi|323144152|ref|ZP_08078788.1| RNA polymerase sigma factor [Succinatimonas hippei YIT 12066]
 gi|322416060|gb|EFY06758.1| RNA polymerase sigma factor [Succinatimonas hippei YIT 12066]
          Length = 311

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 85/285 (29%), Positives = 151/285 (52%), Gaps = 9/285 (3%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
            K++ +       L  YI  +R+ P+L +++E  L  R  + GD+ A + ++TS+LRLV+
Sbjct: 30  EKDIPVPSFSGDLLVSYISSVRRYPLLSQEDEVRLG-RLVQQGDVKARNSMITSNLRLVI 88

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           K+A  YR  G+P+ +++ EGN+GL+ AV KFDPERGFR +TY+ WWI+  ++  ++    
Sbjct: 89  KVARDYRTRGVPMLDLIEEGNLGLIHAVNKFDPERGFRFSTYATWWIRQGIEHAVMNQSR 148

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           LV++       +    + ++K  LQ     + +   V  IAK+L++ E +V SM   +A 
Sbjct: 149 LVRLPFHV--IKDLNQVLKVKKKLQEKA--HGQAVAVKDIAKELDIDEDKVRSMLV-VAE 203

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++ L N  +K+S +    L    D +   L E+        +L   +  LN R++ I
Sbjct: 204 GISISDL-NVKNKDSEKNVSLLDLLADEKTPTLEEQFGNTEIEKLLRSWIDSLNERQKII 262

Query: 243 FEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              R      +  TLE +     ++RERVRQ++      +++ ++
Sbjct: 263 VIHRFGINDNDIKTLEEIGEMLHLTRERVRQLQKTVLISLKKFLK 307


>gi|117926357|ref|YP_866974.1| RNA polymerase, sigma 32 subunit, RpoH [Magnetococcus sp. MC-1]
 gi|117610113|gb|ABK45568.1| RNA polymerase, sigma 32 subunit, RpoH [Magnetococcus sp. MC-1]
          Length = 297

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 110/288 (38%), Positives = 163/288 (56%), Gaps = 9/288 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           ++R     +  GE G  R++ +  + PML   EEY LA  YR H DL AAHRLV +HLRL
Sbjct: 8   ISRPAELALGQGEEGFQRFLKQAAQAPMLSADEEYQLATNYRRHNDLEAAHRLVHAHLRL 67

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+KIA  Y  Y   + ++V EG+IGLM AVKKFD +RG RLATY++WWI+AA+ ++IL +
Sbjct: 68  VLKIAREYLYYRSSLPDLVQEGSIGLMHAVKKFDAQRGNRLATYAVWWIRAAIHDFILNT 127

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
             +VK+ TT  ++ LFF LR+ K  L  +        +   +A K       ++ M+ RL
Sbjct: 128 AHMVKVATTKLKRHLFFKLRQAKSSLAPLNQQ-----EAEELAVKFATDAQTILEMDSRL 182

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           AG D SLN  +        +  + L  +   QE  L   ++++    ++ + +  LN RE
Sbjct: 183 AGADSSLNQPLF---DEGGELIELLEDERPNQELQLQSAQQQQRLGRLVKQGLKQLNERE 239

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           + I  +R + E+    E L+  F++S ERVRQIE RA  K++   Q Q
Sbjct: 240 QAIIISRFMGEHAEPREQLAQRFQISGERVRQIEQRAMAKLRSYFQSQ 287


>gi|291565943|dbj|BAI88215.1| group 2 RNA polymerase sigma factor SigD [Arthrospira platensis
           NIES-39]
          Length = 331

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 67/314 (21%), Positives = 135/314 (42%), Gaps = 52/314 (16%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------------- 43
            +    +  Y+ EI ++P+L  ++E V  K+ ++                          
Sbjct: 18  TSDTDSVRAYLREIGRVPLLTHEQEIVYGKQVQQATLLQEKRNELAKQLAYEPTEAQWAE 77

Query: 44  -------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
                        H    A  ++V ++LRLVV +A  Y    + + +++ EG IG+ + V
Sbjct: 78  LVNLSVAQLQHILHQGQLAKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGTIGMQRGV 137

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +KFDP +G+R +TY+ WWI+ A+   I      +++     +K     L ++K   + + 
Sbjct: 138 EKFDPTKGYRFSTYAYWWIRQAITRAIAEKGRTIRLPIHITEK-----LNKIKKAQRQLA 192

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
               +   +  +A +L+++  ++     +     SL+  +   D   ++  D L    + 
Sbjct: 193 QQLGRAATMNELAAELDLTPKQIREYLEKSRLPLSLD--LRVGDNQDTELVDLLEDTTNS 250

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRER 268
            EQ  +    R +    L   M+ L  ++R++   R   ++   +TL  +     +SRER
Sbjct: 251 PEQFALNSSLRSD----LESLMTDLTDQQRQVLALRFGLDDGQTLTLAKIGDRLNISRER 306

Query: 269 VRQIEARAFKKVQE 282
           VRQIE  A  K+++
Sbjct: 307 VRQIEREALTKLRK 320


>gi|163853281|ref|YP_001641324.1| RNA polymerase factor sigma-32 [Methylobacterium extorquens PA1]
 gi|218532097|ref|YP_002422913.1| RNA polymerase factor sigma-32 [Methylobacterium chloromethanicum
           CM4]
 gi|254563204|ref|YP_003070299.1| RNA polymerase sigma-32 [Methylobacterium extorquens DM4]
 gi|163664886|gb|ABY32253.1| RNA polymerase sigma factor, sigma-70 family [Methylobacterium
           extorquens PA1]
 gi|218524400|gb|ACK84985.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacterium
           chloromethanicum CM4]
 gi|254270482|emb|CAX26482.1| RNA polymerase sigma-32 (sigma H) factor [Methylobacterium
           extorquens DM4]
          Length = 290

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 110/271 (40%), Positives = 175/271 (64%), Gaps = 1/271 (0%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           ++I    + P L + EE  LA  ++E  D  A HRL+++H+RLV+ +A  +R YGLP+++
Sbjct: 10  QFIRTAMEAPFLARDEERGLAVAWKEARDERALHRLISAHMRLVIALAGRFRHYGLPMAD 69

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +V EG++GLM+A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFF
Sbjct: 70  LVQEGHVGLMEAAARFEPEREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKALFF 129

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKN 196
           NLRRL+  L   T+  +  E    IA  + VS  +V  M+ RL+G D SLNA +    + 
Sbjct: 130 NLRRLRARLMQSTEEQVGSEIHGRIATAIGVSREDVALMDARLSGPDMSLNAPVGEESEA 189

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           SS+  D+LV +    ++ +    + + R   L ++++VL+ RE RI   RRL E+  TLE
Sbjct: 190 SSERMDFLVDNAALPDETVSALVDGERRLIWLRQALTVLSERELRILRERRLAEDQATLE 249

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            L     +S+ERVRQIE RA +K++ ++ ++
Sbjct: 250 ALGHRLGISKERVRQIENRALEKLRRALAEK 280


>gi|1017750|gb|AAA79182.1| RpoS [Serratia entomophila]
          Length = 332

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 63  YLGEIGYSPLLTAEEEVYFARR-ALRGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 180

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +     +  
Sbjct: 181 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVHDVSRMLRLNERMPSVDTPL--GGDSEK 234

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
              D L  + D   +   +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 235 ALLDILADEKDNGPE---DTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 291

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 292 DVGREIVLTRERVRQIQVEGLRRLREILQMQ 322


>gi|302036735|ref|YP_003797057.1| RNA polymerase, sigma 32 (sigma H) factor [Candidatus Nitrospira
           defluvii]
 gi|300604799|emb|CBK41131.1| RNA polymerase, sigma 32 (sigma H) factor [Candidatus Nitrospira
           defluvii]
          Length = 340

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 97/288 (33%), Positives = 160/288 (55%), Gaps = 7/288 (2%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +S  +     L +Y+ EIR+ P L K+EE  L + Y+  G   AA +L+ ++LR+ V IA
Sbjct: 55  LSTSLVPVTTLQQYLTEIRRYPYLSKEEELRLFEEYQLRGSRDAAMKLILANLRVSVSIA 114

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y   G    +++ EGN+GL+QA+KKFDP +  R   Y+ WW +A +  Y+L ++ L+K
Sbjct: 115 SEYLHTGADHMDLIQEGNVGLLQAIKKFDPTKNVRFYAYAAWWARAYILRYLLNTYRLIK 174

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE- 184
           +GTT +Q++LF+NL++ K  L+              +A +LNV E +VI M+ RL   E 
Sbjct: 175 VGTTQDQRKLFYNLKKEKAKLE----REGFAPDSKLLADRLNVRERDVIEMDQRLGSWEL 230

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL+  I    +N     D L       ++ L + + +   R  L      L+ RE  I  
Sbjct: 231 SLDQPI--GQENDGTLMDILPAHEQPADERLADTQLKALFRRKLAEFTKTLDEREEDILR 288

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
            R L E P+TLE++ +++ +++ER RQ+EAR  K++++ I+K V+   
Sbjct: 289 NRILSETPLTLEDMGAKYGITKERTRQLEARIIKRLRDYIKKDVKDFD 336


>gi|78188365|ref|YP_378703.1| RNA polymerase sigma factor rpoD (sigma-A) [Chlorobium
           chlorochromatii CaD3]
 gi|78170564|gb|ABB27660.1| RNA polymerase sigma factor rpoD (Sigma-A) [Chlorobium
           chlorochromatii CaD3]
          Length = 299

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 78/299 (26%), Positives = 144/299 (48%), Gaps = 24/299 (8%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD-----------LSAAH 51
           + +  I     + L RY+ EI K  +L  ++E  L K  +E  D             A  
Sbjct: 5   KISKQITNRESLSLDRYLQEIGKYDLLTAEDEVRLTKAIKEGFDMPVDTPEYKRAKRALD 64

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +L+  +LR VV +A  Y+  GL + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ 
Sbjct: 65  KLIKGNLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQ 124

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ + +     +V++    N+      + +    L+   + +        +A  L +   
Sbjct: 125 SILQALAEQSRIVRLP--LNRVGTLNKISKAYSQLEQEYERD---PNTRELASLLEMDSQ 179

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           +V           S++A     D N  +  D L  D    +  L     R +    + RS
Sbjct: 180 DVADTLKIAGRHVSVDAPFAQGDDN--RLLDVLQNDGHMPDYGLT----RDSLTLEVERS 233

Query: 232 MSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +SVL PRE  +  +      +NP+TLE +  +F ++RERVRQI+ +A +++++S   +V
Sbjct: 234 LSVLAPREADVIRSYFGIGMDNPLTLEEIGEKFRLTRERVRQIKEKAIRRLRQSAYSKV 292


>gi|183982017|ref|YP_001850308.1| RNA polymerase sigma factor SigB [Mycobacterium marinum M]
 gi|183175343|gb|ACC40453.1| RNA polymerase sigma factor SigB [Mycobacterium marinum M]
          Length = 333

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 71/312 (22%), Positives = 136/312 (43%), Gaps = 38/312 (12%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREH--------GD---- 46
            ++         +  Y++ I K  +L  + E  LAKR     Y EH        GD    
Sbjct: 25  SDLDAQSPAADLVRVYLNGIGKTALLNAEGEVELAKRIEAGLYAEHLLATRKRLGDNRKR 84

Query: 47  ---------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
                      A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +
Sbjct: 85  ELAAVVRDGAEARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTK 144

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           GF+ +TY+ WWI+ A+   +      +++     ++     L R+K  +     N  +  
Sbjct: 145 GFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLARIKREMHQ---NLGREA 199

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A +  +   ++  +        SL+  + S ++  +   D++    D +      
Sbjct: 200 TDEELAAESGIPVEKINDLLEHSRDPVSLDMPVGSEEE--APLGDFI---EDAEAMSAEN 254

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
               +     +   ++ L+ RE ++   R   ++  P TL+ +   F +SRERVRQIE  
Sbjct: 255 AVIAELLHTDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERD 314

Query: 276 AFKKVQESIQKQ 287
              K++   +  
Sbjct: 315 VMCKLRHGERAD 326


>gi|119897381|ref|YP_932594.1| RNA polymerase sigma factor RpoS [Azoarcus sp. BH72]
 gi|119669794|emb|CAL93707.1| putative RNA polymerase sigma factor [Azoarcus sp. BH72]
          Length = 311

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 78/270 (28%), Positives = 143/270 (52%), Gaps = 13/270 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE  LA+R R  GD  A   ++  +LRLVV IA  Y   G+P+ ++
Sbjct: 44  YLNEIGANPLLSAEEEAALARRVR-AGDFDARQTMIERNLRLVVNIAKHYLNRGIPLLDL 102

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GLM A++KFDPERGFR +TY+ WWI+  ++  I+     +++       +    
Sbjct: 103 VEEGNLGLMHALEKFDPERGFRFSTYATWWIRQNIERAIMNQSRTIRLPVHV--VKELNQ 160

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           + R +  ++A ++ +     +  IA++L+    EV ++        SL+A ++     + 
Sbjct: 161 VLRAQRVVEAASNGDF---SLDEIARRLDKPIEEVRAILALSEHTASLDAPLDI--DPTL 215

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLE 256
              + L  +H    +  I   E +    ++   + +LN ++R +   R        +TLE
Sbjct: 216 SIGESLADEHAETPESQIHNAEIE---GLIRAWIDMLNDKQRLVIRHRYGIGECELMTLE 272

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L++  E++RERVRQI+  A  +++  +++
Sbjct: 273 ELAARLELTRERVRQIQLEALGQLRRILKR 302


>gi|57237826|ref|YP_179074.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni RM1221]
 gi|86150708|ref|ZP_01068924.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 260.94]
 gi|86152585|ref|ZP_01070790.1| RNA polymerase sigma factor rpoD [Campylobacter jejuni subsp.
           jejuni HB93-13]
 gi|121612947|ref|YP_001000680.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 81-176]
 gi|157415258|ref|YP_001482514.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 81116]
 gi|167005602|ref|ZP_02271360.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 81-176]
 gi|205356712|ref|ZP_03223473.1| RNA polymerase sigma factor (sigma 70) [Campylobacter jejuni subsp.
           jejuni CG8421]
 gi|315124489|ref|YP_004066493.1| RNA polymerase sigma factor [Campylobacter jejuni subsp. jejuni
           ICDCCJ07001]
 gi|57166630|gb|AAW35409.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni RM1221]
 gi|85841878|gb|EAQ59124.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 260.94]
 gi|85843470|gb|EAQ60680.1| RNA polymerase sigma factor rpoD [Campylobacter jejuni subsp.
           jejuni HB93-13]
 gi|87249244|gb|EAQ72205.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 81-176]
 gi|157386222|gb|ABV52537.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 81116]
 gi|205345450|gb|EDZ32092.1| RNA polymerase sigma factor (sigma 70) [Campylobacter jejuni subsp.
           jejuni CG8421]
 gi|315018211|gb|ADT66304.1| RNA polymerase sigma factor [Campylobacter jejuni subsp. jejuni
           ICDCCJ07001]
 gi|315932129|gb|EFV11072.1| Phosphatidylserine decarboxylase [Campylobacter jejuni subsp.
           jejuni 327]
          Length = 622

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 74/254 (29%), Positives = 126/254 (49%), Gaps = 14/254 (5%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           E     KR ++  D  A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV K
Sbjct: 366 EILEQIKRGKKISD-EAKGRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDK 424

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RG++ +TY+ WWI+ A+   I      ++I        +   + ++   ++     
Sbjct: 425 FEYKRGYKFSTYATWWIRQAISRAIADQARTIRIPIH-----MIETINQINKIIREHLQK 479

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           + K   V  IAK++ +S  +V  +        SL A I   +++  ++ D++    D   
Sbjct: 480 DGKEPDVSVIAKEVGLSVDKVKQVIKITKEPISLEAPI--GNEDDGKFGDFV---EDRNS 534

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERV 269
              ++   + + +  +   +  LN RE+ +   R      E+  TLE +  E  V+RERV
Sbjct: 535 LSPMDHILKDDLKEQIDEVLDQLNDREKAVIRMRFGLMDDESDRTLEEIGKELNVTRERV 594

Query: 270 RQIEARAFKKVQES 283
           RQIE+ A KK++  
Sbjct: 595 RQIESSAIKKLKHP 608


>gi|172040574|ref|YP_001800288.1| RNA polymerase sigma factor SigB [Corynebacterium urealyticum DSM
           7109]
 gi|171851878|emb|CAQ04854.1| RNA polymerase sigma factor B [Corynebacterium urealyticum DSM
           7109]
          Length = 340

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 65/297 (21%), Positives = 134/297 (45%), Gaps = 38/297 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYRE--------------------------HGDLSAAHR 52
           Y++ I K  +L  ++E  L++R                                 +A   
Sbjct: 47  YLNGIGKTALLTAEDEVELSQRIEAGLYAEQLLKSGEPLTRAKKRDVKILAREGKAARTH 106

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD ++GF+ +TY+ WWI+ A
Sbjct: 107 LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYKKGFKFSTYATWWIRQA 166

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +      +++     ++     L R+K  +          E    +A++  + E  
Sbjct: 167 ITRGMADQSRTIRLPVHLVEQ--VNKLSRIKREMYQHLGREATYE---ELAEESGIPEDR 221

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           +  +  +     SL+  + + ++  +   D++        +  +    R    + +   +
Sbjct: 222 IEMLMKQSRDPVSLDMPVGTDEE--APLGDFIEDSEAEDAEAAVVASLR---HSDIRSVL 276

Query: 233 SVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           + L  RE+ +   R   ++  P TL+ +  +F +SRERVRQIE     K++E  +  
Sbjct: 277 ATLEQREQDVITLRYGLDDGLPRTLDQIGRQFGLSRERVRQIEREVMAKLREGQRAD 333


>gi|124023660|ref|YP_001017967.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Prochlorococcus marinus str. MIT 9303]
 gi|123963946|gb|ABM78702.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Prochlorococcus marinus str. MIT 9303]
          Length = 313

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 76/302 (25%), Positives = 144/302 (47%), Gaps = 36/302 (11%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------EHG-------------------D 46
               +S Y+  I +IP+L   EE  L  + +      + G                    
Sbjct: 16  SSDPVSWYLTTIGRIPLLTPAEEIELGNQVQTMMSLTQDGSVAPDDKEFTTHQRRMIRIG 75

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  R++ ++LRLVV +A  Y+G GL + +++ EG++GL +AV+KFDP RG++ +TY+ 
Sbjct: 76  RRAKERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAF 135

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ +M   I      +++    +++     L  ++     +            IA+ +
Sbjct: 136 WWIRQSMTRAIACQSRTIRLPVHLSER-----LTTIRKVSLDLAHKLGAMPSRSEIAEAM 190

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   E+ S+  +     SL+A +N  ++  S   D +     G+    ++K E++    
Sbjct: 191 DIPVDELDSLLRQALTTSSLDAPVN-GEEGRSFLGDLIADSSLGE---PLDKVEQRIHHE 246

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L R +S L+ +E+ + + R   E  +  TL  +    EVSRERVRQ+E +A +K++   
Sbjct: 247 QLGRWLSHLSEQEQHVLKLRFGLETHDRHTLAEIGRLMEVSRERVRQVELKALRKLRNLT 306

Query: 285 QK 286
           ++
Sbjct: 307 RR 308


>gi|284928680|ref|YP_003421202.1| hypothetical protein UCYN_00890 [cyanobacterium UCYN-A]
 gi|284809139|gb|ADB94844.1| hypothetical protein UCYN_00890 [cyanobacterium UCYN-A]
          Length = 420

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 65/239 (27%), Positives = 121/239 (50%), Gaps = 13/239 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ 
Sbjct: 182 RKAKDKMVHSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYAT 241

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      +++        L+  + R+K   + ++    +      IA ++
Sbjct: 242 WWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKLLSQEMRRKPTEEEIATRM 296

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++  ++  +        SL   I    +  S+  D++  D +  E  + +   R++   
Sbjct: 297 EMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADGETPEDEVAKNLLRED--- 351

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQES 283
            L   +  L+PRER +   R   ++    TLE +   F V+RER+RQIEA+A +K++  
Sbjct: 352 -LENVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHP 409



 Score = 39.0 bits (90), Expect = 0.80,   Method: Composition-based stats.
 Identities = 10/32 (31%), Positives = 18/32 (56%)

Query: 12 GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE 43
           E  +  Y+ EI +I +L  +EE  LA++  +
Sbjct: 62 TEDSIRVYLQEIGRIRLLRAEEEIELARKIAD 93


>gi|291298947|ref|YP_003510225.1| RpoD subfamily RNA polymerase sigma-70 subunit [Stackebrandtia
           nassauensis DSM 44728]
 gi|290568167|gb|ADD41132.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Stackebrandtia
           nassauensis DSM 44728]
          Length = 330

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 83/315 (26%), Positives = 139/315 (44%), Gaps = 43/315 (13%)

Query: 1   MNRKNMSIIVNGEIGLSR-----YIHEIRKIPMLEKQEEYVLAKRY-------REHGD-- 46
           M+ +  + I   E+   R     Y+HEI K P+L+   E  LAK         R  GD  
Sbjct: 1   MSVETTTAIRTDEVAEERDLVGVYLHEISKTPLLDAAAEVDLAKAVEAGLYAQRLIGDDQ 60

Query: 47  -----------------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
                              A  + + ++LRLVV IA  Y   G+P+ +++ EGN GL++A
Sbjct: 61  QPEGVTEAELGRLVLDGQKAKEQFIKANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRA 120

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V+KFD +RGF+ +TY+ WWI+ A+   I +    V++        L  ++ R++   + +
Sbjct: 121 VEKFDYQRGFKFSTYATWWIRQAISRAIAQQERTVRLPVH-----LVEDVNRMRNTARQL 175

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
           T       +   IA  L V+   V  +        SL+  I   D   +   D +    D
Sbjct: 176 TRELGADPEPEQIANALGVTVERVNELIRWSQDTVSLDTPI--GDDGDTNLGDLVA---D 230

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRE 267
             E    +       R  +   +  L+ R   I +AR   E+    +L  ++  F +SRE
Sbjct: 231 SDEPTPEDVVIAGMERERIDMMLGHLDERSAGIVKARYGLEDGREHSLTEVAHRFALSRE 290

Query: 268 RVRQIEARAFKKVQE 282
           R+RQ+E +A  +++E
Sbjct: 291 RIRQLEIQALARLKE 305


>gi|258648419|ref|ZP_05735888.1| RNA polymerase sigma factor [Prevotella tannerae ATCC 51259]
 gi|260851166|gb|EEX71035.1| RNA polymerase sigma factor [Prevotella tannerae ATCC 51259]
          Length = 286

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 76/282 (26%), Positives = 141/282 (50%), Gaps = 12/282 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           + N SI       L +Y+ EI +  ++   EE  LA+R  + GD  A  +L  ++LR VV
Sbjct: 5   KINKSITNRSSAALDKYLVEIGREGLISTDEEVELAQRIHK-GDAEALEKLTKANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL +++++ EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + I     
Sbjct: 64  SVAKQYQNQGLALNDLIDEGNLGLIRAAQKFDETRGFKFISYAVWWIRQSILQAISEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    NQ      L +   + +   +   +   V  +A  L+   ++V         
Sbjct: 124 IVRMP--LNQVGFQSKLTKAIVNFEQEFE---RRPSVQELADILDTDVAKVQEAMGTNGK 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     D NS    D +  ++       +EKE   +    L  ++  L  RER +
Sbjct: 179 KVSVDAPFQDDDSNS--LIDIMTDENAPGTDDQMEKESLSSD---LDAALGTLTERERLV 233

Query: 243 FEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +       N +T E +++   ++RERVRQI+ RA ++++E+
Sbjct: 234 LKMLFGIGRNEMTAEEVANSLSLTRERVRQIKERALRRLREA 275


>gi|311739612|ref|ZP_07713447.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           pseudogenitalium ATCC 33035]
 gi|311305428|gb|EFQ81496.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           pseudogenitalium ATCC 33035]
          Length = 337

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 67/309 (21%), Positives = 138/309 (44%), Gaps = 38/309 (12%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY------------------RE 43
           +R+N +        +  Y++ I K  +L  ++E  LA+                     E
Sbjct: 27  SRRNQTNDNPSADLVRVYLNGIGKTALLSAEDEVELAQAIEVGLYAEYKLNNAEKLTRAE 86

Query: 44  HGD--------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
             D          A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD 
Sbjct: 87  KRDLKILAREGKKARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDY 146

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            +GF+ +TY+ WWI+ A+   +      +++     ++     L R+K  +         
Sbjct: 147 AKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLSRIKREMYQSLGREAT 204

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
            E    ++++  + E+++  +  +     SL+  + + ++  +   D++        +  
Sbjct: 205 NE---ELSEESGIDENKIEMLLRQSRDPVSLDMPVGTDEE--APLGDFIEDAEATDAETA 259

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIE 273
           +    R    + +   +  L  RE+ +   R   ++  P TL+ +   F +SRERVRQIE
Sbjct: 260 VVASMR---HSDIRGVIDTLEKREQDVIRLRYGLDDGVPRTLDQIGRRFGLSRERVRQIE 316

Query: 274 ARAFKKVQE 282
                K+++
Sbjct: 317 REVMAKLRD 325


>gi|307747900|gb|ADN91170.1| RNA polymerase sigma factor rpoD [Campylobacter jejuni subsp.
           jejuni M1]
          Length = 622

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 73/249 (29%), Positives = 125/249 (50%), Gaps = 14/249 (5%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
            KR ++  D  A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ +R
Sbjct: 371 IKRGKKISD-EAKGRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKR 429

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I        +   + ++   ++     + K  
Sbjct: 430 GYKFSTYATWWIRQAISRAIADQARTIRIPIH-----MIETINQINKIIREHLQKDGKEP 484

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
            V  IAK++ +S  +V  +        SL A I   +++  ++ D++    D      ++
Sbjct: 485 DVSVIAKEVGLSVDKVKQVIKITKEPISLEAPI--GNEDDGKFGDFV---EDRNSLSPMD 539

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEA 274
              + + +  +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+
Sbjct: 540 HILKDDLKEQIDEVLDQLNDREKAVIRMRFGLMDDESDRTLEEIGKELNVTRERVRQIES 599

Query: 275 RAFKKVQES 283
            A KK++  
Sbjct: 600 SAIKKLKHP 608


>gi|113954655|ref|YP_729975.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CC9311]
 gi|113882006|gb|ABI46964.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CC9311]
          Length = 313

 Score =  210 bits (536), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 75/312 (24%), Positives = 145/312 (46%), Gaps = 36/312 (11%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL-------------- 47
            R + +        +S Y+  I +IP+L   EE  L  + ++  +L              
Sbjct: 6   ARTSETQRRRSSDPISWYLATIGRIPLLTAAEEIELGNQVQKFMELTQDGSVSPDSEEFS 65

Query: 48  -----------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                       A  R++ ++LRLVV +A  Y+G GL + +++ EG++GL +AV+KFDP 
Sbjct: 66  SKDRRMIRVGQRAKQRMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPT 125

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RG++ +TY+ WWI+ +M   I      +++    +++     L  ++     +       
Sbjct: 126 RGYKFSTYAFWWIRQSMTRAIACQSRTIRLPVHLSER-----LTTIRKVSLDLAHKLGAM 180

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
              + I++ L++   E+ S+  +     SL+A +N  D  S    D +    D   +  +
Sbjct: 181 PSRLEISEALDMPVEELDSLLRQALTTSSLDAPVNGEDGRS-FLGDLIA---DSSAEEPL 236

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEA 274
           +K E++     L R +S L+ +E+ +   R         TL  +    +VSRERVRQ+E 
Sbjct: 237 DKVEQRIHHEQLGRWLSHLSEQEQHVLTLRFGLNGNERHTLAQIGRLLDVSRERVRQVEL 296

Query: 275 RAFKKVQESIQK 286
           ++ +K++   ++
Sbjct: 297 KSLRKLRNLTRR 308


>gi|33866155|ref|NP_897714.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. WH 8102]
 gi|33639130|emb|CAE08136.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 8102]
          Length = 313

 Score =  210 bits (535), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 76/302 (25%), Positives = 142/302 (47%), Gaps = 36/302 (11%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------EHG-------------------D 46
               +S Y+  I +IP+L   EE  L  + +      E G                    
Sbjct: 16  SSDPVSWYLATIGRIPLLTPAEEIELGNQVQAMMTLTEDGSKTFEDHELTGKQRRMLRIG 75

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  R++ ++LRLVV +A  Y+G GL + +++ EG++GL +AV+KFDP RG++ +TY+ 
Sbjct: 76  RRAKERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAF 135

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ +M   I      +++    +++     L  ++     +          V IA+ +
Sbjct: 136 WWIRQSMTRAIACQSRTIRLPVHLSER-----LTTIRKVSLDLAHKLGAMPSRVEIAEAM 190

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   E+ S+  +     SL+A +N  ++  S   D +    D      ++  E++    
Sbjct: 191 DIPLDELDSLLRQALTTSSLDAPVN-GEEGRSFLGDLIA---DSSLDEPLDIVEQRIHHE 246

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L R +S L+ +E+ + + R   E     TL  +    +VSRERVRQ+E +A +K++   
Sbjct: 247 QLGRWLSHLSEQEQHVLKLRFGLEGNERHTLAEIGRLMDVSRERVRQVELKALRKLRNLT 306

Query: 285 QK 286
           ++
Sbjct: 307 RR 308


>gi|254430889|ref|ZP_05044592.1| possible type II alternative RNA polymerase sigma factor [Cyanobium
           sp. PCC 7001]
 gi|197625342|gb|EDY37901.1| possible type II alternative RNA polymerase sigma factor [Cyanobium
           sp. PCC 7001]
          Length = 327

 Score =  210 bits (535), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 73/305 (23%), Positives = 138/305 (45%), Gaps = 44/305 (14%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------------- 43
               +  Y+ EI ++ +L ++EE +LA+  +E                            
Sbjct: 18  SSDPIRLYLREIGRVDLLRQEEEILLARLVQEREELLRQRGDGELTAWAGRCGVPPADLR 77

Query: 44  ---HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
              H    A  R++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV+++DP RGFR
Sbjct: 78  QALHRGRRAKERMLQANLRLVVAVAKKYQRRGLDLLDLIQEGTLGLERAVERYDPRRGFR 137

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+  +   +      +++     +      L R++     +T  + +   + 
Sbjct: 138 FSTYAYWWIRQGITRALASQSRTIRLPVHVTE-----TLNRIRTCQGELTREHGRQPTLA 192

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+ + + E+ + S    +    SL   +       +   D L  DH   EQ L  ++ 
Sbjct: 193 ELARAVGLDEARLRSTLAHIPRPVSLEGRV--GANADTPLVDLLEDDHATPEQTLTRQQL 250

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFK 278
             +    L   +  L+ RE  +   R   ++  P TL  +  + ++SRERVRQIE+RA  
Sbjct: 251 HAD----LEALLDELSAREATVIRQRFGLDDDTPRTLAEIGEQLQLSRERVRQIESRALL 306

Query: 279 KVQES 283
           K+++ 
Sbjct: 307 KLRQP 311


>gi|240169688|ref|ZP_04748347.1| RNA polymerase sigma factor SigB [Mycobacterium kansasii ATCC
           12478]
          Length = 319

 Score =  210 bits (535), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 66/312 (21%), Positives = 133/312 (42%), Gaps = 38/312 (12%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------- 43
            ++         +  Y++ I K  +L   +E  LAKR                       
Sbjct: 11  SDLDAQSPAADLVRVYLNGIGKTALLNAADEVELAKRIEAGLYAEYLLETRKRLGENRKR 70

Query: 44  ------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
                     +A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +
Sbjct: 71  ELAAVVRDGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTK 130

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           GF+ +TY+ WWI+ A+   +      +++     ++     L R+K  +     N  +  
Sbjct: 131 GFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLARIKREMHQ---NLGREA 185

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A++  +   ++  +        SL+  + S ++  +   D++    D +      
Sbjct: 186 TDEELAEESGIPVDKINDLLEHSRDPVSLDMPVGSEEE--APLGDFI---EDAEAMSAEN 240

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
               +     +   ++ L+ RE ++   R   ++  P TL+ +   F +SRERVRQIE  
Sbjct: 241 AVIAELLHTDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERD 300

Query: 276 AFKKVQESIQKQ 287
              K++   +  
Sbjct: 301 VMCKLRHGERAD 312


>gi|310778262|ref|YP_003966595.1| RNA polymerase sigma factor, sigma-70 family [Ilyobacter polytropus
           DSM 2926]
 gi|309747585|gb|ADO82247.1| RNA polymerase sigma factor, sigma-70 family [Ilyobacter polytropus
           DSM 2926]
          Length = 263

 Score =  210 bits (535), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 79/274 (28%), Positives = 142/274 (51%), Gaps = 16/274 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + +S Y+ EI   P+L K+EE   A +  ++GD SA  +LVTS+LRLVV IA  Y   G+
Sbjct: 1   MNISNYLKEISHYPLLTKEEEIEFALK-AQNGDESAHEKLVTSNLRLVVSIAKKYINIGI 59

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGNIGL++AV KFD     R +TY+ +WIK ++  YI  +  +++  T     
Sbjct: 60  PVLDLIQEGNIGLIKAVSKFDTTMDKRFSTYATFWIKQSILRYISSNKGVIRYPTY---- 115

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            ++ N+ ++   ++   +       +  IA  L   + +V         ++SLN+L   S
Sbjct: 116 -IYDNISKINKFIRDYKNKYGSVPSIEVIATGLEFKKKDVEKYLNIF--EQSLNSL-EES 171

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
              +      +  D   +EQ++ +    +   N     + +LN +ER +   R    N  
Sbjct: 172 YGENGDLHSIIPSDDLFEEQIITDSVNEELISN-----LKILNSKERDVIIHRFGLFNKN 226

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            +TLE + +   ++RER+RQI+ +A  K+++  +
Sbjct: 227 VLTLEEIGNHLNLTRERIRQIQLKAIDKLRDKFR 260


>gi|116073370|ref|ZP_01470632.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9916]
 gi|116068675|gb|EAU74427.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9916]
          Length = 313

 Score =  210 bits (535), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 74/302 (24%), Positives = 138/302 (45%), Gaps = 36/302 (11%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------------HGD 46
               +S Y+  I +IP+L   EE  L  + ++                            
Sbjct: 16  SSDPISWYLATIGRIPLLTPAEEIELGNQVQQLMALTQDGTIPIDSDQFSSKDRRIIRVG 75

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  R++ ++LRLVV +A  Y+G GL + ++V EG++GL +AV+KFDP RG++ +TY+ 
Sbjct: 76  RRAKERMMKANLRLVVSVAKKYQGKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAF 135

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ +M   I      +++    +++     L  ++     +          + IA+ +
Sbjct: 136 WWIRQSMTRAIACQSRTIRLPVHLSER-----LTTIRKVSLDLAHKLGAMPSRLEIAEAM 190

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   E+ S+  +     SL+A +N  ++  S   D +    D      + K E+     
Sbjct: 191 DMPLEELDSLLRQALTTSSLDAPVN-GEEGRSFLGDLIA---DNSSDEPLAKVEQSIHHE 246

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L R +S L+ +E+ +   R         TL  +    EVSRER+RQ+E +A +K++   
Sbjct: 247 QLGRWLSHLSDQEQHVLNLRFGLNGNERHTLAEIGRLLEVSRERIRQVELKALRKLRNLT 306

Query: 285 QK 286
           ++
Sbjct: 307 RR 308


>gi|1657704|gb|AAC44535.1| sigma factor MytB [Mycobacterium tuberculosis]
          Length = 345

 Score =  210 bits (535), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 69/312 (22%), Positives = 133/312 (42%), Gaps = 38/312 (12%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREH-------------- 44
            ++         +  Y++ I K  +L    E  LAKR     Y EH              
Sbjct: 37  SDLDAQSPAADLVRVYLNGIGKTALLNPAGEVELAKRIEAGLYAEHLLETRKRLGENRKR 96

Query: 45  -------GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
                     +A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +
Sbjct: 97  DLAAVVRDGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTK 156

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           GF+ +TY+ WWI+ A+   +      +++     ++     L R+K  +          E
Sbjct: 157 GFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLARIKREMHQHLGREATDE 214

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A +  +   ++  +        SL+  + S ++  +   D++    D +      
Sbjct: 215 ---ELAAESGIPIDKINDLLEHSRDPVSLDMPVGSEEE--APLGDFI---EDAEAMSAEN 266

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
               +     +   ++ L+ RE ++   R   ++  P TL+ +   F +SRERVRQIE  
Sbjct: 267 AVIAELLHTDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERD 326

Query: 276 AFKKVQESIQKQ 287
              K++   +  
Sbjct: 327 VMSKLRHGERAD 338


>gi|119511025|ref|ZP_01630145.1| RNA polymerase sigma factor [Nodularia spumigena CCY9414]
 gi|119464276|gb|EAW45193.1| RNA polymerase sigma factor [Nodularia spumigena CCY9414]
          Length = 332

 Score =  210 bits (535), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 73/331 (22%), Positives = 140/331 (42%), Gaps = 52/331 (15%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR------YREHGD----------- 46
             M         +  Y+ EI ++P+L  +EE    K+        E  D           
Sbjct: 13  SAMKTAQTATDLVRTYLREIGRVPLLTHEEEIQYGKQVQFSRILHEVRDSLINQIGREPS 72

Query: 47  ----------------------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
                                  +A  ++V ++LRLVV +A  Y    + + +++ EG+I
Sbjct: 73  LEEWALAANLEVAELNDAIADGETAKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGSI 132

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           G+ + V+KFDP +G+R +TY+ WWI+ A+   I      +++     +K     L ++K 
Sbjct: 133 GMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKARTIRLPIHITEK-----LNKIKK 187

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + ++    +      +A++L+++  +V     R     SL+  +   D   ++  + L
Sbjct: 188 AQRQLSQQLGRAPSAAELAQELDLTPKQVREYLERARLPLSLD--LRLGDNYDTELGEML 245

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEF 262
                  E+ +++     +    L R M  L P+++ + + R   L    +TL  +    
Sbjct: 246 EDPGASPEEFVMQSSLSYD----LERLMEELTPQQKEVIKLRFGLLDGQALTLAKIGDIL 301

Query: 263 EVSRERVRQIEARAFKKVQESIQKQVELSSS 293
            +SRERVRQIE  A  K+++S     E  +S
Sbjct: 302 NISRERVRQIEREALTKLRKSKASMNEYLAS 332


>gi|302338588|ref|YP_003803794.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           smaragdinae DSM 11293]
 gi|301635773|gb|ADK81200.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           smaragdinae DSM 11293]
          Length = 612

 Score =  210 bits (535), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 64/242 (26%), Positives = 117/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +A  RL+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+KF+  +GF+ +TY+ 
Sbjct: 372 KNAKDRLIQANLRLVVSIAKKYTNRGLHFFDLVQEGNIGLIKAVEKFEYSKGFKFSTYAT 431

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      +++        +   + ++    + +     +      +A++L
Sbjct: 432 WWIRQAITRSISDQARTIRVPVH-----MIEQINKVVRESRQLMQILGRDPTDEEVAERL 486

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             +   V S+        SL   I   ++  S   D++    D   +    +      + 
Sbjct: 487 GWTVLRVKSVKNVAREPISLETPI--GEEEDSLLGDFI---EDKDIENPANQTAFTLLQE 541

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   M  L PRE+ + + R   ++   +TLE +   F V+RER+RQIEA+A ++++   
Sbjct: 542 QLQEVMKTLPPREQEVLKMRFGLDDGYSLTLEEVGLYFNVTRERIRQIEAKALRRLRHPK 601

Query: 285 QK 286
           + 
Sbjct: 602 RS 603



 Score = 35.9 bits (82), Expect = 6.3,   Method: Composition-based stats.
 Identities = 11/34 (32%), Positives = 20/34 (58%), Gaps = 1/34 (2%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD 46
           +  +  Y+ EI K  +L  ++E  L+K+  EHG+
Sbjct: 125 DDPIRLYLREIGKESLLTAEQEVELSKQM-EHGE 157


>gi|148823899|ref|YP_001288653.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis F11]
 gi|253798208|ref|YP_003031209.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis KZN
           1435]
 gi|308232219|ref|ZP_07415326.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu001]
 gi|308369834|ref|ZP_07419229.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu002]
 gi|308371106|ref|ZP_07423839.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu003]
 gi|308372374|ref|ZP_07428435.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu004]
 gi|308373485|ref|ZP_07432499.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu005]
 gi|308374669|ref|ZP_07436917.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu006]
 gi|308375503|ref|ZP_07444157.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu007]
 gi|308377104|ref|ZP_07441142.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu008]
 gi|308378072|ref|ZP_07481430.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu009]
 gi|308379289|ref|ZP_07485765.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu010]
 gi|308380449|ref|ZP_07489983.2| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu011]
 gi|148722426|gb|ABR07051.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis F11]
 gi|253319711|gb|ACT24314.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis KZN
           1435]
 gi|308214646|gb|EFO74045.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu001]
 gi|308326293|gb|EFP15144.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu002]
 gi|308329821|gb|EFP18672.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu003]
 gi|308333464|gb|EFP22315.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu004]
 gi|308337459|gb|EFP26310.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu005]
 gi|308341132|gb|EFP29983.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu006]
 gi|308346083|gb|EFP34934.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu007]
 gi|308348958|gb|EFP37809.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu008]
 gi|308353656|gb|EFP42507.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu009]
 gi|308357503|gb|EFP46354.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu010]
 gi|308361457|gb|EFP50308.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu011]
          Length = 345

 Score =  210 bits (535), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 69/312 (22%), Positives = 133/312 (42%), Gaps = 38/312 (12%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREH-------------- 44
            ++         +  Y++ I K  +L    E  LAKR     Y EH              
Sbjct: 37  SDLDAQSPAADLVRVYLNGIGKTALLNAAGEVELAKRIEAGLYAEHLLETRKRLGENRKR 96

Query: 45  -------GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
                     +A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +
Sbjct: 97  DLAAVVRDGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTK 156

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           GF+ +TY+ WWI+ A+   +      +++     ++     L R+K  +          E
Sbjct: 157 GFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLARIKREMHQHLGREATDE 214

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A +  +   ++  +        SL+  + S ++  +   D++    D +      
Sbjct: 215 ---ELAAESGIPIDKINDLLEHSRDPVSLDMPVGSEEE--APLGDFI---EDAEAMSAEN 266

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
               +     +   ++ L+ RE ++   R   ++  P TL+ +   F +SRERVRQIE  
Sbjct: 267 AVIAELLHTDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERD 326

Query: 276 AFKKVQESIQKQ 287
              K++   +  
Sbjct: 327 VMSKLRHGERAD 338


>gi|6010724|gb|AAF01228.1|AF184097_1 mutant RpoS [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
          Length = 326

 Score =  210 bits (535), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 79/271 (29%), Positives = 137/271 (50%), Gaps = 17/271 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     + I      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIHI-----VKELNVY 174

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 175 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 229

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 230 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 285

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 286 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 316


>gi|289208462|ref|YP_003460528.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thioalkalivibrio
           sp. K90mix]
 gi|288944093|gb|ADC71792.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thioalkalivibrio
           sp. K90mix]
          Length = 359

 Score =  210 bits (535), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 76/275 (27%), Positives = 134/275 (48%), Gaps = 13/275 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ +I   P+L  +EE   A R    GD S   R++  +LRLVVKIA  Y   GL
Sbjct: 84  DAIQIYLRDIEYRPLLTPEEERKYA-RLARDGDESGRRRMIECNLRLVVKIARRYLNRGL 142

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGN+GLM AV+KFDPERGFR +TY+ WWI+  ++  ++     ++I    ++ 
Sbjct: 143 PLLDLIEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERALMNQGRTIRIPVHVSK- 201

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                LR      + +T    +      +A++L    +++  +        S++      
Sbjct: 202 ----ELRMHARIARNLTQELGRDPTEEELAQRLGKPVADIQKLRAMSEPSTSMDLPPGPD 257

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--N 251
            + S    D L    D   Q      E ++ ++++   +  L+ ++R +   R       
Sbjct: 258 GERS--LTDILA---DVNAQEPSSLLEDQDIQHLVDEWLGELDYKQREVLVRRFGLHGFE 312

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             TLE + +E  V+RERVRQI+  A K+++  ++ 
Sbjct: 313 RSTLEQVGAEIGVTRERVRQIQMDALKRLRRLLES 347


>gi|281420133|ref|ZP_06251132.1| RNA polymerase sigma-70 factor [Prevotella copri DSM 18205]
 gi|281405933|gb|EFB36613.1| RNA polymerase sigma-70 factor [Prevotella copri DSM 18205]
          Length = 290

 Score =  210 bits (535), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 76/281 (27%), Positives = 136/281 (48%), Gaps = 14/281 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKI 64
           SI       L +Y+ EI + PM+   EE  LA+  R+ G     A ++L+ ++LR VV +
Sbjct: 9   SITNRNSEALDKYLVEIGRAPMVSIDEEIELAQAIRKGGRAGERAKNKLIEANLRFVVSV 68

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y+  GL +++++ EGNIGL++A ++FD  RGF+  +Y++WWI+ ++ + I     +V
Sbjct: 69  AKQYQHQGLTLTDLIDEGNIGLIKAAERFDETRGFKFISYAVWWIRQSILQAIAEQSRIV 128

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           ++           +L ++   +      N +   V  +A +  V E ++           
Sbjct: 129 RLPLNQ-----VGSLNKVNQEINKFEQENQRRPSVEELAARTGVDEDKISQSMAASGHHV 183

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV-LNPRERRIF 243
           S++A  +  D NS         D    +QV     + ++    L + + V L  RE +I 
Sbjct: 184 SIDAPFSDDDDNSMADVMASGDDARTDKQV-----DHESMAQDLRQVLKVCLKDRELKII 238

Query: 244 EARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            A     E    LE +  +  ++RERVRQI  ++  K++ES
Sbjct: 239 CACYGIGETEKGLEEIGDKMGLTRERVRQIREKSITKLRES 279


>gi|284929771|ref|YP_003422293.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase sigma
           factor, cyanobacterial RpoD-like family [cyanobacterium
           UCYN-A]
 gi|284810215|gb|ADB95912.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase sigma
           factor, cyanobacterial RpoD-like family [cyanobacterium
           UCYN-A]
          Length = 318

 Score =  210 bits (535), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 73/318 (22%), Positives = 135/318 (42%), Gaps = 52/318 (16%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS----------------- 48
           M +  +    +  Y+ EI ++P+L  +EE + AKR +   DL                  
Sbjct: 1   MKLTKSNLDPVRSYLREIGRVPLLTHEEEILYAKRVQRFVDLEKYRELFTKETGKEPTET 60

Query: 49  ----------------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
                                 A  ++V ++LRLVV +A  Y    L + +++ EG IG+
Sbjct: 61  QWAQAARISRRELHSAIASGEAAKRKMVEANLRLVVSVAKKYLKRNLDLLDLIQEGTIGM 120

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
            + V+KFDP +G+R +TY+ WWI+ A+   I      +++     +K     L ++K   
Sbjct: 121 QRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEK-----LNKIKKAQ 175

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           + ++    +   +  +A++L+++  +V     R     SL+  +   D   ++  D L  
Sbjct: 176 RELSQARGRDATIAELAEELDLTPKQVREYLERARQPLSLD--LRVGDNQDTELGDLLED 233

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           D    E        + +    L   M  L  +++ +   R       P+TL  +     +
Sbjct: 234 DGPSPEDFATHSSLQFD----LEILMEDLTTQQKEVIALRFGLTDGQPLTLAKIGCRLNI 289

Query: 265 SRERVRQIEARAFKKVQE 282
           SRERVRQIE  A  K+++
Sbjct: 290 SRERVRQIEREALSKLRK 307


>gi|269929031|ref|YP_003321352.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphaerobacter
           thermophilus DSM 20745]
 gi|269788388|gb|ACZ40530.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphaerobacter
           thermophilus DSM 20745]
          Length = 359

 Score =  210 bits (535), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 78/295 (26%), Positives = 137/295 (46%), Gaps = 33/295 (11%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR---------EHGD------------LSAA 50
               + RY  ++    +L  +EE   ++  R         E G+             +A 
Sbjct: 66  TSDAVYRYFRDVGGHQLLTHREEIEYSRAVRAGLEARKRLEAGEDSEELHQIIERAKAAR 125

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            +L+  +LRLVV IA  YR  GLP+ +++ EGNIGLM AV+++DPE G+R +TY+ +WI+
Sbjct: 126 EKLIRHNLRLVVSIAKKYRTSGLPLIDLIQEGNIGLMTAVERYDPELGYRFSTYATFWIR 185

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            A+   +      +++    +   L   +RR +  L+ +   + +P     +A+ L++  
Sbjct: 186 QAIGRAVANQSRTIRVPVHMH--DLISKVRRTEAQLEQL---HGRPATDQELAQALDLDV 240

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
             +      +    SL+  I   +   S   D L    D     ++++      R+ + R
Sbjct: 241 ERIEQARSAIPRTSSLDKPI--GEDGESTIGDLLP---DPASDEVVDQAVTSAIRDQIRR 295

Query: 231 SMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           S+  L+ RER +   R       P TL  ++  + +SRERVRQIE  A  K++ S
Sbjct: 296 SLESLSERERGVLTLRFGLGGQQPQTLAEIAEYYGISRERVRQIEKEALAKLRNS 350


>gi|332526107|ref|ZP_08402245.1| RNA polymerase sigma S (sigma-38) factor transcription regulator
           protein [Rubrivivax benzoatilyticus JA2]
 gi|332109950|gb|EGJ10578.1| RNA polymerase sigma S (sigma-38) factor transcription regulator
           protein [Rubrivivax benzoatilyticus JA2]
          Length = 320

 Score =  210 bits (535), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 79/273 (28%), Positives = 133/273 (48%), Gaps = 9/273 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ +IR+ P++  +EE+  A R R  GD +A   ++  +LRLVV IA  Y G G+P+
Sbjct: 46  LQSYLRDIRRAPLMSAEEEHATAVRAR-AGDFAARQTMIERNLRLVVSIAKHYVGRGMPM 104

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM A  KF+PERGFR +TY+ WWI+ +++  I+    L+++      + L
Sbjct: 105 IDLIEEGNLGLMHATGKFEPERGFRFSTYASWWIRQSIERAIMHQARLIRLPVHVV-REL 163

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              L+  +    +      +P  V  +A  L     EV  +        SL+  +     
Sbjct: 164 NQVLKARRALESSRHGEAERPVSVDEVAAALGRPVDEVAELLKLAEQPTSLDMPLEREGG 223

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PV 253
            S      L    D      +     +   ++L   ++ LN RER +   R    +  P 
Sbjct: 224 ES-----MLDTVADDDAVDPLGLTLSREAVHLLDHGLAELNEREREVLAGRFGLHDREPE 278

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TLE L+    ++RER+RQI+  A  K++  + +
Sbjct: 279 TLEELAVRLGLTRERIRQIQQEALLKLKRRMMR 311


>gi|149200267|ref|ZP_01877288.1| RNA polymerase sigma-A factor [Lentisphaera araneosa HTCC2155]
 gi|149136631|gb|EDM25063.1| RNA polymerase sigma-A factor [Lentisphaera araneosa HTCC2155]
          Length = 274

 Score =  210 bits (535), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 84/280 (30%), Positives = 142/280 (50%), Gaps = 13/280 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
              +  Y+H I    ++ K+EE  LA   +  G   A  +L+ S+LRLVVKIA  ++G G
Sbjct: 5   SDAIRNYMHNISDYSLVTKEEEVDLAADIKL-GSDKAREKLIVSNLRLVVKIAHDFKGLG 63

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP+S+++SEGNIGLM+AV+KFDP +G + ++Y+ WWIK +M+  +      ++I   +  
Sbjct: 64  LPLSDLISEGNIGLMRAVEKFDPAKGAKFSSYAAWWIKQSMRRGLANQSRTIRIPVQSA- 122

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 + +++     + +  ++      IA  L  S+  V  ++       SL A +  
Sbjct: 123 ----GKINKIRNARIELKEKLMREPTDQEIATYLEFSKRTVSGLSTVGGSTISLQAKLQ- 177

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--E 250
            D    + QD +          +I + E  N    + + +  L  RE+ + E R      
Sbjct: 178 -DGEDGEIQDIVADKASQTASDIIGEAESINS---MMKFIVYLTDREKLVLELRFGLLSG 233

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
            P TLE +S     +RERVRQI+ +A KK++E +Q++  L
Sbjct: 234 RPKTLEEVSQAIGRTRERVRQIQNQALKKLRERMQRESLL 273


>gi|16332132|ref|NP_442860.1| RNA polymerase sigma factor RpoD [Synechocystis sp. PCC 6803]
 gi|47717353|sp|P74565|RPOD_SYNY3 RecName: Full=RNA polymerase sigma factor rpoD
 gi|1653761|dbj|BAA18672.1| RNA polymerase sigma factor [Synechocystis sp. PCC 6803]
          Length = 425

 Score =  210 bits (534), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 66/237 (27%), Positives = 121/237 (51%), Gaps = 13/237 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WW
Sbjct: 189 AKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWW 248

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      +++        L+  + R+K   + ++    +      IA+K+ +
Sbjct: 249 IRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKLLSQEMRRKPTEEEIAEKMEM 303

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +  ++  +        SL   I    +  S+  D++  D +  E    ++  +   R  L
Sbjct: 304 TIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADGETPE----DEVSKNLLREDL 357

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQES 283
              +  L+PRER +   R   ++    TLE +   F V+RER+RQIEA+A +K++  
Sbjct: 358 ENVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHP 414



 Score = 39.4 bits (91), Expect = 0.64,   Method: Composition-based stats.
 Identities = 14/49 (28%), Positives = 25/49 (51%), Gaps = 4/49 (8%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
            E  +  Y+ EI +I +L  +EE  LA++  +  +L     L+  +L L
Sbjct: 69  TEDSIRIYLQEIGRIRLLRAEEEIELARQIADLLELE----LIRDNLTL 113


>gi|67921267|ref|ZP_00514786.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
 gi|67857384|gb|EAM52624.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
          Length = 414

 Score =  210 bits (534), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 65/239 (27%), Positives = 120/239 (50%), Gaps = 13/239 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ 
Sbjct: 176 RRAKDKMVHSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYAT 235

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      +++        L+  + R+K   + ++    +      IA ++
Sbjct: 236 WWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKLLSQEMRRKPTEEEIATRM 290

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++  ++  +        SL   I    +  S+  D++  D +  E    ++  +   R 
Sbjct: 291 EMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADGETPE----DEVSKNLLRE 344

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQES 283
            L   +  L+PRER +   R   ++    TLE +   F V+RER+RQIEA+A +K++  
Sbjct: 345 DLENVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHP 403



 Score = 39.0 bits (90), Expect = 0.81,   Method: Composition-based stats.
 Identities = 10/32 (31%), Positives = 18/32 (56%)

Query: 12 GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE 43
           E  +  Y+ EI +I +L  +EE  LA++  +
Sbjct: 58 TEDSIRVYLQEIGRIRLLRAEEEIELARKIAD 89


>gi|187918567|ref|YP_001884130.1| RNA polymerase sigma factor RpoD [Borrelia hermsii DAH]
 gi|119861415|gb|AAX17210.1| RNA polymerase sigma factor RpoD [Borrelia hermsii DAH]
          Length = 630

 Score =  210 bits (534), Expect = 2e-52,   Method: Composition-based stats.
 Identities = 67/257 (26%), Positives = 124/257 (48%), Gaps = 16/257 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE +  K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 378 EEILKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 433

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RGF+ +TY+ WWI+ A+   I      +++        +   + RL    + +   
Sbjct: 434 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVH-----MIEQINRLNRETRYLIQV 488

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             K      ++ +L     +V ++        SL   I   ++  S   D++    D   
Sbjct: 489 LGKDPTDEELSARLGWDLKKVKTVKNVSREPVSLETPI--GEEEDSVLSDFI---EDKAI 543

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +   +       ++ +   +  L  RE+ + + R   E+   +TLE +   F V+RER+R
Sbjct: 544 KNPAKHTSFVVLQDQIRSVLGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIR 603

Query: 271 QIEARAFKKVQESIQKQ 287
           QIE++A ++++   + Q
Sbjct: 604 QIESKALRRLKNPKKTQ 620



 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 43/251 (17%), Positives = 91/251 (36%), Gaps = 33/251 (13%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRL------VTSHLRLVVKI 64
           N E  +  Y+ EI K  +L   +E  LAK+  + G+    + L      + ++  LV  I
Sbjct: 135 NSEDPIRLYLKEIGKEFLLTGNQEVELAKQM-DSGESIIENILKNEGLVIENYYNLVNAI 193

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFD-PERGFRLATYSMWWIKAAMQE---YILRS 120
                       E   E +         FD   +  R+ ++    +K+       YI + 
Sbjct: 194 YSRVDKEEFFKKEKEREKD-------NNFDYYNKKKRITSFYKASLKSFQDRLVKYIEKK 246

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQA--ITDNNLK--PEQVVAIAKKLNVSESEVISM 176
             L ++G    ++ +      +K  L++  +    L+   +  +  A K+   + +  S+
Sbjct: 247 HRLYELGEDIFEESINNERLHIKEMLKSVPLYQEELRIFSDDYIDSASKIKDLKRQQKSI 306

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
             RL  D+  N  I   D    + ++ +    + +E ++         +  +T +   L 
Sbjct: 307 LDRLKIDKVRNLRILGRDLAIPERRERIEQSLNIREDLI---------KEQITEA--QLA 355

Query: 237 PRERRIFEARR 247
            +E    E   
Sbjct: 356 QKELERIEMYY 366


>gi|119489578|ref|ZP_01622338.1| RNA polymerase sigma factor [Lyngbya sp. PCC 8106]
 gi|119454490|gb|EAW35638.1| RNA polymerase sigma factor [Lyngbya sp. PCC 8106]
          Length = 319

 Score =  210 bits (534), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 70/321 (21%), Positives = 141/321 (43%), Gaps = 52/321 (16%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------------------ 43
             +  Y+ EI ++P+L  ++E +  K+ ++                              
Sbjct: 10  DSVRTYLREIGRVPLLTHEQEILYGKQVQQSAILQEGKEKLAKRLGREPSYAEWAENAGV 69

Query: 44  ---------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                        +A  ++V ++LRLVV +A  Y    + + +++ EG IG+ + V+KFD
Sbjct: 70  SLKELKQALEDGQTAKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGTIGMQRGVEKFD 129

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P +G+R +TY+ WWI+ A+   I      +++     +K     L ++K   +++  +  
Sbjct: 130 PTKGYRFSTYAYWWIRQAITRAIAEKGRTIRLPIHITEK-----LNKIKKAQRSLAQDLG 184

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +   +  +A +L+++  ++     R     SL+  +   D   ++  D L  D    E  
Sbjct: 185 RAATIAELADELDLNPKQIREYLERARLPLSLD--LRVGDNQDTELGDLLEDDGASPEDY 242

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQI 272
            ++     + R+ L   M+ L  ++R++   R   EN   +TL  +     +SRERVRQI
Sbjct: 243 ALQ----SSMRSDLEVLMADLTDQQRQVLALRFGLENGQTMTLAKIGDRLNISRERVRQI 298

Query: 273 EARAFKKVQESIQKQVELSSS 293
           E  A  K+++  Q   +  +S
Sbjct: 299 EREALTKLRKRKQDMGDYLAS 319


>gi|149188340|ref|ZP_01866634.1| RNA polymerase sigma factor [Vibrio shilonii AK1]
 gi|148837929|gb|EDL54872.1| RNA polymerase sigma factor [Vibrio shilonii AK1]
          Length = 285

 Score =  210 bits (534), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 94/285 (32%), Positives = 161/285 (56%), Gaps = 6/285 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+  N +I  N    LS Y+  +    +L++ EE  LA     + +     +LV  HLR 
Sbjct: 1   MSHSNAAISFNNSQNLSYYMQYVNSHSILKECEERQLANDLYYNNNEDVISKLVLPHLRY 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA G+ GYGLP+ +++  GNIGL++AVKKF+PE GFRL ++++ WIK+ + ++I+++
Sbjct: 61  VVYIAKGFAGYGLPLVDMIQSGNIGLLKAVKKFNPELGFRLVSFAVHWIKSEITDFIIKN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           WS+VKI TT +Q++LFFNL++ K   + ++++     +   +A KL VS+ +V+SM+ RL
Sbjct: 121 WSIVKIATTKSQRKLFFNLKKYKQSQEWMSES-----EAENLASKLKVSKKDVLSMDGRL 175

Query: 181 AGDES-LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +  +S ++  I   +       +               ++  ++  + L   ++ L+ R 
Sbjct: 176 SARDSYIDPKIGEDEDQVISTGEVFAEPQLDVAIEYETQDWDRHINDELNAGLAKLDARS 235

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R I  +R L    VTL  L+    VS ERVRQIE    +K+++ +
Sbjct: 236 RDIIVSRWLLSEKVTLNELAERHRVSAERVRQIELMTLEKLKDLL 280


>gi|294338839|emb|CAZ87173.1| RNA polymerase sigma factor rpoS [Thiomonas sp. 3As]
          Length = 351

 Score =  210 bits (534), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 79/278 (28%), Positives = 136/278 (48%), Gaps = 11/278 (3%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           +G   L  Y++ IR  P+   ++E+  A R +  GD  A   +V  +LRLVV IA  Y G
Sbjct: 74  SGVSALQAYLNHIRAKPLFTPEQEFETATRAK-AGDFEARQAMVEHNLRLVVSIAKAYVG 132

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            G  + +++ EGN+GL+ A++KF+PERGFR +TY+ WWI+ +++  +++    +++    
Sbjct: 133 RGAALGDLIEEGNLGLIHAIEKFEPERGFRFSTYASWWIRQSIERALMQQVRTIRLPVHV 192

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R    + R + HL+   D   +      +A  L  S  EV  +        SL+AL 
Sbjct: 193 --IRELNQVLRARKHLEQAADYRGQT-SDEDVAALLGRSTEEVTDLLALAEQPTSLDALR 249

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
            +    S   Q       D     + E+ + +    ++   +  L  RER + EAR    
Sbjct: 250 ETQSGESYADQFA-----DQNALSMEEQTQTREVEALVDSWVGELAEREREVIEARFGLH 304

Query: 251 NP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                TLE+L+    ++RERVRQI+  +  K++  + +
Sbjct: 305 GRELETLESLAQRLGLTRERVRQIQQESLLKLKGRLAR 342


>gi|254413477|ref|ZP_05027247.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
 gi|196179584|gb|EDX74578.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
          Length = 331

 Score =  210 bits (534), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 64/305 (20%), Positives = 131/305 (42%), Gaps = 52/305 (17%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYRE----------------------------------- 43
           Y+ EI ++P+L  ++E +  K+ +                                    
Sbjct: 26  YLQEIGRVPLLTHEQEILYGKQVQRLNALEQTKESLFEQLGYEPTLCEWAKASSLSEAEL 85

Query: 44  ----HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                   +A  ++V ++LRLVV +A  Y    + + +++ EG IG+ + V+KFDP +G+
Sbjct: 86  QSCIRAGQTAKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGTIGMQRGVEKFDPTKGY 145

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           R +TY+ WWI+ A+   I      +++     +K     L ++K   + ++    +   +
Sbjct: 146 RFSTYAYWWIRQAITRAIAEKGRTIRLPIHITEK-----LNKIKKAQRQLSQTLGRAATI 200

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +A +L+++  +V     +     SL+  +   D   ++  + L       E       
Sbjct: 201 SELATELDLTPKQVREYLEKARQPLSLD--LRVGDNQDTELGELLEDSGPSPEDFATYSA 258

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAF 277
            + +    L + M+ L  ++R +   R       P+TL  +  + ++SRERVRQIE  A 
Sbjct: 259 MQVD----LEKLMADLTEQQREVLMLRFGLVDGQPMTLAKIGDQLKISRERVRQIEREAL 314

Query: 278 KKVQE 282
            K+++
Sbjct: 315 SKLRK 319


>gi|187931644|ref|YP_001891628.1| RNA polymerase sigma 70 factor RpoD [Francisella tularensis subsp.
           mediasiatica FSC147]
 gi|187712553|gb|ACD30850.1| RNA polymerase sigma 70 factor RpoD [Francisella tularensis subsp.
           mediasiatica FSC147]
          Length = 577

 Score =  210 bits (534), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 64/242 (26%), Positives = 111/242 (45%), Gaps = 12/242 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   ++ ++LRLVV  A  Y   GL   +++ EGNIGLM+AV KFD  +GF+ +TY+ W
Sbjct: 338 QAKKEMIEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKGFKFSTYATW 397

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++            + R+K  +          E+++      N
Sbjct: 398 WIRQAITRSIADQARTIRVPVHM--IETINKVNRIKRQILQEKGREATEEEIIE--HTPN 453

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +++ ++  +        S+ + I   D   S   D++    D      IE    +N R  
Sbjct: 454 MTKEKLKKILNISHTPISMESPI--GDDEDSTVGDFI---EDKNNYSPIEAANLENLREA 508

Query: 228 LTRSMSV-LNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +   +   L  RE ++   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 509 IKELIETGLTEREAKVLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIEAKALRKLKHPS 568

Query: 285 QK 286
           + 
Sbjct: 569 RS 570


>gi|327399101|ref|YP_004339970.1| putative RNA polymerase, sigma 70 family subunit [Hippea maritima
           DSM 10411]
 gi|327181730|gb|AEA33911.1| putative RNA polymerase, sigma 70 family subunit [Hippea maritima
           DSM 10411]
          Length = 289

 Score =  210 bits (534), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 82/294 (27%), Positives = 152/294 (51%), Gaps = 20/294 (6%)

Query: 4   KNMSIIVNGEI------GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSH 57
           KN  + +N E+       L+ Y+ EI KIP+L  +EE  L +R ++ GD  A  +LV  +
Sbjct: 8   KNEQLAINDEVDLAESSALTSYLKEISKIPVLSAEEEKELGRRIKK-GDKEALKKLVKHN 66

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LR VV +A  Y+  G+P+ ++++EGN+GL++A KKFDP+R  +  +Y+ WWIK ++ +YI
Sbjct: 67  LRFVVSVAKKYKNLGIPLLDLINEGNLGLIKAAKKFDPDRNTKFISYAAWWIKQSIMKYI 126

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
               + ++I   A  +     +  +K   +   D      ++  I+   ++SE E+ +  
Sbjct: 127 TEQSTPIRIPLKAKSR--ISKIDTIKEDYRQKFDEEPMNGEISEIS---DLSEREIKNAE 181

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                 +SL+     SD       D +      +EQ + ++  +K+    + + +S L  
Sbjct: 182 LARFYFDSLDD--YVSDDKDILKGDLISL----KEQSIEDEHIQKSLIEEVNKFLSELPE 235

Query: 238 RERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           RE+ I + R    +  P TL  +  ++ +S+ERVRQ+E     K+++  ++  E
Sbjct: 236 REQDIIKLRYGLYDGRPRTLREIGEKYGISKERVRQLENNILNKLKKRFKEYKE 289


>gi|315929035|gb|EFV08275.1| RNA polymerase sigma factor [Campylobacter jejuni subsp. jejuni
           305]
          Length = 622

 Score =  210 bits (534), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 70/239 (29%), Positives = 120/239 (50%), Gaps = 13/239 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ +RG++ +TY+ W
Sbjct: 380 EAKGRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATW 439

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I        +   + ++   ++     + K   V  IAK++ 
Sbjct: 440 WIRQAISRAIADQARTIRIPIH-----MIETINQINKIIREHLQKDGKEPDVSVIAKEVG 494

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V  +        SL A I   +++  ++ D++    D      ++   + + +  
Sbjct: 495 LSVDKVKQVIKITKEPISLEAPI--GNEDDGKFGDFV---EDRNSLSPMDHILKDDLKEQ 549

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++  
Sbjct: 550 IDEVLDQLNDREKAVIRMRFGLMDDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHP 608


>gi|172035791|ref|YP_001802292.1| RNA polymerase sigma factor RpoD [Cyanothece sp. ATCC 51142]
 gi|171697245|gb|ACB50226.1| group 1 sigma-70 RNA polymerase sigma factor A [Cyanothece sp. ATCC
           51142]
          Length = 416

 Score =  210 bits (534), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 65/239 (27%), Positives = 120/239 (50%), Gaps = 13/239 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ 
Sbjct: 178 RKAKDKMVHSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYAT 237

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      +++        L+  + R+K   + ++    +      IA ++
Sbjct: 238 WWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKLLSQEMRRKPTEEEIATRM 292

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++  ++  +        SL   I    +  S+  D++  D +  E    ++  +   R 
Sbjct: 293 EMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADGETPE----DEVSKNLLRE 346

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQES 283
            L   +  L+PRER +   R   ++    TLE +   F V+RER+RQIEA+A +K++  
Sbjct: 347 DLENVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHP 405



 Score = 39.0 bits (90), Expect = 0.84,   Method: Composition-based stats.
 Identities = 10/32 (31%), Positives = 18/32 (56%)

Query: 12 GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE 43
           E  +  Y+ EI +I +L  +EE  LA++  +
Sbjct: 58 TEDSIRVYLQEIGRIRLLRAEEEIELARKIAD 89


>gi|315453594|ref|YP_004073864.1| RNA polymerase sigma factor (sigma-70) [Helicobacter felis ATCC
           49179]
 gi|315132646|emb|CBY83274.1| RNA polymerase sigma factor (sigma-70) [Helicobacter felis ATCC
           49179]
          Length = 621

 Score =  210 bits (534), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 76/296 (25%), Positives = 143/296 (48%), Gaps = 26/296 (8%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEE----------YVLAKRYREHG--DLS 48
           M+++ ++ +V     +  Y+ EI+K+   ++  E            + ++ +        
Sbjct: 323 MSKEEIAAMVPEATMIGSYM-EIKKLFQTKEASEDGFDLEPGKLKEILEQIKRGKLISDK 381

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ E+ +R +TY+ WW
Sbjct: 382 AKNKMARSNLRLVVSIAKRYTSRGLPFLDLIQEGNIGLMKAVDKFEHEKNYRFSTYATWW 441

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           IK A+   I      ++I        +   + R+   ++     N K   +  +AK++ +
Sbjct: 442 IKQAISRAIADQARTIRIPIH-----MIDTINRINKVMRKYMQENGKEPDLDLVAKEVGL 496

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V ++        SL + + + D    ++ D++  D        ++   R++ +  +
Sbjct: 497 PLDKVKNVIKITKEPISLESPVGNDDD--GKFGDFVENDKVVGS---MDHIMREDLKTQI 551

Query: 229 TRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 552 DGVLDQLNEREKSVIRMRFGLLEDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 607



 Score = 41.0 bits (95), Expect = 0.24,   Method: Composition-based stats.
 Identities = 10/31 (32%), Positives = 20/31 (64%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR 42
            +  +  Y+ E+ +IP+L K+EE  L+K+ +
Sbjct: 109 SDSPVRMYLREMGEIPLLSKEEEVELSKQIK 139


>gi|119953489|ref|YP_945698.1| RNA polymerase sigma factor RpoD [Borrelia turicatae 91E135]
 gi|119862260|gb|AAX18028.1| RNA polymerase sigma factor RpoD [Borrelia turicatae 91E135]
          Length = 630

 Score =  210 bits (534), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 67/257 (26%), Positives = 124/257 (48%), Gaps = 16/257 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE +  K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 378 EEILKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 433

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RGF+ +TY+ WWI+ A+   I      +++        +   + RL    + +   
Sbjct: 434 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVH-----MIEQINRLNRETRYLVQV 488

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             K      ++ +L     +V ++        SL   I   ++  S   D++    D   
Sbjct: 489 LGKDPTDEELSSRLGWDLKKVKTVKNVSREPVSLETPI--GEEEDSVLSDFI---EDKAI 543

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +   +       ++ +   +  L  RE+ + + R   E+   +TLE +   F V+RER+R
Sbjct: 544 KNPAKHTSFVVLQDQIRAVLGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIR 603

Query: 271 QIEARAFKKVQESIQKQ 287
           QIE++A ++++   + Q
Sbjct: 604 QIESKALRRLKNPKKTQ 620



 Score = 36.3 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 45/251 (17%), Positives = 91/251 (36%), Gaps = 33/251 (13%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRL------VTSHLRLVVKI 64
           N E  +  Y+ EI K  +L   +E  LAK+  + G+    + L      + ++  LV  I
Sbjct: 135 NSEDPIRLYLKEIGKEFLLTGNQEVELAKQM-DSGESIIENILKNEGLVIENYYNLVNAI 193

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFD-PERGFRLATYSMWWIKAAMQE---YILRS 120
                       E   E +         FD   +  R+ ++    +K        YI R 
Sbjct: 194 YSRVDKEEFFKKEKEREKD-------NNFDYYNKKKRITSFYKASLKPFQDRLIKYIERK 246

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQA--ITDNNLK--PEQVVAIAKKLNVSESEVISM 176
            SL ++G    ++ +      +K  L++  +    L+   +  +  A K+   + +  S+
Sbjct: 247 HSLYELGEDIFEESITSERLHIKEMLKSVPLYQEELRIFSDDYIDSASKIKDLKRQQKSI 306

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
             RL  D+  N  I   D    + ++ +    + +E ++         +  +T +   L 
Sbjct: 307 LDRLKIDKVRNLRILGRDLAIPERRERIEKSLNIREDLI---------KEQITEA--QLA 355

Query: 237 PRERRIFEARR 247
            +E    E   
Sbjct: 356 QKELERIEMYY 366


>gi|13357909|ref|NP_078183.1| RNA polymerase sigma factor [Ureaplasma parvum serovar 3 str. ATCC
           700970]
 gi|170762330|ref|YP_001752432.1| RNA polymerase sigma factor [Ureaplasma parvum serovar 3 str. ATCC
           27815]
 gi|11357048|pir||E82901 RNA polymerase sigma factor UU349 [imported] - Ureaplasma
           urealyticum
 gi|6899329|gb|AAF30758.1|AE002132_2 RNA polymerase sigma factor [Ureaplasma parvum serovar 3 str. ATCC
           700970]
 gi|168827907|gb|ACA33169.1| RNA polymerase sigma factor [Ureaplasma parvum serovar 3 str. ATCC
           27815]
          Length = 448

 Score =  210 bits (534), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 74/289 (25%), Positives = 136/289 (47%), Gaps = 23/289 (7%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSA----AHRLVTSHLRLVVKIAMGY 68
           + G+  Y+  + +  ML   EE   AK      D S      ++L TS++RLV  IA  Y
Sbjct: 154 DDGIKAYLGVLGESKMLRSDEETEYAKMVISD-DPSLVKIGKNQLYTSNMRLVTSIAKKY 212

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
              GL + +++ EG+ GL++A+ KFD E+G + +TY+ WWI+ ++   I      ++I  
Sbjct: 213 LNRGLDLEDLIQEGSSGLLKAIDKFDHEKGHKFSTYATWWIRQSITRAIADQARQIRIPV 272

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN---------VSESEVISMNCR 179
              +      L + + +L      +   E++     K++         ++  +V+ +   
Sbjct: 273 HMVE--TINKLTKAERNLIQELGRDPTAEEIAQAMNKVSQAKNQKEQLITAQKVVEIKKL 330

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
                SL+  I   ++  SQ+ D++  D     +   EK+   ++ N +     VLN  E
Sbjct: 331 NVDPVSLDKQIGHDEE--SQFSDFISDDEIISPEKYTEKKALNDQINEMFE--KVLNDNE 386

Query: 240 RRIFEARRLQ---ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           +R+ + R      E P TLE +     V+RER RQIE++A +K++   +
Sbjct: 387 QRVIKMRYGLLPFERPYTLEEVGEYLGVTRERARQIESKAIRKLKHPSK 435


>gi|296117743|ref|ZP_06836327.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           ammoniagenes DSM 20306]
 gi|295969474|gb|EFG82715.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           ammoniagenes DSM 20306]
          Length = 334

 Score =  210 bits (534), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 67/309 (21%), Positives = 138/309 (44%), Gaps = 38/309 (12%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY------------------RE 43
           +R+  +        +  Y++ I K  +L  ++E  LA+                     E
Sbjct: 24  SRRGQTNDNPSADLVRVYLNGIGKTALLSAEDEVELAQAIEIGLYAEYKLNTAEKLTRAE 83

Query: 44  HGD--------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
             D          A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD 
Sbjct: 84  KRDMKILVKEGKKARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDY 143

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            +GF+ +TY+ WWI+ A+   +      +++     ++     L R+K  +         
Sbjct: 144 AKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLSRIKREMYQSLGREAT 201

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
            E    +A++  + E+++  +  +     SL+  + + ++  +   D++        +  
Sbjct: 202 NE---ELAEESGIEENKIEMLLRQSRDPVSLDMPVGADEE--APLGDFIEDAEATDAETA 256

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIE 273
           +    R    + +   +  L  RE+ +   R   ++  P TL+ +  +F +SRERVRQIE
Sbjct: 257 VVASMR---HSDIRDVIGTLEQREQDVIRLRYGLDDGVPRTLDQIGRKFGLSRERVRQIE 313

Query: 274 ARAFKKVQE 282
                K+++
Sbjct: 314 REVMAKLRD 322


>gi|89256388|ref|YP_513750.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica LVS]
 gi|115314834|ref|YP_763557.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica OSU18]
 gi|156502477|ref|YP_001428542.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica FTNF002-00]
 gi|167010407|ref|ZP_02275338.1| RNA polymerase sigma factor RpoD [Francisella tularensis subsp.
           holarctica FSC200]
 gi|254367725|ref|ZP_04983746.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica 257]
 gi|290953811|ref|ZP_06558432.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica URFT1]
 gi|295312822|ref|ZP_06803554.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica URFT1]
 gi|89144219|emb|CAJ79489.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica LVS]
 gi|115129733|gb|ABI82920.1| DNA-directed RNA polymerase sigma subunit RpoD [Francisella
           tularensis subsp. holarctica OSU18]
 gi|134253536|gb|EBA52630.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica 257]
 gi|156253080|gb|ABU61586.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica FTNF002-00]
          Length = 577

 Score =  209 bits (533), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 65/242 (26%), Positives = 111/242 (45%), Gaps = 12/242 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   ++ ++LRLVV  A  Y   GL   +++ EGNIGLM+AV KFD  +GF+ +TY+ W
Sbjct: 338 QAKKEMIEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKGFKFSTYATW 397

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++            + R+K  +          E+++      N
Sbjct: 398 WIRQAITRSIADQARTIRVPVHM--IETINKVNRIKRQILQEKGREATEEEIIE--HTPN 453

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S+ ++  +        S+ + I   D   S   D++    D      IE    +N R  
Sbjct: 454 MSKEKLKKILNISHTPISMESPI--GDDEDSTVGDFI---EDKNNYSPIEAANLENLREA 508

Query: 228 LTRSMSV-LNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +   +   L  RE ++   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 509 IKELIETGLTEREAKVLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIEAKALRKLKHPS 568

Query: 285 QK 286
           + 
Sbjct: 569 RS 570


>gi|213029652|ref|ZP_03344099.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. 404ty]
          Length = 322

 Score =  209 bits (533), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 75/262 (28%), Positives = 131/262 (50%), Gaps = 13/262 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFK 278
           ++  E  ++RERVRQI+    +
Sbjct: 290 DVGREIGLTRERVRQIQVEGLR 311


>gi|67922139|ref|ZP_00515654.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
 gi|67856039|gb|EAM51283.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
          Length = 318

 Score =  209 bits (533), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 73/318 (22%), Positives = 140/318 (44%), Gaps = 52/318 (16%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR--------------YREHG------ 45
           M +  +    +  Y+ EI ++P+L  +EE + AKR               +E G      
Sbjct: 1   MKLTKSNPDPVRAYLKEIGRVPLLSHEEEILYAKRVQRLINLEKLREEIIQETGKEPTNS 60

Query: 46  -------------------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
                                +A  ++V ++LRLVV +A  Y    L + +++ EG IG+
Sbjct: 61  QWAKAAKLSRKEFCSVVEAGEAAKRKMVEANLRLVVSVAKKYLKRNLDLLDLIQEGTIGM 120

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
            + V+KFDP +G+R +TY+ WWI+ A+   I      +++     +K     L ++K   
Sbjct: 121 QRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEK-----LNKIKKAQ 175

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           + ++    +   +  +A++L+++  +V     R     SL+  +   D   ++  D L  
Sbjct: 176 RELSQQKGRAATISELAEELDLTPKQVRDYLERSRQPLSLD--LRVGDNQDTELGDLLED 233

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           +     Q   +     + +  L + M  L  +++++   R       P+TL  + S   +
Sbjct: 234 EG----QSPEDFATHSSLQFDLEKLMEDLTIQQKQVIALRFGLMDGQPLTLAKIGSRLNI 289

Query: 265 SRERVRQIEARAFKKVQE 282
           SRERVRQIE  A  K+++
Sbjct: 290 SRERVRQIEREALSKLRK 307


>gi|87125501|ref|ZP_01081346.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9917]
 gi|86166801|gb|EAQ68063.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9917]
          Length = 312

 Score =  209 bits (533), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 75/302 (24%), Positives = 139/302 (46%), Gaps = 36/302 (11%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG-------------------------D 46
               +S Y+  I +IP+L   EE  L  + +E                            
Sbjct: 16  SSDPISWYLATIGRIPLLTPAEEIELGNQVQEMMRLTEDGTLAPDHDGFSSHDRRMIRVG 75

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  R++ ++LRLVV +A  Y+G GL + +++ EG++GL +AV+KFDP RG++ +TY+ 
Sbjct: 76  KRAKERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAF 135

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ +M   I      +++    +++     L  ++     +          V IA+ +
Sbjct: 136 WWIRQSMTRAIACQSRTIRLPVHLSER-----LTTIRKVSLDLAHKLGAMPSRVEIAEAM 190

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   E+ ++  +     SL+A +N  ++  S   D +    D      ++K E+     
Sbjct: 191 DMPLDELDALLRQALTTSSLDAPVN-GEEGRSFLGDLIA---DTSHDEPLDKVEQSIHHE 246

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L R +S L+ +E+ +   R         TL  +    EVSRERVRQ+E +A +K++   
Sbjct: 247 QLGRWLSHLSEQEQYVLGLRFGLNGNERHTLAEIGRLMEVSRERVRQVELKALRKLRNLT 306

Query: 285 QK 286
           ++
Sbjct: 307 RR 308


>gi|310779070|ref|YP_003967403.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ilyobacter
           polytropus DSM 2926]
 gi|309748393|gb|ADO83055.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ilyobacter
           polytropus DSM 2926]
          Length = 275

 Score =  209 bits (533), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 83/276 (30%), Positives = 141/276 (51%), Gaps = 15/276 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +S Y+ +IR   +L K+EE  L  R +  G   A H+L+ S+LRLVV IA  Y   G+  
Sbjct: 8   VSLYLEDIRSYNILTKEEELDLLIRAK-SGCEDAKHKLILSNLRLVVNIAKSYVHKGMGF 66

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++SEGN GLM A++KFD E+GFR +TY++WWIK ++ + I+     ++I +  +    
Sbjct: 67  IDLISEGNFGLMHAIEKFDVEKGFRFSTYAVWWIKQSISKAIISKGREIRIPSYKHDL-- 124

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              L ++   +      N     +  IA  L ++  +V  +        SLNA I     
Sbjct: 125 ---LNKVNKFIMEFVMKNSVYPNIEDIALGLEITPKKVQKVMLEFQDLLSLNASI----G 177

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPV 253
           +    +D +       E+ L ++   +  RN +   + VL PRE+ I + R   +     
Sbjct: 178 DDIFLEDTISQPD---EESLEDEVLGEIGRNEINDILEVLKPREKEILKLRYGLDGYEIH 234

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           TLE +   F ++RERVRQIE +  +K++    ++++
Sbjct: 235 TLEEIGKSFSITRERVRQIEKKTLQKLRNKFSEELK 270


>gi|296134902|ref|YP_003642144.1| RNA polymerase sigma factor RpoS [Thiomonas intermedia K12]
 gi|295795024|gb|ADG29814.1| RNA polymerase sigma factor RpoS [Thiomonas intermedia K12]
          Length = 351

 Score =  209 bits (533), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 79/278 (28%), Positives = 136/278 (48%), Gaps = 11/278 (3%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           +G   L  Y++ IR  P+   ++E+  A R +  GD  A   +V  +LRLVV IA  Y G
Sbjct: 74  SGVSALQSYLNHIRAKPLFTPEQEFETATRAK-AGDFEARQAMVEHNLRLVVSIAKAYVG 132

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            G  + +++ EGN+GL+ A++KF+PERGFR +TY+ WWI+ +++  +++    +++    
Sbjct: 133 RGAALGDLIEEGNLGLIHAIEKFEPERGFRFSTYASWWIRQSIERALMQQVRTIRLPVHV 192

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R    + R + HL+   D   +      +A  L  S  EV  +        SL+AL 
Sbjct: 193 --IRELNQVLRARKHLEQAADYRGQT-SDEDVAALLGRSTEEVADLLALAEQPTSLDALR 249

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
            +    S   Q       D     + E+ + +    ++   +  L  RER + EAR    
Sbjct: 250 ETQSGESYADQFA-----DQNALSMEEQTQTREVEALVDSWVGELAEREREVIEARFGLH 304

Query: 251 NP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                TLE+L+    ++RERVRQI+  +  K++  + +
Sbjct: 305 GRELETLESLAQRLGLTRERVRQIQQESLLKLKGRLAR 342


>gi|126659035|ref|ZP_01730176.1| RNA polymerase sigma factor RpoD [Cyanothece sp. CCY0110]
 gi|126619692|gb|EAZ90420.1| RNA polymerase sigma factor RpoD [Cyanothece sp. CCY0110]
          Length = 416

 Score =  209 bits (533), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 65/239 (27%), Positives = 120/239 (50%), Gaps = 13/239 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ 
Sbjct: 178 RKAKDKMVHSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYAT 237

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      +++        L+  + R+K   + ++    +      IA ++
Sbjct: 238 WWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKLLSQEMRRKPTEEEIATRM 292

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++  ++  +        SL   I    +  S+  D++  D +  E    ++  +   R 
Sbjct: 293 EMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADGETPE----DEVSKNLLRE 346

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQES 283
            L   +  L+PRER +   R   ++    TLE +   F V+RER+RQIEA+A +K++  
Sbjct: 347 DLENVLDTLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVTRERIRQIEAKALRKLRHP 405



 Score = 39.0 bits (90), Expect = 0.86,   Method: Composition-based stats.
 Identities = 10/32 (31%), Positives = 18/32 (56%)

Query: 12 GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE 43
           E  +  Y+ EI +I +L  +EE  LA++  +
Sbjct: 58 TEDSIRVYLQEIGRIRLLRAEEEIELARKIAD 89


>gi|171920947|ref|ZP_02932089.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 13 str.
           ATCC 33698]
 gi|185178923|ref|ZP_02964687.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 5 str.
           ATCC 27817]
 gi|188024158|ref|ZP_02996885.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 7 str.
           ATCC 27819]
 gi|188518597|ref|ZP_03004049.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 11 str.
           ATCC 33695]
 gi|188524519|ref|ZP_03004514.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 12 str.
           ATCC 33696]
 gi|195868018|ref|ZP_03080013.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 9 str.
           ATCC 33175]
 gi|198273631|ref|ZP_03206166.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 4 str.
           ATCC 27816]
 gi|209554143|ref|YP_002284749.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 10 str.
           ATCC 33699]
 gi|225550349|ref|ZP_03771298.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 2 str.
           ATCC 27814]
 gi|225551084|ref|ZP_03772030.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 8 str.
           ATCC 27618]
 gi|171903184|gb|EDT49473.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 13 str.
           ATCC 33698]
 gi|184209186|gb|EDU06229.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 5 str.
           ATCC 27817]
 gi|188018789|gb|EDU56829.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 7 str.
           ATCC 27819]
 gi|188997798|gb|EDU66895.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 11 str.
           ATCC 33695]
 gi|195659715|gb|EDX53095.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 12 str.
           ATCC 33696]
 gi|195660310|gb|EDX53572.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 9 str.
           ATCC 33175]
 gi|198249659|gb|EDY74440.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 4 str.
           ATCC 27816]
 gi|209541644|gb|ACI59873.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 10 str.
           ATCC 33699]
 gi|225378899|gb|EEH01264.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 8 str.
           ATCC 27618]
 gi|225379503|gb|EEH01865.1| RNA polymerase sigma factor [Ureaplasma urealyticum serovar 2 str.
           ATCC 27814]
          Length = 448

 Score =  209 bits (533), Expect = 3e-52,   Method: Composition-based stats.
 Identities = 73/292 (25%), Positives = 137/292 (46%), Gaps = 29/292 (9%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSA----AHRLVTSHLRLVVKIAMGY 68
           + G+  Y+  + +  ML   EE   AK    + D +      ++L TS++RLV  IA  Y
Sbjct: 154 DDGIKAYLGVLGESKMLRSDEETEYAKMVISN-DPALIKIGKNQLYTSNMRLVTSIAKKY 212

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
              GL + +++ EG+ GL++A+ KFD E+G + +TY+ WWI+ ++   I      ++I  
Sbjct: 213 LNRGLDLEDLIQEGSSGLLKAIDKFDHEKGHKFSTYATWWIRQSITRAIADQARQIRIPV 272

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN------------VSESEVISM 176
              +      + +L    +++     +      IA+ +N            ++  +V+ +
Sbjct: 273 HMVE-----TINKLTKAERSLIQELGRDPTAEEIAQAMNKASQAKNQKEQLITAQKVVEI 327

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
                   SL+  I   ++  SQ+ D++  D     +   EK+   ++ N +     VLN
Sbjct: 328 KKLNVDPVSLDKQIGHDEE--SQFSDFISDDEIISPEKYTEKKALNDQINEMFE--KVLN 383

Query: 237 PRERRIFEARRLQ---ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             E+R+ + R      E P TLE +     V+RER RQIE++A +K++   +
Sbjct: 384 DNEQRVIKMRYGLLPFERPYTLEEVGEHLGVTRERARQIESKAIRKLKHPSK 435


>gi|134301933|ref|YP_001121902.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis WY96-3418]
 gi|254369360|ref|ZP_04985372.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica FSC022]
 gi|254372870|ref|ZP_04988359.1| DNA-directed RNA polymerase sigma subunit RpoD [Francisella
           tularensis subsp. novicida GA99-3549]
 gi|134049710|gb|ABO46781.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis WY96-3418]
 gi|151570597|gb|EDN36251.1| DNA-directed RNA polymerase sigma subunit RpoD [Francisella
           novicida GA99-3549]
 gi|157122310|gb|EDO66450.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           holarctica FSC022]
          Length = 577

 Score =  209 bits (533), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 64/242 (26%), Positives = 111/242 (45%), Gaps = 12/242 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   ++ ++LRLVV  A  Y   GL   +++ EGNIGLM+AV KFD  +GF+ +TY+ W
Sbjct: 338 QAKKEMIEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKGFKFSTYATW 397

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++            + R+K  +          E+++      N
Sbjct: 398 WIRQAITRSIADQARTIRVPVHM--IETINKVNRIKRQILQEKGREATEEEIIE--HTPN 453

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +++ ++  +        S+ + I   D   S   D++    D      IE    +N R  
Sbjct: 454 MTKEKLKKILNISHTPISMESPI--GDDEDSTVGDFI---EDKNNYSPIEAANLENLREA 508

Query: 228 LTRSMSV-LNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +   +   L  RE ++   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 509 IKELIETGLTEREAKVLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIEAKALRKLKHPS 568

Query: 285 QK 286
           + 
Sbjct: 569 RS 570


>gi|194337394|ref|YP_002019188.1| RNA polymerase, sigma 32 subunit, RpoH [Pelodictyon
           phaeoclathratiforme BU-1]
 gi|194309871|gb|ACF44571.1| RNA polymerase, sigma 32 subunit, RpoH [Pelodictyon
           phaeoclathratiforme BU-1]
          Length = 299

 Score =  209 bits (533), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 75/299 (25%), Positives = 141/299 (47%), Gaps = 24/299 (8%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD-----------LSAAH 51
           + +  I     + L RY+ EI K  +L  ++E  L K  +E  D             A  
Sbjct: 5   KISKQITNRESLSLDRYLQEIGKYDLLTAEDEVKLTKAIKEGFDMPVDTTEYKRAKRALD 64

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +L+  +LR VV +A  Y+  GL + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ 
Sbjct: 65  KLIKGNLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQ 124

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ + +     +V++            L ++      +     +      +A  L +   
Sbjct: 125 SILQALAEQSRIVRLPLNR-----VGTLNKISKAYSQLEQEFERDPNTRELATLLEMDSQ 179

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           +V           S++A     D N  +  D L  D      +      R +    + RS
Sbjct: 180 DVADTLKIAGRHVSVDAPFAQGDDN--RLLDVLQNDG----HLPDYGLNRDSLTLEVERS 233

Query: 232 MSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +SVL PRE  + ++      +NP+TLE +  +F ++RERVRQI+ +A +++++S   ++
Sbjct: 234 LSVLAPREADVIKSYFGIGMDNPLTLEEIGEKFRLTRERVRQIKEKAIRRLRQSAYSKI 292


>gi|225551881|ref|ZP_03772824.1| RNA polymerase sigma factor RpoD [Borrelia sp. SV1]
 gi|225371676|gb|EEH01103.1| RNA polymerase sigma factor RpoD [Borrelia sp. SV1]
          Length = 631

 Score =  209 bits (533), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 67/257 (26%), Positives = 122/257 (47%), Gaps = 16/257 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 379 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 434

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RGF+ +TY+ WWI+ A+   I      +++        +   + RL    + +   
Sbjct: 435 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVH-----MIEQINRLNRETRYLIQV 489

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             K      ++ +L     +V ++        SL   I   ++  S   D++    D   
Sbjct: 490 LGKDPTDEELSDRLGWELKKVKTVKSVSREPVSLETPI--GEEEDSVLSDFI---EDKAI 544

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +           ++ +   +  L  RE+ + + R   E+   +TLE +   F V+RER+R
Sbjct: 545 KNPANHTSFVVLQDQIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIR 604

Query: 271 QIEARAFKKVQESIQKQ 287
           QIE++A ++++   + Q
Sbjct: 605 QIESKALRRLKNPKKTQ 621


>gi|288926163|ref|ZP_06420090.1| RNA polymerase sigma-70 factor [Prevotella buccae D17]
 gi|315608876|ref|ZP_07883849.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella buccae
           ATCC 33574]
 gi|288337055|gb|EFC75414.1| RNA polymerase sigma-70 factor [Prevotella buccae D17]
 gi|315249403|gb|EFU29419.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella buccae
           ATCC 33574]
          Length = 286

 Score =  209 bits (533), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 79/287 (27%), Positives = 147/287 (51%), Gaps = 12/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI    ++  +EE  LA+R R+ GD  A  +L  ++LR VV
Sbjct: 5   KITKSITNRESASLDKYLQEIGHEELVTVEEEVELAQRIRK-GDRHALEKLTKANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + I     
Sbjct: 64  SVAKQYQNQGLSLPDLINEGNMGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++    NQ      + R+   L      N +   +  IA  +++ E ++         
Sbjct: 124 IVRLP--LNQVGSVNKINRM---LNKFEQENERRPSIDEIADSVDLPEDKIEDALKVNTR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     D NS      +    +    +  +    ++ R  ++R++  LN RER I
Sbjct: 179 HVSVDAPFVDGDDNS-----LIDILPNSDAPMADKALVMESLREEISRALRTLNERERNI 233

Query: 243 FEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            E      NP +TLE +  +F ++RERVRQI+ +A ++++ + + +V
Sbjct: 234 IECFFGINNPEMTLEEIGDKFGLTRERVRQIKEKAIRRLRHNTKNRV 280


>gi|254374325|ref|ZP_04989807.1| RNA polymerase sigma-70 factor [Francisella novicida GA99-3548]
 gi|151572045|gb|EDN37699.1| RNA polymerase sigma-70 factor [Francisella novicida GA99-3548]
          Length = 577

 Score =  209 bits (533), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 64/242 (26%), Positives = 111/242 (45%), Gaps = 12/242 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   ++ ++LRLVV  A  Y   GL   +++ EGNIGLM+AV KFD  +GF+ +TY+ W
Sbjct: 338 QAKKEMIEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKGFKFSTYATW 397

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++            + R+K  +          E+++      N
Sbjct: 398 WIRQAITRSIADQARTIRVPVHM--IETINKVNRIKRQILQEKGREATEEEIIE--HTPN 453

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +++ ++  +        S+ + I   D   S   D++    D      IE    +N R  
Sbjct: 454 MTKEKLKKILNISHTPISMESPI--GDDEDSTVGDFI---EDKNNYSPIEAANLENLREA 508

Query: 228 LTRSMSV-LNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +   +   L  RE ++   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 509 IKELIETGLTEREAKVLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIEAKALRKLKHPS 568

Query: 285 QK 286
           + 
Sbjct: 569 RS 570


>gi|118497505|ref|YP_898555.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           novicida U112]
 gi|195536199|ref|ZP_03079206.1| RNA polymerase sigma factor RpoD [Francisella tularensis subsp.
           novicida FTE]
 gi|208779304|ref|ZP_03246650.1| RNA polymerase sigma factor RpoD [Francisella novicida FTG]
 gi|118423411|gb|ABK89801.1| RNA polymerase sigma-70 factor [Francisella novicida U112]
 gi|194372676|gb|EDX27387.1| RNA polymerase sigma factor RpoD [Francisella tularensis subsp.
           novicida FTE]
 gi|208745104|gb|EDZ91402.1| RNA polymerase sigma factor RpoD [Francisella novicida FTG]
          Length = 577

 Score =  209 bits (533), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 64/242 (26%), Positives = 111/242 (45%), Gaps = 12/242 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   ++ ++LRLVV  A  Y   GL   +++ EGNIGLM+AV KFD  +GF+ +TY+ W
Sbjct: 338 QAKKEMIEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKGFKFSTYATW 397

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++            + R+K  +          E+++      N
Sbjct: 398 WIRQAITRSIADQARTIRVPVHM--IETINKVNRIKRQILQEKGREATEEEIIE--HTPN 453

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +++ ++  +        S+ + I   D   S   D++    D      IE    +N R  
Sbjct: 454 MTKEKLKKILNISHTPISMESPI--GDDEDSTVGDFI---EDKNNYSPIEAANLENLREA 508

Query: 228 LTRSMSV-LNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +   +   L  RE ++   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 509 IKELIETGLTEREAKVLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIEAKALRKLKHPS 568

Query: 285 QK 286
           + 
Sbjct: 569 RS 570


>gi|163783667|ref|ZP_02178655.1| RNA polymerase sigma factor RpoS [Hydrogenivirga sp. 128-5-R1-1]
 gi|159881072|gb|EDP74588.1| RNA polymerase sigma factor RpoS [Hydrogenivirga sp. 128-5-R1-1]
          Length = 309

 Score =  209 bits (533), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 88/296 (29%), Positives = 142/296 (47%), Gaps = 38/296 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +++Y+  I KIP+L  +EE  LA++ +E GD  +  +LV S+LR VV +A  Y GYGLP 
Sbjct: 9   INQYLKRISKIPLLSPEEEKELARKAKE-GDEESLKKLVESNLRFVVSVAKQYIGYGLPF 67

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           SE+++ GN+GL++A K+FDPERG +  +Y++WWI+ A+ + + +    V+I     Q  L
Sbjct: 68  SELIAAGNLGLLEAAKRFDPERGVKFISYAVWWIRQAIMQALSQQTGAVRIP--LKQSHL 125

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVA------IAKKL----------------------N 167
              +  +   L    +    PE+V        IAK+L                       
Sbjct: 126 ISKIGTIYAELAKELEREPTPEEVAEQLSKEMIAKELTKELGREPTDEEVQKKFKKEGYK 185

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  EV           SL+A +   +   + + D+L          + E   ++     
Sbjct: 186 ISPEEVEKYLQVCRIPLSLDAPV--GENEDTFFVDFL---SKHGTAEVEESVIQEVLEKE 240

Query: 228 LTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  L  +ERR+ E R       P TL  +     VSRERVRQ+E RA +K++
Sbjct: 241 IYDLLDKLPEKERRVVELRFGLKGNEPKTLREIGDILGVSRERVRQLETRALRKLR 296


>gi|87301096|ref|ZP_01083937.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
 gi|87284064|gb|EAQ76017.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
          Length = 308

 Score =  209 bits (533), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 73/293 (24%), Positives = 137/293 (46%), Gaps = 32/293 (10%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG---------------------DLSAA 50
           G   +S Y+  I ++P+L   EE  L  + +                           A 
Sbjct: 15  GSDPISWYLGTIGRVPLLTPAEEIELGNQVQAMMQLIDSGVEDPPSLRQKQLLRLGRRAK 74

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            R++ ++LRLVV +A  Y+G GL + +++ EG++GL +AV+KFDP RG++ +TY+ WWI+
Sbjct: 75  ERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWWIR 134

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            +M   I      +++    +++     L  ++     +            IA+ + +  
Sbjct: 135 QSMTRAIACQSRTIRLPVHLSER-----LSAVRRVSLELAHKLGAMPSRSEIAEAMAIPI 189

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            E+  +  +     SL+A +N  ++  S   D +    D      +++ ER      L R
Sbjct: 190 QELDGLLRQSLTTSSLDAPVN-GEEGRSFLGDLIA---DSSHDEPLDQVERGMHHEQLER 245

Query: 231 SMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +S L+ +ER++ + R   +     TL  +    +VSRERVRQ+E +A +K++
Sbjct: 246 WLSYLSEQERQVLDLRFGLDGHERHTLAEIGRLLDVSRERVRQVELKALRKLR 298


>gi|158340954|ref|YP_001522121.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158311195|gb|ABW32807.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 268

 Score =  209 bits (533), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 73/275 (26%), Positives = 130/275 (47%), Gaps = 15/275 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ E+ + P+L  +EE  LA++ +  GDL A  R++  +LRLVV IA  ++  GL
Sbjct: 6   DSVQAYLKEMGRYPLLSHEEEIRLARQVK-AGDLKAKQRMIECNLRLVVSIAKKHQHLGL 64

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EG+IGL  AV KFD  +G + +TY+ WWI  A++  +      + I     ++
Sbjct: 65  PLMDLIQEGSIGLNTAVDKFDLAQGCKFSTYAYWWISEAIKRALKSQSRTIYIPIHQWER 124

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                  R+K  ++ +T    +   +  ++    +  S + +         SL+  +   
Sbjct: 125 AH-----RIKKAVRQLTQEKGRTPTLKELSAATGIKSSLIRNTLQSFQAVSSLDQPVGPE 179

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QEN 251
            K++       + D    E   +   +     + LTR M+ L  RER I + R       
Sbjct: 180 QKDA-------LIDLIQTEDAALSIMDGLEIEDALTRCMAYLTERERFIVDQRYGLTDGQ 232

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           P ++  +  +  VSRERVRQI   A KK+   ++ 
Sbjct: 233 PKSMGVIGKQIGVSRERVRQILNIAMKKMTRQVRS 267


>gi|317969130|ref|ZP_07970520.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CB0205]
          Length = 309

 Score =  209 bits (532), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 78/296 (26%), Positives = 142/296 (47%), Gaps = 32/296 (10%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAK------RYREHGDLSA---------------AHR 52
             +S Y+  I ++P+L   EE  L        R  E     A                 R
Sbjct: 18  DPISWYLSTIGRVPLLTPAEEIELGNQVQAMMRLAEEDKGEAYTTHEKKIMRVGKRSKER 77

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ ++LRLVV +A  Y+G GL + +++ EG++GL +AV+KFDP RG++ +TY+ WWI+ +
Sbjct: 78  MMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWWIRQS 137

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           M   I      +++    +++     L  ++     +            IA+++++   E
Sbjct: 138 MTRAIACQSRTIRLPVHLSER-----LTAIRKVSLELAHKLGAMPSRKEIAEEMDMPLDE 192

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           + S+  +     SL+A +N  +  S  +   L+ D    E   +++ ER   +  L R +
Sbjct: 193 LDSLLRQALTTSSLDAPVNGEEGRS--FLGDLIADQSNSE--PLDQVERGIHQEQLGRWL 248

Query: 233 SVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           + L  +ER++ E R     E   TL  +    EVSRERVRQ+E +A +K++   ++
Sbjct: 249 THLTDQERQVLELRFGLEGEERHTLAEIGRMLEVSRERVRQVELKALRKLRHLTRR 304


>gi|186685842|ref|YP_001869038.1| RNA polymerase sigma factor SigD [Nostoc punctiforme PCC 73102]
 gi|186468294|gb|ACC84095.1| RNA polymerase, sigma 70 subunit, RpoD family [Nostoc punctiforme
           PCC 73102]
          Length = 332

 Score =  209 bits (532), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 70/329 (21%), Positives = 135/329 (41%), Gaps = 52/329 (15%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------- 43
           M         +  Y+ EI ++P+L  +EE    K+ +                       
Sbjct: 15  MKTAQTATDLVRTYLREIGRVPLLTHEEEIFYGKQVQRSCTLHESRESLATQLGRQPTLE 74

Query: 44  -----------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
                                 A  ++V ++LRLVV +A  Y    + + +++ EG+IG+
Sbjct: 75  EWAKATKLEPVELNEAIADGEIAKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGSIGM 134

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
            + V+KFDP +G+R +TY+ WWI+ A+   I      +++     +K     L ++K   
Sbjct: 135 QRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKARTIRLPIHITEK-----LNKIKKAQ 189

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           + ++    +      +A++L ++  +V     +     SL+  +   D   ++  + L  
Sbjct: 190 RQLSQKLGRAPTAGELAQELELTPKQVREYLEKARLPLSLD--LRLGDNYDTELGEMLED 247

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
                E+ +++     +    L R M  L P++R +   R        +TL  +     +
Sbjct: 248 PGASPEEFVMQSSLSYD----LDRLMGDLTPQQREVITLRFGLTDGQALTLAKIGEILNI 303

Query: 265 SRERVRQIEARAFKKVQESIQKQVELSSS 293
           SRERVRQIE  A  K+++S     E  +S
Sbjct: 304 SRERVRQIEREALTKLRKSKANMGEYLAS 332


>gi|148238489|ref|YP_001223876.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp. WH
           7803]
 gi|147847028|emb|CAK22579.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 7803]
          Length = 355

 Score =  209 bits (532), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 75/331 (22%), Positives = 141/331 (42%), Gaps = 55/331 (16%)

Query: 2   NRKNMSIIVNGEIGLSR-YIHEIRKIPMLEKQEEYVLAKRYREHGDLSA----------- 49
            +   S     ++ L R Y+ +I ++P+L  Q+E  L ++ +E  DL A           
Sbjct: 32  TKAMASRPSGTDVDLVRSYLRDIGRVPLLSHQQEITLGRQVQELMDLEATEAELQEKRGG 91

Query: 50  -----------------------------AHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
                                          R+V ++LRLVV +A  Y    + + +++ 
Sbjct: 92  EAVPAAELAKAAGLSAVQLKRKLQAGRRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQ 151

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           EG IGL++ V+KFDP RG++ +TY+ WWI+  +   I      +++     +      L 
Sbjct: 152 EGTIGLVRGVEKFDPTRGYKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITE-----MLN 206

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
           +LK   + ++ +  +   V  +A  + + E EV  + CR     SL   +   D + ++ 
Sbjct: 207 KLKKGQRELSQDLGRTPSVTELAAFVELPEDEVKELMCRARQPVSLEMKV--GDGDDTEL 264

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENL 258
            D L  D     ++  E+ E +  +  L   +  L   + R+   R     E+P++L  +
Sbjct: 265 LDLLAGDG----ELPSEQVEGECLKGDLRDLLGQLPELQERVLRMRYGMDGEDPMSLTGI 320

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
                +SR+RVR +E      ++  +  QVE
Sbjct: 321 GRVIGISRDRVRNLERDGLAGLRR-LSDQVE 350


>gi|148242803|ref|YP_001227960.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp.
           RCC307]
 gi|147851113|emb|CAK28607.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. RCC307]
          Length = 309

 Score =  209 bits (532), Expect = 4e-52,   Method: Composition-based stats.
 Identities = 77/298 (25%), Positives = 144/298 (48%), Gaps = 32/298 (10%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------EHGDLS---------------AA 50
           G   +S Y+  I ++P+L   EE  L  + +      E G+ +               + 
Sbjct: 16  GNDPVSWYLSSIGRVPLLTPAEEIELGNQVQTMMTLVEQGEEATYTAREKKLIRVGRRSK 75

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            R++ ++LRLVV +A  Y+G GL + +++ EG++GL +AV+KFDP RG++ +TY+ WWI+
Sbjct: 76  ERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAFWWIR 135

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            +M   I      +++    +++     L  ++     +            IA +L +  
Sbjct: 136 QSMTRAIACQSRTIRLPVHLSER-----LATVRKATMDLAHKLGAMPSRREIATELGMGL 190

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            E+  +  +     SL+A I S ++  S   + +    D + +  ++  ER+     L R
Sbjct: 191 EELDGLLRQALTTSSLDAPI-SGEEGRSFLGELIA---DPRNEEPLDAVERRMHHEQLGR 246

Query: 231 SMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +S L  +E+++ E R     E   TL  +    EVSRERVRQ+E +A +K++   ++
Sbjct: 247 WLSYLTAQEKQVLEMRFGLGGEQRHTLAEIGRLMEVSRERVRQVELKALRKLRNLTRR 304


>gi|320537364|ref|ZP_08037319.1| RNA polymerase sigma factor RpoD [Treponema phagedenis F0421]
 gi|320145829|gb|EFW37490.1| RNA polymerase sigma factor RpoD [Treponema phagedenis F0421]
          Length = 604

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 62/239 (25%), Positives = 112/239 (46%), Gaps = 12/239 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+KF+  +G++ +TY+ 
Sbjct: 364 KKAKDKLINANLRLVVSIAKKYTNRGLLFFDLVQEGNIGLIKAVEKFEYRKGYKFSTYAT 423

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      +++        +   + ++    + +     +      IA +L
Sbjct: 424 WWIRQAITRSISDQARTIRVPVH-----MIEQINKVARESRQLLQKLGRDPTDEEIATQL 478

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             +  +V  +        SL   I   ++  S   D++          + EK      R 
Sbjct: 479 CWTVEKVKQVKNVAREPISLETPI--GEEEDSSLGDFIPDTEIENPSNVTEKILL---RE 533

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +   +S L  RE  + + R   +     TLE +   F+V+RER+RQIEA+A ++++  
Sbjct: 534 EVQSVLSTLPSREHEVLKMRFGLDGDYSQTLEEVGLYFDVTRERIRQIEAKALRRLRHP 592


>gi|308061382|gb|ADO03270.1| RNA polymerase sigma factor RpoD [Helicobacter pylori Cuz20]
          Length = 672

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 70/237 (29%), Positives = 121/237 (51%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ W
Sbjct: 432 RAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATW 491

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WIK A+   I      ++I        +   + R+   ++     N K   +  +A+++ 
Sbjct: 492 WIKQAISRAIADQARTIRIPIH-----MIDTINRINKVMRKHIQENGKEPDLEVVAEEVG 546

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  
Sbjct: 547 LSLDKVKNVIKVTKEPISLETPVGNDDD--GKFGDFV---EDKNIVSSIDHIMREDLKAQ 601

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 602 IESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 658



 Score = 36.3 bits (83), Expect = 5.8,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 19/36 (52%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+  I +L K EE  L+K+ R   D+
Sbjct: 157 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDI 192


>gi|223889384|ref|ZP_03623970.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           64b]
 gi|223885070|gb|EEF56174.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           64b]
          Length = 631

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 67/257 (26%), Positives = 122/257 (47%), Gaps = 16/257 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 379 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 434

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RGF+ +TY+ WWI+ A+   I      +++        +   + RL    + +   
Sbjct: 435 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVH-----MIEQINRLNRETRYLIQV 489

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             K      ++ +L     +V ++        SL   I   ++  S   D++    D   
Sbjct: 490 LGKDPTDEELSDRLGWELKKVKTVKSVSREPVSLETPI--GEEEDSVLSDFI---EDKAI 544

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +           ++ +   +  L  RE+ + + R   E+   +TLE +   F V+RER+R
Sbjct: 545 KNPANHTSFVVLQDQIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIR 604

Query: 271 QIEARAFKKVQESIQKQ 287
           QIE++A ++++   + Q
Sbjct: 605 QIESKALRRLKNPKKTQ 621


>gi|6175927|gb|AAF05340.1|AF182105_2 RNA polymerase sigma subunit [Escherichia coli]
          Length = 313

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 75/264 (28%), Positives = 132/264 (50%), Gaps = 13/264 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL +AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLNRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKV 280
           ++  E  ++RERVRQI+    +++
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRL 313


>gi|56708122|ref|YP_170018.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis SCHU S4]
 gi|110670593|ref|YP_667150.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis FSC198]
 gi|224457213|ref|ZP_03665686.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|254370608|ref|ZP_04986613.1| DNA-directed RNA polymerase sigma subunit RpoD [Francisella
           tularensis subsp. tularensis FSC033]
 gi|254874922|ref|ZP_05247632.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|56604614|emb|CAG45668.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis SCHU S4]
 gi|110320926|emb|CAL09051.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis FSC198]
 gi|151568851|gb|EDN34505.1| DNA-directed RNA polymerase sigma subunit RpoD [Francisella
           tularensis subsp. tularensis FSC033]
 gi|254840921|gb|EET19357.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis MA00-2987]
 gi|282159323|gb|ADA78714.1| RNA polymerase sigma-70 factor [Francisella tularensis subsp.
           tularensis NE061598]
          Length = 577

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 64/242 (26%), Positives = 111/242 (45%), Gaps = 12/242 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   ++ ++LRLVV  A  Y   GL   +++ EGNIGLM+AV KFD  +GF+ +TY+ W
Sbjct: 338 QAKKEMIEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKGFKFSTYATW 397

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++            + R+K  +          E+++      N
Sbjct: 398 WIRQAITRSIADQARTIRVPVHM--IETINKVNRIKRQILQEKGREATEEEIIE--HTPN 453

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +++ ++  +        S+ + I   D   S   D++    D      IE    +N R  
Sbjct: 454 MTKEKLKKILNISHTPISMESPI--GDDEDSTVGDFI---EDKSNYSPIEAANLENLREA 508

Query: 228 LTRSMSV-LNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +   +   L  RE ++   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 509 IKELIETGLTEREAKVLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIEAKALRKLKHPS 568

Query: 285 QK 286
           + 
Sbjct: 569 RS 570


>gi|304320154|ref|YP_003853797.1| RNA polymerase sigma-70 factor family protein [Parvularcula
           bermudensis HTCC2503]
 gi|303299057|gb|ADM08656.1| RNA polymerase sigma-70 factor family protein [Parvularcula
           bermudensis HTCC2503]
          Length = 283

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 97/282 (34%), Positives = 173/282 (61%), Gaps = 5/282 (1%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++++ +  L   I +    P+L  +EE  L +R+ +  D  A  +L  +H+R+ V  A+ 
Sbjct: 1   MVIDNDEYLKATIRQAMSAPLLSIEEERSLMRRWVDDQDERALGKLTRAHMRMAVSTAIK 60

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           +RGYGLP+++++ EG IGL++A K+FDP+R  R  TY+ WWI+A+MQ+YILR+WS+V++G
Sbjct: 61  FRGYGLPLADLIQEGAIGLLEAAKRFDPDREVRFCTYAGWWIRASMQDYILRNWSIVRVG 120

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESL 186
           + +  K +FFNL R++  ++   D   +  ++ A A++ NVSES++  M  RL   D+SL
Sbjct: 121 SKSAHKTIFFNLSRIRSMIED-ADTAPRTARIKA-AERFNVSESDIEFMTSRLGRRDQSL 178

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           NA++  +D    + QD +  + +G + +     ++  R++ + +++  L+ RER I E R
Sbjct: 179 NAML--TDDGDIERQDLIPDEREGPDSLAEGTLDQARRKSWIGKALKTLSNRERMIIEHR 236

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
              E  +TL  L  +  +S+ERVRQIE +A  K++  +  + 
Sbjct: 237 FFTEEKMTLSRLGDDLSLSKERVRQIEKQAMGKLKACLAAEA 278


>gi|254416308|ref|ZP_05030062.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
 gi|196176990|gb|EDX72000.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
          Length = 416

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 68/242 (28%), Positives = 126/242 (52%), Gaps = 13/242 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L A   ++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV+KFDP +G+R +TY+ 
Sbjct: 175 LQAKEHMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTKGYRFSTYAY 234

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   I      +++     +K     L ++K   + I+    +   +  IAK+L
Sbjct: 235 WWIRQGITRAIATQSRTIRLPVHITEK-----LNKIKKAQRKISQEQGRTATIEDIAKEL 289

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V  +  R+    SL   I    +  ++  D L  +    E VL+ +  +++   
Sbjct: 290 EMDAPQVREVLMRVPRSVSLE--IKVGKEKDTELGDLLETEETSPEDVLMREALQRD--- 344

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L + ++ L  RER +   R      +P +L  +    E+SRERVRQIEA+A +K+++  
Sbjct: 345 -LQQLLADLTSRERDVICMRFGLGDGHPYSLAEIGRALELSRERVRQIEAKALQKLRQPK 403

Query: 285 QK 286
           ++
Sbjct: 404 RR 405


>gi|332678201|gb|AEE87330.1| RNA polymerase sigma factor RpoD [Francisella cf. novicida Fx1]
          Length = 577

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 64/242 (26%), Positives = 111/242 (45%), Gaps = 12/242 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   ++ ++LRLVV  A  Y   GL   +++ EGNIGLM+AV KFD  +GF+ +TY+ W
Sbjct: 338 QAKKEMIEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKGFKFSTYATW 397

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++            + R+K  +          E+++      N
Sbjct: 398 WIRQAITRSIADQARTIRVPVHM--IETINKVNRIKRQILQEKGREATEEEIIE--HTPN 453

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +++ ++  +        S+ + I   D   S   D++    D      IE    +N R  
Sbjct: 454 MTKEKLKKILNISHTPISMESPI--GDDEDSTVGDFI---EDKNNYSPIEAANLENLREA 508

Query: 228 LTRSMSV-LNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +   +   L  RE ++   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 509 IKELIETGLTEREAKVLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIEAKALRKLKHPS 568

Query: 285 QK 286
           + 
Sbjct: 569 RS 570


>gi|220907092|ref|YP_002482403.1| RNA polymerase sigma factor SigD [Cyanothece sp. PCC 7425]
 gi|219863703|gb|ACL44042.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7425]
          Length = 318

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 70/318 (22%), Positives = 138/318 (43%), Gaps = 52/318 (16%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------- 43
           M      +  +  Y+ EI ++P+L  ++E +  K+ ++                      
Sbjct: 1   MKTAETSKDLVRAYLREIGRVPLLTHEQEILYGKQVQQLAIVQQVREELSDRLGHEPDLT 60

Query: 44  -----------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
                            +    A  ++V ++LRLVV +A  Y    + + +++ EG IG+
Sbjct: 61  EWATAAKLSEAELQGVVNRGELAKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGTIGM 120

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
            + V+KFDP +G+R +TY+ WWI+ A+   I      +++     +K     L ++K   
Sbjct: 121 QRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKGRTIRLPIHITEK-----LNKIKKAQ 175

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           + ++    +   +  +A++L ++  +V     R     SL+  +   D   ++  + L  
Sbjct: 176 RQLSQQLGRAATIGELAQELELTPKQVREYLERSRQPLSLD--VRVGDNQDTELGELLED 233

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEV 264
                E    +   R +    L R M+ L P++R++   R   E+  P+TL  +     +
Sbjct: 234 TAASPEDFTSQASLRAD----LDRLMADLTPQQRQVLSLRFGLEDGQPLTLAKVGDMLNI 289

Query: 265 SRERVRQIEARAFKKVQE 282
           SRERVRQIE  A  K+++
Sbjct: 290 SRERVRQIEREALSKLRK 307


>gi|224534471|ref|ZP_03675047.1| RNA polymerase sigma factor RpoD [Borrelia spielmanii A14S]
 gi|224514148|gb|EEF84466.1| RNA polymerase sigma factor RpoD [Borrelia spielmanii A14S]
          Length = 631

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 67/257 (26%), Positives = 122/257 (47%), Gaps = 16/257 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 379 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 434

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RGF+ +TY+ WWI+ A+   I      +++        +   + RL    + +   
Sbjct: 435 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVH-----MIEQINRLNRETRYLIQV 489

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             K      ++ +L     +V ++        SL   I   ++  S   D++    D   
Sbjct: 490 LGKDPTDEELSDRLGWELKKVKTVKSVSREPVSLETPI--GEEEDSVLSDFI---EDKAI 544

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +           ++ +   +  L  RE+ + + R   E+   +TLE +   F V+RER+R
Sbjct: 545 KNPANHTSFVVLQDQIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIR 604

Query: 271 QIEARAFKKVQESIQKQ 287
           QIE++A ++++   + Q
Sbjct: 605 QIESKALRRLKNPKKTQ 621


>gi|171920395|ref|ZP_02931720.1| RNA polymerase sigma factor [Ureaplasma parvum serovar 1 str. ATCC
           27813]
 gi|183508771|ref|ZP_02958238.1| RNA polymerase sigma factor [Ureaplasma parvum serovar 14 str. ATCC
           33697]
 gi|186701631|ref|ZP_02971335.1| RNA polymerase sigma factor [Ureaplasma parvum serovar 6 str. ATCC
           27818]
 gi|171902833|gb|EDT49122.1| RNA polymerase sigma factor [Ureaplasma parvum serovar 1 str. ATCC
           27813]
 gi|182675710|gb|EDT87615.1| RNA polymerase sigma factor [Ureaplasma parvum serovar 14 str. ATCC
           33697]
 gi|186700864|gb|EDU19146.1| RNA polymerase sigma factor [Ureaplasma parvum serovar 6 str. ATCC
           27818]
          Length = 448

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 74/289 (25%), Positives = 136/289 (47%), Gaps = 23/289 (7%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSA----AHRLVTSHLRLVVKIAMGY 68
           + G+  Y+  + +  ML   EE   AK      D S      ++L TS++RLV  IA  Y
Sbjct: 154 DDGIKAYLGVLGESKMLRSDEETEYAKMVISD-DPSLVKIGKNQLYTSNMRLVTSIAKKY 212

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
              GL + +++ EG+ GL++A+ KFD E+G + +TY+ WWI+ ++   I      ++I  
Sbjct: 213 LNRGLDLEDLIQEGSSGLLKAIDKFDHEKGHKFSTYATWWIRQSITRAIADQARQIRIPV 272

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN---------VSESEVISMNCR 179
              +      L + + +L      +   E++     K++         ++  +V+ +   
Sbjct: 273 HMVE--TINKLTKAERNLIQELGRDPTAEEIAQAMNKVSQAKNQKEQLITAQKVVEIKKL 330

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
                SL+  I   ++  SQ+ D++  D     +   EK+   ++ N +     VLN  E
Sbjct: 331 NVDPVSLDKQIGHDEE--SQFSDFISDDEIISPEKYTEKKALNDQINEMFE--KVLNDNE 386

Query: 240 RRIFEARRLQ---ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           +R+ + R      E P TLE +     V+RER RQIE++A +K++   +
Sbjct: 387 QRVIKMRYGLLPFERPYTLEEVGEYLGVTRERARQIESKAIRKLKHPSK 435


>gi|307128696|ref|YP_003880726.1| RNA polymerase sigma factor rpoD [Candidatus Sulcia muelleri CARI]
 gi|306483158|gb|ADM90028.1| RNA polymerase sigma factor rpoD [Candidatus Sulcia muelleri CARI]
          Length = 288

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 78/275 (28%), Positives = 143/275 (52%), Gaps = 11/275 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y++EI KIP+L  +EE   AK  R+  ++ A + L+ ++LR VV +A  Y+  GL 
Sbjct: 17  SLDKYLYEIGKIPLLNNEEEIQFAKFARKTYNIKAINFLIKANLRFVVSVAKQYQNQGLN 76

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           +S++++EGN+GL++ + +FD  +GF+  +YS+WWI+ ++ + I      V+  T  N+  
Sbjct: 77  LSDLINEGNLGLIKGIFRFDERKGFKCISYSVWWIRQSILQAIADKSRCVRCPT--NKLA 134

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
            +  + +    L+ I      P  +  I + LN +E E+           SL+A I   +
Sbjct: 135 FYNKVNKKYSELEQIYQI---PPSIKQIGEYLNSNEKEIEEALKNSVKHTSLDAPII--E 189

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV- 253
             +S   D + YD      + +EKE     +  + R +  L+ +E +I       E+   
Sbjct: 190 GENSNLYDIIKYDESPHPDLDLEKESL---KKDIKRLLDTLSEKEAQIITLHYGLESSTI 246

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            LE +S    ++RER RQIE    +++++S +K +
Sbjct: 247 NLEEISFLLNLTRERCRQIEIYGLRRLKQSSRKNI 281


>gi|37522141|ref|NP_925518.1| RNA polymerase sigma factor RpoD [Gloeobacter violaceus PCC 7421]
 gi|35213141|dbj|BAC90513.1| principal RNA polymerase sigma factor [Gloeobacter violaceus PCC
           7421]
          Length = 400

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 66/239 (27%), Positives = 121/239 (50%), Gaps = 13/239 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  ++V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ 
Sbjct: 162 RRAKDKMVQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYAT 221

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      +++        L+  + R+K   + ++    +      IA ++
Sbjct: 222 WWIRQAITRAIADQSRTIRLPVH-----LYETISRIKKTTKLLSQELGRKPTEEEIATRM 276

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++  ++  +        SL   I    +  S+  D++  D +  E    +K  +   R 
Sbjct: 277 EMTIEKLRFIAKSAQLPISLETPI--GKEEDSRLGDFIEADGETPE----DKVAKNLLRE 330

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQES 283
            L   ++ L+PRER +   R   ++    TLE +   F V+RER+RQIEA+A +K++  
Sbjct: 331 DLEAVLNTLSPRERDVLRLRYGLDDGRMKTLEEIGQLFNVTRERIRQIEAKALRKLRHP 389



 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 10/32 (31%), Positives = 17/32 (53%)

Query: 12 GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE 43
           E  +  Y+ EI +I +L   EE  LA++  +
Sbjct: 59 TEDSIRVYLQEIGRIRLLRADEEIELARQIAD 90


>gi|219685543|ref|ZP_03540360.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia garinii
           Far04]
 gi|219672942|gb|EED29964.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia garinii
           Far04]
          Length = 631

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 67/257 (26%), Positives = 122/257 (47%), Gaps = 16/257 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 379 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 434

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RGF+ +TY+ WWI+ A+   I      +++        +   + RL    + +   
Sbjct: 435 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVH-----MIEQINRLNRETRYLVQV 489

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             K      ++ +L     +V ++        SL   I   ++  S   D++    D   
Sbjct: 490 LGKDPTDEELSDRLGWELKKVKTVKSVSREPVSLETPI--GEEEDSVLSDFI---EDKAI 544

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +           ++ +   +  L  RE+ + + R   E+   +TLE +   F V+RER+R
Sbjct: 545 KNPANHTSFVVLQDQIRSILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIR 604

Query: 271 QIEARAFKKVQESIQKQ 287
           QIE++A ++++   + Q
Sbjct: 605 QIESKALRRLKNPKKTQ 621


>gi|307151291|ref|YP_003886675.1| RpoD subfamily RNA polymerase sigma-70 factor [Cyanothece sp. PCC
           7822]
 gi|306981519|gb|ADN13400.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7822]
          Length = 318

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 75/318 (23%), Positives = 134/318 (42%), Gaps = 52/318 (16%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG-------------------- 45
           M    N    +  Y+ EI ++P+L  +EE VLAKR +                       
Sbjct: 1   MKTAKNPTDPVRAYLREIGRVPLLTHEEEIVLAKRVQRSMALQEIKDTLTKNLSREPLEH 60

Query: 46  -------------------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
                                +A  ++V ++LRLVV +A  Y    L + +++ EG IG+
Sbjct: 61  EWAEAAKISEEELRRTMAAGKAAKEKMVEANLRLVVSVAKKYLKRNLDLLDLIQEGTIGM 120

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
            + V+KFDP +G+R +TY+ WWI+ A+   I      +++     +K     L ++K   
Sbjct: 121 QRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEK-----LNKIKKAQ 175

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           + +     +   +  +A++L ++  +V     R     SL+  +   D   ++  + L  
Sbjct: 176 RQLAQKQGRAATISELAQELELTPRQVREYLERARQPLSLD--LRVGDNQDTELGELLED 233

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
                E        + +    L + MS L P++R +   R       P+TL  +     +
Sbjct: 234 TGTSPEDYATHSSLQLD----LEKLMSDLTPQQREVLALRFGLVDGQPLTLAKIGVRLNI 289

Query: 265 SRERVRQIEARAFKKVQE 282
           SRERVRQIE  A  K+++
Sbjct: 290 SRERVRQIEREALSKLRK 307


>gi|227549119|ref|ZP_03979168.1| RNA polymerase sigma factor SigB [Corynebacterium lipophiloflavum
           DSM 44291]
 gi|227078816|gb|EEI16779.1| RNA polymerase sigma factor SigB [Corynebacterium lipophiloflavum
           DSM 44291]
          Length = 331

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 68/309 (22%), Positives = 137/309 (44%), Gaps = 39/309 (12%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------------------- 42
           +R+N +        +  Y++ I K  +L+  EE  LA+R                     
Sbjct: 20  SRRNQTNDNPSADLVRVYLNGIGKTALLDAAEEVELAQRIEVGLYAQFLLDDPDTKLTRA 79

Query: 43  --------EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                         A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD
Sbjct: 80  KKRDLKILAKQGRRARSHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFD 139

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +GF+ +TY+ WWI+ A+   +      +++     ++     L R++  +        
Sbjct: 140 YAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLSRIRREMYQSLGREP 197

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
             E    ++ +  + ES++  +  +     SL+  + + ++  +   D++    D +   
Sbjct: 198 TNE---ELSDESGIEESKIEMLLRQSRDPVSLDMPVGADEE--APLGDFI---EDAEATD 249

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
             +      R + +   +  L  RE+ +   R   ++  P TL+ +  +F +SRERVRQI
Sbjct: 250 AEDAVVSSLRHDDIQDIIGGLEQREQDVIRLRYGLDDGVPRTLDQIGRQFGLSRERVRQI 309

Query: 273 EARAFKKVQ 281
           E     K++
Sbjct: 310 EREVMAKLR 318


>gi|6175921|gb|AAF05336.1|AF182103_2 RNA polymerase sigma subunit [Escherichia coli]
          Length = 313

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 75/264 (28%), Positives = 133/264 (50%), Gaps = 13/264 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLPAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQIEARAFKKV 280
           ++  E  ++RERVRQI+    +++
Sbjct: 290 DVGREIGLTRERVRQIQVEGLRRL 313


>gi|240142885|ref|YP_002967398.1| putative RNA polymerase, sigma 70 (sigma D) factor
           [Methylobacterium extorquens AM1]
 gi|240012832|gb|ACS44057.1| putative RNA polymerase, sigma 70 (sigma D) factor
           [Methylobacterium extorquens AM1]
          Length = 531

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 68/241 (28%), Positives = 122/241 (50%), Gaps = 13/241 (5%)

Query: 44  HGD-LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           HGD   A   LVTS+LRLV  +A  Y    LPI ++V EGNIGLM+A++KFD  RG++ +
Sbjct: 285 HGDLRKARDTLVTSNLRLVFSVAKKYTNRPLPILDLVQEGNIGLMRAIEKFDYRRGWKFS 344

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++WWIK ++   I      +++    ++K     + R    L+A       P     +
Sbjct: 345 TYAIWWIKQSISRSIADHGRTIRLPVHLHEKAA--KIDRTAARLRAELGRPPSPP---EL 399

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+ L++   +V  +        SL+  +   +    ++ D +    D +    +   +  
Sbjct: 400 AQALDIDVRQVERLMNMSRETVSLDLPV--GEDGDVRFGDLV---EDEKAPDPVGLADLA 454

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++ ++ ++  L  RE+ I   R      + +TLE +   F +SRERVRQ+E++A +++
Sbjct: 455 KLKDAVSDAVGDLPEREQTIIRMRFGIGYADQMTLEEIGQHFRISRERVRQVESKAIQRL 514

Query: 281 Q 281
           +
Sbjct: 515 R 515



 Score = 39.0 bits (90), Expect = 0.97,   Method: Composition-based stats.
 Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 6/53 (11%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
             LS Y  EI +  +L ++EE  LAKR       +A   L  S + L   +A 
Sbjct: 58  DALSFYAREIGRHRVLTREEEVALAKRV-----EAARLSLFASFVAL-GSMAR 104


>gi|300312263|ref|YP_003776355.1| RNA polymerase sigma S (sigma38) factor protein [Herbaspirillum
           seropedicae SmR1]
 gi|300075048|gb|ADJ64447.1| RNA polymerase sigma S (sigma38) factor protein [Herbaspirillum
           seropedicae SmR1]
          Length = 337

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 74/272 (27%), Positives = 134/272 (49%), Gaps = 11/272 (4%)

Query: 17  SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
             Y+++I   P+L   EE   A + +  G+  A  +++  +LRLVV IA  Y   G+ + 
Sbjct: 66  QHYLNKIGAKPLLTAAEELHFATQAK-AGEFVARQKMIEHNLRLVVSIAKHYINRGVALL 124

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++ EGN+GLM+A+ KF+PERGFR +TY+ WWI+ +++  I+     V++       R  
Sbjct: 125 DLIEEGNLGLMRAIDKFEPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHM--VREL 182

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
             + R K HL+A    + +      IA  ++    EV  +        SL+  +   +  
Sbjct: 183 NQILRAKYHLEA-QQRDGRDASAEDIAHLVDRPVEEVQDVLALSEHAASLDTPL--DNDP 239

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVT 254
            +   D L       E+    + E +    ++   +  L+ ++R +   R     ++P T
Sbjct: 240 QASLMDLLP---SAVEEHPDTRAESQEMAVLIREWLKSLSEKQRVVVARRFGLDNDDPST 296

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE L+SE  ++RERVRQ++  A  K++  +  
Sbjct: 297 LEQLASEMGITRERVRQVQQEALIKLKRLLTS 328


>gi|83721572|ref|YP_442747.1| RNA polymerase sigma factor RpoS [Burkholderia thailandensis E264]
 gi|167581696|ref|ZP_02374570.1| RNA polymerase sigma factor RpoS [Burkholderia thailandensis TXDOH]
 gi|167619812|ref|ZP_02388443.1| RNA polymerase sigma factor RpoS [Burkholderia thailandensis Bt4]
 gi|257138958|ref|ZP_05587220.1| RNA polymerase sigma factor RpoS [Burkholderia thailandensis E264]
 gi|83655397|gb|ABC39460.1| RpoS [Burkholderia thailandensis E264]
          Length = 363

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 78/280 (27%), Positives = 130/280 (46%), Gaps = 15/280 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+
Sbjct: 83  DTIQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGV 141

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++       
Sbjct: 142 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV--I 199

Query: 134 RLFFNLRRLKGHLQA-----ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           R    + R K HL+            +   +  IA     +  EV  +        SL+A
Sbjct: 200 RELNQVLRAKRHLEKNSLSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDA 259

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +      +S   D L  D        ++  E +    +    +S L+ + R + E R  
Sbjct: 260 PL--DLDPASSLLDLLPDDQSQSPDAEVQHRELE---TLTRAWLSRLSDKHRHVIERRFG 314

Query: 249 QE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                P TLE L+ E  ++RERVRQI+  A  +++     
Sbjct: 315 LNHIEPATLEELADEMGLTRERVRQIQQEALVRLKRFFAS 354


>gi|328676046|gb|AEB28721.1| RNA polymerase sigma factor RpoD [Francisella cf. novicida 3523]
          Length = 577

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 64/242 (26%), Positives = 111/242 (45%), Gaps = 12/242 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   ++ ++LRLVV  A  Y   GL   +++ EGNIGLM+AV KFD  +GF+ +TY+ W
Sbjct: 338 QAKKEMIEANLRLVVSEAKKYTNRGLHFLDIIQEGNIGLMKAVDKFDYRKGFKFSTYATW 397

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++            + R+K  +          E+++      N
Sbjct: 398 WIRQAITRSIADQARTIRVPVHM--IETINKVNRIKRQILQEKGREATEEEIIE--HTPN 453

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +++ ++  +        S+ + I   D   S   D++    D      IE    +N R  
Sbjct: 454 MTKEKLKKILNISHTPISMESPI--GDDEDSTVGDFI---EDKNNYSPIEAANLENLREA 508

Query: 228 LTRSMSV-LNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +   +   L  RE ++   R         TLE +  +F V+RER+RQIEA+A +K++   
Sbjct: 509 IKELIETGLTEREAKVLMMRFGIGMNTDHTLEEVGKQFNVTRERIRQIEAKALRKLKHPS 568

Query: 285 QK 286
           + 
Sbjct: 569 RS 570


>gi|319941926|ref|ZP_08016247.1| hypothetical protein HMPREF9464_01466 [Sutterella wadsworthensis
           3_1_45B]
 gi|319804579|gb|EFW01449.1| hypothetical protein HMPREF9464_01466 [Sutterella wadsworthensis
           3_1_45B]
          Length = 779

 Score =  209 bits (532), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 64/255 (25%), Positives = 130/255 (50%), Gaps = 12/255 (4%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L +Q E   A +  +   + A  +++ ++LRLV+ IA GY   GL +++++ EGN+GLM+
Sbjct: 521 LSEQRELGRAMKLAQTNLMQAKAKMIEANLRLVISIAKGYVNRGLAMTDLIQEGNLGLMK 580

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           AV KF+  RG++ +TY+ WW++ ++   +    + ++I     +        +L+   Q 
Sbjct: 581 AVDKFEYRRGYKFSTYATWWVRQSVTRAVADFGNTIRIPVHMTES-----YNKLRRQKQK 635

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
               + +      +A+  ++   +V  +   + G ES++A I   D+  +   D++  + 
Sbjct: 636 FLQQHGRQPTEQELAELADLPLQKVNLLTQAMRGVESIDAPI--GDEEDATKLDFVRGNE 693

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSR 266
                V  +    ++  + + +S++ LNPRE ++   R         TLE +     ++R
Sbjct: 694 RDDPGVAFQD---RSMIDCIQKSLNELNPREAQVLRLRYGIGTNQDHTLEEVGRTLGLTR 750

Query: 267 ERVRQIEARAFKKVQ 281
           ERVRQIE+ A +K++
Sbjct: 751 ERVRQIESAAIRKLR 765


>gi|218249968|ref|YP_002375211.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           ZS7]
 gi|218165156|gb|ACK75217.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           ZS7]
          Length = 631

 Score =  208 bits (531), Expect = 5e-52,   Method: Composition-based stats.
 Identities = 67/257 (26%), Positives = 122/257 (47%), Gaps = 16/257 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 379 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 434

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RGF+ +TY+ WWI+ A+   I      +++        +   + RL    + +   
Sbjct: 435 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVH-----MIEQINRLNRETRYLIQV 489

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             K      ++ +L     +V ++        SL   I   ++  S   D++    D   
Sbjct: 490 LGKDPTDEELSDRLGWELKKVKTVKSVSREPVSLETPI--GEEEDSVLSDFI---EDKAI 544

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +           ++ +   +  L  RE+ + + R   E+   +TLE +   F V+RER+R
Sbjct: 545 KNPANHTSFVVLQDQIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIR 604

Query: 271 QIEARAFKKVQESIQKQ 287
           QIE++A ++++   + Q
Sbjct: 605 QIESKALRRLKNPKKTQ 621


>gi|88802114|ref|ZP_01117642.1| RNA polymerase sigma-70 factor [Polaribacter irgensii 23-P]
 gi|88782772|gb|EAR13949.1| RNA polymerase sigma-70 factor [Polaribacter irgensii 23-P]
          Length = 287

 Score =  208 bits (531), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 71/276 (25%), Positives = 144/276 (52%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y  EI KI ++   EE  LA + +  GD  A   LV+++LR VV +A  Y+G GL 
Sbjct: 17  SLDKYFQEISKIGLITADEEVELALKIKV-GDSKALDALVSANLRFVVSVAKQYQGQGLK 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           +S++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + +     +V++    N+  
Sbjct: 76  LSDLINEGNLGLVKAAKRFDETRGFKFISYAVWWIRQSIMQALAEQSRIVRLP--LNKIG 133

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               ++++   L+    N  +      IAK+L+++E+EV           S++A     +
Sbjct: 134 SINKIKKIYARLEQ---NEQRMPTHKEIAKQLDMTEAEVEQSLKNSGRHVSMDAPFKEGE 190

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP-- 252
            ++            G       +   ++ +  + R++  L  +E ++ +      N   
Sbjct: 191 DSN-----LYNVLQSGDSPRPDSQLMAQSLKIEIERALGTLTYKEAKVIKMYYGIGNEAM 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +LE +  +F+++RERVRQ++ +A +++Q   + Q+
Sbjct: 246 ASLEEIGEKFDLTRERVRQVKQKAIRRLQSGSKTQM 281


>gi|168009564|ref|XP_001757475.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162691169|gb|EDQ77532.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 591

 Score =  208 bits (531), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 68/322 (21%), Positives = 139/322 (43%), Gaps = 53/322 (16%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--------------------- 45
            I       +  Y+ +I K  +L   EE  L+++ +                        
Sbjct: 267 QISQEPTDPVRAYLRDIGKTKLLTASEEVALSRKIQARDLLVLEKVKSDLQREIGREPSI 326

Query: 46  --------------------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
                                  +  ++V S+LRLVV I   Y+G G+ + +++ EG++G
Sbjct: 327 GEWSRAVGMEQNAFELRVKEGRYSKDKMVNSNLRLVVSIVKNYQGRGMTLPDLIQEGSMG 386

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++  +KFDP++GF+ +TY+ WWI+ A+   I     ++++        L+  + R+   
Sbjct: 387 LIRGAEKFDPDKGFKFSTYAHWWIRQAVTRAIADQSRIIRLPIH-----LYEVISRINKA 441

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            + +   + +  +   +A+ + +S  ++  +        S++ LI      S        
Sbjct: 442 KKMLIQEHGRQPRDEEVAELVGMSVEKLKFIVKSAKTPSSMDRLIGKEKDQSIGEMIA-- 499

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFE 263
              D   +   +   R+  +  +   +  LNPRER +   R   ++    TLE + + F+
Sbjct: 500 ---DKDVESPEDDLIRQVLKQDVDGVLCTLNPREREVLRLRFGLDDGQSRTLEEIGTLFK 556

Query: 264 VSRERVRQIEARAFKKVQESIQ 285
           V+RER+RQIEA+A +K+++  +
Sbjct: 557 VTRERIRQIEAKAMRKLRQPSR 578


>gi|224372659|ref|YP_002607031.1| RNA polymerase sigma factor RpoD [Nautilia profundicola AmH]
 gi|223588464|gb|ACM92200.1| rna polymerase sigma factor [Nautilia profundicola AmH]
          Length = 604

 Score =  208 bits (531), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 67/239 (28%), Positives = 118/239 (49%), Gaps = 13/239 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A  ++  ++LRLVV IA  Y   GLP  +++ EGNIGLM+A+ KF+ E+G++ +TY+ W
Sbjct: 364 EAKEKMARANLRLVVSIAKKYTNRGLPFLDLIQEGNIGLMKAIDKFEFEKGYKFSTYATW 423

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      V+I        +  N+ ++   ++       K   +  IAK++ 
Sbjct: 424 WIRQAISRAIADQARTVRIPIH-----MIENINQINKIVRKYVQEEGKEPSLEVIAKEMK 478

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +   +V  +        SL A +   ++   ++ D++    D       E+   ++ R  
Sbjct: 479 MPIEKVKQILKISKEPVSLEAPV--GEEEDGKFGDFI---EDKTFTNPYEEVVNEDLRKH 533

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +   +  LN RER + + R      ++  TLE +     V+RERVRQIE+ A KK++  
Sbjct: 534 IEEILEQLNERERAVIKMRFGLMPDKSERTLEEIGKALNVTRERVRQIESSAIKKLRHP 592



 Score = 37.5 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 9/31 (29%), Positives = 18/31 (58%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR 42
            +  +  Y+ E+  IP+L+K EE  + +R +
Sbjct: 96  SDSPVRMYLREMGHIPLLDKDEEIEIFRRIQ 126


>gi|159903877|ref|YP_001551221.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9211]
 gi|159889053|gb|ABX09267.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9211]
          Length = 313

 Score =  208 bits (531), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 76/302 (25%), Positives = 144/302 (47%), Gaps = 36/302 (11%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------EHGDLS----------------- 48
               +S Y+  I ++P+L   EE  L  + +      E G +                  
Sbjct: 16  SSDPISWYLSTIGRVPLLTPAEEIELGNQVQVMMNLTEDGSIDVKSEEFTSHQRRLIRIG 75

Query: 49  --AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  R++ ++LRLVV +A  Y+G GL + ++V EG++GL +AV+KFDP RG++ +TY+ 
Sbjct: 76  RRAKERMMKANLRLVVSVAKKYQGKGLELLDLVQEGSLGLERAVEKFDPTRGYKFSTYAF 135

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ +M   I      +++    +++     +R++   L               +A+ +
Sbjct: 136 WWIRQSMTRAIACQSRTIRLPVHLSER--LATIRKISSDL---AHKLGAMPSRAELAEAM 190

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   E+ S+  +     SL+A +N  D   S   D +    D   +  ++K E++  + 
Sbjct: 191 EIDAEELDSILRQALTTSSLDAPVN-GDDGRSFLGDLIA---DSSLEEPLDKVEQRIHQE 246

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L R ++ L+ +E+ + + R   E     TL  +    +VSRERVRQ+E ++ +K++   
Sbjct: 247 QLGRWLTHLSEQEQHVLKLRFGLEGNERHTLAEIGRLLQVSRERVRQVELKSLRKLRNLT 306

Query: 285 QK 286
           +K
Sbjct: 307 RK 308


>gi|195941530|ref|ZP_03086912.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi 80a]
          Length = 631

 Score =  208 bits (531), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 67/257 (26%), Positives = 122/257 (47%), Gaps = 16/257 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 379 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 434

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RGF+ +TY+ WWI+ A+   I      +++        +   + RL    + +   
Sbjct: 435 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVH-----MIEQINRLNRETRYLIQV 489

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             K      ++ +L     +V ++        SL   I   ++  S   D++    D   
Sbjct: 490 LGKDPTDEELSDRLGWELKKVKTVKSVSREPVSLETPI--GEEEDSVLSDFI---EDKAI 544

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +           ++ +   +  L  RE+ + + R   E+   +TLE +   F V+RER+R
Sbjct: 545 KNPANHTSFVVLQDQIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIR 604

Query: 271 QIEARAFKKVQESIQKQ 287
           QIE++A ++++   + Q
Sbjct: 605 QIESKALRRLKNPKKTQ 621


>gi|254821657|ref|ZP_05226658.1| RNA polymerase sigma factor SigB [Mycobacterium intracellulare ATCC
           13950]
          Length = 319

 Score =  208 bits (531), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 69/311 (22%), Positives = 134/311 (43%), Gaps = 38/311 (12%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREH--------------- 44
           ++         +  Y++ I K  +L    E  LAKR     Y EH               
Sbjct: 12  DLDAQSPAADLVRVYLNGIGKTALLNAAGEVELAKRIEAGLYAEHLLETRKRLGENRKRD 71

Query: 45  ------GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
                    +A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +G
Sbjct: 72  LEAVVRDGKAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKG 131

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           F+ +TY+ WWI+ A+   +      +++     ++     L R+K  +     N  +   
Sbjct: 132 FKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLARIKREMHQ---NLGREAT 186

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              +A +  +   ++  +        SL+  + S ++  +   D++    D +       
Sbjct: 187 DEELAAESGIPVDKINDLLEHSRDPVSLDMPVGSEEE--APLGDFI---EDAEAMSAENA 241

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARA 276
              +     +   ++ L+ RE ++   R   ++  P TL+ +   F +SRERVRQIE   
Sbjct: 242 VIAELLHTDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDV 301

Query: 277 FKKVQESIQKQ 287
             K++   +  
Sbjct: 302 MSKLRNGERAD 312


>gi|168009782|ref|XP_001757584.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162691278|gb|EDQ77641.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 583

 Score =  208 bits (531), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 68/321 (21%), Positives = 139/321 (43%), Gaps = 51/321 (15%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------- 43
           K + I+      +  Y+ +I++  +L   EE  L+++ ++                    
Sbjct: 259 KKLQIMRTPSDPIRSYLRDIKRTKLLSASEEVALSRKIQDILKLEKIRAELQRDIGREPT 318

Query: 44  -------------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
                                  SA  +LV S+LRLVV I   Y+G G+ + +++ EG++
Sbjct: 319 LSEWSQAVSLDQTSLELRVKEGRSAKDKLVNSNLRLVVSIVKNYQGRGMTLPDLIQEGSL 378

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++  +KFDPE G++ +TY+ WWI+ A+   I     ++++     +      + R+  
Sbjct: 379 GLIRGAEKFDPEMGYKFSTYATWWIRQAVTRAIADQSRIIRLPVHIYEV-----ISRINK 433

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
               I+    +  +   +A  + +S  +++ +        S++  I    + S    + +
Sbjct: 434 AKMTISQELGRQPRDEEVAAMVGMSVEKLLFIVKSARPPTSMDRPIGKDGEQS--LGEMV 491

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEF 262
                G  +   +    +  +  +   +  LNP ER +   R        +TL++L   F
Sbjct: 492 ADKGVGSPE---DDIMTQVLKQDIEDVLRSLNPMEREVLRLRFGLSGAQSMTLKDLGIIF 548

Query: 263 EVSRERVRQIEARAFKKVQES 283
           +V+RER+RQIEA+A +K++  
Sbjct: 549 KVTRERIRQIEAKALRKLRHP 569


>gi|156742838|ref|YP_001432967.1| RpoD family RNA polymerase sigma factor [Roseiflexus castenholzii
           DSM 13941]
 gi|156234166|gb|ABU58949.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus
           castenholzii DSM 13941]
          Length = 351

 Score =  208 bits (531), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 78/299 (26%), Positives = 127/299 (42%), Gaps = 38/299 (12%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD-------------------------- 46
           +     Y+ EI ++ +L   EE  LA       +                          
Sbjct: 52  DDSTQMYLREIGQVSLLSAAEEVALANDISAGREAQERLNVQHFDSVDERLLLERRVVQA 111

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  RL+ ++LRLVV +A  Y G  L   ++V EGNIGLM+AV+KFD  +G R +TY+ 
Sbjct: 112 EEARRRLIQANLRLVVSVAKKYIGGPLSFMDLVQEGNIGLMRAVEKFDASKGNRFSTYAT 171

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I     L+++    +   +   +RR+   L+   +       +  IA+ +
Sbjct: 172 WWIRQAITRAIAEQSRLIRLPVHLS--DVIAQVRRVARRLEQSLERE---PTIKEIAEAV 226

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E +V  +    A   SL   I +      Q  + L  D        +E   +   + 
Sbjct: 227 GMPERKVKMLLQASAQPISLEQPITN--DGEGQIGELLADDG---ADAPMEIATQHMLQR 281

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            L +++  L  RER +   R         TLE + S F ++RER RQIEA A + ++  
Sbjct: 282 DLEQALMDLPDRERAVLRLRYGLTDGRRRTLEEIGSAFGITRERTRQIEADALRLLRRP 340


>gi|315586085|gb|ADU40466.1| DNA-directed RNA polymerase sigma subunit RpoD [Helicobacter pylori
           35A]
          Length = 680

 Score =  208 bits (531), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 70/237 (29%), Positives = 121/237 (51%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ W
Sbjct: 440 RAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATW 499

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WIK A+   I      ++I        +   + R+   ++     N K   +  +A+++ 
Sbjct: 500 WIKQAISRAIADQARTIRIPIH-----MIDTINRINKVMRKHIQENGKEPDLEVVAEEVG 554

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  
Sbjct: 555 LSLDKVKNVIKVTKEPISLETPVGNDDD--GKFGDFV---EDKNIVSSIDHIMREDLKAQ 609

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 610 IESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 666



 Score = 36.3 bits (83), Expect = 6.0,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 19/36 (52%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+  I +L K EE  L+K+ R   D+
Sbjct: 165 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDI 200


>gi|284051429|ref|ZP_06381639.1| RNA polymerase sigma factor SigD [Arthrospira platensis str.
           Paraca]
          Length = 319

 Score =  208 bits (531), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 66/314 (21%), Positives = 135/314 (42%), Gaps = 52/314 (16%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------------- 43
            +    +  Y+ EI ++P+L  ++E +  K+ ++                          
Sbjct: 6   TSDTDSVRAYLREIGRVPLLTHEQEILYGKQVQQATLLQEKRNELAKQLGYEPTEAQWAE 65

Query: 44  -------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
                        H    A  ++V ++LRLVV +A  Y    + + +++ EG IG+ + V
Sbjct: 66  LVNLSVAQLQHILHQGQLAKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGTIGMQRGV 125

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +KFDP +G+R +TY+ WWI+ A+   I      +++     +K     L ++K   + + 
Sbjct: 126 EKFDPTKGYRFSTYAYWWIRQAITRAIAEKGRTIRLPIHITEK-----LNKIKKAQRQLA 180

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
               +   +  +A +L+++  ++     +     SL+  +   D   ++  D L    + 
Sbjct: 181 QQLGRAATMNELAAELDLTPKQIREYLEKSRLPLSLD--LRVGDNQDTELVDLLEDTTNS 238

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRER 268
            EQ  +    R +    L   M+ L  ++R++   R   ++   +TL  +     +SRER
Sbjct: 239 PEQFALNSSLRSD----LESLMTDLTDQQRQVLALRFGLDDGQTLTLAKIGDRLNISRER 294

Query: 269 VRQIEARAFKKVQE 282
           VRQIE  A  K+++
Sbjct: 295 VRQIEREALTKLRK 308


>gi|297379310|gb|ADI34197.1| RNA polymerase sigma factor RpoD [Helicobacter pylori v225d]
          Length = 677

 Score =  208 bits (531), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 70/237 (29%), Positives = 121/237 (51%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ W
Sbjct: 437 RAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATW 496

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WIK A+   I      ++I        +   + R+   ++     N K   +  +A+++ 
Sbjct: 497 WIKQAISRAIADQARTIRIPIH-----MIDTINRINKVMRKHIQENGKEPDLEVVAEEVG 551

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  
Sbjct: 552 LSLDKVKNVIKVTKEPISLETPVGNDDD--GKFGDFV---EDKNIVSSIDHIMREDLKAQ 606

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 607 IESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 663



 Score = 36.3 bits (83), Expect = 6.1,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 19/36 (52%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+  I +L K EE  L+K+ R   D+
Sbjct: 162 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDI 197


>gi|116071837|ref|ZP_01469105.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. BL107]
 gi|116065460|gb|EAU71218.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. BL107]
          Length = 284

 Score =  208 bits (531), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 78/284 (27%), Positives = 141/284 (49%), Gaps = 31/284 (10%)

Query: 20  IHEIRKIPMLEKQEEYVLA--------------------KRYREHGDLSAAHRLVTSHLR 59
           +  I ++P+L   EE  LA                    ++++      A  R++ ++LR
Sbjct: 1   MSSIGRVPLLTAAEEIELAHHVQDMKQLKELPQEELTSRQKHKIRMGKRARDRMMAANLR 60

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           LVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+  M   I  
Sbjct: 61  LVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQGMTRAIDN 120

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
           S   +++    ++K     L +++   + ++    +    + +A  + +   E+  +  +
Sbjct: 121 SARTIRLPIHISEK-----LSKMRRISRELSHRFGRQPNRLELASAMGIEPRELEDLITQ 175

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
            A   SL+A     +  S+  +  L+ D +G+E   +E  +R  ++  L   +S LN RE
Sbjct: 176 SAPCASLDAHARGEEDRSTLGE--LIPDPNGEE--PMEGMDRSIQKEHLGGWLSQLNERE 231

Query: 240 RRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++I   R     E P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 232 QKILRLRFGLGGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 275


>gi|312149387|gb|ADQ29458.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           N40]
          Length = 631

 Score =  208 bits (531), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 67/257 (26%), Positives = 122/257 (47%), Gaps = 16/257 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 379 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 434

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RGF+ +TY+ WWI+ A+   I      +++        +   + RL    + +   
Sbjct: 435 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVH-----MIEQINRLNRETRYLIQV 489

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             K      ++ +L     +V ++        SL   I   ++  S   D++    D   
Sbjct: 490 LGKDPTDEELSDRLGWELKKVKTVKSVSREPVSLETPI--GEEEDSVLSDFI---EDKAI 544

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +           ++ +   +  L  RE+ + + R   E+   +TLE +   F V+RER+R
Sbjct: 545 KNPANHTSFVVLQDQIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIR 604

Query: 271 QIEARAFKKVQESIQKQ 287
           QIE++A ++++   + Q
Sbjct: 605 QIESKALRRLKNPKKTQ 621


>gi|203284607|ref|YP_002222347.1| RNA polymerase sigma-70 factor [Borrelia duttonii Ly]
 gi|201084050|gb|ACH93641.1| RNA polymerase sigma-70 factor [Borrelia duttonii Ly]
          Length = 630

 Score =  208 bits (531), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 67/257 (26%), Positives = 124/257 (48%), Gaps = 16/257 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE +  K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 378 EEILKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 433

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RGF+ +TY+ WWI+ A+   I      +++        +   + RL    + +   
Sbjct: 434 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVH-----MIEQINRLNRETRYLVQV 488

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             K      ++ +L     +V ++        SL   I   ++  S   D++    D   
Sbjct: 489 LGKDPTDEELSIRLGWDLKKVKTVKNVSREPVSLETPI--GEEEDSVLSDFI---EDKAI 543

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +   +       ++ +   +  L  RE+ + + R   E+   +TLE +   F V+RER+R
Sbjct: 544 KNPAKHTSFVVLQDQIRAVLGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIR 603

Query: 271 QIEARAFKKVQESIQKQ 287
           QIE++A ++++   + Q
Sbjct: 604 QIESKALRRLKNPKKTQ 620



 Score = 37.9 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 43/251 (17%), Positives = 91/251 (36%), Gaps = 33/251 (13%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRL------VTSHLRLVVKI 64
           N E  +  Y+ EI K  +L   +E  LAK+  + G+    + L      + ++  LV  I
Sbjct: 135 NSEDPIRLYLKEIGKEFLLTGNQEVELAKQM-DSGESIIENILKNEGLVIENYYNLVNAI 193

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFD-PERGFRLATYSMWWIKAAMQE---YILRS 120
                       +   E +         FD   +  R+ ++    +K        Y+ R 
Sbjct: 194 YSRVDKEEFFKKDREREKD-------NNFDYYNKKKRITSFYKSLLKPFQDRLVKYVERK 246

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAI----TDNNLKPEQVVAIAKKLNVSESEVISM 176
             L ++G    ++ +     ++K  L++I     +  L  +  +  A K+   + +  S+
Sbjct: 247 HRLYELGEDIFEESITNERLQIKELLKSIPLYQEELRLFSDDYIDSASKIKDLKRQQKSI 306

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
             RL  D+  N  I   D    + ++ +    + +E ++         +  +T +   L 
Sbjct: 307 LDRLKIDKVRNLRILGRDLAIPEKRERIEKSLNIREDLI---------KEQITEA--QLA 355

Query: 237 PRERRIFEARR 247
            +E    E   
Sbjct: 356 QKELERIEMYY 366


>gi|295698783|ref|YP_003603438.1| RNA polymerase sigma factor RpoD [Candidatus Riesia pediculicola
           USDA]
 gi|291157386|gb|ADD79831.1| RNA polymerase sigma factor RpoD [Candidatus Riesia pediculicola
           USDA]
          Length = 607

 Score =  208 bits (531), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 63/230 (27%), Positives = 109/230 (47%), Gaps = 12/230 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 388 RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 447

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            L  +   +   T     PE    +++++
Sbjct: 448 WWIRQAITRSIADQARTIRIPVHM--IETINKLNHISRQILQETGREPSPE---ELSERM 502

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++  +        S+   I   D   S   D++    D   ++ +E    ++ R+
Sbjct: 503 LIPEEKIRKVLKIAREPISMETPI--GDDEDSHLGDFI---EDTTLELPLESATSESLRS 557

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEA 274
                +S L  RE ++   R   +     TLE +  +F+V+RER+RQIEA
Sbjct: 558 ATNEVLSGLTTREAKVLRMRFGIDMHTDHTLEEVGKQFDVTRERIRQIEA 607


>gi|167587040|ref|ZP_02379428.1| RNA polymerase sigma factor RpoS [Burkholderia ubonensis Bu]
          Length = 360

 Score =  208 bits (531), Expect = 6e-52,   Method: Composition-based stats.
 Identities = 78/280 (27%), Positives = 132/280 (47%), Gaps = 15/280 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+
Sbjct: 80  DTIQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGV 138

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++       
Sbjct: 139 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV--I 196

Query: 134 RLFFNLRRLKGHLQAITDN-----NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           R    + R K HL+  + +       +   +  IA     +  EV  +        SL+A
Sbjct: 197 RELNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDA 256

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +      +S   D L  D        ++  E +    +    +S L+ + R + E R  
Sbjct: 257 PL--DLDPASSLLDLLPDDQSQSPDAEVQHRELE---TLTRAWLSRLSDKHRHVIERRFG 311

Query: 249 QE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                P TLE L+ E  ++RERVRQI+  A  +++     
Sbjct: 312 LNHIEPATLEELADEMGLTRERVRQIQQEALVRLKRFFAS 351


>gi|322379076|ref|ZP_08053479.1| RNA polymerase sigma factor RpoD [Helicobacter suis HS1]
 gi|322379940|ref|ZP_08054217.1| RNA polymerase sigma factor RpoD [Helicobacter suis HS5]
 gi|321147638|gb|EFX42261.1| RNA polymerase sigma factor RpoD [Helicobacter suis HS5]
 gi|321148568|gb|EFX43065.1| RNA polymerase sigma factor RpoD [Helicobacter suis HS1]
          Length = 634

 Score =  208 bits (531), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 69/237 (29%), Positives = 120/237 (50%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A +++  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ E+ ++ +TY+ W
Sbjct: 394 RAKNKMARSNLRLVVSIAKRYTSRGLPFLDLIQEGNIGLMKAVDKFEHEKNYKFSTYATW 453

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WIK A+   I      ++I        +   + R+   ++     N K   +  +AK++ 
Sbjct: 454 WIKQAISRAIADQARTIRIPIH-----MIDTINRINKVMRKYMQENGKEPDLDLVAKEVG 508

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +   +V ++        SL + + + D    ++ D++    D      +E   R++ +  
Sbjct: 509 LPLDKVRNVIKITKEPISLESPVGNDDD--GKFGDFV---EDKNVVGSMEHIMREDLKAQ 563

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 564 IDGVLDQLNEREKSVIRMRFGLLEDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 620



 Score = 40.2 bits (93), Expect = 0.43,   Method: Composition-based stats.
 Identities = 11/40 (27%), Positives = 22/40 (55%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR 42
            K +      +  +  Y+ E+ +IP+L K+EE  L+K+ +
Sbjct: 110 EKELPEWSRSDSPVRMYLREMGEIPLLSKEEEVYLSKQIK 149


>gi|301064644|ref|ZP_07205038.1| RNA polymerase sigma factor RpoD [delta proteobacterium NaphS2]
 gi|300441264|gb|EFK05635.1| RNA polymerase sigma factor RpoD [delta proteobacterium NaphS2]
          Length = 590

 Score =  208 bits (531), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 64/241 (26%), Positives = 111/241 (46%), Gaps = 12/241 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   L+ ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ W
Sbjct: 350 RAKSELIQANLRLVVSIAKKYTNRGLMFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATW 409

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I        +   + +L    + +   + +      IA+K+ 
Sbjct: 410 WIRQAITRAIADQARTIRIPVH-----MIETINKLMRTSRYLVQEHGREPTSEEIAEKME 464

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
               +V  +        SL   I   ++  S   D++    D       +          
Sbjct: 465 FPLDKVRKVLKIAKEPISLETPI--GEEEDSHLGDFI---EDKNILSPGDAVVNFGLAEQ 519

Query: 228 LTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             + ++ L PRE ++   R         TLE +  +F V+RER+RQIEA+A +K++   +
Sbjct: 520 TRKVLTTLTPREEKVLRMRFGIGEKADHTLEEVGRDFSVTRERIRQIEAKALRKLRHPSR 579

Query: 286 K 286
            
Sbjct: 580 S 580



 Score = 40.2 bits (93), Expect = 0.36,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 2/54 (3%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
              +  Y+ E+ +I +L +  E  +AKR  E G+  A   L+T  +  V  I  
Sbjct: 98  SDPVKMYLKEMGRISLLTRDGEVEIAKRI-EAGEKEALEALLTCGIG-VEHIIK 149


>gi|254423226|ref|ZP_05036944.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
 gi|196190715|gb|EDX85679.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
          Length = 431

 Score =  208 bits (531), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 62/246 (25%), Positives = 130/246 (52%), Gaps = 13/246 (5%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           ++    A   ++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV+KFDP +G+R +
Sbjct: 186 QNEGTRAKEHMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTKGYRFS 245

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+  +   I      +++     +K     L ++K   + I+    +  +   I
Sbjct: 246 TYAYWWIRQGITRAIATQSRTIRLPVHITEK-----LNKIKKAQRKISQTQGRTAKAEDI 300

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           AK+L+++ +++  +  ++    SL+  +       ++  D L  +    E  L+    R+
Sbjct: 301 AKELDMTVAQIREVLLKVPRSVSLDTKV--GKDRDTELGDLLETEDISPEDRLM----RE 354

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + +  L + ++ L  RE+ +   R   ++  P +L  +    E+SRERVRQIE++A +K+
Sbjct: 355 SLKRELHQLLTDLTTREQEVITLRFGLDDGVPYSLAEIGRTLELSRERVRQIESKALQKL 414

Query: 281 QESIQK 286
           ++  ++
Sbjct: 415 RQPKRR 420



 Score = 37.1 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 12/33 (36%), Positives = 21/33 (63%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAH 51
           Y+ EI ++ +LE+ EE   A+R ++H +L A  
Sbjct: 80  YLQEIGRVSLLERDEEVAEAQRVQQHMELLALR 112


>gi|15595057|ref|NP_212846.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi B31]
 gi|216264471|ref|ZP_03436463.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           156a]
 gi|221217929|ref|ZP_03589396.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           72a]
 gi|225548954|ref|ZP_03769931.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi 94a]
 gi|225549892|ref|ZP_03770853.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi 118a]
 gi|226320452|ref|ZP_03796018.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi 29805]
 gi|226321409|ref|ZP_03796936.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi Bol26]
 gi|3915854|sp|P52323|RPOD_BORBU RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|2688647|gb|AAC67061.1| RNA polymerase sigma-70 factor (rpoD) [Borrelia burgdorferi B31]
 gi|215980944|gb|EEC21751.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           156a]
 gi|221192235|gb|EEE18455.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           72a]
 gi|225369351|gb|EEG98803.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi 118a]
 gi|225370557|gb|EEG99993.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi 94a]
 gi|226233205|gb|EEH31957.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi Bol26]
 gi|226234094|gb|EEH32809.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi 29805]
 gi|312148540|gb|ADQ31199.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia burgdorferi
           JD1]
          Length = 631

 Score =  208 bits (531), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 67/257 (26%), Positives = 122/257 (47%), Gaps = 16/257 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 379 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 434

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RGF+ +TY+ WWI+ A+   I      +++        +   + RL    + +   
Sbjct: 435 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVH-----MIEQINRLNRETRYLIQV 489

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             K      ++ +L     +V ++        SL   I   ++  S   D++    D   
Sbjct: 490 LGKDPTDEELSDRLGWELKKVKTVKSVSREPVSLETPI--GEEEDSVLSDFI---EDKAI 544

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +           ++ +   +  L  RE+ + + R   E+   +TLE +   F V+RER+R
Sbjct: 545 KNPANHTSFVVLQDQIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIR 604

Query: 271 QIEARAFKKVQESIQKQ 287
           QIE++A ++++   + Q
Sbjct: 605 QIESKALRRLKNPKKTQ 621


>gi|289553505|ref|ZP_06442715.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis KZN
           605]
 gi|289438137|gb|EFD20630.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis KZN
           605]
          Length = 338

 Score =  208 bits (531), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 69/312 (22%), Positives = 133/312 (42%), Gaps = 38/312 (12%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREH-------------- 44
            ++         +  Y++ I K  +L    E  LAKR     Y EH              
Sbjct: 30  SDLDAQSPAADLVRVYLNGIGKTALLNAAGEVELAKRIEAGLYAEHLLETRKRLGENRKR 89

Query: 45  -------GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
                     +A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +
Sbjct: 90  DLAAVVRDGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTK 149

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           GF+ +TY+ WWI+ A+   +      +++     ++     L R+K  +          E
Sbjct: 150 GFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLARIKREMHQHLGREATDE 207

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A +  +   ++  +        SL+  + S ++  +   D++    D +      
Sbjct: 208 ---ELAAESGIPIDKINDLLEHSRDPVSLDMPVGSEEE--APLGDFI---EDAEAMSAEN 259

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
               +     +   ++ L+ RE ++   R   ++  P TL+ +   F +SRERVRQIE  
Sbjct: 260 AVIAELLHTDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERD 319

Query: 276 AFKKVQESIQKQ 287
              K++   +  
Sbjct: 320 VMSKLRHGERAD 331


>gi|170078438|ref|YP_001735076.1| sigma factor [Synechococcus sp. PCC 7002]
 gi|169886107|gb|ACA99820.1| sigma factor [Synechococcus sp. PCC 7002]
          Length = 318

 Score =  208 bits (531), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 70/321 (21%), Positives = 137/321 (42%), Gaps = 52/321 (16%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGDLS------------ 48
             +  Y+ EI ++P+L  +EE + ++R +             E  D              
Sbjct: 9   DPVRTYLKEIGRVPLLTHEEEVLYSRRVQKMVNLEKLKAELAEKQDQEPSLKEWAQAANL 68

Query: 49  --------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                         A  ++V ++LRLVV +A  Y    + + +++ EG IG+ + V+KFD
Sbjct: 69  SQRELKKQLLLGKQAKQKMVEANLRLVVSVAKKYIKRNMDLLDLIQEGTIGMQRGVEKFD 128

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P +G+R +TY+ WWI+ A+   I      +++     +K     L ++K   + +   N 
Sbjct: 129 PTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEK-----LNKIKKAQRQLAQANG 183

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +   +  +A +L ++  +V     +     SL+  +   D N ++  + L  D    +  
Sbjct: 184 RSASIPELADELGLTTKQVRDYLEKSRQPLSLD--LRVGDNNDTELIELLEDDGLTPDDY 241

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQI 272
                 +++    L R ++ L  +++ +   R       P TL  +     +SRERVRQI
Sbjct: 242 ATHAALKRD----LARMLNDLTAQQQEVLTLRFGLRDGTPHTLAKIGEHLSISRERVRQI 297

Query: 273 EARAFKKVQESIQKQVELSSS 293
           E  A  K+++   +  E  +S
Sbjct: 298 EREALAKLRKRKAEMGEYLAS 318


>gi|219684458|ref|ZP_03539402.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia garinii PBr]
 gi|219672447|gb|EED29500.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia garinii PBr]
          Length = 631

 Score =  208 bits (531), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 67/257 (26%), Positives = 122/257 (47%), Gaps = 16/257 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 379 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 434

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RGF+ +TY+ WWI+ A+   I      +++        +   + RL    + +   
Sbjct: 435 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVH-----MIEQINRLNRETRYLVQV 489

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             K      ++ +L     +V ++        SL   I   ++  S   D++    D   
Sbjct: 490 LGKDPTDEELSDRLGWELKKVKTVKSVSREPVSLETPI--GEEEDSVLSDFI---EDKAI 544

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +           ++ +   +  L  RE+ + + R   E+   +TLE +   F V+RER+R
Sbjct: 545 KNPANHTSFVVLQDQIRSILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIR 604

Query: 271 QIEARAFKKVQESIQKQ 287
           QIE++A ++++   + Q
Sbjct: 605 QIESKALRRLKNPKKTQ 621


>gi|298490014|ref|YP_003720191.1| RpoD subfamily RNA polymerase sigma 70 subunit ['Nostoc azollae'
           0708]
 gi|298231932|gb|ADI63068.1| RNA polymerase, sigma 70 subunit, RpoD subfamily ['Nostoc azollae'
           0708]
          Length = 332

 Score =  208 bits (531), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 68/319 (21%), Positives = 132/319 (41%), Gaps = 52/319 (16%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------- 43
           M         +  Y+ EI ++P+L  +EE    K+ +                       
Sbjct: 15  MKTAQTATDLVRTYLREIGRVPLLTHEEEIHYGKQVQRCTTLYEVRENLATQLGYQPTLE 74

Query: 44  -----------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
                                 A  R+V ++LRLVV +A  Y    + + +++ EG+IG+
Sbjct: 75  EWAASAQVEPVELNTAIAEGEIAKRRMVEANLRLVVSVAKKYIKRNIDLLDLIQEGSIGM 134

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
            + V+KFDP +G+R +TY+ WWI+ A+   I      +++     +K     L ++K   
Sbjct: 135 QRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKARTIRLPIHITEK-----LNKIKKAQ 189

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           + ++    +    + +A +L ++  +V     +     SL+  +   D   ++  + L  
Sbjct: 190 RQLSQKLGRAPTAIELADELELTPRQVRECLEKARLPLSLD--LRLGDNYDTELGEMLED 247

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
                E  +I+     +    + R M  L P+++ + + R        +TL  +     +
Sbjct: 248 TGATPEDFVIQSSLSSD----IERLMKELTPQQKEVIKLRFGLIDGQALTLSKIGEILNI 303

Query: 265 SRERVRQIEARAFKKVQES 283
           SRERVRQIE  A  K+++S
Sbjct: 304 SRERVRQIEREALTKLRKS 322


>gi|261837545|gb|ACX97311.1| transcription initiation factor sigma-80 [Helicobacter pylori 51]
          Length = 684

 Score =  208 bits (531), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 70/237 (29%), Positives = 121/237 (51%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ W
Sbjct: 444 RAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATW 503

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WIK A+   I      ++I        +   + R+   ++     N K   +  +A+++ 
Sbjct: 504 WIKQAISRAIADQARTIRIPIH-----MIDTINRINKVMRKHIQENGKEPDLEVVAEEVG 558

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  
Sbjct: 559 LSLDKVKNVIKVTKEPISLETPVGNDDD--GKFGDFV---EDKNIVSSIDHIMREDLKAQ 613

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 614 IESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 670



 Score = 36.3 bits (83), Expect = 6.1,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 19/36 (52%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+  I +L K EE  L+K+ R   D+
Sbjct: 169 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDI 204


>gi|256371066|ref|YP_003108890.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidimicrobium
           ferrooxidans DSM 10331]
 gi|256007650|gb|ACU53217.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidimicrobium
           ferrooxidans DSM 10331]
          Length = 337

 Score =  208 bits (530), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 75/298 (25%), Positives = 134/298 (44%), Gaps = 37/298 (12%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD-------------------------L 47
           E  +  Y+ +I    +L K +E  L +R     D                          
Sbjct: 38  EDLVRLYLGDIGSHELLTKDDEAELGRRMDRARDAQRQLDAGVKEPARRAELEELVRQGE 97

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A    + ++LRLVV IA  Y+  GLP+ +++ EGN+GL+ AV+KFD  +GF+ +TY+ W
Sbjct: 98  EAKRAFIQANLRLVVSIAKRYQASGLPLLDLIQEGNMGLIHAVEKFDWRKGFKFSTYATW 157

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I  +   +++   A       +L R++     +     +   V  +A +++
Sbjct: 158 WIRQAITRGIANTGRTIRLPVHA-----GDSLSRVQRAQVQLEVRLGRAPTVRELAAEVD 212

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +   +++      A   SL+  +   D   ++  D +    D Q     +        + 
Sbjct: 213 LPYDKLVEALRFRAEPVSLSEPLR--DDGDAELGDVV---EDSQSATPFDVAAEHLLPSE 267

Query: 228 LTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           ++R ++ L+ RER I   R   +   P TLE +   F ++RER+RQIEARA  K++  
Sbjct: 268 VSRLLAPLDGREREILRLRYGLDRGEPRTLEEVGEYFHLTRERIRQIEARAMSKLRHP 325


>gi|153952229|ref|YP_001397920.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           doylei 269.97]
 gi|152939675|gb|ABS44416.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           doylei 269.97]
          Length = 622

 Score =  208 bits (530), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 71/239 (29%), Positives = 120/239 (50%), Gaps = 13/239 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV KF+ +RG++ +TY+ W
Sbjct: 380 EAKGRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDKFEYKRGYKFSTYATW 439

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I        +   + ++   ++     + K   V  IAK++ 
Sbjct: 440 WIRQAISRAIADQARTIRIPIH-----MIETINQINKIIREHLQKDGKEPNVSVIAKEVG 494

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V  +        SL A I   +++  ++ D++    D      I+   + + +  
Sbjct: 495 LSIDKVKQVIKITKEPISLEAPI--GNEDDGKFGDFV---EDRNSLSPIDHILKDDLKEQ 549

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++  
Sbjct: 550 IDEVLDQLNDREKAVIRMRFGLMDDESDRTLEEIGKELNVTRERVRQIESSAIKKLKHP 608


>gi|224532358|ref|ZP_03672988.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi WI91-23]
 gi|224512665|gb|EEF83036.1| RNA polymerase sigma factor RpoD [Borrelia burgdorferi WI91-23]
          Length = 631

 Score =  208 bits (530), Expect = 7e-52,   Method: Composition-based stats.
 Identities = 67/257 (26%), Positives = 122/257 (47%), Gaps = 16/257 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 379 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 434

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RGF+ +TY+ WWI+ A+   I      +++        +   + RL    + +   
Sbjct: 435 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVH-----MIEQINRLNRETRYLIQV 489

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             K      ++ +L     +V ++        SL   I   ++  S   D++    D   
Sbjct: 490 LGKDPTDEELSDRLGWELKKVKTVKSVSREPVSLETPI--GEEEDSVLSDFI---EDKAI 544

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +           ++ +   +  L  RE+ + + R   E+   +TLE +   F V+RER+R
Sbjct: 545 KNPANHTSFVVLQDQIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIR 604

Query: 271 QIEARAFKKVQESIQKQ 287
           QIE++A ++++   + Q
Sbjct: 605 QIESKALRRLKNPKKTQ 621


>gi|221198089|ref|ZP_03571135.1| RNA polymerase sigma factor RpoS [Burkholderia multivorans CGD2M]
 gi|221204352|ref|ZP_03577369.1| RNA polymerase sigma factor RpoS [Burkholderia multivorans CGD2]
 gi|221175209|gb|EEE07639.1| RNA polymerase sigma factor RpoS [Burkholderia multivorans CGD2]
 gi|221182021|gb|EEE14422.1| RNA polymerase sigma factor RpoS [Burkholderia multivorans CGD2M]
          Length = 338

 Score =  208 bits (530), Expect = 8e-52,   Method: Composition-based stats.
 Identities = 78/280 (27%), Positives = 132/280 (47%), Gaps = 15/280 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+
Sbjct: 58  DTIQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGV 116

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++       
Sbjct: 117 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV--I 174

Query: 134 RLFFNLRRLKGHLQAITDN-----NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           R    + R K HL+  + +       +   +  IA     +  EV  +        SL+A
Sbjct: 175 RELNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDA 234

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +      +S   D L  D        ++  E +    +    +S L+ + R + E R  
Sbjct: 235 PL--DLDPASSLLDLLPDDQSQSPDAEVQHRELE---TLTRAWLSRLSDKHRHVIERRFG 289

Query: 249 QE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                P TLE L+ E  ++RERVRQI+  A  +++     
Sbjct: 290 LNHIEPATLEELADEMGLTRERVRQIQQEALVRLKRFFAS 329


>gi|307824679|ref|ZP_07654903.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Methylobacter
           tundripaludum SV96]
 gi|307734333|gb|EFO05186.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Methylobacter
           tundripaludum SV96]
          Length = 342

 Score =  208 bits (530), Expect = 8e-52,   Method: Composition-based stats.
 Identities = 73/269 (27%), Positives = 134/269 (49%), Gaps = 13/269 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++E+ +  +L   +E +   R    GD +A   ++ S+LRLVVKI+  Y   GLP+ ++
Sbjct: 74  YLNELSRSQLLTADQEKIYGSRALL-GDEAARKIMIESNLRLVVKISRRYLNRGLPLLDL 132

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM AV+KFDPERGFR +TY+ WWI+  ++  I+     +++       +    
Sbjct: 133 IEEGNLGLMHAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHI--VKEMNT 190

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
             + + HL  + ++    E    IA+ L++  ++V  M        S++           
Sbjct: 191 YLKAQRHLSQLLEHEPNAED---IAEHLDIPVNKVEKMLKLNERVTSIDMPGGKDFDKP- 246

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
                +    DG+     EK +    ++ + + +  L+ ++R +   R         TLE
Sbjct: 247 ----LVESISDGESLSPAEKIQEDGIKHNIAKWVFQLSEKQREVICRRYGLCGYEGSTLE 302

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            ++ E  V+RERVRQI+    K+++E ++
Sbjct: 303 QVAQELGVTRERVRQIQMDGLKRMKEILE 331


>gi|158339245|ref|YP_001520422.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158309486|gb|ABW31103.1| RNA polymerase sigma-70 factor, putative [Acaryochloris marina
           MBIC11017]
          Length = 268

 Score =  208 bits (530), Expect = 8e-52,   Method: Composition-based stats.
 Identities = 72/275 (26%), Positives = 131/275 (47%), Gaps = 15/275 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ E+ + P+L  +EE  LA++ +  GDL A  R++  +LRLVV IA  ++  GL
Sbjct: 6   DSVQAYLKEMGRYPLLSHEEEIRLARQVK-AGDLKAKQRMIECNLRLVVSIAKKHQHLGL 64

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EG+IGL  AV KFD  +G + +TY+ WWI  A++  +      + I     ++
Sbjct: 65  PLMDLIQEGSIGLNTAVDKFDLAQGCKFSTYAYWWISEAIKRALKSQSRTIYIPIHQWER 124

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                  R+K  ++ +T    +   +  ++    +  S + +         SL+  +   
Sbjct: 125 AH-----RIKKAVRQLTQEKGRTPTLKELSAATGIKSSLIRNTLQSFQAVSSLDQPVGPE 179

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QEN 251
            K++       + D    E   +   +     + LTR M+ L  RER I + R       
Sbjct: 180 QKDA-------LIDLIQTEDAPLSIMDGLEIEDALTRCMAYLTERERFIVDQRYGLTDGQ 232

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           P ++  +  + ++SRERVRQI   A KK+   ++ 
Sbjct: 233 PKSMGAIGKQIDISRERVRQILNIAMKKMTRQVRS 267


>gi|183220954|ref|YP_001838950.1| RNA polymerase sigma factor RpoD [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Paris)']
 gi|189911049|ref|YP_001962604.1| DNA-directed RNA polymerase sigma sigma70/sigma32 subunit
           [Leptospira biflexa serovar Patoc strain 'Patoc 1
           (Ames)']
 gi|167775725|gb|ABZ94026.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Leptospira biflexa serovar Patoc strain 'Patoc 1
           (Ames)']
 gi|167779376|gb|ABZ97674.1| RNA polymerase sigma factor rpoD (Sigma-70) [Leptospira biflexa
           serovar Patoc strain 'Patoc 1 (Paris)']
          Length = 590

 Score =  208 bits (530), Expect = 8e-52,   Method: Composition-based stats.
 Identities = 58/242 (23%), Positives = 116/242 (47%), Gaps = 12/242 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   LV ++LRLVV IA  Y   G+   +++ EGNIGL++AV KF+ ++G++ +TY+ W
Sbjct: 352 QAKRELVRANLRLVVSIAKRYANRGMHFFDLIQEGNIGLIRAVDKFEYKKGYKFSTYATW 411

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++        +   + ++    +       +      IA++L 
Sbjct: 412 WIRQAITRAISDQARTIRVPVH-----MIEQVNKVIRETRLFVQEFGRDPSNDEIAERLG 466

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
               +V ++        SL   + S  +  S+  D++    D +    +           
Sbjct: 467 WPVQKVKAVKNVAREPISLEIPVGS--EEDSELGDFI---EDKEVISPLNSAASSILSEQ 521

Query: 228 LTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + + +  L  RE+++   R   ++    TLE +  +F+V+RER+RQIEA+A ++++   +
Sbjct: 522 IRQVLQTLPAREQKVIRMRFGLDDGYAQTLEEVGYQFKVTRERIRQIEAKALRRLRHPSR 581

Query: 286 KQ 287
            +
Sbjct: 582 SK 583


>gi|161524626|ref|YP_001579638.1| RNA polymerase sigma factor RpoS [Burkholderia multivorans ATCC
           17616]
 gi|189350618|ref|YP_001946246.1| RNA polymerase sigma factor RpoS [Burkholderia multivorans ATCC
           17616]
 gi|221212761|ref|ZP_03585737.1| RNA polymerase sigma factor RpoS [Burkholderia multivorans CGD1]
 gi|160342055|gb|ABX15141.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia multivorans
           ATCC 17616]
 gi|189334640|dbj|BAG43710.1| RNA polymerase sigma factor RpoS [Burkholderia multivorans ATCC
           17616]
 gi|221166974|gb|EED99444.1| RNA polymerase sigma factor RpoS [Burkholderia multivorans CGD1]
          Length = 361

 Score =  208 bits (530), Expect = 8e-52,   Method: Composition-based stats.
 Identities = 78/280 (27%), Positives = 132/280 (47%), Gaps = 15/280 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+
Sbjct: 81  DTIQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGV 139

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++       
Sbjct: 140 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV--I 197

Query: 134 RLFFNLRRLKGHLQAITDN-----NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           R    + R K HL+  + +       +   +  IA     +  EV  +        SL+A
Sbjct: 198 RELNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDA 257

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +      +S   D L  D        ++  E +    +    +S L+ + R + E R  
Sbjct: 258 PL--DLDPASSLLDLLPDDQSQSPDAEVQHRELE---TLTRAWLSRLSDKHRHVIERRFG 312

Query: 249 QE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                P TLE L+ E  ++RERVRQI+  A  +++     
Sbjct: 313 LNHIEPATLEELADEMGLTRERVRQIQQEALVRLKRFFAS 352


>gi|291280296|ref|YP_003497131.1| DNA-directed RNA polymerase sigma 70 factor [Deferribacter
           desulfuricans SSM1]
 gi|290754998|dbj|BAI81375.1| DNA-directed RNA polymerase sigma 70 factor [Deferribacter
           desulfuricans SSM1]
          Length = 313

 Score =  208 bits (530), Expect = 8e-52,   Method: Composition-based stats.
 Identities = 81/266 (30%), Positives = 136/266 (51%), Gaps = 14/266 (5%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
            E GL  Y++ I +   L ++EEY L KR ++ GD  A  +LV S+L+ VV IA  Y+  
Sbjct: 41  SEDGLKNYLNRISQFQPLSREEEYELGKRIQQ-GDKKALEKLVLSNLKFVVSIANRYKNT 99

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GLP+++++++GN+GL++A K+FDPERG +  +Y++WWI+ A+ + +      VK+     
Sbjct: 100 GLPLADIINQGNLGLLEAAKRFDPERGVKFISYAVWWIRQAIIQALAEQSGTVKLPLKQA 159

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
                  L ++   ++ ++    +      IA  L++  +++ ++        SL A I 
Sbjct: 160 SI-----LYKINEAIEVLSKELGREPTPDEIAVYLDMDPADIENVLRVSRNYLSLEAPIK 214

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--Q 249
             D     + D L       E+ +     + N   ++      LN RE +I + R     
Sbjct: 215 --DGEDRAFIDLLESGGKSVEEEIFLNTLKANIEEIVDE----LNEREAQIIKWRFGLEG 268

Query: 250 ENPVTLENLSSEFEVSRERVRQIEAR 275
           E P TLE +     +SRERVRQIEAR
Sbjct: 269 ETPKTLEEIGEILNISRERVRQIEAR 294


>gi|283954552|ref|ZP_06372071.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 414]
 gi|283793956|gb|EFC32706.1| RNA polymerase sigma factor RpoD [Campylobacter jejuni subsp.
           jejuni 414]
          Length = 622

 Score =  208 bits (530), Expect = 8e-52,   Method: Composition-based stats.
 Identities = 74/254 (29%), Positives = 128/254 (50%), Gaps = 14/254 (5%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           E     KR ++  D  A  R+  S+LRLVV IA  Y   GLP  +++ EGNIGLM+AV K
Sbjct: 366 EILEQIKRGKKISD-EAKGRMAKSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGLMKAVDK 424

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RG++ +TY+ WWI+ A+   I      ++I        +   + ++   ++     
Sbjct: 425 FEYKRGYKFSTYATWWIRQAISRAIADQARTIRIPIH-----MIETINQINKIIREHLQK 479

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           + K   V  IAK++++S  +V  +        SL A I   +++  ++ D++    D   
Sbjct: 480 DGKEPDVSVIAKEVSLSMDKVKQVIKITKEPISLEAPI--GNEDDGKFGDFV---EDRNS 534

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERV 269
              ++   + + +  +   ++ LN RE+ +   R      E+  TLE +  E  V+RERV
Sbjct: 535 LSPMDHILKDDLKEQIDEVLNQLNDREKAVIRMRFGLMDDESDRTLEEIGKELNVTRERV 594

Query: 270 RQIEARAFKKVQES 283
           RQIE+ A KK++  
Sbjct: 595 RQIESSAIKKLKHP 608


>gi|51598964|ref|YP_073152.1| RNA polymerase sigma factor RpoD [Borrelia garinii PBi]
 gi|51573535|gb|AAU07560.1| RNA polymerase sigma-70 factor [Borrelia garinii PBi]
          Length = 631

 Score =  208 bits (530), Expect = 8e-52,   Method: Composition-based stats.
 Identities = 67/257 (26%), Positives = 122/257 (47%), Gaps = 16/257 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 379 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 434

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RGF+ +TY+ WWI+ A+   I      +++        +   + RL    + +   
Sbjct: 435 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVH-----MIEQINRLNRETRYLVQV 489

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             K      ++ +L     +V ++        SL   I   ++  S   D++    D   
Sbjct: 490 LGKDPTDEELSDRLGWELKKVKTVKSVSREPVSLETPI--GEEEDSVLSDFI---EDKAI 544

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +           ++ +   +  L  RE+ + + R   E+   +TLE +   F V+RER+R
Sbjct: 545 KNPANHTSFVVLQDQIRSILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIR 604

Query: 271 QIEARAFKKVQESIQKQ 287
           QIE++A ++++   + Q
Sbjct: 605 QIESKALRRLKNPKKTQ 621


>gi|261879347|ref|ZP_06005774.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           bergensis DSM 17361]
 gi|270334050|gb|EFA44836.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           bergensis DSM 17361]
          Length = 290

 Score =  208 bits (530), Expect = 8e-52,   Method: Composition-based stats.
 Identities = 81/287 (28%), Positives = 140/287 (48%), Gaps = 12/287 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKI 64
           SI       L RY+ EI ++PM+   EE  LA+  R+ G     A  +LV ++LR VV +
Sbjct: 9   SITNRSSEALDRYLVEIGRVPMITVDEEIELAQAIRKGGKEGERAKEKLVKANLRFVVSV 68

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y+  GL +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V
Sbjct: 69  AKQYQHQGLGLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIV 128

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           ++            L ++   +      N +P  V  +A+  N+ E+++           
Sbjct: 129 RLPLNQ-----VGALSKINAEISKFEQENHRPPSVQELARLTNIEEAKIEQTMKADNHHM 183

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           S++A     D NS    D L    D +    ++ E     + + T   +VL  RER I  
Sbjct: 184 SIDAPFQEDDDNS--MADVLSSGDDSRADRQVDYESMS--KELDTVLCNVLKERERTIVR 239

Query: 245 ARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
                  +   LE +  +  ++RERVRQI  ++  K++ES   Q+ +
Sbjct: 240 ECFGIGCHEKGLEEIGDQLGLTRERVRQIREKSIVKLRESGHAQLLI 286


>gi|166367266|ref|YP_001659539.1| RNA polymerase sigma factor SigD [Microcystis aeruginosa NIES-843]
 gi|166089639|dbj|BAG04347.1| group 2 RNA polymerase sigma factor [Microcystis aeruginosa
           NIES-843]
          Length = 318

 Score =  208 bits (530), Expect = 9e-52,   Method: Composition-based stats.
 Identities = 73/319 (22%), Positives = 138/319 (43%), Gaps = 54/319 (16%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------- 43
           M    N    +  Y+ EI ++P+L  +EE + AK+ +                       
Sbjct: 1   MKTSKNPTDPVRAYLREIGRVPLLTHEEEILYAKQVQRLIFLEKIKESLKVKLGSDPSDR 60

Query: 44  ------------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
                              GD  A  ++V ++LRLVV +A  Y    L + +++ EG IG
Sbjct: 61  QWSEAAEISEEQLRRELGAGDF-AKRKMVEANLRLVVSVAKKYLKRNLDLLDLIQEGTIG 119

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           + + V+KFDP +G+R +TY+ WWI+ A+   I      +++     +K     L ++K  
Sbjct: 120 MQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEK-----LNKIKKA 174

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            + +  +  +   +  +A++L+++  +V     R     SL+  +   D   ++  + L 
Sbjct: 175 QRQLAQDKGRAATIAELAEELDLTPKQVRDYLERSRQPLSLDLKV--GDNQDTELGELLE 232

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFE 263
                 E        + +    L + M+ L P+++ +   R   +N  P+TL  +     
Sbjct: 233 DTGLSPEDYTAYSSLQVD----LEKLMADLTPQQKEVICLRFGLDNGQPLTLAKIGVRLN 288

Query: 264 VSRERVRQIEARAFKKVQE 282
           +SRERVRQIE  A  K+++
Sbjct: 289 ISRERVRQIEREAIAKLRK 307


>gi|15609847|ref|NP_217226.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis H37Rv]
 gi|15842248|ref|NP_337285.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis
           CDC1551]
 gi|31793882|ref|NP_856375.1| RNA polymerase sigma factor SigB [Mycobacterium bovis AF2122/97]
 gi|121638585|ref|YP_978809.1| RNA polymerase sigma factor SigB [Mycobacterium bovis BCG str.
           Pasteur 1173P2]
 gi|148662551|ref|YP_001284074.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis H37Ra]
 gi|215412516|ref|ZP_03421250.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis
           94_M4241A]
 gi|215446963|ref|ZP_03433715.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis T85]
 gi|224991077|ref|YP_002645766.1| RNA polymerase sigma factor [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|254365367|ref|ZP_04981412.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis str.
           Haarlem]
 gi|289444252|ref|ZP_06433996.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis T46]
 gi|289448365|ref|ZP_06438109.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           CPHL_A]
 gi|289570886|ref|ZP_06451113.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis T17]
 gi|289575408|ref|ZP_06455635.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis K85]
 gi|289751363|ref|ZP_06510741.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis T92]
 gi|289754812|ref|ZP_06514190.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           EAS054]
 gi|289758838|ref|ZP_06518216.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis T85]
 gi|289762881|ref|ZP_06522259.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis GM
           1503]
 gi|298526180|ref|ZP_07013589.1| RNA polymerase principal sigma factor SigB [Mycobacterium
           tuberculosis 94_M4241A]
 gi|307085405|ref|ZP_07494518.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu012]
 gi|313659647|ref|ZP_07816527.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis KZN
           V2475]
 gi|1171103|gb|AAA86044.1| sigma factor MysB [Mycobacterium tuberculosis H37Rv]
 gi|2182001|emb|CAB09470.1| RNA POLYMERASE SIGMA FACTOR SIGB [Mycobacterium tuberculosis H37Rv]
 gi|13882539|gb|AAK47099.1| RNA polymerase principal sigma factor SigB [Mycobacterium
           tuberculosis CDC1551]
 gi|31619476|emb|CAD94914.1| RNA POLYMERASE SIGMA FACTOR SIGB [Mycobacterium bovis AF2122/97]
 gi|121494233|emb|CAL72711.1| RNA polymerase sigma factor sigB [Mycobacterium bovis BCG str.
           Pasteur 1173P2]
 gi|134150880|gb|EBA42925.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis str.
           Haarlem]
 gi|148506703|gb|ABQ74512.1| RNA polymerase sigma factor [Mycobacterium tuberculosis H37Ra]
 gi|224774192|dbj|BAH26998.1| RNA polymerase sigma factor [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|289417171|gb|EFD14411.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis T46]
 gi|289421323|gb|EFD18524.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           CPHL_A]
 gi|289539839|gb|EFD44417.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis K85]
 gi|289544640|gb|EFD48288.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis T17]
 gi|289691950|gb|EFD59379.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis T92]
 gi|289695399|gb|EFD62828.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           EAS054]
 gi|289710387|gb|EFD74403.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis GM
           1503]
 gi|289714402|gb|EFD78414.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis T85]
 gi|298495974|gb|EFI31268.1| RNA polymerase principal sigma factor SigB [Mycobacterium
           tuberculosis 94_M4241A]
 gi|308365051|gb|EFP53902.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           SUMu012]
 gi|326904326|gb|EGE51259.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis W-148]
          Length = 323

 Score =  208 bits (530), Expect = 9e-52,   Method: Composition-based stats.
 Identities = 69/312 (22%), Positives = 133/312 (42%), Gaps = 38/312 (12%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREH-------------- 44
            ++         +  Y++ I K  +L    E  LAKR     Y EH              
Sbjct: 15  SDLDAQSPAADLVRVYLNGIGKTALLNAAGEVELAKRIEAGLYAEHLLETRKRLGENRKR 74

Query: 45  -------GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
                     +A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +
Sbjct: 75  DLAAVVRDGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTK 134

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           GF+ +TY+ WWI+ A+   +      +++     ++     L R+K  +          E
Sbjct: 135 GFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLARIKREMHQHLGREATDE 192

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A +  +   ++  +        SL+  + S ++  +   D++    D +      
Sbjct: 193 ---ELAAESGIPIDKINDLLEHSRDPVSLDMPVGSEEE--APLGDFI---EDAEAMSAEN 244

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
               +     +   ++ L+ RE ++   R   ++  P TL+ +   F +SRERVRQIE  
Sbjct: 245 AVIAELLHTDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERD 304

Query: 276 AFKKVQESIQKQ 287
              K++   +  
Sbjct: 305 VMSKLRHGERAD 316


>gi|317176909|dbj|BAJ54698.1| RNA polymerase sigma factor RpoD [Helicobacter pylori F16]
          Length = 671

 Score =  208 bits (530), Expect = 9e-52,   Method: Composition-based stats.
 Identities = 70/237 (29%), Positives = 122/237 (51%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ W
Sbjct: 431 RAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATW 490

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WIK A+   I      ++I        +   + R+   ++     N K   +  +A+++ 
Sbjct: 491 WIKQAISRAIADQARTIRIPIH-----MIDTINRINKVMRKHIQENGKEPDLEVVAEEVG 545

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V ++        SL   + + D    ++ D++    D      I++  R++ +  
Sbjct: 546 LSLDKVKNVIKVAKEPISLETPVGNDDD--GKFGDFV---EDKNIVSSIDRIMREDLKAQ 600

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 601 IESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 657



 Score = 35.9 bits (82), Expect = 6.5,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 19/36 (52%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+  I +L K EE  L+K+ R   D+
Sbjct: 156 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDI 191


>gi|308062951|gb|ADO04838.1| RNA polymerase sigma factor RpoD [Helicobacter pylori Sat464]
          Length = 666

 Score =  208 bits (530), Expect = 9e-52,   Method: Composition-based stats.
 Identities = 70/237 (29%), Positives = 121/237 (51%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ W
Sbjct: 426 RAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATW 485

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WIK A+   I      ++I        +   + R+   ++     N K   +  +A+++ 
Sbjct: 486 WIKQAISRAIADQARTIRIPIH-----MIDTINRINKVMRKHIQENGKEPDLEVVAEEVG 540

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  
Sbjct: 541 LSLDKVKNVIKVTKEPISLETPVGNDDD--GKFGDFV---EDKNIVSSIDHIMREDLKAQ 595

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 596 IESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 652



 Score = 36.3 bits (83), Expect = 6.3,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 19/36 (52%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+  I +L K EE  L+K+ R   D+
Sbjct: 151 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDI 186


>gi|170076898|ref|YP_001733536.1| group 2 sigma factor [Synechococcus sp. PCC 7002]
 gi|169884567|gb|ACA98280.1| Group 2 sigma factor [Synechococcus sp. PCC 7002]
          Length = 398

 Score =  208 bits (530), Expect = 9e-52,   Method: Composition-based stats.
 Identities = 64/244 (26%), Positives = 121/244 (49%), Gaps = 13/244 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   ++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV KFDP +G+R +TY+ W
Sbjct: 158 KAKEHMIQANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVDKFDPTKGYRFSTYAYW 217

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+  +   I      +++     +K     L ++K   + I+        +  +A+ L 
Sbjct: 218 WIRQGITRAIATQSRTIRLPVHVTEK-----LNKIKKAQRQISQTQGCTPSLDDVAQALE 272

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++  +V  +  ++    SL   I       ++  D L       E+ L+    R++ +  
Sbjct: 273 MTPEQVREVLQKVPRSVSLE--IRVGKDRDTELGDLLETQDASPEENLV----RESLQRD 326

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVT--LENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L   ++ L  RER + + R    +  T  L  +    E+SRERVRQIEA+A +K+++  +
Sbjct: 327 LHNLLTELTDREREVIQLRYGLGDGKTYSLAEIGRMLELSRERVRQIEAKALQKLRQPKR 386

Query: 286 KQVE 289
           + + 
Sbjct: 387 RNIM 390


>gi|255020686|ref|ZP_05292748.1| RNA polymerase sigma factor RpoH [Acidithiobacillus caldus ATCC
           51756]
 gi|254969922|gb|EET27422.1| RNA polymerase sigma factor RpoH [Acidithiobacillus caldus ATCC
           51756]
          Length = 285

 Score =  208 bits (529), Expect = 9e-52,   Method: Composition-based stats.
 Identities = 111/289 (38%), Positives = 175/289 (60%), Gaps = 12/289 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M +++++ +     G++ Y+  +   P+L  +EE  LA+R R+  D+ AA +LV SHLR 
Sbjct: 6   MTQRDLATV----DGMAAYLRFVHAQPVLSVEEERRLARRLRDEDDVDAAKQLVLSHLRF 61

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV++A  YRGYGLP ++++ EGNIGLM+AVK+FDPE+G RL ++++ WIKA M E+ILR+
Sbjct: 62  VVRVARAYRGYGLPEADLIQEGNIGLMKAVKRFDPEQGVRLVSFAVHWIKAEMHEFILRN 121

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR  +     +       E+  AIA+ L VS+  V+ M  R+
Sbjct: 122 WRIVKVATTKAQRKLFFNLRSARQSSGWLGQ-----EESAAIAEDLGVSQEAVLEMEGRM 176

Query: 181 AG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           AG D SL     S D+        L    +   + LI+++  + R+  L  ++  L+ R+
Sbjct: 177 AGQDYSLQ--YESDDEEGHGRTLELEDPGESSVEALIDRDWDQQRQRGLRAALQSLSERD 234

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           R I + R L ++P TL+ L  E  VS ERVRQ+E    +K++  + + V
Sbjct: 235 RYIIQNRWLSDDPKTLQALGEELGVSAERVRQLEKSGMEKLRSRLLEYV 283


>gi|170703618|ref|ZP_02894360.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia ambifaria
           IOP40-10]
 gi|170131475|gb|EDT00061.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia ambifaria
           IOP40-10]
          Length = 361

 Score =  208 bits (529), Expect = 9e-52,   Method: Composition-based stats.
 Identities = 78/280 (27%), Positives = 132/280 (47%), Gaps = 15/280 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+
Sbjct: 81  DTIQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGV 139

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++       
Sbjct: 140 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV--I 197

Query: 134 RLFFNLRRLKGHLQAITDN-----NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           R    + R K HL+  + +       +   +  IA     +  EV  +        SL+A
Sbjct: 198 RELNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDA 257

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +      +S   D L  D        ++  E +    +    +S L+ + R + E R  
Sbjct: 258 PL--DLDPASSLLDLLPDDQSQSPDAEVQHRELE---TLTRAWLSRLSDKHRHVIERRFG 312

Query: 249 QE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                P TLE L+ E  ++RERVRQI+  A  +++     
Sbjct: 313 LNHIEPATLEELADEMGLTRERVRQIQQEALVRLKRFFAS 352


>gi|20330084|emb|CAD30008.1| RNA polymerase sigma factor [Burkholderia cepacia]
          Length = 362

 Score =  208 bits (529), Expect = 9e-52,   Method: Composition-based stats.
 Identities = 78/280 (27%), Positives = 132/280 (47%), Gaps = 15/280 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+
Sbjct: 82  DTIQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGV 140

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++       
Sbjct: 141 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV--I 198

Query: 134 RLFFNLRRLKGHLQAITDN-----NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           R    + R K HL+  + +       +   +  IA     +  EV  +        SL+A
Sbjct: 199 RELNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDA 258

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +      +S   D L  D        ++  E +    +    +S L+ + R + E R  
Sbjct: 259 PL--DLDPASSLLDLLPDDQSQSPDAEVQHRELE---TLTRAWLSRLSDKHRHVIERRFG 313

Query: 249 QE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                P TLE L+ E  ++RERVRQI+  A  +++     
Sbjct: 314 LNHIEPATLEELADEMGLTRERVRQIQQEALVRLKRFFAS 353


>gi|78066590|ref|YP_369359.1| RNA polymerase sigma factor RpoS [Burkholderia sp. 383]
 gi|77967335|gb|ABB08715.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia sp. 383]
          Length = 362

 Score =  208 bits (529), Expect = 9e-52,   Method: Composition-based stats.
 Identities = 78/280 (27%), Positives = 132/280 (47%), Gaps = 15/280 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+
Sbjct: 82  DTIQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGV 140

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++       
Sbjct: 141 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV--I 198

Query: 134 RLFFNLRRLKGHLQAITDN-----NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           R    + R K HL+  + +       +   +  IA     +  EV  +        SL+A
Sbjct: 199 RELNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDA 258

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +      +S   D L  D        ++  E +    +    +S L+ + R + E R  
Sbjct: 259 PL--DLDPASSLLDLLPDDQSQSPDAEVQHRELE---TLTRAWLSRLSDKHRHVIERRFG 313

Query: 249 QE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                P TLE L+ E  ++RERVRQI+  A  +++     
Sbjct: 314 LNHIEPATLEELADEMGLTRERVRQIQQEALVRLKRFFAS 353


>gi|53719139|ref|YP_108125.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei K96243]
 gi|53723558|ref|YP_103014.1| RNA polymerase sigma factor RpoS [Burkholderia mallei ATCC 23344]
 gi|67639892|ref|ZP_00438721.1| RNA polymerase sigma factor RpoS [Burkholderia mallei GB8 horse 4]
 gi|76810144|ref|YP_333760.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1710b]
 gi|121600326|ref|YP_993163.1| RNA polymerase sigma factor RpoS [Burkholderia mallei SAVP1]
 gi|124385284|ref|YP_001026062.1| RNA polymerase sigma factor RpoS [Burkholderia mallei NCTC 10229]
 gi|126440772|ref|YP_001059233.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 668]
 gi|126450398|ref|YP_001080670.1| RNA polymerase sigma factor RpoS [Burkholderia mallei NCTC 10247]
 gi|126452489|ref|YP_001066500.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1106a]
 gi|134277449|ref|ZP_01764164.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 305]
 gi|167002252|ref|ZP_02268042.1| RNA polymerase sigma factor RpoS [Burkholderia mallei PRL-20]
 gi|167719257|ref|ZP_02402493.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei DM98]
 gi|167738254|ref|ZP_02411028.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 14]
 gi|167815444|ref|ZP_02447124.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 91]
 gi|167823855|ref|ZP_02455326.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 9]
 gi|167845396|ref|ZP_02470904.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei B7210]
 gi|167893937|ref|ZP_02481339.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 7894]
 gi|167902387|ref|ZP_02489592.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei NCTC
           13177]
 gi|167910629|ref|ZP_02497720.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 112]
 gi|167918658|ref|ZP_02505749.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei BCC215]
 gi|217421435|ref|ZP_03452939.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 576]
 gi|226197238|ref|ZP_03792815.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei
           Pakistan 9]
 gi|237812557|ref|YP_002897008.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei
           MSHR346]
 gi|242315690|ref|ZP_04814706.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1106b]
 gi|254178572|ref|ZP_04885227.1| RNA polymerase sigma factor RpoS [Burkholderia mallei ATCC 10399]
 gi|254179542|ref|ZP_04886141.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1655]
 gi|254189067|ref|ZP_04895578.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei Pasteur
           52237]
 gi|254197294|ref|ZP_04903716.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei S13]
 gi|254199960|ref|ZP_04906326.1| RNA polymerase sigma factor RpoS [Burkholderia mallei FMH]
 gi|254206293|ref|ZP_04912645.1| RNA polymerase sigma factor RpoS [Burkholderia mallei JHU]
 gi|254261861|ref|ZP_04952915.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1710a]
 gi|254297419|ref|ZP_04964872.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 406e]
 gi|254358292|ref|ZP_04974565.1| RNA polymerase sigma factor RpoS [Burkholderia mallei 2002721280]
 gi|28394113|gb|AAO34104.1| rpoS [Burkholderia pseudomallei]
 gi|52209553|emb|CAH35506.1| RNA polymerase sigma factor [Burkholderia pseudomallei K96243]
 gi|52426981|gb|AAU47574.1| RNA polymerase sigma factor [Burkholderia mallei ATCC 23344]
 gi|76579597|gb|ABA49072.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1710b]
 gi|121229136|gb|ABM51654.1| RNA polymerase sigma factor RpoS [Burkholderia mallei SAVP1]
 gi|124293304|gb|ABN02573.1| RNA polymerase sigma factor RpoS [Burkholderia mallei NCTC 10229]
 gi|126220265|gb|ABN83771.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 668]
 gi|126226131|gb|ABN89671.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1106a]
 gi|126243268|gb|ABO06361.1| RNA polymerase sigma factor RpoS [Burkholderia mallei NCTC 10247]
 gi|134251099|gb|EBA51178.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 305]
 gi|147749556|gb|EDK56630.1| RNA polymerase sigma factor RpoS [Burkholderia mallei FMH]
 gi|147753736|gb|EDK60801.1| RNA polymerase sigma factor RpoS [Burkholderia mallei JHU]
 gi|148027419|gb|EDK85440.1| RNA polymerase sigma factor RpoS [Burkholderia mallei 2002721280]
 gi|157807858|gb|EDO85028.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 406e]
 gi|157936746|gb|EDO92416.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei Pasteur
           52237]
 gi|160699611|gb|EDP89581.1| RNA polymerase sigma factor RpoS [Burkholderia mallei ATCC 10399]
 gi|169654035|gb|EDS86728.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei S13]
 gi|184210082|gb|EDU07125.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1655]
 gi|217395177|gb|EEC35195.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 576]
 gi|225930617|gb|EEH26627.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei
           Pakistan 9]
 gi|237506433|gb|ACQ98751.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei
           MSHR346]
 gi|238520504|gb|EEP83963.1| RNA polymerase sigma factor RpoS [Burkholderia mallei GB8 horse 4]
 gi|242138929|gb|EES25331.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1106b]
 gi|243062069|gb|EES44255.1| RNA polymerase sigma factor RpoS [Burkholderia mallei PRL-20]
 gi|254220550|gb|EET09934.1| RNA polymerase sigma factor RpoS [Burkholderia pseudomallei 1710a]
          Length = 359

 Score =  208 bits (529), Expect = 9e-52,   Method: Composition-based stats.
 Identities = 78/280 (27%), Positives = 132/280 (47%), Gaps = 15/280 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+
Sbjct: 79  DTIQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGV 137

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++       
Sbjct: 138 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV--I 195

Query: 134 RLFFNLRRLKGHLQAITDN-----NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           R    + R K HL+  + +       +   +  IA     +  EV  +        SL+A
Sbjct: 196 RELNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDA 255

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +      +S   D L  D        ++  E +    +    +S L+ + R + E R  
Sbjct: 256 PL--DLDPASSLLDLLPDDQSQSPDAEVQHRELE---TLTRAWLSRLSDKHRHVIERRFG 310

Query: 249 QE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                P TLE L+ E  ++RERVRQI+  A  +++     
Sbjct: 311 LNHIEPATLEELADEMGLTRERVRQIQQEALVRLKRFFAS 350


>gi|83319868|ref|YP_424476.1| RNA polymerase sigma factor RpoD [Mycoplasma capricolum subsp.
           capricolum ATCC 27343]
 gi|83283754|gb|ABC01686.1| RNA polymerase sigma factor RpoD [Mycoplasma capricolum subsp.
           capricolum ATCC 27343]
          Length = 505

 Score =  208 bits (529), Expect = 9e-52,   Method: Composition-based stats.
 Identities = 70/327 (21%), Positives = 133/327 (40%), Gaps = 67/327 (20%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSA---AHRLVTSHLRLVVKIAMGYRGYG 72
           +  Y ++I + P+L K +E + AK              ++L+ S+L+LV+ +A  +   G
Sbjct: 171 IKTYFYKIGQAPILTKDQEIMYAKMAVSDDPEDVKEGRNKLIESNLKLVISVARKHLNRG 230

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L  ++++ EGNIGLM+AV KF+ E+GF+ +TY+ WWI  A+   I      ++I     +
Sbjct: 231 LDFADLIEEGNIGLMKAVDKFEYEKGFKFSTYATWWISQAITRAIADQARTIRIPVHMVE 290

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 L R++  L          E++     +  ++  +VI +        SL      
Sbjct: 291 --TINKLARVERQLTQELGREPNAEEIANRVGE-GITSDKVIEIKKLSIEPVSLEKPF-- 345

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF--------- 243
            D++ + + D++    D       E  E++  + ++ +    + PRE ++          
Sbjct: 346 GDEDDTHFGDFV---EDKDMVSPSEYTEKEILKEVMDKVFEDMPPREEKVIRMRYGIVPT 402

Query: 244 EARRLQ-----------------------------------------------ENPVTLE 256
             R L                                                ++  TLE
Sbjct: 403 RLRTLLRLAQECNDTNAKELKQAIEELDIHLDTPIEKVRKFNNEIINNNLAKYDSARTLE 462

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQES 283
            +  E  V+RER+RQIEA+  +K+++ 
Sbjct: 463 EVGKELNVTRERIRQIEAKTIRKLKQP 489


>gi|325264732|ref|ZP_08131461.1| RNA polymerase sigma factor RpoD [Clostridium sp. D5]
 gi|324030024|gb|EGB91310.1| RNA polymerase sigma factor RpoD [Clostridium sp. D5]
          Length = 292

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 78/275 (28%), Positives = 131/275 (47%), Gaps = 14/275 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ EI +I  L   EE  L K+  E GD  A  +L  S L LVV IA  Y G GL  
Sbjct: 29  LKIYLKEIGQISPLSSGEELELGKKIAE-GDEGAKLKLEESALCLVVSIAGQYSGRGLLF 87

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGNIGLMQA +K+D  +    + Y+  WI+ A++  +      +++     +   
Sbjct: 88  MDLIQEGNIGLMQAAEKYDYTKDGGFSGYARRWIEDAIKHAVDEQSREIRVPAYVAE--- 144

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKL-NVSESEVISMNCRLAGDESLNALINSSD 194
             N+++++     +     +      IA KL + SE E+ S+   L    SL+A +   D
Sbjct: 145 --NMKKVQKAAYELQQELGREATAGEIAGKLGDKSEEEIESILTFLKNPVSLDAPVEDGD 202

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP-- 252
             + +         D +E+   +      ++  +   +  L+ +ER++   R   E+   
Sbjct: 203 DENLEDTIA-----DREEKTPEDAVNSLIQKEEVLHLLESLSEKERQVISKRFGLEDGRV 257

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            TLE +  E  VSRER+ QIE  A KK++++  K+
Sbjct: 258 HTLEEVGQELNVSRERISQIEEHAMKKLRQAAGKE 292


>gi|167562539|ref|ZP_02355455.1| RNA polymerase sigma factor RpoS [Burkholderia oklahomensis EO147]
 gi|167569723|ref|ZP_02362597.1| RNA polymerase sigma factor RpoS [Burkholderia oklahomensis C6786]
          Length = 362

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 78/280 (27%), Positives = 130/280 (46%), Gaps = 15/280 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+
Sbjct: 82  DTIQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFDARQVMIERNLRLVVSIAKGYLNRGV 140

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++       
Sbjct: 141 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV--I 198

Query: 134 RLFFNLRRLKGHLQA-----ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           R    + R K HL+            +   +  IA     +  EV  +        SL+A
Sbjct: 199 RELNQVLRAKRHLEKNSLSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDA 258

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +      +S   D L  D        ++  E +    +    +S L+ + R + E R  
Sbjct: 259 PL--DLDPASSLLDLLPDDQSQSPDAEVQHRELE---TLTRAWLSRLSDKHRHVIERRFG 313

Query: 249 QE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                P TLE L+ E  ++RERVRQI+  A  +++     
Sbjct: 314 LNHIEPATLEELADEMGLTRERVRQIQQEALVRLKRFFAS 353


>gi|254424042|ref|ZP_05037760.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
 gi|196191531|gb|EDX86495.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
          Length = 319

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 73/309 (23%), Positives = 145/309 (46%), Gaps = 52/309 (16%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGDLS-------------- 48
           +SRY+  I + P+L  ++E  L K  +             E  D                
Sbjct: 11  VSRYLKGIGRFPLLTHEQEITLGKTVQQLMKLEAIRDDLTETMDREPTLAEWAEATNLSP 70

Query: 49  ------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                       A  +++ S+LRLVV IA  YRG  L + +++ EG++GL + V+KFDP 
Sbjct: 71  EALKKTVEIGQQAKDKMMRSNLRLVVSIAKKYRGSKLDMMDLIQEGSLGLCRGVEKFDPL 130

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +G+R +TY+ WWI+ A+   I  +   +++    N+K     L +++   + ++    +P
Sbjct: 131 KGYRFSTYAYWWIRQAITRAIADTGRTIRLPIHINEK-----LSKIRKAQREVSLELGRP 185

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
             V  +A+K+++   +V  +  +     SLN  I S  + +++    L  D    E+   
Sbjct: 186 ATVSEVAEKVSLPAEKVRELQRQSRLPLSLNMRIGS--EQNTELGALLESDSQSPEEYAT 243

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEA 274
           +   +++    + + ++ L  R++ +   R   ++    TL  +  + ++SRERVRQIE 
Sbjct: 244 QNLLKRD----IGQLLARLTERQKDVISMRFGLDDGKKKTLAQIGHDLDISRERVRQIER 299

Query: 275 RAFKKVQES 283
           +A + ++ +
Sbjct: 300 KALRTLRHT 308


>gi|134295851|ref|YP_001119586.1| RNA polymerase sigma factor RpoS [Burkholderia vietnamiensis G4]
 gi|134139008|gb|ABO54751.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia vietnamiensis
           G4]
          Length = 361

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 78/280 (27%), Positives = 132/280 (47%), Gaps = 15/280 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+
Sbjct: 81  DTIQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFDARQVMIERNLRLVVSIAKGYLNRGV 139

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++       
Sbjct: 140 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV--I 197

Query: 134 RLFFNLRRLKGHLQAITDN-----NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           R    + R K HL+  + +       +   +  IA     +  EV  +        SL+A
Sbjct: 198 RELNQVLRAKRHLEKNSMSTGDAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDA 257

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +      +S   D L  D        ++  E +    +    +S L+ + R + E R  
Sbjct: 258 PL--DLDPASSLLDLLPDDQSQSPDAEVQHRELE---TLTRAWLSRLSDKHRHVIERRFG 312

Query: 249 QE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                P TLE L+ E  ++RERVRQI+  A  +++     
Sbjct: 313 LNHIEPATLEELADEMGLTRERVRQIQQEALVRLKRFFAS 352


>gi|167970067|ref|ZP_02552344.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis H37Ra]
 gi|215404675|ref|ZP_03416856.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis
           02_1987]
 gi|215428138|ref|ZP_03426057.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis T92]
 gi|215431649|ref|ZP_03429568.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis
           EAS054]
 gi|218754446|ref|ZP_03533242.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis GM
           1503]
 gi|219558719|ref|ZP_03537795.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis T17]
 gi|254551766|ref|ZP_05142213.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis
           '98-R604 INH-RIF-EM']
 gi|260187727|ref|ZP_05765201.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis
           CPHL_A]
 gi|260201835|ref|ZP_05769326.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis T46]
 gi|260206019|ref|ZP_05773510.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis K85]
 gi|289746512|ref|ZP_06505890.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           02_1987]
 gi|294994199|ref|ZP_06799890.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis 210]
 gi|297635318|ref|ZP_06953098.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis KZN
           4207]
 gi|297732314|ref|ZP_06961432.1| RNA polymerase sigma factor SigB [Mycobacterium tuberculosis KZN
           R506]
 gi|289687040|gb|EFD54528.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           02_1987]
 gi|323718704|gb|EGB27866.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis
           CDC1551A]
 gi|328457981|gb|AEB03404.1| RNA polymerase sigma factor sigB [Mycobacterium tuberculosis KZN
           4207]
          Length = 333

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 69/312 (22%), Positives = 133/312 (42%), Gaps = 38/312 (12%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREH-------------- 44
            ++         +  Y++ I K  +L    E  LAKR     Y EH              
Sbjct: 25  SDLDAQSPAADLVRVYLNGIGKTALLNAAGEVELAKRIEAGLYAEHLLETRKRLGENRKR 84

Query: 45  -------GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
                     +A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +
Sbjct: 85  DLAAVVRDGEAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTK 144

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           GF+ +TY+ WWI+ A+   +      +++     ++     L R+K  +          E
Sbjct: 145 GFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLARIKREMHQHLGREATDE 202

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A +  +   ++  +        SL+  + S ++  +   D++    D +      
Sbjct: 203 ---ELAAESGIPIDKINDLLEHSRDPVSLDMPVGSEEE--APLGDFI---EDAEAMSAEN 254

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
               +     +   ++ L+ RE ++   R   ++  P TL+ +   F +SRERVRQIE  
Sbjct: 255 AVIAELLHTDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERD 314

Query: 276 AFKKVQESIQKQ 287
              K++   +  
Sbjct: 315 VMSKLRHGERAD 326


>gi|325521809|gb|EGD00541.1| RNA polymerase sigma factor RpoS [Burkholderia sp. TJI49]
          Length = 339

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 78/280 (27%), Positives = 132/280 (47%), Gaps = 15/280 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+
Sbjct: 59  DTIQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGV 117

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++       
Sbjct: 118 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV--I 175

Query: 134 RLFFNLRRLKGHLQAITDN-----NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           R    + R K HL+  + +       +   +  IA     +  EV  +        SL+A
Sbjct: 176 RELNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDA 235

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +      +S   D L  D        ++  E +    +    +S L+ + R + E R  
Sbjct: 236 PL--DLDPASSLLDLLPDDQSQSPDAEVQHRELE---TLTRAWLSRLSDKHRHVIERRFG 290

Query: 249 QE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                P TLE L+ E  ++RERVRQI+  A  +++     
Sbjct: 291 LNHIEPATLEELADEMGLTRERVRQIQQEALVRLKRFFAS 330


>gi|218680389|ref|ZP_03528286.1| RNA polymerase factor sigma-32 [Rhizobium etli CIAT 894]
          Length = 209

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 140/194 (72%), Positives = 167/194 (86%)

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           ERGFRLATY+MWWIKA++QEYILRSWSLVK+GTTANQKRLFFNLRRLKG +QAI D +LK
Sbjct: 3   ERGFRLATYAMWWIKASIQEYILRSWSLVKMGTTANQKRLFFNLRRLKGRIQAIDDGDLK 62

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
           PE V  IA KL VSE EVISMN RL+GD SLNA I +++ +S QWQDWLV DHD QE VL
Sbjct: 63  PEHVSEIATKLKVSEEEVISMNRRLSGDASLNAPIKAAEGDSGQWQDWLVDDHDSQEDVL 122

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
           IE++E   RR ML ++MSVLN RERRIFEARRL E+PVTLE+LS+EF++SRERVRQIE R
Sbjct: 123 IEQDELDTRRRMLAKAMSVLNERERRIFEARRLAEDPVTLEDLSTEFDISRERVRQIEVR 182

Query: 276 AFKKVQESIQKQVE 289
           AF+KVQ++++K+ +
Sbjct: 183 AFEKVQDAVRKEAQ 196


>gi|317179895|dbj|BAJ57681.1| RNA polymerase sigma factor RpoD [Helicobacter pylori F32]
          Length = 671

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 70/237 (29%), Positives = 121/237 (51%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ W
Sbjct: 431 RAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATW 490

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WIK A+   I      ++I        +   + R+   ++     N K   +  +A+++ 
Sbjct: 491 WIKQAISRAIADQARTIRIPIH-----MIDTINRINKVMRKHIQENGKEPDLEVVAEEVG 545

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  
Sbjct: 546 LSLDKVKNVIKVTKEPISLETPVGNDDD--GKFGDFV---EDKNIVSSIDHIMREDLKAQ 600

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 601 IESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 657



 Score = 35.9 bits (82), Expect = 6.4,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 19/36 (52%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+  I +L K EE  L+K+ R   D+
Sbjct: 156 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDI 191


>gi|302391919|ref|YP_003827739.1| RNA polymerase, sigma 70 subunit, RpoD [Acetohalobium arabaticum
           DSM 5501]
 gi|302203996|gb|ADL12674.1| RNA polymerase, sigma 70 subunit, RpoD [Acetohalobium arabaticum
           DSM 5501]
          Length = 273

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 73/277 (26%), Positives = 145/277 (52%), Gaps = 13/277 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + +++Y  E+    +L K+EE  LAK   ++GD  A   L+  +LRLVV IA  YRG G+
Sbjct: 1   MSINQYYQEMG-HDLLSKKEEAKLAK-GAQNGDQEARKELIEHNLRLVVSIAKKYRGKGM 58

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+A+ KFDP++G+R +TY+ WWI+ ++   +      +++     +K
Sbjct: 59  EFEDMIQEGNLGLMKAIDKFDPDKGYRFSTYATWWIRQSITRALPE-AKTIRVPVHVWEK 117

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                  ++    + + +   +      I+++  +   +V  +  R++ D++L +L N  
Sbjct: 118 TT-----KVFKAKEKLYNQLNREPTFEEISEETGIDSEKVKEII-RISSDQNLASLNNLV 171

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-- 251
             + +     L+ D D +E   +    R+  +  L   +  L  RE  I   R   ++  
Sbjct: 172 GDDENTELGELIADDDVEE--PMTDLNRQFLQEDLEEVLEELTDREAEIIRLRFGLKDNW 229

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           P TL+ ++  F++SRER+RQI+ +A ++++   + + 
Sbjct: 230 PKTLQEVADRFKLSRERIRQIQEKALRRLRHPSRSKA 266


>gi|319792729|ref|YP_004154369.1| RNA polymerase, sigma 70 family subunit [Variovorax paradoxus EPS]
 gi|315595192|gb|ADU36258.1| putative RNA polymerase, sigma 70 family subunit [Variovorax
           paradoxus EPS]
          Length = 340

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 82/280 (29%), Positives = 137/280 (48%), Gaps = 11/280 (3%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           G   L+ Y+ ++R+  +    EE+  A   R  GD +A   ++  +LRLVV IA GY G 
Sbjct: 58  GADALTIYLRQVRRTELFTPDEEFQAACAAR-SGDFAARQSMIEHNLRLVVNIAKGYLGR 116

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           G+P+S+++ EGN+GLM A+ KF+PERGFR +TY+ WWI+ +++  ++     +++     
Sbjct: 117 GVPLSDLIEEGNLGLMHAITKFEPERGFRFSTYATWWIRQSVERAVMTQARAIRLPVHV- 175

Query: 132 QKRLFFNLRRLKGHLQAITD---NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
             R    + R +  L+   +         +V  IA  L     EV  +        SL+A
Sbjct: 176 -VRELQQVLRARRALEGDAEFVARRPDGVRVEDIAALLGRDVQEVADLLALSEAPRSLDA 234

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
                D+  +        D  G    + +  E +    +L + +  L+ RER + E R  
Sbjct: 235 GDARGDEGFTLADTVASDDEQGNPSGVTQAHEVE---RLLDQWIHALDAREREVLEGRYG 291

Query: 249 QEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             +  P TLE LS    ++RERVRQI+  A  K++  + +
Sbjct: 292 LHDREPETLEVLSVRLGLTRERVRQIQNEALAKMRRQLAR 331


>gi|115351809|ref|YP_773648.1| RNA polymerase sigma factor RpoS [Burkholderia ambifaria AMMD]
 gi|115281797|gb|ABI87314.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia ambifaria
           AMMD]
          Length = 361

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 78/280 (27%), Positives = 132/280 (47%), Gaps = 15/280 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+
Sbjct: 81  DTIQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGV 139

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++       
Sbjct: 140 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV--I 197

Query: 134 RLFFNLRRLKGHLQAITDN-----NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           R    + R K HL+  + +       +   +  IA     +  EV  +        SL+A
Sbjct: 198 RELNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDA 257

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +      +S   D L  D        ++  E +    +    +S L+ + R + E R  
Sbjct: 258 PL--DLDPASSLLDLLPDDQSQSPDAEVQHRELE---TLTRAWLSRLSDKHRHVIERRFG 312

Query: 249 QE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                P TLE L+ E  ++RERVRQI+  A  +++     
Sbjct: 313 LNHIEPATLEELADEMGLTRERVRQIQQEALVRLKRFFAS 352


>gi|186683480|ref|YP_001866676.1| RpoD family RNA polymerase sigma factor [Nostoc punctiforme PCC
           73102]
 gi|186465932|gb|ACC81733.1| RNA polymerase, sigma 70 subunit, RpoD family [Nostoc punctiforme
           PCC 73102]
          Length = 332

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 73/311 (23%), Positives = 136/311 (43%), Gaps = 52/311 (16%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------------------ 43
             +  Y+ EI +IP+L  ++E   AK+ ++                              
Sbjct: 23  DTVRAYLREIGRIPLLTHEQEINFAKQVQKMMALLATKEKLAIQLKRQPTQKEWIENINI 82

Query: 44  ---------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                    H    A  +++ ++LRLVV IA  Y+ + L   +++ EG++GL + V+KFD
Sbjct: 83  GEKSLLQQLHQGQKAKQKMIQANLRLVVSIAKKYQRHNLDFLDLIQEGSLGLERGVEKFD 142

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P +G++ +TY  WWI+ A+   I      +++     +K     L ++K   + +T    
Sbjct: 143 PTKGYKFSTYGYWWIRQAITRAIAEQGRTIRLPIHITEK-----LNKIKRIQRELTQKLG 197

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +    V IA++L++   ++           SL   +        + QD L  +    E  
Sbjct: 198 RTPTAVDIAEELSLDPKQIRDYLLLARQPVSLE--LRVGSDKDIELQDMLEDNGLSPELY 255

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQI 272
              K  ++N +N+L++    LNP++R+I   R      N ++L  +     +SRERVRQI
Sbjct: 256 ADHKFLQQNIQNLLSK----LNPQQRQILTFRFGLTDGNELSLAEIGQRMGISRERVRQI 311

Query: 273 EARAFKKVQES 283
           E +A   ++  
Sbjct: 312 EQQALGSLRRH 322


>gi|56750866|ref|YP_171567.1| RNA polymerase sigma factor SigD [Synechococcus elongatus PCC 6301]
 gi|56685825|dbj|BAD79047.1| group2 RNA polymerase sigma factor RpoD3 [Synechococcus elongatus
           PCC 6301]
          Length = 326

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 72/322 (22%), Positives = 142/322 (44%), Gaps = 54/322 (16%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR--------------EHGDLS------- 48
                 +  Y+ EI ++P+L  +EE VL KR +              E GD         
Sbjct: 12  TPTSDLVRTYLREIGRVPLLTHEEEVVLGKRVQQWMKLQELRQTLQSEEGDRDPSDLEWA 71

Query: 49  -------------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
                              A  +++ ++LRLVV +A  Y    + + +++ EG IG+ + 
Sbjct: 72  AAAGLSIEELRQQQHLGEQAKRKMIEANLRLVVSVAKKYLKRNMDLLDLIQEGTIGMQRG 131

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V+KFDP +G+R +TY+ WWI+ A+   I      +++     +K     L ++K   + +
Sbjct: 132 VEKFDPTKGYRFSTYAYWWIRQAITRAIAEKARTIRLPIHITEK-----LNKIKKMQRQL 186

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
           +    +   +  +A  L+++ ++V     +     SL+  +   D   ++  D L  D  
Sbjct: 187 SQQLGRTATLPELAAALDLTPAQVRDYLEKARHPLSLD--LRVGDNQDTELGDLLETD-- 242

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRE 267
                  E   + + R  + R +  L  ++R++   R   E+   +TL ++    ++SRE
Sbjct: 243 --CTTPEEFTLQASMRRDIDRLLDQLTEQQRQVIALRYGLEDGQVMTLASIGDRLQISRE 300

Query: 268 RVRQIEARAFKKVQESIQKQVE 289
           RVRQ+E  A   ++++ + QV+
Sbjct: 301 RVRQLEREALHTLRQA-RSQVQ 321


>gi|260434805|ref|ZP_05788775.1| RNA polymerase sigma factor RpoD [Synechococcus sp. WH 8109]
 gi|260412679|gb|EEX05975.1| RNA polymerase sigma factor RpoD [Synechococcus sp. WH 8109]
          Length = 312

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 78/302 (25%), Positives = 141/302 (46%), Gaps = 36/302 (11%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------EHGDLS----------------- 48
               +S Y+  I +IP+L   EE  L  + +      E G                    
Sbjct: 15  SSDPVSWYLATIGRIPLLTPAEEIELGNQVQAMMSLTEDGSREFEDGELTTAQRRLLRIG 74

Query: 49  --AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  R++ ++LRLVV +A  Y+G GL + +++ EG++GL +AV+KFDP RG++ +TY+ 
Sbjct: 75  RRAKERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAF 134

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ +M   I      +++    +++     L  ++     +          V IA+ +
Sbjct: 135 WWIRQSMTRAIACQSRTIRLPVHLSER-----LTTIRKVSLDLAHKLGAMPSRVEIAEAM 189

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   E+ S+  +     SL+A +N  ++  S   D +    D      +E  E++    
Sbjct: 190 DIPLDELDSLLRQALTTSSLDAPVN-GEEGRSFLGDLIA---DSSLDEPLEIVEQRIHHE 245

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L R +S L+ +E+ +   R   E     TL  +    EVSRERVRQ+E +A +K++   
Sbjct: 246 QLGRWLSHLSEQEQHVLRMRFGLEGNERHTLAEIGRLMEVSRERVRQVELKALRKLRNLT 305

Query: 285 QK 286
           ++
Sbjct: 306 RR 307


>gi|332672929|gb|AEE69746.1| DNA-directed RNA polymerase sigma subunit RpoD [Helicobacter pylori
           83]
          Length = 674

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 70/237 (29%), Positives = 121/237 (51%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ W
Sbjct: 434 RAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATW 493

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WIK A+   I      ++I        +   + R+   ++     N K   +  +A+++ 
Sbjct: 494 WIKQAISRAIADQARTIRIPIH-----MIDTINRINKVMRKHIQENGKEPDLEVVAEEVG 548

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  
Sbjct: 549 LSLDKVKNVIKVTKEPISLETPVGNDDD--GKFGDFV---EDKNIVSSIDHIMREDLKAQ 603

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 604 IESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 660



 Score = 35.9 bits (82), Expect = 6.5,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 19/36 (52%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+  I +L K EE  L+K+ R   D+
Sbjct: 160 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDI 195


>gi|307636779|gb|ADN79229.1| RNA polymerase sigma factor [Helicobacter pylori 908]
 gi|325995367|gb|ADZ50772.1| RNA polymerase sigma factor [Helicobacter pylori 2018]
 gi|325996964|gb|ADZ49172.1| RNA polymerase sigma factor [Helicobacter pylori 2017]
          Length = 681

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 69/237 (29%), Positives = 120/237 (50%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ W
Sbjct: 441 RAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATW 500

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WIK A+   I      ++I        +   + R+   ++       K   +  +A+++ 
Sbjct: 501 WIKQAISRAIADQARTIRIPIH-----MIDTINRINKVMRKHIQETGKEPDLEVVAEEVG 555

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  
Sbjct: 556 LSLDKVKNVIKVTKEPISLETPVGNDDD--GKFGDFV---EDKNIVSSIDHIMREDLKAQ 610

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 611 IESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 667



 Score = 36.3 bits (83), Expect = 6.0,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 19/36 (52%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+  I +L K EE  L+K+ R   D+
Sbjct: 166 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDI 201


>gi|78212423|ref|YP_381202.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CC9605]
 gi|78196882|gb|ABB34647.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. CC9605]
          Length = 312

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 77/302 (25%), Positives = 141/302 (46%), Gaps = 36/302 (11%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------EHGDLS----------------- 48
               +S Y+  I +IP+L   EE  L  + +      E G                    
Sbjct: 15  SSDPVSWYLATIGRIPLLTPAEEIELGNQVQAMMAFTEDGSREIEDGELTTAQRRLLRIG 74

Query: 49  --AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  R++ ++LRLVV +A  Y+G GL + +++ EG++GL +AV+KFDP RG++ +TY+ 
Sbjct: 75  RRAKERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAF 134

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ +M   I      +++    +++     L  ++     +          V IA+ +
Sbjct: 135 WWIRQSMTRAIACQSRTIRLPVHLSER-----LTTIRKVSLDLAHKLGAMPSRVEIAEAM 189

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   E+ S+  +     SL+A +N  ++  S   D +    D      ++  E++    
Sbjct: 190 DIPLDELDSLLRQALTTSSLDAPVN-GEEGRSFLGDLIA---DSSLDEPLDIVEQRIHHE 245

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L R +S L+ +E+ +   R   E     TL  +    EVSRERVRQ+E +A +K++   
Sbjct: 246 QLGRWLSHLSEQEQHVLRMRFGLEGNERHTLAEIGRLMEVSRERVRQVELKALRKLRNLT 305

Query: 285 QK 286
           ++
Sbjct: 306 RR 307


>gi|328948111|ref|YP_004365448.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           succinifaciens DSM 2489]
 gi|328448435|gb|AEB14151.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           succinifaciens DSM 2489]
          Length = 655

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 61/242 (25%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A +RL+ ++LRLVV IA  Y   GL + +++ EGNIGL++AV+KF+  +G++ +TY+ 
Sbjct: 415 EQAKNRLINANLRLVVSIAKKYTNRGLQLFDLIQEGNIGLIKAVEKFEYRKGYKFSTYAT 474

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      +++        +   + ++    + +     +      IA +L
Sbjct: 475 WWIRQAITRSISDQARTIRVPVH-----MIEQINKVVRESRQLMQKYGREPTDEEIAAQL 529

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +   + V  +        SL   I   ++  S   D++    D + +    +      + 
Sbjct: 530 SWPLARVKQVKNVAREPISLETPI--GEEEDSSLGDFI---EDKEIENPANQTAYTLLQE 584

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +S L  RE+ + + R   ++   +TLE +   F V+RER+RQIEA+A ++++   
Sbjct: 585 QLRSVLSTLPQREQEVLKMRFGLDDGYSLTLEEVGLYFNVTRERIRQIEAKALRRLRHPR 644

Query: 285 QK 286
           + 
Sbjct: 645 RS 646


>gi|208434051|ref|YP_002265717.1| RNA polymerase sigma-80 factor [Helicobacter pylori G27]
 gi|208431980|gb|ACI26851.1| RNA polymerase sigma-80 factor [Helicobacter pylori G27]
          Length = 682

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 70/237 (29%), Positives = 121/237 (51%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ W
Sbjct: 442 RAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATW 501

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WIK A+   I      ++I        +   + R+   ++     N K   +  +A+++ 
Sbjct: 502 WIKQAISRAIADQARTIRIPIH-----MIDTINRINKVMRKHIQENGKEPDLEVVAEEVG 556

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  
Sbjct: 557 LSLDKVKNVIKVTKEPISLETPVGNDDD--GKFGDFV---EDKNIVSSIDHIMREDLKAQ 611

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 612 IESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 668



 Score = 35.9 bits (82), Expect = 7.0,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 19/36 (52%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+  I +L K EE  L+K+ R   D+
Sbjct: 167 SDNPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDI 202


>gi|203288141|ref|YP_002223156.1| RNA polymerase sigma-70 factor [Borrelia recurrentis A1]
 gi|201085361|gb|ACH94935.1| RNA polymerase sigma-70 factor [Borrelia recurrentis A1]
          Length = 630

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 67/257 (26%), Positives = 124/257 (48%), Gaps = 16/257 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE +  K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 378 EEILKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 433

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RGF+ +TY+ WWI+ A+   I      +++        +   + RL    + +   
Sbjct: 434 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVH-----MIEQINRLNRETRYLVQI 488

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             K      ++ +L     +V ++        SL   I   ++  S   D++    D   
Sbjct: 489 LGKDPTDEELSIRLGWDLKKVKTVKNVSREPVSLETPI--GEEEDSVLSDFI---EDKAI 543

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +   +       ++ +   +  L  RE+ + + R   E+   +TLE +   F V+RER+R
Sbjct: 544 KNPAKHTSFVILQDQIRAVLGTLPEREQEVVKMRFGLEDGYSLTLEEVGLYFNVTRERIR 603

Query: 271 QIEARAFKKVQESIQKQ 287
           QIE++A ++++   + Q
Sbjct: 604 QIESKALRRLKNPKKTQ 620



 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 43/251 (17%), Positives = 91/251 (36%), Gaps = 33/251 (13%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRL------VTSHLRLVVKI 64
           N E  +  Y+ EI K  +L   +E  LAK+  + G+    + L      + ++  LV  I
Sbjct: 135 NSEDPIRLYLKEIGKEFLLTGNQEVELAKQM-DSGESIIENILKNEGLVIENYYNLVNAI 193

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFD-PERGFRLATYSMWWIKAAMQE---YILRS 120
                       +   E +         FD   +  R+ ++    +K        Y+ R 
Sbjct: 194 YSRVDKEEFFKKDREREKD-------NNFDYYNKKKRITSFYKSLLKPFQDRLVKYVERK 246

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAI----TDNNLKPEQVVAIAKKLNVSESEVISM 176
             L ++G    ++ +     ++K  L++I     +  L  +  +  A K+   + +  S+
Sbjct: 247 HRLYELGEDIFEESITNERLQIKELLKSIPLYQEELRLFSDDYIDSASKIKDLKRQQKSI 306

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
             RL  D+  N  I   D    + ++ +    + +E ++         +  +T +   L 
Sbjct: 307 LDRLKIDKVRNLRILGRDLAIPEKRERIEKSLNIREDLI---------KEQITEA--QLA 355

Query: 237 PRERRIFEARR 247
            +E    E   
Sbjct: 356 QKELERIEMYY 366


>gi|317013514|gb|ADU80950.1| RNA polymerase sigma factor RpoD [Helicobacter pylori Gambia94/24]
          Length = 681

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 69/237 (29%), Positives = 120/237 (50%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ W
Sbjct: 441 RAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATW 500

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WIK A+   I      ++I        +   + R+   ++       K   +  +A+++ 
Sbjct: 501 WIKQAISRAIADQARTIRIPIH-----MIDTINRINKVMRKHIQETGKEPDLEVVAEEVG 555

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  
Sbjct: 556 LSLDKVKNVIKVTKEPISLETPVGNDDD--GKFGDFV---EDKNIVSSIDHIMREDLKAQ 610

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 611 IESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 667



 Score = 36.3 bits (83), Expect = 6.0,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 19/36 (52%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+  I +L K EE  L+K+ R   D+
Sbjct: 166 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDI 201


>gi|288927698|ref|ZP_06421545.1| RNA polymerase sigma-70 factor [Prevotella sp. oral taxon 317 str.
           F0108]
 gi|288330532|gb|EFC69116.1| RNA polymerase sigma-70 factor [Prevotella sp. oral taxon 317 str.
           F0108]
          Length = 290

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 72/287 (25%), Positives = 134/287 (46%), Gaps = 12/287 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKI 64
           SI       L +Y+ EI + P++   EE  LA++ R+ G     A  +LVT++LR VV +
Sbjct: 9   SITNRSSEALDKYLVEIGRAPLISIDEEIELAQKIRKGGPEGEKAKDKLVTANLRFVVSV 68

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y+  GL +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V
Sbjct: 69  AKQYQHQGLTLTDLIDEGNIGLIKAAQKFDETRGFKFISYAVWWIRQSILQAIAEQSRIV 128

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           ++           +L ++   +      N +   V  ++   N+ E ++           
Sbjct: 129 RLPLNQ-----VGSLNKINHEINKFEQENQRHPSVSELSDATNIDEEKIGQSLMADGHHV 183

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           S++A     + N     D +    D +     + E      N +     VL  RE  I  
Sbjct: 184 SIDAPFQDGEDNC--MLDVMASGDDSRTDKQADHESMALELNSV--LAKVLKDREITIIR 239

Query: 245 ARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
                  +   LE +  +  ++RERVRQI  ++  K+++S   ++ +
Sbjct: 240 ECFGIGCHEKGLEEIGDQLGLTRERVRQIREKSIAKLRDSGNAKILM 286


>gi|296171822|ref|ZP_06852936.1| RNA polymerase principal sigma factor SigB [Mycobacterium
           parascrofulaceum ATCC BAA-614]
 gi|295893958|gb|EFG73726.1| RNA polymerase principal sigma factor SigB [Mycobacterium
           parascrofulaceum ATCC BAA-614]
          Length = 329

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 69/311 (22%), Positives = 134/311 (43%), Gaps = 38/311 (12%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREH--------------- 44
           ++         +  Y++ I K  +L    E  LAKR     Y EH               
Sbjct: 22  DLDAQSPAADLVRVYLNGIGKTALLNAAGEVELAKRIEAGLYAEHLLETRKRLGENRRRD 81

Query: 45  ------GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
                    +A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +G
Sbjct: 82  LEAVVRDGQAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKG 141

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           F+ +TY+ WWI+ A+   +      +++     ++     L R+K  +     N  +   
Sbjct: 142 FKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLARIKREMHQ---NLGREAT 196

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              +A +  +   ++  +        SL+  + S ++  +   D++    D +       
Sbjct: 197 DEELAAESGIPVEKINDLLEHSRDPVSLDMPVGSEEE--APLGDFI---EDAEAMSAENA 251

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARA 276
              +     +   ++ L+ RE ++   R   ++  P TL+ +   F +SRERVRQIE   
Sbjct: 252 VIAELLHTDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDV 311

Query: 277 FKKVQESIQKQ 287
             K++   +  
Sbjct: 312 MSKLRHGERAD 322


>gi|224824776|ref|ZP_03697883.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Lutiella
           nitroferrum 2002]
 gi|224603269|gb|EEG09445.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Lutiella
           nitroferrum 2002]
          Length = 316

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 77/271 (28%), Positives = 139/271 (51%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+++I    +L  QEE  LA R    GD  A  +++  +LRLVV IA  Y   GL + ++
Sbjct: 49  YLNDIGNNALLSPQEEQSLA-RLVVQGDFEARQKMIEHNLRLVVNIAKRYINRGLALLDL 107

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM A++KFDPERGFR +TY+ WWI+ +++  I+     +++       +    
Sbjct: 108 IEEGNIGLMHALEKFDPERGFRFSTYATWWIRQSIERAIMNQSRTIRLPVHV--IKELNV 165

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
             R   HL++        E++  +  K       V+++N R+A   SL+A ++       
Sbjct: 166 YLRASRHLESQIGREPSVEEIAQLVDKPVEDVRRVMNLNERMA---SLDAPLDI--DPML 220

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
              + +  D   + ++ +   + +N    +   M+ LN ++R + E R         TLE
Sbjct: 221 SIGESIPDDQHDEPEIQLHNTQLENF---VHEWMAQLNDKQRMVIERRYGLNGHEICTLE 277

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            L+S   ++RERVRQI+    ++++  ++++
Sbjct: 278 ELASTLSLTRERVRQIQIEGLEQLRRILRRK 308


>gi|109948008|ref|YP_665236.1| RNA polymerase sigma factor RpoD [Helicobacter acinonychis str.
           Sheeba]
 gi|109715229|emb|CAK00237.1| RNA polymerase sigma-70 factor [Helicobacter acinonychis str.
           Sheeba]
          Length = 659

 Score =  208 bits (529), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 70/237 (29%), Positives = 121/237 (51%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ W
Sbjct: 419 RAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEYEKGFKFSTYATW 478

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WIK A+   I      ++I        +   + R+   ++     N K   +  +A+++ 
Sbjct: 479 WIKQAISRAIADQARTIRIPIH-----MIDTINRINKVMRKHMQENGKEPDLEVVAEEVG 533

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  
Sbjct: 534 LSLDKVKNVIKVTKEPISLETPVGNDDD--GKFGDFV---EDKNIVSSIDHIMREDLKVQ 588

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 589 IEGVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 645



 Score = 36.3 bits (83), Expect = 6.2,   Method: Composition-based stats.
 Identities = 11/29 (37%), Positives = 19/29 (65%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
           Y+ E+  I +L+K+EE  L+K+ R   D+
Sbjct: 151 YLREMGNIDLLKKEEEIELSKQIRLGEDI 179


>gi|188526895|ref|YP_001909582.1| RNA polymerase sigma factor RpoD [Helicobacter pylori Shi470]
 gi|188143135|gb|ACD47552.1| RNA polymerase sigma factor RpoD [Helicobacter pylori Shi470]
          Length = 661

 Score =  207 bits (528), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 70/237 (29%), Positives = 121/237 (51%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ W
Sbjct: 421 RAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATW 480

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WIK A+   I      ++I        +   + R+   ++     N K   +  +A+++ 
Sbjct: 481 WIKQAISRAIADQARTIRIPIH-----MIDTINRINKVMRKHIQENGKEPDLEVVAEEVG 535

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  
Sbjct: 536 LSLDKVKNVIKVTKEPISLETPVGNDDD--GKFGDFV---EDKNIVSSIDHIMREDLKVQ 590

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 591 IESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 647



 Score = 36.3 bits (83), Expect = 6.2,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 19/36 (52%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+  I +L K EE  L+K+ R   D+
Sbjct: 146 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDI 181


>gi|317179521|dbj|BAJ57309.1| RNA polymerase sigma factor RpoD [Helicobacter pylori F30]
          Length = 666

 Score =  207 bits (528), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 70/237 (29%), Positives = 121/237 (51%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ W
Sbjct: 426 RAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATW 485

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WIK A+   I      ++I        +   + R+   ++     N K   +  +A+++ 
Sbjct: 486 WIKQAISRAIADQARTIRIPIH-----MIDTINRINKVMRKHIQENGKEPDLEVVAEEVG 540

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  
Sbjct: 541 LSLDKVKNVIKVTKEPISLETPVGNDDD--GKFGDFV---EDKNIVSSIDHIMREDLKAQ 595

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 596 IESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 652



 Score = 35.9 bits (82), Expect = 6.5,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 19/36 (52%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+  I +L K EE  L+K+ R   D+
Sbjct: 151 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDI 186


>gi|15611152|ref|NP_222803.1| RNA polymerase sigma factor RpoD [Helicobacter pylori J99]
 gi|11387124|sp|Q9ZMY3|RPOD_HELPJ RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|4154591|gb|AAD05665.1| RNA POLYMERASE SIGMA FACTOR (SIGMA-70) [Helicobacter pylori J99]
          Length = 681

 Score =  207 bits (528), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 69/237 (29%), Positives = 120/237 (50%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ W
Sbjct: 441 RAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATW 500

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WIK A+   I      ++I        +   + R+   ++       K   +  +A+++ 
Sbjct: 501 WIKQAISRAIADQARTIRIPIH-----MIDTINRINKVMRKHIQETGKEPDLEVVAEEVG 555

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  
Sbjct: 556 LSLDKVKNVIKVTKEPISLETPVGNDDD--GKFGDFV---EDKNIVSSIDHIMREDLKAQ 610

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 611 IESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 667



 Score = 36.3 bits (83), Expect = 6.1,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 19/36 (52%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+  I +L K EE  L+K+ R   D+
Sbjct: 166 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDI 201


>gi|149178485|ref|ZP_01857074.1| transcription initiation factor sigma 70 [Planctomyces maris DSM
           8797]
 gi|148842698|gb|EDL57072.1| transcription initiation factor sigma 70 [Planctomyces maris DSM
           8797]
          Length = 588

 Score =  207 bits (528), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 70/275 (25%), Positives = 127/275 (46%), Gaps = 14/275 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL--SAAHRLVTSHLRLVVKIAMGYRGYGL 73
           L R + E+  + +   ++    ++  +   D    A  +L   +LRLVV IA  YR  GL
Sbjct: 285 LERELSELTIMVVETSEDFQTRSREIKRRFDDWTEAKQQLSGGNLRLVVSIAKKYRNRGL 344

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN GLM+ V+K++  RG++ +TY+ WWI+ A+   +      ++I       
Sbjct: 345 SFLDLIQEGNAGLMRGVEKYEYRRGYKFSTYATWWIRQAITRAVADHARTIRIPVH---- 400

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            +F ++  LK   + I     +   +  +A  + +   E   +        SL+  +   
Sbjct: 401 -MFQSISTLKARSEQIRQETGREPTMEELADSVGLGVEETERIMKTWKHPISLDTPV--G 457

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           +   S + D+L    DG E    +   R+  ++ +   +  L  RER I   R    +  
Sbjct: 458 ESEDSSFGDFL---EDGHESSPADAAMREMLKDKIEHVLKSLTYREREIIRLRYGLGDGY 514

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             TLE     F+V+RER+RQIE++A +K+Q   + 
Sbjct: 515 SYTLEETGRIFKVTRERIRQIESKALRKLQHQTRS 549


>gi|300858635|ref|YP_003783618.1| RNA polymerase sigma factor B [Corynebacterium pseudotuberculosis
           FRC41]
 gi|300686089|gb|ADK29011.1| RNA polymerase sigma factor B [Corynebacterium pseudotuberculosis
           FRC41]
 gi|302206344|gb|ADL10686.1| RNA polymerase sigma factor sigB [Corynebacterium
           pseudotuberculosis C231]
 gi|302330901|gb|ADL21095.1| RNA polymerase sigma factor sigB [Corynebacterium
           pseudotuberculosis 1002]
 gi|308276586|gb|ADO26485.1| RNA polymerase sigma factor sigB [Corynebacterium
           pseudotuberculosis I19]
          Length = 329

 Score =  207 bits (528), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 66/315 (20%), Positives = 138/315 (43%), Gaps = 39/315 (12%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAK---------------------- 39
           +R+  +        +  Y++ I K  +L  ++E  LA+                      
Sbjct: 18  SRRGQTNDNPSADLVRVYLNGIGKTALLSAEDEVELAQTIEVGLYAAHLLEDSEEPLTRA 77

Query: 40  -----RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                +        A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD
Sbjct: 78  MKRDLKVLVKDGRKARAHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFD 137

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +GF+ +TY+ WWI+ A+   +      +++     ++     L R+K  +        
Sbjct: 138 YSKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLSRIKREMYQHLGREA 195

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
             E    +A++  + ES++  +  +     SL+  + + ++  +   D++        + 
Sbjct: 196 TNE---ELAEESGIDESKIEILLRQSRDPVSLDMPVGADEE--APLGDFIEDSEATDAES 250

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
            +    R    + +   +  L  RE+ +   R   ++  P TL+ +  +F +SRERVRQI
Sbjct: 251 AVVASLR---HSDIRSVLDTLERREQDVIRMRYGLDDGVPRTLDQIGRQFGLSRERVRQI 307

Query: 273 EARAFKKVQESIQKQ 287
           E     K+++  +  
Sbjct: 308 EREVMTKLRDGARAD 322


>gi|158337052|ref|YP_001518227.1| RNA polymerase sigma factor SigD [Acaryochloris marina MBIC11017]
 gi|158307293|gb|ABW28910.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 318

 Score =  207 bits (528), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 67/312 (21%), Positives = 136/312 (43%), Gaps = 52/312 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------------- 43
            +  +  Y+ EI ++P+L  +EE    K+ +                             
Sbjct: 7   AKDSVRSYLREIGRVPLLTHEEEVTFGKQVQHLIKLQTIRDELAEQLERQPNDAEWSAAA 66

Query: 44  -----------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                      H   +A  ++V ++LRLVV +A  Y    + + +++ EG IG+ + V+K
Sbjct: 67  KLSEAELQKALHEGEAAKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGTIGMQRGVEK 126

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FDP +G+R +TY+ WWI+ A+   I      +++     +K     L ++K   + ++  
Sbjct: 127 FDPTKGYRFSTYAYWWIRQAITRAIAEKGRTIRLPIHITEK-----LNKIKKTQRQLSQK 181

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +   +  +A  L+++  +V     R     SL+  +   D   ++  + +    +  E
Sbjct: 182 LGRAATISELATSLDLTTKQVREYLERARQPLSLD--VRVGDNQDTELGELIEDPSESPE 239

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVR 270
              ++   R +    L R M+ L  +++++   R   ++  P+TL  +     +SRERVR
Sbjct: 240 NFTLQASLRGD----LERLMADLTDQQQQVLHLRFGLDDGQPLTLAKIGDRLSISRERVR 295

Query: 271 QIEARAFKKVQE 282
           QIE  A  K+++
Sbjct: 296 QIEREALSKLRK 307


>gi|5921146|dbj|BAA84590.1| RNA polymerase sigma 70 [Helicobacter pylori]
          Length = 675

 Score =  207 bits (528), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 70/237 (29%), Positives = 121/237 (51%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ W
Sbjct: 435 RAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATW 494

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WIK A+   I      ++I        +   + R+   ++     N K   +  +A+++ 
Sbjct: 495 WIKQAISRAIADQARTIRIPIH-----MIDTINRINKVMRKHIQENGKEPDLEVVAEEVG 549

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  
Sbjct: 550 LSLDKVKNVIKVTKEPISLETPVGNDDD--GKFGDFV---EDKNIASSIDHIMREDLKAQ 604

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 605 IESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 661



 Score = 35.9 bits (82), Expect = 7.1,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 19/36 (52%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+  I +L K EE  L+K+ R   D+
Sbjct: 160 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDI 195


>gi|325473907|gb|EGC77095.1| RNA polymerase sigma-70 factor family protein [Treponema denticola
           F0402]
          Length = 619

 Score =  207 bits (528), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 65/261 (24%), Positives = 120/261 (45%), Gaps = 14/261 (5%)

Query: 30  EKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
              E   L    +  +    +A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL+
Sbjct: 360 TVDEVIDLTSEIKNGQRMLKNAKDKLINANLRLVVSIAKKYINRGLQFFDLVQEGNIGLI 419

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV+KF+  +G++ +TY+ WWI+ A+   I      +++        +   + ++    +
Sbjct: 420 KAVEKFEYRKGYKFSTYATWWIRQAITRSISDQARTIRVPVH-----MIEQINKVNRESR 474

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
            +     +      IA +L  S  +V  +        SL   I   ++  +   D +   
Sbjct: 475 QLMQKLGREPNDDEIALQLGWSIEKVKQVKNVAREPISLETPI--GEEEDTLLGDLI--- 529

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVS 265
            D   +    + E    +  L   +S L  RE+ + + R   E   P+TLE +   F+V+
Sbjct: 530 EDKGVENPSNRTELTLLQEQLEMVLSSLPEREQEVLKMRFGIEGGYPLTLEEVGLYFDVT 589

Query: 266 RERVRQIEARAFKKVQESIQK 286
           RER+RQIEA+  ++++   + 
Sbjct: 590 RERIRQIEAKGLRRLRHPKRS 610


>gi|317010368|gb|ADU84115.1| RNA polymerase sigma factor RpoD [Helicobacter pylori SouthAfrica7]
          Length = 685

 Score =  207 bits (528), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 70/237 (29%), Positives = 121/237 (51%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ W
Sbjct: 445 RAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATW 504

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WIK A+   I      ++I        +   + R+   ++     N K   +  +A+++ 
Sbjct: 505 WIKQAISRAIADQARTIRIPIH-----MIDTINRINKVMRKYMQENGKEPDLELVAEEVG 559

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  
Sbjct: 560 LSLDKVKNVIKVTKEPISLETPVGNDDD--GKFGDFV---EDKNIVSSIDHIMREDLKAQ 614

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 615 IDGVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 671



 Score = 35.9 bits (82), Expect = 7.0,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 19/36 (52%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+  I +L K EE  L+K+ R   D+
Sbjct: 170 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDI 205


>gi|225849737|ref|YP_002729971.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Persephonella marina EX-H1]
 gi|225645950|gb|ACO04136.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Persephonella marina EX-H1]
          Length = 285

 Score =  207 bits (528), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 90/280 (32%), Positives = 147/280 (52%), Gaps = 13/280 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E G++ Y++ I KIP+L  +EE  +AK+ +E GD  A  +L+ S+LR VV +A  Y GYG
Sbjct: 7   EEGITYYLNSISKIPLLSPEEEKEIAKKAKE-GDKEALEKLIKSNLRFVVNVAKNYTGYG 65

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +P  E++S GNIGL++A K+FDPERG R  +Y++WWIK ++ + I     ++KI      
Sbjct: 66  IPFQELISAGNIGLIEAAKRFDPERGVRFISYAIWWIKQSILQTIQSQKDIIKIP--QKT 123

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK---LNVSESEVISMNCRLAGDESLNAL 189
           + L   +      L+   +   K  ++    K+   +++ E  + +         SL+  
Sbjct: 124 QNLSMKIDTAYLELKERLNREPKYSEIKEYLKEHENIDIDEETIENYLLIKRHSVSLDTP 183

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL- 248
           +   D +   +   L+  H  ++  + E   R++    +   +S L+ RER I   R   
Sbjct: 184 V---DMDEGTFFIDLISKHSTKD--IEENIVRESIEKEIEYILSHLSERERFIIVNRFGL 238

Query: 249 -QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             E P TL  +  E  +SRERVRQIE RA KK++    K+
Sbjct: 239 NGEEPKTLREIGKELGISRERVRQIEIRALKKIRALATKK 278


>gi|42526854|ref|NP_971952.1| RNA polymerase sigma factor RpoD [Treponema denticola ATCC 35405]
 gi|41817169|gb|AAS11863.1| RNA polymerase sigma-70 factor family protein [Treponema denticola
           ATCC 35405]
          Length = 619

 Score =  207 bits (528), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 65/261 (24%), Positives = 120/261 (45%), Gaps = 14/261 (5%)

Query: 30  EKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
              E   L    +  +    +A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL+
Sbjct: 360 TVDEVIDLTSEIKNGQRMLKNAKDKLINANLRLVVSIAKKYINRGLQFFDLVQEGNIGLI 419

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV+KF+  +G++ +TY+ WWI+ A+   I      +++        +   + ++    +
Sbjct: 420 KAVEKFEYRKGYKFSTYATWWIRQAITRSISDQARTIRVPVH-----MIEQINKVNRESR 474

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
            +     +      IA +L  S  +V  +        SL   I   ++  +   D +   
Sbjct: 475 QLMQKLGREPNDDEIALQLGWSIEKVKQVKNVAREPISLETPI--GEEEDTLLGDLI--- 529

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVS 265
            D   +    + E    +  L   +S L  RE+ + + R   E   P+TLE +   F+V+
Sbjct: 530 EDKGVENPSNRTELTLLQEQLEMVLSSLPEREQEVLKMRFGIEGGYPLTLEEVGLYFDVT 589

Query: 266 RERVRQIEARAFKKVQESIQK 286
           RER+RQIEA+  ++++   + 
Sbjct: 590 RERIRQIEAKGLRRLRHPKRS 610


>gi|55980501|ref|YP_143798.1| RNA polymerase pricipal sigma factor RpoD [Thermus thermophilus
           HB8]
 gi|209447478|pdb|3DXJ|F Chain F, Crystal Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme In Complex With The Antibiotic Myxopyronin
 gi|209447484|pdb|3DXJ|P Chain P, Crystal Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme In Complex With The Antibiotic Myxopyronin
 gi|55771914|dbj|BAD70355.1| RNA polymerase pricipal sigma factor (RpoD) [Thermus thermophilus
           HB8]
          Length = 423

 Score =  207 bits (528), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 66/237 (27%), Positives = 111/237 (46%), Gaps = 10/237 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +A   L+ ++LRLVV IA  Y G GL   +++ EGN GL++AV+KF+ +R F+ +TY+ 
Sbjct: 181 EAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYAT 240

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I     +      L R    LQ         E++   A   
Sbjct: 241 WWIRQAINRAIADQARTIRIPVHMVE--TINKLSRTARQLQQELGREPTYEEIAE-AMGP 297

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
                 V           SL   I   D+  S + D++  +H       ++   +     
Sbjct: 298 GWDAKRVEETLKIAQEPVSLETPI--GDEKDSFYGDFIPDEHL---PSPVDAATQSLLSE 352

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L +++S L+ RE  + + R+        TLE + + F V+RER+RQIE +A +K++
Sbjct: 353 ELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLK 409


>gi|46198472|ref|YP_004139.1| RNA polymerase sigma factor rpoD [Thermus thermophilus HB27]
 gi|21730342|pdb|1IW7|F Chain F, Crystal Structure Of The Rna Polymerase Holoenzyme From
           Thermus Thermophilus At 2.6a Resolution
 gi|21730348|pdb|1IW7|P Chain P, Crystal Structure Of The Rna Polymerase Holoenzyme From
           Thermus Thermophilus At 2.6a Resolution
 gi|49259060|pdb|1SMY|F Chain F, Structural Basis For Transcription Regulation By Alarmone
           Ppgpp
 gi|49259066|pdb|1SMY|P Chain P, Structural Basis For Transcription Regulation By Alarmone
           Ppgpp
 gi|78101162|pdb|1ZYR|F Chain F, Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme In Complex With The Antibiotic Streptolydigin
 gi|78101168|pdb|1ZYR|P Chain P, Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme In Complex With The Antibiotic Streptolydigin
 gi|78101224|pdb|2A68|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Rifabutin
 gi|78101230|pdb|2A68|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Rifabutin
 gi|78101236|pdb|2A69|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Rifapentin
 gi|78101242|pdb|2A69|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Rifapentin
 gi|78101248|pdb|2A6E|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme
 gi|78101254|pdb|2A6E|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme
 gi|78101260|pdb|2A6H|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Sterptolydigin
 gi|78101266|pdb|2A6H|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Sterptolydigin
 gi|78101762|pdb|2CW0|F Chain F, Crystal Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme At 3.3 Angstroms Resolution
 gi|78101768|pdb|2CW0|P Chain P, Crystal Structure Of Thermus Thermophilus Rna Polymerase
           Holoenzyme At 3.3 Angstroms Resolution
 gi|83754377|pdb|2BE5|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Inhibitor Tagetitoxin
 gi|83754383|pdb|2BE5|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Inhibitor Tagetitoxin
 gi|210061069|pdb|3EQL|F Chain F, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Myxopyronin
 gi|210061075|pdb|3EQL|P Chain P, Crystal Structure Of The T. Thermophilus Rna Polymerase
           Holoenzyme In Complex With Antibiotic Myxopyronin
 gi|4239959|dbj|BAA74758.1| principal sigma factor [Thermus thermophilus]
 gi|46196094|gb|AAS80512.1| RNA polymerase sigma factor rpoD [Thermus thermophilus HB27]
          Length = 423

 Score =  207 bits (528), Expect = 1e-51,   Method: Composition-based stats.
 Identities = 66/237 (27%), Positives = 111/237 (46%), Gaps = 10/237 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +A   L+ ++LRLVV IA  Y G GL   +++ EGN GL++AV+KF+ +R F+ +TY+ 
Sbjct: 181 EAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYAT 240

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I     +      L R    LQ         E++   A   
Sbjct: 241 WWIRQAINRAIADQARTIRIPVHMVE--TINKLSRTARQLQQELGREPTYEEIAE-AMGP 297

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
                 V           SL   I   D+  S + D++  +H       ++   +     
Sbjct: 298 GWDAKRVEETLKIAQEPVSLETPI--GDEKDSFYGDFIPDEHL---PSPVDAATQSLLSE 352

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L +++S L+ RE  + + R+        TLE + + F V+RER+RQIE +A +K++
Sbjct: 353 ELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKALRKLK 409


>gi|33862619|ref|NP_894179.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9313]
 gi|33634535|emb|CAE20521.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9313]
          Length = 313

 Score =  207 bits (528), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 76/302 (25%), Positives = 144/302 (47%), Gaps = 36/302 (11%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------EHG-------------------D 46
               +S Y+  I +IP+L   EE  L  + +      + G                    
Sbjct: 16  SSDPVSWYLTTIGRIPLLTPAEEIELGNQVQTMMSLTQDGSVAPDDKEFTTHQRRMIRIG 75

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  R++ ++LRLVV +A  Y+G GL + +++ EG++GL +AV+KFDP RG++ +TY+ 
Sbjct: 76  RRAKERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRGYKFSTYAF 135

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ +M   I      +++    +++     L  ++     +            IA+ +
Sbjct: 136 WWIRQSMTRAIACQSRTIRLPVHLSER-----LTTIRKVSLDLAHKLGAIPSRSEIAEAM 190

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   E+ S+  +     SL+A +N  ++  S   D +     G+    ++K E++    
Sbjct: 191 DIPVDELDSLLRQALTTSSLDAPVN-GEERRSFLGDLIADSSLGE---PLDKVEQRIHHE 246

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L R +S L+ +E+ + + R   E  +  TL  +    EVSRERVRQ+E +A +K++   
Sbjct: 247 QLGRWLSHLSEQEQHVLKLRFGLETHDRHTLAEIGRLMEVSRERVRQVELKALRKLRNLT 306

Query: 285 QK 286
           ++
Sbjct: 307 RR 308


>gi|16331222|ref|NP_441950.1| RNA polymerase sigma factor [Synechocystis sp. PCC 6803]
 gi|1001398|dbj|BAA10020.1| RNA polymerase sigma factor [Synechocystis sp. PCC 6803]
          Length = 345

 Score =  207 bits (528), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 67/335 (20%), Positives = 142/335 (42%), Gaps = 56/335 (16%)

Query: 1   MNRKNMSIIVN----GEIGLSRYIHEIRKIPMLEKQEEYVLAKR---------------- 40
           M   N+S   +        +  Y+HEI ++P+L  ++E +L K+                
Sbjct: 18  MPTANLSSPTSPPTFTADMVRSYLHEIGRVPLLTHEQEIILGKQVQQMMALLEHKKALAD 77

Query: 41  ----------YREHGD-------------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
                     + E  D               A  +++ ++LRLVV IA  Y+   +   +
Sbjct: 78  RLGREPSDPEWAEAADLSVTKLHRYLGQGERAKRKMIEANLRLVVAIAKKYQKRNMEFLD 137

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EG++GL + V+KFDP +G++ +TY+ WWI+ A+   I +    +++     +K    
Sbjct: 138 LIQEGSLGLERGVEKFDPTKGYKFSTYAYWWIRQAITRAIAQQGRTIRLPIHITEK---- 193

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L ++K   + ++    +      +AK L +  S++           SL+  +   D   
Sbjct: 194 -LNKIKKTQRELSQQLGRSATPAEVAKALEIDPSQIREYLSLSRQPISLD--VRVGDNQD 250

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTL 255
           ++  + L  +    +  + +    ++ R  L   ++ L P+++ +   R    +   ++L
Sbjct: 251 TELSELLEDEGVSPDAYITQ----ESMRQDLQNLLAELTPQQQAVLTMRFGLNDGQELSL 306

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
             +     +SRERVRQ+E +A  +++       E 
Sbjct: 307 AKIGQHLNISRERVRQLENQALAQLKRRRANMAEY 341


>gi|216263390|ref|ZP_03435385.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia afzelii
           ACA-1]
 gi|215980234|gb|EEC21055.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia afzelii
           ACA-1]
          Length = 631

 Score =  207 bits (528), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 67/257 (26%), Positives = 122/257 (47%), Gaps = 16/257 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 379 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 434

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RGF+ +TY+ WWI+ A+   I      +++        +   + RL    + +   
Sbjct: 435 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVH-----MIEQINRLNRETRYLVQV 489

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             K      ++ +L     +V ++        SL   I   ++  S   D++    D   
Sbjct: 490 LGKDPTDEELSDRLGWELKKVKTVKSVSREPVSLETPI--GEEEDSVLSDFI---EDKAI 544

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +           ++ +   +  L  RE+ + + R   E+   +TLE +   F V+RER+R
Sbjct: 545 KNPANHTSFVVLQDQIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIR 604

Query: 271 QIEARAFKKVQESIQKQ 287
           QIE++A ++++   + Q
Sbjct: 605 QIESKALRRLKNPKKTQ 621


>gi|320160330|ref|YP_004173554.1| RNA polymerase sigma factor [Anaerolinea thermophila UNI-1]
 gi|319994183|dbj|BAJ62954.1| RNA polymerase sigma factor [Anaerolinea thermophila UNI-1]
          Length = 543

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 82/310 (26%), Positives = 141/310 (45%), Gaps = 50/310 (16%)

Query: 16  LSRYIHEIRKIPMLE-----------KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           L  Y+ E+  +P +E             EE    +R  E     A   L+ ++LRLVV I
Sbjct: 238 LMNYLREVHALPRVEFFVEHMPDEDILAEEVEGVRRRAE----DANQTLIRANLRLVVSI 293

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y G G+   +++ EGN+GL++AV KFDP RG++ +TY+ WWI+ ++  YI      +
Sbjct: 294 AKRYLGRGVSFLDLIQEGNLGLLRAVNKFDPTRGYKFSTYATWWIRQSISRYIAEQARTI 353

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV------------------------ 160
           +I     +      L R++  L          E++                         
Sbjct: 354 RIPVHLFES--ITRLLRVQRTLIQQLGREPTAEELALEAGFLSDEDAQAIRKARAEGKSI 411

Query: 161 --AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              + ++ N + S+V  +        SL   +   D++SSQ  D++  D   +    ++ 
Sbjct: 412 DPELMRRWNFATSKVQRVLQSAEEPVSLERPV--GDEDSSQLGDFIEDDEALE---PMDA 466

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARA 276
             R+  R  +  ++S+L+ RER++ E R         TLE +S  F V+RER+RQIEA+A
Sbjct: 467 AAREMLREQVQNALSILSERERQVLELRFGLIDGKDHTLEEVSRYFNVTRERIRQIEAKA 526

Query: 277 FKKVQESIQK 286
            +K++   + 
Sbjct: 527 LRKLRHPTRS 536



 Score = 37.1 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 24/49 (48%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHR 52
           ++++ +   E  +  Y+ EI +I +L+   E+ LA R      L A  +
Sbjct: 84  ESLATLEFSEDPVRLYLKEIGQINLLDADSEFRLAARIEAWRHLEALEK 132


>gi|89901551|ref|YP_524022.1| sigma-70 region 2 [Rhodoferax ferrireducens T118]
 gi|89346288|gb|ABD70491.1| sigma-70 region 2 [Rhodoferax ferrireducens T118]
          Length = 350

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 80/276 (28%), Positives = 142/276 (51%), Gaps = 12/276 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             L+ Y+ ++R+  +   QEE+ LA R R  GD +A   ++  +LRLVV IA  Y G G+
Sbjct: 71  DALTVYLRQVRRTTLFTPQEEFELAGRAR-AGDFAARQSMIEHNLRLVVSIAKAYMGRGV 129

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGN+GLM A+ KF+PERGFR +TY+ WWI+ ++   ++    +V++    N  
Sbjct: 130 PLLDLIEEGNLGLMHAIDKFEPERGFRFSTYATWWIRQSVDRALMCQGRVVRLPV--NVV 187

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQ---VVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
           R    + R +  L++     +       V  +A  L      V  +        SL+A +
Sbjct: 188 RELQQVLRARRALESDAAFVVSRPDGIRVEDVAALLGRDPVHVADLLGLAEAPRSLDAAL 247

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           + S +  + + D LV +       + +  E +    +L   +  L+ RE+ + E R    
Sbjct: 248 DRSGETQT-FGDSLVDEITADPSGVTQVHEVE---RLLEEWVGTLSEREKEVLEGRFGLH 303

Query: 251 N--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +  P TL+ LS+  +++RERVRQ++  A  K++  +
Sbjct: 304 DREPETLDVLSARLDLTRERVRQVQNEALAKLKRYL 339


>gi|332711345|ref|ZP_08431277.1| RNA polymerase sigma factor, sigma-70 family//RpoD-like family
           [Lyngbya majuscula 3L]
 gi|332349894|gb|EGJ29502.1| RNA polymerase sigma factor, sigma-70 family//RpoD-like family
           [Lyngbya majuscula 3L]
          Length = 319

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 70/318 (22%), Positives = 135/318 (42%), Gaps = 52/318 (16%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------- 43
           M    +    +  Y+ EI ++P+L  ++E    K+ ++                      
Sbjct: 1   MKTAQDSTDLVRTYLKEIGRVPLLTHEQEISYGKKVKQLTTLKEVKESLVQQLGREPTFS 60

Query: 44  -----------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
                                SA  ++V ++LRLVV +A  Y    L + +++ EG IGL
Sbjct: 61  EWATASCLTDSQLKSSIAVGESAKRKMVEANLRLVVAVAKKYIKRNLELLDLIQEGTIGL 120

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
            + V+KFDP +G+R +TY+ WWI+ A+   I      +++     +K     L ++K   
Sbjct: 121 QRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKGRTIRLPIHITEK-----LNKIKKAQ 175

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           + ++    +   +  +A +LN++  ++     +     SL   +   D   ++  + L  
Sbjct: 176 RQLSQKLGRTATISELAIELNLTPDQLREYFEQARQPLSLE--LRVGDNKDTELVELLED 233

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
              G E  + +   + +    L + M  L P++R++   R       P+TL  +     +
Sbjct: 234 TGPGPEDFVNQSLMQLD----LEKFMDDLTPQQRQVLRLRYGLAEVEPMTLAKIGQHLNI 289

Query: 265 SRERVRQIEARAFKKVQE 282
           SRERVRQIE  A  K+++
Sbjct: 290 SRERVRQIEREAIAKLRK 307


>gi|210134292|ref|YP_002300731.1| RNA polymerase sigma factor RpoD [Helicobacter pylori P12]
 gi|210132260|gb|ACJ07251.1| RNA polymerase sigma-80 factor [Helicobacter pylori P12]
          Length = 680

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 70/237 (29%), Positives = 121/237 (51%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ W
Sbjct: 440 RAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATW 499

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WIK A+   I      ++I        +   + R+   ++     N K   +  +A+++ 
Sbjct: 500 WIKQAISRAIADQARTIRIPIH-----MIDTINRINKVMRKHIQENGKEPDLEVVAEEVG 554

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  
Sbjct: 555 LSLDKVKNVIKVTKEPISLETPVGNDDD--GKFGDFV---EDKNIVSSIDHIMREDLKAQ 609

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 610 IESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 666



 Score = 35.9 bits (82), Expect = 6.9,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 19/36 (52%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+  I +L K EE  L+K+ R   D+
Sbjct: 165 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDI 200


>gi|256383860|gb|ACU78430.1| RNA polymerase sigma-A factor [Mycoplasma mycoides subsp. capri
           str. GM12]
 gi|256384691|gb|ACU79260.1| RNA polymerase sigma-A factor [Mycoplasma mycoides subsp. capri
           str. GM12]
 gi|296455677|gb|ADH21912.1| RNA polymerase sigma-A factor [synthetic Mycoplasma mycoides
           JCVI-syn1.0]
          Length = 506

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 70/329 (21%), Positives = 137/329 (41%), Gaps = 71/329 (21%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSA---AHRLVTSHLRLVVKIAMGYRGYG 72
           +  Y ++I + P+L K++E + AK              ++L+ S+L+LV+ +A  +   G
Sbjct: 171 IKTYFYKIGQAPILTKEQEIIYAKMAVSDDPEDVQEGRNKLIESNLKLVISVARKHLNRG 230

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L  ++++ EGNIGLM+AV KF+ E+GF+ +TY+ WWI+ A+   I      ++I     +
Sbjct: 231 LDFADLIEEGNIGLMKAVDKFEYEKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 290

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN--VSESEVISMNCRLAGDESLNALI 190
                 + +L    + +T    +      IA ++   ++  +VI +        SL    
Sbjct: 291 -----TINKLARVERQLTQELGREPNADEIANRVGEGITGDKVIEIKKLSIEPVSLEKPF 345

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF------- 243
              D++ + + D++    D       E  E++  + ++ +    + PRE ++        
Sbjct: 346 --GDEDDTHFGDFV---EDKDMVSPNEYTEKEILKEVMDKVFEDMPPREEKVIRMRYGIV 400

Query: 244 --EARRLQ-----------------------------------------------ENPVT 254
               R L                                                ++  T
Sbjct: 401 PTRLRTLLRLAQECNDSNAKELKQAIEELDIHLDTPIEKVRKFNNQIINNNLAKYDSART 460

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQES 283
           LE +  E  V+RER+RQIEA+  +K+++ 
Sbjct: 461 LEEVGKELNVTRERIRQIEAKTIRKLKQP 489


>gi|111115542|ref|YP_710160.1| RNA polymerase sigma factor RpoD [Borrelia afzelii PKo]
 gi|110890816|gb|ABH01984.1| RNA polymerase sigma-70 factor [Borrelia afzelii PKo]
          Length = 631

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 67/257 (26%), Positives = 122/257 (47%), Gaps = 16/257 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 379 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 434

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RGF+ +TY+ WWI+ A+   I      +++        +   + RL    + +   
Sbjct: 435 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVH-----MIEQINRLNRETRYLVQV 489

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             K      ++ +L     +V ++        SL   I   ++  S   D++    D   
Sbjct: 490 LGKDPTDEELSDRLGWELKKVKTVKSVSREPVSLETPI--GEEEDSVLSDFI---EDKAI 544

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +           ++ +   +  L  RE+ + + R   E+   +TLE +   F V+RER+R
Sbjct: 545 KNPANHTSFVVLQDQIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIR 604

Query: 271 QIEARAFKKVQESIQKQ 287
           QIE++A ++++   + Q
Sbjct: 605 QIESKALRRLKNPKKTQ 621


>gi|317011933|gb|ADU82541.1| RNA polymerase sigma factor RpoD [Helicobacter pylori Lithuania75]
          Length = 680

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 70/237 (29%), Positives = 121/237 (51%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ W
Sbjct: 440 RAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATW 499

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WIK A+   I      ++I        +   + R+   ++     N K   +  +A+++ 
Sbjct: 500 WIKQAISRAIADQARTIRIPIH-----MIDTINRINKVMRKHIQENGKEPDLEVVAEEVG 554

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  
Sbjct: 555 LSLDKVKNVIKVTKEPISLETPVGNDDD--GKFGDFV---EDKNIVSSIDHIMREDLKAQ 609

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 610 IESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 666



 Score = 35.9 bits (82), Expect = 6.9,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 19/36 (52%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+  I +L K EE  L+K+ R   D+
Sbjct: 165 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDI 200


>gi|217032875|ref|ZP_03438353.1| hypothetical protein HPB128_1g12 [Helicobacter pylori B128]
 gi|298736968|ref|YP_003729498.1| RNA polymerase primary sigma factor [Helicobacter pylori B8]
 gi|216945415|gb|EEC24081.1| hypothetical protein HPB128_1g12 [Helicobacter pylori B128]
 gi|298356162|emb|CBI67034.1| RNA polymerase primary sigma factor [Helicobacter pylori B8]
          Length = 679

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 70/237 (29%), Positives = 121/237 (51%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ W
Sbjct: 439 RAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATW 498

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WIK A+   I      ++I        +   + R+   ++     N K   +  +A+++ 
Sbjct: 499 WIKQAISRAIADQARTIRIPIH-----MIDTINRINKVMRKHIQENGKEPDLEVVAEEVG 553

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  
Sbjct: 554 LSLDKVKNVIKVTKEPISLETPVGNDDD--GKFGDFV---EDKNIVSSIDHIMREDLKAQ 608

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 609 IESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 665



 Score = 35.9 bits (82), Expect = 6.9,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 19/36 (52%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+  I +L K EE  L+K+ R   D+
Sbjct: 164 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDI 199


>gi|260911629|ref|ZP_05918210.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella sp. oral
           taxon 472 str. F0295]
 gi|260634235|gb|EEX52344.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella sp. oral
           taxon 472 str. F0295]
          Length = 290

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 72/287 (25%), Positives = 134/287 (46%), Gaps = 12/287 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKI 64
           SI       L +Y+ EI + P++   EE  LA++ R+ G     A  +LVT++LR VV +
Sbjct: 9   SITNRSSEALDKYLVEIGRAPLISIDEEIELAQKIRKGGPEGEKAKDKLVTANLRFVVSV 68

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y+  GL +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V
Sbjct: 69  AKQYQHQGLTLTDLIDEGNIGLIKAAQKFDETRGFKFISYAVWWIRQSILQAIAEQSRIV 128

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           ++           +L ++   +      N +   V  ++   N+ E ++           
Sbjct: 129 RLPLNQ-----VGSLNKINHEINKFEQENQRHPSVSELSDATNLDEEKIGQSLMADGHHV 183

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           S++A     + N     D +    D +     + E      N +     VL  RE  I  
Sbjct: 184 SIDAPFQDGEDNC--MLDVMASGDDSRTDKQADHESMALELNSV--LAKVLKDREITIIR 239

Query: 245 ARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
                  +   LE +  +  ++RERVRQI  ++  K+++S   ++ +
Sbjct: 240 ECFGIGCHEKGLEEIGDQLGLTRERVRQIREKSIAKLRDSGNAKILM 286


>gi|149194280|ref|ZP_01871377.1| RNA polymerase sigma factor RpoD [Caminibacter mediatlanticus TB-2]
 gi|149135455|gb|EDM23934.1| RNA polymerase sigma factor RpoD [Caminibacter mediatlanticus TB-2]
          Length = 604

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 64/239 (26%), Positives = 118/239 (49%), Gaps = 13/239 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A  ++  ++LRLVV IA  Y   GLP  +++ EGNIGLM+A+ KF+ E+G++ +TY+ W
Sbjct: 364 EAKEKMARANLRLVVSIAKKYTNRGLPFLDLIQEGNIGLMKAIDKFEFEKGYKFSTYATW 423

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      V+I        +  N+ ++   ++       K   +  IAK++ 
Sbjct: 424 WIRQAISRAIADQARTVRIPIH-----MIENINQINKIIRKYVQEEGKEPSLEVIAKEMK 478

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +   ++  +        SL A +   ++   ++ D++    D       ++   ++ R  
Sbjct: 479 MPVEKIKQILKISKEPISLEAPV--GEEEDGKFGDFI---EDKSFSNPYDEVVLEDLRKH 533

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +   +  LN RE+ + + R      ++  TLE +     V+RERVRQIE+ A KK++  
Sbjct: 534 IDEILENLNEREKAVIKMRFGLMPDKSERTLEEIGKALNVTRERVRQIESSAIKKLRHP 592



 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 9/31 (29%), Positives = 18/31 (58%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR 42
            +  +  Y+ E+  IP+L+K EE  + +R +
Sbjct: 96  SDSPVRMYLREMGHIPLLDKDEEVEIFRRIQ 126


>gi|118463509|ref|YP_882780.1| RNA polymerase sigma factor SigB [Mycobacterium avium 104]
 gi|254776043|ref|ZP_05217559.1| RNA polymerase sigma factor SigB [Mycobacterium avium subsp. avium
           ATCC 25291]
 gi|118164796|gb|ABK65693.1| sigma factor SigB [Mycobacterium avium 104]
          Length = 319

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 69/311 (22%), Positives = 134/311 (43%), Gaps = 38/311 (12%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREH--------------- 44
           ++         +  Y++ I K  +L    E  LAKR     Y EH               
Sbjct: 12  DLDAQSPAADLVRVYLNGIGKTALLNAAGEVELAKRIEAGLYAEHLLETRKRLGENRKRD 71

Query: 45  ------GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
                    +A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +G
Sbjct: 72  LEAVVRDGQAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKG 131

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           F+ +TY+ WWI+ A+   +      +++     ++     L R+K  +     N  +   
Sbjct: 132 FKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLARIKREMHQ---NLGREAT 186

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              +A +  +   ++  +        SL+  + S ++  +   D++    D +       
Sbjct: 187 DEELAAESGIPIDKINDLLEHSRDPVSLDMPVGSEEE--APLGDFI---EDAEAMSAENA 241

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARA 276
              +     +   ++ L+ RE ++   R   ++  P TL+ +   F +SRERVRQIE   
Sbjct: 242 VIAELLHTDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDV 301

Query: 277 FKKVQESIQKQ 287
             K++   +  
Sbjct: 302 MSKLRNGERAD 312


>gi|39132|emb|CAA49185.1| vegetative sigma factor [Agrobacterium tumefaciens str. C58]
          Length = 684

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 66/251 (26%), Positives = 115/251 (45%), Gaps = 15/251 (5%)

Query: 41  YREHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
             + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 435 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 494

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWI+ A+   I      ++I        +   + ++    + +     +  
Sbjct: 495 GYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIETINKIVRTSRQMLHEIGREP 549

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A+KL +   +V  +        SL   +   D+  S   D++    D    + I+
Sbjct: 550 TPEELAEKLAMPLEKVRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKNALLPID 604

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
              +   R   TR ++ L P E R+             TLE +  +F V+RER+RQIEA+
Sbjct: 605 AAIQGFLRETTTRVLASLTPSEERVLRMPFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 664

Query: 276 AFKKVQESIQK 286
           A + V+   + 
Sbjct: 665 ALRNVKHPSRS 675


>gi|596248|gb|AAC44104.1| primary sigma factor [Borrelia burgdorferi]
          Length = 543

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 67/257 (26%), Positives = 122/257 (47%), Gaps = 16/257 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 291 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 346

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RGF+ +TY+ WWI+ A+   I      +++        +   + RL    + +   
Sbjct: 347 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVH-----MIEQINRLNRETRYLIQV 401

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             K      ++ +L     +V ++        SL   I   ++  S   D++    D   
Sbjct: 402 LGKDPTDEELSDRLGWELKKVKTVKSVSREPVSLETPI--GEEEDSVLSDFI---EDKAI 456

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +           ++ +   +  L  RE+ + + R   E+   +TLE +   F V+RER+R
Sbjct: 457 KNPANHTSFVVLQDQIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIR 516

Query: 271 QIEARAFKKVQESIQKQ 287
           QIE++A ++++   + Q
Sbjct: 517 QIESKALRRLKNPKKTQ 533


>gi|148657263|ref|YP_001277468.1| RpoD family RNA polymerase sigma factor [Roseiflexus sp. RS-1]
 gi|148569373|gb|ABQ91518.1| RNA polymerase, sigma 70 subunit, RpoD family [Roseiflexus sp.
           RS-1]
          Length = 345

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 86/311 (27%), Positives = 139/311 (44%), Gaps = 38/311 (12%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD-------------- 46
           ++ K +S     +     Y+ EI ++ +L  +EE  LA   R   +              
Sbjct: 34  LDEKRLSRSETIDDSTQMYLREIGQVSLLSAEEEITLANDIRAGREAQERLKSHRFESLA 93

Query: 47  ------------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                         A  RL+ ++LRLVV IA  Y G  L   ++V EGNIGLM+AV+KFD
Sbjct: 94  ERLLLERRVMQAEEARRRLIQANLRLVVSIAKKYIGGPLSFMDLVQEGNIGLMRAVEKFD 153

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +G R +TY+ WWI+ A+   I     L+++    +   +   LRR+   L+   +   
Sbjct: 154 AGKGNRFSTYATWWIRQAITRAIAEQSRLIRLPVHLSD--VIAQLRRVARRLEQSLERE- 210

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
               V  IA  +++ E +V  +    A   SL   I S      Q  + L  D       
Sbjct: 211 --PTVEEIAAAIDMPEHKVKLLLQASAQPISLEQPITS--DGEGQISELLADDD---ADA 263

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQI 272
            +E   R+  ++ L +++  L  RER + + R    +    TLE + S F ++RER RQI
Sbjct: 264 PMEIATRRMLQHDLAQALMELPDRERAVLQLRYGLTDGRRRTLEEVGSAFGITRERTRQI 323

Query: 273 EARAFKKVQES 283
           EA A ++++  
Sbjct: 324 EADALRQLRRP 334


>gi|331703466|ref|YP_004400153.1| RNA polymerase sigma A factor [Mycoplasma mycoides subsp. capri LC
           str. 95010]
 gi|328802021|emb|CBW54175.1| RNA polymerase sigma A factor [Mycoplasma mycoides subsp. capri LC
           str. 95010]
          Length = 506

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 70/329 (21%), Positives = 137/329 (41%), Gaps = 71/329 (21%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSA---AHRLVTSHLRLVVKIAMGYRGYG 72
           +  Y ++I + P+L K++E + AK              ++L+ S+L+LV+ +A  +   G
Sbjct: 171 IKTYFYKIGQAPILTKEQEIIYAKMAVSDDPEDVQEGRNKLIESNLKLVISVARKHLNRG 230

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L  ++++ EGNIGLM+AV KF+ E+GF+ +TY+ WWI+ A+   I      ++I     +
Sbjct: 231 LDFADLIEEGNIGLMKAVDKFEYEKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 290

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN--VSESEVISMNCRLAGDESLNALI 190
                 + +L    + +T    +      IA ++   ++  +VI +        SL    
Sbjct: 291 -----TINKLARVERQLTQELGREPNADEIANRVGEGITGDKVIEIKKLSIEPVSLEKPF 345

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF------- 243
              D++ + + D++    D       E  E++  + ++ +    + PRE ++        
Sbjct: 346 --GDEDDTHFGDFV---EDKDMVSPNEYTEKEILKEVMDKVFEDMPPREEKVIRMRYGIV 400

Query: 244 --EARRLQ-----------------------------------------------ENPVT 254
               R L                                                ++  T
Sbjct: 401 PTRLRTLLRLAQECNDSNAKELKQAIEELDIHLDTPIEKVRKFNNQIINNNLAKYDSART 460

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQES 283
           LE +  E  V+RER+RQIEA+  +K+++ 
Sbjct: 461 LEEVGKELNVTRERIRQIEAKTIRKLKQP 489


>gi|282899735|ref|ZP_06307698.1| sigD (sigma 28 (flagella/spoulation)) [Cylindrospermopsis
           raciborskii CS-505]
 gi|281195350|gb|EFA70284.1| sigD (sigma 28 (flagella/spoulation)) [Cylindrospermopsis
           raciborskii CS-505]
          Length = 332

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 70/323 (21%), Positives = 135/323 (41%), Gaps = 52/323 (16%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------EHGD-------- 46
           +N   M         +  Y+ EI K+P+L  ++E    K+ +      E  D        
Sbjct: 10  LNSSAMKTAQTPTDIVRTYLREIGKVPLLTHEQEIYYGKQVQKSTALYETKDNLAQELNR 69

Query: 47  -------------------------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
                                      A  ++V ++LRLVV +A  Y    + + +++ E
Sbjct: 70  QPSLEEWAKAAQLDPQELNRLLGQGEIAKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQE 129

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           G+IG+ + V+KFDP +G+R +TY+ WWI+ A+   I      +++     +K     L +
Sbjct: 130 GSIGMQRGVEKFDPSKGYRFSTYAYWWIRQAITRAIAEKARTIRLPIHITEK-----LNK 184

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           +K   + ++    +   +  +A++L ++  +V     +     SL+  +   D   ++  
Sbjct: 185 IKKAQRYLSQTLGRSPSIAELAQELEITPKQVRDCLEKARLPLSLD--LRLGDNYDTELG 242

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLS 259
           + L       E  +I+          L R M+ L P++R + + R        +TL  + 
Sbjct: 243 EMLEDPGASPEDYVIQSSLSSE----LDRMMTHLTPQQREVIKLRFGLVDGQSMTLARIG 298

Query: 260 SEFEVSRERVRQIEARAFKKVQE 282
               +SRERVRQIE  A  +++ 
Sbjct: 299 EVLNISRERVRQIEREALTRLRR 321


>gi|171321354|ref|ZP_02910311.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia ambifaria
           MEX-5]
 gi|171093372|gb|EDT38562.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia ambifaria
           MEX-5]
          Length = 361

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 78/280 (27%), Positives = 132/280 (47%), Gaps = 15/280 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+
Sbjct: 81  DTIQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGV 139

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++       
Sbjct: 140 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV--I 197

Query: 134 RLFFNLRRLKGHLQAITDN-----NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           R    + R K HL+  + +       +   +  IA     +  EV  +        SL+A
Sbjct: 198 RELNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDA 257

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +      +S   D L  D        ++  E +    +    +S L+ + R + E R  
Sbjct: 258 PL--DLDPASSLLDLLPDDQSQSPDAEVQHRELE---TLTRAWLSRLSDKHRHVIERRFG 312

Query: 249 QE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                P TLE L+ E  ++RERVRQI+  A  +++     
Sbjct: 313 LNHIEPATLEELADEMGLTRERVRQIQQEALVRLKRFFAS 352


>gi|298490007|ref|YP_003720184.1| RpoD subfamily RNA polymerase sigma 70 subunit ['Nostoc azollae'
           0708]
 gi|298231925|gb|ADI63061.1| RNA polymerase, sigma 70 subunit, RpoD subfamily ['Nostoc azollae'
           0708]
          Length = 417

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 65/248 (26%), Positives = 130/248 (52%), Gaps = 13/248 (5%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           +   L A   ++ ++LRLVV +A  Y+  GL + ++V EG +GL +AV+KFDP +G+R +
Sbjct: 172 QSQGLQAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFS 231

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+  +   I  S   +++     +K     L ++K   + I+    +   +  +
Sbjct: 232 TYAYWWIRQGITRAIATSSRTIRLPVHITEK-----LNKIKKAQRKISQEKGRTPTLEDL 286

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A +L+++ ++V  +  R+    SL   +       ++  + L  D    E++L+ +  +K
Sbjct: 287 AIELDMTPTQVREVLLRVPRSVSLETKV--GKDKDTELGELLETDSITPEEMLMRESLQK 344

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           +    L   ++ L  RER +   R      +P +L  +    ++SRERVRQIE++A +K+
Sbjct: 345 D----LHHLLADLTSRERDVILMRFGLSDGHPYSLAEIGRALDLSRERVRQIESKALQKL 400

Query: 281 QESIQKQV 288
           ++  ++ +
Sbjct: 401 RQPKRRNL 408


>gi|167836384|ref|ZP_02463267.1| RNA polymerase sigma factor RpoS [Burkholderia thailandensis
           MSMB43]
          Length = 366

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 78/276 (28%), Positives = 130/276 (47%), Gaps = 15/276 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+
Sbjct: 82  DTIQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGV 140

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++       
Sbjct: 141 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV--I 198

Query: 134 RLFFNLRRLKGHLQA-----ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           R    + R K HL+            +   +  IA     +  EV  +        SL+A
Sbjct: 199 RELNQVLRAKRHLEKNSLSTGAAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDA 258

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +      +S   D L  D        ++  E +    +    +S L+ + R + E R  
Sbjct: 259 PL--DLDPASSLLDLLPDDQSQSPDAEVQHRELE---TLTRAWLSRLSDKHRHVIERRFG 313

Query: 249 QE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
                P TLE L+ E  ++RERVRQI+  A  +++ 
Sbjct: 314 LNHIEPATLEELADEMGLTRERVRQIQQEALVRLKR 349


>gi|2267165|gb|AAC64856.1| sigma 80 [Helicobacter pylori]
          Length = 685

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 69/237 (29%), Positives = 120/237 (50%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ W
Sbjct: 445 RAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATW 504

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WIK A+   I      ++I        +   + R+   ++       K   +  +A+++ 
Sbjct: 505 WIKQAISRAIADQARTIRIPIH-----MIDTINRINKVMRKHIQETGKEPDLEVVAEEVG 559

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  
Sbjct: 560 LSLDKVKNVIKVTKEPISLETPVGNDDD--GKFGDFV---EDKNIVSSIDHIMREDLKAQ 614

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 615 IESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 671



 Score = 35.9 bits (82), Expect = 6.3,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 19/36 (52%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+  I +L K EE  L+K+ R   D+
Sbjct: 170 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDI 205


>gi|15644718|ref|NP_206888.1| RNA polymerase sigma factor RpoD [Helicobacter pylori 26695]
 gi|2500785|sp|P55993|RPOD_HELPY RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
 gi|2313167|gb|AAD07156.1| RNA polymerase sigma-70 factor (rpoD) [Helicobacter pylori 26695]
          Length = 671

 Score =  207 bits (527), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 70/237 (29%), Positives = 121/237 (51%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ W
Sbjct: 431 RAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATW 490

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WIK A+   I      ++I        +   + R+   ++     N K   +  +A+++ 
Sbjct: 491 WIKQAISRAIADQARTIRIPIH-----MIDTINRINKVMRKHIQENGKEPDLEVVAEEVG 545

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  
Sbjct: 546 LSLDKVKNVIKVTKEPISLETPVGNDDD--GKFGDFV---EDKNIVSSIDHIMREDLKAQ 600

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 601 IESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 657



 Score = 35.9 bits (82), Expect = 7.1,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 19/36 (52%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+  I +L K EE  L+K+ R   D+
Sbjct: 156 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDI 191


>gi|307718768|ref|YP_003874300.1| RNA polymerase sigma factor [Spirochaeta thermophila DSM 6192]
 gi|306532493|gb|ADN02027.1| RNA polymerase sigma factor [Spirochaeta thermophila DSM 6192]
          Length = 580

 Score =  206 bits (526), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 63/242 (26%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+KF+  +G++ +TY+ 
Sbjct: 340 KTAKDKLIQANLRLVVSIAKKYTNRGLHFFDLVQEGNIGLIKAVEKFEYRKGYKFSTYAT 399

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      +++        +   + +++   + +     +      IA +L
Sbjct: 400 WWIRQAITRSISDQARTIRVPVH-----MIEQINKVQREARQLMQVLGREPTDEEIADRL 454

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
               S V S+        SL + I   ++  S   D++    D        +      + 
Sbjct: 455 GWPLSRVKSVKNVAREPISLESPI--GEEEDSSVGDFI---EDKTAINPSHQTAYALLQQ 509

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +   ++ L PRE+ + + R   E+   +TLE +   F V+RER+RQIEA+A ++++   
Sbjct: 510 QIKDVLATLPPREQEVLKMRFGLEDGYSLTLEEVGLYFNVTRERIRQIEAKALRRLRHPK 569

Query: 285 QK 286
           + 
Sbjct: 570 RS 571



 Score = 36.7 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 9/33 (27%), Positives = 18/33 (54%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE 43
           + +  +  Y+ EI +  +L  +EE  L+K+  E
Sbjct: 91  STDDPIRLYLREIGRENLLTAEEEVSLSKQMEE 123


>gi|206560255|ref|YP_002231019.1| RNA polymerase sigma factor RpoS [Burkholderia cenocepacia J2315]
 gi|198036296|emb|CAR52192.1| RNA polymerase sigma factor [Burkholderia cenocepacia J2315]
          Length = 362

 Score =  206 bits (526), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 78/280 (27%), Positives = 132/280 (47%), Gaps = 15/280 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+
Sbjct: 82  DTIQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGV 140

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++       
Sbjct: 141 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV--I 198

Query: 134 RLFFNLRRLKGHLQAITDN-----NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           R    + R K HL+  + +       +   +  IA     +  EV  +        SL+A
Sbjct: 199 RELNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDA 258

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +      +S   D L  D        ++  E +    +    +S L+ + R + E R  
Sbjct: 259 PL--DLDPASSLLDLLPDDQSQSPDAEVQHRELE---TLTRAWLSRLSDKHRHVIERRFG 313

Query: 249 QE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                P TLE L+ E  ++RERVRQI+  A  +++     
Sbjct: 314 LNHIEPATLEELADEMGLTRERVRQIQQEALVRLKRFFAS 353


>gi|149921032|ref|ZP_01909492.1| RNA polymerase sigma factor RpoD [Plesiocystis pacifica SIR-1]
 gi|149818164|gb|EDM77620.1| RNA polymerase sigma factor RpoD [Plesiocystis pacifica SIR-1]
          Length = 547

 Score =  206 bits (526), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 67/243 (27%), Positives = 118/243 (48%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +A   LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ 
Sbjct: 307 EAAKAELVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYAT 366

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      +++        +  ++ +L    + +     +      IA+K+
Sbjct: 367 WWIRQAITRAISDQARTIRVPVH-----MIESINKLIRTTRQLVQEFGREPTHQEIAEKM 421

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           N+   +V S+        SL   +   +   S   D +    D            ++  +
Sbjct: 422 NMPVEKVRSILRIAKEPISLETPL--GEDGDSSLGDLI---EDKNALDPGSGVVERHLGD 476

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              R+++ L PRE +I   R         TLE +  +F V+RER+RQIEA+A  K++++ 
Sbjct: 477 ETRRALASLTPREEKILRLRFGIGEASDHTLEEVGRDFSVTRERIRQIEAKALSKLRKAD 536

Query: 285 QKQ 287
           + +
Sbjct: 537 RAK 539


>gi|254252249|ref|ZP_04945567.1| Sigma-70 region 2 [Burkholderia dolosa AUO158]
 gi|124894858|gb|EAY68738.1| Sigma-70 region 2 [Burkholderia dolosa AUO158]
          Length = 361

 Score =  206 bits (526), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 78/280 (27%), Positives = 132/280 (47%), Gaps = 15/280 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+
Sbjct: 81  DTIQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGV 139

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++       
Sbjct: 140 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV--I 197

Query: 134 RLFFNLRRLKGHLQAITDN-----NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           R    + R K HL+  + +       +   +  IA     +  EV  +        SL+A
Sbjct: 198 RELNQVLRAKRHLEKNSMSTGDAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDA 257

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +      +S   D L  D        ++  E +    +    +S L+ + R + E R  
Sbjct: 258 PL--DLDPASSLLDLLPDDQSQSPDAEVQHRELE---TLTRAWLSRLSDKHRHVIERRFG 312

Query: 249 QE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                P TLE L+ E  ++RERVRQI+  A  +++     
Sbjct: 313 LNHIEPATLEELADEMGLTRERVRQIQQEALVRLKRFFAS 352


>gi|308183886|ref|YP_003928019.1| RNA polymerase sigma factor RpoD [Helicobacter pylori SJM180]
 gi|308059806|gb|ADO01702.1| RNA polymerase sigma factor RpoD [Helicobacter pylori SJM180]
          Length = 679

 Score =  206 bits (526), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 69/237 (29%), Positives = 120/237 (50%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ W
Sbjct: 439 RAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATW 498

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WIK A+   I      ++I        +   + R+   ++       K   +  +A+++ 
Sbjct: 499 WIKQAISRAIADQARTIRIPIH-----MIDTINRINKVMRKHIQETGKEPDLEVVAEEVG 553

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  
Sbjct: 554 LSLDKVKNVIKVTKEPISLETPVGNDDD--GKFGDFV---EDKNIVSSIDHIMREDLKAQ 608

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 609 IESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 665



 Score = 35.9 bits (82), Expect = 6.4,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 19/36 (52%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+  I +L K EE  L+K+ R   D+
Sbjct: 161 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDI 196


>gi|261838959|gb|ACX98724.1| sigma 70 (RpoD) [Helicobacter pylori 52]
          Length = 685

 Score =  206 bits (526), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 70/237 (29%), Positives = 121/237 (51%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ W
Sbjct: 445 RAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATW 504

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WIK A+   I      ++I        +   + R+   ++     N K   +  +A+++ 
Sbjct: 505 WIKQAISRAIADQARTIRIPIH-----MIDTINRINKVMRKHIQENGKEPDLEVVAEEVG 559

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  
Sbjct: 560 LSLDKVKNVIKVTKEPISLETPVGNDDD--GKFGDFV---EDKNIVSSIDHIMREDLKAQ 614

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 615 IESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 671



 Score = 35.9 bits (82), Expect = 7.1,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 19/36 (52%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+  I +L K EE  L+K+ R   D+
Sbjct: 170 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDI 205


>gi|159026170|emb|CAO88820.1| unnamed protein product [Microcystis aeruginosa PCC 7806]
          Length = 318

 Score =  206 bits (526), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 76/330 (23%), Positives = 142/330 (43%), Gaps = 54/330 (16%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------- 43
           M    N    +  Y+ EI ++P+L  +EE + AK+ +                       
Sbjct: 1   MKTSKNPTDPVRAYLREIGRVPLLSHEEEILYAKQVQRLIFLEKIKESLRAKLGSDPSDR 60

Query: 44  ------------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
                              GD  A  ++V ++LRLVV +A  Y    L + +++ EG IG
Sbjct: 61  QWSEAAEISEEQLRRELGAGDF-AKRKMVEANLRLVVSVAKKYLKRNLDLLDLIQEGTIG 119

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           + + V+KFDP +G+R +TY+ WWI+ A+   I      +++     +K     L ++K  
Sbjct: 120 MQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKSRTIRLPIHITEK-----LNKIKKA 174

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            + +  +  +   +  +A++L+++  +V     R     SL+  +   D   ++  + L 
Sbjct: 175 QRQLAQDKGRAATIAELAEELDLTPKQVRDYLERSRQPLSLDLKV--GDNQDTELGELLE 232

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFE 263
                 E        + +    L + M+ L P+++ +   R   +N  P+TL  +     
Sbjct: 233 DTGLSPEDYTAHSSLQVD----LEKLMADLTPQQKEVICLRFGLDNGQPLTLAKIGVRLN 288

Query: 264 VSRERVRQIEARAFKKVQESIQKQVELSSS 293
           +SRERVRQIE  A  K+++   K  E  +S
Sbjct: 289 ISRERVRQIEREAIAKLRKRKAKIREYLAS 318


>gi|41408924|ref|NP_961760.1| RNA polymerase sigma factor SigB [Mycobacterium avium subsp.
           paratuberculosis K-10]
 gi|41397283|gb|AAS05143.1| SigB [Mycobacterium avium subsp. paratuberculosis K-10]
          Length = 332

 Score =  206 bits (526), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 69/311 (22%), Positives = 134/311 (43%), Gaps = 38/311 (12%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREH--------------- 44
           ++         +  Y++ I K  +L    E  LAKR     Y EH               
Sbjct: 25  DLDAQSPAADLVRVYLNGIGKTALLNAAGEVELAKRIEAGLYAEHLLETRKRLGENRKRD 84

Query: 45  ------GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
                    +A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +G
Sbjct: 85  LEAVVRDGQAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTKG 144

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           F+ +TY+ WWI+ A+   +      +++     ++     L R+K  +     N  +   
Sbjct: 145 FKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLARIKREMHQ---NLGREAT 199

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              +A +  +   ++  +        SL+  + S ++  +   D++    D +       
Sbjct: 200 DEELAAESGIPIDKINDLLEHSRDPVSLDMPVGSEEE--APLGDFI---EDAEAMSAENA 254

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARA 276
              +     +   ++ L+ RE ++   R   ++  P TL+ +   F +SRERVRQIE   
Sbjct: 255 VIAELLHTDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERDV 314

Query: 277 FKKVQESIQKQ 287
             K++   +  
Sbjct: 315 MSKLRNGERAD 325


>gi|330817175|ref|YP_004360880.1| Stationary phase sigma factor [Burkholderia gladioli BSR3]
 gi|327369568|gb|AEA60924.1| Stationary phase sigma factor [Burkholderia gladioli BSR3]
          Length = 366

 Score =  206 bits (526), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 79/280 (28%), Positives = 133/280 (47%), Gaps = 15/280 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+
Sbjct: 86  DTIQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGV 144

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++       
Sbjct: 145 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV--I 202

Query: 134 RLFFNLRRLKGHLQAITDN-----NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           R    + R K HL+  + +       +   +  IA     +  EV  +        SL+A
Sbjct: 203 RELNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDA 262

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +      +S   D L  D        ++  E +    +    +S L+ + R + E R  
Sbjct: 263 PL--DLDPASSLLDLLPDDQSQSPDAEVQHRELE---TLTRAWLSRLSDKHRHVIERRFG 317

Query: 249 QEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             N  P TLE L+ E  ++RERVRQI+  A  +++     
Sbjct: 318 LNNIEPATLEELADEMGLTRERVRQIQQEALVRLKRFFAS 357


>gi|313792143|gb|EFS40244.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL110PA1]
 gi|313801904|gb|EFS43138.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL110PA2]
 gi|313838730|gb|EFS76444.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL086PA1]
 gi|314962802|gb|EFT06902.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL082PA1]
 gi|315078018|gb|EFT50069.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL053PA2]
 gi|327453138|gb|EGE99792.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL092PA1]
          Length = 312

 Score =  206 bits (526), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 69/303 (22%), Positives = 130/303 (42%), Gaps = 41/303 (13%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------------- 41
           ++G+  +  Y+  I + P+L   EE  LA+R                             
Sbjct: 13  IDGKDAVGLYLDGIARTPLLNAAEEVALARRIEAGVFARAILEGHAETTSDTTTKELHQI 72

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
              GD  A  R V ++LRLVV +A  Y    +P+ ++V EGN GL++AV+KFD  +GF+ 
Sbjct: 73  AADGD-EALARFVRANLRLVVSVARKYGRSQMPLLDLVQEGNTGLIRAVEKFDYAKGFKF 131

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY+ WW++ A+   I +   +V++     +      + ++    + +     +  +   
Sbjct: 132 STYATWWVRQAISRGIAQQGRIVRLPVHVAE-----QVNQVSAARRNLERQLGREPETFE 186

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           IA +L ++E  VI +        SL+A +   D   +   D +  +       ++   E 
Sbjct: 187 IADELEITEERVIELIRFGRDHVSLDAPV--EDDGDTSLGDLIARETSPGPDDIVLDAED 244

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVT--LENLSSEFEVSRERVRQIEARAFKK 279
              R+ L   +  L+ R   +   R    +     L ++   + ++ ERVRQIE  A   
Sbjct: 245 ---RSRLEGLLDDLDERSADVVRRRYGLVDGRQAKLADIGKVWGITAERVRQIERAALAS 301

Query: 280 VQE 282
           +++
Sbjct: 302 MRQ 304


>gi|170076992|ref|YP_001733630.1| group II sigma-70 type sigma factor [Synechococcus sp. PCC 7002]
 gi|1769590|gb|AAB95227.1| sigma factor [Synechococcus sp. PCC 7002]
 gi|169884661|gb|ACA98374.1| Group II sigma-70 type sigma factor (RpoD family) [Synechococcus
           sp. PCC 7002]
          Length = 365

 Score =  206 bits (526), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 76/314 (24%), Positives = 134/314 (42%), Gaps = 53/314 (16%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS------------------------ 48
           E  +  +  E+ + P+L+  EE  LA   +   D                          
Sbjct: 51  EDTVGAFFKEMARYPLLKPDEEIQLAHSVKFLNDAEERRLELQEQLGRSPTNEEWASVLG 110

Query: 49  ----------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  +++ S+LRLVV IA  Y   G+P  +++ EG IGL +A +K
Sbjct: 111 LETVKQLNSALYKGRVAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAEK 170

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FDP +G++ +TY+ WWI+ A+   I      +++     +K     L +LK   + +   
Sbjct: 171 FDPNKGYKFSTYAYWWIRQAITRTIANDARTIRLPIHIVEK-----LNKLKKAQRTLKQT 225

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      +A++L+++  ++  +        SLN  +   +   ++  D L  D     
Sbjct: 226 LQRNPTEAELAQELDITADQLHQLLQLRRQSLSLNHRVGKGED--TELVDLLEDDGL--- 280

Query: 213 QVLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERV 269
           Q+  E+      R  L   +  VL  RE+ +   R     E P TLE +   F +SRERV
Sbjct: 281 QLPEERMSEAMMRQELWDVLGDVLTDREKEVIALRYGLSSEQPHTLEEVGGMFNLSRERV 340

Query: 270 RQIEARAFKKVQES 283
           RQI+++A +K++  
Sbjct: 341 RQIQSKAMRKLRRP 354


>gi|288818771|ref|YP_003433119.1| RNA polymerase sigma factor RpoD [Hydrogenobacter thermophilus
           TK-6]
 gi|288788171|dbj|BAI69918.1| RNA polymerase sigma factor RpoD [Hydrogenobacter thermophilus
           TK-6]
 gi|308752357|gb|ADO45840.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Hydrogenobacter
           thermophilus TK-6]
          Length = 570

 Score =  206 bits (526), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 70/242 (28%), Positives = 110/242 (45%), Gaps = 12/242 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   +V  +LRLVV IA  Y   GL   +++ EGNIGLM+AV K+D  +G++ +TY+ W
Sbjct: 332 KAKQVMVKCNLRLVVSIAKKYVNRGLHFLDLIQEGNIGLMKAVDKYDYRKGYKFSTYATW 391

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      ++I           ++ +    L         PE    IAK L 
Sbjct: 392 WIRQAITRAIADQARTIRIPVHM--IETINDITKAHKKLFQELGREPFPE---EIAKYLG 446

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +   +        SL   I   D   +  +D++    D       E+  RK  R  
Sbjct: 447 ISVEKARKVMRTSQEPISLETPI--GDDEETHLKDFI---EDKSVLSPEEQVSRKLLREQ 501

Query: 228 LTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L + +S L  +E+ I   R         TLE +   F V+RER+RQIE +A +K++   +
Sbjct: 502 LIKVLSTLGEKEKEILMYRYGLVDGTEYTLEQIGKMFNVTRERIRQIETKAIRKLRHPAR 561

Query: 286 KQ 287
            +
Sbjct: 562 AK 563



 Score = 41.0 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 10/41 (24%), Positives = 24/41 (58%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY 41
           ++ +N+ +       +  Y+ E+ +IP+L ++EE + AK+ 
Sbjct: 70  VSTENLLLTARDGDPVKLYLREMGRIPLLSREEEIMYAKQI 110


>gi|149200222|ref|ZP_01877244.1| RNA polymerase sigma factor RpoD [Lentisphaera araneosa HTCC2155]
 gi|149136664|gb|EDM25095.1| RNA polymerase sigma factor RpoD [Lentisphaera araneosa HTCC2155]
          Length = 279

 Score =  206 bits (526), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 73/281 (25%), Positives = 136/281 (48%), Gaps = 15/281 (5%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            +  Y+  I  +P++  ++E  LAK   E G   A  +L+ ++L+LVVKIA  Y+  G+P
Sbjct: 7   SIKSYMQSIATLPLVSVEDEIELAKLI-EAGSEDAREKLIIANLKLVVKIAHDYKSLGVP 65

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           +++++SEGNIGLM+AV+KF P  G + ++Y  WWIK A++  +     +++I   +  K 
Sbjct: 66  LADLISEGNIGLMKAVEKFRPGHGAKFSSYGAWWIKQAIRRAVAEQGRVIRIPVQSAVK- 124

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD-ESLNALINSS 193
               +R++      + +   +   +  +A+    S   V  M+        SLN  + + 
Sbjct: 125 ----IRKIHHEAMLLAEKLGRVPSMEEVAEATGFSVRSVRGMSVASTAPAVSLNTTLKTG 180

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV-LNPRERRIFEARRLQE-- 250
           ++   +         D   ++  +     + + +L   +   L  RE+ I + R   +  
Sbjct: 181 EEGVLEDVIP-----DTLLKLPGDNMNETDVKQVLLEVIDSKLTEREQMIIKMRYGLDGH 235

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
              TLE LS     +RERVRQI+ +A +K+   +   +  S
Sbjct: 236 QQKTLEELSDMVGRTRERVRQIQYQALRKLYAHLDSDILAS 276


>gi|172060780|ref|YP_001808432.1| RNA polymerase sigma factor RpoS [Burkholderia ambifaria MC40-6]
 gi|171993297|gb|ACB64216.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia ambifaria
           MC40-6]
          Length = 361

 Score =  206 bits (526), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 78/280 (27%), Positives = 132/280 (47%), Gaps = 15/280 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+
Sbjct: 81  DTIQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGV 139

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++       
Sbjct: 140 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV--I 197

Query: 134 RLFFNLRRLKGHLQAITDN-----NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           R    + R K HL+  + +       +   +  IA     +  EV  +        SL+A
Sbjct: 198 RELNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDA 257

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +      +S   D L  D        ++  E +    +    +S L+ + R + E R  
Sbjct: 258 PL--DLDPASSLLDLLPDDQSQSPDAEVQHRELE---TLTRAWLSRLSDKHRHVIERRFG 312

Query: 249 QE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                P TLE L+ E  ++RERVRQI+  A  +++     
Sbjct: 313 LNHIEPATLEELADEMGLTRERVRQIQQEALVRLKRFFAS 352


>gi|308182264|ref|YP_003926391.1| RNA polymerase sigma factor RpoD [Helicobacter pylori PeCan4]
 gi|308064449|gb|ADO06341.1| RNA polymerase sigma factor RpoD [Helicobacter pylori PeCan4]
          Length = 682

 Score =  206 bits (526), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 70/237 (29%), Positives = 121/237 (51%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ W
Sbjct: 442 RAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATW 501

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WIK A+   I      ++I        +   + R+   ++     N K   +  +A+++ 
Sbjct: 502 WIKQAISRAIADQARTIRIPIH-----MIDTINRINKVMRKHIQENGKEPDLEVVAEEVG 556

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  
Sbjct: 557 LSLDKVKNVIKVTKEPISLETPVGNDDD--GKFGDFV---EDKNIVSSIDHIMREDLKAQ 611

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 612 IESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 668



 Score = 35.9 bits (82), Expect = 7.2,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 19/36 (52%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+  I +L K EE  L+K+ R   D+
Sbjct: 167 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDI 202


>gi|81299483|ref|YP_399691.1| RNA polymerase sigma factor SigD [Synechococcus elongatus PCC 7942]
 gi|123557285|sp|Q31QG5|RPOD3_SYNE7 RecName: Full=RNA polymerase sigma factor rpoD3
 gi|81168364|gb|ABB56704.1| group2 RNA polymerase sigma factor SigD [Synechococcus elongatus
           PCC 7942]
          Length = 320

 Score =  206 bits (526), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 72/322 (22%), Positives = 142/322 (44%), Gaps = 54/322 (16%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR--------------EHGDLS------- 48
                 +  Y+ EI ++P+L  +EE VL KR +              E GD         
Sbjct: 6   TPTSDLVRTYLREIGRVPLLTHEEEVVLGKRVQQWMKLQELRQTLQSEEGDRDPSDLEWA 65

Query: 49  -------------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
                              A  +++ ++LRLVV +A  Y    + + +++ EG IG+ + 
Sbjct: 66  AAAGLSIEELRQQQHLGEQAKRKMIEANLRLVVSVAKKYLKRNMDLLDLIQEGTIGMQRG 125

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V+KFDP +G+R +TY+ WWI+ A+   I      +++     +K     L ++K   + +
Sbjct: 126 VEKFDPTKGYRFSTYAYWWIRQAITRAIAEKARTIRLPIHITEK-----LNKIKKMQRQL 180

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
           +    +   +  +A  L+++ ++V     +     SL+  +   D   ++  D L  D  
Sbjct: 181 SQQLGRTATLPELAAALDLTPAQVRDYLEKARHPLSLD--LRVGDNQDTELGDLLETD-- 236

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRE 267
                  E   + + R  + R +  L  ++R++   R   E+   +TL ++    ++SRE
Sbjct: 237 --CTTPEEFTLQASMRRDIDRLLDQLTEQQRQVIALRYGLEDGQVMTLASIGDRLQISRE 294

Query: 268 RVRQIEARAFKKVQESIQKQVE 289
           RVRQ+E  A   ++++ + QV+
Sbjct: 295 RVRQLEREALHTLRQA-RSQVQ 315


>gi|317181391|dbj|BAJ59175.1| RNA polymerase sigma factor RpoD [Helicobacter pylori F57]
          Length = 665

 Score =  206 bits (526), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 70/237 (29%), Positives = 121/237 (51%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ W
Sbjct: 425 RAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATW 484

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WIK A+   I      ++I        +   + R+   ++     N K   +  +A+++ 
Sbjct: 485 WIKQAISRAIADQARTIRIPIH-----MIDTINRINKVMRKHIQENGKEPDLEVVAEEVG 539

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  
Sbjct: 540 LSLDKVKNVIKVTKEPISLETPVGNDDD--GKFGDFV---EDKNIVSSIDHIMREDLKVQ 594

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 595 IESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 651



 Score = 35.9 bits (82), Expect = 6.7,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 19/36 (52%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+  I +L K EE  L+K+ R   D+
Sbjct: 150 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDI 185


>gi|332709863|ref|ZP_08429819.1| RNA polymerase, sigma subunit, RpsC/SigC [Lyngbya majuscula 3L]
 gi|332351234|gb|EGJ30818.1| RNA polymerase, sigma subunit, RpsC/SigC [Lyngbya majuscula 3L]
          Length = 417

 Score =  206 bits (526), Expect = 2e-51,   Method: Composition-based stats.
 Identities = 66/242 (27%), Positives = 128/242 (52%), Gaps = 13/242 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L A   ++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV+KFDP +G+R +TY+ 
Sbjct: 176 LQAKEHMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTKGYRFSTYAY 235

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   I      +++     +K     L ++K   + I+    +   +  IA +L
Sbjct: 236 WWIRQGITRAIATQSRTIRLPVHITEK-----LNKIKKAQRKISQERGRTATIDDIAVEL 290

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++ ++V  +  R+    SL   I    +  ++  D L  +    E+VL+ +  +++   
Sbjct: 291 EMTAAQVREVLLRVPRSVSLE--IKVGKERDTELGDLLETEETSPEEVLMREALQRD--- 345

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L + ++ L  RER +   R    +  P +L  +    ++SRERVRQIEA+A +K+++  
Sbjct: 346 -LQQLLADLTNRERDVIRMRFGLGDNQPYSLAEIGRALDLSRERVRQIEAKALQKLRQPK 404

Query: 285 QK 286
           ++
Sbjct: 405 RR 406


>gi|114776846|ref|ZP_01451889.1| RNA polymerase sigma factor [Mariprofundus ferrooxydans PV-1]
 gi|114552932|gb|EAU55363.1| RNA polymerase sigma factor [Mariprofundus ferrooxydans PV-1]
          Length = 274

 Score =  206 bits (526), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 102/268 (38%), Positives = 157/268 (58%), Gaps = 9/268 (3%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
            E+RK P L++ EE  LA+ + + GD  AA +LV ++L  V  IA  YR +GLP  +++ 
Sbjct: 15  REMRKTPRLDRAEETRLARLWHDQGDREAARQLVVANLGGVAAIAREYRHFGLPEMDLIQ 74

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           EG +GLM AVK+FDPERGFRL TY+ WW++AA+ ++IL SWS+VK+GT   Q+R+F  L+
Sbjct: 75  EGTLGLMHAVKRFDPERGFRLMTYASWWVRAAIHDFILHSWSIVKLGTNKLQRRVFAGLQ 134

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN-CRLAGDESLNALINSSDKNSSQ 199
           + K  + A   +     +   +A    ++  E        L  D SL+    + D+    
Sbjct: 135 KAKNAIAAFDGS-----RADDVAADFGITAGEYQEAAGAFLQRDLSLD---CACDEGGDA 186

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
               L       EQ++ +    ++R+  L  ++S L  R+R I + R L + P TL++LS
Sbjct: 187 MVHNLESMDASPEQIVTDNNWSEHRQAGLYHALSTLPERDRLILQRRHLSDEPATLKDLS 246

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQ 287
            EF VS ER+RQ+EARA K+++ES+  Q
Sbjct: 247 EEFGVSMERIRQLEARAMKQLRESLVNQ 274


>gi|107029001|ref|YP_626096.1| RNA polymerase sigma factor RpoS [Burkholderia cenocepacia AU 1054]
 gi|105898165|gb|ABF81123.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia cenocepacia AU
           1054]
          Length = 362

 Score =  206 bits (526), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 78/280 (27%), Positives = 132/280 (47%), Gaps = 15/280 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+
Sbjct: 82  DTIQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGV 140

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++       
Sbjct: 141 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV--I 198

Query: 134 RLFFNLRRLKGHLQAITDN-----NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           R    + R K HL+  + +       +   +  IA     +  EV  +        SL+A
Sbjct: 199 RELNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDA 258

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +      +S   D L  D        ++  E +    +    +S L+ + R + E R  
Sbjct: 259 PL--DPDPASSLLDLLPDDQSQSPDAEVQHRELE---TLTRAWLSRLSDKHRHVIERRFG 313

Query: 249 QE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                P TLE L+ E  ++RERVRQI+  A  +++     
Sbjct: 314 LNHIEPATLEELADEMGLTRERVRQIQQEALVRLKRFFAS 353


>gi|217034615|ref|ZP_03440022.1| hypothetical protein HP9810_881g8 [Helicobacter pylori 98-10]
 gi|216942910|gb|EEC22397.1| hypothetical protein HP9810_881g8 [Helicobacter pylori 98-10]
          Length = 671

 Score =  206 bits (526), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 70/237 (29%), Positives = 121/237 (51%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ W
Sbjct: 431 RAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATW 490

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WIK A+   I      ++I        +   + R+   ++     N K   +  +A+++ 
Sbjct: 491 WIKQAISRAIADQARTIRIPIH-----MIDTINRINKVMRKHIQENGKEPDLEVVAEEVR 545

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  
Sbjct: 546 LSLDKVKNVIKVTKEPISLETPVGNDDD--GKFGDFV---EDKNIVSSIDHIMREDLKAQ 600

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 601 IESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 657



 Score = 35.9 bits (82), Expect = 6.7,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 19/36 (52%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+  I +L K EE  L+K+ R   D+
Sbjct: 156 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDI 191


>gi|327330254|gb|EGE72003.1| RNA polymerase principal sigma factor SigA [Propionibacterium acnes
           HL097PA1]
          Length = 312

 Score =  206 bits (525), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 68/303 (22%), Positives = 130/303 (42%), Gaps = 41/303 (13%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------------- 41
           ++G+  +  Y+  I + P+L   EE  LA+R                             
Sbjct: 13  IDGKDAVGLYLDGIARTPLLNAAEEVALARRIEAGVFARAILEGHAETTSDATTKELHQI 72

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
              GD  A    V ++LRLVV +A  Y    +P+ ++V EGN GL++AV+KFD  +GF+ 
Sbjct: 73  AADGD-EALAHFVRANLRLVVSVARKYGRSQMPLLDLVQEGNTGLIRAVEKFDYAKGFKF 131

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY+ WW++ A+   I +   +V++     +      + ++    +++     +  +   
Sbjct: 132 STYATWWVRQAISRGIAQQGRIVRLPVHVAE-----QVNQVSAARRSLERQLGREPETFE 186

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           IA +L ++E  VI +        SL+A +   D   +   D +  +       ++   E 
Sbjct: 187 IADELEITEERVIELIRFGRDHVSLDAPV--EDDGDTSLGDLIARETSPGPDDIVLDAED 244

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVT--LENLSSEFEVSRERVRQIEARAFKK 279
              R+ L   +  L+ R   +   R    +     L ++   + ++ ERVRQIE  A   
Sbjct: 245 ---RSRLEGLLDDLDERSADVVRRRYGLVDGRQAKLADIGKVWGITAERVRQIERAALAS 301

Query: 280 VQE 282
           +++
Sbjct: 302 MRQ 304


>gi|320104559|ref|YP_004180150.1| RNA polymerase sigma-70 subunit RpoD [Isosphaera pallida ATCC
           43644]
 gi|319751841|gb|ADV63601.1| RNA polymerase, sigma 70 subunit, RpoD [Isosphaera pallida ATCC
           43644]
          Length = 592

 Score =  206 bits (525), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 74/273 (27%), Positives = 131/273 (47%), Gaps = 17/273 (6%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGD-----LSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
            E+R + ++  +    LA+R RE  +       A  +L   +LRLVV IA  YR  GL  
Sbjct: 318 KELRDLMLMTLETPAGLARRVREMNERFKEYEKAKRKLSGGNLRLVVSIAKKYRNRGLSF 377

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN GLM+AV K++  RGF+ +TY+ WWI+ A+   I      ++I        +
Sbjct: 378 LDLIQEGNTGLMRAVDKYEWRRGFKFSTYATWWIRQAITRAIADQARTIRIPVH-----M 432

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + +L+   + +     +   +   A+  N+S  E   +        SL+  +   + 
Sbjct: 433 IETMSKLRNVNKKLLQEKGREPTIEETARAANISIEETRRVMKISRHPISLDRPV--GES 490

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--V 253
             S + D++    D   +  I    ++  ++ + + +  L  RER I + R    +    
Sbjct: 491 EDSYFGDFI---EDTTAENPINSATQEMLKDKIDQVLKTLTYREREIIKLRYGLGDGYTY 547

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TLE +   F+V+RERVRQIEA+A +K+Q  ++ 
Sbjct: 548 TLEEVGRIFKVTRERVRQIEAKAVRKLQHPVRS 580



 Score = 39.8 bits (92), Expect = 0.55,   Method: Composition-based stats.
 Identities = 29/175 (16%), Positives = 67/175 (38%), Gaps = 13/175 (7%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSH-LRLVVKIAMGYRGY 71
           +  +  Y+ ++ +IP+L +++E  LA+R            L   + LRLVV +       
Sbjct: 136 DDPVRMYLTQMGEIPLLTREQEISLAERIESTRKRFRRRVLECDYALRLVVDVLKKVDSG 195

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK-AAMQEYILRSWS--LVKIGT 128
            LP    V              + E+   L       +    + +   R +   L   G 
Sbjct: 196 ELPFDRTVKVSM--------TENLEKNQILGRMPHNLVTLEHLMDCNDRDFRDLLRARGD 247

Query: 129 TANQKRLFFNLR-RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
              ++RL   L  R +  ++ + + +++ ++V  + K+L    + +  +  ++  
Sbjct: 248 KEKRRRLARALAIRRRKAVKLVEELSIRTQKVQPLMKRLEQISARMQELLNQIRE 302


>gi|317008763|gb|ADU79343.1| RNA polymerase sigma factor RpoD [Helicobacter pylori India7]
          Length = 676

 Score =  206 bits (525), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 69/237 (29%), Positives = 120/237 (50%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ W
Sbjct: 436 RAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATW 495

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WIK A+   I      ++I        +   + R+   ++       K   +  +A+++ 
Sbjct: 496 WIKQAISRAIADQARTIRIPIH-----MIDTINRINKVMRKHIQETGKEPDLEVVAEEVG 550

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  
Sbjct: 551 LSLDKVKNVIKVTKEPISLETPVGNDDD--GKFGDFV---EDKNIVSSIDHIMREDLKAQ 605

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 606 IESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 662



 Score = 35.9 bits (82), Expect = 6.6,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 19/36 (52%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+  I +L K EE  L+K+ R   D+
Sbjct: 161 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDI 196


>gi|160937287|ref|ZP_02084649.1| hypothetical protein CLOBOL_02177 [Clostridium bolteae ATCC
           BAA-613]
 gi|158439851|gb|EDP17600.1| hypothetical protein CLOBOL_02177 [Clostridium bolteae ATCC
           BAA-613]
          Length = 298

 Score =  206 bits (525), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 76/279 (27%), Positives = 136/279 (48%), Gaps = 22/279 (7%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ +    P+L K+EE  LA   +E G   A  ++++S+LRLV+  A  Y  Y  
Sbjct: 27  DSVQWYLKQAGVGPLLTKEEEIELAYLIQE-GSDEARQKMISSNLRLVINQAKKYVTYTQ 85

Query: 74  PI--SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
            +   +++ EGN+GL++AV+K++PE GFR +TY+ WWIK A+   I      +++     
Sbjct: 86  SLTLLDLIQEGNLGLIKAVEKYNPELGFRFSTYASWWIKQAITRAISVLDKAIRLPVH-- 143

Query: 132 QKRLFFNLRRLKGHLQAITDNN--LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
                 +++++K     I   N  + PE++  I      SE ++  +   +    SL   
Sbjct: 144 ---FCEDIQKVKRATHEIMQQNDIVTPEKLKDIT---GFSEGKIEKILMNMNHTISLETP 197

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL- 248
           +       +   D++    D     + E+      +  ++R M  L PRE+ I   R   
Sbjct: 198 V----GEEATLGDFV---EDTLTPSIEEQAMENAMQREISRQMECLRPREQTILALRFGL 250

Query: 249 -QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             +NP TLE +  +  V+RER+RQIE +A +K++   + 
Sbjct: 251 NGQNPHTLEEVGKQMGVTRERIRQIEMKALRKLRHPNRS 289


>gi|34499137|ref|NP_903352.1| RNA polymerase sigma factor RpoS [Chromobacterium violaceum ATCC
           12472]
 gi|34104988|gb|AAQ61344.1| RNA sigma factor RpoS [Chromobacterium violaceum ATCC 12472]
          Length = 316

 Score =  206 bits (525), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 137/271 (50%), Gaps = 13/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+++I    +L  QEE  LA+R    G+  A  +++  +LRLVV IA  Y   GL + ++
Sbjct: 49  YLNDIGNNALLTPQEELALARRVV-AGEFEARQKMIEHNLRLVVNIAKHYINRGLALLDL 107

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM A++KFDPERGFR +TY+ WWI+ +++  I+     +++      K L   
Sbjct: 108 IEEGNIGLMHALEKFDPERGFRFSTYATWWIRQSIERAIMNQSRTIRLPVHV-IKELNVY 166

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R   HL++        E++  +  K      +V+++N R+A   SL+A ++       
Sbjct: 167 L-RASRHLESQIGREPSVEEIAHLVGKPVEDVRKVLNLNERMA---SLDAPLDID----- 217

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
                     D Q +    +         +   +S LN ++R + E R         TLE
Sbjct: 218 PMLSIGESIPDEQHEEPELQLHNSQLEMFVHDWLSQLNEKQRLVIERRYGLNGYEICTLE 277

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            L++   ++RERVRQI+    ++++  ++++
Sbjct: 278 ELAASLNLTRERVRQIQIEGLEQLRRILRRK 308


>gi|158341079|ref|YP_001522246.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158311320|gb|ABW32932.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 268

 Score =  206 bits (525), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 72/275 (26%), Positives = 129/275 (46%), Gaps = 15/275 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ E+ + P+L  +EE  LA++ +  GDL A  R++  +LRLVV IA  ++  GL
Sbjct: 6   DSVQAYLKEMGRYPLLSHEEEIRLARQVK-AGDLKAKQRMIECNLRLVVSIAKKHQHLGL 64

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EG+IGL  AV KFD  +G + +TY+ WWI  A++  +      + I     ++
Sbjct: 65  PLMDLIQEGSIGLNTAVDKFDLAQGCKFSTYAYWWISEAIKRALKSQSRTIYIPIHQWER 124

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                  R+K  ++ +T    +   +  ++    +  S + +         SL+  +   
Sbjct: 125 AH-----RIKKAVRQLTQEKGRTPTLKELSAATGIKSSLIRNTLQSFQAISSLDQPVGPE 179

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QEN 251
            K++       + D    E   +   +     + LTR M+ L  RER I + R       
Sbjct: 180 QKDA-------LIDLIQTEDAALSIMDGLEIEDALTRCMAYLTERERFIVDQRYGLTDGQ 232

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           P ++  +     +SRERVRQI   A KK+   ++ 
Sbjct: 233 PKSMGAIGKPIGISRERVRQILNIAMKKMTRQVRS 267


>gi|75908113|ref|YP_322409.1| RNA polymerase sigma factor SigD [Anabaena variabilis ATCC 29413]
 gi|75701838|gb|ABA21514.1| Sigma 28 (Flagella/Sporulation) [Anabaena variabilis ATCC 29413]
          Length = 332

 Score =  206 bits (525), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 68/331 (20%), Positives = 132/331 (39%), Gaps = 52/331 (15%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------- 43
             M         +  Y+ EI ++P+L  +EE    K+ +                     
Sbjct: 13  SAMKTAPTATDLVRTYLREIGRVPLLSHEEEIRYGKQVQRSTTLQEVREELATQLGREPS 72

Query: 44  -------------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
                                   A  ++V ++LRLVV +A  Y    + + +++ EG+I
Sbjct: 73  IEEWAKAANINSADLLGAIADGEVAKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGSI 132

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           G+ + V+KFDP +G+R +TY+ WWI+ A+   I      +++     +K     L ++K 
Sbjct: 133 GMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKARTIRLPIHITEK-----LNKIKK 187

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + ++    +      +A +L ++  +V     +     SL+  +   D   ++  + L
Sbjct: 188 AQRQLSQRLGRAPTAGELANELELTPKQVREYLEKARLPLSLD--LRLGDNYDTELGEML 245

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEF 262
                  E  +++     +    L   M  L P+++ +   R        +TL  +    
Sbjct: 246 EDPGASPEDFVMQSSLSND----LEVLMEQLTPQQKEVITLRFGLIDGQALTLARIGEIL 301

Query: 263 EVSRERVRQIEARAFKKVQESIQKQVELSSS 293
            +SRERVRQIE  A  K+++S     E  +S
Sbjct: 302 NISRERVRQIEREALTKLRKSKANMGEYLAS 332


>gi|254421657|ref|ZP_05035375.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family,
           putative [Synechococcus sp. PCC 7335]
 gi|196189146|gb|EDX84110.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family,
           putative [Synechococcus sp. PCC 7335]
          Length = 467

 Score =  206 bits (525), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 70/313 (22%), Positives = 130/313 (41%), Gaps = 52/313 (16%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAK--------------------------------- 39
           +  +  +  E+ + P+L+  EE  LA+                                 
Sbjct: 154 DDAVGAFFKEMARYPLLQPTEEIELARQVRIIVEIEDYSEKASETLKRRPTHAELATAFG 213

Query: 40  ------RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
                 R +     +A  R++ S+LRLVV IA  Y   G+P  +++ EG +GL +A +KF
Sbjct: 214 YTEGQLRQKLRQARAAKRRMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGALGLNRAAEKF 273

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           DP++G++ +TY+ WWI+  +   I      +++     +K     L +LK   + +    
Sbjct: 274 DPDKGYKFSTYAYWWIRQGITRTIANDARTIRLPIHIVEK-----LNKLKKAQRELRKEL 328

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            +    V +A  L ++  ++ ++        SLN  +   +       + +    DG   
Sbjct: 329 QRTPTEVEVAAALEMTPEQLRTLQQVQRKSLSLNHRVGKGEDT-----ELMELLEDGNSL 383

Query: 214 VLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVR 270
               +      R  ++  +  VL  RE+ I   R         TLE +   F++SRERVR
Sbjct: 384 SPESQISESMMRQEISDVLTEVLTEREKEIIALRYGLTTGETHTLEEVGGIFQLSRERVR 443

Query: 271 QIEARAFKKVQES 283
           QI+ +A +K++  
Sbjct: 444 QIQTKAMRKLRRP 456


>gi|220907205|ref|YP_002482516.1| RNA polymerase sigma-70 subunit RpoD subfamily [Cyanothece sp. PCC
           7425]
 gi|219863816|gb|ACL44155.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7425]
          Length = 455

 Score =  206 bits (525), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 64/249 (25%), Positives = 128/249 (51%), Gaps = 14/249 (5%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           + ++ G + A   ++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV+KFDP +G+
Sbjct: 208 QIQKEG-VRAKEHMIQANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTKGY 266

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           R +TY+ WWI+  +   I      +++     +K     L ++K   + I+        +
Sbjct: 267 RFSTYAYWWIRQGITRAIATQSRTIRLPVHITEK-----LNKIKKAQRKISQEKGHTPSI 321

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IA +L ++  +V  +  R+    SL   +       ++  D L  D    E++++   
Sbjct: 322 EDIATELEMTVPQVRELLVRVPRSVSLETKV--GKDKDTELGDLLETDDLSPEEMMM--- 376

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAF 277
            R++    L + ++ L  RER +   R    +    +L ++    ++SRERVRQIEA+A 
Sbjct: 377 -RESLHRELEKLLADLTSRERDVISMRFGLGDGHAYSLADIGRALDLSRERVRQIEAKAL 435

Query: 278 KKVQESIQK 286
           +K+++  ++
Sbjct: 436 QKLRQPKRR 444


>gi|237755496|ref|ZP_04584118.1| RNA polymerase sigma factor RpoD [Sulfurihydrogenibium
           yellowstonense SS-5]
 gi|237692360|gb|EEP61346.1| RNA polymerase sigma factor RpoD [Sulfurihydrogenibium
           yellowstonense SS-5]
          Length = 570

 Score =  206 bits (525), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 72/229 (31%), Positives = 108/229 (47%), Gaps = 12/229 (5%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV K+D ++GF+ +TY+ WWI
Sbjct: 352 KQILVKANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKYDYKKGFKFSTYATWWI 411

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + A+   I      ++I            L R+   L         PE    IAKK  + 
Sbjct: 412 RQAITRAIADQARTIRIPVHM--IETINKLLRISRTLVQELGREPTPE---EIAKKAGMP 466

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             +V  +        SL   I S ++  S   D++    D       +   ++  R  L 
Sbjct: 467 ADKVRKILRTSQDPVSLETPIGSDEE--SHLGDFI---EDKSVLSPEQHMLKQALRLQLD 521

Query: 230 RSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARA 276
             +S L+ RE ++   R   E+    TLE +   F V+RER+RQIEA+A
Sbjct: 522 EVLSTLSEREEQVLRYRFGLEDDTEHTLEQVGKRFGVTRERIRQIEAKA 570


>gi|313665390|ref|YP_004047261.1| RNA polymerase sigma factor RpoD [Mycoplasma leachii PG50]
 gi|312949647|gb|ADR24243.1| putative RNA polymerase sigma factor RpoD [Mycoplasma leachii PG50]
          Length = 498

 Score =  206 bits (525), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 70/327 (21%), Positives = 134/327 (40%), Gaps = 67/327 (20%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSA---AHRLVTSHLRLVVKIAMGYRGYG 72
           +  Y ++I + P+L K +E + AK              ++L+ S+L+LV+ +A  +   G
Sbjct: 163 IKTYFYKIGQAPILTKDQEIMYAKMAVSDDPEDVKEGRNKLIESNLKLVISVARKHLNRG 222

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L  ++++ EGNIGLM+AV KF+ E+GF+ +TY+ WWI+ A+   I      ++I     +
Sbjct: 223 LDFADLIEEGNIGLMKAVDKFEYEKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 282

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 L R++  L          E++     +  ++  +VI +        SL      
Sbjct: 283 --TINKLARVERQLTQELGREPNAEEIANRVGE-GITSDKVIEIKKLSIEPVSLEKPF-- 337

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF--------- 243
            D++ + + D++    D       E  E++  + ++ +    + PRE ++          
Sbjct: 338 GDEDDTHFGDFV---EDKDMVSPNEYTEKEILKEVMDKVFEDMPPREEKVIRMRYGIVPT 394

Query: 244 EARRLQ-----------------------------------------------ENPVTLE 256
             R L                                                ++  TLE
Sbjct: 395 RLRTLLRLAQECNDSSAKELKQAIEELDIHLDTPIEKVRKFNNEIINNNLAKYDSARTLE 454

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQES 283
            +  E  V+RER+RQIEA+  +K+++ 
Sbjct: 455 EVGKELNVTRERIRQIEAKTIRKLKQP 481


>gi|108562514|ref|YP_626830.1| RNA polymerase sigma factor RpoD [Helicobacter pylori HPAG1]
 gi|107836287|gb|ABF84156.1| RNA polymerase sigma-80 factor [Helicobacter pylori HPAG1]
          Length = 692

 Score =  206 bits (525), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 69/237 (29%), Positives = 120/237 (50%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ W
Sbjct: 452 RAKNKMAQSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATW 511

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WIK A+   I      ++I        +   + R+   ++       K   +  +A+++ 
Sbjct: 512 WIKQAISRAIADQARTIRIPIH-----MIDTINRINKVMRKHIQETGKEPDLEVVAEEVG 566

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  
Sbjct: 567 LSLDKVKNVIKVTKEPISLETPVGNDDD--GKFGDFV---EDKNIVSSIDHIMREDLKAQ 621

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 622 IESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 678



 Score = 35.9 bits (82), Expect = 6.9,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 19/36 (52%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+  I +L K EE  L+K+ R   D+
Sbjct: 177 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDI 212


>gi|1769598|gb|AAB39998.1| sigma factor [Synechococcus sp. PCC 7002]
          Length = 398

 Score =  206 bits (525), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 63/244 (25%), Positives = 120/244 (49%), Gaps = 13/244 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   ++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV KFDP +G+R +TY+ W
Sbjct: 158 KAKEHMIQANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVDKFDPTKGYRFSTYAYW 217

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+  +          +++     +K     L ++K   + I+        +  +A+ L 
Sbjct: 218 WIRQGITRGDRTQSRTIRLPVHVTEK-----LNKIKKAQRQISQTQGCTPSLDDVAQALE 272

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++  +V  +  ++    SL   I       ++  D L       E+ L+    R++ +  
Sbjct: 273 MTPEQVREVLQKVPRSVSLE--IRVGKDRDTELGDLLETQDASPEENLV----RESLQRD 326

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVT--LENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L   ++ L  RER + + R    +  T  L  +    +VSRERVRQIEA+A +K+++  +
Sbjct: 327 LHNLLTELTDREREVIQLRYGLGDGKTYSLAEIGRMLDVSRERVRQIEAKALQKLRQPKR 386

Query: 286 KQVE 289
           + + 
Sbjct: 387 RNIM 390


>gi|212550562|ref|YP_002308879.1| RNA polymerase primary sigma factor [Candidatus Azobacteroides
           pseudotrichonymphae genomovar. CFP2]
 gi|212548800|dbj|BAG83468.1| putative RNA polymerase primary sigma factor [Candidatus
           Azobacteroides pseudotrichonymphae genomovar. CFP2]
          Length = 286

 Score =  206 bits (525), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 73/281 (25%), Positives = 139/281 (49%), Gaps = 12/281 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +++ EI    +L  ++E  LA+R R  GD SA  +LV ++LR VV
Sbjct: 5   KITKSITNRESASLDKFLQEISHEELLSIEKEIELARRSRL-GDRSALDKLVRANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + +     
Sbjct: 64  SVAKQYQNQGLSLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQALAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++           +L ++   L      + +      +A++L + E +V         
Sbjct: 124 IVRLPLNR-----VGSLNKISKALSKFEQKHERKPSSEELAQELELPEDKVSETLRISNR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     ++NS    D L  D              ++    +  ++ +LN RE+ I
Sbjct: 179 HISIDAPFADGEENS--LLDVLTNDD---TPAAYHGLIHESLSQEINNALLILNDREKEI 233

Query: 243 FEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            +      +  + LE +   F ++RERVRQI+ +A KK+++
Sbjct: 234 IKMSFGIGQQEMNLEEIGDAFNLTRERVRQIKEKAIKKLKQ 274


>gi|50842514|ref|YP_055741.1| RNA polymerase principal sigma factor HrdD [Propionibacterium acnes
           KPA171202]
 gi|289425060|ref|ZP_06426837.1| sigma-70 region 2 [Propionibacterium acnes SK187]
 gi|289427240|ref|ZP_06428956.1| sigma-70 region 2 [Propionibacterium acnes J165]
 gi|295130591|ref|YP_003581254.1| RNA polymerase principal sigma factor HrdD [Propionibacterium acnes
           SK137]
 gi|50840116|gb|AAT82783.1| RNA polymerase principal sigma factor HrdD [Propionibacterium acnes
           KPA171202]
 gi|289154038|gb|EFD02726.1| sigma-70 region 2 [Propionibacterium acnes SK187]
 gi|289159709|gb|EFD07897.1| sigma-70 region 2 [Propionibacterium acnes J165]
 gi|291376720|gb|ADE00575.1| RNA polymerase principal sigma factor HrdD [Propionibacterium acnes
           SK137]
 gi|313764457|gb|EFS35821.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL013PA1]
 gi|313772161|gb|EFS38127.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL074PA1]
 gi|313807516|gb|EFS46003.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL087PA2]
 gi|313810025|gb|EFS47746.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL083PA1]
 gi|313815996|gb|EFS53710.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL059PA1]
 gi|313818558|gb|EFS56272.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL046PA2]
 gi|313820325|gb|EFS58039.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL036PA1]
 gi|313822868|gb|EFS60582.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL036PA2]
 gi|313825200|gb|EFS62914.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL063PA1]
 gi|313827776|gb|EFS65490.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL063PA2]
 gi|313830353|gb|EFS68067.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL007PA1]
 gi|313833726|gb|EFS71440.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL056PA1]
 gi|314915450|gb|EFS79281.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL005PA4]
 gi|314918267|gb|EFS82098.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL050PA1]
 gi|314920080|gb|EFS83911.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL050PA3]
 gi|314925213|gb|EFS89044.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL036PA3]
 gi|314931602|gb|EFS95433.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL067PA1]
 gi|314955755|gb|EFT00155.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL027PA1]
 gi|314958169|gb|EFT02272.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL002PA1]
 gi|314960004|gb|EFT04106.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL002PA2]
 gi|314967831|gb|EFT11930.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL037PA1]
 gi|314973357|gb|EFT17453.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL053PA1]
 gi|314976035|gb|EFT20130.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL045PA1]
 gi|314978426|gb|EFT22520.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL072PA2]
 gi|314983943|gb|EFT28035.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL005PA1]
 gi|314988127|gb|EFT32218.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL005PA2]
 gi|314989932|gb|EFT34023.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL005PA3]
 gi|315080642|gb|EFT52618.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL078PA1]
 gi|315084315|gb|EFT56291.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL027PA2]
 gi|315085658|gb|EFT57634.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL002PA3]
 gi|315088920|gb|EFT60896.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL072PA1]
 gi|315095902|gb|EFT67878.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL038PA1]
 gi|315098533|gb|EFT70509.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL059PA2]
 gi|315101109|gb|EFT73085.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL046PA1]
 gi|315105655|gb|EFT77631.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL030PA1]
 gi|315108329|gb|EFT80305.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL030PA2]
 gi|327326184|gb|EGE67974.1| RNA polymerase principal sigma factor SigA [Propionibacterium acnes
           HL096PA2]
 gi|327331941|gb|EGE73678.1| RNA polymerase principal sigma factor SigA [Propionibacterium acnes
           HL096PA3]
 gi|327443142|gb|EGE89796.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL013PA2]
 gi|327445926|gb|EGE92580.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL043PA2]
 gi|327448094|gb|EGE94748.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL043PA1]
 gi|327450785|gb|EGE97439.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL087PA3]
 gi|327453871|gb|EGF00526.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL083PA2]
 gi|328753473|gb|EGF67089.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL020PA1]
 gi|328754203|gb|EGF67819.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL087PA1]
 gi|328754545|gb|EGF68161.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL025PA2]
 gi|328760855|gb|EGF74421.1| RNA polymerase principal sigma factor SigA [Propionibacterium acnes
           HL099PA1]
 gi|332675431|gb|AEE72247.1| RNA polymerase principal sigma factor HrdD [Propionibacterium acnes
           266]
          Length = 312

 Score =  206 bits (525), Expect = 3e-51,   Method: Composition-based stats.
 Identities = 68/303 (22%), Positives = 129/303 (42%), Gaps = 41/303 (13%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------------- 41
           ++G+  +  Y+  I + P+L   EE  LA+R                             
Sbjct: 13  IDGKDAVGLYLDGIARTPLLNAAEEVALARRIEAGVFARAILEGHAETTSDTTTKELHQI 72

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
              GD  A    V ++LRLVV +A  Y    +P+ ++V EGN GL++AV+KFD  +GF+ 
Sbjct: 73  AADGD-EALAHFVRANLRLVVSVARKYGRSQMPLLDLVQEGNTGLIRAVEKFDYAKGFKF 131

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY+ WW++ A+   I +   +V++     +      + ++    + +     +  +   
Sbjct: 132 STYATWWVRQAISRGIAQQGRIVRLPVHVAE-----QVNQVSAARRNLERQLGREPETFE 186

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           IA +L ++E  VI +        SL+A +   D   +   D +  +       ++   E 
Sbjct: 187 IADELEITEERVIELIRFGRDHVSLDAPV--EDDGDTSLGDLIARETSPGPDDIVLDAED 244

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVT--LENLSSEFEVSRERVRQIEARAFKK 279
              R+ L   +  L+ R   +   R    +     L ++   + ++ ERVRQIE  A   
Sbjct: 245 ---RSRLEGLLDDLDERSADVVRRRYGLVDGRQAKLADIGKVWGITAERVRQIERAALAS 301

Query: 280 VQE 282
           +++
Sbjct: 302 MRQ 304


>gi|254421571|ref|ZP_05035289.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
 gi|196189060|gb|EDX84024.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
          Length = 390

 Score =  206 bits (524), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 68/316 (21%), Positives = 133/316 (42%), Gaps = 58/316 (18%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEY-----------------VLAKRYREHGDLSA------- 49
             +  Y+HEI ++P+L  ++E                   LA +  E     A       
Sbjct: 74  DAVRSYLHEIGRVPLLSHEDEIVLGKQVQKMMALLAIKEELAAKLSEAEGEEAEVSNADW 133

Query: 50  ---------------------AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
                                  +++ ++LRLVV +A  Y+   L   +++ EG +GL +
Sbjct: 134 AAAASIPESELDHHMRRGQRSKRKMIEANLRLVVAVAKKYQKRNLEFLDLIQEGTLGLER 193

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
            V+KFDP +G++ +TY+ WWI+ A+   I +    +++     +K     L ++K   + 
Sbjct: 194 GVEKFDPMKGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEK-----LNKIKRVQRE 248

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           ++    +      I ++L +   +V           SL+  +   D   ++ QD L  D 
Sbjct: 249 LSQKLGRSPNAAEIGQELELEPKQVREYLSIARQPISLD--VRIGDNQDTELQDLLEDDG 306

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSR 266
              E   +++  R +    + R +S L  +++ +   R      NP++L  +     +SR
Sbjct: 307 ASPEDYTVQQSLRSD----IFRMLSELTSQQQEVINLRFGLADGNPLSLAKVGQRMGISR 362

Query: 267 ERVRQIEARAFKKVQE 282
           ERVRQ+E +A K ++ 
Sbjct: 363 ERVRQLEQQALKHLRR 378


>gi|149177995|ref|ZP_01856592.1| RNA polymerase sigma factor rpoS [Planctomyces maris DSM 8797]
 gi|148843188|gb|EDL57554.1| RNA polymerase sigma factor rpoS [Planctomyces maris DSM 8797]
          Length = 279

 Score =  206 bits (524), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 85/272 (31%), Positives = 139/272 (51%), Gaps = 15/272 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ EI +  +L  +EE  L+ R  EHGD  A  R+V ++LRLVV IA  Y G GLP+
Sbjct: 17  LETYLKEINETALLSAEEERELSNRI-EHGDKEARDRMVRANLRLVVNIARAYSGKGLPL 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GL++AV+ FDPE G R +TY+ +WIK +++  ++ S   ++I   A    L
Sbjct: 76  QDLIEEGNLGLLRAVEGFDPEMGTRFSTYASYWIKQSIKRALVNSAKTIRIP--AYMVEL 133

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
               RR    LQ   D     E+V   A++L++   ++  +   +    S  +  +    
Sbjct: 134 LTKWRRATAQLQDTLDRTPTTEEV---ARELDLPPKKLKIVKKAIQLYNS--SPQSEQHD 188

Query: 196 NSSQWQDWLVYDH-DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENP 252
                 + +  D   G +  L+E +  K+    + R +  +  RE  I   R     + P
Sbjct: 189 AGWSLGEMIPDDRLKGPDDELVENDNLKH----VFRLLKEIPEREANILRMRFGLDGDEP 244

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL+ +     ++RERVRQIE+ A KK+ + I
Sbjct: 245 KTLKEIGQALGLTRERVRQIESEALKKLAKEI 276


>gi|119512139|ref|ZP_01631231.1| RNA polymerase sigma-like factor [Nodularia spumigena CCY9414]
 gi|119463229|gb|EAW44174.1| RNA polymerase sigma-like factor [Nodularia spumigena CCY9414]
          Length = 442

 Score =  206 bits (524), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 68/265 (25%), Positives = 135/265 (50%), Gaps = 18/265 (6%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           I  L  +E     ++ +  G L A   ++ ++LRLVV +A  Y+  GL + ++V EG +G
Sbjct: 185 IAQLTVEE----LEQVQSQG-LQAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLG 239

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L +AV+KFDP +G+R +TY+ WWI+  +   I  S   +++     +K     L ++K  
Sbjct: 240 LERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATSSRTIRLPVHITEK-----LNKIKKA 294

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            + I     +   +  +A +L ++ ++V  +  ++    SL   +       ++  + L 
Sbjct: 295 QRKIAQEKGRTPTLEDLAIELEMTPTQVREVLLKVPRSVSLETKV--GKDKDTELGELLE 352

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFE 263
            D    E++L+ +  +K+    L   ++ L  RER +   R      +P +L  +    +
Sbjct: 353 TDCVTPEEMLMRESLQKD----LHSLLADLTSRERDVILMRFGLSDGHPYSLAEIGRALD 408

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           +SRERVRQIE++A +K+++  ++ +
Sbjct: 409 LSRERVRQIESKALQKLRQPKRRNL 433


>gi|315185629|gb|EFU19397.1| RNA polymerase, sigma 70 subunit, RpoD [Spirochaeta thermophila DSM
           6578]
          Length = 568

 Score =  206 bits (524), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 63/242 (26%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+KF+  +G++ +TY+ 
Sbjct: 328 KTAKDKLIQANLRLVVSIAKKYTNRGLHFFDLVQEGNIGLIKAVEKFEYRKGYKFSTYAT 387

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      +++        +   + +++   + +     +      IA +L
Sbjct: 388 WWIRQAITRSISDQARTIRVPVH-----MIEQINKVQREARQLMQVLGREPTDEEIADRL 442

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
               S V S+        SL + I   ++  S   D++    D        +      + 
Sbjct: 443 GWPLSRVKSVKNVAREPISLESPI--GEEEDSSVGDFI---EDKTAVNPSHQTAYALLQQ 497

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +   ++ L PRE+ + + R   E+   +TLE +   F V+RER+RQIEA+A ++++   
Sbjct: 498 QIKDVLATLPPREQEVLKMRFGLEDGYSLTLEEVGLYFNVTRERIRQIEAKALRRLRHPK 557

Query: 285 QK 286
           + 
Sbjct: 558 RS 559



 Score = 36.3 bits (83), Expect = 5.1,   Method: Composition-based stats.
 Identities = 9/33 (27%), Positives = 18/33 (54%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE 43
           + +  +  Y+ EI +  +L  +EE  L+K+  E
Sbjct: 79  STDDPIRLYLREIGRENLLTAEEEVSLSKQMEE 111


>gi|224531865|ref|ZP_03672497.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia valaisiana
           VS116]
 gi|224511330|gb|EEF81736.1| RNA polymerase sigma factor RpoD (Sigma-70) [Borrelia valaisiana
           VS116]
          Length = 631

 Score =  206 bits (524), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 67/257 (26%), Positives = 122/257 (47%), Gaps = 16/257 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 379 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 434

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RGF+ +TY+ WWI+ A+   I      +++        +   + RL    + +   
Sbjct: 435 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVH-----MIEQINRLNRETRYLIQV 489

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             K      ++ +L     +V ++        SL   I   ++  S   D++    D   
Sbjct: 490 LGKDPTDEELSDRLGWELKKVKTVKSVSREPVSLETPI--GEEEDSVLSDFI---EDKAI 544

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +           ++ +   +  L  RE+ + + R   E+   +TLE +   F V+RER+R
Sbjct: 545 KNPANHTSFVVLQDQIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIR 604

Query: 271 QIEARAFKKVQESIQKQ 287
           QIE++A ++++   + Q
Sbjct: 605 QIESKALRRLKNPKKTQ 621


>gi|313812945|gb|EFS50659.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL025PA1]
          Length = 312

 Score =  206 bits (524), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 68/303 (22%), Positives = 129/303 (42%), Gaps = 41/303 (13%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------------- 41
           ++G+  +  Y+  I + P+L   EE  LA+R                             
Sbjct: 13  IDGKDAVGLYLDGIARTPLLNAAEEVALARRIEAGVFARAILEGHAETTSDATTKELHQI 72

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
              GD  A    V ++LRLVV +A  Y    +P+ ++V EGN GL++AV+KFD  +GF+ 
Sbjct: 73  AADGD-EALAHFVRANLRLVVSVARKYGRSQMPLLDLVQEGNTGLIRAVEKFDYAKGFKF 131

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY+ WW++ A+   I +   +V++     +      + ++    + +     +  +   
Sbjct: 132 STYATWWVRQAISRGIAQQGRIVRLPVHVAE-----QVNQVSAARRNLERQLGREPETFE 186

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           IA +L ++E  VI +        SL+A +   D   +   D +  +       ++   E 
Sbjct: 187 IADELEITEERVIELIRFGRDHVSLDAPV--EDDGDTSLGDLIARETSPGPDDIVLDAED 244

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVT--LENLSSEFEVSRERVRQIEARAFKK 279
              R+ L   +  L+ R   +   R    +     L ++   + ++ ERVRQIE  A   
Sbjct: 245 ---RSRLEGLLDDLDERSADVVRRRYGLVDGRQAKLADIGKVWGITAERVRQIERAALAS 301

Query: 280 VQE 282
           +++
Sbjct: 302 MRQ 304


>gi|307718699|ref|YP_003874231.1| RNA polymerase sigma factor RpoD [Spirochaeta thermophila DSM 6192]
 gi|306532424|gb|ADN01958.1| RNA polymerase sigma factor RpoD [Spirochaeta thermophila DSM 6192]
          Length = 338

 Score =  206 bits (524), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 72/302 (23%), Positives = 138/302 (45%), Gaps = 39/302 (12%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEY--------------VLA-------------KRYR 42
           ++    L+ Y+ +I   P+L  +EE+               L+             +R  
Sbjct: 36  LSDADALALYLKQISSYPLLTPEEEHWIGGEIQRIKLRLRELSSLPEEQRAHHFEEERRL 95

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           +       +R++T++LRLVV IA  Y+  GL + +++ EGNIGL++AV++FD  +G R +
Sbjct: 96  DQRLRELKNRMITANLRLVVSIAKKYQHRGLSLLDLIDEGNIGLIEAVERFDYTKGCRFS 155

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY  WWI+ A+ + +     +++I        +   ++ +    + +     +      +
Sbjct: 156 TYGTWWIRQAIVKSLADKSRVIRIPIH-----MLNTIKNVFMLSKELAQELGRDPTEEEL 210

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           ++   + +  V  +        SL+  I   ++N +   D +  D D   Q   EK   +
Sbjct: 211 SRYTGLPDRRVAEIMQVSQETASLD--ITVDEENMTTLGDLVSDDED---QGPFEKVFHR 265

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
              ++L  ++  L+ RER +   R     E P+TLE       ++RERVRQI+ +A  K+
Sbjct: 266 YLHDVLLEALGDLSERERNVISLRFGLNGEGPLTLEETGKLLGITRERVRQIQEKALAKL 325

Query: 281 QE 282
           +E
Sbjct: 326 RE 327


>gi|213162104|ref|ZP_03347814.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. E00-7866]
          Length = 225

 Score =  206 bits (524), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 60/231 (25%), Positives = 108/231 (46%), Gaps = 12/231 (5%)

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I     
Sbjct: 1   SIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 60

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            ++I            L R+   +         PE    +A+++ + E ++  +      
Sbjct: 61  TIRIPVHM--IETINKLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKE 115

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S+   I   D   S   D++    D   ++ ++    ++ R      ++ L  RE ++
Sbjct: 116 PISMETPI--GDDEDSHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKV 170

Query: 243 FEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
              R   +     TLE +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 171 LRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 221


>gi|300781025|ref|ZP_07090879.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           genitalium ATCC 33030]
 gi|300532732|gb|EFK53793.1| RNA polymerase principal sigma factor SigB [Corynebacterium
           genitalium ATCC 33030]
          Length = 330

 Score =  206 bits (524), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 67/309 (21%), Positives = 138/309 (44%), Gaps = 39/309 (12%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------------------- 42
           +R+N +        +  Y++ I K  +L  +EE  LA++                     
Sbjct: 19  SRRNQTNDNPSADLVRVYLNGIGKTALLNAEEEVELAQQIEVGLYAQHLLDDPDTELTRA 78

Query: 43  --------EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                         A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD
Sbjct: 79  KSRDLKILAKQGRKARAHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFD 138

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +GF+ +TY+ WWI+ A+   +      +++     ++     L R++  +        
Sbjct: 139 YSKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLSRIRREMYQSLGREP 196

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
             E    +A++  + ES++  +  +     SL+  + + ++  +   D++        + 
Sbjct: 197 SNE---ELAEESGIDESKIEMLLRQSRDPVSLDMPVGADEE--APLGDFIEDAEAADAED 251

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
            +    R    + +   ++ L  RE+ +   R   ++  P TL+ +  +F +SRERVRQI
Sbjct: 252 AVVSVLR---HDDIHDIINGLEQREQDVIRLRYGLDDGVPRTLDQIGRKFGLSRERVRQI 308

Query: 273 EARAFKKVQ 281
           E     K++
Sbjct: 309 EREVMSKLR 317


>gi|288799880|ref|ZP_06405339.1| RNA polymerase sigma-70 factor [Prevotella sp. oral taxon 299 str.
           F0039]
 gi|288333128|gb|EFC71607.1| RNA polymerase sigma-70 factor [Prevotella sp. oral taxon 299 str.
           F0039]
          Length = 290

 Score =  206 bits (524), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 70/288 (24%), Positives = 134/288 (46%), Gaps = 14/288 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKI 64
           SI       L +Y+ EI + P++   +E  LA++ ++ G     A  +LVT++LR VV +
Sbjct: 9   SITNRSSEALDKYLVEIGRAPLISIDDEIELAQKIKKGGPEGERAKDKLVTANLRFVVSV 68

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y+  GL +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V
Sbjct: 69  AKQYQHQGLTLTDLIDEGNIGLIKAAQKFDETRGFKFISYAVWWIRQSILQAIAEQSRIV 128

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           ++           +L ++   +      N +   V  ++   N+ E ++           
Sbjct: 129 RLPLNQ-----VGSLNKINHEINKFEQENQRHPSVSELSDATNIDEEKIGQSLMADGHHV 183

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM-SVLNPRERRIF 243
           S++A     + N          D     QV     + ++    L   +  VL  RE  I 
Sbjct: 184 SIDAPFQDGEDNCMLDVMPSSDDSRTDRQV-----DHESMAQELEAVLNKVLKDREITII 238

Query: 244 EARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
                   +   LE +  +  ++RERVRQI  ++  K+++S   ++ +
Sbjct: 239 RECFGIGCHEKGLEEIGDQLGLTRERVRQIREKSIAKLRDSGNAKILM 286


>gi|330447824|ref|ZP_08311472.1| RNA polymerase sigma factor, sigma-70 family protein
           [Photobacterium leiognathi subsp. mandapamensis
           svers.1.1.]
 gi|328492015|dbj|GAA05969.1| RNA polymerase sigma factor, sigma-70 family protein
           [Photobacterium leiognathi subsp. mandapamensis
           svers.1.1.]
          Length = 286

 Score =  206 bits (524), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 138/271 (50%), Gaps = 12/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+++I   P+L K++E   ++++   GD +A   LV S+LRLVV IA  YR   L +S++
Sbjct: 14  YLNDISNKPLLTKEDEIQYSRKFL-MGDTNAKKILVESNLRLVVSIAKKYRASKLSLSDL 72

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM AV KFDPE+GFR +TY+ WWIK  ++  I      +++    +  +    
Sbjct: 73  IDEGNIGLMTAVDKFDPEKGFRFSTYASWWIKQTIERAIHNQNRTIRLPVHVS--KEINT 130

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R    L  + +N    +    IA+ LN   +E+ S+        SL   +   D+NS+
Sbjct: 131 LLRTHRELMKVNNNEPTQDD---IARVLNRDINEISSLLASEVNVVSLEQTLGD-DENSN 186

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
                +  +        ++ ++     NM+   +  L  R+R I   R       P TL+
Sbjct: 187 TVAYLVADEQIASPSAEVDSDDIMKVTNMI---LHKLPSRDREIMCRRYGLMGYEPHTLQ 243

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            ++    ++RER+RQ++ +    ++ S++++
Sbjct: 244 EVADSVGLTRERIRQLQIKTLNTLKRSLERE 274


>gi|307155201|ref|YP_003890585.1| RpoD subfamily RNA polymerase sigma-70 factor [Cyanothece sp. PCC
           7822]
 gi|306985429|gb|ADN17310.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7822]
          Length = 295

 Score =  206 bits (524), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 73/289 (25%), Positives = 139/289 (48%), Gaps = 32/289 (11%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLA-------------------KRYREHGDLSAAHRLV 54
             +  Y+ EI + P+L  Q+E  LA                   KR  + G   A  +++
Sbjct: 7   DNVKAYLQEIGRTPLLNAQQEIELATQVQKMMALIDKENPTPEEKRIIQQG-KRAKRKMI 65

Query: 55  TSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114
            ++LRLVV IA  Y+  GL   +++ EG+IGL++ V+KFDP +G++ +TY+ WWI+ AM 
Sbjct: 66  NANLRLVVSIAKKYQRRGLSFLDLIQEGSIGLIRGVEKFDPSKGYKFSTYAYWWIRQAMT 125

Query: 115 EYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVI 174
             I      +++ +   +      L +LK   + +T    +      +A  L +S  E+ 
Sbjct: 126 RAIADQSRTIRLPSHLTES-----LNKLKRVTRQLTGELGRRPTEQELANALELSLHELH 180

Query: 175 SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV 234
           ++        S +  +   D+  ++ ++ L  + +     + + E     R+M+   +  
Sbjct: 181 AIRQADHRTRSYSLNMKMEDEQ-TELEELLADNSETPNDFVAQIEL----RSMVDELLES 235

Query: 235 LNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           L PR++ I   R   +N   ++LE + +   +SRERVRQ++ RA + ++
Sbjct: 236 LPPRQQEIIALRYGLKNGRQMSLEEVGNYCNLSRERVRQLQNRAMRTLK 284


>gi|282854020|ref|ZP_06263357.1| sigma-70 region 2 [Propionibacterium acnes J139]
 gi|282583473|gb|EFB88853.1| sigma-70 region 2 [Propionibacterium acnes J139]
 gi|314922987|gb|EFS86818.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL001PA1]
 gi|314966764|gb|EFT10863.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL082PA2]
 gi|314981098|gb|EFT25192.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL110PA3]
 gi|315091924|gb|EFT63900.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL110PA4]
 gi|315093320|gb|EFT65296.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL060PA1]
 gi|315103425|gb|EFT75401.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL050PA2]
 gi|327327589|gb|EGE69365.1| RNA polymerase principal sigma factor SigA [Propionibacterium acnes
           HL103PA1]
          Length = 312

 Score =  206 bits (524), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 68/303 (22%), Positives = 129/303 (42%), Gaps = 41/303 (13%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------------- 41
           ++G+  +  Y+  I + P+L   EE  LA+R                             
Sbjct: 13  IDGKDAVGLYLDGIARTPLLNAAEEVALARRIEAGVFARAVLEGHAETTSDATTEELHQI 72

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
              GD  A    V ++LRLVV +A  Y    +P+ ++V EGN GL++AV+KFD  +GF+ 
Sbjct: 73  AADGD-EALAHFVRANLRLVVSVARKYGRSQMPLLDLVQEGNTGLIRAVEKFDYAKGFKF 131

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY+ WW++ A+   I +   +V++     +      + ++    + +     +  +   
Sbjct: 132 STYATWWVRQAISRGIAQQGRIVRLPVHVAE-----QVNQVSAARRNLERQLGREPETFE 186

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           IA +L ++E  VI +        SL+A +   D   +   D +  +       ++   E 
Sbjct: 187 IADELEITEERVIELIRFGRDHVSLDAPV--EDDGDTSLGDLIARETSPGPDDIVLDAED 244

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVT--LENLSSEFEVSRERVRQIEARAFKK 279
              R+ L   +  L+ R   +   R    +     L ++   + ++ ERVRQIE  A   
Sbjct: 245 ---RSRLEGLLDDLDERSADVVRRRYGLVDGRQAKLADIGKVWGITAERVRQIERAALAS 301

Query: 280 VQE 282
           +++
Sbjct: 302 MRQ 304


>gi|330448286|ref|ZP_08311934.1| RNA polymerase sigma factor RpoS [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
 gi|328492477|dbj|GAA06431.1| RNA polymerase sigma factor RpoS [Photobacterium leiognathi subsp.
           mandapamensis svers.1.1.]
          Length = 291

 Score =  206 bits (524), Expect = 4e-51,   Method: Composition-based stats.
 Identities = 79/290 (27%), Positives = 144/290 (49%), Gaps = 15/290 (5%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           ++ K+  +   G+I +  Y+ +I +  +L K++E + +++    GD ++   L+ S+LRL
Sbjct: 3   VSNKDDLLSHGGDI-VHLYLKDIAEKDLLTKEDEVLYSRK-SLAGDENSKKVLIESNLRL 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  YRG  + IS+++ EGNIGL+ AV+KFDPE+GFR +TY+ WWIK  ++  I   
Sbjct: 61  VVSIAKKYRGSPMHISDLIDEGNIGLITAVEKFDPEKGFRFSTYATWWIKQTIERAIHNQ 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR- 179
              +++    +  +    + R    L    +     EQ+  I  K     S  +S     
Sbjct: 121 GRTIRLPVHVS--KEINTIVRAHKQLVKKNNEEPSKEQIANILNKSLHDVSTTLSYETPI 178

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           ++ D+S+N  +N         Q   V   D       +  +      + T  ++ LN R+
Sbjct: 179 ISYDQSVNGEVN--------AQSMAVLIADETMAKPDQHVDDLAIEKITTNVLNCLNKRD 230

Query: 240 RRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           + I   R   L     TL+ ++ E  ++RER+RQ++  +  K++ S+ + 
Sbjct: 231 KEIICRRFGLLGYEAQTLQEVAEEVGLTRERIRQLQVTSLSKLKNSLTRD 280


>gi|116689841|ref|YP_835464.1| RNA polymerase sigma factor RpoS [Burkholderia cenocepacia HI2424]
 gi|170733180|ref|YP_001765127.1| RNA polymerase sigma factor RpoS [Burkholderia cenocepacia MC0-3]
 gi|116647930|gb|ABK08571.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia cenocepacia
           HI2424]
 gi|169816422|gb|ACA91005.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia cenocepacia
           MC0-3]
          Length = 362

 Score =  206 bits (524), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 78/280 (27%), Positives = 132/280 (47%), Gaps = 15/280 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+
Sbjct: 82  DTIQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGV 140

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++       
Sbjct: 141 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV--I 198

Query: 134 RLFFNLRRLKGHLQAITDN-----NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           R    + R K HL+  + +       +   +  IA     +  EV  +        SL+A
Sbjct: 199 RELNQVLRAKRHLEKNSMSTGEAAERREASIDDIAYLTGKTAEEVTDILALNEHTASLDA 258

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +      +S   D L  D        ++  E +    +    +S L+ + R + E R  
Sbjct: 259 PL--DLDPASSLLDLLPDDQSQSPDAEVQHRELE---TLTRAWLSRLSDKHRHVIERRFG 313

Query: 249 QE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                P TLE L+ E  ++RERVRQI+  A  +++     
Sbjct: 314 LNHIEPATLEELADEMGLTRERVRQIQQEALVRLKRFFAS 353


>gi|254778811|ref|YP_003056916.1| RNA polymerase sigma factor RpoD [Helicobacter pylori B38]
 gi|254000722|emb|CAX28640.1| RNA polymerase sigma factor rpoD (Sigma-70) [Helicobacter pylori
           B38]
          Length = 679

 Score =  206 bits (524), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 69/237 (29%), Positives = 120/237 (50%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ W
Sbjct: 439 RAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATW 498

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WIK A+   I      ++I        +   + R+   ++       K   +  +A+++ 
Sbjct: 499 WIKQAISRAIADQARTIRIPIH-----MIDTINRINKVMRKHIQETGKEPDLEVVAEEVG 553

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  
Sbjct: 554 LSLDKVKNVIKVTKEPISLETPVGNDDD--GKFGDFV---EDKNIVSSIDHIMREDLKVQ 608

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 609 IESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQIESSAIKKLR 665



 Score = 35.9 bits (82), Expect = 6.5,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 19/36 (52%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+  I +L K EE  L+K+ R   D+
Sbjct: 164 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDI 199


>gi|319948428|ref|ZP_08022566.1| RNA polymerase sigma factor SigB [Dietzia cinnamea P4]
 gi|319437910|gb|EFV92892.1| RNA polymerase sigma factor SigB [Dietzia cinnamea P4]
          Length = 322

 Score =  205 bits (523), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 65/297 (21%), Positives = 130/297 (43%), Gaps = 38/297 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYRE--------------------------HGDLSAAHR 52
           Y++ I K  +L  ++E  L+KR                                 +A   
Sbjct: 29  YLNGIGKTALLNAEDEVELSKRIEAGLYAKHLLETKKRLGPAKKADLKTIVAEGEAARAH 88

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A
Sbjct: 89  LLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTYATWWIRQA 148

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +      +++     ++     L R+K  L          E++   +    +   +
Sbjct: 149 ITRGMADQSRTIRLPVHLVEQ--VNKLARIKRELHQQLGREATLEELAEES---GIPAHK 203

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           +  +        SL+  + + ++  +   D++    D +              + +   +
Sbjct: 204 IEELLDHSRDPVSLDMPVGADEE--APLGDFI---EDAEATSAENTVVSNVMHSDVRAVL 258

Query: 233 SVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           + L  RE+++   R   ++  P TL+ +   F +SRERVRQIE     K++E  +  
Sbjct: 259 ATLEEREQQVITLRFGLDDGQPRTLDQIGKRFGLSRERVRQIEREVMAKLREGRRAD 315


>gi|1769596|gb|AAB39997.1| sigma factor [Synechococcus sp. PCC 7002]
          Length = 317

 Score =  205 bits (523), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 70/321 (21%), Positives = 139/321 (43%), Gaps = 53/321 (16%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGDLS------------ 48
             +  Y+ EI ++P+L  +EE + ++R +             E  D              
Sbjct: 9   DPVRTYLKEIGRVPLLTHEEEVLYSRRVQKMVNLEKLKAELAEKQDQEPSLKEWAQAANL 68

Query: 49  --------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                         A  ++V ++LRLVV +A  Y    + + +++ EG IG+ + V+KFD
Sbjct: 69  SQRQLKKQLLLGKQAKQKMVEANLRLVVSVAKKYIKRNMDLLDLIQEGTIGMQRGVEKFD 128

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P +G+R +TY+ WWI+ A+   I      +++     +K     L ++K   + +   N 
Sbjct: 129 PTKGYRFSTYAYWWIRQAITRAIAEQSRTIRLPIHITEK-----LNKIKKAQRQLAQANG 183

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +   +  +A +L ++  +V     +     SL+  +   D N ++  + L  D +  +  
Sbjct: 184 RSASIPELADELGLTTKQVRDYLEKSRQPLSLD--LRVGDNNDTELIE-LEDDGELPDDY 240

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQI 272
                 +++    L R ++ L  +++ +   R       P TL  +     +SRERVRQI
Sbjct: 241 ATHAALKRD----LARMLNDLTAQQQEVLTLRFGLRDGTPHTLAKIGEHLNISRERVRQI 296

Query: 273 EARAFKKVQESIQKQVELSSS 293
           E  +  K+++  +K  E  +S
Sbjct: 297 EHGSLAKLRKQKRKLGEYLAS 317


>gi|283781338|ref|YP_003372093.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pirellula staleyi
           DSM 6068]
 gi|283439791|gb|ADB18233.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pirellula staleyi
           DSM 6068]
          Length = 524

 Score =  205 bits (523), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 69/243 (28%), Positives = 116/243 (47%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L   +LRLVV IA  YR  GL   +++ EGN GLM+AV KF+  RGF+  TY+ 
Sbjct: 285 QQAKRELSEGNLRLVVSIAKKYRNRGLSFLDLIQEGNAGLMRAVDKFEYRRGFKFCTYAT 344

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +      + R++   + +     +   +   A+K 
Sbjct: 345 WWIRQAITRAVADQSRTIRIPVHMVE-----TMSRVRNVSRQLLQELGREPTLEETARKA 399

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             +  E   +        SL+  + +S+   S + D L    DG  +       ++  R 
Sbjct: 400 KTTVDEARRVLAMSRYPISLDRPVGNSED--SHFGDLLP---DGTAESPATGASQEMLRT 454

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + + +  L+ RER I + R    +    TLE +   F+V+RER+RQIEA+A +K+Q+  
Sbjct: 455 RINKVLKTLSYREREIIKLRYGLGDGYSYTLEEVGHIFKVTRERIRQIEAKAVRKLQQPS 514

Query: 285 QKQ 287
           + Q
Sbjct: 515 RSQ 517


>gi|218295160|ref|ZP_03495996.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermus aquaticus
           Y51MC23]
 gi|218244363|gb|EED10888.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermus aquaticus
           Y51MC23]
          Length = 439

 Score =  205 bits (523), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 67/237 (28%), Positives = 110/237 (46%), Gaps = 10/237 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +A   L+ ++LRLVV IA  Y G GL   +++ EGN GL++AV+KF+ +R F+ +TY+ 
Sbjct: 197 EAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYAT 256

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I     +      L R    LQ         E++   A   
Sbjct: 257 WWIRQAINRAIADQARTIRIPVHMVE--TINKLSRTARQLQQELGREPSYEEIAE-AMGP 313

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
                 V           SL   I   D+  S + D++    D      +E   +     
Sbjct: 314 GWDAKRVEETLKIAQEPVSLETPI--GDEKDSFYGDFIP---DENLPSPVEAAAQSLLSE 368

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L +++S L+ RE  + + R+        TLE + + F V+RER+RQIE +A +K++
Sbjct: 369 ELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLK 425



 Score = 43.6 bits (102), Expect = 0.032,   Method: Composition-based stats.
 Identities = 14/47 (29%), Positives = 27/47 (57%), Gaps = 2/47 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTS 56
           V+    + +Y+HEI ++P+L  +EE  LA++  E   + A  +L  +
Sbjct: 91  VSTSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEG--MEAIKKLSEA 135


>gi|313673100|ref|YP_004051211.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Calditerrivibrio
           nitroreducens DSM 19672]
 gi|312939856|gb|ADR19048.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Calditerrivibrio
           nitroreducens DSM 19672]
          Length = 327

 Score =  205 bits (523), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 71/285 (24%), Positives = 149/285 (52%), Gaps = 14/285 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
            ++I    +  +  +I++I K   L ++EEY L KR ++ GD  A ++L+ S+++ VV +
Sbjct: 48  EIAISSLTDDSIKDFINKIDKFKPLTREEEYELGKRIQQ-GDQEALNKLILSNIKFVVSM 106

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y+  G+ +S+++++GN+GL++A K+FDP++G +  +Y++WWI+ AM + +      V
Sbjct: 107 ANRYKNTGVSLSDLINQGNLGLVEAAKRFDPDKGVKFISYAVWWIRQAMIQLLAEQSGTV 166

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           K+            L ++   ++ ++    +      I++ LN+ +  + ++        
Sbjct: 167 KLPIKQASL-----LYKINEAIETLSKKYHREPTSEEISEYLNIPKENIENILMVSKNYL 221

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           S  + I   +  +       +   + +   + ++      ++ L   +  L+ RE +I +
Sbjct: 222 SFESPIKDGEDRT------FLDLMESRTIKVEDEVINHTLKDTLQSLIQELDEREAKILK 275

Query: 245 ARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            R     ENP+TLE + +   +SRERVRQIE+RA  K+++   K+
Sbjct: 276 MRYGLDGENPMTLEEVGNILNISRERVRQIESRALSKLRKKAVKK 320


>gi|238027063|ref|YP_002911294.1| RNA polymerase sigma factor RpoS [Burkholderia glumae BGR1]
 gi|76057940|emb|CAJ30487.1| stationary phase sigma factor [Burkholderia plantarii]
 gi|121663602|emb|CAM12359.1| stationary phase sigma factor [Burkholderia glumae]
 gi|237876257|gb|ACR28590.1| Stationary phase sigma factor [Burkholderia glumae BGR1]
          Length = 364

 Score =  205 bits (523), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 78/280 (27%), Positives = 132/280 (47%), Gaps = 15/280 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+
Sbjct: 84  DTIQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGV 142

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++       
Sbjct: 143 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV--I 200

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVA-----IAKKLNVSESEVISMNCRLAGDESLNA 188
           R    + R K HL+  + +  +  +        IA     +  EV  +        SL+A
Sbjct: 201 RELNQVLRAKRHLEKNSMSTGEAAERREAGIDDIAYLTGKTAEEVTDILALNEHTASLDA 260

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +      +S   D L  D        ++  E +    +    +S L+ + R + E R  
Sbjct: 261 PL--DLDPASSLLDLLPDDQSQSPDAEVQHRELE---TLTRAWLSRLSDKHRHVIERRFG 315

Query: 249 QE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                P TLE L+ E  ++RERVRQI+  A  +++     
Sbjct: 316 LNHIEPATLEELADEMGLTRERVRQIQQEALVRLKRFFAS 355


>gi|2522316|gb|AAB81010.1| RNA polymerase principal sigma factor RpoD [Helicobacter pylori]
          Length = 680

 Score =  205 bits (523), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 69/237 (29%), Positives = 120/237 (50%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A +++  S+LRLVV IA  +   GLP  +++ EGNIGLM+AV KF+ E+GF+ +TY+ W
Sbjct: 440 RAKNKMAKSNLRLVVSIAKRFTSRGLPFLDLIQEGNIGLMKAVDKFEHEKGFKFSTYATW 499

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WIK A+   I      ++I        +   + R+   ++       K   +  +A+++ 
Sbjct: 500 WIKQAISRAIADQARTIRIPIH-----MIDTINRINKVMRKHIQETGKEPDLEVVAEEVG 554

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +V ++        SL   + + D    ++ D++    D      I+   R++ +  
Sbjct: 555 LSLDKVKNVIKVTKEPISLETPVGNDDD--GKFGDFV---EDKNIVSSIDHIMREDLKAQ 609

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A KK++
Sbjct: 610 IESVLDQLNEREKAVIRMRFGLLDDESERTLEEIGKELNVTRERVRQIESSAIKKLR 666



 Score = 35.9 bits (82), Expect = 7.2,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 19/36 (52%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+  I +L K EE  L+K+ R   D+
Sbjct: 165 SDSPVRMYLREMGDIKLLSKDEEIELSKQIRLGEDI 200


>gi|239814806|ref|YP_002943716.1| RNA polymerase, sigma 70 family subunit [Variovorax paradoxus S110]
 gi|239801383|gb|ACS18450.1| putative RNA polymerase, sigma 70 family subunit [Variovorax
           paradoxus S110]
          Length = 331

 Score =  205 bits (523), Expect = 5e-51,   Method: Composition-based stats.
 Identities = 81/278 (29%), Positives = 133/278 (47%), Gaps = 11/278 (3%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           G   L+ Y+ ++R+  +   +EEY  A   R  GD +A   ++  +LRLVV IA  Y G 
Sbjct: 49  GADALTIYLRQVRRTELFTPEEEYQAACAAR-AGDFAARQSMIEHNLRLVVNIAKAYLGR 107

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           G+P+S+++ EGN+GLM A+ KF+PERGFR +TY+ WWI+ +++  +L     +++     
Sbjct: 108 GVPLSDLIEEGNLGLMHAITKFEPERGFRFSTYATWWIRQSVERAVLTQARAIRLPVHV- 166

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQ---VVAIAKKLNVSESEVISMNCRLAGDESLNA 188
             R    + R +  L+   +          V  +A  L +    V  +        SL+A
Sbjct: 167 -VRELQQVLRARRTLEGDAEFLAHRPDGVRVEDVAAFLGLEVQAVAELLALAEAPRSLDA 225

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
                D+  +        D  G    +    E      +L + +  L+ RER + E R  
Sbjct: 226 GDAHGDEGFTLADTVASEDEQGDPTDVTHTHEVA---RLLDQWVHALDAREREVLEGRYG 282

Query: 249 QEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             +  P TLE LS    ++RERVRQI+  A  K++  +
Sbjct: 283 LHDREPETLEVLSVRLGLTRERVRQIQNEALAKMRRQL 320


>gi|330469769|ref|YP_004407512.1| RNA polymerase, sigma 70 subunit, rpod subfamily protein
           [Verrucosispora maris AB-18-032]
 gi|328812740|gb|AEB46912.1| RNA polymerase, sigma 70 subunit, rpod subfamily protein
           [Verrucosispora maris AB-18-032]
          Length = 333

 Score =  205 bits (523), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 77/297 (25%), Positives = 133/297 (44%), Gaps = 38/297 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH---------------------GDLSAAHR 52
           Y+HEI + P+L+  +E  L+K      Y EH                         A   
Sbjct: 42  YLHEISRTPLLDAAKEVDLSKAIEAGLYAEHLLGEDRVPEGVTRDELTRLVAEGERAKDL 101

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            + ++LRLVV IA  Y   G+P+ +++ EGN GL++AV+KFD ERG++ +TY+ WWI+ A
Sbjct: 102 FIRANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYERGYKFSTYATWWIRQA 161

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   I +    V++        L  ++ R++   + +T       +   IA  L V+   
Sbjct: 162 ISRAIAQQERTVRLPVH-----LVEDVNRMRNVARQLTRELGSDPEPEQIAAALGVTVER 216

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           V  +        SL+  +   D   +   D +    D       E       R  +   +
Sbjct: 217 VNELVRWSQDTVSLDTPV--GDDGDTNLGDLVA---DSDAPSPEEIVLTGLERQRIEGLL 271

Query: 233 SVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           + L+ R   I  AR   E+    +L  ++S F +SRER+RQ+E +A  +++E  + +
Sbjct: 272 NHLDDRSAGIMRARYGLEDGREHSLTEVASRFSLSRERIRQLEIQALGRLRELARAE 328


>gi|291295726|ref|YP_003507124.1| RNA polymerase sigma 70 subunit, RpoD subfamily [Meiothermus ruber
           DSM 1279]
 gi|290470685|gb|ADD28104.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Meiothermus ruber
           DSM 1279]
          Length = 507

 Score =  205 bits (522), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 64/235 (27%), Positives = 110/235 (46%), Gaps = 10/235 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
               L+ ++LRLVV IA  Y G GL   +++ EGN GL++AV+KF+ +R F+ +TY+ WW
Sbjct: 267 CRQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEFKRRFKFSTYATWW 326

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I     +      L R    +Q         E++ A A     
Sbjct: 327 IRQAINRAIADQARTIRIPVHMVE--TINKLTRTARQMQQELGREPSYEEI-ADAMGPGW 383

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V           SL   I   D+  S + D++  +H       ++   +      L
Sbjct: 384 DAKKVEETFKIAQEPVSLETPI--GDEKDSFYGDFIPDEH---MASPVDSAAQSMLSEEL 438

Query: 229 TRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +++  L+ RE  + + R+        TLE + + F V+RER+RQIE +A +K++
Sbjct: 439 EKALGKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLK 493


>gi|21466021|pdb|1L9Z|H Chain H, Thermus Aquaticus Rna Polymerase HoloenzymeFORK-Junction
           Promoter Dna Complex At 6.5 A Resolution
 gi|11527292|gb|AAG36964.1|AF291720_1 sigma factor SigA [Thermus aquaticus]
          Length = 438

 Score =  205 bits (522), Expect = 6e-51,   Method: Composition-based stats.
 Identities = 67/237 (28%), Positives = 110/237 (46%), Gaps = 10/237 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +A   L+ ++LRLVV IA  Y G GL   +++ EGN GL++AV+KF+ +R F+ +TY+ 
Sbjct: 196 EAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYAT 255

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I     +      L R    LQ         E++   A   
Sbjct: 256 WWIRQAINRAIADQARTIRIPVHMVE--TINKLSRTARQLQQELGREPSYEEIAE-AMGP 312

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
                 V           SL   I   D+  S + D++    D      +E   +     
Sbjct: 313 GWDAKRVEETLKIAQEPVSLETPI--GDEKDSFYGDFIP---DENLPSPVEAAAQSLLSE 367

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L +++S L+ RE  + + R+        TLE + + F V+RER+RQIE +A +K++
Sbjct: 368 ELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLK 424



 Score = 43.6 bits (102), Expect = 0.034,   Method: Composition-based stats.
 Identities = 14/47 (29%), Positives = 27/47 (57%), Gaps = 2/47 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTS 56
           V+    + +Y+HEI ++P+L  +EE  LA++  E   + A  +L  +
Sbjct: 90  VSTSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEG--MEAIKKLSEA 134


>gi|317968274|ref|ZP_07969664.1| putative type II alternative RNA polymerase sigma factor
           [Synechococcus sp. CB0205]
          Length = 382

 Score =  205 bits (522), Expect = 7e-51,   Method: Composition-based stats.
 Identities = 73/245 (29%), Positives = 122/245 (49%), Gaps = 13/245 (5%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           H    A  R++ ++LRLVV +A  Y+  G+ + ++V EG +GL +AV+K+DP RGFR +T
Sbjct: 131 HQGRRARDRMIQANLRLVVAVAKKYQQRGMELLDLVQEGTLGLERAVEKYDPTRGFRFST 190

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI+  +   I      +++     +K     L R+K   + I   + +   V  +A
Sbjct: 191 YAYWWIRQGITRAIATQSRTIRLPVHVTEK-----LNRIKKAQRQIASEHGRLASVADLA 245

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           K+L +SE  +     R+    SL+  +       ++  D L   H   EQ L + +   +
Sbjct: 246 KELGLSEEVIRLTLMRVPRSVSLDTRV--GRDQDTELGDLLEDGHATPEQALTKTQLHDD 303

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
               L   +  L+ RE  +   R   EN  P TL  +  +  +SRERVRQIE RA  K++
Sbjct: 304 ----LEALLEELSGREAEVIRLRFGLENDTPQTLSQIGEDLHLSRERVRQIETRALLKLR 359

Query: 282 ESIQK 286
           +  ++
Sbjct: 360 QPQRR 364


>gi|302519838|ref|ZP_07272180.1| RNA polymerase sigma factor RpoS [Streptomyces sp. SPB78]
 gi|302428733|gb|EFL00549.1| RNA polymerase sigma factor RpoS [Streptomyces sp. SPB78]
          Length = 341

 Score =  205 bits (522), Expect = 7e-51,   Method: Composition-based stats.
 Identities = 72/308 (23%), Positives = 131/308 (42%), Gaps = 39/308 (12%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVL---------AKRYRE----------- 43
           ++MS  +     +  Y+ EI + P+L+  +E  L         A++  +           
Sbjct: 33  RSMSGEIADRDLVGMYLDEIARTPLLDAAKEVELSQTIEAGVFARQILDGETDTKNETSR 92

Query: 44  -------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                       A    + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  
Sbjct: 93  EELEALWEASERAKDVFIRSNLRLVVAVARRYPRAGLPLLDLIQEGNAGLVRAVEKFDYR 152

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +GF+ +TY+ WWI+ A+   I      +++        L   L R++   +     + + 
Sbjct: 153 KGFKFSTYATWWIRQAITRSIADQSRTIRLPVH-----LVEELGRIRRVQREFNREHGRD 207

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
            +   IA +L  +   V  +        SLN  +   D+  +Q+ D L    D       
Sbjct: 208 PEHAEIAAELGSTPERVSDVLDWARDPVSLNMSV--DDEGDTQFGDLL---EDTSAVSPE 262

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEA 274
           +      R   L   +  L+ R   I + R   ++    TL  +  +  ++RER+RQIE 
Sbjct: 263 QSVMTLLRSEELDELIGRLDERTASIIKMRYGIDDGRERTLTEVGKQHGLTRERIRQIEK 322

Query: 275 RAFKKVQE 282
            A  ++++
Sbjct: 323 HALLELKK 330


>gi|186681474|ref|YP_001864670.1| RNA polymerase sigma factor SigC [Nostoc punctiforme PCC 73102]
 gi|186463926|gb|ACC79727.1| RNA polymerase, sigma 70 subunit, RpoD family [Nostoc punctiforme
           PCC 73102]
          Length = 416

 Score =  205 bits (522), Expect = 7e-51,   Method: Composition-based stats.
 Identities = 69/262 (26%), Positives = 134/262 (51%), Gaps = 18/262 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L  +E     ++ +  G L A   ++ ++LRLVV +A  Y+  GL + ++V EG +GL +
Sbjct: 162 LTVEE----LEQVQSQG-LQAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLER 216

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           AV+KFDP +G+R +TY+ WWI+  +   I  S   +++     +K     L ++K   + 
Sbjct: 217 AVEKFDPTKGYRFSTYAYWWIRQGITRAIATSSRTIRLPVHITEK-----LNKIKKAQRK 271

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           I     +   +  +A +L ++ ++V  +  R+    SL   +       ++  + L  D 
Sbjct: 272 IAQEKGRTPTLEDLATELEMTPTQVREVLLRVPRSVSLETKV--GKDKDTELGELLETDC 329

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSR 266
              E++L+    R++ +  L   +S L  RER +   R      +P +L  +    ++SR
Sbjct: 330 VTPEEMLM----RESLQRDLHHLLSDLTSRERDVILMRFGLADGHPYSLAEIGRALDLSR 385

Query: 267 ERVRQIEARAFKKVQESIQKQV 288
           ERVRQIE++A +K+++  ++ +
Sbjct: 386 ERVRQIESKALQKLRQPKRRNL 407


>gi|206889536|ref|YP_002248786.1| RNA polymerase sigma factor RpoD [Thermodesulfovibrio yellowstonii
           DSM 11347]
 gi|206741474|gb|ACI20531.1| RNA polymerase sigma factor RpoD [Thermodesulfovibrio yellowstonii
           DSM 11347]
          Length = 479

 Score =  205 bits (522), Expect = 7e-51,   Method: Composition-based stats.
 Identities = 71/270 (26%), Positives = 128/270 (47%), Gaps = 15/270 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGD--LSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           I +I     L+  E   + ++  +         + L+T +LRLVV IA  Y G GLP+ +
Sbjct: 205 IKKIENESGLKIDELKNIWQKIYKAKCLVEDTKNELITRNLRLVVNIAKNYVGRGLPLLD 264

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF  E+GF+ +TY+ WWI+ A+   ++     +++        +  
Sbjct: 265 LIEEGNIGLMKAVDKFKYEKGFKFSTYATWWIRQAITRALIDQTKTIRVPVH-----MME 319

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
              R+    + +T    +      IA+KL V   +V  +   +     L   I   D   
Sbjct: 320 FYNRVTKASRELTQQLGREPNNEEIAEKLGVPVRKVEEVFRAIQDPIGLQTPIGDED--- 376

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTL 255
           ++ +D++    D      + + ER      + R +  L P+E ++ + R    ++   TL
Sbjct: 377 TELEDFI---GDKTSPSPVSEAERTELSEHIQRILKTLTPKEEKVIKMRFGIGEDRDHTL 433

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           E +     ++RERVRQIE +A +K++   +
Sbjct: 434 EEVGRYLSITRERVRQIETKALRKLKHPSR 463



 Score = 35.9 bits (82), Expect = 8.1,   Method: Composition-based stats.
 Identities = 11/28 (39%), Positives = 18/28 (64%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYRE 43
           +  Y + +  IP+L K+EE  LAK+ +E
Sbjct: 79  VQAYFNSMGDIPILTKEEEVELAKKLQE 106


>gi|16331621|ref|NP_442349.1| RNA polymerase sigma factor SigC [Synechocystis sp. PCC 6803]
 gi|2500787|sp|Q59996|RPSC_SYNY3 RecName: Full=Probable RNA polymerase sigma-C factor
 gi|1001684|dbj|BAA10419.1| RNA polymerase sigma factor [Synechocystis sp. PCC 6803]
          Length = 404

 Score =  205 bits (522), Expect = 7e-51,   Method: Composition-based stats.
 Identities = 63/240 (26%), Positives = 122/240 (50%), Gaps = 13/240 (5%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E   ++A   ++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV+KFDP +G+R +
Sbjct: 159 EKQGITAKAHMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTKGYRFS 218

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TYS WWI+  +   I     ++++     +K     L ++K   + I+       ++  +
Sbjct: 219 TYSYWWIRQGITRAIATQSRMIRLPVHITEK-----LNKIKRAQRKISQEKGHTPKIDEV 273

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A++L ++  +V  +  ++    SL   +       ++  D L  D    E  L+ +  + 
Sbjct: 274 AEELGMTPEQVREVLTQVPRSVSLELKV--GQDKDTELMDLLETDTQSPEDELMREALQN 331

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKV 280
           + + +L      L PRE+ +   R   ++    +L  +     +SRERVRQIEA+A +K+
Sbjct: 332 DMQEILLD----LTPREQEVIALRFGFQDGVAHSLSEIGRILNLSRERVRQIEAKALQKL 387


>gi|325106737|ref|YP_004267805.1| RNA polymerase, sigma 70 subunit, RpoD [Planctomyces brasiliensis
           DSM 5305]
 gi|324967005|gb|ADY57783.1| RNA polymerase, sigma 70 subunit, RpoD [Planctomyces brasiliensis
           DSM 5305]
          Length = 575

 Score =  205 bits (522), Expect = 7e-51,   Method: Composition-based stats.
 Identities = 66/241 (27%), Positives = 116/241 (48%), Gaps = 12/241 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A  +L   +LRLVV IA  YR  GL   +++ EGN GLM+ V+K++  RG++ +TY+ W
Sbjct: 315 EAKQKLSGGNLRLVVSIAKKYRNRGLSFLDLIQEGNAGLMRGVEKYEYRRGYKFSTYATW 374

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   +      ++I        +F ++  LK   + I     +   +  +A  ++
Sbjct: 375 WIRQAITRAVADHARTIRIPVH-----MFQSISTLKAKAEQIRQETGREPTMEELAAAID 429

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  E   +        SL+  +   +   S + D+L  D    E    +   ++  R+ 
Sbjct: 430 MSVEETERIMKTWKHPVSLDTPV--GESEDSSFGDFLQDDS---ENTPADTAMQQMLRDK 484

Query: 228 LTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           +   +  L  RER I + R    +    TLE     F+V+RER+RQIE++A +K+Q   +
Sbjct: 485 INHVLKSLTYREREIIKLRYGLGDGYSYTLEETGRIFKVTRERIRQIESKALRKLQHQTR 544

Query: 286 K 286
            
Sbjct: 545 S 545


>gi|17231302|ref|NP_487850.1| RNA polymerase sigma factor SigD [Nostoc sp. PCC 7120]
 gi|8489797|gb|AAF75755.1|AF262216_2 group 2 sigma 70-type sigma factor D [Nostoc sp. PCC 7120]
 gi|17132944|dbj|BAB75509.1| group 2 sigma 70-type sigma factor D [Nostoc sp. PCC 7120]
          Length = 332

 Score =  205 bits (522), Expect = 7e-51,   Method: Composition-based stats.
 Identities = 68/331 (20%), Positives = 132/331 (39%), Gaps = 52/331 (15%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------- 43
             M         +  Y+ EI ++P+L  +EE    K+ +                     
Sbjct: 13  SAMKTAPTATDLVRTYLREIGRVPLLSHEEEIRYGKQVQRSTTLQEMREELATQSGREPS 72

Query: 44  -------------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
                                   A  ++V ++LRLVV +A  Y    + + +++ EG+I
Sbjct: 73  VEEWAKAANLNPADLLEAIADGEIAKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGSI 132

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           G+ + V+KFDP +G+R +TY+ WWI+ A+   I      +++     +K     L ++K 
Sbjct: 133 GMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKARTIRLPIHITEK-----LNKIKK 187

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + ++    +      +A +L ++  +V     +     SL+  +   D   ++  + L
Sbjct: 188 AQRQLSQRLGRAPTAGELANELELTPKQVREYLEKARLPLSLD--LRLGDNYDTELGEML 245

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEF 262
                  E  +++     +    L   M  L P+++ +   R        +TL  +    
Sbjct: 246 EDPGASPEDFVMQSSLSND----LEVLMEQLTPQQKEVITLRFGLIDGQALTLARIGEIL 301

Query: 263 EVSRERVRQIEARAFKKVQESIQKQVELSSS 293
            +SRERVRQIE  A  K+++S     E  +S
Sbjct: 302 NISRERVRQIEREALTKLRKSKANMGEYLAS 332


>gi|282881579|ref|ZP_06290248.1| sigma-70 region 2 [Prevotella timonensis CRIS 5C-B1]
 gi|281304565|gb|EFA96656.1| sigma-70 region 2 [Prevotella timonensis CRIS 5C-B1]
          Length = 290

 Score =  205 bits (522), Expect = 8e-51,   Method: Composition-based stats.
 Identities = 69/288 (23%), Positives = 136/288 (47%), Gaps = 14/288 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKI 64
           SI       L +Y+ EI + P++   EE  LA++ ++ G     A  +LVT++LR VV +
Sbjct: 9   SITNRSSEALDKYLVEIGRAPLISIDEEIELAQKIKKGGPEGERAKDKLVTANLRFVVSV 68

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y+  GL +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V
Sbjct: 69  AKQYQHQGLTLTDLIDEGNIGLIKAAQKFDETRGFKFISYAVWWIRQSILQAIAEQSRIV 128

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           ++           +L ++   +      + +   +  ++   N+ E ++           
Sbjct: 129 RLPLNQ-----VGSLNKINHEINRFEQEHHRRPSITELSDATNIDEEKIGQSMMADGHHV 183

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM-SVLNPRERRIF 243
           S++A     + N+         D     QV     + ++    L   +  VL  RE  I 
Sbjct: 184 SIDAPFQDGEDNTMLDVMPSGDDSRTDRQV-----DHESMAQELNTVLNKVLKDREITII 238

Query: 244 EARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
           +       +   LE +  +  ++RERVRQI  ++  K+++S   ++ +
Sbjct: 239 KECFGIGCHEKGLEEIGDQLGLTRERVRQIREKSIAKLRDSGNAKILM 286


>gi|108805426|ref|YP_645363.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108766669|gb|ABG05551.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 282

 Score =  205 bits (522), Expect = 8e-51,   Method: Composition-based stats.
 Identities = 80/272 (29%), Positives = 137/272 (50%), Gaps = 12/272 (4%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
            E  L++Y+  IR+  +L   EE  L++R R  GD +A  RL+ S+LRLVV IA  YRG 
Sbjct: 5   TEDVLTQYLGRIREGRLLTAGEEVELSRRAR-AGDGAARRRLIESNLRLVVAIAKRYRGR 63

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           G+P  +++ EGN GL++AV+KFDPE G R +TY+ WWI+ A+   +      V++     
Sbjct: 64  GVPFEDLIQEGNAGLIRAVEKFDPEMGNRFSTYATWWIRQAVTRAVADQGRAVRLPAHV- 122

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
                 ++ RL+    A++    +      +A +L  S  E   +        S++A + 
Sbjct: 123 ----VDSVYRLRRAESALSVELGREPTDEEVAGRLGTSPEEARRLREVSQPISSISARLG 178

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             +++ ++  D L  +   +E   +E       R +L  ++  L  RE R+   R   + 
Sbjct: 179 D-EEDGAELGDLLPDEAASEEYARVEA---GPWRGVLREAVGSLPEREARVLRLRHGLDG 234

Query: 252 P--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
               TL  +S    +S+ER RQ+E +A + ++
Sbjct: 235 ERARTLREVSEILGISQERARQVELKALRTLR 266


>gi|254422659|ref|ZP_05036377.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
 gi|196190148|gb|EDX85112.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Synechococcus sp. PCC 7335]
          Length = 298

 Score =  205 bits (521), Expect = 8e-51,   Method: Composition-based stats.
 Identities = 72/307 (23%), Positives = 131/307 (42%), Gaps = 52/307 (16%)

Query: 27  PMLEKQEEYVLAKRYRE---------------------------------------HGDL 47
           P+L  +EE +L K+ ++                                           
Sbjct: 2   PLLTHEEEILLGKQVQKLMSLIAIHSSLVDTLDREPTRTEWAAAGGISEAELAAIVTAGE 61

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A HR+V ++LRLVV +A  Y    + + +++ EG IG+ + V+KFDP +G+R +TY+ W
Sbjct: 62  QAKHRMVEANLRLVVSVAKKYIKRNVDLLDLIQEGTIGMQRGVEKFDPSKGYRFSTYAYW 121

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++     +K     L ++K   +  T  + +      IA+   
Sbjct: 122 WIRQAITRAIAEKSRTIRLPIHITEK-----LNKIKKAQRQFTQQHGRTPTASEIAQATG 176

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
            +  +V     R     SL+  +   D   +Q  D L  D     Q   +     + ++ 
Sbjct: 177 FTIKQVREYLDRSRQPLSLDLKV--GDNQDTQLGDLLEDDG----QTPDDYATASSLKSD 230

Query: 228 LTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L R M+ L P+++++   R   E+   +TL  + +  ++SRERVRQIE  A  K+++   
Sbjct: 231 LKRIMADLTPQQQQVIALRFGLEDGKNMTLAKIGAMLDISRERVRQIEREALTKLRKRQS 290

Query: 286 KQVELSS 292
              E  +
Sbjct: 291 DMREYLA 297


>gi|295838256|ref|ZP_06825189.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. SPB74]
 gi|197698235|gb|EDY45168.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. SPB74]
          Length = 341

 Score =  205 bits (521), Expect = 8e-51,   Method: Composition-based stats.
 Identities = 72/308 (23%), Positives = 131/308 (42%), Gaps = 39/308 (12%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVL---------AKRYRE----------- 43
           ++MS  +     +  Y+ EI + P+L+  +E  L         A++  +           
Sbjct: 33  RSMSGEIADRDLVGMYLDEIARTPLLDAAKEVELSQTIEAGVFARQILDGETDSKNEASR 92

Query: 44  -------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                       A    + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  
Sbjct: 93  EELEALWEASERAKDVFIRSNLRLVVAVARRYPRAGLPLLDLIQEGNAGLVRAVEKFDYR 152

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +GF+ +TY+ WWI+ A+   I      +++        L   L R++   +     + + 
Sbjct: 153 KGFKFSTYATWWIRQAITRSIADQSRTIRLPVH-----LVEELGRIRRVQREFNREHGRD 207

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
            +   IA +L  +   V  +        SLN  +   D+  +Q+ D L    D       
Sbjct: 208 PEHAEIAAELGSTPERVSDVLDWARDPVSLNMSV--DDEGDTQFGDLL---EDTSAVSPE 262

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEA 274
           +      R   L   +  L+ R   I + R   ++    TL  +  +  ++RER+RQIE 
Sbjct: 263 QSVMTLLRSEELDELIGRLDERTASIIKMRYGIDDGRERTLTEVGKQHGLTRERIRQIEK 322

Query: 275 RAFKKVQE 282
            A  ++++
Sbjct: 323 HALLELKK 330


>gi|307152083|ref|YP_003887467.1| RpoD subfamily RNA polymerase sigma-70 factor [Cyanothece sp. PCC
           7822]
 gi|306982311|gb|ADN14192.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7822]
          Length = 418

 Score =  205 bits (521), Expect = 8e-51,   Method: Composition-based stats.
 Identities = 64/255 (25%), Positives = 128/255 (50%), Gaps = 14/255 (5%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           E    +R ++ G + A  +++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV KF
Sbjct: 165 EVQELERVQKAG-IYAKEQMIKANLRLVVSVAKRYQNRGLELLDLIQEGTLGLERAVDKF 223

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           DP +G+R +TY+ WWI+  +   I     ++++     +K     L ++K   + I    
Sbjct: 224 DPTKGYRFSTYAYWWIRQGITRAIATQSRIIRLPVHITEK-----LNKIKKAQRKIAQLK 278

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
                +  ++++L +S  ++  +  R+    SL   I    +  ++  D L       E 
Sbjct: 279 GATPSIEELSQELEMSPPQIREVLMRVPRSVSLE--IKVGKEKDTELIDLLETTEASPED 336

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQ 271
            +  +  R++    L   ++ L  RER + + R         +L ++    ++SRERVRQ
Sbjct: 337 NIANEALRQD----LHNLLADLTTREREVIQLRYGFKDGKSYSLADIGRTLQLSRERVRQ 392

Query: 272 IEARAFKKVQESIQK 286
           IEA+A +K+++  ++
Sbjct: 393 IEAKAIQKLRQPKRR 407


>gi|289549268|ref|YP_003474256.1| RNA polymerase, sigma 70 family subunit [Thermocrinis albus DSM
           14484]
 gi|289182885|gb|ADC90129.1| putative RNA polymerase, sigma 70 family subunit [Thermocrinis
           albus DSM 14484]
          Length = 310

 Score =  205 bits (521), Expect = 8e-51,   Method: Composition-based stats.
 Identities = 91/300 (30%), Positives = 147/300 (49%), Gaps = 34/300 (11%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L++Y+ ++ KIP+L  +EE  LA+R +E GD  A  +LV S+LR V+ IA  Y+GYGLP+
Sbjct: 10  LAQYLKKVSKIPLLTPEEEKELARRAKE-GDTEALRKLVESNLRFVISIAKQYQGYGLPL 68

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT------- 128
           SE+++ GN GL++A K+FDP+RG +  +Y++WWI+ A+ + + +    V+I         
Sbjct: 69  SELIAAGNYGLVEAAKRFDPDRGVKFISYAVWWIRQAIMQALSQQSGAVRIPLKQSHVIN 128

Query: 129 -----------------TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK--LNVS 169
                            TA +    +    L+  ++         E++    KK  L +S
Sbjct: 129 RIASIYSKLYKEQEKEPTAEEVAYEYTKEILQKEMERELGRPPTEEEIERRIKKEGLKIS 188

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             EV           SL+A I   +              D +E+VL E  E++     + 
Sbjct: 189 PQEVEKCLQICKAPLSLDAPIGEDEDTFFVDLLSKHGSADVEEKVLTEFLEKE-----IE 243

Query: 230 RSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             +  L  +ERR+ E R     E P TL  +     +SRERVRQ+E RA +K++    K+
Sbjct: 244 EMLDKLPEKERRVIELRFGLRGEEPRTLREIGEILNISRERVRQLETRALRKLRNMAMKK 303


>gi|89072392|ref|ZP_01158971.1| hypothetical DNA-directed RNA polymerase, sigma subunit
           [Photobacterium sp. SKA34]
 gi|89051924|gb|EAR57376.1| hypothetical DNA-directed RNA polymerase, sigma subunit
           [Photobacterium sp. SKA34]
          Length = 286

 Score =  205 bits (521), Expect = 8e-51,   Method: Composition-based stats.
 Identities = 79/271 (29%), Positives = 137/271 (50%), Gaps = 12/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+++I   P+L K +E   +++    GD ++   L+ S+LRLVV IA  YR   L +S++
Sbjct: 14  YLNDISNKPLLSKDDEIQYSRK-SLTGDPASKKILIESNLRLVVSIAKKYRAANLSLSDL 72

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM AV+KFDPE+GFR +TY+ WWIK  ++  I      +++    N  +    
Sbjct: 73  IDEGNIGLMTAVEKFDPEKGFRFSTYASWWIKQTIERAIHNQNRTIRLPV--NISKEINT 130

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R    L  + +N    E    IA+ LN    E+ ++        SL+  I   D  +S
Sbjct: 131 LLRTHRELMKLNNNEPTHED---IAQALNKESKEISALFSNEVNVVSLDQTI--GDNENS 185

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
               +LV D   Q      + +  +   +    ++ +N R+R I   R       P TL+
Sbjct: 186 HTIAYLVADE--QITSPSAEVDNDDMIKITNLVLNGINKRDREIICRRFGLMGYEPHTLQ 243

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            ++    ++RER+RQ++ ++   ++ S+ ++
Sbjct: 244 EVADAVGLTRERIRQLQIKSLNSLKRSLARE 274


>gi|22297808|ref|NP_681055.1| RNA polymerase sigma factor SigD [Thermosynechococcus elongatus
           BP-1]
 gi|22293985|dbj|BAC07817.1| group2 RNA polymerase sigma factor [Thermosynechococcus elongatus
           BP-1]
          Length = 315

 Score =  205 bits (521), Expect = 8e-51,   Method: Composition-based stats.
 Identities = 71/305 (23%), Positives = 134/305 (43%), Gaps = 52/305 (17%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYRE----------------------------------- 43
           Y+ EI ++P+L  ++E +  K+ ++                                   
Sbjct: 11  YLREIGRVPLLTHEQEVIYGKQVQQLAAMNEIREKLAAELNREPTRAEWAAAANISEGEL 70

Query: 44  ----HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                    A  ++V ++LRLVV +A  Y    + + +++ EG IG+ + V+KFDP +G+
Sbjct: 71  ETIIENGERAKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGTIGMQRGVEKFDPTKGY 130

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           R +TY+ WWI+ A+   I      +++     +K     L ++K   + ++    +   +
Sbjct: 131 RFSTYAYWWIRQAITRAIAEKGRTIRLPIHITEK-----LNKIKKAQRQLSQRLGRAATI 185

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +A +L ++ ++V     R     SL+  +   D   ++  + L       E    E  
Sbjct: 186 NELAAELELTPAQVREYLERARQPLSLD--VRVGDNQDTELGELLEDSSISPE----EFA 239

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
            +   R+ L R M+ L P++R +   R   EN  P+TL  +     +SRERVRQIE  A 
Sbjct: 240 TQSLLRSDLERLMAELTPQQRHVLSLRFGLENGQPLTLAKVGELLNISRERVRQIEREAL 299

Query: 278 KKVQE 282
            K+++
Sbjct: 300 SKLRK 304


>gi|15827487|ref|NP_301750.1| RNA polymerase sigma factor SigB [Mycobacterium leprae TN]
 gi|221229964|ref|YP_002503380.1| RNA polymerase sigma factor SigB [Mycobacterium leprae Br4923]
 gi|699187|gb|AAA62952.1| u1764a [Mycobacterium leprae]
 gi|13093037|emb|CAC31395.1| RNA polymerase sigma factor [Mycobacterium leprae]
 gi|219933071|emb|CAR71109.1| RNA polymerase sigma factor [Mycobacterium leprae Br4923]
          Length = 319

 Score =  205 bits (521), Expect = 9e-51,   Method: Composition-based stats.
 Identities = 70/312 (22%), Positives = 135/312 (43%), Gaps = 38/312 (12%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREH----------GDLS 48
            ++         +  Y++ I K  +L   +E  LAKR     Y EH          G   
Sbjct: 11  SDLDAQSPAADLVRVYLNGIGKTALLNAADEVELAKRIEAGLYAEHLLQTRKRFGEGRKR 70

Query: 49  AAH-----------RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A              L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  +
Sbjct: 71  ALAAVARDGAAARRHLLEANLRLVVSLAKRYTGRGMPLLDLIQEGNLGLIRAMEKFDYTK 130

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           GF+ +TY+ WWI+ A+   +      +++     ++     L R+K  +     N  +  
Sbjct: 131 GFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVEQ--VNKLARIKREMHQ---NLGREA 185

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A +  +   ++  +        SL+  + S ++  +   D++    D +      
Sbjct: 186 TDEELAAESGIPIEKINDLLEHSRDPVSLDMPVGSEEE--APLGDFI---EDAEAMSAEN 240

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
               +     +   ++ L+ RE ++   R   ++  P TL+ +   F +SRERVRQIE  
Sbjct: 241 AVIAELLHTDIRSVLATLDEREHQVIRLRFGLDDGQPRTLDQIGKLFGLSRERVRQIERD 300

Query: 276 AFKKVQESIQKQ 287
              K++   +  
Sbjct: 301 VMCKLRNGERAD 312


>gi|237751154|ref|ZP_04581634.1| RNA polymerase sigma factor RpoD [Helicobacter bilis ATCC 43879]
 gi|229373599|gb|EEO23990.1| RNA polymerase sigma factor RpoD [Helicobacter bilis ATCC 43879]
          Length = 632

 Score =  205 bits (521), Expect = 9e-51,   Method: Composition-based stats.
 Identities = 71/260 (27%), Positives = 129/260 (49%), Gaps = 15/260 (5%)

Query: 29  LEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           LE ++   + ++ +    +S  A  ++  S+LRLVV IA  Y   GLP  +++ EGNIGL
Sbjct: 371 LEPEKLKEILEQIKRGKRISDTAKTKMSRSNLRLVVSIAKRYTNRGLPFLDLIQEGNIGL 430

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  + ++ +TY+ WWIK A+   I      ++I        +   + ++K  +
Sbjct: 431 MKAVDKFEYRKQYKFSTYATWWIKQAISRAIADQARTIRIPIH-----MIDTINKIKNLM 485

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +       +   V +IA ++ +S  +V ++        SL A I + D    ++ D++  
Sbjct: 486 RKHAQEKGEELDVESIANQVGLSVDKVKNVIKITKEPISLEAPIGNDDD--GKFGDFV-- 541

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFE 263
             D      ++   +++ R  +   +  LN RE+ + + R      E+  TLE +     
Sbjct: 542 -EDKSTMSSMDIMLKEDLREQIDNVLDQLNEREKAVIKMRFGLLEDESDRTLEEIGKALN 600

Query: 264 VSRERVRQIEARAFKKVQES 283
           V+RERVRQIE+ A KK++  
Sbjct: 601 VTRERVRQIESSAIKKLKHP 620



 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 11/36 (30%), Positives = 21/36 (58%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
            +  +  Y+ E+ +IP+L K+EE  L+K   +  D+
Sbjct: 107 SDSPVRMYLREMGQIPLLSKEEEINLSKDMEKGEDI 142


>gi|300113721|ref|YP_003760296.1| RNA polymerase sigma 70 subunit RpoD [Nitrosococcus watsonii C-113]
 gi|299539658|gb|ADJ27975.1| RNA polymerase, sigma 70 subunit, RpoD [Nitrosococcus watsonii
           C-113]
          Length = 578

 Score =  205 bits (521), Expect = 9e-51,   Method: Composition-based stats.
 Identities = 72/238 (30%), Positives = 120/238 (50%), Gaps = 12/238 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  ++V ++LRLVV +A  YR  GL   +++ EGNIGLM+AV KFD  RG++ +TY+ 
Sbjct: 338 QRAKAQMVEANLRLVVSVAKKYRNRGLTFLDLIQEGNIGLMKAVDKFDYHRGYKFSTYAH 397

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I     +K     L R    L+       +PE    +A++L
Sbjct: 398 WWIRQAITRAIDDQSRTIRIPVHVMEK--LSKLNRASYQLRQEKGREGRPE---ELAERL 452

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++SE ++  M+       SL   +       SQ  + +    D Q    +E       + 
Sbjct: 453 DLSEQQIHRMHEIAKQPISLETPL--GKDEDSQLGELM---EDEQVPNPMEVAITAGLQT 507

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              R ++ L+PRE ++   R     +   TL  ++ +F++SRER+RQIEA+A  K++ 
Sbjct: 508 GAQRLLAALSPREAQVVAMRFGIGMDTDHTLGEVARQFDLSRERIRQIEAQALGKLRR 565


>gi|317506478|ref|ZP_07964279.1| sigma-70 protein [Segniliparus rugosus ATCC BAA-974]
 gi|316255239|gb|EFV14508.1| sigma-70 protein [Segniliparus rugosus ATCC BAA-974]
          Length = 348

 Score =  205 bits (521), Expect = 9e-51,   Method: Composition-based stats.
 Identities = 66/313 (21%), Positives = 137/313 (43%), Gaps = 38/313 (12%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAK-----RYREH------------- 44
           ++++         +  Y++ I +  +L  ++E  LAK      Y EH             
Sbjct: 39  QEDLDTQSPAADLVRVYLNGIGRTALLTAEDEVTLAKSIEAGLYAEHLINTSEGLTPQRR 98

Query: 45  --------GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                      +A   L+ ++LRLVV +A  Y G G+P+ +++ EGN+GL++A++KFD  
Sbjct: 99  RELKAVVRDGRAARTHLLEANLRLVVSLAKRYTGRGIPLLDLIQEGNLGLIRAMEKFDYS 158

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +GF+ +TY+ WWI+ A+   +      +++     ++     L R+K  L          
Sbjct: 159 KGFKFSTYATWWIRQAITRGVADQSRTIRLPVHLVEQ--VNKLSRIKRELHQQLGREATS 216

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           E    ++++  + E  +  +        SL+  + + ++  +   D++    D +     
Sbjct: 217 E---ELSRETGIPEHRIADLLDHSRDPVSLDMPVGADEE--APLGDFI---EDSEGASAE 268

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEA 274
                      +   ++ L+  E+++   R   ++  P TL+ +   F +SRERVRQIE 
Sbjct: 269 NAVIAGFLHRDVRSVLATLSDSEQQVIRLRYGLDDGQPRTLDQIGKIFSLSRERVRQIER 328

Query: 275 RAFKKVQESIQKQ 287
               K++   + +
Sbjct: 329 EVMVKLRNGDRAE 341


>gi|67810071|gb|AAY81984.1| RNase polymerase sigma factor [Wolbachia pipientis]
          Length = 571

 Score =  205 bits (521), Expect = 9e-51,   Method: Composition-based stats.
 Identities = 70/248 (28%), Positives = 117/248 (47%), Gaps = 15/248 (6%)

Query: 32  QEEYVLAKRYREHGDL--SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           QE   L KR ++H      A   ++ ++LRLVV IA  Y   GL + +++ EGNIGLM+A
Sbjct: 334 QEFKELIKRIQKHEREVSEAKQEMIKANLRLVVSIAKKYSKRGLDLLDLIQEGNIGLMKA 393

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V KFD +RG++ +TY  WW++ ++   I     +V+I     +      + ++   L+ +
Sbjct: 394 VDKFDYKRGYKFSTYGTWWVRQSITRAIPEQSKVVRIPVHMVEI-----ISKINRALRKM 448

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
           T    +   +  ++ +L +    +  +        SL A     D  SS + D +    D
Sbjct: 449 THEMGREPTLEELSVELTMPLERIRKVMKIARDPVSLEAPTGKDD--SSTFGDCI---ED 503

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSR 266
            +     +     + R + T  ++ L P+E RI   R          TLE +   F V+R
Sbjct: 504 KRVSRPEDAAILADLRGITTNVLATLTPKEERILRMRFGLGKDGKEHTLEEVGKIFNVTR 563

Query: 267 ERVRQIEA 274
           ER+RQIEA
Sbjct: 564 ERIRQIEA 571


>gi|17231292|ref|NP_487840.1| RNA polymerase sigma factor [Nostoc sp. PCC 7120]
 gi|8489801|gb|AAF75758.1|AF262217_2 group 2 sigma 70-type sigma factor E [Nostoc sp. PCC 7120]
 gi|17132934|dbj|BAB75499.1| group 2 sigma 70-type sigma factor E [Nostoc sp. PCC 7120]
          Length = 327

 Score =  205 bits (521), Expect = 9e-51,   Method: Composition-based stats.
 Identities = 67/305 (21%), Positives = 133/305 (43%), Gaps = 52/305 (17%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYRE----------------------------------- 43
           Y+ EI ++P+L +++E V  K+ ++                                   
Sbjct: 23  YLREIGRVPLLTREQEIVYGKQVQQMMSLIDAKEALAKKLDREPSLPEWADHVQKSETEV 82

Query: 44  ----HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                    A  +++ ++LRLVV IA  Y+   +   +++ EG +GL + V+KFDP RG+
Sbjct: 83  KQTVTQGKRAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPMRGY 142

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWI+ A+   I +    +++     +K     L ++K   + +     +    
Sbjct: 143 KFSTYAYWWIRQAITRAIAQQGRTIRLPIHITEK-----LNKIKKVQRELAQTLGRSPSP 197

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IAK+L +  +++           SL+  +   D   ++ Q+ L  D    E    ++ 
Sbjct: 198 AEIAKELELEPAQIREYLNMARQPVSLD--VKVGDNQDTELQEMLEDDGPSPEYYTTQEF 255

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAF 277
            R++    L   ++ L P++R +   R   L  N ++L  +     +SRERVRQ+E +A 
Sbjct: 256 LRQD----LNTLLAELTPQQREVVALRFGLLDGNELSLAKVGERLNLSRERVRQLEHQAL 311

Query: 278 KKVQE 282
             ++ 
Sbjct: 312 AHLRR 316


>gi|319955411|ref|YP_004166678.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Cellulophaga
           algicola DSM 14237]
 gi|319424071|gb|ADV51180.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cellulophaga
           algicola DSM 14237]
          Length = 286

 Score =  205 bits (521), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 77/276 (27%), Positives = 139/276 (50%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y  EI K+ M+   EE  LA + RE GD  A + LV ++LR VV +A  Y+G GL 
Sbjct: 17  SLEKYFQEISKLDMITANEEVELAIKIRE-GDQVALNTLVNANLRFVVSVAKQYQGSGLR 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           +S++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + I     +V++        
Sbjct: 76  LSDLINEGNVGLVKAAKRFDETRGFKFISYAVWWIRQSILQAISELSRMVRLPLNK---- 131

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               + ++      +  +  +P   + IA++L++S S+V           S++A    ++
Sbjct: 132 -IGEIGKINKVFSYLEQSLQRPPNAIEIARELDMSTSQVKLAMKNTGKHLSMDAPF--AE 188

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
             SS   + +           + +E   +    +   +S L  RE  I           P
Sbjct: 189 GESSNLYNVVQSKEANSPDTNLMQESLSSD---IGDLLSTLPSRESDIIRLYYGIGEKAP 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           ++L  +   F++SRERVRQI  +A + ++   QK+V
Sbjct: 246 MSLTEIGEIFDISRERVRQIREKAIRVLRRKSQKEV 281


>gi|313680173|ref|YP_004057912.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Oceanithermus
           profundus DSM 14977]
 gi|313152888|gb|ADR36739.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Oceanithermus
           profundus DSM 14977]
          Length = 484

 Score =  205 bits (521), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 65/235 (27%), Positives = 111/235 (47%), Gaps = 10/235 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV IA  Y G GL   +++ EGN GL++AV+KF+ +R ++ +TY+ WW
Sbjct: 244 ARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRYKFSTYATWW 303

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I     +      L R    LQ          ++ A A     
Sbjct: 304 IRQAINRAIADQARTIRIPVHMVE--TINKLTRTARQLQQELGREATYAEI-ADAMGPGW 360

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V           SL   I   D+  S + D++  +H       ++   +      L
Sbjct: 361 DAKKVEETFKIAQEPVSLETPI--GDEKDSFYGDFIPDEHLAS---PVDSAAQSLLSEEL 415

Query: 229 TRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +++S L+ RE  + + R+        TLE + + F V+RER+RQIE +A +K++
Sbjct: 416 EKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLK 470



 Score = 47.5 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 16/51 (31%), Positives = 28/51 (54%), Gaps = 2/51 (3%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVT 55
            ++  V+    + +Y+HEI ++P+L  +EE  LA+R  E    +A  RL  
Sbjct: 130 TIATRVSTSDPVRQYLHEIGQVPLLTLEEEIDLARRVEEG--EAAVERLAE 178


>gi|283779933|ref|YP_003370688.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pirellula staleyi
           DSM 6068]
 gi|283438386|gb|ADB16828.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pirellula staleyi
           DSM 6068]
          Length = 545

 Score =  205 bits (521), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 75/247 (30%), Positives = 120/247 (48%), Gaps = 13/247 (5%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           YRE+ D +A   L   +LRLVV IA  YR  GL   +++ EGN GLM+AV KF+  RG++
Sbjct: 285 YRENYD-AAKRVLSAGNLRLVVSIAKKYRNRGLSFLDLIQEGNTGLMRAVDKFEYARGYK 343

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      +++            +R +   L         PE+V 
Sbjct: 344 FSTYATWWIRQAITRAIADQSRTIRVPVHM--IDTMSKVRAVTRQLVQELGREPTPEEVA 401

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A         V+ M        SL+  +   D + S + ++L    D +E+  +    
Sbjct: 402 RVAGLTLDDARCVLKM---ARQPLSLDQPV--GDHDDSYFGEFLA---DHREEDPLYDTH 453

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFK 278
           ++  ++ +  +M  LN RER I   R    +    TLE +   F V+RERVRQIE +A +
Sbjct: 454 QQALKHQIEEAMQGLNYREREILRLRYGLTDGYAYTLEEVGKIFSVTRERVRQIETKAVR 513

Query: 279 KVQESIQ 285
           K+Q+  +
Sbjct: 514 KLQQPYR 520


>gi|302543058|ref|ZP_07295400.1| RNA polymerase principal sigma factor HrdD [Streptomyces
           hygroscopicus ATCC 53653]
 gi|302460676|gb|EFL23769.1| RNA polymerase principal sigma factor HrdD [Streptomyces
           himastatinicus ATCC 53653]
          Length = 333

 Score =  205 bits (521), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 72/302 (23%), Positives = 131/302 (43%), Gaps = 41/302 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYR-----------EHGD------------------ 46
           +  Y+ EI + P+L+  +E  L++              E  D                  
Sbjct: 35  VGMYLDEIARTPLLDAAKEVELSQAVEAGVYAQQILDGEAEDTGAAGASREELEAIAAEG 94

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A    + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ 
Sbjct: 95  ARAKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYTKGFKFSTYAT 154

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      +++        L   L R++   +     + +  + + IA++L
Sbjct: 155 WWIRQAITRSIADQSRTIRLPVH-----LVEELGRIRRVQREFNREHGREPEHMEIAEEL 209

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             +   V  +        SLN  +   D+  +Q+ D L    D       +      R  
Sbjct: 210 GSTPERVSDVLDWARDPVSLNMSV--DDEGETQFGDLL---EDTSAVSPEQSVMTLLRSE 264

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ R   I +AR   ++    TL  +  +  ++RER+RQIE  A  ++++  
Sbjct: 265 ELEDLIGRLDDRTASIIKARYGIDDGRERTLTEVGKQHGLTRERIRQIEKHALLELKKMA 324

Query: 285 QK 286
           ++
Sbjct: 325 RQ 326


>gi|113477482|ref|YP_723543.1| RNA polymerase sigma factor SigD [Trichodesmium erythraeum IMS101]
 gi|110168530|gb|ABG53070.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
          Length = 319

 Score =  205 bits (521), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 71/321 (22%), Positives = 136/321 (42%), Gaps = 52/321 (16%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------------------ 43
             +  Y+ EI ++P+L  +EE +  K+ +                               
Sbjct: 10  DSVCTYLREIGRVPLLSHEEEILYGKQVQRLTALQEFNQTLAEALGREPTLLEWAEAKEL 69

Query: 44  ---------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                         A  ++V ++LRLVV +A  Y    + + +++ EG IG+ + V+KFD
Sbjct: 70  SKSELQRIIREGERAKRKMVEANLRLVVSVAKKYIKRNVDLLDLIQEGTIGMQRGVEKFD 129

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P +G+R +TY+ WWI+ A+   I      +++     +K     L ++K   + +T    
Sbjct: 130 PTKGYRFSTYAYWWIRQAITRAIAEKGRTIRLPIHITEK-----LNKIKKVQRQLTQQLG 184

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +      IA++L ++  ++     R     SL+  +   D   ++  D L       E  
Sbjct: 185 RSATTGEIAEELGLTPKQIRECLERARLPLSLD--LRVGDNQDTELGDLLEDTGASPEDY 242

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQI 272
            ++   R +    L   M  L P+++++   R   E+   +TL  + +   +SRERVRQI
Sbjct: 243 ALQSSMRTD----LESIMVDLTPQQKQVLALRFGLEDGQTMTLSKIGAHLNISRERVRQI 298

Query: 273 EARAFKKVQESIQKQVELSSS 293
           E  A  K+++  Q   +  +S
Sbjct: 299 EREALSKLRKRKQDMNDYLAS 319


>gi|325673633|ref|ZP_08153324.1| RNA polymerase principal sigma factor SigA [Rhodococcus equi ATCC
           33707]
 gi|325555654|gb|EGD25325.1| RNA polymerase principal sigma factor SigA [Rhodococcus equi ATCC
           33707]
          Length = 448

 Score =  205 bits (521), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 75/308 (24%), Positives = 134/308 (43%), Gaps = 44/308 (14%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRY----------------------REHGD--- 46
              GL  Y+  IR++ +L   EE  L++                         E  D   
Sbjct: 146 AADGLQWYLKRIRRVDLLTADEEVELSRSIEAGLYASHLLEAYPSRTTRPAPAERRDLRQ 205

Query: 47  -----LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
                 SA  R++ ++LRLVV  A  Y G GL + ++V EGN GL++AV+KFD   G + 
Sbjct: 206 IVQDGRSARTRMIEANLRLVVSTAQNYEGRGLDMLDLVQEGNTGLIRAVEKFDYRLGNKF 265

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY+ WWI+ A+   I      +++     +        R++G ++       +      
Sbjct: 266 STYATWWIRQAITRGIADKSRTIRLPVHVVEDLSRMTTVRVEGEIE-----LGRALTDAE 320

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           +A++ +++  +V  ++       S+ AL +S D      +D   +D         E   R
Sbjct: 321 VAQRADLTLEKVRELDDCDRTVLSIEALTDSDDGAGLDIEDDCAHD-------PYEALHR 373

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKK 279
            + R  +   +  L  RE  + + R    +  P TLE +   ++V+RER+RQIEA+  + 
Sbjct: 374 ADVRERIDIVLETLTEREAGVMKLRHGLVDGVPRTLEEIGKVYKVTRERIRQIEAKTLQL 433

Query: 280 VQESIQKQ 287
           ++E  +  
Sbjct: 434 LREPSRAD 441


>gi|296120487|ref|YP_003628265.1| RNA polymerase sigma factor RpoD [Planctomyces limnophilus DSM
           3776]
 gi|296012827|gb|ADG66066.1| RNA polymerase sigma factor RpoD [Planctomyces limnophilus DSM
           3776]
          Length = 550

 Score =  205 bits (521), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 68/243 (27%), Positives = 112/243 (46%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L   +LRLVV IA  YR  GL   +++ EGN GLM+AV K++  RG++ +TY+ 
Sbjct: 303 EQAMRDLSGGNLRLVVSIAKKYRNRGLSFLDLIQEGNTGLMRAVDKYEYRRGYKFSTYAT 362

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            LR++   L          E+    A   
Sbjct: 363 WWIRQAITRAIADQARTIRIPVHM--IETMSKLRKVAKKLLQEMGREPTLEETAEAA--- 417

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            VS  E   +        SL+  +   +   S + D++  D     +  +    ++  ++
Sbjct: 418 GVSLEETRRVMKISRHPISLDRPV--GESEDSYFGDFIEDD---NTESPVMAATQEMLKD 472

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +   +  L  RER I + R    +    TLE +   F+V+RERVRQIEA+A +K+Q  +
Sbjct: 473 KIDNVLKTLTYREREIIKLRYGLGDGYTYTLEEVGRIFKVTRERVRQIEAKAVRKLQHPV 532

Query: 285 QKQ 287
           + +
Sbjct: 533 RSK 535


>gi|299472559|emb|CBN79861.1| chloroplast RNA-polymerase sigma factor precursor [Ectocarpus
           siliculosus]
          Length = 694

 Score =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 80/318 (25%), Positives = 140/318 (44%), Gaps = 48/318 (15%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREH-------------------------- 44
            G   L+ Y+  + K+ +L+  EE VL ++ ++                           
Sbjct: 46  GGGDALAFYLRTVAKVDLLKPHEEIVLGRQIQKGVSYENTRDHLQLMRGYEPSEEEWAVA 105

Query: 45  --GDLS-----------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
              D             A   ++ ++LRLVV +A  YR   L   +++ EG  GL++A +
Sbjct: 106 LGMDREELVKELSRASKAKMAMLAANLRLVVSVAKRYRFQKLSFQDLIQEGTFGLVKAAE 165

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFDPERGF+ +TY+ WWIK ++   I     ++++    +       L R++     +TD
Sbjct: 166 KFDPERGFKFSTYATWWIKQSIMRGIADQSRIIRLPVHVHD-----FLNRVRKATLEMTD 220

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH--D 209
            N K      +A+ L VS   +           S+ A  N + K S+     +       
Sbjct: 221 KNGKLPTDDELAEHLEVSAVRIQYYRDAAQATLSMEAPRNIASKTSTSPGKKVEMGQGVS 280

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRE 267
           G E+   ++ +    +  +T  +  L+ RE+ + +AR       P TLE +  +F ++RE
Sbjct: 281 GPEKTPDKQAQSDVMKQKVTELLMTLSIREQEVVKARFGLGGALPRTLEEVGRDFRLTRE 340

Query: 268 RVRQIEARAFKKVQESIQ 285
           RVRQIEARA  K+++  +
Sbjct: 341 RVRQIEARALHKLRQPYR 358


>gi|218248849|ref|YP_002374220.1| RNA polymerase sigma-70 subunit RpoD subfamily [Cyanothece sp. PCC
           8801]
 gi|257061911|ref|YP_003139799.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8802]
 gi|218169327|gb|ACK68064.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8801]
 gi|256592077|gb|ACV02964.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8802]
          Length = 417

 Score =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 64/242 (26%), Positives = 130/242 (53%), Gaps = 13/242 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           + A  +++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV+KFDP +G+R +TY+ 
Sbjct: 176 IRAKEQMIKANLRLVVSVAKKYQHRGLELLDLIQEGTLGLERAVEKFDPTKGYRFSTYAY 235

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   I     ++++     +K     L ++K   + ++    +   +  ++K+L
Sbjct: 236 WWIRQGITRAISTQSRIIRLPVHITEK-----LNKIKRAQRKLSQEKGRKATIEEMSKEL 290

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++S  ++  +  R+    SL   +    +  ++  D L  +    E+ LI +  RK+   
Sbjct: 291 DMSAEQIREVLLRIPRSVSLE--VKVGKEKDTELVDLLETECQSPEESLISESLRKD--- 345

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L  RE+ + + R   E+    +L ++    E+SRERVRQIEA+A +K+++  
Sbjct: 346 -LQVLLEDLTEREQDVIKLRYGFEDGTCYSLADIGRVLELSRERVRQIEAKALQKLRQPR 404

Query: 285 QK 286
           ++
Sbjct: 405 RR 406


>gi|281420881|ref|ZP_06251880.1| RNA polymerase sigma-70 factor [Prevotella copri DSM 18205]
 gi|281405173|gb|EFB35853.1| RNA polymerase sigma-70 factor [Prevotella copri DSM 18205]
          Length = 287

 Score =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 72/281 (25%), Positives = 139/281 (49%), Gaps = 11/281 (3%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ +I    +L   EE  LA+R R+ GD  A  RL  ++LR VV
Sbjct: 5   KITQSITNRASASLEKYLQDIAHEELLSTDEEVELAQRIRK-GDRRALERLTKANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  G+ + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + I     
Sbjct: 64  SVAKQYQNQGISLPDLINEGNVGLIKAAQKFDETRGFKFISYAVWWIRQSILQAIAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           LV++    NQ      + R     +   +       V  IA ++++ E ++       + 
Sbjct: 124 LVRLP--LNQVGSVNKINREMSKFEQEFERK---PSVDEIADRIDLPEDKIEDAMKATST 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
              L+     SD       D +    D  ++ L    + ++ R  + R +  L  ++++I
Sbjct: 179 SRHLSVDAPFSDDEDGSMLDLMANSDDPTDKEL----QTESLRAEIERLLKTLPDKDQKI 234

Query: 243 FEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             A      P +TLE + +++ ++RERVRQI+ +  ++++ 
Sbjct: 235 IAAFYGIGTPELTLEEIGTKYHLTRERVRQIKEKTIRRLRN 275


>gi|126642303|ref|YP_001085287.1| EsvH [Acinetobacter baumannii ATCC 17978]
          Length = 233

 Score =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 93/236 (39%), Positives = 142/236 (60%), Gaps = 7/236 (2%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV SHLR VV IA  Y GYGLP  +++ EGN+GLM+AVK+FDP  G RL ++++ WIKA 
Sbjct: 2   LVMSHLRFVVHIARSYAGYGLPQGDLIQEGNLGLMKAVKRFDPNMGVRLVSFAVHWIKAE 61

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           + EY++R+W +VKI TT  Q++LFFNLR LK   + +T      E+  +IA  LNV+  +
Sbjct: 62  IHEYVIRNWRIVKIATTKAQRKLFFNLRSLKKSSKKLT-----LEEAQSIANDLNVTPEQ 116

Query: 173 VISMNCRL-AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR-NMLTR 230
           V+ M  RL A D +  A  +  D          + D+      L+E E+ + +  + L  
Sbjct: 117 VLEMEGRLTAYDAAFEAQGDDDDDTPHTAPVLYLEDNRYDPARLVENEDWEEQSTSALHD 176

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +M+ L+ R R I + R L ++  TL  L++E+ VS ER+RQ+E  A +K++ ++  
Sbjct: 177 AMNQLDDRSRNILQRRWLDDDKSTLHELAAEYNVSAERIRQLEKNAMEKIKVAMSA 232


>gi|86134980|ref|ZP_01053562.1| RNA polymerase sigma-70 factor [Polaribacter sp. MED152]
 gi|85821843|gb|EAQ42990.1| RNA polymerase sigma-70 factor [Polaribacter sp. MED152]
          Length = 287

 Score =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 71/276 (25%), Positives = 138/276 (50%), Gaps = 13/276 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L +Y  EI KI ++   EE  LA + +  GD  A  +LV ++LR VV +A  Y+  GL 
Sbjct: 17  SLEKYFQEIGKIDLITADEEVELALKIK-AGDQRALDKLVKANLRFVVSVAKQYQNQGLK 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           +S++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + +     +V++    N+  
Sbjct: 76  LSDLINEGNLGLVKAAKRFDETRGFKFISYAVWWIRQSIMQSLAEQSRIVRLP--LNKIG 133

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               + ++   L+     N +    V IA +L+ +   V           S++A     +
Sbjct: 134 SISKINKVYSKLEQ---RNERIPTYVEIANELDTTVRNVAQSMKNSGRHVSMDAPFR--E 188

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
              S   + L  D   +    + K+        + R++  L+ +E ++ +      N   
Sbjct: 189 GEDSNLYNVLKSDESPRPDKNLMKQSLDIE---IDRALETLSHKEAKVIKMFFGLGNHTA 245

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +L  +   F+++RERVRQ++ RA +++Q   + +V
Sbjct: 246 SSLSEIGETFDLTRERVRQVKQRAIRRLQNKSRTEV 281


>gi|21221637|ref|NP_627416.1| RNA polymerase principal sigma factor [Streptomyces coelicolor
           A3(2)]
 gi|256787171|ref|ZP_05525602.1| RNA polymerase principal sigma factor [Streptomyces lividans TK24]
 gi|289771070|ref|ZP_06530448.1| RNA polymerase principal sigma factor hrdD [Streptomyces lividans
           TK24]
 gi|19856654|sp|P18249|HRDD_STRCO RecName: Full=RNA polymerase principal sigma factor hrdD
 gi|7799522|emb|CAB90986.1| RNA polymerase principal sigma factor [Streptomyces coelicolor
           A3(2)]
 gi|289701269|gb|EFD68698.1| RNA polymerase principal sigma factor hrdD [Streptomyces lividans
           TK24]
          Length = 332

 Score =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 75/299 (25%), Positives = 130/299 (43%), Gaps = 39/299 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVL---------AKR----YREHG--------------DLS 48
           +  Y+ EI + P+L+  +E  L         A++    Y E G                 
Sbjct: 36  VGMYLDEIARTPLLDAAKEVELSQTIEAGVFARQVLEGYEETGADATREELQALIDESER 95

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A    + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ WW
Sbjct: 96  AKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTYATWW 155

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      +++        L   L R++   +     + +  +   IA +L  
Sbjct: 156 IRQAITRSIADQSRTIRLPVH-----LVEELGRIRRVQREFNREHGREPEPAEIAAELGS 210

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +   V  +        SLN  +   D+  +Q+ D L    D       +      R   L
Sbjct: 211 TPERVTDVLDWARDPVSLNMSV--DDEGETQFGDLL---EDTSAVSPEQSVLTLLRSEEL 265

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              +  L+PR   I + R   ++    TL  +  E  ++RER+RQIE  A  ++++  +
Sbjct: 266 DDLIGRLDPRTASIIKMRYGIDDGRERTLTEVGKEHGLTRERIRQIEKHALLELKKLAR 324


>gi|209525810|ref|ZP_03274346.1| RNA polymerase, sigma 70 subunit, RpoD family [Arthrospira maxima
           CS-328]
 gi|209493783|gb|EDZ94102.1| RNA polymerase, sigma 70 subunit, RpoD family [Arthrospira maxima
           CS-328]
          Length = 407

 Score =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 69/260 (26%), Positives = 133/260 (51%), Gaps = 18/260 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L  +E     K+ +  G L A   ++ ++LRLVV +A  Y+  GL + +++ EG +GL +
Sbjct: 153 LSVEE----LKQVQREG-LQAKDHMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLER 207

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           AV+KFDP RG+R +TYS WWI+  +   I      +++     +K     L ++K   + 
Sbjct: 208 AVEKFDPTRGYRFSTYSYWWIRQGITRAIATQSRTIRLPVHITEK-----LNKIKKAQRK 262

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           I+    +   +  IA +L ++  ++  +  R+    SL   +       ++  D L  + 
Sbjct: 263 ISQEKSRTATIDDIATELKMTPDQIREVLLRVPRSVSLETKV--GTDKDTELGDLLETEE 320

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSR 266
              E++L+    R++    L   ++ L+ +ER + + R      +P +L  +    ++SR
Sbjct: 321 STPEELLM----RESLYRELQNLLADLSGKERAVIQMRYGLGDGHPYSLAEIGRALDLSR 376

Query: 267 ERVRQIEARAFKKVQESIQK 286
           ERVRQIEA+A +K+++  ++
Sbjct: 377 ERVRQIEAKALQKLRQPKRR 396


>gi|21466008|pdb|1L9U|H Chain H, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
           Resolution
 gi|21466014|pdb|1L9U|Q Chain Q, Thermus Aquaticus Rna Polymerase Holoenzyme At 4 A
           Resolution
          Length = 332

 Score =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 67/237 (28%), Positives = 110/237 (46%), Gaps = 10/237 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +A   L+ ++LRLVV IA  Y G GL   +++ EGN GL++AV+KF+ +R F+ +TY+ 
Sbjct: 90  EAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYAT 149

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I     +      L R    LQ         E++   A   
Sbjct: 150 WWIRQAINRAIADQARTIRIPVHMVE--TINKLSRTARQLQQELGREPSYEEIAE-AMGP 206

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
                 V           SL   I   D+  S + D++    D      +E   +     
Sbjct: 207 GWDAKRVEETLKIAQEPVSLETPI--GDEKDSFYGDFIP---DENLPSPVEAAAQSLLSE 261

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L +++S L+ RE  + + R+        TLE + + F V+RER+RQIE +A +K++
Sbjct: 262 ELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLK 318


>gi|195939453|ref|ZP_03084835.1| RNA polymerase sigma factor RpoS [Escherichia coli O157:H7 str.
           EC4024]
          Length = 305

 Score =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 75/256 (29%), Positives = 129/256 (50%), Gaps = 13/256 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVRQI 272
           ++  E  ++RERVRQI
Sbjct: 290 DVGREIGLTRERVRQI 305


>gi|149175263|ref|ZP_01853885.1| transcription initiation factor sigma 70 [Planctomyces maris DSM
           8797]
 gi|148845872|gb|EDL60213.1| transcription initiation factor sigma 70 [Planctomyces maris DSM
           8797]
          Length = 561

 Score =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 73/277 (26%), Positives = 126/277 (45%), Gaps = 14/277 (5%)

Query: 15  GLSRYIHEIRKIPMLEKQ--EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
            L R + ++  + M   +   E + A + R     +A   L   +LRLVV IA  YR  G
Sbjct: 264 NLERELQDLVAMTMETPETLRERIKAVKQRYLDYETAMRELSGGNLRLVVSIAKKYRNRG 323

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L   +++ EGN GLM+AV K++  RG++ +TY+ WWI+ A+   I      ++I      
Sbjct: 324 LSFLDLIQEGNTGLMRAVDKYEYRRGYKFSTYATWWIRQAITRAIADQARTIRIPVHM-- 381

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 LR++   L          E+   +A    +S  E   +        SL+  +  
Sbjct: 382 IETMSKLRKVSKQLLQENGREPTLEETAEVA---GISLEETRRVLKISRHPISLDRPV-- 436

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            +   S + D++    D      +    ++  ++ +   +  L  RER I + R    + 
Sbjct: 437 GESEDSYFGDFI---EDSDSDSPVNTASQEMLKDKIDHVLKTLTYREREIIKLRFGLGDG 493

Query: 253 --VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE +   F+V+RERVRQIEA+A +K+Q  ++ +
Sbjct: 494 YTYTLEEVGRIFKVTRERVRQIEAKAVRKLQHPVRSK 530



 Score = 36.7 bits (84), Expect = 4.1,   Method: Composition-based stats.
 Identities = 11/56 (19%), Positives = 25/56 (44%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSH 57
           +R +  +    +  +  Y+ ++ +IP+L + EE  LAK+            L + +
Sbjct: 72  SRTSDDLSRRIDDPVRMYLTQMGEIPLLTRDEEIRLAKKIEITRRRFRRELLSSDY 127


>gi|19910024|dbj|BAB87263.1| RNA polymerase sigma factor [Cyanophora paradoxa]
          Length = 431

 Score =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 85/319 (26%), Positives = 148/319 (46%), Gaps = 56/319 (17%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRY---------REHG---------DLS----- 48
            E    RY+ EI +I +L+ ++E  LAKR          +EH          D       
Sbjct: 110 SEDSGRRYLQEIGEISLLKAEDEIELAKRIETFRKLEKVKEHMKWKTGVEPTDEEWARAA 169

Query: 49  -----------------AAHRLVTSHLRLVVKIAMGY--RGYGLPISEVVSEGNIGLMQA 89
                            A  RLV ++LR VV +A  Y  +   + + +++ EGNIGL++A
Sbjct: 170 ALSDAEELRHMVRVGTLARDRLVRANLRWVVAVAKKYHKQRGTMSMQDLIQEGNIGLIRA 229

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V+KFDP  G+R  TY+ WWI+ A+   I  S   +++    ++K     + R+K    A+
Sbjct: 230 VEKFDPRMGYRFTTYATWWIRQAITRSIQNSSREIRLPAHRHEK-----INRIKRATVAL 284

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
           + +  +      IA+ + +  S +     +       SL+  IN SD  S+   D++  +
Sbjct: 285 SRSLGRQPTEAEIAEHVGLDPSRMRKFVESAAAVATVSLDVPINESDNQSATIGDFIRSE 344

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSV-LNPRERRIFEARRLQEN--PVTLENLSSEFEV 264
           ++G      ++ ER+  R  + R+++  L+ RE  +   R   ++  P TL  +     V
Sbjct: 345 NEG----PADRAERELMRESVARTLAKALSEREYMVLRMRFGLDDGEPKTLNQVGETLGV 400

Query: 265 SRERVRQIEARAFKKVQES 283
           +RERVRQIE +A +K++  
Sbjct: 401 TRERVRQIEMKALRKLRRP 419


>gi|48743|emb|CAA37174.1| unnamed protein product [Streptomyces coelicolor A3(2)]
          Length = 332

 Score =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 75/299 (25%), Positives = 130/299 (43%), Gaps = 39/299 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVL---------AKR----YREHG--------------DLS 48
           +  Y+ EI + P+L+  +E  L         A++    Y E G                 
Sbjct: 36  VGMYLDEIARTPLLDAAKEVELSQTIEAGVFARQVLEGYEETGADATREELQALIDESER 95

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A    + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ WW
Sbjct: 96  AKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTYATWW 155

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      +++        L   L R++   +     + +  +   IA +L  
Sbjct: 156 IRQAITRSIADQSRTIRLPVH-----LVEELGRIRRVQREFNREHGREPEPAEIAAELGS 210

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +   V  +        SLN  +   D+  +Q+ D L    D       +      R   L
Sbjct: 211 TPERVHDVLDWARDPVSLNMSV--DDEGETQFGDLL---EDTSAVSPEQSVLTLLRSEEL 265

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              +  L+PR   I + R   ++    TL  +  E  ++RER+RQIE  A  ++++  +
Sbjct: 266 DDLIGRLDPRTASIIKMRYGIDDGRERTLTEVGKEHGLTRERIRQIEKHALLELKKLAR 324


>gi|297159879|gb|ADI09591.1| RNA polymerase principal sigma factor hrdD [Streptomyces
           bingchenggensis BCW-1]
          Length = 333

 Score =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 72/302 (23%), Positives = 130/302 (43%), Gaps = 41/302 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRY---------------------REHGDLSA----- 49
           +  Y+ EI + P+L+  +E  L++                          G+L A     
Sbjct: 35  VGMYLDEIARTPLLDAAKEVELSQAIEAGVYAQQILDGEIEDAPAAGASRGELEAIAAEG 94

Query: 50  ---AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                  + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ 
Sbjct: 95  ARAKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYTKGFKFSTYAT 154

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      +++        L   L R++   +     + +  +   IA +L
Sbjct: 155 WWIRQAITRSIADQSRTIRLPVH-----LVEELGRIRRVQREFNREHGREPEHSEIAAEL 209

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             +   V  +        SLN  +   D+  +Q+ D L    D       +      R  
Sbjct: 210 GSTTERVSDVLDWARDPVSLNMSV--DDEGETQFGDLL---EDTSAVSPEQSVMTLLRSE 264

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ R   I +AR   ++    TL  +  +  ++RER+RQIE  A  ++++  
Sbjct: 265 ELEDLIGRLDDRTASIIKARYGIDDGRERTLTEVGKQHGLTRERIRQIEKHALLELKKMA 324

Query: 285 QK 286
           ++
Sbjct: 325 RQ 326


>gi|283780465|ref|YP_003371220.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pirellula staleyi
           DSM 6068]
 gi|283438918|gb|ADB17360.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pirellula staleyi
           DSM 6068]
          Length = 544

 Score =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 70/243 (28%), Positives = 115/243 (47%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +A  +L + +LRLVV IA  YR  GL   +++ EGN GLM+AV K++  RGF+ +TY+ 
Sbjct: 301 EAAKRQLSSGNLRLVVSIAKKYRNRGLSFLDLIQEGNTGLMRAVDKYEYRRGFKFSTYAT 360

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I        +   LR ++  L          E+V A+   +
Sbjct: 361 WWIRQAITRAIADQARTIRIPVHM--IDVLSKLRNVQKKLLQELGREPTTEEVTAL---V 415

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   EV  +        SL+  +  S+ +S     +  +  D      +        R 
Sbjct: 416 DLPLEEVKRVLDIGRHPVSLDRPVGDSEDSS-----FGEFIEDTASDNPVLCATNGILRE 470

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +   +  L  RER I   R    +    TLE +   F+V+RERVRQIEA+A +K+Q  +
Sbjct: 471 RIDGLLKTLTWREREIIRLRYGLCDGYTYTLEEVGRIFKVTRERVRQIEAKAVRKLQHPV 530

Query: 285 QKQ 287
           + +
Sbjct: 531 RSK 533


>gi|253582113|ref|ZP_04859337.1| RNA polymerase [Fusobacterium varium ATCC 27725]
 gi|251836462|gb|EES64999.1| RNA polymerase [Fusobacterium varium ATCC 27725]
          Length = 275

 Score =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 77/276 (27%), Positives = 143/276 (51%), Gaps = 15/276 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +S Y+ +IRK  +L+K EE  L  + +  GD  + ++L+ S+LRLVV IA GY   GL  
Sbjct: 9   ISLYLADIRKYKILDKDEELNLLIKAK-AGDEESKNQLILSNLRLVVNIAKGYINKGLSF 67

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++SEGN+GL+ A++KFD  +GFR +TY++WWIK ++ + ++     ++I +       
Sbjct: 68  IDLISEGNLGLIYAIEKFDITKGFRFSTYAVWWIKQSISKAVIVKGREIRIPSYK----- 122

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           +  L ++  ++ +   +      V  IA +LN+   ++  +        SL+  I     
Sbjct: 123 YDLLNKVNRYVMSRLKDEGNYPPVEEIAAELNIDVDKIQDIIMDFQDPMSLSTQI----G 178

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPV 253
           +    +D L    D   +   E+   +  R  +   ++ L  RE+ I + R   +     
Sbjct: 179 DDIYLEDTLAQQEDFSME---EEIFNEMGRKQVRDMVNQLEEREKEILKLRYGLDGYEIH 235

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           TLE + +   ++RERVRQIE +  +K++    K+++
Sbjct: 236 TLEEIGNTLNITRERVRQIEKKTLQKLRSKYTKELK 271


>gi|291302005|ref|YP_003513283.1| RpoD subfamily RNA polymerase sigma-70 subunit [Stackebrandtia
           nassauensis DSM 44728]
 gi|290571225|gb|ADD44190.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Stackebrandtia
           nassauensis DSM 44728]
          Length = 323

 Score =  204 bits (520), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 73/300 (24%), Positives = 132/300 (44%), Gaps = 40/300 (13%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY--------------------REHGD------- 46
             +  Y++ I K  ++   EE  LAK                      +   D       
Sbjct: 23  DSVRAYLNGIGKHRLINAAEEVDLAKAIETGLFAEWRLSDPARPIDDLQLERDLRQIVAE 82

Query: 47  -LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
              A   L+ ++LRLVV IA  Y G G+ + +++ EGN+GL++AV+KFD  +GF+ +TY+
Sbjct: 83  GRRAKSMLLKANLRLVVSIAKRYVGRGVALLDLIQEGNLGLIRAVEKFDYTKGFKFSTYA 142

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
            WWI+ A+   +      +++     +      + R+    + +T    +  +   IA++
Sbjct: 143 TWWIRQAITRAMADQARTIRVPAHTAE-----QINRIAKIRRELTAEQGREPRHEEIAER 197

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           + +    V+ +        SL+  +  SD   +   D +    D   +      +    R
Sbjct: 198 MGLEPYRVLELLSYDRDPISLDQPV--SDDRQTPLSDLVARPVDPAAEPNPANAQL---R 252

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             L R+++ L  RER +  AR   ++    TLE +  E  +SRERVRQ+E  +  K++E 
Sbjct: 253 QELERALTDLPARERAVLRARFGIDDGRQRTLEEVGEELGLSRERVRQLEKLSLNKLREP 312


>gi|320355021|ref|YP_004196360.1| RpoD subfamily RNA polymerase sigma-70 factor [Desulfobulbus
           propionicus DSM 2032]
 gi|320123523|gb|ADW19069.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfobulbus
           propionicus DSM 2032]
          Length = 533

 Score =  204 bits (519), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 72/261 (27%), Positives = 124/261 (47%), Gaps = 16/261 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           +E Q+E  + +         A   LV ++LRLV+ ++  +   G+ + +++ EGNIGLM+
Sbjct: 279 IEVQQEIEIGRETA----RQAKETLVRANLRLVISVSKKFMNRGMQLPDLIQEGNIGLMK 334

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           AV+K+D +RG++ +TY+ WWI+ A+   I      +++            + R     Q 
Sbjct: 335 AVEKYDYKRGYKFSTYATWWIRQAVTRGIADQGRTIRLPVHM--IETINRMLRFSKDFQR 392

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           I      PE    +AK+L     +V           SL+A +  +D+  +   D++    
Sbjct: 393 IESREPTPE---EMAKQLGTDVEKVQVALKTAKDAISLDAPV--NDEEDTLLSDFI---E 444

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSR 266
           D       E    ++ +  L + M  L PRE ++   R   E     TLE +   F V+R
Sbjct: 445 DHAHPDPQEHSITESLKRCLCKVMGSLTPREEKVLRMRYGIEIGCDHTLEEVGQCFAVTR 504

Query: 267 ERVRQIEARAFKKVQESIQKQ 287
           ER+RQIEA+A KK++   + Q
Sbjct: 505 ERIRQIEAQALKKLRHPARSQ 525


>gi|88608313|ref|YP_506202.1| RNA polymerase sigma factor RpoD [Neorickettsia sennetsu str.
           Miyayama]
 gi|88600482|gb|ABD45950.1| RNA polymerase sigma factor RpoD [Neorickettsia sennetsu str.
           Miyayama]
          Length = 620

 Score =  204 bits (519), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 75/274 (27%), Positives = 130/274 (47%), Gaps = 33/274 (12%)

Query: 37  LAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           L ++   H D +  A HR+V ++LRLV+ IA  Y   G+P  +++ EGNIGLM+AV KFD
Sbjct: 347 LTRKVATHLDNANAAKHRMVEANLRLVISIAKKYTNRGMPFPDLIQEGNIGLMKAVDKFD 406

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             RG + +TY+ WW + A+   I    S+V+     ++        ++    + + + N 
Sbjct: 407 HRRGHKFSTYATWWCRQAITRAIADCGSIVRKPVHIHE-----TANKVMRTRRRLYNLNG 461

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +   V  IA  L +S  +V           SL + +   D NS  + D++    D     
Sbjct: 462 REPTVEEIANLLKISPDKVKKSLKVNQDPISLESPVGD-DSNSGSFGDFI---EDKNAVS 517

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP---------------------- 252
            ++    KN R +L  ++++L+PRE +I   R    N                       
Sbjct: 518 QVDVVLSKNLRKVLDEALAMLSPREEKILRYRFGLCNSVHSPEDEHYLKSLKIDLNRGTN 577

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +TLE +   + V+RER+RQIE+++ +K++   + 
Sbjct: 578 LTLEQVGILYNVTRERIRQIESKSLRKMRSPSRS 611


>gi|304383076|ref|ZP_07365551.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella marshii
           DSM 16973]
 gi|304335762|gb|EFM02017.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella marshii
           DSM 16973]
          Length = 290

 Score =  204 bits (519), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 71/280 (25%), Positives = 133/280 (47%), Gaps = 12/280 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKI 64
           SI       L +Y+ EI + P++   EE  LA++ ++ G     A  +LVT++LR VV +
Sbjct: 9   SITNRSSEALDKYLVEIGRAPLISIDEEIELAQKIKKGGPEGERAKDKLVTANLRFVVSV 68

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y+  GL +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V
Sbjct: 69  AKQYQHQGLTLTDLIDEGNIGLIKAAQKFDETRGFKFISYAVWWIRQSILQAIAEQSRIV 128

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           ++           +L ++   +      N +   V  ++   ++ E ++           
Sbjct: 129 RLPLNQ-----VGSLNKINHEINKFEQENQRHPSVSELSDVTHIDEEKIGQSLMADGHHV 183

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           S++A     ++N     D +    D +   L++ E      N +     VL  RE  I  
Sbjct: 184 SIDAPFQEGEENC--MLDVMAGGEDSRTDRLVDHESMAQELNTV--LCKVLKDREITIIR 239

Query: 245 ARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
                  +   LE +     ++RERVRQI  ++  K+++S
Sbjct: 240 ECFGIGCHEKGLEEIGDRLGLTRERVRQIREKSIAKLRDS 279


>gi|75907387|ref|YP_321683.1| RNA polymerase sigma factor SigC [Anabaena variabilis ATCC 29413]
 gi|75701112|gb|ABA20788.1| RNA polymerase, sigma subunit, RpsC/SigC [Anabaena variabilis ATCC
           29413]
          Length = 416

 Score =  204 bits (519), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 65/256 (25%), Positives = 132/256 (51%), Gaps = 14/256 (5%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
               ++ +  G L +   ++ ++LRLVV +A  Y+  GL + ++V EG +GL +AV+KFD
Sbjct: 164 VEELEKMQSQG-LQSKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFD 222

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P +G+R +TY+ WWI+  +   I  S   +++     +K     L ++K   + I     
Sbjct: 223 PTKGYRFSTYAYWWIRQGITRAIATSSRTIRLPVHITEK-----LNKIKKAQRKIAQEKG 277

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +   +  +A +L+++ ++V  +  R+    SL   +       ++  + L  D    E++
Sbjct: 278 RTPTLEDLAIELDMTPTQVREVLLRVPRSVSLETKV--GKDKDTELGELLETDGVTPEEM 335

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQI 272
           L+    R++ +  L   ++ L  RER +   R      +P +L  +    ++SRERVRQI
Sbjct: 336 LM----RESLQRDLQHLLADLTSRERDVILMRFGLADGHPYSLAEIGRALDLSRERVRQI 391

Query: 273 EARAFKKVQESIQKQV 288
           E++A +K+++  ++ +
Sbjct: 392 ESKALQKLRQPKRRNL 407


>gi|83815083|ref|YP_446059.1| RNA polymerase sigma-70 factor [Salinibacter ruber DSM 13855]
 gi|83756477|gb|ABC44590.1| RNA polymerase sigma-70 factor [Salinibacter ruber DSM 13855]
          Length = 313

 Score =  204 bits (519), Expect = 1e-50,   Method: Composition-based stats.
 Identities = 86/274 (31%), Positives = 149/274 (54%), Gaps = 13/274 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI KI +LE +EE  LA+R  E GD  A H+L  ++LR VV +A  Y+G GL +
Sbjct: 44  LDQYLQEIGKIDLLEPEEEVELARRI-EDGDEEALHKLCRANLRFVVSVAKKYQGQGLSL 102

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           +++++EGN GL++A K+FD  RGF+  +Y++WWI+ A+ + +     +V++    N+   
Sbjct: 103 ADLINEGNYGLIKAAKRFDETRGFKFISYAVWWIRQAILQALAEQSRVVRLP--LNRIGT 160

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              +R+    LQ   D       +  +A++L +   +V       +   S++A  N  D 
Sbjct: 161 ISKIRKASARLQQDLDRK---PNIEELAEELEIDVQKVREAMKHTSRHLSMDAPFNEEDD 217

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPV 253
           NS      L    D       E+   ++ +  + R++S L+ RE  I        +E+P+
Sbjct: 218 NS-----LLDVLPDEDNDSPDEEMLSESVKIDIERALSALHDREAEITRLYFGIGREHPL 272

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           TLE +   F+++RERVRQI+ +A +K+++   KQ
Sbjct: 273 TLEEIGKRFDLTRERVRQIKEKALRKLRQRHSKQ 306


>gi|282900303|ref|ZP_06308254.1| Sigma 28 (Flagella/Sporulation) [Cylindrospermopsis raciborskii
           CS-505]
 gi|281194808|gb|EFA69754.1| Sigma 28 (Flagella/Sporulation) [Cylindrospermopsis raciborskii
           CS-505]
          Length = 399

 Score =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 77/313 (24%), Positives = 138/313 (44%), Gaps = 52/313 (16%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYR---EHGDLSA-------------------- 49
           +  +  +  E+ + P+L+  EE  LA+R R   E  DL A                    
Sbjct: 86  DDAVGAFFKEMARYPLLKPDEEVELARRVRFLEEVKDLQAALEEQLGHSVSKSEVASKFD 145

Query: 50  ----------------AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
                             +++ S+LRLVV IA  Y   G+P  +++ EG +GL +A +KF
Sbjct: 146 LNEKQLESRLYQGRVAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAMGLNRATEKF 205

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           DP++G++ +TY+ WWI+ A+   I      +++     +K     L +LK   + +    
Sbjct: 206 DPDKGYKFSTYAYWWIRQAITRAIANDARTIRLPIHIVEK-----LNKLKKAQRELKQKF 260

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            +    V +A+ L ++  ++  +        SLN  +    +  ++  D L  + +   Q
Sbjct: 261 ARNPTEVEMAEFLEMTVQQLRQLQQLRRQALSLNHRV--GKEEDTELMDLLEDEDN---Q 315

Query: 214 VLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVR 270
               K      R  +   +  VL PRE+ +   R       P TLE + + F +SRERVR
Sbjct: 316 SPEAKMNENMMRQEIWEVLGDVLTPREKDVISLRYGLTTSEPCTLEEVGNMFNLSRERVR 375

Query: 271 QIEARAFKKVQES 283
           QI+++A +K++  
Sbjct: 376 QIQSKAMRKLRRP 388


>gi|126697159|ref|YP_001092045.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9301]
 gi|126544202|gb|ABO18444.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9301]
          Length = 344

 Score =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 69/318 (21%), Positives = 134/318 (42%), Gaps = 53/318 (16%)

Query: 7   SIIVNGEIGLSR-YIHEIRKIPMLEKQEEYVLAKRYRE--------------HGDL---- 47
           S+  + ++ L R Y+ +I ++P+L  ++E  L ++ +E               GD     
Sbjct: 27  SLKASNDVDLVRSYLRDIGRVPLLSHEQEITLGRQVQEYMQVERAELEISELTGDKPSID 86

Query: 48  ---------------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
                                 A  R+V ++LRLVV +A  Y    + + +++ EG IGL
Sbjct: 87  ELSTKLNLSTSVIKKRLRAGQRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGL 146

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++ V+KFDP RG++ +TY+ WWI+  +   I      +++     +      L +LK   
Sbjct: 147 VRGVEKFDPARGYKFSTYAYWWIRQGITRAIAEKSRAIRLPIHITE-----MLNKLKKGQ 201

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           + ++    +   V  +AK + + E +V  + C+     SL   +   +         L+ 
Sbjct: 202 RELSQEMSRTPTVSELAKYVELPEDDVKDLMCKAGQPVSLETKVGDGEDT------VLLD 255

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
              G E +  E+ E    R  L   +  L   + R+   R     + P++L  +     +
Sbjct: 256 LLAGGEDLPDEQIEMDCMRGDLHSLLHQLPDLQCRVLRMRYGMDGDEPMSLTGIGRVLGI 315

Query: 265 SRERVRQIEARAFKKVQE 282
           SR+RVR +E    + ++ 
Sbjct: 316 SRDRVRNLERDGLRGLRR 333


>gi|238060708|ref|ZP_04605417.1| RNA polymerase sigma factor rpoD [Micromonospora sp. ATCC 39149]
 gi|237882519|gb|EEP71347.1| RNA polymerase sigma factor rpoD [Micromonospora sp. ATCC 39149]
          Length = 331

 Score =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 77/297 (25%), Positives = 132/297 (44%), Gaps = 38/297 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAK-----RYREH---------------------GDLSAAHR 52
           Y+HEI + P+L+   E  L+K      Y EH                         A   
Sbjct: 40  YLHEISRTPLLDAATEVDLSKSIEAGLYAEHLLETDRVPAGVDRDDLERVAAEGERAKDL 99

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            + ++LRLVV IA  Y   G+P+ +++ EGN GL++AV+KFD ERGF+ +TY+ WWI+ A
Sbjct: 100 FIRANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQA 159

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   I +    V++        L  ++ R++   + +T       +   IA  L V+   
Sbjct: 160 ISRAIAQQERTVRLPVH-----LVEDVNRMRNAARQLTRELGSDPEPEQIAAALGVTVER 214

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           V  +        SL+  +   D   +   D +    D       +       R  +   +
Sbjct: 215 VNELVRWSQDTVSLDTPV--GDDGDTNLGDLVA---DSDAPSPEDIVLTGLERQRIEGLL 269

Query: 233 SVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           + L+ R   I  AR   E+    +L  ++S F +SRER+RQ+E +A  +++E  + +
Sbjct: 270 NHLDDRSAGIMRARYGLEDGREHSLTEVASRFSLSRERIRQLEIQALGRLRELARAE 326


>gi|188996015|ref|YP_001930266.1| RNA polymerase, sigma 32 subunit, RpoH [Sulfurihydrogenibium sp.
           YO3AOP1]
 gi|188931082|gb|ACD65712.1| RNA polymerase, sigma 32 subunit, RpoH [Sulfurihydrogenibium sp.
           YO3AOP1]
          Length = 285

 Score =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 84/277 (30%), Positives = 138/277 (49%), Gaps = 11/277 (3%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E  +  Y+  I KIP+L K+EE  L K+ +E GD  A  +L+ S+LR V+ IA  Y GYG
Sbjct: 7   EENVDFYLKSIYKIPLLSKEEEESLLKKVKE-GDKEALQKLIISNLRFVINIAKRYAGYG 65

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +P S+++S GNIGL++A KKFD  RG R  +Y++WWI+ ++   I     ++K       
Sbjct: 66  IPFSDLISAGNIGLIEAAKKFDTSRGVRFISYAVWWIRQSIINTIQHESEIIKKPNRMY- 124

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALI 190
                 +     +L+   +     +++++  K   +   + +  N  L      SL+  I
Sbjct: 125 -AYASKINNAYSYLKDTLNREPSIDEIISFLKTQGIKVEKEMVENYFLFKSVFLSLDTPI 183

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-- 248
             +D +        VY+    E+ + E    ++ +  +   +  L+PRER I   R    
Sbjct: 184 EGTDNDLVLEDTISVYNTLDIEKDINE----EDLKRAIEALLDTLSPRERTILIHRFGLN 239

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            E P TL  +     +SRERVRQIE R  KK+++  +
Sbjct: 240 GEEPKTLNEVGEMVGLSRERVRQIENRILKKLRKIAK 276


>gi|17229184|ref|NP_485732.1| RNA polymerase sigma factor SigC [Nostoc sp. PCC 7120]
 gi|20141790|sp|Q03066|RPSC_ANASP RecName: Full=RNA polymerase sigma-C factor
 gi|17135512|dbj|BAB78058.1| RNA polymerase sigma-subunit [Nostoc sp. PCC 7120]
          Length = 416

 Score =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 65/256 (25%), Positives = 132/256 (51%), Gaps = 14/256 (5%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
               ++ +  G L +   ++ ++LRLVV +A  Y+  GL + ++V EG +GL +AV+KFD
Sbjct: 164 VEELEKMQSQG-LQSKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFD 222

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P +G+R +TY+ WWI+  +   I  S   +++     +K     L ++K   + I     
Sbjct: 223 PTKGYRFSTYAYWWIRQGITRAIATSSRTIRLPVHITEK-----LNKIKKAQRKIAQEKG 277

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +   +  +A +L+++ ++V  +  R+    SL   +       ++  + L  D    E++
Sbjct: 278 RTPTLEDLAIELDMTPTQVREVLLRVPRSVSLETKV--GKDKDTELGELLETDGVTPEEM 335

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQI 272
           L+    R++ +  L   ++ L  RER +   R      +P +L  +    ++SRERVRQI
Sbjct: 336 LM----RESLQRDLQHLLADLTSRERDVILMRFGLADGHPYSLAEIGRALDLSRERVRQI 391

Query: 273 EARAFKKVQESIQKQV 288
           E++A +K+++  ++ +
Sbjct: 392 ESKALQKLRQPKRRNL 407


>gi|262038022|ref|ZP_06011434.1| RNA polymerase sigma factor RpoD [Leptotrichia goodfellowii F0264]
 gi|261747975|gb|EEY35402.1| RNA polymerase sigma factor RpoD [Leptotrichia goodfellowii F0264]
          Length = 258

 Score =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 84/262 (32%), Positives = 146/262 (55%), Gaps = 15/262 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +S Y+ +I+K  +L K+EEY L +R RE  D  A   L+ S+LRLV+  A    G GLP+
Sbjct: 9   ISLYLSDIQKFNLLSKEEEYELLRRIREENDEQARQLLILSNLRLVISTAKKLLGNGLPL 68

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++SEGNIGL++A+ KFD E+G R +TY++WWIK ++++ I+ +   ++I +       
Sbjct: 69  IDLISEGNIGLIKAINKFDYEKGHRFSTYAVWWIKQSIKKAIINTGRDIRIPSYK----- 123

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           +  L ++   +        +      IAK++++ ES+VI +        SLN  I  +  
Sbjct: 124 YEQLSKVNKVITDYVAKYGESPPTEYIAKEVDLKESKVILLLNEFQDVISLNETIGDN-- 181

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--V 253
               + + +V + D  E+ +I++++    R +L    ++L  RER I E R    N    
Sbjct: 182 ---IYLEDIVGNTDDVEEKIIKEDQLSEMRELLE---NILTDREREILELRYGLYNNKIH 235

Query: 254 TLENLSSEFEVSRERVRQIEAR 275
           TL+ + ++  ++RERVRQIE +
Sbjct: 236 TLKEIGAKLNITRERVRQIEKK 257


>gi|186684216|ref|YP_001867412.1| RNA polymerase sigma factor [Nostoc punctiforme PCC 73102]
 gi|186466668|gb|ACC82469.1| RNA polymerase, sigma 70 subunit, RpoD family [Nostoc punctiforme
           PCC 73102]
          Length = 327

 Score =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 68/305 (22%), Positives = 133/305 (43%), Gaps = 52/305 (17%)

Query: 19  YIHEIRKIPMLEKQEEYV-----------------LAKRYREHGD--------------- 46
           Y+ EI ++P+L +++E V                 LAK+     D               
Sbjct: 23  YLREIGRVPLLTREQEIVYGKQVQQMMTLIDAKEVLAKKLHREPDMSEWADVVQQSETEV 82

Query: 47  -------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                    A  +++ ++LRLVV IA  Y+   +   +++ EG +GL + V+KFDP RG+
Sbjct: 83  QQTVAQGKRAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPMRGY 142

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWI+ A+   I +    +++     +K     L ++K   + +     +    
Sbjct: 143 KFSTYAYWWIRQAITRAIAQQGRTIRLPIHITEK-----LNKIKKVQRELAQTLGRSPTP 197

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IAK+L +  +++           SL+  +   D   ++ Q+ L       E    ++ 
Sbjct: 198 AEIAKELELEPAQIREYLNMARQPVSLD--VKVGDNQDTELQEMLEDSGPSPEYYTNQEF 255

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
            R++    L   ++ L P++R +   R   E+   ++L  +     +SRERVRQ+E +A 
Sbjct: 256 LRQD----LNNLLAELTPQQREVLALRFGLEDGNEMSLAKVGERLNLSRERVRQLEHQAL 311

Query: 278 KKVQE 282
             ++ 
Sbjct: 312 AHLRR 316


>gi|87307035|ref|ZP_01089181.1| RNA polymerase sigma factor rpoD [Blastopirellula marina DSM 3645]
 gi|87290408|gb|EAQ82296.1| RNA polymerase sigma factor rpoD [Blastopirellula marina DSM 3645]
          Length = 519

 Score =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 70/243 (28%), Positives = 119/243 (48%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L   +LRLVV IA  YR  GL   +++ EGN GLM+AV KF+  RGF+  TY+ 
Sbjct: 280 QQAKRELSEGNLRLVVSIAKKYRNRGLSFLDLIQEGNAGLMRAVDKFEYRRGFKFCTYAT 339

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +      + R++   + +     +   +   A++ 
Sbjct: 340 WWIRQAITRAVADQSRTIRIPVHMVE-----TMSRVRNVARQLLQEKGREPTLEETARRA 394

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             +  E   +        SL+  + +S+   SQ+ D L    DG+ +       ++  R 
Sbjct: 395 GTTVEEARRVLAMSRYPISLDRPVGNSED--SQFGDLLP---DGEAESPAIGAAQEMLRT 449

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            ++R +  L+ RER I + R    +    TLE +   F+V+RER+RQIEA+A +K+Q+  
Sbjct: 450 RISRVLKTLSYREREIIKLRYGLGDGYSYTLEEVGHIFKVTRERIRQIEAKAVRKLQQPS 509

Query: 285 QKQ 287
           + Q
Sbjct: 510 RSQ 512



 Score = 35.9 bits (82), Expect = 8.2,   Method: Composition-based stats.
 Identities = 9/30 (30%), Positives = 19/30 (63%)

Query: 12 GEIGLSRYIHEIRKIPMLEKQEEYVLAKRY 41
           +  +  Y+ ++ +IP+L +QEE  LA++ 
Sbjct: 66 SDDPVRMYLTQMGEIPLLTRQEEIFLARKI 95


>gi|87311289|ref|ZP_01093411.1| transcription initiation factor sigma 70 [Blastopirellula marina
           DSM 3645]
 gi|87286029|gb|EAQ77941.1| transcription initiation factor sigma 70 [Blastopirellula marina
           DSM 3645]
          Length = 567

 Score =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 75/253 (29%), Positives = 122/253 (48%), Gaps = 14/253 (5%)

Query: 39  KRYREHGDL--SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           +RYR   D        L + +LRLVV IA  YR  GL   +++ EGN GLM+AV K++  
Sbjct: 313 ERYRRQFDEYEKVKRELSSGNLRLVVSIAKKYRNRGLSFLDLIQEGNTGLMRAVDKYEYR 372

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RGF+ +TY+ WWI+ A+   I      ++I        +   L +L+   + +     + 
Sbjct: 373 RGFKFSTYATWWIRQAITRAIADQARTIRIPVH-----MIDVLSKLRNVQKRLLQELRRE 427

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
             +  IA++  +   EV  +        SL+  I  S+ +S     +  +  D  E+  I
Sbjct: 428 PTMDEIARRAEIDLEEVRRVMDIGRQPVSLDRPIGESEDSS-----FGEFIEDSHEETPI 482

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEA 274
                +  R+ +   +  L  RER I + R    +    TLE +   F+V+RERVRQIEA
Sbjct: 483 RSASNQILRDRIQGLLKTLTYREREIIKLRYGLGDGYTYTLEEVGRIFKVTRERVRQIEA 542

Query: 275 RAFKKVQESIQKQ 287
           +A +K+Q  ++ Q
Sbjct: 543 KAVRKLQHPVRSQ 555


>gi|323345236|ref|ZP_08085459.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella oralis
           ATCC 33269]
 gi|323093350|gb|EFZ35928.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella oralis
           ATCC 33269]
          Length = 290

 Score =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 70/287 (24%), Positives = 138/287 (48%), Gaps = 12/287 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKI 64
           SI       L +Y+ EI + P++  ++E  LA++ ++ G     A  RLVT++LR VV +
Sbjct: 9   SITNRSSEALDKYLVEIGRAPLISIEDEIELAQKIKKGGPEGERAKERLVTANLRFVVSV 68

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y+  GL +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V
Sbjct: 69  AKQYQHQGLTLTDLIDEGNIGLIKAAQKFDETRGFKFISYAVWWIRQSILQAIAEQSRIV 128

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           ++           +L ++   +      N +   +  ++   N+ E ++           
Sbjct: 129 RLPLNQ-----VGSLNKINHEINKFEQENQRRPSISELSDATNIDEEKIGQSMMADGHHV 183

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           S++A     + N+    D +    D +    ++ E      N +     VL  RE  I +
Sbjct: 184 SIDAPFQDGEDNT--MLDVMPGGDDSRTDRNVDHESMAMELNSVLSR--VLKDREITIIK 239

Query: 245 ARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
                  +   LE +  +  ++RERVRQI  ++  K+++S   ++ +
Sbjct: 240 ECFGIGCHEKGLEEIGDQLGLTRERVRQIREKSIAKLRDSGNAKILM 286


>gi|145596092|ref|YP_001160389.1| RpoD family RNA polymerase sigma factor [Salinispora tropica
           CNB-440]
 gi|145305429|gb|ABP56011.1| RNA polymerase, sigma 70 subunit, RpoD family [Salinispora tropica
           CNB-440]
          Length = 332

 Score =  204 bits (519), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 78/303 (25%), Positives = 135/303 (44%), Gaps = 38/303 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH---------------------GDLSAAHR 52
           Y+HEI + P+L+   E  L+K      Y EH                         A   
Sbjct: 40  YLHEISRTPLLDAATEVDLSKAIEAGLYAEHLLDEDRVPAGVEKAELQRLVAEGARAKDL 99

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            + ++LRLVV IA  Y   G+P+ +++ EGN GL++AV+KFD ERGF+ +TY+ WWI+ A
Sbjct: 100 FIRANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQA 159

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   I +    V++        L  ++ R++   + +T       +   IA  L V+   
Sbjct: 160 ISRAIAQQERTVRLPVH-----LVEDVNRMRNVARQLTRELGSDPEPEQIATALGVTVER 214

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           V  +        SL+  +   D   +   D +    D       +       R  +   +
Sbjct: 215 VNELVRWSQDTVSLDTPV--GDDGDTNLGDLVA---DSDAPSPEDIVLTGLERQRIEGLL 269

Query: 233 SVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
           S L+ R   I  AR   E+    +L  ++S F +SRER+RQ+E +A  +++E  + +   
Sbjct: 270 SHLDDRSAGIMRARYGLEDGREHSLTEVASRFSLSRERIRQLEIQALGRLRELARAEGLQ 329

Query: 291 SSS 293
           +++
Sbjct: 330 AAA 332


>gi|328950970|ref|YP_004368305.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Marinithermus
           hydrothermalis DSM 14884]
 gi|328451294|gb|AEB12195.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Marinithermus
           hydrothermalis DSM 14884]
          Length = 477

 Score =  203 bits (518), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 65/235 (27%), Positives = 110/235 (46%), Gaps = 10/235 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L+ ++LRLVV IA  Y G GL   +++ EGN GL++AV+KF+ +R ++ +TY+ WW
Sbjct: 237 ARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRYKFSTYATWW 296

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      ++I     +      L R    LQ         E++   A     
Sbjct: 297 IRQAINRAIADQARTIRIPVHMVE--TINKLTRTARQLQQEKGREPSYEEIAE-AMGPGW 353

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
               V           SL   I   D+  S + D++  +H       ++   +      L
Sbjct: 354 DAKRVEETFKIAQEPVSLETPI--GDEKDSFYGDFIPDEH---MASPVDAAAQSLLSEEL 408

Query: 229 TRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +++S L+ RE  + + R+        TLE + + F V+RER+RQIE +A +K++
Sbjct: 409 EKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLK 463


>gi|298490639|ref|YP_003720816.1| RpoD subfamily RNA polymerase sigma 70 subunit ['Nostoc azollae'
           0708]
 gi|298232557|gb|ADI63693.1| RNA polymerase, sigma 70 subunit, RpoD subfamily ['Nostoc azollae'
           0708]
          Length = 327

 Score =  203 bits (518), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 65/305 (21%), Positives = 133/305 (43%), Gaps = 52/305 (17%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYRE----------------------------------- 43
           Y+ EI ++P+L +++E V  K+ ++                                   
Sbjct: 23  YLREIGRVPLLTREQEIVYGKQVQQMMTLLDAKEVLAKKLDHEPSLPEWAAHVNQSETEV 82

Query: 44  ----HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                    A  +++ ++LRLVV IA  Y+   +   +++ EG +GL + V+KFDP RG+
Sbjct: 83  KQTVAQGKRAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPMRGY 142

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWI+ A+   I +    +++     +K     L ++K   + +     +    
Sbjct: 143 KFSTYAYWWIRQAITRAIAQQGRTIRLPIHITEK-----LNKIKKVQRELAQKLGRSPSP 197

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IAK+L +  +++           SL+  +   D   ++ Q+ L  +    E    ++ 
Sbjct: 198 TEIAKELELEPAQIREYLNMARQPVSLD--VRVGDNQDTELQEMLEDEGPSPEYYTTQEF 255

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
            R++    L   ++ L P++R +   R   E+   ++L  +     +SRERVRQ+E +A 
Sbjct: 256 LRQD----LNNLLAELTPQQREVLALRFGLEDGNEMSLAKVGERLNLSRERVRQLEHQAL 311

Query: 278 KKVQE 282
             ++ 
Sbjct: 312 AHLRR 316


>gi|116619924|ref|YP_822080.1| RpoD family RNA polymerase sigma factor [Candidatus Solibacter
           usitatus Ellin6076]
 gi|116223086|gb|ABJ81795.1| RNA polymerase, sigma 70 subunit, RpoD family [Candidatus
           Solibacter usitatus Ellin6076]
          Length = 518

 Score =  203 bits (518), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 64/246 (26%), Positives = 114/246 (46%), Gaps = 12/246 (4%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R+ E     A   LV ++LRLVV +A  Y   GL + +++ EGNIGLM+A  KF+  RG+
Sbjct: 270 RHGEAEAERAKKDLVEANLRLVVSVAKKYVNRGLHLLDLIQEGNIGLMRAADKFEYRRGY 329

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWI+ A+   I      ++I    N+      + +     + +     +    
Sbjct: 330 KFSTYATWWIRQAITRAIADQSRTIRIPVHMNES-----MNKFLRATRELEKELGRTPTN 384

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I +++++   +V  +        SL   +       S   D +    D      ++  
Sbjct: 385 DEIGRRMDIPVEKVQKLKTISRDPVSLETPV--GRDGESALGDLI---EDRWVGSPVDAV 439

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAF 277
              N R+     +  L+P+E ++   R     E   TLE +  EF+V+RER+RQIEA+A 
Sbjct: 440 IESNVRDETAGILKTLSPKEEKVIRMRFGIGCEREHTLEEIGQEFDVTRERIRQIEAKAL 499

Query: 278 KKVQES 283
           ++++  
Sbjct: 500 RQLRAP 505



 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 33/180 (18%), Positives = 68/180 (37%), Gaps = 14/180 (7%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHL--RLVVKIAMGYR 69
            +  +  Y+ E+  +P+L ++ E  LA+R  E G L     +  S L  R+VV +A   +
Sbjct: 58  TDDPVRVYLREMGAVPLLTREGEVDLARRM-ERGKLRMQKAISRSALVQRVVVDVADQLK 116

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPE----RGFRLATYSMWWIKAAMQEYILRSWSLVK 125
              + I  VV  G+      V++  P     R      ++   +     + +        
Sbjct: 117 RANIEIESVVDLGD------VEEGSPADVKVRNEAAKHFADIVVLHKKLQQLEDKVEATP 170

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNL-KPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           + +   +KRL   L R K            +  +    A+++  +  E+  ++  +   E
Sbjct: 171 LASKKPRKRLCAKLNRSKVETSLAIRRAPFRLIKWKEFAREIERAVDEISHLDSEIKRLE 230


>gi|71908137|ref|YP_285724.1| RNA polymerase sigma factor RpoS [Dechloromonas aromatica RCB]
 gi|71847758|gb|AAZ47254.1| RNA polymerase, sigma 38 subunit, RpoS [Dechloromonas aromatica
           RCB]
          Length = 309

 Score =  203 bits (518), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 73/270 (27%), Positives = 139/270 (51%), Gaps = 13/270 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L   EE   ++  RE GD SA  R++  +LRLVV IA  Y   G+P+ ++
Sbjct: 42  YLSEIGAKPLLTPAEELATSRLVRE-GDFSARQRMIEHNLRLVVNIAKHYLNRGIPLLDL 100

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL+ A++KFDPERGFR +TY+ WWI+  ++  I+     +++       +    
Sbjct: 101 IEEGNLGLIHALEKFDPERGFRFSTYATWWIRQNIERGIMNQSRTIRLPVHI--VKEINV 158

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           + R   HL++    +   E++  +  +       ++S+N  +A   SL+A +      + 
Sbjct: 159 VLRAMRHLESADKRDSTVERIALLIDRPVADVRRILSLNEHIA---SLDAPLEI--DPNH 213

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLE 256
              + +  D +   + L++  E  +   ++   +  L  R+R + E R         TL+
Sbjct: 214 TMAEVIADDGESDPESLLQSSEVGS---LVDDWLEQLTERQRSVIERRYGLSGADLATLD 270

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            ++ +  ++RERVRQI+     ++++ I++
Sbjct: 271 VIACDLGLTRERVRQIQMEGLDRLRKIIKR 300


>gi|315185771|gb|EFU19537.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           thermophila DSM 6578]
          Length = 338

 Score =  203 bits (518), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 74/302 (24%), Positives = 140/302 (46%), Gaps = 39/302 (12%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEY--------------VLA-------------KRYR 42
           ++    L+ Y+ +I   P+L  +EE+               L+             +R  
Sbjct: 36  LSDADALALYLKQISSYPLLTPEEEHWIGGEIQRIKLRLRELSSLPEEQRAHHFEEERRL 95

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           +       +R++T++LRLVV IA  Y+  GL + +++ EGNIGL++AV++FD  +G R +
Sbjct: 96  DQRLRELKNRMITANLRLVVSIAKKYQHRGLSLLDLIDEGNIGLIEAVERFDYTKGCRFS 155

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY  WWI+ A+ + +     +++I        +   ++ +    + +     +      +
Sbjct: 156 TYGTWWIRQAIVKSLADKSRVIRIPIH-----MLNTIKNVFMLSKELAQELGRDPTEEEL 210

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           ++   + +  V  +        SL+  I   ++N +   D +  D D   Q   EK   +
Sbjct: 211 SRYTGLPDRRVAEIMQVSQETASLD--ITVDEENMTTLGDLVSDDED---QGPFEKVFHR 265

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             R++L  ++S L+ RER +   R     E P+TLE       ++RERVRQI+ +A  K+
Sbjct: 266 YLRDVLLEALSDLSERERNVISLRFGLNGEGPLTLEETGKLLGITRERVRQIQEKALAKL 325

Query: 281 QE 282
           +E
Sbjct: 326 RE 327


>gi|284031338|ref|YP_003381269.1| RpoD subfamily RNA polymerase sigma-70 subunit [Kribbella flavida
           DSM 17836]
 gi|283810631|gb|ADB32470.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Kribbella flavida
           DSM 17836]
          Length = 316

 Score =  203 bits (518), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 73/307 (23%), Positives = 133/307 (43%), Gaps = 45/307 (14%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY----------------REHGD------- 46
           ++G+  +  Y+ EI + P+L  +EE  LA+                  R+ G        
Sbjct: 11  IDGKDSVGLYLEEIARTPLLTAEEEVELAETVEAGLLAEQLLAEGRVGRKKGGAPKYATE 70

Query: 47  ----------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                       A  R VT++LRLVV IA  Y    +P+ ++V EGN GL++AV+KFD  
Sbjct: 71  EELEWLAAEGQRAQQRFVTANLRLVVSIARRYGRSQMPLLDLVQEGNTGLIRAVEKFDYR 130

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +GF+ +TY+ WW++ A+   I +   +V++     +      L ++    + +     + 
Sbjct: 131 KGFKFSTYATWWVRQAITRGIAQQARVVRLPVHVVE-----QLNQIGSARRTLERKLGRE 185

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
            ++  IA +L++ E  V  +        SL+  I   D+  +   D +  +       L+
Sbjct: 186 PEIDEIAAELDLDEERVTELIRIGRDHISLDNPI--DDEGETSLGDLIAAETAPGPDQLV 243

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT--LENLSSEFEVSRERVRQIEA 274
                   R+ L   +  L+PR   +   R    +     L ++ +   +S ERVRQIE 
Sbjct: 244 ADASD---RSGLFSLVDQLDPRSADVIRRRYGLHDGRQAKLADIGAVHGISAERVRQIER 300

Query: 275 RAFKKVQ 281
            A  +++
Sbjct: 301 EALGRLR 307


>gi|77165531|ref|YP_344056.1| hypothetical protein Noc_2066 [Nitrosococcus oceani ATCC 19707]
 gi|76883845|gb|ABA58526.1| RNA polymerase, sigma 70 subunit, RpoD [Nitrosococcus oceani ATCC
           19707]
          Length = 579

 Score =  203 bits (518), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 71/238 (29%), Positives = 119/238 (50%), Gaps = 12/238 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  ++V ++LRLVV +A  YR  GL   +++ EGNIGLM+AV KFD  RG++ +TY+ 
Sbjct: 339 QRAKAQMVEANLRLVVSVAKKYRNRGLTFLDLIQEGNIGLMKAVDKFDYHRGYKFSTYAH 398

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I     +K     L R    L+       +PE    +A++L
Sbjct: 399 WWIRQAITRAIDDQSRTIRIPVHVMEK--LSKLNRASYQLRQEKGREGRPE---ELAERL 453

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +SE ++  M+       SL   +       SQ  + +    D Q    +E       + 
Sbjct: 454 ALSEQQIHRMHEIAKQPISLETPL--GKDEDSQLGELM---EDEQVPNPMEVAITAGLQT 508

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              + ++ L+PRE ++   R     +   TL  ++ +F++SRER+RQIEA+A  K++ 
Sbjct: 509 GAQQLLAALSPREAQVVAMRFGIGMDTDHTLGEVAQQFDLSRERIRQIEAQALGKLRR 566


>gi|119513754|ref|ZP_01632741.1| Sigma 28 (Flagella/Sporulation) [Nodularia spumigena CCY9414]
 gi|119461595|gb|EAW42645.1| Sigma 28 (Flagella/Sporulation) [Nodularia spumigena CCY9414]
          Length = 327

 Score =  203 bits (518), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 64/305 (20%), Positives = 131/305 (42%), Gaps = 52/305 (17%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYRE----------------------------------- 43
           Y+ EI ++P+L + EE +  K+ ++                                   
Sbjct: 23  YLREIGRVPLLTRDEEIIFGKQVQQMMTLLDAKQALAKELDHDPSLPEWAAQVNLPEKEV 82

Query: 44  ----HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                    A  +++ ++LRLVV IA  Y+   +   +++ EG +GL + V+KFDP RG+
Sbjct: 83  TQIVAQGKRAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGY 142

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWI+ A+   I +    +++     +K     L ++K   + +     +    
Sbjct: 143 KFSTYAYWWIRQAITRAIAQQGRTIRLPIHITEK-----LNKIKKVQRELAQKFGRSPTP 197

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IA +L +   ++           SL+  +   D   ++ Q+ L  +    E    ++ 
Sbjct: 198 TEIAHELELEPMQIREYLNMARQPVSLD--VKVGDNQDTELQEMLEDEGPSPEYYTTQEF 255

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
            R++    L   ++ L P++R++   R   E+   ++L  +     +SRERVRQ+E +A 
Sbjct: 256 LRQD----LNNLLAELTPQQRQVLALRFGLEDGNEMSLAKVGERLNLSRERVRQLEHQAL 311

Query: 278 KKVQE 282
             ++ 
Sbjct: 312 AHLRR 316


>gi|327539483|gb|EGF26098.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhodopirellula
           baltica WH47]
          Length = 562

 Score =  203 bits (518), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 76/298 (25%), Positives = 145/298 (48%), Gaps = 23/298 (7%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR------YREHGDLSAAHRLVT 55
           +R  M  + +G+  L   +  + +   L  +    L++R      YR+  D +A   L  
Sbjct: 264 HRSTMPGMPSGD-ELRSELRSLMR---LTYETPRTLSRRVDRCDTYRDDYD-AAKRVLSA 318

Query: 56  SHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQE 115
            +LRLVV IA  YR  GL   +++ EGN GLM+AV KF+  RG++ +TY+ WWI+ A+  
Sbjct: 319 GNLRLVVSIAKKYRNRGLSFLDLIQEGNTGLMRAVDKFEHARGYKFSTYATWWIRQAITR 378

Query: 116 YILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
            I      +++        +   + +++   + +   + +      ++K+  +S  +   
Sbjct: 379 AIADQSRTIRVPVH-----MIDTMNKIRQITRDLVQEHGREPTAEEVSKRSGLSLDDTRV 433

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
           +        SL+  +   D + S + ++L    D ++   + +  R+  ++ +  +M  L
Sbjct: 434 ILKMSRQPLSLDQPV--GDHDDSVFGEFL---QDHRDDDPLVETNREALKHQIDLAMETL 488

Query: 236 NPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           N RER I   R    +    TLE +   F+V+RERVRQIE++A +K+Q+  + +  +S
Sbjct: 489 NYREREILRLRYGLADGYTYTLEEVGRIFQVTRERVRQIESKAVRKLQQPYRAKSLVS 546



 Score = 38.6 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 34/210 (16%), Positives = 76/210 (36%), Gaps = 31/210 (14%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-----REHGDLSAAHRLVT 55
           ++R++       E  +  Y+ ++ +IP+L + +E   A++      R    + A   ++ 
Sbjct: 84  VSRRDEFPTDPTEDPVRMYLMQMGQIPLLTRDQEVAAAQQIEATRERYRHCMMATDFMLQ 143

Query: 56  SHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ- 114
           + L+L+ ++          I   V+        A +K    +           I    + 
Sbjct: 144 AALKLLQQVRDKQLRLDRTIEVSVTN-------AAEKKAIMK----------RIVPNTRT 186

Query: 115 -EYILRSWS---LVKIGTTANQKRLFFNLR----RLKGHLQAITDNNLKPEQVVAIAKKL 166
            +Y+LR      +V I ++   +R     R    R    ++ + + NL+  ++  I +KL
Sbjct: 187 LDYLLRQNRGDYMVAINSSLPMRRRRAAWRNLVIRRNKAVRLVEEMNLRTNKLQPIFEKL 246

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKN 196
             S   +  +   LA           S   
Sbjct: 247 RRSCERMQEIKAILADAHRSTMPGMPSGDE 276


>gi|56752254|ref|YP_172955.1| RNA polymerase sigma factor SigC [Synechococcus elongatus PCC 6301]
 gi|81300658|ref|YP_400866.1| RNA polymerase sigma factor SigC [Synechococcus elongatus PCC 7942]
 gi|56687213|dbj|BAD80435.1| group2 RNA polymerase sigma factor RpoD5 [Synechococcus elongatus
           PCC 6301]
 gi|81169539|gb|ABB57879.1| group2 RNA polymerase sigma factor SigC [Synechococcus elongatus
           PCC 7942]
          Length = 398

 Score =  203 bits (518), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 66/242 (27%), Positives = 122/242 (50%), Gaps = 13/242 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   ++ ++LRLVV +A  Y+  GL + ++V EG +GL +AV+KFDP +G+R +TY+ 
Sbjct: 157 QRAKDHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAY 216

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   I      +++     +K     L R+K   + I     +   +  IA++L
Sbjct: 217 WWIRQGITRAIATQSRTIRLPVHVTEK-----LNRIKKAQRKIAQTKGRTANLEEIAQEL 271

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++  +V  +  R+    SL   +    +  ++  D L    +  +    E+  +++  N
Sbjct: 272 EMTPDQVREVLLRVPKSISLETRV--GKEKDTELGDLL----ETTDFTPEERLTQESLSN 325

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L R +  LN RER +   R    +    +L  +    ++SRERVRQIEA+A +K++   
Sbjct: 326 DLQRLLLELNHRERDVIRMRFGLRDGQIYSLAEIGQVLDLSRERVRQIEAKALQKLRHPR 385

Query: 285 QK 286
           ++
Sbjct: 386 RR 387


>gi|254796694|ref|YP_003081530.1| RNA polymerase sigma-70 factor (RpoD) [Neorickettsia risticii str.
           Illinois]
 gi|254589929|gb|ACT69291.1| RNA polymerase sigma-70 factor (RpoD) [Neorickettsia risticii str.
           Illinois]
          Length = 620

 Score =  203 bits (518), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 75/274 (27%), Positives = 130/274 (47%), Gaps = 33/274 (12%)

Query: 37  LAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           L ++   H D +  A HR+V ++LRLV+ IA  Y   G+P  +++ EGNIGLM+AV KFD
Sbjct: 347 LTRKVATHLDNANAAKHRMVEANLRLVISIAKKYTNRGMPFPDLIQEGNIGLMKAVDKFD 406

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             RG + +TY+ WW + A+   I    S+V+     ++        ++    + + + N 
Sbjct: 407 HRRGHKFSTYATWWCRQAITRAIADCGSIVRKPVHIHE-----TANKVMRTRRRLYNLNG 461

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +   V  IA  L +S  +V           SL + +   D NS  + D++    D     
Sbjct: 462 REPTVEEIANLLKISPDKVKKSLKVNQDPISLESPVGD-DSNSGSFGDFI---EDKNAVS 517

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP---------------------- 252
            ++    KN R +L  ++++L+PRE +I   R    N                       
Sbjct: 518 QVDVVLSKNLRKVLDEALAMLSPREEKILRYRFGLCNSVHSPEDEHYLKSLKIDLNRGTN 577

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +TLE +   + V+RER+RQIE+++ +K++   + 
Sbjct: 578 LTLEQVGILYNVTRERIRQIESKSLRKMRSPSRS 611


>gi|312885799|ref|ZP_07745431.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Mucilaginibacter
           paludis DSM 18603]
 gi|311301606|gb|EFQ78643.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Mucilaginibacter
           paludis DSM 18603]
          Length = 285

 Score =  203 bits (518), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 72/278 (25%), Positives = 134/278 (48%), Gaps = 14/278 (5%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S        L  Y++E+ +  +L  +EE VLA++ R  GD +A  RL  ++LR VV +A 
Sbjct: 9   SFTNRDSQSLETYLNELGRTDLLSAEEEVVLAQKIRL-GDQAALDRLTKTNLRFVVSVAK 67

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y+  GLP+S+++SEGN+GLM+A KKFD  +GF+  +Y++WWI+  +   I     ++++
Sbjct: 68  KYQHQGLPLSDLISEGNVGLMKAAKKFDETKGFKFISYAVWWIRQCILSAIAEHSRMIRL 127

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
                      ++ ++   L  +     +      +A+ L  SE +V           S 
Sbjct: 128 PMNQ-----VGDITKMNKALALLEQQMERQPTTNELAEYLETSEDKVSDALYFATRTASY 182

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           +A   + D+N+      L+    G EQ    +    + +  + + +S L  R++ +    
Sbjct: 183 DAPFRTEDENN------LLDVLPGNEQATDHELMVLSNQQEVRQLLSTLTSRDQEVIRWT 236

Query: 247 RLQENPVTLE--NLSSEFEVSRERVRQIEARAFKKVQE 282
              +    L   +++    +S ERVRQI  +A + ++E
Sbjct: 237 FGLDGKTALPPIDIAPLLGISAERVRQIRNQALQTLRE 274


>gi|269925235|ref|YP_003321858.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
 gi|269788895|gb|ACZ41036.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
          Length = 344

 Score =  203 bits (517), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 74/301 (24%), Positives = 130/301 (43%), Gaps = 37/301 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD-------------------------LS 48
             L  Y+ EI +  +L  +EE  LA+      +                          +
Sbjct: 47  DSLGIYLREIGRAQLLTAEEEVALAQAIERGQEAEQRLQSDDISPEELDDLKKAVEEGKA 106

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A H+L+  +LRLVV IA  Y G+G+P+++++ EGN+GLM+A +KFD  RGFR +TY+ WW
Sbjct: 107 ARHKLIEHNLRLVVSIARRYVGHGMPLADLIEEGNLGLMRAAEKFDWRRGFRFSTYATWW 166

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   +      +++     +      L ++    Q ++    +      +A+   +
Sbjct: 167 IRQAVTRGLAEGGRTIRLPVHVGE-----ALTKIGRETQRLSLELGREPTNQELAEATGL 221

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S   +           SL A +   +   +   + L        + + +          +
Sbjct: 222 SPERIDEYKNASRLPLSLEAPL--GEDGETNLGEVLEDTEAANPEHIADHTMLG---EDI 276

Query: 229 TRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R++  LN R+R I   R       P+TLE    +  V+RER RQIE  A  ++++S  K
Sbjct: 277 KRALERLNERQRAIIIMRYGLYGGQPMTLEAAGRKLGVTRERARQIEQEALNRLRQSDAK 336

Query: 287 Q 287
           Q
Sbjct: 337 Q 337


>gi|116074180|ref|ZP_01471442.1| Possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9916]
 gi|116069485|gb|EAU75237.1| Possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9916]
          Length = 364

 Score =  203 bits (517), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 80/256 (31%), Positives = 123/256 (48%), Gaps = 15/256 (5%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           E   L KR RE     A  R++ ++LRLVV +A  Y+  GL + ++V EG +GL +AV+K
Sbjct: 110 ESKELQKRLREG--RRARDRMIQANLRLVVTVAKKYQQRGLELLDLVQEGTLGLERAVEK 167

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FDP RGFR +TY+ WWI+  +   I      +++     +K     L R+K   Q I  N
Sbjct: 168 FDPTRGFRFSTYAYWWIRQGITRAIATQSRTIRLPVHVTEK-----LNRIKKVQQEIATN 222

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +   +  +++ L +SE  V     R+    SL   +       +Q  D L   H   E
Sbjct: 223 EGRIASISDLSRALGISEETVRLTLMRVPRSVSLETRV--GKDQDTQLGDLLEDCHATPE 280

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVR 270
           Q L +     +    L   +  L  RE  +   R   E+  P+TL  +     +SRERVR
Sbjct: 281 QTLTKNSLHSD----LEELLGELTAREAEVIRRRFGLEDDTPLTLAEIGETMGLSRERVR 336

Query: 271 QIEARAFKKVQESIQK 286
           QIE RA  K+++  ++
Sbjct: 337 QIETRALLKLRQPQRR 352



 Score = 39.8 bits (92), Expect = 0.51,   Method: Composition-based stats.
 Identities = 12/42 (28%), Positives = 24/42 (57%)

Query: 11 NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHR 52
          +G   L  Y+ +I ++ +L  +EE +LA++ ++   L A  R
Sbjct: 5  SGNDLLRLYLQDIGRVDLLTNEEEVLLARQVQQREVLLAEER 46


>gi|142114|gb|AAA22047.1| RNA polymerase sigma-subunit [Nostoc sp. PCC 7120]
          Length = 416

 Score =  203 bits (517), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 65/256 (25%), Positives = 132/256 (51%), Gaps = 14/256 (5%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
               ++ +  G L +   ++ ++LRLVV +A  Y+  GL + ++V EG +GL +AV+KFD
Sbjct: 164 VEELEKMQSQG-LQSKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFD 222

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P +G+R +TY+ WWI+  +   I  S   +++     +K     L ++K   + I     
Sbjct: 223 PTKGYRFSTYAYWWIRQGITRAIATSSRTIRLPVHITEK-----LNKIKKAQRKIAQEKG 277

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +   +  +A +L+++ ++V  +  R+    SL   +       ++  + L  D    E++
Sbjct: 278 RTPTLEDLAIELDMTPTQVREVLLRVPRSVSLETKV--GKDKDTELGELLETDGVTPEEM 335

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQI 272
           L+    R++ +  L   ++ L  RER +   R      +P +L  +    ++SRERVRQI
Sbjct: 336 LM----RESLQRDLQHLLADLTSRERDVILMRFGLADGHPYSLAEIGRALDLSRERVRQI 391

Query: 273 EARAFKKVQESIQKQV 288
           E++A +K+++  ++ +
Sbjct: 392 ESKALQKLRQPKRRNL 407


>gi|88809912|ref|ZP_01125417.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 7805]
 gi|88786102|gb|EAR17264.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 7805]
          Length = 355

 Score =  203 bits (517), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 74/331 (22%), Positives = 139/331 (41%), Gaps = 55/331 (16%)

Query: 2   NRKNMSIIVNGEIGLSR-YIHEIRKIPMLEKQEEYVLAKRYREHGDLS------------ 48
            +   S     ++ L R Y+ +I ++P+L  Q+E  L ++ +E  +L             
Sbjct: 32  AKTTASRPSGTDVDLVRSYLRDIGRVPLLSHQQEITLGRQVQELMELESVEAELQEKRGG 91

Query: 49  ----------------------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
                                       A  R+V ++LRLVV +A  Y    + + +++ 
Sbjct: 92  EAVLAAELAKAAGLSAVQLKRKLQAGRRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQ 151

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           EG IGL++ V+KFDP RG++ +TY+ WWI+  +   I      +++     +      L 
Sbjct: 152 EGTIGLVRGVEKFDPTRGYKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITE-----MLN 206

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
           +LK   + ++    +   V  +A  + + E EV  + CR     SL   +   D + ++ 
Sbjct: 207 KLKKGQRELSQELGRTPSVTELASFVELPEDEVKELMCRARQPVSLEMKV--GDGDDTEL 264

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENL 258
            D L  D     ++  E+ E +  +  L   +  L   + R+   R     E P++L  +
Sbjct: 265 LDLLAGDG----ELPSEQVEGECLKGDLRDLLGQLPELQERVLRMRYGMDGEEPMSLTGI 320

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
                +SR+RVR +E      ++  +  QVE
Sbjct: 321 GRVIGISRDRVRNLERDGLAGLRR-LSDQVE 350


>gi|257452079|ref|ZP_05617378.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. 3_1_5R]
 gi|257466122|ref|ZP_05630433.1| RNA polymerase sigma factor RpoD [Fusobacterium gonidiaformans ATCC
           25563]
 gi|315917279|ref|ZP_07913519.1| RNA polymerase sigma factor RpoD [Fusobacterium gonidiaformans ATCC
           25563]
 gi|317058628|ref|ZP_07923113.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. 3_1_5R]
 gi|313684304|gb|EFS21139.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. 3_1_5R]
 gi|313691154|gb|EFS27989.1| RNA polymerase sigma factor RpoD [Fusobacterium gonidiaformans ATCC
           25563]
          Length = 272

 Score =  203 bits (517), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 82/275 (29%), Positives = 141/275 (51%), Gaps = 16/275 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           LS Y+ +IR+   LEK+EE  L  +  + GD  A ++L+  +LRLVV +A GYR  G+ +
Sbjct: 7   LSLYLKDIRQYRTLEKEEELDLVIK-AQSGDEEAKNQLILCNLRLVVNVAKGYRSKGMNL 65

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++SEGN+GL++A++KFD  +GFR +TY++WWIK ++ + I+     ++I +       
Sbjct: 66  IDLISEGNLGLIRAIEKFDVGKGFRFSTYAVWWIKQSISKAIIFKGREIRIPSYR----- 120

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           +  L ++  ++            V  +A+ L +  ++V  +        SL+  I     
Sbjct: 121 YDILNKINKYVTETVKLCGIYPTVEEVAEYLKMPVNKVEEVMIEFQEPMSLSTEIGED-- 178

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPV 253
                  +L     G E+   EK   K  +  L   +S L  RE+ I + R   +     
Sbjct: 179 ------IYLEDTLSGAEEHFEEKVYYKMMQQRLKDILSRLESREQEILKLRFGLDGYEIH 232

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           TLE++   F ++RERVRQIE    KK++    K++
Sbjct: 233 TLEDIGKNFNITRERVRQIEKNTLKKLKRKYTKEL 267


>gi|218439766|ref|YP_002378095.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
 gi|218172494|gb|ACK71227.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
          Length = 418

 Score =  203 bits (517), Expect = 2e-50,   Method: Composition-based stats.
 Identities = 61/250 (24%), Positives = 131/250 (52%), Gaps = 14/250 (5%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           ++ ++ G + A + ++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV+KFDP +G
Sbjct: 170 EQIQKAG-IEAKNHMIKANLRLVVSVAKRYQNRGLELLDLIQEGTLGLERAVEKFDPTKG 228

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           +R +TY+ WWI+  +   I     ++++     +K     L ++K   + +     +   
Sbjct: 229 YRFSTYAYWWIRQGITRAIATQSRIIRLPVHITEK-----LNKIKKAQRKMAQIKGRTPT 283

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           +  +A +++++  ++  +  R+    SL   I    +  ++  D L       E+ L+ +
Sbjct: 284 MEELAVEVDMTAPQIREVLMRVPRSVSLE--IKVGKEKDTELVDLLETTEASPEESLVNE 341

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARA 276
             R++    L   ++ L  RER + + R         +L ++    ++SRERVRQIEA+A
Sbjct: 342 TLRQD----LQNLLADLTTREREVIQMRYGFKDGKCYSLADIGRALQLSRERVRQIEAKA 397

Query: 277 FKKVQESIQK 286
            +K+++  ++
Sbjct: 398 IQKLRQPKRR 407


>gi|50955189|ref|YP_062477.1| ECF subfamily RNA polymerase sigma-70 factor [Leifsonia xyli subsp.
           xyli str. CTCB07]
 gi|50951671|gb|AAT89372.1| RNA polymerase, sigma-70 family factor [Leifsonia xyli subsp. xyli
           str. CTCB07]
          Length = 308

 Score =  203 bits (517), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 73/309 (23%), Positives = 139/309 (44%), Gaps = 38/309 (12%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------------------ 42
           M    M+++      +  Y++ I +  +L  ++E  LAKR                    
Sbjct: 1   MRGDTMTVLEVTNDPVRDYLNSIGRTWLLTAEDEVSLAKRIEVGVLAGERLATRPGLSPR 60

Query: 43  --------EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                         A  R + ++LRLVV IA  Y G GL + +++ EGN+GL++AV+KFD
Sbjct: 61  EKRELHVLSDDGKRAFERFIEANLRLVVSIAKRYAGRGLAVMDLIQEGNLGLVRAVEKFD 120

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G + +TY+ WWI+ ++   I  +  +++I     +K     L R++  L        
Sbjct: 121 YRTGNKFSTYATWWIRQSILRGIADTARVIRIPVHTVEK--IDKLDRIRRDLG---GELG 175

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +   +  IA   +++ +EV  +    +   SL   +   +   ++  D +    DG    
Sbjct: 176 RTPTLEEIADAASLTPAEVHKLQMSDSETVSLAVPV--GENEGAELGDLI---EDGDAPG 230

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
             E+ E + R   L   +  L  R+ ++   R   +   P+TL+ + + + ++RERVRQ+
Sbjct: 231 PSERVEVEFRHRDLEERLRELPLRDAKVVRMRFGLDGRKPMTLDEVGAVYGITRERVRQL 290

Query: 273 EARAFKKVQ 281
           E R+ K+++
Sbjct: 291 ETRSLKRLR 299


>gi|292491943|ref|YP_003527382.1| RNA polymerase sigma factor, sigma-70 family [Nitrosococcus
           halophilus Nc4]
 gi|291580538|gb|ADE14995.1| RNA polymerase sigma factor, sigma-70 family [Nitrosococcus
           halophilus Nc4]
          Length = 578

 Score =  203 bits (517), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 71/238 (29%), Positives = 118/238 (49%), Gaps = 12/238 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  ++V ++LRLVV +A  YR  GL   +++ EGNIGLM+AV KFD  RG++ +TY+ 
Sbjct: 338 QRAKAQMVEANLRLVVSVAKKYRNRGLTFLDLIQEGNIGLMRAVDKFDYRRGYKFSTYAH 397

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I     +K     L R    L+       +PE    +A++L
Sbjct: 398 WWIRQAITRAIDDQSRTIRIPVHVMEK--LSKLNRASYQLRQEKGREGRPE---ELAERL 452

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +SE ++  M+       SL   +       SQ  + +    D Q    +E       + 
Sbjct: 453 ALSEQQIHHMHEIAKQPISLETPL--GKDEDSQLGELM---EDEQVPNPMEVAISAGLQA 507

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              + ++ L PRE ++   R     +   TL  ++ +F++SRER+RQIEA+A  K++ 
Sbjct: 508 GTQQLLATLTPREAQVVAMRFGIGMDTDHTLGEVAQQFDLSRERIRQIEAQALSKLRR 565


>gi|91203809|emb|CAJ71462.1| strongly similar to transcription initiation factor sigma RpoD
           [Candidatus Kuenenia stuttgartiensis]
          Length = 551

 Score =  203 bits (517), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 69/248 (27%), Positives = 126/248 (50%), Gaps = 14/248 (5%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y+EH   SA  +L  ++LRLVV IA  YR  GL   +++ EGN GLM+AV K++  RG++
Sbjct: 302 YKEH--ESAKRKLSGANLRLVVSIAKKYRNRGLSFLDLIQEGNTGLMRAVDKYEYRRGYK 359

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I        +   + +++   + +  +  +   + 
Sbjct: 360 FSTYATWWIRQAITRSIADQARTIRIPVH-----MIETMSKIRNISKKLLQDKGREPTIE 414

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            IA+++ +S  E   +        SL+  +   +   S + D++    D + +  +    
Sbjct: 415 EIAREVKISVPEARRVLKISRHQISLDRPV--GESEDSSFGDFI---EDEKAESPVAAAT 469

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFK 278
           ++  ++ +   +  L  RER I + R    +    TLE +   F+V+RERVRQIEA+A +
Sbjct: 470 QEMLKDKIESVLETLTYREREIIKLRYGIGDGYTYTLEEVGKIFKVTRERVRQIEAKAVR 529

Query: 279 KVQESIQK 286
           K+Q  I+ 
Sbjct: 530 KLQHPIRS 537



 Score = 36.3 bits (83), Expect = 6.2,   Method: Composition-based stats.
 Identities = 9/29 (31%), Positives = 19/29 (65%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRY 41
           +  +  Y+ ++ +IP+L + EE +LAK+ 
Sbjct: 93  DDPVRMYLTQMGEIPLLTRDEEIMLAKKI 121


>gi|262195942|ref|YP_003267151.1| RNA polymerase, sigma 32 subunit, RpoH [Haliangium ochraceum DSM
           14365]
 gi|262079289|gb|ACY15258.1| RNA polymerase, sigma 32 subunit, RpoH [Haliangium ochraceum DSM
           14365]
          Length = 298

 Score =  203 bits (517), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 108/299 (36%), Positives = 169/299 (56%), Gaps = 13/299 (4%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M+  ++ E G   Y+  + +I  LE++EE  LA+R+REHGD +AA  LV+S LR V+KIA
Sbjct: 1   MARYISEEPGFQTYVDSVERIAALEREEELALARRWREHGDRAAADALVSSQLRSVLKIA 60

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             YRGYG+ +S++V+EGN+GL++AV +F+PERG R  TY+  W++A +  ++L+ WS+V 
Sbjct: 61  RKYRGYGIYLSDLVAEGNLGLLEAVNRFEPERGLRFFTYARHWVRAFILAHVLKHWSIVD 120

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-AIAKKLNVSESEVISMNCRLA-GD 183
           +GTTA Q ++FF L+    H + +T    + +QV   +A     S  +V +   RLA  D
Sbjct: 121 LGTTAQQSKMFFRLQ--SEHARLLTTLGDQSDQVERQLADTFKTSPEQVRANLQRLARRD 178

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SL+  +         + D L  D   QE      E     RN ++     L+ RER I 
Sbjct: 179 ASLDVPVVDG---GITFLDMLQADTTDQETQTAAAELSSVVRNAVSELWPTLDCRERLIV 235

Query: 244 EARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK----QVELSSSPPL 296
           + R L    +P TL  L  +  ++RERVRQ+EA    +++  + +    +VE +   PL
Sbjct: 236 DERLLPADGDPRTLAALGRQLGLTRERVRQLEAGVKDRLRAVLDRLLGGEVEHAQPAPL 294


>gi|291059871|gb|ADD72606.1| RNA polymerase sigma factor RpoD [Treponema pallidum subsp.
           pallidum str. Chicago]
          Length = 610

 Score =  203 bits (517), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 63/239 (26%), Positives = 113/239 (47%), Gaps = 12/239 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+KF+  +G++ +TY+ 
Sbjct: 370 KKAKDKLINANLRLVVSIAKKYTNRGLLFFDLVQEGNIGLIKAVEKFEYRKGYKFSTYAT 429

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      +++        +   + ++    + +     +      IA++L
Sbjct: 430 WWIRQAITRSISDQARTIRVPVH-----MIEQINKVTRESRQLLQKFGREPSDEEIAQQL 484

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             +  +V  +        SL   I   ++  S   D++    D   +      ER   + 
Sbjct: 485 CWTVEKVKQVKSVAREPISLETPI--GEEEDSSLGDFVP---DADVENPSRVTERVLLKE 539

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +   +S L  RE  +   R   +     TLE +   F+V+RER+RQIEA+A K+++  
Sbjct: 540 EVRSILSALPAREHEVLRMRFGLDGDYSQTLEEVGLYFDVTRERIRQIEAKALKRLRHP 598



 Score = 35.6 bits (81), Expect = 9.1,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           +  +  Y+ +I +  +L  ++E +L+KR  E G+      +  S L L 
Sbjct: 116 DDPVKLYLRDIGQEKLLTAEQEVMLSKRM-EEGEGIIKDIITQSGLLLP 163


>gi|162454145|ref|YP_001616512.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
 gi|161164727|emb|CAN96032.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
          Length = 283

 Score =  203 bits (517), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 103/283 (36%), Positives = 166/283 (58%), Gaps = 7/283 (2%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           M    +    +SRYI  +R+IP L ++EE  LA+R+R+HGD  AA  L  ++LR VV IA
Sbjct: 1   MQTSRDQASAVSRYITHVRQIPELSREEEVELARRWRDHGDEQAAAALALANLRHVVSIA 60

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
           + YR YG+P++++++EGN G++ A++K+DP+RG R  TY+ +WI+A +  +++ SWSLV 
Sbjct: 61  ISYRRYGIPLADLIAEGNFGIVHAIRKYDPDRGNRFVTYAAYWIRAYILNHVIHSWSLVG 120

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDE 184
           +G+   + ++FF LRR +  +  +       E    +A+K      +V+ M  RL A D 
Sbjct: 121 VGSGPLRSKMFFRLRRERARIAGLVGEG--EEGDRLLAEKFGAPAEKVLEMAHRLEARDV 178

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL+  +   +  +    D L  D   QE+     EE    R  LT+++  L+PRER I E
Sbjct: 179 SLDTKVF--EDGARSLVDTLPADDQDQEERFSRAEEGALLRERLTQAVENLDPRERYIVE 236

Query: 245 ARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            R + +    ++L  +     VSRER RQ+EARA KK+++ +Q
Sbjct: 237 TRMMADPEEELSLAEIGRRLGVSRERARQLEARAKKKLRDRLQ 279


>gi|254434698|ref|ZP_05048206.1| RNA polymerase sigma factor, sigma-70 family [Nitrosococcus oceani
           AFC27]
 gi|207091031|gb|EDZ68302.1| RNA polymerase sigma factor, sigma-70 family [Nitrosococcus oceani
           AFC27]
          Length = 595

 Score =  203 bits (516), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 71/238 (29%), Positives = 119/238 (50%), Gaps = 12/238 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  ++V ++LRLVV +A  YR  GL   +++ EGNIGLM+AV KFD  RG++ +TY+ 
Sbjct: 355 QRAKAQMVEANLRLVVSVAKKYRNRGLTFLDLIQEGNIGLMKAVDKFDYHRGYKFSTYAH 414

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I     +K     L R    L+       +PE    +A++L
Sbjct: 415 WWIRQAITRAIDDQSRTIRIPVHVMEK--LSKLNRASYQLRQEKGREGRPE---ELAERL 469

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +SE ++  M+       SL   +       SQ  + +    D Q    +E       + 
Sbjct: 470 ALSEQQIHRMHEIAKQPISLETPL--GKDEDSQLGELM---EDEQVPNPMEVAITAGLQT 524

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              + ++ L+PRE ++   R     +   TL  ++ +F++SRER+RQIEA+A  K++ 
Sbjct: 525 GAQQLLAALSPREAQVVAMRFGIGMDTDHTLGEVAQQFDLSRERIRQIEAQALGKLRR 582


>gi|170692344|ref|ZP_02883507.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia graminis
           C4D1M]
 gi|170142774|gb|EDT10939.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia graminis
           C4D1M]
          Length = 359

 Score =  203 bits (516), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 75/280 (26%), Positives = 130/280 (46%), Gaps = 15/280 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+
Sbjct: 79  DTIQHYLNRISVKPLLTVEEEQKYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGV 137

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++       
Sbjct: 138 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV--I 195

Query: 134 RLFFNLRRLKGHLQAITDN-----NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           R    + R K HL+  + N       +   +  IA     +  EV  +        SL+A
Sbjct: 196 RELNQVLRAKRHLEKNSMNSGEAAERRDASIDDIAYLTGKTTDEVTDILALNEHTASLDA 255

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            ++    +S               +V     + +    +    ++ L+ + R + E R  
Sbjct: 256 PLDLDPASSLLDLLSDDQSQSPDAEV-----QHRELETLTRAWLARLSDKHRHVIERRFG 310

Query: 249 QE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                P TLE L+ E  ++RERVRQI+  A  +++     
Sbjct: 311 LNHIEPATLEELADEMGLTRERVRQIQQEALVRLKRFFAS 350


>gi|86608149|ref|YP_476911.1| RNA polymerase sigma factor, group 1 [Synechococcus sp.
           JA-2-3B'a(2-13)]
 gi|86556691|gb|ABD01648.1| RNA polymerase sigma factor, group 1 [Synechococcus sp.
           JA-2-3B'a(2-13)]
          Length = 361

 Score =  203 bits (516), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 69/310 (22%), Positives = 135/310 (43%), Gaps = 51/310 (16%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------------------------- 43
           E  +  Y++ I ++P ++  EE  L+++ ++                             
Sbjct: 49  EDPVDHYLNTIGRVPRIDHAEEIELSRKIQQKLLIDQARQEWRQQRGEDPSDEALAEALQ 108

Query: 44  ----------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
                          A  +L+ ++LRLVV +A  Y   G+P  +++ EGNIGL++A +KF
Sbjct: 109 ISVSTLRSRIRQGEQAQRKLINANLRLVVSVAKKYLNRGVPFLDLIQEGNIGLIRATEKF 168

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           + ERGFR +TY+ WWI+  +   I      +++        +   +R LK   + +    
Sbjct: 169 NAERGFRFSTYAHWWIRQGITRCIANQARTIRLPVH-----MVDKVRLLKRTNRELMKLQ 223

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            +      +A+ L +   ++  +    A   SL+  +    +  S+  D L    D +++
Sbjct: 224 GRRPTEAELAEALGIKVKKLRMIQQAAALPLSLDVPV--GQEGESRLGDLL---QDERQE 278

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQ 271
              +    ++ +  +  +M  L P ER++ E R   +     TL  +   F ++RER+RQ
Sbjct: 279 QPFQGILVQSMQQDVRSAMQTLKPIERQVLELRYGLDGQQARTLREVGDHFNLTRERIRQ 338

Query: 272 IEARAFKKVQ 281
           IE  A +K++
Sbjct: 339 IERDALRKLR 348


>gi|254388870|ref|ZP_05004102.1| RNA polymerase principal sigma factor hrdD [Streptomyces
           clavuligerus ATCC 27064]
 gi|294813166|ref|ZP_06771809.1| RNA polymerase principal sigma factor hrdD [Streptomyces
           clavuligerus ATCC 27064]
 gi|326441537|ref|ZP_08216271.1| RNA polymerase principal sigma factor hrdD [Streptomyces
           clavuligerus ATCC 27064]
 gi|197702589|gb|EDY48401.1| RNA polymerase principal sigma factor hrdD [Streptomyces
           clavuligerus ATCC 27064]
 gi|294325765|gb|EFG07408.1| RNA polymerase principal sigma factor hrdD [Streptomyces
           clavuligerus ATCC 27064]
          Length = 333

 Score =  203 bits (516), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 73/300 (24%), Positives = 123/300 (41%), Gaps = 40/300 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVL---------AKRYREHG-------------------DL 47
           +  Y+ EI + P+L+  +E  L         A++  + G                     
Sbjct: 36  VGMYLDEIARTPLLDAAKEVELSQIIEAGVYARQILDQGVESDAGGATHKELEALVAEGE 95

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A    + S+LRLVV +A  Y   GLP+ ++V EGN GL++AV+KFD  +GF+ +TY+ W
Sbjct: 96  RAKDVFIRSNLRLVVAVARRYPRSGLPLLDLVQEGNAGLVRAVEKFDYSKGFKFSTYATW 155

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++        L   L R++   +       +  +   IA++L 
Sbjct: 156 WIRQAITRSIADQSRTIRLPVH-----LVEELGRIRRVQREFNREKGREPEAAEIAQELG 210

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
            +   V  +        SLN  +   D   +Q+ D L    D       +      R   
Sbjct: 211 STPERVTDVLDWARDPVSLNMAV--DDAGETQFGDLL---EDTSAVSPEQSVLTLLRSEG 265

Query: 228 LTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L   +  L+ R   I   R         TL  +  E  ++RER+RQIE  A  +++   +
Sbjct: 266 LDDLIGKLDQRTASIIRMRYGIMDGRERTLTEVGKEHGLTRERIRQIEKHALLELKRMAR 325


>gi|163846411|ref|YP_001634455.1| sigma-70 family RNA polymerase sigma factor [Chloroflexus
           aurantiacus J-10-fl]
 gi|222524178|ref|YP_002568649.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus sp.
           Y-400-fl]
 gi|163667700|gb|ABY34066.1| RNA polymerase sigma factor, sigma-70 family [Chloroflexus
           aurantiacus J-10-fl]
 gi|222448057|gb|ACM52323.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus sp.
           Y-400-fl]
          Length = 313

 Score =  203 bits (516), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 72/309 (23%), Positives = 135/309 (43%), Gaps = 38/309 (12%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------- 43
           R   +I  +    +  Y++EI   P+L  ++E  LA+   +                   
Sbjct: 2   RNPTTIGRSASDPIVLYLNEIGAEPLLTFEQEQHLAQTMSQGRRAAERLHNEPLLPLAEK 61

Query: 44  -------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                  +    A  +L+ S+LRLVV IA  Y+G+GL + +++ EG++GLM+AV KFD  
Sbjct: 62  QRLIAQVNAGEQARAQLINSNLRLVVSIARRYQGHGLSLLDLIQEGSVGLMRAVDKFDAS 121

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RG + +TY+ +WI+ ++   I      V++     ++     L RL    Q ++    + 
Sbjct: 122 RGLKFSTYATYWIRQSIGRAIADHSRTVRLPVHLGER-----LSRLSRLRQELSQQLDRE 176

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
             +  +A+   +S  +V           SL+     ++       + L    D  +    
Sbjct: 177 PTLEELAQAAGLSVEQVERAEQAGLAPTSLDEP--HTEDGGGALAEIL---TDPLQPTPF 231

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEA 274
           ++      +  +  ++  L+PRER I   R   +     TLE +     ++RERVRQ+E 
Sbjct: 232 DEVSESMLQADVQHALQQLSPRERSILRLRYGLDGEPMHTLEQIGQRLRLTRERVRQLEH 291

Query: 275 RAFKKVQES 283
            A +K+++ 
Sbjct: 292 EALRKLRDP 300


>gi|15639484|ref|NP_218934.1| RNA polymerase sigma factor RpoD [Treponema pallidum subsp.
           pallidum str. Nichols]
 gi|189025724|ref|YP_001933496.1| RNA polymerase sigma factor RpoD [Treponema pallidum subsp.
           pallidum SS14]
 gi|6094131|sp|O83506|RPOD_TREPA RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A;
           AltName: Full=Major vegetative sigma factor
 gi|3322782|gb|AAC65480.1| RNA polymerase sigma-70 factor (rpoD) [Treponema pallidum subsp.
           pallidum str. Nichols]
 gi|189018299|gb|ACD70917.1| RNA polymerase sigma-70 factor [Treponema pallidum subsp. pallidum
           SS14]
          Length = 611

 Score =  203 bits (516), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 63/239 (26%), Positives = 113/239 (47%), Gaps = 12/239 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+KF+  +G++ +TY+ 
Sbjct: 371 KKAKDKLINANLRLVVSIAKKYTNRGLLFFDLVQEGNIGLIKAVEKFEYRKGYKFSTYAT 430

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      +++        +   + ++    + +     +      IA++L
Sbjct: 431 WWIRQAITRSISDQARTIRVPVH-----MIEQINKVTRESRQLLQKFGREPSDEEIAQQL 485

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             +  +V  +        SL   I   ++  S   D++    D   +      ER   + 
Sbjct: 486 CWTVEKVKQVKSVAREPISLETPI--GEEEDSSLGDFVP---DADVENPSRVTERVLLKE 540

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +   +S L  RE  +   R   +     TLE +   F+V+RER+RQIEA+A K+++  
Sbjct: 541 EVRSILSALPAREHEVLRMRFGLDGDYSQTLEEVGLYFDVTRERIRQIEAKALKRLRHP 599



 Score = 35.6 bits (81), Expect = 9.1,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 24/49 (48%), Gaps = 1/49 (2%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           +  +  Y+ +I +  +L  ++E +L+KR  E G+      +  S L L 
Sbjct: 117 DDPVKLYLRDIGQEKLLTAEQEVMLSKRM-EEGEGIIKDIITQSGLLLP 164


>gi|32474487|ref|NP_867481.1| transcription initiation factor sigma 70 [Rhodopirellula baltica SH
           1]
 gi|32445025|emb|CAD75027.1| transcription initiation factor sigma 70 [Rhodopirellula baltica SH
           1]
          Length = 568

 Score =  203 bits (516), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 76/298 (25%), Positives = 144/298 (48%), Gaps = 23/298 (7%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR------YREHGDLSAAHRLVT 55
           +R  M  + +G+  L   +  + +   L  +    L++R      YR+  D +A   L  
Sbjct: 270 HRSTMPGMPSGD-ELRSELRSLMR---LTYETPRTLSRRVDRCDTYRDDYD-AAKRVLSA 324

Query: 56  SHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQE 115
            +LRLVV IA  YR  GL   +++ EGN GLM+AV KF+  RG++ +TY+ WWI+ A+  
Sbjct: 325 GNLRLVVSIAKKYRNRGLSFLDLIQEGNTGLMRAVDKFEHARGYKFSTYATWWIRQAITR 384

Query: 116 YILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
            I      +++        +   + +++   + +   + +      ++K+  +S  +   
Sbjct: 385 AIADQSRTIRVPVH-----MIDTMNKIRQITRDLVQEHGREPTAEEVSKRSGLSLDDTRV 439

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
           +        SL+  +   D + S + ++L    D ++   + +  R+  ++ +  +M  L
Sbjct: 440 ILKMSRQPLSLDQPV--GDHDDSVFGEFL---QDHRDDDPLVETNREALKHQIDLAMETL 494

Query: 236 NPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           N RER I   R         TLE +   F+V+RERVRQIE++A +K+Q+  + +  +S
Sbjct: 495 NYREREILRLRYGLADGYTYTLEEVGRIFQVTRERVRQIESKAVRKLQQPYRAKSLVS 552



 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 34/210 (16%), Positives = 76/210 (36%), Gaps = 31/210 (14%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-----REHGDLSAAHRLVT 55
           ++R++       E  +  Y+ ++ +IP+L + +E   A++      R    + A   ++ 
Sbjct: 90  VSRRDEFPTDPTEDPVRMYLMQMGQIPLLTRDQEVAAAQQIEATRERYRHCMMATDFMLQ 149

Query: 56  SHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ- 114
           + L+L+ ++          I   V+        A +K    +           I    + 
Sbjct: 150 AALKLLQQVRDKQLRLDRTIEVSVTN-------AAEKKAIMK----------RIVPNTRT 192

Query: 115 -EYILRSWS---LVKIGTTANQKRLFFNLR----RLKGHLQAITDNNLKPEQVVAIAKKL 166
            +Y+LR      +V I ++   +R     R    R    ++ + + NL+  ++  I +KL
Sbjct: 193 LDYLLRQNRGDYMVAINSSLPMRRRRAAWRNLVIRRNKAVRLVEEMNLRTNKLQPIFEKL 252

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKN 196
             S   +  +   LA           S   
Sbjct: 253 RRSCERMQEIKAILADAHRSTMPGMPSGDE 282


>gi|320353903|ref|YP_004195242.1| RpoD subfamily RNA polymerase sigma-70 factor [Desulfobulbus
           propionicus DSM 2032]
 gi|320122405|gb|ADW17951.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfobulbus
           propionicus DSM 2032]
          Length = 439

 Score =  203 bits (516), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 63/241 (26%), Positives = 118/241 (48%), Gaps = 13/241 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLVV IA  Y   GL +++++ EGN+GLM+AV +FD ++G + +TY+ WW
Sbjct: 203 AKDSMIRANLRLVVSIAKRYMHQGLTLADLIQEGNLGLMRAVFRFDYKKGNKFSTYASWW 262

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   IL     +++     + R  F          ++     +    V I+K  ++
Sbjct: 263 IRQAITRAILDKTRTIRLPVHFLELRSQFF-----KAFYSLLKELGREPTPVEISKMTDL 317

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +++++        SL   +   D   S   D+L    + + +   +  + +   + +
Sbjct: 318 PMDKILAILEASREPISLETPVGDDD---STLGDFL---ENQESESPYDAVQNRELAHRV 371

Query: 229 TRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           T  +S L  RE +I   R         TLE +   F VSRER+RQIE +A  +++ S ++
Sbjct: 372 TEVLSTLTDREEKIIRLRFGIGEKAEYTLEEIGKRFNVSRERIRQIEKKALNRLRHSSRR 431

Query: 287 Q 287
           +
Sbjct: 432 E 432


>gi|320103352|ref|YP_004178943.1| RNA polymerase sigma-38 subunit RpoS [Isosphaera pallida ATCC
           43644]
 gi|319750634|gb|ADV62394.1| RNA polymerase, sigma 38 subunit, RpoS [Isosphaera pallida ATCC
           43644]
          Length = 287

 Score =  203 bits (516), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 67/269 (24%), Positives = 130/269 (48%), Gaps = 14/269 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ +I + P+L   EE  L +R  E GD  A   LV ++LRLVV IA GY G GL +
Sbjct: 16  LEVYLKQINETPLLSAAEERELGRRVSE-GDYFARDHLVKANLRLVVSIARGYNGKGLGL 74

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ E N+GL++AV+ FD  +  R +TY+ +WIK +++  ++ +   +++        +
Sbjct: 75  DDLIEERNLGLIRAVETFDYSQNIRFSTYASYWIKQSIRRAVMNNGKPIRLPAY-----M 129

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              L + +     +T    +P     + K+L +S  ++  ++  +  + S     +  D+
Sbjct: 130 VTLLAKWRQATTKLTARLGRPPTPEEVGKELRLSPRKIPIVSKAM--EVSKLQPYSEGDE 187

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--- 252
           ++    D ++ D + +    +   +    R  +   +  L+ RE  +   R   +     
Sbjct: 188 DTGVPLDDVLIDGNNRSPDELMAHDDDQARMKI--LLDELDERESAVIRLRFGLDESVPE 245

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKV 280
            +TL  +     ++RERVRQ+E  A  K+
Sbjct: 246 AMTLRQIGERLGLTRERVRQLEQAALTKL 274


>gi|254473016|ref|ZP_05086414.1| RNA polymerase sigma factor [Pseudovibrio sp. JE062]
 gi|211957737|gb|EEA92939.1| RNA polymerase sigma factor [Pseudovibrio sp. JE062]
          Length = 289

 Score =  203 bits (516), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 94/262 (35%), Positives = 158/262 (60%), Gaps = 2/262 (0%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           RK P L K+EEY L + +    D  A  +L  SH RLV+  A+ ++ YG+P+S+++ EG+
Sbjct: 18  RKAPYLSKEEEYKLLEGWITKRDHRALDKLSLSHSRLVIAQALRFKSYGVPLSDLIQEGH 77

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+A  +F   +  R +TY+ WWIK+ +Q+Y+LR+ S+V+ GT++ QK LFF  +R++
Sbjct: 78  IGLMEAANRFKLSKDVRFSTYASWWIKSFIQDYVLRNQSIVRGGTSSRQKMLFFGFKRMR 137

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQD 202
             L +      + +    I+ +   +  ++  M+ RL   D SLNA +  S+ N  Q QD
Sbjct: 138 AELASKHPELSEDQLHQQISNQTGANMRDIKMMSSRLGRSDTSLNATLKGSETN-LQLQD 196

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
            L  D    ++++    + +     L  ++  L PRE+R+   R+L+E+ VTLE L  + 
Sbjct: 197 TLAADEPLPDEIVEVHLDSERAERRLFDAIKTLPPREQRVIRDRKLREDGVTLEALGKKL 256

Query: 263 EVSRERVRQIEARAFKKVQESI 284
            VS+ERVRQIE+RA +K+++++
Sbjct: 257 GVSKERVRQIESRAMQKLKDAM 278


>gi|159039487|ref|YP_001538740.1| RpoD family RNA polymerase sigma factor [Salinispora arenicola
           CNS-205]
 gi|157918322|gb|ABV99749.1| RNA polymerase, sigma 70 subunit, RpoD family [Salinispora
           arenicola CNS-205]
          Length = 329

 Score =  203 bits (516), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 80/297 (26%), Positives = 132/297 (44%), Gaps = 38/297 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR-----YREH---------------------GDLSAAHR 52
           Y+HEI + P+L+   E  L+K      Y EH                         A   
Sbjct: 38  YLHEISRTPLLDAATEVDLSKAIEAGLYAEHLLDEDRVPAGVERAELQRLVAEGERAKDL 97

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            + ++LRLVV IA  Y   G+P+ +++ EGN GL++AV+KFD ERGF+ +TY+ WWI+ A
Sbjct: 98  FIRANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQA 157

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   I +    V++        L  ++ R++   + +T       +   IA  L VS   
Sbjct: 158 ISRAIAQQERTVRLPVH-----LVEDVNRMRNVARQLTRELGSDPEPEQIATALGVSVER 212

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           V  +        SL+  +   D   +   D +    D       E       R  +   +
Sbjct: 213 VNELVRWSQDTVSLDTPV--GDDGDTNLGDLVA---DSDAPSPEEIVLTGLERQRIEGLL 267

Query: 233 SVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           S L+ R   I  AR   E+    +L  ++S F +SRER+RQ+E +A  +++E  + +
Sbjct: 268 SHLDDRSAGIMRARYGLEDGREHSLTEVASRFSLSRERIRQLEIQALGRLRELARAE 324


>gi|149911320|ref|ZP_01899941.1| DNA-directed RNA polymerase, sigma subunit [Moritella sp. PE36]
 gi|149805635|gb|EDM65637.1| DNA-directed RNA polymerase, sigma subunit [Moritella sp. PE36]
          Length = 294

 Score =  203 bits (516), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 84/276 (30%), Positives = 145/276 (52%), Gaps = 12/276 (4%)

Query: 12  GEIGLSRYIHEIRKI-PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
               L  Y  E+++   +L KQEEY  A     +GD +A   ++ S+LRLV+ +A  Y+ 
Sbjct: 5   TSNALDVYFDELQRFSQLLSKQEEYDTAVAAA-NGDKAARDTMIQSNLRLVLMVAKKYQN 63

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
           Y L  +E++ EGN GLM AV KFDPERG R +TY++WWI+  +++YI+     ++I    
Sbjct: 64  YSLDWAEIIQEGNTGLMHAVDKFDPERGCRFSTYAVWWIRNNIEQYIMNHSRTIRIPIHV 123

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              R++  + +    L    D N   E +  IA++L +S  +V+++      + SL+  I
Sbjct: 124 T--RVYKQILKASSELGLDVDTN---EGITKIAQELKISPRKVLNILGHYFNEGSLDKEI 178

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-- 248
           +S D   +  +D +  + D Q  +  EK +     + L   +  L  R + I   R    
Sbjct: 179 HSGDNLLATLKDLVAAEVDCQPDIRYEKCDYYEYMDAL---LEYLPVRSQNIIRLRFGFK 235

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            ++P++L+ ++   ++SRERVRQI      +V+E +
Sbjct: 236 GQDPMSLQAIAQLMDISRERVRQIIRNGLSQVREQL 271


>gi|111018672|ref|YP_701644.1| sigma factor, sigma 70 type, group 2 [Rhodococcus jostii RHA1]
 gi|110818202|gb|ABG93486.1| sigma factor, sigma 70 type, probable group 2 [Rhodococcus jostii
           RHA1]
          Length = 520

 Score =  203 bits (516), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 76/307 (24%), Positives = 137/307 (44%), Gaps = 44/307 (14%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY----------------------REHGD----- 46
             +  Y   I+K  +L   +E  LA+R                       + H D     
Sbjct: 218 DSIRAYSKSIKKRSLLVSGDESELAERIEAGLYAAYLLKEAEDAGEKLSDQRHRDLHRVC 277

Query: 47  ---LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
                A  R + ++LRLVV IA  Y+G GL + ++V EGN+GL++AV+KFD + GF+ +T
Sbjct: 278 RDGQHAKRRFLEANLRLVVSIARRYQGRGLDLLDLVQEGNLGLIRAVEKFDYKTGFKFST 337

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI+ A+   +     +++I     ++     L + +  L   T     P     +A
Sbjct: 338 YATWWIRQAITRALADQSRVIRIPVHMVEQ--IDQLGKERARLTKETGREPTP---SELA 392

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
             L+ +   +  +        SL+ L ++++ +   ++D L         V  E  ER+ 
Sbjct: 393 TALDTTIEHIGDLEKYDQRVLSLDVLTDNAEHDGLDFEDDLAV-------VAEEVAERRR 445

Query: 224 RRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
               L   +S L+ R+ ++   R      +P TL+ +   + V+RER+RQIE++  K ++
Sbjct: 446 FYETLESVLSPLSERDAQVIRLRYGLTGSDPYTLDEIGKIYGVTRERIRQIESKLLKAMK 505

Query: 282 ESIQKQV 288
           E     +
Sbjct: 506 EESVADI 512


>gi|239981636|ref|ZP_04704160.1| RNA polymerase principal sigma factor hrdD [Streptomyces albus
           J1074]
 gi|291453499|ref|ZP_06592889.1| RNA polymerase sigma factor [Streptomyces albus J1074]
 gi|17366575|sp|Q59914|HRDD_STRGR RecName: Full=RNA polymerase principal sigma factor hrdD
 gi|510454|emb|CAA56305.1| sigma factor [Streptomyces griseus]
 gi|291356448|gb|EFE83350.1| RNA polymerase sigma factor [Streptomyces albus J1074]
          Length = 332

 Score =  203 bits (516), Expect = 3e-50,   Method: Composition-based stats.
 Identities = 75/310 (24%), Positives = 129/310 (41%), Gaps = 44/310 (14%)

Query: 7   SIIVNGEIG----LSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------- 43
           S+   GEI     +  Y+ EI + P+L+  +E  L++                       
Sbjct: 22  SVRATGEIADRDLVGMYLDEIARTPLLDAAKEVELSQTIEAGVYAGKILDGEVDSDSAGA 81

Query: 44  ---------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                         A    + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD
Sbjct: 82  SREELEALVAEGERAKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFD 141

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +GF+ +TY+ WWI+ A+   I      +++        L   L R++   +     N 
Sbjct: 142 YAKGFKFSTYATWWIRQAITRSIADQSRTIRLPVH-----LVEELGRIRRVQREFNRENG 196

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +  +   IA +L+ +   V  +        SLN  +   D+  +Q+ D L    D     
Sbjct: 197 RDPEPAEIAAELSSTPERVTDVLDWARDPVSLNMSV--DDEGETQFGDLL---EDTSAVS 251

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
             +      R   L   +  L+ R   I + R   E+    TL  +  +  ++RER+RQI
Sbjct: 252 PEQSVLTLLRSEELDDLIGQLDDRTASIIKMRYGIEDGRERTLTEVGKQHGLTRERIRQI 311

Query: 273 EARAFKKVQE 282
           E  A  +++ 
Sbjct: 312 EKHALLELKR 321


>gi|168704138|ref|ZP_02736415.1| RNA polymerase sigma factor rpoS [Gemmata obscuriglobus UQM 2246]
          Length = 280

 Score =  203 bits (516), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 80/277 (28%), Positives = 132/277 (47%), Gaps = 17/277 (6%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
            K M I   G   +S Y+ EI + P+L   EE  L  R  + GD +A  R+V ++LRLVV
Sbjct: 8   EKPMGISAPGGTAMSAYLREIDRTPLLSATEERELGGRILD-GDPAARDRMVRANLRLVV 66

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A GY G GL + ++V+EGN+GL++AV+ FDP    R +TY+ +WIK ++Q  I+ +  
Sbjct: 67  NLARGYTGRGLSLDDLVAEGNMGLLRAVEGFDPGMSTRFSTYASFWIKQSIQRAIVNTAR 126

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            +++ T      L    RR    L         PE+V A    L+  +  ++ +  ++AG
Sbjct: 127 TIRVPTYMA--ALVARWRRATAALGDELGRAPAPEEV-AGHLGLSRRKLAMVQLALKVAG 183

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
                     +D      +  +    D          +   +  ++   +  LNPR+  +
Sbjct: 184 ------AGTQADDAEGGLEGLIPDTRDSGSD-----ADAAEQLKLVFEQLDRLNPRDADV 232

Query: 243 FEARRL--QENPVTLENLSSEFEVSRERVRQIEARAF 277
              R     E P TL+ +     +++ERVRQIE+ A 
Sbjct: 233 LRLRFGLSGEEPKTLKEVGEALGLTKERVRQIESAAL 269


>gi|51246355|ref|YP_066239.1| RNA polymerase sigma factor (RpoD) [Desulfotalea psychrophila
           LSv54]
 gi|50877392|emb|CAG37232.1| probable RNA polymerase sigma factor (RpoD) [Desulfotalea
           psychrophila LSv54]
          Length = 447

 Score =  203 bits (516), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 67/241 (27%), Positives = 116/241 (48%), Gaps = 13/241 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLVV IA  Y   GL +++++ EGN+GLM+AV +FD  +G + +TY+ WW
Sbjct: 211 AKDTMIRANLRLVVSIAKRYMHQGLTLADLIQEGNLGLMRAVFRFDYTKGNKFSTYASWW 270

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   IL     +++     + R  F          A+     +    + I+K  N+
Sbjct: 271 IRQAITRAILDKTRTIRLPVHFLELRSQFF-----KAFYALFKELGREPTPLEISKTTNL 325

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +++S+        SL   +   D   S   D+L    + + Q   E  + +     +
Sbjct: 326 PMDKILSILEASREPISLETPVGDDD---STLGDFL---ENQESQSPYEAVQNRELSGRV 379

Query: 229 TRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           T  +S L+ RE +I   R         TLE +   F VSRER+RQIE +A  +++ S ++
Sbjct: 380 TEILSTLSDREEKIIRLRFGIGEKAEYTLEEIGKRFNVSRERIRQIEKKALNRLRHSSRR 439

Query: 287 Q 287
            
Sbjct: 440 D 440


>gi|75908126|ref|YP_322422.1| RNA polymerase sigma factor [Anabaena variabilis ATCC 29413]
 gi|75701851|gb|ABA21527.1| Sigma 28 (Flagella/Sporulation) [Anabaena variabilis ATCC 29413]
          Length = 327

 Score =  203 bits (516), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 66/305 (21%), Positives = 133/305 (43%), Gaps = 52/305 (17%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYRE----------------------------------- 43
           Y+ EI ++P+L +++E V  K+ ++                                   
Sbjct: 23  YLREIGRVPLLTREQEIVYGKQVQQMMSLIDAKEALAKKLDREPSLPEWADHVQKSETEV 82

Query: 44  ----HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                    A  +++ ++LRLVV IA  Y+   +   +++ EG +GL + V+KFDP RG+
Sbjct: 83  KQTVTQGKRAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPMRGY 142

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWI+ A+   I +    +++     +K     L ++K   + +     +    
Sbjct: 143 KFSTYAYWWIRQAITRAIAQQGRTIRLPIHITEK-----LNKIKKVQRELAQTLGRSPSP 197

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IAK+L +  +++           SL+  +   D   ++ Q+ L  +    E    ++ 
Sbjct: 198 AEIAKELELEPAQIREYLNMARQPVSLD--VKVGDNQDTELQEMLEDEGPSPEYYTTQEF 255

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAF 277
            R++    L   ++ L P++R +   R   L  N ++L  +     +SRERVRQ+E +A 
Sbjct: 256 LRQD----LNTLLAELTPQQREVVALRFGLLDGNELSLAKVGERLNLSRERVRQLEHQAL 311

Query: 278 KKVQE 282
             ++ 
Sbjct: 312 AHLRR 316


>gi|78211648|ref|YP_380427.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CC9605]
 gi|78196107|gb|ABB33872.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. CC9605]
          Length = 335

 Score =  203 bits (516), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 69/327 (21%), Positives = 136/327 (41%), Gaps = 53/327 (16%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--------------- 48
           K    +      +  Y+ +I ++P+L  ++E  L ++ +E  DL                
Sbjct: 16  KTAKAVTADVDLVRSYLRDIGRVPLLTHEQEITLGRQVQELMDLESLESELKSKAGEKPS 75

Query: 49  ------------------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
                                   A  R+V ++LRLVV +A  Y    + + +++ EG I
Sbjct: 76  RDQLAKASGLSSIQLKRKLQHGRRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTI 135

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++ V+KFDP RG++ +TY+ WWI+  +   I      +++     +      L +LK 
Sbjct: 136 GLVRGVEKFDPTRGYKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITE-----MLNKLKK 190

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + ++    +   V  +A+ + + E +V  + CR     SL   +   D + ++  + L
Sbjct: 191 GQRELSQELGRTPTVTELAEFVELPEDDVKDLMCRARQPVSLEMKV--GDGDDTELLELL 248

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEF 262
             D D     + E   + +    L   +  L   + ++   R     E+P++L  +    
Sbjct: 249 SGDGDLPSDQVEEDCLKGD----LRSLLGQLPHLQEQVLRMRYGMDGEDPMSLTGIGRIL 304

Query: 263 EVSRERVRQIEARAFKKVQESIQKQVE 289
            +SR+RVR +E      ++  +  QVE
Sbjct: 305 GMSRDRVRNLERDGLAGLRR-VSDQVE 330


>gi|146739110|gb|ABQ42602.1| chloroplast RNA-polymerase sigma factor precursor [Heterosigma
           akashiwo]
          Length = 404

 Score =  203 bits (516), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 74/328 (22%), Positives = 146/328 (44%), Gaps = 52/328 (15%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS------------- 48
           N KN    +     +  Y+ ++R + ML  QEE +L ++ +   ++              
Sbjct: 64  NNKNY---LPQSDTMKEYVKDLRTVDMLTAQEEILLTRQIKRGMEIEKALVTLEKTLGRK 120

Query: 49  ---------------------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
                                      +   ++ ++LRLVV  A  Y+  G+   ++V E
Sbjct: 121 PTEEEWVNFVGLKSIDDIRKNLKRASKSKSAIINANLRLVVSTAKAYQYRGVSFQDLVQE 180

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           G  GL +A +KFDP +GFR +TY+ WWIK  +   +     +V++    +     F++RR
Sbjct: 181 GTCGLHKATEKFDPRKGFRFSTYATWWIKQGIMRAVTDQSRVVRLPVHVH--DALFHIRR 238

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
            K +       +L+   +  +A+   ++  +++  +       S++  +    K +S  +
Sbjct: 239 AKANFWT---EHLREPTLAELAEATGLTPQKIVFYDTVKDKVSSIDKTVGIGTKTNSMEK 295

Query: 202 DWLVYDHDGQEQV--LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLEN 257
             +      ++      E  + ++ R  ++R ++ L+PRE+ +   R   ++    TLE 
Sbjct: 296 SQIAISDMCKDSRNKPEETAQVESLRQDISRLINTLSPREQDVVRMRYGLDDGEIRTLEE 355

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + S F V+RERVRQIEARA  K+++  +
Sbjct: 356 IGSIFSVTRERVRQIEARALHKLRQPYR 383


>gi|281420436|ref|ZP_06251435.1| RNA polymerase sigma-70 factor [Prevotella copri DSM 18205]
 gi|281405493|gb|EFB36173.1| RNA polymerase sigma-70 factor [Prevotella copri DSM 18205]
          Length = 291

 Score =  203 bits (516), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 78/285 (27%), Positives = 143/285 (50%), Gaps = 13/285 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRL 60
           + + SI       L +Y+ EI + PM+   EE  LA++ R+ G     A  +LV ++LR 
Sbjct: 5   KISKSITNRSSEALDKYLVEIGREPMVSIDEEIELAQKIRKGGREGERAKEKLVKANLRF 64

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y+  GL +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I   
Sbjct: 65  VVSVAKQYQHQGLSLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQ 124

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
             +V++            L ++   +      N +   V  +A+   + ES++       
Sbjct: 125 SRIVRLPLNQ-----VGALSKISAEISKFEQENQRKPSVAELAQITKMEESKIDQTIKAD 179

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM-SVLNPRE 239
               S++A   S D +++        D    ++      + ++  + L R + SVL  RE
Sbjct: 180 NHHMSIDAPFGSDDDDNAMVDVMASGDDSRTDK----GVDFESMASELDRVLNSVLKDRE 235

Query: 240 RRIF-EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           R+I      +  +   LE + SEF ++RERVRQI  ++  K+++S
Sbjct: 236 RKILCYCYGIGCHEKGLEEIGSEFNLTRERVRQIREKSIIKLRDS 280


>gi|300868700|ref|ZP_07113311.1| RNA polymerase, sigma 28 subunit [Oscillatoria sp. PCC 6506]
 gi|300333261|emb|CBN58503.1| RNA polymerase, sigma 28 subunit [Oscillatoria sp. PCC 6506]
          Length = 462

 Score =  202 bits (515), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 65/242 (26%), Positives = 122/242 (50%), Gaps = 12/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           + A   ++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV+KFDP RG+R +TY+ 
Sbjct: 220 IQAKDHMIQANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTRGYRFSTYAY 279

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   I      +++     +K     L ++K   + I+    +   +  IA +L
Sbjct: 280 WWIRQGITRAIATQSRTIRLPVHITEK-----LNKIKKAQRKISQEKGRTASIEDIAAEL 334

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++  +V  +  R+    SL   +   ++  ++  D L    D       E   R+    
Sbjct: 335 GMTAPQVREVLLRVPRSVSLETKV--GNEKDTELGDLL---DDADSVSPEELLMREALHR 389

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L + ++ L  RER +   R      +P +L  +    ++SRERVRQIEA+A +K+++  
Sbjct: 390 DLQQLLADLTSRERDVILMRFGLGDGHPYSLAEIGRALDLSRERVRQIEAKALQKLRQPK 449

Query: 285 QK 286
           ++
Sbjct: 450 RR 451


>gi|297626467|ref|YP_003688230.1| RNA polymerase principal sigma factor HrdD [Propionibacterium
           freudenreichii subsp. shermanii CIRM-BIA1]
 gi|296922232|emb|CBL56802.1| RNA polymerase principal sigma factor HrdD [Propionibacterium
           freudenreichii subsp. shermanii CIRM-BIA1]
          Length = 309

 Score =  202 bits (515), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 71/304 (23%), Positives = 132/304 (43%), Gaps = 41/304 (13%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------------- 41
           ++G+  +  Y+  I K P+L   EE  LA+                              
Sbjct: 13  IDGKDSVGLYLESIAKTPLLTAAEEVELARLIEVGQYAQAVLRGEVKTKTKATEEELLGI 72

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            E G   A    V ++LRLVV +A  Y    +P+ ++V EGN GL++AV+KFD  +GF+ 
Sbjct: 73  AEEG-ERAMQHFVRANLRLVVSVARKYGRSQMPLLDLVQEGNTGLIRAVEKFDYAKGFKF 131

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY+ WW++ A+   I +   +V++     +      + ++    + +     +  +V  
Sbjct: 132 STYATWWVRQAISRGIAQQGRIVRLPVHVAE-----QVNQISAVRRNLERQLGREPEVSE 186

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           IA +L + E++VI +        SL+A +   D   +   D +  +       L+   E 
Sbjct: 187 IANELGLEENKVIDLIRYSREHVSLDAPV--EDDGDTSLGDLIARETAPGPDELVLDLED 244

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVT--LENLSSEFEVSRERVRQIEARAFKK 279
              R+ L   ++ L+ R   +   R    +     L ++   + ++ ERVRQIE  A  +
Sbjct: 245 ---RSRLEALLANLDDRSADVMRRRYGLLDGHQAKLSDIGKVWGITAERVRQIERAALNQ 301

Query: 280 VQES 283
           ++ S
Sbjct: 302 LRTS 305


>gi|282877365|ref|ZP_06286188.1| putative RNA polymerase sigma factor RpoD [Prevotella buccalis ATCC
           35310]
 gi|281300417|gb|EFA92763.1| putative RNA polymerase sigma factor RpoD [Prevotella buccalis ATCC
           35310]
          Length = 290

 Score =  202 bits (515), Expect = 4e-50,   Method: Composition-based stats.
 Identities = 69/287 (24%), Positives = 137/287 (47%), Gaps = 12/287 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKI 64
           SI       L +Y+ EI + P++   EE  LA++ ++ G     A  +LVT++LR VV +
Sbjct: 9   SITNRSSEALDKYLVEIGRAPLISIDEEIELAQKIKKGGPEGERAKDKLVTANLRFVVSV 68

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y+  GL +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V
Sbjct: 69  AKQYQHQGLSLTDLIDEGNIGLIKAAQKFDETRGFKFISYAVWWIRQSILQAIAEQSRIV 128

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           ++           +L ++   +      N +   +  ++   N+ E ++           
Sbjct: 129 RLPLNQ-----VGSLNKINHEINRFEQENHRRPSISELSDATNIDEDKISQSMMADGHHV 183

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           S++A     + N+    D +    D +    ++ E      + +     VL  RE  I +
Sbjct: 184 SIDAPFQDGEDNT--MLDVMPSGEDSRTDRHVDHESMAQELDAVLN--KVLKEREIIIIK 239

Query: 245 ARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
                  +   LE +  +  ++RERVRQI  ++  K+++S   ++ +
Sbjct: 240 ECFGIGRHEKGLEEIGDQLGLTRERVRQIREKSIAKLRDSGNAKILM 286


>gi|213027483|ref|ZP_03341930.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. 404ty]
          Length = 253

 Score =  202 bits (515), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 95/258 (36%), Positives = 140/258 (54%), Gaps = 8/258 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +     L  YI      PML   EE  LA+R    GDL AA  L+ SHLR 
Sbjct: 1   MTKEMQNLALAPVGNLESYIRAANAWPMLSADEERALAERLHYQGDLEAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVEMVARELGVSSKDVREMESRM 175

Query: 181 -AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE-ERKNRRNMLTRSMSVLNPR 238
            A D + +   +    +        + D        IE +   +   N LT +M  L+ R
Sbjct: 176 AAQDMTFDMSSDDESDSQPMAPVLYLQDKSSNFADGIEDDNWEEQAANRLTDAMQGLDER 235

Query: 239 ERRIFEARRLQEN-PVTL 255
            + I  AR L E+   TL
Sbjct: 236 SQDIIRARWLDEDNKSTL 253


>gi|157414236|ref|YP_001485102.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9215]
 gi|157388811|gb|ABV51516.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9215]
          Length = 344

 Score =  202 bits (515), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 68/318 (21%), Positives = 134/318 (42%), Gaps = 53/318 (16%)

Query: 7   SIIVNGEIGLSR-YIHEIRKIPMLEKQEEYVLAKRYRE--------------HGDL---- 47
           ++  + ++ L R Y+ +I ++P+L  ++E  L ++ +E               GD     
Sbjct: 27  TLKSSNDVDLVRSYLRDIGRVPLLSHEQEITLGRQVQEYMEVERAELEFIELTGDKPSID 86

Query: 48  ---------------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
                                 A  R+V ++LRLVV +A  Y    + + +++ EG IGL
Sbjct: 87  ELSTKLNLSTSIIKKRLRAGQRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGL 146

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++ V+KFDP RG++ +TY+ WWI+  +   I      +++     +      L +LK   
Sbjct: 147 VRGVEKFDPARGYKFSTYAYWWIRQGITRAIAEKSRAIRLPIHITE-----MLNKLKKGQ 201

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           + ++    +   V  +AK + + E +V  + C+     SL   +   +         L+ 
Sbjct: 202 RELSQEMSRTPTVSELAKYVELPEDDVKDLMCKAGQPVSLETKVGDGEDT------VLLD 255

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
              G E +  E+ E    R  L   +  L   + R+   R     + P++L  +     +
Sbjct: 256 LLAGGEDLPDEQIEMDCMRGDLHSLLHQLPDLQCRVLRMRYGMDGDEPMSLTGIGRVLGI 315

Query: 265 SRERVRQIEARAFKKVQE 282
           SR+RVR +E    + ++ 
Sbjct: 316 SRDRVRNLERDGLRGLRR 333


>gi|172036788|ref|YP_001803289.1| group 2 sigma-70 RNA polymerase sigma factor C [Cyanothece sp. ATCC
           51142]
 gi|171698242|gb|ACB51223.1| group 2 sigma-70 RNA polymerase sigma factor C [Cyanothece sp. ATCC
           51142]
          Length = 420

 Score =  202 bits (515), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 63/250 (25%), Positives = 131/250 (52%), Gaps = 14/250 (5%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           +  ++ G + +   ++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV+KFDP +G
Sbjct: 172 EEIQKSG-IRSKDEMIKANLRLVVSVAKKYQHRGLELLDLIQEGTLGLEKAVEKFDPIKG 230

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           +R +TY+ WWI+  +   I     ++++     +K     L ++K   + I+    +   
Sbjct: 231 YRFSTYAYWWIRQGITRAIATQSRIIRLPVHVTEK-----LNKIKQVQRQISQAKGRNAT 285

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           +  I K+LN++ ++V  +  ++    SL   I    +  ++  D L  +    E+ L   
Sbjct: 286 LEEIGKELNMTPTQVREVFMKIPRSVSLE--IKVGKEKDTELVDLLESEDISPEENLA-- 341

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARA 276
              ++ R  +   +  L  RE+ + + R   E+    +L ++    ++SRERVRQIEA+A
Sbjct: 342 --IESLRRDIGILLEDLTEREQEVIKLRYGFEDGVSYSLADIGRTLDLSRERVRQIEAKA 399

Query: 277 FKKVQESIQK 286
            +K+++  ++
Sbjct: 400 LQKLRQPRRR 409


>gi|307729587|ref|YP_003906811.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Burkholderia sp.
           CCGE1003]
 gi|307584122|gb|ADN57520.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Burkholderia sp.
           CCGE1003]
          Length = 362

 Score =  202 bits (515), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 75/280 (26%), Positives = 130/280 (46%), Gaps = 15/280 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+
Sbjct: 82  DTIQHYLNRISVKPLLTVEEEQKYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGV 140

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++       
Sbjct: 141 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV--I 198

Query: 134 RLFFNLRRLKGHLQAITDN-----NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           R    + R K HL+  + N       +   +  IA     +  EV  +        SL+A
Sbjct: 199 RELNQVLRAKRHLEKNSMNSGDAAERRDASIDDIAYLTGKTADEVTDILALNEHTASLDA 258

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            ++    +S               +V     + +    +    ++ L+ + R + E R  
Sbjct: 259 PLDLDPASSLLDLLSDDQSQSPDAEV-----QHRELETLTRAWLARLSDKHRHVIERRFG 313

Query: 249 QE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                P TLE L+ E  ++RERVRQI+  A  +++     
Sbjct: 314 LNHIEPATLEELADEMGLTRERVRQIQQEALVRLKRFFAS 353


>gi|91783466|ref|YP_558672.1| RNA polymerase sigma factor RpoS [Burkholderia xenovorans LB400]
 gi|296157776|ref|ZP_06840610.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Burkholderia sp.
           Ch1-1]
 gi|91687420|gb|ABE30620.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia xenovorans
           LB400]
 gi|295892022|gb|EFG71806.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Burkholderia sp.
           Ch1-1]
          Length = 360

 Score =  202 bits (515), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 75/280 (26%), Positives = 130/280 (46%), Gaps = 15/280 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+
Sbjct: 80  DTIQHYLNRISVKPLLTVEEEQKYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGV 138

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++       
Sbjct: 139 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV--I 196

Query: 134 RLFFNLRRLKGHLQAITDN-----NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           R    + R K HL+  + N       +   +  IA     +  EV  +        SL+A
Sbjct: 197 RELNQVLRAKRHLEKNSMNSGEAAERRDASIDDIAYLTGKTTDEVTDILALNEHTASLDA 256

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            ++    +S               +V     + +    +    ++ L+ + R + E R  
Sbjct: 257 PLDLDPASSLLDLLSDDQSQSPDAEV-----QHRELETLTRAWLARLSDKHRHVIERRFG 311

Query: 249 QE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                P TLE L+ E  ++RERVRQI+  A  +++     
Sbjct: 312 LNHIEPATLEELADEMGLTRERVRQIQQEALVRLKRFFAS 351


>gi|219849586|ref|YP_002464019.1| RpoD subfamily RNA polymerase sigma-70 subunit [Chloroflexus
           aggregans DSM 9485]
 gi|219543845|gb|ACL25583.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Chloroflexus
           aggregans DSM 9485]
          Length = 314

 Score =  202 bits (515), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 72/301 (23%), Positives = 130/301 (43%), Gaps = 38/301 (12%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG------------------------- 45
           +    +  Y++EI   P+L  ++E  LA+   +                           
Sbjct: 10  SASDTIVLYLNEIGAEPLLTFEQEQQLAQTIAQGRRAAERLTNEPSLHSTEKKRLAAQVA 69

Query: 46  -DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
               A  +L+ S+LRLVV IA  Y+G+GL + +++ EG+IGLM+AV KFD  RG + +TY
Sbjct: 70  AGEQARAQLINSNLRLVVSIARRYQGHGLTLLDLIQEGSIGLMRAVDKFDAGRGLKFSTY 129

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + +WI+ ++   I      V++     ++     L RL    Q +     +   +  +A 
Sbjct: 130 ATYWIRQSIGRAIADHSRTVRLPVHLGER-----LSRLARLRQELAQQLDREPTLEELAN 184

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
              +S  +V           SL+     ++       + L    D  +    ++      
Sbjct: 185 AAGLSVEQVERAEQAGLAPTSLDE--AHTEDGGGALSEIL---TDPLQPTPFDEVSEGML 239

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +  +  ++S L+PRER I   R   +     TLE +     ++RERVRQ+E  A +K+++
Sbjct: 240 QADVQAALSQLSPRERNILRLRYGLDGEPMHTLEQIGQRLRLTRERVRQLEYEALRKLRD 299

Query: 283 S 283
            
Sbjct: 300 P 300


>gi|94263318|ref|ZP_01287133.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
 gi|93456273|gb|EAT06403.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
          Length = 442

 Score =  202 bits (515), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 65/241 (26%), Positives = 118/241 (48%), Gaps = 13/241 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLVV IA  Y   GL +++++ EGN+GLM+AV +FD  +G + +TY+ WW
Sbjct: 206 AKDAMIKANLRLVVSIAKRYMHQGLTLADLIQEGNLGLMRAVFRFDYTKGNKFSTYASWW 265

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   IL     +++     + R  F          ++     +    V I++K  +
Sbjct: 266 IRQAITRAILDKTRTIRLPVHFLELRSQFF-----KAFYSLLKELGREPTPVEISEKTGL 320

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +++++        SL   +   D   S   D+L    + +     E  +       +
Sbjct: 321 PMEKILAIFEASREPISLETPVGDDD---STLGDFL---ENQESISPYEAVKGNQLAERV 374

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           T  +S L+PRE +I   R    ++   TLE +   F VSRER+RQIE +A  +++ S ++
Sbjct: 375 TTILSTLSPREEKIIRLRFGIGEDAEYTLEEIGKRFNVSRERIRQIEKKALNRLRHSSRR 434

Query: 287 Q 287
           +
Sbjct: 435 E 435


>gi|291566702|dbj|BAI88974.1| group 2 RNA polymerase sigma factor SigB [Arthrospira platensis
           NIES-39]
          Length = 334

 Score =  202 bits (514), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 67/310 (21%), Positives = 138/310 (44%), Gaps = 52/310 (16%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------------------ 43
             +  Y+HEI ++P+L ++EE +  K+ ++                              
Sbjct: 25  DAVRTYLHEIGRVPLLTREEEIIYGKKVQQMMNLLEVRDELTKELDRDPTPEEWSAKAGL 84

Query: 44  ---------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                    +    A  +++ ++LRLVV IA  Y+   +   +++ EG +GL + V+KFD
Sbjct: 85  SESEMTDIINRGRRAKQKMIEANLRLVVSIAKKYQKRNMEFLDLIQEGTLGLERGVEKFD 144

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P RG++ +TY+ WWI+ A+   I ++   +++     +K     L ++K   + +     
Sbjct: 145 PMRGYKFSTYAYWWIRQAITRAIAQNSRTIRLPIHITEK-----LNKIKRVQRELFQQYG 199

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +      IAK L++  S++           SL+  +   D   ++ QD L  +    +  
Sbjct: 200 RNATPTEIAKALDLEPSQIRDYLLASRHPVSLD--LRVGDNQDTELQDLLEDESASADSY 257

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
           + ++  R++    L   M+ L P++R +   R    +   ++L  +  +  +SRERVRQ+
Sbjct: 258 VTQQLLRQD----LKDMMADLTPQQREVLTLRYGLNDGKEMSLSKVGVQMNISRERVRQL 313

Query: 273 EARAFKKVQE 282
           E +A   ++ 
Sbjct: 314 ENQALNHLRR 323


>gi|284122199|ref|ZP_06386842.1| RNA polymerase, sigma 70 subunit, RpoD family [Candidatus
           Poribacteria sp. WGA-A3]
 gi|283829365|gb|EFC33758.1| RNA polymerase, sigma 70 subunit, RpoD family [Candidatus
           Poribacteria sp. WGA-A3]
          Length = 414

 Score =  202 bits (514), Expect = 5e-50,   Method: Composition-based stats.
 Identities = 65/239 (27%), Positives = 104/239 (43%), Gaps = 13/239 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   LV  +LRLVV IA  + G G+   +++ EGNIGLM+A ++F   +GF+ +TY+ 
Sbjct: 177 ERAKEGLVQHNLRLVVDIAKRFTGRGMGFLDLIQEGNIGLMRAAERFQYRKGFKFSTYAT 236

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WW++  +   +      +++     +   +  + ++   L          E    IA  L
Sbjct: 237 WWVRQGILRAVADQSRTIRVPVHTTE--AWQRMIKISHRLAQKLGREPSNE---EIALAL 291

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            V    V           S +     +    +   D L  DH        E  + +  R+
Sbjct: 292 AVKPERVQHTTQAFLEPISFDQP---NADGETFLGDCLPDDHASPPD---EHLQEEQMRS 345

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            L R + VL PRE ++   R    N    TLE +     V+RER+RQIE  A KK++E 
Sbjct: 346 QLHRLLRVLTPREEQVIRLRFGIGNGQSRTLEEVGKLLNVTRERIRQIEVLAMKKLREP 404


>gi|302560146|ref|ZP_07312488.1| RNA polymerase sigma (70) factor RpoD [Streptomyces griseoflavus
           Tu4000]
 gi|302477764|gb|EFL40857.1| RNA polymerase sigma (70) factor RpoD [Streptomyces griseoflavus
           Tu4000]
          Length = 332

 Score =  202 bits (514), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 71/299 (23%), Positives = 128/299 (42%), Gaps = 39/299 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVL---------AKRYRE------------------HGDLS 48
           +  Y+ EI + P+L+  +E  L         A++  +                       
Sbjct: 36  VGMYLDEIARTPLLDAAKEVELSQIIEAGVFARQILDGTEENKAGATTEELQALYDASER 95

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A    + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ WW
Sbjct: 96  AKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTYATWW 155

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      +++        L   L R++   +     + +  +   +A +L  
Sbjct: 156 IRQAITRSIADQSRTIRLPVH-----LVEELGRIRRVQREFNREHGREPEPAEVAAELGS 210

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +   V+ +        SLN  +   D+  +Q+ D L    D       +      R   L
Sbjct: 211 TPERVVDVLDWARDPVSLNMSV--DDEGETQFGDLL---EDTSAVSPEQSVLTLLRSEEL 265

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              +  L+ R   I + R   E+    TL  +  E  ++RER+RQIE  A  ++++  +
Sbjct: 266 DDLIGRLDQRTASIIKMRYGIEDGRERTLTEVGKEHGLTRERIRQIEKHALLELKKLAR 324


>gi|256370771|ref|YP_003108596.1| RNA polymerase sigma factor rpoD [Candidatus Sulcia muelleri
           SMDSEM]
 gi|256009563|gb|ACU52923.1| RNA polymerase sigma factor rpoD [Candidatus Sulcia muelleri
           SMDSEM]
          Length = 334

 Score =  202 bits (514), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 77/275 (28%), Positives = 140/275 (50%), Gaps = 14/275 (5%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREH---GDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           +Y+ EI KIP+L +++E  LAK  R+    G  +A  +L+ S+LR VV +A  Y+  GL 
Sbjct: 63  KYLEEIGKIPLLSQKKELELAKLARKELNAGCSTALEQLIKSNLRFVVSVAKQYQNQGLS 122

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           +S++++EGN+GL++ + +FD ++GF+  +Y +WWI+ A+ + I      ++  T  N+  
Sbjct: 123 LSDLINEGNLGLIKGISRFDEKKGFKCISYCVWWIRQAILQAIADQARCIRCPT--NKLA 180

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
            +  + +    L+           V  I   LN SE EV           SL+A I   +
Sbjct: 181 FYNKVVKTYSKLEQKLKMQ---PTVNDIVVYLNSSEKEVEEALKNSIQPTSLDAPI--LE 235

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-QENPV 253
              +   D L  +   +    +EKE   +    + R +  L+ +E ++          P+
Sbjct: 236 GEDTNLYDVLKSETSPEPDFKLEKE---SFFKDIKRLLETLSEKESQVISLHYGFGCKPM 292

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           TLE ++   +++RER RQIE    K+++ S +K++
Sbjct: 293 TLEKVAFLLKLTRERCRQIEINGIKRLRISYRKKL 327


>gi|297200336|ref|ZP_06917733.1| RNA polymerase sigma factor RpoS [Streptomyces sviceus ATCC 29083]
 gi|197709451|gb|EDY53485.1| RNA polymerase sigma factor RpoS [Streptomyces sviceus ATCC 29083]
          Length = 332

 Score =  202 bits (514), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 71/300 (23%), Positives = 125/300 (41%), Gaps = 39/300 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------------HGDLS 48
           +  Y+ EI + P+L+  +E  L++                                    
Sbjct: 36  VGMYLDEIARTPLLDAAKEVELSQIIEAGVFARQVLDGFEEAKADATREELEALVEESER 95

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A    + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ WW
Sbjct: 96  AKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTYATWW 155

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      +++        L   L R++   +     + +  +   IA +L  
Sbjct: 156 IRQAITRSIADQSRTIRLPVH-----LVEELGRIRRVQREFNREHGRDPEPAEIAAELGS 210

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +   V+ +        SLN  +   D   +Q+ D L    D       +      R   L
Sbjct: 211 NAERVVDVLDWARDPVSLNMSV--DDDGDTQFGDLL---EDTSAVSPEQSVLTLLRSEEL 265

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +  L+ R   I + R   E+    TL  +  E  ++RER+RQIE  A  ++++  + 
Sbjct: 266 DDLIGRLDQRTASIIKMRYGIEDGRERTLTEVGKEHGLTRERIRQIEKHALLELKKLARS 325


>gi|78780107|ref|YP_398219.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9312]
 gi|78713606|gb|ABB50783.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9312]
          Length = 344

 Score =  202 bits (514), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 69/318 (21%), Positives = 134/318 (42%), Gaps = 53/318 (16%)

Query: 7   SIIVNGEIGLSR-YIHEIRKIPMLEKQEEYVLAKRYRE--------------HGDL---- 47
           S+  + ++ L R Y+ +I ++P+L  ++E  L ++ +E               GD     
Sbjct: 27  SLKASNDVDLVRSYLRDIGRVPLLSHEQEITLGRQVQEYMQVERAELEIIELTGDKPSIE 86

Query: 48  ---------------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
                                 A  R+V ++LRLVV +A  Y    + + +++ EG IGL
Sbjct: 87  ELSSKLNLSIPIIKKRLRAGQRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGL 146

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++ V+KFDP RG++ +TY+ WWI+  +   I      +++     +      L +LK   
Sbjct: 147 VRGVEKFDPARGYKFSTYAYWWIRQGITRAIAEKSRAIRLPIHITE-----MLNKLKKGQ 201

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           + ++    +   V  +AK + + E +V  + C+     SL   +   +         L+ 
Sbjct: 202 RELSQEMSRTPTVSELAKYVELPEEDVKDLMCKAGQPVSLETKVGDGEDT------VLLD 255

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
              G E +  E+ E    R  L   +  L   + R+   R     + P++L  +     +
Sbjct: 256 LLAGGEDLPDEQIEMDCMRGDLHSLLHQLPDLQCRVLRMRYGMDGDEPMSLTGIGRVLGI 315

Query: 265 SRERVRQIEARAFKKVQE 282
           SR+RVR +E    + ++ 
Sbjct: 316 SRDRVRNLERDGLRGLRR 333


>gi|32476381|ref|NP_869375.1| RNA polymerase sigma factor rpoD [Rhodopirellula baltica SH 1]
 gi|32446926|emb|CAD78832.1| RNA polymerase sigma factor rpoD [Rhodopirellula baltica SH 1]
 gi|327539012|gb|EGF25646.1| RNA polymerase sigma factor rpoD [Rhodopirellula baltica WH47]
          Length = 519

 Score =  202 bits (514), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 71/243 (29%), Positives = 119/243 (48%), Gaps = 12/243 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L   +LRLVV IA  YR  GL   +++ EGN GLM+AV KF+  RGF+  TY+ 
Sbjct: 280 QQAKRELSEGNLRLVVSIAKKYRNRGLSFLDLIQEGNAGLMRAVDKFEYRRGFKFCTYAT 339

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      ++I     +      + R++   + +     +   +   A++ 
Sbjct: 340 WWIRQAITRAVADQSRTIRIPVHMVE-----TMSRVRNVARQLLQELGREPSIEETARRA 394

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +V+  E   +        SL+  + +S+   SQ+ D L    DG  +       ++  R 
Sbjct: 395 DVTIEEARRVLTMSRFPISLDRPVGNSED--SQFGDLLP---DGTAESPQIGATQEMLRQ 449

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +T  +  L+ RER I + R    +    TLE +   F+V+RER+RQIEA+A +K+Q+  
Sbjct: 450 RITGVLKSLSYREREIIKLRYGLGDGYSYTLEEVGHIFKVTRERIRQIEAKAVRKLQQPS 509

Query: 285 QKQ 287
           + Q
Sbjct: 510 RSQ 512



 Score = 42.5 bits (99), Expect = 0.085,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 27/50 (54%), Gaps = 1/50 (2%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
            +  +  Y+ ++ +IP+L +++E  LAKR  E        +L+ +H  LV
Sbjct: 66  SDDPVRMYLTQMGEIPLLTRRQEIELAKRIEETR-RRFRTKLLENHYVLV 114


>gi|328883104|emb|CCA56343.1| RNA polymerase principal sigma factor HrdD [Streptomyces venezuelae
           ATCC 10712]
          Length = 333

 Score =  202 bits (514), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 77/315 (24%), Positives = 132/315 (41%), Gaps = 44/315 (13%)

Query: 2   NRKNMSIIVNGEIG----LSRYIHEIRKIPMLEKQEEYVL---------AKRYRE----- 43
            R +    V GEI     +  Y+ EI + P+L+  +E  L         A++  +     
Sbjct: 18  ARASSVRAVGGEIADRDLVGMYLDEIARTPLLDAAKEVELSQTIEAGVYARQILDGEVES 77

Query: 44  --------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
                              A    + S+LRLVV +A  Y   GLP+ +++ EGN GL++A
Sbjct: 78  EAAGASREELEALYAAGERAKDLFIKSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRA 137

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V+KFD  +GF+ +TY+ WWI+ A+   I      +++        L   L R++   +  
Sbjct: 138 VEKFDYAKGFKFSTYATWWIRQAITRSIADQSRTIRLPVH-----LVEELGRIRRVQREF 192

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
              + +  +   IA +L+     V+ +        SLN  +   D+  +Q+ D L    D
Sbjct: 193 NREHGREPEPAEIAAELDTKPERVVDVLDWARDPVSLNMSV--DDEGETQFGDLL---ED 247

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRE 267
                  +      R   L   +  L+ R   I   R   E+    TL  +  E  ++RE
Sbjct: 248 TSAVSPEQSVLTLLRSEELDDLIDKLDHRTASIIRMRYGIEDGRERTLTEVGKEHGLTRE 307

Query: 268 RVRQIEARAFKKVQE 282
           R+RQIE  A  ++++
Sbjct: 308 RIRQIEKHALLELKK 322


>gi|90577256|ref|ZP_01233067.1| hypothetical DNA-directed RNA polymerase, sigma subunit [Vibrio
           angustum S14]
 gi|90440342|gb|EAS65522.1| hypothetical DNA-directed RNA polymerase, sigma subunit [Vibrio
           angustum S14]
          Length = 286

 Score =  202 bits (514), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 74/271 (27%), Positives = 140/271 (51%), Gaps = 12/271 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+++I   P+L K +E   +++    GDL++   L+ S+LRLVV IA  YR   L +S++
Sbjct: 14  YLNDISNKPLLNKDDEIQYSRK-SLTGDLASKKILIESNLRLVVSIAKKYRASNLSLSDL 72

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM AV+KFDPE+GFR +TY+ WWIK  ++  I      +++    +  +    
Sbjct: 73  IDEGNIGLMTAVEKFDPEKGFRFSTYASWWIKQTIERAIHNQNRTIRLPVHIS--KEINT 130

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L R    L  + +N    E    IA+ LN    E+ ++        SL+  I  ++K+ +
Sbjct: 131 LLRTHRELMKLNNNEPTHED---IAQALNKDSKEISALFSNEVNVISLDQTIGDTEKSQT 187

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
                +  +        ++ ++     N++   ++ +N R++ I   R       P TL+
Sbjct: 188 -IAYLVADEQITSPSAEVDNDDMVKITNLI---LNGINARDKEIICRRFGLMGYEPHTLQ 243

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            ++    ++RER+RQ++ ++   ++ S+ ++
Sbjct: 244 EVADAVGLTRERIRQLQIKSLSSLKRSLARE 274


>gi|300726043|ref|ZP_07059501.1| RNA polymerase sigma-70 factor [Prevotella bryantii B14]
 gi|299776650|gb|EFI73202.1| RNA polymerase sigma-70 factor [Prevotella bryantii B14]
          Length = 290

 Score =  202 bits (514), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 74/280 (26%), Positives = 135/280 (48%), Gaps = 12/280 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKI 64
           SI       L +Y+ EI + PM+  +EE  LA++ +  G     A  +LVT++LR VV +
Sbjct: 9   SITNRSSESLDKYLGEISRAPMISIEEEIDLAQQIKRGGREGERAKSKLVTANLRFVVSV 68

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y+  GL +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ A+ + I     +V
Sbjct: 69  AKQYQHQGLTLTDLIDEGNIGLIKAAEKFDETRGFKFISYAVWWIRQAILQAIAEQSRIV 128

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           ++           +L ++   +        +   +  ++++ ++ E ++           
Sbjct: 129 RLPLNQ-----VGSLSKVNQEINKFEQKYQRVPTIQELSQRTDIDEEKIAQSMMASGKHV 183

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           S++A     + NS    D +    D +    ++ E      N +    +VLN RE  I  
Sbjct: 184 SIDAPFQEGEDNS--MVDIMASGEDSRTDKEVDHESMSYDLNQVLE--TVLNEREITIIR 239

Query: 245 ARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
                  P   LE +     ++RERVRQI  ++  K++ES
Sbjct: 240 DCFGIGCPEKGLEEIGDLLGLTRERVRQIREKSITKLRES 279


>gi|194246700|ref|YP_002004339.1| probable RNA polymerase sigma factor RpoD [Candidatus Phytoplasma
           mali]
 gi|193807057|emb|CAP18493.1| probable RNA polymerase sigma factor RpoD [Candidatus Phytoplasma
           mali]
          Length = 419

 Score =  202 bits (514), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 72/305 (23%), Positives = 137/305 (44%), Gaps = 41/305 (13%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAA----------------------- 50
             +  Y+ EI +IP+L  +EE    +   +  +  A                        
Sbjct: 111 DPVKIYLKEIGQIPLLTLEEEQEQFRLVYDGREAEAKLESYRKKEIELSEKEISELNDIL 170

Query: 51  -------HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
                  HRLV ++ RLVV IA  Y   GL   +++ EGN GLM+A++KF+ ++G +L+T
Sbjct: 171 KISNKAKHRLVEANYRLVVSIAKRYIRRGLEFLDLIQEGNRGLMRAIEKFNIDKGCKLST 230

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ +WI   +   +     ++++      +    ++ + K  L+       +   +  ++
Sbjct: 231 YATFWIVQKILRAVADQARIIRLPVHIVDRINIISMAKSKLRLK-----LHREPTIEELS 285

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + +N+SE ++  +        SL A +   +K+ S   +++           + +E  KN
Sbjct: 286 EFINISEKKLRIIEIIKKKPISLEARV--GEKDDSSLGEFISDPDSLSPHDYMLQEIMKN 343

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             N +      L  RE +I   R    N    TLE + + F V+RER+RQIEA+AF++++
Sbjct: 344 TLNEILE--DTLTDREEKILRMRYGLSNGKVHTLEEVGNVFGVTRERIRQIEAKAFRRLR 401

Query: 282 ESIQK 286
              ++
Sbjct: 402 TPARQ 406


>gi|237757189|ref|ZP_04585608.1| RNA polymerase sigma-70 factor [Sulfurihydrogenibium yellowstonense
           SS-5]
 gi|237690651|gb|EEP59840.1| RNA polymerase sigma-70 factor [Sulfurihydrogenibium yellowstonense
           SS-5]
          Length = 285

 Score =  202 bits (514), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 82/280 (29%), Positives = 138/280 (49%), Gaps = 11/280 (3%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
            N E  +  Y+  I KIP+L K+EE  L K+ +E GD  A  +L+ S+LR V+ IA  Y 
Sbjct: 4   FNHEENVDFYLKSIYKIPLLSKEEEESLLKKVKE-GDKEALQKLIISNLRFVINIAKRYA 62

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYG+P S+++S GN+GL++A KKFD  +G R  +Y++WWI+ ++   I     ++K    
Sbjct: 63  GYGIPFSDLISAGNVGLIEAAKKFDTSKGVRFISYAVWWIRQSIINTIQHESEIIKKPNR 122

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLN 187
                    +     +L+   +     +++++  K   +   + +  N  L      SL+
Sbjct: 123 MY--AYASKINNAYSYLKDTLNREPSIDEIISFLKTQGIKVEKEMVENYFLFKSVFLSLD 180

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I  +D +        VY+    E+ + E    ++ +  +   +  L+ RER I   R 
Sbjct: 181 TPIEGTDNDLVLEDTISVYNTLDIEKDINE----EDLKRAIETLLDTLSQRERTILIHRF 236

Query: 248 L--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
               E P TL  +     +SRERVRQIE R  KK+++  +
Sbjct: 237 GLNGEEPKTLNEVGEIVGLSRERVRQIENRVLKKLRKIAK 276


>gi|40353309|gb|AAR84418.1| essential primary sigma 70 factor [Frankia sp. D11]
 gi|40353317|gb|AAR84422.1| essential primary sigma 70 factor [Frankia sp. HR2714]
 gi|40353319|gb|AAR84423.1| essential primary sigma 70 factor [Frankia sp. Flec]
          Length = 255

 Score =  202 bits (514), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 69/265 (26%), Positives = 117/265 (44%), Gaps = 39/265 (14%)

Query: 31  KQEEYVLAKRY-------------------REHGDLSA--------AHRLVTSHLRLVVK 63
            +EE  LAKR                    +   DL A          +LV ++LRLVV 
Sbjct: 1   AEEEVDLAKRIEAGLFASEKLAVATKKTSPQMRRDLEAIERDGQIAKRKLVEANLRLVVS 60

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      
Sbjct: 61  IAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAIADQART 120

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           ++I     +      L R++  L         PE    IAK+++++  +V  +       
Sbjct: 121 IRIPVHMVE--TINKLIRIQRQLLQDLGREPSPE---EIAKEMDLTPDKVREILKVSQEP 175

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SL   I   ++  S   D++    D    V ++       +  L   +  L+ RE+++ 
Sbjct: 176 VSLETPI--GEEEDSHLGDFI---EDCDAVVPVDAASFILLQEQLDSVLHTLSDREKKVI 230

Query: 244 EARRL--QENPVTLENLSSEFEVSR 266
           + R      +P TLE +  EF V+R
Sbjct: 231 QLRFGLTDGHPRTLEEVGREFGVTR 255


>gi|113477826|ref|YP_723887.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
 gi|110168874|gb|ABG53414.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
          Length = 384

 Score =  202 bits (514), Expect = 6e-50,   Method: Composition-based stats.
 Identities = 74/329 (22%), Positives = 148/329 (44%), Gaps = 55/329 (16%)

Query: 1   MNRKNMSIIVNG-----EIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE------------ 43
           MN    +I V+      +  +     ++ + P+L ++EE  LAK  +E            
Sbjct: 52  MNISATTIPVSENQQDIDDAVGALFKQMSRYPLLNQKEEIELAKLIQELVVFEKLPEKLA 111

Query: 44  ---------------------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
                                      H   +A  R+++S+LRLVV IA  Y   G+P  
Sbjct: 112 NDLGRTPTKSEVAVAAGFTESQLDHRLHQCRTAKRRMISSNLRLVVSIAKRYLNRGVPFL 171

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++ EG +GL +A +KFDP++G++ +TY+ WWI+  +   I      +++     +    
Sbjct: 172 DLIQEGALGLNRAAEKFDPDKGYKFSTYAYWWIRQGITRTIANQGRTIRLPVHVVE---- 227

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
             + +L+   + +  +  +      IA++L +S  ++ ++        SLN  + + +  
Sbjct: 228 -QINKLRRVYRDLRRSLNRIPNDTEIAQELEISLPQLRNLQQIRRKTLSLNHRLGTDEN- 285

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVT 254
            ++  D+L  + +   +  +   +   R+++L     VL+ RE+ +   R       P T
Sbjct: 286 -TELLDFLEDNENSTPEAQMN--DMMMRQDILEVLNHVLSNREQDVISLRYGLITGEPHT 342

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQES 283
           L+ +S    +SRERVRQI+A+A +K++  
Sbjct: 343 LDEVSRMINLSRERVRQIQAKAMRKLRRP 371


>gi|302869477|ref|YP_003838114.1| sigma-70 family RNA polymerase [Micromonospora aurantiaca ATCC
           27029]
 gi|315504060|ref|YP_004082947.1| RNA polymerase, sigma 70 subunit, rpod subfamily [Micromonospora
           sp. L5]
 gi|302572336|gb|ADL48538.1| RNA polymerase sigma factor, sigma-70 family [Micromonospora
           aurantiaca ATCC 27029]
 gi|315410679|gb|ADU08796.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Micromonospora
           sp. L5]
          Length = 333

 Score =  202 bits (514), Expect = 7e-50,   Method: Composition-based stats.
 Identities = 78/297 (26%), Positives = 133/297 (44%), Gaps = 38/297 (12%)

Query: 19  YIHEIRKIPMLEKQEEYVLAK---------------RYREHGDLSAAHRL---------- 53
           Y+HEI + P+L+   E  L+K               R  +  D     RL          
Sbjct: 42  YLHEISRTPLLDAAREVDLSKAIEAGLYAEHLLDEDRIPDGVDREDLERLVAEGERAKDL 101

Query: 54  -VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
            + ++LRLVV IA  Y   G+P+ +++ EGN GL++AV+KFD ERGF+ +TY+ WWI+ A
Sbjct: 102 FIRANLRLVVSIARRYVRSGMPMLDLIQEGNTGLVRAVEKFDYERGFKFSTYATWWIRQA 161

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   I +    V++        L  ++ R++   + +T       +   IA  L V+   
Sbjct: 162 ISRAIAQQERTVRLPVH-----LVEDVNRMRNVARQLTRELGSDPEPEQIATALGVTVER 216

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           V  +        SL+  +   D   +   D +    D       E       R  +   +
Sbjct: 217 VNELVRWSQDTVSLDTPV--GDDGDTNLGDLVA---DSDAPSPEEIVLTGLERQRIEGLL 271

Query: 233 SVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           + L+ R   I  AR   E+    +L  ++S F +SRER+RQ+E +A  +++E  + +
Sbjct: 272 NHLDDRSAGIMRARYGLEDGREHSLTEVASRFSLSRERIRQLEIQALGRLRELARAE 328


>gi|307324239|ref|ZP_07603447.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306889970|gb|EFN20948.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 334

 Score =  201 bits (513), Expect = 7e-50,   Method: Composition-based stats.
 Identities = 71/302 (23%), Positives = 129/302 (42%), Gaps = 41/302 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVL---------AKRYREHGDLSA----------------- 49
           +  Y+ EI + P+L+  +E  L         A++  +     A                 
Sbjct: 36  VGMYLDEIARTPLLDAAKEVELSQSIEAGVYAQQILDGEVEEAPAAGASREELAAIAAEG 95

Query: 50  ---AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                  + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ 
Sbjct: 96  ARAKDIFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYTKGFKFSTYAT 155

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      +++        L   L R++   +     + +  +   IA +L
Sbjct: 156 WWIRQAITRSIADQSRTIRLPVH-----LVEELGRIRRVQREFNREHGREPEHAEIAVEL 210

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             +   V  +        SLN  +   D+  +Q+ D L    D       +      R  
Sbjct: 211 GSTMERVSDVLDWARDPVSLNMSV--DDEGETQFGDLL---EDTSAVSPEQSVMTLLRSE 265

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ R   I +AR   ++    TL  +  +  ++RER+RQIE  A  ++++  
Sbjct: 266 ELEDLIGRLDDRTASIIKARYGIDDGRERTLTEVGKQHGLTRERIRQIEKHALLELKKMA 325

Query: 285 QK 286
           ++
Sbjct: 326 RQ 327


>gi|294629875|ref|ZP_06708435.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. e14]
 gi|292833208|gb|EFF91557.1| RNA polymerase sigma (70) factor RpoD [Streptomyces sp. e14]
          Length = 332

 Score =  201 bits (513), Expect = 7e-50,   Method: Composition-based stats.
 Identities = 74/299 (24%), Positives = 129/299 (43%), Gaps = 39/299 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVL---------AKRYREHGDLS------------------ 48
           +  Y+ EI + P+L+  +E  L         A++  +  + S                  
Sbjct: 36  VGMYLDEIARTPLLDAAKEVELSQVIEAGVFARQILDGYEESKTEATPEELQALVDAGER 95

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A    + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ WW
Sbjct: 96  AKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTYATWW 155

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      +++        L   L R++   +     N +  +   IA +L  
Sbjct: 156 IRQAITRSIADQSRTIRLPVH-----LVEELGRIRRVQREFNRENGRDPEPAEIAAELGS 210

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +   V  +        SLN  +   D+  +Q+ D L    D       +      R   L
Sbjct: 211 TPERVADVLDWARDPVSLNMSV--DDEGETQFGDLL---EDTSAVSPEQSVMTLLRSEEL 265

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              +  L+ R   I + R   E+    TL  +  E  ++RER+RQIE  A  ++++  +
Sbjct: 266 DDLIGRLDQRTASIIKMRYGIEDGRERTLTEVGKEHGLTRERIRQIEKHALLELKKLAR 324


>gi|9837536|gb|AAG00589.1|AF288784_1 SigC [Synechococcus elongatus PCC 7942]
          Length = 398

 Score =  201 bits (513), Expect = 7e-50,   Method: Composition-based stats.
 Identities = 66/242 (27%), Positives = 122/242 (50%), Gaps = 13/242 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   ++ ++LRLVV +A  Y+  GL + ++V EG +GL +AV+KFDP +G+R +TY+ 
Sbjct: 157 QRAKDHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLERAVEKFDPTKGYRFSTYAY 216

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   I      +++     +K     L R+K   + I     +   +  IA++L
Sbjct: 217 WWIRQGITRAIATQSRTIRLPVHVTEK-----LTRIKKAQRKIAQTKGRTANLEEIAQEL 271

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++  +V  +  R+    SL   +    +  ++  D L    +  +    E+  +++  N
Sbjct: 272 EMTPDQVREVLLRVPKSISLETRV--GKEKDTELGDLL----ETTDFTPEERLTQESLSN 325

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L R +  LN RER +   R    +    +L  +    ++SRERVRQIEA+A +K++   
Sbjct: 326 DLQRLLLELNHRERDVIRMRFGLRDGQIYSLAEIGQVLDLSRERVRQIEAKALQKLRHPR 385

Query: 285 QK 286
           ++
Sbjct: 386 RR 387


>gi|318056947|ref|ZP_07975670.1| RNA polymerase principal sigma factor [Streptomyces sp. SA3_actG]
 gi|318078687|ref|ZP_07986019.1| RNA polymerase principal sigma factor [Streptomyces sp. SA3_actF]
          Length = 307

 Score =  201 bits (513), Expect = 7e-50,   Method: Composition-based stats.
 Identities = 72/306 (23%), Positives = 129/306 (42%), Gaps = 39/306 (12%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVL---------AKRYRE------------- 43
           MS  +     +  Y+ EI + P+L+  +E  L         A++  +             
Sbjct: 1   MSGEIADRDLVGMYLDEIARTPLLDAAKEVELSQTIEAGVFARQILDGETDTKNETSREE 60

Query: 44  -----HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
                     A    + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +G
Sbjct: 61  LEALWEASERAKDVFIRSNLRLVVAVARRYPRAGLPLLDLIQEGNAGLVRAVEKFDYRKG 120

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           F+ +TY+ WWI+ A+   I      +++        L   L R++   +     + +  +
Sbjct: 121 FKFSTYATWWIRQAITRSIADQSRTIRLPVH-----LVEELGRIRRVQREFNREHGRDPE 175

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              IA +L  +   V  +        SLN  +   D+  +Q+ D L    D       + 
Sbjct: 176 HAEIAAELGSTPERVSDVLDWARDPVSLNMSV--DDEGDTQFGDLL---EDTSAVSPEQS 230

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARA 276
                R   L   +  L+ R   I + R   ++    TL  +  +  ++RER+RQIE  A
Sbjct: 231 VMTLLRSEELDELIGRLDERTASIIKMRYGIDDGRERTLTEVGKQHGLTRERIRQIEKHA 290

Query: 277 FKKVQE 282
             ++++
Sbjct: 291 LLELKK 296


>gi|295676469|ref|YP_003604993.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Burkholderia sp.
           CCGE1002]
 gi|295436312|gb|ADG15482.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Burkholderia sp.
           CCGE1002]
          Length = 362

 Score =  201 bits (513), Expect = 7e-50,   Method: Composition-based stats.
 Identities = 75/280 (26%), Positives = 130/280 (46%), Gaps = 15/280 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+
Sbjct: 82  DTIQHYLNRISVKPLLTVEEEQKYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGV 140

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++       
Sbjct: 141 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV--I 198

Query: 134 RLFFNLRRLKGHLQAITDN-----NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           R    + R K HL+  + N       +   +  IA     +  EV  +        SL+A
Sbjct: 199 RELNQVLRAKRHLEKNSMNSGEAAERRDASIDDIAYLTGKTTDEVTDILALNEHTASLDA 258

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            ++    +S               +V     + +    +    ++ L+ + R + E R  
Sbjct: 259 PLDLDPASSLLDLLSDDQSQSPDAEV-----QHRELETLTRAWLARLSDKHRHVIERRFG 313

Query: 249 QE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                P TLE L+ E  ++RERVRQI+  A  +++     
Sbjct: 314 LNHIEPATLEELADEMGLTRERVRQIQQEALVRLKRFFAS 353


>gi|186475727|ref|YP_001857197.1| RNA polymerase sigma factor RpoS [Burkholderia phymatum STM815]
 gi|184192186|gb|ACC70151.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia phymatum
           STM815]
          Length = 364

 Score =  201 bits (513), Expect = 8e-50,   Method: Composition-based stats.
 Identities = 75/280 (26%), Positives = 130/280 (46%), Gaps = 15/280 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+
Sbjct: 84  DTIQHYLNRISVKPLLTVEEEQRYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGV 142

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++       
Sbjct: 143 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV--I 200

Query: 134 RLFFNLRRLKGHLQAITDN-----NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           R    + R K HL+  + N       +   +  IA     +  EV  +        SL+A
Sbjct: 201 RELNQVLRAKRHLEKNSMNSGEAAERRDASIDDIAYLTGKTTDEVTDILALNEHTASLDA 260

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            ++    +S               +V     + +    +    ++ L+ + R + E R  
Sbjct: 261 PLDLDPASSLLDLLSDDQSQSPDAEV-----QHRELETLTRAWLARLSDKHRHVIERRFG 315

Query: 249 QE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                P TLE L+ E  ++RERVRQI+  A  +++     
Sbjct: 316 LNHIEPATLEELADEMGLTRERVRQIQQEALVRLKRFFAS 355


>gi|311897949|dbj|BAJ30357.1| putative RNA polymerase sigma factor [Kitasatospora setae KM-6054]
          Length = 323

 Score =  201 bits (513), Expect = 8e-50,   Method: Composition-based stats.
 Identities = 74/295 (25%), Positives = 128/295 (43%), Gaps = 38/295 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYR---------EHGD-----------------LSA 49
           +  Y+ EI + P+L+  EE  L+ R           + G+                   A
Sbjct: 29  VGMYLDEIARTPLLDAAEEVELSLRIEAGVFAQHLLDEGEGLDGVSTEELRAIAEDAERA 88

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
               + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ WWI
Sbjct: 89  KDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYSKGFKFSTYATWWI 148

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + A+   I      +++        L   L R++   +       +      IA +L+ +
Sbjct: 149 RQAITRSIADQSRTIRLPVH-----LVEELGRIRKVQREKAKELGREPDPAEIAAELDTT 203

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E  V  +        SLN  +   D+  +Q+ D +    D       +      RR  L 
Sbjct: 204 EQRVKDVLDWARDPVSLNMAV--DDEGETQFGDLV---EDTGAVSPEDAVMVMLRREELD 258

Query: 230 RSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             +  L+ R   I  +R   E+    TL  +  +  ++RER+RQIE  A  ++++
Sbjct: 259 GLIGRLDDRTASIIRSRYGMEDGRERTLTEVGKQHGLTRERIRQIEKHALAELKK 313


>gi|209522220|ref|ZP_03270857.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia sp. H160]
 gi|209497349|gb|EDZ97567.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia sp. H160]
          Length = 363

 Score =  201 bits (512), Expect = 9e-50,   Method: Composition-based stats.
 Identities = 75/280 (26%), Positives = 130/280 (46%), Gaps = 15/280 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+
Sbjct: 83  DTIQHYLNRISVKPLLTVEEEQKYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGV 141

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++       
Sbjct: 142 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV--I 199

Query: 134 RLFFNLRRLKGHLQAITDN-----NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           R    + R K HL+  + N       +   +  IA     +  EV  +        SL+A
Sbjct: 200 RELNQVLRAKRHLEKNSMNSGEAAERRDASIDDIAYLTGKTTDEVTDILALNEHTASLDA 259

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            ++    +S               +V     + +    +    ++ L+ + R + E R  
Sbjct: 260 PLDLDPASSLLDLLSDDQSQSPDAEV-----QHRELETLTRAWLARLSDKHRHVIERRFG 314

Query: 249 QE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                P TLE L+ E  ++RERVRQI+  A  +++     
Sbjct: 315 LNHIEPATLEELADEMGLTRERVRQIQQEALVRLKRFFAS 354


>gi|40353313|gb|AAR84420.1| essential primary sigma 70 factor [Frankia sp. ACN1ag]
          Length = 255

 Score =  201 bits (512), Expect = 9e-50,   Method: Composition-based stats.
 Identities = 69/265 (26%), Positives = 117/265 (44%), Gaps = 39/265 (14%)

Query: 31  KQEEYVLAKRY-------------------REHGDLSA--------AHRLVTSHLRLVVK 63
            +EE  LAKR                    +   DL A          +LV ++LRLVV 
Sbjct: 1   AEEEVDLAKRIEAGLFASEKLAVATKKTSPQMRRDLEAIERDGQIAKRKLVEANLRLVVS 60

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      
Sbjct: 61  IAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAIADQART 120

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           ++I     +      L R++  L         PE    IAK+++++  +V  +       
Sbjct: 121 IRIPVHMVE--TINKLIRIQRQLLQDLGREPSPE---EIAKEMDLTPDKVREILKVSQEP 175

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SL   I   ++  S   D++    D    V ++       +  L   +  L+ RE+++ 
Sbjct: 176 VSLETPI--GEEEDSHLGDFI---EDCDAVVPVDAASFILLQEXLDSVLHTLSDREKKVI 230

Query: 244 EARRL--QENPVTLENLSSEFEVSR 266
           + R      +P TLE +  EF V+R
Sbjct: 231 QLRFGLTDGHPRTLEEVGREFGVTR 255


>gi|209527735|ref|ZP_03276230.1| RNA polymerase, sigma 70 subunit, RpoD family [Arthrospira maxima
           CS-328]
 gi|209491813|gb|EDZ92173.1| RNA polymerase, sigma 70 subunit, RpoD family [Arthrospira maxima
           CS-328]
          Length = 332

 Score =  201 bits (512), Expect = 9e-50,   Method: Composition-based stats.
 Identities = 69/321 (21%), Positives = 141/321 (43%), Gaps = 52/321 (16%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------------------ 43
             +  Y+HEI ++P+L ++EE +  K+ ++                              
Sbjct: 23  DAVRTYLHEIGRVPLLTREEEIIYGKKVQQMMSLLEMRDELTKELDHDPTAAEWSAKAGL 82

Query: 44  ---------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                    +    A  +++ ++LRLVV IA  Y+   +   +++ EG +GL + V+KFD
Sbjct: 83  SESEMTEIMNRGRRAKQKMIEANLRLVVSIAKKYQKRNMEFLDLIQEGTLGLERGVEKFD 142

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P RG++ +TY+ WWI+ A+   I ++   +++     +K     L ++K   + +     
Sbjct: 143 PMRGYKFSTYAYWWIRQAITRAIAQNSRTIRLPIHITEK-----LNKIKRVQRELFQQYG 197

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +      IAK L++  S++           SL+  +   D   ++ QD L  +    +  
Sbjct: 198 RNATPTEIAKALDLEPSQIRDYLLASRHPVSLD--LRVGDNQDTELQDLLEDESASADNY 255

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
           + ++  R++    L   M+ L P++R +   R    +   ++L  +     +SRERVRQ+
Sbjct: 256 VTQQLLRQD----LKDLMADLTPQQREVLTLRYGLNDGKEMSLSKVGVHMNISRERVRQL 311

Query: 273 EARAFKKVQESIQKQVELSSS 293
           E +A   ++    +  E  +S
Sbjct: 312 ENQALNHLRRRKAQVREYLAS 332


>gi|168704760|ref|ZP_02737037.1| transcription initiation factor sigma 70 [Gemmata obscuriglobus UQM
           2246]
          Length = 556

 Score =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 71/273 (26%), Positives = 124/273 (45%), Gaps = 17/273 (6%)

Query: 21  HEIRKIPMLEKQEEYVLAKRY-----REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
            E++ + ++  +E   L +R      R      A   L   +LRLVV IA  YR  GL  
Sbjct: 279 KELQDLMLITLEEPASLRRRVGIMKQRFAEYEQAKRDLSGGNLRLVVSIAKKYRNRGLSF 338

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN GLM+AV K++  RGF+ +TY+ WWI+ A+   I      ++I        +
Sbjct: 339 LDLIQEGNTGLMRAVDKYEHRRGFKFSTYATWWIRQAITRAIADQARTIRIPVH-----M 393

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + +L+   + +     +   V   A    +S  E   +        SL+  +   + 
Sbjct: 394 IETMSKLRNVSKQLLQELGREPTVQETADAAKISYEECKRVLKISRQPISLDRPV--GES 451

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--V 253
             S + D++    D   +  +     +  ++ +   +  L  RER I + R    +    
Sbjct: 452 EDSYFGDFI---EDNSVESPVNAATNEMLKDKIEGVLKTLTYREREIIKLRYGLGDGYTY 508

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TLE +   F+V+RERVRQIEA+A +K+Q  ++ 
Sbjct: 509 TLEEVGRIFKVTRERVRQIEAKAVRKLQHPVRS 541


>gi|149278736|ref|ZP_01884871.1| RNA polymerase sigma-70 factor [Pedobacter sp. BAL39]
 gi|149230355|gb|EDM35739.1| RNA polymerase sigma-70 factor [Pedobacter sp. BAL39]
          Length = 286

 Score =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 74/283 (26%), Positives = 151/283 (53%), Gaps = 13/283 (4%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
            SI       + +Y+ +I +I +L  +EE  LA+R ++ GD +A  +LV ++LR VV +A
Sbjct: 8   QSITNRETNSIDKYLTDIGRIGLLSVEEELGLARRIKK-GDEAALDKLVKTNLRFVVSVA 66

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y+  GL +++++SEGN+GL++A ++FD  +GF+  ++++WWI+ ++ + +     +++
Sbjct: 67  KKYQNKGLQLADLISEGNLGLIKAAQRFDDTKGFKFISFAVWWIRQSIMQALADQKRMIR 126

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           +    NQ      + +    L+ + +   +      +A     SE++V           S
Sbjct: 127 LP--GNQVLGIIKINKAADELEQVLE---RAPTYEELAMATEFSEAKVADYLDSAPLSYS 181

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L+   +  +++     D LV ++      L+ KE        + RS+S+L  RE+ I   
Sbjct: 182 LDMTTH--EESDFSLMDTLVNENTPDTDELMMKESMS---EDVRRSLSILPEREKWIIIF 236

Query: 246 RRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
               +N   +TL++++  F++S+ER+RQ++ RA K ++ S +K
Sbjct: 237 FFGLDNHTALTLDDMTDVFQLSKERIRQLKDRALKTLKTSCRK 279


>gi|323526138|ref|YP_004228291.1| RNA polymerase sigma-70 subunit RpoD subfamily [Burkholderia sp.
           CCGE1001]
 gi|323383140|gb|ADX55231.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Burkholderia sp.
           CCGE1001]
          Length = 358

 Score =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 75/280 (26%), Positives = 130/280 (46%), Gaps = 15/280 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+
Sbjct: 78  DTIQHYLNRISVKPLLTVEEEQKYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGV 136

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++       
Sbjct: 137 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV--I 194

Query: 134 RLFFNLRRLKGHLQAITDN-----NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           R    + R K HL+  + N       +   +  IA     +  EV  +        SL+A
Sbjct: 195 RELNQVLRAKRHLEKNSMNSGEAAERRDASIDDIAYLTGKTTDEVTDILALNEHTASLDA 254

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            ++    +S               +V     + +    +    ++ L+ + R + E R  
Sbjct: 255 PLDLDPASSLLDLLSDDQSQSPDAEV-----QHRELETLTRAWLARLSDKHRHVIERRFG 309

Query: 249 QE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                P TLE L+ E  ++RERVRQI+  A  +++     
Sbjct: 310 LNHIEPATLEELADEMGLTRERVRQIQQEALVRLKRFFAS 349


>gi|33240031|ref|NP_874973.1| putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus subsp. marinus str. CCMP1375]
 gi|33237557|gb|AAP99625.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Prochlorococcus marinus subsp. marinus str. CCMP1375]
          Length = 310

 Score =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 81/303 (26%), Positives = 140/303 (46%), Gaps = 43/303 (14%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYV----------LAKRYREHGD------------------ 46
            LS ++ EI + P+L  +EE            L +R    GD                  
Sbjct: 3   SLSDFLGEIGRHPLLTPEEELTMGRKVQAMVGLIERCHRAGDQGADCVYTEAERRTIKIG 62

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + ++T++LRLVV +A  Y+G GL + +++ EG IGL +AV+K+DP+RG R +TY+ 
Sbjct: 63  EKAKNHMITANLRLVVNLAKKYQGKGLDLLDLIQEGTIGLTRAVEKYDPKRGHRFSTYAY 122

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   +      ++I    N+K     L +L+     +      P     +AKKL
Sbjct: 123 WWIRQGLNRALSTQSRTIRIPVNINEK-----LTKLRAAKSELMQEYGTPPSAEQLAKKL 177

Query: 167 NVSES---EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           +VS+    +++    R +   SL  +I S   + S+  D L  D     ++    E   +
Sbjct: 178 SVSKQIIGDLLECEMR-SITVSLQGVIQSK-TDPSELGDVLPSDEIPPMELAELAERNDS 235

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++L ++   L P+ER I   R   +      TL  ++     SRE  RQ+  RA +K+
Sbjct: 236 AWSLLNKA--NLTPKERTIVSLRFGLDGTNEWRTLAEVAKHMNCSREYCRQVVQRALRKL 293

Query: 281 QES 283
           +++
Sbjct: 294 RKT 296


>gi|1553033|gb|AAC45108.1| primary sigma factor [Borrelia japonica]
          Length = 450

 Score =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 66/250 (26%), Positives = 119/250 (47%), Gaps = 16/250 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 215 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 270

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RGF+ +TY+ WWI+ A+   I      +++        +   + RL    + +   
Sbjct: 271 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVH-----MIEQINRLNRETRYLIQV 325

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             K      ++ +L     +V ++        SL   I   ++  S   D++    D   
Sbjct: 326 LGKDPTDEELSDRLGWELKKVKTVKSVSREPVSLETPI--GEEEDSVLSDFI---EDKAI 380

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +           ++ +   +  L  RE+ + + R   E+   +TLE +   F V+RER+R
Sbjct: 381 KNPANHTSFVVLQDQIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIR 440

Query: 271 QIEARAFKKV 280
           QIE++A +++
Sbjct: 441 QIESKALRRL 450


>gi|218439771|ref|YP_002378100.1| RNA polymerase sigma factor [Cyanothece sp. PCC 7424]
 gi|218172499|gb|ACK71232.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
          Length = 328

 Score =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 64/323 (19%), Positives = 143/323 (44%), Gaps = 53/323 (16%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------------- 43
           +N K      + ++ +  Y+HEI ++P+L  ++E V  K+ ++                 
Sbjct: 6   VNPKTQKPTFSADM-VRTYLHEIGRVPLLTHEQEIVYGKQVQKMMTLLEKKDQLAIELGK 64

Query: 44  ----------------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
                                      A  +++ ++LRLVV IA  Y+   +   +++ E
Sbjct: 65  EPNLTEWANQVQMSEEELNRAIQQGKRAKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQE 124

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           G++GL + V+KFDP +G++ +TY+ WWI+ A+   I +    +++     +K     L +
Sbjct: 125 GSLGLERGVEKFDPTKGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEK-----LNK 179

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           +K   + ++    +      IAK L++  +++           SL+  +   D   ++  
Sbjct: 180 IKKTQRELSQQLGRSATPAEIAKALDLEPAQIREFLSMSRQPISLD--VRVGDNQDTELS 237

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLS 259
           + L  +    +  + ++  R++    L   ++ L P++R +   R   ++   ++L  + 
Sbjct: 238 ELLEDEGISPDNYITQELMRQD----LHDLLAELTPQQREVLSLRFGLQDGKELSLAKIG 293

Query: 260 SEFEVSRERVRQIEARAFKKVQE 282
               +SRERVRQ+E +A  +++ 
Sbjct: 294 QRMNISRERVRQLEHQALSQLRR 316


>gi|186680839|ref|YP_001864035.1| RpoD family RNA polymerase sigma factor [Nostoc punctiforme PCC
           73102]
 gi|186463291|gb|ACC79092.1| RNA polymerase, sigma 70 subunit, RpoD family [Nostoc punctiforme
           PCC 73102]
          Length = 378

 Score =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 75/313 (23%), Positives = 138/313 (44%), Gaps = 52/313 (16%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------------------------------ 42
           +  +  +  E+ + P+L+  EE  LA+R R                              
Sbjct: 65  DDAVGAFFKEMARYPLLKADEEVELARRVRFLEEIRELQAALNLKLGQEPTKLEIASELE 124

Query: 43  ---------EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
                     +    A  +++ S+LRLVV IA  Y   G+P  +++ EG +GL +A +KF
Sbjct: 125 MTEKQLESRLYQGRVAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAMGLNRATEKF 184

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           DP++G++ +TY+ WWI+ A+   I      +++     +K     L +LK   + +    
Sbjct: 185 DPDKGYKFSTYAYWWIRQAITRAIANDARTIRLPIHIVEK-----LNKLKKAQRELKQKL 239

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD-GQE 212
            +      +A+ L++S  ++  +        SLN  +    +  ++  D L  + +   E
Sbjct: 240 CRNPTEGEMAEALDISVQQLRQLQQLRRQALSLNHRV--GKEEDTELMDLLEDEDNLSPE 297

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVR 270
             + E   R+    +L     VL PRE+ +   R       P TLE + + F +SRERVR
Sbjct: 298 AKMNENMMRQEIWEVLG---DVLTPREKDVISLRYGLTTSEPCTLEEVGNMFNLSRERVR 354

Query: 271 QIEARAFKKVQES 283
           QI+++A +K++  
Sbjct: 355 QIQSKAMRKLRRP 367


>gi|296127362|ref|YP_003634614.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Brachyspira
           murdochii DSM 12563]
 gi|296019178|gb|ADG72415.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Brachyspira
           murdochii DSM 12563]
          Length = 309

 Score =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 78/306 (25%), Positives = 141/306 (46%), Gaps = 38/306 (12%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSA----------- 49
           M +K+++    G + +  Y+ +I +I  L K+EE  L +R     D  A           
Sbjct: 1   MLKKDVNQEYKGPVSV--YLKQIGEIRRLSKEEELDLWQRLEVCRDKKALLLEKEDEESK 58

Query: 50  -------------AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                         H+LV S+LRLV+ IA  Y   G+P  +++ EGNIGL++AVK+F+ +
Sbjct: 59  KELESLEKEIDSIQHKLVKSNLRLVISIAKRYYNSGVPFIDIIDEGNIGLIEAVKRFEYK 118

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +GF+ +TY +WWIK ++ + I     +++             +++     + +T    + 
Sbjct: 119 KGFKFSTYGVWWIKQSIVKEISSKRHIIRFPMHIA-----RLIKKSIQTSKVLTQKLGRE 173

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
                IAK++ +    +  +        S+++   +SD N     D      D       
Sbjct: 174 PTTDEIAKEMKIDRKTLSYIMIFTQDTASVDSFFKNSDNN-----DMTSIIEDKNFPSPH 228

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEA 274
           +K    + R+ LT ++  L+ +ER +  +R         TLE+   E  ++RERVRQI+ 
Sbjct: 229 QKAFMDSLRDTLTEALKCLDEKERTVIISRFGLYGKEAKTLEDTGKELNITRERVRQIQI 288

Query: 275 RAFKKV 280
           +A KK+
Sbjct: 289 KAIKKL 294


>gi|291287615|ref|YP_003504431.1| RNA polymerase, sigma 32 subunit, RpoH [Denitrovibrio acetiphilus
           DSM 12809]
 gi|290884775|gb|ADD68475.1| RNA polymerase, sigma 32 subunit, RpoH [Denitrovibrio acetiphilus
           DSM 12809]
          Length = 301

 Score =  201 bits (512), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 74/287 (25%), Positives = 138/287 (48%), Gaps = 15/287 (5%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
             K M   V+ E  L  Y++ I     + K +E+ + +R +  GD  A + L+  +L+ V
Sbjct: 20  TAKVMPAPVS-ETSLKHYLNSISAYKPMTKAQEFAIGERIQ-AGDEDALNTLILCNLKFV 77

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA  YR  GLPI++++++GN+GL++A K+FD  +  +  +Y++WWI+ ++ + +    
Sbjct: 78  VSIANRYRNTGLPIADIINQGNLGLVEAAKRFDHTKDVKFISYAVWWIRQSIIQALAEQS 137

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             VK+            L ++ G  + +     +      +A++L + E+++ ++     
Sbjct: 138 GTVKLPIKQA-----GILYKINGATEKLNKKLNREPTASELAEQLEMDEADIENVLRVSR 192

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              SL A I   +  S       +   +   + + E    K  +  L   +  L+ RE +
Sbjct: 193 NYLSLEAPIKDGEDRS------FIDLLESGTKDIEEDIISKTLKTALDDIVDELDERESQ 246

Query: 242 IFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           I E R       P TLE +    ++SRERVRQ+E RA  K+++   K
Sbjct: 247 IIEWRFGLNEEAPKTLEEIGELMDISRERVRQLETRALSKLRKKAMK 293


>gi|282897491|ref|ZP_06305492.1| sigC (Sigma 28 (Flagella/Sporulation)) [Raphidiopsis brookii D9]
 gi|281197586|gb|EFA72481.1| sigC (Sigma 28 (Flagella/Sporulation)) [Raphidiopsis brookii D9]
          Length = 429

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 68/267 (25%), Positives = 133/267 (49%), Gaps = 18/267 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            +I  L  +E        +  G + A   ++ ++LRLVV +A  Y+  GL + ++V EG 
Sbjct: 170 GEIAQLTVEE----LDEIQSQG-IQAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGT 224

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           +GL +AV+KFDP +G+R +TY+ WWI+  +   I  S   +++     +K     L ++K
Sbjct: 225 LGLERAVEKFDPTKGYRFSTYAYWWIRQGITRAIATSSRTIRLPVHITEK-----LNKIK 279

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
              + I     +   +  +A +L+++ ++V  +  R+    SL   +       ++  + 
Sbjct: 280 KAQRKIAQEKGRTPTLEDLALELDMTPNQVREVLLRVPRSVSLETKV--GKDKDTELGEL 337

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSE 261
           L  D    E+ L+ +  +K+    +   +S L  RER +   R      +  +L  +   
Sbjct: 338 LETDTITPEETLMRESLQKD----IHHLLSDLTTREREVILMRFGLADGHSYSLAEIGRA 393

Query: 262 FEVSRERVRQIEARAFKKVQESIQKQV 288
            E+SRERVRQIE++A +K+++  ++ +
Sbjct: 394 LELSRERVRQIESKALQKLRQPKRRNL 420


>gi|325107209|ref|YP_004268277.1| RNA polymerase, sigma 70 subunit, RpoD [Planctomyces brasiliensis
           DSM 5305]
 gi|324967477|gb|ADY58255.1| RNA polymerase, sigma 70 subunit, RpoD [Planctomyces brasiliensis
           DSM 5305]
          Length = 590

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 67/247 (27%), Positives = 117/247 (47%), Gaps = 12/247 (4%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
           R H   +A   L   +LRLVV IA  YR  G+   +++ EGN GLM+AV K++  RG++ 
Sbjct: 336 RYHDYETAMRELSGGNLRLVVSIAKKYRNRGMNFLDLIQEGNTGLMRAVDKYEYRRGYKF 395

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY+ WWI+ A+   I      ++I        +   + +L+   + +     +   +  
Sbjct: 396 STYATWWIRQAITRAIADQARTIRIPVH-----MIETMSKLRKVGKDLVQELGREPTIEE 450

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           +A+   VS  E   +        SL+  I   +   S + D++    D      +    +
Sbjct: 451 MAEAAEVSLEEARRVMKISRQPISLDRPI--GEGEDSYFGDFI---EDHSTDSPVSTATQ 505

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKK 279
           +  ++ +   +  L  RER I + R    +    TLE +   F+V+RERVRQIEA+A +K
Sbjct: 506 EMLKDKIDHVLKTLTYREREIIKLRYGLGDGYTYTLEEVGRIFKVTRERVRQIEAKAVRK 565

Query: 280 VQESIQK 286
           +Q  ++ 
Sbjct: 566 LQHPVRS 572


>gi|282895663|ref|ZP_06303788.1| sigF (Sigma 28 (Flagella/Sporulation)) [Raphidiopsis brookii D9]
 gi|281199357|gb|EFA74222.1| sigF (Sigma 28 (Flagella/Sporulation)) [Raphidiopsis brookii D9]
          Length = 396

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 75/313 (23%), Positives = 135/313 (43%), Gaps = 52/313 (16%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYR---EHGDLSA-------------------- 49
           +  +  +  E+ + P+L+  EE  LA R R   E  DL A                    
Sbjct: 83  DDAVGAFFKEMARYPLLKPDEEVELAHRVRFLEEVKDLQAALEEQFGHSATKGEIANKFD 142

Query: 50  ----------------AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
                             +++ S+LRLVV IA  Y   G+P  +++ EG +GL +A +KF
Sbjct: 143 LNEKQLENRLYQGRVAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAMGLNRATEKF 202

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           DP++G++ +TY+ WWI+ A+   I      +++     +K     L +LK   + +    
Sbjct: 203 DPDKGYKFSTYAYWWIRQAITRAIANDARTIRLPIHIVEK-----LNKLKKAQRELKQKF 257

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            +      +A+ L ++  ++  +        SLN  +    +  ++  D L  + +   Q
Sbjct: 258 ARNPTEAEMAEFLEMTVQQLRQLQQLRRQALSLNHRV--GKEEDTELMDLLEDEDN---Q 312

Query: 214 VLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVR 270
               K      R  +   +  VL  RE+ +   R       P TLE + + F +SRERVR
Sbjct: 313 SPEAKMNENMMRQEIWEVLGDVLTSREKDVISLRYGLTTSEPCTLEEVGNIFNLSRERVR 372

Query: 271 QIEARAFKKVQES 283
           QI+++A +K++  
Sbjct: 373 QIQSKAMRKLRRP 385


>gi|303235908|ref|ZP_07322511.1| putative RNA polymerase sigma factor RpoD [Prevotella disiens
           FB035-09AN]
 gi|302483781|gb|EFL46773.1| putative RNA polymerase sigma factor RpoD [Prevotella disiens
           FB035-09AN]
          Length = 293

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 69/286 (24%), Positives = 141/286 (49%), Gaps = 12/286 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ +  +  M+   EE  LAKR RE GD  A  RL  ++LR VV
Sbjct: 11  KITKSITNRESTALEKYLQDTSREAMVGLDEEIELAKRIRE-GDEKALERLTKANLRFVV 69

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN GL++A +K+D  RGF+  +Y++WWI+ ++ + I     
Sbjct: 70  SVAKQYQNQGLALPDLINEGNFGLIKAAQKYDETRGFKFISYAVWWIRQSIMQAISEQSR 129

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++           +  R++  +      + +   +  + + +++ E +++        
Sbjct: 130 MVRVPINQ-----MGSANRIRKFINQFEQEHERYPSLSELTEHIDLLEEKIVEALAMATT 184

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A   S+++ S    D L   +      L+  E        +  +++ L+ RE+ I
Sbjct: 185 QVSMDAPFTSNEEGS--LLDVLPNKNAPSADDLLVAESLSTE---VANALASLSEREQII 239

Query: 243 FEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +       P ++LE +     ++RERVRQI+ +A  +++++ Q +
Sbjct: 240 IKCFFGINQPEMSLEEIGERTGLTRERVRQIKEKAIIRLRKNSQSE 285


>gi|1553019|gb|AAC45101.1| primary sigma factor [Borrelia garinii]
          Length = 450

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 66/250 (26%), Positives = 119/250 (47%), Gaps = 16/250 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 215 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 270

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RGF+ +TY+ WWI+ A+   I      +++        +   + RL    + +   
Sbjct: 271 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVH-----MIEQINRLNRETRYLVQV 325

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             K      ++ +L     +V ++        SL   I   ++  S   D++    D   
Sbjct: 326 LGKDPTDEELSDRLGWELKKVKTVKSVSREPVSLETPI--GEEEDSVLSDFI---EDKAI 380

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +           ++ +   +  L  RE+ + + R   E+   +TLE +   F V+RER+R
Sbjct: 381 KNPANHTSFVVLQDQIRSILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIR 440

Query: 271 QIEARAFKKV 280
           QIE++A +++
Sbjct: 441 QIESKALRRL 450


>gi|308273000|emb|CBX29604.1| hypothetical protein N47_J05850 [uncultured Desulfobacterium sp.]
          Length = 326

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 92/275 (33%), Positives = 162/275 (58%), Gaps = 8/275 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY-GLP 74
              Y+ EI +  +L ++EE  LA   ++  D  +A +L+TS+LRLVVKIA  ++ Y    
Sbjct: 46  FQSYLREISQYRLLSREEEIELAINVKDKDDKESASKLITSNLRLVVKIAFNFQHYLANN 105

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++ EGNIGL+ AVKK+DP +G + + Y+ +WI+A + ++I+ +W ++KIGTT  Q++
Sbjct: 106 VPDLIQEGNIGLIHAVKKYDPYKGVKFSYYAAFWIRAYIFKFIMNNWDMLKIGTTQKQRK 165

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALINSS 193
           LFFNL + +   + IT   L PE  + +A++L V E++++ M  RL     SLN  ++  
Sbjct: 166 LFFNLNKER---RQITAEGLNPEPKL-LAERLGVQENDIVQMIPRLDYSPLSLNQPLSED 221

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
            K     ++ +   +      L   E + N    L +   +L   +  IF+ R + ENPV
Sbjct: 222 SKEC--LEERVQDKNASTIDQLSVLESKTNLERELKKFRKLLKGIKADIFDMRIMAENPV 279

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +L+++   +++SRERVRQI+     K+ + ++KQ+
Sbjct: 280 SLQSIGDRYQISRERVRQIQEMIINKIGKWLKKQI 314


>gi|297569039|ref|YP_003690383.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfurivibrio
           alkaliphilus AHT2]
 gi|296924954|gb|ADH85764.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfurivibrio
           alkaliphilus AHT2]
          Length = 445

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 64/241 (26%), Positives = 117/241 (48%), Gaps = 13/241 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   ++ ++LRLVV IA  Y   GL +++++ EGN+GLM+AV +FD  +G + +TY+ WW
Sbjct: 209 AKDAMIKANLRLVVSIAKRYMHQGLTLADLIQEGNLGLMRAVFRFDYTKGNKFSTYASWW 268

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   IL     +++     + R  F          ++     +      I++K  +
Sbjct: 269 IRQAITRAILDKTRTIRLPVHFLELRSQFF-----KAFYSLLKELGREPTPAEISEKTGL 323

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +++++        SL   +   D   S   D+L    + +     E  +       +
Sbjct: 324 PMEKILAIFEASREPISLETPVGDDD---STLGDFL---ENQESVSPYEAVKGNQLAERV 377

Query: 229 TRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           T  +S L+PRE +I   R    ++   TLE +   F VSRER+RQIE +A  +++ S ++
Sbjct: 378 TTILSTLSPREEKIIRLRFGIGEDAEYTLEEIGKRFNVSRERIRQIEKKALNRLRHSSRR 437

Query: 287 Q 287
           +
Sbjct: 438 E 438


>gi|1553017|gb|AAC45100.1| primary sigma factor [Borrelia burgdorferi 297]
          Length = 450

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 66/250 (26%), Positives = 119/250 (47%), Gaps = 16/250 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 215 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 270

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RGF+ +TY+ WWI+ A+   I      +++        +   + RL    + +   
Sbjct: 271 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVH-----MIEQINRLNRETRYLIQV 325

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             K      ++ +L     +V ++        SL   I   ++  S   D++    D   
Sbjct: 326 LGKDPTDEELSDRLGWELKKVKTVKSVSREPVSLETPI--GEEEDSVLSDFI---EDKAI 380

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +           ++ +   +  L  RE+ + + R   E+   +TLE +   F V+RER+R
Sbjct: 381 KNPANHTSFVVLQDQIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIR 440

Query: 271 QIEARAFKKV 280
           QIE++A +++
Sbjct: 441 QIESKALRRL 450


>gi|75907421|ref|YP_321717.1| sigma 28 (flagella/sporulation) [Anabaena variabilis ATCC 29413]
 gi|75701146|gb|ABA20822.1| Sigma 28 (Flagella/Sporulation) [Anabaena variabilis ATCC 29413]
          Length = 378

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 76/313 (24%), Positives = 137/313 (43%), Gaps = 52/313 (16%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYR---EHGDLSA-------------------- 49
           +  +  +  E+ + P+L+  EE  LA+R R   E  DL A                    
Sbjct: 65  DDAVGAFFKEMARYPLLKPDEEVELARRVRFLEEVRDLQADLQLQLGLHPTKAQVAAQLE 124

Query: 50  ----------------AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
                             +++ S+LRLVV IA  Y   G+P  +++ EG +GL +A +KF
Sbjct: 125 ITEKQLENRLYQGRVAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAMGLNRATEKF 184

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           DP++G++ +TY+ WWI+ A+   I      +++     +K     L +LK   + +    
Sbjct: 185 DPDKGYKFSTYAYWWIRQAITRAIANDARTIRLPIHIVEK-----LNKLKKAQRELKQKF 239

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            +      +A+ L +S  ++  +        SLN  +    +  ++  D L  + +   +
Sbjct: 240 SRNPSEAEMAEALEISVPQLRQLQQLRRQALSLNHRV--GKEEDTELMDLLEDEDNLSPE 297

Query: 214 VLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVR 270
               K      R  +   +  VL PRE+ +   R       P TLE + + F +SRERVR
Sbjct: 298 A---KMNENMMRQEIWEVLGDVLTPREKDVISLRYGLTTSEPCTLEEVGNMFNLSRERVR 354

Query: 271 QIEARAFKKVQES 283
           QI+++A +K++  
Sbjct: 355 QIQSKAMRKLRRP 367


>gi|17231741|ref|NP_488289.1| group 2 sigma 70-type sigma factor F [Nostoc sp. PCC 7120]
 gi|8489803|gb|AAF75759.1|AF262218_1 group 2 sigma 70-type sigma factor F [Nostoc sp. PCC 7120]
 gi|17133384|dbj|BAB75948.1| group 2 sigma 70-type sigma factor F [Nostoc sp. PCC 7120]
          Length = 390

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 76/313 (24%), Positives = 137/313 (43%), Gaps = 52/313 (16%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYR---EHGDLSA-------------------- 49
           +  +  +  E+ + P+L+  EE  LA+R R   E  DL A                    
Sbjct: 77  DDAVGAFFKEMARYPLLKPDEEVELARRVRFLEEVRDLQADLQLQIGQHPTKAQVAGQLE 136

Query: 50  ----------------AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
                             +++ S+LRLVV IA  Y   G+P  +++ EG +GL +A +KF
Sbjct: 137 ITEKQLENRLYQGRVAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAMGLNRATEKF 196

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           DP++G++ +TY+ WWI+ A+   I      +++     +K     L +LK   + +    
Sbjct: 197 DPDKGYKFSTYAYWWIRQAITRAIANDARTIRLPIHIVEK-----LNKLKKAQRELKQKF 251

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            +      +A+ L +S  ++  +        SLN  +    +  ++  D L  + +   +
Sbjct: 252 SRNPSEAEMAEALEISVPQLRQLQQLRRQALSLNHRV--GKEEDTELMDLLEDEDNLSPE 309

Query: 214 VLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVR 270
               K      R  +   +  VL PRE+ +   R       P TLE + + F +SRERVR
Sbjct: 310 A---KMNENMMRQEIWEVLGDVLTPREKDVISLRYGLTTSEPCTLEEVGNMFNLSRERVR 366

Query: 271 QIEARAFKKVQES 283
           QI+++A +K++  
Sbjct: 367 QIQSKAMRKLRRP 379


>gi|291566491|dbj|BAI88763.1| group 2 RNA polymerase sigma factor SigC [Arthrospira platensis
           NIES-39]
          Length = 385

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 68/260 (26%), Positives = 133/260 (51%), Gaps = 18/260 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L  +E     K+ +  G + A   ++ ++LRLVV +A  Y+  GL + +++ EG +GL +
Sbjct: 131 LSVEE----LKQVQREG-IQAKDHMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLER 185

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           AV+KFDP RG+R +TYS WWI+  +   I      +++     +K     L ++K   + 
Sbjct: 186 AVEKFDPTRGYRFSTYSYWWIRQGITRAIATQSRTIRLPVHITEK-----LNKIKKAQRK 240

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           I+    +   +  IA +L ++  ++  +  R+    SL   +       ++  D L  + 
Sbjct: 241 ISQEKSRTATIDDIATELKMTPDQIREVLLRVPRSVSLETKV--GTDKDTELGDLLETEE 298

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSR 266
              E++L+    R++    L   ++ L+ +ER + + R      +P +L  +    ++SR
Sbjct: 299 STPEELLM----RESLYRELQHILADLSGKERAVIQMRYGLGDGHPYSLAEIGRALDLSR 354

Query: 267 ERVRQIEARAFKKVQESIQK 286
           ERVRQIEA+A +K+++  ++
Sbjct: 355 ERVRQIEAKALQKLRQPKRR 374


>gi|282896368|ref|ZP_06304389.1| sigD (sigma 28 (flagella/spoulation)) [Raphidiopsis brookii D9]
 gi|281198656|gb|EFA73536.1| sigD (sigma 28 (flagella/spoulation)) [Raphidiopsis brookii D9]
          Length = 332

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 68/323 (21%), Positives = 134/323 (41%), Gaps = 52/323 (16%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------EHGD-------- 46
           +N   M         +  Y+ EI K+P+L  ++E    K+ +      E  D        
Sbjct: 10  LNSNAMKTAQTPTDIVRTYLREIGKVPLLTHEQEIYYGKQVQKSTALYETKDNLAQELNR 69

Query: 47  -------------------------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
                                      A  ++V ++LRL+V +A  Y    + + +++ E
Sbjct: 70  QPSLEEWAKAAQLDPQELNRLLAQGEIAKRKMVEANLRLLVSVAKKYIKRNVDLLDLIQE 129

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           G+IG+ + V+KFDP +G+R +TY+ WWI+ A+   I      +++     +K     L +
Sbjct: 130 GSIGMQRGVEKFDPSKGYRFSTYAYWWIRQAITRAIAEKARTIRLPIHITEK-----LNK 184

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           +K   + ++    +   +  +A++L ++  +V     +     SL+  +   D   ++  
Sbjct: 185 IKKAQRDLSQTLGRSPSIAELAQELEITPKQVRDCLEKARLPLSLD--LRLGDNYDTELG 242

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLS 259
           + L       E  +I+          L R M+ L  ++R + + R        +TL  + 
Sbjct: 243 EMLEDPGASPEDYVIQSSLSSE----LERMMTHLTTQQREVIKLRFGLVDGQSMTLARIG 298

Query: 260 SEFEVSRERVRQIEARAFKKVQE 282
               +SRERVRQIE  A  +++ 
Sbjct: 299 EVLNISRERVRQIEREALTRLRR 321


>gi|300871837|ref|YP_003786710.1| RNA polymerase sigma factor RpoD [Brachyspira pilosicoli 95/1000]
 gi|300689538|gb|ADK32209.1| RNA polymerase sigma factor, RpoD [Brachyspira pilosicoli 95/1000]
          Length = 314

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 81/291 (27%), Positives = 140/291 (48%), Gaps = 36/291 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRY---REHGDL---------------------SAAH 51
           +S Y+ +I +I  L K+EE  L +R    RE+ +                      S  H
Sbjct: 19  VSVYLKQIGEIRRLTKEEELELWQRLEVCRENKNKLIDEDEEKYSKEIEEIDKEIDSIQH 78

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +LV S+LRLV+ IA  Y   G+P  +++ EGNIGL++AVK+F+  +GF+ +TY +WWIK 
Sbjct: 79  KLVKSNLRLVISIAKRYYNSGVPFIDIIDEGNIGLIEAVKRFEYRKGFKFSTYGVWWIKQ 138

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ + I     +++        RL     ++  +L   T    +   +  IAK++ +   
Sbjct: 139 SIVKEISSKRHIIRFPMHIA--RLIKKSIQISKNL---TQQLGREPSIDEIAKEMKIDRK 193

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
            + S+        S+++   +SD N     D   +  D       +    ++ R+ LT +
Sbjct: 194 TLSSIIVFTQETASVDSFFKNSDNN-----DMTSFIEDKNFPSPHQDAFMESLRDTLTEA 248

Query: 232 MSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           +  L+ +ER +   R       P TLE+   E  ++RERVRQI+ +A KK+
Sbjct: 249 LKALDEKERTVIIERFGLYGKEPKTLEDTGKELNITRERVRQIQIKALKKL 299


>gi|218247332|ref|YP_002372703.1| RNA polymerase sigma factor [Cyanothece sp. PCC 8801]
 gi|218167810|gb|ACK66547.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8801]
          Length = 328

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 69/323 (21%), Positives = 143/323 (44%), Gaps = 53/323 (16%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------EHGDL------- 47
           +N K    + + ++ +  Y+HEI ++P+L  ++E V  K+ +      E  D        
Sbjct: 6   VNSKTKQPMYSADM-VRTYLHEIGRVPLLTHEQEIVYGKQVQRMMSLFEMKDQLTQAQGT 64

Query: 48  --------------------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
                                      A  +++ ++LRLVV IA  Y+   +   +++ E
Sbjct: 65  EPSDKEWAKAVNLKEPELKKTIEQGNRAKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQE 124

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           G++GL + V+KFDP +G++ +TY+ WWI+ A+   I +    +++     +K     L +
Sbjct: 125 GSLGLERGVEKFDPTKGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEK-----LNK 179

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           +K   + ++    +      IA  L +  S++           SL+  +   D   ++  
Sbjct: 180 IKKTQRELSQKLGRSATPAEIAAVLEIEPSQIRECLSMARQPISLD--VRVGDNQDTELS 237

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLS 259
           + L       +Q + ++  R++    L   M  L P++R +   R   E+   ++L  + 
Sbjct: 238 ELLEDHEASPDQYITQELLRQD----LKNLMEELTPQQRSVLILRFGLEDGKELSLAKIG 293

Query: 260 SEFEVSRERVRQIEARAFKKVQE 282
            +  +SRERVRQ+E +A  +++ 
Sbjct: 294 KKLNISRERVRQLEHQALAQLRR 316


>gi|300868245|ref|ZP_07112876.1| RNA polymerase sigma factor SigD [Oscillatoria sp. PCC 6506]
 gi|300333769|emb|CBN58060.1| RNA polymerase sigma factor SigD [Oscillatoria sp. PCC 6506]
          Length = 319

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 69/324 (21%), Positives = 132/324 (40%), Gaps = 52/324 (16%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE--------------------------- 43
           +    +  Y+ EI ++P+L  ++E +  K+ +                            
Sbjct: 7   SDTDSVRAYLREIGRVPLLTHEQEILYGKQVQRTTALHEAKNALALELGRDPTRTEWAEA 66

Query: 44  ------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                       H    A   +V ++LRLVV +A  Y    + + +++ EG IG+ + V+
Sbjct: 67  AGLSETELQRTIHAGERAKRMMVEANLRLVVSVAKKYIKRNVDLLDLIQEGTIGMQRGVE 126

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFDP +G+R +TY+ WWI+ A+   I      +++     +K     L ++K   + +  
Sbjct: 127 KFDPTKGYRFSTYAYWWIRQAITRAIAEKGRTIRLPIHITEK-----LNKIKKAQRYLAQ 181

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +      +A +L ++  ++     R     SL+  +   D   ++  D L       
Sbjct: 182 KLGRAATANELAAELELTPKQIREYLERARLPLSLD--LRVGDNQDTELGDLLEDTGASP 239

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE--NLSSEFEVSRERV 269
           E   ++   R +    L   M+ L  ++R +   R   E+  TL    +     +SRERV
Sbjct: 240 EDFALQASLRAD----LEMLMADLTQQQREVLALRFGLEDGQTLTLSKIGDRLNISRERV 295

Query: 270 RQIEARAFKKVQESIQKQVELSSS 293
           RQIE  A  K+++  Q   +  +S
Sbjct: 296 RQIEREALTKLRKRKQDMDDYLAS 319


>gi|282900041|ref|ZP_06308000.1| sigC (Sigma 28 (Flagella/Sporulation)) [Cylindrospermopsis
           raciborskii CS-505]
 gi|281195073|gb|EFA70011.1| sigC (Sigma 28 (Flagella/Sporulation)) [Cylindrospermopsis
           raciborskii CS-505]
          Length = 432

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 67/262 (25%), Positives = 132/262 (50%), Gaps = 18/262 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L  +E      + +  G + A   ++ ++LRLVV +A  Y+  GL + ++V EG +GL +
Sbjct: 178 LTVEE----LDQIQSQG-IQAKEHMIKANLRLVVSVAKKYQNRGLELLDLVQEGTLGLER 232

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           AV+KFDP +G+R +TY+ WWI+  +   I  S   +++     +K     L ++K   + 
Sbjct: 233 AVEKFDPTKGYRFSTYAYWWIRQGITRAIATSSRTIRLPVHITEK-----LNKIKKAQRK 287

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           I     +   +  +A +L+++ ++V  +  R+    SL   +       ++  + L  D 
Sbjct: 288 IAQEKGRTPTLEDLALELDMTPNQVREVLLRVPRSVSLETKV--GKDKDTELGELLETDT 345

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSR 266
              E+ L+ +  +K+    +   +S L  RER +   R      +  +L  +    E+SR
Sbjct: 346 ITPEETLMRESLQKD----IHHLLSDLTTREREVILMRFGLADGHSYSLAEIGRALELSR 401

Query: 267 ERVRQIEARAFKKVQESIQKQV 288
           ERVRQIE++A +K+++  ++ +
Sbjct: 402 ERVRQIESKALQKLRQPKRRNL 423


>gi|119509984|ref|ZP_01629125.1| group 2 sigma 70-type sigma factor F [Nodularia spumigena CCY9414]
 gi|119512944|ref|ZP_01632006.1| group 2 sigma 70-type sigma factor F [Nodularia spumigena CCY9414]
 gi|119462397|gb|EAW43372.1| group 2 sigma 70-type sigma factor F [Nodularia spumigena CCY9414]
 gi|119465308|gb|EAW46204.1| group 2 sigma 70-type sigma factor F [Nodularia spumigena CCY9414]
          Length = 389

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 73/313 (23%), Positives = 135/313 (43%), Gaps = 52/313 (16%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------------------------------ 42
           +  +  +  E+ + P+L+  EE  LA+R R                              
Sbjct: 76  DDAVGAFFKEMARYPLLKPDEEVELARRVRFLEEVREVQAALELELGQPTTKVQVAGQLE 135

Query: 43  ---------EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
                     +    A  +++ S+LRLVV IA  Y   G+P  +++ EG +GL +A +KF
Sbjct: 136 MTEKQLESRLYQGRVAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAMGLNRATEKF 195

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           DP++G++ +TY+ WWI+ A+   I      +++     +K     L +LK   + +    
Sbjct: 196 DPDKGYKFSTYAYWWIRQAITRAIANDARTIRLPIHIVEK-----LNKLKKAQRELKQKL 250

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            +      +A+ L +S  ++  +        SLN  +    +  ++  D L  + +   +
Sbjct: 251 CRNPNEAEMAEALEISVQQLRQLQQLRRQALSLNHRV--GKEEDTELMDLLEDEDNLSPE 308

Query: 214 VLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVR 270
               K      R  +   +  VL PRE+ +   R       P TLE + + F +SRERVR
Sbjct: 309 A---KMNENMMRQEIWEVLGDVLTPREKDVISLRYGLTTSEPCTLEEVGNMFNLSRERVR 365

Query: 271 QIEARAFKKVQES 283
           QI+++A +K++  
Sbjct: 366 QIQSKAMRKLRRP 378


>gi|1553025|gb|AAC45104.1| primary sigma factor [Borrelia garinii]
 gi|1553031|gb|AAC45107.1| primary sigma factor [Borrelia garinii]
          Length = 450

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 66/250 (26%), Positives = 119/250 (47%), Gaps = 16/250 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 215 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 270

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RGF+ +TY+ WWI+ A+   I      +++        +   + RL    + +   
Sbjct: 271 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVH-----MIEQINRLNRETRYLVQV 325

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             K      ++ +L     +V ++        SL   I   ++  S   D++    D   
Sbjct: 326 LGKDPTDEELSDRLGWELKKVKTVKSVSREPVSLETPI--GEEEDSVLSDFI---EDKAI 380

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +           ++ +   +  L  RE+ + + R   E+   +TLE +   F V+RER+R
Sbjct: 381 KNPANHTSFVVLQDQIRSILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIR 440

Query: 271 QIEARAFKKV 280
           QIE++A +++
Sbjct: 441 QIESKALRRL 450


>gi|257061333|ref|YP_003139221.1| RNA polymerase sigma factor [Cyanothece sp. PCC 8802]
 gi|256591499|gb|ACV02386.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8802]
          Length = 328

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 69/323 (21%), Positives = 143/323 (44%), Gaps = 53/323 (16%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------EHGDL------- 47
           +N K    + + ++ +  Y+HEI ++P+L  ++E V  K+ +      E  D        
Sbjct: 6   VNSKTKQPMYSADM-VRTYLHEIGRVPLLTHEQEIVYGKQVQRMMSLFEMKDQLTQAQGT 64

Query: 48  --------------------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
                                      A  +++ ++LRLVV IA  Y+   +   +++ E
Sbjct: 65  EPSDKEWAKAVNLKEPELQKTIEQGNRAKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQE 124

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           G++GL + V+KFDP +G++ +TY+ WWI+ A+   I +    +++     +K     L +
Sbjct: 125 GSLGLERGVEKFDPTKGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEK-----LNK 179

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           +K   + ++    +      IA  L +  S++           SL+  +   D   ++  
Sbjct: 180 IKKTQRELSQKLGRSATPAEIAAVLEIEPSQIRECLSMARQPISLD--VRVGDNQDTELS 237

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLS 259
           + L       +Q + ++  R++    L   M  L P++R +   R   E+   ++L  + 
Sbjct: 238 ELLEDHEASPDQYITQELLRQD----LKNLMEELTPQQRSVLILRFGLEDGKELSLAKIG 293

Query: 260 SEFEVSRERVRQIEARAFKKVQE 282
            +  +SRERVRQ+E +A  +++ 
Sbjct: 294 KKLNISRERVRQLEHQALAQLRR 316


>gi|323453176|gb|EGB09048.1| hypothetical protein AURANDRAFT_53467 [Aureococcus anophagefferens]
          Length = 468

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 79/331 (23%), Positives = 143/331 (43%), Gaps = 58/331 (17%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR---------------------------- 42
           + + GL   I  + +  +L   EE  LA+R +                            
Sbjct: 131 DRDEGLHWQIRNMGQTALLSSDEEKALARRVQRLCTWEGIRANLTASLGREPTELEWGAA 190

Query: 43  --------EHG--------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
                   E+G         L A   ++ ++LRLVV I+  Y+  GL   +V+ EG  GL
Sbjct: 191 ARISRAACENGSFEKARKKCLKAKAAMINANLRLVVSISKRYQHRGLHFQDVIQEGTFGL 250

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
            +AV+KFDPE+GF+ +TY+ WWIK A+   I      +++    +       L+ +K   
Sbjct: 251 TRAVEKFDPEKGFKFSTYATWWIKQAVMRAIADQSRTIRLPVHVHD-----QLQSMKKVT 305

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW--- 203
           + +     +      +A KL+++ +++  +        S++A +  S K SS        
Sbjct: 306 RDLGAELGRECTDEELAGKLDLATTKMDWLRSCERQTMSMDATVRVSGKGSSAGTGGAGN 365

Query: 204 ---LVYDHDGQEQVLIEKEERKNRRNMLTRSMSV-LNPRERRIFEARRLQENP--VTLEN 257
              L  +      +  E+ E K+ ++ +   +   L+ RE  +   R   ++    TLE 
Sbjct: 366 EAKLSDNLADAAALPDERAETKSLQSDIHGLLRTALSDRECDVVRLRFGLDDGKARTLEE 425

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           + + F ++RERVRQIEARA  K+++  +  +
Sbjct: 426 IGTVFSITRERVRQIEARALHKLRQPYRNHM 456


>gi|187923827|ref|YP_001895469.1| RNA polymerase sigma factor RpoS [Burkholderia phytofirmans PsJN]
 gi|187715021|gb|ACD16245.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia phytofirmans
           PsJN]
          Length = 360

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 75/280 (26%), Positives = 130/280 (46%), Gaps = 15/280 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y++ I   P+L  +EE   + R  + G+  A   ++  +LRLVV IA GY   G+
Sbjct: 80  DTIQHYLNRISVKPLLTVEEEQKYS-RLAKAGEFEARQVMIERNLRLVVSIAKGYLNRGV 138

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGN+GLM A++KFDP RGFR +TY+ WWI+ +++  I+     V++       
Sbjct: 139 PLLDLIEEGNLGLMHAIEKFDPTRGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV--I 196

Query: 134 RLFFNLRRLKGHLQAITDN-----NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           R    + R K HL+  + N       +   +  IA     +  EV  +        SL+A
Sbjct: 197 RELNQVLRAKRHLEKNSMNSGEAAERRDASIDDIAYLTGKTTDEVTDILALNEHTASLDA 256

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            ++    +S               +V     + +    +    ++ L+ + R + E R  
Sbjct: 257 PLDLDPASSLLDLLSDDQSQSPDAEV-----QHRELETLTRAWLARLSDKHRHVIERRFG 311

Query: 249 QE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                P TLE L+ E  ++RERVRQI+  A  +++     
Sbjct: 312 LNHIEPATLEELADEMGLTRERVRQIQQEALVRLKRFFAS 351


>gi|239930706|ref|ZP_04687659.1| RNA polymerase principal sigma factor [Streptomyces ghanaensis ATCC
           14672]
 gi|291439071|ref|ZP_06578461.1| sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291341966|gb|EFE68922.1| sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 332

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 72/299 (24%), Positives = 129/299 (43%), Gaps = 39/299 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVL---------AKRYREHGDLS------------------ 48
           +  Y+ EI + P+L+  +E  L         A++  +  + S                  
Sbjct: 36  VGMYLDEIARTPLLDAAKEVELSQIIEAGVFARQILDGYEESKVGATTEELQALVDDAER 95

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A    + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ WW
Sbjct: 96  AKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTYATWW 155

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      +++        L   L R++   +     + +  +   +A +L  
Sbjct: 156 IRQAITRSIADQSRTIRLPVH-----LVEELGRIRRVQREFNREHGRDPEPAEVAAELGS 210

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +   V  +        SLN  +   D+  +Q+ D L    D       +      R   L
Sbjct: 211 TPERVTDVLDWARDPVSLNMSV--DDEGETQFGDLL---EDTSAVSPEQSVLTLLRSEEL 265

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              +  L+ R   I + R   E+    TL  +  E  ++RER+RQIE  A  ++++  +
Sbjct: 266 DDLIGRLDQRTASIIKMRYGIEDGRERTLTEVGKEHGLTRERIRQIEKHALLELKKLAR 324


>gi|149183340|ref|ZP_01861778.1| RNA polymerase sigma factor RpoD [Bacillus sp. SG-1]
 gi|148848937|gb|EDL63149.1| RNA polymerase sigma factor RpoD [Bacillus sp. SG-1]
          Length = 330

 Score =  201 bits (511), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 68/244 (27%), Positives = 115/244 (47%), Gaps = 11/244 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           +N  ++   V     +  Y+ EI ++ +L  QEE  LA R  E GD  A  RL  ++LRL
Sbjct: 98  LNDLSVPPGVKINDPVRMYLKEIGRVDLLSAQEEISLANRI-EEGDEEAKRRLAEANLRL 156

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 157 VVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQ 216

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE    IA++++++  +V  +    
Sbjct: 217 ARTIRIPVHMVE--TINKLIRVQRQLLQDLGREPSPE---EIAEEMDLTPEKVREILKIA 271

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL   I   +++ S   D++    D + Q   E    +  +  L   +  L  RE 
Sbjct: 272 QEPVSLETPI--GEEDDSHLGDFI---EDAEAQSPSEHAAYELLKEQLEDVLDTLTDREE 326

Query: 241 RIFE 244
            +  
Sbjct: 327 NVLR 330


>gi|296121869|ref|YP_003629647.1| RNA polymerase sigma factor, sigma-70 family [Planctomyces
           limnophilus DSM 3776]
 gi|296014209|gb|ADG67448.1| RNA polymerase sigma factor, sigma-70 family [Planctomyces
           limnophilus DSM 3776]
          Length = 290

 Score =  200 bits (510), Expect = 1e-49,   Method: Composition-based stats.
 Identities = 74/274 (27%), Positives = 138/274 (50%), Gaps = 13/274 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  L  Y+ EI +  +L  ++E  LA R   +G+  A  R+V ++LRLVV IA  Y G G
Sbjct: 25  QTPLETYLREINETALLTARDERELANRIA-NGEKEARDRMVRANLRLVVNIARAYVGKG 83

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP+ +++ EGN+GL++AV+ FDP+   R +TY+ +WIK +++  ++     ++I   A  
Sbjct: 84  LPLQDLIEEGNLGLLRAVEGFDPDMNTRFSTYASYWIKQSIKRALINCGKTIRIP--AYM 141

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
             L    R+    L+   D   +P     +A +L + + ++  +   +    S      +
Sbjct: 142 VELLSKWRKATAKLE---DQFKRPPTQEEVAIELGLPKKKLSIVKKAIHLYSS---TPQT 195

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN- 251
            D+ S      +V D   + +   ++    +    +   +  ++ RE +I   R   ++ 
Sbjct: 196 DDEESGWMMSDMVADE--RVKGPDDELLDVDNLKHVYAMLETMDEREAKILRLRFGLDDS 253

Query: 252 -PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            P TL+ +  E  ++RERVRQIE+ A K++ + I
Sbjct: 254 EPKTLKEIGEEMGLTRERVRQIESEALKRIAKRI 287


>gi|1553027|gb|AAC45105.1| primary sigma factor [Borrelia garinii]
          Length = 450

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 66/250 (26%), Positives = 119/250 (47%), Gaps = 16/250 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 215 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 270

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RGF+ +TY+ WWI+ A+   I      +++        +   + RL    + +   
Sbjct: 271 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVH-----MIEQINRLNRETRYLVQV 325

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             K      ++ +L     +V ++        SL   I   ++  S   D++    D   
Sbjct: 326 LGKDPTDEELSDRLGWELKKVKTVKSVSREPVSLETPI--GEEEDSVLSDFI---EDKAI 380

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +           ++ +   +  L  RE+ + + R   E+   +TLE +   F V+RER+R
Sbjct: 381 KNPANHTSFVVLQDQIRSILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIR 440

Query: 271 QIEARAFKKV 280
           QIE++A +++
Sbjct: 441 QIESKALRRL 450


>gi|187250727|ref|YP_001875209.1| RNA polymerase, sigma 70 subunit, RpoD family [Elusimicrobium
           minutum Pei191]
 gi|186970887|gb|ACC97872.1| RNA polymerase, sigma 70 subunit, RpoD family [Elusimicrobium
           minutum Pei191]
          Length = 571

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 65/241 (26%), Positives = 122/241 (50%), Gaps = 12/241 (4%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             +L+ ++LRLVV IA  +    L +S+++ EG +GLM+AV+KF+ +RGF+ +TY+ WWI
Sbjct: 334 KLKLIKANLRLVVSIAKKHVNSNLELSDLIQEGGLGLMKAVEKFEYKRGFKFSTYATWWI 393

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + ++   I    + ++I      K L   L ++    +     + +   +   +K L +S
Sbjct: 394 RQSINRAIADQANTIRIPVHM--KELVSKLTKVTNKFRQ---EHGREPSLEDYSKSLRLS 448

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             +V  +   +    SL+  +   +   S  +D++         V      RK     ++
Sbjct: 449 MEKVKGVLKIMQDPISLSTPV--GEDEDSNLEDFIEDKAGANPTVTASDFLRKQE---VS 503

Query: 230 RSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             ++ L+ RE +I   R   ++  P TLE +   F V+RERVRQIEA+A +K++   + +
Sbjct: 504 EVLNTLSEREAKIIRLRFGIDSGYPRTLEEVGKMFNVTRERVRQIEAKAIRKLRHPSRTK 563

Query: 288 V 288
           +
Sbjct: 564 M 564



 Score = 39.8 bits (92), Expect = 0.46,   Method: Composition-based stats.
 Identities = 13/42 (30%), Positives = 21/42 (50%), Gaps = 2/42 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTS 56
            +  Y+ E+ K+P+L + EE  LA+  RE        +LV  
Sbjct: 85  SIRMYLSEMGKVPLLSRDEEITLARNVRER--EKELRKLVLE 124


>gi|282895449|ref|ZP_06303586.1| sigE (Sigma 28 (Flagella/Sporulation)) [Raphidiopsis brookii D9]
 gi|281199482|gb|EFA74345.1| sigE (Sigma 28 (Flagella/Sporulation)) [Raphidiopsis brookii D9]
          Length = 327

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 64/305 (20%), Positives = 131/305 (42%), Gaps = 52/305 (17%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHG--------------------------------- 45
           Y+ EI ++P+L +++E +  K+ ++                                   
Sbjct: 23  YLREIGRVPLLNREQEIIYGKQVQQMMILVEAKEALAKELGYEPSLSEWAIYVNQSENDL 82

Query: 46  ------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                    A  +++ ++LRLVV IA  Y+   +   +++ EG +GL + V+KFDP  G+
Sbjct: 83  KHKISTGKRAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTMGY 142

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWI+ A+   I +    +++     +K     L ++K   + +     +    
Sbjct: 143 KFSTYAYWWIRQAITRAIAQQGRTIRLPIHITEK-----LNKIKKVQRELAQKLGRSPSP 197

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IAK+L +  +++           SL+  +   D   ++ Q+ L  D    E    ++ 
Sbjct: 198 TEIAKELELEPAQIREYLNIARQPISLD--VRVGDNQDTELQEMLEDDGLSPEHYTTQEF 255

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
                R+ L   ++ L P++R +   R   E+   ++L  +     +SRERVRQ+E +A 
Sbjct: 256 L----RHDLNNLLAELTPQQREVVTLRFGLEDGNEMSLAKVGDRLNISRERVRQLEHQAL 311

Query: 278 KKVQE 282
             ++ 
Sbjct: 312 THLRR 316


>gi|126660028|ref|ZP_01731150.1| RNA polymerase sigma-C factor [Cyanothece sp. CCY0110]
 gi|126618706|gb|EAZ89453.1| RNA polymerase sigma-C factor [Cyanothece sp. CCY0110]
          Length = 418

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 64/242 (26%), Positives = 127/242 (52%), Gaps = 13/242 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           + A   ++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV+KFDP +G+R +TY+ 
Sbjct: 177 IRAKDEMIKANLRLVVSVAKKYQHRGLELLDLIQEGTLGLEKAVEKFDPIKGYRFSTYAY 236

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   I     ++++     +K     L ++K   + I+    +   +  I K+L
Sbjct: 237 WWIRQGITRAIATQSRIIRLPVHITEK-----LNKIKQVQRKISQAKGRSATLEEIGKEL 291

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           N+S ++V  +  ++    SL   I    +  ++  D L  +    E+ L      ++ R 
Sbjct: 292 NMSSTQVRDVLMKIPRSVSLE--IKVGKEKDTELVDLLESEDISPEENLA----IESLRR 345

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +   +  L  RE+ + + R   E+    +L ++    ++SRERVRQIEA+A +K+++  
Sbjct: 346 DIGILLEDLTEREQEVIKLRYGFEDGVSYSLADIGRTLDLSRERVRQIEAKALQKLRQPR 405

Query: 285 QK 286
           ++
Sbjct: 406 RR 407


>gi|168700059|ref|ZP_02732336.1| RNA polymerase sigma factor rpoS [Gemmata obscuriglobus UQM 2246]
          Length = 272

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 78/273 (28%), Positives = 130/273 (47%), Gaps = 13/273 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
              S Y+ EI   P+L   EE  L  R    GD  A  R+V ++LRLVV IA GY G GL
Sbjct: 9   TSFSTYLSEIDHTPLLSAAEERDLGARVL-TGDPQARDRMVRANLRLVVNIARGYTGKGL 67

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + ++VSEGN+GL++AV+ F+P    R +TY+ +WIK +++  I+ +   ++I     + 
Sbjct: 68  ALDDLVSEGNMGLLRAVEGFEPSMNTRFSTYASYWIKQSIKRAIVNTAKTIRIPAYMAE- 126

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            L    RR       ++D   +P     IAK L +S+ ++  +   +      NA   S 
Sbjct: 127 -LLTKWRRATN---QLSDELGRPPTHDEIAKFLGLSKKKLAIIKKAIRV---ANAGTQSD 179

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QEN 251
             ++    +  + D  G       +  + +    +   +  ++ RE  +   R     E 
Sbjct: 180 QSDAGWSIEETLMDSRG--DAPDTELGKSDDLKQVLHLLDRMDQREATVLRMRFGLNDEE 237

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           P TL+ +     ++RERVRQIE  A  K+ + +
Sbjct: 238 PRTLKEIGECLGLTRERVRQIENEALAKLGDGM 270


>gi|33864638|ref|NP_896197.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. WH 8102]
 gi|33632161|emb|CAE06617.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 8102]
          Length = 332

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 66/315 (20%), Positives = 135/315 (42%), Gaps = 53/315 (16%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSA-------------------------- 49
           +  Y+ +I ++P+L  ++E  L ++ ++  D+ A                          
Sbjct: 25  VRSYLRDIGRVPLLTHEQEITLGRQVQDLMDIEAMQTELESRDGDKPSRDKLAKASGLTP 84

Query: 50  -------------AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                          R+V ++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP 
Sbjct: 85  LQLKRKLQHGRRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPT 144

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RG++ +TY+ WWI+  +   I      +++     +      L +LK   + ++    + 
Sbjct: 145 RGYKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITE-----MLNKLKKGQRELSQELGRT 199

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
             +  +A+ + + E +V  + CR     SL   +   D + ++  + L  D D    +  
Sbjct: 200 PTITELAQYVELPEDDVKDLMCRARQPVSLEMKV--GDGDDTELLELLAGDAD----LPS 253

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEA 274
           ++ E    +  L   +  L   + ++   R     E+P++L  +     +SR+RVR +E 
Sbjct: 254 DQVEEDCMKGDLRSLLGQLPHLQEQVLRMRYGMDGEDPMSLTGIGRILGMSRDRVRNLER 313

Query: 275 RAFKKVQESIQKQVE 289
                ++  I  QVE
Sbjct: 314 DGLAGLRR-ISDQVE 327


>gi|11133042|sp|Q60012|HRDD_STRVF RecName: Full=RNA polymerase principal sigma factor hrdD
 gi|1407711|gb|AAB03580.1| sigma factor [Streptomyces viridifaciens]
          Length = 332

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 71/299 (23%), Positives = 127/299 (42%), Gaps = 39/299 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYRE--------HGDLS------------------- 48
           +  Y+ EI + P+L+  +E  L++             G+                     
Sbjct: 36  VGMYLDEIARTPLLDAAKEVELSQTIEAGVFAQQVLDGEEESRTDATREELQALVDAGER 95

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A    + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ WW
Sbjct: 96  AKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTYATWW 155

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      +++        L   L R++   +     + +  +   +A +L  
Sbjct: 156 IRQAITRSIADQSRTIRLPVH-----LVEELGRIRRVQREFNREHGRDPEPAEVAAELGS 210

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +   VI +        SLN  +   D   +Q+ D L    D       +      R   L
Sbjct: 211 TPERVIDVLDWARDPVSLNMAV--DDAGETQFGDLL---EDTSAVSPEQSVLTLLRSEEL 265

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              +  L+ R   I + R   ++    TL  +  E  ++RER+RQIE  A  ++++  +
Sbjct: 266 DDLIGRLDQRTASIIKMRYGIDDGRERTLTEVGKEHGLTRERIRQIEKHALLELKKLAR 324


>gi|288926119|ref|ZP_06420047.1| RNA polymerase sigma-70 factor [Prevotella buccae D17]
 gi|315608396|ref|ZP_07883384.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella buccae
           ATCC 33574]
 gi|288337159|gb|EFC75517.1| RNA polymerase sigma-70 factor [Prevotella buccae D17]
 gi|315249856|gb|EFU29857.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella buccae
           ATCC 33574]
          Length = 290

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 71/280 (25%), Positives = 133/280 (47%), Gaps = 12/280 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD--LSAAHRLVTSHLRLVVKI 64
           SI       L +Y+ EI + PM+  +EE  LA+  +  G     A  +LVT++LR VV +
Sbjct: 9   SITNRASEALDKYLVEIGRAPMVTIEEEIELAQAIKRGGRDAERAKEKLVTANLRFVVSV 68

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y+  GL +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V
Sbjct: 69  AKQYQHQGLTLTDLIDEGNIGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIV 128

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           ++           +L ++   +      + +   V  ++ + ++ E ++           
Sbjct: 129 RLPLNQ-----VGSLNKVNHEINRFEQEHHRRPSVQELSDRTHIDEEKIQQSMMADGHHV 183

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           S++A     + NS    D +    D +    ++ +      N +     VL  RE+ I  
Sbjct: 184 SIDAPFQEGEDNS--MVDVMAGSDDSRTDRQVDHDSMAMELNSVLDR--VLKEREQIIIR 239

Query: 245 ARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
                      LE +  +  ++RERVRQI  ++  K++ES
Sbjct: 240 ECFGIGCQEKGLEEIGDQLGLTRERVRQIREKSITKLRES 279


>gi|240140689|ref|YP_002965169.1| RNA polymerase sigma-32 (sigma H) factor [Methylobacterium
           extorquens AM1]
 gi|240010666|gb|ACS41892.1| RNA polymerase sigma-32 (sigma H) factor [Methylobacterium
           extorquens AM1]
          Length = 262

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 104/251 (41%), Positives = 165/251 (65%), Gaps = 1/251 (0%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A  ++E  D  A HRL+++H+RLV+ +A  +R YGLP++++V EG++GLM+A  +F+PER
Sbjct: 2   AVAWKEARDERALHRLISAHMRLVIALAGRFRHYGLPMADLVQEGHVGLMEAAARFEPER 61

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
             R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFFNLRRL+  L   T+  +  E
Sbjct: 62  EVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRARLMQSTEEQVGSE 121

Query: 158 QVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
               IA  + VS  +V  M+ RL+G D SLNA +    + SS+  D+LV +    ++ + 
Sbjct: 122 IHGRIATAIGVSREDVALMDARLSGPDMSLNAPVGEESEASSERMDFLVDNAALPDETVS 181

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
              + + R   L ++++VL+ RE RI   RRL E+  TLE L     +S+ERVRQIE RA
Sbjct: 182 ALVDGERRLIWLRQALTVLSERELRILRERRLAEDQATLEALGHRLGISKERVRQIENRA 241

Query: 277 FKKVQESIQKQ 287
            +K++ ++ ++
Sbjct: 242 LEKLRRALAEK 252


>gi|149908704|ref|ZP_01897365.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region
           4:Sigma-70region 1.2 [Moritella sp. PE36]
 gi|149808246|gb|EDM68185.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region
           4:Sigma-70region 1.2 [Moritella sp. PE36]
          Length = 284

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 82/287 (28%), Positives = 143/287 (49%), Gaps = 17/287 (5%)

Query: 9   IVNGEIGLSRYIHEIRKI-PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           + N    L  Y++++ +   +L K+EEY  A      GD  A  R++ S+LRLV+ IA  
Sbjct: 3   LSNESNALDVYMYQVNQSSKLLTKEEEYETAMA-SNEGDEKARQRMIQSNLRLVINIAKR 61

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y+   LP+ +++ EGN GL+ AV+KFD  +GFR +TY++WWIK  ++ +I+     +++ 
Sbjct: 62  YQHTSLPLVDIIQEGNTGLIHAVEKFDATKGFRFSTYAVWWIKNNIERFIMNQSRTIRVP 121

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
               +       R LK   +   D       V+ +A+ L +  ++V  +      + SL+
Sbjct: 122 IHIGK----VYKRILKTAREQELDLQCN-HDVMTLAEFLEMQYAQVNEVLSYYFNEASLD 176

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I +   +S+   D L    D       ++ E  +    L   +  L+ R+R+I E R 
Sbjct: 177 KTIVTDRDSSTALVDML---EDYSICKPNDELEDADTLCYLNEVLGHLSERDRKIIELRF 233

Query: 248 LQ--ENPVTLENLSSEFEVSRERVRQIEARAFKK-----VQESIQKQ 287
               E+P+TL  +     +SRER+RQI   + +K     +Q ++QKQ
Sbjct: 234 GLGEEDPLTLHVIGERLSMSRERIRQIINLSLQKIQPELLQNTVQKQ 280


>gi|313837139|gb|EFS74853.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL037PA2]
 gi|314927839|gb|EFS91670.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL044PA1]
 gi|314971910|gb|EFT16008.1| RNA polymerase sigma factor SigB [Propionibacterium acnes HL037PA3]
 gi|328907302|gb|EGG27068.1| sigma-70 region 2 [Propionibacterium sp. P08]
          Length = 312

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 67/303 (22%), Positives = 127/303 (41%), Gaps = 41/303 (13%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------------- 41
           ++G+  +  Y+  I +  +L   EE  LA+R                             
Sbjct: 13  IDGKDAVGLYLDGIARTSLLNAAEEVALARRIEAGVFARAVLEGQAETTSDATTEELHQI 72

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
              GD  A    V ++LRLVV +A  Y    +P+ ++V EGN GL++AV+KFD  +GF+ 
Sbjct: 73  AADGD-EAMAHFVRANLRLVVSVARKYGRSQMPLLDLVQEGNTGLIRAVEKFDYAKGFKF 131

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY+ WW++ A+   I +   +V++     +      + ++    + +     +  +   
Sbjct: 132 STYATWWVRQAISRGIAQQGRIVRLPVHVAE-----QVNQVSAARRNLERQLGREPETSE 186

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           IA +L ++E  VI +        SL+A +   D   +   D +  +       ++   E 
Sbjct: 187 IADELEITEERVIELIRFGRDHVSLDAPV--EDDGDTSLGDLIARETSPGPDDIVLDAED 244

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVT--LENLSSEFEVSRERVRQIEARAFKK 279
              R  L   +  L+ R   +   R    +     L ++   + ++ ERVRQIE  A   
Sbjct: 245 ---RGRLEGLLDNLDERSADVVRRRYGLVDGRQAKLADIGKVWGITAERVRQIERAALDS 301

Query: 280 VQE 282
           +++
Sbjct: 302 MRQ 304


>gi|172035560|ref|YP_001802061.1| RNA polymerase sigma factor [Cyanothece sp. ATCC 51142]
 gi|171697014|gb|ACB49995.1| group 2 sigma-70 RNA polymerase sigma factor B [Cyanothece sp. ATCC
           51142]
          Length = 328

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 65/323 (20%), Positives = 143/323 (44%), Gaps = 53/323 (16%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------------- 43
           +N K      + ++ +  Y+HEI ++P+L  ++E +  K+ ++                 
Sbjct: 6   VNTKTKQPTYSADM-VRTYLHEIGRVPLLTHEQEIIYGKQVQKMMSLLETKEELAQSLGK 64

Query: 44  ----------------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
                                      A  +++ ++LRLVV IA  Y+   +   +++ E
Sbjct: 65  EPSLQEWAKEVNLEEKALTKALEQGERAKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQE 124

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           G++GL + V+KFDP +G++ +TY+ WWI+ A+   I +    +++     +K     L +
Sbjct: 125 GSLGLERGVEKFDPTKGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEK-----LNK 179

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           +K   + ++    +      IA++L +  S++           SL+  +   D   ++  
Sbjct: 180 IKKTQRELSQTLGRSATPAEIAQELEIEPSQIREFLSIARQPISLD--VRVGDNQDTELS 237

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLS 259
           + L       +  + ++  R++    L+  M+ L P++R +   R   E+   ++L  + 
Sbjct: 238 ELLEDQGVSPDIYITQELLRQD----LSNLMAELTPQQRTVLTLRFGLEDGKELSLAKIG 293

Query: 260 SEFEVSRERVRQIEARAFKKVQE 282
               +SRERVRQ+E +A  +++ 
Sbjct: 294 KRLNISRERVRQLEHQALAQLRR 316


>gi|119487601|ref|ZP_01621211.1| RNA polymerase sigma-like factor [Lyngbya sp. PCC 8106]
 gi|119455770|gb|EAW36906.1| RNA polymerase sigma-like factor [Lyngbya sp. PCC 8106]
          Length = 404

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 66/246 (26%), Positives = 124/246 (50%), Gaps = 13/246 (5%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           +   + A   ++ ++LRLVV +A  Y+  GL + +++ EG +GL +AV+KFDP RG+R +
Sbjct: 159 QTEGIKAKDHMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTRGYRFS 218

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TYS WWI+  +   I      +++     +K     L ++K   + I+    +   +  I
Sbjct: 219 TYSYWWIRQGITRAIATQSRTIRLPVHITEK-----LNKIKKAQRKISQEKGRIATIDDI 273

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A +L ++ ++V  +  ++    SL   + S                  +E    ++  R+
Sbjct: 274 AAELEMTPAQVREVLLKVPRSVSLETKVGSDKDTELGELLE------TEEASPEDQLMRE 327

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVT--LENLSSEFEVSRERVRQIEARAFKKV 280
           +    L + ++ L+ RER + + R    N  T  L  +  E E+SRERVRQIEA+A +K+
Sbjct: 328 SLHRDLQQLLADLSDRERDVIQMRYGLGNGHTYSLAEIGRELELSRERVRQIEAKALQKL 387

Query: 281 QESIQK 286
           ++  ++
Sbjct: 388 RQPKRR 393


>gi|159027100|emb|CAO89285.1| rpoD [Microcystis aeruginosa PCC 7806]
          Length = 328

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 62/323 (19%), Positives = 135/323 (41%), Gaps = 54/323 (16%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------------------- 42
             +           +  Y+HEI ++P+L  ++E +  K+ +                   
Sbjct: 6   TNQTQPQPTLNADMVRTYLHEIGRVPLLTHEQEIIYGKQVQRMMSLLEAKEALSKQLGRE 65

Query: 43  ---------------------EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
                                + GD  A  +++ ++LRLVV IA  Y+   +   +++ E
Sbjct: 66  PQHLEWADSVNLSENELDRALKTGDR-AKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQE 124

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           G++GL + V+KFDP +G++ +TY+ WWI+ A+   I +    +++     +K     L +
Sbjct: 125 GSLGLERGVEKFDPTKGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEK-----LNK 179

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           +K   + +     +      IA +L++  +++           SL+  +   D   ++  
Sbjct: 180 IKRTQRELAQKLGRSATPAEIALELDLEPAQIREYLSMARQPISLD--VRVGDNQDTELS 237

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLS 259
           + L       +  + ++  R++    L   ++ L P++R +   R        ++L  + 
Sbjct: 238 ELLEDSGVSPDTFITQELLRQD----LANLLAELTPQQREVITLRFGLTDGKELSLAKIG 293

Query: 260 SEFEVSRERVRQIEARAFKKVQE 282
               +SRERVRQ+E +A   ++ 
Sbjct: 294 QRMNISRERVRQLEHQALAHLRR 316


>gi|1553011|gb|AAC45097.1| primary sigma factor [Borrelia afzelii]
          Length = 450

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 66/250 (26%), Positives = 119/250 (47%), Gaps = 16/250 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 215 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 270

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RGF+ +TY+ WWI+ A+   I      +++        +   + RL    + +   
Sbjct: 271 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVH-----MIEQINRLNRETRYLVQV 325

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             K      ++ +L     +V ++        SL   I   ++  S   D++    D   
Sbjct: 326 LGKDPTDEELSDRLGWELKKVKTVKSVSREPVSLETPI--GEEEDSVLSDFI---EDKAI 380

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +           ++ +   +  L  RE+ + + R   E+   +TLE +   F V+RER+R
Sbjct: 381 KNPANHTSFVVLQDQIRSILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIR 440

Query: 271 QIEARAFKKV 280
           QIE++A +++
Sbjct: 441 QIESKALRRL 450


>gi|1553023|gb|AAC45103.1| primary sigma factor [Borrelia garinii]
          Length = 450

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 66/250 (26%), Positives = 119/250 (47%), Gaps = 16/250 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 215 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 270

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RGF+ +TY+ WWI+ A+   I      +++        +   + RL    + +   
Sbjct: 271 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVH-----MIEQINRLNRETRYLVQV 325

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             K      ++ +L     +V ++        SL   I   ++  S   D++    D   
Sbjct: 326 LGKDPTDEELSDRLGWELKKVKTVKSVSREPVSLETPI--GEEEDSVLSDFI---EDKAI 380

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +           ++ +   +  L  RE+ + + R   E+   +TLE +   F V+RER+R
Sbjct: 381 KNPANHTSFVVLQDQIRSILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIR 440

Query: 271 QIEARAFKKV 280
           QIE++A +++
Sbjct: 441 QIESKALRRL 450


>gi|220907004|ref|YP_002482315.1| RNA polymerase sigma factor [Cyanothece sp. PCC 7425]
 gi|219863615|gb|ACL43954.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7425]
          Length = 327

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 70/305 (22%), Positives = 136/305 (44%), Gaps = 52/305 (17%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYRE----------------------------------- 43
           Y+HEI ++P+L  ++E VL K+ ++                                   
Sbjct: 23  YLHEIGRVPLLTHEQEIVLGKQVQQLMELLEAREKLTTSLDRSPTAEEWAEQANLSVADL 82

Query: 44  ----HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                    A  +++ ++LRLVV +A  Y+   L + +++ EG +GL + V+KFDP RG+
Sbjct: 83  NTAVRRGQRAKQKMIEANLRLVVSVAKKYQKRNLELLDLIQEGTLGLERGVEKFDPTRGY 142

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWI+ A+   I +    V++     +K     L ++K   + ++    +    
Sbjct: 143 KFSTYAYWWIRQAITRAIAQQARTVRLPIHITEK-----LNKIKKAQRVLSQRLGRSATP 197

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IA++L +  S++           SL+  +   D   ++ +D L  D    EQ    + 
Sbjct: 198 AEIAQELELEPSQIREYLTLARQPVSLD--LRVGDNQDTELRDLLEDDSPSPEQYTTGEA 255

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
            R +  ++L      L P++R +   R   E+   ++L  +  +  +SRERVRQ+E +A 
Sbjct: 256 LRDDVNHLLAE----LTPQQREVLTLRFGLEDGKELSLAKVGEQLSLSRERVRQLERQAL 311

Query: 278 KKVQE 282
             ++ 
Sbjct: 312 DHLRR 316


>gi|1553029|gb|AAC45106.1| primary sigma factor [Borrelia garinii]
          Length = 450

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 66/250 (26%), Positives = 119/250 (47%), Gaps = 16/250 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 215 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 270

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RGF+ +TY+ WWI+ A+   I      +++        +   + RL    + +   
Sbjct: 271 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVH-----MIEQINRLNRETRYLVQV 325

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             K      ++ +L     +V ++        SL   I   ++  S   D++    D   
Sbjct: 326 LGKDPTDEELSDRLGWELKKVKTVKSVSREPVSLETPI--GEEEDSVLSDFI---EDKAI 380

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +           ++ +   +  L  RE+ + + R   E+   +TLE +   F V+RER+R
Sbjct: 381 KNPANHTSFVVLQDQIRSILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIR 440

Query: 271 QIEARAFKKV 280
           QIE++A +++
Sbjct: 441 QIESKALRRL 450


>gi|29830237|ref|NP_824871.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29607348|dbj|BAC71406.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 331

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 75/310 (24%), Positives = 134/310 (43%), Gaps = 43/310 (13%)

Query: 10  VNGEIG----LSRYIHEIRKIPMLEKQEEYVL---------AKRYREHGDL--------- 47
           V GEI     +  Y+ EI + P+L+  +E  L         A++  +  +          
Sbjct: 25  VGGEIADRDLVGMYLDEIARTPLLDAAKEVELSQIIEAGVFARQILDGEEEPRAEATREE 84

Query: 48  ---------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
                     A    + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +G
Sbjct: 85  LESLVADSERAKDVFIKSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKG 144

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           F+ +TY+ WWI+ A+   I      +++        L   L R++   +     + +  +
Sbjct: 145 FKFSTYATWWIRQAITRSIADQSRTIRLPVH-----LVEELGRIRRVQREFNREHGREPE 199

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              IA +L+ + + V  +        SLN  +   D+  +Q+ D L    D       + 
Sbjct: 200 PAEIAAELDSNPARVTDVLDWARDPVSLNMHV--DDEGETQFGDLL---EDTSAVSPEQS 254

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARA 276
                R   L   +  L+ R   I + R   ++    TL  +  E  ++RER+RQIE  A
Sbjct: 255 VLTLLRSEELDDLIGRLDQRTASIIKMRYGIDDGRERTLTEVGKEHGLTRERIRQIEKHA 314

Query: 277 FKKVQESIQK 286
             ++++  + 
Sbjct: 315 LLELKKLARS 324


>gi|123969371|ref|YP_001010229.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. AS9601]
 gi|123199481|gb|ABM71122.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. AS9601]
          Length = 344

 Score =  200 bits (510), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 68/318 (21%), Positives = 135/318 (42%), Gaps = 53/318 (16%)

Query: 7   SIIVNGEIGLSR-YIHEIRKIPMLEKQEEYVLAKRYREHGDLS----------------- 48
           SI  + ++ L R Y+ +I ++P+L  ++E  L ++ +E+ ++                  
Sbjct: 27  SIKASNDVDLVRSYLRDIGRVPLLSHEQEITLGRQVQEYMEVERIELEIIELTGEKPSID 86

Query: 49  ----------------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
                                 A  R+V ++LRLVV +A  Y    + + +++ EG IGL
Sbjct: 87  ELSAKLNLTTSTIKKRLRAGQRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGL 146

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++ V+KFDP RG++ +TY+ WWI+  +   I      +++     +      L +LK   
Sbjct: 147 VRGVEKFDPARGYKFSTYAYWWIRQGITRAIAEKSRAIRLPIHITE-----MLNKLKKGQ 201

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           + ++    +   V  +AK + + E +V  + C+     SL   +   +         L+ 
Sbjct: 202 RELSQEMSRTPTVSELAKYVELPEDDVKDLMCKAGQPVSLETKVGDGEDT------VLLD 255

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
              G E +  E+ E    R  L   +  L   + R+   R     + P++L  +     +
Sbjct: 256 LLAGGEDLPDEQIEMDCMRGDLHSLLHQLPDLQCRVLRMRYGMDGDEPMSLTGIGRVLGI 315

Query: 265 SRERVRQIEARAFKKVQE 282
           SR+RVR +E    + ++ 
Sbjct: 316 SRDRVRNLERDGLRGLRR 333


>gi|318040801|ref|ZP_07972757.1| type II alternative RNA polymerase sigma factor [Synechococcus sp.
           CB0101]
          Length = 381

 Score =  200 bits (509), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 74/245 (30%), Positives = 124/245 (50%), Gaps = 13/245 (5%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           H    A  R++ ++LRLVV +A  Y+  G+ + ++V EG +GL +AV+K+DP RGFR +T
Sbjct: 131 HHGRRARDRMIQANLRLVVAVAKKYQQRGMELLDLVQEGTLGLERAVEKYDPTRGFRFST 190

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI+  +   I      +++     +K     L R+K   + I   + +   V  +A
Sbjct: 191 YAYWWIRQGITRAIATQSRTIRLPVHVTEK-----LNRIKKAQRQIATEHGRLASVSDLA 245

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           ++L +SE  V     R+    SL+  +    +  +Q  D L   H   EQ L     R++
Sbjct: 246 RELGLSEEVVRLTLMRVPRSVSLDTRV--GREQDTQLGDLLEDSHATPEQELT----RES 299

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             + L   +  L  RE  +   R   E+  P TL  +  +  +SRERVRQIE+RA  K++
Sbjct: 300 LHDDLESLLEELTAREAAVIRLRYGLEDDTPQTLSQIGEDLHLSRERVRQIESRALLKLR 359

Query: 282 ESIQK 286
           +  ++
Sbjct: 360 QPQRR 364


>gi|186681941|ref|YP_001865137.1| RpoD family RNA polymerase sigma factor [Nostoc punctiforme PCC
           73102]
 gi|186464393|gb|ACC80194.1| RNA polymerase, sigma 70 subunit, RpoD family [Nostoc punctiforme
           PCC 73102]
          Length = 339

 Score =  200 bits (509), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 67/312 (21%), Positives = 134/312 (42%), Gaps = 52/312 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----------------------YREHGDL- 47
            +  +  Y+ EI ++ +L +++E + A++                        +E  D  
Sbjct: 28  TDDIVRSYLQEIGRVDLLTREQEVIFAQQVQLMMNLLAAKEELAVKLDHEPTLQEWADRV 87

Query: 48  ---------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  +++ ++LRLVV +A  Y+   L   +++ EG +GL + V K
Sbjct: 88  ELGAEVLELQLSQGHQAKQKMIQANLRLVVAVAKKYQHRNLEFMDLIQEGTLGLERGVDK 147

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FDP  G++ +TY+ WWI+  +   I +    +++         F  L ++K   + ++  
Sbjct: 148 FDPALGYKFSTYAYWWIRQGITRAIAQQGRTIRLPIHV-----FEKLNKIKRVQRELSQQ 202

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA  L+++ S+V           SL A +   ++  ++ QD L  D    E
Sbjct: 203 LGRVPTTAEIANALSLTPSQVRECLYLARQPFSLEARV--GEQQDTELQDILEDDGPSPE 260

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVR 270
              +E+   ++    L   ++ L+P++R I   R    +   ++L  +     +SRERVR
Sbjct: 261 DYAVEESLHQD----LQDLLAKLSPQQREILTLRFGLTDGYELSLAQIGDRMGISRERVR 316

Query: 271 QIEARAFKKVQE 282
           QIE +A   ++ 
Sbjct: 317 QIEQKALSLLRR 328


>gi|298492420|ref|YP_003722597.1| RpoD subfamily RNA polymerase sigma 70 subunit ['Nostoc azollae'
           0708]
 gi|298234338|gb|ADI65474.1| RNA polymerase, sigma 70 subunit, RpoD subfamily ['Nostoc azollae'
           0708]
          Length = 389

 Score =  200 bits (509), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 77/313 (24%), Positives = 136/313 (43%), Gaps = 52/313 (16%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYR---EHGDLSA-------------------- 49
           +  +  +  E+ + P+L+  EE  LA+R R   E  DL A                    
Sbjct: 76  DDAVGAFFKEMARYPLLKPDEEVELARRVRFLEEVKDLQAALEEELGQQPSRSEVAAKFE 135

Query: 50  ----------------AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
                             +++ S+LRLVV IA  Y   G+P  +++ EG +GL +A +KF
Sbjct: 136 MTEKQLESRLYQGRVAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAMGLNRATEKF 195

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           DP++G++ +TY+ WWI+ A+   I      +++     +K     L +LK   + +    
Sbjct: 196 DPDKGYKFSTYAYWWIRQAITRAIANDARTIRLPIHIVEK-----LNKLKKAQRELKQKL 250

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            +      +A  L +S  ++  +        SLN  +    +  ++  D L  + +   Q
Sbjct: 251 ARNPSEAEMATALEISIQQLRQLQQLRRQALSLNHRV--GKEEDTELMDLLEDEDN---Q 305

Query: 214 VLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVR 270
               K      R  +   +  VL PRE+ +   R       P TLE + + F +SRERVR
Sbjct: 306 SPEAKMNENMMRQEIWEVLGDVLTPREKDVISLRYGLTTSEPCTLEEVGNMFNLSRERVR 365

Query: 271 QIEARAFKKVQES 283
           QI+++A +K++  
Sbjct: 366 QIQSKAMRKLRRP 378


>gi|89074640|ref|ZP_01161105.1| hypothetical DNA-directed RNA polymerase, sigma subunit
           [Photobacterium sp. SKA34]
 gi|89049578|gb|EAR55138.1| hypothetical DNA-directed RNA polymerase, sigma subunit
           [Photobacterium sp. SKA34]
          Length = 284

 Score =  200 bits (509), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 76/272 (27%), Positives = 138/272 (50%), Gaps = 12/272 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y+ +I   P+L K +E   +++Y   GD  A  +L+ S+LRLVV IA  YR   L +
Sbjct: 9   IGLYMKDISSKPLLTKMDEIHYSRKYL-RGDNKAKEKLIESNLRLVVSIAKKYRAAHLLL 67

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GL+ AV+KFDPE+GFR +TY+ WWIK  ++  I      +++    +  + 
Sbjct: 68  GDMIDEGNLGLITAVEKFDPEKGFRFSTYATWWIKQNIERAIHNQNRAIRLPVHVS--KE 125

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              L R    L    ++    E    IA +LN    ++ ++        SL+  I   D+
Sbjct: 126 INALLRTHRDLMKKQNHEPTHED---IALQLNKETQDISTLLSYELNIVSLDQTIGD-DE 181

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPV 253
           +       +V +       ++E+    N    L   ++ + PRER I   R       P 
Sbjct: 182 SKGTIASLVVDEQIPSPSHIVEENSMVNLAEGL---LNKIKPREREILCRRFGMMGYEPQ 238

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           TL+ ++S   ++RERVRQ++ ++ ++++ +++
Sbjct: 239 TLQEVASALGLTRERVRQLQMKSLERLKMNLK 270


>gi|196234461|ref|ZP_03133287.1| RNA polymerase, sigma 32 subunit, RpoH [Chthoniobacter flavus
           Ellin428]
 gi|196221517|gb|EDY16061.1| RNA polymerase, sigma 32 subunit, RpoH [Chthoniobacter flavus
           Ellin428]
          Length = 479

 Score =  200 bits (509), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 71/255 (27%), Positives = 124/255 (48%), Gaps = 13/255 (5%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           E    KR++    L A   +V  +LRLVV IA  Y+  G P  +++ EGNIGLM+AV++F
Sbjct: 228 ELQEMKRWQRKA-LEARTEMVECNLRLVVSIAREYQNRGQPFLDLIQEGNIGLMRAVERF 286

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           +  RG++ AT + WWI+ A+   I      ++I T      +   L +L    + +T  +
Sbjct: 287 EYRRGYKFATCATWWIRQAISRSIANQARTIRIPTH-----MIDLLAKLIRVQRQMTQES 341

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            +      +A +L++    V ++        S++  +   ++  S+  D++    D   +
Sbjct: 342 GRDPTAEDLAGELHLPLRRVRALLKMAEEPISIHTPV--GEEGGSRLGDFI---EDHSVE 396

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQ 271
              ++      R  +   +  L  RER I E R         TLE +   F+V+RERVRQ
Sbjct: 397 DPSKQAAVAMLREKINAVLHTLTEREREILEQRFGLIDGRERTLEEIGRHFKVTRERVRQ 456

Query: 272 IEARAFKKVQESIQK 286
           IEA+A +K++   ++
Sbjct: 457 IEAKALRKMRHPERR 471


>gi|296121158|ref|YP_003628936.1| RNA polymerase sigma factor, sigma-70 family [Planctomyces
           limnophilus DSM 3776]
 gi|296013498|gb|ADG66737.1| RNA polymerase sigma factor, sigma-70 family [Planctomyces
           limnophilus DSM 3776]
          Length = 577

 Score =  200 bits (509), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 71/258 (27%), Positives = 119/258 (46%), Gaps = 12/258 (4%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           G   +  +L   +LRLVV IA  YR  GL   +++ EGN GLM+ V+K++  RG++ +TY
Sbjct: 294 GWTRSKQQLSGGNLRLVVSIAKKYRNRGLSFLDLIQEGNAGLMRGVEKYEFRRGYKFSTY 353

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + WWI+ A+   +      ++I        +F ++  LK   + I     +   +  +A 
Sbjct: 354 ATWWIRQAITRAVADHARTIRIPVH-----MFQSISTLKNKSEQIRQETGREPTIEELAL 408

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            +++S  +   +        SL+  I   +   S + D+L    D  E    +   R+  
Sbjct: 409 AVDMSVEDTERIMKTWKHPMSLDTPI--GESEDSSFGDFL---EDSHESTPADNALREML 463

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           R+ +   +  L  RER I   R    +    TLE     F+V+RER+RQIE++A KK+Q 
Sbjct: 464 RDKIDIVLRSLTYREREIIRLRYGLGDGYSYTLEETGRIFKVTRERIRQIESKALKKLQH 523

Query: 283 SIQKQVELSSSPPLLQKP 300
             +          LL  P
Sbjct: 524 HTRAHHLQGFVEDLLPNP 541


>gi|87300555|ref|ZP_01083397.1| Putative type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 5701]
 gi|87284426|gb|EAQ76378.1| Putative type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 5701]
          Length = 398

 Score =  200 bits (509), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 69/242 (28%), Positives = 117/242 (48%), Gaps = 13/242 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  R++ ++LRLVV +A  Y+  G+ + ++V EG +GL +AV+K+DP RGFR +TY+ 
Sbjct: 156 RRARDRMIQANLRLVVAVAKKYQKRGVELLDLVQEGTLGLERAVEKYDPTRGFRFSTYAY 215

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   I      +++     +K     L R+K   +    ++ +   +  +A+ L
Sbjct: 216 WWIRQGVTRAIATQSRTIRLPVHVTEK-----LNRIKKAQRQFASDHGRTASLAELAEAL 270

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             SE  V     R+    SL A +       +   D L    D  EQ L  ++   +   
Sbjct: 271 QWSEEAVRLTLLRVPRSISLEAKV--GRDQDTPLGDLLEATSDTPEQSLTRQQLHSD--- 325

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R     + P TL  +    ++SRERVRQIE RA  K+++  
Sbjct: 326 -LDALLDELSEREAEVIRLRFGLADDTPRTLAQIGEGMQLSRERVRQIETRALHKLRQPA 384

Query: 285 QK 286
           ++
Sbjct: 385 RR 386


>gi|328954372|ref|YP_004371706.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfobacca
           acetoxidans DSM 11109]
 gi|328454696|gb|AEB10525.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Desulfobacca
           acetoxidans DSM 11109]
          Length = 436

 Score =  200 bits (509), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 74/275 (26%), Positives = 127/275 (46%), Gaps = 16/275 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL--SAAHRLVTSHLRLVVKIAMGYRGYGL 73
           ++R + E+ +      +E   LAK+ RE  +    A   ++ ++LRLVV IA  Y   GL
Sbjct: 166 INRTLKEVLRH-YPNAEEIKQLAKKIREKENEVVRARDEMIKANLRLVVSIAKKYLHRGL 224

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
             S+++ EGN+GLM+AV ++D   G+RL+T++ WWI+  +   I      ++I     + 
Sbjct: 225 SFSDLIQEGNLGLMKAVTRYDYTTGYRLSTFASWWIRQTITRAIYDKTRTIRIPVHLQEI 284

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
           R      R       +     +   +  IA++  V E +++ +        SL   +   
Sbjct: 285 R-----NRCYRAFYDLLKELGREPLLKEIAERSGVPEDKILVVTNLSDEPISLETPVGDE 339

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--EN 251
                +  D++  D   Q     +              +S L PRE +I + R     E 
Sbjct: 340 GD---RLGDFIRND---QAISPFDSIISSELSEKTDAILSTLTPREEKIMKMRFGIGAEV 393

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             TLE +  EF+VSRER+RQIE +A K+++   +K
Sbjct: 394 EHTLEEIGREFKVSRERIRQIEKKALKRLKHPTRK 428


>gi|1553013|gb|AAC45098.1| primary sigma factor [Borrelia afzelii]
 gi|1553015|gb|AAC45099.1| primary sigma factor [Borrelia afzelii]
 gi|1553021|gb|AAC45102.1| primary sigma factor [Borrelia garinii]
          Length = 450

 Score =  200 bits (509), Expect = 2e-49,   Method: Composition-based stats.
 Identities = 66/250 (26%), Positives = 119/250 (47%), Gaps = 16/250 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    K+  +H    A  +L+ ++LRLVV IA  Y   GL   ++V EGNIGL++AV+K
Sbjct: 215 EEIAKGKQMMQH----AKDQLIKANLRLVVSIAKKYANRGLHFFDLVQEGNIGLIKAVEK 270

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RGF+ +TY+ WWI+ A+   I      +++        +   + RL    + +   
Sbjct: 271 FEYKRGFKFSTYATWWIRQAITRSISDQARTIRVPVH-----MIEQINRLNRETRYLVQV 325

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             K      ++ +L     +V ++        SL   I   ++  S   D++    D   
Sbjct: 326 LGKDPTDEELSDRLGWELKKVKTVKSVSREPVSLETPI--GEEEDSVLSDFI---EDKAI 380

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +           ++ +   +  L  RE+ + + R   E+   +TLE +   F V+RER+R
Sbjct: 381 KNPANHTSFVVLQDQIRAILGTLPEREQEVVKMRFGLEDGYSLTLEEVGLHFNVTRERIR 440

Query: 271 QIEARAFKKV 280
           QIE++A +++
Sbjct: 441 QIESKALRRL 450


>gi|284042443|ref|YP_003392783.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Conexibacter
           woesei DSM 14684]
 gi|283946664|gb|ADB49408.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Conexibacter
           woesei DSM 14684]
          Length = 285

 Score =  200 bits (509), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 75/269 (27%), Positives = 130/269 (48%), Gaps = 14/269 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             L   + E R  P+L   EE  LA+R  E GDLSA  R+V S+LRLV+ IA  Y+G GL
Sbjct: 16  DPLQLLMREARNWPLLTPAEEIELARRI-ERGDLSAKERMVNSNLRLVMSIARHYQGQGL 74

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + ++V EG +GL++AV+KFD  +GFR +TY+  WI+ ++Q  +  +   +++     Q+
Sbjct: 75  GMGDLVQEGTLGLIRAVEKFDWRKGFRFSTYATLWIRQSIQRGLENTGRTIRLPVHVGQR 134

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                + R++  L A    +   E++   A+   +   +VI          SL+A +   
Sbjct: 135 A--RKVARIRRELTAKHGRDATDEEIAEAAR---LPVEQVIEAGRADREPTSLDAPV--G 187

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QEN 251
           +   +     +  D    ++ + +      R   + R++  L   E+ +   R     E 
Sbjct: 188 EDGDTALGALIKTDTPEPDEEVAD----TLRHETVQRAIDDLPDNEKTVIHLRFGTAGEP 243

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKV 280
           P TL  +     VS  R R+IE +A +++
Sbjct: 244 PQTLTQIGRRLGVSSSRAREIEEQALRRL 272


>gi|283780188|ref|YP_003370943.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pirellula staleyi
           DSM 6068]
 gi|283438641|gb|ADB17083.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Pirellula staleyi
           DSM 6068]
          Length = 320

 Score =  200 bits (508), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 82/286 (28%), Positives = 138/286 (48%), Gaps = 21/286 (7%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ +  L  Y+ EI +  +L  ++E  LA    + GD+ A  R+V ++LRLVV IA GY 
Sbjct: 37  ISLQTPLESYLREINETALLSARDERELAAAIAD-GDVRARDRMVRANLRLVVNIARGYT 95

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G GL + +++ EGN+GL++AV+ FDP  G R +TY+ +WIK +++  ++ S   ++I   
Sbjct: 96  GKGLSLQDLIEEGNLGLLRAVEGFDPAVGTRFSTYASYWIKQSIKRALINSAKTIRIP-- 153

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA----KKLNVSESEVISMNCRLAGDES 185
           A    L    RR    L         PE+V  +     KKL + +  +   N     D+S
Sbjct: 154 AYMVELLSKWRRATARLTEELGRGPTPEEVARVLGLAKKKLPIIKKAIRIYNSTPQTDQS 213

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
                   +   S  +  +       E  L+E++  K+   ML      ++ RE  +   
Sbjct: 214 --------EAGWSLGEIVMDERLKNPEDELVEQDVLKHVMEMLH----TMDSREATVLRM 261

Query: 246 RRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           R    +  P TL+ +     ++RERVRQIE  A  K+ + ++   E
Sbjct: 262 RFGLGDTTPHTLKEIGESLGLTRERVRQIETEALGKLADGLKDPRE 307


>gi|40353315|gb|AAR84421.1| essential primary sigma 70 factor [Frankia sp. HRX401a]
          Length = 255

 Score =  200 bits (508), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 69/265 (26%), Positives = 116/265 (43%), Gaps = 39/265 (14%)

Query: 31  KQEEYVLAKRY-------------------REHGDLSA--------AHRLVTSHLRLVVK 63
            +EE  LAKR                    +   DL A          +LV ++LRLVV 
Sbjct: 1   AEEEVDLAKRIEAGLFASEKLAVATKKTSPQMRRDLEAIERDGQIAKRKLVEANLRLVVS 60

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y G G+    ++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A+   I      
Sbjct: 61  IAKRYVGRGMLFLHLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAIADQART 120

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           ++I     +      L R++  L         PE    IAK+++++  +V  +       
Sbjct: 121 IRIPVHMVE--TINKLIRIQRQLLQDLGREPSPE---EIAKEMDLTPDKVREILKVSQEP 175

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SL   I   ++  S   D++    D    V ++       +  L   +  L+ RE+++ 
Sbjct: 176 VSLETPI--GEEEDSHLGDFI---EDCDAVVPVDAASFILLQEQLDSVLHTLSDREKKVI 230

Query: 244 EARRL--QENPVTLENLSSEFEVSR 266
           + R      +P TLE +  EF V+R
Sbjct: 231 QLRFGLTDGHPRTLEEVGREFGVTR 255


>gi|221636011|ref|YP_002523887.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Thermomicrobium roseum DSM 5159]
 gi|221157983|gb|ACM07101.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43)
           [Thermomicrobium roseum DSM 5159]
          Length = 334

 Score =  200 bits (508), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 75/295 (25%), Positives = 130/295 (44%), Gaps = 33/295 (11%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------HGDLSAA 50
               + RY  E+    +L  QEE   ++  R                           A 
Sbjct: 41  ANDAVYRYFREVGGHRLLTHQEEIEYSRAVRAGLAARKRIEAGEDTPELRELVRKGQEAR 100

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            +L+  +LRLVV IA  YR   LP+ +++ EGNIGLM AV+++DPE G+R +TY+ +WI+
Sbjct: 101 EKLIRHNLRLVVSIAKRYRSSELPLIDLIQEGNIGLMTAVERYDPELGYRFSTYATFWIR 160

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            A+   +      +++    +       + +++     I     +P     +A+ L +  
Sbjct: 161 QAIGRAVANLSRTIRVPVHMHDL-----IAKIRRAEAQIEQQKGRPATNEELAELLGIDV 215

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           + +     ++    SL+  I   +   S   D L    D +   ++E+      R  + R
Sbjct: 216 ARIEQARTQIPRTSSLDKPI--GEDGESSIGDLLP---DPRSDDVVEEALTNAIREQIRR 270

Query: 231 SMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           S+  L  RER +   R     E P TL  ++   ++SRERVRQ+E  A +K++ S
Sbjct: 271 SLEQLTERERTVLVMRFGLDGEQPRTLAEIADALKISRERVRQVEKEALQKLRNS 325


>gi|254415890|ref|ZP_05029647.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
 gi|196177317|gb|EDX72324.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
          Length = 352

 Score =  200 bits (508), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 66/305 (21%), Positives = 134/305 (43%), Gaps = 52/305 (17%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKR--------------------------YREHGDLS---- 48
           Y+HEI ++P+L  ++E V  K+                          + +H DL     
Sbjct: 48  YLHEIGRVPLLTHEQEIVYGKQVQQMMPLLEAKDALAETLEREPTMQEWADHVDLEESAL 107

Query: 49  ---------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                    A  +++ ++LRLVV IA  Y+   +   +++ EG +GL + V+KFDP RG+
Sbjct: 108 KKIINQGTRAKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGY 167

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWI+ A+   I +    +++     +K     L ++K   + ++    +    
Sbjct: 168 KFSTYAYWWIRQAITRAIAQQARAIRLPIHITEK-----LNKIKKVQRELSQRLGRNATP 222

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I ++L +  +++           SL+  +   D   ++  D L           +   
Sbjct: 223 TEIGQELELEPAQIREYLSIARQPVSLD--VRVGDNQDTELSDLLED----SGPTPVHYT 276

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
            +++ R  L   ++ L P++R +   R   E+   ++L  +     +SRERVRQ+E +A 
Sbjct: 277 TQESLRQDLDNLLAELTPQQREVLALRFGLEDGNELSLAKVGQRLNLSRERVRQLEHQAL 336

Query: 278 KKVQE 282
            +++ 
Sbjct: 337 AQLRR 341


>gi|261880495|ref|ZP_06006922.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           bergensis DSM 17361]
 gi|270332834|gb|EFA43620.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           bergensis DSM 17361]
          Length = 290

 Score =  200 bits (508), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 74/280 (26%), Positives = 133/280 (47%), Gaps = 12/280 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKI 64
           SI       L RY+ EI + P++   EE  L+++ R+ G     A  +L+TS+LR VV +
Sbjct: 9   SITNRSSEALDRYLVEIGRAPLISIDEEIELSQKIRKGGREGQRAKDKLITSNLRFVVSV 68

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y+  GL ++++++EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V
Sbjct: 69  AKQYQHQGLSLTDLINEGNIGLIKATEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIV 128

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           ++            L ++   +      + +      IA+ ++V   ++           
Sbjct: 129 RLPLNQ-----VGTLSKINKEINNFEQRHERRPSTQEIAEAIDVEAGKIRMSMMADGHHV 183

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           S++A     + NS    D +    D +     + E      N +    SVL  RE  I  
Sbjct: 184 SIDAPFQEDESNS--MADIMASGDDTRTDKRADHESMAQELNTVLE--SVLKEREITIIR 239

Query: 245 ARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
                  + + LE +     ++RERVRQI  ++  K++ES
Sbjct: 240 ECFGIGCHELGLEEIGDRLGLTRERVRQIREKSIAKLRES 279


>gi|307152078|ref|YP_003887462.1| RpoD subfamily RNA polymerase sigma-70 factor [Cyanothece sp. PCC
           7822]
 gi|306982306|gb|ADN14187.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7822]
          Length = 328

 Score =  200 bits (508), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 65/323 (20%), Positives = 143/323 (44%), Gaps = 53/323 (16%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------------- 43
           +N KN     + ++ +  Y+HEI ++P+L  ++E V  K+ ++                 
Sbjct: 6   VNPKNQKPTFSADM-VRTYLHEIGRVPLLTHEQEIVYGKQVQKMMTLLEKKDELAIQLER 64

Query: 44  ----------------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
                                      A  +++ ++LRLVV IA  Y+   +   +++ E
Sbjct: 65  EPSLTEWANHVQMSEEELNRAIQQGKRAKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQE 124

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           G++GL + V+KFDP +G++ +TY+ WWI+ A+   I +    +++     +K     L +
Sbjct: 125 GSLGLERGVEKFDPTKGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEK-----LNK 179

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           +K   + ++    +      IAK L++   ++           SL+  +   D   ++  
Sbjct: 180 IKKTQRELSQQLGRSATPSEIAKALDLEPDQIREFLSMSRQPISLD--VRVGDNQDTELS 237

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLS 259
           + L  +    +  + ++  R++    L   ++ L P++R +   R   ++   ++L  + 
Sbjct: 238 ELLEDEGISPDNYITQELMRQD----LQDLLAELTPQQREVLSLRFGLQDGKELSLAKIG 293

Query: 260 SEFEVSRERVRQIEARAFKKVQE 282
               +SRERVRQ+E +A  +++ 
Sbjct: 294 QRMNISRERVRQLEHQALSQLRR 316


>gi|218440063|ref|YP_002378392.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
 gi|218172791|gb|ACK71524.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
          Length = 372

 Score =  200 bits (508), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 79/317 (24%), Positives = 135/317 (42%), Gaps = 53/317 (16%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLA-----------KRYREHGD------------ 46
            N +  +  +  E+ + P+L+ +EE  LA           KR +   D            
Sbjct: 55  TNSDDTVGAFFKEMARYPLLKPEEEIELAYTVKFLMESEEKRQQLQIDLQRPPTKLEWAQ 114

Query: 47  -----------------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
                             SA  +++ S+LRLVV IA  Y   G+P  +++ EG IGL +A
Sbjct: 115 AMGLQNERQLENRLYRGRSAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRA 174

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
            +KFDP +G++ +TY+ WWI+ A+   I      +++     +K     L +LK   + +
Sbjct: 175 AEKFDPNKGYKFSTYAYWWIRQAITRTIANDARTIRLPIHIVEK-----LNKLKKAQRVL 229

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
                +      +A+ L V    +  +        SLN  +   +   ++  D L    D
Sbjct: 230 KQQLHRNPTEKELAQALEVDAENLRQLLQLRRQSLSLNHRVGKGED--TELVDLL---ED 284

Query: 210 GQEQVLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSR 266
              Q+  EK      R  ++  +  VL  RE+ +   R       P TLE +   F +SR
Sbjct: 285 EDLQLPEEKMNEAMMRQDISAVLTDVLTEREKDVIALRYGLSTSQPYTLEEVGGIFNLSR 344

Query: 267 ERVRQIEARAFKKVQES 283
           ERVRQI+++A +K++  
Sbjct: 345 ERVRQIQSKAMRKLRRP 361


>gi|22298374|ref|NP_681621.1| RNA polymerase sigma factor [Thermosynechococcus elongatus BP-1]
 gi|22294553|dbj|BAC08383.1| group 2 RNA polymerase sigma factor [Thermosynechococcus elongatus
           BP-1]
          Length = 309

 Score =  200 bits (508), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 67/316 (21%), Positives = 137/316 (43%), Gaps = 52/316 (16%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYRE----------------------------------- 43
           Y+ EI ++P+L  ++E +L K+ ++                                   
Sbjct: 5   YLQEIGRVPLLTHEQEIILGKQVQQMMALREKRDALTKELGREATFEEWAAACNLTPTEL 64

Query: 44  ----HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                    A  +++ ++LRLVV +A  Y+   L + ++V EG +GL + V+KFDP RG+
Sbjct: 65  CNILKRGERAKQKMIEANLRLVVSVAKKYQKRNLELLDLVQEGTLGLERGVEKFDPTRGY 124

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWI+ A+   I +    +++     +K     L ++K   + +     +    
Sbjct: 125 KFSTYAYWWIRQAITRAIAQQARTIRLPIHITEK-----LNKIKRTQRELAQKLGRSATP 179

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +AK L +   ++           SL+  +   D   ++  + L  D    EQ      
Sbjct: 180 AEVAKALELEPEQIREYLTLARQPVSLD--LRVGDNQDTELGELLEDDSLSPEQF----T 233

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
             ++ R+ +   ++ L P++R++   R    +   ++L  +  +  +SRERVRQ+E +A 
Sbjct: 234 TVESLRDDVNLWLAELTPQQRQVLTLRYGLGDGQELSLAKVGEQLNLSRERVRQLERQAL 293

Query: 278 KKVQESIQKQVELSSS 293
             ++   Q+  E  +S
Sbjct: 294 DHLRRRRQQMYEYLAS 309


>gi|182438069|ref|YP_001825788.1| RNA polymerase principal sigma factor hrdD [Streptomyces griseus
           subsp. griseus NBRC 13350]
 gi|326778714|ref|ZP_08237979.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces cf.
           griseus XylebKG-1]
 gi|178466585|dbj|BAG21105.1| RNA polymerase principal sigma factor hrdD [Streptomyces griseus
           subsp. griseus NBRC 13350]
 gi|326659047|gb|EGE43893.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces cf.
           griseus XylebKG-1]
          Length = 333

 Score =  200 bits (508), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 76/307 (24%), Positives = 130/307 (42%), Gaps = 44/307 (14%)

Query: 10  VNGEIG----LSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------HGD---- 46
           V GEI     +  Y+ EI + P+L+  +E  L++                    GD    
Sbjct: 26  VGGEIADRDLVGMYLDEIARTPLLDAAKEVDLSQTIEAGVFAQQILDGEVESTTGDAKRE 85

Query: 47  ---------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
                      A    + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +
Sbjct: 86  ELEALVAEGERAKDIFIRSNLRLVVAVARRYPRAGLPLLDLIQEGNAGLVRAVEKFDYAK 145

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           GF+ +TY+ WWI+ A+   I      +++        L   L R++   +     + +  
Sbjct: 146 GFKFSTYATWWIRQAITRSIADQSRTIRLPVH-----LVEELGRIRRVQREFNREHGRDP 200

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           +   IA +L+ +   V ++        SLN  +   D   +Q+ D L    D       +
Sbjct: 201 EHAEIAAELDSNAERVGNVLDWARDPVSLNMSV--DDDGDTQFGDLL---EDTSAVSPEQ 255

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
                 R   L   +  L+ R   I + R   E+    TL  +  +  ++RER+RQIE  
Sbjct: 256 SVMTLLRSEELEDLIGKLDNRTASIIKMRYGIEDGRERTLTEVGKQHGLTRERIRQIEKH 315

Query: 276 AFKKVQE 282
           A  +++ 
Sbjct: 316 ALLELKR 322


>gi|113953359|ref|YP_732042.1| RNA polymerase sigma-70 factor family protein [Synechococcus sp.
           CC9311]
 gi|113880710|gb|ABI45668.1| RNA polymerase sigma-70 factor family protein [Synechococcus sp.
           CC9311]
          Length = 376

 Score =  200 bits (508), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 77/249 (30%), Positives = 124/249 (49%), Gaps = 13/249 (5%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           + R      A  R++ ++LRLVV +A  Y+  G+ + ++V EG +GL +AV+KFD  RGF
Sbjct: 127 QLRLRRGRKARDRMIQANLRLVVAVAKKYQHRGMELLDLVQEGTLGLERAVEKFDSTRGF 186

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           R +TYS WWI+  +   I      +++     +K     L R+K   Q I  N  +   +
Sbjct: 187 RFSTYSYWWIRQGITRAIATQSRTIRLPVHITEK-----LNRIKRVQQEIASNEGRTASM 241

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +A++L+VSE  V     R+    SL   +       +Q  + L  +H   EQ L    
Sbjct: 242 TDLARELSVSEDTVRQTLARVPRSVSLETKV--GRDQDTQLGELLEDEHATPEQTLT--- 296

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
            R +  + L   ++ L PRE  +   R   E+  P TL  +  +  +SRERVRQIE RA 
Sbjct: 297 -RDSLHDDLEHLLNELTPREATVIRCRFGLEDDTPRTLAQIGEDMNLSRERVRQIETRAL 355

Query: 278 KKVQESIQK 286
            K+++  ++
Sbjct: 356 LKLRQPQRR 364


>gi|158335492|ref|YP_001516664.1| RNA polymerase sigma factor [Acaryochloris marina MBIC11017]
 gi|158305733|gb|ABW27350.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 327

 Score =  200 bits (508), Expect = 3e-49,   Method: Composition-based stats.
 Identities = 69/322 (21%), Positives = 137/322 (42%), Gaps = 52/322 (16%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------ 43
            ++    +      +  Y+HEI ++P+L  +EE V  K+ +                   
Sbjct: 6   TKQQAISVSPTTDMVRTYLHEIGRVPLLTHEEEIVFGKQVQAMMALLDLQKTVMDELGRE 65

Query: 44  ---------------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
                                H    A  +++ ++LRLVV +A  Y+   L + +++ EG
Sbjct: 66  PSLEEWAEKANLSPSQLELSLHQGQQAKQKMIEANLRLVVSVAKKYQKRNLELLDLIQEG 125

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            +GL + V+KFDP RG++ +TY+ WWI+ A+   I +    +++     +K     L ++
Sbjct: 126 TLGLERGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEK-----LNKI 180

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
           K   + ++    +      IA+ L +  S++           SL+  +   D   ++ +D
Sbjct: 181 KKAQRELSQKLGRSATPAEIAEALELEPSQIRDYLTIARQPISLD--LRVGDNQDTELRD 238

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSS 260
            L  D    EQ    +      R+ + + +  L P++R +   R    N   ++L  +  
Sbjct: 239 LLEDDGQSPEQFTTTEAL----RDDVNQLLKELTPQQRDVLMLRFGLNNGKELSLAKVGQ 294

Query: 261 EFEVSRERVRQIEARAFKKVQE 282
           +  +SRERVRQ+E +A   ++ 
Sbjct: 295 QLSLSRERVRQLERQALDYLRR 316


>gi|126661338|ref|ZP_01732404.1| RNA polymerase sigma factor [Cyanothece sp. CCY0110]
 gi|126617371|gb|EAZ88174.1| RNA polymerase sigma factor [Cyanothece sp. CCY0110]
          Length = 328

 Score =  199 bits (507), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 67/323 (20%), Positives = 145/323 (44%), Gaps = 53/323 (16%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEY-----------------VLAKRYRE 43
           +N K    + + ++ +  Y+HEI ++P+L  ++E                   LA+R  +
Sbjct: 6   VNTKTKQPMYSADM-VRTYLHEIGRVPLLTHEQEIIYGKQVQTMMNLLEKKEELAQRVGK 64

Query: 44  H----------------------GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
                                      A  +++ ++LRLVV IA  Y+   +   +++ E
Sbjct: 65  EPSIQEWAKEVNIEEKALQKALEQGERAKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQE 124

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           G++GL + V+KFDP +G++ +TY+ WWI+ A+   I +    +++     +K     L +
Sbjct: 125 GSLGLERGVEKFDPTKGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEK-----LNK 179

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           +K   + ++ +  +      IA++L +  S++           SL+  +   D   ++  
Sbjct: 180 IKKTQRELSQSLGRSATPAEIAQELEIEPSQIREFLSIARQPISLD--VRVGDNQDTELS 237

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLS 259
           + L       +  + ++  R++    L+  M+ L P++R +   R   E+   ++L  + 
Sbjct: 238 ELLEDQGVSPDIYITQELLRQD----LSNLMAELTPQQRTVLTLRFGLEDGKELSLAKIG 293

Query: 260 SEFEVSRERVRQIEARAFKKVQE 282
               +SRERVRQ+E +A  +++ 
Sbjct: 294 KRLNISRERVRQLEHQALAQLRR 316


>gi|16330349|ref|NP_441077.1| RNA polymerase sigma factor [Synechocystis sp. PCC 6803]
 gi|1652838|dbj|BAA17757.1| RNA polymerase sigma factor [Synechocystis sp. PCC 6803]
          Length = 369

 Score =  199 bits (507), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 75/314 (23%), Positives = 136/314 (43%), Gaps = 51/314 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-----------------------EHGD-- 46
            E  +  +  E+ + P+L   EE  LA++ R                       E G   
Sbjct: 55  SEDTVGAFFKEMARYPLLSAAEEVELARQIRLLVSAEDVRQQLTQQLERTPSLQEWGQAL 114

Query: 47  ---------------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                           +A  R++ S+LRLVV IA  Y   G+P  +++ EG IGL +A +
Sbjct: 115 EFPQVRQFEIWLYQLRAAKRRMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAE 174

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFDP++G++ +TY+ WWI+ A+   I      +++     +K     L ++K   +++  
Sbjct: 175 KFDPDKGYKFSTYAYWWIRQAITRTIANDARTIRLPIHVVEK-----LNKIKKAQRSLKQ 229

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +      +A  L+++ +++  +        SLN  +   +   ++  D L       
Sbjct: 230 ELKRNPNEGELAAALDITPAQLRQLLQLRRQSLSLNHRVGKGED--TELVDLLEDQQLQL 287

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
            + L+   E   RR ++     VL  RE  +   R         TLE + + F +SRERV
Sbjct: 288 PEDLMN--ESMLRREIVEVLAEVLTEREMEVICLRYGIASHQSYTLEEVGNMFNLSRERV 345

Query: 270 RQIEARAFKKVQES 283
           RQI+++A +K++  
Sbjct: 346 RQIQSKAMRKLRRP 359


>gi|6175930|gb|AAF05342.1|AF182106_2 truncated RNA polymerase sigma subunit [Escherichia coli]
          Length = 303

 Score =  199 bits (507), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 73/254 (28%), Positives = 127/254 (50%), Gaps = 13/254 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSRERVR 270
           ++  E  ++RERVR
Sbjct: 290 DVGREIGLTRERVR 303


>gi|4105839|gb|AAD02575.1| RNA polymerase sigma factor [Cyanidium caldarium]
          Length = 589

 Score =  199 bits (507), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 93/348 (26%), Positives = 153/348 (43%), Gaps = 57/348 (16%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYV-----------------LAKRY--- 41
           N+KN           S Y+ EI K+  L  +EE                   L +R    
Sbjct: 245 NKKNRRRRSTNSDSFSTYLTEIGKVHRLSLEEEKEICQEIAFFTHLEAVREDLRRRIGRL 304

Query: 42  -REH------------------GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
            REH                      A +R+V ++LRLV+  A  +R  G+   ++V EG
Sbjct: 305 PREHEWAMETNMSVSELRGKLIKGRRAKNRMVAANLRLVICFAKRFRNRGVAFQDLVQEG 364

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
           +IGL++ V+K+D  RGFR +TY+ WWI+  + + +L    + ++    N+  +   +RR 
Sbjct: 365 SIGLIRGVEKYDANRGFRFSTYASWWIRQGIHKALLECSKMFRLPVHVNE--MIKEIRRC 422

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
              L  I          + IA K+ + E +VI +  R     SL   +  SD   S  + 
Sbjct: 423 SYELMNILGRE---PTKLEIAMKVGMPEEKVIFLLQRAQTALSLEMPLRGSD---SSLES 476

Query: 203 WLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT--LENL 258
             + D           +     + R  L R++S L+ RER +   R   ++  T  L  +
Sbjct: 477 RTLGDVVSSTASPSPEDSAFGTSLRYDLERALSQLDFREREVIRMRFGLDDGRTKSLGEV 536

Query: 259 SSEFEVSRERVRQIEARAFKKVQES-----IQKQVE-LSSSPPLLQKP 300
            S F V+RERVRQIE RA +K+++      +++ +E +S   P ++KP
Sbjct: 537 GSLFCVTRERVRQIETRALRKLRDPRCNIFLKEYMEWISDERPGMKKP 584


>gi|166364164|ref|YP_001656437.1| RNA polymerase sigma factor [Microcystis aeruginosa NIES-843]
 gi|166086537|dbj|BAG01245.1| group 2 RNA polymerase sigma factor [Microcystis aeruginosa
           NIES-843]
          Length = 328

 Score =  199 bits (507), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 63/323 (19%), Positives = 135/323 (41%), Gaps = 54/323 (16%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------------------- 42
             +  S        +  Y+HEI ++P+L  ++E +  K+ +                   
Sbjct: 6   TNQTQSQPTLNADMVRTYLHEIGRVPLLTHEQEIIYGKQVQRMMSLLETKEALSKQLGRE 65

Query: 43  ---------------------EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
                                + GD  A  +++ ++LRLVV IA  Y+   +   +++ E
Sbjct: 66  PDRLEWADSVNLSENELDRALKTGDR-AKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQE 124

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           G++GL + V+KFDP +G++ +TY+ WWI+ A+   I +    +++     +K     L +
Sbjct: 125 GSLGLERGVEKFDPTKGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEK-----LNK 179

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           +K   + +     +      IA +L +  +++           SL+  +   D   ++  
Sbjct: 180 IKRTQRELAQKLGRSATPAEIALELELEPAQIREYLSMARQPISLD--VRVGDNQDTELS 237

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLS 259
           + L       +  + ++  R++    L   ++ L P++R +   R        ++L  + 
Sbjct: 238 ELLEDSGVSPDTFITQELLRQD----LANLLAELTPQQREVITLRFGLTDGKELSLAKIG 293

Query: 260 SEFEVSRERVRQIEARAFKKVQE 282
               +SRERVRQ+E +A   ++ 
Sbjct: 294 QRMNISRERVRQLEHQALAHLRR 316


>gi|225848935|ref|YP_002729099.1| RNA polymerase sigma-70 factor [Sulfurihydrogenibium azorense
           Az-Fu1]
 gi|225644026|gb|ACN99076.1| RNA polymerase sigma-70 factor [Sulfurihydrogenibium azorense
           Az-Fu1]
          Length = 285

 Score =  199 bits (507), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 79/285 (27%), Positives = 151/285 (52%), Gaps = 12/285 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
            N E G+  YI  I KIP+L  ++E  + ++ +  GD  A  +L+ S+LR V+ IA  Y 
Sbjct: 4   FNYEEGVEYYIRSIYKIPLLTPEQEKEILEKIKL-GDKEAFQKLILSNLRFVINIAKRYA 62

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           GYG+P+ +++S GNIGL++A K+FDP +G +  +Y++WWIK ++   + +   +++  T 
Sbjct: 63  GYGIPLQDLISAGNIGLIEAAKRFDPSKGVKFISYAIWWIKQSIINTLSQEGDIIRKPT- 121

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA--IAKKLNVSESEVISMNCRLAGDESLN 187
              + LF  +     +L+   +     +++ +  + + L V +  + +         SL+
Sbjct: 122 -KIQSLFQKISNAYFYLKDSLNREPSVDEIHSFLLREGLEVEKDTIENYLFFNQHFISLD 180

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I S D++     D +    +   + +  K   ++    +   +  L+PRE++I   R 
Sbjct: 181 EPILSQDED-IHLSDTI---SNSGTEDIERKLIDEDILKFIDELLDTLSPREKQILIHRF 236

Query: 248 L--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE-SIQKQVE 289
               E P TL+ + +   +SRERVRQIE R  KK+++ + ++++E
Sbjct: 237 GLYGEEPKTLKEVGNIVGISRERVRQIEIRLLKKLRKLATKRKIE 281


>gi|294507979|ref|YP_003572037.1| RNA polymerase sigma-70 factor [Salinibacter ruber M8]
 gi|294344307|emb|CBH25085.1| RNA polymerase sigma-70 factor [Salinibacter ruber M8]
          Length = 279

 Score =  199 bits (506), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 86/274 (31%), Positives = 149/274 (54%), Gaps = 13/274 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y+ EI KI +LE +EE  LA+R  E GD  A H+L  ++LR VV +A  Y+G GL +
Sbjct: 10  LDQYLQEIGKIDLLEPEEEVELARRI-EDGDEEALHKLCRANLRFVVSVAKKYQGQGLSL 68

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           +++++EGN GL++A K+FD  RGF+  +Y++WWI+ A+ + +     +V++    N+   
Sbjct: 69  ADLINEGNYGLIKAAKRFDETRGFKFISYAVWWIRQAILQALAEQSRVVRLP--LNRIGT 126

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              +R+    LQ   D       +  +A++L +   +V       +   S++A  N  D 
Sbjct: 127 ISKIRKASARLQQDLDRK---PNIEELAEELEIDVQKVREAMKHTSRHLSMDAPFNEEDD 183

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPV 253
           NS      L    D       E+   ++ +  + R++S L+ RE  I        +E+P+
Sbjct: 184 NS-----LLDVLPDEDNDSPDEEMLSESVKIDIERALSALHDREAEITRLYFGIGREHPL 238

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           TLE +   F+++RERVRQI+ +A +K+++   KQ
Sbjct: 239 TLEEIGKRFDLTRERVRQIKEKALRKLRQRHSKQ 272


>gi|33866957|ref|NP_898516.1| type II alternative RNA polymerase sigma factor [Synechococcus sp.
           WH 8102]
 gi|33639558|emb|CAE08942.1| Possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 8102]
          Length = 467

 Score =  199 bits (506), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 73/242 (30%), Positives = 116/242 (47%), Gaps = 13/242 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   ++ ++LRLVV +A  Y+  G+ + ++V EG +GL +AV+KFDP RGFR +TY+ 
Sbjct: 225 RRAKDHMIQANLRLVVAVAKKYQQRGMELLDLVQEGTLGLERAVEKFDPTRGFRFSTYAY 284

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  M   I      +++     +K     L R+K   Q I  N  +   +  +A+ L
Sbjct: 285 WWIRQGMTRAIATQSRTIRLPVHVTEK-----LNRIKRAQQEIATNEGRIASIADLARAL 339

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +SE  V     R+    SL+  +       +Q  D +       EQ L   E   +   
Sbjct: 340 KLSEDTVRQTLARVPRSVSLDTRV--GRDQDTQLGDLIEDGKATPEQTLTHDELHND--- 394

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L  RE  +   R   E+  P TL  +    ++SRERVRQIE RA  K+++  
Sbjct: 395 -LEHLLDELTSREAAVLRRRFGLEDDTPQTLAQIGEALKLSRERVRQIETRALLKLRQPQ 453

Query: 285 QK 286
           ++
Sbjct: 454 RR 455



 Score = 36.3 bits (83), Expect = 5.6,   Method: Composition-based stats.
 Identities = 8/29 (27%), Positives = 16/29 (55%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREH 44
           L  Y+ +I ++ +L  +EE  LA+  +  
Sbjct: 113 LRLYLQDIGRVDLLTNEEEVTLARLVQRR 141


>gi|302344687|ref|YP_003809216.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfarculus baarsii DSM
           2075]
 gi|301641300|gb|ADK86622.1| RNA polymerase, sigma 32 subunit, RpoH [Desulfarculus baarsii DSM
           2075]
          Length = 363

 Score =  199 bits (506), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 66/239 (27%), Positives = 115/239 (48%), Gaps = 13/239 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +A   +V ++LRL V IA  Y   GL  ++++ EGNIGLM+AV ++D   G+R +T++ 
Sbjct: 124 EAAVSEMVEANLRLAVSIAKKYTFRGLSFADLIQEGNIGLMKAVNRYDYRTGYRFSTFAS 183

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   I      ++I     +  L     R+   L         P++V   A+K+
Sbjct: 184 WWIRQTISRAIYDQARTIRIPIHLLE--LRSKYFRVYYGLLKELGREPTPKEV---AEKV 238

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++E +V  +        SL   +    ++  +  D++          ++ + E      
Sbjct: 239 GITEDKVKEIINLTLDSTSLETPVG---EDGDELGDFIENKDAEDPFSMVGETE---MHG 292

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            L  ++  L+ RERRI E R     E+  TLE +   F +SRERVRQIE +A ++++  
Sbjct: 293 HLEAALDSLDGRERRILEMRFGLGDEDEHTLEEVGQVFGLSRERVRQIEKKALQRLRHP 351


>gi|254526733|ref|ZP_05138785.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9202]
 gi|221538157|gb|EEE40610.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9202]
          Length = 333

 Score =  199 bits (506), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 66/308 (21%), Positives = 128/308 (41%), Gaps = 52/308 (16%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYRE--------------HGDL-------------- 47
           +  Y+ +I ++P+L  ++E  L ++ +E               GD               
Sbjct: 26  VRSYLRDIGRVPLLSHEQEITLGRQVQEYMEVERAELELIELAGDKPSIDELSTKLNLST 85

Query: 48  -----------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                       A  R+V ++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP 
Sbjct: 86  SIIKKRLRAGQRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPA 145

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RG++ +TY+ WWI+  +   I      +++     +      L +LK   + ++    + 
Sbjct: 146 RGYKFSTYAYWWIRQGITRAIAEKSRAIRLPIHITE-----MLNKLKKGQRELSQEMSRT 200

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
             V  +AK + + E +V  + C+     SL   +   +         L+    G E +  
Sbjct: 201 PTVSELAKYVELPEDDVKDLMCKAGQPVSLETKVGDGEDT------VLLDLLAGGEDLPD 254

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEA 274
           E+ E    R  L   +  L   + R+   R     + P++L  +     +SR+RVR +E 
Sbjct: 255 EQIEMDCMRGDLHSLLHQLPDLQCRVLRMRYGMDGDEPMSLTGIGRVLGISRDRVRNLER 314

Query: 275 RAFKKVQE 282
              + ++ 
Sbjct: 315 DGLRGLRR 322


>gi|170731361|ref|YP_001763308.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia cenocepacia
           MC0-3]
 gi|169814603|gb|ACA89186.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia cenocepacia
           MC0-3]
          Length = 857

 Score =  199 bits (506), Expect = 4e-49,   Method: Composition-based stats.
 Identities = 61/239 (25%), Positives = 115/239 (48%), Gaps = 14/239 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+  ++L+LV  +A  YR  G P+ ++  EGNIGL++AV++FD  RGF+ +TY+ WW
Sbjct: 515 ARERMAVANLKLVFHLAKKYRYSGEPLDDLAQEGNIGLLKAVERFDWRRGFKFSTYATWW 574

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +  ++      V++    ++K      +RL    QA+     +  ++  IA +LN+
Sbjct: 575 IRQQIGRHLADKCRTVRVPVHVHEKA-----QRLSRETQALESETGRAPELHEIAARLNM 629

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +  +V  +         ++ L            D++  D        ++   +      +
Sbjct: 630 AVQKVAELQRLAPEPLPIHELPIDELIAVEVRSDFVSPD-------PMDIVSKSELLETI 682

Query: 229 TRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            + +S L P+E +    R     E  +TLE +  ++ V+RERVRQIE  A + ++   +
Sbjct: 683 DKLLSTLKPKEEQTLRLRFGIGVEEALTLEEIGCQYGVTRERVRQIEVAALRNLKHPRR 741


>gi|302552062|ref|ZP_07304404.1| RNA polymerase sigma factor RpoS [Streptomyces viridochromogenes
           DSM 40736]
 gi|302469680|gb|EFL32773.1| RNA polymerase sigma factor RpoS [Streptomyces viridochromogenes
           DSM 40736]
          Length = 332

 Score =  199 bits (506), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 74/300 (24%), Positives = 127/300 (42%), Gaps = 39/300 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVL---------------------AKRYREHGD------LS 48
           +  Y+ EI + P+L+   E  L                     A+  RE  +        
Sbjct: 36  VGMYLDEIARTPLLDAAREVELSQVIEAGVFAKQVLDGFEETKAEATREELESLVADAER 95

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A    + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ WW
Sbjct: 96  AKDIFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTYATWW 155

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      +++        L   L R++   +     + +  +   IA +L  
Sbjct: 156 IRQAITRSIADQSRTIRLPVH-----LVEELGRIRRVQREFNREHGRDPEPTEIAAELGS 210

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +   V  +        SLN  +   D+  +Q+ D L    D       +      R   L
Sbjct: 211 TPERVTDVLDWARDPVSLNMSV--DDEGETQFGDLL---EDTSAVSPEQSVLTLLRSEEL 265

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +  L+ R   I + R   E+    TL  +  E  ++RER+RQIE  A  ++++  + 
Sbjct: 266 DDLIGRLDQRTASIIKMRYGIEDGRERTLTEVGKEHGLTRERIRQIEKHALLELKKLARS 325


>gi|88809466|ref|ZP_01124974.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 7805]
 gi|88786685|gb|EAR17844.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 7805]
          Length = 376

 Score =  199 bits (506), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 82/254 (32%), Positives = 125/254 (49%), Gaps = 15/254 (5%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             L +R RE     A  R++ ++LRLVV +A  Y+  G+ + ++V EG +GL +AV+KFD
Sbjct: 124 KELQQRLREG--RRARDRMIQANLRLVVAVAKKYQQRGMELLDLVQEGTLGLERAVEKFD 181

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P RGFR +TY+ WWI+  +   I      +++     +K     L R+K   Q I     
Sbjct: 182 PTRGFRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEK-----LNRIKRVQQEIASEKG 236

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +   V  +AK+L VSE  V     R+    SL   +       +Q  D L   H   EQ 
Sbjct: 237 RLASVSDLAKELGVSEETVRQTLARVPRSVSLETRV--GKDQDTQLGDLLEDGHATPEQT 294

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
           L     R +  + L   +  L+PRE  +  +R   E+  P TL  +     +SRERVRQI
Sbjct: 295 LT----RDSLHDDLEHLLEELSPREAEVIRSRFGLEDDTPRTLAEIGEAMALSRERVRQI 350

Query: 273 EARAFKKVQESIQK 286
           E RA  K+++  ++
Sbjct: 351 ETRALLKLRQPQRR 364



 Score = 37.5 bits (86), Expect = 2.2,   Method: Composition-based stats.
 Identities = 13/55 (23%), Positives = 26/55 (47%), Gaps = 6/55 (10%)

Query: 11 NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           G   L  Y+ +I ++ +L  +EE  L+++ ++        RL+     L  +IA
Sbjct: 17 GGNDLLRLYLQDIGRVDLLTSEEEVTLSRQVQQ------RERLLVQERDLSTRIA 65


>gi|291445451|ref|ZP_06584841.1| sigma factor [Streptomyces roseosporus NRRL 15998]
 gi|291348398|gb|EFE75302.1| sigma factor [Streptomyces roseosporus NRRL 15998]
          Length = 333

 Score =  199 bits (506), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 77/315 (24%), Positives = 134/315 (42%), Gaps = 44/315 (13%)

Query: 2   NRKNMSIIVNGEIG----LSRYIHEIRKIPMLEKQEEYVLAKRY---------------R 42
           +R +    V GEI     +  Y+ EI + P+L+  +E  L++                  
Sbjct: 18  DRASSVRAVGGEIADRDLVGMYLDEIARTPLLDAAKEVDLSQTIEAGVYAQQILDGEVES 77

Query: 43  EHGD-------------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           + GD               A    + S+LRLVV +A  Y   GLP+ +++ EGN GL++A
Sbjct: 78  DAGDAKREELEALVADGERAKDIFIRSNLRLVVAVARRYPRAGLPLLDLIQEGNAGLVRA 137

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V+KFD  +GF+ +TY+ WWI+ A+   I      +++        L   L R++   +  
Sbjct: 138 VEKFDYAKGFKFSTYATWWIRQAITRSIADQSRTIRLPVH-----LVEELGRIRRVQREF 192

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
              + +  +   IA +L+ +   V ++        SLN  +   D   +Q+ D L    D
Sbjct: 193 NREHGRDPEHAEIAAELDSNAERVGNVLDWARDPVSLNMSV--DDDGDTQFGDLL---ED 247

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRE 267
                  +      R   L   +  L+ R   I + R   E+    TL  +  +  ++RE
Sbjct: 248 TSAVSPEQSVMTLLRSEELEDLIGKLDNRTASIIKMRYGIEDGRERTLTEVGKQHGLTRE 307

Query: 268 RVRQIEARAFKKVQE 282
           R+RQIE  A  +++ 
Sbjct: 308 RIRQIEKHALLELKR 322


>gi|281423630|ref|ZP_06254543.1| RNA polymerase sigma-70 factor [Prevotella oris F0302]
 gi|299141293|ref|ZP_07034430.1| RNA polymerase sigma-70 factor [Prevotella oris C735]
 gi|281402182|gb|EFB33013.1| RNA polymerase sigma-70 factor [Prevotella oris F0302]
 gi|298577253|gb|EFI49122.1| RNA polymerase sigma-70 factor [Prevotella oris C735]
          Length = 290

 Score =  199 bits (506), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 69/280 (24%), Positives = 132/280 (47%), Gaps = 12/280 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKI 64
           SI       L +Y+ EI + P++   EE  LA++ ++ G     A  +LVT++LR VV +
Sbjct: 9   SITNRSSEALDKYLVEIGRAPLISIDEEIELAQKIKKGGRDGERAKEKLVTANLRFVVSV 68

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y+  GL +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V
Sbjct: 69  AKQYQHQGLSLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIV 128

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           ++           +L ++   +        +   +  ++    + E ++       +   
Sbjct: 129 RLPLNQ-----VGSLNKINREINKFEQEFQRKPSLAELSSATKIEEEKIDQSLMADSHHV 183

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           S++A     + NS    D +    D +    ++ E        + R   VL  RE  I  
Sbjct: 184 SIDAPFQEGEDNS--MVDVMAGGEDSRTDKQVDHESMALELESVLR--KVLKDREITIIR 239

Query: 245 ARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
                  +   LE +  +  ++RERVRQI  ++  K+++S
Sbjct: 240 ECFGIGCHEKGLEEIGDQLGLTRERVRQIREKSIAKLRDS 279


>gi|260436019|ref|ZP_05789989.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 8109]
 gi|260413893|gb|EEX07189.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 8109]
          Length = 335

 Score =  199 bits (506), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 68/315 (21%), Positives = 134/315 (42%), Gaps = 53/315 (16%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--------------------------- 48
           +  Y+ +I ++P+L  ++E  L ++ +E  DL                            
Sbjct: 28  VRSYLRDIGRVPLLTHEQEITLGRQVQELMDLESLEAELESKAGEKPSRDVLAKASGLSS 87

Query: 49  ------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                       A  R+V ++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP 
Sbjct: 88  MQLKRKLQHGRRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPT 147

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RG++ +TY+ WWI+  +   I      +++     +      L +LK   + ++    + 
Sbjct: 148 RGYKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITE-----MLNKLKKGQRELSQELGRT 202

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
             V  +A+ + + E +V  + CR     SL   +   D + ++  + L  D D     + 
Sbjct: 203 PTVTELAEFVELPEDDVKDLMCRARQPVSLEMKV--GDGDDTELLELLSGDGDLPSDQVE 260

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEA 274
           E   + +    L   +  L   + ++   R     E+P++L  +     +SR+RVR +E 
Sbjct: 261 EDCLKGD----LRSLLGQLPHLQEQVLRMRYGMDGEDPMSLTGIGRILGMSRDRVRNLER 316

Query: 275 RAFKKVQESIQKQVE 289
                ++  +  QVE
Sbjct: 317 DGLAGLRR-VSDQVE 330


>gi|119773417|ref|YP_926157.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)-like
           protein [Shewanella amazonensis SB2B]
 gi|119765917|gb|ABL98487.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)-like
           protein [Shewanella amazonensis SB2B]
          Length = 969

 Score =  199 bits (506), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 67/241 (27%), Positives = 128/241 (53%), Gaps = 19/241 (7%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   ++T +LRLV+ +A  Y G GL ++++V EGNIGLM+AV+KFD  +GF+ +TY+ W
Sbjct: 732 AARDEMITFNLRLVLSVANKYLGRGLELADLVQEGNIGLMKAVEKFDHRKGFKFSTYATW 791

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I     +++I    N+      L +L    + +T    +  ++  ++  L+
Sbjct: 792 WIRQAITRAIADQARIIRIPVHVNES-----LNKLISASKVLTHKFGRGPKISELSLILS 846

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + E++V ++   L  +      +  +D N++ + DW             E+    +R   
Sbjct: 847 MPETKVENLKQILVME-----PVAEADHNTNGYVDW-------AAMSPEEEIIDDDRDTN 894

Query: 228 LTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           +   +  L  +E+++ E R        +TLE +  +F+V+RER+RQIEA++ KK+  + +
Sbjct: 895 IKDLLKGLTDKEKKVLELRFGINAATELTLEEVGQQFDVTRERIRQIEAKSLKKLAHTSR 954

Query: 286 K 286
            
Sbjct: 955 S 955


>gi|317503800|ref|ZP_07961812.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella salivae
           DSM 15606]
 gi|315665097|gb|EFV04752.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella salivae
           DSM 15606]
          Length = 290

 Score =  199 bits (506), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 69/280 (24%), Positives = 132/280 (47%), Gaps = 12/280 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKI 64
           SI       L +Y+ EI + P++   EE  LA++ ++ G     A  +LVT++LR VV +
Sbjct: 9   SITNRSSEALDKYLVEIGRAPLISIDEEIELAQKIKKGGRDGERAKEKLVTANLRFVVSV 68

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y+  GL +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V
Sbjct: 69  AKQYQHQGLSLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIV 128

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           ++           +L ++   +        +   +  ++    + E ++       +   
Sbjct: 129 RLPLNQ-----VGSLNKINREINKFEQEYQRKPSLSELSHATKIEEEKIDQSLMADSHHV 183

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           S++A     + NS    D +    D +    ++ E        + R   VL  RE  I  
Sbjct: 184 SIDAPFQEGEDNS--MVDVMAGGDDSRTDKQVDHESMALELESVLR--KVLKEREITIIR 239

Query: 245 ARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
                  +   LE +  +  ++RERVRQI  ++  K+++S
Sbjct: 240 ECFGIGCHEKGLEEIGDQLGLTRERVRQIREKSIAKLRDS 279


>gi|67924587|ref|ZP_00518002.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
 gi|67853561|gb|EAM48905.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
          Length = 328

 Score =  199 bits (506), Expect = 5e-49,   Method: Composition-based stats.
 Identities = 66/323 (20%), Positives = 145/323 (44%), Gaps = 53/323 (16%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------------- 43
           +N K    + + ++ +  Y+HEI ++P+L  ++E +  K+ ++                 
Sbjct: 6   VNTKTKQPMYSADM-VRTYLHEIGRVPLLTHEQEIIYGKQVQKMMNFLEKKEELADKLGK 64

Query: 44  ----------------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
                                      A  +++ ++LRLVV IA  Y+   +   +++ E
Sbjct: 65  EPTVKEWSKELEIEQKALNQALEQGERAKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQE 124

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           G++GL + V+KFDP +G++ +TY+ WWI+ A+   I +    +++     +K     L +
Sbjct: 125 GSLGLERGVEKFDPTKGYKFSTYAYWWIRQAITRAIAQQSRTIRLPIHITEK-----LNK 179

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           +K   + ++    +      IA++L +  S++           SL+  +   D   ++  
Sbjct: 180 IKKTQRELSQTLGRSATPSEIAQELEIEPSQIREFLSIARQPISLD--VRVGDNQDTELS 237

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLS 259
           + L       +  + ++  R++ RN+    M+ L P++R +   R   E+   ++L  + 
Sbjct: 238 ELLEDQGVSPDLYITQELLRQDLRNL----MAELTPQQRTVLTLRFGLEDGKELSLAKIG 293

Query: 260 SEFEVSRERVRQIEARAFKKVQE 282
               +SRERVRQ+E +A  +++ 
Sbjct: 294 KRMNISRERVRQLEHQALAQLRR 316


>gi|290959686|ref|YP_003490868.1| sigma factor HrdD [Streptomyces scabiei 87.22]
 gi|260649212|emb|CBG72326.1| sigma factor HrdD [Streptomyces scabiei 87.22]
          Length = 332

 Score =  199 bits (506), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 72/299 (24%), Positives = 128/299 (42%), Gaps = 39/299 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVL---------AKRYREHGDLS------------------ 48
           +  Y+ EI + P+L+  +E  L         A++  +  + +                  
Sbjct: 36  VGMYLDEIARTPLLDAAKEVELSQVIEAGVFAQQILDGEEEAQADATREELEALVADSER 95

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A    + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ WW
Sbjct: 96  AKDIFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTYATWW 155

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      +++        L   L R++   +     + +  +   IA +L  
Sbjct: 156 IRQAITRSIADQSRTIRLPVH-----LVEELGRIRRVQREFNREHGRDPEPAEIAAELGS 210

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +   V  +        SLN  +   D   +Q+ D L    D       +      R   L
Sbjct: 211 NADRVTDVLDWARDPVSLNMSV--DDDGDTQFGDLL---EDTSAVSPEQSVLTLLRSEEL 265

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              +  L+ R   I + R   E+    TL  +  E  ++RER+RQIE  A  ++++  +
Sbjct: 266 DDLIGRLDQRTASIIKMRYGIEDGRERTLTEVGKEHGLTRERIRQIEKHALLELKKLAR 324


>gi|304383342|ref|ZP_07365808.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella marshii
           DSM 16973]
 gi|304335510|gb|EFM01774.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella marshii
           DSM 16973]
          Length = 287

 Score =  199 bits (506), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 82/287 (28%), Positives = 152/287 (52%), Gaps = 12/287 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       L +Y+ EI    +L  +EE  LA+R R  GD  A  +L  ++LR VV
Sbjct: 5   KITKSITNRETASLEKYLQEIGHEELLTVEEEVELAQRIR-RGDRQALEKLTKANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ + I     
Sbjct: 64  SVAKQYQNQGLSLPDLINEGNLGLIKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++           ++ R+   L      N +   +  IA K+N+S+ +V  +    + 
Sbjct: 124 IVRLPLNQ-----IGSVNRINKMLNRFEQENERRPSMEEIADKVNLSQEKVADVLKVNSR 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++A     D+ +S        D    ++ L+    R++ R  + R++ VLN RER I
Sbjct: 179 QVSVDAPFTEGDE-TSLLDVLCNNDSPMADRELV----RESLREEINRTLQVLNERERNI 233

Query: 243 FEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            EA         TLE + ++F ++RERVRQI+ +A ++++++ + ++
Sbjct: 234 VEAFFGINQGEKTLEEIGNKFGLTRERVRQIKEKAIRRLRQNTKSRL 280


>gi|144227447|gb|AAZ44150.2| DNA-directed RNA polymerase sigma factor [Mycoplasma hyopneumoniae
           J]
          Length = 676

 Score =  199 bits (506), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 71/293 (24%), Positives = 133/293 (45%), Gaps = 20/293 (6%)

Query: 6   MSIIVNGEIGLSRYIHEIRKI-PMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVV 62
           ++ + +    +  Y+  I K   +L  +EE  LAK+ +  G     A   L+  +LRLVV
Sbjct: 385 LNKLTDTSDMIKWYMRWIGKYGKLLTAEEERELAKKMKIKGRIGKKARDTLIKRNLRLVV 444

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
             A  Y+  GL   +++SEGN+G+++AV K+D  RGF+ +TY+ WWI+ A+   +     
Sbjct: 445 NSAKRYKNRGLGFIDLISEGNLGIIKAVAKYDYTRGFKFSTYATWWIRQAITRAVADQAR 504

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           L++I     +      + +++  LQ     N   E++         S  ++  +      
Sbjct: 505 LIRIPVHMVE--TINKINKVERELQQEKGLNPTAEEISERLDG-EFSPDKIRYIKKINID 561

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS-VLNPRERR 241
             SL+  I    +  S + D++    D      ++   R+ +  +L   +   L+  ER 
Sbjct: 562 PISLDKAI--GKEEDSSFSDFI---KDENMISPVDYAIREEKAKVLLEMIDSTLDYDERD 616

Query: 242 IFEARRLQE--------NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             + R               + E L++   V++ERVRQIEA+  KK++   ++
Sbjct: 617 FIKRRYGVGTNDEGIPYQAHSFEELAAMRRVTKERVRQIEAKILKKLRTPHRR 669


>gi|325109992|ref|YP_004271060.1| RNA polymerase, sigma 38 subunit, RpoS [Planctomyces brasiliensis
           DSM 5305]
 gi|324970260|gb|ADY61038.1| RNA polymerase, sigma 38 subunit, RpoS [Planctomyces brasiliensis
           DSM 5305]
          Length = 286

 Score =  198 bits (505), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 78/271 (28%), Positives = 130/271 (47%), Gaps = 13/271 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ EI +  +L   EE  LA R    GDL A  R+V ++LRLVV IA GY   GLP+
Sbjct: 24  LETYLREINETSLLSADEEKELANRIA-MGDLEARDRMVRANLRLVVNIARGYASKGLPL 82

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GL++AV+ FDP    R +TY+ +WIK +++  ++     ++I   A    L
Sbjct: 83  QDLIEEGNLGLLRAVEGFDPNMNTRFSTYASYWIKQSIKRSLVNCAKTIRIP--AYMVEL 140

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
               R+    LQ   D   +      +A +L + + ++  +   +      N+   S D+
Sbjct: 141 LSKWRKATARLQ---DELNRTPTAEEVAAELGLPKKKLNIVKKAIQL---YNSTPQSDDE 194

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPV 253
            S      +V D   +     E+    +  N + R +  ++ RE  I   R   +   P 
Sbjct: 195 ESGWSLGEMVADE--RAIGPEEELVNNDNLNHVYRMLDDMDDRESTILRMRFGLDHEEPK 252

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           TL+ +     ++RERVRQIE  A  ++   +
Sbjct: 253 TLKEIGESLGLTRERVRQIEQEALNRLNRGL 283


>gi|260436706|ref|ZP_05790676.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 8109]
 gi|260414580|gb|EEX07876.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 8109]
          Length = 377

 Score =  198 bits (505), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 75/249 (30%), Positives = 121/249 (48%), Gaps = 13/249 (5%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           +        A   ++ ++LRLVV +A  Y+  G+ I ++V EG +GL +AV+KFDP RGF
Sbjct: 128 KLALRNGRRAKDHMIQANLRLVVAVAKKYQQRGMEILDLVQEGTLGLERAVEKFDPTRGF 187

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           R +TY+ WWI+  +   I      +++     +K     L R+K   Q I  N  +   +
Sbjct: 188 RFSTYAYWWIRQGITRAIATQSRTIRLPVHVTEK-----LNRIKRVQQEIASNEGRIASI 242

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +A++L +SE  V     R+    SL+  +    +  +Q  D +   H   EQ L   E
Sbjct: 243 ADLARELGISEDTVRQTLARVPRSVSLDTRV--GREQDTQLGDLIEDGHATPEQTLTHDE 300

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
              +    L   +  L  RE  +   R   E+  P TL  +  E ++SRERVRQIE RA 
Sbjct: 301 LHND----LEDLLDELTSREAAVLRRRFGLEDDTPQTLAQIGEELKLSRERVRQIETRAL 356

Query: 278 KKVQESIQK 286
            K+++  ++
Sbjct: 357 LKLRQPQRR 365


>gi|320010254|gb|ADW05104.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 333

 Score =  198 bits (505), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 75/315 (23%), Positives = 131/315 (41%), Gaps = 44/315 (13%)

Query: 2   NRKNMSIIVNGEIG----LSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------- 43
           +R +    V GEI     +  Y+ EI + P+L+  +E  L++                  
Sbjct: 18  DRASSVRAVGGEIADRDLVGMYLDEIARTPLLDAAKEVELSQTIEAGVFAQQILDGVVES 77

Query: 44  --------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
                              A    + S+LRLVV +A  Y   GLP+ +++ EGN GL++A
Sbjct: 78  DAGGAKREELEALVAESERAKDIFIRSNLRLVVAVARRYPRAGLPLLDLIQEGNAGLVRA 137

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V+KFD  +GF+ +TY+ WWI+ A+   I      +++        L   L R++   +  
Sbjct: 138 VEKFDYAKGFKFSTYATWWIRQAITRSIADQSRTIRLPVH-----LVEELGRIRRVQREF 192

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
              + +  +   IA +L+ +   V ++        SLN  +   D   +Q+ D L    D
Sbjct: 193 NREHGRDPEHTEIAAELDTNAERVGNVLDWARDPVSLNMSV--DDDGDTQFGDLL---ED 247

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRE 267
                  +      R   L   +  L+ R   I + R   E+    TL  +  +  ++RE
Sbjct: 248 TSAISPEQSVMTLLRSEELEDLIGKLDNRTASIIKMRYGIEDGRERTLTEVGKQHGLTRE 307

Query: 268 RVRQIEARAFKKVQE 282
           R+RQIE  A  +++ 
Sbjct: 308 RIRQIEKHALLELKR 322


>gi|113954561|ref|YP_729335.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CC9311]
 gi|113881912|gb|ABI46870.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CC9311]
          Length = 335

 Score =  198 bits (505), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 70/316 (22%), Positives = 135/316 (42%), Gaps = 54/316 (17%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSA-------------------------- 49
           +  Y+ +I ++P+L  Q+E  L ++ +E  DL A                          
Sbjct: 27  VRSYLRDIGRVPLLSHQQEITLGRQVQELMDLEALEAELKDQRGGEEVAREEVAKAAGVS 86

Query: 50  --------------AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
                           R+V ++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP
Sbjct: 87  AAQLKRKLQAGRRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDP 146

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            RG++ +TY+ WWI+  +   I      +++     +      L +LK   + ++    +
Sbjct: 147 TRGYKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITE-----MLNKLKKGQRELSQELGR 201

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
              V  +A  + + E EV  + CR     SL   +   D + ++  + L  D     ++ 
Sbjct: 202 TPSVTELASFVELPEEEVKDLMCRARQPVSLEMKV--GDGDDTELLELLAGDG----ELP 255

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIE 273
            ++ E +  +  L   +S L   + ++   R     E P++L  +     +SR+RVR +E
Sbjct: 256 SDQVEGECLKGDLRDLLSQLPELQGKVLRMRYGMDGEEPMSLTGIGRIIGISRDRVRNLE 315

Query: 274 ARAFKKVQESIQKQVE 289
                 ++  +  QVE
Sbjct: 316 RDGLAGLRR-LSPQVE 330


>gi|301320481|gb|ADK69124.1| putative RNA polymerase sigma factor RpoD [Mycoplasma mycoides
           subsp. mycoides SC str. Gladysdale]
          Length = 506

 Score =  198 bits (505), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 71/326 (21%), Positives = 136/326 (41%), Gaps = 65/326 (19%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSA---AHRLVTSHLRLVVKIAMGYRGYG 72
           +  Y ++I + P+L K++E + AK              ++L+ S+L+LV+ +A  +   G
Sbjct: 171 IKTYFYKIGQAPILTKEQEIIYAKMAVSDDPEDVQEGRNKLIESNLKLVISVARKHLNRG 230

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L  ++++ EGNIGLM+AV KF+ E+GF+ +TY+ WWI+ A+   I      ++I     +
Sbjct: 231 LDFADLIEEGNIGLMKAVDKFEYEKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 290

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN--VSESEVISMNCRLAGDESLNALI 190
                 + +L    + +T    +      IA ++   ++  +VI +        SL    
Sbjct: 291 -----TINKLARVERQLTQELGREPNADEIANRVGEGITGDKVIEIKKLSIEPVSLEKPF 345

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM----------------------- 227
              D++ + + D++            EKE  K   +                        
Sbjct: 346 --GDEDDTHFGDFVEDKDMVSPNEYTEKEILKEVMDKVFEDMPPREEKVIRMRYGIVPTR 403

Query: 228 ------------------LTRSMSVLN-----PRER------RIFEARRL-QENPVTLEN 257
                             L +++  L+     P E+      +I        ++  TLE 
Sbjct: 404 LRTLLRLTQECNDTNAKELKQAIEELDIHLDTPIEKVRKFNNQIINNNLAKYDSARTLEE 463

Query: 258 LSSEFEVSRERVRQIEARAFKKVQES 283
           +  E  V+RER+RQIEA+  +K+++ 
Sbjct: 464 VGKELNVTRERIRQIEAKTIRKLKQP 489


>gi|206901861|ref|YP_002251028.1| RNA polymerase sigma factor RpoD [Dictyoglomus thermophilum H-6-12]
 gi|206740964|gb|ACI20022.1| RNA polymerase sigma factor RpoD [Dictyoglomus thermophilum H-6-12]
          Length = 413

 Score =  198 bits (505), Expect = 6e-49,   Method: Composition-based stats.
 Identities = 89/342 (26%), Positives = 152/342 (44%), Gaps = 72/342 (21%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+ EI KIP+L  +EE  LAKR  E GD  A  +L+ ++LRLVV +A  Y G G
Sbjct: 69  DDPVKMYLKEIGKIPLLTPEEEIELAKRV-EQGDEEAKKKLIEANLRLVVSVAKRYIGRG 127

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW----IKAAMQEYILRSWSLVKIGT 128
           L   +++ EGN+GL++AV+KFD  +G++ +TY+ WW    I  A+ +        V +  
Sbjct: 128 LSFLDLIQEGNLGLIKAVEKFDWRKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 187

Query: 129 TANQ-----KRLFFNLRR------------------------------------------ 141
           T N+     + L  NL R                                          
Sbjct: 188 TMNKIHKITRLLTQNLGRKPTEEDIAKFLVIQQKLQEFGVYQESGEKISDDEIIEISKLS 247

Query: 142 --------LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR------LAGDESLN 187
                   ++ HL+A  +     E++   AK+L     E I           + G E L+
Sbjct: 248 LEEIAKKLVEMHLKAKNNKVPTKEEINEKAKELKHVLEEEIRQQTEKVREISMMGQEPLS 307

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             +   +   ++  D++         + ++K  +K+    +   ++ L+ RER I + R 
Sbjct: 308 LEMPVGEDEDNRLADFVENKDLSPADIAVQKSLKKD----IEELLNELSEREREILKLRF 363

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             E+  P TLE +   F V+RER+RQIEA+A ++++   + +
Sbjct: 364 GLEDNQPRTLEEVGKLFNVTRERIRQIEAKALRRLRHPSRSK 405


>gi|239927194|ref|ZP_04684147.1| RNA polymerase principal sigma factor HrdC [Streptomyces ghanaensis
           ATCC 14672]
 gi|291435537|ref|ZP_06574927.1| RNA polymerase principal sigma factor HrdC [Streptomyces ghanaensis
           ATCC 14672]
 gi|291338432|gb|EFE65388.1| RNA polymerase principal sigma factor HrdC [Streptomyces ghanaensis
           ATCC 14672]
          Length = 339

 Score =  198 bits (505), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 73/308 (23%), Positives = 139/308 (45%), Gaps = 42/308 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------------------HG 45
           L +Y+ +I   P+L+ ++E  LA+R                                 H 
Sbjct: 39  LGQYLRQIGATPLLDAEDEVRLAQRIAAGLRAKEEYERAESGGHHLTRERWRELEAAVHD 98

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
             +A  R++ ++LRLVV +A  +   GLP+ +V+ EGN+GL++AV+KFD  +GF+ +TY+
Sbjct: 99  GQAAKDRMIRANLRLVVSMAKRHAHRGLPLLDVIQEGNLGLIRAVEKFDHTKGFKFSTYA 158

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
            WWI+ A++  +      V++     ++     L +++  L    D       V  +A++
Sbjct: 159 TWWIRQAIERGVATHARTVRLPVHVVEQ--LQKLGKVERRLHLSLDRE---PTVEEVARE 213

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
             ++E +V+ +        SL+  +   D   +   D +      Q   + E +      
Sbjct: 214 SGLAEKKVVWLRRVGRQVVSLDTPV--DDTGDTVVGDLIPDTEVLQAPEVAEFQALA--- 268

Query: 226 NMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             L  ++  L PRE  I   R         TL+ ++    ++RERVRQ+E ++  +++E 
Sbjct: 269 EELRGAVDTLAPREALILSLRYGLHDGQTRTLQEVADHVGLTRERVRQLEKQSLAQLRER 328

Query: 284 IQKQVELS 291
            Q +  L+
Sbjct: 329 EQGERLLA 336


>gi|304373196|ref|YP_003856405.1| RNA polymerase sigma factor [Mycoplasma hyorhinis HUB-1]
 gi|304309387|gb|ADM21867.1| RNA polymerase sigma factor [Mycoplasma hyorhinis HUB-1]
          Length = 524

 Score =  198 bits (505), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 68/290 (23%), Positives = 132/290 (45%), Gaps = 20/290 (6%)

Query: 9   IVNGEIGLSRYIHEIRKI-PMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKIA 65
           + +    +  Y+  I K   +L  +EE  LAK+ +  G     A H L+  +LRLV+  A
Sbjct: 236 LSDTNDIIKWYMRWIGKYGKLLTPEEENNLAKQIKNGGRAGKRARHTLINRNLRLVINNA 295

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y+  GL   +++SEGN G+++AV K+D  +G++ +TY+ WWI+ A+   +     +++
Sbjct: 296 KRYKNRGLTFIDLISEGNQGILKAVDKYDYTKGYKFSTYATWWIRQAITRAVADQARIIR 355

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           I     +      + +++  LQ         EQ+  +    + +  +V           S
Sbjct: 356 IPVHMVE--TINKINKIERELQQEYGVTPTDEQIAEVMGG-DFTAEKVRYTKKINIDPIS 412

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS-VLNPRERRIFE 244
           L+  I    +  S + D++    D      I+  ER+ +  +L + +   L+  E+    
Sbjct: 413 LDKAI--GKEEDSSFSDFI---KDESVISPIDYSEREEKTKILKQMIENNLDNDEKVFIM 467

Query: 245 ARRLQENP--------VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R               + + L+ E  V++ER+RQIE++  KK++   +K
Sbjct: 468 KRYGFGTDPNGEQYRIHSFDELAKERGVTKERIRQIESKILKKLRHPQKK 517


>gi|159904297|ref|YP_001551641.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9211]
 gi|159889473|gb|ABX09687.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9211]
          Length = 335

 Score =  198 bits (505), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 70/307 (22%), Positives = 131/307 (42%), Gaps = 52/307 (16%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYRE--------------HG---------------- 45
           +  Y+ +I ++P+L   +E  L +  +E              HG                
Sbjct: 28  IRSYLRDIGRVPLLSNDQEITLGRHVQELMALENLEKDWQSTHGQKPNLDELASAAGLTV 87

Query: 46  ---------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                       A  R+V ++LRLVV IA  Y    + + +++ EG IGL++ V+KFDP 
Sbjct: 88  GALKKKFRLGERAKERMVAANLRLVVSIAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPA 147

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RG++ +TY+ WWI+  +   I      +++     +      L +LK   + ++    + 
Sbjct: 148 RGYKFSTYAYWWIRQGITRAIAEKSRAIRLPIHITE-----MLNKLKKGQRDLSQQLSRT 202

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
             V  +A+ ++VSE EV  +  + +   SL   +   DK+ +   D L  D+D       
Sbjct: 203 PSVAELAEYIDVSEEEVKDLMLKASQPVSLEMKV--GDKDDTVLLDLLSTDNDS----PQ 256

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEA 274
           ++ E    +  L   +  L   + R+   R     E P++L  +     +SR+RVR +E 
Sbjct: 257 QQIELDCMKGDLEILLEKLPELQYRVLRMRYGIDGEEPMSLTGIGRVLGISRDRVRNLER 316

Query: 275 RAFKKVQ 281
              + ++
Sbjct: 317 SGLRGLR 323


>gi|329941264|ref|ZP_08290543.1| RNA polymerase principal sigma factor HrdD [Streptomyces
           griseoaurantiacus M045]
 gi|329299795|gb|EGG43694.1| RNA polymerase principal sigma factor HrdD [Streptomyces
           griseoaurantiacus M045]
          Length = 332

 Score =  198 bits (505), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 74/300 (24%), Positives = 129/300 (43%), Gaps = 39/300 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVL---------AKRYREHGDLS------------------ 48
           +  Y+ EI + P+L+  +E  L         A++  E  + S                  
Sbjct: 36  VGMYLDEIARTPLLDAAKEVELSQVIEAGVFARQILEGEEESRADASREELEALVEAGER 95

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A    + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ WW
Sbjct: 96  AKDVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYRKGFKFSTYATWW 155

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   I      +++        L   L R++   +     + +  +   IA +L  
Sbjct: 156 IRQAITRSIADQSRTIRLPVH-----LVEELGRIRRVQREFNREHGRDPEPAEIAAELGS 210

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +   V  +        SLN  +   D+  +Q+ D L    D       +      R   L
Sbjct: 211 NAERVTDVLDWARDPVSLNMSV--DDEGETQFGDLL---EDTSAVSPEQSVLTLLRSEEL 265

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +  L+ R   I + R   E+    TL  +  E  ++RER+RQIE  A  ++++  + 
Sbjct: 266 DDLIGRLDQRTASIIKMRYGIEDGRERTLTEVGKEHGLTRERIRQIEKHALLELKKLARS 325


>gi|254386169|ref|ZP_05001481.1| RNA polymerase sigma subunit [Streptomyces sp. Mg1]
 gi|194345026|gb|EDX25992.1| RNA polymerase sigma subunit [Streptomyces sp. Mg1]
          Length = 325

 Score =  198 bits (505), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 75/310 (24%), Positives = 132/310 (42%), Gaps = 44/310 (14%)

Query: 10  VNGEIG----LSRYIHEIRKIPMLEKQEEYVLAKRYR--------------EHGDLSAAH 51
           V GEI     +  Y+ EI + P+L+  +E  L++                   G+  A  
Sbjct: 18  VGGEIADRDLVGMYLDEIARTPLLDAAKEVELSQIIEAGVYARQILDGEAEREGEAPARE 77

Query: 52  RL--------------VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
            L              + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +
Sbjct: 78  ELEALAAEGERAKEVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYAK 137

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           GF+ +TY+ WWI+ A+   I      +++        L   L R++   +     + +  
Sbjct: 138 GFKFSTYATWWIRQAITRSIADQSRTIRLPVH-----LVEELGRIRRVQREFNREHGRDP 192

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           +   IA +L+ +   V  +        SLN  +   D   +Q+ D L    D       +
Sbjct: 193 EHTEIAAELDTTAKRVGDVLDWARDPVSLNMSV--DDDGDTQFGDLL---EDTSAISPEQ 247

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
                 R   L   +  L+ R   I + R   ++    TL  +  +  ++RER+RQIE  
Sbjct: 248 SVLSLLRSEELEDLLGKLDQRTASIIKMRYGIDDGRERTLTEVGKQHGLTRERIRQIEKH 307

Query: 276 AFKKVQESIQ 285
           A  ++++  +
Sbjct: 308 ALLELKKMAR 317


>gi|87307232|ref|ZP_01089377.1| transcription initiation factor sigma 70 [Blastopirellula marina
           DSM 3645]
 gi|87289972|gb|EAQ81861.1| transcription initiation factor sigma 70 [Blastopirellula marina
           DSM 3645]
          Length = 507

 Score =  198 bits (505), Expect = 7e-49,   Method: Composition-based stats.
 Identities = 70/257 (27%), Positives = 125/257 (48%), Gaps = 23/257 (8%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           QEEY  AKR    G           +LRLVV IA  YR  GL   +++ EGN GLM+AV 
Sbjct: 251 QEEYDAAKRLLSAG-----------NLRLVVSIAKKYRNRGLSFLDLIQEGNTGLMRAVD 299

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KF+ +RG++ +TY+ WWI+ A+   I      +++        +   + +++   + +  
Sbjct: 300 KFEYQRGYKFSTYATWWIRQAITRAIADQSRTIRVPVH-----MIDTMGKVRAVTRDLLQ 354

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +      +A++  +S  +   +        SL+  +   D + S + ++L    D +
Sbjct: 355 ELGRDPTAEEVAERAGLSIDDARVILKMNRNPLSLDQPV--GDHDDSFFGEFL---EDHR 409

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERV 269
           ++  + +  ++  ++ L   +  LN RER I   R    +    TLE +   F V+RERV
Sbjct: 410 DEDPLYETHQQALKDRLCEVLEALNHREREIIRLRYGLTDGYSYTLEEVGKIFSVTRERV 469

Query: 270 RQIEARAFKKVQESIQK 286
           RQIE++A +K+Q+  + 
Sbjct: 470 RQIESKAVRKLQQPYRS 486


>gi|116071698|ref|ZP_01468966.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. BL107]
 gi|116065321|gb|EAU71079.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. BL107]
          Length = 332

 Score =  198 bits (504), Expect = 8e-49,   Method: Composition-based stats.
 Identities = 65/315 (20%), Positives = 133/315 (42%), Gaps = 53/315 (16%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--------------------------- 48
           +  Y+ +I ++P+L  ++E  L ++ ++  ++                            
Sbjct: 25  VRSYLRDIGRVPLLTHEQEITLGRQVQQLMEIETLEAELESRDGAKPARDQLAKAAELST 84

Query: 49  ------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                       A  R+V ++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP 
Sbjct: 85  VQLKRKLQQGHRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPT 144

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RG++ +TY+ WWI+  +   I      +++     +      L +LK   + ++    + 
Sbjct: 145 RGYKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITE-----MLNKLKKGQRELSQELGRT 199

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
             V  +A+ +++ E EV  + CR     SL   +   D         L+    G  ++  
Sbjct: 200 PTVTELAQFVDLPEDEVKDLMCRARQPVSLEMKVGDGDDTE------LLELLSGDNELPS 253

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEA 274
           ++ E    +  L   +  L   + ++   R     E+P++L  +     +SR+RVR +E 
Sbjct: 254 DQVEEDCLKGDLRSLLGQLPHLQEQVLRMRFGMDGEDPMSLTGIGRILGMSRDRVRNLER 313

Query: 275 RAFKKVQESIQKQVE 289
                ++  +  QVE
Sbjct: 314 DGLAGLRR-VSDQVE 327


>gi|257058077|ref|YP_003135965.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8802]
 gi|256588243|gb|ACU99129.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8802]
          Length = 375

 Score =  198 bits (504), Expect = 8e-49,   Method: Composition-based stats.
 Identities = 76/315 (24%), Positives = 136/315 (43%), Gaps = 53/315 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRY------------------------------ 41
            +  +  +  E+ + P+LE QEE  LA                                 
Sbjct: 60  SDDTVGAFFKEMSRYPLLEAQEEIELAYSVQFLVEAEQKRQQLLEELQHPPTKAQWAQAM 119

Query: 42  ----------REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                     R +   +A  +++ S+LRLVV IA  Y   G+P  +++ EG IGL +A +
Sbjct: 120 GFDSQRQFENRLYRGRTAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAE 179

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFDP +G++ +TY+ WWI+ A+   I      +++     +K     L +LK   + +  
Sbjct: 180 KFDPNKGYKFSTYAYWWIRQAITRTIANDARTIRLPIHIVEK-----LNKLKKAQRILKQ 234

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +      +A++L ++  ++  +        SLN  +   +   ++  D L    D  
Sbjct: 235 KLQRNPNEKELAQELEMTPPQLRQLLQLRRQSLSLNHRVGKGED--TELVDLL---EDQD 289

Query: 212 EQVLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRER 268
            Q+  E+      RN ++  +  VL  RE+ +   R       P TLE +   F +SRER
Sbjct: 290 LQLPEEQMNEGMLRNEISAVLSDVLTEREKDVISLRYGLSTSQPHTLEEVGGMFNLSRER 349

Query: 269 VRQIEARAFKKVQES 283
           VRQI+++A +K++  
Sbjct: 350 VRQIQSKAMRKLRRP 364


>gi|218459714|ref|ZP_03499805.1| RNA polymerase factor sigma-32 [Rhizobium etli Kim 5]
          Length = 198

 Score =  198 bits (504), Expect = 8e-49,   Method: Composition-based stats.
 Identities = 132/184 (71%), Positives = 159/184 (86%)

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +MWWIKA++QEYILRSWSLVK+GTTANQKRLFFNLRRLKG +QAI D +LKPE V  IA 
Sbjct: 1   AMWWIKASIQEYILRSWSLVKMGTTANQKRLFFNLRRLKGRIQAIDDGDLKPEHVSEIAT 60

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           KLNVSE EVISMN RL+GD SLNA I +++ +S QWQDWLV DHD QE VLIE++E + R
Sbjct: 61  KLNVSEEEVISMNRRLSGDASLNAPIKAAEGDSGQWQDWLVDDHDSQEDVLIEQDELETR 120

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R ML+++MSVLN RERRIFEARRL E PVTLE+LS+EF++SRERVRQIE RAF+KVQ+++
Sbjct: 121 RRMLSKAMSVLNERERRIFEARRLAEEPVTLEDLSAEFDISRERVRQIEVRAFEKVQDAV 180

Query: 285 QKQV 288
           +K+ 
Sbjct: 181 RKEA 184


>gi|198283622|ref|YP_002219943.1| RpoD family RNA polymerase sigma-70 subunit [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218667581|ref|YP_002426250.1| RNA polymerase sigm-70 factor family [Acidithiobacillus
           ferrooxidans ATCC 23270]
 gi|198248143|gb|ACH83736.1| RNA polymerase, sigma 70 subunit, RpoD family [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218519794|gb|ACK80380.1| RNA polymerase sigm-70 factor family [Acidithiobacillus
           ferrooxidans ATCC 23270]
          Length = 316

 Score =  198 bits (504), Expect = 9e-49,   Method: Composition-based stats.
 Identities = 76/277 (27%), Positives = 136/277 (49%), Gaps = 14/277 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG-YG 72
             +  Y+ EI   P+L  +EE  L    ++ GD++A +RLV  +LRLVV+IA  Y+  + 
Sbjct: 51  DAIKLYLQEIGHNPLLTAEEEVSLGLSAQQ-GDITARNRLVECNLRLVVRIARRYQRQHT 109

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP+ +++ EGN+GL++A + FDP RGFR +TY+ WWI+  +   I++   +V++ T    
Sbjct: 110 LPLLDLIEEGNLGLIRAAELFDPTRGFRFSTYATWWIRQNIDRGIMQQSRVVRLPTHI-- 167

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
            +    + R    +      + + E V  +  K      + +  + R+    SL+A    
Sbjct: 168 IKNLSAVLRSSRQIAQTMQGDPRVEDVAQVMGKSVAYVEDCLQQDRRV---VSLDAPSRW 224

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE-- 250
             + S      LV   D  +  L    E ++ +  + R++  L+ R R I   R   +  
Sbjct: 225 --EGSPSLAQTLV---DADQADLGASLEEQDLQRQIHRALLGLDVRHRTILIRRFGIDGQ 279

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +  +L  +  E  VS ERVRQ++  A   +++  + Q
Sbjct: 280 DGASLSAIGKELGVSHERVRQLQEEALDLLRQHTELQ 316


>gi|78183723|ref|YP_376157.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CC9902]
 gi|78168017|gb|ABB25114.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. CC9902]
          Length = 332

 Score =  198 bits (504), Expect = 9e-49,   Method: Composition-based stats.
 Identities = 65/315 (20%), Positives = 133/315 (42%), Gaps = 53/315 (16%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--------------------------- 48
           +  Y+ +I ++P+L  ++E  L ++ ++  ++                            
Sbjct: 25  VRSYLRDIGRVPLLTHEQEITLGRQVQQLMEIETLEAELESRDGAKPARDQLAKAAELST 84

Query: 49  ------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                       A  R+V ++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP 
Sbjct: 85  VQLKRKLQQGHRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPT 144

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RG++ +TY+ WWI+  +   I      +++     +      L +LK   + ++    + 
Sbjct: 145 RGYKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITE-----MLNKLKKGQRELSQELGRT 199

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
             V  +A+ +++ E EV  + CR     SL   +   D         L+    G  ++  
Sbjct: 200 PTVTELAQFVDLPEDEVKDLMCRARQPVSLEMKVGDGDDTE------LLELLSGDNELPS 253

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEA 274
           ++ E    +  L   +  L   + ++   R     E+P++L  +     +SR+RVR +E 
Sbjct: 254 DQVEEDCLKGDLRSLLGQLPHLQEQVLRMRFGMDGEDPMSLTGIGRILGMSRDRVRNLER 313

Query: 275 RAFKKVQESIQKQVE 289
                ++  +  QVE
Sbjct: 314 DGLAGLRR-VSDQVE 327


>gi|282865528|ref|ZP_06274579.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces sp.
           ACTE]
 gi|282559572|gb|EFB65123.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Streptomyces sp.
           ACTE]
          Length = 333

 Score =  198 bits (504), Expect = 9e-49,   Method: Composition-based stats.
 Identities = 72/297 (24%), Positives = 125/297 (42%), Gaps = 40/297 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRY---------------REHGD-------------L 47
           +  Y+ EI + P+L+  +E  L++                  E G               
Sbjct: 36  VGMYLDEIARTPLLDAAKEVDLSQTIEAGVYAQQILDGEVESEAGGAKREELEALVAEGE 95

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A    + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ W
Sbjct: 96  RAKDIFIRSNLRLVVAVARRYPRAGLPLLDLIQEGNAGLVRAVEKFDYAKGFKFSTYATW 155

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++        L   L R++   +     + +  +   IA +L 
Sbjct: 156 WIRQAITRSIADQSRTIRLPVH-----LVEELGRIRRVQREFNREHGRDPEHAEIAAELG 210

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
            +   V ++        SLN  +   D   +Q+ D L    D       +      R   
Sbjct: 211 SNTERVGNVLDWARDPVSLNMSV--DDDGDTQFGDLL---EDTSAVSPEQSVMTLLRSEE 265

Query: 228 LTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           L   +  L+ R   I   R   E+    TL  +  +  ++RER+RQIE  A  ++++
Sbjct: 266 LEDLIGKLDNRTASIIRMRYGIEDGRERTLTEVGKQHGLTRERIRQIEKHALLELKK 322


>gi|1519644|gb|AAB07555.1| SigA [Chlorobaculum tepidum]
          Length = 299

 Score =  198 bits (503), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 75/299 (25%), Positives = 144/299 (48%), Gaps = 24/299 (8%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD-----------LSAAH 51
           + +  I     + L RY+ EI K  +L  +      + ++E  D             A  
Sbjct: 5   KISKQITNRESLSLDRYLQEIGKYDLLTARRRGEAHEGHKEGYDMPVDTVEYKRAKRALD 64

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +L+  +LR VV +A  Y+  GL + ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ 
Sbjct: 65  KLIKGNLRFVVSVAKQYQNQGLTLGDLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQ 124

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           ++ + +     +V++    N+      + +    L+   + +        +A  L++   
Sbjct: 125 SILQALAEQSRIVRLP--LNRVGTLNKISKAYSQLEQEYERD---PNTKELADLLDMDSQ 179

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           +V           S++A     D N  +  D L  D    +  L     R +    + RS
Sbjct: 180 DVADTLKIAGRHVSVDAPFAQGDDN--RLLDVLQNDGHMPDYTL----NRDSLSLEVERS 233

Query: 232 MSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +SVL PRE  +  +      +NP+TLE +  +F+++RERVRQI+ +A +++++S   +V
Sbjct: 234 LSVLAPREADVIRSYFGIGMDNPLTLEEIGEKFKLTRERVRQIKEKAIRRLRQSAYNKV 292


>gi|33862185|ref|NP_893746.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus subsp. pastoris str. CCMP1986]
 gi|33634403|emb|CAE20088.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus subsp. pastoris str. CCMP1986]
          Length = 333

 Score =  198 bits (503), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 66/322 (20%), Positives = 133/322 (41%), Gaps = 53/322 (16%)

Query: 7   SIIVNGEIGLSR-YIHEIRKIPMLEKQEEYVLAKRYRE---------------------- 43
           S+  + ++ L R Y+ +I ++P+L  ++E  L ++ +E                      
Sbjct: 16  SLKSSNDVDLVRSYLRDIGRVPLLSHEQEITLGRQVQEYMQVERAEIEIMELTDNKPSPE 75

Query: 44  -----------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
                                 A  R+V ++LRLVV +A  Y    + + +++ EG IGL
Sbjct: 76  ELAEKLNLSTSQIKKRLRAGQRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGL 135

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++ V+KFDP RG++ +TY+ WWI+  +   I      +++     +      L +LK   
Sbjct: 136 VRGVEKFDPARGYKFSTYAYWWIRQGITRAIAEKSRAIRLPIHITE-----MLNKLKKGQ 190

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           + ++    +   +  +AK + + E +V  + C+     SL   +   +         L+ 
Sbjct: 191 RELSQEMSRTPTISELAKYVELPEDDVKDLMCKAGQPVSLETKVGDGEDT------VLLD 244

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
              G E +  E+ E    R  L   +  L   + R+   R     + P++L  +     +
Sbjct: 245 LLAGGEDLPDEQIEMDCMRGDLHSLLHQLPDLQCRVLRMRYGMDGDEPMSLTGIGRVLGI 304

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           SR+RVR +E    + ++   + 
Sbjct: 305 SRDRVRNLERDGLRGLRRLSES 326


>gi|86607249|ref|YP_476012.1| RNA polymerase sigma factor, group 1 [Synechococcus sp. JA-3-3Ab]
 gi|86555791|gb|ABD00749.1| RNA polymerase sigma factor, group 1 [Synechococcus sp. JA-3-3Ab]
          Length = 361

 Score =  198 bits (503), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 70/310 (22%), Positives = 136/310 (43%), Gaps = 51/310 (16%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------------------------- 43
           E  +  Y++ I ++P ++  EE  L+++ ++                             
Sbjct: 49  EDAVDHYLNTIGRVPRIDHAEEIELSRKIQQKLLIDQARREWRQQWGQDPSDEELAAALQ 108

Query: 44  ----------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
                          A  +L+ ++LRLVV +A  Y   G+P  +++ EGN+GL++A +KF
Sbjct: 109 IPVSTLRSRIRQGEQAQRKLINANLRLVVSVAKKYLNRGVPFLDLIQEGNMGLIRATEKF 168

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           + ERGFR +TY+ WWI+  +   I      +++        +   +R LK   + +    
Sbjct: 169 NAERGFRFSTYAHWWIRQGITRCIANQARTIRLPVH-----MVDKVRLLKRTNRELMKAR 223

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            +      +A+ L +   ++  +    A   SL+  +    +  S+  D L    D +++
Sbjct: 224 GRRPTEAELAEALGIKVKKLRMIQQAAALPLSLDVPV--GQEGESRLGDLLP---DERQE 278

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQ 271
              E+   ++ R  +  +M  L P ER++ E R   +     TL  +   F ++RER+RQ
Sbjct: 279 QPFEEILVQSLRQDVRSAMQALKPIERQVLELRYGLDGQRARTLREVGDHFNLTRERIRQ 338

Query: 272 IEARAFKKVQ 281
           IE  A +K++
Sbjct: 339 IERDALRKLR 348


>gi|78214100|ref|YP_382879.1| type II alternative RNA polymerase sigma factor [Synechococcus sp.
           CC9605]
 gi|78198559|gb|ABB36324.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. CC9605]
          Length = 377

 Score =  198 bits (503), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 75/249 (30%), Positives = 121/249 (48%), Gaps = 13/249 (5%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           +        A   ++ ++LRLVV +A  Y+  G+ I ++V EG +GL +AV+KFDP RGF
Sbjct: 128 KLALRNGRRAKDHMIQANLRLVVAVAKKYQQRGMEILDLVQEGTLGLERAVEKFDPTRGF 187

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           R +TY+ WWI+  +   I      +++     +K     L R+K   Q I  N  +   +
Sbjct: 188 RFSTYAYWWIRQGITRAIATQSRTIRLPVHVTEK-----LNRIKRVQQEIASNEGRIASI 242

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +A++L +SE  V     R+    SL+  +    +  +Q  D +   H   EQ L   E
Sbjct: 243 ADLARELGISEDTVRQTLARVPRSVSLDTRV--GREQDTQLGDLIEDGHATPEQTLTHDE 300

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
              +    L   +  L  RE  +   R   E+  P TL  +  E ++SRERVRQIE RA 
Sbjct: 301 LHND----LEHLLDELTSREAAVLRRRFGLEDDTPQTLAQIGEELKLSRERVRQIETRAL 356

Query: 278 KKVQESIQK 286
            K+++  ++
Sbjct: 357 LKLRQPQRR 365


>gi|123967051|ref|YP_001012132.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9515]
 gi|123201417|gb|ABM73025.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9515]
          Length = 333

 Score =  198 bits (503), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 66/321 (20%), Positives = 133/321 (41%), Gaps = 53/321 (16%)

Query: 7   SIIVNGEIGLSR-YIHEIRKIPMLEKQEEYVLAKRYRE---------------------- 43
           S+  + ++ L R Y+ +I ++P+L  ++E  L ++ +E                      
Sbjct: 16  SLKSSNDVDLVRSYLRDIGRVPLLSHEQEITLGRQVQEYMQVERAELEIIELTDNKPSVE 75

Query: 44  -----------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
                                 A  R+V ++LRLVV +A  Y    + + +++ EG IGL
Sbjct: 76  ELAAKLNLSSSQIKKRLRAGQRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGL 135

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++ V+KFDP RG++ +TY+ WWI+  +   I      +++     +      L +LK   
Sbjct: 136 VRGVEKFDPARGYKFSTYAYWWIRQGITRAIAEKSRAIRLPIHITE-----MLNKLKKGQ 190

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           + ++    +   +  +AK + + E +V  + C+     SL   +   +         L+ 
Sbjct: 191 RELSQEMSRTPTISELAKYVELPEDDVKDLMCKAGQPVSLETKVGDGEDT------VLLD 244

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
              G E +  E+ E    R  L   +  L   + R+   R     + P++L  +     +
Sbjct: 245 LLAGGEDLPDEQIEMDCMRGDLHSLLHQLPDLQCRVLRMRYGMDGDEPMSLTGIGRVLGI 304

Query: 265 SRERVRQIEARAFKKVQESIQ 285
           SR+RVR +E    + ++   +
Sbjct: 305 SRDRVRNLERDGLRGLRRLSE 325


>gi|239942002|ref|ZP_04693939.1| RNA polymerase principal sigma factor hrdD [Streptomyces
           roseosporus NRRL 15998]
 gi|239988467|ref|ZP_04709131.1| RNA polymerase principal sigma factor hrdD [Streptomyces
           roseosporus NRRL 11379]
          Length = 308

 Score =  198 bits (503), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 72/297 (24%), Positives = 127/297 (42%), Gaps = 40/297 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRY---------------REHGD-------------L 47
           +  Y+ EI + P+L+  +E  L++                  + GD              
Sbjct: 11  VGMYLDEIARTPLLDAAKEVDLSQTIEAGVYAQQILDGEVESDAGDAKREELEALVADGE 70

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A    + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ W
Sbjct: 71  RAKDIFIRSNLRLVVAVARRYPRAGLPLLDLIQEGNAGLVRAVEKFDYAKGFKFSTYATW 130

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++        L   L R++   +     + +  +   IA +L+
Sbjct: 131 WIRQAITRSIADQSRTIRLPVH-----LVEELGRIRRVQREFNREHGRDPEHAEIAAELD 185

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
            +   V ++        SLN  +   D   +Q+ D L    D       +      R   
Sbjct: 186 SNAERVGNVLDWARDPVSLNMSV--DDDGDTQFGDLL---EDTSAVSPEQSVMTLLRSEE 240

Query: 228 LTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           L   +  L+ R   I + R   E+    TL  +  +  ++RER+RQIE  A  +++ 
Sbjct: 241 LEDLIGKLDNRTASIIKMRYGIEDGRERTLTEVGKQHGLTRERIRQIEKHALLELKR 297


>gi|74316856|ref|YP_314596.1| RNA polymerase sigma factor RpoS [Thiobacillus denitrificans ATCC
           25259]
 gi|74056351|gb|AAZ96791.1| RNA polymerase sigma-70 factor [Thiobacillus denitrificans ATCC
           25259]
          Length = 316

 Score =  198 bits (503), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 78/259 (30%), Positives = 134/259 (51%), Gaps = 13/259 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI + P+L   EE  LA+R    GD  A   ++  +LRLVV IA  Y   GL + ++
Sbjct: 49  YLNEIGQAPLLTAAEEVALARRTVL-GDFEARQTMIERNLRLVVNIAKHYANRGLTLLDL 107

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GL+ A++KFDPERGFR +TY+ WWI+  ++  I+     +++       +    
Sbjct: 108 VEEGNLGLIHALEKFDPERGFRFSTYATWWIRQNIERAIMNQSRTIRLPVHI--IKELNI 165

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
             R + HL+     +   + + A+          ++ +N R+A   SL+A ++     + 
Sbjct: 166 YLRAQRHLETHGVTDATSDDIAALTGHPVADVRRIMQLNERIA---SLDAPLDV--DPTL 220

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLE 256
              + +  D+      +++ EE +N    +   ++ LN ++R + E R         TLE
Sbjct: 221 SLGEAIADDNAHLPDEMLQLEEIENH---VQEWLTQLNDKQRWVIERRFGLNGCEACTLE 277

Query: 257 NLSSEFEVSRERVRQIEAR 275
           +L+ E EV+RERVRQI+  
Sbjct: 278 DLALELEVTRERVRQIQME 296


>gi|323345487|ref|ZP_08085710.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella oralis
           ATCC 33269]
 gi|323093601|gb|EFZ36179.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella oralis
           ATCC 33269]
          Length = 290

 Score =  198 bits (503), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 77/281 (27%), Positives = 141/281 (50%), Gaps = 14/281 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKI 64
           SI       L +Y+ EI ++PM+   EE  LA+  R+ G     A  +L+ ++LR VV +
Sbjct: 9   SITNRSSESLDKYLLEIGRLPMVSIDEETELAQLIRKGGKEGERAKEKLINANLRFVVSV 68

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y+  GL +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V
Sbjct: 69  AKQYQHQGLSLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIV 128

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           ++            L ++   +      + +      +A   N+ E+++           
Sbjct: 129 RLPLNQ-----VGALSKINSEVAKFEQEHQRRPSTQELASLTNIDENKISQTMRADNHHM 183

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV-LNPRERRIF 243
           S++A  +  D+NS    D L    D +   +++   R++  + L  +M+  L PRE  I 
Sbjct: 184 SIDAPFSDDDENS--MADVLASGDDSRADRIVD---RESMNSDLDDAMANALKPREVAIL 238

Query: 244 EARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +           LE +  EF ++RERVRQI  ++ +K++ES
Sbjct: 239 KESFGIGCTEKGLEEIGEEFGLTRERVRQIREKSIQKLRES 279


>gi|282900289|ref|ZP_06308240.1| sigE (Sigma 28 (Flagella/Sporulation)) [Cylindrospermopsis
           raciborskii CS-505]
 gi|281194794|gb|EFA69740.1| sigE (Sigma 28 (Flagella/Sporulation)) [Cylindrospermopsis
           raciborskii CS-505]
          Length = 327

 Score =  197 bits (502), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 63/305 (20%), Positives = 130/305 (42%), Gaps = 52/305 (17%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHG--------------------------------- 45
           Y+ EI ++P+L +++E +  K+ ++                                   
Sbjct: 23  YLREIGRVPLLNREQEIIYGKQVQQMMLLLEVKEALTKELGYEPSLSEWAIYVNQSENDL 82

Query: 46  ------DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                    A  +++ ++LRLVV IA  Y+   +   +++ EG +GL + V+KFDP  G+
Sbjct: 83  KHKISTGKRAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTMGY 142

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWI+ A+   I +    +++     +K     L ++K   + +     +    
Sbjct: 143 KFSTYAYWWIRQAITRAIAQQGRTIRLPIHITEK-----LNKIKKVQRELAQKLGRSPSP 197

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IAK+L +  +++           SL+  +   D   ++ Q+ L       E    ++ 
Sbjct: 198 TEIAKELELEPAQIREYLNIARQPISLD--VRVGDNQDTELQEMLEDHGLSPEHYTTQEF 255

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
                R+ L   ++ L P++R +   R   E+   ++L  +     +SRERVRQ+E +A 
Sbjct: 256 L----RHDLNNLLAELTPQQREVVILRFGLEDGNEMSLAKVGDRLNISRERVRQLEHQAL 311

Query: 278 KKVQE 282
             ++ 
Sbjct: 312 THLRR 316


>gi|218245053|ref|YP_002370424.1| RNA polymerase sigma-70 subunit RpoD subfamily [Cyanothece sp. PCC
           8801]
 gi|218165531|gb|ACK64268.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 8801]
          Length = 375

 Score =  197 bits (502), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 76/315 (24%), Positives = 136/315 (43%), Gaps = 53/315 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRY------------------------------ 41
            +  +  +  E+ + P+LE QEE  LA                                 
Sbjct: 60  SDDTVGAFFKEMSRYPLLEAQEEIELAYSVQFLVEAEQKRQQLLEELQHPPTKAQWAQAM 119

Query: 42  ----------REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                     R +   +A  +++ S+LRLVV IA  Y   G+P  +++ EG IGL +A +
Sbjct: 120 GFDSQRQFENRLYRGRTAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAE 179

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFDP +G++ +TY+ WWI+ A+   I      +++     +K     L +LK   + +  
Sbjct: 180 KFDPNKGYKFSTYAYWWIRQAITRTIANDARTIRLPIHIVEK-----LNKLKKAQRILKQ 234

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +      +A++L ++  ++  +        SLN  +   +   ++  D L    D  
Sbjct: 235 KLQRNPNEKELAQELEMTPPQLRQLLQLRRQSLSLNHRVGKGED--TELVDLL---EDQD 289

Query: 212 EQVLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRER 268
            Q+  E+      RN ++  +  VL  RE+ +   R       P TLE +   F +SRER
Sbjct: 290 LQLPEEQMNEGMLRNEISAVLSDVLTEREKDVISLRYGLSTSQPHTLEEVGGMFNLSRER 349

Query: 269 VRQIEARAFKKVQES 283
           VRQI+++A +K++  
Sbjct: 350 VRQIQSKAMRKLRRP 364


>gi|91202979|emb|CAJ72618.1| similar to DNA-directed RNA polymerase sigma subunit [Candidatus
           Kuenenia stuttgartiensis]
          Length = 256

 Score =  197 bits (502), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 71/262 (27%), Positives = 126/262 (48%), Gaps = 11/262 (4%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           ML  +EE  +A++  + GD  A  +L+ ++LRLVV IA  +   G    +++ EGN+GL+
Sbjct: 1   MLTFEEELEIARKVAK-GDAEAREKLIKANLRLVVSIAKEFVNRGFSFLDLIEEGNLGLI 59

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV+ FD   G R +TY+ WWIK A++  I     +++I +   Q+     + ++K    
Sbjct: 60  RAVEDFDITTGNRFSTYATWWIKQAIRRAIANKARIIRIPSYMLQR-----ISQMKHASS 114

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
            +   + +      IA +++++   V ++   L    SL+A + S         D     
Sbjct: 115 GLLKKHERSPSEQEIAAEIDITAQNVKNIELSLQSMTSLDAPLVSGADIIWALSDITP-- 172

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVS 265
            +G+     E  E    +  L + +  L+ R   +   R         TLE++S   ++S
Sbjct: 173 -NGKTLPPEEGLEETYEKETLKKLLDTLDKRAATVITMRYGLVDGESRTLEDISKILKIS 231

Query: 266 RERVRQIEARAFKKVQESIQKQ 287
           RERVRQIE    +K+   I K+
Sbjct: 232 RERVRQIEKETIQKLHYLITKE 253


>gi|87302558|ref|ZP_01085375.1| Sigma-70 factor family protein [Synechococcus sp. WH 5701]
 gi|87282902|gb|EAQ74859.1| Sigma-70 factor family protein [Synechococcus sp. WH 5701]
          Length = 307

 Score =  197 bits (502), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 77/302 (25%), Positives = 136/302 (45%), Gaps = 41/302 (13%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYR----------------EHGD------------ 46
            LS ++ EI +  +L   +E  L ++ +                E  D            
Sbjct: 4   SLSAFLGEIGRHQLLTPTQELTLGRKVQAMVALNERCALAGGNGEACDYNDVERRTIRTG 63

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  +++T++LRLVV +A  Y+G GL + +++ EG +GL++AV+K+DP RG R +TY+ 
Sbjct: 64  ERAKDQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLVRAVEKYDPTRGHRFSTYAY 123

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   +      ++I    N+K     LR  K  L         P+++ A     
Sbjct: 124 WWIRQGLNRALSTQSRTIRIPVNVNEK--LTKLRAAKARLLQANGLTASPQELAATMHLP 181

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
                +++S   R +   SL  ++ S   + ++  D L  D    E   +E+ E   R  
Sbjct: 182 LAEVEDLLSCELR-SITVSLQGVVKSK-SDPTELVDVLASD----EMPPMERAELSERSA 235

Query: 227 MLTRSMSV--LNPRERRIFEARRLQENPV---TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            + R + V  L PRER +   R   +      TL  ++ +   SRE  RQ+  RA +K++
Sbjct: 236 SVWRLLDVSNLTPRERTVVMLRFGLDGGHEWRTLAEVARQLGCSREYCRQVVQRALRKLR 295

Query: 282 ES 283
           ++
Sbjct: 296 KA 297


>gi|158334481|ref|YP_001515653.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158304722|gb|ABW26339.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 318

 Score =  197 bits (502), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 78/317 (24%), Positives = 140/317 (44%), Gaps = 52/317 (16%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR------------------------- 40
           M   V  +  ++ Y+ EI + P+L  ++E +  K+                         
Sbjct: 1   MKSSVQSKDSITAYLQEIGRFPLLNHEQEIIFGKQVQRMIMLQELKQQLHEQLEREPNLS 60

Query: 41  -YREHGD-------------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
            + +  D              +A  ++V S+LRLVV IA  Y    L   +++ EG IGL
Sbjct: 61  EWADQADIPVSQLQKELKLGQTANRKMVESNLRLVVSIAKKYNKAKLEFLDLIQEGTIGL 120

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
            + V+KFDP +G+R +TY+ WWI+ AM   I      +++    N+K     LR++K  L
Sbjct: 121 QRGVEKFDPTKGYRFSTYAYWWIRQAMTRAIAEQERTIRLPIHINEK--LNKLRKVKRQL 178

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                 +     V  +A ++ +S  +V +         SL+  +   D+ +++  + L  
Sbjct: 179 SLKLHRD---PTVAELATEMELSPKKVEAFLSYARHSISLD--VQVGDQQNTELWELLED 233

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
            H   E        + +    L + ++VLNP++R +   R     +NP+TL  +     V
Sbjct: 234 PHASPEDYATASYLQSD----LAKLLNVLNPQQREVITLRYGLIDQNPLTLAKVGERLNV 289

Query: 265 SRERVRQIEARAFKKVQ 281
           SRE VR++E  AF+ ++
Sbjct: 290 SREWVRRVEREAFQLLR 306


>gi|144575263|gb|AAZ53437.2| DNA-directed RNA polymerase sigma factor [Mycoplasma hyopneumoniae
           7448]
          Length = 676

 Score =  197 bits (502), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 71/293 (24%), Positives = 133/293 (45%), Gaps = 20/293 (6%)

Query: 6   MSIIVNGEIGLSRYIHEIRKI-PMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVV 62
           ++ + +    +  Y+  I K   +L  +EE  LAK+ +  G     A   L+  +LRLVV
Sbjct: 385 LNKLTDTSDMIKWYMRWIGKYGKLLTAEEERELAKKMKIKGRIGKKARDTLIKRNLRLVV 444

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
             A  Y+  GL   +++SEGN+G+++AV K+D  RGF+ +TY+ WWI+ A+   +     
Sbjct: 445 NSAKRYKNRGLGFIDLISEGNLGIIKAVAKYDYTRGFKFSTYATWWIRQAITRAVADQAR 504

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           L++I     +      + +++  LQ     N   E++         S  ++  +      
Sbjct: 505 LIRIPVHMVE--TINKINKVERELQQEKGLNPTAEEISERLGG-EFSPDKIRYIKKINID 561

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS-VLNPRERR 241
             SL+  I    +  S + D++    D      ++   R+ +  +L   +   L+  ER 
Sbjct: 562 PISLDKAI--GKEEDSSFSDFI---KDENMISPVDYAIREEKAKVLLEMIDSTLDYDERD 616

Query: 242 IFEARRLQE--------NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             + R               + E L++   V++ERVRQIEA+  KK++   ++
Sbjct: 617 FIKRRYGVGTNDEGIPYQAHSFEELAAMRRVTKERVRQIEAKILKKLRTPHRR 669


>gi|53987186|gb|AAV27387.1| RNA polymerase sigma factor [Mycoplasma hyopneumoniae 232]
          Length = 676

 Score =  197 bits (502), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 71/293 (24%), Positives = 133/293 (45%), Gaps = 20/293 (6%)

Query: 6   MSIIVNGEIGLSRYIHEIRKI-PMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVV 62
           ++ + +    +  Y+  I K   +L  +EE  LAK+ +  G     A   L+  +LRLVV
Sbjct: 385 LNKLTDTSDMIKWYMRWIGKYGKLLTAEEERELAKKMKIKGRIGKKARDTLIKRNLRLVV 444

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
             A  Y+  GL   +++SEGN+G+++AV K+D  RGF+ +TY+ WWI+ A+   +     
Sbjct: 445 NSAKRYKNRGLGFIDLISEGNLGIIKAVAKYDYTRGFKFSTYATWWIRQAITRAVADQAR 504

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           L++I     +      + +++  LQ     N   E++         S  ++  +      
Sbjct: 505 LIRIPVHMVE--TINKINKVERELQQEKGLNPTAEEISERLGG-EFSPDKIRYIKKINID 561

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS-VLNPRERR 241
             SL+  I    +  S + D++    D      ++   R+ +  +L   +   L+  ER 
Sbjct: 562 PISLDKAI--GKEEDSSFSDFI---KDENMISPVDYAIREEKAKVLLEMIDSTLDYDERD 616

Query: 242 IFEARRLQE--------NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             + R               + E L++   V++ERVRQIEA+  KK++   ++
Sbjct: 617 FIKRRYGVGTNDEGIPYQAHSFEELAAMRRVTKERVRQIEAKILKKLRTPHRR 669


>gi|113474616|ref|YP_720677.1| RNA polymerase sigma factor [Trichodesmium erythraeum IMS101]
 gi|110165664|gb|ABG50204.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
          Length = 336

 Score =  197 bits (502), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 69/328 (21%), Positives = 142/328 (43%), Gaps = 52/328 (15%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------------------- 43
               +    +  Y+HEI ++P+L ++EE V  K+ ++                       
Sbjct: 20  PTTYSSMDTVRTYLHEIGRVPLLTREEEIVYGKQVQQMMQFLELKEKLEEKLNRTATLLE 79

Query: 44  ----------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
                                A  +++ ++LRLVV IA  Y+   +   +++ EG +GL 
Sbjct: 80  WAEHLLVSEKVLKQAIKQGQRAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLE 139

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           + V+KFDP RG++ +TY+ WWI+ A+   I +    +++     +K     L ++K   +
Sbjct: 140 RGVEKFDPTRGYKFSTYAYWWIRQAITRAIAQQARTIRLPIHITEK-----LNKIKRVQR 194

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
            +  +  +      IA+ L +  S++           SL+  +   D   ++ Q+ L  +
Sbjct: 195 ELIQSLGRSPTPSEIAQALELEPSQIREYLLMARHPISLD--LRVGDNQDTELQELLEDE 252

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVS 265
               +  +  +  R++   +L      L+ ++RR+   R   E+   ++L  +  + ++S
Sbjct: 253 TSSPDDYITGELLRQDINTLLAE----LSEQQRRVLVLRFGLEDGKEMSLAKVGDKLQLS 308

Query: 266 RERVRQIEARAFKKVQESIQKQVELSSS 293
           RERVRQ+E +A   ++    K  E  +S
Sbjct: 309 RERVRQLEHQALAFLRRRQAKVREYVAS 336


>gi|149197872|ref|ZP_01874921.1| RNA polymerase sigma factor RpoD [Lentisphaera araneosa HTCC2155]
 gi|149139093|gb|EDM27497.1| RNA polymerase sigma factor RpoD [Lentisphaera araneosa HTCC2155]
          Length = 274

 Score =  197 bits (502), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 72/277 (25%), Positives = 141/277 (50%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +  Y+  I ++P++ + +E  LA+    +G  SA  +L+  +LRLVVKIA  ++  G
Sbjct: 5   DESVRSYMKNIAELPLISRDDEVELAELI-NNGSESAREQLIVGNLRLVVKIAHDFKSLG 63

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +P+++++SEGNIGLM+AV+KF P  G + ++Y  WWIK A++  +     +++I   +  
Sbjct: 64  VPLADLISEGNIGLMKAVEKFKPGMGAKFSSYGAWWIKQAIRRCVAEQSRVIRIPVQSAV 123

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
           K   + ++R+  HL    +   +      IA+  ++S+  V ++         ++   + 
Sbjct: 124 K--MYKIQRVAMHL---AEELGRVPSEKEIAEAADMSQRSVHNLKVAATSPT-ISLSTSL 177

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV-LNPRERRIFEARRL--Q 249
            D      +D L    D   ++   + + ++ +++L   +   L  RE+ I   R     
Sbjct: 178 KDGEDGVLEDMLP---DLMAKMPGGEMDDRDVKSLLQDCVDQHLTEREKLIINMRYGLNG 234

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
               TL+ +S     +RERVRQI+ +A KK+   + +
Sbjct: 235 GEQHTLDEISELIGRTRERVRQIQHKALKKLSRHLDE 271


>gi|206889845|ref|YP_002248858.1| RNA polymerase sigma 70 factor [Thermodesulfovibrio yellowstonii
           DSM 11347]
 gi|206741783|gb|ACI20840.1| RNA polymerase sigma 70 factor [Thermodesulfovibrio yellowstonii
           DSM 11347]
          Length = 427

 Score =  197 bits (502), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 66/237 (27%), Positives = 124/237 (52%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A ++++ S+L+LVV IA  Y G GL + +++ EGNIGLM+AV+KF+ ++GF+ +TYS W
Sbjct: 188 EAKNKMIESNLKLVVSIAKKYTGRGLNLEDLIQEGNIGLMKAVEKFEYKKGFKFSTYSTW 247

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ ++   I      ++I           N+ ++    + +  N+     +  I+  LN
Sbjct: 248 WIRQSINRAIAEHSKTIRIPVHV-----IDNICKINKIYRELYQNSENEPDIEEISLNLN 302

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +   ++           S++  +   D   S  ++++    D       E+    + +++
Sbjct: 303 IPSDKIADFLAISKEPVSIDMSLRDDD---SLLKEFI---EDMNSPNPYEEALHDDLKHL 356

Query: 228 LTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           + +  S+L+ RE+ I   R    +E P +L+ +  EF VSRER+RQIE RA +K++ 
Sbjct: 357 IEKVFSLLSKREKEILMRRYGINEEKPKSLDEVGKEFSVSRERIRQIELRAMRKLKR 413


>gi|312601028|gb|ADQ90283.1| RNA polymerase sigma factor [Mycoplasma hyopneumoniae 168]
          Length = 676

 Score =  197 bits (502), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 71/293 (24%), Positives = 133/293 (45%), Gaps = 20/293 (6%)

Query: 6   MSIIVNGEIGLSRYIHEIRKI-PMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVV 62
           ++ + +    +  Y+  I K   +L  +EE  LAK+ +  G     A   L+  +LRLVV
Sbjct: 385 LNKLTDTSDMIKWYMRWIGKYGKLLTAEEERELAKKMKIKGRIGKKARDTLIKRNLRLVV 444

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
             A  Y+  GL   +++SEGN+G+++AV K+D  RGF+ +TY+ WWI+ A+   +     
Sbjct: 445 NSAKRYKNRGLGFIDLISEGNLGIIKAVAKYDYTRGFKFSTYATWWIRQAITRAVADQAR 504

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           L++I     +      + +++  LQ     N   E++         S  ++  +      
Sbjct: 505 LIRIPVHMVE--TINKINKVERELQQEKGLNPTAEEISERLGG-EFSPDKIRYIKKINID 561

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS-VLNPRERR 241
             SL+  I    +  S + D++    D      ++   R+ +  +L   +   L+  ER 
Sbjct: 562 PISLDKAI--GKEEDSSFSDFI---KDENMISPVDYAIREEKAKVLLEMIDSTLDYDERD 616

Query: 242 IFEARRLQE--------NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             + R               + E L++   V++ERVRQIEA+  KK++   ++
Sbjct: 617 FIKRRYGVGTNDEGIPYQAHSFEELAAMRRVTKERVRQIEAKILKKLRTPHRR 669


>gi|149277811|ref|ZP_01883951.1| RNA polymerase sigma-70 factor [Pedobacter sp. BAL39]
 gi|149231499|gb|EDM36878.1| RNA polymerase sigma-70 factor [Pedobacter sp. BAL39]
          Length = 288

 Score =  197 bits (502), Expect = 1e-48,   Method: Composition-based stats.
 Identities = 79/281 (28%), Positives = 148/281 (52%), Gaps = 12/281 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           R + SI   G   L +Y+ EI KI +L  +EE  LA   RE GD +A  +LV+++LR VV
Sbjct: 5   RISKSITDRGGDSLEKYLSEISKIELLNVEEEVRLASIVRE-GDRAALDKLVSANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  GL +++++SEGN+GL++A  ++D  +GF+  ++++WWI+ ++   I     
Sbjct: 64  SVAKNYQDMGLRLADLISEGNLGLIKAASRYDHTKGFKFISFAVWWIRQSITYAIADQHR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           ++++    NQ      L R    L+   +   +   +  +A+ L++ E++V+        
Sbjct: 124 MIRLP--GNQIVGITRLNRTSDLLEQKLE---RRPSLEEVAEALDLPETKVVDYQMSALK 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             SL+  I   +  ++        + +  + VL  +   +N R    R +S+L PRE++I
Sbjct: 179 TTSLDMPILLGEPGTTFGHMIRNSEVEAADAVLDRQSLAENVR----RLLSILPPREQKI 234

Query: 243 FEARRLQEN-PVT-LENLSSEFEVSRERVRQIEARAFKKVQ 281
                     P T LE++   F +S+ER+RQ++ +A K ++
Sbjct: 235 LSLYYGLGGMPQTRLEDMVPVFHLSKERLRQLKDKAVKTLK 275


>gi|116074383|ref|ZP_01471645.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9916]
 gi|116069688|gb|EAU75440.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9916]
          Length = 341

 Score =  197 bits (502), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 69/316 (21%), Positives = 137/316 (43%), Gaps = 54/316 (17%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSA-------------------------- 49
           +  Y+ +I ++P+L  Q+E  L ++ ++  +L A                          
Sbjct: 33  VRSYLRDIGRVPLLSHQQEITLGRQVQDLMELEALESELKSESGEEVVAPEALAKKAGLS 92

Query: 50  --------------AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
                           R+V ++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP
Sbjct: 93  GVQLKRKLQAGRRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDP 152

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            RG++ +TY+ WWI+  +   I      +++     +      L +LK   + ++    +
Sbjct: 153 TRGYKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITE-----MLNKLKKGQRELSQELGR 207

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
              V  +A+ + + E EV  + CR     SL   +   D + ++  + L  D     ++ 
Sbjct: 208 TPTVTELAEFVELPEEEVKDLMCRARQPVSLEMKV--GDGDDTELLELLAGDG----ELP 261

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIE 273
            E+ E +  +  L   +  L   +R++   R     E+P++L  +     +SR+RVR +E
Sbjct: 262 SEQVEGECLKGDLRDLLEQLPELQRKVLRMRYGMNGEDPMSLTGIGRIIGISRDRVRNLE 321

Query: 274 ARAFKKVQESIQKQVE 289
                 ++  +  QVE
Sbjct: 322 RDGLAGLRR-LSDQVE 336


>gi|332708973|ref|ZP_08428943.1| RNA polymerase sigma factor, sigma-70 family//RpoD-like family
           [Lyngbya majuscula 3L]
 gi|332352162|gb|EGJ31732.1| RNA polymerase sigma factor, sigma-70 family//RpoD-like family
           [Lyngbya majuscula 3L]
          Length = 373

 Score =  197 bits (502), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 75/315 (23%), Positives = 136/315 (43%), Gaps = 52/315 (16%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-------------YREHGDLS--------- 48
             +  +  +  E+ + P+L+  EE  LA+R              +E  D           
Sbjct: 58  GSDDTVGAFFKEMARYPLLKPDEEVDLARRVKFLVEIDHLHNSLQEKLDRKPTKAEVAAA 117

Query: 49  -----------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A  +++ S+LRLVV IA  Y   G+P  +++ EG +GL +A +
Sbjct: 118 VEMTERQLEGNLYRGRVAKRKMIRSNLRLVVSIAKRYINRGVPFLDLIQEGALGLNRAAE 177

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFDP++G++ +TY+ WWI+ A+   I      +++     +K     L +LK   + +  
Sbjct: 178 KFDPDKGYKFSTYAYWWIRQAITRTIANDARTIRLPIHIVEK-----LNKLKKAQRELKQ 232

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +    + +A+ L +S S +  +        SLN  +   +   ++  D L    D  
Sbjct: 233 KLQRNPNELELAQALEISLSHLRQLLELRRRSLSLNHRVGKGED--TELMDLL---EDND 287

Query: 212 EQVLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRER 268
            ++  +K      R  +   +  VL  RE+ +   R       P TLE +   F +SRER
Sbjct: 288 LRLPEDKMNESMMRQEIWEVLSDVLTEREKDVISLRYGLASSEPYTLEEVGGMFNLSRER 347

Query: 269 VRQIEARAFKKVQES 283
           VRQI+++A +K++  
Sbjct: 348 VRQIQSKAMRKLRRP 362


>gi|288819153|ref|YP_003433501.1| RNA polymerase sigma factor RpoS [Hydrogenobacter thermophilus
           TK-6]
 gi|288788553|dbj|BAI70300.1| RNA polymerase sigma factor RpoS [Hydrogenobacter thermophilus
           TK-6]
 gi|308752737|gb|ADO46220.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Hydrogenobacter
           thermophilus TK-6]
          Length = 310

 Score =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 84/301 (27%), Positives = 144/301 (47%), Gaps = 38/301 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +++Y+ ++ KIP+L  +EE  +A+R +E GD  A  +LV S+LR V+ IA  Y GYGLP+
Sbjct: 10  INQYLKKVAKIPLLTPEEEKEVARRAKE-GDQEAFRKLVESNLRFVINIAKQYLGYGLPL 68

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           SE+++ GN GL++A K+FDP+RG +  +Y++WWI+ A+ + + +    V+I     Q  +
Sbjct: 69  SELIAAGNHGLIEAAKRFDPDRGVKFISYAVWWIRQAIMQALSQQTGAVRIP--LKQAHV 126

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVV----------AIAKKLN------------------ 167
              +  +   L    +    PE+V            + ++L                   
Sbjct: 127 INRIGSIYSRLFRELEREPTPEEVAIEYSKEILSRELERELGRKPTKDEVEQRFKKEGFK 186

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  EV           SL+A +   +   + + D+L          + E+   +     
Sbjct: 187 ISPEEVEKCLQVCRIPLSLDAPV--GENEDTFFVDFLSQHGTAD---VEERIINEVLEKE 241

Query: 228 LTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           +   +  L  +ERR+ E R     E P TL  +     +SRERVRQ+E RA +K++    
Sbjct: 242 IGDMLDRLPEKERRVIELRFGLRGEEPRTLREIGDILNISRERVRQLETRALRKLRNMAM 301

Query: 286 K 286
           K
Sbjct: 302 K 302


>gi|172065170|ref|YP_001815882.1| RpoD family RNA polymerase sigma factor [Burkholderia ambifaria
           MC40-6]
 gi|171997412|gb|ACB68329.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           ambifaria MC40-6]
          Length = 621

 Score =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 101/237 (42%), Gaps = 12/237 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L  ++LRLVV IA  Y   GLP ++++ EGNIGL++A++++D  RGFR +TY+ WW
Sbjct: 384 ARTGLFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIERYDYRRGFRFSTYATWW 443

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   +      +++ T          L +L    +              +A  +  
Sbjct: 444 IRQAITHALADLGRTIRVPTH-----TVDALNKLSRLAREHRQRAGTAATPAELAVHMGE 498

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +   +    S +  ++           +     D       +       R  +
Sbjct: 499 PVDKVRDLMAIVKEPVSADVPVSPEGD-----MTFADVAPDTTTPSPEDAAGATQLRRTI 553

Query: 229 TRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
              +  L PRE  + + R     +   +L ++  +  +S ERVRQIEA A  +++ S
Sbjct: 554 AAVIDRLPPREAMVLKLRYGLHTDEGCSLRDIGRQLNLSAERVRQIEASALARLRAS 610



 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 13/56 (23%), Positives = 21/56 (37%), Gaps = 9/56 (16%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREH---------GDLSAAHRLV 54
           +       +  Y+ E+   P+L + EE+  A+R             GD  A   LV
Sbjct: 109 LAPRTTDPVRLYLREMGTTPLLTRDEEFAYARRIERGRAASAAVLCGDPDALDALV 164


>gi|223998999|ref|XP_002289172.1| RNA polymerase [Thalassiosira pseudonana CCMP1335]
 gi|220974380|gb|EED92709.1| RNA polymerase [Thalassiosira pseudonana CCMP1335]
          Length = 318

 Score =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 74/315 (23%), Positives = 134/315 (42%), Gaps = 51/315 (16%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------------------ 43
             +  Y+  +    +L+K EE +LA+  +                               
Sbjct: 1   DSMKYYMKTMGNHDLLQKNEEIILAREIQILIKWEEVREELEGQLLRPPTYQEWANAIEP 60

Query: 44  -----------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                         L A   L  S+LRLV+ IA  Y+G GL + ++  EG +GL +A +K
Sbjct: 61  GMTVTQIKKQIRRSLRAKAALTESNLRLVISIAKRYQGRGLNMQDLCQEGTLGLTRACEK 120

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FDPERGFR +TY+ WWIK  +   I      +++    +       L  ++   + + + 
Sbjct: 121 FDPERGFRFSTYATWWIKQGIMRAIADQARTIRLPVHIHD-----QLSIVRKAERDLQNE 175

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      +A K+ +   ++  +     G  S+   + +S    S      + D D   
Sbjct: 176 LGRDATKEEVAAKVGMKPDKIEFLKRASVGSISMEQELGTSGSERSFTIQDTLGDPD--- 232

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           Q  ++  + +  ++ + R +  LN RE+ +   R   ++    TLE +  +F V+RER+R
Sbjct: 233 QKPVDMAQYRMLQDDVGRLICTLNAREQAVIRMRFGLDDGKAKTLEEIGKKFSVTRERIR 292

Query: 271 QIEARAFKKVQESIQ 285
           QIEARA  K+++  +
Sbjct: 293 QIEARALHKLRQPYR 307


>gi|182416213|ref|YP_001821279.1| RpoD family RNA polymerase sigma factor [Opitutus terrae PB90-1]
 gi|177843427|gb|ACB77679.1| RNA polymerase, sigma 70 subunit, RpoD family [Opitutus terrae
           PB90-1]
          Length = 347

 Score =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 76/275 (27%), Positives = 135/275 (49%), Gaps = 12/275 (4%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           +G   L  Y+ +I + P+L  +EE+ LA+R R  GD  A   ++ ++LRLVV+IA  Y  
Sbjct: 30  DGRSSLQIYLQDIGQTPLLTAREEFALAERVR-RGDAGARDHMIRANLRLVVRIAKDYAQ 88

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
           YGLP+++++SEGN+GL+ AV +FDP  G +L+TY+ WWI+ A++         +++    
Sbjct: 89  YGLPLADLISEGNVGLIHAVDRFDPRIGGKLSTYAAWWIRQAIRRAFAHHARAIRLPVH- 147

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
               +   + RL+    ++++   +      +A +L     ++           SL+A +
Sbjct: 148 ----MLDRIARLRRAQASLSEQFGREATTDELAAELQAPVEKIALWKSAGDAPFSLDAAV 203

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-- 248
                  S+ +       D +      +         L   ++ L+ RE  I   R    
Sbjct: 204 ----GTGSESRRLSETIRDERAPTAFTQLRDATTARDLRAIIATLDVREATILRLRFGLD 259

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            + P TL  +S  F ++RERVRQ+E RA + V+ +
Sbjct: 260 GDEPQTLHAVSLRFGITRERVRQLERRALQNVRNA 294


>gi|5804831|emb|CAB53534.1| RpoS protein [Escherichia coli O157:H7]
 gi|332087634|gb|EGI92761.1| RNA polymerase sigma factor RpoS [Shigella dysenteriae 155-74]
          Length = 298

 Score =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 73/259 (28%), Positives = 131/259 (50%), Gaps = 13/259 (5%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
            +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV
Sbjct: 41  AEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAV 99

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   LR  +     ++
Sbjct: 100 EKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVYLRTAR----ELS 154

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
                      IA++L+    +V  M        S++  +    +     +  L    D 
Sbjct: 155 HKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE-----KALLDILADE 209

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRER 268
           +E    +  +  + +  + + +  LN ++R +   R   L     TLE++  E  ++RER
Sbjct: 210 KENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDVGREIGLTRER 269

Query: 269 VRQIEARAFKKVQESIQKQ 287
           VRQI+    ++++E +Q Q
Sbjct: 270 VRQIQVEGLRRLREILQTQ 288


>gi|317968319|ref|ZP_07969709.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CB0205]
          Length = 260

 Score =  197 bits (501), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 71/250 (28%), Positives = 130/250 (52%), Gaps = 11/250 (4%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           E    ++++      A  R++ ++LRLVV +A  Y+  GL + ++V EG IGL +AV KF
Sbjct: 11  ELTARQKHQIRMGTRARDRMMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKF 70

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           DP  G++ +TY+ WWI+  M   I  S   +++    ++K     L +++   + ++   
Sbjct: 71  DPAMGYKFSTYAYWWIRQGMTRAIDNSARTIRLPIHVSEK-----LSKMRRITRELSHRF 125

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            +    + +A  + +   E+  +  + A   SL+A     D  S+  +  L+ D +  E 
Sbjct: 126 GRQPNRLELAHAMGMQPEELEELITQSAPCASLDAHARGDDDRSTLGE--LIADPNSNES 183

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQ 271
             ++  +R  ++  L   +S LN RER+I E R     + P+TL  +  +  VSRERVRQ
Sbjct: 184 --MDSMDRNLQKEHLGTWLSQLNERERKIIELRFGLAGQEPLTLAEIGRQINVSRERVRQ 241

Query: 272 IEARAFKKVQ 281
           +E++A  K++
Sbjct: 242 LESKAILKLR 251


>gi|330723944|gb|AEC46314.1| RNA polymerase sigma factor [Mycoplasma hyorhinis MCLD]
          Length = 524

 Score =  196 bits (500), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 68/290 (23%), Positives = 132/290 (45%), Gaps = 20/290 (6%)

Query: 9   IVNGEIGLSRYIHEIRKI-PMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKIA 65
           + +    +  Y+  I K   +L  +EE  LAK+ +  G     A H L+  +LRLV+  A
Sbjct: 236 LSDTNDIIKWYMRWIGKYGKLLTPEEENNLAKQIKNGGRAGKRARHTLINRNLRLVINNA 295

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y+  GL   +++SEGN G+++AV K+D  +G++ +TY+ WWI+ A+   +     +++
Sbjct: 296 KRYKNRGLTFIDLISEGNQGILKAVDKYDYTKGYKFSTYATWWIRQAITRAVADQARIIR 355

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           I     +      + +++  LQ         EQ+  +    + +  +V           S
Sbjct: 356 IPVHMVE--TINKINKIERELQQEYGVTPTDEQIAEVMGG-DFTAEKVRYTKKINIDPIS 412

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS-VLNPRERRIFE 244
           L+  I    +  S + D++    D      I+  ER+ +  +L + +   L+  E+    
Sbjct: 413 LDKAI--GKEEYSSFSDFI---KDESVISPIDYSEREEKTKILKQMIENNLDNDEKVFIM 467

Query: 245 ARRLQENP--------VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R               + + L+ E  V++ER+RQIE++  KK++   +K
Sbjct: 468 KRYGFGTDPNGEQYRIHSFDELAKERGVTKERIRQIESKILKKLRHPQKK 517


>gi|196047982|ref|ZP_03115160.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43) [Bacillus
           cereus 03BB108]
 gi|196021238|gb|EDX59967.1| RNA polymerase sigma factor RpoD (Sigma-A) (Sigma-43) [Bacillus
           cereus 03BB108]
          Length = 289

 Score =  196 bits (500), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 72/279 (25%), Positives = 138/279 (49%), Gaps = 10/279 (3%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           N  +  + Y++EI +  +L ++EE +  ++Y+E+GD+ A   L+  +LRLVV +   Y  
Sbjct: 5   NDSVEYNLYLNEIGQHSLLTEEEEKMYLRKYKENGDMEARRILIECNLRLVVSVVNSYPR 64

Query: 71  YG-LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
            G     +++  GN+GL++ ++ F+  +  +LATY  WWI+  +  +I  + + ++   T
Sbjct: 65  VGNCEKMDMIQVGNVGLIRGIEAFEISKNCKLATYVTWWIRHEISRFITFNKNDIRCSVT 124

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
                    + +LK +         +   +  IA++L  S   V+ +   L   ES++  
Sbjct: 125 IQ-----NKMDKLKKYFSNENGKAKRKLNIEQIAEELGYSVETVLQIMDTLMLKESVSLD 179

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL- 248
             SSD++S    + +          LI  EE+  +   L    +VLN +E  +   R   
Sbjct: 180 APSSDEDSRPVMNSVKNAKAPNPVELITSEEQLYQIEEL--LFTVLNEKEESVIRYRFGF 237

Query: 249 -QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             E  +TLE ++  F ++RER++QIE +A  K++  + K
Sbjct: 238 DTEKDLTLEEVARIFGITRERIQQIEKKAIGKLKNRMDK 276


>gi|71893415|ref|YP_278861.1| RNA polymerase sigma factor [Mycoplasma hyopneumoniae J]
          Length = 489

 Score =  196 bits (500), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 71/293 (24%), Positives = 133/293 (45%), Gaps = 20/293 (6%)

Query: 6   MSIIVNGEIGLSRYIHEIRKI-PMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVV 62
           ++ + +    +  Y+  I K   +L  +EE  LAK+ +  G     A   L+  +LRLVV
Sbjct: 198 LNKLTDTSDMIKWYMRWIGKYGKLLTAEEERELAKKMKIKGRIGKKARDTLIKRNLRLVV 257

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
             A  Y+  GL   +++SEGN+G+++AV K+D  RGF+ +TY+ WWI+ A+   +     
Sbjct: 258 NSAKRYKNRGLGFIDLISEGNLGIIKAVAKYDYTRGFKFSTYATWWIRQAITRAVADQAR 317

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           L++I     +      + +++  LQ     N   E++         S  ++  +      
Sbjct: 318 LIRIPVHMVE--TINKINKVERELQQEKGLNPTAEEISERLDG-EFSPDKIRYIKKINID 374

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS-VLNPRERR 241
             SL+  I    +  S + D++    D      ++   R+ +  +L   +   L+  ER 
Sbjct: 375 PISLDKAI--GKEEDSSFSDFI---KDENMISPVDYAIREEKAKVLLEMIDSTLDYDERD 429

Query: 242 IFEARRLQE--------NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             + R               + E L++   V++ERVRQIEA+  KK++   ++
Sbjct: 430 FIKRRYGVGTNDEGIPYQAHSFEELAAMRRVTKERVRQIEAKILKKLRTPHRR 482


>gi|33866043|ref|NP_897602.1| type II alternative RNA polymerase sigma factor [Synechococcus sp.
           WH 8102]
 gi|33639018|emb|CAE08024.1| Possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 8102]
          Length = 308

 Score =  196 bits (500), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 70/300 (23%), Positives = 131/300 (43%), Gaps = 37/300 (12%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------------------------HGD 46
            LS ++ EI +  +L  ++E +L ++ +                                
Sbjct: 4   SLSAFLGEIGRHQLLTPEQELMLGRKVQAMVVITEPCQLAGGSGPSCEYSDEEKAVIRRG 63

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A ++++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG R +TY+ 
Sbjct: 64  ERAKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSTYAY 123

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   +      ++I    N+K     LR  K  L          EQ+    +  
Sbjct: 124 WWIRQGLNRALSTQSRTIRIPVNVNEK--LTKLRAAKARLMQRNGLTPTAEQLADFMEIP 181

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
                ++++   R +   SL  ++ S   + S+  D L  D     +     E   +   
Sbjct: 182 IAEVEDLLACELR-SVTVSLQGVVKSK-SDPSELVDVLPSDELPPMERAEIAERSASVWT 239

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +L ++   L P+ER +   R   +      TL  ++     SRE  RQ+  RA +K++++
Sbjct: 240 LLGKA--NLTPKERTVVTLRFGLDGTNEWRTLAEVARHMNCSREYCRQVVQRALRKLRKT 297


>gi|302535003|ref|ZP_07287345.1| RNA polymerase sigma factor RpoS [Streptomyces sp. C]
 gi|302443898|gb|EFL15714.1| RNA polymerase sigma factor RpoS [Streptomyces sp. C]
          Length = 325

 Score =  196 bits (500), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 75/300 (25%), Positives = 128/300 (42%), Gaps = 40/300 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAK--------------RYREHGDLSAAHRL-------- 53
           +  Y+ EI + P+L+   E  L++                   G+L A   L        
Sbjct: 28  VGMYLDEIARTPLLDAAREVELSQIIEAGVYARQILDGEIERDGELPAREELEALAAEGE 87

Query: 54  ------VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
                 + S+LRLVV +A  Y   GLP+ +++ EGN GL++AV+KFD  +GF+ +TY+ W
Sbjct: 88  RAKEVFIRSNLRLVVAVARRYPRSGLPLLDLIQEGNAGLVRAVEKFDYAKGFKFSTYATW 147

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++        L   L R++   +     N +  +   IA  L+
Sbjct: 148 WIRQAITRSIADQSRTIRLPVH-----LVEELGRIRRIQREFNRENGRDPEHAEIAAALD 202

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
            +E  V  +        SLN  +   D+  +Q+ D L    D       +      R   
Sbjct: 203 STEKRVGDVLDWARDPVSLNMSV--DDEGDTQFGDLL---EDTSAISPEQSVLSLLRSEE 257

Query: 228 LTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L   +  L+ R   I + R   E+    TL  +  +  ++RER+RQIE  A  +++   +
Sbjct: 258 LEDLLGKLDQRTASIIKMRYGIEDGRERTLTEVGKQHGLTRERIRQIEKHALLELKRMAR 317


>gi|269114989|ref|YP_003302752.1| RNA polymerase sigma factor rpoD [Mycoplasma hominis]
 gi|268322614|emb|CAX37349.1| RNA polymerase sigma factor rpoD [Mycoplasma hominis ATCC 23114]
          Length = 538

 Score =  196 bits (500), Expect = 2e-48,   Method: Composition-based stats.
 Identities = 71/289 (24%), Positives = 129/289 (44%), Gaps = 27/289 (9%)

Query: 16  LSRYIHEIRKI-PMLEKQEEYVLAKRYREHGD-------LSAAHRLVTSHLRLVVKIAMG 67
           +  Y+  I K   +L   EE  LAK+ +E  +         A   LV  +LRLV+  A  
Sbjct: 244 VKWYMRWIGKYGKLLTTNEEQALAKKMQEAKEANNYYKYKKARDMLVKRNLRLVINNAKR 303

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y+  GL   +++SEGN G+M+AV K+D  +GF+ +TY+ WWI+ A+   +      V++ 
Sbjct: 304 YKNRGLNFIDLISEGNAGIMKAVSKYDYTKGFKFSTYATWWIRQAITRAVADQARTVRVP 363

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL--NVSESEVISMNCRLAGDES 185
               +      + ++    + +   N  P     IAKK   + +  +V  +        S
Sbjct: 364 VHMVE-----TINKILKIERELQQENGYPPTDEEIAKKYGGDFTAEKVRYIRKINIDPIS 418

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLNPRERRIFE 244
           L+  I    + +S + D++  +           EE       M+   +S  +  +R +  
Sbjct: 419 LDKNI--GKEENSSFSDFVKDESVISPTSYASHEELSVIINEMIEEGLS--DQADRDLIR 474

Query: 245 ARRLQEN-------PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R    +       P TL+ LS E  +S+E+VRQ+E +  +K++   ++
Sbjct: 475 KRFGINDLKGNKYKPHTLDELSKELGISKEKVRQLETKVLRKLKHPQKR 523


>gi|194476921|ref|YP_002049100.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Paulinella chromatophora]
 gi|171191928|gb|ACB42890.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Paulinella chromatophora]
          Length = 321

 Score =  196 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 77/328 (23%), Positives = 139/328 (42%), Gaps = 55/328 (16%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------------- 43
           M   N     + ++ +  Y+ EI +IP+L  ++E  L ++ +E                 
Sbjct: 1   MQTPNDQTSSDADL-VRSYLKEISRIPLLTHEQEITLGRQVQELICIQETEQKLELKNGI 59

Query: 44  -----------------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
                                  HG   A  ++V+S+LRLVV IA  Y    + + ++V 
Sbjct: 60  KPTQEELANSLDLSINQVKRKIIHG-KRAKEQMVSSNLRLVVSIAKKYTKRSMELLDLVQ 118

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           EG IGL++ V+KFDP RG++ +TY+ WWI+  +   I      +++     +      L 
Sbjct: 119 EGTIGLIRGVEKFDPTRGYKFSTYAYWWIRQGITRAISEQSRTIRLPIHITE-----ELN 173

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
           +LK   + ++ +  +   V+ +AK + ++E EV  + C      SL   I   D      
Sbjct: 174 KLKKAQRDLSQSLGRTPTVIELAKMIKLTEKEVKELLCHAKQPVSLEMKIGDGDDT---- 229

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENL 258
              L+     + ++  E   RK  R  L   +  L   + RI + R   +   P+TL  +
Sbjct: 230 --VLLELLPSEIELPEEYVNRKCLRRDLLALVEQLPEIQVRILKMRYGFDSTEPLTLTGI 287

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQK 286
                +SR+RVR +E     ++Q+  + 
Sbjct: 288 GRVLGMSRDRVRNLERDGINRLQKLSKS 315


>gi|189485247|ref|YP_001956188.1| RNA polymerase sigma factor [uncultured Termite group 1 bacterium
           phylotype Rs-D17]
 gi|170287206|dbj|BAG13727.1| RNA polymerase sigma factor [uncultured Termite group 1 bacterium
           phylotype Rs-D17]
          Length = 573

 Score =  196 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 73/262 (27%), Positives = 129/262 (49%), Gaps = 21/262 (8%)

Query: 28  MLEKQEEYVLAKRYRE-----HGDLSAAHRLVTSHLRLVVKIAMGYRG-YGLPISEVVSE 81
           ++  +E     +R RE     H D     +L+ ++ RLVV IA  + G   L +S+++ E
Sbjct: 312 VITPEEMIETDRRIRELEYVIHRD---KMKLIEANFRLVVSIAKKHVGISNLELSDLIQE 368

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           GN+GL +AV+KF+ +RGF+ +TY+ WWI+ ++   I      ++I      K L   L +
Sbjct: 369 GNLGLSKAVEKFEWKRGFKFSTYATWWIRQSINRAIADQARTIRIPVHM--KELISKLTK 426

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
            K   Q    N  +   +   +K L +S   +  +   +    SL   +   ++  S+ +
Sbjct: 427 SKKECQQ---NMGREPTIQEYSKILKLSCDRIRRILKMMQEPVSLAMPV--GEEEDSRLE 481

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLS 259
           D++    D      + K ++   +  L + ++ L PRE  I   R       P TLE + 
Sbjct: 482 DFI---EDQNSPNPVVKTQQYRLQLELEKVLATLAPREAEIIRLRYGIGIGYPSTLEEVG 538

Query: 260 SEFEVSRERVRQIEARAFKKVQ 281
            +F ++RERVRQIEA+A +K++
Sbjct: 539 KKFGITRERVRQIEAKAIRKLK 560


>gi|153311|gb|AAA26765.1| principal sigma-like factor [Streptomyces aureofaciens]
 gi|450079|prf||1920369C RNA polymerase:SUBUNIT=sigma
          Length = 325

 Score =  196 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 77/310 (24%), Positives = 132/310 (42%), Gaps = 44/310 (14%)

Query: 10  VNGEIG----LSRYIHEIRKIPMLEKQEEYVLAKRYR--------------EHGDLSAAH 51
           V GEI     +  Y+ EI + P+L+  +E  L++                   G+  A  
Sbjct: 18  VGGEIADRDLVGMYLDEIARTPLLDAAKEVELSQIIEAGVYARQILDEATPREGESPARE 77

Query: 52  RL--------------VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
            L              + S+LRLVV +   Y   GLP+ +++ EGN GL++AV+KFD  +
Sbjct: 78  ELEALAAEGERAKEVFIRSNLRLVVAVVRRYPRSGLPLLDLIQEGNAGLVRAVEKFDYAK 137

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           GF+ +TY+ WWI+ A+   I      +++        L   L R++   +     N +  
Sbjct: 138 GFKFSTYATWWIRQAITRSIADQSRTIRLPVH-----LVEELGRIRRVQREFNRENGRDP 192

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           +   IA +L+ +E  V  +        SLN  +   D+  +Q+ D L    D       +
Sbjct: 193 EHAEIAAELDSTEKRVGDVLDWARDPVSLNMSV--DDEGDTQFGDLL---EDTSAISPEQ 247

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEAR 275
                 R   L   +  L+ R   I + R   E+    TL  +  +  ++RER+RQIE  
Sbjct: 248 SVLSLLRSEELEDLLGKLDQRTASIIKMRYGIEDGRERTLTEVGKQHGLTRERIRQIEKH 307

Query: 276 AFKKVQESIQ 285
           A  +++   +
Sbjct: 308 ALLELKRMAR 317


>gi|87306425|ref|ZP_01088572.1| RNA polymerase sigma factor rpoS [Blastopirellula marina DSM 3645]
 gi|87290604|gb|EAQ82491.1| RNA polymerase sigma factor rpoS [Blastopirellula marina DSM 3645]
          Length = 296

 Score =  196 bits (500), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 84/290 (28%), Positives = 141/290 (48%), Gaps = 15/290 (5%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  L  Y+ EI +  +L  ++E  LAK   E GD++A  R+V ++LRLVV IA GY G G
Sbjct: 15  QSPLETYLREINETALLSAKDEKDLAKLIGE-GDVNARDRMVRANLRLVVNIARGYTGKG 73

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L + +++ EGN+GL++AV+ FDP  G R +TY+ +WIK +++  ++     ++I   A  
Sbjct: 74  LGLQDLIEEGNLGLLRAVEGFDPAMGTRFSTYASYWIKQSIKRALINCAKTIRIP--AYM 131

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
             L    RR    L         PE    IA+ L + + ++  +   +    S       
Sbjct: 132 VELLSKWRRATNRLTEELGRTPTPE---EIARVLGLPKKKLPIIKKAIKIYNS--TPQTD 186

Query: 193 SDKNSSQWQDWLVYDH-DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE- 250
              +     + ++ D     E  ++E ++ KN   ML      ++ RE  +   R   E 
Sbjct: 187 QADSGWSLGEMVMDDRLKNPEDEMVEHDDLKNVMQMLK----TMDGREATVLRMRFGLEG 242

Query: 251 -NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQK 299
            +P TL+ +  +  ++RERVRQIE  A  K+ E +Q   E     P  ++
Sbjct: 243 MDPHTLKEIGEKLGLTRERVRQIETEALGKLAEGLQDPRERELEGPFRRR 292


>gi|294674467|ref|YP_003575083.1| RNA polymerase sigma-70 factor [Prevotella ruminicola 23]
 gi|294473044|gb|ADE82433.1| RNA polymerase sigma-70 factor [Prevotella ruminicola 23]
          Length = 290

 Score =  196 bits (499), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 78/280 (27%), Positives = 138/280 (49%), Gaps = 12/280 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKI 64
           SI       L +Y+ EI + P++   EE  LA+  R  G     A  RLVT++LR VV +
Sbjct: 9   SITNRSSEALDKYLVEIGRQPLVTIDEEIELAQAIRRGGPEGEKAKERLVTANLRFVVSV 68

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y+  GL +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I     +V
Sbjct: 69  AKQYQHQGLTLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQSRIV 128

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           ++    +       L ++   +      + +   V  +A+   + ES++       +   
Sbjct: 129 RLPLNQS-----GALSKINQEINKFEQQHQRRPSVTELAELTQIEESKIEQTAKADSHHM 183

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           S++A     D NS    D L    D +   L++ E   +  + + R  +VL  RE +I +
Sbjct: 184 SIDAPFGEDDDNS--MADMLSSGEDTRTDKLVDYESLTSDLDNVLR--NVLKDRELKIVK 239

Query: 245 ARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
                      LE + +E  ++RERVRQI  ++  K+ +S
Sbjct: 240 ECFGIGCQERGLEEIGAEMGLTRERVRQIREKSITKLHDS 279


>gi|261879259|ref|ZP_06005686.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           bergensis DSM 17361]
 gi|270334090|gb|EFA44876.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           bergensis DSM 17361]
          Length = 291

 Score =  196 bits (499), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 76/282 (26%), Positives = 144/282 (51%), Gaps = 11/282 (3%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRL 60
           +   +I       L RY+ EI + PML   EE +LA+   + G     A  RLV+ +LR 
Sbjct: 5   KITKNITSRNSEALDRYLSEIAREPMLSPDEEAMLAQAIHKGGPEGDRARDRLVSGNLRF 64

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y+  G+ + ++++EGN+GL++A +KFD  RGF+  +Y++WWI+ ++ E +   
Sbjct: 65  VVSVAKQYQHQGISLIDLINEGNMGLVKAAEKFDETRGFKFISYAVWWIRQSIMEALAVK 124

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
             +V++    NQ  ++  + R     ++    + +      +A+ L V E+++ +     
Sbjct: 125 SRIVRMP--LNQVGIYGKVIR---TTESFLQEHGRVPSNHELAEILQVEEAQITAAMSAG 179

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           A   S++A +  +D++ S        D   +    ++KE      N L R   VL+ RE+
Sbjct: 180 ARATSIDAPLG-NDEDGSMADMLASDDSGMKSDSSLDKESMNQFINDLLR--EVLSAREQ 236

Query: 241 RIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           RI +          +LE ++    ++RER+RQ+  +A +K++
Sbjct: 237 RIIKESFGIGVMEKSLEEIADSMGMTRERIRQVREKALRKIR 278


>gi|114776576|ref|ZP_01451621.1| RNA polymerase sigma factor [Mariprofundus ferrooxydans PV-1]
 gi|114553406|gb|EAU55804.1| RNA polymerase sigma factor [Mariprofundus ferrooxydans PV-1]
          Length = 281

 Score =  196 bits (499), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 101/268 (37%), Positives = 158/268 (58%), Gaps = 11/268 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             L R+  E+R+IP L+++EE  LA++++   DL++  +L+ ++L +V  IA  YR +GL
Sbjct: 11  TSLDRFYQELRRIPKLDREEEDALARKWQRDHDLASVQQLINANLHVVAAIAREYRHFGL 70

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P  +++ EG +GLMQAVK+FDP+RGFRL TY+ +WI+A++ ++ILRSWS+VK+GT   Q+
Sbjct: 71  PEEDLIQEGTLGLMQAVKRFDPDRGFRLKTYAAYWIRASIHDFILRSWSIVKMGTNKLQR 130

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR-LAGDESLNALINS 192
           R+F  L++ +  + A+    L       +A +  VS      +    L  D S++     
Sbjct: 131 RIFAGLQKAECAIAALEGRGL-----EGVASQYGVSGESYQQIAASFLRRDYSID----- 180

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
           SD         L    D  EQ L+ K+ +      L ++M  L+ R+R I   R L E P
Sbjct: 181 SDATEDGNIIELPAPGDTPEQALVAKDWQSFTTMQLKQAMEALSERDRNIIRQRYLVEPP 240

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKV 280
            TL+ LS +  +S ERVRQ+EARA KK+
Sbjct: 241 STLKELSEDLGISIERVRQLEARAMKKI 268


>gi|149907981|ref|ZP_01896649.1| sigma S (sigma 38) factor of RNA polymerase, major sigma
           factorduring stationary phase [Moritella sp. PE36]
 gi|149808987|gb|EDM68918.1| sigma S (sigma 38) factor of RNA polymerase, major sigma
           factorduring stationary phase [Moritella sp. PE36]
          Length = 284

 Score =  196 bits (499), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 77/276 (27%), Positives = 138/276 (50%), Gaps = 12/276 (4%)

Query: 9   IVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           + N    L  Y+ ++ K   +L K++EY  A    E GD  A  R++ S+LRLV+ IA  
Sbjct: 3   LFNESSALDLYMQQVNKTSVLLTKEQEYDTAIAVHE-GDQKARQRMIQSNLRLVINIAKR 61

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y+   L + +++ EGN GL+ AV+KFD  +GFR +TY++WWIK  ++ +I+     +++ 
Sbjct: 62  YQHTSLSLVDIIQEGNTGLIHAVEKFDATKGFRFSTYAVWWIKNNIERFIMNQSRTIRVP 121

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
               +       R LK   + + D     + +  IA  L +   +V+++      + SL+
Sbjct: 122 IHIGK----TYKRILKNAREKVLDLKCNND-LKKIAINLELEFDDVVNVLSYYFTEASLD 176

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             I + + +++   D +    D       ++ E+ +  + L   ++ L  R+R I E R 
Sbjct: 177 KTIATKNDSNTALVDLI---EDSSICKPNDEIEKTDTSSYLITVLNHLCDRDREIIELRF 233

Query: 248 LQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
               E P TL  +     +SRERVRQI   + +K++
Sbjct: 234 GLGREEPQTLNAIGERLFMSRERVRQIITASLQKIK 269


>gi|148240795|ref|YP_001226182.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp. WH
           7803]
 gi|147849334|emb|CAK24885.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 7803]
          Length = 376

 Score =  196 bits (499), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 77/238 (32%), Positives = 117/238 (49%), Gaps = 13/238 (5%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            R++ ++LRLVV +A  Y+  G+ + ++V EG +GL +AV+KFDP RGFR +TY+ WWI+
Sbjct: 138 DRMIQANLRLVVAVAKKYQQRGMELLDLVQEGTLGLERAVEKFDPTRGFRFSTYAYWWIR 197

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
             +   I      +++     +K     L R+K   Q I     +   V  +AK+L VSE
Sbjct: 198 QGITRAIATQSRTIRLPVHITEK-----LNRIKRVQQEIASEQGRLASVSDLAKELGVSE 252

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
             V     R+    SL   +       +Q  D L   H   EQ L       +    L  
Sbjct: 253 DTVRQTLARVPRSVSLETRV--GKDQDTQLGDLLEDGHATPEQTLTRDALHDD----LEH 306

Query: 231 SMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  LNPRE  +  +R   E+  P TL  +     +SRERVRQIE RA  K+++  ++
Sbjct: 307 LLDELNPREAEVIRSRFGLEDDTPRTLAEIGEAMALSRERVRQIETRALLKLRQPQRR 364



 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 13/55 (23%), Positives = 26/55 (47%), Gaps = 6/55 (10%)

Query: 11 NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           G   L  Y+ +I ++ +L  +EE  L+++ ++        RL+     L  +IA
Sbjct: 17 GGNDLLRLYLQDIGRVDLLTSEEEVTLSRQVQQ------RERLLVQERDLSTRIA 65


>gi|72383045|ref|YP_292400.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. NATL2A]
 gi|72002895|gb|AAZ58697.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. NATL2A]
          Length = 335

 Score =  196 bits (499), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 61/309 (19%), Positives = 130/309 (42%), Gaps = 52/309 (16%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------------------- 43
           +  Y+ +I ++P+L  ++E  L ++ ++                                
Sbjct: 28  VRSYLRDIGRVPLLSHEQEITLGRQVQDLVSLENLETELESDLGEKPDINFFADKAGISP 87

Query: 44  -------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                       A  R+V ++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP 
Sbjct: 88  IQLKKKLKSGRRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPT 147

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RG++ +TY+ WWI+  +   I      +++     +      L +LK   + ++    + 
Sbjct: 148 RGYKFSTYAYWWIRQGITRAIAEKSRSIRLPIHITE-----MLNKLKKGQRELSQELSRT 202

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
             +  +++ + + E++V  +  R     SL   I   D   +   D L  + D    +  
Sbjct: 203 PTLKELSEYVELPETDVKDLMSRAGQPVSLETKI--GDGEDTILLDLLSNEID----MPS 256

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEA 274
           E+ E    +  L   +  L   + R+   R     ++P++L  +     +SR+RVR +E 
Sbjct: 257 EQIESDCMKGDLETLLEQLPELQNRVLRMRYGIDGDDPMSLTGIGRVLGISRDRVRNLER 316

Query: 275 RAFKKVQES 283
              + ++++
Sbjct: 317 DGLRGLRKT 325


>gi|172035517|ref|YP_001802018.1| group 2 sigma-70 RNA polymerase sigma factor E [Cyanothece sp. ATCC
           51142]
 gi|171696971|gb|ACB49952.1| group 2 sigma-70 RNA polymerase sigma factor E [Cyanothece sp. ATCC
           51142]
          Length = 374

 Score =  196 bits (499), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 77/315 (24%), Positives = 134/315 (42%), Gaps = 53/315 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAK-------------------------------- 39
            +  +  +  E+ + P+L  +EE  LA                                 
Sbjct: 59  SDDTVGAFFKEMSRYPLLNAEEEVELAHHVQFLVQAEETRQQLQEALQHSPSKAEWAKAM 118

Query: 40  --------RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                    +R H   +A  +++ S+LRLVV IA  Y   G+P  +++ EG IGL +A +
Sbjct: 119 GFETQKQFEHRLHRGRTAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAE 178

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFDP +G++ +TY+ WWI+ A+   I      +++     +K     L +LK   + +  
Sbjct: 179 KFDPNKGYKFSTYAYWWIRQAITRTIANDARTIRLPIHVVEK-----LNKLKKAQRVLKQ 233

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +      +A +L VS S++  +        SLN  +   +   ++  D L    D  
Sbjct: 234 KLQRNPNEKELADELEVSPSQLRQLLQLRRQSLSLNHRVGKGED--TELVDLL---EDQD 288

Query: 212 EQVLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRER 268
            Q+  E       R  ++  +  VL  RE+ +   R       P TLE +   F +SRER
Sbjct: 289 LQLPEELMNEGMLRYEVSAVLSDVLTQREKDVISLRYGLCTSQPHTLEEVGGIFNLSRER 348

Query: 269 VRQIEARAFKKVQES 283
           VRQI+++A +K++  
Sbjct: 349 VRQIQSKAMRKLRRP 363


>gi|126660003|ref|ZP_01731125.1| RNA polymerase sigma factor [Cyanothece sp. CCY0110]
 gi|126618681|gb|EAZ89428.1| RNA polymerase sigma factor [Cyanothece sp. CCY0110]
          Length = 297

 Score =  196 bits (499), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 63/289 (21%), Positives = 135/289 (46%), Gaps = 29/289 (10%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG------------------DLSAAHRLVT 55
             +  Y+  I K P+L   EE  LA+  +                        A  +++ 
Sbjct: 8   DTVRHYLQSIGKTPLLSGAEEIKLAEEIQAMLPLLEKEELNKEEKKIVVIGQRARDKMIQ 67

Query: 56  SHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQE 115
           ++LRLVV IA  Y   GL + +++ EG++GL++ V+KFDP RG++ +TY+ WWI+  +  
Sbjct: 68  ANLRLVVSIAKKYLNSGLSLLDLIQEGSLGLIRGVEKFDPSRGYKFSTYAYWWIRQGITR 127

Query: 116 YILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
            I      +++    N+     NL + +  ++ +T    +      IA+ ++++  ++  
Sbjct: 128 AIAEQSRTIRLPIHINE-----NLNKYRKSIRELTLKLGRKPTQQEIAENMDITVDKLRF 182

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
           +       +S +  I   D+N+++    L  +        ++++E+    + + R +  L
Sbjct: 183 LQQAAFKTKSRSLNIVI-DENNTELGQLLPDEEGVSPSDFVKQQEK---ISQINRMLENL 238

Query: 236 NPRERRIFEARRLQENPVTL--ENLSSEFEVSRERVRQIEARAFKKVQE 282
           +PR++ +   R    +   L  + +  +  +S ER RQI +RA + +++
Sbjct: 239 SPRQKEVIILRFGLRDGKQLSYKAIGEQCGISHERARQIYSRALRILRK 287


>gi|87123422|ref|ZP_01079273.1| Putative type II alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9917]
 gi|86169142|gb|EAQ70398.1| Putative type II alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9917]
          Length = 376

 Score =  196 bits (499), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 74/249 (29%), Positives = 117/249 (46%), Gaps = 13/249 (5%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           + +      A  R++ ++LRLVV +A  Y+  GL + ++V EG +GL +AV+KFDP RGF
Sbjct: 127 KAQLRDGRRARDRMIAANLRLVVTVAKKYQQRGLELLDLVQEGTLGLERAVEKFDPTRGF 186

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           R +TY+ WWI+  +   I      +++     +K     L R+K   Q I     +   +
Sbjct: 187 RFSTYAYWWIRQGITRAIATQSRTIRLPVHVTEK-----LNRIKRVQQEIASQEGRIATL 241

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +A+KL +SE  V     R+    SL   +    +  +Q  D L       EQ L    
Sbjct: 242 TDLAQKLGLSEETVRLTLMRVPRSVSLE--LRVGKEQDTQLGDLLEDGKATPEQELTRDA 299

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
              +    L   +  L  RE  +   R   +N  P TL  +     +SRERVRQIE RA 
Sbjct: 300 LHHD----LEHLLDELTDREAAVIRLRFGLDNDTPCTLAQIGETMALSRERVRQIETRAL 355

Query: 278 KKVQESIQK 286
            K+++  ++
Sbjct: 356 LKLRQPQRR 364



 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 13/47 (27%), Positives = 24/47 (51%), Gaps = 1/47 (2%)

Query: 12 GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHR-LVTSH 57
          G   L  Y+ +I ++ +L  +EE +LA++ +    L    R L  +H
Sbjct: 18 GNDLLRLYLQDIGRVNLLSNEEEVLLARQVQRREQLLRQERELAEAH 64


>gi|113475621|ref|YP_721682.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
 gi|110166669|gb|ABG51209.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
          Length = 410

 Score =  196 bits (499), Expect = 3e-48,   Method: Composition-based stats.
 Identities = 68/250 (27%), Positives = 131/250 (52%), Gaps = 14/250 (5%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           +   + A H++++++LRLVV IA  Y+  G+ + +++ EG +GL +AV+KFDP+RG+R +
Sbjct: 165 QTEGIEARHQMISTNLRLVVSIAKKYQNRGVELLDLIQEGTLGLERAVEKFDPQRGYRFS 224

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+  +   I      +++    ++K     L ++K   Q I        +V  I
Sbjct: 225 TYAYWWIRQGITRAIATQSRTIRLPIHVSEK-----LNKIKKVQQKIFQEKGYTAKVEEI 279

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A++L ++ ++V  +  ++    SL   +       ++  + L       E++LI    R+
Sbjct: 280 ARELKITAAQVREVLVKIPHSVSLETKV--GRDRDTELGELLETKDASPEEMLI----RE 333

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKV 280
           +    L   +  L  RER +   R   E+    +L  ++S  ++SRERVRQIE +A  K+
Sbjct: 334 SLVQALKELLLDLTQRERYVITMRYGLEDGRACSLSEIASALKLSRERVRQIEVKALHKL 393

Query: 281 QES-IQKQVE 289
           ++   + Q++
Sbjct: 394 RQPKFRNQIQ 403


>gi|21219415|ref|NP_625194.1| RNA polymerase principal sigma factor HrdC [Streptomyces coelicolor
           A3(2)]
 gi|256789543|ref|ZP_05527974.1| RNA polymerase principal sigma factor HrdC [Streptomyces lividans
           TK24]
 gi|289773432|ref|ZP_06532810.1| RNA polymerase principal sigma factor hrdC [Streptomyces lividans
           TK24]
 gi|123520|sp|P18184|HRDC_STRCO RecName: Full=RNA polymerase principal sigma factor hrdC
 gi|48741|emb|CAA37173.1| unnamed protein product [Streptomyces coelicolor A3(2)]
 gi|6562877|emb|CAB62686.1| RNA polymerase principal sigma factor HrdC [Streptomyces coelicolor
           A3(2)]
 gi|289703631|gb|EFD71060.1| RNA polymerase principal sigma factor hrdC [Streptomyces lividans
           TK24]
          Length = 339

 Score =  196 bits (499), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 71/307 (23%), Positives = 133/307 (43%), Gaps = 42/307 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------------------HG 45
           L +Y+ +I   P+L  ++E  LA R                                 H 
Sbjct: 39  LGQYLTQIGATPLLTAEDEVRLATRIEAGVRAREELETADTGEPAPTPRRRRTLEETVHD 98

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
              A   +V ++LRLVV +A  +   GLP+ +V+ EGN+GL++AV+KFD  +GF+ +TY+
Sbjct: 99  GQEAKDHMVRANLRLVVSMAKRHAHRGLPLLDVIQEGNLGLIRAVEKFDHTKGFKFSTYA 158

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
            WWI+ A++  +      V++     ++     L +++  L+A  D     E+V A   +
Sbjct: 159 TWWIRQAIERGLATHARTVRLPVHVVEQ--LQKLAKVERKLRAGLDREPTTEEVAA---E 213

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
             +   +V+ +        SL+  +   +   +   D +      +   + E +      
Sbjct: 214 SGIDVDKVVWLRRVGRDAVSLDTPV--DETGDTVVGDLIPDTEVLRAPEVAEFQALA--- 268

Query: 226 NMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             L  ++  L PRE  I   R    +  P TL+ ++    ++RERVRQ+E  +   ++  
Sbjct: 269 AELREAVGTLAPRESLILSLRYGLHDGRPRTLQQVAQHVGLTRERVRQLEKESLAHLRAP 328

Query: 284 IQKQVEL 290
             ++  L
Sbjct: 329 ENRERLL 335


>gi|124026787|ref|YP_001015902.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. NATL1A]
 gi|123961855|gb|ABM76638.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. NATL1A]
          Length = 335

 Score =  196 bits (499), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 61/309 (19%), Positives = 130/309 (42%), Gaps = 52/309 (16%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------------------- 43
           +  Y+ +I ++P+L  ++E  L ++ ++                                
Sbjct: 28  VRSYLRDIGRVPLLSHEQEITLGRQVQDLVVLENLETELESDLGEKPDINFFADKAGLSP 87

Query: 44  -------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                       A  R+V ++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP 
Sbjct: 88  IQLKKKLKSGRRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPT 147

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RG++ +TY+ WWI+  +   I      +++     +      L +LK   + ++    + 
Sbjct: 148 RGYKFSTYAYWWIRQGITRAIAEKSRSIRLPIHITE-----MLNKLKKGQRELSQELSRT 202

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
             +  +++ + + E++V  +  R     SL   I   D   +   D L  + D    +  
Sbjct: 203 PTLKELSEYVELPETDVKDLMSRAGQPVSLETKI--GDGEDTILLDLLSNEID----MPS 256

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEA 274
           E+ E    +  L   +  L   + R+   R     ++P++L  +     +SR+RVR +E 
Sbjct: 257 EQIESDCMKGDLETLLEQLPELQNRVLRMRYGMDGDDPMSLTGIGRVLGISRDRVRNLER 316

Query: 275 RAFKKVQES 283
              + ++++
Sbjct: 317 DGLRGLRKT 325


>gi|328947378|ref|YP_004364715.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           succinifaciens DSM 2489]
 gi|328447702|gb|AEB13418.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           succinifaciens DSM 2489]
          Length = 283

 Score =  196 bits (498), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 68/267 (25%), Positives = 130/267 (48%), Gaps = 16/267 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           +++EI+KIP+L   EE  LA R    GD +A  +L+TS++R V+KIA  Y   GL   ++
Sbjct: 15  HLNEIKKIPLLTNDEEIQLATRAA-AGDKAARDKLLTSNMRFVIKIASQYLNKGLEYEDL 73

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           +SEG +GLM+A+  FD  +G+   +Y++WWI+ ++ + I+     +++    +       
Sbjct: 74  ISEGYLGLMKALDHFDVSKGYHFISYAVWWIRQSIMKAIVDFGRPIRLPVNKD-----AE 128

Query: 139 LRRLKGHLQAITDNNLKP--EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
           L  +K    ++  +  K   E++  +A KL +++  +  M        SL++ I+     
Sbjct: 129 LTEIKRACHSVNPHGKKSEEEELEEVALKLGMTKHHIREMLNISQEMISLDSPISGDSDT 188

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVT 254
           +      LV           +     + +  + ++   L+ +   +   R     +   T
Sbjct: 189 A------LVDTVSAGTFTPEDAAIDASLKTEIDKAFVGLDKKSVEVLNMRYGLNGQGERT 242

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQ 281
           L+ +  +  +SRERVRQIE  A  K++
Sbjct: 243 LKEVGEKMNLSRERVRQIEKHAIAKIR 269


>gi|72080402|ref|YP_287460.1| RNA polymerase sigma factor [Mycoplasma hyopneumoniae 7448]
          Length = 489

 Score =  196 bits (498), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 71/293 (24%), Positives = 133/293 (45%), Gaps = 20/293 (6%)

Query: 6   MSIIVNGEIGLSRYIHEIRKI-PMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVV 62
           ++ + +    +  Y+  I K   +L  +EE  LAK+ +  G     A   L+  +LRLVV
Sbjct: 198 LNKLTDTSDMIKWYMRWIGKYGKLLTAEEERELAKKMKIKGRIGKKARDTLIKRNLRLVV 257

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
             A  Y+  GL   +++SEGN+G+++AV K+D  RGF+ +TY+ WWI+ A+   +     
Sbjct: 258 NSAKRYKNRGLGFIDLISEGNLGIIKAVAKYDYTRGFKFSTYATWWIRQAITRAVADQAR 317

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           L++I     +      + +++  LQ     N   E++         S  ++  +      
Sbjct: 318 LIRIPVHMVE--TINKINKVERELQQEKGLNPTAEEISERLGG-EFSPDKIRYIKKINID 374

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS-VLNPRERR 241
             SL+  I    +  S + D++    D      ++   R+ +  +L   +   L+  ER 
Sbjct: 375 PISLDKAI--GKEEDSSFSDFI---KDENMISPVDYAIREEKAKVLLEMIDSTLDYDERD 429

Query: 242 IFEARRLQE--------NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             + R               + E L++   V++ERVRQIEA+  KK++   ++
Sbjct: 430 FIKRRYGVGTNDEGIPYQAHSFEELAAMRRVTKERVRQIEAKILKKLRTPHRR 482


>gi|42561001|ref|NP_975452.1| RNA polymerase sigma-A factor [Mycoplasma mycoides subsp. mycoides
           SC str. PG1]
 gi|42492498|emb|CAE77094.1| RNA polymerase sigma-A factor [Mycoplasma mycoides subsp. mycoides
           SC str. PG1]
          Length = 522

 Score =  196 bits (498), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 70/326 (21%), Positives = 136/326 (41%), Gaps = 65/326 (19%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSA---AHRLVTSHLRLVVKIAMGYRGYG 72
           +  Y ++I + P+L K++E + AK              ++L+ S+L+LV+ +A  +   G
Sbjct: 187 IKTYFYKIGQAPILTKEQEIIYAKMAVSDDPEDVQEGRNKLIESNLKLVISVARKHLNRG 246

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L  ++++ EGNIGLM+AV KF+ E+GF+ +TY+ WWI+ A+   I      ++I     +
Sbjct: 247 LDFADLIEEGNIGLMKAVDKFEYEKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE 306

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN--VSESEVISMNCRLAGDESLNALI 190
                 + +L    + +T    +      IA ++   ++  +VI +        SL    
Sbjct: 307 -----TINKLARVERQLTQELGREPNADEIANRVGEGITGDKVIEIKKLSIEPVSLEKPF 361

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM----------------------- 227
              D++ + + D++            EK+  K   +                        
Sbjct: 362 --GDEDDTHFGDFVEDKDMVSPNEYTEKKILKEVMDKVFEDMPPREEKVIRMRYGIVPTR 419

Query: 228 ------------------LTRSMSVLN-----PRER------RIFEARRL-QENPVTLEN 257
                             L +++  L+     P E+      +I        ++  TLE 
Sbjct: 420 LRTLLRLTQECNDTNAKELKQAIEELDIHLDTPIEKVRKFNNQIINNNLAKYDSARTLEE 479

Query: 258 LSSEFEVSRERVRQIEARAFKKVQES 283
           +  E  V+RER+RQIEA+  +K+++ 
Sbjct: 480 VGKELNVTRERIRQIEAKTIRKLKQP 505


>gi|108760621|ref|YP_631554.1| RNA polymerase sigma-B factor [Myxococcus xanthus DK 1622]
 gi|108464501|gb|ABF89686.1| RNA polymerase sigma-B factor [Myxococcus xanthus DK 1622]
          Length = 246

 Score =  196 bits (498), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 100/233 (42%), Positives = 147/233 (63%), Gaps = 4/233 (1%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           +VT++LR VVK+A  YR YG+ +S+++ EGNIGLM+AV+KFDP++G RL +Y++WWI+A 
Sbjct: 1   MVTANLRFVVKVAYEYRSYGIKMSDLIQEGNIGLMKAVQKFDPDKGIRLISYAVWWIRAY 60

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +Q YIL+SWSLVK+GTT  Q++LFF+L R +  L+    +      V  IA++L+V   E
Sbjct: 61  IQNYILKSWSLVKLGTTQAQRKLFFSLARTRRELEKF-GSGDAAVNVDDIARRLHVKPGE 119

Query: 173 VISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           V  M  R+ G D SL+A +     NS    D++V     Q+    +KEE       +  +
Sbjct: 120 VREMEQRMGGRDLSLDAPMGEDGGNSH--VDFVVSAAAPQDDEFADKEEAGLINARVRTA 177

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +  L+PRER I E R + E P+TL+ L   F  SRER RQ+E RA  K++  +
Sbjct: 178 LMRLDPRERFIIEQRVMNERPMTLKELGEHFGFSRERARQLEIRAKDKLKSEL 230


>gi|166363676|ref|YP_001655949.1| group 2 RNA polymerase sigma factor [Microcystis aeruginosa
           NIES-843]
 gi|166086049|dbj|BAG00757.1| group 2 RNA polymerase sigma factor [Microcystis aeruginosa
           NIES-843]
          Length = 414

 Score =  196 bits (498), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 69/238 (28%), Positives = 122/238 (51%), Gaps = 13/238 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A  +++ ++LRLVV +A  Y+  GL + +++ EG +GL +AVKKFDP +G+R +TY+ W
Sbjct: 174 RAKEQMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVKKFDPTKGYRFSTYAYW 233

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+  M   I     ++++     +K     L R+K   + I+    +   V  IA++L 
Sbjct: 234 WIRQGMTRAIATKSQIIRLPVHITEK-----LNRIKKAQRKISQMRGRTATVEEIAQELA 288

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++   V  +   +    SL   I    +  ++  D L  +    E   + +  +++ R +
Sbjct: 289 LTPEAVRELLMTVPRSVSLE--IKVGKEKDTELLDLLEIEAVSSENHFVYESLQRDIREL 346

Query: 228 LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           L      L  RER + E R   L     +L ++    E+SRERVRQIE +A +K+++S
Sbjct: 347 LAD----LTAREREVIELRYGFLDGKSHSLADIGRTLELSRERVRQIELKALQKLRQS 400


>gi|57864855|gb|AAW57030.1| putative group 2 RNA polymerase sigma factor [Cyanothece sp. ATCC
           51142]
          Length = 368

 Score =  196 bits (498), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 77/315 (24%), Positives = 134/315 (42%), Gaps = 53/315 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAK-------------------------------- 39
            +  +  +  E+ + P+L  +EE  LA                                 
Sbjct: 53  SDDTVGAFFKEMSRYPLLNAEEEVELAHHVQFLVQAEETRQQLQEALQHSPSKAEWAKAM 112

Query: 40  --------RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                    +R H   +A  +++ S+LRLVV IA  Y   G+P  +++ EG IGL +A +
Sbjct: 113 GFETQKQFEHRLHRGRTAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAE 172

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFDP +G++ +TY+ WWI+ A+   I      +++     +K     L +LK   + +  
Sbjct: 173 KFDPNKGYKFSTYAYWWIRQAITRTIANDARTIRLPIHVVEK-----LNKLKKAQRVLKQ 227

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +      +A +L VS S++  +        SLN  +   +   ++  D L    D  
Sbjct: 228 KLQRNPNEKELADELEVSPSQLRQLLQLRRQSLSLNHRVGKGED--TELVDLL---EDQD 282

Query: 212 EQVLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRER 268
            Q+  E       R  ++  +  VL  RE+ +   R       P TLE +   F +SRER
Sbjct: 283 LQLPEELMNEGMLRYEVSAVLSDVLTQREKDVISLRYGLCTSQPHTLEEVGGIFNLSRER 342

Query: 269 VRQIEARAFKKVQES 283
           VRQI+++A +K++  
Sbjct: 343 VRQIQSKAMRKLRRP 357


>gi|171322946|ref|ZP_02911628.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           MEX-5]
 gi|171091683|gb|EDT37240.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           MEX-5]
          Length = 498

 Score =  196 bits (498), Expect = 4e-48,   Method: Composition-based stats.
 Identities = 57/237 (24%), Positives = 102/237 (43%), Gaps = 12/237 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L  ++LRLVV IA  Y   GLP ++++ EGNIGL++A++++D  RGFR +TY+ WW
Sbjct: 261 ARTGLFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIERYDYRRGFRFSTYATWW 320

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   +      +++ T          L +L    +A             +A  +  
Sbjct: 321 IRQAITHALADLGRTIRVPTH-----TVDALNKLSRLARAHRQRAGTAATPAELAVHMGE 375

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +   +    S +  ++           +     D       +       R  +
Sbjct: 376 PVDKVRDLMAIVKEPVSADVPVSPEGD-----MTFADVAPDTTTPSPEDAAGAAQLRRTI 430

Query: 229 TRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           T  +  L PRE  + + R     +   +L ++  +  +S ERVRQIEA A  +++  
Sbjct: 431 TAVIDRLPPREAMVLKLRYGLHTDEGCSLRDIGRQLNLSAERVRQIEASALARLRAP 487


>gi|113953662|ref|YP_731106.1| type II alternative RNA polymerase sigma factor [Synechococcus sp.
           CC9311]
 gi|113881013|gb|ABI45971.1| Possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. CC9311]
          Length = 307

 Score =  196 bits (498), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 76/300 (25%), Positives = 132/300 (44%), Gaps = 37/300 (12%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------HGD--------------- 46
            LS ++ EI +  +L  ++E  L ++ +               GD               
Sbjct: 3   SLSAFLGEIGRHQLLTPEQELTLGRKVQAMAALTERCTMAGGEGDACVYSDEEKRTIKRG 62

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A ++++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG R +TY+ 
Sbjct: 63  EKAKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSTYAY 122

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   +      ++I    N+K     LR  K  L          EQ+    K  
Sbjct: 123 WWIRQGLNRALSTQSRTIRIPVNVNEK--LTRLRAAKARLMQSNGLAPSAEQLAECMKLP 180

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
                +++    R +   SL  ++ S   + S+  D L  D     +     E   +  N
Sbjct: 181 ISEVEDLLGCELR-SVTVSLQGVVKSK-SDPSELVDVLPSDEIPPMERAEIAERTDSAWN 238

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPV---TLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +L    S L P+ER I   R   +      TL  ++ +   SRE  RQ+  RA +K++++
Sbjct: 239 LLDN--SNLTPKERTIVMLRFGLDGSHEWRTLAEVARQMNCSREYCRQVVQRALRKLRKT 296


>gi|253583872|ref|ZP_04861070.1| RpoD family RNA polymerase sigma factor [Fusobacterium varium ATCC
           27725]
 gi|251834444|gb|EES63007.1| RpoD family RNA polymerase sigma factor [Fusobacterium varium ATCC
           27725]
          Length = 260

 Score =  196 bits (498), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 79/273 (28%), Positives = 145/273 (53%), Gaps = 16/273 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + +S YI +I   P+L  +EE  +A + R  GD  A  +LVTS+LRLV+ IA  Y   G+
Sbjct: 2   LDISEYIKDISTYPLLTPKEEREIAVKAR-SGDREAQEKLVTSNLRLVISIARKYTNMGI 60

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           PI +++ EGN+GL++AV+K++P++  R +TYS +WIK ++  YI  S  L++  +     
Sbjct: 61  PILDLIQEGNMGLIRAVEKYEPDKNIRFSTYSTFWIKQSILRYITSSRGLIRFPSYV--- 117

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
             +  + R+K ++Q   + N     +  I + L++ + E       +   E  N + N  
Sbjct: 118 --YDGISRMKKYVQDYKNKNSHCPSIDEICRSLDMKKKE---AERYIDVLEKGNGIGNEM 172

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQEN 251
                ++   ++YD   +++V+      K+    L + ++ L PRER +   R   L E 
Sbjct: 173 YGEMVEYCSSIIYDDTFEDEVIA-----KSSNIDLMKKVNKLPPREREVLIYRYGLLDEK 227

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +TL  +     +++ER+RQI+  A  +++E +
Sbjct: 228 VLTLGEIGQRMNLTKERIRQIQLEAIDRLREKL 260


>gi|218440090|ref|YP_002378419.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
 gi|218172818|gb|ACK71551.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7424]
          Length = 295

 Score =  196 bits (498), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 66/299 (22%), Positives = 142/299 (47%), Gaps = 32/299 (10%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLA-------------------KRYREHGDLSAAHRLV 54
             +  Y+ EI +IP+L  +EE  LA                   K+  E G + A  +++
Sbjct: 7   DPVRSYLQEIGRIPLLNSEEEVQLATKVQNMLPLLEKENLTAAEKKIVEQGQI-AKRKMI 65

Query: 55  TSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114
            ++LRLVV IA  Y+  GL + +++ EG++GL++AV+KFDP +G++ +TY+ WW++ A+ 
Sbjct: 66  QANLRLVVSIAKRYQRRGLSLLDLIQEGSLGLIRAVEKFDPSKGYKFSTYAYWWVRQAIT 125

Query: 115 EYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVI 174
             +      +++     +     NL +LK  ++ +T    +      +A+++ +   ++ 
Sbjct: 126 RALAEKSRTIRLPIHMTE-----NLNQLKKSVRELTGELGRKPNEQEVAQRMEIPVEKLR 180

Query: 175 SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV 234
            +   +   ++ +  I + D N ++  + L  +      + IE   +      +   +  
Sbjct: 181 EIRHAVYRTDAKSLNI-TLDDNQTELGEVLPDETS----LPIEFVSQWELVTKINDLLED 235

Query: 235 LNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           L PR+R I   R        ++ + +  +  +S ER RQ+  RA + +++   +  E++
Sbjct: 236 LPPRQREIITLRFGLQTGKRMSYKEIGRQCGISHERARQLLNRAMRTLKQKAFRLGEVA 294


>gi|161936260|ref|YP_115577.2| RNA polymerase sigma factor [Mycoplasma hyopneumoniae 232]
          Length = 489

 Score =  195 bits (497), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 71/293 (24%), Positives = 133/293 (45%), Gaps = 20/293 (6%)

Query: 6   MSIIVNGEIGLSRYIHEIRKI-PMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVV 62
           ++ + +    +  Y+  I K   +L  +EE  LAK+ +  G     A   L+  +LRLVV
Sbjct: 198 LNKLTDTSDMIKWYMRWIGKYGKLLTAEEERELAKKMKIKGRIGKKARDTLIKRNLRLVV 257

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
             A  Y+  GL   +++SEGN+G+++AV K+D  RGF+ +TY+ WWI+ A+   +     
Sbjct: 258 NSAKRYKNRGLGFIDLISEGNLGIIKAVAKYDYTRGFKFSTYATWWIRQAITRAVADQAR 317

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           L++I     +      + +++  LQ     N   E++         S  ++  +      
Sbjct: 318 LIRIPVHMVE--TINKINKVERELQQEKGLNPTAEEISERLGG-EFSPDKIRYIKKINID 374

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS-VLNPRERR 241
             SL+  I    +  S + D++    D      ++   R+ +  +L   +   L+  ER 
Sbjct: 375 PISLDKAI--GKEEDSSFSDFI---KDENMISPVDYAIREEKAKVLLEMIDSTLDYDERD 429

Query: 242 IFEARRLQE--------NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             + R               + E L++   V++ERVRQIEA+  KK++   ++
Sbjct: 430 FIKRRYGVGTNDEGIPYQAHSFEELAAMRRVTKERVRQIEAKILKKLRTPHRR 482


>gi|113474981|ref|YP_721042.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
 gi|110166029|gb|ABG50569.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
          Length = 496

 Score =  195 bits (497), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 65/318 (20%), Positives = 140/318 (44%), Gaps = 53/318 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRY------------------------------ 41
            E  +  Y  ++     L  +EE  LA +                               
Sbjct: 185 TEDSIQLYYKQVNSFARLHPEEEIHLAHQIDGLLALEKIYEKLEEKLNRSPNEIEWATEA 244

Query: 42  ---------REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                    R      A +++VT++LRLV  +A  Y+  GL   +++ EG IGL++A +K
Sbjct: 245 KMSKWELCDRLEQGRRAKNQMVTANLRLVTSVAKRYQNRGLDFQDLIQEGVIGLLRATEK 304

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY +WWI+ A+   I     +V++        L+  + ++K  ++ I+  
Sbjct: 305 FDHTKGYKFSTYGIWWIRQAITRAICDYSRIVRLPVY-----LYETISQIKKIVKQIS-I 358

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              P     +A ++ ++  ++  +        SL+  IN  +     +++ + ++ +   
Sbjct: 359 ECSPLTAEEVATRMEMTTEKLQFIIECAQETLSLDYPINKGEN--IIYKEMIKFNGETPT 416

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVR 270
           + + E   +++    +   +  L  RER + + R   ++    TL+ +   F ++RER+R
Sbjct: 417 KYVFENCLQED----VESVLKTLTERERNVLQMRFGLDDGQEKTLKEIGDTFNLTRERIR 472

Query: 271 QIEARAFKKVQESIQKQV 288
           QIEA+A +K+++  +  +
Sbjct: 473 QIEAKALRKLEDPKRNHI 490


>gi|311742672|ref|ZP_07716481.1| RNA polymerase principal sigma factor SigB [Aeromicrobium marinum
           DSM 15272]
 gi|311314300|gb|EFQ84208.1| RNA polymerase principal sigma factor SigB [Aeromicrobium marinum
           DSM 15272]
          Length = 320

 Score =  195 bits (497), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 65/306 (21%), Positives = 119/306 (38%), Gaps = 45/306 (14%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAK-------------------------------- 39
           G   +  Y+ EI + P+L+   E  L+K                                
Sbjct: 17  GRDSVGMYLAEIARTPLLDAGREVELSKTIEAGLFARHLLDTGRVGRAKGGAPKRATAEE 76

Query: 40  -RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
             +       A    + ++LRLVV IA  Y    +P+ ++V EGN GL++AV+KFD  +G
Sbjct: 77  LEWIAAEGERALQEFIQANLRLVVSIARKYGRSAMPMLDLVQEGNTGLIRAVEKFDYVKG 136

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           F+ +TY+ WW++ A+   I +   +V++     +      L ++    + +        +
Sbjct: 137 FKFSTYATWWVRQAITRGIAQQARVVRLPVHVVE-----ELNQVTAARRNLERTLGYDPE 191

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              I+ +L +    VI +        SL+  +   +   +   D +  +           
Sbjct: 192 PAEISAELGMDVDRVIDLLSWGRDHVSLDTPV--DEDGDTSLGDLIARETAPGPDS---S 246

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT--LENLSSEFEVSRERVRQIEARA 276
                 R M+ + +  L  RE  I  AR    +     L ++     +S ERVRQ+E  A
Sbjct: 247 MMSDATRGMIAQLIDHLGEREADIVRARYGLLDGRQQKLADIGKRHGISAERVRQLEREA 306

Query: 277 FKKVQE 282
             K++ 
Sbjct: 307 LAKLRR 312


>gi|320104603|ref|YP_004180194.1| RNA polymerase sigma-38 subunit RpoS [Isosphaera pallida ATCC
           43644]
 gi|319751885|gb|ADV63645.1| RNA polymerase, sigma 38 subunit, RpoS [Isosphaera pallida ATCC
           43644]
          Length = 277

 Score =  195 bits (497), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 80/270 (29%), Positives = 140/270 (51%), Gaps = 13/270 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  L  Y+ EI ++ +L  +EE  LA R  + GD +A  R+V ++LRLVV IA GY G G
Sbjct: 13  QSPLETYLREINEMALLSAEEEKELAARIAK-GDKTARERMVRANLRLVVNIARGYVGKG 71

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L + +++ EGN+GL++AV+ FDP+ G R +TY+ +WIK +++  ++ +   ++I   A  
Sbjct: 72  LALQDLIEEGNLGLLRAVEGFDPKVGTRFSTYASYWIKQSIKRALVNTAKPIRIP--AYM 129

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
             L    RR    LQ   D   +      IA +L + + ++  +   +     +  L+  
Sbjct: 130 VELLCKWRRAAIELQ---DRLGRTPTTDEIAHELRIPKKKLAIVKKAIK----VYNLVPQ 182

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN- 251
           SD+  S W    +   +      +E  E  N + ++ R +  ++ RE  +   R   ++ 
Sbjct: 183 SDQPESGWSLGDMLMDERTRPPDVEMVEADNLK-LVMRRLEEMDKREATVLRMRFGLDDQ 241

Query: 252 -PVTLENLSSEFEVSRERVRQIEARAFKKV 280
            P TL+ +  +  ++RERVRQIE  A  K+
Sbjct: 242 PPCTLKEIGEQLGLTRERVRQIENEALNKL 271


>gi|332708935|ref|ZP_08428906.1| RNA polymerase sigma factor, sigma-70 family//RpoD-like family
           [Lyngbya majuscula 3L]
 gi|332352477|gb|EGJ32046.1| RNA polymerase sigma factor, sigma-70 family//RpoD-like family
           [Lyngbya majuscula 3L]
          Length = 333

 Score =  195 bits (497), Expect = 5e-48,   Method: Composition-based stats.
 Identities = 65/305 (21%), Positives = 134/305 (43%), Gaps = 52/305 (17%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYRE----------------------------------- 43
           Y+HEI ++P+L  ++E V  K+ ++                                   
Sbjct: 29  YLHEIGRVPLLTHEQEIVYGKQVQQMMALLGEKATLAQELEREPTTEEWASYVNKSEAEL 88

Query: 44  ----HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                    A  +++ ++LRLVV IA  Y+   +   +++ EG +GL + V+KFDP RG+
Sbjct: 89  KKAIDQGTRAKRKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVEKFDPTRGY 148

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWI+ A+   I +    +++     +K     L ++K   + ++    +    
Sbjct: 149 KFSTYAYWWIRQAITRAIAQQARAIRLPIHITEK-----LNKIKKVQRELSQTLGRNATP 203

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IAK+L++  +++           SL+  +   D   ++  + L  D        +   
Sbjct: 204 TEIAKELDLEPAQIREYLSIARQPISLD--VRVGDNQDTELSELLEDDGL----TPVNYT 257

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
            +++ R  L   ++ L P++R +   R   E+   ++L  +     +SRERVRQ+E +A 
Sbjct: 258 TQESLRQDLNLLLAELTPQQREVLALRFGLEDGKELSLAKVGKRLNLSRERVRQLEHQAL 317

Query: 278 KKVQE 282
            +++ 
Sbjct: 318 AQLRR 322


>gi|195953303|ref|YP_002121593.1| putative RNA polymerase, sigma 70 family subunit [Hydrogenobaculum
           sp. Y04AAS1]
 gi|195932915|gb|ACG57615.1| putative RNA polymerase, sigma 70 family subunit [Hydrogenobaculum
           sp. Y04AAS1]
          Length = 311

 Score =  195 bits (497), Expect = 6e-48,   Method: Composition-based stats.
 Identities = 80/296 (27%), Positives = 136/296 (45%), Gaps = 37/296 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +++Y+  +  + +L  QEE   AKR +  GD  A   LV ++LR VV +A  Y GYG+P+
Sbjct: 10  INQYMKRVSSVKLLTPQEEKEFAKRAK-AGDKEALKALVEANLRFVVSVAKQYMGYGIPL 68

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT------ 129
           SE+++ GN+GL++A  +FDP++  +  +Y++WW++ A+ + + +    V+I         
Sbjct: 69  SELIAAGNLGLLEAATRFDPDKNVKFISYAVWWVRQAIMQALSQQTGAVRIPVKHSHLIS 128

Query: 130 ---ANQKRLFFNLRRLK---------------GHLQAITDNNLKPEQVVA---IAKKLNV 168
                   L   L R                    +  T      E++        K  V
Sbjct: 129 AVGLAYNELLKELEREPTYKEIADYINKKNIIREFKKETGFAPTEEELEQSMTQEHKYTV 188

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL-VYDHDGQEQVLIEKEERKNRRNM 227
           +E +V           SL+  +   D   + + D L + D D  E+ +I+    K     
Sbjct: 189 TEEDVKKCLQICKTPLSLDTPV--GDNPDTLFVDLLSISDTDEIEEGVIKDVLEKE---- 242

Query: 228 LTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           L   +S L  +ER++ E R       P+TL  +     +SRERVRQ+E RA KK++
Sbjct: 243 LHDIISKLPEKERKVLELRYGLNGNEPLTLREIGDALGISRERVRQLETRAIKKLR 298


>gi|78184480|ref|YP_376915.1| type II alternative RNA polymerase sigma factor [Synechococcus sp.
           CC9902]
 gi|78168774|gb|ABB25871.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. CC9902]
          Length = 309

 Score =  195 bits (497), Expect = 6e-48,   Method: Composition-based stats.
 Identities = 68/302 (22%), Positives = 131/302 (43%), Gaps = 37/302 (12%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------------------------H 44
              LS ++ EI +  +L  ++E +L ++ +                              
Sbjct: 3   SSSLSAFLGEIGRHQLLTPEQELMLGRKVQAMVAITEPCLIAGGTGPSCEYNDNQRFVIR 62

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
               A ++++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG R +TY
Sbjct: 63  RGERAKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSTY 122

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + WWI+  +   +      ++I    N+K     LR  K  +          EQ+     
Sbjct: 123 AYWWIRQGLNRALSTQSRTIRIPVNVNEK--LTKLRAAKARIMQRNGLTATGEQLAEFMN 180

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
                  ++++   R +   SL  ++ S   + S+  D L  D     +     E   + 
Sbjct: 181 VPLTEVEDLLACELR-SVTVSLQGIVKSK-SDPSELVDILPSDEIPPMERAEIAERSASV 238

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             +L+++   L P+E ++   R   +      TL  ++     SRE  RQ+  RA +K++
Sbjct: 239 WALLSKA--NLTPKEHKVVTLRFGLDGTNEWRTLAEVARHMNCSREYCRQVVQRALRKLR 296

Query: 282 ES 283
           ++
Sbjct: 297 KT 298


>gi|225621460|ref|YP_002722719.1| R polymerase sigma factor RpoD [Brachyspira hyodysenteriae WA1]
 gi|225216281|gb|ACN85015.1| R polymerase sigma factor RpoD [Brachyspira hyodysenteriae WA1]
          Length = 309

 Score =  195 bits (496), Expect = 6e-48,   Method: Composition-based stats.
 Identities = 80/306 (26%), Positives = 142/306 (46%), Gaps = 38/306 (12%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR---------EHGDLS--- 48
           M +K+++    G + +  Y+ +I +I  L K+EE  L +R           E+ D     
Sbjct: 1   MLKKDINQEYKGPVSV--YLKQIGEIRRLTKEEELDLWQRLEVCRNDRALLENNDDEESL 58

Query: 49  ------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                         H+LV S+LRLV+ IA  Y   G+P  +++ EGNIGL++AVK+F+ +
Sbjct: 59  KKIEEIDKEIDSIQHKLVKSNLRLVISIAKRYYNSGVPFIDIIDEGNIGLIEAVKRFEYK 118

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +GF+ +TY +WWIK ++ + I     +++        RL     +    L   T    + 
Sbjct: 119 KGFKFSTYGVWWIKQSIVKEISSKRHIIRFPMHIA--RLIKKSIQTSKTL---TQKLGRD 173

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
             +  I+K++ +    +  +        S+++   +SD N     D      D       
Sbjct: 174 PTIDEISKEMKIDRKTLSYIMIFTQDTASVDSFFRNSDNN-----DMTSIIEDKNFPSPH 228

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEA 274
           +K    + R+ LT ++  L+ +ER +  +R         TLE+   E  ++RERVRQI+ 
Sbjct: 229 QKAFMDSLRDTLTEALKCLDEKERTVIISRYGLYGKEAKTLEDTGKELNITRERVRQIQI 288

Query: 275 RAFKKV 280
           +A KK+
Sbjct: 289 KAIKKL 294


>gi|6463980|dbj|BAA86957.1| group 2 sigma factor RpoD3 [Synechococcus sp. PCC 7942]
          Length = 320

 Score =  195 bits (496), Expect = 7e-48,   Method: Composition-based stats.
 Identities = 73/322 (22%), Positives = 144/322 (44%), Gaps = 54/322 (16%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR--------------EHGDLS------- 48
                 +  Y+ EI ++P+L  +EE VL KR +              E GD         
Sbjct: 6   TPTSDLVRTYLREIGRVPLLTHEEEVVLGKRVQQWMKLQELRQTLQSEEGDRDPSDLEWA 65

Query: 49  -------------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
                              A  +++ ++LRLVV +A  Y    + + +++ EG IG+ + 
Sbjct: 66  AAAGLSIEELRQQQHLGEQAKRKMIEANLRLVVSVAKKYLKRNMDLLDLIQEGTIGMQRG 125

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V+KFDP +G+R +TY+ WWI+ A+   I      +++     +K     L ++K   + +
Sbjct: 126 VEKFDPTKGYRFSTYAYWWIRQAITRAIAEKARTIRLPIHITEK-----LNKIKKMQRQL 180

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
           +   L    +  +A  L+++ ++V     +     SL+  +   D   ++  D L  D  
Sbjct: 181 SQQ-LSTATLPELAAALDLTPAQVRDYLEKARHPLSLD--LRVGDNQDTELGDLLETDMQ 237

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRE 267
            + +   E   + + R  + R +  L  ++R++   R   E+   +TL ++    ++SRE
Sbjct: 238 RRRK---EFTLQASMRRDIDRLLDQLTEQQRQVIALRYGLEDGQVMTLASIGDRLQISRE 294

Query: 268 RVRQIEARAFKKVQESIQKQVE 289
           RVRQ+E  A   ++++ + QV+
Sbjct: 295 RVRQLEREALHTLRQA-RSQVQ 315


>gi|172037252|ref|YP_001803753.1| group 2 sigma-70 RNA polymerase sigma factor [Cyanothece sp. ATCC
           51142]
 gi|171698706|gb|ACB51687.1| group 2 sigma-70 RNA polymerase sigma factor [Cyanothece sp. ATCC
           51142]
          Length = 297

 Score =  195 bits (496), Expect = 7e-48,   Method: Composition-based stats.
 Identities = 65/293 (22%), Positives = 135/293 (46%), Gaps = 29/293 (9%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------HGDLSAAHRLVT 55
             +  Y+  I K P+L   EE  LA+  +                        A  +++ 
Sbjct: 8   DTVRHYLQSIGKTPLLSGPEEIKLAEEIQAMLPLLEKEALSKEEEKIVAKGQRARDKMIQ 67

Query: 56  SHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQE 115
           ++LRLVV IA  Y   GL + +++ EG++GL++ V+KFDP RG++ +TY+ WWI+  +  
Sbjct: 68  ANLRLVVSIAKKYLNSGLSLLDLIQEGSLGLIRGVEKFDPSRGYKFSTYAYWWIRQGITR 127

Query: 116 YILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
            I      +++    N+     NL + +  ++ +T    +      IA+ +++S  ++  
Sbjct: 128 AIAEQSRTIRLPIHINE-----NLNKYRKSIRELTLKLGRKPTQQEIAENMDISVDKLRF 182

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
           +       +S +  I   D+N ++    L  +        ++++E+    + + R +  L
Sbjct: 183 LQQAAFKTKSRSLNIVI-DENHTELGQLLPDEDSVSPSDFVKQQEK---ISQINRMLENL 238

Query: 236 NPRERRIFEARRLQENPVTL--ENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +PR++ +   R    +   L  + +  +  +S ER RQI +RA + +++   K
Sbjct: 239 SPRQKEVIILRFGLRDGKQLSYKAIGEQCGISHERARQIYSRALRILRKQSSK 291


>gi|78185801|ref|YP_378235.1| type II alternative RNA polymerase sigma factor [Synechococcus sp.
           CC9902]
 gi|78170095|gb|ABB27192.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. CC9902]
          Length = 377

 Score =  195 bits (496), Expect = 8e-48,   Method: Composition-based stats.
 Identities = 75/249 (30%), Positives = 121/249 (48%), Gaps = 13/249 (5%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           +        A   ++ ++LRLVV +A  Y+  G+ I ++V EG +GL +AV+KFDP RGF
Sbjct: 128 KLSLRNGRRAKDHMIQANLRLVVAVAKKYQQRGMEILDLVQEGTLGLERAVEKFDPTRGF 187

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           R +TY+ WWI+  M   I      +++     +K     L R+K   Q I  N  +   +
Sbjct: 188 RFSTYAYWWIRQGMTRAIATQSRTIRLPVHVTEK-----LNRIKRVQQEIASNEGRIASI 242

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +A++L +SE  V     R+    SL++ +       +Q  D +       E+ L   E
Sbjct: 243 ADLARELGISEDTVRQTLERVPRSVSLDSRV--GKDQDTQLGDLIEDGKATPEETLTHDE 300

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
              +    L   +  L PRE  +   R   E+  P TL  +  E ++SRERVRQIE RA 
Sbjct: 301 LHND----LEGLLDELTPREASVLRRRFGLEDDTPQTLAQIGEELKLSRERVRQIETRAL 356

Query: 278 KKVQESIQK 286
            K+++  ++
Sbjct: 357 LKLRQPQKR 365


>gi|56475838|ref|YP_157427.1| RNA polymerase sigma factor RpoS [Aromatoleum aromaticum EbN1]
 gi|56311881|emb|CAI06526.1| RNA sigma factor RpoS [Aromatoleum aromaticum EbN1]
          Length = 311

 Score =  195 bits (495), Expect = 9e-48,   Method: Composition-based stats.
 Identities = 82/270 (30%), Positives = 140/270 (51%), Gaps = 13/270 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L   EE  LA+R R  GD  A   ++  +LRLVV IA  Y   G+P+ ++
Sbjct: 44  YLNEIGANPLLTAAEEAALARRVR-TGDFPARQIMIERNLRLVVNIAKHYLNRGIPLLDL 102

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GLM A++KFDPERGFR +TY+ WWI+  ++  I+     +++       +    
Sbjct: 103 VEEGNLGLMHALEKFDPERGFRFSTYATWWIRQNIERAIMNQSRTIRLPVHV--VKELNQ 160

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           + R +  L+A  +     EQV   A +L+ S  EV ++        SL+A +      + 
Sbjct: 161 VLRAQRTLEASGNGEFTLEQV---AHRLDKSVDEVRAILALSEHTASLDAPLEI--DPTL 215

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLE 256
              + L  D        I+  E +    ++   + +LN ++R +   R   +    +TLE
Sbjct: 216 SIGESLADDQAEPPDTHIQDAEVE---KLIQEWIGMLNEKQRLVIRHRYGLDECEVMTLE 272

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L+S   ++RERVRQI+  A  +++ ++++
Sbjct: 273 ELASRLCLTRERVRQIQLEALGQLRRTVKR 302


>gi|87124019|ref|ZP_01079869.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9917]
 gi|86168588|gb|EAQ69845.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9917]
          Length = 308

 Score =  195 bits (495), Expect = 9e-48,   Method: Composition-based stats.
 Identities = 74/310 (23%), Positives = 137/310 (44%), Gaps = 37/310 (11%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------------------------HGD 46
            LS ++ EI +  +L  ++E  + ++ +                                
Sbjct: 4   SLSAFLGEIGRHQLLTPEQELTMGRKVQAMVAITDRCMLAGGEGPACDYSEDEKRVIKRG 63

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A ++++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG R +TY+ 
Sbjct: 64  EKAKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSTYAY 123

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   +      ++I    N+K     LR  K  L         PEQ+    K  
Sbjct: 124 WWIRQGLNRALSTQSRTIRIPVNVNEK--LTKLRAAKARLMQQHGQPANPEQLAEAMKIP 181

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
                ++++   R +   SL  ++ S   + S+  D L  D     +     E   +   
Sbjct: 182 LSEVEDLLACELR-SVTVSLQGIVKSK-ADPSELVDVLPSDELPPMERAEIAERTASAWT 239

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPV---TLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +L ++   L P+ER +   R   +      TL  ++     SRE  RQ+  RA +K++++
Sbjct: 240 LLEKA--NLTPKERTVVMLRFGLDGSHEWRTLAEVARHMSCSREYCRQVVQRALRKLRKT 297

Query: 284 IQKQVELSSS 293
             +Q  +SS+
Sbjct: 298 GIQQGLVSSA 307


>gi|332298226|ref|YP_004440148.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           brennaborense DSM 12168]
 gi|332181329|gb|AEE17017.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           brennaborense DSM 12168]
          Length = 332

 Score =  195 bits (495), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 75/308 (24%), Positives = 132/308 (42%), Gaps = 41/308 (13%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL------------------ 47
           M   V     LS Y+ +I +  +L  QEE   A   +EH                     
Sbjct: 24  MGRTVVDPDPLSLYLKQISRYKLLSVQEEQATAAAIQEHKSRIRQLKSGLLEPAENSPAY 83

Query: 48  -----------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                         ++++ ++LRLVV IA  Y+  GL + +++ EGNIGL++AV +F+P 
Sbjct: 84  EEIDRLERDLLVLKNKMIQANLRLVVSIAKRYQHRGLGLLDLIDEGNIGLIEAVDRFEPA 143

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           R  R +TY +WWI+ A+ + +     ++++        +   + +     + +T    + 
Sbjct: 144 RNCRFSTYGIWWIRQAIIKSLADKGRVIRVPVH-----MLNTINKCFFMAKLLTQEYGRE 198

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
                +A+ L V+  +V           SL    N  D NS++  D L    D   +  I
Sbjct: 199 PTTAELARFLCVTNEKVEDYIRLSQEMSSLET--NVDDDNSTRLGDLL---TDENGEAPI 253

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEA 274
           E+       + +   ++ L+ RE  I   R   +   P TL    +   ++RERVRQI+ 
Sbjct: 254 ERVFAAALTDTVNLVLNQLSEREMSIIRLRYGLDGKAPRTLTETGNVLGITRERVRQIQE 313

Query: 275 RAFKKVQE 282
           +  KK++E
Sbjct: 314 KTLKKLRE 321


>gi|28899327|ref|NP_798932.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus RIMD
           2210633]
 gi|28807551|dbj|BAC60816.1| RNA polymerase sigma factor RpoS [Vibrio parahaemolyticus RIMD
           2210633]
          Length = 319

 Score =  195 bits (495), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 69/262 (26%), Positives = 122/262 (46%), Gaps = 13/262 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           R+              Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVV
Sbjct: 41  REEFDASSKSLDATQLYLGEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLVV 99

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           KI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++    
Sbjct: 100 KISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTR 159

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            +++      K L   LR  +     ++           IA +L++   +V  M      
Sbjct: 160 TIRLPIHVV-KELNIYLRTAR----ELSQKLDHEPTAEEIAAQLDIPVEDVSKMLRLNER 214

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++  I           D +   ++   +V  + +   + ++ L   +  LNP+++ +
Sbjct: 215 ISSVDTPI--GGDGEKALLDIIPDANNSDPEVSTQDD---DIKSSLIHWLEELNPKQKEV 269

Query: 243 FEARR--LQENPVTLENLSSEF 262
              R   L   P TLE +    
Sbjct: 270 LARRFGLLGYEPSTLEEVGLRL 291


>gi|59714198|ref|YP_206973.1| sigma-Q factor RpoQ, quorum-sensing regulated RpoS-like sigma
           subunit [Vibrio fischeri ES114]
 gi|59482446|gb|AAW88085.1| sigma-Q factor RpoQ, quorum-sensing regulated RpoS-like sigma
           subunit [Vibrio fischeri ES114]
          Length = 294

 Score =  195 bits (495), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 76/295 (25%), Positives = 135/295 (45%), Gaps = 20/295 (6%)

Query: 1   MNRKNMSIIVNGEIGL----SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTS 56
           M    + + V  E GL    S Y+ EI +  +L  +EE   ++ Y++ GD+SA + L+ S
Sbjct: 1   MAYAKLDMRVCEEQGLNDSYSLYLKEINRYQLLTAEEELAYSRLYKK-GDVSARNTLIES 59

Query: 57  HLRLVVKIAMGYRGYGL---PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           +LRLVVK+A  YR        I +++ EGN+GL++A+ KF+PE G+R +TY++WWI+ ++
Sbjct: 60  NLRLVVKVANKYRKRNQTDLAILDIIEEGNLGLIKAIDKFNPELGYRFSTYAVWWIRESI 119

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
           +  +      V++       +      R    L            +    ++  +  S++
Sbjct: 120 ESALFNHSRTVRLPVHIT--KELNTYLRAARELSKSLKREPSIRDISTYCEEEQIKVSKI 177

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
           IS+          N L   S  +      +     + +         + N    L+  + 
Sbjct: 178 ISLIP--------NQLTCHSACSDELSPKFFELSSNNKALEPDSSLSQNNLEMNLSSWID 229

Query: 234 VLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            LN RE+ I   R         TLE+L  + ++S+ERVRQI++    K+    +K
Sbjct: 230 SLNYREKEIIINRYGLFGCKVKTLEDLGKDLDLSKERVRQIQSETLIKLNTIFKK 284


>gi|87123242|ref|ZP_01079093.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9917]
 gi|86168962|gb|EAQ70218.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9917]
          Length = 309

 Score =  194 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 71/316 (22%), Positives = 135/316 (42%), Gaps = 54/316 (17%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSA-------------------------- 49
           +  Y+ +I ++P+L  Q+E  L ++ +E  +L A                          
Sbjct: 1   MRSYLRDIGRVPLLSHQQEITLGRQVQELMELEALEAELRDQRGGEAVPAAELATAAGLS 60

Query: 50  --------------AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
                           R+V ++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP
Sbjct: 61  ALQLKRKLQAGRRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDP 120

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            RG++ +TY+ WWI+  +   I      +++     +      L +LK   + ++    +
Sbjct: 121 TRGYKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITE-----MLNKLKKGQRELSQELGR 175

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
              V  +A  + + E EV  + CR     SL   +   D + ++  + L  D     ++ 
Sbjct: 176 TPTVTELAGFVELPEEEVKDLMCRARQPVSLEMKV--GDGDDTELLELLAGDG----ELP 229

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIE 273
            E+ E +  +  L   +  L   +RR+   R     E P++L  +     +SR+RVR +E
Sbjct: 230 EEQVEVECLKGDLRDLLEQLPDLQRRVLRMRYGMDGEEPMSLTGIGRVIGISRDRVRNLE 289

Query: 274 ARAFKKVQESIQKQVE 289
                 ++  +  QVE
Sbjct: 290 RDGLAGLRR-LSDQVE 304


>gi|254432638|ref|ZP_05046341.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Cyanobium sp. PCC 7001]
 gi|197627091|gb|EDY39650.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Cyanobium sp. PCC 7001]
          Length = 335

 Score =  194 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 65/327 (19%), Positives = 136/327 (41%), Gaps = 58/327 (17%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------------------- 43
           S    G   +  Y+ +I ++P+L  ++E  L ++ +E                       
Sbjct: 13  SAQSGGGDLVRSYLRDIGRVPLLTHEQEITLGRQVQELMALEEMEQELTMRAGGTAPSAA 72

Query: 44  -----------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
                                 A  R+V ++LRLVV +A  Y    + + +++ EG IGL
Sbjct: 73  ELAKAAGLSPAVLKKRLQAGRRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGL 132

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++ V+KFDP RG++ +TY+ WWI+  +   I      +++     +      L +LK   
Sbjct: 133 VRGVEKFDPTRGYKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITE-----TLNKLKKGQ 187

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           + ++    +   V  +A  + + E EV  + CR     SL   +   D   ++  D L  
Sbjct: 188 RELSQELGRTPTVTELAGYVELPEEEVKDLLCRARQPVSLETKV--GDGEDTELLDLLAG 245

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE-------NPVTLENLS 259
           D     ++  E+ + +  +  L   +  L   + R+ + R   +        P++L +++
Sbjct: 246 DG----ELPEERVDGECLKGDLRALLEQLPELQGRVLKMRYGLDPEGQGLTEPMSLSSIA 301

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQK 286
               +SR++ R +E +A + ++   ++
Sbjct: 302 KNLGMSRDKTRNLERKALEGIRSQSRR 328


>gi|148239880|ref|YP_001225267.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. WH 7803]
 gi|147848419|emb|CAK23970.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 7803]
          Length = 322

 Score =  194 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 68/317 (21%), Positives = 139/317 (43%), Gaps = 53/317 (16%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSA------------------- 49
           ++     +  Y+ +I ++P+L  Q+E  L ++ +E  DL A                   
Sbjct: 6   LLPDADLVRSYLRDIGRVPLLSHQQEITLGRQVQELMDLEATEAELQEKRGGEAVPAAEL 65

Query: 50  ---------------------AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
                                  R+V ++LRLVV +A  Y    + + +++ EG IGL++
Sbjct: 66  AKAAGLSAVQLKRKLQAGRRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVR 125

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
            V+KFDP RG++ +TY+ WWI+  +   I      +++     +      L +LK   + 
Sbjct: 126 GVEKFDPTRGYKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITE-----MLNKLKKGQRE 180

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           ++ +  +   V  +A  + + E EV  + CR     SL   +   D + ++  D L  D 
Sbjct: 181 LSQDLGRTPSVTELAAFVELPEDEVKELMCRARQPVSLEMKV--GDGDDTELLDLLAGDG 238

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSR 266
               ++  E+ E +  +  L   +  L   + R+   R     E+P++L  ++   ++SR
Sbjct: 239 ----ELPSEQVEGECLKGDLRDLLGQLPELQERVLRMRYGMDGEDPMSLTGIAKTLKMSR 294

Query: 267 ERVRQIEARAFKKVQES 283
           +R R++E    + ++++
Sbjct: 295 DRTRRLEREGLESLRQA 311


>gi|94313583|ref|YP_586792.1| RNA polymerase sigma 70 (sigma D) factor [Cupriavidus metallidurans
           CH34]
 gi|93357435|gb|ABF11523.1| RNA polymerase sigma 70 (sigma D) factor [Cupriavidus metallidurans
           CH34]
          Length = 617

 Score =  194 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 61/238 (25%), Positives = 116/238 (48%), Gaps = 12/238 (5%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
             ++ S+LRLVV  A  Y   G+P+ +++ EGN+GLM+AV +FD  RG++ +TY+ WWI+
Sbjct: 380 DEMIRSNLRLVVSNAKKYLHRGMPLLDLIQEGNLGLMRAVDRFDYRRGYKFSTYATWWIR 439

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
             +   I      ++I     +      + ++    + +     +     A+A +L++S 
Sbjct: 440 QGITRAIADKGPTIRIPIHLVEV-----VGKVNRASRELFHETGEAPAPEALAARLSLSV 494

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            +V ++   +    SL   +   +   +   D L  +         E   R + R  L  
Sbjct: 495 KKVKAILDLVKEPLSLEMSV--GESGDALLWDTLTDECSASPD---ESAMRVSLRKDLDE 549

Query: 231 SMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +++ L PRE +I + R   +     TLE +  ++ +SRERVRQ+E +A +K++   + 
Sbjct: 550 ALATLKPREAKIVKMRYGVDAGTDYTLEEIGQQYGLSRERVRQLERQALRKLRNPDRA 607



 Score = 37.5 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 9/27 (33%), Positives = 17/27 (62%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKR 40
             +  Y+ EI  IP+L +++E  +A+R
Sbjct: 95  DPVQLYLREIGTIPLLTREDEVAIARR 121


>gi|115360900|ref|YP_778037.1| RNA polymerase, sigma 28 subunit [Burkholderia ambifaria AMMD]
 gi|115286228|gb|ABI91703.1| RNA polymerase, sigma 28 subunit [Burkholderia ambifaria AMMD]
          Length = 617

 Score =  194 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 101/237 (42%), Gaps = 12/237 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L  ++LRLVV IA  Y   GLP ++++ EGNIGL++A++++D  RGFR +TY+ WW
Sbjct: 380 AKAGLFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIERYDHRRGFRFSTYATWW 439

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   +      +++ T          L +L    +              +A  +  
Sbjct: 440 IRQAITHALADLGRTIRVPTH-----TVDALNKLSRLAREHRQRAGTAATPAELAVHMGE 494

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +   +    S +  ++           +     D       +       R  +
Sbjct: 495 PVDKVRELMAIVKEPVSADVPVSPEGD-----MTFADVAPDTTTPSPEDAAGATQLRRTI 549

Query: 229 TRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
              +  L PRE  + + R     +   +L ++  +  +S ERVRQIEA A  +++ S
Sbjct: 550 AAVIDRLPPREAMVLKLRYGLHTDEGCSLRDIGRQLNLSAERVRQIEASALARLRAS 606



 Score = 41.3 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 20/50 (40%), Gaps = 9/50 (18%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREH---------GDLSAAHRLV 54
             +  Y+ E+   P+L + EE+  A+R             GD  A   LV
Sbjct: 115 DPVRLYLREMGTTPLLTRDEEFAYARRIERGRAASAAVLCGDPDALDALV 164


>gi|307153454|ref|YP_003888838.1| RpoD subfamily RNA polymerase sigma-70 factor [Cyanothece sp. PCC
           7822]
 gi|306983682|gb|ADN15563.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7822]
          Length = 372

 Score =  194 bits (494), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 76/317 (23%), Positives = 135/317 (42%), Gaps = 53/317 (16%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLA------------------------------- 38
            N +  +  +  E+ + P+L+ +EE  LA                               
Sbjct: 55  TNSDDTVGAFFKEMARYPLLKPEEEIELAYTVKFLMESEEKRQELQVQLERPPSKLEWAQ 114

Query: 39  ------KRYREHG---DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
                 +R  E+      +A  +++ S+LRLVV IA  Y   G+P  +++ EG IGL +A
Sbjct: 115 AMGLKNERQLENRLYRGRAAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRA 174

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
            +KFDP +G++ +TY+ WWI+ A+   I      +++     +K     L +LK   + +
Sbjct: 175 AEKFDPNKGYKFSTYAYWWIRQAITRTIANDARTIRLPIHIVEK-----LNKLKKAQRVL 229

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
                +      +A+ L +    +  +        SLN  +   +   ++  D L    D
Sbjct: 230 KQQLHRNPTEQELAQALEIDCEHLRQLLQLRRQSLSLNHRVGKGED--TELVDLL---ED 284

Query: 210 GQEQVLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSR 266
            + Q+  EK      R  +   +  VL  RE+ +   R       P TLE +   F +SR
Sbjct: 285 EELQLPEEKMNEAMMRQDIAAVLTDVLTEREKDVIALRYGLITSQPYTLEEVGGIFNLSR 344

Query: 267 ERVRQIEARAFKKVQES 283
           ERVRQI+++A +K++  
Sbjct: 345 ERVRQIQSKAMRKLRRP 361


>gi|124023525|ref|YP_001017832.1| type II alternative sigma factor, sigma70 family [Prochlorococcus
           marinus str. MIT 9303]
 gi|123963811|gb|ABM78567.1| Putative type II alternative sigma factor, sigma70 family protein
           [Prochlorococcus marinus str. MIT 9303]
          Length = 308

 Score =  194 bits (493), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 71/300 (23%), Positives = 131/300 (43%), Gaps = 37/300 (12%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------------------------HGD 46
            LS Y+ EI +  +L  ++E  + ++ +                                
Sbjct: 4   SLSAYLGEIGRHQLLTPEQELTMGRKVQAMVALTDRCHLAGGAGPECEYSDDQRLTIRRG 63

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A ++++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG R +TY+ 
Sbjct: 64  EKAKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSTYAY 123

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   +      ++I    N+K     LR  K  L          EQ+V   +  
Sbjct: 124 WWIRQGLNRALSTQSRTIRIPVNVNEK--LTKLRAAKSRLMQSNGLPPTAEQLVKTMRLP 181

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
                ++++   R +   SL  ++ S   + S+  D L  +     +     E   +   
Sbjct: 182 MAEVEDLLACELR-SVTVSLQGVVKSK-SDPSELVDVLPSEEIPPMERAEMAERTASVWT 239

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPV---TLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +L R+   L P+ER +   R   +      TL  ++     SRE  RQ+  RA +K++++
Sbjct: 240 LLNRA--NLTPKERMVVTLRFGLDGSHEWRTLAEVARHMSCSREYCRQVVQRALRKLRKT 297


>gi|197336747|ref|YP_002158681.1| RNA polymerase sigma factor RpoS (Sigma-38) [Vibrio fischeri MJ11]
 gi|197313999|gb|ACH63448.1| RNA polymerase sigma factor RpoS (Sigma-38) [Vibrio fischeri MJ11]
          Length = 294

 Score =  194 bits (493), Expect = 1e-47,   Method: Composition-based stats.
 Identities = 77/295 (26%), Positives = 135/295 (45%), Gaps = 20/295 (6%)

Query: 1   MNRKNMSIIVNGEIGL----SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTS 56
           M    + +    E GL    S Y+ EI +  +L  +EE V ++ Y++ GDLSA + L+ S
Sbjct: 1   MAYAKLDMRACEEQGLKDSYSLYLKEINRYQLLTAEEELVYSRLYKK-GDLSARNTLIES 59

Query: 57  HLRLVVKIAMGYRGYGL---PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           +LRLVVK+A  YR        I +++ EGN+GL++A+ KF+PE G+R +TY++WWI+ ++
Sbjct: 60  NLRLVVKVANKYRKRNQTDLAILDIIEEGNLGLIKAIDKFNPELGYRFSTYAVWWIRESI 119

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
           +  +      V++       +      R    L            +    ++  +  S++
Sbjct: 120 ESALFNHSRTVRLPVHIT--KELNTYLRAARELSKSLKREPSIRDISTYCEEEQIKVSKI 177

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
           IS+          N L   S  +      +     + +         + N    L+  + 
Sbjct: 178 ISLIP--------NQLTCHSACSDELSPKFFELSSNNKALEPDNSLSQDNLEMNLSSWID 229

Query: 234 VLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            LN RE+ I   R         TLE+L  + ++S+ERVRQI++    K+    +K
Sbjct: 230 SLNYREKEIIINRYGLFGCKVKTLEDLGKDLDLSKERVRQIQSETLIKLNTIFKK 284


>gi|327539652|gb|EGF26260.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Rhodopirellula
           baltica WH47]
          Length = 567

 Score =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 78/282 (27%), Positives = 125/282 (44%), Gaps = 17/282 (6%)

Query: 21  HEIRKIPMLEKQEEYVLAKRY---REHGD--LSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
            E+R++ ++ ++    L  R    R H D   +    L   +LRLVV IA  YR  GL  
Sbjct: 294 QELRELMLVTQESPTSLHNRMAKVRRHFDQYEATKRELSAGNLRLVVSIAKKYRNRGLSF 353

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN GLM+AV K++  RGF+ +TY+ WWI+ A+   I      ++I        +
Sbjct: 354 LDLIQEGNTGLMRAVDKYEYRRGFKFSTYATWWIRQAITRAIADQARTIRIPVH-----M 408

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              L +L+   + +T    +      IA+  +V   EV  +        SL+  +   + 
Sbjct: 409 IDVLSKLRQAQKRLTQTLRREPTYEDIAEATDVPIEEVRRVMDIGRHPVSLDRPVGEGED 468

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPV 253
           +S     +  +  D +    +        RN +   +  L  RER I   R         
Sbjct: 469 SS-----FGEFVQDSETDNPVRIAASGMLRNKIDELLKTLTFREREIIRLRYGLVDGYSY 523

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPP 295
           TLE     F+V+RERVRQIEA+A  K+Q   + +   S   P
Sbjct: 524 TLEECGRIFKVTRERVRQIEAKAVAKMQSPSRAERLSSYLKP 565



 Score = 37.1 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 12/54 (22%), Positives = 24/54 (44%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSH 57
            +  +    E  +  Y+ ++ +IP+L ++EE  LAK+            L T +
Sbjct: 103 SSADMPKASEDPIRMYLSQMAEIPLLSREEEIALAKKIEITRKQYRRSLLETDY 156


>gi|254432550|ref|ZP_05046253.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Cyanobium sp. PCC 7001]
 gi|197627003|gb|EDY39562.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Cyanobium sp. PCC 7001]
          Length = 319

 Score =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 64/314 (20%), Positives = 128/314 (40%), Gaps = 58/314 (18%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------------------- 43
           +  Y+ +I ++P+L  ++E  L ++ +E                                
Sbjct: 6   VRSYLRDIGRVPLLTHEQEITLGRQVQELMALEEMEQELTMRAGGTAPSAAELAKAAGLS 65

Query: 44  --------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
                        A  R+V ++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP
Sbjct: 66  PAVLKKRLQAGRRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDP 125

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            RG++ +TY+ WWI+  +   I      +++     +      L +LK   + ++    +
Sbjct: 126 TRGYKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITE-----TLNKLKKGQRELSQELGR 180

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
              V  +A  + + E EV  + CR     SL   +   D   ++  D L  D     ++ 
Sbjct: 181 TPTVTELAGYVELPEEEVKDLLCRARQPVSLETKV--GDGEDTELLDLLAGDG----ELP 234

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE-------NPVTLENLSSEFEVSRER 268
            E+ + +  +  L   +  L   + R+ + R   +        P++L  +     +SR+R
Sbjct: 235 EERVDGECLKGDLRALLEQLPELQGRVLKMRYGIDPQSAEMAEPMSLTGIGRILGISRDR 294

Query: 269 VRQIEARAFKKVQE 282
           VR +E      ++ 
Sbjct: 295 VRNLERDGLAGLRR 308


>gi|126659670|ref|ZP_01730799.1| RNA polymerase sigma factor [Cyanothece sp. CCY0110]
 gi|126619015|gb|EAZ89755.1| RNA polymerase sigma factor [Cyanothece sp. CCY0110]
          Length = 369

 Score =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 78/315 (24%), Positives = 135/315 (42%), Gaps = 53/315 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAK-------------------------------- 39
            +  +  +  E+ + P+L  QEE  LA                                 
Sbjct: 54  SDDTVGAFFKEMSRYPLLNAQEEVELANHVQFLVQAEETRQQLREELQRPPTKAEWGQAM 113

Query: 40  --------RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                    +R H   +A  +++ S+LRLVV IA  Y   G+P  +++ EG IGL +A +
Sbjct: 114 GFETQKQFEHRLHRGRTAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAE 173

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFDP +G++ +TY+ WWI+ A+   I      +++     +K     L +LK   + +  
Sbjct: 174 KFDPNKGYKFSTYAYWWIRQAITRTIANDARTIRLPIHVVEK-----LNKLKKAQRVLKQ 228

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +      +A +L VS S++  +        SLN  +   +   ++  D L    D +
Sbjct: 229 KLQRNPNEKELADELEVSPSQLRQLLQLRRQSLSLNHRVGKGED--TELVDLL---EDQE 283

Query: 212 EQVLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRER 268
            Q+  E       R  ++  +  VL  RE+ +   R       P TLE +   F +SRER
Sbjct: 284 LQLPEELMNEGMLRYEVSAVLSDVLTQREKDVISLRYGLCTAQPHTLEEVGGIFNLSRER 343

Query: 269 VRQIEARAFKKVQES 283
           VRQI+++A +K++  
Sbjct: 344 VRQIQSKAMRKLRRP 358


>gi|158340842|ref|YP_001522010.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158311083|gb|ABW32696.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 299

 Score =  194 bits (493), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 74/299 (24%), Positives = 137/299 (45%), Gaps = 31/299 (10%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-----------------EHGDLS 48
            +I+ + +  L  Y+  +    +L   EE  L ++ +                 +     
Sbjct: 2   FTIMRSNKDALGAYLTRMGGYSLLTHAEEVSLGQQIQSALNPPQGISQAELDQIQKRGKR 61

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A HR++  +LRLVV IA  Y+  G+ + +++ EG++GL +AV+KFDP +G+R +TY+ WW
Sbjct: 62  AKHRMICGNLRLVVTIAKKYQKRGMDLIDLIQEGSLGLERAVEKFDPAKGYRFSTYAYWW 121

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ ++   I      ++I     +K     L R+K   + ++    +      +  +L +
Sbjct: 122 IRQSITRAIAMQSHTIRIPVHMTEK-----LNRIKRVRRELSQTLGRTPTHQEMVAELGI 176

Query: 169 SESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +  ++       +++  ESLN  I        +  D L    D Q     E  E+   RN
Sbjct: 177 TLEQLQKTLQAAQISNPESLN--IRVGKDQEMELGDLL---EDLQMPSPNEVVEQDFLRN 231

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            L  +++ LN  ER +   R   E+    +L  +S +  +SRE VR++E  A  K+ +S
Sbjct: 232 ALWSALAQLNDNERTVLILRYGLEDGRERSLYRVSQQMGISREWVRKLEQTAKSKLLQS 290


>gi|89901840|ref|YP_524311.1| sigma 28 [Rhodoferax ferrireducens T118]
 gi|89346577|gb|ABD70780.1| sigma 28 [Rhodoferax ferrireducens T118]
          Length = 726

 Score =  193 bits (492), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 71/292 (24%), Positives = 139/292 (47%), Gaps = 21/292 (7%)

Query: 12  GEIGLSR-YIHEIRKIPMLEKQEE-YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
             +GLSR ++ E+     LE QE     ++  + +    A  ++V ++L+LV+ IA  Y 
Sbjct: 334 ASLGLSRGFLLELADFEQLEVQESAIEFSQAMQAY--RQARDQMVIANLKLVLFIAKKYL 391

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
             G P+ +++ EGNIGL++AV ++D  RGF+L+TY+ WWI+  +  Y+      +++   
Sbjct: 392 YSGQPLDDLLQEGNIGLIKAVDRYDWRRGFKLSTYATWWIRQQVGRYVADKSKTIRLPVH 451

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
                 +   +++     AI     +   +  IAKK+ +  S+V  +   +         
Sbjct: 452 V-----YVKTQQIAHAAHAIELATGRMPTIEEIAKKMEMPASKVAPLALAIPEP----LP 502

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I+  D +S    D      +   +  ++          + R ++ L P++ ++   R   
Sbjct: 503 IHDVDVDSLIAID---AQDNYVARDPMDIVSDSQLIGSIDRFLATLKPKDEQVLRLRFGI 559

Query: 250 E--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ---VELSSSPPL 296
                +TLE + +  EV+RER+RQIEA+A   ++   + +    +L+ +PP 
Sbjct: 560 GAHEAMTLEEIGTRLEVTRERIRQIEAKAICHLKHPARLERLLRDLNGTPPP 611


>gi|33862729|ref|NP_894289.1| RNA polymerase sigma-70 factor family protein [Prochlorococcus
           marinus str. MIT 9313]
 gi|33634645|emb|CAE20631.1| Sigma-70 factor family [Prochlorococcus marinus str. MIT 9313]
          Length = 308

 Score =  193 bits (492), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 70/300 (23%), Positives = 130/300 (43%), Gaps = 37/300 (12%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------------------------HGD 46
            LS Y+ EI +  +L  ++E  + ++ +                                
Sbjct: 4   SLSAYLGEIGRHQLLTPEQELTMGRKVQAMVALTNRCHLAGGAGPECEYSDDQRLTIRRG 63

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A ++++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG R +TY+ 
Sbjct: 64  EKAKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSTYAY 123

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   +      ++I    N+K     LR  K  L          EQ+    +  
Sbjct: 124 WWIRQGLNRALSTQSRTIRIPVNVNEK--LTKLRAAKSRLMQNNGLPPTAEQLAKTMRLP 181

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
                ++++   R +   SL  ++ S   + S+  D L  +     +     E   +   
Sbjct: 182 MAEVEDLLACELR-SVTVSLQGVVKSK-SDPSELADVLPSEEIPPMERAEMSERTASVWT 239

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPV---TLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +L R+   L P+ER +   R   +      TL  ++     SRE  RQ+  RA +K++++
Sbjct: 240 LLNRA--NLTPKERMVVTLRFGLDGSHEWRTLAEVARHMSCSREYCRQVLQRALRKLRKA 297


>gi|32474203|ref|NP_867197.1| transcription initiation factor sigma 70 [Rhodopirellula baltica SH
           1]
 gi|32444741|emb|CAD74742.1| transcription initiation factor sigma 70 [Rhodopirellula baltica SH
           1]
          Length = 567

 Score =  193 bits (492), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 78/282 (27%), Positives = 125/282 (44%), Gaps = 17/282 (6%)

Query: 21  HEIRKIPMLEKQEEYVLAKRY---REHGD--LSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
            E+R++ ++ ++    L  R    R H D   +    L   +LRLVV IA  YR  GL  
Sbjct: 294 QELRELMLVTQESPTSLHNRMAKVRRHFDQYEATKRELSAGNLRLVVSIAKKYRNRGLSF 353

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN GLM+AV K++  RGF+ +TY+ WWI+ A+   I      ++I        +
Sbjct: 354 LDLIQEGNTGLMRAVDKYEYRRGFKFSTYATWWIRQAITRAIADQARTIRIPVH-----M 408

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              L +L+   + +T    +      IA+  +V   EV  +        SL+  +   + 
Sbjct: 409 IDVLSKLRQAQKRLTQTLRREPTYEDIAEATDVPIEEVRRVMDIGRHPVSLDRPVGEGED 468

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPV 253
           +S     +  +  D +    +        RN +   +  L  RER I   R         
Sbjct: 469 SS-----FGEFVQDSETDNPVRIAASGMLRNKIDELLKTLTFREREIIRLRYGLVDGYSY 523

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPP 295
           TLE     F+V+RERVRQIEA+A  K+Q   + +   S   P
Sbjct: 524 TLEECGRIFKVTRERVRQIEAKAVAKMQSPSRAERLSSYLKP 565



 Score = 37.1 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 12/54 (22%), Positives = 24/54 (44%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSH 57
            +  +    E  +  Y+ ++ +IP+L ++EE  LAK+            L T +
Sbjct: 103 SSADMPKASEDPIRMYLSQMAEIPLLSREEEIALAKKIEITRKQYRRSLLETDY 156


>gi|170704115|ref|ZP_02894732.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           ambifaria IOP40-10]
 gi|170130976|gb|EDS99686.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           ambifaria IOP40-10]
          Length = 575

 Score =  193 bits (492), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 101/237 (42%), Gaps = 12/237 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L  ++LRLVV IA  Y   GLP ++++ EGNIGL++A++++D  RGFR +TY+ WW
Sbjct: 338 ARTGLFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIERYDYRRGFRFSTYATWW 397

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   +      +++ T          L +L    +              +A  +  
Sbjct: 398 IRQAITHALADLGRTIRVPTH-----TVDALNKLSRLAREHRQRAGTAATPAELAVHMGE 452

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +   +    S +  ++           +     D       +       R  +
Sbjct: 453 PVDKVRDLMAIVKEPVSADVPVSPEGD-----MTFADVAADTSTPSPEDAAGATQLRRTI 507

Query: 229 TRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
              +  L PRE  + + R     +   +L ++  +  +S ERVRQIEA A  +++ S
Sbjct: 508 AAVIDRLPPREAMVLKLRYGLHADEGCSLRDIGRQLNLSAERVRQIEASALARLRAS 564



 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 13/56 (23%), Positives = 21/56 (37%), Gaps = 9/56 (16%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREH---------GDLSAAHRLV 54
           +       +  Y+ E+   P+L + EE+  A+R             GD  A   LV
Sbjct: 63  LAPRTTDPVRLYLREMGTTPLLTRDEEFAYARRIERGRAASAAVLCGDPDALDALV 118


>gi|67925121|ref|ZP_00518496.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
 gi|67853040|gb|EAM48424.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
          Length = 374

 Score =  193 bits (492), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 75/315 (23%), Positives = 135/315 (42%), Gaps = 53/315 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRY------------------------------ 41
            +  +  +  E+ + P+L  +EE  LA++                               
Sbjct: 59  SDDTVGAFFKEMSRYPLLNAEEEVELAQQVQFLLEVEETKQRLKEELQRTPSKAECAEAL 118

Query: 42  ----------REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                     R H    A  +++ S+LRLVV IA  Y   G+P  +++ EG IGL +A +
Sbjct: 119 GFETAKQFEHRLHKGRIAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAAE 178

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFDP +G++ +TY+ WWI+ A+   I      +++     +K     L +LK   + +  
Sbjct: 179 KFDPNKGYKFSTYAYWWIRQAITRTIANDARTIRLPIHVVEK-----LNKLKKAQRVLKQ 233

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY-DHDG 210
              +      +A +L V+  ++  +        SLN  +   +   ++  D L   D   
Sbjct: 234 KLQRNPNEKELADELEVTPPQLRQLLQLRRQSLSLNHRVGKGED--TELVDLLEDQDLQL 291

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRER 268
            E+++ E   +     +L+    VL  RE+ +   R       P TLE +   F +SRER
Sbjct: 292 PEELMNEGMLQYEVSAVLS---DVLTQREKDVISLRYGLCTSQPHTLEEVGGIFNLSRER 348

Query: 269 VRQIEARAFKKVQES 283
           VRQI+++A +K++  
Sbjct: 349 VRQIQSKAMRKLRRP 363


>gi|254409611|ref|ZP_05023392.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
 gi|196183608|gb|EDX78591.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Microcoleus chthonoplastes PCC 7420]
          Length = 374

 Score =  193 bits (492), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 71/316 (22%), Positives = 136/316 (43%), Gaps = 52/316 (16%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLA-------------KRYREHGDLS-------- 48
            + +  +  +  E+ + P+L+ +EE  LA             +R  +             
Sbjct: 58  TSSDDTVGAFFKEMARYPLLKPEEEIELATQVQFLVEMDEMTERLHQELGRKPTNAELAQ 117

Query: 49  ------------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
                             +  +++ S+LRLVV IA  Y   G+P  +++ EG +GL +A 
Sbjct: 118 ALDLTERQFENRLYRGQISKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGALGLNRAA 177

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +KFDP +G++ +TY+ WWI+ A+   I      +++     +K     L +LK   + + 
Sbjct: 178 EKFDPAKGYKFSTYAYWWIRQAITRTIANDARTIRLPIHIVEK-----LNKLKKVQRELK 232

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
               +      +A+ L++S + +  +        SLN  +   +   ++  D L    D 
Sbjct: 233 QKLQRTPDETELAEALDISRTNLRQLLQLRRRSLSLNHRVGKGED--TELVDLL---EDN 287

Query: 211 QEQVLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRE 267
              +  ++      R  ++  +  VL  RE+ +   R     P   TLE + S F +SRE
Sbjct: 288 DLHLPEQQMSESMMRQEISDVLSDVLTEREKDVISLRYGLATPESYTLEEVGSMFNLSRE 347

Query: 268 RVRQIEARAFKKVQES 283
           RVRQI+++A +K++  
Sbjct: 348 RVRQIQSKAMRKLRRP 363


>gi|14581457|gb|AAK29754.1| stationary phase sigma factor RpoS [Azotobacter vinelandii]
          Length = 238

 Score =  193 bits (492), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 69/249 (27%), Positives = 115/249 (46%), Gaps = 13/249 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           ++EI   P+L   EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + +++
Sbjct: 1   LNEIGFSPLLTPAEEVHFA-RLAQRGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDLI 59

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   L
Sbjct: 60  EEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVYL 118

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
           R  +     +T           IA  L    +EV  M        S++  ++    +   
Sbjct: 119 RAAR----ELTQKLDHEPSAEEIANLLEKPVAEVKRMLGLNERVTSVD--VSLGPDSDKT 172

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLEN 257
             D L  D       L++ ++       + + +  L  ++R +   R         TLE 
Sbjct: 173 LLDVLTDDRPFDPCDLLQDDDLSQS---IDQWLFDLTEKQREVVVRRFGLRGHESCTLEE 229

Query: 258 LSSEFEVSR 266
           +  E  ++R
Sbjct: 230 VGQEIGLTR 238


>gi|300865041|ref|ZP_07109868.1| RNA polymerase sigma factor [Oscillatoria sp. PCC 6506]
 gi|300336978|emb|CBN55018.1| RNA polymerase sigma factor [Oscillatoria sp. PCC 6506]
          Length = 334

 Score =  193 bits (492), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 66/324 (20%), Positives = 138/324 (42%), Gaps = 52/324 (16%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE--------------------------- 43
           +    +  Y+HEI ++ +L +++E +  K+ ++                           
Sbjct: 22  SSTDTVRTYLHEIGRVALLTREQEIIYGKQVQQMMQLLEAKEELAKELRREPTEVEWALQ 81

Query: 44  ------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                       H    A  +++ ++LRLVV IA  Y+   +   +++ EG +GL + V+
Sbjct: 82  VQLSEAELKRLMHQGRRAKQKMIEANLRLVVAIAKKYQKRNMEFLDLIQEGTLGLERGVE 141

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFDP RG++ +TY+ WWI+ A+   I +    +++     +K     L ++K   + +  
Sbjct: 142 KFDPMRGYKFSTYAYWWIRQAITRAIAQHARTIRLPIHITEK-----LNKIKKVQRELAQ 196

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +      I   L +  S++           SL+  +   D   ++ Q+ L  +    
Sbjct: 197 QLGRSPTPAEIGSALELHPSQIREYLLMARHPVSLD--LRVGDNQDTELQELLEDESASP 254

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERV 269
           +  +  +  R++    L   M+ L P++R +   R   E+   ++L  +    ++SRERV
Sbjct: 255 DDYITGELLRQD----LNNLMAELTPQQRDVLSLRFGLEDGHEMSLAKVGERLKLSRERV 310

Query: 270 RQIEARAFKKVQESIQKQVELSSS 293
           RQ+E +A   ++    +  E  +S
Sbjct: 311 RQLEHQALAHLRRRQAQVREYLAS 334


>gi|169883528|gb|ACA97859.1| RNA polymerase sigma factor [Microcystis aeruginosa PCC 7820]
          Length = 377

 Score =  193 bits (492), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 72/316 (22%), Positives = 132/316 (41%), Gaps = 53/316 (16%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLA-------------KRYREH------------- 44
           + E  +  +  E+ + P+L  +EE  LA             ++ +E+             
Sbjct: 61  SNEDTVGAFFKEMARYPLLSAEEEIELAYSVKFLMEAEEVRQKLQENLHRPPTKTEWAIA 120

Query: 45  --------------GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
                            +A  +++ S+LRLVV IA  Y   G+P  +++ EG IGL +A 
Sbjct: 121 LELDNERQLENRLYRGRTAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAA 180

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +KFDP +G++ +TY+ WWI+ A+   I      +++     +K     L +LK   + + 
Sbjct: 181 EKFDPNKGYKFSTYAYWWIRQAITRTIANDARTIRLPIHIVEK-----LNKLKKAQRILK 235

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
            +  +      +A+ L ++  ++  +        SLN  +   +              D 
Sbjct: 236 QDLQRNPNERELAEALEITPEQLRQLLQLRRQSLSLNHRVGKGEDTELVDLLE-----DD 290

Query: 211 QEQVLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRE 267
             Q+  +K      R  +   +  VL  RE+ +   R       P TLE +   F +SRE
Sbjct: 291 DLQLPEDKMNEMMMRQEIFAVLSDVLTEREKDVISLRYGLATSQPYTLEEVGGMFNLSRE 350

Query: 268 RVRQIEARAFKKVQES 283
           RVRQI+ +A +K++  
Sbjct: 351 RVRQIQTKAMRKLRRP 366


>gi|158341157|ref|YP_001522480.1| RNA polymerase sigma-70 factor, putative [Acaryochloris marina
           MBIC11017]
 gi|158311398|gb|ABW33009.1| RNA polymerase sigma-70 factor, putative [Acaryochloris marina
           MBIC11017]
          Length = 274

 Score =  193 bits (491), Expect = 2e-47,   Method: Composition-based stats.
 Identities = 69/272 (25%), Positives = 126/272 (46%), Gaps = 15/272 (5%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
              L  Y+ EI + P+L  +EE +LA++    G+L A  RL+  +LRLVV IA  ++  G
Sbjct: 5   HDSLHFYLKEIARYPILSHEEEILLARQV-NAGNLRAKQRLIECNLRLVVSIAKKHQNRG 63

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP+ +++ EG+IGL  AV KFD  +G R +TY+ WWI+  +   +      + +      
Sbjct: 64  LPLQDLIQEGSIGLSNAVDKFDLAQGCRFSTYAYWWIRQGVTAALRAKSRPIYLPQYQ-- 121

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
              +  + ++K H + +     +   +  +AK  N+    +           SL+  +  
Sbjct: 122 ---WEMISKIKKHFRELNQQLGREPSLSELAKATNLKPKTISRTLHLFQKVSSLDQPVGH 178

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN- 251
             K++       + D    E       E       L++ M+ L+ RE+ +   R   E+ 
Sbjct: 179 QQKDT-------LLDLMAGEDQPTLYLESLQLDEQLSQVMAHLDKREQFVLSQRFGLEDD 231

Query: 252 -PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            P ++  +  +  +SRE +R I  +  KK+Q+
Sbjct: 232 QPKSMREIGEQIGLSREGIRLILNKIMKKLQK 263


>gi|288287|emb|CAA39117.1| unnamed protein product [Myxococcus xanthus]
          Length = 246

 Score =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 99/233 (42%), Positives = 145/233 (62%), Gaps = 4/233 (1%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           +VT++LR VVK+A  YR YG+ +S+++ EGNIGLM+AV+KFDP++G RL +Y++WWI+A 
Sbjct: 1   MVTANLRFVVKVAYEYRSYGIKMSDLIQEGNIGLMKAVQKFDPDKGIRLISYAVWWIRAY 60

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +Q YIL+SWSLVK+GTT    +LFF+L R +  L+    +      V  IA++L+V   E
Sbjct: 61  IQNYILKSWSLVKLGTTQAHGKLFFSLARTRRELEKF-GSGDAAVNVDDIARRLHVKPGE 119

Query: 173 VISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           V  M  R+ G D SL+A +     NS    D++V     Q+    +KEE       +  +
Sbjct: 120 VREMEQRMGGRDLSLDAPMGEDGGNSH--VDFVVSAAAPQDDEFADKEEAGLINARVRTA 177

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +  L+PRER I E R + E P+TL+ L   F  SRER RQ+E RA  K++  +
Sbjct: 178 LMRLDPRERFIIEQRVMNERPMTLKELGEHFGFSRERARQLEIRAKDKLKSEL 230


>gi|166368031|ref|YP_001660304.1| group 2 RNA polymerase sigma factor [Microcystis aeruginosa
           NIES-843]
 gi|166090404|dbj|BAG05112.1| group 2 RNA polymerase sigma factor [Microcystis aeruginosa
           NIES-843]
          Length = 377

 Score =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 72/316 (22%), Positives = 132/316 (41%), Gaps = 53/316 (16%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLA-------------KRYREH------------- 44
           + E  +  +  E+ + P+L  +EE  LA             ++ +E+             
Sbjct: 61  SNEDTVGAFFKEMARYPLLSAEEEIELAYSVKFLMEAEEVRQKLQENLHRPPTKTEWASA 120

Query: 45  --------------GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
                            +A  +++ S+LRLVV IA  Y   G+P  +++ EG IGL +A 
Sbjct: 121 LQLDNERQLENRLYRGRTAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAA 180

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +KFDP +G++ +TY+ WWI+ A+   I      +++     +K     L +LK   + + 
Sbjct: 181 EKFDPNKGYKFSTYAYWWIRQAITRTIANDARTIRLPIHIVEK-----LNKLKKAQRILK 235

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
            +  +      +A+ L ++  ++  +        SLN  +   +              D 
Sbjct: 236 QDLQRNPNERELAEALEMTPEQLRQLLQLRRQSLSLNHRVGKGEDTELVDLLE-----DD 290

Query: 211 QEQVLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRE 267
             Q+  +K      R  +   +  VL  RE+ +   R       P TLE +   F +SRE
Sbjct: 291 DLQLPEDKMNEMMMRQEIFAVLSDVLTEREKDVISLRYGLATSQPYTLEEVGGMFNLSRE 350

Query: 268 RVRQIEARAFKKVQES 283
           RVRQI+ +A +K++  
Sbjct: 351 RVRQIQTKAMRKLRRP 366


>gi|159029420|emb|CAO90796.1| unnamed protein product [Microcystis aeruginosa PCC 7806]
          Length = 377

 Score =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 72/316 (22%), Positives = 132/316 (41%), Gaps = 53/316 (16%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLA-------------KRYREH------------- 44
           + E  +  +  E+ + P+L  +EE  LA             ++ +E+             
Sbjct: 61  SNEDTVGAFFKEMARYPLLSAEEEIELAYLVKFLMEAEEVRQKLQENLHRPPTKTEWAIA 120

Query: 45  --------------GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
                            +A  +++ S+LRLVV IA  Y   G+P  +++ EG IGL +A 
Sbjct: 121 LELDNERQLENRLYRGRTAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAA 180

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +KFDP +G++ +TY+ WWI+ A+   I      +++     +K     L +LK   + + 
Sbjct: 181 EKFDPNKGYKFSTYAYWWIRQAITRTIANDARTIRLPIHIVEK-----LNKLKKAQRILK 235

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
            +  +      +A+ L ++  ++  +        SLN  +   +              D 
Sbjct: 236 QDLQRNPNERELAEALEITPEQLRQLLQLRRQSLSLNHRVGKGEDTELVDLLE-----DD 290

Query: 211 QEQVLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRE 267
             Q+  +K      R  +   +  VL  RE+ +   R       P TLE +   F +SRE
Sbjct: 291 DLQLPEDKMNEMMMRQEIFAVLSDVLTEREKDVISLRYGLATSQPYTLEEVGGMFNLSRE 350

Query: 268 RVRQIEARAFKKVQES 283
           RVRQI+ +A +K++  
Sbjct: 351 RVRQIQTKAMRKLRRP 366


>gi|116071891|ref|ZP_01469159.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. BL107]
 gi|116065514|gb|EAU71272.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. BL107]
          Length = 355

 Score =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 74/249 (29%), Positives = 120/249 (48%), Gaps = 13/249 (5%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           +        A   ++ ++LRLVV +A  Y+  G+ I ++V EG +GL +AV+KFDP RGF
Sbjct: 106 KLSLRNGRRAKDHMIQANLRLVVAVAKKYQQRGMEILDLVQEGTLGLERAVEKFDPTRGF 165

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           R +TY+ WWI+  M   I      +++     +K     L R+K   Q I  N  +   +
Sbjct: 166 RFSTYAYWWIRQGMTRAIATQSRTIRLPVHVTEK-----LNRIKRVQQEIASNEGRIASI 220

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +A++L +SE  V     R+    SL++ +       +Q  D +       E+ L   E
Sbjct: 221 ADLARELGISEDTVRQTLERVPRSVSLDSRV--GKDQDTQLGDLIEDGKATPEETLTHDE 278

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
              +    L   +  L  RE  +   R   E+  P TL  +  E ++SRERVRQIE RA 
Sbjct: 279 LHND----LEGLLDELTTREAAVLRRRFGLEDDTPQTLAQIGEELKLSRERVRQIETRAL 334

Query: 278 KKVQESIQK 286
            K+++  ++
Sbjct: 335 LKLRQPQKR 343


>gi|75812337|ref|YP_319956.1| sigma-28 [Anabaena variabilis ATCC 29413]
 gi|75705093|gb|ABA24767.1| Sigma-28 [Anabaena variabilis ATCC 29413]
          Length = 316

 Score =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 71/308 (23%), Positives = 129/308 (41%), Gaps = 52/308 (16%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------------------- 43
           +  Y+ EI + P+L   +E    ++ ++                                
Sbjct: 9   IRIYLQEIGQFPLLTSDQEITYGRQVQQMIAIQEQQQQLSQQLHREPTTAELANFLNTTQ 68

Query: 44  -------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                       A  +++T++LRLVV IA  Y+   L   ++V EG IGL + ++KFDP 
Sbjct: 69  AQVNQILELGQRAKQKMITANLRLVVSIAKKYQRRNLEFLDLVQEGAIGLQRGIEKFDPN 128

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RG++L+TY+ WW+  A+   I      V++    N+K     L ++K   +       + 
Sbjct: 129 RGYKLSTYAYWWVTQAITRAIAEKSRTVRLPIHVNEK-----LNQIKKVQREFFQTLGRR 183

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
             V  IA+KL +  S++       +G  SL+  +   D   ++  + L  +         
Sbjct: 184 PSVAEIAQKLELEPSQIREYLKVASGTISLDLKV--GDNQETELSELLASEGVS----PN 237

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEA 274
           E    +  R  L+  ++ L P +R +   R   L     +L  +S +  +SRERVRQI+ 
Sbjct: 238 ENTTHEMLRQDLSDLLASLKPMQREVLILRFGLLDNQEQSLAQISEKLNLSRERVRQIQQ 297

Query: 275 RAFKKVQE 282
           +A   ++ 
Sbjct: 298 KAMTALRR 305


>gi|288919497|ref|ZP_06413828.1| RNA polymerase, sigma 32 subunit, RpoH [Frankia sp. EUN1f]
 gi|288349100|gb|EFC83346.1| RNA polymerase, sigma 32 subunit, RpoH [Frankia sp. EUN1f]
          Length = 936

 Score =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 79/293 (26%), Positives = 130/293 (44%), Gaps = 30/293 (10%)

Query: 29  LEKQEEYVLAKRYR-------EHG----------DLSAA--HRLVTSHLRLVVKIAMGYR 69
           L   EE  LA   R       E G          D  A     LV  + RLV  IA+ Y 
Sbjct: 435 LTATEEVGLAMLMRPGRPLHEELGRDFRRQLGPTDERARAHDALVLHNQRLVHSIALKYE 494

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G GL + ++   G IGL++AV+KFD  +G++ +TYS WWI+ A+   +     L+++   
Sbjct: 495 GQGLELEDLSQHGMIGLLRAVQKFDATKGYKFSTYSTWWIRQAITRALADEGRLIRLPAH 554

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             +K     +RR+ G L    D         A        E  +++++ R+ G   L+  
Sbjct: 555 FVEK--VNKVRRVLGQLGMSVDGADVVTVAAAAGLSEQEVERCLLALHQRVVG---LDTP 609

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           +             L    D     +++   RK  R  + RS++ L+PR   +   R   
Sbjct: 610 VGDGGDTVLGELVGLPAPPDTDPDTVLD---RKWLRMAVARSLAELSPRNAEVVRLRFGF 666

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQKP 300
           ++  P TLE +   F V+RER+RQIE +A ++++E ++ QV   ++      P
Sbjct: 667 DDGEPRTLEQIGQVFGVTRERIRQIEKKALEQLREPLR-QVRSDNAVGPGPDP 718


>gi|33241240|ref|NP_876182.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Prochlorococcus marinus subsp. marinus str. CCMP1375]
 gi|33238770|gb|AAQ00835.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)
           [Prochlorococcus marinus subsp. marinus str. CCMP1375]
          Length = 328

 Score =  193 bits (491), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 63/309 (20%), Positives = 130/309 (42%), Gaps = 52/309 (16%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------------------- 43
           +  Y+ +I ++P+L  ++E  L ++ +E                                
Sbjct: 21  VRSYLRDIGRVPLLTNEQEITLGRQVQELISLEKLERELESTNGKKPSKEDLAIDAGISV 80

Query: 44  -------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                     + A  R+V+++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP 
Sbjct: 81  RELSKRLKRGVRAKERMVSANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPA 140

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RG++ +TY+ WWI+  +   I     ++++     +      L +LK   + ++ +  + 
Sbjct: 141 RGYKFSTYAYWWIRQGITRAIAEKSRIIRLPIHITEL-----LNKLKKGQRELSQHLERT 195

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
             +  ++  + +   EV  +  R +   SL + +   D   +   D L  D D    +  
Sbjct: 196 PTMQELSAYVEIPVEEVKDLMFRASQPVSLESKV--GDGEDTSLLDLLAIDTD----LPD 249

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEA 274
           ++ E    +  L   +  L   + R+   R     E P+TL  +     +SR+RVR +  
Sbjct: 250 QQIELDCMKGDLEVLLQKLPELQNRVLRMRFGINGEEPMTLTGIGRMLGISRDRVRNLLR 309

Query: 275 RAFKKVQES 283
              K +++ 
Sbjct: 310 DGLKGLRQY 318


>gi|119717204|ref|YP_924169.1| sigma-70 region 3 domain-containing protein [Nocardioides sp.
           JS614]
 gi|119537865|gb|ABL82482.1| sigma-70 region 3 domain protein [Nocardioides sp. JS614]
          Length = 319

 Score =  193 bits (490), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 66/308 (21%), Positives = 131/308 (42%), Gaps = 45/308 (14%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY----------------REHGD------- 46
           + G   +  Y+ EI + P+L+   E  L+K                  R+ G        
Sbjct: 14  IEGRDSVGLYLDEIARNPLLDAASEVELSKAIEAGLMAEHLLAEGRVGRKKGGAPMTATA 73

Query: 47  ----------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                       A    +T++LRLVV IA  Y    +P+ +++ EGN GL++AV+KFD  
Sbjct: 74  EELEWLAEEGRKAVDTFITANLRLVVSIARKYGRAQMPMLDLIQEGNTGLIRAVEKFDYT 133

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +G++ +TY+ WW++ A+   I +   +V++     +      L ++ G  + +     + 
Sbjct: 134 KGYKFSTYATWWVRQAITRGIAQQARVVRLPVHVVE-----ELNQVGGARRTLERKLGRE 188

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
            +   IA++L +    V+ +        SL++ +   +   +   D +  +      +  
Sbjct: 189 PEPREIAEELGMEVDRVLDLMAWGREHVSLDSPV--DEDGDTSLGDLMAQETAPGPDLNF 246

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT--LENLSSEFEVSRERVRQIEA 274
              E    R+ L   +  L+ R   I  +R    +     L ++ ++  +S ERVRQ+E 
Sbjct: 247 IDVES---RDRLNSLVGKLDDRAADIIRSRYGLVDGRQHKLADIGAKHGISAERVRQLER 303

Query: 275 RAFKKVQE 282
            A +K++ 
Sbjct: 304 EALQKLRR 311


>gi|193222342|emb|CAL62001.1| Putative RNA polymerase sigma-70 factor [Herminiimonas
           arsenicoxydans]
          Length = 808

 Score =  193 bits (490), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 59/244 (24%), Positives = 114/244 (46%), Gaps = 9/244 (3%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  ++  ++L+LV   A  Y   G+   +++ EGNIGL++A++KFD  RGF+ +TY++
Sbjct: 434 EEARSQMAIANLKLVHSTATKYSWSGMEFLDLIQEGNIGLLRAIEKFDYRRGFKFSTYAI 493

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I     L+++        L  ++ +++ H   +     K  +   I+  L
Sbjct: 494 WWIRQAITRAIADQTRLIRVPVH-----LVESINQVERHKNQVEHILGKSLKAQEISDAL 548

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   +V           +++ LI    +N  +    L  +         +   + +   
Sbjct: 549 SMPLRKVEQCLAANVSILNIDDLIERETENQDEAL-VLEENLIDPSATPEQLAIKTSLSK 607

Query: 227 MLTRSMSVLNPRERRIFEARRLQE---NPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +L R +S L  +E  I   R        P TLE +     ++RERVRQIEA+A  +++  
Sbjct: 608 VLNRILSDLPEKEAHILRLRFGLYKNVEPHTLEEVGQLLGITRERVRQIEAKALTRIRYP 667

Query: 284 IQKQ 287
            +++
Sbjct: 668 NRRK 671


>gi|148241197|ref|YP_001226354.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp.
           RCC307]
 gi|147849507|emb|CAK27001.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. RCC307]
          Length = 324

 Score =  193 bits (490), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 65/312 (20%), Positives = 133/312 (42%), Gaps = 52/312 (16%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------------------- 43
           +  Y+ +I ++P+L  ++E  L ++ +E                                
Sbjct: 17  VRSYLRDIGRVPLLSHEQEITLGRQVQELVRLEEAEAEFKMRQGHEPSREELASSFGISP 76

Query: 44  -------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                       A  R+V ++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP 
Sbjct: 77  AVLRRRLINGRRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPT 136

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RG++ +TY+ WWI+  +   I      +++     +      L +LK   + ++    + 
Sbjct: 137 RGYKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITE-----TLNKLKKGQRELSQELGRT 191

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
             V  +A+ L + E EV  +  R     SL   +   D + ++  + L  D     +++ 
Sbjct: 192 PTVGELAEFLELPEPEVKDLLSRARQPVSLEMKV--GDSDDTELCELLQNDAPMPHELVD 249

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEA 274
               + + R++L +    L P + R+ + R   +   P++L  +  E  +SR+RVR +E 
Sbjct: 250 GDCLKGDMRSLLEQ----LPPLQGRVLKMRYGIDVEEPMSLTGIGRELGMSRDRVRNLER 305

Query: 275 RAFKKVQESIQK 286
                ++   + 
Sbjct: 306 DGLAGLRRLSEA 317


>gi|256376033|ref|YP_003099693.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Actinosynnema
           mirum DSM 43827]
 gi|255920336|gb|ACU35847.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Actinosynnema
           mirum DSM 43827]
          Length = 320

 Score =  193 bits (490), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 66/295 (22%), Positives = 128/295 (43%), Gaps = 37/295 (12%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKR-----YREH--------------------GDLSAA 50
             +Y+ ++   P+L   EE VL++R     Y EH                        A 
Sbjct: 25  FGQYLRQVGSTPLLTAAEEVVLSRRIEAGVYAEHLLADTAPTPARRRALNQVVADGRDAK 84

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
             ++ ++LRLVV +A  +   GLP+ +VV EGN+GL++AV+KFD  +G++ +TY++WWI+
Sbjct: 85  DHMIRANLRLVVSVAKKHSFRGLPLLDVVQEGNLGLIRAVEKFDYSKGYKFSTYAIWWIR 144

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            A++  +      V++     +      L ++K   + +     +   V  +A    +  
Sbjct: 145 QAIERGLAEQTRTVRLPVHVVE-----ELSKIKKAERKLRAELDREPTVEELAGATGLRA 199

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
             V  +        SL   +   D+ S+   D +           +E+    +    L  
Sbjct: 200 PRVAELRDAGRATISLETPV--GDEGSASVADLIEDADAASAYDAVEQAAFSSE---LRA 254

Query: 231 SMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +  L  R+  I   R    +    TL+ ++ E  ++RER+RQ+E  + + +++ 
Sbjct: 255 LVETLPARQALIVSRRYGLTDGRVHTLQEVAEELGLTRERIRQLEKESLRFLRDP 309


>gi|288926192|ref|ZP_06420119.1| RNA polymerase sigma-70 factor [Prevotella buccae D17]
 gi|315608841|ref|ZP_07883815.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella buccae
           ATCC 33574]
 gi|288337084|gb|EFC75443.1| RNA polymerase sigma-70 factor [Prevotella buccae D17]
 gi|315249448|gb|EFU29463.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella buccae
           ATCC 33574]
          Length = 290

 Score =  193 bits (490), Expect = 3e-47,   Method: Composition-based stats.
 Identities = 77/284 (27%), Positives = 138/284 (48%), Gaps = 12/284 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRL 60
           + + SI       L +Y+ EI   PM+   EE  LA+  R+ G     A  +LV ++LR 
Sbjct: 5   KISKSITNRSSEALDKYLAEISHEPMVSIDEETELAQAIRKGGREGERAKEKLVRANLRF 64

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y+  GL +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I   
Sbjct: 65  VVSVAKQYQHQGLGLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSIMQAIAEQ 124

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
             +V++    NQ      + ++          + +   +  +A+   + E ++       
Sbjct: 125 SRIVRLP--LNQVGAVSKINQVTSKFVQ---EHNRRPSIQELAQITGIDEQKIEQSLNAD 179

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +   S++A     D NS    D L    D +    ++ E   +  N + +  +VL  RE 
Sbjct: 180 SHHMSIDAPFAEDDDNS--MADVLASGDDSRTDKQVDFESMASELNNVLK--NVLKEREI 235

Query: 241 RIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           RI +       +   LE +  E  ++RERVRQI  ++  K++ES
Sbjct: 236 RIVKECFGIGCHEKGLEEIGEEMGLTRERVRQIREKSILKIRES 279


>gi|67920853|ref|ZP_00514372.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
 gi|67856970|gb|EAM52210.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4:Sigma-70
           region 1.2 [Crocosphaera watsonii WH 8501]
          Length = 297

 Score =  193 bits (490), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 68/291 (23%), Positives = 131/291 (45%), Gaps = 33/291 (11%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------HGDLSAAHRLVT 55
             +  Y+  I K P+L   EE  LA+  +                        A  R++ 
Sbjct: 8   DTVRHYLQSIGKTPLLSSAEEIKLAEEIQAMLPLLEKEQLSREEEKIVAKGQKARERMIE 67

Query: 56  SHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQE 115
           ++LRLVV IA  Y   GL + +++ EG++GL++ V+KFDP RG++ +TY+ WWI+  +  
Sbjct: 68  ANLRLVVSIAKKYLNSGLSLLDLIQEGSLGLIRGVEKFDPARGYKFSTYAYWWIRQGITR 127

Query: 116 YILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
            I      +++    N+     NL + +  ++ +T    +      IA+ + +S   +  
Sbjct: 128 AIAEQSRTIRLPIHINE-----NLNKYRKSIRELTLKLGRKPTQREIAENMEISVDRLQF 182

Query: 176 MNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
           +          SLN +I   D+N ++    L  +        +++EE+    + +   + 
Sbjct: 183 LQQAAFKTKSRSLNVVI---DENQTELGQLLPDEESISPSDFVKQEEK---ISQINNLLE 236

Query: 234 VLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            L PR++ +   R        ++ + +  +  VS ER RQI +RA K +++
Sbjct: 237 SLTPRQKEVIILRFGLRDGKQMSYKAIGEKCGVSHERARQIYSRALKILRK 287


>gi|219130701|ref|XP_002185497.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217403028|gb|EEC42984.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 329

 Score =  193 bits (490), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 72/262 (27%), Positives = 125/262 (47%), Gaps = 16/262 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L K+ R    L A   L  S++RLVV IA  Y+  GL   ++  EG +GL +A +KFDP
Sbjct: 66  DLKKQIRRS--LRAKAALTESNIRLVVSIAKRYQHRGLSFQDLAQEGILGLTRACEKFDP 123

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           ERGFR +TY+ WWIK ++   I      +++    + +     LR+++  L+A    + +
Sbjct: 124 ERGFRFSTYASWWIKQSIMRAIADQGRTIRLPVHIHDQ--INALRKVERELKAELGRDAR 181

Query: 156 PEQV-------VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
            E++           + LN    + +SM   L   +S  +       +       ++ D 
Sbjct: 182 LEEITEKSTLTAEKIEFLNRVSQQDVSMEQELRTSKSKGSSAGLGGPDGGLTLGDVMGD- 240

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSR 266
              E    E+   +  ++ ++R +  LN RE+ +   R   ++    TLE +   F V+R
Sbjct: 241 --PEAQPAEEASYQMLKDDISRLICTLNSREQAVIRMRFGLDDGKAKTLEEIGRRFSVTR 298

Query: 267 ERVRQIEARAFKKVQESIQKQV 288
           ER+RQIE+RA  K+++  +   
Sbjct: 299 ERIRQIESRALHKLRQPYRNHA 320


>gi|9082209|gb|AAF82776.1|AF273254_1 RNA polymerase sigma factor [Coxiella burnetii]
          Length = 410

 Score =  193 bits (490), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 69/286 (24%), Positives = 123/286 (43%), Gaps = 24/286 (8%)

Query: 16  LSRYIHEIRKIPM----------LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVK 63
           L +Y  EI +             L  QE   + +R    E     A   ++ ++LRLV+ 
Sbjct: 125 LEKYSKEIYRAQRNLAQLEEQNNLNIQEIKEINRRVAIGEAKSRRAKKEMIEANLRLVIS 184

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      
Sbjct: 185 IAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQART 244

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           ++I            L R+   +   T     PE    + +++++ E +V  +       
Sbjct: 245 IRIPVHM--IETINKLNRISRQILQETGIEATPE---ELGRRMDMPEEKVRKVLKIAKEP 299

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            S+   I   +   S   D++    D   +  ++            R+     P   ++ 
Sbjct: 300 ISMETPI--GEDEDSNLGDFI---EDINMESPVDFATSAGLMEATRRNFVYAYPARSQVL 354

Query: 244 EARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             R   +     TLE + +  +V+RER+RQIEA+A +K++   + +
Sbjct: 355 RMRFGIDMNTDHTLEEVGNNSDVTRERIRQIEAKALRKLRHPSRAE 400


>gi|307150096|ref|YP_003885480.1| RpoD subfamily RNA polymerase sigma-70 factor [Cyanothece sp. PCC
           7822]
 gi|306980324|gb|ADN12205.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7822]
          Length = 298

 Score =  192 bits (489), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 62/291 (21%), Positives = 135/291 (46%), Gaps = 32/291 (10%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE--------------------HGDLSAAHRL 53
             +  Y+ EI +IP+L  +EE  LA + ++                         A  ++
Sbjct: 7   DPVRSYLQEIGRIPLLNSEEEIQLATKVQKMLSLLELKKDNLAAAEQKIIEQGQRAKQQM 66

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           + ++LRLVV IA  Y+  GL + +++ EG++GL++AV+KFDP +G++ +TY+ WW++ A+
Sbjct: 67  IQANLRLVVSIAKRYQRRGLSLLDLIQEGSLGLIRAVEKFDPSKGYKFSTYAYWWVRQAI 126

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
              +      +++     +     NL  LK  ++ +T    +      +A+++ +   ++
Sbjct: 127 TRALAEKSRTIRLPIHMTE-----NLNHLKKSVRELTGELGRKPTEQEVAQRMEIPLEKL 181

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             +   +   ++ +  I + D N ++  + L  +       + E+E        +   + 
Sbjct: 182 QEIRHAVYRTDAKSLNI-TLDDNQTELGEVLPDETSLPIDFVSERELMT----KVDDLLE 236

Query: 234 VLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            L PR+R I   R        ++ + +  +  +S ER RQ+  RA + +++
Sbjct: 237 DLPPRQREIITLRFGLLTGKRMSYKEIGRQCGISHERARQLLNRAMRTLKQ 287


>gi|17158751|ref|NP_478262.1| transcription initiation factor sigma [Nostoc sp. PCC 7120]
 gi|464687|sp|Q03065|RPSB_ANASP RecName: Full=RNA polymerase sigma-B factor
 gi|424021|pir||B47017 probable transcription initiation factor sigma SigB - Anabaena sp
 gi|142112|gb|AAA22046.1| RNA polymerase sigma-subunit [Nostoc sp. PCC 7120]
 gi|17134700|dbj|BAB77258.1| transcription initiation factor sigma [Nostoc sp. PCC 7120]
          Length = 332

 Score =  192 bits (489), Expect = 4e-47,   Method: Composition-based stats.
 Identities = 71/311 (22%), Positives = 133/311 (42%), Gaps = 52/311 (16%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEY-----------------VLAKRYREHGDLS-------- 48
             +S Y+H+I ++P+L  ++E                   LA++ +    L         
Sbjct: 23  DAVSIYLHKIGRVPLLSHEQEIFFAQQVQQMMVMFTAKEELAEKLQREPTLQEWADKMQL 82

Query: 49  --------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                         A  +++ ++LRLVV IA  Y+   L   +++ EG +GL + V+KFD
Sbjct: 83  KEDVLLQQLSQGQIAKQKMIQANLRLVVSIAKKYQKRNLEFLDLIQEGALGLERGVEKFD 142

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P  G++ +TY+ WWI+  +   I +    +++      K     L ++K   + ++    
Sbjct: 143 PTLGYKFSTYAYWWIRQGITRAIAQQSRTIRLPIHMADK-----LNKIKCVQRELSQKLG 197

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
               V  IA+ LN+  S++      +    SL+  I    +  +Q QD L  D    E+ 
Sbjct: 198 YIAGVTEIAQALNLEPSQIREYLQLVRQPVSLDMRI--GFEQDTQLQDLLKDDGMSPERY 255

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQI 272
                ER+     +   ++ L P+++ +   R        +TL  +S    +SRERVRQ+
Sbjct: 256 ----AERELLYQDIHNLLAKLTPQQKEVLILRFGLAGGCELTLVQISQRMGISRERVRQV 311

Query: 273 EARAFKKVQES 283
           E +A   ++  
Sbjct: 312 EKQALTLLRRY 322


>gi|158339615|ref|YP_001521004.1| RNA polymerase sigma-70 factor, putative [Acaryochloris marina
           MBIC11017]
 gi|158309856|gb|ABW31472.1| RNA polymerase sigma-70 factor, putative [Acaryochloris marina
           MBIC11017]
          Length = 268

 Score =  192 bits (489), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 65/275 (23%), Positives = 126/275 (45%), Gaps = 15/275 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             L  +  EI + P+L  +EE  LA++  + G L A  R++  +LR VV IA  Y+  GL
Sbjct: 6   DSLHFFFKEIARYPLLSHEEEIQLARQ-AQAGSLRAKQRMIECNLRFVVSIAKKYQNRGL 64

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EG+IGL  AV KFD  +G R +TY+ WWI+  +   +      + +       
Sbjct: 65  PLLDLIQEGSIGLSTAVDKFDLAQGCRFSTYAYWWIRQGITAAVRAKSRPIYLPHY---- 120

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
             +  + ++K H + +T    +   +  +++  N+    +           SL+ L+   
Sbjct: 121 -HWDTVGKIKKHFRVLTQQLGREPSLSELSEATNIKPKTISRTLQLFQQISSLDQLVGPQ 179

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QEN 251
            K++       + D    E       E     + L++ M+ L+ RER +   R     ++
Sbjct: 180 QKDT-------LLDMLAGEDQPTHYLESLQLDDELSQVMASLDERERFVLSQRYGLEDDH 232

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           P +++ +  +  +S E +R I  +  +K++   Q 
Sbjct: 233 PKSMKEIGQQIGLSHEGIRLILKKIMQKLERYAQS 267


>gi|158337702|ref|YP_001518878.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158307943|gb|ABW29560.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 318

 Score =  192 bits (489), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 73/311 (23%), Positives = 139/311 (44%), Gaps = 52/311 (16%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKR-------------YREHGDLS---------- 48
            +  ++ Y+ EI + P+L  +EE +  K+              +EH D            
Sbjct: 7   SKDSITTYLREIGRFPLLNHEEEIIFGKQVQRFVALQDLKQDLQEHLDREPTQAEWADKA 66

Query: 49  ----------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
                           A  ++V S+LRLVV IA  Y    +   +++ EG IGL + V+K
Sbjct: 67  EISVSQLQKELKLGHKANRKMVESNLRLVVSIAKKYNKAKVEFLDLIQEGTIGLQRGVEK 126

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FDP +G+R +TY+ WWI+ AM   I      +++    N+K     L +L+   + ++  
Sbjct: 127 FDPMKGYRFSTYAYWWIRQAMTRAIAEQERTIRLPIHINEK-----LSKLRKVRRQLSQK 181

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +   V  +A +++++  ++           SL+  I   D+ +++  + L   ++  +
Sbjct: 182 LHRDPTVQELAVEMDLAPKKIEDYLNYARRSISLD--IQIGDQQNTELWELLEDPNESPD 239

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVR 270
             +     R +    L + +  L+P++R +   R     +NP+TL  +     VSRE VR
Sbjct: 240 TYVTASSLRSD----LAKLLQDLSPQQREVITLRYGLIDQNPLTLAKVGERLNVSREWVR 295

Query: 271 QIEARAFKKVQ 281
           ++E  AFK ++
Sbjct: 296 RVEREAFKILR 306


>gi|300725901|ref|ZP_07059364.1| RNA polymerase sigma-70 factor [Prevotella bryantii B14]
 gi|299776838|gb|EFI73385.1| RNA polymerase sigma-70 factor [Prevotella bryantii B14]
          Length = 290

 Score =  192 bits (489), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 70/284 (24%), Positives = 137/284 (48%), Gaps = 12/284 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRL 60
           + + SI       L +Y+ EI   PM+   +E  LA+  R+ G     A  +LV ++LR 
Sbjct: 5   KISKSITNRSSEALDKYLAEISHEPMINIDQEIELAQAIRKGGRAGERAKDKLVKANLRF 64

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y+  GL +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I   
Sbjct: 65  VVSVAKQYQHQGLSLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQ 124

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
             +V++            L ++   +     +N +   +  I++   + E ++       
Sbjct: 125 SRIVRLPLNQ-----VGALSKINATISKFEQDNQRRPSIQEISRLTGIEEEKIEQSIKAD 179

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               S++A     ++NS    D +    D +    ++ +      + + +  +VL  RE 
Sbjct: 180 NHHTSIDAPFQDGEENS--MVDIMASGEDTRTDRQVDHDSMAQELHSVLK--NVLKDREI 235

Query: 241 RIF-EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +I  E   +  +   LE +     ++RERVRQI  ++  K++E+
Sbjct: 236 KILCECYGIGCHEKGLEEIGDRMGLTRERVRQIREKSILKLREA 279


>gi|87301677|ref|ZP_01084517.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
 gi|87283894|gb|EAQ75848.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
          Length = 349

 Score =  192 bits (489), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 65/324 (20%), Positives = 132/324 (40%), Gaps = 54/324 (16%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------------------- 43
           +  Y+ +I ++P+L  ++E  L ++ +E                                
Sbjct: 38  VRSYLRDIGRVPLLTHEQEITLGRQVQELMRLEEAEQELEMRAGGQKPSAAEWASAAGLS 97

Query: 44  --------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
                        A  R+V ++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP
Sbjct: 98  PALLKRKLSSGRRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDP 157

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            RG++ +TY+ WWI+  +   I      +++     +      L +LK   + ++    +
Sbjct: 158 TRGYKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITE-----TLNKLKKGQRELSQELGR 212

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
              +  +A  + + E EV  + CR     SL   +   D   ++  D L  D      + 
Sbjct: 213 TPTLSELAVCVELPEEEVKDLLCRARQPVSLETKV--GDGEDTELLDLLQGDG----TLP 266

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIE 273
            E  + +  R  +   +  L   +R +   R   +   P++L  +     +SR+R+R +E
Sbjct: 267 AESVDSECLRGDMRALLEQLPELQRSVLSMRYGIDVEEPMSLTGIGRILGMSRDRIRNLE 326

Query: 274 ARAFKKVQESIQKQVELSSSPPLL 297
                 ++  +  QV+  S   ++
Sbjct: 327 RDGLASLRR-LSDQVKDYSDAAMI 349


>gi|162455526|ref|YP_001617893.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
 gi|161166108|emb|CAN97413.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
          Length = 715

 Score =  192 bits (489), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 65/241 (26%), Positives = 120/241 (49%), Gaps = 13/241 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A +R V ++LRLVV IA  Y    LP+ +++ EGNIGLM+AV++FD  RG+R +TY+ W
Sbjct: 483 DAKNRFVKANLRLVVSIARRYNRGRLPLIDLIQEGNIGLMKAVERFDHSRGYRFSTYASW 542

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   +      V+I        +     R+    QAI         +  + K+  
Sbjct: 543 WIRHAISRALADKGRAVRIPVH-----MLDTYNRVARATQAIIARTGHEPTIEELEKETG 597

Query: 168 VSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           V   ++  +    A    SL+  +   D++  ++ D+L  +         +    +   +
Sbjct: 598 VPREKLDKVKDFYAETPFSLDRPV--GDEDGRKFIDFLQEE---NALSPFDHLANRKWSD 652

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + R ++ L P E RI   R     E+ +TL+ +  ++ +SRER+RQ++ +A  K+++ +
Sbjct: 653 EVRRLLTTLTPIESRIIRWRFGLDDEDELTLKEIGDKYNLSRERIRQLQEQALGKIRKQM 712

Query: 285 Q 285
           +
Sbjct: 713 R 713


>gi|157273328|gb|ABV27227.1| sigma 38 RpoS [Candidatus Chloracidobacterium thermophilum]
          Length = 549

 Score =  192 bits (488), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 67/245 (27%), Positives = 113/245 (46%), Gaps = 15/245 (6%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGY--RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
             A   ++ ++LRLVV IA  Y  R  GL  S+++ EGNIGLM+AV+KFD  RG++ +TY
Sbjct: 304 EKARREMIEANLRLVVSIAKNYINRSRGLQFSDLIQEGNIGLMRAVEKFDYRRGYKFSTY 363

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + WWI+ A+   I      +++     +      + ++    + +     +      +A+
Sbjct: 364 ATWWIRQAVTRAIADQGRTIRVPVHMVE-----TINKIVRTARLMVQELGREPTHEELAQ 418

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           + ++  ++V           SL   I   D   S    ++    D       E    K  
Sbjct: 419 RTDLPVAKVRQALKIAQEPISLETPI--GDDGESNLGSFI---EDRNSLNPAEMIVGKGL 473

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQE---NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R      +S L PRE +I + R   +      TLE +   F V+RER+RQIEA+A +K++
Sbjct: 474 REATLEVLSTLTPREEQILKMRFGLDGDGQERTLEEVGRYFHVTRERIRQIEAKALRKLR 533

Query: 282 ESIQK 286
              + 
Sbjct: 534 HPSRS 538


>gi|124021877|ref|YP_001016184.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Prochlorococcus marinus str. MIT 9303]
 gi|123962163|gb|ABM76919.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Prochlorococcus marinus str. MIT 9303]
          Length = 350

 Score =  192 bits (488), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 66/311 (21%), Positives = 130/311 (41%), Gaps = 52/311 (16%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--------------------------- 48
           +  Y+ +I ++P+L  ++E  L ++ +E   L                            
Sbjct: 43  VRSYLRDIGRVPLLSHEQEITLGRQVQELMSLEQLESELEGKTGAPASRKELAKAAGLSE 102

Query: 49  ------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                       A  R+V+++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP 
Sbjct: 103 LQLKKKLQIGRRAKERMVSANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPT 162

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RG++ +TY+ WWI+  +   I      +++     +      L +LK   + ++    + 
Sbjct: 163 RGYKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITE-----MLNKLKKGQRELSQEMGRT 217

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
             V  +A+ + + E EV  + CR     SL   +   D+              G+E++  
Sbjct: 218 PTVSELAEFVELPEEEVKDLMCRARQPMSLEMKVGDGDETELLELLA------GEEELPS 271

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEA 274
           EK E    +  L   +  L   + R+   R   +   P+ L  +    ++SR+RVR +E 
Sbjct: 272 EKVEVDCMKGDLRTLLEKLPELQGRVLRMRYGIDGGEPMNLTGIGRILDISRDRVRNLER 331

Query: 275 RAFKKVQESIQ 285
                +++  +
Sbjct: 332 HGLNGLRQLSE 342


>gi|149908225|ref|ZP_01896889.1| hypothetical DNA-directed RNA polymerase, sigma subunit [Moritella
           sp. PE36]
 gi|149808767|gb|EDM68700.1| hypothetical DNA-directed RNA polymerase, sigma subunit [Moritella
           sp. PE36]
          Length = 284

 Score =  192 bits (488), Expect = 5e-47,   Method: Composition-based stats.
 Identities = 74/270 (27%), Positives = 141/270 (52%), Gaps = 12/270 (4%)

Query: 15  GLSRYIHEIRK-IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
            L  Y+ ++ K   +L K+EEY +A     +GDL A +R++ ++LRLV+ +A  Y+   +
Sbjct: 9   ALDAYLQQVNKKSKLLTKEEEYDIAVAVA-NGDLRAKNRMIEANLRLVISVAKRYQYSVI 67

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGN GL++AV+KFDP +GFR +TY++WWIK  ++  I+ S   ++I       
Sbjct: 68  PLVDIIQEGNTGLIRAVEKFDPNKGFRFSTYAVWWIKNNIERSIMNSDRTIRIPIHVG-- 125

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
           ++  ++ ++   L     ++     +V IAK L     EV+ +      + SL+  I + 
Sbjct: 126 KMHKSIAKVAKELGLDVGSDN---DLVVIAKVLETDVDEVMDVLSYYFSELSLDKGIVTD 182

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QEN 251
           +++ +   D +    D   +    + E  + R+ L   +  L   ER++ E R     E 
Sbjct: 183 NESVTTLVDII---EDQSIRTPSAEIEGGSTRDYLLALLENLPAYERQVVELRFGLTGEE 239

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           P++L  +     +SRE+VR I     ++++
Sbjct: 240 PLSLSRIGERLSMSREKVRIIIRTTLRRLK 269


>gi|58699726|ref|ZP_00374383.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Drosophila
           ananassae]
 gi|58533758|gb|EAL58100.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Drosophila
           ananassae]
          Length = 216

 Score =  192 bits (488), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 97/208 (46%), Positives = 149/208 (71%), Gaps = 2/208 (0%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           ++ V+    L +YI  ++K PML ++EE  LAK + ++ D+S+AH+L+TSHL LVVKIAM
Sbjct: 3   NLCVDSRTNLMQYIARVQKFPMLSQEEEVRLAKNWNQYKDVSSAHKLITSHLNLVVKIAM 62

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            ++ YGL + ++V EGN+GLM AVKKF+P+ GFR +TY++WWI+A+++++IL+SWS VKI
Sbjct: 63  KFKNYGLLLMDLVMEGNMGLMHAVKKFNPDLGFRFSTYAVWWIEASIKDFILKSWSFVKI 122

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNN-LKPEQVVAIAKKLNVSESEVISMNCRLA-GDE 184
           GTT  Q+RLFF+LR++K  +   T+   L  E++ AI+ +L+VSE +V+ MN R+A  D+
Sbjct: 123 GTTQAQRRLFFSLRKIKKRILQYTNRETLNNEEIKAISNELSVSEGDVLQMNYRMACKDQ 182

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQE 212
           SLN  I   D +  + QD +  +   QE
Sbjct: 183 SLNDCIKIGDDSKRELQDMIPCNLVSQE 210


>gi|17233195|ref|NP_490285.1| group 2 sigma 70-type sigma factor [Nostoc sp. PCC 7120]
 gi|17135717|dbj|BAB78263.1| group 2 sigma 70-type sigma factor [Nostoc sp. PCC 7120]
          Length = 316

 Score =  192 bits (488), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 72/305 (23%), Positives = 128/305 (41%), Gaps = 52/305 (17%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYRE----------------------------------- 43
           Y+ EI + P+L   +E   A+  ++                                   
Sbjct: 12  YLQEIGQFPLLTSDQEITYARLVQQMIALQEQQHELTQKLEREPTTLELANFLNKTEAQV 71

Query: 44  ----HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                    A  +++T++LRLVV IA  Y+   L   ++V EG IGL + ++KFDP RG+
Sbjct: 72  NQILELGQRAKQKMITANLRLVVSIAKKYQRRNLEFLDLVQEGAIGLQRGIEKFDPNRGY 131

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           +L+TY+ WW+  A+   I      V++    N+K     L ++K   +       +   V
Sbjct: 132 KLSTYAYWWVTQAITRAIAEKSRTVRLPIHVNEK-----LNQIKKVQREFFQTLGRRATV 186

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IA+KL +  S++       +G  SL+  I   D   ++  + L  +    +    E  
Sbjct: 187 AEIAQKLELEPSQIREYLKVASGTISLDLKI--GDNKETELSELLASEGVSPD----ENI 240

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAF 277
             +  R  L+  ++ L P +R +   R   L     +L  +  +  +SRERVRQI+ +A 
Sbjct: 241 THEMLRQDLSDLLASLKPMQREVLILRFGLLDNQEQSLAQIGEKLNLSRERVRQIQQKAM 300

Query: 278 KKVQE 282
             ++ 
Sbjct: 301 TALRR 305


>gi|119493081|ref|ZP_01624006.1| Sigma 28 (Flagella/Sporulation) [Lyngbya sp. PCC 8106]
 gi|119452826|gb|EAW34001.1| Sigma 28 (Flagella/Sporulation) [Lyngbya sp. PCC 8106]
          Length = 331

 Score =  192 bits (488), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 76/312 (24%), Positives = 137/312 (43%), Gaps = 50/312 (16%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------------------------- 43
           +  +      + + P+L+  EE  LA++ +                              
Sbjct: 18  DDAVGALFKRMARYPLLKANEEIELARQIKALVTFKELEEELTHELGRCPQSSELATATG 77

Query: 44  ----------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
                        + A  ++++S+LRLVV IA  Y   G+P  +++ EG +GL +A +KF
Sbjct: 78  LSEAELNHQFQQGIIAKQKMISSNLRLVVSIAKRYLNRGVPFLDLIQEGALGLNRATEKF 137

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           DP++G++ +TY+ WWI+  +   I      V++     +      L +L+G  Q +  + 
Sbjct: 138 DPDKGYKFSTYAYWWIRQGITRTIANQGRTVRLPVHVVE-----QLNKLQGIHQDLRRSL 192

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            +      +A+ L++S  ++  +        SLN  + S  + +S+  D L        +
Sbjct: 193 RRKPTEDELAEALSISPQQLRLLEQVRRKSLSLNHRVGS--EENSELMDLLEDYESLSPE 250

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQ 271
             I   E   R+ +L    SVLN RE+ I   R       P TL+ +S    +SRERVRQ
Sbjct: 251 SQIN--ELMMRQELLEVLRSVLNEREQDILSLRYGLTTGVPYTLDEVSGMCSLSRERVRQ 308

Query: 272 IEARAFKKVQES 283
           I+A+A +K++  
Sbjct: 309 IQAKAMRKLRRP 320


>gi|86608620|ref|YP_477382.1| RNA polymerase sigma factor [Synechococcus sp. JA-2-3B'a(2-13)]
 gi|86557162|gb|ABD02119.1| RNA polymerase sigma factor [Synechococcus sp. JA-2-3B'a(2-13)]
          Length = 319

 Score =  192 bits (488), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 72/302 (23%), Positives = 137/302 (45%), Gaps = 45/302 (14%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE---------------------- 43
           MS  ++ +  + R++  I +  +L  +EE  LA + +                       
Sbjct: 1   MSESLDLQDAVGRFLKTIGRYSLLTAEEELRLAHQVQRMVTLLEQRQPHESVEGWSQRLG 60

Query: 44  ----------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
                         +A  R+V  +LRLVV IA  YR  GLP  +++ EG IGL +AV+KF
Sbjct: 61  IPLAELQQILRQGEAAKKRMVECNLRLVVSIAKRYRNRGLPFLDLIQEGTIGLTRAVEKF 120

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           DP RG++ +TY+ WWI+ ++   I     ++++        ++  + ++K   + ++   
Sbjct: 121 DPTRGYKFSTYATWWIRQSVNRGIQNKGRMIRLPAH-----MYEKVSQVKRRYRELSAER 175

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
               Q   +   L++ ++    +   +A   SLN  +   D++ ++ Q ++  + +   +
Sbjct: 176 GSRPQAEEVFDSLDIGDNYRELITRHMAEMRSLN--VGVGDEDGTELQHFIPDEDNDPVE 233

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQ 271
            L +   R+  R ++      L+ RER++  AR   +     TL  +     +SRERVRQ
Sbjct: 234 HLTQLARREEVRALV----GQLSERERQVIVARYGLDGSRGLTLREIGEHIGLSRERVRQ 289

Query: 272 IE 273
           IE
Sbjct: 290 IE 291


>gi|320536473|ref|ZP_08036507.1| RNA polymerase sigma factor RpoD family protein [Treponema
           phagedenis F0421]
 gi|320146682|gb|EFW38264.1| RNA polymerase sigma factor RpoD family protein [Treponema
           phagedenis F0421]
          Length = 282

 Score =  192 bits (488), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 73/288 (25%), Positives = 147/288 (51%), Gaps = 16/288 (5%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M +KN++     +  L+ Y+ +I KIP+L  +EE  LA R  E GD +A  +L+ ++LR 
Sbjct: 1   MKKKNIA----TDNVLAGYLRDINKIPLLTLEEEVELATRAAE-GDKAAKDKLIQANLRF 55

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y+  GLP+ +++SEGNIGLM A  +FD  +G++  +Y++WWI+ ++ + I   
Sbjct: 56  VVNVAKKYQNQGLPLMDLISEGNIGLMNAADRFDVTKGYKFISYAVWWIRQSILKAICEK 115

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
             ++++            L +++   + I     + E++  +A  L +    V  +    
Sbjct: 116 SRMIRLPLNR-----VGELIQIEKTRKEIRSTASEEEELKEVADILALDHDTVKMIVNIG 170

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               SL+A +   D  + +  D++    D Q +         + +  + + ++ L  RE 
Sbjct: 171 REPVSLDAPLFD-DAANGKMGDFI---EDAQYEQPEAYMLDVSLKESIDKVINTLPKREA 226

Query: 241 RIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            I   R        ++L+++   F +++ER+RQIE ++ ++++ +  K
Sbjct: 227 EILRYRFGLNGYKQLSLKDVGKIFNLTKERIRQIEKKSLEQLKATSYK 274


>gi|318041996|ref|ZP_07973952.1| RNA polymerase sigma factor, sigma-70 family protein [Synechococcus
           sp. CB0101]
          Length = 318

 Score =  192 bits (488), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 67/302 (22%), Positives = 131/302 (43%), Gaps = 41/302 (13%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------------------------HGD 46
            LS ++ EI +  +L  ++E +L ++ +                                
Sbjct: 13  SLSAFLGEIGRHQLLTPEQELMLGRKVQAMVALHERCHSAGGVGEACSYNDIEKRTMRVG 72

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  +++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG R +TY+ 
Sbjct: 73  ERAKDQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSTYAY 132

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   +      ++I    N+K     L RL+     +   +        +++ +
Sbjct: 133 WWIRQGLNRALSTQSRTIRIPVNVNEK-----LTRLRAAKARLLQRHGSQPSAQQLSEAM 187

Query: 167 NVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           ++   EV  +      +   SL  ++ S   + ++  D L  +     +     E     
Sbjct: 188 DLPVQEVEDLLGCELRSVTVSLQGVVKSK-SDPTELVDVLPSEDLPPMERCELAERNAAV 246

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPV---TLENLSSEFEVSRERVRQIEARAFKKVQ 281
             +L +  S L P+ER +   R   +      TL  ++     SRE  RQ+  RA +K++
Sbjct: 247 WKLLDQ--SNLTPKERTVVMLRFGLDGSHEWRTLAEVARLLGCSREYCRQVVQRALRKLR 304

Query: 282 ES 283
           ++
Sbjct: 305 KA 306


>gi|294673146|ref|YP_003573762.1| RNA polymerase sigma-70 factor [Prevotella ruminicola 23]
 gi|294474130|gb|ADE83519.1| RNA polymerase sigma-70 factor [Prevotella ruminicola 23]
          Length = 290

 Score =  192 bits (488), Expect = 6e-47,   Method: Composition-based stats.
 Identities = 76/294 (25%), Positives = 145/294 (49%), Gaps = 12/294 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRL 60
           + + SI    E  L++Y+ +I +IPM+  ++E  LA+  R+ G     A  +LV ++LR 
Sbjct: 5   KISKSITTRTEESLNKYLTDISRIPMITPEQEVELAQTIRKGGRTGAKAKEKLVNANLRF 64

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y+  G+P+ +++SEGN+GL+ A  KFD  RGF+  +Y++WWI+ ++ + I   
Sbjct: 65  VVSVAKQYQHQGIPLIDLISEGNVGLITAADKFDETRGFKFISYAIWWIRQSILQAIADY 124

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
             +V+   +           ++K    A    N +      +++ +++   ++       
Sbjct: 125 SGMVRRPQSQ-----IAISNKIKNATNAFMLKNQRNPSAEELSEIISLEIEKIEKAIQSE 179

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           A   S++A I  SD +++   D +    +      ++ E      +++    +VL+ RER
Sbjct: 180 AHVASIDAPI--SDDDTTTMADSIASTAEYASDRKVDYE--SMCSDVMLVLGAVLSERER 235

Query: 241 RIFEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
            I         P   L+++ S   +SRERVRQI  R   K+++S    + L  +
Sbjct: 236 AIVVQSFGIGCPERGLDDIGSSMGLSRERVRQIRERGLDKIRKSNMSYILLRHA 289


>gi|257470234|ref|ZP_05634325.1| RpoD family RNA polymerase sigma factor [Fusobacterium ulcerans
           ATCC 49185]
 gi|317064448|ref|ZP_07928933.1| RNA polymerase sigma-A factor [Fusobacterium ulcerans ATCC 49185]
 gi|313690124|gb|EFS26959.1| RNA polymerase sigma-A factor [Fusobacterium ulcerans ATCC 49185]
          Length = 260

 Score =  191 bits (487), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 74/273 (27%), Positives = 140/273 (51%), Gaps = 16/273 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
           + +S YI +I + P+L  +EE  ++ + +  GD  A  +LVTS+LRLV+ IA  Y   G+
Sbjct: 2   LDISEYIKDISRYPLLTPEEEKDISIKAK-AGDKDAQEKLVTSNLRLVISIARKYTNMGI 60

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EGN+GL++AV+K++PE+  R +TYS +WIK ++  YI  S  L++  +     
Sbjct: 61  PLLDLIQEGNMGLIRAVEKYEPEKNIRFSTYSTFWIKQSILRYITSSRGLIRFPSYV--- 117

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
             +  + R+K ++Q   + N     +  I   L++ + E       L     +    N  
Sbjct: 118 --YDGISRMKKYVQDYKNKNSHLPSIEEICSSLDMRKKEAERYIEVLEKGSCIG---NEM 172

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQEN 251
               +++   +++D         +K   KN    L + ++ L  +ER +   R   L E 
Sbjct: 173 YGEIAEYCSSIIFD-----DTFEDKVIAKNSTIDLMKKVNKLPSKEREVLIYRYGLLDEK 227

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +TL  +     +++ER+RQI+  A  K++ ++
Sbjct: 228 VLTLGEIGERMNLTKERIRQIQLEAIDKLRGTL 260


>gi|78212534|ref|YP_381313.1| type II alternative RNA polymerase sigma factor [Synechococcus sp.
           CC9605]
 gi|78196993|gb|ABB34758.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. CC9605]
          Length = 309

 Score =  191 bits (487), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 69/300 (23%), Positives = 132/300 (44%), Gaps = 37/300 (12%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------------------------HGD 46
            LS ++ EI +  +L  ++E ++ ++ +                                
Sbjct: 5   SLSAFLGEIGRHQLLTPEQELMMGRKVQAMVAITERCHLAGGSGPACEYSDEEKGVIRRG 64

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A ++++TS+LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG R +TY+ 
Sbjct: 65  ERAKNQMITSNLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSTYAY 124

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   +      ++I    N+K     LR  K  L      +   EQ+    +  
Sbjct: 125 WWIRQGLNRALSTQSRTIRIPVNVNEK--LTKLRAAKARLMQRNGLSPSGEQLAEFMEIP 182

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
                ++++   R +   SL  ++ S   + S+  D L  D     +     E   +  +
Sbjct: 183 IAEVEDLLACELR-SVTVSLQGVVKSK-SDPSELVDVLPSDELPPMERAEIAERTASVWS 240

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +L ++   L P+E  +   R   +      TL  ++     SRE  RQ+  RA +K++++
Sbjct: 241 LLAKA--NLTPKEHTVVTLRFGLDGTNEWRTLAEVARHMNCSREYCRQVVQRALRKLRKT 298


>gi|303235620|ref|ZP_07322227.1| RNA polymerase sigma factor RpoD family protein [Prevotella disiens
           FB035-09AN]
 gi|302484067|gb|EFL47055.1| RNA polymerase sigma factor RpoD family protein [Prevotella disiens
           FB035-09AN]
          Length = 290

 Score =  191 bits (487), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 72/282 (25%), Positives = 135/282 (47%), Gaps = 12/282 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRL 60
           + + SI       L +Y+ EI + PM+   EE  LA+   + G     A  +L+ ++LR 
Sbjct: 5   KISKSITNRTSEALDKYLVEIGREPMITVDEEIELAQEIHKGGRKGERAKEKLIKANLRF 64

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y+  GL +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I   
Sbjct: 65  VVSVAKQYQHQGLSLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQ 124

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
             +V++    NQ      + ++          + +   +  +A    + E+ +       
Sbjct: 125 SRIVRLP--LNQVGAISKINQVSN---EFIQKHNRRPSIHELADLTGIDEARIRQSQSAD 179

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               S++A  +    + +   D L    D +    ++ E   +  N + +  + L  RER
Sbjct: 180 NHHMSIDAPFSD--DDDNSMSDMLASGDDSRTDKAVDFESMSDDLNAVLQ--NTLKDRER 235

Query: 241 RIFEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           RI         P   LE + +E  ++RERVRQI  +A +K++
Sbjct: 236 RIVIECFGIGCPEKGLEEIGTEMALTRERVRQIREKAIEKIR 277


>gi|119492598|ref|ZP_01623816.1| RNA polymerase sigma factor [Lyngbya sp. PCC 8106]
 gi|119453067|gb|EAW34237.1| RNA polymerase sigma factor [Lyngbya sp. PCC 8106]
          Length = 333

 Score =  191 bits (487), Expect = 7e-47,   Method: Composition-based stats.
 Identities = 68/321 (21%), Positives = 139/321 (43%), Gaps = 52/321 (16%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYR------EHGDL-------------------- 47
             +  Y+HEI ++P+L ++EE    K+ +      E  D                     
Sbjct: 24  DTVRTYLHEIGRVPLLTQEEEIHYGKQVQQMMKQLEEKDKLTKKLEHEPSKTEWANEVEL 83

Query: 48  -------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                         A  +++ ++LRLVV IA  Y+   +   +++ EG +GL + V+KFD
Sbjct: 84  TEDELDRILDCGRRAKQKMIEANLRLVVSIAKKYQKRNMEFLDLIQEGTLGLERGVEKFD 143

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P RG++ +TY+ WW++ A+   I ++   +++     +K     L ++K   + +     
Sbjct: 144 PMRGYKFSTYAYWWVRQAITRAIAQNGRTIRLPIHITEK-----LNKIKRVQRDLVQKYG 198

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +      IA+ L +  S++           SL+  +   D   ++ Q+ L  +    +  
Sbjct: 199 RNPTPTEIAEALELEPSQIREYLLASRHPISLD--LRVGDNQDTELQELLEDETASADNY 256

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
           +  +  R++    L   +  L P++R +   R   E+   ++L  + +   +SRERVRQ+
Sbjct: 257 VTHELLRQD----LKSLIDELTPQQREVILLRYGLEDGKELSLSKVGARMSISRERVRQL 312

Query: 273 EARAFKKVQESIQKQVELSSS 293
           E +A   ++    +  E  +S
Sbjct: 313 ENQALNHLRRRKSQVREYLAS 333


>gi|219883041|ref|YP_002478205.1| RNA polymerase, sigma 32 subunit, RpoH [Arthrobacter
           chlorophenolicus A6]
 gi|219862047|gb|ACL42388.1| RNA polymerase, sigma 32 subunit, RpoH [Arthrobacter
           chlorophenolicus A6]
          Length = 951

 Score =  191 bits (487), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 69/303 (22%), Positives = 131/303 (43%), Gaps = 38/303 (12%)

Query: 5   NMSIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVL-----AKRYREH------------- 44
           + + ++ G IG  +  Y+ +     +L  +E   L     A  Y EH             
Sbjct: 456 SEAPVLEGSIGDDVRLYLEQASSFDLLTHEEVTDLGMAIEAGLYAEHLLGTARPEGRRAI 515

Query: 45  --------GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                       A  +LV+ +LRLVV IA  + G G+   +++ EGN GL +AV+KFD  
Sbjct: 516 LELESVASAGRDAVLKLVSCNLRLVVSIAKRHTGRGMDFLDLIQEGNAGLYRAVQKFDYT 575

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +GF+ +TY+ WWI+ A+   I      +++    +++ +   +       +    +  + 
Sbjct: 576 KGFKFSTYATWWIRQAITRGIADQSRTIRLPVHFHEQVVSVFI-----AERNFLQSEGRD 630

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
                IA+    +  E+ ++        SL+  + +  K   +     +YD D  E    
Sbjct: 631 GTAEEIAEACGKTVDEINAVRRHRTPPASLDWEVPNG-KGGVELLGETLYDPD--EPTAY 687

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIEA 274
           +       ++ +  ++  L+ RE  +   R        +TL+ + + + V+RER+RQIEA
Sbjct: 688 DAAVLAQLQSAVHGALDRLSEREAGVLAYRFGLATGEQLTLDQIGTIYGVTRERIRQIEA 747

Query: 275 RAF 277
           +AF
Sbjct: 748 KAF 750


>gi|317060654|ref|ZP_07925139.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. D12]
 gi|313686330|gb|EFS23165.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. D12]
          Length = 276

 Score =  191 bits (487), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 83/275 (30%), Positives = 143/275 (52%), Gaps = 16/275 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           LS Y+ +IR+   LEK+EE  L  +  + GD  A ++L+  +LRLVV +A GYR  G+ +
Sbjct: 11  LSLYLKDIRQYKTLEKEEELELVIK-AQSGDEEAKNQLILCNLRLVVNVAKGYRSKGMNL 69

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++SEGN+GL++A++KFD E+GFR +TY++WWIK ++ + I+     ++I +       
Sbjct: 70  IDLISEGNLGLIRAIEKFDVEKGFRFSTYAVWWIKQSISKAIIFKGREIRIPSYR----- 124

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           +  L ++  ++            V  +A+ LN+  ++V  +        SL+  I     
Sbjct: 125 YDILNKINRYVTEEIKLYGVYPSVEEVAEYLNMPVNKVEEIMIEFQEPMSLSTEIGED-- 182

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPV 253
                  +L     G E+   EK   K  +  L   ++ L+ RE+ I + R   +     
Sbjct: 183 ------IYLEDTLSGTEEHFEEKVYYKMMQQRLKDILNRLDTREQEILKLRFGLDGYEIH 236

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           TLE +   F ++RERVRQIE    KK++    K++
Sbjct: 237 TLEEIGKNFNITRERVRQIEKNTLKKLKRKYTKEL 271


>gi|1519640|gb|AAB07553.1| SigC [Chloroflexus aurantiacus J-10-fl]
          Length = 312

 Score =  191 bits (487), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 70/309 (22%), Positives = 130/309 (42%), Gaps = 39/309 (12%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSA------------- 49
           R   +I  +    +  Y++EI   P+L  ++E  LA+   + G  +A             
Sbjct: 2   RNPTTIGRSASDPIVLYLNEIGAEPLLTFEQEQHLAQTMSQ-GRRAAERLHNEPLLPLAE 60

Query: 50  -------------AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                          +L+ S+LRLVV IA  Y+G+ L + +++ EG++GLM AV KFD  
Sbjct: 61  KQRLIAQVNAGTGRAQLINSNLRLVVSIARRYQGHALSLLDLIQEGSVGLMGAVDKFDAS 120

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RG + +TY+ +WI+ ++   I      V++     ++     L RL    Q ++    + 
Sbjct: 121 RGLKFSTYATYWIRQSIGRAIADHSRTVRLPVHLGER-----LSRLSRLRQELSQQLDRE 175

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
             +  +A           +         SL+     ++       + L    D  +    
Sbjct: 176 PTLEELAAGCRPERRAGRTAEQAGLAPTSLDEP--HTEDGGGALAEIL---TDPLQPTPF 230

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEA 274
           ++      +  +  ++  L+PRER I   R   +     TLE +     ++RERVRQ+E 
Sbjct: 231 DEVSESMLQADVQHALQQLSPRERSILRLRYGLDGEPMHTLEQIGQRLRLTRERVRQLEH 290

Query: 275 RAFKKVQES 283
            A +K+++ 
Sbjct: 291 EALRKLRDP 299


>gi|123968168|ref|YP_001009026.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. AS9601]
 gi|123198278|gb|ABM69919.1| Putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus str. AS9601]
          Length = 307

 Score =  191 bits (487), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 75/300 (25%), Positives = 131/300 (43%), Gaps = 37/300 (12%)

Query: 15  GLSRYIHEIRKIPMLEKQ----------EEYVLAKRYREHGD------------------ 46
            LS ++ EI +  +L  +          E  VL  R +E G                   
Sbjct: 3   SLSDFLGEIGRHQLLTPERELTMGRKVQEMVVLVNRCQEAGGKGPACEYSEAERKKIKIG 62

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + ++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG R +TY+ 
Sbjct: 63  EKAKNEMITANLRLVVNLAKRYQGKGLELLDLIQEGTLGLTRAVEKYDPSRGHRFSTYAY 122

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   +      ++I    N+K     LR  K  L  +       +++    K  
Sbjct: 123 WWIRQGLNRALSTQSRTIRIPVNINEK--LTKLRSAKSKLMQLKGIPPTSDELAEEMKIT 180

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
                E++S   R +   SL   + S   + S+  D L  D     ++    E   +   
Sbjct: 181 KEEVDELLSCELR-SITVSLQGTVKSK-SDPSELVDILPSDQTPPMELAELAERTASAWK 238

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +L ++   L  +ER+I   R   +      TL  ++     SRE  RQ+  RA +K++++
Sbjct: 239 LLDKA--NLTEKERKIVSLRFGLDGSNEWRTLAEVARHMSCSREYCRQVVQRALRKLRKA 296


>gi|158340730|ref|YP_001521898.1| RNA polymerase sigma-70 factor, putative [Acaryochloris marina
           MBIC11017]
 gi|158310971|gb|ABW32584.1| RNA polymerase sigma-70 factor, putative [Acaryochloris marina
           MBIC11017]
          Length = 269

 Score =  191 bits (487), Expect = 8e-47,   Method: Composition-based stats.
 Identities = 63/275 (22%), Positives = 125/275 (45%), Gaps = 15/275 (5%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++      L  Y+ E+ + P+L  +EE  LA++ +  G L A  R++  +LRLVV IA  
Sbjct: 1   MMATKHDSLHFYLKEMARYPLLSHEEEIELARQAK-AGSLRAKQRMIECNLRLVVSIAKK 59

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           ++  GLP+ +++ EG+IGL  AV KFD  +G R +TY+ WWI+  +   +      + + 
Sbjct: 60  HQNRGLPLLDLIQEGSIGLSTAVDKFDLAQGCRFSTYAYWWIRQGITAALREKSRPIYLP 119

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
                   +    ++K H + +     +   +  +++  ++    +           SL+
Sbjct: 120 H-----NHWDKANKIKKHYRELNQTLGRKPSLSELSEATDIKPKTINRTLQLFQKVSSLD 174

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             +    K+S       + D    +    +  E       L++ M+ L+ RER +   R 
Sbjct: 175 QPVGPEQKDS-------LLDLLAGDDQPTQYMESLQLDEELSQVMANLDERERFVLSQRY 227

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             E+  P +++ +  +  +S E +R I  +  KK+
Sbjct: 228 GLEDNQPKSMKAIGQQIGLSHEAIRLILNKIMKKL 262


>gi|116073053|ref|ZP_01470315.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9916]
 gi|116068358|gb|EAU74110.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9916]
          Length = 321

 Score =  191 bits (486), Expect = 9e-47,   Method: Composition-based stats.
 Identities = 66/319 (20%), Positives = 140/319 (43%), Gaps = 54/319 (16%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSA---------------- 49
           +S++ + ++ +  Y+ +I ++P+L  Q+E  L ++ ++  +L A                
Sbjct: 4   LSLLPDADL-VRSYLRDIGRVPLLSHQQEITLGRQVQDLMELEALESELKSESGEDVVAP 62

Query: 50  ------------------------AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
                                     R+V ++LRLVV +A  Y    + + +++ EG IG
Sbjct: 63  EALAKKAGLSGVQLKRKLQAGRRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIG 122

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++ V+KFDP RG++ +TY+ WWI+  +   I      +++     +      L +LK  
Sbjct: 123 LVRGVEKFDPTRGYKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITE-----MLNKLKKG 177

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            + ++    +   V  +A+ + + E EV  + CR     SL   +   D         L+
Sbjct: 178 QRELSQELGRTPTVTELAEFVELPEEEVKDLMCRARQPVSLEMKVGDGDDTE------LL 231

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFE 263
               G  ++  E+ E +  +  L   +  L   +R++   R     E+P++L  ++   +
Sbjct: 232 ELLSGDGELPSEQVESECLKGDLRDLLEQLPELQRKVLRMRYGMNGEDPMSLTGIAKTLK 291

Query: 264 VSRERVRQIEARAFKKVQE 282
           +SR+R R++E    + ++ 
Sbjct: 292 MSRDRTRRLEREGLEMLRN 310


>gi|218961053|ref|YP_001740828.1| putative RNA polymerase, sigma S (sigma 38) factor [Candidatus
           Cloacamonas acidaminovorans]
 gi|167729710|emb|CAO80622.1| putative RNA polymerase, sigma S (sigma 38) factor [Candidatus
           Cloacamonas acidaminovorans]
          Length = 292

 Score =  191 bits (486), Expect = 9e-47,   Method: Composition-based stats.
 Identities = 77/279 (27%), Positives = 143/279 (51%), Gaps = 12/279 (4%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
            +  L  Y++EI K   L ++EE+ LA + + +GD+ A ++L+ ++L+ VVKIA  Y+  
Sbjct: 9   ADKALQNYLNEISKFKTLSREEEHDLAIKAK-NGDMDAMNKLIQANLKFVVKIASRYQNR 67

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL +SE++SEGNIGL++A++KFDP++  +L +Y++WWIK  +   +    SL+++    +
Sbjct: 68  GLSLSELISEGNIGLIKAIEKFDPDKDIKLISYAIWWIKQRIMLAVSEKSSLIRVPMGKS 127

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
                  L + +   +       K      +++K+N++E  +  +  +L    S + +I 
Sbjct: 128 SAAHRVKLTQDRYFTE-----TGKIATPDELSEKMNIAEKTIEQLQNKLPETSSFDDIIT 182

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           +SD      +D L        Q L  +E     +  +  ++S L+ RE  I         
Sbjct: 183 TSDSQDFTAKDLLEDKDTLDPQSLYYQE---RMQEKIQNAISKLDAREAEIIRNYFGLNE 239

Query: 252 PV---TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
                    ++ +  +SRERVRQI+  A KK+   I+ +
Sbjct: 240 SHESRNFAQIAEKLGLSRERVRQIQKEALKKIMREIKPE 278


>gi|226309754|ref|YP_002769648.1| RNA polymerase sigma factor [Brevibacillus brevis NBRC 100599]
 gi|226092702|dbj|BAH41144.1| RNA polymerase sigma factor [Brevibacillus brevis NBRC 100599]
          Length = 314

 Score =  191 bits (486), Expect = 9e-47,   Method: Composition-based stats.
 Identities = 74/268 (27%), Positives = 131/268 (48%), Gaps = 10/268 (3%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           ++  +   PML+K+EE     RY+  GDL A   +V ++LR VV  A+ +   G+P  ++
Sbjct: 39  FLESVAATPMLDKEEELACLIRYQRDGDLEARETIVRAYLRYVVSTALRHLKRGMPFLDL 98

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EG IGL  A+ KFD  RG RL  YS WWI  A+   I    +L++I    ++      
Sbjct: 99  IQEGTIGLFTAIDKFDVGRGVRLYHYSHWWISQAITRAINDKATLIRIPVHMHE-----Q 153

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR-LAGDESLNALINSSDKNS 197
           +R+ +  +  +     +      IA  L++   +V ++    +   ES++A ++S    +
Sbjct: 154 IRQYQKQVLHLVHALNRTPDRQEIAVLLDIPLEKVEAIELALMMKMESIDAELDSEKWQT 213

Query: 198 SQWQDWLVYDH--DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV-- 253
               + L Y    D     L +  E+ + R+ +  ++  L+PR + I   R    +    
Sbjct: 214 WHEDESLSYAEIMDDGLSSLDDWIEKVDLRSQMRAALDRLSPRAQEIISMRYGLYDDQVY 273

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           TLE +   F ++RER+RQIEA    +++
Sbjct: 274 TLEEVGKMFGLTRERIRQIEATTIDRLR 301


>gi|257463050|ref|ZP_05627452.1| RNA polymerase sigma factor RpoD [Fusobacterium sp. D12]
          Length = 272

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 83/275 (30%), Positives = 143/275 (52%), Gaps = 16/275 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           LS Y+ +IR+   LEK+EE  L  +  + GD  A ++L+  +LRLVV +A GYR  G+ +
Sbjct: 7   LSLYLKDIRQYKTLEKEEELELVIK-AQSGDEEAKNQLILCNLRLVVNVAKGYRSKGMNL 65

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++SEGN+GL++A++KFD E+GFR +TY++WWIK ++ + I+     ++I +       
Sbjct: 66  IDLISEGNLGLIRAIEKFDVEKGFRFSTYAVWWIKQSISKAIIFKGREIRIPSYR----- 120

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           +  L ++  ++            V  +A+ LN+  ++V  +        SL+  I     
Sbjct: 121 YDILNKINRYVTEEIKLYGVYPSVEEVAEYLNMPVNKVEEIMIEFQEPMSLSTEIGED-- 178

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPV 253
                  +L     G E+   EK   K  +  L   ++ L+ RE+ I + R   +     
Sbjct: 179 ------IYLEDTLSGTEEHFEEKVYYKMMQQRLKDILNRLDTREQEILKLRFGLDGYEIH 232

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           TLE +   F ++RERVRQIE    KK++    K++
Sbjct: 233 TLEEIGKNFNITRERVRQIEKNTLKKLKRKYTKEL 267


>gi|296268951|ref|YP_003651583.1| RpoD subfamily RNA polymerase sigma-70 [Thermobispora bispora DSM
           43833]
 gi|296091738|gb|ADG87690.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobispora
           bispora DSM 43833]
          Length = 311

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 71/298 (23%), Positives = 132/298 (44%), Gaps = 41/298 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREH----------------GD------------- 46
           L  Y+ EI ++P+L  +EE  LAKR                    GD             
Sbjct: 18  LGTYLAEIGRVPLLTAEEEVELAKRIEAGLFAEYLLDSALTEPRIGDATDEELERIAISG 77

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A    + ++LRLVV +A  Y G G+P+ ++V EGN+GL++AV+KFD  RG++ +TY+ 
Sbjct: 78  RRAKDEFIKANLRLVVAVARKYAGRGMPLIDLVQEGNVGLVRAVEKFDYRRGYKFSTYAT 137

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      V++ T A ++     L R++  + A  +     E    +A  L
Sbjct: 138 WWIRQAVGRSIHEQGRPVRLPTHAGEQ--MTRLMRVRRDILAEQEMEPSDE---ELADVL 192

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++    V  +    +   SL   +   +++ ++  D +  D     +   ++      + 
Sbjct: 193 DMPIERVRELRRWASDPVSLQLGV--GEEDETELGDMIADDAWADPE---QQAIDTLDKE 247

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            L R ++ L+ R   +   R         TL  +   + + R+R R++E  A + +++
Sbjct: 248 RLERWLTDLDGRLSEMLRWRYGLVDGKEHTLTEVGERYGIGRDRARRMERDALRHLRK 305


>gi|91070519|gb|ABE11426.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [uncultured Prochlorococcus marinus clone HOT0M-3E5]
          Length = 231

 Score =  191 bits (486), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 65/231 (28%), Positives = 121/231 (52%), Gaps = 11/231 (4%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ ++LRLVV +A  Y+  GL + ++V EG IGL +AV KFDP  G++ +TY+ WWI+  
Sbjct: 1   MMAANLRLVVSVAKKYQNQGLELLDLVQEGAIGLERAVDKFDPAMGYKFSTYAYWWIRQG 60

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           M   I  S   +++    ++K     L +++   + ++    +    + +A ++ + + +
Sbjct: 61  MTRAIDNSARTIRLPIHISEK-----LSKMRRVSRELSHKFGRQPTRLEMATEMGIDQKD 115

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           +  +  + A   SL+A     +  S+  +       D   +  +E  +R  ++  L   +
Sbjct: 116 LEDLISQSAPCASLDAHARGEEDRSTLGELI----PDPNCEEPMEGMDRTIQKEHLGTWL 171

Query: 233 SVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           S LN RE++I   R     E P+TL  +  +  VSRERVRQ+EA+A  K++
Sbjct: 172 SQLNEREQKIMRLRFGLDGEEPLTLAEIGRQINVSRERVRQLEAKAILKLR 222


>gi|88808921|ref|ZP_01124430.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 7805]
 gi|88786863|gb|EAR18021.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 7805]
          Length = 322

 Score =  191 bits (485), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 67/320 (20%), Positives = 142/320 (44%), Gaps = 54/320 (16%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS----------------- 48
           ++++ + ++ +  Y+ +I ++P+L  Q+E  L ++ +E  +L                  
Sbjct: 4   LALLPDADL-VRSYLRDIGRVPLLSHQQEITLGRQVQELMELESVEAELQEKRGGEAVLA 62

Query: 49  -----------------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
                                  A  R+V ++LRLVV +A  Y    + + +++ EG IG
Sbjct: 63  AELAKAAGLSAVQLKRKLQAGRRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIG 122

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++ V+KFDP RG++ +TY+ WWI+  +   I      +++     +      L +LK  
Sbjct: 123 LVRGVEKFDPTRGYKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITE-----MLNKLKKG 177

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            + ++    +   V  +A  + + E EV  + CR     SL   +   D + ++  D L 
Sbjct: 178 QRELSQELGRTPSVTELASFVELPEDEVKELMCRARQPVSLEMKV--GDGDDTELLDLLA 235

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFE 263
            D     ++  E+ E +  +  L   +  L   + R+   R     E P++L  ++   +
Sbjct: 236 GDG----ELPSEQVEGECLKGDLRDLLGQLPELQERVLRMRYGMDGEEPMSLTGIAKTLK 291

Query: 264 VSRERVRQIEARAFKKVQES 283
           +SR+R R++E    + ++++
Sbjct: 292 MSRDRTRRLEREGLQSLRQA 311


>gi|81300555|ref|YP_400763.1| group2 RNA polymerase sigma factor SigB [Synechococcus elongatus
           PCC 7942]
 gi|123556657|sp|Q31ME3|RPOD2_SYNE7 RecName: Full=RNA polymerase sigma factor rpoD2
 gi|81169436|gb|ABB57776.1| group2 RNA polymerase sigma factor SigB [Synechococcus elongatus
           PCC 7942]
          Length = 320

 Score =  191 bits (485), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 62/319 (19%), Positives = 134/319 (42%), Gaps = 52/319 (16%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------------------- 43
           +  Y+ EI ++ +L  +EE    ++ +                                 
Sbjct: 13  VRAYLQEIGRVRLLTAEEELCFGRQVQRLMMLLDAQTELRDRLGHEPSKEEWAAAVDLNL 72

Query: 44  -------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                       A  +++ ++LRLVV IA  Y+   +   +++ EG +GL + V+KFDP 
Sbjct: 73  EDLDRQIEQGQRAKRKMIEANLRLVVSIAKKYQKRHMEFLDLIQEGTLGLERGVEKFDPS 132

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +G++ +TY+ WWI+ A+   I +    +++     +K     L +LK   + ++    + 
Sbjct: 133 KGYKFSTYAYWWIRQAITRAIAQQSRTIRLPIHITEK-----LNKLKKTQRELSQQLGRS 187

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
                +A+ L +   +V           SL+  +   D   ++ Q+ L  +       + 
Sbjct: 188 ATASELAEVLELPLEQVREYIQMNRQPVSLD--VKVGDSQDTELQELLEDEQSSPSDYV- 244

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEA 274
              E+++ R  L   M+ L P+++ +   R   +  + ++L  +     +SRERVR++E 
Sbjct: 245 ---EQESLRRDLRNLMAELTPQQQAVIALRYGLDEGDSLSLAKVGERLNISRERVRKLER 301

Query: 275 RAFKKVQESIQKQVELSSS 293
           +A   ++   +   E ++S
Sbjct: 302 QAMDHLRRRSRLLAEYAAS 320


>gi|220906009|ref|YP_002481320.1| RNA polymerase sigma-70 subunit RpoD subfamily [Cyanothece sp. PCC
           7425]
 gi|219862620|gb|ACL42959.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Cyanothece sp.
           PCC 7425]
          Length = 372

 Score =  191 bits (485), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 76/312 (24%), Positives = 134/312 (42%), Gaps = 50/312 (16%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKR-------------------------------- 40
           +  +  ++ ++ + P+L+  EE  LA+R                                
Sbjct: 59  DDAVGAFLKDMARYPLLQPSEEIELARRVKYLVELSELKDQLGRQLGRSATLPEVAAAMN 118

Query: 41  -------YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
                   R +    A  +++ S+LRLVV IA  Y   G+P  ++V EG +GL +A +KF
Sbjct: 119 LTEQQLQIRIYRGQVAKSKMIRSNLRLVVSIAKRYLNRGVPFLDLVQEGALGLNRATEKF 178

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           DPE+GF+ +TY+ WWI+  +   I      +++     +K     L++L+ HL+     N
Sbjct: 179 DPEKGFKFSTYAYWWIRQGITRAIANDSRTIRLPIHIVEK--LNKLKKLQRHLKKELQRN 236

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
                   +A  L ++  ++  +        SLN  +    +  ++  D L  D     +
Sbjct: 237 PTE---QELADALEITLEQLQMLQRARQQALSLNRRV--GREEDTELLDLLEADSTQSPE 291

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQ 271
             + +   +   + L     VL  +ER +   R       P TLE +S  F +SRERVRQ
Sbjct: 292 KQMGEVMMRQEISQLLDL--VLTKQERDVIILRYGLVSGEPNTLEEVSGLFNLSRERVRQ 349

Query: 272 IEARAFKKVQES 283
           I+ +A  K++ S
Sbjct: 350 IQNKAIGKLRRS 361


>gi|117165089|emb|CAJ88642.1| putative RNA polymerase principal sigma factor HrdC [Streptomyces
           ambofaciens ATCC 23877]
          Length = 338

 Score =  191 bits (485), Expect = 1e-46,   Method: Composition-based stats.
 Identities = 66/300 (22%), Positives = 128/300 (42%), Gaps = 42/300 (14%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRY------------REHGD----------------- 46
           L +Y+ +I    +L  ++E  LA+R              + G+                 
Sbjct: 38  LGQYLAQIGATALLTAEDEVTLARRIEAGVRAMEELEAADTGEPAPTPARRRALEETVRD 97

Query: 47  -LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
             +A   +V ++LRLVV +A  +   GLP+ +V+ EGN+GL++AV+KFD  +GF+ +TY+
Sbjct: 98  GRAAKDHMVRANLRLVVSMAKRHAHRGLPLLDVIQEGNLGLIRAVEKFDHTKGFKFSTYA 157

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
            WWI+ A++  +      V++     +      L++L    + +     +      +A +
Sbjct: 158 TWWIRQAIERGLATHARTVRLPVHVVE-----QLQKLAKVERKLRGRLDREPTADEVAAE 212

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
             +   +V+ +        SL+  +   +   +   D +      Q   + E +      
Sbjct: 213 SGIDGDKVVWLRRVGRDAVSLDTPV--DEAGETVVGDLIPDTEVLQAPEVAEFQALA--- 267

Query: 226 NMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             L  ++  L PRE  I   R    +  P TL  ++    ++RERVRQ+E  +   ++  
Sbjct: 268 AELREAVGTLAPREAMILSLRYGLHDGRPRTLHQVAQHVGLTRERVRQLEKASLDHLRAP 327


>gi|225436223|ref|XP_002273602.1| PREDICTED: similar to SIGB (SIGMA FACTOR B); DNA binding /
           DNA-directed RNA polymerase/ transcription factor [Vitis
           vinifera]
          Length = 578

 Score =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 64/250 (25%), Positives = 124/250 (49%), Gaps = 12/250 (4%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R R +  +    +++ S++RLV+ IA  Y+G G+ I ++V EG  GL++  +KFD  +GF
Sbjct: 331 RRRTNYGIRCKDKMIKSNIRLVISIAKNYQGAGMNIQDLVQEGCRGLVRGAEKFDASKGF 390

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWIK A+++ +      +++     +        R+K   + +   N +    
Sbjct: 391 KFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATY-----RVKEARKQLYSENGRHPNN 445

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +A+   +S   + ++        SL+  I     N +     ++ D D   +   E  
Sbjct: 446 EEVAEATGLSMKRLNAVLLTPKAPRSLDQKIGI---NQNLKPSEVIADPDA--ETAEELL 500

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAF 277
            ++  R  L + ++ LNPRE+++   R   E+    TL+ +     VSRER+RQIE+ AF
Sbjct: 501 IKQFMREDLEKVLNSLNPREKQVIRWRYGLEDGRTKTLQEIGELMGVSRERIRQIESCAF 560

Query: 278 KKVQESIQKQ 287
           +K++   + +
Sbjct: 561 RKLKNKRRTK 570


>gi|168000881|ref|XP_001753144.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162695843|gb|EDQ82185.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 581

 Score =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 62/251 (24%), Positives = 127/251 (50%), Gaps = 14/251 (5%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R +E     A  +LV S+LRLVV I   Y+G G+ + +++  G++GL++  +KFDPE GF
Sbjct: 334 RIKEG--QCAKDKLVNSNLRLVVSIVKNYQGRGMTLPDLIQRGSLGLIRGAEKFDPEMGF 391

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWI+ A+   I     ++++     +      + R+      I ++  +  + 
Sbjct: 392 KFSTYATWWIRQAVTRSITDQSRIIRLPVHIYEV-----ISRINKSRMMIAEDQGRQARD 446

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +A  + +S  ++  +        S++ LI   DK+   W+       +  +  L  + 
Sbjct: 447 EEVATAVGISVEKLDFILKSARLPASMDQLIGR-DKDLPLWEMVADKGFNSADDFLTNEV 505

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
            +++    +   +  L+P ER +   R   ++   +TL+++   F+V+RER+RQIE RA 
Sbjct: 506 LKQD----IDGVLQTLSPTEREVLRLRFGLDDAQSMTLKDIGIFFKVTRERIRQIEVRAL 561

Query: 278 KKVQESIQKQV 288
           +K++   ++ +
Sbjct: 562 RKLRHPTRRNI 572


>gi|54401868|gb|AAV34620.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|54401871|gb|AAV34621.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|54401874|gb|AAV34622.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 299

 Score =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 69/250 (27%), Positives = 123/250 (49%), Gaps = 13/250 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    +   
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE--- 231

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
             +  L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 232 --KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 289

Query: 257 NLSSEFEVSR 266
           ++  E  ++R
Sbjct: 290 DVGREIGLTR 299


>gi|302035824|ref|YP_003796146.1| RNA polymerase sigma-70 factor [Candidatus Nitrospira defluvii]
 gi|300603888|emb|CBK40220.1| RNA polymerase sigma-70 factor [Candidatus Nitrospira defluvii]
          Length = 419

 Score =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 62/244 (25%), Positives = 105/244 (43%), Gaps = 13/244 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +A   LV  +LRLVV +A  Y G GL + ++V EGNIGLM+A +++   +GF+ +TY+ 
Sbjct: 182 ETAKDELVRCNLRLVVNVAKHYTGRGLTLLDLVQEGNIGLMKAAERYQHRKGFKFSTYAT 241

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   +      ++I     Q      + R    L        + E+V   A  +
Sbjct: 242 WWIRQGITRSLADQSRTIRIPVH--QTEASNRILRASRRLVQQLGRQPRLEEV---ASTM 296

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +    +           +L   +        +         D Q         R     
Sbjct: 297 RMRPDRLHETIQAFQEPVALEHRVGDGGTELGELL------PDQQAVPPDAHVNRTELTR 350

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + R +  L PRE+ +   R    ++   TLE +     V+RER+RQIEA+A KK++  +
Sbjct: 351 EMDRILGTLTPREQTVIRLRFGIGEDQARTLEQVGQHLSVTRERIRQIEAKALKKLKTPM 410

Query: 285 QKQV 288
            K++
Sbjct: 411 VKEM 414


>gi|2385506|dbj|BAA22190.1| RpoD2 protein [Synechococcus elongatus PCC 7942]
          Length = 320

 Score =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 62/319 (19%), Positives = 134/319 (42%), Gaps = 52/319 (16%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------------------- 43
           +  Y+ EI ++ +L  +EE    ++ +                                 
Sbjct: 13  VRAYLQEIGRVRLLTAEEELCFGRQVQRLMMLLDAQTELRDRLGHEPSKEEWAAAVDLNL 72

Query: 44  -------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                       A  +++ ++LRLVV IA  Y+   +   +++ EG +GL + V+KFDP 
Sbjct: 73  EDLDREIEQGQRAKRKMIEANLRLVVSIAKKYQKRHMEFLDLIQEGTLGLERGVEKFDPS 132

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +G++ +TY+ WWI+ A+   I +    +++     +K     L +LK   + ++    + 
Sbjct: 133 KGYKFSTYAYWWIRQAITRAIAQQSRTIRLPIHITEK-----LNKLKKTQRELSQQLGRS 187

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
                +A+ L +   +V           SL+  +   D   ++ Q+ L  +       + 
Sbjct: 188 ATASELAEVLELPLEQVREYIQMNRQPVSLD--VKVGDSQDTELQELLEDEQSSPSDYV- 244

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEA 274
              E+++ R  L   M+ L P+++ +   R   +  + ++L  +     +SRERVR++E 
Sbjct: 245 ---EQESLRRDLRNLMAELTPQQQAVIALRYGLDEGDSLSLAKVGERLNISRERVRKLER 301

Query: 275 RAFKKVQESIQKQVELSSS 293
           +A   ++   +   E ++S
Sbjct: 302 QAMDHLRRRSRLLAEYAAS 320


>gi|159897807|ref|YP_001544054.1| RNA polymerase, sigma 32 subunit, RpoH [Herpetosiphon aurantiacus
           ATCC 23779]
 gi|159890846|gb|ABX03926.1| RNA polymerase, sigma 32 subunit, RpoH [Herpetosiphon aurantiacus
           ATCC 23779]
          Length = 303

 Score =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 72/302 (23%), Positives = 131/302 (43%), Gaps = 38/302 (12%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVL------AKRYREHG--------------------D 46
           + GL RY++EI + P+L  +EE  L      A++ +                        
Sbjct: 12  DDGLQRYLNEIAETPLLAAEEEQKLTQIVHVARQAQPTPACRIERCPSCALFEQCVTKLK 71

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  +LV ++LRLVV IA  YRG+GLP  +++ EGNIGLM A+++FD  +G R +TY+ 
Sbjct: 72  EPAHEQLVRANLRLVVSIAKRYRGFGLPFQDLIQEGNIGLMNAIERFDATKGVRFSTYAT 131

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +     L+++     +  L   +RR++  L               I+  L
Sbjct: 132 WWIRQAITRSLANQGRLIRLPVHRWE--LLIKVRRIETKLLQALGRE---PSANEISTAL 186

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            V E ++  +        SL      +++      D L  +    E   +E         
Sbjct: 187 GVPEEKICDLLSIAQVPISLATP--KNEETDMLLGDSLPDEDWEDE---LECLLTSIDAQ 241

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                ++ L+ +E+ +   R         +L  + +    +R+R++QIEA A + ++  +
Sbjct: 242 YTRAMLNQLSEQEQEVLTLRYGLKDGKSRSLSEVGAVVGRTRQRIQQIEAGALQVLRTQL 301

Query: 285 QK 286
            +
Sbjct: 302 SQ 303


>gi|1769413|dbj|BAA13122.1| RpoD2 sigma factor [Microcystis aeruginosa]
          Length = 376

 Score =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 73/316 (23%), Positives = 133/316 (42%), Gaps = 54/316 (17%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLA-------------KRYREH------------- 44
           + E  +  +  E+ + P+L  +EE  LA             ++ +E+             
Sbjct: 61  SNEDTVGAFFKEMARYPLLSAEEEIELAYSVKFLMEAEEVRQKLQENLHRPPTKTEWAIA 120

Query: 45  --------------GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
                            +A  +++ S+LRLVV IA  Y   G+P  +++ EG IGL +A 
Sbjct: 121 LELDNERQLENRLYRGRTAKRKMIRSNLRLVVSIAKRYLNRGVPFLDLIQEGAIGLNRAA 180

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +KFDP +G++ +TY+ WWI+ A+   I      +++     +K     L +LK   Q + 
Sbjct: 181 EKFDPNKGYKFSTYAYWWIRQAITRTIANDARTIRLPIHIVEK-----LNKLKKA-QILK 234

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
            +  +      +A++L ++  ++  +        SLN  +   +              D 
Sbjct: 235 QDLQRNPNERELAERLEITPEQLRQLLQLRRQSLSLNHRVGKGEDTELVDLLE-----DD 289

Query: 211 QEQVLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRE 267
             Q+  +K      R  +   +  VL  RE+ +   R       P TLE +   F +SRE
Sbjct: 290 DLQLPEDKMNEMMMRQEIFAVLSDVLTEREKDVISLRYGLATSQPYTLEEVGGMFNLSRE 349

Query: 268 RVRQIEARAFKKVQES 283
           RVRQI+ +A +K++  
Sbjct: 350 RVRQIQTKAMRKLRRP 365


>gi|187251192|ref|YP_001875674.1| DNA-directed RNA polymerase sigma subunit RpoH [Elusimicrobium
           minutum Pei191]
 gi|186971352|gb|ACC98337.1| DNA-directed RNA polymerase, sigma subunit RpoH [Elusimicrobium
           minutum Pei191]
          Length = 380

 Score =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 74/277 (26%), Positives = 149/277 (53%), Gaps = 13/277 (4%)

Query: 14  IGLSRYIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
             +++Y  +I ++   L ++E   L KR ++ GD +A  R++  +LRLV+  A  +    
Sbjct: 6   DSINQYFKKISEVSEDLSREEMEKLWKRIKK-GDTAAKQRMMELNLRLVIPAAKRFMRKD 64

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           + + +++ EGN+GL+QA++KFDP +GFR +TY+++WI  A+++YI      +KI + A  
Sbjct: 65  IDLLDLIEEGNLGLLQAIEKFDPSKGFRFSTYAIYWIDQAIRKYIDEQSGAIKIPSHA-- 122

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL-IN 191
              + ++++      A+ D+  +   +  ++++L+ S  ++ S+   +   + +++L + 
Sbjct: 123 ---WGDIKKWTRTWNALKDSLEREPSLTEMSRELDWSARKIKSILETINAAKGIDSLALA 179

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ-- 249
             +++    +D L  D  G    +     R +  + L  ++  LNPR++ I   R     
Sbjct: 180 IGEEDEVTLEDTLTDDGKGNPDDVF---SRSSSNSALLAALEELNPRDKEILMMRNGLKT 236

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             P+TL  +S    +SRERVRQIE RA   +++   K
Sbjct: 237 NEPMTLSEVSKIMGLSRERVRQIEERAISHIRKKAHK 273


>gi|298250072|ref|ZP_06973876.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297548076|gb|EFH81943.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 319

 Score =  190 bits (484), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 71/297 (23%), Positives = 134/297 (45%), Gaps = 30/297 (10%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------------EHGDLSAA 50
           +N       Y +EI ++ +L K E   LA+R                     ++    A 
Sbjct: 23  MNISDSTHFYRYEIGQVELLSKDEVTDLAQRIEKAQANIRKQRGLSRSARLDDNEAQEAK 82

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            +L+ ++LRLV+ IA  YRG+G+ + +++ EGN+GLM AV KFD ++G+R +TY+ WWI+
Sbjct: 83  RQLIEANLRLVMHIARKYRGFGVDLMDLIQEGNLGLMHAVDKFDYKKGYRFSTYATWWIR 142

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
             +   +     ++++     ++     L R+K  +Q           +  +A ++ +S 
Sbjct: 143 QYITRALSEQAHMIRVPLYKIEE--IKRLGRVKRKMQQ---GETGEPTLEELAVQMEISV 197

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            EVI++        SL+      D   S   + L  D     + ++     +  +  +  
Sbjct: 198 PEVIALLSTNQETISLDMPRKGGDDEIS-LSEVLEDDPIYSPERVV---LTQTLQEQVQD 253

Query: 231 SMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            ++ L PRE+++ + R         +L     +  +S E VRQ+E RA KK+    +
Sbjct: 254 ILNCLTPREKKVLQLRFGLNGNGEHSLTETGKKMGLSHEAVRQMEFRALKKLGHPCR 310


>gi|254526924|ref|ZP_05138976.1| sigma-70 factor family protein [Prochlorococcus marinus str. MIT
           9202]
 gi|221538348|gb|EEE40801.1| sigma-70 factor family protein [Prochlorococcus marinus str. MIT
           9202]
          Length = 307

 Score =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 75/300 (25%), Positives = 131/300 (43%), Gaps = 37/300 (12%)

Query: 15  GLSRYIHEIRKIPMLEKQ----------EEYVLAKRYREHGD------------------ 46
            LS ++ EI +  +L  +          E  VL  R +E G                   
Sbjct: 3   SLSDFLGEIGRHQLLTPERELTMGRKVQEMVVLVNRCQEAGGKGPACEYSEAERKKIKIG 62

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + ++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG R +TY+ 
Sbjct: 63  EKAKNEMITANLRLVVNLAKRYQGKGLELLDLIQEGTLGLTRAVEKYDPSRGHRFSTYAY 122

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   +      ++I    N+K     LR  K  L  +       +++    K  
Sbjct: 123 WWIRQGLNRALSTQSRTIRIPVNINEK--LTKLRSAKSKLMQLKGIPPTSDELAEEMKIT 180

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
                E++S   R +   SL   + S   + S+  D L  D     ++    E   +   
Sbjct: 181 KEEIDELLSCELR-SITVSLQGTVKSK-SDPSELVDILPSDQAPPMELAELAERTASAWK 238

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +L ++   L  +ER+I   R   +      TL  ++     SRE  RQ+  RA +K++++
Sbjct: 239 LLDKA--NLTEKERKIVSLRFGLDGSNEWRTLAEVARHMSCSREYCRQVVQRALRKLRKA 296


>gi|116075407|ref|ZP_01472667.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9916]
 gi|116067604|gb|EAU73358.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9916]
          Length = 310

 Score =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 71/300 (23%), Positives = 129/300 (43%), Gaps = 37/300 (12%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------------------------HGD 46
            LS ++ EI +  +L  ++E  + ++ +                                
Sbjct: 4   SLSAFLGEIGRHQLLTPEQELTMGRKVQAMVAITERCMLAGGTGPACNYSEEEKRTIKKG 63

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A ++++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG R +TY+ 
Sbjct: 64  EKAKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSTYAY 123

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   +      ++I    N+K     LR  K  L         P Q+    +  
Sbjct: 124 WWIRQGLNRALSTQSRTIRIPVNVNEK--LTKLRAAKARLMQRNGQAATPAQLAEAMQIS 181

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
                +++    R +   SL  ++ S   + S+  D L  +     +     E   +   
Sbjct: 182 RAEVDDLLGCELR-SVTVSLQGIVKSK-SDPSELVDVLPSEELPPMEQAEIDERTASAWT 239

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +L R  S L P+ER +   R   +      TL  ++     SRE  RQ+  RA +K+++S
Sbjct: 240 LLDR--SNLTPKERTVVMLRFGLDGSNEWRTLAEVARHMGCSREYCRQVVQRALRKLRKS 297


>gi|309702135|emb|CBJ01450.1| putative RNA polymerase sigma factor [Escherichia coli ETEC H10407]
          Length = 697

 Score =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 59/242 (24%), Positives = 112/242 (46%), Gaps = 10/242 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A    + ++LRLVV IA  + G GL I +++ EGN+GL++AV+KFD  RGF+ +TY+ 
Sbjct: 442 RDAWKGFIHANLRLVVAIAKKHCGRGLDIEDLIQEGNLGLIKAVEKFDFRRGFKFSTYAS 501

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   I     L+++         + + RR +     +         +  + +  
Sbjct: 502 WWIRQKISRAIADQAQLIRLPVH-----FYEHFRRWRSSRDQLLHRQGITPTLRRLQEMT 556

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++ E +++ M         +      +    +      +          ++  E    R 
Sbjct: 557 DLPERQLLQMAKYEEQTVLIGDFHEDAQDREAALSGDALLTRRDFTSAPVQSLEL---RE 613

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            ++  ++ L PRE +I + R         TLE +  +F+V+RER+RQIEA+A +K++   
Sbjct: 614 HISSVLNTLLPRETQIIKMRFGIGMTQDFTLEEVGKQFDVTRERIRQIEAKALRKLRHHS 673

Query: 285 QK 286
           + 
Sbjct: 674 RA 675


>gi|296090195|emb|CBI40014.3| unnamed protein product [Vitis vinifera]
          Length = 575

 Score =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 64/250 (25%), Positives = 124/250 (49%), Gaps = 12/250 (4%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R R +  +    +++ S++RLV+ IA  Y+G G+ I ++V EG  GL++  +KFD  +GF
Sbjct: 328 RRRTNYGIRCKDKMIKSNIRLVISIAKNYQGAGMNIQDLVQEGCRGLVRGAEKFDASKGF 387

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWIK A+++ +      +++     +        R+K   + +   N +    
Sbjct: 388 KFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATY-----RVKEARKQLYSENGRHPNN 442

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +A+   +S   + ++        SL+  I     N +     ++ D D   +   E  
Sbjct: 443 EEVAEATGLSMKRLNAVLLTPKAPRSLDQKIGI---NQNLKPSEVIADPDA--ETAEELL 497

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAF 277
            ++  R  L + ++ LNPRE+++   R   E+    TL+ +     VSRER+RQIE+ AF
Sbjct: 498 IKQFMREDLEKVLNSLNPREKQVIRWRYGLEDGRTKTLQEIGELMGVSRERIRQIESCAF 557

Query: 278 KKVQESIQKQ 287
           +K++   + +
Sbjct: 558 RKLKNKRRTK 567


>gi|133470|sp|P19433|RPSB_MYXXA RecName: Full=RNA polymerase sigma-B factor
          Length = 246

 Score =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 98/233 (42%), Positives = 144/233 (61%), Gaps = 4/233 (1%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           +VT++LR VVK+A  YR YG+ +S+++ EGNIGLM+AV+KFDP++G RL +Y++WWI+A 
Sbjct: 1   MVTANLRFVVKVAYEYRSYGIKMSDLIQEGNIGLMKAVQKFDPDKGIRLISYAVWWIRAY 60

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +Q YIL+SWSLVK+GTT    +LFF+L R +  L+    +      V  IA++L+V   E
Sbjct: 61  IQNYILKSWSLVKLGTTQAHGKLFFSLARTRRELEKF-GSGDAAVNVDDIARRLHVKPGE 119

Query: 173 VISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           V  M  R+ G D SL+A +     NS    D++V     Q+    +KEE       +  +
Sbjct: 120 VREMEQRMGGRDLSLDAPMGEDGGNSH--VDFVVSAAAPQDDEFADKEEAGLINARVRAA 177

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +  L+PRE  I E R + E P+TL+ L   F  SRER RQ+E RA  K++  +
Sbjct: 178 LMRLDPREPFIIEQRVMNERPMTLKELGEHFGFSRERARQLEIRAKDKLKSEL 230


>gi|270487764|ref|ZP_06204838.1| sigma-70, region 4 [Yersinia pestis KIM D27]
 gi|270336268|gb|EFA47045.1| sigma-70, region 4 [Yersinia pestis KIM D27]
          Length = 215

 Score =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 55/221 (24%), Positives = 105/221 (47%), Gaps = 12/221 (5%)

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I      
Sbjct: 1   MQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM-- 58

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 L R+   +         PE    +A+++ + E ++  +        S+   I  
Sbjct: 59  IETINKLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI-- 113

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE-- 250
            D   S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +  
Sbjct: 114 GDDEDSHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGIDMN 170

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
              TLE +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 171 TDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 211


>gi|240047243|ref|YP_002960631.1| RNA polymerase sigma factor [Mycoplasma conjunctivae HRC/581]
 gi|239984815|emb|CAT04802.1| RNA polymerase sigma factor [Mycoplasma conjunctivae]
          Length = 533

 Score =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 63/289 (21%), Positives = 132/289 (45%), Gaps = 18/289 (6%)

Query: 9   IVNGEIGLSRYIHEIRKI-PMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKIA 65
           + +    +  Y+  I K   +L  +EE  LA++    G     A   L+  +LRLV+  A
Sbjct: 245 LTDTNDIIKWYMRWIGKYGKLLTYEEEQELARKMEIPGRVGRKARDTLIKRNLRLVINNA 304

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y+  GL   +++SEGN+G+M+A+ K+D  +GF+ +TY+ WWI+ ++   +     L++
Sbjct: 305 KRYKNRGLNFIDLISEGNLGIMKAISKYDRTKGFKFSTYATWWIRQSITRAVADQARLIR 364

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           I     +      + +++  LQ         E++  +    + +  +V  +        S
Sbjct: 365 IPVHMVE--TINKINKIERELQQKNGVTPSAEEIADV-MGADFTPEKVRYIRKINIDPIS 421

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L+  I    +  S + D++  +         E+EE+   + ++    + L   E+     
Sbjct: 422 LDKAI--GKEEDSSFSDFIKDESVISPSDYAEQEEKS--KVLIEMIKNNLEEEEQEFIMR 477

Query: 246 RRLQENP--------VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R    N          + + L+++  V++ER+RQIE++  KK++   ++
Sbjct: 478 RYGIGNDKNGRQYRAHSYDELAADRGVTKERIRQIESKILKKLRAPQRR 526


>gi|126695941|ref|YP_001090827.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9301]
 gi|126542984|gb|ABO17226.1| Putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus str. MIT 9301]
          Length = 307

 Score =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 75/300 (25%), Positives = 131/300 (43%), Gaps = 37/300 (12%)

Query: 15  GLSRYIHEIRKIPMLEKQ----------EEYVLAKRYREHGD------------------ 46
            LS ++ EI +  +L  +          E  VL  R +E G                   
Sbjct: 3   SLSDFLGEIGRHQLLTPERELTMGRKVQEMVVLVNRCQEAGGKGPACEYSEAERKKIKIG 62

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + ++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG R +TY+ 
Sbjct: 63  EKAKNEMITANLRLVVNLAKRYQGKGLELLDLIQEGTLGLTRAVEKYDPSRGHRFSTYAY 122

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   +      ++I    N+K     LR  K  L  +       +++    K  
Sbjct: 123 WWIRQGLNRALSTQSRTIRIPVNINEK--LTKLRSAKSKLMQLKGIPPSTDELAEEMKIT 180

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
                E++S   R +   SL   + S   + S+  D L  D     ++    E   +   
Sbjct: 181 KEEIDELLSCELR-SITVSLQGTVKSK-SDPSELVDILPSDQTPPMELAELAERTASAWK 238

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +L ++   L  +ER+I   R   +      TL  ++     SRE  RQ+  RA +K++++
Sbjct: 239 LLDKA--NLTEKERKIVSLRFGLDGSNEWRTLAEVARHMSCSREYCRQVVQRALRKLRKA 296


>gi|260590675|ref|ZP_05856133.1| RNA polymerase sigma-70 factor [Prevotella veroralis F0319]
 gi|260537416|gb|EEX20033.1| RNA polymerase sigma-70 factor [Prevotella veroralis F0319]
          Length = 290

 Score =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 71/284 (25%), Positives = 135/284 (47%), Gaps = 12/284 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRL 60
           + + SI       L +Y+ EI + PM+   EE  LA+   + G     A  +L+ ++LR 
Sbjct: 5   KISKSITNRSSEALDKYLVEIGREPMITVDEEIELAQEIHKGGRKGERAKEKLIKANLRF 64

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y+  GL +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I   
Sbjct: 65  VVSVAKQYQHQGLSLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQ 124

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
             +V++    NQ      + ++          + +   +  +A+   + ES +       
Sbjct: 125 SRIVRLP--LNQVGAISKINQVTN---EFVQKHNRRPSIHELAELTGIEESRIRQSQSAD 179

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               S++A  +    + +   D L    D +    ++ E   +    + +  + L  RE 
Sbjct: 180 NHHMSIDAPFSD--DDDNSMSDMLSSGDDSRTDKGVDFESMSDDLRAVLQ--NTLKDREI 235

Query: 241 RIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +I             LE + +E  ++RERVRQI  +A +K++ES
Sbjct: 236 KIVTECFGIGCQEKGLEEIGTEMGLTRERVRQIREKAIEKIRES 279


>gi|288801981|ref|ZP_06407422.1| RNA polymerase sigma-70 factor [Prevotella melaninogenica D18]
 gi|302347072|ref|YP_003815370.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           melaninogenica ATCC 25845]
 gi|288335416|gb|EFC73850.1| RNA polymerase sigma-70 factor [Prevotella melaninogenica D18]
 gi|302150546|gb|ADK96807.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           melaninogenica ATCC 25845]
          Length = 290

 Score =  190 bits (483), Expect = 2e-46,   Method: Composition-based stats.
 Identities = 70/284 (24%), Positives = 135/284 (47%), Gaps = 12/284 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRL 60
           + + SI       L +Y+ EI + PM+   EE  LA+   + G     A  +L+ ++LR 
Sbjct: 5   KISKSITNRSSEALDKYLVEIGREPMITVDEEIELAQEIHKGGRKGERAKEKLIKANLRF 64

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y+  GL +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I   
Sbjct: 65  VVSVAKQYQHQGLSLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQ 124

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
             +V++    NQ      + ++          + +   +  +A+   + E+ +       
Sbjct: 125 SRIVRLP--LNQVGAISKINQVTN---EFVQQHNRRPSIHELAELTGIDEARIRQSQSAD 179

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               S++A  +    + +   D L    D +    ++ E   +    + +  + L  RE 
Sbjct: 180 NHHMSIDAPFSD--DDDNSMSDMLSSGDDSRTDRGVDFESMSDDLRAVLQ--NTLKDREI 235

Query: 241 RIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +I             LE + +E  ++RERVRQI  +A +K++ES
Sbjct: 236 KIVTECFGIGCQEKGLEEIGTEMGLTRERVRQIREKAIEKIRES 279


>gi|56752354|ref|YP_173055.1| group2 RNA polymerase sigma factor RpoD2 [Synechococcus elongatus
           PCC 6301]
 gi|56687313|dbj|BAD80535.1| group2 RNA polymerase sigma factor RpoD2 [Synechococcus elongatus
           PCC 6301]
          Length = 320

 Score =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 61/319 (19%), Positives = 133/319 (41%), Gaps = 52/319 (16%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------------------- 43
           +  Y+ EI ++ +L  +EE    ++ +                                 
Sbjct: 13  VRAYLQEIGRVRLLTAEEELCFGRQVQRLMMLLDAQTELRDRLGHEPSKEEWAAAVDLNL 72

Query: 44  -------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                       A  +++ ++LRLVV IA  Y+   +   +++ EG +GL +  +KFDP 
Sbjct: 73  EDLDRQIEQGQRAKRKMIEANLRLVVSIAKKYQKRHMEFLDLIQEGTLGLERGFEKFDPS 132

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +G++ +TY+ WWI+ A+   I +    +++     +K     L +LK   + ++    + 
Sbjct: 133 KGYKFSTYAYWWIRQAITRAIAQQSRTIRLPIHITEK-----LNKLKKTQRELSQQLGRS 187

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
                +A+ L +   +V           SL+  +   D   ++ Q+ L  +       + 
Sbjct: 188 ATASELAEVLELPLEQVREYIQMNRQPVSLD--VKVGDSQDTELQELLEDEQSSPSDYV- 244

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEA 274
              E+++ R  L   M+ L P+++ +   R   +  + ++L  +     +SRERVR++E 
Sbjct: 245 ---EQESLRRDLRNLMAELTPQQQAVIALRYGLDEGDSLSLAKVGERLNISRERVRKLER 301

Query: 275 RAFKKVQESIQKQVELSSS 293
           +A   ++   +   E ++S
Sbjct: 302 QAMDHLRRRSRLLAEYAAS 320


>gi|13508091|ref|NP_110040.1| RNA polymerase sigma factor [Mycoplasma pneumoniae M129]
 gi|2500786|sp|P78022|RPOD_MYCPN RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A
 gi|1674175|gb|AAB96132.1| Sigma-70 Factor Family [Mycoplasma pneumoniae M129]
 gi|301633308|gb|ADK86862.1| RNA polymerase sigma factor RpoD [Mycoplasma pneumoniae FH]
          Length = 499

 Score =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 71/297 (23%), Positives = 142/297 (47%), Gaps = 22/297 (7%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS---AAHRLVTSH 57
           +  KN+S     +  +  ++  +    ML+ + E  +AK      + S   A ++LVTS+
Sbjct: 197 LTTKNISNRDKVDDNVRFFLGSLDSSKMLDFESEQRIAKVLNSTDEESRKYAINQLVTSN 256

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVV IA  +   GL  ++++ EGN+GL++A+ KF+   G + +TY+ WWIK A+   I
Sbjct: 257 LRLVVSIAKKHLERGLDFNDLIQEGNLGLLKAISKFNWSLGNKFSTYATWWIKQAITRAI 316

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL-----NVSESE 172
                 V+I     +      + RL    +A+     +      +A+K+       +  +
Sbjct: 317 ADQARTVRIPVHMVE-----TINRLAKAERALNQELGREPTAEELAEKMGGQAEGFTVKK 371

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           +  +        SL+  +   ++  SQ+ D++    D   Q+  E  E ++    +   +
Sbjct: 372 IAEIKRLSLDPVSLDKTVGHDEE--SQFGDFV---RDTDAQMPDEFTESRSNYEKIDELL 426

Query: 233 SV-LNPRERRIFEARRLQ---ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           +  L+ +E  I   R          TL+ +S + ++ RE++RQIE +A +K++++++
Sbjct: 427 NNCLSEQEELIVRMRIGMPPYNETKTLDEVSQKIKIPREKIRQIETKAIRKLRQAVR 483


>gi|271963319|ref|YP_003337515.1| RNA polymerase sigma factor RpoD [Streptosporangium roseum DSM
           43021]
 gi|270506494|gb|ACZ84772.1| RNA polymerase sigma factor RpoD [Streptosporangium roseum DSM
           43021]
          Length = 312

 Score =  190 bits (483), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 71/304 (23%), Positives = 132/304 (43%), Gaps = 41/304 (13%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------------REHGDLS-- 48
           V+    L  Y+ EI ++P+L  +EE  LAKR                     +  D    
Sbjct: 14  VSDRDLLGTYLAEIGRVPLLTAEEEVELAKRIEAGLFAEQLLDGGLAEPRIADAADEELE 73

Query: 49  --------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
                   A    + ++LRLVV +A  Y G G+P+ ++V EGN+GL++AV+KFD  RG++
Sbjct: 74  RLAVSGQRAKDEFIQANLRLVVAVARKYSGRGMPLIDLVQEGNLGLVRAVEKFDYRRGYK 133

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ ++   I      V++ T A ++     L R++  + A  D         
Sbjct: 134 FSTYATWWIRQSVGRAIHEQARPVRLPTHAGEQ--MTRLMRVRRDMLAEFDQE---PTDA 188

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A  L +    V  +    +   SL   +   D++ ++  D +  +     +   ++  
Sbjct: 189 DLAAVLELPIERVRELRRWASDPVSLQLGV--GDEDETELGDMIADETWADPE---QQAM 243

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFK 278
               R  L + ++ L  + R +   R         TL  +   + + R+R R+IE  A  
Sbjct: 244 DILERERLEQWLTGLEGQTREMLRWRYGLMDGREHTLTEVGERYGIGRDRARRIERDALA 303

Query: 279 KVQE 282
           ++++
Sbjct: 304 RLRK 307


>gi|325269444|ref|ZP_08136061.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           multiformis DSM 16608]
 gi|325855020|ref|ZP_08171736.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           denticola CRIS 18C-A]
 gi|327313288|ref|YP_004328725.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           denticola F0289]
 gi|324988365|gb|EGC20331.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella
           multiformis DSM 16608]
 gi|325483998|gb|EGC86938.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           denticola CRIS 18C-A]
 gi|326946004|gb|AEA21889.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           denticola F0289]
          Length = 290

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 70/284 (24%), Positives = 135/284 (47%), Gaps = 12/284 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRL 60
           + + SI       L +Y+ EI + PM+   EE  LA+   + G     A  +L+ ++LR 
Sbjct: 5   KISKSITNRSSEALDKYLVEIGREPMITVDEEIELAQEIHKGGRKGERAKEKLIKANLRF 64

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y+  GL +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I   
Sbjct: 65  VVSVAKQYQHQGLSLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQ 124

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
             +V++    NQ      + ++          + +   +  +A+   + E+ +       
Sbjct: 125 SRIVRLP--LNQVGAISKINQVTN---EFVQKHNRRPSIHELAELTGIDEARIRQSQSAD 179

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               S++A  +    + +   D L    D +    ++ E   +    + +  + L  RE 
Sbjct: 180 NHHMSIDAPFSD--DDDNSMSDMLSSGDDSRTDRGVDFESMSDDLRAVLQ--NTLKDREI 235

Query: 241 RIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +I             LE + +E  ++RERVRQI  +A +K++ES
Sbjct: 236 KIVTECFGIGCQEKGLEEIGTEMGLTRERVRQIREKAIEKIRES 279


>gi|33862400|ref|NP_893960.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9313]
 gi|33640513|emb|CAE20302.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9313]
          Length = 335

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 65/311 (20%), Positives = 129/311 (41%), Gaps = 52/311 (16%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------------------- 43
           +  Y+ +I ++P+L  ++E  L ++ +E                                
Sbjct: 28  VRSYLRDIGRVPLLSHEQEITLGRQVQELMSLEQLESELEGQTGEPASRKELAKAAGLSE 87

Query: 44  -------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                       A  R+V+++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP 
Sbjct: 88  LQLKKKLQSGRRAKERMVSANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDPT 147

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RG++ +TY+ WWI+  +   I      +++     +      L +LK   + ++    + 
Sbjct: 148 RGYKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITE-----MLNKLKKGQRELSQEMGRT 202

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
             V  +A+ + + E EV  + CR     SL   +   D+              G+E++  
Sbjct: 203 PTVSELAEFVELPEEEVKDLMCRARQPMSLEMKVGDGDETELLELLA------GEEELPS 256

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEA 274
           EK E    +  L   +  L   + R+   R   +   P+ L  +    ++SR+RVR +E 
Sbjct: 257 EKVEVDCMKGDLRTLLEKLPELQGRVLRMRYGIDGGEPMNLTGIGRILDISRDRVRNLER 316

Query: 275 RAFKKVQESIQ 285
                +++  +
Sbjct: 317 HGLNGLRQLSE 327


>gi|260435993|ref|ZP_05789963.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 8109]
 gi|260413867|gb|EEX07163.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 8109]
          Length = 309

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 70/311 (22%), Positives = 137/311 (44%), Gaps = 37/311 (11%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------------------------HGD 46
            LS ++ EI +  +L  ++E ++ ++ +                                
Sbjct: 5   SLSAFLGEIGRHQLLTPEQELMMGRKVQAMVSITERCHLAGGTGPACEYSDEEKGVIRRG 64

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A ++++TS+LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG R +TY+ 
Sbjct: 65  ERAKNQMITSNLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSTYAY 124

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   +      ++I    N+K     LR  K  L      +   EQ+    +  
Sbjct: 125 WWIRQGLNRALSTQSRTIRIPVNVNEK--LTKLRAAKARLMQRNGLSPSGEQLAEFMEIP 182

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
                ++++   R +   SL  ++ S   + S+  D L  +     +     E   +  +
Sbjct: 183 IAEVEDLLACELR-SVTVSLQGVVKSK-SDPSELVDVLPSEELPPLERAEIAERTASAWS 240

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +L ++   L P+E  +   R   +      TL  ++     SRE  RQ+  RA +K++++
Sbjct: 241 LLAKA--NLTPKEHTVVTLRFGLDGTNEWRTLAEVARHMNCSREYCRQVVQRALRKLRKT 298

Query: 284 IQKQVELSSSP 294
             +   + S+P
Sbjct: 299 GIQSGLVESTP 309


>gi|148239078|ref|YP_001224465.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp. WH
           7803]
 gi|147847617|emb|CAK23168.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. WH 7803]
          Length = 308

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 70/302 (23%), Positives = 132/302 (43%), Gaps = 41/302 (13%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------------------------HGD 46
            LS ++ EI +  +L  ++E  + ++ +                                
Sbjct: 4   SLSAFLGEIGRHQLLTPEQELTMGRKVQAMVSLTERCHLAGGSGPACEYSDDEKRTIKRG 63

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A ++++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG R + Y+ 
Sbjct: 64  EKAKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSNYAY 123

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   +      ++I    N+K     L +L+     +   N        +A  L
Sbjct: 124 WWIRQGLNRALSTQSRTIRIPVNVNEK-----LTKLRASKARLMQRNGLSPSTEQLADDL 178

Query: 167 NVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           N+  SEV  +      +   SL  ++ S   + S+  D L  +     +     E   + 
Sbjct: 179 NLPISEVEDLLGCELRSVTVSLQGVVKSK-SDPSELVDVLPSEEVPPMERAEIAERTASA 237

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             +L +  S L P+ER +   R   +      TL  ++ +   SRE  RQ+  RA +K++
Sbjct: 238 WKLLDK--SNLTPKERTVVMLRFGLDGSNEWRTLAEVARQMNCSREYCRQVVQRALRKLR 295

Query: 282 ES 283
           ++
Sbjct: 296 KT 297


>gi|1542976|gb|AAB08043.1| sigma factor [Thermoanaerobacterium thermosulfurigenes]
          Length = 261

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 74/256 (28%), Positives = 131/256 (51%), Gaps = 12/256 (4%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           +L K+EE +L +R R +GD SA   LV  ++RLV K+A G+   G+   ++V EG IGL+
Sbjct: 4   LLTKEEEKILFERLR-NGDESAKDVLVECNIRLVDKVAAGFLKSGVEFDDLVQEGLIGLL 62

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
            A+ KFD  +G++ +TY+ W+I+ +M+ YI     ++++    N+K     + R+     
Sbjct: 63  TAIDKFDHTKGYKFSTYATWYIQQSMRRYIGNYGKIIRLPIHINEK-----INRILKARY 117

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
            I            I++    +E E+           SLN  +N  ++  ++  +++  D
Sbjct: 118 LIEQKKGSLATTEEISRLTGYTEEEIEGYLSYATDVISLNQYVND-ERVDAELINFIQDD 176

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-QENPVTLENLSSEFEVSR 266
               E++ IEKE +K  R    + +  L  RER I + R     N  TL  + + F ++R
Sbjct: 177 TIDVEEMAIEKEIKKEIR----KILDSLPERERMILKMRFGFGCNLKTLTEIGNIFGLTR 232

Query: 267 ERVRQIEARAFKKVQE 282
           ER+RQI+    K+++ 
Sbjct: 233 ERIRQIQNNTIKELRH 248


>gi|11993459|gb|AAG42748.1|AF299295_2 RNA polymerase sigma factor [Zymomonas mobilis]
          Length = 763

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 56/221 (25%), Positives = 101/221 (45%), Gaps = 12/221 (5%)

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +      GLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        +  
Sbjct: 464 LFRXAISGLMKAVGKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVH-----MIE 518

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + +L    + I     +      +A++L++   +V  +        SL   I   D+  
Sbjct: 519 TINKLVRTSRQILHEIGREPTPEELAERLSMPLEKVRKVMKIAKEPISLETPI--GDEED 576

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
           S   D++    D    + ++   + N +  +TR ++ L PRE R+   R         TL
Sbjct: 577 SHLGDFI---EDKNAIIPVDAAIQANLKETVTRVLASLTPREERVLRMRFGIGMNTDHTL 633

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPL 296
           E +  +F V+RER+RQIEA+A +K++   + +   S   PL
Sbjct: 634 EEVGQQFSVTRERIRQIEAKALRKLKHPSRSRKMRSFPRPL 674


>gi|107103136|ref|ZP_01367054.1| hypothetical protein PaerPA_01004205 [Pseudomonas aeruginosa PACS2]
          Length = 236

 Score =  190 bits (482), Expect = 3e-46,   Method: Composition-based stats.
 Identities = 69/243 (28%), Positives = 118/243 (48%), Gaps = 12/243 (4%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  
Sbjct: 1   MIESNLRLVVKIARRYVNRGLSLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           ++  I+     +++      K L   LR  +     +T           IA  L    +E
Sbjct: 61  IERAIMNQTRTIRLPIHVV-KELNVYLRAAR----ELTHKLDHEPSPEEIANLLEKPVAE 115

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           V  M        S++  ++    +     D L  D       L++ ++       + + +
Sbjct: 116 VKRMLGLNERVTSVD--VSLGPDSDKTLLDTLTDDRPTDPCELLQDDDLS---ESIDQWL 170

Query: 233 SVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
           + L  ++R +   R         TLE +  E  ++RERVRQI+  A K+++E ++K    
Sbjct: 171 TELTDKQREVVIRRFGLRGHESSTLEEVGQEIGLTRERVRQIQVEALKRLREILEKNGLS 230

Query: 291 SSS 293
           S +
Sbjct: 231 SDA 233


>gi|255531277|ref|YP_003091649.1| sigma-70 family RNA polymerase sigma factor [Pedobacter heparinus
           DSM 2366]
 gi|255344261|gb|ACU03587.1| RNA polymerase sigma factor, sigma-70 family [Pedobacter heparinus
           DSM 2366]
          Length = 286

 Score =  189 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 67/281 (23%), Positives = 136/281 (48%), Gaps = 13/281 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +   SI       + +Y+++I +I +L  +EE VLA++ R+ GD SA  RLV ++LR VV
Sbjct: 5   KIEQSITNRDSDSIEKYLYDIARIDLLSVEEEIVLAQKIRK-GDQSALDRLVKANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A  Y+  G+ +S++++EGN+GL++A ++FD  +GF+  ++++WWI+ ++   I     
Sbjct: 64  SVAKKYQNQGIRLSDLIAEGNLGLIKAAQRFDETKGFKFISFAVWWIRQSIMIAIAEQKR 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +V++   ANQ      + +    L+   +   +   +  + + + + E +V+        
Sbjct: 124 IVRLP--ANQIGGIMKINKAMADLEQQLE---RVPSLEEVCEFIELPEEKVVDYLHHAPM 178

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             SL+ +I      +           D   +       + +    + R M  L  RE+ I
Sbjct: 179 TTSLDTVIAEESGFT-----LAETIEDTNVEKTDTTVLQHSVTVDVKRLMRGLPEREKEI 233

Query: 243 FEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                       + L+ +  +  + +ERVRQI+ +A K ++
Sbjct: 234 LSMFYGLGGYPAIGLDEIGGKMNLGKERVRQIKDKALKTLR 274


>gi|78778962|ref|YP_397074.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9312]
 gi|78712461|gb|ABB49638.1| putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus str. MIT 9312]
          Length = 307

 Score =  189 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 75/300 (25%), Positives = 131/300 (43%), Gaps = 37/300 (12%)

Query: 15  GLSRYIHEIRKIPMLEKQ----------EEYVLAKRYREHGD------------------ 46
            LS ++ EI +  +L  +          E  VL  R +E G                   
Sbjct: 3   SLSDFLGEIGRHQLLTPERELTMGRKVQEMVVLVNRCQEAGGKGPACEYSEAERKKIKIG 62

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + ++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG R +TY+ 
Sbjct: 63  EKAKNEMITANLRLVVNLAKRYQGKGLELLDLIQEGTLGLTRAVEKYDPSRGHRFSTYAY 122

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   +      ++I    N+K     LR  K  L  +       +++    K  
Sbjct: 123 WWIRQGLNRALSTQSRTIRIPVNINEK--LTKLRSAKSKLMQLKGITPNSDELAEELKIT 180

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
                E++S   R +   SL   + S   + S+  D L  D     ++    E   +   
Sbjct: 181 KEEIDELLSCELR-SITVSLQGTVKSK-SDPSELVDILPSDQTPPMELAELAERTASAWK 238

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +L ++   L  +ER+I   R   +      TL  ++     SRE  RQ+  RA +K++++
Sbjct: 239 LLDKA--NLTEKERKIVSLRFGLDGSNEWRTLAEVARHMSCSREYCRQVVQRALRKLRKA 296


>gi|170737511|ref|YP_001778771.1| RpoD family RNA polymerase sigma factor [Burkholderia cenocepacia
           MC0-3]
 gi|169819699|gb|ACA94281.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           cenocepacia MC0-3]
          Length = 627

 Score =  189 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 58/236 (24%), Positives = 105/236 (44%), Gaps = 12/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  S+LRLVV +A  Y   GLP S+++ EGNIGLM+AV ++D  RGF+ +TY+ WW
Sbjct: 390 ARTKLFQSNLRLVVSVAKRYADRGLPFSDLIQEGNIGLMKAVDRYDHRRGFKFSTYATWW 449

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   +      +++ T          L +L    +             A++ ++ +
Sbjct: 450 IRQAITHALADLGRTIRVPTH-----TVDTLNKLSRLARLHRQRTGDVADARALSTQMRL 504

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +   +    S +  ++    +     D  +   D       E       R ++
Sbjct: 505 PVDKVRELMSIVREPISADLPVSP--DHDLTLCDVTI---DPDAPTPEEAASAGQLRAVV 559

Query: 229 TRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              +  L  RE  I   R     +N  +L  +  +  +S ERVRQ+E  A +++++
Sbjct: 560 AELIDSLPVREAWILRLRYGIDVDNEYSLREIGRQLNLSAERVRQLEVSALERIRQ 615


>gi|158339957|ref|YP_001521127.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158310198|gb|ABW31813.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 268

 Score =  189 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 66/275 (24%), Positives = 126/275 (45%), Gaps = 15/275 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             L  Y+ E+ + P+L  +EE  LA++ +  G L A  R++  +LRLVV IA  ++  GL
Sbjct: 6   DSLHYYLQEMGRYPLLSHEEEIELARQAK-AGSLRAKQRMIECNLRLVVSIAKKHQNRGL 64

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           P+ +++ EG+IGL  AV KF+  +G R +TY+ WWI+  +   +      + +       
Sbjct: 65  PLLDLIQEGSIGLSTAVDKFEIAQGCRFSTYAYWWIRQGITAALRAKSRPIYLPQYQ--- 121

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
             +  + ++K H + +     +   +  +++   +    +           SL+  +   
Sbjct: 122 --WEMINKIKKHYRELNQKLGREPSLSELSESTEIKPKTINLTLQLFQKISSLDQPVGPE 179

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-- 251
            K+S    D L  D   Q  + +E  +R      L   M+ L+ RER +   R   E+  
Sbjct: 180 QKDS--LLDLLPGD--NQPTLYMESLQRD---EQLFHVMAHLDERERLVLSQRYGLEDDQ 232

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           P ++  +  +  +S E +R I  +  KK++   + 
Sbjct: 233 PKSMREIGEQIGLSHEGIRLILKKIMKKLERYAES 267


>gi|148243538|ref|YP_001228695.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp.
           RCC307]
 gi|147851848|emb|CAK29342.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. RCC307]
          Length = 370

 Score =  189 bits (481), Expect = 4e-46,   Method: Composition-based stats.
 Identities = 68/237 (28%), Positives = 118/237 (49%), Gaps = 13/237 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  R++ ++LRLVV +A  Y+  G+ + ++V EG +GL + V+K+DP RGFR +TY+ 
Sbjct: 129 RRAKERMIQANLRLVVAVAKKYQHRGMELLDLVQEGTLGLERGVEKYDPTRGFRFSTYAY 188

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   I      +++     +K     L R+K   + I     +   +  ++++L
Sbjct: 189 WWIRQGITRAIATQSRTIRLPVHITEK-----LNRIKKAQRDIASRLGRTATLKDLSQEL 243

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +SE  V     R+    SL+  +       ++  D L       EQ L     R+   +
Sbjct: 244 QLSEEVVRQTLMRVPRSVSLDTRV--GRDMDTELGDLLEDGMPTPEQRLT----REKLHD 297

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L   ++ L+ RE R+   R   ++  P TL  +    ++SRERVRQIE+RA  K++
Sbjct: 298 DLLVLLNELSGREARVIRLRFGLDDDTPQTLAEIGKTLDLSRERVRQIESRALHKLR 354



 Score = 35.9 bits (82), Expect = 8.0,   Method: Composition-based stats.
 Identities = 12/53 (22%), Positives = 25/53 (47%), Gaps = 6/53 (11%)

Query: 2  NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLV 54
          NR+  S   +    +  Y+ +I ++ +L  +EE  LA+  ++        +LV
Sbjct: 3  NRQASSKRRSTADLVRLYLQDIGRVDLLSHEEELTLARLVQK------REQLV 49


>gi|168703618|ref|ZP_02735895.1| transcription initiation factor sigma 70 [Gemmata obscuriglobus UQM
           2246]
          Length = 521

 Score =  189 bits (480), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 71/261 (27%), Positives = 117/261 (44%), Gaps = 14/261 (5%)

Query: 30  EKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
              E   L +  R+      +    L  ++LRLVV IA  YR  GLP S+++ EGN GLM
Sbjct: 259 TADELAALVRVLRKRRLAYQAVRKELAEANLRLVVSIAKNYRNRGLPFSDLIQEGNRGLM 318

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV K++    F+  TY+ WW++  +   +  +   V++     Q  L   + +L+G L 
Sbjct: 319 RAVDKYEWRLEFKFGTYATWWVRQGITRALHDNARTVRVPCH--QISLLSRMEKLRGELT 376

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
             T      E    +A+ L V   E  S+        SLN  +          +D+L   
Sbjct: 377 VATGREPTSE---ELAEALGVKPEEARSLRIVGRHPVSLNDSV--GGDGERALEDFLSDT 431

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVS 265
           H        E  +    +  +   +  L PRER + E R       P TL+ ++ ++ ++
Sbjct: 432 HISP---PGEHVDANLLKERIGEVLKSLAPREREVIELRFGLKDGTPKTLDEVAKQYGIT 488

Query: 266 RERVRQIEARAFKKVQESIQK 286
           RER+RQIEAR   K+++  + 
Sbjct: 489 RERIRQIEARGLLKLRQPTRS 509



 Score = 37.5 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 11/37 (29%), Positives = 20/37 (54%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL 47
             +  L  Y+ ++  IP+L +++E  LAKR   H + 
Sbjct: 66  GPDDALGLYLRQMGSIPLLNREKELALAKRLEHHRNR 102


>gi|1173127|sp|P43344|RPOD_SERMA RecName: Full=RNA polymerase sigma factor rpoD; AltName:
           Full=Sigma-70
          Length = 215

 Score =  189 bits (480), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 55/219 (25%), Positives = 104/219 (47%), Gaps = 12/219 (5%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
             +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I        
Sbjct: 3   FLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IE 60

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               L R+   +         PE    +A+++ + E ++  +        S+   I   D
Sbjct: 61  TINKLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GD 115

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NP 252
              S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +    
Sbjct: 116 DEDSHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREXKVLRMRFGIDMNTD 172

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
            TLE +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 173 HTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 211


>gi|291320189|ref|YP_003515450.1| DNA directed RNA polymerase sigma factor [Mycoplasma agalactiae]
 gi|290752521|emb|CBH40493.1| DNA directed RNA polymerase sigma factor(Sigma A) [Mycoplasma
           agalactiae]
          Length = 509

 Score =  189 bits (480), Expect = 5e-46,   Method: Composition-based stats.
 Identities = 67/284 (23%), Positives = 130/284 (45%), Gaps = 22/284 (7%)

Query: 16  LSRYIHEIRKI-PMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  Y+  I K   +L+ +EE+ LA    + G     A  +L+  +LRLV+  A  Y+  G
Sbjct: 226 VKWYMRWIGKYGKLLQPEEEFELATEMDKGGFRGKRARDKLIKRNLRLVINNAKKYKNRG 285

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L   +++SEGN G+++AV+K++  +GF+ +TY+ WWI+ A+   +      V++     +
Sbjct: 286 LSFIDLISEGNSGIIKAVQKYNVNKGFKFSTYATWWIRQAITRAVADQSRTVRVPVHMVE 345

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL--NVSESEVISMNCRLAGDESLNALI 190
                 + ++    + +   N        IA++   + +  +V  +     G  SL+  I
Sbjct: 346 -----TINKITKIERELQQENGVDPTDEEIAQRYGNDFTAEKVRHIRKINIGPISLDKQI 400

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-- 248
               +N S + D++  +           EE     N + +    L+  E  +   R    
Sbjct: 401 --GKENDSSFSDFVKDESVVNPVDYASHEELVETLNAILK--DTLDADEYELICKRYGVG 456

Query: 249 ------QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                 +    +LE L+ E  VS+ER+RQIE +  +K++ S ++
Sbjct: 457 FDNNGEKYKVFSLEELALERNVSKERIRQIENKILRKLKSSPER 500


>gi|158336372|ref|YP_001517546.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
 gi|158306613|gb|ABW28230.1| RNA polymerase sigma-70 factor [Acaryochloris marina MBIC11017]
          Length = 318

 Score =  189 bits (480), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 72/317 (22%), Positives = 139/317 (43%), Gaps = 52/317 (16%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-------------YREHGDLS---- 48
           M      +  ++ Y+ EI + P+L  ++E +  K+              ++H D      
Sbjct: 1   MKNSFVSKDSITTYLREISRFPLLNHEQEVIFGKQVQRLTALQEMKQELQDHLDREPTQK 60

Query: 49  ----------------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
                                 A  ++V S+LRLVV IA  Y    +   +++ EG IGL
Sbjct: 61  EWAEKAQVSVAQLQKELKLGHKANRKMVESNLRLVVSIAKKYNKAKVEFLDLIQEGTIGL 120

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
            + V+KFDP +G+R +TY+ WWI+ AM   I      +++    N+K     L +L+   
Sbjct: 121 QRGVEKFDPMKGYRFSTYAYWWIRQAMTRAIAEQERTIRLPIHINEK-----LSKLRKVR 175

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           + ++    +   V  +A +++++  ++           SL+  I   D+ +++  + L  
Sbjct: 176 RQLSQKLHRDPTVQELAVEMDLAPKKIEDYLNYARRSISLD--IQIGDQQNTELWELLED 233

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
            ++  +        R +    L + +  L+P++R +   R     +NP+TL  +     V
Sbjct: 234 PNESPDTYATASSLRSD----LAKLLQDLSPQQREVITLRYGLIDQNPLTLAKVGERLNV 289

Query: 265 SRERVRQIEARAFKKVQ 281
           SRE VR++E  AFK ++
Sbjct: 290 SREWVRRVEREAFKILR 306


>gi|50365086|ref|YP_053511.1| RNA polymerase sigma factor [Mesoplasma florum L1]
 gi|50363642|gb|AAT75627.1| RNA polymerase sigma factor [Mesoplasma florum L1]
          Length = 471

 Score =  189 bits (480), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 72/327 (22%), Positives = 136/327 (41%), Gaps = 67/327 (20%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHR----LVTSHLRLVVKIAMGYRGY 71
           +  Y   I +  +L K +E V AK      D          L+TS+L+LV+ +A  +   
Sbjct: 137 IKTYFSTIGQTKILTKDQEIVYAK-LANSEDPEERKEGRDMLITSNLKLVISVARKHLNR 195

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL  ++++ EGNIGL++AV KFD E+GF+ +TY+ WWI+ A+   I      ++I     
Sbjct: 196 GLDFADLIEEGNIGLIKAVDKFDYEKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMV 255

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL--NVSESEVISMNCRLAGDESLNAL 189
           +      + +L    + +T    +      +A+++  +++  +V+ +        SL   
Sbjct: 256 E-----TINKLSRIERQLTQELGREPSSKEVAERMGGDMTAEKVVEIKKIAVEPVSLEKP 310

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM---------------------- 227
               D++ + + D++            EKE  +   +                       
Sbjct: 311 F--GDEDDTHFGDFVEDKDMISPTDFTEKEILREVIDKVFEDMPAREEKVIRMRYGIVPT 368

Query: 228 -------------------LTRSMSVLN-----PRER------RIFEARRL-QENPVTLE 256
                              L ++++ L+     P E+      +I +   L  E   TLE
Sbjct: 369 KVRTLIRLAEECNDETAGELAKAINKLDIHLETPVEKIRTVDSKIIQDHLLKYEASKTLE 428

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQES 283
            +  E  V+RER+RQIEA+  +K+++ 
Sbjct: 429 EVGKELNVTRERIRQIEAKTIRKLKQP 455


>gi|123965877|ref|YP_001010958.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9515]
 gi|123200243|gb|ABM71851.1| Putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus str. MIT 9515]
          Length = 307

 Score =  189 bits (480), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 73/302 (24%), Positives = 134/302 (44%), Gaps = 41/302 (13%)

Query: 15  GLSRYIHEIRKIPMLEKQ----------EEYVLAKRYREHGDLSAA-------------- 50
            LS ++ EI +  +L  +          E  VL  R +  G   +A              
Sbjct: 3   SLSDFLGEIGRHQLLTPEKELTMGRKVQEMVVLINRCQTAGGKGSACEYSEVEKKKIKIG 62

Query: 51  ----HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
               + ++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG R +TY+ 
Sbjct: 63  EKAKNAMITANLRLVVNLAKRYQGKGLELLDLIQEGTLGLTRAVEKYDPSRGHRFSTYAY 122

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   +      ++I    N+K     LR  K  L  +      P     +A+++
Sbjct: 123 WWIRQGLNRALSTQSRTIRIPVNINEK--LTKLRAAKSKLMQLKG---FPPTSFELAEEM 177

Query: 167 NVSESEVISMNC--RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            +++ E+  +      +   SL   + S   + S+  D L  D     ++    E   + 
Sbjct: 178 KITKEEIDELLSCELRSITVSLQGTVKSK-SDPSELVDILPSDQTPPMELAELAERTASA 236

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             +L ++   L  +ER+I   R   +      TL  ++     SRE  RQ+  RA +K++
Sbjct: 237 WTLLDKA--NLTEKERKIVSLRFGLDGSNEWKTLAEVARHMSCSREYCRQVVQRALRKLR 294

Query: 282 ES 283
           ++
Sbjct: 295 KA 296


>gi|12045103|ref|NP_072914.1| RNA polymerase sigma factor [Mycoplasma genitalium G37]
 gi|255660251|ref|ZP_05405660.1| RNA polymerase sigma factor [Mycoplasma genitalium G37]
 gi|1350862|sp|P47491|RPOD_MYCGE RecName: Full=RNA polymerase sigma factor rpoD; Short=Sigma-A
 gi|1045940|gb|AAC71469.1| RNA polymerase sigma factor RpoD [Mycoplasma genitalium G37]
 gi|166078711|gb|ABY79329.1| RNA polymerase sigma factor RpoD [synthetic Mycoplasma genitalium
           JCVI-1.0]
          Length = 497

 Score =  188 bits (479), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 71/297 (23%), Positives = 139/297 (46%), Gaps = 22/297 (7%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS---AAHRLVTSH 57
           +  KN+S     +  +  ++  +    ML+ + E  +AK      + S   A ++LVTS+
Sbjct: 195 LTSKNISNRDKVDDNVRFFLGSLDFSKMLDFESEQRIAKVLNSTDEESRKYAINQLVTSN 254

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVV IA  +   GL  ++++ EGN+GL++A+ KF+   G + +TY+ WWIK A+   I
Sbjct: 255 LRLVVSIAKKHLERGLDFNDLIQEGNLGLLKAISKFNWSLGNKFSTYATWWIKQAITRAI 314

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL-----NVSESE 172
                 V+I     +      + RL    +A+     +      +A+K+       +  +
Sbjct: 315 ADQARTVRIPVHMVE-----TINRLAKAERALYQELGREPTDEELAEKMGGQAEGFNVKK 369

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           +  +        SL+  +   ++  SQ+ D++    D   Q   E  E ++    +   +
Sbjct: 370 IAEIKRLSLDPVSLDKTVGHDEE--SQFGDFV---KDTDAQTPDEFTESRSNSEKIDELL 424

Query: 233 -SVLNPRERRIFEARRLQ---ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            + L+ +E  I   R        P TL+ +  +  + RE++RQIE +A +K++ +++
Sbjct: 425 NNNLSEQEELIVRMRIGMPPYNEPKTLDEVGQKILIPREKIRQIENKAIRKLRHAVR 481


>gi|209809124|ref|YP_002264662.1| RNA polymerase sigma factor [Aliivibrio salmonicida LFI1238]
 gi|208010686|emb|CAQ81073.1| RNA polymerase sigma factor [Aliivibrio salmonicida LFI1238]
          Length = 293

 Score =  188 bits (479), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 85/281 (30%), Positives = 134/281 (47%), Gaps = 16/281 (5%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           N     S Y+ EI K  +L   EE   ++ Y   GDL + + L+ S+LRLVVKIA  YR 
Sbjct: 14  NSIDAYSLYLKEINKYKLLTASEELEHSRNYL-SGDLKSRNVLIESNLRLVVKIANKYRH 72

Query: 71  YGL---PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
                    +++ EGN+GLM+AV KFDPE G+R +TY++WWIK +++  +      V++ 
Sbjct: 73  RNQRELAPLDIIEEGNLGLMKAVNKFDPELGYRFSTYAVWWIKESIESALFNHSRTVRLP 132

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
                K L   LR  +     ++    K   +  I+   N    +V  +   +    S  
Sbjct: 133 VHIT-KELNVYLRAARD----LSRTLKKEPSISEISVHCNKDYKKVNKILGLV--PSSST 185

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
               SSD  SS   +    DH   EQ   +   + N  + L+  +++L  RE++I   R 
Sbjct: 186 CHSASSDDMSSNLIELCADDH---EQEPAQSLSKSNLESNLSSWLNLLQCREKQIIINRY 242

Query: 248 L--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                +  TLE L  + ++S+ERVRQI+     K+    +K
Sbjct: 243 GLFGTDVKTLEELGQDLQLSKERVRQIQTETLTKLNTIFKK 283


>gi|72381853|ref|YP_291208.1| putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus str. NATL2A]
 gi|72001703|gb|AAZ57505.1| possible type II alternative RNA polymerase sigma factor
           [Prochlorococcus marinus str. NATL2A]
          Length = 307

 Score =  188 bits (479), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 74/300 (24%), Positives = 135/300 (45%), Gaps = 37/300 (12%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAK----------RYREHGD------------------ 46
            LS ++ EI +  +L  ++E  L +          R ++ G                   
Sbjct: 3   SLSDFLGEIGRHELLTPEQELTLGREVQAMVALNERCQQAGGHGPECEYSSAEKKKFKAG 62

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A ++++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP+RG R +TY+ 
Sbjct: 63  ERAKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPKRGHRFSTYAY 122

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   +      ++I    N+K     LR  K  L      +    Q+    K  
Sbjct: 123 WWIRQGLNRALSTQSRTIRIPVNINEK--LTKLRAAKSRLMQELGVHPSTNQIAIQMKIP 180

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
                E+++   R +   SL   + S   + S+  D L  +     ++    E   +  +
Sbjct: 181 LEEVEELLACELR-SITVSLQGAVKSK-ADPSELVDILPSEEVPPMELAELAERSASAWS 238

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +L +  S L P+ER I   R   +      TL  ++ +   SRE  RQ+  RA +K++++
Sbjct: 239 LLDK--SNLTPKERTILSLRFGLDGSNEWRTLAEVARQMNCSREYCRQVVQRALRKLRKT 296


>gi|124025343|ref|YP_001014459.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. NATL1A]
 gi|123960411|gb|ABM75194.1| Putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus str. NATL1A]
          Length = 307

 Score =  188 bits (479), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 74/300 (24%), Positives = 135/300 (45%), Gaps = 37/300 (12%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAK----------RYREHGD------------------ 46
            LS ++ EI +  +L  ++E  L +          R ++ G                   
Sbjct: 3   SLSDFLGEIGRHELLTPEQELTLGREVQAMVALNERCQQAGGNGPECEYSSAEKKRFKAG 62

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A ++++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP+RG R +TY+ 
Sbjct: 63  ERAKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPKRGHRFSTYAY 122

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   +      ++I    N+K     LR  K  L      +    Q+    K  
Sbjct: 123 WWIRQGLNRALSTQSRTIRIPVNINEK--LTKLRAAKSRLMQELGVHPSTNQIAIQMKIP 180

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
                E+++   R +   SL   + S   + S+  D L  +     ++    E   +  +
Sbjct: 181 LEEVEELLACELR-SITVSLQGAVKSK-ADPSELVDILPSEEVPPMELAELAERSASAWS 238

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +L +  S L P+ER I   R   +      TL  ++ +   SRE  RQ+  RA +K++++
Sbjct: 239 LLDK--SNLTPKERTILSLRFGLDGSNEWRTLAEVARQMNCSREYCRQVVQRALRKLRKT 296


>gi|157412994|ref|YP_001483860.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9215]
 gi|157387569|gb|ABV50274.1| Putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus str. MIT 9215]
          Length = 307

 Score =  188 bits (479), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 75/300 (25%), Positives = 132/300 (44%), Gaps = 37/300 (12%)

Query: 15  GLSRYIHEIRKIPMLEKQ----------EEYVLAKRYREHGD------------------ 46
            LS ++ EI +  +L  +          E  VL  R +E G                   
Sbjct: 3   SLSDFLGEIGRHQLLTPERELTMGRKVQEMVVLVNRCQEAGGKGPACEYSEAERKKIKIG 62

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + ++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG R +TY+ 
Sbjct: 63  EKAKNEMITANLRLVVNLAKRYQGKGLELLDLIQEGTLGLTRAVEKYDPSRGHRFSTYAY 122

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  + + +      ++I    N+K     LR  K  L  +       +++    K  
Sbjct: 123 WWIRQGLNKALSTQSRTIRIPVNINEK--LTKLRSAKSKLMQLKGIPPTSDELSEEMKIT 180

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
                E++S   R +   SL   + S   + S+  D L  D     ++    E   +   
Sbjct: 181 KEEIEELLSCELR-SITVSLQGTVKSK-SDPSELVDILPSDQTPPMELAELAERTASAWK 238

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +L ++   L  +ER+I   R   +      TL  ++     SRE  RQ+  RA +K++++
Sbjct: 239 LLDKA--NLTEKERKIVSLRFGLDGSNEWRTLAEVARHMSCSREYCRQVVQRALRKLRKA 296


>gi|254249954|ref|ZP_04943274.1| DNA-directed RNA polymerase, sigma subunit [Burkholderia
           cenocepacia PC184]
 gi|124876455|gb|EAY66445.1| DNA-directed RNA polymerase, sigma subunit [Burkholderia
           cenocepacia PC184]
          Length = 662

 Score =  188 bits (479), Expect = 6e-46,   Method: Composition-based stats.
 Identities = 57/236 (24%), Positives = 103/236 (43%), Gaps = 12/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  S+LRLVV +A  Y   GLP S+++ EGNIGLM+AV ++D  RGF+ +TY+ WW
Sbjct: 425 ARTKLFQSNLRLVVSVAKRYADRGLPFSDLIQEGNIGLMKAVDRYDHRRGFKFSTYATWW 484

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   +      +++            L +L    +             A++ ++ +
Sbjct: 485 IRQAITHALADLGRTIRVPAH-----TVDTLNKLSRLARLHRQRTGDVADARALSTQMRL 539

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +   +    S +  ++    +     D  +   D       E       R  +
Sbjct: 540 PVDKVRELMSIVREPISADLPVSP--DHDLTLCDVTI---DPDAPTPEEAASAGQLRAAV 594

Query: 229 TRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              +  L  RE  I   R     +N  +L  +  +  +S ERVRQ+E  A +++++
Sbjct: 595 AELIDSLPVREAWILRLRYGIDVDNEYSLREIGRQLNLSAERVRQLEVSALERIRQ 650


>gi|330955107|gb|EGH55367.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae Cit 7]
          Length = 216

 Score =  188 bits (479), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 56/218 (25%), Positives = 101/218 (46%), Gaps = 12/218 (5%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I     
Sbjct: 1   GLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM- 59

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
                  L R+   +         PE    + +++ + E ++  +        S+   I 
Sbjct: 60  -IETINKLNRISRQMLQEMGREPTPE---ELGERMEMPEDKIRKVLKIAKEPISMETPI- 114

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE- 250
             D   S   D++    D   Q  I+    ++ +      +S L  RE ++   R   + 
Sbjct: 115 -GDDEDSHLGDFI---EDSTMQSPIDVATVESLKEATREVLSGLTAREAKVLRMRFGIDM 170

Query: 251 -NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
               TLE +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 171 NTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSE 208


>gi|206564209|ref|YP_002234972.1| putative RNA polymerase sigma-subunit [Burkholderia cenocepacia
           J2315]
 gi|198040249|emb|CAR56232.1| putative RNA polymerase sigma-subunit [Burkholderia cenocepacia
           J2315]
          Length = 628

 Score =  188 bits (479), Expect = 7e-46,   Method: Composition-based stats.
 Identities = 56/236 (23%), Positives = 104/236 (44%), Gaps = 12/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  S+LRLVV +A  Y   GLP ++++ EGNIGLM+AV ++D  RGF+ +TY+ WW
Sbjct: 391 ARTKLFQSNLRLVVSVAKRYADRGLPFADLIQEGNIGLMKAVDRYDHRRGFKFSTYATWW 450

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   +      +++           +L +L    +             A++ ++ +
Sbjct: 451 IRQAITHALADLGRTIRVPAH-----TVDSLNKLSRLARIHRQRTGDVADARALSPQMRL 505

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +   +    S +  ++    +     D  +   D       E       R  +
Sbjct: 506 PVDKVRELMSIVREPISADLPVSP--DHDLTLCDVTI---DADAPTPEEAASAGQLRAAV 560

Query: 229 TRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              +  L  RE  I   R     +N  +L  +  +  +S ERVRQ+E  A +++++
Sbjct: 561 AELIDSLPVREAWILRLRYGIDVDNEYSLREIGRQLNLSAERVRQLEVSALERIRQ 616


>gi|148907004|gb|ABR16646.1| unknown [Picea sitchensis]
          Length = 592

 Score =  188 bits (478), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 51/250 (20%), Positives = 120/250 (48%), Gaps = 12/250 (4%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           + R      +  +++  +LRLV+ +A  Y+  GL + +++  G++GLM++ +KFD  RGF
Sbjct: 345 KMRLEVGRDSFDKIINCNLRLVISVAKNYQNRGLSLQDLIQAGSMGLMRSAEKFDYSRGF 404

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWI+ ++ + +      +++     +      + R++   + +   + +    
Sbjct: 405 KFSTYAYWWIRQSITKALTEQSRTIRLPVHIVES-----MTRIRTAWRLLYQEHKRDPTK 459

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +A+   +S + +  +        SL+           ++ + +   +    + ++ KE
Sbjct: 460 EEVAEVAGISMTRLRHVTRCSRVPTSLDR--CVGKDMDEKFSEIVADTNSESTETIVSKE 517

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAF 277
                +  L R +  L  RE+++   R   ++    +L  +   F +SRERVRQIE +A 
Sbjct: 518 ---LFKKDLDRVLDTLTAREKQVVRLRYGLDDGRMKSLHEVGENFSLSRERVRQIEMKAM 574

Query: 278 KKVQESIQKQ 287
           +K++++ + Q
Sbjct: 575 RKLRQNHRTQ 584


>gi|85813983|emb|CAD20831.2| sigma factor [Spinacia oleracea]
          Length = 575

 Score =  188 bits (478), Expect = 8e-46,   Method: Composition-based stats.
 Identities = 58/236 (24%), Positives = 113/236 (47%), Gaps = 12/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
              +++ S++RLV+ IA  Y+G G+ + ++V EG  GL++  +KFD  +GF+ +TY+ WW
Sbjct: 337 CKDKMIKSNVRLVISIAKNYQGSGMNLQDLVQEGCRGLVRGAEKFDASKGFKFSTYAHWW 396

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           IK A+++ +      +++     +        R+K   + +   N K      +A+   +
Sbjct: 397 IKQAVRKSLSDQSRTIRLPFHMVEATY-----RVKEARKQLLSENGKQPNNEEVAEATGL 451

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S   + ++        SL+  I  +               D + +   +   ++  R  L
Sbjct: 452 SMKRLTAVLMTPKAPRSLDQKIGFNMNLKPSEVIA-----DPEAETAEDLLTKQFMRQDL 506

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQE 282
            + +  L+ RE+++   R   E+    TL+ +     VSRER+RQIE+ AF+K+Q 
Sbjct: 507 EKVLDTLSSREKQVIRWRFGLEDGRMKTLQEIGELMGVSRERIRQIESSAFRKLQN 562


>gi|124024644|ref|YP_001018951.1| type II alternative RNA polymerase sigma factor [Prochlorococcus
           marinus str. MIT 9303]
 gi|123964930|gb|ABM79686.1| Putative type II alternative RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9303]
          Length = 376

 Score =  188 bits (478), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 75/242 (30%), Positives = 116/242 (47%), Gaps = 13/242 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  +++ ++LRLVV +A  Y+  G+ + ++V EG +GL +AV+KFDP RGFR +TY+ 
Sbjct: 134 RRAKDQMIQANLRLVVAVAKKYQQRGIELLDLVQEGTLGLERAVEKFDPARGFRFSTYAY 193

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   I      +++     +K     L R+K   Q I  N  +   +  +AK L
Sbjct: 194 WWIRQGITRAIATQSRTIRLPMHITEK-----LNRIKRVQQEIASNQGRLASIADLAKAL 248

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +SE  V     R+    SL   I    +  SQ  D L            EK  R    N
Sbjct: 249 GLSEETVRLTLMRVPRSISLETRI--GQEQDSQLGDLLED----SNATPEEKLTRDQLHN 302

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R   E+  P TL  +     +SRERVRQIE+ A  K+++  
Sbjct: 303 DLEILLDELSNREATVIRRRFGLEDDTPQTLTQIGEAMHLSRERVRQIESHALLKLRQPQ 362

Query: 285 QK 286
           ++
Sbjct: 363 RR 364



 Score = 35.6 bits (81), Expect = 8.8,   Method: Composition-based stats.
 Identities = 7/43 (16%), Positives = 19/43 (44%)

Query: 2  NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREH 44
           + ++         +  Y+ +I ++ +L  +EE  LA+  +  
Sbjct: 8  TKTSLVRRSGSTDPVRLYLQDIGRVELLTHEEEVTLARLVQRR 50


>gi|113954287|ref|YP_730230.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CC9311]
 gi|113881638|gb|ABI46596.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CC9311]
          Length = 318

 Score =  188 bits (478), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 67/319 (21%), Positives = 141/319 (44%), Gaps = 54/319 (16%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSA---------------- 49
           M+++ + ++ +  Y+ +I ++P+L  Q+E  L ++ +E  DL A                
Sbjct: 1   MALLPDADL-VRSYLRDIGRVPLLSHQQEITLGRQVQELMDLEALEAELKDQRGGEEVAR 59

Query: 50  ------------------------AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
                                     R+V ++LRLVV +A  Y    + + +++ EG IG
Sbjct: 60  DEWAKAAGMSAAQLKRKLQAGRRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIG 119

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++ V+KFDP RG++ +TY+ WWI+  +   I      +++     +      L +LK  
Sbjct: 120 LVRGVEKFDPTRGYKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITE-----MLNKLKKG 174

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            + ++    +   V  +A  + + E EV  + CR     SL   +   D + ++  + L 
Sbjct: 175 QRELSQELGRTPSVTELASFVELPEEEVKDLMCRARQPVSLEMKV--GDGDDTELLELLA 232

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFE 263
            D     ++  ++ E +  +  L   +S L   + ++   R     E P++L  ++   +
Sbjct: 233 GDG----ELPSDQVEGECLKGDLRDLLSQLPELQGKVLRMRYGMDGEEPMSLTGIAKSMK 288

Query: 264 VSRERVRQIEARAFKKVQE 282
           +SR+R R++E    + ++ 
Sbjct: 289 MSRDRTRRLEREGLEMLRR 307


>gi|300727091|ref|ZP_07060510.1| RNA polymerase sigma-70 factor [Prevotella bryantii B14]
 gi|299775635|gb|EFI72226.1| RNA polymerase sigma-70 factor [Prevotella bryantii B14]
          Length = 290

 Score =  188 bits (478), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 73/284 (25%), Positives = 137/284 (48%), Gaps = 12/284 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRL 60
           + + SI       L +Y+ EI + PM+   EE  LA++ R+ G     A  +LV ++LR 
Sbjct: 5   KISKSITNRSSEALDKYLAEISREPMVSIDEETELAQQIRKGGRAGDRAKEKLVKANLRF 64

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y+  GL +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I   
Sbjct: 65  VVSVAKQYQHQGLTLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSIMQAIAEQ 124

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
             +V++    NQ      + ++          + +      +A    +   ++       
Sbjct: 125 SRIVRLP--LNQVGAVSKINQVTAKFVQ---EHNRRPSADELATLTGIDADKIQKSLNAD 179

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +   S++A  +    + +   D L    D +    ++ E  +N    + +  SVL  RE 
Sbjct: 180 SHQMSIDAPFSD--DDDNSMSDMLSSGDDSRTDRQVDYESMQNDMEGVLK--SVLKDREL 235

Query: 241 RIFEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +I +       P   LE +  E  ++RERVRQI  ++  K+++S
Sbjct: 236 KIVKDCFGIGGPEKGLEEIGEEMGLTRERVRQIREKSIMKIRQS 279


>gi|317969234|ref|ZP_07970624.1| RNA polymerase sigma factor, sigma-70 family protein [Synechococcus
           sp. CB0205]
          Length = 311

 Score =  188 bits (478), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 69/301 (22%), Positives = 128/301 (42%), Gaps = 41/301 (13%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------------------------HGD 46
            LS ++ EI +  +L  ++E +L ++ +                                
Sbjct: 4   SLSAFLGEIGRHQLLTPEQELMLGRKVQAMVQLHERCAMAGGVGEACSYNDIEKRTMRVG 63

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  +++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG R +TY+ 
Sbjct: 64  ERAKDQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSTYAY 123

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   +      ++I    N+K     L RL+     +   N        +A  L
Sbjct: 124 WWIRQGLNRALSTQSRTIRIPVNVNEK-----LTRLRAAKARLMQRNGMAPNSQQLATAL 178

Query: 167 NVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            +   E+  +      +   SL  ++ S   + ++  D L  +     +     E     
Sbjct: 179 GLPLDEIEDLLGCELRSVTVSLQGIVKSK-SDPTELVDVLPSEDLPPMERCELAERNAAV 237

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPV---TLENLSSEFEVSRERVRQIEARAFKKVQ 281
             +L +  S L P+ER +   R   +      TL  ++     SRE  RQ+  RA +K++
Sbjct: 238 WKLLDQ--SNLTPKERTVVMLRFGLDGSHEWRTLAEVARLLGCSREYCRQVVQRALRKLR 295

Query: 282 E 282
           +
Sbjct: 296 K 296


>gi|299472557|emb|CBN79859.1| chloroplast RNA-polymerase sigma factor precursor [Ectocarpus
           siliculosus]
          Length = 835

 Score =  188 bits (478), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 65/260 (25%), Positives = 125/260 (48%), Gaps = 14/260 (5%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K E   L +         A   +++++LRLVV +A GYRG GL   +++ EG +GL++
Sbjct: 285 LTKDE---LLRELAVA--DEAKEHMISANLRLVVSMARGYRGRGLAFPDLIQEGTMGLVK 339

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A +KF+PE GF+  TY+ WWIK ++   I     ++++ T  +       L  ++ +   
Sbjct: 340 ACEKFNPEMGFQFYTYARWWIKKSILTGIANQSRVIRLPTQVH-----AFLSSIRKYTYE 394

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK-NSSQWQDWLVYD 207
           +T  + K      +  KL  +  ++          +S++  I +S+K +     D     
Sbjct: 395 LT-VDGKVPTDEELGDKLGATVEKIQHYRQAALRTDSISLDIRASNKVSDGAADDLGTQI 453

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVS 265
            +       +  +    +  +T  ++ L  RE+++  AR   +     TLE +  +  ++
Sbjct: 454 GEKSTPDPEDATQAFYMKGKVTALLATLKDREQKVVRARYGLDGATSKTLEEIGRDLGLT 513

Query: 266 RERVRQIEARAFKKVQESIQ 285
           RERVRQIE++A  K+++  +
Sbjct: 514 RERVRQIESKALSKLRQPYR 533


>gi|269960386|ref|ZP_06174759.1| RNA polymerase sigma-38 factor [Vibrio harveyi 1DA3]
 gi|269834813|gb|EEZ88899.1| RNA polymerase sigma-38 factor [Vibrio harveyi 1DA3]
          Length = 255

 Score =  188 bits (478), Expect = 9e-46,   Method: Composition-based stats.
 Identities = 67/239 (28%), Positives = 121/239 (50%), Gaps = 12/239 (5%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            R++ S+LRLVVKI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+
Sbjct: 14  KRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIR 73

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
             ++  ++     +++      K L   LR  +     ++           IA +L++  
Sbjct: 74  QTIERALMNQTRTIRLPIHVV-KELNIYLRTAR----ELSQKLDHEPTAEEIAAQLDIPV 128

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            +V  M        S++  I           D +   ++   +V  + +   + ++ L  
Sbjct: 129 EDVSKMLRLNERISSVDTPI--GGDGEKALLDIIPDANNSDPEVSTQDD---DIKSSLIH 183

Query: 231 SMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +  LNP+++ +   R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 184 WLEELNPKQKEVLARRFGLLGYEPSTLEEVGREIGLTRERVRQIQVEGLRRLREILIKQ 242


>gi|308189916|ref|YP_003922847.1| RNA polymerase sigma factor [Mycoplasma fermentans JER]
 gi|307624658|gb|ADN68963.1| RNA polymerase sigma factor [Mycoplasma fermentans JER]
          Length = 489

 Score =  188 bits (478), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 70/288 (24%), Positives = 126/288 (43%), Gaps = 18/288 (6%)

Query: 16  LSRYIHEIRKI-PMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  Y+  I K   +L  +EE  LA+   + G     A  +L+  +LRLV+  A  Y+  G
Sbjct: 206 VKWYMRWIGKYGKLLTIEEEKKLAQEMEKGGFRGKRARDKLIKRNLRLVINNAKKYKNRG 265

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L   +++SEGN G+++AV K++  +GF+ +TY+ WWI+ A+   +      +++     +
Sbjct: 266 LSFIDLISEGNSGIVKAVSKYNVSKGFKFSTYATWWIRQAITRAVADQARTIRVPVHMVE 325

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 + +++  LQ         E +            +V  +        SL+  I  
Sbjct: 326 --TINKITKIERELQQELGYEPTDEMIAERYGN-GYDAEKVRYIRKINIDPISLDKQI-- 380

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---Q 249
             +N S + D++  +          +EE     N +      L+  ER +   R      
Sbjct: 381 GKENDSSFSDFVKDESVVNPVDYASQEELVETLNSILE--KSLDDDERILICKRFGVGVD 438

Query: 250 ENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
           EN       +LE L+ E  VS+ER+RQIE +  +K++ S +K   L  
Sbjct: 439 ENGNKYPIHSLEKLAEERNVSKERIRQIENKILRKLKSSTRKGRHLKD 486


>gi|148377531|ref|YP_001256407.1| RNA polymerase sigma factor [Mycoplasma agalactiae PG2]
 gi|148291577|emb|CAL58963.1| DNA directed RNA polymerase sigma factor(Sigma A) [Mycoplasma
           agalactiae PG2]
          Length = 509

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 66/284 (23%), Positives = 129/284 (45%), Gaps = 22/284 (7%)

Query: 16  LSRYIHEIRKI-PMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  Y+  I K   +L+ +EE+ LA    + G     A  +L+  +LRLV+  A  Y+  G
Sbjct: 226 VKWYMRWIGKYGKLLQPEEEFELATEMDKGGFKGKRARDKLIKRNLRLVINNAKKYKNRG 285

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L   +++SEGN G+++AV+K++  +GF+ +TY+ WWI+ A+   +      V++     +
Sbjct: 286 LSFIDLISEGNSGIIKAVQKYNVNKGFKFSTYATWWIRQAITRAVADQSRTVRVPVHMVE 345

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL--NVSESEVISMNCRLAGDESLNALI 190
                 + ++    + +   N        IA++   + +  +V  +        SL+  I
Sbjct: 346 -----TINKITKIERELQQENGVDPTDEEIAQRYGNDFTAEKVRHIRKINIDPISLDKQI 400

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-- 248
               +N S + D++  +           EE     N + +    L+  E  +   R    
Sbjct: 401 --GKENDSSFSDFVKDESVVNPVDYASHEELVETLNAILK--DTLDADEYELICKRYGVG 456

Query: 249 ------QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                 +    +LE L+ E  VS+ER+RQIE +  +K++ S ++
Sbjct: 457 FDNNGEKYKVFSLEELALERNVSKERIRQIENKILRKLKSSPER 500


>gi|149190801|ref|ZP_01869066.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Vibrio shilonii AK1]
 gi|148835363|gb|EDL52335.1| sigma S (sigma 38) factor of RNA polymerase, major sigma factor
           during stationary phase [Vibrio shilonii AK1]
          Length = 289

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 77/279 (27%), Positives = 133/279 (47%), Gaps = 16/279 (5%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           G    S+YIH++  I +L  ++EY  A   R  GD +A   L+ S+LRLVVKIA  Y   
Sbjct: 16  GTDFYSKYIHDVVGIDLLSPEQEYHYATLAR-RGDKAARDVLIESNLRLVVKIARNYTKR 74

Query: 72  G---LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           G     I +++ EGN+GL++A+ KF+PE+GFR +TY++WWI+ +++  ++ +   V++  
Sbjct: 75  GLSNHTILDLIEEGNLGLIKAIDKFEPEKGFRFSTYAVWWIRESIESSLMNTGRTVRLPV 134

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
                     + RL      I  +  +P  V  IA+K   S++++  +       ES ++
Sbjct: 135 HV-----IKEINRLSKQTNEIIADLQRPPSVKEIAEKTAKSQAQISDLIHMSGFIESSSS 189

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
           +     +  S     L            +    +     L   +  L  + R I   R  
Sbjct: 190 VDTIDKEFQS-----LETCKSEAIPEPYDICHNEKLSQSLESVVLSLPEKYRDIVIHRFG 244

Query: 249 QENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
                 +TL+NL   F +S+ERVRQ++     K+Q  ++
Sbjct: 245 LFGKEVLTLDNLGEMFGLSKERVRQLQQEGISKLQNKLK 283


>gi|319777141|ref|YP_004136792.1| putative RNA polymerase sigma factor [Mycoplasma fermentans M64]
 gi|238810060|dbj|BAH69850.1| hypothetical protein [Mycoplasma fermentans PG18]
 gi|318038216|gb|ADV34415.1| Putative RNA polymerase sigma factor [Mycoplasma fermentans M64]
          Length = 489

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 70/288 (24%), Positives = 126/288 (43%), Gaps = 18/288 (6%)

Query: 16  LSRYIHEIRKI-PMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  Y+  I K   +L  +EE  LA+   + G     A  +L+  +LRLV+  A  Y+  G
Sbjct: 206 VKWYMRWIGKYGKLLTIEEEKKLAQEMEKGGFRGKRARDKLIKRNLRLVINNAKKYKNRG 265

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L   +++SEGN G+++AV K++  +GF+ +TY+ WWI+ A+   +      +++     +
Sbjct: 266 LSFIDLISEGNSGIVKAVSKYNVSKGFKFSTYATWWIRQAITRAVADQARTIRVPVHMVE 325

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 + +++  LQ         E +            +V  +        SL+  I  
Sbjct: 326 --TINKITKIERELQQELGYEPTDEMIAERYGN-GYDAEKVRYIRKINIDPISLDKQI-- 380

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---Q 249
             +N S + D++  +          +EE     N +      L+  ER +   R      
Sbjct: 381 GKENDSSFSDFVKDESVVNPVDYASQEELVETLNSILE--KSLDDDERILICKRFGVGVD 438

Query: 250 ENP-----VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
           EN       +LE L+ E  VS+ER+RQIE +  +K++ S +K   L  
Sbjct: 439 ENGNKYPIHSLEKLAEERNVSKERIRQIENKILRKLKSSTRKGRHLKD 486


>gi|254449115|ref|ZP_05062567.1| alternative sigma factor RpoH [gamma proteobacterium HTCC5015]
 gi|198261307|gb|EDY85600.1| alternative sigma factor RpoH [gamma proteobacterium HTCC5015]
          Length = 227

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 89/201 (44%), Positives = 124/201 (61%), Gaps = 11/201 (5%)

Query: 1   MNRK-----NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVT 55
           MN+      NM+ +      L  Y+ ++  IP+L  +EE  LA+R    GDL AA +LV 
Sbjct: 25  MNKSLVMSSNMAPVALSNDTLDAYMQQVSSIPVLGAEEEQELAQRLHREGDLDAARQLVF 84

Query: 56  SHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQE 115
           SHLR V  IA GY+GYGLP+++V+ EGNIGLM+AVK+FDP  G RL ++++ WI+A + E
Sbjct: 85  SHLRFVTHIARGYKGYGLPLADVIQEGNIGLMKAVKRFDPNVGVRLVSFAVHWIRAEIHE 144

Query: 116 YILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
           YILR+W +VK+ TT  Q++LFF LR  K  L  +       E+V  +AK L V  S+V+ 
Sbjct: 145 YILRNWRIVKVATTKAQRKLFFKLRSNKKSLGWLNH-----EEVKTVAKDLGVEASDVME 199

Query: 176 MNCRLAG-DESLNALINSSDK 195
           M  RLAG D + +   N  D 
Sbjct: 200 MESRLAGSDMAYDLPGNDDDD 220


>gi|107025596|ref|YP_623107.1| RNA polymerase, sigma 28 subunit [Burkholderia cenocepacia AU 1054]
 gi|116693222|ref|YP_838755.1| RNA polymerase, sigma 28 subunit [Burkholderia cenocepacia HI2424]
 gi|105894970|gb|ABF78134.1| RNA polymerase, sigma 28 subunit [Burkholderia cenocepacia AU 1054]
 gi|116651222|gb|ABK11862.1| RNA polymerase, sigma 28 subunit [Burkholderia cenocepacia HI2424]
          Length = 628

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 57/236 (24%), Positives = 103/236 (43%), Gaps = 12/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  S+LRLVV +A  Y   GLP S+++ EGNIGLM+AV ++D  RGF+ +TY+ WW
Sbjct: 391 ARTKLFQSNLRLVVSVAKRYADRGLPFSDLIQEGNIGLMKAVDRYDHRRGFKFSTYATWW 450

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   +      +++            L +L    +             A++ ++ +
Sbjct: 451 IRQAITHALADLGRTIRVPAH-----TVDTLNKLSRLARLHRQRTGDVADARALSTQMRL 505

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +   +    S +  ++    +     D  +   D       E       R  +
Sbjct: 506 PVDKVRELMSIVREPISADLPVSP--DHDLTLCDVTI---DPDAPTPEEAASAGQLRAAV 560

Query: 229 TRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              +  L  RE  I   R     +N  +L  +  +  +S ERVRQ+E  A +++++
Sbjct: 561 AELIDSLPVREAWILRLRYGIDVDNEYSLREIGRQLNLSAERVRQLEVSALERIRQ 616


>gi|33861134|ref|NP_892695.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus subsp. pastoris str. CCMP1986]
 gi|33639866|emb|CAE19036.1| Putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus subsp. pastoris str. CCMP1986]
          Length = 307

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 70/302 (23%), Positives = 136/302 (45%), Gaps = 41/302 (13%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYRE-----HGDLSA-------------------- 49
            LS ++ EI +  +L  ++E  + ++ +E     +   +A                    
Sbjct: 3   SLSDFLGEIGRHQLLTPEKELTMGRKVQEMVVLINRCQTAGGKGPDCEYSEEEKKKIKIG 62

Query: 50  ---AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
               + ++T++LRLVV ++  Y+G GL + +++ EG +GL +AV+K+DP RG R +TY+ 
Sbjct: 63  EKAKNEMITANLRLVVNLSKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPSRGHRFSTYAY 122

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   +      ++I    N+K     LR  K  L  +      P   + +A +L
Sbjct: 123 WWIRQGLNRALSTQSRTIRIPVNINEK--LTKLRAAKSKLMQLKG---FPPTSIELANEL 177

Query: 167 NVSESEVISMNC--RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            +++ E+  +      +   SL   + S   + S+  D L  D     ++    E   + 
Sbjct: 178 KITKEEIDELLSCELRSITVSLQGTVKSK-SDPSELVDILPSDQTPPMELAELAERTASA 236

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             +L ++   L  +ER+I   R   +      TL  ++     SRE  RQ+  RA +K++
Sbjct: 237 WTLLDKA--NLTEKERKIVSLRFGLDGSNEWRTLAEVARHMSCSREYCRQVVQRALRKLR 294

Query: 282 ES 283
           ++
Sbjct: 295 KA 296


>gi|18404292|ref|NP_565856.1| SIGF (RNA POLYMERASE SIGMA-SUBUNIT F); DNA binding / DNA-directed
           RNA polymerase/ sigma factor/ transcription factor
           [Arabidopsis thaliana]
 gi|7209640|dbj|BAA92288.1| SigF [Arabidopsis thaliana]
 gi|7688083|emb|CAB89775.1| sigma factor-like protein [Arabidopsis thaliana]
 gi|16604647|gb|AAL24116.1| putative RNA polymerase sigma-70 factor [Arabidopsis thaliana]
 gi|20197948|gb|AAD31584.2| putative RNA polymerase sigma-70 factor [Arabidopsis thaliana]
 gi|20259557|gb|AAM14121.1| putative RNA polymerase sigma-70 factor protein [Arabidopsis
           thaliana]
 gi|330254238|gb|AEC09332.1| RNApolymerase sigma-subunit F [Arabidopsis thaliana]
          Length = 547

 Score =  188 bits (477), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 60/245 (24%), Positives = 123/245 (50%), Gaps = 12/245 (4%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           H   S+  +L+T++LRLVV IA  Y+  GL   +++ EG++GLM++V+KF P+ G R AT
Sbjct: 302 HRGRSSREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFAT 361

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI+ ++++ I ++   +++      + ++  L ++    +              +A
Sbjct: 362 YAYWWIRQSIRKSIFQNSRTIRLP-----ENVYMLLGKVSEARKTCVQEGNYRPSKEELA 416

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
             + VS  ++  +        S+   I S    +     +     D   +       ++ 
Sbjct: 417 GHVGVSTEKLDKLLYNTRTPLSMQQPIWSDQDTT-----FQEITPDSGIETPTMSVGKQL 471

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            RN +   ++VL+P+ERRI + R   +     +L  +   + +S+ERVRQ+E+RA  +++
Sbjct: 472 MRNHVRNLLNVLSPKERRIIKLRFGIDGGKQRSLSEIGEIYGLSKERVRQLESRALYRLK 531

Query: 282 ESIQK 286
           +++  
Sbjct: 532 QNMNS 536


>gi|307718430|ref|YP_003873962.1| RNA polymerase sigma factor [Spirochaeta thermophila DSM 6192]
 gi|306532155|gb|ADN01689.1| RNA polymerase sigma factor [Spirochaeta thermophila DSM 6192]
          Length = 281

 Score =  187 bits (476), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 80/270 (29%), Positives = 129/270 (47%), Gaps = 16/270 (5%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
            Y+ EI++  +L  +EE  L KR R  GD  A  RL+T++LRLVVKIA+ +    +P+ +
Sbjct: 17  AYLREIKRYKLLSPEEERELGKRIR-RGDPEARERLITANLRLVVKIALQFSVPDIPLLD 75

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGL++A +KFD  R  R +TY+ WWI+ A+   ++     +++           
Sbjct: 76  LIQEGNIGLIRAAEKFDYRRNIRFSTYAAWWIRQAIHRALMNKRRPIRLPNRKEDV---- 131

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            LR+++   Q +    ++      IA+ L +   EV  +        SL   IN    + 
Sbjct: 132 -LRKIEKAKQLLEQRLMREPSTEEIAELLGMETEEVEELINLGQEVVSLETQINDGSMD- 189

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS-VLNPRERRIFEARRLQENPV-TL 255
                  ++D         E+  RK  R      +   L+ RE  +   R     P  TL
Sbjct: 190 -------LHDVCPGGASPEEEVCRKACREDTLTLIQRTLDSRESEVVLHRYALTGPRYTL 242

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + LS    +S E VRQIE RA +K++E  +
Sbjct: 243 KTLSEHLGISPETVRQIEIRALRKLRERAE 272


>gi|22298042|ref|NP_681289.1| group 2 RNA polymerase sigma factor [Thermosynechococcus elongatus
           BP-1]
 gi|22294220|dbj|BAC08051.1| group 2 RNA polymerase sigma factor [Thermosynechococcus elongatus
           BP-1]
          Length = 375

 Score =  187 bits (476), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 67/246 (27%), Positives = 125/246 (50%), Gaps = 13/246 (5%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A ++L+ ++LRLVV IA  Y+ +G+   +++ EG++GL +AV+KFDP +GFR +
Sbjct: 130 ERQGQRAKNQLLQANLRLVVNIAKKYQHHGVEFLDLIQEGSLGLERAVEKFDPTKGFRFS 189

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ ++   +      +++     +K     L ++K   + +         +  I
Sbjct: 190 TYAYWWIRQSITRAVASQSRTIRLPIHMVEK-----LNKIKRAQRRLAAQRGAMPSLADI 244

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A++LN+  S+V  +   +    +L   + S  +        L    +       E   R+
Sbjct: 245 AQELNLEVSQVRQVLMAVPKSVALEQRVGSDQETE------LQELIESPAPTPDEVIMRE 298

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE--NLSSEFEVSRERVRQIEARAFKKV 280
           + R  L + +S L+PRER++ E R        LE   ++    +SRER+RQIE RA +K+
Sbjct: 299 SLRTTLKQLLSDLSPRERQVMELRYGLGEQPALELAEVAVLLGLSRERIRQIEHRALQKL 358

Query: 281 QESIQK 286
           ++  ++
Sbjct: 359 RQPQRR 364



 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 9/28 (32%), Positives = 19/28 (67%)

Query: 16 LSRYIHEIRKIPMLEKQEEYVLAKRYRE 43
          + +Y+ EI ++P+L   EE  LA++ ++
Sbjct: 24 VRQYLQEIGRVPLLTPSEELRLAEQVQQ 51


>gi|326332710|ref|ZP_08198972.1| RNA polymerase principal sigma factor SigB [Nocardioidaceae
           bacterium Broad-1]
 gi|325949491|gb|EGD41569.1| RNA polymerase principal sigma factor SigB [Nocardioidaceae
           bacterium Broad-1]
          Length = 315

 Score =  187 bits (476), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 64/307 (20%), Positives = 126/307 (41%), Gaps = 45/307 (14%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------------- 41
           + G   +  Y+ EI +  +L+  +E  L+K                              
Sbjct: 12  IEGRDSVGLYLDEIARNELLDAAKEVELSKAIEAGLMAEHLLAEGRVGRKKAPGGATRAE 71

Query: 42  ----REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
                E G  +     + ++LRLVV IA  Y    +P+ +++ EGN GL++AV+KFD  +
Sbjct: 72  LEWLAEEGHRATRE-FINANLRLVVSIARKYGRAQMPMLDLIQEGNTGLIRAVEKFDYTK 130

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WW++ A+   I +   +V++     +      L ++ G  + +     +  
Sbjct: 131 GYKFSTYATWWVRQAITRGIAQQARVVRLPVHVVE-----ELNQVGGARRTLERQLGRDP 185

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           +   IA +L +    V+ +        SL+  I   +   +   D +  +      + + 
Sbjct: 186 EPEEIAAELGMDIDRVLDLLSWGRDHVSLDTPI--DEDGDTSLGDLMAQESAPSPDMDVI 243

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT--LENLSSEFEVSRERVRQIEAR 275
             E    R  L   +  L+ R   I  +R    +     L ++  +  +S ERVRQ+E  
Sbjct: 244 DVES---RERLNSLVGQLDERSADIVRSRYGLTDGRQHKLADIGVKHGISAERVRQLERE 300

Query: 276 AFKKVQE 282
           A +K++ 
Sbjct: 301 ALQKLRR 307


>gi|282859310|ref|ZP_06268422.1| sigma-70 region 2 [Prevotella bivia JCVIHMP010]
 gi|282587890|gb|EFB93083.1| sigma-70 region 2 [Prevotella bivia JCVIHMP010]
          Length = 290

 Score =  187 bits (476), Expect = 1e-45,   Method: Composition-based stats.
 Identities = 70/284 (24%), Positives = 135/284 (47%), Gaps = 12/284 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRL 60
           + + SI       L +Y+ EI + PM+   EE  LA+   + G     A  +L+ ++LR 
Sbjct: 5   KISKSITNRSSEALDKYLVEIGREPMITVDEEIELAQEIHKGGRKGERAKEKLIKANLRF 64

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y+  GL +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I   
Sbjct: 65  VVSVAKQYQHQGLSLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQ 124

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
             +V++    NQ      + ++          + +   +  +A+   + E+ +       
Sbjct: 125 SRIVRLP--LNQVGAISKINQVTN---EFIQKHNRRPSIHELAEMTGIDEARIRQSQSAD 179

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               S++A  +    + +   D L    D +    ++ E   +    + +  + L  RE 
Sbjct: 180 NHHMSIDAPFSD--DDDNSMSDMLSSGDDSRTDKGVDFESMSDDLRAVLQ--NTLKEREI 235

Query: 241 RIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +I             LE + +E  ++RERVRQI  +A +K++ES
Sbjct: 236 KIVTECFGIGCQEKGLEEIGTEMALTRERVRQIREKAIEKIRES 279


>gi|46201746|ref|ZP_00054445.2| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Magnetospirillum magnetotacticum
           MS-1]
          Length = 756

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 68/248 (27%), Positives = 113/248 (45%), Gaps = 22/248 (8%)

Query: 38  AKRYREHG---DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           A+R  E G      A  R   ++L+LVV  A  + G   P  + + EGN+GL++AV++FD
Sbjct: 513 ARRRMEAGLETARRARERFALANLKLVVWGAKKFGGLTWP--DRIQEGNLGLLKAVERFD 570

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             RG + +TY+ WWIK A+   +      ++I   A +      LRR +  + A+T    
Sbjct: 571 HRRGAKFSTYATWWIKQAVTRAVADKGRTIRIPVHAQE--AMRKLRRAQNEVFALTGREA 628

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            PE+V  + +   +  + V           SL+           +       +   +E  
Sbjct: 629 LPEEVGELTE---IPLARVRRFLAVAEEPASLD----------VEEVGLHAAEMASREPD 675

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQI 272
             E+      + M+   + +L PRE  +   R     E   TLE +  +F V+RER+RQI
Sbjct: 676 PEERLAVAEIKAMVRGQLELLPPREATVIRLRFGIGCEREYTLEEIGQQFGVTRERIRQI 735

Query: 273 EARAFKKV 280
           EA+A +K+
Sbjct: 736 EAKALRKL 743


>gi|26452898|dbj|BAC43527.1| putative plastid RNA polymerase sigma-subunit SIG1 [Arabidopsis
           thaliana]
          Length = 572

 Score =  187 bits (476), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 62/245 (25%), Positives = 117/245 (47%), Gaps = 12/245 (4%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R R H       +++ S++RLV+ IA  Y+G G+ + ++V EG  GL++  +KFD  +GF
Sbjct: 323 RQRIHHGTLCKDKMIKSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKGF 382

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWIK A+++ +     ++++     +        R+K   + +     K  + 
Sbjct: 383 KFSTYAHWWIKQAVRKSLSDQSRMIRLPFHMVEATY-----RVKEARKQLYSETGKHPKN 437

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IA+   +S   ++++        SL+  I  +     Q         D +     +  
Sbjct: 438 EEIAEATGLSMKRLMAVLLSPKPPRSLDQKIGMN-----QNLKPSEVIADPEAVTPEDIL 492

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAF 277
            ++  R  L + +  L  RE+++   R   E+    TL+ +     VSRERVRQIE+ AF
Sbjct: 493 IKEFMRQDLDKVLDSLGTREKQVIRWRFGMEDGRMKTLQEIGEMMGVSRERVRQIESSAF 552

Query: 278 KKVQE 282
           +K++ 
Sbjct: 553 RKLKN 557


>gi|315185550|gb|EFU19319.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           thermophila DSM 6578]
          Length = 281

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 80/271 (29%), Positives = 131/271 (48%), Gaps = 16/271 (5%)

Query: 17  SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
           + Y+ EI++  +L  +EE  L KR R  GD  A  RL+T++LRLVVKIA+ +    +P+ 
Sbjct: 16  TAYLREIKRYKLLSPEEERELGKRIR-RGDPVARERLITANLRLVVKIALQFSVPDIPLL 74

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++ EGNIGL++AV+KFD  R  R +TY+ WWI+ A+   ++     +++          
Sbjct: 75  DLIQEGNIGLIRAVEKFDYRRNIRFSTYAAWWIRQAIHRALMNKRRPIRLPNRKEDV--- 131

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
             LR+++   + +    ++      IA  L +   EV  +        SL   IN    +
Sbjct: 132 --LRKIEKARRLLEQRLMREPSTEEIADLLGMESEEVEELINLGQEVVSLETQINDGSMD 189

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS-VLNPRERRIFEARRLQENPV-T 254
                   ++D         E+  RK  R      +   L+ RE  +   R     P  T
Sbjct: 190 --------LHDVCPGGASPEEEVCRKACREDTLTLIQRTLDSRESEVVLHRYALTGPRYT 241

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L+ LS +  +S E VRQIE RA +K++E  +
Sbjct: 242 LKTLSEQMGISPETVRQIEIRALRKLRERAE 272


>gi|307565781|ref|ZP_07628247.1| sigma-70 region 2 [Prevotella amnii CRIS 21A-A]
 gi|307345508|gb|EFN90879.1| sigma-70 region 2 [Prevotella amnii CRIS 21A-A]
          Length = 290

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 70/284 (24%), Positives = 135/284 (47%), Gaps = 12/284 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRL 60
           + + SI       L +Y+ EI + PM+   EE  LA+   + G     A  +L+ ++LR 
Sbjct: 5   KISKSITNRSSEALDKYLVEIGREPMITVDEEIELAQEIHKGGLKGERAKEKLIKANLRF 64

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A  Y+  GL +++++ EGNIGL++A +KFD  RGF+  +Y++WWI+ ++ + I   
Sbjct: 65  VVSVAKQYQHQGLSLTDLIDEGNIGLVKAAEKFDETRGFKFISYAVWWIRQSILQAIAEQ 124

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
             +V++    NQ      + ++          + +   +  +A+   + E+ +       
Sbjct: 125 SRIVRLP--LNQVGAISKINQVTN---EFIQKHNRRPSIHELAEITGIDEARIRQSQSAD 179

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               S++A  +    + +   D L    D +    ++ E   +    + +  + L  RE 
Sbjct: 180 NHHMSIDAPFSD--DDDNSMSDMLSSGEDSRTDKGVDFESMSDDLRAVLQ--NTLKEREI 235

Query: 241 RIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +I             LE + +E  ++RERVRQI  +A +K++ES
Sbjct: 236 KIVTECFGIGCQEKGLEEIGTEMALTRERVRQIREKAIEKIRES 279


>gi|87303408|ref|ZP_01086196.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
 gi|87282056|gb|EAQ74018.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
          Length = 330

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 63/308 (20%), Positives = 129/308 (41%), Gaps = 53/308 (17%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------------------- 43
           +  Y+ +I ++P+L  ++E  L ++ +E                                
Sbjct: 22  VRSYLRDIGRVPLLTHEQEITLGRQVQELMRLEETEQELEMRAGGQKPSAAEWASAAGLS 81

Query: 44  --------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
                        A  R+V ++LRLVV +A  Y    + + +++ EG IGL++ V+KFDP
Sbjct: 82  PALLKRKLSSGRRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRGVEKFDP 141

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            RG++ +TY+ WWI+  +   I      +++     +      L +LK   + ++    +
Sbjct: 142 TRGYKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITE-----TLNKLKKGQRELSQELGR 196

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
              +  +A  + + E EV  + CR     SL   +   D   ++  D L  D      + 
Sbjct: 197 TPTLSELAVCVELPEEEVKDLLCRARQPVSLETKV--GDGEDTELLDLLQGDG----TLP 250

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIE 273
            E  + +  R  +   +  L   +R +   R     + P++L +++    +SR++ R +E
Sbjct: 251 AESVDSECLRGDMRALLEQLPELQRSVLSMRYGIDGDEPMSLTSIARTLGMSRDKTRNLE 310

Query: 274 ARAFKKVQ 281
            RA + ++
Sbjct: 311 RRALEGIR 318


>gi|159903122|ref|YP_001550466.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9211]
 gi|159888298|gb|ABX08512.1| Putative type II alternative sigma factor, sigma70 family
           [Prochlorococcus marinus str. MIT 9211]
          Length = 312

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 73/300 (24%), Positives = 131/300 (43%), Gaps = 37/300 (12%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------------------------HGD 46
            LS ++ EI +  +L  +EE  + ++ +                                
Sbjct: 3   SLSDFLGEIGRHHLLTPEEELTMGRKVQAMVALLEKSKLSEGKGEACEYTDLERRTIRQG 62

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A ++++TS+LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP+RG R +TY+ 
Sbjct: 63  ERAKNQMITSNLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPKRGHRFSTYAY 122

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   +      ++I    N+K     LR  K  L          E +      L
Sbjct: 123 WWIRQGLNRALSTQSRTIRIPVNINEK--LTKLRAAKSQLMQANGLTPSSEMLAK-KMHL 179

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +  E E +      +   SL  ++ S   + S+  D L  +     +V    E   +  +
Sbjct: 180 SKEEVEELLECELRSITVSLQGVVQSK-SDPSELGDVLPSEEIPPMEVAELAERNDSAWS 238

Query: 227 MLTRSMSVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +L ++   L P+ER I   R   +      TL  ++     SRE  RQ+  RA +K++++
Sbjct: 239 LLNKA--NLTPKERTIVSLRFGLDGSNEWRTLAEVAKHMNCSREYCRQVVQRALRKLRKT 296


>gi|33864481|ref|NP_896041.1| putative type II alternative RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9313]
 gi|33641261|emb|CAE22391.1| Putative type II alternative RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9313]
          Length = 376

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 73/242 (30%), Positives = 115/242 (47%), Gaps = 13/242 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  +++ ++LRLVV +A  Y+  G+ + ++V EG +GL +AV+KFDP RGFR +TY+ 
Sbjct: 134 RRAKDQMIQANLRLVVAVAKKYQQRGIELLDLVQEGTLGLERAVEKFDPTRGFRFSTYAY 193

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+  +   I      +++     +K     L R+K   Q I  +  +   +  +AK L
Sbjct: 194 WWIRQGITRAIATQSRTIRLPMHITEK-----LNRIKRVQQEIASSQGRLASIADLAKAL 248

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +SE  V     R+    SL   I    +  +Q  D L            EK  R    N
Sbjct: 249 GLSEETVRLTLMRVPRSISLETRI--GQEQDTQLGDLLED----SNATPEEKLTRNQLHN 302

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L+ RE  +   R   E+  P TL  +     +SRERVRQIE  A  K+++  
Sbjct: 303 DLEILLDELSNREATVIRRRFGLEDDTPQTLTQIGEAMHLSRERVRQIETHALLKLRQPQ 362

Query: 285 QK 286
           ++
Sbjct: 363 RR 364


>gi|168704590|ref|ZP_02736867.1| RNA polymerase sigma factor rpoS [Gemmata obscuriglobus UQM 2246]
          Length = 278

 Score =  187 bits (475), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 71/277 (25%), Positives = 123/277 (44%), Gaps = 13/277 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  L  Y+ EI +  +L   +E  LA+   + GD  A  ++V ++LRLVV IA GY G G
Sbjct: 13  QSPLETYLREINETALLTADQEKSLARAIAQ-GDTEARDQMVRANLRLVVNIARGYTGKG 71

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L + +++ EGN+GL++AV+ FDP    R +TY+ +WIK +++  ++ +   ++I   A  
Sbjct: 72  LALQDLIEEGNLGLLRAVEGFDPTMNTRFSTYASYWIKQSIKRALVNTAKTIRIP--AYM 129

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
             L    RR    L          E+V  +        + +              A    
Sbjct: 130 VELLAKWRRATNKLSDELGRPPTHEEVGKLLGLPKKKLAIIKKAIRVYNA-----APQAD 184

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QE 250
                   ++ L+ +         E  E  + + +L   +  ++ RE  +   R     E
Sbjct: 185 QGDQGWSIEEMLMDNRAKTPDT--EMVETDDLKQVLI-LLEKMDQREATVLRMRFGLNDE 241

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            P TL+ +     ++RERVRQIE  A  K+ E +  +
Sbjct: 242 EPKTLKEIGECLGLTRERVRQIEGEALAKLGEDLSGE 278


>gi|76799605|ref|ZP_00781725.1| RNA polymerase major sigma factor RpoD [Streptococcus agalactiae
           18RS21]
 gi|76585040|gb|EAO61678.1| RNA polymerase major sigma factor RpoD [Streptococcus agalactiae
           18RS21]
          Length = 278

 Score =  186 bits (474), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 61/190 (32%), Positives = 98/190 (51%), Gaps = 8/190 (4%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             +  Y+ EI  +P+L  +EE  LA    E GDL A  RL  ++LRLVV IA  Y G G+
Sbjct: 97  DPVRMYLKEIGVVPLLTNEEEKELAVAVAE-GDLMAKQRLAEANLRLVVSIAKRYVGRGM 155

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     + 
Sbjct: 156 QFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE- 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                L R + +L      +  PEQ   IA++++++  +V  +        SL   I   
Sbjct: 215 -TINKLVREQRNLLQELGQDPTPEQ---IAERMDMTPDKVREILKIAQEPVSLETPI--G 268

Query: 194 DKNSSQWQDW 203
           +++ S   D+
Sbjct: 269 EEDDSHLGDF 278


>gi|297827203|ref|XP_002881484.1| RNA polymerase sigma-70 factor [Arabidopsis lyrata subsp. lyrata]
 gi|297327323|gb|EFH57743.1| RNA polymerase sigma-70 factor [Arabidopsis lyrata subsp. lyrata]
          Length = 546

 Score =  186 bits (474), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 60/245 (24%), Positives = 122/245 (49%), Gaps = 12/245 (4%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           H   S+  +L+T++LRLVV IA  Y+  GL   +++ EG++GLM++V+KF P+ G R AT
Sbjct: 301 HRGRSSREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFAT 360

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI+ ++++ I ++   +++      + ++  L ++    +              +A
Sbjct: 361 YAYWWIRQSIRKSIFQNSRTIRLP-----ENVYMLLGKVSEARKTCVQEGNYRPSKEQLA 415

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
             + VS  ++  +        S+   I S    +     +     D   +       ++ 
Sbjct: 416 GHVGVSTEKLDKLLYNTRTPLSMQQPIWSDQDTT-----FQEITPDSGIETPTMSVGKQM 470

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            RN +   ++VL+P+ERRI + R   +     +L  +   + +S+ERVRQ+E+RA  +++
Sbjct: 471 MRNHVRNLLNVLSPKERRIIKLRFGIDGGKQRSLSEIGEIYGLSKERVRQLESRALYRLK 530

Query: 282 ESIQK 286
           + +  
Sbjct: 531 QHMNS 535


>gi|328480117|gb|EGF49090.1| RNA polymerase sigma factor RpoD [Lactobacillus rhamnosus MTCC
           5462]
          Length = 206

 Score =  186 bits (474), Expect = 2e-45,   Method: Composition-based stats.
 Identities = 59/213 (27%), Positives = 101/213 (47%), Gaps = 8/213 (3%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+  +    V     +  Y+ EI ++ +L   EE  LA +  E GD  A  RL  ++LRL
Sbjct: 1   MSDMSAPSGVKINDPVRMYLKEIGRVSLLTADEEVALALKI-EQGDQEAKQRLAEANLRL 59

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y G G+   +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I   
Sbjct: 60  VVSIAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQ 119

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I     +      L R++  L         PE++ A   ++++   +V  +    
Sbjct: 120 ARTIRIPVHMVE--TINKLIRIQRQLLQDLGREPTPEEIGA---EMDMPTEKVREILKIA 174

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
               SL   I   +++ S   D++        +
Sbjct: 175 QEPVSLETPI--GEEDDSHLGDFIEDQDATSPE 205


>gi|228949811|ref|ZP_04112021.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228809869|gb|EEM56280.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
          Length = 295

 Score =  186 bits (474), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 74/281 (26%), Positives = 138/281 (49%), Gaps = 17/281 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG-LP 74
           + +Y++EI    +L  ++      +Y+E GD+ +   L+ S+LRLVV +A  +  YG   
Sbjct: 11  MGKYLNEICNYDILTDEQSMEHIIKYKEKGDIDSRDLLICSNLRLVVSVAKSFPCYGNCD 70

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + E++ EG IGLM+ ++ +D  +G +L+TY  WWI+  + +Y+  + S V++ TT  +K 
Sbjct: 71  LMEMIQEGTIGLMKGLEDYDYTKGNKLSTYITWWIRQRISKYLSINRSDVRVATTMQKK- 129

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS--MNCRLAGDESLNALINS 192
               +  +K                  +A+KL   ES VI   +  R+    S+   + +
Sbjct: 130 ----ITEVKNCYYENMGEKGTNLTTKEVAEKLGYKESIVIDALVTDRITNTISIEDDVQN 185

Query: 193 S----DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
                DK  S        +     +V+  +EE+     ++      LNPRE  +   R  
Sbjct: 186 EKTLLDKQQSTLAILANKNAPNPSEVIATEEEKFEFDELM---FVTLNPREESVLRYRFG 242

Query: 249 QEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            ++   +TLE+ +    V+RERV+QIE +A +K+++ +  +
Sbjct: 243 FDDGIELTLEDTARILGVTRERVQQIEKKAIEKMKQRLSSK 283


>gi|134291946|ref|YP_001115715.1| RpoD family RNA polymerase sigma factor [Burkholderia vietnamiensis
           G4]
 gi|134135135|gb|ABO59460.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           vietnamiensis G4]
          Length = 628

 Score =  186 bits (473), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 55/237 (23%), Positives = 104/237 (43%), Gaps = 12/237 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L  ++LRLVV IA  Y   GLP ++++ EGNIGL++A+ ++D  RGFR +TY+ WW
Sbjct: 391 ARMGLFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFSTYATWW 450

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+   +      +++ T          + +L    +     +        +A ++  
Sbjct: 451 IRQAITHALADLGRTIRVPTH-----TVDAINKLTRIAREHRQRSGAAATPHELAVQMGE 505

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +   +    S +A ++   +       ++    D       +       R+ +
Sbjct: 506 PLDKVRDLMSIVKEPMSADAPVSPEGE-----MTFVDVAPDVSTPSPEDAAGAAQLRDTI 560

Query: 229 TRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
              +  L  RE  +   R     +   +L ++  +  +S ERVRQIEA A  +++ S
Sbjct: 561 AAMIGRLPAREATVLRLRYGLHADEGCSLRDIGRQLNLSAERVRQIEASALARLRAS 617



 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 20/50 (40%), Gaps = 9/50 (18%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREH---------GDLSAAHRLV 54
             +  Y+ E+   P+L + EE + A+R             GD  A   LV
Sbjct: 119 DPVRLYLREMGMTPLLTRDEEIMHAQRIERGRAASVAVLCGDPQALDALV 168


>gi|87124760|ref|ZP_01080608.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9917]
 gi|86167639|gb|EAQ68898.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. RS9917]
          Length = 321

 Score =  186 bits (473), Expect = 3e-45,   Method: Composition-based stats.
 Identities = 67/316 (21%), Positives = 136/316 (43%), Gaps = 53/316 (16%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSA------------------- 49
           +++    +  Y+ +I ++P+L  Q+E  L ++ +E  +L A                   
Sbjct: 6   VLSDVDLVRSYLRDIGRVPLLSHQQEITLGRQVQELMELEALEAELRDQRGGEAVPAAEL 65

Query: 50  ---------------------AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
                                  R+V ++LRLVV +A  Y    + + +++ EG IGL++
Sbjct: 66  ATAAGLSALQLKRKLQAGRRAKERMVAANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVR 125

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
            V+KFDP RG++ +TY+ WWI+  +   I      +++     +      L +LK   + 
Sbjct: 126 GVEKFDPTRGYKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITE-----MLNKLKKGQRE 180

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           ++    +   V  +A  + + E EV  + CR     SL   +   D + ++  + L  D 
Sbjct: 181 LSQELGRTPTVTELAGFVELPEEEVKDLMCRARQPVSLEMKV--GDGDDTELLELLAGDG 238

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSR 266
               ++  E+ E +  +  L   +  L   +RR+   R     E P++L  ++    +SR
Sbjct: 239 ----ELPEEQVEVECLKGDLRDLLEQLPDLQRRVLRMRYGMDGEEPMSLTGIAKSLRMSR 294

Query: 267 ERVRQIEARAFKKVQE 282
           +R R++E    + ++ 
Sbjct: 295 DRTRRLEREGLEMLRR 310


>gi|313678638|ref|YP_004056378.1| RNA polymerase sigma factor [Mycoplasma bovis PG45]
 gi|312950821|gb|ADR25416.1| RNA polymerase sigma factor [Mycoplasma bovis PG45]
          Length = 509

 Score =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 66/284 (23%), Positives = 129/284 (45%), Gaps = 22/284 (7%)

Query: 16  LSRYIHEIRKI-PMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  Y+  I K   +L+ +EE+ LA    + G     A  +L+  +LRLV+  A  Y+  G
Sbjct: 226 VKWYMRWIGKYGKLLQPEEEFELATEMDKGGFRGKRARDKLIKRNLRLVINNAKKYKNRG 285

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L   +++SEGN G+++AV+K++  +GF+ +TY+ WWI+ A+   +      V++     +
Sbjct: 286 LSFIDLISEGNSGIIKAVQKYNVNKGFKFSTYATWWIRQAITRAVADQSRTVRVPVHMVE 345

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL--NVSESEVISMNCRLAGDESLNALI 190
                 + ++    + +   N        IA++   + +  +V  +        SL+  I
Sbjct: 346 -----TINKITKIERELQQENGVDPTDEEIAQRYGNDFTAEKVRHIRKINIDPISLDKQI 400

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-- 248
               +N S + D++  +           EE     N + +    L+  E  +   R    
Sbjct: 401 --GKENDSSFSDFVKDESVVNPVEYASHEELVETLNTILK--DTLDADEYELICKRYGVG 456

Query: 249 ------QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                 +    +LE L+ E  VS+ER+RQIE +  +K++ S ++
Sbjct: 457 FDNNGEKYKVFSLEELALERNVSKERIRQIENKILRKLKSSPER 500


>gi|254255220|ref|ZP_04948536.1| DNA-directed RNA polymerase sigma subunit [Burkholderia dolosa
           AUO158]
 gi|124900957|gb|EAY71707.1| DNA-directed RNA polymerase sigma subunit [Burkholderia dolosa
           AUO158]
          Length = 241

 Score =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 55/237 (23%), Positives = 104/237 (43%), Gaps = 12/237 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   L  ++LRLVV IA  YR  GLP ++++ EGNIGL++A++++D  RGFR +TY+ WW
Sbjct: 4   ARIALFDANLRLVVSIAKRYRDRGLPFADLIQEGNIGLLKAIERYDYRRGFRFSTYATWW 63

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ ++   +      +++ T          L +L    +              +A  +  
Sbjct: 64  IRQSVTHALADLGRTIRVPTH-----TVDALNKLARLAREHRQRAGSAATPAQLAAHIGE 118

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              +V  +   +    S +  ++           ++    D       +  +    R  +
Sbjct: 119 PVDKVRDLLAIVKEPVSADLPVSPDGD-----LTFIDVAPDTATPSPEDAADATQLRRTI 173

Query: 229 TRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             ++  L  RE  + + R     +   +L ++  +  +S ERVRQIEA A  +++ S
Sbjct: 174 AAAIERLPQREAMVLKLRYGLHADEGCSLRDIGRQLNLSAERVRQIEASALARLRAS 230


>gi|54401876|gb|AAV34623.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|54401880|gb|AAV34625.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|54401882|gb|AAV34626.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|54401884|gb|AAV34627.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|54401886|gb|AAV34628.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|54401888|gb|AAV34629.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 238

 Score =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 68/249 (27%), Positives = 122/249 (48%), Gaps = 13/249 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           + EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + +++
Sbjct: 1   LGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDLI 59

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   L
Sbjct: 60  EEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVYL 118

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
           R  +     ++           IA++L+    +V  M        S++  +    + +  
Sbjct: 119 RTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA-- 172

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLEN 257
               L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE+
Sbjct: 173 ---LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLED 229

Query: 258 LSSEFEVSR 266
           +  E  ++R
Sbjct: 230 VGREIGLTR 238


>gi|149197281|ref|ZP_01874333.1| RNA polymerase sigma factor RpoD [Lentisphaera araneosa HTCC2155]
 gi|149139827|gb|EDM28228.1| RNA polymerase sigma factor RpoD [Lentisphaera araneosa HTCC2155]
          Length = 404

 Score =  186 bits (473), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 60/235 (25%), Positives = 113/235 (48%), Gaps = 12/235 (5%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           + +V  +LRLV+ IA  Y        +++ EGNIGL+ AV+K+D   G+  +TY+ WWI+
Sbjct: 170 NAMVEGNLRLVISIARKYSNSQEGFLDLIQEGNIGLVSAVEKYDASFGYTFSTYATWWIR 229

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            A+          +K+        +   + ++    + +     +   +  +++ + +S 
Sbjct: 230 QAVSRARTELVRTMKLP-----ANIMVKVNKIYRTERELFQKFGREATIDEVSEAVELSP 284

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           +++ S+        SL   +  S++++ +  D +  D D        + E+K     L  
Sbjct: 285 AKIRSLKRMCQQPISLQTTV--SEEHTGELGDIVSNDDDVLPDA---EVEQKQLHESLVA 339

Query: 231 SMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            + +LN RE+ I   R         TLEN+++EF +SRER+RQIE  A KK++  
Sbjct: 340 MLDILNEREQEILRMRFGLADGEYHTLENIANEFGISRERIRQIETSALKKLRRP 394


>gi|326801849|ref|YP_004319668.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphingobacterium
           sp. 21]
 gi|326552613|gb|ADZ80998.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Sphingobacterium
           sp. 21]
          Length = 285

 Score =  186 bits (472), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 73/279 (26%), Positives = 137/279 (49%), Gaps = 14/279 (5%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           SI       LS Y++E+ K  ++   EE  LA++ RE GD  A  RL  ++LR V+ +A 
Sbjct: 9   SITNRNNRSLSLYLNEVSKFELISADEEVSLAEKIRE-GDQLALERLTKANLRFVISVAK 67

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y+  GL + ++++EGN GL++A ++FD  +GF+  +Y++WWI+ ++   I      V++
Sbjct: 68  QYQHQGLVLEDLINEGNAGLVKAARRFDETKGFKFISYAVWWIRQSIMSAISIQSRAVRL 127

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
               NQ      LRR +  ++   +       V  +A +L  +   +I+         S+
Sbjct: 128 P--GNQISNLIKLRRSQAEMEQRLERE---PSVEELAVELGTTTDRIIASFTNAERQLSI 182

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           +A    S++   +  D L       +Q LI+          +   +  L+ RER+I    
Sbjct: 183 DAPSVFSEEE--RLLDSLASSDPATDQQLIQDSLFL----RIDLVLKKLSSRERQILTMF 236

Query: 247 RLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               N  P TL+ ++ + +++ ER+RQ++ +A   ++ S
Sbjct: 237 YGLSNSEPQTLDEIAYQLKLTPERIRQLKTKALLHIKNS 275


>gi|225440035|ref|XP_002276710.1| PREDICTED: hypothetical protein [Vitis vinifera]
 gi|297741628|emb|CBI32760.3| unnamed protein product [Vitis vinifera]
          Length = 561

 Score =  186 bits (472), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 59/247 (23%), Positives = 119/247 (48%), Gaps = 12/247 (4%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
           + H    +  +L+ ++LR+VV IA  Y+G GL + +++ EG++GLM +V+KF P  G R 
Sbjct: 314 QLHSGNRSRQKLIYANLRMVVHIAKQYQGRGLNLQDLLQEGSMGLMNSVEKFKPNAGCRF 373

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           A+Y+ WWI+ A+++ I +    +++      + ++  L ++K   +              
Sbjct: 374 ASYAYWWIRQAVRKAIFQHSRTIRLP-----ENMYSLLGKVKEAKRLFIQEGHHDPTKEE 428

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           IA+++ ++  ++  +        S+   + +    +     +     D   ++      +
Sbjct: 429 IAERVGITIEKLQRLLLHTRMPLSMQQPVWADQDTT-----FQEVTADTGIEIPDVSVAK 483

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKK 279
           +  R  +   + VL P+ERRI   R    +  P TL  +   F  S+ERVRQ+E RA  K
Sbjct: 484 QLMRQHVRNLLHVLTPKERRIIRLRFGIGDGIPRTLSEIGLVFGFSKERVRQLEQRALHK 543

Query: 280 VQESIQK 286
           +++ +  
Sbjct: 544 LKQCLSS 550


>gi|295133351|ref|YP_003584027.1| RNA polymerase sigma-70 factor [Zunongwangia profunda SM-A87]
 gi|294981366|gb|ADF51831.1| RNA polymerase sigma-70 factor [Zunongwangia profunda SM-A87]
          Length = 284

 Score =  186 bits (472), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 75/289 (25%), Positives = 142/289 (49%), Gaps = 13/289 (4%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
              +    +  L  Y+ +I  I  +  +EE  L ++ +  GD  A H LVTS+LR VV +
Sbjct: 7   TKQVTNRDDASLDFYLKDIGPIARISSEEEVELTRKIK-AGDKKALHTLVTSNLRFVVSV 65

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y+  GL +S++++EGN+GL++A  +FD  RGF+  +Y++WWI+ AM + I  +  +V
Sbjct: 66  AKQYQFKGLSLSDLIAEGNLGLIKAANRFDETRGFKFISYAVWWIRQAMVQSISENARVV 125

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           ++    N+  L   +R+    LQ +       E+V   +  LN+  +E+       A   
Sbjct: 126 RLP--LNKLTLINKIRKANSALQQLLQREASLEEV---SNFLNLPLTEIEEAGKSNATYL 180

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL+  + S+D +       +    +  +Q L+      +  + + + M++L  RE+ +  
Sbjct: 181 SLDKPL-SNDNDDFTLNQLITSKIEDPDQGLL----NVSTSHEINQLMTILEKREKEVII 235

Query: 245 ARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
                      +L ++S+   ++ ERVRQI+     K++ S +  +  S
Sbjct: 236 LLFGLNGGEAKSLRDISTLLGLTSERVRQIKEMGLIKLRRSPKAAILFS 284


>gi|312282671|dbj|BAJ34201.1| unnamed protein product [Thellungiella halophila]
          Length = 547

 Score =  186 bits (472), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 59/245 (24%), Positives = 124/245 (50%), Gaps = 12/245 (4%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           H   S+  +L+T++LRLVV IA  Y+  GL   +++ EG++GLM++V+KF P+ G R AT
Sbjct: 302 HRGRSSREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFAT 361

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI+ ++++ I ++   +++      + ++  L ++    +    +         +A
Sbjct: 362 YAYWWIRQSIRKSIFQNSRTIRLP-----ENVYMLLGKVSEARKTCIQDGNYRPSKEQLA 416

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
             + VS  ++  +        S+   I S    +     +     D   +       ++ 
Sbjct: 417 SHVGVSTEKLDKLLYNTRTPLSMQQPIWSDQDTT-----FQEVTPDSGIETPSMSVGKQL 471

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            RN +   ++VL+P+E+RI + R   +     +L  +   + +S+ERVRQ+E+RA  +++
Sbjct: 472 MRNHVRNLLNVLSPKEKRIIKLRFGIDGGKQRSLSEIGEIYGLSKERVRQLESRALYRLK 531

Query: 282 ESIQK 286
           +++  
Sbjct: 532 QNMSS 536


>gi|255556952|ref|XP_002519509.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
 gi|223541372|gb|EEF42923.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
          Length = 548

 Score =  186 bits (472), Expect = 4e-45,   Method: Composition-based stats.
 Identities = 57/247 (23%), Positives = 126/247 (51%), Gaps = 12/247 (4%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
           + H    +  +L+ ++LR+VV IA  Y+G GL + +++ EG++GLM++++KF P+ G R 
Sbjct: 301 QLHSGNRSREKLINANLRMVVHIAKQYQGRGLSLQDLLQEGSMGLMKSIEKFKPQVGCRF 360

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           ATY+ WWI+  +++ I +    +++      + ++  L ++    ++             
Sbjct: 361 ATYAYWWIRQTVRKAIFQHSRTIRLP-----ENVYHTLGKVSEAKRSYIMEGNHNPTKEE 415

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           +AK++ ++   +  +        S+   + +  + +     +     D + ++      +
Sbjct: 416 LAKRIGITTVRLERLLYMARMPLSMQQTVWADQETT-----FQEITADIEVEIPELCVAK 470

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKK 279
           +  R  +   +++LNPRER+I   R   E+    +L  + S F +S+ERVRQ+E+RA  K
Sbjct: 471 QLMRKHVLSLLNILNPRERKIIRLRYGIEDGKKKSLSEIGSVFGLSKERVRQLESRALYK 530

Query: 280 VQESIQK 286
           +++ +  
Sbjct: 531 LKQCLAS 537


>gi|170077819|ref|YP_001734457.1| sigma-70 factor [Synechococcus sp. PCC 7002]
 gi|169885488|gb|ACA99201.1| sigma-70 factor [Synechococcus sp. PCC 7002]
          Length = 328

 Score =  186 bits (472), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 64/319 (20%), Positives = 139/319 (43%), Gaps = 53/319 (16%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGDLSA-------- 49
           +    +  Y+ EI ++P+L  +EE V  K+ +             E  D  A        
Sbjct: 15  SSADMVRTYLREIGRVPLLTHEEEIVYGKQVQRLMALQEKRQTLEESLDREATREEWAEA 74

Query: 50  ------------------AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                               +++ ++LRLVV IA  Y+   L   +++ EG++GL + V+
Sbjct: 75  AQLTPKQLQRDLQIGERAKRKMIEANLRLVVAIAKKYQKRNLEFLDLIQEGSLGLERGVE 134

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFDP +G++ +TY+ WWI+ A+   I +    +++     +K     L ++K   + +  
Sbjct: 135 KFDPTKGYKFSTYAYWWIRQAITRAIAQQGRTIRLPIHITEK-----LNKIKKTQRQLAQ 189

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
           +  +   +  IA+ L +  +++           SL+  +   D   ++  D L    +  
Sbjct: 190 DLGRAATIAEIAEALELEPAQIREYFRVSRHPISLD--VRVGDNQDTELMDLLEDSGESP 247

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERV 269
           +  +  +  +++ R+++      L P+++ +   R    +   ++L  +     +SRERV
Sbjct: 248 DNNVTYELLKQDLRDLIAD----LTPQQQEVIILRFGLNDGKELSLAKIGKRMNLSRERV 303

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQ+E +A   ++   + Q+
Sbjct: 304 RQLERQALNHLRRR-RSQI 321


>gi|296535367|ref|ZP_06897567.1| possible DNA-directed RNA polymerase sigma subunit SigA [Roseomonas
            cervicalis ATCC 49957]
 gi|296264309|gb|EFH10734.1| possible DNA-directed RNA polymerase sigma subunit SigA [Roseomonas
            cervicalis ATCC 49957]
          Length = 1063

 Score =  185 bits (471), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 70/236 (29%), Positives = 119/236 (50%), Gaps = 13/236 (5%)

Query: 47   LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + A   +V  +L+ VV +A  Y    +P  ++V EG IGL++A+ +FDP+RGFR  TY+ 
Sbjct: 825  IDARQEIVEGNLKRVVWLARRYARAAVPFLDLVQEGQIGLLRAIDRFDPDRGFRFGTYAT 884

Query: 107  WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            WWI+ +M  Y+      V++     ++      +R    L+A T     P+++ A     
Sbjct: 885  WWIRQSMSRYVQDQGRTVRVPVHMLER--IAKAKRASEALRAKTGVVPTPQELAAAL--- 939

Query: 167  NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
               E++V+S+   LA D      I+  D  S   +D  +      E   +      + R 
Sbjct: 940  ---EADVVSVERALAADL---EGISFDDMGSLPDEDAALVAPLVDEATPLTALLHHDLRR 993

Query: 227  MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            +L  S+  L+ R+ RI + R      NP+TLE +   + V+RER+RQIEA++ K++
Sbjct: 994  LLAASLRRLDARQARIIDLRFGLTDGNPLTLEEVGQFYGVTRERIRQIEAKSLKRL 1049


>gi|332976340|gb|EGK13196.1| DNA-directed RNA polymerase sigma subunit SigG [Desmospora sp.
           8437]
          Length = 259

 Score =  185 bits (471), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 60/261 (22%), Positives = 120/261 (45%), Gaps = 16/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+ +E   L +  +E GD SA  +LV  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLKNEEMRALFRSLQEEGDRSAREKLVNGNLRLVLSVIQRFNNRGENVDDLFQVGC 73

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+A+  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 74  IGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVR 130

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L   T  + +   +  I+++LNVS+ EV+     +    SL   I     +     D 
Sbjct: 131 DSL---TYRHSREPTIQEISEELNVSKEEVVFALDAIQDPVSLFEPIYQDGGDPIYVMDQ 187

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L  D +     + E          L  +M  LN RE+ I   R       T   ++ E  
Sbjct: 188 LADDENKDLHWVEEIA--------LREAMGRLNDREKMILSMRFF--EGKTQMEVAEEIG 237

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A +++ + I
Sbjct: 238 ISQAQVSRLEKAAIQQMNKYI 258


>gi|255532556|ref|YP_003092928.1| sigma-70 family RNA polymerase sigma factor [Pedobacter heparinus
           DSM 2366]
 gi|255345540|gb|ACU04866.1| RNA polymerase sigma factor, sigma-70 family [Pedobacter heparinus
           DSM 2366]
          Length = 289

 Score =  185 bits (471), Expect = 5e-45,   Method: Composition-based stats.
 Identities = 70/284 (24%), Positives = 136/284 (47%), Gaps = 15/284 (5%)

Query: 1   MNRKNMSIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHL 58
           M R  +S  +       +  Y+ EI +I + + +EE+ L    R +GD  A HRL+  +L
Sbjct: 1   MKRFTISPSIAKRDSDVVESYLSEIGRISLTDPEEEFRLVSAIR-NGDQEALHRLIKGNL 59

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           R VV +A  Y+  GL + ++++EGNIGL++A  +FD  RGF+  T+++WW++ A+ + I 
Sbjct: 60  RFVVSVAKKYQDKGLKLGDLINEGNIGLIKAAHRFDATRGFKFITFAVWWVRQAILQAIA 119

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
               L+++            + RL   +  +     +   V  +A     +  +V+    
Sbjct: 120 EQRRLIRLPGNQ-----LLGISRLNQAVLKLEQQLERMPTVEELAVYTGFTVDKVMDYTA 174

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
             A   SL+ +I   +++ S   + +  +   Q                L R++ +L+ R
Sbjct: 175 NAAFTYSLDDVIK--EESGSTLMEVIADEATHQTDHFTLAASLSTD---LNRALDILSKR 229

Query: 239 ERRIFEARRLQEN-PVT-LENLSSEFEVSRERVRQIEARAFKKV 280
           E++I          P T +E++    ++S+ER+RQ++ +A K +
Sbjct: 230 EQKIIILFYGLNGYPQTAIEDMQKILKLSKERIRQLKDKAHKTL 273


>gi|328948870|ref|YP_004366207.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           succinifaciens DSM 2489]
 gi|328449194|gb|AEB14910.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           succinifaciens DSM 2489]
          Length = 272

 Score =  185 bits (471), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 72/271 (26%), Positives = 121/271 (44%), Gaps = 14/271 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++ ++K P+L   EE  LAKR +  GD  A + LV S+LRLVV +A  +      I ++
Sbjct: 9   YLNSLKKYPLLSADEEIALAKRIK-SGDKEAFNLLVNSNLRLVVSVAGRFNKGAFCIMDL 67

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GLM A KKFDP  G R +TY+  WI   + ++I  + S + +            
Sbjct: 68  IQEGNLGLMVAAKKFDPAFGTRFSTYAYRWIVQRIMKFISANSSPILLPVHRETL----- 122

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LRR++         N +   V  +A    +SE  +  +        SL+  +    K  S
Sbjct: 123 LRRIQKFQNIFFQQNGREAAVKELALFAGISEERLNDVLETSYTVASLDTEVADEGKTVS 182

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE---NPVTL 255
                L            E   R++ ++ +   M  L   E+ +   R   +   +  +L
Sbjct: 183 -----LGDIIPDTAFSPEELAIREDSKSCVNFFMDSLTGIEKSVLRHRYNFDYDLHSKSL 237

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             +     +S+E VRQ E RA K ++ +++ 
Sbjct: 238 REVGRIVGLSQEAVRQAELRAKKHLKSAMES 268


>gi|148242708|ref|YP_001227865.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp.
           RCC307]
 gi|147851018|emb|CAK28512.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. RCC307]
          Length = 301

 Score =  185 bits (471), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 70/292 (23%), Positives = 130/292 (44%), Gaps = 29/292 (9%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYRE--------------------HGDLSAAHRLV 54
            LS ++ EI +  +L  ++E  L ++ +                          A ++++
Sbjct: 5   SLSAFLGEIGRHKLLTPEQELTLGRKVQAMVPLQDKPVESLSEDEKRALRLGERAKNQMI 64

Query: 55  TSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114
           T++LRLVV +A  Y+G GL + +++ EG +GL +AV+KFDP RG R +TY+ WWI+  + 
Sbjct: 65  TANLRLVVNLAKRYQGKGLELLDLIQEGTLGLTRAVEKFDPTRGHRFSTYAYWWIRQGLN 124

Query: 115 EYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVI 174
             +      ++I    N+K     LR  K  L   T      E++    K       +++
Sbjct: 125 RALSTQSRTIRIPVNINEK--LTKLRAAKARLFQSTGRQPIAEELADYLKLPLDEVEDLL 182

Query: 175 SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV 234
               R +   SL  ++ S   + S+  D L  +     +     E  +    +L ++   
Sbjct: 183 GCELR-SVTVSLQGVVKSK-SDPSELVDVLPSEEMPPMERAELDERTQTVWKLLDQA--N 238

Query: 235 LNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           L P+ER +   R   +      TL  ++ +   SRE  RQ+  R+ +K++ +
Sbjct: 239 LTPKERTVVMLRFGLDGTNEWRTLAEVARQMSCSREYCRQVVQRSLRKLRRA 290


>gi|228988887|ref|ZP_04148936.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228770801|gb|EEM19317.1| RNA polymerase sigma factor RpoD [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
          Length = 295

 Score =  185 bits (470), Expect = 6e-45,   Method: Composition-based stats.
 Identities = 73/281 (25%), Positives = 138/281 (49%), Gaps = 17/281 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG-LP 74
           + +Y++EI    +L  ++      +Y+E GD+ +   L+ S+LRLVV +A  +  YG   
Sbjct: 11  MGKYLNEICNYDILTDEQSMEHIIKYKEKGDIDSRDLLICSNLRLVVSVAKSFPCYGNCD 70

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + E++ EG IGLM+ ++ +D  +G +L+TY  WWI+  + +Y+  + S V++ TT  +K 
Sbjct: 71  LMEMIQEGTIGLMKGLEDYDYTKGNKLSTYITWWIRQRISKYLSINRSDVRVATTMQKK- 129

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS--MNCRLAGDESLNALINS 192
               +  +K                  +A++L   ES VI   +  R+    S+   + +
Sbjct: 130 ----ITEVKNCYYENMGEKGTNLTTKEVAERLGYKESIVIDALVTDRITNTISIEDDVQN 185

Query: 193 S----DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
                DK  S        +     +V+  +EE+     ++      LNPRE  +   R  
Sbjct: 186 EKTLLDKQQSTLAILANKNAPNPSEVIATEEEKFEFDELM---FVTLNPREESVLRYRFG 242

Query: 249 QEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            ++   +TLE+ +    V+RERV+QIE +A +K+++ +  +
Sbjct: 243 FDDGIELTLEDTARILGVTRERVQQIEKKAIEKMKQRLSSK 283


>gi|6273430|emb|CAB60192.1| putative sigma-like transcription factor [Arabidopsis thaliana]
          Length = 487

 Score =  185 bits (470), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 60/245 (24%), Positives = 123/245 (50%), Gaps = 12/245 (4%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           H   S+  +L+T++LRLVV IA  Y+  GL   +++ EG++GLM++V+KF P+ G R AT
Sbjct: 242 HRGRSSREKLITANLRLVVHIAKQYQNRGLNFQDLLQEGSMGLMKSVEKFKPQSGCRFAT 301

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI+ ++++ I ++   +++      + ++  L ++    +              +A
Sbjct: 302 YAYWWIRQSIRKSIFQNSRTIRLP-----ENVYMLLGKVSEARKTCVQEGNYRPSKEELA 356

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
             + VS  ++  +        S+   I S    +     +     D   +       ++ 
Sbjct: 357 GHVGVSTEKLDKLLYNTRTPLSMQQPIWSDQDTT-----FQEITPDSGIETPTMSVGKQL 411

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            RN +   ++VL+P+ERRI + R   +     +L  +   + +S+ERVRQ+E+RA  +++
Sbjct: 412 MRNHVRNLLNVLSPKERRIIKLRFGIDGGKQRSLSEIGEIYGLSKERVRQLESRALYRLK 471

Query: 282 ESIQK 286
           +++  
Sbjct: 472 QNMNS 476


>gi|296125976|ref|YP_003633228.1| RNA polymerase, sigma 32 subunit, RpoH [Brachyspira murdochii DSM
           12563]
 gi|296017792|gb|ADG71029.1| RNA polymerase, sigma 32 subunit, RpoH [Brachyspira murdochii DSM
           12563]
          Length = 285

 Score =  185 bits (470), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 70/270 (25%), Positives = 132/270 (48%), Gaps = 13/270 (4%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  +S Y  + +K  +L ++EE  L KR +E GD  A  +L+ S+LR V+ IA  Y+  G
Sbjct: 14  QNNISLYFADAKKEKLLTREEEIELTKRLKE-GDAEARSKLIRSNLRFVITIAKQYKNSG 72

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L + +++SEGN+GL+ A  +FDP++G+   +Y+++WI+ ++   I     L+++      
Sbjct: 73  LLLEDLISEGNMGLIIAADRFDPDKGYHFISYAVYWIRQSILRAINEKSRLIRLPLNKA- 131

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                +L  L+  +      +     V  +A  LN   ++++ +        SL      
Sbjct: 132 ----MDLVDLERTVHQYYYKSGYTPDVNELAAILNKDPNDILHIMSMSTEHISLE----- 182

Query: 193 SDKNSSQWQDWLVYD-HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
            + N    +D L+    D   + + E    K     L  ++  L+  E++I  AR   + 
Sbjct: 183 GEYNYDGMKDRLIDTIEDKTSKNVEETAINKELMEELKTAIESLSDIEKQIINARYGIDQ 242

Query: 252 PV-TLENLSSEFEVSRERVRQIEARAFKKV 280
              TL+ +   F  ++ER+RQIE +A +K+
Sbjct: 243 ERKTLKEVGEMFSFTKERIRQIEKKALRKM 272


>gi|15223259|ref|NP_172330.1| SIG2 (RNA POLYMERASE SIGMA SUBUNIT 2); DNA binding / DNA-directed
           RNA polymerase/ sigma factor/ transcription factor
           [Arabidopsis thaliana]
 gi|6664315|gb|AAF22897.1|AC006932_14 T27G7.22 [Arabidopsis thaliana]
 gi|9802550|gb|AAF99752.1|AC003981_2 F22O13.2 [Arabidopsis thaliana]
 gi|2443357|dbj|BAA22427.1| SigB [Arabidopsis thaliana]
 gi|2597831|emb|CAA75584.1| sigma factor [Arabidopsis thaliana]
 gi|2879922|dbj|BAA24825.1| plastid RNA polymerase sigma-subunit [Arabidopsis thaliana]
 gi|5478446|dbj|BAA82449.1| sigma factor SigB [Arabidopsis thaliana]
 gi|133778838|gb|ABO38759.1| At1g08540 [Arabidopsis thaliana]
 gi|332190182|gb|AEE28303.1| RNApolymerase sigma subunit 2 [Arabidopsis thaliana]
          Length = 572

 Score =  185 bits (470), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 62/245 (25%), Positives = 117/245 (47%), Gaps = 12/245 (4%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R R H       +++ S++RLV+ IA  Y+G G+ + ++V EG  GL++  +KFD  +GF
Sbjct: 323 RQRIHHGTLCKDKMIKSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKGF 382

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWIK A+++ +     ++++     +        R+K   + +     K  + 
Sbjct: 383 KFSTYAHWWIKQAVRKSLSDQSRMIRLPFHMVEATY-----RVKEARKQLYSETGKHPKN 437

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IA+   +S   ++++        SL+  I  +     Q         D +     +  
Sbjct: 438 EEIAEATGLSMKRLMAVLLSPKPPRSLDQKIGMN-----QNLKPSEVIADPEAVTSEDIL 492

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAF 277
            ++  R  L + +  L  RE+++   R   E+    TL+ +     VSRERVRQIE+ AF
Sbjct: 493 IKEFMRQDLDKVLDSLGTREKQVIRWRFGMEDGRMKTLQEIGEMMGVSRERVRQIESSAF 552

Query: 278 KKVQE 282
           +K++ 
Sbjct: 553 RKLKN 557


>gi|297843640|ref|XP_002889701.1| hypothetical protein ARALYDRAFT_470915 [Arabidopsis lyrata subsp.
           lyrata]
 gi|297335543|gb|EFH65960.1| hypothetical protein ARALYDRAFT_470915 [Arabidopsis lyrata subsp.
           lyrata]
          Length = 572

 Score =  185 bits (470), Expect = 7e-45,   Method: Composition-based stats.
 Identities = 65/256 (25%), Positives = 123/256 (48%), Gaps = 14/256 (5%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           ++  L KR   HG L    +++ S++RLV+ IA  Y+G G+ + ++V EG  GL++  +K
Sbjct: 318 DQKSLRKRIH-HGTL-CKDKMIKSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEK 375

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +GF+ +TY+ WWIK A+++ +     ++++     +        R+K   + +   
Sbjct: 376 FDATKGFKFSTYAHWWIKQAVRKSLSDQSRMIRLPFHMVEATY-----RVKEARKQLYSE 430

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             K  +   IA+   +S   ++++        SL+  I  +     Q         D + 
Sbjct: 431 TGKHPKNEEIAEATGLSMKRLMAVLLSPKPPRSLDQKIGMN-----QNLKPSEVIADPEA 485

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
               +   ++  R  L + +  L  RE+++   R   E+    TL+ +     VSRERVR
Sbjct: 486 VTSEDILIKEFMRQDLDKVLDSLGTREKQVIRWRFGMEDGRMKTLQEIGEMMGVSRERVR 545

Query: 271 QIEARAFKKVQESIQK 286
           QIE+ AF+K++   + 
Sbjct: 546 QIESSAFRKLKNKKRS 561


>gi|116749951|ref|YP_846638.1| RpoD family RNA polymerase sigma factor [Syntrophobacter
           fumaroxidans MPOB]
 gi|116699015|gb|ABK18203.1| RNA polymerase, sigma 70 subunit, RpoD family [Syntrophobacter
           fumaroxidans MPOB]
          Length = 433

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 61/238 (25%), Positives = 113/238 (47%), Gaps = 13/238 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           SA   +V ++LRLV+ IA  YRG G+   +++ EGN+GL++AV +FD  +G R +TY+ W
Sbjct: 196 SAKQEMVKANLRLVLSIAKRYRGRGMSFDDLIQEGNLGLLKAVGRFDHTKGNRFSTYATW 255

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           W++ ++   I      +++     + +  F           +     +      IA++  
Sbjct: 256 WVRQSIIRGIYDKTRTIRLPVHFIELKNLFF-----KVFYELLKELGREPSPQEIAERAK 310

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +   +V  +    A   SL   I    ++  +  D++    D +    +E+   +    +
Sbjct: 311 LPLDKVQMVLTLAAQPISLETPIG---EDEQRLGDFI---EDERAASPMEECSDRELAEI 364

Query: 228 LTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               +S L PRE +I   R   +     TLE +   F+VS+ER+RQIE +A +K++  
Sbjct: 365 TRSLLSSLQPREEKILRLRFGIDGQPAETLEKIGKTFKVSKERIRQIEKKALRKLRNP 422


>gi|156975281|ref|YP_001446188.1| hypothetical protein VIBHAR_03010 [Vibrio harveyi ATCC BAA-1116]
 gi|156526875|gb|ABU71961.1| hypothetical protein VIBHAR_03010 [Vibrio harveyi ATCC BAA-1116]
          Length = 287

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 83/278 (29%), Positives = 140/278 (50%), Gaps = 19/278 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y ++I K  +L   +E   A+R +  GD  A  R++ S+LRLVV IA  Y+G GL   ++
Sbjct: 21  YFNDIGKYALLSADDEREYARRAK-MGDADARTRMINSNLRLVVNIAKRYKGRGLTFLDL 79

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ--KRLF 136
           +SEGNIGLM+AV+KFDPE+GFR +TY+  WI+ +++  ++     V++    N+  KR  
Sbjct: 80  ISEGNIGLMRAVEKFDPEKGFRFSTYATHWIRQSIERELMNQARTVRLPVHINKELKRYV 139

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
              + L    Q IT  +        IA  L +  S V+          SL++     DK 
Sbjct: 140 KATKELSQKTQTITPRD--------IADHLEIPVSSVLKHLEFDKSTISLDS---YQDKE 188

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVT 254
            ++     +  H  +   L  +E+      ML + +  L P  + I   R   +   P +
Sbjct: 189 EAKPLAETMACHRLRCPELELEEDNAFL--MLLQWIEELEPDLKLILTRRYGLDGNTPTS 246

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
           L+ + +E   SRER+R ++ +  KK+ +++ K + +S 
Sbjct: 247 LDTVGTELGYSRERIRHLQMQGIKKL-QNLAKNIPVSG 283


>gi|225620189|ref|YP_002721446.1| DNA-directed RNA polymerase sigma-70/sigma-32 subunit RpoD
           [Brachyspira hyodysenteriae WA1]
 gi|225215008|gb|ACN83742.1| RpoD, DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Brachyspira hyodysenteriae WA1]
          Length = 287

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 71/282 (25%), Positives = 135/282 (47%), Gaps = 13/282 (4%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M+   +      +  +S Y  + +K  +L ++EE  L KR +E GD  A  +L+ S+LR 
Sbjct: 4   MSESRLRTNTEEQNNISLYFADAKKEKLLTREEEIELTKRLKE-GDAEARSKLIRSNLRF 62

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ IA  Y+  GL + +++SEGN+GL+ A  +FDP++G+   +Y+++WI+ ++   I   
Sbjct: 63  VITIAKQYKNSGLLLEDLISEGNLGLIIAADRFDPDKGYHFISYAVYWIRQSILRAINEK 122

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
             L+++           +L  L+  +      +     V  +A  LN   ++++ +    
Sbjct: 123 SRLIRLPLNKA-----MDLVDLERAVHQYYYKSGYTPDVNELATILNKDPNDILHIMSMS 177

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYD-HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
               SL       + N    +D L+    D   + + E    K     L  ++  L+  E
Sbjct: 178 TEHISLE-----GEYNYDGMKDRLIDTIEDKTSKNVEETAINKELMEELKTAIESLSDIE 232

Query: 240 RRIFEARRLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
           ++I  AR   +    TL+ +   F  ++ER+RQIE +A +K+
Sbjct: 233 KQIINARYGIDQERKTLKEVGEMFSFTKERIRQIEKKALRKM 274


>gi|91200070|emb|CAJ73113.1| similar to transcription initiation factor sigma 70 [Candidatus
           Kuenenia stuttgartiensis]
          Length = 491

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 68/240 (28%), Positives = 115/240 (47%), Gaps = 12/240 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R    +LRLVV IA  YR  G+   +++ EGN GLM+AV K+D   GF+ +TY+ WW
Sbjct: 250 ARKRFSEGNLRLVVSIAKKYRKRGMAFHDLIQEGNTGLMRAVDKYDYRMGFKFSTYATWW 309

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           IK A+          ++I        +   + +     +A   ++ +  Q+ AIA+  N 
Sbjct: 310 IKQAIIRATEEKVRTIRIPVH-----MMDVINKSTYVAKAGQGSSAEKIQLEAIARDTNT 364

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              E+  +    +   SL   I S     + ++D++    D +    I   +R   +  +
Sbjct: 365 PLPEIYRLLQITSQPISLETPIGS--DGETMFEDFI---QDKKIDAPIFLAQRSLLKEQI 419

Query: 229 TRSMSVLNPRERRIFEARRLQENPVT--LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + +  L+ RER I + R    +  T  LE +   F ++RER+RQIEA A +K+Q  ++ 
Sbjct: 420 QKVLDTLSYREREIIKLRFGISDGYTHSLEEIGKRFNITRERIRQIEAIALRKLQHPVRS 479



 Score = 39.0 bits (90), Expect = 0.84,   Method: Composition-based stats.
 Identities = 12/29 (41%), Positives = 18/29 (62%)

Query: 14 IGLSRYIHEIRKIPMLEKQEEYVLAKRYR 42
            +  Y++E+ KIP+L   EE  LAK+ R
Sbjct: 39 DSVRLYLNEMAKIPLLTPAEEIYLAKKIR 67


>gi|261416342|ref|YP_003250025.1| RNA polymerase, sigma 32 subunit, RpoH [Fibrobacter succinogenes
           subsp. succinogenes S85]
 gi|261372798|gb|ACX75543.1| RNA polymerase, sigma 32 subunit, RpoH [Fibrobacter succinogenes
           subsp. succinogenes S85]
 gi|302326200|gb|ADL25401.1| RNA polymerase sigma-70 factor [Fibrobacter succinogenes subsp.
           succinogenes S85]
          Length = 282

 Score =  185 bits (469), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 73/280 (26%), Positives = 143/280 (51%), Gaps = 16/280 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR----EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           Y  ++ + P L  QEE  L K  +    E    SA  RL+  +LR VV +A  Y+G GL 
Sbjct: 9   YFRDLNRYPTLTPQEESALLKIIKNGETEEIRKSALQRLIRGNLRFVVSVARKYQGRGLS 68

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++++EGN+GL +A K+FD ++  +  +Y++WWI+ ++Q+ +      V+I        
Sbjct: 69  LLDLINEGNLGLFKAAKRFDMDKDVKFISYAVWWIRQSIQKALFEQVGAVRIP------- 121

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
               L  +    +A+  N    ++ +++ ++    E +++ +  ++  D SL+A I    
Sbjct: 122 -PNKLALVNRFKRALMQNGGDYDKTISM-EEFAPYERDIVEVMEKIV-DISLDAPIGDDA 178

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NP 252
             SS      + D  G +    E  ER+ R+ ++  ++S L  RE  I       +    
Sbjct: 179 GVSSADSVSTLMDVLGSDGNQDEDMEREERKKLIQETLSSLPQREEEILRMFYGLDTVED 238

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
            TL+++  + ++SRERVRQI+ +  +++Q+S + + +L+ 
Sbjct: 239 TTLKDIGEDLKLSRERVRQIKNKTLRRLQKSKEHKEKLAD 278


>gi|218848158|ref|YP_002454701.1| RNA polymerase sigma factor, sigma-70 family [Bacillus cereus
           G9842]
 gi|218546289|gb|ACK98682.1| RNA polymerase sigma factor, sigma-70 family [Bacillus cereus
           G9842]
          Length = 295

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 72/281 (25%), Positives = 139/281 (49%), Gaps = 17/281 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG-LP 74
           + +Y++EI    +L  ++      +Y+E GD+ +   L+ S+LRLVV +A  +  YG   
Sbjct: 11  IGKYLNEICNYDILTDEQSMEHIIKYKEKGDIDSRELLICSNLRLVVSVAKSFPCYGNCD 70

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + E++ EG IGLM+ ++ +D  +G +L+TY  WWI+  + +Y+  + S V++ TT  +K 
Sbjct: 71  LMEMIQEGTIGLMKGLEDYDYTKGNKLSTYITWWIRQRISKYLSINRSDVRVATTMQKK- 129

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS--MNCRLAGDESLNALINS 192
               +  +K                + +A++L   ES VI   +  R+    S+   + +
Sbjct: 130 ----ITEVKNCYYENMGEKGTNLTTMEVAERLGYKESIVIDALVTDRITNTISIEDDVQN 185

Query: 193 S----DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
                D+  S        +     +V+  +EE+     ++      LNPRE  +   R  
Sbjct: 186 EKTLLDRQQSTLAILANKNAPNPSEVMATEEEKFEFDELM---FVTLNPREESVLRYRFG 242

Query: 249 QEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            ++   +TLE+ +    V+RERV+QIE +A +K+++ +  +
Sbjct: 243 FDDGIELTLEDTARILGVTRERVQQIEKKAIEKMKQRLSSK 283


>gi|260220134|emb|CBA27368.1| RNA polymerase sigma-32 factor [Curvibacter putative symbiont of
           Hydra magnipapillata]
          Length = 354

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 88/216 (40%), Positives = 128/216 (59%), Gaps = 8/216 (3%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +V     L  YI    ++PML  +EE   A++++   DL AA +LV SHLRLVV +A  Y
Sbjct: 29  LVPPLGNLDAYISAANRLPMLTLEEEQEFARKFKNENDLEAAGKLVLSHLRLVVSVARQY 88

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            GYGLP  +++ EGN+GLM+AVK+FDPE+G RL +Y++ WIKA + EYIL++W +VK+ T
Sbjct: 89  LGYGLPHGDLIQEGNVGLMKAVKRFDPEQGVRLVSYALHWIKAEIHEYILKNWRMVKVAT 148

Query: 129 TANQKRLFFNLRRLKGHLQAI--------TDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           T  Q++LFFNLR +K   +            + L  EQV  +A++LNV   EV+ M  RL
Sbjct: 149 TKAQRKLFFNLRSMKQRFKGEDAAADLDTHRDTLNSEQVNTMARELNVKPEEVLEMEARL 208

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           AG + L     S D   +      + D + +   +I
Sbjct: 209 AGGDVLLDPSPSDDGEDAFGPIAYLTDTNHEPVAMI 244


>gi|254430393|ref|ZP_05044096.1| possible type II alternative RNA polymerase sigma factor [Cyanobium
           sp. PCC 7001]
 gi|197624846|gb|EDY37405.1| possible type II alternative RNA polymerase sigma factor [Cyanobium
           sp. PCC 7001]
          Length = 302

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 74/303 (24%), Positives = 135/303 (44%), Gaps = 45/303 (14%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAK----------RYREHGD------------------L 47
           +S Y+ EI +  +L  ++E  L +          R RE G                    
Sbjct: 1   MSAYLGEIGRHQLLTPEQELTLGRKVQAMAVLQERCREAGGQGPACEYDDREKRVLRLGE 60

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A ++++T++LRLVV +A  Y+  GL + +++ EG +GL +AV+K+DP RG R +TY+ W
Sbjct: 61  RAKNQMITANLRLVVNLAKRYQNKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSTYAYW 120

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+  +   +      ++I    N+K     L RL+        ++       A+A ++ 
Sbjct: 121 WIRQGLNRALSTQSRTIRIPVNVNEK-----LTRLRAAKARYLQSHGVSPSPKALAGEMQ 175

Query: 168 VSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           +  +EV  +      +   SL  ++ S    S      LV      E   +E+ E   R 
Sbjct: 176 LPLAEVEELLGCELRSITVSLQGVVKSKADPS-----ELVDVLPSPELAPMERAELAERS 230

Query: 226 NMLTRSMSV--LNPRERRIFEARRLQENPV---TLENLSSEFEVSRERVRQIEARAFKKV 280
             + + +    L P+ER +   R   +      TL  ++ + + SRE  RQ+  RA +K+
Sbjct: 231 ASVWKLLESSNLTPKERTVVMLRFGLDGSHEWRTLAEVARQLDCSREYCRQVVQRALRKL 290

Query: 281 QES 283
           +++
Sbjct: 291 RKT 293


>gi|269126860|ref|YP_003300230.1| RpoD subfamily RNA polymerase sigma-70 subunit [Thermomonospora
           curvata DSM 43183]
 gi|268311818|gb|ACY98192.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermomonospora
           curvata DSM 43183]
          Length = 360

 Score =  184 bits (468), Expect = 1e-44,   Method: Composition-based stats.
 Identities = 75/304 (24%), Positives = 132/304 (43%), Gaps = 38/304 (12%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR-----YREH----------------- 44
           S+    +  +  Y+  I +  +L+ QEE  LAK      Y EH                 
Sbjct: 10  SVETQDKDLVGAYLDRIGRTHLLDAQEEVDLAKAIEGGLYAEHLLEEDRVPPGVTRQELE 69

Query: 45  ----GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
                 + A  R V ++LRLVV IA  Y    LP+ +++ EGN+GLM+AV+KFD  RGF+
Sbjct: 70  ELVAAGVRAKQRFVEANLRLVVSIARKYPTDALPLIDLIQEGNLGLMRAVEKFDYRRGFK 129

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ ++   +  +   +++     +      L RL+   + +     +     
Sbjct: 130 FSTYATWWIRQSIGRGLSHTARTIRLPVHVEE-----ELSRLRRAERQLGRELGREPTRE 184

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+ L  +   V  +        SL+A +   D   +   D L    D +      +  
Sbjct: 185 ELAEALGAAVDHVDELLRWRRDPASLDAAV--DDAGETPMGDLL---EDPEGVSPEAEVL 239

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFK 278
             +    L R +  L  RE  I  AR   E+  P++   + + + +S  RVRQI  R+ +
Sbjct: 240 ALDDIAGLARLLDRLPERESAILRARFGIEDGQPLSYAQIGARYGLSHNRVRQITDRSLR 299

Query: 279 KVQE 282
           ++++
Sbjct: 300 RLRQ 303


>gi|2353173|gb|AAB69385.1| sigma factor 2 [Arabidopsis thaliana]
          Length = 574

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 62/245 (25%), Positives = 117/245 (47%), Gaps = 12/245 (4%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R R H       +++ S++RLV+ IA  Y+G G+ + ++V EG  GL++  +KFD  +GF
Sbjct: 325 RQRIHHGTLCKDKMIKSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEKFDATKGF 384

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWIK A+++ +     ++++     +        R+K   + +     K  + 
Sbjct: 385 KFSTYAHWWIKQAVRKSLSDQSRMIRLPFHMVEATY-----RVKEARKQLYSETGKHPKN 439

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IA+   +S   ++++        SL+  I  +     Q         D +     +  
Sbjct: 440 EEIAEATGLSMKRLMAVLLSPKPPRSLDRKIGMN-----QNLKPSEVIADPEAVTSEDIL 494

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAF 277
            ++  R  L + +  L  RE+++   R   E+    TL+ +     VSRERVRQIE+ AF
Sbjct: 495 IKEFMRQDLDKVLDSLGTREKQVIRWRFGMEDGRMKTLQEIGEMMGVSRERVRQIESSAF 554

Query: 278 KKVQE 282
           +K++ 
Sbjct: 555 RKLKN 559


>gi|167916992|ref|ZP_02504083.1| RNA polymerase sigma factor [Burkholderia pseudomallei BCC215]
          Length = 482

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 61/266 (22%), Positives = 127/266 (47%), Gaps = 16/266 (6%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDL---SAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
             +R++P    ++    A+R    G+    +A  R+  ++LRLV+ IA  Y   GL +++
Sbjct: 212 RAMRRLP-TSPEKSDAGAQRAFADGEARISAATARMAEANLRLVLSIARKYASRGLDLAD 270

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGN+GL++A++KF+  RGF+ +TY+ WWI+ A+   I      +++           
Sbjct: 271 LLQEGNLGLLRAIEKFEHRRGFKFSTYATWWIRQAISRAIADRARTIRVPVHV-----GD 325

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
             RR++     I   +     +  +++   +    + ++        SLNA +   D + 
Sbjct: 326 EARRVRKAADRIERRSGVSASLAELSEATGLPAERLRAVLTLPREPRSLNAPL--GDDDQ 383

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTL 255
           +++ D +    D     L +        +++T  +  ++ +E  I   R     + P + 
Sbjct: 384 AEFGDIV---EDTSTPSLFDALAHGQMCDVVTSLLKTMSAQEADILRRRFGIGGDEPWSY 440

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           E +++   VSRE+VR+IE RA + ++
Sbjct: 441 EQIAARAGVSREQVRRIEKRALQTLR 466


>gi|54401878|gb|AAV34624.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 238

 Score =  184 bits (467), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 67/249 (26%), Positives = 122/249 (48%), Gaps = 13/249 (5%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           + EI   P+L  +E+   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + +++
Sbjct: 1   LGEIGYSPLLTAEEKVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDLI 59

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   L
Sbjct: 60  EEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVYL 118

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
           R  +     ++           IA++L+    +V  M        S++  +    + +  
Sbjct: 119 RTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA-- 172

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLEN 257
               L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE+
Sbjct: 173 ---LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLED 229

Query: 258 LSSEFEVSR 266
           +  E  ++R
Sbjct: 230 VGREIGLTR 238


>gi|7363218|emb|CAB83106.1| sigma factor 2 [Sinapis alba]
          Length = 575

 Score =  183 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 59/245 (24%), Positives = 115/245 (46%), Gaps = 12/245 (4%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R R         R++ S++RLV+ IA  Y+G G+   ++V EG  GL++  +KFD  +GF
Sbjct: 323 RKRITHGTQCKDRMIKSNIRLVISIAKNYQGAGMDFQDLVQEGCRGLVRGAEKFDATKGF 382

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWIK A+++ +     ++++     +        R+K   + +     K  + 
Sbjct: 383 KFSTYAHWWIKQAVRKSLSDQSRMIRLPFHMVEATY-----RVKEARKQLYSETGKQPKN 437

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +A+   +S   ++++        SL+  I  +               D + +   +  
Sbjct: 438 EEVAEATGLSMKRLMAVLLSPKPPRSLDQKIGIN-----LNLKPSEVIADPEAETSEDIL 492

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAF 277
            ++  R  L + +  L+ RE+++   R   E+    TL+ +     VSRERVRQI+  AF
Sbjct: 493 MKQFMRQDLDKVLDSLSTREKQVIRWRFGMEDGRMKTLQEIGETMGVSRERVRQIDTSAF 552

Query: 278 KKVQE 282
           +K++ 
Sbjct: 553 RKLKN 557


>gi|255565968|ref|XP_002523972.1| RNA polymerase sigma factor rpoD1, putative [Ricinus communis]
 gi|223536699|gb|EEF38340.1| RNA polymerase sigma factor rpoD1, putative [Ricinus communis]
          Length = 569

 Score =  183 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 63/257 (24%), Positives = 124/257 (48%), Gaps = 14/257 (5%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           ++  L KR   HG +    +++ S++RLV+ IA  Y+G G+ + ++V EG  GL++  +K
Sbjct: 317 DQRTLRKRI-NHGTI-CKDKMIKSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGAEK 374

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +GF+ +TY+ WWIK A+++ +      +++     +        R+K   + +   
Sbjct: 375 FDASKGFKFSTYAHWWIKQAVRKSLSDQSRTIRLPFHMVEATY-----RVKEARKQLYSE 429

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           N +      +A+   +S   + ++        SL+  I  +               D + 
Sbjct: 430 NGRHPDDEEVAEAAGLSMKRLSAVLLTPKAPRSLDQKIGMNMDLKPSEVIA-----DPEA 484

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
           +   E   ++  +  L + ++ LNPRE ++   R   E+    TL+ +     VSRER+R
Sbjct: 485 ETAEELLMKQFMKQDLEKVLNTLNPRETQVVRWRFGLEDGRMKTLQEIGEIMGVSRERIR 544

Query: 271 QIEARAFKKVQESIQKQ 287
           QIE+ AF+K++   + +
Sbjct: 545 QIESSAFRKLKNKKRTK 561


>gi|86605925|ref|YP_474688.1| RNA polymerase sigma factor [Synechococcus sp. JA-3-3Ab]
 gi|86554467|gb|ABC99425.1| RNA polymerase sigma factor [Synechococcus sp. JA-3-3Ab]
          Length = 318

 Score =  183 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 70/295 (23%), Positives = 131/295 (44%), Gaps = 45/295 (15%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE----------------------------- 43
           +  + R++  I +  +L  +EE  LA + +                              
Sbjct: 8   QDAVGRFLKIIGRYSLLTAEEELHLAHQVQRMMALLEQRRQHESLEDWSRRLGIPLEELQ 67

Query: 44  ---HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
                  +A  R+V  +LRLVV IA  YR  GLP  +++ EG IGL +AV+KFDP RG++
Sbjct: 68  QILRQGEAAKKRMVECNLRLVVSIAKRYRNRGLPFLDLIQEGTIGLTRAVEKFDPTRGYK 127

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ ++   I     L+++        ++  + ++K   + ++          
Sbjct: 128 FSTYATWWIRQSVNRGIQNKGRLIRLPAH-----MYEKVSQVKRRYRELSAEKGSRPAAE 182

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +   L++ ++    +   +A   SLN  +   D++ ++ Q ++  + +      IE   
Sbjct: 183 EVFDSLDIGDNYRELITRHMAEIRSLN--VGVGDEDGTELQHFIPDEDND----PIEHLN 236

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIE 273
           R      +   +S L+ RE+++  AR   +    +TL  +     +SRERVRQIE
Sbjct: 237 RVAHCEEVRALVSQLSEREQQVIVARYGLDGSKGLTLREIGEHIGLSRERVRQIE 291


>gi|168036108|ref|XP_001770550.1| plastid sigma factor SIG1 [Physcomitrella patens subsp. patens]
 gi|14669828|dbj|BAB62006.1| PpSIG1 [Physcomitrella patens]
 gi|14669830|dbj|BAB62007.1| PpSIG1 [Physcomitrella patens]
 gi|162678258|gb|EDQ64719.1| plastid sigma factor SIG1 [Physcomitrella patens subsp. patens]
          Length = 677

 Score =  183 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 86/321 (26%), Positives = 145/321 (45%), Gaps = 53/321 (16%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYR------------------------------ 42
           +  L+ Y+ EI KI +L KQEE  L+K+ R                              
Sbjct: 354 QDYLTTYLREITKINLLTKQEEVFLSKKLRIGLNLLEERKKLAAELGYVPSNEEWAPHMN 413

Query: 43  -EHGD--------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
              GD          A  ++V ++LRLVV +A  Y  +GL +++++ EG+IGL++ V+KF
Sbjct: 414 LSVGDLVRKLGEAEWARDKMVMANLRLVVSVAKQYHSFGLEMADLIQEGSIGLLRGVEKF 473

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D  RG++L+TY  WWI+  +   I      V++    +       +R+ K  L +     
Sbjct: 474 DHTRGYKLSTYVHWWIRQGVTRAIADHSRTVRLPVHVHD--TLGRIRKAKSTLLS----E 527

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI--NSSDKNSSQWQDWLVYDHDGQ 211
                V  I++  N++ +++ +         SL+  I  N+      +    LV D D  
Sbjct: 528 GCTASVQEISEATNLTGTKIKNTLQVTKKLVSLDKEIGRNTLQSGDGETLHSLVADRD-I 586

Query: 212 EQVLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARRL----QENPVTLENLSSEFEVSR 266
           E       ER   ++ + + + S L PRER I            + ++LE++S  + VSR
Sbjct: 587 ENQPWTIVERMLMKDDVDKLLTSQLGPRERDIVRLHYGVGREDGSVMSLESISYRYGVSR 646

Query: 267 ERVRQIEARAFKKVQESIQKQ 287
           ERVRQ+E  A +K+Q   ++Q
Sbjct: 647 ERVRQLETAAMRKLQIKSREQ 667


>gi|161899381|ref|XP_001712917.1| sigma 2 transcription factor [Bigelowiella natans]
 gi|75756411|gb|ABA27305.1| sigma 2 transcription factor [Bigelowiella natans]
          Length = 389

 Score =  183 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 55/234 (23%), Positives = 109/234 (46%), Gaps = 10/234 (4%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+   L+L++ IA  Y G GL   ++++EG +GLM+ ++K+D  +G + +TY+ WWI
Sbjct: 151 KEILIKRSLKLIISIAKRYNGCGLSFEDLIAEGILGLMKGIRKYDFSKGHKFSTYAHWWI 210

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + ++   I     ++++      K +   + ++K             E    I+  + + 
Sbjct: 211 RQSISRSIDDQSRIIRLPVYV--KEILSKINKIKNKFYEDKKRYPTEE---EISLLIGIP 265

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             ++  +        SL++LI +   +S+   D +        +V       K+ +  L 
Sbjct: 266 LKKLRKLLLSCNDLISLDSLIENDSNDSNMLNDSIEDSKVINSEVY---AIEKSLKQDLN 322

Query: 230 RSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +++  L+ RE  +   R   ++    TLE +     V+RER RQIE +A KK+Q
Sbjct: 323 KALLTLSDRESAVIRLRYGLDDGNERTLEEIGEYLNVTRERARQIEIKALKKLQ 376


>gi|224144900|ref|XP_002325455.1| predicted protein [Populus trichocarpa]
 gi|222862330|gb|EEE99836.1| predicted protein [Populus trichocarpa]
          Length = 564

 Score =  183 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 56/236 (23%), Positives = 111/236 (47%), Gaps = 12/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
              +++ S++RLV+ IA  Y+G G+ + ++V EG  GL++ V+KFD  +GF+ +TY+ WW
Sbjct: 326 CKDKMIKSNIRLVISIAKNYQGAGMNLQDLVQEGCRGLVRGVEKFDASKGFKFSTYAHWW 385

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A++  +      +++        +     R+K   +     N +      +A+   +
Sbjct: 386 IRQAVRRSLSDQSRTIRLPFH-----MVDATYRVKEARKQFYSENGRHPDDKEVAEATGL 440

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S   + ++        SL+  +  +               D + +   +   ++  +  L
Sbjct: 441 SMKRLSAVLLTPKAPRSLDQKMGFNMD-----LKLSEVTADPEAETAEDLLMKEFMKKDL 495

Query: 229 TRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQE 282
            R +  L+PRE ++   R   E+    TL+ +     VSRER+RQIE  AF+K++ 
Sbjct: 496 ERVLESLSPRENQVIRWRFGMEDGRMKTLQEIGELMGVSRERIRQIELSAFRKLKN 551


>gi|332982148|ref|YP_004463589.1| RNA polymerase sigma subunit RpsG/SigG [Mahella australiensis 50-1
           BON]
 gi|332699826|gb|AEE96767.1| RNA polymerase, sigma subunit, RpsG/SigG [Mahella australiensis
           50-1 BON]
          Length = 257

 Score =  183 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 57/261 (21%), Positives = 112/261 (42%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L  ++   L KR +E GD +A    +  +LRLV+ I   +   G  + ++   G 
Sbjct: 14  SKLPVLTDKQMKDLLKRIKE-GDKAAREEFIRGNLRLVLSIIQRFNNRGEHVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD  +  + +TY++  I   ++ Y+  + S +++      + L     +  
Sbjct: 73  IGLIKAIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVS-----RSLRDTAYKAL 126

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
              + +   N K   V  IAK + +   EV+     +    SL   +     ++    D 
Sbjct: 127 QVREQLVAQNGKEPTVEEIAKAMELPAEEVVFAMDAIQDPISLFEPVYHDGGDAIYVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  D +  +  L            L  +M  L+ RE+ I   R  Q    T   ++ E  
Sbjct: 187 VSDDKNQDDNWLETIA--------LKEAMQKLSEREKTILAMRFFQG--RTQMEVAEEIG 236

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A   +++ I
Sbjct: 237 ISQAQVSRLEKSALSHMRKYI 257


>gi|126453822|ref|YP_001064420.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1106a]
 gi|167736534|ref|ZP_02409308.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 14]
 gi|217424965|ref|ZP_03456461.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 576]
 gi|242317344|ref|ZP_04816360.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1106b]
 gi|254188239|ref|ZP_04894751.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei Pasteur
           52237]
 gi|254295684|ref|ZP_04963141.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 406e]
 gi|126227464|gb|ABN91004.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1106a]
 gi|157805995|gb|EDO83165.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 406e]
 gi|157935919|gb|EDO91589.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei Pasteur
           52237]
 gi|217391985|gb|EEC32011.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 576]
 gi|242140583|gb|EES26985.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1106b]
          Length = 482

 Score =  183 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 61/266 (22%), Positives = 127/266 (47%), Gaps = 16/266 (6%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDL---SAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
             +R++P    ++    A+R    G+    +A  R+  ++LRLV+ IA  Y   GL +++
Sbjct: 212 RAMRRLP-TSPEKSDAGAQRAFADGEARISAATARMAEANLRLVLSIARKYASRGLDLAD 270

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGN+GL++A++KF+  RGF+ +TY+ WWI+ A+   I      +++           
Sbjct: 271 LLQEGNLGLLRAIEKFEHRRGFKFSTYATWWIRQAISRAIADRARTIRVPVHV-----GD 325

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
             RR++     I   +     +  +++   +    + ++        SLNA +   D + 
Sbjct: 326 EARRVRKAADRIERRSGVSASLAELSEATGLPAERLRAVLTLPREPRSLNAPL--GDDDQ 383

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTL 255
           +++ D +    D     L +        +++T  +  ++ +E  I   R     + P + 
Sbjct: 384 AEFGDIV---EDTSTPSLFDALAHGQMCDVVTSLLKTMSAQEADILRRRFGIGGDEPWSY 440

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           E +++   VSRE+VR+IE RA + ++
Sbjct: 441 EQIAARAGVSREQVRRIEKRALQTLR 466


>gi|262197687|ref|YP_003268896.1| RNA polymerase, sigma 32 subunit, RpoH [Haliangium ochraceum DSM
           14365]
 gi|262081034|gb|ACY17003.1| RNA polymerase, sigma 32 subunit, RpoH [Haliangium ochraceum DSM
           14365]
          Length = 465

 Score =  183 bits (466), Expect = 2e-44,   Method: Composition-based stats.
 Identities = 62/254 (24%), Positives = 128/254 (50%), Gaps = 11/254 (4%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R  EH   +A +  V ++LRLVV IA  +    + +++++ EGN+GL++AV+++D  RGF
Sbjct: 220 RAAEHAARNARNEFVKANLRLVVSIARRFNHGRMSLADLIQEGNLGLIKAVERYDYRRGF 279

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           R +TY+ WWI+ A+   +      V++        +     RL      +T+   +    
Sbjct: 280 RFSTYASWWIRHAIGRALADKGREVRLPVH-----MLDAHHRLLKAQHQLTNTLGRQPTS 334

Query: 160 VAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
             +++  N+S  ++  M   L     SL+  +N  D  S      ++ D  G+E   +  
Sbjct: 335 EELSEAANLSVEKIEKMRTHLLDQALSLDRPMNDEDGRSVA---EVLQDPHGEEHSALNV 391

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARA 276
             ++   + + +++  L P E  I   R   +N   +TL+ +  ++ +SRER+RQ++ +A
Sbjct: 392 LAQRTMSDEVRKTLQTLRPIEADILRRRFGLDNDEELTLKQIGEQYNLSRERIRQLQEQA 451

Query: 277 FKKVQESIQKQVEL 290
             K++ +++++  +
Sbjct: 452 LTKMRVALRRKAMM 465


>gi|134284106|ref|ZP_01770800.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 305]
 gi|167900733|ref|ZP_02487938.1| RNA polymerase sigma factor [Burkholderia pseudomallei NCTC 13177]
 gi|167908960|ref|ZP_02496051.1| RNA polymerase sigma factor [Burkholderia pseudomallei 112]
 gi|226194652|ref|ZP_03790247.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei
           Pakistan 9]
 gi|134244558|gb|EBA44662.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 305]
 gi|225933353|gb|EEH29345.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei
           Pakistan 9]
          Length = 482

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 61/266 (22%), Positives = 127/266 (47%), Gaps = 16/266 (6%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDL---SAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
             +R++P    ++    A+R    G+    +A  R+  ++LRLV+ IA  Y   GL +++
Sbjct: 212 RAMRRLP-TSPEKSDAGAQRAFADGEARISAATARMAEANLRLVLSIARKYASRGLDLAD 270

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGN+GL++A++KF+  RGF+ +TY+ WWI+ A+   I      +++           
Sbjct: 271 LLQEGNLGLLRAIEKFEHRRGFKFSTYATWWIRQAISRAIADRARTIRVPVHV-----GD 325

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
             RR++     I   +     +  +++   +    + ++        SLNA +   D + 
Sbjct: 326 EARRVRKAADRIERRSGVSASLAELSEATGLPAERLRAVLTLPREPRSLNAPL--GDDDQ 383

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTL 255
           +++ D +    D     L +        +++T  +  ++ +E  I   R     + P + 
Sbjct: 384 AEFGDIV---EDTSTPSLFDALAHGQMCDVVTSLLKTMSAQEADILRRRFGIGGDEPWSY 440

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           E +++   VSRE+VR+IE RA + ++
Sbjct: 441 EQIAARAGVSREQVRRIEKRALQTLR 466


>gi|14530750|emb|CAC42416.1| RpoH protein [Ralstonia metallidurans CH34]
          Length = 317

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 92/249 (36%), Positives = 137/249 (55%), Gaps = 9/249 (3%)

Query: 6   MSIIVNGEIG-LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
            ++   G +G L  YI  + +IPML  +EE  LA+  R++  + AA R+V SHLRLVV I
Sbjct: 47  FALTFPGTLGNLDSYIQAVHRIPMLTPEEELSLARDLRDNDSVDAARRMVMSHLRLVVSI 106

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y GYGLP ++++ EGNIGLM+AVK+FDPE+            +  + EY+L++W +V
Sbjct: 107 ARQYLGYGLPHADLIQEGNIGLMKAVKRFDPEQACAWCRTRCTGSRPEIHEYVLKNWRMV 166

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGD 183
           K+ TT  Q++LFFNLR  K        +   PEQ+ A+A++LNV   EV+ M  R+  GD
Sbjct: 167 KVATTKAQRKLFFNLRSHKQ-----GSHTFTPEQIEAVARELNVKPEEVMEMETRMSGGD 221

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            +L   I   ++         + D+  +   ++E + R +      R      P +RRI 
Sbjct: 222 MALEGQIEDGEEE--FAPIAYLADNHNEPTQVLEAKRRPSAGRGPGRGADEAGPAQRRII 279

Query: 244 EARRLQENP 252
           EAR L  N 
Sbjct: 280 EARWLDVND 288


>gi|225175855|ref|ZP_03729848.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Dethiobacter
           alkaliphilus AHT 1]
 gi|225168779|gb|EEG77580.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Dethiobacter
           alkaliphilus AHT 1]
          Length = 268

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 59/263 (22%), Positives = 120/263 (45%), Gaps = 17/263 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+      L K+ +  GD  A   L+  +LRLV+ +   ++  G  + ++   G I
Sbjct: 15  KLPVLKSARMKELFKKMQ-SGDEHARQELINGNLRLVLSVLQRFKNRGENLDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+AV  F  +     +TY++  I   ++ Y+  +   V++  +           + + 
Sbjct: 74  GLMKAVDNFSLDHNVHFSTYAVPMIIGEIKRYLRDNN-AVRVSRSLKMLAH-----KAQQ 127

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + +T   L+   +  IA  L+++  EV+     +    SL+  +   D     +   L
Sbjct: 128 SREELTRKLLREPTLKEIAADLDITPEEVVFAYQAINDPLSLHDPVFQ-DTTDPVFVMDL 186

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           V D     ++ +E          L ++M +L+ RERRI E+R       T   +++E  +
Sbjct: 187 VSDQSSSAEIWVEDIT-------LRQAMEILSERERRILESRFF--EGRTQTEIANEIGI 237

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           S+ +V +IE  A ++V+  + ++
Sbjct: 238 SQAQVSRIEKSALRQVRHHLAEE 260


>gi|53717743|ref|YP_106729.1| RNA polymerase sigma factor [Burkholderia pseudomallei K96243]
 gi|52208157|emb|CAH34087.1| RNA polymerase sigma factor [Burkholderia pseudomallei K96243]
          Length = 482

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 61/266 (22%), Positives = 127/266 (47%), Gaps = 16/266 (6%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDL---SAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
             +R++P    ++    A+R    G+    +A  R+  ++LRLV+ IA  Y   GL +++
Sbjct: 212 RAMRRLP-TSPEKSDAGAQRAFADGEARISAATARMAEANLRLVLSIARKYASRGLDLAD 270

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGN+GL++A++KF+  RGF+ +TY+ WWI+ A+   I      +++           
Sbjct: 271 LLQEGNLGLLRAIEKFEHRRGFKFSTYATWWIRQAISRAIADRARTIRVPVHV-----GD 325

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
             RR++     I   +     +  +++   +    + ++        SLNA +   D + 
Sbjct: 326 EARRVRKAADRIERRSGVNASLAELSEATGLPAERLRAVLTLPREPRSLNAPL--GDDDQ 383

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTL 255
           +++ D +    D     L +        +++T  +  ++ +E  I   R     + P + 
Sbjct: 384 AEFGDIV---EDTSTPSLFDALAHGQMCDVVTSLLKTMSAQEADILRRRFGIGGDEPWSY 440

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           E +++   VSRE+VR+IE RA + ++
Sbjct: 441 EQIAARAGVSREQVRRIEKRALQTLR 466


>gi|312111757|ref|YP_003990073.1| RNA polymerase, sigma 28 subunit, SigG [Geobacillus sp. Y4.1MC1]
 gi|311216858|gb|ADP75462.1| RNA polymerase, sigma 28 subunit, SigG [Geobacillus sp. Y4.1MC1]
          Length = 271

 Score =  183 bits (465), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 60/262 (22%), Positives = 118/262 (45%), Gaps = 17/262 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+ +E   L KR  E GDL A  +LV  +LRLV+ +   +   G  + ++   G 
Sbjct: 26  SKLPVLKNEEMRELFKRMHE-GDLEAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGC 84

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+++  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 85  IGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVR 141

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
              + +     K      IA  L +   EV+     +    SL   I +   +     D 
Sbjct: 142 ---EKLMGEAAKEPTTEEIANVLGIPHEEVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQ 198

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L  + +G  Q + E          L   +  LN RE+ I   R  Q    T   ++ E  
Sbjct: 199 LSDERNGDSQWIEEIA--------LKEGLCRLNEREKMIIRKRFFQG--KTQMEVAEEIG 248

Query: 264 VSRERVRQIEARAFKKVQESIQ 285
           +S+ +V ++E  A +++ ++IQ
Sbjct: 249 ISQAQVSRLEKAAIRQMNKNIQ 270


>gi|302555769|ref|ZP_07308111.1| RNA polymerase sigma factor RpoS [Streptomyces viridochromogenes
           DSM 40736]
 gi|302473387|gb|EFL36480.1| RNA polymerase sigma factor RpoS [Streptomyces viridochromogenes
           DSM 40736]
          Length = 339

 Score =  183 bits (464), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 67/307 (21%), Positives = 131/307 (42%), Gaps = 42/307 (13%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYR------------------------------EHG 45
           L +Y+ +I   P+L  ++E  LA+R                                   
Sbjct: 39  LGQYLAQIGATPLLTAEDEVRLARRMEAGVRALEELDRSDADDDGLAPGRRGELEETARD 98

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
              A   +V ++LRLVV +A  +   GLP+ +V+ EGN+GL++AV+KFD  +GF+ +TY+
Sbjct: 99  GQRAKDHMVRANLRLVVSMARRHAHRGLPLLDVIQEGNLGLIRAVEKFDHTKGFKFSTYA 158

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
            WWI+ +++  +      V++     +      L+++    + +  +  +   V  +A++
Sbjct: 159 TWWIRQSIERGLAAHARTVRLPMQVVE-----QLQKIAKVERRLQLDLGREPSVAEVARE 213

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
             ++E  +  +        SL+  +   D   +   D +      Q     E  E     
Sbjct: 214 SGLAEDRIDWLRRVGRQAVSLDTPV--DDTGETVVGDLIPDTEVLQAP---EVAEYTALA 268

Query: 226 NMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             L  ++  L PRE  I   R      +  T + ++    ++RERVRQ+E  +  +++E 
Sbjct: 269 EELREAVGTLGPREAMILSLRYGLHDGHTRTRDEVARRVGLTRERVRQLEKASLARLREP 328

Query: 284 IQKQVEL 290
             ++  L
Sbjct: 329 ENRERLL 335


>gi|88854620|ref|ZP_01129287.1| RNA polymerase sigma factor [marine actinobacterium PHSC20C1]
 gi|88816428|gb|EAR26283.1| RNA polymerase sigma factor [marine actinobacterium PHSC20C1]
          Length = 1108

 Score =  183 bits (464), Expect = 3e-44,   Method: Composition-based stats.
 Identities = 66/302 (21%), Positives = 128/302 (42%), Gaps = 40/302 (13%)

Query: 21  HEIRKIPMLEKQEEYVLAK----------------------------RYREHGDLSAAHR 52
             +   P+L   +E +LA+                            ++       A  R
Sbjct: 627 QRLNDFPLLSADQEVLLAREIEAGLFAQEQFDLLDRREQRSPSGRELQWVAKNGEKAFAR 686

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
              S+ RLV  IA  Y   GL  ++++ EG +GL++A++KFD  +GF+ +TY+ WW++ A
Sbjct: 687 FAASNYRLVFSIARRYVNNGLDYADLIQEGALGLLRAIQKFDYMKGFKFSTYATWWVRQA 746

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +    S ++I     +++      +L+   ++    N +   +  +A    V+E +
Sbjct: 747 ITRALADLGSTIRIPVHMVEQQ-----NKLRQAARSFELQNDRKPTISELAAGAEVTEQD 801

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
                       S++  ++  +   S   + LV +      +LI  E     R  +   +
Sbjct: 802 ASRALGYEYSFLSIDKELDPGEGFGS-LHNLLVDESVAPVDLLIHAE----FRGAMNNVL 856

Query: 233 SVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
           S L  RE    + R     ++P TL+++   F V+RER+RQIE +  + ++ S + Q  L
Sbjct: 857 SALPKRESTTIQMRFGIGGQDPATLDHIGDIFGVTRERIRQIEKKTMESLRSSAEVQGRL 916

Query: 291 SS 292
             
Sbjct: 917 GD 918


>gi|124022691|ref|YP_001016998.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Prochlorococcus marinus str. MIT 9303]
 gi|123962977|gb|ABM77733.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Prochlorococcus marinus str. MIT 9303]
          Length = 320

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 65/316 (20%), Positives = 131/316 (41%), Gaps = 52/316 (16%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------------- 43
           +++    +  Y+ +I ++P+L  ++E  L ++ +E                         
Sbjct: 6   VLSDVDLVRSYLRDIGRVPLLSHEQEITLGRQVQELMSLEQLESELEGKTGAPASRKELA 65

Query: 44  --------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
                              A  R+V+++LRLVV +A  Y    + + +++ EG IGL++ 
Sbjct: 66  KAAGLSELQLKKKLQSGRRAKERMVSANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRG 125

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V+KFDP RG++ +TY+ WWI+  +   I      +++     +      L +LK   + +
Sbjct: 126 VEKFDPTRGYKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITE-----MLNKLKKGQREL 180

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
           +    +   V  +A+ + + E EV  + CR     SL   +   D+              
Sbjct: 181 SQEMGRTPTVSELAEFVELPEEEVKDLMCRARQPMSLEMKVGDGDETELLELLA------ 234

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRE 267
           G+E++  EK E    +  L   +  L   + R+   R   +   P+ L  ++    +SR+
Sbjct: 235 GEEELPSEKVEVDCMKGDLRTLLEKLPELQGRVLRMRYGIDGGEPMNLTGIAKTLGMSRD 294

Query: 268 RVRQIEARAFKKVQES 283
           R R++E      ++ S
Sbjct: 295 RTRRLEREGLALMRTS 310


>gi|251797866|ref|YP_003012597.1| sporulation sigma factor SigG [Paenibacillus sp. JDR-2]
 gi|247545492|gb|ACT02511.1| RNA polymerase, sigma 28 subunit, SigG [Paenibacillus sp. JDR-2]
          Length = 260

 Score =  183 bits (464), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 54/261 (20%), Positives = 116/261 (44%), Gaps = 16/261 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L   E   L    +   + +A  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLTNAEMRELFTALQTQNEWAAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGCI 74

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A+  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++ 
Sbjct: 75  GLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVRD 131

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L   T+ N +   +  I++ LNV + +V+     +    SL   I     +     D +
Sbjct: 132 SL---TNQNSREPTIFEISEALNVPKEDVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQI 188

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             D +     + E          L  +M  LN RE+ I   R       T   ++ E  +
Sbjct: 189 SDDKNKDVSWIEEIA--------LREAMHKLNDREKMILSMRFF--EGKTQMEVADEIGI 238

Query: 265 SRERVRQIEARAFKKVQESIQ 285
           S+ +V ++E  A +++Q+ ++
Sbjct: 239 SQAQVSRLEKSAIQQMQKHVK 259


>gi|76812098|ref|YP_331741.1| RNA polymerase sigma factor [Burkholderia pseudomallei 1710b]
 gi|254261622|ref|ZP_04952676.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1710a]
 gi|76581551|gb|ABA51026.1| RNA polymerase sigma factor [Burkholderia pseudomallei 1710b]
 gi|254220311|gb|EET09695.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1710a]
          Length = 482

 Score =  182 bits (463), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 60/266 (22%), Positives = 127/266 (47%), Gaps = 16/266 (6%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDL---SAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
             +R++P    ++    A+R    G+    +A  R+  ++LRLV+ IA  Y   GL +++
Sbjct: 212 RAMRRLP-TSPEKSDAGAQRAFADGEARISAATARMAEANLRLVLSIARKYASRGLDLAD 270

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGN+GL++A++KF+  RGF+ +TY+ WWI+ A+   +      +++           
Sbjct: 271 LLQEGNLGLLRAIEKFEHRRGFKFSTYATWWIRQAISRAVADRARTIRVPVHV-----GD 325

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
             RR++     I   +     +  +++   +    + ++        SLNA +   D + 
Sbjct: 326 EARRVRKAADRIERRSGVSASLAELSEATGLPAERLRAVLTLPREPRSLNAPL--GDDDQ 383

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTL 255
           +++ D +    D     L +        +++T  +  ++ +E  I   R     + P + 
Sbjct: 384 AEFGDIV---EDTSTPSLFDALAHGQMCDVVTSLLKTMSAQEADILRRRFGIGGDEPWSY 440

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           E +++   VSRE+VR+IE RA + ++
Sbjct: 441 EQIAARAGVSREQVRRIEKRALQTLR 466


>gi|295399724|ref|ZP_06809705.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|294978127|gb|EFG53724.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
          Length = 271

 Score =  182 bits (463), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 60/262 (22%), Positives = 117/262 (44%), Gaps = 17/262 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+ +E   L KR  E GDL A  +LV  +LRLV+ +   +   G  + ++   G 
Sbjct: 26  SKLPVLKNEEMRELFKRMHE-GDLEAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGC 84

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+++  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 85  IGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVR 141

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
              + +     K      IA  L +   EV+     +    SL   I +   +     D 
Sbjct: 142 ---EKLMGEAAKEPTTEEIANVLGIPHEEVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQ 198

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L  +  G  Q + E          L   +  LN RE+ I   R  Q    T   ++ E  
Sbjct: 199 LSDERSGDNQWIEEIA--------LKEGLCRLNEREKMIIRKRFFQG--KTQMEVAEEIG 248

Query: 264 VSRERVRQIEARAFKKVQESIQ 285
           +S+ +V ++E  A +++ ++IQ
Sbjct: 249 ISQAQVSRLEKAAIRQMNKNIQ 270


>gi|161833810|ref|YP_001598006.1| RNA polymerase sigma factor rpoD [Candidatus Sulcia muelleri GWSS]
 gi|152206300|gb|ABS30610.1| RNA polymerase sigma factor rpoD [Candidatus Sulcia muelleri GWSS]
          Length = 351

 Score =  182 bits (463), Expect = 4e-44,   Method: Composition-based stats.
 Identities = 78/329 (23%), Positives = 144/329 (43%), Gaps = 58/329 (17%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR---------------------------- 42
           +  + L +++ EI  IP+L ++EE+  AK  R                            
Sbjct: 29  SESLSLDKFLLEISNIPLLSQEEEFFWAKLARVGYIYNSEIESILKKFKIFKKLKKLNKL 88

Query: 43  -------------------EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
                              +     A   LV ++LR V+ IA  Y+  GL +S++++EGN
Sbjct: 89  KKLKKIKKLTAVLIKKFDKKGIKKYALDNLVKANLRFVISIAKQYQNQGLSLSDLINEGN 148

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
            GL++ + +FD  +GF+  +Y +WWI+ ++ + I      V+  T  N+   +  + +  
Sbjct: 149 FGLIKGINRFDERKGFKCISYCVWWIRQSILQAISDKARCVRYPT--NKLAFYNKVNKTY 206

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L+        P  +  I+  LNVSE +V           SL+A +   + ++S   D 
Sbjct: 207 SKLEQKLKM---PPSIKYISDYLNVSEKDVEEALINSIKHTSLDAPL--GEGDNSNLYDV 261

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-PVTLENLSSEF 262
           +  D   +    +EKE  +    +L   +  L+ RE +I           + LE ++   
Sbjct: 262 IKIDESPKTDHSLEKESLQQDIKIL---LETLSERESQIITLHYGLGCFSMNLEKIAYLL 318

Query: 263 EVSRERVRQIEARAFKKVQESIQKQVELS 291
           +++RER RQIE  A K++++S +K++ LS
Sbjct: 319 KLTRERCRQIEMHAIKRLKKSSRKEILLS 347


>gi|269102892|ref|ZP_06155589.1| RNA polymerase sigma factor RpoS [Photobacterium damselae subsp.
           damselae CIP 102761]
 gi|268162790|gb|EEZ41286.1| RNA polymerase sigma factor RpoS [Photobacterium damselae subsp.
           damselae CIP 102761]
          Length = 282

 Score =  182 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 70/271 (25%), Positives = 134/271 (49%), Gaps = 20/271 (7%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ ++R   +L K+EE  L+ + +  GD  A  +L+ S+LRLVV IA   +  GL + ++
Sbjct: 10  YLKQLRSRALLTKEEEIELSIKVQ-AGDQKARAKLIESNLRLVVSIAKKMQHRGLDLDDL 68

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK--RLF 136
           ++EGNIGL+ AV+KF+P+ G+R +TY+ WWIK AM   I      V++    +++   ++
Sbjct: 69  INEGNIGLITAVEKFNPDYGYRFSTYATWWIKQAMDRAIHNHSREVRLPVHISKELCTIY 128

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
              + +    + +T        +  ++      + E+  +        SL+   +   K 
Sbjct: 129 SAFKEMSTKSEQVT--------IDQVSALTGSPKEEIEKILKYERRYSSLDDQFDEGAKF 180

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVT 254
           S    D    DH        E    +++  +L   ++ L PR++ I   R       P T
Sbjct: 181 SEIIPDHSKLDH-------TELLNEEDQTEVLAMLLAELKPRDQEIIARRFGLFGYEPHT 233

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L+ +++   ++RERVRQ++  A +++   ++
Sbjct: 234 LQEVATAVNLTRERVRQLQILAQQRLAAKMR 264


>gi|237810316|ref|YP_002894767.1| RNA polymerase sigma factor [Burkholderia pseudomallei MSHR346]
 gi|237504080|gb|ACQ96398.1| RNA polymerase sigma factor [Burkholderia pseudomallei MSHR346]
          Length = 482

 Score =  182 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 60/266 (22%), Positives = 127/266 (47%), Gaps = 16/266 (6%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDL---SAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
             +R++P    ++    A+R    G+    +A  R+  ++LRLV+ IA  Y   GL +++
Sbjct: 212 RAMRRLP-TSPEKSDAGAQRAFADGEARISAATARMAEANLRLVLSIARKYASRGLDLAD 270

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGN+GL++A++KF+  RGF+ +TY+ WWI+ A+   +      +++           
Sbjct: 271 LLQEGNLGLLRAIEKFEHRRGFKFSTYATWWIRQAISRAVADRARTIRVPVHV-----GD 325

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
             RR++     I   +     +  +++   +    + ++        SLNA +   D + 
Sbjct: 326 EARRVRKAADRIERRSGVSASLAELSEATGLPAERLRAVLTLPREPRSLNAPL--GDDDQ 383

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTL 255
           +++ D +    D     L +        +++T  +  ++ +E  I   R     + P + 
Sbjct: 384 AEFGDIV---EDTSTPSLFDALAHGQMCDVVTSLLKTMSAQEADILRRRFGIGGDEPWSY 440

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           E +++   VSRE+VR+IE RA + ++
Sbjct: 441 EQIAARAGVSREQVRRIEKRALQTLR 466


>gi|254182275|ref|ZP_04888872.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1655]
 gi|184212813|gb|EDU09856.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 1655]
          Length = 482

 Score =  182 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 60/266 (22%), Positives = 127/266 (47%), Gaps = 16/266 (6%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDL---SAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
             +R++P    ++    A+R    G+    +A  R+  ++LRLV+ IA  Y   GL +++
Sbjct: 212 RAMRRLP-TSPEKSDAGAQRAFADGEARISAATARMAEANLRLVLSIARKYASRGLDLAD 270

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGN+GL++A++KF+  RGF+ +TY+ WWI+ A+   +      +++           
Sbjct: 271 LLQEGNLGLLRAIEKFEHRRGFKFSTYATWWIRQAISRAVADRARTIRVPVHV-----GD 325

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
             RR++     I   +     +  +++   +    + ++        SLNA +   D + 
Sbjct: 326 EARRVRKAADRIERRSGVSASLAELSEATGLPAERLRAVLTLPREPRSLNAPL--GDDDQ 383

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTL 255
           +++ D +    D     L +        +++T  +  ++ +E  I   R     + P + 
Sbjct: 384 AEFGDIV---EDTSTPSLFDALAHGQMCDVVTSLLKTMSAQEADILRRRFGIGGDEPWSY 440

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           E +++   VSRE+VR+IE RA + ++
Sbjct: 441 EQIAARAGVSREQVRRIEKRALQTLR 466


>gi|221212018|ref|ZP_03584996.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           multivorans CGD1]
 gi|221168103|gb|EEE00572.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           multivorans CGD1]
          Length = 625

 Score =  182 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 57/238 (23%), Positives = 103/238 (43%), Gaps = 12/238 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   L  ++LRLVV IA  Y   GLP ++++ EGNIGL++A+ ++D  RGFR +TY+ W
Sbjct: 387 AAKMALFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFSTYATW 446

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ ++   +      +++ T          + +L    +              +A ++ 
Sbjct: 447 WIRQSITHALADLGRTIRVPTH-----TVDAINKLARLAREHRQRAGAAATPDELAAQMG 501

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
               +V  +   +    S++  I            ++    D       +  +   RR  
Sbjct: 502 EPVDKVRELMAIVKEPVSVDLPIAPDGD-----MTFVDVVPDASTPSPEDAADAAQRRAA 556

Query: 228 LTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +  ++  L PRE  I   R         +L ++     +S ERVRQIEA A  +++ S
Sbjct: 557 IAAAIDRLPPREALIVRLRYGLHAGEGCSLRDIGRRLNLSAERVRQIEASALARLRAS 614



 Score = 39.8 bits (92), Expect = 0.54,   Method: Composition-based stats.
 Identities = 12/55 (21%), Positives = 19/55 (34%), Gaps = 9/55 (16%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREH---------GDLSAAHRL 53
           +       +  Y+ E+  +P+L   EE   A+R             GD  A   L
Sbjct: 121 LAPRTTDPVRLYLREMGTVPLLTHDEEIAYAQRIERGRAASVAVLCGDPDALDAL 175


>gi|124386302|ref|YP_001028216.1| putative RNA polymerase sigma factor RpoD [Burkholderia mallei NCTC
           10229]
 gi|126449023|ref|YP_001081831.1| RNA polymerase sigma factor [Burkholderia mallei NCTC 10247]
 gi|126450673|ref|YP_001081854.1| RNA polymerase sigma factor RpoD [Burkholderia mallei NCTC 10247]
 gi|124294322|gb|ABN03591.1| putative RNA polymerase sigma factor RpoD [Burkholderia mallei NCTC
           10229]
 gi|126241893|gb|ABO04986.1| RNA polymerase sigma factor [Burkholderia mallei NCTC 10247]
 gi|126243543|gb|ABO06636.1| RNA polymerase sigma factor RpoD [Burkholderia mallei NCTC 10247]
          Length = 482

 Score =  182 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 61/266 (22%), Positives = 127/266 (47%), Gaps = 16/266 (6%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDL---SAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
             +R++P    ++    A+R    G+    +A  R+  ++LRLV+ IA  Y   GL +++
Sbjct: 212 RAMRRLP-TSPEKSDAGAQRAFADGEARISAATARMAEANLRLVLSIARKYASRGLDLAD 270

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGN+GL++A++KF+  RGF+ +TY+ WWI+ A+   I      +++           
Sbjct: 271 LLQEGNLGLLRAIEKFEHRRGFKFSTYATWWIRQAISRAIAERARTIRVPVHV-----GD 325

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
             RR++     I   +     +  +++   +    + ++        SLNA +   D + 
Sbjct: 326 EARRVRKAADRIERRSGVSASLAELSEATGLPAERLRAVLTLPREPRSLNAPL--GDDDQ 383

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTL 255
           +++ D +    D     L +        +++T  +  ++ +E  I   R     + P + 
Sbjct: 384 AEFGDIV---EDTSTPSLFDALAHGQMCDVVTSLLKTMSAQEADILRRRFGIGGDEPWSY 440

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           E +++   VSRE+VR+IE RA + ++
Sbjct: 441 EQIAARAGVSREQVRRIEKRALQTLR 466


>gi|126441635|ref|YP_001057174.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 668]
 gi|126221128|gb|ABN84634.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 668]
          Length = 482

 Score =  182 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 61/266 (22%), Positives = 127/266 (47%), Gaps = 16/266 (6%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDL---SAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
             +R++P    ++    A+R    G+    +A  R+  ++LRLV+ IA  Y   GL +++
Sbjct: 212 RAMRRLP-TSPEKSDAGAQRAFADGEARISAATARMAEANLRLVLSIARKYASRGLDLAD 270

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGN+GL++A++KF+  RGF+ +TY+ WWI+ A+   I      +++           
Sbjct: 271 LLQEGNLGLLRAIEKFEHRRGFKFSTYATWWIRQAISRAIAERARTIRVPVHV-----GD 325

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
             RR++     I   +     +  +++   +    + ++        SLNA +   D + 
Sbjct: 326 EARRVRKAADRIERRSGVSASLAELSEATGLPAERLRAVLTLPREPRSLNAPL--GDDDQ 383

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTL 255
           +++ D +    D     L +        +++T  +  ++ +E  I   R     + P + 
Sbjct: 384 AEFGDIV---EDTSTPSLFDALAHGQMCDVVTSLLKTMSAQEADILRRRFGIGGDEPWSY 440

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           E +++   VSRE+VR+IE RA + ++
Sbjct: 441 EQIAARAGVSREQVRRIEKRALQTLR 466


>gi|20808063|ref|NP_623234.1| sporulation sigma factor SigG [Thermoanaerobacter tengcongensis
           MB4]
 gi|20516644|gb|AAM24838.1| DNA-directed RNA polymerase sigma subunits (sigma70/sigma32)
           [Thermoanaerobacter tengcongensis MB4]
          Length = 264

 Score =  182 bits (463), Expect = 5e-44,   Method: Composition-based stats.
 Identities = 56/261 (21%), Positives = 117/261 (44%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+  ++  L  R + +GD  A    + S+LRLV+ +   +   G  + ++   G 
Sbjct: 21  SKLPVLKPSKQRELLIRMK-NGDKKAREEFINSNLRLVLSVIQRFNNRGESVDDLFQVGC 79

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD ++  + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 80  IGLIKAIDNFDLDQNVKFSTYAVPMIIGEIRRYLRDNT-PIRVSRSL--RDIAYKALQVR 136

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L      N K   V  IAK+L++   EV+     +    SL   I     ++    D 
Sbjct: 137 DKL---VSENSKEPTVGEIAKELDLPSEEVVMALDAIQEPVSLFEPIYHDGGDAIYVMDQ 193

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  D +  E  L         +  L  ++  LN RE+ I   R       T   ++ E  
Sbjct: 194 VSDDKNVDEVWLE--------KIALKEALEKLNEREKMILTMRFF--EGKTQMEVAKEIG 243

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A   +++ I
Sbjct: 244 ISQAQVSRLEKAALNHMRKYI 264


>gi|289746505|ref|ZP_06505883.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           02_1987]
 gi|289687033|gb|EFD54521.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           02_1987]
          Length = 216

 Score =  182 bits (462), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 50/216 (23%), Positives = 100/216 (46%), Gaps = 12/216 (5%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            S    + + G  ++V+KFD  +G++ +TY+ WWI+ A+   +      ++I     +  
Sbjct: 5   FSTSSRKAHSGADRSVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE-- 62

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +   L R++  L         PE    +AK+++++  +V+ +        SL+  I   D
Sbjct: 63  VINKLGRIQRELLQDLGREPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GD 117

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENP 252
           +  SQ  D++    D +  V ++       ++ L   +  L+ RE  +   R       P
Sbjct: 118 EGDSQLGDFI---EDSEAVVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQP 174

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            TL+ +   + V+RER+RQIE++   K++   + QV
Sbjct: 175 RTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQV 210


>gi|304404022|ref|ZP_07385684.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
 gi|304347000|gb|EFM12832.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
          Length = 272

 Score =  182 bits (462), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 53/262 (20%), Positives = 115/262 (43%), Gaps = 16/262 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L   E   L    +   + +A  +LV  +LRLV+ +   +   G  + ++   G 
Sbjct: 26  SKLPVLTNAEMRELFTALQTRNERAAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGC 85

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+A+  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 86  IGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVR 142

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L   T+ N +   +  I++ L V + +V+     +    SL   I     +     D 
Sbjct: 143 DSL---TNANSREPTIFEISEALGVPKEDVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQ 199

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  D +     + E          L  +M  LN RE+ I   R       T   ++ E  
Sbjct: 200 ISDDKNKDISWIEEIA--------LREAMHKLNDREKMILSMRFF--EGKTQMEVADEIG 249

Query: 264 VSRERVRQIEARAFKKVQESIQ 285
           +S+ +V ++E  A +++Q+ ++
Sbjct: 250 ISQAQVSRLEKSAIQQMQKHVK 271


>gi|53724654|ref|YP_101962.1| RNA polymerase sigma factor RpoD [Burkholderia mallei ATCC 23344]
 gi|121599433|ref|YP_994127.1| putative RNA polymerase sigma factor RpoD [Burkholderia mallei
           SAVP1]
 gi|167001162|ref|ZP_02266961.1| RNA polymerase sigma factor [Burkholderia mallei PRL-20]
 gi|238561900|ref|ZP_00441190.2| RNA polymerase sigma factor RpoD [Burkholderia mallei GB8 horse 4]
 gi|254176911|ref|ZP_04883568.1| RNA polymerase sigma factor RpoD [Burkholderia mallei ATCC 10399]
 gi|254203640|ref|ZP_04910000.1| RNA polymerase sigma factor RpoD [Burkholderia mallei FMH]
 gi|254208616|ref|ZP_04914964.1| RNA polymerase sigma factor RpoD [Burkholderia mallei JHU]
 gi|254360328|ref|ZP_04976598.1| RNA polymerase sigma factor RpoD [Burkholderia mallei 2002721280]
 gi|52428077|gb|AAU48670.1| RNA polymerase sigma factor RpoD, putative [Burkholderia mallei
           ATCC 23344]
 gi|121228243|gb|ABM50761.1| putative RNA polymerase sigma factor RpoD [Burkholderia mallei
           SAVP1]
 gi|147745152|gb|EDK52232.1| RNA polymerase sigma factor RpoD [Burkholderia mallei FMH]
 gi|147750492|gb|EDK57561.1| RNA polymerase sigma factor RpoD [Burkholderia mallei JHU]
 gi|148029568|gb|EDK87473.1| RNA polymerase sigma factor RpoD [Burkholderia mallei 2002721280]
 gi|160697952|gb|EDP87922.1| RNA polymerase sigma factor RpoD [Burkholderia mallei ATCC 10399]
 gi|238523583|gb|EEP87020.1| RNA polymerase sigma factor RpoD [Burkholderia mallei GB8 horse 4]
 gi|243062992|gb|EES45178.1| RNA polymerase sigma factor [Burkholderia mallei PRL-20]
          Length = 482

 Score =  182 bits (462), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 61/266 (22%), Positives = 127/266 (47%), Gaps = 16/266 (6%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDL---SAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
             +R++P    ++    A+R    G+    +A  R+  ++LRLV+ IA  Y   GL +++
Sbjct: 212 RAMRRLP-TSPEKSDAGAQRAFADGEARISAATARMAEANLRLVLSIARKYASRGLDLAD 270

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGN+GL++A++KF+  RGF+ +TY+ WWI+ A+   I      +++           
Sbjct: 271 LLQEGNLGLLRAIEKFEHRRGFKFSTYATWWIRQAISRAIAERARTIRVPVHV-----GD 325

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
             RR++     I   +     +  +++   +    + ++        SLNA +   D + 
Sbjct: 326 EARRVRKAADRIERRSGVSASLAELSEATGLPAERLRAVLTLPREPRSLNAPL--GDDDQ 383

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTL 255
           +++ D +    D     L +        +++T  +  ++ +E  I   R     + P + 
Sbjct: 384 AEFGDIV---EDTSTPSLFDALAHGQMCDVVTSLLKTMSAQEADILRRRFGIGGDEPWSY 440

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           E +++   VSRE+VR+IE RA + ++
Sbjct: 441 EQIAARAGVSREQVRRIEKRALQTLR 466


>gi|326518320|dbj|BAJ88189.1| predicted protein [Hordeum vulgare subsp. vulgare]
 gi|326533296|dbj|BAJ93620.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 552

 Score =  182 bits (462), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 70/251 (27%), Positives = 126/251 (50%), Gaps = 15/251 (5%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E  L KR  +HG +   +R+VTS++RLV+ IA  + G GL + +++ EG  GL++  +K
Sbjct: 297 DENTLRKRL-DHG-IHCKNRMVTSNVRLVISIAREFEGPGLELYDLIQEGMQGLIRGAEK 354

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +GFR +TYS WWIK AM++ +     + ++     +        R+K   + +   
Sbjct: 355 FDASKGFRFSTYSHWWIKQAMRKSVSEQTQIFRLPAHMVEASY-----RVKECTKRLRRK 409

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA  + +    V +         SL++ I S+D        +     D   
Sbjct: 410 LKRRPSNEEIAVDIGMPVKRVEAAVSLPKYSVSLDSKIGSTD------MTYQEVTADPSA 463

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +   E   R + +  + +++  L+PRER++ + R    +    TL+ + +   VSRER+R
Sbjct: 464 ETAEEMLNRMSMKKDVHQALDTLSPRERQVVKLRFGINDGRIRTLQEIGNIMGVSRERIR 523

Query: 271 QIEARAFKKVQ 281
           QIE+ AF+K++
Sbjct: 524 QIESGAFRKLR 534


>gi|110004382|emb|CAK98720.1| probable rna polymerase sigma-a factor protein [Spiroplasma citri]
          Length = 445

 Score =  182 bits (462), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 73/325 (22%), Positives = 129/325 (39%), Gaps = 66/325 (20%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAA---HRLVTSHLRLVVKIAMGYRGYG 72
           +  Y + +    +L ++EE   AK               +L+TS+L+LVV +A  +   G
Sbjct: 111 IKAYFNILGTSKILTREEEIKYAKMLESSDPEEIRFGRDKLITSNLKLVVSVARKHLNRG 170

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L  S+++ EGNIGLM+AV KFD +RGF+ +TY+ WWI+ A    I      ++I     +
Sbjct: 171 LDFSDLIEEGNIGLMKAVDKFDYKRGFKFSTYATWWIRQATTRAIADQARTIRIPVHMVE 230

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN--VSESEVISMNCRLAGDESLNALI 190
                 + +L    + +T    +      IA+K+   +   +V  +        SL   I
Sbjct: 231 -----TINKLTRIERQLTQELGREPSYNEIAEKMGQGMVGEKVREIKRLSIEPVSLEKPI 285

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN-------------MLTRSMSVLNP 237
              D++ + + D++            EKE  +   +             ++     +L  
Sbjct: 286 --GDEDDTHFGDFVDDKDIFTPDEYTEKESLREVIDEVFHEILSAREEKVIRMRFGLLPT 343

Query: 238 RERRIFEARRLQEN-----------------------------------------PVTLE 256
           + R +    +  E+                                         P TLE
Sbjct: 344 KLRTVLRLAKECEDETFPELVQTVKALDIHYDTPIEKVQSQKHALIDKHLSKYDSPKTLE 403

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQ 281
            +  EF+V+RER+RQIEA+  +K +
Sbjct: 404 EVGKEFKVTRERIRQIEAKTIRKFK 428


>gi|302389526|ref|YP_003825347.1| RNA polymerase, sigma subunit, RpsG/SigG [Thermosediminibacter
           oceani DSM 16646]
 gi|302200154|gb|ADL07724.1| RNA polymerase, sigma subunit, RpsG/SigG [Thermosediminibacter
           oceani DSM 16646]
          Length = 257

 Score =  182 bits (462), Expect = 6e-44,   Method: Composition-based stats.
 Identities = 55/261 (21%), Positives = 116/261 (44%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L   +   L  R ++ GD  A  +L+  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLSNSKMKELFLRVKQ-GDKEAREKLIHGNLRLVLSVIQRFNNRGEYVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+A+  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 73  IGLMKAIDNFDLNQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVR 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L    + N +   +  IAK++N+   E++     +    SL   I     +     D 
Sbjct: 130 DSL---VNKNSREPSIEEIAKEMNIPSEEIVMALDAIQEPISLFEPIYHDGGDPIFVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  D +  E  L        R   +  +M  LN RE+ I   R       T   ++ E  
Sbjct: 187 ISDDKNNDENWL--------RSISIKEAMQKLNEREKLILTLRFF--EGKTQMEVAQEIG 236

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A K +++ +
Sbjct: 237 ISQAQVSRLEKAALKHLKKYM 257


>gi|148909485|gb|ABR17840.1| unknown [Picea sitchensis]
          Length = 495

 Score =  182 bits (462), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 51/250 (20%), Positives = 120/250 (48%), Gaps = 12/250 (4%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           + R      +  +++  +LRLV+ +A  Y+  GL + +++  G++GLM++ +KFD  RGF
Sbjct: 248 KMRLEVGRDSFDKIINCNLRLVISVAKNYQNRGLSLQDLIQAGSMGLMRSAEKFDYSRGF 307

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWI+ ++ + +      +++     +      + R++   + +   + +    
Sbjct: 308 KFSTYAYWWIRQSITKALTEQSRTIRLPVHIVES-----MTRIRTAWRLLYQEHKRDPTK 362

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +A+   +S + +  +        SL+           ++ + +   +    + ++ KE
Sbjct: 363 EEVAEVAGISMTRLRHVTRCSRVPTSLDR--CVGKDMDEKFSEIVADTNSESTETIVSKE 420

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAF 277
                +  L R +  L  RE+++   R   ++    +L  +   F +SRERVRQIE +A 
Sbjct: 421 ---LFKKDLDRVLDTLTAREKQVVRLRYGLDDGRMKSLHEVGENFSLSRERVRQIEMKAM 477

Query: 278 KKVQESIQKQ 287
           +K++++ + Q
Sbjct: 478 RKLRQNHRTQ 487


>gi|225175484|ref|ZP_03729478.1| RNA polymerase, sigma 28 subunit, SigG [Dethiobacter alkaliphilus
           AHT 1]
 gi|225168813|gb|EEG77613.1| RNA polymerase, sigma 28 subunit, SigG [Dethiobacter alkaliphilus
           AHT 1]
          Length = 277

 Score =  181 bits (461), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 55/261 (21%), Positives = 118/261 (45%), Gaps = 17/261 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+  E   L  R RE GD SA  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 34  KLPVLKNDEMRRLFARLRE-GDESAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 92

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + + + +++ 
Sbjct: 93  GLIKAIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKVLQVRD 149

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L    +   +   +  IAK+LN+   +++     +    SL   I     +     D +
Sbjct: 150 SL---ANRFAREPTISEIAKELNLKREDIVFALDAIQEPVSLFEPIYHDGGDPIFVMDQI 206

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             D +   + L            +  ++  LN RE+ I   R  +    T   ++ E  +
Sbjct: 207 SDDKNHDNKWLEVLA--------INEALHKLNEREKLILTLRFYRG--KTQMEVADEIGI 256

Query: 265 SRERVRQIEARAFKKVQESIQ 285
           S+ +V ++E  A   +++ +Q
Sbjct: 257 SQAQVSRLEKAALSHLRKHVQ 277


>gi|33863339|ref|NP_894899.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Prochlorococcus marinus str. MIT 9313]
 gi|33640788|emb|CAE21243.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           [Prochlorococcus marinus str. MIT 9313]
          Length = 320

 Score =  181 bits (461), Expect = 7e-44,   Method: Composition-based stats.
 Identities = 65/316 (20%), Positives = 131/316 (41%), Gaps = 52/316 (16%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------------- 43
           +++    +  Y+ +I ++P+L  ++E  L ++ +E                         
Sbjct: 6   VLSDVDLVRSYLRDIGRVPLLSHEQEITLGRQVQELMSLEQLESELEGQTGEPASRKELA 65

Query: 44  --------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
                              A  R+V+++LRLVV +A  Y    + + +++ EG IGL++ 
Sbjct: 66  KAAGLSELQLKKKLQSGRRAKERMVSANLRLVVSVAKKYTKRNMELLDLIQEGTIGLVRG 125

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V+KFDP RG++ +TY+ WWI+  +   I      +++     +      L +LK   + +
Sbjct: 126 VEKFDPTRGYKFSTYAYWWIRQGITRAIAEKSRTIRLPIHITE-----MLNKLKKGQREL 180

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
           +    +   V  +A+ + + E EV  + CR     SL   +   D+              
Sbjct: 181 SQEMGRTPTVSELAEFVELPEEEVKDLMCRARQPMSLEMKVGDGDETELLELLA------ 234

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRE 267
           G+E++  EK E    +  L   +  L   + R+   R   +   P+ L  ++    +SR+
Sbjct: 235 GEEELPSEKVEVDCMKGDLRTLLEKLPELQGRVLRMRYGIDGGEPMNLTGIAKTLGMSRD 294

Query: 268 RVRQIEARAFKKVQES 283
           R R++E      ++ S
Sbjct: 295 RTRRLEREGLALMRTS 310


>gi|293363636|ref|ZP_06610388.1| putative RNA polymerase sigma factor RpoD [Mycoplasma alligatoris
           A21JP2]
 gi|292552792|gb|EFF41550.1| putative RNA polymerase sigma factor RpoD [Mycoplasma alligatoris
           A21JP2]
          Length = 492

 Score =  181 bits (461), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 68/290 (23%), Positives = 134/290 (46%), Gaps = 21/290 (7%)

Query: 16  LSRYIHEIRKI-PMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  Y+  I K   +L+  +E  LAK+  + G     A  +L+  +LRLV+  A  Y+  G
Sbjct: 207 VKWYMRWIGKYGELLKPDQEKQLAKQMEKGGFRGKRARDKLIMRNLRLVINNAKKYKNRG 266

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L   +++SEGN G+++AV+K++ E+GF+ +TY+ WWI+ A+   +      +++     +
Sbjct: 267 LTFIDLISEGNAGILKAVQKYNVEKGFKFSTYATWWIRQAITRAVADQARTIRVPVHMVE 326

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 + +++  LQ    +     Q+ A     + +E +V  +        SL+  I  
Sbjct: 327 --TINKITKIERELQQELGHEPTDSQI-ANRFGNDYTEEKVRYIRKINVDPISLDKQI-- 381

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS-VLNPRERRIFEARRL--- 248
             +N S + D++  D+       ++   ++    +L   +   L   ER +   R     
Sbjct: 382 GKENDSSFSDFVKDDNILN---PVDYASQEQLSELLIDLIDKSLEKDERELICKRYGVGV 438

Query: 249 -----QENPVTLENLSSEF-EVSRERVRQIEARAFKKVQESIQKQVELSS 292
                +    +L+ L+ E   VS+ER+RQIE +  +K++ S +    L  
Sbjct: 439 DSNGEKYRVHSLDELARERGGVSKERIRQIENKILRKLKNSSKNGRHLKD 488


>gi|189348175|ref|YP_001941371.1| RNA polymerase sigma 28 subunit [Burkholderia multivorans ATCC
           17616]
 gi|189338313|dbj|BAG47381.1| RNA polymerase sigma 28 subunit [Burkholderia multivorans ATCC
           17616]
          Length = 612

 Score =  181 bits (461), Expect = 8e-44,   Method: Composition-based stats.
 Identities = 58/243 (23%), Positives = 103/243 (42%), Gaps = 12/243 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E    +A   L  ++LRLVV IA  Y   GLP ++++ EGNIGL++A+ ++D  RGFR +
Sbjct: 369 ERATRAAKTALFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFS 428

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ ++   +      +++ T          + +L    +              +
Sbjct: 429 TYATWWIRQSITHALADLGRTIRVPTH-----TVDAINKLARLAREHRQRAGATATPAEL 483

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A ++     +V  +   +    S +  I            ++    D       +  +  
Sbjct: 484 AAQMGEPVDKVRDLMAIVKEPVSADLPIAPDGD-----MTFVDVVPDASTPSPEDAADAA 538

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            RR  +  ++  L PRE  I   R         +L ++     +S ERVRQIEA A  ++
Sbjct: 539 QRRAAIAAAIDRLPPREALIVRLRYGLHAGEGCSLRDIGRRLNLSAERVRQIEASALARL 598

Query: 281 QES 283
           + S
Sbjct: 599 RAS 601



 Score = 40.6 bits (94), Expect = 0.33,   Method: Composition-based stats.
 Identities = 12/55 (21%), Positives = 20/55 (36%), Gaps = 9/55 (16%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREH---------GDLSAAHRL 53
           ++      +  Y+ E+  +P+L   EE   A+R             GD  A   L
Sbjct: 108 LVPRTTDPVRLYLREMGTVPLLTHDEEIAYAQRIERGRAASVAVLCGDPDALDAL 162


>gi|304317193|ref|YP_003852338.1| RNA polymerase, sigma 28 subunit, SigG [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
 gi|302778695|gb|ADL69254.1| RNA polymerase, sigma 28 subunit, SigG [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
          Length = 256

 Score =  181 bits (461), Expect = 9e-44,   Method: Composition-based stats.
 Identities = 57/261 (21%), Positives = 118/261 (45%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+  ++  L  R + +GD +A    +  +LRLV+ +   +   G  + ++   G 
Sbjct: 13  SKLPVLKGAKQKELLIRMK-NGDKNAREEFINGNLRLVLSVIQRFNNRGEYVDDLFQVGC 71

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD  +  + +TY++  I   ++ Y+  + S +++  +   + + +   +++
Sbjct: 72  IGLIKAIDNFDLNQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSL--RDVAYKALQIR 128

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L    + N K   V  IAK+LN+   EV+     +    SL   I     ++    D 
Sbjct: 129 DKL---VNENSKEPTVGDIAKELNIPREEVVFALDAIQDPVSLFEPIYHDGGDAIYVMDQ 185

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  D +  E  L +          L  ++  LN RE+ I   R       T   ++ E  
Sbjct: 186 IGDDKNVDEVWLEQIA--------LKEAIKKLNDREKMILTMRFF--EGKTQMEVAREIG 235

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A   +++ I
Sbjct: 236 ISQAQVSRLEKSALTHMRKYI 256


>gi|161522996|ref|YP_001585925.1| RpoD family RNA polymerase sigma factor [Burkholderia multivorans
           ATCC 17616]
 gi|160346549|gb|ABX19633.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           multivorans ATCC 17616]
          Length = 625

 Score =  181 bits (461), Expect = 9e-44,   Method: Composition-based stats.
 Identities = 58/243 (23%), Positives = 103/243 (42%), Gaps = 12/243 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E    +A   L  ++LRLVV IA  Y   GLP ++++ EGNIGL++A+ ++D  RGFR +
Sbjct: 382 ERATRAAKTALFDANLRLVVSIAKRYPDRGLPFADLIQEGNIGLLKAIDRYDHRRGFRFS 441

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ ++   +      +++ T          + +L    +              +
Sbjct: 442 TYATWWIRQSITHALADLGRTIRVPTH-----TVDAINKLARLAREHRQRAGATATPAEL 496

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A ++     +V  +   +    S +  I            ++    D       +  +  
Sbjct: 497 AAQMGEPVDKVRDLMAIVKEPVSADLPIAPDGD-----MTFVDVVPDASTPSPEDAADAA 551

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            RR  +  ++  L PRE  I   R         +L ++     +S ERVRQIEA A  ++
Sbjct: 552 QRRAAIAAAIDRLPPREALIVRLRYGLHAGEGCSLRDIGRRLNLSAERVRQIEASALARL 611

Query: 281 QES 283
           + S
Sbjct: 612 RAS 614



 Score = 40.2 bits (93), Expect = 0.34,   Method: Composition-based stats.
 Identities = 12/55 (21%), Positives = 20/55 (36%), Gaps = 9/55 (16%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREH---------GDLSAAHRL 53
           ++      +  Y+ E+  +P+L   EE   A+R             GD  A   L
Sbjct: 121 LVPRTTDPVRLYLREMGTVPLLTHDEEIAYAQRIERGRAASVAVLCGDPDALDAL 175


>gi|218194307|gb|EEC76734.1| hypothetical protein OsI_14770 [Oryza sativa Indica Group]
          Length = 563

 Score =  181 bits (461), Expect = 9e-44,   Method: Composition-based stats.
 Identities = 69/251 (27%), Positives = 124/251 (49%), Gaps = 15/251 (5%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E  L KR  +HG +   +R+VTS++RLV+ IA  + G G+ + +++ EG  GL++  +K
Sbjct: 308 DERTLRKRL-DHG-IYCKNRMVTSNVRLVISIAREFEGPGMELYDLIQEGMQGLIRGAEK 365

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +GFR +TYS WWIK AM++ +     + ++     +        R+K  ++ +   
Sbjct: 366 FDASKGFRFSTYSHWWIKQAMRKSVSEQSQIFRLPAHMVEASY-----RVKECIKRLRRK 420

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA    +    V +         SL++ I S+D        +     D   
Sbjct: 421 LKRRPTNEEIAADTGMPIKRVEAAVNLPKYSVSLDSKIGSTD------MTYQEVTADPTA 474

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +   E   R + +  + +++  L  RER++   R   E+    TL+ + +   VSRER+R
Sbjct: 475 ETAEEMLNRLSMKRDVHKALDTLTTRERQVVTLRFGLEDGRIRTLQEIGNTMGVSRERIR 534

Query: 271 QIEARAFKKVQ 281
           QIE+ AF+K++
Sbjct: 535 QIESAAFRKLR 545


>gi|238786819|ref|ZP_04630620.1| RNA polymerase sigma factor rpoS [Yersinia frederiksenii ATCC
           33641]
 gi|238725187|gb|EEQ16826.1| RNA polymerase sigma factor rpoS [Yersinia frederiksenii ATCC
           33641]
          Length = 306

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 66/271 (24%), Positives = 119/271 (43%), Gaps = 39/271 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R                           Y   GL + ++
Sbjct: 63  YLGEIGYSPLLTAEEEVYFARR---------------------------YSNRGLALLDL 95

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 96  IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 154

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 155 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 209

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
                L    D  E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 210 ----LLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 265

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 266 DVGREIGLTRERVRQIQVEGLRRLREILQGQ 296


>gi|167843756|ref|ZP_02469264.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei B7210]
 gi|254197157|ref|ZP_04903580.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei S13]
 gi|169653899|gb|EDS86592.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei S13]
          Length = 482

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 61/266 (22%), Positives = 127/266 (47%), Gaps = 16/266 (6%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDL---SAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
             +R++P    ++    A+R    G+    +A  R+  ++LRLV+ IA  Y   GL +++
Sbjct: 212 RAMRRLP-TSPKKSDAGAQRAFADGEARISAATARMAEANLRLVLSIARKYASRGLDLAD 270

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGN+GL++A++KF+  RGF+ +TY+ WWI+ A+   I      +++           
Sbjct: 271 LLQEGNLGLLRAIEKFEHRRGFKFSTYATWWIRQAISRAIADRARTIRVPVHV-----GD 325

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
             RR++     I   +     +  +++   +    + ++        SLNA +   D + 
Sbjct: 326 EARRVRKAADRIERRSGVSASLAELSEATGLPAERLRAVLTLPREPRSLNAPL--GDDDQ 383

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTL 255
           +++ D +    D     L +        +++T  +  ++ +E  I   R     + P + 
Sbjct: 384 AEFGDIV---EDTSTPSLFDALAHGQMCDVVTSLLKTMSAQEADILRRRFGIGGDEPWSY 440

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           E +++   VSRE+VR+IE RA + ++
Sbjct: 441 EQIAARAGVSREQVRRIEKRALQTLR 466


>gi|297611772|ref|NP_001067832.2| Os11g0448400 [Oryza sativa Japonica Group]
 gi|62701714|gb|AAX92787.1| Sigma-70 region 3, putative [Oryza sativa Japonica Group]
 gi|108864350|gb|ABA93405.2| Sigma-70 region 3 family protein, expressed [Oryza sativa Japonica
           Group]
 gi|255680064|dbj|BAF28195.2| Os11g0448400 [Oryza sativa Japonica Group]
          Length = 564

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 69/251 (27%), Positives = 124/251 (49%), Gaps = 15/251 (5%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E  L KR  +HG +   +R+VTS++RLV+ IA  + G G+ + +++ EG  GL++  +K
Sbjct: 309 DERTLRKRL-DHG-IYCKNRMVTSNVRLVISIAREFEGPGMELYDLIQEGMQGLIRGAEK 366

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +GFR +TYS WWIK AM++ +     + ++     +        R+K  ++ +   
Sbjct: 367 FDASKGFRFSTYSHWWIKQAMRKSVSEQSQIFRLPAHMVEASY-----RVKECIKRLRRK 421

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA    +    V +         SL++ I S+D        +     D   
Sbjct: 422 LKRRPTNEEIAADTGMPIKRVEAAVNLPKYSVSLDSKIGSTD------MTYQEVTADPTA 475

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +   E   R + +  + +++  L  RER++   R   E+    TL+ + +   VSRER+R
Sbjct: 476 ETAEEMLNRLSMKRDVHKALDTLTTRERQVVTLRFGLEDGRIRTLQEIGNTMGVSRERIR 535

Query: 271 QIEARAFKKVQ 281
           QIE+ AF+K++
Sbjct: 536 QIESAAFRKLR 546


>gi|78043932|ref|YP_360874.1| sporulation sigma factor SigG [Carboxydothermus hydrogenoformans
           Z-2901]
 gi|77996047|gb|ABB14946.1| RNA polymerase sigma-G factor [Carboxydothermus hydrogenoformans
           Z-2901]
          Length = 257

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 56/261 (21%), Positives = 118/261 (45%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L  QE   L  + +E GD+ A  +L++ +LRLV+ I   +   G  + ++   G 
Sbjct: 14  SKLPVLTNQEMKKLFLKVKE-GDMEARQKLISGNLRLVLSIIQRFTNRGEYVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD E+  + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 73  IGLIKAIDNFDLEQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDVAYKALQVR 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
            +L        +   V  IA++L V + EV+     +    SL   I     +     D 
Sbjct: 130 DNL---VGRFSREPTVSEIAQELKVPQEEVVFALDAIQDPVSLFEPIYQDGGDPIFVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  + +     L        +   L  ++  LN RER I + R       T   ++ E  
Sbjct: 187 IKDEKNTDHNWL--------QGIALKEALERLNERERLILKLRFY--EGKTQMEVAEEIG 236

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A   +++ +
Sbjct: 237 ISQAQVSRLEKAALNHLRKFV 257


>gi|149923127|ref|ZP_01911542.1| RNA polymerase sigma-C factor [Plesiocystis pacifica SIR-1]
 gi|149816035|gb|EDM75549.1| RNA polymerase sigma-C factor [Plesiocystis pacifica SIR-1]
          Length = 304

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 96/281 (34%), Positives = 151/281 (53%), Gaps = 15/281 (5%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           S + + +    RY+  +     ++ + E  LA+ Y E GD  A  RL+ +HLR VV IA 
Sbjct: 12  SRVSSRDRDFERYVAHVSSFEEIDGERERELARAYHE-GDRLAGQRLIEAHLRDVVAIAR 70

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           GYR YG P++E+V+EGN+GL++A++ FDPERG R  TY  +W++A +  ++ RSWSLV++
Sbjct: 71  GYRNYGHPMAELVAEGNVGLVRALESFDPERGLRFMTYGRYWVRARILAHVQRSWSLVRV 130

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DES 185
           G+++   RLF+ L R +G  QA         +  A+A+    SE+ V +M  R+ G D S
Sbjct: 131 GSSSAHTRLFYGLHRARGRFQATAGERDGAAERAALAEYFGCSEAHVEAMAARIDGRDLS 190

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L+                 +      E  + E+E  +  R  +   +  L+PRER I   
Sbjct: 191 LD-----------HPSSAALVSESTVEATIFEREVGELVRERIAAVIRELDPRERVILRR 239

Query: 246 RRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R L E  +P +L  +  E  +SRER RQ+E R   K++  +
Sbjct: 240 RLLDESGSPPSLVEVGRELGLSRERTRQLEQRVKTKLRRRL 280


>gi|78062752|ref|YP_372660.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia sp. 383]
 gi|77970637|gb|ABB12016.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia sp. 383]
          Length = 511

 Score =  181 bits (460), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 52/230 (22%), Positives = 102/230 (44%), Gaps = 13/230 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   ++ ++LRLV+ IA  Y   G+ + ++V +G++GLM+A++KF+  RGF+ +TY+ 
Sbjct: 272 RDATRAMLEANLRLVLSIARKYMNRGVDLPDLVQDGSLGLMRAIEKFEYRRGFKFSTYAT 331

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      +++             +R++ H         +      +A + 
Sbjct: 332 WWIRQAITRAVADRARTIRVPVHV-----GDQYQRVQRHALRFRQRTGRRATPAELAAET 386

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++ ++    A   SL+A +  +D    +         D       E+      R 
Sbjct: 387 GLDEDKLRAVLALPAEPVSLDAPLPDADTGLVELI------EDQASASPFEQLADTRMRE 440

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEA 274
            +   +  + P E  +   R       P T + ++ +  +SRERVRQIE 
Sbjct: 441 CVRSLLRSVTPAEADVLRRRFGLGGTEPDTYDAIAQDAGMSRERVRQIEK 490


>gi|300870272|ref|YP_003785143.1| DNA directed RNA polymerase sigma subunit [Brachyspira pilosicoli
           95/1000]
 gi|300687971|gb|ADK30642.1| DNA directed RNA polymerase sigma subunit [Brachyspira pilosicoli
           95/1000]
          Length = 284

 Score =  181 bits (459), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 65/267 (24%), Positives = 126/267 (47%), Gaps = 11/267 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            +S Y  + ++  +L ++EE  L +R ++ GD  A  +L+ S+LR V+ IA  Y+  GL 
Sbjct: 15  NISLYFADAKREKLLTREEEIELTQRLKK-GDSQARAKLIRSNLRFVISIAKQYKNSGLL 73

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++ EGN+GL+ A  +FDP++G+   +Y+++WI+ ++   I     L+++        
Sbjct: 74  LEDLIGEGNLGLIIATDRFDPDKGYHFISYAVYWIRQSILRAINEKSRLIRLPLNKA--- 130

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
              +L  L+  +            V  +A  L     E+ ++        SL     + D
Sbjct: 131 --MDLVDLERAVHQCYYKTGHMPDVEDLAAILKKEPREIRNIMSMNNEYVSLEK-DFNMD 187

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE-NPV 253
               +  D +    D   + + +    K     L  +M  L+  E+ I  AR   +    
Sbjct: 188 GVKDRLADVV---EDKNSKTVEDILSDKELTEELKIAMEELSDIEKEIINARYGLDQEKK 244

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKV 280
           TL+ +  ++  ++ER+RQIE +A KK+
Sbjct: 245 TLKEVGEKYSFTKERIRQIEKKALKKM 271


>gi|162449128|ref|YP_001611495.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
 gi|161159710|emb|CAN91015.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
          Length = 275

 Score =  181 bits (459), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 92/274 (33%), Positives = 148/274 (54%), Gaps = 19/274 (6%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
             S Y  E+     L  + E  LA R+R  GD  A  RL+ + L  V+ IA+ YR +GLP
Sbjct: 9   AFSAYRTELANYATLSPEAERELALRWR-AGDRDAGRRLIEACLPFVMTIALEYRRWGLP 67

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++V EGNIGL++A ++FDP+RG RLATY+ +WI+A ++E++ R + +V++G++ +++R
Sbjct: 68  MEDIVQEGNIGLLKAAERFDPDRGCRLATYAAYWIRAEIREHVARGYRIVRLGSSKSERR 127

Query: 135 LFFNLRRLKGHLQAITDN--NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                R+      A+      L  E+   +   L             +A D SL     S
Sbjct: 128 ALRIYRKTHEKDPAVLAELSGLSEERAAELLPLL-------------MARDVSLE---RS 171

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
             ++     + L       E    + +ER      L + ++ L+PRER I   R L ++P
Sbjct: 172 PTEDGIAPVERLASSAHTPEDEACDADERAQLSRALLQVVNELSPRERSIMNQRWLTDSP 231

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           VTLE L ++F VS+ERVRQIE RA K+++  I++
Sbjct: 232 VTLEQLGADFGVSKERVRQIEERAKKRMRARIEE 265


>gi|94502401|ref|ZP_01308854.1| RNA polymerase sigma factor rpoD [Candidatus Sulcia muelleri str.
           Hc (Homalodisca coagulata)]
 gi|94451042|gb|EAT14014.1| RNA polymerase sigma factor rpoD [Candidatus Sulcia muelleri str.
           Hc (Homalodisca coagulata)]
          Length = 341

 Score =  181 bits (459), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 78/329 (23%), Positives = 144/329 (43%), Gaps = 58/329 (17%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR---------------------------- 42
           +  + L +++ EI  IP+L ++EE+  AK  R                            
Sbjct: 19  SESLSLDKFLLEISNIPLLGQEEEFFWAKLARVGYIYNSEIESILKKFKIFKKLKKLNKL 78

Query: 43  -------------------EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
                              +     A   LV ++LR V+ IA  Y+  GL +S++++EGN
Sbjct: 79  KKLKKIKKLTAVLIKKFDKKGIKKYALDNLVKANLRFVISIAKQYQNQGLSLSDLINEGN 138

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
            GL++ + +FD  +GF+  +Y +WWI+ ++ + I      V+  T  N+   +  + +  
Sbjct: 139 FGLIKGINRFDERKGFKCISYCVWWIRQSILQAISDKARCVRYPT--NKLAFYNKVNKTY 196

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L+        P  +  I+  LNVSE +V           SL+A +   + ++S   D 
Sbjct: 197 SKLEQKLKM---PPSIKYISDYLNVSEKDVEEALINSIKHTSLDAPL--GEGDNSNLYDV 251

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-PVTLENLSSEF 262
           +  D   +    +EKE  +    +L   +  L+ RE +I           + LE ++   
Sbjct: 252 IKIDESPKTDHSLEKESLQQDIKIL---LETLSERESQIITLHYGLGCFSMNLEKIAYLL 308

Query: 263 EVSRERVRQIEARAFKKVQESIQKQVELS 291
           +++RER RQIE  A K++++S +K++ LS
Sbjct: 309 KLTRERCRQIEMHAIKRLKKSSRKEILLS 337


>gi|154485093|ref|ZP_02027541.1| hypothetical protein EUBVEN_02816 [Eubacterium ventriosum ATCC
           27560]
 gi|149734046|gb|EDM50165.1| hypothetical protein EUBVEN_02816 [Eubacterium ventriosum ATCC
           27560]
          Length = 258

 Score =  181 bits (459), Expect = 1e-43,   Method: Composition-based stats.
 Identities = 54/262 (20%), Positives = 115/262 (43%), Gaps = 17/262 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L + E+  L K  ++ G+  A  + +  +LRLV+ I   +      + ++   G 
Sbjct: 14  SKLPLLTEDEKKELFKEIKK-GNEVAREKYIRGNLRLVLSILQRFSNSNENVDDLFQIGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++AV  FD     + +TY++  I   ++ Y+  +   +++  +           +  
Sbjct: 73  IGLIKAVDNFDDTLNVKFSTYAVPMISGELKRYLRDNA-AIRVSRSIKDIAYKAIYCK-- 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
              + I     +   VV IAK++ V   +V+     +    SL   +     ++    D 
Sbjct: 130 ---ENIIKTTHREPTVVEIAKEIGVEPEDVVYALDAIQSPVSLYDPVYDQGGDTLYVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    +        KEE+     +L  ++  L+ RER+I + R    N  T   ++ E  
Sbjct: 187 ISDKKN--------KEEKWVENIVLNEALKGLSERERKIIDMRFF--NGKTQMEIADEIG 236

Query: 264 VSRERVRQIEARAFKKVQESIQ 285
           +S+ +V ++E  A K +++ ++
Sbjct: 237 ISQAQVSRLEKNALKAMKKYME 258


>gi|224068757|ref|XP_002326192.1| predicted protein [Populus trichocarpa]
 gi|222833385|gb|EEE71862.1| predicted protein [Populus trichocarpa]
          Length = 535

 Score =  181 bits (459), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 56/247 (22%), Positives = 124/247 (50%), Gaps = 12/247 (4%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           + + H    +  +L+ ++LR+VV IA  Y+  GL + +++ EG +GLM++++KF P+ G 
Sbjct: 286 KLQLHSGNRSREKLINANLRMVVHIAKRYQNRGLGLQDLLQEGTVGLMKSIEKFKPQAGC 345

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           R ATY+ WWI+  + + I +    +++      + ++  L ++    ++           
Sbjct: 346 RFATYAYWWIRQTITKAIFQHSRTIRLP-----ENVYGLLGKVMEAKRSYIQEGNHQPTA 400

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IA+++ ++  ++  + C      S+   + S      Q   +     D + ++     
Sbjct: 401 EEIARRVGIAIDKLEKLLCFTRTPLSMQQTVWSD-----QNTTFQEITADTEIEIPDMSV 455

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAF 277
            ++  R  +   +++L+ +ERRI   R   E+    +L  + + F +S+ERVRQ+E+RA 
Sbjct: 456 AKQLMRKHIRGLLNILSLKERRIIRLRFGIEDGKQKSLSEIGNVFGLSKERVRQLESRAL 515

Query: 278 KKVQESI 284
            K+++ +
Sbjct: 516 YKLKQCV 522


>gi|125543279|gb|EAY89418.1| hypothetical protein OsI_10924 [Oryza sativa Indica Group]
          Length = 540

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 66/251 (26%), Positives = 119/251 (47%), Gaps = 15/251 (5%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E  L KR   +  +S  + +V S++RLV+ IA  + G G+  S+++ EG  GL++  +K
Sbjct: 285 DENTLRKRL--NYGISCKNTMVKSNVRLVISIAREFEGPGMEFSDLIQEGIQGLVRGAEK 342

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +GFR +TYS WWIK A+++ +L    ++++     +        R+K   + +   
Sbjct: 343 FDASKGFRFSTYSHWWIKQAIRKSVLEQTQIIRLPAHMAEAS-----SRVKECRRRLRRQ 397

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA    +    V +         SL + +  +D        +     D   
Sbjct: 398 LKRLPTNEEIASDTGMPLRRVEAAMSLPKYTVSLTSKVGCTD------MTYQEITPDTST 451

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +   E   R   +  + R++  L+PRER++   R   ++    TL ++     VSRER+R
Sbjct: 452 ETAEEMLHRWLMKEDVDRALDGLSPRERQVIRYRFGMDDGRLRTLHDIGRLMGVSRERIR 511

Query: 271 QIEARAFKKVQ 281
           QIE  AF+K++
Sbjct: 512 QIELVAFRKLR 522


>gi|149917806|ref|ZP_01906301.1| sigma 70 (RpoD) [Plesiocystis pacifica SIR-1]
 gi|149821326|gb|EDM80728.1| sigma 70 (RpoD) [Plesiocystis pacifica SIR-1]
          Length = 431

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 69/256 (26%), Positives = 123/256 (48%), Gaps = 13/256 (5%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           EYV   R       SA ++ V ++LRLVV IA  +    +P+ +++ EGNIGLM+AV +F
Sbjct: 182 EYVANVRRSSRKLRSAKNKFVKANLRLVVSIARRFNHGRMPLQDLIQEGNIGLMKAVDRF 241

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D  +GFR +TY  WWI+ A+   I      V++         +  + + +  L+A     
Sbjct: 242 DYRKGFRFSTYGSWWIRHAISRAIADKGRQVRLPVHM--IDAYHKVNKARRELEAKLGRE 299

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              E    +A+   ++ +++  M   L     SL+  +  SD +  +  D+L    D   
Sbjct: 300 PTRE---ELAQHTGIALAKIERMGTMLVDNPISLDKPV--SDADGRKMGDFL---EDENA 351

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVR 270
           +   E  E       + R +S L P E  I   R     +  +TL+ +  ++ +SRER+R
Sbjct: 352 EDPGEGLEADALNEQVKRLVSKLRPIEADIIRKRFGLIDDEELTLKEIGGQYSLSRERIR 411

Query: 271 QIEARAFKKVQESIQK 286
           Q++ +A  K++  +++
Sbjct: 412 QLQEQALGKIRRELKR 427


>gi|186687052|ref|YP_001870195.1| RpoD family RNA polymerase sigma factor [Nostoc punctiforme PCC
           73102]
 gi|186469355|gb|ACC85154.1| RNA polymerase, sigma 70 subunit, RpoD family [Nostoc punctiforme
           PCC 73102]
          Length = 316

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 65/315 (20%), Positives = 132/315 (41%), Gaps = 52/315 (16%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------------ 43
           ++      +  Y+ EI + P+L   +E   A+  ++                        
Sbjct: 1   MLSPTTDSVRSYLKEIGRYPLLTPDQEITNARLVQQMMAVEEQRSNLALQLNRQPTDLEL 60

Query: 44  ---------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
                               A  ++VT++LRLVV +A  Y+ Y L   +++ EG +GL +
Sbjct: 61  ATSLGQNEAELQSVIQQGQKAKQKMVTANLRLVVSVAKKYQNYSLDFLDLLQEGALGLQR 120

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
            ++KFDP +G++L+TY  WWI  ++   +      +++    N+K     L +++   Q 
Sbjct: 121 GIEKFDPNKGYKLSTYVYWWITQSITRAVADKSRTIRLPIHINEK-----LNKIRRVQQQ 175

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           ++ +  +P  V  IA+ LN+S +++           SL   +   D+  S+  D L  D 
Sbjct: 176 LSQSLGRPPVVAEIAESLNLSPNQIREYLQISKPLVSLEKRV--GDEGESELADILPMDG 233

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSR 266
              ++ +  +  +++   +L        PR+R +   R        +TL  ++    +SR
Sbjct: 234 ISLDEQITLESLQQDLAKLLALL----KPRQREVLTLRFGLSDNQQLTLSQVAKRLNLSR 289

Query: 267 ERVRQIEARAFKKVQ 281
           E +R+ E  A   ++
Sbjct: 290 ETIRKTEHLALSILR 304


>gi|269926941|ref|YP_003323564.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
 gi|269790601|gb|ACZ42742.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thermobaculum
           terrenum ATCC BAA-798]
          Length = 596

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 55/239 (23%), Positives = 111/239 (46%), Gaps = 12/239 (5%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           ++   GD+ A  RL+ ++LRLVV IA  Y G G+ + +++ EGNIGL++AV+KF  ++G+
Sbjct: 247 KWIAEGDI-ARKRLIEANLRLVVSIAKKYTGRGITLLDLIQEGNIGLIKAVEKFRHQKGY 305

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWI+ A+   I      ++I     +      + ++    + +T    +    
Sbjct: 306 KFSTYATWWIRQAITRAIADQARTIRIPVHMGE-----AINKIAQARRRLTQELGREPTE 360

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IA  L +   ++  +        SL   +   ++  +   D++    D +    ++  
Sbjct: 361 QEIANYLGIPVEKIREVQKISQEPISLENPV--GEEEDTSLGDFI---QDHKAPAPMDAA 415

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAF 277
            +   R+ + + +  L+ RER +   R   +  P     ++    VS  +V Q E+R  
Sbjct: 416 SQSLLRDQIDQVLKHLSERERGVLLMRFGLDCEPRPYREVAHILAVSPNQVMQAESRVL 474



 Score = 76.4 bits (187), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 39/163 (23%), Positives = 70/163 (42%), Gaps = 10/163 (6%)

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL----AGDESLNALINSSDKN 196
           R +G L      + +P     +A  L VS ++V+    R+    A   S        D+ 
Sbjct: 434 RERGVLLMRFGLDCEPRPYREVAHILAVSPNQVMQAESRVLDMVAARLSPEDYQMLLDRF 493

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNR---RNMLTRSMSVLNPRERRIFEARRLQE--N 251
               +  +  +    +  L + + R+     R  L   M  +   ER +   R   +   
Sbjct: 494 GHLDRSPMSEESFRLKYKLTQTQLREIDQKLREALASVMLHVPAPERDMMRFRFGLDIGQ 553

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI-QKQVELSSS 293
           P TLE +   F V+RER+RQIE++A +K++  + ++Q+E   S
Sbjct: 554 PRTLEEVGRAFGVTRERIRQIESKALRKLRRDVFRRQLEDLLS 596



 Score = 35.9 bits (82), Expect = 7.4,   Method: Composition-based stats.
 Identities = 9/31 (29%), Positives = 18/31 (58%)

Query: 10 VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR 40
           N +  +  Y+ EI K  +L +++E  LA++
Sbjct: 69 TNLDDPIRLYLREIGKENLLSQEQEIELARK 99


>gi|258648463|ref|ZP_05735932.1| RNA polymerase sigma factor [Prevotella tannerae ATCC 51259]
 gi|260851219|gb|EEX71088.1| RNA polymerase sigma factor [Prevotella tannerae ATCC 51259]
          Length = 283

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 75/281 (26%), Positives = 139/281 (49%), Gaps = 12/281 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           +I       L RY+ EI + P +  +EE  L +R + +GD +A  RLV ++LR VV +A 
Sbjct: 10  AITNRNNESLERYLSEISREPRITVEEEVELGRRAK-NGDEAAVERLVRANLRFVVSVAK 68

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y+G G+ + ++++EGN+GL+QA  +FD  RGF+  +Y++WWI+ ++   I     L+++
Sbjct: 69  QYQGQGISLIDLINEGNLGLIQAAHRFDDTRGFKFISYAVWWIRQSILLAITEKSRLIRL 128

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
               NQ      + R         +   +P  +  I +++ V+E  V           S+
Sbjct: 129 P--QNQMSSIQKILRFYNQYMQDYE---RPPSIEEICEQMQVTEERVRLALQLQNKPLSI 183

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           +A +  ++  +    + L  D        + KE     R  + R +++L P ER + E  
Sbjct: 184 DAPL--TEDEARTLSERLRSDKGSSADGPLLKEAE---RWKVERMLNLLPPLERSVIEYY 238

Query: 247 -RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +   ++LE + +   +SRERVRQI+ +A   ++   + 
Sbjct: 239 LGFKGQGISLEEIGNRIGLSRERVRQIKVKAIMILRRHHES 279


>gi|125972969|ref|YP_001036879.1| sporulation sigma factor SigG [Clostridium thermocellum ATCC 27405]
 gi|256004766|ref|ZP_05429741.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium thermocellum
           DSM 2360]
 gi|281417180|ref|ZP_06248200.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           thermocellum JW20]
 gi|125713194|gb|ABN51686.1| RNA polymerase, sigma subunit, RpsG/SigG [Clostridium thermocellum
           ATCC 27405]
 gi|255991216|gb|EEU01323.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium thermocellum
           DSM 2360]
 gi|281408582|gb|EFB38840.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           thermocellum JW20]
 gi|316940795|gb|ADU74829.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium thermocellum
           DSM 1313]
          Length = 257

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 55/261 (21%), Positives = 119/261 (45%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L  +++  L +R  + GD SA    +  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLTNEQKKELFERMHK-GDTSAREEFIKGNLRLVLSVIQRFNNRGEYVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   + K
Sbjct: 73  IGLIKAIDNFDVTQNVKFSTYAVPMIIGEIRRYLRDNN-AIRVSRSL--RDIAYKALQAK 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
              + +T+ N K   +  IAK+L + + EV+     +    SL   +     ++    D 
Sbjct: 130 ---EKLTNQNSKEPTIEEIAKELGLPKEEVVFALDAIQDPISLFESVYHDGGDAIYVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  + +  E  L            L+ +M  LN RE+ I   R    +  T   ++ E  
Sbjct: 187 VKDEKNNDENWLEGIA--------LSEAMRKLNDREKLILNLRFF--DGRTQMEVAEEIG 236

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A   +++ I
Sbjct: 237 ISQAQVSRLEKTALMHMRKYI 257


>gi|62734062|gb|AAX96171.1| Sigma-70 region 3, putative [Oryza sativa Japonica Group]
 gi|125589330|gb|EAZ29680.1| hypothetical protein OsJ_13741 [Oryza sativa Japonica Group]
          Length = 563

 Score =  180 bits (458), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 69/251 (27%), Positives = 124/251 (49%), Gaps = 15/251 (5%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E  L KR  +HG +   +R+VTS++RLV+ IA  + G G+ + +++ EG  GL++  +K
Sbjct: 309 DERTLRKRL-DHG-IYCKNRMVTSNVRLVISIAREFEGPGMELYDLIQEGMQGLIRGAEK 366

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +GFR +TYS WWIK AM++ +     + ++     +        R+K  ++ +   
Sbjct: 367 FDASKGFRFSTYSHWWIKQAMRKSVSEQSQIFRLPAHMVEASY-----RVKECIKRLRRK 421

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA    +    V +         SL++ I S+D        +     D   
Sbjct: 422 LKRRPTNEEIAADTGMPIKRVEAAVNLPKYSVSLDSKIGSTD------MTYQEVTADPTA 475

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +   E   R + +  + +++  L  RER++   R   E+    TL+ + +   VSRER+R
Sbjct: 476 ETAEEMLNRLSMKRDVHKALDTLTTRERQVVTLRFGLEDGRIRTLQEIGNTMGVSRERIR 535

Query: 271 QIEARAFKKVQ 281
           QIE+ AF+K++
Sbjct: 536 QIESAAFRKLR 546


>gi|148242910|ref|YP_001228067.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp.
           RCC307]
 gi|147851220|emb|CAK28714.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. RCC307]
          Length = 293

 Score =  180 bits (457), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 73/296 (24%), Positives = 131/296 (44%), Gaps = 23/296 (7%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD----------------LSAAH 51
           ++          ++ I +  +L  +EE  L ++ R   D                L A  
Sbjct: 1   MVKGSNDCFGWMLNGIGRHALLSPEEEVSLGRQVRAWQDHPGGPGQAPAAVQKRGLRARG 60

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RLV ++LRLVV +A      GL + ++V EG+IGL +A +K+DP  G+R +TY+ WWIK 
Sbjct: 61  RLVQANLRLVVHLAKKQHLRGLAMEDLVQEGSIGLQRAAEKYDPSTGYRFSTYAYWWIKQ 120

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           A+   I      +++    +++     LR  +  L        +PE++   A    + + 
Sbjct: 121 ALHRAIQLQTPALRLPCRVSER--LGRLRSTRQRLSQELGRQPRPEELAE-AMGERIDQL 177

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           + +     ++   SL+     SD +     D L  D       L +    +    +L+ +
Sbjct: 178 QELERAQVISRGCSLDTP-MGSDPDHGSLVDLLEDDRTSPMDQLEQALRSEQLAELLSSA 236

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              L+ RE  + +AR   E  +  + L+  F +SRER RQ+E  A +K++   + Q
Sbjct: 237 --GLSEREATVVQARH-SEEHIPYQQLADRFGISRERTRQLEHNALRKLRHCAEAQ 289


>gi|115452175|ref|NP_001049688.1| Os03g0271100 [Oryza sativa Japonica Group]
 gi|29893614|gb|AAP06868.1| unknown protein [Oryza sativa Japonica Group]
 gi|32351880|dbj|BAC78529.1| plastid sigma factor 2B [Oryza sativa Japonica Group]
 gi|108707414|gb|ABF95209.1| Sigma-70 region 3 family protein, expressed [Oryza sativa Japonica
           Group]
 gi|113548159|dbj|BAF11602.1| Os03g0271100 [Oryza sativa Japonica Group]
 gi|215704451|dbj|BAG93885.1| unnamed protein product [Oryza sativa Japonica Group]
 gi|215765869|dbj|BAG87566.1| unnamed protein product [Oryza sativa Japonica Group]
          Length = 540

 Score =  180 bits (457), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 66/251 (26%), Positives = 119/251 (47%), Gaps = 15/251 (5%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E  L KR   +  +S  + +V S++RLV+ IA  + G G+  S+++ EG  GL++  +K
Sbjct: 285 DENTLRKRL--NYGISCKNTMVKSNVRLVISIAREFEGPGMEFSDLIQEGIQGLVRGAEK 342

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +GFR +TYS WWIK A+++ +L    ++++     +        R+K   + +   
Sbjct: 343 FDASKGFRFSTYSHWWIKQAIRKSVLEQTQIIRLPAHMAEAS-----SRVKECRRRLRRQ 397

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA    +    V +         SL + +  +D        +     D   
Sbjct: 398 LKRLPTNEEIASDTGMPLRRVEAAMSLPKYTVSLTSKVGCTD------MTYQEITPDTST 451

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +   E   R   +  + R++  L+PRER++   R   ++    TL ++     VSRER+R
Sbjct: 452 ETAEEMLHRWLMKEDVDRALDGLSPRERQVIRYRFGMDDGRLRTLHDIGRLMGVSRERIR 511

Query: 271 QIEARAFKKVQ 281
           QIE  AF+K++
Sbjct: 512 QIELVAFRKLR 522


>gi|254478776|ref|ZP_05092144.1| RNA polymerase sigma-G factor [Carboxydibrachium pacificum DSM
           12653]
 gi|214035288|gb|EEB75994.1| RNA polymerase sigma-G factor [Carboxydibrachium pacificum DSM
           12653]
          Length = 258

 Score =  180 bits (457), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 55/261 (21%), Positives = 116/261 (44%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+  ++  L    + +GD  A    + S+LRLV+ +   +   G  + ++   G 
Sbjct: 15  SKLPVLKPSKQRELLITMK-NGDKKAREEFINSNLRLVLSVIQRFNNRGESVDDLFQVGC 73

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD ++  + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 74  IGLIKAIDNFDLDQNVKFSTYAVPMIIGEIRRYLRDNT-PIRVSRSL--RDIAYKALQVR 130

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L      N K   V  IAK+L++   EV+     +    SL   I     ++    D 
Sbjct: 131 DKL---VSENSKEPTVGEIAKELDLPSEEVVMALDAIQEPVSLFEPIYHDGGDAIYVMDQ 187

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  D +  E  L         +  L  ++  LN RE+ I   R       T   ++ E  
Sbjct: 188 VSDDKNVDEVWLE--------KIALKEALEKLNEREKMILTMRFF--EGKTQMEVAKEIG 237

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A   +++ I
Sbjct: 238 ISQAQVSRLEKAALNHMRKYI 258


>gi|134293382|ref|YP_001117118.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia vietnamiensis
           G4]
 gi|134136539|gb|ABO57653.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia vietnamiensis
           G4]
          Length = 518

 Score =  180 bits (457), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 52/239 (21%), Positives = 108/239 (45%), Gaps = 13/239 (5%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
             ++ ++LRLV+ IA  Y   G+ + ++V +G +GLM+A++KF+  RGF+ +TY+ WWI+
Sbjct: 283 RAMLEANLRLVLSIARKYVNRGVDLPDLVQDGCLGLMRAIEKFEYRRGFKFSTYATWWIR 342

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            A+   +      +++      +      +R++ H       + +      +A    ++E
Sbjct: 343 QAVARAVADRSRTIRVPVHVGDQS-----QRVQRHALRFRQRHGRRATPAELAADTGLAE 397

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            ++ ++    A   SL+  +  ++              D       E+      R  ++ 
Sbjct: 398 DKLRALLALPAEPLSLDTPLPDAETGLVDLI------EDQTSASPFERLANTRMRECVSS 451

Query: 231 SMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +  + P E  +   R       P T + ++ +  +SRERVRQIE RA   ++ + Q +
Sbjct: 452 LLRSVTPTEADVLRRRFGLGGAEPDTYDAIAQDAGMSRERVRQIEKRALATLRTAAQAE 510


>gi|302851352|ref|XP_002957200.1| hypothetical protein VOLCADRAFT_109400 [Volvox carteri f.
           nagariensis]
 gi|300257450|gb|EFJ41698.1| hypothetical protein VOLCADRAFT_109400 [Volvox carteri f.
           nagariensis]
          Length = 733

 Score =  180 bits (457), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 67/249 (26%), Positives = 117/249 (46%), Gaps = 15/249 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           V+A   R    L A   L+ S+ RLV+ +   Y G G+ + ++VSEG  GL++ V+ +D 
Sbjct: 461 VMAYNMRYDAGLKAKELLLKSNYRLVMTVCKRYIGKGMHLQDLVSEGVKGLLRGVEMYDA 520

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            RGFR  TY+ WWI+ A+   +  +   V++        +   L +LK    A+     +
Sbjct: 521 SRGFRFGTYAHWWIRQAVSRSMAETGRAVRLPVH-----MIEQLTKLKNATAALAMELNR 575

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
              V  +A+ + +  S V  +        S+ + I   D          + D    E++ 
Sbjct: 576 EPSVEEMAEAVGLPPSRVELLLDAARAASSMESAIGGDDG-------LTIKDAVQDERMA 628

Query: 216 IEKEERKN-RRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQI 272
            ++    +  R  +   +  L+ RE  +   R   E+ V  TLE++ S   V+RER+RQ+
Sbjct: 629 ADEAFGSDSMRADVESMLEGLSDREACVLRLRFGLEDGVEWTLEDIGSRLGVTRERIRQL 688

Query: 273 EARAFKKVQ 281
           EA+A +K+Q
Sbjct: 689 EAKALRKLQ 697


>gi|262197834|ref|YP_003269043.1| RNA polymerase, sigma 32 subunit, RpoH [Haliangium ochraceum DSM
           14365]
 gi|262081181|gb|ACY17150.1| RNA polymerase, sigma 32 subunit, RpoH [Haliangium ochraceum DSM
           14365]
          Length = 436

 Score =  180 bits (457), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 54/241 (22%), Positives = 112/241 (46%), Gaps = 9/241 (3%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            +  V ++LRLVV +A  Y   G+P+++++ EGN+GLM AV +FD  RG R +TY+ WWI
Sbjct: 203 RNEFVHANLRLVVTMARRYDRGGMPLADLIQEGNLGLMHAVSRFDYRRGLRFSTYACWWI 262

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + A+   +      V+I     + +    L +++  L         P ++   A+     
Sbjct: 263 RHAIGRALADKSRAVRIPVHMLEAQ--QQLAKVQAKLIGELGREPTPSELAKAAQVPLAK 320

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
            +++      +    SL+  +   D    +    ++ D   ++   ++    +   + + 
Sbjct: 321 LNQMHRYL--MGQPMSLDRPLYDDDD---RAFGDMLADPLSEDSSPVDDLTTQTLTSRVE 375

Query: 230 RSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             +  L P E  +   R     +   T   +  ++++SRER+RQI+  A  K++ ++++ 
Sbjct: 376 TLLDHLTPIEADVLRQRFGLMDDEERTFREIGDQYDLSRERIRQIQNAALGKLRRALERA 435

Query: 288 V 288
           V
Sbjct: 436 V 436


>gi|172063054|ref|YP_001810705.1| RpoD family RNA polymerase sigma factor [Burkholderia ambifaria
           MC40-6]
 gi|171995571|gb|ACB66489.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           ambifaria MC40-6]
          Length = 520

 Score =  180 bits (457), Expect = 2e-43,   Method: Composition-based stats.
 Identities = 52/239 (21%), Positives = 106/239 (44%), Gaps = 13/239 (5%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
             ++ ++LRLV+ IA  Y   G+ + ++V +G +GLM+A++KF+  RGF+ +TY+ WWI+
Sbjct: 285 RAMLEANLRLVLSIARKYMNRGVDLPDLVQDGCLGLMRAIEKFEYRRGFKFSTYATWWIR 344

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            A+   +      +++             +R++ H         +      +A +  + E
Sbjct: 345 QAVARAVADRSRTIRVPVHV-----GDQYQRVQRHALRFRQRTGRRATPAELAAETGLPE 399

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            ++ ++    A   SL+  +  ++              D       E+      R  +T 
Sbjct: 400 GKLRAVLALPAEPLSLDTPLPDAETGLVDLI------EDQASASPFERLADTRMRECVTS 453

Query: 231 SMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +  + P E  +   R       P T + ++ +  +SRERVRQIE RA   ++ + + +
Sbjct: 454 LLRSVTPAEADVLRRRFGLGGAEPDTYDAIAQDAGMSRERVRQIEKRALATLRTAAEAE 512


>gi|159470255|ref|XP_001693275.1| chloroplast RNA polymerase sigma factor, c [Chlamydomonas
           reinhardtii]
 gi|42742499|gb|AAM88387.2|AF525691_1 RNA polymerase sigma factor [Chlamydomonas reinhardtii]
 gi|47076042|emb|CAF25319.1| sigma-like transcription factor [Chlamydomonas reinhardtii]
 gi|158277533|gb|EDP03301.1| chloroplast RNA polymerase sigma factor, c [Chlamydomonas
           reinhardtii]
          Length = 752

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 62/244 (25%), Positives = 112/244 (45%), Gaps = 12/244 (4%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           + R    L A   L+ S+ +LV+ +   + G G  I ++VSEG  GL++ V+K+D  +GF
Sbjct: 481 KLRYDAGLKAKELLLKSNYKLVMTVCKSFVGKGPHIQDLVSEGVKGLLKGVEKYDATKGF 540

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           R  TY+ WWI+ A+   +  +   V++        +   L RLK     +     +   +
Sbjct: 541 RFGTYAHWWIRQAVSRSLAETGRAVRLPMH-----MIEQLTRLKNLSAKLQTQLAREPTL 595

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +AK   +  + V  +        SL+  I  ++   +  +D +  + +  ++      
Sbjct: 596 PELAKAAGLPVTRVQMLMETARSAASLDTPIGGNELGPT-VKDSVEDEREAADEEFGSDS 654

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAF 277
            R +   ML      L  RE R+   R   ++    TLE +     V+RER+RQIEA+A 
Sbjct: 655 LRNDMEAMLLE----LPEREARVVRLRFGLDDGKEWTLEEIGEALNVTRERIRQIEAKAL 710

Query: 278 KKVQ 281
           +K++
Sbjct: 711 RKLR 714


>gi|323706111|ref|ZP_08117680.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
 gi|323534555|gb|EGB24337.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
          Length = 256

 Score =  180 bits (457), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 57/261 (21%), Positives = 118/261 (45%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+  ++  L  R + +GD SA    +  +LRLV+ +   +   G  + ++   G 
Sbjct: 13  SKLPVLKGAKQKELLLRMK-NGDKSAREEFINGNLRLVLSVIQRFNNRGEYVDDLFQVGC 71

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD  +  + +TY++  I   ++ Y+  + S +++  +   + + +   +++
Sbjct: 72  IGLIKAIDNFDLNQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSL--RDVAYKALQVR 128

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L    + N K   V  IAK+LN+   EV+     +    SL   I     ++    D 
Sbjct: 129 DKL---VNENSKEPTVGDIAKELNIPREEVVFALDAIQDPVSLFEPIYHDGGDAIYVMDQ 185

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  + +  E  L +          L  ++  LN RE+ I   R       T   ++ E  
Sbjct: 186 IGDEKNVDEVWLEQIA--------LKEAIKKLNDREKMILTMRFF--EGKTQMEVAKEIG 235

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A   +++ I
Sbjct: 236 ISQAQVSRLEKSALSHMRKYI 256


>gi|170700559|ref|ZP_02891561.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           ambifaria IOP40-10]
 gi|170134549|gb|EDT02875.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           ambifaria IOP40-10]
          Length = 519

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 52/239 (21%), Positives = 106/239 (44%), Gaps = 13/239 (5%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
             ++ ++LRLV+ IA  Y   G+ + ++V +G +GLM+A++KF+  RGF+ +TY+ WWI+
Sbjct: 284 RAMLEANLRLVLSIARKYMNRGVDLPDLVQDGCLGLMRAIEKFEYRRGFKFSTYATWWIR 343

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            A+   +      +++             +R++ H         +      +A +  + E
Sbjct: 344 QAVARAVADRSRTIRVPVHV-----GDQYQRVQRHALRFRQRTGRRATPAELAAESGLPE 398

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            ++ ++    A   SL+  +  ++              D       E+      R  +T 
Sbjct: 399 GKLRAVLALPAEPLSLDTPLPDAETGLVDLI------EDQASASPFERLADTRMRECVTS 452

Query: 231 SMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +  + P E  +   R       P T + ++ +  +SRERVRQIE RA   ++ + + +
Sbjct: 453 LLRSVTPAEADVLRRRFGLGGAEPDTYDAIAQDAGMSRERVRQIEKRALATLRTAAEAE 511


>gi|15615117|ref|NP_243420.1| sporulation sigma factor SigG [Bacillus halodurans C-125]
 gi|10175174|dbj|BAB06273.1| RNA polymerase sporulation forespore-specific (late) sigma-G factor
           [Bacillus halodurans C-125]
          Length = 261

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 61/263 (23%), Positives = 117/263 (44%), Gaps = 15/263 (5%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+ QE   L  R +  GD SA   LV  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLKNQEMRELFARLQ-SGDTSARETLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+++  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 73  IGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVR 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L        K   V  IAK+L V + +V+     +    SL   I +   +     D 
Sbjct: 130 DQLMGEKQRE-KEPTVQEIAKELGVPKEDVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQ 188

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  D +   Q + E          L  +M  LN RE+ I   R  Q    T   ++ E  
Sbjct: 189 ISDDRNKDVQWVDEIA--------LKEAMVRLNDREKLILNMRFYQG--KTQMEVAEEIG 238

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+ +V ++E  A +++ +  Q 
Sbjct: 239 ISQAQVSRLEKAAIQQMSKHAQS 261


>gi|83720670|ref|YP_440648.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis E264]
 gi|167617444|ref|ZP_02386075.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis Bt4]
 gi|83654495|gb|ABC38558.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis E264]
          Length = 483

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 56/236 (23%), Positives = 118/236 (50%), Gaps = 12/236 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  R+  ++LRLV+ IA  Y   GL +++++ EGN+GL++A++KF+  RGF+ +TY+ W
Sbjct: 242 AATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEYRRGFKFSTYATW 301

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++             RR++     I   +     +  +++   
Sbjct: 302 WIRQAISRAIADRARTIRVPVHV-----GDEARRVRKVADRIERRSGARASLAELSEATG 356

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S   + ++        SLNA +   D + +++ D +    D     L +   +    ++
Sbjct: 357 LSAERLRAVLMLPREPRSLNAPL--GDDDQAEFGDIV---EDASTPSLFDALAQGQMCDV 411

Query: 228 LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +T  +  ++ +E  I   R     + P + E ++++  VSRE++R+IE RA + ++
Sbjct: 412 VTSLLKTMSAQEADILRRRFGIGGDEPWSYEQIAAQAGVSREQIRRIEKRALQTLR 467


>gi|237653675|ref|YP_002889989.1| RNA polymerase sigma factor RpoS [Thauera sp. MZ1T]
 gi|237624922|gb|ACR01612.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Thauera sp. MZ1T]
          Length = 312

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 82/260 (31%), Positives = 138/260 (53%), Gaps = 13/260 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE V+A+R R  GD  A   ++  +LRLVV IA  Y   G+P+ ++
Sbjct: 45  YLNEIGANPLLTAEEELVIARRVR-MGDFDARQTMIERNLRLVVNIAKHYLNRGIPLLDL 103

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EGN+GLM A++KFDPERGFR +TY+ WWI+  ++  I+     +++       +    
Sbjct: 104 VEEGNLGLMHALEKFDPERGFRFSTYATWWIRQNIERAIMNQSRTIRLPVHV--VKELNQ 161

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           + R + H++A  +     EQ   IA +L  +  EV S+        SL+A ++     S 
Sbjct: 162 VLRAQRHIEADCNGESSLEQ---IANRLGKTIEEVRSILALGEHTASLDAPLDI--DPSL 216

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLE 256
              + L  +      + I+  E +    ++   +++LN ++R +   R   +    +TLE
Sbjct: 217 SIGESLADEQHISADLRIQCSEVEQ---LVREWLAILNDKQRMVIRHRYGIDECELLTLE 273

Query: 257 NLSSEFEVSRERVRQIEARA 276
            L+   E++RERVRQI+  A
Sbjct: 274 ELAERLELTRERVRQIQLEA 293


>gi|317121713|ref|YP_004101716.1| RNA polymerase, sigma subunit, RpsG/SigG [Thermaerobacter
           marianensis DSM 12885]
 gi|315591693|gb|ADU50989.1| RNA polymerase, sigma subunit, RpsG/SigG [Thermaerobacter
           marianensis DSM 12885]
          Length = 261

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 58/259 (22%), Positives = 122/259 (47%), Gaps = 17/259 (6%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L  ++  VL +R R+ GD  A  +LV  +LRLV+ +   +   G P+ ++   G IG
Sbjct: 20  LPVLTNEQMRVLFRRMRQ-GDEEARQQLVQGNLRLVLSVIQRFNHRGEPVDDLFQVGCIG 78

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           LM+A+  FD E+  R +TY++  I   ++ Y+  +   +++  +   + + +   +++  
Sbjct: 79  LMKAIDNFDLEQNVRFSTYAVPMIIGEIRRYLRDNT-PIRVSRSL--RDVAYKALQVRD- 134

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
              +T  + +   +  IA++L +   EV+     +    SL   I     +     D + 
Sbjct: 135 --QLTHRHGREPTLEEIARELGLPREEVVHALDAIQDPVSLFEPIYQDGGDPIYVVDQVS 192

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            D    EQ L            +  +M+ L+ RE+ I   R  Q    T   +++E  +S
Sbjct: 193 DDKQRDEQWLETIA--------VREAMARLDEREQLIITKRFYQG--KTQMEVANEIGIS 242

Query: 266 RERVRQIEARAFKKVQESI 284
           + +V ++E  A +++++ +
Sbjct: 243 QAQVSRLEKAALQRMRKYM 261


>gi|167037237|ref|YP_001664815.1| sporulation sigma factor SigG [Thermoanaerobacter pseudethanolicus
           ATCC 33223]
 gi|167040623|ref|YP_001663608.1| sporulation sigma factor SigG [Thermoanaerobacter sp. X514]
 gi|300914664|ref|ZP_07131980.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X561]
 gi|307267689|ref|ZP_07549143.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|307724102|ref|YP_003903853.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter sp. X513]
 gi|320115656|ref|YP_004185815.1| RNA polymerase sigma-G factor [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
 gi|166854863|gb|ABY93272.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Thermoanaerobacter sp. X514]
 gi|166856071|gb|ABY94479.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Thermoanaerobacter pseudethanolicus ATCC 33223]
 gi|300889599|gb|EFK84745.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X561]
 gi|306917291|gb|EFN47611.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|307581163|gb|ADN54562.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X513]
 gi|319928747|gb|ADV79432.1| RNA polymerase sigma-G factor [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
          Length = 256

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 54/261 (20%), Positives = 116/261 (44%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+  ++  L +R + +GD  A    +  +LRLV+ +   +   G  + ++   G 
Sbjct: 13  SKLPVLKPSKQKELLQRMK-NGDKKAREEFINGNLRLVLSVIQRFNNRGEYVDDLFQVGC 71

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 72  IGLIKAIDNFDLNQNVKFSTYAVPMIIGEIRRYLRDNT-PIRVSRSL--RDIAYKALQVR 128

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L      N K   V  IAK+L++   EV+     +    SL   I     ++    D 
Sbjct: 129 DKL---VSENSKEPTVGEIAKELDLPREEVVMALDAIQEPVSLFEPIYHDGGDAIYVMDQ 185

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  D +  E  L         +  L  ++  L+ RE+ I   R       T   ++ E  
Sbjct: 186 VSDDKNMDEVWLE--------KIALKEAIQKLSEREKMILTMRFF--EGKTQMEVAKEIG 235

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A   +++ I
Sbjct: 236 ISQAQVSRLEKAALNHMRKYI 256


>gi|149916650|ref|ZP_01905152.1| RNA polymerase sigma factor rpoD [Plesiocystis pacifica SIR-1]
 gi|149822367|gb|EDM81756.1| RNA polymerase sigma factor rpoD [Plesiocystis pacifica SIR-1]
          Length = 398

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 71/245 (28%), Positives = 122/245 (49%), Gaps = 17/245 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +  V ++LRLVV IA  Y    +P+S+++ EGNIGLM+AV +FD +RG+R +TY+ WW
Sbjct: 160 AKNEFVQANLRLVVTIARRYDQRLMPLSDLIQEGNIGLMKAVDRFDGKRGYRFSTYATWW 219

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ ++   +      V++    +      +++R++   + +     +   V  +AK+  +
Sbjct: 220 IRHSINRALANKGRTVRLPAHVS-----ADIQRIQRATRELETRTGESPSVDELAKETGL 274

Query: 169 SESEVISMN-CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           S++ V  ++   L    SL+A   SSD +S    D L    D     L +  E ++    
Sbjct: 275 SKTRVRKLSKLSLHNPVSLDAP--SSDDDSRGLLDRL---EDSSAPRLADMVELEDMSEH 329

Query: 228 LTRSMSVLNPRERRIFEARRLQE------NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           L  +MS L P E  I   R            +TL  L    ++SRER+RQ++ RA  K++
Sbjct: 330 LREAMSALEPIEADILRRRYGLGVAGEEFEAMTLRELGEMHQLSRERIRQLQQRALNKLR 389

Query: 282 ESIQK 286
               +
Sbjct: 390 REFAR 394


>gi|32351878|dbj|BAC78528.1| plastid sigma factor 2A [Oryza sativa Japonica Group]
          Length = 564

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 69/251 (27%), Positives = 124/251 (49%), Gaps = 15/251 (5%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E  L KR  +HG +   +R+VTS++RLV+ IA  + G G+ + +++ EG  GL++  +K
Sbjct: 309 DERTLRKRL-DHG-IYCKNRMVTSNVRLVISIAREFEGPGMELYDLIQEGMQGLIRGAEK 366

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +GFR +TYS WWIK AM++ +     + ++     +        R+K  ++ +   
Sbjct: 367 FDASKGFRFSTYSHWWIKQAMRKSVSEQSQIFRLPAHMVEASY-----RVKECIKRLRRK 421

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA    +    V +         SL++ I S+D        +     D   
Sbjct: 422 LKRRPTNEEIAADTGMPIKRVEAAVNLPKYSVSLDSKIGSTD------MTYQEVTADPTA 475

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +   E   R + +  + +++  L  RER++   R   E+    TL+ + +   VSRER+R
Sbjct: 476 ETAEEMLNRLSMKRDVHKALDTLTTRERQVVTLRFGLEDGRIRTLQEIGNTMGVSRERIR 535

Query: 271 QIEARAFKKVQ 281
           QIE+ AF+K++
Sbjct: 536 QIESAAFRKLR 546


>gi|312964996|ref|ZP_07779236.1| RNA polymerase sigma factor RpoS [Escherichia coli 2362-75]
 gi|312290552|gb|EFR18432.1| RNA polymerase sigma factor RpoS [Escherichia coli 2362-75]
          Length = 237

 Score =  180 bits (456), Expect = 3e-43,   Method: Composition-based stats.
 Identities = 66/237 (27%), Positives = 119/237 (50%), Gaps = 12/237 (5%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           ++  I+     +++      K L   LR  +     ++           IA++L+    +
Sbjct: 61  IERAIMNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDD 115

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           V  M        S++  +    +     +  L    D +E    +  +  + +  + + +
Sbjct: 116 VSRMLRLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWL 170

Query: 233 SVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             LN ++R +   R   L     TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 171 FELNAKQREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 227


>gi|115358293|ref|YP_775431.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia ambifaria
           AMMD]
 gi|115283581|gb|ABI89097.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia ambifaria
           AMMD]
          Length = 516

 Score =  180 bits (456), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 52/239 (21%), Positives = 106/239 (44%), Gaps = 13/239 (5%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
             ++ ++LRLV+ IA  Y   G+ + ++V +G +GLM+A++KF+  RGF+ +TY+ WWI+
Sbjct: 281 RAMLEANLRLVLSIARKYMNRGVDLPDLVQDGCLGLMRAIEKFEYRRGFKFSTYATWWIR 340

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            A+   +      +++             +R++ H         +      +A +  + E
Sbjct: 341 QAVARAVADRSRTIRVPVHV-----GDQYQRVQRHALRFRQRTGRRATPAELAAESGLPE 395

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            ++ ++    A   SL+  +  ++              D       E+      R  +T 
Sbjct: 396 GKLRAVLALPAEPLSLDTPLPDAETGLVDLI------EDQASASPFERLADTRMRECVTS 449

Query: 231 SMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +  + P E  +   R       P T + ++ +  +SRERVRQIE RA   ++ + + +
Sbjct: 450 LLRSVTPAEADVLRRRFGLGGAEPDTYDAIAQDAGMSRERVRQIEKRALATLRTAAEAE 508


>gi|254253854|ref|ZP_04947171.1| DNA-directed RNA polymerase sigma subunit [Burkholderia dolosa
           AUO158]
 gi|124898499|gb|EAY70342.1| DNA-directed RNA polymerase sigma subunit [Burkholderia dolosa
           AUO158]
          Length = 547

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 53/239 (22%), Positives = 106/239 (44%), Gaps = 13/239 (5%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
             ++ ++LRLV+ IA  Y   G+ + ++V +G +GLM+A++KF+  RGF+ +TY+ WWI+
Sbjct: 312 RAMLEANLRLVLSIARKYMNRGVDLPDLVQDGCVGLMRAIEKFEYRRGFKFSTYATWWIR 371

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            A+   +      +++             +R++ H         +      +A +  + E
Sbjct: 372 QAVARAVADRSRTIRVPVHV-----GDQYQRVQRHALRFRQRTGRRATPAELAAETGLDE 426

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            ++ ++    A   SL+  +  +D         +    D       E+      R  +T 
Sbjct: 427 DKLRAILALPAEPVSLDTPLPDTDTG------LVDTIEDQASASPFERLADARMRECVTS 480

Query: 231 SMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +  + P E  +   R       P T + ++ +  +SRERVRQIE RA   ++   + +
Sbjct: 481 LLRSVTPTEADVLRRRFGLGGAEPDTYDAIAQDAGMSRERVRQIEKRALAALRTVAEAE 539


>gi|256751992|ref|ZP_05492861.1| RNA polymerase, sigma 28 subunit, SigG [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|256749102|gb|EEU62137.1| RNA polymerase, sigma 28 subunit, SigG [Thermoanaerobacter
           ethanolicus CCSD1]
          Length = 256

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 54/261 (20%), Positives = 117/261 (44%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+  ++  L +R + +GD  A    +  +LRLV+ +   +   G  + ++   G 
Sbjct: 13  SKLPVLKPSKQKELLQRMK-NGDKKAREEFINGNLRLVLSVIQRFNNRGEYVDDLFQVGC 71

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD ++  + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 72  IGLIKAIDNFDLDQNVKFSTYAVPMIIGEIRRYLRDNT-PIRVSRSL--RDIAYKALQVR 128

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L      N K   V  IAK+L++   EV+     +    SL   I     ++    D 
Sbjct: 129 DKL---VSENSKEPTVGEIAKELDLPREEVVMALDAIQEPVSLFEPIYHDGGDAIYVMDQ 185

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  D +  E  L         +  L  ++  L+ RE+ I   R       T   ++ E  
Sbjct: 186 VSDDKNMDEVWLE--------KIALKEAIQKLSEREKMILTMRFF--EGKTQMEVAKEIG 235

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A   +++ I
Sbjct: 236 ISQAQVSRLEKAALNHMRKYI 256


>gi|218442621|ref|YP_002380941.1| RNA polymerase, sigma 32 subunit, RpoH [Cyanothece sp. PCC 7424]
 gi|218174979|gb|ACK73711.1| RNA polymerase, sigma 32 subunit, RpoH [Cyanothece sp. PCC 7424]
          Length = 308

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 72/311 (23%), Positives = 128/311 (41%), Gaps = 53/311 (17%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYRE-------------------------------- 43
           L  Y+    +  +L   +E  L ++ ++                                
Sbjct: 11  LDSYLKNFTRYELLNSSQEIDLGQKIQKWQKLKHQFVQFQKKTGKKTSVFDFCSDFQLEE 70

Query: 44  -------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                       A ++LV  +LRLV+ +A  Y G GL   +++ EGNIGL++A + F+P 
Sbjct: 71  AEFYLVYEEGQQAKNQLVQGNLRLVINLAKKYLGRGLSFEDLLQEGNIGLIRAAELFEPS 130

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +G++ +TY+ WWI+  +   I  S   +++        +   L R+K     +     + 
Sbjct: 131 KGYKFSTYAYWWIRQQIIRAINNSARTIRLPVH-----IIARLNRIKKTQHKLAAQLGRT 185

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
             V  IA  L +S  E+           SL+ ++   D+   +    L+ D + Q   L 
Sbjct: 186 PTVQEIATSLQMSAQEIEKYREVAQKTISLSTIV---DEQGRETLQDLIADPNPQPDFL- 241

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
              ER      +   M  L PR + I + R  +E   TLE + +  ++S+ERVRQI  +A
Sbjct: 242 ---ERVFSYEQILEKMETLPPRYQDILKKRIYEEQ--TLEAIGTSTKLSKERVRQIFQKA 296

Query: 277 FKKVQESIQKQ 287
             +++E   K 
Sbjct: 297 LSRLREEFLKD 307


>gi|167579340|ref|ZP_02372214.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis TXDOH]
          Length = 482

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 56/236 (23%), Positives = 118/236 (50%), Gaps = 12/236 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  R+  ++LRLV+ IA  Y   GL +++++ EGN+GL++A++KF+  RGF+ +TY+ W
Sbjct: 241 AATARMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIEKFEYRRGFKFSTYATW 300

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++             RR++     I   +     +  +++   
Sbjct: 301 WIRQAISRAIADRARTIRVPVHV-----GDEARRVRKVADRIERRSGARASLAELSEATG 355

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S   + ++        SLNA +   D + +++ D +    D     L +   +    ++
Sbjct: 356 LSAERLRAVLMLPREPRSLNAPL--GDDDQAEFGDIV---EDASTPSLFDALAQGQMCDV 410

Query: 228 LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +T  +  ++ +E  I   R     + P + E ++++  VSRE++R+IE RA + ++
Sbjct: 411 VTSLLKTMSAQEADILRRRFGIGGDEPWSYEQIAAQAGVSREQIRRIEKRALQTLR 466


>gi|326392135|ref|ZP_08213612.1| RNA polymerase, sigma 28 subunit, SigG [Thermoanaerobacter
           ethanolicus JW 200]
 gi|325991822|gb|EGD50337.1| RNA polymerase, sigma 28 subunit, SigG [Thermoanaerobacter
           ethanolicus JW 200]
          Length = 256

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 54/261 (20%), Positives = 116/261 (44%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+  ++  L +R + +GD  A    +  +LRLV+ +   +   G  + ++   G 
Sbjct: 13  SKLPVLKPSKQKELLQRMK-NGDEKAREEFINGNLRLVLSVIQRFNNRGEYVDDLFQVGC 71

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 72  IGLIKAIDNFDLNQNVKFSTYAVPMIIGEIRRYLRDNT-PIRVSRSL--RDIAYKALQVR 128

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L      N K   V  IAK+L++   EV+     +    SL   I     ++    D 
Sbjct: 129 DKL---VSENSKEPTVGEIAKELDLPREEVVMALDAIQEPVSLFEPIYHDGGDAIYVMDQ 185

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  D +  E  L         +  L  ++  L+ RE+ I   R       T   ++ E  
Sbjct: 186 VSDDKNMDEVWLE--------KIALKEAIQKLSEREKMILTMRFF--EGKTQMEVAKEIG 235

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A   +++ I
Sbjct: 236 ISQAQVSRLEKAALNHMRKYI 256


>gi|313901760|ref|ZP_07835186.1| RNA polymerase, sigma subunit, RpsG/SigG [Thermaerobacter
           subterraneus DSM 13965]
 gi|313467966|gb|EFR63454.1| RNA polymerase, sigma subunit, RpsG/SigG [Thermaerobacter
           subterraneus DSM 13965]
          Length = 261

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 59/259 (22%), Positives = 123/259 (47%), Gaps = 17/259 (6%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L  ++  VL +R RE GD  A  +LV  +LRLV+ +   +   G P+ ++   G IG
Sbjct: 20  LPVLSNEQMRVLFRRMRE-GDEEARQQLVQGNLRLVLSVIQRFNHRGEPVDDLFQVGCIG 78

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           LM+A+  FD E+  R +TY++  I   ++ Y+  +   +++  +   + + +   +++  
Sbjct: 79  LMKAIDNFDLEQNVRFSTYAVPMIIGEIRRYLRDNT-PIRVSRSL--RDVAYKALQVRD- 134

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
              +T  + +   +  IA++L     EV+     +    SL   I     +     D + 
Sbjct: 135 --QLTHRHGREPTLEEIAQELGQPREEVVHALDAIQDPVSLFEPIYQDGGDPIFVVDQVS 192

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            D         +++ER      +  +MS L+ RE+ I   R  Q    T   +++E  +S
Sbjct: 193 DDK--------QRDERWLETIAVREAMSRLDEREQLIITKRFYQG--KTQMEVANEIGIS 242

Query: 266 RERVRQIEARAFKKVQESI 284
           + +V ++E  A +++++ +
Sbjct: 243 QAQVSRLEKAALQRMRKYM 261


>gi|186682180|ref|YP_001865376.1| SigH/RpoD family RNA polymerase sigma factor [Nostoc punctiforme
           PCC 73102]
 gi|186464632|gb|ACC80433.1| RNA polymerase, sigma 70 subunit SigH, RpoD family [Nostoc
           punctiforme PCC 73102]
          Length = 321

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 64/301 (21%), Positives = 128/301 (42%), Gaps = 52/301 (17%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------------------ 43
             +  Y+ EI +IP+L +++E + A+  ++                              
Sbjct: 20  DTVRAYLKEIGRIPLLTQEQEIIFAQEVQQLMTILAESEKLTIELKRTPTLSEWANQMQL 79

Query: 44  ---------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                    +    A H+++T++LRLVV IA  Y+   L + +++ EG +GL + V+KF+
Sbjct: 80  SEQELLQQLNQGKKAKHKMITANLRLVVSIAKQYQRRNLELMDLIQEGTLGLERGVEKFN 139

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P  G+R +TY+ WWI+  +   I +    +++    N+K     L ++K   + ++    
Sbjct: 140 PALGYRFSTYAYWWIRQGITRAIAQQGRAIRLPIHINEK-----LNKIKRVQRELSQTLG 194

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +      IA  L++  S++           SL+  I  S +   + QD +          
Sbjct: 195 RIPTSTEIANALSLKPSQIREFLLLATRTISLD--IRVSSEKDLRLQDLIEDYKYSSNSY 252

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQI 272
           + E+   +     +   +S L+ +++ I            ++L+ +     +SRERVRQI
Sbjct: 253 ITEESLNQE----VNSLLSNLSRQQQEILNLHFGLTDGEELSLQQIGQRLGISRERVRQI 308

Query: 273 E 273
           E
Sbjct: 309 E 309


>gi|218200736|gb|EEC83163.1| hypothetical protein OsI_28384 [Oryza sativa Indica Group]
          Length = 537

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 58/243 (23%), Positives = 115/243 (47%), Gaps = 13/243 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                ++  S+ RLV+ +A  Y GYGL I ++V +G  GLM+  +KF+P +G R  TY+ 
Sbjct: 296 RRCREKMARSNFRLVIHVARKYEGYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAY 355

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ ++++ I ++  L+++  +       + L R  G  +       +      +A++ 
Sbjct: 356 WWIRQSIKKSIFKNSRLIRLPESV------YALLRKVGKARMECIMEGEQPTNANVARRA 409

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++  ++  +  +     S+   + S +  +     +     D   +      +R   R 
Sbjct: 410 GITIEKLAKLRAKTRKPRSMQDHVWSDEGVT-----FQEITEDPNVEPPDLSVDRMMMRQ 464

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +   + +L+PRE+ I E R       P TL  +   F +S+ER+RQ++ RA +K++ S 
Sbjct: 465 QVRDFLGILSPREKEIIEHRFGIHDGEPKTLHVIGDMFGLSKERIRQLQNRALEKLKRSA 524

Query: 285 QKQ 287
             Q
Sbjct: 525 SLQ 527


>gi|170691127|ref|ZP_02882293.1| sigma-70 region 3 domain protein [Burkholderia graminis C4D1M]
 gi|170144376|gb|EDT12538.1| sigma-70 region 3 domain protein [Burkholderia graminis C4D1M]
          Length = 202

 Score =  179 bits (455), Expect = 4e-43,   Method: Composition-based stats.
 Identities = 49/203 (24%), Positives = 91/203 (44%), Gaps = 12/203 (5%)

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            + R+   +
Sbjct: 1   MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQI 58

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
              T     P     +A+K+ + E ++  +        S+   I   D + S   D++  
Sbjct: 59  LQETGLEPDPAT---LAEKMEMPEDKIRKIMKIAKEPISMETPI--GDDDDSHLGDFI-- 111

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D       +     + R+++   +  L PRE ++   R   E     TLE +  +F+V
Sbjct: 112 -EDTNTVAPADAALHASMRDVVKDVLDSLTPREAKVLRMRFGIEMSTDHTLEEVGKQFDV 170

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RER+RQIEA+A +K++   +  
Sbjct: 171 TRERIRQIEAKALRKLRHPSRSD 193


>gi|294155544|ref|YP_003559928.1| DNA-directed RNA polymerase, sigma-70 factor [Mycoplasma crocodyli
           MP145]
 gi|291599870|gb|ADE19366.1| DNA-directed RNA polymerase, sigma-70 factor [Mycoplasma crocodyli
           MP145]
          Length = 490

 Score =  179 bits (454), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 67/292 (22%), Positives = 130/292 (44%), Gaps = 25/292 (8%)

Query: 16  LSRYIHEIRKI-PMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  Y+  I K   +L+  EE  LAK   + G     A  +L+  +LRLV+  A  Y+  G
Sbjct: 205 VKWYMRWIGKYGELLKPDEERRLAKLMEKGGFRGKRARDKLIMRNLRLVINNAKKYKNRG 264

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L   +++SEGN G+++AV+K++ E+GF+ +TY+ WWI+ A+   +      +++     +
Sbjct: 265 LTFIDLISEGNAGILKAVQKYNVEKGFKFSTYATWWIRQAITRAVADQARTIRVPVHMVE 324

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN--VSESEVISMNCRLAGDESLNALI 190
                 + ++    + +            IA +     +E +V  +        SL+  I
Sbjct: 325 -----TINKITKIERELQQELGHEPTDAQIANRFGNEYTEEKVRYIRKINIDPISLDKQI 379

Query: 191 NSSDKNSSQWQDWLVYDHDGQE-QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL- 248
               +N S + D++  D          +++  +    ++ +S+      ER +   R   
Sbjct: 380 --GKENDSSFSDFVKDDSVMTPVDFASQEQLSELLLELINKSLER---DERELICKRFGV 434

Query: 249 -------QENPVTLENLSSEF-EVSRERVRQIEARAFKKVQESIQKQVELSS 292
                  +    +L+ L+ E   VS+ERVRQIE +  +K++ S +    L  
Sbjct: 435 GVDSEGNKYRVHSLDELAKERGGVSKERVRQIENKILRKLKNSSKNGRHLRD 486


>gi|260773542|ref|ZP_05882458.1| RNA polymerase sigma factor RpoS [Vibrio metschnikovii CIP 69.14]
 gi|260612681|gb|EEX37884.1| RNA polymerase sigma factor RpoS [Vibrio metschnikovii CIP 69.14]
          Length = 297

 Score =  179 bits (454), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 69/254 (27%), Positives = 117/254 (46%), Gaps = 12/254 (4%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           ++              Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVV
Sbjct: 36  KEEYDASSKSLDATQMYLSEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLVV 94

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           KI+  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++    
Sbjct: 95  KISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTR 154

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            +++      K L   LR  +     ++           IA +L+    +V  M      
Sbjct: 155 TIRLPIHVV-KELNIYLRTAR----ELSQRLDHEPTAEEIAAELDKPVEDVNKMLRLNER 209

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++  I           D L    D          + ++ R  L   +  LNP+++ +
Sbjct: 210 ISSVDTPI--GGDGDKALLDILP---DSNHSDPEVSTQDEDIRLSLLNWLDELNPKQKEV 264

Query: 243 FEARRLQENPVTLE 256
             ARRL    + L+
Sbjct: 265 L-ARRLDYWVMNLQ 277


>gi|261405674|ref|YP_003241915.1| sporulation sigma factor SigG [Paenibacillus sp. Y412MC10]
 gi|315646040|ref|ZP_07899161.1| sporulation sigma factor SigG [Paenibacillus vortex V453]
 gi|329922674|ref|ZP_08278226.1| RNA polymerase sigma-G factor [Paenibacillus sp. HGF5]
 gi|261282137|gb|ACX64108.1| RNA polymerase, sigma 28 subunit, SigG [Paenibacillus sp. Y412MC10]
 gi|315278801|gb|EFU42115.1| sporulation sigma factor SigG [Paenibacillus vortex V453]
 gi|328942016|gb|EGG38299.1| RNA polymerase sigma-G factor [Paenibacillus sp. HGF5]
          Length = 260

 Score =  179 bits (454), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 54/262 (20%), Positives = 117/262 (44%), Gaps = 16/262 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L   E   L    +++ + SA  +LV  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLTNVEMRELFHNLQQNNERSAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGC 73

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+A+  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 74  IGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVR 130

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
                +T+ N +   +  I++ LNV + +V+     +    SL   I     +     D 
Sbjct: 131 D---QLTNANSREPTIFEISEALNVPKEDVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQ 187

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  D +     + E          L  +M  L  RE+ I   R       T   ++ E  
Sbjct: 188 ISDDKNKDVSWIEEIA--------LREAMHKLGQREKMILSMRFY--EGKTQMEVADEIG 237

Query: 264 VSRERVRQIEARAFKKVQESIQ 285
           +S+ +V ++E  A K++Q+ ++
Sbjct: 238 ISQAQVSRLEKSAIKQMQKHVK 259


>gi|149377551|ref|ZP_01895291.1| group 2 sigma 70-type sigma factor F [Marinobacter algicola DG893]
 gi|149358164|gb|EDM46646.1| group 2 sigma 70-type sigma factor F [Marinobacter algicola DG893]
          Length = 332

 Score =  179 bits (454), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 75/305 (24%), Positives = 137/305 (44%), Gaps = 52/305 (17%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYR-------------------------EHGDLSA---- 49
           Y  +  +  +L  + E  L++R                             GD  A    
Sbjct: 26  YFRDASRYELLTNESERRLSRRLTFCYRIISAELSLPEGTPQTFREVVGSLGDACAFSTR 85

Query: 50  -----------AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
                        RL+ S+LRL V IA  Y   G+P+S+V+ + N+GL++AV++FDP +G
Sbjct: 86  CRRAYHLATSSRQRLIRSNLRLAVHIARRYANRGIPMSDVIQDANVGLIKAVERFDPTKG 145

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           FR +TY+ WWI   ++  + R   LV        + +   +R L+    A+     +   
Sbjct: 146 FRFSTYAYWWISEEVKRCMKRGTRLVHTP-----ENVVDEIRLLQRTSLALYQTLGRTPS 200

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
              +A+++ VS S +  +    + + S++  + S++ N +  +     D    +  + + 
Sbjct: 201 QTELAREIEVSPSRIGELRALASMEVSVDLPV-STEGNITLGESLSADDQSAPDHDMAQ- 258

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARA 276
              ++R+  L   ++ L+ RE+ +   R   +   P TL+ +S +  +SRERVRQIE  A
Sbjct: 259 ---RDRKRTLATLLAELSSREKDVLARRYGLDLPEPETLQVISDDLGISRERVRQIEKSA 315

Query: 277 FKKVQ 281
            KK+Q
Sbjct: 316 LKKLQ 320


>gi|23098931|ref|NP_692397.1| sporulation sigma factor SigG [Oceanobacillus iheyensis HTE831]
 gi|22777159|dbj|BAC13432.1| stage III sporulation protein G (RNA polymerase
           sporulation-specific sigma G factor) [Oceanobacillus
           iheyensis HTE831]
          Length = 260

 Score =  179 bits (454), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 56/261 (21%), Positives = 118/261 (45%), Gaps = 16/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+ +E   L  R +E GD++A   LV  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLKNEEMKKLFVRMQEDGDITAREELVNGNLRLVLSVIQRFNNRGEYVDDLFQVGC 73

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+++  FD     R +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 74  IGLMKSIDNFDLSHNVRFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVR 130

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L + T     P     IAK++++ +++V+     +    SL   I +   +     D 
Sbjct: 131 EKLISKTSKEPSP---AEIAKEMDIPQTDVVFALDAIQDPVSLFEPIYNDGGDPIFVMDQ 187

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  + D     +         +  L   M  LN RE+ I   R  Q    T   ++ E  
Sbjct: 188 ISDEKDKDSSWV--------DKLSLKEGMHQLNEREKMILNKRFFQG--KTQMEVADEIG 237

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A  ++ + +
Sbjct: 238 ISQAQVSRLEKAAISQMNKQM 258


>gi|307107488|gb|EFN55731.1| hypothetical protein CHLNCDRAFT_35462 [Chlorella variabilis]
          Length = 267

 Score =  179 bits (454), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 59/242 (24%), Positives = 113/242 (46%), Gaps = 8/242 (3%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT-YS 105
           L A   +V  ++RLVV IA  Y G GL + ++V+EG +GL +AV KFD     ++   Y+
Sbjct: 24  LQAREHMVNCNMRLVVSIAKKYVGRGLALQDLVAEGMVGLQRAVDKFDASTRLQVTPAYA 83

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
            WWI+ ++   I     +V++    ++      + +++   QA+ D         A+A +
Sbjct: 84  HWWIRQSVTRAISDQARVVRLPVHLHE-----AMGKVRRAEQALWDETGLLPAPQAVADR 138

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
             ++ S+++++        S + +      +         +  +  E+   E    +  +
Sbjct: 139 CGLTHSKLMALYKSFRAPTSRDGVPTLGAGSVDAKAPGEQWVEEVGEEDPAELAHHRMMK 198

Query: 226 NMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             L   +  L  RE  I + R   ++    TLE +   F V+RER+RQIEA+A +K++  
Sbjct: 199 EDLNHVLLTLTERECGIIKMRYGLDDGEEKTLEEVGRAFNVTRERIRQIEAKAIRKLRSP 258

Query: 284 IQ 285
            +
Sbjct: 259 SR 260


>gi|187918623|ref|YP_001884188.1| RNA polymerase sigma factor RpoS [Borrelia hermsii DAH]
 gi|119861471|gb|AAX17266.1| RNA polymerase sigma factor RpoS [Borrelia hermsii DAH]
          Length = 267

 Score =  178 bits (453), Expect = 6e-43,   Method: Composition-based stats.
 Identities = 76/272 (27%), Positives = 143/272 (52%), Gaps = 18/272 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+  +R+  ++  +EE  LAK+ +  GDL A ++++ ++LRLV+KI   Y G GL +
Sbjct: 9   LNIYLKSVREHRLITHEEEIELAKQIKL-GDLKAKNKMINANLRLVLKIIKRYAGKGLKV 67

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GL++A +K+DP +  + +TY+ +WIK ++Q  +     LVK+         
Sbjct: 68  EDLIQEGNLGLIRAAEKYDPSKNTKFSTYASFWIKQSLQRALNTKTRLVKVPYRKE---- 123

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + ++  +L        K  +   I ++ N++ ++ + +   L  + SL+  +  S+ 
Sbjct: 124 -NLILQINKYLME----EEKSPKKEDIMERFNLTTAQYVKIIPYLEKEYSLDKKLEGSEN 178

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN---P 252
             S   +    +    E  L +    K+  ++L    + LN +ER I   R   +N    
Sbjct: 179 --STLLNLYEDNSFNPESTLEQNSTLKHLNHILE---TKLNDKERYIIRKRYNLDNNDKK 233

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL+++SSE  +S E VRQIE R  KK++E +
Sbjct: 234 STLKDISSELGISSETVRQIEKRVLKKLREEL 265


>gi|320537570|ref|ZP_08037508.1| RNA polymerase sigma factor RpoD family protein [Treponema
           phagedenis F0421]
 gi|320145572|gb|EFW37250.1| RNA polymerase sigma factor RpoD family protein [Treponema
           phagedenis F0421]
          Length = 274

 Score =  178 bits (453), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 73/281 (25%), Positives = 133/281 (47%), Gaps = 16/281 (5%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           GE   S+Y+ +I++ P+L  QEE  LA + + +GD  A  +L+ S+LRLVVK+A      
Sbjct: 2   GENIFSQYLKDIKRYPLLTAQEELCLADKIQ-NGDRGALQQLINSNLRLVVKMAKDRTPS 60

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
              + +++ EGN+GLM A +KF      R ++Y+ WWI+ ++  Y+      +++     
Sbjct: 61  ENLLMDLIQEGNMGLMIAAEKFSSSFNARFSSYACWWIRQSLNRYLNGKHETIRLPFRKA 120

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
                  LR+++  +    +   +      IA+ + V    VI +        S ++ + 
Sbjct: 121 DL-----LRKIEKTIDLFKEKYRRTPSYEEIAEIIQVPLKSVIQICVFTEKPISFDSPLQ 175

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQ 249
                S+   D    +    E+    K + +  R  L    + L  RE+ I E R     
Sbjct: 176 IH--FSANLYDLTENNDYNPEKEYFRKVQIEAFRKFLQ---NTLKSREKDIIEERLPITD 230

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ---ESIQKQ 287
           +NP +L +L  ++ +S E VRQ E RA KK++   + ++ +
Sbjct: 231 KNPKSLRSLGIKYGISAESVRQTEIRALKKLRMHEKYLKSE 271


>gi|119953545|ref|YP_945755.1| RNA polymerase sigma factor RpoS [Borrelia turicatae 91E135]
 gi|119862316|gb|AAX18084.1| RNA polymerase sigma factor RpoS [Borrelia turicatae 91E135]
          Length = 267

 Score =  178 bits (453), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 77/272 (28%), Positives = 143/272 (52%), Gaps = 18/272 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+  +R+  ++  +EE  LAK+ +  GDL A ++++ ++LRLV+KI   Y G GL +
Sbjct: 9   LNIYLKSVREHRLITHEEEIELAKQIKL-GDLKAKNKMINANLRLVLKIIKRYAGKGLKV 67

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GL++A +K+DP +  + +TY+ +WIK ++Q  +     LVK+         
Sbjct: 68  EDLIQEGNLGLIRAAEKYDPSKNTKFSTYASFWIKQSLQRALNTKTRLVKVPYRKE---- 123

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + ++  +L        K  +   I ++ N++ ++ I +   L  + SL+  I  S+ 
Sbjct: 124 -NLILQINKYLME----EEKSPKKEDIMERFNLTTAQYIKIIPYLEKEYSLDKKIEGSEN 178

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN---P 252
             S   +    +    E  L +    K+  ++L    + LN +ER I   R   +N    
Sbjct: 179 --STLLNLYEDNSFNPESTLEQNSTLKHLNHILE---TKLNEKERYIIIKRYNLDNSDKK 233

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL+++S+E  +S E VRQIE R  KK++E +
Sbjct: 234 STLKDISNELGISSETVRQIEKRVLKKLKEEL 265


>gi|138894663|ref|YP_001125116.1| sporulation sigma factor SigG [Geobacillus thermodenitrificans
           NG80-2]
 gi|134266176|gb|ABO66371.1| Sporulation-specific sigma factor [Geobacillus thermodenitrificans
           NG80-2]
          Length = 264

 Score =  178 bits (453), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 61/262 (23%), Positives = 119/262 (45%), Gaps = 17/262 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+ +E   L +R  E GDL A  +LV  +LRLV+ +   +   G  + ++   G 
Sbjct: 19  SKLPVLKNEEMRELFQRMHE-GDLEAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGC 77

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+++  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 78  IGLMKSIDNFDLNQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVR 134

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L        K      IAK+L V+  EV+     +    SL   I +   +     D 
Sbjct: 135 ERL---MGETAKEPSTEEIAKELGVAHEEVVLALDAIQDPVSLFEPIYNDGGDPIYVMDQ 191

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L  + +   Q + E          L   +  LN RE+ I   R  Q    T   ++ E  
Sbjct: 192 LSDERNRDSQWIEEIA--------LKEGLRRLNEREKMIIRKRFFQG--KTQMEVAEEIG 241

Query: 264 VSRERVRQIEARAFKKVQESIQ 285
           +S+ +V ++E  A +++ ++IQ
Sbjct: 242 ISQAQVSRLEKAAIRQMNKNIQ 263


>gi|326791409|ref|YP_004309230.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium lentocellum DSM
           5427]
 gi|326542173|gb|ADZ84032.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium lentocellum DSM
           5427]
          Length = 257

 Score =  178 bits (453), Expect = 7e-43,   Method: Composition-based stats.
 Identities = 54/260 (20%), Positives = 114/260 (43%), Gaps = 17/260 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L  +++  L K   E GD  A    +  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPILTNEQKETLFKLI-EQGDNKAREEYIRGNLRLVLSVIQRFNNRGEHVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD  +  R +TY++  I   ++ Y+  +   +++      + L     +   
Sbjct: 74  GLIKAIDNFDVTQNVRFSTYAVPMIIGEIRRYLRDNN-AIRVS-----RSLRDTAYKALQ 127

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + +T  N K   V  IA +L + + +++     +    SL   +   + ++    D +
Sbjct: 128 TKEQLTRKNAKEPTVQEIADELGIKKEDIVFALDAIQDPISLFEPVYHDESDTLYIMDQV 187

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             D +  +  L            L  +M  +N RE++I   R       T   +++E  +
Sbjct: 188 SDDKNQDDVWLENIA--------LKEAMKRINDREKQILMLRFFAG--KTQMEVANEIGI 237

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ +V ++E  A K +++ I
Sbjct: 238 SQAQVSRLEKTALKHMKKYI 257


>gi|83589704|ref|YP_429713.1| sporulation sigma factor SigG [Moorella thermoacetica ATCC 39073]
 gi|83572618|gb|ABC19170.1| RNA polymerase, sigma subunit, RpsG/SigG [Moorella thermoacetica
           ATCC 39073]
          Length = 272

 Score =  178 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 53/261 (20%), Positives = 118/261 (45%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+  E   L ++ +  G+  A  +L+T +LRLV+ +   +   G  + ++   G 
Sbjct: 29  SKLPLLKSDEIRQLFQQMQ-AGETGAREKLITGNLRLVLSVIQRFTNRGEHVDDLFQVGC 87

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+A+  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 88  IGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDVAYKALQIR 144

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L    +   +   +  +A++L++ + EVI     +    SL   I     +     D 
Sbjct: 145 DTL---VNKLAREPSLAEVAQQLDLPQEEVIFALDAIQEPVSLFEPIYHDGGDPIFVMDQ 201

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  + +     L            +  +M+ LNPRER I   R       T   ++ E  
Sbjct: 202 IGDEKNQDSSWLENIA--------IKEAMNKLNPRERLILSLRFF--EGKTQMEVADEIG 251

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A + +++ I
Sbjct: 252 ISQAQVSRLEKAALQHMRKYI 272


>gi|52080136|ref|YP_078927.1| sporulation sigma factor SigG [Bacillus licheniformis ATCC 14580]
 gi|52785510|ref|YP_091339.1| sporulation sigma factor SigG [Bacillus licheniformis ATCC 14580]
 gi|319646086|ref|ZP_08000316.1| RNA polymerase sigma-G factor [Bacillus sp. BT1B_CT2]
 gi|52003347|gb|AAU23289.1| RNA polymerase sporulation-specific sigma factor (sigma-G)
           [Bacillus licheniformis ATCC 14580]
 gi|52348012|gb|AAU40646.1| SigG [Bacillus licheniformis ATCC 14580]
 gi|317391836|gb|EFV72633.1| RNA polymerase sigma-G factor [Bacillus sp. BT1B_CT2]
          Length = 259

 Score =  178 bits (453), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 59/261 (22%), Positives = 119/261 (45%), Gaps = 16/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+ +E   L K+ ++ GD +A  +LV  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLKNEEMRKLFKQMQDEGDTTAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGC 73

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+++  FD     + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 74  IGLMKSIDNFDLSHNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVR 130

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L + T           IAK+L VS  E++     +    SL   I +   +     D 
Sbjct: 131 ERLISETSRE---PTAQEIAKELEVSHEEIVFALDAIQDPVSLFEPIYNDGGDPIYVMDQ 187

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  + +   Q + E          L   M  LN RE+ I   R  Q    T   ++ E  
Sbjct: 188 ISDERNKDSQWIEELA--------LKEGMRRLNEREKMILRKRFFQG--KTQMEVADEIG 237

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A K++ ++I
Sbjct: 238 ISQAQVSRLEKAAIKQMNKNI 258


>gi|291561536|emb|CBL40335.1| RNA polymerase, sigma subunit, RpsG/SigG [butyrate-producing
           bacterium SS3/4]
          Length = 258

 Score =  178 bits (452), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 56/261 (21%), Positives = 119/261 (45%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L  +E+  L +R + +GD  A    +  +LRLV+ +   + G    + ++   G 
Sbjct: 14  SKLPLLTNEEKTDLFRRIQ-NGDTDARETYIKGNLRLVLSVIQRFSGSSENLDDLFQIGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD  +  + +TY++  I   ++ Y+  + S +++      + L     +  
Sbjct: 73  IGLIKAIDNFDLSQNVKFSTYAVPMILGEVRRYLRDNNS-IRVS-----RSLRDTAYKAL 126

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
              + +T  NL+   ++ IA ++ +S+ E+      +    SL   +  +D         
Sbjct: 127 SARELLTKRNLREPTIMEIADEVGISKEEITYAMDAIQSPVSLYEPVY-TDGGDPLCVMD 185

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
            + D   +E+  +E+         L+ +M  L  RERRI + R       T   ++ E  
Sbjct: 186 QISDKKNREENWVEQLS-------LSEAMKRLPARERRIIDMRFF--EGKTQTEVAGEVG 236

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A K ++  +
Sbjct: 237 ISQAQVSRLEKNALKAMKSYL 257


>gi|18310743|ref|NP_562677.1| sporulation sigma factor SigG [Clostridium perfringens str. 13]
 gi|18145424|dbj|BAB81467.1| probable transcription initiation factor sigma G [Clostridium
           perfringens str. 13]
          Length = 270

 Score =  178 bits (452), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 56/260 (21%), Positives = 115/260 (44%), Gaps = 17/260 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+++E   L  + + +GD SA  + +  +LRLV+ +   +   G  + ++   G I
Sbjct: 28  KLPVLKEKEMKELLLQMQ-NGDTSAREKFIKGNLRLVLSVIQRFNNRGENVDDLFQVGCI 86

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD  +  + +TY++  I   ++ Y+  +   +++  +         L R K 
Sbjct: 87  GLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-TIRVSRSLRDIAYKALLVRDK- 144

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
               + + N K   V  IAK+L +   +V+     +    SL   I     ++    D +
Sbjct: 145 ----LVNENNKEPTVSQIAKELKIPREDVVFALDAIQDPVSLFEPIYHDGGDAIYVMDQI 200

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               +  +  L            +  +M  LN RE+ I   R    N  T   ++ E  +
Sbjct: 201 SDSKNQDDSWLENIA--------IKEAMKKLNDREKLILNLRFF--NGRTQMEVADEIGI 250

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ +V ++E  A K +++ +
Sbjct: 251 SQAQVSRLEKIALKHMRKYV 270


>gi|47459124|ref|YP_015986.1| RNA polymerase sigma factor [Mycoplasma mobile 163K]
 gi|47458453|gb|AAT27775.1| DNA-directed RNA polymerase sigma factor [Mycoplasma mobile 163K]
          Length = 488

 Score =  178 bits (452), Expect = 8e-43,   Method: Composition-based stats.
 Identities = 66/288 (22%), Positives = 134/288 (46%), Gaps = 26/288 (9%)

Query: 16  LSRYIHEIRKI-PMLEKQEEYVLAKRYREHGD----LSAAHRLVTSHLRLVVKIAMGYRG 70
           +  Y+  + K   +L+K+EE   +K+  E  +      A + L+  +LRLV+  A  Y+ 
Sbjct: 201 VKWYMSWVGKHGKVLDKEEEIKYSKQIEEDRNGRKGKKAFNALIHHNLRLVINNAKKYKN 260

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            GL   +++SEGN GL++A  K+D  RGF+ +TY+ WW++ A+   +     +V++    
Sbjct: 261 RGLSFIDLISEGNAGLIKAATKYDYRRGFKFSTYATWWVRQAITRAVADQARIVRVPVHM 320

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL--NVSESEVISMNCRLAGDESLNA 188
            +      + ++    + +      P     IA+K   N +  +V  +        SL+ 
Sbjct: 321 VE-----TINKIIKIERELHQELGVPPTDKQIAEKYGNNFTAEKVQYIRKINIDPISLDK 375

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS-VLNPRERRIFEARR 247
            I   D   S + D++    D      +E   +     +LT  +   L+  ER + + R 
Sbjct: 376 SIGKDDD--SSFSDFV---KDESVVSPLEFASQNELSGILTDILEKHLDEAERDLIKKRF 430

Query: 248 LQE--------NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
                      +  +LE L++E ++S+E+VR +E++  +K++   +++
Sbjct: 431 GIGVDKDGNRISSHSLEELAAELQISKEKVRSLESKILRKLKHPQKRK 478


>gi|255531368|ref|YP_003091740.1| sigma-70 family RNA polymerase sigma factor [Pedobacter heparinus
           DSM 2366]
 gi|255344352|gb|ACU03678.1| RNA polymerase sigma factor, sigma-70 family [Pedobacter heparinus
           DSM 2366]
          Length = 286

 Score =  178 bits (452), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 77/277 (27%), Positives = 138/277 (49%), Gaps = 13/277 (4%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           SI    +  L+RY+ EI K P+L+ +EE VL KR +E GD  A  RLV+S+LR VV +A 
Sbjct: 9   SITNRSQDSLARYLQEISKYPLLDAEEEIVLGKRIKE-GDWDALQRLVSSNLRFVVTVAK 67

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y    L +++++S+GNIGL++A ++FD +RGF+  +Y++WWI+ ++ + +  S  +V +
Sbjct: 68  KYESPDLSLADLISDGNIGLIKAAERFDEKRGFKFISYAVWWIRQSILQGMNTSKRMVHL 127

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
             +         +R++K     +     +      +A  +  +E  V           SL
Sbjct: 128 PMSQ-----ISGIRQVKRSEIKLEQELQRIPCREELAGFMKTAEEVVYDYLYISGSQVSL 182

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           +A     D         + YD        +E+E  +     + R M +L+PRER I    
Sbjct: 183 DAPTEGQDG--VLIPCIVQYDKGPAPDASLERESLE---KDVQRMMDILSPRERSILFLA 237

Query: 247 RLQENPVTLE--NLSSEFEVSRERVRQIEARAFKKVQ 281
               N   L+  ++S+   +S E +R+ + +A  +++
Sbjct: 238 YGMGNNRPLQNDDISTLLGLSTETIRRSKNKALDRLR 274


>gi|310642978|ref|YP_003947736.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
 gi|309247928|gb|ADO57495.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
          Length = 260

 Score =  178 bits (452), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 54/262 (20%), Positives = 117/262 (44%), Gaps = 16/262 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L   E   L    +++ + SA  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLTNAEMRELFTSLQQNNERSAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGCI 74

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A+  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++ 
Sbjct: 75  GLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVRD 131

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L   T+ N +   +  I++ LNV + +V+     +    SL   I     +     D +
Sbjct: 132 SL---TNLNSREPTIFEISEVLNVPKEDVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQI 188

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             D +     + E          L  +M  L  RE+ I   R       T   ++ E  +
Sbjct: 189 SDDRNKDVSWIEEIA--------LREAMHRLGQREKMILSMRFY--EGKTQMEVADEIGI 238

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+ +V ++E  A +++Q+ ++ 
Sbjct: 239 SQAQVSRLEKSAIQQMQKHVKS 260


>gi|308173495|ref|YP_003920200.1| RNA polymerase sporulation-specific sigma factor sigma-G [Bacillus
           amyloliquefaciens DSM 7]
 gi|307606359|emb|CBI42730.1| RNA polymerase sporulation-specific sigma factor (sigma-G)
           [Bacillus amyloliquefaciens DSM 7]
 gi|328553575|gb|AEB24067.1| sporulation sigma factor SigG [Bacillus amyloliquefaciens TA208]
 gi|328911632|gb|AEB63228.1| RNA polymerase sporulation-specific sigma factor (sigma-G)
           [Bacillus amyloliquefaciens LL3]
          Length = 260

 Score =  178 bits (452), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 60/263 (22%), Positives = 119/263 (45%), Gaps = 16/263 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+ +E   L K+ ++ GD SA  +LV  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLKNEEMRKLFKQLQDEGDDSAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGC 73

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+++  FD     + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 74  IGLMKSIDNFDLSHNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVR 130

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L + T      E    IAK L V   E++     +    SL   I +   +     D 
Sbjct: 131 ERLISETSREPTAE---EIAKVLEVPHEEIVFALDAIQDPVSLFEPIYNDGGDPIYVMDQ 187

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  + +   Q + E          L   M  LN RE+ I   R  Q    T   ++ E  
Sbjct: 188 ISDERNKDTQWIEELA--------LKEGMRRLNEREKMILRKRFFQG--KTQMEVAEEIG 237

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+ +V ++E  A K++ ++I +
Sbjct: 238 ISQAQVSRLEKAAIKQMNKNIHQ 260


>gi|110799379|ref|YP_696447.1| sporulation sigma factor SigG [Clostridium perfringens ATCC 13124]
 gi|168207288|ref|ZP_02633293.1| RNA polymerase sigma-G factor [Clostridium perfringens E str.
           JGS1987]
 gi|168210606|ref|ZP_02636231.1| RNA polymerase sigma-G factor [Clostridium perfringens B str. ATCC
           3626]
 gi|168214238|ref|ZP_02639863.1| RNA polymerase sigma-G factor [Clostridium perfringens CPE str.
           F4969]
 gi|168217048|ref|ZP_02642673.1| RNA polymerase sigma-G factor [Clostridium perfringens NCTC 8239]
 gi|169342669|ref|ZP_02863710.1| RNA polymerase sigma-G factor [Clostridium perfringens C str.
           JGS1495]
 gi|182625828|ref|ZP_02953594.1| RNA polymerase sigma-G factor [Clostridium perfringens D str.
           JGS1721]
 gi|110674026|gb|ABG83013.1| RNA polymerase sigma-G factor [Clostridium perfringens ATCC 13124]
 gi|169299175|gb|EDS81245.1| RNA polymerase sigma-G factor [Clostridium perfringens C str.
           JGS1495]
 gi|170661342|gb|EDT14025.1| RNA polymerase sigma-G factor [Clostridium perfringens E str.
           JGS1987]
 gi|170711289|gb|EDT23471.1| RNA polymerase sigma-G factor [Clostridium perfringens B str. ATCC
           3626]
 gi|170714329|gb|EDT26511.1| RNA polymerase sigma-G factor [Clostridium perfringens CPE str.
           F4969]
 gi|177908862|gb|EDT71354.1| RNA polymerase sigma-G factor [Clostridium perfringens D str.
           JGS1721]
 gi|182380954|gb|EDT78433.1| RNA polymerase sigma-G factor [Clostridium perfringens NCTC 8239]
          Length = 257

 Score =  178 bits (452), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 56/260 (21%), Positives = 115/260 (44%), Gaps = 17/260 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+++E   L  + + +GD SA  + +  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKEKEMKELLLQMQ-NGDTSAREKFIKGNLRLVLSVIQRFNNRGENVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD  +  + +TY++  I   ++ Y+  +   +++  +         L R K 
Sbjct: 74  GLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-TIRVSRSLRDIAYKALLVRDK- 131

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
               + + N K   V  IAK+L +   +V+     +    SL   I     ++    D +
Sbjct: 132 ----LVNENNKEPTVSQIAKELKIPREDVVFALDAIQDPVSLFEPIYHDGGDAIYVMDQI 187

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               +  +  L            +  +M  LN RE+ I   R    N  T   ++ E  +
Sbjct: 188 SDSKNQDDSWLENIA--------IKEAMKKLNDREKLILNLRFF--NGRTQMEVADEIGI 237

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ +V ++E  A K +++ +
Sbjct: 238 SQAQVSRLEKIALKHMRKYV 257


>gi|308069872|ref|YP_003871477.1| RNA polymerase sigma-G factor (stage III sporulation protein G)
           [Paenibacillus polymyxa E681]
 gi|305859151|gb|ADM70939.1| RNA polymerase sigma-G factor (Stage III sporulation protein G)
           [Paenibacillus polymyxa E681]
          Length = 260

 Score =  178 bits (452), Expect = 9e-43,   Method: Composition-based stats.
 Identities = 54/262 (20%), Positives = 117/262 (44%), Gaps = 16/262 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L   E   L    +++ + SA  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLTNAEMRELFTSLQQNNERSAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGCI 74

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A+  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++ 
Sbjct: 75  GLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVRD 131

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L   T+ N +   +  I++ LNV + +V+     +    SL   I     +     D +
Sbjct: 132 SL---TNLNSREPTIFEISEALNVPKEDVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQI 188

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             D +     + E          L  +M  L  RE+ I   R       T   ++ E  +
Sbjct: 189 SDDRNKDVSWIEEIA--------LREAMHRLGQREKMILSMRFY--EGKTQMEVADEIGI 238

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+ +V ++E  A +++Q+ ++ 
Sbjct: 239 SQAQVSRLEKSAIQQMQKHVKS 260


>gi|326319203|ref|YP_004236875.1| RpoD subfamily RNA polymerase sigma-70 subunit [Acidovorax avenae
           subsp. avenae ATCC 19860]
 gi|323376039|gb|ADX48308.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidovorax avenae
           subsp. avenae ATCC 19860]
          Length = 878

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 52/244 (21%), Positives = 107/244 (43%), Gaps = 17/244 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  R+  ++L+L    A  Y   G  + ++  EGN+GL++AV +++  RGFR +TY+ WW
Sbjct: 521 ARDRMTAANLKLAFFHARKYLYSGETLDDLAQEGNVGLLKAVDRYNWRRGFRFSTYATWW 580

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           ++  +  Y+      +++     +K       R+    + + D   +   +  +A+++ +
Sbjct: 581 VRQQISRYVADKARTIRMPVHIYEKA--QRAERIAQRFEMLAD---RAPSLDELAERMEM 635

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              ++ ++         +       D++       L            +  E    R  L
Sbjct: 636 PRHKLAALLRIAPEPSRI-------DESPVDELISLDARDAYWLPDPADAVETHQVRAAL 688

Query: 229 TRSMSVLNPR---ERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            R +S L+ R   E  +   R        +TL+ +   F V+RER+RQIEA+A +K++  
Sbjct: 689 DRYISSLSTRDRKEEHVLRLRYGIGVHEALTLDEVGQRFGVTRERIRQIEAKAIRKLKHH 748

Query: 284 IQKQ 287
            + +
Sbjct: 749 ARSE 752


>gi|115475493|ref|NP_001061343.1| Os08g0242800 [Oryza sativa Japonica Group]
 gi|30698490|dbj|BAC76602.1| Sig6 [Oryza sativa Japonica Group]
 gi|40253642|dbj|BAD05586.1| Sig6, plastid RNA polymerase sigma factor [Oryza sativa Japonica
           Group]
 gi|40253689|dbj|BAD05631.1| Sig6, plastid RNA polymerase sigma factor [Oryza sativa Japonica
           Group]
 gi|113623312|dbj|BAF23257.1| Os08g0242800 [Oryza sativa Japonica Group]
 gi|215712228|dbj|BAG94355.1| unnamed protein product [Oryza sativa Japonica Group]
          Length = 572

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 58/243 (23%), Positives = 115/243 (47%), Gaps = 13/243 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                ++  S+ RLV+ +A  Y GYGL I ++V +G  GLM+  +KF+P +G R  TY+ 
Sbjct: 331 RRCREKMARSNFRLVIHVARKYEGYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAY 390

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ ++++ I ++  L+++  +       + L R  G  +       +      +A++ 
Sbjct: 391 WWIRQSIKKSIFKNSRLIRLPESV------YALLRKVGKARMECIMEGEQPTNANVARRA 444

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++  ++  +  +     S+   + S +  +     +     D   +      +R   R 
Sbjct: 445 GITIEKLAKLRAKTRKPRSMQDHVWSDEGVT-----FQEITEDPNVEPPDLSVDRMMMRQ 499

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +   + +L+PRE+ I E R       P TL  +   F +S+ER+RQ++ RA +K++ S 
Sbjct: 500 QVRDFLGILSPREKEIIEHRFGIHDGEPKTLHVIGDMFGLSKERIRQLQNRALEKLKRSA 559

Query: 285 QKQ 287
             Q
Sbjct: 560 SLQ 562


>gi|193216688|ref|YP_001999930.1| RNA polymerase sigma factor [Mycoplasma arthritidis 158L3-1]
 gi|193002011|gb|ACF07226.1| RNA polymerase sigma-70 factor [Mycoplasma arthritidis 158L3-1]
          Length = 513

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 66/290 (22%), Positives = 130/290 (44%), Gaps = 27/290 (9%)

Query: 16  LSRYIHEIRKI-PMLEKQEEYVLAKRYREH-------GDLSAAHRLVTSHLRLVVKIAMG 67
           +  Y+  I K   +L  ++E  LA +  E            A   LV  +LRLV+  A  
Sbjct: 219 VKWYMRWIGKYGKLLTPKKERELAIKMEEALANNNYYRYKRARDMLVKRNLRLVINNAKR 278

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y+  GL   +++SEGN G+M+AV K+D ++GF+ +TY+ WWI+ A+   +      +++ 
Sbjct: 279 YKNRGLSFIDLISEGNSGIMKAVSKYDYKKGFKFSTYATWWIRQAITRAVADQARTIRVP 338

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL--NVSESEVISMNCRLAGDES 185
               +      + ++    + +      P     IAKK   + +  +V  +        S
Sbjct: 339 VHMVE-----TINKILKIERELQQEFGYPPTDEEIAKKFGGDFTAEKVRYIRKINIDPIS 393

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L+  I    + +S + D++  +          ++E     N +    S L+P ++ +   
Sbjct: 394 LDKNI--GKEENSSFSDFVKDESVISPNDFASQQELAVILNEMIN--SSLDPEDQALIRK 449

Query: 246 RRLQEN--------PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           R             P TL+ L+ E  +S+E+VR++EA+  +K++   +++
Sbjct: 450 RYGVGQDPSGVPYRPHTLDELAKELNISKEKVRKLEAKILRKLKHPQKRK 499


>gi|239826533|ref|YP_002949157.1| sporulation sigma factor SigG [Geobacillus sp. WCH70]
 gi|239806826|gb|ACS23891.1| RNA polymerase, sigma 28 subunit, SigG [Geobacillus sp. WCH70]
          Length = 259

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 63/262 (24%), Positives = 119/262 (45%), Gaps = 17/262 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+ +E   L KR  E GDL A  +LV  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLKNEEMRELFKRMHE-GDLEAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+++  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 73  IGLMKSIDNFDLNQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVR 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L + T    K      IAK L +   EV+     +    SL   I +   +     D 
Sbjct: 130 EKLMSET---AKEPSAEEIAKVLGIPHEEVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L  + +   Q + E          L   M  LN RE+ I   R  Q    T   ++ E  
Sbjct: 187 LSDERNRDSQWIEEIA--------LKEGMRRLNEREKMIIRKRFFQG--KTQMEVAEEIG 236

Query: 264 VSRERVRQIEARAFKKVQESIQ 285
           +S+ +V ++E  A +++ ++IQ
Sbjct: 237 ISQAQVSRLEKAAIRQMNKNIQ 258


>gi|224126061|ref|XP_002319746.1| predicted protein [Populus trichocarpa]
 gi|222858122|gb|EEE95669.1| predicted protein [Populus trichocarpa]
          Length = 567

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 59/248 (23%), Positives = 117/248 (47%), Gaps = 12/248 (4%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L  R R +  +    +++ S++RLV+ IA  Y+G G+ + ++V EG  GL++  +KFD  
Sbjct: 317 LTLRKRLNYGILCKDKMIKSNVRLVISIAKNYQGTGMNLQDLVQEGCRGLVRGAEKFDAS 376

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +GF+ +TY+ WWIK A+++ +      +++        +     R+K   + +   N + 
Sbjct: 377 KGFKFSTYAHWWIKQAVRKSLSDRSRTIRLPFH-----MVDATYRVKEARKQLYSENGRH 431

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
                +A+   +S   + ++        SL+  +  +               D + +   
Sbjct: 432 PDDKEVAEAAGLSMKRLSAVLLTPKAPRSLDQKMGFNMD-----LKLSEVTADPEAETAE 486

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEA 274
           +   ++  +  L + +  L+PRE ++   R   E+    TL+ +     VSRERVRQIE 
Sbjct: 487 DLLMKEFMKKDLAKVLGSLSPRENQVVRWRFGMEDGRMKTLQEIGELMGVSRERVRQIEL 546

Query: 275 RAFKKVQE 282
            AF+K++ 
Sbjct: 547 SAFRKLKN 554


>gi|222528794|ref|YP_002572676.1| sporulation sigma factor SigG [Caldicellulosiruptor bescii DSM
           6725]
 gi|222455641|gb|ACM59903.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor bescii DSM 6725]
          Length = 255

 Score =  178 bits (452), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 59/259 (22%), Positives = 121/259 (46%), Gaps = 17/259 (6%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L  +E+  L KR +E GD  A    +  +LRLV+ +   +   G  + ++   G IG
Sbjct: 14  LPVLSHEEKLELLKRMKE-GDKEARRIFIEGNLRLVLSVVQKFANRGENLDDLFQVGCIG 72

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A+  FD  +  + +TY++  I   ++ Y+  + S+ +I  +   K   +   ++K  
Sbjct: 73  LIKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNSM-RISRSL--KDTAYKALKIK-- 127

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            +   +NN K   +  IAK+L++++ +++     +    SL   +   D   + +    +
Sbjct: 128 -EKYINNNQKEPTLEEIAKELSITKEDLVFALDSIQEPISLYEPVFQ-DSTDTMYVVERL 185

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            DH   E V +E+         L  ++S L  RE+ I   R  +    T   ++    +S
Sbjct: 186 CDHKSCESVWLEEIS-------LKDALSKLTKREKEILYLRYYKG--KTQMEVAKIVGIS 236

Query: 266 RERVRQIEARAFKKVQESI 284
           + +V +IE  A   +++ I
Sbjct: 237 QAQVSRIEKSAIGHIKKYI 255


>gi|110802253|ref|YP_699047.1| sporulation sigma factor SigG [Clostridium perfringens SM101]
 gi|110682754|gb|ABG86124.1| RNA polymerase sigma-G factor [Clostridium perfringens SM101]
          Length = 257

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 56/260 (21%), Positives = 115/260 (44%), Gaps = 17/260 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+++E   L  + + +GD SA  + +  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKEKEMKELLLQMQ-NGDTSAREKFIKGNLRLVLSVIQRFNNRGENVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD  +  + +TY++  I   ++ Y+  +   +++  +         L R K 
Sbjct: 74  GLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-TIRVSRSLRDIAYKALLVRDK- 131

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
               + + N K   V  IAK+L +   +V+     +    SL   I     ++    D +
Sbjct: 132 ----LVNENNKEPTVSQIAKELKIPREDVVFALDAIQDPVSLFEPIYYDGGDAIYVMDQI 187

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               +  +  L            +  +M  LN RE+ I   R    N  T   ++ E  +
Sbjct: 188 SDSKNQDDSWLENIA--------IKEAMKKLNDREKLILNLRFF--NGRTQMEVADEIGI 237

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ +V ++E  A K +++ +
Sbjct: 238 SQAQVSRLEKIALKHMRKYV 257


>gi|56419663|ref|YP_146981.1| sporulation sigma factor SigG [Geobacillus kaustophilus HTA426]
 gi|261419325|ref|YP_003253007.1| sporulation sigma factor SigG [Geobacillus sp. Y412MC61]
 gi|297530705|ref|YP_003671980.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
 gi|319766141|ref|YP_004131642.1| RNA polymerase, sigma 28 subunit, SigG [Geobacillus sp. Y412MC52]
 gi|56379505|dbj|BAD75413.1| DNA-directed RNA polymerase sporulation-specific sigma factor
           (sigma-G) [Geobacillus kaustophilus HTA426]
 gi|261375782|gb|ACX78525.1| RNA polymerase, sigma 28 subunit, SigG [Geobacillus sp. Y412MC61]
 gi|297253957|gb|ADI27403.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
 gi|317111007|gb|ADU93499.1| RNA polymerase, sigma 28 subunit, SigG [Geobacillus sp. Y412MC52]
          Length = 259

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 62/262 (23%), Positives = 121/262 (46%), Gaps = 17/262 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+ +E   L +R  E GDL A  +LV  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLKNEEMRELFRRMHE-GDLEAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+++  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 73  IGLMKSIDNFDLNQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVR 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L + T      E    IAK+L V+  EV+     +    SL   I +   +     D 
Sbjct: 130 ERLMSETAKEPSTE---EIAKELGVAHEEVVFALDAIQDPVSLFEPIYNDGGDPIYVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L  + +   Q + E          L   +  LN RE+ I   R  Q    T   ++ E  
Sbjct: 187 LSDERNRDSQWIEEIA--------LKEGLRRLNEREKMIIRKRFFQG--KTQMEVAEEIG 236

Query: 264 VSRERVRQIEARAFKKVQESIQ 285
           +S+ +V ++E  A +++ ++IQ
Sbjct: 237 ISQAQVSRLEKAAIRQMNKNIQ 258


>gi|167822153|ref|ZP_02453624.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 9]
          Length = 299

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 61/266 (22%), Positives = 127/266 (47%), Gaps = 16/266 (6%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDL---SAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
             +R++P    ++    A+R    G+    +A  R+  ++LRLV+ IA  Y   GL +++
Sbjct: 29  RAMRRLP-TSPEKSDAGAQRAFADGEARISAATARMAEANLRLVLSIARKYASRGLDLAD 87

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGN+GL++A++KF+  RGF+ +TY+ WWI+ A+   I      +++           
Sbjct: 88  LLQEGNLGLLRAIEKFEHRRGFKFSTYATWWIRQAISRAIADRARTIRVPVHV-----GD 142

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
             RR++     I   +     +  +++   +    + ++        SLNA +   D + 
Sbjct: 143 EARRVRKAADRIERRSGVSASLAELSEATGLPAERLRAVLTLPREPRSLNAPL--GDDDQ 200

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTL 255
           +++ D +    D     L +        +++T  +  ++ +E  I   R     + P + 
Sbjct: 201 AEFGDIV---EDTSTPSLFDALAHGQMCDVVTSLLKTMSAQEADILRRRFGIGGDEPWSY 257

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           E +++   VSRE+VR+IE RA + ++
Sbjct: 258 EQIAARAGVSREQVRRIEKRALQTLR 283


>gi|167813607|ref|ZP_02445287.1| RNA polymerase sigma factor RpoD [Burkholderia pseudomallei 91]
          Length = 302

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 61/266 (22%), Positives = 127/266 (47%), Gaps = 16/266 (6%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDL---SAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
             +R++P    ++    A+R    G+    +A  R+  ++LRLV+ IA  Y   GL +++
Sbjct: 32  RAMRRLP-TSPEKSDAGAQRAFADGEARISAATARMAEANLRLVLSIARKYASRGLDLAD 90

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGN+GL++A++KF+  RGF+ +TY+ WWI+ A+   I      +++           
Sbjct: 91  LLQEGNLGLLRAIEKFEHRRGFKFSTYATWWIRQAISRAIADRARTIRVPVHV-----GD 145

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
             RR++     I   +     +  +++   +    + ++        SLNA +   D + 
Sbjct: 146 EARRVRKAADRIERRSGVSASLAELSEATGLPAERLRAVLTLPREPRSLNAPL--GDDDQ 203

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTL 255
           +++ D +    D     L +        +++T  +  ++ +E  I   R     + P + 
Sbjct: 204 AEFGDIV---EDTSTPSLFDALAHGQMCDVVTSLLKTMSAQEADILRRRFGIGGDEPWSY 260

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           E +++   VSRE+VR+IE RA + ++
Sbjct: 261 EQIAARAGVSREQVRRIEKRALQTLR 286


>gi|107026582|ref|YP_624093.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia cenocepacia AU
           1054]
 gi|116692228|ref|YP_837761.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia cenocepacia
           HI2424]
 gi|105895956|gb|ABF79120.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia cenocepacia AU
           1054]
 gi|116650228|gb|ABK10868.1| RNA polymerase, sigma 38 subunit, RpoS [Burkholderia cenocepacia
           HI2424]
          Length = 514

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 52/230 (22%), Positives = 103/230 (44%), Gaps = 13/230 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   ++ ++LRLV+ IA  Y   G+ +S++V +G +GLM+A++KF+  RGF+ +TY+ 
Sbjct: 275 RDATRAMLEANLRLVLSIARKYLNRGVDLSDLVQDGCLGLMRAIEKFEYRRGFKFSTYAT 334

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      +++             +R++ H         +      +A + 
Sbjct: 335 WWIRQAIARAVADRSRTIRVPVHV-----GDQYQRVQRHALRFRQRTGRRATPAELAAET 389

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++E ++ ++    A   SL+  +  +D    +         D       E+      R+
Sbjct: 390 GLAEDKLRAVLALPAEPVSLDTPLPDADTGLVELI------EDQASASPFEQLADTRMRD 443

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEA 274
            +   +  + P E  +   R       P T + ++ +  +SRERVRQIE 
Sbjct: 444 CVRSLLRSVTPTEADVLRRRFGLGGAEPDTYDAIAQDAGMSRERVRQIEK 493


>gi|254519266|ref|ZP_05131322.1| sporulation sigma factor SigG [Clostridium sp. 7_2_43FAA]
 gi|226913015|gb|EEH98216.1| sporulation sigma factor SigG [Clostridium sp. 7_2_43FAA]
          Length = 259

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 60/261 (22%), Positives = 115/261 (44%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+++E+  L  + R+ GD  A    +  +LRLV+ +   +   G  + ++   G 
Sbjct: 16  SKLPILKEKEKRELLLKMRD-GDKGARETFIKGNLRLVLSVIQRFNNRGENVDDLFQVGC 74

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+A+  FD  +  + +TY++  I   ++ Y+  + S +++  +         L R +
Sbjct: 75  IGLMKAIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRDIAYKALLVRDR 133

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
                +   N K   V  IAK+LN+   EV+     +    SL   I     ++    D 
Sbjct: 134 -----LIKENNKEPTVSQIAKELNLPREEVVFALDAIQDPVSLFEPIYHDGGDAIYVMDQ 188

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    +  E  L            +  +M  LN RE+ I   R    N  T   ++ E  
Sbjct: 189 ISDSKNSDESWLEN--------ISIKEAMKKLNDREKLILTLRFF--NGRTQMEVADEIG 238

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A K +++ +
Sbjct: 239 ISQAQVSRLEKTALKHMRKYV 259


>gi|67925817|ref|ZP_00519113.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4 [Crocosphaera
           watsonii WH 8501]
 gi|67852341|gb|EAM47804.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4 [Crocosphaera
           watsonii WH 8501]
          Length = 386

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 59/238 (24%), Positives = 122/238 (51%), Gaps = 10/238 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  +++ ++LRLVV ++  Y+G GL   ++VSEGN+GL++AV+KF+ ++G++ +TY+ 
Sbjct: 21  KRAKEKMIQANLRLVVAVSKKYQGKGLEFMDLVSEGNLGLIRAVEKFEYDKGYKFSTYAY 80

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            WI+ A+   I      +++    N+      + +LK     I     +   V  ++++L
Sbjct: 81  HWIRQALVRAICDKGRTIRVPVHINE-----EISKLKKVQLEIRQKYGRSATVRELSERL 135

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +S  ++  +        SL+  +   + NS+      + D +G  Q  ++       + 
Sbjct: 136 EISPEKIRVLRSVNNPMLSLDQKVLGDEDNSTLL--SFLADPNGDLQKFLDNL---GNKE 190

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++ + +  L P+E+R+     L+   +TL  +  +  +SRERVR I+  A  K+++ I
Sbjct: 191 LVEQCLCGLKPQEQRVLREYYLETPSLTLNEIGKKMNLSRERVRHIKNNALDKLKQVI 248


>gi|312794092|ref|YP_004027015.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
 gi|312181232|gb|ADQ41402.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
          Length = 255

 Score =  178 bits (451), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 61/259 (23%), Positives = 121/259 (46%), Gaps = 17/259 (6%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L  +E+  L KR +E GD  A    +  +LRLV+ +   +   G  + ++   G IG
Sbjct: 14  LPVLSHEEKLELLKRMKE-GDKEARRIFIEGNLRLVLSVVQKFANRGENLDDLFQVGCIG 72

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A+  FD  +  + +TY++  I   ++ Y+  + S+ +I  +   K   +   ++K  
Sbjct: 73  LIKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNSM-RISRSL--KDTAYKALKIK-- 127

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            +   +NN K   +  IAK+L+V++ E++     +    SL   +   D   + +    +
Sbjct: 128 -EKYINNNQKEPTLEEIAKELSVTKEELVFALDSIQEPISLYEPVFQ-DSTDTMYVVEKL 185

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            DH   E V +E+         L  ++S L  RE+ I   R  +    T   ++    +S
Sbjct: 186 CDHKSCENVWLEEIS-------LKDALSRLTKREKEILYLRYYKG--KTQMEVARIVGIS 236

Query: 266 RERVRQIEARAFKKVQESI 284
           + +V +IE  A   +++ I
Sbjct: 237 QAQVSRIEKSAIGHIKKYI 255


>gi|289578664|ref|YP_003477291.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter italicus Ab9]
 gi|297544884|ref|YP_003677186.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
 gi|289528377|gb|ADD02729.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter italicus Ab9]
 gi|296842659|gb|ADH61175.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
          Length = 256

 Score =  177 bits (450), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 55/261 (21%), Positives = 116/261 (44%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+  ++  L  R + +GD  A    +  +LRLV+ +   +   G  + ++   G 
Sbjct: 13  SKLPVLKPSKQKELLIRMK-NGDKKAREEFINGNLRLVLSVIQRFNNRGEYVDDLFQVGC 71

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD ++  + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 72  IGLIKAIDNFDLDQNVKFSTYAVPMIIGEIRRYLRDNT-PIRVSRSL--RDIAYKALQVR 128

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L      N K   V  IAK+L++   EV+     +    SL   I     ++    D 
Sbjct: 129 DKL---VSENSKEPTVGEIAKELDLPREEVVMALDAIQEPVSLFEPIYHDGGDAIYVMDQ 185

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  D +  E  L         +  L  ++  LN RE+ I   R       T   ++ E  
Sbjct: 186 VSDDKNIDEVWLE--------KIALKEAIQKLNEREKLILTLRFF--EGKTQMEVAKEIG 235

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A   +++ I
Sbjct: 236 ISQAQVSRLEKAALNHMRKYI 256


>gi|1769588|gb|AAB95226.1| sigma factor [Synechococcus sp. PCC 7002]
          Length = 328

 Score =  177 bits (450), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 63/319 (19%), Positives = 138/319 (43%), Gaps = 53/319 (16%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------------EHGDLS--------- 48
           +    +  Y+ EI ++P+L  +EE V  K+ +             E  D           
Sbjct: 15  SSADMVRTYLREIGRVPLLTHEEEIVYGKQVQRLMALQEKRQTLEESLDRERTREEWAEA 74

Query: 49  -----------------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A  +++ ++LRLVV IA   +   L   +++ EG++GL + V+
Sbjct: 75  AQLTPKQLQRDLQIGERAKRKMIEANLRLVVAIARNIKKRNLEFLDLIQEGSLGLERGVE 134

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFDP +G++ +TY+ WWI+ A+   I +    +++     +K     L ++K   + +  
Sbjct: 135 KFDPTKGYKFSTYAYWWIRQAITRAIAQQGRTIRLPIHITEK-----LNKIKKTQRQLAQ 189

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
           +  +   +  IA+ L +  +++           SL+  +   D   ++  D L    +  
Sbjct: 190 DLGRAATIAEIAEALELEPAQIREYFRVSRHPISLD--VRVGDNQDTELMDLLEDSGESP 247

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERV 269
           +  +  +  +++ R+++      L P+++ +   R    +   ++L  +     +SRERV
Sbjct: 248 DNNVTYELLKQDLRDLIAD----LTPQQQEVIILRFGLNDGKELSLAKIGKRMNLSRERV 303

Query: 270 RQIEARAFKKVQESIQKQV 288
           RQ+E +A   ++   + Q+
Sbjct: 304 RQLERQALNHLRRR-RSQI 321


>gi|309786170|ref|ZP_07680798.1| RNA polymerase sigma factor RpoS [Shigella dysenteriae 1617]
 gi|308925915|gb|EFP71394.1| RNA polymerase sigma factor RpoS [Shigella dysenteriae 1617]
          Length = 237

 Score =  177 bits (450), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 66/237 (27%), Positives = 120/237 (50%), Gaps = 12/237 (5%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           ++  I+     +++      K L   LR  +     ++           IA++L+    +
Sbjct: 61  IERAIMNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDD 115

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           V  M        S++  +    +     +  L    D +E    +  +  + +  + + +
Sbjct: 116 VSRMLRLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWL 170

Query: 233 SVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             LN ++R +   R   L     TLE++  E +++RERVRQI+    ++++E +Q Q
Sbjct: 171 FELNAKQREVLARRFGLLGYEAATLEDVGREIDLTRERVRQIQVEGLRRLREILQTQ 227


>gi|162450883|ref|YP_001613250.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
 gi|161161465|emb|CAN92770.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
          Length = 463

 Score =  177 bits (450), Expect = 1e-42,   Method: Composition-based stats.
 Identities = 63/237 (26%), Positives = 118/237 (49%), Gaps = 13/237 (5%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V ++LRLV   A   R  G+P+ +++ EGN+GL++A +KFD  RG+R +TY+MWWIK A+
Sbjct: 231 VRANLRLVAAAARQLRHRGVPLLDLIQEGNLGLIRAAEKFDYRRGYRFSTYAMWWIKQAL 290

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
              +L    ++++     + R     RR     + +   + +      +A++  +S  ++
Sbjct: 291 SRALLYQGQVIRVPVHIAETR-----RRALQARRELEQEHAREAAPEEVAERSGLSMEKL 345

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
            ++         L+A +   D + ++  D+   +    +++L+     +     ++  + 
Sbjct: 346 QALREMALPPVYLDAPV--GDDDGARQGDFFASEGAAPDELLV----HRRLHAQVSALLE 399

Query: 234 VLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            L PRER +   R   +   P TL  +   F VSRERVRQIE  A  K++   ++Q 
Sbjct: 400 SLTPRERDVLRLRFGLDGGQPHTLAEIGGMFSVSRERVRQIEESALSKLRTLSRRQA 456


>gi|973980|gb|AAB05357.1| RNA polymerase sigma factor [Cyanidium caldarium]
          Length = 609

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 72/343 (20%), Positives = 143/343 (41%), Gaps = 79/343 (23%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYR--------------EHGDL------------- 47
            +  ++ EI  +P+L + +   LA+  R              E+G               
Sbjct: 260 SMGAFLKEIGSVPLLTESQVVSLAREIRKLALWNATRIQLRHEYGKEPDRTEWAKALNMS 319

Query: 48  ------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
                        A   LV ++LRLVV +A  +   GL + +++ EG+IGL++  ++FD 
Sbjct: 320 AEELTRNLLRAQRARESLVAANLRLVVSVAKQFTNRGLSMQDLIQEGSIGLIKGAERFDY 379

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
             GFR +TY+MWWI+ AMQ  I  +   ++I +T     +     RL      ++    +
Sbjct: 380 RTGFRFSTYAMWWIRQAMQRAIADTSRPIRIPSTITDLSVQIYRARL-----ELSSTLGR 434

Query: 156 PEQVVAIAKKLNVSESEV--ISMNCRLAGDESLNALIN--------------SSDKNSS- 198
                 +A  L++S   +  + +    +   SL+A ++               +D  SS 
Sbjct: 435 DPTDAELADFLDISVQRLQDVKLYTNQSATVSLDAPVSRQVTNTCIKSKGTGDTDVFSSK 494

Query: 199 --------------QWQDWLVYDHDGQEQVLIEKEERKN--RRNMLTRSMSVLNPRERRI 242
                         +  D+ + D    ++ +  +    +   R+ +  ++S+LNP ER +
Sbjct: 495 ADGKLSKNGYGSRHKLGDFTLGDTVQTDESVSPEHMMADSLMRDDIECALSLLNPYEREV 554

Query: 243 FEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQES 283
              R   ++    +++ + + + V   R+R+IEARA +K++  
Sbjct: 555 IRMRFGLDDGRMKSVDEVCAYYCVQTSRIRRIEARALRKLRHP 597


>gi|260906263|ref|ZP_05914585.1| RNA polymerase, sigma 32 subunit, RpoH [Brevibacterium linens BL2]
          Length = 903

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 70/292 (23%), Positives = 120/292 (41%), Gaps = 44/292 (15%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKR--------------------------YR 42
           + + +  L  Y+ +I + P+L   EE  +AKR                          + 
Sbjct: 572 VTDTDDLLGVYLKQIGQYPLLSAAEEVAVAKRIEAGMYATHVLSLGQYQTRRERRALEWV 631

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           +    +A   +VTS+LRLVV IA  +    L + +++ EGN+GL++AV+KFD  +G + +
Sbjct: 632 KADGAAAYEEMVTSNLRLVVSIAKRFNRSKLDLLDLIQEGNLGLVRAVQKFDYTKGNKFS 691

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL-FFNLRRLKGHLQAITDNNLKPEQVVA 161
           TY+ WWI+  +   I  +   +++     +K   F+N  R      A   ++ K EQ + 
Sbjct: 692 TYATWWIRQGIDRGIGDTAKTIRLPIHLFEKASEFWNCMRDDESRAACDHDHSKVEQALR 751

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           +         + +S+         L    +     S    D  + D D        K   
Sbjct: 752 M---------QPVSLEGY------LELQWDGHYAESLMSFDDRIADPDVFTDNPETKIVD 796

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQ 271
                 +   +  L  RE  I   R     E P TL+ + + F V+RER+RQ
Sbjct: 797 GELLETVNSVVDSLPAREAEIIRRRFGWNGEPPQTLDAIGNRFAVTRERIRQ 848


>gi|154685949|ref|YP_001421110.1| sporulation sigma factor SigG [Bacillus amyloliquefaciens FZB42]
 gi|154351800|gb|ABS73879.1| SigG [Bacillus amyloliquefaciens FZB42]
          Length = 260

 Score =  177 bits (450), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 59/263 (22%), Positives = 119/263 (45%), Gaps = 16/263 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+ +E   L ++ ++ GD SA  +LV  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLKNEEMRKLFRQLQDEGDDSAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGC 73

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+++  FD     + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 74  IGLMKSIDNFDLSHNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVR 130

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L + T      E    IAK L V   E++     +    SL   I +   +     D 
Sbjct: 131 ERLISETSREPTAE---EIAKVLEVPHEEIVFALDAIQDPVSLFEPIYNDGGDPIYVMDQ 187

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  + +   Q + E          L   M  LN RE+ I   R  Q    T   ++ E  
Sbjct: 188 ISDERNKDTQWIEELA--------LKEGMRRLNEREKMILRKRFFQG--KTQMEVAEEIG 237

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+ +V ++E  A K++ ++I +
Sbjct: 238 ISQAQVSRLEKAAIKQMNKNIHQ 260


>gi|297580668|ref|ZP_06942594.1| LOW QUALITY PROTEIN: RNA polymerase sigma factor RpoS [Vibrio
           cholerae RC385]
 gi|297535084|gb|EFH73919.1| LOW QUALITY PROTEIN: RNA polymerase sigma factor RpoS [Vibrio
           cholerae RC385]
          Length = 236

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 60/224 (26%), Positives = 105/224 (46%), Gaps = 12/224 (5%)

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     ++
Sbjct: 9   RRYSNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIR 68

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           +      K L   LR  +     ++           IA +L+    +V  M        S
Sbjct: 69  LPIHVV-KELNIYLRTAR----ELSQRLDHEPTPEEIALELDRPVDDVTKMLRLNERISS 123

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           ++  I           D L   H+   +   + +   + R  L   +  LNP+++ +   
Sbjct: 124 VDTPI--GGDGDKALLDILPDSHNADPEFSTQDD---DIRESLLNWLDELNPKQKEVLAR 178

Query: 246 RR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 179 RFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVKQ 222


>gi|317051905|ref|YP_004113021.1| sigma-70 family RNA polymerase sigma factor [Desulfurispirillum
           indicum S5]
 gi|316946989|gb|ADU66465.1| RNA polymerase sigma factor, sigma-70 family [Desulfurispirillum
           indicum S5]
          Length = 305

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 79/282 (28%), Positives = 143/282 (50%), Gaps = 13/282 (4%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           +     L  Y+  I +I +L  +EE  LA+R    GD  A   LV S+LR VVKIAM YR
Sbjct: 29  IPSGDSLRDYLRRISRITLLTAEEEKELARRIS-AGDEQAFRVLVESNLRFVVKIAMKYR 87

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
             G+ + ++++EGNIGL++A ++FDPERG R  TY++WWIK ++ + I+ S + V++   
Sbjct: 88  DIGINLLDLINEGNIGLLEAARRFDPERGNRFITYAVWWIKQSIIQAIISSSNTVRLP-- 145

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             Q R    L   +       D++ +      +  +  +  S +  +        SL+  
Sbjct: 146 GKQARFASKLNSARREF--ARDHDGREPTEQELRDEYGLDISNIEDILRATRSYISLDTP 203

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   D+ + +       +   +EQ + +K   +     +   ++ L  R+  + + R   
Sbjct: 204 IGEDDERTLKDVLESPEESSTEEQYVRQKISTE-----IRSIIAELESRDALVVDLRFGI 258

Query: 250 EN--PVTLENLSSEFEVSRERVRQIEARAFKKV-QESIQKQV 288
               P TL+ + +   +S+ERVRQIE RA K++ ++++ +++
Sbjct: 259 SEGIPQTLDEVGTRLGLSKERVRQIEERALKRLQRKAMNRKL 300


>gi|293977922|ref|YP_003543352.1| sigma-70 family RNA polymerase sigma factor [Candidatus Sulcia
           muelleri DMIN]
 gi|292667853|gb|ADE35488.1| RNA polymerase sigma factor, sigma-70 family [Candidatus Sulcia
           muelleri DMIN]
          Length = 342

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 67/244 (27%), Positives = 123/244 (50%), Gaps = 11/244 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   LV ++LR V+ IA  Y+  GL +S++++EGN GL++ + +FD  +GF+  +Y +WW
Sbjct: 105 ALDNLVKANLRFVISIAKQYQNQGLSLSDLINEGNFGLIKGINRFDERKGFKCISYCVWW 164

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ ++ + I      V+  T  N+   +  + +    L+        P  +  I+  LNV
Sbjct: 165 IRQSILQAISDKARCVRYPT--NKLAFYNKVNKTYSKLEQKLKM---PPSIKYISDYLNV 219

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SE +V           SL+A +   + ++S   D +  D   +    +EKE  +    +L
Sbjct: 220 SEKDVEEALINSIKHTSLDAPL--GEGDNSNLYDVIKIDESPKTDHSLEKESLQQDIKIL 277

Query: 229 TRSMSVLNPRERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              +  L+ RE +I           + LE ++   +++RER RQIE  A K++++S +K+
Sbjct: 278 ---LETLSERESQIITLHYGLGCFSMNLEKIAYLLKLTRERCRQIEMHAIKRLKKSSRKE 334

Query: 288 VELS 291
           + LS
Sbjct: 335 ILLS 338



 Score = 36.3 bits (83), Expect = 5.3,   Method: Composition-based stats.
 Identities = 15/45 (33%), Positives = 26/45 (57%), Gaps = 3/45 (6%)

Query: 1  MNRKNMSIIVNGE---IGLSRYIHEIRKIPMLEKQEEYVLAKRYR 42
          M ++N+  I   E   + L +++ EI  IP+L ++EE+  AK  R
Sbjct: 1  MKKQNIITIPESESESLSLDKFLLEISNIPLLSQEEEFFWAKLAR 45


>gi|23978337|dbj|BAC21138.1| principal sigma factor [Pseudanabaena sp. PCC 7367]
          Length = 203

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 53/214 (24%), Positives = 102/214 (47%), Gaps = 13/214 (6%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+
Sbjct: 1   VQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
              I      +++        L+  + R+K   + ++    +      IA ++ ++  ++
Sbjct: 61  TRAIADQSRTIRLPVH-----LYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKL 115

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             +        SL   I    +  S+  D++  D     +   ++  +   R  L   + 
Sbjct: 116 RFIAKSAQLPISLETPI--GKEEDSRLGDFIESDG----ETPDDQVAKNLLREDLENVLG 169

Query: 234 VLNPRERRIFEARRLQENPV--TLENLSSEFEVS 265
            L+PRER + + R   ++    TLE +   F V+
Sbjct: 170 TLSPRERDVLKLRYGLDDGRMKTLEEIGQIFNVT 203


>gi|303238906|ref|ZP_07325437.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302593539|gb|EFL63256.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 257

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 56/261 (21%), Positives = 118/261 (45%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L   ++ VL +R  + GD SA    +  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLTNDQKKVLFERMHK-GDTSAREEFIKGNLRLVLSVIQRFNNRGEYVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD  +  + +TY++  I   ++ Y+  + S +++  +   + + +   + K
Sbjct: 73  IGLIKAIDNFDVSQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSL--RDIAYKALQAK 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L   T+ N K   V  I+K+L + + +++     +    SL   +     ++    D 
Sbjct: 130 ERL---TNKNSKEPTVDDISKELGIPKEDIVFALDAIQDPISLFESVYHDGGDAIYVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  + +  E  L            L  +M  LN RE+ I   R    +  T   ++ E  
Sbjct: 187 VKDEKNHDENWLEGIA--------LNEAMRKLNDREKLILNLRFF--DGRTQMEVAEEIG 236

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A   +++ I
Sbjct: 237 ISQAQVSRLEKTALMHMRKYI 257


>gi|167717486|ref|ZP_02400722.1| RNA polymerase sigma factor [Burkholderia pseudomallei DM98]
          Length = 294

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 60/266 (22%), Positives = 127/266 (47%), Gaps = 16/266 (6%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDL---SAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
             +R++P    ++    A+R    G+    +A  R+  ++LRLV+ IA  Y   GL +++
Sbjct: 24  RAMRRLP-TSPEKSDAGAQRAFADGEARISAATARMAEANLRLVLSIARKYASRGLDLAD 82

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGN+GL++A++KF+  RGF+ +TY+ WWI+ A+   +      +++           
Sbjct: 83  LLQEGNLGLLRAIEKFEHRRGFKFSTYATWWIRQAISRAVADRARTIRVPVHV-----GD 137

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
             RR++     I   +     +  +++   +    + ++        SLNA +   D + 
Sbjct: 138 EARRVRKAADRIERRSGVSASLAELSEATGLPAERLRAVLTLPREPRSLNAPL--GDDDQ 195

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTL 255
           +++ D +    D     L +        +++T  +  ++ +E  I   R     + P + 
Sbjct: 196 AEFGDIV---EDTSTPSLFDALAHGQMCDVVTSLLKTMSAQEADILRRRFGIGGDEPWSY 252

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           E +++   VSRE+VR+IE RA + ++
Sbjct: 253 EQIAARAGVSREQVRRIEKRALQTLR 278


>gi|23978369|dbj|BAC21149.1| principal sigma factor [Pseudanabaena sp. PCC 7403]
          Length = 203

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 53/214 (24%), Positives = 101/214 (47%), Gaps = 13/214 (6%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+
Sbjct: 1   VQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
              I      +++        L+  + R+K   + ++    +      IA ++ ++  ++
Sbjct: 61  TRAIADQSRTIRLPVH-----LYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKL 115

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             +        SL   I    +  S+  D++  D     +   ++  +   R  L   + 
Sbjct: 116 RFIAKSAQLPISLETPI--GKEEDSRLGDFIESDG----ETPDDQVAKSLLREDLESVLG 169

Query: 234 VLNPRERRIFEARRLQENPV--TLENLSSEFEVS 265
            L+PRER +   R   ++    TLE +   F V+
Sbjct: 170 TLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVT 203


>gi|206563110|ref|YP_002233873.1| RNA polymerase sigma factor [Burkholderia cenocepacia J2315]
 gi|198039150|emb|CAR55114.1| RNA polymerase sigma factor [Burkholderia cenocepacia J2315]
          Length = 508

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 52/230 (22%), Positives = 103/230 (44%), Gaps = 13/230 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   ++ ++LRLV+ IA  Y   G+ +S++V +G +GLM+A++KF+  RGF+ +TY+ 
Sbjct: 269 RDATRAMLEANLRLVLSIARKYLNRGVDLSDLVQDGCLGLMRAIEKFEYRRGFKFSTYAT 328

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      +++             +R++ H         +      +A + 
Sbjct: 329 WWIRQAIARAVADRSRTIRVPVHV-----GDQYQRVQRHALRFRQRTGRRATPAELAAET 383

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++E ++ ++    A   SL+  +  +D    +         D       E+      R+
Sbjct: 384 GLAEDKLRAVLALPAEPVSLDTPLPDADTGLVELI------EDQASASPFEQLADTRMRD 437

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEA 274
            +   +  + P E  +   R       P T + ++ +  +SRERVRQIE 
Sbjct: 438 CVRSLLRSVTPTEADVLRRRFGLGGAEPDTYDAIAQDAGMSRERVRQIEK 487


>gi|254282580|ref|ZP_04957548.1| RNA polymerase principal sigma factor SigA [gamma proteobacterium
           NOR51-B]
 gi|219678783|gb|EED35132.1| RNA polymerase principal sigma factor SigA [gamma proteobacterium
           NOR51-B]
          Length = 429

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 64/240 (26%), Positives = 109/240 (45%), Gaps = 12/240 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   LV  +LRLV  IA  Y+G G+   ++V EG +GL++A +KF+ E+G+R +TY   
Sbjct: 187 KARDALVMHNLRLVYSIAARYKGRGVNYLDLVQEGTLGLIRAAEKFEFEKGYRFSTYCFN 246

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI  +++ Y+    SL++  T   +      + RL       T           +AK L 
Sbjct: 247 WITQSVRRYVGDVGSLIRFPTHVQE-----QMGRLYREKALETARTGIEPDEETLAKNLG 301

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +   +   +        SL+A     D+ +    D +  D  G  +   +  E+ +    
Sbjct: 302 MDLDKTRELLQLRNLGVSLDAPRFDDDEGT--MVDSMTGDTFGDTE---DTAEQDSLNRF 356

Query: 228 LTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           LT ++  L P ER +  AR       P++   ++ +  VSRE VRQ+E    KK++   +
Sbjct: 357 LTNAIDTLEPAERDVVTARWGLHSGPPLSRAEIADKLGVSREWVRQLERSGLKKLRGQSE 416


>gi|196247722|ref|ZP_03146424.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
 gi|196212506|gb|EDY07263.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
          Length = 259

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 61/262 (23%), Positives = 119/262 (45%), Gaps = 17/262 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+ +E   L +R  E GDL A  +LV  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLKNEEMRELFQRMHE-GDLEAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+++  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 73  IGLMKSIDNFDLNQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVR 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L        K      IAK+L V+  EV+     +    SL   I +   +     D 
Sbjct: 130 ERL---MGETAKEPSTEEIAKELGVAHEEVVLALDAIQDPVSLFEPIYNDGGDPIYVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L  + +   Q + E          L   +  LN RE+ I   R  Q    T   ++ E  
Sbjct: 187 LSDERNRDSQWIEEIA--------LKEGLRRLNEREKMIIRKRFFQG--KTQMEVAEEIG 236

Query: 264 VSRERVRQIEARAFKKVQESIQ 285
           +S+ +V ++E  A +++ ++IQ
Sbjct: 237 ISQAQVSRLEKAAIRQMNKNIQ 258


>gi|332297914|ref|YP_004439836.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           brennaborense DSM 12168]
 gi|332181017|gb|AEE16705.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Treponema
           brennaborense DSM 12168]
          Length = 269

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 70/273 (25%), Positives = 127/273 (46%), Gaps = 15/273 (5%)

Query: 17  SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
           + Y+ +I++ P+L  ++E  L+     +GD SA  +LV S+LRLVV IA  Y    + + 
Sbjct: 7   ASYMAQIQRYPLLTPEQEKKLSADIH-NGDTSAKLKLVQSNLRLVVSIANKYVSDRIGVM 65

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++ EGN+GL+ A  KF      R +TY+  WI   +  +I      + +     +    
Sbjct: 66  DLIQEGNLGLLTAASKFHYSFNTRFSTYAYSWITQYILRFIQNKIPYITLPHRKEE---- 121

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
             LR++      +         +  IA  ++VSES++           S++A I     +
Sbjct: 122 -MLRKIHMAKIDLMQQLQSEPTLREIASYMDVSESDISGALMHEYVYSSIDAEI--DGTS 178

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN---PV 253
           +    D +       EQ+ ++  E ++ R+++      L  RER++   R   +N   P 
Sbjct: 179 NLTCADMIADPSPSPEQLCLKNLEAEDIRSLV----ETLPDRERQVIYYRFNFDNSRKPW 234

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TL  +S    +S E VRQ+E RA + ++ +  K
Sbjct: 235 TLRQISEMLGISAETVRQMELRALQFLRTAAVK 267


>gi|326204636|ref|ZP_08194492.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium papyrosolvens
           DSM 2782]
 gi|325985203|gb|EGD46043.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium papyrosolvens
           DSM 2782]
          Length = 257

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 55/261 (21%), Positives = 117/261 (44%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L  +++ VL +R  + GD SA    +  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLTNEQKKVLFERMHK-GDNSARDEFINGNLRLVLSVIQRFNNRGEYVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD  +  + +TY++  I   ++ Y+  + S +++  +   + + +   + K
Sbjct: 73  IGLIKAIDNFDVSQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSL--RDIAYKALQAK 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L   T  N K   +  +A++L + + +++     +    SL   +     ++    D 
Sbjct: 130 ERL---TTQNSKEPTIAELAQELQLPKEDIVFALDAIQDPISLFESVYHDGGDAIYVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  D +  E  L            L  +M  LN RE+ I   R       T   ++ E  
Sbjct: 187 VSDDKNIDENWLE--------TISLKEAMRKLNDREKLILNLRFF--EGRTQMEVADEIG 236

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A   +++ I
Sbjct: 237 ISQAQVSRLEKTALMHMKKYI 257


>gi|17158744|ref|NP_478255.1| group 2 sigma 70-type sigma factor [Nostoc sp. PCC 7120]
 gi|17134693|dbj|BAB77251.1| group 2 sigma 70-type sigma factor [Nostoc sp. PCC 7120]
          Length = 323

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 61/305 (20%), Positives = 133/305 (43%), Gaps = 51/305 (16%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYRE----------------------------------- 43
           Y+ +I ++P+L  +EE V +K+ ++                                   
Sbjct: 18  YLQDIVRVPLLTHEEEIVYSKQVQQMMVLQKKKETLKKQLNHEPSQKELAKYVQLSEIEV 77

Query: 44  ----HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
                    A  +++ ++LRLVV IA  Y+   L + +++ EG++GL + V+KFDP RG+
Sbjct: 78  KDIFQQGTQAKQKMMVANLRLVVAIAKKYQRRNLELMDLIQEGSLGLERGVEKFDPTRGY 137

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WWI  AM   I +    +++     +K     L + K   + ++    +    
Sbjct: 138 KFSTYAYWWISQAMTRAISQQSRTIRLPIHITEK-----LNKFKKVQRELSQKLKRSPSA 192

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IA+K+ ++ +++  +        SL+  +   D   ++ Q+ L    +   ++   + 
Sbjct: 193 DEIAEKMKLNPAQIRELLMISRQPASLDKQV--GDNEDTELQELLTEVPETSPEI---QV 247

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
            +   R  +  S+  L P+++++       E+   +TL  ++    +S  RVR +E +A 
Sbjct: 248 TQNLMRQDIYLSLRELTPQQQQVLILHYGLEDNYELTLTQVAQHLNISERRVRYLEKQAL 307

Query: 278 KKVQE 282
             ++ 
Sbjct: 308 SYLRR 312


>gi|32472693|ref|NP_865687.1| RNA polymerase sigma factor rpoS [Rhodopirellula baltica SH 1]
 gi|32443930|emb|CAD73372.1| RNA polymerase sigma factor rpoS [Rhodopirellula baltica SH 1]
          Length = 355

 Score =  177 bits (449), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 75/275 (27%), Positives = 135/275 (49%), Gaps = 13/275 (4%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
            +  L  Y+ EI + P+L  +EE  LA R  + GD+ A  ++V ++LRLVV I+ GY G 
Sbjct: 84  AQSPLETYLREINETPLLSAEEELELAARIAQ-GDVMARDQMVRANLRLVVNISRGYTGK 142

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL + +++ EGN+GL++AV+ FDP  G R +TY+ +WIK +++  ++ S   ++I   A 
Sbjct: 143 GLGLQDLIEEGNLGLLRAVEGFDPIHGTRFSTYASYWIKQSIKRALINSAKTIRIP--AY 200

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
              L    RR    L          E+V   A+ L + + ++  +   +  + S     +
Sbjct: 201 MVELLSKWRRATARLNEELGRTPTNEEV---ARVLGLPKKKLPIIRKAIKINNS--TPQS 255

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE- 250
              +      D +    D + +   E+    +        +  L  RE  + + R     
Sbjct: 256 DQTEAGWSLGDMV---QDERLKAPDEEMLDHDILKHAMSLLGDLEERESTVLKLRFGLGG 312

Query: 251 -NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             P+TL+ + +E  ++RERVRQIE  A +++ + +
Sbjct: 313 VEPMTLKEIGAELGLTRERVRQIETEALRRLADGL 347


>gi|16078597|ref|NP_389416.1| sporulation sigma factor SigG [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221309407|ref|ZP_03591254.1| sporulation sigma factor SigG [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221313732|ref|ZP_03595537.1| sporulation sigma factor SigG [Bacillus subtilis subsp. subtilis
           str. NCIB 3610]
 gi|221318656|ref|ZP_03599950.1| sporulation sigma factor SigG [Bacillus subtilis subsp. subtilis
           str. JH642]
 gi|221322929|ref|ZP_03604223.1| sporulation sigma factor SigG [Bacillus subtilis subsp. subtilis
           str. SMY]
 gi|321315298|ref|YP_004207585.1| sporulation sigma factor SigG [Bacillus subtilis BSn5]
 gi|133475|sp|P19940|RPSG_BACSU RecName: Full=RNA polymerase sigma-G factor; AltName: Full=Stage
           III sporulation protein G
 gi|143430|gb|AAA22703.1| sporulation-specific sigma factor [Bacillus subtilis]
 gi|580764|emb|CAA40771.1| sigma-G factor [Bacillus subtilis subsp. subtilis str. 168]
 gi|2633906|emb|CAB13407.1| RNA polymerase sporulation-specific sigma factor (sigma-G)
           [Bacillus subtilis subsp. subtilis str. 168]
 gi|320021572|gb|ADV96558.1| sporulation sigma factor SigG [Bacillus subtilis BSn5]
          Length = 260

 Score =  176 bits (448), Expect = 2e-42,   Method: Composition-based stats.
 Identities = 59/263 (22%), Positives = 119/263 (45%), Gaps = 16/263 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+ +E   L ++ ++ GD SA  +LV  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLKNEEMRKLFRQLQDEGDDSAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGC 73

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+++  FD     + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 74  IGLMKSIDNFDLSHNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVR 130

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L + T      E    IAK L V   E++     +    SL   I +   +     D 
Sbjct: 131 ERLISETSKEPTAED---IAKVLEVPHEEIVFALDAIQDPVSLFEPIYNDGGDPIYVMDQ 187

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  + +   Q + E          L   M  LN RE+ I   R  Q    T   ++ E  
Sbjct: 188 ISDERNTDSQWIEELA--------LKEGMRRLNDREKMILRKRFFQG--KTQMEVAEEIG 237

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+ +V ++E  A K++ ++I +
Sbjct: 238 ISQAQVSRLEKAAIKQMNKNIHQ 260


>gi|149916815|ref|ZP_01905317.1| RNA polymerase sigma factor RpoD [Plesiocystis pacifica SIR-1]
 gi|149822532|gb|EDM81921.1| RNA polymerase sigma factor RpoD [Plesiocystis pacifica SIR-1]
          Length = 421

 Score =  176 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 71/247 (28%), Positives = 115/247 (46%), Gaps = 20/247 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            ++ V ++LRLVV IA  +    +P+ ++V EGN+GLM+AV +FDP RG+R +TY+ WWI
Sbjct: 181 KNKFVKANLRLVVTIARRFDHGLMPLQDLVQEGNLGLMKAVDRFDPTRGYRFSTYATWWI 240

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + A+   +      V++    +       LRR+   L+A T     PEQ+   A    +S
Sbjct: 241 RHAINRALANKGRTVRLPAHVSAD--LQRLRRVTRELEAKTGETPTPEQLAQAA---GLS 295

Query: 170 ESEVISMN-CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           ++ V  ++   L    SL+A  +  D         L    D    V  +  E +     L
Sbjct: 296 KTRVRKLSKLTLDPTVSLDAPSHDDDARG-----LLDRLEDASVPVAADILEHQALNEHL 350

Query: 229 TRSMSVLNPRERRIFEARRL---------QENPVTLENLSSEFEVSRERVRQIEARAFKK 279
             ++  L P E  I + R              P+TL  L     +SRER+RQ++ RA  K
Sbjct: 351 RDALYNLQPIELDILKRRYGIATSEAESVDFEPMTLRQLGERHSLSRERIRQLQERALTK 410

Query: 280 VQESIQK 286
           ++    +
Sbjct: 411 LRREFAR 417


>gi|312622917|ref|YP_004024530.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
 gi|312203384|gb|ADQ46711.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
          Length = 255

 Score =  176 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 57/259 (22%), Positives = 120/259 (46%), Gaps = 17/259 (6%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L  +E+  L KR +E GD  A    +  +LRLV+ +   +   G  + ++   G IG
Sbjct: 14  LPVLSHEEKLELLKRMKE-GDKEARRIFIEGNLRLVLSVVQKFANRGENLDDLFQVGCIG 72

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A+  FD  +  + +TY++  I   ++ Y+  + S+ +I  +   K   +   ++K  
Sbjct: 73  LIKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNSM-RISRSL--KDTAYKALKIK-- 127

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            +   + N K   +  IAK+L++++ +++     +    SL   +   D   + +    +
Sbjct: 128 -EKYINKNQKEPTLEEIAKELSITKEDLVFALDSIQEPISLYEPVFQ-DSTDTMYVVERL 185

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            DH   E V +E+         L  ++S L  RE+ I   R  +    T   ++    +S
Sbjct: 186 CDHKSCESVWLEEIS-------LKDALSKLTKREKEILYLRYYKG--KTQMEVAKIVGIS 236

Query: 266 RERVRQIEARAFKKVQESI 284
           + +V +IE  A   +++ +
Sbjct: 237 QAQVSRIEKSAIGHIKKYV 255


>gi|312128104|ref|YP_003992978.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor hydrothermalis 108]
 gi|311778123|gb|ADQ07609.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor hydrothermalis 108]
          Length = 255

 Score =  176 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 58/259 (22%), Positives = 120/259 (46%), Gaps = 17/259 (6%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L  +E+  L KR +E GD  A    +  +LRLV+ +   +   G  + ++   G IG
Sbjct: 14  LPVLSHEEKLELLKRMKE-GDKEARRIFIEGNLRLVLSVVQKFANRGENLDDLFQVGCIG 72

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A+  FD  +  + +TY++  I   ++ Y+  + S+ +I  +   K   +   ++K  
Sbjct: 73  LIKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNSM-RISRSL--KDTAYKALKIK-- 127

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            +   + N +   +  IAK+L++++ E++     +    SL   +   D   + +    +
Sbjct: 128 -EKYINKNHREPTLEEIAKELSITKEELVFALDSIQEPISLYEPVFQ-DSTDTMYVVEKL 185

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            DH   E V +E+         L  ++S L  RE+ I   R  +    T   ++    +S
Sbjct: 186 CDHKSCENVWLEEIS-------LKDALSKLTKREKEILYLRYYKG--KTQMEVARIVGIS 236

Query: 266 RERVRQIEARAFKKVQESI 284
           + +V +IE  A   +++ I
Sbjct: 237 QAQVSRIEKSAIGHIKKYI 255


>gi|162458688|ref|NP_001104923.1| sigma factor SIG2A [Zea mays]
 gi|4336606|gb|AAD17854.1| sigma factor SIG2A [Zea mays]
          Length = 539

 Score =  176 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 66/251 (26%), Positives = 119/251 (47%), Gaps = 15/251 (5%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E  L KR   +  +   +R+VTS++RLV+ IA  + G G+   +++ EG  GL++  +K
Sbjct: 284 DEKTLRKRL--NYGIYCKNRMVTSNVRLVISIAREFEGPGMDFYDLIQEGMQGLIRGAEK 341

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +GFR +TYS WWIK AM++ +     + ++     +        R+K   + +   
Sbjct: 342 FDSSKGFRFSTYSHWWIKQAMRKSVSEQSQIFRLPAHMVEASY-----RVKECTKRLRRK 396

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA    +    V +         SL++ I S+D        +     D   
Sbjct: 397 LRRRPTNEEIAVDTGIPIKRVEAAVNLPKYSVSLDSKIGSTD------MTYQEVTADPSA 450

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +   E   R + +  +  ++  L  RE+++   R   E+    TL+ + +   VSRER+R
Sbjct: 451 ETAEEMLNRMSMKKDVHMALDTLTTREKQVVVLRFGLEDGRIRTLQEIGNIMGVSRERIR 510

Query: 271 QIEARAFKKVQ 281
           QIE+ AF+K++
Sbjct: 511 QIESGAFRKLR 521


>gi|296331109|ref|ZP_06873583.1| sporulation sigma factor SigG [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|305674264|ref|YP_003865936.1| sporulation-specific sigma factor sigma-G [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|296151753|gb|EFG92628.1| sporulation sigma factor SigG [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|305412508|gb|ADM37627.1| sporulation-specific sigma factor sigma-G [Bacillus subtilis subsp.
           spizizenii str. W23]
          Length = 260

 Score =  176 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 59/263 (22%), Positives = 119/263 (45%), Gaps = 16/263 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+ +E   L ++ ++ GD SA  +LV  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLKNEEMRKLFRQLQDEGDDSAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGC 73

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+++  FD     + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 74  IGLMKSIDNFDLSHNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVR 130

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L + T      E    IAK L V   E++     +    SL   I +   +     D 
Sbjct: 131 ERLISETSKEPTAED---IAKVLEVPHEEIVFALDAIQDPVSLFEPIYNDGGDPIYVMDQ 187

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  + +   Q + E          L   M  LN RE+ I   R  Q    T   ++ E  
Sbjct: 188 ISDERNKDSQWIEELA--------LKEGMRRLNDREKMILRKRFFQG--KTQMEVAEEIG 237

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+ +V ++E  A K++ ++I +
Sbjct: 238 ISQAQVSRLEKAAIKQMNKNIHQ 260


>gi|229815207|ref|ZP_04445543.1| hypothetical protein COLINT_02253 [Collinsella intestinalis DSM
           13280]
 gi|229809217|gb|EEP44983.1| hypothetical protein COLINT_02253 [Collinsella intestinalis DSM
           13280]
          Length = 261

 Score =  176 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 60/260 (23%), Positives = 119/260 (45%), Gaps = 17/260 (6%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           +K++   L +R++E GD+ A  +LV SHL LV  IA  ++  G PI +++  G +GL++A
Sbjct: 12  DKEKTRELFRRFKEEGDMDAREKLVMSHLNLVRFIANKFKNRGEPIDDLIQVGYLGLLKA 71

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +FDP RG    T++   I   ++ +       V++      +RL     ++      +
Sbjct: 72  IDRFDPSRGLEFTTFATPTIMGEIKRHFRDKGWSVRVP-----RRLQELSAKVNQATDTL 126

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVYD 207
           T    +   +  IA  L+ +  EV+            SL A   + D ++    D    +
Sbjct: 127 TSQLQRSPTIAEIADYLDATVDEVLEAMESSSAYSSVSLEAPSGADDDDTPSVIDRYATE 186

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
                          + R ++  +++  +PRER + E R L+   +T   ++ +  +S+ 
Sbjct: 187 DS--------DLAFTDDRIIIEEALASFSPRERDVIEMRFLKG--MTQIEIAEKLGISQV 236

Query: 268 RVRQIEARAFKKVQESIQKQ 287
           +V ++  R  KK+Q+ I  +
Sbjct: 237 QVSRLLRRTLKKIQDKIDPE 256


>gi|332799104|ref|YP_004460603.1| RNA polymerase sigma-28 subunit SigG [Tepidanaerobacter sp. Re1]
 gi|332696839|gb|AEE91296.1| RNA polymerase, sigma 28 subunit, SigG [Tepidanaerobacter sp. Re1]
          Length = 257

 Score =  176 bits (448), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 52/261 (19%), Positives = 115/261 (44%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L   +   L  + ++ GD SA  +L++ +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLSNAKMKELFLQLQK-GDKSAREKLISGNLRLVLSVIQRFNNRGEYVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD  +  + +TY++  I   ++ Y+  +   +++      + L     +  
Sbjct: 73  IGLIKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-QIRVS-----RSLRDTAYKAL 126

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
               ++   N +   +  +AK++N+   EV+     +    SL   I     +     D 
Sbjct: 127 QVRDSLVTKNSREPSINEVAKEMNMPSEEVVFALDAIQEPVSLFEPIYHDGGDPIFVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  + +  +Q L        +   +  +M  L  RE++I   R       T   ++ E  
Sbjct: 187 ISDEKNQDDQWL--------QGISIKEAMQRLGEREKKILNLRFF--EGKTQMEVAQEIG 236

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A K +++ I
Sbjct: 237 ISQAQVSRLEKAALKHMRKFI 257


>gi|311068054|ref|YP_003972977.1| sporulation sigma factor SigG [Bacillus atrophaeus 1942]
 gi|310868571|gb|ADP32046.1| sporulation sigma factor SigG [Bacillus atrophaeus 1942]
          Length = 260

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 59/263 (22%), Positives = 119/263 (45%), Gaps = 16/263 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+ +E   L ++ ++ GD SA  +LV  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLKNEEMRKLFRQLQDEGDDSAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGC 73

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+++  FD     + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 74  IGLMKSIDNFDLSHNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVR 130

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L + T      E    IAK L V   E++     +    SL   I +   +     D 
Sbjct: 131 ERLISETSKEPTAED---IAKVLEVPHEEIVFALDAIQDPVSLFEPIYNDGGDPIYVMDQ 187

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  + +   Q + E          L   M  LN RE+ I   R  Q    T   ++ E  
Sbjct: 188 ISDERNKDTQWIEELA--------LKEGMRRLNDREKMILRKRFFQG--KTQMEVAEEIG 237

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+ +V ++E  A K++ ++I +
Sbjct: 238 ISQAQVSRLEKAAIKQMNKNIHQ 260


>gi|260589168|ref|ZP_05855081.1| RNA polymerase sigma-G factor [Blautia hansenii DSM 20583]
 gi|260540249|gb|EEX20818.1| RNA polymerase sigma-G factor [Blautia hansenii DSM 20583]
          Length = 266

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 48/262 (18%), Positives = 111/262 (42%), Gaps = 17/262 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            ++P+L  +E+  L  R +E GD  A  + +  +LRLV+ +   +        ++   G 
Sbjct: 21  SRLPILTNEEKDALFVRIKE-GDPEAREQYIKGNLRLVLSVIKRFSSSNENADDLFQIGC 79

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           +GL++A+  FD     + +TY++  I   ++ Y+  +   +++  +           +  
Sbjct: 80  VGLIKAIDNFDTTLNVKFSTYAVPMIIGEIRRYLRDNN-AIRVSRSLRDVAYKAIYAK-- 136

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
              +     NLK   +  IA+++ + + E++     +    SL   +  ++   + +   
Sbjct: 137 ---ENYVKQNLKEPTINEIAEEIGIDKEEIVYALDAIQSPVSLYEPVY-TEGGDTLYVMD 192

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
            + D   +E   IE          L  ++  L+ RE+ I   R       T   ++ E  
Sbjct: 193 QISDKKNKEDNWIENI-------ALKEALKKLDDREQHIVTMRFY--EGKTQMEVAEEIG 243

Query: 264 VSRERVRQIEARAFKKVQESIQ 285
           +S+ +V ++E  A K ++  ++
Sbjct: 244 ISQAQVSRLEKHALKTMRNYLR 265


>gi|167770711|ref|ZP_02442764.1| hypothetical protein ANACOL_02057 [Anaerotruncus colihominis DSM
           17241]
 gi|167667306|gb|EDS11436.1| hypothetical protein ANACOL_02057 [Anaerotruncus colihominis DSM
           17241]
          Length = 263

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 57/261 (21%), Positives = 118/261 (45%), Gaps = 18/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+ +L+++E+  L K+ R+ GD  A   ++  +LRLV+ +   +   G  + ++   G 
Sbjct: 21  SKLTVLKEKEKIELLKKIRQ-GDQKARQEMINGNLRLVLSVVQKFTNRGENLDDLFQVGC 79

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FDP +  R +TY +  I   ++ ++  + S V++  +   + L +   + K
Sbjct: 80  IGLIKAIDNFDPNQNVRFSTYGVPMIIGEIRRHLRDNNS-VRVSRSL--RDLAYKAMQAK 136

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
              +A+ + N K   V  IAK++   + +V+     +    SL   + S   ++    D 
Sbjct: 137 ---EALINRNSKEPTVEEIAKEMGAKKEDVVLALEAIVEPMSLYDPVYSDGGDTIYVMDQ 193

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +   +          E       +   +M  L  RE++I   R       T   ++ E  
Sbjct: 194 IGDKNS---------ESDWMDEIVFREAMKNLGDREKQILSLRFFGG--KTQMEVAKEIG 242

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A   V++ I
Sbjct: 243 ISQAQVSRLEKGALDWVKKHI 263


>gi|239623454|ref|ZP_04666485.1| RNA polymerase [Clostridiales bacterium 1_7_47_FAA]
 gi|239521485|gb|EEQ61351.1| RNA polymerase [Clostridiales bacterium 1_7_47FAA]
          Length = 258

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 57/260 (21%), Positives = 115/260 (44%), Gaps = 17/260 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L  +E+  L KR   +GD  A  + +  +LRLV+ +   +      I ++   G I
Sbjct: 15  KLPLLSNEEKEELFKRIL-NGDKDAREQYIKGNLRLVLSVIQRFSNSQENIDDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD  +  + +TY++  I   ++ Y+  + S +++      + L     +   
Sbjct: 74  GLIKAIDNFDITQNVKFSTYAVPMILGEVRRYLRDNNS-IRVS-----RSLRDTAYKALY 127

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + +T  N K   +V IA+++ VS+ ++      +    SL   +  +D     +    
Sbjct: 128 AREQLTRVNSKEPTLVEIAQEIGVSKEDITYALDAIQTPVSLYEPVY-TDGGDPLYVMDQ 186

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           + D    E+  +E          L  +M  L  RER I + R       T   ++ E  +
Sbjct: 187 ISDKKNLEENWVEDLS-------LVEAMKRLPERERHIIDMRFF--EGKTQTEVAEEIHI 237

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ +V ++E  A K ++  +
Sbjct: 238 SQAQVSRLEKNALKSMKTYL 257


>gi|26665386|dbj|BAC44904.1| principal sigma factor [Fischerella major NIES-592]
          Length = 203

 Score =  176 bits (447), Expect = 3e-42,   Method: Composition-based stats.
 Identities = 53/214 (24%), Positives = 102/214 (47%), Gaps = 13/214 (6%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+
Sbjct: 1   VQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
              I      +++        L+  + R+K   + ++    +      IA ++ ++  ++
Sbjct: 61  TRAIADQSRTIRLPVH-----LYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKL 115

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             +        SL   I    +  S+  D++  D     +   ++  +   R  L + + 
Sbjct: 116 RFIVKSAQLPISLETPI--GKEEDSRLGDFIESDG----ETPEDQVSKNLLREDLEKVLD 169

Query: 234 VLNPRERRIFEARRLQENPV--TLENLSSEFEVS 265
            L+PRER +   R   ++    TLE +   F V+
Sbjct: 170 SLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVT 203


>gi|255525678|ref|ZP_05392611.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium carboxidivorans
           P7]
 gi|296185436|ref|ZP_06853846.1| RNA polymerase sigma-G factor [Clostridium carboxidivorans P7]
 gi|255510664|gb|EET86971.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium carboxidivorans
           P7]
 gi|296050270|gb|EFG89694.1| RNA polymerase sigma-G factor [Clostridium carboxidivorans P7]
          Length = 257

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 58/260 (22%), Positives = 120/260 (46%), Gaps = 17/260 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+++E   L    R +GD+S   + + S+LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKEKEMKELLLSMR-NGDVSCREKFIKSNLRLVLSVIQRFNNRGENVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++++  FD  +  + +TY++  I   ++ Y+  + S +++  +          R L+ 
Sbjct: 74  GLIKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRDI----AYRALQV 128

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + I++NN K   V  IAK+L V   EV+     +    SL   I     ++    D +
Sbjct: 129 RDRLISENN-KEPTVSQIAKELKVPREEVVFALDAIQDPVSLFEPIYHDGGDAIYVMDQI 187

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             + +  +  L            +  +M  LN RE+ I   R    +  T   ++ E  +
Sbjct: 188 SDNKNMDDSWLENIA--------IKEAMKKLNDREKLILNLRFF--DGRTQMEVADEIGI 237

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ +V ++E  A + +++ +
Sbjct: 238 SQAQVSRLEKTALRHMRKYV 257


>gi|325475291|gb|EGC78476.1| region 2 family RNA polymerase sigma-70 factor [Treponema denticola
           F0402]
          Length = 275

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 71/273 (26%), Positives = 133/273 (48%), Gaps = 14/273 (5%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
            E  L +YI + +K P+L  ++E  LA   ++ G+  A   LVTS+LRLV+K+A  +   
Sbjct: 2   TENLLLQYIKDSKKYPLLSAEQEAELADEVKK-GNTEAIEVLVTSNLRLVIKMAKKFSSN 60

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
              I E++ EGN+GLM+A  KF      R ++Y+ WWIK +   Y+  +  ++K+     
Sbjct: 61  ENQILELIQEGNMGLMKAASKFSKSFKVRFSSYAAWWIKQSFIRYLNSADKVIKLPVR-- 118

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
           ++ L   + + + + +          Q+  I K+     ++V S N       SL+  + 
Sbjct: 119 KEALIRQVNKEEENYKIKYGILPSYSQLAEIMKEKVDIIAQVKSFN--YTDICSLDDPV- 175

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             ++ S+   D++  +    E+  I+ E     +  L + + +LN RE+ +   R   + 
Sbjct: 176 -DNERSANLYDFIPCNTYNPEEEFIDNE----FKEKLNKCLEILNDREKDVLRNRYGLDG 230

Query: 252 PV---TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +   T   L  ++ +S E +RQ + RA KK++
Sbjct: 231 TMTSTTFAVLGKKYSISAESIRQTQLRALKKLR 263


>gi|323486723|ref|ZP_08092043.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323692138|ref|ZP_08106382.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
 gi|323399942|gb|EGA92320.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323503825|gb|EGB19643.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
          Length = 258

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 57/261 (21%), Positives = 111/261 (42%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L   E+  L KR  + GD+ A  + +  +LRLV+ +   +      + ++   G 
Sbjct: 14  SKLPLLSNDEKEELFKRILD-GDMDAREQYIKGNLRLVLSVIQRFSNSSENVDDLFQIGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD  +  R +TY++  I   ++ Y+  + S +++  +           R  
Sbjct: 73  IGLIKAIDNFDITQNVRFSTYAVPMILGEVKRYLRDNNS-IRVSRSLRDTAYKAIYAR-- 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
              + +   NLK   +  IA ++ VS+  +      +    SL   +  +D     +   
Sbjct: 130 ---EGLMKRNLKEPTICEIADEIGVSKESITYALDAIQSPVSLYEPVY-TDGGDPLYVMD 185

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
            + D    E+  IE          L  +M  L  RER I + R       T   ++ E  
Sbjct: 186 QLSDKKCSEEHWIEDIS-------LNEAMKRLPERERHIIDMRFF--EGKTQTEVAEEIH 236

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A K ++  +
Sbjct: 237 ISQAQVSRLEKSALKNMRNYL 257


>gi|260893400|ref|YP_003239497.1| RNA polymerase, sigma 28 subunit, SigG [Ammonifex degensii KC4]
 gi|260865541|gb|ACX52647.1| RNA polymerase, sigma 28 subunit, SigG [Ammonifex degensii KC4]
          Length = 256

 Score =  176 bits (447), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 49/261 (18%), Positives = 113/261 (43%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L  Q+   L +  +  GD +A   L+  +LRLV+ +   +   G  + ++   G 
Sbjct: 13  SKLPVLTAQQMCRLFEAMK-RGDGNARSELIKGNLRLVLSVVQRFANRGEHLDDLFQVGC 71

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD ++  + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 72  IGLIKAIDNFDLDQNVKFSTYAVPMIIGEIRRYLRDNN-AIRVSRSL--RDIAYKALQVR 128

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L        +   V  IA+ L + + EV+     +    SL   +     +     D 
Sbjct: 129 DVL---ASQYAREPSVAEIAEALKLPQEEVVMALEAIQDPVSLFEPVYHDGGDPIYVMDQ 185

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  + +     L            +  +M  L+ RER+I + R       T   ++ E  
Sbjct: 186 VGDEKNQDVNWLENIA--------IKEAMKRLSERERQIIKMRFF--EGKTQMEVAEEIG 235

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A   +++ +
Sbjct: 236 ISQAQVSRLEKAALNHMRKYV 256


>gi|213421295|ref|ZP_03354361.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. E01-6750]
          Length = 191

 Score =  176 bits (446), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 78/196 (39%), Positives = 117/196 (59%), Gaps = 5/196 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +     L  YI      PML   EE  LA+R    GDL AA  L+ SHLR 
Sbjct: 1   MTKEMQNLALAPVGNLESYIRAANAWPMLSADEERALAERLHYQGDLEAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           W +VK+ TT  Q++LFFNLR+ K  L          ++V  +A++L VS  +V  M  R+
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DEVEMVARELGVSSKDVREMESRM 175

Query: 181 AGDESLNALINSSDKN 196
           A  +    + +  + +
Sbjct: 176 AAQDMTFDMSSDDESD 191


>gi|125585746|gb|EAZ26410.1| hypothetical protein OsJ_10293 [Oryza sativa Japonica Group]
          Length = 497

 Score =  176 bits (446), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 66/251 (26%), Positives = 119/251 (47%), Gaps = 15/251 (5%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E  L KR   +  +S  + +V S++RLV+ IA  + G G+  S+++ EG  GL++  +K
Sbjct: 242 DENTLRKRL--NYGISCKNTMVKSNVRLVISIAREFEGPGMEFSDLIQEGIQGLVRGAEK 299

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +GFR +TYS WWIK A+++ +L    ++++     +        R+K   + +   
Sbjct: 300 FDASKGFRFSTYSHWWIKQAIRKSVLEQTQIIRLPAHMAEAS-----SRVKECRRRLRRQ 354

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA    +    V +         SL + +  +D        +     D   
Sbjct: 355 LKRLPTNEEIASDTGMPLRRVEAAMSLPKYTVSLTSKVGCTD------MTYQEITPDTST 408

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +   E   R   +  + R++  L+PRER++   R   ++    TL ++     VSRER+R
Sbjct: 409 ETAEEMLHRWLMKEDVDRALDGLSPRERQVIRYRFGMDDGRLRTLHDIGRLMGVSRERIR 468

Query: 271 QIEARAFKKVQ 281
           QIE  AF+K++
Sbjct: 469 QIELVAFRKLR 479


>gi|225389920|ref|ZP_03759644.1| hypothetical protein CLOSTASPAR_03670 [Clostridium asparagiforme
           DSM 15981]
 gi|225044021|gb|EEG54267.1| hypothetical protein CLOSTASPAR_03670 [Clostridium asparagiforme
           DSM 15981]
          Length = 258

 Score =  176 bits (446), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 58/260 (22%), Positives = 115/260 (44%), Gaps = 17/260 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L  +E+ VL KR  + GD  A  + +  +LRLV+ +   + G    I ++   G I
Sbjct: 15  KLPLLSNEEKEVLFKRILD-GDKEAREQYIKGNLRLVLSVIQRFSGNQENIDDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD  +  + +TY++  I   ++ Y+  + S +++  +           R   
Sbjct: 74  GLIKAIDNFDITQNVKFSTYAVPMILGEVRRYLRDNNS-IRVSRSLRDTAYKAIYAR--- 129

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + +T  N K   +  IA+++ VS+ ++      +    SL   +  +D     +    
Sbjct: 130 --EQLTRLNSKEPTLAEIAQEIGVSKEDITYALDAIQTPVSLYEPVY-TDGGDPLYVMDQ 186

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           + D    E+  +E          L  +M  L  RER I + R       T   ++ E  +
Sbjct: 187 ISDKKNLEENWVEDLS-------LGEAMKRLPERERHIIDLRFF--EGKTQTEVAEEIHI 237

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ +V ++E  A K ++  +
Sbjct: 238 SQAQVSRLEKNALKTMKTYL 257


>gi|203284664|ref|YP_002222404.1| RNA polymerase sigma factor [Borrelia duttonii Ly]
 gi|201084107|gb|ACH93698.1| RNA polymerase sigma factor [Borrelia duttonii Ly]
          Length = 267

 Score =  176 bits (446), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 76/272 (27%), Positives = 142/272 (52%), Gaps = 18/272 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+  +R+  ++  +EE  LAK+ +  G L A ++++ ++LRLV+KI   Y G GL I
Sbjct: 9   LNIYLKSVREHRLITHEEEIELAKQIKL-GSLKAKNQMINANLRLVLKIIKRYAGKGLKI 67

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GL++A +K+DP +  + +TY+ +WIK ++Q  +     LVK+         
Sbjct: 68  EDLIQEGNLGLIRAAEKYDPSKNTKFSTYASFWIKQSLQRALNTKTRLVKVPYRKE---- 123

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + ++  +L        K  +   I ++ N++ ++ + +   L  + SL+  I  S+ 
Sbjct: 124 -NLILQINKYLME----EEKSPKKEDIMERFNLTTAQYVKIIPYLEKEYSLDKKIEGSEN 178

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN---P 252
             S   +    +    E  L +    K+   +L    + LN +ER I + R   +N    
Sbjct: 179 --STLLNLYEDNSFNPESTLEQNSTLKHLNYILE---TKLNEKERYIIKKRYNLDNSDKK 233

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL+++S+E  +S E VRQIE R  KK++E +
Sbjct: 234 STLKDISTELGISSETVRQIEKRVLKKLREEL 265


>gi|323099956|gb|ADX23556.1| RNA polymerase sigma-G factor [Bacillus mycoides]
          Length = 292

 Score =  176 bits (446), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 62/261 (23%), Positives = 121/261 (46%), Gaps = 17/261 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+ +E   L +  +  G++SA  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 48  KLPVLKNEEMRKLFREMQ-SGEISAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 106

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++ 
Sbjct: 107 GLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVRE 163

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L A    N K    + IAK L V+  E++     +    SL   I +   +     D L
Sbjct: 164 KLIA---ENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGGDPIFVMDQL 220

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             +    EQ + E          L   M  LN RE+ I   R  Q    T   ++ E  +
Sbjct: 221 SDEKQKDEQWVEELA--------LKEGMKRLNDREKMIIRKRFFQG--KTQMEVAEEIGI 270

Query: 265 SRERVRQIEARAFKKVQESIQ 285
           S+ +V ++E  A K++ ++IQ
Sbjct: 271 SQAQVSRLEKSAIKQMNKTIQ 291


>gi|167630136|ref|YP_001680635.1| RNA polymerase sigma-g factor, putative [Heliobacterium
           modesticaldum Ice1]
 gi|167592876|gb|ABZ84624.1| RNA polymerase sigma-g factor, putative [Heliobacterium
           modesticaldum Ice1]
          Length = 265

 Score =  176 bits (446), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 52/261 (19%), Positives = 111/261 (42%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L   E   L +  +  G+ SA  +L++ +LRLV+ +   +   G  + ++   G 
Sbjct: 22  SKLPVLTNAEMRTLFQAMQ-SGERSAREKLISGNLRLVLSVIQRFTNRGEYVDDLFQVGC 80

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+A+  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 81  IGLMKAIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVR 137

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
            HL    +   +   V  IA  L     EV+     +    SL   I     +     D 
Sbjct: 138 DHL---VNELSREPTVTEIADALGFPREEVVFALDAIQEPISLFEPIYHDGGDPIFVMDQ 194

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  + +   Q L            +  ++  LN RE+ I   R       T   ++ E  
Sbjct: 195 IGDEKNQDAQWLEGIA--------VREALRRLNDREKLILTLRFF--EGKTQMEVADEIG 244

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A   +++ +
Sbjct: 245 ISQAQVSRLEKAALTHMRKHV 265


>gi|269963639|ref|ZP_06177962.1| conserved hypothetical protein [Vibrio harveyi 1DA3]
 gi|269831652|gb|EEZ85788.1| conserved hypothetical protein [Vibrio harveyi 1DA3]
          Length = 279

 Score =  176 bits (446), Expect = 4e-42,   Method: Composition-based stats.
 Identities = 65/279 (23%), Positives = 123/279 (44%), Gaps = 17/279 (6%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY--- 68
           G+   + Y+ +I  I +L +++E   AK     GD  A   ++ S+LRLVVKIA  Y   
Sbjct: 8   GKDPYAHYLKDIVGIDLLSREDELHYAK-LNRAGDKEAREVMIESNLRLVVKIAKSYLKR 66

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            G    + +++ EGNIGL++A+ K+DPE G+R +TY++WWI+  ++  ++ +   V++  
Sbjct: 67  TGNNFTLLDLIEEGNIGLIKAIDKYDPEPGYRFSTYAVWWIRENIEAALMNNGRTVRLPA 126

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
                     +  L       +    K   +  ++    V    V  +   L+G   ++ 
Sbjct: 127 HV-----CKEINSLASKKHDASKTMSKDISISELSHCSGVKVERVDELVA-LSGFIDVST 180

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +     + +     L            +  E       L   ++ L  + +++   R  
Sbjct: 181 TV-----DLNHAPFVLEQCESEYTTDPQQDCEDHCFTQALEHVVNTLPVKLQQVLIHRFG 235

Query: 249 Q--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
               N  TL  +     VS ERVRQ++  A +++Q+ +Q
Sbjct: 236 LFEHNVKTLAEVGDLLNVSNERVRQMQKEAVERIQKRLQ 274


>gi|157692208|ref|YP_001486670.1| sporulation sigma factor SigG [Bacillus pumilus SAFR-032]
 gi|194014766|ref|ZP_03053383.1| RNA polymerase sigma-G factor [Bacillus pumilus ATCC 7061]
 gi|157680966|gb|ABV62110.1| DNA-directed RNA polymerase sigma subunit SigG [Bacillus pumilus
           SAFR-032]
 gi|194013792|gb|EDW23357.1| RNA polymerase sigma-G factor [Bacillus pumilus ATCC 7061]
          Length = 259

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 59/261 (22%), Positives = 117/261 (44%), Gaps = 16/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+  E   L ++ ++ GD +A  +LV  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLKNDEMRKLFRQLQDEGDDTAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGC 73

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+++  FD     R +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 74  IGLMKSIDNFDLSHNVRFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVR 130

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L + T      E    IAK L V   E++     +    SL   I +   +     D 
Sbjct: 131 ERLISETSKEPTAED---IAKVLEVPHEEIVFALDAIQDPVSLFEPIYNDGGDPIYVMDQ 187

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  + +   Q + E          L   M  LN RE+ I   R  Q    T   ++ E  
Sbjct: 188 ISDERNKDTQWVEELA--------LKEGMRRLNDREKMILRKRFFQG--KTQMEVAEEIG 237

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A K++ ++I
Sbjct: 238 ISQAQVSRLEKAAIKQMNKNI 258


>gi|170735771|ref|YP_001777031.1| RpoD family RNA polymerase sigma factor [Burkholderia cenocepacia
           MC0-3]
 gi|169817959|gb|ACA92541.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           cenocepacia MC0-3]
          Length = 511

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 52/230 (22%), Positives = 101/230 (43%), Gaps = 13/230 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   ++ ++LRLV+ IA  Y   G+ +S++V +G +GLM+A++KF+  RGF+ +TY+ 
Sbjct: 272 RDATRAMLEANLRLVLSIARKYLNRGVDLSDLVQDGCLGLMRAIEKFEYRRGFKFSTYAT 331

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      +++             +R++ H         +      +A + 
Sbjct: 332 WWIRQAIARAVADRSRTIRVPVHV-----GDQYQRVQRHALRFRQRTGRRATPAELAAET 386

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E ++ ++    A   SL+  +  +D    +         D       E+      R 
Sbjct: 387 GLDEGKLRAVLALPAEPVSLDTPLPDADTGLVELI------EDQASASPFEQLADTRMRE 440

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEA 274
            +   +  + P E  +   R       P T + ++ +  +SRERVRQIE 
Sbjct: 441 CVRALLRSVTPTEADVLRRRFGLGGAEPDTYDAIAQDAGMSRERVRQIEK 490


>gi|9621765|gb|AAF89531.1|AF160964_1 RNA polymerase sigma factor [Peanut witches'-broom phytoplasma]
          Length = 458

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 55/236 (23%), Positives = 100/236 (42%), Gaps = 11/236 (4%)

Query: 55  TSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114
            S+LR+VV IA      G    +++ EGN+GLM+ V KFD  +GF+ +TY+ WWI+ A+ 
Sbjct: 221 LSNLRIVVSIAKKQSERGQYFLDLIHEGNMGLMKTVDKFDYTKGFKFSTYATWWIRQAIT 280

Query: 115 EYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVI 174
             +      ++     +   +       K  L        +  +   IAK +N+   ++ 
Sbjct: 281 RAVADQSRTIRCPVHVS--DILNKNFAFKSKLTQDLARKARKAENHEIAKAMNIETKKL- 337

Query: 175 SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV 234
            M  +          I S  +       +          + + +  +K     L  +   
Sbjct: 338 -MIYKWLKRNDFFRNIYSWWRWFFFRWFYKRSLRYFASWLYVTRNFKKTLEESLEEA--- 393

Query: 235 LNPRERRIFEARR----LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           L PRE+ + + R           TLE + ++  V+RER+RQIE +A +K++   + 
Sbjct: 394 LTPREQLVLKMRYGILEGDNRVHTLEEVGAKLGVTRERIRQIETKALRKLRHPSRS 449


>gi|203288197|ref|YP_002223212.1| RNA polymerase sigma factor [Borrelia recurrentis A1]
 gi|201085417|gb|ACH94991.1| RNA polymerase sigma factor [Borrelia recurrentis A1]
          Length = 267

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 76/272 (27%), Positives = 142/272 (52%), Gaps = 18/272 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+  +R+  ++  +EE  LAK+ +  G L A ++++ ++LRLV+KI   Y G GL I
Sbjct: 9   LNIYLKSVREHRLITHEEEIELAKQIKL-GSLKAKNQMINANLRLVLKIIKRYAGKGLKI 67

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GL++A +K+DP +  + +TY+ +WIK ++Q  +     LVK+         
Sbjct: 68  EDLIQEGNLGLIRAAEKYDPSKNTKFSTYASFWIKQSLQRALNTKTRLVKVPYRKE---- 123

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + ++  +L        K  +   I ++ N++ ++ + +   L  + SL+  I  S+ 
Sbjct: 124 -NLILQINKYLME----EEKSPKKEDIMERFNLTTAQYVKIIPYLEKEYSLDKKIEGSEN 178

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN---P 252
             S   +    +    E  L +    K+   +L    + LN +ER I + R   +N    
Sbjct: 179 --STLLNLYEDNSLNPESTLEQNSTLKHLNYILE---TKLNEKERYIIKKRYNLDNSDKK 233

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL+++S+E  +S E VRQIE R  KK++E +
Sbjct: 234 STLKDISTELGISSETVRQIEKRVLKKLREEL 265


>gi|153953967|ref|YP_001394732.1| sporulation sigma factor SigG [Clostridium kluyveri DSM 555]
 gi|219854581|ref|YP_002471703.1| hypothetical protein CKR_1238 [Clostridium kluyveri NBRC 12016]
 gi|146346848|gb|EDK33384.1| SigG [Clostridium kluyveri DSM 555]
 gi|219568305|dbj|BAH06289.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 257

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 53/261 (20%), Positives = 117/261 (44%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+++E   L  + ++ GD  A  + +  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLKEKEMKELLIKMQQ-GDNDAREKFIKGNLRLVLSVIQRFNNRGENVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD  +  + +TY++  I   ++ Y+  + S +++  +   + + +   +++
Sbjct: 73  IGLIKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSL--RDIAYKALQVR 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L      N K   +  IAK+L +   EV+     +    SL   I     ++    D 
Sbjct: 130 DKL---IRENNKEPTISQIAKELELPREEVVFALDAIQDPVSLFEPIYHDGGDAIYVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    +  E  L            +  +M  LN RE+ I   R    +  T   ++ E  
Sbjct: 187 ISDTKNVDENWLEN--------ISIKEAMKKLNDREKLILNLRFF--DGRTQMEVAHEIG 236

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A + +++ +
Sbjct: 237 ISQAQVSRLEKTALRHMRKYV 257


>gi|23978350|dbj|BAC21142.1| principal sigma factor [Xenococcus sp. PCC 7307]
          Length = 203

 Score =  176 bits (446), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 53/214 (24%), Positives = 101/214 (47%), Gaps = 13/214 (6%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+
Sbjct: 1   VQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
              I      +++        L+  + R+K   + ++    +      IA ++ ++  ++
Sbjct: 61  TRAIADQSRTIRLPVH-----LYETISRIKKTTKLLSQERGRKPTEEEIATRMEMTIEKL 115

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             +        SL   I    +  S+  D++  D     +   ++  +   R  L   + 
Sbjct: 116 RFIAKSAQLPISLETPI--GKEEDSRLGDFIEADG----ETPEDQVSKSLLREDLESVLD 169

Query: 234 VLNPRERRIFEARRLQENPV--TLENLSSEFEVS 265
            L+PRER +   R   ++    TLE +   F V+
Sbjct: 170 TLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVT 203


>gi|154500348|ref|ZP_02038386.1| hypothetical protein BACCAP_04015 [Bacteroides capillosus ATCC
           29799]
 gi|150270853|gb|EDM98136.1| hypothetical protein BACCAP_04015 [Bacteroides capillosus ATCC
           29799]
          Length = 256

 Score =  175 bits (445), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 59/261 (22%), Positives = 115/261 (44%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+ +L+ +E   L KR +E GD +A   L+  +LRLV+ +   +   G  + ++   G 
Sbjct: 13  SKLKVLKNEETVALLKRTKE-GDTAAREELIAGNLRLVLSVIQKFSNRGENVDDLFQVGC 71

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  F+ +   R +TY +  I   ++ Y+  + S+     + + +   + + + K
Sbjct: 72  IGLIKAIDNFNTDLDVRFSTYGVPMIVGEIRRYLRDNSSMR---VSRSMRDTAYKVLQAK 128

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
               A        E    IAK L++   +V+     +    SL   + S   ++    D 
Sbjct: 129 EKFMAEHQREPTME---EIAKMLDLKREDVVFAMDAIMDPVSLYEPVYSDGGDAICVMDQ 185

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    +  E  L            L  ++S L+ RER I   R       T   +S+E  
Sbjct: 186 VKDSKNTDESWLE--------HIALKEAISHLSDRERHILSLRFF--EGRTQMEVSAEIG 235

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A  K+++S+
Sbjct: 236 ISQAQVSRLEKSAIWKIRKSL 256


>gi|23978360|dbj|BAC21145.1| principal sigma factor [Pleurocapsa sp. PCC 7314]
          Length = 203

 Score =  175 bits (445), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 53/214 (24%), Positives = 101/214 (47%), Gaps = 13/214 (6%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+
Sbjct: 1   VHSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
              I      +++        L+  + R+K   + ++    +      IA ++ ++  ++
Sbjct: 61  TRAIADQSRTIRLPVH-----LYETISRIKKTTKLLSQERGRKPTEEEIATRMEMTIEKL 115

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             +        SL   I    +  S+  D++  D     +   ++  +   R  L   + 
Sbjct: 116 RFIAKSAQLPISLETPI--GKEEDSRLGDFIEADG----ETPEDQVSKSLLREDLESVLD 169

Query: 234 VLNPRERRIFEARRLQENPV--TLENLSSEFEVS 265
            L+PRER +   R   ++    TLE +   F V+
Sbjct: 170 TLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVT 203


>gi|302871380|ref|YP_003840016.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
 gi|302574239|gb|ADL42030.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
          Length = 255

 Score =  175 bits (445), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 57/259 (22%), Positives = 121/259 (46%), Gaps = 17/259 (6%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L  +E++ L KR +E GD  A    +  +LRLV+ +   +   G  + ++   G IG
Sbjct: 14  LPVLSHEEKFELLKRMKE-GDKEARRIFIEGNLRLVLSVVQKFANRGENLDDLFQVGCIG 72

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A+  FD  +  + +TY++  I   ++ Y+  + S+ +I  +   K   +   ++K  
Sbjct: 73  LIKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNSM-RISRSL--KDTAYKALKIK-- 127

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            +   + N +   +  IAK+L++++ E++     +    SL   +   D + + +    +
Sbjct: 128 -EKYINKNHREPTLEEIAKELSITKEELVFALDSIQEPISLYEPVFQ-DSSDTMYVVEKL 185

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            D    E V +E+         L  ++S L  RE+ I   R  +    T   ++    +S
Sbjct: 186 CDQKSCENVWLEEIS-------LKDALSKLTKREKEILYLRYYKG--KTQMEVARIVGIS 236

Query: 266 RERVRQIEARAFKKVQESI 284
           + +V +IE  A   +++ I
Sbjct: 237 QAQVSRIEKSAIGHIKKYI 255


>gi|167834949|ref|ZP_02461832.1| RNA polymerase sigma factor RpoD [Burkholderia thailandensis
           MSMB43]
          Length = 301

 Score =  175 bits (445), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 56/236 (23%), Positives = 117/236 (49%), Gaps = 12/236 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  R+  ++LRLV+ IA  +   GL +++++ EGN+GL++A++KF+  RGF+ +TY+ W
Sbjct: 60  AATARMAEANLRLVLSIARKHASRGLDLADLLQEGNLGLLRAIEKFEYRRGFKFSTYATW 119

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   I      +++            +RR++     I   +     +  ++    
Sbjct: 120 WIRQAISRAIADRARTIRVPVHV-----GDEVRRVRKVADRIERRSGARASLAELSAATG 174

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +    + +M        SLNA + + D+  +++ D +    D     L +        ++
Sbjct: 175 LPVERLRAMLMLPREPRSLNAPLGNDDQ--AEFGDLV---EDASTPSLFDALAHGQMCDV 229

Query: 228 LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +T  +  ++ +E  I   R     + P + E ++++  VSRE+VR+IE RA + ++
Sbjct: 230 VTSLLKTMSAQEADILRRRFGIGGDEPWSYEQIAAQTGVSREQVRRIEKRALQTLR 285


>gi|167561013|ref|ZP_02353929.1| RNA polymerase sigma factor [Burkholderia oklahomensis EO147]
          Length = 476

 Score =  175 bits (445), Expect = 5e-42,   Method: Composition-based stats.
 Identities = 53/236 (22%), Positives = 116/236 (49%), Gaps = 12/236 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  ++  ++LRLV+ IA  Y   GL +++++ EGN+GL++A++KF+  RGF+ +TY+ W
Sbjct: 235 AATGKMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIQKFEYRRGFKFSTYATW 294

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   +      +++             RR++     I   +     +  +++   
Sbjct: 295 WIRQAISRAVADRARTIRLPVHV-----GDQARRVRKIADRIKQRSGMRASLAELSEATE 349

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S   + ++        SLN  +   D + +++ D +    D     L +       R++
Sbjct: 350 LSTERLRAVLELPREPRSLNTPL--GDDDQAEFGDLV---EDASTPSLFDALAGAQMRDV 404

Query: 228 LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  ++ +E  I   R     + P + E ++++  VSRE++R+IE RA + ++
Sbjct: 405 VASLLKTMSAQEADILRRRFGIGGDEPWSYEQIAAQSGVSREQIRRIEKRALQTLR 460


>gi|300854419|ref|YP_003779403.1| putative RNA polymerase sigma-G factor [Clostridium ljungdahlii DSM
           13528]
 gi|300434534|gb|ADK14301.1| predicted RNA polymerase sigma-G factor [Clostridium ljungdahlii
           DSM 13528]
          Length = 257

 Score =  175 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 53/261 (20%), Positives = 117/261 (44%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+ +E   L  + ++ GD  +  + +  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLKGKEMKELLIKMQQ-GDNESREKFIKGNLRLVLSVIQRFNNRGENVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD  +  + +TY++  I   ++ Y+  + S +++  +   + + +   +++
Sbjct: 73  IGLIKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSL--RDIAYKALQVR 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L      N K   +  IA++LN+   EV+     +    SL   I     ++    D 
Sbjct: 130 DKL---IRENNKEPTISQIAEELNIPREEVVFALDAIQDPVSLFEPIYHDGGDAIYVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    +  E  L            +  +M  LN RE+ I   R    +  T   ++ E  
Sbjct: 187 ISDTKNLDENWLEN--------ISIKEAMKKLNDREKLILNLRFF--DGRTQMEVADEIG 236

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A + +++ I
Sbjct: 237 ISQAQVSRLEKTALRHMRKYI 257


>gi|167568274|ref|ZP_02361148.1| RNA polymerase sigma factor [Burkholderia oklahomensis C6786]
          Length = 483

 Score =  175 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 53/236 (22%), Positives = 116/236 (49%), Gaps = 12/236 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  ++  ++LRLV+ IA  Y   GL +++++ EGN+GL++A++KF+  RGF+ +TY+ W
Sbjct: 242 AATGKMAEANLRLVLSIARKYASRGLDLADLLQEGNLGLLRAIQKFEYRRGFKFSTYATW 301

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   +      +++             RR++     I   +     +  +++   
Sbjct: 302 WIRQAISRAVADRARTIRLPVHV-----GDQARRVRKIADRIKQRSGMRASLAELSEATE 356

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S   + ++        SLN  +   D + +++ D +    D     L +       R++
Sbjct: 357 LSTERLRAVLELPREPRSLNTPL--GDDDQAEFGDLV---EDASTPSLFDALAGAQMRDV 411

Query: 228 LTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   +  ++ +E  I   R     + P + E ++++  VSRE++R+IE RA + ++
Sbjct: 412 VASLLKTMSAQEADILRRRFGIGGDEPWSYEQIAAQSGVSREQIRRIEKRALQTLR 467


>gi|295696452|ref|YP_003589690.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
 gi|295412054|gb|ADG06546.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
          Length = 261

 Score =  175 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 56/264 (21%), Positives = 121/264 (45%), Gaps = 17/264 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            ++P+L   E   L   ++  GDLSA  RL+  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SQLPVLTNAEMRKLFAEFQ-AGDLSARERLIHGNLRLVLSVIQRFNNRGENVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+A+  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 73  IGLMKAIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVR 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
                +T+  L+   +  I+++LN+ + +V+     +    SL   I     +     D 
Sbjct: 130 D---QLTNERLREPTITEISEQLNLPKEDVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  D +     + E          L  +M+ L  RE++I   R       T   ++ E  
Sbjct: 187 IRDDRNQDVLWVEEIA--------LREAMNKLGQREQKILAMRFF--EGKTQMEVAEEIG 236

Query: 264 VSRERVRQIEARAFKKVQESIQKQ 287
           +S+ +V ++E  A + +Q+ I+ Q
Sbjct: 237 ISQAQVSRLEKSAIQHMQKFIKIQ 260


>gi|220929478|ref|YP_002506387.1| sporulation sigma factor SigG [Clostridium cellulolyticum H10]
 gi|219999806|gb|ACL76407.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium cellulolyticum
           H10]
          Length = 257

 Score =  175 bits (445), Expect = 6e-42,   Method: Composition-based stats.
 Identities = 54/261 (20%), Positives = 117/261 (44%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L  +++  L +R  + GD SA    +  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLTNEQKKELFERMHK-GDNSARDEFIKGNLRLVLSVIQRFNNRGEYVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++++  FD  +  + +TY++  I   ++ Y+  + S +++  +   + + +   + K
Sbjct: 73  IGLIKSIDNFDVTQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSL--RDIAYKALQAK 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L   T  N K   +V +A++L + + +++     +    SL   +     ++    D 
Sbjct: 130 ERL---TTQNSKEPTIVELAQELQLPKEDIVFALDAIQDPISLFESVYHDGGDAIYVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  D +  E  L            L  +M  LN RE+ I   R       T   ++ E  
Sbjct: 187 VSDDKNIDENWLE--------TISLKEAMRKLNDREKLILNLRFF--EGRTQMEVADEIG 236

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A   +++ I
Sbjct: 237 ISQAQVSRLEKTALMHMKKYI 257


>gi|302338308|ref|YP_003803514.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           smaragdinae DSM 11293]
 gi|301635493|gb|ADK80920.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Spirochaeta
           smaragdinae DSM 11293]
          Length = 281

 Score =  175 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 75/276 (27%), Positives = 134/276 (48%), Gaps = 15/276 (5%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  L  Y  EI++  +L  +EE  L+++ +  GD +A HRL+ ++LRLVVKIA  Y   G
Sbjct: 11  DDALRSYFDEIKQHKLLTFEEELELSRKIQ-SGDEAARHRLIEANLRLVVKIAKSYVTPG 69

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
             + +++ EGN+GL++A +K+D  +  R +TY+ WWI+ ++   I +    +++    N 
Sbjct: 70  FGLLDLIQEGNMGLIRAAEKYDHRKQVRFSTYAAWWIRQSIVRAIAKKQKAIRLPHRKN- 128

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                 L++++     ++           IA ++ +  S V  M        SL+     
Sbjct: 129 ----NLLKKIQRTYYQLSQELEHEPSAEEIAVEIGIEPSIVDQMLQVGNPVVSLD---CE 181

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQE 250
              ++S   D L       E+V I K  +++  + L      L  RER+I   R      
Sbjct: 182 IGDDASTLLDMLEDSTYEPERVCINKSMQEDTMHFLDH----LKERERQILLYRFAFFGG 237

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              TL+ +  E  +S E VRQIE RA +K+++  ++
Sbjct: 238 KKYTLKKIGMEMGISPETVRQIEMRAIRKLRDHAEE 273


>gi|160935677|ref|ZP_02083052.1| hypothetical protein CLOBOL_00567 [Clostridium bolteae ATCC
           BAA-613]
 gi|158441421|gb|EDP19131.1| hypothetical protein CLOBOL_00567 [Clostridium bolteae ATCC
           BAA-613]
          Length = 258

 Score =  175 bits (445), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 55/260 (21%), Positives = 115/260 (44%), Gaps = 17/260 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L  +E+  L +R  + GD  A  + +  +LRLV+ +   +      I ++   G I
Sbjct: 15  KLPLLSNEEKEELFQRILD-GDKEAREQYIKGNLRLVLSVIQRFSNSQENIDDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD  +  + +TY++  I   ++ Y+  + S +++      + L     +   
Sbjct: 74  GLIKAIDNFDITQNVKFSTYAVPMILGEVRRYLRDNNS-IRVS-----RSLRDTAYKALY 127

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + +T  N K   ++ IA+++ VS+ ++      +    SL   +  +D     +    
Sbjct: 128 AREQLTRTNSKEPTLMEIAQEIGVSKEDITYALDAIQTPVSLYEPVY-TDGGDPLFVMDQ 186

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           + D    E+  +E          L  +M  L  RER I + R       T   ++ E  +
Sbjct: 187 ISDKKNLEENWVEDLS-------LVEAMKRLPERERHIIDMRFF--EGKTQTEVAQEIHI 237

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ +V ++E  A K ++  +
Sbjct: 238 SQAQVSRLEKNALKSMKSYL 257


>gi|331082586|ref|ZP_08331709.1| RNA polymerase sigma-G factor [Lachnospiraceae bacterium 6_1_63FAA]
 gi|330400205|gb|EGG79847.1| RNA polymerase sigma-G factor [Lachnospiraceae bacterium 6_1_63FAA]
          Length = 259

 Score =  175 bits (444), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 48/263 (18%), Positives = 111/263 (42%), Gaps = 17/263 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            ++P+L  +E+  L  R +E GD  A  + +  +LRLV+ +   +        ++   G 
Sbjct: 14  SRLPILTNEEKDALFVRIKE-GDPEAREQYIKGNLRLVLSVIKRFSSSNENADDLFQIGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           +GL++A+  FD     + +TY++  I   ++ Y+  +   +++  +           +  
Sbjct: 73  VGLIKAIDNFDTTLNVKFSTYAVPMIIGEIRRYLRDNN-AIRVSRSLRDVAYKAIYAK-- 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
              +     NLK   +  IA+++ + + E++     +    SL   +  ++   + +   
Sbjct: 130 ---ENYVKQNLKEPTINEIAEEIGIDKEEIVYALDAIQSPVSLYEPVY-TEGGDTLYVMD 185

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
            + D   +E   IE          L  ++  L+ RE+ I   R       T   ++ E  
Sbjct: 186 QISDKKNKEDNWIENI-------ALKEALKKLDDREQHIVTMRFY--EGKTQMEVAEEIG 236

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+ +V ++E  A K ++  ++ 
Sbjct: 237 ISQAQVSRLEKHALKTMRTYLRS 259


>gi|312134672|ref|YP_004002010.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|311774723|gb|ADQ04210.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor owensensis OL]
          Length = 255

 Score =  175 bits (444), Expect = 7e-42,   Method: Composition-based stats.
 Identities = 57/259 (22%), Positives = 121/259 (46%), Gaps = 17/259 (6%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L  +E++ L KR +E GD  A    +  +LRLV+ +   +   G  + ++   G IG
Sbjct: 14  LPVLSHEEKFELLKRMKE-GDKEARRIFIEGNLRLVLSVVQKFANRGENLDDLFQVGCIG 72

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A+  FD  +  + +TY++  I   ++ Y+  + S+ +I  +   K   +   ++K  
Sbjct: 73  LIKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNSM-RISRSL--KDTAYKALKIK-- 127

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            +   + N +   +  IAK+L++++ E++     +    SL   +   D + + +    +
Sbjct: 128 -EKYINKNQREPTLEEIAKELSITKEELVFALDSIQEPISLYEPVFQ-DSSDTMYVVEKL 185

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            D    E V +E+         L  ++S L  RE+ I   R  +    T   ++    +S
Sbjct: 186 CDQKSCENVWLEEIS-------LKDALSKLTKREKEILYLRYYKG--KTQMEVARIVGIS 236

Query: 266 RERVRQIEARAFKKVQESI 284
           + +V +IE  A   +++ I
Sbjct: 237 QAQVSRIEKSAIGHIKKYI 255


>gi|168180582|ref|ZP_02615246.1| RNA polymerase sigma-G factor [Clostridium botulinum NCTC 2916]
 gi|168182609|ref|ZP_02617273.1| RNA polymerase sigma-G factor [Clostridium botulinum Bf]
 gi|170757556|ref|YP_001782076.1| sporulation sigma factor SigG [Clostridium botulinum B1 str. Okra]
 gi|170761503|ref|YP_001787848.1| sporulation sigma factor SigG [Clostridium botulinum A3 str. Loch
           Maree]
 gi|187778872|ref|ZP_02995345.1| hypothetical protein CLOSPO_02467 [Clostridium sporogenes ATCC
           15579]
 gi|226949887|ref|YP_002804978.1| sporulation sigma factor SigG [Clostridium botulinum A2 str. Kyoto]
 gi|237795971|ref|YP_002863523.1| sporulation sigma factor SigG [Clostridium botulinum Ba4 str. 657]
 gi|169122768|gb|ACA46604.1| RNA polymerase sigma-G factor [Clostridium botulinum B1 str. Okra]
 gi|169408492|gb|ACA56903.1| RNA polymerase sigma-G factor [Clostridium botulinum A3 str. Loch
           Maree]
 gi|182668579|gb|EDT80558.1| RNA polymerase sigma-G factor [Clostridium botulinum NCTC 2916]
 gi|182674221|gb|EDT86182.1| RNA polymerase sigma-G factor [Clostridium botulinum Bf]
 gi|187772497|gb|EDU36299.1| hypothetical protein CLOSPO_02467 [Clostridium sporogenes ATCC
           15579]
 gi|226842131|gb|ACO84797.1| RNA polymerase sigma-G factor [Clostridium botulinum A2 str. Kyoto]
 gi|229263792|gb|ACQ54825.1| RNA polymerase sigma-G factor [Clostridium botulinum Ba4 str. 657]
          Length = 257

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 54/261 (20%), Positives = 110/261 (42%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+ +E   L  R R +G+       +  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLKDKEMKKLLVRIR-NGETECREEFIQGNLRLVLSVIKRFNNRGENVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD  +  + +TY++  I   ++ Y+  + S +++  +           +  
Sbjct: 73  IGLIKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRDIAY-----KAL 126

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
                +  NN K   V  IAK+L +   EV+     +    SL   I     ++    D 
Sbjct: 127 QARDKLIKNNNKEPTVSQIAKELELPREEVVFALDAIQDPVSLFEPIYHDGGDAIFVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    +  E  +            +  +M  LN RE+ I   R    +  T   ++ E  
Sbjct: 187 ISDTKNVDENWIEN--------ISIKEAMKKLNDREKLILNLRFF--DGRTQMEVADEIG 236

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A K +++ +
Sbjct: 237 ISQAQVSRLEKTALKHMRKYV 257


>gi|108707415|gb|ABF95210.1| Sigma-70 region 3 family protein, expressed [Oryza sativa Japonica
           Group]
 gi|215695353|dbj|BAG90544.1| unnamed protein product [Oryza sativa Japonica Group]
          Length = 343

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 66/251 (26%), Positives = 119/251 (47%), Gaps = 15/251 (5%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E  L KR   +  +S  + +V S++RLV+ IA  + G G+  S+++ EG  GL++  +K
Sbjct: 88  DENTLRKRL--NYGISCKNTMVKSNVRLVISIAREFEGPGMEFSDLIQEGIQGLVRGAEK 145

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +GFR +TYS WWIK A+++ +L    ++++     +        R+K   + +   
Sbjct: 146 FDASKGFRFSTYSHWWIKQAIRKSVLEQTQIIRLPAHMAEAS-----SRVKECRRRLRRQ 200

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA    +    V +         SL + +  +D        +     D   
Sbjct: 201 LKRLPTNEEIASDTGMPLRRVEAAMSLPKYTVSLTSKVGCTD------MTYQEITPDTST 254

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +   E   R   +  + R++  L+PRER++   R   ++    TL ++     VSRER+R
Sbjct: 255 ETAEEMLHRWLMKEDVDRALDGLSPRERQVIRYRFGMDDGRLRTLHDIGRLMGVSRERIR 314

Query: 271 QIEARAFKKVQ 281
           QIE  AF+K++
Sbjct: 315 QIELVAFRKLR 325


>gi|163941643|ref|YP_001646527.1| sporulation sigma factor SigG [Bacillus weihenstephanensis KBAB4]
 gi|229134713|ref|ZP_04263522.1| RNA polymerase sigma-G factor [Bacillus cereus BDRD-ST196]
 gi|163863840|gb|ABY44899.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           weihenstephanensis KBAB4]
 gi|228648759|gb|EEL04785.1| RNA polymerase sigma-G factor [Bacillus cereus BDRD-ST196]
 gi|322510150|gb|ADX05464.1| RNA polymerase sigma-G factor [Bacillus mycoides]
          Length = 292

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 62/261 (23%), Positives = 121/261 (46%), Gaps = 17/261 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+ +E   L +  +  G++SA  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 48  KLPVLKNEEMRKLFREMQ-SGEISAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 106

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++ 
Sbjct: 107 GLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVRE 163

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L A    N K    + IAK L V+  E++     +    SL   I +   +     D L
Sbjct: 164 KLIA---ENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGGDPIFVMDQL 220

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             +    EQ + E          L   M  LN RE+ I   R  Q    T   ++ E  +
Sbjct: 221 KDEKQKDEQWVEELA--------LKEGMKRLNDREKMIIRKRFFQG--KTQMEVAEEIGI 270

Query: 265 SRERVRQIEARAFKKVQESIQ 285
           S+ +V ++E  A K++ ++IQ
Sbjct: 271 SQAQVSRLEKSAIKQMNKTIQ 291


>gi|298500963|ref|ZP_07010764.1| RNA polymerase sigma factor RpoS [Vibrio cholerae MAK 757]
 gi|297540211|gb|EFH76271.1| RNA polymerase sigma factor RpoS [Vibrio cholerae MAK 757]
          Length = 233

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 62/229 (27%), Positives = 109/229 (47%), Gaps = 12/229 (5%)

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           +VKI+  Y    L + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++  
Sbjct: 1   MVKISRRYSNRRLTLLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQ 60

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              +++      K L   LR  +     ++           IA +L+    +V  M    
Sbjct: 61  TRTIRLPIHVV-KELNIYLRTAR----ELSQRLDHEPTPEEIALELDRPVDDVTKMLRLN 115

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               S++  I           D L   H+   +   + +   + R  L   +  LNP+++
Sbjct: 116 ERISSVDTPI--GGDGDKALLDILPDSHNADPEFSTQDD---DIRESLLNWLDELNPKQK 170

Query: 241 RIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R   L   P TLE +  E  ++RERVRQI+    ++++E + KQ
Sbjct: 171 EVLARRFGLLGYEPSTLEEVGREINLTRERVRQIQVEGLRRLREILVKQ 219


>gi|218676616|ref|YP_002395435.1| RpoS-like sigma factor [Vibrio splendidus LGP32]
 gi|218324884|emb|CAV26646.1| RpoS-like sigma factor [Vibrio splendidus LGP32]
          Length = 298

 Score =  175 bits (444), Expect = 8e-42,   Method: Composition-based stats.
 Identities = 67/276 (24%), Positives = 127/276 (46%), Gaps = 19/276 (6%)

Query: 17  SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY---RGYGL 73
           + Y+ +I  I +L +++E   AK     GD  A   ++ S+LRLVVKIA  Y   +G   
Sbjct: 30  AHYLKDIVGIDLLSREDELYYAK-LNRAGDKQARDIMIESNLRLVVKIAKSYLKRKGNNF 88

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++ EGNIGL++A+ K+DPE G+R +TY++WWI+  ++  ++     V++       
Sbjct: 89  TLLDLIEEGNIGLIKAIDKYDPEPGYRFSTYAVWWIRENIEAALMNKGRTVRLPAHV--- 145

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                +  L      ++    K   +  ++    V    V  +   L+G   +   +  S
Sbjct: 146 --CKEINSLASKKLDVSKKMRKEISISELSNSSGVKAERVDQLVA-LSGFIDVTTTVGIS 202

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QEN 251
                  Q    Y  D Q     +  E ++  + L + ++ L P+ +++   R       
Sbjct: 203 HAPLVLDQCESEYIPDPQ-----QDCEDQSFTHALEQIINTLPPKLQKVLIHRFGFFDNK 257

Query: 252 PVTLENLSSEF--EVSRERVRQIEARAFKKVQESIQ 285
             TL  +       VS ERVRQ++  A +++Q+ ++
Sbjct: 258 VKTLSEVGQMLDVNVSNERVRQMQKEAVERIQKRLK 293


>gi|215404668|ref|ZP_03416849.1| RNA polymerase sigma factor [Mycobacterium tuberculosis 02_1987]
 gi|298526173|ref|ZP_07013582.1| hypothetical protein TBAG_01589 [Mycobacterium tuberculosis
           94_M4241A]
 gi|298495967|gb|EFI31261.1| hypothetical protein TBAG_01589 [Mycobacterium tuberculosis
           94_M4241A]
          Length = 197

 Score =  175 bits (443), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 47/201 (23%), Positives = 94/201 (46%), Gaps = 12/201 (5%)

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           ++KFD  +G++ +TY+ WWI+ A+   +      ++I     +  +   L R++  L   
Sbjct: 1   MEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQD 58

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
                 PE    +AK+++++  +V+ +        SL+  I   D+  SQ  D++    D
Sbjct: 59  LGREPTPE---ELAKEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---ED 110

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRE 267
            +  V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RE
Sbjct: 111 SEAVVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRE 170

Query: 268 RVRQIEARAFKKVQESIQKQV 288
           R+RQIE++   K++   + QV
Sbjct: 171 RIRQIESKTMSKLRHPSRSQV 191


>gi|312876365|ref|ZP_07736350.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
 gi|311796859|gb|EFR13203.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
          Length = 255

 Score =  175 bits (443), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 60/259 (23%), Positives = 120/259 (46%), Gaps = 17/259 (6%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L  +E+  L KR +E GD  A    +  +LRLV+ +   +   G  + ++   G IG
Sbjct: 14  LPVLSHEEKLELLKRMKE-GDKEARRIFIEGNLRLVLSVVQKFANRGENLDDLFQVGCIG 72

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A+  FD  +  + +TY++  I   ++ Y+  + S+ +I  +   K   +   ++K  
Sbjct: 73  LIKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNSM-RISRSL--KDTAYKALKIK-- 127

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            +    NN K   +  IAK+L++++ E++     +    SL   +   D   + +    +
Sbjct: 128 -EKYISNNQKEPTLEEIAKELSITKEELVFTLDSIQEPISLYEPVFQ-DSTDTMYVVEKL 185

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
           YDH   E V +E+         L  ++S L  RE+ I      +    T   ++    +S
Sbjct: 186 YDHKSSENVWLEEIS-------LKDALSRLTKREKEILYLHYYKG--KTQMEVARIVGIS 236

Query: 266 RERVRQIEARAFKKVQESI 284
           + +V +IE  A   +++ I
Sbjct: 237 QAQVSRIEKSAIGHIKKYI 255


>gi|325265256|ref|ZP_08131981.1| RNA polymerase sigma-G factor [Clostridium sp. D5]
 gi|324029435|gb|EGB90725.1| RNA polymerase sigma-G factor [Clostridium sp. D5]
          Length = 259

 Score =  175 bits (443), Expect = 9e-42,   Method: Composition-based stats.
 Identities = 59/263 (22%), Positives = 120/263 (45%), Gaps = 23/263 (8%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+++E+  L  R +  GD  A    +  +LRLV+ +   +        ++   G +
Sbjct: 15  KLPLLKEEEKEALFTRIK-AGDEEAREEYIKGNLRLVLSVIKRFSNSNENADDLFQIGCV 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ---KRLFFNLRR 141
           GLM+AV  FDP R  + +TY++  I   ++ Y+  + S +++  +      K ++     
Sbjct: 74  GLMKAVDHFDPNRLVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRDTAYKAIYAKEGY 132

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           +K HL        K   V  IA+++ +S+ +++     +    SL+  + S   ++    
Sbjct: 133 MKKHL--------KEPTVQEIAEEIGISKEDIVFALDAIQMPMSLHEPVYSDGGDTLYVM 184

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           D +    + +E  + E          L  +M  LN RER I   R       T   ++ E
Sbjct: 185 DQVSDKKNKEENWVEELS--------LEAAMERLNERERYIITLRFF--EGKTQMEVAEE 234

Query: 262 FEVSRERVRQIEARAFKKVQESI 284
            ++S+ +V ++E  A K +++ +
Sbjct: 235 IKISQAQVSRLEKNALKVMKQYL 257


>gi|148380489|ref|YP_001255030.1| RNA polymerase sigma-G factor [Clostridium botulinum A str. ATCC
           3502]
 gi|153933176|ref|YP_001384712.1| sporulation sigma factor SigG [Clostridium botulinum A str. ATCC
           19397]
 gi|153936833|ref|YP_001388233.1| sporulation sigma factor SigG [Clostridium botulinum A str. Hall]
 gi|153938804|ref|YP_001391829.1| sporulation sigma factor SigG [Clostridium botulinum F str.
           Langeland]
 gi|148289973|emb|CAL84086.1| RNA polymerase sigma-G factor [Clostridium botulinum A str. ATCC
           3502]
 gi|152929220|gb|ABS34720.1| RNA polymerase sigma-G factor [Clostridium botulinum A str. ATCC
           19397]
 gi|152932747|gb|ABS38246.1| RNA polymerase sigma-G factor [Clostridium botulinum A str. Hall]
 gi|152934700|gb|ABS40198.1| RNA polymerase sigma-G factor [Clostridium botulinum F str.
           Langeland]
 gi|295319855|gb|ADG00233.1| RNA polymerase sigma-G factor [Clostridium botulinum F str. 230613]
 gi|322806802|emb|CBZ04371.1| RNA polymerase sporulation specific sigma factor SigG [Clostridium
           botulinum H04402 065]
          Length = 257

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 54/261 (20%), Positives = 110/261 (42%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+ +E   L  R R +G+       +  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLKDKEMKKLLVRIR-NGETECREEFIQGNLRLVLSVIKRFNNRGENVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD  +  + +TY++  I   ++ Y+  + S +++  +           +  
Sbjct: 73  IGLIKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRDIAY-----KAL 126

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
                +  NN K   V  IAK+L +   EV+     +    SL   I     ++    D 
Sbjct: 127 QARDKLIKNNNKEPTVSQIAKELELPREEVVFALDAIQDPVSLFEPIYHDGGDAIFVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    +  E  +            +  +M  LN RE+ I   R    +  T   ++ E  
Sbjct: 187 ISDTKNIDENWIEN--------ISIKEAMKKLNDREKLILNLRFF--DGRTQMEVADEIG 236

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A K +++ +
Sbjct: 237 ISQAQVSRLEKTALKHMRKYV 257


>gi|281357254|ref|ZP_06243743.1| RNA polymerase, sigma 32 subunit, RpoH [Victivallis vadensis ATCC
           BAA-548]
 gi|281316285|gb|EFB00310.1| RNA polymerase, sigma 32 subunit, RpoH [Victivallis vadensis ATCC
           BAA-548]
          Length = 428

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 64/267 (23%), Positives = 127/267 (47%), Gaps = 24/267 (8%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
            EIRK  +LE  EE             +   +++ ++LRLV+ IA  YR  GLP ++++ 
Sbjct: 171 GEIRK--LLEIHEEL-----------QNLRQKMIEANLRLVISIAQKYRNRGLPFNDLIQ 217

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           EGN+GL++A++KFD   G + +TY+ WWIK  +   I     +++I        +   + 
Sbjct: 218 EGNLGLLRALEKFDFRLGNKFSTYASWWIKHNISRSIAEQSRVIRIPAH-----MVHAIN 272

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
            +    Q    ++ +  ++  +A  L +  + + ++        SL A ++SS+   +  
Sbjct: 273 SMTWAEQRFIQSHGREPEIDELAAVLEMPVARISAIRKMSCQTISLQAPVSSSEDG-AML 331

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENL 258
           +D +  D        +    RK   + L   +  L  R+++I   R     +  + L ++
Sbjct: 332 EDLIADDSTAN---PVRDFARKILYDKLYEMLRTLPERDQQIIILRFGLFGQPCLPLVDI 388

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQ 285
           S  F ++RER+RQ+EA+  + ++   +
Sbjct: 389 SRRFNLTRERIRQLEAKIIENLRSPAK 415


>gi|253576139|ref|ZP_04853471.1| RNA polymerase sigma-G factor [Paenibacillus sp. oral taxon 786
           str. D14]
 gi|251844482|gb|EES72498.1| RNA polymerase sigma-G factor [Paenibacillus sp. oral taxon 786
           str. D14]
          Length = 260

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 52/262 (19%), Positives = 114/262 (43%), Gaps = 16/262 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L   E   L    ++    SA  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLTNAEMRELFHSLQQDHVRSAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 74

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A+  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++ 
Sbjct: 75  GLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQMRD 131

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
           +L   T+ N +   +  I++ L + + +V+     +    SL   I     +     D +
Sbjct: 132 NL---TNQNSREPTIFEISEALGLPKEDVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQI 188

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             D +     + E          L  +M  L  RE+ I   R       T   ++ E  +
Sbjct: 189 SDDKNKDVSWIEEIA--------LREAMQRLGNREKMILSMRFF--EGKTQMEVADEIGI 238

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+ +V ++E  A  ++Q+ ++ 
Sbjct: 239 SQAQVSRLEKSAILQMQKHVKS 260


>gi|256371989|ref|YP_003109813.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidimicrobium
           ferrooxidans DSM 10331]
 gi|256008573|gb|ACU54140.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Acidimicrobium
           ferrooxidans DSM 10331]
          Length = 302

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 70/271 (25%), Positives = 130/271 (47%), Gaps = 14/271 (5%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           G   +  ++ ++ K P+    E+  LAKR RE GD  A   +V ++LRLVV  A  Y+  
Sbjct: 33  GADSIRLFLDDLAKHPLPSAAEQVELAKRVRE-GDEDAKAEMVAANLRLVVHWARRYQDR 91

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           G+ +++++ EG  GL++AV+KFD  RGF+ +TY+ WW++ ++Q  +      +++   A 
Sbjct: 92  GVELADLIQEGTFGLIRAVEKFDWRRGFKFSTYATWWVRQSLQRAVHNHGQAIRLPMEAA 151

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
           ++      RR+    + +  +  +      IA   N+S S++  +        SL+  + 
Sbjct: 152 ERS-----RRVDNVTRELAADLGRAPTEEEIAMAANLSASQLADVRHAARVVASLDQAVG 206

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--Q 249
              + S      L      Q+    E+ +    R ML R++  L+  ER++   R     
Sbjct: 207 PEGETS------LGDLVVAQDTSFEEEVDESISREMLRRAVEELDELERQVVTLRFGLQG 260

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + P +LE  +    +   R R++EA A  K+
Sbjct: 261 DRPASLEATARILGIGPRRARRLEASALAKL 291


>gi|229541192|ref|ZP_04430252.1| RNA polymerase, sigma 28 subunit, SigG [Bacillus coagulans 36D1]
 gi|229325612|gb|EEN91287.1| RNA polymerase, sigma 28 subunit, SigG [Bacillus coagulans 36D1]
          Length = 258

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 60/262 (22%), Positives = 120/262 (45%), Gaps = 17/262 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+ +E   L K+    GD SA  +LV  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLKNEEMRDLLKKMH-AGDASAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+++  FD  +  R +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 73  IGLMKSIDNFDLNQNVRFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVR 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L + T      E    IA++L+V   +++     +    SL   I +   +     D 
Sbjct: 130 EKLMSATSKEPTTE---EIARELDVPHEDIVFALDAIQDPVSLFEPIYNDGGDPIYVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  + +   Q + E          L   M  LN RE+ I   R  Q    T   ++ E  
Sbjct: 187 VSDEKNKDSQWIEEIA--------LQEGMRRLNEREKMIIRKRFFQG--KTQMEVAEEIG 236

Query: 264 VSRERVRQIEARAFKKVQESIQ 285
           +S+ +V ++E  A K++ ++IQ
Sbjct: 237 ISQAQVSRLEKAAIKQMNKNIQ 258


>gi|26665382|dbj|BAC44902.1| principal sigma factor [Anabaena planctonica TAC421]
          Length = 203

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 52/214 (24%), Positives = 101/214 (47%), Gaps = 13/214 (6%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+
Sbjct: 1   VQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
              I      +++        L+  + R+K   + ++    +      IA ++ ++  ++
Sbjct: 61  TRAIADQSRTIRLPVH-----LYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKL 115

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             +        SL   I    +  S+  D++  +     +   ++  +   R  L + + 
Sbjct: 116 RFIAKSAQSPISLETPI--GKEEDSRLGDFIESEG----ETPEDQVSKNLLREDLEKVLD 169

Query: 234 VLNPRERRIFEARRLQENPV--TLENLSSEFEVS 265
            L PRER +   R   ++    TLE +   F V+
Sbjct: 170 SLGPRERDVLRLRYGLDDGRMKTLEEIGQIFNVT 203


>gi|160880600|ref|YP_001559568.1| sporulation sigma factor SigG [Clostridium phytofermentans ISDg]
 gi|160429266|gb|ABX42829.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           phytofermentans ISDg]
          Length = 260

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 56/261 (21%), Positives = 119/261 (45%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+ +E+  L +R ++ GD  A    +  +LRLV+ I   +      + ++   G 
Sbjct: 14  SKLPLLKGEEKDALFERIKQ-GDKEARELYIKGNLRLVLSIIQRFSNSNENVDDLFQIGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+A+  FD  +G + +TY++  I   ++ Y+  +   +++      + L     +  
Sbjct: 73  IGLMKAIDNFDITQGVKFSTYAVPMIIGEIRRYLRDNN-AIRVS-----RSLRDTAYKAI 126

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
              + +   N K   V  IA ++ +S+ ++++    +    SL   + S   ++    D 
Sbjct: 127 YAKEMLLKKNDKEPTVCEIANEVGISQEDIVAALDAIQSPVSLYEPVYSEGGDTLYIMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    + +E  + E          L  +M+ L+PRE  I   R  Q    T   ++ E +
Sbjct: 187 VSDKKNKEENWVEE--------ISLKEAMARLSPRENNIINLRFFQG--KTQMEVAEEIQ 236

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A K ++  +
Sbjct: 237 ISQAQVSRLEKNALKNMRNYL 257


>gi|119503379|ref|ZP_01625463.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2080]
 gi|119461025|gb|EAW42116.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2080]
          Length = 430

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 67/256 (26%), Positives = 119/256 (46%), Gaps = 14/256 (5%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           +LE++    L +  R +    A  +LV  +LRLV  IA  Y+G G+   ++V EG +GL+
Sbjct: 169 VLERETMKALRRELRIY--TEARDKLVMHNLRLVYSIAGRYKGRGVSYLDLVQEGTLGLI 226

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +A +KF+ E+GFR +TY   WI  A++ Y+    +L+++ T   +      + RL     
Sbjct: 227 RAAEKFEFEKGFRFSTYCFNWITQAVRRYVGDVGTLIRLPTHVQE-----QMGRLYKEKA 281

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                         +A KL +   +   +        SL+A     D+ +    D L  +
Sbjct: 282 IEQLRTGVEPDEETLAAKLGMDIEKTRQLLQMRNLGVSLDAPRFDDDEGT--LLDTLSGE 339

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVS 265
             G  +   +  E+ +    L  ++  L P E+R+  AR    +  P++   ++    VS
Sbjct: 340 PYGGTE---DSAEQASLHKFLGGAVDALEPSEQRVVVARWGLHDGPPLSRAEVADSLGVS 396

Query: 266 RERVRQIEARAFKKVQ 281
           RE VRQ+E  A +K++
Sbjct: 397 REWVRQLERSALRKLK 412


>gi|194696078|gb|ACF82123.1| unknown [Zea mays]
 gi|323388703|gb|ADX60156.1| SIGMA70-like transcription factor [Zea mays]
          Length = 541

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 61/245 (24%), Positives = 120/245 (48%), Gaps = 16/245 (6%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                ++  S+ RLV+ +A  Y G GL I ++V +G  GLM+  +KF+P +G R  TY+ 
Sbjct: 299 RRCREKMARSNFRLVIHVARKYEGCGLDIQDLVQDGCCGLMKTFEKFNPSKGCRFPTYAY 358

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL-KGHLQAITDNNLKPEQVVAIAKK 165
           WWI+ ++++ I ++  L+++  +      +  LR++ K  ++ I D      +V  +A++
Sbjct: 359 WWIRQSIKKSIFKNSRLIRLPESV-----YALLRKVGKARMECIMDGEQPTNEV--VARR 411

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
             ++  ++  +  +     S+   + S D  + Q         D   +      +R   R
Sbjct: 412 AGITIEKLAKLRAKTRKVRSMQDRVWSDDGVTYQ-----EITEDPNIEGPEVSVDRLMMR 466

Query: 226 NMLTRSM-SVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             +   +  +L+PRE+ I E R       P TL  +   + +S+ER+RQ++ +A  K++ 
Sbjct: 467 QQVRSFLTGILSPREKEIIEHRFGIHDGQPKTLHVIGDMYGLSKERIRQVQNKALDKLRN 526

Query: 283 SIQKQ 287
           SI  Q
Sbjct: 527 SISAQ 531


>gi|162458769|ref|NP_001105507.1| sigma-like factor6 [Zea mays]
 gi|4336610|gb|AAD17856.1| sigma factor SIG6 [Zea mays]
          Length = 541

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 61/245 (24%), Positives = 120/245 (48%), Gaps = 16/245 (6%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                ++  S+ RLV+ +A  Y G GL I ++V +G  GLM+  +KF+P +G R  TY+ 
Sbjct: 299 RRCREKMARSNFRLVIHVARKYEGCGLDIQDLVQDGCCGLMKTFEKFNPSKGCRFPTYAY 358

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL-KGHLQAITDNNLKPEQVVAIAKK 165
           WWI+ ++++ I ++  L+++  +      +  LR++ K  ++ I D      +V  +A++
Sbjct: 359 WWIRQSIKKSIFKNSRLIRLPESV-----YALLRKVGKARMECIMDGEQPTNEV--VARR 411

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
             ++  ++  +  +     S+   + S D  + Q         D   +      +R   R
Sbjct: 412 AGITIEKLAKLRAKTRKVRSMQDRVWSDDGVTYQ-----EITEDPNIEGPEVSVDRLMMR 466

Query: 226 NMLTRSM-SVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             +   +  +L+PRE+ I E R       P TL  +   + +S+ER+RQ++ +A  K++ 
Sbjct: 467 QQVRSFLTGILSPREKEIIEHRFGIHDGQPKTLHVIGDMYGLSKERIRQVQNKALDKLRN 526

Query: 283 SIQKQ 287
           SI  Q
Sbjct: 527 SISAQ 531


>gi|125602683|gb|EAZ42008.1| hypothetical protein OsJ_26557 [Oryza sativa Japonica Group]
          Length = 497

 Score =  175 bits (443), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 58/243 (23%), Positives = 115/243 (47%), Gaps = 13/243 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                ++  S+ RLV+ +A  Y GYGL I ++V +G  GLM+  +KF+P +G R  TY+ 
Sbjct: 256 RRCREKMARSNFRLVIHVARKYEGYGLDIQDLVQDGCSGLMKTFEKFNPSKGCRFPTYAY 315

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ ++++ I ++  L+++  +       + L R  G  +       +      +A++ 
Sbjct: 316 WWIRQSIKKSIFKNSRLIRLPESV------YALLRKVGKARMECIMEGEQPTNANVARRA 369

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++  ++  +  +     S+   + S +  +     +     D   +      +R   R 
Sbjct: 370 GITIEKLAKLRAKTRKPRSMQDHVWSDEGVT-----FQEITEDPNVEPPDLSVDRMMMRQ 424

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +   + +L+PRE+ I E R       P TL  +   F +S+ER+RQ++ RA +K++ S 
Sbjct: 425 QVRDFLGILSPREKEIIEHRFGIHDGEPKTLHVIGDMFGLSKERIRQLQNRALEKLKRSA 484

Query: 285 QKQ 287
             Q
Sbjct: 485 SLQ 487


>gi|150016005|ref|YP_001308259.1| sporulation sigma factor SigG [Clostridium beijerinckii NCIMB 8052]
 gi|149902470|gb|ABR33303.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           beijerinckii NCIMB 8052]
          Length = 257

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 55/261 (21%), Positives = 113/261 (43%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+++E+  L  + +  GD +A    +  +LRLV+ +   +   G  I ++   G 
Sbjct: 14  SKLPILKEKEKKQLFLQMQ-AGDKNARETFIKGNLRLVLSVIQRFNNRGENIDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+++  FD  +  + +TY++  I   ++ Y+  + S +++  +         + R  
Sbjct: 73  IGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRDIAYKALIMR-- 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
              +    +N K   +  IAK+L +   EV+     +    SL   I     ++    D 
Sbjct: 130 ---EKFIKDNNKEPTISQIAKELELPREEVVFALDAIQDPVSLFEPIYHDGGDAIYVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    +  E  L            +  +M  L  RE+ I   R    N  T   ++ E  
Sbjct: 187 ISDAKNTDEHWLEN--------ISIKEAMKKLTDREKLILNLRFF--NGRTQMEVADEIG 236

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A K +++ +
Sbjct: 237 ISQAQVSRLEKTALKHMRKHV 257


>gi|158833995|gb|ABW81803.1| RNA polymerase sigma 38 [Candidatus Regiella insecticola]
          Length = 268

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 64/229 (27%), Positives = 111/229 (48%), Gaps = 11/229 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD  +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 51  YLGEIGYSPLLTAEEEVYFARR-ALCGDQQSRRRMIESNLRLVVKIARRYGNRGLALLDL 109

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 110 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 168

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            IA++L+    +V  M        S+++ +     +  
Sbjct: 169 LRTAR----ELAHKLDHEPSAEEIAEQLDRPVDDVSRMLRLNERITSVDSPL--GGDSEK 222

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
              D L  D    E    +  +  + ++ + + +  LN ++R +   R 
Sbjct: 223 ALLDILSDDS---ENGPEDTTQNDDMKHSIVKWLFELNAKQREVLARRF 268


>gi|302386721|ref|YP_003822543.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           saccharolyticum WM1]
 gi|302197349|gb|ADL04920.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           saccharolyticum WM1]
          Length = 258

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 59/261 (22%), Positives = 116/261 (44%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L  +E+ VL KR   +GD  A    +  +LRLV+ +   + G    + ++   G 
Sbjct: 14  SKLPLLSNEEKEVLFKRIL-NGDKKAREDYIKGNLRLVLSVIQRFSGSNENVDDLFQIGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD  +  R +TY++  I   ++ Y+  + S +++      + L     +  
Sbjct: 73  IGLIKAIDNFDITQNVRFSTYAVPMILGEVRRYLRDNNS-IRVS-----RSLRDTAYKAI 126

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
              + +   NLK   ++ IA+++ VS+ ++      +    SL   + S D     +   
Sbjct: 127 YAKENLMKKNLKEPTLMEIAEEIGVSKEDITYALDAIQSPVSLYEPVYS-DGGDPLFVMD 185

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
            + D    E+  +E          L  +M  L  RER I + R       T   ++ E  
Sbjct: 186 QISDKKNLEENWVEDIS-------LNEAMRRLPERERHIIDMRFF--EGKTQTEVAEEIH 236

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A K ++  +
Sbjct: 237 ISQAQVSRLEKNALKTMKNYL 257


>gi|158833999|gb|ABW81805.1| RNA polymerase sigma 38 [Candidatus Regiella insecticola]
          Length = 268

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 64/229 (27%), Positives = 111/229 (48%), Gaps = 11/229 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD  +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 51  YLGEIGYSPLLTAEEEVYFARR-ALCGDQQSRRRMIESNLRLVVKIARRYGNRGLALLDL 109

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 110 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQSRTIRLPIHIV-KELNVY 168

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            IA++L+    +V  M        S+++ +     +  
Sbjct: 169 LRTAR----ELAHKLDHEPSAEEIAEQLDRPVDDVSRMLRLNERITSVDSPL--GGDSEK 222

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
              D L  D    E    +  +  + ++ + + +  LN ++R +   R 
Sbjct: 223 ALLDILSDDS---ENGPEDTTQNDDMKHSIVKWLFELNAKQREVLARRF 268


>gi|210633875|ref|ZP_03297890.1| hypothetical protein COLSTE_01807 [Collinsella stercoris DSM 13279]
 gi|210159044|gb|EEA90015.1| hypothetical protein COLSTE_01807 [Collinsella stercoris DSM 13279]
          Length = 261

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 64/257 (24%), Positives = 120/257 (46%), Gaps = 17/257 (6%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           +K++   L +R++E GD+ A  +LV SHL LV  IA  ++  G PI ++V  G +GL++A
Sbjct: 12  DKEKTRELFRRFKEEGDMDAREKLVMSHLNLVRFIANKFKNRGEPIDDLVQVGYLGLLKA 71

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +FDP RG    T++   I   ++ +       V++      +RL     ++      +
Sbjct: 72  IDRFDPARGLEFTTFATPTIMGEIKRHFRDKGWSVRVP-----RRLQELSAKVNQATDTL 126

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVYD 207
           T    +   +  IA+ L+ +  EV+            SL A     D ++    D    +
Sbjct: 127 TSQLQRSPTIAEIAEYLDATVDEVLEAMESSSAYSSVSLEAPSGMEDDDAPSVIDRYATE 186

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
                    E+    + R ++  +++  +PRER + E R LQ   +T   ++ +  +S+ 
Sbjct: 187 D--------EELAFTDDRIIIEEALASFSPREREVIEMRFLQG--MTQIEIAEKLGISQV 236

Query: 268 RVRQIEARAFKKVQESI 284
           +V ++  R  KK+QE I
Sbjct: 237 QVSRLLRRTLKKIQEKI 253


>gi|182418893|ref|ZP_02950150.1| RNA polymerase sigma-G factor [Clostridium butyricum 5521]
 gi|237667291|ref|ZP_04527275.1| RNA polymerase sigma-G factor [Clostridium butyricum E4 str. BoNT E
           BL5262]
 gi|182377176|gb|EDT74744.1| RNA polymerase sigma-G factor [Clostridium butyricum 5521]
 gi|237655639|gb|EEP53195.1| RNA polymerase sigma-G factor [Clostridium butyricum E4 str. BoNT E
           BL5262]
          Length = 257

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 57/261 (21%), Positives = 114/261 (43%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+++E+  L  + +  GD SA    +  +LRLV+ +   +   G  I ++   G 
Sbjct: 14  SKLPILKEKEKKQLLLQMK-AGDKSARETFIKGNLRLVLSVIQRFNNRGENIDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+++  FD  +  + +TY++  I   ++ Y+  + S +++  +         + R  
Sbjct: 73  IGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRDIAYKALIVR-- 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
              +    +N K   +  IAK+L +   EV+     +    SL   I     ++    D 
Sbjct: 130 ---EKFIKDNNKEPTISQIAKELELPREEVVFALDAIQDPVSLYEPIYHDGGDAIYVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    D  E  L            +  +M  L+ RE+ I   R    N  T   ++ E  
Sbjct: 187 ISDSKDTDENWLEN--------ISIKEAMKKLSDREKLILNLRFF--NGRTQMEVADEIG 236

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A K +++ +
Sbjct: 237 ISQAQVSRLEKTALKHMRKHV 257


>gi|158320421|ref|YP_001512928.1| sporulation sigma factor SigG [Alkaliphilus oremlandii OhILAs]
 gi|158140620|gb|ABW18932.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           oremlandii OhILAs]
          Length = 257

 Score =  174 bits (442), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 58/261 (22%), Positives = 115/261 (44%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            ++P+L+  +  VL  R  + GD SA    +  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SELPVLKNSQMRVLFDRIHK-GDNSAREEFIQGNLRLVLSVIQRFNNRGEHVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD     R +TY++  I   ++ Y+  + S +++      + L     +  
Sbjct: 73  IGLIKAIDNFDLSHNVRFSTYAVPMIIGEIRRYLRDNNS-IRVS-----RSLRDTAYKAL 126

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
              + + + N K   +  IA++LN+   +V+     +    SL   I     ++    D 
Sbjct: 127 QVREQLINKNSKEPTIAQIAEELNLPREDVVFALDAIQDPVSLFEPIYQDSGDAIFVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
            V D   +++  I+          L  +M  LN RE+ I   R       T   ++ E  
Sbjct: 187 -VCDEKSEDECWIDGI-------ALREAMRKLNSREKHILSLRFF--EGRTQMEVADEIG 236

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A K +++ I
Sbjct: 237 ISQAQVSRLEKTALKHMRKYI 257


>gi|288553150|ref|YP_003425085.1| sporulation sigma factor SigG [Bacillus pseudofirmus OF4]
 gi|288544310|gb|ADC48193.1| sporulation sigma factor SigG [Bacillus pseudofirmus OF4]
          Length = 261

 Score =  174 bits (441), Expect = 1e-41,   Method: Composition-based stats.
 Identities = 58/263 (22%), Positives = 117/263 (44%), Gaps = 15/263 (5%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+  E   L  + +  GD SA   LV  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLKNTEMRELFTQLQ-SGDDSAREVLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+++  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 73  IGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVR 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L A      +P  V  IAK L+V + +V+     +    SL   I +   +     D 
Sbjct: 130 DQLMAEKKRENEP-TVQEIAKVLDVPKEDVVFALDAIQDPVSLFEPIYNDGGDPIFVMDQ 188

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  + +     + E          L  +M  LN RE+ I   R  Q    T   ++ E  
Sbjct: 189 ISDERNKDVNWVEEIA--------LKEAMIRLNDREKMILNMRFFQG--KTQMEVADEIG 238

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+ +V ++E  A +++ +  Q 
Sbjct: 239 ISQAQVSRLEKAAIQQMNKHAQS 261


>gi|291087795|ref|ZP_06347503.2| RNA polymerase sigma-G factor [Clostridium sp. M62/1]
 gi|291073935|gb|EFE11299.1| RNA polymerase sigma-G factor [Clostridium sp. M62/1]
          Length = 291

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 55/260 (21%), Positives = 114/260 (43%), Gaps = 17/260 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L  +E+  L  R  + GD  A  + +  +LRLV+ +   + G    + ++   G I
Sbjct: 48  KLPLLTNEEKEELFARILK-GDREAREQYIKGNLRLVLSVIQRFSGSSENVDDLFQIGCI 106

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD  +  R +TY++  I   ++ Y+  + S +++  +           R   
Sbjct: 107 GLIKAIDNFDITQNVRFSTYAVPMILGEVKRYLRDNNS-IRVSRSLRDTAYKAIYAR--- 162

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             +++   NLK   +  IA+++ VS+ ++      +    SL   + +   +     D L
Sbjct: 163 --ESLMKKNLKEPTLCEIAEEVGVSKEDITYALDAIQSPVSLYEPVYTDGGDPLYVMDQL 220

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               + +E  + +          L+ +M  L  RER I   R       T   ++ E  +
Sbjct: 221 SDKKNSEENWIED--------ISLSEAMRRLPERERHIIGMRFF--EGKTQTEVAEEIHI 270

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ +V ++E  A K ++  +
Sbjct: 271 SQAQVSRLEKNALKAMKNYL 290


>gi|146295967|ref|YP_001179738.1| sporulation sigma factor SigG [Caldicellulosiruptor saccharolyticus
           DSM 8903]
 gi|145409543|gb|ABP66547.1| RNA polymerase, sigma subunit, RpsG/SigG [Caldicellulosiruptor
           saccharolyticus DSM 8903]
          Length = 255

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 55/259 (21%), Positives = 117/259 (45%), Gaps = 17/259 (6%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +PML  +E+  L K+ + +GD  A  + +  +LRLV+ +   +   G  + ++   G IG
Sbjct: 14  LPMLSHEEKIELLKKMK-NGDKEARKQFIEGNLRLVLSVVQKFANRGENLDDLFQVGCIG 72

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A+  FD  +  + +TY++  I   ++ Y+  + ++ +I  +   K   +   ++K  
Sbjct: 73  LIKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNAM-RISRSL--KDTAYKALKIKER 129

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
                  N +   +  IA +L +S+ +++     +    SL   I   D   + +    V
Sbjct: 130 ---YISQNYREPTLEEIANELCISKEDLVFALDSIQEPISLYEPIFQ-DSTDTMYVVDQV 185

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            D    E + +E+         L  ++S L  RE+ I   R  +    T   +++   +S
Sbjct: 186 SDQKSCENLWLEEIS-------LKDALSRLTKREKEILYLRYYKG--KTQMEVATIIGIS 236

Query: 266 RERVRQIEARAFKKVQESI 284
           + +V +IE  A   +++ I
Sbjct: 237 QAQVSRIEKSAIGHIKKYI 255


>gi|226313413|ref|YP_002773307.1| sporulation sigma factor SigG [Brevibacillus brevis NBRC 100599]
 gi|226096361|dbj|BAH44803.1| RNA polymerase sigma-G factor [Brevibacillus brevis NBRC 100599]
          Length = 259

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 55/263 (20%), Positives = 121/263 (46%), Gaps = 17/263 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L  +E   L +R +  G+L+A  +LV  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLTNKEMRDLFERLQ-SGELAAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+A+  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 73  IGLMKAIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVR 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
            +L   T+ + +   ++ I+++LNV++ +V+     +    SL   I     +     D 
Sbjct: 130 DNL---TNKHSREPTIIEISQELNVAKEDVVFALDAIQDPVSLFEPIYQDGGDPIYVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  + +     + E          L   M  L  RE+ I   R       T   ++ E  
Sbjct: 187 ISDEKNKDVTWVEEIA--------LREGMQRLGDREKMILSMRFY--EGKTQMEVAEEIG 236

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+ +V ++E  A   +Q+ +Q 
Sbjct: 237 ISQAQVSRLEKAAIAHMQKHVQS 259


>gi|197302592|ref|ZP_03167647.1| hypothetical protein RUMLAC_01321 [Ruminococcus lactaris ATCC
           29176]
 gi|197298490|gb|EDY33035.1| hypothetical protein RUMLAC_01321 [Ruminococcus lactaris ATCC
           29176]
          Length = 259

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 58/261 (22%), Positives = 118/261 (45%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L + E+  L +R ++ GD  A    +  +LRLV+ +   +        ++   G 
Sbjct: 13  SKLPLLREDEKEELFRRIQK-GDEKAREEYIKGNLRLVLSVIKRFDSSSESADDLFQIGC 71

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           +GLM+AV  FDPER  R +TY++  I   ++ Y+  + S +++      + L     +  
Sbjct: 72  VGLMKAVDNFDPERLVRFSTYAVPMIVGEIRRYLRDNSS-IRVS-----RSLRDTAYKAI 125

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
              +      +K   V  IA ++ +++ +V+     +    SL+  +  +D   + +   
Sbjct: 126 YAKEGYVRRYMKEPTVQEIADEIGIAKEDVVFALDAVQTPMSLHEPVY-NDGGDALYVMD 184

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
            V D   +E+  +E+         L  +M  LN RER I   R       T   ++ +  
Sbjct: 185 QVSDKKNREENWVEELS-------LEAAMERLNERERYIISLRFF--EGKTQTEVAGQIG 235

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A K +++ +
Sbjct: 236 ISQAQVSRLEKNALKTMRQYL 256


>gi|212639646|ref|YP_002316166.1| sporulation sigma factor SigG [Anoxybacillus flavithermus WK1]
 gi|212561126|gb|ACJ34181.1| DNA-directed RNA polymerase specialized sigma subunit sigG
           [Anoxybacillus flavithermus WK1]
          Length = 259

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 58/262 (22%), Positives = 121/262 (46%), Gaps = 17/262 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+ +E   L ++ +  GD+SA  +L+T +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLKNEEMRELFRQMQ-AGDISAREKLITGNLRLVLSVIQRFNNRGEYVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+++  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 73  IGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVR 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             + + T    K      IAK L+V   E++     +    SL   I +   +     D 
Sbjct: 130 EKMMSET---AKEPTAEEIAKILDVPHEEIVFALDAIQDPVSLFEPIYNDGGDPIYVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L  + +     + E          L   +  LN RE+ I   R  Q    T   ++ E  
Sbjct: 187 LSDEKNRDTNWIEEIA--------LKEGLRRLNEREKMIIRKRFFQG--KTQMEVAEEIG 236

Query: 264 VSRERVRQIEARAFKKVQESIQ 285
           +S+ +V ++E  A K++ ++IQ
Sbjct: 237 ISQAQVSRLEKAAIKQMNKNIQ 258


>gi|86145220|ref|ZP_01063551.1| RpoS-like sigma factor [Vibrio sp. MED222]
 gi|85836797|gb|EAQ54917.1| RpoS-like sigma factor [Vibrio sp. MED222]
          Length = 298

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 64/276 (23%), Positives = 124/276 (44%), Gaps = 19/276 (6%)

Query: 17  SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY---RGYGL 73
           + Y+ +I  I +L +++E   AK     GD  A   ++ S+LRLVVKIA  Y   +G   
Sbjct: 30  AHYLKDIVGIDLLSREDELYYAK-LNRAGDKHARDIMIESNLRLVVKIAKSYLKRKGNNF 88

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++ EGNIGL++A+ K+DPE G+R +TY++WWI+  ++  ++     V++       
Sbjct: 89  TLLDLIEEGNIGLIKAIDKYDPEPGYRFSTYAVWWIRENIEAALMNKGRTVRLPAHV--- 145

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                +  L      ++    K   +  ++    V    V  +   L+G   +   +   
Sbjct: 146 --CKEINSLASKKLDVSKKMRKEISISELSNISGVKAERVDQLVA-LSGFIDVTTTVGI- 201

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QEN 251
               S     L            +  E ++  + L + ++ L P+ +++   R       
Sbjct: 202 ----SHAPLVLEQCESEYIPDPQQDCEDQSFTHALEQIINTLPPKLQKVLIHRFGFFDNK 257

Query: 252 PVTLENLSSEF--EVSRERVRQIEARAFKKVQESIQ 285
             TL  +       VS ERVRQ++  A +++Q+ ++
Sbjct: 258 VKTLSEVGQMLDVNVSNERVRQMQKEAVERIQKRLK 293


>gi|229075660|ref|ZP_04208642.1| RNA polymerase sigma-G factor [Bacillus cereus Rock4-18]
 gi|229098374|ref|ZP_04229319.1| RNA polymerase sigma-G factor [Bacillus cereus Rock3-29]
 gi|229117400|ref|ZP_04246776.1| RNA polymerase sigma-G factor [Bacillus cereus Rock1-3]
 gi|228666010|gb|EEL21476.1| RNA polymerase sigma-G factor [Bacillus cereus Rock1-3]
 gi|228684991|gb|EEL38924.1| RNA polymerase sigma-G factor [Bacillus cereus Rock3-29]
 gi|228707436|gb|EEL59627.1| RNA polymerase sigma-G factor [Bacillus cereus Rock4-18]
          Length = 289

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 62/261 (23%), Positives = 121/261 (46%), Gaps = 17/261 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+ +E   L +  +  G++SA  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 45  KLPVLKNEEMRKLFREMQ-SGEISAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 103

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++ 
Sbjct: 104 GLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVRE 160

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L A    N K    + IAK L V+  E++     +    SL   I +   +     D L
Sbjct: 161 KLIA---ENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGGDPIFVMDQL 217

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             +    EQ + E          L   M  LN RE+ I   R  Q    T   ++ E  +
Sbjct: 218 SDEKQKDEQWVEELA--------LKEGMKRLNDREKMIIRKRFFQG--KTQMEVAEEIGI 267

Query: 265 SRERVRQIEARAFKKVQESIQ 285
           S+ +V ++E  A K++ ++IQ
Sbjct: 268 SQAQVSRLEKSAIKQMNKTIQ 288


>gi|42525589|ref|NP_970687.1| sigma-70 family RNA polymerase sigma factor [Treponema denticola
           ATCC 35405]
 gi|41815600|gb|AAS10568.1| RNA polymerase sigma-70 factor, region 2 family [Treponema
           denticola ATCC 35405]
          Length = 275

 Score =  174 bits (441), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 70/273 (25%), Positives = 133/273 (48%), Gaps = 14/273 (5%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
            E  L +YI + +K P+L  ++E  LA   ++ G+  A   LVTS+LRLV+K+A  +   
Sbjct: 2   TENLLLQYIKDSKKYPLLSAEQEAELADEVKK-GNTEAIEVLVTSNLRLVIKMAKKFSSN 60

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
              I E++ EGN+GLM+A  KF      R ++Y+ WWIK +   Y+  +  ++K+     
Sbjct: 61  ENQILELIQEGNMGLMKAASKFSKSFKVRFSSYAAWWIKQSFIRYLNSADKVIKLPVR-- 118

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
           ++ L   + + + + +          Q+  I K+     +++ S N       SL+  + 
Sbjct: 119 KEALIRQVHKEEENYKIKYGILPSYSQLAEIMKEKVDIIAQIKSFN--YTDICSLDDPV- 175

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             ++ S+   D++  +    E+  I+ E     +  L + + +LN RE+ +   R   + 
Sbjct: 176 -DNERSANLYDFIPCNTYNPEEEFIDNE----FKEKLNKCLEILNDREKDVLRNRYGLDG 230

Query: 252 PV---TLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +   T   L  ++ +S E +RQ + RA KK++
Sbjct: 231 TMTSTTFAVLGKKYSISAESIRQTQLRALKKLR 263


>gi|89895050|ref|YP_518537.1| hypothetical protein DSY2304 [Desulfitobacterium hafniense Y51]
 gi|89334498|dbj|BAE84093.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 260

 Score =  173 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 52/269 (19%), Positives = 119/269 (44%), Gaps = 19/269 (7%)

Query: 20  IHEIR--KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + E+   + P+L  +E   L  R  ++GD  A  RL+  +L+L+  +   +   G  + +
Sbjct: 5   LTEMNLPRFPLLSDEEMMDLLHR-AQNGDAEARERLINCNLKLIFNLVQRFSHRGYELED 63

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +   G IGL++A+ KFD   G + +TY++  I   ++ ++      VK+  +   K L +
Sbjct: 64  LFQIGTIGLIKAIDKFDFTYGVKFSTYAVPMIIGEIRRFLRDD-HPVKVPRS--YKELVY 120

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + + +  L A    +     +  IA+ + V   +++S    +    S++  +   D + 
Sbjct: 121 KVNKARESLSATLGRD---PTIGEIAESIGVDREDIVSALEAVQSPTSIHDTLYQDDSDP 177

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
               D L  + D +             +  L   +  L  RE+R+   R  ++   T   
Sbjct: 178 IYILDQLPMEKDLEAGWFE--------KIALKEVLDKLPEREKRVLMMRFYED--KTQSE 227

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +++   +S+ ++ +IE  A  ++++ + +
Sbjct: 228 IAALLNLSQVQISRIERAALHRIRQYLHE 256


>gi|322384112|ref|ZP_08057830.1| sporulation sigma factor SigG-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321151192|gb|EFX44501.1| sporulation sigma factor SigG-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 272

 Score =  173 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 51/261 (19%), Positives = 114/261 (43%), Gaps = 16/261 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L   E   L    +   + +A  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 27  KLPVLTNTEMRELFALLQTKNERAAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGCI 86

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A+  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++ 
Sbjct: 87  GLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVRD 143

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
               +T+ N +   +  I++ LNV + +V+     +    SL   I     +     D +
Sbjct: 144 ---QLTNRNSREPTIYEISEVLNVPKEDVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQI 200

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             + +        K+        L  +M  L  RE+ I   R       T   ++ E  +
Sbjct: 201 SDERN--------KDLFWIEGIALREAMRKLGSREKMILSMRFF--EGKTQMEVADEIGI 250

Query: 265 SRERVRQIEARAFKKVQESIQ 285
           S+ +V ++E  A  ++Q+ ++
Sbjct: 251 SQAQVSRLEKSAINQMQKHVK 271


>gi|205373280|ref|ZP_03226084.1| sporulation sigma factor SigG [Bacillus coahuilensis m4-4]
          Length = 258

 Score =  173 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 55/262 (20%), Positives = 111/262 (42%), Gaps = 17/262 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+ +E   L ++ +  GD  +  +LV  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLKNEEMRELFRKMQ-AGDTYSREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+++  FD  +  R +TY++  I   ++ Y+  +   +++  +           +  
Sbjct: 73  IGLMKSIDNFDLSQNVRFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLRDIAY-----KAL 126

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
              + +     K      IAK L+V   +++     +    SL   I +   +     D 
Sbjct: 127 QAREKLMGETSKEPTAEEIAKVLDVPHEDIVFALDAIQDPVSLFEPIYNDGGDPIFVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L  + +     + E          L   +  LN RE+ I   R  Q    T   ++ E  
Sbjct: 187 LSDERNRDVNWIEEIA--------LKEGLRRLNDREKMIIRKRFFQG--KTQMEVADEIG 236

Query: 264 VSRERVRQIEARAFKKVQESIQ 285
           +S+ +V ++E  A K + ++IQ
Sbjct: 237 ISQAQVSRLEKAAIKHMNKNIQ 258


>gi|158833997|gb|ABW81804.1| RNA polymerase sigma 38 [Candidatus Regiella insecticola]
          Length = 268

 Score =  173 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 64/229 (27%), Positives = 111/229 (48%), Gaps = 11/229 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD  +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 51  YLGEIGYSPLLTAEEEVYFARR-ALCGDQQSRRRMIESNLRLVVKIARRYGNRGLALLDL 109

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 110 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 168

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     +            IA++L+    +V  M        S+++ +     +  
Sbjct: 169 LRTAR----ELAHKLDHEPSAEEIAEQLDRPVDDVSRMLRLNERITSVDSPL--GGDSEK 222

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
              D L  D    E    +  +  + ++ + + +  LN ++R +   R 
Sbjct: 223 ALLDILSDDS---ENGPEDTTQNDDMKHSIVKWLFELNAKQREVLARRF 268


>gi|238926534|ref|ZP_04658294.1| DNA-directed RNA polymerase sigma subunit RpoD [Selenomonas
           flueggei ATCC 43531]
 gi|238885480|gb|EEQ49118.1| DNA-directed RNA polymerase sigma subunit RpoD [Selenomonas
           flueggei ATCC 43531]
          Length = 352

 Score =  173 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 65/254 (25%), Positives = 120/254 (47%), Gaps = 21/254 (8%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIA----MGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
             + G+L A   L   + +LV K A      YR   L   ++   G IGL+ A KKFD  
Sbjct: 102 MIQQGNLQAEQDLCVKNKKLVDKYALGYEKRYRHR-LDFDDIEQAGFIGLITAAKKFDIS 160

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
            G+  +TY++WWIK A+   I+    +++I        +   + ++ G     ++ N + 
Sbjct: 161 MGYSFSTYAVWWIKQAITREIMDHGFVIRIPVH-----MMEQIIKVAGVENMFSELN-RE 214

Query: 157 EQVVAIAKKLNVSESEVIS---MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
           E++V +  +    E  V     +   +    SLN  +   +  + +  ++L  D     +
Sbjct: 215 ERIVKVMDETGYKEERVRECMMLKEYVLTYSSLN--VTVGEDETVELGEFLSDDGAISIE 272

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQ 271
            +IE +E    R ML   ++ L  +E+++ + R   E+    TLE +   F V+RER+RQ
Sbjct: 273 EMIENKEL---RRMLDDVLNTLTEKEKKVIKLRFGLEDNRQWTLEEVGKLFNVTRERIRQ 329

Query: 272 IEARAFKKVQESIQ 285
           IE++A +K++   +
Sbjct: 330 IESKALRKLRHPSR 343


>gi|327538655|gb|EGF25307.1| RNA polymerase sigma factor rpoS [Rhodopirellula baltica WH47]
          Length = 330

 Score =  173 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 75/275 (27%), Positives = 135/275 (49%), Gaps = 13/275 (4%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
            +  L  Y+ EI + P+L  +EE  LA R  + GD+ A  ++V ++LRLVV I+ GY G 
Sbjct: 59  AQSPLETYLREINETPLLSAEEELELAARIAQ-GDVMARDQMVRANLRLVVNISRGYTGK 117

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL + +++ EGN+GL++AV+ FDP  G R +TY+ +WIK +++  ++ S   ++I   A 
Sbjct: 118 GLGLQDLIEEGNLGLLRAVEGFDPIHGTRFSTYASYWIKQSIKRALINSAKTIRIP--AY 175

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
              L    RR    L          E+V   A+ L + + ++  +   +  + S     +
Sbjct: 176 MVELLSKWRRATARLNEELGRTPTNEEV---ARVLGLPKKKLPIIRKAIKINNS--TPQS 230

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE- 250
              +      D +    D + +   E+    +        +  L  RE  + + R     
Sbjct: 231 DQTEAGWSLGDMV---QDERLKAPDEEMLDHDILKHAMSLLGDLEERESTVLKLRFGLGG 287

Query: 251 -NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             P+TL+ + +E  ++RERVRQIE  A +++ + +
Sbjct: 288 VEPMTLKEIGAELGLTRERVRQIETEALRRLADGL 322


>gi|167748837|ref|ZP_02420964.1| hypothetical protein ANACAC_03611 [Anaerostipes caccae DSM 14662]
 gi|167651807|gb|EDR95936.1| hypothetical protein ANACAC_03611 [Anaerostipes caccae DSM 14662]
          Length = 275

 Score =  173 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 56/259 (21%), Positives = 113/259 (43%), Gaps = 17/259 (6%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L  +E+  L  R  E GD  A  + +  +LRLV+ +   + G      ++   G IG
Sbjct: 33  LPLLTNEEKEELFIRI-EQGDQEAREQYIKGNLRLVLSVIQRFSGSNENADDLFQVGCIG 91

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           LM+A+  FD     + +TY++  I   ++ Y+  + S+ ++  +           +    
Sbjct: 92  LMKAIDNFDRSLNVKFSTYAVPMIIGEVRRYLRDNNSM-RVSRSLRDIAY-----KAITA 145

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            +A+T    K   + AIA+++ + + +V+     +A   SL   +   D   + +    V
Sbjct: 146 KEALTKKFNKEPTIEAIAEEIEMKKEDVLFALDAIATPLSLYEPVYQ-DGGDTLFLMDQV 204

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            D   +E++ +E          L  +M  L  RE  I   R    +  T   ++ E  +S
Sbjct: 205 KDKKNKEELWVESI-------ALKDAMEHLPEREYNIIRLRFF--DGKTQTEVADEISIS 255

Query: 266 RERVRQIEARAFKKVQESI 284
           + +V ++E  A K ++  +
Sbjct: 256 QAQVSRLEKNALKHMKHYL 274


>gi|266624907|ref|ZP_06117842.1| RNA polymerase sigma-G factor [Clostridium hathewayi DSM 13479]
 gi|288863210|gb|EFC95508.1| RNA polymerase sigma-G factor [Clostridium hathewayi DSM 13479]
          Length = 258

 Score =  173 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 58/261 (22%), Positives = 115/261 (44%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L  +E+  L KR  + GD+ A    +  +LRLV+ +   + G    + ++   G 
Sbjct: 14  SKLPLLNNEEKEALFKRILD-GDMEAREEYIKGNLRLVLSVIQRFSGSNENVDDLFQIGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD  +  R +TY++  I   ++ Y+  + S +++      + L     +  
Sbjct: 73  IGLIKAIDNFDITQNVRFSTYAVPMILGEVRRYLRDNNS-IRVS-----RSLRDTAYKAI 126

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
              + +   NLK   ++ IA ++ VS+ ++      +    SL   + S D     +   
Sbjct: 127 YAKENLMKKNLKEPTIMEIADEIGVSKEDITYALDAIQNPVSLYEPVYS-DGGDPLFVMD 185

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
            + D    E+  +E          L  +M  L  RER I + R       T   ++ E  
Sbjct: 186 QISDKKNLEENWVEDIS-------LNEAMKRLPERERHIIDMRFF--EGKTQTEVAEEIH 236

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A K ++  +
Sbjct: 237 ISQAQVSRLEKNALKSMKGYL 257


>gi|23978340|dbj|BAC21139.1| principal sigma factor [Stanieria cyanosphaera str. PCC 7437]
          Length = 203

 Score =  173 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 52/214 (24%), Positives = 100/214 (46%), Gaps = 13/214 (6%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+
Sbjct: 1   VQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
              I      +++        L+  + R+K   + ++    +      IA ++ ++  ++
Sbjct: 61  TRAIADQSRTIRLPVH-----LYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKL 115

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             +        SL   I    +  S+  D++  D     +   ++  +   R  L   + 
Sbjct: 116 RFIAKSAQLPISLETPI--GKEEDSRLGDFIEADG----ETPEDQVSKSLLREDLENVLD 169

Query: 234 VLNPRERRIFEARRLQENPV--TLENLSSEFEVS 265
            L+P ER +   R   ++    TLE +   F V+
Sbjct: 170 TLSPSERDVLRLRYGLDDGRMKTLEEIGQIFNVT 203


>gi|219669461|ref|YP_002459896.1| RNA polymerase, sigma 28 subunit, SigF [Desulfitobacterium
           hafniense DCB-2]
 gi|219539721|gb|ACL21460.1| RNA polymerase, sigma 28 subunit, SigF [Desulfitobacterium
           hafniense DCB-2]
          Length = 261

 Score =  173 bits (440), Expect = 2e-41,   Method: Composition-based stats.
 Identities = 52/269 (19%), Positives = 119/269 (44%), Gaps = 19/269 (7%)

Query: 20  IHEIR--KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + E+   + P+L  +E   L  R  ++GD  A  RL+  +L+L+  +   +   G  + +
Sbjct: 6   LTEMNLPRFPLLSDEEMMDLLHR-AQNGDAEARERLINCNLKLIFNLVQRFSHRGYELED 64

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +   G IGL++A+ KFD   G + +TY++  I   ++ ++      VK+  +   K L +
Sbjct: 65  LFQIGTIGLIKAIDKFDFTYGVKFSTYAVPMIIGEIRRFLRDD-HPVKVPRS--YKELVY 121

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + + +  L A    +     +  IA+ + V   +++S    +    S++  +   D + 
Sbjct: 122 KVNKARESLSATLGRD---PTIGEIAESIGVDREDIVSALEAVQSPTSIHDTLYQDDSDP 178

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
               D L  + D +             +  L   +  L  RE+R+   R  ++   T   
Sbjct: 179 IYILDQLPMEKDLEAGWFE--------KIALKEVLDKLPEREKRVLMMRFYED--KTQSE 228

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +++   +S+ ++ +IE  A  ++++ + +
Sbjct: 229 IAALLNLSQVQISRIERAALHRIRQYLHE 257


>gi|51599021|ref|YP_073209.1| RNA polymerase sigma factor [Borrelia garinii PBi]
 gi|51573592|gb|AAU07617.1| RNA polymerase sigma factor [Borrelia garinii PBi]
          Length = 266

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 77/273 (28%), Positives = 140/273 (51%), Gaps = 20/273 (7%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+  +R+  ++  +EE  LA + +  G+  A ++++ ++LRLV+KI   Y G GL I
Sbjct: 9   LNIYLKSVREHKLITHEEEIKLASQIQ-RGNAQAKNKMINANLRLVLKIIKRYAGKGLKI 67

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GL++A +K+DP +  + +TY+ +WIK ++Q  +     LVK+         
Sbjct: 68  EDLIQEGNLGLIRAAEKYDPNKNTKFSTYASFWIKQSLQRALNTKTRLVKVPYRKE---- 123

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + ++  +L     +     +   I K+ N+S ++ I +   L  + SL+  I  S+ 
Sbjct: 124 -NLILQINKYLTEEEKSP----KKEEIMKRFNLSPAQYIKIIPYLEKEYSLDKEIEGSEN 178

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV-LNPRERRIFEARRLQEN--- 251
             S   +    +    E  L    E+ +    L   +   LN +ER I + R   +N   
Sbjct: 179 --STLLNLYEDNSFNPEITL----EQDSTIKHLNYVLETKLNEKERYIIKKRYNLDNNPK 232

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL+++S+E  +S E VRQIE R  KK++E I
Sbjct: 233 KSTLKDISTELGISSETVRQIEKRVLKKLKEEI 265


>gi|228973923|ref|ZP_04134498.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228980512|ref|ZP_04140822.1| RNA polymerase sigma-G factor [Bacillus thuringiensis Bt407]
 gi|228779332|gb|EEM27589.1| RNA polymerase sigma-G factor [Bacillus thuringiensis Bt407]
 gi|228785789|gb|EEM33793.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
          Length = 289

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 62/261 (23%), Positives = 121/261 (46%), Gaps = 17/261 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+ +E   L +  +  G++SA  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 45  KLPVLKNEEMRKLFREMQ-SGEISAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 103

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++ 
Sbjct: 104 GLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVRE 160

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L A    N K    + IAK L V+  E++     +    SL   I +   +     D L
Sbjct: 161 KLIA---ENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGGDPIFVMDQL 217

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             +    EQ + E          L   M  LN RE+ I   R  Q    T   ++ E  +
Sbjct: 218 SDEKQKDEQWVEELA--------LKEGMKRLNDREKMIIRKRFFQG--KTQMEVAEEIGI 267

Query: 265 SRERVRQIEARAFKKVQESIQ 285
           S+ +V ++E  A K++ ++IQ
Sbjct: 268 SQAQVSRLEKSAIKQMNKTIQ 288


>gi|331086150|ref|ZP_08335232.1| hypothetical protein HMPREF0987_01535 [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|330406309|gb|EGG85823.1| hypothetical protein HMPREF0987_01535 [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 259

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 55/260 (21%), Positives = 122/260 (46%), Gaps = 17/260 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L  +E+  L  + +E GD +A  R +  +LRLV+ +   +      + ++   G +
Sbjct: 15  KLPLLSNEEKEALFVKIKE-GDEAARERYIKGNLRLVLSVIKRFASSNENVDDLFQIGCV 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A+  F+ +   + +TY++  I   ++ Y+  + S +++      + L     +   
Sbjct: 74  GLMKAIDNFNTDLQVKFSTYAVPMIIGEIRRYLRDNNS-IRVS-----RSLRDTAYKAIY 127

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             +     +LK   V  IA+++ +++ ++I     +    SLN  +  +D   + +    
Sbjct: 128 AKEGYMKRHLKEPTVEEIAEEIGIAKEDIIFALDAIQAPMSLNEPVY-NDSGDALYVMDQ 186

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           + D   +E+  +E          L  +M  LN RER I + R       T   ++S+ ++
Sbjct: 187 ISDKKNREEYWVEGLS-------LEAAMERLNERERFIIQLRFF--EGKTQMEVASQVKI 237

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ +V ++E  A K +++ +
Sbjct: 238 SQAQVSRLEKNALKTMRQYL 257


>gi|226226008|ref|YP_002760114.1| RNA polymerase sigma factor [Gemmatimonas aurantiaca T-27]
 gi|226089199|dbj|BAH37644.1| RNA polymerase sigma factor [Gemmatimonas aurantiaca T-27]
          Length = 302

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 81/276 (29%), Positives = 144/276 (52%), Gaps = 14/276 (5%)

Query: 13  EIGLSRYIHEIRKIPMLE-KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
                +Y+H+I+K+P++    EE  LA R  + GD +AA RLVT++LR V+     Y+G+
Sbjct: 23  STAFDQYLHDIQKLPLITDAAEERRLA-RLAQKGDEAAAERLVTANLRFVISYVKKYQGH 81

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL +SE+V+ GN GL++AV+KFDP++G +  +Y++WW++ A+ + +      V+I    N
Sbjct: 82  GLDLSELVAIGNEGLLKAVRKFDPDQGVKFISYAVWWVRQAVLKALAEQTRSVRIPLNQN 141

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
                  L R+      ++    +      ++K L     +V +     + + SL+A I+
Sbjct: 142 -----SQLIRMARGEMILSQVLNREPTDAELSKLLEEPVEQVRNARQISSTEVSLDAPID 196

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQE 250
             D+ +S   +    +       + +  + +  R  + R     L PRER+I       +
Sbjct: 197 RQDREASTLGERFAGE---THADIEDGTDFRLMREFIDRVFRKYLTPRERKILYLYYGLD 253

Query: 251 NP---VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
                +TLE + +   V+RER+RQI  RAF+K++ES
Sbjct: 254 EGAEAMTLERIGALMGVTRERIRQIRERAFEKLRES 289


>gi|15894973|ref|NP_348322.1| sporulation sigma factor SigG [Clostridium acetobutylicum ATCC 824]
 gi|1350864|sp|P33658|RPSG_CLOAB RecName: Full=RNA polymerase sigma-G factor
 gi|15024660|gb|AAK79662.1|AE007679_8 Specialized DNA-dependent RNA polymerase sigma subunit [Clostridium
           acetobutylicum ATCC 824]
 gi|580960|emb|CAA80621.1| putative sigma factor G [Clostridium acetobutylicum ATCC 824]
 gi|706854|gb|AAC43310.1| putative sigma factor G [Clostridium acetobutylicum ATCC 824]
 gi|325509110|gb|ADZ20746.1| sporulation sigma factor SigG [Clostridium acetobutylicum EA 2018]
          Length = 257

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 57/261 (21%), Positives = 119/261 (45%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+++E   L    R +G+ +A  + +  +LRLV+ +   +   G    ++   G 
Sbjct: 14  SKLPVLKEKEMRELLISMR-NGNTTAREKFIKGNLRLVLSVIQRFNNRGENADDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++++  FD  +  + +TY++  I   ++ Y+  + S +++  +          R L+
Sbjct: 73  IGLIKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRDI----AYRALQ 127

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
              + I+ NN K   V  IAK+L +   EVI     +    SL   I   D ++    D 
Sbjct: 128 VRDRLISKNN-KEPTVSQIAKELKIPREEVIFALDAIQDPISLFEPIYHDDGDAIYVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  + +  +  L        +   +  +M  L+ RE+ I   R    +  T   ++ E  
Sbjct: 187 ISDNKNLDDSWL--------QNISIKEAMKKLSDREKMILNMRFF--DGRTQMEVADEIG 236

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A K +++ +
Sbjct: 237 ISQAQVSRLEKTALKHMKKYV 257


>gi|325289982|ref|YP_004266163.1| RNA polymerase, sigma subunit, RpoX/SigF [Syntrophobotulus
           glycolicus DSM 8271]
 gi|324965383|gb|ADY56162.1| RNA polymerase, sigma subunit, RpoX/SigF [Syntrophobotulus
           glycolicus DSM 8271]
          Length = 257

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 53/267 (19%), Positives = 117/267 (43%), Gaps = 19/267 (7%)

Query: 20  IHEIR--KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + E+   + P+L++QE   L  +  + GD  A  +L+  +L+L+  +   +   G  + +
Sbjct: 5   LTEMNLPRFPLLKEQEMTELLHK-AQAGDHDAREQLINCNLKLIFNLIQRFTHRGYELED 63

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +   G IGL++A+ KFD   G + +TY++  I   ++ ++      +K+  +   K L +
Sbjct: 64  LFQIGTIGLIKAIDKFDFSYGVKFSTYAVPMIIGEIRRFLRDD-HPIKVPRS--YKELVY 120

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + R +  L    +       V  IA+ LNV   E+++    +    S+N  +   D + 
Sbjct: 121 KIHRSREKLSLELNRE---PTVNEIAQDLNVGSEEIVTALDAVQSPTSINDTLYQDDSDP 177

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
               D +  + D       E          L   ++ L  RE+++   R  ++   T   
Sbjct: 178 IYILDQIPVEKDLVPAWFEEVA--------LKDVLNKLPEREKQVLVMRFYED--KTQSE 227

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESI 284
           ++    +S+ ++ +IE  A   +++ +
Sbjct: 228 IAKRLNLSQVQISRIERAALLHLKQMM 254


>gi|317470325|ref|ZP_07929717.1| RNA polymerase sigma-G factor [Anaerostipes sp. 3_2_56FAA]
 gi|316902189|gb|EFV24111.1| RNA polymerase sigma-G factor [Anaerostipes sp. 3_2_56FAA]
          Length = 258

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 56/259 (21%), Positives = 113/259 (43%), Gaps = 17/259 (6%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L  +E+  L  R  E GD  A  + +  +LRLV+ +   + G      ++   G IG
Sbjct: 16  LPLLTNEEKEELFIRI-EQGDQEAREQYIKGNLRLVLSVIQRFSGSNENADDLFQVGCIG 74

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           LM+A+  FD     + +TY++  I   ++ Y+  + S+ ++  +           +    
Sbjct: 75  LMKAIDNFDRSLNVKFSTYAVPMIIGEVRRYLRDNNSM-RVSRSLRDIAY-----KAITA 128

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            +A+T    K   + AIA+++ + + +V+     +A   SL   +   D   + +    V
Sbjct: 129 KEALTKKFNKEPTIEAIAEEIEMKKEDVLFALDAIATPLSLYEPVYQ-DGGDTLFLMDQV 187

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            D   +E++ +E          L  +M  L  RE  I   R    +  T   ++ E  +S
Sbjct: 188 KDKKNKEELWVESI-------ALKDAMEHLPEREYNIIRLRFF--DGKTQTEVADEISIS 238

Query: 266 RERVRQIEARAFKKVQESI 284
           + +V ++E  A K ++  +
Sbjct: 239 QAQVSRLEKNALKHMKHYL 257


>gi|23978365|dbj|BAC21147.1| principal sigma factor [Leptolyngbya sp. PCC 7375]
          Length = 203

 Score =  173 bits (439), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 53/214 (24%), Positives = 101/214 (47%), Gaps = 13/214 (6%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V S+LRLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+
Sbjct: 1   VQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
              I      +++        L+  + R+K   + ++    +      IA ++ ++  ++
Sbjct: 61  TRAIADQSRTIRLPVH-----LYETISRIKKTTKLLSQELGRKPTEEEIATRMEMTIEKL 115

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             +        SL   I    +  S+  D++  D     +   ++  +   R  L   +S
Sbjct: 116 RFIAKSAQLPISLETPI--GKEEDSRLGDFIESDG----ETPEDEVSKSLLREDLEGVLS 169

Query: 234 VLNPRERRIFEARRLQENPV--TLENLSSEFEVS 265
            L+P ER +   R   ++    TLE +   F V+
Sbjct: 170 TLSPSERDVLRLRYGLDDGRMKTLEEIGQIFNVT 203


>gi|23978335|dbj|BAC21137.1| principal sigma factor [Phormidium sp. IAM M-99]
          Length = 203

 Score =  173 bits (438), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 51/214 (23%), Positives = 101/214 (47%), Gaps = 13/214 (6%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V S+ RLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+
Sbjct: 1   VQSNFRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
              I      +++        L+  + R+K   + ++    +      IA ++ ++  ++
Sbjct: 61  TRAIADQSRTIRLPVH-----LYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKL 115

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             +        SL   I    +  S+  D++  D +  E    ++  +   R  L   ++
Sbjct: 116 RFIAKSAQLPISLETPI--GKEEDSRLGDFIESDGETPE----DQVSKNLLREDLEGVLA 169

Query: 234 VLNPRERRIFEARRLQENPV--TLENLSSEFEVS 265
            L+PRE+ +       ++    TLE +   F V+
Sbjct: 170 TLSPREKDVLRLHYGLDDGRMKTLEEIGQIFNVT 203


>gi|133473|sp|P26764|RPSF_BACLI RecName: Full=RNA polymerase sigma-F factor; AltName:
           Full=Sporulation sigma factor; AltName: Full=Stage II
           sporulation protein AC
 gi|304173|gb|AAA22797.1| sporulation protein [Bacillus licheniformis]
          Length = 255

 Score =  173 bits (438), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 57/256 (22%), Positives = 113/256 (44%), Gaps = 19/256 (7%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L+  E   L K   ++GD  A   L+  ++RLV  +   +   G    ++   G IGL++
Sbjct: 14  LKDHEVKELIKN-SQNGDQKARDLLIEKNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLK 72

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           +V KFD     R +TY++  I   +Q +I      VK+  +   K L   +RR K   + 
Sbjct: 73  SVDKFDLSYDVRFSTYAVPMIIGEIQRFIRDDG-TVKVSRSL--KELGNKIRRAK---EE 126

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           ++ +N +   V  IA  L +S  EV+     +    S++  +  +D +     D +    
Sbjct: 127 LSKSNGRIPTVQEIADYLEISSEEVVMAQEAVRSPSSIHETVYENDGDPITLLDQIAD-- 184

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
                   + EE+   +  L  ++  L+ RE+ I   R  ++   T   ++    +S+ +
Sbjct: 185 --------QSEEKWFDKIALKEAIKDLDEREKLIVYLRYYKD--KTQSEVADRLGISQVQ 234

Query: 269 VRQIEARAFKKVQESI 284
           V ++E +  K+++  +
Sbjct: 235 VSRLEKKILKQIKNQM 250


>gi|228992638|ref|ZP_04152564.1| RNA polymerase sigma-G factor [Bacillus pseudomycoides DSM 12442]
 gi|228998684|ref|ZP_04158271.1| RNA polymerase sigma-G factor [Bacillus mycoides Rock3-17]
 gi|229006186|ref|ZP_04163872.1| RNA polymerase sigma-G factor [Bacillus mycoides Rock1-4]
 gi|228755027|gb|EEM04386.1| RNA polymerase sigma-G factor [Bacillus mycoides Rock1-4]
 gi|228761152|gb|EEM10111.1| RNA polymerase sigma-G factor [Bacillus mycoides Rock3-17]
 gi|228766970|gb|EEM15607.1| RNA polymerase sigma-G factor [Bacillus pseudomycoides DSM 12442]
          Length = 259

 Score =  173 bits (438), Expect = 3e-41,   Method: Composition-based stats.
 Identities = 63/261 (24%), Positives = 121/261 (46%), Gaps = 17/261 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+ +E   L +  +  G++SA  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKNEEMRKLFREMQ-SGEISAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++ 
Sbjct: 74  GLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVRE 130

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L A    N K    + IAK L V+  E++     +    SL   I +   +     D L
Sbjct: 131 KLIA---ENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGGDPIFVMDQL 187

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             D    EQ + E          L   M  LN RE+ I   R  Q    T   ++ E  +
Sbjct: 188 SDDKQRDEQWVEELA--------LKEGMKRLNDREKMIIRKRFFQG--KTQMEVAEEIGI 237

Query: 265 SRERVRQIEARAFKKVQESIQ 285
           S+ +V ++E  A K++ ++IQ
Sbjct: 238 SQAQVSRLEKSAIKQMNKTIQ 258


>gi|219684379|ref|ZP_03539323.1| RNA polymerase sigma factor [Borrelia garinii PBr]
 gi|219685569|ref|ZP_03540385.1| RNA polymerase sigma factor [Borrelia garinii Far04]
 gi|219672368|gb|EED29421.1| RNA polymerase sigma factor [Borrelia garinii PBr]
 gi|219672847|gb|EED29870.1| RNA polymerase sigma factor [Borrelia garinii Far04]
          Length = 266

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 77/273 (28%), Positives = 140/273 (51%), Gaps = 20/273 (7%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+  +R+  ++  +EE  LA + +  G+  A ++++ ++LRLV+KI   Y G GL I
Sbjct: 9   LNIYLKSVREHKLITHEEEIKLAGQIQ-RGNAQAKNKMINANLRLVLKIIKRYAGKGLKI 67

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GL++A +K+DP +  + +TY+ +WIK ++Q  +     LVK+         
Sbjct: 68  EDLIQEGNLGLIRAAEKYDPNKNTKFSTYASFWIKQSLQRALNTKTRLVKVPYRKE---- 123

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + ++  +L     +     +   I K+ N+S ++ I +   L  + SL+  I  S+ 
Sbjct: 124 -NLILQINKYLTEEEKSP----KKEEIMKRFNLSPAQYIKIIPYLEKEYSLDKEIEGSEN 178

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV-LNPRERRIFEARRLQEN--- 251
             S   +    +    E  L    E+ +    L   +   LN +ER I + R   +N   
Sbjct: 179 --STLLNLYEDNSFNPEITL----EQDSTIKHLNYVLETKLNEKERYIIKKRYNLDNNPK 232

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL+++S+E  +S E VRQIE R  KK++E I
Sbjct: 233 KSTLKDISTELGISSETVRQIEKRVLKKLKEEI 265


>gi|144575120|gb|AAZ43865.2| DNA-directed RNA polymerase sigma factor [Mycoplasma synoviae 53]
          Length = 798

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 67/284 (23%), Positives = 128/284 (45%), Gaps = 24/284 (8%)

Query: 16  LSRYIHEIRKI-PMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  Y+  I K   +L  QEE  LA+   + G     A   ++  +LRLVV  A  Y+  G
Sbjct: 502 VKWYMRWIGKYGKLLTPQEEKDLAEEMDKGGSRGKRARDLIIKRNLRLVVNAAKKYKNRG 561

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L   ++VSEGN GL++A +KFD ++GF+ +TY+ WWI+ ++   +     ++++     +
Sbjct: 562 LSFIDLVSEGNAGLLKAAQKFDIKKGFKFSTYATWWIRQSISRAVADQARIIRVPVHMVE 621

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIA--KKLNVSESEVISMNCRLAGDESLNALI 190
                 + +++  +Q      +  E++ A    K      S +  +        SL+  +
Sbjct: 622 --TINKIYKIEREIQQENGGEIIDEEIAARLGGKSKKYDASYIRYIRKINTSPISLDKQV 679

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
               +N S + D++  +         +KEE   + N     +  L+  E  + +      
Sbjct: 680 --GKENDSFFGDFVKDESIISPVEFADKEELITKINYYVEKL--LSEAEADLIKRYHGIG 735

Query: 251 --------NPVTLENLSSEF-----EVSRERVRQIEARAFKKVQ 281
                      TL+ +S +F     ++S+ERVRQI  + +KK++
Sbjct: 736 YDAKGNPVRSATLDEISKDFRGEGKKISKERVRQIITKIYKKLR 779


>gi|213425678|ref|ZP_03358428.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. E02-1180]
          Length = 304

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 65/271 (23%), Positives = 120/271 (44%), Gaps = 39/271 (14%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LR                   
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLR------------------- 100

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
                  L++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 101 -------LIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 152

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    +   
Sbjct: 153 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE--- 205

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLE 256
             +  L    D +E    +  +  + +  + + +  LN ++R +   R   L     TLE
Sbjct: 206 --KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLE 263

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 264 DVGREIGLTRERVRQIQVEGLRRLREILQTQ 294


>gi|4100832|gb|AAD00998.1| RpoS [Escherichia coli]
          Length = 269

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 63/231 (27%), Positives = 113/231 (48%), Gaps = 11/231 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 48  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 106

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 107 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 165

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 166 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 220

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
                L    D +E    +  +  + +  + + +  LN ++R +   R   
Sbjct: 221 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGL 267


>gi|42782996|ref|NP_980243.1| sporulation sigma factor SigG [Bacillus cereus ATCC 10987]
 gi|49186753|ref|YP_030005.1| sporulation sigma factor SigG [Bacillus anthracis str. Sterne]
 gi|49478441|ref|YP_037965.1| sporulation sigma factor SigG [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|52141585|ref|YP_085244.1| sporulation sigma factor SigG [Bacillus cereus E33L]
 gi|118479123|ref|YP_896274.1| sporulation sigma factor SigG [Bacillus thuringiensis str. Al
           Hakam]
 gi|196038711|ref|ZP_03106019.1| RNA polymerase sigma-G factor [Bacillus cereus NVH0597-99]
 gi|222097349|ref|YP_002531406.1| sporulation sigma factor sigg [Bacillus cereus Q1]
 gi|228928952|ref|ZP_04091984.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228935219|ref|ZP_04098045.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228947623|ref|ZP_04109913.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228987048|ref|ZP_04147173.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|229092950|ref|ZP_04224083.1| RNA polymerase sigma-G factor [Bacillus cereus Rock3-42]
 gi|229123417|ref|ZP_04252621.1| RNA polymerase sigma-G factor [Bacillus cereus 95/8201]
 gi|229186144|ref|ZP_04313313.1| RNA polymerase sigma-G factor [Bacillus cereus BGSC 6E1]
 gi|254683387|ref|ZP_05147247.1| sporulation sigma factor SigG [Bacillus anthracis str. CNEVA-9066]
 gi|254739809|ref|ZP_05197502.1| sporulation sigma factor SigG [Bacillus anthracis str. Kruger B]
 gi|254750999|ref|ZP_05203038.1| sporulation sigma factor SigG [Bacillus anthracis str. Vollum]
 gi|254757943|ref|ZP_05209970.1| sporulation sigma factor SigG [Bacillus anthracis str. Australia
           94]
 gi|301055394|ref|YP_003793605.1| RNA polymerase sigma-G factor [Bacillus anthracis CI]
 gi|42738923|gb|AAS42851.1| RNA polymerase sigma-G factor [Bacillus cereus ATCC 10987]
 gi|49180680|gb|AAT56056.1| RNA polymerase sigma-G factor [Bacillus anthracis str. Sterne]
 gi|49329997|gb|AAT60643.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|51975054|gb|AAU16604.1| RNA polymerase sigma-G factor [Bacillus cereus E33L]
 gi|118418348|gb|ABK86767.1| RNA polymerase, sigma subunit, RpsG/SigG [Bacillus thuringiensis
           str. Al Hakam]
 gi|196030434|gb|EDX69033.1| RNA polymerase sigma-G factor [Bacillus cereus NVH0597-99]
 gi|221241407|gb|ACM14117.1| RNA polymerase sigma-G factor [Bacillus cereus Q1]
 gi|228597320|gb|EEK54971.1| RNA polymerase sigma-G factor [Bacillus cereus BGSC 6E1]
 gi|228660193|gb|EEL15829.1| RNA polymerase sigma-G factor [Bacillus cereus 95/8201]
 gi|228690454|gb|EEL44238.1| RNA polymerase sigma-G factor [Bacillus cereus Rock3-42]
 gi|228772642|gb|EEM21083.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228812143|gb|EEM58474.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228824384|gb|EEM70190.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228830759|gb|EEM76364.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|300377563|gb|ADK06467.1| RNA polymerase sigma-G factor [Bacillus cereus biovar anthracis
           str. CI]
 gi|324327802|gb|ADY23062.1| sporulation sigma factor SigG [Bacillus thuringiensis serovar
           finitimus YBT-020]
          Length = 289

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 62/261 (23%), Positives = 120/261 (45%), Gaps = 17/261 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+  E   L +  +  G++SA  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 45  KLPVLKNDEMRKLFREMQ-SGEISAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 103

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++ 
Sbjct: 104 GLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVRE 160

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L A    N K    + IAK L V+  E++     +    SL   I +   +     D L
Sbjct: 161 KLIA---ENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGGDPIFVMDQL 217

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             +    EQ + E          L   M  LN RE+ I   R  Q    T   ++ E  +
Sbjct: 218 SDEKQKDEQWVEELA--------LKEGMKRLNDREKMIIRKRFFQG--KTQMEVAEEIGI 267

Query: 265 SRERVRQIEARAFKKVQESIQ 285
           S+ +V ++E  A K++ ++IQ
Sbjct: 268 SQAQVSRLEKSAIKQMNKTIQ 288


>gi|139436946|ref|ZP_01771106.1| Hypothetical protein COLAER_00079 [Collinsella aerofaciens ATCC
           25986]
 gi|133776593|gb|EBA40413.1| Hypothetical protein COLAER_00079 [Collinsella aerofaciens ATCC
           25986]
          Length = 263

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 60/257 (23%), Positives = 124/257 (48%), Gaps = 17/257 (6%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           +K++   L +RY+E GD  A  +LV SH+ LV  +A  ++  G P+ +++  G +GL++A
Sbjct: 13  DKEKTRELFRRYKETGDPDAREQLVMSHMNLVRFLANKFKNRGEPLDDLMQVGYLGLLKA 72

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +FDPERG    T++   I   ++ +       V++      +RL     ++      +
Sbjct: 73  IDRFDPERGLEFTTFATPTILGEIKRHFRDKGWSVRVP-----RRLQELSAKVNQATDKL 127

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYD 207
           T+   +  +V  IA+ L+V+  EV+      +   S  + A   S   ++    D    D
Sbjct: 128 TNELQRSPKVEEIAEYLDVTVDEVLEAMESSSAYTSVPIEAPGASDSDDAPSILDRYADD 187

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            +        + +  + R ++  ++   +PRER + E R ++   +T   ++ +  +S+ 
Sbjct: 188 DN--------ELDFTDDRLVIEEAIRDFSPREREVIELRFVKG--MTQIEIAKKLGISQV 237

Query: 268 RVRQIEARAFKKVQESI 284
           +V ++  R  KK+Q+ I
Sbjct: 238 QVSRLLRRTLKKIQDKI 254


>gi|15595116|ref|NP_212905.1| RNA polymerase sigma factor (rpoS) [Borrelia burgdorferi B31]
 gi|195941591|ref|ZP_03086973.1| RNA polymerase sigma factor (rpoS) [Borrelia burgdorferi 80a]
 gi|216264706|ref|ZP_03436698.1| RNA polymerase sigma factor (rpoS) [Borrelia burgdorferi 156a]
 gi|218249170|ref|YP_002375269.1| RNA polymerase sigma factor (rpoS) [Borrelia burgdorferi ZS7]
 gi|221217974|ref|ZP_03589441.1| RNA polymerase sigma factor [Borrelia burgdorferi 72a]
 gi|223889406|ref|ZP_03623992.1| RNA polymerase sigma factor [Borrelia burgdorferi 64b]
 gi|224532620|ref|ZP_03673242.1| RNA polymerase sigma factor [Borrelia burgdorferi WI91-23]
 gi|225548870|ref|ZP_03769847.1| RNA polymerase sigma factor [Borrelia burgdorferi 94a]
 gi|225550031|ref|ZP_03770992.1| RNA polymerase sigma factor [Borrelia burgdorferi 118a]
 gi|225551867|ref|ZP_03772810.1| RNA polymerase sigma factor [Borrelia sp. SV1]
 gi|226320640|ref|ZP_03796199.1| RNA polymerase sigma factor [Borrelia burgdorferi 29805]
 gi|226321470|ref|ZP_03796997.1| RNA polymerase sigma factor [Borrelia burgdorferi Bol26]
 gi|2688700|gb|AAC67109.1| RNA polymerase sigma factor (rpoS) [Borrelia burgdorferi B31]
 gi|215981179|gb|EEC21986.1| RNA polymerase sigma factor (rpoS) [Borrelia burgdorferi 156a]
 gi|218164358|gb|ACK74419.1| RNA polymerase sigma factor (rpoS) [Borrelia burgdorferi ZS7]
 gi|221192280|gb|EEE18500.1| RNA polymerase sigma factor [Borrelia burgdorferi 72a]
 gi|223885092|gb|EEF56196.1| RNA polymerase sigma factor [Borrelia burgdorferi 64b]
 gi|224512476|gb|EEF82855.1| RNA polymerase sigma factor [Borrelia burgdorferi WI91-23]
 gi|225369490|gb|EEG98942.1| RNA polymerase sigma factor [Borrelia burgdorferi 118a]
 gi|225370473|gb|EEG99909.1| RNA polymerase sigma factor [Borrelia burgdorferi 94a]
 gi|225371662|gb|EEH01089.1| RNA polymerase sigma factor [Borrelia sp. SV1]
 gi|226233266|gb|EEH32018.1| RNA polymerase sigma factor [Borrelia burgdorferi Bol26]
 gi|226233963|gb|EEH32685.1| RNA polymerase sigma factor [Borrelia burgdorferi 29805]
 gi|312148432|gb|ADQ31091.1| RNA polymerase sigma factor [Borrelia burgdorferi JD1]
 gi|312149704|gb|ADQ29775.1| RNA polymerase sigma factor [Borrelia burgdorferi N40]
          Length = 266

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 78/272 (28%), Positives = 138/272 (50%), Gaps = 18/272 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+  +R+  ++  +EE  LA + +  G+  A ++++ ++LRLV+KI   Y G GL I
Sbjct: 9   LNIYLKSVREHKLITHEEEIKLAGQIQ-RGNAKAKNKMINANLRLVLKIIKRYAGKGLKI 67

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GL++A +K+DP +  + +TY+ +WIK ++Q  +     LVK+        L
Sbjct: 68  EDLIQEGNLGLIRAAEKYDPNKNTKFSTYASFWIKQSLQRALNTKTRLVKVPYRKENLIL 127

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
                     +        K  +   I K+ N+S ++ I +   L  + SL+  I  S+ 
Sbjct: 128 ---------QINKYLTEEEKSPKKEEIMKRFNLSPAQYIKIIPYLEKEYSLDKEIEGSEN 178

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN---P 252
             S   +    +    E  L +    K+   +L    + LN +ER I + R   +N    
Sbjct: 179 --STLLNLYEDNSFNPEITLEQDSTLKHLNYILE---TKLNEKERYIIKKRYNLDNSPKK 233

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL+++S+E  +S E VRQIE R  KK++E I
Sbjct: 234 STLKDISTELGISSETVRQIEKRVLKKLKEEI 265


>gi|229031535|ref|ZP_04187535.1| RNA polymerase sigma-G factor [Bacillus cereus AH1271]
 gi|228729824|gb|EEL80804.1| RNA polymerase sigma-G factor [Bacillus cereus AH1271]
          Length = 289

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 62/261 (23%), Positives = 120/261 (45%), Gaps = 17/261 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+  E   L +  +  G++SA  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 45  KLPVLKNDEMRKLFREMQ-SGEISAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 103

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++ 
Sbjct: 104 GLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDN-DPIRVSRSL--RDIAYKALQVRE 160

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L A    N K    + IAK L V+  E++     +    SL   I +   +     D L
Sbjct: 161 KLIA---ENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGGDPIFVMDQL 217

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             +    EQ + E          L   M  LN RE+ I   R  Q    T   ++ E  +
Sbjct: 218 SDEKQKDEQWVEELA--------LKEGMKRLNDREKMIIRKRFFQG--KTQMEVAEEIGI 267

Query: 265 SRERVRQIEARAFKKVQESIQ 285
           S+ +V ++E  A K++ ++IQ
Sbjct: 268 SQAQVSRLEKSAIKQMNKTIQ 288


>gi|306841478|ref|ZP_07474178.1| RNA polymerase factor sigma-32 [Brucella sp. BO2]
 gi|306288442|gb|EFM59798.1| RNA polymerase factor sigma-32 [Brucella sp. BO2]
          Length = 198

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 86/195 (44%), Positives = 128/195 (65%), Gaps = 1/195 (0%)

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
            R +TY+ WWI+A+MQ+YILR+WS+V+ GT++ QK LFFNLRRL+  L    DN  K E 
Sbjct: 1   MRFSTYASWWIRASMQDYILRNWSIVRGGTSSAQKALFFNLRRLRSKLAQTDDNMTKAEI 60

Query: 159 VVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
              I+ +L VS S+V  M+ RL+G D SL+A +N  +  +S+  D+LV DH  Q+++   
Sbjct: 61  YREISDQLGVSTSDVEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIAES 120

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
             + + R   LTR++  LN RE  I   RRL ++ VTLE L  +  +S+ERVRQIE+RA 
Sbjct: 121 SIDMERRNRWLTRALDTLNERELHIIRERRLDDDGVTLEALGEKLGISKERVRQIESRAM 180

Query: 278 KKVQESIQKQVELSS 292
           +K++ ++  Q EL++
Sbjct: 181 EKLKIALLSQHELAA 195


>gi|87310114|ref|ZP_01092246.1| transcription initiation factor sigma 70 [Blastopirellula marina
           DSM 3645]
 gi|87287104|gb|EAQ79006.1| transcription initiation factor sigma 70 [Blastopirellula marina
           DSM 3645]
          Length = 516

 Score =  173 bits (438), Expect = 4e-41,   Method: Composition-based stats.
 Identities = 65/238 (27%), Positives = 115/238 (48%), Gaps = 16/238 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   + +++LRLVV IA  +RG GL   +++ EGN+GLM+AV+KFDP  G++ ATY+ W
Sbjct: 270 RAQRAITSANLRLVVSIAKSFRGRGLSYLDLIQEGNLGLMRAVEKFDPSLGYKFATYATW 329

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+ + +      +++       R+   ++++      ++  +     +   AK+  
Sbjct: 330 WIRQAVMKGLADQGRTIRLP-----ARMQDRIQKINVAKAILSQEHRSEPPIELTAKQAE 384

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++E EV++ +       SL+   N  D                 EQ L            
Sbjct: 385 LTEREVVAADRLGRTIMSLDVSNNDDDSFGDTLASGDAEQSSADEQRLPLA--------- 435

Query: 228 LTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQES 283
           + + +  L  RE+ I   R    +    TLE +S  F V+RER+RQIE+ A +K+++ 
Sbjct: 436 INQLLQELTSREQEIVRRRFGMFDGRVQTLEEVSQAFSVTRERIRQIESAAIRKLRQP 493


>gi|167628452|ref|YP_001678951.1| RNA polymerase sigma-f factor, putative [Heliobacterium
           modesticaldum Ice1]
 gi|167591192|gb|ABZ82940.1| RNA polymerase sigma-f factor, putative [Heliobacterium
           modesticaldum Ice1]
          Length = 264

 Score =  172 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 64/278 (23%), Positives = 122/278 (43%), Gaps = 25/278 (8%)

Query: 20  IHEIR--KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + E+   + P+L ++E   L  R  + GD  A  RL+  +LRLV  +   ++  G  + +
Sbjct: 5   LSEMNLPRFPLLGEEETTRLL-RLAKDGDGDARERLIQCNLRLVFNLVQRFQHRGYELED 63

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +   G IGL++A+ KFD     R +TY++  I   ++ ++    S VK+  +  +     
Sbjct: 64  LFQIGVIGLIKAIDKFDLSYNVRFSTYAVPMIVGEIRRFLRDD-SPVKVSRSYKEIA--- 119

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
             +R+    Q +  +  +   V  IA  +N+   +V+     +    S++  +   D + 
Sbjct: 120 --QRIHRVRQELNGSLGREPTVQEIAGAMNMPVEDVVEALEAVQLPTSIHETLYQDDGDP 177

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
               D L          +  +E        L   +S L  RER I E R  Q+   T   
Sbjct: 178 IFLLDQLAS--------VGTEESAWFDHLALKDVLSRLAAREREILEMRFFQD--KTQTE 227

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPP 295
           +++   +S+ ++ +IE  A KK+++       LS +PP
Sbjct: 228 VATLVGLSQVQISRIERAALKKIRD------MLSQTPP 259


>gi|240144182|ref|ZP_04742783.1| RNA polymerase sigma-G factor [Roseburia intestinalis L1-82]
 gi|257203785|gb|EEV02070.1| RNA polymerase sigma-G factor [Roseburia intestinalis L1-82]
          Length = 259

 Score =  172 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 53/260 (20%), Positives = 119/260 (45%), Gaps = 17/260 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+++E+  L  R ++ GD +A    +  +LRLV+ +   + G    + ++   G I
Sbjct: 15  KLPILKEEEKDALFARIKQ-GDTAARETYIKGNLRLVLSVIKRFSGNHENVDDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++++  FDP  G + +TY++  I   ++ Y+  + S +++      + L     +   
Sbjct: 74  GLIKSIDNFDPTIGVKFSTYAVPMIIGEIRRYLRDNNS-IRVS-----RSLRDTAYKAIH 127

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + ++    K   +  IA +  +S+ +++     +    SL   +  +D   + +    
Sbjct: 128 TKEILSKTENKEPTLDEIAAESGISKEDIVFALDAIQSPLSLYDPVY-TDGGDTLYVMDQ 186

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           + D   +E+  IE+         L  ++  LN RE  I + R       T   ++ E  +
Sbjct: 187 ISDKKNREENWIEELS-------LNDALDRLNERENYILKLRFF--EGKTQMEVADEIHI 237

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ +V ++E  A K ++  +
Sbjct: 238 SQAQVSRLEKSALKSIRHYL 257


>gi|291536437|emb|CBL09549.1| RNA polymerase, sigma subunit, RpsG/SigG [Roseburia intestinalis
           M50/1]
          Length = 259

 Score =  172 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 52/260 (20%), Positives = 119/260 (45%), Gaps = 17/260 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+++E+  L  R ++ GD +A    +  +LRLV+ +   + G    + ++   G I
Sbjct: 15  KLPILKEEEKDALFARIKQ-GDTAARETYIKGNLRLVLSVIKRFSGNHENVDDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++++  FDP  G + +TY++  I   ++ Y+  + S +++      + L     +   
Sbjct: 74  GLIKSIDNFDPTIGVKFSTYAVPMIIGEIRRYLRDNNS-IRVS-----RSLRDTAYKAIH 127

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + ++    K   +  IA +  +S+ +++     +    SL   +  +D   + +    
Sbjct: 128 TKEILSKTENKEPTLDEIAAESGISKEDIVFALDAIQSPLSLYDPVY-TDGGDTLYVMDQ 186

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           + D   +E+  +E+         L  ++  LN RE  I + R       T   ++ E  +
Sbjct: 187 ISDKKNREENWVEELS-------LNDALDRLNERENYILKLRFF--EGKTQMEVADEIHI 237

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ +V ++E  A K ++  +
Sbjct: 238 SQAQVSRLEKSALKSIRHYL 257


>gi|161521004|ref|YP_001584431.1| RpoD family RNA polymerase sigma factor [Burkholderia multivorans
           ATCC 17616]
 gi|189352818|ref|YP_001948445.1| RNA polymerase sigma 38 subunit [Burkholderia multivorans ATCC
           17616]
 gi|160345054|gb|ABX18139.1| RNA polymerase, sigma 70 subunit, RpoD family [Burkholderia
           multivorans ATCC 17616]
 gi|189336840|dbj|BAG45909.1| RNA polymerase sigma 38 subunit [Burkholderia multivorans ATCC
           17616]
          Length = 525

 Score =  172 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 52/230 (22%), Positives = 101/230 (43%), Gaps = 13/230 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   ++ ++LRLV+ IA  Y   G+ +S++V +G IGLM+A++KF+  RGF+ +TY+ 
Sbjct: 286 RDATRAMLEANLRLVLSIARKYLNRGVDLSDLVQDGCIGLMRAIEKFEYRRGFKFSTYAT 345

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      +++      +      +R++           +      +A + 
Sbjct: 346 WWIRQAIARAVADRARTIRVPVHVGDQH-----QRVRRQALRFRQRTGRQPTPAELAAET 400

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++E ++ ++    A   SL+  +  +D              D       E+      R 
Sbjct: 401 GLAEDKLRAILALPAEPVSLDTPLPDADTGLVDLI------EDETSASPFEQLAGTRMRE 454

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEA 274
            +   +  + P E  +   R       P T + ++ +  +SRERVRQIE 
Sbjct: 455 CVRSLLRSVTPTEADVLRRRFGLGGTEPDTYDAIAKDAGMSRERVRQIEK 504


>gi|120553093|ref|YP_957444.1| RNA polymerase, sigma 32 subunit, RpoH [Marinobacter aquaeolei VT8]
 gi|120322942|gb|ABM17257.1| RNA polymerase, sigma 32 subunit, RpoH [Marinobacter aquaeolei VT8]
          Length = 330

 Score =  172 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 68/237 (28%), Positives = 119/237 (50%), Gaps = 12/237 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L+  HRL+ S+LRL V IA  Y  +G+ +S+++ + N+GL++AV+++DP +GFR +TY+ 
Sbjct: 94  LACRHRLIQSNLRLAVHIARRYGHHGIAMSDLIQDANVGLIKAVERYDPGKGFRFSTYAY 153

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI   ++  + R   +V        + +   +R+L+     +  +  +      +A+++
Sbjct: 154 WWISEEVRRCLQRGVRVVHTP-----ENVVEEIRQLQKVSMRLHQSLGREPTQSELAREM 208

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             + S +  +    A + S +  +   +  S    D L    D +        +R  R  
Sbjct: 209 EATPSRIGELRALAAREVSTDVPLV--EDGSVTLADSLDAGADTRPDQPFRARDRMIR-- 264

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L R M  L+ RER I   R       P TL+ +S +  +SRERVRQIE  A +K+Q
Sbjct: 265 -LERMMGALSDRERDILTRRYGLGLIEPETLQTISEQLGLSRERVRQIEKGALRKLQ 320


>gi|52080862|ref|YP_079653.1| sporulation sigma factor SigF [Bacillus licheniformis ATCC 14580]
 gi|52786234|ref|YP_092063.1| sporulation sigma factor SigF [Bacillus licheniformis ATCC 14580]
 gi|319645181|ref|ZP_07999414.1| RNA polymerase sigma-F factor [Bacillus sp. BT1B_CT2]
 gi|52004073|gb|AAU24015.1| RNA polymerase sporulation-specific sigma factor (sigma-F)
           [Bacillus licheniformis ATCC 14580]
 gi|52348736|gb|AAU41370.1| SigF [Bacillus licheniformis ATCC 14580]
 gi|317392990|gb|EFV73784.1| RNA polymerase sigma-F factor [Bacillus sp. BT1B_CT2]
          Length = 255

 Score =  172 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 58/256 (22%), Positives = 112/256 (43%), Gaps = 19/256 (7%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L+  E   L K   ++GD  A   L+  ++RLV  +   +   G    ++   G IGL++
Sbjct: 14  LKDHEVKELIKN-SQNGDQKARDLLIEKNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLK 72

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           +V KFD     R +TY++  I   +Q +I      VK+  +   K L   +RR K  L  
Sbjct: 73  SVDKFDLSYDVRFSTYAVPMIIGEIQRFIRDDG-TVKVSRSL--KELGNKIRRAKDEL-- 127

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
            + +N +   V  IA  L +S  EV+     +    S++  +  +D +     D +    
Sbjct: 128 -SKSNGRIPTVQEIADYLEISSEEVVMAQEAVRSPSSIHETVYENDGDPITLLDQIAD-- 184

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
                   + EE+   +  L  ++  L+ RE+ I   R  ++   T   ++    +S+ +
Sbjct: 185 --------QSEEKWFDKIALKEAIKDLDEREKLIVYLRYYKD--KTQSEVADRLGISQVQ 234

Query: 269 VRQIEARAFKKVQESI 284
           V ++E +  K+++  +
Sbjct: 235 VSRLEKKILKQIKNQM 250


>gi|126700256|ref|YP_001089153.1| sporulation sigma factor SigG [Clostridium difficile 630]
 gi|254976235|ref|ZP_05272707.1| sporulation sigma factor SigG [Clostridium difficile QCD-66c26]
 gi|255093622|ref|ZP_05323100.1| sporulation sigma factor SigG [Clostridium difficile CIP 107932]
 gi|255101810|ref|ZP_05330787.1| sporulation sigma factor SigG [Clostridium difficile QCD-63q42]
 gi|255307677|ref|ZP_05351848.1| sporulation sigma factor SigG [Clostridium difficile ATCC 43255]
 gi|255315370|ref|ZP_05356953.1| sporulation sigma factor SigG [Clostridium difficile QCD-76w55]
 gi|255518035|ref|ZP_05385711.1| sporulation sigma factor SigG [Clostridium difficile QCD-97b34]
 gi|255651151|ref|ZP_05398053.1| sporulation sigma factor SigG [Clostridium difficile QCD-37x79]
 gi|255656619|ref|ZP_05402028.1| sporulation sigma factor SigG [Clostridium difficile QCD-23m63]
 gi|260684217|ref|YP_003215502.1| sporulation sigma factor SigG [Clostridium difficile CD196]
 gi|260687876|ref|YP_003219010.1| sporulation sigma factor SigG [Clostridium difficile R20291]
 gi|296449925|ref|ZP_06891689.1| RNA polymerase sigma-G factor [Clostridium difficile NAP08]
 gi|296878307|ref|ZP_06902315.1| RNA polymerase sigma-G factor [Clostridium difficile NAP07]
 gi|306521001|ref|ZP_07407348.1| sporulation sigma factor SigG [Clostridium difficile QCD-32g58]
 gi|115251693|emb|CAJ69528.1| RNA polymerase sigma-G factor [Clostridium difficile]
 gi|260210380|emb|CBA64761.1| RNA polymerase sigma-G factor [Clostridium difficile CD196]
 gi|260213893|emb|CBE05925.1| RNA polymerase sigma-G factor [Clostridium difficile R20291]
 gi|296261195|gb|EFH08026.1| RNA polymerase sigma-G factor [Clostridium difficile NAP08]
 gi|296430605|gb|EFH16444.1| RNA polymerase sigma-G factor [Clostridium difficile NAP07]
          Length = 257

 Score =  172 bits (437), Expect = 5e-41,   Method: Composition-based stats.
 Identities = 56/261 (21%), Positives = 117/261 (44%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            ++P+L+ ++   L  + + +GD  A  + V  +LRLV+ +   +   G  I ++   G 
Sbjct: 14  SELPVLKNKQMKELLLQIK-NGDEEARQQFVRGNLRLVLSVIKKFNNRGENIDDLFQIGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD  +  R +TY++  I   ++ Y+  +   +++  +   K + +   +++
Sbjct: 73  IGLIKAIDNFDLSQNVRFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--KDIAYKALQVR 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L      N K   V  IAK+L +    V+     +    SL   +   + ++    D 
Sbjct: 130 ERL---IRTNSKEPTVSEIAKELELEVESVVMALDAIQDPISLFDPVYQDNGDAIFVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    D  E  L E          L  ++  LN RE+ + + R  +    T   ++ E  
Sbjct: 187 VQDKKDTDENWLQE--------ISLKEAIKKLNSREKLVLDLRFYKG--RTQIEVADEIG 236

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V +IE  A K +++ +
Sbjct: 237 ISQAQVSRIEKNALKNMRKYV 257


>gi|2564653|gb|AAC45358.1| group 2 alternative sigma factor [Nostoc punctiforme PCC 73102]
          Length = 321

 Score =  172 bits (436), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 64/301 (21%), Positives = 126/301 (41%), Gaps = 52/301 (17%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------------------ 43
             +  Y+ EI +IP+L +++E + A+  ++                              
Sbjct: 20  DTVRAYLKEIGRIPLLTQEQEIIFAQEVQQLMTILAESEKLTIELKRTPTLSEWANQMQL 79

Query: 44  ---------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                    +    A H+++T++LRLVV IA  Y+   L + +++ EG +GL + V+KF+
Sbjct: 80  SEQELLQQLNQGKKAKHKMITANLRLVVSIAKQYQRRNLELMDLIQEGTLGLERGVEKFN 139

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P  G+R  TY+ WWI+  +   I +    +++    N+K     L ++K   + ++    
Sbjct: 140 PALGYRKTTYAYWWIRQGITRAIAQQGRAIRLPIHINEK-----LNKIKRVQRELSQTLG 194

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +      IA  L++  S++           SL+  I  S     + QD +          
Sbjct: 195 RIPTSTEIANALSLKPSQIREFLLLATRTISLD--IRVSSAKDLRLQDLIEDYKYSSNSY 252

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQI 272
           + E+   +     +   +S L+ +++ I            ++L+ +     +SRERVRQI
Sbjct: 253 ITEESLNQE----VNSLLSNLSRQQQEILNLHFGLTDGEELSLQQIGQRLGISRERVRQI 308

Query: 273 E 273
           E
Sbjct: 309 E 309


>gi|295092809|emb|CBK78916.1| RNA polymerase, sigma subunit, RpsG/SigG [Clostridium cf.
           saccharolyticum K10]
          Length = 258

 Score =  172 bits (436), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 55/260 (21%), Positives = 114/260 (43%), Gaps = 17/260 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L  +E+  L  R  + GD  A  + +  +LRLV+ +   + G    + ++   G I
Sbjct: 15  KLPLLTNEEKEELFARILK-GDREAREQYIKGNLRLVLSVIQRFSGSSENVDDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD  +  R +TY++  I   ++ Y+  + S +++  +           R   
Sbjct: 74  GLIKAIDNFDITQNVRFSTYAVPMILGEVKRYLRDNNS-IRVSRSLRDTAYKAIYAR--- 129

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             +++   NLK   +  IA+++ VS+ ++      +    SL   + +   +     D L
Sbjct: 130 --ESLMKKNLKEPTLCEIAEEVGVSKEDITYALDAIQSPVSLYEPVYTDGGDPLYVMDQL 187

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               + +E  + +          L+ +M  L  RER I   R       T   ++ E  +
Sbjct: 188 SDKKNSEENWIED--------ISLSEAMRRLPERERHIIGMRFF--EGKTQTEVAEEIHI 237

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ +V ++E  A K ++  +
Sbjct: 238 SQAQVSRLEKNALKAMKNYL 257


>gi|4100834|gb|AAD00999.1| RpoS [Escherichia coli]
          Length = 258

 Score =  172 bits (436), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 63/231 (27%), Positives = 113/231 (48%), Gaps = 11/231 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 37  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 95

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 96  IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 154

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 155 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 209

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
                L    D +E    +  +  + +  + + +  LN ++R +   R   
Sbjct: 210 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGL 256


>gi|302874724|ref|YP_003843357.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium cellulovorans
           743B]
 gi|302577581|gb|ADL51593.1| RNA polymerase, sigma 28 subunit, SigG [Clostridium cellulovorans
           743B]
          Length = 256

 Score =  172 bits (436), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 57/261 (21%), Positives = 118/261 (45%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L++ E   L  + +  GD  +  + +  +LRLV+ +   +   G    ++   G 
Sbjct: 13  SKLPVLKEHEMRELLDKMK-AGDYISREKFIRGNLRLVLSVIQRFNNRGENADDLFQVGC 71

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD  +  + +TY++  I   ++ Y+  + S +++  +          R L+
Sbjct: 72  IGLIKALDNFDLTQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRDI----AYRALQ 126

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
              + +T+NN K   V  IAK+L+V++ EVI     +    SL   I     ++    D 
Sbjct: 127 VRDKLLTENN-KEPTVYQIAKELDVAKEEVIFALDAIQEPVSLFEPIYHDGGDAIYVMDQ 185

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    +  E  L            +  +M  L+ RE+ I   R    +  T   ++ E  
Sbjct: 186 ISDSKNLDESWLENIA--------IKEAMKRLSDREKLILNMRFF--DGRTQMEVADEIG 235

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A + +++ +
Sbjct: 236 ISQAQVSRLEKNALRHMRKHV 256


>gi|149198541|ref|ZP_01875585.1| RNA polymerase sigma factor RpoD [Lentisphaera araneosa HTCC2155]
 gi|149138256|gb|EDM26665.1| RNA polymerase sigma factor RpoD [Lentisphaera araneosa HTCC2155]
          Length = 282

 Score =  172 bits (436), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 64/273 (23%), Positives = 127/273 (46%), Gaps = 12/273 (4%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+  +    +++   E  LA +  + GD SA   L  ++LRLVV IA  +   G+ 
Sbjct: 5   ALDNYLKNLSDYDLIDSDREIALANKIAK-GDESAIQELTLANLRLVVTIAKQFMNRGVA 63

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + E+++EGN GL++A ++F P  G + A+Y+ WWIK  ++  I     +V++   +    
Sbjct: 64  LGELIAEGNHGLVKAAQRFRPGHGAKFASYAAWWIKQNIRRAIRDDKRIVRVPVQS---- 119

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSS 193
               ++++K     I           A+AK++ +S   V + +  +     S+N  I S 
Sbjct: 120 -LLRMQKIKNARLKIQQETGDASNDKAVAKEVGISPRLVRTTSLHVDTSSFSINEQI-SQ 177

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP- 252
           D  +++  + +          ++E  +    + ++      L  RE +I  AR   ++  
Sbjct: 178 DGKATEKGELIPDSQAQTPGEVMEFHD--GYKTLMEIVRQELTEREYKILSARFGLDDGE 235

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             TL   S    ++ ERVRQ++  A ++++  +
Sbjct: 236 AKTLAETSELVGLTSERVRQLQQEALRRLRCKL 268


>gi|51892360|ref|YP_075051.1| sporulation sigma factor SigG [Symbiobacterium thermophilum IAM
           14863]
 gi|51856049|dbj|BAD40207.1| RNA polymerase sigma factor similar to B. subtilis SigG
           [Symbiobacterium thermophilum IAM 14863]
          Length = 256

 Score =  172 bits (436), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 53/260 (20%), Positives = 115/260 (44%), Gaps = 17/260 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L   +   L  R R  G+ +A   L+T +LRLV+ +   +   G  + ++   G I
Sbjct: 14  KLPVLTNAQMRELFVRMR-SGEKAARDELITGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 72

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A+  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++ 
Sbjct: 73  GLMKAIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVRD 129

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
              A+ +   +   V  IA +L +   E++     +    SL   +  +D     +    
Sbjct: 130 ---ALVNRLSREPTVQEIADELGLPLEEIVYALDSIQEPVSLFEPLY-NDGGDPIYVMDQ 185

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           V D   Q+   +E          + +++  LN RER I   R       T   ++ E  +
Sbjct: 186 VSDESQQDSQWLEGIS-------IRQALHRLNERERLILTLRFF--EGKTQMEVAEEIGI 236

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ +V ++E  A   +++ +
Sbjct: 237 SQAQVSRLEKAALSHMRKYV 256


>gi|229086468|ref|ZP_04218640.1| RNA polymerase sigma-G factor [Bacillus cereus Rock3-44]
 gi|228696785|gb|EEL49598.1| RNA polymerase sigma-G factor [Bacillus cereus Rock3-44]
          Length = 259

 Score =  172 bits (436), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 63/261 (24%), Positives = 121/261 (46%), Gaps = 17/261 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+ +E   L +  +  G++SA  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKNEEMRKLFREMQ-SGEISAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++ 
Sbjct: 74  GLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVRE 130

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L A    N K    + IAK L V+  E++     +    SL   I +   +     D L
Sbjct: 131 KLIA---ENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGGDPIFVMDQL 187

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             D    EQ + E          L   M  LN RE+ I   R  Q    T   ++ E  +
Sbjct: 188 SDDKQRDEQWVEELA--------LKEGMKRLNDREKMIIRKRFFQG--KTQMEVAEEIGI 237

Query: 265 SRERVRQIEARAFKKVQESIQ 285
           S+ +V ++E  A K++ ++IQ
Sbjct: 238 SQAQVSRLEKSAIKQMNKTIQ 258


>gi|169831582|ref|YP_001717564.1| sporulation sigma factor SigG [Candidatus Desulforudis audaxviator
           MP104C]
 gi|169638426|gb|ACA59932.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Candidatus
           Desulforudis audaxviator MP104C]
          Length = 255

 Score =  172 bits (436), Expect = 6e-41,   Method: Composition-based stats.
 Identities = 52/261 (19%), Positives = 115/261 (44%), Gaps = 18/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L   E   L +  +  GD SA  +L+  +LRLV+ +   +   G  + ++   G 
Sbjct: 13  SKLPVLTAAEMRQLFQEMQ-AGDPSARSKLINGNLRLVLSVIQRFTNRGEFVDDLFQVGC 71

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 72  IGLIKAIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDVAYKALQIR 128

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
            +L    +   +   V  IA++LN+   E++     +    SL   I   D +     D 
Sbjct: 129 DNL---ANRFSREPSVSEIAQELNIPREEIVFALDSIQEPISLFEPIYH-DGDPIFVMDQ 184

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  + +     L +          +  ++  LN RE+ I   R       T   ++ E  
Sbjct: 185 VSDERNADANWLEDIA--------IRDAIRKLNEREKLILTLRFF--EGKTQMEVAEEIG 234

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A   +++ I
Sbjct: 235 ISQAQVSRLEKAALSHMRKYI 255


>gi|311696748|gb|ADP99621.1| RNA polymerase, sigma 70 subunit, RpoD family [marine bacterium
           HP15]
          Length = 332

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 66/241 (27%), Positives = 117/241 (48%), Gaps = 12/241 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +   +L+ S+LRL V IA  Y  +G+P+S+++ + N+GL++AV++FDP +GFR +TY+ W
Sbjct: 95  ACRRKLIQSNLRLAVHIARRYGQHGIPMSDLIQDANVGLIKAVERFDPTKGFRFSTYAYW 154

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI   ++  + R   LV        + +   +R+L      +  +  +      +A+++ 
Sbjct: 155 WISEEVKRCLQRGTRLVHTP-----ENVVDEIRQLHKVSLRMHQSLGRTPSQSELAREME 209

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
            S S +  +      + S +  +   +  S    D L           +     ++R+  
Sbjct: 210 ASPSRIGELRALATREISTDVPLV--EDGSVTLGDSLDAGDQMAPDHPM---SDRDRQRT 264

Query: 228 LTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L   +S LN RE+ I   R       P TL+ +S +  +SRERVRQIE  A KK+Q   +
Sbjct: 265 LKSMLSELNDREKDILSRRYGLGLPEPETLQVISDDLGISRERVRQIEKTALKKLQSRYE 324

Query: 286 K 286
            
Sbjct: 325 S 325


>gi|89099621|ref|ZP_01172496.1| sporulation sigma factor SigG [Bacillus sp. NRRL B-14911]
 gi|89085774|gb|EAR64900.1| sporulation sigma factor SigG [Bacillus sp. NRRL B-14911]
          Length = 259

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 61/263 (23%), Positives = 117/263 (44%), Gaps = 17/263 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+ +E   L K+  E GD  A   LV  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLKNEEMRKLFKQMHE-GDTYARECLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+++  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 73  IGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVR 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L + T      E    IA+ L V   E++     +    SL   I +   +     D 
Sbjct: 130 ERLMSETSKEPTAE---EIARVLEVPHEEIVFALDAIQDPVSLFEPIYNDGGDPIFVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L  + +   Q + E          L   M  LN RE+ I   R  Q    T   ++ E  
Sbjct: 187 LSDERNKDIQWIEEIA--------LKEGMRRLNEREKLILRKRFFQG--KTQMEVAEEIG 236

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+ +V ++E  A K++ ++IQ 
Sbjct: 237 ISQAQVSRLEKAAIKQMNKNIQS 259


>gi|255280674|ref|ZP_05345229.1| RNA polymerase sigma-G factor [Bryantella formatexigens DSM 14469]
 gi|255268611|gb|EET61816.1| RNA polymerase sigma-G factor [Bryantella formatexigens DSM 14469]
          Length = 258

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 53/262 (20%), Positives = 117/262 (44%), Gaps = 17/262 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L  +E+  L +R R+ GD+ A    +  +LRLV+ +   +        ++   G 
Sbjct: 14  SKLPVLTNEEKEELFERIRQ-GDMEARELYIKGNLRLVLSVIKRFSASNENADDLFQIGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+A+  F+ E   + +TY++  I   ++ Y+  + S +++      + L     +  
Sbjct: 73  IGLMKAIDNFNTEMDVKFSTYAVPMIIGEIRRYLRDNNS-IRVS-----RSLRDTAYKAL 126

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
              +A    +LK   +  +A+++ +S  +++     +    SL   + S   ++    D 
Sbjct: 127 YTREAYMKKHLKEPTINELAEEIGISREDIVFAMDAIQSPLSLYDPVYSEGGDTLYVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    + +E  +            L  +M  L+ RER+I   R       T   +++E  
Sbjct: 187 ISDKKNKEENWVESLA--------LQEAMKRLSDRERKIINMRFF--EGKTQMEVAAEIC 236

Query: 264 VSRERVRQIEARAFKKVQESIQ 285
           +S+ +V ++E  A K ++  ++
Sbjct: 237 ISQAQVSRLEKSALKSMRNFLR 258


>gi|317129288|ref|YP_004095570.1| RNA polymerase, sigma 28 subunit, SigG [Bacillus cellulosilyticus
           DSM 2522]
 gi|315474236|gb|ADU30839.1| RNA polymerase, sigma 28 subunit, SigG [Bacillus cellulosilyticus
           DSM 2522]
          Length = 261

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 55/263 (20%), Positives = 121/263 (46%), Gaps = 15/263 (5%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+ +E  VL ++ + +GD  A   LV  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLKNKEMRVLFEKMQ-NGDEFAREELVNGNLRLVLSVIQRFNNRGEYVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+++  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 73  IGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVR 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
            ++        +   V  IAK L+V + +++     +    SL   I +   +     D 
Sbjct: 130 DNMMNEKKRE-REPTVQEIAKVLDVPKEDIVFALDAIQDPVSLFEPIYNDGGDPIYVMDQ 188

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  D     Q + E          L  +M  LN RE+ I + R  Q    T   ++ E  
Sbjct: 189 ISDDKQKDIQWIEEIA--------LKEAMIRLNDREKMILDMRFFQG--KTQMEVADEIG 238

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+ +V ++E  A +++ +  ++
Sbjct: 239 ISQAQVSRLEKAAIQQMNKHAKE 261


>gi|225574955|ref|ZP_03783565.1| hypothetical protein RUMHYD_03034 [Blautia hydrogenotrophica DSM
           10507]
 gi|225037802|gb|EEG48048.1| hypothetical protein RUMHYD_03034 [Blautia hydrogenotrophica DSM
           10507]
          Length = 259

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 49/262 (18%), Positives = 111/262 (42%), Gaps = 17/262 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L  +E+  L +R ++ GD  A    +  +LRLV+ +   +        ++   G I
Sbjct: 15  KLPILSNEEKEELFRRIKQ-GDQQAREEYIKGNLRLVLSVIKRFSNSNENADDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD     + +TY++  I   ++ Y+  + S +++  +           + + 
Sbjct: 74  GLIKAIDNFDTTLDVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRDIAYKAIYAKER- 131

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
               I    LK   +  I+K++ + +  ++     +    SL   + +   ++    D +
Sbjct: 132 ----IVKEELKEPTIEEISKEIGIEKEMIVYALDAIQNPVSLFEPVYTEGGDALYVMDQI 187

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               + +E  + E          L  +M  L  RE+ I + R       T   ++ E  +
Sbjct: 188 SDKKNKEEHWVEELS--------LREAMDRLGEREKHIIDLRFY--EGKTQMEVAREIGI 237

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+ +V ++E  A K ++  ++ 
Sbjct: 238 SQAQVSRLEKNALKTMRTYLRS 259


>gi|148656381|ref|YP_001276586.1| RNA polymerase, sigma 32 subunit, RpoH [Roseiflexus sp. RS-1]
 gi|148568491|gb|ABQ90636.1| RNA polymerase, sigma 32 subunit, RpoH [Roseiflexus sp. RS-1]
          Length = 398

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 63/256 (24%), Positives = 118/256 (46%), Gaps = 16/256 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR--GYGLPISEVVSEGNIGL 86
           L   ++Y   +R +      A   L+  +LRLV KIA  Y      L   +++ EG IGL
Sbjct: 140 LSSVQQYAAERRIKAS--EEAIDTLMRCNLRLVAKIATRYMPYARHLTFDDLLQEGRIGL 197

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+++FD     RL+TY+++WI+ ++Q  +     +V++     +      L RL+   
Sbjct: 198 LKAIERFDQNCRGRLSTYAVYWIRQSIQRALADQDRMVRLPVHIVE-----QLHRLRKTC 252

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +     + +      +A  L VS ++V S+        S++  +      ++   + +  
Sbjct: 253 EQFRCIHGREPGDAELANALGVSLAKVRSLWRVAQHHTSIDRPV--GADTNTFLGELIAD 310

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           D +     + E++       +L   +  L+ RER I E R         TLE +   F +
Sbjct: 311 DREEGPDFICEQQLL---HAVLREVLGHLSSRERDILERRYGLIDGQTHTLEEIGQIFGL 367

Query: 265 SRERVRQIEARAFKKV 280
           +RER+RQIE +A K++
Sbjct: 368 TRERIRQIERKALKRL 383


>gi|152976264|ref|YP_001375781.1| sporulation sigma factor SigG [Bacillus cereus subsp. cytotoxis NVH
           391-98]
 gi|152025016|gb|ABS22786.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           cytotoxicus NVH 391-98]
          Length = 259

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 61/261 (23%), Positives = 120/261 (45%), Gaps = 17/261 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+  E   L +  +  G+ SA  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKNDEMRKLFREMQ-SGETSAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++ 
Sbjct: 74  GLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVRE 130

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L A    N K    + IA+ L+V+  E++     +    SL   I +   +     D L
Sbjct: 131 KLIA---ENSKEPTAMDIAQVLDVTHEEIVFALDAIQDPVSLFEPIYNDGGDPIFVMDQL 187

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             +    EQ + E          L   M  LN RE+ I   R  Q    T   ++ E  +
Sbjct: 188 SDEKQKDEQWVEELA--------LKEGMKRLNDREKMIIRKRFFQG--KTQMEVAEEIGI 237

Query: 265 SRERVRQIEARAFKKVQESIQ 285
           S+ +V ++E  A K++ ++IQ
Sbjct: 238 SQAQVSRLEKSAIKQMNKTIQ 258


>gi|221196694|ref|ZP_03569741.1| RNA polymerase sigma factor RpoD (Sigma-70) [Burkholderia
           multivorans CGD2M]
 gi|221203363|ref|ZP_03576382.1| RNA polymerase sigma factor RpoD (Sigma-70) [Burkholderia
           multivorans CGD2]
 gi|221177297|gb|EEE09725.1| RNA polymerase sigma factor RpoD (Sigma-70) [Burkholderia
           multivorans CGD2]
 gi|221183248|gb|EEE15648.1| RNA polymerase sigma factor RpoD (Sigma-70) [Burkholderia
           multivorans CGD2M]
          Length = 524

 Score =  172 bits (436), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 52/230 (22%), Positives = 101/230 (43%), Gaps = 13/230 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   ++ ++LRLV+ IA  Y   G+ +S++V +G IGLM+A++KF+  RGF+ +TY+ 
Sbjct: 285 RDATRAMLEANLRLVLSIARKYLNRGVDLSDLVQDGCIGLMRAIEKFEYRRGFKFSTYAT 344

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      +++      +      +R++           +      +A + 
Sbjct: 345 WWIRQAIARAVADRARTIRVPVHVGDQH-----QRVRRQALRFRQRTGRQPTPAELAAET 399

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++E ++ ++    A   SL+  +  +D              D       E+      R 
Sbjct: 400 GLAEDKLRAILALPAEPVSLDTPLPDADTGLVDLI------EDETSASPFEQLAGARMRE 453

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEA 274
            +   +  + P E  +   R       P T + ++ +  +SRERVRQIE 
Sbjct: 454 CVRSLLRSVTPAEADVLRRRFGLGGTEPDTYDAIAKDAGMSRERVRQIEK 503


>gi|167465669|ref|ZP_02330758.1| sporulation sigma factor SigG [Paenibacillus larvae subsp. larvae
           BRL-230010]
          Length = 260

 Score =  171 bits (435), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 50/261 (19%), Positives = 113/261 (43%), Gaps = 16/261 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L   E   L    +   + +A  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLTNTEMRELFALLQTKNERAAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGCI 74

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A+  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++ 
Sbjct: 75  GLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVRD 131

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
               +T+ N +   +  I++ LNV + +V+     +    SL   I     +     D +
Sbjct: 132 ---QLTNRNSREPTIYEISEVLNVPKEDVVFALDAIQDPVSLFEPIYHDGGDPIYVMDQI 188

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             + +     +            L  +M  L  RE+ I   R       T   ++ E  +
Sbjct: 189 SDERNKDLFWIEGIA--------LREAMRKLGSREKMILSMRFF--EGKTQMEVADEIGI 238

Query: 265 SRERVRQIEARAFKKVQESIQ 285
           S+ +V ++E  A  ++Q+ ++
Sbjct: 239 SQAQVSRLEKSAINQMQKHVK 259


>gi|320103437|ref|YP_004179028.1| RpoD subfamily RNA polymerase sigma-70 factor [Isosphaera pallida
           ATCC 43644]
 gi|319750719|gb|ADV62479.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Isosphaera
           pallida ATCC 43644]
          Length = 286

 Score =  171 bits (435), Expect = 7e-41,   Method: Composition-based stats.
 Identities = 73/262 (27%), Positives = 130/262 (49%), Gaps = 9/262 (3%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           +L  +EE  LA+R    GD SA  R++ ++LRLV  +A  YRG GL   ++V EGN+GL+
Sbjct: 32  LLTAEEERELARRVL-RGDASARRRMIEANLRLVAMVAARYRGLGLDWEDLVGEGNLGLI 90

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV  +DP+RG R +TY+  WI+  ++  +  + + +++      K   +     +    
Sbjct: 91  RAVSSYDPDRGVRFSTYAAHWIRQTIRVALTTTAATIRLPAHMVTKLALW-----RRAEA 145

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
            +T N  +      +A +L  S S  +SM   +      +    +++   S+ +  +   
Sbjct: 146 RLTRNLGRSPTFEEVADELGWSSSTRLSMKRAMESGRVHHEEPGATEGRGSESRRPIDQA 205

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVS 265
            D + +   E E R      L RS+  L  RER +   R    +  P  L  +++   V+
Sbjct: 206 VDPRPEPAWEIERRDELLE-LRRSLQRLGERERLVLALRYGLGDIAPKPLREVATTLGVT 264

Query: 266 RERVRQIEARAFKKVQESIQKQ 287
           RE VR+IEARA +++ E ++ +
Sbjct: 265 REWVRRIEARALRQLHEEVEPE 286


>gi|221212711|ref|ZP_03585688.1| RNA polymerase sigma factor RpoD (Sigma-70) [Burkholderia
           multivorans CGD1]
 gi|221167810|gb|EEE00280.1| RNA polymerase sigma factor RpoD (Sigma-70) [Burkholderia
           multivorans CGD1]
          Length = 522

 Score =  171 bits (435), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 52/230 (22%), Positives = 101/230 (43%), Gaps = 13/230 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   ++ ++LRLV+ IA  Y   G+ +S++V +G IGLM+A++KF+  RGF+ +TY+ 
Sbjct: 283 RDATRAMLEANLRLVLSIARKYLNRGVDLSDLVQDGCIGLMRAIEKFEYRRGFKFSTYAT 342

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      +++      +      +R++           +      +A + 
Sbjct: 343 WWIRQAIARAVADRARTIRVPVHVGDQH-----QRVRRQALRFRQRTGRQPTPAELAAET 397

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++E ++ ++    A   SL+  +  +D              D       E+      R 
Sbjct: 398 GLAEDKLRAILALPAEPVSLDTPLPDADTGLVDLI------EDETSASPFEQLAGTRMRE 451

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEA 274
            +   +  + P E  +   R       P T + ++ +  +SRERVRQIE 
Sbjct: 452 CVRSLLRSVTPTEADVLRRRFGLGGTEPDTYDAIAKDAGMSRERVRQIEK 501


>gi|167751709|ref|ZP_02423836.1| hypothetical protein EUBSIR_02718 [Eubacterium siraeum DSM 15702]
 gi|167655517|gb|EDR99646.1| hypothetical protein EUBSIR_02718 [Eubacterium siraeum DSM 15702]
 gi|291558002|emb|CBL35119.1| RNA polymerase, sigma subunit, RpsG/SigG [Eubacterium siraeum
           V10Sc8a]
          Length = 261

 Score =  171 bits (435), Expect = 8e-41,   Method: Composition-based stats.
 Identities = 55/260 (21%), Positives = 125/260 (48%), Gaps = 18/260 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+ +L++ E+  L ++ R  GD +A  +L+  +LRLV+ +   + G G    ++   G I
Sbjct: 20  KLKVLKESEKTELLRQMR-SGDPTAREKLINGNLRLVLSVIQRFSGRGENPDDLFQVGCI 78

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A+  F  +   R +TY++  I   ++ Y+  S S +++  +   + L +   + + 
Sbjct: 79  GLMKAIDNFSTDFNVRFSTYAVPMIMGELRRYLRDSGS-IRVSRSM--RDLAYKAMQAR- 134

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + +T++N K   +  IAK+++    +V+     ++   SL   + S   ++    D +
Sbjct: 135 --EKLTNDNSKEPTIEQIAKEIDAKREDVVIALEAVSDPISLYEPVFSESGDTIYMMDQI 192

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             ++D +                L  ++  L+ RE+ I + R  +    T   ++ E  +
Sbjct: 193 GDNNDDR---------NWLDEIALKEAIIGLDDREKNILKLRFFRG--KTQVEVAQEIGI 241

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ +V ++E  A  K+++++
Sbjct: 242 SQAQVSRLEKGALGKIKKAL 261


>gi|216263458|ref|ZP_03435453.1| RNA polymerase sigma factor (rpoS) [Borrelia afzelii ACA-1]
 gi|215980302|gb|EEC21123.1| RNA polymerase sigma factor (rpoS) [Borrelia afzelii ACA-1]
          Length = 266

 Score =  171 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 77/272 (28%), Positives = 139/272 (51%), Gaps = 18/272 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+  +R+  ++  +EE  LA + +  G   A ++++ ++LRLV+KI   Y G GL I
Sbjct: 9   LNIYLKSVREHKLITHEEEIQLAGQIQ-RGSAKAKNKMINANLRLVLKIIKRYAGKGLKI 67

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GL++A +K+DP +  + +TY+ +WIK ++Q  +     LVK+        L
Sbjct: 68  EDLIQEGNLGLIRAAEKYDPNKNTKFSTYASFWIKQSLQRALNTKTRLVKVPYRKENLIL 127

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
                     +        K  +   I K+ N+S ++ I +   L  + SL+  I    +
Sbjct: 128 ---------QINKYLTEEEKAPKKEEIMKRFNLSPAQYIKIIPYLEKEYSLDKEI-EGSE 177

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN---P 252
           NS+     L  D+    ++ +E++      N +    + L  +ER I + R   +N    
Sbjct: 178 NSTLLN--LYEDNSFNPEITLEQDSTLQHLNYILE--TKLTEKERYIIKKRYNLDNSPKK 233

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL+++S+E  +S E VRQIE R  KK++E I
Sbjct: 234 STLKDISTELGISSETVRQIEKRVLKKLKEEI 265


>gi|121535240|ref|ZP_01667054.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
 gi|121306125|gb|EAX47053.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
          Length = 257

 Score =  171 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 48/260 (18%), Positives = 109/260 (41%), Gaps = 17/260 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L   +   L +  ++ G+  A  +L+  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLSANKMRELFEIMQQ-GNPEAREQLIYGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A+  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++ 
Sbjct: 74  GLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSM--RDIAYKALQVRD 130

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L +          +  IA +L +   E+I     +    SL   I     +     D +
Sbjct: 131 ALVSKFSRE---PSINEIADELKIPREEIIFALDAIQEPVSLFEPIYHDGGDPIFVMDQI 187

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             D +     L            +  ++  L+ RE+ I   R       T   ++ E  +
Sbjct: 188 SDDKNQDMNWLEGVA--------IKEALRKLSDREKHILTLRFF--EGKTQMEVADEIGI 237

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ +V ++E  A   +++ I
Sbjct: 238 SQAQVSRLEKAALGHMRKYI 257


>gi|40353299|gb|AAR84413.1| alternative primary sigma 70 factor [Frankia sp. ORS020607]
          Length = 220

 Score =  171 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 47/204 (23%), Positives = 95/204 (46%), Gaps = 10/204 (4%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  +LV+++LRLVV +A  Y G G+ + ++V EGN+GL++AV+KFD  +G++ +TY+ W
Sbjct: 22  AAKQQLVSANLRLVVSVAKKYSGRGMTLLDLVQEGNLGLIRAVEKFDYAKGYKFSTYATW 81

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A+   +      ++I     +      + ++    + +     +      +A +L+
Sbjct: 82  WIRQAIGRALADQARTIRIPVHVVE-----QINKITRLQRQLVSTLGREPTDEELALELD 136

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +   +V+ +        SL   +   D   S   D++    D       +       ++ 
Sbjct: 137 MPIEQVVELRRYAQDTVSLETSV--GDDGDSVLGDFI---EDSDATSPADAASYGAMQDE 191

Query: 228 LTRSMSVLNPRERRIFEARRLQEN 251
           +   +  L+PRER +   R    N
Sbjct: 192 IENVLGGLSPREREVMRLRFGLTN 215


>gi|224534531|ref|ZP_03675107.1| RNA polymerase sigma factor [Borrelia spielmanii A14S]
 gi|224514208|gb|EEF84526.1| RNA polymerase sigma factor [Borrelia spielmanii A14S]
          Length = 266

 Score =  171 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 76/272 (27%), Positives = 140/272 (51%), Gaps = 18/272 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+  +R+  ++  +EE  LA + +  G+  A ++++ ++LRLV+KI   Y G GL I
Sbjct: 9   LNIYLKSVREHKLITHEEEIQLAGQIQ-RGNAQAKNKMINANLRLVLKIIKRYAGKGLKI 67

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GL++A +K+DP +  + +TY+ +WIK ++Q  +     LVK+         
Sbjct: 68  EDLIQEGNLGLIRAAEKYDPNKNTKFSTYASFWIKQSLQRALNTKTRLVKVPYRKE---- 123

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + ++  +L     +     +   I K+ N+S ++ I +   L  + SL+  I  S+ 
Sbjct: 124 -NLILQINKYLTEEEKSP----KKEEIMKRFNLSPAQYIKIIPYLEKEYSLDKEIEGSEN 178

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN---P 252
             S   +    +    E  L +    K+   +L    + L  +ER I + R   +N    
Sbjct: 179 --STLLNLYEDNSFNPEITLEQDSTIKHLNYILE---TKLTEKERYIIKKRYNLDNSPKK 233

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL+++S+E  +S E VRQIE R  KK++E I
Sbjct: 234 STLKDISTELGISSETVRQIEKRVLKKLKEEI 265


>gi|168186812|ref|ZP_02621447.1| RNA polymerase sigma-G factor [Clostridium botulinum C str. Eklund]
 gi|169295146|gb|EDS77279.1| RNA polymerase sigma-G factor [Clostridium botulinum C str. Eklund]
          Length = 256

 Score =  171 bits (435), Expect = 9e-41,   Method: Composition-based stats.
 Identities = 54/261 (20%), Positives = 118/261 (45%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+++E   L  + ++ GD  +  + V  +LRLV+ +   +   G  + ++   G 
Sbjct: 13  SKLPVLKEKEMKELLLKMKD-GDNLSREKFVRGNLRLVLSVIQRFNNRGENVDDLFQVGC 71

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD  +  + +TY++  I   ++ Y+  + S +++  +   + + +   +++
Sbjct: 72  IGLIKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSL--RDIAYKALQVR 128

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
                I     K   V  IAK+L++   EV+     +    SL   I     ++    D 
Sbjct: 129 DR---IIKKENKDPNVSQIAKELDLPREEVVFALDAIQDPVSLFEPIYHDGGDALYVMDQ 185

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  + +  E  +            +  +M  LN RE+ I   R  Q    T   ++ E  
Sbjct: 186 ISDNKNADESWIEN--------ISIKEAMKRLNEREKLILNMRFFQG--RTQMEVADEIG 235

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A K +++ +
Sbjct: 236 ISQAQVSRLEKTALKHMRKYV 256


>gi|171322339|ref|ZP_02911166.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           MEX-5]
 gi|171092333|gb|EDT37699.1| RNA polymerase, sigma 32 subunit, RpoH [Burkholderia ambifaria
           MEX-5]
          Length = 234

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 51/237 (21%), Positives = 103/237 (43%), Gaps = 13/237 (5%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ ++LRLV+ IA  Y   G+ + ++V +G +GLM+A++KF+  RGF+ +TY+ WWI+ A
Sbjct: 1   MLEANLRLVLSIARKYMNRGVDLPDLVQDGCLGLMRAIEKFEYRRGFKFSTYATWWIRQA 60

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +      +++             +R++ H         +      +  +  + E +
Sbjct: 61  VARAVADRSRTIRVPVHV-----GDQYQRVQRHALRFRQRTGRRATPAELIAETGLPEGK 115

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           + ++    A   SL+  +  ++              D       E       R  +T  +
Sbjct: 116 LRAVLALPAEPLSLDTPLPDAETGLVDLI------EDQASASPFEHLADTRMRECVTSLL 169

Query: 233 SVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             + P E  +   R       P T + ++ +  +SRERVRQIE RA   ++   + +
Sbjct: 170 RSVTPAEADVLRRRFGLGGAEPDTYDAIAQDAGMSRERVRQIEKRALATLRTVAEAE 226


>gi|307822780|ref|ZP_07653011.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacter tundripaludum
           SV96]
 gi|307736384|gb|EFO07230.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacter tundripaludum
           SV96]
          Length = 448

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 64/251 (25%), Positives = 125/251 (49%), Gaps = 12/251 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           + E   LS+   L  ++  LV+ +A  Y+   L   ++V EG  GL++A+ KFD   GF+
Sbjct: 205 FAEQLWLSSRQALAEANSGLVLFLANQYKCGFLDFDDLVQEGQTGLLRAIDKFDYHLGFQ 264

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ +WIK A+   + R+  +V++     Q      + R K  L + T      +++ 
Sbjct: 265 FSTYAAYWIKQAISRALSRNERVVRVPC--EQVANIHKVLRAKNELLSKTGREPSIKELT 322

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
             +K  +   + ++S++      E+L+      D++S    D+L            +K E
Sbjct: 323 EYSKIPDDQINVILSISQTAVSLENLD-----DDEDSLAPIDFL---EQQVFANPFKKIE 374

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFK 278
           + + +  L +++ +L+PRE ++          N +TL+ + +E  ++RERVRQI+ +A  
Sbjct: 375 QSDLKAWLGKAIKILDPRELKVICCHFGINTGNEMTLQEIGAELNLTRERVRQIQVKALN 434

Query: 279 KVQESIQKQVE 289
           K++ S  KQ+ 
Sbjct: 435 KMKLSYGKQLM 445


>gi|331090618|ref|ZP_08339469.1| hypothetical protein HMPREF9477_00112 [Lachnospiraceae bacterium
           2_1_46FAA]
 gi|330401058|gb|EGG80653.1| hypothetical protein HMPREF9477_00112 [Lachnospiraceae bacterium
           2_1_46FAA]
          Length = 259

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 52/260 (20%), Positives = 116/260 (44%), Gaps = 17/260 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+++E+  L  R +  GD  A    +  +LRLV+ +   +        ++   G I
Sbjct: 15  KLPLLKEEEKEALFVRIK-AGDEEAKEEYIKGNLRLVLSVIKRFSNSNENPDDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  F+ E   + +TY++  I   ++ Y+  + S +++      + L     +   
Sbjct: 74  GLIKAINNFNTELNVKFSTYAVPMIIGEIRRYMRDNNS-IRVS-----RSLRDTAYKAIY 127

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             +     +LK   +  IA ++ +S+ E++     +    SL+  I +   ++    D +
Sbjct: 128 AKEGYMKTHLKEPTIQEIASEIGISKEEIVQALDAIQMPMSLHEPIYNDGGDTLYVMDQI 187

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               + +E  + E          L  +M  L  RER+I + R       T   ++ E  +
Sbjct: 188 SDKKNKEENWVEELS--------LAEAMERLGERERKIIQMRFF--EGKTQMEIAKEIHI 237

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ +V ++E  A + +++ +
Sbjct: 238 SQAQVSRLEKNALEFMKQYL 257


>gi|26665384|dbj|BAC44903.1| principal sigma factor [Gloeobacter violaceus PCC 8105]
          Length = 203

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 54/214 (25%), Positives = 102/214 (47%), Gaps = 13/214 (6%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V S+LRLVV IA+ Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+
Sbjct: 1   VQSNLRLVVSIALKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
              I      +++        L+  + R+K   + ++    +      IA ++ ++  ++
Sbjct: 61  TRAIADQSRTIRLPVH-----LYETISRIKKTTKLLSQELGRKPTEEEIATRMEMTIEKL 115

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             +        SL   I    +  S+  D+   D     +   +K  +   R  L   ++
Sbjct: 116 RFIAKSAQLPISLETPI--GKEEDSRLGDFSEADG----ETPEDKVAKNLLREDLEAVLN 169

Query: 234 VLNPRERRIFEARRLQENPV--TLENLSSEFEVS 265
            L+PRER +   R   ++    TLE +   F V+
Sbjct: 170 TLSPRERDVLRLRYGLDDGRMKTLEEIGQLFNVT 203


>gi|23978293|dbj|BAC21127.1| principal sigma factor [Arthrospira platensis]
          Length = 203

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 52/214 (24%), Positives = 100/214 (46%), Gaps = 13/214 (6%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V S+LRLVV IA  Y   GL   +++ EG++GL++A +K D E+G++ +TY+ WWI+ A+
Sbjct: 1   VQSNLRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKLDHEKGYKFSTYATWWIRQAI 60

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
              I      +++        L+  + R+K   + ++    +      IA ++ ++  ++
Sbjct: 61  TRAIADQSRTIRLPV-----LLYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKL 115

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             +        SL   I    +  S+  D++  D     +   ++  +   R  L   + 
Sbjct: 116 RFIAKSAQLPISLETPI--GKEEDSRLGDFIESDG----ETPEDQVSKNLLREDLESVLD 169

Query: 234 VLNPRERRIFEARRLQENPV--TLENLSSEFEVS 265
            L+PRER +   R   ++    TLE +   F V+
Sbjct: 170 TLSPRERDVLRLRYGLDDGRMKTLEEIGQIFNVT 203


>gi|291538695|emb|CBL11806.1| RNA polymerase, sigma subunit, RpsG/SigG [Roseburia intestinalis
           XB6B4]
          Length = 259

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 52/260 (20%), Positives = 118/260 (45%), Gaps = 17/260 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+++E+  L  R ++ GD +A    +  +LRLV+ +   + G    + ++   G I
Sbjct: 15  KLPILKEEEKDALFARIKQ-GDTAARETYIKGNLRLVLSVIKRFSGNHENVDDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++++  FDP  G + +TY++  I   ++ Y+  + S +++      + L     +   
Sbjct: 74  GLIKSIDNFDPTIGVKFSTYAVPMIIGEIRRYLRDNNS-IRVS-----RSLRDTAYKAIH 127

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + ++    K   +  IA +  +S+ +++     +    SL   +  +D   + +    
Sbjct: 128 TKEILSKTENKEPTLDEIAAESGISKEDIVFALDAIQSPLSLYDPVY-TDGGDTLYVMDQ 186

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           + D   +E+  IE+         L  ++  LN RE  I + R       T   ++ E  +
Sbjct: 187 ISDKKNREENWIEELS-------LNDALDRLNERENYILKLRFF--EGKTQMEVADEIHI 237

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ +V ++E  A   ++  +
Sbjct: 238 SQAQVSRLEKSALNSIRHYL 257


>gi|242041441|ref|XP_002468115.1| hypothetical protein SORBIDRAFT_01g039810 [Sorghum bicolor]
 gi|241921969|gb|EER95113.1| hypothetical protein SORBIDRAFT_01g039810 [Sorghum bicolor]
          Length = 528

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 69/268 (25%), Positives = 126/268 (47%), Gaps = 20/268 (7%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E  L +R   HG +   +R+V S++RLV+ IA  + G G+  S+++ EG  GL++  +K
Sbjct: 273 DENTLRRRL-NHG-VYCKNRMVKSNVRLVISIAKEHEGPGMEFSDLIQEGMQGLIRGAEK 330

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +GFR +TYS WWIK A+++ +L    ++++     +        R+K   + +   
Sbjct: 331 FDASKGFRFSTYSHWWIKQAIRKSVLEQTQIIRLPAHMAEAS-----SRVKECCRRLRRE 385

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA    ++   V +         S  + +  +D    +         D   
Sbjct: 386 LKRLPSNEEIAVDTGMTIRRVEAAMSLPKYSVSFTSKVGCTDVTYQEIM------PDTSA 439

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVR 270
           +   E   R   +  +  ++  L+PRE+ +   R   E   P TL ++     VSRER+R
Sbjct: 440 ETAEEVLHRWLMKKDVNTALESLSPREKLVMRYRFGIEGGRPRTLHDIGQIMGVSRERIR 499

Query: 271 QIEARAFKKVQ-----ESIQKQVELSSS 293
           QIE  AF+K++     +S+Q  ++ + S
Sbjct: 500 QIELGAFRKLRSKKRVQSLQHYLQPAES 527


>gi|323702540|ref|ZP_08114203.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
 gi|323532514|gb|EGB22390.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
          Length = 260

 Score =  171 bits (434), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 56/260 (21%), Positives = 114/260 (43%), Gaps = 17/260 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           + P+L  +E   L K+  + GD  A  RLV  +L+LV  +   +   G  + ++   G I
Sbjct: 13  RFPLLGDKEMRDLIKK-AQAGDADARERLVNCNLKLVFNLVQRFNNRGYELEDLFQIGCI 71

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A+ KFD     + +TY++  I   ++ ++    S VK+  +  +        +++ 
Sbjct: 72  GLMKAIDKFDLSYDVKFSTYAVPMIVGEIRRFLRDD-SPVKVSRSLKE-----TAYKIQQ 125

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
               +T    +   +  IA++L     EV+S         S+   ++  D +     D L
Sbjct: 126 TRDRLTARLGRDPSINEIAQELGCHREEVVSALEAAQTPTSIYETLHQDDGDPIYILDQL 185

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               DG    L +          + + +  L  R+R+I   R  ++   T   ++    +
Sbjct: 186 SGADDGDSPWLEKLA--------VKQLLIELPERDRQILLWRFFED--KTQSEVALRLGL 235

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ +V ++E +A +K++E +
Sbjct: 236 SQVQVSRLERQALRKLKELM 255


>gi|162458864|ref|NP_001104924.1| sigma-like factor2B [Zea mays]
 gi|4336608|gb|AAD17855.1| sigma factor SIG2B [Zea mays]
          Length = 527

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 66/253 (26%), Positives = 120/253 (47%), Gaps = 19/253 (7%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E  L +R   HG +   +R+V S++RLV+ IA  + G G+  S+++ +G  GL++  +K
Sbjct: 272 DENTLRRRL-NHG-VYCKNRMVKSNVRLVISIAKEHEGPGMEFSDLIQDGMQGLIRGAEK 329

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ--KRLFFNLRRLKGHLQAIT 150
           FD  +GFR +TYS WWIK A+++ +L    ++++     +   R+    RRL   L+ + 
Sbjct: 330 FDASKGFRFSTYSHWWIKQAIRKSVLEQTQIIRLPAHMAEASSRVKECCRRLGRELKRL- 388

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
                      IA    ++   V +         S  + +  +D    +         D 
Sbjct: 389 ------PSNEEIAVDTGMTIRRVEAAMSLPKYSVSFTSKVGCTDVTYQEIM------PDT 436

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRER 268
             +   E   R   +  +  ++  L+PR++++   R   E     TL ++     VSRER
Sbjct: 437 SAETAEETLHRWLMKKDVNTALDSLSPRKKQVMRYRFGIEGGRARTLHDIGQLMGVSRER 496

Query: 269 VRQIEARAFKKVQ 281
           +RQIE  AF+K++
Sbjct: 497 IRQIELGAFRKLR 509


>gi|330980004|gb|EGH78270.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. aptata
           str. DSM 50252]
          Length = 214

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 79/204 (38%), Positives = 119/204 (58%), Gaps = 6/204 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+H +  IP+L  ++E  LA+      DL AA ++V +HLR VV IA  Y GYGL 
Sbjct: 16  NLEAYVHTVNSIPLLTPEQERELAESLYYEQDLDAARQMVLAHLRFVVHIARSYSGYGLA 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++
Sbjct: 76  QADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           LFFNLR  K  L  + +     ++V  +A+ L V   EV  M  RL G +        +D
Sbjct: 136 LFFNLRSQKKRLAWLNN-----DEVHRVAESLGVEPREVREMESRLTGHDMAFDPAAEAD 190

Query: 195 KNSS-QWQDWLVYDHDGQEQVLIE 217
            +S+ Q     + DH       +E
Sbjct: 191 DDSAFQSPANYLEDHRYDPARQLE 214


>gi|30021992|ref|NP_833623.1| sporulation sigma factor SigG [Bacillus cereus ATCC 14579]
 gi|206971353|ref|ZP_03232304.1| RNA polymerase sigma-G factor [Bacillus cereus AH1134]
 gi|218899057|ref|YP_002447468.1| RNA polymerase sigma-G factor [Bacillus cereus G9842]
 gi|228902409|ref|ZP_04066563.1| RNA polymerase sigma-G factor [Bacillus thuringiensis IBL 4222]
 gi|228909729|ref|ZP_04073552.1| RNA polymerase sigma-G factor [Bacillus thuringiensis IBL 200]
 gi|228922656|ref|ZP_04085956.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228940992|ref|ZP_04103550.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228954180|ref|ZP_04116208.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228960121|ref|ZP_04121785.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228966857|ref|ZP_04127901.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|229019106|ref|ZP_04175941.1| RNA polymerase sigma-G factor [Bacillus cereus AH1273]
 gi|229025350|ref|ZP_04181768.1| RNA polymerase sigma-G factor [Bacillus cereus AH1272]
 gi|229047588|ref|ZP_04193178.1| RNA polymerase sigma-G factor [Bacillus cereus AH676]
 gi|229071403|ref|ZP_04204625.1| RNA polymerase sigma-G factor [Bacillus cereus F65185]
 gi|229081156|ref|ZP_04213666.1| RNA polymerase sigma-G factor [Bacillus cereus Rock4-2]
 gi|229104466|ref|ZP_04235133.1| RNA polymerase sigma-G factor [Bacillus cereus Rock3-28]
 gi|229111373|ref|ZP_04240926.1| RNA polymerase sigma-G factor [Bacillus cereus Rock1-15]
 gi|229129181|ref|ZP_04258154.1| RNA polymerase sigma-G factor [Bacillus cereus BDRD-Cer4]
 gi|229146475|ref|ZP_04274846.1| RNA polymerase sigma-G factor [Bacillus cereus BDRD-ST24]
 gi|229162839|ref|ZP_04290796.1| RNA polymerase sigma-G factor [Bacillus cereus R309803]
 gi|229180179|ref|ZP_04307523.1| RNA polymerase sigma-G factor [Bacillus cereus 172560W]
 gi|229192073|ref|ZP_04319042.1| RNA polymerase sigma-G factor [Bacillus cereus ATCC 10876]
 gi|296504397|ref|YP_003666097.1| sporulation sigma factor SigG [Bacillus thuringiensis BMB171]
 gi|29897548|gb|AAP10824.1| RNA polymerase sigma-G factor [Bacillus cereus ATCC 14579]
 gi|206734125|gb|EDZ51296.1| RNA polymerase sigma-G factor [Bacillus cereus AH1134]
 gi|218543268|gb|ACK95662.1| RNA polymerase sigma-G factor [Bacillus cereus G9842]
 gi|228591399|gb|EEK49249.1| RNA polymerase sigma-G factor [Bacillus cereus ATCC 10876]
 gi|228603388|gb|EEK60865.1| RNA polymerase sigma-G factor [Bacillus cereus 172560W]
 gi|228620721|gb|EEK77590.1| RNA polymerase sigma-G factor [Bacillus cereus R309803]
 gi|228637108|gb|EEK93567.1| RNA polymerase sigma-G factor [Bacillus cereus BDRD-ST24]
 gi|228654418|gb|EEL10283.1| RNA polymerase sigma-G factor [Bacillus cereus BDRD-Cer4]
 gi|228672149|gb|EEL27440.1| RNA polymerase sigma-G factor [Bacillus cereus Rock1-15]
 gi|228678908|gb|EEL33118.1| RNA polymerase sigma-G factor [Bacillus cereus Rock3-28]
 gi|228702200|gb|EEL54676.1| RNA polymerase sigma-G factor [Bacillus cereus Rock4-2]
 gi|228711694|gb|EEL63647.1| RNA polymerase sigma-G factor [Bacillus cereus F65185]
 gi|228723835|gb|EEL75190.1| RNA polymerase sigma-G factor [Bacillus cereus AH676]
 gi|228735935|gb|EEL86512.1| RNA polymerase sigma-G factor [Bacillus cereus AH1272]
 gi|228742206|gb|EEL92371.1| RNA polymerase sigma-G factor [Bacillus cereus AH1273]
 gi|228792956|gb|EEM40514.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228799637|gb|EEM46590.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228805500|gb|EEM52091.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228818671|gb|EEM64738.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228837085|gb|EEM82426.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228850018|gb|EEM94849.1| RNA polymerase sigma-G factor [Bacillus thuringiensis IBL 200]
 gi|228857153|gb|EEN01659.1| RNA polymerase sigma-G factor [Bacillus thuringiensis IBL 4222]
 gi|296325449|gb|ADH08377.1| sporulation sigma factor SigG [Bacillus thuringiensis BMB171]
 gi|326941673|gb|AEA17569.1| sporulation sigma factor SigG [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 259

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 62/261 (23%), Positives = 121/261 (46%), Gaps = 17/261 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+ +E   L +  +  G++SA  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKNEEMRKLFREMQ-SGEISAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++ 
Sbjct: 74  GLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVRE 130

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L A    N K    + IAK L V+  E++     +    SL   I +   +     D L
Sbjct: 131 KLIA---ENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGGDPIFVMDQL 187

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             +    EQ + E          L   M  LN RE+ I   R  Q    T   ++ E  +
Sbjct: 188 SDEKQKDEQWVEELA--------LKEGMKRLNDREKMIIRKRFFQG--KTQMEVAEEIGI 237

Query: 265 SRERVRQIEARAFKKVQESIQ 285
           S+ +V ++E  A K++ ++IQ
Sbjct: 238 SQAQVSRLEKSAIKQMNKTIQ 258


>gi|164686360|ref|ZP_02210390.1| hypothetical protein CLOBAR_02798 [Clostridium bartlettii DSM
           16795]
 gi|164601962|gb|EDQ95427.1| hypothetical protein CLOBAR_02798 [Clostridium bartlettii DSM
           16795]
          Length = 257

 Score =  171 bits (433), Expect = 1e-40,   Method: Composition-based stats.
 Identities = 52/261 (19%), Positives = 116/261 (44%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            ++P+ +  +   L  + ++ GD  A  + V  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SELPVFKADQMRELLVKIKQ-GDEDARQKFVKGNLRLVLSVIQKFNNRGENVDDLFQIGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           +GL++A+  FD  +  R +TY++  I   ++ Y+  +   +++  +   K + +   +++
Sbjct: 73  VGLIKAIDNFDLSQNVRFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--KDIAYKALQVR 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L      N K   +  IAK+L++    V+     +    SL   +   + ++    D 
Sbjct: 130 ERL---IRTNSKEPTISEIAKELDMEVESVVMALDAIQDPISLFDPVYQDNGDAIFVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    D  E  L E          L  ++  L+ RE+ + + R  +    T   ++ E  
Sbjct: 187 VQDKKDTDENWLEEIA--------LKEAIKKLSSREKLVLDLRFYKG--RTQIEVADEIG 236

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V +IE  A K +++ I
Sbjct: 237 ISQAQVSRIEKNALKNMRKYI 257


>gi|288917890|ref|ZP_06412250.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Frankia sp.
           EUN1f]
 gi|288350679|gb|EFC84896.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Frankia sp.
           EUN1f]
          Length = 392

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 58/246 (23%), Positives = 105/246 (42%), Gaps = 21/246 (8%)

Query: 44  HGDLS---AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
            GD        +LV  HL LV  +A  +R  G P+ ++V    IGL+++V +FDPERG  
Sbjct: 159 EGDPERAALRDQLVRMHLPLVEYLARRFRNRGEPLDDLVQVATIGLIKSVDRFDPERGVE 218

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+   I   ++ +       +++     + +L      L      ++ +  +   V 
Sbjct: 219 FSTYATPTIVGEIKRHFRDKGWAIRVPRRLQELKLS-----LTKATSELSQSLGRSPTVS 273

Query: 161 AIAKKLNVSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            IA+ L ++E EV+    +       SL+A  +  D+  +      V D         E 
Sbjct: 274 EIARHLEMTEEEVLEGLESANAYSAVSLDAPDSGDDEAPAVADTLGVQD---------ES 324

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
            E    R  L   +  L PRE+RI   R      +T   +++E  +S+  V ++ AR   
Sbjct: 325 LEGVEYRESLKPLLEKLPPREKRILLLRFFGN--MTQSQIANELGISQMHVSRLLARTLA 382

Query: 279 KVQESI 284
           +++  +
Sbjct: 383 QLRRGL 388


>gi|261415107|ref|YP_003248790.1| RNA polymerase, sigma 32 subunit, RpoH [Fibrobacter succinogenes
           subsp. succinogenes S85]
 gi|261371563|gb|ACX74308.1| RNA polymerase, sigma 32 subunit, RpoH [Fibrobacter succinogenes
           subsp. succinogenes S85]
 gi|302326239|gb|ADL25440.1| RNA polymerase sigma-70 factor [Fibrobacter succinogenes subsp.
           succinogenes S85]
          Length = 270

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 66/277 (23%), Positives = 128/277 (46%), Gaps = 30/277 (10%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           I + +  L RY+ +IR+   L ++EE +L ++ +E GD  A  +L+++++R V+K+A+ Y
Sbjct: 3   IDSTDTTLKRYLEDIRRTAPLSREEEQILFQKAKE-GDKIARKKLISANMRFVLKVAIQY 61

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           RG  +P+ ++VSEG +GL++A++ F+  RG +  +Y +WWIKA +   I    +L+++  
Sbjct: 62  RGCPIPLPDLVSEGAMGLVRAIESFEHTRGLKFISYGVWWIKAYITRAINEQGNLIRLP- 120

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
                    +LR  K   +      +                 E+  +        S ++
Sbjct: 121 ------ANQHLRVRKALHEQSRGKEIN---------------EEIRELIQIGQRGVSFDS 159

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            + +  K +     +     D          E ++   +    M  L  RE R+      
Sbjct: 160 PLKADSKAT-----YAEVLPDSGASNPEADSEIQSVEALARDLMEQLPEREARVITGIFG 214

Query: 249 --QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             QE P TL  +     +S ERVRQ+  +A +++++ 
Sbjct: 215 INQEAPQTLREVGESMNISHERVRQLRDQALRRIRKY 251


>gi|224531828|ref|ZP_03672460.1| RNA polymerase sigma factor [Borrelia valaisiana VS116]
 gi|224511293|gb|EEF81699.1| RNA polymerase sigma factor [Borrelia valaisiana VS116]
          Length = 266

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 78/272 (28%), Positives = 136/272 (50%), Gaps = 18/272 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+  +R+  ++  +EE  LA + +  G   A ++++ ++LRLV+KI   Y G GL I
Sbjct: 9   LNIYLKSVREHKLITHEEEIKLAGQIQ-RGSAQAKNKMINANLRLVLKIIKRYAGKGLKI 67

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GL++A +K+DP +  + +TY+ +WIK ++Q  +     LVK+        L
Sbjct: 68  EDLIQEGNLGLIRAAEKYDPNKNTKFSTYASFWIKQSLQRALNTKTRLVKVPYRKENLIL 127

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
                     +        K  +   I K+ N+S ++ I +   L  + SL+  I  S+ 
Sbjct: 128 ---------QINKYLTEEEKSPKKEEIMKRFNLSPAQYIKIIPYLEKEYSLDKEIEGSEN 178

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN---P 252
             S   +    +    E  L +    K+   +L    + LN +ER I + R   +N    
Sbjct: 179 --STLLNLYEDNSFNPEITLEQDSTLKHLNYVLE---TKLNEKERYIIKKRYNLDNSPKK 233

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL+++S E  +S E VRQIE R  KK++E I
Sbjct: 234 STLKDISMELGISSETVRQIEKRVLKKLKEEI 265


>gi|147677561|ref|YP_001211776.1| DNA-directed RNA polymerase specialized sigma subunit
           [Pelotomaculum thermopropionicum SI]
 gi|146273658|dbj|BAF59407.1| DNA-directed RNA polymerase specialized sigma subunit
           [Pelotomaculum thermopropionicum SI]
          Length = 259

 Score =  171 bits (433), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 52/260 (20%), Positives = 118/260 (45%), Gaps = 17/260 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           + P+L+ +E   L ++ +  GD  A  +LV  +L+LV  +   ++  G  + ++   G I
Sbjct: 12  RFPLLKDREMRELLQKAK-AGDSYARDKLVNCNLKLVFNLVKRFQNRGYELEDLFQIGCI 70

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A+ KFD     + +TY++  I   ++ ++      +K+  +  +K       R++ 
Sbjct: 71  GLMKAIDKFDVSYDVKFSTYAVPMIVGEIRRFLRDDN-PIKVSRSLKEKAY-----RVQQ 124

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
               +T    +   V  ++ +L +S  EV++         S+   ++  D +     D +
Sbjct: 125 ARDLLTARLGREPTVGEVSAELGLSREEVVNALEAAQVPASIYETLHQDDGDPIYLLDQI 184

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               +G    L         +  +   ++ L  R+R+I   R  ++   T  +++    +
Sbjct: 185 KGSEEGDVPWLE--------KITVKELLNKLPERDRQILAWRFFED--RTQSDIAKRLGL 234

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ +V ++E +A KK++E +
Sbjct: 235 SQVQVSRLERQALKKLKELM 254


>gi|258514354|ref|YP_003190576.1| sporulation sigma factor SigG [Desulfotomaculum acetoxidans DSM
           771]
 gi|257778059|gb|ACV61953.1| RNA polymerase, sigma 28 subunit, SigG [Desulfotomaculum
           acetoxidans DSM 771]
          Length = 257

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 51/260 (19%), Positives = 114/260 (43%), Gaps = 17/260 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P++   +   L +  ++ GD SA  +L+  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVIPNSKMRELFEAIQQ-GDTSARPQLINGNLRLVLSVIQRFTNRGEYVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A+  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++ 
Sbjct: 74  GLMKAIDNFDLAQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDVAYKALQVRD 130

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L    + + +   V  IAK+L +   EV+     +    SL   I     +     D +
Sbjct: 131 TL---VNKHSREPSVNEIAKELKMPREEVVFALDAIQEPISLFEPIYHDGGDPIFVMDQI 187

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             D +     L            +  ++  L+ RE+ I   R    +  T   ++ E  +
Sbjct: 188 SDDKNQDLNWLEGIA--------IKDALRKLSDREKHILTLRFF--DGKTQMEVADEIGI 237

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ +V ++E  A   +++ I
Sbjct: 238 SQAQVSRLEKAALHHMRKYI 257


>gi|302876248|ref|YP_003844881.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium cellulovorans
           743B]
 gi|307686980|ref|ZP_07629426.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium cellulovorans
           743B]
 gi|302579105|gb|ADL53117.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium cellulovorans
           743B]
          Length = 281

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 68/267 (25%), Positives = 123/267 (46%), Gaps = 20/267 (7%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM-GYRGYGLPISEVVSEGNIGLM 87
           L  +E   L   Y+ + D++A   L+ ++ RLV K A        L   ++V EG IGLM
Sbjct: 11  LTNEELVTL---YQTNKDITARDYLIINNKRLVYKAASLKKDTSLLAYDDLVQEGLIGLM 67

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
             ++KF+ +   + +TY  +WIK  +   I  + + +++      K         K +++
Sbjct: 68  IGIEKFNADYNSKFSTYIYYWIKQRIDRAIYNTGTSIRLPIHLINKINKVMYVENKNNVK 127

Query: 148 AITDNNLKPEQVVAIAKK-------LNVSESEVISMNCRLAGDES--LNALINSSDKNSS 198
           ++ +++      + I  K       L      +IS+N  L  D S     LI+  D+NSS
Sbjct: 128 SLDNDSTDLCTDLDITDKQYDYYKFLVKQFKNIISLNSALLSDNSEGDEELIDFIDENSS 187

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLE 256
            + D    ++     ++ E+         L   +  LN RE+ +   R   ++    TLE
Sbjct: 188 NFGDPGSKNYSIDSNIIKEELSHD-----LNEVLKTLNEREQHVLRMRFGLDDGEMKTLE 242

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQES 283
            + + F V+RER+RQIE++A KK++  
Sbjct: 243 QIGNHFNVTRERIRQIESKALKKLRNP 269


>gi|258511274|ref|YP_003184708.1| RNA polymerase, sigma 28 subunit, SigG [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
 gi|257478000|gb|ACV58319.1| RNA polymerase, sigma 28 subunit, SigG [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
          Length = 259

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 55/263 (20%), Positives = 117/263 (44%), Gaps = 17/263 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            ++P+L   +   L ++ R  GD SA  +LV  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SQLPVLTNAQMRELFEQLR-AGDPSAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+A+  FD  +  R +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 73  IGLMKAIDNFDLNQNVRFSTYAVPMIVGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVR 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L      NL+   +V IA ++N+ + EV+     +    S+   I     +     D 
Sbjct: 130 DML---ASKNLREPSIVEIANEMNLPKEEVVFALDAIQDPVSMFEPIYHDGGDPIYVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  + +     +            L  +M  L+ RE++I   R       T   ++ E  
Sbjct: 187 IHDEREKDSAWVEGIA--------LREAMRKLSDREKKILAKRFY--EGKTQMEVADEIG 236

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+ +V ++E  A  ++ + IQ 
Sbjct: 237 ISQAQVSRLEKAAIHRMYKHIQS 259


>gi|188585937|ref|YP_001917482.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|179350624|gb|ACB84894.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 269

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 53/262 (20%), Positives = 118/262 (45%), Gaps = 17/262 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDL-SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
            K+P+L   E   L ++ R   D   A  +L+  +LRLV+ +   +   G  + ++   G
Sbjct: 14  SKLPVLNNSEMKELFEKMRVGDDEDEARQKLINGNLRLVLSVIQRFNNRGEYVDDLFQVG 73

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            +GL++A+  FD  +  + +TY++  I   ++ Y+  + S +++  +   + + +   ++
Sbjct: 74  CVGLIKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSL--RDIAYKALQI 130

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
           +  L    + N +   +  IA+KL+VSE +V+     +    SL   I     +     D
Sbjct: 131 RDEL---VEKNSREPAISEIAEKLDVSEEQVVFALDAIQDPVSLFEPIYHDGGDPIFVMD 187

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
            +  + +     L E          +   +  L+ RE+ I   R  +    T   ++ E 
Sbjct: 188 QISDEKNQDRTWLEEIA--------IKEGLHRLSSREKLIVNLRFFKG--KTQMEVAEEI 237

Query: 263 EVSRERVRQIEARAFKKVQESI 284
            +S+ +V ++E  A  +++++I
Sbjct: 238 GISQAQVSRLEKAALSQLKKNI 259


>gi|325288838|ref|YP_004265019.1| RNA polymerase, sigma subunit, RpsG/SigG [Syntrophobotulus
           glycolicus DSM 8271]
 gi|324964239|gb|ADY55018.1| RNA polymerase, sigma subunit, RpsG/SigG [Syntrophobotulus
           glycolicus DSM 8271]
          Length = 257

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 54/261 (20%), Positives = 113/261 (43%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L   +   L  + +  GD +   +L+  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLSGAKMKELFTKMQ-AGDGTIREQLIKGNLRLVLSVIQRFSNRGEHVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+A+  FD  +  + +TY++  I   ++ Y+  + S +++  +   + + +   +++
Sbjct: 73  IGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSL--RDIAYKALQIR 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L            +  IA KL   + EVI     +    SL   I   D     +   
Sbjct: 130 DKLATECSRE---PTIQEIAAKLETPQEEVILALDAIQEPVSLFEPIYH-DGGDPIYVMD 185

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
            + DH   +++ +E          +   +  L  RE+RI   R  Q    T   ++ E  
Sbjct: 186 QIGDHKQSDRIWLESLS-------IKEGIERLGEREKRIISLRFFQG--KTQMEVAEEIG 236

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A K +++ +
Sbjct: 237 ISQAQVSRLEKAALKHMRKHV 257


>gi|91227014|ref|ZP_01261551.1| RpoS-like sigma factor [Vibrio alginolyticus 12G01]
 gi|91188816|gb|EAS75102.1| RpoS-like sigma factor [Vibrio alginolyticus 12G01]
 gi|210148643|gb|ACJ09227.1| RpoS-like sigma factor [Vibrio alginolyticus]
          Length = 279

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 67/280 (23%), Positives = 131/280 (46%), Gaps = 19/280 (6%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           G+   + Y+ +I  I +L ++EE   AK     GD  A   L+ S+LRLVVKIA GY   
Sbjct: 8   GKDPYAHYLKDIVGIDLLSREEELHYAK-LNRAGDEEAREMLIESNLRLVVKIAKGYLKR 66

Query: 72  ---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
                 + +++ EGNIGL++AV KFDPE G+R +TY++WWI+  ++  ++ +   V++  
Sbjct: 67  PGNNFTLLDLIEEGNIGLIKAVDKFDPEPGYRFSTYAVWWIRENIEAALMNNGRTVRLPA 126

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
              ++     L++L       + +  K   +  +++   V    +  +        +L+ 
Sbjct: 127 HVCKEINSLALKKL-----DASKSESKELSISELSRCSGVKAERIDEL-------VALSG 174

Query: 189 LINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
            I+ S         +++   + +      +  E +     +   +  L  + +++   R 
Sbjct: 175 FIDVSTTADLHRVPFVLELCESEYTPDPQQDCENQCFTQAIENIIKTLPTKLQKVLIHRF 234

Query: 248 LQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              +    TL  +     VS ERVRQ++  A ++VQ+ ++
Sbjct: 235 GLFDQRVKTLSEIGLLLNVSNERVRQMQIEAVERVQKRLR 274


>gi|226311983|ref|YP_002771877.1| sporulation sigma factor SigF [Brevibacillus brevis NBRC 100599]
 gi|226094931|dbj|BAH43373.1| RNA polymerase sigma-F factor [Brevibacillus brevis NBRC 100599]
          Length = 251

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 49/259 (18%), Positives = 106/259 (40%), Gaps = 19/259 (7%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   +   L  +  + GD  A   LV S++RLV  +   +   G    ++   G IGL
Sbjct: 11  PFLTNDQVKELIAK-SQAGDTEARELLVNSNIRLVWSVVQRFINRGYEADDLFQIGCIGL 69

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV KFD     R +TY++  I   +Q ++      VK+  +  +        +++   
Sbjct: 70  LKAVDKFDLSYDVRFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKE-----TANKVRRTK 123

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
             +     +   +  +A  + ++  EV+          S++  +  +D +     D +  
Sbjct: 124 DELYKQFGRAPTIAEVADAVGITPEEVVFAQEANRAPSSIHETVFENDGDPITLIDQIAD 183

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
                     E   +   +  L  ++S L+ RE+ I   R  ++   T   ++    +S+
Sbjct: 184 ----------EGVNKWFEKIALKDAISRLSEREQLIVYLRYYKDQ--TQSEVAERLGISQ 231

Query: 267 ERVRQIEARAFKKVQESIQ 285
            +V ++E R  + +++ I+
Sbjct: 232 VQVSRLEKRILQTIKDQIE 250


>gi|75764482|ref|ZP_00743967.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|74488029|gb|EAO51760.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
          Length = 260

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 62/261 (23%), Positives = 116/261 (44%), Gaps = 16/261 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+ +E   L +  +  G++SA  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKNEEMRKLFREMQ-SGEISAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD  +  + +TY++  I   ++ Y+  +   ++      +  L   L     
Sbjct: 74  GLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRFCAFLGRYALINXL----Q 128

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + +   N K    + IAK L V+  E++     +    SL   I +   +     D L
Sbjct: 129 VREKLIAENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGGDPIFVMDQL 188

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             +    EQ + E          L   M  LN RE+ I   R  Q    T   ++ E  +
Sbjct: 189 SDEKQKDEQWVEELA--------LKEGMKRLNDREKMIIRKRFFQG--KTQMEVAEEIGI 238

Query: 265 SRERVRQIEARAFKKVQESIQ 285
           S+ +V ++E  A K++ ++IQ
Sbjct: 239 SQAQVSRLEKSAIKQMNKTIQ 259


>gi|118443097|ref|YP_878334.1| sporulation sigma factor SigG [Clostridium novyi NT]
 gi|118133553|gb|ABK60597.1| Specialized DNA-dependent RNA polymerase sigma subunit [Clostridium
           novyi NT]
          Length = 256

 Score =  170 bits (432), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 56/261 (21%), Positives = 119/261 (45%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+++E   L  + ++ GD  +  + V  +LRLV+ +   +   G  + ++   G 
Sbjct: 13  SKLPVLKEKEMKELLLKMKD-GDNLSREKFVRGNLRLVLSVIQRFNNRGENVDDLFQVGC 71

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD  +  + +TY++  I   ++ Y+  + S +++  +   + + +   +++
Sbjct: 72  IGLIKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSL--RDIAYKALQVR 128

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
                I     K   V  IAK+L++   EV+     +    SL   I   D   + +   
Sbjct: 129 D---KIIKKENKDPNVSRIAKELDLPREEVVFALDAIQDPVSLFEPIYH-DGGDALYVMD 184

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
            + D    ++  IE          +  +M  LN RE+ I   R  Q    T   ++ E  
Sbjct: 185 QISDSKNVDESWIENIS-------IKEAMKRLNEREKMILNMRFFQG--RTQMEVADEIG 235

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A K +++ +
Sbjct: 236 ISQAQVSRLEKTALKHMRKYV 256


>gi|218289914|ref|ZP_03494104.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
 gi|218240054|gb|EED07240.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
          Length = 259

 Score =  170 bits (431), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 56/263 (21%), Positives = 118/263 (44%), Gaps = 17/263 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            ++P+L   +   L ++ R  GDLSA  +LV  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SQLPVLTNAQMRELFEQLR-AGDLSAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+A+  FD  +  R +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 73  IGLMKAIDNFDLNQNVRFSTYAVPMIVGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVR 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L      NL+   +V IA ++N+ + EV+     +    S+   I     +     D 
Sbjct: 130 DML---ASKNLREPSIVEIANEMNLPKEEVVFALDAIQDPVSMFEPIYHDGGDPIYVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  + +     +            L  +M  L+ RE++I   R       T   ++ E  
Sbjct: 187 IHDEREKDSAWVEGIA--------LREAMRKLSDREKKILAKRFY--EGKTQMEVADEIG 236

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+ +V ++E  A  ++ + IQ 
Sbjct: 237 ISQAQVSRLEKAAIHRMYKHIQS 259


>gi|23978372|dbj|BAC21150.1| principal sigma factor [Synechococcus sp. PCC 7001]
          Length = 203

 Score =  170 bits (431), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 54/214 (25%), Positives = 104/214 (48%), Gaps = 13/214 (6%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V S  RLVV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+
Sbjct: 1   VQSKFRLVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAI 60

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
              I      +++        L+  + R+K   + ++    +      IA+ + ++  ++
Sbjct: 61  TRAIADQSRTIRLPVH-----LYETISRIKKTTKTLSQEFGRKPTEEEIAESMEMTIEKL 115

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             +        SL   I    +  S+  D++  D +  EQ + +   R++    L   ++
Sbjct: 116 RFIAKSAQLPISLETPI--GKEEDSRLGDFIEADIENPEQDVAKNLLRED----LEGVLA 169

Query: 234 VLNPRERRIFEARRLQENPV--TLENLSSEFEVS 265
            L+PRER +   R   ++    TLE +   F+V+
Sbjct: 170 TLSPRERDVLRLRYGLDDGRMKTLEEIGQIFDVT 203


>gi|294501013|ref|YP_003564713.1| RNA polymerase sigma-G factor [Bacillus megaterium QM B1551]
 gi|295706362|ref|YP_003599437.1| RNA polymerase sigma-G factor [Bacillus megaterium DSM 319]
 gi|294350950|gb|ADE71279.1| RNA polymerase sigma-G factor [Bacillus megaterium QM B1551]
 gi|294804021|gb|ADF41087.1| RNA polymerase sigma-G factor [Bacillus megaterium DSM 319]
          Length = 259

 Score =  170 bits (431), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 59/263 (22%), Positives = 119/263 (45%), Gaps = 17/263 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+ +E   L K+ +  GD +A  +LV+ +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLKNEEMRKLFKQMQ-AGDGTAREKLVSGNLRLVLSVIQRFNNRGEFVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+++  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 73  IGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVR 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L + T      E    I+K L V   E++     +    SL   I +   +     D 
Sbjct: 130 ERLMSETSKEPTAE---EISKVLEVPHEEIVFALDAIQDPVSLFEPIYNDGGDPIYVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L  + +     + E          L   M  LN RE+ I   R  Q    T   ++ E  
Sbjct: 187 LSDERNRDSTWIEEIA--------LQEGMRRLNEREKLILRKRFFQG--KTQMEVAEEIG 236

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+ +V ++E  A K++ ++IQ 
Sbjct: 237 ISQAQVSRLEKAAIKQMNKNIQS 259


>gi|30263905|ref|NP_846282.1| sporulation sigma factor SigG [Bacillus anthracis str. Ames]
 gi|47778237|ref|YP_020684.2| sporulation sigma factor SigG [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|165872304|ref|ZP_02216941.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0488]
 gi|167641114|ref|ZP_02399369.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0193]
 gi|170688856|ref|ZP_02880059.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0465]
 gi|170708817|ref|ZP_02899253.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0389]
 gi|177654919|ref|ZP_02936636.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0174]
 gi|190565736|ref|ZP_03018655.1| RNA polymerase sigma-G factor [Bacillus anthracis Tsiankovskii-I]
 gi|196035947|ref|ZP_03103349.1| RNA polymerase sigma-G factor [Bacillus cereus W]
 gi|196045922|ref|ZP_03113151.1| RNA polymerase sigma-G factor [Bacillus cereus 03BB108]
 gi|206976720|ref|ZP_03237624.1| RNA polymerase sigma-G factor [Bacillus cereus H3081.97]
 gi|217961324|ref|YP_002339892.1| sporulation sigma factor SigG [Bacillus cereus AH187]
 gi|218233406|ref|YP_002368703.1| sporulation sigma factor SigG [Bacillus cereus B4264]
 gi|218905033|ref|YP_002452867.1| RNA polymerase sigma-G factor [Bacillus cereus AH820]
 gi|225865885|ref|YP_002751263.1| RNA polymerase sigma-G factor [Bacillus cereus 03BB102]
 gi|227813187|ref|YP_002813196.1| RNA polymerase sigma-G factor [Bacillus anthracis str. CDC 684]
 gi|228916541|ref|ZP_04080107.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|229140552|ref|ZP_04269107.1| RNA polymerase sigma-G factor [Bacillus cereus BDRD-ST26]
 gi|229152101|ref|ZP_04280296.1| RNA polymerase sigma-G factor [Bacillus cereus m1550]
 gi|229157482|ref|ZP_04285559.1| RNA polymerase sigma-G factor [Bacillus cereus ATCC 4342]
 gi|229174570|ref|ZP_04302100.1| RNA polymerase sigma-G factor [Bacillus cereus MM3]
 gi|229198015|ref|ZP_04324729.1| RNA polymerase sigma-G factor [Bacillus cereus m1293]
 gi|229602177|ref|YP_002868139.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0248]
 gi|254721437|ref|ZP_05183226.1| sporulation sigma factor SigG [Bacillus anthracis str. A1055]
 gi|30258549|gb|AAP27768.1| RNA polymerase sigma-G factor [Bacillus anthracis str. Ames]
 gi|47551942|gb|AAT33159.2| RNA polymerase sigma-G factor [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|164711980|gb|EDR17520.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0488]
 gi|167510894|gb|EDR86285.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0193]
 gi|170126302|gb|EDS95193.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0389]
 gi|170667211|gb|EDT17971.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0465]
 gi|172080430|gb|EDT65517.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0174]
 gi|190562655|gb|EDV16621.1| RNA polymerase sigma-G factor [Bacillus anthracis Tsiankovskii-I]
 gi|195991596|gb|EDX55562.1| RNA polymerase sigma-G factor [Bacillus cereus W]
 gi|196023362|gb|EDX62040.1| RNA polymerase sigma-G factor [Bacillus cereus 03BB108]
 gi|206745030|gb|EDZ56433.1| RNA polymerase sigma-G factor [Bacillus cereus H3081.97]
 gi|217067470|gb|ACJ81720.1| RNA polymerase sigma-G factor [Bacillus cereus AH187]
 gi|218161363|gb|ACK61355.1| RNA polymerase sigma-G factor [Bacillus cereus B4264]
 gi|218537241|gb|ACK89639.1| RNA polymerase sigma-G factor [Bacillus cereus AH820]
 gi|225788717|gb|ACO28934.1| RNA polymerase sigma-G factor [Bacillus cereus 03BB102]
 gi|227002358|gb|ACP12101.1| RNA polymerase sigma-G factor [Bacillus anthracis str. CDC 684]
 gi|228585494|gb|EEK43598.1| RNA polymerase sigma-G factor [Bacillus cereus m1293]
 gi|228608875|gb|EEK66167.1| RNA polymerase sigma-G factor [Bacillus cereus MM3]
 gi|228625932|gb|EEK82682.1| RNA polymerase sigma-G factor [Bacillus cereus ATCC 4342]
 gi|228631450|gb|EEK88084.1| RNA polymerase sigma-G factor [Bacillus cereus m1550]
 gi|228643113|gb|EEK99389.1| RNA polymerase sigma-G factor [Bacillus cereus BDRD-ST26]
 gi|228843120|gb|EEM88202.1| RNA polymerase sigma-G factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|229266585|gb|ACQ48222.1| RNA polymerase sigma-G factor [Bacillus anthracis str. A0248]
          Length = 259

 Score =  170 bits (431), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 62/261 (23%), Positives = 120/261 (45%), Gaps = 17/261 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+  E   L +  +  G++SA  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKNDEMRKLFREMQ-SGEISAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++ 
Sbjct: 74  GLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVRE 130

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L A    N K    + IAK L V+  E++     +    SL   I +   +     D L
Sbjct: 131 KLIA---ENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGGDPIFVMDQL 187

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             +    EQ + E          L   M  LN RE+ I   R  Q    T   ++ E  +
Sbjct: 188 SDEKQKDEQWVEELA--------LKEGMKRLNDREKMIIRKRFFQG--KTQMEVAEEIGI 237

Query: 265 SRERVRQIEARAFKKVQESIQ 285
           S+ +V ++E  A K++ ++IQ
Sbjct: 238 SQAQVSRLEKSAIKQMNKTIQ 258


>gi|253578148|ref|ZP_04855420.1| sporulation sigma factor SigG [Ruminococcus sp. 5_1_39B_FAA]
 gi|251850466|gb|EES78424.1| sporulation sigma factor SigG [Ruminococcus sp. 5_1_39BFAA]
          Length = 259

 Score =  170 bits (431), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 51/262 (19%), Positives = 113/262 (43%), Gaps = 17/262 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L  +E+  L +R + +GD  A    +  +LRLV+ +   ++       ++   G 
Sbjct: 14  SKLPVLTAEEKAELFRRIK-NGDEQARELYIKGNLRLVLSVIRRFQNSSENADDLFQIGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD     + +TY++  I   ++ Y+  + S +++  +           R  
Sbjct: 73  IGLIKAIDNFDTTLQVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRDIAYKAIYTR-- 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
              +     +LK   V  IA+++ + +  ++     +    SL   + +   ++    D 
Sbjct: 130 ---ENYMKQHLKEPTVTEIAQEIGIEKEMIVYALDAIQNPVSLFEPVYTEGGDTLYVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    + +E+ +            L  +M  LN RE+ I E R       T   ++ E  
Sbjct: 187 ISDKKNKEERWIENLA--------LREAMQRLNSREKHIIELRFY--EGKTQMEVAQEIG 236

Query: 264 VSRERVRQIEARAFKKVQESIQ 285
           +S+ +V ++E  A K ++  ++
Sbjct: 237 ISQAQVSRLEKNALKSMRNYLR 258


>gi|229013088|ref|ZP_04170253.1| RNA polymerase sigma-G factor [Bacillus mycoides DSM 2048]
 gi|229061509|ref|ZP_04198853.1| RNA polymerase sigma-G factor [Bacillus cereus AH603]
 gi|229168644|ref|ZP_04296366.1| RNA polymerase sigma-G factor [Bacillus cereus AH621]
 gi|228614800|gb|EEK71903.1| RNA polymerase sigma-G factor [Bacillus cereus AH621]
 gi|228717743|gb|EEL69393.1| RNA polymerase sigma-G factor [Bacillus cereus AH603]
 gi|228748342|gb|EEL98202.1| RNA polymerase sigma-G factor [Bacillus mycoides DSM 2048]
          Length = 259

 Score =  170 bits (431), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 62/261 (23%), Positives = 121/261 (46%), Gaps = 17/261 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+ +E   L +  +  G++SA  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKNEEMRKLFREMQ-SGEISAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++ 
Sbjct: 74  GLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVRE 130

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L A    N K    + IAK L V+  E++     +    SL   I +   +     D L
Sbjct: 131 KLIA---ENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGGDPIFVMDQL 187

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             +    EQ + E          L   M  LN RE+ I   R  Q    T   ++ E  +
Sbjct: 188 KDEKQKDEQWVEELA--------LKEGMKRLNDREKMIIRKRFFQG--KTQMEVAEEIGI 237

Query: 265 SRERVRQIEARAFKKVQESIQ 285
           S+ +V ++E  A K++ ++IQ
Sbjct: 238 SQAQVSRLEKSAIKQMNKTIQ 258


>gi|308233741|ref|ZP_07664478.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Atopobium vaginae DSM
           15829]
 gi|328943730|ref|ZP_08241195.1| DNA-directed RNA polymerase sigma subunit SigB [Atopobium vaginae
           DSM 15829]
 gi|327491699|gb|EGF23473.1| DNA-directed RNA polymerase sigma subunit SigB [Atopobium vaginae
           DSM 15829]
          Length = 286

 Score =  170 bits (431), Expect = 2e-40,   Method: Composition-based stats.
 Identities = 57/255 (22%), Positives = 116/255 (45%), Gaps = 11/255 (4%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           +KQ+   L KRY+E GD  A  +LV +HL L   +A  ++  G  + ++V    IGL++A
Sbjct: 29  DKQKTKELFKRYKETGDEQAREQLVLAHLNLARFLASKFKNRGESLDDLVQVATIGLIKA 88

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +FD  RG    T++   I   ++ +       V++      +RL     ++      +
Sbjct: 89  IDRFDISRGLEFTTFATPTIMGEIKRHFRDKGWSVRVP-----RRLQELSAKVTQVSDKL 143

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
           T+   +   V  IA+ L VS  EV+          S++  +   D +       ++    
Sbjct: 144 TEKLQRSPSVDEIAQALGVSVDEVLEAMESAHAYSSVSLDVPQGDDDDGTQSSTVID--- 200

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
            +  ++ E  E  + R +L +++   + RE++I   R L     T   ++ + ++S+ +V
Sbjct: 201 -KYALVDEDLESSDDRIVLEQAIKDFSEREQQIIRMRFL--EGFTQVEIAQKLQISQVQV 257

Query: 270 RQIEARAFKKVQESI 284
            ++  +  +K QE +
Sbjct: 258 SRLLRKTLQKFQEKL 272


>gi|317132579|ref|YP_004091893.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Ethanoligenens harbinense YUAN-3]
 gi|315470558|gb|ADU27162.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Ethanoligenens harbinense YUAN-3]
          Length = 256

 Score =  169 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 54/261 (20%), Positives = 118/261 (45%), Gaps = 18/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+ +L + ++  L KR ++ GDL+A   L++ +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLKVLTESQKTALLKRVKQ-GDLAAREELISGNLRLVLSVIQRFTNRGENLDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+++  FD  +  R +TY++  I   ++ Y+  +   +++  +   + + +   + K
Sbjct: 73  IGLMKSIDNFDISQNVRFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKAMQCK 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L            +  +AK++++ + E++     +    SL   + S D   + +   
Sbjct: 130 ERLMNANQRE---PTIEEMAKEMDMPKEEIVMALESVVEPVSLYEPVYS-DGGDTIYVMD 185

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
            + D       L E          L  ++  L+ RE+RI   R       T   ++SE  
Sbjct: 186 QIGDKTVDSDWLDE--------ITLKEAVGALSEREKRILYLRFF--EGHTQMEVASEIG 235

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A  K++  +
Sbjct: 236 ISQAQVSRLEKGALSKIKSQM 256


>gi|253681759|ref|ZP_04862556.1| RNA polymerase sigma-G factor [Clostridium botulinum D str. 1873]
 gi|253561471|gb|EES90923.1| RNA polymerase sigma-G factor [Clostridium botulinum D str. 1873]
          Length = 257

 Score =  169 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 56/261 (21%), Positives = 118/261 (45%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+ +E   L  + R+ GD  +  + +  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLKDKEMKELLIKMRD-GDYFSREKFIRGNLRLVLSVIQRFNNRGENVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD  +  + +TY++  I   ++ Y+  + S +++  +   + + +   +++
Sbjct: 73  IGLIKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSL--RDIAYKALQVR 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L    + + K   V  IAK+L +   EV+     +    SL   I   D   + +   
Sbjct: 130 DRL---INKDNKDPNVSQIAKELELPREEVVFALDAIQDPVSLFEPIYH-DGGDALYVMD 185

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
            + D    +   IE          +  +M  LN RE+ I   R  Q    T   ++ E  
Sbjct: 186 QISDSKNADDSWIENIS-------IKEAMKRLNKREKLILNMRFFQG--RTQMEVADEIG 236

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A K +++ +
Sbjct: 237 ISQAQVSRLEKTALKHMRKYV 257


>gi|327438872|dbj|BAK15237.1| DNA-directed RNA polymerase [Solibacillus silvestris StLB046]
          Length = 425

 Score =  169 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 59/259 (22%), Positives = 119/259 (45%), Gaps = 21/259 (8%)

Query: 35  YVLAKRYREHGDLSAAHR----LVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLM 87
               K+     D    ++    LV ++ +LV KI   Y G    G   +++   G IGL+
Sbjct: 163 IEYLKQIHSE-DEFKRNKSLSNLVEANRKLVWKIVKHYSGLATVGFDENDMYQVGFIGLL 221

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +A +KFD   G++ +TY+ WWI+ A+   I    +L++I     +K     + +      
Sbjct: 222 KAAEKFDVSLGYQFSTYATWWIRQAITRGIADYSTLIRIPVHYREK-----MNKFIKIEN 276

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLV 205
            + +   +P     I+K++    + +  +   ++    +SL+ L+   D  ++   + ++
Sbjct: 277 ELWNELARPATTFEISKEMEEPTNVIEELRFYISQSNLDSLDRLV--GDDENTSLGELVL 334

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFE 263
            D+         K E +N    + +  S L  RE ++   R     +   TLE +   + 
Sbjct: 335 DDNLKMPDEEYYKIELRNTIGEIFQ--SNLTEREMQVLYYRFGFKNDETKTLEEVGQIYN 392

Query: 264 VSRERVRQIEARAFKKVQE 282
           ++RER+RQIEA+A +K+++
Sbjct: 393 LTRERIRQIEAKALRKLRK 411


>gi|116070855|ref|ZP_01468124.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. BL107]
 gi|116066260|gb|EAU72017.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. BL107]
          Length = 239

 Score =  169 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 59/234 (25%), Positives = 111/234 (47%), Gaps = 9/234 (3%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG R +TY+ WWI+  
Sbjct: 1   MITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSTYAYWWIRQG 60

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +      ++I    N+K     LR  K  +          EQ+            +
Sbjct: 61  LNRALSTQSRTIRIPVNVNEK--LTKLRAAKARVMQRNGLTATAEQLAEFMNLPLTEVED 118

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           +++   R +   SL  ++ S   + S+  D L  +     +     E   +   +L+++ 
Sbjct: 119 LLACELR-SVTVSLQGIVKSK-SDPSELVDILPSEEIPPMERAEIAERSASVWALLSKA- 175

Query: 233 SVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             L P+E ++   R   +      TL  ++     SRE  RQ+  RA +K++++
Sbjct: 176 -NLTPKEHKVVTLRFGLDGTNEWRTLAEVARHMNCSREYCRQVVQRALRKLRKT 228


>gi|299783172|gb|ADJ41170.1| RNA polymerase sigma factor [Lactobacillus fermentum CECT 5716]
          Length = 287

 Score =  169 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 54/179 (30%), Positives = 89/179 (49%), Gaps = 6/179 (3%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
                 +     +  Y+ EI ++ +L   EE  LA R  E GD +A   L  ++LRLVV 
Sbjct: 99  TTAPSSIKINDPVRMYLKEIGRVNLLTADEEVALALRI-EKGDETAKQELAEANLRLVVS 157

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y G G+   +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I      
Sbjct: 158 IAKRYVGRGMQFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQART 217

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           ++I     +      L R++  L         PE++ A   ++++   +V  +   L G
Sbjct: 218 IRIPVHMVE--TINKLIRIQRQLLQDLGREPLPEEIGA---EMDMDTQKVRDILNDLPG 271


>gi|138895880|ref|YP_001126333.1| sporulation sigma factor SigF [Geobacillus thermodenitrificans
           NG80-2]
 gi|134267393|gb|ABO67588.1| RNA polymerase sigma-F factorr [Geobacillus thermodenitrificans
           NG80-2]
          Length = 252

 Score =  169 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 56/253 (22%), Positives = 110/253 (43%), Gaps = 19/253 (7%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           QE   L +R +E GD  A   ++  ++RLV  +   +   G    ++   G IGL+++V 
Sbjct: 17  QEMKELIRRSQE-GDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVD 75

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD     + +TY++  I   +Q ++      VK+  +   K +   +R+ K  L     
Sbjct: 76  KFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSL--KEMGNKIRKAKDELSKTRG 132

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +   +  IA  L VS  EV+     +    S++  +  +D +     D +    D  
Sbjct: 133 ---RAPTITEIADHLGVSPEEVVLAQEAVRSPASIHETVYENDGDPITLLDQIA---DAD 186

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E    EK         L +++  L+ RER I   R  ++   T   +++   +S+ +V +
Sbjct: 187 EASWFEKI-------ALKKAIEELDERERLIVYLRYYKDQ--TQSEVAARLGISQVQVSR 237

Query: 272 IEARAFKKVQESI 284
           +E +  + ++E +
Sbjct: 238 LEKKILQHIKEKM 250


>gi|226327187|ref|ZP_03802705.1| hypothetical protein PROPEN_01052 [Proteus penneri ATCC 35198]
 gi|225204405|gb|EEG86759.1| hypothetical protein PROPEN_01052 [Proteus penneri ATCC 35198]
          Length = 201

 Score =  169 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 49/207 (23%), Positives = 95/207 (45%), Gaps = 12/207 (5%)

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 1   MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 58

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    +A+++ + E ++  +        S+   I   D   S   D++  
Sbjct: 59  LQEMGREPSPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 111

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   ++ ++    ++ R+     ++ L  RE ++   R   +     TLE +  +F+V
Sbjct: 112 -EDTTLELPLDSATSESLRSATHEVLAGLTLREAKVLRMRFGIDMNTDHTLEEVGKQFDV 170

Query: 265 SRERVRQIEARAFKKVQESIQKQVELS 291
           +RER+RQIEA+A +K++   + +V  S
Sbjct: 171 TRERIRQIEAKALRKLRHPSRSEVLRS 197


>gi|311029938|ref|ZP_07708028.1| sporulation sigma factor SigG [Bacillus sp. m3-13]
          Length = 259

 Score =  169 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 60/263 (22%), Positives = 119/263 (45%), Gaps = 17/263 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+ +E   L +  +  G+LSA  +LV  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLKNEEMRKLFREMQ-GGELSAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+++  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 73  IGLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVR 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L + T      E    IAK L V   E++     +    SL   I +   +     D 
Sbjct: 130 ERLMSETSREPTAE---EIAKVLEVPHEEIVFALDAIQDPVSLFEPIYNDGGDPIYVLDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  + +   Q + E          L   M  LN RE+ I   R  Q    T   ++ E  
Sbjct: 187 ISDEKNKDIQWIEEIA--------LKEGMRRLNDREKLILRKRFFQG--KTQMEVADEIG 236

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+ +V ++E  A K++ ++IQ 
Sbjct: 237 ISQAQVSRLEKAAIKQMNKNIQS 259


>gi|261417856|ref|YP_003251538.1| sporulation sigma factor SigF [Geobacillus sp. Y412MC61]
 gi|297529524|ref|YP_003670799.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
 gi|319767332|ref|YP_004132833.1| RNA polymerase, sigma 28 subunit, SigF [Geobacillus sp. Y412MC52]
 gi|261374313|gb|ACX77056.1| RNA polymerase, sigma 28 subunit, SigF [Geobacillus sp. Y412MC61]
 gi|297252776|gb|ADI26222.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
 gi|317112198|gb|ADU94690.1| RNA polymerase, sigma 28 subunit, SigF [Geobacillus sp. Y412MC52]
          Length = 252

 Score =  169 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 52/253 (20%), Positives = 108/253 (42%), Gaps = 19/253 (7%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           QE   L +R +E GD  A   ++  ++RLV  +   +   G    ++   G IGL+++V 
Sbjct: 17  QEMKELIRRSQE-GDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVD 75

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD     + +TY++  I   +Q ++      VK+  +   K +   +R+ K  L     
Sbjct: 76  KFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSL--KEMGNKIRKAKDELSKTRG 132

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +   V  IA  L +S  +V+     +    S++  +  +D +     D +       
Sbjct: 133 ---RAPTVTEIADHLGISPEDVVLAQEAVRSPTSIHETVYENDGDPITLLDQIAD----- 184

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
                  E     +  L +++  L+ RER I   R  ++   T   ++S   +S+ +V +
Sbjct: 185 -----ADEASWFDKIALKKAIEELDERERLIVYLRYYKDQ--TQSEVASRLGISQVQVSR 237

Query: 272 IEARAFKKVQESI 284
           +E +  + +++ +
Sbjct: 238 LEKKILQHIKDKM 250


>gi|46241495|gb|AAS82950.1| chloroplast RPOD [Chlamydomonas reinhardtii]
          Length = 311

 Score =  169 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 62/244 (25%), Positives = 112/244 (45%), Gaps = 12/244 (4%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           + R    L A   L+ S+ +LV+ +   + G G  I ++VSEG  GL++ V+K+D  +GF
Sbjct: 40  KLRYDAGLKAKELLLKSNYKLVMTVCKSFVGKGPHIQDLVSEGVKGLLKGVEKYDATKGF 99

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           R  TY+ WWI+ A+   +  +   V++        +   L RLK     +     +   +
Sbjct: 100 RFGTYAHWWIRQAVSRSLAETGRAVRLPMH-----MIEQLTRLKNLSAKLQTQLAREPTL 154

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +AK   +  + V  +        SL+  I  ++   +  +D +  + +  ++      
Sbjct: 155 PELAKAAGLPVTRVQMLMETARSAASLDTPIGGNELGPT-VKDSVEDEREAADEEFGSDS 213

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAF 277
            R +   ML      L  RE R+   R   ++    TLE +     V+RER+RQIEA+A 
Sbjct: 214 LRNDMEAMLLE----LPEREARVVRLRFGLDDGKEWTLEEIGEALNVTRERIRQIEAKAL 269

Query: 278 KKVQ 281
           +K++
Sbjct: 270 RKLR 273


>gi|224533396|ref|ZP_03673990.1| RNA polymerase sigma factor [Borrelia burgdorferi CA-11.2a]
 gi|224513561|gb|EEF83918.1| RNA polymerase sigma factor [Borrelia burgdorferi CA-11.2a]
          Length = 266

 Score =  169 bits (430), Expect = 3e-40,   Method: Composition-based stats.
 Identities = 77/272 (28%), Positives = 144/272 (52%), Gaps = 18/272 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+  +R+  ++  +EE  LA + +  G+  A ++++ ++LRLV+KI   Y G GL I
Sbjct: 9   LNIYLKSVREHKLITHEEEIKLAGQIQ-RGNAKAKNKMINANLRLVLKIIKRYAGKGLKI 67

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GL++A +K+DP +  + +TY+ +WIK ++Q  +     LVK+         
Sbjct: 68  EDLIQEGNLGLIRAAEKYDPNKNTKFSTYASFWIKQSLQRALNTKTRLVKVPYRKE---- 123

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + ++  +L     +     +   I K+ N+S ++ I +   L  + SL+  I    +
Sbjct: 124 -NLILQINKYLTEEEKSP----KKEEIMKRFNLSPAQYIKIIPYLEKEYSLDKEI-EGSE 177

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN---P 252
           NS+     L  D+    ++ +E++      N +  + S  N +ER I + R   +N    
Sbjct: 178 NSTLLN--LYEDNSFNPEITLEQDSTLKHLNYILETKS--NEKERYIIKKRYNLDNSPKK 233

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL+++S+E  +S E VRQIE R  KK++E I
Sbjct: 234 STLKDISTELGISSETVRQIEKRVLKKLKEEI 265


>gi|89895640|ref|YP_519127.1| sporulation sigma factor SigG [Desulfitobacterium hafniense Y51]
 gi|89335088|dbj|BAE84683.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 266

 Score =  169 bits (430), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 49/261 (18%), Positives = 109/261 (41%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L   +   L   Y+  G+  A  +L+  +LRLV+ +   +   G  + ++   G 
Sbjct: 23  SKLPVLSSAKMKELFVAYQ-SGEKEAREKLIYGNLRLVLSVIQRFTNRGEYVDDLFQVGC 81

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+A+  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 82  IGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVR 138

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
                + +   +   V  IA KL +   EVI     +    SL   I     +     D 
Sbjct: 139 D---QLVNECSREPTVSEIADKLTLPREEVIFALDAIQEPISLFEPIYHDGGDPIFVMDQ 195

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  +       L            +  ++  L+ RE+ I   R    +  T   ++ E  
Sbjct: 196 IGDEKHSDNSWLEGIA--------VREALRRLSEREKLILSLRFF--HGKTQMEVADEIG 245

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A   +++ +
Sbjct: 246 ISQAQVSRLEKAALGHMRKYV 266


>gi|47570318|ref|ZP_00240965.1| RNA polymerase sigma-G factor [Bacillus cereus G9241]
 gi|47553027|gb|EAL11431.1| RNA polymerase sigma-G factor [Bacillus cereus G9241]
          Length = 257

 Score =  169 bits (430), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 62/261 (23%), Positives = 119/261 (45%), Gaps = 17/261 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L   E   L +  +  G++SA  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 13  KLPVLXNDEMRKLFREMQ-SGEISAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 71

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++ 
Sbjct: 72  GLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVRE 128

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L A    N K    + IAK L V+  E++     +    SL   I +   +     D L
Sbjct: 129 KLIA---ENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGGDPIFVMDQL 185

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             +    EQ + E          L   M  LN RE+ I   R  Q    T   ++ E  +
Sbjct: 186 SDEKQKDEQWVEELA--------LKEGMKRLNDREKMIIRKRFFQG--KTQMEVAEEIGI 235

Query: 265 SRERVRQIEARAFKKVQESIQ 285
           S+ +V ++E  A K++ ++IQ
Sbjct: 236 SQAQVSRLEKSAIKQMNKTIQ 256


>gi|196248769|ref|ZP_03147469.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
 gi|196211645|gb|EDY06404.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
          Length = 250

 Score =  169 bits (430), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 56/253 (22%), Positives = 110/253 (43%), Gaps = 19/253 (7%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           QE   L +R +E GD  A   ++  ++RLV  +   +   G    ++   G IGL+++V 
Sbjct: 15  QEMKELIRRSQE-GDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVD 73

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD     + +TY++  I   +Q ++      VK+  +   K +   +R+ K  L     
Sbjct: 74  KFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSL--KEMGNKIRKAKDELSKTRG 130

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +   +  IA  L VS  EV+     +    S++  +  +D +     D +    D  
Sbjct: 131 ---RAPTITEIADHLGVSPEEVVLAQEAVRSPASIHETVYENDGDPITLLDQIA---DAD 184

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E    EK         L +++  L+ RER I   R  ++   T   +++   +S+ +V +
Sbjct: 185 EASWFEKI-------ALKKAIEELDERERLIVYLRYYKDQ--TQSEVAARLGISQVQVSR 235

Query: 272 IEARAFKKVQESI 284
           +E +  + ++E +
Sbjct: 236 LEKKILQHIKEKM 248


>gi|15558898|dbj|BAB64922.1| chloroplast RNA polymerase sigma factor [Chlamydomonas reinhardtii]
          Length = 250

 Score =  169 bits (430), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 64/244 (26%), Positives = 113/244 (46%), Gaps = 15/244 (6%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R R HG   A   L+ S+ +LV+ +   + G G  I ++VSEG  GL++ V+K+D  +GF
Sbjct: 1   RIRVHG---AKELLLKSNYKLVMTVCKSFVGKGPHIQDLVSEGVKGLLKGVEKYDATKGF 57

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           R  TY+ WWI+ A+   +  +   V++        +   L RLK     +     +   +
Sbjct: 58  RFGTYAHWWIRQAVSRSLAETGRAVRLPMH-----MIEQLTRLKNLSAKLQTQLAREPTL 112

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +AK   +  + V  +        SL+  I  ++   +  +D +  + +  ++      
Sbjct: 113 PELAKAAGLPVTRVQMLMETARSAASLDTPIGGNELGPT-VKDSVEDEREAADEEFGSDS 171

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAF 277
            R +   ML      L  RE R+   R   ++    TLE +     V+RER+RQIEA+A 
Sbjct: 172 LRNDMEAMLLE----LPEREARVVRLRFGLDDGKEWTLEEIGEALNVTRERIRQIEAKAL 227

Query: 278 KKVQ 281
           +K++
Sbjct: 228 RKLR 231


>gi|40353311|gb|AAR84419.1| essential primary sigma 70 factor [Frankia sp. ACN14a]
          Length = 214

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 53/202 (26%), Positives = 96/202 (47%), Gaps = 10/202 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A  +LV ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +
Sbjct: 23  ERDGQIAKRKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFS 82

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I     +      L R++  L         PE    I
Sbjct: 83  TYATWWIRQAITRAIADQARTIRIPVHMVE--TINKLIRIQRQLLQDLGREPSPE---EI 137

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           AK+++++  +V  +        SL   I   ++  S   D++    D    V ++     
Sbjct: 138 AKEMDLTPDKVREILKVSQEPVSLETPI--GEEEDSHLGDFI---EDCDAVVPVDAASFI 192

Query: 223 NRRNMLTRSMSVLNPRERRIFE 244
             +  L   +  L+ RE+++ +
Sbjct: 193 LLQEQLDSVLHTLSDREKKVIQ 214


>gi|56420843|ref|YP_148161.1| sporulation sigma factor SigF [Geobacillus kaustophilus HTA426]
 gi|56380685|dbj|BAD76593.1| DNA-directed RNA polymerase sporulation-specific sigma factor
           (sigma-F) (stage II sporulation protein AC) [Geobacillus
           kaustophilus HTA426]
          Length = 250

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 52/253 (20%), Positives = 108/253 (42%), Gaps = 19/253 (7%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           QE   L +R +E GD  A   ++  ++RLV  +   +   G    ++   G IGL+++V 
Sbjct: 15  QEMKELIRRSQE-GDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVD 73

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD     + +TY++  I   +Q ++      VK+  +   K +   +R+ K  L     
Sbjct: 74  KFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSL--KEMGNKIRKAKDELSKTRG 130

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +   V  IA  L +S  +V+     +    S++  +  +D +     D +       
Sbjct: 131 ---RAPTVTEIADHLGISPEDVVLAQEAVRSPTSIHETVYENDGDPITLLDQIAD----- 182

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
                  E     +  L +++  L+ RER I   R  ++   T   ++S   +S+ +V +
Sbjct: 183 -----ADEASWFDKIALKKAIEELDERERLIVYLRYYKDQ--TQSEVASRLGISQVQVSR 235

Query: 272 IEARAFKKVQESI 284
           +E +  + +++ +
Sbjct: 236 LEKKILQHIKDKM 248


>gi|20808499|ref|NP_623670.1| DNA-directed RNA polymerase sigma subunits (sigma70/sigma32)
           [Thermoanaerobacter tengcongensis MB4]
 gi|20517120|gb|AAM25274.1| DNA-directed RNA polymerase sigma subunits (sigma70/sigma32)
           [Thermoanaerobacter tengcongensis MB4]
          Length = 265

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 67/260 (25%), Positives = 129/260 (49%), Gaps = 15/260 (5%)

Query: 28  MLEKQ--EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG-YGLPISEVVSEGNI 84
           +L K+  +E+ L +R R +GD  A   +V  ++ LVV IA  +   YG+ + +++ EG I
Sbjct: 4   VLTKEKTDEFELFERLR-NGDKKARDEIVEKNIGLVVSIAANFSKAYGVELDDLIQEGFI 62

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL+ A++ FD  +G+R +TY++++IK  +Q YI      + +     QK     +   + 
Sbjct: 63  GLLAAIEGFDHTKGYRFSTYAVFYIKQKIQRYIWGRSRTIHLPVKTYQK--LNQVLSAQL 120

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L+ +       E    IA++  +   EV+++        SLN  +  +D   ++  D +
Sbjct: 121 KLEQVKGEAFPEE----IAEETGIKTEEVVNLLSLKNPTVSLNQQLYENDN--TELIDVI 174

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-PVTLENLSSEFE 263
           + +    E  +      +  R +L   + VL  +ER + E R      P+TL+ ++    
Sbjct: 175 LDEQSENE--IDRNYSLEELRKILKECLEVLPEKERSVLEMRYGLNGTPMTLKQIAEILN 232

Query: 264 VSRERVRQIEARAFKKVQES 283
           +S++R  QIE RA ++++ S
Sbjct: 233 ISKQRAGQIEKRALQRLRNS 252


>gi|295696440|ref|YP_003589678.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
 gi|295412042|gb|ADG06534.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
          Length = 256

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 51/256 (19%), Positives = 109/256 (42%), Gaps = 19/256 (7%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L  Q+   L  +  + GD  A   LV  + RLV  +   + G G    ++   G IGLM+
Sbjct: 14  LTDQQVRELIAQ-SQSGDAGARETLVLFNQRLVWSVVQRFLGRGYEPEDLFQIGCIGLMK 72

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A+ KFD     + +TY++  I   +Q ++      VK+  +  +       R ++     
Sbjct: 73  AIDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSVKE-----TARHIRRARDE 126

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           +     +   +  +A++L +  +EV+     +    S++  +  +D +     D +    
Sbjct: 127 LAKRLGRQPHINELAEELGMDPAEVVFTQDAMRAPASIHETVFENDGDPILLMDQIAD-- 184

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
                   E++E+   R  LT +++ L  RER I   R  ++   T   ++    +S+ +
Sbjct: 185 --------EEQEKWFDRLALTDALNRLPERERLIVFLRFFRD--KTQSEVAEVLGISQVQ 234

Query: 269 VRQIEARAFKKVQESI 284
           V ++E +   +++  +
Sbjct: 235 VSRLEKKILNRIRRQL 250


>gi|219670064|ref|YP_002460499.1| sporulation sigma factor SigG [Desulfitobacterium hafniense DCB-2]
 gi|219540324|gb|ACL22063.1| RNA polymerase, sigma 28 subunit, SigG [Desulfitobacterium
           hafniense DCB-2]
          Length = 257

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 49/261 (18%), Positives = 109/261 (41%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L   +   L   Y+  G+  A  +L+  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLSSAKMKELFVAYQ-SGEKEAREKLIYGNLRLVLSVIQRFTNRGEYVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+A+  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 73  IGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVR 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
                + +   +   V  IA KL +   EVI     +    SL   I     +     D 
Sbjct: 130 D---QLVNECSREPTVSEIADKLTLPREEVIFALDAIQEPISLFEPIYHDGGDPIFVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  +       L            +  ++  L+ RE+ I   R    +  T   ++ E  
Sbjct: 187 IGDEKHSDNSWLEGIA--------VREALRRLSEREKLILSLRFF--HGKTQMEVADEIG 236

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A   +++ +
Sbjct: 237 ISQAQVSRLEKAALGHMRKYV 257


>gi|302391629|ref|YP_003827449.1| RNA polymerase, sigma subunit, RpsG/SigG [Acetohalobium arabaticum
           DSM 5501]
 gi|302203706|gb|ADL12384.1| RNA polymerase, sigma subunit, RpsG/SigG [Acetohalobium arabaticum
           DSM 5501]
          Length = 260

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 51/264 (19%), Positives = 113/264 (42%), Gaps = 17/264 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            ++P+L  +E   L K+ + +GD  A   +V  +L+LV+ +   +   G PI ++   G 
Sbjct: 13  SELPVLSNEEMRELFKKMQ-NGDREARQTIVGGNLKLVLSVLQRFNNRGEPIDDLFQVGC 71

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+A+  FD  R  + +TY++  I   ++ ++      +++  +   +   +   ++K
Sbjct: 72  IGLMKAIDNFDLSRNVKFSTYAVPMIIGEIRRHLRDHN-PIRVSRSL--RDTAYKALQMK 128

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L+  T        +  IA++L +   E++     +    SL   I     +     D 
Sbjct: 129 ESLENKTSEE---PTLTEIAQELGIPREEIVQALDAIQDPISLFEPIYQDGGDPIYVMDQ 185

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  D    E  L            +  ++  L  RE+ I   R  +    T   ++    
Sbjct: 186 VSDDDSEDESWLEGIA--------VREALRQLEDREKLILSMRFYKG--KTQMEVADNIG 235

Query: 264 VSRERVRQIEARAFKKVQESIQKQ 287
           +S+ +V ++E  A + +++ + ++
Sbjct: 236 ISQAQVSRLEKAALENLEKYVSEE 259


>gi|160892497|ref|ZP_02073287.1| hypothetical protein CLOL250_00024 [Clostridium sp. L2-50]
 gi|156865538|gb|EDO58969.1| hypothetical protein CLOL250_00024 [Clostridium sp. L2-50]
          Length = 258

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 55/261 (21%), Positives = 112/261 (42%), Gaps = 17/261 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           ++P+L  +E+  L  R  E GD++A    +  +LRLV+ +   +        ++   G I
Sbjct: 15  RLPLLTDKEKDELFDRI-EQGDMAARETFIKGNLRLVLSVIQRFSNSNENPDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD     + +TY++  I    + Y+  + S +++  +   + + +     K 
Sbjct: 74  GLIKAIDNFDRSLNVKFSTYAVPMILGECRRYLRDNNS-IRVSRSL--RDIAYKAIYTKD 130

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L    D       V  IAK+++V+  ++ +    ++   SL   +     ++    D L
Sbjct: 131 ALLKKLDRE---PTVDEIAKEIDVAPEDITTALDAISTPVSLYEPVYQEGGDTLYIVDQL 187

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               + +E  +            L  +M  LN RE  I   R       T   ++SE  +
Sbjct: 188 SDKKNKEENWVEN--------ISLKEAMKKLNEREYNILRLRFF--EGKTQTEVASEIAI 237

Query: 265 SRERVRQIEARAFKKVQESIQ 285
           S+ +V +IE  A K ++  ++
Sbjct: 238 SQAQVSRIEKSAIKSLKGYLR 258


>gi|111115602|ref|YP_710220.1| RNA polymerase sigma factor [Borrelia afzelii PKo]
 gi|110890876|gb|ABH02044.1| RNA polymerase sigma factor [Borrelia afzelii PKo]
          Length = 266

 Score =  169 bits (429), Expect = 4e-40,   Method: Composition-based stats.
 Identities = 76/272 (27%), Positives = 138/272 (50%), Gaps = 18/272 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+  +R+  ++  +EE  L  + +  G   A ++++ ++LRLV+KI   Y G GL I
Sbjct: 9   LNIYLKSVREHKLITHEEEIQLVGQIQ-RGSAKAKNKMINANLRLVLKIIKRYAGKGLKI 67

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GL++A +K+DP +  + +TY+ +WIK ++Q  +     LVK+        L
Sbjct: 68  EDLIQEGNLGLIRAAEKYDPNKNTKFSTYASFWIKQSLQRALNTKTRLVKVPYRKENLIL 127

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
                     +        K  +   I K+ N+S ++ I +   L  + SL+  I    +
Sbjct: 128 ---------QINKYLTEEEKAPKKEEIMKRFNLSPAQYIKIIPYLEKEYSLDKEI-EGSE 177

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN---P 252
           NS+     L  D+    ++ +E++      N +    + L  +ER I + R   +N    
Sbjct: 178 NSTLLN--LYEDNSFNPEITLEQDSTLQHLNYILE--TKLTEKERYIIKKRYNLDNSPKK 233

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            TL+++S+E  +S E VRQIE R  KK++E I
Sbjct: 234 STLKDISTELGISSETVRQIEKRVLKKLKEEI 265


>gi|16079402|ref|NP_390226.1| sporulation sigma factor SigF [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221310263|ref|ZP_03592110.1| sporulation sigma factor SigF [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221314586|ref|ZP_03596391.1| sporulation sigma factor SigF [Bacillus subtilis subsp. subtilis
           str. NCIB 3610]
 gi|221319509|ref|ZP_03600803.1| sporulation sigma factor SigF [Bacillus subtilis subsp. subtilis
           str. JH642]
 gi|221323785|ref|ZP_03605079.1| sporulation sigma factor SigF [Bacillus subtilis subsp. subtilis
           str. SMY]
 gi|321311821|ref|YP_004204108.1| sporulation sigma factor SigF [Bacillus subtilis BSn5]
 gi|133474|sp|P07860|RPSF_BACSU RecName: Full=RNA polymerase sigma-F factor; AltName:
           Full=Sporulation sigma factor; AltName: Full=Stage II
           sporulation protein AC
 gi|143611|gb|AAA22788.1| sporulation-specific sigma factor [Bacillus subtilis]
 gi|1304000|dbj|BAA12655.1| SpoIIAC [Bacillus subtilis]
 gi|2634780|emb|CAB14277.1| RNA polymerase sporulation-specific sigma factor (sigma-F)
           [Bacillus subtilis subsp. subtilis str. 168]
 gi|291484775|dbj|BAI85850.1| sporulation sigma factor SigF [Bacillus subtilis subsp. natto
           BEST195]
 gi|320018095|gb|ADV93081.1| sporulation sigma factor SigF [Bacillus subtilis BSn5]
          Length = 255

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 57/258 (22%), Positives = 109/258 (42%), Gaps = 19/258 (7%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K   L+  E   L K+  ++GD  A   L+  ++RLV  +   +   G    ++   G 
Sbjct: 9   GKNAQLKDHEVKELIKQ-SQNGDQQARDLLIEKNMRLVWSVVQRFLNRGYEPDDLFQIGC 67

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL+++V KFD     R +TY++  I   +Q +I      VK+  +   K L   +RR K
Sbjct: 68  IGLLKSVDKFDLTYDVRFSTYAVPMIIGEIQRFIRDDG-TVKVSRSL--KELGNKIRRAK 124

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L        +   V  IA  L +   +V+     +    S++  +  +D +     D 
Sbjct: 125 DELSKTLG---RVPTVQEIADHLEIEAEDVVLAQEAVRAPSSIHETVYENDGDPITLLDQ 181

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  +           EE+   +  L  ++S L  RE+ I   R  ++   T   ++    
Sbjct: 182 IADN----------SEEKWFDKIALKEAISDLEEREKLIVYLRYYKDQ--TQSEVAERLG 229

Query: 264 VSRERVRQIEARAFKKVQ 281
           +S+ +V ++E +  K+++
Sbjct: 230 ISQVQVSRLEKKILKQIK 247


>gi|257886121|ref|ZP_05665774.1| RNA polymerase sigma-70 factor [Enterococcus faecium 1,231,501]
 gi|257821977|gb|EEV49107.1| RNA polymerase sigma-70 factor [Enterococcus faecium 1,231,501]
          Length = 383

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 67/254 (26%), Positives = 125/254 (49%), Gaps = 16/254 (6%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPER 97
           Y+   D S+   LV ++ RLV+KIA  Y  Y    L I ++   G IGL++A  KFD  +
Sbjct: 121 YQRERDNSSLDALVKANRRLVLKIAQRYNKYLTSSLDIDDLEQFGMIGLLKAADKFDLSK 180

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
            +  +TY+ +WI+ ++   I+ +   V++     +K     L RL+  +      N    
Sbjct: 181 EYAFSTYATYWIRQSISRGIMDTSLTVRLPVHIFEK--INKLNRLEARMM----TNSSTT 234

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESL-NALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
            + +I K++++SE +   +    +   SL +          +   D L  ++   E+V+ 
Sbjct: 235 DISSILKEMDISEEQYYDLLAIRSTYLSLPSLDTPIGIDGDATIGDMLPDNNYDIEEVI- 293

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEA 274
              +    R  + +SM+ L  +ER +   R     E   TLE + + F V+RER+RQIEA
Sbjct: 294 ---DLGFLREDIKKSMTYLKEKEREVLYLRFGFDGEGRKTLEEIGNIFGVTRERIRQIEA 350

Query: 275 RAFKKVQESIQKQV 288
           +A +K+++ + +++
Sbjct: 351 KAIRKMKKKVNREL 364


>gi|213417289|ref|ZP_03350433.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
          Length = 277

 Score =  169 bits (429), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 63/228 (27%), Positives = 113/228 (49%), Gaps = 11/228 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 233

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
                L    D +E    +  +  + +  + + +  LN ++R +   R
Sbjct: 234 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARR 277


>gi|157692844|ref|YP_001487306.1| sporulation sigma factor SigF [Bacillus pumilus SAFR-032]
 gi|194016850|ref|ZP_03055463.1| RNA polymerase sigma-F factor [Bacillus pumilus ATCC 7061]
 gi|157681602|gb|ABV62746.1| DNA-directed RNA polymerase sigma subunit SigF [Bacillus pumilus
           SAFR-032]
 gi|194011456|gb|EDW21025.1| RNA polymerase sigma-F factor [Bacillus pumilus ATCC 7061]
          Length = 255

 Score =  169 bits (428), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 56/259 (21%), Positives = 113/259 (43%), Gaps = 19/259 (7%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L   E   L K+  + GD  A   LV  ++RLV  +   +   G    ++   G IGL++
Sbjct: 14  LSNDEVKELIKK-SQDGDQQARDLLVEKNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLK 72

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           +V KFD     + +TY++  I   +Q +I      VK+  +   K L   +RR +  L  
Sbjct: 73  SVDKFDLSYDVKFSTYAVPMIIGEIQRFIRDDG-TVKVSRSL--KELGNKIRRARDEL-- 127

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
            + ++ +   V  IA+ L+++  +V+     +    S++  +  +D +     D +    
Sbjct: 128 -SKSHGRMPTVQEIAEYLDITPEDVVLAQEAVRTPSSIHETVYENDGDPITLLDQIAD-- 184

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
                     EER   +  L  ++  L  RE+ I   R  ++   T   ++    +S+ +
Sbjct: 185 --------HSEERWFDKIALKEAIKELEEREKLIVYLRYYKDQ--TQSEVAERLGISQVQ 234

Query: 269 VRQIEARAFKKVQESIQKQ 287
           V ++E +  K++Q  + ++
Sbjct: 235 VSRLEKKILKQIQMQMDQK 253


>gi|40353301|gb|AAR84414.1| essential primary sigma 70 factor [Frankia sp. ORS020607]
 gi|40353303|gb|AAR84415.1| essential primary sigma 70 factor [Frankia sp. CcI3]
 gi|40353305|gb|AAR84416.1| essential primary sigma 70 factor [Frankia sp. CeD]
          Length = 217

 Score =  169 bits (428), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 53/202 (26%), Positives = 96/202 (47%), Gaps = 10/202 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A  +LV ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +
Sbjct: 26  ERDGQIAKRKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFS 85

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I     +      L R++  L         PE    I
Sbjct: 86  TYATWWIRQAITRAIADQARTIRIPVHMVE--TINKLIRIQRQLLQDLGREPSPE---EI 140

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           AK+++++  +V  +        SL   I   ++  S   D++    D    V ++     
Sbjct: 141 AKEMDLTPDKVREILKVSQEPVSLETPI--GEEEDSHLGDFI---EDCDAVVPVDAASFI 195

Query: 223 NRRNMLTRSMSVLNPRERRIFE 244
             +  L   +  L+ RE+++ +
Sbjct: 196 LLQEQLDSVLHTLSDREKKVIQ 217


>gi|297616994|ref|YP_003702153.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
 gi|297144831|gb|ADI01588.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
          Length = 256

 Score =  169 bits (428), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 55/261 (21%), Positives = 113/261 (43%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
             +P+L+ +    L  R +++ D  A   L+  +LRLV+ +   +   G  + ++   G 
Sbjct: 13  SNLPVLKNERMRDLFLRVKQN-DRQAREELIRGNLRLVLSVIQRFNHRGEYVDDLFQVGC 71

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD E+  R +TY++  I   ++ Y+  +   V++  +   + + +   +++
Sbjct: 72  IGLIKAIDNFDLEQNVRFSTYAVPMIIGEIRRYLRDNN-PVRVSRSL--RDVAYKALQVR 128

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L A          +  IA +L VS+ EV+     +    SL   I +   +     D 
Sbjct: 129 EQLLAEKSRE---PTIAEIADRLEVSQEEVVFALDAIQEPVSLFEPIYNDGGDPILVMDQ 185

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  D    E  L            +  ++  L+ RE+ I   R       T   ++ E  
Sbjct: 186 ISDDKTTDELWLEG--------ISIREALKKLSEREKLILTLRFF--EGKTQMEVAEEIG 235

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A K +++ I
Sbjct: 236 ISQAQVSRLEKAALKHMKKYI 256


>gi|56964115|ref|YP_175846.1| sporulation sigma factor SigG [Bacillus clausii KSM-K16]
 gi|56910358|dbj|BAD64885.1| DNA-directed RNA polymerase sigma factor sigma-G [Bacillus clausii
           KSM-K16]
          Length = 261

 Score =  169 bits (428), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 53/261 (20%), Positives = 112/261 (42%), Gaps = 15/261 (5%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L+  E   L  + +  G   A   LV  +LRLV+ +   +   G  + ++   G IG
Sbjct: 16  LPVLKNAEMRELFTKLQ-AGYEPARETLVNGNLRLVLSVIQRFNNRGENVDDLFQVGCIG 74

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           LM+++  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++  
Sbjct: 75  LMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVRDQ 131

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           + A      K   V  IA  L V + +V+     +    SL   I +   +     D + 
Sbjct: 132 MMAEKKRE-KEPTVQEIAAVLEVPKEDVVFALDAIQDPVSLFEPIYNDGGDPIFVMDQIS 190

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            + +     + E          L  +M  LN RE+ I   R  Q    T   ++ E  +S
Sbjct: 191 DERNKDINWVEEIA--------LKEAMVRLNDREKTILNMRFFQG--KTQMEVAEEIGIS 240

Query: 266 RERVRQIEARAFKKVQESIQK 286
           + +V ++E  A +++ + I+ 
Sbjct: 241 QAQVSRLEKGAIQQMNKHIES 261


>gi|330874700|gb|EGH08849.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv.
           morsprunorum str. M302280PT]
          Length = 202

 Score =  169 bits (428), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 75/184 (40%), Positives = 112/184 (60%), Gaps = 5/184 (2%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+H +  IP+L  + E  LA+      DL AA ++V +HLR VV IA  Y GYGL 
Sbjct: 16  NLEAYVHTVNSIPLLTPERERELAESLYYEQDLDAARQMVLAHLRFVVHIARSYSGYGLA 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++++ EGN+GLM+AVK+F+PE G RL ++++ WIKA + E+ILR+W +VK+ TT  Q++
Sbjct: 76  QADLIQEGNVGLMKAVKRFNPEMGVRLVSFAVHWIKAEIHEFILRNWRIVKVATTKAQRK 135

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           LFFNLR  K  L  + +     ++V  +A+ L V   EV  M  RL G +        +D
Sbjct: 136 LFFNLRSQKKRLAWLNN-----DEVHRVAESLGVEPREVREMESRLTGHDMAFDPAAEAD 190

Query: 195 KNSS 198
            +S+
Sbjct: 191 DDSA 194


>gi|15639996|ref|NP_219449.1| RNA polymerase sigma-43 factor (sigA) [Treponema pallidum subsp.
           pallidum str. Nichols]
 gi|189026235|ref|YP_001934007.1| RNA polymerase sigma-43 factor [Treponema pallidum subsp. pallidum
           SS14]
 gi|3323340|gb|AAC65963.1| RNA polymerase sigma-43 factor (sigA) [Treponema pallidum subsp.
           pallidum str. Nichols]
 gi|189018810|gb|ACD71428.1| RNA polymerase sigma-43 factor [Treponema pallidum subsp. pallidum
           SS14]
          Length = 311

 Score =  169 bits (428), Expect = 5e-40,   Method: Composition-based stats.
 Identities = 62/293 (21%), Positives = 131/293 (44%), Gaps = 23/293 (7%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E  L+ Y++++++IP++  ++E          GD  A + LV +++R V+ +A  YR  G
Sbjct: 25  ENTLTAYLNDLKRIPLMN-EKEEYACACAAYAGDAQAKNALVRANVRFVISVARHYRTCG 83

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP+++++SEGNIGL+ A ++F+P RG R  +Y+  WI+ ++ + +     ++++  +   
Sbjct: 84  LPLADLISEGNIGLLTAAERFNPARGCRFISYAACWIRQSILKALNEKARIIRLPVS--- 140

Query: 133 KRLFFNLRRLKGHLQAI------------TDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
                 +R  K   + I            T    +  +  A   +   +  EV   +  L
Sbjct: 141 -----RIRAAKSTYEYIPPVTSVNVGISKTQGGNRYGKRRATMCRAVPTVEEVHIWHTPL 195

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           + D  L A  +  +              D       E       +  + + + +L  R+ 
Sbjct: 196 SLDAPLGASGSRGESGDVDGLRIGDCVPDDLYAQPEEHMLACALQADIAKILRLLPARDA 255

Query: 241 RIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           ++   R         +L+ +   F++++ERVRQIE +A  +++   ++    S
Sbjct: 256 QVIRYRFGLGGYERRSLQEIGEIFQITKERVRQIEKKALLRIRSCARQHRLDS 308


>gi|297737220|emb|CBI26421.3| unnamed protein product [Vitis vinifera]
          Length = 555

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 57/240 (23%), Positives = 117/240 (48%), Gaps = 8/240 (3%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  S++RLV+ IA  Y   G  ++++V  G IGL++ ++KFD  +GF+++TY  WW
Sbjct: 312 AREKLAMSNVRLVMSIAQRYDNMGAEMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 371

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   ++ +   +++ +  +++       +++   + IT        +  IA+ LN+
Sbjct: 372 IRQGVSRALVENSRTLRLPSHLHERLSLIRNAKIRLEEKGIT------PSIDRIAECLNM 425

Query: 169 SESEVISMNCRLAGDESLN-ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           S+ +V +    ++   SL+     S +    +     + D   +       +E   +  +
Sbjct: 426 SQKKVRNATEAISKVFSLDREAFPSLNGLPGETLHSYIADVRLENNPWHGVDEWALKDEV 485

Query: 228 LTRSMSVLNPRERRIFEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                + L  RER I       +N  +T E++S    +SRERVRQ+   A +K++ + +K
Sbjct: 486 NKLINTTLGERERDIIRLYYGLDNECLTWEDISKRIGLSRERVRQVGLVALEKLKNAARK 545


>gi|296332278|ref|ZP_06874740.1| sporulation sigma factor SigF [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|305674979|ref|YP_003866651.1| sporulation sigma factor SigmaF [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|296150592|gb|EFG91479.1| sporulation sigma factor SigF [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|305413223|gb|ADM38342.1| sporulation sigma factor SigmaF [Bacillus subtilis subsp.
           spizizenii str. W23]
          Length = 255

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 57/258 (22%), Positives = 109/258 (42%), Gaps = 19/258 (7%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K   L+  E   L K+  ++GD  A   L+  ++RLV  +   +   G    ++   G 
Sbjct: 9   GKNAQLKDHEVKELIKQ-SQNGDQQARDLLIEKNMRLVWSVVQRFLNRGYEPDDLFQIGC 67

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL+++V KFD     R +TY++  I   +Q +I      VK+  +   K L   +RR K
Sbjct: 68  IGLLKSVDKFDLTYDVRFSTYAVPMIIGEIQRFIRDDG-TVKVSRSL--KELGNKIRRAK 124

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L        +   V  IA  L +   +V+     +    S++  +  +D +     D 
Sbjct: 125 DELSKTLG---RVPTVQEIADHLEIEAEDVVLAQEAVRAPSSIHETVYENDGDPITLLDQ 181

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  +           EE+   +  L  ++S L  RE+ I   R  ++   T   ++    
Sbjct: 182 IADN----------SEEKWFDKIALKEAISDLEEREKLIVYLRYYKDQ--TQSEVAERLG 229

Query: 264 VSRERVRQIEARAFKKVQ 281
           +S+ +V ++E +  K+++
Sbjct: 230 ISQVQVSRLEKKILKQIK 247


>gi|224146103|ref|XP_002325882.1| predicted protein [Populus trichocarpa]
 gi|222862757|gb|EEF00264.1| predicted protein [Populus trichocarpa]
          Length = 509

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 54/240 (22%), Positives = 114/240 (47%), Gaps = 8/240 (3%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  S++RLV+ IA  Y   G  ++++V  G IGL++ ++KFD  +GF+++TY  WW
Sbjct: 266 AREKLAMSNVRLVMSIAQKYDNMGAEMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 325

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   ++ +   +++    +++       +++       +       +  IA+ LN+
Sbjct: 326 IRQGVSRALVDNSRTLRLPNHLHERLGLIRNAKIR------LEEKGVTPSIDRIAESLNM 379

Query: 169 SESEVISMNCRLAGDESLN-ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           S+ +V +    ++   SL+     S +    +     + D+  +       +E   +  +
Sbjct: 380 SQRKVRNATEAISKVFSLDREAFPSLNGLPGETHHSYIADNRPENNPWHGVDEWALKEEV 439

Query: 228 LTRSMSVLNPRERRIFEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                S L  RE+ I       +   +T E++S    +SRERVRQ+   A +K++ + +K
Sbjct: 440 NKLIDSTLQEREKEIIRLYHGLDQECLTWEDISKRMGLSRERVRQVGLVALEKLKHAARK 499


>gi|269968333|ref|ZP_06182353.1| conserved hypothetical protein [Vibrio alginolyticus 40B]
 gi|269827051|gb|EEZ81365.1| conserved hypothetical protein [Vibrio alginolyticus 40B]
          Length = 296

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 67/280 (23%), Positives = 131/280 (46%), Gaps = 19/280 (6%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           G+   + Y+ +I  I +L ++EE   AK     GD  A   L+ S+LRLVVKIA GY   
Sbjct: 25  GKDPYAHYLKDIVGIDLLSREEELHYAK-LNRVGDEEAREMLIESNLRLVVKIAKGYLKR 83

Query: 72  ---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
                 + +++ EGNIGL++AV KFDPE G+R +TY++WWI+  ++  ++ +   V++  
Sbjct: 84  PGNNFTLLDLIEEGNIGLIKAVDKFDPEPGYRFSTYAVWWIRENIEAALMNNGRTVRLPA 143

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
              ++     L++L       + +  K   +  +++   V    +  +        +L+ 
Sbjct: 144 HVCKEINSLALKKL-----DASKSESKELSISELSRCSGVKAERIDEL-------VALSG 191

Query: 189 LINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
            I+ S         +++   + +      +  E +     +   +  L  + +++   R 
Sbjct: 192 FIDVSTTADLHRVPFVLELCESEYTPDPQQDCENQCFTQAIENIIKTLPIKLQKVLIHRF 251

Query: 248 LQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              +    TL  +     VS ERVRQ++  A ++VQ+ ++
Sbjct: 252 GLFDQRVKTLSEIGLLLNVSNERVRQMQIEAVERVQKRLR 291


>gi|11762220|gb|AAG40388.1|AF325036_1 At1g64860 [Arabidopsis thaliana]
          Length = 502

 Score =  169 bits (428), Expect = 6e-40,   Method: Composition-based stats.
 Identities = 58/240 (24%), Positives = 116/240 (48%), Gaps = 8/240 (3%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  S++RLV+ IA  Y   G  +S++V  G IGL++ ++KFD  +GFR++TY  WW
Sbjct: 259 AREKLAMSNVRLVMSIAQRYNNLGAEMSDLVQGGLIGLLRGIEKFDSSKGFRISTYVYWW 318

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   ++ +   +++ T  +++       +L+   + IT        +  IA+ LN+
Sbjct: 319 IRQGVSRALVDNSRTLRLPTHLHERLGLIRNAKLRLQEKGIT------PSIDRIAESLNM 372

Query: 169 SESEVISMNCRLAGDESLN-ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           S+ +V +    ++   SL+     S +    +     + D   +       ++   +  +
Sbjct: 373 SQKKVRNATEAVSKVFSLDRDAFPSLNGLPGETHHSYIADTRLENNPWHGYDDLALKEEV 432

Query: 228 LTRSMSVLNPRERRIFEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                + L  RE+ I       +   +T E++S    +SRERVRQ+   A +K++ + +K
Sbjct: 433 SKLISATLGEREKEIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 492


>gi|225568653|ref|ZP_03777678.1| hypothetical protein CLOHYLEM_04731 [Clostridium hylemonae DSM
           15053]
 gi|225162581|gb|EEG75200.1| hypothetical protein CLOHYLEM_04731 [Clostridium hylemonae DSM
           15053]
          Length = 259

 Score =  168 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 52/261 (19%), Positives = 118/261 (45%), Gaps = 17/261 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+++E+  L  R +  GD  A    +  +LRLV+ +   + G      ++   G I
Sbjct: 15  KLPILKEEEKEALFARIK-AGDEEAKEEYIKGNLRLVLSVIKRFGGSNENPDDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  F+ E   + +TY++  I   ++ Y+  + S +++      + L     +   
Sbjct: 74  GLIKAINNFNTELDVKFSTYAVPMIIGEIRRYMRDNNS-IRVS-----RSLRDTAYKAIY 127

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             +     NLK   V  IA+++ +S+ +++     +    SL   + +   ++    D +
Sbjct: 128 AKENYVKRNLKEPTVQEIAEEIGISKEDIVFALDAIQVPMSLQEPVYNDGGDALYVMDQI 187

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               + +E+ + +          L  +M  L  RER I + R       T   ++ E  +
Sbjct: 188 SDTKNKEEKWVEDLS--------LEAAMEHLGERERYIIKLRFF--EGKTQMEVAEEINI 237

Query: 265 SRERVRQIEARAFKKVQESIQ 285
           S+ +V ++E  A + +++ ++
Sbjct: 238 SQAQVSRLEKNALRVMKQYLE 258


>gi|153811113|ref|ZP_01963781.1| hypothetical protein RUMOBE_01504 [Ruminococcus obeum ATCC 29174]
 gi|149833001|gb|EDM88084.1| hypothetical protein RUMOBE_01504 [Ruminococcus obeum ATCC 29174]
          Length = 259

 Score =  168 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 52/261 (19%), Positives = 113/261 (43%), Gaps = 17/261 (6%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L+  E+  L ++ ++ GD  A  + +  +LRLV+ +   ++       ++   G IG
Sbjct: 16  LPILKSDEKEALFQKIKK-GDSEAREQYIKGNLRLVLSVIKRFQNSNENADDLFQIGCIG 74

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           LM+AV  FD     + +TY++  I   ++ Y+    S +++  +           +    
Sbjct: 75  LMKAVDNFDDTLNVKFSTYAVPMIIGEIRRYLRDYNS-IRVSRSLRDIAYKAIYTK---- 129

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            + +   NLK   +  IA ++ + +  ++     +    SL   + S +   + +    +
Sbjct: 130 -ENMIKKNLKEPTIDEIADEIGIEKEMIVYALDAIQSPVSLFEPVYS-EGGDTLYVMDQI 187

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            D   +E   +E          L  +M+ LN RE+ I E R       T   ++ E  +S
Sbjct: 188 SDQKNKEDHWLENLS-------LREAMNRLNQREKHIIEMRFY--EGRTQMEVADEIGIS 238

Query: 266 RERVRQIEARAFKKVQESIQK 286
           + +V ++E  A K ++  ++ 
Sbjct: 239 QAQVSRLEKNALKTMKNYLRS 259


>gi|291545415|emb|CBL18523.1| RNA polymerase, sigma subunit, RpsG/SigG [Ruminococcus sp. SR1/5]
          Length = 259

 Score =  168 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 49/260 (18%), Positives = 112/260 (43%), Gaps = 17/260 (6%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L+++E+  L KR +  GD  A    +  +LRLV+ +   ++       ++   G IG
Sbjct: 16  LPVLDQEEKAELFKRIK-AGDEEARELYIKGNLRLVLSVIRRFQNSSENPDDLFQIGCIG 74

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A+  FD     + +TY++  I   ++ Y+  + S +++  +           R    
Sbjct: 75  LIKAIDNFDTTLQVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRDIAYKTIYTR---- 129

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            +     +LK   +  IA ++ + +  ++     +    SL   + S   ++    D + 
Sbjct: 130 -ENYMRQHLKEPTIAEIADEIGIDKEMIVYAMDAIQSPVSLFEPVYSEGGDTLYVMDQIS 188

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
              + +E  + +          L  +M+ L  RER I + R       T   ++ E  +S
Sbjct: 189 DKKNLEENWVED--------ISLRDAMNRLGERERHIIDLRFY--EGKTQMEVADEIGIS 238

Query: 266 RERVRQIEARAFKKVQESIQ 285
           + +V ++E  A + ++  ++
Sbjct: 239 QAQVSRLEKHALRSMRNYLR 258


>gi|126650128|ref|ZP_01722361.1| sporulation sigma factor SigF [Bacillus sp. B14905]
 gi|126593300|gb|EAZ87262.1| sporulation sigma factor SigF [Bacillus sp. B14905]
          Length = 263

 Score =  168 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 54/257 (21%), Positives = 113/257 (43%), Gaps = 19/257 (7%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           +L ++E   L  R ++ GD  A  R+V  + RLV  I   +   G+ + ++   G IGLM
Sbjct: 11  LLSQEEMRDLIARAQK-GDHEARKRMVEGNTRLVWSIVQRFTTRGVELEDLFQIGCIGLM 69

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           ++V KFD     + +TY++  I   +Q ++     +VK+  +  +        +++    
Sbjct: 70  KSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-MVKVSRSIRELNF-----KIRHATD 123

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                N  P  +  +A+ L V+  E+++ +  L    SL+  +  S+ +S    D +  +
Sbjct: 124 EFIKKNEHPPTIQELAQVLGVTTEEIVTASDALRDPASLHEQLYESEGDSITLMDQMKDE 183

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
              Q    I           L   ++ L PRE+ I   R   +   T   +++   +S+ 
Sbjct: 184 KSEQPFDYIP----------LKEVLTRLEPREQSIIYLRYFSD--CTQTEIANRLGISQV 231

Query: 268 RVRQIEARAFKKVQESI 284
           +V ++E +   +++  +
Sbjct: 232 QVSRLEKKILAQLKSWM 248


>gi|294501135|ref|YP_003564835.1| RNA polymerase sigma-F factor [Bacillus megaterium QM B1551]
 gi|295706482|ref|YP_003599557.1| RNA polymerase sigma-F factor [Bacillus megaterium DSM 319]
 gi|464690|sp|P35145|RPSF_BACME RecName: Full=RNA polymerase sigma-F factor; AltName:
           Full=Sporulation sigma factor; AltName: Full=Stage II
           sporulation protein AC
 gi|39654|emb|CAA45288.1| spoIIAC [Bacillus megaterium]
 gi|294351072|gb|ADE71401.1| RNA polymerase sigma-F factor [Bacillus megaterium QM B1551]
 gi|294804141|gb|ADF41207.1| RNA polymerase sigma-F factor [Bacillus megaterium DSM 319]
 gi|383708|prf||1904152C spoIIAC gene
          Length = 253

 Score =  168 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 53/258 (20%), Positives = 111/258 (43%), Gaps = 19/258 (7%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L+  E   L KR  + GD  A   +V  ++RLV  +   +   G    ++   G IGL
Sbjct: 12  PYLKDHEVKDLIKR-SQQGDQIARDTIVQKNMRLVWSVVQRFINRGYEPDDLFQIGCIGL 70

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           +++V KFD     + +TY++  I   +Q +I      VK+  +   K +   +R+ K  L
Sbjct: 71  LKSVDKFDLSYDVKFSTYAVPMIIGEIQRFIRDDG-TVKVSRSL--KEMSNKIRKAKDEL 127

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
             +     +   V  +A+ L+++  EV+          S++  +  +D +     D +  
Sbjct: 128 SKLLG---RVPTVAEVAEHLDLTPEEVVLAQEANRAPSSIHETVYENDGDPITLLDQIAD 184

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
                       E +   +  L  ++  L+ RE+ I   R  ++   T   +++   +S+
Sbjct: 185 ----------HTEAKWFDKIALKEAIEELDEREKLIVYLRYYKDQ--TQSEVAARLGISQ 232

Query: 267 ERVRQIEARAFKKVQESI 284
            +V ++E +  K+++  +
Sbjct: 233 VQVSRLEKKILKQMKLHM 250


>gi|212638845|ref|YP_002315365.1| sporulation sigma factor SigF [Anoxybacillus flavithermus WK1]
 gi|212560325|gb|ACJ33380.1| Stage II sporulation protein AC, DNA-directed RNA polymerase
           sporulation-specific sigma factor (sigma-F)
           [Anoxybacillus flavithermus WK1]
          Length = 247

 Score =  168 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 54/254 (21%), Positives = 112/254 (44%), Gaps = 20/254 (7%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           E   L +R  + GD  A   ++  ++RLV  +   +   G    ++   G IGLM++V K
Sbjct: 14  EIKELIRR-SQQGDQQARDEIIEKNMRLVWSVVQRFLNRGYEPEDLFQIGCIGLMKSVDK 72

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD     + +TY++  I   +Q +I    S VK+  +   K +   +R+ K  L   +  
Sbjct: 73  FDLSYDVKFSTYAVPMILGEIQRFIRDDGS-VKVSRSL--KEIGNKIRKAKDEL---SKQ 126

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           N +   V  IA+ L +S  +V+     +    S++  +  +D +     D +  + D   
Sbjct: 127 NGRVPTVNEIAQFLQISPEDVVLAQEAVRSPTSIHETVYENDGDPITLLDQIADEQDVWF 186

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
                       +  L ++M  L+ RER I   R  ++   T   +++   +S+ +V ++
Sbjct: 187 D-----------KIALKKAMEELDERERLIVYLRYYKDQ--TQSEVAARLGISQVQVSRL 233

Query: 273 EARAFKKVQESIQK 286
           E +  ++++  + +
Sbjct: 234 EKKILQQMKARMDE 247


>gi|2398851|dbj|BAA22214.1| plastid RNA polymerase sigma-subunit [Arabidopsis thaliana]
          Length = 502

 Score =  168 bits (427), Expect = 7e-40,   Method: Composition-based stats.
 Identities = 58/240 (24%), Positives = 116/240 (48%), Gaps = 8/240 (3%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  S++RLV+ IA  Y   G  +S++V  G IGL++ ++KFD  +GFR++TY  WW
Sbjct: 259 AREKLAMSNVRLVMSIAQRYDNLGAEMSDLVQGGLIGLLRGIEKFDSSKGFRISTYVYWW 318

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   ++ +   +++ T  +++       +L+   + IT        +  IA+ LN+
Sbjct: 319 IRQGVSRALVDNSRTLRLPTHLHERLGLIRNAKLRLQEKGIT------PSIDRIAESLNM 372

Query: 169 SESEVISMNCRLAGDESLN-ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           S+ +V +    ++   SL+     S +    +     + D   +       ++   +  +
Sbjct: 373 SQKKVRNATEAVSKVFSLDRDAFPSLNGLPGETHHSYIADTRLENNPWHGYDDLALKEEV 432

Query: 228 LTRSMSVLNPRERRIFEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                + L  RE+ I       +   +T E++S    +SRERVRQ+   A +K++ + +K
Sbjct: 433 SKLISATLGEREKEIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 492


>gi|331028036|ref|YP_004421751.1| group 2 RNA polymerase sigma factor [Synechococcus phage S-CBS3]
 gi|294805649|gb|ADF42487.1| group 2 RNA polymerase sigma factor [Synechococcus phage S-CBS3]
          Length = 299

 Score =  168 bits (427), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 67/299 (22%), Positives = 128/299 (42%), Gaps = 37/299 (12%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------EHGD---------------LSAAH 51
             ++ Y+ +I + P+L   EE   +++ +       EH D                 A  
Sbjct: 2   DPVADYLKQIGRHPLLTATEEIEYSRQIQAMLAVQAEHPDSSTHTHQQRVIIRRGQRAKE 61

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPIS--EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           R++  +LRLVV IA  Y      +   ++V +GN+GL +A + FDP RG++ +TY+ WWI
Sbjct: 62  RMIVRNLRLVVTIAKKYVKRCTSLEMLDLVQDGNMGLARATELFDPSRGYKFSTYAYWWI 121

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + ++   +     ++++    ++K +     + + ++        K   +   A  ++  
Sbjct: 122 RQSISRGLQDRDRMIRLPIHRHEKVI-----KARAYMNHQLAMTGKMPTIAECAAAVDAD 176

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             E+ +         SL+A  +  D  S       + D       L + +E    R +L 
Sbjct: 177 PHELQASLVMAQDVCSLDAKASGRDDLSP------ILDLIPDPASLHKDDEYLIEREILH 230

Query: 230 RSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            ++++L+  E+ I            VTL  L  E  VSRE +RQ   +A  KV++ I +
Sbjct: 231 DAINMLSEDEQDIVRRHNGLGGAPKVTLGQLGQERGVSREAIRQKHTKAMNKVRQQIGR 289


>gi|26665380|dbj|BAC44901.1| principal sigma factor [Chlorogloeopsis fritschii PCC 6912]
          Length = 198

 Score =  168 bits (427), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 49/209 (23%), Positives = 98/209 (46%), Gaps = 13/209 (6%)

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           +VV IA  Y   GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+   I  
Sbjct: 1   MVVSIAKKYMNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIAD 60

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
               +++        L+  + R+K   + ++    +      IA ++ ++  ++  +   
Sbjct: 61  QSRTIRLPVH-----LYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKS 115

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
                SL   I    +  S+  D++  D     +   ++  +   R  L + +  L+PRE
Sbjct: 116 AQLPISLETPI--GKEEDSRLGDFIESDG----ETPEDQVSKNLLREDLEKVLDSLSPRE 169

Query: 240 RRIFEARRLQENPV--TLENLSSEFEVSR 266
           R +   R   ++    TLE +   F V+R
Sbjct: 170 RDVLRLRYGLDDGRMKTLEEIGQIFNVTR 198


>gi|2385344|emb|CAA74896.1| sigma factorB [Arabidopsis thaliana]
          Length = 500

 Score =  168 bits (427), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 58/240 (24%), Positives = 116/240 (48%), Gaps = 8/240 (3%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  S++RLV+ IA  Y   G  +S++V  G IGL++ ++KFD  +GFR++TY  WW
Sbjct: 257 AREKLAMSNVRLVMSIAQRYDNLGAEMSDLVQGGLIGLLRGIEKFDSSKGFRISTYVYWW 316

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   ++ +   +++ T  +++       +L+   + IT        +  IA+ LN+
Sbjct: 317 IRQGVSRALVDNSRTLRLPTHLHERLGLIRNAKLRLQEKGIT------PSIDRIAESLNM 370

Query: 169 SESEVISMNCRLAGDESLN-ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           S+ +V +    ++   SL+     S +    +     + D   +       ++   +  +
Sbjct: 371 SQKKVRNATEAVSKVFSLDRDAFPSLNGLPGETHHSYIADTRLENNPWHGYDDLALKEEV 430

Query: 228 LTRSMSVLNPRERRIFEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                + L  RE+ I       +   +T E++S    +SRERVRQ+   A +K++ + +K
Sbjct: 431 SKLISATLGEREKEIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 490


>gi|297837779|ref|XP_002886771.1| RNA polymerase sigma subunit 1 [Arabidopsis lyrata subsp. lyrata]
 gi|297332612|gb|EFH63030.1| RNA polymerase sigma subunit 1 [Arabidopsis lyrata subsp. lyrata]
          Length = 503

 Score =  168 bits (427), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 59/240 (24%), Positives = 117/240 (48%), Gaps = 8/240 (3%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  S++RLV+ IA  Y   G  +S++V  G IGL++ ++KFD  +GFR++TY  WW
Sbjct: 260 AREKLAMSNVRLVMSIAQRYDNLGAEMSDLVQGGLIGLLRGIEKFDSSKGFRISTYVYWW 319

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   ++ +   +++ T  +++       +L+   + IT        +  IA+ LN+
Sbjct: 320 IRQGVSRALVDNSRTLRLPTHLHERLGLIRNAKLRLQEKGIT------PSIDRIAESLNM 373

Query: 169 SESEVISMNCRLAGDESLN-ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           S+ +V +    ++   SL+     S +    +     + D+  +       ++   +  +
Sbjct: 374 SQKKVRNATEAVSKIFSLDRDAFPSLNGLPGETHHSYIADNRVENNPWHGYDDLALKEEV 433

Query: 228 LTRSMSVLNPRERRIFEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                + L  RER I       +   +T E++S    +SRERVRQ+   A +K++ + +K
Sbjct: 434 SKLISATLGEREREIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 493


>gi|255566078|ref|XP_002524027.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
 gi|223536754|gb|EEF38395.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
          Length = 508

 Score =  168 bits (427), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 54/241 (22%), Positives = 114/241 (47%), Gaps = 8/241 (3%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  S++RLV+ IA  Y   G  ++++V  G IGL++ ++KFD  +GFR++TY  WW
Sbjct: 265 AREKLAMSNVRLVMSIAQRYDNMGAEMADLVQGGLIGLLRGIEKFDSSKGFRISTYVYWW 324

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   ++ +   +++    +++       +++       +       +  IA+ LN+
Sbjct: 325 IRQGVSRALVENSRTLRLPNHLHERLGLIRNAKIR------LEEKGVTPSIDRIAESLNI 378

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S+ +V +    ++   SL+     S               +  E       +    ++ +
Sbjct: 379 SQKKVRNATEAVSKVFSLDREAFPSLNGLPGETHHSYIADNCLENNPWHGVDDWALKDEV 438

Query: 229 TRSMS-VLNPRERRIFEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + ++  L  RE+ I       +N  +T E++S    +SRERVRQ+   A +K++ + +K
Sbjct: 439 NKLINLTLQEREQEIIRLYYGLDNESLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 498

Query: 287 Q 287
           +
Sbjct: 499 K 499


>gi|83590339|ref|YP_430348.1| sigma 28 (flagella/sporulation) [Moorella thermoacetica ATCC 39073]
 gi|83573253|gb|ABC19805.1| RNA polymerase, sigma subunit, RpoX/SigF [Moorella thermoacetica
           ATCC 39073]
          Length = 270

 Score =  168 bits (427), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 55/284 (19%), Positives = 122/284 (42%), Gaps = 19/284 (6%)

Query: 20  IHEIR--KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + E+   + P+L + E   L +R +  GD  A  RL+  +L+LV  +   +      + +
Sbjct: 3   LSEMNLPRFPLLSEAETDELLRRAK-AGDKEARERLINCNLKLVFNLVQRFEKRNYELED 61

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +   G IGL++A+ KFD     R +TY++  I   ++ ++    S VK+  +  +     
Sbjct: 62  LFQIGTIGLIKAIDKFDLSYKVRFSTYAVPMILGEIRRFLRDD-SAVKVSRSLKETAF-- 118

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
              ++    + +     +   +  IA+ L++S  E+I+    +    S++  +   D + 
Sbjct: 119 ---KVNRTREELAKKFGREPAIGEIAEALDLSREEIIAALEAVQMPSSIHDTVYQDDGDP 175

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
               D L  +   + + L         +  L   +  L  + RR+   R  Q+   T   
Sbjct: 176 IYVLDQLASEDGEEPEWL--------DKIALKEVLRQLPEKHRRVLVLRFFQD--KTQAE 225

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQKPR 301
           +++   +S+ ++ +IE +A ++++E +Q +         L   R
Sbjct: 226 VAARMGLSQVQISRIERQALQRIRELLQAEGSWDGDSVPLPGCR 269


>gi|323701302|ref|ZP_08112977.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
 gi|323533904|gb|EGB23768.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
          Length = 257

 Score =  168 bits (426), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 45/261 (17%), Positives = 111/261 (42%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L   +   L +  ++ G+  A ++L+  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLTNSQMRTLFEAMQQ-GNKEARNQLINGNLRLVLSVIQRFTNRGEYVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+A+  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 73  IGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDVAYKALQVR 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L    +   +   +  IA +L +   E++     +    SL   I     +     D 
Sbjct: 130 DSL---VNKFSREPSINEIAGELKMPREEIVFALDAIQEPISLFEPIYHDGGDPIFVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  + +     L            +  ++  L+ RE+ I   R       T   ++ E  
Sbjct: 187 ISDEKNMDLSWLEG--------ISIRDALRRLSDREKHILTLRFF--EGKTQMEVADEIG 236

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A   +++ +
Sbjct: 237 ISQAQVSRLEKAALNHMRKYV 257


>gi|15217767|ref|NP_176666.1| SIGA (SIGMA FACTOR A); DNA binding / DNA-directed RNA polymerase/
           sigma factor/ transcription factor [Arabidopsis
           thaliana]
 gi|5042421|gb|AAD38260.1|AC006193_16 RNA polymerase sigma subunit 1 [Arabidopsis thaliana]
 gi|2353171|gb|AAB69384.1| sigma factor 1 [Arabidopsis thaliana]
 gi|2443408|dbj|BAA22421.1| SigA [Arabidopsis thaliana]
 gi|2558514|emb|CAA74640.1| plastid RNA polymerase sigma factor [Arabidopsis thaliana]
 gi|5478439|dbj|BAA82448.1| sigma factor SigA [Arabidopsis thaliana]
 gi|17064900|gb|AAL32604.1| RNA polymerase sigma subunit 1 [Arabidopsis thaliana]
 gi|20259916|gb|AAM13305.1| RNA polymerase sigma subunit 1 [Arabidopsis thaliana]
 gi|222423019|dbj|BAH19492.1| AT1G64860 [Arabidopsis thaliana]
 gi|332196177|gb|AEE34298.1| sigma factor A [Arabidopsis thaliana]
          Length = 502

 Score =  168 bits (426), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 58/240 (24%), Positives = 116/240 (48%), Gaps = 8/240 (3%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  S++RLV+ IA  Y   G  +S++V  G IGL++ ++KFD  +GFR++TY  WW
Sbjct: 259 AREKLAMSNVRLVMSIAQRYDNLGAEMSDLVQGGLIGLLRGIEKFDSSKGFRISTYVYWW 318

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   ++ +   +++ T  +++       +L+   + IT        +  IA+ LN+
Sbjct: 319 IRQGVSRALVDNSRTLRLPTHLHERLGLIRNAKLRLQEKGIT------PSIDRIAESLNM 372

Query: 169 SESEVISMNCRLAGDESLN-ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           S+ +V +    ++   SL+     S +    +     + D   +       ++   +  +
Sbjct: 373 SQKKVRNATEAVSKVFSLDRDAFPSLNGLPGETHHSYIADTRLENNPWHGYDDLALKEEV 432

Query: 228 LTRSMSVLNPRERRIFEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                + L  RE+ I       +   +T E++S    +SRERVRQ+   A +K++ + +K
Sbjct: 433 SKLISATLGEREKEIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 492


>gi|296133647|ref|YP_003640894.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           sp. JR]
 gi|296032225|gb|ADG82993.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           potens JR]
          Length = 257

 Score =  168 bits (426), Expect = 8e-40,   Method: Composition-based stats.
 Identities = 51/261 (19%), Positives = 113/261 (43%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L   E   + ++ +  GD SA  +L+  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLSSSEMRKIFEQMQ-AGDKSARTKLINGNLRLVLSVIQRFTNRGEYVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+A+  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 73  IGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDVAYKALQVR 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
               A+ +   +   +  IA +L +   EV+     +    SL   I     +     D 
Sbjct: 130 D---ALVNKYSREPSINEIASELKMPREEVVFALDAIQEPISLFEPIYHDGGDPIYVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  + +     L            +  +M  LN RE+ I   R       T   ++ E  
Sbjct: 187 IGDEKNLDGNWLEG--------ISVREAMRKLNEREKLILTLRFF--EGKTQMEVAEEIG 236

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A K +++ +
Sbjct: 237 ISQAQVSRLEKAALKHMRKYM 257


>gi|291529642|emb|CBK95228.1| RNA polymerase sigma factor, sigma-70 family [Eubacterium rectale
           M104/1]
          Length = 340

 Score =  168 bits (426), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 73/294 (24%), Positives = 131/294 (44%), Gaps = 29/294 (9%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRL----VTSHLRLVVKIAMGYR 69
             LS Y++E+ K     ++EE  + K   E        +L     + ++RLVV +A  Y 
Sbjct: 42  DPLSMYMYEMSKWQPFTEEEEKQVFKELSETESEDKKKQLKDEIFSRNIRLVVYVAKRYY 101

Query: 70  GYGLPIS--EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
                +   +++ E ++GL++A+ ++D   G++ +TY+ WWI  A    I     L++  
Sbjct: 102 KNLKHMEPIDLIDEASLGLLKAIDRYDYTTGYKFSTYAYWWINQACTRSIANDNDLIRQP 161

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              ++      +++ +       DNN     V  IAK+LNVSE +V ++   +    +  
Sbjct: 162 VHIHE--FIIKVKKAQRKWGQTHDNN---APVDYIAKELNVSEEKVRNILIIIDCQSNYI 216

Query: 188 ALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMS------------ 233
           +L  +  K S +  D  V +   D +  V  EK E    +N +   +S            
Sbjct: 217 SLDCTMSKGSEEPGDTEVGEIVLDPKGNVDFEKVEVNQFQNRIIEILSKANNKTSAKSNR 276

Query: 234 --VLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQES 283
                 R   + + R   +N    TLE ++  + VSRER+RQIEA+A K ++  
Sbjct: 277 SVEQTKRMIDVIKRRFGFDNCRIETLEEIAQSYGVSRERIRQIEAQALKILRNP 330


>gi|188587460|ref|YP_001919005.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|179352147|gb|ACB86417.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 273

 Score =  168 bits (426), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 57/264 (21%), Positives = 120/264 (45%), Gaps = 17/264 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P++  +E   L +R  E GD  A   L+  +LRLV+ +   ++  G  + ++   G +
Sbjct: 15  KLPVISSEETQKLFERL-EQGDEQAKQELINGNLRLVLSVINKFKNRGENLDDLFQVGCL 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++AV  FDP++G + +TY++  I   ++ Y+     + ++  +   K L     + K 
Sbjct: 74  GLVKAVDNFDPKQGVKFSTYAVPMIMGEIKRYLRDDSPM-RVSRSL--KLLGQEAAKAKE 130

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L+           +  +A +LN+S  E++      +   SL   + S   +     D +
Sbjct: 131 KLRK---EKPYEPTIEELASELNISREELVEALNSSSEPLSLYDPVYSDSTDPVLLVDQI 187

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             +         E+ E       L  +++ L  R+R I   R  +    T   +S E  +
Sbjct: 188 KDEE--------ERLENWVENMTLKEAIAKLPERQRNIVNRRFFKGQ--TQVEVSDELNI 237

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+ +V ++E  A  ++++ ++++V
Sbjct: 238 SQAQVSRLEKSALLQLRKLVKEEV 261


>gi|295399044|ref|ZP_06809026.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|312110351|ref|YP_003988667.1| RNA polymerase, sigma 28 subunit, SigF [Geobacillus sp. Y4.1MC1]
 gi|294978510|gb|EFG54106.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|311215452|gb|ADP74056.1| RNA polymerase, sigma 28 subunit, SigF [Geobacillus sp. Y4.1MC1]
          Length = 250

 Score =  168 bits (426), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 51/257 (19%), Positives = 112/257 (43%), Gaps = 19/257 (7%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           +L+  E   L +R +E GD  A + ++  ++RLV  +   +   G    ++   G IGL+
Sbjct: 11  LLKDHEMKKLIRRSQE-GDQQARNEIIQKNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLL 69

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           ++V KFD     + +TY++  I   +Q +I      VK+  +  +        +++    
Sbjct: 70  KSVDKFDLSYDVKFSTYAVPMIIGEIQRFIRDDG-TVKVSRSLKE-----TGNKIRKARD 123

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
            ++  + +   V  IA  L +S  EV+     +    S++  +  +D +     D +   
Sbjct: 124 ELSKKHGRAPTVTEIADYLEISPEEVVLAQEAVRSPASIHETVYENDGDPITLLDQIAD- 182

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
                      E     +  L +++  L+ RER I   R  ++   T   ++S   +S+ 
Sbjct: 183 ---------ADEASWFDKIALKKAIEELDERERLIVYLRYYKDQ--TQSEVASRLGISQV 231

Query: 268 RVRQIEARAFKKVQESI 284
           +V ++E +  ++++E +
Sbjct: 232 QVSRLEKKILQQIKERM 248


>gi|239827600|ref|YP_002950224.1| sporulation sigma factor SigF [Geobacillus sp. WCH70]
 gi|239807893|gb|ACS24958.1| RNA polymerase, sigma 28 subunit, SigF [Geobacillus sp. WCH70]
          Length = 250

 Score =  168 bits (426), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 54/253 (21%), Positives = 110/253 (43%), Gaps = 19/253 (7%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           QE   L +R +E GD  A   ++  ++RLV  +   +   G    ++   G IGL+++V 
Sbjct: 15  QEMKELIRRSQE-GDQEARDEIIEKNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLKSVD 73

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD     + +TY++  I   +Q +I      VK+  +   K +   +R+ K  L   + 
Sbjct: 74  KFDLSYDVKFSTYAVPMIIGEIQRFIRDDG-TVKVSRSL--KEMGNKIRKAKDEL---SK 127

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +   V  IA  L +S  +V+     +    S++  +  +D +     D +       
Sbjct: 128 KQGRAPTVTEIADYLEISPEDVVLAQEAIRSPASIHETVYENDGDPITLLDQIADSD--- 184

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
                  E     +  L +++  L+ RER I   R  ++   T   ++S   +S+ +V +
Sbjct: 185 -------EVSWFDKIALKKAIEELDERERLIVYLRYYKDQ--TQSEVASRLGISQVQVSR 235

Query: 272 IEARAFKKVQESI 284
           +E +  ++++E +
Sbjct: 236 LEKKILQQIKERM 248


>gi|332653369|ref|ZP_08419114.1| RNA polymerase sigma-G factor [Ruminococcaceae bacterium D16]
 gi|332518515|gb|EGJ48118.1| RNA polymerase sigma-G factor [Ruminococcaceae bacterium D16]
          Length = 256

 Score =  168 bits (426), Expect = 9e-40,   Method: Composition-based stats.
 Identities = 56/260 (21%), Positives = 115/260 (44%), Gaps = 17/260 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+ +L+ +E   L +R +E GD  A   L+  +LRLV+ +   +   G  + ++   G I
Sbjct: 14  KLKVLKNEETQALLRRAKE-GDKQAREELIAGNLRLVLSVIHKFANRGENVDDLFQVGCI 72

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD     + +TY +  I   ++ Y+  + ++     +   +   + + + K 
Sbjct: 73  GLIKAIDNFDTSLDVKFSTYGVPMIVGEIRRYLRDNSAMR---VSRAMRDTAYKVLQAK- 128

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             ++    + K   V  IA+ L +   EV+     +    SL   I S   ++    D +
Sbjct: 129 --ESYMAQHQKEPSVEEIAQMLGIKREEVVFALDAILDPVSLYEPIYSDSGDTVCVMDQV 186

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               +  E  L            L  ++S L+ RE++I   R  Q    T   +S E  +
Sbjct: 187 KDSRNTDEMWLE--------HIALKEAVSRLSEREQKILAMRFYQ--SKTQVEVSREIGI 236

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ +V ++E  A +++++ +
Sbjct: 237 SQAQVSRLEKNALRQIRKEL 256


>gi|293375845|ref|ZP_06622113.1| putative RNA polymerase sigma factor RpoD [Turicibacter sanguinis
           PC909]
 gi|325844994|ref|ZP_08168319.1| RNA polymerase sigma factor RpoD family protein [Turicibacter sp.
           HGF1]
 gi|292645524|gb|EFF63566.1| putative RNA polymerase sigma factor RpoD [Turicibacter sanguinis
           PC909]
 gi|325488967|gb|EGC91357.1| RNA polymerase sigma factor RpoD family protein [Turicibacter sp.
           HGF1]
          Length = 331

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 63/270 (23%), Positives = 119/270 (44%), Gaps = 20/270 (7%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL---PISEVVSEGNIGLMQAVKK 92
              K+YR   D +A   L+ ++  LV KI   Y  +        ++ S G  GLM+A++K
Sbjct: 66  EYLKKYRLENDETALEWLIFNNTNLVHKIIGRYTKFYHHKLDYDDLFSVGLEGLMKAIEK 125

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD       +TY+ +W+K A+   I      ++I        +F ++ ++  + Q   D 
Sbjct: 126 FDFTFDNNFSTYATYWVKQAVTRTIADEGFTIRIPVH-----MFESINQVMRYEQK-ADQ 179

Query: 153 NLKPEQVVAIAKKLNVSESE---VISMNCRLAGDESLNALINSSDKNS------SQWQDW 203
             +P  V  +  +L +   +   V  +   +    SLN  ++  D+++      S   + 
Sbjct: 180 EDEPVDVDNLCGELKIPIEKYEAVKRVQTYMLKPTSLNGFVSKEDEDTELQDLISNENEM 239

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSE 261
           LV           ++   ++ +  + + +  LNPRE+ +   R     E   TLE +   
Sbjct: 240 LVEGMSRIYDNPEKQAMDEDLKAYMDKMILSLNPREQFVIIHRFGLNGEEKKTLEEIGEI 299

Query: 262 FEVSRERVRQIEARAFKKVQESIQKQVELS 291
             V+RER+RQIEA+A +K++  + +  E  
Sbjct: 300 EGVTRERIRQIEAKAMRKLRTLLMRYKEYL 329


>gi|85860024|ref|YP_462226.1| RNA polymerase sigma factor [Syntrophus aciditrophicus SB]
 gi|85723115|gb|ABC78058.1| RNA polymerase sigma factor [Syntrophus aciditrophicus SB]
          Length = 580

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 56/206 (27%), Positives = 88/206 (42%), Gaps = 10/206 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A  +LV ++LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +
Sbjct: 340 EKKAEEAKRKLVEANLRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFS 399

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            L R   +L         P+    I
Sbjct: 400 TYATWWIRQAITRAIADQARTIRIPVHM--IETINKLIRTSRYLVQELGREPSPD---EI 454

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A K+     +V  +        SL   I   ++  S   D++    D +     E     
Sbjct: 455 ANKMEYPLEKVRKVLKIAKEPISLETPI--GEEEDSHLGDFI---EDKKIMSPSEATISM 509

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRL 248
           +      + +S L PRE ++   R  
Sbjct: 510 DLAEQTRKILSTLTPREEKVLRMRFG 535


>gi|291060369|gb|ADD73104.1| RNA polymerase sigma-43 factor [Treponema pallidum subsp. pallidum
           str. Chicago]
          Length = 296

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 62/293 (21%), Positives = 131/293 (44%), Gaps = 23/293 (7%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           E  L+ Y++++++IP++  ++E          GD  A + LV +++R V+ +A  YR  G
Sbjct: 10  ENTLTAYLNDLKRIPLMN-EKEEYACACAAYAGDAQAKNALVRANVRFVISVARHYRTCG 68

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           LP+++++SEGNIGL+ A ++F+P RG R  +Y+  WI+ ++ + +     ++++  +   
Sbjct: 69  LPLADLISEGNIGLLTAAERFNPARGCRFISYAACWIRQSILKALNEKARIIRLPVS--- 125

Query: 133 KRLFFNLRRLKGHLQAI------------TDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
                 +R  K   + I            T    +  +  A   +   +  EV   +  L
Sbjct: 126 -----RIRAAKSTYEYIPPVTSVNVGISKTQGGNRYGKRRATMCRAVPTVEEVHIWHTPL 180

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           + D  L A  +  +              D       E       +  + + + +L  R+ 
Sbjct: 181 SLDAPLGASGSRGESGDVDGLRIGDCVPDDLYAQPEEHMLACALQADIAKILRLLPARDA 240

Query: 241 RIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           ++   R         +L+ +   F++++ERVRQIE +A  +++   ++    S
Sbjct: 241 QVIRYRFGLGGYERRSLQEIGEIFQITKERVRQIEKKALLRIRSCARQHRLDS 293


>gi|147678180|ref|YP_001212395.1| sporulation sigma factor SigG [Pelotomaculum thermopropionicum SI]
 gi|146274277|dbj|BAF60026.1| DNA-directed RNA polymerase specialized sigma subunit
           [Pelotomaculum thermopropionicum SI]
          Length = 257

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 51/261 (19%), Positives = 114/261 (43%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L   +   L +   + GD SA  +L+  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLTGSQMKALFEAMHK-GDASARTKLINGNLRLVLSVIQRFTNRGEYVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+A+  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 73  IGLMKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDVAYKALQVR 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
               A+ +   +   +  IA +L +   E++     +    SL   I   D     +   
Sbjct: 130 D---ALVNKYSREPSINEIACELKMPREEIVFALDAIQEPISLFEPIYH-DGGDPIFVMD 185

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
            + D   Q+Q  +E          +  ++  L+ RE+ I   R       T   ++ E  
Sbjct: 186 QISDEKNQDQNWLEGI-------AIRDALRKLSDREKLILTLRFY--EGKTQMEVAEEIG 236

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A   +++ I
Sbjct: 237 ISQAQVSRLEKAALNHMKKHI 257


>gi|291522675|emb|CBK80968.1| RNA polymerase, sigma subunit, RpsG/SigG [Coprococcus catus GD/7]
          Length = 259

 Score =  168 bits (426), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 54/262 (20%), Positives = 121/262 (46%), Gaps = 17/262 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L++ E+ +L KR + H DL A  R +  +LRLV+ +   + G    ++++   G I
Sbjct: 15  KLPLLKEDEKEMLMKRIKSH-DLRARERFINGNLRLVLSVIQRFSGTNENVNDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD  +G R +TY++  I   ++ ++  + S +++  +           R   
Sbjct: 74  GLIKAIDNFDLTQGVRFSTYAVPMIVGEIRRFLRDN-SAIRVSRSLRDTAYKAIYAR--- 129

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             +A+   N +   V+ IA++  + + +++     +    SL   + +   ++    D +
Sbjct: 130 --EALITRNNREPTVMEIAEETGIPKEDIVFALDAIQSPMSLYEPVYTDGGDALCIMDQV 187

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               +G+   +            L  +M  L+ RE RI + R       T   ++ E  +
Sbjct: 188 SDRKNGENSWVENLA--------LNDAMKRLSHRENRIIKMRFY--EGKTQMEVADELAI 237

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+ ++ +IE  A + ++  ++ 
Sbjct: 238 SQAQISRIEKSALQNMRTYLRA 259


>gi|158833963|gb|ABW81787.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
          Length = 225

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 66/229 (28%), Positives = 120/229 (52%), Gaps = 11/229 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD S+  R++ S+LRLVVKI+  Y   GLP+ ++
Sbjct: 8   YLGEIGYSPLLTAEEEIYFARRVL-CGDESSRRRMIESNLRLVVKISRRYINRGLPLLDL 66

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 67  IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 125

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +  L    D++  PE++     K     S ++ +N R++   S++    ++ +   
Sbjct: 126 LRAAR-ELSHKLDHDPSPEEIAEQLNKPVDYVSRMLRLNERIS---SVDTSFGNAAEKG- 180

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
              D L  + D   +   + +   + +  + + +  L+ ++R +   R 
Sbjct: 181 -LLDVLSDETDSDPENTTQND---DMKKSVVKWLFELSTKQREVLARRF 225


>gi|158312828|ref|YP_001505336.1| FliA/WhiG family RNA polymerase sigma factor [Frankia sp. EAN1pec]
 gi|158108233|gb|ABW10430.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Frankia sp.
           EAN1pec]
          Length = 376

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 59/246 (23%), Positives = 105/246 (42%), Gaps = 21/246 (8%)

Query: 44  HGDLS---AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
            GD        +LV  HL LV  +A  +R  G P+ ++V    IGL+++V +FDPERG  
Sbjct: 143 EGDPERAALRDQLVRMHLPLVEYLARRFRNRGEPLDDLVQVATIGLIKSVDRFDPERGVE 202

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+   I   ++ +       +++     + +L      L      ++ +  +   V 
Sbjct: 203 FSTYATPTIVGEIKRHFRDKGWAIRVPRRLQELKLS-----LTKATSELSQSLGRSPTVS 257

Query: 161 AIAKKLNVSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            IA+ L +SE EV+    +       SL+A  +  D+  +      V D         E 
Sbjct: 258 EIARHLEMSEEEVLEGLESANAYSAVSLDAPDSGDDEAPAVADTLGVQD---------ES 308

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
            E    R  L   +  L PRE+RI   R      +T   +++E  +S+  V ++ AR   
Sbjct: 309 LEGVEYRESLKPLLEKLPPREKRILLLRFFGN--MTQSQIANELGISQMHVSRLLARTLA 366

Query: 279 KVQESI 284
           +++  +
Sbjct: 367 QLRRGL 372


>gi|312194695|ref|YP_004014756.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Frankia sp.
           EuI1c]
 gi|311226031|gb|ADP78886.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Frankia sp.
           EuI1c]
          Length = 393

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 61/257 (23%), Positives = 106/257 (41%), Gaps = 23/257 (8%)

Query: 35  YVLAKRYRE--HGDLS---AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             L  R  E   GD        +LV  HL LV  +A  +R  G P+ ++V    IGL+++
Sbjct: 149 RALFARLVELPEGDAERAAIRDQLVRMHLPLVEYLARRFRNRGEPLDDLVQVATIGLIKS 208

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V +FDPERG   +TY+   I   ++ +       +++     + +L      L      +
Sbjct: 209 VDRFDPERGVEFSTYATPTIVGEIKRHFRDKGWAIRVPRRLQELKLS-----LTKATSEL 263

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
           +    +   V  IA  L ++E EV+    +       SL+A  +  D++ +      V D
Sbjct: 264 SQKLGRSPTVAEIAAHLEMTEEEVLEGLESANAYSAVSLDAPDSGDDESPAVADTLGVQD 323

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
                    E  E    R  L   +  L PRE+RI   R      +T   ++ E  +S+ 
Sbjct: 324 ---------ESLEGVEYRESLKPLLEKLPPREKRILLLRFFGN--MTQSQIAIELGISQM 372

Query: 268 RVRQIEARAFKKVQESI 284
            V ++ AR   +++  +
Sbjct: 373 HVSRLLARTLAQLRRGL 389


>gi|40353307|gb|AAR84417.1| essential primary sigma 70 factor [Frankia sp. ARgP5ag]
          Length = 217

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 53/202 (26%), Positives = 96/202 (47%), Gaps = 10/202 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A  +LV ++LRLVV IA  Y G G+   +++ EGN+GL++AV+KFD  +G++ +
Sbjct: 26  ERDGQIAKRKLVEANLRLVVSIAKRYVGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFS 85

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I     +      L R++  L         PE    I
Sbjct: 86  TYATWWIRQAITRAIADQARTIRIPVHMVE--TINKLIRIQRQLLQDLGREPSPE---VI 140

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           AK+++++  +V  +        SL   I   ++  S   D++    D    V ++     
Sbjct: 141 AKEMDLTPDKVREILKVSQEPVSLETPI--GEEEDSHLGDFI---EDCDAVVPVDAASFI 195

Query: 223 NRRNMLTRSMSVLNPRERRIFE 244
             +  L   +  L+ RE+++ +
Sbjct: 196 LLQEQLDSVLHTLSDREKKVIQ 217


>gi|6682871|dbj|BAA88922.1| sigma factor [Nicotiana tabacum]
          Length = 502

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 57/242 (23%), Positives = 116/242 (47%), Gaps = 12/242 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  S++RLV+ IA  Y   G  +++++  G IGL++ ++KFD  RGF+++TY  WW
Sbjct: 259 AREKLAMSNVRLVMSIAQRYDTNGTEMADLIQGGLIGLLRGIEKFDHSRGFKISTYVYWW 318

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   ++ +   +++    +++       ++K         N     +  IA+ LN+
Sbjct: 319 IRQGVSRALVENSRTLRLPIHLHERLSLIRNAKIK------LKENGITPSIEKIAECLNM 372

Query: 169 SESEVISMNCRLAGDESLN--ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           S+ +V +     +   SL+  A  + +         ++  +    E +     +    ++
Sbjct: 373 SQKKVRNATEASSKVFSLDREAFPSLNGLPGETLHSYIADNR--LENIPWHGVDEWMLKD 430

Query: 227 MLTRSM-SVLNPRERRIFEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +   + S L  RER I       +N  +T E++S    +SRERVRQ+   A +K++ + 
Sbjct: 431 EVNNLISSTLREREREIVRLYYGLDNECLTWEDISRRIGLSRERVRQVGLVALEKLKHAA 490

Query: 285 QK 286
           +K
Sbjct: 491 RK 492


>gi|281355585|ref|ZP_06242079.1| RNA polymerase, sigma 32 subunit, RpoH [Victivallis vadensis ATCC
           BAA-548]
 gi|281318465|gb|EFB02485.1| RNA polymerase, sigma 32 subunit, RpoH [Victivallis vadensis ATCC
           BAA-548]
          Length = 248

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 72/238 (30%), Positives = 122/238 (51%), Gaps = 11/238 (4%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
             L+  +LRLV KIA  + G GLP  ++VSEGN GLM A +++DP RG R +TYS WWIK
Sbjct: 16  KALIEENLRLVQKIANDFLGRGLPWEDLVSEGNRGLMTAARRYDPSRGARFSTYSAWWIK 75

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            A+++ I     +V++      +  +  +RR+   L     +    E+V   A     + 
Sbjct: 76  QAIRQAIAEQAQMVRVP--IGTQTHWRKIRRIVNELTEALGHAPSDEEVAEAANLPLATV 133

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD-HDGQEQVLIEKEERKNRRNMLT 229
           + +     R    +SLNA I+  D +  ++QD+   D     +Q LI+ E+ +N  ++L 
Sbjct: 134 NRLRG--SRQIDVQSLNAPISDGDPDGGEFQDFFQDDTEPAPDQQLIKLEDVENLLSLLE 191

Query: 230 RSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
                   RE+++   R   +     TL+ + +E   + ERVRQI+ +A +K+   ++
Sbjct: 192 TLTE----REQKVLRLRFGLDGEPIRTLDEVGTELNCTNERVRQIQNQALRKLHAQLE 245


>gi|2565297|gb|AAB81958.1| RNA polymerase sigma subunit 1 [Arabidopsis thaliana]
          Length = 502

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 58/240 (24%), Positives = 116/240 (48%), Gaps = 8/240 (3%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  S++RLV+ IA  Y   G  +S++V  G IGL++ ++KFD  +GFR++TY  WW
Sbjct: 259 AREKLAMSNVRLVMSIAQRYDNLGAEMSDLVQGGLIGLLRGIEKFDSSKGFRISTYVYWW 318

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   ++ +   +++ T  +++       +L+   + IT        +  IA+ LN+
Sbjct: 319 IRQGVSRALVDNSRTLRLPTHLHERLGLIRNAKLRLQEKGIT------PSIDRIAESLNM 372

Query: 169 SESEVISMNCRLAGDESLN-ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           S+ +V +    ++   SL+     S +    +     + D   +       ++   +  +
Sbjct: 373 SQKKVRNATEAVSKVFSLDRDAFPSLNGLPGETHHSYIADTRLENNPWHGYDDLALKEEV 432

Query: 228 LTRSMSVLNPRERRIFEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                + L  RE+ I       +   +T E++S    +SRERVRQ+   A +K++ + +K
Sbjct: 433 SKLISATLGEREKEIIRLYYGLDKECLTWEDISKRIGLSRERVRQVGLVALEKLKHAARK 492


>gi|323388685|gb|ADX60147.1| SIGMA70-like transcription factor [Zea mays]
          Length = 428

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 67/253 (26%), Positives = 120/253 (47%), Gaps = 19/253 (7%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E  L +R   HG +   +R+V S++RLV+ IA  + G G+  S+++ +G  GL++  +K
Sbjct: 173 DENTLRRRL-NHG-VYCKNRMVKSNVRLVISIAKEHEGPGMEFSDLIQDGMQGLIRGAEK 230

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ--KRLFFNLRRLKGHLQAIT 150
           FD  +GFR +TYS WWIK A+++ +L    ++++     +   R+    RRL   L+ + 
Sbjct: 231 FDASKGFRFSTYSHWWIKQAIRKSVLEQTQIIRLPAHMAEASSRVKECCRRLGRELKRL- 289

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
                      IA    ++   V +         S  + +  +D    +         D 
Sbjct: 290 ------PSNEEIAVDTGMTIRRVEAAMSLPKYSVSFTSKVGCTDVTYQEIM------PDT 337

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRER 268
             +   E   R   +  +  ++  L+PRE+++   R   E     TL ++     VSRER
Sbjct: 338 SAETAEETLHRWLMKKDVNTALDSLSPREKQVMRYRFGIEGGRARTLHDIGQLMGVSRER 397

Query: 269 VRQIEARAFKKVQ 281
           +RQIE  AF+K++
Sbjct: 398 IRQIELGAFRKLR 410


>gi|260361298|ref|ZP_05774403.1| RNA polymerase sigma-32 factor [Vibrio parahaemolyticus K5030]
 gi|308111826|gb|EFO49366.1| RNA polymerase sigma-32 factor [Vibrio parahaemolyticus K5030]
          Length = 158

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 70/156 (44%), Positives = 102/156 (65%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++   + +  +  L  YI  +   PML   EE  LA+R    G++ AA  L+ SHLR 
Sbjct: 1   MTKEAYPMALVTQDSLDSYIRSVNSYPMLTADEERELAERLHYKGEIEAAKGLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A GY GYGLP++++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           W +VKI TT  Q++LFFNLR+ K  L    +  ++ 
Sbjct: 121 WRIVKIATTKAQRKLFFNLRKSKKRLGWFNNGEVET 156


>gi|225450015|ref|XP_002272444.1| PREDICTED: hypothetical protein [Vitis vinifera]
          Length = 426

 Score =  168 bits (425), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 59/239 (24%), Positives = 122/239 (51%), Gaps = 12/239 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             +  R+  S+ RLVV IA  Y+G GL + +++ EG+IGL++  ++FDP+RG++L+TY  
Sbjct: 187 RESRERINQSYRRLVVSIAARYQGKGLSLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVY 246

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I     ++++  +     +   + ++      ++    +      IA+ +
Sbjct: 247 WWIRQAIVRAIANKSRIIRLPGS-----ICEMVAKIAEARTVLSRRLRRLPTYDEIAEFI 301

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +V+ S V  ++ R     S++  + S  +     Q+ +    +   Q +++   R+  + 
Sbjct: 302 DVNVSTVRLVSERSRTPISVDQAVTS--QGCMTLQEIIPGPDETTPQKMVK---RQLMKQ 356

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            + R+++ L  RE  I         E P++ E +    ++SRERVRQI + A  K++++
Sbjct: 357 EVERALNTLCEREAYILRLYFGINGETPLSFEEIGRLMKLSRERVRQINSIALSKLRQT 415


>gi|291454068|ref|ZP_06593458.1| RNA polymerase sigma factor [Streptomyces albus J1074]
 gi|291357017|gb|EFE83919.1| RNA polymerase sigma factor [Streptomyces albus J1074]
          Length = 365

 Score =  167 bits (424), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 58/237 (24%), Positives = 103/237 (43%), Gaps = 15/237 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              +RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDPERG   +TY+  
Sbjct: 140 ELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPERGVEFSTYATP 199

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +   ++ +       V++     + RL      L      ++  + +   V  +A+KL 
Sbjct: 200 TVVGEIKRHFRDKGWAVRVPRRLQELRLS-----LTSATAELSQRHGRSPTVHELAEKLG 254

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +SE EV+          +L+  +  +D  S    D L  +         E  E    R  
Sbjct: 255 ISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGSED--------EALEGVEYRES 306

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 307 LKPLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLREKL 361


>gi|253761922|ref|XP_002489335.1| hypothetical protein SORBIDRAFT_0010s016080 [Sorghum bicolor]
 gi|241946983|gb|EES20128.1| hypothetical protein SORBIDRAFT_0010s016080 [Sorghum bicolor]
          Length = 238

 Score =  167 bits (424), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 61/231 (26%), Positives = 112/231 (48%), Gaps = 13/231 (5%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           +VTS++RLV+ IA  + G G+ + +++ EG  GL++  +KFD  +GFR +TYS WWIK A
Sbjct: 1   MVTSNVRLVISIAREFEGPGMDLYDLIQEGMQGLIRGAEKFDASKGFRFSTYSHWWIKQA 60

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           M++ +     + ++     +        R+K   + +     +      IA    +    
Sbjct: 61  MRKSVSEQSQIFRLPAHMVEASY-----RVKECTKRLRRKLRRRPTNEEIALDTGMPIKR 115

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           V +         SL++ I S+D        +     D   +   E   R + +  + +++
Sbjct: 116 VEAAVNLPKYSVSLDSKIGSTD------MTYQEVTADPSAETAEEMLNRMSMKKDVHKAL 169

Query: 233 SVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             L  RE+++   R   E+    TL+ + +   VSRER+RQIE+ AF+K++
Sbjct: 170 DTLTTREKQVVVLRFGLEDDRIRTLQEIGNIMGVSRERIRQIESGAFRKLR 220


>gi|1621026|gb|AAB17121.1| RpoS [Yersinia enterocolitica]
          Length = 277

 Score =  167 bits (424), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 61/225 (27%), Positives = 107/225 (47%), Gaps = 11/225 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 62  YLGEIGYSPLLTAEEEVYFARR-ALRGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 120

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+ L++AV+KFDPE GFR +TYS WWI+  ++  I+     +++        +   
Sbjct: 121 IEEGNLCLIRAVEKFDPEPGFRFSTYSHWWIRQTIERAIMNQTRTIRLPIH-----IVKE 175

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L    G  + ++           IA++LN    +V  M        S++  +    + S 
Sbjct: 176 LNVYFGTARELSHKLDHEPSAEEIAEQLNKPVDDVSRMLRLNERITSVDTPLGGDSEKS- 234

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
                L    D  E    +  +  + +  + + +  LN ++R + 
Sbjct: 235 ----LLDILSDENENGPEDTTQDDDMKQSIVKWLFELNAKQREVL 275


>gi|303232785|ref|ZP_07319470.1| putative RNA polymerase sigma-B factor [Atopobium vaginae
           PB189-T1-4]
 gi|302481271|gb|EFL44346.1| putative RNA polymerase sigma-B factor [Atopobium vaginae
           PB189-T1-4]
          Length = 287

 Score =  167 bits (424), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 56/257 (21%), Positives = 115/257 (44%), Gaps = 15/257 (5%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           +KQ    L  +++ HGD  A ++LV +HL L   +A  ++  G  + +++    IGL++A
Sbjct: 40  DKQRTRELFIKFKRHGDEEARNQLVLNHLNLARFLASKFKNRGESLDDLIQVATIGLIKA 99

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +FD +RG    T++   I   ++ +       V++      +RL     ++      +
Sbjct: 100 IDRFDIDRGLEFTTFATPTILGEIKRHFRDRSWSVRVP-----RRLQELSSKVSQATDML 154

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVYD 207
           T+       V  IA++L+VS  EV+      R     SL+     +D  S+       Y 
Sbjct: 155 TEKLQHSPSVEEIARELDVSVDEVLEAMESSRAYSSVSLDVPTVDNDDGSAATSVLDTY- 213

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
                  + +  E  + + +L   +     RE++I   R L  + +T   ++ + +VS+ 
Sbjct: 214 -----ASVDDDLESCDDKLVLQEIIKNCTEREQQIIRMRFL--DGMTQVEIADKLQVSQV 266

Query: 268 RVRQIEARAFKKVQESI 284
           +V ++     +K+QE +
Sbjct: 267 QVSRLLRNTLRKLQEKL 283


>gi|257055481|ref|YP_003133313.1| RNA polymerase sigma factor, sigma-70 family [Saccharomonospora
           viridis DSM 43017]
 gi|256585353|gb|ACU96486.1| RNA polymerase sigma factor, sigma-70 family [Saccharomonospora
           viridis DSM 43017]
          Length = 315

 Score =  167 bits (424), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 77/300 (25%), Positives = 139/300 (46%), Gaps = 41/300 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRY---------------------REHGDLS--------A 49
           Y+ E+ + P+L   +E  LAKR                       +  DL         A
Sbjct: 19  YLDEVGETPLLTANQEVELAKRIEAGVYAAELLRRADEGEITLDYDRRDLEIVARDGQRA 78

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              ++ ++LRLVV  A   R   LP+ + + EGN+GL++AV+KFD  +GF+ +TY+MWWI
Sbjct: 79  KDHMIRANLRLVVTAARKNRHTNLPLLDAIQEGNLGLIRAVEKFDYAKGFKFSTYAMWWI 138

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + A+Q       + +++    +++     L RL+  LQ+ +++ L  E++ A A+   + 
Sbjct: 139 RQAIQRGNAFQSNAIRLPMHVSEQ--VAKLDRLERTLQSRSNHELTVEELAAAAE---MP 193

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
              V ++        SL+    S D++   +   LV D  G    + E  ER+   + + 
Sbjct: 194 VERVEALRQAGRSTVSLD---MSLDEDGELYLRDLVAD--GTVPAVGEGIERQAMVDQVR 248

Query: 230 RSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            ++  L P E  +   R      +  T+  +S    +SR+RVR +E RA   ++E  + +
Sbjct: 249 ATIDSLPPMEAAVVSLRYGLRDGHQHTIPEISQRLGLSRKRVRTLEQRAMAMLREPQRSE 308


>gi|222832154|gb|EEE70631.1| predicted protein [Populus trichocarpa]
          Length = 299

 Score =  167 bits (424), Expect = 1e-39,   Method: Composition-based stats.
 Identities = 83/237 (35%), Positives = 131/237 (55%), Gaps = 25/237 (10%)

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AVK+FDP++  RL +Y+M WIKA + EYIL++W +VK+ TT  Q++LFFNLR +K  L
Sbjct: 1   MKAVKRFDPDQNVRLVSYAMHWIKAEIHEYILKNWRMVKVATTKAQRKLFFNLRSMKQGL 60

Query: 147 Q---------AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
           +         A+  + L   ++ A+A+KLNV   EV+ M  RLAG + L     S D   
Sbjct: 61  KSDAAMAEDGAMLRDTLTSGEIDAVAEKLNVKREEVMEMETRLAGGDVLLDPSPSDDGEQ 120

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKN-RRNMLTRSMSVLNPRERRIFEARRL-----QEN 251
           +      + D   +   +IE  +R +   + +  ++  L+ R RRI E R L        
Sbjct: 121 AFGPIAYLADGAHEPTAMIESRQRDHLATDGIAMALDSLDDRSRRIVEERWLKVNDDGSG 180

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI----------QKQVELSSSPPLLQ 298
            +TL  L++ + VS ER+RQIE  A KK+++++           +Q  L+++PPL Q
Sbjct: 181 GMTLHELAAVYGVSAERIRQIEVAAMKKMKKALADLCGPHAPHARQRHLATTPPLRQ 237


>gi|291559903|emb|CBL38703.1| RNA polymerase, sigma subunit, RpsG/SigG [butyrate-producing
           bacterium SSC/2]
          Length = 258

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 57/259 (22%), Positives = 112/259 (43%), Gaps = 17/259 (6%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L ++E+  L +R  E GDL A    +  +LRLV+ I   + G      ++   G IG
Sbjct: 16  LPLLSEEEKEDLFERI-EQGDLLAREHYIKGNLRLVLSIIQRFSGSNENADDLFQVGCIG 74

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           LM+A+  FD     + +TY++  I   ++ Y+  + S+ ++      + L     +    
Sbjct: 75  LMKAIDNFDRNLNVKFSTYAVPMIIGEVKRYLRDNHSM-RVS-----RSLRDTAYKAINA 128

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            + +T        +  IAK++++ + +V+     +A   SL   +     ++    D  V
Sbjct: 129 REVLTKKLNHEPTIDVIAKEIDMKKEDVLFALDAIATPLSLYEPVYQDGGDTLYLMDQ-V 187

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            D   +E   +E          L  +M  L  RE  I + R       T   ++ E  +S
Sbjct: 188 KDKKNKEDSWVESI-------ALKEAMEHLPDREYDIIKMRFF--EGKTQTEVADEIAIS 238

Query: 266 RERVRQIEARAFKKVQESI 284
           + +V ++E  A K ++  +
Sbjct: 239 QAQVSRLEKNALKHMKNHL 257


>gi|297608012|ref|NP_001061065.2| Os08g0163400 [Oryza sativa Japonica Group]
 gi|255678168|dbj|BAF22979.2| Os08g0163400 [Oryza sativa Japonica Group]
          Length = 520

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 68/254 (26%), Positives = 121/254 (47%), Gaps = 10/254 (3%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L  R  E     A   L  S+LRLV+ IA  Y   G+ +++++  G IGL++ ++KFD 
Sbjct: 266 ELRSRMHES--FLAREMLTMSNLRLVISIAQKYDNLGVELADLIQGGLIGLLRGIEKFDA 323

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            RGFR++TY  WWI+  +   +  +    ++ T  +++     L  ++G    + D  + 
Sbjct: 324 SRGFRISTYVYWWIRQGVSRALAENSKTFRLPTYLHER-----LIAIRGAKYELEDQGIA 378

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQV 214
           P  +  IA  LN+SE +V++    +    SL+     S +    +     + D +     
Sbjct: 379 P-TIENIAGSLNISEKKVLNATEAVNKVLSLDQQAFPSLNGLPGETLHSYIEDQNVANDP 437

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIE 273
               EE   +  +     S LN RER I        +   T E++S +F +SRERVRQ+ 
Sbjct: 438 WHGFEEWYLKEEVNKLLNSTLNERERDIIRLYHGIGKQCHTWEDISRQFGLSRERVRQVG 497

Query: 274 ARAFKKVQESIQKQ 287
             A +K++ + +++
Sbjct: 498 LIAMEKLKHAARRK 511


>gi|2529275|gb|AAB81194.1| sigma factor [Geobacillus stearothermophilus]
          Length = 250

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 51/253 (20%), Positives = 108/253 (42%), Gaps = 19/253 (7%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           QE   L +R +E GD  A   ++  ++RLV  +   +   G    ++   G IGL+++V 
Sbjct: 15  QEMKELIRRSQE-GDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVD 73

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD     + +TY++  I   +Q ++      VK+  +   K +   +R+ K  L     
Sbjct: 74  KFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSL--KEMGNKIRKAKDELSKTRG 130

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +   +  IA  L +S  +V+     +    S++  +  +D +     D +       
Sbjct: 131 ---RSPTITEIADHLGISPEDVVLAQEAVRLPTSIHETVYENDGDPITLLDQIAD----- 182

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
                  E     +  L +++  L+ RER I   R  ++   T   ++S   +S+ +V +
Sbjct: 183 -----ADEASWFDKIALKKAIEELDERERLIVYLRYYRD--RTQSEVASRLGISQVQVSR 235

Query: 272 IEARAFKKVQESI 284
           +E +  + +++ +
Sbjct: 236 LEKKILQHIKDKM 248


>gi|290769931|gb|ADD61700.1| putative protein [uncultured organism]
          Length = 259

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 49/260 (18%), Positives = 111/260 (42%), Gaps = 17/260 (6%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L ++E+  L KR +  GD  A    +  +LRLV+ +   ++       ++   G IG
Sbjct: 16  LPVLNQEEKEELFKRIK-AGDEEARELYIKGNLRLVLSVIRRFQNSSENPDDLFQIGCIG 74

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A+  FD     + +TY++  I   ++ Y+  + S +++  +           R    
Sbjct: 75  LIKAIDNFDTTLQVKFSTYAVPMIVGEIRRYLRDNNS-IRVSRSLRDIAYKTIYTR---- 129

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            +     +LK   +  IA ++ + +  ++     +    SL   + S   ++    D + 
Sbjct: 130 -ENYMRQHLKEPTIAEIADEIGIDKEMIVYAMDAIQSPVSLFEPVYSEGGDTLYVMDQIS 188

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
              + +E  + +          L  +M+ L  RER I + R       T   ++ E  +S
Sbjct: 189 DKKNREENWVED--------ISLRDAMNRLGERERHIIDLRFY--EGKTQMEVADEIGIS 238

Query: 266 RERVRQIEARAFKKVQESIQ 285
           + +V ++E  A + ++  ++
Sbjct: 239 QAQVSRLEKHALRSMRNYLR 258


>gi|225375609|ref|ZP_03752830.1| hypothetical protein ROSEINA2194_01234 [Roseburia inulinivorans DSM
           16841]
 gi|225212588|gb|EEG94942.1| hypothetical protein ROSEINA2194_01234 [Roseburia inulinivorans DSM
           16841]
          Length = 259

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 53/260 (20%), Positives = 121/260 (46%), Gaps = 17/260 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L++ E+  L  R R+ GD  A    +  +LRLV+ +   + G    + ++   G I
Sbjct: 15  KLPILKETEKEALFARIRQ-GDQEAREMYIKGNLRLVLSVIKRFSGSHENLDDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++++  F+P+   + +TY++  I   ++ Y+  + S +++      + L     +   
Sbjct: 74  GLIKSIDNFNPDLQVKFSTYAVPMIIGEIRRYLRDNNS-IRVS-----RSLRDTAYKAIH 127

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + ++ N+ K   +  IA++  V+  +++     +    SL   +  +D   + +    
Sbjct: 128 AKEVLSKNSFKEPTLQEIAEESGVAAEDILYALDAIQSPVSLYDPVY-TDGGDTLYVMDQ 186

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           + D   +E+  +EK         L+ +M+ L+ RE  I   R       T   ++ E  +
Sbjct: 187 ISDKKNKEENWVEKLS-------LSDAMNHLSERENFIINLRFF--EGKTQMEVADEIHI 237

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ +V ++E  A K +++ +
Sbjct: 238 SQAQVSRLEKSALKTIRQYL 257


>gi|125602291|gb|EAZ41616.1| hypothetical protein OsJ_26150 [Oryza sativa Japonica Group]
          Length = 420

 Score =  167 bits (424), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 68/254 (26%), Positives = 121/254 (47%), Gaps = 10/254 (3%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L  R  E     A   L  S+LRLV+ IA  Y   G+ +++++  G IGL++ ++KFD 
Sbjct: 166 ELRSRMHES--FLAREMLTMSNLRLVISIAQKYDNLGVELADLIQGGLIGLLRGIEKFDA 223

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            RGFR++TY  WWI+  +   +  +    ++ T  +++     L  ++G    + D  + 
Sbjct: 224 SRGFRISTYVYWWIRQGVSRALAENSKTFRLPTYLHER-----LIAIRGAKYELEDQGIA 278

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQV 214
           P  +  IA  LN+SE +V++    +    SL+     S +    +     + D +     
Sbjct: 279 P-TIENIAGSLNISEKKVLNATEAVNKVLSLDQQAFPSLNGLPGETLHSYIEDQNVANDP 337

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIE 273
               EE   +  +     S LN RER I        +   T E++S +F +SRERVRQ+ 
Sbjct: 338 WHGFEEWYLKEEVNKLLNSTLNERERDIIRLYHGIGKQCHTWEDISRQFGLSRERVRQVG 397

Query: 274 ARAFKKVQESIQKQ 287
             A +K++ + +++
Sbjct: 398 LIAMEKLKHAARRK 411


>gi|332977445|gb|EGK14221.1| DNA-directed RNA polymerase sigma subunit SigF [Desmospora sp.
           8437]
          Length = 254

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 54/256 (21%), Positives = 114/256 (44%), Gaps = 19/256 (7%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L   E   L ++  + GD  A  RLV  ++RLV  +   +   G    ++   G IGL++
Sbjct: 13  LSDTEVKELIQK-SQKGDTEARDRLVQHNIRLVWSVVQRFLNRGYEAEDLFQIGCIGLLK 71

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           AV KFD     + +TY++  I   +Q ++     +VK+  +   K L   +R++K  +  
Sbjct: 72  AVDKFDLAYDVKFSTYAVPMIIGEIQRFLRDDG-MVKVSRSL--KELSNRIRKVKDEM-- 126

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
            T    +   +  +++++ V+  E++          S++  +  +D +     D +    
Sbjct: 127 -TKGLGRSPTIQELSEEMGVTPEEIVFAQEANRTPTSIHETVYENDGDPITLMDQIAD-- 183

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
                   E+EE    R  L  ++  L  RER I   R  ++   T   ++    +S+ +
Sbjct: 184 --------EEEEGWFDRMALKEAIRQLEERERLIVYLRFFKDQ--TQSEVAQRLGISQVQ 233

Query: 269 VRQIEARAFKKVQESI 284
           V ++E +  ++++++I
Sbjct: 234 VSRLEKKIIRRMRDAI 249


>gi|331269711|ref|YP_004396203.1| FliA/WhiG family RNA polymerase sigma 28 subunit [Clostridium
           botulinum BKT015925]
 gi|329126261|gb|AEB76206.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           botulinum BKT015925]
          Length = 242

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 55/258 (21%), Positives = 117/258 (45%), Gaps = 17/258 (6%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+L+ +E   L  + R+ GD  +  + +  +LRLV+ +   +   G  + ++   G IGL
Sbjct: 2   PVLKDKEMKELLIKMRD-GDYFSREKFIRGNLRLVLSVIQRFNNRGENVDDLFQVGCIGL 60

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+  FD  +  + +TY++  I   ++ Y+  + S +++  +   + + +   +++  L
Sbjct: 61  IKAIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSL--RDIAYKALQVRDRL 117

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
               + + K   V  IAK+L +   EV+     +    SL   I   D   + +    + 
Sbjct: 118 ---INKDNKDPNVSQIAKELELPREEVVFALDAIQDPVSLFEPIYH-DGGDALYVMDQIS 173

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           D+   +   IE          +  +M  LN RE+ I   R  Q    T   ++ E  +S+
Sbjct: 174 DNKSVDDSWIENIS-------IKEAMKRLNEREKLILNMRFFQG--RTQMEVADEIGISQ 224

Query: 267 ERVRQIEARAFKKVQESI 284
            +V ++E  A K +++ +
Sbjct: 225 AQVSRLEKTALKHMRKYV 242


>gi|158833975|gb|ABW81793.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833979|gb|ABW81795.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
          Length = 225

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 67/229 (29%), Positives = 119/229 (51%), Gaps = 11/229 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L   EE   A+R    GD S+  R++ S+LRLVVKI+  Y   GLP+ ++
Sbjct: 8   YLSEIGYSPLLTAAEEIYFARRVL-CGDESSRRRMIESNLRLVVKISRRYINRGLPLLDL 66

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY  WWI+  ++  I+     +++      K L   
Sbjct: 67  IEEGNLGLIRAVEKFDPERGFRFSTYDTWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 125

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +  L    D++  PE++     K     S ++ +N R++   S++    ++ +   
Sbjct: 126 LRAAR-ELSHKLDHDPSPEEIAEQLNKPVDYVSRMLRLNERIS---SVDTSFGNAAEKG- 180

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
              D L  + D   +   + +   + +  + + +S L+ ++R +   R 
Sbjct: 181 -LLDVLSDETDNDPENTTQND---DMKKSVVKWLSELSTKQREVLARRF 225


>gi|158833951|gb|ABW81781.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833953|gb|ABW81782.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833955|gb|ABW81783.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833957|gb|ABW81784.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833961|gb|ABW81786.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833965|gb|ABW81788.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833981|gb|ABW81796.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833983|gb|ABW81797.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833985|gb|ABW81798.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833989|gb|ABW81800.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
          Length = 225

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 66/229 (28%), Positives = 119/229 (51%), Gaps = 11/229 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L   EE   A+R    GD S+  R++ S+LRLVVKI+  Y   GLP+ ++
Sbjct: 8   YLGEIGYSPLLTAAEEIYFARRVL-CGDESSRRRMIESNLRLVVKISRRYINRGLPLLDL 66

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 67  IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 125

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +  L    D++  PE++     K     S ++ +N R++   S++    ++ +   
Sbjct: 126 LRAAR-ELSHKLDHDPSPEEIAEQLNKPVDYVSRMLRLNERIS---SVDTSFGNAAEKG- 180

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
              D L  + D   +   + +   + +  + + +  L+ ++R +   R 
Sbjct: 181 -LLDVLSDETDNDPENTTQND---DMKKSVVKWLFELSTKQREVLARRF 225


>gi|158833993|gb|ABW81802.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
          Length = 225

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 66/229 (28%), Positives = 119/229 (51%), Gaps = 11/229 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L   EE   A+R    GD S+  R++ S+LRLVVKI+  Y   GLP+ ++
Sbjct: 8   YLGEIGYSPLLTAAEEIYFARRVL-CGDESSRRRMIESNLRLVVKISRRYINRGLPLLDL 66

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 67  IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 125

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +  L    D++  PE++     K     S ++ +N R++   S++    ++ +   
Sbjct: 126 LRAAR-ELSHKLDHDPSPEEIAEQLNKPVDYVSRMLRLNERIS---SVDTSFGNAAEKG- 180

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
              D L  + D   +   + +   + +  + + +  L+ ++R +   R 
Sbjct: 181 -LLDVLSDETDNDPENTTQND---DMKKSVVKWLFELSTKQREVLARRF 225


>gi|2780746|dbj|BAA24364.1| plastid RNA polymerase sigma factor [Oryza sativa Japonica Group]
          Length = 519

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 68/254 (26%), Positives = 121/254 (47%), Gaps = 10/254 (3%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L  R  E     A   L  S+LRLV+ IA  Y   G+ +++++  G IGL++ ++KFD 
Sbjct: 265 ELRSRMHES--FLAREMLTMSNLRLVISIAQKYDNLGVELADLIQGGLIGLLRGIEKFDA 322

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            RGFR++TY  WWI+  +   +  +    ++ T  +++     L  ++G    + D  + 
Sbjct: 323 SRGFRISTYVYWWIRQGVSRALAENSKTFRLPTYLHER-----LIAIRGAKYELEDQGIA 377

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQV 214
           P  +  IA  LN+SE +V++    +    SL+     S +    +     + D +     
Sbjct: 378 P-TIENIAGSLNISEKKVLNATEAVNKVLSLDQQAFPSLNGLPGETLHSYIEDQNVANDP 436

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIE 273
               EE   +  +     S LN RER I        +   T E++S +F +SRERVRQ+ 
Sbjct: 437 WHGFEEWYLKEEVNKLLNSTLNERERDIIRLYHGIGKQCHTWEDISRQFGLSRERVRQVG 496

Query: 274 ARAFKKVQESIQKQ 287
             A +K++ + +++
Sbjct: 497 LIAMEKLKHAARRK 510


>gi|15240693|ref|NP_196877.1| SIG4 (SIGMA FACTOR 4); DNA binding / DNA-directed RNA polymerase/
           sigma factor/ transcription factor [Arabidopsis
           thaliana]
 gi|3983260|gb|AAC97954.1| sigma-like factor [Arabidopsis thaliana]
 gi|4972296|dbj|BAA78110.1| RNA polymerase sigma subunit SigD [Arabidopsis thaliana]
 gi|9758039|dbj|BAB08700.1| sigma-like factor [Arabidopsis thaliana]
 gi|332004550|gb|AED91933.1| sigma factor 4 [Arabidopsis thaliana]
          Length = 419

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 80/287 (27%), Positives = 133/287 (46%), Gaps = 27/287 (9%)

Query: 13  EIGLSRYIHEIRKIPML-EKQEEYV-----LA----KRYREHGD-----LSAAHRLVTSH 57
           E+ L  Y+ E  K+  L    EE       LA    K+ R   +       A  ++   +
Sbjct: 128 EVQLCLYLKEGAKLENLGTSVEENEMVSVLLASGRGKKKRSANEILCRRKEAREKITRCY 187

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
            RLVV IA GY+G GL + +++ EG+IGL++  ++FDP+RG++L+TY  WWIK A+   I
Sbjct: 188 RRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAILRAI 247

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
                LVK+  +  +        ++      +T    +      IA+ LN++ S V    
Sbjct: 248 AHKSRLVKLPGSMWELTA-----KVAEASNVLTRKLRRQPSCEEIAEHLNLNVSAVRLAV 302

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
            R     SL+     + +N       +V   D  E    E  +R++ ++ + + +  L  
Sbjct: 303 ERSRSPVSLD---RVASQNGRMTLQEIVRGPD--ETRPEEMVKREHMKHEIEQLLGSLTA 357

Query: 238 RERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           RE R+         E P++ E +    ++SRERVRQI   A KK++ 
Sbjct: 358 RESRVLGLYFGLNGETPMSFEEIGKSLKLSRERVRQINGIALKKLRN 404


>gi|210608669|ref|ZP_03287946.1| hypothetical protein CLONEX_00125 [Clostridium nexile DSM 1787]
 gi|210152926|gb|EEA83932.1| hypothetical protein CLONEX_00125 [Clostridium nexile DSM 1787]
          Length = 259

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 47/261 (18%), Positives = 117/261 (44%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+++E+  L  + +  GD  A  + +  +LRLV+ +   +        ++   G 
Sbjct: 14  SKLPLLKEEEKNALFAKIK-AGDEGAKEQYIKGNLRLVLSVIKRFTNSNENPDDLFQIGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  F+ E   + +TY++  I   ++ Y+  + S +++      + L     +  
Sbjct: 73  IGLIKAINNFNTELDVKFSTYAVPMIIGEIRRYMRDNNS-IRVS-----RSLRDTAYKAI 126

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
              +     NL+   +  I++++ +++ +++     +    SLN  + +   ++    D 
Sbjct: 127 YAKEGYMKRNLREPTLQEISEEIGIAKEDIVFAMDAIQAPMSLNEPVYNDGGDALYVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    + +E  + E          L  +M  L  RE+ I   R       T   ++ + +
Sbjct: 187 ISDKKNKEENWIEELA--------LQAAMEHLGEREKYIIRLRFF--EGRTQMEVAEDID 236

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A K +++ +
Sbjct: 237 ISQAQVSRLEKHALKVMRQYL 257


>gi|313887713|ref|ZP_07821395.1| putative RNA polymerase sigma-B factor [Peptoniphilus harei
           ACS-146-V-Sch2b]
 gi|312846322|gb|EFR33701.1| putative RNA polymerase sigma-B factor [Peptoniphilus harei
           ACS-146-V-Sch2b]
          Length = 261

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 55/264 (20%), Positives = 120/264 (45%), Gaps = 17/264 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K+E   L K Y E  D      L+  HL +   ++  Y G G+   ++    +IGL+ 
Sbjct: 13  LTKEERKDLFKEYHETKDQEIRDILIEEHLYIAEILSKKYTGRGIDYDDIYQVASIGLIY 72

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++++DPE+GF  ++++   I   +++Y   +   +++     +       +++     +
Sbjct: 73  AIERYDPEKGFEFSSFATPTIIGEIKKYFRDNGWTIRVPRRIQELS-----KKISNATVS 127

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVY 206
           ++    K   +  IA+ L+ +  EV+      ++   +SL+    S D++     D +  
Sbjct: 128 LSQKYQKTPTIDEIAEYLDSTPEEVMEAMEASKVYTPQSLDVTYESGDESEVNLSDLI-- 185

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
              G E+   +K E  +      ++M  L+  ER I   R    N  T   ++ +  +S+
Sbjct: 186 ---GVEEAYFDKIESNDF---FKKAMENLDEVERTILIDRYF--NKKTQVVIAKKLNISQ 237

Query: 267 ERVRQIEARAFKKVQESIQKQVEL 290
             V +IE +  +K+++ + K +E+
Sbjct: 238 MTVSRIEKKVLEKMRKEVAKTMEV 261


>gi|220931759|ref|YP_002508667.1| sporulation sigma factor SigG [Halothermothrix orenii H 168]
 gi|219993069|gb|ACL69672.1| sporulation sigma factor SigG [Halothermothrix orenii H 168]
          Length = 260

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 50/264 (18%), Positives = 120/264 (45%), Gaps = 17/264 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            ++P+L  +E   L K+ ++ GD SA  +++  +LRLV+ +   +   G  + ++   G 
Sbjct: 13  SELPVLSNEEMRKLFKKMQQ-GDWSARQKIINGNLRLVLSVIQRFNNRGENVDDLFQVGC 71

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD  +  R +TY++  I   ++ Y+  +   +++  +   +   +   ++K
Sbjct: 72  IGLIKAIDNFDLSQNVRFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDTAYKALQMK 128

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
              +++ +   +   +  ++++L +  SE+I     +    SL   I     +     D 
Sbjct: 129 ---ESLKNKKSEEPSLKEVSEELGIPRSEIIFALDAIQDPISLFEPIYHDGGDPIFVMDQ 185

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  +    E  L            +   +  L+PRE+ I   R       T   +++E  
Sbjct: 186 ISDEKTEDENWLEGIA--------VREGLRKLSPREKLILAYRFY--EGKTQMEVANEIG 235

Query: 264 VSRERVRQIEARAFKKVQESIQKQ 287
           +S+ +V ++E  A K+++  +++ 
Sbjct: 236 ISQAQVSRLEKAALKRLKRHVKED 259


>gi|311068942|ref|YP_003973865.1| sporulation sigma factor SigF [Bacillus atrophaeus 1942]
 gi|310869459|gb|ADP32934.1| sporulation sigma factor SigF [Bacillus atrophaeus 1942]
          Length = 255

 Score =  167 bits (423), Expect = 2e-39,   Method: Composition-based stats.
 Identities = 57/253 (22%), Positives = 107/253 (42%), Gaps = 19/253 (7%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L+  E   L KR  + GD  A   L+  ++RLV  +   +   G    ++   G IGL++
Sbjct: 14  LKDHEVKDLIKR-SQDGDQQARDLLIEKNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLK 72

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           +V KFD     R +TY++  I   +Q +I      VK+  +   K L   +RR K  L  
Sbjct: 73  SVDKFDLSYDVRFSTYAVPMIIGEIQRFIRDDG-TVKVSRSL--KELGNKIRRAKDELSK 129

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                 +   V  IA+ L +   +V+     +    S++  +  +D +     D +    
Sbjct: 130 TYG---RVPTVQEIAEHLEIDAEDVVLAQEAVRAPSSIHETVYENDGDPITLLDQIAD-- 184

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
                     EE+   +  L  ++S L  RE+ I   R  ++   T   ++    +S+ +
Sbjct: 185 --------HSEEKWFDKIALKEAISDLEEREKLIVYLRYYKDQ--TQSEVAERLGISQVQ 234

Query: 269 VRQIEARAFKKVQ 281
           V ++E +  K+++
Sbjct: 235 VSRLEKKILKQIK 247


>gi|254974392|ref|ZP_05270864.1| RNA polymerase sigma-F factor [Clostridium difficile QCD-66c26]
 gi|255091783|ref|ZP_05321261.1| RNA polymerase sigma-F factor [Clostridium difficile CIP 107932]
 gi|255099887|ref|ZP_05328864.1| RNA polymerase sigma-F factor [Clostridium difficile QCD-63q42]
 gi|255305776|ref|ZP_05349948.1| RNA polymerase sigma-F factor [Clostridium difficile ATCC 43255]
 gi|255313518|ref|ZP_05355101.1| RNA polymerase sigma-F factor [Clostridium difficile QCD-76w55]
 gi|255516203|ref|ZP_05383879.1| RNA polymerase sigma-F factor [Clostridium difficile QCD-97b34]
 gi|255649300|ref|ZP_05396202.1| RNA polymerase sigma-F factor [Clostridium difficile QCD-37x79]
 gi|255654820|ref|ZP_05400229.1| RNA polymerase sigma-F factor [Clostridium difficile QCD-23m63]
 gi|260682470|ref|YP_003213755.1| RNA polymerase sigma-F factor [Clostridium difficile CD196]
 gi|260686069|ref|YP_003217202.1| RNA polymerase sigma-F factor [Clostridium difficile R20291]
 gi|296449564|ref|ZP_06891341.1| RNA polymerase sigma-F factor [Clostridium difficile NAP08]
 gi|296878113|ref|ZP_06902128.1| RNA polymerase sigma-F factor [Clostridium difficile NAP07]
 gi|306519396|ref|ZP_07405743.1| RNA polymerase sigma-F factor [Clostridium difficile QCD-32g58]
 gi|260208633|emb|CBA61376.1| RNA polymerase sigma-F factor [Clostridium difficile CD196]
 gi|260212085|emb|CBE02685.1| RNA polymerase sigma-F factor [Clostridium difficile R20291]
 gi|296261628|gb|EFH08446.1| RNA polymerase sigma-F factor [Clostridium difficile NAP08]
 gi|296430866|gb|EFH16698.1| RNA polymerase sigma-F factor [Clostridium difficile NAP07]
          Length = 254

 Score =  166 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 54/260 (20%), Positives = 123/260 (47%), Gaps = 16/260 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K P+L  +E   L ++ + +GD  A   L++S+L LV  +   +   G    ++   G+I
Sbjct: 10  KKPLLSHEETLELIEKVQ-NGDEEAKEILISSNLGLVRSVVSRFLNIGYDREDLFQLGSI 68

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++++ KFDP+   + +TY++  I   ++ Y+     ++K+  +  Q  +     + K 
Sbjct: 69  GLIKSIYKFDPKFNVKFSTYAVPMILGEIKRYLRDDG-MIKVSRSLKQIAV-----KAKM 122

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             +A+T    +   +  +AK ++V + +++         E L  +I+  + +     D +
Sbjct: 123 ESEALTKKLGREPSIEELAKAIDVEKEDLVMAMEANFNVEYLQGVIHEEEGSPICLIDKI 182

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               + +E+ +++         +L   +  L+ RER+I   R  ++  +T   +     +
Sbjct: 183 SMKGESEEEKVVDNI-------LLKDILGRLDKRERQIIVLRYFED--MTQSEIGEMLNI 233

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ +V +IE +   K++E I
Sbjct: 234 SQVQVSRIEKKVLSKLKEYI 253


>gi|328955594|ref|YP_004372927.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Coriobacterium
           glomerans PW2]
 gi|328455918|gb|AEB07112.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Coriobacterium
           glomerans PW2]
          Length = 262

 Score =  166 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 59/265 (22%), Positives = 123/265 (46%), Gaps = 17/265 (6%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           +K++ + L +RY+E GD  A  +LV SH+ LV  +A  ++  G P+ +++  G +GL++A
Sbjct: 13  DKEKTHELFRRYKEDGDDDAREKLVMSHMNLVRFLANKFKNRGEPLDDLMQVGYLGLLKA 72

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +F+P RG    TY+   I   ++ +       V++      +RL     ++      +
Sbjct: 73  IDRFEPARGLEFTTYATPTILGEIKRHFRDKGWSVRVP-----RRLQELSAKVNQATDLL 127

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYD 207
           T    +  +V  IA+ L+ +  EV+      +   S  L    +S + ++    D    D
Sbjct: 128 TTELQRSPKVEEIAEYLDATVDEVLEAMESSSAYSSVPLEGTGSSENDDAPSIIDRYAID 187

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            +             + R ++  ++   +PRER +   R L+   +T   ++ +  +S+ 
Sbjct: 188 DNV--------LSFTDDRLIIEDALESFSPREREVVNLRFLKG--MTQIEIAEQLGISQV 237

Query: 268 RVRQIEARAFKKVQESIQKQVELSS 292
           +V ++  R  KK+Q+ I  +  +S 
Sbjct: 238 QVSRLLRRTLKKIQDRIDPEGVMSQ 262


>gi|126698352|ref|YP_001087249.1| RNA polymerase sigma-F factor [Clostridium difficile 630]
 gi|115249789|emb|CAJ67606.1| RNA polymerase sigma-F factor [Clostridium difficile]
          Length = 254

 Score =  166 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 54/260 (20%), Positives = 123/260 (47%), Gaps = 16/260 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K P+L  +E   L ++ + +GD  A   L++S+L LV  +   +   G    ++   G+I
Sbjct: 10  KKPLLSHEETLELIEKVQ-NGDEEAKEILISSNLGLVRSVVSRFLNIGYDREDLFQLGSI 68

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++++ KFDP+   + +TY++  I   ++ Y+     ++K+  +  Q  +     + K 
Sbjct: 69  GLIKSIYKFDPKFNVKFSTYAVPMILGEIKRYLRDDG-MIKVSRSLKQIAI-----KAKM 122

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             +A+T    +   +  +AK ++V + +++         E L  +I+  + +     D +
Sbjct: 123 ESEALTKKLGREPSIEELAKAIDVEKEDLVMAMEANFNVEYLQGVIHEEEGSPICLIDKI 182

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               + +E+ +++         +L   +  L+ RER+I   R  ++  +T   +     +
Sbjct: 183 SMKGESEEEKVVDNI-------LLKDILGRLDKRERQIIVLRYFED--MTQSEIGEMLNI 233

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ +V +IE +   K++E I
Sbjct: 234 SQVQVSRIEKKVLSKLKEYI 253


>gi|325002338|ref|ZP_08123450.1| RpoD family RNA polymerase sigma factor [Pseudonocardia sp. P1]
          Length = 425

 Score =  166 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 72/295 (24%), Positives = 122/295 (41%), Gaps = 57/295 (19%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR---------EHGDLS-------------- 48
                 RY  E  +  +++  EE VLA+            E+GD +              
Sbjct: 146 ATDSFWRYRQETGRAGLIDAGEEVVLARAIEVGLLAAERLENGDETTPAALPLRLLIAAG 205

Query: 49  --AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  R VT++LRLV+ IA GY   GL   ++V EG +GL++AV+KFD  +G + +TY+ 
Sbjct: 206 EGAYERFVTANLRLVLSIASGYGAPGLDALDLVQEGTLGLIRAVQKFDIAQGTKFSTYAT 265

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++      ++   F+ R L     A  +        V      
Sbjct: 266 WWIRQAITRAIADQSRTIRYPVHLVERLNAFSRRALPDDDSATAELVATLPTTVPFESAR 325

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +V   EV+            +      D  +   + + V D                   
Sbjct: 326 DVLGEEVLQ-----------DVADRYLDPPAPDLRGFTVED------------------- 355

Query: 227 MLTRSMSVLNPRERRIFEARRLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            +  ++S+L+ RER I + R     +  TL+ +  E  V+RER+RQI+++A  ++
Sbjct: 356 -VAAALSILSERERTIVDRRFGFVGDAATLDVIGGELGVTRERIRQIQSKALGRL 409


>gi|158833949|gb|ABW81780.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
          Length = 225

 Score =  166 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 65/229 (28%), Positives = 119/229 (51%), Gaps = 11/229 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L   EE   A+R    GD S+  R++ S+LRLVVKI+  Y   GLP+ ++
Sbjct: 8   YLGEIGYSPLLTAAEEIYFARRVL-CGDESSRRRMIESNLRLVVKISRRYINRGLPLLDL 66

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 67  IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 125

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +  L    D++  PE++     K     + ++ +N R++   S++    ++ +   
Sbjct: 126 LRAAR-ELSHKLDHDPSPEEIAEQLNKPVDYVNRMLRLNERIS---SVDTSFGNAAEKG- 180

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
              D L  + D   +   + +   + +  + + +  L+ ++R +   R 
Sbjct: 181 -LLDVLSDETDNDPENTTQND---DMKKSVVKWLFELSTKQREVLARRF 225


>gi|329939708|ref|ZP_08289009.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
 gi|329301278|gb|EGG45173.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
          Length = 387

 Score =  166 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 57/237 (24%), Positives = 103/237 (43%), Gaps = 15/237 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              +RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+  
Sbjct: 162 ELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATP 221

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +   ++ +       V++     + RL      L      ++  + +   V  +A+KL 
Sbjct: 222 TVVGEIKRHFRDKGWAVRVPRRLQELRLA-----LTTATAELSQLHGRSPTVHELAEKLA 276

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +SE EV+          +L+  +  +D  S    D L  +         E  E    R  
Sbjct: 277 ISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAED--------EALEGVEYRES 328

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 329 LKPLLEDLPPREKRILLLRFFAN--MTQSQIAQEVGISQMHVSRLLARTLAQLREKL 383


>gi|223986354|ref|ZP_03636363.1| hypothetical protein HOLDEFILI_03674 [Holdemania filiformis DSM
           12042]
 gi|223961703|gb|EEF66206.1| hypothetical protein HOLDEFILI_03674 [Holdemania filiformis DSM
           12042]
          Length = 257

 Score =  166 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 57/259 (22%), Positives = 121/259 (46%), Gaps = 17/259 (6%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L+ Q+   L  + ++ GDLSA  +L+  +L+LV+ I   +      + ++   G IG
Sbjct: 16  LPVLKSQQMTELFIQLQD-GDLSAKEKLINGNLKLVLSIVQRFAHRTENMDDLFQIGCIG 74

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A+  FD     R +TY++  I   ++ Y+  +  ++++      K L + + + K  
Sbjct: 75  LIKAIDNFDLSHEVRFSTYAVPMIIGEIKRYLRDNQ-MIRVSRHL--KDLAYKVLKEK-- 129

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            +A    N +   +  +A+ + V E ++      L    S+   I + D ++    D + 
Sbjct: 130 -EAFIHANQREPSLAELAEIMGVKEKDIAESLESLQSVVSIFEPIYNDDGDTLYLLDQIK 188

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            DHD        +  + +    L  SM  L+ +E +I   R  Q    T   ++SE  +S
Sbjct: 189 DDHD--------EIGKLSSLIALKESMKHLSDKEAQIINKRYYQGQ--TQTEIASELGIS 238

Query: 266 RERVRQIEARAFKKVQESI 284
           + +V ++E  A + ++++ 
Sbjct: 239 QAQVSRLEKSALQCLKKNF 257


>gi|2529271|gb|AAB81191.1| sigma factor [Lysinibacillus sphaericus]
          Length = 263

 Score =  166 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 53/257 (20%), Positives = 112/257 (43%), Gaps = 19/257 (7%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           +L ++E   L  R ++ GD  A  R+V  + RLV  I   +   G+ + ++   G IGLM
Sbjct: 11  LLSQEEMRDLIARAQQ-GDHEARKRMVEGNTRLVWSIVQRFTTRGVELEDLFQIGCIGLM 69

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           ++V KFD     + +TY++  I   +Q ++     +VK+  +  +        +++    
Sbjct: 70  KSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-MVKVSRSIRELNF-----KIRHATD 123

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                N     +  +A+ L V+  E+++ +  L    SL+  +  S+ +S    D +  +
Sbjct: 124 EFIKRNEHRPTIQELAQVLGVTTEEIVTASDALRDPASLHEQLYESEGDSITLMDQMKDE 183

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
              Q    I           L   ++ L PRE+ I   R   +   T   +++   +S+ 
Sbjct: 184 KSEQPFDYIP----------LKEVLTRLEPREQSIIYLRYFSD--CTQTEIANRLGISQV 231

Query: 268 RVRQIEARAFKKVQESI 284
           +V ++E +   +++  +
Sbjct: 232 QVSRLEKKILAQLKSWM 248


>gi|154686587|ref|YP_001421748.1| sporulation sigma factor SigF [Bacillus amyloliquefaciens FZB42]
 gi|308174131|ref|YP_003920836.1| RNA polymerase sporulation-specific sigma factor sigma-F [Bacillus
           amyloliquefaciens DSM 7]
 gi|63146682|emb|CAG28933.1| Sigma F [Bacillus amyloliquefaciens FZB42]
 gi|154352438|gb|ABS74517.1| SigF [Bacillus amyloliquefaciens FZB42]
 gi|307606995|emb|CBI43366.1| RNA polymerase sporulation-specific sigma factor (sigma-F)
           [Bacillus amyloliquefaciens DSM 7]
 gi|328552736|gb|AEB23228.1| sporulation sigma factor SigF [Bacillus amyloliquefaciens TA208]
 gi|328912466|gb|AEB64062.1| RNA polymerase sigma factor [Bacillus amyloliquefaciens LL3]
          Length = 255

 Score =  166 bits (422), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 57/253 (22%), Positives = 107/253 (42%), Gaps = 19/253 (7%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L+  E   L K+ +E GD  A   L+  ++RLV  +   +   G    ++   G IGL++
Sbjct: 14  LKDHEVKELIKKSQE-GDQQARDLLIEKNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLK 72

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           +V KFD     R +TY++  I   +Q +I      VK+  +   K L   +RR K  L  
Sbjct: 73  SVDKFDLSYDVRFSTYAVPMIIGEIQRFIRDDG-TVKVSRSL--KELGNKIRRAKDELSK 129

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                 +   V  IA  L +   +V+     +    S++  +  +D +     D +    
Sbjct: 130 TYG---RVPTVQEIADHLEIDAEDVVLAQEAVRAPSSIHETVYENDGDPITLLDQIAD-- 184

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
                     EE+   +  L  ++S L  RE+ I   R  ++   T   ++    +S+ +
Sbjct: 185 --------HSEEKWFDKIALKEAISDLEEREKLIVYLRYYKDQ--TQSEVAERLGISQVQ 234

Query: 269 VRQIEARAFKKVQ 281
           V ++E +  K+++
Sbjct: 235 VSRLEKKILKQIK 247


>gi|313810026|gb|EFS47747.1| sigma-70 region 2 [Propionibacterium acnes HL083PA1]
          Length = 464

 Score =  166 bits (421), Expect = 3e-39,   Method: Composition-based stats.
 Identities = 53/220 (24%), Positives = 99/220 (45%), Gaps = 34/220 (15%)

Query: 2   NRKNMSIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRY------------------ 41
           +    +++V G     +  Y+ +I K+ +L   EE  LAKR                   
Sbjct: 198 DEPEQTVMVAGATADPVKDYLKQIGKVALLNAVEEVDLAKRIEAGLFAGEQLADPDAKIR 257

Query: 42  -REHGDLS--------AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
            ++  D          A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+K
Sbjct: 258 EKDREDYEWIAEDGKVAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEK 317

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G++ +TY+ WWIK A+   +      ++I     +  +   L R++  +      
Sbjct: 318 FDYTKGYKFSTYATWWIKQAITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGR 375

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
              PE    +A +L+++  +VI +        SL+     
Sbjct: 376 EPTPE---ELASELDMTAEKVIEVQKYGREPISLHTPHWV 412


>gi|158833967|gb|ABW81789.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833969|gb|ABW81790.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833971|gb|ABW81791.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833973|gb|ABW81792.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833977|gb|ABW81794.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
 gi|158833987|gb|ABW81799.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
          Length = 225

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 67/229 (29%), Positives = 119/229 (51%), Gaps = 11/229 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L   EE   A+R    GD S+  R++ S+LRLVVKI+  Y   GLP+ ++
Sbjct: 8   YLSEIGYSPLLTAAEEIYFARRVL-CGDESSRRRVIESNLRLVVKISRRYINRGLPLLDL 66

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY  WWI+  ++  I+     +++      K L   
Sbjct: 67  IEEGNLGLIRAVEKFDPERGFRFSTYDTWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 125

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +  L    D++  PE++     K     S ++ +N R++   S++    ++ +   
Sbjct: 126 LRAAR-ELSHKLDHDPSPEEIAEQLNKPVDYVSRMLRLNERIS---SVDTSFGNAAEKG- 180

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
              D L  + D   +   + +   + +  + + +S L+ ++R +   R 
Sbjct: 181 -LLDVLSDETDNDPENTTQND---DMKKSVVKWLSELSTKQREVLARRF 225


>gi|261415258|ref|YP_003248941.1| RNA polymerase, sigma 32 subunit, RpoH [Fibrobacter succinogenes
           subsp. succinogenes S85]
 gi|261371714|gb|ACX74459.1| RNA polymerase, sigma 32 subunit, RpoH [Fibrobacter succinogenes
           subsp. succinogenes S85]
 gi|302327293|gb|ADL26494.1| RNA polymerase sigma-70 factor [Fibrobacter succinogenes subsp.
           succinogenes S85]
          Length = 283

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 67/270 (24%), Positives = 136/270 (50%), Gaps = 15/270 (5%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +Y+++I + P+L +++E +L ++  E G+ +A   LV S+LR VV IA  Y+G GL I E
Sbjct: 15  QYLNDISRYPLLTREQETILLQKSAE-GNKAALDMLVNSNLRFVVNIANLYKGRGLDIME 73

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +++EGN+GL++A ++FD     +  +Y++WWI+  +   I     +++I  +A ++ +  
Sbjct: 74  LINEGNMGLIEAARRFDRSLKIKFISYAVWWIRQNITRAISEKGRMIRI--SAEKELMLR 131

Query: 138 NLRRLKGHLQAITDNNLK-PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
              R    +Q +         Q +    K   SE E I M        SL+A +  ++  
Sbjct: 132 RFNRHAKDVQQVIGGTFTINTQSLEGLSKYKASEIEKILMMGN--STSSLDAPV--NEDG 187

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS-VLNPRERRIFEARRL--QENPV 253
            +   D +       +    E  +  NR  +  + +   L+ +E+ I +       ++ +
Sbjct: 188 DATLGDTISDSQSRTD----ELADNNNRAEVFDKVLDKNLSNQEKEIIKLYYGFKMDSDL 243

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQES 283
            L+ ++    +S+ERVRQ++  A  K++++
Sbjct: 244 NLKEIAPMVGLSKERVRQLKENALNKLRDA 273


>gi|260438829|ref|ZP_05792645.1| RNA polymerase sigma-G factor [Butyrivibrio crossotus DSM 2876]
 gi|292808819|gb|EFF68024.1| RNA polymerase sigma-G factor [Butyrivibrio crossotus DSM 2876]
          Length = 260

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 51/263 (19%), Positives = 114/263 (43%), Gaps = 17/263 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L  +E+  L  + + +GD +A  R +  +LRLV+ +   + G G  + ++   G 
Sbjct: 14  SKLPLLSTKEKEELIIKVK-NGDKAARERYIKCNLRLVLSVVKRFSGNGENMDDLFQIGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD     + +TY++  I   ++ ++  + S +++  +           + +
Sbjct: 73  IGLIKAIDNFDMSLNVKFSTYAVPMIIGEIRRFLRDN-SQIRVSRSLKDVAFRAIYAKER 131

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
                I         V  +A ++ VS+ E++     +    SL   I +   +     D 
Sbjct: 132 -----IMKTGKDEPTVNELATEIGVSKEELVMALDAIQTPVSLYEPIYTDGGDMLYVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    + +E  + E          L  ++  L  RE+ I + R    +  T   +S    
Sbjct: 187 IGDKKNTEENWVNEMA--------LKDAIKRLPDREKEIIKLRYF--DGKTQMEVSKMVR 236

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+ +V ++E  A K ++  +++
Sbjct: 237 ISQAQVSRLEKSAIKNMENYLRR 259


>gi|323704529|ref|ZP_08116107.1| RNA polymerase, sigma 32 subunit, RpoH [Thermoanaerobacterium
           xylanolyticum LX-11]
 gi|323535991|gb|EGB25764.1| RNA polymerase, sigma 32 subunit, RpoH [Thermoanaerobacterium
           xylanolyticum LX-11]
          Length = 339

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 60/269 (22%), Positives = 120/269 (44%), Gaps = 17/269 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSE 81
           KI  L  ++  +L     + G+  A   LV  + +LV+  A          +   ++V  
Sbjct: 74  KIKFLTNEQLCIL----YQQGNKWALEALVDRNKKLVMSRAYKCFKRYKLNIDEDDLVQY 129

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           G  GL++A ++FD +R  +  TY+ WWI  A++  I     ++++        +   L  
Sbjct: 130 GYFGLIKAAERFDIKRETKFVTYATWWIDQAIKRSICDYGFIIRLPVHYFD-EINKVLNI 188

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           L  H       +L  E ++ I ++  +S+ +   +   +    S+++L    + NS    
Sbjct: 189 LSIHF------DLSKEAIIKILEENGISKDKYDDIMFVIENVLSIDSLNKYVNPNSGDGD 242

Query: 202 DWLVYD-HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENL 258
             L+    D     + E+ + K  +  +   +  L  RE+ +   R   +  + +TLE +
Sbjct: 243 TELLDLIVDKTNPTVEEEIDLKLLKETINNILDTLKSREKEVIRMRFGLDGGDEMTLERI 302

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             EF ++RER+RQIE +A KK++   + +
Sbjct: 303 GKEFNITRERIRQIEEKAIKKLRHPSRSK 331


>gi|51892950|ref|YP_075641.1| sporulation sigma factor SigF [Symbiobacterium thermophilum IAM
           14863]
 gi|51856639|dbj|BAD40797.1| RNA polymerase sigma factor similar to B. subtilis
           sporulation-specific sigma-F [Symbiobacterium
           thermophilum IAM 14863]
          Length = 255

 Score =  166 bits (421), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 58/254 (22%), Positives = 112/254 (44%), Gaps = 15/254 (5%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
             EE          GD  A  RLV  +LRLV  +   +   G    ++   G IGL++A+
Sbjct: 13  PDEEVRRLVALARAGDKEARDRLVEGNLRLVRSLVSRFSASGADPEDLFQIGCIGLLKAI 72

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
            +FD     R +TY++  I   ++ ++     + ++  +  Q  L    RR++  L A  
Sbjct: 73  DRFDLNYDVRFSTYAVPLIMGEIRRHLRDDGPM-RVSRSLKQ--LAQQARRVRERLAAQM 129

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
           + +     V  +A +L VS  EV++    +    S++  ++  D +     D L  D   
Sbjct: 130 ERD---PTVAEVAAELGVSPEEVVAALDGVRPPTSIHQTVHEGDGDPIYLLDQLAADDGQ 186

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
           +E V ++       R  L   ++ L+ RER +   R  ++   T   ++S    S+ +V 
Sbjct: 187 REGVWLD-------RVALREGLNQLDERERTVILLRFFRD--KTQTEVASILGCSQVQVS 237

Query: 271 QIEARAFKKVQESI 284
           ++E RA ++++  +
Sbjct: 238 RLERRALERIRNYV 251


>gi|167758779|ref|ZP_02430906.1| hypothetical protein CLOSCI_01121 [Clostridium scindens ATCC 35704]
 gi|167663519|gb|EDS07649.1| hypothetical protein CLOSCI_01121 [Clostridium scindens ATCC 35704]
          Length = 258

 Score =  166 bits (420), Expect = 4e-39,   Method: Composition-based stats.
 Identities = 52/260 (20%), Positives = 118/260 (45%), Gaps = 17/260 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+++E+  L  R +  GD  A    +  +LRLV+ +   + G      ++   G I
Sbjct: 15  KLPILKEEEKEALFARIK-AGDAEAKEEYIKGNLRLVLSVIKRFGGSNENPDDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  F+ E   + +TY++  I   ++ Y+  + S +++      + L     +   
Sbjct: 74  GLIKAINNFNTELDVKFSTYAVPMIIGEIRRYMRDNNS-IRVS-----RSLRDTAYKAIY 127

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             +     NLK   V  IA+++ +S+ +++     +    SL   + +   ++    D +
Sbjct: 128 AKENYIKQNLKEPTVQEIAEEIGISKEDIVFALDAIQVPMSLQEPVYNDGGDALYVMDQI 187

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               + +E+ + +          L  +M  L  RER I + R       T   ++ E ++
Sbjct: 188 SDTKNKEEKWVEDLS--------LEAAMQHLGERERYIIKLRFF--EGKTQMEVADEIKI 237

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ +V ++E  A + +++ +
Sbjct: 238 SQAQVSRLEKNALRLMRQYL 257


>gi|302554830|ref|ZP_07307172.1| RNA polymerase sigma factor rpoD [Streptomyces viridochromogenes
           DSM 40736]
 gi|302472448|gb|EFL35541.1| RNA polymerase sigma factor rpoD [Streptomyces viridochromogenes
           DSM 40736]
          Length = 481

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 81/284 (28%), Positives = 135/284 (47%), Gaps = 25/284 (8%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++  GE GL R     R +P     EE     R  E     A   LV  + RLV KIA+G
Sbjct: 211 LLRGGEDGLGRSDRLGRDVP----AEEIAALPRGSER--WRAYECLVLHNQRLVWKIALG 264

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y+G GL   ++V  G IGLM+AV+KFD  +GF+ +TY+ WWIK A+   I    +L+++ 
Sbjct: 265 YQGRGLDTEDLVQHGTIGLMRAVRKFDATKGFKFSTYATWWIKQAITRAIADEGTLIRLP 324

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              ++K     + ++    + +  N  +P  V  +A    ++ +EV  +       +SL+
Sbjct: 325 AHVHEK-----VSKVAVAERKLL-NEGRPRTVDNVAYVSGLTFAEVEKVRRISRSTDSLD 378

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
            +I     + +   D ++         ++    RK  +  L   +  L+ RER +   R 
Sbjct: 379 RII----GDDTALGDLIIGPSRLPGPDVV--LIRKEFQARLRHVVEHLSERERHVLVRRT 432

Query: 248 L--QENPVTLENLSSEFEVSRERVRQIEARAFKK-----VQESI 284
               + P TLE++   F V+RER+RQIE +A  K     ++  +
Sbjct: 433 GLDGDEPDTLEDIGVVFGVTRERIRQIEPKAKAKFEGQLLRHGL 476


>gi|23099294|ref|NP_692760.1| sporulation sigma factor SigF [Oceanobacillus iheyensis HTE831]
 gi|22777523|dbj|BAC13795.1| stage II sporulation protein AC (RNA polymerase sigma-F factor)
           [Oceanobacillus iheyensis HTE831]
          Length = 250

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 49/256 (19%), Positives = 107/256 (41%), Gaps = 20/256 (7%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L  ++   L  R  + GD SA  RLV  ++RLV  +   +   G    ++   G+IGL++
Sbjct: 12  LSDEQVKELI-RLSQQGDQSARDRLVEKNIRLVWSVVQRFINRGYDPDDLFQIGSIGLIK 70

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           ++ KFD     + +TY++  I   +Q +I    S +K+  +  +        +++     
Sbjct: 71  SIDKFDLSYDVKFSTYAVPMIIGEIQRFIRDDGS-IKVSRSLKEIG-----NKIRRKKDE 124

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           +T    +   V  +A+ L +   EV+         +S+   +  +D +     D +    
Sbjct: 125 MTKQYGRSPTVNELAEALELQPEEVVHAQEAAKSPQSIYETVFENDGDPITLLDQIADQD 184

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
               + L            L  ++  L  RER I   R  ++   T   ++    +S+ +
Sbjct: 185 SKWFEKL-----------SLQEAIRSLTERERLIIYLRYYKD--KTQTEVAERLGISQVQ 231

Query: 269 VRQIEARAFKKVQESI 284
           V ++E +  + +++++
Sbjct: 232 VSRLEKKILEDMKKNM 247


>gi|293401521|ref|ZP_06645664.1| RNA polymerase sigma-G factor [Erysipelotrichaceae bacterium
           5_2_54FAA]
 gi|291305159|gb|EFE46405.1| RNA polymerase sigma-G factor [Erysipelotrichaceae bacterium
           5_2_54FAA]
          Length = 259

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 56/258 (21%), Positives = 119/258 (46%), Gaps = 17/258 (6%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           +L  +E   L K+Y+  GD  A   L+  +L+LV+ I   +      + ++   G IGL+
Sbjct: 18  VLSNEEMKELFKKYQ-SGDEQAKEDLIQGNLKLVLSIVQRFSNRCENMDDLFQVGCIGLV 76

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +++  FD +   R +TY++  I   ++ Y+  +  ++++      K L + + RLK   +
Sbjct: 77  KSIDNFDLKHEVRFSTYAVPMIMGEIKRYLRDNQ-VIRVSRHL--KDLAYKVFRLK---E 130

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                + K   +  +A++L V E +V+          S+   + ++D +     D +  D
Sbjct: 131 EYIHEHQKEPTIHWLAEQLQVKEKDVVDALDSTQSVVSIFEPVYNTDGDELYLLDQIKDD 190

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            D        + ER +    L +SM  L  +E+ I + R  Q+   T   +++E  +S+ 
Sbjct: 191 KD--------EIERLSNYMTLKKSMRNLKGKEKDIIQKRYYQD--KTQTEIANELGISQA 240

Query: 268 RVRQIEARAFKKVQESIQ 285
           +V ++E  A   +++  +
Sbjct: 241 QVSRLEKNAIALLKKEFE 258


>gi|158320823|ref|YP_001513330.1| FliA/WhiG family RNA polymerase sigma factor [Alkaliphilus
           oremlandii OhILAs]
 gi|158141022|gb|ABW19334.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           oremlandii OhILAs]
          Length = 256

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 55/262 (20%), Positives = 119/262 (45%), Gaps = 16/262 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           ++ +LE      L  +  + G++ A   LV  +L LV  +   +   G    ++   G I
Sbjct: 10  QVEILEHDRTIELILQ-AQSGNMEAQEILVNHNLGLVRSVIRRFANRGYEREDLFQLGCI 68

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+KKFD     R +TY++  I   ++ ++     ++K+  +  Q        R+K 
Sbjct: 69  GLIKAIKKFDTSFDVRFSTYAVPMIIGEIKRFLRDDG-IIKVSRSLKQ-----TAARVKM 122

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + +   N +   +  IA  +  ++ E++      A  E L  +I+  D +     D +
Sbjct: 123 TKEKLQKENGREPTLQEIADDMGATKEEIVMALDSSASPEYLYDVIHQDDGSPIHLIDKI 182

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             +   ++  +I+       R +L  ++S L PRER+I   R  ++   T   ++    +
Sbjct: 183 SENDTLEDSEVID-------RIVLQEAISKLEPRERQIIFLRYFKDQ--TQTQIAQVLGI 233

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+ +V +IE +  + +++ ++K
Sbjct: 234 SQVQVSRIEKKVLQNMKDIMKK 255


>gi|6682869|dbj|BAA88921.1| sigma factor [Nicotiana tabacum]
          Length = 508

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 61/242 (25%), Positives = 118/242 (48%), Gaps = 12/242 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  RL  S++RLV+ IA  Y   G  ++++V  G IGL++ ++KFDP +G++++TY  WW
Sbjct: 265 ARERLAMSNVRLVMSIAQRYDNVGAEMADLVQGGLIGLLRGIEKFDPSKGYKISTYVYWW 324

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   ++ +   +++ T  +++       + +   + IT        V  IA  LN+
Sbjct: 325 IRQGVSRALVENSRTLRLPTYLHERLSLIRNAKARLEEKGIT------PSVNNIAASLNM 378

Query: 169 SESEVISMNCRLAGDESLN--ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           S+ +V +     +   SL+  A  + +         ++  +H   E       +    ++
Sbjct: 379 SQKKVRNATEASSKMYSLDREAFPSLNGLPGETLHSYIADNH--LENNPWHGVDVWALKD 436

Query: 227 MLTRSM-SVLNPRERRIFEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +   + S L  RER I       +N  +T E++S    +SRERVRQ+   A +K++ + 
Sbjct: 437 EVNNLISSTLRDREREIIRLYYGLDNECLTWEDISKRIGLSRERVRQVGLVALEKLKHAA 496

Query: 285 QK 286
           +K
Sbjct: 497 RK 498


>gi|209883307|ref|YP_002287164.1| RNA polymerase sigma factor RpoD [Oligotropha carboxidovorans OM5]
 gi|209871503|gb|ACI91299.1| RNA polymerase sigma factor RpoD [Oligotropha carboxidovorans OM5]
          Length = 387

 Score =  166 bits (420), Expect = 5e-39,   Method: Composition-based stats.
 Identities = 67/283 (23%), Positives = 119/283 (42%), Gaps = 34/283 (12%)

Query: 29  LEKQEEYVLAKRYREHGD--------------------LSAAHRLVTSHLRLVVKIAMGY 68
           L + EE  L +  R   D                      A  R V S+L  V K+A   
Sbjct: 106 LNEMEERELGRTIRLAKDIQYAALEDLNQYERQLVHRAEKAKARFVESNLLYVRKLANRK 165

Query: 69  RGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           R        ++  EG +GL++A + FDPE GFR  TY+ WWI+  M   +      +++ 
Sbjct: 166 RNLKHLTADDLFQEGLMGLLKATELFDPELGFRFKTYATWWIQQYMSRALDDGDRTIRLP 225

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              ++       R++K     +T    +   +  +A +L +    +  +  RL   E + 
Sbjct: 226 VHRHE-----YFRKIKRKTAKLTFELGREPTLNELATELGLERERLAKLLWRLHVTECVE 280

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           A     +  +      ++     +   +++    +  R M+ R ++ L PRE RI   R 
Sbjct: 281 ADAPIGEDTT------VLSYKADESPSILDLVALQQLRTMVARVLATLVPREERIIRMRF 334

Query: 248 LQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
             +     TLE + + F V+RER+RQIEA+A +K++   + + 
Sbjct: 335 GLDGSGEQTLEAIGNVFGVTRERIRQIEAKALRKLKHPSRSRA 377


>gi|158833959|gb|ABW81785.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
          Length = 225

 Score =  165 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 66/229 (28%), Positives = 118/229 (51%), Gaps = 11/229 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L   EE   A+R    GD S+  R++ S+LRLVVKI+  Y   GLP+ ++
Sbjct: 8   YLSEIGYSPLLTAAEEIYFARRVL-CGDESSRRRMIESNLRLVVKISRRYINRGLPLLDL 66

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     + +      K L   
Sbjct: 67  IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIHLPIHIV-KELNVY 125

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +  L    D++  PE++     K     S ++ +N R++   S++    ++ +   
Sbjct: 126 LRAAR-ELAHKLDHDPSPEEIAEQLNKPVDYVSRMLRLNERIS---SVDTSFGNAAEKG- 180

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
              D L  + D   +   + +   + +  + + +  L+ ++R +   R 
Sbjct: 181 -LLDVLSDETDNDPENTTQND---DMKKSVVKWLFELSTKQREVLARRF 225


>gi|150390630|ref|YP_001320679.1| sporulation sigma factor SigG [Alkaliphilus metalliredigens QYMF]
 gi|149950492|gb|ABR49020.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           metalliredigens QYMF]
          Length = 257

 Score =  165 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 55/261 (21%), Positives = 108/261 (41%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            ++P+L+      L    ++ GD SA    +  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SELPVLKNDYMRHLFGLIKQ-GDNSAREEFIQGNLRLVLSVIQRFNNRGEHVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD     R +TY++  I   ++ Y+  + S +++      + L     +  
Sbjct: 73  IGLIKAIDNFDLRHNVRFSTYAVPMIIGEIRRYLRDNNS-IRVS-----RSLRDTAYKAL 126

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
                +T+   K   V  IA  LN+   +V+     +    SL   I     ++    D 
Sbjct: 127 QVRDQLTNQKSKEPSVAEIAANLNIPREDVVFALDAIQDPVSLFEPIYHDSGDAIFVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  +    E  +            L  +M  LN RE+ I   R       T   ++ E  
Sbjct: 187 IRDEKSEDETWIDGIA--------LREAMRRLNNREKHILNLRFF--EGRTQMEVADEIG 236

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A K ++++I
Sbjct: 237 ISQAQVSRLEKTALKHMRKNI 257


>gi|4100836|gb|AAD01000.1| RpoS [Escherichia coli]
          Length = 259

 Score =  165 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 63/231 (27%), Positives = 112/231 (48%), Gaps = 12/231 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L   EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 39  YLGEIGYSPLLTA-EEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 96

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 97  IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 155

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    + + 
Sbjct: 156 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA- 210

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
                L    D +E    +  +  + +  + + +  LN ++R +   R   
Sbjct: 211 ----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGL 257


>gi|4103484|gb|AAD01787.1| sigma-D factor [Myxococcus xanthus]
          Length = 297

 Score =  165 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 75/272 (27%), Positives = 123/272 (45%), Gaps = 50/272 (18%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           GLS Y+  +     L +++EY LA+R R+ GD SA     +S+L  VV +A  +   G  
Sbjct: 11  GLSHYLRNLGGHQQLTREQEYELARRARK-GDESARQTTASSNLAFVVAVAKKFANRGAR 69

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++ EGN+GLM+A++ FDP++  R ATY++WWI+A +  Y+  + S V+ G       
Sbjct: 70  LDDLIQEGNVGLMKAIEHFDPKKNVRFATYAVWWIRAYITRYLKDNRSQVRGG------- 122

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
                                              E+E  SM      D SL+A I   +
Sbjct: 123 -----------------------------------EAERGSMV-----DFSLDATI--DE 140

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
              + + D L  +    +QV +  E+    +  L +    +      I   R  Q+ P+T
Sbjct: 141 DGETTFLDRLEDNSPSPQQVFLAHEQDTEIQEALAKVRKRIGDLGWDILTERLTQDKPLT 200

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           LE L   + VSRE VRQ+E +    ++  +Q 
Sbjct: 201 LEELGQRWGVSREPVRQVELKTKNFLERYLQA 232


>gi|167765669|ref|ZP_02437722.1| hypothetical protein CLOSS21_00157 [Clostridium sp. SS2/1]
 gi|167712644|gb|EDS23223.1| hypothetical protein CLOSS21_00157 [Clostridium sp. SS2/1]
          Length = 271

 Score =  165 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 57/259 (22%), Positives = 112/259 (43%), Gaps = 17/259 (6%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L ++E+  L +R  E GDL A    +  +LRLV+ I   + G      ++   G IG
Sbjct: 29  LPLLSEEEKEDLFERI-EQGDLLAREHYIKGNLRLVLSIIQRFSGSNENADDLFQVGCIG 87

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           LM+A+  FD     + +TY++  I   ++ Y+  + S+ ++      + L     +    
Sbjct: 88  LMKAIDNFDRNLNVKFSTYAVPMIIGEVKRYLRDNHSM-RVS-----RSLRDTAYKAINA 141

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            + +T        +  IAK++++ + +V+     +A   SL   +     ++    D  V
Sbjct: 142 REVLTKKLNHEPTIDVIAKEIDMKKEDVLFALDAIATPLSLYEPVYQDGGDTLYLMDQ-V 200

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            D   +E   +E          L  +M  L  RE  I + R       T   ++ E  +S
Sbjct: 201 KDKKNKEDSWVESI-------ALKEAMEHLPDREYDIIKMRFF--EGKTQTEVADEIAIS 251

Query: 266 RERVRQIEARAFKKVQESI 284
           + +V ++E  A K ++  +
Sbjct: 252 QAQVSRLEKNALKHMKNHL 270


>gi|258515296|ref|YP_003191518.1| RNA polymerase, sigma 28 subunit, SigF [Desulfotomaculum
           acetoxidans DSM 771]
 gi|257779001|gb|ACV62895.1| RNA polymerase, sigma 28 subunit, SigF [Desulfotomaculum
           acetoxidans DSM 771]
          Length = 259

 Score =  165 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 50/265 (18%), Positives = 119/265 (44%), Gaps = 17/265 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           + P+L+ +E   L  + +  GD  A  RLV  +L+LV  +   +   G  + ++   G+I
Sbjct: 12  RFPLLKDEEMRQLLAKAKL-GDAVARERLVNCNLKLVFNLVKRFNNRGYELEDLFQIGSI 70

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A+ KFD     + +TY++  I   ++ ++      VK+  +  +        +++ 
Sbjct: 71  GLMKAIDKFDLNYDVKFSTYAVPMIVGEIRRFLRDDN-PVKVSRSVKEIAY-----KVQQ 124

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + +     +   +  +A+++ +S+ EV+          S+   ++  D +     D L
Sbjct: 125 TKERLIGKLGREPSIGEVAEEIGLSKEEVVIALEAAQSPTSIYETLHQDDGDPIYLLDQL 184

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
                     L + E        +   ++ L+ R+R+I   R  ++   T  +++    +
Sbjct: 185 SSKEGNDLFWLDQIE--------VKELLNNLHERDRQILIWRFFED--KTQSDIARRLGL 234

Query: 265 SRERVRQIEARAFKKVQESIQKQVE 289
           S+ +V ++E +A  K++E + + ++
Sbjct: 235 SQVQVSRLERQALNKLKEVMAENIK 259


>gi|2529267|gb|AAB81186.1| sigma factor [Paenibacillus polymyxa]
          Length = 251

 Score =  165 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 54/256 (21%), Positives = 110/256 (42%), Gaps = 19/256 (7%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           LE  E   L     + GD  A   L+ S++RLV  +   +   G    ++   G IGL++
Sbjct: 13  LEDTEVKRLI-ALSQSGDNDARETLINSNIRLVWSVVQRFMNRGYEPDDLFQIGCIGLLK 71

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           +V KFD     + +TY++  I   +Q ++      +K+  +   K     +R++K  L  
Sbjct: 72  SVDKFDLSYEVKFSTYAVPMIIGEIQRFLRDDG-TLKVSRSL--KETANKVRKMKDELSK 128

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
             +       V  +A +L V+  +V+          S++  +  +D +     D +    
Sbjct: 129 PLNRL---PTVKEVADELGVTPEDVVFAQEANKPPTSIHETVFENDGDPITLMDQIAD-- 183

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
                   E +ER   +  L  ++  L+ RER I   R  ++   T   ++S   +S+ +
Sbjct: 184 --------ESQERWFDKLALNEAIDGLSERERLIVYLRYYRDQ--TQSEVASRLGISQVQ 233

Query: 269 VRQIEARAFKKVQESI 284
           V ++E +  +++++ I
Sbjct: 234 VSRLEKKILQQIRDQI 249


>gi|134298555|ref|YP_001112051.1| sporulation sigma factor SigG [Desulfotomaculum reducens MI-1]
 gi|134051255|gb|ABO49226.1| RNA polymerase, sigma subunit, RpsG/SigG [Desulfotomaculum reducens
           MI-1]
          Length = 257

 Score =  165 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 46/261 (17%), Positives = 112/261 (42%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+  +   L +  ++ GD  A  +L+  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPVLKNTQMRTLFEAMQQ-GDKDARSQLINGNLRLVLSVIQRFTNRGEYVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+A+  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 73  IGLMKAIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDVAYKALQVR 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L    +   +   +  IA +L +   +++     +    SL   I     +     D 
Sbjct: 130 DTL---VNKYSREPSINEIAGELKMPREDIVFALDAIQEPISLFEPIYHDGGDPIFVLDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  + +     L E          +  ++  L+ RE+ I   R       T   ++ E  
Sbjct: 187 ISDEKNLDLSWLEE--------ISIRDALRRLSDREKHILTLRFF--EGKTQMEVADEIG 236

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A   +++ +
Sbjct: 237 ISQAQVSRLEKAALNHMKKFV 257


>gi|261366888|ref|ZP_05979771.1| RNA polymerase sigma-G factor [Subdoligranulum variabile DSM 15176]
 gi|282571002|gb|EFB76537.1| RNA polymerase sigma-G factor [Subdoligranulum variabile DSM 15176]
          Length = 260

 Score =  165 bits (419), Expect = 6e-39,   Method: Composition-based stats.
 Identities = 60/263 (22%), Positives = 115/263 (43%), Gaps = 18/263 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            ++P+L + E+  L +  R  GD  A  +++  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SQLPVLSETEKSALIRAAR-AGDAEARRKMIQGNLRLVLSVVQKFANRGENLDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FDP    R +TY +  I   ++ ++  +   V++  +   + L ++  R +
Sbjct: 73  IGLIKAIDHFDPSLQVRFSTYGVPMIVGEIRRFLRDNN-AVRVSRSI--RDLAYHSMRAR 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             LQ     N +  ++  IA ++  S   V      +    SL   + S  ++S    D 
Sbjct: 130 EALQK---ENGRDPKISEIAARVGASPENVAMALESVVEPASLYEPVYSDGEDSFAIVDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L              EE      M   ++  L+ RERRI   R L     T   ++ E  
Sbjct: 187 LHD---------ATGEESWISDIMFRDTVKSLSARERRIIAMRYLGG--KTQMQVAREIG 235

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+ +V ++E  A  +++E I  
Sbjct: 236 ISQAQVSRLEKGALNRIKEQISS 258


>gi|326566650|gb|EGE16791.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis 12P80B1]
          Length = 585

 Score =  165 bits (419), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 52/204 (25%), Positives = 87/204 (42%), Gaps = 10/204 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 379 IGEAKARRAKKDMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 438

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            + R+   L         PE   
Sbjct: 439 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKINRVSRQLLQEMGREPTPE--- 493

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            + ++L++ E++V  +        S+   I   D   S   D++    D      IE   
Sbjct: 494 ELGERLDMDEAKVRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDNTISSPIENAT 548

Query: 221 RKNRRNMLTRSMSVLNPRERRIFE 244
            +  R      +  L  RE ++ +
Sbjct: 549 AEGLREATREVLDNLTEREAKVLK 572


>gi|238917256|ref|YP_002930773.1| RNA polymerase sporulation-specific sigma factor [Eubacterium
           eligens ATCC 27750]
 gi|238872616|gb|ACR72326.1| RNA polymerase sporulation-specific sigma factor [Eubacterium
           eligens ATCC 27750]
          Length = 258

 Score =  165 bits (419), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 48/259 (18%), Positives = 116/259 (44%), Gaps = 17/259 (6%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L+  +   L  + +  GD  A    +  +LRLV+ I   +   G  + ++   G IG
Sbjct: 16  LPLLKPAQAKELLVKIK-SGDTQARETFIKGNLRLVLSIVQRFSQSGENLDDLFQIGCIG 74

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           +++A+  FD     + +TY++  I   ++ ++  + S +++      + L     +    
Sbjct: 75  MIKAIDNFDISLNVQFSTYAVPMIIGEIKRFLRDN-STIRVS-----RSLKDTAYKAITT 128

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            + +   NLK   +  IA+++ +S+++++     +    SL   + +   ++    D + 
Sbjct: 129 RETLMKKNLKEPSITEIAEEIGISKADIVIALEAVTPSISLYEPVFNDGGDTLYVIDQVK 188

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
              +         E+R  R   L  +++ L+PRER+I   R      +T   ++    +S
Sbjct: 189 DKKNT--------EDRWVRNIALQEAINRLSPRERQIIILRFFDC--LTQTEVAKGLGIS 238

Query: 266 RERVRQIEARAFKKVQESI 284
           + +V ++E  A + ++  +
Sbjct: 239 QAQVSRLEKCALRDMKRHL 257


>gi|326512474|dbj|BAJ99592.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 506

 Score =  165 bits (419), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 68/254 (26%), Positives = 120/254 (47%), Gaps = 10/254 (3%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L  R RE     A   L  S++RLV+ IA  Y   G+ +S+++  G IGL++ ++KFD 
Sbjct: 252 ELRSRMRES--FLAREVLTMSNIRLVISIAQKYDKLGVELSDLIQGGLIGLLRGIEKFDA 309

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            RGFR++TY  WWI+  +   +  +    ++ T  +++     L  ++    A+ D  + 
Sbjct: 310 SRGFRISTYVYWWIRQGVSRALADNSRTFRLPTYMHER-----LIAIRAAKYALEDQGVS 364

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQV 214
           P     IA+ LN+SE +V +    +    SL+     S +          + D +     
Sbjct: 365 P-TTQNIAELLNISEKKVHNATEAVNKALSLDQQAFPSLNGLPGDTLHSYIEDQNVANDP 423

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIE 273
               EE   +  +    +S L  RER I        +   T E++S +F +SRERVRQ+ 
Sbjct: 424 WHGFEEWYLKEEVNNLLISNLTERERHIIRLYHGIGKQCHTWEDISRQFGLSRERVRQVG 483

Query: 274 ARAFKKVQESIQKQ 287
             A +K++ + +++
Sbjct: 484 LIAMEKLKHAARRK 497


>gi|71894468|ref|YP_278576.1| RNA polymerase sigma factor [Mycoplasma synoviae 53]
          Length = 490

 Score =  165 bits (419), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 67/284 (23%), Positives = 128/284 (45%), Gaps = 24/284 (8%)

Query: 16  LSRYIHEIRKI-PMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  Y+  I K   +L  QEE  LA+   + G     A   ++  +LRLVV  A  Y+  G
Sbjct: 194 VKWYMRWIGKYGKLLTPQEEKDLAEEMDKGGSRGKRARDLIIKRNLRLVVNAAKKYKNRG 253

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L   ++VSEGN GL++A +KFD ++GF+ +TY+ WWI+ ++   +     ++++     +
Sbjct: 254 LSFIDLVSEGNAGLLKAAQKFDIKKGFKFSTYATWWIRQSISRAVADQARIIRVPVHMVE 313

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIA--KKLNVSESEVISMNCRLAGDESLNALI 190
                 + +++  +Q      +  E++ A    K      S +  +        SL+  +
Sbjct: 314 --TINKIYKIEREIQQENGGEIIDEEIAARLGGKSKKYDASYIRYIRKINTSPISLDKQV 371

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
               +N S + D++  +         +KEE   + N     +  L+  E  + +      
Sbjct: 372 --GKENDSFFGDFVKDESIISPVEFADKEELITKINYYVEKL--LSEAEADLIKRYHGIG 427

Query: 251 --------NPVTLENLSSEF-----EVSRERVRQIEARAFKKVQ 281
                      TL+ +S +F     ++S+ERVRQI  + +KK++
Sbjct: 428 YDAKGNPVRSATLDEISKDFRGEGKKISKERVRQIITKIYKKLR 471


>gi|225019126|ref|ZP_03708318.1| hypothetical protein CLOSTMETH_03078 [Clostridium methylpentosum
           DSM 5476]
 gi|224948099|gb|EEG29308.1| hypothetical protein CLOSTMETH_03078 [Clostridium methylpentosum
           DSM 5476]
          Length = 288

 Score =  165 bits (418), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 50/258 (19%), Positives = 116/258 (44%), Gaps = 18/258 (6%)

Query: 28  MLEKQEEYVLAKRYREHGDLS-AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           +L+++E+  L  R + +     A  +L++ +L+LV+ +   +   G  + ++   G IGL
Sbjct: 48  VLKEKEKIELLTRIKNNDRPEQAREKLISGNLKLVLSVIQRFTNRGENLDDLFQVGCIGL 107

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+  FD  +  R +TY++  I   ++ Y+  + S V++      + L     +     
Sbjct: 108 IKAIDNFDISQNVRFSTYAVPMIIGEIRRYLRDNNS-VRVS-----RSLKDTAYKAMQAK 161

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           + +T  +LK   +  I++++ V   +V+     +    SL   + S   ++    D +  
Sbjct: 162 EKLTTAHLKEPTIDEISQEMGVRREDVVLALESIVDPVSLYEPVYSDGGDTIYVMDQIGD 221

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
             D +                +  ++  LN RE++I   R    N  T   ++ +  +S+
Sbjct: 222 KSDDK---------NWLDEIAIKEAIKNLNEREKKILSLRFF--NGKTQVEVAEDIGISQ 270

Query: 267 ERVRQIEARAFKKVQESI 284
            +V ++E  A  ++++SI
Sbjct: 271 AQVSRLEKGALDRIKKSI 288


>gi|125560253|gb|EAZ05701.1| hypothetical protein OsI_27933 [Oryza sativa Indica Group]
          Length = 372

 Score =  165 bits (418), Expect = 7e-39,   Method: Composition-based stats.
 Identities = 68/254 (26%), Positives = 121/254 (47%), Gaps = 10/254 (3%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L  R  E     A   L  S+LRLV+ IA  Y   G+ +++++  G IGL++ ++KFD 
Sbjct: 118 ELRSRMHES--FLAREMLTMSNLRLVISIAQKYDNLGVELADLIQGGLIGLLRGIEKFDA 175

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            RGFR++TY  WWI+  +   +  +    ++ T  +++     L  ++G    + D  + 
Sbjct: 176 SRGFRISTYVYWWIRQGVSRALAENSKTFRLPTYLHER-----LIAIRGAKYELEDQGIA 230

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQV 214
           P  +  IA  LN+SE +V++    +    SL+     S +    +     + D +     
Sbjct: 231 P-TIENIAGSLNISEKKVLNATEAVNKVLSLDQQAFPSLNGLPGETLHSYIEDQNVANDP 289

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIE 273
               EE   +  +     S LN RER I        +   T E++S +F +SRERVRQ+ 
Sbjct: 290 WHGFEEWYLKEEVNKLLNSTLNERERDIIRLYHGIGKQCHTWEDISRQFGLSRERVRQVG 349

Query: 274 ARAFKKVQESIQKQ 287
             A +K++ + +++
Sbjct: 350 LIAMEKLKHAARRK 363


>gi|258592807|emb|CBE69116.1| RNA polymerase sigma factor RpoS [NC10 bacterium 'Dutch sediment']
          Length = 286

 Score =  165 bits (418), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 81/271 (29%), Positives = 138/271 (50%), Gaps = 14/271 (5%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
            +  L  Y+  I ++P+L+K+EE  L K   + GD  A  +LV ++LR VVK+A+ YRG 
Sbjct: 14  SDDALGAYLKRIAQVPLLKKEEELKLGKA-TQRGDEKALKQLVEANLRFVVKVALRYRGC 72

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL + ++++EGNIGL++A +++ P+   +  TY++WWI+ A+ + +  S   V++     
Sbjct: 73  GLSLPDLINEGNIGLLEAARRYSPDYNVKFITYAVWWIRQAIMQALAISGGAVRLPLRKA 132

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
             RL   L  ++  L           +V     +L++S S++     R         L  
Sbjct: 133 --RLASQLDDVRADLSQQLQAEPTDSEVTE---ELDLSASDLEGALHRAGQ------LAF 181

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ-- 249
            SD+   + +  +      Q      +  R++ R  + R +  LN RER I E R     
Sbjct: 182 LSDEIGLEQRIGMELYESKQLPPADYELIRRSLREEVERMLRSLNDRERLIVELRFGLGK 241

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           E  +TL+ +    ++SRERVRQIE RA +K+
Sbjct: 242 EEAMTLKEVGKRLKLSRERVRQIEERAKQKL 272


>gi|37806470|dbj|BAC99905.1| putative plastid RNA polymerase sigma factor [Oryza sativa Japonica
           Group]
          Length = 388

 Score =  165 bits (418), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 68/254 (26%), Positives = 121/254 (47%), Gaps = 10/254 (3%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L  R  E     A   L  S+LRLV+ IA  Y   G+ +++++  G IGL++ ++KFD 
Sbjct: 134 ELRSRMHES--FLAREMLTMSNLRLVISIAQKYDNLGVELADLIQGGLIGLLRGIEKFDA 191

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            RGFR++TY  WWI+  +   +  +    ++ T  +++     L  ++G    + D  + 
Sbjct: 192 SRGFRISTYVYWWIRQGVSRALAENSKTFRLPTYLHER-----LIAIRGAKYELEDQGIA 246

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQV 214
           P  +  IA  LN+SE +V++    +    SL+     S +    +     + D +     
Sbjct: 247 P-TIENIAGSLNISEKKVLNATEAVNKVLSLDQQAFPSLNGLPGETLHSYIEDQNVANDP 305

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIE 273
               EE   +  +     S LN RER I        +   T E++S +F +SRERVRQ+ 
Sbjct: 306 WHGFEEWYLKEEVNKLLNSTLNERERDIIRLYHGIGKQCHTWEDISRQFGLSRERVRQVG 365

Query: 274 ARAFKKVQESIQKQ 287
             A +K++ + +++
Sbjct: 366 LIAMEKLKHAARRK 379


>gi|187935615|ref|YP_001885389.1| sporulation sigma factor SigG [Clostridium botulinum B str. Eklund
           17B]
 gi|187723768|gb|ACD24989.1| RNA polymerase sigma-G factor [Clostridium botulinum B str. Eklund
           17B]
          Length = 257

 Score =  165 bits (418), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 57/261 (21%), Positives = 111/261 (42%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+PML K++E        + GDLSA    +  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPML-KEKEKKQLLLALKKGDLSARETFIKGNLRLVLSVIQRFNNRGENVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+++  FD  +  + +TY++  I   ++ Y+  + S +++  +         + R K
Sbjct: 73  IGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRDIAYKALIVRDK 131

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
                   +N K   +  IAK+L +   EV+     +    SL   I     ++    D 
Sbjct: 132 -----FIKDNNKEPTISQIAKELELPREEVVFALDAIQDPVSLFEPIYHDGGDAIFVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    +  E  L            +  +M  L  RE+ I   R  +    T   ++ E  
Sbjct: 187 ISDSKNTDESWLEN--------ISIKEAMKKLTDREKLILNLRFFRG--RTQMEVADEIG 236

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A K +++ +
Sbjct: 237 ISQAQVSRLEKTALKHMRKHV 257


>gi|150389982|ref|YP_001320031.1| FliA/WhiG family RNA polymerase sigma factor [Alkaliphilus
           metalliredigens QYMF]
 gi|149949844|gb|ABR48372.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           metalliredigens QYMF]
          Length = 258

 Score =  165 bits (418), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 55/259 (21%), Positives = 116/259 (44%), Gaps = 16/259 (6%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           +L  +E   L +   + GDL A  +LV+ +L L+  +   +   G    ++   G+IGL+
Sbjct: 14  VLPHEETMTLIQ-MAQKGDLQAQEKLVSHNLGLIRSVIKRFSNRGYDREDLFQLGSIGLI 72

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +A++KFD     R +TY++  I   ++ ++     ++K+  +  Q        R+K   +
Sbjct: 73  KAIRKFDISFNVRFSTYAVPMIIGEIKRFLRDDG-IIKVSRSLKQ-----TASRVKVTKE 126

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
            +     +   +  IAK L +++ E++         E L  +I+  D +     D +   
Sbjct: 127 KLFKEFGREPTLHEIAKVLEITKEEIVMALDSNMYPEYLYEVIHQDDGSPIHLIDKISET 186

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
               +  +I+K        ML   +  L PRER+I   R  ++   T   ++    +S+ 
Sbjct: 187 DSLDDSEVIDKI-------MLKEVIGRLEPRERQIIILRYFKD--KTQTEIAKVLGISQV 237

Query: 268 RVRQIEARAFKKVQESIQK 286
           +V +IE +  + +++ + K
Sbjct: 238 QVSRIEKKVLQTMKDMMSK 256


>gi|56963560|ref|YP_175291.1| sporulation sigma factor SigF [Bacillus clausii KSM-K16]
 gi|56909803|dbj|BAD64330.1| DNA-directed RNA polymerase sigma factor sigma-F [Bacillus clausii
           KSM-K16]
          Length = 254

 Score =  165 bits (418), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 52/261 (19%), Positives = 109/261 (41%), Gaps = 19/261 (7%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K   L  ++   L  + +E GD  A   +V  + RLV  +   +   G    ++   G 
Sbjct: 9   GKKKPLSDKQVKELIAKSQE-GDTEARDSIVNHNTRLVWSVVQRFLNRGYEADDLFQIGC 67

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL+++V KFD     + +TY++  I   +Q ++      VK+  +   K L   +R+ K
Sbjct: 68  IGLIKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSI--KELSNKIRKAK 124

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L   T    +   +  IA+ L V+  E++          S++  +  +D +     D 
Sbjct: 125 DEL---TKTLRRAPTINEIAEHLGVTPEEIVFAGDANRSLSSIHETVYENDGDPITLLDQ 181

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +              + +   +  L  ++  L  RER I   R  ++   T   ++    
Sbjct: 182 IAD----------HSQVKWFDKIALKEAICDLGERERLIVYLRYYKDQ--TQSEVAERLG 229

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E +  ++++E++
Sbjct: 230 ISQVQVSRLEKKILEQMKETM 250


>gi|296133159|ref|YP_003640406.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           sp. JR]
 gi|296031737|gb|ADG82505.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           potens JR]
          Length = 260

 Score =  165 bits (418), Expect = 8e-39,   Method: Composition-based stats.
 Identities = 52/267 (19%), Positives = 111/267 (41%), Gaps = 19/267 (7%)

Query: 20  IHEIR--KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + E+   + P+L  +E   L  + + +GD +A  +LV  +L+LV  +   +   G    +
Sbjct: 5   LSEMNLPRFPLLSDKEMKELLIKAK-NGDQAAREKLVNCNLKLVFNLVQRFCNRGYEPED 63

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +   G IGL++A+ KFD     + +TY++  I   ++ ++      VK+  +   K    
Sbjct: 64  LFQIGTIGLIKAIDKFDLSYDVKFSTYAVPLIIGEIRRFLRDDN-PVKVSRSV--KETAN 120

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + R +  L A    +     +  IAK++ +   E+++         S+   +   D + 
Sbjct: 121 KINRAREKLSASLGRD---PTISEIAKEVGMEREEIVNAMEASQLPTSIYETLYQDDGDP 177

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
               D +      + Q              L   +  L  RE+++   R  ++   T   
Sbjct: 178 IYVMDAITGSSGDEGQWFE--------HMALKDVLQKLPEREKKVLLLRFFED--KTQTQ 227

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESI 284
           ++    +S+ +V +IE +A K ++  I
Sbjct: 228 VAEILGISQVQVSRIERQALKTIRSMI 254


>gi|149181668|ref|ZP_01860161.1| sporulation sigma factor SigF [Bacillus sp. SG-1]
 gi|148850646|gb|EDL64803.1| sporulation sigma factor SigF [Bacillus sp. SG-1]
          Length = 253

 Score =  164 bits (417), Expect = 9e-39,   Method: Composition-based stats.
 Identities = 58/256 (22%), Positives = 109/256 (42%), Gaps = 19/256 (7%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L+  E   L KR +E GD SA   +V  ++RLV  +   +   G    ++   G IGL++
Sbjct: 14  LKDTEVKELIKRSQE-GDQSARDTIVQKNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLK 72

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           +V KFD     + +TY++  I   +Q +I      VK+  +   K +   +RR K  L  
Sbjct: 73  SVDKFDLSYDVKFSTYAVPMIIGEIQRFIRDDG-TVKVSRSL--KEMGNRIRRAKDEL-- 127

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
            +    +   V  IA  L +S  EV+          S++  +  +D +     D +    
Sbjct: 128 -SKTFGRVPTVNEIAAHLELSPEEVVMAQEASRSPSSIHETVYENDGDPITLLDQISDTS 186

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D          ++   +  L  ++  L+ RER I   R  ++   T   ++    +S+ +
Sbjct: 187 D----------QKWFDKIALKEAIRELDERERLIVYLRYYKDQ--TQSEVADRLGISQVQ 234

Query: 269 VRQIEARAFKKVQESI 284
           V ++E +    ++E +
Sbjct: 235 VSRLEKKILHNMKEKL 250


>gi|251796351|ref|YP_003011082.1| sporulation sigma factor SigF [Paenibacillus sp. JDR-2]
 gi|247543977|gb|ACT00996.1| RNA polymerase, sigma 28 subunit, SigF [Paenibacillus sp. JDR-2]
          Length = 251

 Score =  164 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 54/258 (20%), Positives = 108/258 (41%), Gaps = 19/258 (7%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L+  E   L     + GD  A   LV  ++RLV  +   +   G    ++   G IGL
Sbjct: 11  PYLDDAEVKRLI-ALSQSGDTIARDTLVQCNIRLVWSVVQRFINRGYEPEDLFQIGCIGL 69

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           +++V KFD     + +TY++  I   +Q ++      +K+  +   K     +R++K  L
Sbjct: 70  LKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TLKVSRSL--KETANKVRKMKDEL 126

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                       V  +A +L ++  +V+          S++  +  +D +     D +  
Sbjct: 127 SKTLGRL---PTVSEVADRLGITPEDVVFAQEANKPPTSIHETVFENDGDPITLMDQIAD 183

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           D           +ER   +  L  ++  L+ RER I   R  ++   T   ++S   +S+
Sbjct: 184 D----------SQERWFDKLALIEAIEGLSERERLIVYLRYYRD--KTQSEVASRLGISQ 231

Query: 267 ERVRQIEARAFKKVQESI 284
            +V ++E +  + ++E I
Sbjct: 232 VQVSRLEKKILQSIREQI 249


>gi|302554065|ref|ZP_07306407.1| RNA polymerase sigma-G factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302471683|gb|EFL34776.1| RNA polymerase sigma-G factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 381

 Score =  164 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 59/255 (23%), Positives = 108/255 (42%), Gaps = 20/255 (7%)

Query: 35  YVLAKRYREHGD-----LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             L  + R   D         ++LV  HL LV  +A  +R  G P+ ++     IGL+++
Sbjct: 138 RELFLKLRALPDGSPEYAELRNQLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKS 197

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V +FDP+RG   +TY+   +   ++ +       V++     + RL      L      +
Sbjct: 198 VDRFDPDRGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLA-----LTTATAEL 252

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
           +  + +   V  +A+KL++SE EV+          +L+  +  +D  S    D L  +  
Sbjct: 253 SQLHGRSPTVHELAEKLSISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAED- 311

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
                  E  E    R  L   +  L PRE+RI   R      +T   ++ E  +S+  V
Sbjct: 312 -------EALEGVEYRESLKPLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHV 362

Query: 270 RQIEARAFKKVQESI 284
            ++ AR   +++E +
Sbjct: 363 SRLLARTLAQLREKL 377


>gi|2706544|emb|CAA75859.1| Sig1 [Sinapis alba]
          Length = 481

 Score =  164 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 61/241 (25%), Positives = 120/241 (49%), Gaps = 10/241 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  S++RLV+ IA  Y   G  +S++V  G IGL++ ++KFD  +GFR++TY  WW
Sbjct: 238 AREKLAMSNVRLVMSIAQRYDNMGAEMSDLVQGGLIGLLRGIEKFDSSKGFRISTYVYWW 297

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   ++ +   +++ T  +++       +L+   + IT        +  IA+ LN+
Sbjct: 298 IRQGVSRALVDNSRTLRLPTHLHERLGLIRNAKLRLQEKGIT------PSIDRIAESLNM 351

Query: 169 SESEVISMNCRLAGDESLN-ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           S+ +V +    ++   SL+     S +    +     + D +  E       +    ++ 
Sbjct: 352 SQKKVRNATEAVSKIFSLDRDAFPSLNGLPGETHHSYIAD-NRLENNPWHGYDALALKDE 410

Query: 228 LTRSMS-VLNPRERRIFEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           +++ +S  L  RER I       +   +T E++S    +SRERVRQ+   A +K++ + +
Sbjct: 411 VSKLISVTLGEREREIIRLYYGLDKECLTWEDISQRIGLSRERVRQVGLVALEKLKHAAR 470

Query: 286 K 286
           K
Sbjct: 471 K 471


>gi|188588400|ref|YP_001920536.1| sporulation sigma factor SigG [Clostridium botulinum E3 str. Alaska
           E43]
 gi|251778549|ref|ZP_04821469.1| RNA polymerase sigma-G factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
 gi|188498681|gb|ACD51817.1| RNA polymerase sigma-G factor [Clostridium botulinum E3 str. Alaska
           E43]
 gi|243082864|gb|EES48754.1| RNA polymerase sigma-G factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
          Length = 257

 Score =  164 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 56/261 (21%), Positives = 111/261 (42%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+PML K++E        + GDLSA    +  +LRLV+ +   +   G  + ++   G 
Sbjct: 14  SKLPML-KEKEKKQLLLALKKGDLSARETFIKGNLRLVLSVIQRFNNRGENVDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+++  FD  +  + +TY++  I   ++ Y+  + S +++  +         + R K
Sbjct: 73  IGLMKSIDNFDLSQNVKFSTYAVPMIIGEIRRYLRDNNS-IRVSRSLRDIAYKALIVRDK 131

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
                   +N +   +  IAK+L +   EV+     +    SL   I     ++    D 
Sbjct: 132 -----FIKDNNREPTISQIAKELELPREEVVFALDAIQDPVSLFEPIYHDGGDAIFVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    +  E  L            +  +M  L  RE+ I   R  +    T   ++ E  
Sbjct: 187 ISDSKNTDESWLEN--------ISIKEAMKKLTDREKLILNLRFFRG--RTQMEVADEIG 236

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A K +++ +
Sbjct: 237 ISQAQVSRLEKTALKHMRKHV 257


>gi|291484084|dbj|BAI85159.1| sporulation sigma factor SigG [Bacillus subtilis subsp. natto
           BEST195]
          Length = 237

 Score =  164 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 55/250 (22%), Positives = 111/250 (44%), Gaps = 16/250 (6%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L ++ ++ GD SA  +LV  +LRLV+ +   +   G  + ++   G IGLM+++  FD  
Sbjct: 4   LFRQLQDEGDDSAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCIGLMKSIDNFDLS 63

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
              + +TY++  I   ++ Y+  +   +++  +   + + +   +++  L + T      
Sbjct: 64  HNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVRERLISETSKEPTA 120

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           E    IAK L V   E++     +    SL   I +   +     D +  + +   Q + 
Sbjct: 121 ED---IAKVLEVPHEEIVFALDAIQDPVSLFEPIYNDGGDPIYVMDQISDERNTDSQWIE 177

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           E          L   M  LN RE+ I   R  Q    T   ++ E  +S+ +V ++E  A
Sbjct: 178 ELA--------LKEGMRRLNDREKMILRKRFFQG--KTQMEVAEEIGISQAQVSRLEKAA 227

Query: 277 FKKVQESIQK 286
            K++ ++I +
Sbjct: 228 IKQMNKNIHQ 237


>gi|160878636|ref|YP_001557604.1| FliA/WhiG family RNA polymerase sigma factor [Clostridium
           phytofermentans ISDg]
 gi|160427302|gb|ABX40865.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           phytofermentans ISDg]
          Length = 238

 Score =  164 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 52/245 (21%), Positives = 108/245 (44%), Gaps = 16/245 (6%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R  + GD  A  R+VT ++ LV  I   + G G    ++   G+IGLM+A+ KFD     
Sbjct: 8   RLSKQGDKVARDRVVTENVGLVWSIVRRFMGRGHEAEDLFQIGSIGLMKAIDKFDLSYDV 67

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY++  I   ++ ++     ++K+  +  +      L R     + +   N +   +
Sbjct: 68  KFSTYAVPMITGEIKRFLRDDG-MIKVSRSLKETAGKIRLMR-----ETLESKNGREPTI 121

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I + L +++ EV+      A  ESL   I   D N+    D +    D  ++++    
Sbjct: 122 EEIGEALELAKEEVVMALESGAEVESLYKTIYQGDGNAIFLIDKIEQTDDASDEMI---- 177

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
                   L   M  L+ +E+ I   R  ++   T   ++ +  +S+ +V ++E +  + 
Sbjct: 178 ----DHMALREVMDSLDEKEKDIIRLRYFKD--KTQTEIAKQLGISQVQVSRLERKILRT 231

Query: 280 VQESI 284
           ++E +
Sbjct: 232 MRERM 236


>gi|294631337|ref|ZP_06709897.1| RNA polymerase sigma factor [Streptomyces sp. e14]
 gi|292834670|gb|EFF93019.1| RNA polymerase sigma factor [Streptomyces sp. e14]
          Length = 379

 Score =  164 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 103/237 (43%), Gaps = 15/237 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              ++LV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+  
Sbjct: 154 ELRNQLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATP 213

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +   ++ +       V++     + RL      L      ++  + +   V  +A+KL 
Sbjct: 214 TVVGEIKRHFRDKGWAVRVPRRLQELRLA-----LTTATAELSQLHGRSPTVHELAEKLA 268

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +SE EV+          +L+  +  +D  S    D L  +         E  E    R  
Sbjct: 269 ISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAED--------EALEGVEYRES 320

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 321 LKPLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLREKL 375


>gi|218132880|ref|ZP_03461684.1| hypothetical protein BACPEC_00741 [Bacteroides pectinophilus ATCC
           43243]
 gi|217991753|gb|EEC57757.1| hypothetical protein BACPEC_00741 [Bacteroides pectinophilus ATCC
           43243]
          Length = 259

 Score =  164 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 52/260 (20%), Positives = 115/260 (44%), Gaps = 17/260 (6%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L+ +E+  L ++  + GD  A  + +  +LRLV+ +   + G G    ++   G IG
Sbjct: 16  LPLLKNEEKDELLRKAID-GDSKAREKYIKGNLRLVLSVIQRFAGNGENADDLFQIGCIG 74

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           LM+A+  FD  +  R +TY++  I   ++ Y+    S +++      + L     +    
Sbjct: 75  LMKAIDNFDVTQNVRFSTYAVPMIMGEVRRYMRDYNS-IRVS-----RSLRDTAYKAIHA 128

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
              +T  N     V+ IA ++ + + E++     +    SL   + S   ++    D + 
Sbjct: 129 RDMLTKKNQHEPTVMEIAAEVGLPKEEIVMALDAMQTPLSLYEPVFSEGGDTLYVMDQIS 188

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
              + ++  + +          L  ++S L  RER I   R    +  T   ++ +  +S
Sbjct: 189 DKKNREDNWVEDIA--------LREAVSRLPERERNIIRLRFF--DGRTQMEVARDVGIS 238

Query: 266 RERVRQIEARAFKKVQESIQ 285
           + +V ++E  A + ++  +Q
Sbjct: 239 QAQVSRLEKNALRSMKNYLQ 258


>gi|166031183|ref|ZP_02234012.1| hypothetical protein DORFOR_00869 [Dorea formicigenerans ATCC
           27755]
 gi|166029030|gb|EDR47787.1| hypothetical protein DORFOR_00869 [Dorea formicigenerans ATCC
           27755]
          Length = 278

 Score =  164 bits (417), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 52/260 (20%), Positives = 118/260 (45%), Gaps = 17/260 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+++E+  L  R +  GD  A    +  +LRLV+ +   +        ++   G I
Sbjct: 33  KLPILKEEEKEALFARIK-AGDDEAKEEYIKGNLRLVLSVIKRFHSSNENPDDLFQIGCI 91

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  F+ E   + +TY++  I   ++ Y+  + S +++      + L     +   
Sbjct: 92  GLIKAINNFNTELDVKFSTYAVPMIIGEIRRYMRDNSS-IRVS-----RSLRDTAYKAIY 145

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             +     N++   V  IA+++ +++ +++     +    SL   + S D   + +    
Sbjct: 146 AKENYVKQNMREPTVQEIAQEIGIAKEDIVYALDAIQAPMSLQEPVYS-DGGDALYVMDQ 204

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           + DH  +E+  +E          L  +M  LN RER I   R    +  T   ++ +  +
Sbjct: 205 ISDHKNKEEKWVESLS-------LQAAMEHLNERERYIISLRFF--DGRTQMEVARDVGI 255

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ +V ++E  A + +++ +
Sbjct: 256 SQAQVSRLEKNALRIMRQYL 275


>gi|225454597|ref|XP_002264928.1| PREDICTED: hypothetical protein isoform 1 [Vitis vinifera]
          Length = 507

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 57/240 (23%), Positives = 117/240 (48%), Gaps = 8/240 (3%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  S++RLV+ IA  Y   G  ++++V  G IGL++ ++KFD  +GF+++TY  WW
Sbjct: 264 AREKLAMSNVRLVMSIAQRYDNMGAEMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 323

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   ++ +   +++ +  +++       +++   + IT        +  IA+ LN+
Sbjct: 324 IRQGVSRALVENSRTLRLPSHLHERLSLIRNAKIRLEEKGIT------PSIDRIAECLNM 377

Query: 169 SESEVISMNCRLAGDESLN-ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           S+ +V +    ++   SL+     S +    +     + D   +       +E   +  +
Sbjct: 378 SQKKVRNATEAISKVFSLDREAFPSLNGLPGETLHSYIADVRLENNPWHGVDEWALKDEV 437

Query: 228 LTRSMSVLNPRERRIFEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                + L  RER I       +N  +T E++S    +SRERVRQ+   A +K++ + +K
Sbjct: 438 NKLINTTLGERERDIIRLYYGLDNECLTWEDISKRIGLSRERVRQVGLVALEKLKNAARK 497


>gi|221195774|ref|ZP_03568827.1| RNA polymerase sigma-F factor [Atopobium rimae ATCC 49626]
 gi|221184248|gb|EEE16642.1| RNA polymerase sigma-F factor [Atopobium rimae ATCC 49626]
          Length = 276

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 62/268 (23%), Positives = 115/268 (42%), Gaps = 20/268 (7%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           R  P  +K     L  +Y+E  D     +L+ SHL LV  +A  ++  G P+ +++  G 
Sbjct: 21  RGTPAWDKDRTRKLFAQYQETHDSEVRDQLIVSHLNLVRFLASKFKNRGEPLDDLIQVGT 80

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+ +FDP RG    TY+   I   ++ +       V++      +RL     ++ 
Sbjct: 81  IGLIKAIDRFDPSRGLEFTTYATPTIMGEIKRHFRDKGWSVRVP-----RRLQELSAKVN 135

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL----NALINSSDKNSSQ 199
                +T    +   +  IAKKL VS  EV+          S+           D+  S 
Sbjct: 136 QITDELTTELQRSPSIEEIAKKLGVSVDEVLEAMESSGAYSSVPLEGGGSSVDGDEAPSI 195

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
              ++  D         E     + R +L  +++  +PRE+ I   R +    +T   ++
Sbjct: 196 IDQYITED---------EALAGSDDRIVLEDAIADFSPREQEIIRMRFV--EGLTQVEIA 244

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +  +S+ +V ++  R  K++QE I  +
Sbjct: 245 EKLGISQVQVSRLLRRTLKRIQEKIDPE 272


>gi|158833991|gb|ABW81801.1| RNA polymerase sigma 38 [Candidatus Hamiltonella defensa]
          Length = 225

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 66/229 (28%), Positives = 119/229 (51%), Gaps = 11/229 (4%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L   EE   A+R    GD S+  R++ S+LRLVVKI+  Y   GLP+ ++
Sbjct: 8   YLGEICYSPLLTAAEEIYFARRVL-CGDGSSRRRMIESNLRLVVKISRRYINRGLPLLDL 66

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 67  IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 125

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +  L    D++  PE++     K     S ++ +N R++   S++    ++ +   
Sbjct: 126 LRAAR-ELSHKLDHDPSPEEIAEQLNKPVDYVSRMLRLNERIS---SVDTSFGNAAEKG- 180

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
              D L  + D   +   + +   + +  + + +  L+ ++R +   R 
Sbjct: 181 -LLDVLSDETDNDPENTTQND---DMKKSVVKWLFELSTKQREVLARRF 225


>gi|284044896|ref|YP_003395236.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Conexibacter
           woesei DSM 14684]
 gi|283949117|gb|ADB51861.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Conexibacter
           woesei DSM 14684]
          Length = 300

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 64/271 (23%), Positives = 121/271 (44%), Gaps = 16/271 (5%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG-YG 72
             L  ++    + P+L   EE  L++R  E GDL+A  RLV  +LRLVV IA  ++G   
Sbjct: 29  DALQLFLRRASRYPLLTPAEELALSRRI-ERGDLAAKERLVNHNLRLVVSIARRFQGVSE 87

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           L + ++V EG +GL++A +KFD  RGFR +TY+  WI+ A+Q  I      +++     Q
Sbjct: 88  LTLLDLVQEGVVGLIRAAEKFDWRRGFRFSTYATLWIRQAIQRGIATHGRTIRLPVNVAQ 147

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
           +      R++    + +     +   V  I+   ++   +V  +        SL+ ++ +
Sbjct: 148 RE-----RKVAAAARRLEAELGRAPTVEEISSASDLPPDQVADLREVSRTLASLDQVVTA 202

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
               +      L      +   + E+ +   +   + R++  L   +R + + R   E  
Sbjct: 203 DTDTT------LGELLPSEAPEVEEQVDALLQAETVRRTVEHLPSPQRDVIKLRFGLEED 256

Query: 253 VTL---ENLSSEFEVSRERVRQIEARAFKKV 280
            T      +     ++  +VR IE  A  ++
Sbjct: 257 RTPLPHAQIGRRLALATAQVRAIEREALARL 287


>gi|225028119|ref|ZP_03717311.1| hypothetical protein EUBHAL_02389 [Eubacterium hallii DSM 3353]
 gi|224954589|gb|EEG35798.1| hypothetical protein EUBHAL_02389 [Eubacterium hallii DSM 3353]
          Length = 278

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 56/263 (21%), Positives = 115/263 (43%), Gaps = 17/263 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            ++P+L  +E+  L  +  E G++ A  + V  +LRLV+ +   +        ++   G 
Sbjct: 33  SELPLLSDEEKENLFIQI-EQGNMDAREQYVKGNLRLVLSVIQRFSSNHEHADDLFQVGC 91

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+A+  FD     + +TY++  I   ++ Y+  + S +++      + L     +  
Sbjct: 92  IGLMKAIDNFDRTLNVKFSTYAVPMILGEVRRYLRDNNS-IRVS-----RSLRDTAYKAI 145

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
              + +T +  +   +  ++KK  + E ++I     +A   SL   +   D N   +   
Sbjct: 146 YAKEQLTKSMNRTPTIEEVSKKTEIPEEDIIYALDAIATPMSLFEPVYQ-DGNDPLFLMD 204

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
            + D   +E   IE          L  +M+ L+ RE  I E R       T   ++ E  
Sbjct: 205 QICDKKNKEDTWIEHLS-------LQEAMNQLSGREYHIIEKRFF--EGKTQTEVADEIS 255

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+ +V ++E  A K ++  I++
Sbjct: 256 ISQAQVSRLEKNALKSIRNFIER 278


>gi|261405990|ref|YP_003242231.1| sporulation sigma factor SigF [Paenibacillus sp. Y412MC10]
 gi|329929773|ref|ZP_08283449.1| RNA polymerase sigma-F factor [Paenibacillus sp. HGF5]
 gi|261282453|gb|ACX64424.1| RNA polymerase, sigma 28 subunit, SigF [Paenibacillus sp. Y412MC10]
 gi|328935751|gb|EGG32212.1| RNA polymerase sigma-F factor [Paenibacillus sp. HGF5]
          Length = 251

 Score =  164 bits (416), Expect = 1e-38,   Method: Composition-based stats.
 Identities = 49/256 (19%), Positives = 106/256 (41%), Gaps = 19/256 (7%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L+  E   L     + GD  A   LV  ++RLV  +   +   G    ++   G IGL++
Sbjct: 13  LDDAEVKRLI-ALSQSGDNVARDTLVNCNIRLVWSVVQRFMNRGYEPDDLFQIGCIGLLK 71

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           +V KFD     + +TY++  I   +Q ++      +K+  +  +        +++     
Sbjct: 72  SVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TLKVSRSLKEMA-----NKVRKKRDE 125

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           ++    +   V  +A++L V+  EV+          S++  +  +D +     D +  D 
Sbjct: 126 LSKQLDRLPTVKEVAEELGVTPEEVVFAQEANKPPTSIHETVFENDGDPITLMDQIADD- 184

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
                     +ER   +  L  ++  L  RER I   R  ++   T   +++   +S+ +
Sbjct: 185 ---------SQERWFDKLALNEAIGGLTERERLIVYLRYYRDQ--TQSEVATRLGISQVQ 233

Query: 269 VRQIEARAFKKVQESI 284
           V ++E +  + ++  I
Sbjct: 234 VSRLEKKILQSIRNEI 249


>gi|312135430|ref|YP_004002768.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|311775481|gb|ADQ04968.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor owensensis OL]
          Length = 240

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 53/253 (20%), Positives = 109/253 (43%), Gaps = 17/253 (6%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
            K  +  L  + + +GD  A  +L+ S+L LV  +   +   G+ + ++   G IGL++A
Sbjct: 2   SKASQEELISKAK-NGDKVARQQLIESNLALVWSVVKKFAAKGVELEDLFQIGCIGLIKA 60

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V +FDP    R +TY++  I   ++ Y+      +K+      +++  N  ++K      
Sbjct: 61  VDRFDPSFNVRFSTYAVPMIIGEIKRYLRDDGR-IKVS-----RKIKENQGKIKKLRNQF 114

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
             +N +   +  I++   +S  E++      +   SLN ++N  +       D    + D
Sbjct: 115 VSSNGREPTISEISQLTGLSSDEILLCLDASSEVASLNEVVNQEEGKPITLMDIASDEED 174

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
              ++L            L   +  L  RER I   R  +    T   ++ +  +S+  V
Sbjct: 175 YSTKLLDLMA--------LKEGLKKLKGRERYIIFMRYFKN--KTQSEIAKQLNISQVHV 224

Query: 270 RQIEARAFKKVQE 282
            +IE RA ++++ 
Sbjct: 225 SRIEKRALERIKR 237


>gi|1526450|dbj|BAA13238.1| RNA polymerase sigma subunit, truncated form of sigma-38
           [Escherichia coli W3110]
 gi|23306704|gb|AAN15271.1| C-terminal truncated RNA polymerase sigma factor S [Escherichia
           coli]
          Length = 269

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 61/220 (27%), Positives = 109/220 (49%), Gaps = 11/220 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +    +   
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE--- 231

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
             +  L    D +E    +  +  + +  + + +  LN +
Sbjct: 232 --KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAK 269


>gi|153854687|ref|ZP_01995937.1| hypothetical protein DORLON_01935 [Dorea longicatena DSM 13814]
 gi|149752791|gb|EDM62722.1| hypothetical protein DORLON_01935 [Dorea longicatena DSM 13814]
          Length = 258

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 54/260 (20%), Positives = 117/260 (45%), Gaps = 17/260 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L ++E+  L  R +  GD  A    +  +LRLV+ +   +   G    ++   G I
Sbjct: 15  KLPILNEKEKEALFVRIK-AGDQEAKEEYIKGNLRLVLSVIRRFGASGENPDDLFQIGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  F+ E   + +TY++  I   ++ Y+  + S +++      + L     +   
Sbjct: 74  GLIKAINNFNTELEVKFSTYAVPMIIGEIRRYMRDNNS-IRVS-----RSLRDTAYKAIY 127

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             +     N K   V  IA+++ +S+ +++     +    SL   + +   ++    D L
Sbjct: 128 AKENYMKKNQKEPTVQEIAEEIGISKEDIVFALDAIQVPMSLQEPVYNDGGDALYVMDQL 187

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               + +E+ + +          L  +M  L  RER I + R  Q    T   ++ E ++
Sbjct: 188 SDQTNKEEKWIEDLS--------LEEAMKHLGERERYIIKLRFFQG--KTQMEVADEIQI 237

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ +V ++E  A K +++ +
Sbjct: 238 SQAQVSRLEKNALKTMRQYL 257


>gi|29829555|ref|NP_824189.1| RNA polymerase sigma factor, sigH [Streptomyces avermitilis
           MA-4680]
 gi|29606663|dbj|BAC70724.1| putative RNA polymerase sigma factor, sigH [Streptomyces
           avermitilis MA-4680]
          Length = 391

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 58/237 (24%), Positives = 103/237 (43%), Gaps = 15/237 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              +RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDPERG   +TY+  
Sbjct: 166 ELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPERGVEFSTYATP 225

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +   ++ +       V++     + RL      L      ++  + +   V  +A+KL 
Sbjct: 226 TVVGEIKRHFRDKGWAVRVPRRLQELRLA-----LTTATAELSQQHGRSPTVHELAEKLA 280

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +SE EV+          +L+  +  +D  S    D L  +         E  E    R  
Sbjct: 281 ISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAED--------EALEGVEYRES 332

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 333 LKPLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLREKL 387


>gi|33946401|gb|AAQ55816.1| truncated stationary phase specific sigma factor [Pseudomonas
           syringae]
          Length = 252

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 63/195 (32%), Positives = 100/195 (51%), Gaps = 10/195 (5%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L   EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 66  YLNEIGFSPLLSPAEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 124

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 125 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVY 183

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNS 197
           LR  +  L    D+   PE++  + +K       ++ +N R++  D SL         + 
Sbjct: 184 LRAAR-ELTQKLDHEPSPEEIANLLEKPVAEVKRMLGLNERVSSVDVSL------GPDSD 236

Query: 198 SQWQDWLVYDHDGQE 212
               D L  D     
Sbjct: 237 KTLLDTLTDDRPTDP 251


>gi|302335912|ref|YP_003801119.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Olsenella uli DSM
           7084]
 gi|301319752|gb|ADK68239.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Olsenella uli DSM
           7084]
          Length = 276

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 61/260 (23%), Positives = 115/260 (44%), Gaps = 17/260 (6%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           +K+    L +RY+  GD  A  +LV SHL LV  +A  ++  G P+ ++V  G IGL++A
Sbjct: 28  DKERTRELFRRYKVEGDEDAREQLVMSHLNLVRFLASKFKNRGEPLDDLVQVGTIGLIKA 87

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +FDPERG    T++   I   ++ +       V++      +RL     ++      +
Sbjct: 88  IDRFDPERGLEFTTFATPTIMGEIKRHFRDKGWSVRVP-----RRLQELSAKVNQVTDEL 142

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYD 207
           T +  +   V  IA  L+ +  EV+      +   S  L      +D ++    D     
Sbjct: 143 TKDLQRSPSVEEIAAALDTTVDEVLEAMESSSAYSSVPLEGTGPGADDDAPSVIDHYA-- 200

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
                  + E     + R ++  ++   +PRE+ I   R +    +T   ++    +S+ 
Sbjct: 201 ------TVDEDLAASDDRMVIEETVRDFSPREQEIIRMRFI--EGLTQVEIARRLGISQV 252

Query: 268 RVRQIEARAFKKVQESIQKQ 287
           +V ++  R  +KVQE I  +
Sbjct: 253 QVSRLLRRTLQKVQEKIDPE 272


>gi|291544789|emb|CBL17898.1| RNA polymerase, sigma subunit, RpsG/SigG [Ruminococcus sp. 18P13]
          Length = 257

 Score =  164 bits (415), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 57/258 (22%), Positives = 115/258 (44%), Gaps = 17/258 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+ +L++ E+  L +  +  G   A  +L+  +LRLV+ +   + G G  I ++   G 
Sbjct: 14  SKLTVLKESEKIELLREIQRTGSKEARDKLINGNLRLVLSVIQRFAGRGEDIDDLFQIGV 73

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD  +  R +TY +  I   ++ ++        I  + + + L +   + K
Sbjct: 74  IGLIKAINNFDLSKEVRFSTYCVPMISGELRRFLRDYN---HIKVSRSLRDLAYKAMQAK 130

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
              + +T    K   +  IAK+++   S+V+     +    SL   + S D   + +   
Sbjct: 131 ---EQLTAEQQKEPTMDEIAKRIDAKRSDVVLALESVTDPVSLYEPVYS-DAGDTLYVLD 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
            + D +  +  L E          L  ++  L PRE+RI   R  Q    T   ++ E  
Sbjct: 187 QISDQNSVDSWLDEIA--------LRDAIKALQPREKRILYLRFFQG--KTQVEVAQEIG 236

Query: 264 VSRERVRQIEARAFKKVQ 281
           +S+ +V ++E  A  +++
Sbjct: 237 ISQAQVSRLEKGALNQIK 254


>gi|317128506|ref|YP_004094788.1| RNA polymerase, sigma 28 subunit, SigF [Bacillus cellulosilyticus
           DSM 2522]
 gi|315473454|gb|ADU30057.1| RNA polymerase, sigma 28 subunit, SigF [Bacillus cellulosilyticus
           DSM 2522]
          Length = 252

 Score =  163 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 49/256 (19%), Positives = 110/256 (42%), Gaps = 19/256 (7%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L+ +E   L K  ++ G   A  ++V ++ RLV  +   +   G    ++   G IGL++
Sbjct: 15  LDDKEVKRLIKEAQD-GAQEARDQIVNANTRLVWSVVQRFLNRGYEADDLFQIGCIGLIK 73

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           +V KFD     + +TY++  I   +Q ++      VK+  +  +        +++   + 
Sbjct: 74  SVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSIKESA-----NKIRKMKEE 127

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           ++    +   V  IA+KL+++  EV+          S++  +  +D +     D +  D 
Sbjct: 128 LSKTLGRTPTVNEIAEKLDLTPEEVVFAQEASRQLTSIHETVYENDGDPITLLDQISDDG 187

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D           +   +  L   +  L+ RE+ I   R  ++   T   ++    +S+ +
Sbjct: 188 D----------MKWFDKIALRDEIDKLDEREKLIVYLRYYKDQ--TQSQVAERLGISQVQ 235

Query: 269 VRQIEARAFKKVQESI 284
           V ++E +  K ++E +
Sbjct: 236 VSRLEKKILKVLKEQL 251


>gi|194699556|gb|ACF83862.1| unknown [Zea mays]
 gi|223944677|gb|ACN26422.1| unknown [Zea mays]
          Length = 496

 Score =  163 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 71/254 (27%), Positives = 122/254 (48%), Gaps = 10/254 (3%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L  R RE     A   L  S+ RLV+ IA  Y   G+ + +++  G IGL++ ++KFD 
Sbjct: 242 ELRARMRES--FLAREMLAMSNTRLVISIAQKYDNLGVELPDLIQGGLIGLLRGIEKFDA 299

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            RGFR++TY  WWI+  +   +  +    ++ T  +++     L  ++G   A+ D  + 
Sbjct: 300 SRGFRISTYVYWWIRQGVSRALADNSRSFRLPTYLHER-----LVAIRGAKYALEDQGIA 354

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQV 214
           P  V  IA+ LN+SE +V +    +    SL+     S +          + D +     
Sbjct: 355 P-TVENIAESLNISEKKVHNATEAVHKVISLDQQAFPSLNGLPGDTLHSYIEDQNVANDP 413

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIE 273
               EER  +  + +   S LN RER I        +   T E++S +F +SRERVRQ+ 
Sbjct: 414 WHGFEERYLKEEVNSLINSTLNERERDIIRLYHGIGKQCHTWEDISRQFGLSRERVRQVG 473

Query: 274 ARAFKKVQESIQKQ 287
             A +K++ + +++
Sbjct: 474 LVAMEKLKHAARRE 487


>gi|198284078|ref|YP_002220399.1| RNA polymerase sigma-32 subunit RpoH [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218665176|ref|YP_002426733.1| RNA polymerase sigm-70 factor family [Acidithiobacillus
           ferrooxidans ATCC 23270]
 gi|198248599|gb|ACH84192.1| RNA polymerase, sigma 32 subunit, RpoH [Acidithiobacillus
           ferrooxidans ATCC 53993]
 gi|218517389|gb|ACK77975.1| RNA polymerase sigm-70 factor family [Acidithiobacillus
           ferrooxidans ATCC 23270]
          Length = 285

 Score =  163 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 71/280 (25%), Positives = 133/280 (47%), Gaps = 19/280 (6%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
            V     LS ++ +    P L +++E  L +R R  GD  A   L+++H+ LV  +A GY
Sbjct: 18  PVTDPPPLSDFVDDENGGPFLSQKQELQLIRRLR-RGDECARATLISAHMPLVRAVARGY 76

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           R  GL   +++ EG +GL++AV +F    G R ++Y+ WWI+ AMQ  ++R    +++  
Sbjct: 77  RNKGLSQEDLLQEGYMGLLRAVDRFQEGLGTRFSSYATWWIREAMQRALIR-SRFIRLPD 135

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
              +    +    ++   +  +D  ++ EQ       L V ES + +++       SL+ 
Sbjct: 136 YLAKSLHAY----MQSGAEEDSDAGVRREQRRE---ALGVRESTMRALDFADIRVFSLDE 188

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            I+       Q    +       ++  I K         L   ++ LN ++R +   R  
Sbjct: 189 EISDGPGRIEQVTGDVASPDSDYDRDAICKA--------LREHLTELNEKQREVMVFRYG 240

Query: 249 --QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              + P+TLE ++    VSRE VRQ++ RA  ++++S+ +
Sbjct: 241 MHGDAPMTLEAVAERMGVSREAVRQLQVRALTRLRQSLSE 280


>gi|225454599|ref|XP_002264964.1| PREDICTED: hypothetical protein isoform 2 [Vitis vinifera]
          Length = 496

 Score =  163 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 57/240 (23%), Positives = 117/240 (48%), Gaps = 8/240 (3%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  S++RLV+ IA  Y   G  ++++V  G IGL++ ++KFD  +GF+++TY  WW
Sbjct: 253 AREKLAMSNVRLVMSIAQRYDNMGAEMADLVQGGLIGLLRGIEKFDSSKGFKISTYVYWW 312

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   ++ +   +++ +  +++       +++   + IT        +  IA+ LN+
Sbjct: 313 IRQGVSRALVENSRTLRLPSHLHERLSLIRNAKIRLEEKGIT------PSIDRIAECLNM 366

Query: 169 SESEVISMNCRLAGDESLN-ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           S+ +V +    ++   SL+     S +    +     + D   +       +E   +  +
Sbjct: 367 SQKKVRNATEAISKVFSLDREAFPSLNGLPGETLHSYIADVRLENNPWHGVDEWALKDEV 426

Query: 228 LTRSMSVLNPRERRIFEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                + L  RER I       +N  +T E++S    +SRERVRQ+   A +K++ + +K
Sbjct: 427 NKLINTTLGERERDIIRLYYGLDNECLTWEDISKRIGLSRERVRQVGLVALEKLKNAARK 486


>gi|311030733|ref|ZP_07708823.1| sporulation sigma factor SigF [Bacillus sp. m3-13]
          Length = 251

 Score =  163 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 52/258 (20%), Positives = 111/258 (43%), Gaps = 19/258 (7%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L+  E   L KR  + G+  A   +V  ++RLV  +   +   G    ++   G IGL++
Sbjct: 13  LKDHEVKELIKR-SQSGEQEARDTIVQKNMRLVWSVVQRFMNRGYEPDDLFQIGCIGLLK 71

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           +V KFD     + +TY++  I   +Q +I    S VK+  +   K +   +R+ K  L  
Sbjct: 72  SVDKFDLSYDVKFSTYAVPMIIGEIQRFIRDDGS-VKVSRSL--KEVANKIRKAKDEL-- 126

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
            +    +   +  IA+ L ++  EV+          S++  +  +D +     D +    
Sbjct: 127 -SKRYGRVPTINEIAEFLEITAEEVVLAQEAARAPSSIHETVYENDGDPITLLDQIAD-- 183

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
                     E R   +  L  ++  L+ RE+ I   R  ++   T   ++    +S+ +
Sbjct: 184 --------HSEHRWFDKIALKEAIEELDEREKLIVYLRYYKDQ--TQTEVAQRLGISQVQ 233

Query: 269 VRQIEARAFKKVQESIQK 286
           V ++E +  +++++ + +
Sbjct: 234 VSRLEKKILQQMKDRMDE 251


>gi|326523529|dbj|BAJ92935.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 506

 Score =  163 bits (414), Expect = 2e-38,   Method: Composition-based stats.
 Identities = 68/254 (26%), Positives = 120/254 (47%), Gaps = 10/254 (3%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L  R RE     A   L  S++RLV+ IA  Y   G+ +S+++  G IGL++ ++KFD 
Sbjct: 252 ELRSRMRES--FLAREVLTMSNIRLVISIAQKYDKLGVELSDLIQGGLIGLLRGIEKFDA 309

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            RGFR++TY  WWI+  +   +  +    ++ T  +++     L  ++    A+ D  + 
Sbjct: 310 SRGFRISTYVYWWIRQGVSRALADNSKTFRLPTYMHER-----LIAIRAAKYALEDQGVS 364

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQV 214
           P     IA+ LN+SE +V +    +    SL+     S +          + D +     
Sbjct: 365 P-TTQNIAELLNISEKKVHNATEAVNKALSLDQQAFPSLNGLPGDTLHSYIEDQNVANDP 423

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIE 273
               EE   +  +    +S L  RER I        +   T E++S +F +SRERVRQ+ 
Sbjct: 424 WHGFEEWYLKEEVNNLLISNLTERERHIIRLYHGIGKQCHTWEDISRQFGLSRERVRQVG 483

Query: 274 ARAFKKVQESIQKQ 287
             A +K++ + +++
Sbjct: 484 LIAMEKLKHAARRK 497


>gi|315646368|ref|ZP_07899486.1| sporulation sigma factor SigF [Paenibacillus vortex V453]
 gi|315278011|gb|EFU41331.1| sporulation sigma factor SigF [Paenibacillus vortex V453]
          Length = 251

 Score =  163 bits (414), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 50/256 (19%), Positives = 106/256 (41%), Gaps = 19/256 (7%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L+  E   L     + GD  A   LV  ++RLV  +   +   G    ++   G IGL++
Sbjct: 13  LDDAEVKRLI-ALSQSGDNVARDTLVNCNIRLVWSVVQRFMNRGYEPDDLFQIGCIGLLK 71

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           +V KFD     + +TY++  I   +Q ++      +K+  +  +        +++     
Sbjct: 72  SVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TLKVSRSLKEMA-----NKVRKKRDE 125

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           ++    +   V  +A++L V+  EV+          S++  +  +D +     D +    
Sbjct: 126 LSKQLDRLPTVKEVAEELGVTPEEVVFAQEANKPPTSIHETVFENDGDPITLMDQIAD-- 183

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
                   E +ER   +  L  ++  L  RER I   R  ++   T   ++S   +S+ +
Sbjct: 184 --------ESQERWFDKLALNEAIGGLTERERLIVYLRYYRDQ--TQSEVASRLGISQVQ 233

Query: 269 VRQIEARAFKKVQESI 284
           V ++E +  + ++  I
Sbjct: 234 VSRLEKKILQSIRNEI 249


>gi|84385871|ref|ZP_00988901.1| RNA polymerase sigma factor RpoS [Vibrio splendidus 12B01]
 gi|84379187|gb|EAP96040.1| RNA polymerase sigma factor RpoS [Vibrio splendidus 12B01]
          Length = 262

 Score =  163 bits (414), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 65/267 (24%), Positives = 121/267 (45%), Gaps = 19/267 (7%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEG 82
           I +L +++E   AK     GD  A   ++ S+LRLVVKIA  Y   +G    + +++ EG
Sbjct: 3   IDLLSREDEVYYAK-LNRAGDKQARDIMIESNLRLVVKIAKSYLKRKGNNFTLLDLIEEG 61

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
           NIGL++A+ K+DPE G+R +TY++WWI+  ++  ++     V++            +  L
Sbjct: 62  NIGLIKAIDKYDPEPGYRFSTYAVWWIRENIEAALMNKGRTVRLPAHV-----CKEINSL 116

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
                 ++    K   +  ++    V    V  +   L+G   +   + ++       Q 
Sbjct: 117 ASKKLDVSKKMSKEISISELSDSSGVKAKRVDQLVA-LSGFIDVTTTVGTNHAPMVLDQC 175

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSS 260
              Y  D Q        E ++    L + +S L P+ +++   R         TL  +  
Sbjct: 176 ESEYIPDPQRDC-----EDQSFTQALEQIISTLPPKLQKVLIHRFGFFDNKVKTLSEVGQ 230

Query: 261 EF--EVSRERVRQIEARAFKKVQESIQ 285
                VS ERVRQ++  A +++Q+ ++
Sbjct: 231 MLDVNVSSERVRQMQKEAVERIQKRLK 257


>gi|308069565|ref|YP_003871170.1| RNA polymerase sigma-F factor (stage II sporulation protein AC)
           (sporulation sigma factor) [Paenibacillus polymyxa E681]
 gi|305858844|gb|ADM70632.1| RNA polymerase sigma-F factor (Stage II sporulation protein AC)
           (Sporulation sigma factor) [Paenibacillus polymyxa E681]
          Length = 251

 Score =  163 bits (414), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 55/256 (21%), Positives = 110/256 (42%), Gaps = 19/256 (7%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           LE  E   L     + GD  A   LV S++RLV  +   +   G    ++   G IGL++
Sbjct: 13  LEDAEVKQLI-ALSQSGDNEARETLVNSNIRLVWSVVQRFMNRGYEPDDLFQIGCIGLLK 71

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           +V KFD     + +TY++  I   +Q ++      +K+  +   K     +R++K  L  
Sbjct: 72  SVDKFDLSYEVKFSTYAVPMIIGEIQRFLRDDG-TLKVSRSL--KETANKVRKMKDEL-- 126

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
            +    +   V  +A +L V+  +V+          S++  +  +D +     D +    
Sbjct: 127 -SKRLNRLPTVKEVADELGVTPEDVVFAQEANKPPTSIHETVFENDGDPITLMDQIAD-- 183

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
                   E +ER   +  L  ++  L+ RER I   R  ++   T   ++S   +S+ +
Sbjct: 184 --------ESQERWFDKLALNEAIGGLSERERLIVYLRYYRDQ--TQSEVASRLGISQVQ 233

Query: 269 VRQIEARAFKKVQESI 284
           V ++E +  + +++ I
Sbjct: 234 VSRLEKKILQLIRDQI 249


>gi|258511711|ref|YP_003185145.1| sporulation sigma factor SigF [Alicyclobacillus acidocaldarius
           subsp. acidocaldarius DSM 446]
 gi|257478437|gb|ACV58756.1| RNA polymerase, sigma 28 subunit, SigF [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
          Length = 256

 Score =  163 bits (414), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 55/265 (20%), Positives = 115/265 (43%), Gaps = 19/265 (7%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           H + +   L  +E   L +R   +GD  A  RL+  + RLV  +   + G G    ++  
Sbjct: 11  HHVDEYEKLSDEEVRELLER-SHNGDAEARERLIVHNQRLVWAVVQRFLGRGYEAEDLFQ 69

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
            G IGLM+AV KFD     + +TY++  I   +Q ++    S VK+  +  +       +
Sbjct: 70  IGCIGLMKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDD-STVKVSRSLKE-----TAK 123

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
           +++     +     +   +  IA+ + +  SE++     L    S++  +  +D +    
Sbjct: 124 QIRHVRDRLAKELGRQPHITEIAEAMGMEPSEIVFAQEALRAPASIHETVYENDGDPIYL 183

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
            D +            E+ E K  +  L   +  L  RER I   R  ++   T  +++ 
Sbjct: 184 MDQIAD----------EETEGKFDKVELHEIIGRLPERERFIVYMRFFRD--KTQSDVAR 231

Query: 261 EFEVSRERVRQIEARAFKKVQESIQ 285
              +S+ +V ++E R  +++++ ++
Sbjct: 232 VLGISQVQVSRLEKRILQQIRQELE 256


>gi|291447660|ref|ZP_06587050.1| RNA polymerase sigma factor [Streptomyces roseosporus NRRL 15998]
 gi|291350607|gb|EFE77511.1| RNA polymerase sigma factor [Streptomyces roseosporus NRRL 15998]
          Length = 318

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 103/237 (43%), Gaps = 15/237 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              +RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+  
Sbjct: 93  ELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATP 152

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +   ++ +       V++     + RL      L      ++  + +   V  +A++L 
Sbjct: 153 TVVGEIKRHFRDKGWAVRVPRRLQELRLS-----LTTATAELSQQHGRSPTVHELAERLG 207

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +SE EV+          +L+  +  +D  S    D L  +         E  E    R  
Sbjct: 208 ISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGSED--------EALEGVEYRES 259

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 260 LKPLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLRERL 314


>gi|319649652|ref|ZP_08003808.1| FliA/WhiG family RNA polymerase [Bacillus sp. 2_A_57_CT2]
 gi|317398814|gb|EFV79496.1| FliA/WhiG family RNA polymerase [Bacillus sp. 2_A_57_CT2]
          Length = 236

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 57/253 (22%), Positives = 114/253 (45%), Gaps = 17/253 (6%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
              L K+  + GD++A  +LV  +LRLV+ +   +   G  + ++   G IGLM+++  F
Sbjct: 1   MRELFKQMHK-GDITAREKLVNGNLRLVLSVIQRFNNRGEFVDDLFQVGCIGLMKSIDNF 59

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++  L + T   
Sbjct: 60  DLSQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVRERLMSKTSRE 116

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
              E    IAK+L+V   E++     +    SL   I +   +     D L  + +   Q
Sbjct: 117 PTAE---EIAKELDVPHEEIVFALDAIQDPVSLFEPIYNDGGDPIYVMDQLSDERNKDIQ 173

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
            + E          L   M  LN RE+ I   R  Q    T   ++ E  +S+ +V ++E
Sbjct: 174 WIEEIA--------LKEGMRRLNEREKLILRKRFFQG--KTQMEVAEEIGISQAQVSRLE 223

Query: 274 ARAFKKVQESIQK 286
             A K++ ++IQ 
Sbjct: 224 KAAIKQMNKNIQS 236


>gi|229543947|ref|ZP_04433006.1| RNA polymerase, sigma 28 subunit, SigF [Bacillus coagulans 36D1]
 gi|229325086|gb|EEN90762.1| RNA polymerase, sigma 28 subunit, SigF [Bacillus coagulans 36D1]
          Length = 252

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 52/270 (19%), Positives = 113/270 (41%), Gaps = 19/270 (7%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +   + +  K   L+ +E   L +R +E GD  A   +V  ++RLV  +   +   G   
Sbjct: 1   MDAELKKAEKKTRLKDEEVKNLIRRSQE-GDQGARDLIVEKNMRLVWSVVQRFLNRGYEP 59

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++   G IGL+++V KFD     + +TY++  I   +Q ++      VK+  +  +   
Sbjct: 60  DDLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKE--- 115

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
                R++     +T    +   V  IA +L +   EV+          S++  +  +D 
Sbjct: 116 --TGNRIRKTRDELTKKLGRSPTVHEIASELGMPVEEVVMAQEAGKAPSSIHETVYENDG 173

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
           +     D +   +D          ++   +  L  ++  L  RER I   R  ++   T 
Sbjct: 174 DPITLLDQISDQND----------QKWFDQIALQEAIRGLEERERLIVYLRYYKDQ--TQ 221

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             ++    +S+ +V ++E +  + ++E ++
Sbjct: 222 SEVAERLGISQVQVSRLEKKILEVMKERME 251


>gi|182436064|ref|YP_001823783.1| RNA polymerase sigma factor [Streptomyces griseus subsp. griseus
           NBRC 13350]
 gi|326776688|ref|ZP_08235953.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
 gi|178464580|dbj|BAG19100.1| RNA polymerase sigma factor [Streptomyces griseus subsp. griseus
           NBRC 13350]
 gi|326657021|gb|EGE41867.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
          Length = 318

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 62/255 (24%), Positives = 109/255 (42%), Gaps = 20/255 (7%)

Query: 35  YVLAKRYREHGDLSA-----AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             L    RE  D SA      +RLV  HL LV  +A  +R  G P+ ++     IGL+++
Sbjct: 75  RALFFELRELPDGSAEKAELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKS 134

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V +FDP+RG   +TY+   +   ++ +       V++     + RL      L      +
Sbjct: 135 VDRFDPDRGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLS-----LTTATAEL 189

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
           +  + +   V  +A++L +SE EV+          +L+  +  +D  S    D L  +  
Sbjct: 190 SQQHGRSPTVHELAERLGISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGSED- 248

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
                  E  E    R  L   +  L PRE+RI   R      +T   ++ E  +S+  V
Sbjct: 249 -------EALEGVEYRESLKPLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHV 299

Query: 270 RQIEARAFKKVQESI 284
            ++ AR   +++E +
Sbjct: 300 SRLLARTLAQLRERL 314


>gi|242078297|ref|XP_002443917.1| hypothetical protein SORBIDRAFT_07g004340 [Sorghum bicolor]
 gi|241940267|gb|EES13412.1| hypothetical protein SORBIDRAFT_07g004340 [Sorghum bicolor]
          Length = 500

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 71/254 (27%), Positives = 123/254 (48%), Gaps = 10/254 (3%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L  R RE     A   L  S++RLV+ IA  Y   G+ +++++  G IGL++ ++KFD 
Sbjct: 246 ELRARMRES--FLAREMLTMSNIRLVISIAQKYDNLGVELADLIQGGLIGLLRGIEKFDA 303

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            RGFR++TY  WWI+  +   +  +    ++ T  +++     L  ++G   A+ D  + 
Sbjct: 304 SRGFRISTYVYWWIRQGVSRALADNSKAFRLPTYLHER-----LIAIRGAKYALEDQGIA 358

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQV 214
           P  V  IA+ LN+SE +V +    +    SL+     S +          + D +     
Sbjct: 359 P-TVENIAESLNISEKKVHNATEAVNKVLSLDQQAFPSLNGLPGDTLHSYIEDQNVANDP 417

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIE 273
               EER  +  +     S LN RER I        +   T E++S +F +SRERVRQ+ 
Sbjct: 418 WHGFEERYLKEEVNNLINSTLNERERDIIRLYHGIGKQCHTWEDISRQFGLSRERVRQVG 477

Query: 274 ARAFKKVQESIQKQ 287
             A +K++ + +++
Sbjct: 478 LVAMEKLKHAARRK 491


>gi|167932999|ref|ZP_02520086.1| RNA polymerase sigma factor RpoD [candidate division TM7
           single-cell isolate TM7b]
          Length = 211

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 50/162 (30%), Positives = 91/162 (56%), Gaps = 6/162 (3%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
            +  +  Y+ EI KIP+L  +EE  LA R  + GD  A  ++  +++RLVV IA  Y G 
Sbjct: 47  SDDSVRLYLREIGKIPLLSAEEEMELAHRVVQ-GDKKAKDKMAEANMRLVVSIAKRYSGR 105

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL   +++ EGN GL++AV+KFDP++GF+ +TY+ WWI+ A+   I     +++I     
Sbjct: 106 GLDFLDLIQEGNTGLLRAVEKFDPDKGFKFSTYATWWIRQAITRAIADQARVIRIPVHMV 165

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
           +      + +L    + +T    +   +  ++K+L++   ++
Sbjct: 166 E-----TINKLLRTQRRMTQELNREPTIEELSKELDMEPDKI 202


>gi|253576354|ref|ZP_04853684.1| RNA polymerase sigma-F factor [Paenibacillus sp. oral taxon 786
           str. D14]
 gi|251844247|gb|EES72265.1| RNA polymerase sigma-F factor [Paenibacillus sp. oral taxon 786
           str. D14]
          Length = 251

 Score =  163 bits (413), Expect = 3e-38,   Method: Composition-based stats.
 Identities = 47/251 (18%), Positives = 105/251 (41%), Gaps = 18/251 (7%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           E        + GD +A  RLV  ++RLV  +   +   G    ++   G IGL+++V KF
Sbjct: 17  EVKRLIALSQSGDNAARDRLVNCNIRLVWSVVQRFMNRGYEPEDLFQIGCIGLLKSVDKF 76

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D     + +TY++  I   +Q ++      +K+  +  +        +++     ++   
Sbjct: 77  DLSYDVKFSTYAVPMIIGEIQRFLRDDG-TLKVSRSLKEMA-----NKVRKKKDELSKQL 130

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            +   V  +A +L V+  +V+          S++  +  +D +     D +         
Sbjct: 131 GRLPTVKEVADELGVTPEDVVFAQEANKPPASIHETVFENDGDPITLMDQIAD------- 183

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
              E +ER   +  L  ++  L  RER I   R  ++   T   +++   +S+ +V ++E
Sbjct: 184 ---ETQERWFDKLALHEAIDGLTDRERLIVYLRYYRDQ--TQSEVATRLGISQVQVSRLE 238

Query: 274 ARAFKKVQESI 284
            +  + +++ I
Sbjct: 239 KKILQSIRDQI 249


>gi|302871563|ref|YP_003840199.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
 gi|302574422|gb|ADL42213.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
          Length = 240

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 53/253 (20%), Positives = 109/253 (43%), Gaps = 17/253 (6%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
            K  +  L  + + +GD  A  +L+ S+L LV  +   +   G+ + ++   G IGL++A
Sbjct: 2   SKASQEELISKAK-NGDKVARQQLIESNLALVWSVVKKFAAKGVELEDLFQIGCIGLIKA 60

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V +FDP    R +TY++  I   ++ Y+      +K+      +++  N  ++K      
Sbjct: 61  VDRFDPSFNVRFSTYAVPMIIGEIKRYLRDDGR-IKVS-----RKIKENQSKIKKLRNQF 114

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
             +N +   +  I++   +S  E++      +   SL+ +IN  +       D    + D
Sbjct: 115 VSDNGREPTISEISQLTGLSSEEILLCMDASSEVASLSEVINQEEGKPITLMDLASDEED 174

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
              ++L            L   +  L  RER I   R  +    T   ++ +  +S+  V
Sbjct: 175 YSTKLLDLMA--------LKEGLKKLKGRERYIIFMRYFKN--KTQSEIAKQLNISQVHV 224

Query: 270 RQIEARAFKKVQE 282
            +IE RA ++++ 
Sbjct: 225 SRIEKRALERIKR 237


>gi|297202300|ref|ZP_06919697.1| RNA polymerase sigma-F factor [Streptomyces sviceus ATCC 29083]
 gi|297148082|gb|EDY54214.2| RNA polymerase sigma-F factor [Streptomyces sviceus ATCC 29083]
          Length = 381

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 103/237 (43%), Gaps = 15/237 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              ++LV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+  
Sbjct: 156 ELRNQLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATP 215

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +   ++ +       V++     + RL      L      ++  + +   V  +A+KL 
Sbjct: 216 TVVGEIKRHFRDKGWAVRVPRRLQELRLS-----LTTATAELSQQHGRSPTVHELAEKLA 270

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +SE EV+          +L+  +  +D  S    D L  +         E  E    R  
Sbjct: 271 ISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAED--------EALEGVEYRES 322

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 323 LKPLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLREKL 377


>gi|196038743|ref|ZP_03106051.1| RNA polymerase sigma-F factor [Bacillus cereus NVH0597-99]
 gi|196030466|gb|EDX69065.1| RNA polymerase sigma-F factor [Bacillus cereus NVH0597-99]
          Length = 252

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 54/263 (20%), Positives = 117/263 (44%), Gaps = 19/263 (7%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           +K P L+ QE   L ++  + GD  A   +V S++RLV  +   +   G    ++   G 
Sbjct: 9   KKKPQLKDQELKALIQK-SQDGDQQARDTIVQSNMRLVWSVVQRFLNRGYEPDDLFQIGC 67

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL+++V KFD     + +TY++  I   +Q ++    S VK+  +   K     +R+++
Sbjct: 68  IGLLKSVDKFDLSFDVKFSTYAVPMIIGEIQRFLRDDGS-VKVSRSL--KETGNKIRKMR 124

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L   +    +   +  +A+ L ++  EV+          S++  +  +D +     D 
Sbjct: 125 DEL---SKEFGRAPTINEVAEALELTPEEVVLAQEASRAPSSIHETVYENDGDPITILDQ 181

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +            + E +   +  L  ++  L+ RER I   R  ++   T   ++    
Sbjct: 182 IAD----------QSETKWFDKIALKEAIRELDERERLIVYLRYYKDQ--TQSEVAERIG 229

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+ +V ++E +  K++++ I +
Sbjct: 230 ISQVQVSRLEKKILKQMKDRIDE 252


>gi|329895346|ref|ZP_08270971.1| RNA polymerase sigma factor [gamma proteobacterium IMCC3088]
 gi|328922359|gb|EGG29703.1| RNA polymerase sigma factor [gamma proteobacterium IMCC3088]
          Length = 424

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 64/240 (26%), Positives = 115/240 (47%), Gaps = 12/240 (5%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            G L+A  +LV  ++RLV K+A   +  G+ + ++V EG IGL++A +KFD   GFR +T
Sbjct: 181 QGYLAARDKLVMHNVRLVYKLAREKQNRGIAVRDLVQEGIIGLVRAAEKFDYRLGFRFST 240

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+  W    +Q     + SLV   T   Q+     L R++       D   +   +  +A
Sbjct: 241 YAYNWTNQHIQRVCEGNGSLVTYPTHVTQE--VNALYRVRNEW---MDRRGEEPSLAELA 295

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           +    +   V  +        S+ +     D++++   +  + D        +E+ + ++
Sbjct: 296 EHSGFTLERVRELTQLTNLTVSIQS---DDDEDTNALPESALVDEAANPA--LEQAQSRS 350

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            + +L + +  L+ RE+ I  AR   +     TL  L+ + EVSRE VRQ+E  A +K+Q
Sbjct: 351 LKRLLEQQLKQLDRREQMIVTARWGLDGRPSRTLAQLADQLEVSRELVRQLEKSALRKLQ 410


>gi|134298969|ref|YP_001112465.1| FliA/WhiG family RNA polymerase sigma factor [Desulfotomaculum
           reducens MI-1]
 gi|134051669|gb|ABO49640.1| RNA polymerase, sigma subunit, RpoX/SigF [Desulfotomaculum reducens
           MI-1]
          Length = 260

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 54/262 (20%), Positives = 118/262 (45%), Gaps = 17/262 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           + P+L  +E   L K+  + G+  A  RLV  +L+LV  +   +   G  + ++   G I
Sbjct: 13  RFPLLGDKEMRGLLKK-AQSGNSEARERLVNCNLKLVFNLVQRFSNRGYELEDLFQIGCI 71

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A+ KFD     + +TY++  I   ++ ++    S VK+  +  +        +++ 
Sbjct: 72  GLMKAIDKFDLSYDVKFSTYAVPMIVGEIRRFLRDD-SPVKVSRSLKE-----TAYKIQQ 125

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
               +T    +   +  IA++L+ S  EV++         S+   ++  D +     D L
Sbjct: 126 TRDRLTARLGREPSINEIAEELSYSREEVVNALEAAQMPTSIYETLHQDDGDPIYILDQL 185

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             + +G    L +          + + +  L  R+R+I   R  ++   T   ++    +
Sbjct: 186 SGEDEGDAPWLEKLA--------VKQILIQLPERDRQILLWRFFED--KTQSEVALRLGL 235

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+ +V ++E +A +K++E + +
Sbjct: 236 SQVQVSRLERQALRKLKELMHQ 257


>gi|312793875|ref|YP_004026798.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
 gi|312181015|gb|ADQ41185.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
          Length = 240

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 54/253 (21%), Positives = 109/253 (43%), Gaps = 17/253 (6%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
            K  +  L  + + +GD  A  +L+ S+L LV  +   +   G+ + ++   G IGL++A
Sbjct: 2   SKASQEELISKAK-NGDKLARQQLIESNLALVWSVVKKFAAKGVELEDLFQIGCIGLIKA 60

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V +FDP    R +TY++  I   ++ Y+      +K+      +++  N  ++K      
Sbjct: 61  VDRFDPSFNVRFSTYAVPMIIGEIKRYLRDDGK-IKVS-----RKIKENQSKIKKLRNQF 114

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
             +N +   +  I++   +S  E++      +   SLN ++N  +       D    + D
Sbjct: 115 VSSNGREPTISEISQLTGLSSDEILLCMDATSEVASLNDVVNQEEGKPITLMDIASDEED 174

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
              ++L            L   +  L  RER I   R  +    T   ++ E  +S+  V
Sbjct: 175 YSTKLLDLMA--------LKEGLKKLKGRERYIIFMRYFKN--KTQSEIAKELNISQVHV 224

Query: 270 RQIEARAFKKVQE 282
            +IE RA ++++ 
Sbjct: 225 SRIEKRALERIKR 237


>gi|293376228|ref|ZP_06622471.1| RNA polymerase sigma-G factor [Turicibacter sanguinis PC909]
 gi|325845152|ref|ZP_08168461.1| RNA polymerase sigma-G factor [Turicibacter sp. HGF1]
 gi|292645120|gb|EFF63187.1| RNA polymerase sigma-G factor [Turicibacter sanguinis PC909]
 gi|325488817|gb|EGC91217.1| RNA polymerase sigma-G factor [Turicibacter sp. HGF1]
          Length = 259

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 52/262 (19%), Positives = 116/262 (44%), Gaps = 17/262 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+ +L   E   L K ++ +G++ A   L+  +LRLV+ I   +   G  + ++   G +
Sbjct: 15  KLEVLSNAEMTELFKSFQ-NGNVEARESLIKGNLRLVLSIIKKFNHRGENLDDLFQVGCL 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A+  FD     + +TY++  I   ++ Y+  + S   +  + + +   + + ++K 
Sbjct: 74  GLMKAIDHFDLSHEVKFSTYAVPMIIGEIRRYLRDNNS---LRVSRSLRDTAYKVLQVKD 130

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L      +   E    IA  + V   +V+     ++   S+ + I +   ++    D +
Sbjct: 131 QLSIELQRDPTNE---EIAAAIGVEPIDVVLSVEAISDPVSIFSPIYNDGGDTIHLIDQI 187

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             D           +++ + + ML      L  RE+RI   R       T   +++E  +
Sbjct: 188 KDDSIT--------DDKWSVKLMLEEGFKRLGKREKRIIHDRYFMG--KTQMEIAAEIGI 237

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+ +V ++E  A + ++E ++ 
Sbjct: 238 SQAQVSRLEKNALQVMEEMMKS 259


>gi|27884311|dbj|BAC55891.1| RNA polymerase sigma factor [Streptomyces griseus subsp. griseus]
          Length = 318

 Score =  163 bits (412), Expect = 4e-38,   Method: Composition-based stats.
 Identities = 62/255 (24%), Positives = 109/255 (42%), Gaps = 20/255 (7%)

Query: 35  YVLAKRYREHGDLSA-----AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             L    RE  D SA      +RLV  HL LV  +A  +R  G P+ ++     IGL+++
Sbjct: 75  RALFFELRELPDGSAEKAELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKS 134

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V +FDP+RG   +TY+   +   ++ +       V++     + RL      L      +
Sbjct: 135 VDRFDPDRGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLS-----LTTATAEL 189

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
           +  + +   V  +A++L +SE EV+          +L+  +  +D  S    D L  +  
Sbjct: 190 SQQHGRSPTVHELAERLGISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGSED- 248

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
                  E  E    R  L   +  L PRE+RI   R      +T   ++ E  +S+  V
Sbjct: 249 -------EALEGVEYRESLKPLLEALPPREKRILLLRFFGN--MTQSQIAQEVGISQMHV 299

Query: 270 RQIEARAFKKVQESI 284
            ++ AR   +++E +
Sbjct: 300 SRLLARTLAQLRERL 314


>gi|90580452|ref|ZP_01236258.1| hypothetical DNA-directed RNA polymerase, sigma subunit [Vibrio
           angustum S14]
 gi|90438361|gb|EAS63546.1| hypothetical DNA-directed RNA polymerase, sigma subunit [Vibrio
           angustum S14]
          Length = 231

 Score =  162 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 59/226 (26%), Positives = 112/226 (49%), Gaps = 11/226 (4%)

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           + IA  YR   L + +++ EGN+GL+ AV+KFDPE+GFR +TY+ WWIK  ++  I    
Sbjct: 1   MSIAKKYRAAHLLLGDMIDEGNLGLITAVEKFDPEKGFRFSTYATWWIKQNIERAIHNQN 60

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
             +++    +  +    L R    L    ++    E    IA++LN    ++  +     
Sbjct: 61  RTIRLPVHVS--KEINGLLRTHRDLMKKQNHEPTHED---IAQQLNKETHDISILFSYEQ 115

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
              SL+  I   D+N+      +V +       ++E+    N    +   ++ + PRER 
Sbjct: 116 KIVSLDQTIGD-DENTGTIASLIVDEQIPSPSHIVEENSMVNLAEDI---LNKIKPRERE 171

Query: 242 IFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           I   R       P TL+ ++    ++RERVRQ++A++ ++++ +++
Sbjct: 172 ILCRRFGVMGYEPQTLQEVALALGITRERVRQLQAKSLERLKMNLK 217


>gi|239982221|ref|ZP_04704745.1| RNA polymerase sigma factor, sigH [Streptomyces albus J1074]
          Length = 287

 Score =  162 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 58/237 (24%), Positives = 103/237 (43%), Gaps = 15/237 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              +RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDPERG   +TY+  
Sbjct: 62  ELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPERGVEFSTYATP 121

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +   ++ +       V++     + RL      L      ++  + +   V  +A+KL 
Sbjct: 122 TVVGEIKRHFRDKGWAVRVPRRLQELRLS-----LTSATAELSQRHGRSPTVHELAEKLG 176

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +SE EV+          +L+  +  +D  S    D L  +         E  E    R  
Sbjct: 177 ISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGSED--------EALEGVEYRES 228

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 229 LKPLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLREKL 283


>gi|86742435|ref|YP_482835.1| sigma 28 subunit [Frankia sp. CcI3]
 gi|86569297|gb|ABD13106.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Frankia sp. CcI3]
          Length = 338

 Score =  162 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 59/253 (23%), Positives = 108/253 (42%), Gaps = 19/253 (7%)

Query: 35  YVLAKRYREHGDLSA-AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
             LA+   +  + SA   +LV  HL LV  +A  +R  G P+ ++V    IGL+++V +F
Sbjct: 98  VRLAELPEDDPERSAVRDQLVRMHLPLVEYLARRFRNRGEPLDDLVQVATIGLIKSVDRF 157

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           DPERG   +TY+   I   ++ +       +++     + +L      L      ++   
Sbjct: 158 DPERGVEFSTYATPTIVGEIKRHFRDKGWAIRVPRRLQELKLS-----LTKATSELSQTL 212

Query: 154 LKPEQVVAIAKKLNVSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
            +   V  IA+ L +SE +V+    +       SL+A  +  D+  +      V D    
Sbjct: 213 GRSPTVSEIARHLQMSEDDVLEGLESANAYSAVSLDAPDSGDDEAPAVADTLGVQD---- 268

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
                E  E    R  L   +  L  RE+RI   R      +T   +++E  +S+  V +
Sbjct: 269 -----ESLEGVEYRESLKPLLEKLPAREKRILLLRFFGN--MTQSQIATELGISQMHVSR 321

Query: 272 IEARAFKKVQESI 284
           + AR   +++  +
Sbjct: 322 LLARTLAQLRRGL 334


>gi|297736323|emb|CBI24961.3| unnamed protein product [Vitis vinifera]
          Length = 319

 Score =  162 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 59/239 (24%), Positives = 122/239 (51%), Gaps = 12/239 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             +  R+  S+ RLVV IA  Y+G GL + +++ EG+IGL++  ++FDP+RG++L+TY  
Sbjct: 80  RESRERINQSYRRLVVSIAARYQGKGLSLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVY 139

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I     ++++  +     +   + ++      ++    +      IA+ +
Sbjct: 140 WWIRQAIVRAIANKSRIIRLPGS-----ICEMVAKIAEARTVLSRRLRRLPTYDEIAEFI 194

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +V+ S V  ++ R     S++  + S  +     Q+ +    +   Q +++   R+  + 
Sbjct: 195 DVNVSTVRLVSERSRTPISVDQAVTS--QGCMTLQEIIPGPDETTPQKMVK---RQLMKQ 249

Query: 227 MLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            + R+++ L  RE  I         E P++ E +    ++SRERVRQI + A  K++++
Sbjct: 250 EVERALNTLCEREAYILRLYFGINGETPLSFEEIGRLMKLSRERVRQINSIALSKLRQT 308


>gi|288555973|ref|YP_003427908.1| sporulation sigma factor SigF [Bacillus pseudofirmus OF4]
 gi|288547133|gb|ADC51016.1| sporulation sigma factor SigF [Bacillus pseudofirmus OF4]
          Length = 256

 Score =  162 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 55/259 (21%), Positives = 115/259 (44%), Gaps = 19/259 (7%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             +E   L  R +E GD  A   +V  + RLV  +   +   G    ++   G IGL+++
Sbjct: 17  SDKEVKELIARSQE-GDQQARDLIVNRNTRLVWSVVQRFMNRGYEADDLFQIGCIGLIKS 75

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V KFD     + +TY++  I   +Q ++      VK+  +   K L   +R++K  L   
Sbjct: 76  VDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSI--KELGNKIRKMKDEL--- 129

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
           T +  +   V  IA++L ++  EV+          S++  +  +D +     D +     
Sbjct: 130 TKSLGRVPTVNEIAEQLEITPEEVVFAGEASRSLTSIHETVYENDGDPITLLDQIAD--- 186

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
                  + E +   +  L  ++  L+ RER I   R  ++   T   +++   +S+ +V
Sbjct: 187 -------QTETKWFDKIALKEAIRDLDERERLIVFLRYYKDQ--TQSEVATRLGISQVQV 237

Query: 270 RQIEARAFKKVQESIQKQV 288
            ++E +  ++++E + +Q+
Sbjct: 238 SRLEKKILEQMKEVMGEQI 256


>gi|37806471|dbj|BAC99906.1| putative plastid RNA polymerase sigma factor [Oryza sativa Japonica
           Group]
          Length = 342

 Score =  162 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 68/254 (26%), Positives = 121/254 (47%), Gaps = 10/254 (3%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L  R  E     A   L  S+LRLV+ IA  Y   G+ +++++  G IGL++ ++KFD 
Sbjct: 88  ELRSRMHES--FLAREMLTMSNLRLVISIAQKYDNLGVELADLIQGGLIGLLRGIEKFDA 145

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            RGFR++TY  WWI+  +   +  +    ++ T  +++     L  ++G    + D  + 
Sbjct: 146 SRGFRISTYVYWWIRQGVSRALAENSKTFRLPTYLHER-----LIAIRGAKYELEDQGIA 200

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQV 214
           P  +  IA  LN+SE +V++    +    SL+     S +    +     + D +     
Sbjct: 201 P-TIENIAGSLNISEKKVLNATEAVNKVLSLDQQAFPSLNGLPGETLHSYIEDQNVANDP 259

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIE 273
               EE   +  +     S LN RER I        +   T E++S +F +SRERVRQ+ 
Sbjct: 260 WHGFEEWYLKEEVNKLLNSTLNERERDIIRLYHGIGKQCHTWEDISRQFGLSRERVRQVG 319

Query: 274 ARAFKKVQESIQKQ 287
             A +K++ + +++
Sbjct: 320 LIAMEKLKHAARRK 333


>gi|282861039|ref|ZP_06270104.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
 gi|282563697|gb|EFB69234.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
          Length = 323

 Score =  162 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 62/255 (24%), Positives = 108/255 (42%), Gaps = 20/255 (7%)

Query: 35  YVLAKRYREHGDLSA-----AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             L    RE  D SA      +RLV  HL LV  +A  +R  G P+ ++     IGL+++
Sbjct: 80  RALFVELRELPDGSAEKAELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKS 139

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V +FDP+RG   +TY+   +   ++ +       V++     + RL      L      +
Sbjct: 140 VDRFDPDRGVEFSTYATPTVVGEIKRHFRDKGWAVRVPRRLQELRLS-----LTTATAEL 194

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
           +    +   V  +A++L +SE EV+          +L+  +  +D  S    D L  +  
Sbjct: 195 SQQYGRSPTVHELAERLGISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGSED- 253

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
                  E  E    R  L   +  L PRE+RI   R      +T   ++ E  +S+  V
Sbjct: 254 -------EALEGVEYRESLKPLLEGLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHV 304

Query: 270 RQIEARAFKKVQESI 284
            ++ AR   +++E +
Sbjct: 305 SRLLARTLAQLRERL 319


>gi|160933256|ref|ZP_02080645.1| hypothetical protein CLOLEP_02102 [Clostridium leptum DSM 753]
 gi|156868330|gb|EDO61702.1| hypothetical protein CLOLEP_02102 [Clostridium leptum DSM 753]
          Length = 260

 Score =  162 bits (411), Expect = 5e-38,   Method: Composition-based stats.
 Identities = 57/264 (21%), Positives = 117/264 (44%), Gaps = 20/264 (7%)

Query: 24  RKIPMLEKQEEYVLAKRYRE---HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
            K+ +L ++E+  L  + +         A   L+  +LRLV+ +   +   G  + ++  
Sbjct: 14  SKLKVLTEKEKRALLTQMKNGTPQEQKKAREELINGNLRLVLSVIQRFTNRGENLDDLFQ 73

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
            G IGL++A+  FD  +  R +TY +  I   ++ ++  + S V++  +   +   +   
Sbjct: 74  VGCIGLIKAIDNFDISQDVRFSTYGVPMIIGEIRRFLRDNNS-VRVSRSL--RDTAYKAM 130

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
           ++K  L   T  N K   +  IAK+L + + +V+     +    SL   + S D N + +
Sbjct: 131 QVKERL---TTQNNKEPSIEEIAKELELPKEDVVLALEAIVEPVSLYEPVFS-DGNDTIF 186

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
               V D +     L E          L  ++  L PRE++I   R  Q    T   ++ 
Sbjct: 187 VMDQVGDKNDDNNWLDEIA--------LKEAIRNLGPREKKILNLRFFQG--KTQMEVAK 236

Query: 261 EFEVSRERVRQIEARAFKKVQESI 284
           E  +S+ +V ++E  + ++++  I
Sbjct: 237 EIGISQAQVSRLEKGSLERIKNHI 260


>gi|20151162|pdb|1L0O|C Chain C, Crystal Structure Of The Bacillus Stearothermophilus Anti-
           Sigma Factor Spoiiab With The Sporulation Sigma Factor
           Sigmaf
          Length = 243

 Score =  162 bits (410), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 51/250 (20%), Positives = 106/250 (42%), Gaps = 19/250 (7%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           QE   L +R +E GD  A   ++  ++RLV  +   +   G    ++   G IGL+++V 
Sbjct: 13  QEMKELIRRSQE-GDQEARDEIIEKNMRLVWSVVQRFLNRGYEADDLFQIGCIGLLKSVD 71

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD     + +TY++  I   +Q ++      VK+  +   K +   +R+ K  L     
Sbjct: 72  KFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSL--KEMGNKIRKAKDELSKTRG 128

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +   V  IA  L +S  +V+     +    S++  +  +D +     D +       
Sbjct: 129 ---RAPTVTEIADHLGISPEDVVLAQEAVRLPTSIHETVYENDGDPITLLDQIAD----- 180

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
                  E     +  L +++  L+ RER I   R  ++   T   ++S   +S+ ++ +
Sbjct: 181 -----ADEASWFDKIALKKAIEELDERERLIVYLRYYKDQ--TQSEVASRLGISQVQMSR 233

Query: 272 IEARAFKKVQ 281
           +E +  + ++
Sbjct: 234 LEKKILQHIK 243


>gi|310642622|ref|YP_003947380.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
 gi|309247572|gb|ADO57139.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
          Length = 251

 Score =  162 bits (410), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 51/254 (20%), Positives = 108/254 (42%), Gaps = 18/254 (7%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           +  E        + GD  A   LV S++RLV  +   +   G    ++   G IGL+++V
Sbjct: 14  EDTEVKRLIALSQSGDNDARETLVNSNIRLVWSVVQRFMNRGYEPDDLFQIGCIGLLKSV 73

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
            KFD     + +TY++  I   +Q ++    +   +  + + K     +R++K  L   +
Sbjct: 74  DKFDLSYEVKFSTYAVPMIIGEIQRFLRDDGT---LKVSRSLKETANKVRKMKDEL---S 127

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
               +   V  +A +L V+  +V+          S++  +  +D +     D +      
Sbjct: 128 KRLNRLPTVKEVADELGVTPEDVVFAQEANKPPTSIHETVFENDGDPITLMDQIAD---- 183

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                 E +ER   +  L  ++  L+ RER I   R  ++   T   ++S   +S+ +V 
Sbjct: 184 ------ESQERWFDKLALNEAIDGLSERERLIVYLRYYRDQ--TQSEVASRLGISQVQVS 235

Query: 271 QIEARAFKKVQESI 284
           ++E +  + +++ I
Sbjct: 236 RLEKKILQLIRDQI 249


>gi|311898315|dbj|BAJ30723.1| putative RNA polymerase sigma factor [Kitasatospora setae KM-6054]
          Length = 360

 Score =  162 bits (410), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 54/237 (22%), Positives = 103/237 (43%), Gaps = 15/237 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              ++LV  H+ LV  +A  +R  G P+ ++     IGL+++V +FD ERG   +TY+  
Sbjct: 135 EIRNQLVRMHIPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDHERGVEFSTYATP 194

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I   ++ +       V++     + RL      L      ++  + +   V  +A+ L 
Sbjct: 195 TIVGEIKRHFRDKGWAVRVPRRLQELRLS-----LTTATSELSQRHGRSPTVHELAEHLG 249

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +SE +V+          +L+  +  SD  S    D L            E  E    R  
Sbjct: 250 ISEEDVLEGLESANAYSTLSLDVPDSDDESPAVADTLGATD--------EALEGVEYRES 301

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   ++ L PRE++I   R  +   +T   +++E  +S+  V ++ AR   +++E +
Sbjct: 302 LKPLLAQLPPREQKILVLRFFRN--MTQSQIAAEVGISQMHVSRLLARTLAQLREKL 356


>gi|121535758|ref|ZP_01667560.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
 gi|121305657|gb|EAX46597.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
          Length = 243

 Score =  162 bits (410), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 58/258 (22%), Positives = 113/258 (43%), Gaps = 17/258 (6%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           MLE  E     KR  + GD  A   ++  ++ LV  I   +   G    ++   G IGLM
Sbjct: 1   MLEDAELKEWIKR-AQAGDKQAKEYILEHNVNLVRSIVHRFLNRGYEWDDLFQIGCIGLM 59

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +A+++FD     + +TY++  +   ++ +I       K+      K L + + R +  LQ
Sbjct: 60  KAIERFDLNFNVKFSTYAVPMVIGEIRRFIRDDNPT-KVSRPV--KELAYRVYRTQERLQ 116

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
           ++         +  +AK+L ++  E++S    +    SL       D +     D +   
Sbjct: 117 SLLGRE---PTIHEVAKELALAPQEIVSALEAMQPPASLFEQAYHDDGDPISRLDQIAQ- 172

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            DGQ+    EK         L   +S L P+ER +   R  ++   T   +++   +S+ 
Sbjct: 173 CDGQDNAYFEKL-------ALREVLSRLPPKERYVIHLRFFED--KTQAEIANMIGLSQV 223

Query: 268 RVRQIEARAFKKVQESIQ 285
           +V +IE +A + +++ +Q
Sbjct: 224 QVSRIEKQALRLIRDLMQ 241


>gi|224088962|ref|XP_002308586.1| predicted protein [Populus trichocarpa]
 gi|222854562|gb|EEE92109.1| predicted protein [Populus trichocarpa]
          Length = 559

 Score =  162 bits (410), Expect = 6e-38,   Method: Composition-based stats.
 Identities = 58/236 (24%), Positives = 116/236 (49%), Gaps = 12/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
               L+ +   LV+ IA  YRG G+ + +++  GN+GL+Q  ++FDP RG+R +TY  +W
Sbjct: 321 CRDELIKNTHSLVLYIARNYRGMGIAMEDLIQAGNLGLLQGAERFDPTRGYRFSTYVQYW 380

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ +M + + R    ++I        L  ++ +++   +A+++++ +      +AK   +
Sbjct: 381 IRKSMLKIVERHARGIQIPY-----ALSRSINKIQKARKALSNSHGRYPDDWEVAKFTGL 435

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S +++ S    L    SL+  I         +  +  +  D   Q   E   R++ R  +
Sbjct: 436 SLAKIESAQKCLRVVASLDQKI-----GEGHYAKYSEFIPDMSIQNPEEAVMRQHMREEI 490

Query: 229 TRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              +  L+ RE+++   R       P +L  +   F VS+ERVR+IE +   K+++
Sbjct: 491 YDLLRGLDSREKQVMVLRYGFKDNQPKSLAEIGRLFRVSKERVRKIEKKIMIKLRD 546


>gi|114566373|ref|YP_753527.1| sporulation sigma factor SigG [Syntrophomonas wolfei subsp. wolfei
           str. Goettingen]
 gi|114337308|gb|ABI68156.1| RNA polymerase sigma-G factor [Syntrophomonas wolfei subsp. wolfei
           str. Goettingen]
          Length = 234

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 52/241 (21%), Positives = 109/241 (45%), Gaps = 16/241 (6%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            G   A  +L+  ++RLV+ +   +   G  + ++   G IGL++++  FD  +  R +T
Sbjct: 10  QGKTQAREKLIQGNIRLVLSVIQRFTNRGEYVDDLFQVGCIGLIKSIDNFDLSQNVRFST 69

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y++  I   ++ Y+  +   V++  +   + + +   +++   + + ++N     V  IA
Sbjct: 70  YAVPMIIGEIRRYLRDNN-AVRVSRSL--RDIAYKALQVR---EKLINDNSAEPTVSQIA 123

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + L+VS  EV+     +    SL   I +   +     D L  +  G EQ L E      
Sbjct: 124 QHLDVSREEVVFALDAIQEPVSLFEPIYNDGGDPILVMDQLSDERSGDEQWLEE------ 177

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               +  +M  LN RE+ I   R       T   ++ E  +S+ +V ++E  A K++++ 
Sbjct: 178 --ISIKEAMKKLNDREKHIVSLRFFAG--KTQMEVAEEIGISQAQVSRLEKAALKQLRKY 233

Query: 284 I 284
           +
Sbjct: 234 V 234


>gi|164687591|ref|ZP_02211619.1| hypothetical protein CLOBAR_01232 [Clostridium bartlettii DSM
           16795]
 gi|164603365|gb|EDQ96830.1| hypothetical protein CLOBAR_01232 [Clostridium bartlettii DSM
           16795]
          Length = 255

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 51/258 (19%), Positives = 117/258 (45%), Gaps = 16/258 (6%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           +L  +E   L ++ + +GD  A   L++S+L LV  +   +   G    ++   G+IGL+
Sbjct: 13  LLSHEETLDLIQKVQ-NGDEEAKALLISSNLGLVRSVIGKFSNIGYERDDLFQLGSIGLI 71

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +A+ KFDP    + +TY++  I   ++ Y+     +VK+  +  Q  +     ++K   +
Sbjct: 72  KAIYKFDPSYNVKFSTYAVPMILGEIKRYLRDDG-MVKVSRSLKQLAI-----KVKMQGE 125

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
            ++    +   +  +A+ + V + +V+         E L  +I+  + +     D +   
Sbjct: 126 MLSKKLGRDPTIEELAEAIGVEKEDVVMAIESNFSVEYLQGVIHEEEGSPICLIDKISQK 185

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            + +E  +++         +L   +  L+ RER+I   R  ++   T   +     +S+ 
Sbjct: 186 GEAEEDKVVDNI-------LLKEVLGKLDKRERQIIMLRYFED--KTQSEIGELLNISQV 236

Query: 268 RVRQIEARAFKKVQESIQ 285
           +V +IE +   K++  I+
Sbjct: 237 QVSRIEKKVLHKLKLYIE 254


>gi|2624403|emb|CAA74653.1| plastid RNA polymerase sigma factor [Sorghum bicolor]
          Length = 500

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 71/254 (27%), Positives = 123/254 (48%), Gaps = 10/254 (3%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L  R RE     A   L  S++RLV+ IA  Y   G+ +++++  G IGL++ ++KFD 
Sbjct: 246 ELRARMRES--FLAREMLTMSNIRLVISIAQKYDNLGVELADLIQGGLIGLLRGIEKFDA 303

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            RGFR++TY  WWI+  +   +  +    ++ T  +++     L  ++G   A+ D  + 
Sbjct: 304 SRGFRISTYVYWWIRQGVSRALADNSKAFRLPTYLHER-----LIAIRGAKYALEDQGIA 358

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQV 214
           P  V  IA+ LN+SE +V +    +    SL+     S +          + D +     
Sbjct: 359 P-TVENIAESLNISEKKVHNATEAVNKVLSLDQQAFPSLNGLPGDTLHSYIEDQNVANDP 417

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIE 273
               EER  +  +     S LN RER I        +   T E++S +F +SRERVRQ+ 
Sbjct: 418 WHGFEERYLKEEVNNLINSNLNERERDIIRLYHGIGKQCHTWEDISRQFGLSRERVRQVG 477

Query: 274 ARAFKKVQESIQKQ 287
             A +K++ + +++
Sbjct: 478 LVAMEKLKHAARRK 491


>gi|294673921|ref|YP_003574537.1| RNA polymerase sigma-70 factor [Prevotella ruminicola 23]
 gi|294472533|gb|ADE81922.1| RNA polymerase sigma-70 factor [Prevotella ruminicola 23]
          Length = 250

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 61/278 (21%), Positives = 130/278 (46%), Gaps = 49/278 (17%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +  L+RY+ EI +  +L  +EE  LA+R  + GD  A  +L+ ++L+ VV +A  Y+G G
Sbjct: 19  DSALNRYLDEIGREQLLTNEEERELAERIAK-GDERALSKLIEANLKFVVSVARQYKGKG 77

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           + + ++VSEGN+GLM+A  KFD  +G R   ++  +I+ ++++ I +   L ++     Q
Sbjct: 78  VDMEDLVSEGNLGLMKAAAKFDASKGVRFVNFAFVYIRQSIEKAIDQQGGLYQVPKDVKQ 137

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                                           ++   +++ +S++  L    +++     
Sbjct: 138 --------------------------------EVARQQAQAVSVDAPLGHRTNMSL---- 161

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
                      L    +    +  E+   +   + +  ++  L+ RERR+  A       
Sbjct: 162 -----------LSVLVNKDAPLADERVHSEAIEDAIEFALGTLDARERRVINAFYGINQE 210

Query: 253 V-TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
             T+  ++ + +V RERVRQI  +A +K++++ + +++
Sbjct: 211 HETMAEIAEDMDVKRERVRQIREKAVRKLRKAYRNKLK 248


>gi|256372040|ref|YP_003109864.1| RNA polymerase, sigma 32 subunit, RpoH [Acidimicrobium ferrooxidans
           DSM 10331]
 gi|256008624|gb|ACU54191.1| RNA polymerase, sigma 32 subunit, RpoH [Acidimicrobium ferrooxidans
           DSM 10331]
          Length = 294

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 68/268 (25%), Positives = 124/268 (46%), Gaps = 24/268 (8%)

Query: 29  LEKQEEYVLAKRYREHGDLS------------AAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
           L   EE  L+   +E  +              A  R V  ++ LVV IA  Y   G+ + 
Sbjct: 24  LLPDEEVALSIVLQEAQEAEDVPPDVAAVVQAARERFVEGNMGLVVSIARRYVQPGISLD 83

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           ++V EG IGL++A+  +D  RGFR +TY+ WWI+ A+ + + R+   V +      + + 
Sbjct: 84  DLVQEGTIGLLRAIDLYDGRRGFRFSTYATWWIRQAIAQALTRTRRDVVLP-----RGIA 138

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
             L R++   + +     +   +  +A    + E  V  +        SL+  +   ++ 
Sbjct: 139 AELARVEVQRRELEQALGRQPSMAELAAASGIDELRVRELQGYARSVLSLDQAV--GEER 196

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVT 254
                D +    D   + + E  E  + R ++  +++ L PRER +   R   E   P +
Sbjct: 197 DVTLADIVP---DRDAEPIEETIEHADLRTVIAGALAHLEPREREVLAFRFGLEGNEPHS 253

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQE 282
           LE+ ++ F ++RER+RQIEARA  +++ 
Sbjct: 254 LEDAAAYFGIARERIRQIEARAIARLRR 281


>gi|162448460|ref|YP_001610827.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
 gi|161159042|emb|CAN90347.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
          Length = 446

 Score =  162 bits (410), Expect = 7e-38,   Method: Composition-based stats.
 Identities = 70/247 (28%), Positives = 122/247 (49%), Gaps = 14/247 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   LV ++LRL V IA  ++ +G+P+ ++V EGN+GL++A  KF+  RG R  TY+ W
Sbjct: 208 QAKSELVQANLRLAVAIAREHQRFGVPLLDLVQEGNLGLIRAADKFEYRRGHRFGTYAAW 267

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WIK A++  IL     V++       R      ++    + +     +   V  IA++  
Sbjct: 268 WIKQAIKRTILNQGKPVRMPVHLTAIR-----SQVVRARRDLVQERGREPSVEEIAERSG 322

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++  +V  ++       SL+A +   ++  +++ D L  D      +L  +   +  R +
Sbjct: 323 LTVEKVRVISELALEPLSLDAPV--GEEGDTRYGDLLANDEPTPADMLARRRLIEQTREL 380

Query: 228 LTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L      L PRER +   R   +     TLE +   F ++RER+RQIEA+  +K++   +
Sbjct: 381 L----DSLQPRERELLRRRFGLDGNEDETLEEIGQSFSLTRERIRQIEAKLLEKLRTRSR 436

Query: 286 KQVELSS 292
            Q EL S
Sbjct: 437 -QRELGS 442


>gi|299538362|ref|ZP_07051645.1| RNA polymerase sigma-F factor [Lysinibacillus fusiformis ZC1]
 gi|298725949|gb|EFI66541.1| RNA polymerase sigma-F factor [Lysinibacillus fusiformis ZC1]
          Length = 247

 Score =  161 bits (409), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 52/251 (20%), Positives = 108/251 (43%), Gaps = 19/251 (7%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
              L  R ++ GD  A  R+V  + RLV  I   +   G+ + ++   G IGLM++V KF
Sbjct: 1   MRDLIARAQQ-GDHEARKRMVEGNTRLVWSIVQRFTTRGVELEDLFQIGCIGLMKSVDKF 59

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D     + +TY++  I   +Q ++     +VK+  +  +        +++         N
Sbjct: 60  DLTYDVKFSTYAVPMIIGEIQRFLRDDG-MVKVSRSIRELNF-----KIRHATDEFIKKN 113

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
             P  +  +A+ L V+  E+++ +  L    SL+  +  S+ +S    D +  +   Q  
Sbjct: 114 EHPPTIQELAQVLGVTTEEIVTASDALRDPASLHEQLYESEGDSITLMDQMKDEKSEQPF 173

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
             I           L   ++ L PRE+ I   R   +   T   +++   +S+ +V ++E
Sbjct: 174 DYIP----------LKEVLTRLEPREQSIIYLRYFSD--CTQTEIANRLGISQVQVSRLE 221

Query: 274 ARAFKKVQESI 284
            +   +++  +
Sbjct: 222 KKILAQLKSWM 232


>gi|300728464|ref|ZP_07061824.1| RNA polymerase sigma-43 factor [Prevotella bryantii B14]
 gi|299774265|gb|EFI70897.1| RNA polymerase sigma-43 factor [Prevotella bryantii B14]
          Length = 251

 Score =  161 bits (409), Expect = 8e-38,   Method: Composition-based stats.
 Identities = 72/286 (25%), Positives = 128/286 (44%), Gaps = 51/286 (17%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +    +       L  Y+ EI K  +L +QEE  L+ + + +GD SA  +L T++LR VV
Sbjct: 5   KTGKPLSEQENDSLQTYLSEIGKENLLSEQEEQELSAKIQ-NGDESAIEKLTTANLRFVV 63

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA  Y+  GL I++++SEGN GL++A +KFD  +G R   Y++ +I+ A++  I     
Sbjct: 64  SIAKRYQDRGLGINDLISEGNFGLIKAARKFDAAKGQRFVQYAVHFIRQAIENAIQEQSG 123

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +  +  + +                                  + + +S+  S++  L  
Sbjct: 124 IYTLPHSMD--------------------------------DPVELKQSKAFSVDAPLVQ 151

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
            ++ + L   SD N+       + D                 R  L RS+SVLN RERR+
Sbjct: 152 GKTASLLHVLSDPNAVIPDKPYLDD---------------VLRQGLIRSLSVLNDRERRV 196

Query: 243 FEARRLQEN---PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
                   +    +T E + ++  + RERVR I  +A +K+++  +
Sbjct: 197 VSMFYGLNDQNAGLTYEEIGTQLGLKRERVRDIRKKAERKMKKYTK 242


>gi|15614101|ref|NP_242404.1| sporulation sigma factor SigF [Bacillus halodurans C-125]
 gi|10174155|dbj|BAB05257.1| RNA polymerase sigma-F factor (stage II sporulation protein AC)
           [Bacillus halodurans C-125]
          Length = 252

 Score =  161 bits (409), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 54/253 (21%), Positives = 107/253 (42%), Gaps = 18/253 (7%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            EE        + GD  A  ++V+ + RLV  +   +   G    ++   G IGL+++V 
Sbjct: 16  DEEIKQLIAQSQAGDQEARDQIVSRNTRLVWSVVQRFLNRGYEADDLFQIGCIGLIKSVD 75

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD     + +TY++  I   +Q ++      VK+  +   K L   +R+LK  +   T 
Sbjct: 76  KFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSI--KELGNKIRKLKDDM---TK 129

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +   V  IA++L ++  EV+          S++  +  +D +     D L       
Sbjct: 130 TLGRTPTVNEIAEQLEITPEEVVFAGDASRSLSSIHETVYENDGDPITLLDQLED----- 184

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
                + E R   +  L  ++  L  RER I   R  ++   T   ++    +S+ +V +
Sbjct: 185 -----QSETRWFDKIALKEAIHNLEERERLIVYLRYYKDQ--TQSEVAQRLGISQVQVSR 237

Query: 272 IEARAFKKVQESI 284
           +E +  + ++ +I
Sbjct: 238 LEKKILETMKANI 250


>gi|126215762|gb|ABN81001.1| putative RNA polymerase sigma-B factor [Rhodococcus opacus]
          Length = 194

 Score =  161 bits (409), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 44/204 (21%), Positives = 97/204 (47%), Gaps = 12/204 (5%)

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +P+ +++ EGN+GL++A++KFD  +GF+ +TY+ WWI+ A+   +      +++     +
Sbjct: 1   MPLLDLIQEGNLGLIRAMEKFDYAKGFKFSTYATWWIRQAITRGMADQSRTIRLPVHLVE 60

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
           +     L R+K  L        +      +A++  +   ++  +        SL+  + +
Sbjct: 61  Q--VNKLARIKRELHQ---QLGREATDDELAEESGIPAHKIADLLDHSRDPVSLDMPVGN 115

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN- 251
            ++  +   D++    D +              + +   ++ L+ RE+++   R   ++ 
Sbjct: 116 DEE--APLGDFI---EDSEATSAENAVIAGLLHSDVRSVLATLDEREQQVIRLRYGLDDG 170

Query: 252 -PVTLENLSSEFEVSRERVRQIEA 274
            P TL+ +   F +SRERVRQIE 
Sbjct: 171 QPRTLDQIGKLFGLSRERVRQIER 194


>gi|239929001|ref|ZP_04685954.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291437340|ref|ZP_06576730.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291340235|gb|EFE67191.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 374

 Score =  161 bits (409), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 103/237 (43%), Gaps = 15/237 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              ++LV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+  
Sbjct: 149 ELRNQLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATP 208

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +   ++ +       V++     + RL      L      ++  + +   V  +A+KL 
Sbjct: 209 TVVGEIKRHFRDKGWAVRVPRRLQELRLA-----LTTATAELSQLHGRSPTVHELAEKLA 263

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +SE EV+          +L+  +  +D  S    D L  +         E  E    R  
Sbjct: 264 ISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAED--------EALEGVEYRES 315

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 316 LKPLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLREKL 370


>gi|328884955|emb|CCA58194.1| RNA polymerase sigma factor [Streptomyces venezuelae ATCC 10712]
          Length = 344

 Score =  161 bits (409), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 102/237 (43%), Gaps = 15/237 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              ++LV  HL LV  +A  +R  G P+ ++     IGL+++V +FDPERG   +TY+  
Sbjct: 119 ELRNQLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPERGVEFSTYATP 178

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +   ++ +       V++     + RL      L      ++  + +   V  +A++L 
Sbjct: 179 TVVGEIKRHFRDKGWAVRVPRRLQELRLS-----LTTATAELSQQHGRSPTVHELAERLG 233

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +SE EV+          +L+  +  +D  S    D L  +         E  E    R  
Sbjct: 234 ISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAED--------EALEGVEYRES 285

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR    ++E +
Sbjct: 286 LKPLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLASLREKL 340


>gi|152976482|ref|YP_001375999.1| sporulation sigma factor SigF [Bacillus cereus subsp. cytotoxis NVH
           391-98]
 gi|152025234|gb|ABS23004.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           cytotoxicus NVH 391-98]
          Length = 252

 Score =  161 bits (409), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 54/263 (20%), Positives = 116/263 (44%), Gaps = 19/263 (7%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           +K P L+  E   L ++  + GD  A   +V S++RLV  +   +   G    ++   G 
Sbjct: 9   KKNPQLKDHELKALIQK-SQDGDQGARDTIVQSNMRLVWSVVQRFLNRGYEPDDLFQIGC 67

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL+++V KFD     + +TY++  I   +Q ++    S VK+  +   K     +R++K
Sbjct: 68  IGLLKSVDKFDLSFDVKFSTYAVPMIIGEIQRFLRDDGS-VKVSRSL--KETGNKIRKMK 124

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L   +    +   +  +A+ L ++  EV+          S++  +  +D +     D 
Sbjct: 125 DEL---SKEYGRAPTINEVAEALELTPEEVVLAQEASRTPSSIHETVYENDGDPITILDQ 181

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +            + E +   +  L  ++  L+ RER I   R  ++   T   ++    
Sbjct: 182 IAD----------QAETKWFDKIALKEAIRELDERERLIVYLRYYKDQ--TQSEVAERIG 229

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+ +V ++E +  K++++ I +
Sbjct: 230 ISQVQVSRLEKKILKQMKDRIDE 252


>gi|312127292|ref|YP_003992166.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor hydrothermalis 108]
 gi|311777311|gb|ADQ06797.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor hydrothermalis 108]
          Length = 240

 Score =  161 bits (409), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 54/253 (21%), Positives = 109/253 (43%), Gaps = 17/253 (6%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
            K  +  L  + + +GD  A  +L+ S+L LV  +   +   G+ + ++   G IGL++A
Sbjct: 2   SKASQEELISKAK-NGDKLARQQLIESNLALVWSVVKKFAAKGVELEDLFQIGCIGLIKA 60

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V +FDP    R +TY++  I   ++ Y+      +K+      +++  N  ++K      
Sbjct: 61  VDRFDPSFNVRFSTYAVPMIIGEIKRYLRDDGK-IKVS-----RKIKENQGKIKKLRNQF 114

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
             N+ +   +  I++   +S  E++      +   SL+ +IN  +       D    + D
Sbjct: 115 VSNHGREPTISEISQLTGLSSDEILLCLDASSEVASLSEVINQEEGKPITLMDIASDEED 174

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
              ++L            L   +  L  RER I   R  +    T   ++ E  +S+  V
Sbjct: 175 YSTKLLDLMA--------LKEGLKKLKGRERYIIFMRYFKN--KTQSEIAKELNISQVHV 224

Query: 270 RQIEARAFKKVQE 282
            +IE RA ++++ 
Sbjct: 225 SRIEKRALERIKR 237


>gi|310822395|ref|YP_003954753.1| RNA polymerase sigma factor [Stigmatella aurantiaca DW4/3-1]
 gi|309395467|gb|ADO72926.1| RNA polymerase sigma factor [Stigmatella aurantiaca DW4/3-1]
          Length = 245

 Score =  161 bits (409), Expect = 9e-38,   Method: Composition-based stats.
 Identities = 77/275 (28%), Positives = 126/275 (45%), Gaps = 54/275 (19%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           GLS Y+  +     L +++EY LA+  R+ GD SA   L TS+L  VV +A  +   G  
Sbjct: 11  GLSHYLRHLGGHHQLTREQEYELARAARK-GDESARQTLATSNLAFVVAVAKKFANRGAR 69

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++ EGN+GLM+A++ FDP++  R ATY++WWI+A +  Y+  + S V+ G       
Sbjct: 70  LDDLIQEGNVGLMKAIEHFDPKKNVRFATYAVWWIRAYITRYLKDNRSQVRGG------- 122

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
                                              ESE  SM      D SL+A I   +
Sbjct: 123 -----------------------------------ESERGSMV-----DFSLDATI--DE 140

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
           +  + + D L         V + +E+ +     L +    +      I + R  Q+ P+T
Sbjct: 141 EGETTFMDRLEDGGPSPSDVYLSREQDQEVHEALVKVRKRIGDLGWDILQERLTQDKPLT 200

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           LE L   + VSRERVRQ+E +     +  +++ +E
Sbjct: 201 LEELGQRWGVSRERVRQVELKT----KSFLERYLE 231


>gi|302389825|ref|YP_003825646.1| RNA polymerase, sigma subunit, RpoX/SigF [Thermosediminibacter
           oceani DSM 16646]
 gi|302200453|gb|ADL08023.1| RNA polymerase, sigma subunit, RpoX/SigF [Thermosediminibacter
           oceani DSM 16646]
          Length = 241

 Score =  161 bits (409), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 52/249 (20%), Positives = 108/249 (43%), Gaps = 17/249 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L K+ +E GD  A   LV+ +L LV  I   +   G  I ++   G+IGL++A++KFD 
Sbjct: 8   ELLKKAKE-GDQEAKSELVSLNLGLVWSIVKRFTNRGYEIEDLFQIGSIGLLKAIEKFDF 66

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
               + +TY++  I   ++ YI      +K+  +     +     +++   + +     +
Sbjct: 67  SYNVKFSTYAVPMIIGEIRRYIRDD-RPIKMTRSLRDFSI-----KIQNAKERLAKELNR 120

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
              +  +A++L  +  E++          SLN +    D +   + D L  D   Q Q L
Sbjct: 121 EPTIAELAEELGATPEELVVGLEAAQPIISLNDVAFQEDGSPIYYMDQLNSDEHHQNQWL 180

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
                       L  ++S L+  ER+I   R  ++   T   ++    +++ +V ++E +
Sbjct: 181 --------DTIALKEALSKLDKLERQIIILRYFKD--KTQTEVAKILGITQVQVSRLERK 230

Query: 276 AFKKVQESI 284
              K++  +
Sbjct: 231 ILAKIRNML 239


>gi|30022159|ref|NP_833790.1| sporulation sigma factor SigF [Bacillus cereus ATCC 14579]
 gi|30264150|ref|NP_846527.1| sporulation sigma factor SigF [Bacillus anthracis str. Ames]
 gi|42783188|ref|NP_980435.1| sporulation sigma factor SigF [Bacillus cereus ATCC 10987]
 gi|47529588|ref|YP_020937.1| sporulation sigma factor SigF [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|47568126|ref|ZP_00238830.1| sigma-B, putative [Bacillus cereus G9241]
 gi|49186981|ref|YP_030233.1| sporulation sigma factor SigF [Bacillus anthracis str. Sterne]
 gi|49478518|ref|YP_038132.1| sporulation sigma factor SigF [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|52141420|ref|YP_085409.1| sporulation sigma factor SigF [Bacillus cereus E33L]
 gi|65321467|ref|ZP_00394426.1| COG1191: DNA-directed RNA polymerase specialized sigma subunit
           [Bacillus anthracis str. A2012]
 gi|75762406|ref|ZP_00742276.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|118479276|ref|YP_896427.1| sporulation sigma factor SigF [Bacillus thuringiensis str. Al
           Hakam]
 gi|165871124|ref|ZP_02215774.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0488]
 gi|167633745|ref|ZP_02392069.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0442]
 gi|167639441|ref|ZP_02397712.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0193]
 gi|170687128|ref|ZP_02878346.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0465]
 gi|170705887|ref|ZP_02896350.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0389]
 gi|177652593|ref|ZP_02935009.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0174]
 gi|190565830|ref|ZP_03018749.1| RNA polymerase sigma-F factor [Bacillus anthracis Tsiankovskii-I]
 gi|196035002|ref|ZP_03102409.1| RNA polymerase sigma-F factor [Bacillus cereus W]
 gi|196045861|ref|ZP_03113090.1| RNA polymerase sigma-F factor [Bacillus cereus 03BB108]
 gi|206971277|ref|ZP_03232228.1| RNA polymerase sigma-F factor [Bacillus cereus AH1134]
 gi|206977400|ref|ZP_03238296.1| RNA polymerase sigma-F factor [Bacillus cereus H3081.97]
 gi|217961566|ref|YP_002340136.1| sporulation sigma factor SigF [Bacillus cereus AH187]
 gi|218234550|ref|YP_002368877.1| sporulation sigma factor SigF [Bacillus cereus B4264]
 gi|218899234|ref|YP_002447645.1| RNA polymerase sigma-F factor [Bacillus cereus G9842]
 gi|218905210|ref|YP_002453044.1| RNA polymerase sigma-F factor [Bacillus cereus AH820]
 gi|222097523|ref|YP_002531580.1| sporulation sigma factor sigf [Bacillus cereus Q1]
 gi|225866059|ref|YP_002751437.1| RNA polymerase sigma-F factor [Bacillus cereus 03BB102]
 gi|227816852|ref|YP_002816861.1| RNA polymerase sigma-F factor [Bacillus anthracis str. CDC 684]
 gi|228902583|ref|ZP_04066734.1| RNA polymerase sigma-F factor [Bacillus thuringiensis IBL 4222]
 gi|228909904|ref|ZP_04073725.1| RNA polymerase sigma-F factor [Bacillus thuringiensis IBL 200]
 gi|228916713|ref|ZP_04080278.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228922825|ref|ZP_04086123.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228929122|ref|ZP_04092149.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228935394|ref|ZP_04098212.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228941224|ref|ZP_04103777.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228947793|ref|ZP_04110080.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228954358|ref|ZP_04116384.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228960339|ref|ZP_04121992.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228967106|ref|ZP_04128142.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228974156|ref|ZP_04134726.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228980748|ref|ZP_04141053.1| RNA polymerase sigma-F factor [Bacillus thuringiensis Bt407]
 gi|228987264|ref|ZP_04147385.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|229019284|ref|ZP_04176110.1| RNA polymerase sigma-F factor [Bacillus cereus AH1273]
 gi|229025528|ref|ZP_04181938.1| RNA polymerase sigma-F factor [Bacillus cereus AH1272]
 gi|229047765|ref|ZP_04193345.1| RNA polymerase sigma-F factor [Bacillus cereus AH676]
 gi|229071577|ref|ZP_04204795.1| RNA polymerase sigma-F factor [Bacillus cereus F65185]
 gi|229081330|ref|ZP_04213833.1| RNA polymerase sigma-F factor [Bacillus cereus Rock4-2]
 gi|229093131|ref|ZP_04224253.1| RNA polymerase sigma-F factor [Bacillus cereus Rock3-42]
 gi|229111546|ref|ZP_04241097.1| RNA polymerase sigma-F factor [Bacillus cereus Rock1-15]
 gi|229123596|ref|ZP_04252791.1| RNA polymerase sigma-F factor [Bacillus cereus 95/8201]
 gi|229129353|ref|ZP_04258324.1| RNA polymerase sigma-F factor [Bacillus cereus BDRD-Cer4]
 gi|229140809|ref|ZP_04269354.1| RNA polymerase sigma-F factor [Bacillus cereus BDRD-ST26]
 gi|229146647|ref|ZP_04275014.1| RNA polymerase sigma-F factor [Bacillus cereus BDRD-ST24]
 gi|229152275|ref|ZP_04280468.1| RNA polymerase sigma-F factor [Bacillus cereus m1550]
 gi|229157657|ref|ZP_04285732.1| RNA polymerase sigma-F factor [Bacillus cereus ATCC 4342]
 gi|229186319|ref|ZP_04313484.1| RNA polymerase sigma-F factor [Bacillus cereus BGSC 6E1]
 gi|229192285|ref|ZP_04319250.1| RNA polymerase sigma-F factor [Bacillus cereus ATCC 10876]
 gi|229198196|ref|ZP_04324905.1| RNA polymerase sigma-F factor [Bacillus cereus m1293]
 gi|229603990|ref|YP_002868374.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0248]
 gi|254683842|ref|ZP_05147702.1| sporulation sigma factor SigF [Bacillus anthracis str. CNEVA-9066]
 gi|254721677|ref|ZP_05183466.1| sporulation sigma factor SigF [Bacillus anthracis str. A1055]
 gi|254736189|ref|ZP_05193895.1| sporulation sigma factor SigF [Bacillus anthracis str. Western
           North America USA6153]
 gi|254744078|ref|ZP_05201761.1| sporulation sigma factor SigF [Bacillus anthracis str. Kruger B]
 gi|254754142|ref|ZP_05206177.1| sporulation sigma factor SigF [Bacillus anthracis str. Vollum]
 gi|254758168|ref|ZP_05210195.1| sporulation sigma factor SigF [Bacillus anthracis str. Australia
           94]
 gi|296504567|ref|YP_003666267.1| sporulation sigma factor SigF [Bacillus thuringiensis BMB171]
 gi|301055569|ref|YP_003793780.1| sporulation sigma factor SigF [Bacillus anthracis CI]
 gi|29897716|gb|AAP10991.1| RNA polymerase sigma-F factor [Bacillus cereus ATCC 14579]
 gi|30258795|gb|AAP28013.1| RNA polymerase sigma-F factor [Bacillus anthracis str. Ames]
 gi|42739116|gb|AAS43043.1| RNA polymerase sigma-F factor [Bacillus cereus ATCC 10987]
 gi|47504736|gb|AAT33412.1| RNA polymerase sigma-F factor [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|47555116|gb|EAL13463.1| sigma-B, putative [Bacillus cereus G9241]
 gi|49180908|gb|AAT56284.1| RNA polymerase sigma-F factor [Bacillus anthracis str. Sterne]
 gi|49330074|gb|AAT60720.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|51974889|gb|AAU16439.1| RNA polymerase sigma-F factor [Bacillus cereus E33L]
 gi|74490099|gb|EAO53445.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|118418501|gb|ABK86920.1| RNA polymerase, sigma subunit, RpoX/SigF [Bacillus thuringiensis
           str. Al Hakam]
 gi|164713043|gb|EDR18570.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0488]
 gi|167512500|gb|EDR87875.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0193]
 gi|167531151|gb|EDR93838.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0442]
 gi|170129427|gb|EDS98291.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0389]
 gi|170668745|gb|EDT19490.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0465]
 gi|172081928|gb|EDT66996.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0174]
 gi|190562749|gb|EDV16715.1| RNA polymerase sigma-F factor [Bacillus anthracis Tsiankovskii-I]
 gi|195992541|gb|EDX56502.1| RNA polymerase sigma-F factor [Bacillus cereus W]
 gi|196023301|gb|EDX61979.1| RNA polymerase sigma-F factor [Bacillus cereus 03BB108]
 gi|206734049|gb|EDZ51220.1| RNA polymerase sigma-F factor [Bacillus cereus AH1134]
 gi|206744391|gb|EDZ55802.1| RNA polymerase sigma-F factor [Bacillus cereus H3081.97]
 gi|217063378|gb|ACJ77628.1| RNA polymerase sigma-F factor [Bacillus cereus AH187]
 gi|218162507|gb|ACK62499.1| RNA polymerase sigma-F factor [Bacillus cereus B4264]
 gi|218540139|gb|ACK92537.1| RNA polymerase sigma-F factor [Bacillus cereus AH820]
 gi|218540957|gb|ACK93351.1| RNA polymerase sigma-F factor [Bacillus cereus G9842]
 gi|221241581|gb|ACM14291.1| RNA polymerase sigma-F factor [Bacillus cereus Q1]
 gi|225790809|gb|ACO31026.1| RNA polymerase sigma-F factor [Bacillus cereus 03BB102]
 gi|227007915|gb|ACP17658.1| RNA polymerase sigma-F factor [Bacillus anthracis str. CDC 684]
 gi|228585356|gb|EEK43465.1| RNA polymerase sigma-F factor [Bacillus cereus m1293]
 gi|228591235|gb|EEK49089.1| RNA polymerase sigma-F factor [Bacillus cereus ATCC 10876]
 gi|228597113|gb|EEK54768.1| RNA polymerase sigma-F factor [Bacillus cereus BGSC 6E1]
 gi|228625614|gb|EEK82366.1| RNA polymerase sigma-F factor [Bacillus cereus ATCC 4342]
 gi|228631237|gb|EEK87873.1| RNA polymerase sigma-F factor [Bacillus cereus m1550]
 gi|228636817|gb|EEK93280.1| RNA polymerase sigma-F factor [Bacillus cereus BDRD-ST24]
 gi|228642599|gb|EEK98885.1| RNA polymerase sigma-F factor [Bacillus cereus BDRD-ST26]
 gi|228653958|gb|EEL09825.1| RNA polymerase sigma-F factor [Bacillus cereus BDRD-Cer4]
 gi|228659731|gb|EEL15376.1| RNA polymerase sigma-F factor [Bacillus cereus 95/8201]
 gi|228671928|gb|EEL27221.1| RNA polymerase sigma-F factor [Bacillus cereus Rock1-15]
 gi|228690280|gb|EEL44073.1| RNA polymerase sigma-F factor [Bacillus cereus Rock3-42]
 gi|228701952|gb|EEL54435.1| RNA polymerase sigma-F factor [Bacillus cereus Rock4-2]
 gi|228711513|gb|EEL63470.1| RNA polymerase sigma-F factor [Bacillus cereus F65185]
 gi|228723557|gb|EEL74922.1| RNA polymerase sigma-F factor [Bacillus cereus AH676]
 gi|228735810|gb|EEL86395.1| RNA polymerase sigma-F factor [Bacillus cereus AH1272]
 gi|228741969|gb|EEL92143.1| RNA polymerase sigma-F factor [Bacillus cereus AH1273]
 gi|228772493|gb|EEM20938.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228778917|gb|EEM27179.1| RNA polymerase sigma-F factor [Bacillus thuringiensis Bt407]
 gi|228785496|gb|EEM33505.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228792475|gb|EEM40041.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228799363|gb|EEM46327.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228805290|gb|EEM51883.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228811780|gb|EEM58114.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228818383|gb|EEM64455.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228824146|gb|EEM69960.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228830412|gb|EEM76022.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228836880|gb|EEM82223.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228842900|gb|EEM87983.1| RNA polymerase sigma-F factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228849739|gb|EEM94572.1| RNA polymerase sigma-F factor [Bacillus thuringiensis IBL 200]
 gi|228857024|gb|EEN01533.1| RNA polymerase sigma-F factor [Bacillus thuringiensis IBL 4222]
 gi|229268398|gb|ACQ50035.1| RNA polymerase sigma-F factor [Bacillus anthracis str. A0248]
 gi|296325619|gb|ADH08547.1| sporulation sigma factor SigF [Bacillus thuringiensis BMB171]
 gi|300377738|gb|ADK06642.1| sporulation sigma factor SigF [Bacillus cereus biovar anthracis
           str. CI]
 gi|324327980|gb|ADY23240.1| sporulation sigma factor SigF [Bacillus thuringiensis serovar
           finitimus YBT-020]
 gi|326941847|gb|AEA17743.1| sporulation sigma factor SigF [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 252

 Score =  161 bits (409), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 53/263 (20%), Positives = 116/263 (44%), Gaps = 19/263 (7%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           +K P L+  E   L ++  + GD  A   +V S++RLV  +   +   G    ++   G 
Sbjct: 9   KKKPQLKDHELKALIQK-SQDGDQQARDTIVQSNMRLVWSVVQRFLNRGYEPDDLFQIGC 67

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL+++V KFD     + +TY++  I   +Q ++    S VK+  +   K     +R+++
Sbjct: 68  IGLLKSVDKFDLSFDVKFSTYAVPMIIGEIQRFLRDDGS-VKVSRSL--KETGNKIRKMR 124

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L   +    +   +  +A+ L ++  EV+          S++  +  +D +     D 
Sbjct: 125 DEL---SKEFGRAPTINEVAEALELTPEEVVLAQEASRAPSSIHETVYENDGDPITILDQ 181

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +            + E +   +  L  ++  L+ RER I   R  ++   T   ++    
Sbjct: 182 IAD----------QSETKWFDKIALKEAIRELDERERLIVYLRYYKDQ--TQSEVAERIG 229

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+ +V ++E +  K++++ I +
Sbjct: 230 ISQVQVSRLEKKILKQMKDRIDE 252


>gi|3769432|gb|AAC78468.1| RNA polymerase sigma factor 2 [Zea mays]
          Length = 349

 Score =  161 bits (409), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 68/254 (26%), Positives = 121/254 (47%), Gaps = 10/254 (3%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L  R RE     A   L  S++RLV+ IA  Y   G+ +++++  G IGL++ ++KFD 
Sbjct: 95  ELRARMRES--FLAREMLTMSNIRLVISIAHKYDNLGVDLADLIQGGLIGLLRGIEKFDA 152

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            RGFR++TY  WWI+  +   +  +    ++ T  +++     L  ++G   A+ D  + 
Sbjct: 153 SRGFRISTYVYWWIRQGVSRALADNSKTFRLPTYLHER-----LLAIRGAKYALEDQGIA 207

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQV 214
           P  +  IA+ LN+S  +V +    +    SL+     S +          + D +     
Sbjct: 208 P-TIENIAESLNISVKKVHNATEAVHKVLSLDQQAFPSLNGLPGDTLHSYIEDQNVANDP 266

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIE 273
               EE   +  +     S LN RER I        +   T E++S +F +SRERVRQ+ 
Sbjct: 267 WHGFEEMYLKEEVNNLINSNLNERERDIIRLYHGIGKQCHTWEDISRQFGLSRERVRQVR 326

Query: 274 ARAFKKVQESIQKQ 287
             A +K++ + +++
Sbjct: 327 LVAMEKLKHAARRK 340


>gi|333024500|ref|ZP_08452564.1| putative RNA polymerase sigma-F factor [Streptomyces sp. Tu6071]
 gi|332744352|gb|EGJ74793.1| putative RNA polymerase sigma-F factor [Streptomyces sp. Tu6071]
          Length = 356

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 104/237 (43%), Gaps = 15/237 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              +RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDPERG   +TY+  
Sbjct: 131 ELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPERGVEFSTYATP 190

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +   ++ +       V++     + RL      L      ++  + +   V  +A++L+
Sbjct: 191 TVVGEIKRHFRDKGWAVRVPRRLQELRLS-----LTSATAELSQQHGRSPTVHELAQRLS 245

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +SE EV+          +L+  +  +D  S    D L  +         E  E    R  
Sbjct: 246 ISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAED--------EALEGVEYRES 297

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   ++++ +
Sbjct: 298 LKPLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLRDKL 352


>gi|290957490|ref|YP_003488672.1| sigma factor [Streptomyces scabiei 87.22]
 gi|260647016|emb|CBG70115.1| putative sigma factor [Streptomyces scabiei 87.22]
          Length = 388

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 57/237 (24%), Positives = 103/237 (43%), Gaps = 15/237 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              +RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+  
Sbjct: 163 ELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATP 222

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +   ++ +       V++     + RL      L      ++  + +   V  +A+KL 
Sbjct: 223 TVVGEIKRHFRDKGWAVRVPRRLQELRLA-----LTTATAELSQQHGRSPTVHELAEKLA 277

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +SE EV+          +L+  +  +D  S    D L  +         E  E    R  
Sbjct: 278 ISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAED--------EALEGVEYRES 329

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 330 LKPLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLREKL 384


>gi|312877562|ref|ZP_07737521.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
 gi|311795637|gb|EFR12007.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
          Length = 240

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 53/253 (20%), Positives = 108/253 (42%), Gaps = 17/253 (6%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
            K  +  L  + + +GD  A  +L+ S+L LV  +   +   G+ + ++   G IGL++A
Sbjct: 2   SKASQEELISKAK-NGDKLARQQLIESNLALVWSVVKKFAAKGVELDDLFQIGCIGLIKA 60

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V +F P    R +TY++  I   ++ Y+      +K+      +++  N  ++K      
Sbjct: 61  VDRFAPSFNLRFSTYAVPMIIGEIKRYLRDDGK-IKVS-----RKIKENQSKIKKLRNQF 114

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
             +N +   +  I++   +S  E++      +   SLN ++N  +       D    + D
Sbjct: 115 VSSNGREPTISEISQLTGLSSDEILLCMDASSEVASLNEVVNQEEGKPITLMDIASDEED 174

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
              ++L            L   +  L  RER I   R  +    T   ++ E  +S+  V
Sbjct: 175 YSTKLLDLMA--------LKEGLKKLKGRERYIIFMRYFKN--KTQSEIAKELNISQVHV 224

Query: 270 RQIEARAFKKVQE 282
            +IE RA ++++ 
Sbjct: 225 SRIEKRALERIKR 237


>gi|307592489|ref|YP_003900080.1| RNA polymerase sigma-32 factor RpoH [Cyanothece sp. PCC 7822]
 gi|306986134|gb|ADN18014.1| RNA polymerase, sigma 32 subunit, RpoH [Cyanothece sp. PCC 7822]
          Length = 307

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 60/243 (24%), Positives = 116/243 (47%), Gaps = 17/243 (6%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R    G   AA  LV ++L+ V+ IA  Y G GL +S+++ EG++GL++A ++FDP  G+
Sbjct: 74  RILYQG-KKAADTLVRANLKFVIFIANRYVGRGLELSDLIQEGSLGLIRAAERFDPSLGY 132

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+ WW++A M   +      +++ +  N K     L ++K     +     +    
Sbjct: 133 QFSTYANWWVRAFMTRALANQSRTIRLPSQVNDK-----LNKIKKTRHNLAQLLGRSPSS 187

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +A+ L +S  ++ S+        SL+  +   ++     QD +    +      ++ +
Sbjct: 188 SELAQALGISVLQLHSLAQLDKKTISLS--VWVDEQGRETLQDLIPSSDEPSLDETLKPD 245

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           E       + + +  L+PR + I   R L     TL  +   F +SRERVR+I  R+   
Sbjct: 246 E-------IEQLLQTLSPRNQEIVRLRIL--EGKTLSEIGQSFHLSRERVRKICLRSLTI 296

Query: 280 VQE 282
           +++
Sbjct: 297 LRQ 299


>gi|89099055|ref|ZP_01171934.1| sporulation sigma factor SigF [Bacillus sp. NRRL B-14911]
 gi|89086185|gb|EAR65307.1| sporulation sigma factor SigF [Bacillus sp. NRRL B-14911]
          Length = 252

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 50/256 (19%), Positives = 110/256 (42%), Gaps = 19/256 (7%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L+  E   L ++  + GD  A   +V  ++RLV  +   +   G    ++   G IGL++
Sbjct: 14  LKDHEVKELIQK-SQAGDQGARDTIVQKNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLK 72

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           +V KFD     + +TY++  I   +Q +I      VK+  +   K +   +R+ K  L  
Sbjct: 73  SVDKFDLSYDVKFSTYAVPMIIGEIQRFIRDDG-TVKVSRSL--KEMGNKIRKAKDEL-- 127

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
            T    +   V  ++  L +   ++I          S++  +  +D +     D +   +
Sbjct: 128 -TKTFGRIPTVTELSAYLEIPPEDIILAQEAGRTPSSIHETVYENDGDPITLLDQIDDGN 186

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           DG          +   +  L  ++  L+ RER I   R  ++   T   +++   +S+ +
Sbjct: 187 DG----------KWFDQIALKEAIRELDERERLIVYLRYYKDQ--TQSEVAARLGISQVQ 234

Query: 269 VRQIEARAFKKVQESI 284
           V ++E +  +++++ +
Sbjct: 235 VSRLEKKILQQMKDRM 250


>gi|229180352|ref|ZP_04307695.1| RNA polymerase sigma-F factor [Bacillus cereus 172560W]
 gi|228603099|gb|EEK60577.1| RNA polymerase sigma-F factor [Bacillus cereus 172560W]
          Length = 252

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 53/263 (20%), Positives = 116/263 (44%), Gaps = 19/263 (7%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           +K P L+  E   L ++  + GD  A   +V S++RLV  +   +   G    ++   G 
Sbjct: 9   KKKPQLKDHELKALIQK-SQDGDQQARDTIVQSNMRLVWSVVQRFLNRGYEPDDLFQIGC 67

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL+++V KFD     + +TY++  I   +Q ++    S VK+  +   K     +R+++
Sbjct: 68  IGLLKSVDKFDLSFDVKFSTYAVPMIIGEIQRFLRDDGS-VKVSRSL--KETGNKIRKMR 124

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L   +    +   +  +A+ L ++  EV+          S++  +  +D +     D 
Sbjct: 125 DEL---SKEFGRAPTINEVAEALELTPEEVVLAQEASRAPSSIHETVYENDGDPITILDQ 181

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +            + E +   +  L  ++  L+ RER I   R  ++   T   ++    
Sbjct: 182 IAD----------QSEAKWFDKIALKEAIRELDERERLIVYLRYYKDQ--TQSEVAERIG 229

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+ +V ++E +  K++++ I +
Sbjct: 230 ISQVQVSRLEKKILKQMKDRIDE 252


>gi|197247378|ref|YP_002147821.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
 gi|197211081|gb|ACH48478.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
          Length = 269

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 59/208 (28%), Positives = 103/208 (49%), Gaps = 8/208 (3%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           LR  +     ++           IA++L+    +V  M        S++  +     +  
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPL--GGDSEK 232

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRN 226
              D L  + +   +   + ++ K    
Sbjct: 233 ALLDILADEKENGPEDTTQDDDMKQSTE 260


>gi|229075781|ref|ZP_04208758.1| RNA polymerase sigma-F factor [Bacillus cereus Rock4-18]
 gi|229098543|ref|ZP_04229484.1| RNA polymerase sigma-F factor [Bacillus cereus Rock3-29]
 gi|229104680|ref|ZP_04235342.1| RNA polymerase sigma-F factor [Bacillus cereus Rock3-28]
 gi|229117569|ref|ZP_04246941.1| RNA polymerase sigma-F factor [Bacillus cereus Rock1-3]
 gi|228665889|gb|EEL21359.1| RNA polymerase sigma-F factor [Bacillus cereus Rock1-3]
 gi|228678744|gb|EEL32959.1| RNA polymerase sigma-F factor [Bacillus cereus Rock3-28]
 gi|228684865|gb|EEL38802.1| RNA polymerase sigma-F factor [Bacillus cereus Rock3-29]
 gi|228707333|gb|EEL59529.1| RNA polymerase sigma-F factor [Bacillus cereus Rock4-18]
          Length = 252

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 53/263 (20%), Positives = 116/263 (44%), Gaps = 19/263 (7%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           +K P L+  E   L ++  + GD  A   +V S++RLV  +   +   G    ++   G 
Sbjct: 9   KKKPQLKDHELKALIQK-SQGGDQQARDTIVQSNMRLVWSVVQRFLNRGYEPDDLFQIGC 67

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL+++V KFD     + +TY++  I   +Q ++    S VK+  +   K     +R+++
Sbjct: 68  IGLLKSVDKFDLSFDVKFSTYAVPMIIGEIQRFLRDDGS-VKVSRSL--KETGNKIRKMR 124

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L   +    +   +  +A+ L ++  EV+          S++  +  +D +     D 
Sbjct: 125 DEL---SKEFGRAPTINEVAEALELTPEEVVLAQEASRPPSSIHETVYENDGDPITILDQ 181

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +            + E +   +  L  ++  L+ RER I   R  ++   T   ++    
Sbjct: 182 IAD----------QSETKWFDKIALKEAIRELDERERLIVYLRYYKDQ--TQSEVAERIG 229

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+ +V ++E +  K++++ I +
Sbjct: 230 ISQVQVSRLEKKILKQMKDRIDE 252


>gi|289642895|ref|ZP_06475030.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Frankia
           symbiont of Datisca glomerata]
 gi|289507278|gb|EFD28242.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Frankia
           symbiont of Datisca glomerata]
          Length = 332

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 58/246 (23%), Positives = 102/246 (41%), Gaps = 21/246 (8%)

Query: 44  HGDL---SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
            GD        +LV  HL LV  +A  +R  G P+ ++     IGL+++V +FDPERG  
Sbjct: 99  EGDQQRAEIRDQLVRMHLPLVEYLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPERGVE 158

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+   I   ++ +       +++     + +L      L      ++    +   V 
Sbjct: 159 FSTYATPTIVGEIKRHFRDKGWAIRVPRRLQELKLS-----LTKATSELSQTLGRSPTVS 213

Query: 161 AIAKKLNVSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            IA  L +SE EV+    +       SL+A  +  D+  +      V D         E 
Sbjct: 214 EIAAHLQMSEEEVLEGLESANAYSAVSLDAPDSGDDEAPAVADTLGVQD---------ES 264

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
            E    R  L   +  L PRE+RI   R      +T   +++E  +S+  V ++ AR   
Sbjct: 265 LEGVEYRESLKPLLEKLPPREKRILLLRFFGN--MTQSQIATELGISQMHVSRLLARTLA 322

Query: 279 KVQESI 284
           +++  +
Sbjct: 323 QLRRGL 328


>gi|239990645|ref|ZP_04711309.1| RNA polymerase sigma factor [Streptomyces roseosporus NRRL 11379]
          Length = 309

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 103/237 (43%), Gaps = 15/237 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              +RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+  
Sbjct: 84  ELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATP 143

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +   ++ +       V++     + RL      L      ++  + +   V  +A++L 
Sbjct: 144 TVVGEIKRHFRDKGWAVRVPRRLQELRLS-----LTTATAELSQQHGRSPTVHELAERLG 198

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +SE EV+          +L+  +  +D  S    D L  +         E  E    R  
Sbjct: 199 ISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGSED--------EALEGVEYRES 250

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 251 LKPLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLRERL 305


>gi|21223610|ref|NP_629389.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
 gi|5912531|emb|CAB56114.2| SigH protein [Streptomyces coelicolor A3(2)]
 gi|9968693|emb|CAC05976.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
          Length = 361

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 57/237 (24%), Positives = 104/237 (43%), Gaps = 15/237 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              +RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+  
Sbjct: 136 ELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATP 195

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +   ++ +       V++     + RL      L      ++  + +   V  +A+KL+
Sbjct: 196 TVVGEIKRHFRDKGWAVRVPRRLQELRLA-----LTTATAELSQLHGRSPTVHELAEKLS 250

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +SE EV+          +L+  +  +D  S    D L  +         E  E    R  
Sbjct: 251 ISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAED--------EALEGVEYRES 302

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 303 LKPLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLREKL 357


>gi|289769170|ref|ZP_06528548.1| SigH protein [Streptomyces lividans TK24]
 gi|289699369|gb|EFD66798.1| SigH protein [Streptomyces lividans TK24]
          Length = 361

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 57/237 (24%), Positives = 104/237 (43%), Gaps = 15/237 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              +RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+  
Sbjct: 136 ELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATP 195

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +   ++ +       V++     + RL      L      ++  + +   V  +A+KL+
Sbjct: 196 TVVGEIKRHFRDKGWAVRVPRRLQELRLA-----LTTATAELSQLHGRSPTVHELAEKLS 250

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +SE EV+          +L+  +  +D  S    D L  +         E  E    R  
Sbjct: 251 ISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAED--------EALEGVEYRES 302

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 303 LKPLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLREKL 357


>gi|228992811|ref|ZP_04152736.1| RNA polymerase sigma-F factor [Bacillus pseudomycoides DSM 12442]
 gi|228998857|ref|ZP_04158442.1| RNA polymerase sigma-F factor [Bacillus mycoides Rock3-17]
 gi|229006374|ref|ZP_04164053.1| RNA polymerase sigma-F factor [Bacillus mycoides Rock1-4]
 gi|228754873|gb|EEM04239.1| RNA polymerase sigma-F factor [Bacillus mycoides Rock1-4]
 gi|228760873|gb|EEM09834.1| RNA polymerase sigma-F factor [Bacillus mycoides Rock3-17]
 gi|228766860|gb|EEM15498.1| RNA polymerase sigma-F factor [Bacillus pseudomycoides DSM 12442]
          Length = 252

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 54/263 (20%), Positives = 116/263 (44%), Gaps = 19/263 (7%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           +K P L+  E   L ++  + GD  A   +V S++RLV  +   +   G    ++   G 
Sbjct: 9   KKKPQLKDHELKALIQK-SQDGDQQARDTIVQSNMRLVWSVVQRFLNRGYEPDDLFQIGC 67

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL+++V KFD     + +TY++  I   +Q ++    S VK+  +   K     +R++K
Sbjct: 68  IGLLKSVDKFDLSFDVKFSTYAVPMIIGEIQRFLRDDGS-VKVSRSL--KETGNKIRKMK 124

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L   +    +   +  +A+ L ++  EV+          S++  +  +D +     D 
Sbjct: 125 DEL---SKEYGRAPTINEVAEALELTPEEVVLAQEASRTPSSIHETVYENDGDPITILDQ 181

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +            + E +   +  L  ++  L+ RER I   R  ++   T   ++    
Sbjct: 182 IAD----------QTETKWFDKIALKEAIRELDERERLIVYLRYYKDQ--TQSEVAERIG 229

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+ +V ++E +  K++++ I +
Sbjct: 230 ISQVQVSRLEKKILKQMKDRIDE 252


>gi|329936108|ref|ZP_08285907.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
 gi|329304426|gb|EGG48305.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
          Length = 310

 Score =  161 bits (408), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 59/237 (24%), Positives = 104/237 (43%), Gaps = 15/237 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              +RLV  HL LV  +A  YR  G P+ ++     IGL+++V +FDP+RG   +TY+  
Sbjct: 85  ELRNRLVRMHLPLVEHLARRYRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATP 144

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +   ++ +       V++     + RL      L      ++  + +   V  +A+KL 
Sbjct: 145 TVVGEIKRHFRDKGWAVRVPRRLQELRLA-----LTTATAELSQQHGRSPTVHELAEKLA 199

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +SE EV+          +L+  +  +D ++    D L  D    E V          R  
Sbjct: 200 ISEEEVLEGLESANAYSTLSLDVPDTDDDAPAVADRLGADEAALESV--------EYRAS 251

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   K++E +
Sbjct: 252 LRLLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAKLRERL 306


>gi|320008631|gb|ADW03481.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 320

 Score =  161 bits (407), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 103/237 (43%), Gaps = 15/237 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              +RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+  
Sbjct: 95  ELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATP 154

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +   ++ +       V++     + RL      L      ++  + +   V  +A++L 
Sbjct: 155 TVVGEIKRHFRDKGWAVRVPRRLQELRLS-----LTTATAELSQQHGRSPTVHELAERLG 209

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +SE EV+          +L+  +  +D  S    D L  +         E  E    R  
Sbjct: 210 ISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGSED--------EALEGVEYRES 261

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 262 LKPLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLRERL 316


>gi|219111033|ref|XP_002177268.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217411803|gb|EEC51731.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 324

 Score =  161 bits (407), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 61/246 (24%), Positives = 116/246 (47%), Gaps = 14/246 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  R+V S++RLVV IA  Y   G+ + ++V EG++GL +A +KF+P++GF+ +TY+ 
Sbjct: 69  REAKQRMVQSNMRLVVSIARKYSNVGVSLQDLVQEGSLGLSRAAEKFEPKKGFKFSTYAS 128

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      +++    +   L   +R+++ +LQ         E    +A++L
Sbjct: 129 WWIQQAVFRSIAYHSRTIRLPVHVH--NLLNRVRKVRNNLQRELSRTPTNE---EMAEEL 183

Query: 167 NVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDG------QEQVLIEKE 219
            ++  +   M        SL      S+ K+       L+ D          E    ++ 
Sbjct: 184 GMTLQKYNKMLRLTKRSISLETPKYQSNPKDLGHESHDLLGDTISASSALFDESTPEKRV 243

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAF 277
           +R      L   + +L+  ERR+  +R    +    T+  ++S+ + S+  VR  E RA 
Sbjct: 244 DRGIFHEDLHEMLEILDEDERRVICSRYGLSDGLTRTVTAVASQMKQSKAWVRSQECRAL 303

Query: 278 KKVQES 283
           +K++  
Sbjct: 304 RKLRRP 309


>gi|302536824|ref|ZP_07289166.1| RNA polymerase sigma-F factor [Streptomyces sp. C]
 gi|302445719|gb|EFL17535.1| RNA polymerase sigma-F factor [Streptomyces sp. C]
          Length = 332

 Score =  161 bits (407), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 103/237 (43%), Gaps = 15/237 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              +RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+  
Sbjct: 107 ELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATP 166

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +   ++ +       V++     + RL      L      ++  + +   V  +A++L 
Sbjct: 167 TVVGEIKRHFRDKGWAVRVPRRLQELRLS-----LTTATAELSQQHGRSPTVHELAERLG 221

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +SE EV+          +L+  +  +D  S    D L  +         E  E    R  
Sbjct: 222 ISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGSED--------EALEGVEYRES 273

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 274 LKPLLEGLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLREKL 328


>gi|229163011|ref|ZP_04290967.1| RNA polymerase sigma-F factor [Bacillus cereus R309803]
 gi|229174749|ref|ZP_04302273.1| RNA polymerase sigma-F factor [Bacillus cereus MM3]
 gi|228608739|gb|EEK66037.1| RNA polymerase sigma-F factor [Bacillus cereus MM3]
 gi|228620417|gb|EEK77287.1| RNA polymerase sigma-F factor [Bacillus cereus R309803]
          Length = 252

 Score =  161 bits (407), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 53/263 (20%), Positives = 116/263 (44%), Gaps = 19/263 (7%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           +K P L+  E   L ++  + GD  A   +V S++RLV  +   +   G    ++   G 
Sbjct: 9   KKKPQLKDHELKALIQQ-SQDGDQQARDTIVQSNMRLVWSVVQRFLNRGYEPDDLFQIGC 67

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL+++V KFD     + +TY++  I   +Q ++    S VK+  +   K     +R+++
Sbjct: 68  IGLLKSVDKFDLSFDVKFSTYAVPMIIGEIQRFLRDDGS-VKVSRSL--KETGNKIRKMR 124

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L   +    +   +  +A+ L ++  EV+          S++  +  +D +     D 
Sbjct: 125 DEL---SKEFGRAPTINEVAEALELTPEEVVLAQEASRAPSSIHETVYENDGDPITILDQ 181

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +            + E +   +  L  ++  L+ RER I   R  ++   T   ++    
Sbjct: 182 IAD----------QSETKWFDKIALKEAIRELDDRERLIVYLRYYKDQ--TQSEVAERIG 229

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+ +V ++E +  K++++ I +
Sbjct: 230 ISQVQVSRLEKKILKQMKDRIDE 252


>gi|318060190|ref|ZP_07978913.1| RNA polymerase sigma factor, sigH [Streptomyces sp. SA3_actG]
 gi|318078835|ref|ZP_07986167.1| RNA polymerase sigma factor, sigH [Streptomyces sp. SA3_actF]
          Length = 356

 Score =  161 bits (407), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 104/237 (43%), Gaps = 15/237 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              +RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDPERG   +TY+  
Sbjct: 131 ELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPERGVEFSTYATP 190

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +   ++ +       V++     + RL      L      ++  + +   V  +A++L+
Sbjct: 191 TVVGEIKRHFRDKGWAVRVPRRLQELRLS-----LTSATAELSQQHGRSPTVHELAQRLS 245

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +SE EV+          +L+  +  +D  S    D L  +         E  E    R  
Sbjct: 246 ISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAED--------EALEGVEYRES 297

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   ++++ +
Sbjct: 298 LKPLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLRDKL 352


>gi|229031716|ref|ZP_04187709.1| RNA polymerase sigma-F factor [Bacillus cereus AH1271]
 gi|228729600|gb|EEL80587.1| RNA polymerase sigma-F factor [Bacillus cereus AH1271]
          Length = 252

 Score =  161 bits (407), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 53/263 (20%), Positives = 116/263 (44%), Gaps = 19/263 (7%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           +K P L+  E   L ++  + GD  A   +V S++RLV  +   +   G    ++   G 
Sbjct: 9   KKKPQLKDHELKALIQQ-SQDGDQQARDTIVQSNMRLVWSVVQRFLNRGYEPDDLFQIGC 67

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL+++V KFD     + +TY++  I   +Q ++    S VK+  +   K     +R+++
Sbjct: 68  IGLLKSVDKFDLSFDVKFSTYAVPMIIGEIQRFLRDDGS-VKVSRSL--KETGNKIRKMR 124

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L   +    +   +  +A+ L ++  EV+          S++  +  +D +     D 
Sbjct: 125 DEL---SKEFGRAPTINEVAEALELTPEEVVLAQEASRAPSSIHETVYENDGDPITILDQ 181

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +            + E +   +  L  ++  L+ RER I   R  ++   T   ++    
Sbjct: 182 IAD----------QSETKWFDKIALKEAIRELDERERLIVYLRYYKDQ--TQSEVAERIG 229

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+ +V ++E +  K++++ I +
Sbjct: 230 ISQVQVSRLEKKILKQMKDRIDE 252


>gi|291531212|emb|CBK96797.1| RNA polymerase, sigma subunit, RpsG/SigG [Eubacterium siraeum 70/3]
          Length = 255

 Score =  161 bits (407), Expect = 1e-37,   Method: Composition-based stats.
 Identities = 54/251 (21%), Positives = 119/251 (47%), Gaps = 18/251 (7%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+ +L++ E+  L ++ R  GD +A  +L+  +LRLV+ +   + G G    ++   G I
Sbjct: 20  KLKVLKESEKTELLRQMR-SGDPTAREKLINGNLRLVLSVIQRFSGRGENPDDLFQVGCI 78

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A+  F  +   R +TY++  I   ++ Y+  S S +++  +   + L +   + + 
Sbjct: 79  GLMKAIDNFSTDFNVRFSTYAVPMIMGELRRYLRDSGS-IRVSRSM--RDLAYKAMQAR- 134

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + +T++N K   +  IAK+++    +V+     ++   SL   + S   ++    D +
Sbjct: 135 --EKLTNDNSKEPTIEQIAKEIDAKREDVVIALEAVSDPISLYEPVFSESGDTIYMMDQI 192

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             ++D +                L  ++  L+ RE+ I + R  +    T   ++ E  +
Sbjct: 193 GDNNDDR---------NWLDEIALKEAIIGLDDREKNILKLRFFRG--KTQVEVAQEIGI 241

Query: 265 SRERVRQIEAR 275
           S+ +V ++E R
Sbjct: 242 SQAQVSRLEKR 252


>gi|239944189|ref|ZP_04696126.1| RNA polymerase sigma factor [Streptomyces roseosporus NRRL 15998]
          Length = 284

 Score =  161 bits (407), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 103/237 (43%), Gaps = 15/237 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              +RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+  
Sbjct: 59  ELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATP 118

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +   ++ +       V++     + RL      L      ++  + +   V  +A++L 
Sbjct: 119 TVVGEIKRHFRDKGWAVRVPRRLQELRLS-----LTTATAELSQQHGRSPTVHELAERLG 173

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +SE EV+          +L+  +  +D  S    D L  +         E  E    R  
Sbjct: 174 ISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGSED--------EALEGVEYRES 225

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 226 LKPLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLRERL 280


>gi|302518878|ref|ZP_07271220.1| RNA polymerase sigma factor RpoS [Streptomyces sp. SPB78]
 gi|302427773|gb|EFK99588.1| RNA polymerase sigma factor RpoS [Streptomyces sp. SPB78]
          Length = 201

 Score =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 50/198 (25%), Positives = 88/198 (44%), Gaps = 12/198 (6%)

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++AV+KFD  RGF+ +TY+ WWI+ AM   +      +++     +      + R+   
Sbjct: 1   LIRAVEKFDYTRGFKFSTYATWWIRQAMSRALADQARTIRVPVHVVEL-----INRVVRV 55

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            + +            +A  L +++  V  +        SL+  +   D+      D + 
Sbjct: 56  QRGLLQERGHEPSHAEVAALLGLTKERVGEVLRLAQEPVSLHTPVGGEDE--VALGDLI- 112

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFE 263
              DG      E       R  L   +S L  RER++ + R   ++  P TLE + + F 
Sbjct: 113 --EDGDAPSPPESAALLLLRRHLEDVLSTLGERERQVVQLRYGLDDGRPRTLEEIGTLFG 170

Query: 264 VSRERVRQIEARAFKKVQ 281
           V+RER+RQIEA+   K++
Sbjct: 171 VTRERIRQIEAKTLAKLR 188


>gi|312622111|ref|YP_004023724.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
 gi|312202578|gb|ADQ45905.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
          Length = 240

 Score =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 53/247 (21%), Positives = 108/247 (43%), Gaps = 17/247 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L  R + +GD  A  +L+ S+L LV  +   +   G+ + ++   G+IGL++AV +FDP
Sbjct: 8   ELISRAK-NGDKLARQQLIESNLALVWSVVKKFAAKGVELEDLFQIGSIGLIKAVDRFDP 66

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
               R +TY++  I   ++ Y+      +K+      +++  N  ++K        N+ +
Sbjct: 67  SFNVRFSTYAVPMIIGEIKRYLRDDGK-IKVS-----RKIKENQGKIKKLRNQFVSNHGR 120

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
              +  I++   +S  E++      +   SL+ +IN  +       D    + D   ++L
Sbjct: 121 EPTISEISQLTGLSNDEILLCLDASSEVASLSEVINQEEGKPITLMDIASDEEDYSTKLL 180

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
                       L   +  L  RER I   R  +    T   ++ +  +S+  V +IE R
Sbjct: 181 DLMA--------LKEGLKKLKGRERYIIFMRYFKN--KTQSEIAKQLNISQVHVSRIEKR 230

Query: 276 AFKKVQE 282
           A ++++ 
Sbjct: 231 ALERIKR 237


>gi|254384657|ref|ZP_04999996.1| RNA polymerase sigma factor [Streptomyces sp. Mg1]
 gi|194343541|gb|EDX24507.1| RNA polymerase sigma factor [Streptomyces sp. Mg1]
          Length = 334

 Score =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 103/237 (43%), Gaps = 15/237 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              +RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+  
Sbjct: 109 ELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATP 168

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +   ++ +       V++     + RL      L      ++  + +   V  +A++L 
Sbjct: 169 TVVGEIKRHFRDKGWAVRVPRRLQELRLS-----LTTATAELSQQHGRSPTVHELAERLG 223

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +SE EV+          +L+  +  +D  S    D L  +         E  E    R  
Sbjct: 224 ISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGSED--------EALEGVEYRES 275

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 276 LKPLLEGLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLREKL 330


>gi|326201325|ref|ZP_08191197.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium papyrosolvens
           DSM 2782]
 gi|325988893|gb|EGD49717.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium papyrosolvens
           DSM 2782]
          Length = 248

 Score =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 49/243 (20%), Positives = 108/243 (44%), Gaps = 15/243 (6%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + GD  A   LV  ++ LV  I   ++  G  + ++   G+IGL++A+ KFD     + 
Sbjct: 16  AKAGDKQAQSVLVERNVGLVWSIVKRFQNRGYEVDDLFQIGSIGLIKAINKFDTSYDVKF 75

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY++  I   ++ +I     ++K+  +  +        + +   + ++    +   +  
Sbjct: 76  STYAVPMIIGEIKRFIRDDG-IIKVSRSLKEIS-----SKARITKEIMSKELGREPTINE 129

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           IA+++N+S  E++         ESL + I   D +     D +    +  E  LI+K   
Sbjct: 130 IAQRMNISPEELVMAIEAGCTPESLYSTIGDGDNSPILLIDRIDAADNNCEVDLIDKI-- 187

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                 + + +  L+ RER+I   R  +E   T   ++    +S+ +V +IE +  + ++
Sbjct: 188 -----AIRQILDTLDTRERQIIILRYFKE--KTQVQIAKLLGISQVQVSRIEKKILRDIK 240

Query: 282 ESI 284
             +
Sbjct: 241 SKM 243


>gi|163941815|ref|YP_001646699.1| sporulation sigma factor SigF [Bacillus weihenstephanensis KBAB4]
 gi|229013283|ref|ZP_04170424.1| RNA polymerase sigma-F factor [Bacillus mycoides DSM 2048]
 gi|229061746|ref|ZP_04199079.1| RNA polymerase sigma-F factor [Bacillus cereus AH603]
 gi|229134882|ref|ZP_04263689.1| RNA polymerase sigma-F factor [Bacillus cereus BDRD-ST196]
 gi|229168817|ref|ZP_04296536.1| RNA polymerase sigma-F factor [Bacillus cereus AH621]
 gi|163864012|gb|ABY45071.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           weihenstephanensis KBAB4]
 gi|228614665|gb|EEK71771.1| RNA polymerase sigma-F factor [Bacillus cereus AH621]
 gi|228648557|gb|EEL04585.1| RNA polymerase sigma-F factor [Bacillus cereus BDRD-ST196]
 gi|228717492|gb|EEL69156.1| RNA polymerase sigma-F factor [Bacillus cereus AH603]
 gi|228748050|gb|EEL97914.1| RNA polymerase sigma-F factor [Bacillus mycoides DSM 2048]
          Length = 252

 Score =  160 bits (406), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 50/263 (19%), Positives = 114/263 (43%), Gaps = 19/263 (7%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           +K P L+  E   L ++  + GD  A   +V S++RLV  +   +   G    ++   G 
Sbjct: 9   KKKPQLKDHELKALIQK-SQDGDQQARDTIVQSNMRLVWSVVQRFLNRGYEPDDLFQIGC 67

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL+++V KFD     + +TY++  I   +Q ++    S VK+  +  +        +++
Sbjct: 68  IGLLKSVDKFDLSFDVKFSTYAVPMIIGEIQRFLRDDGS-VKVSRSLKE-----TGNKVR 121

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
                ++    +   +  +A+ L ++  EV+          S++  +  +D +     D 
Sbjct: 122 KMRDELSKEFGRAPTINEVAQALELTPEEVVLAQEASRAPSSIHETVYENDGDPITILDQ 181

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +            + E +   +  L  ++  L+ RER I   R  ++   T   ++    
Sbjct: 182 IAD----------QSETKWFDKIALKEAIRELDERERLIVYLRYYKDQ--TQSEVAERIG 229

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+ +V ++E +  K++++ I +
Sbjct: 230 ISQVQVSRLEKKILKQMKDRIDE 252


>gi|256785278|ref|ZP_05523709.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
          Length = 354

 Score =  160 bits (405), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 57/237 (24%), Positives = 104/237 (43%), Gaps = 15/237 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              +RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+  
Sbjct: 129 ELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATP 188

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +   ++ +       V++     + RL      L      ++  + +   V  +A+KL+
Sbjct: 189 TVVGEIKRHFRDKGWAVRVPRRLQELRLA-----LTTATAELSQLHGRSPTVHELAEKLS 243

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +SE EV+          +L+  +  +D  S    D L  +         E  E    R  
Sbjct: 244 ISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAED--------EALEGVEYRES 295

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 296 LKPLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLREKL 350


>gi|5732893|gb|AAD49326.1|AF162936_2 RNA polymerase alternative sigma factor [Streptomyces coelicolor
           A3(2)]
          Length = 354

 Score =  160 bits (405), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 57/237 (24%), Positives = 104/237 (43%), Gaps = 15/237 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              +RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+  
Sbjct: 129 ELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATP 188

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +   ++ +       V++     + RL      L      ++  + +   V  +A+KL+
Sbjct: 189 TVVGEIKRHFRDKGWAVRVPRRLQELRLA-----LTTATAELSQLHGRSPTVHELAEKLS 243

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +SE EV+          +L+  +  +D  S    D L  +         E  E    R  
Sbjct: 244 ISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAED--------EALEGVEYRES 295

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 296 LKPLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLREKL 350


>gi|153814532|ref|ZP_01967200.1| hypothetical protein RUMTOR_00746 [Ruminococcus torques ATCC 27756]
 gi|317500575|ref|ZP_07958796.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|331089324|ref|ZP_08338225.1| hypothetical protein HMPREF1025_01808 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|145848026|gb|EDK24944.1| hypothetical protein RUMTOR_00746 [Ruminococcus torques ATCC 27756]
 gi|316898008|gb|EFV20058.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|330405505|gb|EGG85037.1| hypothetical protein HMPREF1025_01808 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 260

 Score =  160 bits (405), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 49/242 (20%), Positives = 107/242 (44%), Gaps = 16/242 (6%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A  + +  +LRLV+ +   +        ++   G +GLM+AV  FDP R  + +
Sbjct: 32  KAGDEEAREKYIKGNLRLVLSVIKRFENSSENADDLFQIGCVGLMKAVDHFDPGRMVKFS 91

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I   ++ Y+  + S +++      + L     +     +     ++K   V  I
Sbjct: 92  TYAVPMIIGEIRRYLRDN-SPIRVS-----RSLRDTAYKAIYAKEGYIKRHMKEPTVQEI 145

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+++ +++ E++     +    SL+  + S  +++    D +    + +E  + E     
Sbjct: 146 AEEIGIAKEEIVYALDAIQMPMSLHEPVYSDGQDALFVMDQVSDKKNKEENWIEELS--- 202

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
                L  +M  LN RER I   R       T   ++ +  +S+ +V ++E  A K +++
Sbjct: 203 -----LEAAMERLNERERYIITLRFF--EGKTQMEVAEQINISQAQVSRLEKNALKIMRK 255

Query: 283 SI 284
            +
Sbjct: 256 YL 257


>gi|319651418|ref|ZP_08005547.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
 gi|317396949|gb|EFV77658.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
          Length = 252

 Score =  160 bits (405), Expect = 2e-37,   Method: Composition-based stats.
 Identities = 53/256 (20%), Positives = 112/256 (43%), Gaps = 19/256 (7%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L+  E   L K+  + GD  A  ++V  ++RLV  +   +   G    ++   G IGL++
Sbjct: 14  LKDNEVKELIKQ-SQSGDQGARDKIVQKNMRLVWSVVQRFLNRGYEPDDLFQIGCIGLLK 72

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           +V KFD     + +TY++  I   +Q +I      VK+  +   K +   +R+ K  L  
Sbjct: 73  SVDKFDLSYDVKFSTYAVPMIIGEIQRFIRDDG-TVKVSRSL--KEMGNKIRKAKDELSK 129

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                 +   V  +++ L +S  ++I          S++  +  +D +     D +    
Sbjct: 130 TLG---RIPTVTELSEFLEISPEDIILAQEASRIPSSIHETVYENDGDPITLLDQI---D 183

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           DG E    +K         L  ++  L+ RER I   R  ++   T   +++   +S+ +
Sbjct: 184 DGNEGKWFDKI-------ALKEAIRELDERERLIVYLRYYKDQ--TQSEVAARLGISQVQ 234

Query: 269 VRQIEARAFKKVQESI 284
           V ++E +  +++++ +
Sbjct: 235 VSRLEKKILQQMKDRM 250


>gi|302558487|ref|ZP_07310829.1| RNA polymerase sigma factor [Streptomyces griseoflavus Tu4000]
 gi|302476105|gb|EFL39198.1| RNA polymerase sigma factor [Streptomyces griseoflavus Tu4000]
          Length = 281

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 57/237 (24%), Positives = 103/237 (43%), Gaps = 15/237 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              +RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+  
Sbjct: 56  ELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATP 115

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +   ++ +       V++     + RL      L      ++  + +   V  +A+KL 
Sbjct: 116 TVVGEIKRHFRDKGWAVRVPRRLQELRLA-----LTTATAELSQLHGRSPTVHELAEKLA 170

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +SE EV+          +L+  +  +D  S    D L  +         E  E    R  
Sbjct: 171 ISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAED--------EALEGVEYRES 222

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 223 LKPLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLREKL 277


>gi|224124068|ref|XP_002319237.1| predicted protein [Populus trichocarpa]
 gi|222857613|gb|EEE95160.1| predicted protein [Populus trichocarpa]
          Length = 499

 Score =  160 bits (405), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 52/240 (21%), Positives = 109/240 (45%), Gaps = 8/240 (3%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  S++RLV+ IA      G  ++++V  G IGL++ ++KFD  +GF+++TY  WW
Sbjct: 256 AREKLAMSNVRLVMSIAQKNDNMGAEMADLVQAGLIGLLRGIEKFDSSKGFKISTYVYWW 315

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   ++ +   +++    +++       +++       +       +  IA+ LN+
Sbjct: 316 IRQGVSRALVENPRTLRLPNHLHERLGLIRNAKIR------LEEKGVTPSIDRIAESLNM 369

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S+ +V +    ++   SL+     S               +  E       +    +  +
Sbjct: 370 SQRKVRNATEAISKVFSLDREAFPSLNGLPGETHHSYIADNRLENNPWHGVDEWALKEEV 429

Query: 229 TRSMSV-LNPRERRIFEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + +   L  RER I       +   +T E++S    +SRERVRQ+   A +K++ + +K
Sbjct: 430 NKLIDSALQEREREIIRLYHGLDKECLTWEDISKRMGLSRERVRQVGLVALEKLKHAARK 489


>gi|3893860|gb|AAC78467.1| RNA polymerase sigma factor 1 [Zea mays]
          Length = 398

 Score =  159 bits (404), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 71/254 (27%), Positives = 122/254 (48%), Gaps = 10/254 (3%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L  R RE     A   L  S+ RLV+ IA  Y   G+ + +++  G IGL++ ++KFD 
Sbjct: 144 ELRARMRES--FLAREMLAMSNTRLVISIAQKYDNLGVELPDLIQGGLIGLLRGIEKFDA 201

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            RGFR++TY  WWI+  +   +  +    ++ T  +++     L  ++G   A+ D  + 
Sbjct: 202 SRGFRISTYVYWWIRQGVSRALADNSRSFRLPTYLHER-----LVAIRGAKYALEDQGIA 256

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQV 214
           P  V  IA+ LN+SE +V +    +    SL+     S +          + D +     
Sbjct: 257 P-TVENIAESLNISEKKVHNATEAVHKVISLDQQAFPSLNGLPGDTLHSYIEDQNVANDP 315

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIE 273
               EER  +  + +   S LN RER I        +   T E++S +F +SRERVRQ+ 
Sbjct: 316 WHGFEERYLKEEVNSLINSTLNERERDIIRLYHGIGKQCHTWEDISRQFGLSRERVRQVG 375

Query: 274 ARAFKKVQESIQKQ 287
             A +K++ + +++
Sbjct: 376 LVAMEKLKHAARRE 389


>gi|154503856|ref|ZP_02040916.1| hypothetical protein RUMGNA_01682 [Ruminococcus gnavus ATCC 29149]
 gi|153795455|gb|EDN77875.1| hypothetical protein RUMGNA_01682 [Ruminococcus gnavus ATCC 29149]
          Length = 259

 Score =  159 bits (404), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 53/245 (21%), Positives = 110/245 (44%), Gaps = 17/245 (6%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R +E GD  A  + +  +LRLV+ +   +        ++   G +GLM+AV  FDP R  
Sbjct: 30  RIKE-GDEDAREQYIKGNLRLVLSVIKRFSSSSENADDLFQIGCVGLMKAVDHFDPSRLV 88

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY++  I   ++ Y+  + S +++      + L     +     +       K   V
Sbjct: 89  KFSTYAVPMIIGEIRRYLRDNNS-IRVS-----RSLRDTAYKAIYAKEGFVKKYSKEPTV 142

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IA+++ +S+ +++     +    SL+  + S D   + +    V D   +E+  +E+ 
Sbjct: 143 QEIAEEIGISKEDIVFALDAIQMPVSLHEPVYS-DGGDTLYIMDQVSDKKNREENWVEEL 201

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
                   L  +M  LN RER I + R       T   ++ + ++S+ +V ++E  A K 
Sbjct: 202 S-------LEAAMERLNERERFIIQLRFF--EGKTQMEVAEQIQISQAQVSRLEKNALKI 252

Query: 280 VQESI 284
           +++ +
Sbjct: 253 MKQYL 257


>gi|304407011|ref|ZP_07388665.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
 gi|304343998|gb|EFM09838.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
          Length = 251

 Score =  159 bits (404), Expect = 3e-37,   Method: Composition-based stats.
 Identities = 52/258 (20%), Positives = 107/258 (41%), Gaps = 19/258 (7%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE  E   L     + GD  +   LV  ++RLV  +   +   G    ++   G IGL
Sbjct: 11  PYLEDAEVKRLI-ALSQSGDNVSRDTLVHCNIRLVWSVVQRFMNRGYEPEDLFQIGCIGL 69

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           +++V KFD     + +TY++  I   +Q ++      +K+  +   K     +R++K  L
Sbjct: 70  LKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TLKVSRSL--KETANKVRKMKDEL 126

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                       +  +A+ L ++  +V+          S++  +  +D +     D +  
Sbjct: 127 SKTLGRL---PTITEVAEGLGITPEDVVFAQEANKPPTSIHETVFENDGDPITLMDQIAD 183

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           D           +ER   +  L  ++  L  RER I   R  ++   T   ++S   +S+
Sbjct: 184 D----------SQERWFDKLALAEAIEGLAERERLIVYLRYYRDQ--TQSEVASRLGISQ 231

Query: 267 ERVRQIEARAFKKVQESI 284
            +V ++E +  + +++ I
Sbjct: 232 VQVSRLEKKILQLIKDQI 249


>gi|1552544|emb|CAA90874.1| sigma factor [Bacillus coagulans]
          Length = 252

 Score =  159 bits (404), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 51/270 (18%), Positives = 109/270 (40%), Gaps = 19/270 (7%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +   + +      L+ +E   L +R  E GD  A   +V  ++RLV  +   +   G   
Sbjct: 1   MDAELKKAENKARLKDEEVKNLIRR-TEEGDQEARDLIVEKNIRLVWSVVHRFLNRGYEP 59

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++   G IGL+++V KFD     + +TY++  I   +Q ++      VK+  +  +   
Sbjct: 60  DDLFQIGCIGLLKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-TVKVSRSLKE--- 115

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
                R++     +T    +   V  IA +L +   EV+          S++  +  +D 
Sbjct: 116 --TGNRIRKIRDELTKKLGRSPTVHEIASELGMPVEEVVMAQEAGKAPSSIHETVYENDG 173

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
           +     D +   +D          ++   +  L  ++  L  RER I   R  ++   T 
Sbjct: 174 DPITLLDQISDQND----------QKWFDQIALQEAIRGLEERERLIVYLRYYKDQ--TQ 221

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
                   +S+ +V ++E +  + ++E ++
Sbjct: 222 SEAGERLGISQVQVSRLEKKILRVMKERME 251


>gi|309778067|ref|ZP_07673006.1| RNA polymerase sigma-G factor [Erysipelotrichaceae bacterium
           3_1_53]
 gi|308914161|gb|EFP59962.1| RNA polymerase sigma-G factor [Erysipelotrichaceae bacterium
           3_1_53]
          Length = 259

 Score =  159 bits (404), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 59/276 (21%), Positives = 121/276 (43%), Gaps = 22/276 (7%)

Query: 16  LSRYIHEIR-----KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           +SRY  EI      ++ +L   E   L  + ++ GD  A   L+  +L+LV+ I   +  
Sbjct: 1   MSRYKVEISGINTAQLKVLTNAEMKELFVQLQQ-GDEQAKETLINGNLKLVLSIVQRFSN 59

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
               + ++   G IGL++++  FD +   R +TY++  I   ++ Y+  +  ++++    
Sbjct: 60  RCENMDDLFQVGCIGLVKSIDNFDLKHEVRFSTYAVPMIMGEIKRYLRDN-QVIRVSRHL 118

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
             K L +   +LK   +     N K   +  +A++L V E +++          S+   +
Sbjct: 119 --KDLAYRAFKLK---EEYVHKNQKEPTIAWLAEQLEVKEKDIVDALDSTQSVLSIFEPV 173

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
            +SD +     D +  D D        + E  N    L RS+  L  +E  I + R  Q+
Sbjct: 174 YNSDGDELFLLDQIKDDKD--------EIEHLNNIMALKRSLKRLKGKELDIIQKRYYQD 225

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             +T   ++ E  +S+ +V ++E  A   +++    
Sbjct: 226 --MTQTEIAGELGISQAQVSRLEKNAIAVLKKEFDS 259


>gi|229086642|ref|ZP_04218811.1| RNA polymerase sigma-F factor [Bacillus cereus Rock3-44]
 gi|228696724|gb|EEL49540.1| RNA polymerase sigma-F factor [Bacillus cereus Rock3-44]
          Length = 252

 Score =  159 bits (404), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 54/263 (20%), Positives = 116/263 (44%), Gaps = 19/263 (7%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           +K P L+  E   L ++  + GD  A   +V S++RLV  +   +   G    ++   G 
Sbjct: 9   KKKPQLKDHELKALIQK-SQDGDQGARDTIVQSNMRLVWSVVQRFLNRGYEPDDLFQIGC 67

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL+++V KFD     + +TY++  I   +Q ++    S VK+  +   K     +R++K
Sbjct: 68  IGLLKSVDKFDLSFEVKFSTYAVPMIIGEIQRFLRDDGS-VKVSRSL--KETGNKIRKMK 124

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L   +    +   +  +A+ L ++  EV+          S++  +  +D +     D 
Sbjct: 125 DEL---SKEYGRAPTINEVAEALELTPEEVVLAQEASRTPSSIHETVYENDGDPITILDQ 181

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +            + E +   +  L  ++  L+ RER I   R  ++   T   ++    
Sbjct: 182 IAD----------QTETKWFEKIALKEAIRELDERERLIVYLRYYKDQ--TQSEVAERIG 229

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+ +V ++E +  K++++ I +
Sbjct: 230 ISQVQVSRLEKKILKQMKDRIDE 252


>gi|299535877|ref|ZP_07049197.1| sporulation sigma factor SigG [Lysinibacillus fusiformis ZC1]
 gi|298728629|gb|EFI69184.1| sporulation sigma factor SigG [Lysinibacillus fusiformis ZC1]
          Length = 257

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 55/257 (21%), Positives = 114/257 (44%), Gaps = 17/257 (6%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L+ +E   L  R +  G+      LV  +LRLV+ I   +   G    ++   G IG
Sbjct: 15  LPILKHEEMKELFIRLQ-AGETEIREELVMCNLRLVLSIVGRFAYRGEQADDLFQVGCIG 73

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           LM+A+  FD +   R +TY++  I   ++ ++    +L ++  +          + ++  
Sbjct: 74  LMKAIDHFDLKHNVRFSTYAVPMIIGEIRRHLRDHHAL-RVSRSLRDI----AYKAMQAK 128

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            Q ITD NL+   +  IA+ +++ + +V+     +    SL   I S   ++    D L 
Sbjct: 129 EQWITD-NLREPTIEEIAEMIDMKKEDVLFALDAIQDPVSLQEPIYSDGGDAVYMMDQLR 187

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            D   ++Q +            +  S+  L+ R++ I   R       T   ++ E  +S
Sbjct: 188 DDDVSEDQWVA--------YVSVKESLQKLDERQQMIVAKRFYYGE--TQTEIAKELGIS 237

Query: 266 RERVRQIEARAFKKVQE 282
           + ++ ++E  A + +Q+
Sbjct: 238 QAQISRLEKNAIETMQK 254


>gi|325479184|gb|EGC82281.1| sigma-70, region 4 [Anaerococcus prevotii ACS-065-V-Col13]
          Length = 343

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 62/272 (22%), Positives = 126/272 (46%), Gaps = 17/272 (6%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISE 77
            ++ K+  L  ++     +     G+ +A   LV  +  LV   A  +    G  L + +
Sbjct: 83  KDMMKLSDLTNEQIVEQFQI----GNQNALAALVEKNQGLVRSRASYFFRSHGNDLDLED 138

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +V  G +G+++A +KFD   G++  TY+  WI  A+++ I +    ++I      K    
Sbjct: 139 LVQSGMLGMIRAAEKFDLSLGYKFTTYAYKWIDKAIRKAINKEGHTIRIPAGKYLK--LN 196

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L+++       +D  L   +++           ++  +N       SLN  ++S D   
Sbjct: 197 KLKQILKANPEASDEELY--RILENEGIDKKQADDLFLINRNQVNSTSLNINLDSEDSTG 254

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTL 255
            +  D +  +    + +++E    K+  N L +++  L  RE++I   R   +N  P TL
Sbjct: 255 DELMDMVGDESTPVDMLILE----KDMENFLLKALDQLTDREKQIIIYRYGLDNEKPKTL 310

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +   +++SRER+RQIE +A  K++E  +++
Sbjct: 311 EEIGKIYDLSRERIRQIENQALGKLKEFSERE 342


>gi|302542626|ref|ZP_07294968.1| putative RNA polymerase sigma factor [Streptomyces hygroscopicus
           ATCC 53653]
 gi|302460244|gb|EFL23337.1| putative RNA polymerase sigma factor [Streptomyces himastatinicus
           ATCC 53653]
          Length = 351

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 53/237 (22%), Positives = 101/237 (42%), Gaps = 15/237 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              + LV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+  
Sbjct: 126 ELRNNLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATP 185

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +   ++ +       V++     + RL      L      ++  + +   V  +A+ L 
Sbjct: 186 TVVGEIKRHFRDKGWAVRVPRRLQELRLS-----LTTATAELSQRHGRAPTVHELAEHLA 240

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +SE EV+          +L+  +  +D  S    D L  +         E  E    R  
Sbjct: 241 ISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAED--------EALEGVEYRES 292

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   +  L PRE++I   R      +T   ++ E  +S+  V ++ AR   ++++ +
Sbjct: 293 LKPLLEDLPPREKKILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLRDRL 347


>gi|307824191|ref|ZP_07654417.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacter tundripaludum
           SV96]
 gi|307734571|gb|EFO05422.1| RNA polymerase, sigma 32 subunit, RpoH [Methylobacter tundripaludum
           SV96]
          Length = 391

 Score =  159 bits (403), Expect = 4e-37,   Method: Composition-based stats.
 Identities = 57/250 (22%), Positives = 117/250 (46%), Gaps = 10/250 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                +++  ++RL   +A  ++   L   +++ EG +GL++AV +FDP RG++ +TY++
Sbjct: 146 QRLRQQMIAGNVRLAAFVAHKHKTTVLSFDDLLQEGVVGLIKAVDRFDPYRGYQFSTYAI 205

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            WIK A+   I++   +V++     ++           +LQ       +   +  +    
Sbjct: 206 PWIKQAISRLIVKQEKIVRLPVALAERACAVFEAMRNAYLQTE-----RWPSIEQLKSLC 260

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++SE E+ ++        SL+A     D    + Q  +      Q  + +++   +N   
Sbjct: 261 DLSEDEIKTIRNYYQATHSLDA---VGDAEEDEGQALMARMKQRQFALPLDELIDRNLGR 317

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L + ++ L  +E  I   R   +N   +TL+ ++ + +VSRERVRQI+  A KK++   
Sbjct: 318 YLDQVVATLPDKEAAILNMRFGLKNHTEMTLQAIADQLQVSRERVRQIQNDALKKLKNQF 377

Query: 285 QKQVELSSSP 294
              + L   P
Sbjct: 378 GYDLMLFLEP 387


>gi|303241077|ref|ZP_07327586.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302591337|gb|EFL61076.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 246

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 53/253 (20%), Positives = 116/253 (45%), Gaps = 16/253 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           E   L K+ +  GD  A   LV  ++ LV  I   ++  G    ++   G IGL++A+KK
Sbjct: 8   ETLELIKKAK-SGDKQAQSILVERNVGLVWSIVKRFQNRGYETDDIYQIGCIGLIKAIKK 66

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD     + +TY++  I   ++ +I     ++K+  +  +        +++   + +   
Sbjct: 67  FDDSFDVKFSTYAVPMIIGEIKRFIRDDG-IIKVSRSLKELS-----NKIRVTKEIMMKE 120

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +   +  I+ +++V+  E++         ESL   +  SD ++    D L  + + +E
Sbjct: 121 LGREPSISEISLRMDVAAEELVMAMEANCSPESLYNTVGDSDTSTVLLIDKLNNESNDEE 180

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
             L++K +       L   ++ L PRE++I   R  +E   T   ++    +S+ +V +I
Sbjct: 181 VDLVDKID-------LRLVLNTLKPREKQIIILRYFKE--KTQVQIAKMLGISQVQVSRI 231

Query: 273 EARAFKKVQESIQ 285
           E +   ++++ I+
Sbjct: 232 EKKILDEIKKKIK 244


>gi|167462564|ref|ZP_02327653.1| sporulation sigma factor SigF [Paenibacillus larvae subsp. larvae
           BRL-230010]
          Length = 251

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 51/256 (19%), Positives = 107/256 (41%), Gaps = 19/256 (7%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L+ QE   L     + GD  A   LV  ++RLV  +   +   G    ++   G IGL++
Sbjct: 13  LDDQEVKRLI-ALSQSGDTIARDTLVNCNIRLVWSVVQRFLNRGYEADDLFQIGCIGLLK 71

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           +V KF+     + +TY++  I   +Q ++      +K+  +   K L   +R+ K  L  
Sbjct: 72  SVDKFNLSYEVKFSTYAVPMIIGEIQRFLRDDG-TLKVSRSL--KELANKVRKTKDELSK 128

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
             +       +  +A  L ++  EV+          S++  +  +D +     D +  D 
Sbjct: 129 NLERL---PTLKEVANALGITPEEVVFAQEANKPLSSIHETVFENDWDPITLMDQIADD- 184

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
                     +E+   +  L  ++  L+ RER I   R  ++   T   +++   +S+ +
Sbjct: 185 ---------SQEKWFDKLALNEAIEGLSERERLIVYLRYFKDQ--TQSEVANRLGISQVQ 233

Query: 269 VRQIEARAFKKVQESI 284
           V ++E +  + ++  I
Sbjct: 234 VSRLEKKILQSIRNQI 249


>gi|149916583|ref|ZP_01905097.1| RNA polymerase sigma factor [Roseobacter sp. AzwK-3b]
 gi|149809510|gb|EDM69370.1| RNA polymerase sigma factor [Roseobacter sp. AzwK-3b]
          Length = 189

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 95/190 (50%), Positives = 133/190 (70%), Gaps = 4/190 (2%)

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           +A++QEYILRSWS+VK+GTT+ QK+LFFNLR+ K  + A+ + +L+PE V  IA  L V+
Sbjct: 1   RASIQEYILRSWSMVKLGTTSAQKKLFFNLRKAKAKIGALEEGDLRPENVKQIAHDLGVT 60

Query: 170 ESEVISMNCRL-AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           E+EVISMN R+  GD SLNA I S  + S +WQDWL  +   Q      ++E + RR ML
Sbjct: 61  ETEVISMNRRMSGGDASLNAQIGSDGEGSMEWQDWLEDEDADQASDYERRDELEARREML 120

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
             +M VLN RER I   RRL +  VTLE+LS++++VSRER+RQIE RAF+K+Q+ ++   
Sbjct: 121 ALAMDVLNERERDILTQRRLSDETVTLEDLSTQYDVSRERIRQIEVRAFEKLQDRMR--- 177

Query: 289 ELSSSPPLLQ 298
           EL++   +L 
Sbjct: 178 ELAAEKGMLP 187


>gi|254455073|ref|ZP_05068509.1| RNA polymerase, sigma 32 subunit, RpoH [Octadecabacter antarcticus
           238]
 gi|198263775|gb|EDY88046.1| RNA polymerase, sigma 32 subunit, RpoH [Octadecabacter antarcticus
           238]
          Length = 249

 Score =  159 bits (403), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 73/208 (35%), Positives = 120/208 (57%), Gaps = 5/208 (2%)

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           +   NIGL++A  +FDP++GFR +TY+ WWI+A +Q+Y L+ WSLVK+  +A  ++LF+N
Sbjct: 1   MQHANIGLLKAADRFDPDKGFRFSTYAAWWIRAEIQDYKLQGWSLVKLPNSAFGRKLFYN 60

Query: 139 LRRLKGHLQAITDNNLKPEQ-VVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSDKN 196
           L+R++  L  + +  + PE  V  IA  L V+  +V+ M  RLA  + SLN  + S D  
Sbjct: 61  LKRVETRL--VAEGEVPPEHLVDRIATDLGVTPEQVVLMQQRLAAPDGSLNRPV-SDDGG 117

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           ++Q QD L       E+ +  + + +     L+  ++ L+ RE+ I     + + P TL 
Sbjct: 118 TAQLQDLLEDPDADVEKEVSARLDSRAFWTTLSFHLNRLSKREQEIIIEIYVSDTPKTLY 177

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
            L  +F VS ER+RQI   A  +++ S 
Sbjct: 178 ELGEQFSVSHERIRQIREAALTRLRASF 205


>gi|15828925|ref|NP_326285.1| RNA polymerase sigma factor [Mycoplasma pulmonis UAB CTIP]
 gi|14089868|emb|CAC13627.1| DNA-DIRECTED RNA POLYMERASE SIGMA FACTOR (SIGMA-A) [Mycoplasma
           pulmonis]
          Length = 461

 Score =  159 bits (402), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 64/298 (21%), Positives = 131/298 (43%), Gaps = 20/298 (6%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKI-PMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLR 59
            K  S ++     +  Y+  I K   +L   EE  LA   ++ G     A  +L+  +LR
Sbjct: 165 EKLKSKLIETNDIVKWYMRWIGKYGTLLTAAEEKQLAIDMKKGGLKGKIAKDKLINRNLR 224

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           LV+  A  Y+  GL   +++SEGN G+++AV+KFD  +GF+ +TY+ WWI+ ++   +  
Sbjct: 225 LVINNAKKYKNRGLSFIDLISEGNAGIIKAVQKFDESKGFKFSTYATWWIRQSITRAVAD 284

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
               ++I     +      + +++  LQ     N   EQ+       +    +V  +   
Sbjct: 285 QARTIRIPVHMVE--TINKIIKIERELQQELGVNPTDEQIAERYGN-DYDAKKVRYIRKM 341

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
                SL+  +    +N S + D++    D      I+   +++    L   ++     E
Sbjct: 342 NIDPISLDKTV--GKENDSFFSDFV---KDESVISPIDHAAKEDLNEHLLELLNEQLTEE 396

Query: 240 RRIFEA-RRLQENP--------VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            R+    R               T + L++E   S+E++RQ E +  ++++ + ++++
Sbjct: 397 ERVLIMKRYGIGEDENGVPYQVHTFDQLATEKNTSKEKIRQWENKILRRLKATKKRKI 454


>gi|75812393|ref|YP_320012.1| sigma-70 [Anabaena variabilis ATCC 29413]
 gi|75705149|gb|ABA24823.1| Sigma-70 [Anabaena variabilis ATCC 29413]
          Length = 314

 Score =  159 bits (402), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 61/306 (19%), Positives = 125/306 (40%), Gaps = 52/306 (16%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------------------ 43
             +  Y+ EI K PML  ++E  LA++ ++                              
Sbjct: 6   DSVGIYLREISKYPMLTPEQEITLARQVKQMTVVQQHKQVLEEQLHQQLNIQQLAADMGK 65

Query: 44  ---------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                         A  +++ ++LRLVV IA  YR   L   ++V EG+IGL +AV++FD
Sbjct: 66  SETEVFQILRLGQKAKEKMIAANLRLVVAIAKKYRWSQLEFLDLVQEGSIGLQKAVERFD 125

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P RG++ +T + WWI+  + + I    + ++  +  N +     L +LK   + +     
Sbjct: 126 PNRGYKFSTCAYWWIRQEITKAIANKSTTIRTPSHMNDR-----LIKLKKVQRELVKILG 180

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +   +  IA+   +  ++V           SL+  +   D+    + + L  D     + 
Sbjct: 181 REPNIAEIAEFAELEPNQVRECLIAFRHPLSLDRPMGQEDEVD--FLEILPADGTSPNEY 238

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQI 272
           L E   R++    L   +  L P ++++   R      + ++ + ++    + + +V   
Sbjct: 239 LDEGFLRQD----LANCLITLKPLQKQVLMLRFGLGSVDKLSTKQIAERLNIKQAKVGTT 294

Query: 273 EARAFK 278
           + +A K
Sbjct: 295 QKQAIK 300


>gi|254389000|ref|ZP_05004231.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|294814936|ref|ZP_06773579.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|197702718|gb|EDY48530.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|294327535|gb|EFG09178.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 358

 Score =  159 bits (402), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 55/237 (23%), Positives = 103/237 (43%), Gaps = 15/237 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              ++LV  HL LV  +A  +R  G P+ ++     IGL+++V +FDPERG   +TY+  
Sbjct: 133 ELRNQLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPERGVEFSTYATP 192

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +   ++ +       V++     + RL      L      ++  + +   V  +A++L 
Sbjct: 193 TVVGEIKRHFRDKGWAVRVPRRLQELRLA-----LTTATAELSQLHGRSPTVHELAERLG 247

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +SE EV+          +L+  +  +D  S    D L  +         E  E    R  
Sbjct: 248 ISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAED--------EALEGVEYRES 299

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   ++++ +
Sbjct: 300 LKPLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLRDKL 354


>gi|302392455|ref|YP_003828275.1| RNA polymerase, sigma subunit, RpoX/SigF [Acetohalobium arabaticum
           DSM 5501]
 gi|302204532|gb|ADL13210.1| RNA polymerase, sigma subunit, RpoX/SigF [Acetohalobium arabaticum
           DSM 5501]
          Length = 253

 Score =  159 bits (402), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 59/263 (22%), Positives = 125/263 (47%), Gaps = 17/263 (6%)

Query: 22  EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
            I +  +L + E   L K+  + GD  A  +LV  +++LV+K+A  +        E+   
Sbjct: 7   NIPQKELLSEAETKELLKK-AQAGDQKAKDKLVNHNVKLVLKVAHRFANKNYDYEELFQI 65

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           G+IGL++A+++FD ER  + +TY++  I   ++ ++      VK+  +  ++       R
Sbjct: 66  GSIGLLKAIERFDLERDVKFSTYAVPLIIGEIKRFLRDD-DAVKVSRSLKRRAH-----R 119

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           +    +++T    +   +  IA+++ V + E+++    +    S+ + +  ++ NS +  
Sbjct: 120 INEVKESLTAELNREPTIQEIAEEMEVDKEEIVNALEAVREPTSIYSPVYENEGNSIELV 179

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           D L            E +E++  R  L   +  L  RER I + R   E   T + ++  
Sbjct: 180 DQLAASS--------ENQEQEIDRLALREVIDELKTRERLILKLRFFDE--KTQQEVADR 229

Query: 262 FEVSRERVRQIEARAFKKVQESI 284
             VS+ +V ++E +   KV+E +
Sbjct: 230 IGVSQVQVSRLERKIIDKVREEL 252


>gi|222529665|ref|YP_002573547.1| Sig B/F/G subfamily RNA polymerase sigma-28 factor
           [Caldicellulosiruptor bescii DSM 6725]
 gi|222456512|gb|ACM60774.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor bescii DSM 6725]
          Length = 232

 Score =  159 bits (402), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 50/241 (20%), Positives = 106/241 (43%), Gaps = 16/241 (6%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            ++GD  A  +L+ ++L LV  +   +   G+ + ++   G+IGL++AV +FDP    R 
Sbjct: 5   AKNGDKLARQQLIENNLALVWSVVKKFAAKGVELEDLFQIGSIGLIKAVDRFDPSFNVRF 64

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY++  I   ++ Y+      +K+      +++  N  ++K        N+ +   +  
Sbjct: 65  STYAVPMIIGEIKRYLRDDGK-IKVS-----RKIKENQGKIKKLRNQFVSNHGREPTISE 118

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           I++   +S  E++      +   SL+ +IN  +       D    + D   ++L      
Sbjct: 119 ISQLTGLSNDEILLCLDASSEVASLSEVINQEEGKPITLMDIASDEEDYSTKLLDLMA-- 176

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                 L   +  L  RER I   R  +    T   ++ +  +S+  V +IE RA ++++
Sbjct: 177 ------LKEGLKKLKGRERYIIFMRYFKN--KTQSEIAKQLNISQVHVSRIEKRALERIK 228

Query: 282 E 282
            
Sbjct: 229 R 229


>gi|300814743|ref|ZP_07094991.1| putative RNA polymerase sigma-B factor [Peptoniphilus sp. oral
           taxon 836 str. F0141]
 gi|300511130|gb|EFK38382.1| putative RNA polymerase sigma-B factor [Peptoniphilus sp. oral
           taxon 836 str. F0141]
          Length = 258

 Score =  159 bits (402), Expect = 5e-37,   Method: Composition-based stats.
 Identities = 57/264 (21%), Positives = 118/264 (44%), Gaps = 17/264 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K+E+  L   Y +  D      L+  +L +   ++  Y G G+   ++    +IGL+ 
Sbjct: 10  LTKEEKKELFLEYYKTKDQDLRTILIEEYLYIAEILSKKYIGKGIDYDDIYQVASIGLIY 69

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           +V +FDP +G+  ++++   I   +++Y       +++     +  L   +   K  L  
Sbjct: 70  SVDRFDPTKGYEFSSFATPTIIGEIKKYFRDKGWTIRVPRRIQE--LSKKIMIAKNKLSQ 127

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVY 206
                 +   V  IA+ LN S  E+I      ++   +SL+ + +S D      QD +  
Sbjct: 128 EYQ---RTPTVEDIAEFLNASPEEIIESMEASKVYTPQSLDIVYDSGDDKKMSLQDLIGE 184

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           D    +++        + ++ L +SM  LN  E+ I   R    N  T   ++ +  +S+
Sbjct: 185 DEKYFDKI--------DLKDFLLKSMKNLNEVEKTILIDRYF--NKKTQIVIAKKLNISQ 234

Query: 267 ERVRQIEARAFKKVQESIQKQVEL 290
             V +IE +  +K+++ I+K +E+
Sbjct: 235 MTVSRIEKKVLEKMRKEIKKTMEV 258


>gi|313901043|ref|ZP_07834531.1| RNA polymerase sigma-G factor [Clostridium sp. HGF2]
 gi|312954001|gb|EFR35681.1| RNA polymerase sigma-G factor [Clostridium sp. HGF2]
          Length = 259

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 61/276 (22%), Positives = 124/276 (44%), Gaps = 22/276 (7%)

Query: 16  LSRYIHEIR-----KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           +SRY  EI      ++ +L   E   L  + ++ GD SA   L+  +L+LV+ I   +  
Sbjct: 1   MSRYKVEISGINTAQLKVLTNAEMKELFVKLQQ-GDESAKETLINGNLKLVLSIVQRFSN 59

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
               + ++   G IGL++++  FD +   R +TY++  I   ++ Y+  +  ++++    
Sbjct: 60  RCENMDDLFQVGCIGLVKSIDNFDLKHEVRFSTYAVPMIMGEIKRYLRDN-QVIRVSRHL 118

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
             K L +   +LK   +     + K   V  +A++L V E +++          S+   +
Sbjct: 119 --KDLAYRAFKLK---EEYVHKHQKEPSVSWLAQQLEVKEKDIVDALDSTQSVLSIFEPV 173

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
            +SD +     D +  D D        + ER N    L RS++ L  +E  I + R  Q+
Sbjct: 174 YNSDGDELFLLDQIKDDKD--------EIERLNNLMALKRSLTRLKGKELDIIQKRYYQD 225

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             +T   ++ E  +S+ +V ++E  A   +++    
Sbjct: 226 --MTQTEIAGELGISQAQVSRLEKNAIAVLKKEFDS 259


>gi|318060769|ref|ZP_07979492.1| RNA polymerase sigma factor [Streptomyces sp. SA3_actG]
 gi|318078700|ref|ZP_07986032.1| RNA polymerase sigma factor [Streptomyces sp. SA3_actF]
 gi|333025872|ref|ZP_08453936.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
 gi|332745724|gb|EGJ76165.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
          Length = 367

 Score =  159 bits (402), Expect = 6e-37,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 96/237 (40%), Gaps = 17/237 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +
Sbjct: 143 RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTV 202

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +   V  +AK L VS
Sbjct: 203 VGEIKRFFRDTSWSVRVPRRLQELRLA-----LTKTSDELAQKLDRSPTVPELAKALGVS 257

Query: 170 ESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E +V+            SL++     D       D L Y+    E V          R  
Sbjct: 258 EDDVVDGLAVGNAYTASSLDSPAPEDDGGEGSLADRLGYEDTALEGV--------EYRES 309

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   ++ L PRERRI   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 310 LKPLLAKLPPRERRIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 364


>gi|323456432|gb|EGB12299.1| hypothetical protein AURANDRAFT_12561 [Aureococcus anophagefferens]
          Length = 233

 Score =  158 bits (401), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 62/239 (25%), Positives = 112/239 (46%), Gaps = 23/239 (9%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            SA   LV +++RLVV +A  Y G GL +S++V EG++GLM+A  KFDP RG + +TY+ 
Sbjct: 5   RSARQALVATNMRLVVSVAKRYTGLGLGLSDLVQEGSLGLMRAATKFDPARGCKFSTYAC 64

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +     L+++    +Q     +L +LK   +  T  + +      +A+ L
Sbjct: 65  WWIQQAILRAVAFQSRLIRLPMHVHQ-----DLAKLKRGTRDFTAAHGREPSDGELAELL 119

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++ +++  +       ++L                 L      +E       E      
Sbjct: 120 EMTPAKLRKVRAAARQGDTL----------------KLEDTLASKEPTGETAVELALLHE 163

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            L  +M  L+  E+R+   R   E+  P T   +++    S+E VR+ E RA +K+++ 
Sbjct: 164 DLHAAMDDLDADEKRVISLRYGLEDGVPCTPAQVAASCAESKEWVRRCEMRAIRKLRKP 222


>gi|297588048|ref|ZP_06946692.1| RNA polymerase general stress sigma factor(sigma B) [Finegoldia
           magna ATCC 53516]
 gi|297574737|gb|EFH93457.1| RNA polymerase general stress sigma factor(sigma B) [Finegoldia
           magna ATCC 53516]
          Length = 258

 Score =  158 bits (401), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 58/267 (21%), Positives = 120/267 (44%), Gaps = 19/267 (7%)

Query: 29  LEKQEE---YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           + K+E+     L  +++E  D      LV  +L +   +A  Y G G+   ++     IG
Sbjct: 6   ISKEEQENIKELFLKFQETRDKKTRDTLVEKNLYIAEILAKKYTGRGIEYDDLYQVACIG 65

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L+ A+ ++DP +G+  ++Y+   I   +++Y      ++++     +  L   +   K H
Sbjct: 66  LIYAIDRYDPSKGYEFSSYATPTIVGEIKKYFRDKGWVIRVPRRIQE--LNKKVANAKIH 123

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDW 203
           L        K   V  IA  L++S  EV+ +    ++   +SL+  I+ S  +       
Sbjct: 124 LAQTMQ---KSPTVEDIADYLSISNEEVLEVLEGAKVYAPQSLDQSIDQSSDDRDTNLSD 180

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L+ + D           +   R+++ R M  LN  E++I   R    +  T   ++ E +
Sbjct: 181 LIGEEDKDM-------LKFENRDLINRCMEDLNEVEKKILLGRYF--DKKTQIVIAEELD 231

Query: 264 VSRERVRQIEARAFKKVQESIQKQVEL 290
           +S+  V ++E +  KK + S+++Q+E 
Sbjct: 232 ISQMTVSRMEKKILKKFKASLKEQLEF 258


>gi|295109704|emb|CBL23657.1| RNA polymerase, sigma subunit, RpsG/SigG [Ruminococcus obeum
           A2-162]
          Length = 259

 Score =  158 bits (401), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 53/260 (20%), Positives = 113/260 (43%), Gaps = 17/260 (6%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L+++E+  L +R ++ GD  A  + +  +LRLV+ +   ++       ++   G IG
Sbjct: 16  LPILKQEEKDELFRRIKQ-GDTKAREQYIKGNLRLVLSVIRRFQNSNENPDDLFQIGCIG 74

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           LM+AV  FD     + +TY++  I   ++ Y+    S +++  +           +    
Sbjct: 75  LMKAVDNFDDTLMVKFSTYAVPMIIGEIRRYLRDYNS-IRVSRSLRDIAYKAIYAK---- 129

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            +     NLK   +  IA+++ + +  ++     +    SL   + S   ++    D + 
Sbjct: 130 -ENYIRQNLKEPTMEEIAEEIGIEKEMIVYALDAIQSPVSLYEPVYSEGGDTLYVMDQIS 188

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
              + +E  L            L  +M+ L  RER I E R       T   ++ E  +S
Sbjct: 189 DRKNKEEHWLENLS--------LKEAMNRLGSRERHIIEMRFY--EGKTQMEVADEIGIS 238

Query: 266 RERVRQIEARAFKKVQESIQ 285
           + +V ++E  A K ++  ++
Sbjct: 239 QAQVSRLEKNALKTMRNYLR 258


>gi|262273681|ref|ZP_06051494.1| RNA polymerase sigma factor RpoS [Grimontia hollisae CIP 101886]
 gi|262222096|gb|EEY73408.1| RNA polymerase sigma factor RpoS [Grimontia hollisae CIP 101886]
          Length = 246

 Score =  158 bits (401), Expect = 7e-37,   Method: Composition-based stats.
 Identities = 60/208 (28%), Positives = 99/208 (47%), Gaps = 8/208 (3%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
            +           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+
Sbjct: 41  FATSTKALDATQLYLSEIGYSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLVVKIS 99

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y   GL + ++V EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     ++
Sbjct: 100 RRYSNRGLALLDLVEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIR 159

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           +      K L   LR  +     +            IA +L+    +V  M        S
Sbjct: 160 LPIHVV-KELNVYLRTAR----ELAQKLDHEPTAEDIAFQLDKPVEDVNRMLRLNERISS 214

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQ 213
           ++  I     +     D +  + +G  +
Sbjct: 215 VDNPI--GGDSEKALLDIIPDEKEGGPE 240


>gi|229082715|ref|ZP_04215161.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock4-2]
 gi|228700606|gb|EEL53146.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock4-2]
          Length = 323

 Score =  158 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 73/268 (27%), Positives = 123/268 (45%), Gaps = 13/268 (4%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP--ISE 77
           I EI    +L KQE   L +RY+ HG+      L   ++ LV+ IA  Y+         +
Sbjct: 40  IKEIGNYKVLSKQESLKLFQRYK-HGEKDLRDYLFHVNVGLVLSIARKYKNKHPDIEFDD 98

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR-SWSLVKIGTTANQKRLF 136
           +V EGN G+++A++ F+P  G+  +TY+ WWIK +M   I R      KI    NQ    
Sbjct: 99  LVQEGNEGMLRAMEDFNPALGYCFSTYAFWWIKKSMLGIICRKKSGPFKIPNYVNQ---- 154

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
           FNLR ++   + +   N  P  V  +AK+LNV+   VI  N       ++   +++ +++
Sbjct: 155 FNLRYVELEDKYLQMYNRTP-SVEEVAKELNVTSETVIKYNVYYKRATTMTLDVDTINED 213

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPVTL 255
                 +  YD         E         +      VLNP+++ +      L +  V L
Sbjct: 214 IGILNPF--YDDSSTIPSTNEMVIEDLNYEIWLIFDEVLNPKQKMVLNLCFGLLDGKVYL 271

Query: 256 E-NLSSEFEVSRERVRQIEARAFKKVQE 282
              ++    ++ ERV QI+  A KK+++
Sbjct: 272 HKEIAKALMITTERVSQIKDEAIKKLKK 299


>gi|282881777|ref|ZP_06290435.1| RNA polymerase sigma-B factor [Peptoniphilus lacrimalis 315-B]
 gi|281298387|gb|EFA90825.1| RNA polymerase sigma-B factor [Peptoniphilus lacrimalis 315-B]
          Length = 261

 Score =  158 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 57/264 (21%), Positives = 118/264 (44%), Gaps = 17/264 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K+E+  L   Y +  D      L+  +L +   ++  Y G G+   ++    +IGL+ 
Sbjct: 13  LTKEEKKELFLEYYKTKDQDLRTILIEEYLYIAEILSKKYIGKGIDYDDIYQVASIGLIY 72

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           +V +FDP +G+  ++++   I   +++Y       +++     +  L   +   K  L  
Sbjct: 73  SVDRFDPTKGYEFSSFATPTIIGEIKKYFRDKGWTIRVPRRIQE--LSKKIMIAKNKLSQ 130

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVY 206
                 +   V  IA+ LN S  E+I      ++   +SL+ + +S D      QD +  
Sbjct: 131 EYQ---RTPTVEDIAEFLNASPEEIIESMEASKVYTPQSLDIVYDSGDDKKMSLQDLIGE 187

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           D    +++        + ++ L +SM  LN  E+ I   R    N  T   ++ +  +S+
Sbjct: 188 DEKYFDKI--------DLKDFLLKSMKNLNEIEKTILIDRYF--NKKTQIVIAKKLNISQ 237

Query: 267 ERVRQIEARAFKKVQESIQKQVEL 290
             V +IE +  +K+++ I+K +E+
Sbjct: 238 MTVSRIEKKVLEKMRKEIKKTMEV 261


>gi|240142271|ref|YP_002966781.1| putative RNA polymerase sigma factor protein (Sigma-70)
           [Methylobacterium extorquens AM1]
 gi|240012215|gb|ACS43440.1| putative RNA polymerase sigma factor protein (Sigma-70)
           [Methylobacterium extorquens AM1]
          Length = 253

 Score =  158 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 71/262 (27%), Positives = 116/262 (44%), Gaps = 31/262 (11%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           +  +L   EE  L   YR  G   +  RLV +H R+   +A  +      + ++  EG I
Sbjct: 10  RETLLSPDEESGLVDAYRNDGCRKSLDRLVRTHARMAFSVARRWSNNEAHMQDLAQEGMI 69

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           G+M+A  KF+P  G R A Y  WWI +++     R+  +V +    ++  +    +RL+G
Sbjct: 70  GIMRAADKFNPSFGKRFAQYCRWWILSSIS---SRASEVVCVVDMPDRVFVAHRRKRLEG 126

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
              A+    +                   +S++  L G           D+  +   D L
Sbjct: 127 ADAALVGAAVTA-----------------VSISEPLGG-----------DEGGATVGDML 158

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           V D    E   ++ E     R  +  +M  L  RER I   RRL E P TLE ++  F++
Sbjct: 159 VSDETSPESAAVQSEMNWYYRTAVQTAMQGLTEREREILSRRRLAETPETLEVVADFFDL 218

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           +RER+RQIE  A  KV+ +++ 
Sbjct: 219 TRERIRQIENAAMAKVERNLRA 240


>gi|148241530|ref|YP_001226687.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp.
           RCC307]
 gi|147849840|emb|CAK27334.1| Alternative RNA polymerase sigma factor, sigma-70 family
           [Synechococcus sp. RCC307]
          Length = 280

 Score =  158 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 66/277 (23%), Positives = 122/277 (44%), Gaps = 31/277 (11%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHR------------------LVTSH 57
           +  Y+ +I +  +L  ++E  LA+  +    L    +                  ++ ++
Sbjct: 5   VRAYLEQIGRYALLRPEQEVELARLVQRAQQLEQQLQLSPTEQRELRRGRRARERMIQAN 64

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVV +A  Y+G GL + ++V EG++GL++AV+KFDP  G+R +TY+  WI+ A+   +
Sbjct: 65  LRLVVTVAKTYQGRGLDLMDLVQEGSLGLIRAVEKFDPTLGYRFSTYAWNWIRQAISRGL 124

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
                 +++     Q      LR L+   + +    L  + V A+A +  V         
Sbjct: 125 ETKGRTLRLPIHVTQ-----QLRALRRAHERLWQQGLSTDLV-AVAAEAGVDLKAASLAL 178

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
               G  SL+     S+ +       L+      E   +++ ER +    + R +  L  
Sbjct: 179 RMAPGTLSLDTPAAGSESD-------LLQLLPSAEPSPLDEAERHDGWERMGRQLRHLPE 231

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
           R++++ + R L      L  +  +   SRER RQIE 
Sbjct: 232 RDQQVLQWRYLTPERQKLSVVGEQLGCSRERARQIEQ 268


>gi|227501074|ref|ZP_03931123.1| DNA-directed RNA polymerase sigma subunit RpoD [Anaerococcus
           tetradius ATCC 35098]
 gi|227216847|gb|EEI82245.1| DNA-directed RNA polymerase sigma subunit RpoD [Anaerococcus
           tetradius ATCC 35098]
          Length = 344

 Score =  158 bits (401), Expect = 8e-37,   Method: Composition-based stats.
 Identities = 62/272 (22%), Positives = 126/272 (46%), Gaps = 17/272 (6%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISE 77
            ++ K+  L  ++     +     G+ +A   LV  +  LV   A  +    G  L + +
Sbjct: 84  RDMMKLSDLTNEQIVEQFQI----GNQNALAALVEKNQGLVRSRASYFFRSHGNDLDLED 139

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +V  G +G+++A +KFD   G++  TY+  WI  A+++ I +    ++I      K    
Sbjct: 140 LVQSGMLGMIRAAEKFDLSLGYKFTTYAYKWIDKAIRKAINKEGHTIRIPAGKYLK--LN 197

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L+++       +D  L   +++           ++  +N       SLN  ++S D   
Sbjct: 198 KLKQILKANPEASDEELY--RILENEGIDKKQADDLFLINRNQVNSTSLNINLDSEDSTG 255

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTL 255
            +  D +  +    + +++E    K+  N L +++  L  RE++I   R   +N  P TL
Sbjct: 256 DELMDMVGDESTPVDMLILE----KDMENFLLKALDQLTDREKQIIIYRYGLDNEKPKTL 311

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           E +   +++SRER+RQIE +A  K++E  +++
Sbjct: 312 EEIGKIYDLSRERIRQIENQALGKLKEFSERE 343


>gi|302876403|ref|YP_003845036.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium cellulovorans
           743B]
 gi|307687066|ref|ZP_07629512.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium cellulovorans
           743B]
 gi|302579260|gb|ADL53272.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium cellulovorans
           743B]
          Length = 427

 Score =  158 bits (400), Expect = 9e-37,   Method: Composition-based stats.
 Identities = 62/245 (25%), Positives = 110/245 (44%), Gaps = 18/245 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYG---LPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
             A   LV ++ +LV +IA+ Y+ +       S++   G +GLM+A +KFD  +G + +T
Sbjct: 179 EQALDNLVNANKKLVWEIALRYKQFSTVSFDNSDMYQAGVLGLMKAAEKFDISKGNQFST 238

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WW++ ++   I    + ++I     +K + +             + N +      +A
Sbjct: 239 YATWWVRQSITRSIADYSTTIRIPVHMREKIIKYV-----STENKFWNENGRVASKEELA 293

Query: 164 KKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD-HDGQEQVLIEKEE 220
             L +S  EV  + +   +A   SL+  I       S   +++  D H   E+   E E 
Sbjct: 294 NLLGISSEEVNYLQVYQDVANLTSLDIPI--GADEGSFLGEFIPDDKHRSPEKSAEEGEL 351

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFK 278
           ++  + +       L P+E RI   R         TLE +     V+RER+RQIEA+A  
Sbjct: 352 KRELKEICE---GRLTPKETRILNFRFGFIDGRTHTLEEIGHVENVTRERIRQIEAKAIS 408

Query: 279 KVQES 283
           K+Q  
Sbjct: 409 KLQNP 413


>gi|323454681|gb|EGB10551.1| hypothetical protein AURANDRAFT_23034 [Aureococcus anophagefferens]
          Length = 388

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 63/260 (24%), Positives = 110/260 (42%), Gaps = 18/260 (6%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R      + A   L +++LRLVV IA  YR  GL   +++ EG  GL +AV++FDPERGF
Sbjct: 124 RAARSRGVDARSTLTSANLRLVVSIAKRYRFCGLAQEDLLQEGAFGLSRAVERFDPERGF 183

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           R +TY+ +WI+ A+         ++++    +       L  ++     ++    +    
Sbjct: 184 RFSTYATFWIRQAVLRACAEQSRVIRLPAHVHD-----QLASMRKASAELSRRLGRDATD 238

Query: 160 VAIAKKLNVSESEVISMNCR--LAGDESLNA--------LINSSDKNSSQWQDWLVYDHD 209
             +A  L + + E ++   R       SL+           +     ++          D
Sbjct: 239 DELADHLELEKPEKLAFLRRCAAQDPSSLDEKHAIHAGRGSSVGGGGAAGATTIAESLSD 298

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSV-LNPRERRIFEARRLQEN--PVTLENLSSEFEVSR 266
               V  E       R  +   ++   N RER +   R       P++   ++    VSR
Sbjct: 299 DTILVPDEFVAEAASREYVGDLLATVCNDRERDVLGMRFGLYGNAPISKTKIAERLAVSR 358

Query: 267 ERVRQIEARAFKKVQESIQK 286
           ERVRQIE RA  K++++ + 
Sbjct: 359 ERVRQIEVRALTKLRQTHRA 378


>gi|2398853|dbj|BAA22215.1| plastid RNA polymerase sigma-subunit [Arabidopsis thaliana]
          Length = 571

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 59/236 (25%), Positives = 114/236 (48%), Gaps = 11/236 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
               LV S   LV+ +A  YRG G+   +++  G +G++Q  ++FD  RG++ +TY  +W
Sbjct: 332 CRDELVKSTRSLVLFLARNYRGMGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYW 391

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ +M   + R    V I ++    R   ++++ +  L+  T + +K      IAK    
Sbjct: 392 IRKSMSTMVSRHARGVHIPSSI--IRTINHIQKARKTLK--TSHGIKYAADEEIAKLTGH 447

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  ++ + N  L    S++  +            +L +  D   +   E   R++ R  +
Sbjct: 448 SVKKIRAANQCLKVVGSIDKKVGDC-----FTTKFLEFTPDTTMESPEEAVMRQSARRDI 502

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              +  L PRE+++   R   ++  P +LE +   F+VS+E +R+IE RA  K+++
Sbjct: 503 HDLLEGLEPREKQVMVLRYGLQDYRPKSLEEIGKLFKVSKEWIRKIERRAMAKLRD 558


>gi|47565382|ref|ZP_00236424.1| RNA polymerase sigma-43 factor, putative [Bacillus cereus G9241]
 gi|208742286|ref|YP_002267738.1| RNA polymerase sigma factor (sigma-A) (sigma-43) [Bacillus cereus]
 gi|47557736|gb|EAL16062.1| RNA polymerase sigma-43 factor, putative [Bacillus cereus G9241]
          Length = 325

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 70/273 (25%), Positives = 124/273 (45%), Gaps = 13/273 (4%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP--ISE 77
           I  I    +L KQE   L +RY+ HG+      L   ++ LV+ IA  Y+         +
Sbjct: 42  IKGIGNYKVLSKQESLKLFQRYK-HGEKDLRDYLFHVNVGLVLSIARKYKNKHPDIEFDD 100

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLF 136
           +V EGN G+++A++ F+P  G+  +TY+ WWI+ +M   I  +     KI  + NQ    
Sbjct: 101 LVQEGNEGMLRAMEDFNPALGYCFSTYAFWWIQKSMLGIICKKKSGPFKIPNSVNQ---- 156

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
           FNLR ++   + +     +P  V  + K+LNV+   VI  N       ++   +++ +++
Sbjct: 157 FNLRYVELEDKYL-QMYNRPPSVEEVVKELNVTSETVIKHNVYYKRATTMTLDVDTINED 215

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPVTL 255
                 +   D            E  N    L     VLNP+++ +      L +  V L
Sbjct: 216 IGILNPFY-DDSSAIPSTNEMVIEDLNYEIWLIFD-EVLNPKQKMVLNLCFGLLDGKVYL 273

Query: 256 E-NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              ++    ++ ERV QI+  A KK+++   K+
Sbjct: 274 HKEIAKALMITTERVSQIKDEAIKKLKKCDYKE 306


>gi|326443307|ref|ZP_08218041.1| sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 351

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 55/237 (23%), Positives = 103/237 (43%), Gaps = 15/237 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              ++LV  HL LV  +A  +R  G P+ ++     IGL+++V +FDPERG   +TY+  
Sbjct: 126 ELRNQLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPERGVEFSTYATP 185

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +   ++ +       V++     + RL      L      ++  + +   V  +A++L 
Sbjct: 186 TVVGEIKRHFRDKGWAVRVPRRLQELRLA-----LTTATAELSQLHGRSPTVHELAERLG 240

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +SE EV+          +L+  +  +D  S    D L  +         E  E    R  
Sbjct: 241 ISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAED--------EALEGVEYRES 292

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   ++++ +
Sbjct: 293 LKPLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLRDKL 347


>gi|169827020|ref|YP_001697178.1| sporulation sigma factor SigG [Lysinibacillus sphaericus C3-41]
 gi|168991508|gb|ACA39048.1| RNA polymerase sigma-G factor (Stage III sporulation protein G)
           [Lysinibacillus sphaericus C3-41]
          Length = 257

 Score =  158 bits (400), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 54/257 (21%), Positives = 113/257 (43%), Gaps = 17/257 (6%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L+ +E   L  R +  G+      LV  +LRLV+ I   +   G    ++   G IG
Sbjct: 15  LPILKHEEMKELFIRLQ-AGETEIREELVMCNLRLVLSIVGRFAYRGEQADDLFQVGCIG 73

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           LM+A+  FD +   R +TY++  I   ++ ++    +L ++  +          + ++  
Sbjct: 74  LMKAIDHFDLKHNVRFSTYAVPMIIGEIRRHLRDHHAL-RVSRSLRDI----AYKAMQAK 128

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            Q IT+ NL+   +  IA  +++ + +V+     +    SL   I S   ++    D L 
Sbjct: 129 EQWITE-NLREPTIEEIADMIDMKKEDVLFALDAIQDPMSLQEPIYSDGGDAVYMMDQLR 187

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            D   ++Q +            +  S+  L+ R++ I   R       T   ++ E  +S
Sbjct: 188 DDDVSEDQWVA--------YVSVKESLQKLDERQQMIVAKRFYYGE--TQTEIAKELGIS 237

Query: 266 RERVRQIEARAFKKVQE 282
           + ++ ++E  A + +Q+
Sbjct: 238 QAQISRLEKNAIETMQK 254


>gi|297192165|ref|ZP_06909563.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
 gi|197720190|gb|EDY64098.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
          Length = 349

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 103/237 (43%), Gaps = 15/237 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              ++LV  HL LV  +A  +R  G P+ ++     IGL+++V +FDPERG   +TY+  
Sbjct: 124 ELRNQLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPERGVEFSTYATP 183

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +   ++ +       V++     + RL      L      ++  + +   V  +A++L 
Sbjct: 184 TVVGEIKRHFRDKGWAVRVPRRLQELRLS-----LTTATAELSQQHGRSPTVHELAERLG 238

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +SE EV+          +L+  +  +D  S    D L  +         E  E    R  
Sbjct: 239 ISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAED--------EALEGVEYRES 290

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 291 LKPLLEGLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLRERL 345


>gi|166031695|ref|ZP_02234524.1| hypothetical protein DORFOR_01395 [Dorea formicigenerans ATCC
           27755]
 gi|166028672|gb|EDR47429.1| hypothetical protein DORFOR_01395 [Dorea formicigenerans ATCC
           27755]
          Length = 244

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 56/249 (22%), Positives = 108/249 (43%), Gaps = 17/249 (6%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             L +R  E GD  A  RLV  +  LV  I   +   G+   ++   GNIGL++A+ KFD
Sbjct: 5   IALIQRSHE-GDEEARARLVEENAGLVWCIVKRFHNRGVETEDLFQIGNIGLIKAIDKFD 63

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
                + +TY++  I   ++ ++     ++K+  +  +      L +     + + +   
Sbjct: 64  LSYDVKFSTYAVPMISGEIKRFLRDDG-MIKVSRSLKELAYKAYLLK-----EDLQNQWG 117

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +   V  ++++L V + E++         ESL+  I   D    +  D L    +  EQV
Sbjct: 118 REPTVGELSERLGVEQEELVMALDAGGDVESLHKPIYQKDGQEIRLMDKLEEKSEEHEQV 177

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
           L           +LT  + VLN  E+R+   R   E   T   +  E  +S+ +V ++E 
Sbjct: 178 L--------NHIVLTELLGVLNQDEKRLIYLRYFAEQ--TQSQVGRELGISQVQVSRMEK 227

Query: 275 RAFKKVQES 283
           +   +++ +
Sbjct: 228 KILGQLKNA 236


>gi|302802267|ref|XP_002982889.1| hypothetical protein SELMODRAFT_117159 [Selaginella moellendorffii]
 gi|302818650|ref|XP_002990998.1| hypothetical protein SELMODRAFT_132663 [Selaginella moellendorffii]
 gi|300141329|gb|EFJ08042.1| hypothetical protein SELMODRAFT_132663 [Selaginella moellendorffii]
 gi|300149479|gb|EFJ16134.1| hypothetical protein SELMODRAFT_117159 [Selaginella moellendorffii]
          Length = 292

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 69/261 (26%), Positives = 120/261 (45%), Gaps = 14/261 (5%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           E   L ++ +          +V+S+L LV+K+A  +   G  I +++ EG  GL+  V+K
Sbjct: 33  EPQELRRKLKHA--KRCRTNMVSSNLGLVIKVARKFGLKGTTIEDLIQEGINGLLHGVEK 90

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  RGFRL+TY +WWI+ +++   ++   + ++        LF    R+      I + 
Sbjct: 91  FDTSRGFRLSTYVLWWIELSVRRASVKRSIMCQVPMH-----LFDTHTRVLKTRARIFEE 145

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
                    +A  L  +  +V      +   +SL+  +   D  +      L    D + 
Sbjct: 146 RGTFPTNEEVATILGTTAQKVHLAANLMRHPKSLDDNVPGCDNVT-----LLEILPDPEV 200

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVR 270
           +  +   E+   +  L + +++L PRE+ +   R    +    TLE LS  F +SRERVR
Sbjct: 201 ESSLLVAEKALLKEQLDKVLNLLKPREKEVLTLRYGIGDGRDRTLEELSHHFNLSRERVR 260

Query: 271 QIEARAFKKVQESIQKQVELS 291
           QIE RA  K+ E   K++  S
Sbjct: 261 QIEKRALAKIHELGGKELLAS 281


>gi|302520387|ref|ZP_07272729.1| RNA polymerase sigma-B factor [Streptomyces sp. SPB78]
 gi|302429282|gb|EFL01098.1| RNA polymerase sigma-B factor [Streptomyces sp. SPB78]
          Length = 338

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 96/237 (40%), Gaps = 17/237 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +
Sbjct: 114 RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTV 173

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +   V  +AK L VS
Sbjct: 174 VGEIKRFFRDTSWSVRVPRRLQELRLA-----LTKTSDELAQKLDRSPTVPELAKALGVS 228

Query: 170 ESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E +V+            SL++     D       D L Y+    E V          R  
Sbjct: 229 EDDVVDGLAVGNAYTASSLDSPAPEDDGGEGSLADRLGYEDTALEGV--------EYRES 280

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   ++ L PRERRI   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 281 LKPLLAKLPPRERRIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 335


>gi|295836570|ref|ZP_06823503.1| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
 gi|295826098|gb|EDY44232.2| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
          Length = 338

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 104/237 (43%), Gaps = 15/237 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              +RLV  HL LV  +A  +R  G P+ ++     IGL+++V +FDPERG   +TY+  
Sbjct: 113 ELRNRLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPERGVEFSTYATP 172

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +   ++ +       V++     + RL      L      ++  + +   V  +A++L+
Sbjct: 173 TVVGEIKRHFRDKGWAVRVPRRLQELRLS-----LTSATAELSQLHGRSPTVHELAQRLS 227

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +SE EV+          +L+  +  +D  S    D L  +         E  E    R  
Sbjct: 228 ISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAED--------EALEGVEYRES 279

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   +  L PRE+RI   R      +T   ++ E  +S+  V ++ AR   ++++ +
Sbjct: 280 LKPLLEDLPPREKRILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLRDKL 334


>gi|220929692|ref|YP_002506601.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium cellulolyticum
           H10]
 gi|220000020|gb|ACL76621.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium cellulolyticum
           H10]
          Length = 249

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 45/243 (18%), Positives = 107/243 (44%), Gaps = 14/243 (5%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + GD  A   LV  ++ LV  I   ++  G  + ++   G+IGL++A+ KFD     + 
Sbjct: 16  AKAGDKQAQSVLVEKNVGLVWSIVKRFQNRGYEVDDLFQIGSIGLIKAINKFDTSYDVKF 75

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY++  I   ++ +I     ++K+  +  +        + +   + ++    +   +  
Sbjct: 76  STYAVPMIIGEIKRFIRDDG-IIKVSRSLKEVS-----SKARITKEIMSKELGREPTINE 129

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           IA+ +N+S  E++         ESL + I   + +     D +   ++   +V +     
Sbjct: 130 IAQHMNISPEELVMAIEAGCTPESLYSTIGDGENSPILLIDRIDAANNNSCEVDL----- 184

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  + + +  L+ RER+I   R  +E   T   ++    +S+ +V +IE +  + ++
Sbjct: 185 -IDKIAIRQILDTLDTRERQIIILRYFKE--KTQVQIAKLLGISQVQVSRIEKKILRDIK 241

Query: 282 ESI 284
             +
Sbjct: 242 SKM 244


>gi|318041080|ref|ZP_07973036.1| DNA-directed RNA polymerase sigma subunit (sigma70/sigma32)-like
           protein [Synechococcus sp. CB0101]
          Length = 279

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 64/290 (22%), Positives = 122/290 (42%), Gaps = 37/290 (12%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLA---KRYREHGD---------LSAAHRLVTSHLRL 60
                 Y+  I +IP+L  QEE  L    K + E  D           A  R+VT++LRL
Sbjct: 2   SDAFGDYLRTIGRIPLLTAQEEVHLGTIVKDWMESNDPSPALQRRGRRALQRIVTANLRL 61

Query: 61  VVKIAMGYRGY----GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           VV +A+ Y            ++V  GN+GL++A +K+DP RG++ +TY  WWI+ ++  Y
Sbjct: 62  VVTVALRYIRRLKHLAHDPMDLVQAGNLGLLRAAEKYDPTRGYKFSTYGYWWIRQSINRY 121

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVI-- 174
           +      ++I           NL  L     ++      P  V  +A+ L  S   ++  
Sbjct: 122 LQEHSGSIRIPV---------NLVSLANRADSLQSLRSHPMSVEQLAEALQESPQRLLYA 172

Query: 175 SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV 234
                 +   SL+  ++ SD + +   D +  DH              +    +   +  
Sbjct: 173 MAIQHRSNTVSLDQQLSGSDGDMT-LLDTVTDDHQP---------LITDDYRWMHSQLQH 222

Query: 235 LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L+  E  + + R  ++   +   ++     S+++V+++E  A  K++  +
Sbjct: 223 LSTPELTVIQLRYGEDKQRSFAEVARLIGRSKDQVQRLERHALTKLRRHL 272


>gi|332970514|gb|EGK09503.1| RNA polymerase sigma factor SigB [Desmospora sp. 8437]
          Length = 261

 Score =  158 bits (399), Expect = 1e-36,   Method: Composition-based stats.
 Identities = 56/252 (22%), Positives = 113/252 (44%), Gaps = 16/252 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L +RY+E  D      LV     LV  +A  +     P  ++V  G IGL+ A+K++DP
Sbjct: 17  DLIRRYQEESDEEIQEVLVDHFTPLVETLASKFTKGSEPFEDLVQVGMIGLLAALKRYDP 76

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           + G    ++++  I   ++ +I      V +     +        R+K   + +T    +
Sbjct: 77  DFGKSFESFAVPTIVGEIKRHIRDKTWSVHVPRRIKELG-----PRIKKAAEELTIRYQR 131

Query: 156 PEQVVAIAKKLNVSESEVISMNC--RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
              V  IA+ L+V+  EV+      R     S+++ I ++++ S      LV + D    
Sbjct: 132 SPSVDEIAQYLDVTPEEVLETMEMGRSYNAVSVDSPIEANNEGSQVTLLDLVGNRDA--- 188

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
                 E+ +++ +L ++  VL  RE+ I          ++ + +  E  +S+  V +++
Sbjct: 189 ----GFEKVDQQLLLQKAFQVLTDREQAIIRMTFFDN--LSQKQVGDELGISQMHVSRLQ 242

Query: 274 ARAFKKVQESIQ 285
            RA  K++E+I+
Sbjct: 243 RRALGKLREAIR 254


>gi|4218586|emb|CAA10725.1| chloroplast sigma factor [Triticum aestivum]
          Length = 461

 Score =  157 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 70/254 (27%), Positives = 121/254 (47%), Gaps = 10/254 (3%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L  R RE     A   L  S++RLV+ IA  Y   G+ +S+++  G IGL++ ++KFD 
Sbjct: 207 ELRSRMRES--FLAREVLTMSNIRLVISIAQKYDKLGVELSDLIQGGLIGLLRGIEKFDA 264

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            RGFR++TY  WWI+  +   +  +    ++ T  +++     L  ++G   A+ D  + 
Sbjct: 265 SRGFRISTYVYWWIRQGVSRALADNSKTFRLPTYLHER-----LIAIRGAKYALEDQGVS 319

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQV 214
           P     IAK LN+SE +V +    +    SL+     S +          + D +     
Sbjct: 320 P-TTQNIAKLLNISEKKVHNATEAVNKALSLDQQAFPSLNGLPGDTLHSYIEDQNVANDP 378

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIE 273
               EE   +  +     S L  RER I +      +   T E++S +F +SRERVRQ+ 
Sbjct: 379 WHGFEEWYLKEEVNKLLNSNLTERERDIIQLYHGIGKQCHTWEDISRQFGLSRERVRQVG 438

Query: 274 ARAFKKVQESIQKQ 287
             A +K+++  +++
Sbjct: 439 LIAMEKLKQRARRK 452


>gi|218133795|ref|ZP_03462599.1| hypothetical protein BACPEC_01684 [Bacteroides pectinophilus ATCC
           43243]
 gi|217991170|gb|EEC57176.1| hypothetical protein BACPEC_01684 [Bacteroides pectinophilus ATCC
           43243]
          Length = 256

 Score =  157 bits (398), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 56/256 (21%), Positives = 112/256 (43%), Gaps = 15/256 (5%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             L ++    GD  A +RLVT ++ L+  I   + G G  + ++   G+IGL++A+ KFD
Sbjct: 9   KELIEQAH-RGDKEARNRLVTENMGLIWSIVKRFTGRGHELEDLFQIGSIGLIKAIDKFD 67

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
                R +TY++  I   ++ ++     ++K+  +   K +   ++R +  LQ       
Sbjct: 68  TSYDVRFSTYAVPMITGEVKRFLRDDG-MIKVSRSL--KEIVVKVQRAREQLQKEMGEEP 124

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
             E    IA+ ++V E +++      +  ES+   I  SD N     D +         +
Sbjct: 125 SME---MIARAIDVPEEDIVMALEAGSEIESIYKTIYQSDGNEITLIDRVADRGSSGAGI 181

Query: 215 LIEKEERKNRRNM------LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           + E E     +        L + +  L   E+ +   R  ++   T   ++ E  +S+ +
Sbjct: 182 VPECEWTDYEKEQLINHMVLKQILDELPENEKNLILLRYFRDQ--TQTQVAKEMGISQVQ 239

Query: 269 VRQIEARAFKKVQESI 284
           V +IE R   +++E I
Sbjct: 240 VSRIEKRILLRLREKI 255


>gi|257784260|ref|YP_003179477.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Atopobium
           parvulum DSM 20469]
 gi|257472767|gb|ACV50886.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Atopobium
           parvulum DSM 20469]
          Length = 284

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 55/262 (20%), Positives = 115/262 (43%), Gaps = 12/262 (4%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           IP  +K     L  +Y+E  D     +L+ SHL LV  +A  ++  G P+ +++  G IG
Sbjct: 31  IPAWDKDRTRQLFAQYKETKDSEVRDQLIVSHLNLVRFLASKFKNRGEPLDDLIQVGTIG 90

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A+ +F+P+RG    TY+   I   ++ +       V++      +RL     ++   
Sbjct: 91  LIKAIDRFEPDRGLEFTTYATPTIMGEIKRHFRDKGWSVRVP-----RRLQELSSKINQV 145

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
              +T    +   +  IA++L+ +  E++      +   S+      S  +  +    + 
Sbjct: 146 TDDLTKELQRSPSIEEIAQRLDTNVEEILEAMESSSAYSSVPLEGGGSGADGDETPSII- 204

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
                Q     E     + R +L  ++   +PRE+ I   R +    +T   ++ +  +S
Sbjct: 205 ----DQYVTEDEDLAGSDDRIVLDEAIRDFSPREQEIIRMRFV--EGLTQVEIAEKLNIS 258

Query: 266 RERVRQIEARAFKKVQESIQKQ 287
           + +V ++  R  K++QE I  +
Sbjct: 259 QVQVSRLLRRTLKRIQEKIDPE 280


>gi|224007213|ref|XP_002292566.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220971428|gb|EED89762.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 338

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 65/334 (19%), Positives = 139/334 (41%), Gaps = 64/334 (19%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYR-------EHGDLS------------------ 48
             +S YI  + +  +L K++E +L ++ R       +  DL                   
Sbjct: 1   DSISTYIKSLGQHELLYKEDEVLLGRQVRLLMGLEGKRRDLEEELLRPPTFAQWASATNH 60

Query: 49  --------------AAHRLVTSHLRLVVKIAMG-----------YRGYGLPISEVVSEGN 83
                         A   L+ ++LRLV+ +A             +    +   +   +G 
Sbjct: 61  TVPSLKQQIRRSQRAKAALIEANLRLVITVARQAVKKSPFRSSSHAASSVQFQDACQQGI 120

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL +A +KFDPE GFR +TY++WWI+  + + +      V++  +A        +  ++
Sbjct: 121 IGLTRATEKFDPELGFRFSTYAIWWIQKEVAKNVNEQSRTVRVPGSA-----IKKINDIR 175

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS-------SDKN 196
              + + +   +      +A+K  ++  ++          +SL+  I+S       +   
Sbjct: 176 IQERVLMNELGRRPSDDEVAEKCGLTVEKLNFYRQSAKEVKSLDKKIDSRTGKGSAASGG 235

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVT 254
               +   ++  D +     E  +++  +  + R +  L+PRE+ +   R   ++  P T
Sbjct: 236 DDDGKTMEIFVRDTEHPSPSELIDQQMMQQDIRRLVKTLSPREQAVIRLRFGLDDGKPQT 295

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           L ++  +F V +ER+++IEARA  K+++  +  V
Sbjct: 296 LGDIGEKFGVEKERIKKIEARALLKLRQPSRSSV 329


>gi|295837881|ref|ZP_06824814.1| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
 gi|295826719|gb|EDY46528.2| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
          Length = 286

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 96/237 (40%), Gaps = 17/237 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +
Sbjct: 62  RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTV 121

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +   V  +AK L VS
Sbjct: 122 VGEIKRFFRDTSWSVRVPRRLQELRLA-----LTKTSDELAQKLDRSPTVPELAKALGVS 176

Query: 170 ESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E +V+            SL++     D       D L Y+    E V          R  
Sbjct: 177 EDDVVDGLAVGNAYTASSLDSPAPEDDGGEGSLADRLGYEDTALEGV--------EYRES 228

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   ++ L PRERRI   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 229 LKPLLAKLPPRERRIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 283


>gi|169823706|ref|YP_001691317.1| RNA polymerase sigma B factor [Finegoldia magna ATCC 29328]
 gi|302380124|ref|ZP_07268597.1| RNA polymerase sigma-70 factor, sigma-B/F/G family protein
           [Finegoldia magna ACS-171-V-Col3]
 gi|303234447|ref|ZP_07321085.1| RNA polymerase sigma-70 factor, sigma-B/F/G family protein
           [Finegoldia magna BVS033A4]
 gi|167830511|dbj|BAG07427.1| RNA polymerase sigma B factor [Finegoldia magna ATCC 29328]
 gi|302312066|gb|EFK94074.1| RNA polymerase sigma-70 factor, sigma-B/F/G family protein
           [Finegoldia magna ACS-171-V-Col3]
 gi|302494402|gb|EFL54170.1| RNA polymerase sigma-70 factor, sigma-B/F/G family protein
           [Finegoldia magna BVS033A4]
          Length = 258

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 58/267 (21%), Positives = 122/267 (45%), Gaps = 19/267 (7%)

Query: 29  LEKQEE---YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           + K+E+     L  +++E  D      LV  +L +   +A  Y G G+   ++     IG
Sbjct: 6   ISKEEQENIKELFLKFQETRDKKTRDTLVEKNLYIAEILAKKYTGRGIEYDDLYQVACIG 65

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L+ A+ ++DP +G+  ++Y+   I   +++Y      ++++     +  L   +   K H
Sbjct: 66  LIYAIDRYDPSKGYEFSSYATPTIVGEIKKYFRDKGWVIRVPRRIQE--LNKKVATAKVH 123

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDW 203
           L        K   V  IA  L++S  EV+ +    ++   +SL+  I+ S+++       
Sbjct: 124 LSQTMQ---KSPTVEDIADYLSISNEEVLEVLEGAKVYAPQSLDQSIDQSNEDRETNLSD 180

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L+ + D           +   R+++ R M  LN  ER+I   R    +  T   ++ E +
Sbjct: 181 LIGEEDKDM-------LKFENRDLINRCMQDLNKVERKILLGRYF--DKKTQIVIAEELD 231

Query: 264 VSRERVRQIEARAFKKVQESIQKQVEL 290
           +S+  V ++E +  KK + ++++Q+E 
Sbjct: 232 ISQMTVSRMEKKILKKFKAALKEQLEF 258


>gi|323490578|ref|ZP_08095784.1| RNA polymerase sigma-B factor [Planococcus donghaensis MPA1U2]
 gi|323395844|gb|EGA88684.1| RNA polymerase sigma-B factor [Planococcus donghaensis MPA1U2]
          Length = 260

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 56/261 (21%), Positives = 120/261 (45%), Gaps = 24/261 (9%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
            K++     + Y++  D  A   LV ++ RLV  IA  Y        ++   G +GL+ A
Sbjct: 11  TKEQVLDWIEAYQKTEDEEAQTNLVLNYKRLVESIARKYSNGKSYHEDIAQVGMLGLLGA 70

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           ++++DP  G     +++  I   ++ ++      + +     +        R+K  ++ +
Sbjct: 71  IRRYDPSYGRSFEAFAVPTIIGEIKRFLRDKTWAIHVPRRIKELG-----PRIKATVEVL 125

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDW 203
           T    +  QV  IA+ L+V E +++           L+ D SL A    SD ++    D 
Sbjct: 126 TTELQRSPQVWEIAEYLDVEEDDILEAMEMGKSYQALSMDHSLEA---DSDGSTITLFDV 182

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  + DG         E+ ++R ++  +M+VL+ RE++I +   +    ++ +    +  
Sbjct: 183 VGQEDDGY--------EKADQRMLVAEAMNVLSEREKQIIQFTYI--EQLSQKEAGDKLG 232

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+  V +++ +A KK+QE+I
Sbjct: 233 ISQMHVSRLQRKAIKKLQEAI 253


>gi|197723817|gb|ACH72688.1| RNA polymerase sigma-37 factor [Listeria marthii]
          Length = 256

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 61/263 (23%), Positives = 121/263 (46%), Gaps = 24/263 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 11  KEKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 70

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +++D   G     +++  I   ++ ++      V +     +        ++K  ++ +T
Sbjct: 71  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELT 125

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWL 204
                  Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +
Sbjct: 126 RELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVV 182

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++
Sbjct: 183 GGTDDGF--------ERVNQRMLLEKVLPVLDEREQKILQYTFIEN--RSQKETGELLDI 232

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           S+  V +I+ +A KK++E++Q +
Sbjct: 233 SQMHVSRIQRQAIKKLREALQNE 255


>gi|126649718|ref|ZP_01721954.1| sporulation sigma factor SigG [Bacillus sp. B14905]
 gi|126593437|gb|EAZ87382.1| sporulation sigma factor SigG [Bacillus sp. B14905]
          Length = 257

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 54/257 (21%), Positives = 113/257 (43%), Gaps = 17/257 (6%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L+ +E   L  R +  G++     LV  +LRLV+ I   +   G    ++   G IG
Sbjct: 15  LPILKHEEMKELFIRLQ-AGEIEIREELVMCNLRLVLSIVGRFAYRGEQADDLFQVGCIG 73

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           LM+A+  FD +   R +TY++  I   ++ ++    +L ++  +          + ++  
Sbjct: 74  LMKAIDHFDLKHNVRFSTYAVPMIIGEIRRHLRDHHAL-RVSRSLRDI----AYKAMQAK 128

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            Q IT+ NL+   +  IA  + + + +V+     +    SL   I S   ++    D L 
Sbjct: 129 EQWITE-NLREPTIEEIADMIEMKKEDVLFALDAIQDPMSLQEPIYSDGGDAVYMMDQLR 187

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            D   ++Q +            +  S+  L+ R++ I   R       T   ++ E  +S
Sbjct: 188 DDDVSEDQWVA--------YVSVKESLQKLDERQQMIVAKRFYYGE--TQTEIAKELGIS 237

Query: 266 RERVRQIEARAFKKVQE 282
           + ++ ++E  A + +Q+
Sbjct: 238 QAQISRLEKNAIETMQK 254


>gi|260589293|ref|ZP_05855206.1| RNA polymerase sigma-F factor [Blautia hansenii DSM 20583]
 gi|331082700|ref|ZP_08331823.1| hypothetical protein HMPREF0992_00747 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|260540374|gb|EEX20943.1| RNA polymerase sigma-F factor [Blautia hansenii DSM 20583]
 gi|330400319|gb|EGG79961.1| hypothetical protein HMPREF0992_00747 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 237

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 64/241 (26%), Positives = 113/241 (46%), Gaps = 16/241 (6%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GD SA   L   ++ LV  IA  ++  G  + ++V  G IGL++A+ KFD     R +T
Sbjct: 13  QGDKSARDILTEKNMGLVHSIARRFQNRGAELEDLVQIGCIGLLKAIDKFDLSYEVRFST 72

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y++  I   ++ ++     +VK+  +  +        +     + +     +   +  IA
Sbjct: 73  YAVPMITGEIKRFLRDDG-MVKVSRSLKEAA-----GKAYAVREELLMKTGQEPSMEEIA 126

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           K+L+VSE E+I      A  ESL   I  SD +    +D L Y+ D QE+VL        
Sbjct: 127 KELSVSEEELIMAMESSAQVESLQKTIYQSDGSDIALEDKLPYEKDEQEEVL-------- 178

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            + +L   +  LN RER +   R  +E   T  +++    +S+ +V ++E +  K ++E 
Sbjct: 179 DKLLLEDILGSLNARERELIYLRFFKE--KTQTSIAKMMGMSQVQVSRLEKKILKALRER 236

Query: 284 I 284
           I
Sbjct: 237 I 237


>gi|300689719|ref|YP_003750714.1| RNA polymerase sigma factor [Ralstonia solanacearum PSI07]
 gi|299076779|emb|CBM09897.1| putative RNA polymerase sigma factor [Ralstonia solanacearum PSI07]
          Length = 907

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 54/245 (22%), Positives = 107/245 (43%), Gaps = 19/245 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              ++ ++LRLV+ IA      GL + +++ EGN+GL++AV +FD  RGFR +T ++WWI
Sbjct: 550 RDHMMQANLRLVMDIARHRMHSGLRVEDLIQEGNLGLLKAVDRFDWRRGFRFSTMAIWWI 609

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           K  +   I  +   +++    +QK     + R +   ++      KP  +   A   N++
Sbjct: 610 KQQIGRGIFDTALEIRLPVHIHQK-----ISRGRRETESFEHVRGKPASLSERATICNMT 664

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             +       L+   S+            +    + Y    +      +    +   ++ 
Sbjct: 665 LDKFELAARALSEPLSI------------EGAQQVGYFKSEESDEPFARMSEDDDARLVE 712

Query: 230 RSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             ++ L  ++  +   R        +TLE +     V+RERVRQIEA A +K+     ++
Sbjct: 713 EVLTKLKTKDAEVLRLRFGIGVLEALTLEQIGEILGVTRERVRQIEAAAMQKLSSPFSRE 772

Query: 288 VELSS 292
             + +
Sbjct: 773 ALMKA 777


>gi|160939297|ref|ZP_02086648.1| hypothetical protein CLOBOL_04191 [Clostridium bolteae ATCC
           BAA-613]
 gi|158438260|gb|EDP16020.1| hypothetical protein CLOBOL_04191 [Clostridium bolteae ATCC
           BAA-613]
          Length = 240

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 56/255 (21%), Positives = 114/255 (44%), Gaps = 16/255 (6%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
              +E +        GD +A  +LV  ++ L+  I   + G G  + ++   G+IGL++A
Sbjct: 2   TAMDETMKLINMAHEGDKAARDQLVMDNVGLIWSIVRRFSGRGYEMEDLFQIGSIGLIKA 61

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + KFD     + +TY++  I   ++ ++     ++K+  +  +  +     +++   + +
Sbjct: 62  IDKFDTGFDVKFSTYAVPMITGEIKRFLRDDG-MIKVSRSIKELGV-----KVRAAREEM 115

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
           T    +   +  IA +L  S  EV +     A  ESL    +S D+NS+   D L  D++
Sbjct: 116 TYALGREPTIEEIAGRLGTSREEVAASLEAAAEVESLYRPADSGDENSTYLMDRLAQDNN 175

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
             E +L         R +L   M  L   +R I   R       T   ++ E  +S+ +V
Sbjct: 176 DHEDLL--------NRMVLKDLMEGLEEEQREIILRRYFYNE--TQTQIAGELGISQVQV 225

Query: 270 RQIEARAFKKVQESI 284
            ++E R  K++++ +
Sbjct: 226 SRLEKRILKEMRKKL 240


>gi|256004731|ref|ZP_05429707.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium thermocellum
           DSM 2360]
 gi|281416836|ref|ZP_06247856.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium thermocellum
           JW20]
 gi|255991324|gb|EEU01430.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium thermocellum
           DSM 2360]
 gi|281408238|gb|EFB38496.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium thermocellum
           JW20]
 gi|316941118|gb|ADU75152.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium thermocellum
           DSM 1313]
          Length = 248

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 47/233 (20%), Positives = 107/233 (45%), Gaps = 15/233 (6%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  ++ LV  I   ++  G    ++   G IGL++A+ KFD     + +TY++  I   
Sbjct: 29  LVEKNVGLVWSIVRRFQNRGYEAEDIFQIGCIGLIKAINKFDCSYDVKFSTYAVPMIIGE 88

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           ++ +I     ++K+  +  +        + +   + ++    +   V  I+++L +   E
Sbjct: 89  IKRFIRDDG-MIKVSRSLKELA-----NKARITKEIMSKELGREPTVGEISEQLGIPVEE 142

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           V+         ESL + +   D +S+   D +  + + QE  +++       R  L + +
Sbjct: 143 VVMAMEASCTPESLYSTLGEGDNSSTLLIDKIANESENQEVDIVD-------RIDLRKVL 195

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             L PRE++I   R  +E   T   ++    +S+ +V +IE +  +++++ I+
Sbjct: 196 DTLKPREKQIIVLRYFKE--KTQVQIAKMLGISQVQVSRIEKKILEEIRKKIK 246


>gi|125972644|ref|YP_001036554.1| RNA polymerase, sigma 28 subunit [Clostridium thermocellum ATCC
           27405]
 gi|125712869|gb|ABN51361.1| RNA polymerase, sigma subunit, RpoX/SigF [Clostridium thermocellum
           ATCC 27405]
          Length = 246

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 47/233 (20%), Positives = 107/233 (45%), Gaps = 15/233 (6%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  ++ LV  I   ++  G    ++   G IGL++A+ KFD     + +TY++  I   
Sbjct: 27  LVEKNVGLVWSIVRRFQNRGYEAEDIFQIGCIGLIKAINKFDCSYDVKFSTYAVPMIIGE 86

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           ++ +I     ++K+  +  +        + +   + ++    +   V  I+++L +   E
Sbjct: 87  IKRFIRDDG-MIKVSRSLKELA-----NKARITKEIMSKELGREPTVGEISEQLGIPVEE 140

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           V+         ESL + +   D +S+   D +  + + QE  +++       R  L + +
Sbjct: 141 VVMAMEASCTPESLYSTLGEGDNSSTLLIDKIANESENQEVDIVD-------RIDLRKVL 193

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             L PRE++I   R  +E   T   ++    +S+ +V +IE +  +++++ I+
Sbjct: 194 DTLKPREKQIIVLRYFKE--KTQVQIAKMLGISQVQVSRIEKKILEEIRKKIK 244


>gi|197723819|gb|ACH72689.1| RNA polymerase sigma-37 factor [Listeria marthii]
          Length = 257

 Score =  157 bits (397), Expect = 2e-36,   Method: Composition-based stats.
 Identities = 61/263 (23%), Positives = 121/263 (46%), Gaps = 24/263 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +++D   G     +++  I   ++ ++      V +     +        ++K  ++ +T
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELT 126

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWL 204
                  Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +
Sbjct: 127 RELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVV 183

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++
Sbjct: 184 GGTDDGF--------ERVNQRMLLEKVLPVLDEREQKILQYTFIEN--RSQKETGELLDI 233

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           S+  V +I+ +A KK++E++Q +
Sbjct: 234 SQMHVSRIQRQAIKKLREALQNE 256


>gi|323450165|gb|EGB06048.1| hypothetical protein AURANDRAFT_11909 [Aureococcus anophagefferens]
          Length = 325

 Score =  156 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 64/258 (24%), Positives = 116/258 (44%), Gaps = 26/258 (10%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +    L+  +LRLV+ +A  Y   GL  +++  EGN GL +A  +FDP +GFR +TY++
Sbjct: 76  KACREELIQRNLRLVLSVAKRYGDCGLAFTDLCQEGNFGLAKACDRFDPSKGFRFSTYAV 135

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   +      +++ T  ++K     LRR+K H  A+     +      IA+++
Sbjct: 136 WWIRQAVAHAVAHQSRTIRLPTHVHEK-----LRRMKKHKVALEKQTGRDATDDEIAREM 190

Query: 167 NVSESEVISMNCRLAGDESLNALINS----------------SDKNSSQWQDWLVYDHDG 210
           ++   ++  +     G  S +    +                S  + +Q  D L      
Sbjct: 191 SLDADKLRRLRRAARGTVSTDVDAENLGSRRGAAPGNGRRGASYASGAQLADLLHDATQH 250

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRER 268
            E+   E   +   R ML   +     RE  +       +   P TL  ++  F+++RER
Sbjct: 251 PERDAAESLLKDEVRRMLDDDLED---REEDVLNRHFGLDGRRPETLAEIAVRFDLTRER 307

Query: 269 VRQIEARAFKKVQESIQK 286
           +RQIE  AF K+++  + 
Sbjct: 308 IRQIEKSAFAKLRQPHRS 325


>gi|310815187|ref|YP_003963151.1| RNA polymerase, sigma 32 subunit, RpoH [Ketogulonicigenium vulgare
           Y25]
 gi|308753922|gb|ADO41851.1| RNA polymerase, sigma 32 subunit, RpoH [Ketogulonicigenium vulgare
           Y25]
          Length = 809

 Score =  156 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 54/242 (22%), Positives = 103/242 (42%), Gaps = 21/242 (8%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            SA   L+  HL  V + A      G    +V     +GL ++ ++FDPERG+R   Y+ 
Sbjct: 578 ESATEHLIREHLPYVRRFASRNVDEGEDPEDVFQVAFMGLQRSTRRFDPERGYRFLIYAT 637

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           +W++ A+  +     + ++I    N+K     + +L   L+ +          + +A++L
Sbjct: 638 YWMRQAITRWRADEGAAIRIPVHRNEK-----ITKLDRALERLDVRVGGAVSDLELAEEL 692

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             +  EV                I    +  +   DW   D+   E    +  ++     
Sbjct: 693 EWTIDEVKQ-----------FRGIPREAEYPASLDDW---DNLLPEPSEADVFDQTETER 738

Query: 227 MLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +L  +++ L  R+  +   R    +E  +TLE +   + V+RER+RQIEA+A   +    
Sbjct: 739 ILADALAELPERQADVLRMRFGIGRETDMTLEEVGQIYGVTRERIRQIEAKALDHLSHPG 798

Query: 285 QK 286
           +K
Sbjct: 799 RK 800


>gi|238924598|ref|YP_002938114.1| sporulation sigma factor SigG [Eubacterium rectale ATCC 33656]
 gi|238876273|gb|ACR75980.1| sporulation sigma factor SigG [Eubacterium rectale ATCC 33656]
          Length = 259

 Score =  156 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 46/263 (17%), Positives = 114/263 (43%), Gaps = 17/263 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+  E+  L ++ ++ GD +A  + +  +LRLV+ +   +  +   + ++   G 
Sbjct: 14  SKLPVLKDDEKEELFEKIKK-GDKAAREKYIRGNLRLVLSVIRRFSNHNENMDDLFQIGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+++  FDP  G + +TY++  I   ++ Y+  + S  +I      + L     +  
Sbjct: 73  IGLMKSIDNFDPTIGVKFSTYAVPMIIGEVRRYLRDN-SAYRIP-----RSLRDTAYQAI 126

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
              + ++   +    +  I+K   + E++++     +    SL   + +   ++    D 
Sbjct: 127 KSKEKLSRKLVHEPSLAEISKDCGIPENDILYALDAIQTPLSLFDPVYTDGGDTLYVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    + +E  +         + +  R+        R+I + R       T   ++ E  
Sbjct: 187 ISDKKNKEEAWVKNLVLDDALKLLDDRA--------RQIIKLRFF--EGKTQIEVAEEIN 236

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+ +V ++E  A K +   ++ 
Sbjct: 237 ISQAQVSRLEKNALKNMHGYLEA 259


>gi|16802936|ref|NP_464421.1| RNA polymerase sigma factor SigB [Listeria monocytogenes EGD-e]
 gi|47094902|ref|ZP_00232516.1| RNA polymerase sigma-B factor [Listeria monocytogenes str. 1/2a
           F6854]
 gi|224499433|ref|ZP_03667782.1| RNA polymerase sigma factor SigB [Listeria monocytogenes Finland
           1988]
 gi|224503136|ref|ZP_03671443.1| RNA polymerase sigma factor SigB [Listeria monocytogenes FSL
           R2-561]
 gi|254827839|ref|ZP_05232526.1| SigB [Listeria monocytogenes FSL N3-165]
 gi|254832139|ref|ZP_05236794.1| RNA polymerase sigma factor SigB [Listeria monocytogenes 10403S]
 gi|254898932|ref|ZP_05258856.1| RNA polymerase sigma factor SigB [Listeria monocytogenes J0161]
 gi|254911580|ref|ZP_05261592.1| RNA polymerase sigma-B factor [Listeria monocytogenes J2818]
 gi|254935906|ref|ZP_05267603.1| RNA polymerase sigma-B factor [Listeria monocytogenes F6900]
 gi|284801225|ref|YP_003413090.1| RNA polymerase sigma factor SigB [Listeria monocytogenes 08-5578]
 gi|284994367|ref|YP_003416135.1| RNA polymerase sigma factor SigB [Listeria monocytogenes 08-5923]
 gi|289434163|ref|YP_003464035.1| RNA polymerase sigma-B factor SigB [Listeria seeligeri serovar 1/2b
           str. SLCC3954]
 gi|315281577|ref|ZP_07870178.1| RNA polymerase sigma-B factor [Listeria marthii FSL S4-120]
 gi|22770508|gb|AAN06629.1|AF497201_1 sigma factor B [Listeria monocytogenes]
 gi|22770512|gb|AAN06631.1|AF497203_1 sigma factor B [Listeria monocytogenes]
 gi|22770532|gb|AAN06641.1|AF497213_1 sigma factor B [Listeria monocytogenes]
 gi|3298587|gb|AAC38791.1| Sigma B [Listeria monocytogenes]
 gi|16410298|emb|CAC98973.1| RNA polymerase sigma-37 factor (sigma-B) [Listeria monocytogenes
           EGD-e]
 gi|47016784|gb|EAL07703.1| RNA polymerase sigma-B factor [Listeria monocytogenes str. 1/2a
           F6854]
 gi|66968488|gb|AAY59623.1| SigB [Listeria seeligeri]
 gi|112363462|gb|ABI16056.1| sigma B [Listeria monocytogenes]
 gi|153582303|emb|CAO79793.1| sigma factor B [Listeria monocytogenes]
 gi|153582305|emb|CAO79794.1| sigma factor B [Listeria monocytogenes]
 gi|223700498|gb|ACN20365.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700502|gb|ACN20368.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700506|gb|ACN20371.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700514|gb|ACN20377.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700518|gb|ACN20380.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700522|gb|ACN20383.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700526|gb|ACN20386.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700530|gb|ACN20389.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700534|gb|ACN20392.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700538|gb|ACN20395.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700542|gb|ACN20398.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700546|gb|ACN20401.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700550|gb|ACN20404.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700554|gb|ACN20407.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700558|gb|ACN20410.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700562|gb|ACN20413.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700566|gb|ACN20416.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700570|gb|ACN20419.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700574|gb|ACN20422.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700578|gb|ACN20425.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700582|gb|ACN20428.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700586|gb|ACN20431.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700590|gb|ACN20434.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700594|gb|ACN20437.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700598|gb|ACN20440.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700602|gb|ACN20443.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700606|gb|ACN20446.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700610|gb|ACN20449.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700614|gb|ACN20452.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700618|gb|ACN20455.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700622|gb|ACN20458.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700626|gb|ACN20461.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700630|gb|ACN20464.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700634|gb|ACN20467.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700638|gb|ACN20470.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700642|gb|ACN20473.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700646|gb|ACN20476.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700650|gb|ACN20479.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700654|gb|ACN20482.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700658|gb|ACN20485.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700662|gb|ACN20488.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700666|gb|ACN20491.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700670|gb|ACN20494.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700674|gb|ACN20497.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700678|gb|ACN20500.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700682|gb|ACN20503.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700686|gb|ACN20506.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700690|gb|ACN20509.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700694|gb|ACN20512.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700698|gb|ACN20515.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700702|gb|ACN20518.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700706|gb|ACN20521.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700710|gb|ACN20524.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700714|gb|ACN20527.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700718|gb|ACN20530.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700722|gb|ACN20533.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700726|gb|ACN20536.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700730|gb|ACN20539.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700734|gb|ACN20542.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700738|gb|ACN20545.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700742|gb|ACN20548.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700746|gb|ACN20551.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700750|gb|ACN20554.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700754|gb|ACN20557.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700758|gb|ACN20560.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700762|gb|ACN20563.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700766|gb|ACN20566.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700770|gb|ACN20569.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700774|gb|ACN20572.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700778|gb|ACN20575.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700782|gb|ACN20578.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700786|gb|ACN20581.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700790|gb|ACN20584.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700794|gb|ACN20587.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700798|gb|ACN20590.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700802|gb|ACN20593.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700806|gb|ACN20596.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700810|gb|ACN20599.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700814|gb|ACN20602.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700818|gb|ACN20605.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700822|gb|ACN20608.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700826|gb|ACN20611.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700830|gb|ACN20614.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700834|gb|ACN20617.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700838|gb|ACN20620.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700842|gb|ACN20623.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700846|gb|ACN20626.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700850|gb|ACN20629.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700854|gb|ACN20632.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700858|gb|ACN20635.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700862|gb|ACN20638.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700866|gb|ACN20641.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700870|gb|ACN20644.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700874|gb|ACN20647.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700878|gb|ACN20650.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700882|gb|ACN20653.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700886|gb|ACN20656.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700890|gb|ACN20659.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700894|gb|ACN20662.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700898|gb|ACN20665.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700902|gb|ACN20668.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700906|gb|ACN20671.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700910|gb|ACN20674.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700914|gb|ACN20677.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700918|gb|ACN20680.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700922|gb|ACN20683.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700926|gb|ACN20686.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700930|gb|ACN20689.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700934|gb|ACN20692.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700938|gb|ACN20695.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700942|gb|ACN20698.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700946|gb|ACN20701.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700950|gb|ACN20704.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700954|gb|ACN20707.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700958|gb|ACN20710.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700962|gb|ACN20713.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700966|gb|ACN20716.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700970|gb|ACN20719.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700974|gb|ACN20722.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700978|gb|ACN20725.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700982|gb|ACN20728.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700986|gb|ACN20731.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700990|gb|ACN20734.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700994|gb|ACN20737.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|223700998|gb|ACN20740.1| RNA polymerase sigma factor SigB [Listeria monocytogenes]
 gi|258600220|gb|EEW13545.1| SigB [Listeria monocytogenes FSL N3-165]
 gi|258608494|gb|EEW21102.1| RNA polymerase sigma-B factor [Listeria monocytogenes F6900]
 gi|284056787|gb|ADB67728.1| RNA polymerase sigma factor SigB [Listeria monocytogenes 08-5578]
 gi|284059834|gb|ADB70773.1| RNA polymerase sigma factor SigB [Listeria monocytogenes 08-5923]
 gi|289170407|emb|CBH26947.1| RNA polymerase sigma-B factor SigB [Listeria seeligeri serovar 1/2b
           str. SLCC3954]
 gi|293589526|gb|EFF97860.1| RNA polymerase sigma-B factor [Listeria monocytogenes J2818]
 gi|302034427|gb|ADK92367.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|302034429|gb|ADK92368.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|302034431|gb|ADK92369.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|302034433|gb|ADK92370.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|302034439|gb|ADK92373.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|302034441|gb|ADK92374.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|302034443|gb|ADK92375.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|302034445|gb|ADK92376.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|313614786|gb|EFR88329.1| RNA polymerase sigma-B factor [Listeria marthii FSL S4-120]
          Length = 259

 Score =  156 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 61/263 (23%), Positives = 121/263 (46%), Gaps = 24/263 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +++D   G     +++  I   ++ ++      V +     +        ++K  ++ +T
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELT 126

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWL 204
                  Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +
Sbjct: 127 RELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVV 183

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++
Sbjct: 184 GGTDDGF--------ERVNQRMLLEKVLPVLDEREQKILQYTFIEN--RSQKETGELLDI 233

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           S+  V +I+ +A KK++E++Q +
Sbjct: 234 SQMHVSRIQRQAIKKLREALQNE 256


>gi|313619763|gb|EFR91370.1| RNA polymerase sigma-B factor [Listeria innocua FSL S4-378]
          Length = 259

 Score =  156 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 61/263 (23%), Positives = 121/263 (46%), Gaps = 24/263 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQENGDEDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +++D   G     +++  I   ++ ++      V +     +        ++K  ++ +T
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELT 126

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWL 204
                  Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +
Sbjct: 127 RELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVV 183

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++
Sbjct: 184 GGTDDGF--------ERVNQRMLLEKVLPVLDEREQKILQYTFIEN--RSQKETGELLDI 233

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           S+  V +I+ +A KK++E++Q +
Sbjct: 234 SQMHVSRIQRQAIKKLREALQNE 256


>gi|297157365|gb|ADI07077.1| putative sigma factor [Streptomyces bingchenggensis BCW-1]
          Length = 242

 Score =  156 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 54/237 (22%), Positives = 103/237 (43%), Gaps = 15/237 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              + LV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+  
Sbjct: 17  ELRNTLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATP 76

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +   ++ +       V++     + RL      L      ++  + +   V  +A++L+
Sbjct: 77  TVVGEIKRHFRDKGWAVRVPRRLQELRLS-----LTTATAELSQRHGRAPTVHELAEQLS 131

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +SE EV+          +L+  +  +D  S    D L  +         E  E    R  
Sbjct: 132 ISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAED--------EALEGVEYRES 183

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   +  L PRE++I   R      +T   ++ E  +S+  V ++ AR   +++E +
Sbjct: 184 LKPLLEDLPPREKKILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLRERL 238


>gi|82949200|dbj|BAE53364.1| sigma factor [Streptomyces sp. AJ9463]
          Length = 195

 Score =  156 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 50/198 (25%), Positives = 93/198 (46%), Gaps = 31/198 (15%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYRE--------------------------HGDLSAAHR 52
           Y+ +I K+P+L  ++E  LAKR                                  A + 
Sbjct: 2   YLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANSDKLAPKLKRELEIIAEDGRRAKNH 61

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ A
Sbjct: 62  LLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQA 121

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +      ++I     +  +   L R++  +         PE    +AK+L+++  +
Sbjct: 122 ITRAMADQARTIRIPVHMVE--VINKLARVQRQMLQDLGREPTPE---ELAKELDMTPEK 176

Query: 173 VISMNCRLAGDESLNALI 190
           VI +        SL+  +
Sbjct: 177 VIEVQKYGREPISLHTPL 194


>gi|111225338|ref|YP_716132.1| SigH putative RNA polymerase sigma factor [Frankia alni ACN14a]
 gi|111152870|emb|CAJ64617.1| SigH putative RNA polymerase sigma factor [Frankia alni ACN14a]
          Length = 299

 Score =  156 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 61/257 (23%), Positives = 107/257 (41%), Gaps = 23/257 (8%)

Query: 35  YVLAKRYRE--HGDLS---AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             L  R  E   GD        +LV  HL LV  +A  +R  G P+ ++V    IGL+++
Sbjct: 55  RALFVRLAELPEGDAERAAIRDQLVRMHLPLVEYLARRFRNRGEPLDDLVQVATIGLIKS 114

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V +FDPERG   +TY+   I   ++ +       +++     + +L      L      +
Sbjct: 115 VDRFDPERGVEFSTYATPTIVGEIKRHFRDKGWAIRVPRRLQELKLS-----LTKATSEL 169

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
           +    +   V  IA+ L +SE +V+    +       SL+A  +  D+  +      V D
Sbjct: 170 SQTLGRSPTVSEIARHLQMSEEDVLEGLESANAYSAVSLDAPDSGDDEAPAVADTLGVQD 229

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
                    E  E    R  L   +  L PRE+RI   R      +T   +++E  +S+ 
Sbjct: 230 ---------ESLEGVEYRESLKPLLEKLPPREKRILLLRFFGN--MTQSQIATELGISQM 278

Query: 268 RVRQIEARAFKKVQESI 284
            V ++ AR   +++  +
Sbjct: 279 HVSRLLARTLAQLRRGL 295


>gi|255022641|ref|ZP_05294627.1| RNA polymerase sigma factor SigB [Listeria monocytogenes FSL
           J1-208]
 gi|22770504|gb|AAN06627.1|AF497199_1 sigma factor B [Listeria monocytogenes]
          Length = 259

 Score =  156 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 61/263 (23%), Positives = 121/263 (46%), Gaps = 24/263 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQENGDEDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +++D   G     +++  I   ++ ++      V +     +        ++K  ++ +T
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELT 126

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWL 204
                  Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +
Sbjct: 127 RELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVV 183

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++
Sbjct: 184 GGTDDGF--------ERVNQRMLLEKVLPVLDEREQKILQFTFIEN--RSQKETGELLDI 233

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           S+  V +I+ +A KK++E++Q +
Sbjct: 234 SQMHVSRIQRQAIKKLREALQNE 256


>gi|15232364|ref|NP_190960.1| SIGC (RNA POLYMERASE SIGMA-SUBUNIT C); DNA binding / DNA-directed
           RNA polymerase/ sigma factor/ transcription factor
           [Arabidopsis thaliana]
 gi|2353175|gb|AAB69386.1| sigma factor 3 [Arabidopsis thaliana]
 gi|2463554|dbj|BAA22530.1| SigC [Arabidopsis thaliana]
 gi|5478585|dbj|BAA82450.1| sigma factor SigC [Arabidopsis thaliana]
 gi|7630012|emb|CAB88354.1| sigma factor SigC [Arabidopsis thaliana]
 gi|133778870|gb|ABO38775.1| At3g53920 [Arabidopsis thaliana]
 gi|332645638|gb|AEE79159.1| RNApolymerase sigma-subunit C [Arabidopsis thaliana]
          Length = 571

 Score =  156 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 58/236 (24%), Positives = 113/236 (47%), Gaps = 11/236 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
               LV S   LV+ +A  YRG G+   +++  G +G++Q  ++FD  RG++ +TY  +W
Sbjct: 332 CRDELVKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYW 391

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ +M   + R    V I ++    R   ++++ +  L+  T + +K      IAK    
Sbjct: 392 IRKSMSTMVSRHARGVHIPSSI--IRTINHIQKARKTLK--TSHGIKYAADEEIAKLTGH 447

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  ++ + N  L    S++  +            +L +  D   +   E   R++ R  +
Sbjct: 448 SVKKIRAANQCLKVVGSIDKKVGDC-----FTTKFLEFTPDTTMESPEEAVMRQSARRDI 502

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              +  L PRE+++   R   ++  P +LE +    +VS+E +R+IE RA  K+++
Sbjct: 503 HDLLEGLEPREKQVMVLRYGLQDYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLRD 558


>gi|46907127|ref|YP_013516.1| RNA polymerase sigma factor SigB [Listeria monocytogenes serotype
           4b str. F2365]
 gi|47092103|ref|ZP_00229896.1| RNA polymerase sigma-B factor [Listeria monocytogenes str. 4b
           H7858]
 gi|217965008|ref|YP_002350686.1| RNA polymerase sigma-B factor [Listeria monocytogenes HCC23]
 gi|226223514|ref|YP_002757621.1| RNA polymerase sigma-37 factor (sigma-B) [Listeria monocytogenes
           Clip81459]
 gi|254823836|ref|ZP_05228837.1| RNA polymerase sigma-B factor [Listeria monocytogenes FSL J1-194]
 gi|254852389|ref|ZP_05241737.1| RNA polymerase sigma-B factor [Listeria monocytogenes FSL R2-503]
 gi|254931278|ref|ZP_05264637.1| RNA polymerase sigma B [Listeria monocytogenes HPB2262]
 gi|254994246|ref|ZP_05276436.1| RNA polymerase sigma factor SigB [Listeria monocytogenes FSL
           J2-064]
 gi|255521165|ref|ZP_05388402.1| RNA polymerase sigma factor SigB [Listeria monocytogenes FSL
           J1-175]
 gi|290892914|ref|ZP_06555904.1| RNA polymerase sigma-B factor [Listeria monocytogenes FSL J2-071]
 gi|300764104|ref|ZP_07074099.1| RNA polymerase sigma-B factor [Listeria monocytogenes FSL N1-017]
 gi|22770514|gb|AAN06632.1|AF497204_1 sigma factor B [Listeria monocytogenes]
 gi|22770518|gb|AAN06634.1|AF497206_1 sigma factor B [Listeria monocytogenes]
 gi|22770520|gb|AAN06635.1|AF497207_1 sigma factor B [Listeria monocytogenes]
 gi|22770522|gb|AAN06636.1|AF497208_1 sigma factor B [Listeria monocytogenes]
 gi|22770524|gb|AAN06637.1|AF497209_1 sigma factor B [Listeria monocytogenes]
 gi|22770526|gb|AAN06638.1|AF497210_1 sigma factor B [Listeria monocytogenes]
 gi|22770528|gb|AAN06639.1|AF497211_1 sigma factor B [Listeria monocytogenes]
 gi|22770530|gb|AAN06640.1|AF497212_1 sigma factor B [Listeria monocytogenes]
 gi|3298584|gb|AAC38789.1| sigma B [Listeria monocytogenes]
 gi|3298589|gb|AAC38792.1| Sigma B [Listeria monocytogenes]
 gi|26000673|gb|AAN75465.1| SigB [Listeria monocytogenes]
 gi|46880394|gb|AAT03693.1| RNA polymerase sigma-B factor [Listeria monocytogenes serotype 4b
           str. F2365]
 gi|47019543|gb|EAL10283.1| RNA polymerase sigma-B factor [Listeria monocytogenes str. 4b
           H7858]
 gi|112960117|gb|ABI27557.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960121|gb|ABI27560.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960125|gb|ABI27563.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960129|gb|ABI27566.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960133|gb|ABI27569.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960137|gb|ABI27572.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960141|gb|ABI27575.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960145|gb|ABI27578.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960149|gb|ABI27581.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960153|gb|ABI27584.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960157|gb|ABI27587.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960161|gb|ABI27590.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960165|gb|ABI27593.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960169|gb|ABI27596.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960173|gb|ABI27599.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960177|gb|ABI27602.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960181|gb|ABI27605.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960185|gb|ABI27608.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960189|gb|ABI27611.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960193|gb|ABI27614.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960197|gb|ABI27617.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960201|gb|ABI27620.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960205|gb|ABI27623.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960209|gb|ABI27626.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960213|gb|ABI27629.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960217|gb|ABI27632.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960221|gb|ABI27635.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960225|gb|ABI27638.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960229|gb|ABI27641.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960233|gb|ABI27644.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960237|gb|ABI27647.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960241|gb|ABI27650.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960245|gb|ABI27653.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960249|gb|ABI27656.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960253|gb|ABI27659.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960257|gb|ABI27662.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960261|gb|ABI27665.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960265|gb|ABI27668.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960269|gb|ABI27671.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960273|gb|ABI27674.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960277|gb|ABI27677.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960281|gb|ABI27680.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960285|gb|ABI27683.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960289|gb|ABI27686.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960293|gb|ABI27689.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960297|gb|ABI27692.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960301|gb|ABI27695.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960305|gb|ABI27698.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960309|gb|ABI27701.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960313|gb|ABI27704.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960317|gb|ABI27707.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960321|gb|ABI27710.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960325|gb|ABI27713.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960329|gb|ABI27716.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960333|gb|ABI27719.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960337|gb|ABI27722.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960341|gb|ABI27725.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960345|gb|ABI27728.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960349|gb|ABI27731.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960353|gb|ABI27734.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960357|gb|ABI27737.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112960361|gb|ABI27740.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962434|gb|ABI28932.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962439|gb|ABI28936.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962444|gb|ABI28940.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962449|gb|ABI28944.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962454|gb|ABI28948.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962459|gb|ABI28952.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962464|gb|ABI28956.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962469|gb|ABI28960.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962474|gb|ABI28964.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962479|gb|ABI28968.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962484|gb|ABI28972.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962489|gb|ABI28976.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962494|gb|ABI28980.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962499|gb|ABI28984.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962504|gb|ABI28988.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962509|gb|ABI28992.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962514|gb|ABI28996.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962519|gb|ABI29000.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962524|gb|ABI29004.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962529|gb|ABI29008.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962534|gb|ABI29012.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962539|gb|ABI29016.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962544|gb|ABI29020.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962549|gb|ABI29024.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962554|gb|ABI29028.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962559|gb|ABI29032.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962564|gb|ABI29036.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962569|gb|ABI29040.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962574|gb|ABI29044.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962579|gb|ABI29048.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962584|gb|ABI29052.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962589|gb|ABI29056.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962594|gb|ABI29060.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962599|gb|ABI29064.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962604|gb|ABI29068.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962609|gb|ABI29072.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962614|gb|ABI29076.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962619|gb|ABI29080.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962624|gb|ABI29084.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962629|gb|ABI29088.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962634|gb|ABI29092.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962644|gb|ABI29100.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962649|gb|ABI29104.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962654|gb|ABI29108.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962659|gb|ABI29112.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962664|gb|ABI29116.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962669|gb|ABI29120.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962674|gb|ABI29124.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962679|gb|ABI29128.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962684|gb|ABI29132.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962689|gb|ABI29136.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962694|gb|ABI29140.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962699|gb|ABI29144.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962704|gb|ABI29148.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962709|gb|ABI29152.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962714|gb|ABI29156.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962719|gb|ABI29160.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962724|gb|ABI29164.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962729|gb|ABI29168.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962734|gb|ABI29172.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962739|gb|ABI29176.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|112962744|gb|ABI29180.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
 gi|118084623|gb|ABI16055.2| sigma B [Listeria monocytogenes]
 gi|118084625|gb|ABI16057.2| sigma B [Listeria monocytogenes]
 gi|153582301|emb|CAO79792.1| sigma factor B [Listeria monocytogenes]
 gi|153582307|emb|CAO79795.1| sigma factor B [Listeria monocytogenes]
 gi|217334278|gb|ACK40072.1| RNA polymerase sigma-B factor [Listeria monocytogenes HCC23]
 gi|225875976|emb|CAS04680.1| RNA polymerase sigma-37 factor (sigma-B) [Listeria monocytogenes
           serotype 4b str. CLIP 80459]
 gi|258605695|gb|EEW18303.1| RNA polymerase sigma-B factor [Listeria monocytogenes FSL R2-503]
 gi|290557490|gb|EFD91014.1| RNA polymerase sigma-B factor [Listeria monocytogenes FSL J2-071]
 gi|293582827|gb|EFF94859.1| RNA polymerase sigma B [Listeria monocytogenes HPB2262]
 gi|293593059|gb|EFG00820.1| RNA polymerase sigma-B factor [Listeria monocytogenes FSL J1-194]
 gi|300515094|gb|EFK42146.1| RNA polymerase sigma-B factor [Listeria monocytogenes FSL N1-017]
 gi|302034435|gb|ADK92371.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|302034437|gb|ADK92372.1| RNA polymerase sigma factor [Listeria monocytogenes]
 gi|307570432|emb|CAR83611.1| RNA polymerase sigma-B factor [Listeria monocytogenes L99]
 gi|313609777|gb|EFR85233.1| RNA polymerase sigma-B factor [Listeria monocytogenes FSL F2-208]
 gi|328467051|gb|EGF38146.1| RNA polymerase sigma factor SigB [Listeria monocytogenes 1816]
 gi|328475458|gb|EGF46224.1| RNA polymerase sigma factor SigB [Listeria monocytogenes 220]
 gi|332311302|gb|EGJ24397.1| RNA polymerase sigma-B factor [Listeria monocytogenes str. Scott A]
          Length = 259

 Score =  156 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 61/263 (23%), Positives = 121/263 (46%), Gaps = 24/263 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +++D   G     +++  I   ++ ++      V +     +        ++K  ++ +T
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELT 126

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWL 204
                  Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +
Sbjct: 127 RELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVV 183

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++
Sbjct: 184 GGTDDGF--------ERVNQRMLLEKVLPVLDEREQKILQFTFIEN--RSQKETGELLDI 233

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           S+  V +I+ +A KK++E++Q +
Sbjct: 234 SQMHVSRIQRQAIKKLREALQNE 256


>gi|213580121|ref|ZP_03361947.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-0664]
          Length = 143

 Score =  156 bits (396), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 68/143 (47%), Positives = 95/143 (66%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  ++ +     L  YI      PML   EE  LA+R    GDL AA  L+ SHLR 
Sbjct: 1   MTKEMQNLALAPVGNLESYIRAANAWPMLSADEERALAERLHYQGDLEAAKTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFFNLRRLK 143
           W +VK+ TT  Q++LFFNLR+ K
Sbjct: 121 WRIVKVATTKAQRKLFFNLRKTK 143


>gi|266620503|ref|ZP_06113438.1| RNA polymerase sigma-F factor [Clostridium hathewayi DSM 13479]
 gi|288867868|gb|EFD00167.1| RNA polymerase sigma-F factor [Clostridium hathewayi DSM 13479]
          Length = 237

 Score =  156 bits (395), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 60/253 (23%), Positives = 115/253 (45%), Gaps = 17/253 (6%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            E   L +   E GD  A  RLVT ++ L+  I   + G G    ++   G+IGLM+A+ 
Sbjct: 2   DETMRLIEMAHE-GDKEARDRLVTENMGLIWSIVRRFTGRGYDPEDLFQIGSIGLMKAID 60

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD     + +TY++  I   ++ ++     ++K+  +  +        R     +A+  
Sbjct: 61  KFDMSFDVKFSTYAVPMITGEIKRFLRDDG-MIKVSRSIKEMGTRVKCVR-----EALGF 114

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +   +  IA +L  S+ EV +     A  ESL   +N +D+NS    D +  +   Q
Sbjct: 115 TLGREPTIEEIAGELGASKEEVAASIEAGAEVESLYRTVNKNDENSILLIDKIEEESSAQ 174

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E++L         R +L   ++ L+ ++R I   R       T   ++S   +S+ +V +
Sbjct: 175 EELL--------NRMVLRELLTGLSDKDREIIIRRYYYNE--TQSQIASHLGISQVQVSR 224

Query: 272 IEARAFKKVQESI 284
           +E +  K+++E +
Sbjct: 225 LEKKILKQMREKL 237


>gi|238800552|gb|ACR56097.1| RNA polymerase sigma factor SigB [Listeria innocua]
          Length = 248

 Score =  156 bits (395), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 61/263 (23%), Positives = 121/263 (46%), Gaps = 24/263 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 1   KEKVYIWIAAYQENGDEDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 60

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +++D   G     +++  I   ++ ++      V +     +        ++K  ++ +T
Sbjct: 61  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELT 115

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWL 204
                  Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +
Sbjct: 116 RELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVV 172

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++
Sbjct: 173 GGTDDGF--------ERVNQRMLLEKVLPVLDEREQKILQYTFIEN--RSQKETGELLDI 222

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           S+  V +I+ +A KK++E++Q +
Sbjct: 223 SQMHVSRIQRQAIKKLREALQNE 245


>gi|328883832|emb|CCA57071.1| RNA polymerase sigma factor SigB [Streptomyces venezuelae ATCC
           10712]
          Length = 303

 Score =  156 bits (395), Expect = 3e-36,   Method: Composition-based stats.
 Identities = 59/260 (22%), Positives = 100/260 (38%), Gaps = 27/260 (10%)

Query: 37  LAKRYREHGDLSA----------AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L  R R   D  A             L+  +L LV   A  +R    P+ ++V  G IGL
Sbjct: 56  LFLRLRALDDEGAAADSPERTYVRDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGL 115

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+ +FD ERG    T++M  +   ++ +   +   V++     + RL      L    
Sbjct: 116 IKAIDRFDCERGVEFPTFAMPTVVGEIKRFFRDTSWSVRVPRRLQELRLA-----LTKAS 170

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWL 204
             +     +   V  +A  L VSE +V+            SL++     D       D L
Sbjct: 171 DELAQKLDRSPTVTELAAVLGVSEEDVVDGLAVGNAYTASSLDSPSPEDDGGEGSLADRL 230

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
            Y+    E V          R  L   ++ L PRER+I   R      +T   +  E  +
Sbjct: 231 GYEDTALEGV--------EYRESLKPLLAKLPPRERQIIMLRFFAN--MTQSQIGEEVGI 280

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+  V ++  R   +++E +
Sbjct: 281 SQMHVSRLLTRTLAQLREGL 300


>gi|167950928|ref|ZP_02538002.1| RNA polymerase sigma factor RpoS [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 216

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 55/217 (25%), Positives = 101/217 (46%), Gaps = 12/217 (5%)

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           + + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      
Sbjct: 1   MALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV- 59

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
           K +   LR  +     +  +         IA  L+   SEV  M        S++     
Sbjct: 60  KEINVYLRAAR----QLAQSLDHEPTSEEIADLLDKPISEVKRMLGLNERVTSVDTPF-- 113

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QE 250
                    D +  +      V I+ +        L   +  LN ++R + E R      
Sbjct: 114 GKDADKPLLDTIPDERVQDPTVNIQNDGLNTN---LDTWLLKLNDKQREVVERRFGLHGY 170

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              TLE +++E  V+RERVRQI+  A +++++ +++ 
Sbjct: 171 ENSTLEQVANELGVTRERVRQIQMDALRRLRDILERD 207


>gi|319654668|ref|ZP_08008747.1| sigma factor B [Bacillus sp. 2_A_57_CT2]
 gi|317393584|gb|EFV74343.1| sigma factor B [Bacillus sp. 2_A_57_CT2]
          Length = 264

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 64/269 (23%), Positives = 119/269 (44%), Gaps = 24/269 (8%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
            K+E   L K Y+ H D  A + LV  +  LV  IA  Y        ++V  G IGL+ A
Sbjct: 11  SKEETNALIKAYQLHQDEDAQNTLVLQYQNLVEAIARKYSKGRSYHEDIVQVGIIGLLGA 70

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           ++++D   G     +++  I   ++ ++      V +     +        ++K  ++ +
Sbjct: 71  IRRYDESFGKTFEAFAVPTIIGEIKRFLRDKTWSVHVPRRIKELG-----PKIKATVEEL 125

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDW 203
           T    +  +V  IA  L VSE EV+           L+ D S+ A    SD  +    D 
Sbjct: 126 TTELHRSPRVDEIADVLGVSEEEVLEAMEMGKSYQALSVDHSIEA---DSDGGTVTLLDI 182

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  + +G E+V        N+  +L + + VL+ RE+ I +   L+   ++ +    +  
Sbjct: 183 VGNEDEGYEKV--------NQMLVLDKVLHVLSEREKLIIQYTYLEN--MSQKEAGDKLG 232

Query: 264 VSRERVRQIEARAFKKVQESIQKQVELSS 292
           +S+  V +++ RA KK+QE+I  +   S 
Sbjct: 233 ISQMHVSRLQRRAIKKLQEAIHSETNNSE 261


>gi|30266015|gb|AAN16085.1| SigB [Listeria welshimeri]
          Length = 259

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 61/263 (23%), Positives = 120/263 (45%), Gaps = 24/263 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +++D   G     +++  I   ++ ++      V +     +        ++K  ++ +T
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELT 126

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWL 204
                  Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +
Sbjct: 127 RELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVV 183

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               DG         ER N+R +L + + VL+ RE+ I +   ++    + +      ++
Sbjct: 184 GGTDDGF--------ERVNQRMLLEKVLPVLDEREQMILQYTFIEN--RSQKETGELLDI 233

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           S+  V +I+ +A KK++E++Q +
Sbjct: 234 SQMHVSRIQRQAIKKLREALQNE 256


>gi|291525265|emb|CBK90852.1| RNA polymerase, sigma subunit, RpsG/SigG [Eubacterium rectale DSM
           17629]
 gi|291529276|emb|CBK94862.1| RNA polymerase, sigma subunit, RpsG/SigG [Eubacterium rectale
           M104/1]
          Length = 259

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 46/263 (17%), Positives = 114/263 (43%), Gaps = 17/263 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+  E+  L ++ ++ GD +A  + +  +LRLV+ +   +  +   + ++   G 
Sbjct: 14  SKLPVLKDDEKEELFEKIKK-GDKAAREKYIRGNLRLVLSVIRRFSNHNENMDDLFQIGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+++  FDP  G + +TY++  I   ++ Y+  + S  +I      + L     +  
Sbjct: 73  IGLMKSIDNFDPTIGVKFSTYAVPMIIGEVRRYLRDN-SAYRIP-----RSLRDTAYQAI 126

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
              + ++   +    +  I+K   + E++++     +    SL   + +   ++    D 
Sbjct: 127 KSKEKLSRKLVHDPSLAEISKDCGIPENDILYALDAIQTPLSLFDPVYTDGGDTLYVMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    + +E  +         + +  R+        R+I + R       T   ++ E  
Sbjct: 187 ISDKKNKEEAWVKNLVLDDALKLLDDRA--------RQIIKLRFF--EGKTQIEVAEEIN 236

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+ +V ++E  A K +   ++ 
Sbjct: 237 ISQAQVSRLEKNALKNMHGYLEA 259


>gi|118443643|ref|YP_877879.1| sporulation sigma factor SigF [Clostridium novyi NT]
 gi|118134099|gb|ABK61143.1| RNA polymerase sigma-F factor [Clostridium novyi NT]
          Length = 251

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 51/249 (20%), Positives = 108/249 (43%), Gaps = 17/249 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L K+ +  GD  A   LV  +L LV  I+  +   G    ++   G++GL++A+  FD 
Sbjct: 18  ELIKKAKL-GDKKALDELVEKNLPLVTAISKKFLNRGYEYEDIFQIGSMGLIKAINNFDS 76

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
               + +TY++  I   ++ +I     L+K+  +       +  R+L    + +T    +
Sbjct: 77  SYNVQFSTYAVPMIMGEIRRFIRDDG-LIKVSRSVK-----YTARKLHFDKEKLTKKLNR 130

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
              V  ++K   + + ++I     +   + L   I+  D +     D +V          
Sbjct: 131 EPTVEELSKFSGIDKEQIIFATEAINEPKYLYDTIHQDDGSPIYLIDKVVLKD------- 183

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
            E E  +  +  L  ++S L+ R R+I   R  ++  +T   ++    +S+ +V +IE +
Sbjct: 184 -ESEIDELDKIALKEALSKLDQRSRQIIILRYFKD--ITQVKVAKMLGISQVQVSRIEKK 240

Query: 276 AFKKVQESI 284
             K ++E +
Sbjct: 241 VLKTMKEKL 249


>gi|3298591|gb|AAC38793.1| Sigma B [Listeria innocua]
          Length = 259

 Score =  156 bits (395), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 61/263 (23%), Positives = 121/263 (46%), Gaps = 24/263 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQENGDEDAQYNLVIHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +++D   G     +++  I   ++ ++      V +     +        ++K  ++ +T
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELT 126

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWL 204
                  Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +
Sbjct: 127 RELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVV 183

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++
Sbjct: 184 GGTDDGF--------ERVNQRMLLEKVLPVLDEREQKILQYTFIEN--RSQKETGELLDI 233

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           S+  V +I+ +A KK++E++Q +
Sbjct: 234 SQMHVSRIQRQAIKKLREALQNE 256


>gi|331269204|ref|YP_004395696.1| FliA/WhiG family RNA polymerase sigma 28 subunit [Clostridium
           botulinum BKT015925]
 gi|329125754|gb|AEB75699.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           botulinum BKT015925]
          Length = 252

 Score =  156 bits (394), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 52/249 (20%), Positives = 112/249 (44%), Gaps = 17/249 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L K+ +  GD  A  +LV  +L LV  I+  +   G    ++   G++GL++A+  FD 
Sbjct: 19  ELIKQAKL-GDKKAVDQLVQKNLPLVSAISKKFLNRGYEYEDIFQIGSMGLIKAINNFDS 77

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
               + +TY++  I   ++ +I     L+K+  +       +  ++L    + +T    +
Sbjct: 78  SYNVQFSTYAVPMIMGEIKRFIRDDG-LIKVSRSVK-----YTAKKLHYDKEKLTKQLNR 131

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
              +  ++K   +S+ E+I  +  +   + L   I+  D +     D +V D  G     
Sbjct: 132 EPSIEELSKFSGISKEEIIFSSEAINEPKYLYDTIHQDDGSPIYLIDKVVVDDKG----- 186

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
              E  +  +  L  ++S L+ R R+I   R  ++  +T   ++    +S+ +V +IE +
Sbjct: 187 ---EIDELDKIALKEALSKLDQRSRQIIILRYFKD--ITQVKVAKMLGISQVQVSRIEKK 241

Query: 276 AFKKVQESI 284
             K ++E +
Sbjct: 242 VLKSMKEKL 250


>gi|168335364|ref|ZP_02693458.1| sporulation sigma factor SigG [Epulopiscium sp. 'N.t. morphotype
           B']
          Length = 243

 Score =  156 bits (394), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 51/246 (20%), Positives = 104/246 (42%), Gaps = 17/246 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P L  Q++  L +     GD  A    +  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPTLTNQQKEHLFELIG-AGDNMAREEYIRGNLRLVLSVIQRFNNRGEHVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FD  +G + +TY++  I   ++ Y+  +   +++  +   +   +   ++K 
Sbjct: 74  GLIKAIDNFDTTQGVKFSTYAVPMIIGEIRRYLRDNN-AIRVSRSL--RDTAYKALQVK- 129

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + +   N K   +  IA  L ++   ++     +    SL   +   D ++    D  
Sbjct: 130 --EKLLRQNSKEPTIEEIAAVLEIATENIVFALDAIQDPISLFEPVYHDDGDALFIMDQ- 186

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           V D   Q+ + +E          L  +M  LN RE+ I   R       T   ++ E  +
Sbjct: 187 VSDEKSQDDIWLENI-------ALKEAMKRLNDREKHILTLRFFAG--KTQMEVADEIGI 237

Query: 265 SRERVR 270
           S+ +V 
Sbjct: 238 SQAQVS 243


>gi|30266005|gb|AAN16080.1| SigB [Listeria seeligeri]
 gi|30266007|gb|AAN16081.1| SigB [Listeria seeligeri]
 gi|66968476|gb|AAY59617.1| SigB [Listeria seeligeri]
 gi|66968478|gb|AAY59618.1| SigB [Listeria seeligeri]
 gi|66968480|gb|AAY59619.1| SigB [Listeria seeligeri]
 gi|66968482|gb|AAY59620.1| SigB [Listeria seeligeri]
 gi|66968484|gb|AAY59621.1| SigB [Listeria seeligeri]
 gi|66968486|gb|AAY59622.1| SigB [Listeria seeligeri]
 gi|313634111|gb|EFS00776.1| RNA polymerase sigma-B factor [Listeria seeligeri FSL N1-067]
 gi|313638716|gb|EFS03817.1| RNA polymerase sigma-B factor [Listeria seeligeri FSL S4-171]
          Length = 259

 Score =  156 bits (394), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 61/263 (23%), Positives = 122/263 (46%), Gaps = 24/263 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  + +LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQENGDQDAQYNLVVHYKKLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +++D   G     +++  I   ++ ++      V +     +        ++K  ++ +T
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELT 126

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWL 204
                  Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +
Sbjct: 127 RELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVV 183

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++
Sbjct: 184 GGTDDGF--------ERVNQRMLLEKVLPVLDEREQKILQYTFIEN--RSQKETGELLDI 233

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           S+  V +I+ +A KK++E++Q +
Sbjct: 234 SQMHVSRIQRQAIKKLREALQNE 256


>gi|315302306|ref|ZP_07873197.1| RNA polymerase sigma-B factor [Listeria ivanovii FSL F6-596]
 gi|313629329|gb|EFR97571.1| RNA polymerase sigma-B factor [Listeria ivanovii FSL F6-596]
          Length = 259

 Score =  156 bits (394), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 61/263 (23%), Positives = 120/263 (45%), Gaps = 24/263 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQEDGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +++D   G     +++  I   ++ ++      V +     +        ++K  ++ +T
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELT 126

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWL 204
                  Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +
Sbjct: 127 RELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVV 183

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++
Sbjct: 184 GGTDDGF--------ERVNQRMLLEKVLPVLDEREQKILQYTFIEN--RSQKETGELLDI 233

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           S+  V +I+ +A KK++E++Q +
Sbjct: 234 SQMHVSRIQRQAIKKLREALQNE 256


>gi|311897125|dbj|BAJ29533.1| putative RNA polymerase sigma factor [Kitasatospora setae KM-6054]
          Length = 296

 Score =  156 bits (394), Expect = 4e-36,   Method: Composition-based stats.
 Identities = 55/260 (21%), Positives = 101/260 (38%), Gaps = 22/260 (8%)

Query: 35  YVLAKRYR--EHGDLS---AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             L +R    E G          L+  +L LV   +  +R    P+ ++V  G IGL++A
Sbjct: 52  RALFRRLAGLESGSAEHTYVRDTLIELNLPLVRYASARFRSRNEPMEDIVQVGTIGLIKA 111

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +FDP+RG    T++M  +   ++ +   +   V++     + RL      L      +
Sbjct: 112 IDRFDPDRGVEFPTFAMPTVVGEIKRFFRDTSWSVRVPRRLQELRLA-----LTKAGDEL 166

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
           +    +   V  +A  L V+E +V+            SL++     D       D L Y+
Sbjct: 167 SQRLDRSPTVPELAAYLGVTEDDVVEGLAVGNAYTASSLDSTPAEDDGGDGPLADRLGYE 226

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
               E V          R  L   ++ L PRERRI   R      +T   +  E  +S+ 
Sbjct: 227 DLALEGV--------EYRESLKPLLAKLPPRERRIIMLRFFGN--LTQSQIGEEIGISQM 276

Query: 268 RVRQIEARAFKKVQESIQKQ 287
            V ++  +    ++  +  +
Sbjct: 277 HVSRLLTKTLAHLRAGLTAE 296


>gi|269127892|ref|YP_003301262.1| B/F/G subfamily RNA polymerase sigma-28 subunit [Thermomonospora
           curvata DSM 43183]
 gi|268312850|gb|ACY99224.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Thermomonospora curvata DSM 43183]
          Length = 276

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 59/260 (22%), Positives = 109/260 (41%), Gaps = 23/260 (8%)

Query: 35  YVLAKRYRE--HGDLS---AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
            VL +R  +   GD         LV  HL LV  +A  +R  G  + +++    IGL+++
Sbjct: 32  RVLFERLHQLPEGDPERQRVRDELVELHLPLVEYLARRFRNRGEWLDDLIQVATIGLIKS 91

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +FD +RG   +TY+   I   ++ +       V++     + +L      L   +  +
Sbjct: 92  IDRFDLDRGVEFSTYATPTIVGEIKRHFRDKGWAVRVPRRLQELKLS-----LTKAISDL 146

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                +   V  +A+ L +SE EV+    +       SL+A   S D+++    D L   
Sbjct: 147 AQREGRAPTVSELAEHLQMSEEEVLEGLESANAYSTVSLDAPD-SGDEDAPAVADSLGMV 205

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            D  E V          R  L   +  L  RE+RI   R      +T   +++E  +S+ 
Sbjct: 206 DDSLEGV--------EYRESLKPLLEKLPAREKRILLLRFFGN--MTQSQIANELGISQM 255

Query: 268 RVRQIEARAFKKVQESIQKQ 287
            V ++ AR   +++E +  +
Sbjct: 256 HVSRLLARTLAQLREGLTAE 275


>gi|116872297|ref|YP_849078.1| RNA polymerase sigma factor SigB [Listeria welshimeri serovar 6b
           str. SLCC5334]
 gi|55535652|gb|AAV52891.1| SigB [Listeria welshimeri]
 gi|116741175|emb|CAK20295.1| RNA polymerase sigma-37 (sigma-B) [Listeria welshimeri serovar 6b
           str. SLCC5334]
          Length = 259

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 61/263 (23%), Positives = 120/263 (45%), Gaps = 24/263 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +++D   G     +++  I   ++ ++      V +     +        ++K  ++ +T
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELT 126

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWL 204
                  Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +
Sbjct: 127 RELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVV 183

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               DG         ER N+R +L + + VL+ RE+ I +   ++    + +      ++
Sbjct: 184 GGTDDGF--------ERVNQRMLLEKVLPVLDEREQMILQYTFIEN--RSQKETGELLDI 233

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           S+  V +I+ +A KK++E++Q +
Sbjct: 234 SQMHVSRIQRQAIKKLREALQNE 256


>gi|295102494|emb|CBL00039.1| RNA polymerase, sigma subunit, RpsG/SigG [Faecalibacterium
           prausnitzii L2-6]
          Length = 255

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 60/253 (23%), Positives = 115/253 (45%), Gaps = 18/253 (7%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L +QE+  L  R R  GD  A   ++  +LRLV+ +   +   G  + ++   G IG
Sbjct: 15  LPILSEQEKRDLLTRAR-AGDKKARQSMIEGNLRLVLSVVQRFSQRGENMDDLFQVGCIG 73

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A+  FDP +  R +TY +  I   ++ ++  + +L ++      + L     R    
Sbjct: 74  LIKAIDNFDPAQQVRFSTYGVPMIIGEIRRFLRDNNAL-RVS-----RSLRDTAYRAMQS 127

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            + +     +   V  IA+K  +S  EV +    +    SL   +  +D   + +    V
Sbjct: 128 REELEKQLGREPTVDEIAQKTGLSRREVSAALESVVEPLSLEEPVY-ADGGDAVYVIDQV 186

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            D DG++  +   + R+          + L PRE+RI E R L+    T   ++ E  +S
Sbjct: 187 RDPDGEDSWISGLQFRQTV--------AGLTPREKRIMELRYLKG--KTQMEVAREIGIS 236

Query: 266 RERVRQIEARAFK 278
           + +V ++E  A +
Sbjct: 237 QAQVSRLEKAALE 249


>gi|147865632|emb|CAN83254.1| hypothetical protein VITISV_036980 [Vitis vinifera]
          Length = 611

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 57/236 (24%), Positives = 107/236 (45%), Gaps = 12/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
               L+ S   LV+ IA  YRG G+   +++  GN+G++Q  ++FD  +G+R +TY  +W
Sbjct: 373 CRDELLRSTHSLVLYIARNYRGMGVAFEDILQAGNLGVLQGAERFDHTKGYRFSTYVQYW 432

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ +M   + R    VKI  T N       + +++   +A+  ++ +      IAK   +
Sbjct: 433 IRKSMSTLVARHARGVKIPFTLN-----RAIGQIQKARKALYKSHGRYPDDNEIAKFTGL 487

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S +++ S    L    S +                L +  D   +   E   ++ +R  +
Sbjct: 488 SLAKIRSAGNCLRVVGSTDQSFQDC-----WGATILEFTPDTSIKSPEEGFMQQCKRKDI 542

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              +  L+PRER+I   R         +LE +   F VS+E +R++E  A   +++
Sbjct: 543 HNLLKGLDPRERQILVLRYGFGEQQRKSLEEIGRRFNVSKEWIRKLEKTALANLRD 598


>gi|225429414|ref|XP_002275831.1| PREDICTED: hypothetical protein [Vitis vinifera]
 gi|296081598|emb|CBI20603.3| unnamed protein product [Vitis vinifera]
          Length = 561

 Score =  156 bits (394), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 57/236 (24%), Positives = 107/236 (45%), Gaps = 12/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
               L+ S   LV+ IA  YRG G+   +++  GN+G++Q  ++FD  +G+R +TY  +W
Sbjct: 323 CRDELLRSTHSLVLYIARNYRGMGVAFEDILQAGNLGVLQGAERFDHTKGYRFSTYVQYW 382

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ +M   + R    VKI  T N       + +++   +A+  ++ +      IAK   +
Sbjct: 383 IRKSMSTLVARHARGVKIPFTLN-----RAIGQIQKARKALYKSHGRYPDDNEIAKFTGL 437

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S +++ S    L    S +                L +  D   +   E   ++ +R  +
Sbjct: 438 SLAKIRSAGNCLRVVGSTDQSFQDC-----WGATILEFTPDTSIKSPEEGFMQQCKRKDI 492

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              +  L+PRER+I   R         +LE +   F VS+E +R++E  A   +++
Sbjct: 493 HNLLKGLDPRERQILVLRYGFGEQQRKSLEEIGRRFNVSKEWIRKLEKTALANLRD 548


>gi|255019642|ref|ZP_05291721.1| RNA polymerase, sigma 70 subunit, RpoD family [Acidithiobacillus
           caldus ATCC 51756]
 gi|254970865|gb|EET28348.1| RNA polymerase, sigma 70 subunit, RpoD family [Acidithiobacillus
           caldus ATCC 51756]
          Length = 285

 Score =  155 bits (393), Expect = 5e-36,   Method: Composition-based stats.
 Identities = 63/269 (23%), Positives = 122/269 (45%), Gaps = 21/269 (7%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           + E    P L  ++E  +  + R  GD +A   LV++H+ LV  IA  YR  GL   ++V
Sbjct: 31  LQESG--PFLSPEQESAVIAQIR-SGDEAARATLVSAHMPLVRAIARSYRNKGLSQEDLV 87

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EG +GLM+A+ +F    G R ++Y+ WWI+ AMQ  ++R    +++     +       
Sbjct: 88  QEGYMGLMRAMDRFQEGLGTRFSSYATWWIREAMQRALIR-ARFIRLPDYLAKSLHAL-- 144

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
                  +++ + +    Q     + L V +S + +++       SL+  +         
Sbjct: 145 -----QQKSLDEVDGHDAQRAQRREALGVRDSTMRALDFADVRVCSLDEEMADG------ 193

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLEN 257
                +    G      +  +R      L   + +LN ++R +   R     + P+TLE 
Sbjct: 194 --PSRIEQVVGNVASPAQDYDRDASVRALREHLKLLNEKQREVMIYRFGLHGDAPMTLEA 251

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ++    VSRE VRQ++ RA  ++++++ +
Sbjct: 252 IAERLGVSREAVRQLQVRALLRLRQALSE 280


>gi|319935952|ref|ZP_08010376.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
 gi|319809066|gb|EFW05562.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
          Length = 241

 Score =  155 bits (393), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 54/243 (22%), Positives = 103/243 (42%), Gaps = 22/243 (9%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A  ++V  +L LV  I   ++       ++   G IGLM+A+  FDP    + +TY
Sbjct: 16  GDEQAKEQVVKDNLGLVWSIVHRFKNSYYDKEDLFQIGCIGLMKAINHFDPSYNVQFSTY 75

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           ++  I   ++ Y       +K+  +   K L   + + K  LQA  +       V  +A+
Sbjct: 76  AVPIIMGEIKRYFRDDG-TIKVSRSL--KELNIKVTKAKEILQAENNEE---PTVEEVAR 129

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY--DHDGQEQVLIEKEERK 222
            L V   +V+          SL+  I   D ++   +D L+   DH   E++ +E E   
Sbjct: 130 YLEVDVHDVVEAIDSSYYPTSLSEPIYEKDGSTISMEDRLIDKSDHMWFEKIALEME--- 186

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
                    M  L+ +E+ I   R   +     E ++    +S+ +V ++E +   K++ 
Sbjct: 187 ---------MEKLDEKEKMIIYMRYQLD--YNQEAIAQRLGISQVQVSRLEKKIVTKLRT 235

Query: 283 SIQ 285
            ++
Sbjct: 236 RLK 238


>gi|307330885|ref|ZP_07610018.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306883426|gb|EFN14479.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 263

 Score =  155 bits (393), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 53/237 (22%), Positives = 103/237 (43%), Gaps = 15/237 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              + LV  HL LV  +A  +R  G P+ ++     IGL+++V +FDP+RG   +TY+  
Sbjct: 38  EMRNHLVRMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKSVDRFDPDRGVEFSTYATP 97

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +   ++ +       V++     + RL      L      ++  + +   V  +A++L+
Sbjct: 98  TVVGEIKRHFRDKGWAVRVPRRLQELRLS-----LTTATAELSQRHGRAPTVHELAEQLS 152

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +SE EV+          +L+  +  +D  S    D L  +         E  E    R  
Sbjct: 153 ISEEEVLEGLESANAYSTLSLDVPDTDDESPAVADTLGAED--------EALEGVEYRES 204

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   +  L PRE++I   R      +T   ++ E  +S+  V ++ AR   ++++ +
Sbjct: 205 LKPLLEDLPPREKKILLLRFFGN--MTQSQIAQEVGISQMHVSRLLARTLAQLRDKL 259


>gi|29830729|ref|NP_825363.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29607842|dbj|BAC71898.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 307

 Score =  155 bits (393), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 55/237 (23%), Positives = 96/237 (40%), Gaps = 17/237 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +
Sbjct: 83  RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTV 142

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      ++    +   V  +A  L VS
Sbjct: 143 VGEIKRFFRDTSWSVRVPRRLQELRLA-----LTKASDELSQKLDRSPTVAELAAVLGVS 197

Query: 170 ESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E +V+            SL++     D       D L Y+    E V          R  
Sbjct: 198 EEDVVDGLAVGNAYTASSLDSPAPEDDGGEGSLADRLGYEDTALEGV--------EYRES 249

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   ++ L PRERRI   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 250 LKPLLAKLPPRERRIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 304


>gi|67078088|ref|YP_245708.1| RNA polymerase sigma factor (sigma-A) (sigma-43) [Bacillus cereus
           E33L]
 gi|66970394|gb|AAY60370.1| RNA polymerase sigma factor (sigma-A) (sigma-43) [Bacillus cereus
           E33L]
          Length = 323

 Score =  155 bits (393), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 69/268 (25%), Positives = 118/268 (44%), Gaps = 13/268 (4%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP--ISE 77
           I EI    +L KQE   L +RY+ HG+      L   ++ LV+ IA  Y+         +
Sbjct: 40  IKEIGNYQVLSKQESLNLFQRYK-HGEKDLRDYLFHVNVGLVLSIARKYKNKHPDIEFDD 98

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS-LVKIGTTANQKRLF 136
           +V EGN G+++A++ F+P+ G+  +TY+ WWIK  M   I +  S   KI    NQ  L 
Sbjct: 99  LVQEGNEGMLRAMEDFNPDLGYCFSTYAFWWIKKRMLGIICKKRSGPFKIPNYVNQFNLK 158

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
           +                 +P  V  + K+L+V+   VI  N       ++   I++ +++
Sbjct: 159 YV-----ELEDKYLQMYNRPPSVEEVVKELDVTSEIVIRHNVYYKRVTTMTLDIDTINED 213

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPVTL 255
                 +   D      +     E  N    L     VLNP+++ +      L +  V L
Sbjct: 214 IGISNSFY-DDKSAIPSINEMVIEDLNYEIWLIFD-EVLNPKQKMVLNLCFGLLDGKVYL 271

Query: 256 E-NLSSEFEVSRERVRQIEARAFKKVQE 282
              ++    ++ ERV QI+  A KK+++
Sbjct: 272 HKEIAKALMITTERVSQIKEEAIKKLKK 299


>gi|134036998|gb|ABO47837.1| truncated sigma 38 factor [Escherichia coli]
 gi|134037001|gb|ABO47839.1| truncated sigma 38 factor [Escherichia coli]
          Length = 240

 Score =  155 bits (393), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 56/177 (31%), Positives = 94/177 (53%), Gaps = 6/177 (3%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           LR  +     ++           IA++L+    +V  M        S++  +    +
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231


>gi|16799967|ref|NP_470235.1| RNA polymerase sigma factor SigB [Listeria innocua Clip11262]
 gi|16413344|emb|CAC96126.1| RNA polymerase sigma-37 factor (sigma-B) [Listeria innocua
           Clip11262]
 gi|30266013|gb|AAN16084.1| SigB [Listeria monocytogenes]
          Length = 259

 Score =  155 bits (393), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 61/263 (23%), Positives = 120/263 (45%), Gaps = 24/263 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQEDGDEDAQYNLVIHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +++D   G     +++  I   ++ ++      V +     +        ++K  ++ +T
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELT 126

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWL 204
                  Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +
Sbjct: 127 RELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVV 183

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++
Sbjct: 184 GGTDDGF--------ERVNQRMLLEKVLPVLDEREQKILQYTFIEN--RSQKETGELLDI 233

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           S+  V +I+ +A KK++E++Q +
Sbjct: 234 SQMHVSRIQRQAIKKLREALQNE 256


>gi|229118995|ref|ZP_04248338.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock1-3]
 gi|228664438|gb|EEL19936.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock1-3]
          Length = 294

 Score =  155 bits (393), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 65/268 (24%), Positives = 119/268 (44%), Gaps = 13/268 (4%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP--ISE 77
           I EI    +L KQE   L +RY+ HG+      L   ++ LV+ IA  Y+         +
Sbjct: 11  IKEIGNYKVLSKQESLKLFQRYK-HGEKDLRDYLFHVNVGLVLSIARKYKNKHPDIEFDD 69

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLF 136
           +V EGN G+++A++ F+P  G+  +TY+ WWI+ +M   I  +     KI    NQ  L 
Sbjct: 70  LVQEGNEGMLRAMEDFNPALGYCFSTYAFWWIQKSMLGIICKKKSGPFKIPNYVNQFNLK 129

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
           +                 +   V  + K+L+V+   VI  N       ++   I++ +++
Sbjct: 130 YV-----ELEDKYLQMYNRTPTVEEVVKELDVTSETVIRHNVYYKRATTMTLDIDTINED 184

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPVTL 255
               + +  YD +    ++ E         +      VLNP+++ +      L +  V L
Sbjct: 185 IGMSKPF--YDDNSAIPLINEIVIEDLNYEIWLIFDEVLNPKQKMVLNLCFGLLDGKVYL 242

Query: 256 E-NLSSEFEVSRERVRQIEARAFKKVQE 282
              ++    ++ ERV QI+  A KK+++
Sbjct: 243 HKEIAKALMITTERVSQIKEEAIKKLKK 270


>gi|313647807|gb|EFS12253.1| RNA polymerase sigma factor rpoS [Shigella flexneri 2a str. 2457T]
          Length = 254

 Score =  155 bits (393), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 56/171 (32%), Positives = 92/171 (53%), Gaps = 6/171 (3%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
           LR  +     ++           IA++L+    +V  M        S++  
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTP 225


>gi|229100411|ref|ZP_04231282.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock3-29]
 gi|229107324|ref|ZP_04237193.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock3-28]
 gi|228676119|gb|EEL31095.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock3-28]
 gi|228683031|gb|EEL37038.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock3-29]
          Length = 323

 Score =  155 bits (393), Expect = 6e-36,   Method: Composition-based stats.
 Identities = 65/268 (24%), Positives = 119/268 (44%), Gaps = 13/268 (4%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP--ISE 77
           I EI    +L KQE   L +RY+ HG+      L   ++ LV+ IA  Y+         +
Sbjct: 40  IKEIGNYKVLSKQESLKLFQRYK-HGEKDLRDYLFHVNVGLVLSIARKYKNKHPDIEFDD 98

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLF 136
           +V EGN G+++A++ F+P  G+  +TY+ WWI+ +M   I  +     KI    NQ  L 
Sbjct: 99  LVQEGNEGMLRAMEDFNPALGYCFSTYAFWWIQKSMLGIICKKKSGPFKIPNYVNQFNLK 158

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
           +                 +   V  + K+L+V+   VI  N       ++   I++ +++
Sbjct: 159 YV-----ELEDKYLQMYNRTPTVEEVVKELDVTSETVIRHNVYYKRATTMTLDIDTINED 213

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPVTL 255
               + +  YD +    ++ E         +      VLNP+++ +      L +  V L
Sbjct: 214 IGMSKPF--YDDNSAIPLINEIVIEDLNYEIWLIFDEVLNPKQKMVLNLCFGLLDGKVYL 271

Query: 256 E-NLSSEFEVSRERVRQIEARAFKKVQE 282
              ++    ++ ERV QI+  A KK+++
Sbjct: 272 HKEIAKALMITTERVSQIKEEAIKKLKK 299


>gi|307102796|gb|EFN51063.1| hypothetical protein CHLNCDRAFT_33233 [Chlorella variabilis]
          Length = 288

 Score =  155 bits (393), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 57/258 (22%), Positives = 115/258 (44%), Gaps = 31/258 (12%)

Query: 57  HLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           ++RLV+ IA  Y G G+ I +++ EG +GL +++ +FD  +GF+ +TY+ WWI+ ++   
Sbjct: 4   NVRLVINIAKRYVGNGIDIVDLIPEGLVGLSKSLDRFDASKGFKFSTYAHWWIRQSISRA 63

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVI-- 174
           +     +V++ +          L R+   + ++T+   +      IA  +++    VI  
Sbjct: 64  VCDQARVVRLPSHV-----CETLYRINRAITSMTEQRDEMPSYEEIAAAVDLPVRRVIHY 118

Query: 175 -SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ------EQVLIEKEERKNRRNM 227
             ++    G  S           SS  +       D        E+   E+ + ++ R M
Sbjct: 119 LRLSKLPGGAASARDRPTQYLSGSSLKEVTYEALEDCAEDEDPGEEGEEEEAQHESIRQM 178

Query: 228 LTRSMSVLNPRERRIFEARRL-----------------QENPVTLENLSSEFEVSRERVR 270
               +S L  RER I   R                       ++L  ++S + +S+ER+R
Sbjct: 179 TDLLLSTLEKRERNILRLRYGLLGWGPAAGGLSWDDNVDGGSMSLGEVASAYGLSKERIR 238

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE +A + +++  ++Q+
Sbjct: 239 QIEDKAMRALRKPWRQQL 256


>gi|30266009|gb|AAN16082.1| SigB [Listeria ivanovii]
 gi|30266011|gb|AAN16083.1| SigB [Listeria ivanovii]
          Length = 259

 Score =  155 bits (393), Expect = 7e-36,   Method: Composition-based stats.
 Identities = 60/263 (22%), Positives = 121/263 (46%), Gaps = 24/263 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           +++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  REKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +++D   G     +++  I   ++ ++      V +     +        ++K  ++ +T
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELT 126

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWL 204
                  Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +
Sbjct: 127 RELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVV 183

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++
Sbjct: 184 GGTDDGF--------ERVNQRMLLEKVLPVLDEREQKILQYTFIEN--RSQKETGELLDI 233

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           S+  V +I+ +A KK++E++Q +
Sbjct: 234 SQMHVSRIQRQAIKKLREALQNE 256


>gi|326790567|ref|YP_004308388.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium lentocellum DSM
           5427]
 gi|326541331|gb|ADZ83190.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium lentocellum DSM
           5427]
          Length = 239

 Score =  155 bits (392), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 61/249 (24%), Positives = 115/249 (46%), Gaps = 17/249 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L +R ++ GD  A + LV  +L LV  +   +   G  + ++   G+IGL++++ KFD 
Sbjct: 6   ELIQRAQQ-GDEIAKNILVQENLGLVWSLVRRFSNRGYDMEDLFQIGSIGLLKSIDKFDL 64

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
               + +TY++  I   ++ ++     ++K+  +   K   + +R LK  L    +    
Sbjct: 65  SFNVKFSTYAVPMIVGEIKRFLRDDG-MIKVSRSL--KETAYKVRILKDELIRELNRE-- 119

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
              +  IA  L++   EV+      A  ESLNA+I   D       D +  +    +  L
Sbjct: 120 -PTISEIAAGLDLQVEEVVEALESNAEIESLNAVIYQGDGKPITLSDKI-DEVPTLQNSL 177

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
           ++K        +LT  +  L P ER I   R  ++   T   ++S  ++S+ +V +IE R
Sbjct: 178 VDKM-------ILTELIERLLPIEREIIHMRYFED--RTQTEIASALDISQVQVSRIEKR 228

Query: 276 AFKKVQESI 284
             KK++E +
Sbjct: 229 ILKKMREML 237


>gi|169831385|ref|YP_001717367.1| FliA/WhiG family RNA polymerase sigma factor [Candidatus
           Desulforudis audaxviator MP104C]
 gi|169638229|gb|ACA59735.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Candidatus
           Desulforudis audaxviator MP104C]
          Length = 257

 Score =  155 bits (392), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 49/263 (18%), Positives = 111/263 (42%), Gaps = 17/263 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
             P+L+ +E   L  R  + GD+ A   L+ ++L+LV  +   + G G    ++   G I
Sbjct: 11  NHPLLKDRETRRLL-RLSQQGDVLARETLINANLKLVCNVIRRFEGRGYDPDDLFQIGCI 69

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+ KFD     + +TY++  I   ++ ++     L ++  +  +        + + 
Sbjct: 70  GLIKAIDKFDLRFKVKFSTYAVPMIIGEIRRFLRDDTPL-RVSRSLKELAW-----KAQS 123

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + +     +   +  +A++L +   E++          SL  +++  + +     D +
Sbjct: 124 TREQLQVRLDRDPTIGELAEELGIPREELVGALEAAQSPTSLYEVLHQDEGDPIHVMDQV 183

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
                   Q   E E     R  L   +  L  R+RRI   R  ++   T   ++    +
Sbjct: 184 --------QNKEENEGAWVERIALQELLDSLPERDRRIVVWRFFED--KTQAEVARNLGL 233

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           S+ +V ++E  A +K++   + +
Sbjct: 234 SQVQVSRLEREALRKLKSMARAK 256


>gi|78043803|ref|YP_360778.1| RNA polymerase sigma-F factor [Carboxydothermus hydrogenoformans
           Z-2901]
 gi|77995918|gb|ABB14817.1| RNA polymerase sigma-F factor [Carboxydothermus hydrogenoformans
           Z-2901]
          Length = 257

 Score =  155 bits (392), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 54/260 (20%), Positives = 120/260 (46%), Gaps = 17/260 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           + P L +QE   L ++ ++ GD++A  +L+  +L+LV K+   +   G  + ++   G I
Sbjct: 12  RFPRLGEQEIKELIEKAQK-GDVAAREKLINCNLKLVFKVVERFLHRGYEVEDLFQIGTI 70

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+ KFD ++  + +TY++  I   ++ ++      ++I  +  +  +     ++  
Sbjct: 71  GLIKAIDKFDLKQQVKFSTYAVPMIVGEIRRFLRDDQ-AIRISRSTKELGV-----KILK 124

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             +A+T    +   +  + + L  S   ++          SL   ++  D +     D +
Sbjct: 125 EKEALTVKLGREPTIAELEETLGYSREAIVEALEAGQSLASLFETVHQDDGDPIYLLDQI 184

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             + D +EQ L+E          +   +S L PRER I   R  +E   T   ++    +
Sbjct: 185 KQEGD-EEQTLLENIS-------IKEVLSKLEPRERYILINRFFKE--KTQMEIARTLGI 234

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+ +V ++E +A  K++  +
Sbjct: 235 SQVQVSRLERQALLKLKRYL 254


>gi|163815157|ref|ZP_02206538.1| hypothetical protein COPEUT_01315 [Coprococcus eutactus ATCC 27759]
 gi|158449566|gb|EDP26561.1| hypothetical protein COPEUT_01315 [Coprococcus eutactus ATCC 27759]
          Length = 260

 Score =  155 bits (392), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 53/264 (20%), Positives = 116/264 (43%), Gaps = 17/264 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P L + E+  L  R  E GD SA    +  +LRLV+ +   +        ++   G 
Sbjct: 14  SKLPYLTEDEKNKLFDRM-EQGDESARDEFIEGNLRLVLSVIQRFGSSNENPDDLFQVGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD     + +TY++  I    + Y+  +   +++  +   + + +     K
Sbjct: 73  IGLIKALDNFDRSLNVKFSTYAVPMIIGECRRYLRDNN-AIRVSRSL--RDIAYKAIYAK 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
            +LQ   D   K   +  IA+++++ + +++     ++   SL   +     ++    D 
Sbjct: 130 ENLQKTRD---KEPTIEEIAEEISIPKEDIVMSLDAISAPLSLYEPVYQEGGDTLYIMDQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  D   +E++ +E  +       L  +M  L  RE+ I   R       T   ++ E  
Sbjct: 187 I-KDGKSREELWVENLD-------LREAMGRLCDREKNIVRLRFF--EGKTQTEVAEEIS 236

Query: 264 VSRERVRQIEARAFKKVQESIQKQ 287
           +S+ +V ++E  A K ++  ++ +
Sbjct: 237 ISQAQVSRLEKNAIKSLRRYLEDK 260


>gi|88705109|ref|ZP_01102821.1| RNA polymerase sigma factor 70 family protein [Congregibacter
           litoralis KT71]
 gi|88700804|gb|EAQ97911.1| RNA polymerase sigma factor 70 family protein [Congregibacter
           litoralis KT71]
          Length = 439

 Score =  155 bits (392), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 59/235 (25%), Positives = 103/235 (43%), Gaps = 12/235 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   L   +LRLV  IA  YRG G+   +++ EG +GL++A +K+D  +GFR +TY   
Sbjct: 197 DARDTLTMHNLRLVYSIAGRYRGKGVNYLDLIQEGTLGLIRAAEKYDHSKGFRFSTYCFN 256

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI  A++ ++  +  L++  T   ++     L RL+   +  T          A+A+   
Sbjct: 257 WITQAIRRHVGDTGGLIRYPTHVQEQ--VNKLYRLRVTEKQRTGEEPG---DAALAEAAG 311

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++  +   +        SL+A     D  +            G       + E ++  + 
Sbjct: 312 LTLEKTRDLLQLRNLGVSLDAPQFDDDDGTLLDTM-----SGGPFDASESEAETESLHDR 366

Query: 228 LTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
           L   M  L+  ER +  AR    +  P++   ++    VSRE VRQ+E  A  K+
Sbjct: 367 LLLEMEELDKAEREVVIARWGLHDGPPLSRAEIADRMSVSREWVRQLERAALTKL 421


>gi|169837518|ref|ZP_02870706.1| RNA polymerase sigma factor rpoD [candidate division TM7
           single-cell isolate TM7a]
          Length = 149

 Score =  155 bits (392), Expect = 8e-36,   Method: Composition-based stats.
 Identities = 51/155 (32%), Positives = 85/155 (54%), Gaps = 6/155 (3%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
            Y+ EI +IP+L  +EE   A+R   +G+  A  +L+ S+LRLVV IA  +   GL + +
Sbjct: 1   MYLREIGQIPLLSYEEEIDYAQRVL-NGEEEAKQKLIESNLRLVVSIAKKHTNRGLKMLD 59

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGN+GLM+AV+KF+ E+GF+ +TY+ WWI+ A+   I      ++I        +  
Sbjct: 60  LIQEGNMGLMKAVEKFEYEKGFKFSTYATWWIRQAITRAIADQGRTIRIPVH-----MIE 114

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
            + ++K   + I     K      +AKKL +    
Sbjct: 115 TINKIKKESRIILQETGKEPTAEELAKKLELPVER 149


>gi|329938753|ref|ZP_08288149.1| SigH-like stress response sigma factor [Streptomyces
           griseoaurantiacus M045]
 gi|329302244|gb|EGG46136.1| SigH-like stress response sigma factor [Streptomyces
           griseoaurantiacus M045]
          Length = 291

 Score =  155 bits (392), Expect = 9e-36,   Method: Composition-based stats.
 Identities = 54/237 (22%), Positives = 97/237 (40%), Gaps = 17/237 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FDP+RG    T++M  +
Sbjct: 67  RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDPDRGVEFPTFAMPTV 126

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      ++    +   V  +A  L VS
Sbjct: 127 VGEIKRFFRDTSWSVRVPRRLQELRLA-----LTKASDELSQKLDRSPTVAELAVVLGVS 181

Query: 170 ESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E +V+            SL++     D       D L Y+    E V          R  
Sbjct: 182 EEDVVDGLAVGNAYTASSLDSPAPEDDGGEGSLADRLGYEDTALEGV--------EYRES 233

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   ++ L PRER+I   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 234 LKPLLAKLPPRERQIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 288


>gi|22770510|gb|AAN06630.1|AF497202_1 sigma factor B [Listeria monocytogenes]
          Length = 259

 Score =  155 bits (392), Expect = 9e-36,   Method: Composition-based stats.
 Identities = 60/263 (22%), Positives = 120/263 (45%), Gaps = 24/263 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +++D   G     +++  I   ++ ++      V +     +        ++K  ++ + 
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELX 126

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWL 204
                  Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +
Sbjct: 127 RELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVV 183

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++
Sbjct: 184 GGTDDGF--------ERVNQRMLLEKVLPVLDEREQKILQYTFIEN--RSQKETGELLDI 233

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           S+  V +I+ +A KK++E++Q +
Sbjct: 234 SQMHVSRIQRQAIKKLREALQNE 256


>gi|6010732|gb|AAF01232.1|AF184101_1 mutant RpoS [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
          Length = 242

 Score =  154 bits (391), Expect = 9e-36,   Method: Composition-based stats.
 Identities = 56/177 (31%), Positives = 94/177 (53%), Gaps = 6/177 (3%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           LR  +     ++           IA++L+    +V  M        S++  +    +
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSE 231


>gi|160943880|ref|ZP_02091110.1| hypothetical protein FAEPRAM212_01380 [Faecalibacterium prausnitzii
           M21/2]
 gi|158444556|gb|EDP21560.1| hypothetical protein FAEPRAM212_01380 [Faecalibacterium prausnitzii
           M21/2]
 gi|295104729|emb|CBL02273.1| RNA polymerase, sigma subunit, RpsG/SigG [Faecalibacterium
           prausnitzii SL3/3]
          Length = 255

 Score =  154 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 57/255 (22%), Positives = 113/255 (44%), Gaps = 18/255 (7%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            ++P+L + E+  L       GD +A  R+V  +LRLV+ +   +   G  + ++   G 
Sbjct: 13  GQLPVLTEAEKRQLLT-LAHAGDKAARARMVEGNLRLVLSVVQRFAQRGENLDDLFQVGC 71

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FDP +  R +TY +  I   ++ ++  + +L ++  T     L     R  
Sbjct: 72  IGLIKAIDNFDPAQPVRFSTYGVPMIIGEIRRFLRDNNAL-RVSRT-----LRDTAYRAM 125

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
              + +     +   +  IA    ++  EV +    +    SL+  +  +D   + +   
Sbjct: 126 QARETLEKQLGREPTMDEIAAAAGLARREVTAALESVVEPLSLDEPVY-TDGGDAMYVID 184

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
            V D D +E  +   + R           + L+PRE+RI E R L+    T   ++ E  
Sbjct: 185 QVRDPDSEESWISGLQFRDTV--------AALSPREKRIMELRYLRG--KTQMEVAQEIG 234

Query: 264 VSRERVRQIEARAFK 278
           +S+ +V ++E  A +
Sbjct: 235 ISQAQVSRLEKGALQ 249


>gi|255030138|ref|ZP_05302089.1| RNA polymerase sigma factor SigB [Listeria monocytogenes LO28]
          Length = 245

 Score =  154 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 60/259 (23%), Positives = 118/259 (45%), Gaps = 24/259 (9%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G     +++  I   ++ ++      V +     +        ++K  ++ +T    
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQ 116

Query: 155 KPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +    
Sbjct: 117 SSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTD 173

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++S+  
Sbjct: 174 DGF--------ERVNQRMLLEKVLPVLDEREQKILQYTFIEN--RSQKETGELLDISQMH 223

Query: 269 VRQIEARAFKKVQESIQKQ 287
           V +I+ +A KK++E++Q +
Sbjct: 224 VSRIQRQAIKKLREALQNE 242


>gi|282863440|ref|ZP_06272499.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
 gi|282561775|gb|EFB67318.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
          Length = 288

 Score =  154 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 55/237 (23%), Positives = 96/237 (40%), Gaps = 17/237 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +
Sbjct: 64  RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTV 123

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +   V  +AK L VS
Sbjct: 124 VGEIKRFFRDTSWSVRVPRRLQELRLA-----LTKASDELAQKLDRSPTVPELAKALGVS 178

Query: 170 ESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E +V+            SL++     D       D L Y+    E V          R  
Sbjct: 179 EEDVVDGLAVGNAYTASSLDSPSPEDDGGEGSLADRLGYEDAALEGV--------EYRES 230

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   ++ L PRER+I   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 231 LKPLLAKLPPRERQIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLTQLREGL 285


>gi|317056324|ref|YP_004104791.1| Sig B/F/G subfamily RNA polymerase sigma-28 subunit [Ruminococcus
           albus 7]
 gi|315448593|gb|ADU22157.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Ruminococcus
           albus 7]
          Length = 256

 Score =  154 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 51/261 (19%), Positives = 112/261 (42%), Gaps = 18/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
             + +L + E+  L KR    GD +A  +L+  +LRLV+ +   Y G      ++   G 
Sbjct: 14  GDLKILTESEKQELLKR-SADGDKTAREKLIKGNLRLVLSVLQKYSGGKENPDDLFQVGV 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           +GL++A+  FD     R +TY++  I   ++ Y +R +  +++  +   + L + + + K
Sbjct: 73  VGLIKAIDNFDVGLNVRFSTYAVPMILGEIKRY-MRDFRPIRVSRSM--RDLAYRVMQAK 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
               A          +  IA+  N   +++++    +    S+   + +   +     D 
Sbjct: 130 ERFIAEKQRE---PSIDEIAEITNEKRADIVTALESVTDPVSIYEPVYTDGGDPLCIADQ 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    D  +   +E+   K        ++  L PRE+ I   R  +    T   ++ E  
Sbjct: 187 ICDSTD--DSSWLEELTMK-------EALKELRPREKNILFLRFFKG--HTQVEVAHEIG 235

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A  K++  +
Sbjct: 236 ISQAQVSRLEKNALNKIKSQL 256


>gi|47777365|gb|AAT37999.1| putative RNA polymerase sigma factor [Oryza sativa Japonica Group]
          Length = 882

 Score =  154 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 61/252 (24%), Positives = 109/252 (43%), Gaps = 14/252 (5%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E +L  R +E        RL+ +   LV  IA  Y G G    +++  G +G++   +K
Sbjct: 630 DEALLRSRLQEGYC--CRERLLVTTEWLVKYIAKTYAGMGTAFEDLLQAGKMGVLNGAEK 687

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD ++G + +TY  +WI+ AM   +  +  ++++       R+   +R+++   +AI  N
Sbjct: 688 FDSQKGCKFSTYVKYWIRKAMLALLAENSGVIQLP-----ARMEGIIRKVREARRAIRYN 742

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA  + VS + V           SL   I        Q   ++    D   
Sbjct: 743 TGRNPPDAEIAALIGVSVANVRLARKCSRRVVSLYTEIGVG-----QNAKFVEVTPDTSL 797

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +   E   R   R  L   +  L PRE  + + R   E+    +LE + S + VS+E +R
Sbjct: 798 EAPDEAMFRMQLRERLLHVLDRLPPREGHVLKLRHGLEDGKCRSLEQIGSIYHVSKEWIR 857

Query: 271 QIEARAFKKVQE 282
           +IE  A  K++ 
Sbjct: 858 KIEKSAMSKLRN 869


>gi|205373764|ref|ZP_03226566.1| sporulation sigma factor SigF [Bacillus coahuilensis m4-4]
          Length = 244

 Score =  154 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 51/247 (20%), Positives = 105/247 (42%), Gaps = 19/247 (7%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L+ +E   L KR  + GD+ A   +V  ++RLV  +   +   G    ++   G+IGL++
Sbjct: 14  LKDEEIKQLIKR-SQDGDVDARDMIVNRNMRLVWSVVQRFLNRGYEPDDLFQIGSIGLLK 72

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           +V KFD     + +TY++  I   +Q +I      VK+  +   K     +RR K  L  
Sbjct: 73  SVDKFDLSYDVKFSTYAVPMIIGEIQRFIRDDG-TVKVSRSL--KETGNKIRRAKEELSK 129

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
             +   +   +  +A  L ++  EV+          S++  +  +D +     D +   +
Sbjct: 130 TLN---RVPTISELADFLEITPEEVVLAQEASRTPSSIHETVYENDGDPITLLDQIADQN 186

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D          ++   +  L  ++  L+ RER I   R  ++   T   ++    +S+ +
Sbjct: 187 D----------QKWFDKIALKEAIRELDERERLIVFLRYYKDQ--TQSEVADRLGISQVQ 234

Query: 269 VRQIEAR 275
           V ++  +
Sbjct: 235 VSRLRKK 241


>gi|149183717|ref|ZP_01862127.1| sigma factor B [Bacillus sp. SG-1]
 gi|148848576|gb|EDL62816.1| sigma factor B [Bacillus sp. SG-1]
          Length = 265

 Score =  154 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 59/264 (22%), Positives = 121/264 (45%), Gaps = 12/264 (4%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
            K++     K Y+E  D  A   LV  +  LV+ IA  Y        ++V  G IGL+ A
Sbjct: 11  TKEQVKKWIKAYQEDNDDEAQSNLVLHYENLVISIARKYSKGKSFHEDIVQVGMIGLLGA 70

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           ++++D   G     +++  I   ++ ++      V +     +        ++K  ++ +
Sbjct: 71  IRRYDDSFGKTFEAFAIPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKSTVEEL 125

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
           T+   +  +V  IA  + V+E EV+         ++L+  ++ S +  S+     + D  
Sbjct: 126 TNTLERSPKVEEIADYIGVTEEEVLEAMEMGKSYQALS--VDHSIEADSEGSTVTLLDIV 183

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
           G      E  ER N++ +L + + VL+ RER I +   L    ++ ++   +  +S+  V
Sbjct: 184 GNVD---EGYERINQKLVLEKVLHVLSERERLIIQYTYLDN--LSQKDAGEKLGISQMHV 238

Query: 270 RQIEARAFKKVQESIQKQVELSSS 293
            +++ RA KK++E+I  ++  S S
Sbjct: 239 SRLQRRAIKKLKEAIDAEMRNSES 262


>gi|3386359|gb|AAC34827.1| RNA polymerase sigma B [Listeria monocytogenes]
          Length = 266

 Score =  154 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 61/263 (23%), Positives = 121/263 (46%), Gaps = 24/263 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 19  KEKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 78

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +++D   G     +++  I   ++ ++      V +     +        ++K  ++ +T
Sbjct: 79  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELT 133

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWL 204
                  Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +
Sbjct: 134 RELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVV 190

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++
Sbjct: 191 GGTDDGF--------ERVNQRMLLEKVLPVLDEREQKILQFTFIEN--RSQKETGELLDI 240

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           S+  V +I+ +A KK++E++Q +
Sbjct: 241 SQMHVSRIQRQAIKKLREALQNE 263


>gi|119384818|ref|YP_915874.1| RNA polymerase, sigma 32 subunit, RpoH [Paracoccus denitrificans
           PD1222]
 gi|119374585|gb|ABL70178.1| RNA polymerase, sigma 32 subunit, RpoH [Paracoccus denitrificans
           PD1222]
          Length = 728

 Score =  154 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 54/245 (22%), Positives = 106/245 (43%), Gaps = 27/245 (11%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            SA   L+  HL  V + A      G    +V     +GL ++ ++FDPERG+R   Y+ 
Sbjct: 497 ESATEHLIREHLPYVRRFASRNVEEGEDPEDVFQVAFMGLQRSTRRFDPERGYRFLIYAT 556

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           +W++ A+  +     + ++I    N+K     + +L   L+ +          + +AK+L
Sbjct: 557 YWMRQAITRWRSDEGAAIRIPVHRNEK-----ITKLDRALERLDVRVGGAVSDLELAKEL 611

Query: 167 NVSESEV---ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
             +  EV    S+       ESL+                  +D    E   ++  +   
Sbjct: 612 EWTIDEVTQFRSIPREAEYPESLDD-----------------WDDLLPEPSGVDVFDEAE 654

Query: 224 RRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              ++T +++ L  R+  +   R    +++ +TLE +   + V+RER+RQIEA+   ++ 
Sbjct: 655 TERIVTDALADLPERQADVIRMRFGIGRDSDMTLEEIGQIYGVTRERIRQIEAKGLDRLS 714

Query: 282 ESIQK 286
              +K
Sbjct: 715 HPGRK 719


>gi|302385959|ref|YP_003821781.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           saccharolyticum WM1]
 gi|302196587|gb|ADL04158.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           saccharolyticum WM1]
          Length = 240

 Score =  154 bits (391), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 59/253 (23%), Positives = 118/253 (46%), Gaps = 17/253 (6%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            E   L +   E GD +A  +LVT +  LV  I   + G G    ++   G+IGLM+A+ 
Sbjct: 5   DETMRLIQMAHE-GDKAARDQLVTDNFGLVWSIVRRFTGRGYEAEDLFQIGSIGLMKAID 63

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD     + +TY++  I   ++ ++     ++K+  +  +  L     ++K   + +  
Sbjct: 64  KFDLSYEVKFSTYAVPMITGEIKRFLRDDG-MIKVSRSIKEMGL-----KVKNVREELIY 117

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +   V  IA ++  S+ EV +     A  ESL   +N +D+NS    D +  +   Q
Sbjct: 118 RLGREPTVEEIAGEIGASKEEVAASIEAGAEVESLYRSVNKNDENSILLIDKIEEESSAQ 177

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E++L         R +L   ++ L+ ++R I   R       T   ++++  +S+ +V +
Sbjct: 178 EELL--------NRMVLRELLTALSDKDREIIIRRYYYNE--TQSQIAAKLGISQVQVSR 227

Query: 272 IEARAFKKVQESI 284
           +E +  K+++E +
Sbjct: 228 LEKKILKQMREKL 240


>gi|327438482|dbj|BAK14847.1| DNA-directed RNA polymerase specialized sigma subunit [Solibacillus
           silvestris StLB046]
          Length = 261

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 59/257 (22%), Positives = 112/257 (43%), Gaps = 16/257 (6%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
            K+E       Y+  G   +   LV  + +LV  IA  Y        ++V  G +GL+ A
Sbjct: 11  SKEEVLNWIAEYQASGCEESQTNLVLHYQQLVESIARKYSHGKSYYDDIVQVGMLGLLGA 70

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +++FDP  G     +++  I   ++ ++      V +     +        R+K  ++A+
Sbjct: 71  IRRFDPSFGRSFEAFAVPTIVGEIKRFLRDKTWDVHVPRRIKELG-----PRIKAAVEAL 125

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNC--RLAGDESLNALINSSDKNSSQWQDWLVYD 207
           T +  +   +  IA  L V + +V+      R     S++  I S    S+     +V  
Sbjct: 126 TTSLQRSPSITEIATYLEVQDEDVLEAMEMGRSYQALSMDHSIESDSDGSTVTLFDVVGR 185

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            D   +V        NRR ++  +M+VLN RER+I +   L    ++ +       +S+ 
Sbjct: 186 EDTGYEV-------TNRRMIVADAMNVLNERERQIIQLTYL--EQLSQKEAGERLGISQM 236

Query: 268 RVRQIEARAFKKVQESI 284
            V +I+ +A KK+Q++I
Sbjct: 237 HVSRIQRKAIKKLQDAI 253


>gi|318041016|ref|ZP_07972972.1| type II alternative sigma-70 family RNA polymerase sigma factor
           [Synechococcus sp. CB0101]
          Length = 323

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 58/322 (18%), Positives = 131/322 (40%), Gaps = 53/322 (16%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAK---------------RYREHGD------------ 46
             +SR++  I ++P+L   EE  L +               + R  G+            
Sbjct: 13  DAISRHLRAIGRVPLLTADEEISLGRAVQNGRLLLEAAEELKLRAGGEAPSLEAWASSVN 72

Query: 47  -------------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
                          A+ ++VT++LRLVV +A       L + +++ EG +GL++AV++F
Sbjct: 73  LSPRQLQRQLRLAERASEQMVTANLRLVVSLARRISHRRLDLDDLIQEGTLGLIRAVQRF 132

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           DP RG++ +TY+ WWI+  M   + +    +++      +     L+RL+     +    
Sbjct: 133 DPSRGYKFSTYATWWIREGMGRALQQQSRTIRLPAHMQDR-----LQRLRRCQMELRQML 187

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            +   +  +A+   +   ++     R     SL++       +  +    L+       Q
Sbjct: 188 GREPNLEELAEATELKPLDIREALFRAQEPLSLDS------GHGPEDDLRLLDTLRCGAQ 241

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQ 271
           +  ++    + +  L   +  L  +E  +   R   + P  + L  ++ +  +SR++ R 
Sbjct: 242 LPSDQLTAAHLQTDLVALLDELPEKEAELLRLRYGIDQPAPMNLSAVARQMGLSRDQARG 301

Query: 272 IEARAFKKVQESIQKQVELSSS 293
           +E RA   ++    + ++   +
Sbjct: 302 MERRANAAIRRLSDRVIDYLEA 323


>gi|68171972|ref|ZP_00545278.1| Sigma-70 region 4 [Ehrlichia chaffeensis str. Sapulpa]
 gi|67998602|gb|EAM85349.1| Sigma-70 region 4 [Ehrlichia chaffeensis str. Sapulpa]
          Length = 205

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 88/197 (44%), Positives = 126/197 (63%), Gaps = 3/197 (1%)

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P  GFRL+TY++WWIKA +++YIL+SWS +KIGTT  Q++LFF+LR++K  L    ++N+
Sbjct: 1   PTLGFRLSTYAIWWIKAFIKDYILKSWSCIKIGTTQAQRKLFFSLRKIKKKLFKY-NHNI 59

Query: 155 KPEQVVAIAKKLNVSESEVISMNCR-LAGDESLNALINSSDK-NSSQWQDWLVYDHDGQE 212
             E +  IA K + SE EV  MN   L  D SLN L+ S+D  N  + Q+ +  D   QE
Sbjct: 60  TKEDIKLIANKCSTSEQEVEQMNRYFLYRDRSLNELVFSNDNQNGVELQEIIKCDTPNQE 119

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
              +  EE   ++ ++++++S LN R R IF  RRL E P TL+ LS E+ +S+ERVRQI
Sbjct: 120 DTYLLNEELNIKKALISQALSTLNERYRDIFIRRRLIEEPDTLDKLSQEYNISKERVRQI 179

Query: 273 EARAFKKVQESIQKQVE 289
           E  AF KV+  I  + E
Sbjct: 180 EMHAFTKVKNFIISERE 196


>gi|227485585|ref|ZP_03915901.1| DNA-directed RNA polymerase sigma subunit RpoD [Anaerococcus
           lactolyticus ATCC 51172]
 gi|227236451|gb|EEI86466.1| DNA-directed RNA polymerase sigma subunit RpoD [Anaerococcus
           lactolyticus ATCC 51172]
          Length = 340

 Score =  154 bits (390), Expect = 1e-35,   Method: Composition-based stats.
 Identities = 61/271 (22%), Positives = 124/271 (45%), Gaps = 17/271 (6%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISE 77
            ++ K+  L  +E     +     G+ +A   LV  +  LV   A  +    G  L + +
Sbjct: 80  KDMMKLSDLNNEEIVEQFQL----GNQNALAALVEKNQGLVRSRASYFFRSHGNDLDLED 135

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +V  G +G+++A +KFD   G++  TY+  WI  A+++ I +    ++I      K    
Sbjct: 136 LVQSGMLGMIRAAEKFDLTLGYKFTTYAYKWIDKAIRKAINKEGHTIRIPAGKYLK--LN 193

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L+++       +D  +   +++           ++  +N       SLN  ++S D   
Sbjct: 194 KLKQILKANPEASDEEIY--RILENEGINKKQADDLFLINRNQVNSTSLNINLDSEDSTG 251

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTL 255
            +  D +  +    + +++E    K+  N L +++  L  RE++I   R   +N  P TL
Sbjct: 252 DELMDMVGDESTPVDMLILE----KDMENFLMQALDQLTDREKQIIIYRYGLDNEKPKTL 307

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E + + +++SRER+RQIE +A  K+++    
Sbjct: 308 EQIGAIYDLSRERIRQIENQALGKLKDYSDS 338


>gi|256396809|ref|YP_003118373.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Catenulispora acidiphila DSM 44928]
 gi|256363035|gb|ACU76532.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Catenulispora acidiphila DSM 44928]
          Length = 353

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 58/255 (22%), Positives = 103/255 (40%), Gaps = 19/255 (7%)

Query: 35  YVLAKRYRE-----HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             L  R  E              LV  HL LV  +A  +R  G P+ ++     IGL+++
Sbjct: 109 RELFARLNELPEGSTERKQIRDELVQMHLPLVEHLARRFRNRGEPLDDLTQVATIGLIKS 168

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V +FD ERG   +TY+   +   ++ +       V++     + RL      L      +
Sbjct: 169 VDRFDTERGVEFSTYATPTVIGEIKRHFRDKGWAVRVPRRLQELRLS-----LTSATSEL 223

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
           +  N +   V  +A+ L +SE EV+          +L+  ++      S      V D  
Sbjct: 224 SQRNRRSPTVAELAEYLKISEEEVLEGLESANAYSTLSLDVSEGGDEDS----PAVADSL 279

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
           G E   +E  E    R  L   +  L PRE++I   R      +T   ++ E  +S+  V
Sbjct: 280 GSEDEALEGVE---YRESLKPLLEQLPPREKKILLLRFFGN--MTQSQIAEEIGISQMHV 334

Query: 270 RQIEARAFKKVQESI 284
            ++ AR  ++++  +
Sbjct: 335 SRLLARTLEQLRAQL 349


>gi|225389231|ref|ZP_03758955.1| hypothetical protein CLOSTASPAR_02977 [Clostridium asparagiforme
           DSM 15981]
 gi|225044710|gb|EEG54956.1| hypothetical protein CLOSTASPAR_02977 [Clostridium asparagiforme
           DSM 15981]
          Length = 239

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 59/255 (23%), Positives = 110/255 (43%), Gaps = 17/255 (6%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            E   L  R  E GD +A  +LV  ++ L+  I   + G G  + ++   G+IGLM+A+ 
Sbjct: 2   DETLKLILRAHE-GDKTARDQLVMDNVGLIWSIVRRFAGRGYEMEDLFQIGSIGLMKAID 60

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD     + +TY++  I   ++ ++     ++K+  +  +  L     R     + +T 
Sbjct: 61  KFDTTFEVKFSTYAVPMITGEIKRFLRDDG-MIKVSRSIKELGLKVKCAR-----EEMTY 114

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +   +  IA  + VS  EV +     A  ESL   +  SD N     D L  +++  
Sbjct: 115 ELGREPTIEEIAGSVGVSREEVAASMEAGAEVESLYRPVGGSDDNQLCLMDRLEEENNEH 174

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E ++         R +L   +S L   ER I   R       T   ++ +  +S+ +V +
Sbjct: 175 EALI--------NRMVLKELLSSLEEGEREIIVRRYFHNQ--TQTQIAQDLGISQVQVSR 224

Query: 272 IEARAFKKVQESIQK 286
           +E R  K +++  + 
Sbjct: 225 LEKRILKAMRKRFES 239


>gi|268608170|ref|ZP_06141897.1| sporulation sigma factor SigG [Ruminococcus flavefaciens FD-1]
          Length = 259

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 51/261 (19%), Positives = 113/261 (43%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            ++ ++++ E+  L +  +  G   A  +L+  +LRLV+ +   + G G  I ++   G 
Sbjct: 14  SELKVMKEDEKMALLREIKATGSKEARDKLIKGNLRLVLSVIQRFTGRGEDIDDLFQIGV 73

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++A+  FD  +  R +TY +  I   ++ ++        +  + + + L +   + K
Sbjct: 74  IGLIKAINNFDLTKEVRFSTYCVPMISGELRRHLRDYS---HVKVSRSLRDLAYKAIQSK 130

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
             L   T    +   +  IA+ +    SE++     ++   SL   + S   ++    D 
Sbjct: 131 ERL---TVRLQREPSIDEIAEDIGEKRSEIVIALESISDPVSLYEPVYSDSDDTLFIMDQ 187

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +   +D          E +     +  +++ L  RER I   R  +    T   ++ E  
Sbjct: 188 ISDRND---------IESRLNELTIRDAINQLGQRERNILYLRFFRG--KTQTEVAGEIG 236

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A + V+ S+
Sbjct: 237 ISQAQVSRLEKSAIRTVKGSL 257


>gi|239980906|ref|ZP_04703430.1| RNA polymerase sigma factor, sigma L [Streptomyces albus J1074]
 gi|291452768|ref|ZP_06592158.1| sigma L [Streptomyces albus J1074]
 gi|291355717|gb|EFE82619.1| sigma L [Streptomyces albus J1074]
          Length = 340

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 55/237 (23%), Positives = 95/237 (40%), Gaps = 17/237 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +
Sbjct: 116 RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTV 175

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +   V  +A  L VS
Sbjct: 176 IGEIKRFFRDTSWSVRVPRRLQELRLA-----LTKTSDELAQKLDRSPTVPELAHALGVS 230

Query: 170 ESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E +V+            SL++     D       D L Y+    E V          R  
Sbjct: 231 EEDVVDGLAVGNAYTASSLDSPAPEDDGGEGSLADRLGYEDTALEGV--------EYRES 282

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   ++ L PRERRI   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 283 LKPLLAKLPPRERRIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 337


>gi|255026033|ref|ZP_05298019.1| RNA polymerase sigma factor SigB [Listeria monocytogenes FSL
           J2-003]
          Length = 259

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 61/263 (23%), Positives = 121/263 (46%), Gaps = 24/263 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +++D   G     +++  I   ++ ++      V +     +        ++K  ++ +T
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELT 126

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWL 204
                  Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +
Sbjct: 127 RELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVV 183

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++
Sbjct: 184 GGTDDGF--------ERVNQRMLLEKVLPVLDEREQKILQFTFIEN--RSQKETGELLDI 233

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           S+  V +I+ +A KK++E++Q +
Sbjct: 234 SQMHVSRIQRQAXKKLREALQNE 256


>gi|257067128|ref|YP_003153384.1| RNA polymerase, sigma 32 subunit, RpoH [Anaerococcus prevotii DSM
           20548]
 gi|256799008|gb|ACV29663.1| RNA polymerase, sigma 32 subunit, RpoH [Anaerococcus prevotii DSM
           20548]
          Length = 343

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 60/248 (24%), Positives = 118/248 (47%), Gaps = 13/248 (5%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
           G+ +A   LV  +  LV   A  +    G  L + ++V  G +G+++A +KFD   G++ 
Sbjct: 103 GNQNALAALVEKNQGLVRSRASYFFRSHGNDLDLEDLVQSGMLGMIRAAEKFDLSLGYKF 162

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
            TY+  WI  A+++ I +    ++I      K     L+++       +D  L   +++ 
Sbjct: 163 TTYAYKWIDKAIRKAINKEGHTIRIPAGKYLK--LNKLKQILKANPEASDEELY--RILE 218

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
                     ++  +N       SLN  ++S D    +  D +  +    + +++E    
Sbjct: 219 KEGIDKKQADDLFLINRNQVNSTSLNINLDSEDSTGDELMDMVGDESTPVDMLILE---- 274

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKK 279
           K+  N L +++  L  RE++I   R   +N  P TLE +   +++SRER+RQIE +A  K
Sbjct: 275 KDMENFLLKALDQLTDREKQIIIFRYGLDNEKPKTLEEIGKIYDLSRERIRQIENQALGK 334

Query: 280 VQESIQKQ 287
           ++E  +++
Sbjct: 335 LKEFSERE 342


>gi|72160963|ref|YP_288620.1| RNA polymerase sigma factor [Thermobifida fusca YX]
 gi|71914695|gb|AAZ54597.1| RNA polymerase sigma factor [Thermobifida fusca YX]
          Length = 267

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 58/276 (21%), Positives = 111/276 (40%), Gaps = 32/276 (11%)

Query: 25  KIPMLEKQEEY---------VLAKRYRE-HGD----LSAAHRLVTSHLRLVVKIAMGYRG 70
           + P L  Q E+          L +R  E   D          LV  HL LV  +A  +R 
Sbjct: 4   RGPALTAQTEHSTPDRARARELFERLGELDPDSPERQRIRDELVELHLPLVEYLARRFRN 63

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            G  + ++     IGL++++ +FD  RG   +TY+   I   ++ +       V++    
Sbjct: 64  RGEWLDDLTQVATIGLIKSIDRFDLSRGVEFSTYATPTIVGEIKRHFRDKGWAVRVPRRL 123

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS--MNCRLAGDESLNA 188
            + +L      L   +  ++  + +   V  +A+ L +SE EV+    +       SL+A
Sbjct: 124 QELKLS-----LTKAVSELSQRHGRAPTVAELAEYLKMSEEEVLEGLESANAYSTVSLDA 178

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
             N  +   +      + D         E  E    R  L   +  L PRE++I   R  
Sbjct: 179 PDNGDEDAPAVADSLGIMD---------ESLEGVEYRESLKPLLERLPPREKKILLLRFF 229

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
               +T   +++E  +S+  V ++ AR   ++++++
Sbjct: 230 GN--MTQSQIAAELGISQMHVSRLLARTLAQLRQAL 263


>gi|229542547|ref|ZP_04431607.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Bacillus
           coagulans 36D1]
 gi|229326967|gb|EEN92642.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Bacillus
           coagulans 36D1]
          Length = 259

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 56/270 (20%), Positives = 132/270 (48%), Gaps = 18/270 (6%)

Query: 23  IRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           + K+P  ++ +   L + ++++GD  A   LV  + +LV  +A  Y        ++   G
Sbjct: 1   MSKLPQPDQIDVNQLIQSFQQNGDKEAQEILVAHYQKLVESLARKYSKGRAYQEDIFQVG 60

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            IGL+ A+++FDP  G    ++++  I   ++ ++      V +     +        R+
Sbjct: 61  IIGLLGAIQRFDPNIGKSFESFAIPTIIGEIKRFLRDKTWSVHVPRRIKELG-----PRI 115

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL---NALINSSDKNSSQ 199
           K  ++ +T+   +  ++  IA  L +SE EV+          +L   +++ + SD ++  
Sbjct: 116 KSTVEKLTNELQRSPKIAEIAAHLEISEEEVLEAMEMSKSYHALSVDHSIESDSDGSTVT 175

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
             D +  + DG E+V        N+R +L + + VL+ RER++     ++   ++ ++  
Sbjct: 176 LLDMVGSEDDGYEKV--------NQRLVLEKVLHVLSERERQVIHYTYIEN--LSQKDTG 225

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQVE 289
            +  +S+  V +++ RA KK++++I+ +++
Sbjct: 226 EKLGISQMHVSRLQRRAIKKLRDAIEGELQ 255


>gi|21222437|ref|NP_628216.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
 gi|256786489|ref|ZP_05524920.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
 gi|289770380|ref|ZP_06529758.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
 gi|13122198|emb|CAC32374.1| putative RNA polymerase sigma factor [Streptomyces coelicolor
           A3(2)]
 gi|289700579|gb|EFD68008.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
          Length = 318

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 55/237 (23%), Positives = 96/237 (40%), Gaps = 17/237 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +
Sbjct: 94  RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTV 153

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      ++    +   V  +A  L VS
Sbjct: 154 VGEIKRFFRDTSWSVRVPRRLQELRLA-----LTKASDELSQKLDRSPTVGELAAVLGVS 208

Query: 170 ESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E +V+            SL++     D       D L Y+    E V          R  
Sbjct: 209 EEDVVDGLAVGNAYTASSLDSPAPEDDGGEGSLADRLGYEDTALEGV--------EYRES 260

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   ++ L PRERRI   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 261 LKPLLAKLPPRERRIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLSQLREGL 315


>gi|222632746|gb|EEE64878.1| hypothetical protein OsJ_19735 [Oryza sativa Japonica Group]
          Length = 1012

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 61/252 (24%), Positives = 109/252 (43%), Gaps = 14/252 (5%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E +L  R +E        RL+ +   LV  IA  Y G G    +++  G +G++   +K
Sbjct: 760 DEALLRSRLQEGYC--CRERLLVTTEWLVKYIAKTYAGMGTAFEDLLQAGKMGVLNGAEK 817

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD ++G + +TY  +WI+ AM   +  +  ++++       R+   +R+++   +AI  N
Sbjct: 818 FDSQKGCKFSTYVKYWIRKAMLALLAENSGVIQLP-----ARMEGIIRKVREARRAIRYN 872

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA  + VS + V           SL   I        Q   ++    D   
Sbjct: 873 TGRNPPDAEIAALIGVSVANVRLARKCSRRVVSLYTEIGVG-----QNAKFVEVTPDTSL 927

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +   E   R   R  L   +  L PRE  + + R   E+    +LE + S + VS+E +R
Sbjct: 928 EAPDEAMFRMQLRERLLHVLDRLPPREGHVLKLRHGLEDGKCRSLEQIGSIYHVSKEWIR 987

Query: 271 QIEARAFKKVQE 282
           +IE  A  K++ 
Sbjct: 988 KIEKSAMSKLRN 999


>gi|253682486|ref|ZP_04863283.1| RNA polymerase sigma-F factor [Clostridium botulinum D str. 1873]
 gi|253562198|gb|EES91650.1| RNA polymerase sigma-F factor [Clostridium botulinum D str. 1873]
          Length = 252

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 51/249 (20%), Positives = 111/249 (44%), Gaps = 17/249 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L K+ +  GD  A   LV  +L LV  I+  +   G    ++   G++GL++A+  FD 
Sbjct: 19  ELIKQAKL-GDKKAVDELVQKNLPLVSSISKKFLNRGYEYEDIFQIGSMGLIKAINNFDS 77

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
               + +TY++  I   ++ +I     L+K+  +       +  ++L    + +T    +
Sbjct: 78  SYDVQFSTYAVPMIMGEIKRFIRDDG-LIKVSRSVK-----YTAKKLHYDKEKLTKELNR 131

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
              +  ++K   +S+ ++I  +  +   + L   I+  D +     D +V D  G     
Sbjct: 132 EPSLEELSKFSGISKEDIIFSSEAINEPKYLYDTIHQDDGSPIYLIDKVVLDDKG----- 186

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
              E  +  +  L  ++S L+ R R+I   R  ++  +T   ++    +S+ +V +IE +
Sbjct: 187 ---EIDELDKIALKEALSKLDQRSRQIIILRYFKD--ITQVKVAKMLGISQVQVSRIEKK 241

Query: 276 AFKKVQESI 284
             K ++E +
Sbjct: 242 VLKSMKEKL 250


>gi|290959142|ref|YP_003490324.1| SigH-like stress response sigma factor [Streptomyces scabiei 87.22]
 gi|260648668|emb|CBG71781.1| SigH-like stress response sigma factor [Streptomyces scabiei 87.22]
          Length = 306

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 55/237 (23%), Positives = 96/237 (40%), Gaps = 17/237 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +
Sbjct: 82  RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTV 141

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      ++    +   V  +A  L VS
Sbjct: 142 VGEIKRFFRDTSWSVRVPRRLQELRLA-----LTKASDELSQKLDRSPTVTELAAVLGVS 196

Query: 170 ESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E +V+            SL++     D       D L Y+    E V          R  
Sbjct: 197 EEDVVDGLAVGNAYTASSLDSPAPEDDGGEGSLADRLGYEDTALEGV--------EYRES 248

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   ++ L PRERRI   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 249 LKPLLAKLPPRERRIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 303


>gi|255550882|ref|XP_002516489.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
 gi|223544309|gb|EEF45830.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
          Length = 560

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 60/236 (25%), Positives = 114/236 (48%), Gaps = 12/236 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
               L+ S   LV+  A  YRG G+ + +++  GN+G+++  ++FD  RG+R +TY  +W
Sbjct: 322 CRDELIKSTRSLVLYFARNYRGTGIALEDLLQAGNLGVLEGAERFDHTRGYRFSTYVQYW 381

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ +M + + R    ++I  T     L   + +++   +A+T +N K      IAK   +
Sbjct: 382 IRKSMSKIVSRLARGIQIPCT-----LSRAIYQIQKARKALTTSNGKYPDDDEIAKYTGL 436

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S +++ S +  L    S++  I       S    +L +  D   Q   E   R++    +
Sbjct: 437 SLAKIESASRCLRVVGSIDQKI-----GESLNAKYLEFLPDTSVQSPEEVVMRQHMIQDM 491

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              +  L+ RER++   R    +  P +LE +   F VS+E VR++E R   +++ 
Sbjct: 492 HNLLRSLDSRERQVLILRFGLNDYQPKSLEEIGRHFHVSKEWVRRLEKRVMTRLRN 547


>gi|30266017|gb|AAN16086.1| SigB [Listeria welshimeri]
          Length = 259

 Score =  154 bits (389), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 60/263 (22%), Positives = 120/263 (45%), Gaps = 24/263 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+G+  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQENGNQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +++D   G     +++  I   ++ ++      V +     +        ++K  ++ +T
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELT 126

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWL 204
                  Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +
Sbjct: 127 RELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVV 183

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               DG         ER N+R +L + + VL+ RE+ I +   ++    + +      ++
Sbjct: 184 GGTDDGF--------ERVNQRMLLEKVLPVLDEREQMILQYTFIEN--RSQKETGELLDI 233

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           S+  V +I+ +A KK++E++Q +
Sbjct: 234 SQMHVSRIQRQAIKKLREALQNE 256


>gi|168187412|ref|ZP_02622047.1| RNA polymerase sigma-F factor [Clostridium botulinum C str. Eklund]
 gi|169294714|gb|EDS76847.1| RNA polymerase sigma-F factor [Clostridium botulinum C str. Eklund]
          Length = 251

 Score =  153 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 50/249 (20%), Positives = 109/249 (43%), Gaps = 17/249 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L K+ +  GD  A   LV  +L LV  I+  +   G    ++   G++GL++A+  FD 
Sbjct: 18  ELIKKAKL-GDKKALDELVEKNLPLVSAISKKFLNRGYEYEDIFQIGSMGLIKAINNFDS 76

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
               + +TY++  I   ++ +I     L+K+  +       +  R+L    + +T    +
Sbjct: 77  SYNVQFSTYAVPMIMGEIRRFIRDDG-LIKVSRSVK-----YTARKLHFDKEKLTKKLHR 130

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
              +  ++K   + + ++I     +   + L   I+  D +     D +V        V 
Sbjct: 131 EPTLEELSKFSGIEKEQIIFAMEAINEPKYLYDTIHQDDGSPIYLIDKVV--------VK 182

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
            E E  +  +  L  +++ L+ R R+I   R  ++  +T   ++    +S+ +V +IE +
Sbjct: 183 DESEVDELDKIALKEALNKLDQRSRQIIILRYFKD--ITQVKVAKMLGISQVQVSRIEKK 240

Query: 276 AFKKVQESI 284
             K ++E +
Sbjct: 241 VLKTMKEKL 249


>gi|112962639|gb|ABI29096.1| RNA polymerase sigma-B factor [Listeria monocytogenes]
          Length = 258

 Score =  153 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 60/262 (22%), Positives = 121/262 (46%), Gaps = 23/262 (8%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +++D   G     +++  I   ++ ++      V +     +        ++K  ++ +T
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELT 126

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNC-----RLAGDESLNALINSSDKNSSQWQDWLV 205
                  Q+  IA  + V+E  + +M        L+ D S+ A    SD ++    D + 
Sbjct: 127 RELQSSPQISDIADFIGVTEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVG 183

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
              DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++S
Sbjct: 184 GTDDGF--------ERVNQRMLLEKVLPVLDEREQKILQFTFIEN--RSQKETGELLDIS 233

Query: 266 RERVRQIEARAFKKVQESIQKQ 287
           +  V +I+ +A KK++E++Q +
Sbjct: 234 QMHVSRIQRQAIKKLREALQNE 255


>gi|299143454|ref|ZP_07036534.1| RNA polymerase sigma-B factor [Peptoniphilus sp. oral taxon 386
           str. F0131]
 gi|298517939|gb|EFI41678.1| RNA polymerase sigma-B factor [Peptoniphilus sp. oral taxon 386
           str. F0131]
          Length = 260

 Score =  153 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 56/260 (21%), Positives = 118/260 (45%), Gaps = 16/260 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L+K E   L + Y+ + D      L+  HL +   ++  Y G G+   ++    +IGL+ 
Sbjct: 13  LDKSERKELFEAYKLNKDPEIRDILIEEHLYIAEILSKKYSGRGIDYDDIFQVASIGLIY 72

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A+ ++D E+G+  ++++   I   +++Y       +++     +       +++      
Sbjct: 73  AIDRYDFEKGYEFSSFATPTIIGEIKKYFRDKGWTIRVPRRIQELS-----KKINNAKTQ 127

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +T    +   V  IA  L  +  EVI      ++   +SL+   +++  +    ++  + 
Sbjct: 128 LTQELQRIPTVEDIADYLETTPEEVIEAMEASKVYTPQSLDVTYDTNGDD----KELNLA 183

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           D  G+ +   EK E K+    L R+MS LN  ER I   R       T   ++ + ++S+
Sbjct: 184 DLVGENEKYFEKIEMKDF---LERAMSELNDMERTILIERYF--EKKTQVAIAEKLDISQ 238

Query: 267 ERVRQIEARAFKKVQESIQK 286
             + +IE +  KK++E I+K
Sbjct: 239 MTISRIEKKVLKKMREEIKK 258


>gi|332753462|gb|EGJ83842.1| RNA polymerase sigma factor rpoS domain protein [Shigella flexneri
           4343-70]
          Length = 215

 Score =  153 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 54/215 (25%), Positives = 104/215 (48%), Gaps = 12/215 (5%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K 
Sbjct: 1   MLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KE 59

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           L   LR  +     ++           IA++L+    +V  M        S++  +    
Sbjct: 60  LNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDS 115

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENP 252
           +     +  L    D +E    +  +  + +  + + +  LN ++R +   R   L    
Sbjct: 116 E-----KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLARRFGLLGYEA 170

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 171 ATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 205


>gi|254384440|ref|ZP_04999781.1| hypothetical protein SSAG_04083 [Streptomyces sp. Mg1]
 gi|194343326|gb|EDX24292.1| hypothetical protein SSAG_04083 [Streptomyces sp. Mg1]
          Length = 1094

 Score =  153 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 69/297 (23%), Positives = 129/297 (43%), Gaps = 35/297 (11%)

Query: 28  MLEKQEEYVLAKRYREHGDL--------------------SAAHRLVTSHLRLVVKIAMG 67
           ML  +EE  LA   R   D                      A +  V  +  L   IA+ 
Sbjct: 220 MLTAEEEVGLAVLVRGGADRIESRPTEAEIAALAATDLRVRARNCFVVHNQGLAHGIALR 279

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           + G GL   +++  G +GL++A  KFDP +G++ +TY+ WWI+ +M   +    ++++I 
Sbjct: 280 HAGQGLDHEDLLQHGALGLIRAAVKFDPVKGYKFSTYATWWIRQSMSRAVADEGAVIRIP 339

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              ++      +R++    + +  +  +P   V +A   ++S   V  +       +SL+
Sbjct: 340 VHFHE-----QIRKVAAAERRL-QSEGRPWSAVHVAVACDLSVQRVEEIRRVSRRTDSLD 393

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
            +I     +     D +  D        +  EE  ++   L   ++  + R+ RI   R 
Sbjct: 394 RVI----GDGVHLGDLVALDRPLPSAEHLAMEEMGHKH--LLSLLTRFDARDARILLRRT 447

Query: 248 LQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ-VELSSSPPLLQKPR 301
             +  +  TL++L  EF V+RER+RQ+E +AF   +E +    +    + P   KPR
Sbjct: 448 GLDGGDRSTLDDLGKEFGVTRERIRQVEVKAFAAFREMLLANGIGPGHAEPPDPKPR 504


>gi|307328850|ref|ZP_07608020.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306885515|gb|EFN16531.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 276

 Score =  153 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 54/237 (22%), Positives = 96/237 (40%), Gaps = 17/237 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +
Sbjct: 52  RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTV 111

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      ++    +   V  +A  L VS
Sbjct: 112 VGEIKRFFRDTSWSVRVPRRLQELRLA-----LTKASDELSQRLDRSPTVPELATALGVS 166

Query: 170 ESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E +V+            SL++     D       D L Y+    E V          R  
Sbjct: 167 EEDVVDGLAVGNAYTASSLDSPSPEDDGGEGSLADRLGYEDSALEGV--------EYRES 218

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   ++ L PRER+I   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 219 LKPLLAKLPPRERQIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 273


>gi|260762513|ref|ZP_05874850.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 2 str.
           86/8/59]
 gi|260672939|gb|EEX59760.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 2 str.
           86/8/59]
          Length = 184

 Score =  153 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 79/181 (43%), Positives = 117/181 (64%), Gaps = 1/181 (0%)

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           MQ+YILR+WS+V+ GT++ QK LFFNLRRL+  L    DN  K E    I+ +L VS S+
Sbjct: 1   MQDYILRNWSIVRGGTSSAQKALFFNLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTSD 60

Query: 173 VISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           V  M+ RL+G D SL+A +N  +  +S+  D+LV DH  Q+++     + + R   LTR+
Sbjct: 61  VEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTRA 120

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           +  LN RE  I   RRL ++ VTLE L  +  +S+ERVRQIE+RA +K++ ++  Q EL+
Sbjct: 121 LDTLNERELHIIRERRLDDDGVTLEALGEKLGISKERVRQIESRAMEKLKIALLSQHELA 180

Query: 292 S 292
           +
Sbjct: 181 A 181


>gi|283796413|ref|ZP_06345566.1| RNA polymerase sigma-F factor [Clostridium sp. M62/1]
 gi|291075823|gb|EFE13187.1| RNA polymerase sigma-F factor [Clostridium sp. M62/1]
 gi|295091441|emb|CBK77548.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase
           sigma-70 factor, sigma-B/F/G subfamily [Clostridium cf.
           saccharolyticum K10]
 gi|295114800|emb|CBL35647.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase
           sigma-70 factor, sigma-B/F/G subfamily
           [butyrate-producing bacterium SM4/1]
          Length = 245

 Score =  153 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 54/238 (22%), Positives = 103/238 (43%), Gaps = 17/238 (7%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD +A  RLV  ++ LV  I   + G G    ++   G+IGL++A+ KFD     R +TY
Sbjct: 20  GDKAARDRLVEENMGLVWSIVRRFAGRGCETEDLFQIGSIGLIKAIDKFDTSYDVRFSTY 79

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           ++  I   ++ ++     ++K+  +  +  +     ++    + +     +   +  IA 
Sbjct: 80  AVPMIAGEIRRFLRDDG-MIKVSRSVKEMGI-----KVSAAREKLAGTLGREPTLEEIAG 133

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            +  S  EV +     A  ESL A     D  +    D L  +    E+VL         
Sbjct: 134 SVGASREEVAASLEAGAQVESLYAP-AGGDDTNLSLLDRLSQESRENEEVL--------D 184

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           R +L + +  L  +ER +   R       T   ++ +  +S+ +V ++E R  KK++E
Sbjct: 185 RMVLKKLLGSLGEKERELIVRRYFYGQ--TQTKIAGQMGISQVQVSRMEKRILKKMRE 240


>gi|302338101|ref|YP_003803307.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Spirochaeta
           smaragdinae DSM 11293]
 gi|301635286|gb|ADK80713.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Spirochaeta
           smaragdinae DSM 11293]
          Length = 262

 Score =  153 bits (388), Expect = 2e-35,   Method: Composition-based stats.
 Identities = 58/263 (22%), Positives = 119/263 (45%), Gaps = 19/263 (7%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL---PISEVVSEGNI 84
           +LE++ E  L + YR   D     R +  +  LV  +A              ++V  G  
Sbjct: 5   LLEEKTEAELWELYRNSRDPKIRDRFIEQYSPLVKYVAGKVAIGMPQNVEFDDLVGFGVF 64

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL  A++KFDPE+  +  TY++  I+ A+ + + RS   V        + +   + RL+ 
Sbjct: 65  GLFDAIEKFDPEKHVKFKTYAVTRIRGAIYDEL-RSIDWVPRSVRQKAREIEETIHRLEA 123

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSS-QWQ 201
            L        +      IA +L +S ++   +  +++G    SLN +  + D+N +    
Sbjct: 124 SL-------GRAASDKEIADELGISVADFQKLMLKISGTSVLSLNDVWYTGDENDTVAIV 176

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           D +         ++IEKEE    R ++ +++S L  +E+++      ++  +TL+ +   
Sbjct: 177 DGIESPQSLNPDIIIEKEE---IRRVIVQAISELPEKEKKVLVLYYYED--LTLKEIGKV 231

Query: 262 FEVSRERVRQIEARAFKKVQESI 284
            +V+  RV Q+  +A  +++  +
Sbjct: 232 LDVTESRVSQLHTKAIMRLRSKL 254


>gi|218677311|ref|ZP_03525208.1| RNA polymerase factor sigma-32 [Rhizobium etli CIAT 894]
          Length = 171

 Score =  153 bits (388), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 74/169 (43%), Positives = 114/169 (67%), Gaps = 1/169 (0%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L +QEE+ LA R+++H D  A +++  +H+RLV+ +A  +R +GLP+S++V EG +GL
Sbjct: 3   PYLARQEEHDLAIRWKDHDDRGARNQIAMAHMRLVISMAGKFRNFGLPMSDLVQEGYVGL 62

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A  +F+P+R  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 63  LEAAARFEPDRDVRFSTYASWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRAKL 122

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
                          IA  L VS ++V +M+ RL+G D SL A   S D
Sbjct: 123 AKGDTQLTLQSIHQEIAAALGVSLADVQTMDARLSGNDASLQAPSVSGD 171


>gi|254698073|ref|ZP_05159901.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 2 str.
           86/8/59]
          Length = 188

 Score =  153 bits (388), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 80/185 (43%), Positives = 121/185 (65%), Gaps = 1/185 (0%)

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           ++A+MQ+YILR+WS+V+ GT++ QK LFFNLRRL+  L    DN  K E    I+ +L V
Sbjct: 1   MRASMQDYILRNWSIVRGGTSSAQKALFFNLRRLRSKLAQTDDNMTKAEIYREISDQLGV 60

Query: 169 SESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           S S+V  M+ RL+G D SL+A +N  +  +S+  D+LV DH  Q+++     + + R   
Sbjct: 61  STSDVEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIAESSIDMERRNRW 120

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           LTR++  LN RE  I   RRL ++ VTLE L  +  +S+ERVRQIE+RA +K++ ++  Q
Sbjct: 121 LTRALDTLNERELHIIRERRLDDDGVTLEALGEKLGISKERVRQIESRAMEKLKIALLSQ 180

Query: 288 VELSS 292
            EL++
Sbjct: 181 HELAA 185


>gi|325845925|ref|ZP_08169123.1| putative RNA polymerase sigma factor RpoD [Anaerococcus
           hydrogenalis ACS-025-V-Sch4]
 gi|325481831|gb|EGC84863.1| putative RNA polymerase sigma factor RpoD [Anaerococcus
           hydrogenalis ACS-025-V-Sch4]
          Length = 333

 Score =  153 bits (387), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 64/271 (23%), Positives = 129/271 (47%), Gaps = 23/271 (8%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISE 77
            +I ++  L  ++         + G+ +A   LV  +  LV   A  +    G  L + +
Sbjct: 74  SDIIRLSDLTNEQIVEQF----QEGNQNALGALVDKNQGLVRSRASYFYRSHGNDLELED 129

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +V  G +G+++A +KFD   G++  TY+  WI  A+++ I +    ++I         + 
Sbjct: 130 LVQSGMLGMIRAAEKFDLTLGYKFTTYAYKWIDKAIRKAINKEGHTIRIPAGK-----YL 184

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE---SEVISMNCRLAGDESLNALINSSD 194
            L +LK  L+A  +     E++  I K+  + +    ++  +N       SLN  ++S D
Sbjct: 185 KLNKLKQILKA--NPEASEEELYKILKQEGIDKKQADDLFLINRNQVNSTSLNINLDSED 242

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
               +  D +  D    +  ++    +K+  + L +++  L+ RE++I   R   +N  P
Sbjct: 243 STGDELMDMVGDDSIPVDDQIL----KKDMEDFLMKALDQLSDREKQIIIYRYGLDNEKP 298

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            TLE + + + +SRER+RQIE +A  K+++ 
Sbjct: 299 KTLEEIGTIYSLSRERIRQIENQALGKLKQY 329


>gi|6010722|gb|AAF01227.1|AF184096_1 mutant RpoS [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
          Length = 228

 Score =  153 bits (387), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 56/171 (32%), Positives = 92/171 (53%), Gaps = 6/171 (3%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
           LR  +     ++           IA++L+    +V  M        S++  
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDTP 225


>gi|212695902|ref|ZP_03304030.1| hypothetical protein ANHYDRO_00435 [Anaerococcus hydrogenalis DSM
           7454]
 gi|212677025|gb|EEB36632.1| hypothetical protein ANHYDRO_00435 [Anaerococcus hydrogenalis DSM
           7454]
          Length = 333

 Score =  153 bits (387), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 64/271 (23%), Positives = 129/271 (47%), Gaps = 23/271 (8%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISE 77
            +I ++  L  ++         + G+ +A   LV  +  LV   A  +    G  L + +
Sbjct: 74  SDIIRLSDLTNEQIVEQF----QEGNQNALGALVDKNQGLVRSRASYFYRSHGNDLELED 129

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +V  G +G+++A +KFD   G++  TY+  WI  A+++ I +    ++I         + 
Sbjct: 130 LVQSGMLGMIRAAEKFDLTLGYKFTTYAYKWIDKAIRKAINKEGHTIRIPAGK-----YL 184

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE---SEVISMNCRLAGDESLNALINSSD 194
            L +LK  L+A  +     E++  I K+  + +    ++  +N       SLN  ++S D
Sbjct: 185 KLNKLKQILKA--NPEASEEELYKILKQEGIDKKQADDLFLINRNQVNSTSLNINLDSED 242

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
               +  D +  D    +  ++    +K+  + L +++  L+ RE++I   R   +N  P
Sbjct: 243 STGDELMDMVGDDSIPVDDQIL----KKDMEDFLMKALDQLSDREKQIIIYRYGLDNEKP 298

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            TLE + + + +SRER+RQIE +A  K+++ 
Sbjct: 299 KTLEEIGTIYSLSRERIRQIENQALGKLKQY 329


>gi|6010720|gb|AAF01226.1|AF184095_1 mutant RpoS [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
          Length = 254

 Score =  153 bits (387), Expect = 3e-35,   Method: Composition-based stats.
 Identities = 56/170 (32%), Positives = 92/170 (54%), Gaps = 6/170 (3%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           LR  +     ++           IA++L+    +V  M        S++ 
Sbjct: 179 LRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVDT 224


>gi|256546106|ref|ZP_05473459.1| RNA polymerase sigma factor RpoD (sigma-A) [Anaerococcus vaginalis
           ATCC 51170]
 gi|256398223|gb|EEU11847.1| RNA polymerase sigma factor RpoD (sigma-A) [Anaerococcus vaginalis
           ATCC 51170]
          Length = 333

 Score =  153 bits (387), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 64/271 (23%), Positives = 129/271 (47%), Gaps = 23/271 (8%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISE 77
            +I ++  L  ++         + G+ +A   LV  +  LV   A  +    G  L + +
Sbjct: 74  SDIIRLSDLTNEQIVEQF----QEGNQNALGALVDKNQGLVRSRASYFYRSHGNDLELED 129

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +V  G +G+++A +KFD   G++  TY+  WI  A+++ I +    ++I         + 
Sbjct: 130 LVQSGMLGMIRAAEKFDLTLGYKFTTYAYKWIDKAIRKAINKEGHTIRIPAGK-----YL 184

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE---SEVISMNCRLAGDESLNALINSSD 194
            L +LK  L+A  +     E++  I K+  + +    ++  +N       SLN  ++S D
Sbjct: 185 KLNKLKQILKA--NPEASEEELYKILKQEGIDKKQADDLFLINRNQVNSTSLNINLDSED 242

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
               +  D +  D    +  ++    +K+  + L +++  L+ RE++I   R   +N  P
Sbjct: 243 STGDELMDMVGDDSIPVDDQIL----KKDMEDFLMKALDQLSDREKQIIIYRYGLDNEKP 298

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            TLE + + + +SRER+RQIE +A  K+++ 
Sbjct: 299 KTLEEIGTIYNLSRERIRQIENQALGKLKQY 329


>gi|197723821|gb|ACH72690.1| RNA polymerase sigma-37 factor [Listeria marthii]
          Length = 238

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 59/255 (23%), Positives = 115/255 (45%), Gaps = 24/255 (9%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G     +++  I   ++ ++      V +     +        ++K  ++ +T    
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQ 116

Query: 155 KPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +    
Sbjct: 117 SSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTD 173

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++S+  
Sbjct: 174 DGF--------ERVNQRMLLEKVLPVLDEREQKILQYTFIEN--RSQKETGELLDISQMH 223

Query: 269 VRQIEARAFKKVQES 283
           V +I+ +A KK++E+
Sbjct: 224 VSRIQRQAIKKLREA 238


>gi|298250481|ref|ZP_06974285.1| RNA polymerase, sigma 32 subunit, RpoH [Ktedonobacter racemifer DSM
           44963]
 gi|297548485|gb|EFH82352.1| RNA polymerase, sigma 32 subunit, RpoH [Ktedonobacter racemifer DSM
           44963]
          Length = 313

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 73/308 (23%), Positives = 126/308 (40%), Gaps = 68/308 (22%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDL--------------------SAAHRLVTSHL 58
           Y  +I    +L   E   LA+R    G                       A +RLV ++L
Sbjct: 20  YKRDIAGFSLLSPDEVVGLAQRIEGAGKQRGTRLQFRTVSADGANPDVQQAKNRLVEANL 79

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           RLV  +A  YRG+G+ I +++ EGNIGL+ AV+KFDP +G+R +TY+  WI+  +   + 
Sbjct: 80  RLVRSVAYQYRGFGVDIMDLIQEGNIGLIHAVEKFDPTKGYRFSTYATHWIRQYICRELA 139

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
           R    ++I     +        +L+   +A T  + +  Q  A AK +       ++   
Sbjct: 140 RQIHKIRIPLYLQE--------QLRHLPEAPTTPDGQAMQDQAHAKLM-------VAYER 184

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
             A   S +A+    +  +              EQ  ++  +R+    +  R+   L  R
Sbjct: 185 SKATHVSFDAVPFEFEDPAPTP-----------EQYCMQGAQRQLLHQLFLRA--GLTQR 231

Query: 239 ERRIFEARRLQ--------------------ENPVTLENLSSEFEVSRERVRQIEARAFK 278
           ER++   R                       ++  T   + ++  +S E VRQIE RA  
Sbjct: 232 ERQVLVLRYGLQQQREEGLEALLSGAISDQKQDESTYPQIGTQLGLSHEAVRQIEMRALL 291

Query: 279 KVQESIQK 286
           K++  +Q 
Sbjct: 292 KLRYQVQA 299


>gi|291547959|emb|CBL21067.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase
           sigma-70 factor, sigma-B/F/G subfamily [Ruminococcus sp.
           SR1/5]
          Length = 260

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 61/246 (24%), Positives = 109/246 (44%), Gaps = 16/246 (6%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GD +A   L   +  L+  +A  + G G+ + ++   G+IGL++AV KFD     + +T
Sbjct: 13  QGDKAARDLLFEENTGLIYSVAKRFLGRGVEMEDLFQIGSIGLLKAVDKFDMSYDVKFST 72

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y++  I   ++ Y+         G     + L  N  R+    +A+T    +      +A
Sbjct: 73  YAVPMIIGEIKRYLRDD------GILKVSRSLKENHYRIYQVREALTRRLEREPTTGEMA 126

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           +++ +S  E++      A  ESL+  I   +       D L    + QE+VL        
Sbjct: 127 EEMGISIEELVMTMESGAEVESLHKTIYQGEGTEISLMDKLPEKENRQEKVL-------- 178

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            R  L   +  L  +ERR+   R  Q   +T   ++ E  VS+ +V ++E R  + +QES
Sbjct: 179 DRIFLEEILGTLEAKERRLIYMRYFQN--MTQMEIAHELGVSQVQVSRMEKRILRSLQES 236

Query: 284 IQKQVE 289
            +K  E
Sbjct: 237 AEKNKE 242


>gi|297158639|gb|ADI08351.1| RNA polymerase sigma factor, sigma L [Streptomyces bingchenggensis
           BCW-1]
          Length = 276

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 54/237 (22%), Positives = 96/237 (40%), Gaps = 17/237 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +
Sbjct: 52  RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTV 111

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      ++    +   V  +A  L VS
Sbjct: 112 VGEIKRFFRDTSWSVRVPRRLQELRLA-----LTKTSDELSQKLDRSPTVTELATALGVS 166

Query: 170 ESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E +V+            SL++     D       D L Y+    E V          R  
Sbjct: 167 EEDVVDGLAVGNAYTASSLDSPSPEDDGGEGSLADRLGYEDSALEGV--------EYRES 218

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   ++ L PRER+I   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 219 LKPLLAKLPPRERQIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 273


>gi|22770516|gb|AAN06633.1|AF497205_1 sigma factor B [Listeria monocytogenes]
          Length = 259

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 61/263 (23%), Positives = 120/263 (45%), Gaps = 24/263 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +++D   G     +++  I   ++ ++      V +     +        ++K  ++ +T
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELT 126

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWL 204
                  Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +
Sbjct: 127 RELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVV 183

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++
Sbjct: 184 GGTDDGF--------ERVNQRMLLEKVLPVLDEREQKILQFTFIEN--RSQKETGELLDI 233

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           S+  V +I+ +A KK+ E++Q +
Sbjct: 234 SQMHVSRIQRQAIKKLLEALQNE 256


>gi|22770506|gb|AAN06628.1|AF497200_1 sigma factor B [Listeria monocytogenes]
          Length = 259

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 61/263 (23%), Positives = 120/263 (45%), Gaps = 24/263 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQENGDEDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +++D   G     +++  I   ++ ++      V +     +        ++K  ++ +T
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELT 126

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWL 204
                  Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +
Sbjct: 127 RELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVV 183

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++
Sbjct: 184 GGTDDGF--------ERVNQRMLLEKVLPVLDEREQKILQFTFIEN--RSQKETGELLDI 233

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           S+  V +I+ +A KK+ E++Q +
Sbjct: 234 SQMHVSRIQRQAIKKLLEALQNE 256


>gi|326203397|ref|ZP_08193262.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Clostridium
           papyrosolvens DSM 2782]
 gi|325986655|gb|EGD47486.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Clostridium
           papyrosolvens DSM 2782]
          Length = 249

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 43/253 (16%), Positives = 109/253 (43%), Gaps = 15/253 (5%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E  L   Y   G+    + +V+++L L   ++  +   G+   ++     + L++AV++
Sbjct: 12  DEAQLFSLYISTGNQDYRNEIVSNYLSLAEYLSKKFLNRGVDFDDIYQVACLALIKAVER 71

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F PE+G +  +++   I   ++ +     + +KI     + R   N  R       +T  
Sbjct: 72  FSPEKGVKFISFATPTILGEIKRFFRDKSTTIKIPRRIYESRQGVNKAR-----DELTQK 126

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +  +   IA+ + +S   V+ +    +     +   + + +N S+  D L YD    E
Sbjct: 127 LSRVPRADEIAEYMGISVDTVLEILEAGSSSIVKSLDQSINQENDSELGDTLGYDEKTYE 186

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
            +        + ++ L ++++  N  E+   + R +Q   +T + ++    VS+  + ++
Sbjct: 187 MI--------DNKDFLEKALTSFNDIEKEFIKYRYIQN--MTQKQIAEILGVSQMYISRM 236

Query: 273 EARAFKKVQESIQ 285
           E +   K +  ++
Sbjct: 237 EKKILDKFRTYLK 249


>gi|320009626|gb|ADW04476.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 288

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 55/237 (23%), Positives = 96/237 (40%), Gaps = 17/237 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +
Sbjct: 64  RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTV 123

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +   V  +AK L VS
Sbjct: 124 VGEIKRFFRDTSWSVRVPRRLQELRLA-----LTKTSDELAQKLDRSPTVPELAKALGVS 178

Query: 170 ESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E +V+            SL++     D       D L Y+    E V          R  
Sbjct: 179 EEDVVDGLAVGNAYTASSLDSPSPEDDGGEGSLADRLGYEDAALEGV--------EYRES 230

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   ++ L PRER+I   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 231 LKPLLAKLAPRERQIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLTQLREGL 285


>gi|302552550|ref|ZP_07304892.1| RNA polymerase sigma-E factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302470168|gb|EFL33261.1| RNA polymerase sigma-E factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 301

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 55/237 (23%), Positives = 96/237 (40%), Gaps = 17/237 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +
Sbjct: 77  RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTV 136

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      ++    +   V  +A  L VS
Sbjct: 137 VGEIKRFFRDTSWSVRVPRRLQELRLA-----LTKASDELSQKLDRSPTVTELASVLGVS 191

Query: 170 ESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E +V+            SL++     D       D L Y+    E V          R  
Sbjct: 192 EEDVVDGLAVGNAYTASSLDSPAPEDDGGEGSLADRLGYEDTALEGV--------EYRES 243

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   ++ L PRERRI   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 244 LKPLLAKLPPRERRIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 298


>gi|296270865|ref|YP_003653497.1| Sig B/F/G subfamily RNA polymerase sigma-28 [Thermobispora bispora
           DSM 43833]
 gi|296093652|gb|ADG89604.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Thermobispora bispora DSM 43833]
          Length = 259

 Score =  153 bits (386), Expect = 4e-35,   Method: Composition-based stats.
 Identities = 53/243 (21%), Positives = 103/243 (42%), Gaps = 18/243 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                 LV  H+ LV  +A  +R  G  + ++     IGL++++ +FD  RG   +TY+ 
Sbjct: 32  QRIRDELVELHMPLVEYLARRFRNRGEWLDDLTQVATIGLIKSIDRFDLSRGVEFSTYAT 91

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I   ++ +       V++     + +L      L   +  ++    +   V  +A+ L
Sbjct: 92  PTIVGEIKRHFRDKGWAVRVPRRLQELKLS-----LTKAISELSQRESRAPTVAELAEHL 146

Query: 167 NVSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            +SE EV+    +       SL+A   S D+++    D L         ++ E  E    
Sbjct: 147 QMSEEEVLEGLESANAYSTVSLDAPD-SGDEDAPAVSDSLG--------IVDESLEGVEY 197

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L   +  L PRE+RI   R      +T   +++E  +S+  V ++ AR   +++E +
Sbjct: 198 RESLKPLLERLPPREKRILLLRFFGN--MTQSQIANELGISQMHVSRLLARTLAQLREGL 255

Query: 285 QKQ 287
             +
Sbjct: 256 TAE 258


>gi|23978347|dbj|BAC21141.1| principal sigma factor [Oscillatoria sp. PCC 7112]
          Length = 188

 Score =  152 bits (385), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 43/199 (21%), Positives = 90/199 (45%), Gaps = 13/199 (6%)

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
              GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+   I      +++  
Sbjct: 1   MNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV 60

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
                 L+  + R+K   + ++    +      IA ++ ++  ++  +        SL  
Sbjct: 61  H-----LYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLET 115

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            I    +  S+  D++  D     +   ++  +   R  L   +  L+PRER +   R  
Sbjct: 116 PI--GKEEDSRLGDFIESDG----ETPEDQVSKNLLREDLESVLDTLSPRERDVLRLRYG 169

Query: 249 QENPV--TLENLSSEFEVS 265
            ++    TLE +   F V+
Sbjct: 170 LDDGRMKTLEEIGQIFNVT 188


>gi|297200783|ref|ZP_06918180.1| RNA polymerase sigma-G factor [Streptomyces sviceus ATCC 29083]
 gi|197712353|gb|EDY56387.1| RNA polymerase sigma-G factor [Streptomyces sviceus ATCC 29083]
          Length = 297

 Score =  152 bits (385), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 54/237 (22%), Positives = 96/237 (40%), Gaps = 17/237 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +
Sbjct: 73  RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTV 132

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      ++    +   V  +A  L VS
Sbjct: 133 VGEIKRFFRDTSWSVRVPRRLQELRLA-----LTKASDELSQKLDRSPTVAELASVLGVS 187

Query: 170 ESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E +V+            SL++     D       D L Y+    E V          R  
Sbjct: 188 EEDVVDGLAVGNAYTASSLDSPAPEDDGGEGSLADRLGYEDTALEGV--------EYRES 239

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   ++ L PRER+I   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 240 LKPLLAKLPPRERQIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 294


>gi|332799331|ref|YP_004460830.1| RNA polymerase sigma-28 subunit SigF [Tepidanaerobacter sp. Re1]
 gi|332697066|gb|AEE91523.1| RNA polymerase, sigma 28 subunit, SigF [Tepidanaerobacter sp. Re1]
          Length = 240

 Score =  152 bits (385), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 48/249 (19%), Positives = 110/249 (44%), Gaps = 17/249 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L K  +  G+  A   LV+ +L LV  I   +   G    ++   G+IGL++A++KFD 
Sbjct: 8   ELLKEAK-RGEKKARDELVSLNLGLVWSIVKRFNNRGYEPEDLFQIGSIGLLKAIEKFDF 66

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
               + +TY++  I   ++ YI      +K+  +  +        +++   + +T+   +
Sbjct: 67  SYDVKFSTYAVPMIMGEIRRYIRDD-KPIKVSRSLKELGY-----KIQKTQEELTNTLDR 120

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
              +  I+ ++ V   E++          SLN ++   D +     D L  +        
Sbjct: 121 EPTINEISDEMEVPVEEIVMAMEASQSLVSLNDVVYQDDGSPIYLIDQLNENE------- 173

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
             +E   + +  L  ++S L+  ER+I   R  ++  +T  +++ +  +++ +V ++E +
Sbjct: 174 -YQENLLHDKIALKEALSKLDRDERQIITLRYFKD--MTQIDVAKKLNMTQVQVSRLERK 230

Query: 276 AFKKVQESI 284
              KV+  +
Sbjct: 231 VLTKVKNLL 239


>gi|254390381|ref|ZP_05005598.1| sigma L [Streptomyces clavuligerus ATCC 27064]
 gi|294813859|ref|ZP_06772502.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|197704085|gb|EDY49897.1| sigma L [Streptomyces clavuligerus ATCC 27064]
 gi|294326458|gb|EFG08101.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 314

 Score =  152 bits (385), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 54/237 (22%), Positives = 95/237 (40%), Gaps = 17/237 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +
Sbjct: 90  RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTV 149

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +   V  +A  L VS
Sbjct: 150 VGEIKRFFRDTSWSVRVPRRLQELRLA-----LTKASDELAQRLDRSPTVPELAAVLGVS 204

Query: 170 ESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E EV+            SL++     D       D L Y+    E V          R  
Sbjct: 205 EEEVVDGLAVGNAYTASSLDSPSPEDDGGEGSLADRLGYEDTALEGV--------EYRES 256

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   ++ L PRER+I   R      +T   +  E  +S+  V ++  R   ++++ +
Sbjct: 257 LKPLLAKLPPRERQIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLRDGL 311


>gi|300856558|ref|YP_003781542.1| RNA polymerase sigma-F factor [Clostridium ljungdahlii DSM 13528]
 gi|300436673|gb|ADK16440.1| RNA polymerase sigma-F factor [Clostridium ljungdahlii DSM 13528]
          Length = 251

 Score =  152 bits (385), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 44/245 (17%), Positives = 107/245 (43%), Gaps = 16/245 (6%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           +Y + GD  A ++LV  +L LV  I+  +   G    ++   G +GLM+AV  F+ E   
Sbjct: 21  KYAKKGDKDALNKLVELNLPLVASISKKFLNRGYEYEDIFQIGCMGLMKAVNNFNEEYNV 80

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY++  I   ++ ++     ++K+  +          +++    +A+T    +   +
Sbjct: 81  KFSTYAVPMILGEIKRFLRDDG-MIKVSRSVK-----NTAKKIHYDREALTKKLNREPTI 134

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +A+   V   E+I      +  + L   I+  D +     D +  +     +++    
Sbjct: 135 QELAEYSGVEVEELIFATESASSLQYLYDTIHQDDGSPVLLIDKISENPKEDVEMV---- 190

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
                +  L  +++ L+ + R+I   R  ++   T   ++    +++ +V +IE +  K 
Sbjct: 191 ----DKIALKEALNNLDVKSRQIIMLRYFKD--KTQVQVAKMLGINQVQVSRIEKKVLKT 244

Query: 280 VQESI 284
           ++E +
Sbjct: 245 MREIL 249


>gi|332981002|ref|YP_004462443.1| RNA polymerase sigma-28 subunit SigF [Mahella australiensis 50-1
           BON]
 gi|332698680|gb|AEE95621.1| RNA polymerase, sigma 28 subunit, SigF [Mahella australiensis 50-1
           BON]
          Length = 256

 Score =  152 bits (385), Expect = 5e-35,   Method: Composition-based stats.
 Identities = 45/259 (17%), Positives = 106/259 (40%), Gaps = 19/259 (7%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           +L +QE   L  + R+ G+  AA  L   +L LV  +   +   G    ++   G++GL+
Sbjct: 16  LLTQQEIEDLIVKVRQ-GNKQAAEILAERNLGLVHNVVRKFMNRGYEYDDLFQVGSMGLV 74

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL-VKIGTTANQKRLFFNLRRLKGHL 146
           +A+  +D     + +TY++  I   ++ ++    S+ V         ++     R+K  L
Sbjct: 75  KAINNYDLSYNVKFSTYAVPMIMGEIKRFLRDDGSIKVSRSVKIAAYKIHNAQDRIKKEL 134

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                   +   V  +A  L++  ++V+          SL        ++S    D +  
Sbjct: 135 -------GREPSVQELATALDMEPADVVYAMEADTVPVSLYDSAYEDGESSISLIDRISD 187

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
             +    V+         R  L   ++ L+ + R++   R  ++   T   ++    +++
Sbjct: 188 GDELDTDVI--------DRVALKECIAQLDAKGRQVILLRYFKD--KTQSEVAQMLGITQ 237

Query: 267 ERVRQIEARAFKKVQESIQ 285
            +V +IE +  + +++ I+
Sbjct: 238 VQVCRIEKKVLEFMRQYIK 256


>gi|302559791|ref|ZP_07312133.1| RNA polymerase sigma-F factor [Streptomyces griseoflavus Tu4000]
 gi|302477409|gb|EFL40502.1| RNA polymerase sigma-F factor [Streptomyces griseoflavus Tu4000]
          Length = 301

 Score =  152 bits (385), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 54/240 (22%), Positives = 97/240 (40%), Gaps = 17/240 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +
Sbjct: 76  RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTV 135

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      ++    +   V  +A  L VS
Sbjct: 136 VGEIKRFFRDTSWSVRVPRRLQELRLA-----LTKASDELSQKLDRSPTVPELAAVLGVS 190

Query: 170 ESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E +V+            SL++     D       D L Y+    E V          R  
Sbjct: 191 EEDVVDGLAVGNAYTASSLDSPAPEDDGGEGSLADRLGYEDTALEGV--------EYRES 242

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   ++ L PRER+I   R      +T   +  E  +S+  V ++  R   +++E +  +
Sbjct: 243 LKPLLAKLPPRERQIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGLISE 300


>gi|119715950|ref|YP_922915.1| sigma-70 region 2 domain-containing protein [Nocardioides sp.
           JS614]
 gi|119536611|gb|ABL81228.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Nocardioides sp.
           JS614]
          Length = 270

 Score =  152 bits (385), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 57/265 (21%), Positives = 109/265 (41%), Gaps = 23/265 (8%)

Query: 29  LEKQEEYVLAKRYREHGDLSAA-----HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           L +     L    R+ G  +A        LV  HL LV   A  +R  G P+ ++V  G 
Sbjct: 20  LTRLRSAELFAMLRDDGAPAARRDAAREGLVHLHLPLVEHCARRFRNRGEPLEDLVQVGT 79

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL+++V +FD +RG   +TY+   I   ++ Y       +++     + R+     ++ 
Sbjct: 80  IGLIKSVDRFDADRGVEFSTYATPTIIGEIKRYFRDKGWAIRVPRRLQELRM-----QIS 134

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQ 201
                +T +  +      +A  +  +  E++    +       SL+A  +  D  +S   
Sbjct: 135 TASAELTQSLGRSPTPRELAGAIGCTVEEIVEGIESSNAYSTLSLDATDDGDDNTASMLD 194

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
              V D         E  E    R  L   +  L PRE++I   R  +   +T   ++ E
Sbjct: 195 AIGVDD---------EGLEHVEIRESLKPLLDRLEPREKKILLLRFFKN--MTQSQIAEE 243

Query: 262 FEVSRERVRQIEARAFKKVQESIQK 286
             VS+  V ++  R  ++++ S+++
Sbjct: 244 IGVSQMHVSRLLNRTLEQLRVSLEE 268


>gi|226329393|ref|ZP_03804911.1| hypothetical protein PROPEN_03298 [Proteus penneri ATCC 35198]
 gi|225202579|gb|EEG84933.1| hypothetical protein PROPEN_03298 [Proteus penneri ATCC 35198]
          Length = 137

 Score =  152 bits (385), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 62/137 (45%), Positives = 93/137 (67%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++  S+ +  +  +  YI      PML  +EE  LA+R    GDL AA  L+ SHLR 
Sbjct: 1   MTKEMQSLALVPQGSIEAYIRAANSYPMLTAEEEKELAERLHYEGDLDAARTLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V+ +A  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VIHVARSYSGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVKIGTTANQKRLFF 137
           W +VK+ TT +Q++LFF
Sbjct: 121 WRIVKVATTKSQRKLFF 137


>gi|229113622|ref|ZP_04243069.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock1-15]
 gi|228669818|gb|EEL25214.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock1-15]
 gi|324323938|gb|ADY24981.1| RNA polymerase sigma-43 factor [Bacillus thuringiensis serovar
           finitimus YBT-020]
          Length = 323

 Score =  152 bits (385), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 65/268 (24%), Positives = 114/268 (42%), Gaps = 13/268 (4%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP--ISE 77
           I  I    +L K+E   L KRY+ HG+      L   +  LV+ +A  Y+         +
Sbjct: 40  IRGIGNYKVLSKEESLHLFKRYK-HGEKDLRDYLFHVNEGLVLSVARNYKNKHPDIEFDD 98

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLF 136
           +V EGN G+++A++ F+P+ G+  +TY+ WWI+ +M   I  +     KI T  NQ  L 
Sbjct: 99  LVQEGNEGMLRAMEDFNPDLGYCFSTYAFWWIQKSMLGIIRKKKSGPFKIPTHVNQFNLK 158

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
           +                 +   V  + K+LNV+   VI          ++   I++ +++
Sbjct: 159 YV-----ELEDKYLQRYNRTPSVEEVVKELNVTRETVIRHKVYYKRATTMTLDIDTINED 213

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPVTL 255
                +    D            E  N    L     VLNP+++ +      L +  V L
Sbjct: 214 VG-ISNPFFDDRSAIPSTNEMIIEDLNYEIWLIFD-EVLNPKQKMVLNLCFGLLDGKVYL 271

Query: 256 E-NLSSEFEVSRERVRQIEARAFKKVQE 282
              ++    ++ ERV QI+  A KK+++
Sbjct: 272 HKEIAKALMITTERVSQIKDEAIKKLKK 299


>gi|146296669|ref|YP_001180440.1| FliA/WhiG family RNA polymerase sigma factor [Caldicellulosiruptor
           saccharolyticus DSM 8903]
 gi|145410245|gb|ABP67249.1| RNA polymerase, sigma subunit, RpoX/SigF [Caldicellulosiruptor
           saccharolyticus DSM 8903]
          Length = 231

 Score =  152 bits (385), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 51/241 (21%), Positives = 98/241 (40%), Gaps = 17/241 (7%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            ++GD  A   L+ ++L LV  I   +   G+   ++   G IGL++AV +FD     R 
Sbjct: 5   AKNGDKKARQELIENNLALVWSIVKKFVVKGIEADDLFQIGCIGLIKAVDRFDLSFNVRF 64

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY++  I   ++ Y+      +KI      +++  N  +LK         N +   +  
Sbjct: 65  STYAVPMIIGEIKRYLRDDGK-IKIS-----RKIKENQNKLKRFRDEFLFQNGREPTISE 118

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           I++   +S+ +++          SLN +IN  +       D    +             R
Sbjct: 119 ISEATGLSQDDILLCIDASLDVTSLNEVINQEEGKPITLMDIAADEDYSS---------R 169

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                 L   +  L  RER I   R  +    T   ++ E  +S+  V +IE +A ++++
Sbjct: 170 LLDIMALKEGLRKLKGRERYIIFMRYFKN--KTQSEIAKELNISQVHVSRIEKKALERIK 227

Query: 282 E 282
            
Sbjct: 228 R 228


>gi|2660755|gb|AAC29510.1| sigma-B general stress transcription factor [Bacillus
           licheniformis]
          Length = 265

 Score =  152 bits (384), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 65/283 (22%), Positives = 126/283 (44%), Gaps = 30/283 (10%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K   L K E   L K+Y++  D  A   LV ++  LV  +A  Y        ++   G 
Sbjct: 7   SKTTKLTKTEVDTLIKKYQDSQDEDAQLTLVQTYKNLVETLAKKYSKGKSFHEDLCQVGM 66

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           +GL+ A+K++DP+ G     +++  I   ++ ++      V +     +        R+K
Sbjct: 67  LGLLGAIKRYDPDVGKSFEAFAIPTIIGEIKRFLRDKTWSVHVPRRIKELG-----PRIK 121

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNS 197
             +  +T+   +  +V  IA+ L+V+E EV+           L+ D S+ A    +D ++
Sbjct: 122 MAVDHLTNETQRSPKVDEIAEFLDVTEEEVLETMEMGKSYQALSVDHSIEA---DADGST 178

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
               D +    +G E+V        N++ ML   + VL+ RE++I E   +Q    + + 
Sbjct: 179 VTILDIVGSQEEGYEKV--------NQKLMLESVLHVLSDREKQIIELTYIQN--KSQKE 228

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQKP 300
                 +S+  V +++ +A KK++E+      L+  P +  KP
Sbjct: 229 TGDMLGISQMHVSRLQRKAVKKLREA------LAEDPFMELKP 265


>gi|224000633|ref|XP_002289989.1| plastid RNA polymerase sigma factor [Thalassiosira pseudonana
           CCMP1335]
 gi|220975197|gb|EED93526.1| plastid RNA polymerase sigma factor [Thalassiosira pseudonana
           CCMP1335]
          Length = 321

 Score =  152 bits (384), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 60/246 (24%), Positives = 110/246 (44%), Gaps = 14/246 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  R+V  ++RLVV IA  Y G G+ + ++V EG++GL +A +KFDP++GF+ +TY+ 
Sbjct: 60  KEAKQRMVQCNMRLVVSIARRYHGVGVNVQDLVQEGSLGLARAAEKFDPKKGFKFSTYAS 119

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      +++    +   L   +RR +  LQ         E    +A ++
Sbjct: 120 WWIQQAVFRSIAYHSRTIRLPVHVH--NLLNKVRRARQVLQQELGRTPTNE---EMAVEM 174

Query: 167 NVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDG------QEQVLIEKE 219
           +++  +   M        SL      ++ K+     + LV D          E+   +  
Sbjct: 175 DMTIEKYNKMIRTTRNAISLERPKYKNNPKDLGHESEALVGDMVDSSAVIFDEKTPEQNV 234

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAF 277
           +     N +   +  L   ER +   R    +    T+  ++SE   ++  VR  E RA 
Sbjct: 235 DHGLLHNDIEYMLGKLGEDERSVLCLRYGINDGITRTVTLVASEMRQTKSWVRSQECRAL 294

Query: 278 KKVQES 283
           +K++  
Sbjct: 295 RKLRRP 300


>gi|299473209|emb|CBN78785.1| RNA polymerase [Ectocarpus siliculosus]
          Length = 627

 Score =  152 bits (384), Expect = 6e-35,   Method: Composition-based stats.
 Identities = 59/249 (23%), Positives = 116/249 (46%), Gaps = 19/249 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYG------LPISEVVSEGNIGLMQAVKKFDPERGFR 100
            +A  R+++ +LRLVV IA      G      + + +++ +G  GL++AV++FDPE+GFR
Sbjct: 233 KAARDRMISCNLRLVVHIARRKFYKGASGTLKVSLEDMIQDGTAGLVKAVERFDPEKGFR 292

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WW+   +         +V++  + +   +   + RL+    A+ D   +   V 
Sbjct: 293 FSTYATWWVHQGIHCGFADCGRVVRLPMSLH--TMVCKVMRLQT---AMVDQLGRQPTVQ 347

Query: 161 AIAKKLNVSESEVIS-MNCRLAGDESLNA-----LINSSDKNSSQWQDWLVYDHDGQEQV 214
            ++ +  + E +V   +        SL+        + + +NS + +         QE  
Sbjct: 348 ELSLESGLDERKVEKCLRVNQVEPISLDGYRKSKSGHLNFENSFRRERVGDSVKSVQETE 407

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
            ++  +    +  +   +  L+ RE  +   R       P TLE +  E +V+RERVRQI
Sbjct: 408 PVDGADVSLLKTDVDTILGDLSEREAYVLRMRFGIGGSSPSTLETVGQELQVTRERVRQI 467

Query: 273 EARAFKKVQ 281
           +  A +K++
Sbjct: 468 QIAAIQKLR 476


>gi|26665390|dbj|BAC44906.1| principal sigma factor [Scytonema sp. IAM M-262]
          Length = 188

 Score =  152 bits (384), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 43/199 (21%), Positives = 91/199 (45%), Gaps = 13/199 (6%)

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
              GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+   I      +++  
Sbjct: 1   MNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV 60

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
                 L+  + R+K   + ++    +      IA ++ ++  ++  +        SL  
Sbjct: 61  H-----LYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLET 115

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            I    +  S+  D++  D     +   ++  +   R  L + +  L+PRER +   R  
Sbjct: 116 PI--GKEEDSRLGDFIESDS----ETPEDQVSKNLLREDLEKVLDSLSPRERDVLRLRYG 169

Query: 249 QENPV--TLENLSSEFEVS 265
            ++    TLE +   F V+
Sbjct: 170 LDDGRMKTLEEIGQIFNVT 188


>gi|23978302|dbj|BAC21129.1| principal sigma factor [Oscillatoria agardhii]
          Length = 188

 Score =  152 bits (384), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 42/199 (21%), Positives = 90/199 (45%), Gaps = 13/199 (6%)

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
              GL   +++ EG++GL++A +KF+ E+G++ +TY+ WWI+ A+   I      +++  
Sbjct: 1   MNRGLSFQDLIQEGSLGLIRAAEKFEHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV 60

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
                 L+  + R+K   + ++    +      IA ++ ++  ++  +        SL  
Sbjct: 61  H-----LYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLET 115

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            I    +  S+  D++  D     +   ++  +   R  L   +  L+PRER +   R  
Sbjct: 116 PI--GKEEDSRLGDFIESDG----ETPEDQVSKNLLREDLENVLDTLSPRERDVLRLRYG 169

Query: 249 QENPV--TLENLSSEFEVS 265
            ++    TLE +   F V+
Sbjct: 170 LDDGRMKTLEEIGQIFNVT 188


>gi|23978319|dbj|BAC21133.1| principal sigma factor [Microcystis wesenbergii]
          Length = 188

 Score =  152 bits (384), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 44/199 (22%), Positives = 90/199 (45%), Gaps = 13/199 (6%)

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
              GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+   I      +++  
Sbjct: 1   MNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV 60

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
                 L+  + R+K   + ++    +      IA K+ ++  ++  +        SL  
Sbjct: 61  H-----LYETISRIKKTTKILSQEMRRKPTEEEIATKMEMTIEKLRFIAKSAQLPISLET 115

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            I    +  S+  D++  D     +   ++  +   R  L   +  L+PRER +   R  
Sbjct: 116 PI--GKEEDSRLGDFIEADG----ETPEDEVSKNLLREDLENVLDTLSPRERDVLRLRYG 169

Query: 249 QENPV--TLENLSSEFEVS 265
            ++    TLE +   F V+
Sbjct: 170 LDDGRMKTLEEIGQIFNVT 188


>gi|39840783|emb|CAD20832.1| sigma factor [Spinacia oleracea]
          Length = 548

 Score =  152 bits (384), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 58/234 (24%), Positives = 117/234 (50%), Gaps = 11/234 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
               L+ S   LV+ ++  YRG G+   +++  GNIG++Q  ++FD  RG++ +TY  +W
Sbjct: 311 CRDELLKSGRSLVLYLSRYYRGLGVAHEDLMQAGNIGILQGAERFDHTRGYQFSTYVQYW 370

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ AM + + R    +K+ TT     L   + R++   + +  +  K    V ++K   +
Sbjct: 371 IRKAMSQLVSRHGRGIKVPTT-----LSTTINRVQKARKILKRSQGKHPDDVEVSKSTGL 425

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  ++ S +  L    SL+  +            +L    D   ++  +   +++ RN +
Sbjct: 426 SLDKIKSADNCLRIVGSLDQKVGHFIN-----MKYLECTPDTALEMPEKTVMKQHMRNDV 480

Query: 229 TRSMSVLNPRERRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            + +  L+P+ERR+   R   E + ++L  +   F+VS+E +R++E RA  K++
Sbjct: 481 HKLLQELDPKERRVLIHRYGLEGHCMSLHEVGKVFDVSKEWIRKMEKRALTKLR 534


>gi|239930292|ref|ZP_04687245.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291438640|ref|ZP_06578030.1| sigma L factor [Streptomyces ghanaensis ATCC 14672]
 gi|291341535|gb|EFE68491.1| sigma L factor [Streptomyces ghanaensis ATCC 14672]
          Length = 300

 Score =  152 bits (384), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 55/237 (23%), Positives = 96/237 (40%), Gaps = 17/237 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +
Sbjct: 76  RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTV 135

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      ++    +   V  +A  L VS
Sbjct: 136 VGEIKRFFRDTSWSVRVPRRLQELRLA-----LTKTSDELSQKLDRSPTVTELATALGVS 190

Query: 170 ESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E +V+            SL++     D       D L Y+    E V          R  
Sbjct: 191 EEDVVDGLAVGNAYTASSLDSPAPEDDGGEGSLADRLGYEDTALEGV--------EYRES 242

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   ++ L PRERRI   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 243 LKPLLAKLPPRERRIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 297


>gi|23978298|dbj|BAC21128.1| principal sigma factor [Anabaena variabilis]
 gi|23978312|dbj|BAC21131.1| principal sigma factor [Nostoc linckia]
 gi|23978323|dbj|BAC21134.1| principal sigma factor [Anabaena variabilis]
 gi|23978327|dbj|BAC21135.1| principal sigma factor [Anabaenopsis circularis]
 gi|23978343|dbj|BAC21140.1| principal sigma factor [Chlorogloeopsis sp. PCC 6718]
 gi|23978354|dbj|BAC21143.1| principal sigma factor [Fischerella muscicola]
 gi|23978367|dbj|BAC21148.1| principal sigma factor [Chroococcidiopsis sp. PCC 7431]
 gi|26665388|dbj|BAC44905.1| principal sigma factor [Tolypothrix sp. IAM M-259]
 gi|26665392|dbj|BAC44907.1| principal sigma factor [Fischerella sp. IAM M-263]
 gi|26665394|dbj|BAC44908.1| principal sigma factor [Hapalosiphon sp. IAM M-264]
 gi|26665396|dbj|BAC44909.1| principal sigms factor [Hapalosiphon delicatulus IAM M-266]
 gi|26665398|dbj|BAC44910.1| principal sigma factor [Nostoc entophytum IAM M-267]
          Length = 188

 Score =  152 bits (384), Expect = 7e-35,   Method: Composition-based stats.
 Identities = 43/199 (21%), Positives = 91/199 (45%), Gaps = 13/199 (6%)

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
              GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+   I      +++  
Sbjct: 1   MNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV 60

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
                 L+  + R+K   + ++    +      IA ++ ++  ++  +        SL  
Sbjct: 61  H-----LYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLET 115

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            I    +  S+  D++  D     +   ++  +   R  L + +  L+PRER +   R  
Sbjct: 116 PI--GKEEDSRLGDFIESDG----ETPEDQVSKNLLREDLEKVLDSLSPRERDVLRLRYG 169

Query: 249 QENPV--TLENLSSEFEVS 265
            ++    TLE +   F V+
Sbjct: 170 LDDGRMKTLEEIGQIFNVT 188


>gi|260892756|ref|YP_003238853.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Ammonifex
           degensii KC4]
 gi|260864897|gb|ACX52003.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Ammonifex
           degensii KC4]
          Length = 245

 Score =  152 bits (384), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 61/259 (23%), Positives = 115/259 (44%), Gaps = 19/259 (7%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           +L+++    L  R +E GD  A   LV ++L LV K+   + G G    ++   G IGL+
Sbjct: 6   LLDQKTTRALLLRAQE-GDPQARELLVRANLGLVGKVVRRFAGQGREGEDLFQIGCIGLL 64

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +A+ +FDP+RG   +TY++  I   ++ ++     ++K+  +  +       RR+     
Sbjct: 65  KAIDRFDPQRGTCFSTYAVATILGEIRRFLRDDG-MLKVSRSLKE-----TSRRVIRTRA 118

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
           ++     +   V  IA+ L ++  EV+           L   +    + +  W+D L   
Sbjct: 119 SLKMALGREPSVAEIAESLGIAVEEVVMALEAGKAPAFLQEPLAGEGEEALCWEDCLSS- 177

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
                    EKEE       L  S+  L  RER I   R       T E ++ +  +S+ 
Sbjct: 178 ---------EKEESWLETLSLRESLRRLPAREREIIWWRFFAG--YTQEEVAKQLGISQA 226

Query: 268 RVRQIEARAFKKVQESIQK 286
           +V ++E  A +K++E ++ 
Sbjct: 227 QVSRLERNALQKLREELEA 245


>gi|169351116|ref|ZP_02868054.1| hypothetical protein CLOSPI_01895 [Clostridium spiroforme DSM 1552]
 gi|169292178|gb|EDS74311.1| hypothetical protein CLOSPI_01895 [Clostridium spiroforme DSM 1552]
          Length = 239

 Score =  152 bits (384), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 51/250 (20%), Positives = 103/250 (41%), Gaps = 19/250 (7%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             L ++ R  GD  A   +V  +L LV  I   ++       ++   G IGLM+A+  FD
Sbjct: 7   IELIEKAR-CGDEIAKELVVNQNLGLVWSIVHRFKNNYYDKEDLFQIGCIGLMKAINNFD 65

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G + +TY++  I   ++ Y       +K+  +   K L   + ++K   + + +   
Sbjct: 66  TNYGVQFSTYAVPIIMGEIKRYFRDDG-TIKVSRSL--KELNLKINKVK---ELLINQTG 119

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +   V AIAK LN+   +V+          SL+  I   D +S   ++ +   H+     
Sbjct: 120 QDPTVEAIAKYLNIDVQDVVEAIDSSYYPTSLSEPIYEKDGSSISMEERVEDKHNK---- 175

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
                     +  L   +  L+ +E+ I   R   +     E ++    +S+ +V ++E 
Sbjct: 176 ------MWFEKIALKMEIDKLDEKEKLILYLRYQLD--FNQEKVAKRLNISQVQVSRLEK 227

Query: 275 RAFKKVQESI 284
           +   K++  +
Sbjct: 228 KIIAKLRSHL 237


>gi|220927856|ref|YP_002504765.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Clostridium
           cellulolyticum H10]
 gi|219998184|gb|ACL74785.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Clostridium
           cellulolyticum H10]
          Length = 249

 Score =  152 bits (384), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 47/255 (18%), Positives = 108/255 (42%), Gaps = 19/255 (7%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E  L  +Y   G+L   + +V+++L L   ++  +   G+   ++     + L+ AV++
Sbjct: 12  DEVQLFSQYISTGNLEYRNEIVSNYLSLAEYLSKKFLNRGVDFDDIYQVACLALINAVER 71

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F P++G +  +++   I   ++ +     + +KI     + R   N  R       +T  
Sbjct: 72  FSPDKGVKFISFATPTILGEIKRFFRDKSTTIKIPRRIYESRQGVNKAR-----DELTQK 126

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDG 210
             +  +   IA+ + +    V+ +    +     SL+  IN    N ++  D L YD   
Sbjct: 127 LSRVPRADEIAEYMGIPVETVLEIIEAGSSTIVKSLDQTINQ--DNDAELGDTLGYDEKT 184

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
            E +        + ++ L + +   N  ER+    R +Q    T + ++    VS+  V 
Sbjct: 185 YEMI--------DNKDFLEKVLISFNDVERQFVTYRYIQN--KTQKQIAEILGVSQMYVS 234

Query: 271 QIEARAFKKVQESIQ 285
           ++E +   K ++ ++
Sbjct: 235 RMERKILDKFRKYLK 249


>gi|49328110|gb|AAT58808.1| hypothetical protein [Oryza sativa Japonica Group]
          Length = 799

 Score =  152 bits (384), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 61/252 (24%), Positives = 109/252 (43%), Gaps = 14/252 (5%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E +L  R +E        RL+ +   LV  IA  Y G G    +++  G +G++   +K
Sbjct: 547 DEALLRSRLQEGYC--CRERLLVTTEWLVKYIAKTYAGMGTAFEDLLQAGKMGVLNGAEK 604

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD ++G + +TY  +WI+ AM   +  +  ++++       R+   +R+++   +AI  N
Sbjct: 605 FDSQKGCKFSTYVKYWIRKAMLALLAENSGVIQLP-----ARMEGIIRKVREARRAIRYN 659

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA  + VS + V           SL   I        Q   ++    D   
Sbjct: 660 TGRNPPDAEIAALIGVSVANVRLARKCSRRVVSLYTEIGVG-----QNAKFVEVTPDTSL 714

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +   E   R   R  L   +  L PRE  + + R   E+    +LE + S + VS+E +R
Sbjct: 715 EAPDEAMFRMQLRERLLHVLDRLPPREGHVLKLRHGLEDGKCRSLEQIGSIYHVSKEWIR 774

Query: 271 QIEARAFKKVQE 282
           +IE  A  K++ 
Sbjct: 775 KIEKSAMSKLRN 786


>gi|167755690|ref|ZP_02427817.1| hypothetical protein CLORAM_01205 [Clostridium ramosum DSM 1402]
 gi|237734438|ref|ZP_04564919.1| sporulation sigma factor sigF [Mollicutes bacterium D7]
 gi|167704629|gb|EDS19208.1| hypothetical protein CLORAM_01205 [Clostridium ramosum DSM 1402]
 gi|229382668|gb|EEO32759.1| sporulation sigma factor sigF [Coprobacillus sp. D7]
          Length = 240

 Score =  151 bits (383), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 49/253 (19%), Positives = 102/253 (40%), Gaps = 19/253 (7%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             L ++    GD  A   +V+ +L LV  I   ++       ++   G IGLM+AV  FD
Sbjct: 7   IELIEQAH-RGDDRAKELVVSQNLGLVWSIVHRFKNNYYDKEDLFQIGCIGLMKAVNNFD 65

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G + +TY++  I   ++ Y       +K+  +  +  L     ++    + +T+   
Sbjct: 66  TNYGVQFSTYAVPIIMGEIKRYFRDDG-TIKVSRSLKELNL-----KINKARELLTNQTG 119

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +   V  IA  L+V   +V+          SL+  I   D +S   ++ +   H+     
Sbjct: 120 QDPTVEQIAAYLDVDVQDVVEAIDSSYYPTSLSEPIYEKDGSSISMEERIENKHNK---- 175

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
                     +  L   +  L+ +E+ I   R   +     E ++    +S+ +V ++E 
Sbjct: 176 ------MWFEKIALEMEIDKLDEKEKLILYMRYQLD--FNQERVAQRLNISQVQVSRLEK 227

Query: 275 RAFKKVQESIQKQ 287
           +   K++  + +Q
Sbjct: 228 KIIAKLRSHLNEQ 240


>gi|297193425|ref|ZP_06910823.1| sigma L [Streptomyces pristinaespiralis ATCC 25486]
 gi|197723192|gb|EDY67100.1| sigma L [Streptomyces pristinaespiralis ATCC 25486]
          Length = 304

 Score =  151 bits (383), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 54/237 (22%), Positives = 95/237 (40%), Gaps = 17/237 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +
Sbjct: 80  RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTV 139

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +   V  +A  L VS
Sbjct: 140 VGEIKRFFRDTSWSVRVPRRLQELRLA-----LTKASDELAQKLDRSPTVPELAAVLGVS 194

Query: 170 ESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E +V+            SL++     D       D L Y+    E V          R  
Sbjct: 195 EEDVVDGLAVGNAYTASSLDSPSPEDDGGEGSLADRLGYEDSALEGV--------EYRES 246

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   ++ L PRER+I   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 247 LKPLLAKLPPRERQIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 301


>gi|119474993|ref|ZP_01615346.1| RNA polymerase sigma-70 factor family protein [marine gamma
           proteobacterium HTCC2143]
 gi|119451196|gb|EAW32429.1| RNA polymerase sigma-70 factor family protein [marine gamma
           proteobacterium HTCC2143]
          Length = 491

 Score =  151 bits (383), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 65/255 (25%), Positives = 122/255 (47%), Gaps = 15/255 (5%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           +    L    +E+ D    + +V  +LRLV  IA  Y    LP+ E++ EG  GL++AV+
Sbjct: 234 ERVKELGALKKEYVDY--RNVMVNHNLRLVYHIAKRYNSGTLPMLELIQEGVFGLVRAVE 291

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KF P  G R +TY+  WI+A ++    +  SLV++ ++  Q     ++ +L+  ++  + 
Sbjct: 292 KFQPASGNRFSTYAYLWIEAKVRLTHEKLNSLVRLPSSNFQ-----DVIKLRRSMEQ-SR 345

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
           +  +      +A KL+++++ V  +    +   SL+  +   D + S      +      
Sbjct: 346 STGERFSTRNVAAKLDMTQAHVELLLRTKSQPLSLDQPVGGEDNDLSLSGTLQLEQPPVS 405

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERV 269
             VL       + +  +T  +S L  RE  I + R    +  P++ E++     +SRERV
Sbjct: 406 SLVL-----NSDMQRQVTELLSELTSREAYILQHRFGLGDMEPMSRESIGKNIGLSRERV 460

Query: 270 RQIEARAFKKVQESI 284
           RQIE  A   ++E +
Sbjct: 461 RQIEKAALISLKELL 475


>gi|225569422|ref|ZP_03778447.1| hypothetical protein CLOHYLEM_05506 [Clostridium hylemonae DSM
           15053]
 gi|225161630|gb|EEG74249.1| hypothetical protein CLOHYLEM_05506 [Clostridium hylemonae DSM
           15053]
          Length = 237

 Score =  151 bits (383), Expect = 8e-35,   Method: Composition-based stats.
 Identities = 53/250 (21%), Positives = 105/250 (42%), Gaps = 17/250 (6%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             L K+  + GD  A  +LV  +  LV  I   +   G    ++   GNIGL++A+ KFD
Sbjct: 5   IALIKKSHQ-GDEKARAQLVEENAGLVWCIVKRFYNRGAEAEDLFQVGNIGLLKAIDKFD 63

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
                + +TY++  I   ++ ++     ++K+  +  +      L +     + + +   
Sbjct: 64  MSYEVKFSTYAVPMISGEIKRFLRDDG-MIKVSRSLKELSYKAYLCQ-----EKLQEALG 117

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +   +  IA+ L V   E+          ESL+  I   +    +  D L     G+E++
Sbjct: 118 REPTITEIAEYLEVDREELTMALDASGDIESLHKPIYQKEGQEIRLMDKLPEKEGGEEKI 177

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
           L           +L + +  LN  ER++   R       T   +  E  +S+ +V ++E 
Sbjct: 178 L--------NHMLLQQLLEYLNKDERQLIYLRYFANQ--TQSQVGQELGISQVQVSRLEK 227

Query: 275 RAFKKVQESI 284
           +  K+++E I
Sbjct: 228 KILKRLRERI 237


>gi|194016072|ref|ZP_03054687.1| RNA polymerase sigma-B factor [Bacillus pumilus ATCC 7061]
 gi|194012427|gb|EDW21994.1| RNA polymerase sigma-B factor [Bacillus pumilus ATCC 7061]
          Length = 262

 Score =  151 bits (383), Expect = 9e-35,   Method: Composition-based stats.
 Identities = 59/260 (22%), Positives = 114/260 (43%), Gaps = 12/260 (4%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K E   L + Y+ + D  A   LV  +  LV  +A  Y        ++   G IGL+ 
Sbjct: 10  LTKDEVDRLIQSYQSNQDEQAQLTLVECYTNLVDMLAKKYSKGKSFHEDLRQVGMIGLLG 69

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A+K++DP  G     +++  I   ++ ++      V +     +        R+K  +  
Sbjct: 70  AIKRYDPLVGKSFEAFAIPTIIGEIKRFLRDKTWSVHVPRRIKELG-----PRIKMAVDH 124

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           +T    K  QV  IA+ L+V+E EV+         ++L+  ++   +  S+     + D 
Sbjct: 125 LTTETQKSPQVQEIAEYLDVTEEEVLETMEMGKSYQALS--VDQGVEADSEGSTVTILDV 182

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
            G ++   E  ER N++ ML   + VL  RE+ I     LQ    + +       +S+  
Sbjct: 183 VGSQE---EGYERVNQKMMLESVLHVLTDREKEIINLTYLQN--KSQKETGDLLGISQMH 237

Query: 269 VRQIEARAFKKVQESIQKQV 288
           V +++ +A KK+++++ +  
Sbjct: 238 VSRLQRKAVKKLRDALSEDA 257


>gi|302544114|ref|ZP_07296456.1| RNA polymerase sigma-F factor [Streptomyces hygroscopicus ATCC
           53653]
 gi|302461732|gb|EFL24825.1| RNA polymerase sigma-F factor [Streptomyces himastatinicus ATCC
           53653]
          Length = 293

 Score =  151 bits (383), Expect = 9e-35,   Method: Composition-based stats.
 Identities = 53/237 (22%), Positives = 95/237 (40%), Gaps = 17/237 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +
Sbjct: 69  RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTV 128

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +   V  +A  L VS
Sbjct: 129 VGEIKRFFRDTSWSVRVPRRLQELRLA-----LTKASDELAQTLDRSPTVTELATALGVS 183

Query: 170 ESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E +V+            SL++     +       D L Y+    E V          R  
Sbjct: 184 EEDVVDGLAVGNAYTASSLDSPSPEDEGGEGSLADRLGYEDSALEGV--------EYRES 235

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   ++ L PRER+I   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 236 LKPLLAKLPPRERQIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 290


>gi|225055401|gb|ACN80687.1| Tsr7 [Streptomyces laurentii]
          Length = 336

 Score =  151 bits (383), Expect = 9e-35,   Method: Composition-based stats.
 Identities = 53/234 (22%), Positives = 101/234 (43%), Gaps = 15/234 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDP+RG +  T++M  +
Sbjct: 113 RGALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFPTFAMPTV 172

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ Y   +   V +      +RL     ++ G  + +T  + +      IA++L + 
Sbjct: 173 VGEIKRYFRDNVRTVHVP-----RRLHELWVQVNGATEDLTTAHGRSPTTAEIAERLKIG 227

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E EV++         + +              D L Y+      V          R+++ 
Sbjct: 228 EDEVLACIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALAGV--------EHRDLVR 279

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +  L  RE+RI   R      +T   +S E  VS+  V ++ AR+F +++ +
Sbjct: 280 HLLVQLPEREQRILMLRYYSN--LTQSQISQELGVSQMHVSRLLARSFARLRSA 331


>gi|219124053|ref|XP_002182327.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217406288|gb|EEC46228.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 317

 Score =  151 bits (383), Expect = 9e-35,   Method: Composition-based stats.
 Identities = 60/266 (22%), Positives = 120/266 (45%), Gaps = 29/266 (10%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGY-------------RGYGLPISEVVSEGNIG 85
           +R  + G   A   LV ++L LV  +A                 G  L + +++ EG +G
Sbjct: 54  RRVLDEG-QQARAALVAANLGLVTALAKRQLSTLQTATEAGRGVGTILTLQDLIQEGTLG 112

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           LM+A ++F+PERG+R +TY+ WW++  + + +  S   +++    +       +++ K  
Sbjct: 113 LMKAAERFEPERGWRFSTYATWWVRQRILKSVSDSSRTIRLPAHVH--GTLQRIQKAKAW 170

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS----SDKNSSQWQ 201
            QA    + +   + ++A+ L +   +V           SL   +       D+N+    
Sbjct: 171 FQA----HGEEATLSSLAQYLELPVEKVRLYTDSSRNVMSLETPLKGRSAFKDENTRTLG 226

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLS 259
           D L  D    E+ +  +  R +  +++T+   VL   E+ +   R   E+    ++E  +
Sbjct: 227 DTLASDEKTPEEDVEAQALRLDLEHVMTQ---VLTDVEQNVLRRRFGLEDGTCWSVEETA 283

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQ 285
            +  VSR+R+R +E RA  K++   Q
Sbjct: 284 RQLGVSRDRIRLVETRALNKLRHPQQ 309


>gi|28211847|ref|NP_782791.1| sporulation sigma factor SigF [Clostridium tetani E88]
 gi|28204289|gb|AAO36728.1| RNA polymerase sigma-F factor [Clostridium tetani E88]
          Length = 255

 Score =  151 bits (383), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 44/248 (17%), Positives = 105/248 (42%), Gaps = 16/248 (6%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L     ++GD  A  +LV  +L LV  I+  +   G    ++   G +GL++A+  FD  
Sbjct: 21  LLLEKAKNGDKKATDKLVELNLPLVSAISKKFLNRGYDYEDIYQIGCMGLVKAINNFDSS 80

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
              + +TY++  I   ++ +I     ++K+      + L    R+L  H + +     + 
Sbjct: 81  YNVKFSTYAVPMIMGEIKRFIRDDG-IIKVS-----RSLKIMARKLYYHRETLCKKLGRE 134

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
             +  +++   +   E++      +  + L+ +I+  D       D +  ++     ++ 
Sbjct: 135 PSIEELSEYTGLEIEEIVYAMESSSNLQYLHDVIHQDDGAPIMLIDKISENYSEDSDII- 193

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
                   +  L  ++  L+ + R+I   R  ++   T   ++    +S+ +V +IE R 
Sbjct: 194 -------NKLALKEALGKLDAKSRQIIMLRYFKD--KTQIEVAKMLGISQVQVSRIEKRV 244

Query: 277 FKKVQESI 284
            K ++E +
Sbjct: 245 LKTMKEKL 252


>gi|161898923|gb|ABX80451.1| SigB [Listeria monocytogenes]
          Length = 236

 Score =  151 bits (383), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 58/253 (22%), Positives = 113/253 (44%), Gaps = 24/253 (9%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G     +++  I   ++ ++      V +     +        ++K  ++ +T    
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQ 116

Query: 155 KPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +    
Sbjct: 117 SSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTD 173

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++S+  
Sbjct: 174 DGF--------ERVNQRMLLEKVLPVLDEREQKILQYTFIEN--RSQKETGELLDISQMH 223

Query: 269 VRQIEARAFKKVQ 281
           V +I+ +A KK++
Sbjct: 224 VSRIQRQAIKKLR 236


>gi|310777993|ref|YP_003966326.1| RNA polymerase, sigma 32 subunit, RpoH [Ilyobacter polytropus DSM
           2926]
 gi|309747316|gb|ADO81978.1| RNA polymerase, sigma 32 subunit, RpoH [Ilyobacter polytropus DSM
           2926]
          Length = 329

 Score =  151 bits (383), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 71/268 (26%), Positives = 131/268 (48%), Gaps = 19/268 (7%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L +Y H+I     + K++E  + K+ ++ GD  A   LVTS+L+LV KIAM Y   G+  
Sbjct: 71  LEQYFHDISLYTPIPKEKEKDIVKKAQD-GDEEAREMLVTSNLKLVAKIAMKYSKSGVNY 129

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ +G IGL+ A+ K+D  +G    +YS+WWIK  +   I    + +KI +       
Sbjct: 130 IDLIQDGTIGLIAAIDKYDLSKGHSFTSYSVWWIKREIINSIANRINAIKIPSYV----- 184

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           +   ++++       + N K      I++ LN+S  EV  M      + S   +   +D 
Sbjct: 185 YLMNKKIRIFEDDFMERNNKKPSYQEISEALNLSLEEVEKM-----KEASEIGVGGFADG 239

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
           N     D+   D   +E  L+E+      R+ ++  M  ++P E+++ E     ++   L
Sbjct: 240 NEPDLGDFNTVDQIDKELNLLEE------RSKISNLMRKISPEEQKVVEMYYGLDDNKRL 293

Query: 256 --ENLSSEFEVSRERVRQIEARAFKKVQ 281
             + +S    VS E+V+ ++ RA  K++
Sbjct: 294 GFKEISKIMGVSVEKVKFLKERAILKLK 321


>gi|161898889|gb|ABX80434.1| SigB [Listeria monocytogenes]
 gi|161898893|gb|ABX80436.1| SigB [Listeria monocytogenes]
 gi|161898909|gb|ABX80444.1| SigB [Listeria monocytogenes]
          Length = 236

 Score =  151 bits (383), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 58/253 (22%), Positives = 113/253 (44%), Gaps = 24/253 (9%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G     +++  I   ++ ++      V +     +        ++K  ++ +T    
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQ 116

Query: 155 KPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +    
Sbjct: 117 SSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTD 173

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++S+  
Sbjct: 174 DGF--------ERVNQRMLLEKVLPVLDEREQKILQFTFIEN--RSQKETGELLDISQMH 223

Query: 269 VRQIEARAFKKVQ 281
           V +I+ +A KK++
Sbjct: 224 VSRIQRQAIKKLR 236


>gi|149921691|ref|ZP_01910139.1| RNA polymerase sigma factor RpoD [Plesiocystis pacifica SIR-1]
 gi|149817429|gb|EDM76901.1| RNA polymerase sigma factor RpoD [Plesiocystis pacifica SIR-1]
          Length = 384

 Score =  151 bits (383), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 60/235 (25%), Positives = 109/235 (46%), Gaps = 13/235 (5%)

Query: 55  TSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114
            ++LRLVV +A       LP+ +++ EGNIGL++A+++FD  +GFR +TY+ WWI+ ++ 
Sbjct: 156 KANLRLVVSLARRLSNGRLPLQDLIQEGNIGLLKAIERFDHRKGFRFSTYASWWIRHSIS 215

Query: 115 EYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVI 174
             I      V++        +   + R++   +A        E    IA ++ V  ++V 
Sbjct: 216 RAIYNKGRQVRLPVHVY--DVHQKITRVRRRYEAQIGREPTHE---EIANEIGVPLAKVE 270

Query: 175 SMNC-RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
            +    L    SL+A ++ +D  S      +    D        + E       L  ++S
Sbjct: 271 KIAAIELGPIVSLDAPLSRNDDRSG-----VDLLEDQVSPGPGFELELGELEEGLEDALS 325

Query: 234 VLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L P E  I   R   +     TL  +   + +SRER+RQ++ RA  +++E   +
Sbjct: 326 ALRPMEADILRRRYGLDGVEKETLREIGERYALSRERIRQLQERAVSRMREEFAR 380


>gi|23978358|dbj|BAC21144.1| principal sigma factor [Nodularia sp. PCC 73104]
          Length = 188

 Score =  151 bits (383), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 44/199 (22%), Positives = 91/199 (45%), Gaps = 13/199 (6%)

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
              GL   +++ EG++GL++A +KFD E+G+R +TY+ WWI+ A+   I      +++  
Sbjct: 1   MNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYRFSTYATWWIRQAITRAIADQSRTIRLPV 60

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
                 L+  + R+K   + ++    +      IA ++ ++  ++  +        SL  
Sbjct: 61  H-----LYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLET 115

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            I    +  S+  D++  D     +   ++  +   R  L + +  L+PRER +   R  
Sbjct: 116 PI--GKEEDSRLGDFIESDG----ETPEDQVSKNLLREDLEKVLDSLSPRERDVLRLRYG 169

Query: 249 QENPV--TLENLSSEFEVS 265
            ++    TLE +   F V+
Sbjct: 170 LDDGRMKTLEEIGQIFNVT 188


>gi|161898913|gb|ABX80446.1| SigB [Listeria monocytogenes]
 gi|161898915|gb|ABX80447.1| SigB [Listeria monocytogenes]
 gi|161898939|gb|ABX80459.1| SigB [Listeria monocytogenes]
          Length = 237

 Score =  151 bits (383), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 58/253 (22%), Positives = 113/253 (44%), Gaps = 24/253 (9%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 3   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 62

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G     +++  I   ++ ++      V +     +        ++K  ++ +T    
Sbjct: 63  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQ 117

Query: 155 KPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +    
Sbjct: 118 SSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTD 174

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++S+  
Sbjct: 175 DGF--------ERVNQRMLLEKVLPVLDEREQKILQYTFIEN--RSQKETGELLDISQMH 224

Query: 269 VRQIEARAFKKVQ 281
           V +I+ +A KK++
Sbjct: 225 VSRIQRQAIKKLR 237


>gi|161898857|gb|ABX80418.1| SigB [Listeria monocytogenes]
          Length = 236

 Score =  151 bits (383), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 58/253 (22%), Positives = 113/253 (44%), Gaps = 24/253 (9%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQENGDEDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G     +++  I   ++ ++      V +     +        ++K  ++ +T    
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQ 116

Query: 155 KPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +    
Sbjct: 117 SSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTD 173

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++S+  
Sbjct: 174 DGF--------ERVNQRMLLEKVLPVLDEREQKILQFTFIEN--RSQKETGELLDISQMH 223

Query: 269 VRQIEARAFKKVQ 281
           V +I+ +A KK++
Sbjct: 224 VSRIQRQAIKKLR 236


>gi|225574676|ref|ZP_03783286.1| hypothetical protein RUMHYD_02753 [Blautia hydrogenotrophica DSM
           10507]
 gi|225038103|gb|EEG48349.1| hypothetical protein RUMHYD_02753 [Blautia hydrogenotrophica DSM
           10507]
          Length = 239

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 55/252 (21%), Positives = 112/252 (44%), Gaps = 17/252 (6%)

Query: 34  EYVLAKRYREH-GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           E+ LA   R H GD  A   +   ++ L+  I   ++  G+ + ++   G+IGL++AV K
Sbjct: 4   EHTLALIARAHQGDKEARDTIFEENIGLIWSIVKRFQNRGVELEDLFQIGSIGLLKAVDK 63

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD     + +TY++  I   ++ ++     ++K+  +  +      L R     + +   
Sbjct: 64  FDLSYDVKFSTYAVPMISGEIKRFLRDDG-MIKVSRSLKEVCYKAYLAR-----EKLEKE 117

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +  Q+  +A ++ + + E++         ESL   I   + N  +  D L    + QE
Sbjct: 118 LGRDPQIAEMAGEIGIPQEELMMALDSNVEIESLQKTIYQGEGNDIRLIDKLEEKKNRQE 177

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           + L         R +L   +  L   ERR+   R  QE   T   ++ E  VS+ +V ++
Sbjct: 178 ESL--------NRILLEEILGQLTVSERRLIYMRYFQE--RTQTEIARELGVSQVQVSRM 227

Query: 273 EARAFKKVQESI 284
           E +  K++++ +
Sbjct: 228 EKKILKRLRDKM 239


>gi|294630218|ref|ZP_06708778.1| RNA polymerase sigma-F factor [Streptomyces sp. e14]
 gi|292833551|gb|EFF91900.1| RNA polymerase sigma-F factor [Streptomyces sp. e14]
          Length = 302

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 54/237 (22%), Positives = 96/237 (40%), Gaps = 17/237 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +
Sbjct: 78  RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTV 137

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      ++    +   V  +A  L VS
Sbjct: 138 VGEIKRFFRDTSWSVRVPRRLQELRLA-----LTKASDELSQKLDRSPTVAELAAVLGVS 192

Query: 170 ESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E +V+            SL++     D       D L Y+    E V          R  
Sbjct: 193 EEDVVDGLAVGNAYTASSLDSPAPEDDGGEGSLADRLGYEDSALEGV--------EYRES 244

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   ++ L PRERRI   R      +T   +  E  +S+  V ++  R   ++++ +
Sbjct: 245 LKPLLAKLPPRERRIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLRDGL 299


>gi|161898845|gb|ABX80412.1| SigB [Listeria monocytogenes]
 gi|161898851|gb|ABX80415.1| SigB [Listeria monocytogenes]
 gi|161898853|gb|ABX80416.1| SigB [Listeria monocytogenes]
 gi|161898861|gb|ABX80420.1| SigB [Listeria monocytogenes]
 gi|161898863|gb|ABX80421.1| SigB [Listeria monocytogenes]
 gi|161898867|gb|ABX80423.1| SigB [Listeria monocytogenes]
 gi|161898869|gb|ABX80424.1| SigB [Listeria monocytogenes]
 gi|161898873|gb|ABX80426.1| SigB [Listeria monocytogenes]
 gi|161898875|gb|ABX80427.1| SigB [Listeria monocytogenes]
 gi|161898877|gb|ABX80428.1| SigB [Listeria monocytogenes]
 gi|161898879|gb|ABX80429.1| SigB [Listeria monocytogenes]
 gi|161898887|gb|ABX80433.1| SigB [Listeria monocytogenes]
 gi|161898891|gb|ABX80435.1| SigB [Listeria monocytogenes]
 gi|161898901|gb|ABX80440.1| SigB [Listeria monocytogenes]
 gi|161898911|gb|ABX80445.1| SigB [Listeria monocytogenes]
 gi|161898919|gb|ABX80449.1| SigB [Listeria monocytogenes]
 gi|161898925|gb|ABX80452.1| SigB [Listeria monocytogenes]
 gi|161898927|gb|ABX80453.1| SigB [Listeria monocytogenes]
 gi|161898929|gb|ABX80454.1| SigB [Listeria monocytogenes]
 gi|161898935|gb|ABX80457.1| SigB [Listeria monocytogenes]
 gi|161898941|gb|ABX80460.1| SigB [Listeria monocytogenes]
 gi|161898943|gb|ABX80461.1| SigB [Listeria monocytogenes]
          Length = 237

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 58/253 (22%), Positives = 113/253 (44%), Gaps = 24/253 (9%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 3   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 62

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G     +++  I   ++ ++      V +     +        ++K  ++ +T    
Sbjct: 63  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQ 117

Query: 155 KPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +    
Sbjct: 118 SSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTD 174

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++S+  
Sbjct: 175 DGF--------ERVNQRMLLEKVLPVLDEREQKILQFTFIEN--RSQKETGELLDISQMH 224

Query: 269 VRQIEARAFKKVQ 281
           V +I+ +A KK++
Sbjct: 225 VSRIQRQAIKKLR 237


>gi|297562622|ref|YP_003681596.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
 gi|296847070|gb|ADH69090.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
          Length = 267

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 59/276 (21%), Positives = 112/276 (40%), Gaps = 32/276 (11%)

Query: 25  KIPMLEKQEEY---------VLAKRYRE-----HGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           + P L  + E+          L +R  E              LV  HL LV  +A  +R 
Sbjct: 4   RGPALTAKTEHAVPDRARARELFERLGELEADSEERRRIRDELVELHLPLVEYLARRFRN 63

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            G  + ++     IGL++++ +FD ERG   +TY+   I   ++ +       V++    
Sbjct: 64  RGEWLDDLTQVATIGLIKSIDRFDLERGVEFSTYATPTIVGEIKRHFRDKGWAVRVPRRL 123

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS--MNCRLAGDESLNA 188
            + +L      L   +  ++    +   V  +A  L ++E EV+    +       SL+A
Sbjct: 124 QELKLS-----LTKAVSDLSQREGRSPTVAELAAHLQMTEEEVLEGLESANAYSTVSLDA 178

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
              S D+++    D L         ++ E  E    R  L   +  L PRE+RI   R  
Sbjct: 179 PD-SGDEDAPAVADSLG--------IVDESLEGVEYRESLKPLLEQLPPREKRILLLRFF 229

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
               +T   ++ E  +S+  V ++ AR   ++++++
Sbjct: 230 GN--MTQSQIAQELGISQMHVSRLLARTLAQLRQAL 263


>gi|291563747|emb|CBL42563.1| RNA polymerase, sigma subunit, RpoX/SigF [butyrate-producing
           bacterium SS3/4]
          Length = 239

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 56/251 (22%), Positives = 109/251 (43%), Gaps = 17/251 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L KR    GD  A  RLV  +  LV  I   + G G    ++   GNIGL++A+  FD 
Sbjct: 6   ELLKR-SHAGDKEARDRLVMENAGLVWSIVRRFIGRGPEPDDLFQIGNIGLIKAIDHFDT 64

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           E G R +TY++  I   ++ ++     ++K+      K L   +   +  L+A       
Sbjct: 65  ELGVRFSTYAVPMITGEIRRFLRDDG-MIKVSRPL--KELAGKVGAAREKLEADLGRE-- 119

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
              V  +A+ +  S  EV +     A   S+    ++ D++     D +       ++VL
Sbjct: 120 -PTVEELARSVGASREEVAASMEAGARVGSIYEPFDAGDESGGCLADKIAEKTSENDRVL 178

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
                    R +L   +S L  +E++I + R  +   +T   ++    +S+ +V ++E +
Sbjct: 179 --------DRIVLAELLSGLGEKEQQIIKMRYFEN--MTQTVIAGRLGISQVQVSRMEKK 228

Query: 276 AFKKVQESIQK 286
             ++++E +  
Sbjct: 229 ILREMRERLTS 239


>gi|182437345|ref|YP_001825064.1| RNA polymerase sigma factor, sigma L [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|326777955|ref|ZP_08237220.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
 gi|178465861|dbj|BAG20381.1| RNA polymerase sigma factor, sigma L [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|326658288|gb|EGE43134.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
          Length = 288

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 54/237 (22%), Positives = 96/237 (40%), Gaps = 17/237 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +
Sbjct: 64  RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTV 123

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +   V  +A+ L VS
Sbjct: 124 VGEIKRFFRDTSWSVRVPRRLQELRLA-----LTKTSDELAQKLDRSPTVPELARALGVS 178

Query: 170 ESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E +V+            SL++     D       D L Y+    E V          R  
Sbjct: 179 EEDVVDGLAVGNAYTASSLDSPSPEDDGGEGSLADRLGYEDAALEGV--------EYRES 230

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   ++ L PRER+I   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 231 LKPLLAKLAPRERQIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 285


>gi|119514602|gb|ABL76113.1| SigB [Listeria monocytogenes]
 gi|119514606|gb|ABL76115.1| SigB [Listeria monocytogenes]
 gi|119514608|gb|ABL76116.1| SigB [Listeria monocytogenes]
 gi|119514610|gb|ABL76117.1| SigB [Listeria monocytogenes]
 gi|119514614|gb|ABL76119.1| SigB [Listeria monocytogenes]
 gi|119514618|gb|ABL76121.1| SigB [Listeria monocytogenes 690]
 gi|119514626|gb|ABL76125.1| SigB [Listeria monocytogenes]
 gi|119514630|gb|ABL76127.1| SigB [Listeria monocytogenes]
 gi|119514632|gb|ABL76128.1| SigB [Listeria monocytogenes]
          Length = 249

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 59/256 (23%), Positives = 115/256 (44%), Gaps = 24/256 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +++D   G     +++  I   ++ ++      V +     +        ++K  ++ +T
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELT 126

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWL 204
                  Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +
Sbjct: 127 RELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVV 183

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++
Sbjct: 184 GGTDDGF--------ERVNQRMLLEKVLPVLDEREQKILQYTFIEN--RSQKETGELLDI 233

Query: 265 SRERVRQIEARAFKKV 280
           S+  V +I+ +A KK+
Sbjct: 234 SQMHVSRIQRQAIKKL 249


>gi|239942800|ref|ZP_04694737.1| RNA polymerase sigma factor, sigma L [Streptomyces roseosporus NRRL
           15998]
          Length = 288

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 54/237 (22%), Positives = 96/237 (40%), Gaps = 17/237 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +
Sbjct: 64  RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTV 123

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +   V  +A+ L VS
Sbjct: 124 VGEIKRFFRDTSWSVRVPRRLQELRLA-----LTKTSDELAQKLDRSPTVPELARALGVS 178

Query: 170 ESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E +V+            SL++     D       D L Y+    E V          R  
Sbjct: 179 EEDVVDGLAVGNAYTASSLDSPSPEDDGGEGSLADRLGYEDTALEGV--------EYRES 230

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   ++ L PRER+I   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 231 LKPLLAKLAPRERQIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 285


>gi|326442277|ref|ZP_08217011.1| RNA polymerase sigma factor, sigma L [Streptomyces clavuligerus
           ATCC 27064]
          Length = 292

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 54/237 (22%), Positives = 95/237 (40%), Gaps = 17/237 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +
Sbjct: 68  RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTV 127

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +   V  +A  L VS
Sbjct: 128 VGEIKRFFRDTSWSVRVPRRLQELRLA-----LTKASDELAQRLDRSPTVPELAAVLGVS 182

Query: 170 ESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E EV+            SL++     D       D L Y+    E V          R  
Sbjct: 183 EEEVVDGLAVGNAYTASSLDSPSPEDDGGEGSLADRLGYEDTALEGV--------EYRES 234

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   ++ L PRER+I   R      +T   +  E  +S+  V ++  R   ++++ +
Sbjct: 235 LKPLLAKLPPRERQIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLRDGL 289


>gi|22135904|gb|AAM91534.1| sigma factor SigC [Arabidopsis thaliana]
          Length = 291

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 58/236 (24%), Positives = 113/236 (47%), Gaps = 11/236 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
               LV S   LV+ +A  YRG G+   +++  G +G++Q  ++FD  RG++ +TY  +W
Sbjct: 52  CRDELVKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYW 111

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ +M   + R    V I ++    R   ++++ +  L+  T + +K      IAK    
Sbjct: 112 IRKSMSTMVSRHARGVHIPSSI--IRTINHIQKARKTLK--TSHGIKYAADEEIAKLTGH 167

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  ++ + N  L    S++  +            +L +  D   +   E   R++ R  +
Sbjct: 168 SVKKIRAANQCLKVVGSIDKKVGDC-----FTTKFLEFTPDTTMESPEEAVMRQSARRDI 222

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              +  L PRE+++   R   ++  P +LE +    +VS+E +R+IE RA  K+++
Sbjct: 223 HDLLEGLEPREKQVMVLRYGLQDYRPKSLEEIGKLLKVSKEWIRKIERRAMAKLRD 278


>gi|161898883|gb|ABX80431.1| SigB [Listeria monocytogenes]
          Length = 235

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 58/253 (22%), Positives = 113/253 (44%), Gaps = 24/253 (9%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 1   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 60

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G     +++  I   ++ ++      V +     +        ++K  ++ +T    
Sbjct: 61  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQ 115

Query: 155 KPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +    
Sbjct: 116 SSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTD 172

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++S+  
Sbjct: 173 DGF--------ERVNQRMLLEKVLPVLDEREQKILQFTFIEN--RSQKETGELLDISQMH 222

Query: 269 VRQIEARAFKKVQ 281
           V +I+ +A KK++
Sbjct: 223 VSRIQRQAIKKLR 235


>gi|89099505|ref|ZP_01172381.1| sigma factor B [Bacillus sp. NRRL B-14911]
 gi|89085891|gb|EAR65016.1| sigma factor B [Bacillus sp. NRRL B-14911]
          Length = 264

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 63/264 (23%), Positives = 120/264 (45%), Gaps = 24/264 (9%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
            K+E   L K Y+E+ D  A   LV ++  LV  IA  Y        ++   G IGL+ A
Sbjct: 11  SKEEINELIKAYQENQDEEAQEILVRNYKALVETIARKYSKGRSYHEDIAQVGIIGLLGA 70

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           ++++D   G     +++  I   ++ ++      V +     +        ++K  ++ +
Sbjct: 71  IRRYDETFGKSFEAFAVPTIIGEIKRFLRDKTWSVHVPRRIKELG-----PKIKTTVEEL 125

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDW 203
           T    +  +V  IA ++ VSE EV+           L+ D S+ A    SD  +    D 
Sbjct: 126 TTQLHRSPRVDEIADEIGVSEEEVLEAMEMGKSYQALSVDHSIEA---DSDGGTVTLLDI 182

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    +G E+V        N+R +L R + VL  RE++I +   L+   ++ ++   +  
Sbjct: 183 VGNVDEGFEKV--------NQRMVLERVLHVLTDREKQIIQYTYLEN--MSQKDAGDKLG 232

Query: 264 VSRERVRQIEARAFKKVQESIQKQ 287
           +S+  V +++ RA KK+QE+I  +
Sbjct: 233 ISQMHVSRLQRRAIKKLQEAINAE 256


>gi|157691239|ref|YP_001485701.1| RNA polymerase sigma factor SigB [Bacillus pumilus SAFR-032]
 gi|157679997|gb|ABV61141.1| DNA-directed RNA polymerase sigma subunit SigB [Bacillus pumilus
           SAFR-032]
          Length = 262

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 58/260 (22%), Positives = 114/260 (43%), Gaps = 12/260 (4%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K E   L + Y+ + D  A   LV  +  LV  +A  Y        ++   G IGL+ 
Sbjct: 10  LTKDEVDRLIQSYQSNQDEQAQLTLVECYTNLVDMLAKKYSKGKSFHEDLRQVGMIGLLG 69

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A+K++DP  G     +++  I   ++ ++      V +     +        R+K  +  
Sbjct: 70  AIKRYDPLVGKSFEAFAIPTIIGEIKRFLRDKTWSVHVPRRIKELG-----PRIKMAVDH 124

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           +T    K  +V  IA+ L+V+E EV+         ++L+  ++   +  S+     + D 
Sbjct: 125 LTTETQKSPKVQEIAEYLDVTEEEVLETMEMGKSYQALS--VDQGVEADSEGSTVTILDV 182

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
            G ++   E  ER N++ ML   + VL  RE+ I     LQ    + +       +S+  
Sbjct: 183 VGSQE---EGYERVNQKMMLESVLHVLTDREKEIINLTYLQN--KSQKETGDLLGISQMH 237

Query: 269 VRQIEARAFKKVQESIQKQV 288
           V +++ +A KK+++++ +  
Sbjct: 238 VSRLQRKAVKKLRDALSEDA 257


>gi|119514598|gb|ABL76111.1| SigB [Listeria monocytogenes]
 gi|119514600|gb|ABL76112.1| SigB [Listeria monocytogenes]
 gi|119514604|gb|ABL76114.1| SigB [Listeria monocytogenes]
 gi|119514612|gb|ABL76118.1| SigB [Listeria monocytogenes]
 gi|119514616|gb|ABL76120.1| SigB [Listeria monocytogenes]
 gi|119514620|gb|ABL76122.1| SigB [Listeria monocytogenes]
 gi|119514622|gb|ABL76123.1| SigB [Listeria monocytogenes]
 gi|119514624|gb|ABL76124.1| SigB [Listeria monocytogenes]
 gi|119514628|gb|ABL76126.1| SigB [Listeria monocytogenes]
 gi|119514634|gb|ABL76129.1| SigB [Listeria monocytogenes]
 gi|119514636|gb|ABL76130.1| SigB [Listeria monocytogenes]
 gi|119514638|gb|ABL76131.1| SigB [Listeria monocytogenes]
          Length = 249

 Score =  151 bits (382), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 59/256 (23%), Positives = 115/256 (44%), Gaps = 24/256 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +++D   G     +++  I   ++ ++      V +     +        ++K  ++ +T
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELT 126

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWL 204
                  Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +
Sbjct: 127 RELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVV 183

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++
Sbjct: 184 GGTDDGF--------ERVNQRMLLEKVLPVLDEREQKILQFTFIEN--RSQKETGELLDI 233

Query: 265 SRERVRQIEARAFKKV 280
           S+  V +I+ +A KK+
Sbjct: 234 SQMHVSRIQRQAIKKL 249


>gi|239989259|ref|ZP_04709923.1| RNA polymerase sigma factor, sigma L [Streptomyces roseosporus NRRL
           11379]
          Length = 288

 Score =  151 bits (381), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 55/237 (23%), Positives = 96/237 (40%), Gaps = 17/237 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +
Sbjct: 64  RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTV 123

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +   V  +A+ L VS
Sbjct: 124 VGEIKRFFRDTSWSVRVPRRLQELRLA-----LTKTSDELAQKLDRSPTVPELARALGVS 178

Query: 170 ESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E +VI            SL++     D       D L Y+    E V          R  
Sbjct: 179 EEDVIDGLAVGNAYTASSLDSPSPEDDGGEGSLADRLGYEDTALEGV--------EYRES 230

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   ++ L PRER+I   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 231 LKPLLAKLAPRERQIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 285


>gi|161898865|gb|ABX80422.1| SigB [Listeria monocytogenes]
          Length = 237

 Score =  151 bits (381), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 58/253 (22%), Positives = 112/253 (44%), Gaps = 24/253 (9%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 3   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 62

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G     +++  I   ++ ++      V +     +        ++K  ++ +T    
Sbjct: 63  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQ 117

Query: 155 KPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D      
Sbjct: 118 SSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVAGGTD 174

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++S+  
Sbjct: 175 DGF--------ERVNQRMLLEKVLPVLDEREQKILQYTFIEN--RSQKETGELLDISQMH 224

Query: 269 VRQIEARAFKKVQ 281
           V +I+ +A KK++
Sbjct: 225 VSRIQRQAIKKLR 237


>gi|291446269|ref|ZP_06585659.1| sigma L [Streptomyces roseosporus NRRL 15998]
 gi|291349216|gb|EFE76120.1| sigma L [Streptomyces roseosporus NRRL 15998]
          Length = 307

 Score =  151 bits (381), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 54/237 (22%), Positives = 96/237 (40%), Gaps = 17/237 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +
Sbjct: 83  RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTV 142

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +   V  +A+ L VS
Sbjct: 143 VGEIKRFFRDTSWSVRVPRRLQELRLA-----LTKTSDELAQKLDRSPTVPELARALGVS 197

Query: 170 ESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E +V+            SL++     D       D L Y+    E V          R  
Sbjct: 198 EEDVVDGLAVGNAYTASSLDSPSPEDDGGEGSLADRLGYEDTALEGV--------EYRES 249

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   ++ L PRER+I   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 250 LKPLLAKLAPRERQIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 304


>gi|52079008|ref|YP_077799.1| RNA polymerase sigma factor SigB [Bacillus licheniformis ATCC
           14580]
 gi|319648688|ref|ZP_08002899.1| RNA polymerase sigma factor [Bacillus sp. BT1B_CT2]
 gi|52002219|gb|AAU22161.1| RNA polymerase sigma-37 factor (sigma-B) [Bacillus licheniformis
           ATCC 14580]
 gi|317389107|gb|EFV69923.1| RNA polymerase sigma factor [Bacillus sp. BT1B_CT2]
          Length = 263

 Score =  151 bits (381), Expect = 1e-34,   Method: Composition-based stats.
 Identities = 65/283 (22%), Positives = 126/283 (44%), Gaps = 30/283 (10%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K   L K E   L K+Y+E+ D  A   LV ++  LV  +A  Y        ++   G 
Sbjct: 5   SKTTKLTKTEVDTLIKKYQENQDEDAQLTLVQTYKNLVETLAKKYSKGKSFHEDLCQVGM 64

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           +GL+ A+K++DP+ G     +++  I   ++ ++      V +     +        R+K
Sbjct: 65  LGLLGAIKRYDPDVGKSFEAFAIPTIIGEIKRFLRDKTWSVHVPRRIKELG-----PRIK 119

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNS 197
             +  +T    +  +V  IA+ L+V+E EV+           L+ D S+ A    +D ++
Sbjct: 120 MAVDHLTTETQRSPRVDEIAEFLDVTEEEVLETMEMGKSYQALSVDHSIEA---DADGST 176

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
               D +    +G E+V        N++ ML   + VL+ RE++I E   +Q    + + 
Sbjct: 177 VTILDIVGSQEEGYEKV--------NQKLMLESVLHVLSDREKQIIELTYIQN--KSQKE 226

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQKP 300
                 +S+  V +++ +A K+++E+      L+  P +  KP
Sbjct: 227 TGEMLGISQMHVSRLQRKAVKRLREA------LAEDPYMELKP 263


>gi|23978331|dbj|BAC21136.1| principal sigma factor [Synechococcus leopoliensis]
          Length = 188

 Score =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 45/199 (22%), Positives = 93/199 (46%), Gaps = 13/199 (6%)

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
              GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+   I      +++  
Sbjct: 1   MNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV 60

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
                 L+  + R+K   + ++    +      IA ++ ++  ++  +        SL  
Sbjct: 61  H-----LYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLET 115

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            I    +  S+  D++  D +  E  + +   R++    L   +S L+PRER +   R  
Sbjct: 116 PI--GKEEDSRLGDFIEADGETPEDEVAKNLLRED----LEGVLSTLSPRERDVLRLRYG 169

Query: 249 QENPV--TLENLSSEFEVS 265
            ++    TLE +   F V+
Sbjct: 170 LDDGRMKTLEEIGQLFNVT 188


>gi|161898855|gb|ABX80417.1| SigB [Listeria monocytogenes]
          Length = 237

 Score =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 58/253 (22%), Positives = 112/253 (44%), Gaps = 24/253 (9%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 3   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 62

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G     +++  I   ++ ++      V +     +        ++K  ++ +T    
Sbjct: 63  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQ 117

Query: 155 KPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D      
Sbjct: 118 SSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVAGGTD 174

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++S+  
Sbjct: 175 DGF--------ERVNQRMLLEKVLPVLDEREQKILQFTFIEN--RSQKETGELLDISQMH 224

Query: 269 VRQIEARAFKKVQ 281
           V +I+ +A KK++
Sbjct: 225 VSRIQRQAIKKLR 237


>gi|225026792|ref|ZP_03715984.1| hypothetical protein EUBHAL_01044 [Eubacterium hallii DSM 3353]
 gi|224955911|gb|EEG37120.1| hypothetical protein EUBHAL_01044 [Eubacterium hallii DSM 3353]
          Length = 245

 Score =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 54/247 (21%), Positives = 113/247 (45%), Gaps = 17/247 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L K+ +E G+  A   LV  +  L+  +   ++G G    ++   G+IGL++ ++ FD 
Sbjct: 6   ELIKQAKE-GNKEAQSILVEENSGLIWSVVKRFQGRGYDKEDLFQIGSIGLLKCIENFDL 64

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           ER  + +TY++  I   ++ ++     +VK+  +   K   + ++R K H Q + +    
Sbjct: 65  ERNVKFSTYAVPLIMGEIKRFLRDDG-IVKVSRSL--KEASYKIKREKEHYQKLYNRE-- 119

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
              +  IA  L++ ES+++          SL+ +I  S+ +    +D L    D  EQ +
Sbjct: 120 -PTLKEIAVTLDMDESDILMAMESGQEVCSLHQVIYQSEGDEIHLEDKLEQQADLIEQTV 178

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
                       +   +  LN +ER+I   R  Q    T   ++ +  +S+ +V ++E +
Sbjct: 179 --------DNIYVQELLKKLNEQERQIIHMRYFQNQ--TQAAIAKKIGISQVQVSRMEKK 228

Query: 276 AFKKVQE 282
              K+++
Sbjct: 229 ILNKLRK 235


>gi|52784380|ref|YP_090209.1| RNA polymerase sigma factor SigB [Bacillus licheniformis ATCC
           14580]
 gi|52346882|gb|AAU39516.1| SigB [Bacillus licheniformis ATCC 14580]
          Length = 264

 Score =  151 bits (381), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 65/283 (22%), Positives = 126/283 (44%), Gaps = 30/283 (10%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K   L K E   L K+Y+E+ D  A   LV ++  LV  +A  Y        ++   G 
Sbjct: 6   SKTTKLTKTEVDTLIKKYQENQDEDAQLTLVQTYKNLVETLAKKYSKGKSFHEDLCQVGM 65

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           +GL+ A+K++DP+ G     +++  I   ++ ++      V +     +        R+K
Sbjct: 66  LGLLGAIKRYDPDVGKSFEAFAIPTIIGEIKRFLRDKTWSVHVPRRIKELG-----PRIK 120

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNS 197
             +  +T    +  +V  IA+ L+V+E EV+           L+ D S+ A    +D ++
Sbjct: 121 MAVDHLTTETQRSPRVDEIAEFLDVTEEEVLETMEMGKSYQALSVDHSIEA---DADGST 177

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
               D +    +G E+V        N++ ML   + VL+ RE++I E   +Q    + + 
Sbjct: 178 VTILDIVGSQEEGYEKV--------NQKLMLESVLHVLSDREKQIIELTYIQN--KSQKE 227

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQKP 300
                 +S+  V +++ +A K+++E+      L+  P +  KP
Sbjct: 228 TGEMLGISQMHVSRLQRKAVKRLREA------LAEDPYMELKP 264


>gi|23978363|dbj|BAC21146.1| principal sigma factor [Pleurocapsa sp. PCC 7327]
          Length = 188

 Score =  150 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 44/199 (22%), Positives = 91/199 (45%), Gaps = 13/199 (6%)

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
              GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+   I      +++  
Sbjct: 1   MNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV 60

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
                 L+  + R+K   + ++    +      IA ++ ++  ++  +        SL  
Sbjct: 61  H-----LYETISRIKKTTKILSQEMRRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLET 115

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            I    +  S+  D++  D +  E    ++  +   R  L   +  L+PRER +   R  
Sbjct: 116 PI--GKEEDSRLGDFIEADGETPE----DEVSKNLLREDLENVLDTLSPRERDVLRLRYG 169

Query: 249 QENPV--TLENLSSEFEVS 265
            ++    TLE +   F V+
Sbjct: 170 LDDGRMKTLEEIGQIFNVT 188


>gi|89094249|ref|ZP_01167191.1| RNA polymerase sigma factor [Oceanospirillum sp. MED92]
 gi|89081504|gb|EAR60734.1| RNA polymerase sigma factor [Oceanospirillum sp. MED92]
          Length = 411

 Score =  150 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 57/254 (22%), Positives = 118/254 (46%), Gaps = 15/254 (5%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             +E   L  RY          +L+  +LRLV  +A+ ++  G+ + +++ EGNIGL++A
Sbjct: 161 TTEEVDSLISRY-----EKLRSKLIEKNLRLVYVVALRFKSSGVSLDDLIQEGNIGLLKA 215

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
             +F+   G+R +TY+ W I+  ++  + +++  +   +   +K     L  +K      
Sbjct: 216 ADRFNFVHGYRFSTYAFWCIQNVLKTALQKNYHTISRPSYLQEK-----LSVIKRESVRF 270

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
            +   +      +++  ++ E+ +  +    A   SL+  ++ S +      +  + D  
Sbjct: 271 LNQYGRYPGTTELSELTSIPEAMLEKIKSFPAEPLSLSQPVSRSQEGEDLTVESTLED-- 328

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRE 267
                  ++ +   +R ML R    LN RE ++ + R   +     TLE +S +  VS E
Sbjct: 329 -NAMAAEKETDIALKRRMLERMSLRLNEREYKVLKMRFGIDCHTEHTLEEISHQLNVSVE 387

Query: 268 RVRQIEARAFKKVQ 281
           RVRQ++  A +K+Q
Sbjct: 388 RVRQLQKIALEKLQ 401


>gi|284990614|ref|YP_003409168.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Geodermatophilus obscurus DSM 43160]
 gi|284063859|gb|ADB74797.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Geodermatophilus obscurus DSM 43160]
          Length = 360

 Score =  150 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 48/243 (19%), Positives = 96/243 (39%), Gaps = 18/243 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                 LV  HL LV   A  +   G P  +++  G +GL+ A+ +FDP RG    ++++
Sbjct: 134 ERLREVLVEEHLPLVRHFARRFSNRGEPFDDLLQVGTLGLIAAIDRFDPTRGVEFLSFAV 193

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I   ++ +       V++     +  L      L   +  +   N +      +A+ L
Sbjct: 194 PTITGEIKRHFRDQGWSVRVPRRLQELHLS-----LNAAVGELAQKNGRAPTPSELAEHL 248

Query: 167 NVSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            +  +EV+            SL+  + S + +S      L  +    E V          
Sbjct: 249 GIPRAEVLEGLAVANAYRSSSLDERL-SGEDDSPTLAATLGEEDSALEGV--------EY 299

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L   ++ +  RERRI   R      +T   ++++  +S+  V ++ ++   K++E +
Sbjct: 300 RESLQPLLATIPARERRILILRFFGN--MTQSQIAADIGISQMHVSRLLSQTLAKLREGL 357

Query: 285 QKQ 287
            K 
Sbjct: 358 LKD 360


>gi|255505890|ref|ZP_05348671.3| RNA polymerase sigma-F factor [Bryantella formatexigens DSM 14469]
 gi|255265373|gb|EET58578.1| RNA polymerase sigma-F factor [Bryantella formatexigens DSM 14469]
          Length = 238

 Score =  150 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 48/249 (19%), Positives = 111/249 (44%), Gaps = 17/249 (6%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L +R  + GD +A  +LV  +L LV  IA  + G G  + ++   G+IGL++A+  F+  
Sbjct: 7   LIERAHQ-GDKAAREQLVEENLGLVFTIAKRFTGRGTDVEDLFQIGSIGLLKAIDNFNLS 65

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
              + +TY++  I   ++ ++     ++K+  +  +        R     + +     + 
Sbjct: 66  YDVKFSTYAVPMIAGEIRRFLRDDG-MLKVSRSLKE-----TAGRAAAAREQLEKKLGRE 119

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
             +  ++ ++ ++  E++      A  ESL+  +   D  +   +D +       E+VL 
Sbjct: 120 PTMEELSGEVGITREEIVLAMEAAAEVESLHRPVYQGDGTAIYLEDRIEEKESMNEKVLD 179

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
                     +LT  M  L P E+ +   R  ++   T   ++     ++ +V ++E + 
Sbjct: 180 NM--------VLTEVMEKLEPEEQFLIIMRYFKD--KTQSQVAELLGRTQVQVSRMEKKI 229

Query: 277 FKKVQESIQ 285
            KK+++++Q
Sbjct: 230 LKKMRDALQ 238


>gi|153005080|ref|YP_001379405.1| RNA polymerase sigma-32 subunit RpoH [Anaeromyxobacter sp. Fw109-5]
 gi|152028653|gb|ABS26421.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter sp.
           Fw109-5]
          Length = 241

 Score =  150 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 69/270 (25%), Positives = 119/270 (44%), Gaps = 51/270 (18%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+  +R  P L + EE+ LA R R+ GD+ A  +LV  +L  VV IA   R   + +
Sbjct: 16  LAPYLKAVRDFPPLSRDEEHALALRARK-GDVRAKQKLVRHNLAFVVAIARKQRRGTVRL 74

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM+AV+KFDP  G R +TY++WWI+A + +Y+  + S V+  +       
Sbjct: 75  DDLIQEGNVGLMRAVEKFDPHAGTRFSTYAVWWIRAYIGKYLKEARSTVRPQS------- 127

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
                                                 +S++  +             ++
Sbjct: 128 -------------------------------GTVAQPDLSLDSAI------------DEE 144

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
             +   + +  D  G E   ++ E   + R+ L +    +      I   R  Q+ P TL
Sbjct: 145 GDATHLERIEDDGPGPEDTYLQAEGDSDVRDALGKVRKRIGELGWDIVHNRLEQDQPRTL 204

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           E +   + VSRERVRQ+E +  + +   +Q
Sbjct: 205 EEIGKRWGVSRERVRQVELKTKQFLHRYLQ 234


>gi|197723815|gb|ACH72687.1| RNA polymerase sigma-37 factor [Listeria marthii]
          Length = 242

 Score =  150 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 59/256 (23%), Positives = 115/256 (44%), Gaps = 24/256 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 5   KEKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 64

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +++D   G     +++  I   ++ ++      V +     +        ++K  ++ +T
Sbjct: 65  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELT 119

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWL 204
                  Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +
Sbjct: 120 RELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVV 176

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++
Sbjct: 177 GGTDDGF--------ERVNQRMLLEKVLPVLDEREQKILQYTFIEN--RSQKETGELLDI 226

Query: 265 SRERVRQIEARAFKKV 280
           S+  V +I+ +A KK+
Sbjct: 227 SQMHVSRIQRQAIKKL 242


>gi|288927103|ref|ZP_06420991.1| RNA polymerase sigma-70 factor [Prevotella buccae D17]
 gi|288336130|gb|EFC74523.1| RNA polymerase sigma-70 factor [Prevotella buccae D17]
          Length = 287

 Score =  150 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 70/288 (24%), Positives = 122/288 (42%), Gaps = 49/288 (17%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
            +K+  +  N    L+ Y+ EI +   L  ++E  LA   +  GD  A  +L  ++L+ V
Sbjct: 41  TKKSKDMDSNERNALNTYLDEIGQESPLTPEKEQDLAACIQ-AGDRGALEQLTRANLKFV 99

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V +A  +RG GL  S+++SEGNIGLM+A  KFD  RG R   Y+  +++ AM+  + +  
Sbjct: 100 VAMARRFRGRGLAQSDLISEGNIGLMEAAGKFDGSRGNRFVAYAAPYVRKAMERAVEQQA 159

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            L ++                                   I ++ +  E +  S++  L+
Sbjct: 160 GLYRVPR--------------------------------DIMRQKSRHEVQPASVDAPLS 187

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
                  L    +K++         D D   Q +IE          L   ++ L+ RE+R
Sbjct: 188 EGNKFTLLDILENKDAIHP------DDDYNVQAMIEA---------LESLVATLDEREQR 232

Query: 242 IFEARRLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +            +L  ++ +  + RER RQI  RA +K+  S Q + 
Sbjct: 233 VVRGFYGLGTGRISLAEIAEQMGIKRERARQIRDRALRKIARSTQNRA 280


>gi|253580606|ref|ZP_04857870.1| RNA polymerase [Ruminococcus sp. 5_1_39B_FAA]
 gi|251847977|gb|EES75943.1| RNA polymerase [Ruminococcus sp. 5_1_39BFAA]
          Length = 237

 Score =  150 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 55/242 (22%), Positives = 112/242 (46%), Gaps = 16/242 (6%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A   +   +  LV  +A  + G  + + ++V  G+IGL++A+ +FD     + +
Sbjct: 12  QQGDKEARDTVFKENAGLVYSMAKRFAGRSVEMEDIVQIGSIGLLKAIDRFDISYDVKFS 71

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I   ++ Y+     ++K+      + L  N  R+    +A+     +   +  +
Sbjct: 72  TYAVPMIIGEIRRYLRDDG-MLKVS-----RNLKENCARIYSAREALEKELGREPILEEV 125

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           AK   +S  EV+      A  ESL+ +I   D N     D L    +GQ+  L       
Sbjct: 126 AKATELSVDEVVMSMESGAEVESLHKIIYQGDGNDISLMDRLQEKENGQDAAL------- 178

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             R  L   +  L+ RER++   R  ++  +T   +++E  +S+ +V ++E R  K++++
Sbjct: 179 -NRIFLDEILKKLDARERQLIGMRYFKD--MTQTEIAAEMGISQVQVSRMEKRILKELKK 235

Query: 283 SI 284
            +
Sbjct: 236 QV 237


>gi|161898881|gb|ABX80430.1| SigB [Listeria monocytogenes]
 gi|161898907|gb|ABX80443.1| SigB [Listeria monocytogenes]
          Length = 233

 Score =  150 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 57/247 (23%), Positives = 111/247 (44%), Gaps = 24/247 (9%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D   G  
Sbjct: 5   YQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKS 64

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
              +++  I   ++ ++      V +     +        ++K  ++ +T       Q+ 
Sbjct: 65  FEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQSSPQIS 119

Query: 161 AIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            IA  + V+E EV+           L+ D S+ A    SD ++    D +    DG    
Sbjct: 120 DIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTDDGF--- 173

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
                ER N+R +L + + VL+ RE++I +   ++    + +      ++S+  V +I+ 
Sbjct: 174 -----ERVNQRMLLEKVLPVLDEREQKILQYTFIEN--RSQKETGELLDISQMHVSRIQR 226

Query: 275 RAFKKVQ 281
           +A KK++
Sbjct: 227 QAIKKLR 233


>gi|161898895|gb|ABX80437.1| SigB [Listeria monocytogenes]
 gi|161898903|gb|ABX80441.1| SigB [Listeria monocytogenes]
          Length = 237

 Score =  150 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 57/253 (22%), Positives = 112/253 (44%), Gaps = 24/253 (9%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 3   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 62

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G     +++  I   ++ ++      V +     +        ++   ++ +T    
Sbjct: 63  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKINNAVEELTRELQ 117

Query: 155 KPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +    
Sbjct: 118 SSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTD 174

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++S+  
Sbjct: 175 DGF--------ERVNQRMLLEKVLPVLDEREQKILQFTFIEN--RSQKETGELLDISQMH 224

Query: 269 VRQIEARAFKKVQ 281
           V +I+ +A KK++
Sbjct: 225 VSRIQRQAIKKLR 237


>gi|271969498|ref|YP_003343694.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Streptosporangium roseum DSM 43021]
 gi|270512673|gb|ACZ90951.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Streptosporangium roseum DSM 43021]
          Length = 266

 Score =  150 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 51/243 (20%), Positives = 98/243 (40%), Gaps = 18/243 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                 LV  HL LV  +A  +R  G  + ++     IGL++++ +FD  RG   +TY+ 
Sbjct: 39  QRIRDELVELHLPLVEYLARRFRNRGEWLDDLTQVATIGLIKSIDRFDLGRGVEFSTYAT 98

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I   ++ +       V++     + +L      L   +  ++    +   V  +A  L
Sbjct: 99  PTIVGEIKRHFRDKGWAVRVPRRLQELKLS-----LTKAISELSQREGRAPTVGELAAFL 153

Query: 167 NVSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            +SE EV+    +       SL+A  +  D   +      + D         +  E    
Sbjct: 154 KMSEEEVLEGLESANAYSTVSLDAPDSGDDDAPAVADSLGIVD---------DSLEGVEY 204

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L   +  L PRE+RI   R      +T   +++E  +S+  V ++ AR   +++E +
Sbjct: 205 RESLKPLLERLPPREKRILLLRFFGN--MTQSQIATELGISQMHVSRLLARTLAQLREGL 262

Query: 285 QKQ 287
             +
Sbjct: 263 TAE 265


>gi|84502385|ref|ZP_01000521.1| RNA polymerase sigma-70 factor family protein [Oceanicola batsensis
           HTCC2597]
 gi|84389197|gb|EAQ01994.1| RNA polymerase sigma-70 factor family protein [Oceanicola batsensis
           HTCC2597]
          Length = 249

 Score =  150 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 67/265 (25%), Positives = 120/265 (45%), Gaps = 32/265 (12%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           I    KIP+L+  EE    +R+++HGD  A   L+ SH R    +A  +    + + ++ 
Sbjct: 6   IQAAAKIPLLDIDEERNAIRRWQDHGDREALTLLLRSHARQAWSMAARWTDNPVHLEDLA 65

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
           +EG IGL++A   FD  +  R +TY+ WW+   +     R  S++ +   A         
Sbjct: 66  AEGVIGLIRAADNFDLGQDVRFSTYAAWWVMNGVSAAAARIRSVIDVPPRAV-------- 117

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
                                  + +L   ++ VI+M   + G  +L+A +      +  
Sbjct: 118 -------------------TEMRSGRLADEDNTVITM--AMQGIVALDAPVGDG---THS 153

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
             D LV      E+    +     +R ++ ++MS LN +E  I   RRLQ  P TLE+L+
Sbjct: 154 LLDALVSSDLTPEETAAAESLHDVQRRLIAKAMSGLNAQEAEIIRRRRLQAVPETLEDLA 213

Query: 260 SEFEVSRERVRQIEARAFKKVQESI 284
               ++R+R+RQ+E RA  +++  +
Sbjct: 214 DAMNMTRDRLRQVERRAMTRLRRFL 238


>gi|86158019|ref|YP_464804.1| sigma 32 (RpoH) [Anaeromyxobacter dehalogenans 2CP-C]
 gi|197122674|ref|YP_002134625.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter sp. K]
 gi|220917457|ref|YP_002492761.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter
           dehalogenans 2CP-1]
 gi|85774530|gb|ABC81367.1| sigma 32 (RpoH) [Anaeromyxobacter dehalogenans 2CP-C]
 gi|196172523|gb|ACG73496.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter sp. K]
 gi|219955311|gb|ACL65695.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter
           dehalogenans 2CP-1]
          Length = 241

 Score =  150 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 73/272 (26%), Positives = 124/272 (45%), Gaps = 51/272 (18%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             L+ Y+  +R  P L +++E+ LA R R+ G++SA  +LV  +L  VV IA   R   +
Sbjct: 14  DELAPYLKAVRDFPPLTREDEHALAIRARK-GEVSAKQKLVRHNLAFVVAIARKQRRGTV 72

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++ EGN+GLM+AV+KFDP  G R +TY++WWI+A + +Y+  + S V+        
Sbjct: 73  RLDDLIQEGNVGLMRAVEKFDPHAGTRFSTYAVWWIRAYIGKYLKEARSTVR-------- 124

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                                   Q   +A+                  D SL++ I   
Sbjct: 125 -----------------------PQSGTVAQP-----------------DLSLDSAI--D 142

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           ++  +   + +  D  G E   +  E  +  R+ L +    +      I   R  Q+ P 
Sbjct: 143 EEGDATHLERIEDDGPGPEDTYLSGEGDREVRDALGKVRKRIGELGWDIVHNRLEQDQPR 202

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           TLE +   + VSRERVRQ+E +  + +   +Q
Sbjct: 203 TLEEIGKRWGVSRERVRQVELKTKQFLHRYLQ 234


>gi|161898931|gb|ABX80455.1| SigB [Listeria monocytogenes]
 gi|161898937|gb|ABX80458.1| SigB [Listeria monocytogenes]
          Length = 237

 Score =  150 bits (380), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 58/253 (22%), Positives = 112/253 (44%), Gaps = 24/253 (9%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 3   YIWIAAYQEDGDEDAQYNLVIHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 62

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G     +++  I   ++ ++      V +     +        ++K  ++ +T    
Sbjct: 63  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQ 117

Query: 155 KPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +    
Sbjct: 118 SSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTD 174

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++S+  
Sbjct: 175 DGF--------ERVNQRMLLEKVLPVLDEREQKILQFTFIEN--RSQKETGELLDISQMH 224

Query: 269 VRQIEARAFKKVQ 281
           V +I+ +A KK++
Sbjct: 225 VSRIQRQAIKKLR 237


>gi|3451022|gb|AAC32644.1| RNA polymerase sigma factor [Escherichia coli RS218]
          Length = 220

 Score =  150 bits (379), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 57/162 (35%), Positives = 92/162 (56%), Gaps = 3/162 (1%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 178

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           LR  +  L    D+    E++     K     S ++ +N R+
Sbjct: 179 LRTAR-ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERI 219


>gi|310826431|ref|YP_003958788.1| RinA family phage transcriptional regulator [Eubacterium limosum
           KIST612]
 gi|308738165|gb|ADO35825.1| RinA family phage transcriptional regulator [Eubacterium limosum
           KIST612]
          Length = 250

 Score =  150 bits (379), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 58/257 (22%), Positives = 109/257 (42%), Gaps = 16/257 (6%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
            KQE   L   Y++ GD     RL+ + L +   +   Y      + ++     +GLM A
Sbjct: 8   TKQESKKLFIEYKKTGDKEIRDRLIENFLYIPKLLVKKYAYRSNDVEDIYQVACLGLMYA 67

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V+++DP+RGF   T++   I   +++Y      ++++     +  L   + R K  L+  
Sbjct: 68  VERYDPDRGFEFDTFASPTIIGEIKKYYRDKQWIIRVPRRIQE--LNREINRAKTTLE-- 123

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNC--RLAGDESLNALINSSDKNSSQWQDWLVYD 207
               +K   +  IA  L V+E  VI       +   +SL+    S+          L+ +
Sbjct: 124 -HKLMKTPTISEIADYLEVTEEAVIEAMEGNNVFYPKSLSTEFESNADGQEATLLDLIGE 182

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            D       E+ E       L + +  LNP ER I E R    N  T + +++    S+ 
Sbjct: 183 ED-------ERIENIGNVEDLRQRLESLNPVERMIIEERYY--NGKTQKEVAAIIGKSQM 233

Query: 268 RVRQIEARAFKKVQESI 284
            V ++E +  +K++ ++
Sbjct: 234 TVSRLEKKVMEKLRANL 250


>gi|161898897|gb|ABX80438.1| SigB [Listeria monocytogenes]
          Length = 235

 Score =  150 bits (379), Expect = 2e-34,   Method: Composition-based stats.
 Identities = 58/253 (22%), Positives = 112/253 (44%), Gaps = 24/253 (9%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 1   YIWIAAYQEDGDEDAQYNLVIHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 60

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G     +++  I   ++ ++      V +     +        ++K  ++ +T    
Sbjct: 61  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQ 115

Query: 155 KPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +    
Sbjct: 116 SSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTD 172

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++S+  
Sbjct: 173 DGF--------ERVNQRMLLEKVLPVLDEREQKILQYTFIEN--RSQKETGELLDISQMH 222

Query: 269 VRQIEARAFKKVQ 281
           V +I+ +A KK++
Sbjct: 223 VSRIQRQAIKKLR 235


>gi|1396060|dbj|BAA13043.1| part of principal sigma factor homolog [Synechocystis sp.]
          Length = 186

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 44/197 (22%), Positives = 91/197 (46%), Gaps = 13/197 (6%)

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+   I      +++    
Sbjct: 1   RGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPVH- 59

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
               L+  + R+K   + ++    +      IA+K+ ++  ++  +        SL   I
Sbjct: 60  ----LYETISRIKKTTKLLSQEMRRKPTEEEIAEKMEMTIEKLRFIAKSAQLPISLETPI 115

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
               +  S+  D++  D     +   ++  +   R  L   +  L+PRER +   R   +
Sbjct: 116 --GKEEDSRLGDFIEADG----ETPEDEVSKNLLREDLENVLDTLSPRERDVLRLRYGLD 169

Query: 251 NPV--TLENLSSEFEVS 265
           +    TLE +   F V+
Sbjct: 170 DGRMKTLEEIGQIFNVT 186


>gi|260439092|ref|ZP_05792908.1| RNA polymerase sigma-F factor [Butyrivibrio crossotus DSM 2876]
 gi|292808404|gb|EFF67609.1| RNA polymerase sigma-F factor [Butyrivibrio crossotus DSM 2876]
          Length = 241

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 52/245 (21%), Positives = 106/245 (43%), Gaps = 14/245 (5%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
               G+  A   LV  ++ LV  IA  +   G  + ++VS G IGL++A+ KFD      
Sbjct: 10  LAHEGNKEARDMLVMHNMGLVYSIAKRFANRGYEMDDIVSIGTIGLIKAIDKFDLNMDVM 69

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
           L+TY++  I   ++ +I     ++KI  +  +    + + + K +L       +    + 
Sbjct: 70  LSTYAVPMISGEIKRFIRDDG-IIKISRSIKEN--GWKINQAKDYLSQKLKREV---TIE 123

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I+K+  +   +++         ES+   I  SD N     D L               +
Sbjct: 124 EISKETGICTEDIVVAMEASKDVESIYQTIYQSDGNQIYVVDKLA------ASAKESDHD 177

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           +     ML  +M++L   E+ I E R  QE   T   ++    +S+ +V ++E +   ++
Sbjct: 178 KIMNHVMLEETMNILEKDEKTIIEMRYFQE--KTQSEVAKILGISQVQVSRMEKKILLRM 235

Query: 281 QESIQ 285
           +++++
Sbjct: 236 RKNME 240


>gi|164690667|dbj|BAF98617.1| putative DNA helicase [Streptomyces argenteolus]
          Length = 1064

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 64/287 (22%), Positives = 121/287 (42%), Gaps = 33/287 (11%)

Query: 28  MLEKQEEYVLA--KRYREHGD-----------------LSAAHRLVTSHLRLVVKIAMGY 68
           +L  +EE  LA   R R+  D                   A   LV  ++RLV      Y
Sbjct: 112 LLRAEEEVGLAVLMRGRDRMDHEPGKGFAAGLAPLDERRRAFDALVLHNIRLVHAAVAPY 171

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            G G+   ++V  G +G+M+A +KFDP  G R +TY+ WWI+ A+   +    S ++I  
Sbjct: 172 LGQGVDREDLVQHGVLGVMRAAEKFDPRAGTRFSTYATWWIRQAVSRAVADEGSTIRIPA 231

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
                 L   +   +       +  L+P +   +A +L++   + +++  R++     ++
Sbjct: 232 HVRDVVLKVAVACRRSR-----ERGLRP-RPQDLAAELDLPP-DTVNLALRVSRPA--DS 282

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
           L   +D          + D     +  +     +   + L   +  L  R   I   R  
Sbjct: 283 LDRVADGVRPAELAISLRDAIPGPEETLRAAFGRQWVDWL---LEPLPARNADIVRRRNG 339

Query: 249 --QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
             +  P TL+++   + V+RER+RQ E RA   +++ +   V++ +S
Sbjct: 340 VIKGEPQTLKDIGVLYGVTRERIRQNEKRALAVLRDRLGAPVKVPAS 386


>gi|297820128|ref|XP_002877947.1| predicted protein [Arabidopsis lyrata subsp. lyrata]
 gi|297323785|gb|EFH54206.1| predicted protein [Arabidopsis lyrata subsp. lyrata]
          Length = 568

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 59/236 (25%), Positives = 116/236 (49%), Gaps = 11/236 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
               L+ S   LV+ +A  YRG G+   +++  G +G++Q  ++FD  RG++ +TY  +W
Sbjct: 329 CRDELLKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVQYW 388

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ +M   + R    V I ++    R    +++ +  L+  T + +K      I+K  ++
Sbjct: 389 IRKSMSMMVSRHARGVHIPSSI--IRTINQIQKARKTLK--TSHGIKYPADEDISKLTSL 444

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  ++ + N  L    S+   +   D  S++   +L +  D   +   E   R++ R  +
Sbjct: 445 SVKKIRAANQCLKVVGSIEKKV--GDCFSTK---FLEFTPDTTMESPEEAVMRQSARRDI 499

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              +  L PRE+++   R   +N  P +LE +     VS+E +R+IE RA  K+++
Sbjct: 500 HDLLEGLEPREKQVMVLRYGLQNYRPKSLEEIGKLLRVSKEWIRKIERRAMAKLRD 555


>gi|291550016|emb|CBL26278.1| RNA polymerase, sigma subunit, RpsG/SigG [Ruminococcus torques
           L2-14]
          Length = 260

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 60/261 (22%), Positives = 120/261 (45%), Gaps = 17/261 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L ++E+  L +R R+ GD  A    +  +LRLV+ +   +        ++   G 
Sbjct: 14  SKLPLLREKEKEELFRRIRQ-GDKLAREEYIKGNLRLVLSVMKRFDSSNENADDLFQIGC 72

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           +GL++AV  FDP+R  + +TY++  I   ++ Y+  + SL ++  +           R  
Sbjct: 73  VGLVKAVDNFDPDRQVKFSTYAVPMIIGEIRRYLRDNSSL-RVSRSLRDIAYKVIYTR-- 129

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
              +     N+K   +  IA+++ +S+ EV+     +    SL   +  +D   + +   
Sbjct: 130 ---EGYIRKNMKEPSIQEIAEEIGLSKEEVVYALDAVQTPMSLQEPVY-NDGGDALYVMD 185

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
            V D   +E+  +E+         L  +M  LN RERR+   R       T   +S +  
Sbjct: 186 QVSDKKNREENWVEELS-------LEAAMERLNERERRLIRLRFF--EGKTQMEVSEQIG 236

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+ +V ++E  A K +++ +
Sbjct: 237 ISQAQVSRLEKNALKTMRQYL 257


>gi|161898847|gb|ABX80413.1| SigB [Listeria monocytogenes]
          Length = 233

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 57/247 (23%), Positives = 111/247 (44%), Gaps = 24/247 (9%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D   G  
Sbjct: 5   YQENGDEDAQYNLVIHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKS 64

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
              +++  I   ++ ++      V +     +        ++K  ++ +T       Q+ 
Sbjct: 65  FEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQSSPQIS 119

Query: 161 AIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            IA  + V+E EV+           L+ D S+ A    SD ++    D +    DG    
Sbjct: 120 DIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTDDGF--- 173

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
                ER N+R +L + + VL+ RE++I +   ++    + +      ++S+  V +I+ 
Sbjct: 174 -----ERVNQRMLLEKVLPVLDEREQKILQFTFIEN--RSQKETGELLDISQMHVSRIQR 226

Query: 275 RAFKKVQ 281
           +A KK++
Sbjct: 227 QAIKKLR 233


>gi|161898871|gb|ABX80425.1| SigB [Listeria monocytogenes]
          Length = 229

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 57/247 (23%), Positives = 111/247 (44%), Gaps = 24/247 (9%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D   G  
Sbjct: 1   YQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKS 60

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
              +++  I   ++ ++      V +     +        ++K  ++ +T       Q+ 
Sbjct: 61  FEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQSSPQIS 115

Query: 161 AIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            IA  + V+E EV+           L+ D S+ A    SD ++    D +    DG    
Sbjct: 116 DIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTDDGF--- 169

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
                ER N+R +L + + VL+ RE++I +   ++    + +      ++S+  V +I+ 
Sbjct: 170 -----ERVNQRMLLEKVLPVLDEREQKILQFTFIEN--RSQKETGELLDISQMHVSRIQR 222

Query: 275 RAFKKVQ 281
           +A KK++
Sbjct: 223 QAIKKLR 229


>gi|30024623|dbj|BAC75680.1| sigma L [Streptomyces griseus]
          Length = 288

 Score =  150 bits (379), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 53/237 (22%), Positives = 95/237 (40%), Gaps = 17/237 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +
Sbjct: 64  RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTV 123

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +   V  + + L VS
Sbjct: 124 VGEIKRFFRDTSWSVRVPRRLQELRLA-----LTKTSDELAQKLDRSPTVPELVRALGVS 178

Query: 170 ESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E +V+            SL++     D       D L Y+    E V          R  
Sbjct: 179 EEDVVDGLAVGNAYTASSLDSPSPEDDGGEGSLADRLGYEDAALEGV--------EYRES 230

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   ++ L PRER+I   R      +T   +  E  +S+  V ++  R   +++E +
Sbjct: 231 LKPLLAKLAPRERQIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLREGL 285


>gi|167759902|ref|ZP_02432029.1| hypothetical protein CLOSCI_02266 [Clostridium scindens ATCC 35704]
 gi|167662521|gb|EDS06651.1| hypothetical protein CLOSCI_02266 [Clostridium scindens ATCC 35704]
          Length = 237

 Score =  149 bits (378), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 51/241 (21%), Positives = 103/241 (42%), Gaps = 16/241 (6%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GD  A  RLV  +  LV  I   +   G+   ++   GNIGL++A+ KFD     + +T
Sbjct: 13  DGDEEARARLVEENAGLVWCIVKRFYNRGVEAEDLFQVGNIGLLKAIDKFDMSYDVKFST 72

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y++  I   ++ ++     ++K+  +  +      L + +     + +   +   +  IA
Sbjct: 73  YAVPMISGEIKRFLRDDG-MIKVSRSLKELAYKAYLCQER-----LQEQWGRDPTITEIA 126

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + LNV   E+          ESL+  I   +    +  D L     G++++L        
Sbjct: 127 ESLNVEREELTMALDASGDIESLHKPIYQKEGQEIRLMDKLPEKEGGEDKIL-------- 178

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
              +L + ++ L+  ER++   R       T   +  E  +S+ +V ++E +  K ++E 
Sbjct: 179 NHMLLQQLLNYLDKDERQLIYLRYFANQ--TQTQVGRELGISQVQVSRMEKKILKNLRER 236

Query: 284 I 284
           I
Sbjct: 237 I 237


>gi|188589198|ref|YP_001920238.1| sporulation sigma factor SigF [Clostridium botulinum E3 str. Alaska
           E43]
 gi|251778416|ref|ZP_04821336.1| RNA polymerase sigma-F factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
 gi|188499479|gb|ACD52615.1| RNA polymerase sigma-F factor [Clostridium botulinum E3 str. Alaska
           E43]
 gi|243082731|gb|EES48621.1| RNA polymerase sigma-F factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
          Length = 251

 Score =  149 bits (378), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 44/246 (17%), Positives = 101/246 (41%), Gaps = 16/246 (6%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             + GD  A +RL+  +L LV  I+  +   G    ++   G+IGL++A+  FD     +
Sbjct: 22  LAKDGDTEAMNRLIEMNLPLVASISKKFLNRGYDYEDIFQIGSIGLVKAINNFDLSYNVK 81

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY++  I   ++ ++     ++K+             +R+    + +T    +   + 
Sbjct: 82  FSTYAVPMIIGEIKRFLRDDG-MIKVSRNVKSLA-----KRIHFTKEELTKKLNRSPTIE 135

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+   V + E+I         + L   I+  D       D L            E + 
Sbjct: 136 ELAEYSGVDKEEIIFAIESATSLQYLYDTIHQDDGAPVLLIDKLSEKG--------EDDI 187

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
               +  L  ++  L+ + R+I   R  ++   T   ++    +S+ +V +IE +   K+
Sbjct: 188 GMINKIALKEALRSLDEKARQIIVLRYFKD--KTQVQVAKLLGISQVQVSRIEKKVLLKM 245

Query: 281 QESIQK 286
           ++ +++
Sbjct: 246 RDKLEE 251


>gi|296332841|ref|ZP_06875301.1| RNA polymerase sigma factor SigB [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305673187|ref|YP_003864859.1| RNA polymerase sigma factor SigB [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|296150121|gb|EFG91010.1| RNA polymerase sigma factor SigB [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305411431|gb|ADM36550.1| RNA polymerase sigma factor SigB [Bacillus subtilis subsp.
           spizizenii str. W23]
          Length = 262

 Score =  149 bits (378), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 62/267 (23%), Positives = 115/267 (43%), Gaps = 24/267 (8%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K   L K E   L   Y+ + D  A   LV  +  LV  +A  Y        ++   G 
Sbjct: 5   SKTTKLTKDEVDRLISDYQTNQDEQAQETLVRVYTNLVDMLAKKYSKGKSFHEDLRQVGM 64

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL+ A+K++DP  G     +++  I   ++ ++      V +     +        R+K
Sbjct: 65  IGLLGAIKRYDPVVGKSFEAFAIPTIIGEIKRFLRDKTWSVHVPRRIKELG-----PRIK 119

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNS 197
             +  +T    +  +V  IA+ L+VSE EV+           L+ D S+ A    +D ++
Sbjct: 120 MAVDQLTTETQRSPKVEEIAEFLDVSEEEVLETMEMGKSYQALSVDHSIEA---DADGST 176

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
               D +    DG         ER N++ ML   + VL+ RE++I +   +Q    + + 
Sbjct: 177 VTILDIVGSQEDGY--------ERVNQQMMLQSVLHVLSDREKQIIDLTYIQN--KSQKE 226

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESI 284
                 +S+  V +++ +A KK++E++
Sbjct: 227 TGDILGISQMHVSRLQRKAVKKLREAL 253


>gi|305644360|gb|ADM53781.1| RNA polymerase sigma factor [Aeromonas hydrophila]
 gi|305644362|gb|ADM53782.1| RNA polymerase sigma factor [Aeromonas hydrophila]
          Length = 176

 Score =  149 bits (378), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 43/186 (23%), Positives = 78/186 (41%), Gaps = 12/186 (6%)

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+  
Sbjct: 1   GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISR 58

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            +         PE    +A ++ + E ++  +        S+   I   D   S   D++
Sbjct: 59  QMLQEMGREPNPE---ELAMRMGMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI 113

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEF 262
               D    +  +    ++ RN     ++ L  RE ++   R   +     TLE +  +F
Sbjct: 114 ---EDTTLALPADAATSESLRNATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQF 170

Query: 263 EVSRER 268
           +V+RER
Sbjct: 171 DVTRER 176


>gi|55274976|gb|AAV49287.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 204

 Score =  149 bits (378), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 56/214 (26%), Positives = 102/214 (47%), Gaps = 12/214 (5%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           ++  I+     +++      K L   LR  +     ++           IA++L+    +
Sbjct: 61  IERAIMNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDD 115

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           V  M        S++  +    +     +  L    D +E    +  +  + +  + + +
Sbjct: 116 VSRMLRLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWL 170

Query: 233 SVLNPRERRIFEARR--LQENPVTLENLSSEFEV 264
             LN ++R +   R   L     TLE++  E  +
Sbjct: 171 FELNAKQREVLARRFGLLGYEAATLEDVGREIGL 204


>gi|23978307|dbj|BAC21130.1| principal sigma factor [Calothrix brevissima]
          Length = 188

 Score =  149 bits (378), Expect = 3e-34,   Method: Composition-based stats.
 Identities = 43/199 (21%), Positives = 90/199 (45%), Gaps = 13/199 (6%)

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
              GL   +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+   I      +++  
Sbjct: 1   MNRGLSFQDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLSV 60

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
                 L+  + R+K   + ++    +      IA ++ ++  ++  +        SL  
Sbjct: 61  H-----LYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLET 115

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            I    +  S+  D++  D     +   ++  +   R  L + +  L+PRER +   R  
Sbjct: 116 PI--GKEEDSRLGDFIESDG----ETPEDQVSKNLLREDLEKVLDSLSPRERDVLRLRYG 169

Query: 249 QENPV--TLENLSSEFEVS 265
             +    TLE +   F V+
Sbjct: 170 LGDGRMKTLEEIGQIFNVT 188


>gi|238917528|ref|YP_002931045.1| RNA polymerase sporulation-specific sigma factor [Eubacterium
           eligens ATCC 27750]
 gi|238872888|gb|ACR72598.1| RNA polymerase sporulation-specific sigma factor [Eubacterium
           eligens ATCC 27750]
          Length = 249

 Score =  149 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 47/250 (18%), Positives = 99/250 (39%), Gaps = 17/250 (6%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             L  +   + D  A  +LVT +L L+  I   ++G G    ++   G IGL++A+  F+
Sbjct: 15  RELIAKAHNN-DKEAREKLVTDNLGLIWNIIKRFKGRGTEQEDLFQIGCIGLIKAIDNFN 73

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
            +     +TY++  I   ++ ++     +VK+  +  +  +     +       + D   
Sbjct: 74  LDMDVAFSTYAVPMITGEIRRFLRDDG-MVKVSRSIKENAV-----KSMKAAGQLRDTLG 127

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
               V  IA    +S  ++          ES+   I   D +     D L    D     
Sbjct: 128 CEPTVEQIAAACELSVEDITLSMSASMEVESIYKTIYQGDGSEVMLMDKLEDKADIG--- 184

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
                E  + +  L + M  L+ RE+ +   R   +   T   ++ EF +S+ +V ++E 
Sbjct: 185 -----ETASSKVALVQLMETLSQREKELIRMRYYDD--YTQMQVAKEFGISQVQVSRMEK 237

Query: 275 RAFKKVQESI 284
           +    +++ +
Sbjct: 238 KILSGMRKRL 247


>gi|220931546|ref|YP_002508454.1| sporulation sigma factor SigF [Halothermothrix orenii H 168]
 gi|219992856|gb|ACL69459.1| sporulation sigma factor SigF [Halothermothrix orenii H 168]
          Length = 257

 Score =  149 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 49/262 (18%), Positives = 118/262 (45%), Gaps = 15/262 (5%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+ +L ++E     K+ + + D  A  +LV  +LRLV+K+   ++  G    ++   G I
Sbjct: 10  KVRLLSEEETRHYIKKAQNN-DQKALDKLVEHNLRLVLKVINRFKSSGYDPQDLFQIGVI 68

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+K FD +RG + +TY++  I   ++ +I     ++K+  +  +         ++ 
Sbjct: 69  GLIKAIKNFDLDRGVKFSTYAVSRIIGEIRLHIRDDG-IIKVSRSLKKIA-----NDVRK 122

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             + +   N     ++ ++KK   S+ E++          S+   +   D +     D L
Sbjct: 123 KEEELKKKNNCSPSILELSKKTGYSKEEIVQALEANKAPTSIYETVYEDDGSELYVVDNL 182

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             +   +E++    +                  R R+I   R  ++   T + ++ E  V
Sbjct: 183 ANESKDEEKIPDFNKILLVDLLKKLD------ERSRKIIYLRYFED--KTQQEVADEIGV 234

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+ ++ ++E +   K+++++++
Sbjct: 235 SQVQISRLEKKILHKLRDNLEE 256


>gi|55274915|gb|AAV49259.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274917|gb|AAV49260.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274923|gb|AAV49263.1| RNA polymerase subunit sigma-38 [Shigella flexneri]
 gi|55274925|gb|AAV49264.1| RNA polymerase subunit sigma-38 [Shigella boydii]
 gi|55274928|gb|AAV49265.1| RNA polymerase subunit sigma-38 [Shigella sonnei]
 gi|55274932|gb|AAV49267.1| RNA polymerase subunit sigma-38 [Shigella boydii]
 gi|55274939|gb|AAV49270.1| RNA polymerase subunit sigma-38 [Shigella boydii]
 gi|55274949|gb|AAV49274.1| RNA polymerase subunit sigma-38 [Shigella dysenteriae]
 gi|55274955|gb|AAV49277.1| RNA polymerase subunit sigma-38 [Shigella dysenteriae]
 gi|55274957|gb|AAV49278.1| RNA polymerase subunit sigma-38 [Shigella dysenteriae]
 gi|55274959|gb|AAV49279.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274961|gb|AAV49280.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274974|gb|AAV49286.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274980|gb|AAV49289.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274991|gb|AAV49293.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274993|gb|AAV49294.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 204

 Score =  149 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 57/214 (26%), Positives = 102/214 (47%), Gaps = 12/214 (5%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+ 
Sbjct: 1   RMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQ 60

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            ++  I+     +++      K L   LR  +     ++           IA++L+    
Sbjct: 61  TIERAIMNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVD 115

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           +V  M        S++  +    + +      L    D +E    +  +  + +  + + 
Sbjct: 116 DVSRMLRLNERITSVDTPLGGDSEKA-----LLDILADEKENGPEDTTQDDDMKQSIVKW 170

Query: 232 MSVLNPRERRIFEARR--LQENPVTLENLSSEFE 263
           +  LN ++R +   R   L     TLE++  E  
Sbjct: 171 LFELNAKQREVLARRFGLLGYEAATLEDVGREIG 204


>gi|317505016|ref|ZP_07962964.1| RNA polymerase sigma factor rpoD [Prevotella salivae DSM 15606]
 gi|315663898|gb|EFV03617.1| RNA polymerase sigma factor rpoD [Prevotella salivae DSM 15606]
          Length = 260

 Score =  149 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 63/281 (22%), Positives = 118/281 (41%), Gaps = 50/281 (17%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRL 60
           +    +       L+ Y++EI K  +L   EE  L+++ ++ G     A ++L +++LR 
Sbjct: 14  KTGKPLSERESESLNLYLNEIGKEELLSDDEENKLSQQIQQGGASSERAINKLTSANLRF 73

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y   G+ I +++SEGNIGLM+A   FD  RG R   Y+  +++ A++  +   
Sbjct: 74  VVAIAKQYTDRGVAILDLISEGNIGLMKAAMSFDGSRGLRFVGYAEPFVRRAIEAAVNEQ 133

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
             + ++    N                        PE+                      
Sbjct: 134 SGIFRLPKHEN-----------------------SPEEKAN------------------- 151

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           +   S++A +      + +    L    D       ++    + +  L ++M++LN RE+
Sbjct: 152 SRAFSVDAPL-----ENGKNMSLLSVLSDPNAARPDQEVLEASVKEELMQAMNILNQREK 206

Query: 241 RIFEARRLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
            + EA      P  T   ++ +  + RERVRQI  +A +K+
Sbjct: 207 NVVEAFYGIGQPHLTFAEIAEKMGLKRERVRQIRNKAVRKL 247


>gi|55274937|gb|AAV49269.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 204

 Score =  149 bits (378), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 57/214 (26%), Positives = 102/214 (47%), Gaps = 12/214 (5%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+ 
Sbjct: 1   RMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQ 60

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            ++  I+     +++      K L   LR  +     ++           IA++L+    
Sbjct: 61  TIERAIMNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVD 115

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           +V  M        S++  +    +     +  L    D +E    +  +  + +  + + 
Sbjct: 116 DVSRMLRLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDNDMKQSIVKW 170

Query: 232 MSVLNPRERRIFEARR--LQENPVTLENLSSEFE 263
           +  LN ++R +   R   L     TLE++  E  
Sbjct: 171 LFELNAKQREVLARRFGLLGYEAATLEDVGREIG 204


>gi|315608976|ref|ZP_07883948.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella buccae
           ATCC 33574]
 gi|315249356|gb|EFU29373.1| DNA-directed RNA polymerase sigma subunit RpoD [Prevotella buccae
           ATCC 33574]
          Length = 287

 Score =  149 bits (377), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 70/288 (24%), Positives = 122/288 (42%), Gaps = 49/288 (17%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
            +K+  +  N    L+ Y+ EI +   L  ++E  LA   +  GD  A  +L  ++L+ V
Sbjct: 41  TKKSKDMDSNERNALNTYLDEIGQESPLTPEKEQDLAACIQ-AGDRGALEQLTRANLKFV 99

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V +A  +RG GL  S+++SEGNIGLM+A  KFD  RG R   Y+  +++ AM+  + +  
Sbjct: 100 VAMARRFRGRGLAQSDLISEGNIGLMEAAGKFDGSRGNRFVAYAAPYVRKAMERAVEQQA 159

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            L ++                                   I ++ +  E +  S++  L+
Sbjct: 160 GLYRVPR--------------------------------DIMRQKSRHEVQPASVDAPLS 187

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
                  L    +K++         D D   Q +IE          L   ++ L+ RE+R
Sbjct: 188 EGNKFTLLDILENKDAIHP------DDDYNVQAMIEA---------LESLVATLDEREQR 232

Query: 242 IFEARRLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +            +L  ++ +  + RER RQI  RA +K+  S Q + 
Sbjct: 233 VVRGFYGLGTGRISLAEIAEQMGIKRERARQIRDRALRKIARSTQNRA 280


>gi|125975381|ref|YP_001039291.1| RNA polymerase, sigma 28 subunit [Clostridium thermocellum ATCC
           27405]
 gi|281419342|ref|ZP_06250357.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Clostridium
           thermocellum JW20]
 gi|125715606|gb|ABN54098.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Clostridium
           thermocellum ATCC 27405]
 gi|281406962|gb|EFB37225.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Clostridium
           thermocellum JW20]
 gi|316939496|gb|ADU73530.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Clostridium
           thermocellum DSM 1313]
          Length = 252

 Score =  149 bits (377), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 46/253 (18%), Positives = 118/253 (46%), Gaps = 19/253 (7%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L + Y+E   +   +++V+ +L L   +A  +   G+   ++    +I L++AV++FDP
Sbjct: 17  ELFREYKETKSVEVRNKIVSKYLYLSDILAKKFLNRGIDYEDIYQVASIALIKAVERFDP 76

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           ++G +  +++   I   ++ Y     S+++I      +R++   +++    +++T    +
Sbjct: 77  DKGVKFISFATPTIIGEIKRYFRDKGSVIRIP-----RRIYEVYQKINHARESLTQELKR 131

Query: 156 PEQVVAIAKKLNVSESEVISMNCR--LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
           P ++  +A+ LN+SE  V+ +         +S +  + ++D+        ++ D D    
Sbjct: 132 PPRIDELARHLNISEESVVEIIESYNAYNIQSFSQNVYANDE---LELHEVIGDQDSTF- 187

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
                 ER   R+ L +S+   +  E+     R       T ++++ +  VS+  + ++E
Sbjct: 188 ------ERIENRDFLEKSLDKFSDVEKEFISMRYFDN--KTQKDIAQKMGVSQMYISRLE 239

Query: 274 ARAFKKVQESIQK 286
            +  +K +  + K
Sbjct: 240 RKVLEKFRRMLAK 252


>gi|55274951|gb|AAV49275.1| RNA polymerase subunit sigma-38 [Shigella flexneri]
          Length = 205

 Score =  149 bits (377), Expect = 4e-34,   Method: Composition-based stats.
 Identities = 57/215 (26%), Positives = 102/215 (47%), Gaps = 12/215 (5%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            R++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+
Sbjct: 1   RRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIR 60

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
             ++  I+     +++      K L   LR  +     ++           IA++L+   
Sbjct: 61  QTIERAIMNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPV 115

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            +V  M        S++  +    + +      L    D +E    +  +  + +  + +
Sbjct: 116 DDVSRMLRLNERITSVDTPLGGDSEKA-----LLDILADEKENGPEDTTQDDDMKQSIVK 170

Query: 231 SMSVLNPRERRIFEARR--LQENPVTLENLSSEFE 263
            +  LN ++R +   R   L     TLE++  E  
Sbjct: 171 WLFELNAKQREVLARRFGLLGYEAATLEDVGREIG 205


>gi|239623681|ref|ZP_04666712.1| RNA polymerase [Clostridiales bacterium 1_7_47_FAA]
 gi|239521712|gb|EEQ61578.1| RNA polymerase [Clostridiales bacterium 1_7_47FAA]
          Length = 239

 Score =  149 bits (377), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 56/255 (21%), Positives = 113/255 (44%), Gaps = 17/255 (6%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            E   L     E GD +A  +LV  ++ L+  I   + G G  + ++   G+IGL++A+ 
Sbjct: 2   DETMKLINMAHE-GDKAARDQLVMDNVGLIWSIVRRFSGRGYEMEDLFQIGSIGLIKAID 60

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD     + +TY++  I   ++ ++     ++K+  +  +        +++   + +T 
Sbjct: 61  KFDTGFEVKFSTYAVPMITGEIKRFLRDDG-MIKVSRSIKELGF-----KVRAAREEMTY 114

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
           +  +   +  IA +L+ S  EV +     A  ESL     + D N+    D L  +++  
Sbjct: 115 SLGREPTIEEIAARLDTSREEVAASMEAGAEVESLYRPTGNGDDNTMFLMDRLEEENNDH 174

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E++L         R +L   M  L   +R I   R       T   ++ E  +S+ +V +
Sbjct: 175 EELL--------NRMVLKELMEDLGEEQREIIVRRYFYNQ--TQTQIAKELGISQVQVSR 224

Query: 272 IEARAFKKVQESIQK 286
           +E R  K+++   +K
Sbjct: 225 LEKRILKEMRMRYEK 239


>gi|23978316|dbj|BAC21132.1| principal sigma factor [Anabaena cylindrica]
          Length = 188

 Score =  149 bits (377), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 42/199 (21%), Positives = 90/199 (45%), Gaps = 13/199 (6%)

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
              GL   +++ EG++GL++A +K D E+G++ +TY+ WWI+ A+   I      +++  
Sbjct: 1   MNRGLSFQDLIQEGSLGLIRAAEKLDHEKGYKFSTYATWWIRQAITRAIADQSRTIRLPV 60

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
                 L+  + R+K   + ++    +      IA ++ ++  ++  +        SL  
Sbjct: 61  H-----LYETISRIKKTTKLLSQEMGRKPTEEEIATRMEMTIEKLRFIAKSAQLPISLET 115

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            I    +  S+  D++  D     +   ++  +   R  L + +  L+PRER +   R  
Sbjct: 116 PI--GKEEDSRLGDFIESDG----ETPEDQVSKNLLREDLEKVLDSLSPRERDVLRLRYG 169

Query: 249 QENPV--TLENLSSEFEVS 265
            ++    TLE +   F V+
Sbjct: 170 LDDGRMKTLEEIGQIFNVT 188


>gi|311071144|ref|YP_003976067.1| RNA polymerase sigma factor SigB [Bacillus atrophaeus 1942]
 gi|310871661|gb|ADP35136.1| RNA polymerase sigma factor SigB [Bacillus atrophaeus 1942]
          Length = 262

 Score =  149 bits (376), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 63/267 (23%), Positives = 116/267 (43%), Gaps = 24/267 (8%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K   L K E   L   Y+ + D SA   LV  +  LV  +A  Y        ++   G 
Sbjct: 5   SKTTKLTKDEVDRLINEYQTNQDDSAQETLVQVYTNLVEVLAKKYSKGKSFHEDLRQVGM 64

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL+ A+K++DP  G     +++  I   ++ ++      V +     +        R+K
Sbjct: 65  IGLLGAIKRYDPVVGKSFEAFAIPTIIGEIKRFLRDKTWSVHVPRRIKELG-----PRIK 119

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNS 197
             +  +T    +  +V  IA+ L+VSE EV+           L+ D S+ A    +D ++
Sbjct: 120 MAVDTLTTETQRSPKVEEIAEYLDVSEEEVLETMEMGKSYQALSVDHSIEA---DADGST 176

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
               D +    DG         ER N++ ML   + VL+ RE++I +   +Q    + + 
Sbjct: 177 VTILDIVGSQEDGY--------ERVNQQMMLKSVLHVLSEREKQIIDLTYIQN--KSQKE 226

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESI 284
                 +S+  V +++ +A KK++E++
Sbjct: 227 TGDILGISQMHVSRLQRKAVKKLREAL 253


>gi|169351193|ref|ZP_02868131.1| hypothetical protein CLOSPI_01972 [Clostridium spiroforme DSM 1552]
 gi|169292255|gb|EDS74388.1| hypothetical protein CLOSPI_01972 [Clostridium spiroforme DSM 1552]
          Length = 258

 Score =  149 bits (376), Expect = 5e-34,   Method: Composition-based stats.
 Identities = 60/283 (21%), Positives = 124/283 (43%), Gaps = 25/283 (8%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
             N  II+NG        HE RK   L  +E Y L   Y++  D     +LV  +++LV+
Sbjct: 1   MNNYQIIING-------YHEPRKK--LTTKETYALIDEYQKTKDERIKEKLVNDNIKLVI 51

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +   +        ++   G IGL++A++ F+     + +TY++  I   M+ Y+  +  
Sbjct: 52  SMTKRFYNRSDGCDDLFQVGMIGLIKAIENFNTSYDLKFSTYAVPLIIGEMKRYLRDN-H 110

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            +KI  +   K + + + ++K       +   +   +  +AKKL++ +S ++        
Sbjct: 111 QIKISRSL--KDIAYKILKIKD---EYLNKFQREPTIKELAKKLDIDQSVIVEALLSTNS 165

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             SL   + +SD NS +  D L  +  G          + N R  L  ++  L+ +E  +
Sbjct: 166 VASLQEEVKNSDGNSLKMIDSLSDEKAG--------VLKTNERIDLYDALKSLSQKEHDV 217

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            + R      ++   ++ E  +S+ +V +IE +A   +   ++
Sbjct: 218 IKQRYF--EGLSQSEIAKELFISQAQVSRIEKKALNTLHNYLK 258


>gi|254514436|ref|ZP_05126497.1| RNA polymerase sigma factor SigB [gamma proteobacterium NOR5-3]
 gi|219676679|gb|EED33044.1| RNA polymerase sigma factor SigB [gamma proteobacterium NOR5-3]
          Length = 432

 Score =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 60/235 (25%), Positives = 104/235 (44%), Gaps = 12/235 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   L   +LRLV  IA  YRG G+   +++ EG +GL++A +K+D  +GFR +TY   
Sbjct: 190 DARDTLTMHNLRLVYSIAGRYRGKGVNYLDLIQEGTLGLIRAAEKYDHNKGFRFSTYCFN 249

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI  A++ ++  +  L++  T   ++     L RL+   +  T          A+A+   
Sbjct: 250 WITQAIRRHVGDTGGLIRYPTHVQEQ--VNKLYRLRITEKQRTGEEPG---DAALAEAAG 304

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +   +        SL+A     D  +            G  +    + E ++  + 
Sbjct: 305 LSLEKTRELLQLRNLGISLDAPQYDDDDGTLLDTM-----SGGPFEACEAEAETESLHDR 359

Query: 228 LTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
           L   M  L+  ER +  AR    +  P++   ++    VSRE VRQ+E  A  K+
Sbjct: 360 LLVEMQGLDQAEREVVIARWGLHDGPPLSRAEIADRMSVSREWVRQLERAALTKL 414


>gi|2338708|gb|AAC46374.1| sigma factor RpoS [Vibrio cholerae]
          Length = 168

 Score =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 55/169 (32%), Positives = 91/169 (53%), Gaps = 6/169 (3%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE + A+R    GD +A  R++ S+LRLVVKI+  Y   GL + ++
Sbjct: 6   YLSEIGFSPLLTAEEEVLYARR-ALRGDEAARKRMIESNLRLVVKISRRYSNRGLALLDL 64

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  ++     +++      K L   
Sbjct: 65  IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERALMNQTRTIRLPIHVV-KELNIY 123

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
           LR  +     ++           IA +L+    +V  M        S++
Sbjct: 124 LRTAR----ELSQRLDHEPTPEEIALELDRPVDDVTKMLRLNERITSVD 168


>gi|20807766|ref|NP_622937.1| DNA-directed RNA polymerase specialized sigma subunit
           [Thermoanaerobacter tengcongensis MB4]
 gi|20516321|gb|AAM24541.1| DNA-directed RNA polymerase specialized sigma subunit
           [Thermoanaerobacter tengcongensis MB4]
          Length = 240

 Score =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 50/256 (19%), Positives = 119/256 (46%), Gaps = 18/256 (7%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K+EE +   +  ++ D ++  +L+  +  L+  I   +   G  + ++   G IG ++AV
Sbjct: 2   KEEENLELIKLAKNNDKASLEKLILENSGLIWSIVKKFANRGYELEDLYQIGCIGFVKAV 61

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +KFD     + +TY++  I   ++ ++     L+K+  +  +        +     + ++
Sbjct: 62  QKFDESYNVKFSTYAVPIIMGEIKRFLRDDG-LIKVSRSLKELSSKAFYMK-----EVLS 115

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
           +   +   +  IA++LNV+  E+       A  ESL   I S ++   Q  + +    D 
Sbjct: 116 NELNREPTINEIAERLNVTPEEIAMAFESAATAESLYDSI-SHEEEDRQLIEMVGDKEDS 174

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                ++ EE+      L   +  L PRE+++   R  ++  +T   +++   +S+ +V 
Sbjct: 175 -----VDLEEKLT----LHMIIDKLKPREKQVIFLRYFKD--MTQTEVANILGISQVQVS 223

Query: 271 QIEARAFKKVQESIQK 286
           +IE +  +K+++ ++K
Sbjct: 224 RIEKKVLEKIRKELEK 239


>gi|221308296|ref|ZP_03590143.1| RNA polymerase sigma factor SigB [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221312618|ref|ZP_03594423.1| RNA polymerase sigma factor SigB [Bacillus subtilis subsp. subtilis
           str. NCIB 3610]
 gi|221317541|ref|ZP_03598835.1| RNA polymerase sigma factor SigB [Bacillus subtilis subsp. subtilis
           str. JH642]
 gi|221321817|ref|ZP_03603111.1| RNA polymerase sigma factor SigB [Bacillus subtilis subsp. subtilis
           str. SMY]
 gi|255767137|ref|NP_388354.2| RNA polymerase sigma factor SigB [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|321314147|ref|YP_004206434.1| RNA polymerase sigma factor SigB [Bacillus subtilis BSn5]
 gi|133469|sp|P06574|RPSB_BACSU RecName: Full=RNA polymerase sigma-B factor; AltName: Full=General
           stress protein 84; Short=GSP84; AltName: Full=Sigma-37
 gi|143538|gb|AAA22754.1| sigma-37 RNA polymerase [Bacillus subtilis]
 gi|225184764|emb|CAB12280.2| RNA polymerase sigma-37 factor (sigma(B)) [Bacillus subtilis subsp.
           subtilis str. 168]
 gi|291482882|dbj|BAI83957.1| RNA polymerase sigma factor SigB [Bacillus subtilis subsp. natto
           BEST195]
 gi|320020421|gb|ADV95407.1| RNA polymerase sigma factor SigB [Bacillus subtilis BSn5]
          Length = 262

 Score =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 63/267 (23%), Positives = 114/267 (42%), Gaps = 24/267 (8%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K   L K E   L   Y+   D  A   LV  +  LV  +A  Y        ++   G 
Sbjct: 5   SKTTKLTKDEVDRLISDYQTKQDEQAQETLVRVYTNLVDMLAKKYSKGKSFHEDLRQVGM 64

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL+ A+K++DP  G     +++  I   ++ ++      V +     +        R+K
Sbjct: 65  IGLLGAIKRYDPVVGKSFEAFAIPTIIGEIKRFLRDKTWSVHVPRRIKELG-----PRIK 119

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNS 197
             +  +T    +  +V  IA+ L+VSE EV+           L+ D S+ A    SD ++
Sbjct: 120 MAVDQLTTETQRSPKVEEIAEFLDVSEEEVLETMEMGKSYQALSVDHSIEA---DSDGST 176

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
               D +    DG         ER N++ ML   + VL+ RE++I +   +Q    + + 
Sbjct: 177 VTILDIVGSQEDGY--------ERVNQQLMLQSVLHVLSDREKQIIDLTYIQN--KSQKE 226

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESI 284
                 +S+  V +++ +A KK++E++
Sbjct: 227 TGDILGISQMHVSRLQRKAVKKLREAL 253


>gi|182440445|ref|YP_001828164.1| RNA polymerase sigma factor [Streptomyces griseus subsp. griseus
           NBRC 13350]
 gi|326781114|ref|ZP_08240379.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
 gi|178468961|dbj|BAG23481.1| RNA polymerase sigma factor [Streptomyces griseus subsp. griseus
           NBRC 13350]
 gi|326661447|gb|EGE46293.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
          Length = 293

 Score =  149 bits (376), Expect = 6e-34,   Method: Composition-based stats.
 Identities = 54/239 (22%), Positives = 105/239 (43%), Gaps = 13/239 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + L+  +L LV   A  +R  G   + ++V  G IGL++A+ +FD  R     ++++ 
Sbjct: 61  ARNTLIEMNLSLVRFAANRFRNRGSGDMEDIVQVGTIGLIKAIDRFDLSREVEFTSFAVP 120

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +I   ++ +   +   V +     + R+  +L + K  L  + D +        +A+ L 
Sbjct: 121 YIVGEIKRFFRDTSWAVHVPRRLQELRV--DLAKAKEALAGVLDRD---PTAKELAEYLG 175

Query: 168 VSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           + ESEV        G    SL+   ++++    Q       D  G     +E  E     
Sbjct: 176 IEESEVTEGIVASNGYTAGSLDMPTDTAEAGPGQTAGRTFADVLGDPDPAMEAVE---NL 232

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + L   +  L+ RERRI + R  QE  +T   + +E  +S+  V ++ +R   K++  +
Sbjct: 233 HALAPLLDELDERERRIIDMRFGQE--MTQAQIGAELGISQMHVSRLLSRMLGKLRSGM 289


>gi|304439070|ref|ZP_07398989.1| RNA polymerase sigma-B factor [Peptoniphilus duerdenii ATCC
           BAA-1640]
 gi|304372429|gb|EFM26016.1| RNA polymerase sigma-B factor [Peptoniphilus duerdenii ATCC
           BAA-1640]
          Length = 260

 Score =  149 bits (376), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 52/250 (20%), Positives = 111/250 (44%), Gaps = 16/250 (6%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
            + Y +  D     +L+  +L +   +A  Y G G+   ++    +IGL+ AV ++DP +
Sbjct: 17  FEEYNKTRDPELREKLIEDNLYIAEILAKKYYGRGIDYDDIYQVASIGLIYAVDRYDPSK 76

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           GF  ++++   I   +++Y       +++     +       +++      +  N  K  
Sbjct: 77  GFEFSSFATPTIIGEIKKYFRDKGWTIRVPRRIQELS-----KKINNARVYLAQNLQKAP 131

Query: 158 QVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
            V  IA+ LN +E EV+      R+   +SL+     S ++ S  ++  + D  GQ++  
Sbjct: 132 TVSDIAEYLNTTEEEVLEAIEASRVYQPQSLD----ISYESQSDDKEVNLADIIGQDEEY 187

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
            EK E  +    L      LN  E+ I   R    N  T   ++ +  +S+  V +IE +
Sbjct: 188 FEKIEMNDLMESL---FKNLNEVEKTILVERYF--NRKTQVAIAEQLNISQMTVSRIEKK 242

Query: 276 AFKKVQESIQ 285
             +++++ ++
Sbjct: 243 VLERLKKDVE 252


>gi|210617641|ref|ZP_03291672.1| hypothetical protein CLONEX_03896 [Clostridium nexile DSM 1787]
 gi|210149188|gb|EEA80197.1| hypothetical protein CLONEX_03896 [Clostridium nexile DSM 1787]
          Length = 237

 Score =  149 bits (376), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 48/245 (19%), Positives = 103/245 (42%), Gaps = 16/245 (6%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R    GD  A  +LV  ++ L+  I   + G G    ++   G+IGL++A+ KFD     
Sbjct: 9   RQSHDGDEKAREQLVEENIGLIWCIVKRFYGRGAEPEDLFQIGSIGLLKAIDKFDMTYDV 68

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY++  I   ++ ++     ++K+  +  +        + K     + +   +   +
Sbjct: 69  KFSTYAVPMISGEIKRFLRDDG-MIKVSRSLKELSYKAYFAKEK-----LQEKLGRDPTL 122

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +A+ + V + E++         ESL+  I   D N  Q  D L      +E+VL    
Sbjct: 123 EELAETMEVEKEELVMAMESSGEVESLHKPIYQKDGNEIQLMDKLEETGAQEEKVL---- 178

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
                + +L + +  L   ER++   R       T   +     +S+ +V ++E +  K 
Sbjct: 179 ----NQMLLAQLLEGLEKEERQLIYLRYFANQ--TQSQVGKTLGISQVQVSRLEKKILKN 232

Query: 280 VQESI 284
           +++ +
Sbjct: 233 LRQKV 237


>gi|228931462|ref|ZP_04094387.1| RNA polymerase sigma-43 factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|229188107|ref|ZP_04315191.1| RNA polymerase sigma-43 factor [Bacillus cereus BGSC 6E1]
 gi|228595348|gb|EEK53084.1| RNA polymerase sigma-43 factor [Bacillus cereus BGSC 6E1]
 gi|228828268|gb|EEM73978.1| RNA polymerase sigma-43 factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
          Length = 323

 Score =  148 bits (375), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 67/268 (25%), Positives = 111/268 (41%), Gaps = 13/268 (4%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP--ISE 77
           I EI    +L KQE   L +RY+ HG+      L   ++ LV+ IA  Y+         +
Sbjct: 40  IKEIGNYQVLSKQESLNLFQRYK-HGEKDLRDYLFHVNVGLVLSIARKYKNKHPDIEFDD 98

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS-LVKIGTTANQKRLF 136
           +V EGN G+++A++ F+P  G+  +TY+  WI+  M   I +  S   KI    NQ  L 
Sbjct: 99  LVQEGNEGMLRAMEDFNPALGYCFSTYAFCWIQKRMLGIICKKRSGPFKIPNYVNQFNLK 158

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
           +                 +P  V  + K L+V+   VI  N       ++  L   +   
Sbjct: 159 YV-----ELEDKYLQMYNRPPSVEEVVKDLDVTSEIVIRHNVYYKRATTM-TLDIDTINE 212

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPVTL 255
                +    D      +     E  N    L     VLNP+++ +      L +  V L
Sbjct: 213 DIGISNSSHDDKSAIPSINEMVIEDLNYEIWLIFD-EVLNPKQKMVLNLCFGLLDGKVYL 271

Query: 256 E-NLSSEFEVSRERVRQIEARAFKKVQE 282
              ++    ++ ERV QI+  A KK+++
Sbjct: 272 HKEIAKALMITTERVSQIKEEAIKKLKK 299


>gi|54401894|gb|AAV34632.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|54401896|gb|AAV34633.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274921|gb|AAV49262.1| RNA polymerase subunit sigma-38 [Shigella boydii]
 gi|55274982|gb|AAV49290.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 203

 Score =  148 bits (375), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 56/213 (26%), Positives = 101/213 (47%), Gaps = 12/213 (5%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           ++  I+     +++      K L   LR  +     ++           IA++L+    +
Sbjct: 61  IERAIMNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDD 115

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           V  M        S++  +    +     +  L    D +E    +  +  + +  + + +
Sbjct: 116 VSRMLRLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWL 170

Query: 233 SVLNPRERRIFEARR--LQENPVTLENLSSEFE 263
             LN ++R +   R   L     TLE++  E  
Sbjct: 171 FELNAKQREVLARRFGLLGYEAATLEDVGREIG 203


>gi|302535694|ref|ZP_07288036.1| RNA polymerase sigma-E factor [Streptomyces sp. C]
 gi|302444589|gb|EFL16405.1| RNA polymerase sigma-E factor [Streptomyces sp. C]
          Length = 300

 Score =  148 bits (375), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 52/237 (21%), Positives = 94/237 (39%), Gaps = 17/237 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +
Sbjct: 76  RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTV 135

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +   V  +A  L V+
Sbjct: 136 VGEIKRFFRDTSWSVRVPRRLQELRLA-----LTKASDELAQKLDRSPTVPELAAVLGVT 190

Query: 170 ESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E EV+            SL++     +       D L Y+    E V          R  
Sbjct: 191 EEEVVDGLAVGNAYTASSLDSPSPEDEGGEGSLADRLGYEDSALEGV--------EYRES 242

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   ++ L PRER+I   R      +T   +  E  +S+  V ++  R   +++  +
Sbjct: 243 LKPLLAKLPPRERQIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLRTGL 297


>gi|239982297|ref|ZP_04704821.1| RNA polymerase sigma factor [Streptomyces albus J1074]
 gi|291454142|ref|ZP_06593532.1| sigma factor [Streptomyces albus J1074]
 gi|291357091|gb|EFE83993.1| sigma factor [Streptomyces albus J1074]
          Length = 298

 Score =  148 bits (375), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 58/242 (23%), Positives = 105/242 (43%), Gaps = 13/242 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + L+  +L LV   A  +R  G   + ++V  G IGL++A+ +FD  R     T+++ 
Sbjct: 66  ARNTLIEMNLSLVRYAAGRFRHRGPGEMEDIVQVGTIGLIKAIDRFDLSREVEFTTFAVP 125

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +I   ++ +   +   V +     + R+  ++ + K  L A  D       V  +A KL 
Sbjct: 126 YIVGEIKRFFRDTSWAVHVPRRLQELRV--DMAKAKESLAAELDRE---PTVKELAAKLE 180

Query: 168 VSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
            +E EV+       G    SL+    S D N +      + D  G      E  E     
Sbjct: 181 RTEEEVVEGLVAANGYTAGSLDVPTESGDDNRAGGSPRSLADTLGAPDPAQELVED---L 237

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + L   +  L+ RERRI E R  QE  +T   + +E  +S+  V ++ +R   +++  + 
Sbjct: 238 HALAPLLETLDERERRIVEMRFGQE--LTQSQIGAELGISQMHVSRLLSRILTRLRSGML 295

Query: 286 KQ 287
            +
Sbjct: 296 AE 297


>gi|256379368|ref|YP_003103028.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Actinosynnema mirum DSM 43827]
 gi|255923671|gb|ACU39182.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Actinosynnema mirum DSM 43827]
          Length = 268

 Score =  148 bits (375), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 51/242 (21%), Positives = 100/242 (41%), Gaps = 18/242 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                 LVT HL +   IA  +   G P  ++V    +GL+ AV +FDPERG    ++++
Sbjct: 43  ERLRDELVTEHLPVARHIARRFGHRGEPHDDLVQVATVGLINAVDRFDPERGSDFLSFAV 102

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I   +++Y   S   V++     +  L  N    +     ++    +      +A+ L
Sbjct: 103 PTIMGEVRKYFRDSSWSVRMPRRLKELHLAINAGSAR-----LSQELGRAPTPSELAQHL 157

Query: 167 NVSESEVISMNCR--LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            +S  EV             SL+ L+  +D +S      L  +    E +         +
Sbjct: 158 GLSREEVHEGLAAGNAYHSASLDDLL-VADDSSISLGSTLGEEDPELEAI--------EQ 208

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L   +  L  RERRI   R      +T   ++ +  +S+  V ++ A+  +++++ +
Sbjct: 209 RESLHPLLEKLPERERRIVVMRFFGN--MTQTQIAQKVGISQMHVSRLLAKTLRQLRDGL 266

Query: 285 QK 286
           ++
Sbjct: 267 EQ 268


>gi|255526140|ref|ZP_05393061.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium carboxidivorans
           P7]
 gi|296187150|ref|ZP_06855547.1| RNA polymerase sigma-F factor [Clostridium carboxidivorans P7]
 gi|255510189|gb|EET86508.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium carboxidivorans
           P7]
 gi|296048185|gb|EFG87622.1| RNA polymerase sigma-F factor [Clostridium carboxidivorans P7]
          Length = 251

 Score =  148 bits (375), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 44/245 (17%), Positives = 105/245 (42%), Gaps = 16/245 (6%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           +Y  +G+  A ++L+  +L LV  I+  +   G    ++   G +GL++AV  FD +   
Sbjct: 21  KYARNGNKDALNKLIEVNLPLVSAISKKFLNRGYEYEDIFQIGCMGLVKAVNNFDEKYNV 80

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY++  I   ++ +I     ++K+  +          ++L    +A+T    +   +
Sbjct: 81  KFSTYAVPMILGEIKRFIRDDG-MIKVSRSVK-----NTAKKLHYAKEALTKQISREPTI 134

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +++   +   ++I         + L   I+  D       D L    D   +++    
Sbjct: 135 EELSEYSGIGVEDIIFAMESSNSLQYLYDTIHQDDGAPVLLIDKLSESSDRDSEIV---- 190

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
                R  L  ++  L+ + R+I   R  ++   T   ++    +S+ +V +IE +  K 
Sbjct: 191 ----DRIALKEALKNLDVKSRQIIMLRYFKD--KTQIQVAKMLGISQVQVSRIEKKVLKV 244

Query: 280 VQESI 284
           ++E++
Sbjct: 245 MRENL 249


>gi|160914281|ref|ZP_02076502.1| hypothetical protein EUBDOL_00291 [Eubacterium dolichum DSM 3991]
 gi|158433908|gb|EDP12197.1| hypothetical protein EUBDOL_00291 [Eubacterium dolichum DSM 3991]
          Length = 260

 Score =  148 bits (375), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 51/257 (19%), Positives = 115/257 (44%), Gaps = 17/257 (6%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           +L   +   L  R ++ GD +A   L+  +L+LV+ I   +      + ++   G IGL+
Sbjct: 18  VLNNTQMKELFLRMQK-GDQNAKEELINGNLKLVLSIVQRFANRCENMDDLFQVGCIGLV 76

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +++  FD +   R +TY++  I   ++ Y+  +  ++++      K L +   RLK   +
Sbjct: 77  KSIDHFDLKHEVRFSTYAVPMIMGEIKRYLRDN-QVLRVSRHL--KDLAYKCFRLK---E 130

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                + K   +  +A++L V E +++          S+   + +SD +     D +  +
Sbjct: 131 EYVHQHQKEPSITWLAEQLEVREKDIVDALDSTQNVLSIFEPVYNSDGDELYLLDQIRDE 190

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            D        + +  N    L  S+  L  +E  I + R  Q+  +T   +++E  +S+ 
Sbjct: 191 KD--------EIDLLNNVLSLRSSLKQLKEKELEILDKRYYQD--MTQTEIANELGISQA 240

Query: 268 RVRQIEARAFKKVQESI 284
           +V ++E  A   +++ +
Sbjct: 241 QVSRLEKSAISTLRKEM 257


>gi|143460|gb|AAA22713.1| 37 kd minor sigma factor (rpoF, sigB; ttg start codon) [Bacillus
           subtilis]
 gi|143463|gb|AAA22715.1| 37 kd minor sigma factor (ttg start codon) [Bacillus subtilis]
 gi|1881283|dbj|BAA19310.1| RNA POLYMERASE SIGMA-B FACTOR (SIGMA-37) [Bacillus subtilis]
          Length = 264

 Score =  148 bits (375), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 63/267 (23%), Positives = 114/267 (42%), Gaps = 24/267 (8%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K   L K E   L   Y+   D  A   LV  +  LV  +A  Y        ++   G 
Sbjct: 7   SKTTKLTKDEVDRLISDYQTKQDEQAQETLVRVYTNLVDMLAKKYSKGKSFHEDLRQVGM 66

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL+ A+K++DP  G     +++  I   ++ ++      V +     +        R+K
Sbjct: 67  IGLLGAIKRYDPVVGKSFEAFAIPTIIGEIKRFLRDKTWSVHVPRRIKELG-----PRIK 121

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNS 197
             +  +T    +  +V  IA+ L+VSE EV+           L+ D S+ A    SD ++
Sbjct: 122 MAVDQLTTETQRSPKVEEIAEFLDVSEEEVLETMEMGKSYQALSVDHSIEA---DSDGST 178

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
               D +    DG         ER N++ ML   + VL+ RE++I +   +Q    + + 
Sbjct: 179 VTILDIVGSQEDGY--------ERVNQQLMLQSVLHVLSDREKQIIDLTYIQN--KSQKE 228

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESI 284
                 +S+  V +++ +A KK++E++
Sbjct: 229 TGDILGISQMHVSRLQRKAVKKLREAL 255


>gi|88799025|ref|ZP_01114606.1| RNA polymerase sigma factor [Reinekea sp. MED297]
 gi|88778252|gb|EAR09446.1| RNA polymerase sigma factor [Reinekea sp. MED297]
          Length = 339

 Score =  148 bits (375), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 60/243 (24%), Positives = 105/243 (43%), Gaps = 15/243 (6%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           LS    L+ S++RLV K+A  +   GL + ++  EG  GL++A+++F  ++  R +TY+ 
Sbjct: 106 LSVREFLIASNIRLVFKVAHRHTERGLSLLDLAQEGQFGLVRALERFRCDKELRFSTYAT 165

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            WI   ++  I +    V I T         +L R    L        +P  V   A+  
Sbjct: 166 HWITQYIRLAIKKQTRTVPIPTNVQD-----DLARTNRALARAQQQQGRPVSVTEFARLS 220

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD-HDGQEQVLIEKEERKNRR 225
           N S      +        SLNA + S D+  S   +    D  D        + ER + +
Sbjct: 221 NQSTDAAEHLM-------SLNAPVQSLDERLSDDSEVSALDLLDSDLARPESEHERSDNQ 273

Query: 226 NMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +   ++ L  RE++I   R             ++ +  +SRERVRQ+E +A   ++  
Sbjct: 274 ERVQALLAHLTSREQQILAMRYGIGMGAEYGYREIADQLNLSRERVRQLEKQALGFLRAQ 333

Query: 284 IQK 286
           ++K
Sbjct: 334 MEK 336


>gi|297560730|ref|YP_003679704.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
 gi|296845178|gb|ADH67198.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
          Length = 287

 Score =  148 bits (375), Expect = 7e-34,   Method: Composition-based stats.
 Identities = 54/253 (21%), Positives = 106/253 (41%), Gaps = 15/253 (5%)

Query: 34  EYVLAKRYREHGDL----SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           E +LA+ +    D          +V  +  LV K+A  Y G G P+ ++     +GL++A
Sbjct: 36  EELLAELHGLDDDDPRAVRLREEVVVRYQPLVNKLARRYNGRGEPLEDLKQTAMVGLVKA 95

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           ++ + P+RG    +Y M  +   ++ +       +++     + R+     +L+  L   
Sbjct: 96  IRGYRPDRGKPFISYLMPTVTGEIKRHFRDHTWAIRVPRRHQENRI-----KLRQVLNTF 150

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
              + +      IAK++ + E EV+ +        SL+     S  +  Q    L  DH 
Sbjct: 151 QQTHARVPTNAEIAKEMGLDEEEVVELVQASESYRSLSLDAPDSSDSDGQEGSRL-EDHL 209

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
           G E    E  ER  +R  L  +++ L  RER I + R   +   T   ++     S+  V
Sbjct: 210 GSED---EGLERVVQRESLKPALARLPEREREILKLRFFGD--HTQTEIADRMGYSQMHV 264

Query: 270 RQIEARAFKKVQE 282
            ++     ++++E
Sbjct: 265 SRLLKNTLEQLRE 277


>gi|161898917|gb|ABX80448.1| SigB [Listeria monocytogenes]
          Length = 236

 Score =  148 bits (375), Expect = 8e-34,   Method: Composition-based stats.
 Identities = 57/252 (22%), Positives = 111/252 (44%), Gaps = 24/252 (9%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 3   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 62

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G     +++  I   ++ ++      V +     +        ++   ++ +T    
Sbjct: 63  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKINNAVEELTRELQ 117

Query: 155 KPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +    
Sbjct: 118 SSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTD 174

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++S+  
Sbjct: 175 DGF--------ERVNQRMLLEKVLPVLDEREQKILQFTFIEN--RSQKETGELLDISQMH 224

Query: 269 VRQIEARAFKKV 280
           V +I+ +A KK+
Sbjct: 225 VSRIQRQAIKKL 236


>gi|218197356|gb|EEC79783.1| hypothetical protein OsI_21197 [Oryza sativa Indica Group]
          Length = 557

 Score =  148 bits (375), Expect = 8e-34,   Method: Composition-based stats.
 Identities = 61/252 (24%), Positives = 109/252 (43%), Gaps = 14/252 (5%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E +L  R +E        RL+ +   LV  IA  Y G G    +++  G +G++   +K
Sbjct: 305 DEALLRSRLQEGYC--CRERLLVTTEWLVKYIAKTYAGMGTAFEDLLQAGKMGVLNGAEK 362

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD ++G + +TY  +WI+ AM   +  +  ++++       R+   +R+++   +AI  N
Sbjct: 363 FDSQKGCKFSTYVKYWIRKAMLALLAENSGVIQLP-----ARMEGIIRKVREARRAIRYN 417

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA  + VS + V           SL   I        Q   ++    D   
Sbjct: 418 TGRNPPDAEIAALIGVSVANVRLARKCSRRVVSLYTEIGVG-----QNAKFVEVTPDTSL 472

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +   E   R   R  L   +  L PRE  + + R   E+    +LE + S + VS+E +R
Sbjct: 473 EAPDEAMFRMQLRERLLHVLDRLPPREGHVLKLRHGLEDGKCRSLEQIGSIYHVSKEWIR 532

Query: 271 QIEARAFKKVQE 282
           +IE  A  K++ 
Sbjct: 533 KIEKSAMSKLRN 544


>gi|313901496|ref|ZP_07834946.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Thermaerobacter
           subterraneus DSM 13965]
 gi|313468234|gb|EFR63698.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Thermaerobacter
           subterraneus DSM 13965]
          Length = 258

 Score =  148 bits (375), Expect = 8e-34,   Method: Composition-based stats.
 Identities = 63/259 (24%), Positives = 116/259 (44%), Gaps = 18/259 (6%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLM 87
           +QE   L +RYR   D  +   L+  HL LV  +A     +    + + +++S G  GLM
Sbjct: 8   RQERAELWRRYRTAADPESWEALIREHLPLVRYLAGRLVVHLPPQVELDDLISYGIFGLM 67

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +A+K++DP RG +  TY+   I+ AM + + R+   V  G     + +    RRL+  L 
Sbjct: 68  EAIKRYDPSRGVKFETYAYTRIRGAMLDGL-RAMDWVPQGLRRRAREVEACYRRLENRL- 125

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLV 205
                  +P +   +A +L ++  E   +   LA     SL+ ++ S   + +   D L 
Sbjct: 126 ------GRPAEDAEVAAELGLTPDEFGELLKDLARTTVISLDDVLRSESDDPAAVLDRLA 179

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
              D      +      + R  L ++++VL  RER +          +T++ ++    VS
Sbjct: 180 ---DPGAADPLAAATLADLRQRLAQALAVLPERERLVITLYYY--EGLTVKEIAEVMGVS 234

Query: 266 RERVRQIEARAFKKVQESI 284
             RV Q+  RA  +++  +
Sbjct: 235 PSRVSQLHTRAILRLRARL 253


>gi|238063793|ref|ZP_04608502.1| RNA polymerase sigma factor [Micromonospora sp. ATCC 39149]
 gi|237885604|gb|EEP74432.1| RNA polymerase sigma factor [Micromonospora sp. ATCC 39149]
          Length = 294

 Score =  148 bits (375), Expect = 8e-34,   Method: Composition-based stats.
 Identities = 50/237 (21%), Positives = 93/237 (39%), Gaps = 18/237 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             R + + L L   +A  Y G G P  ++     +GL++A+ KFDP RG   A Y++  I
Sbjct: 70  RDRAIEAWLPLANHLAHRYSGRGEPTDDLAQTAAVGLIKAIDKFDPSRGVDFAGYAIPTI 129

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA--KKLN 167
              ++ +       +++     + RL      +      +     +   V  IA   KL 
Sbjct: 130 IGELKRHFRDRTWDIRVPRRLQELRLA-----ISDANSTLLQTLGRSPTVADIAAHLKLT 184

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
             E        R     SL+      D  +++  D L  +          + E    R  
Sbjct: 185 EEEVLEGLEGARAYNAVSLSTPTGDGD-RATELGDMLGGEDT--------EFELAELRVA 235

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L  +++ L+ RE++I   R      +T   ++ +  VS+  V ++ ARA  K++  +
Sbjct: 236 LGPALATLDEREQKILTLRFYGN--LTQSQIADQIGVSQMHVSRLLARALTKLRGQL 290


>gi|312281919|dbj|BAJ33825.1| unnamed protein product [Thellungiella halophila]
          Length = 562

 Score =  148 bits (375), Expect = 9e-34,   Method: Composition-based stats.
 Identities = 58/256 (22%), Positives = 118/256 (46%), Gaps = 13/256 (5%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           E +L +    H        L+ S   LV+ ++  YRG G+   +++  GN+G++Q  ++F
Sbjct: 310 EILLMRNL--HYGWYCRDELLKSTRSLVLFLSRNYRGLGIAHEDLIQAGNVGVLQGAERF 367

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D  RG++ +TY  +WI+ +M   + R    V I ++    R    +++ +  L+  T + 
Sbjct: 368 DHTRGYKFSTYVQYWIRKSMSMMVSRHARGVYIPSSV--IRTMSQIQKARKTLK--TSHG 423

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
           +K      I+K+   S  ++ + N  L    S++  +            +L +  D   +
Sbjct: 424 IKYPADEEISKETGYSLKKIRAANQCLKVVGSIDKKVGDC-----FTTKFLEFTPDTTME 478

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQ 271
              E   R++    +   +  L PRE+++   R   +   P +LE +    +VS+E +R+
Sbjct: 479 SPEEAVMRQSAWRDVHDLLQGLEPREKQVMVLRYGLQGFRPKSLEEIGKLLKVSKEWIRK 538

Query: 272 IEARAFKKVQESIQKQ 287
           IE RA  K+++    +
Sbjct: 539 IERRAMAKLRDQANAE 554


>gi|323487067|ref|ZP_08092375.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323694575|ref|ZP_08108741.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
 gi|323399568|gb|EGA91958.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323501343|gb|EGB17239.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
          Length = 237

 Score =  148 bits (375), Expect = 9e-34,   Method: Composition-based stats.
 Identities = 51/252 (20%), Positives = 111/252 (44%), Gaps = 16/252 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E +        GD +A  RLV  ++ LV  I   + G G    ++   G+IGL++A+ K
Sbjct: 2   DETMKLIEMAHSGDKAARERLVMDNVGLVWSIVRRFTGRGCETEDLFQIGSIGLIKAIDK 61

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD     R +TY++  I   ++ ++     ++K+  +  +        ++    ++++ +
Sbjct: 62  FDTSYDVRFSTYAVPMITGEIKRFLRDDG-MIKVSRSIKELGF-----KVSAVRESLSGS 115

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +   +  I++ L VS+ EV +        ESL A   S + N+    D +  + +  E
Sbjct: 116 LGREPTLEEISEALEVSKEEVAASLEAGCQVESLYAPSGSGEDNTLSLIDKVAEEKEENE 175

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
            +L         R +L   +  L  ++R I   R       T   ++    +S+ +V ++
Sbjct: 176 MLL--------DRMVLGELLKSLEKKQREIIVRRYFYNQ--TQTQIAEILGISQVQVSRM 225

Query: 273 EARAFKKVQESI 284
           E +  ++++E +
Sbjct: 226 ERKILREMREKL 237


>gi|303242484|ref|ZP_07328964.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302589952|gb|EFL59720.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 252

 Score =  148 bits (374), Expect = 9e-34,   Method: Composition-based stats.
 Identities = 54/258 (20%), Positives = 123/258 (47%), Gaps = 17/258 (6%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
              + + L + ++    +   + +V+ +L L   I+  +   G+   ++    +I L++A
Sbjct: 11  SNDDSHSLFENFKNSQSVEVRNEIVSKYLYLAEIISKKFVNRGIDYEDIYQVASIALIKA 70

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V++FDP++G + A+++   +   ++ +     S+++I      +R++   +++    +++
Sbjct: 71  VERFDPDKGVKFASFATPTLIGEIKRFFRDKASVIRIP-----RRIYEVYQKVSHARESL 125

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDH 208
           T    +P ++  IAK LN+SE  V+ +       ES NA  + S D+N     D  +++ 
Sbjct: 126 TQELSRPPRIDEIAKYLNISEETVMEII------ESNNAHNLQSFDQNVYTDDDLELHET 179

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
            G+E    EK E    R+ L +S+   N  E+   + R    N  T + ++    VS+  
Sbjct: 180 IGEEDATFEKIE---NRDFLKKSLDKFNDAEKEFIDMRYF--NNRTQKEIAERLGVSQMY 234

Query: 269 VRQIEARAFKKVQESIQK 286
           V ++E +   + +  + K
Sbjct: 235 VSRLEKKVLDRFRRLLIK 252


>gi|168700394|ref|ZP_02732671.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Gemmata obscuriglobus UQM 2246]
          Length = 335

 Score =  148 bits (374), Expect = 9e-34,   Method: Composition-based stats.
 Identities = 63/239 (26%), Positives = 109/239 (45%), Gaps = 15/239 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            HRL ++++RL   +A  +R + L  S+++ E   GLMQA+ +FD   G RLATY+ WWI
Sbjct: 100 KHRLASANIRLAAHVAKRFRHHSLAYSDLLQEAVCGLMQAIDRFDVSHGTRLATYATWWI 159

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           +  +Q  + R   LV +     Q      L  L+   +A+            +A +   S
Sbjct: 160 RQTLQIAVARQSHLVSLSPHHLQ-----ELGLLQQESEALAHGGKHLPSPQELASRTGSS 214

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
              +  +        SLNA++   D +  +  + +        Q      E   R+  L+
Sbjct: 215 LEHLTHLQTATRTPVSLNAVL--DDDSDFKLTEAMPDTGTLVMQ------ENNERQEALS 266

Query: 230 RSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             M  L PRER++ + R         +L  +     +S+ERVRQI+ RA +K++ + ++
Sbjct: 267 FLMENLRPRERKVLDLRFGLTGNGTHSLRQIGHLLRISKERVRQIQNRALEKLKANAER 325


>gi|7363220|emb|CAB83107.1| sigma factor 3 [Sinapis alba]
          Length = 567

 Score =  148 bits (374), Expect = 9e-34,   Method: Composition-based stats.
 Identities = 58/236 (24%), Positives = 110/236 (46%), Gaps = 11/236 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
               LV S   LV+ +A  YRG G+   +++  G +G++Q  ++FD  RG++ +TY  +W
Sbjct: 328 CRDELVKSTRSLVLFLARNYRGLGIAHEDLIQAGYVGVLQGAERFDHTRGYKFSTYVRYW 387

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ +M   + R    V I   A+  R    +++ +  L+  T   +K      I+K    
Sbjct: 388 IRKSMSTMVSRHARGVHIP--ASIIRTMSQIQKARKTLK--TSQGIKYPADEEISKLTGY 443

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  ++ + N  L    S++  +            +L +  D   +   E   R++ R  +
Sbjct: 444 SLKKIRAANQCLKVVGSIDKKVGDC-----FTTRFLEFTPDPTMESPEEAVMRQSARGEV 498

Query: 229 TRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              +  L PRE+++   R   ++  P +LE +     VS+E +R+IE RA  K+++
Sbjct: 499 HNLLEGLEPREKQVMVLRYGLQDYSPKSLEEIGKILRVSKEGIRKIERRAMAKLRD 554


>gi|15613092|ref|NP_241395.1| RNA polymerase sigma factor SigB [Bacillus halodurans C-125]
 gi|10173142|dbj|BAB04248.1| RNA polymerase general stress sigma factor(sigma B) [Bacillus
           halodurans C-125]
          Length = 261

 Score =  148 bits (374), Expect = 9e-34,   Method: Composition-based stats.
 Identities = 55/261 (21%), Positives = 116/261 (44%), Gaps = 14/261 (5%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            E Y   + Y++  D     +LV  +  LV  +A  +        +++  G +GL+ A +
Sbjct: 13  DEVYDWIESYQQGADEEIQTKLVKHYEPLVHSLARKFSRSRAHDDDLIQVGMVGLLAAFE 72

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           ++DP+ G    ++++  I   ++ +I      V +     +        ++K     +  
Sbjct: 73  RYDPKYGRSFESFAVPTIIGEIKRFIRDKTWSVHVPRRIKELG-----PKIKKAADELAS 127

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +  +V  IA  L VSE EV+         ++L+  ++ S +   +  +  + D  GQ
Sbjct: 128 ELQRSPRVEEIADFLGVSEEEVLETMEMGKSYQALS--VDRSLEADPEGGEVTLLDLVGQ 185

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E    EK +++    +L ++  VL+ RE++I          ++ +       +S+  V +
Sbjct: 186 EDGGYEKADQQM---LLEKAFQVLDEREKQILLCTYF--EHLSQKETGHRLGISQMHVSR 240

Query: 272 IEARAFKKVQESIQKQVELSS 292
           ++ RA KK+++SI+  VELS 
Sbjct: 241 LQRRALKKLRDSIR--VELSE 259


>gi|330466807|ref|YP_004404550.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily protein
           [Verrucosispora maris AB-18-032]
 gi|328809778|gb|AEB43950.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily protein
           [Verrucosispora maris AB-18-032]
          Length = 273

 Score =  148 bits (374), Expect = 9e-34,   Method: Composition-based stats.
 Identities = 50/239 (20%), Positives = 95/239 (39%), Gaps = 18/239 (7%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +   R + + L L   +A  Y G G P  ++     +GL++A+ KFDP RG   A Y++ 
Sbjct: 47  ALRDRAIEAWLPLANHLAHRYSGRGEPTDDLAQTAAVGLIKAIDKFDPTRGVDFAGYAIP 106

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA--KK 165
            I   ++ +       +++     + RL      +     ++     +   V  IA   K
Sbjct: 107 TIIGELKRHFRDRTWDIRVPRRLQELRLA-----ISDANSSLLQTLGRSPTVADIAAHLK 161

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           L   E        R     SL+      D  +++  D L  +          + E    R
Sbjct: 162 LTEEEVLEGLEGARAYNAVSLSTPTGDGD-RATELGDMLGGEDS--------EFELAELR 212

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             L  +++ L+ RE++I   R      +T   ++ +  VS+  V ++ ARA  K++  +
Sbjct: 213 VALGPALATLDEREQKILTLRFYGN--LTQSQIAEQIGVSQMHVSRLLARALTKLRGQL 269


>gi|161898933|gb|ABX80456.1| SigB [Listeria monocytogenes]
          Length = 236

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 59/253 (23%), Positives = 112/253 (44%), Gaps = 25/253 (9%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y   G    E    GNIGL+ A++++D
Sbjct: 3   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQ-GKSFHEDSQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G     +++  I   ++ ++      V +     +        ++K  ++ +T    
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQ 116

Query: 155 KPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +    
Sbjct: 117 SSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTD 173

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++S+  
Sbjct: 174 DGF--------ERVNQRMLLEKVLPVLDEREQKILQFTFIEN--RSQKETGELLDISQMH 223

Query: 269 VRQIEARAFKKVQ 281
           V +I+ +A KK++
Sbjct: 224 VSRIQRQAIKKLR 236


>gi|154684976|ref|YP_001420137.1| RNA polymerase sigma factor SigB [Bacillus amyloliquefaciens FZB42]
 gi|126363073|emb|CAM35801.1| RNA polymerase sigma-B factor [Bacillus amyloliquefaciens FZB42]
 gi|154350827|gb|ABS72906.1| SigB [Bacillus amyloliquefaciens FZB42]
          Length = 262

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 60/267 (22%), Positives = 116/267 (43%), Gaps = 24/267 (8%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K   L K E   L + ++ H +  A   LV  +  LV  +A  Y        ++   G 
Sbjct: 5   SKTTKLTKDEVDRLIRDFQTHDNKEAQETLVEVYTNLVEMLAKKYSKGKSFHEDLRQVGM 64

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL+ A+K++DPE G     +++  I   ++ ++      V +     +        R+K
Sbjct: 65  IGLLGAIKRYDPEVGKSFEAFAIPTIIGEIKRFLRDKTWSVHVPRRIKELG-----PRIK 119

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNS 197
             +  +T    +  +V  IA  L+VSE EV+           L+ D S+ A    +D ++
Sbjct: 120 MAVDQLTTETQRSPKVEEIAAFLDVSEEEVLETMEMGKSYQALSVDHSIEA---DADGST 176

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
               D +    +G         ER N++ M+   + VL+ RE++I +   +Q    + + 
Sbjct: 177 VTILDIVGSQEEGY--------ERVNQQMMIKSVLHVLSDREKQIIDLTFVQN--KSQKE 226

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESI 284
                 +S+  V +++ +A KK++E++
Sbjct: 227 TGDILGISQMHVSRLQRKAVKKLREAL 253


>gi|213026208|ref|ZP_03340655.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. 404ty]
          Length = 445

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 47/189 (24%), Positives = 84/189 (44%), Gaps = 9/189 (4%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 256 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 315

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 316 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 373

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R+   +         PE    +A+++ + E ++  +        S+   I   D   
Sbjct: 374 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDED 428

Query: 198 SQWQDWLVY 206
           S   D++  
Sbjct: 429 SHLGDFIED 437


>gi|55274945|gb|AAV49272.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 204

 Score =  148 bits (374), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 56/214 (26%), Positives = 102/214 (47%), Gaps = 12/214 (5%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ S+LRL+VKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+ 
Sbjct: 1   RMIESNLRLMVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQ 60

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            ++  I+     +++      K L   LR  +     ++           IA++L+    
Sbjct: 61  TIERAIMNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVD 115

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           +V  M        S++  +    + +      L    D +E    +  +  + +  + + 
Sbjct: 116 DVSRMLRLNERITSVDTPLGGDSEKA-----LLDILADEKENGPEDTTQDDDMKQSIVKW 170

Query: 232 MSVLNPRERRIFEARR--LQENPVTLENLSSEFE 263
           +  LN ++R +   R   L     TLE++  E  
Sbjct: 171 LFELNAKQREVLARRFGLLGYEAATLEDVGREIG 204


>gi|187934214|ref|YP_001885077.1| sporulation sigma factor SigF [Clostridium botulinum B str. Eklund
           17B]
 gi|187722367|gb|ACD23588.1| RNA polymerase sigma-F factor [Clostridium botulinum B str. Eklund
           17B]
          Length = 251

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 44/246 (17%), Positives = 101/246 (41%), Gaps = 16/246 (6%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             + GD  A +RL+  +L LV  I+  +   G    ++   G+IGL++A+  FD     +
Sbjct: 22  LAKDGDNEAMNRLIEMNLPLVASISKKFLNRGYDYEDIFQIGSIGLVKAINNFDLSYNVK 81

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY++  I   ++ ++     ++K+             +R+    + +T    +   + 
Sbjct: 82  FSTYAVPMIIGEIKRFLRDDG-MIKVSRNVKSLA-----KRIHFTKEELTKKLNRSPTIE 135

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+   V + E+I         + L   I+  D       D L            E + 
Sbjct: 136 ELAEYSGVDKEEIIFAIESATSLQYLYDTIHQDDGAPVLLIDKLSEKG--------EDDI 187

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
               +  L  ++  L+ + R+I   R  ++   T   ++    +S+ +V +IE +   ++
Sbjct: 188 GMINKIALKEALRSLDEKARQIIVLRYFKD--KTQVQVAKLLGISQVQVSRIEKKVLLRM 245

Query: 281 QESIQK 286
           +E +++
Sbjct: 246 REKLEE 251


>gi|163938900|ref|YP_001643784.1| RNA polymerase sigma factor SigB [Bacillus weihenstephanensis
           KBAB4]
 gi|163861097|gb|ABY42156.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           weihenstephanensis KBAB4]
          Length = 257

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 55/265 (20%), Positives = 121/265 (45%), Gaps = 17/265 (6%)

Query: 22  EIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           EI+  P  L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++ 
Sbjct: 2   EIQSQPTDLTKEDVIKLIAEFQQNQCDEAQERLVNHYKNLVYSIAYRYSKGGPMHEDIIQ 61

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
            G +GL+ A++++D   G     +++  I   +++Y+      V +      +R+     
Sbjct: 62  VGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGVHVP-----RRIKDLGG 116

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSS 198
           ++K  ++ +TD+  +  +++ IA  L +SE EV+ +          SL+ ++ +S   SS
Sbjct: 117 KIKLAIEELTDHLQRSPKIIEIANHLGLSEEEVLEIMDAKNNYQVSSLDDVVENSSDGSS 176

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
             +   V +       + +  E+  RR +L    +VLN  E+ +      +   +  ++ 
Sbjct: 177 VARIESVGE-------VEQGYEQTERRLVLDDIFNVLNDTEKSVIHYIFGEN--LNQKDT 227

Query: 259 SSEFEVSRERVRQIEARAFKKVQES 283
                +S+  V +I+ +A  K++++
Sbjct: 228 GERLGISQMHVSRIKRQAISKLKQA 252


>gi|296133019|ref|YP_003640266.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           sp. JR]
 gi|296031597|gb|ADG82365.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           potens JR]
          Length = 262

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 48/254 (18%), Positives = 109/254 (42%), Gaps = 14/254 (5%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKF 93
           L  R+++  DL+A  +L+  +  LV  +A        P     +++S G  GL+ A++KF
Sbjct: 13  LWDRFKKERDLAAREQLILKYAPLVKYVAGRLAISLPPNVQQDDLISYGIFGLIDAIEKF 72

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           +PER  +  TY++  IK A+ + + RS   +        K L     RL+  L       
Sbjct: 73  EPERNIKFETYAISRIKGAIWDGL-RSMDWIPYSIRQKAKELEETYARLENEL------- 124

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQE 212
            +P     + + L +++ +  S+    +    L+   +   D++ +     +    D + 
Sbjct: 125 GRPATDEEMCETLGITKQQFYSLLQETSCTSLLSLEDLFVFDRDGTNGVKMIDTIADSRV 184

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
              +     + ++ +L  +++ L  RE+ +          +TL+ +     V+  R+ Q+
Sbjct: 185 PDPVAAVMFEEQKKILGEAINKLPEREKMVIALYYY--EGLTLKEIGKVLGVTESRISQL 242

Query: 273 EARAFKKVQESIQK 286
             +A  +++  + +
Sbjct: 243 HTKAILRLRGRLSR 256


>gi|297811483|ref|XP_002873625.1| hypothetical protein ARALYDRAFT_909325 [Arabidopsis lyrata subsp.
           lyrata]
 gi|297319462|gb|EFH49884.1| hypothetical protein ARALYDRAFT_909325 [Arabidopsis lyrata subsp.
           lyrata]
          Length = 273

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 58/217 (26%), Positives = 105/217 (48%), Gaps = 12/217 (5%)

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y+G GL + +++ EG+IGL++  ++FDP+RG++L+TY  WWIK A+   I     LVK+ 
Sbjct: 52  YQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAILRAIAHKSRLVKLP 111

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
            +  +        ++      +T    +      IA+ LN+  S V     R     SL+
Sbjct: 112 GSMWELTA-----KVAEASNVLTRKLRRQPSCEEIAEHLNLHVSAVRLAVERSRSPVSLD 166

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
            +++ + + + Q            E    E  +R++ ++ + + +  L  RE R+     
Sbjct: 167 RVVSQNGRMTLQEIV-----RGPDETRPEEMVKREHMKHEIEQLLGSLTARESRVLGLYF 221

Query: 248 L--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
               E P++ E +    ++SRERVRQI   A KK++ 
Sbjct: 222 GLNGETPMSFEEIGKSLKLSRERVRQINGIALKKLRN 258


>gi|260592476|ref|ZP_05857934.1| RNA polymerase sigma-43 factor [Prevotella veroralis F0319]
 gi|260535522|gb|EEX18139.1| RNA polymerase sigma-43 factor [Prevotella veroralis F0319]
          Length = 228

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 70/270 (25%), Positives = 115/270 (42%), Gaps = 47/270 (17%)

Query: 17  SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
            +YI EI +  +L  +EE  LA + +  GD  A  +L  ++L+ VV +A  Y+  GL   
Sbjct: 5   EKYIEEIVQEQLLSSEEEQTLAAKIKL-GDAKALEKLTKANLKFVVSLAHHYKNQGLGED 63

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           ++VSEGNIG+M A +KFD  +G R  +Y+  +I+ AM+E I    +L K+      K   
Sbjct: 64  DLVSEGNIGMMHAAQKFDGTKGIRFVSYAAPYIRKAMEEAIKEQTALYKLP-----KDEK 118

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
               R + H                                       S++  I     N
Sbjct: 119 SKFERKRTHA-------------------------------------ISIDQPIPVGSSN 141

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV-TL 255
           +   Q  L  +   Q    + KE        + + ++ LN RE+RI  A         T+
Sbjct: 142 NFTLQHVLENEDAPQADEHLNKELLNFE---IQKGLNELNEREKRIIIAIYGLNGTHYTM 198

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             ++    + RERVRQI  +A +K+ + ++
Sbjct: 199 AEIAENMGLKRERVRQIRNKALRKLHKKMK 228


>gi|299822364|ref|ZP_07054250.1| RNA polymerase sigma-B factor [Listeria grayi DSM 20601]
 gi|299815893|gb|EFI83131.1| RNA polymerase sigma-B factor [Listeria grayi DSM 20601]
          Length = 259

 Score =  148 bits (373), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 58/260 (22%), Positives = 117/260 (45%), Gaps = 24/260 (9%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y   K Y+E  D  A   LV  +  LV  IA  Y        ++V  G IGL+ A+
Sbjct: 12  KEKVYEWIKLYQETADDDAQTNLVLHYHNLVESIARKYSQGKSFHEDLVQVGVIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           K++DP+ G     +++  I   ++ ++      V +     +        ++K  ++ +T
Sbjct: 72  KRYDPDFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELT 126

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWL 204
                  Q+  IA  +  +E E++           L+ D S+ A    SD ++    D +
Sbjct: 127 RELQSSPQISDIANFIGATEEEILEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVV 183

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               +G EQV        N+R +L + + VL+ RE++I +   ++    + +      ++
Sbjct: 184 GGVDEGFEQV--------NQRMILEKILPVLDEREQKILQYTFIEN--RSQKETGELLDI 233

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+  V +++ +A KK++E++
Sbjct: 234 SQMHVSRVQRQAIKKLREAL 253


>gi|256005472|ref|ZP_05430434.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Clostridium
           thermocellum DSM 2360]
 gi|255990527|gb|EEU00647.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Clostridium
           thermocellum DSM 2360]
          Length = 252

 Score =  147 bits (372), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 46/253 (18%), Positives = 118/253 (46%), Gaps = 19/253 (7%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L + Y+E   +   +++V+ +L L   +A  +   G+   ++    +I L++AV++FDP
Sbjct: 17  ELFREYKETKSVEVRNKIVSKYLYLSDILAKKFLNRGIDYEDIYQVVSIALIKAVERFDP 76

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           ++G +  +++   I   ++ Y     S+++I      +R++   +++    +++T    +
Sbjct: 77  DKGVKFISFATPTIIGEIKRYFRDKGSVIRIP-----RRIYEVYQKINHARESLTQELKR 131

Query: 156 PEQVVAIAKKLNVSESEVISMNCR--LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
           P ++  +A+ LN+SE  V+ +         +S +  + ++D+        ++ D D    
Sbjct: 132 PPRIDELARHLNISEESVVEIIESYNAYNIQSFSQNVYANDE---LELHEVIGDQDSTF- 187

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
                 ER   R+ L +S+   +  E+     R       T ++++ +  VS+  + ++E
Sbjct: 188 ------ERIENRDFLEKSLDKFSDVEKEFISMRYFDN--KTQKDIAQKMGVSQMYISRLE 239

Query: 274 ARAFKKVQESIQK 286
            +  +K +  + K
Sbjct: 240 RKVLEKFRRMLAK 252


>gi|117927772|ref|YP_872323.1| RNA polymerase, sigma 28 subunit [Acidothermus cellulolyticus 11B]
 gi|117648235|gb|ABK52337.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Acidothermus
           cellulolyticus 11B]
          Length = 287

 Score =  147 bits (372), Expect = 1e-33,   Method: Composition-based stats.
 Identities = 56/238 (23%), Positives = 101/238 (42%), Gaps = 14/238 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                 LV +HL LV  +A  +R  G P  ++V    IGL++A+ +FD ERG   +TY+ 
Sbjct: 60  QEIRSELVQTHLPLVEYLARRFRNRGEPHDDLVQVATIGLIKAIDRFDVERGVEFSTYAT 119

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I   ++ Y       +++     + ++      L      ++    +   V  +A  L
Sbjct: 120 PTIVGEIKRYFRDRGWAIRVPRRLQELKMS-----LAKATSELSQQYGRAPTVSELADHL 174

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +SE E++       G ES NA    S  ++ +  D            + E  E    R 
Sbjct: 175 GMSEDEILE------GLESANAYSTIS-LDTPETDDADALAVADTLGNIDEALEGVEYRE 227

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L PRE+RI   R  +   +T   +++E  +S+  V ++ AR   +++E +
Sbjct: 228 SLKPLLEKLPPREKRILLLRFFRN--MTQSQIAAELGISQMHVSRLLARTLARLREGL 283


>gi|55274943|gb|AAV49271.1| RNA polymerase subunit sigma-38 [Shigella dysenteriae]
          Length = 204

 Score =  147 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 56/214 (26%), Positives = 101/214 (47%), Gaps = 12/214 (5%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+ 
Sbjct: 1   RMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQ 60

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            ++  I+     +++      K L   LR  +     ++           IA++L+    
Sbjct: 61  TIERAIMNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVD 115

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           +   M        S++  +    +     +  L    D +E    +  +  + +  + + 
Sbjct: 116 DFSRMLRLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKW 170

Query: 232 MSVLNPRERRIFEARR--LQENPVTLENLSSEFE 263
           +  LN ++R +   R   L     TLE++  E  
Sbjct: 171 LFELNAKQREVLARRFGLLGYEAATLEDVGREIG 204


>gi|47564960|ref|ZP_00236004.1| sigma-B [Bacillus cereus G9241]
 gi|47558333|gb|EAL16657.1| sigma-B [Bacillus cereus G9241]
          Length = 257

 Score =  147 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 51/257 (19%), Positives = 116/257 (45%), Gaps = 16/257 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++  G +GL+ 
Sbjct: 10  LTKEDVIKLIAEFQQNQCDEAQERLVEHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLG 69

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++++D   G     +++  I   +++Y+      + +      +R+     ++K  ++ 
Sbjct: 70  AIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRIKDLGGKIKLAIEE 124

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +TD+  +  +++ IA  L +SE EV+ +          SL+ ++ +S   SS  +   V 
Sbjct: 125 LTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENSSDGSSVARIESVG 184

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           +       + +  E   RR +L    +VLN  E+ +      +   +  ++      +S+
Sbjct: 185 E-------VEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGEN--LNQKDTGERLGISQ 235

Query: 267 ERVRQIEARAFKKVQES 283
             V +I+ +A  K++++
Sbjct: 236 MHVSRIKRQAISKLKQA 252


>gi|320007063|gb|ADW01913.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 297

 Score =  147 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 59/241 (24%), Positives = 105/241 (43%), Gaps = 20/241 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYG-LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + L+  +L LV   A  +R  G     +++  G IGL++A+ +FD  R    AT+++ 
Sbjct: 68  ARNTLIEMNLSLVRFAASRFRNRGGDDTEDIIQVGTIGLIKAIDRFDLSREVEFATFAVP 127

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +I   ++ +   +   V +     + R+   L + K  L    D +     V  +A  L+
Sbjct: 128 YIVGEIKRFFRDTTWSVHVPRRLQELRV--ELAKAKEQLSTKLDRD---PTVAELAAHLD 182

Query: 168 VSESEVISMNCRLAGDE--SLNALINSSDKNSSQ--WQDWLVYDHDGQEQVLIEKEERKN 223
           + E E+I       G    SL+     SD  S Q  + D L  D  G E V         
Sbjct: 183 LPEEEIIEGLVAANGYSAGSLDTPNADSDSGSEQRAYADLLGEDDPGMESV--------E 234

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             + L   +  L+ RER+I   R  QE  +T   + +E  VS+  V ++ +R  ++++  
Sbjct: 235 NLHTLAPLLRQLDDRERKIVRMRFGQE--MTQAQIGAELGVSQMHVSRLLSRIVQRLRAG 292

Query: 284 I 284
           +
Sbjct: 293 M 293


>gi|116328490|ref|YP_798210.1| RNA polymerase sigma factor WhiG [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116331220|ref|YP_800938.1| RNA polymerase sigma factor WhiG [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
 gi|116121234|gb|ABJ79277.1| RNA polymerase sigma subunit [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116124909|gb|ABJ76180.1| RNA polymerase sigma subunit [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
          Length = 266

 Score =  147 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 64/261 (24%), Positives = 123/261 (47%), Gaps = 19/261 (7%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL---PISEVVSEGNIGLMQ 88
           Q+E  L K YR+  D      LV  +  LV  +A              ++VS G  GL+ 
Sbjct: 11  QDETELWKSYRDTKDQDIRSYLVEKYSPLVKHVAGRIAIGMPQNVEFDDLVSYGVFGLLD 70

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++KFDP+R  +  TY+M  I+ ++ + +    S+  I  +  QK      ++L+  +  
Sbjct: 71  AIEKFDPDRLIKFKTYAMTRIRGSIFDELR---SIDWIPRSIRQKA-----KQLEQIIGM 122

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD--ESLNALINSSDKNSS-QWQDWLV 205
           + +   +     AIAK+L +S  E  S+  +++G    SLN +    D+N    + + L 
Sbjct: 123 LENKEGQQVDDDAIAKELGISMEEYNSLLTKISGTSLVSLNDIWFLGDENDEVSFMETLE 182

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
              +     +IEKEE    +N++  ++  L  +E+++      ++  +TL+ +    EV+
Sbjct: 183 SPMNMNPDTIIEKEE---IKNVIVEAIKTLPEKEKKVIVLYYYED--LTLKEIGEVLEVT 237

Query: 266 RERVRQIEARAFKKVQESIQK 286
             R+ Q+  RA  +++  + K
Sbjct: 238 ESRISQLHTRAVSRLRSKLGK 258


>gi|5360738|dbj|BAA82139.1| sigma factor of sigB family [Streptomyces griseus]
          Length = 259

 Score =  147 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 54/239 (22%), Positives = 105/239 (43%), Gaps = 13/239 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + L+  +L LV   A  +R  G   + ++V  G IGL++A+ +FD  R     ++++ 
Sbjct: 27  ARNTLIEMNLSLVRFAANRFRNRGSGDMEDIVQVGTIGLIKAIDRFDLSREVEFTSFAVP 86

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +I   ++ +   +   V +     + R+  +L + K  L  + D +        +A+ L 
Sbjct: 87  YIVGEIKRFFRDTSWAVHVPRRLQELRV--DLAKAKEALAGVLDRD---PTAKELAEYLG 141

Query: 168 VSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           + ESEV        G    SL+   ++++    Q       D  G     +E  E     
Sbjct: 142 IEESEVTEGIVASNGYTAGSLDMPTDTAEAGPGQTAGRTFADVLGDPDPAMEAVE---NL 198

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + L   +  L+ RERRI + R  QE  +T   + +E  +S+  V ++ +R   K++  +
Sbjct: 199 HALAPLLDELDERERRIIDMRFGQE--MTQAQIGAELGISQMHVSRLLSRMLGKLRTGM 255


>gi|219123705|ref|XP_002182160.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217406121|gb|EEC46061.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 319

 Score =  147 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 57/255 (22%), Positives = 109/255 (42%), Gaps = 22/255 (8%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGY-------------RGYGLPISEVVSEGNIGLMQAVKKF 93
             A   LV ++L LV  +A                 G  L + +++ EG +GLM+A ++F
Sbjct: 63  QQARAALVAANLGLVTALAKRQLSTLQTATEAGRGVGTILTLQDLIQEGTLGLMKAAERF 122

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           +PERG+R +TY+ WW++  + + +  S   +++    +       +++ K   +A    +
Sbjct: 123 EPERGWRFSTYATWWVRQRILKSVSDSSRTIRLPAHVH--GTLQRIQKAKAWFRA----H 176

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            +   + ++A+ L +   +V           SL   +        +    L       E+
Sbjct: 177 GEEATLSSLAQYLELPVEKVRLYTDSSRNVMSLETPLKGRSAFKDENTRTLGDTLASDEK 236

Query: 214 VLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVR 270
              E  E +  R  L   M  VL   E+ +   R   E+    +LE  + +  +SR+R+R
Sbjct: 237 TPEENVEAQALRLDLEHVMIKVLTDVEQNVLRRRFGLEDGTSWSLEETAKQLGMSRDRIR 296

Query: 271 QIEARAFKKVQESIQ 285
            +EARA  K++   Q
Sbjct: 297 LVEARALNKLRRPQQ 311


>gi|207743452|ref|YP_002259844.1| sigma factor, ecf;peptidase aspartic, active site;;; protein
           [Ralstonia solanacearum IPO1609]
 gi|206594849|emb|CAQ61776.1| sigma factor, ecf;peptidase aspartic, active site;;; protein
           [Ralstonia solanacearum IPO1609]
          Length = 203

 Score =  147 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 53/203 (26%), Positives = 94/203 (46%), Gaps = 10/203 (4%)

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M A++KFDPERGFR +TY+ WWI+ +++  I+     V++       R    + R K HL
Sbjct: 1   MHAIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV--IRELNQVLRAKRHL 58

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +  +  + +   +  IA  L  +  EV  +        SL+        + +   D+L  
Sbjct: 59  EK-SGIDGRDASIEDIAHLLGKTTEEVQDVLSLNEHTTSLDTPF--DLDSGTSLLDFLSD 115

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
           +H        ++   +    ++   ++ L+ + R + E R       P TLE L++E  +
Sbjct: 116 EHGASPD---QEVAHRELSQLMKSWLARLSDKHRYVVERRFGLNHIEPATLEELAAEMGL 172

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +RERVRQI+  A  K++     Q
Sbjct: 173 TRERVRQIQQEALVKLKRHFASQ 195


>gi|325263641|ref|ZP_08130375.1| RNA polymerase sigma-F factor [Clostridium sp. D5]
 gi|324031350|gb|EGB92631.1| RNA polymerase sigma-F factor [Clostridium sp. D5]
          Length = 238

 Score =  147 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 48/248 (19%), Positives = 109/248 (43%), Gaps = 17/248 (6%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             L K+  + GD  A  +LV  ++ LV  +   + G G    ++   G+IGL++A+ KFD
Sbjct: 5   IALIKKSHD-GDKKAREQLVEENVGLVWCVVKRFYGRGTEAEDLFQIGSIGLLKAIDKFD 63

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
                + +TY++  I   ++ ++     ++K+  +  +        ++    +A+T +  
Sbjct: 64  LSYEVKFSTYAVPMISGEIKRFLRDDG-MIKVSRSLKELSY-----KIFQTREALTGSLG 117

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +   +  +A  +NV + E++         ESL   I+  + N  +  D L      +E++
Sbjct: 118 REPTLEELANTMNVDKEEIVQAMEAGGEVESLYKPIHQKEGNEIRLVDKLEEKERKEEKI 177

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
           L           +L + +  L+  ER++   R   +   T   +  +  +S+ +V ++E 
Sbjct: 178 L--------DHMLLAQLLESLDKEERQLIYLRYFADE--TQSQVGKKLGISQVQVSRMEK 227

Query: 275 RAFKKVQE 282
           R  + ++ 
Sbjct: 228 RIIENLRR 235


>gi|24215303|ref|NP_712784.1| RNA polymerase sigma factor WhiG [Leptospira interrogans serovar
           Lai str. 56601]
 gi|45657258|ref|YP_001344.1| RNA polymerase sigma factor WhiG [Leptospira interrogans serovar
           Copenhageni str. Fiocruz L1-130]
 gi|24196402|gb|AAN49802.1| RNA polymerase sigma factor WhiG [Leptospira interrogans serovar
           Lai str. 56601]
 gi|45600496|gb|AAS69981.1| RNA polymerase sigma-28 factor [Leptospira interrogans serovar
           Copenhageni str. Fiocruz L1-130]
          Length = 266

 Score =  147 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 66/261 (25%), Positives = 123/261 (47%), Gaps = 19/261 (7%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL---PISEVVSEGNIGLMQ 88
           Q+E  L K YRE  D      LV  +  LV  +A              ++VS G  GL+ 
Sbjct: 11  QDETELWKSYRETKDQDIRSYLVEKYSPLVKHVAGRIAIGMPQNVEFDDLVSYGVFGLLD 70

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++KFDPER  +  TY+M  I+ ++ + +    S+  I  +  QK      ++L+  +  
Sbjct: 71  AIEKFDPERLIKFKTYAMTRIRGSIFDELR---SIDWIPRSIRQKA-----KQLEQIIGM 122

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD--ESLNALINSSDKNSS-QWQDWLV 205
           + +   +     AIAK+L +S  E  S+  +++G    SLN +    D+N    + + L 
Sbjct: 123 LENKEGQQVDDDAIAKELGISMEEYNSLLTKISGTSLVSLNDIWFLGDENDEVSFMETLE 182

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
              +     +IEKEE    +N++  ++  L  +E+++      ++  +TL+ +    EV+
Sbjct: 183 SPMNMNPDTIIEKEE---IKNVIVEAIKTLPEKEKKVIVLYYYED--LTLKEIGEVLEVT 237

Query: 266 RERVRQIEARAFKKVQESIQK 286
             R+ Q+  RA  +++  + K
Sbjct: 238 ESRISQLHTRAVSRLRSKLGK 258


>gi|302765387|ref|XP_002966114.1| hypothetical protein SELMODRAFT_266972 [Selaginella moellendorffii]
 gi|300165534|gb|EFJ32141.1| hypothetical protein SELMODRAFT_266972 [Selaginella moellendorffii]
          Length = 249

 Score =  147 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 59/237 (24%), Positives = 111/237 (46%), Gaps = 17/237 (7%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ S+LRLVV IA  Y   G+ I +++ EG +GL+  ++KFD  RGF+ +TY+ WWI  A
Sbjct: 1   MILSNLRLVVAIARRYENMGVEIGDLIQEGTLGLIHGLEKFDVSRGFKFSTYAYWWIFQA 60

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           M   + +    V+      +      + +L+         + +P  V  + + L +  + 
Sbjct: 61  MIRSLDKRGKCVRYPFHLCE--AIRKINQLRNR-----QVDDRPVSVETMMQVLKLPRAR 113

Query: 173 V-ISMNCRLAGDESLNALINS--SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           + I++        SL+  + +    +     +D++V  +   +  L+   ER   +  L 
Sbjct: 114 IEIALQASNYRLTSLDRHVANKRCFEEGDPLEDFIVDQNVENQPWLM--AERDAVKEELD 171

Query: 230 RSMSV-LNPRERRIFEARRLQE----NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R +   L+ RER +   R        +P++   +     +SRERVRQ+E  A  K++
Sbjct: 172 RLLESKLDAREREVIRKRFGLHPNQTSPLSRHEIGRSCGISRERVRQLENDAMAKLR 228


>gi|167755749|ref|ZP_02427876.1| hypothetical protein CLORAM_01264 [Clostridium ramosum DSM 1402]
 gi|167704688|gb|EDS19267.1| hypothetical protein CLORAM_01264 [Clostridium ramosum DSM 1402]
          Length = 258

 Score =  147 bits (372), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 54/257 (21%), Positives = 110/257 (42%), Gaps = 16/257 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L   E Y L   Y+   + +   RLV  + +LV+ +A  + G    + ++   G IGL++
Sbjct: 18  LTTDETYKLIDEYQATKNEAIKDRLVNDNTKLVLSMARRFYGREDSMDDLFQVGMIGLIK 77

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++ F+   G + +TY++  I   M+ Y+  +   +KI  +   + L + + ++K     
Sbjct: 78  AIENFNTSFGLKFSTYAVPLIIGEMKRYLRDN-HQIKISRSI--RDLAYKVLKVKDSYIT 134

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
             +       +  +A +L V  S VI          SL   + + D N+ +  D +  D 
Sbjct: 135 KLNRE---PTINELANELEVEPSAVIEALLSTNSVSSLQEEVKNDDGNNLKMIDSITDDK 191

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
                       R N    L  ++  LN +E R+ + R      ++   ++ E  +S+ +
Sbjct: 192 TV--------VSRTNETIDLYDALKSLNQKEHRVIKQRYF--EGLSQSEIAKELFISQAQ 241

Query: 269 VRQIEARAFKKVQESIQ 285
           V +IE +A   +   ++
Sbjct: 242 VSRIERKALDNLHNYLK 258


>gi|239930293|ref|ZP_04687246.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 305

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 53/234 (22%), Positives = 104/234 (44%), Gaps = 15/234 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDP+RG +  T++M  +
Sbjct: 82  RAALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFPTFAMPTV 141

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ Y   +   V +      +RL     ++ G  + +T    +      IA++L ++
Sbjct: 142 VGEIKRYFRDNVRTVHVP-----RRLHELWVQVNGATEDLTTAFGRSPSTAEIAERLRIT 196

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E +V+S         + +              D L Y+    + V          R+++ 
Sbjct: 197 EEDVLSCIEAGRSYHATSLEAAQEGDGMPGLLDRLGYEDPALDGV--------EHRDLVR 248

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +  L  RE+RI   R      +T   +S+E  VS+  V ++ AR+F++++ +
Sbjct: 249 HLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLLARSFQRLRSA 300


>gi|302867457|ref|YP_003836094.1| RNA polymerase sigma-70 factor [Micromonospora aurantiaca ATCC
           27029]
 gi|315506134|ref|YP_004085021.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily
           [Micromonospora sp. L5]
 gi|302570316|gb|ADL46518.1| RNA polymerase sigma-70 factor, sigma-B/F/G subfamily
           [Micromonospora aurantiaca ATCC 27029]
 gi|315412753|gb|ADU10870.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Micromonospora sp. L5]
          Length = 269

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 50/239 (20%), Positives = 103/239 (43%), Gaps = 18/239 (7%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +  ++++ + L L   +A  Y G G P  ++     +GL++AV +FD  RG   A +++ 
Sbjct: 44  ALRNQVIEAWLPLANHLAARYSGRGEPAGDLAQTAALGLIKAVDRFDASRGVDFAGFAIP 103

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I   ++ +       +++     + RL     R+      +T    +   V  IA  L+
Sbjct: 104 TILGEIKRHFRDRTWNIRVPRRLQELRL-----RISEANSTLTQTLNRAPTVADIAAHLD 158

Query: 168 VS--ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           V+  E        R     SL+  I   D ++++  D L  + +        + E  + R
Sbjct: 159 VTEEEVLEGLEGARAYNAVSLSTPIGDGD-SATELGDTLGTEDN--------EYELADLR 209

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             L  +++ L+ RE++I   R      +T   +++   VS+  V ++ ARA  K++  +
Sbjct: 210 ASLGPALATLDEREQKILTLRFYGN--LTQSEIAARVGVSQMHVSRLLARALTKLRGQL 266


>gi|254384107|ref|ZP_04999452.1| sigma factor [Streptomyces sp. Mg1]
 gi|194342997|gb|EDX23963.1| sigma factor [Streptomyces sp. Mg1]
          Length = 301

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 53/234 (22%), Positives = 93/234 (39%), Gaps = 17/234 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+  +L LV   A  +R    P+ ++V  G IGL++A+ +FD ERG    T++M  +
Sbjct: 77  RDTLIELNLPLVRYAAARFRSRNEPMEDIVQVGTIGLIKAIDRFDCERGVEFPTFAMPTV 136

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +   V  +A  L VS
Sbjct: 137 VGEIKRFFRDTSWSVRVPRRLQELRLA-----LTKASDELAQKLDRSPTVPELAAVLGVS 191

Query: 170 ESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E EV+            SL++     +       D L Y+    E V          R  
Sbjct: 192 EEEVVDGLAVGNAYTASSLDSPSPEDEGGEGSLADRLGYEDTALEGV--------EYRES 243

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           L   ++ L PRER+I   R      +T   +  E  +S+  V ++  R   +++
Sbjct: 244 LKPLLAKLPPRERQIIMLRFFAN--MTQSQIGEEVGISQMHVSRLLTRTLAQLR 295


>gi|288802544|ref|ZP_06407983.1| RNA polymerase sigma-70 factor [Prevotella melaninogenica D18]
 gi|288335072|gb|EFC73508.1| RNA polymerase sigma-70 factor [Prevotella melaninogenica D18]
          Length = 257

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 61/270 (22%), Positives = 115/270 (42%), Gaps = 47/270 (17%)

Query: 17  SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
            +YI +I    +L  +EE  LA++ +  GD  A  +L  ++L+ VV +A  Y   GL   
Sbjct: 34  EKYIEDIANEQLLSDKEEQDLAEKIKV-GDARALEKLTKANLKFVVSLAHQYHNRGLGED 92

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++SEGNIG+M A +KFD  +G R   ++  +I+ AM+E I    +L K+          
Sbjct: 93  DLISEGNIGMMYAAQKFDGSKGVRFVVFAAPYIRKAMEEAIKEQATLYKLP--------- 143

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
                                            ++E      + +   S++  +     N
Sbjct: 144 ---------------------------------KNETSRFEQKRSHAISIDQPVPVGSNN 170

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV-TL 255
           +   Q  L  ++       + +E   N    + + + VL+ RE+R+            T+
Sbjct: 171 NFTLQHILENENAKHADEHLNQEILSNE---IQKGLDVLDEREKRVITYIYGLTGAHYTM 227

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             ++ +  + RERVRQI  +A +K+ + ++
Sbjct: 228 AEIAEDMGLKRERVRQIRDKALRKLHKKMK 257


>gi|229051333|ref|ZP_04194847.1| RNA polymerase sigma-43 factor [Bacillus cereus AH676]
 gi|229125362|ref|ZP_04254451.1| RNA polymerase sigma-43 factor [Bacillus cereus 95/8201]
 gi|228658091|gb|EEL13842.1| RNA polymerase sigma-43 factor [Bacillus cereus 95/8201]
 gi|228722026|gb|EEL73457.1| RNA polymerase sigma-43 factor [Bacillus cereus AH676]
          Length = 325

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 65/266 (24%), Positives = 113/266 (42%), Gaps = 13/266 (4%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP--ISEVVSEGN 83
             +L K+E   L KRY+ HG+      L   +  LV+ IA  Y+         ++V EGN
Sbjct: 48  YKVLSKEESLHLFKRYK-HGEKDLRDYLFHVNEGLVLSIARNYKNKHPDIEFDDLVQEGN 106

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRL 142
            G+++A++ F+P+ G+  +TY+ WWI+ +M   I  +     KI T  NQ  L +     
Sbjct: 107 EGMLRAMEDFNPDLGYCFSTYAFWWIQKSMLGIIRKKKSGPFKIPTHVNQFNLKYV---- 162

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
                       +   V  + K+LNV+   VI          ++   I++ +++      
Sbjct: 163 -ELEDKYLQRYNRTPSVEEVVKELNVTRETVIRHKVYYKRATTMTLDIDTINEDVGISTP 221

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPVTLE-NLSS 260
           +   D            E  N    L     VLNP+++ +      L +  V L   ++ 
Sbjct: 222 FF-DDKSAIPSTNEMIIEDLNYEIWLIFD-EVLNPKQKMVLNLCFGLLDGKVYLHKEIAK 279

Query: 261 EFEVSRERVRQIEARAFKKVQESIQK 286
              ++ ERV QI+  A KK+++   K
Sbjct: 280 ALMITTERVSQIKDEAIKKLKKCQHK 305


>gi|161898859|gb|ABX80419.1| SigB [Listeria monocytogenes]
          Length = 236

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 59/253 (23%), Positives = 111/253 (43%), Gaps = 25/253 (9%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E GD  A + LV  +  LV  IA  Y   G    E    GNIGL+ A++++D
Sbjct: 3   YIWIAAYQEDGDEDAQYNLVIHYKNLVESIARKYSQ-GKSFHEDSQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G     +++  I   ++ ++      V +     +        ++K  ++ +T    
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQ 116

Query: 155 KPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +    
Sbjct: 117 SSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTD 173

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++S+  
Sbjct: 174 DGF--------ERVNQRMLLEKVLPVLDEREQKILQFTFIEN--RSQKETGELLDISQMH 223

Query: 269 VRQIEARAFKKVQ 281
           V +I+ +A KK++
Sbjct: 224 VSRIQRQAIKKLR 236


>gi|296501716|ref|YP_003663416.1| RNA polymerase sigma factor SigB [Bacillus thuringiensis BMB171]
 gi|296322768|gb|ADH05696.1| RNA polymerase sigma factor SigB [Bacillus thuringiensis BMB171]
          Length = 257

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 54/265 (20%), Positives = 120/265 (45%), Gaps = 17/265 (6%)

Query: 22  EIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           EI+  P  L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++ 
Sbjct: 2   EIQSQPTNLTKEDVIKLIADFQQNQCDEAQERLVEHYKNLVYSIAYRYSKGGPMHEDIIQ 61

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
            G +GL+ A++++D   G     +++  I   +++Y+      + +      +R+     
Sbjct: 62  VGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRIKDLGG 116

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSS 198
           ++K  ++ +TD+  +  +++ IA  L +SE EV+ +          SL+ ++ +S   SS
Sbjct: 117 KIKLAIEELTDHLQRSPKIIEIANHLGLSEEEVLEIMDAKNNYRVSSLDDVVENSSDGSS 176

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
             +   V +       + +  E   RR +L    +VLN  E+ +      +   +  ++ 
Sbjct: 177 VARIESVGE-------VEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGEN--LNQKDT 227

Query: 259 SSEFEVSRERVRQIEARAFKKVQES 283
                +S+  V +I+ +A  K++++
Sbjct: 228 GERLGISQMHVSRIKRQAISKLKQA 252


>gi|182418456|ref|ZP_02949750.1| RNA polymerase sigma-F factor [Clostridium butyricum 5521]
 gi|237666966|ref|ZP_04526951.1| RNA polymerase sigma-F factor [Clostridium butyricum E4 str. BoNT E
           BL5262]
 gi|182377838|gb|EDT75382.1| RNA polymerase sigma-F factor [Clostridium butyricum 5521]
 gi|237658165|gb|EEP55720.1| RNA polymerase sigma-F factor [Clostridium butyricum E4 str. BoNT E
           BL5262]
          Length = 252

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 44/246 (17%), Positives = 105/246 (42%), Gaps = 15/246 (6%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             + GD  A ++L+  +L LV  I+  +   G    ++   G+IGL++A+  FD     +
Sbjct: 22  LAKKGDNDAMNKLIEINLPLVASISKKFLNRGYDYEDIFQIGSIGLVKAINNFDLNYNVK 81

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY++  I   ++ ++     ++K+             R++  + + +T+   +   + 
Sbjct: 82  FSTYAVPMIMGEIKRFLRDDG-MIKVSRNVKSLA-----RKIHYYREQLTNKLKRSPTIE 135

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+   V + E++         + L   I+  D       D L       +  LIEK  
Sbjct: 136 ELAEYAGVEKEEIVFAIESANSLQYLYDTIHQDDGAPVMLIDKLSEKKGEDDVNLIEKI- 194

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                  L  ++  L+ + R+I   R  ++   T   ++    +S+ +V +IE +   ++
Sbjct: 195 ------ALKEALRSLDEKARQIIMLRYFKD--KTQIQVAKMLGISQVQVSRIEKKVLLQM 246

Query: 281 QESIQK 286
           ++ +++
Sbjct: 247 KKKLEE 252


>gi|54401900|gb|AAV34635.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 203

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 56/213 (26%), Positives = 100/213 (46%), Gaps = 12/213 (5%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ S+LRLVVKIA  Y   GL + +++ EGN+GL +AV+KFDPERGFR +TY+ WWI+  
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLNRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           ++  I+     +++      K L   LR  +     ++           IA++L+    +
Sbjct: 61  IERAIMNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDD 115

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           V  M        S++  +    +     +  L    D +E    +  +  + +  + + +
Sbjct: 116 VSRMLRLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWL 170

Query: 233 SVLNPRERRIFEARR--LQENPVTLENLSSEFE 263
             LN ++R +   R   L     TLE++  E  
Sbjct: 171 FELNAKQREVLARRFGLLGYEAATLEDVGREIG 203


>gi|317121977|ref|YP_004101980.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermaerobacter marianensis DSM 12885]
 gi|315591957|gb|ADU51253.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermaerobacter marianensis DSM 12885]
          Length = 250

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 56/251 (22%), Positives = 111/251 (44%), Gaps = 20/251 (7%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           E  L  R R  GD  A  RLV  H+ LV  +A  + G+G  + ++V  G IGL+QA+  F
Sbjct: 2   EAELWARAR-RGDAEARERLVALHMPLVRHVARRFAGFGHEMDDLVQAGTIGLLQAIDGF 60

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           DP RG++ +TY++  I   ++ ++  S      G T   +     +RR+   ++    + 
Sbjct: 61  DPARGYQFSTYAVPAILGEIRRWLRASDPA---GLTRAMRARVAAIRRVAEAMEQELGH- 116

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
                  A+A++L    ++V           SL+  ++S    S++ Q            
Sbjct: 117 --RPPAAAVAERLGCDVADVTFALEASQVPVSLDEPLSSDPDASARGQRLAAPAEPDWSD 174

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
            +            +  +++ L PR R I   R  ++  +T   +++   +S+ +V ++E
Sbjct: 175 AVA-----------VRAALTQLPPRLRTIVTLRFFRD--MTQAEVAAAVGLSQPQVSRLE 221

Query: 274 ARAFKKVQESI 284
             A  ++++ +
Sbjct: 222 KLALGQLRQLL 232


>gi|685227|dbj|BAA04283.1| sigma factor [Streptomyces setonii]
          Length = 259

 Score =  147 bits (371), Expect = 2e-33,   Method: Composition-based stats.
 Identities = 53/242 (21%), Positives = 106/242 (43%), Gaps = 13/242 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + L+  +L LV   A  +R  G   + ++V  G IGL++A+ +FD  R     ++++ 
Sbjct: 27  ARNTLIEMNLSLVRFAANRFRNRGSGDMEDIVQVGTIGLIKAIDRFDLSREVEFTSFAVP 86

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +I   ++ +   +   V +     + R+      L    +++  +  +   V  +A+ L 
Sbjct: 87  YIVGEIKRFFRDTSWAVHVPRRLQELRVD-----LAKAKESLAGDLDRDPTVRELAQDLG 141

Query: 168 VSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           + ESEV        G    SL+   ++++    Q       D  G+    +E  E     
Sbjct: 142 IEESEVTEGIVASNGYTAGSLDMPTDTAEAGPGQHSGRTFADVLGEPDPAMETVE---NL 198

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + L   +  L+ RERRI + R  QE  +T   + +E  +S+  V ++ +R   K++  + 
Sbjct: 199 HALAPLLGELDERERRIIDMRFGQE--MTQAQIGAELGISQMHVSRLLSRMLGKLRNGML 256

Query: 286 KQ 287
            Q
Sbjct: 257 TQ 258


>gi|291438641|ref|ZP_06578031.1| transcription initiation factor sigma F [Streptomyces ghanaensis
           ATCC 14672]
 gi|291341536|gb|EFE68492.1| transcription initiation factor sigma F [Streptomyces ghanaensis
           ATCC 14672]
          Length = 303

 Score =  146 bits (370), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 53/234 (22%), Positives = 104/234 (44%), Gaps = 15/234 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDP+RG +  T++M  +
Sbjct: 80  RAALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFPTFAMPTV 139

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ Y   +   V +      +RL     ++ G  + +T    +      IA++L ++
Sbjct: 140 VGEIKRYFRDNVRTVHVP-----RRLHELWVQVNGATEDLTTAFGRSPSTAEIAERLRIT 194

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E +V+S         + +              D L Y+    + V          R+++ 
Sbjct: 195 EEDVLSCIEAGRSYHATSLEAAQEGDGMPGLLDRLGYEDPALDGV--------EHRDLVR 246

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +  L  RE+RI   R      +T   +S+E  VS+  V ++ AR+F++++ +
Sbjct: 247 HLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLLARSFQRLRSA 298


>gi|55275000|gb|AAV49297.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 203

 Score =  146 bits (370), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 56/213 (26%), Positives = 100/213 (46%), Gaps = 12/213 (5%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ S+LRLVVKIA  Y   GL +  ++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           ++  I+     +++      K L   LR  +     ++           IA++L+    +
Sbjct: 61  IERAIMNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDD 115

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           V  M        S++  +    +     +  L    D +E    +  +  + +  + + +
Sbjct: 116 VSRMLRLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWL 170

Query: 233 SVLNPRERRIFEARR--LQENPVTLENLSSEFE 263
             LN ++R +   R   L     TLE++  E  
Sbjct: 171 FELNAKQREVLARRFGLLGYEAATLEDVGREIG 203


>gi|218896055|ref|YP_002444466.1| RNA polymerase sigma-B factor [Bacillus cereus G9842]
 gi|218544560|gb|ACK96954.1| RNA polymerase sigma-B factor [Bacillus cereus G9842]
          Length = 257

 Score =  146 bits (370), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 54/265 (20%), Positives = 121/265 (45%), Gaps = 17/265 (6%)

Query: 22  EIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           EI+  P  L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++ 
Sbjct: 2   EIQSQPTTLTKEDVIKLIAEFQQNQCNEAQERLVDHYKNLVYSIAYRYSKGGPMHEDIIQ 61

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
            G +GL+ A++++D   G     +++  I   +++Y+      + +      +R+     
Sbjct: 62  VGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRIKDLGG 116

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSS 198
           ++K  ++ +TD+  +  +++ IA  L +SE EV+ +          SL+ ++ +S   SS
Sbjct: 117 KIKLAIEELTDHLQRSPKIIEIANHLGLSEEEVLEIMDAKNNYRVSSLDDVVENSSDGSS 176

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
             +   V +       + +  E+  RR +L    +VLN  E+ +      +   +  ++ 
Sbjct: 177 VARIESVGE-------VEQGYEQTERRLVLEDIFNVLNDTEKSVIHYIFGEN--LNQKDT 227

Query: 259 SSEFEVSRERVRQIEARAFKKVQES 283
                +S+  V +I+ +A  K++++
Sbjct: 228 GERLGISQMHVSRIKRQAISKLKQA 252


>gi|305644358|gb|ADM53780.1| RNA polymerase sigma factor [Aeromonas hydrophila]
          Length = 176

 Score =  146 bits (370), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 42/186 (22%), Positives = 77/186 (41%), Gaps = 12/186 (6%)

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+  
Sbjct: 1   GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISR 58

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            +         PE    +A ++ + E ++  +        S+   I   D   S   D++
Sbjct: 59  QMLQEMGREPNPE---ELAMRMGMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI 113

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEF 262
               D    +  +    ++ RN     ++ L  RE ++   R   +     TLE +  +F
Sbjct: 114 ---EDTTLALPADAATSESLRNATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQF 170

Query: 263 EVSRER 268
           +V+ ER
Sbjct: 171 DVTVER 176


>gi|284033085|ref|YP_003383016.1| B/F/G subfamily RNA polymerase sigma-28 subunit [Kribbella flavida
           DSM 17836]
 gi|283812378|gb|ADB34217.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Kribbella
           flavida DSM 17836]
          Length = 264

 Score =  146 bits (370), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 53/241 (21%), Positives = 100/241 (41%), Gaps = 18/241 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   LV+ H+ LV  +A  +R  G P  ++V    IGL++A+ +FD +RG   +TY+   
Sbjct: 40  ARDGLVSLHMPLVEHLARRFRNRGEPYDDLVQVATIGLIKAIDRFDSDRGVEFSTYATPT 99

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I   ++ Y       +++     + RL      L      +T    +   V  ++ +L +
Sbjct: 100 ILGEIKRYFRDKGWAIRVPRRLQELRLS-----LTAATAELTQELGRAPTVAELSTRLGL 154

Query: 169 SESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           S+  VI    +       SL+A   +    ++        D         E  E    R 
Sbjct: 155 SQDLVIEGLESANAYNTLSLDAPDQNEADATTVLDGLGGED---------EALESVEFRE 205

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L   ++ L  RE+RI   R  +   +T   ++ E  +S+  V ++ AR   +++  + K
Sbjct: 206 SLKPLLAQLETREKRILTLRFFRG--MTQSQIAEEIGISQMHVSRLLARTLTELRAGLLK 263

Query: 287 Q 287
           +
Sbjct: 264 E 264


>gi|217958581|ref|YP_002337129.1| RNA polymerase sigma factor SigB [Bacillus cereus AH187]
 gi|217065197|gb|ACJ79447.1| RNA polymerase sigma-B factor [Bacillus cereus AH187]
          Length = 257

 Score =  146 bits (370), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 50/257 (19%), Positives = 115/257 (44%), Gaps = 16/257 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++  G +GL+ 
Sbjct: 10  LTKEDVIKLIAEFQQNQCDEAQERLVEHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLG 69

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++++D   G     +++  I   +++Y+      + +      +R+     ++K  ++ 
Sbjct: 70  AIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRIKDLGGKIKLAIEE 124

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +TD   +  +++ IA  L +SE EV+ +          SL+ ++ ++   SS  +   V 
Sbjct: 125 LTDRLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENASDGSSVARIESVG 184

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           +       + +  E   RR +L    +VLN  E+ +      +   +  ++      +S+
Sbjct: 185 E-------VEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGEN--LNQKDTGERLGISQ 235

Query: 267 ERVRQIEARAFKKVQES 283
             V +I+ +A  K++++
Sbjct: 236 MHVSRIKRQAISKLKQA 252


>gi|284043529|ref|YP_003393869.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
 gi|283947750|gb|ADB50494.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
          Length = 261

 Score =  146 bits (370), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 49/244 (20%), Positives = 100/244 (40%), Gaps = 17/244 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L +RYRE GD     R + S + LV K+A  Y     P+ ++V    +GL++A+ +FDP
Sbjct: 28  DLIRRYRETGDPRCRTRAIESFMPLVHKLARRYHPGPEPLDDLVQVACVGLVKAIDRFDP 87

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           + G R A++++  I   ++ +   +   V +     +  L     RL+  +  +++   +
Sbjct: 88  DAGPRFASFAIPTITGELRRHFRDTTWSVHVPRRVQEDAL-----RLRHAMTELSERPGR 142

Query: 156 PEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
              +  ++    + + ++             SL+  +   D  S+   D L  D  G   
Sbjct: 143 SPTIHELSAATGLDDEQITEALHATTAKAASSLDRPVPGQDDGSATIGDTLGCDEYGFA- 201

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
                      R  +   +  L  R+R I   R  ++  +T   ++     S+ +V ++ 
Sbjct: 202 -------LAEHRTTIGPRLRALPLRDREILYLRFAED--MTQHEIAQRIGCSQMQVSRLL 252

Query: 274 ARAF 277
            RA 
Sbjct: 253 RRAL 256


>gi|239980907|ref|ZP_04703431.1| RNA polymerase sigma factor, sigma F [Streptomyces albus J1074]
 gi|291452769|ref|ZP_06592159.1| transcription initiation factor sigma F [Streptomyces albus J1074]
 gi|291355718|gb|EFE82620.1| transcription initiation factor sigma F [Streptomyces albus J1074]
          Length = 294

 Score =  146 bits (369), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 53/234 (22%), Positives = 103/234 (44%), Gaps = 15/234 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDP+RG +  T++M  +
Sbjct: 71  RSALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFPTFAMPTV 130

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ Y   +   V +      +RL     ++    + +T  + +      IA++L +S
Sbjct: 131 VGEIKRYFRDNVRTVHVP-----RRLHELWVQVTSATEDLTTAHGRSPTTAEIAERLRIS 185

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E EV++         + +              D L Y+    + V          R+++ 
Sbjct: 186 EDEVLACIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALDGV--------EHRDLVR 237

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +  L  RE+RI   R      +T   +S+E  VS+  V ++ AR+F +++ +
Sbjct: 238 HLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLLARSFARLRSA 289


>gi|326775053|ref|ZP_08234318.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
 gi|326655386|gb|EGE40232.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
          Length = 300

 Score =  146 bits (369), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 54/242 (22%), Positives = 107/242 (44%), Gaps = 12/242 (4%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYG-LPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           H    A + L+  +L LV   A  +R  G     +++  G IGL++A+ +FD  R    A
Sbjct: 66  HEHQYARNTLIEMNLSLVRFAASRFRNRGGDDTEDIIQVGTIGLIKAIDRFDLSREVEFA 125

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           T+++ +I   ++ +   +   V +     + R+      L    + ++    +   V  +
Sbjct: 126 TFAVPYIVGEIKRFFRDTTWSVHVPRRLQELRVD-----LAKAKEQLSGELDRDPTVKEL 180

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A  L++ E E+I       G  + +    S+D +S Q Q     D  G+    +E  E  
Sbjct: 181 AAHLDLPEEEIIEGLVAANGYSAGSLDTPSADSDSGQEQRAYA-DVLGEADPGMETVE-- 237

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              + L   +  L+ RERRI + R   E  +T   + +E  VS+  V ++ +R  +++++
Sbjct: 238 -NLHTLAPLLDQLDERERRIVQMRFGAE--MTQSQIGAELGVSQMHVSRLLSRIVQQLRK 294

Query: 283 SI 284
            +
Sbjct: 295 GM 296


>gi|313901877|ref|ZP_07835297.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermaerobacter subterraneus DSM 13965]
 gi|313467870|gb|EFR63364.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermaerobacter subterraneus DSM 13965]
          Length = 251

 Score =  146 bits (369), Expect = 3e-33,   Method: Composition-based stats.
 Identities = 54/251 (21%), Positives = 114/251 (45%), Gaps = 20/251 (7%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           E  L +R R+ GD  A  RLV  H+ LV  +A  +  +G  + +++  G IGL+QA+  F
Sbjct: 2   EDRLWERARQ-GDGEARERLVALHMPLVRHVARRFASFGHDLDDLIQAGTIGLLQAIDGF 60

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           DP RG++ +TY++  I   ++ ++  S      G +   +     +RR+   ++      
Sbjct: 61  DPSRGYQFSTYAVPVILGEIRRWLRASDPA---GLSRAMRARVAEIRRVADAMEQ---EL 114

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            +     A+A++L    ++V           SL+  + S++ +++   D L    D    
Sbjct: 115 GRRPPAAAVAQRLACDVADVTFALEAAQSPVSLDEPL-SAEPDAACRGDRLPAPGDPD-- 171

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
                    +    +  +++ L PR R I   R  ++  +T   +++   +S+ +V ++E
Sbjct: 172 --------WSDTVAVRAALAQLPPRLRTIIALRFFRD--LTQAEVAAAVGLSQPQVSRLE 221

Query: 274 ARAFKKVQESI 284
             A  +++  +
Sbjct: 222 KMALARLRSLL 232


>gi|326938732|gb|AEA14628.1| RNA polymerase sigma factor SigB [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 257

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 54/265 (20%), Positives = 120/265 (45%), Gaps = 17/265 (6%)

Query: 22  EIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           EI+  P  L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++ 
Sbjct: 2   EIQSQPTTLTKEDVIKLIAEFQQNQCNEAQERLVDHYKNLVYSIAYRYSKGGPMHEDIIQ 61

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
            G +GL+ A++++D   G     +++  I   +++Y+      + +      +R+     
Sbjct: 62  VGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRIKDLGG 116

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSS 198
           ++K  ++ +TD+  +  +++ IA  L +SE EV+ +          SL+ ++ +S   SS
Sbjct: 117 KIKLAIEELTDHLQRSPKIIEIANHLGLSEEEVLEIMDAKNNYRVSSLDDVVENSSDGSS 176

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
             +   V +       + +  E   RR +L    +VLN  E+ +      +   +  ++ 
Sbjct: 177 VARIESVGE-------VEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGEN--LNQKDT 227

Query: 259 SSEFEVSRERVRQIEARAFKKVQES 283
                +S+  V +I+ +A  K++++
Sbjct: 228 GERLGISQMHVSRIKRQAISKLKQA 252


>gi|46204236|ref|ZP_00050286.2| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Magnetospirillum magnetotacticum
           MS-1]
          Length = 182

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 77/168 (45%), Positives = 115/168 (68%), Gaps = 1/168 (0%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L + EE  LA  ++E  D  A HRL+++H+RLV+ +A  +R YGLP++++V EG++GL
Sbjct: 4   PFLARDEERGLAVAWKEERDERALHRLISAHMRLVIALAGRFRHYGLPMADLVQEGHVGL 63

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFFNLRRL+  L
Sbjct: 64  MEAAARFEPEREVRFSTYATWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRARL 123

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSS 193
              T+  +  E    IA  + VS  +V  M+ RL+G D SLNA +   
Sbjct: 124 MQSTEEQVGSEIHGRIATAIGVSREDVALMDARLSGPDMSLNAPVGEE 171


>gi|291537993|emb|CBL11104.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase
           sigma-70 factor, sigma-B/F/G subfamily [Roseburia
           intestinalis XB6B4]
          Length = 248

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 49/240 (20%), Positives = 101/240 (42%), Gaps = 10/240 (4%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A   L+  +L LV  IA  +   G    E+   G IGLM+AV KFD       +TY
Sbjct: 14  GDKGARDTLIAGNLGLVHTIANRFEHRGHEREELFQIGCIGLMKAVDKFDLSLNLAFSTY 73

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           ++  I   ++ ++     +VK+  T  +     N  +     + +     +   ++ IA+
Sbjct: 74  AVPVIMGEIRRFLRDDG-MVKVSRTLKE-----NAYKAGRAKEELWGELGREPGLLEIAE 127

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +  +S  E+I         ES+   +   D +     D L    +  +    +  E    
Sbjct: 128 RTGLSSGEIIMAMESARDVESIYQPVYEKDGDELLMVDQLCEKEENGKDEPEK--EAVLN 185

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R ++ + M +L+ RE+ +   R  +    T    + E  +++ +V ++E +    +++++
Sbjct: 186 RMVIEQLMELLDEREQNLIRCRYFEN--RTQSETAKELGMTQVQVSRLEKKILLCLRKNL 243


>gi|30261116|ref|NP_843493.1| RNA polymerase sigma factor SigB [Bacillus anthracis str. Ames]
 gi|47526271|ref|YP_017620.1| RNA polymerase sigma factor SigB [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|65318395|ref|ZP_00391354.1| COG1191: DNA-directed RNA polymerase specialized sigma subunit
           [Bacillus anthracis str. A2012]
 gi|165871654|ref|ZP_02216299.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0488]
 gi|167635453|ref|ZP_02393766.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0442]
 gi|167638886|ref|ZP_02397160.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0193]
 gi|170687593|ref|ZP_02878809.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0465]
 gi|170707965|ref|ZP_02898414.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0389]
 gi|177653505|ref|ZP_02935679.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0174]
 gi|190566700|ref|ZP_03019617.1| RNA polymerase sigma-B factor [Bacillus anthracis Tsiankovskii-I]
 gi|196037492|ref|ZP_03104803.1| RNA polymerase sigma-B factor [Bacillus cereus NVH0597-99]
 gi|227816152|ref|YP_002816161.1| RNA polymerase sigma-B factor [Bacillus anthracis str. CDC 684]
 gi|229604478|ref|YP_002865547.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0248]
 gi|254682827|ref|ZP_05146688.1| RNA polymerase sigma factor SigB [Bacillus anthracis str.
           CNEVA-9066]
 gi|254725613|ref|ZP_05187395.1| RNA polymerase sigma factor SigB [Bacillus anthracis str. A1055]
 gi|254734239|ref|ZP_05191952.1| RNA polymerase sigma factor SigB [Bacillus anthracis str. Western
           North America USA6153]
 gi|254740112|ref|ZP_05197804.1| RNA polymerase sigma factor SigB [Bacillus anthracis str. Kruger B]
 gi|254753453|ref|ZP_05205489.1| RNA polymerase sigma factor SigB [Bacillus anthracis str. Vollum]
 gi|254758550|ref|ZP_05210577.1| RNA polymerase sigma factor SigB [Bacillus anthracis str. Australia
           94]
 gi|17369088|sp|Q9K5J6|RPSB_BACAN RecName: Full=RNA polymerase sigma-B factor
 gi|8670945|emb|CAB95034.1| sigB [Bacillus anthracis]
 gi|30254730|gb|AAP24979.1| RNA polymerase sigma-B factor [Bacillus anthracis str. Ames]
 gi|47501419|gb|AAT30095.1| RNA polymerase sigma-B factor [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|164712555|gb|EDR18087.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0488]
 gi|167513016|gb|EDR88388.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0193]
 gi|167529071|gb|EDR91825.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0442]
 gi|170127125|gb|EDS96003.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0389]
 gi|170668406|gb|EDT19153.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0465]
 gi|172081309|gb|EDT66383.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0174]
 gi|190562252|gb|EDV16220.1| RNA polymerase sigma-B factor [Bacillus anthracis Tsiankovskii-I]
 gi|196031734|gb|EDX70330.1| RNA polymerase sigma-B factor [Bacillus cereus NVH0597-99]
 gi|227003869|gb|ACP13612.1| RNA polymerase sigma-B factor [Bacillus anthracis str. CDC 684]
 gi|229268886|gb|ACQ50523.1| RNA polymerase sigma-B factor [Bacillus anthracis str. A0248]
          Length = 257

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 51/257 (19%), Positives = 118/257 (45%), Gaps = 16/257 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++  G +GL+ 
Sbjct: 10  LTKEDVIKLIAEFQQNQCGEAQERLVDHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLG 69

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++++D   G     +++  I   +++Y+      + +      +R+     ++K  ++ 
Sbjct: 70  AIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRIKDLGGKIKLAIEE 124

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +TD+  +  +++ IA  L +SE EV+ +          SL+ ++ ++   SS  +   V 
Sbjct: 125 LTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENASDGSSVARIESVG 184

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           +       + +  E+  RR +L    +VLN  E+ +     + E  +  ++      +S+
Sbjct: 185 E-------VEQGYEQTERRLVLKDIFNVLNETEKSVIH--YIFEENLNQKDTGERLGISQ 235

Query: 267 ERVRQIEARAFKKVQES 283
             V +I+ +A  K++++
Sbjct: 236 MHVSRIKRQAISKLKQA 252


>gi|55274911|gb|AAV49257.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274963|gb|AAV49281.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 202

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 56/212 (26%), Positives = 101/212 (47%), Gaps = 12/212 (5%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           ++  I+     +++      K L   LR  +     ++           IA++L+    +
Sbjct: 61  IERAIMNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDD 115

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           V  M        S++  +    + +      L    D +E    +  +  + +  + + +
Sbjct: 116 VSRMLRLNERITSVDTPLGGDSEKA-----LLDILADEKENGPEDTTQDDDMKQSIVKWL 170

Query: 233 SVLNPRERRIFEARR--LQENPVTLENLSSEF 262
             LN ++R +   R   L     TLE++  E 
Sbjct: 171 FELNAKQREVLARRFGLLGYEAATLEDVGREI 202


>gi|206968111|ref|ZP_03229067.1| RNA polymerase sigma-B factor [Bacillus cereus AH1134]
 gi|206737031|gb|EDZ54178.1| RNA polymerase sigma-B factor [Bacillus cereus AH1134]
          Length = 257

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 54/265 (20%), Positives = 119/265 (44%), Gaps = 17/265 (6%)

Query: 22  EIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           EI+  P  L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++ 
Sbjct: 2   EIQSQPTNLTKEDVIKLIADFQQNQCDEAQERLVNHYKNLVYSIAYRYSKGGPMHEDIIQ 61

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
            G +GL+ A++++D   G     +++  I   +++Y+      + +      +R+     
Sbjct: 62  VGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRIKDLGG 116

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSS 198
           ++K  ++ +TD   +  +++ IA  L +SE EV+ +          SL+ ++ +S   SS
Sbjct: 117 KIKLAIEELTDRFQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENSSDGSS 176

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
             +   V +       + +  E   RR +L    +VLN  E+ +      +   +  ++ 
Sbjct: 177 VARIESVGE-------VEQGYEETERRLVLKDIFNVLNETEKSVIHYIFGEN--LNQKDT 227

Query: 259 SSEFEVSRERVRQIEARAFKKVQES 283
                +S+  V +I+ +A  K++++
Sbjct: 228 GERLGISQMHVSRIKRQAISKLKQA 252


>gi|302552488|ref|ZP_07304830.1| RNA polymerase sigma-B factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302470106|gb|EFL33199.1| RNA polymerase sigma-B factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 285

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 46/238 (19%), Positives = 105/238 (44%), Gaps = 16/238 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A + L+  ++ LV   A  +R  G  + +VV  G IGL++A+ +F+  R  +  ++++ +
Sbjct: 58  ARNTLIEMNMSLVRFAARRFRSSGQAMEDVVQVGVIGLIKAIDRFEVSREVQFTSFAVPY 117

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I   ++ +   +   V +     + R       L    + +     +  +V  +A  +N+
Sbjct: 118 IVGEIKRFFRDTSWAVHVPRRLQEART-----ELAKATEELASRLGRAPRVAELAALMNL 172

Query: 169 SESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           SE EV+       G    SL+A I+   ++S       + + D   +++ +        +
Sbjct: 173 SEEEVVEAQVAANGYLSSSLDATISGDSEDSDSTLSEFIGEEDPGLELVEDF-------H 225

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   ++ L+ R+R I   R ++E  +T   +     +S+  V ++ AR   +++  +
Sbjct: 226 ALAPLIAELDERQRLILHLRFVEE--LTQAEIGKRLGISQMHVSRLIARTVARLRSGM 281


>gi|54401890|gb|AAV34630.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274947|gb|AAV49273.1| RNA polymerase subunit sigma-38 [Shigella dysenteriae]
          Length = 203

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 57/213 (26%), Positives = 102/213 (47%), Gaps = 12/213 (5%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            R++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+
Sbjct: 1   RRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIR 60

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
             ++  I+     +++      K L   LR  +     ++           IA++L+   
Sbjct: 61  QTIERAIMNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPV 115

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            +V  M        S++  +    + +      L    D +E    +  +  + +  + +
Sbjct: 116 DDVSRMLRLNERITSVDTPLGGDSEKA-----LLDILADEKENGPEDTTQDDDMKQSIVK 170

Query: 231 SMSVLNPRERRIFEARR--LQENPVTLENLSSE 261
            +  LN ++R +   R   L     TLE++  E
Sbjct: 171 WLFELNAKQREVLARRFGLLGYEAATLEDVGRE 203


>gi|182434526|ref|YP_001822245.1| putative RNA polymerase sigma factor [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|178463042|dbj|BAG17562.1| putative RNA polymerase sigma factor [Streptomyces griseus subsp.
           griseus NBRC 13350]
          Length = 300

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 54/242 (22%), Positives = 107/242 (44%), Gaps = 12/242 (4%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYG-LPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           H    A + L+  +L LV   A  +R  G     +++  G IGL++A+ +FD  R    A
Sbjct: 66  HEHQYARNTLIEMNLSLVRFAASRFRNRGGDDTEDIIQVGTIGLIKAIDRFDLSREVEFA 125

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           T+++ +I   ++ +   +   V +     + R+      L    + ++    +   V  +
Sbjct: 126 TFAVPYIVGEIKRFFRDTTWSVHVPRRLQELRVD-----LAKAKEQLSGELDRDPTVKEL 180

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A  L++ E E+I       G  + +    S+D +S Q Q     D  G+    +E  E  
Sbjct: 181 AAHLDLPEEEIIEGLVAANGYSAGSLDTPSADSDSGQEQRAYA-DVLGEADPGMETVE-- 237

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              + L   +  L+ RERRI + R   E  +T   + +E  VS+  V ++ +R  +++++
Sbjct: 238 -NLHTLAPLLDQLDERERRIVQMRFGAE--MTQSQIGAELGVSQMHVSRLLSRIVQQLRK 294

Query: 283 SI 284
            +
Sbjct: 295 GM 296


>gi|324325029|gb|ADY20289.1| RNA polymerase sigma factor SigB [Bacillus thuringiensis serovar
           finitimus YBT-020]
          Length = 257

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 51/257 (19%), Positives = 117/257 (45%), Gaps = 16/257 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++  G +GL+ 
Sbjct: 10  LTKEDVMKLIAEFQQNQCDEAQERLVEHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLG 69

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++++D   G     +++  I   +++Y+      + +      +R+     ++K  ++ 
Sbjct: 70  AIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRIKDLGGKIKLAIEE 124

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +TD+  +  +++ IA  L +SE EV+ +          SL+ ++ ++   SS  +   V 
Sbjct: 125 LTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENASDGSSVARIESVG 184

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           +       + +  E   RR +L    +VLN  E+ +     + E  +  ++      +S+
Sbjct: 185 E-------VEQGYEETERRLVLKDIFNVLNETEKSVIH--YIFEENLNQKDTGERLGISQ 235

Query: 267 ERVRQIEARAFKKVQES 283
             V +I+ +A  K++++
Sbjct: 236 MHVSRIKRQAISKLKQA 252


>gi|218232670|ref|YP_002365766.1| RNA polymerase sigma factor SigB [Bacillus cereus B4264]
 gi|218160627|gb|ACK60619.1| RNA polymerase sigma-B factor [Bacillus cereus B4264]
          Length = 257

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 54/265 (20%), Positives = 119/265 (44%), Gaps = 17/265 (6%)

Query: 22  EIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           EI+  P  L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++ 
Sbjct: 2   EIQSQPTNLTKEDVIKLIADFQQNQCDEAQERLVNHYKNLVYSIAYRYSKGGPMHEDIIQ 61

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
            G +GL+ A++++D   G     +++  I   +++Y+      + +      +R+     
Sbjct: 62  VGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRIKDLGG 116

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSS 198
           ++K  ++ +TD   +  +++ IA  L +SE EV+ +          SL+ ++ +S   SS
Sbjct: 117 KIKLAIEELTDRFQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENSSDGSS 176

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
             +   V +       + +  E   RR +L    +VLN  E+ +      +   +  ++ 
Sbjct: 177 VARIESVGE-------VEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGEN--LNQKDT 227

Query: 259 SSEFEVSRERVRQIEARAFKKVQES 283
                +S+  V +I+ +A  K++++
Sbjct: 228 GERLGISQMHVSRIKRQAISKLKQA 252


>gi|30019159|ref|NP_830790.1| RNA polymerase sigma factor SigB [Bacillus cereus ATCC 14579]
 gi|29894702|gb|AAP07991.1| RNA polymerase sigma-B factor [Bacillus cereus ATCC 14579]
          Length = 258

 Score =  146 bits (369), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 51/257 (19%), Positives = 116/257 (45%), Gaps = 16/257 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++  G +GL+ 
Sbjct: 11  LTKEDVIKLIADFQQNQCDEAQERLVEHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLG 70

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++++D   G     +++  I   +++Y+      + +      +R+     ++K  ++ 
Sbjct: 71  AIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRIKDLGGKIKLAIEE 125

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +TD+  +  +++ IA  L +SE EV+ +          SL+ ++ +S   SS  +   V 
Sbjct: 126 LTDHLQRSPRIIEIANHLGLSEEEVLEIMDAKNNYRVSSLDDVVENSSDGSSVARIESVG 185

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           +       + +  E   RR +L    +VLN  E+ +      +   +  ++      +S+
Sbjct: 186 E-------VEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGEN--LNQKDTGERLGISQ 236

Query: 267 ERVRQIEARAFKKVQES 283
             V +I+ +A  K++++
Sbjct: 237 MHVSRIKRQAISKLKQA 253


>gi|167745425|ref|ZP_02417552.1| hypothetical protein ANACAC_00116 [Anaerostipes caccae DSM 14662]
 gi|317473026|ref|ZP_07932327.1| RNA polymerase sigma-70 factor [Anaerostipes sp. 3_2_56FAA]
 gi|167655146|gb|EDR99275.1| hypothetical protein ANACAC_00116 [Anaerostipes caccae DSM 14662]
 gi|316899509|gb|EFV21522.1| RNA polymerase sigma-70 factor [Anaerostipes sp. 3_2_56FAA]
          Length = 241

 Score =  146 bits (368), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 45/253 (17%), Positives = 108/253 (42%), Gaps = 17/253 (6%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            E   L K  +E GD  A  ++V  ++ L+  +   + G G    ++   G+IGL++AV 
Sbjct: 2   DETRELLKLTKE-GDQDAREKIVLDNMGLIWSVVKRFTGRGHEPEDLFQIGSIGLLKAVD 60

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD     + +TY++  I   ++ ++     ++K+  +  +        +++   +A   
Sbjct: 61  KFDLSYDVKFSTYAVPMITGEIKRFLRDDG-MIKVSRSLKEIAY-----QVRQAGEAFAM 114

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +   +  ++++  ++  E++         ES+      SD +     D L  + +  
Sbjct: 115 KYNREATIDELSRETKIARDEIVVALEANKDVESIYQPSYQSDDSQVLLVDKLPGEENES 174

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           + V+           ML   M  L+  ER +   R    +  T + ++ +  +S+ +V +
Sbjct: 175 DTVI--------NHVMLEELMDTLSGDERELITMRYF--HGKTQQEIAKKLSISQVQVSR 224

Query: 272 IEARAFKKVQESI 284
           +E +   ++++ I
Sbjct: 225 MEKKILLRMRKQI 237


>gi|296506459|ref|YP_003667693.1| RNA polymerase sigma-43 factor [Bacillus thuringiensis BMB171]
 gi|296327046|gb|ADH09973.1| RNA polymerase sigma-43 factor [Bacillus thuringiensis BMB171]
          Length = 323

 Score =  146 bits (368), Expect = 4e-33,   Method: Composition-based stats.
 Identities = 65/266 (24%), Positives = 113/266 (42%), Gaps = 13/266 (4%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP--ISEVVSEGN 83
             +L K+E   L KRY+ HG+      L   +  LV+ IA  Y+         ++V EGN
Sbjct: 46  YKVLSKEESLHLFKRYK-HGEKDLRDYLFHVNEGLVLSIARNYKNKHPDIEFDDLVQEGN 104

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRL 142
            G+++A++ F+P+ G+  +TY+ WWI+ +M   I  +     KI T  NQ  L +     
Sbjct: 105 EGMLRAMEDFNPDLGYCFSTYAFWWIQKSMLGIIRKKKSGPFKIPTHVNQFNLKYV---- 160

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
                       +   V  + K+LNV+   VI          ++   I++ +++      
Sbjct: 161 -ELEDKYLQRYNRTPSVEEVVKELNVTRETVIRHKVYYKRATTMTLDIDTINEDVGISTP 219

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPVTLE-NLSS 260
           +   D            E  N    L     VLNP+++ +      L +  V L   ++ 
Sbjct: 220 FF-DDRSAIPSTNEMIIEDLNYEIWLIFD-EVLNPKQKMVLNLCFGLLDGKVYLHKEIAK 277

Query: 261 EFEVSRERVRQIEARAFKKVQESIQK 286
              ++ ERV QI+  A KK+++   K
Sbjct: 278 ALMITTERVSQIKDEAIKKLKKCQHK 303


>gi|225862940|ref|YP_002748318.1| RNA polymerase sigma-B factor [Bacillus cereus 03BB102]
 gi|225786058|gb|ACO26275.1| RNA polymerase sigma-B factor [Bacillus cereus 03BB102]
          Length = 257

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 51/257 (19%), Positives = 117/257 (45%), Gaps = 16/257 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++  G +GL+ 
Sbjct: 10  LTKEDVIKLIAEFQQNQCGEAQERLVNHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLG 69

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++++D   G     +++  I   +++Y+      + +      +R+     ++K  ++ 
Sbjct: 70  AIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRIKDLGGKIKLAIEE 124

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +TD+  +  +++ IA  L +SE EV+ +          SL+ ++ ++   SS  +   V 
Sbjct: 125 LTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENASDGSSVARIESVG 184

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           +       + +  E   RR +L    +VLN  E+ +     + E  +  ++      +S+
Sbjct: 185 E-------VEQGYEETERRLVLKDIFNVLNETEKSVIH--YIFEENLNQKDTGERLGISQ 235

Query: 267 ERVRQIEARAFKKVQES 283
             V +I+ +A  K++++
Sbjct: 236 MHVSRIKRQAISKLKQA 252


>gi|49183950|ref|YP_027202.1| RNA polymerase sigma factor SigB [Bacillus anthracis str. Sterne]
 gi|49177877|gb|AAT53253.1| RNA polymerase sigma-B factor [Bacillus anthracis str. Sterne]
          Length = 258

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 51/257 (19%), Positives = 118/257 (45%), Gaps = 16/257 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++  G +GL+ 
Sbjct: 11  LTKEDVIKLIAEFQQNQCGEAQERLVDHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLG 70

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++++D   G     +++  I   +++Y+      + +      +R+     ++K  ++ 
Sbjct: 71  AIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRIKDLGGKIKLAIEE 125

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +TD+  +  +++ IA  L +SE EV+ +          SL+ ++ ++   SS  +   V 
Sbjct: 126 LTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENASDGSSVARIESVG 185

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           +       + +  E+  RR +L    +VLN  E+ +     + E  +  ++      +S+
Sbjct: 186 E-------VEQGYEQTERRLVLKDIFNVLNETEKSVIH--YIFEENLNQKDTGERLGISQ 236

Query: 267 ERVRQIEARAFKKVQES 283
             V +I+ +A  K++++
Sbjct: 237 MHVSRIKRQAISKLKQA 253


>gi|321309570|ref|YP_004191899.1| RNA polymerase sigma factor rpoD [Mycoplasma haemofelis str.
           Langford 1]
 gi|319801414|emb|CBY92060.1| RNA polymerase sigma factor rpoD [Mycoplasma haemofelis str.
           Langford 1]
          Length = 524

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 56/250 (22%), Positives = 108/250 (43%), Gaps = 16/250 (6%)

Query: 17  SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--AAHRLVTSHLRLVVKIAMGYRGYGLP 74
             ++  +    ML  +EE  LAK   ++ DL   A  +L+TS+LRLV+ IA  Y   G  
Sbjct: 202 KSFLSTLHFSKMLTAEEERKLAKLM-DNPDLRPFAVKQLMTSNLRLVISIAKKYLNRGFS 260

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + ++V EG  GLM++++KFD + G + +TY+ WWI+ ++   I     +++I     +  
Sbjct: 261 LGDLVQEGVFGLMKSIQKFDYKFGNKFSTYATWWIRQSITRAIADQARIIRIPVHMVE-- 318

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKK--LNVSESEVISMNCRLAGDESLNALINS 192
           +     + +  L          EQ+    +K     +  +V  +        SL+  I  
Sbjct: 319 VINKFVKAEKDLILKNGEEPTIEQLAQEMQKYSPQYTVQKVSDIKKLNIDLVSLDKPIAH 378

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQEN 251
           ++  +S + D++  +     +   E     ++  +L   + S L   E  +         
Sbjct: 379 NE--TSNFSDFVQDEEAASSE---EVAASTHKSMVLQEFLESTLEDDELLMIHMHYGLME 433

Query: 252 ---PVTLENL 258
              P T+E +
Sbjct: 434 YKSPHTIEQI 443


>gi|326775534|ref|ZP_08234799.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
 gi|326655867|gb|EGE40713.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
          Length = 292

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 47/239 (19%), Positives = 99/239 (41%), Gaps = 16/239 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + L+  +L LV   A  +R  G   + +++  G IGL++A+ +F+  R     ++++ 
Sbjct: 63  ARNTLIEMNLSLVHFAAKRFRNRGSGEMEDIIQVGTIGLIKAIDRFELSREVEFTSFAIP 122

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +I   ++ +   S   V +     + R+      L    +A++    +   V  +A  L 
Sbjct: 123 YIVGEIKRFFRDSTWAVHVPRRLQELRVT-----LAKTREALSTRLDREPTVAELAHHLE 177

Query: 168 VSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           ++E EVI       G    SL+  I +   ++       +         L+E        
Sbjct: 178 LTEEEVIEGLIAANGYTAGSLDLPIGADQNSAETVTYGDIKGDVDPAMELVEDL------ 231

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + L   +  L+ RER I   R  +E  +T   +     +S+  V ++ +R   K+++ +
Sbjct: 232 HTLAPLLEQLDEREREIVAMRFGRE--MTQAQIGEHLGISQMHVSRLLSRLLTKLRKDM 288


>gi|282862754|ref|ZP_06271815.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
 gi|282562440|gb|EFB67981.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
          Length = 298

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 58/241 (24%), Positives = 105/241 (43%), Gaps = 20/241 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYG-LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + L+  +L LV   A  +R  G     +++  G IGL++A+ +FD  R    AT+++ 
Sbjct: 69  ARNTLIEMNLSLVRYAASRFRNRGGDDTEDIIQVGTIGLIKAIDRFDLSREVEFATFAVP 128

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +I   ++ +   +   V +     + R+   L + K  L A  D +     V  +A  L+
Sbjct: 129 YIVGEIKRFFRDTTWSVHVPRRLQELRV--ELAKAKETLSAQLDRD---PTVAELATHLD 183

Query: 168 VSESEVISMNCRLAGDE--SLNALINSSDKNSSQ--WQDWLVYDHDGQEQVLIEKEERKN 223
           + E E+I       G    SL+     S+  + Q  + D L  D  G E V         
Sbjct: 184 LPEEEIIEGLVAANGYSAGSLDTPSADSESGNEQRAYADLLGEDDPGMESV--------E 235

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             + L   +  L+ RER I   R  QE  +T   + +E  VS+  V ++ +R  ++++  
Sbjct: 236 NLHALAPLLRQLDDRERTIVRMRFGQE--MTQAQIGAELGVSQMHVSRLLSRIVQRLRTG 293

Query: 284 I 284
           +
Sbjct: 294 M 294


>gi|196035080|ref|ZP_03102486.1| RNA polymerase sigma-B factor [Bacillus cereus W]
 gi|195992144|gb|EDX56106.1| RNA polymerase sigma-B factor [Bacillus cereus W]
          Length = 257

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 51/257 (19%), Positives = 118/257 (45%), Gaps = 16/257 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++  G +GL+ 
Sbjct: 10  LTKEDVIKLIAEFQQNQCGEAQERLVDHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLG 69

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++++D   G     +++  I   +++Y+      + +      +R+     ++K  ++ 
Sbjct: 70  AIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRIKDLGGKIKLAIEE 124

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +TD+  +  +++ IA  L +SE EV+ +          SL+ ++ ++   SS  +   V 
Sbjct: 125 LTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENASDGSSVARIESVG 184

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           +       + +  E+  RR +L    +VLN  E+ +     + E  +  ++      +S+
Sbjct: 185 E-------VEQGYEQTERRLVLEDIFNVLNETEKSVIH--YIFEENLNQKDTGERLGISQ 235

Query: 267 ERVRQIEARAFKKVQES 283
             V +I+ +A  K++++
Sbjct: 236 MHVSRIKRQAISKLKQA 252


>gi|320010407|gb|ADW05257.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 326

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 52/238 (21%), Positives = 99/238 (41%), Gaps = 18/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            + LV  +L LV   A  +R    P+ ++V  G IGL++A+ +F+  RG    T++M  I
Sbjct: 100 RNTLVELNLALVKFAASRFRTRSEPMEDIVQVGTIGLIKAIDRFELSRGVEFPTFAMPTI 159

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      ++    +   V  +A +L +S
Sbjct: 160 VGEIKRFFRDTSWSVRVPRRLQELRLD-----LAKAGDELSQQLDRAPTVAELADRLGLS 214

Query: 170 ESEVIS--MNCRLAGDESLNA-LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             EV+            SL+A   +  D N     D L Y+ +G E +            
Sbjct: 215 RDEVVEGMAASNAYTASSLDAKPDDHGDGNEGALADRLGYEDNGLEGI--------EYIE 266

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   ++ L  R+R I   R +    +T   +  E  +S+  V ++ +R   K+++ +
Sbjct: 267 SLKPLIASLPLRDRTILSMRFVSN--MTQSEIGEELGISQMHVSRLLSRTLVKLRKGL 322


>gi|302559792|ref|ZP_07312134.1| RNA polymerase sigma-F factor [Streptomyces griseoflavus Tu4000]
 gi|302477410|gb|EFL40503.1| RNA polymerase sigma-F factor [Streptomyces griseoflavus Tu4000]
          Length = 298

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 55/234 (23%), Positives = 103/234 (44%), Gaps = 15/234 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDPERG +  T++M  +
Sbjct: 75  RAALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQFPTFAMPTV 134

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ Y   +   V +      +RL     ++    + +T    +      IA++L +S
Sbjct: 135 VGEIKRYFRDNVRTVHVP-----RRLHELWVQVNSATEDLTTAFGRSPSTAEIAERLRIS 189

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E EV+S         + +              D L Y+    + V          R+++ 
Sbjct: 190 EDEVLSCIEAGRSYHATSLEAAQEGDGMPGLLDRLGYEDPALDGV--------EHRDLVR 241

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +  L  RE+RI   R      +T   +S+E  VS+  V ++ AR+F++++ +
Sbjct: 242 HLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLLARSFQRLRSA 293


>gi|323345486|ref|ZP_08085709.1| RNA polymerase sigma-43 factor [Prevotella oralis ATCC 33269]
 gi|323093600|gb|EFZ36178.1| RNA polymerase sigma-43 factor [Prevotella oralis ATCC 33269]
          Length = 238

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 67/276 (24%), Positives = 115/276 (41%), Gaps = 48/276 (17%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
            G+  +  Y+ EI    +L   EE  LA++ + +GD +A  RL  ++L+ VV IA  Y+ 
Sbjct: 4   TGKSSMKLYLDEIGGESLLTSLEEMKLAEKIQ-NGDEAALERLTKANLKFVVFIAKQYQH 62

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            G+ + ++VSEGNIGL+ A KK+ P +  R A ++  +I+  +++ +LR  +        
Sbjct: 63  QGVDMEDLVSEGNIGLLYAAKKYTPSKEKRFAPFAAPFIRKQIEQLLLRQGA-------D 115

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
           +Q RL                                       S+        S+ A I
Sbjct: 116 SQSRLSA-------------------------------------SLTSESKKVVSVEAPI 138

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-Q 249
            +  +NS      L   +       I  E  K     L R   VL+ R++++        
Sbjct: 139 PAGSRNSFNLLHVLKDTNALMADEHINDESFKAELERLMRR--VLDQRQQQVISLFFGIG 196

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
               TL  +     + RERVRQI  +A +K+++  +
Sbjct: 197 CEKHTLMEIGDFMNLKRERVRQIRDKALQKIRKIAK 232


>gi|305644356|gb|ADM53779.1| RNA polymerase sigma factor [Aeromonas hydrophila]
          Length = 176

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 42/186 (22%), Positives = 77/186 (41%), Gaps = 12/186 (6%)

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+  
Sbjct: 1   GLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISR 58

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            +         PE    +A ++ + E ++  +        S+   I   D   S   D++
Sbjct: 59  QMLQEMGREPNPE---ELAMRMGMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI 113

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEF 262
               D    +  +    ++ RN     ++ L  RE ++   R   +     TLE +  +F
Sbjct: 114 ---EDTTLALPADAATSESLRNATREVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQF 170

Query: 263 EVSRER 268
           +V+ ER
Sbjct: 171 DVTWER 176


>gi|222094730|ref|YP_002528790.1| RNA polymerase sigma factor sigb [Bacillus cereus Q1]
 gi|221238788|gb|ACM11498.1| RNA polymerase sigma-B factor [Bacillus cereus Q1]
          Length = 257

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 50/257 (19%), Positives = 115/257 (44%), Gaps = 16/257 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++  G +GL+ 
Sbjct: 10  LTKEDVMKLIAEFQQNQCDEAQERLVEHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLG 69

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++++D   G     +++  I   +++Y+      + +      +R+     ++K  ++ 
Sbjct: 70  AIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRIKDLGGKIKLAIEE 124

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +TD   +  +++ IA  L +SE EV+ +          SL+ ++ ++   SS  +   V 
Sbjct: 125 LTDRLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENASDGSSVARIESVG 184

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           +       + +  E   RR +L    +VLN  E+ +      +   +  ++      +S+
Sbjct: 185 E-------VEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGEN--LNQKDTGERLGISQ 235

Query: 267 ERVRQIEARAFKKVQES 283
             V +I+ +A  K++++
Sbjct: 236 MHVSRIKRQAISKLKQA 252


>gi|302525186|ref|ZP_07277528.1| RNA polymerase sigma-G factor [Streptomyces sp. AA4]
 gi|302434081|gb|EFL05897.1| RNA polymerase sigma-G factor [Streptomyces sp. AA4]
          Length = 282

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 57/259 (22%), Positives = 109/259 (42%), Gaps = 21/259 (8%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG----LPISEVVSEGNIGLMQAV 90
             L +++ +  D ++  RLV  +  LV  +A    G G    + + ++V  G  GL+ A+
Sbjct: 36  QALWQQFADKPDQTSRDRLVLHYAPLVKYVAGR-VGTGLPTHVDVGDLVQSGIFGLVDAI 94

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +KFDPERG R  TY+M  I+ A+ + +      V     +  K     L RL   L    
Sbjct: 95  EKFDPERGLRFETYAMQRIRGAILDDLRSQ-DWVPRAVRSKAKETARALERLGARLH--- 150

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
               +      +A ++ +S  ++       RL    +L  L+ +  K++    D L  D 
Sbjct: 151 ----RTPTDAELAGEMGISLDDLRDFYGQLRLTSVVALEDLVAAG-KDAGSLVDTLPDDG 205

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
                 ++     ++ R  L  +++ L  R++ +          +TL  +     V+  R
Sbjct: 206 AVDPVAVL---VDQDNRRQLAEAIAQLTDRDKIVVSLYYF--ESLTLAEIGKVLGVTESR 260

Query: 269 VRQIEARAFKKVQESIQKQ 287
           V Q+  RA  +++  + +Q
Sbjct: 261 VSQLHTRAVMRLRAKLMEQ 279


>gi|225376836|ref|ZP_03754057.1| hypothetical protein ROSEINA2194_02478 [Roseburia inulinivorans DSM
           16841]
 gi|225211332|gb|EEG93686.1| hypothetical protein ROSEINA2194_02478 [Roseburia inulinivorans DSM
           16841]
          Length = 244

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 45/246 (18%), Positives = 102/246 (41%), Gaps = 11/246 (4%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R  + GD  A  ++V+ +L LV  I   +   G    E+   G IGL++A+  FD     
Sbjct: 9   RQAQDGDKKARDKVVSDNLGLVHAIVRRFEKRGHDREELFQIGCIGLIKAIDHFDLSLNL 68

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
             +TY++  I   ++ ++     +VK+  +  +     N  ++    + +T    +   +
Sbjct: 69  AFSTYAVPMITGEIRRFLRDDG-MVKVSRSLKE-----NGYKISRAKEVLTTELGRDPSL 122

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           + ++    +   E++       G ES+   +  SD +     D +    D  E+   E  
Sbjct: 123 LELSAMTELGTEEIVMALDANRGVESIYQPVCGSDGDELLLIDQIGDQSDVYEEPEKEAV 182

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
             K    ++ + M  L+  E++I   R  +    T   ++    V++ ++ + E +   K
Sbjct: 183 LNKM---VIRQLMDTLDETEQQIIRLRYFEN--KTQCEVAGILAVTQVQISRNERKILAK 237

Query: 280 VQESIQ 285
           ++  ++
Sbjct: 238 LRAKLE 243


>gi|168333394|ref|ZP_02691674.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family protein
           [Epulopiscium sp. 'N.t. morphotype B']
          Length = 249

 Score =  146 bits (368), Expect = 5e-33,   Method: Composition-based stats.
 Identities = 57/253 (22%), Positives = 117/253 (46%), Gaps = 18/253 (7%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           E+  L     + GD+SA   LV  +L LV  +   +   G  + ++   G+IGL+++++K
Sbjct: 11  EKTRLLILKAQGGDISAKELLVEQNLGLVWSLVKRFTNRGYDLDDLFQVGSIGLLKSIEK 70

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD +     +TY++  I   ++ ++     L+K+  +   K L    R +K   +     
Sbjct: 71  FDLKYPVAFSTYAVPMIVGEIKRFLRDDG-LIKVSRSL--KDLASKARNVK---EDFQRQ 124

Query: 153 NLKPEQVVAIAKKLNVSESEV-ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
             +   +  I+  LNV   E+ +S+   +   ESLNA++N +   +    + +    D Q
Sbjct: 125 ENREPTLKEISDILNVPCEEIAVSLEANM-EVESLNAVVNPNSSATITLAEKIDQSPDEQ 183

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           + +             L   +  L+  ER+I   R  ++  +T   +++   VS+ ++ +
Sbjct: 184 KNIFEN--------IYLKEIIKTLSSVERQIVNYRYFED--LTQLEIANRLGVSQVQISR 233

Query: 272 IEARAFKKVQESI 284
           IE R  +K+++SI
Sbjct: 234 IEKRVLEKLRQSI 246


>gi|54401898|gb|AAV34634.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274877|gb|AAV49241.1| RNA polymerase subunit sigma-38 [Escherichia albertii]
 gi|55274996|gb|AAV49295.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 201

 Score =  146 bits (368), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 56/211 (26%), Positives = 101/211 (47%), Gaps = 12/211 (5%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           ++  I+     +++      K L   LR  +     ++           IA++L+    +
Sbjct: 61  IERAIMNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDD 115

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           V  M        S++  +    + +      L    D +E    +  +  + +  + + +
Sbjct: 116 VSRMLRLNERITSVDTPLGGDSEKA-----LLDILADEKENGPEDTTQDDDMKQSIVKWL 170

Query: 233 SVLNPRERRIFEARR--LQENPVTLENLSSE 261
             LN ++R +   R   L     TLE++  E
Sbjct: 171 FELNAKQREVLARRFGLLGYEAATLEDVGRE 201


>gi|240146182|ref|ZP_04744783.1| RNA polymerase sigma-F factor [Roseburia intestinalis L1-82]
 gi|257201716|gb|EEV00001.1| RNA polymerase sigma-F factor [Roseburia intestinalis L1-82]
 gi|291536709|emb|CBL09821.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase
           sigma-70 factor, sigma-B/F/G subfamily [Roseburia
           intestinalis M50/1]
          Length = 248

 Score =  146 bits (368), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 49/240 (20%), Positives = 100/240 (41%), Gaps = 10/240 (4%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A   L+  +L LV  IA  +   G    E+   G IGLM+AV KFD       +TY
Sbjct: 14  GDKGARDTLIAGNLGLVHTIANRFEHRGHEREELFQIGCIGLMKAVDKFDLSLNLAFSTY 73

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           ++  I   ++ ++     +VK+  T  +     N  +     + +     +   ++ IA+
Sbjct: 74  AVPVIMGEIRRFLRDDG-MVKVSRTLKE-----NAYKAGRAKEELWGELGREPGLLEIAE 127

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +  +S  E+I         ES+   +   D +     D L    +       +  E    
Sbjct: 128 RTGLSSGEIIMAMESARDVESIYQPVYEKDGDELLMVDQLCEKEENGRDEPEK--EAVLN 185

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R ++ + M +L+ RE+ +   R  +    T    + E  +++ +V ++E +    +++++
Sbjct: 186 RMVIEQLMELLDEREQNLIRCRYFEN--RTQSETAKELGMTQVQVSRLEKKILLCLRKNL 243


>gi|320105081|ref|YP_004180672.1| RNA polymerase sigma-32 subunit RpoH [Isosphaera pallida ATCC
           43644]
 gi|319752363|gb|ADV64123.1| RNA polymerase, sigma 32 subunit, RpoH [Isosphaera pallida ATCC
           43644]
          Length = 322

 Score =  145 bits (367), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 62/241 (25%), Positives = 117/241 (48%), Gaps = 20/241 (8%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
               +L  +++RLV  +A  +R  G+  S+++ EG  GL++A+ +FD   G +LATY+ W
Sbjct: 90  ELRSKLALANMRLVAHVAKRFRDRGVSYSDLLQEGFCGLLEAIDRFDLAHGTKLATYATW 149

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ AMQ  +  +   V++           +LR+L  + + I +   +P      + + +
Sbjct: 150 WIRQAMQRAVAATAYPVRLS--------PRHLRQLARNQEEI-ERGGQPRTRKKASDEES 200

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           VS   +  ++       SL+A +   D +SS      + D +G     ++ +E       
Sbjct: 201 VSPEMIQRIHAATRPTVSLDATV---DSDSSFSLLHTMSDPEGDRTGEVDMDET------ 251

Query: 228 LTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + + M  L PRE ++   R         +L  +    +VS+ERVRQI+ RA +K++  +Q
Sbjct: 252 IVKLMENLRPREIQVLSLRFGLNGATRHSLSQVGKVLDVSKERVRQIQDRALEKLRLCVQ 311

Query: 286 K 286
           +
Sbjct: 312 E 312


>gi|49480184|ref|YP_035252.1| RNA polymerase sigma factor SigB [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|49331740|gb|AAT62386.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           konkukian str. 97-27]
          Length = 258

 Score =  145 bits (367), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 51/257 (19%), Positives = 117/257 (45%), Gaps = 16/257 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++  G +GL+ 
Sbjct: 11  LTKEDVIKLIAEFQQNQCDEAQERLVDHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLG 70

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++++D   G     +++  I   +++Y+      + +      +R+     ++K  ++ 
Sbjct: 71  AIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRIKDLGGKIKLAIEE 125

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +TD+  +  +++ IA  L +SE EV+ +          SL+ ++ ++   SS  +   V 
Sbjct: 126 LTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENASDGSSVARIESVG 185

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           +       + +  E   RR +L    +VLN  E+ +     + E  +  ++      +S+
Sbjct: 186 E-------VEQGYEETERRLVLKDIFNVLNETEKSVIH--YIFEENLNQKDTGERLGISQ 236

Query: 267 ERVRQIEARAFKKVQES 283
             V +I+ +A  K++++
Sbjct: 237 MHVSRIKRQAISKLKQA 253


>gi|307564926|ref|ZP_07627446.1| sigma-70, region 4 [Prevotella amnii CRIS 21A-A]
 gi|307346366|gb|EFN91683.1| sigma-70, region 4 [Prevotella amnii CRIS 21A-A]
          Length = 228

 Score =  145 bits (367), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 63/270 (23%), Positives = 115/270 (42%), Gaps = 47/270 (17%)

Query: 17  SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
            +YI +I    +L  +EE  L+ R +  GD  A  +L  ++L  VV IA  Y+  GL   
Sbjct: 5   EKYIGDIIGENLLSDEEEVQLSNRIK-IGDAKALEKLTKANLTFVVSIAHQYKEQGLDED 63

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++SEGNIG+M A +KFD  +G R   ++  +I+ A+++ I    +L K+     + +LF
Sbjct: 64  DLISEGNIGMMYAAQKFDGSKGIRFVKFAAPYIRKAIEKSIKEQTTLYKVP--KKENKLF 121

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
              R                                        A   SL+  I     N
Sbjct: 122 EKKR----------------------------------------AKPVSLDQPIPVGSNN 141

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF-EARRLQENPVTL 255
               Q+ +  +++       +         +L +S++ LN RE+ +  +   +    +T+
Sbjct: 142 KLTLQNLIPNNNNKDTD---DSVNSNILNTILMQSINCLNEREKAVITQLYGINGTSLTM 198

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             +++   + RERVRQI   A +K+   ++
Sbjct: 199 AEVATSLGLKRERVRQIRNTALRKLYRKMR 228


>gi|297200782|ref|ZP_06918179.1| RNA polymerase sigma-E factor [Streptomyces sviceus ATCC 29083]
 gi|197712352|gb|EDY56386.1| RNA polymerase sigma-E factor [Streptomyces sviceus ATCC 29083]
          Length = 285

 Score =  145 bits (367), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 53/234 (22%), Positives = 104/234 (44%), Gaps = 15/234 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+ ++L LV   A  +R    P+ +V+  G IGL+ A+ +FDP+RG +  T++M  +
Sbjct: 62  RTALIEANLPLVRYAAARFRSRNEPMEDVIQVGTIGLINAIDRFDPDRGVQFPTFAMPTV 121

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ Y   +   V +      +RL     ++ G  + +T    +      IA++L ++
Sbjct: 122 VGEIKRYFRDNVRTVHVP-----RRLHELWVQVNGATEDLTTAFGRTPTTAEIAQRLRIT 176

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E EV+S         + +              D L Y+    + V          R+++ 
Sbjct: 177 EDEVLSCIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALDGV--------EHRDLVR 228

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +  L  RE+RI   R      +T   +S+E  VS+  V ++ AR+F++++ +
Sbjct: 229 HLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLLARSFQRLRSA 280


>gi|52144331|ref|YP_082499.1| RNA polymerase sigma factor SigB [Bacillus cereus E33L]
 gi|51977800|gb|AAU19350.1| RNA polymerase sigma-B factor [Bacillus cereus E33L]
          Length = 258

 Score =  145 bits (367), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 51/257 (19%), Positives = 118/257 (45%), Gaps = 16/257 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++  G +GL+ 
Sbjct: 11  LTKEDVIKLIAEFQQNQCGEAQERLVDHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLG 70

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++++D   G     +++  I   +++Y+      + +      +R+     ++K  ++ 
Sbjct: 71  AIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRIKDLGGKIKLAIEE 125

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +TD+  +  +++ IA  L +SE EV+ +          SL+ ++ ++   SS  +   V 
Sbjct: 126 LTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENASDGSSVARIESVG 185

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           +       + +  E+  RR +L    +VLN  E+ +     + E  +  ++      +S+
Sbjct: 186 E-------VEQGYEQTERRLVLEDIFNVLNETEKSVIH--YIFEENLNQKDTGERLGISQ 236

Query: 267 ERVRQIEARAFKKVQES 283
             V +I+ +A  K++++
Sbjct: 237 MHVSRIKRQAISKLKQA 253


>gi|297158638|gb|ADI08350.1| RNA polymerase sigma factor, sigma F [Streptomyces bingchenggensis
           BCW-1]
          Length = 277

 Score =  145 bits (367), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 56/241 (23%), Positives = 105/241 (43%), Gaps = 17/241 (7%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           EHG       L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDPERG +  
Sbjct: 49  EHG--RVRDALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQFP 106

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           T++M  +   ++ Y   +   V +      +RL     ++ G  + +T  + +      I
Sbjct: 107 TFAMPTVVGEIKRYFRDNVRTVHVP-----RRLHELWVQVNGATEDLTVLHGRSPTTAEI 161

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A++L + E EV++         + +              D L Y+      V        
Sbjct: 162 AERLGLGEDEVLACIEAGRSYHATSLEAAQEGDGLPGLVDRLGYEDPALAGV-------- 213

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             R+++   +  L  RE+RI   R      +T   +S+E  VS+  V ++ +R+F +++ 
Sbjct: 214 EHRDLVRHLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLLSRSFARLRS 271

Query: 283 S 283
           +
Sbjct: 272 A 272


>gi|196044126|ref|ZP_03111362.1| RNA polymerase sigma-B factor [Bacillus cereus 03BB108]
 gi|218902186|ref|YP_002450020.1| RNA polymerase sigma-B factor [Bacillus cereus AH820]
 gi|196024765|gb|EDX63436.1| RNA polymerase sigma-B factor [Bacillus cereus 03BB108]
 gi|218534787|gb|ACK87185.1| RNA polymerase sigma-B factor [Bacillus cereus AH820]
          Length = 257

 Score =  145 bits (367), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 51/257 (19%), Positives = 117/257 (45%), Gaps = 16/257 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++  G +GL+ 
Sbjct: 10  LTKEDVIKLIAEFQQNQCGEAQERLVDHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLG 69

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++++D   G     +++  I   +++Y+      + +      +R+     ++K  ++ 
Sbjct: 70  AIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRIKDLGGKIKLAIEE 124

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +TD+  +  +++ IA  L +SE EV+ +          SL+ ++ ++   SS  +   V 
Sbjct: 125 LTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENASDGSSVARIESVG 184

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           +       + +  E   RR +L    +VLN  E+ +     + E  +  ++      +S+
Sbjct: 185 E-------VEQGYEETERRLVLKDIFNVLNETEKSVIH--YIFEENLNQKDTGERLGISQ 235

Query: 267 ERVRQIEARAFKKVQES 283
             V +I+ +A  K++++
Sbjct: 236 MHVSRIKRQAISKLKQA 252


>gi|300783890|ref|YP_003764181.1| RNA polymerase sigma factor [Amycolatopsis mediterranei U32]
 gi|299793404|gb|ADJ43779.1| RNA polymerase sigma factor [Amycolatopsis mediterranei U32]
          Length = 282

 Score =  145 bits (367), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 56/258 (21%), Positives = 109/258 (42%), Gaps = 21/258 (8%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG----LPISEVVSEGNIGLMQAVK 91
            L +++ +  D ++  RLV  +  LV  +A    G G    + + ++V  G  GL+ A++
Sbjct: 37  ALWQQFADSPDQASRDRLVLHYAPLVKYVAGR-VGTGLPTHIDVGDLVQSGIFGLVDAIE 95

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFDPERG R  TY+M  I+ A+ + +      V     +  K     + RL   L     
Sbjct: 96  KFDPERGLRFETYAMQRIRGAILDDLRSQ-DWVPRAVRSKAKEAERAMERLGARLH---- 150

Query: 152 NNLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
              +      +A +L +   ++       +L    +L  L+ +  K+S    D L  D  
Sbjct: 151 ---RTPTDAELAAELGIGLDDLRDFYGQLQLTSVVALEDLVAAG-KDSGSLVDTLPDDDA 206

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
                ++     ++ R  L ++++ L  R++ +          +TL  +     V+  RV
Sbjct: 207 VDPVAVL---VDQDNRRQLAQAIAQLTERDKIVVSLYYF--ESLTLAEIGKVLGVTESRV 261

Query: 270 RQIEARAFKKVQESIQKQ 287
            Q+  RA  +++  + +Q
Sbjct: 262 SQLHTRAVMRLRAKLVEQ 279


>gi|161898849|gb|ABX80414.1| SigB [Listeria monocytogenes]
          Length = 236

 Score =  145 bits (367), Expect = 6e-33,   Method: Composition-based stats.
 Identities = 57/253 (22%), Positives = 112/253 (44%), Gaps = 25/253 (9%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 3   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 62

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G     +++  I   ++ ++      V +     +        ++K  ++ +T    
Sbjct: 63  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQ 117

Query: 155 KPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +    
Sbjct: 118 SSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTD 174

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++S+  
Sbjct: 175 DGF--------ERVNQRMLLEKVLPVLDEREQKILQFTFIEN--RSQKETGELLDISQMH 224

Query: 269 VRQIEARAFKKVQ 281
           V +I+ +A  K++
Sbjct: 225 VSRIQRQAI-KLR 236


>gi|54401892|gb|AAV34631.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 200

 Score =  145 bits (367), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 56/210 (26%), Positives = 101/210 (48%), Gaps = 12/210 (5%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+ 
Sbjct: 1   RMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQ 60

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            ++  I+     +++      K L   LR  +     ++           IA++L+    
Sbjct: 61  TIERAIMNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVD 115

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           +V  M        S++  +    +     +  L    D +E    +  +  + +  + + 
Sbjct: 116 DVSRMLRLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKW 170

Query: 232 MSVLNPRERRIFEARR--LQENPVTLENLS 259
           +  LN ++R +   R   L     TLE++ 
Sbjct: 171 LFELNAKQREVLARRFGLLGYEAATLEDVG 200


>gi|226325489|ref|ZP_03801007.1| hypothetical protein COPCOM_03294 [Coprococcus comes ATCC 27758]
 gi|225206232|gb|EEG88586.1| hypothetical protein COPCOM_03294 [Coprococcus comes ATCC 27758]
          Length = 239

 Score =  145 bits (367), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 49/252 (19%), Positives = 109/252 (43%), Gaps = 17/252 (6%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             L +R  E GD +A  +LV  +  L+  +   + G G    ++   G+IGL++A+ KFD
Sbjct: 5   IALIRRAHE-GDENARAQLVEENTGLIWCVVKRFYGRGTEAEDLFQIGSIGLLKAIDKFD 63

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
                + +TY++  I   ++ ++     ++K+  +  +        +     +A+T+   
Sbjct: 64  LGYDVKFSTYAVPMITGEIKRFLRDDG-MLKVSRSLKEIAY-----KAYQAKEALTEKLG 117

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +   +  IA++  V + E++         ESL+  +   D N     + +      +E++
Sbjct: 118 REPLLEEIAEETGVEKEELVMAMEAAGEVESLHRPVGMKDGNEVMLLEKIADTGGAEEKI 177

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
           L           +LT  +  L   ER++   R   +   T   +  E  +S+ +V ++E 
Sbjct: 178 L--------DHLLLTELIKELKKDERKLLYLRYFAD--KTQTEIGEELGISQVQVSRMEK 227

Query: 275 RAFKKVQESIQK 286
           +  K ++E  ++
Sbjct: 228 KILKTMREHAKE 239


>gi|161898905|gb|ABX80442.1| SigB [Listeria monocytogenes]
          Length = 236

 Score =  145 bits (367), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 57/250 (22%), Positives = 110/250 (44%), Gaps = 24/250 (9%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 3   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 62

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G     +++  I   ++ ++      V +     +        ++K  ++ +T    
Sbjct: 63  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQ 117

Query: 155 KPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +    
Sbjct: 118 SSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTD 174

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++S+  
Sbjct: 175 DGF--------ERVNQRMLLEKVLPVLDEREQKILQFTFIEN--RSQKETGELLDISQMH 224

Query: 269 VRQIEARAFK 278
           V +I+ +A K
Sbjct: 225 VSRIQRQAIK 234


>gi|308172341|ref|YP_003919046.1| RNA polymerase sigma-37 factor sigma B [Bacillus amyloliquefaciens
           DSM 7]
 gi|307605205|emb|CBI41576.1| RNA polymerase sigma-37 factor (sigma(B)) [Bacillus
           amyloliquefaciens DSM 7]
 gi|328552153|gb|AEB22645.1| RNA polymerase sigma factor SigB [Bacillus amyloliquefaciens TA208]
 gi|328910426|gb|AEB62022.1| RNA polymerase sigma-37 factor (sigma(B)) [Bacillus
           amyloliquefaciens LL3]
          Length = 262

 Score =  145 bits (367), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 60/267 (22%), Positives = 115/267 (43%), Gaps = 24/267 (8%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K   L K E   L   ++ H +  A   LV  +  LV  +A  Y        ++   G 
Sbjct: 5   SKTTKLTKDEVDRLILDFQIHDNKEAQETLVEVYTNLVEMLAKKYSKGKSFHEDLRQVGM 64

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL+ A+K++DPE G     +++  I   ++ ++      V +     +        R+K
Sbjct: 65  IGLLGAIKRYDPEVGKSFEAFAIPTIIGEIKRFLRDKTWSVHVPRRIKELG-----PRIK 119

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNS 197
             +  +T    +  +V  IA  L+VSE EV+           L+ D S+ A    +D ++
Sbjct: 120 MAVDQLTTETQRSPKVEEIAAFLDVSEEEVLETMEMGKSYQALSVDHSIEA---DADGST 176

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
               D +    +G         ER N++ M+   + VL+ RE++I +   +Q    + + 
Sbjct: 177 VTILDIVGSQEEGY--------ERVNQQMMIKSVLHVLSDREKQIIDLTFVQN--KSQKE 226

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESI 284
                 +S+  V +++ +A KK++E++
Sbjct: 227 TGDILGISQMHVSRLQRKAVKKLREAL 253


>gi|167040197|ref|YP_001663182.1| FliA/WhiG family RNA polymerase sigma factor [Thermoanaerobacter
           sp. X514]
 gi|300914281|ref|ZP_07131597.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacter sp.
           X561]
 gi|307265137|ref|ZP_07546696.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacter wiegelii
           Rt8.B1]
 gi|307724483|ref|YP_003904234.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter sp. X513]
 gi|326391064|ref|ZP_08212611.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacter
           ethanolicus JW 200]
 gi|166854437|gb|ABY92846.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Thermoanaerobacter sp. X514]
 gi|300889216|gb|EFK84362.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacter sp.
           X561]
 gi|306919759|gb|EFN49974.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacter wiegelii
           Rt8.B1]
 gi|307581544|gb|ADN54943.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X513]
 gi|325992849|gb|EGD51294.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacter
           ethanolicus JW 200]
          Length = 246

 Score =  145 bits (366), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 51/255 (20%), Positives = 117/255 (45%), Gaps = 19/255 (7%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            E   L +  +++ D  +  +L+  +  L+  I   +   G  + ++   G IG ++A++
Sbjct: 10  DENLELIRAAQKN-DKESLEKLILENSGLIWSIVKKFSNRGYELEDLYQIGCIGFVKAIQ 68

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD     +L+TY++  I   ++ ++     L+K+  +  +        +     + +++
Sbjct: 69  KFDESYNVKLSTYAVPIIMGEIKRFLRDDG-LIKVSRSLKELSTKAFYVK-----EILSN 122

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +   +  IA++LNVS  E+       A  ESL       +       D L+ +   +
Sbjct: 123 ELNREPTINEIAERLNVSPEEIAMAFESAATAESLYDNATHDED------DRLLIEMVSE 176

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E    EKE   + +  L   ++ L PRE++I   R  ++  +T   ++S   +S+ +V +
Sbjct: 177 E----EKEVDIDDKLALQMVINKLKPREKQIIFLRYFKD--MTQMEVASVLGISQVQVSR 230

Query: 272 IEARAFKKVQESIQK 286
           IE +  +K+++ +++
Sbjct: 231 IEKKVLQKLRKELEE 245


>gi|281425346|ref|ZP_06256259.1| RNA polymerase sigma-43 factor [Prevotella oris F0302]
 gi|281400509|gb|EFB31340.1| RNA polymerase sigma-43 factor [Prevotella oris F0302]
          Length = 252

 Score =  145 bits (366), Expect = 7e-33,   Method: Composition-based stats.
 Identities = 62/281 (22%), Positives = 113/281 (40%), Gaps = 50/281 (17%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD--LSAAHRLVTSHLRL 60
           +    +       L+ Y++EI K  +L   EE  L+++    G     A  +L +++LR 
Sbjct: 5   KTGKPLSERESESLNIYLNEIGKETILSDDEEKQLSQQIMAGGAAAEQAIGKLTSANLRF 64

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y   G+ I +++SEGNIGLM+A + FD  RG R   Y+  +++ A++  +   
Sbjct: 65  VVSIAKQYVDRGVAILDLISEGNIGLMKAARSFDGSRGLRFVGYAEPFVRKAVEAAVNEQ 124

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
             + ++    +      N R                                        
Sbjct: 125 SGIFRLPKHEHSAEEKANSRAF-------------------------------------- 146

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               S++A + +      +  + L    D       ++    + +  L  +M++L+ RER
Sbjct: 147 ----SVDAPLQNG-----KNVNLLSILSDPTAARPDQEALETSVKEELLEAMNILDNRER 197

Query: 241 RIFEARRLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
            + EA      P  T   +  +  + RERVRQI  +A +K+
Sbjct: 198 NVVEAFYGIGQPHLTFAEIGEKMGLKRERVRQIRNKAVRKL 238


>gi|118476614|ref|YP_893765.1| RNA polymerase sigma factor SigB [Bacillus thuringiensis str. Al
           Hakam]
 gi|301052635|ref|YP_003790846.1| sigma factor B [Bacillus anthracis CI]
 gi|118415839|gb|ABK84258.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Bacillus thuringiensis
           str. Al Hakam]
 gi|300374804|gb|ADK03708.1| sigma factor B [Bacillus cereus biovar anthracis str. CI]
          Length = 258

 Score =  145 bits (366), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 51/257 (19%), Positives = 117/257 (45%), Gaps = 16/257 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++  G +GL+ 
Sbjct: 11  LTKEDVIKLIAEFQQNQCGEAQERLVDHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLG 70

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++++D   G     +++  I   +++Y+      + +      +R+     ++K  ++ 
Sbjct: 71  AIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRIKDLGGKIKLAIEE 125

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +TD+  +  +++ IA  L +SE EV+ +          SL+ ++ ++   SS  +   V 
Sbjct: 126 LTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENASDGSSVARIESVG 185

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           +       + +  E   RR +L    +VLN  E+ +     + E  +  ++      +S+
Sbjct: 186 E-------VEQGYEETERRLVLKDIFNVLNETEKSVIH--YIFEENLNQKDTGERLGISQ 236

Query: 267 ERVRQIEARAFKKVQES 283
             V +I+ +A  K++++
Sbjct: 237 MHVSRIKRQAISKLKQA 253


>gi|85706634|ref|ZP_01037726.1| RNA polymerase sigma subunit [Roseovarius sp. 217]
 gi|85668692|gb|EAQ23561.1| RNA polymerase sigma subunit [Roseovarius sp. 217]
          Length = 830

 Score =  145 bits (366), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 51/245 (20%), Positives = 103/245 (42%), Gaps = 27/245 (11%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            SA   L+  HL  V + A      G    +V     +GL ++ ++FDPERG+R   Y+ 
Sbjct: 497 ESATEHLIREHLPYVRRFASRNVEEGEEPEDVFQVAFMGLQRSTRRFDPERGYRFLIYAT 556

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           +W++ A+  +     + ++I    N+K       +L   L  +          + +A++L
Sbjct: 557 YWMRQAIMRWRADEGAAIRIPVHRNEKVT-----KLDRALDRLDVRVGGAVSDLDLAEEL 611

Query: 167 NVSESEVIS---MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
             +  EV     +  +     SL+                  +D+   E   ++  ++  
Sbjct: 612 EWAIDEVRQFRCIPRKAEYPASLDD-----------------WDNLLPEPSEVDVLDQAE 654

Query: 224 RRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              ++T +++ L  R+  +   R     ++ +TLE +   + V+RER+RQIEA+    + 
Sbjct: 655 TERIVTEALADLPERQADVIRMRFGIGHDSEMTLEEIGQIYGVTRERIRQIEAKGLDLLS 714

Query: 282 ESIQK 286
              +K
Sbjct: 715 HPGRK 719


>gi|327441148|dbj|BAK17513.1| DNA-directed RNA polymerase specialized sigma subunit [Solibacillus
           silvestris StLB046]
          Length = 256

 Score =  145 bits (366), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 50/260 (19%), Positives = 108/260 (41%), Gaps = 18/260 (6%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L+  E   L  R ++ G+     +LV  +LRLV+ I   Y   G    ++   G IG
Sbjct: 15  LPVLKPDEMKDLFIRLQQ-GEWIVREQLVFCNLRLVLSIVGRYAYRGEQADDLFQVGCIG 73

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A+  FD +   R +TY++  I   ++ ++    +   +  + + + + +   + K  
Sbjct: 74  LLKAIDNFDLKHNVRFSTYAVPMIMGEIRRHLRDHHA---LRVSRSLRDIAYKAMKAK-- 128

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            +     +L    +  +A+ + + + +V+     +    SL   I S   ++    D + 
Sbjct: 129 -EQFIAEHLTEPTIEQLAQAIEMKKEDVLFALDAIQDPMSLQEPIYSDGGDAIFMIDQIK 187

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
                        EE       L  SM  LN R++ I E R       T   ++    +S
Sbjct: 188 DKV---------TEEHWVGSISLQESMKKLNSRQKMIIEKRFFLGE--TQTEIAQSLGIS 236

Query: 266 RERVRQIEARAFKKVQESIQ 285
           + ++ ++E  A + ++   +
Sbjct: 237 QAQISRLEKSAVELMKRDFR 256


>gi|239945848|ref|ZP_04697785.1| putative RNA polymerase sigma factor [Streptomyces roseosporus NRRL
           15998]
 gi|239992317|ref|ZP_04712981.1| putative RNA polymerase sigma factor [Streptomyces roseosporus NRRL
           11379]
 gi|291449304|ref|ZP_06588694.1| sigma factor [Streptomyces roseosporus NRRL 15998]
 gi|291352251|gb|EFE79155.1| sigma factor [Streptomyces roseosporus NRRL 15998]
          Length = 298

 Score =  145 bits (366), Expect = 8e-33,   Method: Composition-based stats.
 Identities = 58/242 (23%), Positives = 109/242 (45%), Gaps = 12/242 (4%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYG-LPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           H    A + L+  +L LV   A  +R  G     +++  G IGL++A+ +FD  R    A
Sbjct: 64  HEHQYARNTLIEMNLSLVRFAASRFRNRGGDDTEDIIQVGTIGLIKAIDRFDLSREVEFA 123

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           T+++ +I   ++ +   +   V +     + R+  +L + K  L A  D +     V  +
Sbjct: 124 TFAVPYIVGEIKRFFRDTTWSVHVPRRLQELRV--DLAKAKEQLSAELDRD---PTVKEL 178

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A  L++ E E+I       G  + +    S+D +S Q Q     D  G+    +E  E  
Sbjct: 179 ATHLDLPEEEIIEGLVAANGYSAGSLDTPSADSDSGQEQRAYA-DVLGEADPGMETVE-- 235

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              + L   +  L+ RERRI + R   E  +T   +  E  VS+  V ++ +R  +++++
Sbjct: 236 -NLHTLAPLLEQLDDRERRIVQMRFGAE--MTQSQIGEELGVSQMHVSRLLSRIVQQLRK 292

Query: 283 SI 284
            +
Sbjct: 293 GM 294


>gi|297193426|ref|ZP_06910824.1| RNA polymerase sigma-F factor [Streptomyces pristinaespiralis ATCC
           25486]
 gi|197723191|gb|EDY67099.1| RNA polymerase sigma-F factor [Streptomyces pristinaespiralis ATCC
           25486]
          Length = 282

 Score =  145 bits (366), Expect = 9e-33,   Method: Composition-based stats.
 Identities = 53/234 (22%), Positives = 101/234 (43%), Gaps = 15/234 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDP+RG +  T++M  +
Sbjct: 59  RAALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFPTFAMPTV 118

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ Y   +   V +      +RL     ++ G  + +T  + +      IA++L + 
Sbjct: 119 VGEIKRYFRDNVRTVHVP-----RRLHELWVQVNGATEDLTTAHGRSPTTAEIAERLKIG 173

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E EV++         + +              D L Y+      V          R+++ 
Sbjct: 174 EDEVLACIEAGRSYHATSLEAAQEGDGMPGLLDRLGYEDPALAGV--------EHRDLVR 225

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +  L  RE+RI   R      +T   +S E  VS+  V ++ AR+F +++ +
Sbjct: 226 HLLVQLPEREQRILMLRYYSN--LTQSQISQELGVSQMHVSRLLARSFARLRSA 277


>gi|182435018|ref|YP_001822737.1| putative RNA polymerase sigma factor [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|178463534|dbj|BAG18054.1| putative RNA polymerase sigma factor [Streptomyces griseus subsp.
           griseus NBRC 13350]
          Length = 292

 Score =  145 bits (366), Expect = 9e-33,   Method: Composition-based stats.
 Identities = 47/239 (19%), Positives = 99/239 (41%), Gaps = 16/239 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + L+  +L LV   A  +R  G   + +++  G IGL++A+ +F+  R     ++++ 
Sbjct: 63  ARNTLIEMNLSLVHFAAKRFRNRGSGEMEDIIQVGTIGLIKAIDRFELSREVEFTSFAIP 122

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +I   ++ +   S   V +     + R+      L    +A++    +   V  +A  L 
Sbjct: 123 YIVGEIKRFFRDSTWAVHVPRRLQELRVT-----LAKTREALSTRLDREPTVAELAHHLE 177

Query: 168 VSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           ++E EVI       G    SL+  I +   ++       +         L+E        
Sbjct: 178 LTEEEVIEGLIAANGYTAGSLDLPIGADQNSAETVTYGDIKGDVDPAMELVEDL------ 231

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + L   +  L+ RER I   R  +E  +T   +     +S+  V ++ +R   K+++ +
Sbjct: 232 HTLAPLLERLDEREREIVAMRFGRE--MTQAQIGEHLGISQMHVSRLLSRLLTKLRKDM 288


>gi|133478|sp|P12254|RPSK_BACSU RecName: Full=RNA polymerase sigma-K factor; AltName:
           Full=Sigma-27; AltName: Full=Stage IV sporulation
           protein CB; Flags: Precursor
          Length = 294

 Score =  145 bits (366), Expect = 9e-33,   Method: Composition-based stats.
 Identities = 54/281 (19%), Positives = 104/281 (37%), Gaps = 19/281 (6%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +  +V   + L  Y+        L   EE    +   + GD  A + L+  +LRLV  I 
Sbjct: 9   LGFVVKELVFLVSYVKNNAFPQPLSSSEEKKYLELMAK-GDEHARNMLIEHNLRLVAHIV 67

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA--MQEYILRSWSL 123
             +   G    +++S G IGL++ ++ +   +G +LATY+   I+    + +      SL
Sbjct: 68  KKFENTGEDAEDLISIGTIGLIKGIESYSAGKGTKLATYAARCIENEIVITKGGCIHPSL 127

Query: 124 VKIGTT-ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           ++            F   ++                   I   L            +   
Sbjct: 128 IRFNIYGVRIHNGNFFHDKVNNCFFIFKSMPPLFVMNNEILMHL--------RALKKTKK 179

Query: 183 DESLNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           D SL+  I    + N     D L  ++    + +I+  +       + + + +L+ RE+ 
Sbjct: 180 DVSLHDPIGQDKEGNEISLIDVLKSEN----EDVIDTIQLNMELEKVKQYIDILDDREKE 235

Query: 242 IFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           +   R   +     T   ++ E  +SR  V +IE RA  K+
Sbjct: 236 VIVGRFGLDLKKEKTQREIAKELGISRSYVSRIEKRALMKM 276


>gi|222151972|ref|YP_002561132.1| sigma factor B [Macrococcus caseolyticus JCSC5402]
 gi|222121101|dbj|BAH18436.1| sigma factor B [Macrococcus caseolyticus JCSC5402]
          Length = 255

 Score =  145 bits (366), Expect = 9e-33,   Method: Composition-based stats.
 Identities = 48/262 (18%), Positives = 111/262 (42%), Gaps = 24/262 (9%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             +E     K Y++  D  A   LV  + +LV  +A  Y        ++V  G +GL+ A
Sbjct: 10  TPEEINAWIKLYQDTQDEFAQKELVLHYQKLVESLAYRYSKGQSHHEDLVQVGMVGLLGA 69

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +FD     +   + +  +   ++ Y+      V +     +        ++K     +
Sbjct: 70  INRFDVTFERKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIG-----PKIKRATDEL 124

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNC------RLAGDESLNALINSSDKNSSQWQDW 203
           T+   +  +++ IA+++  +E EV+           L+ D S+ A     D ++    D 
Sbjct: 125 TNELGRSPKIIEIAQRIEATEEEVLEAMEMGQSYNALSVDHSIEA---DKDGSTVTLLDV 181

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    +G         +   +R +L + + +L+ RER I +   L  + ++ +    +  
Sbjct: 182 MGNTEEGY--------DLTEKRMILEKVLPILSDREREIIQCTFL--DGLSQKETGEKIG 231

Query: 264 VSRERVRQIEARAFKKVQESIQ 285
           +S+  V +++  A KK+++++Q
Sbjct: 232 LSQMHVSRLQRTAIKKLRDAVQ 253


>gi|289578665|ref|YP_003477292.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter italicus Ab9]
 gi|289528378|gb|ADD02730.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter italicus Ab9]
          Length = 241

 Score =  145 bits (366), Expect = 9e-33,   Method: Composition-based stats.
 Identities = 57/264 (21%), Positives = 110/264 (41%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L  +EE  L  +  E GD  A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 39  PPLSVEEETYLVSKM-EKGDNEAKTVLIERNLRLVVYIAKKFENTGVGIEDLISIGTIGL 97

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+  F+P++  +LATY+   I+  +  Y+ R+                          
Sbjct: 98  IKAINTFNPKKKIKLATYASRCIENEILMYLRRNSKT----------------------- 134

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                             KL VS  E ++++                D N     D L  
Sbjct: 135 ------------------KLEVSFEEPLNVD---------------WDGNELLLSDILGT 161

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEV 264
           D++   + + ++ E    R +LT ++  L  RE++I   R   +     T + ++    +
Sbjct: 162 DNETVYKYIEDEVE----RELLTSALKKLPDREKKIIGLRFGLDGGVEKTQKEVADMLGI 217

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E +  K++++ + + +
Sbjct: 218 SQSYISRLEKKILKRLKKEMNRLI 241


>gi|207723755|ref|YP_002254153.1| rna polymerase sigma d (sigma-70) factor protein [Ralstonia
           solanacearum MolK2]
 gi|206588959|emb|CAQ35921.1| rna polymerase sigma d (sigma-70) factor protein [Ralstonia
           solanacearum MolK2]
          Length = 773

 Score =  145 bits (366), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 44/161 (27%), Positives = 74/161 (45%), Gaps = 7/161 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 571 ERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 630

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I            + R+   +   T N   P     +
Sbjct: 631 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGNEPDPAT---L 685

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
           A+K+ + E ++  +        S+   I   D + S   D+
Sbjct: 686 AEKMEMPEDKIRKIMKIAKEPISMKTPI--GDDDDSHLGDF 724


>gi|282863441|ref|ZP_06272500.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
 gi|282561776|gb|EFB67319.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
          Length = 285

 Score =  144 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 56/234 (23%), Positives = 104/234 (44%), Gaps = 15/234 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDPERG +  T++M  +
Sbjct: 62  RTALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQFPTFAMPTV 121

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ Y   +   V +      +RL     ++ G  + +T  + +      IA++L +S
Sbjct: 122 VGEIKRYFRDNVRTVHVP-----RRLHELWVQVTGATEDLTTAHGRSPTTAEIAQRLKIS 176

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E EV++         + +              D L Y+      V          R+++ 
Sbjct: 177 EEEVLACIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALAGV--------EHRDLVR 228

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +  L  RE+RI   R    N +T   +S+E  VS+  V ++ AR+F +++ +
Sbjct: 229 HLLVQLPEREQRILLLRYY--NNLTQSQISAELGVSQMHVSRLLARSFARLRSA 280


>gi|55274913|gb|AAV49258.1| RNA polymerase subunit sigma-38 [Escherichia coli]
 gi|55274972|gb|AAV49285.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 200

 Score =  144 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 55/210 (26%), Positives = 100/210 (47%), Gaps = 12/210 (5%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           ++  I+     +++      K L   LR  +     ++           IA++L+    +
Sbjct: 61  IERAIMNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDD 115

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           V  M        S++  +    +     +  L    D +E    +  +  + +  + + +
Sbjct: 116 VSRMLRLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWL 170

Query: 233 SVLNPRERRIFEARR--LQENPVTLENLSS 260
             LN ++R +   R   L     TLE++  
Sbjct: 171 FELNAKQREVLARRFGLLGYEAATLEDVGR 200


>gi|108804196|ref|YP_644133.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108765439|gb|ABG04321.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 258

 Score =  144 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 56/265 (21%), Positives = 106/265 (40%), Gaps = 17/265 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
              P  +K     L +RY   GD  A  +++   L L   +A  + G G P+ ++V   +
Sbjct: 3   GGYPRPDKARTRRLLERYHREGDRQAREQVIQEQLPLAEFLARKFAGRGEPLEDLVQVAS 62

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           +GL++AV +FD +R    +TY+   I   ++ +       +++     + R     + +K
Sbjct: 63  VGLIKAVDRFDVDRNIEFSTYATPNILGEIKRHFRDKGWAMRVPRGLQELR-----QAVK 117

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC--RLAGDESLNALINSSDKNSSQWQ 201
             ++  T    +   +  +A++L+     V       R     SL+A I+  D       
Sbjct: 118 EAIREETVRTGRSPTMDELAERLDTDVESVAEALTLGRAYNTTSLDAPISQDDAEGDTIM 177

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           D         E   IE  E K    +L  +M  L  ++R I   R       T   ++  
Sbjct: 178 DLQAD-----ENQPIEGIEDKL---LLQEAMRGLREQQREILRLRF--NEGKTQTEIAER 227

Query: 262 FEVSRERVRQIEARAFKKVQESIQK 286
             VS+  V ++  RA   ++ S+ +
Sbjct: 228 IGVSQMHVSRLLRRAIADLRRSLSE 252


>gi|167037236|ref|YP_001664814.1| sporulation sigma factor SigE [Thermoanaerobacter pseudethanolicus
           ATCC 33223]
 gi|307266545|ref|ZP_07548078.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|307267688|ref|ZP_07549142.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|320115655|ref|YP_004185814.1| RNA polymerase sigma-E factor [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
 gi|326392136|ref|ZP_08213613.1| RNA polymerase, sigma 28 subunit, SigE [Thermoanaerobacter
           ethanolicus JW 200]
 gi|166856070|gb|ABY94478.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Thermoanaerobacter pseudethanolicus ATCC 33223]
 gi|306917290|gb|EFN47610.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|306918464|gb|EFN48705.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|319928746|gb|ADV79431.1| RNA polymerase sigma-E factor [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
 gi|325991823|gb|EGD50338.1| RNA polymerase, sigma 28 subunit, SigE [Thermoanaerobacter
           ethanolicus JW 200]
          Length = 241

 Score =  144 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 57/262 (21%), Positives = 109/262 (41%), Gaps = 63/262 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L  +EE  L  +  E GD  A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 39  PPLSVEEEIYLISKM-EKGDNEAKTVLIERNLRLVVYIAKKFENTGVGIEDLISIGTIGL 97

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+  F+P++  +LATY+   I+  +  Y+ R+                          
Sbjct: 98  IKAINTFNPKKKIKLATYASRCIENEILMYLRRNSKT----------------------- 134

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                             KL VS  E ++++                D N     D L  
Sbjct: 135 ------------------KLEVSFDEPLNVD---------------WDGNELLLSDILGT 161

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEV 264
           D++   + + ++ E    + +LT ++  L  RE++I   R   E     T + ++    +
Sbjct: 162 DNETVYKYIEDEVE----KELLTSALKKLPDREKKIIGLRFGLEGGVEKTQKEVADMLGI 217

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+  + ++E +  K++++ + +
Sbjct: 218 SQSYISRLEKKILKRLKKEMNR 239


>gi|161898837|gb|ABX80408.1| SigB [Listeria monocytogenes]
          Length = 236

 Score =  144 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 57/250 (22%), Positives = 110/250 (44%), Gaps = 24/250 (9%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 3   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 62

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G     +++  I   ++ ++      V +     +        ++K  ++ +T    
Sbjct: 63  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVKELTRELQ 117

Query: 155 KPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +    
Sbjct: 118 SSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTD 174

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++S+  
Sbjct: 175 DGF--------ERVNQRMLLEKVLPVLDEREQKILQFTFIEN--RSQKETGELLDISQMH 224

Query: 269 VRQIEARAFK 278
           V +I+ +A K
Sbjct: 225 VSRIQRQAIK 234


>gi|320009625|gb|ADW04475.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 285

 Score =  144 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 56/234 (23%), Positives = 104/234 (44%), Gaps = 15/234 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDPERG +  T++M  +
Sbjct: 62  RTALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQFPTFAMPTV 121

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ Y   +   V +      +RL     ++ G  + +T  + +      IA++L +S
Sbjct: 122 VGEIKRYFRDNVRTVHVP-----RRLHELWVQVTGATEDLTTAHGRSPTTGEIAERLKIS 176

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E EV++         + +              D L Y+      V          R+++ 
Sbjct: 177 EDEVLACIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALAGV--------EHRDLVR 228

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +  L  RE+RI   R    N +T   +S+E  VS+  V ++ AR+F +++ +
Sbjct: 229 HLLVQLPEREQRILLLRYY--NNLTQSQISAELGVSQMHVSRLLARSFARLRSA 280


>gi|207723156|ref|YP_002253555.1| sigma factor, ecf;peptidase aspartic, active site;;; protein
           [Ralstonia solanacearum MolK2]
 gi|206588350|emb|CAQ35313.1| sigma factor, ecf;peptidase aspartic, active site;;; protein
           [Ralstonia solanacearum MolK2]
          Length = 229

 Score =  144 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 52/201 (25%), Positives = 92/201 (45%), Gaps = 10/201 (4%)

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++KFDPERGFR +TY+ WWI+ +++  I+     V++       R    + R K HL+ 
Sbjct: 29  AIEKFDPERGFRFSTYATWWIRQSIERAIMNQARTVRLPVHV--IRELNQVLRAKRHLEK 86

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
            +  + +   +  IA  L  +  EV  +        SL+          +   D+L  +H
Sbjct: 87  -SGIDGRDASIEDIAHLLGKTTEEVQDVLSLNEHTTSLDTPF--DLDPGTSLLDFLSDEH 143

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSR 266
                   ++   +    ++   ++ L+ + R + E R       P TLE L++E  ++R
Sbjct: 144 GASPD---QEVAHRELSQLMKSWLARLSDKHRYVVERRFGLNHIEPATLEELAAEMGLTR 200

Query: 267 ERVRQIEARAFKKVQESIQKQ 287
           ERVRQI+  A  K++     Q
Sbjct: 201 ERVRQIQQEALVKLKRHFASQ 221


>gi|182437344|ref|YP_001825063.1| RNA polymerase sigma factor, sigma F [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|326777954|ref|ZP_08237219.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
 gi|178465860|dbj|BAG20380.1| RNA polymerase sigma factor, sigma F [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|326658287|gb|EGE43133.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
          Length = 292

 Score =  144 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 54/237 (22%), Positives = 103/237 (43%), Gaps = 15/237 (6%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                 L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDP+RG +  T++M
Sbjct: 66  RRVRTALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFPTFAM 125

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +   ++ Y   +   V +      +RL     ++ G  + +T  + +      IA++L
Sbjct: 126 PTVVGEIKRYFRDNVRTVHVP-----RRLHELWVQVTGATEDLTTAHGRSPTTAEIAERL 180

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +SE EV++         + +              D L Y+      V          R+
Sbjct: 181 KISEDEVLACIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALAGV--------EHRD 232

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           ++   +  L  RE+RI   R      +T   +S+E  VS+  V ++ AR+F +++ +
Sbjct: 233 LVRHLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLLARSFARLRSA 287


>gi|29830728|ref|NP_825362.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29607841|dbj|BAC71897.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 309

 Score =  144 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 53/234 (22%), Positives = 102/234 (43%), Gaps = 15/234 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDP+RG +  T++M  +
Sbjct: 86  RGALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFPTFAMPTV 145

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ Y   +   V +      +RL     ++    + +T    +      IA++L ++
Sbjct: 146 VGEIKRYFRDNVRTVHVP-----RRLHELWVQVNSATEDLTTAFGRSPTTAEIAERLRIT 200

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E EV+S         + +              D L Y+    + V          R+++ 
Sbjct: 201 EEEVLSCIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALDGV--------EHRDLVR 252

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +  L  RE+RI   R      +T   +S+E  VS+  V ++ AR+F +++ +
Sbjct: 253 HLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLLARSFARLRSA 304


>gi|154503257|ref|ZP_02040317.1| hypothetical protein RUMGNA_01081 [Ruminococcus gnavus ATCC 29149]
 gi|153796251|gb|EDN78671.1| hypothetical protein RUMGNA_01081 [Ruminococcus gnavus ATCC 29149]
          Length = 238

 Score =  144 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 46/239 (19%), Positives = 107/239 (44%), Gaps = 16/239 (6%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           +GD  A  +LV  ++ L+  +   + G G+   ++   G+IGL++A+ KFD     + +T
Sbjct: 13  NGDKEAREQLVEENIGLIWCVVKRFYGRGIEAEDLFQIGSIGLIKAIDKFDLSYDVKFST 72

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y++  I   ++ ++     ++K+  +  +        R+    + +TD   +   +  ++
Sbjct: 73  YAVPMISGEIKRFLRDDG-MIKVSRSLKELSY-----RIFQTREKMTDGLGREPTLEELS 126

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           +++ V + E++         ESL   I+  + +     D L             +EE+  
Sbjct: 127 QEMGVEKEELVQAMEASGEVESLYRPIHQKEGSEISLLDKLEEKE--------HREEKIL 178

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            R +L + +  L+ +ER +   R   E   T   +  E  +S+ +V ++E +  + ++E
Sbjct: 179 DRMLLGQLLEKLDGQERTLIYLRYFAE--KTQSAVGKEMGISQVQVSRMEKKIIQNLRE 235


>gi|4102217|gb|AAD11814.1| sigma-like factor [Streptomyces sp. A21]
          Length = 343

 Score =  144 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 59/241 (24%), Positives = 107/241 (44%), Gaps = 20/241 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYG-LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + L+  +L LV   A  +R  G     +++  G IGL++A+ +FD  R    AT+++ 
Sbjct: 114 ARNTLIEMNLSLVRFAASRFRNRGGDDTEDIIQVGTIGLIKAIDRFDLSREVEFATFAVP 173

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +I   ++ +   +   V +     + R+   L + K  L A  D +     V  +A +L+
Sbjct: 174 YIVGEIKRFFRDTTWSVHVPRRLQELRV--ELAKAKEALSADLDRD---PTVAELAARLD 228

Query: 168 VSESEVISMNCRLAGDE--SLNALINSSDKNSSQ--WQDWLVYDHDGQEQVLIEKEERKN 223
           +SE E+I       G    SL+     S+  + Q  + D L  D  G E V         
Sbjct: 229 LSEEEIIEGLVAANGYSAGSLDTPSADSESGNEQRAYADLLGEDDPGMESV--------E 280

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             + L   +  L+ RER I   R  QE  +T   + +E  VS+  V ++ +R  ++++  
Sbjct: 281 NLHALAPLLRQLDDRERAIVRMRFGQE--MTQAQIGAELGVSQMHVSRLLSRIVRRLRTG 338

Query: 284 I 284
           +
Sbjct: 339 M 339


>gi|206975667|ref|ZP_03236579.1| RNA polymerase sigma-B factor [Bacillus cereus H3081.97]
 gi|206746129|gb|EDZ57524.1| RNA polymerase sigma-B factor [Bacillus cereus H3081.97]
          Length = 257

 Score =  144 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 51/257 (19%), Positives = 116/257 (45%), Gaps = 16/257 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++  G +GL+ 
Sbjct: 10  LTKEDVIKLIAEFQQNQCDEAQERLVDHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLG 69

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++++D   G     +++  I   +++Y+      + +      +R+     ++K  ++ 
Sbjct: 70  AIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRIKDLGGKIKLAIEE 124

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +TD   +  +++ IA  L +SE EV+ +          SL+ ++ ++   SS  +   V 
Sbjct: 125 LTDCLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENASDGSSVARIESVG 184

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           +       + +  E   RR +L    +VLN  E+ +     + E  +  ++      +S+
Sbjct: 185 E-------VEQGYEETERRLVLKDIFNVLNETEKSVIH--YIFEENLNQKDTGERLGISQ 235

Query: 267 ERVRQIEARAFKKVQES 283
             V +I+ +A  K++++
Sbjct: 236 MHVSRIKRQAISKLKQA 252


>gi|55274978|gb|AAV49288.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 200

 Score =  144 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 56/210 (26%), Positives = 100/210 (47%), Gaps = 12/210 (5%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           + S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  +
Sbjct: 1   IESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTI 60

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
           +  I+     +++      K L   LR  +     ++           IA++L+    +V
Sbjct: 61  ERAIMNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDV 115

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             M        S++  +    +     +  L    D +E    +  +  + +  + + + 
Sbjct: 116 SRMLRLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWLF 170

Query: 234 VLNPRERRIFEARR--LQENPVTLENLSSE 261
            LN ++R +   R   L     TLE++  E
Sbjct: 171 ELNAKQREVLARRFGLLGYEAATLEDVGRE 200


>gi|299141532|ref|ZP_07034668.1| RNA polymerase sigma-70 factor [Prevotella oris C735]
 gi|298576868|gb|EFI48738.1| RNA polymerase sigma-70 factor [Prevotella oris C735]
          Length = 252

 Score =  144 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 62/281 (22%), Positives = 113/281 (40%), Gaps = 50/281 (17%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGD--LSAAHRLVTSHLRL 60
           +    +       L+ Y++EI K  +L   EE  L+++    G     A  +L +++LR 
Sbjct: 5   KTGKPLSERESESLNIYLNEIGKETILSDDEEKQLSQQIMAGGAAAERAIGKLTSANLRF 64

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  Y   G+ I +++SEGNIGLM+A + FD  RG R   Y+  +++ A++  +   
Sbjct: 65  VVSIAKQYVDRGVAILDLISEGNIGLMKAARSFDGSRGLRFVGYAEPFVRKAVEAAVNEQ 124

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
             + ++    +      N R                                        
Sbjct: 125 SGIFRLPKHEHSAEEKANSRAF-------------------------------------- 146

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               S++A + +      +  + L    D       ++    + +  L  +M++L+ RER
Sbjct: 147 ----SVDAPLQNG-----KNVNLLSILSDPTAARPDQEALETSVKEELLEAMNILDNRER 197

Query: 241 RIFEARRLQENPV-TLENLSSEFEVSRERVRQIEARAFKKV 280
            + EA      P  T   +  +  + RERVRQI  +A +K+
Sbjct: 198 NVVEAFYGIGQPHLTFAEIGEKMGLKRERVRQIRNKAVRKL 238


>gi|197303315|ref|ZP_03168355.1| hypothetical protein RUMLAC_02038 [Ruminococcus lactaris ATCC
           29176]
 gi|197297599|gb|EDY32159.1| hypothetical protein RUMLAC_02038 [Ruminococcus lactaris ATCC
           29176]
          Length = 237

 Score =  144 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 50/245 (20%), Positives = 109/245 (44%), Gaps = 16/245 (6%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R   HGD  A  +LV  ++ LV  +   + G G    ++   G+IGL++A+ KFD     
Sbjct: 9   RKSHHGDKEAREQLVKENVGLVWCVVKRFYGRGAEPEDLFQIGSIGLLKAIDKFDLSYDV 68

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY++  I   ++ ++     ++K+  +   K+L +   + K   + +T+   +   +
Sbjct: 69  QFSTYAVPMISGEIRRFLRDDG-MIKVSRSL--KKLSYKCGKKK---EELTERMGREPTM 122

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +A  L   + E++         ES+   I+    +     D L      +E +L    
Sbjct: 123 EELATSLGTEKEELVQAMEAATEVESIYRPIHQEGDSQLSILDRLEEKSRPEEHLL---- 178

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
                R ML++ +  L+  ER++   R  QE   T   +     +S+ +V ++E +  ++
Sbjct: 179 ----NRMMLSQILDGLDKEERQLIYLRYFQE--KTQAAVGEILGISQVQVSRMEKKILER 232

Query: 280 VQESI 284
           +++ +
Sbjct: 233 MRKQM 237


>gi|294813860|ref|ZP_06772503.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|326442278|ref|ZP_08217012.1| RNA polymerase sigma factor, sigma F [Streptomyces clavuligerus
           ATCC 27064]
 gi|294326459|gb|EFG08102.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 335

 Score =  144 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 53/234 (22%), Positives = 101/234 (43%), Gaps = 15/234 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDP+RG +  T++M  +
Sbjct: 112 RGALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFPTFAMPTV 171

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ Y   +   V +      +RL     ++ G  + +T  + +      IA++L + 
Sbjct: 172 VGEIKRYFRDNVRTVHVP-----RRLHELWVQVNGATEDLTTAHGRIPTTAEIAERLRIG 226

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E EV++         + +              D L Y+      V          R+++ 
Sbjct: 227 EDEVLACIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALAGV--------EHRDLVR 278

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +  L  RE+RI   R      +T   +S E  VS+  V ++ AR+F +++ +
Sbjct: 279 HLLVQLPEREQRILMLRYYSN--LTQSQISQELGVSQMHVSRLLARSFARLRSA 330


>gi|290959143|ref|YP_003490325.1| SigF-like sigma factor [Streptomyces scabiei 87.22]
 gi|260648669|emb|CBG71782.1| SigF-like sigma factor [Streptomyces scabiei 87.22]
          Length = 287

 Score =  144 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 52/234 (22%), Positives = 102/234 (43%), Gaps = 15/234 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDP+RG +  T++M  +
Sbjct: 64  RGALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFPTFAMPTV 123

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ Y   +   V +      +RL     ++    + +T    +      IA++L ++
Sbjct: 124 IGEIKRYFRDNVRTVHVP-----RRLHELWVQVNSATEDLTTAFGRTPSTAEIAERLRIT 178

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E EV+S         + +              D L Y+          + +    R+++ 
Sbjct: 179 EEEVLSCIEAGRSYHATSLEAAQEGDGMPGLLDRLGYEDP--------ELDGVEHRDLVR 230

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +  L  RE+RI   R      +T   +S+E  VS+  V ++ AR+F +++ +
Sbjct: 231 HLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLLARSFARLRSA 282


>gi|254384106|ref|ZP_04999451.1| RNA polymerase sigma-F factor [Streptomyces sp. Mg1]
 gi|194342996|gb|EDX23962.1| RNA polymerase sigma-F factor [Streptomyces sp. Mg1]
          Length = 302

 Score =  144 bits (365), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 54/234 (23%), Positives = 103/234 (44%), Gaps = 15/234 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDP+RG +  T++M  +
Sbjct: 79  RGALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFPTFAMPTV 138

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ Y   +   V +      +RL     ++    + +T  + +      IA++L ++
Sbjct: 139 VGEIKRYFRDNVRTVHVP-----RRLHELWVQVNAATEDLTTLHGRTPTTPEIAERLRIT 193

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E EV+S         + +              D L Y+      V          R+++ 
Sbjct: 194 EEEVLSCIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPELAGV--------EHRDLVR 245

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +  L  RE+RI   R    N +T   +S+E  VS+  V ++ AR+F +++ +
Sbjct: 246 HLLVQLPEREQRILLLRYY--NNLTQSQISAELGVSQMHVSRLLARSFARLRSA 297


>gi|315503089|ref|YP_004081976.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily
           [Micromonospora sp. L5]
 gi|315409708|gb|ADU07825.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Micromonospora sp. L5]
          Length = 273

 Score =  144 bits (364), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 50/240 (20%), Positives = 94/240 (39%), Gaps = 18/240 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +   R + + L L   +A  Y G G P  ++     IGL++A+ KFDP RG   A Y++
Sbjct: 46  PALRDRAIEAWLPLANHLAHRYSGRGEPNDDLAQTAAIGLIKAIDKFDPSRGVDFAGYAI 105

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA--K 164
             I   ++ +       +++     + RL      +      +     +   V  IA   
Sbjct: 106 PTIIGELKRHFRDRTWDIRVPRRLQELRLA-----ISDANSTLLQTLGRSPTVADIAAHL 160

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           KL   E        R     SL+      +  +++  D L  +          + E    
Sbjct: 161 KLTEEEVLEGLEGARAYNAVSLSTPTGDGE-RATELGDLLGGEDG--------EFELAEM 211

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L  +++ L+ RE++I   R      +T   ++ +  VS+  V ++ ARA  K++  +
Sbjct: 212 RVALGPALATLDQREQKILTLRFYGN--LTQSQIAEQIGVSQMHVSRLLARALTKLRGQL 269


>gi|297544885|ref|YP_003677187.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
 gi|296842660|gb|ADH61176.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
          Length = 241

 Score =  144 bits (364), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 57/264 (21%), Positives = 110/264 (41%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L  +EE  L  +  E GD  A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 39  PPLSMEEETYLVSKM-EKGDNEAKTVLIERNLRLVVYIAKKFENTGVGIEDLISIGTIGL 97

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+  F+P++  +LATY+   I+  +  Y+ R+                          
Sbjct: 98  IKAINTFNPKKKIKLATYASRCIENEILMYLRRNSKT----------------------- 134

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                             KL VS  E ++++                D N     D L  
Sbjct: 135 ------------------KLEVSFEEPLNVD---------------WDGNELLLSDILGT 161

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEV 264
           D++   + + ++ E    R +LT ++  L  RE++I   R   +     T + ++    +
Sbjct: 162 DNETVYKYIEDEVE----RELLTSALKKLPDREKKIIGLRFGLDGGVEKTQKEVADMLGI 217

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E +  K++++ + + +
Sbjct: 218 SQSYISRLEKKILKRLKKEMNRLI 241


>gi|160946612|ref|ZP_02093815.1| hypothetical protein PEPMIC_00570 [Parvimonas micra ATCC 33270]
 gi|158446996|gb|EDP23991.1| hypothetical protein PEPMIC_00570 [Parvimonas micra ATCC 33270]
          Length = 254

 Score =  144 bits (364), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 48/257 (18%), Positives = 117/257 (45%), Gaps = 15/257 (5%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           + +E   L + Y E+       +L+  +L +   +A  Y   G+   ++    ++GL+ A
Sbjct: 9   DSEEIKSLFREYFENPTPELRDKLIEKNLYMAEILAKKYVNRGIDYDDLFQVASLGLIYA 68

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + ++D  +GF  ++++M  I   ++ Y      ++++      +R+  N +++      +
Sbjct: 69  IDRYDISKGFEFSSFAMPTIVGEIKRYFRDKGWVIRVP-----RRIQENSKKVNNAKYHL 123

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVYD 207
           T    +   +  IA  + +SE EV+ +    ++   +SL+    S + + S+ +D  + D
Sbjct: 124 TQELGRTPTIKDIADYVELSEEEVLEIMEASKVYTPQSLD---QSFENSDSEDKDTNLID 180

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
             G+E    +  + ++    + +++  L   E++I   R       T   L+ E  +S+ 
Sbjct: 181 IVGEEDKEFDFIDNQDF---IRKTLDKLTEVEKQIILGRYF--EQKTQVALAKELNISQM 235

Query: 268 RVRQIEARAFKKVQESI 284
            V ++E +A  K +E +
Sbjct: 236 TVSRLEKKALAKFREEL 252


>gi|161898841|gb|ABX80410.1| SigB [Listeria monocytogenes]
          Length = 234

 Score =  144 bits (364), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 57/250 (22%), Positives = 110/250 (44%), Gaps = 24/250 (9%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 3   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 62

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G     +++  I   ++ ++      V +     +        ++K  ++ +T    
Sbjct: 63  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVKELTRELQ 117

Query: 155 KPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +    
Sbjct: 118 SSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTD 174

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++S+  
Sbjct: 175 DGF--------ERVNQRMLLEKVLPVLDEREQKILQFTFIEN--RSQKETGELLDISQMH 224

Query: 269 VRQIEARAFK 278
           V +I+ +A K
Sbjct: 225 VSRIQRQAIK 234


>gi|167037535|ref|YP_001665113.1| FliA/WhiG family RNA polymerase sigma factor [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|256752057|ref|ZP_05492925.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|320115950|ref|YP_004186109.1| RNA polymerase sigma-F factor [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
 gi|166856369|gb|ABY94777.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Thermoanaerobacter pseudethanolicus ATCC 33223]
 gi|256749067|gb|EEU62103.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|319929041|gb|ADV79726.1| RNA polymerase sigma-F factor [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
          Length = 246

 Score =  144 bits (364), Expect = 1e-32,   Method: Composition-based stats.
 Identities = 49/255 (19%), Positives = 117/255 (45%), Gaps = 19/255 (7%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            E   L +  +++ D  +  +L+  +  L+  I   +   G  + ++   G IG ++A++
Sbjct: 10  DENLELIRAAQKN-DKESLEKLILENSGLIWSIVKKFSNRGYELEDLYQIGCIGFVKAIQ 68

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD     +L+TY++  I   ++ ++     L+K+  +  +        +     + +++
Sbjct: 69  KFDESYNVKLSTYAVPIIMGEIKRFLRDDG-LIKVSRSLKELSTKAFYVK-----EILSN 122

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +   +  IA++LNVS  E+       A  ESL       +       D L+ +   +
Sbjct: 123 ELNREPTINEIAERLNVSPEEIAMAFESAATAESLYDNATHDED------DKLLIEMVSE 176

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E    EKE   + +  L   ++ L PRE++I   R  ++  +T   +++   +S+ +V +
Sbjct: 177 E----EKEVDIDDKLALQMVINKLKPREKQIIFLRYFKD--MTQMEVANILGISQVQVSR 230

Query: 272 IEARAFKKVQESIQK 286
           +E +  +K+++ +++
Sbjct: 231 LEKKVLQKLRKELEE 245


>gi|55274919|gb|AAV49261.1| RNA polymerase subunit sigma-38 [Shigella flexneri]
          Length = 201

 Score =  144 bits (364), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 55/211 (26%), Positives = 101/211 (47%), Gaps = 12/211 (5%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ S+LRLVVKIA  Y   GL + +++ EG++GL++AV+KFDPERGFR +TY+ WWI+ 
Sbjct: 1   RMIESNLRLVVKIARRYGNRGLALLDLIEEGSLGLIRAVEKFDPERGFRFSTYATWWIRQ 60

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            ++  I+     +++      K L   LR  +     ++           IA++L+    
Sbjct: 61  TIERAIMNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVD 115

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           +V  M        S++  +    + +      L    D +E    +  +  + +  + + 
Sbjct: 116 DVSRMLRLNERITSVDTPLGGDSEKA-----LLDILADEKENGPEDTTQDDDMKQSIVKW 170

Query: 232 MSVLNPRERRIFEARR--LQENPVTLENLSS 260
           +  LN ++R +   R   L     TLE++  
Sbjct: 171 LFELNAKQREVLARRFGLLGYEAATLEDVGR 201


>gi|163941644|ref|YP_001646528.1| sporulation sigma factor SigE [Bacillus weihenstephanensis KBAB4]
 gi|229013089|ref|ZP_04170254.1| RNA polymerase sigma-35 factor [Bacillus mycoides DSM 2048]
 gi|163863841|gb|ABY44900.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           weihenstephanensis KBAB4]
 gi|228748343|gb|EEL98203.1| RNA polymerase sigma-35 factor [Bacillus mycoides DSM 2048]
 gi|322510149|gb|ADX05463.1| RNA polymerase sigma-35 factor [Bacillus mycoides]
          Length = 239

 Score =  144 bits (364), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 67/264 (25%), Positives = 114/264 (43%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL  +   +GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLTKEEEAVLLNKL-PNGDQAARSMLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  ++ R+                          
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMHLRRN-------------------------- 129

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                               N + SEV       + DE LN      D N     D L  
Sbjct: 130 --------------------NKNRSEV-------SFDEPLN---IDWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           D D    ++ +  E    R++L +++  LN RE++I E R         T ++++    +
Sbjct: 160 DDD----IITKDLEATVDRHLLMKALHQLNDREKQIMELRFGLAGGEEKTQKDVADMLGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 216 SQSYISRLEKRIIKRLRKEFNKMV 239


>gi|254432127|ref|ZP_05045830.1| group2 RNA polymerase sigma factor RpoD6 [Cyanobium sp. PCC 7001]
 gi|197626580|gb|EDY39139.1| group2 RNA polymerase sigma factor RpoD6 [Cyanobium sp. PCC 7001]
          Length = 335

 Score =  144 bits (364), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 75/291 (25%), Positives = 131/291 (45%), Gaps = 37/291 (12%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLA---KRYREHGDL---------SAAHRLVTSHLR 59
           G  GLS Y+  I ++P+L   EE  LA   + + +H D           A +R+VT++LR
Sbjct: 55  GGDGLSDYLRLIARVPLLTPAEELHLAGTVQEWLQHPDPPLSLRRRGTRARNRMVTANLR 114

Query: 60  LVVKIAMGYRGYGLPIS----EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQE 115
           LVV +   YRG    +     ++   GNIGLM+AV+ FDP RG+RL+TY+  WI  A+Q 
Sbjct: 115 LVVMVCRRYRGRIGNLQLEMLDLYQAGNIGLMRAVELFDPSRGYRLSTYAFSWIHQAVQR 174

Query: 116 YILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
            +  + + ++I T          LR +    Q +     +P  + AIA  L   E  + +
Sbjct: 175 CMTATGNGIRIPT---------ALRNIAYRAQLLEACAEQPLSIGAIAALLGEKEQRLQT 225

Query: 176 MNC--RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
                R     SL+    S  ++++  +  ++ D  G            +    L   + 
Sbjct: 226 ALTVVRQCSTTSLDKPSASMGEDTTLIE--VIPDRRGNVPH--------DDYRWLHEHLD 275

Query: 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L+ R+R++ + R   +   +    +    VS+  V+ +E R  K ++  +
Sbjct: 276 ALDLRDRQVLQLRYGDDESRSCSKTARVLGVSKSCVQSVERRTLKNLRRRL 326


>gi|149191506|ref|ZP_01869755.1| RNA polymerase sigma factor [Vibrio shilonii AK1]
 gi|148834694|gb|EDL51682.1| RNA polymerase sigma factor [Vibrio shilonii AK1]
          Length = 125

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 58/125 (46%), Positives = 83/125 (66%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  +   + +  +  L  YI  +   PML   EE  LA+R    G++ AA  L+ SHLR 
Sbjct: 1   MANQAYPMALVTQDSLDGYIRSVNSYPMLTADEERELAERLHYDGEIEAAKGLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A GY GYGLP++++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120

Query: 121 WSLVK 125
           W +VK
Sbjct: 121 WRIVK 125


>gi|307328849|ref|ZP_07608019.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306885514|gb|EFN16530.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 277

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 52/234 (22%), Positives = 103/234 (44%), Gaps = 15/234 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+ ++L LV   A  +R    P+ +V+  G IGL+ A+ +FDP+RG +  T++M  +
Sbjct: 54  RAALIEANLPLVRYAAARFRSRNEPMEDVIQVGTIGLINAIDRFDPDRGVQFPTFAMPTV 113

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ Y   +   V +      +RL     ++ G  + +T  + +      IA++L +S
Sbjct: 114 VGEIKRYFRDNVRTVHVP-----RRLHELWVQVNGATEDLTVLHGRSPTTAEIAERLKLS 168

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E EV++         + +              D L Y+      V          R+++ 
Sbjct: 169 EEEVLACIEAGRSYHATSLEAAQEGDGLPGLVDRLGYEDPALAGV--------EHRDLVR 220

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +  L  RE+RI   R      +T   +S+E  VS+  V ++ +R+F +++ +
Sbjct: 221 HLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLLSRSFARLRSA 272


>gi|282866278|ref|ZP_06275324.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
 gi|282558864|gb|EFB64420.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
          Length = 318

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 52/236 (22%), Positives = 97/236 (41%), Gaps = 16/236 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            + LV  +L LV   A  +R    P+ ++V  G IGL++A+ +F+  RG    T++M  I
Sbjct: 94  RNTLVELNLALVKFAAARFRSRSEPMEDIVQVGTIGLIKAIDRFELSRGVEFPTFAMPTI 153

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +   VV +A++L ++
Sbjct: 154 IGEIKRFFRDTSWSVRVPRRLQELRLD-----LAKAGDELAQQLDRAPTVVELAERLGIT 208

Query: 170 ESEVIS-MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
             EV+  M    A   S        D N     D L Y+ +G E +             L
Sbjct: 209 HEEVVEGMTASNAYTASSLDAKPEDDDNEGALADRLGYEDNGLEGI--------EYIESL 260

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              ++ L  R+R I   R +    +T   +  E  +S+  V ++ +R   K++  +
Sbjct: 261 KPLIASLPLRDRTILSLRFVAN--MTQSEIGEELGISQMHVSRLLSRTLVKLRRGL 314


>gi|239941779|ref|ZP_04693716.1| putative RNA polymerase sigma factor [Streptomyces roseosporus NRRL
           15998]
 gi|239988239|ref|ZP_04708903.1| putative RNA polymerase sigma factor [Streptomyces roseosporus NRRL
           11379]
 gi|291445225|ref|ZP_06584615.1| RNA polymerase sigma factor [Streptomyces roseosporus NRRL 15998]
 gi|291348172|gb|EFE75076.1| RNA polymerase sigma factor [Streptomyces roseosporus NRRL 15998]
          Length = 329

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 48/236 (20%), Positives = 98/236 (41%), Gaps = 16/236 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            + LV  +L LV   A  +R    P+ ++V  G IGL++A+ +F+  RG    T++M  I
Sbjct: 105 RNTLVELNLALVKFAASRFRSRSEPMEDIVQVGTIGLIKAIDRFELSRGVEFPTFAMPTI 164

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      ++    +   V  ++++L ++
Sbjct: 165 VGEIKRFFRDTSWSVRVPRRLQELRLD-----LAKAGDELSQQLDRAPTVAELSERLGIT 219

Query: 170 ESEVIS-MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
             EV+  M+   A   S        D +     D + Y+  G E +             L
Sbjct: 220 PDEVVEGMSASNAYTASSLDAKPEEDDSEGALADRIGYEDHGLEGI--------EYVESL 271

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              ++ L  R+R I   R +    +T   +  E  +S+  V ++ +R   K+++ +
Sbjct: 272 KPLIAALPARDRMILSLRFVSN--MTQSEIGEELNISQMHVSRLLSRTLTKLRKGL 325


>gi|302866675|ref|YP_003835312.1| RNA polymerase sigma-70 factor [Micromonospora aurantiaca ATCC
           27029]
 gi|302569534|gb|ADL45736.1| RNA polymerase sigma-70 factor, sigma-B/F/G subfamily
           [Micromonospora aurantiaca ATCC 27029]
          Length = 273

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 50/240 (20%), Positives = 94/240 (39%), Gaps = 18/240 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +   R + + L L   +A  Y G G P  ++     IGL++A+ KFDP RG   A Y++
Sbjct: 46  PALRDRAIEAWLPLANHLAHRYSGRGEPNDDLAQTAAIGLIKAIDKFDPSRGVDFAGYAI 105

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA--K 164
             I   ++ +       +++     + RL      +      +     +   V  IA   
Sbjct: 106 PTIIGELKRHFRDRTWDIRVPRRLQELRLA-----ISDANSTLLQTLGRSPTVADIAAHL 160

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           KL   E        R     SL+      +  +++  D L  +          + E    
Sbjct: 161 KLTEEEVLEGLEGARAYNAVSLSTPTGDGE-RATELGDLLGGEDG--------EFELAEM 211

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L  +++ L+ RE++I   R      +T   ++ +  VS+  V ++ ARA  K++  +
Sbjct: 212 RVALGPALATLDQREQKILTLRFYGN--LTQSQIAEQIGVSQMHVSRLLARALTKLRGQL 269


>gi|167040624|ref|YP_001663609.1| sporulation sigma factor SigE [Thermoanaerobacter sp. X514]
 gi|300914665|ref|ZP_07131981.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X561]
 gi|307724101|ref|YP_003903852.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter sp. X513]
 gi|166854864|gb|ABY93273.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Thermoanaerobacter sp. X514]
 gi|300889600|gb|EFK84746.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X561]
 gi|307581162|gb|ADN54561.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X513]
          Length = 241

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 57/262 (21%), Positives = 109/262 (41%), Gaps = 63/262 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L  +EE  L  +  E GD  A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 39  PPLSVEEEMYLISKM-EKGDNEAKTVLIERNLRLVVYIAKKFENTGVGIEDLISIGTIGL 97

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+  F+P++  +LATY+   I+  +  Y+ R+                          
Sbjct: 98  IKAINTFNPKKKIKLATYASRCIENEILMYLRRNSKT----------------------- 134

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                             KL VS  E ++++                D N     D L  
Sbjct: 135 ------------------KLEVSFDEPLNVD---------------WDGNELLLSDILGT 161

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEV 264
           D++   + + ++ E    + +LT ++  L  RE++I   R   E     T + ++    +
Sbjct: 162 DNETVYKYIEDEVE----KELLTSALKKLPDREKKIIGLRFGLEGGVEKTQKEVADMLGI 217

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+  + ++E +  K++++ + +
Sbjct: 218 SQSYISRLEKKILKRLKKEMNR 239


>gi|239942801|ref|ZP_04694738.1| RNA polymerase sigma factor, sigma F [Streptomyces roseosporus NRRL
           15998]
 gi|239989260|ref|ZP_04709924.1| RNA polymerase sigma factor, sigma F [Streptomyces roseosporus NRRL
           11379]
 gi|291446270|ref|ZP_06585660.1| sigma F [Streptomyces roseosporus NRRL 15998]
 gi|291349217|gb|EFE76121.1| sigma F [Streptomyces roseosporus NRRL 15998]
          Length = 285

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 55/237 (23%), Positives = 103/237 (43%), Gaps = 15/237 (6%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                 L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDPERG +  T++M
Sbjct: 59  RRVRAALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQFPTFAM 118

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +   ++ Y   +   V +      +RL     ++ G  + +T  + +      IA++L
Sbjct: 119 PTVVGEIKRYFRDNVRTVHVP-----RRLHELWVQVTGATEDLTTAHGRSPTTAEIAERL 173

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +SE EV++         + +              D L Y+      V          R+
Sbjct: 174 KISEDEVLACIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALAGV--------EHRD 225

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           ++   +  L  RE+RI   R      +T   +S+E  VS+  V ++ AR+F +++ +
Sbjct: 226 LVRHLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLLARSFARLRSA 280


>gi|331697274|ref|YP_004333513.1| SigB/F/G subfamily RNA polymerase sigma-28 subunit [Pseudonocardia
           dioxanivorans CB1190]
 gi|326951963|gb|AEA25660.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Pseudonocardia dioxanivorans CB1190]
          Length = 296

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 46/233 (19%), Positives = 98/233 (42%), Gaps = 17/233 (7%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           +  HL L   IA  +   G P+ ++     +GL+ AV +FDP RG     +++  I   +
Sbjct: 32  IIEHLPLARHIAKRFSQRGEPLQDLEQVAVLGLINAVDRFDPARGPEFLAFAIPTITGEV 91

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
             +       +++     +  +      +      +T    +      IA +L+V+ S+V
Sbjct: 92  LRWFRDRAWTIRVPRRLKELDMS-----ISTAADRLTQELGRAPTPSEIAARLDVALSDV 146

Query: 174 I-SMNCRLA-GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           + S+  R A    SL+  +++  ++ S     L     G   V          R +L+  
Sbjct: 147 VESIQAREAYRCVSLDVPLSTESEDESVHNGILARTDPGVALV--------EDREVLSPL 198

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +  L  RE+RI   R  ++  +T   +  E  +S+  V ++   A +++++++
Sbjct: 199 VDALTEREQRIVLLRFFED--MTQNEIGQEIGISQMHVSRVLTAALERLRQAL 249


>gi|306821834|ref|ZP_07455426.1| RNA polymerase sigma-B factor [Eubacterium yurii subsp. margaretiae
           ATCC 43715]
 gi|304550141|gb|EFM38140.1| RNA polymerase sigma-B factor [Eubacterium yurii subsp. margaretiae
           ATCC 43715]
          Length = 268

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 46/253 (18%), Positives = 112/253 (44%), Gaps = 12/253 (4%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             L   Y E  D++  + L+  +L +   ++  Y   G+   ++    ++GL+ A++++D
Sbjct: 27  KELFLMYSEKRDIAIRNELIQRNLYIAEILSKKYINKGIEYEDIYQVASLGLIYAIERYD 86

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +GF  ++++   I   +++Y       +++     +  L   +  +K  LQ  T    
Sbjct: 87  ITKGFEFSSFATPTIIGEIKKYFRDKGWSIRVPRRIQE--LSKRVNTVKNELQQETH--- 141

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           K  ++  IA+KL +++ EV+           ++  +     N  + +D  +++  G++  
Sbjct: 142 KTPRISDIAEKLGITQEEVLETMDAAGAYAPISLDVKY--DNEGEDKDVALHELIGKDDK 199

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
              + E  +    L   M  L+  E++I   R       T   ++ E ++S+  V ++E 
Sbjct: 200 SFAEIEDGDF---LRNVMESLSEVEKKIIMDRYFDN--KTQMTVAKELDISQMTVSRMEK 254

Query: 275 RAFKKVQESIQKQ 287
           +   K+++  +KQ
Sbjct: 255 KILTKLKKEYEKQ 267


>gi|254390382|ref|ZP_05005599.1| RNA polymerase sigma-F factor [Streptomyces clavuligerus ATCC
           27064]
 gi|197704086|gb|EDY49898.1| RNA polymerase sigma-F factor [Streptomyces clavuligerus ATCC
           27064]
          Length = 326

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 53/234 (22%), Positives = 101/234 (43%), Gaps = 15/234 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDP+RG +  T++M  +
Sbjct: 103 RGALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFPTFAMPTV 162

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ Y   +   V +      +RL     ++ G  + +T  + +      IA++L + 
Sbjct: 163 VGEIKRYFRDNVRTVHVP-----RRLHELWVQVNGATEDLTTAHGRIPTTAEIAERLRIG 217

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E EV++         + +              D L Y+      V          R+++ 
Sbjct: 218 EDEVLACIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALAGV--------EHRDLVR 269

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +  L  RE+RI   R      +T   +S E  VS+  V ++ AR+F +++ +
Sbjct: 270 HLLVQLPEREQRILMLRYYSN--LTQSQISQELGVSQMHVSRLLARSFARLRSA 321


>gi|161898921|gb|ABX80450.1| SigB [Listeria monocytogenes]
          Length = 231

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 56/244 (22%), Positives = 108/244 (44%), Gaps = 24/244 (9%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D   G  
Sbjct: 6   YQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKS 65

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
              +++  I   ++ ++      V +     +        ++K  ++ +T       Q+ 
Sbjct: 66  FEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQSSPQIS 120

Query: 161 AIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            IA  + V+E EV+           L+ D S+ A    SD ++    D +    DG    
Sbjct: 121 DIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTDDGF--- 174

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
                ER N+R +L + + VL+ RE++I +   ++    + +      ++S+  V +I+ 
Sbjct: 175 -----ERVNQRMLLEKVLPVLDEREQKILQFTFIEN--RSQKETGELLDISQMHVSRIQR 227

Query: 275 RAFK 278
           +A K
Sbjct: 228 QAIK 231


>gi|284030454|ref|YP_003380385.1| putative RNA polymerase, sigma 70 family subunit [Kribbella flavida
           DSM 17836]
 gi|283809747|gb|ADB31586.1| putative RNA polymerase, sigma 70 family subunit [Kribbella flavida
           DSM 17836]
          Length = 301

 Score =  144 bits (363), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 64/315 (20%), Positives = 121/315 (38%), Gaps = 57/315 (18%)

Query: 3   RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLA----------KRYREHGDLSA--- 49
              M        GL  Y+ ++ +  +L   E Y L+          +R        A   
Sbjct: 1   MAEMDCDAADVTGLVAYLRDLGRHDLLSPDEVYELSSWIEAGVLAGERLARAAPSEAVAP 60

Query: 50  -------------------AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
                                R++  +LRLVV +A  Y G GL + +++ EGNIGLM+AV
Sbjct: 61  EEQVERADLAALAELGEAARRRMIEGNLRLVVSLAKRYTGKGLSLLDLIQEGNIGLMRAV 120

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           ++FD + G R +TY++WWI+ A+   I     LV++   A     + +  R+    + + 
Sbjct: 121 ERFDYKLGHRFSTYAIWWIRQALGRAISDRSRLVRMPAQA-----YVDAGRVAVVQRELI 175

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
               +   +  +A+  +++ + V          E L+              D ++ D   
Sbjct: 176 QRLEREPTIEELARATSLTVARVERALAWKLRPEPLD----------GHDSDQVIDDET- 224

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRER 268
                    +R   R  L   +  L+  ++ +   R    N    +LE  +    +   R
Sbjct: 225 -------LLQRAALRRDLHCQLEFLDDLKQDVLRLRYGLHNTPQSSLEETAEYLSLPPAR 277

Query: 269 VRQIEARAFKKVQES 283
           VR +E  A + ++++
Sbjct: 278 VRSLELEALRHLRKA 292


>gi|302544115|ref|ZP_07296457.1| RNA polymerase sigma-F factor [Streptomyces hygroscopicus ATCC
           53653]
 gi|302461733|gb|EFL24826.1| RNA polymerase sigma-F factor [Streptomyces himastatinicus ATCC
           53653]
          Length = 284

 Score =  143 bits (362), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 51/234 (21%), Positives = 101/234 (43%), Gaps = 15/234 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+ ++L LV   A  +R    P+ +V+  G IGL+ A+ +FDP RG +  T++M  +
Sbjct: 59  RDALIEANLPLVRYAAARFRSRNEPMEDVIQVGTIGLINAIDRFDPGRGVQFPTFAMPTV 118

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ Y   +   V +      +RL     ++ G  + +T  + +      IA++L + 
Sbjct: 119 VGEIKRYFRDNVRTVHVP-----RRLHELWVQVNGATEDLTVLHGRSPTTAEIAERLGLG 173

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E EV++         + +              D L Y+      V          R+++ 
Sbjct: 174 EDEVLACIEAGRSYHATSLEAAQEGDGLPGLVDRLGYEDPALAGV--------EHRDLVR 225

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +  L  RE+RI   R      +T   +S+E  VS+  V ++ +R+F +++ +
Sbjct: 226 HLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLLSRSFARLRSA 277


>gi|328880523|emb|CCA53762.1| RNA polymerase sigma factor SigB [Streptomyces venezuelae ATCC
           10712]
          Length = 325

 Score =  143 bits (362), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 50/259 (19%), Positives = 105/259 (40%), Gaps = 22/259 (8%)

Query: 36  VLAKRYREHGDLSA-----AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
            L +R R   + +A      + LV  +L LV   A  +R       ++V  G +GL++A+
Sbjct: 52  ALFERLRSLEEGTASYSYVRNTLVELNLSLVKYAATRFRHSSENWEDLVQVGTVGLIKAI 111

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
            +FDP RG    ++++  +   ++ ++  +   V +     + RL      +     A+ 
Sbjct: 112 NRFDPARGNEFMSFALPTVLGEIRRHLRDTSWSVHVPRRLQELRLD-----VAKANDALE 166

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDH 208
               +P     ++ +L+++E E+        G    SL+  ++  D         L  D 
Sbjct: 167 QELGRPPTAAELSDRLHITEDELREGRIAANGFASRSLDVPVDDEDAGPGMLARCLGSDD 226

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D  E+VL            L   ++ L+ R+R I   R   E  +T   +     +S+  
Sbjct: 227 DAFEKVL--------NLEALKPLVAALSERDRTILALRFGGE--LTQAEIGERLGLSQMH 276

Query: 269 VRQIEARAFKKVQESIQKQ 287
           V ++ +R    ++ ++  +
Sbjct: 277 VSRLLSRILGGLRTALTTE 295


>gi|183220350|ref|YP_001838346.1| RNA polymerase sigma factor WhiG [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Paris)']
 gi|189910466|ref|YP_001962021.1| RNA polymerase sigma factor WhiG [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Ames)']
 gi|167775142|gb|ABZ93443.1| RNA polymerase sigma subunit [Leptospira biflexa serovar Patoc
           strain 'Patoc 1 (Ames)']
 gi|167778772|gb|ABZ97070.1| RNA polymerase sigma factor for flagellar operon [Leptospira
           biflexa serovar Patoc strain 'Patoc 1 (Paris)']
          Length = 266

 Score =  143 bits (362), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 64/260 (24%), Positives = 120/260 (46%), Gaps = 19/260 (7%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL---PISEVVSEGNIGLMQA 89
           +E  L K+YR   D      LV  +  LV  +A              ++VS G  GL+ A
Sbjct: 12  DETDLWKQYRVKKDAEIRSYLVEKYSPLVKHVAGRIAIGMPQNVEFEDLVSYGVFGLLDA 71

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           ++KFDP R  +  TY+M  I+ ++ + +    S+  I  +  QK      ++L+  +  +
Sbjct: 72  IEKFDPSREIKFKTYAMTRIRGSIFDELR---SVDWIPRSIRQKA-----KQLENIIAML 123

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD--ESLNALINSSDKNSS-QWQDWLVY 206
            +   K      IAK+L VS  E  S+  +L+G    SLN +    D+N    + + L  
Sbjct: 124 ENKEGKKVDDEEIAKELGVSMEEYNSLLAKLSGTSLVSLNDIWFLGDENDEVSFMETLES 183

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
             +     +IEKEE    +N++  ++  L  +E+++      ++  +TL+ +    EV+ 
Sbjct: 184 PMNMNPDNIIEKEE---IKNVIVEAIQSLPEKEKKVIVLYYYED--LTLKEIGEVLEVTE 238

Query: 267 ERVRQIEARAFKKVQESIQK 286
            R+ Q+  +A  +++  + K
Sbjct: 239 SRISQLHTKAVARLRSKLSK 258


>gi|169829726|ref|YP_001699884.1| RNA polymerase sigma-B factor [Lysinibacillus sphaericus C3-41]
 gi|168994214|gb|ACA41754.1| RNA polymerase sigma-B factor (Sigma-37) (General stress protein
           84) (GSP84) [Lysinibacillus sphaericus C3-41]
          Length = 261

 Score =  143 bits (362), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 60/261 (22%), Positives = 117/261 (44%), Gaps = 24/261 (9%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
            K++     + Y+   D  A   LV  +  LV  IA  Y        ++V  G +GL+ A
Sbjct: 11  SKEDVLKWIELYQSTEDDEAQTNLVIHYRYLVESIARKYSNGKSYYDDIVQVGMLGLLGA 70

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +++FDP  G     +++  I   ++ ++      V +     +        R+K  ++A+
Sbjct: 71  IRRFDPNVGRSFEAFAVPTIVGEIKRFLRDKTWDVHVPRRIKEIG-----PRIKTTVEAL 125

Query: 150 TDNNLKPEQVVAIAKKLNVSES------EVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
           T    +   +  IA++L V+E       E+      L+ D S+ +    SD ++    D 
Sbjct: 126 TIELQRSPSIQEIAERLEVAEEEVLEAMEMSRSYQALSMDHSIES---DSDGSTVTLFDI 182

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L  + DG         E  ++R +++ +M VLN RE++I +   L    ++ +    +  
Sbjct: 183 LGREDDGY--------EMTDKRMIVSEAMVVLNEREKQIIQLTYL--EQLSQKEAGEQLG 232

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+  V +I+ +A KK+QE+I
Sbjct: 233 ISQMHVSRIQRKAIKKLQEAI 253


>gi|293392779|ref|ZP_06637097.1| DNA-directed RNA polymerase sigma subunit RpoS [Serratia odorifera
           DSM 4582]
 gi|291424638|gb|EFE97849.1| DNA-directed RNA polymerase sigma subunit RpoS [Serratia odorifera
           DSM 4582]
          Length = 202

 Score =  143 bits (362), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 53/143 (37%), Positives = 83/143 (58%), Gaps = 3/143 (2%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 63  YLGEIGYSPLLTAEEEVYFARR-ALRGDVPSRRRMIESNLRLVVKIARRYSNRGLALLDL 121

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   
Sbjct: 122 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVY 180

Query: 139 LRRLKGHLQAITDNNLKPEQVVA 161
           LR  +  L    D+    E++  
Sbjct: 181 LRTAR-ELSHKLDHEPSAEEIAE 202


>gi|290956130|ref|YP_003487312.1| sigma factor [Streptomyces scabiei 87.22]
 gi|260645656|emb|CBG68747.1| putative sigma factor [Streptomyces scabiei 87.22]
          Length = 1033

 Score =  143 bits (362), Expect = 2e-32,   Method: Composition-based stats.
 Identities = 64/290 (22%), Positives = 120/290 (41%), Gaps = 34/290 (11%)

Query: 28  MLEKQEEYVLAKRYR--------EHGDLS------------AAHRLVTSHLRLVVKIAMG 67
           +L  + E  LA   R        E  D              A   LV  + RLV  +   
Sbjct: 209 LLTAEAEVGLAVLLRGGTDSVGQEPEDEELSGLPSDDIRVRARDCLVLHNQRLVHSLIRS 268

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
               GL   ++V  G +GLM+A +KFDP +G++ +TY+ WW++ ++   I    +L+++ 
Sbjct: 269 CLDQGLEYEDLVQHGVLGLMRAARKFDPAKGYKFSTYATWWVRQSVSRAIADEGALIRVP 328

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              ++      +R++    +A+     +P   V +A + +++   V  +       +SL+
Sbjct: 329 VHMHE-----QMRKVAAAERALAAQG-RPAGNVDVAVQCDMTLDRVEEIRKLTRRTDSLD 382

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
            +I     + +   D++          +            +   +   + R  RI   R 
Sbjct: 383 RII----GDGATLGDFVG--KRQALPSVENDVLHVLLMEDVMGVVGTFSERSARILVRRL 436

Query: 248 L--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPP 295
               E P TL+ L  EF V+RER+RQ+E +A  + +  ++    LS   P
Sbjct: 437 GLDGEEPSTLDELGREFGVTRERIRQLEGKARSEFRCRLRAAGLLSGHGP 486


>gi|126651479|ref|ZP_01723683.1| sigma factor B [Bacillus sp. B14905]
 gi|126591732|gb|EAZ85828.1| sigma factor B [Bacillus sp. B14905]
          Length = 261

 Score =  143 bits (362), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 60/261 (22%), Positives = 117/261 (44%), Gaps = 24/261 (9%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
            K++     + Y+   D  A   LV  +  LV  IA  Y        ++V  G +GL+ A
Sbjct: 11  SKEDVLKWIELYQSTEDDEAQTNLVIHYRYLVESIARKYSNGKSYYDDIVQVGMLGLLGA 70

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +++FDP  G     +++  I   ++ ++      V +     +        R+K  ++A+
Sbjct: 71  IRRFDPNVGRSFEAFAVPTIVGEIKRFLRDKTWDVHVPRRIKEIG-----PRIKSTVEAL 125

Query: 150 TDNNLKPEQVVAIAKKLNVSES------EVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
           T    +   +  IA++L V+E       E+      L+ D S+ +    SD ++    D 
Sbjct: 126 TIELQRSPSIQEIAERLEVAEEEVLEAMEMSRSYQALSMDHSIES---DSDGSTVTLFDI 182

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L  + DG         E  ++R +++ +M VLN RE++I +   L    ++ +    +  
Sbjct: 183 LGREDDGY--------EMTDKRMIVSEAMVVLNEREKQIIQLTYL--EQLSQKEAGEQLG 232

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+  V +I+ +A KK+QE+I
Sbjct: 233 ISQMHVSRIQRKAIKKLQEAI 253


>gi|317499023|ref|ZP_07957304.1| RNA polymerase sigma-F factor [Lachnospiraceae bacterium 5_1_63FAA]
 gi|291560723|emb|CBL39523.1| RNA polymerase, sigma subunit, RpoX/SigF [butyrate-producing
           bacterium SSC/2]
 gi|316893673|gb|EFV15874.1| RNA polymerase sigma-F factor [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 241

 Score =  143 bits (362), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 43/245 (17%), Positives = 107/245 (43%), Gaps = 16/245 (6%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R  + G+ +A  +++ +++ L+  +   +   G    ++   G+IGLM+AV KFD     
Sbjct: 9   RLTKEGNEAAREQIILNNVGLIWSVVRRFTNRGYESEDLFQIGSIGLMKAVDKFDLSYDV 68

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY++  I   ++ ++     ++K+  +  +     N+ ++    +       +   +
Sbjct: 69  KFSTYAVPMITGEIRRFLRDDG-MIKVSRSLKE-----NVYKIMKAREKFCQQYQREATI 122

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I++   ++  E+++        ES++      D +     D L    +  E+V+    
Sbjct: 123 EEISEITKITREEIVTSLEASNEVESIHQSAYQKDGSEISLLDKLSKGENESEKVV---- 178

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
                  +L  +M  L  +E+++   R       T + ++  F +S+ +V +IE R  KK
Sbjct: 179 ----DHVLLKEAMKHLEQKEQQMIYYRYF--EGKTQQEIAKIFHISQVQVSRIEKRILKK 232

Query: 280 VQESI 284
           ++  +
Sbjct: 233 LRRQM 237


>gi|228992639|ref|ZP_04152565.1| RNA polymerase sigma-35 factor [Bacillus pseudomycoides DSM 12442]
 gi|228998685|ref|ZP_04158272.1| RNA polymerase sigma-35 factor [Bacillus mycoides Rock3-17]
 gi|229006188|ref|ZP_04163874.1| RNA polymerase sigma-35 factor [Bacillus mycoides Rock1-4]
 gi|228755029|gb|EEM04388.1| RNA polymerase sigma-35 factor [Bacillus mycoides Rock1-4]
 gi|228761153|gb|EEM10112.1| RNA polymerase sigma-35 factor [Bacillus mycoides Rock3-17]
 gi|228766971|gb|EEM15608.1| RNA polymerase sigma-35 factor [Bacillus pseudomycoides DSM 12442]
          Length = 239

 Score =  143 bits (362), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 67/264 (25%), Positives = 114/264 (43%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL  +  + GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLTKEEEEVLLNKLPK-GDQAARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  ++ R+                          
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMHLRRN-------------------------- 129

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                               N + SEV       + DE LN      D N     D L  
Sbjct: 130 --------------------NKNRSEV-------SFDEPLN---IDWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           D D    ++ +  E    R++L +++  LN RE++I E R         T ++++    +
Sbjct: 160 DDD----IITKDLEANVDRHLLKKALHQLNDREKQIMELRFGLAGGEEKTQKDVADMLGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 216 SQSYISRLEKRIIKRLRKEFNKMV 239


>gi|108798252|ref|YP_638449.1| RNA polymerase sigma factor SigF [Mycobacterium sp. MCS]
 gi|119867348|ref|YP_937300.1| RNA polymerase sigma factor SigF [Mycobacterium sp. KMS]
 gi|126433912|ref|YP_001069603.1| RNA polymerase sigma factor SigF [Mycobacterium sp. JLS]
 gi|108768671|gb|ABG07393.1| RNA polymerase, sigma 28 subunit [Mycobacterium sp. MCS]
 gi|119693437|gb|ABL90510.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Mycobacterium
           sp. KMS]
 gi|126233712|gb|ABN97112.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Mycobacterium
           sp. JLS]
          Length = 263

 Score =  143 bits (362), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 49/236 (20%), Positives = 98/236 (41%), Gaps = 13/236 (5%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             R+V   L L   IA  + G G P  ++V    +GL+ AV +FD + G    ++++  I
Sbjct: 41  RDRIVERCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVIRFDVDAGSDFVSFAVPTI 100

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   VK+     +  L     RL      ++    +      +A++L + 
Sbjct: 101 MGEVRRHFRDNSWSVKVPRRLKELHL-----RLGSATAELSQRLGRAPTASELAEELGMD 155

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             EV+     L    S N L   S  NS       + D  G   + +++ E    R  L 
Sbjct: 156 RDEVVE---GLVAGSSYNTLSIDSGGNSGNEDAPAIADTLGDVDLGLDQIE---NREALR 209

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             ++ L  RER +   R  +   +T   ++    +S+  V ++ A++  ++++ +Q
Sbjct: 210 PLLAALPERERMVLLLRFFEN--LTQTQIAERVGISQMHVSRLLAKSLTRLRDQLQ 263


>gi|15895573|ref|NP_348922.1| sporulation sigma factor SigF [Clostridium acetobutylicum ATCC 824]
 gi|15025312|gb|AAK80262.1|AE007731_7 Sporulation-specific sigma factor F [Clostridium acetobutylicum
           ATCC 824]
 gi|325509722|gb|ADZ21358.1| sporulation sigma factor SigF [Clostridium acetobutylicum EA 2018]
          Length = 252

 Score =  143 bits (361), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 47/269 (17%), Positives = 115/269 (42%), Gaps = 22/269 (8%)

Query: 23  IRKIPMLEKQEEYV-----LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + K   L+K+E        L K   E G+  A ++++ ++L LV  I+  +   G    +
Sbjct: 1   MGKENTLKKEEPNYNDNEKLIKSVHE-GNKEALNKIIENNLPLVSAISRKFLNRGYEYDD 59

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +   G +GL++AV  F+ +   + +TY++  I   ++ ++     ++K+  +        
Sbjct: 60  IFQIGCMGLVKAVNNFNSDYKVKFSTYAVPMIMGEIKRFLRDDG-IIKVSRSVK-----S 113

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
             R+L    + +     +   +  ++K   + + E+I         + L  +++  D + 
Sbjct: 114 TARQLHYDREKLVKELNREPTIDELSKFSGIDKEEIIMATESTTSMQYLYDVVHQDDGSP 173

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
               D L   +     V+         + +L + +  L+ + ++I   R  ++   T   
Sbjct: 174 VLLIDKLSDPYSEDSDVI--------DKIVLKQIIKSLDNKSKQIIMLRYFKD--KTQTQ 223

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +++   +S+ +V +IE R  K ++E + K
Sbjct: 224 VANMLGISQVQVSRIEKRILKAIREKLTK 252


>gi|585927|sp|P37970|RPOF_STRAU RecName: Full=RNA polymerase sigma-F factor
 gi|153450|gb|AAA93050.1| minor sigma-like factor [Streptomyces aureofaciens]
          Length = 297

 Score =  143 bits (361), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 56/237 (23%), Positives = 103/237 (43%), Gaps = 15/237 (6%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                 L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDPERG +  T++M
Sbjct: 71  ERVRGALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQFPTFAM 130

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +   ++ Y   +   V +      +RL     ++    + +T  + +      IA++L
Sbjct: 131 PTVVGEIKRYFRDNVRTVHVP-----RRLHELWVQVNAATEDLTTLHGRTPTTPEIAERL 185

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +SE EV+S         + +              D L Y+      V          R+
Sbjct: 186 RISEDEVLSCIEAGRSYHATSLEAAQEGDGMPGLLDRLGYEDPELAGV--------EHRD 237

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           ++   +  L  RE+RI   R    N +T   +S+E  VS+  V ++ AR+F +++ +
Sbjct: 238 LVRHLLVQLPEREQRILLLRYY--NNLTQSQISAELGVSQMHVSRLLARSFARLRSA 292


>gi|21222438|ref|NP_628217.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
 gi|585925|sp|P37971|RPOF_STRCO RecName: Full=RNA polymerase sigma-F factor
 gi|153455|gb|AAA93052.1| sigma factor [Streptomyces coelicolor A3(2)]
 gi|13122128|emb|CAC32306.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
          Length = 287

 Score =  143 bits (361), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 54/234 (23%), Positives = 103/234 (44%), Gaps = 15/234 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDPERG +  T++M  +
Sbjct: 64  RAALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQFPTFAMPTV 123

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ Y   +   V +      +RL     ++    + +T    +      IA++L ++
Sbjct: 124 VGEIKRYFRDNVRTVHVP-----RRLHELWVQVNSATEDLTTAFGRSPTTAEIAERLRIT 178

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E EV+S         + +              D L Y+    + V          R+++ 
Sbjct: 179 EEEVLSCIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALDGV--------EHRDLVR 230

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +  L  RE+RI   R      +T   +S+E  VS+  V ++ AR+F++++ +
Sbjct: 231 HLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLLARSFQRLRSA 282


>gi|302346408|ref|YP_003814706.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           melaninogenica ATCC 25845]
 gi|302150820|gb|ADK97081.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           melaninogenica ATCC 25845]
          Length = 228

 Score =  143 bits (361), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 62/270 (22%), Positives = 116/270 (42%), Gaps = 47/270 (17%)

Query: 17  SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
            +YI +I    +L  +EE  LA++ +  GD  A  +L  ++L+ VV +A  YR  GL   
Sbjct: 5   EKYIEDIANEQLLSDKEEQELAEKIKV-GDARALEKLTKANLKFVVSLAHQYRNRGLGED 63

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++SEGNIG+M A +KFD  +G R   ++  +I+ AM+E I    +L K+          
Sbjct: 64  DLISEGNIGMMYAAQKFDGSKGVRFVIFAAPYIRKAMEETIKEQATLYKLP--------- 114

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
                                            ++E      + +   S++  +     N
Sbjct: 115 ---------------------------------KNETSRFEQKRSHAISIDQPVPVGSNN 141

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV-TL 255
           +   Q  L  ++       + +E   N    + + + VL+ RE+R+            T+
Sbjct: 142 NFTLQHILENENAKHADEHLNQEILSNE---IQKGLDVLDEREKRVITYIYGLTGAHYTM 198

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             ++ +  + RERVRQI  +A +K+ + ++
Sbjct: 199 AEIAEDMGLKRERVRQIRDKALRKLHKKMK 228


>gi|302520386|ref|ZP_07272728.1| RNA polymerase sigma-G factor [Streptomyces sp. SPB78]
 gi|318060770|ref|ZP_07979493.1| RNA polymerase sigma factor [Streptomyces sp. SA3_actG]
 gi|318078699|ref|ZP_07986031.1| RNA polymerase sigma factor [Streptomyces sp. SA3_actF]
 gi|333025873|ref|ZP_08453937.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
 gi|302429281|gb|EFL01097.1| RNA polymerase sigma-G factor [Streptomyces sp. SPB78]
 gi|332745725|gb|EGJ76166.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
          Length = 274

 Score =  143 bits (361), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 58/241 (24%), Positives = 109/241 (45%), Gaps = 17/241 (7%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           EHG + AA  L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDP+RG +  
Sbjct: 46  EHGRVRAA--LIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFP 103

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           T++M  +   ++ Y   +   V +      +RL     ++    + +T  + +      I
Sbjct: 104 TFAMPTVVGEIKRYFRDNVRTVHVP-----RRLHELWVQVNSAAEDLTTAHGRSPTTAEI 158

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A++L + E EV++         + +              D L Y+    + V        
Sbjct: 159 AERLRIGEDEVLACIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALDGV-------- 210

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             R+++   +  L  RE+RI   R    N +T   +S+E  VS+  V ++ AR+F +++ 
Sbjct: 211 EHRDLVRHLLVQLPEREQRILLLRYY--NNLTQSQISAELGVSQMHVSRLLARSFARLRS 268

Query: 283 S 283
           +
Sbjct: 269 A 269


>gi|29827282|ref|NP_821916.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29604380|dbj|BAC68451.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 279

 Score =  143 bits (361), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 50/239 (20%), Positives = 104/239 (43%), Gaps = 18/239 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + L+  ++ LV   A  +R      + ++V  G IGL++A+ +F+  R     ++++ 
Sbjct: 52  ARNTLIEMNVTLVRFAAARFRSRSQDEMEDIVQVGTIGLIKAIDRFELTREVEFTSFAVP 111

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +I   ++ +   +   V +     + R+     +L    + +     +   V  +++ + 
Sbjct: 112 YIVGEIKRFFRDTSWAVHVPRRLQEARI-----QLAKATEELQSRLDRMPTVKELSELMC 166

Query: 168 VSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           +SE EV        G    SL+A I+SS+   +   D++  D +          E     
Sbjct: 167 LSEEEVNEARLASNGYTSSSLDATISSSNDGEAALADFIGTDDN--------ALELVEDF 218

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           N L   ++ L+ RERRI   R + E  +T   +     VS+  V ++ +R   K++E +
Sbjct: 219 NALAPMIAELDDRERRIIHMRFVDE--LTQAQIGEHLGVSQMHVSRLLSRTLAKLREGM 275


>gi|328883833|emb|CCA57072.1| RNA polymerase sigma factor SigB [Streptomyces venezuelae ATCC
           10712]
          Length = 281

 Score =  143 bits (361), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 53/234 (22%), Positives = 101/234 (43%), Gaps = 15/234 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDP+RG +  T++M  +
Sbjct: 58  RGALIEANLPLVRYAADRFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFPTFAMPTV 117

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ Y   +   V +      +RL     ++ G  + +T  + +      IA++L + 
Sbjct: 118 VGEIKRYFRDNVRTVHVP-----RRLHELWVQVNGATEDLTTAHGRSPTTAEIAERLRIG 172

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E EV++         + +              D L Y+      V          R+++ 
Sbjct: 173 EDEVLACIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALAGV--------EHRDLVR 224

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +  L  RE+RI   R      +T   +S E  VS+  V ++ AR+F +++ +
Sbjct: 225 HLLVQLPEREQRILMLRYYSN--LTQSQISQELGVSQMHVSRLLARSFARLRSA 276


>gi|320012478|gb|ADW07328.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 290

 Score =  143 bits (361), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 54/242 (22%), Positives = 103/242 (42%), Gaps = 13/242 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + L+  +L LV   A  +R  G   + ++V  G IGL++A+ +FD  R     ++++ 
Sbjct: 58  ARNTLIEMNLSLVRFAAGRFRNRGSGDMEDIVQVGTIGLIKAIDRFDLAREVEFTSFAVP 117

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +I   ++ +   +   V +     + R+  +L + K  L    D +     V  +A  L+
Sbjct: 118 YIVGEIKRFFRDTTWAVHVPRRLQELRV--DLAKAKEALAVELDRD---PTVQELAGYLD 172

Query: 168 VSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           + E E+        G    SL    ++ D            D  G+    +E  E     
Sbjct: 173 LEEEEITEGLVAANGYTAGSLEMPADAGDHAGRTTAGRTYADVLGEPDPAMETVE---NL 229

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + L   +  L+ RERRI + R  QE  +T   +  E  +S+  V ++ +R  +K+ + + 
Sbjct: 230 HALAPLLGELDARERRIIDMRFGQE--MTQAQIGDELGISQMHVSRLLSRILRKLHDGML 287

Query: 286 KQ 287
            Q
Sbjct: 288 AQ 289


>gi|148381038|ref|YP_001255579.1| RNA polymerase sigma-F factor [Clostridium botulinum A str. ATCC
           3502]
 gi|153933259|ref|YP_001385409.1| sporulation sigma factor SigF [Clostridium botulinum A str. ATCC
           19397]
 gi|153935896|ref|YP_001388816.1| sporulation sigma factor SigF [Clostridium botulinum A str. Hall]
 gi|153939970|ref|YP_001392365.1| sporulation sigma factor SigF [Clostridium botulinum F str.
           Langeland]
 gi|170754271|ref|YP_001782722.1| sporulation sigma factor SigF [Clostridium botulinum B1 str. Okra]
 gi|226950516|ref|YP_002805607.1| RNA polymerase sigma-F factor [Clostridium botulinum A2 str. Kyoto]
 gi|148290522|emb|CAL84650.1| RNA polymerase sigma-F factor [Clostridium botulinum A str. ATCC
           3502]
 gi|152929303|gb|ABS34803.1| RNA polymerase sigma-F factor [Clostridium botulinum A str. ATCC
           19397]
 gi|152931810|gb|ABS37309.1| RNA polymerase sigma-F factor [Clostridium botulinum A str. Hall]
 gi|152935866|gb|ABS41364.1| RNA polymerase sigma-F factor [Clostridium botulinum F str.
           Langeland]
 gi|169119483|gb|ACA43319.1| RNA polymerase sigma-F factor [Clostridium botulinum B1 str. Okra]
 gi|226844449|gb|ACO87115.1| RNA polymerase sigma-F factor [Clostridium botulinum A2 str. Kyoto]
 gi|295320356|gb|ADG00734.1| RNA polymerase sigma-F factor [Clostridium botulinum F str. 230613]
 gi|322807388|emb|CBZ04962.1| RNA polymerase sporulation specific sigma factor SigF [Clostridium
           botulinum H04402 065]
          Length = 251

 Score =  143 bits (361), Expect = 3e-32,   Method: Composition-based stats.
 Identities = 40/253 (15%), Positives = 107/253 (42%), Gaps = 17/253 (6%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           ++   L ++ R  G+  A  +LV  +L LV  I+  +   G    ++   G IGL++A+ 
Sbjct: 14  EDNMELMEKAR-SGNKEALDKLVEVNLPLVSAISKKFLNRGYEYDDIFQIGCIGLVKAIN 72

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
            F+ +   + +TY++  I   ++ ++     ++K+  +          ++L    + +  
Sbjct: 73  NFETKYNVKFSTYAVPMIMGEIKRFLRDDG-IIKVSRSIK-----TAAKKLHYDKEKLCK 126

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +   +  +++    +  E++      +  + L  +I+  D       D +  +    
Sbjct: 127 ELNREPTIEELSQFSGYTVDEILMATESSSSPQYLYDVIHQDDGAPVLLIDKISEN---- 182

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
                E++ +      L  ++  L+ + R+I   R  ++   T   ++ +  +S+ +V +
Sbjct: 183 ----TEEDNKIVDNIALKEALKNLDIKSRQIIILRYFKD--KTQIEVAKQLGISQVQVSR 236

Query: 272 IEARAFKKVQESI 284
           IE +  K ++E +
Sbjct: 237 IEKKVLKLMKEKL 249


>gi|219856135|ref|YP_002473257.1| hypothetical protein CKR_2792 [Clostridium kluyveri NBRC 12016]
 gi|219569859|dbj|BAH07843.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 254

 Score =  143 bits (361), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 49/255 (19%), Positives = 107/255 (41%), Gaps = 17/255 (6%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            +   L K  RE GD  A ++LV  +L LV  I+  +   G    ++   G +GLM+AV 
Sbjct: 17  DDNLKLIKCARE-GDKEALNKLVELNLPLVSAISKKFLNRGYEYEDIFQIGCMGLMKAVN 75

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
            FD     + +TY++  I   ++ ++     ++K+  +          ++L    +A+T 
Sbjct: 76  NFDETYNVKFSTYAVPMILGEIKRFLRDDG-MIKVSRSIK-----NTAKKLHYDREALTK 129

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +   +  +A+   V   E++         + L   I+  D +     D +  +    
Sbjct: 130 KLNREPTIEELAEYSGVKTEELLFATESTNSLQYLYDTIHQDDGSPVLLIDKISENPKED 189

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
            +V+         R  L  ++  L+ + R+I   R  ++   T   ++    +++ +V +
Sbjct: 190 VEVI--------DRIALKEALRNLDVKSRQIIMLRYFKD--KTQVQVAKMLGINQVQVSR 239

Query: 272 IEARAFKKVQESIQK 286
           IE +  K ++E + +
Sbjct: 240 IEKKVLKTMREILSE 254


>gi|319937136|ref|ZP_08011543.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
 gi|319807502|gb|EFW04095.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
          Length = 259

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 50/262 (19%), Positives = 106/262 (40%), Gaps = 16/262 (6%)

Query: 23  IRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           I++   L  QE   L  +Y +  D +   +LV S+L+LV+ +   Y      + ++   G
Sbjct: 13  IQEYEKLSHQETMNLLDQYHQTNDENIKEKLVLSNLKLVLSLVQKYHQRVSNLDDLFQVG 72

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            IGL++A+  FD     R +TY++  I   ++ YI  +  + +I  +         L   
Sbjct: 73  VIGLIKAIDHFDTSLDVRFSTYAVPLIIGEIKRYIRDNSPM-RIPRSMRDLAYKALL--- 128

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
               +     + K      ++K L+V E  ++          SL+  + +        + 
Sbjct: 129 --ANEEYMKKHHKEASTKELSKILDVDEFLLVEALSSTNSVTSLSQEVQNDGNGQIDLES 186

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
            +    +  E +             L  +M+ L+ +E +I   R  +    T   ++ E 
Sbjct: 187 QIPDRKNQMEDM--------QNSIDLYEAMNHLDEKELQIINERYFKG--HTQSEIAKEL 236

Query: 263 EVSRERVRQIEARAFKKVQESI 284
            +S+ +V +IE +A   +++ +
Sbjct: 237 FISQAQVSRIEKQALSHLKKYM 258


>gi|289578314|ref|YP_003476941.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter italicus Ab9]
 gi|297544594|ref|YP_003676896.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
 gi|289528027|gb|ADD02379.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter italicus Ab9]
 gi|296842369|gb|ADH60885.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
          Length = 246

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 50/247 (20%), Positives = 110/247 (44%), Gaps = 18/247 (7%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R  +  D  +  +L+  +  L+  I   +   G  + ++   G +G ++AV+KFD     
Sbjct: 17  RAAQKNDKESLEKLILENSGLIWSIVKKFSNRGYELEDLYQIGCMGFVKAVQKFDESYNV 76

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           +L+TY++  I   ++ ++     L+K+  +  +        +     + ++    +   +
Sbjct: 77  KLSTYAVPIIMGEIKRFLRDDG-LIKVSRSLKELSTKAFYLK-----EVLSSELNREPTI 130

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IA++L VS  EV       A  ESL       +       D L+ +   +E    EKE
Sbjct: 131 NEIAERLKVSPEEVAMAFESAATAESLYDNATHDED------DRLLIEMVSEE----EKE 180

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
              + +  L   ++ L PRE++I   R  ++  +T   ++S   +S+ +V +IE +  +K
Sbjct: 181 VDIDDKLALQMVINKLKPREKQIIFLRYFKD--MTQMEIASILGISQVQVSRIEKKVLQK 238

Query: 280 VQESIQK 286
           +++ + +
Sbjct: 239 LRKELDE 245


>gi|153955768|ref|YP_001396533.1| sporulation sigma factor SigF [Clostridium kluyveri DSM 555]
 gi|146348626|gb|EDK35162.1| RNA polymerase sigma-F factor [Clostridium kluyveri DSM 555]
          Length = 251

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 49/255 (19%), Positives = 107/255 (41%), Gaps = 17/255 (6%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            +   L K  RE GD  A ++LV  +L LV  I+  +   G    ++   G +GLM+AV 
Sbjct: 14  DDNLKLIKCARE-GDKEALNKLVELNLPLVSAISKKFLNRGYEYEDIFQIGCMGLMKAVN 72

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
            FD     + +TY++  I   ++ ++     ++K+  +          ++L    +A+T 
Sbjct: 73  NFDETYNVKFSTYAVPMILGEIKRFLRDDG-MIKVSRSIK-----NTAKKLHYDREALTK 126

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +   +  +A+   V   E++         + L   I+  D +     D +  +    
Sbjct: 127 KLNREPTIEELAEYSGVKTEELLFATESTNSLQYLYDTIHQDDGSPVLLIDKISENPKED 186

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
            +V+         R  L  ++  L+ + R+I   R  ++   T   ++    +++ +V +
Sbjct: 187 VEVI--------DRIALKEALRNLDVKSRQIIMLRYFKD--KTQVQVAKMLGINQVQVSR 236

Query: 272 IEARAFKKVQESIQK 286
           IE +  K ++E + +
Sbjct: 237 IEKKVLKTMREILSE 251


>gi|282858710|ref|ZP_06267864.1| sigma-70 region 2 [Prevotella bivia JCVIHMP010]
 gi|282588514|gb|EFB93665.1| sigma-70 region 2 [Prevotella bivia JCVIHMP010]
          Length = 228

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 66/270 (24%), Positives = 109/270 (40%), Gaps = 47/270 (17%)

Query: 17  SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
            +YI  I    +L  +EE  LA R +  GD  A  +L  ++L  VV IA  Y+  GL  +
Sbjct: 5   KKYIENIIGETILTNEEERQLADRIKV-GDAKALEKLTKANLTFVVSIAHQYKEQGLDEN 63

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++SEGNIG+M A +KFD  +G R   ++  +I+ AM++ I    +L K+    N+K  F
Sbjct: 64  DLISEGNIGMMYAAQKFDGTKGVRFVNFAASYIRKAMEDAIKEQTALYKVP--KNEKNRF 121

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
              R                                        A   SL+  +     N
Sbjct: 122 EQKR----------------------------------------AKAISLDQPVPVGSNN 141

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV-TL 255
           +   Q+ +V           +          L +SM  LN RE  +       +    T+
Sbjct: 142 NFTLQNVIVNGDTANTD---DDVTTNMLNTALKQSMKFLNERETAVITQLYGLDGVHFTM 198

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             ++    + RER+RQI   A +K+  +++
Sbjct: 199 AEVAETLGLKRERIRQIRNTALRKLHRNLK 228


>gi|302560279|ref|ZP_07312621.1| RNA polymerase sigma factor [Streptomyces griseoflavus Tu4000]
 gi|302477897|gb|EFL40990.1| RNA polymerase sigma factor [Streptomyces griseoflavus Tu4000]
          Length = 304

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 49/236 (20%), Positives = 97/236 (41%), Gaps = 16/236 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            + LV  +L LV   A  +R    P+ +++  G IGL++A+ +F+  RG    T++M  I
Sbjct: 80  RNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRGVEFPTFAMPTI 139

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +   V  +A++L ++
Sbjct: 140 IGEIKRFFRDTSWSVRVPRRLQELRLD-----LAKAGDELAQQLDRSPTVAELAERLGIT 194

Query: 170 ESEVIS-MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
             EV+  M    A   S        D       D + Y+  G E +             L
Sbjct: 195 NEEVVEGMAASNAYTASSLDAQPEEDDAEGALADRIGYEDHGLEGI--------EYVESL 246

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              ++ L PR+R+I   R +    +T   +  E  +S+  V ++ +R   K+++ +
Sbjct: 247 KPLIAELPPRDRKILSLRFVAG--MTQSEIGEELGISQMHVSRLLSRTLVKLRKGL 300


>gi|168179581|ref|ZP_02614245.1| RNA polymerase sigma-F factor [Clostridium botulinum NCTC 2916]
 gi|168181777|ref|ZP_02616441.1| RNA polymerase sigma-F factor [Clostridium botulinum Bf]
 gi|170761116|ref|YP_001788407.1| sporulation sigma factor SigF [Clostridium botulinum A3 str. Loch
           Maree]
 gi|237796543|ref|YP_002864095.1| sporulation sigma factor SigF [Clostridium botulinum Ba4 str. 657]
 gi|169408105|gb|ACA56516.1| RNA polymerase sigma-F factor [Clostridium botulinum A3 str. Loch
           Maree]
 gi|182669805|gb|EDT81781.1| RNA polymerase sigma-F factor [Clostridium botulinum NCTC 2916]
 gi|182675139|gb|EDT87100.1| RNA polymerase sigma-F factor [Clostridium botulinum Bf]
 gi|229260985|gb|ACQ52018.1| RNA polymerase sigma-F factor [Clostridium botulinum Ba4 str. 657]
          Length = 251

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 40/253 (15%), Positives = 107/253 (42%), Gaps = 17/253 (6%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           ++   L ++ R  G+  A  +LV  +L LV  I+  +   G    ++   G IGL++A+ 
Sbjct: 14  EDNMELMEKAR-SGNKEALDKLVEVNLPLVSAISKKFLNRGYEYDDIFQIGCIGLVKAIN 72

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
            F+ +   + +TY++  I   ++ ++     ++K+  +          ++L    + +  
Sbjct: 73  NFETKYNVKFSTYAVPMIMGEIKRFLRDDG-IIKVSRSIK-----TAAKKLHYDKEKLCK 126

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +   +  +++    +  E++      +  + L  +I+  D       D +  +    
Sbjct: 127 ELNREPTIEELSQFSGYTVDEILMATESSSSPQYLYDVIHQDDGAPVLLIDKISEN---- 182

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
                E++ +      L  ++  L+ + R+I   R  ++   T   ++ +  +S+ +V +
Sbjct: 183 ----TEEDNKIIDNIALKEALKNLDIKSRQIIILRYFKD--KTQIEVAKQLGISQVQVSR 236

Query: 272 IEARAFKKVQESI 284
           IE +  K ++E +
Sbjct: 237 IEKKVLKLMKEKL 249


>gi|302552549|ref|ZP_07304891.1| RNA polymerase sigma-B factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302470167|gb|EFL33260.1| RNA polymerase sigma-B factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 289

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 53/234 (22%), Positives = 104/234 (44%), Gaps = 15/234 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDP+RG +  T++M  +
Sbjct: 66  RGALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFPTFAMPTV 125

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ Y   +   V +      +RL     ++    + +T +  +      IA++L ++
Sbjct: 126 VGEIKRYFRDNVRTVHVP-----RRLHELWVQVNSATEDLTTSFGRTPTTAEIAERLRIT 180

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E EV+S         + +              D L Y+    + V          R+++ 
Sbjct: 181 EDEVLSCIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALDGV--------EHRDLVR 232

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +  L  RE+RI   R      +T   +S+E  VS+  V ++ AR+F++++ +
Sbjct: 233 HLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLLARSFQRLRSA 284


>gi|55274989|gb|AAV49292.1| RNA polymerase subunit sigma-38 [Shigella flexneri]
          Length = 199

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 56/209 (26%), Positives = 101/209 (48%), Gaps = 12/209 (5%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+ 
Sbjct: 1   RMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQ 60

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            ++  I+     +++      K L   LR  +     ++           IA++L+    
Sbjct: 61  TIERAIMNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVD 115

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           +V  M        S++  +    + +      L    D +E    +  +  + +  + + 
Sbjct: 116 DVSRMLRLNERITSVDTPLGGDSEKA-----LLDILADEKENGPEDTTQDDDMKQSIVKW 170

Query: 232 MSVLNPRERRIFEARR--LQENPVTLENL 258
           +  LN ++R +   R   L     TLE++
Sbjct: 171 LFELNAKQREVLARRFGLLGYEAATLEDV 199


>gi|313115569|ref|ZP_07801028.1| RNA polymerase sigma-G factor [Faecalibacterium cf. prausnitzii
           KLE1255]
 gi|310622084|gb|EFQ05580.1| RNA polymerase sigma-G factor [Faecalibacterium cf. prausnitzii
           KLE1255]
          Length = 255

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 57/257 (22%), Positives = 115/257 (44%), Gaps = 18/257 (7%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L + E+  L  R       +A  ++V  +LRLV+ +   +   G  + ++   G I
Sbjct: 14  KLPVLTEAEKRELLARAHAGD-AAAREQMVEGNLRLVLSVVQRFAQRGENLDDLFQVGCI 72

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FDP +  R +TY +  I   ++ ++  + +L ++      + L     R   
Sbjct: 73  GLIKAIDHFDPAQPVRFSTYGVPMIIGEIRRFLRDNNAL-RVS-----RSLRDTAYRAMQ 126

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             +A+     +   +  IA+   ++  EV +    +    SL   +  +D   + +    
Sbjct: 127 SREALEKQLGREPTMDEIAQAAGLARREVTAALESVVEPISLEEPVY-TDGGDAMYVIDQ 185

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           V D DG++  +   + R+          + L PRE+RI E R LQ    T   ++ E  +
Sbjct: 186 VRDPDGEDSWISGLQFRQTV--------AGLTPREKRIMELRYLQG--KTQMEVAREIGI 235

Query: 265 SRERVRQIEARAFKKVQ 281
           S+ +V ++E  A  + +
Sbjct: 236 SQAQVSRLEKGALSQFR 252


>gi|115394497|gb|ABI97158.1| RNA polymerase sigma factor [Fusobacterium necrophorum]
          Length = 185

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 43/187 (22%), Positives = 82/187 (43%), Gaps = 12/187 (6%)

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++K   +       K      +
Sbjct: 1   TYAPWWIRQAITRAIADQGRTIRIPVH-----MIETINKIKKEARIYLQETGKDATPEIL 55

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A++L +   +V S+        SL   + S  +  S+  D++    D +     E   R 
Sbjct: 56  AERLGMEVEKVKSIQEMNQDPISLETPVGS--EEDSELGDFV---EDQKMLTPYELTNRS 110

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             R  L   +  L+ RE ++   R   ++  P TLE +   F+V+RER+RQIE +A +K+
Sbjct: 111 LLREQLDSVLGSLSSREEKVLRYRYGLDDGSPKTLEEVGKIFKVTRERIRQIEVKALRKL 170

Query: 281 QESIQKQ 287
           +   +++
Sbjct: 171 RHPSRRK 177


>gi|297560171|ref|YP_003679145.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
 gi|296844619|gb|ADH66639.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
          Length = 313

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 57/254 (22%), Positives = 109/254 (42%), Gaps = 16/254 (6%)

Query: 36  VLAKRYRE--HGDLSA---AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
            L  + RE    D  A     R+V  +  L+ KIA  Y G G P+ ++     +GL++AV
Sbjct: 63  ELISQLRELAEDDPRADELRERVVVLYQPLINKIARRYGGRGEPLEDLKQTAMVGLVKAV 122

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           + +DP RG    +Y +  +   ++ +       V++     + R+   LRR+ G  Q   
Sbjct: 123 RGYDPARGKPFISYLLPTVTGEIKRHFRDHTWAVRVPRRHQENRV--KLRRVTGEFQQA- 179

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
             + +   V  +++++ + E+EV  +        SL+     S  +  Q    L  DH G
Sbjct: 180 --HARTPTVHELSEEMGLPEAEVGELIQVSESYRSLSLDAPDSSDSEGQEGTRL-EDHLG 236

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
            E   ++   R   R  L  +++ L  RER I   R   +   T   ++     S+  V 
Sbjct: 237 CEDAALD---RVVERESLKPALARLPAREREILRLRFFGD--HTQSEIADRLGYSQMHVS 291

Query: 271 QIEARAFKKVQESI 284
           ++ +   ++++E +
Sbjct: 292 RLLSGVLEQLREEV 305


>gi|294497070|ref|YP_003560770.1| RNA polymerase sigma-B factor [Bacillus megaterium QM B1551]
 gi|295702435|ref|YP_003595510.1| RNA polymerase sigma-B factor [Bacillus megaterium DSM 319]
 gi|294347007|gb|ADE67336.1| RNA polymerase sigma-B factor [Bacillus megaterium QM B1551]
 gi|294800094|gb|ADF37160.1| RNA polymerase sigma-B factor [Bacillus megaterium DSM 319]
          Length = 264

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 51/270 (18%), Positives = 116/270 (42%), Gaps = 24/270 (8%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K++     +R+++  D  A   LV  +  LV  IA  Y        ++V  G +GL+ 
Sbjct: 10  LTKEQVQERIERFQKTQDEEAQSDLVVHYKNLVESIARRYSKGRSLHEDIVQVGMLGLLG 69

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++++D   G    ++++  I   ++ ++      V +     +        ++K  ++ 
Sbjct: 70  AIRRYDASFGRSFESFAVPTIIGEIKRFLRDKTWSVHVPRRIKELG-----PKIKAAVEE 124

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQD 202
           +T    +  QV  IA  + V+E E++           L+ D S+ A    SD ++    D
Sbjct: 125 LTTRLQRSPQVKEIADHIGVTEEEILETMEMGQSYQALSVDHSIEA---DSDGSTVTILD 181

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
            +     G         E+ ++R +L + + VL+ RE+ +     ++   ++ ++   + 
Sbjct: 182 LVGEQESGY--------EKTDQRLVLEKILHVLSDREKEVIRYTFIEN--LSQKDAGEKL 231

Query: 263 EVSRERVRQIEARAFKKVQESIQKQVELSS 292
            +S+  V +++ RA  K++ + +     S 
Sbjct: 232 GISQMHVSRLQRRALDKLRTAARSDSNDSE 261


>gi|297559507|ref|YP_003678481.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
 gi|296843955|gb|ADH65975.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
          Length = 285

 Score =  143 bits (360), Expect = 4e-32,   Method: Composition-based stats.
 Identities = 56/258 (21%), Positives = 107/258 (41%), Gaps = 15/258 (5%)

Query: 30  EKQEEYVLAKRYREHGDLSA---AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
             +E   +  R  E GD  A     R++  +  L+ KIA  Y G G P+ ++     +GL
Sbjct: 32  TAEELLSVLVRLGE-GDPQANGLRERVMVLYQPLINKIARRYGGRGEPLEDLKQTAMVGL 90

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
            +AV+ +DP RG    +Y +  +   ++ +       V++     + R+   LRR+    
Sbjct: 91  AKAVRGYDPARGKPFISYLLPTVTGEIKRHFRDHTWAVRVPRRHQENRV--KLRRVTSEF 148

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           Q     + +   +  +A  + + E+EV  +        SL+     S  +  Q    L  
Sbjct: 149 QQ---RHARTPTIAELAHDMGLPEAEVSELTQVSESYRSLSLDAPDSSDSEGQEGTRL-E 204

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           DH G E   ++   R   R  L  +++ L  RER I   R   +   T   ++     S+
Sbjct: 205 DHLGCEDAALD---RVVERESLKPALARLPAREREILRLRFFGD--HTQSEIADRLGYSQ 259

Query: 267 ERVRQIEARAFKKVQESI 284
             V ++ +   ++++E +
Sbjct: 260 MHVSRLLSGVLEQLREEV 277


>gi|331083018|ref|ZP_08332137.1| RNA polymerase sigma-35 factor [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|330399755|gb|EGG79416.1| RNA polymerase sigma-35 factor [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 241

 Score =  143 bits (360), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 59/272 (21%), Positives = 104/272 (38%), Gaps = 65/272 (23%)

Query: 18  RYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
            YI     +P  L  QEE  +       G   A   L+  +LRLVV IA  +   G+ + 
Sbjct: 26  HYIGGAEVLPAPLTAQEEGEMLDALAGEGKEEARACLIEHNLRLVVYIAKKFDNTGVGVE 85

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++S G IGL++A+  FDP +  +LATY+   I+  +  Y+ R+                
Sbjct: 86  DLISIGTIGLIKAINTFDPVKKIKLATYASRCIENEILMYLRRNSKT------------- 132

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
                                       KL VS  E ++++                D N
Sbjct: 133 ----------------------------KLEVSIDEPLNVD---------------WDGN 149

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL----QENP 252
                D L  D D    V+ +  E +  R +L +++  L  RE+ I   R          
Sbjct: 150 ELLLSDILGTDED----VIYKDIENEVERKLLGKAIGKLTKREQTIVRLRFGINMPDGGE 205

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            T + ++    +S+  + ++E +  K++++ I
Sbjct: 206 KTQKEVADLLGISQSYISRLEKKIMKRLKKEI 237


>gi|255017998|ref|ZP_05290124.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes FSL
           F2-515]
          Length = 209

 Score =  143 bits (360), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 49/120 (40%), Positives = 73/120 (60%), Gaps = 3/120 (2%)

Query: 4   KNMSIIVNGEIG--LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
            +MS+    +I   +  Y+ EI ++ +L   EE  LAKR  E GD+ A  RL  ++LRLV
Sbjct: 91  TDMSVPPGVKINDPVRMYLKEIGRVDLLTADEEIALAKRI-EAGDIEAKGRLAEANLRLV 149

Query: 62  VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
           V IA  Y G G+   +++ EGN+GLM+AV+KFD  +GF+ +TY+ WWI+ A+   I    
Sbjct: 150 VSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQA 209


>gi|330375231|gb|AEC12842.1| RNA polymerase sigma factor RpoS [Pseudomonas fluorescens]
          Length = 200

 Score =  143 bits (360), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 55/208 (26%), Positives = 98/208 (47%), Gaps = 14/208 (6%)

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           AV+KFDPERGFR +TY+ WWI+  ++  I+     +++      K L   LR  +   Q 
Sbjct: 1   AVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHVV-KELNVYLRAARELTQK 59

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYD 207
           + D+   PE++  + +K       ++ +N R++  D SL         +     D L  D
Sbjct: 60  L-DHEPSPEEIANLLEKPVAEVKRMLGLNERVSSVDVSL------GPDSDKTLLDTLTDD 112

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVS 265
                  L++ ++       + + +S L  ++R +   R         TLE++  E  ++
Sbjct: 113 RPTDPCELLQDDDLSQS---IDQWLSELTEKQREVVVRRFGLRGHESSTLEDVGLEIGLT 169

Query: 266 RERVRQIEARAFKKVQESIQKQVELSSS 293
           RERVRQI+    K+++E ++K    S S
Sbjct: 170 RERVRQIQVEGLKRLREILEKNGLSSES 197


>gi|289770379|ref|ZP_06529757.1| transcription initiation factor sigma F [Streptomyces lividans
           TK24]
 gi|289700578|gb|EFD68007.1| transcription initiation factor sigma F [Streptomyces lividans
           TK24]
          Length = 287

 Score =  143 bits (360), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 54/234 (23%), Positives = 103/234 (44%), Gaps = 15/234 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDPERG +  T++M  +
Sbjct: 64  RAALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQFPTFAMPTV 123

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ Y   +   V +      +RL     ++    + +T    +      IA++L ++
Sbjct: 124 VGEIKRYFRDNVRTVHVP-----RRLHELWVQVNSATEDLTTAFGRSPTTAEIAERLRIT 178

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E EV+S         + +              D L Y+    + V          R+++ 
Sbjct: 179 EEEVLSCIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALDGV--------EHRDLVR 230

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +  L  RE+RI   R      +T   +S+E  VS+  V ++ AR+F++++ +
Sbjct: 231 HLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLLARSFQRLRSA 282


>gi|229061510|ref|ZP_04198854.1| RNA polymerase sigma-35 factor [Bacillus cereus AH603]
 gi|229134714|ref|ZP_04263523.1| RNA polymerase sigma-35 factor [Bacillus cereus BDRD-ST196]
 gi|229168645|ref|ZP_04296367.1| RNA polymerase sigma-35 factor [Bacillus cereus AH621]
 gi|228614801|gb|EEK71904.1| RNA polymerase sigma-35 factor [Bacillus cereus AH621]
 gi|228648760|gb|EEL04786.1| RNA polymerase sigma-35 factor [Bacillus cereus BDRD-ST196]
 gi|228717744|gb|EEL69394.1| RNA polymerase sigma-35 factor [Bacillus cereus AH603]
          Length = 232

 Score =  143 bits (360), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 67/264 (25%), Positives = 114/264 (43%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL  +   +GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 30  PPLTKEEEAVLLNKL-PNGDQAARSMLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 88

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  ++ R+                          
Sbjct: 89  IKAVNTFNPEKKIKLATYASRCIENEILMHLRRN-------------------------- 122

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                               N + SEV       + DE LN      D N     D L  
Sbjct: 123 --------------------NKNRSEV-------SFDEPLN---IDWDGNELLLSDVLGT 152

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           D D    ++ +  E    R++L +++  LN RE++I E R         T ++++    +
Sbjct: 153 DDD----IITKDLEATVDRHLLMKALHQLNDREKQIMELRFGLAGGEEKTQKDVADMLGI 208

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 209 SQSYISRLEKRIIKRLRKEFNKMV 232


>gi|256786488|ref|ZP_05524919.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
          Length = 291

 Score =  142 bits (359), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 54/234 (23%), Positives = 103/234 (44%), Gaps = 15/234 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDPERG +  T++M  +
Sbjct: 68  RAALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQFPTFAMPTV 127

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ Y   +   V +      +RL     ++    + +T    +      IA++L ++
Sbjct: 128 VGEIKRYFRDNVRTVHVP-----RRLHELWVQVNSATEDLTTAFGRSPTTAEIAERLRIT 182

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E EV+S         + +              D L Y+    + V          R+++ 
Sbjct: 183 EEEVLSCIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALDGV--------EHRDLVR 234

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +  L  RE+RI   R      +T   +S+E  VS+  V ++ AR+F++++ +
Sbjct: 235 HLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLLARSFQRLRSA 286


>gi|324998294|ref|ZP_08119406.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily protein
           [Pseudonocardia sp. P1]
          Length = 258

 Score =  142 bits (359), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 46/239 (19%), Positives = 100/239 (41%), Gaps = 14/239 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                RLVT +L +   IA  +   G P+ ++V    +GL+ A+ +FDP++G    ++++
Sbjct: 28  EQLRDRLVTGYLPVAQHIARRFNHRGEPLDDLVQVATVGLINAIDRFDPDKGGEFFSFAV 87

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I   ++ +       +++      +RL      + G +  ++    +  +   IA+ L
Sbjct: 88  PTISGEVRRHFRDQSWSMRVP-----RRLKDMHVSINGAVSELSQTLGRSPRPSEIAEHL 142

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   EV+          S +     S ++       LV D D        + +R + R 
Sbjct: 143 GLPVPEVLEGLEAAEAYRSSSLDEMLSSEDGGATVGELVGDADA-------ELDRVDYRE 195

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            L   ++ L PRER I   R       T   +++E  +S+  V ++ ++   +++  ++
Sbjct: 196 SLRPLLAELAPRERTIVMLRFFGN--RTQTQIANEVGISQMHVSRLLSQTLSRLRNRLE 252


>gi|307328229|ref|ZP_07607407.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306886063|gb|EFN17071.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 307

 Score =  142 bits (359), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 49/240 (20%), Positives = 102/240 (42%), Gaps = 15/240 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            + L+  +L LV   A  +    + + ++V  G IGL++A+ +FD  R     T+++ +I
Sbjct: 80  RNTLIELNLSLVRYAARRFHNRSVEMEDIVQVGTIGLIKAIDRFDLSREVEFTTFAVPYI 139

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V +     + R+      L    + +     +      +A+ L +S
Sbjct: 140 VGEIKRFFRDTSWAVHVPRRLQELRID-----LAKANEELFQRLDRSPTTAELAEHLQLS 194

Query: 170 ESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E EV+       G    SL+A    +++ S   +     D  G     +E  E     + 
Sbjct: 195 EDEVVDGLVASNGYLTSSLDAP---AEQESGATRVTTYADRFGDVDPAMEAVE---NLHA 248

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   +  L  R+RRI + R  +E  +T   + +E  VS+  V ++ +RA  +++  +  +
Sbjct: 249 LKPLVEELGERDRRILQLRFGEE--MTQSEIGAELGVSQMHVSRLLSRALSRLRRGMLAE 306


>gi|3077738|dbj|BAA25787.1| SigB [Cyanidium caldarium]
          Length = 424

 Score =  142 bits (359), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 68/289 (23%), Positives = 118/289 (40%), Gaps = 44/289 (15%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY----------------------- 68
           +EE     R R      A  RLV S+LRLV+ IA  Y                       
Sbjct: 130 EEEV----RKRIERGRRARERLVASNLRLVLAIANRYKLRAVVCSAWKSRSKGGMDMPSH 185

Query: 69  ------RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
                 R + + + +++ EG +GL++A +KFDP +GF+ +TY+ WWI+ A+Q  +     
Sbjct: 186 EKVRLQRQHNIFLGDLIQEGALGLIRAAEKFDPSKGFKFSTYATWWIRQAIQRCVSEHSR 245

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            +++     +      + R++  LQ +       E+V   A  + +   + I+ +     
Sbjct: 246 TIRLPNHVTES--LRQIYRMRARLQHVLKRPPTDEEVAE-ACNMTLKRLKKITQHAWETQ 302

Query: 183 DESLNALINSSD-----KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
             SL    NS           +    +    +  E+   E  ER   R  +   +  L  
Sbjct: 303 TLSLEGPPNSEAHSLYKSQQGEAPLSIGSIIEATEETPEEALERNCMREDVECVLRTLPF 362

Query: 238 RERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +ER I   R      E P + E LS+ F++    +R IE+RA +K++  
Sbjct: 363 QEREILRLRYGISDDERPHSTEELSARFQLPVHTIRLIESRALRKLRHP 411


>gi|325662347|ref|ZP_08150956.1| hypothetical protein HMPREF0490_01695 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|325471349|gb|EGC74572.1| hypothetical protein HMPREF0490_01695 [Lachnospiraceae bacterium
           4_1_37FAA]
          Length = 234

 Score =  142 bits (359), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 50/226 (22%), Positives = 105/226 (46%), Gaps = 15/226 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L  +E+  L  + +E GD +A  R +  +LRLV+ +   +      + ++   G +
Sbjct: 15  KLPLLSNEEKEALFVKIKE-GDEAARERYIKGNLRLVLSVIKRFASSNENVDDLFQIGCV 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+A+  F+ +   + +TY++  I   ++ Y+  + S +++      + L     +   
Sbjct: 74  GLMKAIDNFNTDLQVKFSTYAVPMIIGEIRRYLRDNNS-IRVS-----RSLRDTAYKAIY 127

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             +     +LK   V  IA+++ +++ ++I     +    SLN  +  +D   + +    
Sbjct: 128 AKEGYMKRHLKEPTVEEIAEEIGIAKEDIIFALDAIQAPMSLNEPVY-NDSGDALYVMDQ 186

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           + D   +E+  +E          L  +M  LN RER I + R L+E
Sbjct: 187 ISDKKNREEYWVEGLS-------LEAAMERLNERERFIIQLRFLKE 225


>gi|169334044|ref|ZP_02861237.1| hypothetical protein ANASTE_00437 [Anaerofustis stercorihominis DSM
           17244]
 gi|169258761|gb|EDS72727.1| hypothetical protein ANASTE_00437 [Anaerofustis stercorihominis DSM
           17244]
          Length = 253

 Score =  142 bits (359), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 48/259 (18%), Positives = 107/259 (41%), Gaps = 20/259 (7%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P L  +E   +  R + +G+    +  +  +LRLV+ +   +      + ++   G IG
Sbjct: 15  LPNLNNKEIEDMLIRIK-NGEEDLKNEFIRCNLRLVLSVVQRFSNRNENMDDLFQVGCIG 73

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A+  FD + G + +TY++  I   ++ Y+  +   +++  +                
Sbjct: 74  LIKAIDNFDVKFGVKFSTYAVPMIIGEVRRYLRDNG-TIRVSRSLKDM--------AYKA 124

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           L+    +         IAKKL V E ++      +    SL   + + + +S    D + 
Sbjct: 125 LKYKEAHKDTNPTNREIAKKLGVKEKDLNFALDSIVEPCSLYDQMYNDNGDSISLIDQVG 184

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            + +        +EE    +  L  ++  L  RE+ I   R       T   +++E  +S
Sbjct: 185 DEKN--------REENWTEKLSLKEAVEKLKGREKEIILKRYYLG--RTQIEVANEIGIS 234

Query: 266 RERVRQIEARAFKKVQESI 284
           + +V ++E    +K++  I
Sbjct: 235 QAQVSRLEKSGLRKIKNEI 253


>gi|54025575|ref|YP_119817.1| putative sigma factor [Nocardia farcinica IFM 10152]
 gi|54017083|dbj|BAD58453.1| putative sigma factor [Nocardia farcinica IFM 10152]
          Length = 315

 Score =  142 bits (359), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 47/242 (19%), Positives = 99/242 (40%), Gaps = 18/242 (7%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +    L++  + L   IA  + G G P  ++     +GL+ AV +FDP RG    ++++ 
Sbjct: 90  ALRDELISRCVPLADHIARKFSGRGEPFDDLTQVARVGLVHAVDRFDPARGSNFLSFAVP 149

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I   ++ Y       +++     +  L     R+   +  ++ +  +      IA +L 
Sbjct: 150 TIMGEVRRYFRDHTWAMRVPRRVKETHL-----RIGAAIDTLSQSLGRSPTAKEIAAELR 204

Query: 168 VSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           V   EV    +        S++A     + ++S        D  G+E+   E+ E     
Sbjct: 205 VDPDEVTQAVIAGNAYQPSSIDAAALGRESDASLL------DTLGEEEAQFERVEEYV-- 256

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             +   ++ L  RERRI   R      +T   ++ +  +S+  V +I A+   +++E   
Sbjct: 257 -AIRPLLAGLPERERRILTMRFF--ESMTQTQIAKQMGISQMHVSRILAKTLARLRELSA 313

Query: 286 KQ 287
           ++
Sbjct: 314 RE 315


>gi|18311030|ref|NP_562964.1| sporulation sigma factor SigF [Clostridium perfringens str. 13]
 gi|110799417|ref|YP_696728.1| sporulation sigma factor SigF [Clostridium perfringens ATCC 13124]
 gi|110803821|ref|YP_699329.1| sporulation sigma factor SigF [Clostridium perfringens SM101]
 gi|168205856|ref|ZP_02631861.1| RNA polymerase sigma-F factor [Clostridium perfringens E str.
           JGS1987]
 gi|168208750|ref|ZP_02634375.1| RNA polymerase sigma-F factor [Clostridium perfringens B str. ATCC
           3626]
 gi|168212915|ref|ZP_02638540.1| RNA polymerase sigma-F factor [Clostridium perfringens CPE str.
           F4969]
 gi|168215675|ref|ZP_02641300.1| RNA polymerase sigma-F factor [Clostridium perfringens NCTC 8239]
 gi|182623955|ref|ZP_02951743.1| RNA polymerase sigma-F factor [Clostridium perfringens D str.
           JGS1721]
 gi|18145712|dbj|BAB81754.1| RNA polymerase sigma-F factor [Clostridium perfringens str. 13]
 gi|110674064|gb|ABG83051.1| RNA polymerase sigma-F factor [Clostridium perfringens ATCC 13124]
 gi|110684322|gb|ABG87692.1| RNA polymerase sigma-F factor [Clostridium perfringens SM101]
 gi|170662589|gb|EDT15272.1| RNA polymerase sigma-F factor [Clostridium perfringens E str.
           JGS1987]
 gi|170712973|gb|EDT25155.1| RNA polymerase sigma-F factor [Clostridium perfringens B str. ATCC
           3626]
 gi|170715517|gb|EDT27699.1| RNA polymerase sigma-F factor [Clostridium perfringens CPE str.
           F4969]
 gi|177910848|gb|EDT73202.1| RNA polymerase sigma-F factor [Clostridium perfringens D str.
           JGS1721]
 gi|182382022|gb|EDT79501.1| RNA polymerase sigma-F factor [Clostridium perfringens NCTC 8239]
          Length = 251

 Score =  142 bits (359), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 39/247 (15%), Positives = 101/247 (40%), Gaps = 17/247 (6%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             + G+  A ++L+  +  LV  I   +   G    ++   G++GL++A+  F+     +
Sbjct: 22  MAKEGNKEAMNKLIEVNTPLVSSICKRFTNRGYDYEDIFQIGSMGLVKAINNFNDSFNVK 81

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY++  I   ++ ++     ++K+  +        +  +     + +     +   V 
Sbjct: 82  FSTYAVPMIIGEIKRFLRDDG-IIKVSRSTKTLAKKLHYNK-----EELIKKLNRDPTVD 135

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A+   V + EVI      +  + L   I+  +       D L    +  + V      
Sbjct: 136 ELAEYSGVDKEEVIVALESASSMQYLYDTIHHDEGTPVLLIDKLSEKGEDDDMV------ 189

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
               +  L  ++S L+ + ++I   R  ++   T   ++    +S+ +V +IE +  K +
Sbjct: 190 ---NKIALREAISSLDSKGKQIIMLRYFKD--KTQIQVAKMLGISQVQVSRIEKKVLKIM 244

Query: 281 QESIQKQ 287
           +E +++ 
Sbjct: 245 KEKLEED 251


>gi|260589594|ref|ZP_05855507.1| RNA polymerase sigma-E factor [Blautia hansenii DSM 20583]
 gi|260540162|gb|EEX20731.1| RNA polymerase sigma-E factor [Blautia hansenii DSM 20583]
          Length = 252

 Score =  142 bits (359), Expect = 5e-32,   Method: Composition-based stats.
 Identities = 59/272 (21%), Positives = 104/272 (38%), Gaps = 65/272 (23%)

Query: 18  RYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
            YI     +P  L  QEE  +       G   A   L+  +LRLVV IA  +   G+ + 
Sbjct: 37  HYIGGAEVLPAPLTAQEEGEMLDALAGEGKEEARACLIEHNLRLVVYIAKKFDNTGVGVE 96

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++S G IGL++A+  FDP +  +LATY+   I+  +  Y+ R+                
Sbjct: 97  DLISIGTIGLIKAINTFDPVKKIKLATYASRCIENEILMYLRRNSKT------------- 143

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
                                       KL VS  E ++++                D N
Sbjct: 144 ----------------------------KLEVSIDEPLNVD---------------WDGN 160

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL----QENP 252
                D L  D D    V+ +  E +  R +L +++  L  RE+ I   R          
Sbjct: 161 ELLLSDILGTDED----VIYKDIENEVERKLLGKAIGKLTKREQTIVRLRFGINMPDGGE 216

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            T + ++    +S+  + ++E +  K++++ I
Sbjct: 217 KTQKEVADLLGISQSYISRLEKKIMKRLKKEI 248


>gi|320181954|gb|EFW56860.1| RNA polymerase sigma factor RpoH [Shigella boydii ATCC 9905]
          Length = 186

 Score =  142 bits (359), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 62/191 (32%), Positives = 101/191 (52%), Gaps = 8/191 (4%)

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
            RL ++++ WIKA + EY+LR+W +VK+ TT  Q++LFFNLR+ K  L          ++
Sbjct: 1   MRLVSFAVHWIKAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQ-----DE 55

Query: 159 VVAIAKKLNVSESEVISMNCRLA-GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           V  +A++L V+  +V  M  R+A  D + +   +    +        + D        IE
Sbjct: 56  VEMVARELGVTSKDVREMESRMAAQDMTFDLSSDDDSDSQPMAPVLYLQDKSSNFADGIE 115

Query: 218 KE-ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEAR 275
            +   +   N LT +M  L+ R + I  AR L E+   TL+ L+  + VS ERVRQ+E  
Sbjct: 116 DDNWEEQAANRLTDAMQGLDERSQDIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKN 175

Query: 276 AFKKVQESIQK 286
           A KK++ +I+ 
Sbjct: 176 AMKKLRAAIEA 186


>gi|150015700|ref|YP_001307954.1| sporulation sigma factor SigF [Clostridium beijerinckii NCIMB 8052]
 gi|149902165|gb|ABR32998.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           beijerinckii NCIMB 8052]
          Length = 251

 Score =  142 bits (359), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 44/246 (17%), Positives = 104/246 (42%), Gaps = 16/246 (6%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
               GD  A + L+  +L LV  I+  +   G    ++   G+IGL++A+  FD     +
Sbjct: 22  LARSGDTDAMNTLIEMNLPLVSSISKKFLNRGYDYEDIFQIGSIGLVKAINNFDLNYNVK 81

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY++  I   ++ ++     ++K+             R++    + +T    +   + 
Sbjct: 82  FSTYAVPMIIGEIKRFLRDDG-MIKVSRNVKSLA-----RKIHFQKEILTKKLKRSPTIE 135

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A   NV + E++         + L   I+  D       D L  +    ++ LIEK  
Sbjct: 136 ELADYANVDKEEILFAIESSNSLQYLYDTIHQDDGAPVLLIDKL-SEKSADDENLIEKI- 193

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                  L  +++ L+ + ++I   R  ++   T   ++    +S+ +V +IE +   ++
Sbjct: 194 ------ALKEALNSLDNKAKQIIMLRYFKD--KTQVQVAKMLGISQVQVSRIEKKVLAEM 245

Query: 281 QESIQK 286
           ++ +++
Sbjct: 246 RKKLEE 251


>gi|47122|emb|CAA48660.1| whiG-Stv [Streptomyces griseocarneus]
          Length = 278

 Score =  142 bits (358), Expect = 6e-32,   Method: Composition-based stats.
 Identities = 51/254 (20%), Positives = 106/254 (41%), Gaps = 16/254 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
            L + Y+  GD     +L+  +  LV  +A          +  ++ VS G  GL+ A++K
Sbjct: 31  ELWRSYKASGDERLREQLILHYSPLVKYVAGRVSVGLPPNVEQADFVSSGIFGLIDAIEK 90

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FDP R  +  TY++  I+ AM + + R+   +        + +      L+  L+     
Sbjct: 91  FDPARAIKFETYAITRIRGAMIDEL-RALDWIPRSVRQKARAVERAYATLEAELR----- 144

Query: 153 NLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
             +      +A ++ ++  E+ S+     LA   +L  L+++ D+   +    +    D 
Sbjct: 145 --RTPTEAEVAAEMGIALEELHSVFSQLSLANVVALEDLLHAGDEGGERL-SLMDTLEDT 201

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                +E  E    R +L R+++ L  RE+ +          +TL  +     V+  RV 
Sbjct: 202 AADDPVEVAEDHELRRLLARAINTLPEREKTVVTLYYY--EGLTLAEIGQVLGVTESRVS 259

Query: 271 QIEARAFKKVQESI 284
           QI  ++  +++  +
Sbjct: 260 QIHTKSVLQLRAKL 273


>gi|168186139|ref|ZP_02620774.1| RNA polymerase sigma-D factor [Clostridium botulinum C str. Eklund]
 gi|169295860|gb|EDS77993.1| RNA polymerase sigma-D factor [Clostridium botulinum C str. Eklund]
          Length = 242

 Score =  142 bits (358), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 54/242 (22%), Positives = 107/242 (44%), Gaps = 19/242 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              +V  ++ LV  IA      +   +   +++  G +GLM A  KFD  +G + +TY+ 
Sbjct: 10  KEEIVKKYIPLVKYIASRVIIGKTKYIEFEDLLGYGMLGLMDAFNKFDKSKGMKFSTYAS 69

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ +M + I ++  +         K     L +    ++ +   NL    +  IA++L
Sbjct: 70  IRIRGSMIDEIRKNSPI--------SKGAMDKLNKYNAAIENLQRKNLSEPNIKDIAQEL 121

Query: 167 NVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +++ S+V  +   +      SL  LI S D + S     +    D       E+ ER  +
Sbjct: 122 DMTVSQVGEIENFINYISIVSLEDLIFSDDDDIS----LIGTIEDINSPDPEEEFERDEK 177

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              L++ + +LN ++R +      +E  +TL+ +     VS  RV Q+ +RA   +++ +
Sbjct: 178 LEYLSKGLDMLNDKDRTVLSLYYYEE--MTLKEIGKVLGVSESRVCQLHSRAIVHLRKEL 235

Query: 285 QK 286
            K
Sbjct: 236 AK 237


>gi|302556259|ref|ZP_07308601.1| RNA polymerase sigma-B factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302473877|gb|EFL36970.1| RNA polymerase sigma-B factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 281

 Score =  142 bits (358), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 47/239 (19%), Positives = 106/239 (44%), Gaps = 18/239 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + L+  ++ LV   A  +R  G   + ++V  G IGL++A+ +FD  R     ++++ 
Sbjct: 54  ARNTLIEMNMSLVRFAAGRFRSRGPEEMEDIVQVGMIGLIKAIDRFDLSREAEFTSFAVP 113

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +I   ++ +   +   V +     + R+     +L    + +     +   V  +++ ++
Sbjct: 114 YIVGEIKRFFRDTTWAVHVPRRLQEARV-----QLARATEELRSRLGRTPTVKELSELMS 168

Query: 168 VSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           + E EV        G    SL+A I+ SD   +  QD++  +         +  E     
Sbjct: 169 LPEQEVREARIAANGYNSSSLDATISGSDDGEAALQDFIGAED--------QAMELVEDF 220

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + L   ++ L+ R+R I   R ++E  +T   +     VS+ +V ++ +R   +++E +
Sbjct: 221 HALAPLLAELDERDRHIIRMRFVEE--LTQAQIGERLGVSQMQVSRLLSRTLARLREGM 277


>gi|257054261|ref|YP_003132093.1| RNA polymerase sigma factor, sigma-70 family [Saccharomonospora
           viridis DSM 43017]
 gi|256584133|gb|ACU95266.1| RNA polymerase sigma factor, sigma-70 family [Saccharomonospora
           viridis DSM 43017]
          Length = 267

 Score =  142 bits (358), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 48/240 (20%), Positives = 98/240 (40%), Gaps = 14/240 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
               RLVT HL L   IA  + G G+   ++V    +GL+ AV +FDP RG    ++++ 
Sbjct: 38  ELRDRLVTGHLPLAEHIAQRFSGRGVAKEDLVQVARVGLINAVDRFDPSRGSDFLSFAVP 97

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +   ++ +   +  ++++     +  L      +      ++    +      IA  L 
Sbjct: 98  TVMGEVRRHFRDTGWVIRVPRRLKELHLS-----INNASTQLSQRLGRAPTPSEIADHLG 152

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++  EV           S++      +  S+  ++  + D  G+E   +   E       
Sbjct: 153 LTLEEVFEGLEAGNAYHSMSL----DEVLSADTENLALGDTLGEEDAALAGVE---NHET 205

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   +  L  RER I   R +    +T   ++    +S+  V ++ AR  KK++E + ++
Sbjct: 206 LQPLVKQLPERERTILALRFVHN--MTQTQIAERIGISQMHVSRLLARTLKKLREGLVEE 263


>gi|182438259|ref|YP_001825978.1| putative RNA polymerase sigma factor [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|326778910|ref|ZP_08238175.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
 gi|178466775|dbj|BAG21295.1| putative RNA polymerase sigma factor [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|326659243|gb|EGE44089.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
          Length = 323

 Score =  142 bits (358), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 48/236 (20%), Positives = 96/236 (40%), Gaps = 16/236 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            + LV  +L LV   A  +R    P+ ++V  G IGL++A+ +F+  RG    T++M  I
Sbjct: 99  RNTLVELNLALVKFAAARFRSRSEPMEDIVQVGTIGLIKAIDRFELSRGVEFPTFAMPTI 158

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      ++    +   V  ++++L +S
Sbjct: 159 VGEIKRFFRDTSWSVRVPRRLQELRLD-----LAKAGDELSQQLDRAPTVAELSERLGIS 213

Query: 170 ESEVIS-MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
             EV+  M+   A   S        D       D + Y+    E +             L
Sbjct: 214 PEEVVEGMSASNAYTASSLDAKPEEDDGEGALADRIGYEDHSLEGI--------EYVESL 265

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              ++ L  R+R I   R +    +T   +  E  +S+  V ++ +R   K+++ +
Sbjct: 266 KPLIAALPARDRMILSLRFVSN--MTQSEIGEELNISQMHVSRLLSRTLTKLRKGL 319


>gi|55274998|gb|AAV49296.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 198

 Score =  142 bits (358), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 55/208 (26%), Positives = 100/208 (48%), Gaps = 12/208 (5%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           ++  I+     +++      K L   LR  +     ++           IA++L+    +
Sbjct: 61  IERAIMNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDD 115

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           V  M        S++  +    +     +  L    D +E    +  +  + +  + + +
Sbjct: 116 VSRMLRLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWL 170

Query: 233 SVLNPRERRIFEARR--LQENPVTLENL 258
             LN ++R +   R   L     TLE++
Sbjct: 171 FELNAKQREVLARRFGLLGYEAATLEDV 198


>gi|55274901|gb|AAV49252.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 198

 Score =  142 bits (358), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 55/208 (26%), Positives = 97/208 (46%), Gaps = 12/208 (5%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           +     +++      K L   LR  +     ++           IA++L+    +V  M 
Sbjct: 61  MNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRML 115

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                  S++  +    +     +  L    D +E    +  +  + +  + + +  LN 
Sbjct: 116 RLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNA 170

Query: 238 RERRIFEARR--LQENPVTLENLSSEFE 263
           ++R +   R   L     TLE++  E  
Sbjct: 171 KQREVLARRFGLLGYEAATLEDVGREIG 198


>gi|291439213|ref|ZP_06578603.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291342108|gb|EFE69064.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 304

 Score =  142 bits (358), Expect = 7e-32,   Method: Composition-based stats.
 Identities = 49/236 (20%), Positives = 96/236 (40%), Gaps = 16/236 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            + LV  +L LV   A  +R    P+ +++  G IGL++A+ +F+  RG    T++M  I
Sbjct: 80  RNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFEMSRGVEFPTFAMPTI 139

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +   V  +A++L ++
Sbjct: 140 IGEIKRFFRDTSWSVRVPRRLQELRLD-----LAKAGDELAQQLDRAPTVAELAERLGIT 194

Query: 170 ESEVIS-MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
             EV+  M    A   S        D       D + Y+  G E +             L
Sbjct: 195 NDEVVEGMAASNAYTASSLDAQPEEDDAEGALADRIGYEDHGLEGI--------EYIESL 246

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              ++ L PR+R+I   R +    +T   +  E  +S+  V ++ +R   K++  +
Sbjct: 247 KPLIAELPPRDRKILSLRFVAG--MTQSEIGEELGISQMHVSRLLSRTLVKLRRGL 300


>gi|113955141|ref|YP_730472.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CC9311]
 gi|113882492|gb|ABI47450.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CC9311]
          Length = 282

 Score =  142 bits (358), Expect = 8e-32,   Method: Composition-based stats.
 Identities = 66/288 (22%), Positives = 125/288 (43%), Gaps = 33/288 (11%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVL-----------AKRYREHGDLSAAHRLVTS 56
           +       + +++ EI + P+L   EE  L           A   ++     A  R++ +
Sbjct: 1   MPFPDNGNIDQFLDEIGRTPLLTAAEEITLGTSVRMSQSPEATPAQKRAGKRAKDRMIKA 60

Query: 57  HLRLVVKIAMGYRGYGL---PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           +LRLVV ++  Y    L      ++V EG+IGL +AV+KFDPE G++ +TY+ WWI+ ++
Sbjct: 61  NLRLVVTVSRKYLHRQLGQLEFGDLVQEGSIGLNRAVEKFDPELGYKFSTYAYWWIRQSI 120

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK-KLNVSESE 172
              I ++ + +++ T+ N   +   L +L   L       L       +   +       
Sbjct: 121 SRAIDQTSATIRVPTSMNL--VLAKLNQLPQGLNDEQICELLEVSDTQLKNLRHAFVAKR 178

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           + S++ +L  D   + L        S                  E +    +R++  ++ 
Sbjct: 179 IASLDMKLGADRDGSTLTELLCDEQSTLN-------------YDEFQWEAVKRSLGDQAK 225

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             LN  +      RR   +  +L+++++E  +SRERVRQ   RA K +
Sbjct: 226 IALNNDQEL---LRRNVVDEQSLQSIANEIGISRERVRQKVDRAKKHL 270


>gi|295837882|ref|ZP_06824815.1| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
 gi|197699594|gb|EDY46527.1| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
          Length = 274

 Score =  142 bits (358), Expect = 8e-32,   Method: Composition-based stats.
 Identities = 59/241 (24%), Positives = 110/241 (45%), Gaps = 17/241 (7%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           EHG + AA  L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDPERG +  
Sbjct: 46  EHGRVRAA--LIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQFP 103

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           T++M  +   ++ Y   +   V +      +RL     ++    + +T  + +      I
Sbjct: 104 TFAMPTVVGEIKRYFRDNVRTVHVP-----RRLHELWVQVNSAAEDLTTAHGRSPTTAEI 158

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A++L ++E EV++         + +              D L Y+    + V        
Sbjct: 159 AERLRIAEDEVLACIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALDGV-------- 210

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             R+++   +  L  RE+RI   R    N +T   +S+E  VS+  V ++ AR+F +++ 
Sbjct: 211 EHRDLVRHLLVQLPEREQRILLLRYY--NNLTQSQISAELGVSQMHVSRLLARSFARLRS 268

Query: 283 S 283
           +
Sbjct: 269 A 269


>gi|167641125|ref|ZP_02399380.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0193]
 gi|167510905|gb|EDR86296.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0193]
          Length = 239

 Score =  141 bits (357), Expect = 9e-32,   Method: Composition-based stats.
 Identities = 67/264 (25%), Positives = 114/264 (43%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL  +  + GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLTKEEEEVLLNKLPK-GDQAARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  ++ R+                          
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMHLRRN-------------------------- 129

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                               N + SEV       + DE LN      D N     D L  
Sbjct: 130 --------------------NKNRSEV-------SFDEPLN---IDWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           D D    ++ +  E    R++L +++  LN RE++I E R         T ++++    +
Sbjct: 160 DDD----IITKDLEATVDRHLLMKALHQLNDREKQIMELRFGLAGGEEKTQKDVADMLGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 216 SQSYISRLEKRIIKRLRKKFNKMV 239


>gi|296125231|ref|YP_003632483.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Brachyspira murdochii
           DSM 12563]
 gi|296017047|gb|ADG70284.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Brachyspira murdochii
           DSM 12563]
          Length = 272

 Score =  141 bits (357), Expect = 9e-32,   Method: Composition-based stats.
 Identities = 52/273 (19%), Positives = 114/273 (41%), Gaps = 19/273 (6%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR-----GYGLPI 75
            E  KIP +    E    + ++          L+  +  LV  +A            +  
Sbjct: 6   KEKGKIPNITNDNEQEYWQEFKNTQSPYIREALIIKYSPLVKYVASKISVNMGSHKHIEF 65

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++V  G+ GLM A+ K++P R  +  TY++  I+ A+ + + +   L +     + ++ 
Sbjct: 66  QDLVGFGSFGLMDAIDKYNPNRDIKFKTYAVTRIRGAIYDELRKLDYLPR-----SIRKD 120

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL--AGDESLNALINSS 193
              + + +  L+A    N+KP     IA  L +  S+      R   A   SL+ +    
Sbjct: 121 VKEIEKAREILEARLSRNIKP---QEIADMLGIPISKYNETMKRYIEASPTSLSDVWYVG 177

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D +        +  +D      +   ER++ +N +  ++  L  +E+++       +  +
Sbjct: 178 DDSDEISVIDTLKSNDKTNPEYL--AEREDVKNKIVAALKKLPEKEKQVLILYYYDD--L 233

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TL+ +    EVS  R+ Q+  +A ++++ S+ +
Sbjct: 234 TLKEIGKVLEVSESRISQLHTKAIQQLRYSLSE 266


>gi|302535695|ref|ZP_07288037.1| RNA polymerase sigma-B factor [Streptomyces sp. C]
 gi|302444590|gb|EFL16406.1| RNA polymerase sigma-B factor [Streptomyces sp. C]
          Length = 355

 Score =  141 bits (357), Expect = 9e-32,   Method: Composition-based stats.
 Identities = 56/234 (23%), Positives = 103/234 (44%), Gaps = 15/234 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDPERG +  T++M  +
Sbjct: 132 RGALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQFPTFAMPTV 191

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ Y   +   V +      +RL     ++    + +T  + +      IA++L +S
Sbjct: 192 VGEIKRYFRDNVRTVHVP-----RRLHELWVQVNAATEDLTTLHGRTPTTPEIAERLRIS 246

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E EV+S         + +              D L Y+      V          R+++ 
Sbjct: 247 EDEVLSCIEAGRSYHATSLEAAQEGDGMPGLLDRLGYEDPELAGV--------EHRDLVR 298

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +  L  RE+RI   R    N +T   +S+E  VS+  V ++ AR+F +++ +
Sbjct: 299 HLLVQLPEREQRILLLRYY--NNLTQSQISAELGVSQMHVSRLLARSFARLRSA 350


>gi|75761672|ref|ZP_00741618.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|74490828|gb|EAO54098.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
          Length = 258

 Score =  141 bits (357), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 51/257 (19%), Positives = 117/257 (45%), Gaps = 16/257 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++  G +GL+ 
Sbjct: 11  LTKEDVIKLIAEFQQNQCNEAQERLVDHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLG 70

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++++D   G     +++  I   +++Y+      + +      +R+     ++K  ++ 
Sbjct: 71  AIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRIKDLGGKIKLAIEE 125

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +TD+  +  +++ IA  L +SE EV+ +          SL+ ++ +S   SS  +   V 
Sbjct: 126 LTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENSSDGSSVARIESVG 185

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           +       + +  E+  RR +L    +VLN  E+ +      +   +  ++      +S+
Sbjct: 186 E-------VEQGYEQTERRLVLEDIFNVLNDMEKSVIHYIFGEN--LNQKDTRERLGISQ 236

Query: 267 ERVRQIEARAFKKVQES 283
             V +I+ +A  K++++
Sbjct: 237 MHVSRIKRQAISKLKQA 253


>gi|301055395|ref|YP_003793606.1| sporulation sigma factor SigE [Bacillus anthracis CI]
 gi|300377564|gb|ADK06468.1| sporulation sigma factor SigE [Bacillus cereus biovar anthracis
           str. CI]
          Length = 238

 Score =  141 bits (357), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 67/264 (25%), Positives = 114/264 (43%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL  +  + GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 36  PPLTKEEEEVLLNKLPK-GDQAARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 94

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  ++ R+                          
Sbjct: 95  IKAVNTFNPEKKIKLATYASRCIENEILMHLRRN-------------------------- 128

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                               N + SEV       + DE LN      D N     D L  
Sbjct: 129 --------------------NKNRSEV-------SFDEPLN---IDWDGNELLLSDVLGT 158

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           D D    ++ +  E    R++L +++  LN RE++I E R         T ++++    +
Sbjct: 159 DDD----IITKDLEATVDRHLLMKALHQLNDREKQIMELRFGLAGGEEKTQKDVADMLGI 214

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 215 SQSYISRLEKRIIKRLRKEFNKMV 238


>gi|323099955|gb|ADX23555.1| RNA polymerase sigma-35 factor [Bacillus mycoides]
          Length = 239

 Score =  141 bits (357), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 67/264 (25%), Positives = 114/264 (43%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL  +  + GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLTKEEEEVLLNKLPK-GDQAARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  ++ R+                          
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMHLRRN-------------------------- 129

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                               N + SEV       + DE LN      D N     D L  
Sbjct: 130 --------------------NKNRSEV-------SFDEPLN---IDWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           D D    ++ +  E    R++L +++  LN RE++I E R         T ++++    +
Sbjct: 160 DDD----IITKDLEATVDRHLLMKALHQLNDREKQIMELRFGLAGGEEKTQKDVADMLGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 216 SQSYISRLEKRIIKRLRKEFNKMV 239


>gi|239930843|ref|ZP_04687796.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 308

 Score =  141 bits (357), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 49/236 (20%), Positives = 96/236 (40%), Gaps = 16/236 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            + LV  +L LV   A  +R    P+ +++  G IGL++A+ +F+  RG    T++M  I
Sbjct: 84  RNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFEMSRGVEFPTFAMPTI 143

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +   V  +A++L ++
Sbjct: 144 IGEIKRFFRDTSWSVRVPRRLQELRLD-----LAKAGDELAQQLDRAPTVAELAERLGIT 198

Query: 170 ESEVIS-MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
             EV+  M    A   S        D       D + Y+  G E +             L
Sbjct: 199 NDEVVEGMAASNAYTASSLDAQPEEDDAEGALADRIGYEDHGLEGI--------EYIESL 250

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              ++ L PR+R+I   R +    +T   +  E  +S+  V ++ +R   K++  +
Sbjct: 251 KPLIAELPPRDRKILSLRFVAG--MTQSEIGEELGISQMHVSRLLSRTLVKLRRGL 304


>gi|118443948|ref|YP_877996.1| RNA polymerase sigma factor for flagellar operon fliA [Clostridium
           novyi NT]
 gi|118134404|gb|ABK61448.1| RNA polymerase sigma factor for flagellar operon fliA [Clostridium
           novyi NT]
          Length = 242

 Score =  141 bits (357), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 53/242 (21%), Positives = 105/242 (43%), Gaps = 19/242 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              +V  ++ LV  IA      +   +   +++  G +GLM A  KFD  +G + +TY+ 
Sbjct: 10  KEEIVKKYIPLVKYIASRVIIGKTKYIEFEDLLGYGMLGLMDAFNKFDKSKGMKFSTYAS 69

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ +M + I ++  +         K     L +    ++++   NL    +  IAK+L
Sbjct: 70  IRIRGSMIDEIRKNSPI--------SKGAMDKLNKYNSAIESLQKRNLAEPNIKDIAKEL 121

Query: 167 NVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +++  +V  +   +      SL  LI S D + S          D       E+ E   +
Sbjct: 122 DMTVKQVGEIENFINYISIVSLEDLIFSEDDDISLMGTI----EDINSPNPEEEYENDEK 177

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              L++ + +LN ++R +      +E  +TL+ +     VS  RV Q+ +RA   +++ +
Sbjct: 178 LEYLSKGLDMLNEKDRTVLSLYYYEE--MTLKEIGKILGVSESRVCQLHSRAIVHLRKEL 235

Query: 285 QK 286
            K
Sbjct: 236 AK 237


>gi|229086469|ref|ZP_04218641.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock3-44]
 gi|228696786|gb|EEL49599.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock3-44]
          Length = 239

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 68/264 (25%), Positives = 115/264 (43%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL  +  + GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLTKEEEEVLLNKLPK-GDQAARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  ++ R+                          
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMHLRRN-------------------------- 129

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                               N + SEV       + DE LN      D N     D L  
Sbjct: 130 --------------------NKNRSEV-------SFDEPLN---IDWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           D D    ++ +  E    R++L +++  LN RE++I E R     E   T ++++    +
Sbjct: 160 DED----IITKDLEATVDRHLLMKALHQLNDREKQIMELRFGLAGEEEKTQKDVADMLGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 216 SQSYISRLEKRIIKRLRKEFNKMV 239


>gi|87303841|ref|ZP_01086550.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
 gi|87281651|gb|EAQ73647.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. WH 5701]
          Length = 215

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 51/204 (25%), Positives = 103/204 (50%), Gaps = 10/204 (4%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           +R    G   A  R++ ++LRLVV +A  Y+G GL + +++ EG++GL +AV+KFDP RG
Sbjct: 22  RRMLRIG-RRAKERMMKANLRLVVSVAKKYQGKGLELLDLIQEGSLGLERAVEKFDPTRG 80

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           ++ +TY+ WWI+ +M   I      +++    +++     L  ++     +         
Sbjct: 81  YKFSTYAFWWIRQSMTRAIACQSRTIRLPVHLSER-----LTTIRKVSLDLAHKLGAMPN 135

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            + IA+ +++   E+ S+  +     SL+A +N  ++  S   D +    D      ++ 
Sbjct: 136 RLEIAEAMDIPVEELDSLLRQALTTSSLDAPVN-GEEGRSFLGDLIA---DSSADEPLDI 191

Query: 219 EERKNRRNMLTRSMSVLNPRERRI 242
            E++     L R +S L+ +E+ +
Sbjct: 192 VEQRIHHEQLGRWLSHLSEQEQNV 215


>gi|282864142|ref|ZP_06273199.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
 gi|282561220|gb|EFB66765.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
          Length = 290

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 57/241 (23%), Positives = 104/241 (43%), Gaps = 17/241 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + L+  +L LV   A  +R  G   + ++V  G +GL++A+ +FD  R     ++++ 
Sbjct: 58  ARNTLIEMNLSLVRFAAGRFRSRGSGDMEDIVQVGTVGLIKAIDRFDLAREVEFTSFAVP 117

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +I   ++ +   +   V +     + R+  +L R K  L    D +     V  +A  L 
Sbjct: 118 YIVGEIKRFFRDTTWSVHVPRRLQELRV--DLARAKETLAVGLDRD---PTVQELAAHLG 172

Query: 168 VSESEV----ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + E EV    ++ N   AG  SL+    + D            D  G+    +E  E   
Sbjct: 173 LDEQEVTDGIVAANGYTAG--SLDMPAEAGDPAGRATGGRTFADVLGEPDPAMETVE--- 227

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             + L   +  L+ RERRI E R  QE  +T   +  E  +S+  V ++  R  +K++  
Sbjct: 228 NLHALAPLLEDLDARERRIIEMRFGQE--LTQAQIGDELGISQMHVSRLLGRTLRKLRAG 285

Query: 284 I 284
           +
Sbjct: 286 M 286


>gi|299538306|ref|ZP_07051591.1| RNA polymerase sigma-B factor [Lysinibacillus fusiformis ZC1]
 gi|298726508|gb|EFI67098.1| RNA polymerase sigma-B factor [Lysinibacillus fusiformis ZC1]
          Length = 261

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 60/261 (22%), Positives = 115/261 (44%), Gaps = 24/261 (9%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
            K++     + Y+   D  A   LV  +  LV  IA  Y        ++V  G +GL+ A
Sbjct: 11  SKEDVLKWIEMYQSTEDDEAQTNLVIHYRYLVESIARKYSNGKSYYDDIVQVGMLGLLGA 70

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +++FDP  G     +++  I   ++ ++      V +     +        R+K  ++A+
Sbjct: 71  IRRFDPNVGRSFEAFAVPTIVGEIKRFLRDKTWDVHVPRRIKELG-----PRIKSTVEAL 125

Query: 150 TDNNLKPEQVVAIAKKLNVSES------EVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
           T    +   +  IA++L V+E       E+      L+ D S+ +    SD ++    D 
Sbjct: 126 TIELQRSPSIKDIAERLEVAEEEVLEAMEMSRSYQALSMDHSIES---DSDGSTVTLFDI 182

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L  + DG         E  N+R ++  ++ VLN RE++I +   L    ++ +       
Sbjct: 183 LGREDDGY--------EMTNQRMIVQDALVVLNEREKQIIQLTYL--EQLSQKEAGERLG 232

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+  V +I+ +A KK+QE+I
Sbjct: 233 ISQMHVSRIQRKAIKKLQEAI 253


>gi|30021993|ref|NP_833624.1| sporulation sigma factor SigE [Bacillus cereus ATCC 14579]
 gi|30263906|ref|NP_846283.1| sporulation sigma factor SigE [Bacillus anthracis str. Ames]
 gi|42782997|ref|NP_980244.1| sporulation sigma factor SigE [Bacillus cereus ATCC 10987]
 gi|47529336|ref|YP_020685.1| sporulation sigma factor SigE [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49186754|ref|YP_030006.1| sporulation sigma factor SigE [Bacillus anthracis str. Sterne]
 gi|49478442|ref|YP_037966.1| sporulation sigma factor SigE [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|52141583|ref|YP_085245.1| sporulation sigma factor SigE [Bacillus cereus E33L]
 gi|162382776|ref|YP_896275.2| sporulation sigma factor SigE [Bacillus thuringiensis str. Al
           Hakam]
 gi|165872323|ref|ZP_02216960.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0488]
 gi|167636583|ref|ZP_02394877.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0442]
 gi|170688850|ref|ZP_02880053.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0465]
 gi|170708793|ref|ZP_02899229.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0389]
 gi|177654897|ref|ZP_02936614.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0174]
 gi|190566146|ref|ZP_03019065.1| RNA polymerase sigma-29 factor [Bacillus anthracis Tsiankovskii-I]
 gi|196035954|ref|ZP_03103356.1| RNA polymerase sigma-29 factor [Bacillus cereus W]
 gi|196038626|ref|ZP_03105934.1| RNA polymerase sigma-29 factor [Bacillus cereus NVH0597-99]
 gi|196045866|ref|ZP_03113095.1| RNA polymerase sigma-29 factor [Bacillus cereus 03BB108]
 gi|206971306|ref|ZP_03232257.1| RNA polymerase sigma-29 factor [Bacillus cereus AH1134]
 gi|206976716|ref|ZP_03237620.1| RNA polymerase sigma-29 factor [Bacillus cereus H3081.97]
 gi|217961326|ref|YP_002339894.1| sporulation sigma factor SigE [Bacillus cereus AH187]
 gi|218234749|ref|YP_002368704.1| sporulation sigma factor SigE [Bacillus cereus B4264]
 gi|218899058|ref|YP_002447469.1| RNA polymerase sigma-29 factor [Bacillus cereus G9842]
 gi|218905035|ref|YP_002452869.1| RNA polymerase sigma-29 factor [Bacillus cereus AH820]
 gi|222097350|ref|YP_002531407.1| sporulation sigma factor sige [Bacillus cereus Q1]
 gi|225865886|ref|YP_002751264.1| RNA polymerase sigma-29 factor [Bacillus cereus 03BB102]
 gi|227813186|ref|YP_002813195.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. CDC 684]
 gi|228902410|ref|ZP_04066564.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis IBL 4222]
 gi|228909730|ref|ZP_04073553.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis IBL 200]
 gi|228916542|ref|ZP_04080108.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228922657|ref|ZP_04085957.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228928953|ref|ZP_04091985.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228935220|ref|ZP_04098046.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228940993|ref|ZP_04103551.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228947624|ref|ZP_04109914.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228954181|ref|ZP_04116209.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228960122|ref|ZP_04121786.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228966858|ref|ZP_04127902.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           sotto str. T04001]
 gi|228973924|ref|ZP_04134499.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228980513|ref|ZP_04140823.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis Bt407]
 gi|228987049|ref|ZP_04147174.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|229047589|ref|ZP_04193179.1| RNA polymerase sigma-35 factor [Bacillus cereus AH676]
 gi|229071404|ref|ZP_04204626.1| RNA polymerase sigma-35 factor [Bacillus cereus F65185]
 gi|229081157|ref|ZP_04213667.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock4-2]
 gi|229092951|ref|ZP_04224084.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock3-42]
 gi|229111374|ref|ZP_04240927.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock1-15]
 gi|229123418|ref|ZP_04252622.1| RNA polymerase sigma-35 factor [Bacillus cereus 95/8201]
 gi|229129182|ref|ZP_04258155.1| RNA polymerase sigma-35 factor [Bacillus cereus BDRD-Cer4]
 gi|229140553|ref|ZP_04269108.1| RNA polymerase sigma-35 factor [Bacillus cereus BDRD-ST26]
 gi|229146476|ref|ZP_04274847.1| RNA polymerase sigma-35 factor [Bacillus cereus BDRD-ST24]
 gi|229152102|ref|ZP_04280297.1| RNA polymerase sigma-35 factor [Bacillus cereus m1550]
 gi|229180180|ref|ZP_04307524.1| RNA polymerase sigma-35 factor [Bacillus cereus 172560W]
 gi|229186145|ref|ZP_04313314.1| RNA polymerase sigma-35 factor [Bacillus cereus BGSC 6E1]
 gi|229192074|ref|ZP_04319043.1| RNA polymerase sigma-35 factor [Bacillus cereus ATCC 10876]
 gi|229198016|ref|ZP_04324730.1| RNA polymerase sigma-35 factor [Bacillus cereus m1293]
 gi|229601447|ref|YP_002868140.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0248]
 gi|254683386|ref|ZP_05147246.1| sporulation sigma factor SigE [Bacillus anthracis str. CNEVA-9066]
 gi|254721438|ref|ZP_05183227.1| sporulation sigma factor SigE [Bacillus anthracis str. A1055]
 gi|254735943|ref|ZP_05193649.1| sporulation sigma factor SigE [Bacillus anthracis str. Western
           North America USA6153]
 gi|254739808|ref|ZP_05197501.1| sporulation sigma factor SigE [Bacillus anthracis str. Kruger B]
 gi|254750998|ref|ZP_05203037.1| sporulation sigma factor SigE [Bacillus anthracis str. Vollum]
 gi|254757944|ref|ZP_05209971.1| sporulation sigma factor SigE [Bacillus anthracis str. Australia
           94]
 gi|296504398|ref|YP_003666098.1| sporulation sigma factor SigE [Bacillus thuringiensis BMB171]
 gi|49065841|sp|P62177|RP35_BACAN RecName: Full=RNA polymerase sigma-35 factor; Flags: Precursor
 gi|49065842|sp|P62178|RP35_BACCR RecName: Full=RNA polymerase sigma-35 factor; Flags: Precursor
 gi|49065843|sp|P62179|RP35_BACTK RecName: Full=RNA polymerase sigma-35 factor; Flags: Precursor
 gi|40335|emb|CAA40026.1| sigma factor 35 [Bacillus thuringiensis serovar kurstaki]
 gi|19918914|gb|AAL99378.1| sigma factor 35 [Bacillus thuringiensis serovar israelensis]
 gi|29897549|gb|AAP10825.1| RNA polymerase sigma-E factor [Bacillus cereus ATCC 14579]
 gi|30258550|gb|AAP27769.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. Ames]
 gi|42738924|gb|AAS42852.1| RNA polymerase sigma-29 factor [Bacillus cereus ATCC 10987]
 gi|47504484|gb|AAT33160.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49180681|gb|AAT56057.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. Sterne]
 gi|49329998|gb|AAT60644.1| RNA polymerase sporulation-specific sigma E factor [Bacillus
           thuringiensis serovar konkukian str. 97-27]
 gi|51975052|gb|AAU16602.1| RNA polymerase sporulation-specific sigma E factor [Bacillus cereus
           E33L]
 gi|164711999|gb|EDR17539.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0488]
 gi|165973128|gb|ABY76243.1| sigma factor [Bacillus thuringiensis]
 gi|167528006|gb|EDR90812.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0442]
 gi|170126278|gb|EDS95169.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0389]
 gi|170667205|gb|EDT17965.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0465]
 gi|172080408|gb|EDT65495.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0174]
 gi|190563065|gb|EDV17031.1| RNA polymerase sigma-29 factor [Bacillus anthracis Tsiankovskii-I]
 gi|195991603|gb|EDX55569.1| RNA polymerase sigma-29 factor [Bacillus cereus W]
 gi|196023306|gb|EDX61984.1| RNA polymerase sigma-29 factor [Bacillus cereus 03BB108]
 gi|196030349|gb|EDX68948.1| RNA polymerase sigma-29 factor [Bacillus cereus NVH0597-99]
 gi|206734078|gb|EDZ51249.1| RNA polymerase sigma-29 factor [Bacillus cereus AH1134]
 gi|206745026|gb|EDZ56429.1| RNA polymerase sigma-29 factor [Bacillus cereus H3081.97]
 gi|217065302|gb|ACJ79552.1| RNA polymerase sigma-29 factor [Bacillus cereus AH187]
 gi|218162706|gb|ACK62698.1| RNA polymerase sigma-29 factor [Bacillus cereus B4264]
 gi|218537297|gb|ACK89695.1| RNA polymerase sigma-29 factor [Bacillus cereus AH820]
 gi|218544009|gb|ACK96403.1| RNA polymerase sigma-29 factor [Bacillus cereus G9842]
 gi|221241408|gb|ACM14118.1| RNA polymerase sporulation-specific sigma E factor [Bacillus cereus
           Q1]
 gi|225791008|gb|ACO31225.1| RNA polymerase sigma-29 factor [Bacillus cereus 03BB102]
 gi|227003693|gb|ACP13436.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. CDC 684]
 gi|228585495|gb|EEK43599.1| RNA polymerase sigma-35 factor [Bacillus cereus m1293]
 gi|228591400|gb|EEK49250.1| RNA polymerase sigma-35 factor [Bacillus cereus ATCC 10876]
 gi|228597321|gb|EEK54972.1| RNA polymerase sigma-35 factor [Bacillus cereus BGSC 6E1]
 gi|228603389|gb|EEK60866.1| RNA polymerase sigma-35 factor [Bacillus cereus 172560W]
 gi|228631451|gb|EEK88085.1| RNA polymerase sigma-35 factor [Bacillus cereus m1550]
 gi|228637109|gb|EEK93568.1| RNA polymerase sigma-35 factor [Bacillus cereus BDRD-ST24]
 gi|228643114|gb|EEK99390.1| RNA polymerase sigma-35 factor [Bacillus cereus BDRD-ST26]
 gi|228654419|gb|EEL10284.1| RNA polymerase sigma-35 factor [Bacillus cereus BDRD-Cer4]
 gi|228660194|gb|EEL15830.1| RNA polymerase sigma-35 factor [Bacillus cereus 95/8201]
 gi|228672150|gb|EEL27441.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock1-15]
 gi|228690455|gb|EEL44239.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock3-42]
 gi|228702201|gb|EEL54677.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock4-2]
 gi|228711695|gb|EEL63648.1| RNA polymerase sigma-35 factor [Bacillus cereus F65185]
 gi|228723836|gb|EEL75191.1| RNA polymerase sigma-35 factor [Bacillus cereus AH676]
 gi|228772643|gb|EEM21084.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228779333|gb|EEM27590.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis Bt407]
 gi|228785790|gb|EEM33794.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228792957|gb|EEM40515.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           sotto str. T04001]
 gi|228799638|gb|EEM46591.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228805501|gb|EEM52092.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228812144|gb|EEM58475.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228818672|gb|EEM64739.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228824385|gb|EEM70191.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228830760|gb|EEM76365.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228837086|gb|EEM82427.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228843121|gb|EEM88203.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228850019|gb|EEM94850.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis IBL 200]
 gi|228857154|gb|EEN01660.1| RNA polymerase sigma-35 factor [Bacillus thuringiensis IBL 4222]
 gi|229265855|gb|ACQ47492.1| RNA polymerase sigma-29 factor [Bacillus anthracis str. A0248]
 gi|296325450|gb|ADH08378.1| sporulation sigma factor SigE [Bacillus thuringiensis BMB171]
 gi|308154178|gb|ADA55132.3| sporulation specific sigma factor E [Bacillus thuringiensis serovar
           aizawai]
 gi|308154180|gb|ADA55133.2| sporulation specific sigma factor E [Bacillus thuringiensis serovar
           aizawai]
 gi|324327803|gb|ADY23063.1| sporulation sigma factor SigE [Bacillus thuringiensis serovar
           finitimus YBT-020]
 gi|326941674|gb|AEA17570.1| sporulation sigma factor SigE [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 239

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 67/264 (25%), Positives = 114/264 (43%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL  +  + GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLTKEEEEVLLNKLPK-GDQAARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  ++ R+                          
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMHLRRN-------------------------- 129

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                               N + SEV       + DE LN      D N     D L  
Sbjct: 130 --------------------NKNRSEV-------SFDEPLN---IDWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           D D    ++ +  E    R++L +++  LN RE++I E R         T ++++    +
Sbjct: 160 DDD----IITKDLEATVDRHLLMKALHQLNDREKQIMELRFGLAGGEEKTQKDVADMLGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 216 SQSYISRLEKRIIKRLRKEFNKMV 239


>gi|294631664|ref|ZP_06710224.1| RNA polymerase sigma factor WhiG [Streptomyces sp. e14]
 gi|292834997|gb|EFF93346.1| RNA polymerase sigma factor WhiG [Streptomyces sp. e14]
          Length = 280

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 48/256 (18%), Positives = 104/256 (40%), Gaps = 16/256 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
            L + Y+  GD     +L+  +  LV  +A          +  ++ VS G  GL+ A++K
Sbjct: 33  ELWRSYKATGDERLREQLILHYSPLVKYVAGRVSVGLPPNVEQADFVSSGVFGLIDAIEK 92

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD +R  +  TY++  I+ AM + + R+   +        + +      L+  L+     
Sbjct: 93  FDIDREIKFETYAITRIRGAMIDEL-RALDWIPRSVRQKARNVERAYATLEARLR----- 146

Query: 153 NLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
             +      +A ++ ++  E+ ++     LA   +L  L++           ++    D 
Sbjct: 147 --RTPTETEVAGEMGIAVDELHAVFSQLSLANVVALEELLHVG-GEDGDGLSFMDTLEDT 203

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                +E  E +  R  L R+++ L  RE+ +          +TL  + +   V+  RV 
Sbjct: 204 AADNPVEVAEDRELRRFLARAINTLPEREKTVVTLYYY--EGLTLAEIGNVLGVTESRVS 261

Query: 271 QIEARAFKKVQESIQK 286
           QI  ++  +++  +  
Sbjct: 262 QIHTKSVLQLRAKLAS 277


>gi|294813001|ref|ZP_06771644.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|326441452|ref|ZP_08216186.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|294325600|gb|EFG07243.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 306

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 48/240 (20%), Positives = 102/240 (42%), Gaps = 18/240 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            + LV  +L LV   A  +R    P+ ++V  G IGL++A+ +F+  RG    T++M  +
Sbjct: 82  RNTLVELNLSLVRFAAARFRSRSEPMDDIVQVGTIGLIKAIDRFELSRGVEFPTFAMPTV 141

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +T    +   V  +A+ L + 
Sbjct: 142 IGEIKRFFRDTSWSVRVPRRLQELRLD-----LARAGDELTARLDRSPTVAELAEYLGIG 196

Query: 170 ESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
             EV+   +        SL+A    ++++     + + Y+  G E V             
Sbjct: 197 ADEVVEGMVASNAYTPSSLDAR-PQNEEHDGTLAERIGYEDGGLEGV--------EYIES 247

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   ++ L  R+RRI   R   +  +T  ++  E  +S+ +V ++ +R   +++  +  +
Sbjct: 248 LKPLIAGLPDRDRRILSLRFGAD--MTQSDIGEELGISQMQVSRLLSRTLVRLRRGLTAE 305


>gi|108803518|ref|YP_643455.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108764761|gb|ABG03643.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 274

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 65/255 (25%), Positives = 115/255 (45%), Gaps = 13/255 (5%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG-YGLPISEVVSEGNIGLMQAVKK 92
           E  L +R    GD  A  R++ SHL L   +A  Y   + +P  +++ EG + L+ AV  
Sbjct: 24  EQALLERAA-SGDREARRRVIESHLGLAAALARRYARRWVVPFEDLLQEGALALVHAVDH 82

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           +DP RG R +TY+ WW+K A++   +     +++      +R +    RL    + +   
Sbjct: 83  YDPSRGMRFSTYATWWVKQAIRRAAMAYARPMRVP-----ERTWRLSERLAEAERELRAE 137

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +  +   +   L  SE E+  +   +    SL + +   +++     D +    D   
Sbjct: 138 LGREIEDRDLRSGLGWSEEELSEVRRAMGPVVSLESPVGEEEEDV--LGDLVA---DENA 192

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ-ENPVTLENLSSEFEVSRERVRQ 271
           +   E   R + R  L  ++S L  RER +   R      P T  +L  E  VSRER RQ
Sbjct: 193 EDPAELAARNDARRRLAHALSALPRRERAVLAGRYGLTGEPRTFVDLGRELGVSRERARQ 252

Query: 272 IEARAFKKVQESIQK 286
           +E  A ++++E  ++
Sbjct: 253 LERAAAERLREHGRR 267


>gi|229031536|ref|ZP_04187536.1| RNA polymerase sigma-35 factor [Bacillus cereus AH1271]
 gi|229075661|ref|ZP_04208643.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock4-18]
 gi|229098375|ref|ZP_04229320.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock3-29]
 gi|229104467|ref|ZP_04235134.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock3-28]
 gi|229117401|ref|ZP_04246777.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock1-3]
 gi|229162840|ref|ZP_04290797.1| RNA polymerase sigma-35 factor [Bacillus cereus R309803]
 gi|229174571|ref|ZP_04302101.1| RNA polymerase sigma-35 factor [Bacillus cereus MM3]
 gi|228608876|gb|EEK66168.1| RNA polymerase sigma-35 factor [Bacillus cereus MM3]
 gi|228620722|gb|EEK77591.1| RNA polymerase sigma-35 factor [Bacillus cereus R309803]
 gi|228666011|gb|EEL21477.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock1-3]
 gi|228678909|gb|EEL33119.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock3-28]
 gi|228684992|gb|EEL38925.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock3-29]
 gi|228707437|gb|EEL59628.1| RNA polymerase sigma-35 factor [Bacillus cereus Rock4-18]
 gi|228729825|gb|EEL80805.1| RNA polymerase sigma-35 factor [Bacillus cereus AH1271]
          Length = 239

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 68/264 (25%), Positives = 115/264 (43%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL  +  + GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLTKEEEEVLLNKLPK-GDQAARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  ++ R+                          
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMHLRRN-------------------------- 129

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                               N + SEV       + DE LN      D N     D L  
Sbjct: 130 --------------------NKNRSEV-------SFDEPLN---IDWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           D D    ++ +  E    R++L +++  LN RE++I E R     E   T ++++    +
Sbjct: 160 DDD----IITKDLEATVDRHLLMKALHQLNDREKQIMELRFGLAGEEEKTQKDVADMLGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 216 SQSYISRLEKRIIKRLRKEFNKMV 239


>gi|330862244|emb|CBX72405.1| RNA polymerase sigma factor rpoD [Yersinia enterocolitica W22703]
          Length = 553

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 43/170 (25%), Positives = 78/170 (45%), Gaps = 7/170 (4%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 386 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 445

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 446 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 503

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
            L R+   +         PE    +A+++ + E ++  +        S+ 
Sbjct: 504 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPISME 550


>gi|158319069|ref|YP_001511576.1| FliA/WhiG family RNA polymerase sigma factor [Alkaliphilus
           oremlandii OhILAs]
 gi|158139268|gb|ABW17580.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           oremlandii OhILAs]
          Length = 270

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 51/259 (19%), Positives = 111/259 (42%), Gaps = 18/259 (6%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           E  L K Y    D+   + L+  HL +   ++  +   G+   ++    ++GL+ A++++
Sbjct: 27  EKELFKEYALTRDIEIRNELINRHLYIAEILSKKFLNKGIEYEDIYQVASLGLIYAIERY 86

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D  +GF  ++++   I   +++Y       +++     +  L   +   K  LQ      
Sbjct: 87  DVTKGFEFSSFATPTIIGEIKKYFRDKGWSIRVPRRIQE--LSKKVNVSKNTLQQTLQ-- 142

Query: 154 LKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDG 210
            +   V  IA+ LN +E EVI      ++   +SL+ +  N  D    Q  D +      
Sbjct: 143 -RTPTVKDIAEYLNCTEEEVIEAMEASQVYTPKSLDLIYDNDGDDKDIQLLDLIGELDKR 201

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
            + +          ++   +++  LN  E+++ + R    N  T   +S E  VS+  V 
Sbjct: 202 FDDI--------ENKDFFQKAIDKLNEVEKKVLKDRFF--NNKTQMKVSEELNVSQMTVS 251

Query: 271 QIEARAFKKVQESIQKQVE 289
           ++E R  +K ++ + + +E
Sbjct: 252 RMEKRIIEKFKKELDRSME 270


>gi|229019107|ref|ZP_04175942.1| RNA polymerase sigma-35 factor [Bacillus cereus AH1273]
 gi|229025351|ref|ZP_04181769.1| RNA polymerase sigma-35 factor [Bacillus cereus AH1272]
 gi|228735936|gb|EEL86513.1| RNA polymerase sigma-35 factor [Bacillus cereus AH1272]
 gi|228742207|gb|EEL92372.1| RNA polymerase sigma-35 factor [Bacillus cereus AH1273]
          Length = 232

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 67/264 (25%), Positives = 114/264 (43%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL  +  + GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 30  PPLTKEEEEVLLNKLPK-GDQAARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 88

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  ++ R+                          
Sbjct: 89  IKAVNTFNPEKKIKLATYASRCIENEILMHLRRN-------------------------- 122

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                               N + SEV       + DE LN      D N     D L  
Sbjct: 123 --------------------NKNRSEV-------SFDEPLN---IDWDGNELLLSDVLGT 152

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           D D    ++ +  E    R++L +++  LN RE++I E R         T ++++    +
Sbjct: 153 DDD----IITKDLEATVDRHLLMKALHQLNDREKQIMELRFGLAGGEEKTQKDVADMLGI 208

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 209 SQSYISRLEKRIIKRLRKEFNKMV 232


>gi|118418349|gb|ABK86768.1| RNA polymerase, sigma 29 subunit, SigE [Bacillus thuringiensis str.
           Al Hakam]
          Length = 248

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 67/264 (25%), Positives = 114/264 (43%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL  +  + GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 46  PPLTKEEEEVLLNKLPK-GDQAARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 104

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  ++ R+                          
Sbjct: 105 IKAVNTFNPEKKIKLATYASRCIENEILMHLRRN-------------------------- 138

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                               N + SEV       + DE LN      D N     D L  
Sbjct: 139 --------------------NKNRSEV-------SFDEPLN---IDWDGNELLLSDVLGT 168

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           D D    ++ +  E    R++L +++  LN RE++I E R         T ++++    +
Sbjct: 169 DDD----IITKDLEATVDRHLLMKALHQLNDREKQIMELRFGLAGGEEKTQKDVADMLGI 224

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 225 SQSYISRLEKRIIKRLRKEFNKMV 248


>gi|302542195|ref|ZP_07294537.1| RNA polymerase sigma factor WhiG [Streptomyces hygroscopicus ATCC
           53653]
 gi|302459813|gb|EFL22906.1| RNA polymerase sigma factor WhiG [Streptomyces himastatinicus ATCC
           53653]
          Length = 277

 Score =  141 bits (356), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 52/254 (20%), Positives = 107/254 (42%), Gaps = 16/254 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
            L + Y+  GD     +L+  +  LV  +A          +  ++ VS G  GL+ A++K
Sbjct: 30  ELWRSYKATGDGRLREQLILHYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEK 89

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FDPER  +  TY++  I+ AM + + R+   +        + +      L+  L+     
Sbjct: 90  FDPERAIKFETYAITRIRGAMIDEL-RALDWIPRSVRQKARAVERAYATLEAALR----- 143

Query: 153 NLKPEQVVAIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
             +    V +A ++++S  E+  +     LA   +L  L++   +   +    +    D 
Sbjct: 144 --RTPTEVEVAAEMDISVDELHGVFSQLSLANVVALEELLHVGGEGGDRL-SLMDTLEDT 200

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                +E  E +  R +L R+++ L  RE+ +          +TL  +     V+  RV 
Sbjct: 201 AADNPVEVAEDRELRRLLARAINTLPEREKTVVTLYYY--EGLTLAEIGQVLGVTESRVS 258

Query: 271 QIEARAFKKVQESI 284
           QI  ++  +++  +
Sbjct: 259 QIHTKSVLQLRAKL 272


>gi|257055039|ref|YP_003132871.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Saccharomonospora
           viridis DSM 43017]
 gi|256584911|gb|ACU96044.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Saccharomonospora
           viridis DSM 43017]
          Length = 295

 Score =  141 bits (355), Expect = 1e-31,   Method: Composition-based stats.
 Identities = 53/255 (20%), Positives = 102/255 (40%), Gaps = 15/255 (5%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVK 91
             L K +          RLV  +  LV  +A          + +++++  G  GL+ A++
Sbjct: 45  QALWKEFVRSPSQRVRDRLVLHYAPLVKYVAGRVGTGLPTHIDVADLIQSGIFGLVDAIE 104

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFDPERG R  TY+M  I+ A+ + +      V     +  + +     RL   L+    
Sbjct: 105 KFDPERGLRFETYAMQRIRGAILDDLRSQ-DWVPRAVRSRAREIERAHERLGARLR---- 159

Query: 152 NNLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
              +      +A +L ++  E+  +    RL    +L+ L+ +S  N +          D
Sbjct: 160 ---RTPTDAEVAAELGITLRELRDLYGQLRLTSVLALDDLMGASKDNGNGTGSPADTLPD 216

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
                       ++ R  L  +++ LN R+R +      +   +TL  +     V+  RV
Sbjct: 217 DGAVDPAAVLVDQDNRRQLAEAIAQLNERDRIVVSLYYFEN--LTLAEIGKVLGVTESRV 274

Query: 270 RQIEARAFKKVQESI 284
            Q+  RA  +++  +
Sbjct: 275 SQLHTRAVLRLRAKL 289


>gi|317121837|ref|YP_004101840.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Thermaerobacter
           marianensis DSM 12885]
 gi|315591817|gb|ADU51113.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Thermaerobacter
           marianensis DSM 12885]
          Length = 261

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 59/259 (22%), Positives = 111/259 (42%), Gaps = 18/259 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKK 92
            L +RYR   D  +   L+  HL LV  +A     +    + + +++S G  GLM+A+++
Sbjct: 13  ELWRRYRTTADPESWEALIREHLPLVRYLAGRMIIHLPPQVELDDLISYGIFGLMEAIRR 72

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           +DP RG +  TY+   I+ AM + + R+   V        + +    RRL+  L      
Sbjct: 73  YDPARGVKFETYAYTRIRGAMLDGL-RAMDWVPQTLRRRARDVEACYRRLENRL------ 125

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYDHDG 210
             +P     +A +L +   E   +   LA     SL+ ++ S   + +   D L    D 
Sbjct: 126 -GRPANDDEVAAELGLKPEEFAGLLQELARTTVVSLDDVLPSDSDDPAAVLDRLA---DP 181

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                ++     + R  L  +++ L  RER +          +T++ ++    VS  RV 
Sbjct: 182 GATDPLQAATLADLRRRLADALAGLPERERLVVSLYYY--EGLTVKEIAEVMGVSPSRVS 239

Query: 271 QIEARAFKKVQESIQKQVE 289
           Q+  RA  +++  +  + E
Sbjct: 240 QLHTRAILRLRARLGAEEE 258


>gi|187778269|ref|ZP_02994742.1| hypothetical protein CLOSPO_01861 [Clostridium sporogenes ATCC
           15579]
 gi|187771894|gb|EDU35696.1| hypothetical protein CLOSPO_01861 [Clostridium sporogenes ATCC
           15579]
          Length = 251

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 40/253 (15%), Positives = 106/253 (41%), Gaps = 17/253 (6%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           ++   L +  R  G+  A  +LV  +L LV  I+  +   G    ++   G IGL++A+ 
Sbjct: 14  EDNMELMEEAR-SGNKQALDKLVEVNLPLVSAISKKFLNRGYEYDDIFQIGCIGLVKAIN 72

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
            F+ +   + +TY++  I   ++ ++     ++K+  +          ++L    + +  
Sbjct: 73  NFETKYNVKFSTYAVPMIMGEIKRFLRDDG-IIKVSRSIK-----TAAKKLHYDKEKLCK 126

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +   +  +++    +  E++      +  + L  +I+  D       D +  +    
Sbjct: 127 ELNREPTIEELSQFSGYTVDEILMATESSSSPQYLYDVIHQDDGAPVLLIDKISEN---- 182

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
                E++ +      L  ++  L+ + R+I   R  ++   T   ++ +  +S+ +V +
Sbjct: 183 ----TEEDNKIIDNIALKEALKNLDIKSRQIIILRYFKD--KTQIEVAKQLGISQVQVSR 236

Query: 272 IEARAFKKVQESI 284
           IE +  K ++E +
Sbjct: 237 IEKKVLKLMKEKL 249


>gi|297202660|ref|ZP_06920057.1| RNA polymerase sigma-G factor [Streptomyces sviceus ATCC 29083]
 gi|197713235|gb|EDY57269.1| RNA polymerase sigma-G factor [Streptomyces sviceus ATCC 29083]
          Length = 280

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 48/256 (18%), Positives = 104/256 (40%), Gaps = 16/256 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
            L + Y+  GD     +L+  +  LV  +A          +  ++ VS G  GL+ A++K
Sbjct: 33  ELWRSYKATGDERLREQLILHYSPLVKYVAGRVSVGLPPNVEQADFVSSGVFGLIDAIEK 92

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD +R  +  TY++  I+ AM + + R+   +        + +      L+  L+     
Sbjct: 93  FDLDREIKFETYAITRIRGAMIDEL-RALDWIPRSVRQKARNVERAYATLEARLR----- 146

Query: 153 NLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
             +      +A +L ++  ++ ++     LA   +L  L++           ++    D 
Sbjct: 147 --RTPTEGEVAGELGIAVDDLHAVFSQLSLANVVALEELLHVG-GEGGDGLSFMDTLEDP 203

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                +E  E +  R  L R+++ L  RE+ +          +TL  + +   V+  RV 
Sbjct: 204 AADNPVEVAEDRELRRFLARAINTLPEREKTVVTLYYY--EGLTLAEIGNVLGVTESRVS 261

Query: 271 QIEARAFKKVQESIQK 286
           QI  ++  +++  +  
Sbjct: 262 QIHTKSVLQLRAKLAS 277


>gi|291549326|emb|CBL25588.1| RNA polymerase sigma-F factor [Ruminococcus torques L2-14]
          Length = 239

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 44/247 (17%), Positives = 106/247 (42%), Gaps = 16/247 (6%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R    GD  A   LV  ++ L+  +   + G G    ++   G+IGL++A+ KFD     
Sbjct: 9   RKSHDGDKKAREELVEKNIGLIWCVVKRFYGRGAEPEDLFQIGSIGLLKAIDKFDFSYEV 68

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY++  I   ++ ++     ++K+  +   + L +   + +   + +T    +   +
Sbjct: 69  QFSTYAVPMISGEIRRFLRDDG-MIKVSRSL--RELSYKSLQAR---EKMTRILGREPTL 122

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             ++++L +   E++         ES+   I+  + +     D L      +E+VL    
Sbjct: 123 KELSEELQIDCEEIVQAMESSVEVESIYKPIHQKEGSEILLMDKLEEKDRQEEKVL---- 178

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
                R +L   +  L  +ER I   R       T   +  +  +S+ +V + E +  ++
Sbjct: 179 ----DRIVLKEVLETLEAKERTIIYLRYFAG--KTQAEIGKKMGMSQVQVSRTEKKVLER 232

Query: 280 VQESIQK 286
           +++ +++
Sbjct: 233 MRKEMKR 239


>gi|296168913|ref|ZP_06850582.1| RNA polymerase sigma-F factor [Mycobacterium parascrofulaceum ATCC
           BAA-614]
 gi|295896382|gb|EFG76035.1| RNA polymerase sigma-F factor [Mycobacterium parascrofulaceum ATCC
           BAA-614]
          Length = 262

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 46/236 (19%), Positives = 95/236 (40%), Gaps = 13/236 (5%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             ++V   L L   IA  + G G P  ++V    +GL+ AV +FD + G    ++++  I
Sbjct: 40  RDKIVERCLPLADHIARRFEGRGEPRDDLVQVARVGLVNAVVRFDVDAGSDFVSFAVPTI 99

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   VK+     +  L     RL      ++    +      +A +L + 
Sbjct: 100 MGEVRRHFRDNSWSVKVPRRLKELHL-----RLGTATAELSQRLGRAPTATELAAELGMD 154

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             EV+     L    S N L   S   S + +   + D  G     +++ E +     L 
Sbjct: 155 REEVVE---GLVAGSSYNTLSIDSGGGSDEDEARAIADTLGDVDTGLDRIEDQ---ESLR 208

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             +  L  RER +   R      +T   ++    +S+  V ++ A++  ++++ +Q
Sbjct: 209 PLLEALPERERTVLVLRFF--ESMTQTQIAERVGISQMHVSRLLAKSLTRLRDQLQ 262


>gi|291004131|ref|ZP_06562104.1| putative RNA polymerase sigma factor [Saccharopolyspora erythraea
           NRRL 2338]
          Length = 328

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 59/259 (22%), Positives = 113/259 (43%), Gaps = 21/259 (8%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAV 90
             L K + +  D     RLV  +  LV  +A    G GLP    +S+++  G  GL+ A+
Sbjct: 84  VALWKAFGQQRDQELRDRLVLHYAPLVKYVAGR-VGTGLPSHVEVSDLIQSGIFGLVDAI 142

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +KF+PERG +  TY+M  I+ A+ + +      V     +  + +   L RL+  LQ   
Sbjct: 143 EKFEPERGLKFETYAMQRIRGAILDDLRAQ-DWVPRSVRSRARDVERALERLEAKLQ--- 198

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
               +      +A++L +S  E+  +    ++    +L+ LI +    SS          
Sbjct: 199 ----RTASDAELAEELELSVDELRELFAQLQMTSVVALDDLIGAGQTTSS----LAETLP 250

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D + +  +     ++ R  L  ++  L+ R+R +      +   +TL  +     V+  R
Sbjct: 251 DDRAEDPVATLVDRDSRRQLAEAVERLSDRDRIVVTLYYFEN--LTLAEIGKVLGVTESR 308

Query: 269 VRQIEARAFKKVQESIQKQ 287
           V Q+  RA  +++  + +Q
Sbjct: 309 VCQLHTRAVLRLRTKLTEQ 327


>gi|23098085|ref|NP_691551.1| RNA polymerase sigma factor SigB [Oceanobacillus iheyensis HTE831]
 gi|22776310|dbj|BAC12586.1| RNA polymerase general stress sigma factor (sigma B)
           [Oceanobacillus iheyensis HTE831]
          Length = 263

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 54/260 (20%), Positives = 114/260 (43%), Gaps = 20/260 (7%)

Query: 33  EEYVLAKRY--REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           +E      Y  ++  +     ++V  +  LV  IA  Y        ++V  G IGL+ AV
Sbjct: 13  DEVYQWIEYLQKDPTNEEIQEKIVLKYQDLVGSIARKYSKNSAIHEDLVQVGMIGLLAAV 72

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +++DP  G    ++++  I   ++ +I      V +     +        +++  +  +T
Sbjct: 73  RRYDPTYGKSFESFAIPTIIGEIKRFIRDKTWSVHVPRRIKELG-----PKIRKGVDELT 127

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA---LINSSDKNSSQWQDWLVYD 207
            +N K   V  IAK +  SE EV+         ++L+    +   SD ++    D +   
Sbjct: 128 TDNQKSPTVAEIAKYIGTSEEEVLETMEMGQSYKALSVDRKIEADSDGSTVAILDLVGNS 187

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            DG + V         +R ML + + +L+ RE++I E    +   ++ +       +S+ 
Sbjct: 188 EDGYDNV--------EQRMMLEKILPILSEREQQILECTYFKN--MSQKETGELLGISQM 237

Query: 268 RVRQIEARAFKKVQESIQKQ 287
            V +++ R+ +K++E+IQ +
Sbjct: 238 HVSRLQRRSLRKLREAIQSE 257


>gi|284043274|ref|YP_003393614.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
 gi|283947495|gb|ADB50239.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
          Length = 258

 Score =  141 bits (355), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 46/254 (18%), Positives = 100/254 (39%), Gaps = 17/254 (6%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
             +E+ L +R+ E  D  A   L+   + LV  +A  Y   G P+ ++   G +GL++AV
Sbjct: 14  AADEHELLRRWHEERDEDARRALIERMMPLVRSLARRYANRGEPLDDLEQVGCVGLIKAV 73

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
            +FD  R  R +T+++  I   ++ +       V++     +        R+      ++
Sbjct: 74  DRFDLSRELRFSTFAVPTILGEIKRHFRDRAWSVRVSRGLQELSA-----RVTREADRLS 128

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
               +   +  +A+  N +  +V+          ++       D      +         
Sbjct: 129 TKLGRSPTIEDLAEATNSTPEQVLEALQGAQAYSTVPLEEPLGDDGEPVARIGAEDPE-- 186

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                    E    R  L+R + VL+ RERRI   R      +T   ++    +S+  V 
Sbjct: 187 --------FELAEERIELSRGLHVLSERERRIVLLRFFAG--LTQREIAERVGISQMHVS 236

Query: 271 QIEARAFKKVQESI 284
           ++  R+ +++ +++
Sbjct: 237 RLLRRSLERMGDTM 250


>gi|330946209|gb|EGH47399.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. pisi
           str. 1704B]
          Length = 230

 Score =  140 bits (354), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 46/180 (25%), Positives = 79/180 (43%), Gaps = 9/180 (5%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L+  E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 55  LKIAEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 114

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 115 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 172

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                    PE    + +++ + E ++  +        S+   I   D   S   D++  
Sbjct: 173 LQEMGREPTPE---ELGERMEMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFIED 227


>gi|297582861|ref|YP_003698641.1| LuxR family transcriptional regulator [Bacillus selenitireducens
           MLS10]
 gi|297141318|gb|ADH98075.1| transcriptional regulator, LuxR family [Bacillus selenitireducens
           MLS10]
          Length = 268

 Score =  140 bits (354), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 53/258 (20%), Positives = 118/258 (45%), Gaps = 16/258 (6%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           +K+ +  +   ++E GD     +LV  +  LV  +A  +        ++V  G IGL+ A
Sbjct: 18  DKERQLKMIAEFQETGDDEIQTQLVLEYENLVHALARKFSRGQRHDEDLVQVGMIGLLAA 77

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +++FDP  G    ++++  I   ++ +I      V +     +        ++K  ++ +
Sbjct: 78  LRRFDPSFGRSFESFAVPTIVGEIKRFIRDKTWSVHVPRRIKELG-----PKIKSAVENL 132

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNC--RLAGDESLNALINSSDKNSSQWQDWLVYD 207
           T    +  QV  IA  L VSE E++      +     S++  I + D+ S+     LV  
Sbjct: 133 TTELQRSPQVEEIADYLEVSEEEILETMEMGKSYQALSVDRSIEADDEGSAVTLLDLVG- 191

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
                  +    E+ +++ +L ++  VL  RE++I +    +   ++ +    +  +S+ 
Sbjct: 192 ------SVESGYEQTDQQLLLEKAFQVLTDREKQILQLTYFEN--MSQKETGEQLGISQM 243

Query: 268 RVRQIEARAFKKVQESIQ 285
            V +++ RA +K+++SI+
Sbjct: 244 HVSRLQRRALQKLKDSIR 261


>gi|325660705|ref|ZP_08149334.1| RNA polymerase sigma-F factor [Lachnospiraceae bacterium 4_1_37FAA]
 gi|331085570|ref|ZP_08334654.1| RNA polymerase sigma-F factor [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|325473012|gb|EGC76221.1| RNA polymerase sigma-F factor [Lachnospiraceae bacterium 4_1_37FAA]
 gi|330407457|gb|EGG86959.1| RNA polymerase sigma-F factor [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 240

 Score =  140 bits (354), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 52/251 (20%), Positives = 105/251 (41%), Gaps = 17/251 (6%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             L +R  + GD  A  +LV  +  LV  I   + G G    ++   G+IGL++A+ KFD
Sbjct: 5   IALIQRSHD-GDEKAREQLVEENTGLVWCIVKRFFGRGTDSEDLFQIGSIGLLKAIDKFD 63

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
                + +TY++  I   ++ ++     ++K+  +  +      L R +     +     
Sbjct: 64  LNYDVKFSTYAVPMISGEIRRFLRDDG-MIKVSRSLKETAYKAFLARER-----LQKKYN 117

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +   +  +A +L V + E+          ESL+  I   D N  Q  D L  +   +E +
Sbjct: 118 REPTMEELAAELEVEKEELAMALDASGEVESLHKPIYQKDGNEIQLLDKLEEEEGQEETI 177

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
           L           ++ + +  L+  ER++   R       T   +  +  +S+ +V ++E 
Sbjct: 178 L--------NHMLIRQLLEELDREERQLIYLRYFANQ--TQSEIGKKLGISQVQVSRLEK 227

Query: 275 RAFKKVQESIQ 285
           +  K ++  IQ
Sbjct: 228 KILKNMRTKIQ 238


>gi|297199468|ref|ZP_06916865.1| RNA polymerase sigma-B factor [Streptomyces sviceus ATCC 29083]
 gi|197712989|gb|EDY57023.1| RNA polymerase sigma-B factor [Streptomyces sviceus ATCC 29083]
          Length = 282

 Score =  140 bits (354), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 46/239 (19%), Positives = 102/239 (42%), Gaps = 18/239 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + L+  ++ LV   A  +R      + ++V  G IGL++A+ +F+  R     ++S+ 
Sbjct: 55  ARNTLIEMNISLVRYAASRFRSRDPEEMEDIVQVGVIGLIKAIDRFELSREVEFTSFSIP 114

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +I   ++ +   +   V +     + R+     +L    + ++    +   V  +A+ +N
Sbjct: 115 YIVGEIKRFFRDTTWAVHVPRRLQEARV-----QLARATEELSTRLGRTPTVAELAQLMN 169

Query: 168 VSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           + E EVI   +        SL+A I + D   +   D++  D            E     
Sbjct: 170 LEEKEVIEARLASNGYRSSSLDAAIGNGDDGETALADFIGTDDG--------ALELVEDF 221

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + L   ++ L+ R R+I   R ++E   T   +     +S+  V ++ +R   +++E +
Sbjct: 222 HALAPMIAALDERSRKILHWRFVEE--ATQAQIGERLGISQMHVSRLLSRTLAQLREGM 278


>gi|330468593|ref|YP_004406336.1| RNA polymerase sigma-70 factor [Verrucosispora maris AB-18-032]
 gi|328811564|gb|AEB45736.1| RNA polymerase sigma-70 factor [Verrucosispora maris AB-18-032]
          Length = 292

 Score =  140 bits (354), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 59/253 (23%), Positives = 111/253 (43%), Gaps = 25/253 (9%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   LV   L    ++A  YRG G P+ ++     +GL+ AV ++DPERG     Y+  
Sbjct: 41  EARDDLVRFALPFAGRLARRYRGRGEPLEDLEQVARLGLVNAVDRYDPERGS-FTAYAAI 99

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I   ++ +       V +      +RL   +  +     A+T    +   V  ++K+L+
Sbjct: 100 TIVGEIKRHFRDRTWGVHVP-----RRLRDLILEVGQATAALTSELSRAPTVAELSKRLD 154

Query: 168 VSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
             E E+++     AG    SLNA +    ++S+++ D +       E V        + R
Sbjct: 155 TPEEEILAALESAAGYSPASLNAPV--GGESSAEFGDLVGESDIALESV--------DDR 204

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             ++  +  L  RERRI   R       T   +++ F +S+  V ++ +RA   +++++ 
Sbjct: 205 VTVSGLLHRLPWRERRILAMRFYGNQ--TQAEIAARFGISQMHVSRLLSRALTWLRQAM- 261

Query: 286 KQVELSSSPPLLQ 298
               L+ +PP  Q
Sbjct: 262 ----LADAPPPWQ 270


>gi|117928753|ref|YP_873304.1| RNA polymerase sigma factor WhiG [Acidothermus cellulolyticus 11B]
 gi|117649216|gb|ABK53318.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Acidothermus
           cellulolyticus 11B]
          Length = 289

 Score =  140 bits (354), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 54/259 (20%), Positives = 117/259 (45%), Gaps = 18/259 (6%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAV 90
             L +R++E GD     RL+  +  LV  +A    G GLP     +++VS G  GL+ A+
Sbjct: 40  RDLWRRFKETGDPELRERLILHYSPLVKYVAGR-VGVGLPPNIEQADLVSYGIFGLIDAI 98

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +KFD +R  +  TY++  IK A+ + + R+   +            +  R ++    A+ 
Sbjct: 99  EKFDLDRAIKFETYAINRIKGAIIDEL-RAIDWIPRSVR-------YKAREVEKAYAALE 150

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDH 208
               +      +A +L +S  E+ ++  +++     +L+ L+N       +    +    
Sbjct: 151 HKLHRTPTEAEVAAELGISLDELHAIFSQVSFVNVIALDELLNVGGDRGDRL-SLVDTLE 209

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D + +  +E  E +  + +L+R+++ L  RE+ +          +TL  +     V+  R
Sbjct: 210 DTKAEDPVEAFETEETKYLLSRAINALPEREKIVITLYYY--EGLTLAEIGQVLGVTESR 267

Query: 269 VRQIEARAFKKVQESIQKQ 287
           + Q+  +A  +++  + +Q
Sbjct: 268 ICQMHTKAVLQLRAKLAEQ 286


>gi|197302589|ref|ZP_03167644.1| hypothetical protein RUMLAC_01318 [Ruminococcus lactaris ATCC
           29176]
 gi|197298487|gb|EDY33032.1| hypothetical protein RUMLAC_01318 [Ruminococcus lactaris ATCC
           29176]
          Length = 248

 Score =  140 bits (354), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 57/262 (21%), Positives = 107/262 (40%), Gaps = 64/262 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE ++E  +  R     D  A   L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 43  PPLENEKEEEVIGRLGTEDDQEAKKLLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGL 102

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+  F+P +  +LATY+   I+  +  Y+ R+                          
Sbjct: 103 IKAINTFNPTKKIKLATYASRCIENEILMYLRRNSKT----------------------- 139

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                             KL VS  E ++++                D N     D L  
Sbjct: 140 ------------------KLEVSIDEPLNVD---------------WDGNELLLSDILGT 166

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP----VTLENLSSEF 262
           D D   + L  + ERK    +L R+++ L+ RE+ I   R   ++P    +T + ++   
Sbjct: 167 DEDTIYKDLENEAERK----ILFRALNKLSGREKMIVRMRFGLDHPEGKEMTQKEVADLL 222

Query: 263 EVSRERVRQIEARAFKKVQESI 284
            +S+  + ++E +   +++  +
Sbjct: 223 GISQSYISRLEKKIMTRLRREM 244


>gi|152976265|ref|YP_001375782.1| sporulation sigma factor SigE [Bacillus cereus subsp. cytotoxis NVH
           391-98]
 gi|152025017|gb|ABS22787.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           cytotoxicus NVH 391-98]
          Length = 239

 Score =  140 bits (353), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 67/264 (25%), Positives = 113/264 (42%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL  +  + GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLTKEEEEVLLNKLPK-GDQAARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  ++ R+                          
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMHLRRN-------------------------- 129

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                               N + SEV       + DE LN      D N     D L  
Sbjct: 130 --------------------NKNRSEV-------SFDEPLN---IDWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           D D    ++ +  E    R +L +++  LN RE++I E R         T ++++    +
Sbjct: 160 DDD----IITKDLEANVDRYLLMKALHQLNDREKQIMELRFGLAGGEEKTQKDVADMLGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 216 SQSYISRLEKRIIKRLRKEFNKMV 239


>gi|307330048|ref|ZP_07609199.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306884309|gb|EFN15344.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 277

 Score =  140 bits (353), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 51/254 (20%), Positives = 106/254 (41%), Gaps = 16/254 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
            L + Y+  GD     +L+  +  LV  +A          +  ++ VS G  GL+ A++K
Sbjct: 30  ELWRSYKTTGDGRLREQLILHYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEK 89

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FDPER  +  TY++  I+ AM + + R+   +        + +      L+  L+     
Sbjct: 90  FDPERAIKFETYAITRIRGAMIDEL-RALDWIPRSVRQKARAVERAYATLEAQLR----- 143

Query: 153 NLKPEQVVAIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
             +      +A ++++S  E+  +     LA   +L  L++   +   +    +    D 
Sbjct: 144 --RTPSEAEVAAEMDISIEELHGVFSQLSLANVVALEELLHVGGEGGDRL-SLMDTLEDT 200

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                +E  E +  R +L R+++ L  RE+ +          +TL  +     V+  RV 
Sbjct: 201 AADNPVEVAEDRELRRLLARAINTLPEREKTVVTLYYY--EGLTLAEIGQVLGVTESRVS 258

Query: 271 QIEARAFKKVQESI 284
           QI  ++  +++  +
Sbjct: 259 QIHTKSVLQLRAKL 272


>gi|295109465|emb|CBL23418.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase
           sigma-70 factor, sigma-B/F/G subfamily [Ruminococcus
           obeum A2-162]
          Length = 238

 Score =  140 bits (353), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 48/254 (18%), Positives = 108/254 (42%), Gaps = 17/254 (6%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
            ++   L  R  + GD  A  RL   +  L+   A  + G G+ + ++   G+IGL++AV
Sbjct: 2   PEDTLALIGRAHQ-GDKEARERLFHENTGLIYCAAKRFLGRGVDMEDLFQIGSIGLLKAV 60

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
            KFD     + +TY++  I   ++ ++     ++K+  +  +     N  R+    + + 
Sbjct: 61  DKFDTSYDVKFSTYAVPMIIGEIKRFLRDDG-ILKVSRSVKE-----NQYRIGRKREELE 114

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
               +   +  +A+ + +   E+          ES+  +I   + N  +  D +    + 
Sbjct: 115 KTLGREPTLGELAESVQMLPEELAMTMDAANDVESIYQIIYQGEGNELRLLDKIPEKEN- 173

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                    +R   +  L   +  LN  ER++   R  +E  +T   ++ EF VS+ ++ 
Sbjct: 174 -------LHDRLLNKIFLEELLRSLNAEERKLLYMRYFRE--MTQTEVADEFGVSQVQIS 224

Query: 271 QIEARAFKKVQESI 284
           ++E +   +++  I
Sbjct: 225 RMEKKILNRLRAII 238


>gi|329938754|ref|ZP_08288150.1| SigF-like sigma factor [Streptomyces griseoaurantiacus M045]
 gi|329302245|gb|EGG46137.1| SigF-like sigma factor [Streptomyces griseoaurantiacus M045]
          Length = 305

 Score =  140 bits (353), Expect = 2e-31,   Method: Composition-based stats.
 Identities = 54/234 (23%), Positives = 101/234 (43%), Gaps = 15/234 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDPERG +  T++M  +
Sbjct: 82  RGALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPERGVQFPTFAMPTV 141

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ Y   +   V +      +RL     ++    + +T    +      IA++L + 
Sbjct: 142 VGEIKRYFRDNVRTVHVP-----RRLHELWVQVNSATEDLTTAFGRSPTTAEIAERLRIG 196

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E EV+S         + +              D L Y+    + V          R+++ 
Sbjct: 197 EEEVLSCIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALDGV--------EHRDLVR 248

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +  L  RE+RI   R      +T   +S+E  VS+  V ++ AR+F +++ +
Sbjct: 249 HLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLLARSFARLRSA 300


>gi|239981813|ref|ZP_04704337.1| RNA polymerase sigma factor [Streptomyces albus J1074]
          Length = 328

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 49/236 (20%), Positives = 95/236 (40%), Gaps = 16/236 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            + LV  +L LV   A  +R    P+ +++  G IGL++A+ +F+  RG    T++M  I
Sbjct: 104 RNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRGVEFPTFAMPTI 163

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +   V  +A +L +S
Sbjct: 164 IGEIKRFFRDTSWSVRVPRRLQELRLD-----LAKAGDELAQKLDRAPTVRELADRLGLS 218

Query: 170 ESEVIS-MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           + EV+  M    A   S        D +     D + Y+  G E +             L
Sbjct: 219 QEEVVEGMAASNAYTASSLDAQPEEDDSEGALADRIGYEDHGIEGI--------EYVESL 270

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              ++ L  R+RRI   R      +T   +  E  +S+  V ++  R   ++++ +
Sbjct: 271 KPLIAELPARDRRILSLRFTAN--MTQSEIGEELGISQMHVSRLLTRTLNRLRKGL 324


>gi|55274897|gb|AAV49250.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 198

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 55/208 (26%), Positives = 96/208 (46%), Gaps = 12/208 (5%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL +  ++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           +     +++      K L   LR  +     ++           IA++L+    +V  M 
Sbjct: 61  MNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRML 115

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                  S++  +    +     +  L    D +E    +  +  + +  + + +  LN 
Sbjct: 116 RLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNA 170

Query: 238 RERRIFEARR--LQENPVTLENLSSEFE 263
           ++R +   R   L     TLE++  E  
Sbjct: 171 KQREVLARRFGLLGYEAATLEDVGREIG 198


>gi|154685948|ref|YP_001421109.1| sporulation sigma factor SigE [Bacillus amyloliquefaciens FZB42]
 gi|154351799|gb|ABS73878.1| SigE [Bacillus amyloliquefaciens FZB42]
          Length = 239

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 64/264 (24%), Positives = 112/264 (42%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL  +    GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLSKEEEQVLLLKL-PSGDQAARAILIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+                    +++   
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN-------------------NKIRSE- 135

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                            ++ DE LN      D N     D L  
Sbjct: 136 ---------------------------------VSFDEPLN---IDWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           D D    ++ +  E    + +L +++  LN RE++I E R     E   T ++++    +
Sbjct: 160 DDD----IITKDIEANVDKKLLKKALEQLNEREKQIMELRFGLVGEEEKTQKDVADMMGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 216 SQSYISRLEKRIIKRLRKEFNKMV 239


>gi|319893019|ref|YP_004149894.1| RNA polymerase sigma factor SigB [Staphylococcus pseudintermedius
           HKU10-03]
 gi|317162715|gb|ADV06258.1| RNA polymerase sigma factor SigB [Staphylococcus pseudintermedius
           HKU10-03]
          Length = 256

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 50/263 (19%), Positives = 107/263 (40%), Gaps = 24/263 (9%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             ++     + Y+   D  A  +LV  + +L+  +A  Y        ++V  G +GL+ A
Sbjct: 12  SPEQINQWIQAYQNDEDHEAQEKLVKHYEKLIESLAYKYSKGQSHHEDLVQVGMVGLIGA 71

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +FD     +   + +  +   ++ Y+      V +     +        R+K     +
Sbjct: 72  INRFDLSFDRKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIG-----PRIKKVSDEL 126

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNC------RLAGDESLNALINSSDKNSSQWQDW 203
           T+   +   +  IA++L VS+ +V+           L+ D S+ A     D ++    D 
Sbjct: 127 TNELGRSPSISEIAERLEVSDEDVLEAMEMGQSYNALSVDHSIEA---DKDGSTVTLLDI 183

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    D          E   +R +L R + +L  RER I +   +  + ++ +       
Sbjct: 184 MGQHDDNY--------ELTEKRMILERILPILTDREREIIQCTFI--DGLSQKETGERIG 233

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+  V +++  A KK+QE+ +K
Sbjct: 234 LSQMHVSRLQRTAIKKLQEAARK 256


>gi|297561355|ref|YP_003680329.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
 gi|296845803|gb|ADH67823.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
          Length = 285

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 52/255 (20%), Positives = 105/255 (41%), Gaps = 15/255 (5%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTS----HLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           E +LA+ +    D   A  L       +  LV K+A  Y G G P+ ++     +GL++A
Sbjct: 34  EDMLAELHGLDRDDPRADDLCERVVVLYQPLVNKLARRYNGRGEPLDDLQQTAMLGLVKA 93

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +  F+P+RG    +Y +  +   ++ +       V++     + R+     +L+  L   
Sbjct: 94  IHGFNPDRGKPFISYLLPTVTGEIKRHFRDHTWAVRVSRRHQENRI-----KLRQALNDF 148

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
              + +   V  +++++ + E+EV  +        SL+     +  +  Q    L  DH 
Sbjct: 149 QQAHARTPTVHELSEEMGLPEAEVGELIQVSESYRSLSLDAPDTSDSDGQEGTRL-EDHL 207

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
           G E    E  E   +R  L  +++ L  RER I   R   +   T   ++     S+  V
Sbjct: 208 GSED---EGLELVVQRESLKPALARLPEREREILMLRFFGD--HTQSEIADCLGYSQMHV 262

Query: 270 RQIEARAFKKVQESI 284
            ++      +++E +
Sbjct: 263 SRLLNGVLGQLREEM 277


>gi|290962991|ref|YP_003494173.1| sigma factor [Streptomyces scabiei 87.22]
 gi|260652517|emb|CBG75650.1| sigma factor [Streptomyces scabiei 87.22]
          Length = 283

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 50/239 (20%), Positives = 103/239 (43%), Gaps = 18/239 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + L+  ++ LV   A  +R  G   + ++V  G IGL++A+ +F+  R     T+++ 
Sbjct: 56  ARNTLIEMNISLVRYAAGRFRSRGADEMEDIVQVGMIGLIKAIDRFELSREVEFTTFAVP 115

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +I   ++ +   +   V +     + R+      L      ++    +   V  +A+ +N
Sbjct: 116 YIVGEIRRFFRDTSWAVHVPRRLKEARV-----ELARATDELSSRLGRSPTVKELAELMN 170

Query: 168 VSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           +SE EVI       G    SL+A I   +   +   D++  +  G E V           
Sbjct: 171 LSEDEVIEARLAANGYNSSSLDAAIGGDETGEAALADFIGSEDAGMELV--------EDF 222

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + L   +S L  R+RRI   R ++E  +T   ++     S+  V ++ +R   +++  +
Sbjct: 223 HALAPLLSELGDRDRRIIHMRFVEE--LTQAQIAEHLGCSQMHVSRLLSRTLARLRRGM 279


>gi|297616993|ref|YP_003702152.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
 gi|297144830|gb|ADI01587.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
          Length = 241

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 66/262 (25%), Positives = 112/262 (42%), Gaps = 63/262 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L  +EE  L +R  E GD      L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 39  PPLSSEEESTLLQRL-EQGDNGVKSTLIEHNLRLVVYIAKKFENTGINIEDLVSIGTIGL 97

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+P +  +LATY+   I+  +  Y+ R+                     LK   
Sbjct: 98  IKAVNTFEPRKNIKLATYASRCIENEILMYLRRN---------------------LKTRA 136

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +                          +S++  L  D          D N     D L  
Sbjct: 137 E--------------------------VSLDEPLNVD---------WDGNELLLSDVLGT 161

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEV 264
           D D   + + E+ E+K    +L++++  L PRE+RI + R   E+    T + ++    +
Sbjct: 162 DGDMIYKTIEEEVEKK----LLSQAILRLPPREKRIIQLRFGLEDGYEKTQKEVADILGI 217

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+  + ++E R  K+++  I+K
Sbjct: 218 SQSYISRLEKRILKRLRREIRK 239


>gi|323463926|gb|ADX76079.1| RNA polymerase sigma-B factor [Staphylococcus pseudintermedius
           ED99]
          Length = 256

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 50/263 (19%), Positives = 106/263 (40%), Gaps = 24/263 (9%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             ++     + Y+   D  A  +LV  + +L+  +A  Y        ++V  G +GL+ A
Sbjct: 12  SPEQINQWIQAYQNDEDHEAQEKLVKHYEKLIESLAYKYSKGQSHHEDLVQVGMVGLIGA 71

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +FD     +   + +  +   ++ Y+      V +     +        R+K     +
Sbjct: 72  INRFDLSFDRKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIG-----PRIKKVSDEL 126

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNC------RLAGDESLNALINSSDKNSSQWQDW 203
           T+   +   +  IA +L VS+ +V+           L+ D S+ A     D ++    D 
Sbjct: 127 TNELGRSPSISEIADRLEVSDEDVLEAMEMGQSYNALSVDHSIEA---DKDGSTVTLLDI 183

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    D          E   +R +L R + +L  RER I +   +  + ++ +       
Sbjct: 184 MGQHDDNY--------ELTEKRMILERILPILTDREREIIQCTFI--DGLSQKETGERIG 233

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+  V +++  A KK+QE+ +K
Sbjct: 234 LSQMHVSRLQRTAIKKLQEAARK 256


>gi|294630217|ref|ZP_06708777.1| RNA polymerase sigma-F factor [Streptomyces sp. e14]
 gi|292833550|gb|EFF91899.1| RNA polymerase sigma-F factor [Streptomyces sp. e14]
          Length = 314

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 53/234 (22%), Positives = 103/234 (44%), Gaps = 15/234 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDP+RG +  T++M  +
Sbjct: 91  RGALIEANLPLVRYAAGRFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFPTFAMPTV 150

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ Y   +   V +      +RL     ++    + +T    +      IA++L ++
Sbjct: 151 VGEIKRYFRDNVRTVHVP-----RRLHELWVQVNSATEDLTTAFGRSPTTAEIAERLRIT 205

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E EV+S         + +              D L Y+    + V          R+++ 
Sbjct: 206 EEEVLSCIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALDGV--------EHRDLVR 257

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +  L  RE+RI   R      +T   +S+E  VS+  V ++ AR+F++++ +
Sbjct: 258 HLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLLARSFQRLRSA 309


>gi|302558130|ref|ZP_07310472.1| RNA polymerase sigma factor WhiG [Streptomyces griseoflavus Tu4000]
 gi|302475748|gb|EFL38841.1| RNA polymerase sigma factor WhiG [Streptomyces griseoflavus Tu4000]
          Length = 280

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 50/254 (19%), Positives = 103/254 (40%), Gaps = 16/254 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
            L + Y+  GD     +L+  +  LV  +A          +   + VS G  GL+ A++K
Sbjct: 33  ELWRSYKATGDERLREQLILHYSPLVKYVAGRVSVGLPPNVDQGDFVSSGVFGLIDAIEK 92

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD +R  +  TY++  I+ AM + + R+   +        + +      L+  L+     
Sbjct: 93  FDVDREIKFETYAITRIRGAMIDEL-RALDWIPRSVRQKARNVERAYATLEARLR----- 146

Query: 153 NLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
             +      +A +L ++  E+ ++     LA   +L  L++     S      +    D 
Sbjct: 147 --RTPSESEVAGELGIAVDELHAVFSQLSLANVVALEELLHVG-GESGDRLSLMDTLEDT 203

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                +E  E +  R  L R+++ L  RE+ +          +TL  + +   V+  RV 
Sbjct: 204 AADDPVEVAEDRELRRFLARAINTLPEREKTVVTLYYY--EGLTLAEIGNVLGVTESRVS 261

Query: 271 QIEARAFKKVQESI 284
           QI  ++  +++  +
Sbjct: 262 QIHTKSVLQLRAKL 275


>gi|159037890|ref|YP_001537143.1| anti-sigma-factor antagonist [Salinispora arenicola CNS-205]
 gi|157916725|gb|ABV98152.1| anti-sigma-factor antagonist [Salinispora arenicola CNS-205]
          Length = 374

 Score =  140 bits (353), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 59/254 (23%), Positives = 111/254 (43%), Gaps = 25/254 (9%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   LV   L    ++A  YRG G P+ ++     +GL+ AV ++DPERG     Y+ 
Sbjct: 40  QEARDDLVRFALPFAGRLARRYRGRGEPLEDLEQVARLGLVNAVDRYDPERGS-FTAYAA 98

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I   ++ +       V +      +RL   +  +     A+T    +   V  +A++L
Sbjct: 99  ITIVGEIKRHFRDRTWGVHVP-----RRLRDLILEVGQATAALTSELSRAPTVAELARRL 153

Query: 167 NVSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
              E E+++     AG    SLNA +    ++S+++ D +    +  E V        + 
Sbjct: 154 ETPEEEILAALESAAGYSPASLNAPV--GGESSAEFGDLVGESDNALESV--------DD 203

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  ++  +  L  RERRI   R       T   +++ F +S+  V ++ +RA   +++++
Sbjct: 204 RVTVSGLLHRLPWRERRILAMRFYGNQ--TQAEIAARFGISQMHVSRLLSRALTWLRQAM 261

Query: 285 QKQVELSSSPPLLQ 298
                L+ +PP  Q
Sbjct: 262 -----LADAPPPWQ 270


>gi|229157483|ref|ZP_04285560.1| RNA polymerase sigma-35 factor [Bacillus cereus ATCC 4342]
 gi|228625933|gb|EEK82683.1| RNA polymerase sigma-35 factor [Bacillus cereus ATCC 4342]
          Length = 223

 Score =  139 bits (352), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 67/264 (25%), Positives = 114/264 (43%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL  +  + GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 21  PPLTKEEEEVLLNKLPK-GDQAARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 79

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  ++ R+                          
Sbjct: 80  IKAVNTFNPEKKIKLATYASRCIENEILMHLRRN-------------------------- 113

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                               N + SEV       + DE LN      D N     D L  
Sbjct: 114 --------------------NKNRSEV-------SFDEPLN---IDWDGNELLLSDVLGT 143

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           D D    ++ +  E    R++L +++  LN RE++I E R         T ++++    +
Sbjct: 144 DDD----IITKDLEATVDRHLLMKALHQLNDREKQIMELRFGLAGGEEKTQKDVADMLGI 199

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 200 SQSYISRLEKRIIKRLRKEFNKMV 223


>gi|328880278|emb|CCA53517.1| RNA polymerase sigma factor SigB [Streptomyces venezuelae ATCC
           10712]
          Length = 290

 Score =  139 bits (352), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 58/253 (22%), Positives = 111/253 (43%), Gaps = 16/253 (6%)

Query: 35  YVLAKRYR-EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
             LA R     G     + L+  ++ LVV  A  +R  G  + ++V  G IGL++A+ +F
Sbjct: 44  RELAAREEGTEGHQYVRNTLIEMNMSLVVYAAGRFRARGDEMEDIVQVGMIGLIKAIDRF 103

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D  R    AT+++ +I   ++ +   S   V +     + R+      L      ++   
Sbjct: 104 DLSREVEFATFAVPYIVGEIKRFFRDSTWAVHVPRRLQEARV-----ELAKATDELSSRL 158

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQ 211
            +  +V  +A  +++SE +V+       G    SL+A +   D   S+  D  + D  GQ
Sbjct: 159 GRAPRVAELAPAMDLSEEQVVEAQVAANGYHSTSLDAAVAGGD---SEDDDAALADLIGQ 215

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E   IE  E  +    L  ++    PR+R +   R ++E  +T   +     VS+  V +
Sbjct: 216 EDPAIELFEDFHTLAPLVEALG---PRDRLLLHLRFVEE--LTQSEIGERLGVSQMHVSR 270

Query: 272 IEARAFKKVQESI 284
           + AR  ++++  +
Sbjct: 271 LLARNIERLRAGM 283


>gi|20808064|ref|NP_623235.1| sporulation sigma factor SigE [Thermoanaerobacter tengcongensis
           MB4]
 gi|20516645|gb|AAM24839.1| DNA-directed RNA polymerase sigma subunits (sigma70/sigma32)
           [Thermoanaerobacter tengcongensis MB4]
          Length = 241

 Score =  139 bits (352), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 57/262 (21%), Positives = 108/262 (41%), Gaps = 63/262 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L  +EE  L  +  E GD  A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 39  PPLSVEEESYLISKM-EKGDNEAKSILIERNLRLVVYIAKKFENTGVGIEDLISIGTIGL 97

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+  F+P +  +LATY+   I+  +  Y+ R+                          
Sbjct: 98  IKAINTFNPRKKIKLATYASRCIENEILMYLRRNNKT----------------------- 134

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                             +L VS  E ++++                D N     D L  
Sbjct: 135 ------------------RLEVSFDEPLNVD---------------WDGNELLLSDILGT 161

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEV 264
           D++   + + ++ E    R +LT ++  L  RE++I   R   E     T + ++    +
Sbjct: 162 DNETVYKYIEDEVE----RELLTSALKKLPDREKKIIRLRFGLEGGTEKTQKEVADMLGI 217

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+  + ++E +  K++++ + +
Sbjct: 218 SQSYISRLEKKILKRLKKEMNR 239


>gi|297156863|gb|ADI06575.1| RNA polymerase sigma factor WhiG [Streptomyces bingchenggensis
           BCW-1]
          Length = 277

 Score =  139 bits (352), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 56/252 (22%), Positives = 105/252 (41%), Gaps = 12/252 (4%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
            L + Y+  GD     +L+  +  LV  +A          +  ++ VS G  GL+ A++K
Sbjct: 30  ELWRSYKSTGDGRLREQLILHYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEK 89

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FDPER  +  TY++  I+ AM + +    +L  I  +  QK     + R    L+A    
Sbjct: 90  FDPERAIKFETYAITRIRGAMIDELR---ALDWIPRSVRQKA--RAVERAYATLEAALRR 144

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
                +V A    + + E   +     LA   +L  L+++S     +    +    D   
Sbjct: 145 TPSEAEVAA-EMDIGLDELHGVFSQLSLANVVALEDLLHAS-GEGGERLSLMDTLEDTAA 202

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
              +E  E +  R +L R+++ L  RE+ +          +TL  +     V+  RV QI
Sbjct: 203 DNPVEVAEDRELRRLLARAINTLPEREKTVVTLYYY--EGLTLAEIGQVLGVTESRVSQI 260

Query: 273 EARAFKKVQESI 284
             ++  +++  +
Sbjct: 261 HTKSVLQLRAKL 272


>gi|213621937|ref|ZP_03374720.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 197

 Score =  139 bits (352), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 52/200 (26%), Positives = 95/200 (47%), Gaps = 10/200 (5%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             R++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI
Sbjct: 1   RRRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWI 60

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           +  ++  I+     +++      K L   LR  +     ++           IA++L+  
Sbjct: 61  RQTIERAIMNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKP 115

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             +V  M        S++  +    + +      L    D +E    +  +  + +  + 
Sbjct: 116 VDDVSRMLRLNERITSVDTPLGGDSEKA-----LLDILADEKENGPEDTTQDDDMKQSIV 170

Query: 230 RSMSVLNPRERRIFEARRLQ 249
           + +  LN ++R +   R   
Sbjct: 171 KWLFELNAKQREVLARRFGL 190


>gi|291453672|ref|ZP_06593062.1| SigI protein [Streptomyces albus J1074]
 gi|291356621|gb|EFE83523.1| SigI protein [Streptomyces albus J1074]
          Length = 285

 Score =  139 bits (352), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 49/236 (20%), Positives = 95/236 (40%), Gaps = 16/236 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            + LV  +L LV   A  +R    P+ +++  G IGL++A+ +F+  RG    T++M  I
Sbjct: 61  RNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRGVEFPTFAMPTI 120

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +   V  +A +L +S
Sbjct: 121 IGEIKRFFRDTSWSVRVPRRLQELRLD-----LAKAGDELAQKLDRAPTVRELADRLGLS 175

Query: 170 ESEVIS-MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           + EV+  M    A   S        D +     D + Y+  G E +             L
Sbjct: 176 QEEVVEGMAASNAYTASSLDAQPEEDDSEGALADRIGYEDHGIEGI--------EYVESL 227

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              ++ L  R+RRI   R      +T   +  E  +S+  V ++  R   ++++ +
Sbjct: 228 KPLIAELPARDRRILSLRFTAN--MTQSEIGEELGISQMHVSRLLTRTLNRLRKGL 281


>gi|75764483|ref|ZP_00743968.1| RNA polymerase sigma-E factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|74488030|gb|EAO51761.1| RNA polymerase sigma-E factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
          Length = 224

 Score =  139 bits (352), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 67/264 (25%), Positives = 114/264 (43%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL  +  + GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 22  PPLTKEEEEVLLNKLPK-GDQAARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 80

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  ++ R+                          
Sbjct: 81  IKAVNTFNPEKKIKLATYASRCIENEILMHLRRN-------------------------- 114

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                               N + SEV       + DE LN      D N     D L  
Sbjct: 115 --------------------NKNRSEV-------SFDEPLN---IDWDGNELLLSDVLGT 144

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           D D    ++ +  E    R++L +++  LN RE++I E R         T ++++    +
Sbjct: 145 DDD----IITKDLEATVDRHLLMKALHQLNDREKQIMELRFGLAGGEEKTQKDVADMLGI 200

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 201 SQSYISRLEKRIIKRLRKEFNKMV 224


>gi|145594674|ref|YP_001158971.1| sigma-70 region 2 domain-containing protein [Salinispora tropica
           CNB-440]
 gi|145304011|gb|ABP54593.1| sigma-70 region 2 domain protein [Salinispora tropica CNB-440]
          Length = 284

 Score =  139 bits (352), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 59/254 (23%), Positives = 111/254 (43%), Gaps = 25/254 (9%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   LV   L    ++A  YRG G P+ ++     +GL+ AV ++DPERG     Y+ 
Sbjct: 40  QEARDDLVRFALPFAGRLARRYRGRGEPLEDLEQVARLGLVNAVDRYDPERGS-FTAYAA 98

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I   ++ +       V +      +RL   +  +     A+T    +   V  +A++L
Sbjct: 99  ITIVGEIKRHFRDRTWGVHVP-----RRLRDLILEVGQATAALTSELSRAPTVAELARRL 153

Query: 167 NVSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
              E E+++     AG    SLNA +    ++S+++ D +    +  E V        + 
Sbjct: 154 ETPEEEILAALESAAGYSPASLNAPV--GGESSAEFGDLVGESDNALESV--------DD 203

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  ++  +  L  RERRI   R       T   +++ F +S+  V ++ +RA   +++++
Sbjct: 204 RVTVSGLLHRLPWRERRILAMRFYGNQ--TQAEIAARFGISQMHVSRLLSRALTWLRQAM 261

Query: 285 QKQVELSSSPPLLQ 298
                L+ +PP  Q
Sbjct: 262 -----LADAPPPWQ 270


>gi|325674621|ref|ZP_08154308.1| DNA-directed RNA polymerase sigma subunit SigB [Rhodococcus equi
           ATCC 33707]
 gi|325554207|gb|EGD23882.1| DNA-directed RNA polymerase sigma subunit SigB [Rhodococcus equi
           ATCC 33707]
          Length = 262

 Score =  139 bits (352), Expect = 3e-31,   Method: Composition-based stats.
 Identities = 46/246 (18%), Positives = 94/246 (38%), Gaps = 18/246 (7%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           +    +   R+V   L L   IA  +   G  + ++     +GL+ AV +FDP +G   A
Sbjct: 33  DERGTALRDRIVAQSLPLARNIARRFSSRGEEMDDLYQVACVGLINAVDRFDPAQGSSFA 92

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
            Y++  I   ++ Y        ++        L      +    +A++    +      +
Sbjct: 93  AYAVPTIMGEVRRYFRDHAWAARVPRRLKDLTLD-----VGKATEALSQRLGRSPTAHEL 147

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
           A +L      V+            SL++ +   D  S+   D L  D    EQ  +    
Sbjct: 148 ATELGTDPDSVMEAIAAAGAYQTHSLDSPVGR-DGESATLADTLATDDVDLEQTELHLA- 205

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                  L   +  L PRE+RI   R  +E   T   ++ E  VS+ ++ ++ ++   ++
Sbjct: 206 -------LQPLIDQLEPREKRIVVMRFFEE--RTQTEIAREIGVSQVQISRLLSKILARI 256

Query: 281 QESIQK 286
           + ++ +
Sbjct: 257 RTNLDE 262


>gi|150387863|ref|YP_001317912.1| RinA family phage transcriptional regulator [Alkaliphilus
           metalliredigens QYMF]
 gi|149947725|gb|ABR46253.1| phage transcriptional regulator, RinA family [Alkaliphilus
           metalliredigens QYMF]
          Length = 266

 Score =  139 bits (352), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 49/258 (18%), Positives = 115/258 (44%), Gaps = 16/258 (6%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           E  L   Y+E+  +   + LV  +L +   ++  +   G+   ++    ++GL+ A+++F
Sbjct: 23  EKELFIEYQENKKVEVRNELVNRYLYIAEILSKKFLNKGIDYEDIYQVASLGLIYAIERF 82

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D  RGF  ++++   I   ++++       +++     +     N  ++      +  N 
Sbjct: 83  DLSRGFEFSSFATPTIIGEIKKHFRDKGWSIRVPRRIQELSKKVNTAKMT-----LHQNL 137

Query: 154 LKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
            +   +  IA+ LN ++ EV+      ++   +SL+   ++  ++       L+ + D  
Sbjct: 138 QRTPMIKDIAEYLNCTQEEVMEAMEASQVYTPKSLDLTYDNDGEDKDIQLIDLIGEKDKN 197

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
              +         R+ L ++M  LN  E+++ E R    N  T  N++ E  VS+  V +
Sbjct: 198 FDEI-------ENRDFLKKAMRNLNEVEKKVLEDRFF--NSKTQMNVAEELNVSQMTVSR 248

Query: 272 IEARAFKKVQESIQKQVE 289
           +E R  +K ++ + K +E
Sbjct: 249 MEKRIIEKFRKELNKSME 266


>gi|55274930|gb|AAV49266.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 198

 Score =  139 bits (352), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 56/208 (26%), Positives = 99/208 (47%), Gaps = 12/208 (5%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            R++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+
Sbjct: 1   RRMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIR 60

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
             ++  I+     +++      K L   LR  +     ++           IA++L+   
Sbjct: 61  QTIERAIMNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPV 115

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            +V  M        S++  +    + +      L    D +E    +  +  + +  + +
Sbjct: 116 DDVSRMLRLNERITSVDTPLGGDSEKA-----LLDILADEKENGPEDTTQDDDMKQSIVK 170

Query: 231 SMSVLNPRERRIFEARR--LQENPVTLE 256
            +  LN ++R +   R   L     TLE
Sbjct: 171 WLFELNAKQREVLARRFGLLGYEAATLE 198


>gi|284046869|ref|YP_003397209.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
 gi|283951090|gb|ADB53834.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
          Length = 276

 Score =  139 bits (352), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 51/241 (21%), Positives = 99/241 (41%), Gaps = 21/241 (8%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            A   +V  HL L   +A  Y   G P+ ++V   ++GL++AV +FDP RG   A+Y++ 
Sbjct: 49  DARKAMVEQHLGLAHHLARRYSDRGEPLDDLVQVASLGLLKAVDRFDPARGVSFASYAVP 108

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I   ++ +       + +     +  L            A+  +  +      + K+  
Sbjct: 109 TILGELRRHFRDRGWAIHVPRDLKEAAL--------RVESALAGHAGRSPTPSQLGKETG 160

Query: 168 VSESEVISMNCRLAGDE--SLNALINSSDKNSS-QWQDWLVYDHDGQEQVLIEKEERKNR 224
           +    V+            SL+A   + ++ ++    D L  D D        + +R   
Sbjct: 161 LDVEAVLEALEVAGAHRALSLDAPAGNEEEGTTATLVDRLGRDDD--------ELDRAGD 212

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  + R  SVL PRER I   R +++  +T   + +   VS+  V ++   A  +++ + 
Sbjct: 213 RATIERLASVLEPREREILRLRFVED--MTQSEIGARVGVSQMHVSRLIRTALTRMRLAS 270

Query: 285 Q 285
           Q
Sbjct: 271 Q 271


>gi|221309406|ref|ZP_03591253.1| sporulation sigma factor SigE [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221313731|ref|ZP_03595536.1| sporulation sigma factor SigE [Bacillus subtilis subsp. subtilis
           str. NCIB 3610]
 gi|221318655|ref|ZP_03599949.1| sporulation sigma factor SigE [Bacillus subtilis subsp. subtilis
           str. JH642]
 gi|221322928|ref|ZP_03604222.1| sporulation sigma factor SigE [Bacillus subtilis subsp. subtilis
           str. SMY]
 gi|255767354|ref|NP_389415.2| sporulation sigma factor SigE [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|296331108|ref|ZP_06873582.1| sporulation sigma factor SigE [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|305674263|ref|YP_003865935.1| sporulation-specific sigma factor sigma-E [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|321315297|ref|YP_004207584.1| sporulation sigma factor SigE [Bacillus subtilis BSn5]
 gi|133472|sp|P06222|RPSE_BACSU RecName: Full=RNA polymerase sigma-E factor; AltName: Full=P31;
           AltName: Full=Sigma-29; AltName: Full=Stage II
           sporulation protein GB; Flags: Precursor
 gi|40169|emb|CAA25620.1| unnamed protein product [Bacillus subtilis]
 gi|225184981|emb|CAB13406.2| RNA polymerase sporulation-specific sigma-29 factor (sigma-E)
           [Bacillus subtilis subsp. subtilis str. 168]
 gi|291484083|dbj|BAI85158.1| sporulation sigma factor SigE [Bacillus subtilis subsp. natto
           BEST195]
 gi|296151752|gb|EFG92627.1| sporulation sigma factor SigE [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|305412507|gb|ADM37626.1| sporulation-specific sigma factor sigma-E [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|320021571|gb|ADV96557.1| sporulation sigma factor SigE [Bacillus subtilis BSn5]
 gi|224259|prf||1012299A spoIIG gene
          Length = 239

 Score =  139 bits (352), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 64/264 (24%), Positives = 112/264 (42%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K EE VL  +   +GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLSKDEEQVLLMKL-PNGDQAARAILIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+                    +++   
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN-------------------NKIRSE- 135

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                            ++ DE LN      D N     D L  
Sbjct: 136 ---------------------------------VSFDEPLN---IDWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           D D    ++ +  E    + +L +++  LN RE++I E R     E   T ++++    +
Sbjct: 160 DDD----IITKDIEANVDKKLLKKALEQLNEREKQIMELRFGLVGEEEKTQKDVADMMGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 216 SQSYISRLEKRIIKRLRKEFNKMV 239


>gi|55274986|gb|AAV49291.1| RNA polymerase subunit sigma-38 [Shigella flexneri]
          Length = 196

 Score =  139 bits (352), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 53/206 (25%), Positives = 95/206 (46%), Gaps = 12/206 (5%)

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           LVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+ 
Sbjct: 1   LVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMN 60

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
               +++      K L   LR  +     ++           IA++L+    +V  M   
Sbjct: 61  QTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRL 115

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
                S++  +    +     +  L    D +E    +  +  + +  + + +  LN ++
Sbjct: 116 NERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQ 170

Query: 240 RRIFEARR--LQENPVTLENLSSEFE 263
           R +   R   L     TLE++  E  
Sbjct: 171 REVLARRFGLLGYEAATLEDVGREIG 196


>gi|29829172|ref|NP_823806.1| RNA polymerase sigma factor WhiG [Streptomyces avermitilis MA-4680]
 gi|29606278|dbj|BAC70341.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 280

 Score =  139 bits (352), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 49/256 (19%), Positives = 104/256 (40%), Gaps = 16/256 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
            L + Y+  GD     +L+  +  LV  +A          +  ++ VS G  GL+ A++K
Sbjct: 33  ELWRSYKATGDERLREQLILHYSPLVKYVAGRVSVGLPPNVEQADFVSSGVFGLIDAIEK 92

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  R  +  TY++  I+ AM + + R+   +        + +      L+  L+     
Sbjct: 93  FDIGREIKFETYAITRIRGAMIDEL-RALDWIPRSVRQKARNVERAYATLEARLR----- 146

Query: 153 NLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
             +      +A ++ ++  E+ S+     LA   +L  L++   +   +    +    D 
Sbjct: 147 --RTPTEGEVATEMGIAVDELHSVFSQLSLANVVALEELLHVGGEGGDRL-SLMDTLEDT 203

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                +E  E +  R  L R+++ L  RE+ +          +TL  + +   V+  RV 
Sbjct: 204 AADNPVEVAEDRELRRFLARAINTLPDREKTVVTLYYY--EGLTLAEIGNVLGVTESRVS 261

Query: 271 QIEARAFKKVQESIQK 286
           QI  ++  +++  +  
Sbjct: 262 QIHTKSVLQLRAKLAS 277


>gi|308173494|ref|YP_003920199.1| RNA polymerase sporulation-specific sigma-29 factor sigma-E
           [Bacillus amyloliquefaciens DSM 7]
 gi|307606358|emb|CBI42729.1| RNA polymerase sporulation-specific sigma-29 factor (sigma-E)
           [Bacillus amyloliquefaciens DSM 7]
 gi|328553576|gb|AEB24068.1| sporulation sigma factor SigE [Bacillus amyloliquefaciens TA208]
 gi|328911631|gb|AEB63227.1| RNA polymerase sporulation-specific sigma-29 factor (sigma-E)
           [Bacillus amyloliquefaciens LL3]
          Length = 239

 Score =  139 bits (352), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 64/264 (24%), Positives = 112/264 (42%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL  +    GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLSKEEEQVLLLKL-PSGDQAARAILIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+                    +++   
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN-------------------NKIRSE- 135

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                            ++ DE LN      D N     D L  
Sbjct: 136 ---------------------------------VSFDEPLN---IDWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           D D    ++ +  E    + +L +++  LN RE++I E R     E   T ++++    +
Sbjct: 160 DDD----IITKDIEANVDKKLLKKALEQLNDREKQIMELRFGLIGEEEKTQKDVADMMGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 216 SQSYISRLEKRIIKRLRKEFNKMV 239


>gi|302554440|ref|ZP_07306782.1| RNA polymerase sigma-G factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302472058|gb|EFL35151.1| RNA polymerase sigma-G factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 280

 Score =  139 bits (352), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 55/254 (21%), Positives = 104/254 (40%), Gaps = 12/254 (4%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
            L + Y+  GD     +L+  +  LV  +A          +  ++ VS G  GL+ A++K
Sbjct: 33  ELWRSYKATGDERLREQLILHYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEK 92

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD +R  +  TY++  I+ AM + +    +L  I  +  QK    N+ R    L+A    
Sbjct: 93  FDIDREIKFETYAITRIRGAMIDELR---ALDWIPRSVRQKA--RNVERAYATLEARLRR 147

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
                +V A    + V E   +     LA   +L  L+++           +    D   
Sbjct: 148 TPTEGEVAA-EMGIGVEELHAVFSQLSLANVVALEELLHAG-GEGGDGLSVMDTLEDTAA 205

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
              +E  E +  R +L R+++ L  RE+ +          +TL  + +   V+  RV QI
Sbjct: 206 DNPVEVAEDRELRRLLARAINTLPEREKTVVTLYYY--EGLTLAEIGNVLGVTESRVSQI 263

Query: 273 EARAFKKVQESIQK 286
             ++  +++  +  
Sbjct: 264 HTKSVLQLRAKLAS 277


>gi|161898899|gb|ABX80439.1| SigB [Listeria monocytogenes]
          Length = 229

 Score =  139 bits (352), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 55/246 (22%), Positives = 107/246 (43%), Gaps = 24/246 (9%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G     +++  I   ++ ++      V +     +        ++K  ++ +T    
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQ 116

Query: 155 KPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +    
Sbjct: 117 SSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTD 173

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++S+  
Sbjct: 174 DGF--------ERVNQRMLLEKVLPVLDEREQKILQFTFIEN--RSQKETGELLDISQMH 223

Query: 269 VRQIEA 274
           V +I+ 
Sbjct: 224 VSRIQR 229


>gi|327485473|gb|AEA79879.1| RNA polymerase sigma factor RpoH [Vibrio cholerae LMA3894-4]
          Length = 185

 Score =  139 bits (352), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 60/187 (32%), Positives = 105/187 (56%), Gaps = 11/187 (5%)

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           ++++ WIKA + EY+LR+W +VKI TT  Q++LFFNLR+ K  L    +      +V  +
Sbjct: 2   SFAVHWIKAEIHEYVLRNWRIVKIATTKAQRKLFFNLRKSKKRLGWFNNG-----EVETV 56

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A++L V  +EV  M  RLA  ++   +    D+N   +   ++Y  D     L +  E +
Sbjct: 57  ARELGVEPAEVREMESRLAAQDAAFEMSAEDDENGMAYTAPVLYLEDKHSD-LADNLEAE 115

Query: 223 NRR----NMLTRSMSVLNPRERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAF 277
           N        L+ +++ L+ R + I  AR L ++   TL++L+  + VS ER+RQ+E  A 
Sbjct: 116 NWEAHTTQRLSMALASLDERSQHIVRARWLDDDNKTTLQDLAEMYGVSAERIRQLEKNAM 175

Query: 278 KKVQESI 284
           +K++E++
Sbjct: 176 RKLKEAV 182


>gi|261405539|ref|YP_003241780.1| sporulation sigma factor SigK [Paenibacillus sp. Y412MC10]
 gi|315645904|ref|ZP_07899025.1| sporulation sigma factor SigK [Paenibacillus vortex V453]
 gi|329925929|ref|ZP_08280639.1| RNA polymerase sigma-K factor [Paenibacillus sp. HGF5]
 gi|261282002|gb|ACX63973.1| RNA polymerase, sigma 28 subunit, SigK [Paenibacillus sp. Y412MC10]
 gi|315278665|gb|EFU41979.1| sporulation sigma factor SigK [Paenibacillus vortex V453]
 gi|328939580|gb|EGG35929.1| RNA polymerase sigma-K factor [Paenibacillus sp. HGF5]
          Length = 233

 Score =  139 bits (352), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 58/275 (21%), Positives = 108/275 (39%), Gaps = 64/275 (23%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+        L ++EE    +R  E GD  + ++L+  +LRLV  I   +   G  +
Sbjct: 18  LVSYVKNNAFPQPLTEEEEAKHLQRMAE-GDPQSRNKLIEHNLRLVAHIVKKFDNTGEDL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++S G IGL++A++ F P +G +LAT++   I+  +                      
Sbjct: 77  EDLISIGTIGLIKAIESFRPNKGTKLATFAARCIENEI---------------------- 114

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
             +LR LK                            + +S++  +  D          + 
Sbjct: 115 LMHLRSLKKT-------------------------RKDVSLHDPIGTD---------KEG 140

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE---NP 252
           N     D L  + D     +++  + K  ++ + R++ +L+ RE+ +   R   E     
Sbjct: 141 NEITLIDILGTEADD----IVDAVQLKIEKSKIYRNLDILDDREKEVVIGRFGLEAGGEE 196

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            T   ++ E  +SR  V +IE RA  K+     KQ
Sbjct: 197 RTQREIAKELGISRSYVSRIEKRALMKLYHEFYKQ 231


>gi|254382042|ref|ZP_04997404.1| RNA polymerase sigma subunit [Streptomyces sp. Mg1]
 gi|194340949|gb|EDX21915.1| RNA polymerase sigma subunit [Streptomyces sp. Mg1]
          Length = 278

 Score =  139 bits (352), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 49/254 (19%), Positives = 108/254 (42%), Gaps = 16/254 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
            L + Y+E GD     +L+  +  LV  +A          +  ++ VS G  GL+ A++K
Sbjct: 31  ALWRAYKESGDERLRQQLILHYSPLVKYVAGRVSVGLPPNVEQADFVSSGVFGLIDAIEK 90

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD +R  +  TY++  I+ AM + + R+   +        + +      L+  L+     
Sbjct: 91  FDIDRSIKFETYAITRIRGAMIDEL-RALDWIPRSVRQKARAVERAYATLEAQLR----- 144

Query: 153 NLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
             +      +A ++ ++  E+ ++     LA   +L+ L++   +   +    +    D 
Sbjct: 145 --RTPTECEVADEMGIAVEELHTVFSQLSLANVVALDELLHVGGEGGDRL-SLMDTLEDT 201

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                +E  E +  R +L R+++ L  RE+ +          +TL  + +   V+  RV 
Sbjct: 202 AADNPVEVAEGRELRRLLARAINTLPEREKTVVTLYYY--EGLTLAEIGNVLGVTESRVS 259

Query: 271 QIEARAFKKVQESI 284
           QI  ++  +++  +
Sbjct: 260 QIHTKSVLQLRAKL 273


>gi|239623450|ref|ZP_04666481.1| RNA polymerase [Clostridiales bacterium 1_7_47_FAA]
 gi|239521481|gb|EEQ61347.1| RNA polymerase [Clostridiales bacterium 1_7_47FAA]
          Length = 246

 Score =  139 bits (352), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 59/262 (22%), Positives = 106/262 (40%), Gaps = 64/262 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE +EE  +        D  A   L+  +LRLVV IA  +    + + +++S G IGL
Sbjct: 41  PPLESEEESRMIGLLGGEDDKGARSTLIEHNLRLVVYIAKKFDNTSVGVEDLISIGTIGL 100

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+  F P++  +LATY+   I+  +  Y+ R+                          
Sbjct: 101 IKAINTFKPDKNIKLATYASRCIENEILMYLRRNNKT----------------------- 137

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                             +L VS  E ++++                D N     D L  
Sbjct: 138 ------------------RLEVSIDEPLNVD---------------WDGNELLLSDILGT 164

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL----QENPVTLENLSSEF 262
           D D    V+    E +  +N+L  ++S LNPRER+I E R          +T + ++   
Sbjct: 165 DED----VIYHDIEDEIEKNLLNNAISRLNPRERKIVELRYGLTNEDGEEMTQKEVADLL 220

Query: 263 EVSRERVRQIEARAFKKVQESI 284
            +S+  + ++E +  K++++ I
Sbjct: 221 GISQSYISRLEKKIMKRLKKEI 242


>gi|119476594|ref|ZP_01616904.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2143]
 gi|119449850|gb|EAW31086.1| RNA polymerase sigma factor [marine gamma proteobacterium HTCC2143]
          Length = 194

 Score =  139 bits (352), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 45/201 (22%), Positives = 88/201 (43%), Gaps = 12/201 (5%)

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           PERGFR +TY+ WWI+  ++  I+     +++       +      R    L    D+  
Sbjct: 1   PERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHV--VKELNVYLRAARELTQKLDHEP 58

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            PE++  +  +       ++ +N R+A   S++  + +    S    D +   H      
Sbjct: 59  TPEEIAELLDRPVADVKRMLRLNERVA---SVDTPLGADSDKS--LLDTIPDTHVSD--- 110

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQI 272
             E  +  + +  ++  +  L  ++R +   R         TLE +  E  ++RERVRQI
Sbjct: 111 PAEMLQDDDMKASISEWIGELTEKQREVVARRFGLRGYETSTLEEVGREIGLTRERVRQI 170

Query: 273 EARAFKKVQESIQKQVELSSS 293
           +  A K++++ ++KQ   S S
Sbjct: 171 QVEALKRLRDILEKQGLSSES 191


>gi|187935068|ref|YP_001885063.1| RNA polymerase sigma-D factor [Clostridium botulinum B str. Eklund
           17B]
 gi|187723221|gb|ACD24442.1| RNA polymerase sigma-D factor [Clostridium botulinum B str. Eklund
           17B]
          Length = 242

 Score =  139 bits (352), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 60/246 (24%), Positives = 113/246 (45%), Gaps = 19/246 (7%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           D     ++V  ++ LV  IA      +   +   ++VS G IGLM A+ KF+PE+G + +
Sbjct: 6   DNDVKEQIVKEYIPLVKYIASRIMIGKNKYMEYEDLVSYGIIGLMDAISKFNPEKGMKFS 65

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           +Y+   IK A+ + I ++  +         K     L R  G ++A+ +  L+   ++ I
Sbjct: 66  SYASIRIKGAIIDQIRKNRPI--------TKGAMDKLNRYNGAIEALQNKLLREPNILEI 117

Query: 163 AKKLNVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
           AK L +S  EV  +   +      SL  +I S D+  +          D        + E
Sbjct: 118 AKYLELSLEEVSQIENYINHISMVSLENIIFSDDEEVNLLGII----EDKNSPSPEGELE 173

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            K +  +L+ ++ +L  +E+ I          +TL+ + +   VS  RV Q+ AR+   +
Sbjct: 174 EKEKLEVLSDAIKLLKEKEQLILNLYYY--EKLTLKEIGAILSVSESRVCQLHARSISNL 231

Query: 281 QESIQK 286
           +E+++K
Sbjct: 232 REAMKK 237


>gi|126348115|emb|CAJ89836.1| putative RNA polymerase sigma factor [Streptomyces ambofaciens ATCC
           23877]
          Length = 295

 Score =  139 bits (352), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 48/236 (20%), Positives = 106/236 (44%), Gaps = 11/236 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A + L+  ++ LV   A  +RG G  + +VV  G IGL++A+ +F+  R     ++++ +
Sbjct: 64  ARNTLIEMNMSLVRFAAGRFRGRGDDMDDVVQTGMIGLIKAIDRFELSREVEFTSFALPY 123

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I   ++ +   +   V +     + R+      L    + ++    +   V  +A  +N+
Sbjct: 124 IVGEIKRFFRDTTWAVHVPRRLQELRV-----ELAKAREELSSRLDREPTVAELATLMNI 178

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SE+EV+       G  S ++L  +   +  +  + ++ D  G E+  +   E  +    L
Sbjct: 179 SENEVVEGQIASNGYNS-SSLDAALTGDGPEGGESVLADFIGVEEDGLRLVEDFHS---L 234

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              M+ L+ R+R+I   R ++E   T   +      S+  V ++  R   +++E +
Sbjct: 235 APLMAELSERDRQIIHMRFVEE--ATQAEIGERLGCSQMHVSRLIKRIITRLREGM 288


>gi|297157938|gb|ADI07650.1| SigL-like sigma factor [Streptomyces bingchenggensis BCW-1]
          Length = 322

 Score =  139 bits (352), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 49/236 (20%), Positives = 97/236 (41%), Gaps = 16/236 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            + LV  +L LV   A  +R    P+ ++V  G IGL++A+ +F+  RG    T++M  I
Sbjct: 98  RNTLVELNLALVKFAASRFRSRSEPMEDIVQVGTIGLIKAIDRFELSRGVEFPTFAMPTI 157

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +      +A++L ++
Sbjct: 158 VGEIKRFFRDTSWSVRVPRRLQELRLD-----LAKAGDELAQRLDRAPTAGELAERLGLT 212

Query: 170 ESEVIS-MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            +EVI  M    A   S        D       D + Y+  G E +             L
Sbjct: 213 TAEVIEGMAASNAYTASSLDAQPEEDDTEGALADRIGYEDHGLEGI--------EYVESL 264

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              ++ L+PR+R+I   R +    +T   +  E  +S+  V ++ +R   +++  +
Sbjct: 265 KPLIADLSPRDRKILSLRFVAN--MTQSEIGDELGISQMHVSRLLSRTLVRLRRGL 318


>gi|254519896|ref|ZP_05131952.1| sporulation sigma factor SigF [Clostridium sp. 7_2_43FAA]
 gi|226913645|gb|EEH98846.1| sporulation sigma factor SigF [Clostridium sp. 7_2_43FAA]
          Length = 251

 Score =  139 bits (351), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 43/246 (17%), Positives = 102/246 (41%), Gaps = 16/246 (6%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             + G+  A ++++  +L LV  I+  +   G    ++   G+IGL++A+  FD +   +
Sbjct: 22  LAKAGNQDAMNKVIEMNLPLVSSISKKFLNRGYDYEDIFQIGSIGLVKAINNFDDKFNVK 81

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY++  I   ++ +I     ++K+             R+L    + +T    +   + 
Sbjct: 82  FSTYAVPMIIGEIKRFIRDDG-IIKVSRNVKSLA-----RKLHFDKEQLTKKLDREPTIE 135

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +++   V + E++      A  + L   I+  D       D L            E + 
Sbjct: 136 ELSQFSGVDKEEILFAIESSASMQYLYDTIHQDDGAPVLLIDKLSEKG--------EDDS 187

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
               R  L  ++  L+ + R+I   R  ++   T   ++    +S+ +V +IE +    +
Sbjct: 188 DMINRIALKEALRSLDSKARQIIMLRYFKD--KTQVQVAKMLGISQVQVSRIEKKVLVLM 245

Query: 281 QESIQK 286
           ++ +Q+
Sbjct: 246 KQKLQE 251


>gi|312138386|ref|YP_004005722.1| sigma-70 factor [Rhodococcus equi 103S]
 gi|311887725|emb|CBH47037.1| putative sigma-70 factor [Rhodococcus equi 103S]
          Length = 262

 Score =  139 bits (351), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 46/246 (18%), Positives = 94/246 (38%), Gaps = 18/246 (7%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           +    +   R+V   L L   IA  +   G  + ++     +GL+ AV +FDP +G   A
Sbjct: 33  DERGTALRDRIVAQSLPLARNIARRFSSRGEEMDDLYQVACVGLINAVDRFDPAQGSSFA 92

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
            Y++  I   ++ Y        ++        L      +    +A++    +      +
Sbjct: 93  AYAVPTIMGEVRRYFRDHAWAARVPRRLKDLTLD-----VGKATEALSQRLGRSPTAHEL 147

Query: 163 AKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
           A +L      V+            SL++ +   D  S+   D L  D    EQ  +    
Sbjct: 148 ATELGTDPDSVMEAIAAAGAYQTHSLDSPVGR-DGESATLADTLATDDVDLEQTELHLA- 205

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                  L   +  L PRE+RI   R  +E   T   ++ E  VS+ ++ ++ ++   ++
Sbjct: 206 -------LRPLIDQLEPREKRIVVMRFFEE--RTQTEIAREIGVSQVQISRLLSKILARI 256

Query: 281 QESIQK 286
           + ++ +
Sbjct: 257 RTNLDE 262


>gi|315506253|ref|YP_004085140.1| anti-sigma-factor antagonist [Micromonospora sp. L5]
 gi|315412872|gb|ADU10989.1| anti-sigma-factor antagonist [Micromonospora sp. L5]
          Length = 377

 Score =  139 bits (351), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 57/254 (22%), Positives = 108/254 (42%), Gaps = 25/254 (9%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   LV   L    ++A  YRG G P+ ++     +GL+ AV ++DPERG     Y+ 
Sbjct: 40  QEARDDLVRFALPFAGRLARRYRGRGEPLEDLEQVARLGLVNAVDRYDPERGS-FTAYAA 98

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I   ++ +       V +      +RL   +  +      +T    +   V  ++ +L
Sbjct: 99  ITIVGEIKRHFRDRTWGVHVP-----RRLRDLILEVGQATATLTSELSRAPTVAELSARL 153

Query: 167 NVSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
              E E+++     AG    SLNA +    ++S+++ D +       E V        + 
Sbjct: 154 ETPEEEILAALESAAGYSPASLNAPV--GGESSAEFGDLVGESDHALESV--------DD 203

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  ++  +  L  RERRI   R       T   +++ F +S+  V ++ +RA   +++++
Sbjct: 204 RVTVSGLLHRLPWRERRILAMRFYGNQ--TQAEIAARFGISQMHVSRLLSRALTWLRQAM 261

Query: 285 QKQVELSSSPPLLQ 298
                L+ +PP  Q
Sbjct: 262 -----LADAPPPWQ 270


>gi|257438785|ref|ZP_05614540.1| RNA polymerase sigma-G factor [Faecalibacterium prausnitzii A2-165]
 gi|257198753|gb|EEU97037.1| RNA polymerase sigma-G factor [Faecalibacterium prausnitzii A2-165]
          Length = 254

 Score =  139 bits (351), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 55/258 (21%), Positives = 116/258 (44%), Gaps = 18/258 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           ++P+L + E+  L  R R     +A   ++  +LRLV+ +   +   G  + ++   G I
Sbjct: 14  QLPVLSEAEKRQLLTRARAGD-AAARQAMIEGNLRLVLSVVQRFAQRGENLDDLFQVGCI 72

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++A+  FDP +  R +TY +  I   ++ ++  + +L ++      + L     +   
Sbjct: 73  GLIKAIDNFDPAQPVRFSTYGVPMIIGEIRRFLRDNNAL-RVS-----RSLRDAAYKAMQ 126

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             +A+     +   V  +A++  +S  EV +    +    SL   +  +D   + +    
Sbjct: 127 AREALEKQLGREPTVDEVARQAGLSRREVNAALESVVEPISLEEPLY-TDGGDAMYVIDQ 185

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           V D D ++  +   E R+          + L PRE+RI E R L+    T   ++ E  +
Sbjct: 186 VRDPDSEDSWISGLEFRQTV--------AGLTPREKRIMELRYLKGE--TQMEVAREIGI 235

Query: 265 SRERVRQIEARAFKKVQE 282
           S+ +V ++E  A ++ + 
Sbjct: 236 SQAQVSRLEKAALEQFRH 253


>gi|260893401|ref|YP_003239498.1| RNA polymerase, sigma 28 subunit, SigE [Ammonifex degensii KC4]
 gi|260865542|gb|ACX52648.1| RNA polymerase, sigma 28 subunit, SigE [Ammonifex degensii KC4]
          Length = 242

 Score =  139 bits (351), Expect = 4e-31,   Method: Composition-based stats.
 Identities = 65/261 (24%), Positives = 108/261 (41%), Gaps = 63/261 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L+ +EE  L KR  E GD S  + LV  +LRLVV IA  Y   G+ + ++VS G+IGL
Sbjct: 38  PPLDAEEEAHLLKRL-EAGDQSVRNTLVERNLRLVVYIARKYESTGINLEDLVSIGSIGL 96

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+P+R  +LATY+   I+  +  ++ R    ++                     
Sbjct: 97  IKAVNTFNPQRKVKLATYASRCIENEILMFLRRQSRTLR--------------------- 135

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                            ++ DE LN      D N     D L  
Sbjct: 136 -------------------------------QEVSFDEPLNT---DWDGNELLLSDVLGT 161

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFE 263
           + D   + L E+ +    R +L  +++ L+ RER I E R          T + ++    
Sbjct: 162 EGDVTSRHLEEEVD----RRVLKLALASLSGRERVIMELRFGLGADGEEKTQKEVADLLG 217

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+  + ++E R  K+++  I
Sbjct: 218 ISQSYISRLEKRILKRLRREI 238


>gi|255523683|ref|ZP_05390649.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           carboxidivorans P7]
 gi|296186687|ref|ZP_06855089.1| putative RNA polymerase sigma factor WhiG [Clostridium
           carboxidivorans P7]
 gi|255512552|gb|EET88826.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           carboxidivorans P7]
 gi|296048724|gb|EFG88156.1| putative RNA polymerase sigma factor WhiG [Clostridium
           carboxidivorans P7]
          Length = 241

 Score =  139 bits (351), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 59/245 (24%), Positives = 104/245 (42%), Gaps = 19/245 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           L     LV  ++ LV  IA      +   +   ++VS G +GLM A+ KFD  RG + +T
Sbjct: 7   LDVKEELVKKYIPLVKYIASRVIIGKTKYIEYEDLVSYGMLGLMDAIGKFDNTRGMKFST 66

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           YS   IK AM + I ++  +         K     L R    ++ +     +      IA
Sbjct: 67  YSSIRIKGAMIDEIRKNSPI--------SKGAMDKLNRYNAAVERLQKTLGREPSDKEIA 118

Query: 164 KKLNVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
            +LN++  E+I +   +      SL  LI S D +       +    D +     +  E 
Sbjct: 119 NELNITLKEMIEIENYINYISIVSLEDLIFSEDDDIP----LIGTIQDNKSPSPEKSLEE 174

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           K     L +++ +LN +++ +          +TL+ +     VS  RV Q+ +RA   ++
Sbjct: 175 KEELEYLAKALDLLNEKDKTVLSLYYY--EGLTLKEIGKVLSVSESRVCQLHSRAIVHLR 232

Query: 282 ESIQK 286
            ++QK
Sbjct: 233 NAMQK 237


>gi|118470482|ref|YP_886176.1| RNA polymerase sigma factor SigF [Mycobacterium smegmatis str. MC2
           155]
 gi|25396413|dbj|BAC24795.1| alternative sigma factor SigF [Mycobacterium smegmatis]
 gi|118171769|gb|ABK72665.1| RNA polymerase sigma-F factor [Mycobacterium smegmatis str. MC2
           155]
          Length = 250

 Score =  139 bits (351), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 45/237 (18%), Positives = 96/237 (40%), Gaps = 16/237 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             ++V   L L   IA  + G G P  ++V    +GL+ AV +FD E G    ++++  I
Sbjct: 29  REKIVERCLPLADHIARRFDGRGEPREDLVQVARVGLVNAVNRFDVEAGSDFVSFAVPTI 88

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   VK+     +  L     RL      ++    +      +A +L++ 
Sbjct: 89  MGEVRRHFRDNSWSVKVPRRLKELHL-----RLGAATAELSQRLGRAPTASELAHELDMD 143

Query: 170 ESEVISMNCRLAGDESLN-ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
             EV+      +   +L+       D+ +    D L     G +Q+        + R  L
Sbjct: 144 REEVVEGLIAGSSYNTLSIDSGGGGDEEAPAIVDTLGDLDMGLDQI--------DNRESL 195

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              ++ L  RER +   R      +T   ++    +S+  V ++ A++  ++++ +Q
Sbjct: 196 RPLLASLPERERTVLVLRFF--ESMTQTQIAERVGISQMHVSRLLAKSLARLRDQLQ 250


>gi|302521363|ref|ZP_07273705.1| RNA polymerase sigma-B factor [Streptomyces sp. SPB78]
 gi|302430258|gb|EFL02074.1| RNA polymerase sigma-B factor [Streptomyces sp. SPB78]
          Length = 312

 Score =  139 bits (351), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 51/236 (21%), Positives = 96/236 (40%), Gaps = 16/236 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            + LV  +L LV   A  +R    P+ +++  G IGL++A+ +F+  RG    T++M  I
Sbjct: 88  RNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRGVEFPTFAMPTI 147

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +      +A+KL + 
Sbjct: 148 IGEIKRFFRDTSWSVRVPRRLQELRLD-----LAKAGDELAQRLDRAPTPSELAEKLGIE 202

Query: 170 ESEVIS-MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
             EVI  M    A   S        D + S   D L Y+  G E +             L
Sbjct: 203 REEVIEGMAASNAYTASSLDAQPEEDDSESALADRLGYEDHGLEGI--------EYIESL 254

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              ++ L  R+R+I   R +    +T   +  E  +S+  V ++ +R   K+++ +
Sbjct: 255 KPMIARLPQRDRKILSLRFVAN--MTQSEIGEELGISQMHVSRLLSRTLVKLRKGL 308


>gi|282861385|ref|ZP_06270450.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Streptomyces sp. ACTE]
 gi|282564043|gb|EFB69580.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Streptomyces sp. ACTE]
          Length = 278

 Score =  139 bits (351), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 51/254 (20%), Positives = 106/254 (41%), Gaps = 16/254 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
            L + Y+  GD     +L+  +  LV  +A          +  ++ VS G  GL+ A++K
Sbjct: 31  ELWRSYKSTGDERLREQLILHYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEK 90

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD ER  +  TY++  I+ AM + + R+   +        + +      L+  L+     
Sbjct: 91  FDLERAIKFETYAITRIRGAMIDEL-RALDWIPRSVRQKARNVERAYATLEAQLR----- 144

Query: 153 NLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
             +      +A ++ ++  E+ S+     LA   +L  L++   +   +    +    D 
Sbjct: 145 --RTPTEAEVAAEMGIALEELHSVFSQLSLANVVALEELLHVGGEGGDRL-SLMDTLEDT 201

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                +E  E +  R ML R+++ L  RE+ +          +TL  + +   V+  RV 
Sbjct: 202 AADNPVEIAEDRELRRMLARAINTLPEREKTVVTLYYY--EGLTLAEIGNVLGVTESRVS 259

Query: 271 QIEARAFKKVQESI 284
           QI  ++  +++  +
Sbjct: 260 QIHTKSVLQLRAKL 273


>gi|311031146|ref|ZP_07709236.1| RNA polymerase sigma factor SigB [Bacillus sp. m3-13]
          Length = 261

 Score =  139 bits (351), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 52/252 (20%), Positives = 112/252 (44%), Gaps = 18/252 (7%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           +L +RY++ G   +  +LV  +  LV  IA  Y        ++   G IGL+ A+K+FD 
Sbjct: 14  MLLERYQQDGCEVSQLQLVEHYTALVESIARKYSRGKAFHEDLSQVGMIGLLGAMKRFDA 73

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
             G     +++  I   ++ ++      V +     +        ++K  ++ +T+   +
Sbjct: 74  SFGRSFEAFAVPTIIGEIKRFLRDKTWSVHVPRRIKEIG-----PKIKSAVEELTNELQR 128

Query: 156 PEQVVAIAKKLNVSESEV---ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +V  IA  L V+E EV   + M+         NA+   SD ++    D +     G +
Sbjct: 129 SPKVFEIADYLEVTEEEVLEAMEMSQNYQALSVDNAIEADSDGSTVTILDIVGNQDAGFD 188

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           QV        +++ +L +   VL+ RE++I E    +   ++ +    +  +S+  V ++
Sbjct: 189 QV--------DQQLLLQKIFHVLSEREKQIIECTFFKN--MSQKETGEKLGISQMHVSRL 238

Query: 273 EARAFKKVQESI 284
           + +A  K++++ 
Sbjct: 239 QRKALTKLKQAF 250


>gi|212639647|ref|YP_002316167.1| sporulation sigma factor SigE [Anoxybacillus flavithermus WK1]
 gi|212561127|gb|ACJ34182.1| DNA-directed RNA polymerase specialized sigma subunit sigE
           [Anoxybacillus flavithermus WK1]
          Length = 239

 Score =  139 bits (351), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 66/264 (25%), Positives = 113/264 (42%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE +L K+    GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLTKEEEEMLLKKL-PSGDETARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+                          
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRNN------------------------- 130

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                    +V S    ++ DE LN      D N     D L  
Sbjct: 131 -------------------------KVRS---EVSFDEPLN---IDWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           + D    V+ +  E    RN+L R++  L+ RE++I E R         T ++++    +
Sbjct: 160 EDD----VITKDLEANIDRNLLFRALDQLSDREKQIMELRFGLSGGEEKTQKDVADLLGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K +
Sbjct: 216 SQSYISRLEKRIIKRLRKEFNKMM 239


>gi|229827370|ref|ZP_04453439.1| hypothetical protein GCWU000182_02758 [Abiotrophia defectiva ATCC
           49176]
 gi|229788308|gb|EEP24422.1| hypothetical protein GCWU000182_02758 [Abiotrophia defectiva ATCC
           49176]
          Length = 268

 Score =  139 bits (351), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 54/261 (20%), Positives = 111/261 (42%), Gaps = 13/261 (4%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVK 91
             L ++Y +        +L+  +  LV  IA     Y GY +   ++V  G  GL+ A+ 
Sbjct: 15  IKLWEQYAKKPTQELREKLIIEYANLVKIIAGRMSIYLGYNVEYDDLVGYGIFGLIDAID 74

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G +  TY+   IK A+ + I +   +  I  T  Q++     ++L+   +AI +
Sbjct: 75  KFDHVKGVKFETYASLRIKGAILDQIRK---MDWIPRTMRQRQ-----KKLEAAERAIEE 126

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
              +      IA +L +S  E  S   +++    ++        +               
Sbjct: 127 KYGRMATDEEIAAELGISVDEYGSWQSQVSMSGIISLDDYLEQGSDLVADKSGSKLGISG 186

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
            +   E  E++  +  L  ++  L  +E+++      +E  +TL+ +S    VS  RV Q
Sbjct: 187 FEQPEEAVEKEELKESLAVAIEGLTEKEQKVIALYYYEE--LTLKEISRVLSVSESRVSQ 244

Query: 272 IEARAFKKVQESIQKQVELSS 292
           +  +A  K++E +   +++ +
Sbjct: 245 LHTKALTKLKEKLGDYIDIFT 265


>gi|225568655|ref|ZP_03777680.1| hypothetical protein CLOHYLEM_04733 [Clostridium hylemonae DSM
           15053]
 gi|225162583|gb|EEG75202.1| hypothetical protein CLOHYLEM_04733 [Clostridium hylemonae DSM
           15053]
          Length = 246

 Score =  139 bits (351), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 61/275 (22%), Positives = 111/275 (40%), Gaps = 67/275 (24%)

Query: 18  RYI--HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
            YI   EI   P LE +EE  +        D  A   L+  +LRLVV IA  +   G+ +
Sbjct: 31  HYIGGSEILPAP-LEAEEESAVINDLGSEYDEKAKKVLIEHNLRLVVYIAKKFDNTGVGV 89

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++S G IGL++A+  F+PE+  +LATY+   I+  +  Y+ R+               
Sbjct: 90  EDLISIGTIGLIKAINTFNPEKNIKLATYASRCIENEILMYLRRNNKT------------ 137

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
                                        K+ VS  E ++++                D 
Sbjct: 138 -----------------------------KMEVSIDEPLNVD---------------WDG 153

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--- 252
           N     D L  + D   + L  + E+K    +L +++S L+ RER I + R     P   
Sbjct: 154 NELLLSDILGTEEDTIYKDLENEVEQK----LLLKAISRLSGRERTIIQMRFGLGTPDGE 209

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             T + ++    +S+  + ++E +  ++++  + K
Sbjct: 210 EKTQKEVADMLGISQSYISRLEKKIMQRLRREMVK 244


>gi|254387389|ref|ZP_05002636.1| sigma factor [Streptomyces sp. Mg1]
 gi|194346181|gb|EDX27147.1| sigma factor [Streptomyces sp. Mg1]
          Length = 266

 Score =  139 bits (351), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 48/240 (20%), Positives = 98/240 (40%), Gaps = 12/240 (5%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY--GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            + L+  +  LV      +R    G  I +VV  G IGL++A+ +FDP R    +T +M 
Sbjct: 31  RNTLIEMNASLVQYAVRRFRSRCDGGDIEDVVQVGTIGLIKAIDRFDPARENEFSTLAMP 90

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +I   ++ +   +   V++     + R+      +    + +T    +   V  +A  L 
Sbjct: 91  YITGEIKRHFRDTSWAVRVPRRLQELRID-----IAKAKEELTVRLDRSPTVTDLAGHLG 145

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +++ EV+       G  S +     SD          + D  G+E+  +   E       
Sbjct: 146 LTDEEVVEGLVAANGHTSGSLDAPHSDHGDGPTTGHTLADVMGEEEPALALVEDVQ---A 202

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   +  L+ RER +   R  +E  +T   + +   +S+ +V ++  R    ++ S+  +
Sbjct: 203 LAPLLQRLSERERSMLRMRFGEE--LTQAQIGTALGISQMQVSRLLNRILAHLRASLLAE 260


>gi|300788069|ref|YP_003768360.1| RNA polymerase sigma factor [Amycolatopsis mediterranei U32]
 gi|299797583|gb|ADJ47958.1| RNA polymerase sigma factor [Amycolatopsis mediterranei U32]
          Length = 273

 Score =  139 bits (351), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 47/239 (19%), Positives = 94/239 (39%), Gaps = 18/239 (7%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +   RL+T HL L   IA  + G G P  +++     GL++AV ++  +RG    ++++ 
Sbjct: 48  ALRERLITEHLPLAEHIARRFSGRGEPFEDLLQVARTGLIRAVDRYAADRGSDFVSFAVP 107

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I   ++ +       +++      K L   L +    L         P     +A+ L+
Sbjct: 108 TIMGEVRRHFRDVGWSMRVPR--ALKDLKQKLAKASDVLAHELGRAPTP---SELARHLD 162

Query: 168 VSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           +    V    +  +     SL+      + + +        D            ER    
Sbjct: 163 LDIETVREGLLAAQAYRATSLDTPAREGEDDFAAAGRLAEDDS---------GFERFENH 213

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             L  +M+ L PRER I + R   E  +T   ++    VS+  V ++ A+  +++++ I
Sbjct: 214 IALRAAMATLEPRERAIVKMRFADE--LTQSQIAQRIGVSQMHVSRLLAKTLEQLRQHI 270


>gi|302867341|ref|YP_003835978.1| RNA polymerase sigma-70 factor [Micromonospora aurantiaca ATCC
           27029]
 gi|302570200|gb|ADL46402.1| RNA polymerase sigma-70 factor, sigma-B/F/G subfamily
           [Micromonospora aurantiaca ATCC 27029]
          Length = 377

 Score =  139 bits (350), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 57/254 (22%), Positives = 108/254 (42%), Gaps = 25/254 (9%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   LV   L    ++A  YRG G P+ ++     +GL+ AV ++DPERG     Y+ 
Sbjct: 40  QEARDDLVRFALPFAGRLARRYRGRGEPLEDLEQVARLGLVNAVDRYDPERGS-FTAYAA 98

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I   ++ +       V +      +RL   +  +      +T    +   V  ++ +L
Sbjct: 99  ITIVGEIKRHFRDRTWGVHVP-----RRLRDLILEVGQATATLTSELSRAPTVAELSARL 153

Query: 167 NVSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
              E E+++     AG    SLNA +    ++S+++ D +       E V        + 
Sbjct: 154 ETPEEEILAALESAAGYSPASLNAPV--GGESSAEFGDLVGESDHALESV--------DD 203

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  ++  +  L  RERRI   R       T   +++ F +S+  V ++ +RA   +++++
Sbjct: 204 RVTVSGLLHRLPWRERRILAMRFYGNQ--TQAEIAARFGISQMHVSRLLSRALTWLRQAM 261

Query: 285 QKQVELSSSPPLLQ 298
                L+ +PP  Q
Sbjct: 262 -----LADAPPPWQ 270


>gi|210624023|ref|ZP_03294140.1| hypothetical protein CLOHIR_02092 [Clostridium hiranonis DSM 13275]
 gi|210153230|gb|EEA84236.1| hypothetical protein CLOHIR_02092 [Clostridium hiranonis DSM 13275]
          Length = 255

 Score =  139 bits (350), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 49/254 (19%), Positives = 106/254 (41%), Gaps = 17/254 (6%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             L + Y ++ D+   + L+  HL L   +A  Y   G+   ++    ++ L+ A+ ++D
Sbjct: 16  KELFRLYSDNKDIDIRNILIERHLYLARILAKKYINKGVDYEDIYQVASLALIYAIDRYD 75

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +GF  ++++   I   +++Y       +++     +       +++     AI     
Sbjct: 76  ISKGFEFSSFATPTIIGEIKKYFRDKVWTMRVPRRIQELS-----KKISNAKIAIEQEKK 130

Query: 155 KPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +   V  IA+ +   E +V+            SL+A      ++     D  + D  G E
Sbjct: 131 RHPSVKDIAEYIGCREEDVLEAMEASYSYQPVSLDASSGDDSED-----DLTLSDRVGVE 185

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           +      E+K+    L R M  LN  E +I E R       T   +++E  +S+  V ++
Sbjct: 186 EKDFGNIEQKDF---LNRFMQTLNELEVKILEDRFFHN--KTQSVIATELNISQMTVSRL 240

Query: 273 EARAFKKVQESIQK 286
           E +  +K+++  +K
Sbjct: 241 EKKVVEKLRKEYEK 254


>gi|304317194|ref|YP_003852339.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium thermosaccharolyticum DSM 571]
 gi|302778696|gb|ADL69255.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium thermosaccharolyticum DSM 571]
          Length = 241

 Score =  139 bits (350), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 56/262 (21%), Positives = 109/262 (41%), Gaps = 63/262 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L  +EE  L  +  E GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 39  PPLSTEEEIFLIAKM-ESGDNAAKSMLIERNLRLVVYIAKKFENTGVGIEDLISIGTIGL 97

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+  F+P +  +LATY+   I+  +  Y+ R+                          
Sbjct: 98  IKAINTFNPHKKIKLATYASRCIENEILMYLRRNSKT----------------------- 134

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                             ++ VS  E ++++                D N     D L  
Sbjct: 135 ------------------RMEVSFDEPLNID---------------WDGNELLLSDILGT 161

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEV 264
           D+    +++ +  E +  + +L  ++  L+ RE+RI   R        +T + ++    +
Sbjct: 162 DN----EIVYKMIEDEVDKQLLKTALKKLSEREKRIIGLRFGLGGGAEMTQKEVADMLGI 217

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+  + ++E R  K++++ I +
Sbjct: 218 SQSYISRLEKRILKRLKKEINR 239


>gi|332297782|ref|YP_004439704.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Treponema
           brennaborense DSM 12168]
 gi|332180885|gb|AEE16573.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Treponema
           brennaborense DSM 12168]
          Length = 262

 Score =  139 bits (350), Expect = 5e-31,   Method: Composition-based stats.
 Identities = 51/258 (19%), Positives = 110/258 (42%), Gaps = 21/258 (8%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQA 89
           E  L   Y++    +     +  ++ LV  +A      G+P      ++V  G  GL+ A
Sbjct: 11  EDELWLEYKKTKSPALRDAFIRQYMPLVKYVAGK-VATGMPGSVEFDDLVGFGQFGLLDA 69

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + K+DP++  +  TY++  I+ ++ + + R    V    +  QK      R ++  + A+
Sbjct: 70  INKYDPDKNVKFKTYAVTRIRGSIFDEL-RQLDWV--PRSVRQKA-----REIEDAIVAL 121

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNS-SQWQDWLVY 206
                +P     +A  + +SE+E      R++G    SLN +  S D +      D +  
Sbjct: 122 ESRLGRPASDAEVAGSMGISEAEFQQTVMRVSGTSVLSLNDVWYSGDDSDHVSIGDSIES 181

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
                  V++E+EE    R ++  +++ L  +E+ +          +T + +     VS 
Sbjct: 182 PASLNPDVIVEREE---IRRVIAEAITELPEKEKMVLVLYY--HEDLTFKEIGQVLNVSE 236

Query: 267 ERVRQIEARAFKKVQESI 284
            R+ Q+  +A  +++  +
Sbjct: 237 SRISQLHTKANMRLRSKL 254


>gi|323706112|ref|ZP_08117681.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
 gi|323534556|gb|EGB24338.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
          Length = 241

 Score =  139 bits (350), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 56/262 (21%), Positives = 109/262 (41%), Gaps = 63/262 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L  +EE  L  +  E GD  A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 39  PPLSAEEEMFLIAKM-ESGDNEAKSMLIERNLRLVVYIAKKFENTGVGIEDLISIGTIGL 97

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++++  F+P +  +LATY+   I+  +  Y+ R+                          
Sbjct: 98  IKSINTFNPRKKIKLATYASRCIENEILMYLRRNSKT----------------------- 134

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                             ++ VS  E ++++                D N     D L  
Sbjct: 135 ------------------RMEVSFDEPLNID---------------WDGNELLLSDILGT 161

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           D+    +++ +  E +  + +LT ++  L+ RE+RI   R        +T + ++    +
Sbjct: 162 DN----ELVYKIIEDEVDKQLLTNALKKLSDREKRIIGLRFGLSGGTEMTQKEVADLLGI 217

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+  + ++E R  K++++ I +
Sbjct: 218 SQSYISRLEKRILKRLKKEINR 239


>gi|311029937|ref|ZP_07708027.1| sporulation sigma factor SigE [Bacillus sp. m3-13]
          Length = 239

 Score =  139 bits (350), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 64/264 (24%), Positives = 111/264 (42%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE  L  +   +GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLSKEEEAHLLIKL-PNGDQAARSILIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+                          
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRNN------------------------- 130

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                    +V S    ++ DE LN      D N     D L  
Sbjct: 131 -------------------------KVRS---EVSFDEPLN---IDWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           + D    ++ +  E    R +L +++  LN RE++I E R         T ++++    +
Sbjct: 160 EED----IITKDLEANVDRKLLLKALEQLNDREKQIMELRFGLIGGEEKTQKDVADMLGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 216 SQSYISRLEKRIIKRLRKEFNKMV 239


>gi|320537994|ref|ZP_08037899.1| RNA polymerase sigma factor WhiG [Treponema phagedenis F0421]
 gi|320145151|gb|EFW36862.1| RNA polymerase sigma factor WhiG [Treponema phagedenis F0421]
          Length = 262

 Score =  139 bits (350), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 54/257 (21%), Positives = 109/257 (42%), Gaps = 19/257 (7%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLMQAV 90
           E  L   Y++ G+       +  +  LV  +A      +   +   ++VS G  GL  A+
Sbjct: 11  EEELWLEYKKTGNAKIREFFIIQYAPLVKYVASKIAVGKPGSIEFDDLVSYGIFGLFDAI 70

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
            K+DPE+  R  TY++  I+ A+ + + RS   V        K++   +  ++  L    
Sbjct: 71  DKYDPEKNIRFNTYAVTRIRGAIYDEL-RSIDWVPRSVRQQIKQIEDTIAAIEAKL---- 125

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SL-NALINSSDKNSSQWQDWLVYD 207
               +      IA +LN+S  E   +  +++G    SL +      D       D +   
Sbjct: 126 ---GRSATDEEIAFELNISLEEYHQLLLKISGTSVISLADTKFGGEDSGQIAVGDSIEAP 182

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
                 V++E+EE    + ++  ++  L+ RE+++      ++  +TL+ +    +V+  
Sbjct: 183 ASLNPDVIVEREE---IKRVIVEAIKELSEREQQVLILYYYED--MTLKEIGKVLKVTES 237

Query: 268 RVRQIEARAFKKVQESI 284
           RV QI   A  K++  +
Sbjct: 238 RVSQIHTSANLKLKAKL 254


>gi|328948392|ref|YP_004365729.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Treponema
           succinifaciens DSM 2489]
 gi|328448716|gb|AEB14432.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Treponema
           succinifaciens DSM 2489]
          Length = 262

 Score =  139 bits (350), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 53/264 (20%), Positives = 117/264 (44%), Gaps = 19/264 (7%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIG 85
           L++ EE  L   Y++   ++   RL+  ++ LV  +A              ++V  G  G
Sbjct: 6   LDENEEAELWHEYKKSKSVAIRDRLIRQYMPLVKWVAGRVSTGMPDSVEFDDLVGFGQFG 65

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L+ A+ KFD ++G +  TY+   I+ A+ + +     L  +  +  QK      R ++  
Sbjct: 66  LLDAINKFDIDKGVKFKTYATTRIRGAIFDELRE---LDWVPRSVRQKS-----REIEDT 117

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNS-SQWQD 202
           +  +     +      IAK +N++E+E  S   +++G    SLN +  S D++      D
Sbjct: 118 IVELESKLGRTASDAEIAKAMNMTEAEYQSAVMKVSGTSVLSLNDVWYSGDESEHVSIGD 177

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
            +   +     V++E+EE    R ++ ++++ L   E+ +          ++ + +    
Sbjct: 178 SIEAPNSLNPDVIVEREE---IRRVIIQAINELPKNEKMVIVLYY--HEDLSFKEIGQVL 232

Query: 263 EVSRERVRQIEARAFKKVQESIQK 286
            VS  R+ Q+ ++A  +++  +  
Sbjct: 233 NVSESRISQLHSKANLRLRAKLTS 256


>gi|317127083|ref|YP_004093365.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Bacillus
           cellulosilyticus DSM 2522]
 gi|315472031|gb|ADU28634.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Bacillus
           cellulosilyticus DSM 2522]
          Length = 262

 Score =  139 bits (350), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 51/257 (19%), Positives = 118/257 (45%), Gaps = 16/257 (6%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++       Y+  G+     +LV     LV  +A  +        +++  G IGL+ A+
Sbjct: 13  KEQVLQWIAEYQSTGNKEIQTKLVLEFESLVHALARKFSRGQRHDEDLIQVGMIGLLAAI 72

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           ++FDP  G    ++++  I   ++ +I      V +      +R+     ++K  +  +T
Sbjct: 73  RRFDPTIGKSFESFAVPTIIGEIKRFIRDKTWSVHVP-----RRIKEMGPKVKNAVDTLT 127

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNC--RLAGDESLNALINSSDKNSSQWQDWLVYDH 208
               +  +V  IA  ++ SE EV+      +     S++  I + D+ S+     LV   
Sbjct: 128 TQLQRSPKVEEIAAHIDASEEEVLETMEMGKSYQALSVDRSIEADDEGSAVTLLDLVGST 187

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           +G         E+ +++ +L ++ +VL+ RE++I      +   ++ ++   +  +S+  
Sbjct: 188 EGGY-------EKTDQQMLLEKAFTVLSDREKQILHLTYFEN--LSQKDTGEKLGISQMH 238

Query: 269 VRQIEARAFKKVQESIQ 285
           V +++ RA +K++ES++
Sbjct: 239 VSRLQRRALQKLRESLK 255


>gi|312139980|ref|YP_004007316.1| sigma-70 factor sigf [Rhodococcus equi 103S]
 gi|311889319|emb|CBH48635.1| sigma-70 factor SigF [Rhodococcus equi 103S]
          Length = 259

 Score =  139 bits (350), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 46/246 (18%), Positives = 90/246 (36%), Gaps = 17/246 (6%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E G       ++T  L L   IA  +   G P  ++V   +IGL+ AV ++D ERG    
Sbjct: 29  EPGHAELRESIITRCLPLAQHIARRFDRRGEPFEDLVQVASIGLVNAVDRYDVERGSDFL 88

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
            +++  I   ++ +   +   V++     +  L      L      ++    +      +
Sbjct: 89  AFAVPTIMGEVRRHFRDTGWAVRVPRRLKELHLD-----LVKTSAQLSQRLGRSPTTREM 143

Query: 163 AKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
           A++L +   EV        G +  S++A   S     S   D L  +      V      
Sbjct: 144 AEELGIEVEEVAQGLQAANGYQALSVDAAAGSGPDTGSTLGDLLGDNDSDIAGV------ 197

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                  L   +  L  RER +   R       T   +++   VS+  V +I +    ++
Sbjct: 198 --EDHETLRVVLEGLPERERTVLLLRFFGNQ--TQSQIAAHVGVSQMHVSRILSDTLARL 253

Query: 281 QESIQK 286
           +  +++
Sbjct: 254 RAQVER 259


>gi|94499982|ref|ZP_01306517.1| RNA polymerase sigma-A factor [Oceanobacter sp. RED65]
 gi|94427840|gb|EAT12815.1| RNA polymerase sigma-A factor [Oceanobacter sp. RED65]
          Length = 368

 Score =  139 bits (350), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 49/268 (18%), Positives = 118/268 (44%), Gaps = 18/268 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
              Y+  I ++     ++  VL +RY ++      ++LV ++LRL + +A  Y G G+ +
Sbjct: 110 FDLYLQHIHELKGRLYKQAQVLKRRYEDY-----RNQLVQANLRLAMHVARQYTGKGMEL 164

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            E++ EG +GL++  ++++  +G+R  TY+ WWI+ A++  +     +V+I T    +  
Sbjct: 165 EELIQEGTLGLIKGAERYNINKGYRFTTYAYWWIQQAIKGALSEKRGIVRIPTNVTDR-- 222

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              + +++         N +      I+  L +    + S        +S++  I     
Sbjct: 223 ---IVKVERCKYEFFKANGRYPNAKEISSILGMDVDHIRSTLAVTNVGDSIDEPIY---D 276

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT- 254
                Q+ +  +        +++E+ +     L + +  L  R++ I           T 
Sbjct: 277 EGLTMQESMASESIATPSSQLDEEDGEAF---LEKLIGELPKRQQFIVRLYHGIGIGQTY 333

Query: 255 -LENLSSEFEVSRERVRQIEARAFKKVQ 281
             + ++ +  V+ ER RQ+   + ++++
Sbjct: 334 PFKEIAPQIGVTLERTRQLYHESIRQLK 361


>gi|161898843|gb|ABX80411.1| SigB [Listeria monocytogenes]
          Length = 228

 Score =  139 bits (350), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 54/241 (22%), Positives = 106/241 (43%), Gaps = 24/241 (9%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D   G  
Sbjct: 6   YQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKS 65

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
              +++  I   ++ ++      V +     +        ++K  ++ +T       Q+ 
Sbjct: 66  FEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQSSPQIS 120

Query: 161 AIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            IA  + V+E EV+           L+ D S+ A    SD ++    D +    DG    
Sbjct: 121 DIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTDDGF--- 174

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
                ER N+R +L + + VL+ RE++I +   ++    + +      ++S+  V +I+ 
Sbjct: 175 -----ERVNQRMLLEKVLPVLDEREQKILQFTFIEN--RSQKETGELLDISQMHVSRIQR 227

Query: 275 R 275
           +
Sbjct: 228 Q 228


>gi|302551910|ref|ZP_07304252.1| RNA polymerase sigma-E factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302469528|gb|EFL32621.1| RNA polymerase sigma-E factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 304

 Score =  139 bits (350), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 49/236 (20%), Positives = 98/236 (41%), Gaps = 16/236 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            + LV  +L LV   A  +R    P+ +++  G IGL++A+ +F+  RG    T++M  I
Sbjct: 80  RNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRGVEFPTFAMPTI 139

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +   V  +A++L +S
Sbjct: 140 VGEIKRFFRDTSWSVRVPRRLQELRLD-----LAKAGDELAQKLDRAPTVTELAERLGIS 194

Query: 170 ESEVIS-MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
             EV+  M    A   S        D +     D + Y+  G E +             L
Sbjct: 195 NDEVVEGMAASNAYTASSLDAQPEEDDSEGALADRIGYEDHGLEGI--------EYVESL 246

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              ++ L PR+R+I   R +    +T   +  E  +S+  V ++ +R   ++++ +
Sbjct: 247 KPLIAELPPRDRKILSLRFVAG--LTQSEIGEELGISQMHVSRLLSRTLVRLRKGL 300


>gi|331269335|ref|YP_004395827.1| RNA polymerase sigma 28 subunit FliA/WhiG [Clostridium botulinum
           BKT015925]
 gi|329125885|gb|AEB75830.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium botulinum
           BKT015925]
          Length = 242

 Score =  139 bits (350), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 54/242 (22%), Positives = 106/242 (43%), Gaps = 19/242 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              +V  ++ LV  IA      +   +   +++  G IGLM A+ KFD  +G + +TY+ 
Sbjct: 10  REHIVKKYIPLVKYIASRVIIGKSKYIEFEDLLGYGMIGLMDALNKFDESKGMKFSTYAS 69

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ +M + I ++  +         K     L R    ++ +   NL    +  IA++L
Sbjct: 70  IRIRGSMIDEIRKNSPI--------SKGAMDKLNRYNNAIETLQKKNLTEPNIKDIAQEL 121

Query: 167 NVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            ++ +EV  +   +      SL  LI S D + S     +  +     +   E +ER   
Sbjct: 122 QMTVNEVGEIENFINYISIVSLEDLIFSEDDDIS-LMGTIEDEKSPNPEKDFEDQER--- 177

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              L +++ +LN +++ +          +TL+ + S   VS  RV Q+ +RA   +++ +
Sbjct: 178 LEYLAKALDMLNDKDKTVLSLYYY--EGMTLKEIGSVLGVSESRVCQLHSRAIVHLRKML 235

Query: 285 QK 286
            K
Sbjct: 236 GK 237


>gi|295836990|ref|ZP_06823923.1| RNA polymerase sigma factor [Streptomyces sp. SPB74]
 gi|197697450|gb|EDY44383.1| RNA polymerase sigma factor [Streptomyces sp. SPB74]
          Length = 312

 Score =  139 bits (350), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 50/236 (21%), Positives = 95/236 (40%), Gaps = 16/236 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            + LV  +L LV   A  +R    P+ +++  G IGL++A+ +F+  RG    T++M  I
Sbjct: 88  RNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRGVEFPTFAMPTI 147

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +      +A +L + 
Sbjct: 148 IGEIKRFFRDTSWSVRVPRRLQELRLD-----LAKAGDELAQRLDRAPTPSELADRLGIE 202

Query: 170 ESEVIS-MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
             EVI  M    A   S        D + S   D L Y+  G E +             L
Sbjct: 203 REEVIEGMAASNAYTASSLDAQPEEDDSESALADRLGYEDHGLEGI--------EYIESL 254

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              ++ L  R+R+I   R +    +T   +  E  +S+  V ++ +R   K+++ +
Sbjct: 255 KPMIARLPQRDRKILSLRFVAN--MTQSEIGEELGISQMHVSRLLSRTLVKLRKGL 308


>gi|330936784|gb|EGH40944.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. pisi
           str. 1704B]
          Length = 176

 Score =  139 bits (350), Expect = 6e-31,   Method: Composition-based stats.
 Identities = 46/108 (42%), Positives = 72/108 (66%), Gaps = 1/108 (0%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y++EI   P+L  +EE   A R  + GD +   R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 67  YLNEIGFSPLLSPEEEVHFA-RLSQSGDPAGRKRMIESNLRLVVKIARRYVNRGLSLLDL 125

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           + EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++
Sbjct: 126 IEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRL 173


>gi|157692207|ref|YP_001486669.1| sporulation sigma factor SigE [Bacillus pumilus SAFR-032]
 gi|157680965|gb|ABV62109.1| DNA-directed RNA polymerase sigma subunit SigE [Bacillus pumilus
           SAFR-032]
          Length = 239

 Score =  139 bits (350), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 63/264 (23%), Positives = 109/264 (41%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K EE  L  +  + GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLSKDEEQELLVKLPK-GDQTARAILIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+                    +++   
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN-------------------NKIRSE- 135

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                            ++ DE LN      D N     D L  
Sbjct: 136 ---------------------------------VSFDEPLN---IDWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           D D    ++    E    + +L +++  LN RE++I E R         T ++++    +
Sbjct: 160 DDD----IITRDIEANVDKKLLKKALEQLNDREKQIMELRFGLVGGEEKTQKDVADMLGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++Q+   K V
Sbjct: 216 SQSYISRLEKRIIKRLQKEFNKMV 239


>gi|311068053|ref|YP_003972976.1| sporulation sigma factor SigE [Bacillus atrophaeus 1942]
 gi|310868570|gb|ADP32045.1| sporulation sigma factor SigE [Bacillus atrophaeus 1942]
          Length = 239

 Score =  139 bits (350), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 64/264 (24%), Positives = 111/264 (42%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K EE VL  +    GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLSKDEEQVLLLKL-PSGDQAARAILIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+                    +++   
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN-------------------NKIRSE- 135

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                            ++ DE LN      D N     D L  
Sbjct: 136 ---------------------------------VSFDEPLN---IDWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           D D    ++ +  E    + +L +++  LN RE++I E R     E   T ++++    +
Sbjct: 160 DDD----IITKDIEANVDKKLLKKALEQLNDREKQIMELRFGLVGEEEKTQKDVADMMGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 216 SQSYISRLEKRIIKRLRKEFNKMV 239


>gi|328948495|ref|YP_004365832.1| RNA polymerase, sigma 32 subunit, RpoH [Treponema succinifaciens
           DSM 2489]
 gi|328448819|gb|AEB14535.1| RNA polymerase, sigma 32 subunit, RpoH [Treponema succinifaciens
           DSM 2489]
          Length = 349

 Score =  139 bits (350), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 55/248 (22%), Positives = 100/248 (40%), Gaps = 24/248 (9%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRG-YGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
            + G++ A +R+   +LR V++I+  +         E    G IGL++A+K FD      
Sbjct: 114 AQSGNVYAFNRMTEMYLRGVLRISYNFAKENYCDFEEAFQNGTIGLIRAIKNFDVTSPNS 173

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            A+Y    + + MQ       S   +    +QK  F  L  +  +L         PE+ +
Sbjct: 174 FASYYSLSVLSEMQRKYSVKNSFFDLPVHFSQK-TFEFLGIISKYLAK----GKTPEESI 228

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I       E     +         L+A+   +       +D ++Y              
Sbjct: 229 GIISDDFYLEINP-KLKMYFLPYLDLDAISYENFAFDIHIEDDIIY-------------- 273

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFK 278
            ++ +  L   +  L  RER++ E R    N   +TLE +   + VSRER+RQIE +A +
Sbjct: 274 -ESLKEQLNEVLHTLPERERKVLEMRFGLNNLKQMTLEEVGKYYNVSRERIRQIEKKALR 332

Query: 279 KVQESIQK 286
           +++   + 
Sbjct: 333 RLRHPHRA 340


>gi|223994539|ref|XP_002286953.1| plastid RNA polymerase sigma factor [Thalassiosira pseudonana
           CCMP1335]
 gi|220978268|gb|EED96594.1| plastid RNA polymerase sigma factor [Thalassiosira pseudonana
           CCMP1335]
          Length = 298

 Score =  139 bits (350), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 47/243 (19%), Positives = 101/243 (41%), Gaps = 14/243 (5%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           +    +  +L+T ++ LV  IA  Y      +  ++ EG +G+M+A +++DP +GFR +T
Sbjct: 57  NKGQESRTKLITGNVGLVTLIAKRYYNM---LRNLIQEGYMGIMEAAERYDPSKGFRFST 113

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y   WI+  +   I  S  ++++            +R +    +       +   +  +A
Sbjct: 114 YGTHWIRQRIVRAIAESSRMIRLPVHVQ-----ATIRNINKKHEEFEATIGRSPSLPELA 168

Query: 164 KKLNVSESEVISMNCRLAGDESLN-ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
            ++ VS  ++           SL  A+   S +++    D +            E    +
Sbjct: 169 HEMGVSLDKLHLYQHLSRNVISLERAVDQHSPEDNRTLGDRIACTELPTPD---EDAMSE 225

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             R  +   +  L   ER +   R   ++  P TL+  +    +S + VR +EA+A  ++
Sbjct: 226 ALRGEVHSMLDALRDNERIVLTHRFGLDDGRPKTLKETAYGMGISIDSVRAVEAKALNRL 285

Query: 281 QES 283
           ++ 
Sbjct: 286 RQP 288


>gi|21223976|ref|NP_629755.1| RNA polymerase sigma factor WhiG [Streptomyces coelicolor A3(2)]
 gi|256784937|ref|ZP_05523368.1| RNA polymerase sigma factor WhiG [Streptomyces lividans TK24]
 gi|289768830|ref|ZP_06528208.1| RNA polymerase sigma factor whiG [Streptomyces lividans TK24]
 gi|133480|sp|P17211|RPSW_STRCO RecName: Full=RNA polymerase sigma factor whiG
 gi|153486|gb|AAA26828.1| sigma factor (whiG) (put. alt.); putative [Streptomyces coelicolor]
 gi|3192014|emb|CAA19413.1| RNA polymerase sigma factor WhiG [Streptomyces coelicolor A3(2)]
 gi|289699029|gb|EFD66458.1| RNA polymerase sigma factor whiG [Streptomyces lividans TK24]
          Length = 280

 Score =  139 bits (350), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 47/254 (18%), Positives = 107/254 (42%), Gaps = 16/254 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
            L + Y+  GD     +L+  +  LV  +A          +  ++ VS G  GL+ A++K
Sbjct: 33  ELWRSYKTTGDERLREQLILHYSPLVKYVAGRVSVGLPPNVEQADFVSSGVFGLIDAIEK 92

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD +R  +  TY++  I+ AM + + R+   +        + +      L+  L+     
Sbjct: 93  FDVDREIKFETYAITRIRGAMIDEL-RALDWIPRSVRQKARNVERAYATLEARLR----- 146

Query: 153 NLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
             +      +A ++ ++  ++ ++     LA   +L  L+++  +   +    +    D 
Sbjct: 147 --RTPSESEVAVEMGIAVEDLHAVFSQLSLANVVALEELLHAGGEGGGRL-SLMDTLEDT 203

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                +E  E +  R +L R+++ L  RE+ +          +TL  + +   V+  RV 
Sbjct: 204 AADNPVEVAEDRELRRLLARAINTLPEREKTVVTLYYY--EGLTLAEIGNVLGVTESRVS 261

Query: 271 QIEARAFKKVQESI 284
           QI  ++  +++  +
Sbjct: 262 QIHTKSVLQLRAKL 275


>gi|312134334|ref|YP_004001672.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|311774385|gb|ADQ03872.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor owensensis OL]
          Length = 256

 Score =  138 bits (349), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 47/235 (20%), Positives = 110/235 (46%), Gaps = 15/235 (6%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L + Y++  D+   + LV  HL +   IA  +   G+   ++     + L+ AV++F+P 
Sbjct: 18  LFEEYQKTKDVKLRNELVNRHLYIAEIIAKKFVNRGIDYDDLYQVACVALINAVERFEPN 77

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +G++  +++   I   ++ Y     S++++      +R++    ++K   + ++    +P
Sbjct: 78  KGYKFTSFATPTIMGEIKRYFRDRASIIRLP-----RRIYETSAKIKLATEVLSTKLKRP 132

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
            +V  IA+ LN+S  EV+ +      + S + L  S D+   + ++  + D  G+     
Sbjct: 133 PKVEEIAQHLNMSTEEVLEVM-----EASNSYLPQSLDQTMYEDEEMTLGDVLGKSD--- 184

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E   +      + +++  L+P ER   + R  +E   T + ++ E  VS+  + +
Sbjct: 185 ESILQVENVEAVKKAIERLSPFEREFLQKRFFEE--KTQKEIAEEMNVSQMYISR 237


>gi|253573548|ref|ZP_04850891.1| RNA polymerase sigma factor [Paenibacillus sp. oral taxon 786 str.
           D14]
 gi|251847076|gb|EES75081.1| RNA polymerase sigma factor [Paenibacillus sp. oral taxon 786 str.
           D14]
          Length = 262

 Score =  138 bits (349), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 60/261 (22%), Positives = 117/261 (44%), Gaps = 20/261 (7%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
            L +R++EHGDL A  +L+  +L +V  ++          +   ++ S G +GL+ AV+K
Sbjct: 13  DLWERWKEHGDLEAKKQLIEKYLPIVDYVSGRLAVGLPKNVSKDDLASNGVMGLIDAVEK 72

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD +RG +  TY+ W ++ A+ + + R    V        K       +++   Q +   
Sbjct: 73  FDYKRGLQFETYASWRVRGAILDGL-RQGDWVPRSVREKAK-------KIEEGYQHLEQQ 124

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDG 210
            L+      ++  LNVSE E  SM   +A     SL   I   ++ S      LV +   
Sbjct: 125 YLRSVTDAEMSSYLNVSEKEFQSMLQEVAVMTLCSLEDPIR--EEESETRLTLLVDEKAK 182

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                + +      R  L + +  L  +ER +      ++  ++L  ++    +S  R+ 
Sbjct: 183 NPDYKVREFYL---RESLAKGIEKLTEKERTVVSLLYYED--LSLSEIAEVMSLSPSRIS 237

Query: 271 QIEARAFKKVQESIQKQVELS 291
           Q+ ++A  +++ S++KQ +L 
Sbjct: 238 QLHSKAILRLRGSLEKQRDLL 258


>gi|258511273|ref|YP_003184707.1| sporulation sigma factor SigE [Alicyclobacillus acidocaldarius
           subsp. acidocaldarius DSM 446]
 gi|257477999|gb|ACV58318.1| RNA polymerase, sigma 28 subunit, SigE [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
          Length = 249

 Score =  138 bits (349), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 66/264 (25%), Positives = 106/264 (40%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE  L +R    GD S    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 47  PPLTKEEEQYLLERL-PSGDPSVRSMLIERNLRLVVYIARKFENTGVNIEDLVSIGTIGL 105

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FDP +  +LATY+   I+  +  Y+ R+                    +L+   
Sbjct: 106 IKAVNTFDPSKKIKLATYASRCIENEILMYLRRN-------------------NKLRAE- 145

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                            ++ DE LN      D N     D L  
Sbjct: 146 ---------------------------------VSLDEPLN---VDWDGNELLLSDVLGT 169

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEV 264
           D D     +    E +  R +L  ++  L+ RER I E R        +T ++++    +
Sbjct: 170 DSD----TIYRNLEDEVDRELLYDALDKLSERERTIMELRFGLGTGQEMTQKDVADLLGI 225

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++Q    K +
Sbjct: 226 SQSYISRLEKRILKRLQREFNKMM 249


>gi|224477054|ref|YP_002634660.1| RNA polymerase sigma factor SigB [Staphylococcus carnosus subsp.
           carnosus TM300]
 gi|222421661|emb|CAL28475.1| sigma factor B [Staphylococcus carnosus subsp. carnosus TM300]
          Length = 256

 Score =  138 bits (349), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 47/264 (17%), Positives = 109/264 (41%), Gaps = 24/264 (9%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           +  ++     ++++   +  A  +LV  + +L+  +A  Y        ++V  G +GL+ 
Sbjct: 11  ISPEQINEWIRQHQNDENTDAQDKLVKHYQKLIESLAFKYSKGQSHHEDLVQVGMVGLIG 70

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A+ +FD   G +   + +  +   ++ Y+      V +     +        R+K     
Sbjct: 71  AINRFDINFGRKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIG-----PRIKKTTDE 125

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNC------RLAGDESLNALINSSDKNSSQWQD 202
           +T+   +   +  IA++L V++ EV+           L+ D S+ A     D ++    D
Sbjct: 126 LTNELERSPSISEIAERLEVTDEEVLEAMEMGQSYNALSVDHSIEA---DKDGSTVTLLD 182

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
            +     G         +   +R +L R + +L  RER I +   +    ++ +      
Sbjct: 183 IMGEQEGGY--------DLTEKRMILERILPILTDREREIIQCTFI--EGLSQKETGERI 232

Query: 263 EVSRERVRQIEARAFKKVQESIQK 286
            +S+  V +++  A KK+Q++ +K
Sbjct: 233 GLSQMHVSRLQRNAIKKLQQAAKK 256


>gi|229195303|ref|ZP_04322075.1| RNA polymerase sigma-B factor [Bacillus cereus m1293]
 gi|228588158|gb|EEK46204.1| RNA polymerase sigma-B factor [Bacillus cereus m1293]
          Length = 242

 Score =  138 bits (349), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 49/249 (19%), Positives = 113/249 (45%), Gaps = 16/249 (6%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L   ++++    A  RLV  +  LV  IA  Y   G    +++  G +GL+ A++++D  
Sbjct: 3   LIAEFQQNQCDEAQERLVDHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYDYS 62

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
            G     +++  I   +++Y+      + +      +R+     ++K  ++ +TD+  + 
Sbjct: 63  IGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRIKDLGGKIKLAIEELTDHLQRS 117

Query: 157 EQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            +++ IA  L +SE EV+ +          SL+ ++ ++   SS  +   V +       
Sbjct: 118 PKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENASDGSSVARIESVGE------- 170

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
           + +  E   RR +L    +VLN  E+ +     + E  +  ++      +S+  V +I+ 
Sbjct: 171 VEQGYEETERRLVLKDIFNVLNETEKSVIH--YIFEENLNQKDTGERLGISQMHVSRIKR 228

Query: 275 RAFKKVQES 283
           +A  K++++
Sbjct: 229 QAISKLKQA 237


>gi|55274970|gb|AAV49284.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 196

 Score =  138 bits (349), Expect = 7e-31,   Method: Composition-based stats.
 Identities = 55/206 (26%), Positives = 98/206 (47%), Gaps = 12/206 (5%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+ 
Sbjct: 1   RMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQ 60

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            ++  I+     +++      K L   LR  +     ++           IA++L+    
Sbjct: 61  TIERAIMNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVD 115

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           +V  M        S++  +    +     +  L    D +E    +  +  + +  + + 
Sbjct: 116 DVSRMLRLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKW 170

Query: 232 MSVLNPRERRIFEARR--LQENPVTL 255
           +  LN ++R +   R   L     TL
Sbjct: 171 LFELNAKQREVLARRFGLLGYEAATL 196


>gi|302535451|ref|ZP_07287793.1| RNA polymerase sigma-E factor [Streptomyces sp. C]
 gi|302444346|gb|EFL16162.1| RNA polymerase sigma-E factor [Streptomyces sp. C]
          Length = 288

 Score =  138 bits (349), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 49/237 (20%), Positives = 99/237 (41%), Gaps = 16/237 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            + LV  +L LV   A  +RG   P+ ++V  G IGL++A+ +FDPERG    T++M  I
Sbjct: 62  RNTLVELNLSLVKYAARRFRGRSEPMEDIVQVGTIGLIKAINRFDPERGVEFTTFAMPTI 121

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   VK+     + R+            A+  +  +      +A++L+V+
Sbjct: 122 SGEIKRFFRDTSWAVKVPRRLQELRIDSA-----KAHDALEQDLGREPTDTEMARELDVT 176

Query: 170 ESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
             E        +     SL+A +    +     +   + + +          +R      
Sbjct: 177 PEEFSEGRKAASAYSARSLDAPVQEDSERDPAAERASLGEEEPAY-------DRIECLES 229

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   ++VL  RER +   R  QE  +T   + +   +S+  V ++  R   +++  +
Sbjct: 230 LKPMLAVLPERERELLSLRFGQE--LTQSEIGARLGLSQMHVSRLLNRTLTRLRGGL 284


>gi|240171602|ref|ZP_04750261.1| RNA polymerase sigma factor SigF [Mycobacterium kansasii ATCC
           12478]
          Length = 262

 Score =  138 bits (349), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 45/236 (19%), Positives = 93/236 (39%), Gaps = 13/236 (5%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             ++V   L L   IA  + G G P  +++    +GL+ AV +FD E G    ++++  I
Sbjct: 40  RDKIVERCLPLADHIARRFEGRGEPRDDLIQVARVGLVNAVVRFDVETGSDFVSFAVPTI 99

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   VK+     +  L     RL      ++    +      +A +L + 
Sbjct: 100 MGEVRRHFRDNSWSVKVPRRLKELHL-----RLGTATAELSQRLGRAPTATELAAELGMD 154

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             EV+     L    S N L   S   +       + D  G     +++ E    R  L 
Sbjct: 155 RGEVVE---GLVAGSSYNTLSIDSGGGNEDDDARAIADTLGDMDAGLDRIED---RESLR 208

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             +  L  RER +   R      +T   ++    +S+  V ++ A++  ++++ ++
Sbjct: 209 PLLEALPERERTVLILRFF--ESMTQTQIAERVGISQMHVSRLLAKSLARLRDQLE 262


>gi|290959865|ref|YP_003491047.1| SigL-like sigma factor [Streptomyces scabiei 87.22]
 gi|260649391|emb|CBG72506.1| SigL-like sigma factor [Streptomyces scabiei 87.22]
          Length = 304

 Score =  138 bits (349), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 48/236 (20%), Positives = 98/236 (41%), Gaps = 16/236 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            + LV  +L LV   A  +R    P+ +++  G IGL++A+ +F+  RG    T++M  I
Sbjct: 80  RNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRGVEFPTFAMPTI 139

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +   V  +A++L ++
Sbjct: 140 VGEIKRFFRDTSWSVRVPRRLQELRLD-----LAKAGDELAQKLDRAPTVGELAERLGLT 194

Query: 170 ESEVIS-MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
             EV+  M    A   S        D +     D + Y+  G E +             L
Sbjct: 195 NDEVVEGMAASNAYTASSLDAQPEEDDSEGALADRIGYEDHGLEGI--------EYVESL 246

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              ++ L PR+R+I   R +    +T   +  E  +S+  V ++ +R   ++++ +
Sbjct: 247 KPLIAGLPPRDRQILSLRFVAN--MTQSEIGDELGISQMHVSRLLSRTLVRLRKGL 300


>gi|294501014|ref|YP_003564714.1| RNA polymerase sigma-E factor [Bacillus megaterium QM B1551]
 gi|295706363|ref|YP_003599438.1| RNA polymerase sigma-E factor [Bacillus megaterium DSM 319]
 gi|294350951|gb|ADE71280.1| RNA polymerase sigma-E factor [Bacillus megaterium QM B1551]
 gi|294804022|gb|ADF41088.1| RNA polymerase sigma-E factor [Bacillus megaterium DSM 319]
          Length = 239

 Score =  138 bits (349), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 63/264 (23%), Positives = 111/264 (42%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K EE VL K+    GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLTKDEEEVLLKKL-PSGDEAARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+                    +++   
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN-------------------NKIRSE- 135

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                            ++ DE LN      D N     D +  
Sbjct: 136 ---------------------------------VSFDEPLN---IDWDGNELLLSDVMGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           + D    ++ +  E    R +L +++  LN RE++I E R         T ++++    +
Sbjct: 160 EED----IITKDLEANVDRKLLLKALHQLNDREKQIMELRFGLAGGEEKTQKDVADMLGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 216 SQSYISRLEKRIIKRLRKEFNKMV 239


>gi|291550014|emb|CBL26276.1| RNA polymerase, sigma 29 subunit, SigE [Ruminococcus torques L2-14]
          Length = 264

 Score =  138 bits (349), Expect = 8e-31,   Method: Composition-based stats.
 Identities = 54/262 (20%), Positives = 109/262 (41%), Gaps = 64/262 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE ++E  + +      D  A   L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 59  PPLENEKEREVVRWLGTDRDEKARKILIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGL 118

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+  F+P +  +LATY+   I+  +  Y+ R+                          
Sbjct: 119 IKAINTFNPSKKIKLATYASRCIENEILMYLRRNSKT----------------------- 155

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                             K+ VS  E ++++                D N     D L  
Sbjct: 156 ------------------KMEVSIDEPLNVD---------------WDGNELLLSDILGT 182

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP----VTLENLSSEF 262
           + D   + L ++ ERK    +L R+++ L+ RE+ I   R   ++P    +T + ++ + 
Sbjct: 183 EEDTIYRDLEDEAERK----ILFRALNKLSGREKLIVRMRFGLDHPEGKEMTQKEVADQL 238

Query: 263 EVSRERVRQIEARAFKKVQESI 284
            +S+  + ++E +   +++  +
Sbjct: 239 GISQSYISRLEKKIMHRLRMEM 260


>gi|194014382|ref|ZP_03052999.1| RNA polymerase sigma-E factor [Bacillus pumilus ATCC 7061]
 gi|194013408|gb|EDW22973.1| RNA polymerase sigma-E factor [Bacillus pumilus ATCC 7061]
          Length = 239

 Score =  138 bits (349), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 63/264 (23%), Positives = 109/264 (41%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K EE  L  +  + GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLSKDEEQELLVKLPK-GDQTARAILIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+                    +++   
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN-------------------NKIRSE- 135

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                            ++ DE LN      D N     D L  
Sbjct: 136 ---------------------------------VSFDEPLN---IDWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           D D    ++    E    + +L +++  LN RE++I E R         T ++++    +
Sbjct: 160 DDD----IITRDIEANVDKKLLKKALEQLNDREKQIMELRFGLIGGEEKTQKDVADMLGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++Q+   K V
Sbjct: 216 SQSYISRLEKRIIKRLQKEFNKMV 239


>gi|238064463|ref|ZP_04609172.1| sigma-70 region 2 domain-containing protein [Micromonospora sp.
           ATCC 39149]
 gi|237886274|gb|EEP75102.1| sigma-70 region 2 domain-containing protein [Micromonospora sp.
           ATCC 39149]
          Length = 305

 Score =  138 bits (349), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 57/254 (22%), Positives = 110/254 (43%), Gaps = 25/254 (9%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   LV   L    ++A  YRG G P+ ++     +GL+ AV ++DPERG     Y+ 
Sbjct: 63  QEARDDLVRFALPFAGRLARRYRGRGEPLEDLEQVARLGLVNAVDRYDPERGS-FTAYAA 121

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I   ++ +       V +      +RL   +  +      +T    +   V  +A++L
Sbjct: 122 ITIVGEIKRHFRDRTWGVHVP-----RRLRDLILEVGQATATLTSELSRAPTVAELAERL 176

Query: 167 NVSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
              + E+++     AG    SLNA +    ++S+++ D +    +  E V        + 
Sbjct: 177 ETPQEEILAALESAAGYSPASLNAPV--GGESSAEFGDLVGESDNALESV--------DD 226

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  ++  +  L  RERRI   R       T   +++ F +S+  V ++ +RA   +++++
Sbjct: 227 RVTISGLLHRLPWRERRILAMRFYGNQ--TQAEIAARFGISQMHVSRLLSRALTWLRQAM 284

Query: 285 QKQVELSSSPPLLQ 298
                L+ +PP  Q
Sbjct: 285 -----LADAPPPWQ 293


>gi|318056726|ref|ZP_07975449.1| SigL-like sigma factor [Streptomyces sp. SA3_actG]
 gi|318075360|ref|ZP_07982692.1| SigL-like sigma factor [Streptomyces sp. SA3_actF]
          Length = 316

 Score =  138 bits (349), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 51/236 (21%), Positives = 96/236 (40%), Gaps = 16/236 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            + LV  +L LV   A  +R    P+ +++  G IGL++A+ +F+  RG    T++M  I
Sbjct: 92  RNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRGVEFPTFAMPTI 151

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +      +A+KL + 
Sbjct: 152 IGEIKRFFRDTSWSVRVPRRLQELRLD-----LAKAGDELAQRLDRAPTPSELAEKLGIE 206

Query: 170 ESEVIS-MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
             EVI  M    A   S        D + S   D L Y+  G E +             L
Sbjct: 207 REEVIEGMAASNAYTASSLDAQPEEDDSESALADRLGYEDHGLEGI--------EYIESL 258

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              ++ L  R+R+I   R +    +T   +  E  +S+  V ++ +R   K+++ +
Sbjct: 259 KPMIARLPQRDRKILSLRFVAN--MTQSEIGEELGISQMHVSRLLSRTLVKLRKGL 312


>gi|297196939|ref|ZP_06914336.1| RNA polymerase sigma-B factor [Streptomyces sviceus ATCC 29083]
 gi|197715922|gb|EDY59956.1| RNA polymerase sigma-B factor [Streptomyces sviceus ATCC 29083]
          Length = 281

 Score =  138 bits (349), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 48/239 (20%), Positives = 108/239 (45%), Gaps = 18/239 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + L+  ++ LV   A  +R  G   + ++V  G IGL++A+ +F+  R     ++++ 
Sbjct: 54  ARNTLIEMNMSLVRFAAGRFRSRGPEEMEDIVQVGMIGLIKAIDRFELTREVEFTSFAIP 113

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +I   ++ +   +   V +     + R+     +L    + +     +   V  +++ ++
Sbjct: 114 YIVGEIKRFFRDTTWAVHVPRRLQEARV-----QLARATEELRSRLGRTPTVKELSELMS 168

Query: 168 VSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           +SE EV    +        SL+A I+ S+   S   D++     G E   +E  E  +  
Sbjct: 169 LSEEEVREARLASNSYNSSSLDAAISGSEDGESALADFI-----GAEDRALELVEDFH-- 221

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             L   ++ L+ R+R+I   R ++E  +T   +     VS+  V ++ +R   +++E +
Sbjct: 222 -ALAPLIAALDDRDRQIIHMRFVEE--LTQAQIGERLGVSQMHVSRLLSRTLARLREGM 277


>gi|312794377|ref|YP_004027300.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
 gi|312876651|ref|ZP_07736632.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
 gi|311796604|gb|EFR12952.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
 gi|312181517|gb|ADQ41687.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
          Length = 256

 Score =  138 bits (348), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 52/245 (21%), Positives = 114/245 (46%), Gaps = 17/245 (6%)

Query: 29  LEKQEEY--VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           LE  +E    L + Y++  D+   + LV  HL +   IA  +   G+   ++     I L
Sbjct: 8   LEIDDEKIDRLFEEYQKTKDIKLRNELVNKHLYIAEIIAKKFVNRGIDYEDLYQVACIAL 67

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           + AV++F+P +G+R  +++   I   ++ Y     S++++      +R++    ++K   
Sbjct: 68  INAVERFEPNKGYRFTSFATPTIMGEIKRYFRDRASIIRLP-----RRIYETSAKIKLAT 122

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           + ++    +P +V  IA+ LN+S  EV+ +      + S + L  S D+   + ++  + 
Sbjct: 123 EILSTKLKRPPKVEEIAQHLNMSTEEVLEVM-----EASSSYLPQSLDQTMYEDEEMTLG 177

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           D  G+     E   +      + +++  L+P ER   + R  +E   T + ++ E  VS+
Sbjct: 178 DVLGKSD---ENILQVENVEAVKKAIERLSPFEREFVQKRFFEE--KTQKEIAEEMNVSQ 232

Query: 267 ERVRQ 271
             + +
Sbjct: 233 MYISR 237


>gi|325674546|ref|ZP_08154234.1| RNA polymerase sigma-F factor [Rhodococcus equi ATCC 33707]
 gi|325554806|gb|EGD24480.1| RNA polymerase sigma-F factor [Rhodococcus equi ATCC 33707]
          Length = 259

 Score =  138 bits (348), Expect = 9e-31,   Method: Composition-based stats.
 Identities = 45/244 (18%), Positives = 89/244 (36%), Gaps = 17/244 (6%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           G       ++T  L L   IA  +   G P  ++V   +IGL+ AV ++D ERG     +
Sbjct: 31  GHAELRESIITRCLPLAEHIARRFDRRGEPFEDLVQVASIGLVNAVDRYDVERGSDFLAF 90

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           ++  I   ++ +   +   V++     +  L      L      ++    +      +A+
Sbjct: 91  AVPTIMGEVRRHFRDTGWAVRVPRRLKELHLD-----LVKTSAQLSQRLGRSPTTREMAE 145

Query: 165 KLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           +L +   EV        G +  S++A   S     S   D L  +      V        
Sbjct: 146 ELGIEVEEVAQGLQAANGYQALSVDAAAGSGPDTGSTLGDLLGDNDSDIAGV-------- 197

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
                L   +  L  RER +   R       T   +++   VS+  V +I +    +++ 
Sbjct: 198 EDHETLRVVLEGLPERERTVLLLRFFGNQ--TQSQIAAHVGVSQMHVSRILSDTLARLRA 255

Query: 283 SIQK 286
            +++
Sbjct: 256 QVER 259


>gi|290962881|ref|YP_003494063.1| sigma factor [Streptomyces scabiei 87.22]
 gi|260652407|emb|CBG75540.1| putative sigma factor [Streptomyces scabiei 87.22]
          Length = 275

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 51/237 (21%), Positives = 106/237 (44%), Gaps = 15/237 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            + L+  +L LV   A  +RG    + ++V  G IGL++A+ +F+  R     T+++ +I
Sbjct: 46  RNTLIEMNLSLVRYAASRFRGREDSLEDIVQVGTIGLIKAIDRFELSREVEFTTFAVPYI 105

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V +     + R+      L      +     +      +++ +++S
Sbjct: 106 VGEIKRFFRDTSWAVHVPRRLQEARV-----ELARATDELQSRLGRMPTTRELSELMSLS 160

Query: 170 ESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E EVI       G    SL+A + S   +     D ++ D  G+E   ++  E  +    
Sbjct: 161 EEEVIEARKASNGYNTSSLDAALTSDGGDDG---DAVLGDLIGEEDHALQLVEDFHS--- 214

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   ++ L+ RERRI   R ++E   T   ++ E  VS+  V ++ +R  K+++  +
Sbjct: 215 LAPLIAQLDDRERRIIHLRFVEE--WTQSQIAEELGVSQMHVSRLISRIIKRLRTGL 269


>gi|239928675|ref|ZP_04685628.1| RNA polymerase sigma factor WhiG [Streptomyces ghanaensis ATCC
           14672]
 gi|291436999|ref|ZP_06576389.1| RNA polymerase sigma factor WhiG [Streptomyces ghanaensis ATCC
           14672]
 gi|291339894|gb|EFE66850.1| RNA polymerase sigma factor WhiG [Streptomyces ghanaensis ATCC
           14672]
          Length = 280

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 49/256 (19%), Positives = 105/256 (41%), Gaps = 16/256 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
            L + Y+  GD     +L+  +  LV  +A          +  ++ VS G  GL+ A++K
Sbjct: 33  ELWRSYKATGDERLREQLILHYSPLVKYVAGRVSVGLPSNVEQADFVSSGIFGLIDAIEK 92

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD +R  +  TY++  I+ AM + + R+   +        + +      L+  L+     
Sbjct: 93  FDVDREIKFETYAITRIRGAMIDEL-RALDWIPRSVRQKARNVERAYATLEARLR----- 146

Query: 153 NLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
             +      +A +L ++  E+ ++     LA   +L  L++   +   +    +    D 
Sbjct: 147 --RTPSESEVAGELGIAVEELHAVFSQLSLANVVALEELLHVGGEGGDRL-SLMDTLEDT 203

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                +E  E +  R  L R+++ L  RE+ +          +TL  + +   V+  RV 
Sbjct: 204 AADNPVEVAEDRELRRFLVRAINTLPEREKTVVTLYYY--EGLTLAEIGNVLGVTESRVS 261

Query: 271 QIEARAFKKVQESIQK 286
           QI  ++  +++  +  
Sbjct: 262 QIHTKSVLQLRAKLAS 277


>gi|42528183|ref|NP_973281.1| RNA polymerase sigma factor WhiG [Treponema denticola ATCC 35405]
 gi|41819453|gb|AAS13200.1| RNA polymerase sigma-27 factor [Treponema denticola ATCC 35405]
 gi|325474612|gb|EGC77798.1| RNA polymerase sigma-27 factor [Treponema denticola F0402]
          Length = 262

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 49/257 (19%), Positives = 108/257 (42%), Gaps = 19/257 (7%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQA 89
           E  L  +Y++  D       +  +  LV  +A    G G+P      ++V  G  GL+ A
Sbjct: 11  EEELWDKYKKTSDPKIREYFILKYAPLVKYVAGK-VGIGMPTNVEFDDLVGYGVFGLLDA 69

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           ++K+D ++  +  TY++  I+ A+ + +    S+  +  +  QK      R ++  +  +
Sbjct: 70  IEKYDLDKNVKFNTYAVNRIRGAIFDELR---SIDWVPRSVRQKS-----REIEETIADL 121

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYD 207
                +      IA  + +   E  S+  +++     SL  L  S+D +       ++  
Sbjct: 122 EARLGRSASNEEIAYAMGLDIEEYNSLLLKISATSVISLTDLRFSNDDSEEFSVGDIIEA 181

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
                  +I   ER++ + ++  ++  L  RE+++      ++  +TL  +     V+  
Sbjct: 182 PSSLNPDVI--VEREDIKRVIVEAIKELPDREKKVLIMYYYED--MTLREIGEVLHVTES 237

Query: 268 RVRQIEARAFKKVQESI 284
           RV QI   A  K++  +
Sbjct: 238 RVSQIHTSANIKLRAKL 254


>gi|297197437|ref|ZP_06914834.1| RNA polymerase sigma-E factor [Streptomyces sviceus ATCC 29083]
 gi|197716285|gb|EDY60319.1| RNA polymerase sigma-E factor [Streptomyces sviceus ATCC 29083]
          Length = 298

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 48/236 (20%), Positives = 104/236 (44%), Gaps = 11/236 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A + L+  ++ LV   A  +RG G  + ++V  G IGL++A+ +F+  R     ++++ +
Sbjct: 67  ARNTLIEMNMSLVRFAAGRFRGRGDDMEDIVQTGMIGLIKAIDRFEISREVEFTSFALPY 126

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I   ++ +   +   V +     + R+      L    + +     +   V  +A  +N+
Sbjct: 127 IVGEIKRFFRDTTWAVHVPRRLQELRV-----ELAKAREELASRLDRDPTVAELATLMNI 181

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SE EVI       G  S ++L  +   +  +  + ++ D  G E+  +   E  +    L
Sbjct: 182 SEKEVIEAQIASNGYNS-SSLDAALTGDGPEGGEAVLADFIGVEEDGLRLVEDFHS---L 237

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              M+ L+ R+R+I   R ++E   T   +      S+  V ++  R   +++E +
Sbjct: 238 APLMAELSERDRQIIHMRFVEE--ATQSEIGERLGCSQMHVSRLIKRIITRLREGM 291


>gi|40787125|gb|AAR90090.1| WhiG-like protein [Streptomyces ambofaciens]
          Length = 280

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 52/254 (20%), Positives = 110/254 (43%), Gaps = 16/254 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
            L + Y+  GD     +L+  +  LV  +A          +  ++ VS G  GL+ A++K
Sbjct: 33  ELWRSYKATGDERLREQLILHYSPLVKYVAGRVSVGLPPNVEQADFVSSGVFGLIDAIEK 92

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD +R  +  TY++  I+ AM + +    +L  I  +  QK    N+ R    L+A    
Sbjct: 93  FDVDREIKFETYAITRIRGAMIDELR---ALDWIPRSVRQKA--RNVERAYTTLEA---R 144

Query: 153 NLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
             +      +A ++ ++  ++ ++     LA   +L  L+++  +   +    +    D 
Sbjct: 145 LRRTPSESEVAVEMGIAVEDLHAVFSQLSLANVVALEELLHAGGEGGGRL-SLMDTLEDT 203

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                +E  E +  R +L R+++ L  RE+ +          +TL  + +   V+  RV 
Sbjct: 204 AADNPVEVAEDRELRRLLARAINTLPEREKTVVTLYYY--EGLTLAEIGNVLGVTESRVS 261

Query: 271 QIEARAFKKVQESI 284
           QI  ++  +++  +
Sbjct: 262 QIHTKSVLQLRAKL 275


>gi|55274885|gb|AAV49245.1| RNA polymerase subunit sigma-38 [Shigella boydii]
 gi|255312609|gb|ACU01714.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312611|gb|ACU01715.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312613|gb|ACU01716.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312615|gb|ACU01717.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312617|gb|ACU01718.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312619|gb|ACU01719.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312621|gb|ACU01720.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312623|gb|ACU01721.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312625|gb|ACU01722.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312627|gb|ACU01723.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312629|gb|ACU01724.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312631|gb|ACU01725.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312635|gb|ACU01727.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312637|gb|ACU01728.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312649|gb|ACU01734.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312651|gb|ACU01735.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312655|gb|ACU01737.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312657|gb|ACU01738.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312667|gb|ACU01743.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312673|gb|ACU01746.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312675|gb|ACU01747.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312677|gb|ACU01748.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312679|gb|ACU01749.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312681|gb|ACU01750.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312683|gb|ACU01751.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312685|gb|ACU01752.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312687|gb|ACU01753.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312691|gb|ACU01755.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312693|gb|ACU01756.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312695|gb|ACU01757.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312699|gb|ACU01759.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312701|gb|ACU01760.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312703|gb|ACU01761.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312705|gb|ACU01762.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 54/205 (26%), Positives = 96/205 (46%), Gaps = 12/205 (5%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           +     +++      K L   LR  +     ++           IA++L+    +V  M 
Sbjct: 61  MNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRML 115

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                  S++  +    +     +  L    D +E    +  +  + +  + + +  LN 
Sbjct: 116 RLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNA 170

Query: 238 RERRIFEARR--LQENPVTLENLSS 260
           ++R +   R   L     TLE++  
Sbjct: 171 KQREVLARRFGLLGYEAATLEDVGR 195


>gi|315445714|ref|YP_004078593.1| RNA polymerase sigma factor, sigma-70 family [Mycobacterium sp.
           Spyr1]
 gi|315264017|gb|ADU00759.1| RNA polymerase sigma factor, sigma-70 family [Mycobacterium sp.
           Spyr1]
          Length = 262

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 47/236 (19%), Positives = 94/236 (39%), Gaps = 13/236 (5%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             R+V   L L   IA  + G G P  ++V    +GL+ AV +FD   G    ++++  I
Sbjct: 40  RDRIVERCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVIRFDVNAGSDFVSFAVPTI 99

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   VK+     +  L     RL      ++    +      +A +L + 
Sbjct: 100 MGEVRRHFRDNSWSVKVPRRLKELHL-----RLGAATAELSQRLGRAPTPSELAAELEMD 154

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             EV+     L    S N L   S   S       + D  G   + +++ E    R  L 
Sbjct: 155 RDEVVE---GLVAGSSYNTLSIDSGGGSGNEDAPAIADTLGDVDLTLDQIE---NREALR 208

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             ++ L  RER +   R      +T   ++    +S+  V ++ A++  ++++ ++
Sbjct: 209 PLLAALPERERTVLVLRFF--ESMTQTQIAERVGISQMHVSRLLAKSLTRLRDQLE 262


>gi|108799609|ref|YP_639806.1| RNA polymerase, sigma 28 subunit [Mycobacterium sp. MCS]
 gi|119868720|ref|YP_938672.1| FliA/WhiG family RNA polymerase sigma factor [Mycobacterium sp.
           KMS]
 gi|108770028|gb|ABG08750.1| RNA polymerase, sigma 28 subunit [Mycobacterium sp. MCS]
 gi|119694809|gb|ABL91882.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Mycobacterium
           sp. KMS]
          Length = 284

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 46/255 (18%), Positives = 104/255 (40%), Gaps = 22/255 (8%)

Query: 36  VLAKRYREHGDLSAAHR----LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            L  R  E  D S   R    ++T+ + +   IA  + G G P  +V+    IGL++ V 
Sbjct: 28  RLFDRLAESADDSERERWRRHIITACVPIADHIAYRFVGRGEPSEDVIQVARIGLIKTVD 87

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           ++DP++G     +++  I+  ++ +   +   V++     + +L     R++  +  ++ 
Sbjct: 88  RYDPDKGH-FLAFAVPTIRGEIRRHFRDNTWTVRVPRKVQETQL-----RMRDAVNTLSQ 141

Query: 152 NNLKPEQVVAIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
              +    V +A +L+V   E+             SL+A + ++  +          D  
Sbjct: 142 RLNRTPTGVELADELDVGSEELGDCQAATTAYRPVSLDAPLLTAQNDGDTVGSMQGGDDP 201

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
           G          R     +L  ++S L+PR R I          +T   ++    VS+ ++
Sbjct: 202 GYG--------RVEDLILLQEAISDLDPRRRAIVGMIFFDC--LTQREVARRLHVSQVQI 251

Query: 270 RQIEARAFKKVQESI 284
            ++   A  ++++ +
Sbjct: 252 SRLLNDALARIRQRV 266


>gi|254973932|ref|ZP_05270404.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile QCD-66c26]
 gi|255091318|ref|ZP_05320796.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile CIP 107932]
 gi|255312976|ref|ZP_05354559.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile QCD-76w55]
 gi|255515735|ref|ZP_05383411.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile QCD-97b34]
 gi|255648829|ref|ZP_05395731.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile QCD-37x79]
 gi|260682047|ref|YP_003213332.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile CD196]
 gi|260685645|ref|YP_003216778.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile R20291]
 gi|306518943|ref|ZP_07405290.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile QCD-32g58]
 gi|260208210|emb|CBA60565.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile CD196]
 gi|260211661|emb|CBE01928.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile R20291]
          Length = 233

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 57/241 (23%), Positives = 109/241 (45%), Gaps = 19/241 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGY--RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              L+  ++ LV  IA  +   G G    ++V+ G IGL+ A+ KFD E+G + ++YS  
Sbjct: 3   REELIKENMPLVKSIARKFFIPGKGFEYQDLVNSGVIGLIDAINKFDAEKGAKFSSYSYI 62

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            IK+A+ + I     +         K     + +    ++ +    L+      IAK+LN
Sbjct: 63  KIKSAILDEIRNQSPI--------SKHNLTKVNKYNRVVEKLQSKLLREPTSYEIAKELN 114

Query: 168 VSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           VSE E+  +   +      SLN +I      + Q         D +E+      E + + 
Sbjct: 115 VSEKELHDIESNIDMLNIVSLNYVIFEDTNETVQDVI-----SDREEEAPENIIEEEEKL 169

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            +L++++S LN RE+ I      ++  + L+ +     VS  RV Q+  ++ + ++  I+
Sbjct: 170 EILSKAISNLNEREKLILSLYYYED--LNLKEIGKVLGVSESRVSQLHRKSIRNLRNKIK 227

Query: 286 K 286
           +
Sbjct: 228 E 228


>gi|325270141|ref|ZP_08136748.1| RNA polymerase sigma-43 factor [Prevotella multiformis DSM 16608]
 gi|324987442|gb|EGC19418.1| RNA polymerase sigma-43 factor [Prevotella multiformis DSM 16608]
          Length = 228

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 62/270 (22%), Positives = 112/270 (41%), Gaps = 47/270 (17%)

Query: 17  SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
            +Y+ EI     L  +EE  LA R +  GD  A  +L  ++L+ VV +A  YR  GL   
Sbjct: 5   EKYMEEIAGGQPLSDREERTLAGRIKV-GDAQALEKLTKANLKYVVSLAHQYRNRGLGED 63

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++SEGNIG+M A ++FD  RG R   ++  +I+ AM+E I    +L ++      +   
Sbjct: 64  DLISEGNIGMMHAAQRFDGSRGVRFVVFAAPYIRKAMEEAIKEQAALYRLPRNEKNRS-- 121

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
                                                     + +   S++  +     N
Sbjct: 122 ----------------------------------------EQKRSHAISIDQPVPVGSSN 141

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV-TL 255
           +   Q+ L  D+        E+  ++   + + + + VLN RER++            T+
Sbjct: 142 NFTLQNVLENDNAPHAD---EQLNQEILSSEIQKGLGVLNERERQVIACLYGLSGVHYTM 198

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              +    + RERVRQI  +A +K+ + ++
Sbjct: 199 AEAAEHMGLKRERVRQIRDKALRKLHKRLK 228


>gi|188585936|ref|YP_001917481.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|179350623|gb|ACB84893.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 239

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 61/262 (23%), Positives = 108/262 (41%), Gaps = 63/262 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L  +EE  L ++ +  GD      L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLTNEEEKDLLEKLK-AGDKKVRSTLIERNLRLVVYIARKFENTGVNIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FDP++  +LATY+   I+  +  Y+ R+                    +LK   
Sbjct: 96  IKAVNTFDPQKKIKLATYASKCIENEILMYLRRN-------------------NKLKNE- 135

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                            ++ DE LN      D N     D L  
Sbjct: 136 ---------------------------------VSIDEPLN---IDWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
           D D    ++ +  E+K  +N+L  ++  L+ RE+ I + R         T + ++    +
Sbjct: 160 DID----IIHQNIEQKVNKNLLKMALEKLSQREKTIMKLRFGLGRQEGKTQKEVADILGI 215

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+  + ++E R   ++++ I K
Sbjct: 216 SQSYISRLEKRIINRMRKEINK 237


>gi|126435251|ref|YP_001070942.1| FliA/WhiG family RNA polymerase sigma factor [Mycobacterium sp.
           JLS]
 gi|126235051|gb|ABN98451.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Mycobacterium
           sp. JLS]
          Length = 284

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 46/255 (18%), Positives = 105/255 (41%), Gaps = 22/255 (8%)

Query: 36  VLAKRYREHGDLSAAHR----LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            L  R  E  D S   R    ++T+ + +   IA  + G G P  +V+    IGL++ V 
Sbjct: 28  RLFDRLAESADDSERQRWRRHIITACVPIADHIAYRFVGRGEPSEDVIQVARIGLIKTVD 87

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           ++DP++G     +++  I+  ++ +   +   V++     + +L     R++  +  ++ 
Sbjct: 88  RYDPDKGH-FLAFAVPTIRGEIRRHFRDNTWTVRVPRKVQETQL-----RMRDAVNTLSQ 141

Query: 152 NNLKPEQVVAIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
              +    V +A++L+V   E+             SL+A + ++  +          D  
Sbjct: 142 RLNRTPTGVELAEELDVGSEELGDCQAATTAYRPVSLDAPLLTAQNDGDTVGSMQGGDDP 201

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
           G          R     +L  ++S L+PR R I          +T   ++    VS+ ++
Sbjct: 202 GYG--------RVEDLILLQEAISDLDPRRRAIVGMIFFDC--LTQREVARRLHVSQVQI 251

Query: 270 RQIEARAFKKVQESI 284
            ++   A  ++++ +
Sbjct: 252 SRLLNDALARIRQRV 266


>gi|134102478|ref|YP_001108139.1| putative RNA polymerase sigma factor [Saccharopolyspora erythraea
           NRRL 2338]
 gi|133915101|emb|CAM05214.1| putative RNA polymerase sigma factor [Saccharopolyspora erythraea
           NRRL 2338]
          Length = 311

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 59/259 (22%), Positives = 113/259 (43%), Gaps = 21/259 (8%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAV 90
             L K + +  D     RLV  +  LV  +A    G GLP    +S+++  G  GL+ A+
Sbjct: 67  VALWKAFGQQRDQELRDRLVLHYAPLVKYVAGR-VGTGLPSHVEVSDLIQSGIFGLVDAI 125

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +KF+PERG +  TY+M  I+ A+ + +      V     +  + +   L RL+  LQ   
Sbjct: 126 EKFEPERGLKFETYAMQRIRGAILDDLRAQ-DWVPRSVRSRARDVERALERLEAKLQ--- 181

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
               +      +A++L +S  E+  +    ++    +L+ LI +    SS          
Sbjct: 182 ----RTASDAELAEELELSVDELRELFAQLQMTSVVALDDLIGAGQTTSS----LAETLP 233

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D + +  +     ++ R  L  ++  L+ R+R +      +   +TL  +     V+  R
Sbjct: 234 DDRAEDPVATLVDRDSRRQLAEAVERLSDRDRIVVTLYYFEN--LTLAEIGKVLGVTESR 291

Query: 269 VRQIEARAFKKVQESIQKQ 287
           V Q+  RA  +++  + +Q
Sbjct: 292 VCQLHTRAVLRLRTKLTEQ 310


>gi|145225367|ref|YP_001136045.1| RNA polymerase sigma factor SigF [Mycobacterium gilvum PYR-GCK]
 gi|145217853|gb|ABP47257.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Mycobacterium
           gilvum PYR-GCK]
          Length = 262

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 47/236 (19%), Positives = 94/236 (39%), Gaps = 13/236 (5%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             R+V   L L   IA  + G G P  ++V    +GL+ AV +FD   G    ++++  I
Sbjct: 40  RDRIVERCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVIRFDVTAGSDFVSFAVPTI 99

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   VK+     +  L     RL      ++    +      +A +L + 
Sbjct: 100 MGEVRRHFRDNSWSVKVPRRLKELHL-----RLGAATAELSQRLGRAPTPSELAAELEMD 154

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             EV+     L    S N L   S   S       + D  G   + +++ E    R  L 
Sbjct: 155 RDEVVE---GLVAGSSYNTLSIDSGGGSGNEDAPAIADTLGDVDLTLDQIE---NREALR 208

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             ++ L  RER +   R      +T   ++    +S+  V ++ A++  ++++ ++
Sbjct: 209 PLLAALPERERTVLVLRFF--ESMTQTQIAERVGISQMHVSRLLAKSLTRLRDQLE 262


>gi|253682632|ref|ZP_04863429.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           D str. 1873]
 gi|253562344|gb|EES91796.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           D str. 1873]
          Length = 242

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 52/242 (21%), Positives = 105/242 (43%), Gaps = 19/242 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              +V  ++ LV  IA      +   +   +++  G IGLM A+ KFD  +G + +TY+ 
Sbjct: 10  REHIVKKYIPLVKYIASRVIIGKSKYIEFEDLLGYGMIGLMDALNKFDESKGMKFSTYAS 69

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ +M + I ++  +         K     L +    ++ +   NL    +  IA++L
Sbjct: 70  IRIRGSMIDEIRKNSPI--------SKGAMDKLNKYNSAIETLQKRNLTEPNIKDIAEEL 121

Query: 167 NVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            ++ +EV  +   +      SL  LI S D + S     +  +     +   E +ER   
Sbjct: 122 EMTVNEVGEIENFINYISVVSLEDLIFSEDDDIS-LMGTIEDEKSPNPEKDFEDQER--- 177

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              L +++ +LN +++ +          +TL+ +     VS  RV Q+ +RA   +++ +
Sbjct: 178 LEYLAKALDMLNDKDKTVLSLYYY--EGMTLKEIGIVLGVSESRVCQLHSRAIVHLRKML 235

Query: 285 QK 286
            K
Sbjct: 236 GK 237


>gi|333024988|ref|ZP_08453052.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
 gi|332744840|gb|EGJ75281.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
          Length = 316

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 51/236 (21%), Positives = 95/236 (40%), Gaps = 16/236 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            H LV  +L LV   A  +R    P+ +++  G IGL++A+ +F+  RG    T++M  I
Sbjct: 92  RHTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRGVEFPTFAMPTI 151

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +      +A+KL + 
Sbjct: 152 IGEIKRFFRDTSWSVRVPRRLQELRLD-----LAKAGDELAQRLDRAPTPSELAEKLGIE 206

Query: 170 ESEVIS-MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
             EVI  M    A   S        D + S   D L Y+    E +             L
Sbjct: 207 REEVIEGMAASNAYTASSLDAQPEEDDSESALADRLGYEDHSLEGI--------EYIESL 258

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              ++ L  R+R+I   R +    +T   +  E  +S+  V ++ +R   K+++ +
Sbjct: 259 KPMIARLPQRDRKILSLRFVAN--MTQSEIGEELGISQMHVSRLLSRTLVKLRKGL 312


>gi|182418318|ref|ZP_02949613.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           butyricum 5521]
 gi|237666658|ref|ZP_04526643.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium butyricum
           E4 str. BoNT E BL5262]
 gi|182377700|gb|EDT75244.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           butyricum 5521]
 gi|237657857|gb|EEP55412.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium butyricum
           E4 str. BoNT E BL5262]
          Length = 243

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 54/242 (22%), Positives = 108/242 (44%), Gaps = 19/242 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             +++  ++ LV  IA      +   +   ++VS G IGL+ A+ KFD  +G + ++Y+ 
Sbjct: 11  KEQIIEEYIPLVKYIASRVMFAKNKYMEYEDLVSYGMIGLIDAINKFDNSKGMKFSSYAS 70

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             IK AM + + ++  +         K     L R    ++ +    L+      I+  L
Sbjct: 71  IRIKGAMIDELRKNRPI--------SKGAMDKLNRYNKAIEELQGRLLREPTTQEISNYL 122

Query: 167 NVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            +S SEV  +   +      SL ++I S D++     + +    D          E K +
Sbjct: 123 GISSSEVAEIENYINYISMVSLESVIFSDDED----VNLMGVIEDKNSPSPHSYLEDKEK 178

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             +LT+++ +L  ++R I          +TL+ +    EVS  RV Q+ +R+ + ++E +
Sbjct: 179 LEILTQAIELLKEKDRMILNLYYY--EGLTLKEIGKILEVSESRVCQLHSRSIRNLRECM 236

Query: 285 QK 286
           +K
Sbjct: 237 KK 238


>gi|302774234|ref|XP_002970534.1| hypothetical protein SELMODRAFT_147096 [Selaginella moellendorffii]
 gi|300162050|gb|EFJ28664.1| hypothetical protein SELMODRAFT_147096 [Selaginella moellendorffii]
          Length = 458

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 54/259 (20%), Positives = 116/259 (44%), Gaps = 22/259 (8%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG--YGLPISEVVSEGNIGLMQAVKK 92
             L +R +     +A ++L+  + RLV+ +A  Y        + ++  EG  GL+ A+  
Sbjct: 207 RTLRRRLQLG--EAAQNKLIEHNCRLVLFLARRYERDAGSFSLEDLCQEGVKGLIDAMDH 264

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+P +G R +TY+++WI+ A+   I R+  ++++  +   K++   +R+ +  L+     
Sbjct: 265 FNPGKGTRFSTYAIFWIRTAIVRAITRTGQVIRLPFSFAAKKV--EIRKARRELRVELGR 322

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           N   E+V+       V    +   +       SLN  +  +D+       +L Y  +  +
Sbjct: 323 NPSDEEVMERTGLDPVQFWNIYYYSNFRVR--SLNETVRGTDEE------FLEYLPETGD 374

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP----VTLENLSSEFEVSRER 268
            V     E    R  +  ++  L  +ER + + R   E+      +L  +     +S+E 
Sbjct: 375 IV----SESSEVREEIVTALQRLKDKERMVLQHRYGLEDGALAVKSLREVGRRLNMSQEM 430

Query: 269 VRQIEARAFKKVQESIQKQ 287
           VR+ EA A ++++   + +
Sbjct: 431 VRRYEASALERLRHQEEAK 449


>gi|302793696|ref|XP_002978613.1| hypothetical protein SELMODRAFT_177039 [Selaginella moellendorffii]
 gi|300153962|gb|EFJ20599.1| hypothetical protein SELMODRAFT_177039 [Selaginella moellendorffii]
          Length = 458

 Score =  138 bits (348), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 55/259 (21%), Positives = 116/259 (44%), Gaps = 22/259 (8%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG--YGLPISEVVSEGNIGLMQAVKK 92
             L +R +     +A ++L+  + RLV+ +A  Y        + ++  EG  GL+ A+  
Sbjct: 207 RTLRRRLQLG--EAAQNKLIEHNCRLVLFLARRYERDAGSFSLEDLCQEGVKGLIDAMDH 264

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+P +G R +TY+++WI+ AM   I R+  ++++  +   K++   +R+ +  L+     
Sbjct: 265 FNPGKGTRFSTYAIFWIRTAMVRAITRTGQVIRLPFSFAAKKV--EIRKARRELRVELGR 322

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           N   E+V+       V    +   +       SLN  +  +D+       +L Y  +  +
Sbjct: 323 NPSDEEVMERTGLDPVQFWNIYYYSNFRVR--SLNETVRGTDEE------FLEYLPETGD 374

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP----VTLENLSSEFEVSRER 268
            V     E    R  +  ++  L  +ER + + R   E+      +L  +     +S+E 
Sbjct: 375 IV----SESSEVREEIVTALQRLKDKERMVLQHRYGLEDGAIAVKSLREVGRRLNMSQEM 430

Query: 269 VRQIEARAFKKVQESIQKQ 287
           VR+ EA A ++++   + +
Sbjct: 431 VRRYEASALERLRHQEEAK 449


>gi|182440616|ref|YP_001828335.1| putative RNA polymerase sigma factor [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|178469132|dbj|BAG23652.1| putative RNA polymerase sigma factor [Streptomyces griseus subsp.
           griseus NBRC 13350]
          Length = 290

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 44/239 (18%), Positives = 96/239 (40%), Gaps = 16/239 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + L+  +L LV   A  +R  G   + ++V  G IGL++A+ +F+  R     ++++ 
Sbjct: 61  ARNTLIEMNLSLVHFAAKRFRNRGSGEMEDIVQVGTIGLIKAIDRFELSREVEFTSFAIP 120

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +I   ++ +   S   V +     + R+      L    + +     +   V  +A  L 
Sbjct: 121 YIVGEIKRFFRDSTWAVHVPRRLQELRVT-----LAKAKEELAGRLDRDPTVGELAAHLG 175

Query: 168 VSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           +++ EV+       G    SL+  I +   ++       +         L+E        
Sbjct: 176 LTDEEVVEGLIASNGYTAGSLDLPIGTEQNSAETITYGDIKGDLDPAIELVENL------ 229

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + L   +  L  R+R I   R  QE  +T   +     +S+  V ++  R   ++++++
Sbjct: 230 HALAPLLEGLGDRDREIVAMRFGQE--LTQAQIGERLGISQMHVSRLLNRLLTQLRKNM 286


>gi|302544308|ref|ZP_07296650.1| RNA polymerase sigma-F factor [Streptomyces hygroscopicus ATCC
           53653]
 gi|302461926|gb|EFL25019.1| RNA polymerase sigma-F factor [Streptomyces himastatinicus ATCC
           53653]
          Length = 288

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 49/233 (21%), Positives = 100/233 (42%), Gaps = 15/233 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            + L+  +L LV   A  +R   + + +VV  G IGL++A+ +FD  R     T+++ +I
Sbjct: 44  RNTLIELNLSLVRYAARRFRNRSVEMEDVVQVGTIGLIKAIDRFDLSREVEFTTFAVPYI 103

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V +     + R+      L    + +     +      +A+ LN+S
Sbjct: 104 VGEIKRFFRDTSWAVHVPRRLQELRID-----LAKANEELFQRFDRSPTTTELAEHLNLS 158

Query: 170 ESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E EV+   +        SL+A    +D  +   +     D  G+    +E  E     + 
Sbjct: 159 EDEVLDGLVASNGYSTSSLDAP---ADPETGTTRVTTYADRIGEVDPAMEVVE---NLHA 212

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           L   +  L  R+RRI + R  +E  +T   + +E  VS+  V ++  ++  ++
Sbjct: 213 LKPLVEQLGERDRRILQMRFGEE--MTQSEIGAELGVSQMHVSRLLTKSLTRL 263


>gi|255312639|gb|ACU01729.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312641|gb|ACU01730.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312643|gb|ACU01731.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312645|gb|ACU01732.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 53/205 (25%), Positives = 95/205 (46%), Gaps = 12/205 (5%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           L LVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LGLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           +     +++      K L   LR  +     ++           IA++L+    +V  M 
Sbjct: 61  MNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRML 115

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                  S++  +    +     +  L    D +E    +  +  + +  + + +  LN 
Sbjct: 116 RLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNA 170

Query: 238 RERRIFEARR--LQENPVTLENLSS 260
           ++R +   R   L     TLE++  
Sbjct: 171 KQREVLARRFGLLGYEAATLEDVGR 195


>gi|326781290|ref|ZP_08240555.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
 gi|326661623|gb|EGE46469.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
          Length = 290

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 45/239 (18%), Positives = 96/239 (40%), Gaps = 16/239 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + L+  +L LV   A  +R  G   + ++V  G IGL++A+ +F+  R     ++++ 
Sbjct: 61  ARNTLIEMNLSLVHFAAKRFRNRGSGEMEDIVQVGTIGLIKAIDRFELSREVEFTSFAIP 120

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +I   ++ +   S   V +     + R+      L    + +     +   V  +A  L 
Sbjct: 121 YIVGEIKRFFRDSTWAVHVPRRLQELRVT-----LAKAKEELAGRLDRDPTVGELAAHLG 175

Query: 168 VSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           +++ EVI       G    SL+  I +   ++       +         L+E        
Sbjct: 176 LTDEEVIEGLIASNGYTAGSLDLPIGTEQNSAETITYGDIKGDLDPAIELVENL------ 229

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + L   +  L  R+R I   R  QE  +T   +     +S+  V ++  R   ++++++
Sbjct: 230 HALAPLLEGLGDRDREIVAMRFGQE--LTQAQIGERLGISQMHVSRLLNRLLTQLRKNM 286


>gi|302386724|ref|YP_003822546.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           saccharolyticum WM1]
 gi|302197352|gb|ADL04923.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           saccharolyticum WM1]
          Length = 246

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 62/286 (21%), Positives = 116/286 (40%), Gaps = 68/286 (23%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           K + +   GEI    YI     +P  L+ ++E  +        D  A   L+  +LRLVV
Sbjct: 20  KTLMMPNQGEI---HYIGGADILPPPLDNEKEAQIIALLGSDDDQRAKSELIEHNLRLVV 76

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA  +    + + +++S G IGL++A+  F+P +  +LATY+   I+  +  Y+ R+  
Sbjct: 77  YIAKKFDNTSVGVEDLISIGTIGLIKAINTFNPNKNIKLATYASRCIENEILMYLRRNNK 136

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
                                                     K+ VS  E ++++     
Sbjct: 137 T-----------------------------------------KMEVSIDEPLNVD----- 150

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
                      D N     D L  + D    V+ +  E +  RN+L  ++S L+PRER+I
Sbjct: 151 ----------WDGNELLLSDILGTEED----VIYKDLETEVERNLLNTAISRLSPRERKI 196

Query: 243 FEARRLQ----ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            E R          +T + ++    +S+  + ++E +  K++++ I
Sbjct: 197 VELRFGLTDEEGEEMTQKEVADLLGISQSYISRLEKKIMKRLKKEI 242


>gi|239932973|ref|ZP_04689926.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291441326|ref|ZP_06580716.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291344221|gb|EFE71177.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 295

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 49/255 (19%), Positives = 108/255 (42%), Gaps = 16/255 (6%)

Query: 35  YVLAKRYRE-----HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
               +R  E     H    A + L+  ++ LV   A  +RG G  + ++V  G IGL++A
Sbjct: 45  RQFFRRLAELEEGTHEYQYARNTLIEMNMSLVRFAAGRFRGRGDDMDDIVQTGMIGLIKA 104

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +F+  R     ++++ +I   ++ +   +   V +     + R+      L    + +
Sbjct: 105 IDRFELSREVEFTSFALPYIVGEIKRFFRDTTWAVHVPRRLQELRV-----ELAKAREEL 159

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
                +   V  +A  +N++E +VI       G  S ++L  +   +  +  + ++ D  
Sbjct: 160 ASRLDREPTVAELATLMNITEDQVIEGQIAANGYNS-SSLDAALTGDGPENGEAVLADFI 218

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
           G E+  +   E  +    L   M+ L+ R+R+I   R ++E   T   +      S+  V
Sbjct: 219 GVEEEGLRLVEDFH---ALAPLMAELSERDRQIIHMRFVEE--ATQAEIGERLGCSQMHV 273

Query: 270 RQIEARAFKKVQESI 284
            ++  R   +++E +
Sbjct: 274 SRLIKRIIARLREGM 288


>gi|118618107|ref|YP_906439.1| RNA polymerase sigma factor SigF [Mycobacterium ulcerans Agy99]
 gi|183981270|ref|YP_001849561.1| alternate RNA polymerase sigma factor SigF [Mycobacterium marinum
           M]
 gi|118570217|gb|ABL04968.1| alternate RNA polymerase sigma factor SigF [Mycobacterium ulcerans
           Agy99]
 gi|183174596|gb|ACC39706.1| alternate RNA polymerase sigma factor SigF [Mycobacterium marinum
           M]
          Length = 262

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 47/236 (19%), Positives = 94/236 (39%), Gaps = 13/236 (5%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              +V   L L   IA  + G G P  ++V    +GL+ AV +FD E G    ++++  I
Sbjct: 40  RDTIVERCLPLADHIARRFEGRGEPRDDLVQVARVGLVNAVVRFDVETGSDFVSFAVPTI 99

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   VK+     +  L     RL      ++    +      +A +L + 
Sbjct: 100 MGEVRRHFRDNSWSVKVPRRLKELHL-----RLGAATAELSQRLGRAPTATELAAELEMD 154

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
            +EV+     L    S N L   S   S       + D  G     +++ E    R  L 
Sbjct: 155 RAEVVE---GLVAGSSYNTLSIDSGSGSEDDDARAIADTLGDMDAGLDRIED---RESLR 208

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             +  L  RER +   R    + +T   ++    +S+  V ++ A++  ++++ ++
Sbjct: 209 PLLEALPERERTVLVLRFF--DSMTQTQIAERVGISQMHVSRLLAKSLARLRDQLE 262


>gi|21219133|ref|NP_624912.1| RNA polymerase sigma factor sig8 [Streptomyces coelicolor A3(2)]
 gi|256789847|ref|ZP_05528278.1| RNA polymerase sigma factor sig8 [Streptomyces lividans TK24]
 gi|289773730|ref|ZP_06533108.1| SigB [Streptomyces lividans TK24]
 gi|6670923|gb|AAF23070.1|AF068267_4 SigB [Streptomyces coelicolor A3(2)]
 gi|6448735|emb|CAB61294.1| RNA polymerase sigma factor sig8 [Streptomyces coelicolor A3(2)]
 gi|289703929|gb|EFD71358.1| SigB [Streptomyces lividans TK24]
          Length = 281

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 46/239 (19%), Positives = 107/239 (44%), Gaps = 18/239 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + L+  ++ LV   A  +R  G   + ++V  G IGL++A+ +F+  R     ++++ 
Sbjct: 54  ARNTLIEMNMSLVRFAAGRFRSRGPEEMEDIVQVGMIGLIKAIDRFELTREVEFTSFAVP 113

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +I   ++ +   +   V +     + R+     +L    + +     +      +++ ++
Sbjct: 114 YIVGEIKRFFRDTSWAVHVPRRLQEARV-----QLARATEELRSRLGRTPTTAELSELMS 168

Query: 168 VSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           + E EV+       G    SL+A IN S+   S   D++  D      V        +  
Sbjct: 169 LPEDEVVEARLAANGYNSASLDAAINGSEDGESALADFIGADDAALALV--------DDF 220

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + L   ++ L+ R+R+I   R ++E  +T +++     VS+  V ++ +R   +++E +
Sbjct: 221 HALAPMIAELDERDRQIIHWRFVEE--LTQKDIGERLGVSQMHVSRLISRLLARLREGM 277


>gi|302549129|ref|ZP_07301471.1| RNA polymerase sigma-E factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302466747|gb|EFL29840.1| RNA polymerase sigma-E factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 295

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 45/236 (19%), Positives = 105/236 (44%), Gaps = 11/236 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A + L+  ++ LV   A  +RG G  + ++V  G IGL++A+ +F+  R     ++++ +
Sbjct: 64  ARNTLIEMNMSLVRFAAGRFRGRGDDMEDIVQTGMIGLIKAIDRFELSREVEFTSFALPY 123

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I   ++ +   +   V +     + R+      L    + +     +   V  +A  +N+
Sbjct: 124 IVGEIKRFFRDTTWAVHVPRRLQELRVD-----LAKAREELASRLDREPTVAELATLMNI 178

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SE++V+       G  S ++L  +   +  +  + ++ D  G E+  +   E  +    L
Sbjct: 179 SENQVVEGQIAANGYNS-SSLDAALTGDGPEGGEAVLADFIGVEEDGLRLVEDFHS---L 234

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              M+ L+ R+R+I   R ++E   T   +      S+  V ++  R   ++++ +
Sbjct: 235 APLMAELSERDRQIIHMRFVEE--ATQAEIGERLGCSQMHVSRLIKRIITRLRQGM 288


>gi|3077740|dbj|BAA25788.1| SigC [Cyanidium caldarium]
          Length = 424

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 65/289 (22%), Positives = 116/289 (40%), Gaps = 44/289 (15%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY-------------------- 71
           +EE     R        A  RLV S+LRLV+ IA  Y+                      
Sbjct: 130 EEEV----RNEIERGRRARARLVASNLRLVLAIANRYKSRAVVRSAWKSRSKGGMDMPSH 185

Query: 72  ---------GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
                     + + +++ EG +GL++A +KFDP +GF+ +TY+ WWI+ A+Q  +     
Sbjct: 186 EKVRLQRQHNIFLGDLIQEGALGLIRAAEKFDPSKGFKFSTYATWWIRQAIQRCVSEHSR 245

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            +++     +      + R++  LQ +       E+V   A  + +   + I+ +     
Sbjct: 246 TIRLPNHVTES--LRQIYRMRARLQHVLKRPPTDEEVAE-ACNMTLKRLKKITQHAWKTQ 302

Query: 183 DESLNALINSSD-----KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
             SL    N+           +    +    +  E+   E  ER   R  +   +  L  
Sbjct: 303 TLSLEGPPNNEAHSLYKSQQGEAPLSIGSIIEATEETPEEALERNCMREDVECVLRTLPF 362

Query: 238 RERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +ER I   R      E P + E LS+ F++    +R IE+RA +K++  
Sbjct: 363 QEREILRLRYGISDDERPHSTEELSARFQLPVHTIRLIESRALRKLRHP 411


>gi|167630319|ref|YP_001680818.1| RNA polymerase sigma factor, flia/whig family [Heliobacterium
           modesticaldum Ice1]
 gi|167593059|gb|ABZ84807.1| RNA polymerase sigma factor, flia/whig family [Heliobacterium
           modesticaldum Ice1]
          Length = 266

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 51/256 (19%), Positives = 106/256 (41%), Gaps = 16/256 (6%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKKF 93
           L   Y++H D +A   L+  +  LV  +A        P     +++S G  GLM A++KF
Sbjct: 17  LWASYKDHKDPAAREELILIYAPLVKFVAGRLAISLPPNVEREDLISYGVFGLMDAIEKF 76

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D  RG +  TY++  I+ +M + + R+   V +             R L+     ++   
Sbjct: 77  DLARGLKFETYAIARIRGSMLDGL-RAMDWVPVSVR-------QKTRELEKTYATLSQRL 128

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYDHDGQ 211
            +      +A+ L ++ +E   +   +      SL+     +D +       +    D Q
Sbjct: 129 GREATDEEVAQALGLTLNEFAKLLQDVQATTIMSLDEY-WLTDSDKGDPVRLIDSLADEQ 187

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
            +      E +  R +L +++  L  +ER +          +TL+ + +   VS  R+ Q
Sbjct: 188 VEEPTAALEFEETRLLLAQAIDKLPEKERTVIALYYY--EGLTLKEIGAVIGVSESRISQ 245

Query: 272 IEARAFKKVQESIQKQ 287
           +  +A  +++  + +Q
Sbjct: 246 LHTKAILRLRGQLARQ 261


>gi|154503852|ref|ZP_02040912.1| hypothetical protein RUMGNA_01678 [Ruminococcus gnavus ATCC 29149]
 gi|153795451|gb|EDN77871.1| hypothetical protein RUMGNA_01678 [Ruminococcus gnavus ATCC 29149]
          Length = 246

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 57/262 (21%), Positives = 108/262 (41%), Gaps = 64/262 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE + E  + +R     D  A   L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 41  PPLETERETEVIRRLGSEYDQEAKKMLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGL 100

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+  F+P +  +LATY+   I+  +  Y+ R+                          
Sbjct: 101 IKAINTFNPTKKIKLATYASRCIENEILMYLRRNSKT----------------------- 137

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                             K+ VS  E ++++                D N     D L  
Sbjct: 138 ------------------KMEVSIDEPLNVD---------------WDGNELLLSDILGT 164

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP----VTLENLSSEF 262
           + D   + L  + ERK    +L R+++ L+ RE+ I + R   +NP     T + ++   
Sbjct: 165 EEDTIYRDLETEAERK----LLVRAINQLSSREKLIVKMRFGLDNPDGIEKTQKEVADLL 220

Query: 263 EVSRERVRQIEARAFKKVQESI 284
            +S+  + ++E +  ++++  I
Sbjct: 221 GISQSYISRLEKKIMQRLKREI 242


>gi|21221509|ref|NP_627288.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
 gi|289771198|ref|ZP_06530576.1| SigI protein [Streptomyces lividans TK24]
 gi|5911753|emb|CAB55836.1| SigI protein [Streptomyces coelicolor A3(2)]
 gi|7672251|emb|CAB89440.1| putative RNA polymerase sigma factor [Streptomyces coelicolor
           A3(2)]
 gi|289701397|gb|EFD68826.1| SigI protein [Streptomyces lividans TK24]
          Length = 304

 Score =  138 bits (347), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 48/236 (20%), Positives = 96/236 (40%), Gaps = 16/236 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            + LV  +L LV   A  +R    P+ +++  G IGL++A+ +F+  RG    T++M  I
Sbjct: 80  RNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRGVEFPTFAMPTI 139

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +   V  +A+ L +S
Sbjct: 140 IGEIKRFFRDTSWSVRVPRRLQELRLD-----LAKAGDELAQRLDRAPTVSELAEHLGLS 194

Query: 170 ESEVIS-MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           + EV+  M    A   S        D       D + Y+  G E +             L
Sbjct: 195 KDEVVEGMAASNAYTASSLDAQPEEDDAEGALADRIGYEDHGLEGI--------EYVESL 246

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              ++ L  R+R+I   R +    +T   +  E  +S+  V ++ +R   ++++ +
Sbjct: 247 KPLIAELPSRDRKILSLRFVAG--MTQSEIGEELGISQMHVSRLLSRTLVRLRKGL 300


>gi|54401902|gb|AAV34636.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 194

 Score =  138 bits (347), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 54/204 (26%), Positives = 97/204 (47%), Gaps = 12/204 (5%)

Query: 57  HLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           +LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  
Sbjct: 1   NLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERA 60

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
           I+     +++      K L   LR  +     ++           IA++L+    +V  M
Sbjct: 61  IMNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRM 115

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
                   S++  +    +     +  L    D +E    +  +  + +  + + +  LN
Sbjct: 116 LRLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELN 170

Query: 237 PRERRIFEARR--LQENPVTLENL 258
            ++R +   R   L     TLE++
Sbjct: 171 AKQREVLARRFGLLGYEAATLEDV 194


>gi|315186365|gb|EFU20125.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Spirochaeta
           thermophila DSM 6578]
          Length = 262

 Score =  137 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 49/257 (19%), Positives = 111/257 (43%), Gaps = 17/257 (6%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAV 90
           E  L K Y++  D       +  +  LV  +A          +   +++  G  GL+ A+
Sbjct: 11  EDELWKEYQKTRDPQIREYFIKQYAPLVKYVAGKIAVGLPSSVEFDDLIGFGTFGLLDAI 70

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +KFDPE+  +  TY++  I+ A+ + + R+   V        K +   L RL+  L    
Sbjct: 71  EKFDPEKHVKFKTYAVTRIRGAIYDEL-RAMDWVPRSVRQKSKEIEDALHRLESSL---- 125

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDH 208
               +      +A+++N+S  E+     +++     SL  L  + D+N       ++   
Sbjct: 126 ---GRAATDEELAREMNMSSRELQKTLQKISSTSILSLQELWYTGDENDRVAIADML--E 180

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
             Q      + ER+  + ++  ++  L  +E+++      ++  +TL+ + +   V+  R
Sbjct: 181 APQAYDPAARVEREEIKRVVAEAIKELPEKEKKVLVLYYYED--LTLKEIGAILNVTESR 238

Query: 269 VRQIEARAFKKVQESIQ 285
           V Q+  +A  +++  ++
Sbjct: 239 VSQLHTKAISRLRVKLR 255


>gi|149183912|ref|ZP_01862300.1| sporulation sigma factor SigE [Bacillus sp. SG-1]
 gi|148848376|gb|EDL62638.1| sporulation sigma factor SigE [Bacillus sp. SG-1]
          Length = 239

 Score =  137 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 63/264 (23%), Positives = 113/264 (42%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL K+   +GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLSKEEEAVLLKKL-PNGDKTARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+                    +++   
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN-------------------NKIRSE- 135

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                            ++ DE LN      D N     D L  
Sbjct: 136 ---------------------------------VSFDEPLN---IDWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           + D    ++ +  E    R +L  +++ L+ RE++I E R         T ++++    +
Sbjct: 160 EED----IITKDLEATVDRKLLFNALTELSDREKQIMELRFGLMGGEEKTQKDVADMLGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 216 SQSYISRLEKRIIKRLKKEFNKMV 239


>gi|255312697|gb|ACU01758.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score =  137 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 54/205 (26%), Positives = 95/205 (46%), Gaps = 12/205 (5%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL +  ++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLNLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           +     +++      K L   LR  +     ++           IA++L+    +V  M 
Sbjct: 61  MNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRML 115

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                  S++  +    +     +  L    D +E    +  +  + +  + + +  LN 
Sbjct: 116 RLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNA 170

Query: 238 RERRIFEARR--LQENPVTLENLSS 260
           ++R +   R   L     TLE++  
Sbjct: 171 KQREVLARRFGLLGYEAATLEDVGR 195


>gi|256371428|ref|YP_003109252.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Acidimicrobium
           ferrooxidans DSM 10331]
 gi|256008012|gb|ACU53579.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Acidimicrobium
           ferrooxidans DSM 10331]
          Length = 254

 Score =  137 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 59/252 (23%), Positives = 114/252 (45%), Gaps = 18/252 (7%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFD 94
            +R++  GDL A +RL+  +  LV  +A          +  +++ S G  GL+ A++KF+
Sbjct: 11  WRRFKHDGDLEARNRLLEHYASLVRFVASRVAVGLPASVDPNDLASYGTFGLIDALEKFE 70

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           PERG +  TY++  IK A+ + + R+   V     A  K +      L+  L        
Sbjct: 71  PERGIKFETYAITRIKGAIIDEL-RAIDWVPRSVRAKAKSVEQAYAALEARLH------- 122

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +P     +A +L +SE E++++  +++  G   L+ ++ S ++         + D     
Sbjct: 123 RPPTDAEVASELGMSEDELLAIYSKISFLGLVGLDEVVMSGERGEGMTLGDTLADRRQSA 182

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
               E++ER   R ML  S++ L  RE+ +           TL  +     V+  R+ QI
Sbjct: 183 GGAFEEQER---RRMLADSINQLADREKTVLVLYYY--EGFTLAEIGRILGVTESRICQI 237

Query: 273 EARAFKKVQESI 284
            ++A   ++  +
Sbjct: 238 HSKAVLALRGKL 249


>gi|3249729|gb|AAC26667.1| RNA polymerase sigma-like factor [Streptomyces bluensis]
          Length = 161

 Score =  137 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 36/171 (21%), Positives = 70/171 (40%), Gaps = 12/171 (7%)

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI+ A+   +      ++I     +  +   L R+   +         PE    +A
Sbjct: 1   YATWWIRQAITRAMADQARTIRIPVHMVE--VINKLARVSRQMLQDLGREPTPE---ELA 55

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           K+L+++  +VI +        SL+  +   +   +Q+ D +    D +  V  +      
Sbjct: 56  KELDMTPEKVIEVQKYGREPISLHTPL--GEDGDTQFGDLI---EDSEAVVPADAVSFTL 110

Query: 224 RRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQI 272
            +  L   +  L+ RE  +   R       P TL+ +   + V+RER+RQI
Sbjct: 111 LQEQLHSVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGVTRERIRQI 161


>gi|255312633|gb|ACU01726.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score =  137 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 54/205 (26%), Positives = 95/205 (46%), Gaps = 12/205 (5%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           +     +++      K L   LR  +     ++           I ++L+    +V  M 
Sbjct: 61  MNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEITEQLDKPVDDVSRML 115

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                  S++  +    +     +  L    D +E    +  E  + +  + + +  LN 
Sbjct: 116 RLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTEDDDMKQSIVKWLFELNA 170

Query: 238 RERRIFEARR--LQENPVTLENLSS 260
           ++R +   R   L     TLE++  
Sbjct: 171 KQREVLARRFGLLGYEAATLEDVGR 195


>gi|52080135|ref|YP_078926.1| sporulation sigma factor SigE [Bacillus licheniformis ATCC 14580]
 gi|52785509|ref|YP_091338.1| sporulation sigma factor SigE [Bacillus licheniformis ATCC 14580]
 gi|319646087|ref|ZP_08000317.1| RNA polymerase sigma-E factor [Bacillus sp. BT1B_CT2]
 gi|52003346|gb|AAU23288.1| RNA polymerase sporulation-specific sigma-29 factor (sigma-E)
           [Bacillus licheniformis ATCC 14580]
 gi|52348011|gb|AAU40645.1| SigE [Bacillus licheniformis ATCC 14580]
 gi|317391837|gb|EFV72634.1| RNA polymerase sigma-E factor [Bacillus sp. BT1B_CT2]
          Length = 239

 Score =  137 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 62/264 (23%), Positives = 112/264 (42%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K EE VL  +  + GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLSKDEEQVLLHKLPD-GDQAARAILIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+                    +++   
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN-------------------NKIRSE- 135

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                            ++ DE LN      D N     D L  
Sbjct: 136 ---------------------------------VSFDEPLN---IDWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           ++D    ++ +  E    + +L +++  LN RE++I E R         T ++++    +
Sbjct: 160 END----IITKDIEANVDKKLLKKALEQLNDREKQIMELRFGLVGGEEKTQKDVADMLGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 216 SQSYISRLEKRIIKRLRKEFNKMV 239


>gi|167758775|ref|ZP_02430902.1| hypothetical protein CLOSCI_01117 [Clostridium scindens ATCC 35704]
 gi|167663515|gb|EDS07645.1| hypothetical protein CLOSCI_01117 [Clostridium scindens ATCC 35704]
          Length = 247

 Score =  137 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 59/274 (21%), Positives = 108/274 (39%), Gaps = 65/274 (23%)

Query: 18  RYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
            YI     +P  L  +EE           +  A   L+  +LRLVV IA  +   G+ + 
Sbjct: 32  HYIGGSDILPAPLNTEEETAAINDLGSEDEEEAKKTLIEHNLRLVVYIAKKFDNTGVGVE 91

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++S G IGL++A+  F+PE+  +LATY+   I+  +  Y+ R+                
Sbjct: 92  DLISIGTIGLIKAINTFNPEKNIKLATYASRCIENEILMYLRRNNKT------------- 138

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
                                       K+ VS  E ++++                D N
Sbjct: 139 ----------------------------KMEVSIDEPLNVD---------------WDGN 155

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP---- 252
                D L  D D   + L  + ERK    +L +++S L+ RER I + R     P    
Sbjct: 156 ELLLSDILGTDEDTIYKDLENEVERK----LLVKAISRLSGRERTIIKMRFGLGTPDGEE 211

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            T + ++    +S+  + ++E +  ++++  + K
Sbjct: 212 KTQKEVADMLGISQSYISRLEKKIMQRLKREMVK 245


>gi|229541193|ref|ZP_04430253.1| RNA polymerase, sigma 28 subunit, SigE [Bacillus coagulans 36D1]
 gi|229325613|gb|EEN91288.1| RNA polymerase, sigma 28 subunit, SigE [Bacillus coagulans 36D1]
          Length = 239

 Score =  137 bits (346), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 63/264 (23%), Positives = 111/264 (42%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE +L K+    GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLSKEEEEMLLKKL-PAGDKAARSILIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+                    +L+   
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN-------------------NKLRSE- 135

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                            ++ DE LN      D N     D L  
Sbjct: 136 ---------------------------------VSFDEPLN---IDWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           D D    ++    E    + +L  ++  L+ RE++I E R     +   T ++++    +
Sbjct: 160 DDD----IITRDLEANVDKKLLYSALHRLSDREKQIMELRFGLKGQEEKTQKDVADMLGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 216 SQSYISRLEKRIIKRLRKEFNKMV 239


>gi|297191780|ref|ZP_06909178.1| sporulation sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
 gi|197721703|gb|EDY65611.1| sporulation sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
          Length = 278

 Score =  137 bits (345), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 50/254 (19%), Positives = 105/254 (41%), Gaps = 16/254 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
            L + Y+  GD     +L+  +  LV  +A          +  ++ VS G  GL+ A++K
Sbjct: 31  ELWRSYKATGDGRLREQLILHYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEK 90

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD ER  +  TY++  I+ AM + + R+   +        + +      L+  L+     
Sbjct: 91  FDIERSIKFETYAITRIRGAMIDEL-RALDWIPRSVRQKARAVERAYATLEAQLR----- 144

Query: 153 NLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
             +      +A ++ ++  E+ S+     LA   +L  L++       +    +    D 
Sbjct: 145 --RTPSESEVAAEMGITVDELHSVFSQLSLANVVALEELLHVG-GEGGERLSLMDTLEDT 201

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                +E  E +  R +L R+++ L  RE+ +          +TL  + +   V+  RV 
Sbjct: 202 AADNPVEVAEGRELRRLLARAINTLPDREKTVVTLYYY--EGLTLAEIGNVLGVTESRVS 259

Query: 271 QIEARAFKKVQESI 284
           QI  ++  +++  +
Sbjct: 260 QIHTKSVLQLRAKL 273


>gi|254381148|ref|ZP_04996513.1| RNA polymerase sigma factor [Streptomyces sp. Mg1]
 gi|194340058|gb|EDX21024.1| RNA polymerase sigma factor [Streptomyces sp. Mg1]
          Length = 306

 Score =  137 bits (345), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 51/241 (21%), Positives = 109/241 (45%), Gaps = 15/241 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           A + L+  ++ LV   A  +      G+ + +V+  G IGL++A+ +FDP+R    +T +
Sbjct: 73  ARNTLIEMNISLVRFAARRFTARINAGIELDDVIQVGTIGLIKAIDRFDPDREVEFSTLA 132

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
           + +I   ++ Y   +   V +     + R+      L    + +T+   +   V  IA+ 
Sbjct: 133 LPYITGEIKRYFRDTTWAVHVPRRLQELRV-----ELAKCQETLTEVLGRAPSVKEIAEH 187

Query: 166 LNVSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           L +SE EVI       G    SL++   ++D+ ++  +   + D  G     +   E  +
Sbjct: 188 LELSEEEVIEGLVAANGYSSASLDSTAGTTDRPAALSEGRPLADTVGDIDPAMVLFEDVH 247

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               L   +S L+ R+ +I   R  +E  +T   + +E  +S+ +V ++  R   +++  
Sbjct: 248 T---LAPLLSELDERDLQILRMRFARE--MTQAEIGTELGISQMQVSRLLTRILTRLRSG 302

Query: 284 I 284
           +
Sbjct: 303 M 303


>gi|134100730|ref|YP_001106391.1| RNA polymerase sigma factor [Saccharopolyspora erythraea NRRL 2338]
 gi|291006467|ref|ZP_06564440.1| RNA polymerase sigma factor [Saccharopolyspora erythraea NRRL 2338]
 gi|133913353|emb|CAM03466.1| RNA polymerase sigma factor [Saccharopolyspora erythraea NRRL 2338]
          Length = 268

 Score =  137 bits (345), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 53/252 (21%), Positives = 102/252 (40%), Gaps = 20/252 (7%)

Query: 36  VLAKRYREHGDLSA-AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
            LA+   + G   A   RLVT HL +   IA  +R  G    ++V    +GL++AV +FD
Sbjct: 21  ELAELDEQDGRYQALRDRLVTEHLPVAEHIARRFRHRGETHDDLVQVATLGLIKAVDRFD 80

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P RG    +Y++  I   ++ +   +   V++     +  L      +   + A++    
Sbjct: 81  PGRGVGFMSYAVPTIMGEVRRHFRDAGWSVRMPRRMQELHLS-----VSAGISALSQELG 135

Query: 155 KPEQVVAIAKKLNVSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +      +A  L +S  +V             SL+ L+  +D       + + +D     
Sbjct: 136 RAPTPSELAAHLKLSVDDVQQGLEAGNAYRSASLDDLLTGTDD--VPLGEAIGFDDSELA 193

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           +V          R  +   ++ L  RERRI   R  +   +T   ++ +  VS+  V ++
Sbjct: 194 EV--------EDRETIRPLLAELPERERRILVMRFFRG--MTQTEIAEQVGVSQMHVSRL 243

Query: 273 EARAFKKVQESI 284
             R    ++E +
Sbjct: 244 LTRTLSWLRERL 255


>gi|256787303|ref|ZP_05525734.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
          Length = 308

 Score =  137 bits (345), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 48/236 (20%), Positives = 96/236 (40%), Gaps = 16/236 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            + LV  +L LV   A  +R    P+ +++  G IGL++A+ +F+  RG    T++M  I
Sbjct: 84  RNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRGVEFPTFAMPTI 143

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +   V  +A+ L +S
Sbjct: 144 IGEIKRFFRDTSWSVRVPRRLQELRLD-----LAKAGDELAQRLDRAPTVSELAEHLGLS 198

Query: 170 ESEVIS-MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           + EV+  M    A   S        D       D + Y+  G E +             L
Sbjct: 199 KDEVVEGMAASNAYTASSLDAQPEEDDAEGALADRIGYEDHGLEGI--------EYVESL 250

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              ++ L  R+R+I   R +    +T   +  E  +S+  V ++ +R   ++++ +
Sbjct: 251 KPLIAELPSRDRKILSLRFVAG--MTQSEIGEELGISQMHVSRLLSRTLVRLRKGL 304


>gi|29830033|ref|NP_824667.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29607143|dbj|BAC71202.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 306

 Score =  137 bits (345), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 48/236 (20%), Positives = 97/236 (41%), Gaps = 16/236 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            + LV  +L LV   A  +R    P+ +++  G IGL++A+ +F+  RG    T++M  I
Sbjct: 82  RNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRGVEFPTFAMPTI 141

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +   V  +A++L +S
Sbjct: 142 VGEIKRFFRDTSWSVRVPRRLQELRLD-----LAKAGDELAQRLDRAPTVSELAERLGIS 196

Query: 170 ESEVIS-MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
             EV+  M    A   S        D +     D + Y+  G E +             L
Sbjct: 197 NGEVVEGMAASNAYTASSLDAQPEEDDSEGALADRIGYEDHGLEGI--------EFVESL 248

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              ++ L  R+R+I   R +    +T   +  E  +S+  V ++ +R   ++++ +
Sbjct: 249 KPLIAQLPSRDRKILSLRFVAN--MTQSEIGDELGISQMHVSRLLSRTLVRLRKGL 302


>gi|114566161|ref|YP_753315.1| sigma 28 (flagella/sporulation) [Syntrophomonas wolfei subsp.
           wolfei str. Goettingen]
 gi|114337096|gb|ABI67944.1| sigma 28 (flagella/sporulation) [Syntrophomonas wolfei subsp.
           wolfei str. Goettingen]
          Length = 243

 Score =  137 bits (345), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 44/246 (17%), Positives = 107/246 (43%), Gaps = 17/246 (6%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R  + GD  A  +L  +++ L+  +   ++       ++   G +GL++A+++FD     
Sbjct: 15  RLAQGGDQEAKAQLYEANVGLIYLVLERFKNTSYDQEDLFQVGAMGLLKAIERFDFSFDV 74

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           R +TY++  I   +++++     +VK+     Q+ +     R++     +  +  +   V
Sbjct: 75  RFSTYAVPMIIGEIKKFLRDDG-MVKV-----QRGIKELYARVRWAQDKLRGDLGREPGV 128

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IA  L + + +++           ++ ++ S +K      D LV++            
Sbjct: 129 NEIASLLEMEKEDIVVAMEACQAPAYIHDVVPSEEKEQLSLLDKLVHEEGNVAI------ 182

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
                +  L  +++ L+ RER +   R  Q+   T   ++ +  VS+ ++ +IE  A  K
Sbjct: 183 ---LEKLALREALAKLDERERVVIIRRFFQDE--TQTVIAEDLGVSQVQISRIEKSAILK 237

Query: 280 VQESIQ 285
           ++  +Q
Sbjct: 238 LRSLLQ 243


>gi|331695379|ref|YP_004331618.1| SigB/F/G subfamily RNA polymerase sigma-28 subunit [Pseudonocardia
           dioxanivorans CB1190]
 gi|326950068|gb|AEA23765.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Pseudonocardia dioxanivorans CB1190]
          Length = 259

 Score =  137 bits (345), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 39/241 (16%), Positives = 95/241 (39%), Gaps = 14/241 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +    LV  +L +   IA  +   G P+ ++     +GL+ A+ +F P++G    ++++
Sbjct: 29  EALRDELVRGYLPVAQHIARRFAHRGEPLDDLTQVATVGLINAIDRFAPDKGSDFFSFAV 88

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I   ++ +       +++        +      L G +  ++    +  +   IA+ L
Sbjct: 89  PTISGEVRRHFRDLGWSMRVPRRLKDLHVS-----LNGAVSDLSQRLGRAPKPTEIAEYL 143

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +  ++V+          S +     S +  S     LV + D        + +R + R 
Sbjct: 144 GMPVADVLEGLEAADAYRSSSLDEMLSSEQGSATVGELVGEADA-------ELDRVDTRQ 196

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L   ++ L  RER I   R      +T   ++ +  +S+  V ++ A+   +++  + +
Sbjct: 197 ALRPVLAELGERERTIVMLRFFGN--MTQTQIAEKVGISQMHVSRLLAQTLDRLRSRLDQ 254

Query: 287 Q 287
            
Sbjct: 255 D 255


>gi|297617167|ref|YP_003702326.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
 gi|297145004|gb|ADI01761.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
          Length = 258

 Score =  137 bits (345), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 55/258 (21%), Positives = 114/258 (44%), Gaps = 18/258 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY----RGYGLPISEVVSEGNIGLMQAVK 91
            L  RY++ GD+ A   L+  +  LV  IA         + + + E++S G  GL+ AV 
Sbjct: 8   ELWSRYKDEGDIEARDELILHYAGLVKYIAARLFPNLSSHQVELDELISYGIEGLIDAVH 67

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           +FDP+R  +  TY++  IK A+ + + R+   + +      K L      L+  L     
Sbjct: 68  RFDPKRKVKFETYALARIKGAIIDGL-RAMDWIPVSLRHKAKELEKAYCLLEHRL----- 121

Query: 152 NNLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
              +      +A +L +S  E  ++     LA    L  LI   + + ++    ++ D  
Sbjct: 122 --GRAATDEEMACELGMSIPEFQNLLKEVNLATIIYLEDLIPGDEGDKNKRIADVIKDER 179

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
            ++   +E  E +  + +L  ++++L  +ER +          +TL+ +     +S  R+
Sbjct: 180 AEDG--LELIEFEESKRLLAEAIALLPEKERTVVTLYYY--EGLTLKEIGEVLGLSESRI 235

Query: 270 RQIEARAFKKVQESIQKQ 287
            Q+  +A  +++  + K+
Sbjct: 236 SQLHTKAILRLRGRLGKK 253


>gi|302874610|ref|YP_003843243.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           cellulovorans 743B]
 gi|307690779|ref|ZP_07633225.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           cellulovorans 743B]
 gi|302577467|gb|ADL51479.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           cellulovorans 743B]
          Length = 241

 Score =  137 bits (345), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 54/241 (22%), Positives = 107/241 (44%), Gaps = 19/241 (7%)

Query: 51  HRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
             ++T ++ LV  IA      +   +   ++VS G +GLM A+ KFD  +G + ++Y+  
Sbjct: 11  EEIITKYIPLVKYIASRVIIGKSKHIEFDDLVSNGILGLMDALNKFDESKGMKFSSYASI 70

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            IK AM + + R+  +         K     L R    + ++ +  L+   V  IA ++ 
Sbjct: 71  RIKGAMIDELRRNSPI--------PKGAMDKLNRYNSAIDSLRNTLLREPTVDEIACEMA 122

Query: 168 VSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           +  ++VI +   +      SL  LI S D +       +    D +     +  E K + 
Sbjct: 123 IDIADVIEIENHINYLSVVSLEELIYSEDDDMP----LIGTIKDNKSPSPEKDLEDKEKM 178

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             L +++ +LN +++ +          +TL+ +    EVS  RV Q+  RA   +++++ 
Sbjct: 179 EYLAKAIELLNEKDKLVLNLYYY--EGLTLKEIGKILEVSESRVCQLHTRAIAHLRKNLS 236

Query: 286 K 286
           K
Sbjct: 237 K 237


>gi|312621597|ref|YP_004023210.1| RNA polymerase, sigma 28 subunit, flia/whig [Caldicellulosiruptor
           kronotskyensis 2002]
 gi|312202064|gb|ADQ45391.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Caldicellulosiruptor
           kronotskyensis 2002]
          Length = 246

 Score =  137 bits (345), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 55/256 (21%), Positives = 113/256 (44%), Gaps = 19/256 (7%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKF 93
           L +++ +  D     +L+  ++ LV  +A     Y G  +   ++VS G+IGL+ A++KF
Sbjct: 6   LWEKFTKTKDPKIKEQLIIKYMPLVKLVAGRMAIYFGGNVEYDDLVSYGSIGLLDAIEKF 65

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D ++G +  TY+   IK A+ + +        +  +  QK       +         +  
Sbjct: 66  DSQKGVKFETYAYTRIKGAIIDCVRNQDF---LPRSIRQK------AKEIERAYIEIEKE 116

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            K      +AK++ +S  E+  +  R++    ++          S+     + D   Q +
Sbjct: 117 GKTPTNQEVAKRIGISVEELQKLQDRISSGMIISLESFLEQNYESKIGG--LEDFVSQPE 174

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
             IE EE    R +L + +  L   ER +      ++  ++++ ++    VS  RV Q+ 
Sbjct: 175 HFIENEEL---RKVLRQQIDNLMENERMVIVLYYYED--LSIKEIAKVLGVSESRVSQLH 229

Query: 274 ARAFKKVQESIQKQVE 289
            RA  K++ ++QK +E
Sbjct: 230 TRALLKLRSALQKYLE 245


>gi|89099620|ref|ZP_01172495.1| sporulation sigma factor SigE [Bacillus sp. NRRL B-14911]
 gi|89085773|gb|EAR64899.1| sporulation sigma factor SigE [Bacillus sp. NRRL B-14911]
          Length = 239

 Score =  137 bits (345), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 61/264 (23%), Positives = 111/264 (42%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL  +  + GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLSKEEEEVLLIKLPK-GDKAARSMLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+                    +++   
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN-------------------NKIRSE- 135

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                            ++ DE LN      D N     D L  
Sbjct: 136 ---------------------------------VSFDEPLN---IDWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEV 264
           + D    ++ +  E    + +L +++  L  RE++I E R         T ++++    +
Sbjct: 160 EED----IITKDLEANVDKKLLLKALHQLTDREKQIMELRFGLGSGEEKTQKDVADMLGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 216 SQSYISRLEKRIIKRLKKEFNKMV 239


>gi|160935680|ref|ZP_02083055.1| hypothetical protein CLOBOL_00570 [Clostridium bolteae ATCC
           BAA-613]
 gi|158441424|gb|EDP19134.1| hypothetical protein CLOBOL_00570 [Clostridium bolteae ATCC
           BAA-613]
          Length = 246

 Score =  137 bits (345), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 60/272 (22%), Positives = 109/272 (40%), Gaps = 65/272 (23%)

Query: 18  RYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
            YI     +P  LE +EE  +        D  A   L+  +LRLVV IA  +    + + 
Sbjct: 31  HYIGGADILPAPLETEEEGRMISLLGSEDDKEARAALIEHNLRLVVYIAKKFDNTSVGVE 90

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++S G IGL++A+  F P++  +LATY+   I+  +  Y+ R+                
Sbjct: 91  DLISIGTIGLIKAINTFKPDKNIKLATYASRCIENEILMYLRRNNKT------------- 137

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
                                       +L VS  E ++++                D N
Sbjct: 138 ----------------------------RLEVSIDEPLNVD---------------WDGN 154

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL----QENP 252
                D L  D D    V+    E +  +++L  ++S LNPRER+I E R          
Sbjct: 155 ELLLSDILGTDED----VIYHDIEDEIEKSLLNNAISRLNPRERKIVELRYGLTNEDGEE 210

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +T + ++    +S+  + ++E +  K++++ I
Sbjct: 211 MTQKEVADLLGISQSYISRLEKKIMKRLKKEI 242


>gi|55274967|gb|AAV49283.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 194

 Score =  137 bits (345), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 54/204 (26%), Positives = 96/204 (47%), Gaps = 12/204 (5%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           + S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  +
Sbjct: 1   IESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTI 60

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
           +  I+     +++      K L   LR  +     ++           IA++L+    +V
Sbjct: 61  ERAIMNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDV 115

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             M        S++  +    +     +  L    D +E    +  +  + +  + + + 
Sbjct: 116 SRMLRLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWLF 170

Query: 234 VLNPRERRIFEARR--LQENPVTL 255
            LN ++R +   R   L     TL
Sbjct: 171 ELNAKQREVLARRFGLLGYEAATL 194


>gi|302558953|ref|ZP_07311295.1| RNA polymerase sigma-F factor [Streptomyces griseoflavus Tu4000]
 gi|302476571|gb|EFL39664.1| RNA polymerase sigma-F factor [Streptomyces griseoflavus Tu4000]
          Length = 282

 Score =  137 bits (345), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 49/239 (20%), Positives = 105/239 (43%), Gaps = 18/239 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + L+  ++ LV   A  +R  G   + ++V  G IGL++A+ +F+  R     ++++ 
Sbjct: 55  ARNTLIEMNMSLVRYAAGRFRSRGPEEMEDIVQVGMIGLIKAIDRFELSREVEFTSFAIP 114

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +I   ++ +   +   V +     + R+     +L    + +     +   V  +A+ ++
Sbjct: 115 YIVGEIKRFFRDTSWSVHVPRRLQEARV-----QLARATEELRSRLGRTPTVGELAQLMS 169

Query: 168 VSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           ++E EV        G    SL+A I S     S   D++     G E   +E  E  +  
Sbjct: 170 LTEEEVNEARIASNGYNSASLDAAIGSEPDGESVLADFI-----GSEDAALELVEDFH-- 222

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             L   ++ L+ RER+I   R ++E  +T   +      S+  V ++ +R  K+++  +
Sbjct: 223 -ALAPMIADLDERERKIVHWRFVEE--LTQAEIGQRLGCSQMHVSRLLSRTLKRLRAGM 278


>gi|302537203|ref|ZP_07289545.1| RNA polymerase sigma-G factor [Streptomyces sp. C]
 gi|302446098|gb|EFL17914.1| RNA polymerase sigma-G factor [Streptomyces sp. C]
          Length = 278

 Score =  137 bits (345), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 50/254 (19%), Positives = 108/254 (42%), Gaps = 16/254 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
           VL + Y++ GD     +L+  +  LV  +A          +  ++ VS G  GL+ A++K
Sbjct: 31  VLWRSYKDSGDERLREQLILHYSPLVKYVAGRVSVGLPPNVEQADFVSSGVFGLIDAIEK 90

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD ER  +  TY++  I+ AM + + R+   +        + +      L+  L+     
Sbjct: 91  FDIERSIKFETYAITRIRGAMIDEL-RALDWIPRSVRQKARAVERAYATLEAQLR----- 144

Query: 153 NLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
             +      +A ++ ++  E+ ++     LA   +L  L++   +   +    +    D 
Sbjct: 145 --RTPTEGEVAGEMGIAVEELHTVFSQLSLANVVALEELLHVGGEGGDRL-SLMDTLEDT 201

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                +E  E +  R +L R+++ L  RE+ +          +TL  + +   V+  RV 
Sbjct: 202 AADNPVEVAEDRELRRLLARAINTLPDREKTVVTLYYY--EGLTLAEIGNVLGVTESRVS 259

Query: 271 QIEARAFKKVQESI 284
           QI  ++  +++  +
Sbjct: 260 QIHTKSVLQLRAKL 273


>gi|297616717|ref|YP_003701876.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
 gi|297144554|gb|ADI01311.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
          Length = 248

 Score =  137 bits (345), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 50/247 (20%), Positives = 103/247 (41%), Gaps = 16/247 (6%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           +  + GD  A   +  S+L LV      ++       ++   G IGL++A+ +FD   G 
Sbjct: 17  KAAQAGDRDAEEAVFQSNLGLVYMALERFKNTPYDFEDLFQIGAIGLLKAIARFDFGYGV 76

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY++  I   ++ Y+         G    Q+ +     R+K     +     K   +
Sbjct: 77  KFSTYAVPMIIGELKRYLRDD------GILKVQRSIKEIYYRVKSAQDDLRREFGKEPTI 130

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IA++L +  ++V+           +  L+   +K         V D +G E +L    
Sbjct: 131 GEIAERLGLELNDVVMAVEACQPPTYIYNLLPGDEKEQPLPLISKVSDREGTEDLLE--- 187

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
                +  L  ++  L+PRER +   R  ++   T   ++ +  +S+ +V ++E RA KK
Sbjct: 188 -----KVALKEAVMRLDPREREVIVRRFFKDE--TQSAIAEDLGISQVQVSRLEKRALKK 240

Query: 280 VQESIQK 286
           ++  +  
Sbjct: 241 LRGLLDS 247


>gi|284045116|ref|YP_003395456.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Conexibacter woesei
           DSM 14684]
 gi|283949337|gb|ADB52081.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Conexibacter woesei
           DSM 14684]
          Length = 262

 Score =  137 bits (345), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 54/260 (20%), Positives = 112/260 (43%), Gaps = 16/260 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQA 89
           E   L +RY+  GD  A  RLV ++  LV  +A          +  ++++S G IGL+ A
Sbjct: 9   ELKDLWRRYKASGDGRARERLVVAYSPLVKYVAGRMASGLPAHVEEADLISYGLIGLISA 68

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +++FD  R  +  TY++  I+ A+ + + RS   V     A  + +     +L+  LQ  
Sbjct: 69  IERFDLGREIKFETYAIPRIRGAIIDEL-RSLDWVPRSVRAKAREIERANAKLEHKLQ-- 125

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYD 207
                +      +A +L++S  E      +++     +L+ L   SD +  Q    L   
Sbjct: 126 -----RAPTDEEMAHELDMSMDEFQDALIQISNSTIAALDELWTVSDASGDQI-SLLDTL 179

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            D       +  +    ++ +  +++ L  RE+ +      +   +TL  +     V+  
Sbjct: 180 QDPDAPDPEKIVDASELKDRVADAIARLPEREKLVIALYYYEN--LTLREIGEVLGVTES 237

Query: 268 RVRQIEARAFKKVQESIQKQ 287
           R+ Q+  +A  +++  +Q +
Sbjct: 238 RISQLHTKAVLRLRSRLQNE 257


>gi|332196178|gb|AEE34299.1| sigma factor A [Arabidopsis thaliana]
          Length = 498

 Score =  137 bits (345), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 50/221 (22%), Positives = 102/221 (46%), Gaps = 9/221 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L  S++RLV+ IA  Y   G  +S++V  G IGL++ ++KFD  +GFR++TY  WW
Sbjct: 259 AREKLAMSNVRLVMSIAQRYDNLGAEMSDLVQGGLIGLLRGIEKFDSSKGFRISTYVYWW 318

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+  +   ++ +   +++ T  +++       +L+   + IT        +  IA+ LN+
Sbjct: 319 IRQGVSRALVDNSRTLRLPTHLHERLGLIRNAKLRLQEKGIT------PSIDRIAESLNM 372

Query: 169 SESEVISMNCRLAGDESLN-ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           S+ +V +    ++   SL+     S +    +     + D   +       ++   +  +
Sbjct: 373 SQKKVRNATEAVSKVFSLDRDAFPSLNGLPGETHHSYIADTRLENNPWHGYDDLALKEEV 432

Query: 228 LTRSMSVLNPRERRIFEARRLQENP-VTLENLSSEFEVSRE 267
                + L  RE+ I       +   +T E++S    + RE
Sbjct: 433 SKLISATLGEREKEIIRLYYGLDKECLTWEDISKRI-IERE 472


>gi|153440|gb|AAC36891.1| minor sigma-like factor [Streptomyces aureofaciens]
 gi|743686|prf||2013252A RNA polymerase:SUBUNIT=sigma factor
          Length = 278

 Score =  137 bits (345), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 50/254 (19%), Positives = 107/254 (42%), Gaps = 16/254 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
           VL + Y++ GD     +L+  +  LV  +A          +  ++ VS G  GL+ A++K
Sbjct: 31  VLWRSYKDSGDERLREQLILHYSPLVKYVAGRVSVGLPPNVEQADFVSSGVFGLIDAIEK 90

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD ER  +  TY++  I+ AM + + R+   +        + +      L+  L+     
Sbjct: 91  FDIERSIKFETYAITRIRGAMIDEL-RALDWIPRSVRQKARAVERAYATLEAQLR----- 144

Query: 153 NLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
             +      +A ++ +   E+ ++     LA   +L  L++   +   +    +    D 
Sbjct: 145 --RTPTEGEVAGEMGIGVEELHTVFSQLSLANVVALEELLHVGGEGGDRL-SLMDTLEDH 201

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                +E  E +  R +L R+++ L  RE+ +          +TL  + +   V+  RV 
Sbjct: 202 AADDPVEVAEDRELRRLLARAINTLPEREKTVVTLYYY--EGLTLAEIGNVLGVTESRVS 259

Query: 271 QIEARAFKKVQESI 284
           QI  ++  +++  +
Sbjct: 260 QIHTKSVLQLRAKL 273


>gi|255305293|ref|ZP_05349465.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile ATCC 43255]
          Length = 233

 Score =  137 bits (345), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 56/241 (23%), Positives = 108/241 (44%), Gaps = 19/241 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGY--RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              L+  ++ LV  IA  +   G G    ++V+ G IGL+ A+ KFD E+G + ++YS  
Sbjct: 3   REELIKENMPLVKSIARKFFIPGKGFEYQDLVNSGVIGLIDAINKFDTEKGAKFSSYSYI 62

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            IK+A+ + I     +         K     + +    ++ +    L+      IAK+L 
Sbjct: 63  KIKSAILDEIRNQSPI--------SKHNLTKVNKYNRVVEKLQSKLLREPTSYEIAKELK 114

Query: 168 VSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           VSE E+  +   +      SLN +I      + Q         D +E+      E + + 
Sbjct: 115 VSEKELHDIESNIDMLNIVSLNYVIFEDTNETVQDVI-----SDREEEAPENIIEEEEKL 169

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            +L++++S LN RE+ I      ++  + L+ +     VS  RV Q+  ++ + ++  I+
Sbjct: 170 EILSKAISNLNEREKLILSLYYYED--LNLKEIGKVLGVSESRVSQLHRKSIRNLRNKIK 227

Query: 286 K 286
           +
Sbjct: 228 E 228


>gi|302872543|ref|YP_003841179.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
 gi|302575402|gb|ADL43193.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
          Length = 246

 Score =  137 bits (345), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 56/262 (21%), Positives = 122/262 (46%), Gaps = 23/262 (8%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQA 89
           +E +L +++ +  D     +L+  ++ LV  +A     Y G  +   ++VS G+IGL+ A
Sbjct: 2   DEALLWEKFIKTKDPKIKEQLIIKYMPLVKLVAGRMAIYFGGNVEYDDLVSYGSIGLLDA 61

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           ++KFD ++G +  TY+   IK A+ + +        +  +  QK       +        
Sbjct: 62  IEKFDSQKGVKFETYAYTRIKGAIIDCVRSQDF---LPRSIRQK------AKEIEKAYIE 112

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYD 207
            +   +      +AK++ +S SE+  +  +++     SL++ +    + + + +   + D
Sbjct: 113 IEREGRTPTDDEVAKRVGLSISELQKLQEKISSGMIVSLDSFL----EQNYESKIGGLED 168

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
              Q +  IE EE    + +L + +  L   ER +      +E  ++++ ++    VS  
Sbjct: 169 FVSQPEHFIENEEL---KEVLRQQIDNLLENERMVIVLYYYEE--LSIKEIAKILGVSES 223

Query: 268 RVRQIEARAFKKVQESIQKQVE 289
           RV Q+  RA  K++ ++QK +E
Sbjct: 224 RVSQLHTRALLKLRSALQKYLE 245


>gi|307718622|ref|YP_003874154.1| hypothetical protein STHERM_c09340 [Spirochaeta thermophila DSM
           6192]
 gi|306532347|gb|ADN01881.1| hypothetical protein STHERM_c09340 [Spirochaeta thermophila DSM
           6192]
          Length = 262

 Score =  136 bits (344), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 48/257 (18%), Positives = 111/257 (43%), Gaps = 17/257 (6%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAV 90
           E  L K Y++  D       +  +  LV  +A          +   +++  G  GL+ A+
Sbjct: 11  EDELWKEYQKTRDPQIREYFIKQYAPLVKYVAGKIAVGLPSSVEFDDLIGFGTFGLLDAI 70

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +KFDPE+  +  TY++  I+ A+ + + R+   V        + +   L RL+  L    
Sbjct: 71  EKFDPEKHVKFKTYAVTRIRGAIYDEL-RAMDWVPRSVRQKSREIEDALHRLESSL---- 125

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDH 208
               +      +A+++N+S  E+     +++     SL  L  + D+N       ++   
Sbjct: 126 ---GRAATDEELAREMNMSSRELQKTLQKISSTSILSLQELWYTGDENDRVAIADML--E 180

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
             Q      + ER+  + ++  ++  L  +E+++      ++  +TL+ + +   V+  R
Sbjct: 181 APQAYDPAARVEREEIKRVVAEAIKELPEKEKKVLVLYYYED--LTLKEIGAILNVTESR 238

Query: 269 VRQIEARAFKKVQESIQ 285
           V Q+  +A  +++  ++
Sbjct: 239 VSQLHTKAISRLRVKLR 255


>gi|312126848|ref|YP_003991722.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor hydrothermalis 108]
 gi|311776867|gb|ADQ06353.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor hydrothermalis 108]
          Length = 248

 Score =  136 bits (344), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 56/258 (21%), Positives = 118/258 (45%), Gaps = 23/258 (8%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKF 93
           L +++ +  D     +L+  ++ LV  +A     Y G  +   ++VS G+IGL+ A++KF
Sbjct: 8   LWEKFIKTKDPKIKEQLIIKYMPLVKLVAGRMAIYFGGNVEYDDLVSYGSIGLLDAIEKF 67

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D ++G +  TY+   IK A+ + +        +  +  QK       +         +  
Sbjct: 68  DSQKGVKFETYAYTRIKGAIIDCVRSQDF---LPRSIRQK------AKEIEKAYIEIEKE 118

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQ 211
            K      +AK++ +S  E+  +  R++     SL++ +    + + + +   + D   Q
Sbjct: 119 GKTPTDQEVAKRIGISVDELQKLQDRISSGMIISLDSFL----EQNYESKIGGLEDFVSQ 174

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
            +  IE EE    + +L + +  L   ER +      +E  ++++ ++    VS  RV Q
Sbjct: 175 PEHFIENEEL---KTVLRQQIDNLMENERMVIVLYYYEE--LSIKEIAKVLGVSESRVSQ 229

Query: 272 IEARAFKKVQESIQKQVE 289
           +  RA  K++ ++QK +E
Sbjct: 230 LHTRALLKLRSALQKYLE 247


>gi|328880412|emb|CCA53651.1| RNA polymerase sigma factor SigB [Streptomyces venezuelae ATCC
           10712]
          Length = 283

 Score =  136 bits (344), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 42/238 (17%), Positives = 105/238 (44%), Gaps = 16/238 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A + L+  ++ LV   A  +R  G  + ++V  G IGL++A+ +F+  R     T+++ +
Sbjct: 56  ARNTLIEMNMSLVRYAAGRFRHRGDEMEDIVQVGMIGLIKAIDRFELSREVEFTTFAVPY 115

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I   ++ +   +   V +     + R+      L    + ++    +      +A+ +++
Sbjct: 116 IVGEIKRFFRDTSWAVHVPRRLQEARV-----ELAKATEELSTRLGRTPTSKELAELMSL 170

Query: 169 SESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +E EV        G    SL+A ++  +++S       +   D   +++ +        +
Sbjct: 171 TEEEVNEARLASNGYHSSSLDAALSGENEDSEASLADFIGSEDPAMELVEDF-------H 223

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   ++ L+ R+R+I   R ++E  +T   +      S+  V ++ +R  K +++ +
Sbjct: 224 ALAPLIAELDERDRQIIHLRFVEE--LTQAQIGERLGCSQMHVSRLLSRTIKSLRQGL 279


>gi|222530110|ref|YP_002573992.1| FliA/WhiG subfamily RNA polymerase sigma-28 factor
           [Caldicellulosiruptor bescii DSM 6725]
 gi|222456957|gb|ACM61219.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Caldicellulosiruptor
           bescii DSM 6725]
          Length = 246

 Score =  136 bits (344), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 56/256 (21%), Positives = 114/256 (44%), Gaps = 19/256 (7%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKF 93
           L +++ +  D     +L+  ++ LV  +A     Y G  +   ++VS G+IGL+ A++KF
Sbjct: 6   LWEKFTKTKDPKIKEQLIIKYMPLVKLVAGRMAIYFGGNVEYDDLVSYGSIGLLDAIEKF 65

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D ++G +  TY+   IK A+ + +        +  +  QK       +    +    +  
Sbjct: 66  DSQKGVKFETYAYTRIKGAIIDCVRSQDF---LPRSIRQK------AKEIERVYIEIEKE 116

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            K      +AK++ +S  E+  +  R++    ++          S+     + D   Q +
Sbjct: 117 GKTPTNQEVAKRIGISVEELQKLQDRISSGMIISLESFLEQNYESKIGG--LEDFVSQPE 174

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
             IE EE    R +L + +  L   ER +      +E  ++++ ++    VS  RV Q+ 
Sbjct: 175 HFIENEEL---REVLRQQIDNLLENERMVIVLYYYEE--LSIKEIAKVLGVSESRVSQLH 229

Query: 274 ARAFKKVQESIQKQVE 289
            RA  K++ ++QK +E
Sbjct: 230 TRALLKLRSALQKYLE 245


>gi|25991939|gb|AAN76997.1|AF481773_1 putative sigma 70 transcription factor [Frankia sp. ACoN24d]
          Length = 185

 Score =  136 bits (344), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 37/178 (20%), Positives = 77/178 (43%), Gaps = 10/178 (5%)

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            G G+ + ++V EGN+GL++ VKKFD  +G++ +TY+ WWI+ A+   +      ++I  
Sbjct: 1   SGRGMTLLDLVQEGNLGLIRPVKKFDYAKGYKFSTYATWWIRQAIGRALADQGRTIRIPV 60

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
              +      + ++    + +     +      +A +L++   +V+ +        SL  
Sbjct: 61  XVVE-----QINKITRLQRQLVSTLGREPTDEELALELDMPIEQVVELRRYAQDTVSLET 115

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
            +   D   S   D++    D       +       ++ +   +  LNPRER +   R
Sbjct: 116 SV--GDDGDSVLGDFI---EDSDATSPADAASYGAMQDEIENVLGGLNPREREVMRLR 168


>gi|55274875|gb|AAV49240.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 193

 Score =  136 bits (344), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 51/197 (25%), Positives = 94/197 (47%), Gaps = 10/197 (5%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  
Sbjct: 1   MIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQT 60

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           ++  I+     +++      K L   LR  +     ++           IA++L+    +
Sbjct: 61  IERAIMNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDD 115

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           V  M        S++  +    +     +  L    D +E    +  +  + +  + + +
Sbjct: 116 VSRMLRLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWL 170

Query: 233 SVLNPRERRIFEARRLQ 249
             LN ++R +   R   
Sbjct: 171 FELNAKQREVLARRFGL 187


>gi|213616352|ref|ZP_03372178.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 508

 Score =  136 bits (344), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 43/168 (25%), Positives = 77/168 (45%), Gaps = 7/168 (4%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 346 LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 405

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 406 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 463

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
            L R+   +         PE    +A+++ + E ++  +        S
Sbjct: 464 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIRKVLKIAKEPIS 508


>gi|312135825|ref|YP_004003163.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|311775876|gb|ADQ05363.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor owensensis OL]
          Length = 246

 Score =  136 bits (344), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 58/262 (22%), Positives = 122/262 (46%), Gaps = 23/262 (8%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQA 89
           +E +L +++ +  D     +L+  ++ LV  +A     Y G  +   ++VS G+IGL+ A
Sbjct: 2   DEALLWEKFIKTKDQKIKEQLIIKYMPLVKLVAGRMAIYFGGNVEYDDLVSYGSIGLLDA 61

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           ++KFD ++G +  TY+   I+ A+ + +        +  +  QK       +        
Sbjct: 62  IEKFDSQKGVKFETYAYTRIRGAIIDCVRSQDF---LPRSIRQK------AKEIEKAYIE 112

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYD 207
            +   +      +AK+L +S SE+  +  +++     SL + +    + S + +   + D
Sbjct: 113 IEREGRTPTDYEVAKRLGISISELQKLQEKISSGMIVSLESFL----EQSYESKIGGLED 168

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
              Q +  IE EE KN   +L + +  L   ER +      +E  ++++ ++    +S  
Sbjct: 169 FVSQPEHFIENEELKN---VLRQQIDNLMENERMVIMLYYYEE--LSIKEIAKILGISES 223

Query: 268 RVRQIEARAFKKVQESIQKQVE 289
           RV Q+  RA  K++ ++QK +E
Sbjct: 224 RVSQLHTRALLKLRSALQKYLE 245


>gi|320008281|gb|ADW03131.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Streptomyces
           flavogriseus ATCC 33331]
          Length = 278

 Score =  136 bits (344), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 50/254 (19%), Positives = 106/254 (41%), Gaps = 16/254 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
            L + Y+  GD     +L+  +  LV  +A          +  ++ VS G  GL+ A++K
Sbjct: 31  ELWRSYKTTGDGRLREQLILHYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEK 90

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD ER  +  TY++  I+ AM + + R+   +        + +      L+  L+     
Sbjct: 91  FDIERAIKFETYAITRIRGAMIDEL-RALDWIPRSVRQKARNVERAYATLEAQLR----- 144

Query: 153 NLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
             +      +A ++ V+  E+ ++     LA   +L  L++   +   +    +    D 
Sbjct: 145 --RTPSEAEVASEMGVALEELHAVFSQLSLANVVALEELLHVGGEGGDRL-SLMDTLEDT 201

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                +E  E +  R +L R+++ L  RE+ +          +TL  + +   V+  RV 
Sbjct: 202 AADDPVEVAEDRELRRLLARAINTLPEREKTVVTLYYY--EGLTLAEIGNVLGVTESRVS 259

Query: 271 QIEARAFKKVQESI 284
           QI  ++  +++  +
Sbjct: 260 QIHTKSVLQLRAKL 273


>gi|126697838|ref|YP_001086735.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile 630]
 gi|255099435|ref|ZP_05328412.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           difficile QCD-63q42]
 gi|115249275|emb|CAJ67088.1| RNA polymerase sigma-28factor for flagellar operon [Clostridium
           difficile]
          Length = 233

 Score =  136 bits (344), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 56/241 (23%), Positives = 108/241 (44%), Gaps = 19/241 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGY--RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              L+  ++ LV  IA  +   G G    ++V+ G IGL+ A+ KFD E+G + ++YS  
Sbjct: 3   REELIKENMPLVKSIARKFFIPGKGFEYQDLVNSGVIGLIDAINKFDAEKGAKFSSYSYI 62

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            IK+A+ + I     +         K     + +    ++ +    L+      IAK+L 
Sbjct: 63  KIKSAILDEIRNQSPI--------SKHNLTKVNKYNRVVEKLQSKLLREPTSYEIAKELK 114

Query: 168 VSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           VSE E+  +   +      SLN +I      + Q         D +E+      E + + 
Sbjct: 115 VSEKELHDIESNIDMLNIVSLNYVIFEDTNETVQDVI-----SDREEEAPENIIEEEEKL 169

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            +L++++S LN RE+ I      ++  + L+ +     VS  RV Q+  ++ + ++  I+
Sbjct: 170 EILSKAISNLNEREKLILSLYYYED--LNLKEIGKVLGVSESRVSQLHRKSIRNLRNKIK 227

Query: 286 K 286
           +
Sbjct: 228 E 228


>gi|239826532|ref|YP_002949156.1| sporulation sigma factor SigE [Geobacillus sp. WCH70]
 gi|239806825|gb|ACS23890.1| RNA polymerase, sigma 28 subunit, SigE [Geobacillus sp. WCH70]
          Length = 239

 Score =  136 bits (344), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 62/264 (23%), Positives = 111/264 (42%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE +L K+    GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLTKEEEEMLIKKLS-SGDETARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+                    +++   
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN-------------------NKVRAE- 135

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                            ++ DE LN      D N     D L  
Sbjct: 136 ---------------------------------VSFDEPLN---IDWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           + D    V+ +  E    R +L  ++  L+ RE++I E R         T ++++    +
Sbjct: 160 EDD----VITKDLEADVDRRLLFNALRQLSDREKQIMELRFGLSGGEEKTQKDVADLLGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K +
Sbjct: 216 SQSYISRLEKRIIKRLRKEFNKMM 239


>gi|297200169|ref|ZP_06917566.1| RNA polymerase sigma-E factor [Streptomyces sviceus ATCC 29083]
 gi|197713380|gb|EDY57414.1| RNA polymerase sigma-E factor [Streptomyces sviceus ATCC 29083]
          Length = 304

 Score =  136 bits (344), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 48/237 (20%), Positives = 98/237 (41%), Gaps = 18/237 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            + LV  +L LV   A  +R    P+ +++  G IGL++A+ +F+  RG    T++M  I
Sbjct: 80  RNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRGVEFPTFAMPTI 139

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +   V  +A +L +S
Sbjct: 140 VGEIKRFFRDTSWSVRVPRRLQELRLD-----LAKAGDELAQKLDRAPTVAELADRLGLS 194

Query: 170 ESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + EV+            SL+A     D +     D + Y+  G E +             
Sbjct: 195 KEEVVEGMAASNAYTAASLDAQ-PEEDDSEGALADRIGYEDHGLEGI--------EYVES 245

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   ++ L  R+R+I   R +    +T   +  E  +S+  V ++ +R   ++++ +
Sbjct: 246 LKPLIAELPSRDRQILSLRFVAG--MTQSEIGEELGISQMHVSRLLSRTLVRLRKGL 300


>gi|291448259|ref|ZP_06587649.1| LOW QUALITY PROTEIN: RNA polymerase sigma factor RpoD [Streptomyces
           roseosporus NRRL 15998]
 gi|291351206|gb|EFE78110.1| LOW QUALITY PROTEIN: RNA polymerase sigma factor RpoD [Streptomyces
           roseosporus NRRL 15998]
          Length = 360

 Score =  136 bits (344), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 41/154 (26%), Positives = 76/154 (49%), Gaps = 28/154 (18%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY---------------------- 41
           + +++       +  Y+ +I K+P+L  ++E  LAKR                       
Sbjct: 207 QQVAVAGATADPVKDYLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANADKLAPKLKR 266

Query: 42  -----REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                 E G   A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  
Sbjct: 267 ELEIIAEDG-RRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYT 325

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
           +G++ +TY+ WWI+ A+   +      ++I   +
Sbjct: 326 KGYKFSTYATWWIRQAITRAMADQARTIRIPVHS 359


>gi|255312671|gb|ACU01745.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score =  136 bits (344), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 53/205 (25%), Positives = 95/205 (46%), Gaps = 12/205 (5%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           +     +++      K L   LR  +     ++            A++L+    +V  M 
Sbjct: 61  MNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEESAEQLDKPVDDVSRML 115

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                  S++  +    +     +  L    D +E    +  +  + +  + + +  LN 
Sbjct: 116 RLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNA 170

Query: 238 RERRIFEARR--LQENPVTLENLSS 260
           ++R +   R   L     TLE++  
Sbjct: 171 KQREVLARRFGLLGYEAATLEDVGR 195


>gi|225619299|ref|YP_002720525.1| RNA polymerase sigma factor WhiG [Brachyspira hyodysenteriae WA1]
 gi|225214118|gb|ACN82852.1| RNA polymerase sigma factor WhiG [Brachyspira hyodysenteriae WA1]
          Length = 275

 Score =  136 bits (344), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 50/268 (18%), Positives = 113/268 (42%), Gaps = 19/268 (7%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR-----GYGLPISEVVS 80
           IP +  + E      +++         L+  +  LV  +A            +   ++V 
Sbjct: 14  IPNITNENEQEYWLEFKKTLSPYIREALIIKYSPLVKYVASKISVNMGSHKHIEFQDLVG 73

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
            G+ GLM A+ K++P R  +  TY++  I+ A+ + + +   L +     + ++    + 
Sbjct: 74  FGSFGLMDAIDKYNPNRDIKFKTYAVTRIRGAIYDELRKLDYLPR-----SIRKDVKEIE 128

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL--AGDESLNALINSSDKNSS 198
           + +  L+A    N+KP     IA  L +  S+      R   A   SL+ +    D +  
Sbjct: 129 KAREILEARLSRNIKP---QEIADMLGIPISKYNETMKRYIEASPTSLSDVWYVGDDSDE 185

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
                 +  +D      +   ER++ +N +  ++  L  +E+++       +  +TL+ +
Sbjct: 186 ISVIDTLKSNDKTNPEYL--AEREDVKNKIIAALKKLPEKEQQVLILYYYDD--LTLKEI 241

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQK 286
               EVS  R+ Q+  +A ++++ S+ +
Sbjct: 242 GKVLEVSESRISQLHTKAIQQLRYSLSE 269


>gi|255312689|gb|ACU01754.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score =  136 bits (344), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 55/205 (26%), Positives = 97/205 (47%), Gaps = 12/205 (5%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           +     +++      K L   LR  +     ++           IA++L+    +V  M 
Sbjct: 61  MNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRML 115

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                  S++  +    +     +  L    D +E    +  +  + +  + +S+  LN 
Sbjct: 116 RLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKSLFELNA 170

Query: 238 RERRIFEARR--LQENPVTLENLSS 260
           ++R +   R   L     TLE++  
Sbjct: 171 KQREVLARRFGLLGYEAATLEDVGR 195


>gi|254392909|ref|ZP_05008077.1| sigma factor of sigB family [Streptomyces clavuligerus ATCC 27064]
 gi|294811525|ref|ZP_06770168.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|326440088|ref|ZP_08214822.1| putative RNA polymerase sigma factor [Streptomyces clavuligerus
           ATCC 27064]
 gi|197706564|gb|EDY52376.1| sigma factor of sigB family [Streptomyces clavuligerus ATCC 27064]
 gi|294324124|gb|EFG05767.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 289

 Score =  136 bits (344), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 47/237 (19%), Positives = 98/237 (41%), Gaps = 16/237 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            + L+  +L LV   A  +R     + +++  G IGL++A+ +F+  R    AT+++ +I
Sbjct: 63  RNTLIELNLALVKYAAGRFRNRAEQMEDIIQVGTIGLIKAIDRFELSREVEFATFAVPYI 122

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V +     + R+      L      ++    +      +A+ L + 
Sbjct: 123 VGEIKRFFRDTSWAVHVPRRLQELRID-----LAKATDDLSQRLDRSPTTRELAEHLGID 177

Query: 170 ESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E EVI       G    S++  +  S  +++      + D  G     +E  E       
Sbjct: 178 EQEVIEGVVAANGYTAGSIDMPLEDSSDHTTSS----LSDRLGAPDAGLEIAENVQ---A 230

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   +  L  R+RRI   R  +E  +T   + +E  VS+  V ++  R   +++E +
Sbjct: 231 LKPLIEELGERDRRILRMRFGEE--LTQSEIGAELGVSQMHVSRLLTRITTRLREGL 285


>gi|227500978|ref|ZP_03931027.1| possible DNA-directed RNA polymerase sigma subunit SigB
           [Anaerococcus tetradius ATCC 35098]
 gi|227216751|gb|EEI82149.1| possible DNA-directed RNA polymerase sigma subunit SigB
           [Anaerococcus tetradius ATCC 35098]
          Length = 256

 Score =  136 bits (343), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 40/244 (16%), Positives = 105/244 (43%), Gaps = 16/244 (6%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
            ++Y +  D      L+  H+ +V  ++  Y G G+   ++    ++GL+ A++++DP +
Sbjct: 17  FEQYYKTKDKKLRDELIEEHMYIVDILSNKYVGKGIEKDDLYQVASLGLIYAIERYDPSK 76

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           GF  ++++   I   ++ Y      ++++      +R+    +++    + +     +  
Sbjct: 77  GFAFSSFATPTIMGELKRYFRDKGWVIRVP-----RRIQNLYKKINTAKKILPQELQRTP 131

Query: 158 QVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
            V  IA  L   E  ++      ++   +SL+         ++     ++ + D     +
Sbjct: 132 TVADIADYLGEDEETILETMEASKVYTPQSLDMKYQVQKGENAVDLSDMIGEEDKNFDSI 191

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
                    ++++ +SM  LN  E+ I E R       T  ++++  ++S+  V +IE +
Sbjct: 192 -------ELKDLIDKSMERLNDLEKEILELRYY--EGRTQVDIANSLDISQMTVSRIEKK 242

Query: 276 AFKK 279
             +K
Sbjct: 243 ILQK 246


>gi|220931758|ref|YP_002508666.1| sporulation sigma factor SigE [Halothermothrix orenii H 168]
 gi|219993068|gb|ACL69671.1| sporulation sigma factor SigE [Halothermothrix orenii H 168]
          Length = 245

 Score =  136 bits (343), Expect = 3e-30,   Method: Composition-based stats.
 Identities = 59/263 (22%), Positives = 107/263 (40%), Gaps = 64/263 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE+ EE  L KR  E GD S    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 42  PPLEEDEEDYLLKRLSE-GDNSVRQLLIKHNLRLVVYIARKFSNTGIDIEDLVSIGTIGL 100

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AVK FD  +  +LATY+   I+  +  Y+ ++                          
Sbjct: 101 IKAVKTFDVNKNIKLATYASRCIENEILMYLRKNSR------------------------ 136

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                            KK  +S  + ++++                D N  +  D +  
Sbjct: 137 -----------------KKAEISFDDPLNID---------------WDGNELKLSDVMGT 164

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ---ENPVTLENLSSEFE 263
           + D    ++    E +    +L  +M  L+ RE++I   R          T ++++    
Sbjct: 165 EGD----IIYRNIESEIDWELLKDAMKTLSDREKKILILRFGLLNSGETKTQKDVADLLG 220

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+  + ++E R  +K++  + +
Sbjct: 221 ISQSYISRLEKRIIRKLKREVAR 243


>gi|255312665|gb|ACU01742.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312669|gb|ACU01744.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 54/205 (26%), Positives = 95/205 (46%), Gaps = 12/205 (5%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           +      ++      K L   LR  +     ++           IA++L+    +V  M 
Sbjct: 61  MNQTRTNRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRML 115

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                  S++  +    +     +  L    D +E    +  +  + +  + + +  LN 
Sbjct: 116 RLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNA 170

Query: 238 RERRIFEARR--LQENPVTLENLSS 260
           ++R +   R   L     TLE++  
Sbjct: 171 KQREVLARRFGLLGYEAATLEDVGR 195


>gi|329936708|ref|ZP_08286415.1| RNA polymerase sigma factor WhiG [Streptomyces griseoaurantiacus
           M045]
 gi|329303938|gb|EGG47821.1| RNA polymerase sigma factor WhiG [Streptomyces griseoaurantiacus
           M045]
          Length = 279

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 51/254 (20%), Positives = 105/254 (41%), Gaps = 17/254 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
            L + Y+  GD     +L+  +  LV  +A          +  ++ VS G  GL+ A++K
Sbjct: 33  ELWRTYKATGDERLREQLILHYSPLVKYVAGRVSVGLPPNVEQADFVSSGVFGLIDAIEK 92

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           +D  R  +  TY++  I+ AM + +    +L  I  +  QK    N+ R    L+A    
Sbjct: 93  YDIGREIKFETYAITRIRGAMIDELR---ALDWIPRSVRQKA--RNVERAYTTLEA---R 144

Query: 153 NLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
             +      +A +L +   ++ ++     LA   +L  +++   +         +   D 
Sbjct: 145 LRRTPTESEVAAELGIRVDDLHAVFSQLSLANVVALEEILHIGGEGGGLSLMDTL--EDT 202

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                +E  E +  R  L R+++ L  RE+ +          +TL  + +   V+  RV 
Sbjct: 203 SADNPVEVAEDRELRRFLARAINTLPEREKTVVTLYYF--EGLTLAEIGNVLGVTESRVS 260

Query: 271 QIEARAFKKVQESI 284
           QI  ++  +++  +
Sbjct: 261 QIHTKSVLQLRAKL 274


>gi|313799121|gb|ADR82155.1| RNA polymerase sigma factor [Mycoplasma sp. 1220]
 gi|313799126|gb|ADR82156.1| RNA polymerase sigma factor [Mycoplasma anatis]
 gi|313799129|gb|ADR82157.1| RNA polymerase sigma factor [Mycoplasma anatis]
          Length = 183

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 44/187 (23%), Positives = 85/187 (45%), Gaps = 12/187 (6%)

Query: 23  IRKI-PMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           I K   +L   EE  LAK     G     A  +L+  +LRLV+  A  Y+  GL   +++
Sbjct: 3   IGKYGELLSADEEVELAKTMNLGGFRGKRARDKLIKRNLRLVINNAKKYKNRGLSFIDLI 62

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
           SEGN G+++A +K++ ++GF+ +TY+ WWI+ A+   +      +++     +      +
Sbjct: 63  SEGNAGILKAAQKYNVDKGFKFSTYATWWIRQAITRAVADQARTIRVPVHMVE-----TI 117

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLN--VSESEVISMNCRLAGDESLNALINSSDKNS 197
            ++    + +     +      IA K     +  +V  +        SL+  I    +N 
Sbjct: 118 NKITKIERELQQELGREPLDEEIAAKFGNAYTAEKVRYIRKINIDPISLDKQI--GKEND 175

Query: 198 SQWQDWL 204
           S + D++
Sbjct: 176 SSFSDFV 182


>gi|188589224|ref|YP_001920224.1| RNA polymerase sigma-D factor [Clostridium botulinum E3 str. Alaska
           E43]
 gi|251778902|ref|ZP_04821822.1| RNA polymerase sigma-D factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
 gi|188499505|gb|ACD52641.1| RNA polymerase sigma-D factor [Clostridium botulinum E3 str. Alaska
           E43]
 gi|243083217|gb|EES49107.1| RNA polymerase sigma-D factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
          Length = 242

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 56/244 (22%), Positives = 111/244 (45%), Gaps = 19/244 (7%)

Query: 48  SAAHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
               ++V  ++ LV  IA      +   +   ++VS G IGLM A+ KF+P++G + ++Y
Sbjct: 8   DVKEQIVKEYIPLVKYIASRIMIGKNKYMEYEDLVSYGIIGLMDAISKFNPDKGMKFSSY 67

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +   IK A+ + I ++  +         K     L R    ++++ +  L+   ++ IA+
Sbjct: 68  ASIRIKGAIIDQIRKNRPI--------TKGAMDKLNRYNSAIESLQNKLLREPNILEIAQ 119

Query: 165 KLNVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
            L +S  EV  +   +      SL  +I S D+  +          D        + E K
Sbjct: 120 YLELSLQEVSQIENYINHISMVSLENIIFSDDEEVNLLGII----EDKNSPSPEGELEEK 175

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            +  +L+ ++ +L  +E+ I          +TL+ + S   VS  RV Q+ AR+   ++E
Sbjct: 176 EQLEVLSDAIKLLKEKEQLILNLYYY--EKLTLKEIGSILSVSESRVCQLHARSISNLRE 233

Query: 283 SIQK 286
           +++K
Sbjct: 234 AMKK 237


>gi|266626024|ref|ZP_06118959.1| RNA polymerase sigma-E factor [Clostridium hathewayi DSM 13479]
 gi|288862073|gb|EFC94371.1| RNA polymerase sigma-E factor [Clostridium hathewayi DSM 13479]
          Length = 246

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 64/286 (22%), Positives = 116/286 (40%), Gaps = 68/286 (23%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           K + +   GEI    YI     +P  L+ + E  +        D SA   L+  +LRLVV
Sbjct: 20  KTLMMPKQGEI---HYIGGADILPAPLDNESEARVIAMLGGEDDQSAKSELIEHNLRLVV 76

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA  +    + + +++S G IGL++A+  F+P +  +LATY+   I+  +  Y+ R+  
Sbjct: 77  YIAKKFDNTSVGVEDLISIGTIGLIKAINTFNPGKNIKLATYASRCIENEILMYLRRNNK 136

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
                                                     K+ VS  E ++++     
Sbjct: 137 T-----------------------------------------KMEVSIDEPLNVD----- 150

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
                      D N     D L  D D    V+ +  E +  RN+L  ++S L+PRER+I
Sbjct: 151 ----------WDGNELLLSDILGTDED----VIYKDLETEVERNLLNSAISRLSPRERKI 196

Query: 243 FEARRLQ----ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            E R          +T + ++    +S+  + ++E +  K++++ I
Sbjct: 197 VELRFGLSDEEGEEMTQKEVADLLGISQSYISRLEKKIMKRLKKEI 242


>gi|55274953|gb|AAV49276.1| RNA polymerase subunit sigma-38 [Shigella flexneri 2a]
          Length = 193

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 51/196 (26%), Positives = 93/196 (47%), Gaps = 10/196 (5%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           + S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  +
Sbjct: 1   IESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTI 60

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
           +  I+     +++      K L   LR  +     ++           IA++L+    +V
Sbjct: 61  ERAIMNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDV 115

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             M        S++  +    +     +  L    D +E    +  +  + +  + + + 
Sbjct: 116 SRMLRLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWLF 170

Query: 234 VLNPRERRIFEARRLQ 249
            LN ++R +   R   
Sbjct: 171 ELNAKQREVLARRFGL 186


>gi|182435659|ref|YP_001823378.1| RNA polymerase sigma factor WhiG [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|326776293|ref|ZP_08235558.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Streptomyces cf.
           griseus XylebKG-1]
 gi|178464175|dbj|BAG18695.1| putative RNA polymerase sigma factor WhiG [Streptomyces griseus
           subsp. griseus NBRC 13350]
 gi|326656626|gb|EGE41472.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Streptomyces cf.
           griseus XylebKG-1]
          Length = 278

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 48/254 (18%), Positives = 105/254 (41%), Gaps = 16/254 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
            L + Y+  GD     +L+  +  LV  +A          +  ++ VS G  GL+ A++K
Sbjct: 31  ELWRSYKTTGDERLREQLILHYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEK 90

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD ER  +  TY++  I+ AM + + R+   +        + +      L+   +     
Sbjct: 91  FDIERAIKFETYAITRIRGAMIDEL-RALDWIPRSVRQKARNVERAYATLEAQFR----- 144

Query: 153 NLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
             +      +A ++ ++  E+ ++     LA   +L  L++   +   +    +    D 
Sbjct: 145 --RTPSEAEVASEMGIALEELHAVFSQLSLANVVALEELLHVGGEGGDRL-SLMDTLEDT 201

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                +E  E +  R +L R+++ L  RE+ +          +TL  + +   V+  RV 
Sbjct: 202 AADNPVEVAEDRELRRLLARAINTLPDREKTVVTLYYY--EGLTLAEIGNVLGVTESRVS 259

Query: 271 QIEARAFKKVQESI 284
           QI  ++  +++  +
Sbjct: 260 QIHTKSVLQLRAKL 273


>gi|255312647|gb|ACU01733.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|255312653|gb|ACU01736.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 53/205 (25%), Positives = 95/205 (46%), Gaps = 12/205 (5%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           L LVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LLLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           +     +++      K L   LR  +     ++           IA++L+    +V  M 
Sbjct: 61  MNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRML 115

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                  S++  +    +     +  L    D +E    +  +  + +  + + +  LN 
Sbjct: 116 RLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNA 170

Query: 238 RERRIFEARR--LQENPVTLENLSS 260
           ++R +   R   L     TLE++  
Sbjct: 171 KQREVLARRFGLLGYEAATLEDVGR 195


>gi|297195554|ref|ZP_06912952.1| sigma factor [Streptomyces pristinaespiralis ATCC 25486]
 gi|197721376|gb|EDY65284.1| sigma factor [Streptomyces pristinaespiralis ATCC 25486]
          Length = 291

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 44/237 (18%), Positives = 101/237 (42%), Gaps = 16/237 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            + L+  +L LV   A  +R     + +++  G IGL++A+ +F+  R    AT+++ +I
Sbjct: 65  RNTLIELNLALVKYAAGRFRNRAEQMEDIIQVGTIGLIKAIDRFELSREVEFATFAVPYI 124

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V +     + R+      L   +  ++           +A+ L + 
Sbjct: 125 IGEIKRFFRDTSWAVHVPRRLQELRID-----LAKAVDELSQKLDHTPTTAELAEHLGMD 179

Query: 170 ESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E E+I       G    S++  ++ +  + +      + D  G     +E  E       
Sbjct: 180 EEEIIEGVVASNGYTAGSIDMPMDDASDHGAVP----LSDRLGAPDAELEIAENVQ---A 232

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   +  L+ R+R+I + R  +E  +T   + +E  VS+  V ++ +R   +++E +
Sbjct: 233 LKPLIEELDERDRQILQMRFGEE--MTQSEIGAELGVSQMHVSRLLSRITARLREGL 287


>gi|55274894|gb|AAV49249.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 195

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 54/205 (26%), Positives = 95/205 (46%), Gaps = 12/205 (5%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL +  ++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLALIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           +     +++      K L   LR  +     ++           IA++L+    +V  M 
Sbjct: 61  MNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRML 115

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                  S++  +    +     +  L    D +E    +  +  + +  + + +  LN 
Sbjct: 116 RLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNA 170

Query: 238 RERRIFEARR--LQENPVTLENLSS 260
           ++R +   R   L     TLE++  
Sbjct: 171 KQREVLARRFGLLGYEAATLEDVGR 195


>gi|153487|gb|AAA26829.1| sigma factor (whiG) (put. alt.) (gtg start codon); putative
           [Streptomyces coelicolor]
          Length = 258

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 47/254 (18%), Positives = 107/254 (42%), Gaps = 16/254 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
            L + Y+  GD     +L+  +  LV  +A          +  ++ VS G  GL+ A++K
Sbjct: 11  ELWRSYKTTGDERLREQLILHYSPLVKYVAGRVSVGLPPNVEQADFVSSGVFGLIDAIEK 70

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD +R  +  TY++  I+ AM + + R+   +        + +      L+  L+     
Sbjct: 71  FDVDREIKFETYAITRIRGAMIDEL-RALDWIPRSVRQKARNVERAYATLEARLR----- 124

Query: 153 NLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
             +      +A ++ ++  ++ ++     LA   +L  L+++  +   +    +    D 
Sbjct: 125 --RTPSESEVAVEMGIAVEDLHAVFSQLSLANVVALEELLHAGGEGGGRL-SLMDTLEDT 181

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                +E  E +  R +L R+++ L  RE+ +          +TL  + +   V+  RV 
Sbjct: 182 AADNPVEVAEDRELRRLLARAINTLPEREKTVVTLYYY--EGLTLAEIGNVLGVTESRVS 239

Query: 271 QIEARAFKKVQESI 284
           QI  ++  +++  +
Sbjct: 240 QIHTKSVLQLRAKL 253


>gi|15615119|ref|NP_243422.1| sporulation sigma factor SigE [Bacillus halodurans C-125]
 gi|10175176|dbj|BAB06275.1| RNA polymerase sporulation mother cell-specific (early) sigma-29
           factor [Bacillus halodurans C-125]
          Length = 237

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 64/264 (24%), Positives = 109/264 (41%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE  L K+    GD +    L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 35  PPLSKEEEAHLLKKL-PSGDKAVRSMLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 93

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+                    +++   
Sbjct: 94  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN-------------------NKIRSE- 133

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                            ++ DE LN      D N     D L  
Sbjct: 134 ---------------------------------VSFDEPLN---IDWDGNELLLSDVLGT 157

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           D D    ++    E K  R +L +++  L  RE++I E R         T ++++    +
Sbjct: 158 DDD----IITRGIEEKVDRKLLMKALHTLTDREKQIMELRFGLAGGEEKTQKDVADLLGI 213

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++Q+   K V
Sbjct: 214 SQSYISRLEKRIIKRLQKEFNKMV 237


>gi|225389924|ref|ZP_03759648.1| hypothetical protein CLOSTASPAR_03674 [Clostridium asparagiforme
           DSM 15981]
 gi|225044004|gb|EEG54250.1| hypothetical protein CLOSTASPAR_03674 [Clostridium asparagiforme
           DSM 15981]
          Length = 223

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 60/272 (22%), Positives = 109/272 (40%), Gaps = 65/272 (23%)

Query: 18  RYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
            YI     +P  LE +EE  +        D  A   L+  +LRLVV IA  +    + + 
Sbjct: 8   HYIGGADILPAPLEPEEESRMIGMLSGEEDQKARAALIEHNLRLVVYIAKKFDNTSVGVE 67

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++S G IGL++A+  F P++  +LATY+   I+  +  Y+ R+                
Sbjct: 68  DLISIGTIGLIKAINTFKPDKNIKLATYASRCIENEILMYLRRNNKT------------- 114

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
                                       ++ VS  E ++++                D N
Sbjct: 115 ----------------------------RMEVSIDEPLNVD---------------WDGN 131

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL----QENP 252
                D L  D D    V+    E +  +N+L  ++S LNPRER+I E R          
Sbjct: 132 ELLLSDILGTDED----VIYHDIEDEIEKNLLNNAISRLNPRERKIVELRYGLTNEDGEE 187

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +T + ++    +S+  + ++E +  K++++ I
Sbjct: 188 MTQKEVADLLGISQSYISRLEKKIMKRLRKEI 219


>gi|5911749|emb|CAB55833.1| SigJ protein [Streptomyces coelicolor A3(2)]
          Length = 266

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 46/239 (19%), Positives = 107/239 (44%), Gaps = 18/239 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + L+  ++ LV   A  +R  G   + ++V  G IGL++A+ +F+  R     ++++ 
Sbjct: 39  ARNTLIEMNMSLVRFAAGRFRSRGPEEMEDIVQVGMIGLIKAIDRFELTREVEFTSFAVP 98

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +I   ++ +   +   V +     + R+     +L    + +     +      +++ ++
Sbjct: 99  YIVGEIKRFFRDTSWAVHVPRRLQEARV-----QLARATEELRSRLGRTPTTAELSELMS 153

Query: 168 VSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           + E EV+       G    SL+A IN S+   S   D++  D      V        +  
Sbjct: 154 LPEDEVVEARLAANGYNSASLDAAINGSEDGESALADFIGADDAALALV--------DDF 205

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + L   ++ L+ R+R+I   R ++E  +T +++     VS+  V ++ +R   +++E +
Sbjct: 206 HALAPMIAELDERDRQIIHWRFVEE--LTQKDIGERLGVSQMHVSRLISRLLARLREGM 262


>gi|254818833|ref|ZP_05223834.1| RNA polymerase sigma factor SigF [Mycobacterium intracellulare ATCC
           13950]
          Length = 242

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 46/259 (17%), Positives = 101/259 (38%), Gaps = 29/259 (11%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
             E +  A++            +V   L L   +A  +   G  + +++    +GLM AV
Sbjct: 9   PAESHEYARQ---------REYIVARCLPLADHVASHFARRGEGLEDLIQVARLGLMNAV 59

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
            +FDP +G     +++  +   ++ Y       +++     +  +     ++      + 
Sbjct: 60  NRFDPAKGPSFIGFAVPTMMGEVRRYFRDYSWGMRVPRRLRELHV-----QISRATADLA 114

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD----ESLNALINSSDKNSSQWQDWLVY 206
               +      +++ L V   E++   C +AGD    +SL+A + +    + +     V 
Sbjct: 115 QQLGRAPNAGELSQMLEVPREEIVE--CLVAGDAYRLDSLDAPLGADSSGTPRSVADSVG 172

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           D D Q        E    R  L   ++ L PRER +   R      +T   ++    VS+
Sbjct: 173 DIDPQ-------IEHITNREALRALVATLPPRERDVLRMRFF--ESMTQSQIAERIGVSQ 223

Query: 267 ERVRQIEARAFKKVQESIQ 285
            +V +I A   + +++ ++
Sbjct: 224 MQVSRILANTLRCLRDQLE 242


>gi|302874980|ref|YP_003843613.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium cellulovorans
           743B]
 gi|307690403|ref|ZP_07632849.1| sporulation sigma factor SigF [Clostridium cellulovorans 743B]
 gi|302577837|gb|ADL51849.1| RNA polymerase, sigma 28 subunit, SigF [Clostridium cellulovorans
           743B]
          Length = 265

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 40/247 (16%), Positives = 103/247 (41%), Gaps = 17/247 (6%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             L K   + GD  A + L+  ++ LV  I+  +   G    ++   G +GL++AV  F+
Sbjct: 31  VELIK-LAQGGDNEALNDLIKKNMPLVAAISKKFLNRGYEYDDIFQIGCMGLIKAVNNFN 89

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
            +   + +TY++  I   ++ ++     ++KI  +          ++L    + +T+   
Sbjct: 90  TDFNVKFSTYAVPMIMGEIKRFLRDDG-IIKISRSIK-----ATAKKLHYDRENLTNILN 143

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +   +  ++K   +S+ ++I         + L  +I+  D +     D +    +  + +
Sbjct: 144 REPTIEELSKYSGISKDDIIMATESSGSLQYLYDVIHQDDGSPVLLIDKISETGEDDKDM 203

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
           + +   +     + T        + R+I   R  ++   T   ++    +S+ +V +IE 
Sbjct: 204 IDKLALKDALLKLDT--------KSRQIILLRYFKD--KTQIQVAKMLGISQVQVSRIEK 253

Query: 275 RAFKKVQ 281
           +  K ++
Sbjct: 254 KVLKLMK 260


>gi|323486720|ref|ZP_08092041.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323692141|ref|ZP_08106384.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
 gi|323400101|gb|EGA92478.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323503715|gb|EGB19534.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
          Length = 246

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 60/274 (21%), Positives = 114/274 (41%), Gaps = 65/274 (23%)

Query: 18  RYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
            YI     +P  L  +EE  + K      D  A  +L+  +LRLVV IA  +    + + 
Sbjct: 31  HYIGGADILPAPLGSKEEAEVLKELGTERDAQAKSKLIEHNLRLVVYIAKKFDNTSVGVE 90

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++S G+IGL++A+  F+ ++  +LATY+   I+  +  Y+ R+                
Sbjct: 91  DLISIGSIGLIKAINTFNIDKNIKLATYASRCIENEILMYLRRNNKT------------- 137

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
                                       K+ VS  E ++++                D N
Sbjct: 138 ----------------------------KMEVSIDEPLNVD---------------WDGN 154

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ----ENP 252
                D L  D D    V+    E +  +++L  ++S LNPRE++I E R       E+ 
Sbjct: 155 ELLLSDILGTDED----VIYRDLEDEIEKSLLNTAISRLNPREQKIVELRFGLGTENEDE 210

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +T + ++    +S+  + ++E +  K++++ I K
Sbjct: 211 MTQKEVADLLGISQSYISRLEKKIMKRLKKEIVK 244


>gi|3929539|gb|AAC79983.1| HasR [Streptomyces ambofaciens]
 gi|117164812|emb|CAJ88361.1| putative sigma factor [Streptomyces ambofaciens ATCC 23877]
          Length = 281

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 45/239 (18%), Positives = 107/239 (44%), Gaps = 18/239 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + L+  ++ LV   A  +R  G   + ++V  G IGL++A+ +F+  R     ++++ 
Sbjct: 54  ARNTLIEMNMSLVRFAAGRFRSRGPEEMEDIVQVGMIGLIKAIDRFELTREVEFTSFAVP 113

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +I   ++ +   +   V +     + R+     +L    + +     +      +++ ++
Sbjct: 114 YIVGEIKRFFRDTSWAVHVPRRLQEARV-----QLARATEELRSRLGRNPTTKELSELMS 168

Query: 168 VSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           + E EV+       G    SL+A I+ S+   S   D++  D      V        +  
Sbjct: 169 LPEDEVVEARLAANGYNSASLDAAISGSEDGESALADFIGADDATLALV--------DDF 220

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + L   ++ L+ R+R+I   R ++E  +T +++     VS+  V ++ +R   +++E +
Sbjct: 221 HALAPMIAELDERDRQIIHWRFVEE--LTQKDIGERLGVSQMHVSRLISRLLARLREGM 277


>gi|329937605|ref|ZP_08287124.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
 gi|329303004|gb|EGG46892.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
          Length = 292

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 47/247 (19%), Positives = 110/247 (44%), Gaps = 16/247 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A + L+  ++ LV   A  +R  G  + ++V  G IGL++A+ +F+  R     ++++ +
Sbjct: 58  ARNTLIEMNMSLVRFAAGRFRNRGDDMEDIVQVGMIGLIKAIDRFEISREVEFTSFALPY 117

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I   ++ +   +   V +     + R+      L    + ++    +   V  +A  +N+
Sbjct: 118 IVGEIKRFFRDTTWAVHVPRRLQELRV-----ELAKAREELSSRLDRDPTVAELATLMNL 172

Query: 169 SESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            E +V+       G    SL+A ++  D++     + ++ D  G E   +   E  +   
Sbjct: 173 PEKDVVEAQIAANGYNSSSLDAALSGEDQDG----EAVLSDFIGAEDEAMGLVEDFHT-- 226

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L   ++ L+ R+RRI   R ++E   T  ++ ++   S+  V ++  R  ++++  +  
Sbjct: 227 -LAPLVAELSERDRRIIHMRFVEE--ATQADIGAQLGCSQMHVSRLIKRIIEQLRTGMLA 283

Query: 287 QVELSSS 293
            V+   S
Sbjct: 284 DVDRVES 290


>gi|29827628|ref|NP_822262.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29604728|dbj|BAC68797.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 295

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 46/239 (19%), Positives = 105/239 (43%), Gaps = 12/239 (5%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
            + L+  +L LV   A  +R  G   + ++V  G IGL++A+ +F+  R    A++++ +
Sbjct: 65  RNTLIEMNLTLVRYAASRFRSRGSGEMEDIVQVGTIGLIKAIDRFELSREVEFASFAVPY 124

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I   ++ +   +   V +     + R+      L      ++    +   V  +A+ +++
Sbjct: 125 IVGEIKRFFRDTSWAVHVPRRLQEARV-----ELAQATDELSRRTGRTPTVRELAELMSL 179

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +E EVI          S ++L  S   + S   + ++ D  G+E+  +E  E  +    L
Sbjct: 180 TEEEVIEARKAANAYRS-SSLDASLSGDGSADNESVLADFIGREETALELIEDMHS---L 235

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              ++ L+ R+RRI   R + E  +T   +     +S+  V ++  +    ++  +  +
Sbjct: 236 APLVAQLDERDRRILHLRFVDE--LTQAQIGERLGISQMHVSRLINKIITTLRAGLLSE 292


>gi|312792676|ref|YP_004025599.1| RNA polymerase, sigma 28 subunit, flia/whig [Caldicellulosiruptor
           kristjanssonii 177R1B]
 gi|312179816|gb|ADQ39986.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Caldicellulosiruptor
           kristjanssonii 177R1B]
          Length = 246

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 56/258 (21%), Positives = 119/258 (46%), Gaps = 23/258 (8%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKF 93
           L +++ +  D     +L+  ++ LV  +A     Y G  +   ++VS G+IGL+ A++KF
Sbjct: 6   LWEKFIKTKDPKIKEQLIIKYMPLVKLVAGRMAIYFGGNVEYDDLVSYGSIGLLDAIEKF 65

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D ++G +  TY+   IK A+ + +        +  +  QK       +         +  
Sbjct: 66  DSQKGVKFETYAYTRIKGAIIDCVRSQDF---LPRSIRQK------AKEIEKAYVEIERE 116

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQ 211
            K      +AK++ +S +E+  +  R++     SL++ +    + + + +   + D   Q
Sbjct: 117 GKTPTDQEVAKRVGISVNELQKLQERISSGMIISLDSFL----EQNYESKIGGLEDFVSQ 172

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
            +  IE EE    + +L + +  L   ER +      +E  ++++ ++    VS  RV Q
Sbjct: 173 PEHFIENEEL---KEVLRQQIENLMENERMVIVLYYYEE--LSIKEIAKVLGVSESRVSQ 227

Query: 272 IEARAFKKVQESIQKQVE 289
           +  RA  K++ ++QK +E
Sbjct: 228 LHTRALLKLKAALQKYLE 245


>gi|256392583|ref|YP_003114147.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Catenulispora acidiphila DSM 44928]
 gi|256358809|gb|ACU72306.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Catenulispora acidiphila DSM 44928]
          Length = 262

 Score =  136 bits (343), Expect = 4e-30,   Method: Composition-based stats.
 Identities = 41/237 (17%), Positives = 100/237 (42%), Gaps = 17/237 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              ++  ++     +A  +R  G   +++     +GL++AV  FDP+ G    TY+   I
Sbjct: 38  REFVIGEYMSYARYVAGRFRQRGESQADLEQVAYLGLVKAVDNFDPDYGAAFLTYATPMI 97

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V +     +  L      ++   + +T           IA++L++S
Sbjct: 98  AGEVRRHFRDTTWDVHVPRRVQENALA-----VRAAERELTQQLGHAPSAAQIAERLDLS 152

Query: 170 ESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
             EV       A     SL+  +  +D + +   + +  D  G + V+         R  
Sbjct: 153 ADEVAEAYEASAAHHTASLDVPVAMADGDGASMGELMGDDDPGYDLVV--------DREA 204

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   ++ L+PR++RI   +  +   ++   + +E  VS+ +V ++ ++   ++++ +
Sbjct: 205 LKPLLAELSPRDKRILLMKFFRN--MSQAQIGAELGVSQMQVSRLLSQILGRLRDQV 259


>gi|167766746|ref|ZP_02438799.1| hypothetical protein CLOSS21_01252 [Clostridium sp. SS2/1]
 gi|167711500|gb|EDS22079.1| hypothetical protein CLOSS21_01252 [Clostridium sp. SS2/1]
          Length = 232

 Score =  136 bits (342), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 40/239 (16%), Positives = 103/239 (43%), Gaps = 16/239 (6%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R  + G+ +A  +++ +++ L+  +   +   G    ++   G+IGLM+AV KFD     
Sbjct: 9   RLTKEGNEAAREQIILNNVGLIWSVVRRFTNRGYESEDLFQIGSIGLMKAVDKFDLSYDV 68

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY++  I   ++ ++     ++K+  +  +     N+ ++    +       +   +
Sbjct: 69  KFSTYAVPMITGEIRRFLRDDG-MIKVSRSLKE-----NVYKIMKAREKFCQQYQREATI 122

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I++   ++  E+++        ES++      D +     D L    +  E+V+    
Sbjct: 123 EEISEITKITREEIVTSLEASNEVESIHQSAYQKDGSEISLLDKLSKGENESEKVV---- 178

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                  +L  +M  L  +E+++   R       T + ++  F +S+ +V +I+ +  K
Sbjct: 179 ----DHVLLKEAMKHLEQKEQQMIYYRYF--EGKTQQEIAKIFHISQVQVSRIQKKILK 231


>gi|325973333|ref|YP_004250397.1| RNA polymerase sigma factor rpoD [Mycoplasma suis str. Illinois]
 gi|325989768|ref|YP_004249467.1| RNA polymerase sigma factor [Mycoplasma suis KI3806]
 gi|323574853|emb|CBZ40513.1| RNA polymerase sigma factor [Mycoplasma suis]
 gi|323651935|gb|ADX98017.1| RNA polymerase sigma factor rpoD [Mycoplasma suis str. Illinois]
          Length = 530

 Score =  136 bits (342), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 57/241 (23%), Positives = 103/241 (42%), Gaps = 12/241 (4%)

Query: 28  MLEKQEEYVLAKRYREHGDLS-AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           ML   EE  +A+        S A  +L+TS+LRLV+ +A  Y   G  + +++ EG  GL
Sbjct: 214 MLTADEEKKIAQLMDIPEKRSFAEKQLMTSNLRLVISVAKKYLNCGFNLGDLIQEGVFGL 273

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
            +A+ KFD + G + +TY+ WWI+ A+   I     +++I     +  +   + + +  L
Sbjct: 274 RKAITKFDYKFGNKFSTYATWWIRQAITRSIADQSKIIRIPVHMME--VINKMTKAEKEL 331

Query: 147 QAITDNNLKPEQVVAIAKKLN--VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
              T N    E++ +  +K     +  ++  +        SL+  I +++  SS + D++
Sbjct: 332 VLKTGNPPTLEELSSEMQKYGTQFTPIKISEIKKINVDLVSLDKPILNNE--SSNFADFV 389

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQEN--PVTLENLSSE 261
             D D  E        +      L   +   L   E  I        N    T+E +S  
Sbjct: 390 REDGD--EANPEWIASKNIYEEKLKSLLQETLKKDEYLILALHFGLNNQESHTVEQISQL 447

Query: 262 F 262
           F
Sbjct: 448 F 448


>gi|291448094|ref|ZP_06587484.1| sporulation sigma factor [Streptomyces roseosporus NRRL 15998]
 gi|1655819|gb|AAB41960.1| sporulation sigma factor [Streptomyces filamentosus]
 gi|291351041|gb|EFE77945.1| sporulation sigma factor [Streptomyces roseosporus NRRL 15998]
          Length = 278

 Score =  136 bits (342), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 48/254 (18%), Positives = 105/254 (41%), Gaps = 16/254 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
            L + Y+  GD     +L+  +  LV  +A          +  ++ VS G  GL+ A++K
Sbjct: 31  ELWRSYKTTGDERLREQLILHYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEK 90

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD ER  +  TY++  I+ AM + + R+   +        + +      L+   +     
Sbjct: 91  FDIERAIKFETYAITRIRGAMIDEL-RALDWIPRSVRQKARNVERAYATLEAQFR----- 144

Query: 153 NLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
             +      +A ++ ++  E+ ++     LA   +L  L++   +   +    +    D 
Sbjct: 145 --RTPSEAEVASEMGIALEELHAVFSQLSLANVVALEELLHVGGEGGDRL-SLMDTLEDT 201

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                +E  E +  R +L R+++ L  RE+ +          +TL  + +   V+  RV 
Sbjct: 202 AADNPVEVAEDRELRRLLARAINTLPDREKTVVTLYYY--EGLTLAEIGNVLGVTESRVS 259

Query: 271 QIEARAFKKVQESI 284
           QI  ++  +++  +
Sbjct: 260 QIHTKSVLQLRAKL 273


>gi|222528460|ref|YP_002572342.1| Sig B/F/G subfamily RNA polymerase sigma-28 factor
           [Caldicellulosiruptor bescii DSM 6725]
 gi|222455307|gb|ACM59569.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor bescii DSM 6725]
          Length = 256

 Score =  136 bits (342), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 51/245 (20%), Positives = 114/245 (46%), Gaps = 17/245 (6%)

Query: 29  LEKQEEY--VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           LE  +E    L + Y++   +   + LV  +L +   IA  + G G+   ++     I L
Sbjct: 8   LEIDDEKIDRLFEEYQKTKSIELRNELVNKYLYIAEIIAKKFVGRGIDYEDLYQVACIAL 67

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           + AV++F+P +G++  +++   I   ++ Y     S++++      +R++    ++K   
Sbjct: 68  INAVERFEPNKGYKFTSFATPTIMGEIKRYFRDRASIIRLP-----RRIYETSAKIKLAT 122

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           + ++    +P +V  IA+ LN+S  EV+ +      + S N L  S D+   + ++  + 
Sbjct: 123 EVLSTKLKRPPKVEEIAQHLNMSAEEVLEVM-----EASNNYLPQSLDQTMYEDEEMTLG 177

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           D  G+     E   +      + +++  L+P ER   + R  +E   T + ++ E  VS+
Sbjct: 178 DVLGKSD---ENILQVENVEAVKKAIERLSPFEREFVQKRFFEE--KTQKEIAEEMNVSQ 232

Query: 267 ERVRQ 271
             + +
Sbjct: 233 MYISR 237


>gi|215432251|ref|ZP_03430170.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis
           EAS054]
 gi|289755409|ref|ZP_06514787.1| stress response/stationary phase sigma factor SigF [Mycobacterium
           tuberculosis EAS054]
 gi|289695996|gb|EFD63425.1| stress response/stationary phase sigma factor SigF [Mycobacterium
           tuberculosis EAS054]
          Length = 261

 Score =  136 bits (342), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 39/236 (16%), Positives = 94/236 (39%), Gaps = 14/236 (5%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             ++V   L L   IA  + G G P  +++    +GL+ A  +FD + G    ++++  I
Sbjct: 40  RDKIVQRCLPLADHIARRFEGRGEPRDDLIQVARVGLVNAAVRFDMKTGSDFVSFAVPTI 99

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   VK+     +  L     RL      ++    +      +A +L + 
Sbjct: 100 MGEVRRHFRDNSWSVKVPRRLKELHL-----RLGTATADLSQRLGRAPSASELAAELGMD 154

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
            +EVI      +   +L+        + ++     + D D          ++   R +L 
Sbjct: 155 RAEVIEGLLAGSSYHTLSIDSGGGSDDDARAITDTLGDVDA-------GLDQIENREVLR 207

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             +  L  RER +   R    + +T   ++    +S+  V ++ A++  ++++ ++
Sbjct: 208 PLLEALPERERTVLVLRFF--DSMTQTQIAERVGISQMHVSRLLAKSLARLRDQLE 261


>gi|23098930|ref|NP_692396.1| sporulation sigma factor SigE [Oceanobacillus iheyensis HTE831]
 gi|22777158|dbj|BAC13431.1| stage II sporulation protein GB (RNA polymerase
           sporulation-specific sigma E factor) [Oceanobacillus
           iheyensis HTE831]
          Length = 239

 Score =  136 bits (342), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 63/264 (23%), Positives = 111/264 (42%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L KQEE  L  R  + GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLSKQEEQELLIRLPK-GDKAARAMLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+                    +LK   
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN-------------------NKLKSE- 135

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                            ++ DE LN      D N     D +  
Sbjct: 136 ---------------------------------VSFDEPLN---IDWDGNELLLSDVMGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           + D    ++ +  E    + +L  ++  LN RE++I E R     E   T ++++    +
Sbjct: 160 EED----IITKNLESTVDKTLLKSALEKLNAREKQIMELRFGLIGEEEKTQKDVADMLGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E +  +++++   K V
Sbjct: 216 SQSYISRLEKKIIRRLKKEFNKMV 239


>gi|260899647|ref|ZP_05908042.1| RNA polymerase sigma-C factor [Vibrio parahaemolyticus AQ4037]
 gi|308106738|gb|EFO44278.1| RNA polymerase sigma-C factor [Vibrio parahaemolyticus AQ4037]
          Length = 120

 Score =  136 bits (342), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 55/120 (45%), Positives = 80/120 (66%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M ++   + +  +  L  YI  +   PML   EE  LA+R    G++ AA  L+ SHLR 
Sbjct: 1   MTKEAYPMALVTQDSLDSYIRSVNSYPMLTADEERELAERLHYKGEIEAAKGLILSHLRF 60

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV +A GY GYGLP++++V EGNIGLM+AVK+F+PE G RL ++++ WIKA + EY+LR+
Sbjct: 61  VVHVARGYSGYGLPMADLVQEGNIGLMKAVKRFNPEVGVRLVSFAVHWIKAEIHEYVLRN 120


>gi|332982149|ref|YP_004463590.1| RNA polymerase sigma-29 subunit SigE [Mahella australiensis 50-1
           BON]
 gi|332699827|gb|AEE96768.1| RNA polymerase, sigma 29 subunit, SigE [Mahella australiensis 50-1
           BON]
          Length = 239

 Score =  136 bits (342), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 59/260 (22%), Positives = 108/260 (41%), Gaps = 62/260 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EE  + KR  + GD S    L+  +LRLVV IA  +   G+P+ +++S G IGL
Sbjct: 36  PPLSADEEQDIMKRLSD-GDESVKSILIERNLRLVVYIARRFENTGIPVEDLISIGTIGL 94

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FDP++  +LATY+   I+  +  Y+ R+    K   +                 
Sbjct: 95  IKAVNTFDPDKKIKLATYASRCIENEILMYLRRNCRFNKTEVSI---------------- 138

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                               DE LN      D N     D L  
Sbjct: 139 ------------------------------------DEPLNT---DWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEV 264
           + D    ++ ++ +    + +L  +++ L+ RE+RI + R   ++    T + ++    +
Sbjct: 160 EVDLVYNIIEDEVD----KQLLNIALNKLSSREQRIMQLRFGLDDGVEKTQKEVADMLGI 215

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+  + ++E R  K++++ I
Sbjct: 216 SQSYISRLEKRIIKRLKKEI 235


>gi|238916673|ref|YP_002930190.1| RNA polymerase sporulation-specific sigma factor [Eubacterium
           eligens ATCC 27750]
 gi|238872033|gb|ACR71743.1| RNA polymerase sporulation-specific sigma factor [Eubacterium
           eligens ATCC 27750]
          Length = 250

 Score =  136 bits (342), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 59/288 (20%), Positives = 112/288 (38%), Gaps = 68/288 (23%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           KN  ++  G++    YI     +P  L   EE    +      D  A H L+  +LRLVV
Sbjct: 24  KNFCLLKQGDV---HYIGGTDILPAPLGASEEQDAIEALGTASDAEAKHTLIEHNLRLVV 80

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA  +   G+ + +++S G IGL++A+  +D ++  +LATY+   I+  +  Y+ R+  
Sbjct: 81  YIAKKFDNTGVGVEDLISIGTIGLIKAINSYDKDKNIKLATYASRCIENEILMYLRRNS- 139

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
                             ++K                                    ++ 
Sbjct: 140 ------------------KIKAE----------------------------------VSI 147

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
           DE LN      D N     D +  D D    ++    E +    ML R+++ L  RER I
Sbjct: 148 DEPLN---VDWDGNELLLSDIIGTDED----IIYRDIETEVECKMLKRAINQLPERERII 200

Query: 243 FEARRL----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + R           T + ++    +S+  + ++E +  +++++ + K
Sbjct: 201 VDLRFGLSSEDGEEKTQKEVADMLGISQSYISRLEKKIMRQLRKEMVK 248


>gi|325860122|ref|ZP_08173248.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           denticola CRIS 18C-A]
 gi|325482407|gb|EGC85414.1| RNA polymerase sigma factor RpoD family protein [Prevotella
           denticola CRIS 18C-A]
          Length = 228

 Score =  136 bits (342), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 63/270 (23%), Positives = 109/270 (40%), Gaps = 47/270 (17%)

Query: 17  SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
            +YI EI     L   EE  LA+R +  GD  A  +L  ++L+ VV +A  YR  GL   
Sbjct: 5   EKYIEEIAGGQPLSDVEERTLAERIKV-GDAHALEKLTKANLKYVVSLAHQYRNRGLGED 63

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++SEGNIG+M A ++FD  RG R   ++  +I+ AM+E I     L ++      +   
Sbjct: 64  DLISEGNIGMMHAAQRFDGTRGVRFVVFAAPYIRKAMEEAIKEQAVLYRLPRNEKNRS-- 121

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
                                                     + +   S++  +     N
Sbjct: 122 ----------------------------------------EQKRSHAISIDQPVPVGSSN 141

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV-TL 255
           +   Q+ L  D+        E+  ++     + + + VLN RER++            T+
Sbjct: 142 NFTLQNVLENDNAPHAD---EQLNQEILSAEIQKGLGVLNERERQVITCLYGLSGIHYTM 198

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              +    + RERVRQI   A +K+ + ++
Sbjct: 199 AEAAEHMGLKRERVRQIRDGALRKLHKRMK 228


>gi|28211312|ref|NP_782256.1| RNA polymerase sigma factor for flagellar operon fliA [Clostridium
           tetani E88]
 gi|28203752|gb|AAO36193.1| RNA polymerase sigma factor for flagellar operon fliA [Clostridium
           tetani E88]
          Length = 242

 Score =  136 bits (342), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 57/244 (23%), Positives = 109/244 (44%), Gaps = 19/244 (7%)

Query: 48  SAAHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
                LV  ++ LV  IA      +   +   ++V  G +GLM A++KFDP +G + +TY
Sbjct: 8   DVKEGLVKKYIPLVKYIASRVIIGKTKYIDYDDLVGYGMLGLMDAMQKFDPSKGMKFSTY 67

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +   I+ +M + + R   +         K     L R    ++ +   N K  ++  +AK
Sbjct: 68  ASIRIRGSMIDELRRISPI--------SKSAMDKLNRYNEAVEKLQMKNFKEPKLEEVAK 119

Query: 165 KLNVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           +L++S  EV  +   +      SL   I S +++ S     +  +    E++L EKE   
Sbjct: 120 ELDMSLKEVAQIENYINYISIVSLEDFIFSDEEDMSLMATVVDKNSPSPEKILEEKELI- 178

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
                L ++++ L  R+R +          +TL+ +    +VS  RV Q+ +RA   ++ 
Sbjct: 179 ---EYLEKAINKLKERDRIVLSLYYY--ERLTLKEIGKVLDVSESRVCQLHSRAIVHLRS 233

Query: 283 SIQK 286
            ++K
Sbjct: 234 ELKK 237


>gi|167464139|ref|ZP_02329228.1| DNA-directed RNA polymerase sigma subunit D [Paenibacillus larvae
           subsp. larvae BRL-230010]
 gi|322382365|ref|ZP_08056272.1| RNA polymerase sigma factor SigD-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321153718|gb|EFX46093.1| RNA polymerase sigma factor SigD-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 262

 Score =  136 bits (342), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 53/256 (20%), Positives = 110/256 (42%), Gaps = 20/256 (7%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKK 92
            L K ++E G L A   L+  +L LV  ++          +   ++ S G +GLM AV+K
Sbjct: 13  ELWKAWKEAGCLEAKQSLLEQYLPLVDYVSSRMSNGLPRNVAKEDLASFGVLGLMDAVEK 72

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  RG +  TY+ W I  A+ + + R    V        + L    ++++   Q +  +
Sbjct: 73  FDHTRGLQFETYASWRILGAVIDGL-RQGDWVP-------RSLREKAKKIEDAYQKLEQH 124

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDG 210
            L+      I++ L V E E   M   +      S++  I   ++ S      L+ +   
Sbjct: 125 YLRTVTDAEISEYLGVEEEEFRQMLQEINVTSICSVDDPIK--EEESETRLSLLIDEKAK 182

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
             +  + +      +  L R++  L  +E+ +      +E  ++L  ++    +S  R+ 
Sbjct: 183 NPEYKVNEFYL---KETLARAIEKLTEKEKIVVSLFYFEE--LSLSEIAEVMSLSPSRIS 237

Query: 271 QIEARAFKKVQESIQK 286
           Q+ ++A  +++ ++ K
Sbjct: 238 QLHSKAILRLRGTLNK 253


>gi|153953960|ref|YP_001394725.1| sporulation sigma factor SigK [Clostridium kluyveri DSM 555]
 gi|219854574|ref|YP_002471696.1| hypothetical protein CKR_1231 [Clostridium kluyveri NBRC 12016]
 gi|146346841|gb|EDK33377.1| SigE1 [Clostridium kluyveri DSM 555]
 gi|219568298|dbj|BAH06282.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 233

 Score =  136 bits (342), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 60/279 (21%), Positives = 110/279 (39%), Gaps = 63/279 (22%)

Query: 9   IVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           I+   + ++ Y+      P  L  +EE    ++ +E GDL A   LV  +LRLV  I   
Sbjct: 10  ILGNVVFMTAYVTNNSSFPQPLNDEEERYYLRKLKE-GDLLAKSILVERNLRLVAHIVKK 68

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y   G  + +++S G +GL++A+  FD  +G RLATY+   I+  +   I  +       
Sbjct: 69  YSYPGKDVDDLISIGTVGLIKAIDSFDSCKGTRLATYAAKCIENEILMLIRNN------- 121

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
                       +++K                              + +   +  D    
Sbjct: 122 ------------KKIKNE----------------------------VYLQDPIGVD---- 137

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
                 + N     D L  D D   +++ +K + K   + +    + L+ RE+ + E R 
Sbjct: 138 -----KEGNEISLMDVLSSDEDSIIEIVEQKIQVKKLYSKIN---TCLSQREKSVVEMRY 189

Query: 248 --LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             L+  P T   ++    +SR  V +IE +A KK+ + +
Sbjct: 190 GLLEGKPKTQREIAKILGISRSYVSRIEKKALKKLYKEL 228


>gi|319649653|ref|ZP_08003809.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
 gi|317398815|gb|EFV79497.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
          Length = 239

 Score =  136 bits (342), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 60/264 (22%), Positives = 112/264 (42%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE +L  +  + GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLSKEEEEMLLIKLPK-GDKAARSILIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+                    +++   
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN-------------------NKIRSE- 135

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                            ++ DE LN      D N     D L  
Sbjct: 136 ---------------------------------VSFDEPLN---IDWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEV 264
           + D    ++ +  E    + +L +++  L+ RE++I E R         T ++++    +
Sbjct: 160 EDD----IITKDLEANVDKKLLLKALHQLSDREKQIMELRFGLGSGEEKTQKDVADMLGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 216 SQSYISRLEKRIIKRLKKEFNKMV 239


>gi|15610422|ref|NP_217803.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis H37Rv]
 gi|15842877|ref|NP_337914.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis
           CDC1551]
 gi|31794466|ref|NP_856959.1| RNA polymerase sigma factor SigF [Mycobacterium bovis AF2122/97]
 gi|121639175|ref|YP_979399.1| RNA polymerase sigma factor SigF [Mycobacterium bovis BCG str.
           Pasteur 1173P2]
 gi|148663149|ref|YP_001284672.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis H37Ra]
 gi|148824488|ref|YP_001289242.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis F11]
 gi|167968918|ref|ZP_02551195.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis H37Ra]
 gi|215405299|ref|ZP_03417480.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis
           02_1987]
 gi|215413164|ref|ZP_03421865.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis
           94_M4241A]
 gi|215428770|ref|ZP_03426689.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis T92]
 gi|215447591|ref|ZP_03434343.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis T85]
 gi|218755069|ref|ZP_03533865.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis GM
           1503]
 gi|219559346|ref|ZP_03538422.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis T17]
 gi|224991668|ref|YP_002646357.1| RNA polymerase sigma factor [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|253800329|ref|YP_003033330.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis KZN
           1435]
 gi|254233896|ref|ZP_04927221.1| alternate RNA polymerase sigma factor sigF [Mycobacterium
           tuberculosis C]
 gi|254365909|ref|ZP_04981954.1| alternate RNA polymerase sigma factor sigF [Mycobacterium
           tuberculosis str. Haarlem]
 gi|254552388|ref|ZP_05142835.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis
           '98-R604 INH-RIF-EM']
 gi|260188335|ref|ZP_05765809.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis
           CPHL_A]
 gi|260202448|ref|ZP_05769939.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis T46]
 gi|260206638|ref|ZP_05774129.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis K85]
 gi|289444868|ref|ZP_06434612.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis T46]
 gi|289448975|ref|ZP_06438719.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           CPHL_A]
 gi|289555564|ref|ZP_06444774.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis KZN
           605]
 gi|289571513|ref|ZP_06451740.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis T17]
 gi|289576006|ref|ZP_06456233.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis K85]
 gi|289747104|ref|ZP_06506482.1| sigma factor SigF [Mycobacterium tuberculosis 02_1987]
 gi|289751981|ref|ZP_06511359.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis T92]
 gi|289759427|ref|ZP_06518805.1| sigma factor SigF [Mycobacterium tuberculosis T85]
 gi|289763474|ref|ZP_06522852.1| alternate RNA polymerase sigma factor sigF [Mycobacterium
           tuberculosis GM 1503]
 gi|294993773|ref|ZP_06799464.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis 210]
 gi|297635940|ref|ZP_06953720.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis KZN
           4207]
 gi|297732937|ref|ZP_06962055.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis KZN
           R506]
 gi|298526762|ref|ZP_07014171.1| sigma factor SigF [Mycobacterium tuberculosis 94_M4241A]
 gi|306777615|ref|ZP_07415952.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu001]
 gi|306782337|ref|ZP_07420674.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu002]
 gi|306786159|ref|ZP_07424481.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu003]
 gi|306790527|ref|ZP_07428849.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu004]
 gi|306795048|ref|ZP_07433350.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu005]
 gi|306799245|ref|ZP_07437547.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu006]
 gi|306805094|ref|ZP_07441762.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu008]
 gi|306809281|ref|ZP_07445949.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu007]
 gi|306969383|ref|ZP_07482044.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu009]
 gi|306973735|ref|ZP_07486396.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu010]
 gi|307081445|ref|ZP_07490615.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu011]
 gi|307086048|ref|ZP_07495161.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu012]
 gi|313660269|ref|ZP_07817149.1| RNA polymerase sigma factor SigF [Mycobacterium tuberculosis KZN
           V2475]
 gi|5917771|gb|AAD56032.1|AF181975_3 sigma factor SigF [Mycobacterium bovis]
 gi|1877341|emb|CAB07069.1| ALTERNATE RNA POLYMERASE SIGMA FACTOR SIGF [Mycobacterium
           tuberculosis H37Rv]
 gi|13883208|gb|AAK47728.1| stress response/stationary phase sigma factor SigF [Mycobacterium
           tuberculosis CDC1551]
 gi|31620062|emb|CAD95406.1| PROBABLE RNA POLYMERASE SIGMA FACTOR SIGF [Mycobacterium bovis
           AF2122/97]
 gi|121494823|emb|CAL73304.1| Probable rna polymerase sigma factor sigF [Mycobacterium bovis BCG
           str. Pasteur 1173P2]
 gi|124599425|gb|EAY58529.1| alternate RNA polymerase sigma factor sigF [Mycobacterium
           tuberculosis C]
 gi|134151422|gb|EBA43467.1| alternate RNA polymerase sigma factor sigF [Mycobacterium
           tuberculosis str. Haarlem]
 gi|148507301|gb|ABQ75110.1| sigma factor SigF [Mycobacterium tuberculosis H37Ra]
 gi|148723015|gb|ABR07640.1| alternate RNA polymerase sigma factor sigF [Mycobacterium
           tuberculosis F11]
 gi|224774783|dbj|BAH27589.1| RNA polymerase sigma factor [Mycobacterium bovis BCG str. Tokyo
           172]
 gi|253321832|gb|ACT26435.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis KZN
           1435]
 gi|289417787|gb|EFD15027.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis T46]
 gi|289421933|gb|EFD19134.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           CPHL_A]
 gi|289440196|gb|EFD22689.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis KZN
           605]
 gi|289540437|gb|EFD45015.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis K85]
 gi|289545267|gb|EFD48915.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis T17]
 gi|289687632|gb|EFD55120.1| sigma factor SigF [Mycobacterium tuberculosis 02_1987]
 gi|289692568|gb|EFD59997.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis T92]
 gi|289710980|gb|EFD74996.1| alternate RNA polymerase sigma factor sigF [Mycobacterium
           tuberculosis GM 1503]
 gi|289714991|gb|EFD79003.1| sigma factor SigF [Mycobacterium tuberculosis T85]
 gi|298496556|gb|EFI31850.1| sigma factor SigF [Mycobacterium tuberculosis 94_M4241A]
 gi|308214036|gb|EFO73435.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu001]
 gi|308325087|gb|EFP13938.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu002]
 gi|308329308|gb|EFP18159.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu003]
 gi|308333139|gb|EFP21990.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu004]
 gi|308336826|gb|EFP25677.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu005]
 gi|308340659|gb|EFP29510.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu006]
 gi|308344393|gb|EFP33244.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu007]
 gi|308348397|gb|EFP37248.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu008]
 gi|308353234|gb|EFP42085.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu009]
 gi|308356974|gb|EFP45825.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu010]
 gi|308360831|gb|EFP49682.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu011]
 gi|308364515|gb|EFP53366.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           SUMu012]
 gi|323718155|gb|EGB27337.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis
           CDC1551A]
 gi|326902486|gb|EGE49419.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis W-148]
 gi|328460063|gb|AEB05486.1| RNA polymerase sigma factor sigF [Mycobacterium tuberculosis KZN
           4207]
          Length = 261

 Score =  136 bits (342), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 39/236 (16%), Positives = 94/236 (39%), Gaps = 14/236 (5%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             ++V   L L   IA  + G G P  +++    +GL+ A  +FD + G    ++++  I
Sbjct: 40  RDKIVQRCLPLADHIARRFEGRGEPRDDLIQVARVGLVNAAVRFDVKTGSDFVSFAVPTI 99

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   VK+     +  L     RL      ++    +      +A +L + 
Sbjct: 100 MGEVRRHFRDNSWSVKVPRRLKELHL-----RLGTATADLSQRLGRAPSASELAAELGMD 154

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
            +EVI      +   +L+        + ++     + D D          ++   R +L 
Sbjct: 155 RAEVIEGLLAGSSYHTLSIDSGGGSDDDARAITDTLGDVDA-------GLDQIENREVLR 207

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             +  L  RER +   R    + +T   ++    +S+  V ++ A++  ++++ ++
Sbjct: 208 PLLEALPERERTVLVLRFF--DSMTQTQIAERVGISQMHVSRLLAKSLARLRDQLE 261


>gi|310657328|ref|YP_003935049.1| RNA polymerase sigma-37 factor (sigma-b) [Clostridium sticklandii
           DSM 519]
 gi|308824106|emb|CBH20144.1| RNA polymerase sigma-37 factor (sigma-B) [Clostridium sticklandii]
          Length = 273

 Score =  136 bits (342), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 47/254 (18%), Positives = 112/254 (44%), Gaps = 16/254 (6%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             L   Y E+  +   + LV  HL +   ++  +   G+   ++    ++GL+ A+++FD
Sbjct: 31  KELFLIYSENKAIELRNELVKRHLYIAEILSKKFLNKGIEYEDIYQVASLGLIFAIERFD 90

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +GF  ++++   I   +++Y       +++     +  L   +   K +LQ       
Sbjct: 91  VSKGFEFSSFATPTIIGEIKKYFRDKGWSIRVPRRIQE--LSKKVNTAKSYLQQELH--- 145

Query: 155 KPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +  ++  IAK L+ +E EV+       +   +SL+   ++   +       LV D D   
Sbjct: 146 RVPKIEDIAKYLDCTEEEVLEAIEASHVYKPKSLDLSYDNEGDDKDILLLDLVGDEDKSF 205

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
            ++         ++ +  ++S LN  E +I + R  +    T  +++++  VS+  V ++
Sbjct: 206 NMI-------ENKDFIENALSKLNEIETKIIKDRFFKN--KTQMHVANDLGVSQMTVSRM 256

Query: 273 EARAFKKVQESIQK 286
           E +   K+++  +K
Sbjct: 257 EKKILAKLKKDYEK 270


>gi|332981685|ref|YP_004463126.1| RNA polymerase sigma-27/28 subunit,RpsK/SigK [Mahella australiensis
           50-1 BON]
 gi|332699363|gb|AEE96304.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Mahella
           australiensis 50-1 BON]
          Length = 236

 Score =  136 bits (342), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 61/275 (22%), Positives = 98/275 (35%), Gaps = 63/275 (22%)

Query: 16  LSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           L+ Y+      P  L  +EE    + Y E GD  A + L+  +LRLV  I   Y      
Sbjct: 19  LTSYVSNNNSFPQPLSYEEERHYLELY-EQGDQQAKNILIEHNLRLVAHIVKKYNNAVKD 77

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
             +++S G IGL++ +  FD  +G RLATY+   I+  +  Y+  S              
Sbjct: 78  PEDLISIGTIGLIKGITTFDSNKGTRLATYAARCIENEILMYVRAS-------------- 123

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
                                              E + + +   +  D          +
Sbjct: 124 ---------------------------------KKEKKEVFLQEPIGTD---------KE 141

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENP 252
            N     D L  D D     + +K +      +  +  SVL  RER I E R      N 
Sbjct: 142 GNEVTLIDILGTDEDTITDQVSDKMQIA---KLYKKMGSVLKDRERLILELRYGLINGND 198

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            T   ++    +SR  V +IE +A  K+ + +Q +
Sbjct: 199 KTQREIAQMLGISRSYVSRIEKKALNKLNKELQTE 233


>gi|55274887|gb|AAV49246.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 199

 Score =  136 bits (342), Expect = 5e-30,   Method: Composition-based stats.
 Identities = 58/206 (28%), Positives = 100/206 (48%), Gaps = 9/206 (4%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           +     +++      K L   LR  +  L    D+    E+   IA++L+    +V  M 
Sbjct: 61  MNQTRTIRLPIHIV-KELNVYLRTAR-ELSHKLDHEPSAEEAEEIAEQLDKPVDDVSRML 118

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                  S++  +    +     +  L    D +E    +  +  + +  + + +  LN 
Sbjct: 119 RLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNA 173

Query: 238 RERRIFEARR--LQENPVTLENLSSE 261
           ++R +   R   L     TLE++  E
Sbjct: 174 KQREVLARRFGLLGYEAATLEDVGRE 199


>gi|146295518|ref|YP_001179289.1| FliA/WhiG family RNA polymerase sigma factor [Caldicellulosiruptor
           saccharolyticus DSM 8903]
 gi|145409094|gb|ABP66098.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Caldicellulosiruptor
           saccharolyticus DSM 8903]
          Length = 257

 Score =  136 bits (342), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 47/243 (19%), Positives = 114/243 (46%), Gaps = 15/243 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L+  E   L + YR+  D++  + LV  HL +   +A  +   G+   ++     + L+ 
Sbjct: 10  LDVAEIDKLFEEYRKTKDINLRNELVNRHLYIAEIVAKKFINRGIEYDDLYQVACMALIN 69

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           AV++F+P +G++  +++   I   ++ Y     SL+++      +R++    ++K   + 
Sbjct: 70  AVERFEPNKGYKFTSFATPTIMGEIKRYFRDRASLIRLP-----RRIYETSAKIKLATEI 124

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           ++    +P ++  IA+ + ++  EV+ +      + S N L  S D+   + ++  + D 
Sbjct: 125 LSAKLKQPPKIEEIAQYIGITPEEVLEVM-----EASNNYLPQSLDQTMYEDEEMTLGDV 179

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
            G+    + + E       + +++  L+P ER   + R  +E   T   ++ E +VS+  
Sbjct: 180 LGKSDENLVQIENT---ETVKKAIDKLSPLEREFVQKRFFEE--KTQREIADEMKVSQMY 234

Query: 269 VRQ 271
           + +
Sbjct: 235 ISR 237


>gi|254439671|ref|ZP_05053165.1| RNA polymerase sigma factor, sigma-70 family [Octadecabacter
           antarcticus 307]
 gi|198255117|gb|EDY79431.1| RNA polymerase sigma factor, sigma-70 family [Octadecabacter
           antarcticus 307]
          Length = 235

 Score =  135 bits (341), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 71/235 (30%), Positives = 120/235 (51%), Gaps = 6/235 (2%)

Query: 60  LVVKIAMGYRGYGLPIS-EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           +   +A  +         ++V + NIGLM+A  +FDPERG+R +TYS+WWI+A +Q Y L
Sbjct: 1   MARTMAKRFSAGLQAAEPDLVQQANIGLMKAADRFDPERGYRFSTYSVWWIRAEIQSYKL 60

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
            S S+V+   +A+ +     L RL   +      N + +    +AK L V+   +  +  
Sbjct: 61  ASMSIVRRPNSADFRNAVGKLGRLDEAVSNDPTIN-RTDADALVAKALGVNLQRLNDLRQ 119

Query: 179 RLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
           +++G D SLN      D    +    LV     ++   + + + K  R +L   +  L  
Sbjct: 120 QVSGTDYSLNLPSFGDDGE--ERMARLVDPASTEDADTMHRLDIKKLRGLLVEIIGSLPD 177

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI-QKQVELS 291
           RER+I  A +LQ+ P TL  L   F +S ERVRQ+    F++++ ++ Q+ +EL 
Sbjct: 178 RERKIIMATQLQDPPATLTALGIHFGISTERVRQLREMGFERLRTTMTQRDLELE 232


>gi|169334413|ref|ZP_02861606.1| hypothetical protein ANASTE_00813 [Anaerofustis stercorihominis DSM
           17244]
 gi|169259130|gb|EDS73096.1| hypothetical protein ANASTE_00813 [Anaerofustis stercorihominis DSM
           17244]
          Length = 250

 Score =  135 bits (341), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 45/245 (18%), Positives = 110/245 (44%), Gaps = 16/245 (6%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            ++GD ++   L   +  L+  I   Y  Y +   ++   G IGL++A+K+F  E   + 
Sbjct: 22  AQNGDKNSLEELTVINTPLINSILKRYLSYSISYDDLFQIGAIGLIKAIKRFSFEFNTKF 81

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY+++ I    + Y      ++K+G     + L     + K   +     N     +  
Sbjct: 82  STYAVYVINGEYKRYFRDEG-IIKVG-----RNLKTIYLKTKTIREDYVKKNGVEPSIDY 135

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           +++K+ VS  +V+         ESL+  +N+++       D +  ++D  E+++ + +  
Sbjct: 136 LSEKIGVSSEDVLMALEACRQPESLSKELNNNENTPILLMDKIKDENDSNEKIVEKLD-- 193

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                 L  ++  L  R+R+I   R  +    T + ++    +S+ +V ++E +  + ++
Sbjct: 194 ------LKNAIMNLEKRDRQIIVLRYFKN--KTQKEVAEVLGLSQVQVSRLEKKIIENMK 245

Query: 282 ESIQK 286
           ++ + 
Sbjct: 246 KTFES 250


>gi|328885347|emb|CCA58586.1| RNA polymerase sigma factor for flagellar operon [Streptomyces
           venezuelae ATCC 10712]
          Length = 258

 Score =  135 bits (341), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 50/254 (19%), Positives = 107/254 (42%), Gaps = 16/254 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
            L + Y+E GD     +L+  +  LV  +A          +  ++ VS G  GL+ A++K
Sbjct: 11  ELWRSYKETGDERLREQLILHYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEK 70

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD ER  +  TY++  I+ AM + + R+   +        + +      L+  L+     
Sbjct: 71  FDVERAIKFETYAITRIRGAMIDEL-RALDWIPRSVRQKARNVERAYATLEAQLR----- 124

Query: 153 NLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
             +      +A ++++S  ++ ++     LA   +L  L++   +   +    +    D 
Sbjct: 125 --RTPSETEVAAEMDISLEDLHAVFSQLSLANVVALEELLHVGGEGGDRL-SLMDTLEDT 181

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                +E  E +  R +L R+++ L  RE+ +          +TL  +     V+  RV 
Sbjct: 182 AADNPVEVAEDRELRRLLARAINTLPEREKTVVTLYYY--EGLTLAEIGHVLGVTESRVS 239

Query: 271 QIEARAFKKVQESI 284
           QI  ++  +++  +
Sbjct: 240 QIHTKSVLQLRAKL 253


>gi|254479124|ref|ZP_05092475.1| RNA polymerase sigma-K factor [Carboxydibrachium pacificum DSM
           12653]
 gi|214034938|gb|EEB75661.1| RNA polymerase sigma-K factor [Carboxydibrachium pacificum DSM
           12653]
          Length = 234

 Score =  135 bits (341), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 59/269 (21%), Positives = 96/269 (35%), Gaps = 63/269 (23%)

Query: 19  YIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           Y+      P  L  +EE    + YR  GD  A + L+  +LRLV  +   Y G G  + +
Sbjct: 24  YLTNTNSFPSPLSPEEERKYLEAYR-RGDEEARNILIERNLRLVAHVVKKYSGTGRDLDD 82

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++S G IGL++A+  +D E+G  LATY+   I+  +   I                    
Sbjct: 83  LISIGTIGLIKAIDTYDFEKGTHLATYAAKCIENEILMSIR------------------- 123

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
                                      K  V   + I ++                + N 
Sbjct: 124 ----------------------AEKKMKGEVFLQDPIGVDK---------------EGNE 146

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTL 255
               D L  D D   + + +K + K   + L   +     RER I E R    N    T 
Sbjct: 147 ISLMDVLGTDEDEVSEQVEKKIQIKKLYSKLNSVLKN---RERMIIEMRYGLYNGRVRTQ 203

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESI 284
             ++    +SR  V +IE +A  K+ + +
Sbjct: 204 REIAKMLGISRSYVSRIEKKALNKLYKEL 232


>gi|257056691|ref|YP_003134523.1| RNA polymerase sigma factor, sigma-70 family [Saccharomonospora
           viridis DSM 43017]
 gi|256586563|gb|ACU97696.1| RNA polymerase sigma factor, sigma-70 family [Saccharomonospora
           viridis DSM 43017]
          Length = 266

 Score =  135 bits (341), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 41/235 (17%), Positives = 88/235 (37%), Gaps = 15/235 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              ++T  L L   IA  + G G P  ++V    +GL+ A+ +FD  RG     +++  I
Sbjct: 45  REEIITRCLPLAEHIARRFVGRGEPRDDLVQVARLGLLNAIDRFDASRGTEFVAFAVPTI 104

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   S   V++     +  L      L      +     +      +A +L +S
Sbjct: 105 MGEVRRHFRDSSWAVRVPRRLKELHLS-----LSQASSKLAQRLGRAPTPSELAAELGLS 159

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             +V          +S++      D+ +    + + +D          + E       L 
Sbjct: 160 PEDVWDGLLAGNAYQSVSMDAAYDDEGTLPLAETVGHDDV--------ELEHVEYHESLQ 211

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             ++ L  RERR+   R      +T   ++    +S+  V ++ AR  + ++  +
Sbjct: 212 PLLASLPERERRVLILRFFGN--MTQTQIAERVGISQMHVSRLLARTLEFLRSQL 264


>gi|163784595|ref|ZP_02179438.1| RNA polymerase sigma factor RpoS [Hydrogenivirga sp. 128-5-R1-1]
 gi|159880134|gb|EDP73795.1| RNA polymerase sigma factor RpoS [Hydrogenivirga sp. 128-5-R1-1]
          Length = 154

 Score =  135 bits (341), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 55/156 (35%), Positives = 89/156 (57%), Gaps = 6/156 (3%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
           N E G++ Y+ +I  IP++  +EE  LAK+ +E GD  A  +LV ++LR V+ +A  Y G
Sbjct: 5   NYEEGVTYYLKQIADIPLISPEEEKNLAKKIKE-GDKQALDKLVKANLRFVINVAKNYIG 63

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
           YG+P  E++S GNIGL++A K+FDP+RG R  +Y++WWIK ++ + I +   L++I    
Sbjct: 64  YGVPFQELISAGNIGLIEAAKRFDPDRGVRFISYAIWWIKQSIFQTIQQQKDLIRIPH-- 121

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
              R      R+      + +   +      I  KL
Sbjct: 122 ---RTSNMAVRIDKVYLELKEKLGREPTYKEIKSKL 154


>gi|327314688|ref|YP_004330125.1| sigma-70, region 4 [Prevotella denticola F0289]
 gi|326944846|gb|AEA20731.1| sigma-70, region 4 [Prevotella denticola F0289]
          Length = 228

 Score =  135 bits (341), Expect = 6e-30,   Method: Composition-based stats.
 Identities = 63/270 (23%), Positives = 110/270 (40%), Gaps = 47/270 (17%)

Query: 17  SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
            +YI EI     L   EE  LA+R +  GD  A  +L  ++L+ VV +A  YR  GL   
Sbjct: 5   EKYIEEIAGGQPLSDVEERTLAERIKV-GDAHALEKLTKANLKYVVSLAHQYRNRGLGED 63

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++SEGNIG+M A ++FD  RG R   ++  +I+ AM+E I    +L ++      +   
Sbjct: 64  DLISEGNIGMMHAAQRFDGARGVRFVVFAAPYIRKAMEEAIKEQAALYRLPRNEKNRS-- 121

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
                                                     + +   S++  +     N
Sbjct: 122 ----------------------------------------EQKRSHAISIDQPVPVGSSN 141

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV-TL 255
           +   Q+ L  D+        E+  ++     + + + VLN RER++            T+
Sbjct: 142 NFTLQNVLENDNAPHAD---EQLNQEILSAEIQKGLGVLNERERQVITCLYGLSGIHYTM 198

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              +    + RERVRQI   A +K+ + ++
Sbjct: 199 AEAAEHMGLKRERVRQIRDGALRKLHKRMK 228


>gi|261880927|ref|ZP_06007354.1| RNA polymerase sigma factor rpoD [Prevotella bergensis DSM 17361]
 gi|270332314|gb|EFA43100.1| RNA polymerase sigma factor rpoD [Prevotella bergensis DSM 17361]
          Length = 243

 Score =  135 bits (341), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 65/268 (24%), Positives = 114/268 (42%), Gaps = 48/268 (17%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL 73
             ++RY+++I    +L  +EE  LA R +  GD  A   L +++L  V+ +A  Y   GL
Sbjct: 8   DSINRYLNDIGHHNLLSNEEELQLADRIQ-AGDSQAIEELTSANLTYVITLANQYVKRGL 66

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++SEGNIG++QA  KF  + G R   ++  +I+ AM++ I +   L ++       
Sbjct: 67  ALEDLISEGNIGMLQAATKFSRDAGKRFVAFAAPYIRDAMEQAIEQQAGLYRVPRN---- 122

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
                                      A   KL    S+ +S++  L G   L+      
Sbjct: 123 ---------------------------ADNNKLEKKRSKALSIDEPLCGSHELSLGHVIP 155

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE-NP 252
           D+N++               V  E  E+      LT  ++ L+ RE+++  A        
Sbjct: 156 DRNAT---------------VPDEDLEKDMLLGELTELIADLDQREQQVIRALYGIGTEA 200

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKV 280
            T+        + RERVRQI  +A +K+
Sbjct: 201 KTMLETGMAMGLKRERVRQIRNKAIRKI 228


>gi|21225555|ref|NP_631334.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
 gi|256783425|ref|ZP_05521856.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
 gi|289767301|ref|ZP_06526679.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
 gi|4835317|emb|CAB42939.1| putative RNA polymerase sigma factor [Streptomyces coelicolor
           A3(2)]
 gi|289697500|gb|EFD64929.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
          Length = 295

 Score =  135 bits (341), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 46/236 (19%), Positives = 104/236 (44%), Gaps = 11/236 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A + L+  ++ LV   A  +RG G  + ++V  G IGL++A+ +F+  R     ++++ +
Sbjct: 64  ARNTLIEMNMSLVRFAAGRFRGRGNDMEDIVQTGMIGLIKAIDRFELSREVEFTSFALPY 123

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I   ++ +   +   V +     + R+      L    + ++    +   V  +A  +N+
Sbjct: 124 IVGEIKRFFRDTTWAVHVPRRLQELRV-----ELARAREELSTRLDREPTVAELATLMNI 178

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E +VI       G  S ++L  +   +  +  + ++ D  G E+  +   E  +    L
Sbjct: 179 GEDQVIEGQIASNGYNS-SSLDAALTGDGPENGESVLADFIGVEEDGLRLVEDFHS---L 234

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              M+ L+ R+R+I   R ++E   T   +      S+  V ++  R   +++E +
Sbjct: 235 APLMAELSERDRQIIHLRFVEE--ATQAEIGERLGCSQMHVSRLIKRIITRLREGM 288


>gi|153953795|ref|YP_001394560.1| RNA polymerase sigma factor [Clostridium kluyveri DSM 555]
 gi|219854411|ref|YP_002471533.1| hypothetical protein CKR_1068 [Clostridium kluyveri NBRC 12016]
 gi|146346676|gb|EDK33212.1| RNA polymerase sigma factor [Clostridium kluyveri DSM 555]
 gi|219568135|dbj|BAH06119.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 241

 Score =  135 bits (341), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 58/251 (23%), Positives = 107/251 (42%), Gaps = 19/251 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLMQAVKKFDPER 97
                +L+    LV  +L LV  IA      +   +   ++VS G +GLM A+ KFD +R
Sbjct: 1   MALANELNIKEELVKKYLPLVKYIASRVIIGKTKYIEYEDLVSYGTLGLMDAINKFDKDR 60

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G + +TY+   IK +M + + R+  +         K     L R    ++ +     +  
Sbjct: 61  GMKFSTYASIRIKGSMIDELRRNSPI--------SKGAMDKLNRYNAAVEYLQGELGREP 112

Query: 158 QVVAIAKKLNVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
             V IA KL +S  E++ +   +      SL  L+ S + N            D +    
Sbjct: 113 NSVEIASKLGISLKEMMEIENYINYISMVSLEDLVFSDEDNIPIMGTI----EDTKSPSP 168

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
               E K +   L +++ +LN ++  +      +E  +TL+ +     VS  RV Q+ +R
Sbjct: 169 ERNLEEKEKLKYLAKALELLNEKDNLVLTLYYYEE--LTLKEIGHILNVSESRVCQLHSR 226

Query: 276 AFKKVQESIQK 286
           A   +++++ K
Sbjct: 227 AIVHLRKAMAK 237


>gi|312876527|ref|ZP_07736510.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Caldicellulosiruptor
           lactoaceticus 6A]
 gi|311796738|gb|EFR13084.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Caldicellulosiruptor
           lactoaceticus 6A]
          Length = 246

 Score =  135 bits (341), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 56/258 (21%), Positives = 119/258 (46%), Gaps = 23/258 (8%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKF 93
           L +++ +  D     +L+  ++ LV  +A     Y G  +   ++VS G+IGL+ A++KF
Sbjct: 6   LWEKFIKTKDPKIKEQLIIKYMPLVKLVAGRMAIYFGGNVEYDDLVSYGSIGLLDAIEKF 65

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D ++G +  TY+   IK A+ + +        +  +  QK       +         +  
Sbjct: 66  DSQKGVKFETYAYTRIKGAIIDCVRSQDF---LPRSIRQK------AKEIEKAYVEIERE 116

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQ 211
            K      +AK++ +S +E+  +  R++     SL++ +    + + + +   + D   Q
Sbjct: 117 GKTPTDQEVAKRVGISVNELQKLKERISSGMIISLDSFL----EQNYESKIGGLEDFVSQ 172

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
            +  IE EE    + +L + +  L   ER +      +E  ++++ ++    VS  RV Q
Sbjct: 173 PEHFIENEEL---KEVLRQQIENLMENERMVIVLYYYEE--LSIKEIAKVLGVSESRVSQ 227

Query: 272 IEARAFKKVQESIQKQVE 289
           +  RA  K++ ++QK +E
Sbjct: 228 LHTRALLKLKAALQKYLE 245


>gi|289758832|ref|ZP_06518210.1| predicted protein [Mycobacterium tuberculosis T85]
 gi|289714396|gb|EFD78408.1| predicted protein [Mycobacterium tuberculosis T85]
          Length = 170

 Score =  135 bits (341), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 37/174 (21%), Positives = 75/174 (43%), Gaps = 12/174 (6%)

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
           +      ++I     +  +   L R++  L         PE    +AK+++++  +V+ +
Sbjct: 1   MADQARTIRIPVHMVE--VINKLGRIQRELLQDLGREPTPE---ELAKEMDITPEKVLEI 55

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
                   SL+  I   D+  SQ  D++    D +  V ++       ++ L   +  L+
Sbjct: 56  QQYAREPISLDQTI--GDEGDSQLGDFI---EDSEAVVAVDAVSFTLLQDQLQSVLDTLS 110

Query: 237 PRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            RE  +   R       P TL+ +   + V+RER+RQIE++   K++   + QV
Sbjct: 111 EREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIESKTMSKLRHPSRSQV 164


>gi|55274883|gb|AAV49244.1| RNA polymerase subunit sigma-38 [Shigella boydii]
 gi|55274899|gb|AAV49251.1| RNA polymerase subunit sigma-38 [Escherichia albertii]
          Length = 193

 Score =  135 bits (341), Expect = 7e-30,   Method: Composition-based stats.
 Identities = 54/203 (26%), Positives = 96/203 (47%), Gaps = 12/203 (5%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           +     +++      K L   LR  +     ++           IA++L+    +V  M 
Sbjct: 61  MNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRML 115

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                  S++  +    +     +  L    D +E    +  +  + +  + + +  LN 
Sbjct: 116 RLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNA 170

Query: 238 RERRIFEARR--LQENPVTLENL 258
           ++R +   R   L     TLE++
Sbjct: 171 KQREVLARRFGLLGYEAATLEDV 193


>gi|294629742|ref|ZP_06708302.1| RNA polymerase sigma factor [Streptomyces sp. e14]
 gi|292833075|gb|EFF91424.1| RNA polymerase sigma factor [Streptomyces sp. e14]
          Length = 305

 Score =  135 bits (341), Expect = 8e-30,   Method: Composition-based stats.
 Identities = 47/236 (19%), Positives = 97/236 (41%), Gaps = 16/236 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            + LV  +L LV   A  +R    P+ +++  G IGL++A+ +F+  RG    T++M  I
Sbjct: 81  RNTLVELNLALVKFAASRFRSRSEPMEDIIQVGTIGLIKAIDRFELSRGVEFPTFAMPTI 140

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +   V  +A+ L +S
Sbjct: 141 IGEIKRFFRDTSWSVRVPRRLQELRLD-----LAKAGDELAQRLDRAPTVSELAEHLGLS 195

Query: 170 ESEVIS-MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
             EV+  M    A   S        +++     D + Y+  G E +             L
Sbjct: 196 AEEVVEGMAASNAYTASSLDAQPEENESEGALADRIGYEDHGIEGI--------EYVESL 247

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              ++ L  R+R+I   R +    +T   +  E  +S+  V ++ +R   ++++ +
Sbjct: 248 KPLIAELPSRDRKILSLRFVAN--MTQSEIGEELGISQMHVSRLLSRTLVRLRKGL 301


>gi|163816725|ref|ZP_02208088.1| hypothetical protein COPEUT_02915 [Coprococcus eutactus ATCC 27759]
 gi|158447982|gb|EDP24977.1| hypothetical protein COPEUT_02915 [Coprococcus eutactus ATCC 27759]
          Length = 224

 Score =  135 bits (340), Expect = 8e-30,   Method: Composition-based stats.
 Identities = 55/244 (22%), Positives = 107/244 (43%), Gaps = 28/244 (11%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R  + GD++A  RL+T ++ LVV +A  Y G G  + +++  G IGL++AV +FD E   
Sbjct: 9   RLAKEGDITARDRLITENMGLVVSVAKRYIGRGQELEDLIQIGLIGLIKAVDRFDLEYDV 68

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
             +TYS+  I+  ++ ++     LV++      + L     R + + Q     N +   V
Sbjct: 69  MFSTYSVPLIQGEIRRFLRDDG-LVRVS-----RNLKTIHYRAEKYRQEYQRTNGREPTV 122

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I  K+     E++ M    A D S                     +  G+ Q    +E
Sbjct: 123 DEICAKIGSDPEELV-MAMESAVDIS-------------------NIEEMGELQTSRREE 162

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           ER   +  + + +  L  RE+++   R   E   T   +     +S+ +V ++E +  ++
Sbjct: 163 ERVVEKLYVKQLLDTLPEREKKLITLRYFGE--KTQGEIGRILGMSQVQVSRLEKKILRE 220

Query: 280 VQES 283
           ++ +
Sbjct: 221 LKRA 224


>gi|56419662|ref|YP_146980.1| sporulation sigma factor SigE [Geobacillus kaustophilus HTA426]
 gi|56379504|dbj|BAD75412.1| DNA-directed RNA polymerase sigma-29 factor precursor (sigma-E)
           (stage II sporulation protein GB) [Geobacillus
           kaustophilus HTA426]
          Length = 239

 Score =  135 bits (340), Expect = 8e-30,   Method: Composition-based stats.
 Identities = 63/264 (23%), Positives = 109/264 (41%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE  L  R    GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLTKEEEEQLIARLA-AGDDTARSLLIERNLRLVVYIARKFENTGIHIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+                    +++   
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN-------------------NKVRAE- 135

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                            ++ DE LN      D N     D L  
Sbjct: 136 ---------------------------------VSFDEPLN---IDWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           D D    V+ +  E    R +L  ++  L+ RE++I E R         T ++++    +
Sbjct: 160 DDD----VITKDLEADVDRRLLLNALRQLSDREKQIMELRFGLSGGEEKTQKDVADLLGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K +
Sbjct: 216 SQSYISRLEKRIIKRLRKEFNKMM 239


>gi|166031185|ref|ZP_02234014.1| hypothetical protein DORFOR_00871 [Dorea formicigenerans ATCC
           27755]
 gi|166029032|gb|EDR47789.1| hypothetical protein DORFOR_00871 [Dorea formicigenerans ATCC
           27755]
          Length = 246

 Score =  135 bits (340), Expect = 8e-30,   Method: Composition-based stats.
 Identities = 60/288 (20%), Positives = 112/288 (38%), Gaps = 68/288 (23%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           +       GEI    YI     +P  LE  +E           D  A   L+  +LRLVV
Sbjct: 20  RTFLFPDGGEI---HYIGGSDILPAPLEADDEARAIGYLGSAHDEEARKLLIEHNLRLVV 76

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA  +   G+ + +++S G IGL++A+  F+P +  +LATY+   I+  +  Y+ R+  
Sbjct: 77  YIAKKFDNTGIGVEDLISIGTIGLIKAINTFNPTKNIKLATYASRCIENEILMYLRRNNK 136

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
                                                     KL VS  E ++++     
Sbjct: 137 T-----------------------------------------KLEVSIDEPLNVD----- 150

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
                      D N     D L  + D   + L ++ ERK    +L +++++L+ RER I
Sbjct: 151 ----------WDGNELLLSDILGTEEDTIYKDLEQEAERK----ILIKALNLLSARERSI 196

Query: 243 FEARRL----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + R           T + ++    +S+  + ++E +   ++++ + K
Sbjct: 197 IQMRFGIGTVDGEEKTQKEVADLLGISQSYISRLEKKIMVRLRKEMVK 244


>gi|41409504|ref|NP_962340.1| RNA polymerase sigma factor SigF [Mycobacterium avium subsp.
           paratuberculosis K-10]
 gi|254776692|ref|ZP_05218208.1| RNA polymerase sigma factor SigF [Mycobacterium avium subsp. avium
           ATCC 25291]
 gi|41398335|gb|AAS05956.1| SigF_2 [Mycobacterium avium subsp. paratuberculosis K-10]
          Length = 262

 Score =  135 bits (340), Expect = 8e-30,   Method: Composition-based stats.
 Identities = 46/236 (19%), Positives = 95/236 (40%), Gaps = 13/236 (5%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             ++V   L L   IA  + G G P  ++V    +GL+ AV +FD + G    ++++  I
Sbjct: 40  RDKIVERCLPLADHIARRFEGRGEPRDDLVQVARVGLVNAVVRFDVDAGSDFVSFAVPTI 99

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   VK+     +  L     RL      ++    +      +A +L + 
Sbjct: 100 MGEVRRHFRDNSWSVKVPRRLKELHL-----RLGTATADLSQRLGRAPTATELAAELEMD 154

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             EV+     L    S N L   S   S + +   + D  G     +++ E +     L 
Sbjct: 155 REEVVE---GLVAGSSYNTLSIDSGGGSEEEEVRAIADTLGDVDTGLDRIEDQ---ESLR 208

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             +  L  RER +   R      +T   ++    +S+  V ++ A++  ++++ +Q
Sbjct: 209 PLLEALPERERTVLVLRFF--ESMTQTQIAERVGISQMHVSRLLAKSLTRLRDQLQ 262


>gi|78044685|ref|YP_360875.1| sporulation sigma factor SigE [Carboxydothermus hydrogenoformans
           Z-2901]
 gi|77996800|gb|ABB15699.1| RNA polymerase sigma-E factor [Carboxydothermus hydrogenoformans
           Z-2901]
          Length = 237

 Score =  135 bits (340), Expect = 8e-30,   Method: Composition-based stats.
 Identities = 63/260 (24%), Positives = 112/260 (43%), Gaps = 63/260 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L  +EE  L     + GD +A   L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 35  PPLSSEEENTLLTLLVQ-GDAAAKSTLIERNLRLVVYIARKFENTGVNIEDLVSIGTIGL 93

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+  +                       
Sbjct: 94  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRNSKI----------------------- 130

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                             +L VS  E ++++                D N     D L  
Sbjct: 131 ------------------RLEVSFDEPLNVD---------------WDGNELLLSDVLGT 157

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEV 264
           + D   +V+ ++ E+K    +L  ++S LN RER+I E R    +    T + ++    +
Sbjct: 158 EGDIIYKVMEDEVEKK----LLKVALSKLNQRERKIMELRFGLTDGYERTQKEVADLLGI 213

Query: 265 SRERVRQIEARAFKKVQESI 284
           S+  + ++E +  K++++ I
Sbjct: 214 SQSYISRLEKKILKRLKKEI 233


>gi|56962590|ref|YP_174316.1| RNA polymerase sigma factor SigB [Bacillus clausii KSM-K16]
 gi|56908828|dbj|BAD63355.1| DNA-directed RNA polymerase general stress sigma factor sigma-B
           [Bacillus clausii KSM-K16]
          Length = 261

 Score =  135 bits (340), Expect = 8e-30,   Method: Composition-based stats.
 Identities = 48/255 (18%), Positives = 116/255 (45%), Gaps = 12/255 (4%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K + Y+  ++Y++ G   A  +LV     LV  ++  +        ++   G +GL+ A+
Sbjct: 12  KDDIYLWIEQYQKTGSEEAQIKLVNHFEALVRSLSRKFSKGREYDEDLYQVGMVGLLAAM 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           K+++ + G    ++++  +   ++ +I      V +     +        ++K     +T
Sbjct: 72  KRYNEDYGRSFESFAVPTVVGEIKRFIRDKTWSVHVPRRIKELG-----PKIKKAADTLT 126

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
               +   V  IA+ L V+E EV+         ++L+  +N   +   +  +  + D  G
Sbjct: 127 IELQRSPYVHEIAEYLQVTEEEVLETMEMSKSYQALS--VNRPLEADQEGGEVTLLDLVG 184

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
            E+   E+ ++K    +L ++  VLN RE+ I +    +   ++ +    +  +S+  V 
Sbjct: 185 NEEAGYEQADQKL---LLEKAFEVLNEREKDILQCTYYEN--LSQKETGEKLGISQMHVS 239

Query: 271 QIEARAFKKVQESIQ 285
           +++ RA +K+++SI+
Sbjct: 240 RLQRRALQKLRDSIR 254


>gi|318075685|ref|ZP_07983017.1| RNA polymerase sigma factor WhiG [Streptomyces sp. SA3_actF]
          Length = 259

 Score =  135 bits (340), Expect = 8e-30,   Method: Composition-based stats.
 Identities = 50/256 (19%), Positives = 105/256 (41%), Gaps = 16/256 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
            L + Y+  GD     +L+  +  LV  +A          +  ++ VS G  GL+ A++K
Sbjct: 12  ELWRMYKTTGDARLREQLILHYSPLVKYVAGRVSVGLPPNVEQADFVSSGVFGLIDAIEK 71

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD ER  +  TY++  I+ AM + + R+   +        + +      L+  L      
Sbjct: 72  FDIERSIKFETYAITRIRGAMIDEL-RALDWIPRSVRQKARNVERAYATLEAKLH----- 125

Query: 153 NLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
             +    V +A ++ V   ++ ++     LA   +L  L++   +   +    +    D 
Sbjct: 126 --RTPTEVEVASEMGVGVEDLHAVFSQLSLANVVALEELLSVGSEGGGRL-SIMDTLEDT 182

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                +E  E +  R +L+R+++ L  RE+ +          +TL  +     V+  RV 
Sbjct: 183 GADNPVEVAEGRELRQLLSRAINSLPDREKTVVMLYYY--EGLTLAEIGHVLGVTESRVS 240

Query: 271 QIEARAFKKVQESIQK 286
           QI  ++  +++  +  
Sbjct: 241 QIHTKSVLQLRAKLSS 256


>gi|210608671|ref|ZP_03287948.1| hypothetical protein CLONEX_00127 [Clostridium nexile DSM 1787]
 gi|210152928|gb|EEA83934.1| hypothetical protein CLONEX_00127 [Clostridium nexile DSM 1787]
          Length = 247

 Score =  135 bits (340), Expect = 8e-30,   Method: Composition-based stats.
 Identities = 57/273 (20%), Positives = 104/273 (38%), Gaps = 68/273 (24%)

Query: 20  IHEIRKIPMLEK----QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           IH I    +L      +EE           D  A   L+  +LRLVV IA  +   G+ +
Sbjct: 30  IHYIGGSEVLPAPLAVEEEAEAINELGSKDDEYAKKVLIEHNLRLVVYIAKKFDNTGVGV 89

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++S G IGL++A+  F+P +  +LATY+   I+  +  Y+ R+               
Sbjct: 90  EDLISIGTIGLIKAINTFNPTKNIKLATYASRCIENEILMYLRRNNKT------------ 137

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
                                        KL VS  E ++++                D 
Sbjct: 138 -----------------------------KLEVSIDEPLNVD---------------WDG 153

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR----LQEN 251
           N     D L  + D   + L  + ERK    +L +++  L+ RER I   R     L   
Sbjct: 154 NELLLSDILGTEEDTIYRDLENEAERK----LLVKAIGRLSNRERMIVRMRFGLGTLDGE 209

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             T + ++    +S+  + ++E +  ++++  +
Sbjct: 210 EKTQKEVADLLGISQSYISRLEKKIMQRLKREM 242


>gi|302532223|ref|ZP_07284565.1| RNA polymerase sigma-F factor [Streptomyces sp. C]
 gi|302441118|gb|EFL12934.1| RNA polymerase sigma-F factor [Streptomyces sp. C]
          Length = 307

 Score =  135 bits (340), Expect = 8e-30,   Method: Composition-based stats.
 Identities = 53/242 (21%), Positives = 105/242 (43%), Gaps = 16/242 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGY----GLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           A + L+  +L LV   A  +R      GL + +V+  G IGL++A+ +FD +R    +T 
Sbjct: 73  ARNTLIEMNLSLVHYAARRFRARVSGGGLDMDDVIQVGTIGLIKAIDRFDLDREVEFSTL 132

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           ++ +I   ++ +   +   V +     + R       L    +++T+   +   V  +A+
Sbjct: 133 ALPYITGEIKRHFRDTTWAVHVPRRLQELR-----SELAKAQESLTEALHRAPTVKEVAQ 187

Query: 165 KLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
            L +SE EVI       G    SL+    + +   +      + +  G+    +E  E  
Sbjct: 188 HLGLSEEEVIDGLVAANGYTSGSLDTADEAEEARGTGRPARALAEKLGESDPAMELFEDF 247

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +    L   +  L PRER I   R  QE   T   + +E  +S+ +V ++ +R   +++ 
Sbjct: 248 HT---LAPLLRELQPRERLILSMRFGQE--KTQAEIGAELHISQMQVSRLLSRTLARLRA 302

Query: 283 SI 284
            +
Sbjct: 303 GM 304


>gi|255312659|gb|ACU01739.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score =  135 bits (340), Expect = 8e-30,   Method: Composition-based stats.
 Identities = 53/205 (25%), Positives = 95/205 (46%), Gaps = 12/205 (5%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFD ERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDLERGFRFSTYATWWIRQTIERAI 60

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           +     +++      K L   LR  +     ++           IA++L+    +V  M 
Sbjct: 61  MNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRML 115

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                  S++  +    +     +  L    D +E    +  +  + +  + + +  LN 
Sbjct: 116 RLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNA 170

Query: 238 RERRIFEARR--LQENPVTLENLSS 260
           ++R +   R   L     TLE++  
Sbjct: 171 KQREVLARRFGLLGYEAATLEDVGR 195


>gi|256390724|ref|YP_003112288.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Catenulispora
           acidiphila DSM 44928]
 gi|256356950|gb|ACU70447.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Catenulispora
           acidiphila DSM 44928]
          Length = 411

 Score =  135 bits (340), Expect = 8e-30,   Method: Composition-based stats.
 Identities = 57/260 (21%), Positives = 106/260 (40%), Gaps = 24/260 (9%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKF 93
           L   ++  GDL    RL+  +  LV  +A   R      L  ++ VS G  GL+ A+++F
Sbjct: 166 LWDDFKRTGDLGLRERLILHYSPLVKYVAGRVRVGLPGALDSADFVSSGIFGLIDAIERF 225

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           +P R  +  TY++  I+ A+ + +    +L  I  +  QK      R ++     +    
Sbjct: 226 EPHRHVKFETYAIARIRGAIIDELR---ALDWIPRSLRQKA-----REIEQASVRLEQEF 277

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRL------AGDESLNALINSSDKNSSQWQDWLVYD 207
            +      IA++L +   E+  +  +L      A DE L     S D+        +   
Sbjct: 278 GRTPSESEIARELGIGLGELRQIFSKLSLVNVAALDELLALPTQSGDR-----IPLMETL 332

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            DG     +   E +  R +L R+++ L  R++ +          +TL  +     VS  
Sbjct: 333 EDGDAPDPVALFEVQETRALLARAVNSLPERDKTVVTLYYF--EGMTLAQIGEVLGVSES 390

Query: 268 RVRQIEARAFKKVQESIQKQ 287
           RV QI  +A   ++  +  +
Sbjct: 391 RVCQIHTKAVLTLRGKLSAK 410


>gi|302670750|ref|YP_003830710.1| flagellar biosynthesis sigma factor FliA [Butyrivibrio
           proteoclasticus B316]
 gi|302395223|gb|ADL34128.1| flagellar biosynthesis sigma factor FliA [Butyrivibrio
           proteoclasticus B316]
          Length = 257

 Score =  135 bits (340), Expect = 9e-30,   Method: Composition-based stats.
 Identities = 56/263 (21%), Positives = 114/263 (43%), Gaps = 20/263 (7%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKF 93
           L + Y          +L+  +  LV  +A     Y G+ +   ++V  G  GL+ A+ KF
Sbjct: 9   LWEEYHNTKSAEVREKLILEYAPLVKLVAGRLSMYLGFNVEYDDLVGYGIFGLIDAIDKF 68

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D  +  +  TY+   I+ A+ + I +   +  I  T  Q++     ++++  ++ I  + 
Sbjct: 69  DLMKDVKFETYASLRIRGAILDQIRK---MDWIPRTIRQRQ-----KKIEAAIREIERDG 120

Query: 154 LKPEQVVAIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
                   IA K+ +SE E        ++ G  SLN  ++               +    
Sbjct: 121 GHVATDAEIAAKMQISEDEYANWQNQMKVTGVVSLNEFMDQGADIPED-----SNNRSSG 175

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
                E  E++  + ML +S+  L  +E+++      +E  +TL+ +S   EVS  RV Q
Sbjct: 176 FVKPEEAIEKEELKKMLAQSLESLTDKEKKVILLYYYEE--LTLKEISQVLEVSESRVSQ 233

Query: 272 IEARAFKKVQESIQKQVELSSSP 294
           +  +A +K++E +   + + ++P
Sbjct: 234 LHTKALQKMREKLGDYLGILTNP 256


>gi|317129289|ref|YP_004095571.1| RNA polymerase, sigma 28 subunit, SigE [Bacillus cellulosilyticus
           DSM 2522]
 gi|315474237|gb|ADU30840.1| RNA polymerase, sigma 28 subunit, SigE [Bacillus cellulosilyticus
           DSM 2522]
          Length = 238

 Score =  135 bits (340), Expect = 9e-30,   Method: Composition-based stats.
 Identities = 65/264 (24%), Positives = 112/264 (42%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE  L K+    GD S    L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 36  PPLSKEEEAYLLKKL-PSGDDSVRSVLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 94

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FDPE+  +LATY+   I+  +  Y+ R+                    +++   
Sbjct: 95  IKAVSTFDPEKKIKLATYASRCIENEILMYLRRN-------------------NKIRSE- 134

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                            ++ DE LN      D N     D L  
Sbjct: 135 ---------------------------------VSFDEPLN---IDWDGNELLLSDVLGT 158

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           + D    ++ +  E K  R +L +++  LN RE++I E R     +   T ++++    +
Sbjct: 159 EED----IITKGIEDKVDRKLLVKALEALNDREKQIMELRFGLAGDEEKTQKDVADMLGI 214

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++Q+   K +
Sbjct: 215 SQSYISRLEKRIIKRLQKEFNKML 238


>gi|160880601|ref|YP_001559569.1| sporulation sigma factor SigE [Clostridium phytofermentans ISDg]
 gi|160429267|gb|ABX42830.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           phytofermentans ISDg]
          Length = 246

 Score =  135 bits (340), Expect = 9e-30,   Method: Composition-based stats.
 Identities = 58/272 (21%), Positives = 109/272 (40%), Gaps = 65/272 (23%)

Query: 18  RYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
            YI     +P  L+ + E     +     D+ A   LV  +LRLVV IA  +   G+ + 
Sbjct: 31  HYIGGAEVLPAPLDAKREADAIMKLGTPDDVEAKSLLVEHNLRLVVYIAKKFDNTGVGVE 90

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++S G IGL++A+  F+P++  +LATY+   I+  +  Y+ R+                
Sbjct: 91  DLISIGTIGLIKAINTFNPDKNIKLATYASRCIENEILMYLRRNSKT------------- 137

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
                                       KL VS  E ++++                D N
Sbjct: 138 ----------------------------KLEVSIDEPLNVD---------------WDGN 154

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL----QENP 252
                D L  + D    V+ +  E +  + +L R++S LN RE+ I   R        N 
Sbjct: 155 ELLLSDILGTEED----VIYKNIEDEVDKKLLGRALSKLNDREKIIVSLRFGLNTADGNE 210

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            T + ++    +S+  + ++E +  K++++ +
Sbjct: 211 RTQKEVADMLGISQSYISRLEKKIIKRLKKEM 242


>gi|20807708|ref|NP_622879.1| sporulation sigma factor SigK [Thermoanaerobacter tengcongensis
           MB4]
 gi|20516259|gb|AAM24483.1| DNA-directed RNA polymerase sigma subunits (sigma70/sigma32)
           [Thermoanaerobacter tengcongensis MB4]
          Length = 231

 Score =  135 bits (340), Expect = 9e-30,   Method: Composition-based stats.
 Identities = 59/269 (21%), Positives = 96/269 (35%), Gaps = 63/269 (23%)

Query: 19  YIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           Y+      P  L  +EE    + YR  GD  A + L+  +LRLV  +   Y G G  + +
Sbjct: 21  YLTNTNSFPSPLSPEEERKYLEAYR-RGDEEARNILIERNLRLVAHVVKKYSGTGRDLDD 79

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++S G IGL++A+  +D E+G  LATY+   I+  +   I                    
Sbjct: 80  LISIGTIGLIKAIDTYDFEKGTHLATYAAKCIENEILMSIR------------------- 120

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
                                      K  V   + I ++                + N 
Sbjct: 121 ----------------------AEKKMKGEVFLQDPIGVDK---------------EGNE 143

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTL 255
               D L  D D   + + +K + K   + L   +     RER I E R    N    T 
Sbjct: 144 ISLMDVLGTDEDEVSEQVEKKIQIKKLYSKLNSVLKN---RERMIIEMRYGLYNGRVRTQ 200

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESI 284
             ++    +SR  V +IE +A  K+ + +
Sbjct: 201 REIAKMLGISRSYVSRIEKKALNKLYKEL 229


>gi|312623242|ref|YP_004024855.1| RNA polymerase, sigma 28 subunit, sig b/f/g subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
 gi|312203709|gb|ADQ47036.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
          Length = 256

 Score =  135 bits (340), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 51/245 (20%), Positives = 114/245 (46%), Gaps = 17/245 (6%)

Query: 29  LEKQEEY--VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           LE  +E    L + Y++   +   + LV  +L +   IA  + G G+   ++     I L
Sbjct: 8   LEIDDEKIDRLFEEYQKTKSIELRNELVNRYLYIAEIIAKKFVGRGIDYEDLYQVACIAL 67

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           + AV++F+P +G++  +++   I   ++ Y     S++++      +R++    ++K   
Sbjct: 68  INAVERFEPNKGYKFTSFATPTIMGEIKRYFRDRASIIRLP-----RRIYETSAKIKLAT 122

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           + ++    +P +V  IA+ LN+S  EV+ +      + S N L  S D+   + ++  + 
Sbjct: 123 EVLSTKLKRPPKVEEIAQHLNMSTEEVLEVM-----EASNNYLPQSLDQTMYEDEEMTLG 177

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           D  G+     E   +      + +++  L+P ER   + R  +E   T + ++ E  VS+
Sbjct: 178 DVLGKSD---ENILQVENVEAVKKAIERLSPFEREFVQKRFFEE--KTQKEIAEEMNVSQ 232

Query: 267 ERVRQ 271
             + +
Sbjct: 233 MYISR 237


>gi|254478671|ref|ZP_05092042.1| RNA polymerase sigma-F factor [Carboxydibrachium pacificum DSM
           12653]
 gi|214035358|gb|EEB76061.1| RNA polymerase sigma-F factor [Carboxydibrachium pacificum DSM
           12653]
          Length = 215

 Score =  134 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 45/232 (19%), Positives = 105/232 (45%), Gaps = 18/232 (7%)

Query: 55  TSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114
             +  L+  I   +   G  + ++   G IG ++AV+KFD     + +TY++  I   ++
Sbjct: 1   MENSGLIWSIVKKFANRGYELEDLYQIGCIGFVKAVQKFDESYNVKFSTYAVPIIMGEIK 60

Query: 115 EYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVI 174
            ++     L+K+  +  +        +     + +++   +   +  IA++LNV+  E+ 
Sbjct: 61  RFLRDDG-LIKVSRSLKELSSKAFYMK-----EVLSNELNREPTINEIAERLNVTPEEIA 114

Query: 175 SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV 234
                 A  ESL   I S ++   Q  + +    D      ++ EE+      L   +  
Sbjct: 115 MAFESAATAESLYDSI-SHEEEDRQLIEMVGDKEDS-----VDLEEKLT----LHMIIDK 164

Query: 235 LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           L PRE+++   R  ++  +T   +++   +S+ +V +IE +  +K+++ ++K
Sbjct: 165 LKPREKQVIFLRYFKD--MTQTEVANILGISQVQVSRIEKKVLEKIRKELEK 214


>gi|300854227|ref|YP_003779211.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           ljungdahlii DSM 13528]
 gi|300434342|gb|ADK14109.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           ljungdahlii DSM 13528]
          Length = 241

 Score =  134 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 52/245 (21%), Positives = 102/245 (41%), Gaps = 19/245 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           L     LV  +L LV  IA      +   +   ++VS G +GL+ A+ KFD +RG + +T
Sbjct: 7   LDIKEELVKKYLPLVKYIASRVIIGKTKYIEYEDLVSYGMLGLIDAINKFDKDRGMKFST 66

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   IK +M + + R+  +         K     L +    + ++     +      IA
Sbjct: 67  YASIRIKGSMIDELRRNSPI--------SKGAMDKLNKYNAAMDSLRTKLGREPSSEEIA 118

Query: 164 KKLNVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
            +L +   +++ +   +      SL  LI S D +            D +     +  E+
Sbjct: 119 NELGMPLKKMMEIENYINYISIVSLEDLIFSEDDDIPLMGTV----EDTKSPSPEKSLEK 174

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           K     L +++ +LN ++  +          +TL+ +     VS  RV Q+ +RA   ++
Sbjct: 175 KEMLEYLAKALDLLNEKDNLVITLYYY--EKLTLKEIGHILNVSESRVCQLHSRAILHLR 232

Query: 282 ESIQK 286
           +++ K
Sbjct: 233 KNMTK 237


>gi|167770714|ref|ZP_02442767.1| hypothetical protein ANACOL_02060 [Anaerotruncus colihominis DSM
           17241]
 gi|167667309|gb|EDS11439.1| hypothetical protein ANACOL_02060 [Anaerotruncus colihominis DSM
           17241]
          Length = 243

 Score =  134 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 62/271 (22%), Positives = 116/271 (42%), Gaps = 64/271 (23%)

Query: 19  YIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           YI+    +P  L ++EE ++ ++  EH D +A   L   +LRLVV IA  +   G+ + +
Sbjct: 32  YINGPETLPAPLSREEEQIVFRKLEEH-DEAAKETLTVHNLRLVVYIAKKFESTGICVED 90

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++S G IGL++AV  F P++  +LATY+   I+  +  ++ ++ S        N+     
Sbjct: 91  LISIGTIGLIKAVNTFCPQKNIKLATYASRCIENEILMHLRKNQS------HKNE----- 139

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
                                                     ++ DE LN      D N 
Sbjct: 140 ------------------------------------------ISIDEPLN---IDWDGNE 154

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTL 255
               D L  D D   + + ++ E    +N+L  ++  L+ RER I + R   L     T 
Sbjct: 155 LLLSDILGTDPDSINRPIEDEAE----KNLLLGAIDRLDGRERMIMQLRFGLLGAEEKTQ 210

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           + ++    +S+  + ++E R  KK+++ ++K
Sbjct: 211 KEVADIIGISQSYISRLEKRIIKKLKKDLEK 241


>gi|227485765|ref|ZP_03916081.1| possible DNA-directed RNA polymerase sigma subunit SigB
           [Anaerococcus lactolyticus ATCC 51172]
 gi|227236320|gb|EEI86335.1| possible DNA-directed RNA polymerase sigma subunit SigB
           [Anaerococcus lactolyticus ATCC 51172]
          Length = 258

 Score =  134 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 40/241 (16%), Positives = 97/241 (40%), Gaps = 16/241 (6%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           + +  D      L+  HL +V  ++  Y G G+   ++    ++GL+ AV ++DP +G+ 
Sbjct: 21  FHKTRDKKLRDELIEEHLYIVDILSNKYVGKGIEKDDLYQVASLGLINAVDRYDPSKGYA 80

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            ++++   I   ++ Y      ++K+      + L+  +   K  L        +   + 
Sbjct: 81  FSSFATPTIMGEIKRYFRDKGWVIKVPRRI--QNLYKKINVAKKVLPQELQ---RVPTIA 135

Query: 161 AIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            IA  L   E  ++      ++   +SL+   +     ++     ++ + D     +   
Sbjct: 136 DIADYLGEDEETILETMEASKVYTPQSLDMKYSVQKGENAIDLAEIIGEEDKNFDSV--- 192

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                 ++++ +S   L   E+ I E R       T  +++   ++S+  V +IE +   
Sbjct: 193 ----ELKDLIEKSKERLTDLEKEILELRYY--EGRTQVDIAESLDISQMTVSRIEKKILN 246

Query: 279 K 279
           K
Sbjct: 247 K 247


>gi|17226799|gb|AAL37943.1|AF359562_4 SigB [Staphylococcus epidermidis]
          Length = 256

 Score =  134 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 50/263 (19%), Positives = 111/263 (42%), Gaps = 24/263 (9%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             ++     K+++E+ D  A  +LV  + +L+  +A  Y        ++V  G +GL+ A
Sbjct: 12  SPEQINQWIKQHQENEDSQAQDKLVKHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGA 71

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +FD     +   + +  +   ++ Y+      V +     +        R+K     +
Sbjct: 72  INRFDLSFDRKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIG-----PRIKKVSDEL 126

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNC------RLAGDESLNALINSSDKNSSQWQDW 203
           T+   +   +  IA++L VS+ EV+           L+ D S+ A     D ++    D 
Sbjct: 127 TNELERSPSISEIAQRLEVSDEEVLEAMEMGQSYNALSVDHSIEA---DKDGSTVTLLDI 183

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    D          +   +R +L R + +L+ RER+I +   +    ++ +       
Sbjct: 184 MGQQDDNY--------DLTEKRMILERILPILSERERQIIQCTFI--EGLSQKETGERIG 233

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+  V +++  A KK+QE+ ++
Sbjct: 234 LSQMHVSRLQRTAIKKLQEAARQ 256


>gi|1276889|gb|AAC44103.1| stress response/stationary phase sigma factor [Mycobacterium
           tuberculosis H37Rv]
 gi|1589717|prf||2211432A RNA polymerase sigma factor
          Length = 261

 Score =  134 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 39/236 (16%), Positives = 94/236 (39%), Gaps = 14/236 (5%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             ++V   L L   IA  + G G P  +++    +GL+ A  +FD + G    ++++  I
Sbjct: 40  RDKIVQRCLPLADHIARRFEGRGEPRDDLIQVARVGLVNAAVRFDVKTGSDFVSFAVPTI 99

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   VK+     +  L     RL      ++    +      +A +L + 
Sbjct: 100 MGEVRRHFRDNSWSVKVPRRLKELHL-----RLGTATADLSQRLGRAPSASELAAELGMD 154

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
            +EVI      +   +L+        + ++     + D D          ++   R +L 
Sbjct: 155 RAEVIEGLLAGSSYHTLSIDSGGGSDDDARAITDTLGDVDA-------GLDQIENREVLR 207

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             +  L  RER +   R    + +T   ++    +S+  V ++ A++  ++++ ++
Sbjct: 208 PLLEALPERERTVLVLRFF--DSMTQTQIAERVGISQMHVSRVLAKSLARLRDQLE 261


>gi|329735692|gb|EGG71975.1| RNA polymerase sigma-B factor [Staphylococcus epidermidis VCU028]
          Length = 256

 Score =  134 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 50/263 (19%), Positives = 111/263 (42%), Gaps = 24/263 (9%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             ++     K+++E+ D  A  +LV  + +L+  +A  Y        ++V  G +GL+ A
Sbjct: 12  SPEQINQWIKQHQENEDSQAQDKLVKHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGA 71

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +FD     +   + +  +   ++ Y+      V +     +        R+K     +
Sbjct: 72  INRFDLSFDRKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIG-----PRIKKVSDEL 126

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNC------RLAGDESLNALINSSDKNSSQWQDW 203
           T+   +   +  IA++L VS+ EV+           L+ D S+ A     D ++    D 
Sbjct: 127 TNELERSPSISEIAQRLEVSDEEVLEAMEMGQSYNALSVDHSIEA---DKDGSTVTLLDI 183

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    D          +   +R +L R + +L+ RER+I +   +    ++ +       
Sbjct: 184 MGQQDDNY--------DLTEKRMILERILPILSERERQIIQCTFI--EGLSQKETGERIG 233

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+  V +++  A KK+QE+ ++
Sbjct: 234 LSQMHVSRLQRTAIKKLQEAARQ 256


>gi|86605313|ref|YP_474076.1| RNA polymerase sigma factor SigF [Synechococcus sp. JA-3-3Ab]
 gi|86553855|gb|ABC98813.1| RNA polymerase sigma factor, group 3 [Synechococcus sp. JA-3-3Ab]
          Length = 299

 Score =  134 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 52/261 (19%), Positives = 110/261 (42%), Gaps = 17/261 (6%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQA 89
           K +   L + Y +  D +  +RLV  +L LV K A  +R        ++V  G IGL+QA
Sbjct: 52  KAQTAALLRLYHQTRDPALRNRLVEINLGLVRKEAHHWRNQCDEGYDDLVQVGCIGLIQA 111

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +++FD  RG   ++++M +I+  +Q Y+      ++I      +R     R+ K  +  +
Sbjct: 112 IERFDISRGLAFSSFAMPYIRGEIQHYLRDKSPTIRIP-----RRWATLQRQAKKVIARL 166

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYD 207
                +      + + L ++E E   +          SL+A +   +++S    D +   
Sbjct: 167 RQELGRSPSEAEVREALQLTEQEWRELELAQQNSLLLSLDAPVQV-EEDSVALGDTIPDQ 225

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
                Q+  E       R  L  +++ L  R R+I E     +  +T +  +    +S  
Sbjct: 226 RYRSFQLAEED------RIRLQNALAKLEERTRQILEFVFFYD--LTQKETAERLGISAV 277

Query: 268 RVRQIEARAFKKVQESIQKQV 288
            V +   +  +++ + + + +
Sbjct: 278 TVSRQVKKGLERLAKLLSQDI 298


>gi|288555607|ref|YP_003427542.1| sporulation sigma factor SigK [Bacillus pseudofirmus OF4]
 gi|288546767|gb|ADC50650.1| sporulation sigma factor SigK [Bacillus pseudofirmus OF4]
          Length = 235

 Score =  134 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 61/278 (21%), Positives = 103/278 (37%), Gaps = 65/278 (23%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +S  V   I    Y+        L+K +E    K  +E GD  A + L+  +LRLV  I 
Sbjct: 8   LSYFVKEVIVFVSYVKNNAFPQPLKKDDERKYLKLMQE-GDAEARNLLIEHNLRLVAHIV 66

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             +        +++S G IGL++A++ +   +G +LATY+   I+  +            
Sbjct: 67  KKFENTREDTEDLISIGTIGLIKAIESYSDGKGTKLATYAARCIENEI------------ 114

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
                       +LR LK                                    +  D S
Sbjct: 115 ----------LMHLRALKK-----------------------------------VKKDVS 129

Query: 186 LNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           L+  I +  + N     D L  D D    V+  K E+K     +     VL+ RE+ +  
Sbjct: 130 LHDPIGTDKEGNEISLIDVLQEDADDIVDVIQTKMEKKQIYEYIH----VLDEREKEVIV 185

Query: 245 ARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            R   +  + +T   ++ +  +SR  V +IE RA  K+
Sbjct: 186 GRFGLDMEDELTQREIAKKLGISRSYVSRIEKRALMKL 223


>gi|302391540|ref|YP_003827360.1| RNA polymerase, sigma 29 subunit, SigE [Acetohalobium arabaticum
           DSM 5501]
 gi|302203617|gb|ADL12295.1| RNA polymerase, sigma 29 subunit, SigE [Acetohalobium arabaticum
           DSM 5501]
          Length = 247

 Score =  134 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 67/263 (25%), Positives = 107/263 (40%), Gaps = 64/263 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L  +EE  L  + +E GD +    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 42  PPLSNEEESYLLSKLKE-GDKAVRSVLIERNLRLVVYIARKFENTGIDIEDLVSIGTIGL 100

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FD  +  +LATY+   I+  +  Y+             N+K+            
Sbjct: 101 IKAVNTFDVSKRIKLATYASRCIENEILMYLR----------RNNKKK------------ 138

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                            ++ DE LN      D N  +  D L  
Sbjct: 139 -------------------------------SEISFDEPLN---IDWDGNELKLSDVLGT 164

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN---PVTLENLSSEFE 263
           D D   Q + E  +    R +L ++M VL  RER+I   R         +T + ++    
Sbjct: 165 DMDLIYQYIEEDVD----RELLLQAMEVLTDRERKIMILRFGLGEDREEMTQKEVADILG 220

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+  + ++E R  KK+Q+ I K
Sbjct: 221 ISQSYISRLEKRIIKKLQQEISK 243


>gi|45643442|gb|AAC79984.2| HasL [Streptomyces ambofaciens]
 gi|126347729|emb|CAJ89446.1| putative sigma factor [Streptomyces ambofaciens ATCC 23877]
          Length = 281

 Score =  134 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 46/239 (19%), Positives = 108/239 (45%), Gaps = 18/239 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + L+  ++ LV   A  +R  G   + ++V  G IGL++A+ +F+  R     ++++ 
Sbjct: 54  ARNTLIEMNMSLVRFAAGRFRSRGPEEMEDIVQVGMIGLIKAIDRFELTREVEFTSFAVP 113

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +I   ++ +   +   V +     + R+     +L    + +     +      +++ ++
Sbjct: 114 YIVGEIKRFFRDTSWAVHVPRRLQEARV-----QLARATEELRSRLGRNPTTKELSELMS 168

Query: 168 VSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           + E EV+       G    SL+A I+ S+   S   D++     G E   +   E  +  
Sbjct: 169 LPEDEVVEARLAANGYNSASLDAAISGSEDGESALADFI-----GAEDTALALVEDFH-- 221

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             L   ++ L+ R+R+I   R ++E  +T +++     VS+  V ++ +R   +++E +
Sbjct: 222 -ALAPMIAELDERDRQIIHWRFVEE--LTQKDIGERLGVSQMHVSRLISRLLARLREGM 277


>gi|120402666|ref|YP_952495.1| RNA polymerase sigma factor SigF [Mycobacterium vanbaalenii PYR-1]
 gi|119955484|gb|ABM12489.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Mycobacterium
           vanbaalenii PYR-1]
          Length = 262

 Score =  134 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 43/236 (18%), Positives = 93/236 (39%), Gaps = 14/236 (5%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             R+V   L L   IA  + G G P  ++V    +GL+ AV +FD   G    ++++  I
Sbjct: 41  RDRIVERCLPLADHIARRFDGRGEPRDDLVQVARVGLVNAVIRFDVNAGSDFVSFAVPTI 100

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   VK+     +  L     RL      ++    +      +A +L + 
Sbjct: 101 MGEVRRHFRDNSWSVKVPRRLKELHL-----RLGAATAELSQRLGRAPTATELAAELEMD 155

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             EV+      +   +L+         S       + D  G   + +++ E    R  L 
Sbjct: 156 RDEVVEGLVAGSSYNTLS----IDSGGSGNEDAPAIADTLGDVDLSLDQIE---NREALR 208

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             ++ L  RER +   R      +T   ++    +S+  V ++ A++  ++++ ++
Sbjct: 209 PLLAALPERERTVLALRFF--ESMTQTQIAERVGISQMHVSRLLAKSLARLRDQLE 262


>gi|167745312|ref|ZP_02417439.1| hypothetical protein ANACAC_00003 [Anaerostipes caccae DSM 14662]
 gi|167655033|gb|EDR99162.1| hypothetical protein ANACAC_00003 [Anaerostipes caccae DSM 14662]
          Length = 243

 Score =  134 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 57/274 (20%), Positives = 109/274 (39%), Gaps = 65/274 (23%)

Query: 18  RYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
            YI     +P  LE +EE  +  +     +  A  +L+  +LRLVV IA  +   G+ + 
Sbjct: 26  HYIGGAEILPAPLEAKEEEKMIHKLGTAEEPEARAKLIERNLRLVVYIAKKFDNTGIGVE 85

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++S G IGL++A+  F+P +  +LATY+   I+  +  Y+ R+                
Sbjct: 86  DLISIGTIGLIKAINTFNPAKKIKLATYASRCIENEILMYLRRNNKT------------- 132

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
                                       K+ VS  E ++++                D N
Sbjct: 133 ----------------------------KMEVSIDEPLNVD---------------WDGN 149

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL----QENP 252
                D L  D D    ++    E +  R +L  +M +L+ RER+I E R          
Sbjct: 150 ELLLSDILGTDED----IIYRDLEHEVDRKLLLNAMKILSDRERKIIELRFGINQKDGEE 205

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            T + ++    +S+  + ++E +  K+++  + +
Sbjct: 206 KTQKEVADLMGISQSYISRLEKKIIKRLKREMSR 239


>gi|42780162|ref|NP_977409.1| RNA polymerase sigma factor SigB [Bacillus cereus ATCC 10987]
 gi|42736080|gb|AAS40017.1| RNA polymerase sigma-B factor [Bacillus cereus ATCC 10987]
          Length = 257

 Score =  134 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 51/257 (19%), Positives = 116/257 (45%), Gaps = 16/257 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K++   L   ++++    A  RLV  +  LV  IA  Y   G    +++  G +GL+ 
Sbjct: 10  LTKEDVMKLIAEFQQNQCDEAQERLVEHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLG 69

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++++D   G     +++  I   +++Y+      + +      +R+     ++K  ++ 
Sbjct: 70  AIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRIKDLGGKIKLAIEE 124

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +TD   +  +++ IA  L +SE EV+ +          SL+ ++ ++   SS  +   V 
Sbjct: 125 LTDQLQRSPKIIEIADHLELSEEEVLEIMDAKNNYRVSSLDDVVENASDGSSVARIESVG 184

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           +       + +  E   RR +L    +VLN  E+ +     + E  +  ++      +S+
Sbjct: 185 E-------VEQGYEETERRLVLKDIFNVLNETEKSVIH--YIFEENLNQKDTGERLGISQ 235

Query: 267 ERVRQIEARAFKKVQES 283
             V +I+ +A  K++++
Sbjct: 236 MHVSRIKRQAISKLKQA 252


>gi|15613848|ref|NP_242151.1| sporulation sigma factor SigK [Bacillus halodurans C-125]
 gi|10173901|dbj|BAB05004.1| RNA polymerase sigma factor (sigma K) precursor [Bacillus
           halodurans C-125]
          Length = 235

 Score =  134 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 59/265 (22%), Positives = 97/265 (36%), Gaps = 63/265 (23%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
            Y+        L K+EE    KR  E GD  A +RL+  +LRLV  I   +        +
Sbjct: 20  SYVKNNAFPQPLSKEEERHYLKRMAE-GDEEARNRLIEHNLRLVAHIVKKFENTREHTED 78

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++S G IGL++A++ F   +G +LATY+   I+  +                        
Sbjct: 79  LISIGTIGLIKAIESFSEGKGTKLATYAARCIENEI----------------------LM 116

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
           +LR LK                            + +S++  +  D          + N 
Sbjct: 117 HLRALKK-------------------------VKKDVSLHDPIGTD---------KEGNE 142

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
               D L  D +     +  K E+K     +     VL+ RE+ +   R   +     T 
Sbjct: 143 ITLIDVLQEDSEDIADSIQLKMEKKQIYEYIH----VLDDREKEVIVGRFGLDLEEERTQ 198

Query: 256 ENLSSEFEVSRERVRQIEARAFKKV 280
             ++ E  +SR  V +IE RA  K+
Sbjct: 199 REIAKELGISRSYVSRIEKRALMKL 223


>gi|317122054|ref|YP_004102057.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Thermaerobacter
           marianensis DSM 12885]
 gi|315592034|gb|ADU51330.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Thermaerobacter
           marianensis DSM 12885]
          Length = 251

 Score =  134 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 66/289 (22%), Positives = 106/289 (36%), Gaps = 64/289 (22%)

Query: 10  VNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           V G + L  Y+   R  P  L  +EE    +R R HGD  A   L+  +LRLV  IA  +
Sbjct: 14  VRGLLYLVGYLQTGRSFPQPLTPEEEAHYLERMR-HGDERARDVLIERNLRLVAHIAKKF 72

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
              G    +++S G +GL++ V  +DP +G RLATY+   I+  +  ++           
Sbjct: 73  DETGEDPEDLISIGTVGLIKGVDTYDPSKGTRLATYAARCIENEILMHLR---------- 122

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
                                T  N +                  + +   +  D     
Sbjct: 123 --------------------ATRRNRRE-----------------VFLQNPIGVDR---- 141

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
                + N     D L  D D  E  +  +   +  R  +      L PRERR+ E R  
Sbjct: 142 -----EGNEVTLMDMLPADDDAVEDTVGRRLLARRIREAVRE----LGPRERRVLELRFG 192

Query: 249 QENPV--TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPP 295
            +     T   ++    +SR  V +IE RA +K+   +  +  L +  P
Sbjct: 193 LDGQRRYTQREVARVLGISRSYVSRIEKRAVRKLTRHVLDEPGLPAGGP 241


>gi|150019061|ref|YP_001311315.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           beijerinckii NCIMB 8052]
 gi|149905526|gb|ABR36359.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           beijerinckii NCIMB 8052]
          Length = 242

 Score =  134 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 55/251 (21%), Positives = 108/251 (43%), Gaps = 19/251 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLMQAVKKFDPER 97
                D+    +++  ++ LV  IA      +   +   ++VS G +GLM A+ KFD  +
Sbjct: 1   MHALKDVDGKEQIIQEYIPLVKYIASRVMFGKNKYMEYEDLVSYGMVGLMDALNKFDDTK 60

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G + ++Y+   IK AM + + R+  +         K     L +    +  +    L+  
Sbjct: 61  GMKFSSYASIRIKGAMIDELRRNRPI--------SKGAMDKLNKYNKAVDTLQLELLREP 112

Query: 158 QVVAIAKKLNVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
               IAK L +S SEV  +   +      SL  +I S D++     + +    D      
Sbjct: 113 TNDEIAKYLGISMSEVAEIENYINYISMVSLENVIFSDDED----VNLIGIIEDKNSPSP 168

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
               + K +  +LT+++ +L  ++R +          +TL+ + +   VS  RV Q+ +R
Sbjct: 169 DAYLQDKEQLEILTKAIDLLKEKDRIVLNLYYY--EGLTLKEIGTVLSVSESRVCQLHSR 226

Query: 276 AFKKVQESIQK 286
           A   ++E ++K
Sbjct: 227 AISSLRECMRK 237


>gi|257457436|ref|ZP_05622606.1| RNA polymerase sigma-D factor [Treponema vincentii ATCC 35580]
 gi|257445165|gb|EEV20238.1| RNA polymerase sigma-D factor [Treponema vincentii ATCC 35580]
          Length = 262

 Score =  134 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 53/257 (20%), Positives = 104/257 (40%), Gaps = 19/257 (7%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLMQAV 90
           E  L   Y+   D       +  +  LV  +A          +   ++V  G  GL+ A+
Sbjct: 11  EDELWLEYKHTQDPQLREFFIVKYAPLVKYVAGKVAVGMPNNVEFDDLVGYGVFGLLDAI 70

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
            K+DPE+  +  TY++  I+ A+ + + RS   V        + +   +  L+  L    
Sbjct: 71  DKYDPEKNVKFNTYAVTRIRGAIFDEL-RSIDWVPRSVRQQSREIEEVIADLEARLGHAA 129

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNAL-INSSDKNSSQWQDWLVYD 207
                      IA+ L +S  E   +  +++G    SL  L   + D   +   D +   
Sbjct: 130 -------TDSEIAEALGMSVEEFHQVLLKISGTSIISLTDLRFGADDSEQTPVADSIEAP 182

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
                 V++E+EE    + ++  +++ L  RE+++      ++  +TL  +    EV+  
Sbjct: 183 TSLNPDVIVEREE---MKRIIVDAINELPDREKKVLIMYYYED--MTLREIGKVLEVTES 237

Query: 268 RVRQIEARAFKKVQESI 284
           RV QI   A  K++  +
Sbjct: 238 RVSQIHTSANLKLKAKL 254


>gi|2224777|emb|CAA80617.1| putative pro-sigma factor E [Clostridium acetobutylicum ATCC 824]
          Length = 235

 Score =  134 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 62/265 (23%), Positives = 104/265 (39%), Gaps = 65/265 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K EE  L  +   +GD S    L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 33  PPLSKDEEDDLVNKLV-NGDESIRSILIERNLRLVVYIARKFENTGVGVEDLISVGTIGL 91

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FDP +  +LATY    I+  +                         LRR     
Sbjct: 92  IKAVNTFDPTKKIKLATYGSRCIENEI----------------------LMYLRR----- 124

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS-DKNSSQWQDWLV 205
                                         N ++  + S    +N   D N     D L 
Sbjct: 125 ------------------------------NSKVKAEISFYEPLNIDWDGNKPLLSDILG 154

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFE 263
            D+D    ++    E +  + +L  ++  LN RE+RI E R         T + ++    
Sbjct: 155 TDNDCVYNLI----EGEVDKQLLLFALKKLNEREKRIVELRYGLTGVGEKTQKEVADMLG 210

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           +S+  + ++E R  K++++ I K +
Sbjct: 211 ISQSYISRLEKRIIKRLKKEINKML 235


>gi|145224454|ref|YP_001135132.1| FliA/WhiG family RNA polymerase sigma factor [Mycobacterium gilvum
           PYR-GCK]
 gi|145216940|gb|ABP46344.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Mycobacterium gilvum
           PYR-GCK]
          Length = 270

 Score =  134 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 46/236 (19%), Positives = 90/236 (38%), Gaps = 14/236 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                R++   L L    A  +RG G    ++    ++GL+ AVK+FDP+ G     Y++
Sbjct: 29  RRLHERIIAMTLPLAQHTARRFRGRGQSHDDLFQVASVGLVNAVKRFDPDSGSDFLAYAV 88

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I   ++ Y       VK+      K L   L + +  L         P +V A    L
Sbjct: 89  PTIMGEVRRYFRDCSWAVKVPRRL--KDLNSQLAKARAELTQQLGRAPTPSEVAA---HL 143

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   EV+      +   +L+    S            + + D +   +++ E       
Sbjct: 144 GIDREEVVQATIASSNYATLSTDSTSGPDGDFVALRETLGEPDARLDAVVDNET------ 197

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            +   +  L PRE+ + + R   E  +T   ++     S+  V ++ A+A   +++
Sbjct: 198 -IRPLIEKLPPREQAVLKLRFFDE--MTQTQIAERMGYSQMHVSRLLAKALATLRD 250


>gi|261419324|ref|YP_003253006.1| sporulation sigma factor SigE [Geobacillus sp. Y412MC61]
 gi|297530706|ref|YP_003671981.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
 gi|319766140|ref|YP_004131641.1| RNA polymerase, sigma 28 subunit, SigE [Geobacillus sp. Y412MC52]
 gi|261375781|gb|ACX78524.1| RNA polymerase, sigma 28 subunit, SigE [Geobacillus sp. Y412MC61]
 gi|297253958|gb|ADI27404.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
 gi|317111006|gb|ADU93498.1| RNA polymerase, sigma 28 subunit, SigE [Geobacillus sp. Y412MC52]
          Length = 239

 Score =  134 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 62/264 (23%), Positives = 109/264 (41%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE  L  R    GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLTKEEEEQLIARLA-AGDDTARSLLIERNLRLVVYIARKFENTGIHIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+                    +++   
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN-------------------NKVRAE- 135

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                            ++ DE LN      D N     D L  
Sbjct: 136 ---------------------------------VSFDEPLN---IDWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           + D    V+ +  E    R +L  ++  L+ RE++I E R         T ++++    +
Sbjct: 160 EDD----VITKDLEADVDRRLLLNALRQLSDREKQIMELRFGLSGGEEKTQKDVADLLGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K +
Sbjct: 216 SQSYISRLEKRIIKRLRKEFNKMM 239


>gi|220929439|ref|YP_002506348.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           cellulolyticum H10]
 gi|219999767|gb|ACL76368.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           cellulolyticum H10]
          Length = 254

 Score =  134 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 46/252 (18%), Positives = 109/252 (43%), Gaps = 17/252 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKK 92
            L K+Y E  D +A  +L+  +  L+  +A     Y G  +   ++V  G  GL+ A++K
Sbjct: 8   HLWKQYIETKDAAAKEKLIIQYAYLIKYVAGRLSIYFGSNVEFDDLVGYGAFGLIDAIEK 67

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           +D  +G +  TY+   I+ ++ + I     +  +  +  QK      + L+     I + 
Sbjct: 68  YDLAKGVKFETYASLRIRGSIIDSIRD---MDWVPRSLRQKN-----KELEKVYVEIENE 119

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
                    +A+K+ +S S+   +      D +++++++  +     ++  L    +  E
Sbjct: 120 KGHTATDKEVAEKMGLSMSDFYKLL----NDVNVSSMMSLDEFMEQNYERGLEIFSESTE 175

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
                  E    + +L   +  L  +E+ +      +E  +TL+ +S+   V+  R+ Q+
Sbjct: 176 DKPEASLEFNEMKQLLADCIDKLPEKEKAVITFYYFEE--LTLKEISAIMNVTESRISQL 233

Query: 273 EARAFKKVQESI 284
             +A  +++  +
Sbjct: 234 HTKALLRMKGKL 245


>gi|30024622|dbj|BAC75679.1| sigma F [Streptomyces griseus]
          Length = 293

 Score =  134 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 53/237 (22%), Positives = 103/237 (43%), Gaps = 14/237 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                 L+ ++L LV   A  +R    P+ +VV  G IGL+ A+ +FDP+RG +  T++M
Sbjct: 66  RRVRTALIEANLPLVRYAAARFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFPTFAM 125

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +   ++ Y   + +      + +  RL     ++ G  + +T  + +      IA++L
Sbjct: 126 PTVVGEIKRYFRDNCA----HPSTSPDRLHELWVQVTGATEDLTTAHGRSPTTAEIAERL 181

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +SE EV++         + +              D L Y+      V          R+
Sbjct: 182 KISEDEVLACIEAGRSYHATSLEAAQEGDGLPGLLDRLGYEDPALAGV--------EHRD 233

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           ++   +  L  RE+RI   R      +T   +S+E  VS+  V ++ AR+F +++ +
Sbjct: 234 LVRHLLVQLPEREQRILLLRYYSN--LTQSQISAELGVSQMHVSRLLARSFARLRSA 288


>gi|312622918|ref|YP_004024531.1| RNA polymerase, sigma 28 subunit, sige [Caldicellulosiruptor
           kronotskyensis 2002]
 gi|312203385|gb|ADQ46712.1| RNA polymerase, sigma 28 subunit, SigE [Caldicellulosiruptor
           kronotskyensis 2002]
          Length = 244

 Score =  134 bits (339), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 53/262 (20%), Positives = 100/262 (38%), Gaps = 62/262 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EE  +  +    G       LV  +LRLVV IA  +    + + ++VS G IGL
Sbjct: 41  PPLTPDEEAQILYKIHYQGKEELKKILVERNLRLVVYIARRFENTKINLEDLVSIGTIGL 100

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+  ++P +  +LATY+   I+  +  ++ R+ +                        
Sbjct: 101 IKAINTYNPNKNIKLATYASKCIENEILMFLRRNSN------------------------ 136

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                            KKL +S  E ++++                D N     D L  
Sbjct: 137 -----------------KKLELSIDEPLNVD---------------WDGNELLLSDVLGT 164

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEV 264
           D     + +  + E    R  L R++  L  RE+RI E R         T + ++    +
Sbjct: 165 D----TEEIYNRIESSVEREALLRAIQKLPSREKRIVELRFGFGDGGEKTQKEVADMLGI 220

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+  + ++E +   ++++ + K
Sbjct: 221 SQSYISRLEKKIITRLKKELAK 242


>gi|294815383|ref|ZP_06774026.1| RNA polymerase sigma factor whiG [Streptomyces clavuligerus ATCC
           27064]
 gi|294327982|gb|EFG09625.1| RNA polymerase sigma factor whiG [Streptomyces clavuligerus ATCC
           27064]
          Length = 278

 Score =  134 bits (338), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 49/254 (19%), Positives = 107/254 (42%), Gaps = 16/254 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
            L + Y+  GD     +L+  +  LV  +A          +  ++ VS G  GL+ A++K
Sbjct: 31  ELWRSYKVTGDERLREQLILHYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEK 90

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD ER  +  TY++  I+ AM + + R+   +        + +      L+  L+     
Sbjct: 91  FDIERSIKFETYAITRIRGAMIDEL-RALDWIPRSVRQKARAVERAYATLEAQLR----- 144

Query: 153 NLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
             +      +A+++ ++  E+ ++     LA   +L  L++   +   +    +    D 
Sbjct: 145 --RTPSEGEVAEEMGIAVEELHAVFSQLSLANVVALEELLHVGGEGGDRL-SLMDTLEDT 201

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                +E  E +  R +L R+++ L  RE+ +          +TL  + +   V+  RV 
Sbjct: 202 AADDPVEVAEGRELRRLLARAINTLPDREKTVVTLYYY--EGLTLAEIGNVLGVTESRVS 259

Query: 271 QIEARAFKKVQESI 284
           QI  ++  +++  +
Sbjct: 260 QIHTKSVLQLRAKL 273


>gi|295695806|ref|YP_003589044.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
 gi|295411408|gb|ADG05900.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
          Length = 238

 Score =  134 bits (338), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 58/270 (21%), Positives = 101/270 (37%), Gaps = 63/270 (23%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
            YI        L ++EE    K+  E GD  A + L+  +LRLV  I   +   G    +
Sbjct: 20  SYIKNSAFPHPLSEEEEEQYLKQMAE-GDERARNLLIEHNLRLVAHIVKKFENTGEDTED 78

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++S G IGL++A++ F P +G +LATY+   I+  +                        
Sbjct: 79  LISIGTIGLIKAIESFQPHKGTKLATYAARCIENEI----------------------LM 116

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
           +LR LK                            + +S++  +  D          + N 
Sbjct: 117 HLRALKKT-------------------------RKDVSLHDPIGTD---------KEGNE 142

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTL 255
               D L  D D     +++  E K  ++ +   +  L+ RE+ +   R         T 
Sbjct: 143 VTLLDILSSDADD----VVDIVEMKLEKHQIYEKLQELDEREQEVIRGRFGLQNGEEKTQ 198

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             ++ E  +SR  V +IE RA  K+   ++
Sbjct: 199 REIAEELGISRSYVSRIEKRALMKLLHDLR 228


>gi|295399723|ref|ZP_06809704.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|312111758|ref|YP_003990074.1| RNA polymerase, sigma 28 subunit, SigE [Geobacillus sp. Y4.1MC1]
 gi|294978126|gb|EFG53723.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|311216859|gb|ADP75463.1| RNA polymerase, sigma 28 subunit, SigE [Geobacillus sp. Y4.1MC1]
          Length = 239

 Score =  134 bits (338), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 61/264 (23%), Positives = 112/264 (42%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE +L  +  + GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLTKEEEEMLIGKLSD-GDETARSLLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  ++ R+                    +++   
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMHLRRN-------------------NKVRAE- 135

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                            ++ DE LN      D N     D L  
Sbjct: 136 ---------------------------------VSFDEPLN---IDWDGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           + D    V+ +  E    RN+L  ++  L+ RE++I E R         T ++++    +
Sbjct: 160 EDD----VITKDLEADVDRNLLFNALRQLSDREKQIMELRFGLSGGEEKTQKDVADLLGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K +
Sbjct: 216 SQSYISRLEKRIIKRLRKEFNKMM 239


>gi|55274872|gb|AAV49239.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 179

 Score =  134 bits (338), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 54/214 (25%), Positives = 94/214 (43%), Gaps = 37/214 (17%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++ S+LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+ 
Sbjct: 1   RMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQ 60

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            ++  I+     +++      K L   LR  +     ++           IA++L+    
Sbjct: 61  TIERAIMNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVD 115

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           +V  M        S++                                +  + +  + + 
Sbjct: 116 DVSRMLRLNERITSVDTP------------------------------QDDDMKQSIVKW 145

Query: 232 MSVLNPRERRIFEARR--LQENPVTLENLSSEFE 263
           +  LN ++R +   R   L     TLE++  E  
Sbjct: 146 LFELNAKQREVLARRFGLLGYEAATLEDVGREIG 179


>gi|315444787|ref|YP_004077666.1| RNA polymerase sigma factor, sigma-70 family [Mycobacterium sp.
           Spyr1]
 gi|315263090|gb|ADT99831.1| RNA polymerase sigma factor, sigma-70 family [Mycobacterium sp.
           Spyr1]
          Length = 270

 Score =  134 bits (338), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 46/236 (19%), Positives = 90/236 (38%), Gaps = 14/236 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                R++   L L    A  +RG G    ++    ++GL+ AVK+FDP+ G     Y++
Sbjct: 29  RRLHERIIAMTLPLAQHTARRFRGRGQSHDDLFQVASVGLVNAVKRFDPDSGSDFLAYAV 88

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I   ++ Y       VK+      K L   L + +  L         P +V A    L
Sbjct: 89  PTIMGEVRRYFRDCSWAVKVPRRL--KDLNSQLAKARAELTQQLGRAPTPSEVAA---HL 143

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   EV+      +   +L+    S            + + D +   +++ E       
Sbjct: 144 GIDREEVVQATIASSNYATLSTDSTSGPDGDFVALRETLGEPDARLDAVVDNET------ 197

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            +   +  L PRE+ + + R   E  +T   ++     S+  V ++ A+A   +++
Sbjct: 198 -IRPLIEKLPPREQAVLKLRFFDE--MTQTQIAERMGYSQMHVSRLLAKALATLRD 250


>gi|283798349|ref|ZP_06347502.1| RNA polymerase sigma-E factor [Clostridium sp. M62/1]
 gi|291073934|gb|EFE11298.1| RNA polymerase sigma-E factor [Clostridium sp. M62/1]
 gi|295092808|emb|CBK78915.1| RNA polymerase, sigma 29 subunit, SigE [Clostridium cf.
           saccharolyticum K10]
          Length = 246

 Score =  134 bits (338), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 66/288 (22%), Positives = 116/288 (40%), Gaps = 68/288 (23%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           K + +   GEI    YI     +P  L+ +EE  +        D  A  RL+  +LRLVV
Sbjct: 20  KTLLMQKEGEI---HYIGGADILPAPLDSKEEAEVLGELGTEKDREAKSRLIEHNLRLVV 76

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA  +    + + +++S G IGL++A+  F+  +  +LATY+   I+  +  Y+ R+  
Sbjct: 77  YIAKKFDNTSVGVEDLISIGTIGLIKAINTFNTGKNIKLATYASRCIENEILMYLRRNNK 136

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
                                                     KL VS  E ++++     
Sbjct: 137 T-----------------------------------------KLEVSIDEPLNVD----- 150

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
                      D N     D L  D D    V+    E +  RN+L  ++S LNPRE++I
Sbjct: 151 ----------WDGNELLLSDILGTDED----VIYRDLEDEIERNLLNTAISRLNPREKKI 196

Query: 243 FEARRLQ----ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            E R          +T + ++    +S+  + ++E +  K++++ I K
Sbjct: 197 VELRFGLNSENGEEMTQKEVADLLGISQSYISRLEKKIMKRLKKEIVK 244


>gi|329941096|ref|ZP_08290375.1| SigL-like sigma factor [Streptomyces griseoaurantiacus M045]
 gi|329299627|gb|EGG43526.1| SigL-like sigma factor [Streptomyces griseoaurantiacus M045]
          Length = 319

 Score =  134 bits (338), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 48/236 (20%), Positives = 95/236 (40%), Gaps = 16/236 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            H LV  +L LV   A  +R    P+ +++  G IGL++A+ +F+  RG    T++M  I
Sbjct: 95  RHTLVELNLALVKFAAARFRTRSEPMEDIIQVGTIGLIKAIDRFELSRGVEFPTFAMPTI 154

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +   V  +A +L +S
Sbjct: 155 IGEIKRFFRDTSWSVRVPRRLQELRLD-----LAKAGDELAQQLDRAPTVTELADRLGLS 209

Query: 170 ESEVIS-MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
             EV+  M    A   S        D +     D + Y+          + E       L
Sbjct: 210 NEEVVEGMVASNAYTASSLDAQPEEDDSEGALADRIGYED--------HELEGVEYVESL 261

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              ++ L  R+R+I   R +    +T   +  E  +S+  V ++ +R   ++++ +
Sbjct: 262 KPLIAGLPQRDRKILSLRFVAN--MTQSEIGEELGISQMHVSRLLSRTLVRLRKGL 315


>gi|312794093|ref|YP_004027016.1| RNA polymerase, sigma 28 subunit, sige [Caldicellulosiruptor
           kristjanssonii 177R1B]
 gi|312181233|gb|ADQ41403.1| RNA polymerase, sigma 28 subunit, SigE [Caldicellulosiruptor
           kristjanssonii 177R1B]
          Length = 244

 Score =  134 bits (338), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 49/262 (18%), Positives = 102/262 (38%), Gaps = 62/262 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EE  +  R    G+      L+  +LRLVV IA  +    + + ++VS G IGL
Sbjct: 41  PPLTPDEEAQILYRIHYQGEEGLKKLLIERNLRLVVYIAKRFENTKVNLEDLVSIGTIGL 100

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+  ++P +  +LATY+   I+  +  ++ R+ +                        
Sbjct: 101 IKAINTYNPNKNIKLATYASKCIENEILMFLRRNSN------------------------ 136

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                            KKL +S  E ++++                D N     + L  
Sbjct: 137 -----------------KKLEMSIDEPLNVD---------------WDGNELLLSEVLGT 164

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEV 264
           D     + +  + E    +  L +++  L  RE++I E R     +   T + ++    +
Sbjct: 165 D----TEEIYNRIENNVEKEALLQAIQKLPSREKKIVELRFGFGDDGEKTQKEVADMLGI 220

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+  + ++E +   ++++ + K
Sbjct: 221 SQSYISRLEKKIITRLKKELAK 242


>gi|304316726|ref|YP_003851871.1| RNA polymerase, sigma 28 subunit, SigK [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
 gi|302778228|gb|ADL68787.1| RNA polymerase, sigma 28 subunit, SigK [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
          Length = 231

 Score =  134 bits (338), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 57/265 (21%), Positives = 98/265 (36%), Gaps = 63/265 (23%)

Query: 19  YIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           Y+      P  L  +EE    + Y+ +GD  A + L+  +LRLV  I   Y   G  + +
Sbjct: 21  YLTNASSFPQPLTAEEEKKYFEAYK-NGDEEAKNILIERNLRLVAHIVKKYSNTGKDVDD 79

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++S G IGL++A+  +D  +G  LATY+   I+  +   +                    
Sbjct: 80  LISIGTIGLIKAISTYDASKGTHLATYAARCIENEILMSLRSE----------------- 122

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
             +++K                              IS+   +  D          + N+
Sbjct: 123 --KKIKSE----------------------------ISLQDPIGID---------KEGNA 143

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTL 255
               D L  + D   +V  + E     + + ++  SVL  RER I E R         T 
Sbjct: 144 ISLIDILGTETD---EVSDQVELEMQIKKLYSKINSVLKNRERLIIELRYGLVNGGAKTQ 200

Query: 256 ENLSSEFEVSRERVRQIEARAFKKV 280
             ++    +SR  V +IE +A  K+
Sbjct: 201 REIAKMLGISRSYVSRIEKKALSKL 225


>gi|293366035|ref|ZP_06612723.1| RNA polymerase sigma-B factor [Staphylococcus epidermidis
           M23864:W2(grey)]
 gi|291319758|gb|EFE60116.1| RNA polymerase sigma-B factor [Staphylococcus epidermidis
           M23864:W2(grey)]
          Length = 256

 Score =  134 bits (338), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 50/263 (19%), Positives = 111/263 (42%), Gaps = 24/263 (9%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             ++     K+++E+ D  A  +LV  + +L+  +A  Y        ++V  G +GL+ A
Sbjct: 12  SPEQINQWIKQHQENEDSQAQDKLVKHYRKLIESLAYRYSKGQSHHEDLVQVGMVGLIGA 71

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +FD     +   + +  +   ++ Y+      V +     +        R+K     +
Sbjct: 72  INRFDLSFDRKFEVFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIG-----PRIKKVSDEL 126

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNC------RLAGDESLNALINSSDKNSSQWQDW 203
           T+   +   +  IA++L VS+ EV+           L+ D S+ A     D ++    D 
Sbjct: 127 TNELERSPSISEIAQRLEVSDEEVLEAMEMGQSYNALSVDHSIEA---DKDGSTVTLLDI 183

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    D          +   +R +L R + +L+ RER+I +   +    ++ +       
Sbjct: 184 MGQQDDNY--------DLTEKRMILERILPILSERERQIIQCTFI--EGLSQKETGERIG 233

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+  V +++  A KK+QE+ ++
Sbjct: 234 LSQMHVSRLQRTAIKKLQEAARQ 256


>gi|197303735|ref|ZP_03168772.1| hypothetical protein RUMLAC_02464 [Ruminococcus lactaris ATCC
           29176]
 gi|197297255|gb|EDY31818.1| hypothetical protein RUMLAC_02464 [Ruminococcus lactaris ATCC
           29176]
          Length = 265

 Score =  134 bits (338), Expect = 1e-29,   Method: Composition-based stats.
 Identities = 60/256 (23%), Positives = 98/256 (38%), Gaps = 62/256 (24%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L   EE    ++Y E GDL A H L+  +LRLV  I   Y+  G  + +++S G IGL+
Sbjct: 66  PLTPDEEKYYFQKYTE-GDLEAKHILIERNLRLVAHIVRKYQNLGEEMEDLISIGTIGLI 124

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV  FDPE+G RLA Y+   ++  +  Y+                       R +    
Sbjct: 125 KAVISFDPEKGNRLAAYASRCVENEILMYL-----------------------RARKKGG 161

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                                     IS+   +  D          D N  +  D +   
Sbjct: 162 KE------------------------ISLYEPIGTDR---------DGNEIRLYDII--- 185

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVS 265
                 V  +   ++N + +  +  S L+PRER + + R         T   ++S   +S
Sbjct: 186 ETTDTDVPEKLYLKENIQKLYEKVESELSPRERLVLKMRYGLYNGEEYTQREIASLLGIS 245

Query: 266 RERVRQIEARAFKKVQ 281
           R  V +IE  A +K++
Sbjct: 246 RSYVSRIEKSAVEKLR 261


>gi|331696957|ref|YP_004333196.1| SigB/F/G subfamily RNA polymerase sigma-28 subunit [Pseudonocardia
           dioxanivorans CB1190]
 gi|326951646|gb|AEA25343.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Pseudonocardia dioxanivorans CB1190]
          Length = 288

 Score =  134 bits (338), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 52/223 (23%), Positives = 91/223 (40%), Gaps = 20/223 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             RLVT HL +V  IA  + G G P+ ++   G +GL+ AV +FDP RG    +Y++  I
Sbjct: 67  RERLVTGHLPVVRHIARRFAGRGEPVDDLEQAGTVGLINAVDRFDPARGVDFLSYAVPTI 126

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +       +++      +RL      +   +  +     +  +   IA ++   
Sbjct: 127 TGEVRRHFRDRTWSMRVP-----RRLKELQSSINSAVGGLAQELGRAPRPSEIADRIGRD 181

Query: 170 ESEVIS-MNCR-LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
             EVI  +  R +    SL+ L+  SD   S+              +   + E+ + R  
Sbjct: 182 VDEVIEGLEARQVYRSTSLDELVADSDAMLSETLG-----------IADAELEKVDYRQT 230

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
           L   +  L  RER I   R      +T   ++ E  VS+  V 
Sbjct: 231 LAPLLDELPTRERTILVLRFFAG--MTQTQIADEVGVSQMHVS 271


>gi|29827692|ref|NP_822326.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29604792|dbj|BAC68861.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 295

 Score =  134 bits (338), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 48/266 (18%), Positives = 112/266 (42%), Gaps = 21/266 (7%)

Query: 35  YVLAKRYRE-----HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
               +R  E     H    A + L+  ++ LV   A  +R  G  + ++V  G IGL++A
Sbjct: 43  RQFFRRLSELEEGTHDYQYARNTLIEMNMSLVRFAAGRFRNRGDDMEDIVQVGMIGLIKA 102

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +F+  R     ++++ +I   ++ +   +   V +     + R+      L    + +
Sbjct: 103 IDRFEISREVEFTSFALPYIVGEIKRFFRDTTWAVHVPRRLQELRV-----ELAKAREEL 157

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYD 207
           +    +   V  +A  +N+SE+EV+       G    SL+A ++  D+         + +
Sbjct: 158 SSRLDREPSVAELATLMNLSENEVVEAQIASNGYNSSSLDAALSGDDQEGEAVLADFIGE 217

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            D   Q++ +        + L   ++ L+ R+R+I   R ++E   T  ++ +    S+ 
Sbjct: 218 EDDGMQLVEDF-------HTLAPLVAELSDRDRQIIHMRFVEE--ATQADIGARLGCSQM 268

Query: 268 RVRQIEARAFKKVQESIQKQVELSSS 293
            V ++  R  ++++  +   +    S
Sbjct: 269 HVSRLIKRIIEQLRTGMLSDLHRVES 294


>gi|332653851|ref|ZP_08419595.1| RNA polymerase sigma-E factor [Ruminococcaceae bacterium D16]
 gi|332516937|gb|EGJ46542.1| RNA polymerase sigma-E factor [Ruminococcaceae bacterium D16]
          Length = 231

 Score =  134 bits (338), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 62/265 (23%), Positives = 102/265 (38%), Gaps = 66/265 (24%)

Query: 24  RKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
              P  L+ +EE    +R  + GDL A + LV  +LRLV  I   Y        +++S G
Sbjct: 24  GSFPRPLKAEEERKYLERCAQ-GDLEARNILVEHNLRLVAHIVKKYYAQTGDQDDLISIG 82

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            IGL++ +  F  ++  RLATY+   I+  +  +                        R 
Sbjct: 83  TIGLIKGISTFKADKNVRLATYASRCIENEILMHF-----------------------RA 119

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL-NALINSSDKNSSQWQ 201
           +  LQ                                  G+ SL + + N  D NS    
Sbjct: 120 QKKLQ----------------------------------GEVSLSDTMENGGDGNSLSLM 145

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLS 259
           D +  D +    +L + + R   R +       LNPRER I   R   ++  P T   ++
Sbjct: 146 DVIAVDDN----MLEDLDTRDACRRVRQCVGECLNPRERAIITLRYGLDDQPPRTQREVA 201

Query: 260 SEFEVSRERVRQIEARAFKKVQESI 284
           +   +SR  V +IE RA  K+++++
Sbjct: 202 ARCGISRSYVSRIEKRALAKLEQAM 226


>gi|222528793|ref|YP_002572675.1| sporulation sigma factor SigE [Caldicellulosiruptor bescii DSM
           6725]
 gi|222455640|gb|ACM59902.1| RNA polymerase, sigma 28 subunit, SigE [Caldicellulosiruptor bescii
           DSM 6725]
          Length = 244

 Score =  134 bits (338), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 52/262 (19%), Positives = 100/262 (38%), Gaps = 62/262 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EE  +  +    G       LV  +LRLVV IA  +    + + ++VS G IGL
Sbjct: 41  PPLTPDEEAQILYKIHYQGKEELKKLLVERNLRLVVYIARRFENTKINLEDLVSIGTIGL 100

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+  ++P +  +LATY+   I+  +  ++ R+ +                        
Sbjct: 101 IKAINTYNPNKNIKLATYASKCIENEILMFLRRNSN------------------------ 136

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                            KKL +S  E ++++                D N     D L  
Sbjct: 137 -----------------KKLELSIDEPLNVD---------------WDGNELLLSDVLGT 164

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEV 264
           D     + +  + E    R  L R++  L  RE++I E R         T + ++    +
Sbjct: 165 D----TEEIYNRIESSVEREALLRAIQKLPSREKKIVELRFGFGDGGEKTQKEVADMLGI 220

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+  + ++E +   ++++ + K
Sbjct: 221 SQSYISRLEKKIITRLKKELAK 242


>gi|27468586|ref|NP_765223.1| RNA polymerase sigma factor SigB [Staphylococcus epidermidis ATCC
           12228]
 gi|57867587|ref|YP_189242.1| RNA polymerase sigma factor SigB [Staphylococcus epidermidis RP62A]
 gi|251812213|ref|ZP_04826686.1| DNA-directed RNA polymerase sigma subunit FliA [Staphylococcus
           epidermidis BCM-HMP0060]
 gi|282876523|ref|ZP_06285389.1| RNA polymerase sigma-B factor [Staphylococcus epidermidis SK135]
 gi|27316133|gb|AAO05267.1|AE016749_213 sigma factor B [Staphylococcus epidermidis ATCC 12228]
 gi|57638245|gb|AAW55033.1| RNA polymerase sigma-37 factor [Staphylococcus epidermidis RP62A]
 gi|251804310|gb|EES56967.1| DNA-directed RNA polymerase sigma subunit FliA [Staphylococcus
           epidermidis BCM-HMP0060]
 gi|281294775|gb|EFA87303.1| RNA polymerase sigma-B factor [Staphylococcus epidermidis SK135]
 gi|329726159|gb|EGG62631.1| RNA polymerase sigma-B factor [Staphylococcus epidermidis VCU144]
 gi|329734176|gb|EGG70494.1| RNA polymerase sigma-B factor [Staphylococcus epidermidis VCU045]
          Length = 256

 Score =  134 bits (338), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 50/263 (19%), Positives = 111/263 (42%), Gaps = 24/263 (9%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             ++     K+++E+ D  A  +LV  + +L+  +A  Y        ++V  G +GL+ A
Sbjct: 12  SPEQINQWIKQHQENEDSQAQDKLVKHYRKLIESLAYRYSKGQSHHEDLVQVGMVGLIGA 71

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +FD     +   + +  +   ++ Y+      V +     +        R+K     +
Sbjct: 72  INRFDLSFDRKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIG-----PRIKKVSDEL 126

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNC------RLAGDESLNALINSSDKNSSQWQDW 203
           T+   +   +  IA++L VS+ EV+           L+ D S+ A     D ++    D 
Sbjct: 127 TNELERSPSISEIAQRLEVSDEEVLEAMEMGQSYNALSVDHSIEA---DKDGSTVTLLDI 183

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    D          +   +R +L R + +L+ RER+I +   +    ++ +       
Sbjct: 184 MGQQDDNY--------DLTEKRMILERILPILSERERQIIQCTFI--EGLSQKETGERIG 233

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+  V +++  A KK+QE+ ++
Sbjct: 234 LSQMHVSRLQRTAIKKLQEAARQ 256


>gi|312128105|ref|YP_003992979.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor hydrothermalis 108]
 gi|311778124|gb|ADQ07610.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor hydrothermalis 108]
          Length = 244

 Score =  134 bits (338), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 50/262 (19%), Positives = 101/262 (38%), Gaps = 62/262 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EE  +  R    G+      L+  +LRLVV IA  +    + + ++VS G IGL
Sbjct: 41  PPLTPDEEAQILYRIHYQGEEGLKKLLIERNLRLVVYIAKRFENTKINLEDLVSIGTIGL 100

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+  ++P +  +LATY+   I+  +  ++ R+ +                        
Sbjct: 101 IKAINTYNPNKNIKLATYASKCIENEILMFLRRNSN------------------------ 136

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                            +KL +S  E ++++                D N     D L  
Sbjct: 137 -----------------RKLELSIDEPLNVD---------------WDGNELLLSDVLGT 164

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEV 264
           D     + +  K E    +  L +++  L  RE++I E R         T + ++    +
Sbjct: 165 D----TEEIYNKIESSVEKEALLQAIQKLPSREKKIVELRFGFGDGGEKTQKEVADMLGI 220

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+  + ++E +   ++++ + K
Sbjct: 221 SQSYISRLEKKIITRLKKELAK 242


>gi|294501329|ref|YP_003565029.1| RNA polymerase sigma-K factor [Bacillus megaterium QM B1551]
 gi|295706676|ref|YP_003599751.1| RNA polymerase sigma-K factor [Bacillus megaterium DSM 319]
 gi|294351266|gb|ADE71595.1| RNA polymerase sigma-K factor [Bacillus megaterium QM B1551]
 gi|294804335|gb|ADF41401.1| RNA polymerase sigma-K factor [Bacillus megaterium DSM 319]
          Length = 242

 Score =  134 bits (338), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 55/268 (20%), Positives = 93/268 (34%), Gaps = 65/268 (24%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+        L   EE        E GD  A + L+  +LRLV  I   +   G   
Sbjct: 18  LVSYVKNNAFPQPLSAAEEKRYLSLM-EQGDQEARNLLIEHNLRLVAHIVKKFENTGEDA 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++S G IGL++A++ +   +G +LATY+   I+  +                      
Sbjct: 77  EDLISIGTIGLIKAIESYSQGKGTKLATYAARCIENEI---------------------- 114

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS-D 194
             +LR LK                                       D SL+  I    +
Sbjct: 115 LMHLRALKKT-----------------------------------KKDVSLHDPIGQDKE 139

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NP 252
            N     D L  + D     +I+  +       +   + +L+ RE+ +   R   +  + 
Sbjct: 140 GNEISLIDVLKSESDD----VIDMIQLNMELEKIKEYIDILDDREKEVIVGRFGLDLQDE 195

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKV 280
            T   ++ E  +SR  V +IE RA  K+
Sbjct: 196 KTQREIAKELNISRSYVSRIEKRALMKM 223


>gi|326443735|ref|ZP_08218469.1| RNA polymerase sigma factor WhiG [Streptomyces clavuligerus ATCC
           27064]
          Length = 258

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 49/254 (19%), Positives = 107/254 (42%), Gaps = 16/254 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
            L + Y+  GD     +L+  +  LV  +A          +  ++ VS G  GL+ A++K
Sbjct: 11  ELWRSYKVTGDERLREQLILHYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEK 70

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD ER  +  TY++  I+ AM + + R+   +        + +      L+  L+     
Sbjct: 71  FDIERSIKFETYAITRIRGAMIDEL-RALDWIPRSVRQKARAVERAYATLEAQLR----- 124

Query: 153 NLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
             +      +A+++ ++  E+ ++     LA   +L  L++   +   +    +    D 
Sbjct: 125 --RTPSEGEVAEEMGIAVEELHAVFSQLSLANVVALEELLHVGGEGGDRL-SLMDTLEDT 181

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                +E  E +  R +L R+++ L  RE+ +          +TL  + +   V+  RV 
Sbjct: 182 AADDPVEVAEGRELRRLLARAINTLPDREKTVVTLYYY--EGLTLAEIGNVLGVTESRVS 239

Query: 271 QIEARAFKKVQESI 284
           QI  ++  +++  +
Sbjct: 240 QIHTKSVLQLRAKL 253


>gi|254381060|ref|ZP_04996425.1| sigma factor [Streptomyces sp. Mg1]
 gi|194339970|gb|EDX20936.1| sigma factor [Streptomyces sp. Mg1]
          Length = 302

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 53/243 (21%), Positives = 110/243 (45%), Gaps = 15/243 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L+  ++ LV   A  +R     G+ I ++V  G IGL++A+ +FDP+R    +T ++
Sbjct: 70  RNTLIEMNISLVNFAARRFRSRAGGGVDIEDIVQVGTIGLIKAIDRFDPDREVEFSTLAL 129

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            +I   ++ +   +   V +     + R       L     A+T+   +   V  IA+ L
Sbjct: 130 PYISGEIKRFFRDTTWAVHVPRRLQELR-----SELAKSQDALTEVFGRAPTVKEIAEHL 184

Query: 167 NVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            +SE +VI       G    S++A  +S  + S + +   + +  G+    +E  E  + 
Sbjct: 185 ELSEDDVIEGLVAANGYTSGSIDAATSSRQRTSGETEGRSLAETVGEVDPDMELFEEFHT 244

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              L   +  L  R+RRI   R  +E  +T   + +E  +S+ +V ++  R   +++ ++
Sbjct: 245 ---LAPLLQSLKERDRRILAMRFGEE--MTQAEIGTELGISQMQVSRLLTRVLTRLRTAM 299

Query: 285 QKQ 287
             +
Sbjct: 300 LAE 302


>gi|153852719|ref|ZP_01994156.1| hypothetical protein DORLON_00138 [Dorea longicatena DSM 13814]
 gi|149754361|gb|EDM64292.1| hypothetical protein DORLON_00138 [Dorea longicatena DSM 13814]
          Length = 237

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 47/250 (18%), Positives = 102/250 (40%), Gaps = 17/250 (6%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             L ++  E GD  A  ++V  +  LV  I   + G G  + ++   G IGL++A+ KFD
Sbjct: 5   IALIQKSHE-GDEEARAQIVEENTGLVWCIVRRFTGRGTELEDLFQIGTIGLLKAIDKFD 63

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
                + +TY++  I   ++ ++     ++K+  +  +              + +     
Sbjct: 64  LSYEVKFSTYAVPMISGEIKRFLRDDG-MIKVSRSLKELSYKGY-----QAQEVLGRKLG 117

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +   V  +A+ L+VS  E+          ESL+  +   +       + +  +   +E+V
Sbjct: 118 REPSVTELAEYLDVSPEELTMAMDACTDVESLHRPVYKKEGQEISLMEKVGKEDGAEERV 177

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
           L     ++   ++           ER++   R   E   T   +  E  +S+ +V ++E 
Sbjct: 178 LDHLLLKELLTSLDKE--------ERKLIYLRYFAE--KTQTQIGKEMGISQVQVSRMEK 227

Query: 275 RAFKKVQESI 284
           +  K ++E I
Sbjct: 228 KILKNLRERI 237


>gi|194017684|ref|ZP_03056294.1| RNA polymerase sigma-K factor [Bacillus pumilus ATCC 7061]
 gi|194010584|gb|EDW20156.1| RNA polymerase sigma-K factor [Bacillus pumilus ATCC 7061]
          Length = 289

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 52/279 (18%), Positives = 98/279 (35%), Gaps = 63/279 (22%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
             M ++V   + L  Y+        L   +E        + GD  A + L+  +LRLV  
Sbjct: 54  TAMGLMVKELVFLVSYVKNNAFPQPLSGDDEKKYLALMAQ-GDEHARNMLIEHNLRLVAH 112

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           I   +   G    +++S G IGL++A++ +   +G +LATY+   I+  +          
Sbjct: 113 IVKKFENTGEDAEDLISIGTIGLIKAIESYSSGKGTKLATYAARCIENEI---------- 162

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
                         +LR LK                                       D
Sbjct: 163 ------------LMHLRALKKT-----------------------------------KKD 175

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SL+  I    + +   +  L+     + + +I+  +       +   + +L+ RE+ + 
Sbjct: 176 VSLHDPIGQDKEGN---EISLIDVLKSESEDVIDTIQLNMELEKVKEYIDILDGREKEVI 232

Query: 244 EARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             R   +     T   ++ E  +SR  V +IE RA  K+
Sbjct: 233 VGRFGLDLKKEKTQREIAKELGISRSYVSRIEKRALMKM 271


>gi|325264805|ref|ZP_08131534.1| RNA polymerase sigma-E factor [Clostridium sp. D5]
 gi|324030097|gb|EGB91383.1| RNA polymerase sigma-E factor [Clostridium sp. D5]
          Length = 246

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 57/272 (20%), Positives = 110/272 (40%), Gaps = 65/272 (23%)

Query: 18  RYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
            YI     +P  LE + E  + +      D  A   L+  +LRLVV IA  +   G+ + 
Sbjct: 31  HYIGGSEVLPAPLETERETEVIEHLGSEYDQEAKKLLIEHNLRLVVYIAKKFDNTGVGVE 90

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++S G IGL++A+  F+P +  +LATY+   I+  +  Y+ R+                
Sbjct: 91  DLISIGTIGLIKAINTFNPTKKIKLATYASRCIENEILMYLRRNSKT------------- 137

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
                                       K+ VS  E ++++                D N
Sbjct: 138 ----------------------------KMEVSIDEPLNVD---------------WDGN 154

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP---- 252
                D L  D D   + L  + ERK    +L ++++ L+ RE+ I + R   +NP    
Sbjct: 155 ELLLSDILGTDEDTIYKDLENEAERK----LLVKAINKLSSREKMIVKMRFGLDNPEGEE 210

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            T + ++    +S+  + ++E +  ++++  +
Sbjct: 211 KTQKEVADLLGISQSYISRLEKKIMQRLKREM 242


>gi|255312661|gb|ACU01740.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 53/205 (25%), Positives = 94/205 (45%), Gaps = 12/205 (5%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           L LVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LLLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           +     +++      K L   LR  +     ++           IA++L+    +V  M 
Sbjct: 61  MNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRML 115

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                  S +  +    +     +  L    D +E    +  +  + +  + + +  LN 
Sbjct: 116 RLNERITSEDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNA 170

Query: 238 RERRIFEARR--LQENPVTLENLSS 260
           ++R +   R   L     TLE++  
Sbjct: 171 KQREVLARRFGLLGYEAATLEDVGR 195


>gi|258514023|ref|YP_003190245.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfotomaculum
           acetoxidans DSM 771]
 gi|257777728|gb|ACV61622.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfotomaculum
           acetoxidans DSM 771]
          Length = 249

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 59/259 (22%), Positives = 124/259 (47%), Gaps = 14/259 (5%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQA 89
           E   L + Y  + D  A  +L+  +L LV  ++         G+   ++   G +GL+++
Sbjct: 2   EPKKLWEAYISNRDKKAREKLILMYLPLVKHLSGRLAVRLPIGISYEDLEGYGVVGLIES 61

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           ++KF+P +G    T++   I+ A+ + + +   L  +  T  QK  F  +   +  L+ I
Sbjct: 62  IEKFNPAKGVSFETFAYRRIRGAIIDEVRK---LYWVPRTLWQK--FQAVNAERERLRRI 116

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
             +N+  EQV A    ++++E    S         SL+ ++ SSD +S +  + +    D
Sbjct: 117 NGDNVTDEQVAASLN-ISIAELHKTSNCYNQLNMNSLDEVLTSSDGDSVRLGNLIP---D 172

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
                 ++  E ++ R +L  +++ LN ++R +       +  +TL+ +    EVS  RV
Sbjct: 173 PNSPDPLDVVEEQDGRRILAEAVNSLNEKDRLVMALYY--QERLTLKEIGQVLEVSESRV 230

Query: 270 RQIEARAFKKVQESIQKQV 288
            Q+ ARA  ++++ I++ +
Sbjct: 231 CQLHARAMSRLRQKIKEML 249


>gi|226359630|ref|YP_002777408.1| RNA polymerase sigma factor [Rhodococcus opacus B4]
 gi|226238115|dbj|BAH48463.1| RNA polymerase sigma factor [Rhodococcus opacus B4]
          Length = 265

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 42/237 (17%), Positives = 91/237 (38%), Gaps = 14/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +    ++T  L L   IA  + G G    +++    +GL++AV +FDP+RGF   +Y++ 
Sbjct: 40  ALRDEIITRCLPLADHIARRFGGRGEAHEDLLQVARLGLVKAVDRFDPDRGFDFVSYAVP 99

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I   ++ Y   +   +++     +         +   +  ++    +      IA +L 
Sbjct: 100 TIMGEVRRYFRDTGWSMRVPRRMQELHAL-----IAKAVDELSQELGRSPSASEIAAELE 154

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +   EV          ++L+      D          + + D +   +            
Sbjct: 155 LDVREVSEGLLAKNAYQTLSMDAAMGDDPDDLPLAETLGEEDPELANVESHAS------- 207

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +  ++  L P ERR+   R      +T   ++    VS+ +V +I AR    ++E +
Sbjct: 208 VRPALEKLPPLERRVLMLRFFG--SMTQTEIAQRVGVSQMQVSRILARTLSGLREQL 262


>gi|295840299|ref|ZP_06827232.1| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
 gi|295827905|gb|EDY46913.2| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
          Length = 286

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 53/245 (21%), Positives = 104/245 (42%), Gaps = 19/245 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+  ++ LV   A  +R  G  + +VV  G IGL++A+ +F+  R     T+++
Sbjct: 56  QDARNTLIEMNMSLVRFAARRFRSRGDDMEDVVQVGTIGLIKAIDRFELSREVEFTTFAV 115

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            +I   ++ +   +   V +     + R+      L    + ++    +  +V  +A  +
Sbjct: 116 PYIVGEIKRFFRDTTWAVHVPRRLQEARV-----ELAKANEELSTRLGRAPRVSELAALM 170

Query: 167 NVSESEVISMNCRLAG--DESLNALINSSDKNSSQ--WQDWLVYDHDGQEQVLIEKEERK 222
           N+SE +V+       G    SL+A I   D    +    D++  D  G E V        
Sbjct: 171 NLSEQQVVEAQIAANGYSSSSLDATIGGEDSGEGEAVLSDFIGADDPGMELV-------- 222

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              + L   ++ L PR+R+I E R  QE  +T   +     VS+  V ++  R    ++ 
Sbjct: 223 EDLHALAPLLAGLEPRDRQILELRFGQE--LTQAQIGERLGVSQMHVSRLLNRTLGTLRA 280

Query: 283 SIQKQ 287
            +  +
Sbjct: 281 GLMSE 285


>gi|331269717|ref|YP_004396209.1| RNA polymerase sigma-K factor [Clostridium botulinum BKT015925]
 gi|329126267|gb|AEB76212.1| RNA polymerase sigma-K factor [Clostridium botulinum BKT015925]
          Length = 226

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 60/275 (21%), Positives = 105/275 (38%), Gaps = 63/275 (22%)

Query: 9   IVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           +++G   L+ Y+      P  L + EE    K++++ GD  A   L+  +LRLV  I   
Sbjct: 1   MIDGMTFLTAYVSNGTSFPQPLNEDEERYYLKKFKD-GDTLAKGILIERNLRLVAHIVKK 59

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y      I +++S G +GL++A+  FD  +G RLATY+   I+  +              
Sbjct: 60  YSYPNKDIDDLISIGTVGLIKAIDSFDISKGTRLATYAARCIENEILM------------ 107

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
                  L  N +++K                              + +   +  D    
Sbjct: 108 -------LIRNTKKIKSE----------------------------VYLQDPIGVD---- 128

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
                 + N     D L  D +   +V+   E R   + +  +    L  RE+ I + R 
Sbjct: 129 -----KEGNEISLMDVLSSDENSVIEVV---ENRMQVKKLYDKINECLTDREKIIIKMRY 180

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
              +  P T   +++   +SR  V +IE RA KK+
Sbjct: 181 GLNDGKPKTQREIAAFLNISRSYVSRIEKRALKKM 215


>gi|312876364|ref|ZP_07736349.1| RNA polymerase, sigma 28 subunit, SigE [Caldicellulosiruptor
           lactoaceticus 6A]
 gi|311796858|gb|EFR13202.1| RNA polymerase, sigma 28 subunit, SigE [Caldicellulosiruptor
           lactoaceticus 6A]
          Length = 244

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 49/262 (18%), Positives = 102/262 (38%), Gaps = 62/262 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EE  +  R    G+      L+  +LRLVV IA  +    + + ++VS G IGL
Sbjct: 41  PPLTPDEEAQILYRIHYQGEEGLKKLLIERNLRLVVYIAKRFENTKVNLEDLVSIGTIGL 100

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+  ++P +  +LATY+   I+  +  ++ R+ +                        
Sbjct: 101 IKAINTYNPNKNIKLATYASKCIENEILMFLRRNSN------------------------ 136

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                            KKL +S  E ++++                D N     + L  
Sbjct: 137 -----------------KKLEMSIDEPLNVD---------------WDGNELLLSEVLGT 164

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEV 264
           D     + +  + E    +  L +++  L  RE++I E R     +   T + ++    +
Sbjct: 165 D----TEEIYNRIENNVEKEALLQAIQKLPSREKKIVELRSGFGDDGEKTQKEVADMLGI 220

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+  + ++E +   ++++ + K
Sbjct: 221 SQSYISRLEKKIITRLKKELAK 242


>gi|160915290|ref|ZP_02077503.1| hypothetical protein EUBDOL_01299 [Eubacterium dolichum DSM 3991]
 gi|158433089|gb|EDP11378.1| hypothetical protein EUBDOL_01299 [Eubacterium dolichum DSM 3991]
          Length = 240

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 51/247 (20%), Positives = 102/247 (41%), Gaps = 21/247 (8%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A RY   GD  A  + V ++  LV  I   +    +   ++   G IGLM+A+  FD   
Sbjct: 12  AIRY---GDEEALEQFVEANQPLVYAIVKRFHNRRISQEDLFQIGCIGLMKAIHNFDAAY 68

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
             + +TY++  I   ++ +     S ++I  +   K  +  + ++K   + +T    K  
Sbjct: 69  EVKFSTYAVPIIMGEIKRFFRDDGS-IRISRSL--KEGYLQMLKIK---EQLTQTLGKEP 122

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               IA+ +N+   EVI          SL+  I  +D ++   +D +             
Sbjct: 123 TYAQIAQAMNIEVGEVILAFEANQFMYSLDEPIYENDGSAIVLEDRVEDP---------- 172

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
           K+     +  L +  + L  RE+ I   R         E+++    +S+ +V ++E +  
Sbjct: 173 KQTDIVMKLSLRKEFARLEQREQLILHYRYDLNMK--QEDIAKRLHISQVQVSRLEKKIL 230

Query: 278 KKVQESI 284
            K++E +
Sbjct: 231 WKLKERL 237


>gi|251797416|ref|YP_003012147.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Paenibacillus sp.
           JDR-2]
 gi|247545042|gb|ACT02061.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Paenibacillus sp.
           JDR-2]
          Length = 256

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 57/256 (22%), Positives = 109/256 (42%), Gaps = 20/256 (7%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
            L + ++E GDL A  RL+   L LV  +           +   ++ S G +GL+ A++K
Sbjct: 8   DLWRAWKEEGDLEAKKRLIEQFLPLVDYVTNRMAIGLPKNVLKDDLASNGVMGLIDAIEK 67

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  RG +  TY+ W I+ ++ + + R    V        K       R++   Q++   
Sbjct: 68  FDYCRGLQFETYASWRIRGSIIDGL-RQGDWVPRSVREKAK-------RIEEAYQSLEQK 119

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDG 210
            L+      I++ LNVSE E  +M   +A     SL   I   +  +      L    D 
Sbjct: 120 YLRSVSDAEISQYLNVSEKEFTTMLHEIAITTVCSLEDPIREEESET-----RLSLLIDE 174

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
           + +    K      ++ L   +  L  +ER +      +E  ++L  ++    +S  R+ 
Sbjct: 175 RAKNPDHKAHEFFLKDSLISGIEKLTEKERTVISLFYYEE--LSLSEIAEVMSLSPSRIS 232

Query: 271 QIEARAFKKVQESIQK 286
           Q+ ++A  +++ ++ K
Sbjct: 233 QLHSKAILRLRGALAK 248


>gi|153854689|ref|ZP_01995939.1| hypothetical protein DORLON_01937 [Dorea longicatena DSM 13814]
 gi|149752793|gb|EDM62724.1| hypothetical protein DORLON_01937 [Dorea longicatena DSM 13814]
          Length = 246

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 55/274 (20%), Positives = 106/274 (38%), Gaps = 65/274 (23%)

Query: 18  RYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
            YI     +P  LE   E    K      D +A   L+  +LRLVV IA  +   G+ + 
Sbjct: 31  HYIGGSDILPAPLEAAAEKKAIKDLGTEKDENARKILIEHNLRLVVYIAKKFDNTGVGVE 90

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++S G IGL++A+  F+P++  +LATY+   I+  +  Y+ R+                
Sbjct: 91  DLISIGTIGLIKAINTFNPDKNIKLATYASRCIENEILMYLRRNNKT------------- 137

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
                                       ++ VS  E ++++                D N
Sbjct: 138 ----------------------------RMEVSIDEPLNVD---------------WDGN 154

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL----QENP 252
                D L  + D   + L  + E+K    +L R++  L+ RE+ I   R          
Sbjct: 155 ELLLSDILGTEEDAIYKDLENEAEKK----VLIRAIGRLSGREQMIIRMRFGLGTEDGEE 210

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            T + ++    +S+  + ++E +  ++++  + K
Sbjct: 211 KTQKEVADMLGISQSYISRLEKKIMQRLRREMVK 244


>gi|46240842|dbj|BAD15074.1| RNA polymerase alternative sigma factor [Saccharopolyspora
           erythraea]
          Length = 280

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 48/244 (19%), Positives = 99/244 (40%), Gaps = 19/244 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                RLVT HL +   IA  +   G    ++     +GL+ AV +FDP RG    +Y++
Sbjct: 38  EQLRDRLVTEHLPVAEHIARRFSHRGESQEDLTQVATLGLINAVDRFDPGRGVDFLSYAV 97

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I   ++ +   +   V++     +  L      +   +  ++    +      IA+ L
Sbjct: 98  PTIMGEVRRHFRDTGWAVRMPRRLQELHLS-----VSAAIARLSQEFGRAPTPSEIAEHL 152

Query: 167 NVSESEVI--SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            +S ++V             SL+ L+  +D+         + D  G     +++ E    
Sbjct: 153 GISTNDVYHGLEAGNAYRSASLDELLTDTDE-------IPLGDAIGSNDAELDEVE---N 202

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  +   ++ L  RERRI   R  +   +T   ++ +  +S+  V ++ +R    ++E +
Sbjct: 203 RETIRPLLAELEERERRILVMRFFRG--MTQTQIAEQVGISQMHVSRLLSRTLAWLRERL 260

Query: 285 QKQV 288
           +  V
Sbjct: 261 ETDV 264


>gi|134102136|ref|YP_001107797.1| RNA polymerase sigma factor [Saccharopolyspora erythraea NRRL 2338]
 gi|291007613|ref|ZP_06565586.1| RNA polymerase sigma factor [Saccharopolyspora erythraea NRRL 2338]
 gi|133914759|emb|CAM04872.1| RNA polymerase sigma factor [Saccharopolyspora erythraea NRRL 2338]
          Length = 280

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 48/244 (19%), Positives = 99/244 (40%), Gaps = 19/244 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                RLVT HL +   IA  +   G    ++     +GL+ AV +FDP RG    +Y++
Sbjct: 38  EQLRDRLVTEHLPVAEHIARRFSHRGESQEDLTQVATLGLINAVDRFDPGRGVDFLSYAV 97

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I   ++ +   +   V++     +  L      +   +  ++    +      IA+ L
Sbjct: 98  PTIMGEVRRHFRDTGWAVRMPRRLQELHLS-----VSAAIARLSQEFGRAPTPSEIAEHL 152

Query: 167 NVSESEVI--SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            +S ++V             SL+ L+  +D+         + D  G     +++ E    
Sbjct: 153 GISTNDVYHGLEAGNAYRSASLDELLTDTDE-------IPLGDAIGSNDAELDEVE---N 202

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  +   ++ L  RERRI   R  +   +T   ++ +  +S+  V ++ +R    ++E +
Sbjct: 203 RETIRPLLAELEERERRILVMRFFRG--MTQTQIAEQVGISQMHVSRLLSRTLAWLRERL 260

Query: 285 QKQV 288
           +  V
Sbjct: 261 ETDV 264


>gi|15895412|ref|NP_348761.1| sigma factor of SigD/WhiG family [Clostridium acetobutylicum ATCC
           824]
 gi|15025135|gb|AAK80101.1|AE007715_6 Sigma factor of SigD/WhiG family [Clostridium acetobutylicum ATCC
           824]
 gi|325509558|gb|ADZ21194.1| Sigma factor of SigD/WhiG family [Clostridium acetobutylicum EA
           2018]
          Length = 241

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 61/248 (24%), Positives = 103/248 (41%), Gaps = 19/248 (7%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
            G +     L+  ++ LV  IA      +   +   ++V  G IGLM A+KKFD  +G +
Sbjct: 4   DGIVDDREALIKKYIPLVKYIASRVIIGKSKYIEYEDLVGYGMIGLMDALKKFDQSKGMK 63

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TYS   IK AM + + ++  +         K     L R    ++ +     +    +
Sbjct: 64  FSTYSSIRIKGAMIDELRKNSPI--------SKGAMDKLNRYNLVVERLEKELSREPTEL 115

Query: 161 AIAKKLNVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
            IA  L V   EV  +   +      SL  LI S D +               E+ L EK
Sbjct: 116 EIASGLGVGRKEVGEIEGYINYISVVSLEDLIFSEDDDMPLIGTIEDEKSPSPEKALEEK 175

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           EE       L + + +LN ++R +          +TL+ + +   VS  RV Q+  RA  
Sbjct: 176 EEI----EYLAKGIELLNEKDRMVLSLYYY--EGLTLKKIGNILNVSESRVCQLHTRAIM 229

Query: 279 KVQESIQK 286
            +++S++K
Sbjct: 230 HLRKSLKK 237


>gi|332799103|ref|YP_004460602.1| RNA polymerase sigma-28 subunit SigE [Tepidanaerobacter sp. Re1]
 gi|332696838|gb|AEE91295.1| RNA polymerase, sigma 28 subunit, SigE [Tepidanaerobacter sp. Re1]
          Length = 239

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 55/264 (20%), Positives = 107/264 (40%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EE    K+ +  GD +    L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLTSDEEVFYLKKLQ-MGDQTVKTVLIERNLRLVVYIARKFENTGICIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+  FDP +  +LATY+   I+  +  Y+ R+                          
Sbjct: 96  IKAINTFDPNKKIKLATYASKCIENEILMYLRRNNKT----------------------- 132

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                             ++ VS  E ++++                D N     D L  
Sbjct: 133 ------------------RMEVSFDEPLNID---------------WDGNELLLSDILGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEV 264
           D+D   + + ++ +    R +L  +M  L+ RER I + R         T + ++    +
Sbjct: 160 DNDMIYKYIEDEVD----RELLYTAMKRLSQRERCIIKLRFGLNGGVEKTQKEVADLLGI 215

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E +  K++++ + + +
Sbjct: 216 SQSYISRLEKKIIKRLKKEMVRMM 239


>gi|256004813|ref|ZP_05429788.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           thermocellum DSM 2360]
 gi|281417227|ref|ZP_06248247.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           thermocellum JW20]
 gi|255991263|gb|EEU01370.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           thermocellum DSM 2360]
 gi|281408629|gb|EFB38887.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           thermocellum JW20]
 gi|316940748|gb|ADU74782.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           thermocellum DSM 1313]
          Length = 256

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 47/254 (18%), Positives = 114/254 (44%), Gaps = 17/254 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKK 92
            L K+Y +  + +   +L+  +  +V  IA     Y G  +   +++  G  GL+ A++K
Sbjct: 10  ELWKQYADTKNPAIKEQLIIEYSNIVKYIAGRLSIYFGSNVEYDDLIGYGIFGLIDAIEK 69

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G +  TY+   I+ ++ + I     L  +  +  QK      + L+     I + 
Sbjct: 70  FDINKGVKFETYASLRIRGSIIDSIRE---LDWVPRSLRQKN-----KELEKVYAEIENE 121

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      +A KL ++  E      +L  + +L+++I+  +     ++  +    + ++
Sbjct: 122 LGRSASDKEVADKLGITVDE----LNKLLNEVNLSSMISLEEFLEQNYEIGVTTAPESRD 177

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           +      E    R +L  ++S L  +E+ +      ++  +TL+ +S+  +VS  R+ Q+
Sbjct: 178 EKPEGYIEMAELREILADAISKLPEKEKMVITLYYFED--LTLKEISAIMKVSESRISQL 235

Query: 273 EARAFKKVQESIQK 286
             +A  +++  + +
Sbjct: 236 HTKAILRLRGKLAR 249


>gi|226304764|ref|YP_002764722.1| RNA polymerase sigma factor [Rhodococcus erythropolis PR4]
 gi|226183879|dbj|BAH31983.1| RNA polymerase sigma factor [Rhodococcus erythropolis PR4]
          Length = 272

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 42/240 (17%), Positives = 96/240 (40%), Gaps = 18/240 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
               + ++   L L   +A  Y+G G P  ++     +GL+QAV++FD ++G    ++++
Sbjct: 45  EKITNSIIELCLPLATHVARRYQGRGQPFEDLEQVARVGLVQAVQRFDVDKGSDFLSFAV 104

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +   ++++       V++  +  ++ L      L   L +++    +   V  +A +L
Sbjct: 105 PTVMGEVRKHFRDHGWSVRVPRSLQERHLA-----LNRALTSLSQTLGRAPTVAELATEL 159

Query: 167 NVSESEVISMNCR--LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           ++   EV              L+   ++ D +     D L            E   R + 
Sbjct: 160 DIEPDEVEQGLTAGNSYRTTPLDT-ASAGDGSGLTLIDTLGQYD--------EAISRIDN 210

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              L  ++  L  RER I   R      +T   ++ +  +S+  V +I  +  K+++  +
Sbjct: 211 HETLRPALLALPERERTIVVLRFFGH--LTQSQIAEKIGISQMHVSRILTQTLKQLRTEM 268


>gi|114566413|ref|YP_753567.1| RNA polymerase sigma factor [Syntrophomonas wolfei subsp. wolfei
           str. Goettingen]
 gi|114337348|gb|ABI68196.1| putative RNA polymerase sigma factor [Syntrophomonas wolfei subsp.
           wolfei str. Goettingen]
          Length = 260

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 53/259 (20%), Positives = 114/259 (44%), Gaps = 17/259 (6%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKF 93
           L  R +E+ D+ A  +L+     LV  +A     +    + + E++S G  GL+ A++KF
Sbjct: 12  LWIRLKENEDIEARDQLIIHFAHLVKYVASRLAIHLSSLVELDELISYGIEGLIDAIEKF 71

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D +R  +  TY++  I+ +M + + RS   + +      K L      ++  L       
Sbjct: 72  DHKRNIKFETYAITRIRGSMIDGL-RSMDWIPVSLRQKSKELEKAYMNVEARL------- 123

Query: 154 LKPEQVVAIAKKLNVSESE--VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
            +      +A++L ++  E  V+  +       SL+  +   D    +    L+ DH+  
Sbjct: 124 GRSASDAEVAEELGLNLDEFAVLLRDVAATTIISLDDFLPGEDGEQKKRMLDLLEDHNSI 183

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
                E  E    +++L +++S L  +E+ +          +TL+ + +   +S  R+ Q
Sbjct: 184 SAS--EIVEFNEVKDLLAKAISRLPDKEKLVVYLYYY--EGLTLKEIGATISLSESRISQ 239

Query: 272 IEARAFKKVQESIQKQVEL 290
           +  +A  +++ S+ K+  L
Sbjct: 240 LHTKAILRLRGSLSKKKNL 258


>gi|168180934|ref|ZP_02615598.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum NCTC 2916]
 gi|182668292|gb|EDT80271.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum NCTC 2916]
          Length = 242

 Score =  134 bits (337), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 58/242 (23%), Positives = 107/242 (44%), Gaps = 19/242 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              +V  ++ LV  IA      +   +   ++VS G IGLM A+ KFD  +G + +TY+ 
Sbjct: 11  KEEIVKKYIPLVKYIASRVIIGKTKYIEYEDLVSYGMIGLMDALNKFDESKGMKFSTYAS 70

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             IK +M + + R+  +         K     L R    ++ +     K   ++ IA +L
Sbjct: 71  IRIKGSMIDELRRNSPI--------SKGAMDKLNRYNEAIEKLQKKLNKEPNLIQIADEL 122

Query: 167 NVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           NVS  EV  +   +      SL  LI SS+         +    D +     +  E   +
Sbjct: 123 NVSLKEVSEIENYINYISVISLEDLIFSSEDEVP----LIGTIKDEKSPSPEKHVEENEQ 178

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + L +++ +LN ++R +      +E  +TL+ +     VS  RV Q+ +RA   +++++
Sbjct: 179 LDYLAKAIELLNEKDRLVVTLYYYEE--LTLKEIGKILNVSESRVCQLHSRAIIHLKKAM 236

Query: 285 QK 286
            K
Sbjct: 237 AK 238


>gi|255312663|gb|ACU01741.1| RNA polymerase sigma S factor [Escherichia coli]
          Length = 195

 Score =  133 bits (336), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 53/205 (25%), Positives = 95/205 (46%), Gaps = 12/205 (5%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL + +++ EGN+ L++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLVLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           +     +++      K L   LR  +     ++           IA++L+    +V  M 
Sbjct: 61  MNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRML 115

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                  S++  +    +     +  L    D +E    +  +  + +  + + +  LN 
Sbjct: 116 RLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNA 170

Query: 238 RERRIFEARR--LQENPVTLENLSS 260
           ++R +   R   L     TLE++  
Sbjct: 171 KQREVLARRFGLLGYEAATLEDVGR 195


>gi|149183910|ref|ZP_01862298.1| sporulation sigma factor SigG [Bacillus sp. SG-1]
 gi|148848374|gb|EDL62636.1| sporulation sigma factor SigG [Bacillus sp. SG-1]
          Length = 227

 Score =  133 bits (336), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 46/218 (21%), Positives = 95/218 (43%), Gaps = 15/218 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K+P+L+ +E   L +  +  GD+SA  +LV  +LRLV+ +   +   G  + ++   G 
Sbjct: 25  SKLPVLKNEEMRKLFREMQ-AGDISAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGC 83

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGLM+++  FD  +  R +TY++  I   ++ Y+  +   +++  +   + + +   +++
Sbjct: 84  IGLMKSIDNFDLGQNVRFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVR 140

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
              + +     K      IAK L+V   +++     +    SL   I +   +     D 
Sbjct: 141 ---EKLMGETSKEPTAEEIAKVLDVPHEDIVFAMDAIQDPVSLFEPIYNDGGDPIFVMDQ 197

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           L  + +     + E          L   M  LN RE+ 
Sbjct: 198 LSDERNRDHTWIEEIA--------LQEGMRRLNDREKM 227


>gi|55274965|gb|AAV49282.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 193

 Score =  133 bits (336), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 53/203 (26%), Positives = 95/203 (46%), Gaps = 12/203 (5%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           +     +++      K L   LR  +     ++            A++L+    +V  M 
Sbjct: 61  MNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEESAEQLDKPVDDVSRML 115

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                  S++  +    +     +  L    D +E    +  +  + +  + + +  LN 
Sbjct: 116 RLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNA 170

Query: 238 RERRIFEARR--LQENPVTLENL 258
           ++R +   R   L     TLE++
Sbjct: 171 KQREVLARRFGLLGYEAATLEDV 193


>gi|312134671|ref|YP_004002009.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|311774722|gb|ADQ04209.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor owensensis OL]
          Length = 244

 Score =  133 bits (336), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 51/262 (19%), Positives = 102/262 (38%), Gaps = 62/262 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EE  +  R    G+      L+  +LRLVV IA  +    + + ++VS G IGL
Sbjct: 41  PPLTPDEEAQILYRIHYQGEEELKKLLIERNLRLVVYIARRFENTKVNLEDLVSIGTIGL 100

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+  ++P +  +LATY+   I+  +  ++ R+ +                        
Sbjct: 101 IKAINTYNPNKNIKLATYASKCIENEILMFLRRNSN------------------------ 136

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                            KKL +S  E ++++                D N     D L  
Sbjct: 137 -----------------KKLELSIDEPLNVD---------------WDGNELLLSDVLGT 164

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEV 264
           D     + +  + E    +  L +++  L  RE++I E R     E   T + ++    +
Sbjct: 165 D----TEEIYNRIESNVEKEALLQAIQKLPSREKKIVELRFGFGDEGEKTQKEVADMLGI 220

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+  + ++E +   ++++ + K
Sbjct: 221 SQSYISRLEKKIITRLKKELAK 242


>gi|312128428|ref|YP_003993302.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor hydrothermalis 108]
 gi|311778447|gb|ADQ07933.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor hydrothermalis 108]
          Length = 256

 Score =  133 bits (336), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 49/236 (20%), Positives = 109/236 (46%), Gaps = 15/236 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L + Y+    +   + LV  HL +   IA  + G G+   ++     I L+ AV++F+P
Sbjct: 17  RLFEEYQRTKAIELRNELVNKHLYIAEIIAKKFVGRGIDYEDLYQVACIALINAVERFEP 76

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            +G++  +++   I   ++ Y     S++++      +R++    ++K   + ++    +
Sbjct: 77  NKGYKFTSFATPTIMGEIKRYFRDRASIIRLP-----RRIYETSAKIKLATEVLSTKLKR 131

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
           P +V  IA+ LN+S  EV+ +      + S N L  S D+   + ++  + D  G+    
Sbjct: 132 PPKVEEIARHLNMSTEEVLEVM-----EASNNYLPQSLDQTMYEDEEMTLGDVLGKSD-- 184

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
            E   +      + +++  L+P ER   + R  +E   T + ++ E  VS+  + +
Sbjct: 185 -ENILQVENVEAVKKAIERLSPFEREFVQKRFFEE--KTQKEIAEEMNVSQMYISR 237


>gi|302522171|ref|ZP_07274513.1| RNA polymerase sigma-G factor [Streptomyces sp. SPB78]
 gi|318056578|ref|ZP_07975301.1| RNA polymerase sigma factor WhiG [Streptomyces sp. SA3_actG]
 gi|302431066|gb|EFL02882.1| RNA polymerase sigma-G factor [Streptomyces sp. SPB78]
          Length = 279

 Score =  133 bits (336), Expect = 2e-29,   Method: Composition-based stats.
 Identities = 50/256 (19%), Positives = 105/256 (41%), Gaps = 16/256 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
            L + Y+  GD     +L+  +  LV  +A          +  ++ VS G  GL+ A++K
Sbjct: 32  ELWRMYKTTGDARLREQLILHYSPLVKYVAGRVSVGLPPNVEQADFVSSGVFGLIDAIEK 91

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD ER  +  TY++  I+ AM + + R+   +        + +      L+  L      
Sbjct: 92  FDIERSIKFETYAITRIRGAMIDEL-RALDWIPRSVRQKARNVERAYATLEAKLH----- 145

Query: 153 NLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
             +    V +A ++ V   ++ ++     LA   +L  L++   +   +    +    D 
Sbjct: 146 --RTPTEVEVASEMGVGVEDLHAVFSQLSLANVVALEELLSVGSEGGGRL-SIMDTLEDT 202

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                +E  E +  R +L+R+++ L  RE+ +          +TL  +     V+  RV 
Sbjct: 203 GADNPVEVAEGRELRQLLSRAINSLPDREKTVVMLYYY--EGLTLAEIGHVLGVTESRVS 260

Query: 271 QIEARAFKKVQESIQK 286
           QI  ++  +++  +  
Sbjct: 261 QIHTKSVLQLRAKLSS 276


>gi|290957086|ref|YP_003488268.1| sporulation-specific sigma factor WhiG [Streptomyces scabiei 87.22]
 gi|260646612|emb|CBG69709.1| sporulation-specific sigma factor WhiG [Streptomyces scabiei 87.22]
          Length = 258

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 48/256 (18%), Positives = 106/256 (41%), Gaps = 16/256 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKK 92
            L + Y+  GD     +L+  +  LV  +A          +  ++ VS G  GL+ A++K
Sbjct: 11  ELWRTYKTSGDERLREQLILHYSPLVKYVAGRVSVGLPANVEQADFVSSGVFGLIDAIEK 70

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD +R  +  TY++  I+ AM + + R+   +        + +      L+  L+     
Sbjct: 71  FDIDREIKFETYAITRIRGAMIDEL-RALDWIPRSVRQKARNVERAYATLESRLR----- 124

Query: 153 NLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
             +      +A ++ ++  E+ ++     LA   +L  L+++  +   +    +    D 
Sbjct: 125 --RTPSEGEVAAEMGIAVDELHAVFSQLSLANVVALEELLHAGGEGGDRL-SLMDTLEDT 181

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                +E  E +  R  L R+++ L  RE+ +          +TL  + +   V+  RV 
Sbjct: 182 AADDPVEVAEDRELRRFLARAINTLPEREKTVVTLYYY--EGLTLAEIGNVLGVTESRVS 239

Query: 271 QIEARAFKKVQESIQK 286
           QI  ++  +++  +  
Sbjct: 240 QIHTKSVLQLRAKLAS 255


>gi|284028684|ref|YP_003378615.1| B/F/G subfamily RNA polymerase sigma-28 subunit [Kribbella flavida
           DSM 17836]
 gi|283807977|gb|ADB29816.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Kribbella
           flavida DSM 17836]
          Length = 275

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 48/256 (18%), Positives = 99/256 (38%), Gaps = 18/256 (7%)

Query: 35  YVLAKRYREHGDLSAAHRL----VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
             L  R     D      L    +  +L +   IA  +RG G+   ++     +GL++A 
Sbjct: 27  RELLSRRAATTDEELQQALLNEAIELNLGIAHSIASRFRGRGVESDDLDQVAYLGLLKAA 86

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           + ++P  G     Y++  I+  ++ Y       V+I     +  L  ++  ++  L    
Sbjct: 87  RSYNPSTGTPFLAYAVPTIRGEVKRYFRDCSWTVRIPRRLQE--LQGSIASVRPQLVQDL 144

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
             +     +  +A +L    +EV +          L+        +++   D +  + D 
Sbjct: 145 QRD---PTLEELAAELGTDVAEVEAAIAADGCFSVLSLDRPVDGDSTANLADTIADEEDT 201

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                    ER     ML   ++ L PRER+I E R +     T  ++ +E  VS+ +V 
Sbjct: 202 SF-------ERTEAVAMLEPVLNDLTPRERKILELRFI--EGHTQADIGAEIGVSQMQVS 252

Query: 271 QIEARAFKKVQESIQK 286
           ++      +++E I+ 
Sbjct: 253 RLLRGILDRLREQIES 268


>gi|322806971|emb|CBZ04541.1| RNA polymerase sigma factor for flagellar operon [Clostridium
           botulinum H04402 065]
          Length = 242

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 57/242 (23%), Positives = 107/242 (44%), Gaps = 19/242 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              +V  ++ LV  IA      +   +   ++VS G IGLM A+ KFD  +G + +TY+ 
Sbjct: 11  KEEIVKKYIPLVKYIASRVIIGKTKYIEYEDLVSYGMIGLMDALNKFDESKGMKFSTYAS 70

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             IK +M + + R+  +         K     L R    ++ +     K   ++ IA +L
Sbjct: 71  IRIKGSMIDELRRNSPI--------SKGAMDKLNRYNEAIEKLQKKLNKEPNLIQIADEL 122

Query: 167 NVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           N+S  EV  +   +      SL  LI SS+         +    D +     +  E   +
Sbjct: 123 NISLKEVSEIENYINYISVISLEDLIFSSEDEVP----LIGTIKDEKSPSPEKHVEENEQ 178

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + L +++ +LN ++R +      +E  +TL+ +     VS  RV Q+ +RA   +++++
Sbjct: 179 LDYLAKAIELLNEKDRLVVTLYYYEE--LTLKEIGKILNVSESRVCQLHSRAIIHLKKAM 236

Query: 285 QK 286
            K
Sbjct: 237 AK 238


>gi|169629597|ref|YP_001703246.1| RNA polymerase sigma factor SigF [Mycobacterium abscessus ATCC
           19977]
 gi|169241564|emb|CAM62592.1| Alternative sigma factor SigF [Mycobacterium abscessus]
          Length = 272

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 44/248 (17%), Positives = 97/248 (39%), Gaps = 19/248 (7%)

Query: 41  YREHGDLSAA--HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
             EH D        +VT  L L   +A  +   G  + +++    +GL+ AV +FDPE+G
Sbjct: 39  LAEHSDAYQRKHEEIVTRCLPLADNVARHFDRRGEDLEDLIQVARVGLLNAVNRFDPEKG 98

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
                +++  +   ++ +       + +      +       ++      +T    +   
Sbjct: 99  ASFLGFAVPTMMGEVRRHFRDHGWSLHVPRAIRDRHA-----QISRATAELTQELQRAPT 153

Query: 159 VVAIAKKLNVSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
              +A +L +   EV+   +       +S+ A ++  D+ S    D L  +    E V  
Sbjct: 154 AGELAAELGIDREEVVESLIAADAYQPQSIEAPLSHGDQESKHLSDLLGNEDPALEHV-- 211

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
                   R  +   ++ L  RER + E R  +   +T   ++++  VS+  V +I +  
Sbjct: 212 ------TNREAVRPLLANLPLRERTVLELRFFKG--MTQSQIAAQIGVSQMHVSRILSDT 263

Query: 277 FKKVQESI 284
            + ++E +
Sbjct: 264 LRYLREQM 271


>gi|158333719|ref|YP_001514891.1| RNA polymerase sigma factor SigF [Acaryochloris marina MBIC11017]
 gi|158303960|gb|ABW25577.1| RNA polymerase sigma factor [Acaryochloris marina MBIC11017]
          Length = 264

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 50/265 (18%), Positives = 118/265 (44%), Gaps = 16/265 (6%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQA 89
           K E   L ++Y++       +RLV  +L LV + A  + G+      +++  G++GL++A
Sbjct: 10  KSESLELLQQYQQSSCTELRNRLVQMNLGLVRREAHRWVGHSTESFDDLMQVGSLGLIRA 69

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +++FDP +G   +++++ +I+  +Q Y+      V+I    ++ +     R+     + +
Sbjct: 70  IERFDPFKGHAFSSFAVPYIRGEIQHYLRDKSPQVRIPRKWHELQ-----RQAINVTREM 124

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYD 207
            D   +    V +A  L++ + E   +          SL+A +++S++ S    + L   
Sbjct: 125 RDELQRQPTDVEVAAALDICQKEWQEVKLASCNRSVLSLDAPVHNSEQESMSLGELLPDR 184

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           H    Q+  E + R      L +++S L  R   + E     +  +T +  +    +S  
Sbjct: 185 HYHSFQLAQEDQIR------LRQALSKLEKRTSDVLEFVFFHD--LTQKETAEVLGISAV 236

Query: 268 RVRQIEARAFKKVQESIQKQVELSS 292
            V +   +    +++ ++   E + 
Sbjct: 237 TVSRQVKKGLVALRQMLKGSEETAE 261


>gi|125973527|ref|YP_001037437.1| sporulation sigma factor SigK [Clostridium thermocellum ATCC 27405]
 gi|256003345|ref|ZP_05428336.1| RNA polymerase, sigma 28 subunit, SigK [Clostridium thermocellum
           DSM 2360]
 gi|281417730|ref|ZP_06248750.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           thermocellum JW20]
 gi|125713752|gb|ABN52244.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Clostridium
           thermocellum ATCC 27405]
 gi|255992635|gb|EEU02726.1| RNA polymerase, sigma 28 subunit, SigK [Clostridium thermocellum
           DSM 2360]
 gi|281409132|gb|EFB39390.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           thermocellum JW20]
 gi|316940233|gb|ADU74267.1| RNA polymerase, sigma 28 subunit, SigK [Clostridium thermocellum
           DSM 1313]
          Length = 236

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 62/282 (21%), Positives = 105/282 (37%), Gaps = 63/282 (22%)

Query: 9   IVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           I+N    L  YI  +   P  L  +EE       ++ GD  A + L+  +LRLV  I   
Sbjct: 12  ILNNIFFLLGYISNVNSFPQPLSPEEEQHYLDLLKK-GDEEARNILIERNLRLVAHIVKK 70

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y        +++S G IGL++A+  F+ E+G RLATY+   I+  +  +I  +       
Sbjct: 71  YSSTINDSDDLISIGTIGLIKAISTFNHEKGTRLATYAARCIENEILMHIRSNKKT---- 126

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
                                                     +SEV S+   +  D    
Sbjct: 127 ------------------------------------------QSEV-SLQDPIGVDR--- 140

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
                 D N     D +    +  E V+ E E +   + +  +   VL  RE+ + E R 
Sbjct: 141 ------DGNEIALIDVI---GNESESVVEEVELKMQVKRLYNKMKDVLKAREKMVLELRY 191

Query: 248 LQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
                   T   ++    +SR  V +IE +A KK+ + ++ +
Sbjct: 192 GLLNGTGKTQREIAKMLGISRSYVSRIEKKAIKKLGKELKSE 233


>gi|308068681|ref|YP_003870286.1| RNA polymerase sigma-D factor (Sigma-28) [Paenibacillus polymyxa
           E681]
 gi|305857960|gb|ADM69748.1| RNA polymerase sigma-D factor (Sigma-28) [Paenibacillus polymyxa
           E681]
          Length = 262

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 55/261 (21%), Positives = 116/261 (44%), Gaps = 20/261 (7%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
            L ++++EHGD  A  +L+  +L +V  ++          +   ++ S G +GL+ A++K
Sbjct: 13  ELWEQWKEHGDKEAKKQLIEKYLHIVEYVSGRLAVGLPKNVSKDDLASNGVMGLIDALEK 72

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD ERG +  TY+ W ++ A+ + + R    V        K       +++   Q +   
Sbjct: 73  FDYERGLQFETYASWRVRGAILDGL-RQGDWVPRSVREKAK-------KIEDAYQHLEQR 124

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDG 210
            L+      ++  L+VSE E  +M   +A     SL   I   ++ S      LV +   
Sbjct: 125 YLRTVSDEEMSHYLDVSEKEFQNMIQEVAVMSIVSLEDPIR--EEESETRLSLLVDEKAK 182

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                + +      R+ L + +  L  +ER +      ++  ++L  ++    +S  R+ 
Sbjct: 183 NPDHKVNEFTL---RDALAQGIDKLTEKERIVVSLLYYED--LSLSEIAEVMSLSPSRIS 237

Query: 271 QIEARAFKKVQESIQKQVELS 291
           Q+ ++A  +++ ++ KQ +L 
Sbjct: 238 QLHSKAILRLRATLDKQRDLL 258


>gi|153938360|ref|YP_001391942.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum F str. Langeland]
 gi|152934256|gb|ABS39754.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum F str. Langeland]
 gi|295319962|gb|ADG00340.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum F str. 230613]
          Length = 242

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 57/242 (23%), Positives = 107/242 (44%), Gaps = 19/242 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              +V  ++ LV  IA      +   +   ++VS G IGLM A+ KFD  +G + +TY+ 
Sbjct: 11  KEEIVKKYIPLVKYIASRVIIGKTKYIEYEDLVSYGMIGLMDALNKFDESKGMKFSTYAS 70

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             IK +M + + R+  +         K     L R    ++ +     K   ++ IA +L
Sbjct: 71  IRIKGSMIDELRRNSPI--------SKGAMDKLNRYNEAIEKLQKKLNKEPNLIQIAGEL 122

Query: 167 NVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           N+S  EV  +   +      SL  LI SS+         +    D +     +  E   +
Sbjct: 123 NISLKEVSEIENYINYISVISLEDLIFSSEDEVP----LIGTIKDEKSPSPEKHVEENEQ 178

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + L +++ +LN ++R +      +E  +TL+ +     VS  RV Q+ +RA   +++++
Sbjct: 179 LDYLAKAIELLNEKDRLVVTLYYYEE--LTLKEIGKILNVSESRVCQLHSRAIIHLKKAM 236

Query: 285 QK 286
            K
Sbjct: 237 AK 238


>gi|42566466|gb|AAS21045.1| major sigma factor 70 [Meiothermus silvanus DSM 9946]
          Length = 168

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 39/176 (22%), Positives = 69/176 (39%), Gaps = 10/176 (5%)

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I     +      L R    +Q         E++   
Sbjct: 1   TYATWWIRQAINRAIADQARTIRIPVHMVE--TINKLTRTARQMQQELGREPTYEEISE- 57

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A        +V           SL   I   D+  S + D++  +H       ++   + 
Sbjct: 58  AMGPGWDAKKVEETFKIAQEPVSLETPI--GDEKDSFYGDFIPDEH---MASPVDSAAQS 112

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARA 276
                L +++  L+ RE  + + R+        TLE + + F V+RER+RQIE +A
Sbjct: 113 MLSEELEKALGKLSDREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKA 168


>gi|333023850|ref|ZP_08451914.1| putative RNA polymerase sigma-F factor [Streptomyces sp. Tu6071]
 gi|332743702|gb|EGJ74143.1| putative RNA polymerase sigma-F factor [Streptomyces sp. Tu6071]
          Length = 294

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 55/240 (22%), Positives = 101/240 (42%), Gaps = 8/240 (3%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + L+  +  LV   A  +R  G   + +++  G IGL++A+ +FD  R     ++++ 
Sbjct: 61  ARNTLIEMNQSLVRFAARRFRNRGNGDMEDILQVGTIGLIKAIDRFDLTREAEFTSFAIP 120

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +I   ++ Y   S   V +     + R+  +L R K  L    D +     V  +A +LN
Sbjct: 121 YIVGEIKRYFRDSTWAVHVPRRLQELRV--DLARAKERLAVELDRDPG---VKELAAELN 175

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +SE EVI       G  S +  + +    S +        +           E       
Sbjct: 176 ISEEEVIDGLIAANGYMSDSLDLPADSSTSGKPDQKTATTYADFLGDWDPAMELVENFTA 235

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   +  L+ RER + E R  QE  +T   + +E  VS+  V ++ +R   K++E +  +
Sbjct: 236 LRPLLGTLDDRERYLLELRFGQE--LTQAQIGAELGVSQMHVSRLLSRTLGKLREGLLSE 293


>gi|318059283|ref|ZP_07978006.1| RNA polymerase sigma factor [Streptomyces sp. SA3_actG]
 gi|318075250|ref|ZP_07982582.1| RNA polymerase sigma factor [Streptomyces sp. SA3_actF]
          Length = 294

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 54/240 (22%), Positives = 100/240 (41%), Gaps = 8/240 (3%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + L+  +  LV   A  +R  G   + +++  G IGL++A+ +FD  R     ++++ 
Sbjct: 61  ARNTLIEMNQSLVRFAARRFRNRGNGDMEDILQVGTIGLIKAIDRFDLTREAEFTSFAIP 120

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +I   ++ Y   S   V +     + R+  +L R K  L    D +     V  +A +L 
Sbjct: 121 YIVGEIKRYFRDSTWAVHVPRRLQELRV--DLARAKERLAVELDRDPG---VKELAAELG 175

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +SE EVI       G  S +  + +    S +        +           E       
Sbjct: 176 ISEEEVIDGLIAANGYMSDSLDLPADSSTSGKPDQKTATTYADFLGDWDPAMELVENFTA 235

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   +  L+ RER + E R  QE  +T   + +E  VS+  V ++ +R   K++E +  +
Sbjct: 236 LRPLLGTLDDRERYLLELRFGQE--LTQAQIGAELGVSQMHVSRLLSRTLGKLREGLLSE 293


>gi|168029696|ref|XP_001767361.1| plastid sigma factor SIG5 [Physcomitrella patens subsp. patens]
 gi|56603661|dbj|BAD80742.1| plastid sigma factor PpSIG5 [Physcomitrella patens]
 gi|162681425|gb|EDQ67852.1| plastid sigma factor SIG5 [Physcomitrella patens subsp. patens]
          Length = 632

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 55/253 (21%), Positives = 103/253 (40%), Gaps = 15/253 (5%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI--SEVVSEGNIGLMQAVKKFD 94
           L  R R     +A  +L+  +LRLV+  A  Y    + +   ++  EG IGLMQAV KFD
Sbjct: 382 LIMRRRLALGRAARTKLIQRNLRLVLSQAYKYHKDSMSLSIQDLCQEGVIGLMQAVDKFD 441

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P +G+R +TY ++WI+ ++     +S  +++     +  R+     ++      +     
Sbjct: 442 PGKGYRFSTYGIYWIRNSILRAQTKSGHMLRSPHNVSTHRVNIQRAKV-----ELFSELG 496

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +      I K L ++      +        SL+     +     +  + LV + D  + +
Sbjct: 497 RQPTNDEIRKHLGITADRFRDILRTNMRTSSLHEHDRIT---GREKVENLVSEEDALDTL 553

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQI 272
                     +  L   +  L P+E  +   R   +     +L  +     +SRE VR+ 
Sbjct: 554 AGG---TSMVQYGLDDVLDSLRPKENLVLRQRFGLDGKGQRSLSEVGLILNLSREMVRRY 610

Query: 273 EARAFKKVQESIQ 285
           E R   K+Q   +
Sbjct: 611 ELRGILKLQHPTR 623


>gi|256393983|ref|YP_003115547.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Catenulispora acidiphila DSM 44928]
 gi|256360209|gb|ACU73706.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Catenulispora acidiphila DSM 44928]
          Length = 265

 Score =  133 bits (336), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 42/241 (17%), Positives = 102/241 (42%), Gaps = 17/241 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +    ++  ++     +A  +R  G   +++     +GL++AV  FDP+ G    TY+ 
Sbjct: 36  EALREYVIGEYMSYARFVAARFRLRGETQADLEQVAYLGLVKAVDNFDPDYGATFLTYAT 95

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I   ++ +   +   V +   A +  L      ++   + +T    +      I ++L
Sbjct: 96  PMIAGEVRRHFRDTTWHVHVPRRAQENALA-----VRAVERELTQQLGRAPSAAEIGRRL 150

Query: 167 NVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           ++S  EV       A     SL+  +  +D + +   D L  +  G + V+         
Sbjct: 151 DLSADEVAEAYEASAAHHTASLDVPVAMADGDGASLGDLLGDEDPGFDSVV--------D 202

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L   ++ L+PR++RI   +  +   ++   + +E  VS+ +V ++ ++    +++ +
Sbjct: 203 REALKPLLAELSPRDKRILLMKFFRN--MSQAQIGAEIGVSQMQVSRLLSQIIGSLRDRL 260

Query: 285 Q 285
           +
Sbjct: 261 E 261


>gi|302522454|ref|ZP_07274796.1| RNA polymerase sigma-F factor [Streptomyces sp. SPB78]
 gi|302431349|gb|EFL03165.1| RNA polymerase sigma-F factor [Streptomyces sp. SPB78]
          Length = 297

 Score =  133 bits (335), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 54/240 (22%), Positives = 100/240 (41%), Gaps = 8/240 (3%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + L+  +  LV   A  +R  G   + +++  G IGL++A+ +FD  R     ++++ 
Sbjct: 64  ARNTLIEMNQSLVRFAARRFRNRGNGDMEDILQVGTIGLIKAIDRFDLTREAEFTSFAIP 123

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +I   ++ Y   S   V +     + R+  +L R K  L    D +     V  +A +L 
Sbjct: 124 YIVGEIKRYFRDSTWAVHVPRRLQELRV--DLARAKERLAVELDRDPG---VKELAAELG 178

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +SE EVI       G  S +  + +    S +        +           E       
Sbjct: 179 ISEEEVIDGLIAANGYMSDSLDLPADSSTSGKPDQKTATTYADFLGDWDPAMELVENFTA 238

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   +  L+ RER + E R  QE  +T   + +E  VS+  V ++ +R   K++E +  +
Sbjct: 239 LRPLLGTLDDRERYLLELRFGQE--LTQAQIGAELGVSQMHVSRLLSRTLGKLREGLLSE 296


>gi|148380599|ref|YP_001255140.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum A str. ATCC 3502]
 gi|153931945|ref|YP_001384886.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum A str. ATCC 19397]
 gi|153937160|ref|YP_001388355.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum A str. Hall]
 gi|168182725|ref|ZP_02617389.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum Bf]
 gi|170754752|ref|YP_001782258.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum B1 str. Okra]
 gi|226950054|ref|YP_002805145.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum A2 str. Kyoto]
 gi|237796081|ref|YP_002863633.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum Ba4 str. 657]
 gi|148290083|emb|CAL84202.1| RNA polymerase sigma factor [Clostridium botulinum A str. ATCC
           3502]
 gi|152927989|gb|ABS33489.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum A str. ATCC 19397]
 gi|152933074|gb|ABS38573.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum A str. Hall]
 gi|169119964|gb|ACA43800.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum B1 str. Okra]
 gi|182674219|gb|EDT86180.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum Bf]
 gi|226840945|gb|ACO83611.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum A2 str. Kyoto]
 gi|229261699|gb|ACQ52732.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum Ba4 str. 657]
          Length = 242

 Score =  133 bits (335), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 57/242 (23%), Positives = 107/242 (44%), Gaps = 19/242 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              +V  ++ LV  IA      +   +   ++VS G IGLM A+ KFD  +G + +TY+ 
Sbjct: 11  KEEIVKKYIPLVKYIASRVIIGKTKYIEYEDLVSYGMIGLMDALNKFDESKGMKFSTYAS 70

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             IK +M + + R+  +         K     L R    ++ +     K   ++ IA +L
Sbjct: 71  IRIKGSMIDELRRNSPI--------SKGAMDKLNRYNEAIEKLQKKLNKEPNLIQIADEL 122

Query: 167 NVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           N+S  EV  +   +      SL  LI SS+         +    D +     +  E   +
Sbjct: 123 NISLKEVSEIENYINYISVISLEDLIFSSEDEVP----LIGTIKDEKSPSPEKHVEENEQ 178

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + L +++ +LN ++R +      +E  +TL+ +     VS  RV Q+ +RA   +++++
Sbjct: 179 LDYLAKAIELLNEKDRLVVTLYYYEE--LTLKEIGKILNVSESRVCQLHSRAIIHLKKAM 236

Query: 285 QK 286
            K
Sbjct: 237 AK 238


>gi|319399556|gb|EFV87811.1| RNA polymerase sigma-B factor [Staphylococcus epidermidis FRI909]
          Length = 256

 Score =  133 bits (335), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 50/263 (19%), Positives = 111/263 (42%), Gaps = 24/263 (9%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             ++     K+++E+ D  A  +LV  + +L+  +A  Y        ++V  G +GL+ A
Sbjct: 12  SPEQINQWIKQHQENEDSLAQDKLVKHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGA 71

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +FD     +   + +  +   ++ Y+      V +     +        R+K     +
Sbjct: 72  INRFDLSFDRKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIG-----PRIKKVSDEL 126

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNC------RLAGDESLNALINSSDKNSSQWQDW 203
           T+   +   +  IA++L VS+ EV+           L+ D S+ A     D ++    D 
Sbjct: 127 TNELERSPSISEIAQRLEVSDEEVLEAMEMGQSYNALSVDHSIEA---DKDGSTVTLLDI 183

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    D          +   +R +L R + +L+ RER+I +   +    ++ +       
Sbjct: 184 MGQQDDNY--------DLTEKRMILERILPILSERERQIIQCTFI--EGLSQKETGERIG 233

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+  V +++  A KK+QE+ ++
Sbjct: 234 LSQMHVSRLQRTAIKKLQEAARQ 256


>gi|311897124|dbj|BAJ29532.1| putative RNA polymerase sigma factor [Kitasatospora setae KM-6054]
          Length = 301

 Score =  133 bits (335), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 51/232 (21%), Positives = 100/232 (43%), Gaps = 15/232 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+  ++ LV   A+ +R    P+ +VV  G IGL+ A+ +FDP+RG +  TY++  I
Sbjct: 78  RSALIEINIPLVRYAAIRFRSRNEPMEDVVQVGTIGLINAIDRFDPDRGVQFPTYALPTI 137

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ Y   +   + +      +RL     ++ G ++ +T  + +  +V  IA  L + 
Sbjct: 138 LGEIKRYFRDNVRTMHVP-----RRLQELWVQVSGAMEELTVAHGRAPKVPEIAANLRIP 192

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E +V +         + +       +      D L Y+      V          R+M+ 
Sbjct: 193 EEDVRACLDAGRAYNAASLEAAQEHEGGLALLDRLGYEDSALTDV--------EHRDMVR 244

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             +  L  RERRI   R      +T   +S+E  +S+  V ++ +R   +++
Sbjct: 245 HLLVQLPERERRIIMLRFFAN--LTQSQISTELGMSQMHVSRLLSRILSRLR 294


>gi|55274903|gb|AAV49253.1| RNA polymerase subunit sigma-38 [Escherichia albertii]
          Length = 192

 Score =  133 bits (335), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 50/201 (24%), Positives = 92/201 (45%), Gaps = 12/201 (5%)

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           KIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+    
Sbjct: 2   KIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTR 61

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            +++      K L   LR  +     ++           IA++L+    +V  M      
Sbjct: 62  TIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNER 116

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S++  +    +     +  L    D +E    +  +  + +  + + +  LN ++R +
Sbjct: 117 ITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREV 171

Query: 243 FEARR--LQENPVTLENLSSE 261
              R   L     TLE++  E
Sbjct: 172 LARRFGLLGYEAATLEDVGRE 192


>gi|303237309|ref|ZP_07323879.1| sigma-70, region 4 [Prevotella disiens FB035-09AN]
 gi|302482696|gb|EFL45721.1| sigma-70, region 4 [Prevotella disiens FB035-09AN]
          Length = 235

 Score =  133 bits (335), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 67/258 (25%), Positives = 110/258 (42%), Gaps = 48/258 (18%)

Query: 17  SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
            +YI +I    +L  +EE  LAK+ +  GD  A  +L  S+L+ VV IA  Y+  GL   
Sbjct: 7   EKYIKDIANEQLLSDKEEQELAKQIK-IGDAKALEKLTKSNLKFVVSIAHQYKNRGLGED 65

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++SEGNIG+M A +KFD  +G R   ++  +I+ AM+E I       K+     Q +  
Sbjct: 66  DLISEGNIGMMYAAQKFDGTKGTRFVKFAAPYIRKAMEEAINEQLETFKV-----QNKDE 120

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
              R+                                     R A   S++  I +    
Sbjct: 121 KKPRK-------------------------------------RTAHRVSIDQPIPAGSNG 143

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVT 254
           +   Q  L    +   Q   E   ++  R  + ++MSVL+ R+R++         E   T
Sbjct: 144 TFTLQTIL---ENANSQHADENLTKQIVREEIKKAMSVLDARQRKVISLLYAIKDEEAYT 200

Query: 255 LENLSSEFEVSRERVRQI 272
           ++  +   ++ RERVRQI
Sbjct: 201 MQETADIMDIKRERVRQI 218


>gi|238924140|ref|YP_002937656.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Eubacterium rectale
           ATCC 33656]
 gi|238875815|gb|ACR75522.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Eubacterium rectale
           ATCC 33656]
 gi|291524873|emb|CBK90460.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Eubacterium
           rectale DSM 17629]
 gi|291529014|emb|CBK94600.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Eubacterium
           rectale M104/1]
          Length = 255

 Score =  133 bits (335), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 60/257 (23%), Positives = 121/257 (47%), Gaps = 21/257 (8%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQA 89
           E+  L + Y+++       +L+  + +LV  +A     Y G+ +   ++VS G  GL+ A
Sbjct: 5   EKEKLWEEYQKNPTPKLREQLIIEYAQLVRLVAGRLSMYLGHNVEYDDLVSYGIFGLIDA 64

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + KF+ E+  +  TY+   I+ A+ + I +   +  I  T  Q++     R++   ++ I
Sbjct: 65  IDKFNLEKNVKFETYASLRIRGAILDQIRK---MDWIPRTVRQRQ-----RKIDEAIKNI 116

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYD 207
                K      +AK+L++SE E+ S   +L      SL+        + S  +  +   
Sbjct: 117 ELRTGKTANDADLAKELSISEDELCSWQSQLKVTNVVSLDEF------DESGPEPVMDAA 170

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           H+       E   ++  + ML +S+  L  +ERR+ E    ++  +TL+ +S+  EVS  
Sbjct: 171 HNSHYAQPEEIVTQEELKTMLVKSLDNLTEKERRVIELYYYED--LTLKEISNILEVSES 228

Query: 268 RVRQIEARAFKKVQESI 284
           RV Q+  +   K+++ +
Sbjct: 229 RVSQLHTKGLIKMRKVM 245


>gi|256391118|ref|YP_003112682.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Catenulispora acidiphila DSM 44928]
 gi|256357344|gb|ACU70841.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Catenulispora acidiphila DSM 44928]
          Length = 366

 Score =  133 bits (335), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 40/237 (16%), Positives = 85/237 (35%), Gaps = 16/237 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+  H+     +A  +        ++     + L++AV  FDP RG     Y    +
Sbjct: 129 RDELIAEHMNYARYVASRFSVPADTAEDLEQVAYLALIKAVDNFDPARGTAFLGYLTPMV 188

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ Y   S   V +     +  L  +        + +     +   +  +A+ L   
Sbjct: 189 AGEIKRYFRDSTWDVHVPRRMQELSLALHG----APAEQLERRLGRSPTIAELAEHLGAQ 244

Query: 170 ESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
             E++      A     SL   +   D+  +   + L  D D  E V+         R  
Sbjct: 245 PEEIVEAFDASAAYSATSLERPLVPGDEQGASLGETLGGDDDAYEWVV--------DREA 296

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   ++ L  +++RI   R  +   +T   + +E  VS+ +V +   R    +++++
Sbjct: 297 LKPLLAALPEKDKRILLMRFFRG--MTQSQIGTELGVSQMQVSRYLTRILSTLRDAV 351


>gi|295836278|ref|ZP_06823211.1| RNA polymerase sigma-27 factor [Streptomyces sp. SPB74]
 gi|197697357|gb|EDY44290.1| RNA polymerase sigma-27 factor [Streptomyces sp. SPB74]
          Length = 279

 Score =  133 bits (335), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 49/256 (19%), Positives = 106/256 (41%), Gaps = 16/256 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
            L + Y+  GD     +L+  +  LV  +A          +  ++ VS G  GL+ A++K
Sbjct: 32  ELWRMYKTTGDARLREQLILHYSPLVKYVAGRVSVGLPPNVEQADFVSSGVFGLIDAIEK 91

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD ER  +  TY++  I+ AM + + R+   +        + +      L+  L+     
Sbjct: 92  FDIERSIKFETYAITRIRGAMIDEL-RALDWIPRSVRQKARNVERAYATLEAKLR----- 145

Query: 153 NLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
             +      +A+++ V   ++ ++     LA   +L  L++   +   +    +    D 
Sbjct: 146 --RTPSEAEVAREMGVGVEDLHAVFSQLSLANVVALEELLSVGSEGGGRL-SIMDTLEDT 202

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                +E  E +  R +L+R+++ L  RE+ +          +TL  +     V+  RV 
Sbjct: 203 DADNPVEVAEGRELRRLLSRAINSLPEREKTVVMLYYY--EGLTLAEIGHVLGVTESRVS 260

Query: 271 QIEARAFKKVQESIQK 286
           QI  ++  +++  +  
Sbjct: 261 QIHTKSVLQLRAKLSS 276


>gi|170760209|ref|YP_001787962.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum A3 str. Loch Maree]
 gi|169407198|gb|ACA55609.1| RNA polymerase sigma factor for flagellar operon FliA [Clostridium
           botulinum A3 str. Loch Maree]
          Length = 242

 Score =  133 bits (335), Expect = 3e-29,   Method: Composition-based stats.
 Identities = 57/242 (23%), Positives = 107/242 (44%), Gaps = 19/242 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              +V  ++ LV  IA      +   +   ++VS G IGLM A+ KFD  +G + +TY+ 
Sbjct: 11  KEEIVKKYIPLVKYIASRVIIGKTKYIEYEDLVSYGMIGLMDALNKFDESKGMKFSTYAS 70

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             IK +M + + R+  +         K     L R    ++ +     K   ++ IA +L
Sbjct: 71  IRIKGSMIDELRRNSPI--------SKGAMDKLNRYNEAIEKLQKKLNKEPNLIQIADEL 122

Query: 167 NVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           N+S  EV  +   +      SL  LI SS+         +    D +     +  E   +
Sbjct: 123 NISLKEVSEIENYINYISVISLEDLIFSSEDEVP----LIGTIKDEKSPSPEKHVEENEQ 178

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + L +++ +LN ++R +      +E  +TL+ +     VS  RV Q+ +RA   +++++
Sbjct: 179 LDYLAKAIELLNEKDRLVVTLYYYEE--LTLKEIGKILNVSESRVCQLHSRAIVHLKKAM 236

Query: 285 QK 286
            K
Sbjct: 237 VK 238


>gi|163816759|ref|ZP_02208122.1| hypothetical protein COPEUT_02949 [Coprococcus eutactus ATCC 27759]
 gi|158448016|gb|EDP25011.1| hypothetical protein COPEUT_02949 [Coprococcus eutactus ATCC 27759]
          Length = 207

 Score =  133 bits (335), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 60/262 (22%), Positives = 96/262 (36%), Gaps = 64/262 (24%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L   +E     R    GD  A   L+  +LRLV  I   Y        +++S G IGL+
Sbjct: 7   PLTPDKEKEYINRCI-SGDNEARRVLIEYNLRLVAHIVKKYSSSVRDPEDLLSIGTIGLI 65

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +A+  + PE+G +LA Y+   I                      +  L  NLR+ K   +
Sbjct: 66  KAIDSYKPEKGCKLAGYAAKCI----------------------ENELLMNLRQEKKKSR 103

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                                     +SM   +  D+  N ++             ++  
Sbjct: 104 E-------------------------VSMYEPIGTDKEGNEIV-------------IMDI 125

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSV-LNPRERRIFEARR--LQENPVTLENLSSEFEV 264
               E   +EK   ++  N L   M+  L PRE  I + R   L E P+T +  +    +
Sbjct: 126 ISTSESCPLEKLITEDHLNHLPSCMNQILTPREYHIIQMRYGILGEAPLTQKETAKILGI 185

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           SR  V +IE RA  K++  + K
Sbjct: 186 SRSYVSRIEKRALSKLRGCLDK 207


>gi|288554854|ref|YP_003426789.1| RNA polymerase sigma factor SigB [Bacillus pseudofirmus OF4]
 gi|288546014|gb|ADC49897.1| RNA polymerase sigma factor SigB [Bacillus pseudofirmus OF4]
          Length = 261

 Score =  133 bits (335), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 50/258 (19%), Positives = 108/258 (41%), Gaps = 18/258 (6%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K E Y   + Y+E G+     +LV  +  LV  +A  +        ++   G +GL+ A+
Sbjct: 12  KDEVYEWIRLYQETGEEEVQVKLVKHYEALVRSLARKFSKGREYDEDLYQVGMVGLLAAL 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
            +FD E G    ++++  I   ++ +I      V +      K L   +++    L    
Sbjct: 72  TRFDSEFGRSFESFAVPTIVGEIKRFIRDKTWSVHVPRRI--KELGPKIKKAVESLTVEL 129

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMN---CRLAGDESLNALINSSDKNSSQWQDWLVYD 207
           + +    ++ A  +       E + M+     L+ D SL A     +       D +  +
Sbjct: 130 NRSPLVHEIAAYLEVSEEEVLETMEMSKSYQALSVDRSLEA---DQEGGEVTLLDLVGNE 186

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
             G         E+ +++ +L ++  VLN RE++I          ++ +    +  +S+ 
Sbjct: 187 DSGF--------EKTDQKMLLQKAFQVLNEREKQILMLTYYDN--LSQKETGEKLGISQM 236

Query: 268 RVRQIEARAFKKVQESIQ 285
            V +++ RA +K+++SI+
Sbjct: 237 HVSRLQRRALQKLRDSIK 254


>gi|229492301|ref|ZP_04386108.1| RNA polymerase sigma-F factor [Rhodococcus erythropolis SK121]
 gi|229320710|gb|EEN86524.1| RNA polymerase sigma-F factor [Rhodococcus erythropolis SK121]
          Length = 260

 Score =  133 bits (335), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 43/234 (18%), Positives = 96/234 (41%), Gaps = 18/234 (7%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++   L L   +A  Y+G G P  ++     +GL+QAV++FD ++G    ++++  +   
Sbjct: 39  IIELCLPLATHVARRYQGRGQPFEDLEQVARVGLIQAVQRFDVDKGSDFLSFAVPTVMGE 98

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           ++++       V++  +  ++ L      L   L  ++    +   V  +AK+L++   E
Sbjct: 99  VRKHFRDHGWSVRVPRSLQERHLA-----LNRALTTLSQTLGRAPTVAELAKELDIEPDE 153

Query: 173 VISMNCR--LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           V              L+   ++ D +     D L            E   R +    L  
Sbjct: 154 VEQGLTAGNSYRTTPLDT-ASAGDGSGLTLIDTLGQYD--------EAISRIDNHETLRP 204

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++  L  RER I   R      +T   ++ +  +S+  V +I  ++ K+++  +
Sbjct: 205 ALLALPERERTIVVLRFFGH--LTQSQIAEKVGISQMHVSRILTQSLKQLRTEM 256


>gi|310641572|ref|YP_003946330.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
 gi|309246522|gb|ADO56089.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
          Length = 262

 Score =  133 bits (335), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 55/261 (21%), Positives = 116/261 (44%), Gaps = 20/261 (7%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
            L ++++E+GD  A  +L+  +L +V  ++          +   ++ S G +GL+ A++K
Sbjct: 13  DLWEQWKEYGDKEAKKQLIEKYLHIVEYVSGRLAVGLPKNVSKDDLASNGVMGLIDALEK 72

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD ERG +  TY+ W ++ A+ + + R    V        K       +++   Q +   
Sbjct: 73  FDYERGLQFETYASWRVRGAILDGL-RQGDWVPRSVREKAK-------KIEDAYQHLEQR 124

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDG 210
            L+      ++  L+VSE E  SM   +A     SL   I   ++ S      LV +   
Sbjct: 125 YLRTVSDEEMSHYLDVSEKEFQSMIQEVAVMSIVSLEDPIR--EEESETRLSLLVDEKAK 182

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                + +      R+ L + +  L  +ER +      ++  ++L  ++    +S  R+ 
Sbjct: 183 NPDHKVNEFTL---RDALAQGIDKLTEKERIVVSLLYYED--LSLSEIAEVMSLSPSRIS 237

Query: 271 QIEARAFKKVQESIQKQVELS 291
           Q+ ++A  +++ ++ KQ +L 
Sbjct: 238 QLHSKAILRLRATLDKQRDLL 258


>gi|111017120|ref|YP_700092.1| sigma factor, sigma 70 type, group 3 [Rhodococcus jostii RHA1]
 gi|110816650|gb|ABG91934.1| sigma factor, sigma 70 type, group 3 [Rhodococcus jostii RHA1]
          Length = 265

 Score =  133 bits (335), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 41/237 (17%), Positives = 90/237 (37%), Gaps = 14/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +    ++T  L L   IA  + G G    +++    +GL++AV +FDP+RGF   +Y++ 
Sbjct: 40  ALRDEVITRCLPLADHIARRFGGRGEAHEDLLQVARLGLVKAVDRFDPDRGFDFVSYAVP 99

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I   ++ Y   +   +++     +         +   +  ++    +      IA +L 
Sbjct: 100 TIMGEVRRYFRDTGWSMRVPRRMQELHAL-----ITKAVDELSQELGRSPSASEIAAQLE 154

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +   EV          ++L+      D          + + D +   +            
Sbjct: 155 LDVREVSEGLLAKNAYQTLSMDAAMGDDPDDLPLAETLGEEDPELANVESHA-------A 207

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +  ++  L P ERR+   R      +T   ++    VS+ +V +I AR    ++  +
Sbjct: 208 VRPALQKLPPLERRVLMLRFFG--SMTQTEIAQRVGVSQMQVSRILARTLSGLRAQL 262


>gi|146296307|ref|YP_001180078.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Caldicellulosiruptor
           saccharolyticus DSM 8903]
 gi|145409883|gb|ABP66887.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG
           [Caldicellulosiruptor saccharolyticus DSM 8903]
          Length = 245

 Score =  133 bits (335), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 51/259 (19%), Positives = 114/259 (44%), Gaps = 19/259 (7%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQA 89
           +E  L ++Y +  D     +L   ++ LV  IA     Y G  +   ++VS G++GL+ A
Sbjct: 2   DEAFLWEKYSKTKDPKIKEQLTLRYMPLVKLIAGRMAMYFGGNVEYDDLVSYGSLGLLDA 61

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           ++K+D ++G +  TY+   I+ A+ + +        +  +  QK       +        
Sbjct: 62  IEKYDSQKGVKFETYAYTRIRGAIIDCVRSQDW---VPRSIRQK------AKEVEKAYIE 112

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
            +   K      +AK+  ++ SE   +  +++    L+       + + + +   + D  
Sbjct: 113 IEKEGKIPTDEEVAKRTGLTLSEFQKLKEKISSGMILSLEGFL--EQNYEIKIGGLEDFV 170

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
              +V IE EE    + +L + +  L+  E+ +      +E  ++++ ++    VS  RV
Sbjct: 171 SHPEVFIENEEL---KEVLRQEIENLSENEKMVILLYYFEE--LSIKEIAKILGVSESRV 225

Query: 270 RQIEARAFKKVQESIQKQV 288
            Q+  RA  K++  ++K +
Sbjct: 226 SQLHTRALLKLRAKLEKHL 244


>gi|326773494|ref|ZP_08232777.1| RNA polymerase sigma (70) factor RpoD [Actinomyces viscosus C505]
 gi|326636724|gb|EGE37627.1| RNA polymerase sigma (70) factor RpoD [Actinomyces viscosus C505]
          Length = 164

 Score =  133 bits (334), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 41/143 (28%), Positives = 71/143 (49%), Gaps = 27/143 (18%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY----------REHGD----------------- 46
             +  Y+ +I K+ +L  ++E  LAKR            E G+                 
Sbjct: 22  DPVKDYLKQIGKVALLNAEQEVELAKRIEAGLYAEHRLAEEGNDLPAKLRRELHWVAQDG 81

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ 
Sbjct: 82  QRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYAT 141

Query: 107 WWIKAAMQEYILRSWSLVKIGTT 129
           WWI+ A+   +      ++I   
Sbjct: 142 WWIRQAITRAMADQARTIRIPVH 164


>gi|294634103|ref|ZP_06712658.1| RNA polymerase sigma factor [Streptomyces sp. e14]
 gi|292829917|gb|EFF88271.1| RNA polymerase sigma factor [Streptomyces sp. e14]
          Length = 294

 Score =  133 bits (334), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 46/236 (19%), Positives = 105/236 (44%), Gaps = 11/236 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A + L+  ++ LV   A  +R     + ++V  G IGL++A+ +F+  R     ++++ +
Sbjct: 63  ARNTLIEMNMSLVRFAAGRFRNRSDDMEDIVQTGMIGLIKAIDRFELSREVEFTSFALPY 122

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I   ++ +   +   V +     + R+      L    + ++    +   V  +A  +N+
Sbjct: 123 IVGEIKRFFRDTTWAVHVPRRLQELRV-----ELARAREELSSRLDRDPTVAELATLMNL 177

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SESEV+       G  S ++L  +   +  +  + ++ D  G E+  I   E  +    L
Sbjct: 178 SESEVVEAQIASNGYNS-SSLDAALTGDGPEGGEAVLADFIGVEEHGIRLVEDFH---AL 233

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              ++ L+ R+RRI   R ++E   T   +  +   S+  V ++  R   ++++ +
Sbjct: 234 APLVADLSERDRRIIHLRFVEE--ATQAEIGEQLGCSQMHVSRLIKRIITQLRQGM 287


>gi|302556969|ref|ZP_07309311.1| RNA polymerase sigma factor [Streptomyces griseoflavus Tu4000]
 gi|302474587|gb|EFL37680.1| RNA polymerase sigma factor [Streptomyces griseoflavus Tu4000]
          Length = 295

 Score =  133 bits (334), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 46/233 (19%), Positives = 103/233 (44%), Gaps = 11/233 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A + L+  ++ LV   A  +RG G  + +VV  G IGL++A+ +F+  R     ++++ +
Sbjct: 64  ARNTLIEMNMSLVRFAAGRFRGRGDDMDDVVQTGMIGLIKAIDRFELAREVEFTSFALPY 123

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I   ++ +   +   V +     + R+      L    + +     +   V  +A  +N+
Sbjct: 124 IVGEIKRFFRDTTWAVHVPRRLQELRV-----ELAKAREELASRLDREPTVAELATLMNI 178

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +E +V+       G  S ++L  +   +  ++ + ++ D  G E+  +   E  +    L
Sbjct: 179 TEQQVVEGQIAANGYNS-SSLDAALTGDGPEYGEAVLADFIGVEEEGLRLVEDFHS---L 234

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              M+ L+PR+R I   R ++E   T   +      S+  V ++  R   +++
Sbjct: 235 APLMAELSPRDREILHLRFVEE--ATQAEIGERLGCSQMHVSRLIKRIIARLR 285


>gi|256379908|ref|YP_003103568.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Actinosynnema mirum
           DSM 43827]
 gi|255924211|gb|ACU39722.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Actinosynnema mirum
           DSM 43827]
          Length = 272

 Score =  133 bits (334), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 57/261 (21%), Positives = 109/261 (41%), Gaps = 17/261 (6%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG----LPISEVVSEGNIGLMQAV 90
             L   Y +  +     RLV  +  LV  +A    G G    + +++++  G  GL+ A+
Sbjct: 22  IALWHTYGQSREQGLRDRLVLHYAPLVKYVAGR-VGTGLPAHVDVADLIQSGIFGLVDAI 80

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +KF+PERG +  TY+M  I+ A+ + +      V     +  + +   L RL G LQ   
Sbjct: 81  EKFEPERGLKFETYAMQRIRGAILDDLRSQ-DWVPRSVRSRARDVERALERLGGRLQ--- 136

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCR--LAGDESLNALINSSDKNSSQWQDWLVYDH 208
               +      +A +L +   E+  +  +  L    +L+ LI +     S          
Sbjct: 137 ----RTPTDRELAAELKIGLGELRELYAQFQLTSVVALDELIAAGRAAGSAGSSLAESLP 192

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D   +  +     ++ R  L  +++ L  R+R +      +   +TL  +     V+  R
Sbjct: 193 DEGAEDPVASLVDQDSRRQLADAIAQLAERDRVVVTLYYFEN--LTLAEIGKVLGVTESR 250

Query: 269 VRQIEARAFKKVQESIQKQVE 289
           V Q+  RA  +++  I +Q+E
Sbjct: 251 VCQLHTRAVLRLRTKINEQLE 271


>gi|323452445|gb|EGB08319.1| hypothetical protein AURANDRAFT_5759 [Aureococcus anophagefferens]
          Length = 239

 Score =  133 bits (334), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 63/251 (25%), Positives = 118/251 (47%), Gaps = 23/251 (9%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRG-----YGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           A H LV ++  LVV IA GY+          + ++V EG +GL++AV+K++PERG R  T
Sbjct: 1   AKHALVRANGGLVVSIARGYQRLRTGAGVEALDDLVQEGTLGLIRAVEKYEPERGIRFGT 60

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+  WIKA++  ++ R  +++K+ +      L     R      A+ ++  +      +A
Sbjct: 61  YATAWIKASISAWLKRGDAMIKVPSRVADLGL-----RAARSSSALQNDLGRDATAEEVA 115

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + L  S + V +    L G   ++   ++   + S +   L            E     +
Sbjct: 116 RDLGASTAAVEAAASALHGSRVVSYDASAGGDSESNFVACLAD----------EDCAVGD 165

Query: 224 RRNMLTRSM-SVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKV 280
            +  LT ++ +VL+ RE R+   R   ++    +    ++   + +E VRQI  +AF+K+
Sbjct: 166 LKADLTNALAAVLDDRELRVVRLRYGLDDGTQRSTRECAAALGIGKESVRQICLKAFRKL 225

Query: 281 QESIQKQVELS 291
           + + Q    LS
Sbjct: 226 RGTAQGSALLS 236


>gi|328882855|emb|CCA56094.1| RNA polymerase sigma factor SigB [Streptomyces venezuelae ATCC
           10712]
          Length = 296

 Score =  133 bits (334), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 47/235 (20%), Positives = 97/235 (41%), Gaps = 11/235 (4%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            + LV  +L LV   A  +     P+ ++V  G IGL++A+ +F+  RG    T++M  I
Sbjct: 69  RNTLVELNLALVRFAAARFGTRSEPMEDIVQVGTIGLIKAIDRFELTRGVEFPTFAMPTI 128

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V +     + RL      L      +     +   V  +A++L ++
Sbjct: 129 IGEIKRFFRDTSWSVHVPRRLQELRLD-----LARAGDTLAQRLDRAPTVAELAEELGIA 183

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             EV+      +   + ++L    D+      +  + D  G E   +   E       L 
Sbjct: 184 PEEVVE-GMAASNAYTASSLDAQPDEEEGGGGEATLADRLGYEDHGLTGIE---YIASLK 239

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             ++ L  RER+I   R +    +T   + +E  +S+  V ++ AR   +++  +
Sbjct: 240 PMIASLPARERQILSLRFVSG--LTQSEIGTELGISQMHVSRLLARTLARLRRGL 292


>gi|225574950|ref|ZP_03783560.1| hypothetical protein RUMHYD_03029 [Blautia hydrogenotrophica DSM
           10507]
 gi|225037797|gb|EEG48043.1| hypothetical protein RUMHYD_03029 [Blautia hydrogenotrophica DSM
           10507]
          Length = 225

 Score =  133 bits (334), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 59/273 (21%), Positives = 110/273 (40%), Gaps = 65/273 (23%)

Query: 19  YIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           YI     +P  L+ Q+E  + ++     +  A   L+  +LRLVV IA  +   G+ + +
Sbjct: 11  YIGGADVLPAPLDAQQEEKVIQKLGTEQEKEAKALLIEHNLRLVVYIAKKFDNTGVGVED 70

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++S G IGL++A+  F+P +  +LATY+   I+  +  Y+ R+                 
Sbjct: 71  LISIGTIGLIKAINTFNPVKKIKLATYASRCIENEILMYLRRNSKT-------------- 116

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
                                      K+ VS  E ++++                D N 
Sbjct: 117 ---------------------------KMEVSIDEPLNVD---------------WDGNE 134

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL----QENPV 253
               D L  D D    V+    E +  R++L  ++S L+PRE+ I   R           
Sbjct: 135 LLLSDILGTDED----VISRGIEDEVERDLLGNAISKLSPREQTIVTLRFGLHSVDGKEK 190

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           T + ++    +S+  + ++E R  K++++ I K
Sbjct: 191 TQKEVADLLGISQSYISRLEKRIMKRLKKEIVK 223


>gi|55274934|gb|AAV49268.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 191

 Score =  133 bits (334), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 52/201 (25%), Positives = 94/201 (46%), Gaps = 12/201 (5%)

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           LVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+ 
Sbjct: 1   LVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMN 60

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
               +++      K L   LR  +     ++           IA++L+    +V  M   
Sbjct: 61  QTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRL 115

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
                S++  +    +     +  L    D +E    +  +  + +  + + +  LN ++
Sbjct: 116 NERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQ 170

Query: 240 RRIFEARR--LQENPVTLENL 258
           R +   R   L     TLE++
Sbjct: 171 REVLARRFGLLGYEAATLEDV 191


>gi|15894972|ref|NP_348321.1| sporulation sigma factor SigE [Clostridium acetobutylicum ATCC 824]
 gi|585930|sp|P33657|RPSE_CLOAB RecName: Full=RNA polymerase sigma-E factor
 gi|15024659|gb|AAK79661.1|AE007679_7 DNA-dependent RNA polymerase sigma subunit [Clostridium
           acetobutylicum ATCC 824]
 gi|460971|gb|AAC43309.1| putative sigma factor E [Clostridium acetobutylicum ATCC 824]
 gi|325509109|gb|ADZ20745.1| sporulation sigma factor SigE [Clostridium acetobutylicum EA 2018]
          Length = 235

 Score =  133 bits (334), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 62/265 (23%), Positives = 104/265 (39%), Gaps = 65/265 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K EE  L  +   +GD S    L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 33  PPLSKDEEDDLVNKLV-NGDESIRSILIERNLRLVVYIARKFENTGVGVEDLISVGTIGL 91

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FDP +  +LATY    I+  +                         LRR     
Sbjct: 92  IKAVNTFDPTKKIKLATYGSRCIENEI----------------------LMYLRR----- 124

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS-DKNSSQWQDWLV 205
                                         N ++  + S    +N   D N     D L 
Sbjct: 125 ------------------------------NSKVKAEISFYEPLNIDWDGNKLLLSDILG 154

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFE 263
            D+D    ++    E +  + +L  ++  LN RE+RI E R         T + ++    
Sbjct: 155 TDNDCVYNLI----EGEVDKQLLLFALKKLNEREKRIVELRYGLTGVGEKTQKEVADMLG 210

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           +S+  + ++E R  K++++ I K +
Sbjct: 211 ISQSYISRLEKRIIKRLKKEINKML 235


>gi|255553456|ref|XP_002517769.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
 gi|223543041|gb|EEF44576.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
          Length = 389

 Score =  133 bits (334), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 55/224 (24%), Positives = 103/224 (45%), Gaps = 12/224 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             +  R+  ++ RLV+ IA  YRG GL + +++ EG+IGL++  ++FDP+RG +L+TY  
Sbjct: 174 RQSRERITGNYRRLVLSIANRYRGKGLSLQDLIQEGSIGLLRGAERFDPKRGNKLSTYVY 233

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWIK A+   I  +  +V+   +   +       ++      +T+   +      IAK+L
Sbjct: 234 WWIKEAIITSISINSRIVRQPRSLWDRTTKIAEAKIS-----LTERLGRLPSYREIAKEL 288

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           NV  S V  +  R     SL+  +  SD+     Q+ +    +   + +++K+     + 
Sbjct: 289 NVHVSTVRLVFSRSRSTVSLDQAV--SDQGGMTLQEIIPGPEEMMPENMVKKQLL---KK 343

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRER 268
            L   +  L  RE              P + + +    ++ RER
Sbjct: 344 ELEELIQTLGKREAHTLRLIFGLNGQTPQSCDEIGRSLKLCRER 387


>gi|295696453|ref|YP_003589691.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
 gi|295412055|gb|ADG06547.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
          Length = 242

 Score =  133 bits (334), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 60/264 (22%), Positives = 112/264 (42%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L ++EE  L  R  E GD S    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 40  PPLTREEEEALLVRLIE-GDESVRSTLIERNLRLVVYIARKFENTGIYIEDLVSIGTIGL 98

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FDP++  +LATY+   I+  +  ++ R+                    +++   
Sbjct: 99  IKAVNTFDPQKRIKLATYASRCIENEILMFLRRN-------------------NKVRAE- 138

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                            ++ DE LN      D N     D L  
Sbjct: 139 ---------------------------------VSFDEPLN---VDWDGNELLLSDVLGT 162

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           ++D   + + E+ +    +++L  ++  L  RER+I E R        +T ++++    +
Sbjct: 163 ENDTIYRNIEEQID----KHLLYDALGKLTERERKIMELRFGLAGGQEMTQKDVADLLGI 218

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   + +
Sbjct: 219 SQSYISRLEKRIIKRLRKEFNRML 242


>gi|254380542|ref|ZP_04995908.1| sigma factor [Streptomyces sp. Mg1]
 gi|194339453|gb|EDX20419.1| sigma factor [Streptomyces sp. Mg1]
          Length = 304

 Score =  133 bits (334), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 54/259 (20%), Positives = 106/259 (40%), Gaps = 16/259 (6%)

Query: 35  YVLAKRYR--EHGDLS---AAHRLVTSHLRLVVKIAMGYRGY----GLPISEVVSEGNIG 85
            V  +R R  E G        + L+   L LV   A  +R      GL + +++  G IG
Sbjct: 50  RVFFRRLRTLEEGTREYQYTRNTLIEMSLSLVQFAARRFRARVLGGGLDMDDIIQVGTIG 109

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A+ +FDPER    +T ++ +I   ++ +   +   V +     + R       L   
Sbjct: 110 LIKAIDRFDPEREVEFSTLALPYIVGEIKRHFRDTTWSVHVPRRLQELR-----SELAKA 164

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            +A+TD   +   V  +A+ L ++E +VI       G  S +    + +  +S       
Sbjct: 165 QEALTDVLGRAPTVKEVAEHLELTEEQVIDGLVAANGYTSGSLDAAAGESETSPSTGRST 224

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
                    +    E     + L   +  L+ R+R I + R  Q+   T   + SE  +S
Sbjct: 225 RPLADLVGDVDPAMELFEDLHTLAPLLRQLDERDRLILQMRFGQD--RTQAEIGSELGIS 282

Query: 266 RERVRQIEARAFKKVQESI 284
           + +V ++ +R   +++  +
Sbjct: 283 QMQVSRLLSRTLARLRTGM 301


>gi|33322905|gb|AAQ07189.1|AF496497_1 RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           lactis]
          Length = 167

 Score =  133 bits (334), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 36/169 (21%), Positives = 70/169 (41%), Gaps = 12/169 (7%)

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
               ++I     +      L R++  L      + +PE    IA ++++   +V  +   
Sbjct: 1   QARTIRIPVHMVE--TINKLIRIQRQLLQDLGRDPEPE---EIAAEMDLPVKKVREVLKV 55

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
                SL   I   +++ S   D++    D       +    +  ++ L   +  L  RE
Sbjct: 56  AQEPVSLETPI--GEEDDSHLGDFI---EDKDATSPEQHAASEMLKDQLAEVLDTLTDRE 110

Query: 240 RRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             +   R   ++  P TLE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 111 ENVLRLRFGLDDGNPRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRS 159


>gi|226313041|ref|YP_002772935.1| RNA polymerase sigma-D factor [Brevibacillus brevis NBRC 100599]
 gi|226095989|dbj|BAH44431.1| RNA polymerase sigma-D factor [Brevibacillus brevis NBRC 100599]
          Length = 262

 Score =  133 bits (334), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 52/262 (19%), Positives = 116/262 (44%), Gaps = 18/262 (6%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGL 86
           EK +E+     +++ G   A   L+T  L LV K+A          +   +++S G  GL
Sbjct: 8   EKAKEFDKWVMWKQEGSREAEVDLITRFLPLVDKVANRLAINLPANVDKDDLISYGRFGL 67

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           + A+ KFD  RG +  TY+MW I+ AM + +  +     I  T   K      ++++   
Sbjct: 68  LDALAKFDHTRGLQFETYAMWRIRGAMIDGLRENDW---IPRTVRDKA-----KKIEEAY 119

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             +    L+      ++  L +S+ E+  + +   LA   S++  +   D+  +    ++
Sbjct: 120 TTLEQQMLRMPTDQEVSDYLGISKKELQQVFLETSLASMVSIDEAVGDEDEQKTARHSYI 179

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           + +   +   +    E  + + +L   +  L  +ER +      +E  +TL  ++    +
Sbjct: 180 IDELTPRPDNV---AEVSSLKEVLVTVIDKLPEKERLVISLFYFEE--MTLSEIAEIMSL 234

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S  R+ Q+ ++A  +++ ++ +
Sbjct: 235 SPSRISQLHSKALFRLRSALSR 256


>gi|313902394|ref|ZP_07835797.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Thermaerobacter
           subterraneus DSM 13965]
 gi|313467325|gb|EFR62836.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Thermaerobacter
           subterraneus DSM 13965]
          Length = 247

 Score =  133 bits (334), Expect = 4e-29,   Method: Composition-based stats.
 Identities = 66/294 (22%), Positives = 106/294 (36%), Gaps = 70/294 (23%)

Query: 10  VNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           V G + L  Y+   R  P  L  +EE    +R R  GD  A   L+  +LRLV  IA  +
Sbjct: 14  VRGLLYLVGYLQTGRSFPQPLSPEEEAHYLERMR-CGDERAREVLIERNLRLVAHIAKKF 72

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
              G    +++S G +GL++ V  +DP +G RLATY+   I+  +  ++           
Sbjct: 73  DETGEDPEDLISIGTVGLIKGVDTYDPSKGTRLATYAARCIENEILMHLR---------- 122

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
                                T  N +                  + +   +  D     
Sbjct: 123 --------------------ATRRNRRE-----------------VFLQNPIGVDR---- 141

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
                + N     D L  D D  E+ +  +   +  R  +      L PRERR+ E R  
Sbjct: 142 -----EGNEVTLMDMLPADEDAVEETVGRRLLARRIREAVRE----LGPRERRVLELRFG 192

Query: 249 QENPV--TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQKP 300
            +     T   ++    +SR  V +IE RA +K+         +   P  L +P
Sbjct: 193 LDGRRRYTQREVARVLGISRSYVSRIEKRAVRKL------TRHVLDEPGPLPEP 240


>gi|261405673|ref|YP_003241914.1| sporulation sigma factor SigE [Paenibacillus sp. Y412MC10]
 gi|329922715|ref|ZP_08278267.1| RNA polymerase sigma-E factor [Paenibacillus sp. HGF5]
 gi|261282136|gb|ACX64107.1| RNA polymerase, sigma 28 subunit, SigE [Paenibacillus sp. Y412MC10]
 gi|328942057|gb|EGG38340.1| RNA polymerase sigma-E factor [Paenibacillus sp. HGF5]
          Length = 240

 Score =  133 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 69/264 (26%), Positives = 113/264 (42%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE  L K+    GD +    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 38  PPLTKEEEEFLLKKL-PTGDAATRAMLIERNLRLVVYIARKFENTGINIEDLVSIGAIGL 96

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FDPE+  +LATY+   I+  +  Y+ R+                          
Sbjct: 97  IKAVNTFDPEKKIKLATYASRCIENEILMYLRRN-------------------------- 130

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                               N + SEV       + DE LN      D N     D L  
Sbjct: 131 --------------------NKTRSEV-------SFDEPLN---IDWDGNELLLSDVLGT 160

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           ++D   + + E+ +RK    +L +++  L+ RER I E R         T ++++    +
Sbjct: 161 ENDTIYRNIEEQVDRK----LLQKALDKLSDRERMIMELRFGLQDGEEKTQKDVADLLGI 216

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 217 SQSYISRLEKRIIKRLRKEFNKMV 240


>gi|242371561|ref|ZP_04817135.1| DNA-directed RNA polymerase sigma subunit FliA [Staphylococcus
           epidermidis M23864:W1]
 gi|242350713|gb|EES42314.1| DNA-directed RNA polymerase sigma subunit FliA [Staphylococcus
           epidermidis M23864:W1]
          Length = 256

 Score =  133 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 49/263 (18%), Positives = 111/263 (42%), Gaps = 24/263 (9%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             ++     K ++E+ +  A  +LVT + +L+  +A  Y        ++V  G +GL+ A
Sbjct: 12  SPEQINQWIKEHQENENSQAQDKLVTHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGA 71

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +FD     +   + +  +   ++ Y+      V +     +        R+K     +
Sbjct: 72  INRFDLSFDRKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIG-----PRIKKVSDEL 126

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNC------RLAGDESLNALINSSDKNSSQWQDW 203
           T+   +   +  IA++L V++ EV+           L+ D S+ A     D ++    D 
Sbjct: 127 TNELERSPSINEIAERLEVTDEEVLEAMEMGQSYNALSVDHSIEA---DKDGSTVTLLDI 183

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    D          +   +R +L R + +L+ RER+I +   +    ++ +       
Sbjct: 184 MGQQDDNY--------DLTEKRMILERILPILSDRERQIIQCTFI--EGLSQKETGERIG 233

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+  V +++  A KK+QE+ ++
Sbjct: 234 LSQMHVSRLQRTAIKKLQEAAKQ 256


>gi|253682196|ref|ZP_04862993.1| RNA polymerase sigma-K factor [Clostridium botulinum D str. 1873]
 gi|253561908|gb|EES91360.1| RNA polymerase sigma-K factor [Clostridium botulinum D str. 1873]
          Length = 235

 Score =  133 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 60/275 (21%), Positives = 104/275 (37%), Gaps = 63/275 (22%)

Query: 9   IVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           +++G   L+ Y+      P  L + EE    K+++  GD  A   L+  +LRLV  I   
Sbjct: 10  MIDGMTFLTAYVSNGTSFPQPLNEDEERYYLKKFK-GGDALAKGILIERNLRLVAHIVKK 68

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y      I +++S G +GL++A+  FD  +G RLATY+   I+  +              
Sbjct: 69  YSYPNKDIDDLISIGTVGLIKAIDSFDISKGTRLATYAARCIENEILM------------ 116

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
                  L  N +++K                              + +   +  D    
Sbjct: 117 -------LIRNTKKIKSE----------------------------VYLQDPIGVD---- 137

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
                 + N     D L  D +   +V+   E R   + +  +    L  RE+ I + R 
Sbjct: 138 -----KEGNEISLMDVLSSDENSVIEVV---ENRMQIKKLYDKINECLTEREKIIIKMRY 189

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
              +  P T   +++   +SR  V +IE RA KK+
Sbjct: 190 GLNDGKPKTQREIAAFLNISRSYVSRIEKRALKKM 224


>gi|323705266|ref|ZP_08116841.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
 gi|323535168|gb|EGB24944.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
          Length = 231

 Score =  133 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 55/265 (20%), Positives = 98/265 (36%), Gaps = 63/265 (23%)

Query: 19  YIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           Y+      P  L  +EE    + ++ +GD  A + L+  +LRLV  +   Y   G  + +
Sbjct: 21  YLTNANSFPQPLTAEEERKYFEAFK-NGDEEAKNILIERNLRLVAHVVKKYSNAGKDVDD 79

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++S G IGL++A+  +D  +G  LATY+   I+  +   +              +K++  
Sbjct: 80  LISIGTIGLIKAILTYDSSKGTHLATYAARCIENEILMSLR------------AEKKIKS 127

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
                                               IS++  +  D          + N 
Sbjct: 128 E-----------------------------------ISLHDPIGVD---------KEGNE 143

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTL 255
               D L  + D   +V  + E R   + +  +  SVL  RE+ I E R         T 
Sbjct: 144 ISLIDILGTETD---EVSDQVELRMQVKKLYHKLNSVLKNREKLIIELRYGLINGGAKTQ 200

Query: 256 ENLSSEFEVSRERVRQIEARAFKKV 280
             ++    +SR  V +IE +A  K+
Sbjct: 201 REIAKMLGISRSYVSRIEKKALNKL 225


>gi|296164736|ref|ZP_06847300.1| RNA polymerase sigma-F factor [Mycobacterium parascrofulaceum ATCC
           BAA-614]
 gi|295899907|gb|EFG79349.1| RNA polymerase sigma-F factor [Mycobacterium parascrofulaceum ATCC
           BAA-614]
          Length = 288

 Score =  133 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 47/258 (18%), Positives = 100/258 (38%), Gaps = 29/258 (11%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
             E +  A++           R+V   L L   +A  +   G  + ++V    +GLM AV
Sbjct: 55  PAESHEYARQ---------RERIVARCLPLADHVASHFARRGEGLDDLVQVARLGLMNAV 105

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
            +FDP++G     +++  +   ++ Y       +++     +  +     ++      + 
Sbjct: 106 NRFDPDKGPSFIGFAVPTMMGEVRRYFRDYSWGMRVPRRLRELHV-----QISRTTGDLA 160

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD----ESLNALINSSDKNSSQWQDWLVY 206
               +      +++ L V   E++   C +AGD    +SL+A + +    + +     V 
Sbjct: 161 QKLGRAPTAGELSRALEVPHEEIVE--CLVAGDAYRLDSLDAPMGTDSSGTPRLVADAVG 218

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
             D Q        E    R  L   ++ L  RER +   R      +T   ++    VS+
Sbjct: 219 GIDPQ-------IEHITNREALRVLVAALPEREREVLRMRFF--ESMTQSQIAERIGVSQ 269

Query: 267 ERVRQIEARAFKKVQESI 284
            +V +I A   + ++E +
Sbjct: 270 MQVSRILAGTLRCLREQL 287


>gi|254819525|ref|ZP_05224526.1| RNA polymerase sigma factor SigF [Mycobacterium intracellulare ATCC
           13950]
          Length = 262

 Score =  133 bits (334), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 45/236 (19%), Positives = 94/236 (39%), Gaps = 13/236 (5%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             ++V   L L   IA  + G G P  ++V    +GL+ AV +FD + G    ++++  I
Sbjct: 40  RDKIVERCLPLADHIARRFEGRGEPRDDLVQVARVGLVNAVVRFDVDAGSDFVSFAVPTI 99

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   VK+     +  L     RL      ++    +      +A +L + 
Sbjct: 100 MGEVRRHFRDNSWSVKVPRRLKELHL-----RLGTATADLSQRLGRAPTATELAAELEMD 154

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             EV+     L    S N L   S     + +   + D  G     +++ E +     L 
Sbjct: 155 REEVVE---GLVAGSSYNTLSIDSGGGGEEEEARAIADTLGDVDTGLDRIEDQ---ESLR 208

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             +  L  RER +   R      +T   ++    +S+  V ++ A++  ++++ +Q
Sbjct: 209 PLLEALPERERTVLVLRFF--ESMTQTQIAERVGISQMHVSRLLAKSLTRLRDQLQ 262


>gi|167037477|ref|YP_001665055.1| sporulation sigma factor SigK [Thermoanaerobacter pseudethanolicus
           ATCC 33223]
 gi|167040139|ref|YP_001663124.1| sporulation sigma factor SigK [Thermoanaerobacter sp. X514]
 gi|256752531|ref|ZP_05493387.1| RNA polymerase, sigma 28 subunit, SigK [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|300914223|ref|ZP_07131539.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X561]
 gi|307724542|ref|YP_003904293.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter sp. X513]
 gi|320115891|ref|YP_004186050.1| RNA polymerase sigma-K factor [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
 gi|166854379|gb|ABY92788.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Thermoanaerobacter sp. X514]
 gi|166856311|gb|ABY94719.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Thermoanaerobacter pseudethanolicus ATCC 33223]
 gi|256748597|gb|EEU61645.1| RNA polymerase, sigma 28 subunit, SigK [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|300889158|gb|EFK84304.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X561]
 gi|307581603|gb|ADN55002.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X513]
 gi|319928982|gb|ADV79667.1| RNA polymerase sigma-K factor [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
          Length = 231

 Score =  132 bits (333), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 62/266 (23%), Positives = 100/266 (37%), Gaps = 65/266 (24%)

Query: 19  YIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           Y+      P  L  +EE    + Y+ +GD  A + L+  +LRLV  +   Y G G  I +
Sbjct: 21  YLTNTNSFPNPLTPEEEKKYLEAYK-NGDEEARNILIERNLRLVAHVVKKYSGTGKDIDD 79

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++S G IGL++A+  FD  +G  LATY+   I+  +   I                    
Sbjct: 80  LISIGTIGLIKAISTFDSSKGTHLATYAARCIENEILMSI-------------------R 120

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
             +++KG                             + +   +  D          + N 
Sbjct: 121 TEKKMKGE----------------------------VFLQDPIGVD---------KEGNE 143

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQENP--VT 254
               D L  + D     + E+ E+K +   L   M SVL  RE+ I E R    N    T
Sbjct: 144 ISLMDVLGTEED----EISEQVEKKLQIKKLYSKMNSVLKNREKLIIEMRYGLYNGKVRT 199

Query: 255 LENLSSEFEVSRERVRQIEARAFKKV 280
              ++    +SR  V +IE +A  K+
Sbjct: 200 QREIAKMLGISRSYVSRIEKKALNKL 225


>gi|223043961|ref|ZP_03614002.1| RNA polymerase sigma-B factor [Staphylococcus capitis SK14]
 gi|314934140|ref|ZP_07841501.1| RNA polymerase sigma-B factor [Staphylococcus caprae C87]
 gi|222442676|gb|EEE48780.1| RNA polymerase sigma-B factor [Staphylococcus capitis SK14]
 gi|313653045|gb|EFS16806.1| RNA polymerase sigma-B factor [Staphylococcus caprae C87]
          Length = 256

 Score =  132 bits (333), Expect = 5e-29,   Method: Composition-based stats.
 Identities = 50/263 (19%), Positives = 111/263 (42%), Gaps = 24/263 (9%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             ++     K ++E+ +  A  +LVT + +L+  +A  Y        ++V  G +GL+ A
Sbjct: 12  SPEQINQWIKEHQENENSQAQDKLVTHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGA 71

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +FD     +   + +  +   ++ Y+      V +     +        R+K     +
Sbjct: 72  INRFDLSFDRKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIG-----PRIKKISDEL 126

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNC------RLAGDESLNALINSSDKNSSQWQDW 203
           T+   +   +  IA++L VS+ EV+           L+ D S+ A     D ++    D 
Sbjct: 127 TNELERSPSISEIAQRLEVSDEEVLEAMEMGQSYNALSVDHSIEA---DKDGSTVTLLDI 183

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    D          +   +R +L R + +L+ RER+I +   +    ++ +       
Sbjct: 184 MGQQDDNY--------DLTEKRMILERILPILSDRERQIIQCTFI--EGLSQKETGERIG 233

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+  V +++  A KK+QE+ ++
Sbjct: 234 LSQMHVSRLQRTAIKKLQEAAKQ 256


>gi|169831144|ref|YP_001717126.1| FliA/WhiG family RNA polymerase sigma factor [Candidatus
           Desulforudis audaxviator MP104C]
 gi|169637988|gb|ACA59494.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Candidatus
           Desulforudis audaxviator MP104C]
          Length = 256

 Score =  132 bits (333), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 59/274 (21%), Positives = 101/274 (36%), Gaps = 63/274 (22%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           ++NG + L  +I        L ++EE    +R    GD  A + L   +LRLV  I   Y
Sbjct: 34  LINGVVLLLSHITNNSFPQPLSREEEKEYVRRML-AGDEHARNILTERNLRLVAHIIKKY 92

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
              G    +++S G IGL++A+  F+P +G RLATY+   I+  +               
Sbjct: 93  DSTGEDTDDLISIGTIGLIKAINTFNPHKGARLATYAARCIENEI--------------- 137

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
                    +LR +K                                         SL  
Sbjct: 138 -------LMHLRTVKKTRFE-----------------------------------VSLQD 155

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            I    + +   +  L+       +V+ +K E    +  L   M  L+ RE+++   R  
Sbjct: 156 PIGVDKEGN---EITLIDILGTNPEVVEDKVETHFEQRRLLEKMHKLSRREKKVLALRFG 212

Query: 249 --QENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
              +   T + ++ +  +SR  V +IE RA  K+
Sbjct: 213 LVDDTRQTQQEIAQDLGISRSYVSRIEKRALNKL 246


>gi|57996874|emb|CAI45885.1| negative response regulator [Escherichia coli]
 gi|57996882|emb|CAI45889.1| negative response regulator [Escherichia coli]
          Length = 191

 Score =  132 bits (333), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 54/201 (26%), Positives = 94/201 (46%), Gaps = 12/201 (5%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           +     +++      K L   LR  +     ++           IA++L+    +V  M 
Sbjct: 61  MNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRML 115

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                  S++  +    +     +  L    D +E    +  +  + +  + + +  LN 
Sbjct: 116 RLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNA 170

Query: 238 RERRIFEARR--LQENPVTLE 256
           ++R +   R   L     TLE
Sbjct: 171 KQREVLARRFGLLGYEAATLE 191


>gi|311898622|dbj|BAJ31030.1| putative RNA polymerase sigma factor [Kitasatospora setae KM-6054]
          Length = 276

 Score =  132 bits (333), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 53/256 (20%), Positives = 111/256 (43%), Gaps = 18/256 (7%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAV 90
             L + Y+E GD     +L+  +  LV  +A    G GLP     ++ VS G  GL+ A+
Sbjct: 29  QALWRSYKESGDHRLRDQLILHYSPLVKYVAGR-VGVGLPANVEQADFVSSGVFGLIDAI 87

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +KFD +R  +  TY++  I+ A+ + + R+   +        K +      L+  L+   
Sbjct: 88  EKFDIDRAIKFETYAISRIRGAIIDEL-RALDWIPRSVRQKAKAVERAYATLEARLR--- 143

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
               +      +A ++ +S  ++ ++     LA   +L+ L++S+ +   +    +    
Sbjct: 144 ----RTPYDPEVAAEMGISLDDLHTIFSQLSLANVVALDELLHSAGEGGDRLT-LMETLP 198

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D      +E  E +  R +L  +++ L  RE+ +          +TL  +     V+  R
Sbjct: 199 DSGADNPVEIAEDRELRRLLASAVNTLPEREKTVVTLYYY--EGLTLAEIGQVLGVTESR 256

Query: 269 VRQIEARAFKKVQESI 284
           V QI  ++  +++  +
Sbjct: 257 VSQIHTKSVLQLRAKM 272


>gi|44662845|gb|AAS47504.1| major sigma factor 70 [Meiothermus ruber DSM 1279]
          Length = 168

 Score =  132 bits (333), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 40/176 (22%), Positives = 70/176 (39%), Gaps = 10/176 (5%)

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I     +      L R    +Q         E++ A 
Sbjct: 1   TYATWWIRQAINRAIADQARTIRIPVHMVE--TINKLTRTARRMQQELGREPSYEEI-AD 57

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A        +V           SL   I   D+  S + D++  +H       ++   + 
Sbjct: 58  AMGPGWDAKKVEETFKIAQEPVSLETPI--GDEKDSFYGDFIPDEH---MASPVDSAAQS 112

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARA 276
                L +++  L+ RE  + + R+        TLE + + F V+RER+RQIE +A
Sbjct: 113 MLSEELEKALGKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKA 168


>gi|260438830|ref|ZP_05792646.1| RNA polymerase sigma-E factor [Butyrivibrio crossotus DSM 2876]
 gi|292808820|gb|EFF68025.1| RNA polymerase sigma-E factor [Butyrivibrio crossotus DSM 2876]
          Length = 246

 Score =  132 bits (333), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 62/288 (21%), Positives = 117/288 (40%), Gaps = 68/288 (23%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
           KN  +   G+I    YI     +P  LE  EE  +        D  A   L+  +LRLVV
Sbjct: 20  KNFLLDRKGDI---HYIGGADVLPAPLEPAEEAEVIADLGTEYDTKAKTMLIEHNLRLVV 76

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA  +   G+ + +++S G IGL++A+  FD  +  +LATY+   I+  +  Y+ R+  
Sbjct: 77  YIAKKFDNTGVGVEDLISIGTIGLIKAINSFDINKKIKLATYASRCIENEILMYLRRNHK 136

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
                                                     ++ VS  E ++++     
Sbjct: 137 T-----------------------------------------RMEVSIDEPLNVD----- 150

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
                      D N     D L  D D   + L ++ E+K    +L ++++ L+ RER I
Sbjct: 151 ----------WDGNELLLSDILGTDEDIIYRNLEDEAEKK----LLLKAVNKLSERERTI 196

Query: 243 FEARRLQENP----VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + R    +P    +T + ++    +S+  + ++E +  K++++ + K
Sbjct: 197 IDLRFGLNSPDGKELTQKEVADMLGISQSYISRLEKKIIKRLKKEMIK 244


>gi|289578255|ref|YP_003476882.1| RNA polymerase, sigma 28 subunit, SigK [Thermoanaerobacter italicus
           Ab9]
 gi|289527968|gb|ADD02320.1| RNA polymerase, sigma 28 subunit, SigK [Thermoanaerobacter italicus
           Ab9]
          Length = 231

 Score =  132 bits (333), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 56/265 (21%), Positives = 94/265 (35%), Gaps = 63/265 (23%)

Query: 19  YIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           Y+      P  L  +EE    + Y+ +GD  A + L+  +LRLV  +   Y G G  I +
Sbjct: 21  YLTNTNSFPNPLTPEEEKKYLEAYK-NGDEEARNILIERNLRLVAHVVKKYSGTGKDIDD 79

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++S G IGL++A+  FD  +G  LATY+   I+  +   +                    
Sbjct: 80  LISIGTIGLIKAISTFDSSKGTHLATYAARCIENEILMSVR------------------- 120

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
                                      K  V   + I ++                + N 
Sbjct: 121 ----------------------AEKKMKGEVFLQDPIGVDK---------------EGNE 143

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTL 255
               D L  + +   + + +K + K   N +   +     RER I E R    N    T 
Sbjct: 144 ISLMDVLGTEENEISEQVEKKIQIKKLYNKMNNVLKN---RERLIIEMRYGLYNGKVRTQ 200

Query: 256 ENLSSEFEVSRERVRQIEARAFKKV 280
             ++    +SR  V +IE +A  K+
Sbjct: 201 REIAKMLGISRSYVSRIEKKALNKL 225


>gi|160943881|ref|ZP_02091111.1| hypothetical protein FAEPRAM212_01381 [Faecalibacterium prausnitzii
           M21/2]
 gi|158444557|gb|EDP21561.1| hypothetical protein FAEPRAM212_01381 [Faecalibacterium prausnitzii
           M21/2]
 gi|295104730|emb|CBL02274.1| RNA polymerase, sigma 29 subunit, SigE [Faecalibacterium
           prausnitzii SL3/3]
          Length = 234

 Score =  132 bits (333), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 64/263 (24%), Positives = 102/263 (38%), Gaps = 63/263 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L  ++E  L  R    GD +A   L+T +LRLVV +A  Y   G+P  ++VS G IGL
Sbjct: 33  PPLTPEQEKALLDRMA-AGDAAAREELITHNLRLVVYLAKKYENSGVPAEDLVSIGTIGL 91

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F P R  +LATY+   I   +  Y                      LR+     
Sbjct: 92  IKAVNTFTPARSIKLATYASRCIGNEILMY----------------------LRKSSNRR 129

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           Q                                 + DE LN      D N     D L  
Sbjct: 130 QEA-------------------------------SIDEPLN---VDGDGNELLLSDILGS 155

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEV 264
           D +   Q L +  E    R +L  +++ L+ RER+I E R    +    T +  +    +
Sbjct: 156 DANAVSQQLEQDAE----RAVLRSAVAALSARERQIMELRFGLTDGVERTQKEAADALGI 211

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           S+  + ++E R  + ++  ++ +
Sbjct: 212 SQSYISRLEKRIIRTLKARLESE 234


>gi|302871075|ref|YP_003839711.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
 gi|302573934|gb|ADL41725.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
          Length = 256

 Score =  132 bits (333), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 49/245 (20%), Positives = 112/245 (45%), Gaps = 17/245 (6%)

Query: 29  LEKQEEY--VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           LE  +E    L + Y+    +   + LV  +L +   IA  +   G+   ++     + L
Sbjct: 8   LEIDDEKIDRLFEEYQRTKAIELRNELVNKYLYIAEIIAKKFVNRGIDYDDLYQVACVAL 67

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           + AV++F+P +G++  +++   I   ++ Y     S++++      +RL+    ++K   
Sbjct: 68  INAVERFEPNKGYKFTSFATPTIMGEIKRYFRDRASIIRLP-----RRLYETSAKIKLVT 122

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           + ++    +P +V  IA+ LN+S  EV+ +      + S + L  S D+   + ++  + 
Sbjct: 123 EMLSSKLKRPPKVEEIAQHLNMSTEEVLEVM-----EASNSYLPQSLDQTMYEDEEMTLG 177

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           D  G+     E   +      + +++  L+P ER   + R  +E   T + ++ E  VS+
Sbjct: 178 DVLGKSD---ENILQIENVEAVKKAIERLSPFEREFVQKRFFEE--KTQKEIAEEMNVSQ 232

Query: 267 ERVRQ 271
             + +
Sbjct: 233 MYISR 237


>gi|78045111|ref|YP_359473.1| sporulation sigma factor SigK [Carboxydothermus hydrogenoformans
           Z-2901]
 gi|77997226|gb|ABB16125.1| RNA polymerase sigma-K factor [Carboxydothermus hydrogenoformans
           Z-2901]
          Length = 234

 Score =  132 bits (333), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 61/278 (21%), Positives = 105/278 (37%), Gaps = 65/278 (23%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           ++++V G + L  Y+        L ++EE     R  + GD  A   L   +LRLV  I 
Sbjct: 8   ITLVVEGLLFLLGYLAGSAFPQPLSEEEEAYYIDRLLQ-GDREARDVLAERNLRLVAHIV 66

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             + G G    +++S G IGL++A+  F P++G +LATY+   +                
Sbjct: 67  KKFEGTGEATEDLISIGTIGLIKAIDTFRPDKGTKLATYAAKCV---------------- 110

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
                 +  +  +LR  K +                                    G+ S
Sbjct: 111 ------ENEILMHLRATKKN-----------------------------------RGEVS 129

Query: 186 LNALI-NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           L   I    + N     D L    D    +++E+  R      + +++  L PRER++ E
Sbjct: 130 LYDPIGFDKEGNEITLLDILGTRGD----IVLEQVVRMLDAETIEKNLKKLTPRERKVIE 185

Query: 245 ARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKV 280
            R         T   ++ +  +SR  V +IE RA  K+
Sbjct: 186 ERFGLSQTPRKTQREIAKKMGISRSYVSRIEKRAILKL 223


>gi|315646039|ref|ZP_07899160.1| sporulation sigma factor SigE [Paenibacillus vortex V453]
 gi|315278800|gb|EFU42114.1| sporulation sigma factor SigE [Paenibacillus vortex V453]
          Length = 240

 Score =  132 bits (333), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 69/264 (26%), Positives = 113/264 (42%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE  L K+    GD +    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 38  PPLTKEEEEFLLKKL-PSGDAATRAMLIERNLRLVVYIARKFENTGINIEDLVSIGAIGL 96

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FDPE+  +LATY+   I+  +  Y+ R+                          
Sbjct: 97  IKAVNTFDPEKKIKLATYASRCIENEILMYLRRN-------------------------- 130

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                               N + SEV       + DE LN      D N     D L  
Sbjct: 131 --------------------NKTRSEV-------SFDEPLN---IDWDGNELLLSDVLGT 160

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           ++D   + + E+ +RK    +L +++  L+ RER I E R         T ++++    +
Sbjct: 161 ENDTIYRNIEEQVDRK----LLQKALDKLSDRERMIMELRFGLQDGEEKTQKDVADLLGI 216

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 217 SQSYISRLEKRIIKRLRKEFNKMV 240


>gi|295109522|emb|CBL23475.1| RNA polymerase, sigma 29 subunit, SigE [Ruminococcus obeum A2-162]
          Length = 243

 Score =  132 bits (333), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 55/263 (20%), Positives = 106/263 (40%), Gaps = 64/263 (24%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            LE + E  +  + +   +  A   L+  +LRLVV IA  +   G+ + +++S G IGL+
Sbjct: 39  PLEPKREAYVISKLKTEQEQEARSLLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLI 98

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +A+  F+P +  +LATY+   I+  +  Y+ R+                           
Sbjct: 99  KAINTFNPVKNIKLATYASRCIENEILMYLRRNSKT------------------------ 134

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                            K+ VS  E ++++                D N     D L  D
Sbjct: 135 -----------------KMEVSIDEPLNVD---------------WDGNELLLSDILGTD 162

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN----PVTLENLSSEFE 263
            D    V+  + E +    +L ++++ L+PRE+ I   R    N      T + ++    
Sbjct: 163 ED----VISRRMEDEVEITLLAKAINKLSPREQTIIRLRFGLNNAEGKEKTQKEVADLLG 218

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+  + ++E R  K++++ I K
Sbjct: 219 ISQSYISRLEKRIMKRLKKEIVK 241


>gi|321309571|ref|YP_004191900.1| RNA polymerase sigma factor rpoD [Mycoplasma haemofelis str.
           Langford 1]
 gi|319801415|emb|CBY92061.1| RNA polymerase sigma factor rpoD [Mycoplasma haemofelis str.
           Langford 1]
          Length = 424

 Score =  132 bits (333), Expect = 6e-29,   Method: Composition-based stats.
 Identities = 60/246 (24%), Positives = 102/246 (41%), Gaps = 19/246 (7%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLS-AAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           +  I K   L  +EE  L K        + A  RL   +LRLV   A  Y  YG P+ ++
Sbjct: 109 LKLIGK---LTFEEETALFKLLENPETRNFAVKRLTIFNLRLVWSSARKYLNYGFPMEDL 165

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V EG  GL++A+ KFD   G R +TY+ WWI+ AM   +     ++++        +  N
Sbjct: 166 VQEGIFGLVKAIHKFDCAFGNRFSTYATWWIRQAMLRAVEDKSRIIRVPVHMVP--VINN 223

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLN--VSESEVISMNCRLAGDESLNALINSSDKN 196
           L R++  L          EQ+    +K +   +  +V  +        SL+ LI+  +  
Sbjct: 224 LARIEKALILENGEEPTIEQLTQEMQKYDSQYTVQKVSDIKKLNIDWVSLDKLIDYDEN- 282

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQ---ENP 252
                 +L    D +     E+    ++  +L   + S L   E  + +        E+P
Sbjct: 283 ------FLDSVPDEEVISSEEEAILTHKSMVLQEFLESTLEDDELLVLDMHYGLMEFESP 336

Query: 253 VTLENL 258
            T+E +
Sbjct: 337 NTIEQI 342


>gi|317472443|ref|ZP_07931767.1| RNA polymerase sigma-E factor [Anaerostipes sp. 3_2_56FAA]
 gi|316900087|gb|EFV22077.1| RNA polymerase sigma-E factor [Anaerostipes sp. 3_2_56FAA]
          Length = 238

 Score =  132 bits (332), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 57/274 (20%), Positives = 109/274 (39%), Gaps = 65/274 (23%)

Query: 18  RYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
            YI     +P  LE +EE  +  +     +  A  +L+  +LRLVV IA  +   G+ + 
Sbjct: 21  HYIGGAEILPAPLEAKEEEKMIHKLGTAEEPEARAKLIERNLRLVVYIAKKFDNTGIGVE 80

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++S G IGL++A+  F+P +  +LATY+   I+  +  Y+ R+                
Sbjct: 81  DLISIGTIGLIKAINTFNPAKKIKLATYASRCIENEILMYLRRNNKT------------- 127

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
                                       K+ VS  E ++++                D N
Sbjct: 128 ----------------------------KMEVSIDEPLNVD---------------WDGN 144

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL----QENP 252
                D L  D D    ++    E +  R +L  +M +L+ RER+I E R          
Sbjct: 145 ELLLSDILGTDED----IIYRDLEHEVDRKLLLNAMKILSDRERKIIELRFGINQKDGEE 200

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            T + ++    +S+  + ++E +  K+++  + +
Sbjct: 201 KTQKEVADLMGISQSYISRLEKKIIKRLKREMSR 234


>gi|297616583|ref|YP_003701742.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
 gi|297144420|gb|ADI01177.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Syntrophothermus lipocalidus DSM 12680]
          Length = 235

 Score =  132 bits (332), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 62/275 (22%), Positives = 110/275 (40%), Gaps = 66/275 (24%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +  G + L  Y++ +     L ++EE +  ++ RE GD  A H L+  +LRLV  +   +
Sbjct: 13  LTKGMLMLFSYLNNLVFPHPLSEEEERIYLEKTRE-GDEEAKHILIEHNLRLVAHVIKKF 71

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            G G    +++S G IGL++A+  FD  RG RLATY+   I+  +  +            
Sbjct: 72  EGTGEDTEDLISIGTIGLIKAINTFDYARGTRLATYAARCIENEVLMW------------ 119

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
                  F N R++K                                         S+  
Sbjct: 120 -------FRNSRKVKQE--------------------------------------VSIYE 134

Query: 189 LI-NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
            I    + N   + D L  D++     +++  E + +   + + +  L+ RER++ E R 
Sbjct: 135 PIGYDKEGNEITFLDILTTDNE-----IVDVVETRLQEEKIRQKLGALSKRERQVIEMRY 189

Query: 248 LQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                   T   ++ +  +SR  V +IE RA KK+
Sbjct: 190 GLFSGLKATQREIARKLGISRSYVSRIEKRALKKL 224


>gi|326390169|ref|ZP_08211730.1| RNA polymerase, sigma 28 subunit, SigK [Thermoanaerobacter
           ethanolicus JW 200]
 gi|325993817|gb|EGD52248.1| RNA polymerase, sigma 28 subunit, SigK [Thermoanaerobacter
           ethanolicus JW 200]
          Length = 231

 Score =  132 bits (332), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 63/266 (23%), Positives = 97/266 (36%), Gaps = 65/266 (24%)

Query: 19  YIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           Y+      P  L  +EE    + YR +GD  A + L+  +LRLV  +   Y G G  I +
Sbjct: 21  YLTNTNSFPNPLTPEEEKKYLEAYR-NGDEEARNILIERNLRLVAHVVKKYSGTGKDIDD 79

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++S G IGL++A+  FD  +G  LATY+   I+  +   I                    
Sbjct: 80  LISIGTIGLIKAISTFDSSKGTHLATYAARCIENEILMSIR------------------- 120

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
                                      K  +   + I ++                + N 
Sbjct: 121 ----------------------AEKKMKGEIFLQDPIGVDK---------------EGNE 143

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQENP--VT 254
               D L  + D     + E+ E+K +   L   M SVL  RER I E R    N    T
Sbjct: 144 ISLMDVLGTEED----EISEQVEKKLQIKKLYSKMNSVLKNRERLIIEMRYGLYNGKVRT 199

Query: 255 LENLSSEFEVSRERVRQIEARAFKKV 280
              ++    +SR  V +IE +A  K+
Sbjct: 200 QREIAKMLGISRSYVSRIEKKALNKL 225


>gi|315648111|ref|ZP_07901212.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Paenibacillus vortex
           V453]
 gi|315276757|gb|EFU40100.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Paenibacillus vortex
           V453]
          Length = 262

 Score =  132 bits (332), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 51/259 (19%), Positives = 109/259 (42%), Gaps = 16/259 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
            L   ++E GD  A  +L+  HL +V  ++          +   ++ S G +GL+ A++K
Sbjct: 13  ELWSAWKEDGDHEAKKKLIEYHLHIVDYVSSRLAIGLPKNVSKGDLASNGVMGLIDAIEK 72

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD +RG +  TY+ W ++ A+ + + R    V        K       R++   Q +   
Sbjct: 73  FDYKRGLQFETYASWRVRGAILDSL-RQGDWVPRSVREKAK-------RIETAYQQLEQK 124

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
            L+      ++  L+V+E E   M   +A     +      ++ S      LV +     
Sbjct: 125 YLRSVSDSEMSDYLDVTEKEFRHMLQEVAVMTLTSLEDPIREEESETRMSLLVDEKAKNP 184

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
              + +      R  L + +  L P+ER +      ++  ++L  ++    +S  R+ Q+
Sbjct: 185 DHKVHEFYL---REALMKGIGKLTPKERTVVSLLYYED--LSLSEIAEVMSLSPSRISQL 239

Query: 273 EARAFKKVQESIQKQVELS 291
            ++A  +++ ++ K  +L 
Sbjct: 240 HSKAILRLRGALDKDRDLL 258


>gi|332799375|ref|YP_004460874.1| RNA polymerase sigma-28 subunit SigK [Tepidanaerobacter sp. Re1]
 gi|332697110|gb|AEE91567.1| RNA polymerase, sigma 28 subunit, SigK [Tepidanaerobacter sp. Re1]
          Length = 240

 Score =  132 bits (332), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 55/260 (21%), Positives = 94/260 (36%), Gaps = 64/260 (24%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L  +EE      Y + GD  A + L+  +LRLV  I   +   G  + +++S G IGL+
Sbjct: 35  PLTPEEEKKYILLYSK-GDEEARNILIEHNLRLVAHIVKKFASTGEDMDDLISIGTIGLI 93

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +A+  F+  +G RLATY+   I+  +                        NLR  K    
Sbjct: 94  KAISTFNYSKGSRLATYAARCIENEI----------------------LMNLRSTKK--- 128

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS-DKNSSQWQDWLVY 206
                                           +  +  L   I    + N     D L  
Sbjct: 129 --------------------------------IKSEVYLQEPIGVDKEGNEISLIDVLGT 156

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEV 264
           + D     + +K + +     ++ S+     +ER++ E R    N    T   ++    +
Sbjct: 157 EVDAVTDEITKKFQNEKLYEKISTSLKS---QERKVIELRYGLFNGVTKTQREIAKILGI 213

Query: 265 SRERVRQIEARAFKKVQESI 284
           SR  V +IE RA KK+ + +
Sbjct: 214 SRSYVSRIEKRAIKKLSKEL 233


>gi|229917800|ref|YP_002886446.1| RNA polymerase sigma factor SigB [Exiguobacterium sp. AT1b]
 gi|229469229|gb|ACQ71001.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Exiguobacterium sp. AT1b]
          Length = 266

 Score =  132 bits (332), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 54/263 (20%), Positives = 115/263 (43%), Gaps = 25/263 (9%)

Query: 30  EKQEEYVLAKRYREH-GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
              E     +RY++   +      L+  +  LV  +A  +        ++V  G IGL+ 
Sbjct: 11  SDDEVLEWIERYQQDDQNEEVQMLLINRYSDLVEALARKFSRGRAIHDDLVQVGMIGLLA 70

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A+++FDPE G    ++++  I   ++ +I      V +     +        ++K  ++ 
Sbjct: 71  ALRRFDPEFGRSFESFAVPTIIGEIKRFIRDKTWSVHVPRRIKELG-----PKIKKTVEE 125

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQD 202
           +T    +  ++  IA  L VS+ E++           L+ D S+ A    ++ ++    D
Sbjct: 126 LTTELQRSPRIDEIADHLGVSDEEILETLEMGKSYQALSVDSSIEA---DNEGSTVTLLD 182

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
            +     G E V        ++R +L ++ +VLN RER I E    +   ++ +      
Sbjct: 183 LVGSQERGYESV--------DQRLILEKAFNVLNERERAILECAYYKN--MSQKETGELL 232

Query: 263 EVSRERVRQIEARAFKKVQESIQ 285
            +S+  V +++ RA +K++E+I+
Sbjct: 233 GISQMHVSRLQRRALEKLREAIK 255


>gi|332976341|gb|EGK13197.1| DNA-directed RNA polymerase sigma subunit SigE [Desmospora sp.
           8437]
          Length = 240

 Score =  132 bits (332), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 63/264 (23%), Positives = 111/264 (42%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L ++EE  L  R    GD +    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 38  PPLTREEEEHLLIRL-PSGDAAVRAMLIERNLRLVVYIARKFENTGINIEDLVSIGTIGL 96

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FDP +  +LATY+   I+  +  ++ R+                    +++   
Sbjct: 97  IKAVNTFDPSKKIKLATYASRCIENEILMFLRRN-------------------NKIRSE- 136

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                            ++ DE LN      D N     D +  
Sbjct: 137 ---------------------------------VSFDEPLN---MDWDGNELLLSDVMGT 160

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           D+D   + + E+ +RK    +L  ++S L+ RER+I E R         T ++++    +
Sbjct: 161 DNDTIYRNIEEQVDRK----ILRTALSRLSERERKIMELRFGLNGGEEKTQKDVADLLGI 216

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++   K V
Sbjct: 217 SQSYISRLEKRIIKRLRKEFNKMV 240


>gi|326791514|ref|YP_004309335.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           lentocellum DSM 5427]
 gi|326542278|gb|ADZ84137.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           lentocellum DSM 5427]
          Length = 249

 Score =  132 bits (332), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 54/260 (20%), Positives = 103/260 (39%), Gaps = 22/260 (8%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGL 86
           EK++   +   Y    D +    L+  ++ LV  +A     Y    +   ++V  G +GL
Sbjct: 2   EKKDMNAVWAEYVGTRDTALKSSLIEHYVYLVKLVAGRLGIYLNQYVDSDDLVGYGVLGL 61

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           + AV KFDP +  +  TY+   I+ A+ + I R    V       QK        +    
Sbjct: 62  IDAVDKFDPGKNVKFETYASLRIRGAILDAI-RKLDWVPRTLRKKQKD-------IDKAY 113

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
             +     +      +A  L +S  E   +      + ++++LI+       ++      
Sbjct: 114 IELEGRLGRQPLDEEVADFLEISIEEYNELLK----EVNISSLISID-----EYMYQFES 164

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
             D    +     E    + ML   +  L  RE+++      +E  +TL+ +S   EVS 
Sbjct: 165 VKDPSAPIPENYIEDTEVKEMLAEFIDSLPEREKKVIFLYYYEE--LTLKEISHVLEVSE 222

Query: 267 ERVRQIEARAFKKVQESIQK 286
            RV Q+  +A  +++  +QK
Sbjct: 223 SRVSQLHTKAVSRLRAYMQK 242


>gi|164686436|ref|ZP_02210464.1| hypothetical protein CLOBAR_00001 [Clostridium bartlettii DSM
           16795]
 gi|164604447|gb|EDQ97912.1| hypothetical protein CLOBAR_00001 [Clostridium bartlettii DSM
           16795]
          Length = 256

 Score =  132 bits (332), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 55/257 (21%), Positives = 114/257 (44%), Gaps = 17/257 (6%)

Query: 33  EEYVLAKRYREHG-DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           E   L   Y     +      L+  +L LV  +A  Y   G+   ++   G++ L+ A++
Sbjct: 14  ETKELFNIYSNDKSNKEVRDILIERNLYLVSILAKKYINKGVEFEDLYQVGSLALIYAIE 73

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           ++D  +G+  ++++   I   +++Y       +++     +  L   +   K  L+    
Sbjct: 74  RYDISKGYEFSSFATPTIIGEIKKYFRDKVWTMRVPRRVQE--LNKKVNEAKLLLEQ--- 128

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHD 209
            N K  +V  IA+ +   E EV+       G    SL++ +NS   +S + +  L+    
Sbjct: 129 QNKKKPKVNEIAEYIGCREEEVLEALEASYGYQPVSLDSPVNS---DSEEAEISLIDKIG 185

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
            QE    + E     ++ + +  S LN  ER IFE R  +E   T   L+ E ++S+  +
Sbjct: 186 SQENNFSDIE----YKDFIEKFTSKLNELERNIFEGRFFKE--KTQSALAKELDISQMTI 239

Query: 270 RQIEARAFKKVQESIQK 286
            +IE +  +K+++  ++
Sbjct: 240 SRIERKVVQKLRKEYER 256


>gi|164688589|ref|ZP_02212617.1| hypothetical protein CLOBAR_02234 [Clostridium bartlettii DSM
           16795]
 gi|164603002|gb|EDQ96467.1| hypothetical protein CLOBAR_02234 [Clostridium bartlettii DSM
           16795]
          Length = 234

 Score =  132 bits (332), Expect = 7e-29,   Method: Composition-based stats.
 Identities = 55/260 (21%), Positives = 99/260 (38%), Gaps = 63/260 (24%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L  +EE       +   +  A   LV  ++RLV  I+  Y   G  + +++S G IGL+
Sbjct: 10  PLTPEEEVYYLNLLKNENNKEAKEVLVQRNMRLVAHISKKYNNSGEELDDLISIGTIGLI 69

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +A+  F+ ++G RLATY+   I+  +   I  +                           
Sbjct: 70  KAIDTFNVDKGIRLATYASKCIENEILMNIRSNKK------------------------- 104

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                            K+ VS  + I ++                + N+    D L  D
Sbjct: 105 ----------------NKMQVSLQDPIGVDK---------------EGNAISLIDILGTD 133

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMS-VLNPRERRIFEARRLQ--ENPVTLENLSSEFEV 264
            D     +++K E K + + L   +  VL  RE+ I + R         T   ++ + ++
Sbjct: 134 ED----YIVDKVELKMKISKLYEKIEKVLTEREKEIIKLRYGLTPSGYKTQREIAQQLDI 189

Query: 265 SRERVRQIEARAFKKVQESI 284
           SR  V +IE +A KK++  +
Sbjct: 190 SRSYVSRIEKKALKKLKREL 209


>gi|261407955|ref|YP_003244196.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Paenibacillus sp.
           Y412MC10]
 gi|329929288|ref|ZP_08283041.1| RNA polymerase sigma factor, FliA/WhiG family [Paenibacillus sp.
           HGF5]
 gi|261284418|gb|ACX66389.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Paenibacillus sp.
           Y412MC10]
 gi|328936657|gb|EGG33100.1| RNA polymerase sigma factor, FliA/WhiG family [Paenibacillus sp.
           HGF5]
          Length = 262

 Score =  132 bits (332), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 50/259 (19%), Positives = 109/259 (42%), Gaps = 16/259 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
            L   ++E GD  A  +L+  HL +V  ++          +   ++ S G +GL+ A++K
Sbjct: 13  DLWSAWKEDGDHEAKKKLIEYHLHIVDYVSSRLAIGLPKNVSKGDLASNGVMGLIDAIEK 72

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD +RG +  TY+ W ++ A+ + + R    V        K       +++   Q +   
Sbjct: 73  FDYKRGLQFETYASWRVRGAILDSL-RQGDWVPRSVREKAK-------KIETAYQQLEQK 124

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
            L+      ++  L+V+E E   M   +A     +      ++ S      LV +     
Sbjct: 125 YLRSVSDSEMSDYLDVTEKEFRHMLQEVAVMTLTSLEDPIREEESETRMSLLVDEKAKNP 184

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
              + +      R  L + +  L P+ER +      ++  ++L  ++    +S  R+ Q+
Sbjct: 185 DHKVHEFYL---REALMKGIGKLTPKERTVVSLLYYED--LSLSEIAEVMSLSPSRISQL 239

Query: 273 EARAFKKVQESIQKQVELS 291
            ++A  +++ ++ K  +L 
Sbjct: 240 HSKAILRLRGALDKDRDLL 258


>gi|242241477|ref|ZP_04795922.1| DNA-directed RNA polymerase sigma subunit FliA [Staphylococcus
           epidermidis W23144]
 gi|242235020|gb|EES37331.1| DNA-directed RNA polymerase sigma subunit FliA [Staphylococcus
           epidermidis W23144]
          Length = 256

 Score =  132 bits (332), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 50/263 (19%), Positives = 111/263 (42%), Gaps = 24/263 (9%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             ++     K+++E+ D  A  +LV  + +L+  +A  Y        ++V  G +GL+ A
Sbjct: 12  SPEQINQWIKQHQENEDSLAQDKLVKHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGA 71

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +FD     +   + +  +   ++ Y+      V +     +        R+K     +
Sbjct: 72  INRFDLSFDRKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIG-----PRIKKVSDEL 126

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNC------RLAGDESLNALINSSDKNSSQWQDW 203
           T+   +   +  IA++L VS+ EV+           L+ D S+ A     D ++    D 
Sbjct: 127 TNELERSPSISEIAQRLEVSDEEVLEAMEMGQSYNALSVDHSIEA---DKDGSTVTLLDI 183

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    D          +   +R +L R + +L+ RER+I +   +    ++ +       
Sbjct: 184 MGQQDDNY--------DLTEKRMILERILPILSERERQIIQCTFI--EGLSQKETGERIG 233

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+  V +++  A KK+QE+ ++
Sbjct: 234 LSQMHVSRLQRTAVKKLQEAARQ 256


>gi|118464372|ref|YP_883398.1| RNA polymerase sigma factor SigF [Mycobacterium avium 104]
 gi|118165659|gb|ABK66556.1| RNA polymerase sigma-F factor [Mycobacterium avium 104]
          Length = 241

 Score =  132 bits (332), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 46/236 (19%), Positives = 95/236 (40%), Gaps = 13/236 (5%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             ++V   L L   IA  + G G P  ++V    +GL+ AV +FD + G    ++++  I
Sbjct: 19  RDKIVERCLPLADHIARRFEGRGEPRDDLVQVARVGLVNAVVRFDVDAGSDFVSFAVPTI 78

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   VK+     +  L     RL      ++    +      +A +L + 
Sbjct: 79  MGEVRRHFRDNSWSVKVPRRLKELHL-----RLGTATADLSQRLGRAHTATELAAELEMD 133

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             EV+     L    S N L   S   S + +   + D  G     +++ E +     L 
Sbjct: 134 REEVVE---GLVAGSSYNTLSIDSGGGSEEEEVRAIADTLGDVDTGLDRIEDQ---ESLR 187

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             +  L  RER +   R      +T   ++    +S+  V ++ A++  ++++ +Q
Sbjct: 188 PLLEALPERERTVLVLRFF--ESMTQTQIAERVGISQMHVSRLLAKSLTRLRDQLQ 241


>gi|325846834|ref|ZP_08169712.1| putative RNA polymerase sigma-B factor [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
 gi|325481206|gb|EGC84249.1| putative RNA polymerase sigma-B factor [Anaerococcus hydrogenalis
           ACS-025-V-Sch4]
          Length = 256

 Score =  132 bits (332), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 40/257 (15%), Positives = 109/257 (42%), Gaps = 16/257 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K  +  K+E     +++ +  D    + L+  H+ +V  ++  Y G G+   ++    ++
Sbjct: 5   KASLERKKEIKEKFEQFYKTRDKDLRNELIEDHMYIVDILSNKYVGKGIEKDDLYQVASL 64

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL+ A+ ++DP +G+  ++++   I   ++ Y      ++++      +R+    +++  
Sbjct: 65  GLIYAIDRYDPSKGYEFSSFATPTIMGELKRYFRDKGWVIRVP-----RRIQNLYKKINV 119

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQD 202
             + +     +   +  IA  L   E  ++      ++   +SL+         +S    
Sbjct: 120 AKKILPQELQRTPTIKDIAAYLGEDEETILETMEASKVYTPQSLDMKYQVQKGENSVDLS 179

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
            ++ + D     +         ++++ +S   LN  E++I E R       T  +++ + 
Sbjct: 180 DMIGEDDKNFDSI-------ELKDLIEKSTERLNDLEKQILELRYY--EGRTQVDIAKKL 230

Query: 263 EVSRERVRQIEARAFKK 279
            +S+  V +IE +  +K
Sbjct: 231 SISQMTVSRIEKKILQK 247


>gi|291454422|ref|ZP_06593812.1| RNA polymerase sigma factor WhiG [Streptomyces albus J1074]
 gi|291357371|gb|EFE84273.1| RNA polymerase sigma factor WhiG [Streptomyces albus J1074]
          Length = 279

 Score =  132 bits (332), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 54/256 (21%), Positives = 107/256 (41%), Gaps = 15/256 (5%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
            L   Y+  GD     +L+  +  LV  +A          +  ++ VS G  GL+ A++K
Sbjct: 31  ELWSSYKATGDARLREQLILHYSPLVKYVAGRVSVGLPPNVEQADFVSSGIFGLIDAIEK 90

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FDPER  +  TY++  I+ AM + +    +L  I  +  QK    N+ R    L+A    
Sbjct: 91  FDPERSIKFETYAITRIRGAMIDELR---ALDWIPRSVRQKA--RNVERAYASLEAELHR 145

Query: 153 NLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
                    +A ++ ++  ++ ++     LA   +L  L++   +        +    D 
Sbjct: 146 ---TPTEAEVAAEMGIAVEDLHAVFSQLSLANVVALEELLHGGGEGGGDRLSIMDTLEDT 202

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                +E  E +  R +L R++++L  RE+ +          +TL  +     V+  RV 
Sbjct: 203 SADNPVELAEDRELRRLLARAINLLPEREKTVVTLYYY--EGLTLAEIGHVLGVTESRVS 260

Query: 271 QIEARAFKKVQESIQK 286
           QI  ++  +++  +  
Sbjct: 261 QIHTKSVLQLRAKLSS 276


>gi|134300227|ref|YP_001113723.1| FliA/WhiG family RNA polymerase sigma factor [Desulfotomaculum
           reducens MI-1]
 gi|134052927|gb|ABO50898.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Desulfotomaculum
           reducens MI-1]
          Length = 251

 Score =  132 bits (332), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 56/257 (21%), Positives = 105/257 (40%), Gaps = 18/257 (7%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKKF 93
           L ++Y    D  A  +++  HL LV  +A              ++ S G IGLM+A+ K+
Sbjct: 6   LWEKYITLRDPEARQKIILLHLPLVKHLAGRVAVKLPSFILREDLESYGVIGLMEALDKY 65

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           DP  G    +Y+   I+ AM + + R   L +     NQ         LK   + +    
Sbjct: 66  DPAMGHSFDSYAYHRIRGAMLDEVRRQNWLPRTAWQKNQL--------LKNTRERLEREQ 117

Query: 154 LKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
            +      +AK++ +   EV  +  N      +SL+  +   D         L    D  
Sbjct: 118 GEVITNEVLAKEMGIPVEEVRQLIFNANKMYIQSLDEEVAGHDG---SQMSKLELLEDTN 174

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
               +   E K  + +L  ++  L+ RE+ I          +TL+ +    EVS  RV Q
Sbjct: 175 SPDPLSIVEEKESKRLLAEAIETLSEREKLILALYY--SEGLTLKEIGQVLEVSESRVCQ 232

Query: 272 IEARAFKKVQESIQKQV 288
           + ++  K+++++++  +
Sbjct: 233 LHSQVMKRLKKTLESML 249


>gi|288553151|ref|YP_003425086.1| sporulation sigma factor SigE [Bacillus pseudofirmus OF4]
 gi|288544311|gb|ADC48194.1| sporulation sigma factor SigE [Bacillus pseudofirmus OF4]
          Length = 237

 Score =  132 bits (332), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 67/264 (25%), Positives = 108/264 (40%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE VL K+    GD +    L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 35  PPLSKEEEAVLLKKL-PTGDKAVRSMLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 93

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I                      +  +   LRR     
Sbjct: 94  IKAVNTFNPEKKIKLATYASRCI----------------------ENEILMYLRRNNKTR 131

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                            ++ DE LN      D N     D L  
Sbjct: 132 SE-------------------------------VSFDEPLN---IDWDGNELLLSDVLGT 157

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           + D    ++    E K  R +L +++  LN RE++I E R     E   T ++++    +
Sbjct: 158 EED----IITRGIEEKVDRKLLVKALHTLNEREKQIMELRFGLAGEEEKTQKDVADMLGI 213

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++Q+   K V
Sbjct: 214 SQSYISRLEKRIIKRLQKEFNKMV 237


>gi|302538372|ref|ZP_07290714.1| RNA polymerase sigma-E factor [Streptomyces sp. C]
 gi|302447267|gb|EFL19083.1| RNA polymerase sigma-E factor [Streptomyces sp. C]
          Length = 323

 Score =  132 bits (332), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 48/256 (18%), Positives = 104/256 (40%), Gaps = 14/256 (5%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGL----PISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
            + L+  +  LV      +RG        + ++V  G IGL++A+ +FDP R    AT +
Sbjct: 78  RNTLIEMNASLVQYAVRRFRGRAEGAAGDVDDLVQVGTIGLIKAIDRFDPARENEFATLA 137

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
           M +I   ++ +   +   V +     + R+      +    + +T    +   V  +A  
Sbjct: 138 MPYITGEIKRHFRDTAWAVHVPRRLQELRID-----IAKAKEELTIRLDRSPTVRDLAAY 192

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           L+++E +VI       G  S +     ++      +   + +  G+E+  +E  E     
Sbjct: 193 LDLTEEQVIEGLVAANGHTSGSLDAPHAEHGDGPAEGHTLAEVLGEEEPALELVEDIQT- 251

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             L   +  L+ RER +   R  +E  +T   + +   +S+ +V ++ +R    ++ S+ 
Sbjct: 252 --LAPLLERLSERERTMLRMRFGEE--LTQAQMGAALGISQMQVSRLLSRLLAHLRTSML 307

Query: 286 KQVELSSSPPLLQKPR 301
              +    P   +  R
Sbjct: 308 SDPDPHPEPGPGRPGR 323


>gi|134298554|ref|YP_001112050.1| sporulation sigma factor SigE [Desulfotomaculum reducens MI-1]
 gi|134051254|gb|ABO49225.1| RNA polymerase, sigma 29 subunit, SigE [Desulfotomaculum reducens
           MI-1]
          Length = 241

 Score =  132 bits (332), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 66/262 (25%), Positives = 112/262 (42%), Gaps = 63/262 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EE  L +R  + GDL   + L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 39  PPLSIDEEIDLIERLGD-GDLKVKNVLIERNLRLVVYIARKFENTGIGIEDLVSIGTIGL 97

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FDP +  +LATY+   I+  +  ++ R+                          
Sbjct: 98  IKAVNTFDPHKKIKLATYASRCIENEILMHLRRN-------------------------- 131

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                               N + SEV       + DE LN      D N     D L  
Sbjct: 132 --------------------NKTRSEV-------SFDEPLN---IDWDGNELLLSDVLGT 161

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEV 264
           ++D    ++ +  E +  + +L +++  L+ RERRI E R    N    T + ++    +
Sbjct: 162 END----IIYKNIEEEVDKKLLHQALLKLSGRERRIMELRFGLNNGSEKTQKEVADMLGI 217

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+  + ++E R  K++++ I +
Sbjct: 218 SQSYISRLEKRIIKRLKKEIHR 239


>gi|289422547|ref|ZP_06424390.1| RNA polymerase sigma-B factor [Peptostreptococcus anaerobius 653-L]
 gi|289157119|gb|EFD05741.1| RNA polymerase sigma-B factor [Peptostreptococcus anaerobius 653-L]
          Length = 257

 Score =  132 bits (332), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 49/249 (19%), Positives = 107/249 (42%), Gaps = 13/249 (5%)

Query: 35  YVLAKRYREHGDLSA-AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
             L K + E  D  A  + L+  HL L   ++  Y   G+   ++    ++ L+ A+ ++
Sbjct: 15  KDLFKIFSEDKDNIAIRNILIEKHLYLAKILSRKYMNKGVDYEDIFQVASLALIFAIDRY 74

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D  +GF  ++++   I   +++Y       +++     +  L   +   K  L+     +
Sbjct: 75  DVSKGFEFSSFATPTIVGEIKKYFRDKVWTLRVPRRIQE--LSKKISNTKTLLEQELKRS 132

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            KP   + IA+ L V   +V+       G + ++    S++ N  + +D  + D  G E+
Sbjct: 133 PKP---IEIAEYLEVDLEDVLEAMEASYGYQPMSLDTPSNEDN--EDKDITLGDKIGFEE 187

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
               + E  +    L + M  LN  E  I + R  +    T   ++ E  +S+  V ++E
Sbjct: 188 KNFSQIEDMDF---LDKFMETLNELEVSIVKGRFFEN--KTQSVIAGELGISQMTVSRLE 242

Query: 274 ARAFKKVQE 282
            +  +K+++
Sbjct: 243 KKIVEKLKK 251


>gi|253578603|ref|ZP_04855875.1| sporulation sigma factor SigE [Ruminococcus sp. 5_1_39B_FAA]
 gi|251850921|gb|EES78879.1| sporulation sigma factor SigE [Ruminococcus sp. 5_1_39BFAA]
          Length = 238

 Score =  132 bits (332), Expect = 8e-29,   Method: Composition-based stats.
 Identities = 59/290 (20%), Positives = 111/290 (38%), Gaps = 73/290 (25%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           MNR      + G   L            LE + E  + ++     +  A   L+  +LRL
Sbjct: 16  MNRSGEVFYIGGNDVLPA---------PLEPKREAFILQKLGTGQEEEAKSVLIEHNLRL 66

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           VV IA  +   G+ + +++S G IGL++A+  F+P +  +LATY+   I+  +  Y+ R+
Sbjct: 67  VVYIAKKFDNTGVGVEDLISIGTIGLIKAINTFNPVKNIKLATYASRCIENEILMYLRRN 126

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
                                                       K+ VS  E ++++   
Sbjct: 127 SKT-----------------------------------------KMEVSIDEPLNVD--- 142

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
                        D N     D L  D D   + L ++ E      +L++++  L+PRE+
Sbjct: 143 ------------WDGNELLLSDILGTDEDVISRRLEDEVEIS----LLSKAIRKLSPREQ 186

Query: 241 RIFEARRLQEN----PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            I   R           T + ++    +S+  + ++E R  K++++ I K
Sbjct: 187 TIIRLRFGLGKENAAEKTQKEVADLLGISQSYISRLEKRIMKRLKKEIVK 236


>gi|284044899|ref|YP_003395239.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
 gi|283949120|gb|ADB51864.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
          Length = 273

 Score =  131 bits (331), Expect = 9e-29,   Method: Composition-based stats.
 Identities = 55/238 (23%), Positives = 98/238 (41%), Gaps = 17/238 (7%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             L +RY   GD  A   L+T  L L  ++A+ Y     P+ ++V   ++GL++AV +F+
Sbjct: 33  RRLLERYHLRGDERAREELITRFLPLARQLALRYYHGREPLDDLVQVASVGLVKAVDRFE 92

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             R    A+Y++  +   ++ Y   +   + +     ++ L  +  R    LQ       
Sbjct: 93  VRRTTAFASYAVPVMLGELRRYFRDNGWALHVPRGLQERALAVD--RTADRLQVAQGAAP 150

Query: 155 KPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
            P Q   IA++L ++  EV+      R     SL+A   S+D       D L  D     
Sbjct: 151 TPAQ---IAEQLKLTVEEVVEAMAAARATDTVSLDAPRPSADGERDALVDSLGADDS--- 204

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                + E    R  +  ++  L  RER I   R   E   T   +++   VS+ ++ 
Sbjct: 205 -----RLELVEYREAIAGALDALPVREREILRLRF--EEDRTQSEIAARLGVSQMQIS 255


>gi|212697380|ref|ZP_03305508.1| hypothetical protein ANHYDRO_01950 [Anaerococcus hydrogenalis DSM
           7454]
 gi|212675572|gb|EEB35179.1| hypothetical protein ANHYDRO_01950 [Anaerococcus hydrogenalis DSM
           7454]
          Length = 256

 Score =  131 bits (331), Expect = 9e-29,   Method: Composition-based stats.
 Identities = 40/257 (15%), Positives = 109/257 (42%), Gaps = 16/257 (6%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K  +  K+E     +++ +  D    + L+  H+ +V  ++  Y G G+   ++    ++
Sbjct: 5   KASLERKKEIKEKFEQFYKTRDKDLRNELIEDHMYIVDILSNKYVGKGIEKDDLYQVASL 64

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL+ A+ ++DP +G+  ++++   I   ++ Y      ++++      +R+    +++  
Sbjct: 65  GLIYAIDRYDPSKGYEFSSFATPTIMGELKRYFRDKGWVIRVP-----RRIQNLYKKINV 119

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQD 202
             + +     +   +  IA  L   E  ++      ++   +SL+         +S    
Sbjct: 120 AKKILPQELQRTPTIKDIAAYLGEDEETILETMEASKVYTPQSLDMKYQVQKGENSVDLS 179

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
            ++ + D     +         ++++ +S   LN  E++I E R       T  +++ + 
Sbjct: 180 DMIGEDDKNFDSI-------ELKDLIEKSTERLNDLEKQILELRYY--EGRTQVDIAQKL 230

Query: 263 EVSRERVRQIEARAFKK 279
            +S+  V +IE +  +K
Sbjct: 231 SISQMTVSRIEKKILQK 247


>gi|147678403|ref|YP_001212618.1| DNA-directed RNA polymerase specialized sigma subunit
           [Pelotomaculum thermopropionicum SI]
 gi|146274500|dbj|BAF60249.1| DNA-directed RNA polymerase specialized sigma subunit
           [Pelotomaculum thermopropionicum SI]
          Length = 256

 Score =  131 bits (331), Expect = 9e-29,   Method: Composition-based stats.
 Identities = 61/260 (23%), Positives = 116/260 (44%), Gaps = 14/260 (5%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKK 92
            L + YR   D    H +V S+L LV  +A          +   ++ S G +GL++AV+K
Sbjct: 6   ELWREYRRSRDEKLKHEIVMSYLPLVKYLAGRLAVKLPACIGQEDLESFGILGLLEAVEK 65

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           ++P+ G     Y+   I+ A+ +   +   L  I  T  QK    +L   +  LQ     
Sbjct: 66  YNPDYGVSFKAYAYNRIRGAIIDEFRK---LNWIPRTMWQK--IQSLNNTRERLQGEAGE 120

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
            +  E  +A A  +++ E   ++ +       SL+  +  +D    +W D +        
Sbjct: 121 TVTSET-LAGAMGISLPELHKLAWHASRLSLSSLDETVALADGELVRWGDMIQDPESPDP 179

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
             +IEKEE    R +L +++  L  ++R +       +  +TL+ + +  EVS  RV Q+
Sbjct: 180 LDIIEKEE---GRRLLVQAIEELPEKDRLVLSLYY--QEGLTLKEIGAVMEVSESRVCQL 234

Query: 273 EARAFKKVQESIQKQVELSS 292
             RA  ++++ +++   LS 
Sbjct: 235 HTRAINRLRKKLEQASGLSR 254


>gi|331090017|ref|ZP_08338907.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium 3_1_46FAA]
 gi|330402931|gb|EGG82497.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium 3_1_46FAA]
          Length = 245

 Score =  131 bits (331), Expect = 9e-29,   Method: Composition-based stats.
 Identities = 56/262 (21%), Positives = 104/262 (39%), Gaps = 64/262 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE   E  +  R        A   L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 40  PPLEGMRESEMINRLGTEYAEDAKKVLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGL 99

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+  F+P +  +LATY+   I+  +  Y+ R+                          
Sbjct: 100 IKAINTFNPTKKIKLATYASRCIENEILMYLRRNSKT----------------------- 136

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                             K+ VS  E ++++                D N     D L  
Sbjct: 137 ------------------KMEVSIDEPLNVD---------------WDGNELLLSDILGT 163

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP----VTLENLSSEF 262
           + D   + L  + ERK    +L R+++ LN RE+ I   R   +NP     T + ++   
Sbjct: 164 EEDTIYKDLENEAERK----LLIRALNKLNSREKLIVSMRFGLDNPDGKEKTQKEVADLL 219

Query: 263 EVSRERVRQIEARAFKKVQESI 284
            +S+  + ++E +  ++++  +
Sbjct: 220 GISQSYISRLEKKIMQRLKREM 241


>gi|257065529|ref|YP_003151785.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Anaerococcus
           prevotii DSM 20548]
 gi|256797409|gb|ACV28064.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Anaerococcus
           prevotii DSM 20548]
          Length = 255

 Score =  131 bits (331), Expect = 9e-29,   Method: Composition-based stats.
 Identities = 39/244 (15%), Positives = 104/244 (42%), Gaps = 16/244 (6%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
            + Y +  DL     L+  H+ +V  ++  Y G G+   ++    ++GL+ AV+++DP +
Sbjct: 17  FEEYYQTRDLKLRDELIKEHMYIVDILSNKYVGKGIEKDDLYQVASLGLIYAVERYDPTK 76

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G+  ++++   I   ++ Y      ++++      +R+    +++    + +     +  
Sbjct: 77  GYAFSSFATPTIMGELKRYFRDKGWVIRVP-----RRIQNLYKKINTAKKILPQELQRTP 131

Query: 158 QVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
            +  IA  L   E  ++      ++   +SL+         ++     ++ + D     +
Sbjct: 132 TIADIADYLGEDEETILETMEASKVYTPQSLDMKYQVQKGENAIDLSDMIGEEDKNFDSI 191

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
                    ++++ +S   LN  E+ I E R       T  ++++  ++S+  V +IE +
Sbjct: 192 -------ELKDLIDKSKERLNDLEKEILELRYY--EGRTQVDIANTLDISQMTVSRIEKK 242

Query: 276 AFKK 279
             +K
Sbjct: 243 ILQK 246


>gi|57996876|emb|CAI45886.1| negative response regulator [Escherichia coli]
          Length = 191

 Score =  131 bits (331), Expect = 9e-29,   Method: Composition-based stats.
 Identities = 54/201 (26%), Positives = 93/201 (46%), Gaps = 12/201 (5%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL +  ++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLNLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           +     +++      K L   LR  +     ++           IA++L+    +V  M 
Sbjct: 61  MNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRML 115

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                  S++  +    +     +  L    D +E    +  +  + +  + + +  LN 
Sbjct: 116 RLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNA 170

Query: 238 RERRIFEARR--LQENPVTLE 256
           ++R +   R   L     TLE
Sbjct: 171 KQREVLARRFGLLGYEAATLE 191


>gi|297544535|ref|YP_003676837.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
 gi|296842310|gb|ADH60826.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
          Length = 231

 Score =  131 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 57/265 (21%), Positives = 94/265 (35%), Gaps = 63/265 (23%)

Query: 19  YIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           Y+      P  L  +EE    + Y+ +GD  A + L+  +LRLV  +   Y G G  I +
Sbjct: 21  YLTNTNSFPNPLTPEEEKKYLEAYK-NGDEEARNILIERNLRLVAHVVKKYSGTGKDIDD 79

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++S G IGL++A+  FD  +G  LATY+   I+  +   I                    
Sbjct: 80  LISIGTIGLIKAISTFDSSKGTHLATYAARCIENEILMSIR------------------- 120

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
                                      K  V   + I ++                + N 
Sbjct: 121 ----------------------AEKKMKGEVFLQDPIGVDK---------------EGNE 143

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTL 255
               D L  + +   + + +K + K   N +   +     RE+ I E R    N    T 
Sbjct: 144 ISLMDVLGTEENEISEQVEKKIQIKKLYNKMNNVLKN---REKLIIEMRYGLYNGKVRTQ 200

Query: 256 ENLSSEFEVSRERVRQIEARAFKKV 280
             ++    +SR  V +IE RA  K+
Sbjct: 201 REIAKMLGISRSYVSRIEKRALNKL 225


>gi|239926901|ref|ZP_04683854.1| RNA polymerase sigma factor sig8 [Streptomyces ghanaensis ATCC
           14672]
 gi|291435248|ref|ZP_06574638.1| HasL [Streptomyces ghanaensis ATCC 14672]
 gi|291338143|gb|EFE65099.1| HasL [Streptomyces ghanaensis ATCC 14672]
          Length = 281

 Score =  131 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 49/239 (20%), Positives = 104/239 (43%), Gaps = 18/239 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + L+  ++ LV   A  +R  G   + ++V  G IGL++A+ +F+  R     ++++ 
Sbjct: 54  ARNTLIEMNMSLVRFAAGRFRSRGPEEMEDIVQVGMIGLIKAIDRFELSREVEFTSFAIP 113

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +I   M+ +   +   V +     + R+     +L    + +     +      +A+ ++
Sbjct: 114 YIVGEMKRFFRDTSWSVHVPRRLQEARV-----QLARATEELRTRLGRTPTTRELAQLMS 168

Query: 168 VSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           ++E EV        G    SL+A I S     S   D++     G E   +E  E  +  
Sbjct: 169 LTEEEVNEARIAANGYNSASLDAAIGSEPDGESVLADFI-----GSEDAALELVEDFH-- 221

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             L   ++ L+ RER+I   R ++E  +T   +      S+  V ++ +R  K+++  +
Sbjct: 222 -ALAPMIAELDERERKIIHWRFVEE--LTQAEIGERLGCSQMHVSRLISRILKRLRAGL 277


>gi|187778769|ref|ZP_02995242.1| hypothetical protein CLOSPO_02364 [Clostridium sporogenes ATCC
           15579]
 gi|187772394|gb|EDU36196.1| hypothetical protein CLOSPO_02364 [Clostridium sporogenes ATCC
           15579]
          Length = 242

 Score =  131 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 57/242 (23%), Positives = 107/242 (44%), Gaps = 19/242 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              +V  ++ LV  IA      +   +   ++VS G IGLM A+ KFD  +G + +TY+ 
Sbjct: 11  KEEIVKKYIPLVKYIASRVIIGKTKYIEYEDLVSYGMIGLMDALNKFDESKGMKFSTYAS 70

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             IK +M + + R+  +         K     L R    ++ +     K   ++ IA +L
Sbjct: 71  IRIKGSMIDELRRNSPI--------SKGAMDKLNRYNEAIERLQKKLNKEPNLIQIADEL 122

Query: 167 NVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           N+S  EV  +   +      SL  LI SS+         +    D +     +  E   +
Sbjct: 123 NISLKEVSEIENYINYISVISLEDLIFSSEDEVP----LIGTIKDDKSPSPEKHVEENEQ 178

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + L +++ +LN ++R +      +E  +TL+ +     VS  RV Q+ +RA   +++++
Sbjct: 179 LDYLAKAIELLNEKDRLVVTLYYYEE--LTLKEIGKILSVSESRVCQLHSRAIIHLKKAM 236

Query: 285 QK 286
            K
Sbjct: 237 TK 238


>gi|297529299|ref|YP_003670574.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
 gi|297252551|gb|ADI25997.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
          Length = 245

 Score =  131 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 61/276 (22%), Positives = 100/276 (36%), Gaps = 67/276 (24%)

Query: 16  LSRYIHEIRKIPMLEK-QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           L  YI        L   +EE  LA      GD  A +RL+  +LRLV  I   +   G  
Sbjct: 26  LVSYIKNNAFPQPLSAQEEEKYLA--LMAKGDEQARNRLIEHNLRLVAHIVKKFENTGEE 83

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++S G IGL++A++ + P +G +LATY+   I+  +                     
Sbjct: 84  VEDLISIGTIGLIKAIESYSPGKGTKLATYAARCIENEI--------------------- 122

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS- 193
              +LR LK                                       D SL+  I    
Sbjct: 123 -LMHLRSLKKT-----------------------------------RKDVSLHEPIGQDK 146

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-- 251
           + N     D L  +     Q ++++         + + +SVL+ RE+ +   R       
Sbjct: 147 EGNEISLLDILKAEG----QDIVDEIHLNMELEQVKQYISVLDEREKEVIINRFGLGRQR 202

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             T   ++ E  +SR  V +IE RA  K+     +Q
Sbjct: 203 EKTQREIAKELGISRSYVSRIEKRALMKMFHEFYRQ 238


>gi|153812463|ref|ZP_01965131.1| hypothetical protein RUMOBE_02862 [Ruminococcus obeum ATCC 29174]
 gi|149831388|gb|EDM86476.1| hypothetical protein RUMOBE_02862 [Ruminococcus obeum ATCC 29174]
          Length = 243

 Score =  131 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 55/263 (20%), Positives = 106/263 (40%), Gaps = 64/263 (24%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            LE + E  +  R +   +  A   L+  +LRLVV IA  +   G+ + +++S G IGL+
Sbjct: 39  PLEPKREAYVISRLKTDQEQEARSLLIEHNLRLVVYIARKFDNTGVGVEDLISIGTIGLI 98

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +A+  F+P +  +LATY+   I+  +  Y+ R+                           
Sbjct: 99  KAINTFNPVKNIKLATYASRCIENEILMYLRRNSKT------------------------ 134

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                            ++ VS  E ++++                D N     D L  D
Sbjct: 135 -----------------RMEVSIDEPLNVD---------------WDGNELLLSDILGTD 162

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN----PVTLENLSSEFE 263
            D   + L ++ E      +L ++++ L+PRE+ I   R    N      T + ++    
Sbjct: 163 DDVISRKLEDEVEIT----LLGKAINKLSPREQTIIRLRFGLNNADGKEKTQKEVADLLG 218

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+  + ++E R  K++++ I K
Sbjct: 219 ISQSYISRLEKRIMKRLKKEIVK 241


>gi|333028638|ref|ZP_08456702.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
 gi|332748490|gb|EGJ78931.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
          Length = 310

 Score =  131 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 52/243 (21%), Positives = 104/243 (42%), Gaps = 15/243 (6%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+  ++ LV   A  +R  G  + +VV  G IGL++A+ +F+  R     T+++
Sbjct: 80  QDARNTLIEMNMSLVRFAARRFRSRGDDMEDVVQVGTIGLIKAIDRFELSREVEFTTFAV 139

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            +I   ++ +   +   V +     + R+      L    + ++    +  +V  +A  +
Sbjct: 140 PYIVGEIKRFFRDTTWAVHVPRRLQEARV-----ELAKANEELSTRLGRAPKVSELAALM 194

Query: 167 NVSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           ++SE +V+       G    SL+A I   D    +     + D  G E   +E  E    
Sbjct: 195 SLSEQQVVEAQIAANGYSSSSLDATIGGEDSGEGEAA---LSDFIGAEDPGMELVED--- 248

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + L   ++ L PR+R+I E R  QE  +T   +     VS+  V ++  R    ++  +
Sbjct: 249 LHALAPLLAGLEPRDRQILELRFGQE--LTQAQIGERLGVSQMHVSRLLNRTLGTLRAGL 306

Query: 285 QKQ 287
             +
Sbjct: 307 MSE 309


>gi|161898839|gb|ABX80409.1| SigB [Listeria monocytogenes]
          Length = 222

 Score =  131 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 53/240 (22%), Positives = 103/240 (42%), Gaps = 24/240 (10%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 1   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 60

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G     +++  I   ++ ++      V +     +        ++K  ++ +T    
Sbjct: 61  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVKELTRELQ 115

Query: 155 KPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +    
Sbjct: 116 SSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTD 172

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++S+  
Sbjct: 173 DGF--------ERVNQRMLLEKVLPVLDEREQKILQFTFIEN--RSQKETGELLDISQMH 222


>gi|157693076|ref|YP_001487538.1| sporulation sigma factor SigK [Bacillus pumilus SAFR-032]
 gi|157681834|gb|ABV62978.1| DNA-directed RNA polymerase sigma subunit SigK carboxy-terminus
           [Bacillus pumilus SAFR-032]
          Length = 289

 Score =  131 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 54/280 (19%), Positives = 98/280 (35%), Gaps = 65/280 (23%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
             M ++V   + L  Y+        L   +E        + GD  A + L+  +LRLV  
Sbjct: 54  TAMGLMVKELVFLVSYVKNNAFPQPLSGDDEKKYLALMAQ-GDEHARNMLIEHNLRLVAH 112

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           I   +   G    +++S G IGL++A++ +   +G +LATY+   I+  +          
Sbjct: 113 IVKKFENTGEDAEDLISIGTIGLIKAIESYSSGKGTKLATYAARCIENEI---------- 162

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
                         +LR LK                                       D
Sbjct: 163 ------------LMHLRALKKT-----------------------------------KKD 175

Query: 184 ESLNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
            SL+  I    + N     D L  ++    + +I+  +       +   + +L+ RE+ +
Sbjct: 176 VSLHDPIGQDKEGNEISLIDVLKSEN----EDVIDTIQLNMELEKVKEYIDILDGREKEV 231

Query: 243 FEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
              R   +     T   ++ E  +SR  V +IE RA  K+
Sbjct: 232 IVGRFGLDLKKEKTQREIAKELGISRSYVSRIEKRALMKM 271


>gi|188011759|gb|ACD45176.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011761|gb|ACD45177.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011765|gb|ACD45179.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011767|gb|ACD45180.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011769|gb|ACD45181.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011771|gb|ACD45182.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011773|gb|ACD45183.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011775|gb|ACD45184.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011777|gb|ACD45185.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011779|gb|ACD45186.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011781|gb|ACD45187.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011783|gb|ACD45188.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011785|gb|ACD45189.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011787|gb|ACD45190.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011789|gb|ACD45191.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011791|gb|ACD45192.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011793|gb|ACD45193.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011795|gb|ACD45194.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011797|gb|ACD45195.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011799|gb|ACD45196.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011801|gb|ACD45197.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011803|gb|ACD45198.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011805|gb|ACD45199.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011807|gb|ACD45200.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011809|gb|ACD45201.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011811|gb|ACD45202.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011813|gb|ACD45203.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011815|gb|ACD45204.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011817|gb|ACD45205.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011819|gb|ACD45206.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011821|gb|ACD45207.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011823|gb|ACD45208.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011825|gb|ACD45209.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011827|gb|ACD45210.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011829|gb|ACD45211.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011831|gb|ACD45212.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011833|gb|ACD45213.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011835|gb|ACD45214.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011837|gb|ACD45215.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011839|gb|ACD45216.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011841|gb|ACD45217.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011843|gb|ACD45218.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011845|gb|ACD45219.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011847|gb|ACD45220.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011849|gb|ACD45221.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011851|gb|ACD45222.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011853|gb|ACD45223.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011855|gb|ACD45224.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011857|gb|ACD45225.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011859|gb|ACD45226.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011861|gb|ACD45227.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011863|gb|ACD45228.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011867|gb|ACD45230.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011869|gb|ACD45231.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011875|gb|ACD45234.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011877|gb|ACD45235.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011879|gb|ACD45236.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011881|gb|ACD45237.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011883|gb|ACD45238.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011885|gb|ACD45239.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011887|gb|ACD45240.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011889|gb|ACD45241.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011891|gb|ACD45242.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011893|gb|ACD45243.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011895|gb|ACD45244.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011899|gb|ACD45246.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011903|gb|ACD45248.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011905|gb|ACD45249.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011907|gb|ACD45250.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011909|gb|ACD45251.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011911|gb|ACD45252.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011913|gb|ACD45253.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011917|gb|ACD45255.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011919|gb|ACD45256.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011921|gb|ACD45257.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011923|gb|ACD45258.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011925|gb|ACD45259.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011927|gb|ACD45260.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011929|gb|ACD45261.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011931|gb|ACD45262.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011933|gb|ACD45263.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011935|gb|ACD45264.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011937|gb|ACD45265.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011939|gb|ACD45266.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011941|gb|ACD45267.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011943|gb|ACD45268.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|281324217|gb|ADA60650.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324221|gb|ADA60652.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324239|gb|ADA60661.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324273|gb|ADA60678.1| RNA polymerase sigma factor B [Listeria monocytogenes]
          Length = 222

 Score =  131 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 53/240 (22%), Positives = 104/240 (43%), Gaps = 24/240 (10%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           ++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++
Sbjct: 1   EKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIR 60

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           ++D   G     +++  I   ++ ++      V +     +        ++K  ++ +T 
Sbjct: 61  RYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTR 115

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLV 205
                 Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D + 
Sbjct: 116 ELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVG 172

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
              DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++S
Sbjct: 173 GTDDGF--------ERVNQRMLLEKVLPVLDEREQKILQYTFIEN--RSQKETGELLDIS 222


>gi|188011585|gb|ACD45089.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011587|gb|ACD45090.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011589|gb|ACD45091.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011591|gb|ACD45092.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011593|gb|ACD45093.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011595|gb|ACD45094.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011597|gb|ACD45095.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011599|gb|ACD45096.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011601|gb|ACD45097.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011603|gb|ACD45098.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011605|gb|ACD45099.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011607|gb|ACD45100.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011609|gb|ACD45101.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011611|gb|ACD45102.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011613|gb|ACD45103.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011615|gb|ACD45104.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011617|gb|ACD45105.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011619|gb|ACD45106.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011621|gb|ACD45107.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011623|gb|ACD45108.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011625|gb|ACD45109.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011627|gb|ACD45110.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011629|gb|ACD45111.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011631|gb|ACD45112.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011633|gb|ACD45113.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011635|gb|ACD45114.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011637|gb|ACD45115.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011639|gb|ACD45116.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011641|gb|ACD45117.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011643|gb|ACD45118.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011645|gb|ACD45119.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011647|gb|ACD45120.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011649|gb|ACD45121.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011651|gb|ACD45122.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011653|gb|ACD45123.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011655|gb|ACD45124.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011657|gb|ACD45125.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011659|gb|ACD45126.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011661|gb|ACD45127.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011663|gb|ACD45128.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011665|gb|ACD45129.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011667|gb|ACD45130.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011669|gb|ACD45131.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011671|gb|ACD45132.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011673|gb|ACD45133.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011675|gb|ACD45134.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011677|gb|ACD45135.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011679|gb|ACD45136.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011681|gb|ACD45137.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011683|gb|ACD45138.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011685|gb|ACD45139.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011687|gb|ACD45140.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011689|gb|ACD45141.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011691|gb|ACD45142.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011693|gb|ACD45143.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011695|gb|ACD45144.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011697|gb|ACD45145.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011699|gb|ACD45146.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011701|gb|ACD45147.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011703|gb|ACD45148.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011705|gb|ACD45149.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011707|gb|ACD45150.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011709|gb|ACD45151.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011711|gb|ACD45152.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011713|gb|ACD45153.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011715|gb|ACD45154.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011717|gb|ACD45155.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011719|gb|ACD45156.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011721|gb|ACD45157.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011723|gb|ACD45158.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011725|gb|ACD45159.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011727|gb|ACD45160.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011729|gb|ACD45161.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011731|gb|ACD45162.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011733|gb|ACD45163.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011735|gb|ACD45164.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011737|gb|ACD45165.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011739|gb|ACD45166.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011741|gb|ACD45167.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011743|gb|ACD45168.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011745|gb|ACD45169.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011747|gb|ACD45170.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011749|gb|ACD45171.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011751|gb|ACD45172.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011753|gb|ACD45173.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011755|gb|ACD45174.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011757|gb|ACD45175.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011763|gb|ACD45178.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011865|gb|ACD45229.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011871|gb|ACD45232.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011873|gb|ACD45233.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011945|gb|ACD45269.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011947|gb|ACD45270.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011949|gb|ACD45271.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|211906951|gb|ACJ11994.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|211906953|gb|ACJ11995.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|211906955|gb|ACJ11996.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|211906957|gb|ACJ11997.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|211906959|gb|ACJ11998.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|211906961|gb|ACJ11999.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|211906963|gb|ACJ12000.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|281324219|gb|ADA60651.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324223|gb|ADA60653.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324225|gb|ADA60654.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324227|gb|ADA60655.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324229|gb|ADA60656.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324231|gb|ADA60657.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324233|gb|ADA60658.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324235|gb|ADA60659.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324237|gb|ADA60660.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324241|gb|ADA60662.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324243|gb|ADA60663.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324245|gb|ADA60664.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324247|gb|ADA60665.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324249|gb|ADA60666.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324251|gb|ADA60667.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324253|gb|ADA60668.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324255|gb|ADA60669.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324257|gb|ADA60670.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324259|gb|ADA60671.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324261|gb|ADA60672.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324263|gb|ADA60673.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324265|gb|ADA60674.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324267|gb|ADA60675.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324269|gb|ADA60676.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324271|gb|ADA60677.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324275|gb|ADA60679.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324277|gb|ADA60680.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324279|gb|ADA60681.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324281|gb|ADA60682.1| RNA polymerase sigma factor B [Listeria monocytogenes]
 gi|281324283|gb|ADA60683.1| RNA polymerase sigma factor B [Listeria monocytogenes]
          Length = 222

 Score =  131 bits (331), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 53/240 (22%), Positives = 104/240 (43%), Gaps = 24/240 (10%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           ++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++
Sbjct: 1   EKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIR 60

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           ++D   G     +++  I   ++ ++      V +     +        ++K  ++ +T 
Sbjct: 61  RYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTR 115

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLV 205
                 Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D + 
Sbjct: 116 ELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVG 172

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
              DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++S
Sbjct: 173 GTDDGF--------ERVNQRMLLEKVLPVLDEREQKILQFTFIEN--RSQKETGELLDIS 222


>gi|255527843|ref|ZP_05394691.1| RNA polymerase, sigma 28 subunit, SigK [Clostridium carboxidivorans
           P7]
 gi|296185444|ref|ZP_06853854.1| RNA polymerase sigma-K factor [Clostridium carboxidivorans P7]
 gi|255508454|gb|EET84846.1| RNA polymerase, sigma 28 subunit, SigK [Clostridium carboxidivorans
           P7]
 gi|296050278|gb|EFG89702.1| RNA polymerase sigma-K factor [Clostridium carboxidivorans P7]
          Length = 233

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 67/281 (23%), Positives = 114/281 (40%), Gaps = 67/281 (23%)

Query: 9   IVNGEIGLSRYIHEIRKIP--MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           +    + L+ YI      P  + +K+EEY L K+++E GDL A + LV  +LRLV  I  
Sbjct: 10  LAGSMVFLTAYITNNSSFPQPLNDKEEEYYL-KKFKE-GDLLAKNILVERNLRLVAHIVK 67

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y   G  + +++S G +GL++A+  FD  +G RLATY+   I+  +   I  +      
Sbjct: 68  KYSYPGKEVDDLISIGTVGLIKAIDSFDASKGTRLATYAAKCIENEILMLIRNNKKT--- 124

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
                                                 K  +   + I ++     + SL
Sbjct: 125 --------------------------------------KGEIYLQDPIGIDKE-GNEISL 145

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV-LNPRERRIFEA 245
             +++S + +                  +IE  E K +   L   M+  L  RE+ + E 
Sbjct: 146 LDVLSSDEDS------------------IIEIVESKIQVKKLYDKMNTCLAEREKSVVEM 187

Query: 246 RR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R   L+  P T   ++    +SR  V +IE RA KK+ + +
Sbjct: 188 RYGLLEGKPKTQREIAKILGISRSYVSRIEKRALKKLYKEL 228


>gi|211906943|gb|ACJ11990.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|211906945|gb|ACJ11991.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|211906947|gb|ACJ11992.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
 gi|211906949|gb|ACJ11993.1| RNA polymerase sigma factor sigma B [Listeria monocytogenes]
          Length = 222

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 53/240 (22%), Positives = 104/240 (43%), Gaps = 24/240 (10%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           ++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++
Sbjct: 1   EKVYIWIAAYQENGDEDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIR 60

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           ++D   G     +++  I   ++ ++      V +     +        ++K  ++ +T 
Sbjct: 61  RYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTR 115

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLV 205
                 Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D + 
Sbjct: 116 ELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVG 172

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
              DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++S
Sbjct: 173 GTDDGF--------ERVNQRMLLEKVLPVLDEREQKILQFTFIEN--RSQKETGELLDIS 222


>gi|153814605|ref|ZP_01967273.1| hypothetical protein RUMTOR_00819 [Ruminococcus torques ATCC 27756]
 gi|317501234|ref|ZP_07959439.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|145848099|gb|EDK25017.1| hypothetical protein RUMTOR_00819 [Ruminococcus torques ATCC 27756]
 gi|316897410|gb|EFV19476.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
          Length = 246

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 56/262 (21%), Positives = 104/262 (39%), Gaps = 64/262 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE   E  +  R        A   L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 41  PPLEGMRESEMINRLGTEYAEDAKKVLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGL 100

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+  F+P +  +LATY+   I+  +  Y+ R+                          
Sbjct: 101 IKAINTFNPTKKIKLATYASRCIENEILMYLRRNSKT----------------------- 137

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                             K+ VS  E ++++                D N     D L  
Sbjct: 138 ------------------KMEVSIDEPLNVD---------------WDGNELLLSDILGT 164

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP----VTLENLSSEF 262
           + D   + L  + ERK    +L R+++ LN RE+ I   R   +NP     T + ++   
Sbjct: 165 EEDTIYKDLENEAERK----LLIRALNKLNSREKLIVSMRFGLDNPDGKEKTQKEVADLL 220

Query: 263 EVSRERVRQIEARAFKKVQESI 284
            +S+  + ++E +  ++++  +
Sbjct: 221 GISQSYISRLEKKIMQRLKREM 242


>gi|146295966|ref|YP_001179737.1| sporulation sigma factor SigE [Caldicellulosiruptor saccharolyticus
           DSM 8903]
 gi|145409542|gb|ABP66546.1| RNA polymerase, sigma 29 subunit, SigE [Caldicellulosiruptor
           saccharolyticus DSM 8903]
          Length = 246

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 51/262 (19%), Positives = 101/262 (38%), Gaps = 62/262 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L  +EE  +  +            LV  +LRLVV IA  +    + + ++VS G IGL
Sbjct: 43  PPLTPEEESEILNKIHYERREELKKVLVERNLRLVVYIARKFENTKINLEDLVSIGTIGL 102

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+  ++P++  +LATY+   I+  +  ++ R+                          
Sbjct: 103 IKAINTYNPDKNIKLATYASKCIENEILMFLRRNSH------------------------ 138

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                            +KL +S  E ++++                D N     D L  
Sbjct: 139 -----------------RKLELSIDEPLNVD---------------WDGNELLLSDVLGT 166

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           D +G    +    E    +  L +++  L  RE+RI E R     E   T + ++    +
Sbjct: 167 DSEGVYSSIESSVE----KEALLKAIQKLPKREKRIVELRFGFSDEGEKTQKEVADMLGI 222

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+  + ++E +   ++++ + K
Sbjct: 223 SQSYISRLEKKIITRLKKELAK 244


>gi|293401517|ref|ZP_06645660.1| RNA polymerase sigma-E factor [Erysipelotrichaceae bacterium
           5_2_54FAA]
 gi|291305155|gb|EFE46401.1| RNA polymerase sigma-E factor [Erysipelotrichaceae bacterium
           5_2_54FAA]
          Length = 238

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 60/271 (22%), Positives = 116/271 (42%), Gaps = 63/271 (23%)

Query: 18  RYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
            YI     +P  LEK+EE   A    E+GD  A ++L+  +LRLVV IA  Y    + + 
Sbjct: 23  WYIQGSDVLPKPLEKEEELA-ALIALENGDEEARNKLIEHNLRLVVYIAKRYETNPIFME 81

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++S G+IGL++AV  F  ++  +L TY+   I+  +  ++ +                 
Sbjct: 82  DLISIGSIGLIKAVNTFKRDKNIKLVTYASRCIENEILMFLRKKSR-------------- 127

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
                                      +K+ VS  E ++++                D N
Sbjct: 128 ---------------------------RKVEVSFDEPLNIDY---------------DGN 145

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE-NPVTL 255
                D L  D D    ++ ++ E++  +  L  +M+ L  RER+I + R   E   +T 
Sbjct: 146 ELLLSDILGTDDD----IVTKEFEKQENKRELLAAMATLKDRERQILQMRYGIEHEELTQ 201

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ++++    +S+  + ++E R  +K++  ++K
Sbjct: 202 KDIAKRLGISQSYISRLEKRIIQKLKVQMKK 232


>gi|226310092|ref|YP_002769986.1| RNA polymerase sigma-B factor [Brevibacillus brevis NBRC 100599]
 gi|226093040|dbj|BAH41482.1| RNA polymerase sigma-B factor [Brevibacillus brevis NBRC 100599]
          Length = 262

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 54/267 (20%), Positives = 113/267 (42%), Gaps = 19/267 (7%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             +E   L   Y E  D +   +LV ++  LV  +A  +    +   ++V  G IGL+ +
Sbjct: 11  SPEELKELIHLYGETKDPTIQEQLVRAYTPLVESLAKKFVRGQVMYEDLVQVGLIGLLAS 70

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
            ++FDP       ++++  I   ++ YI      V +     +        ++K  +  +
Sbjct: 71  FRRFDPSFERTFESFAIPTIVGEIKRYIRDKTWSVYVPRRVKELS-----PKIKRVVDEL 125

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA---LINSSDKNSSQWQDWLVY 206
           T    +  Q+  IA  L VSE  ++          SL+    L    D N+    D +  
Sbjct: 126 TIKLQRSPQIADIANSLGVSEEAILETLEMGRSYHSLSMDSELEADLDGNTISLLDLVGT 185

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
             +G   V         +  ML R++ +L+ RE+ I +    Q   ++ +       +S+
Sbjct: 186 MEEGYGAV--------EQNLMLERALQILDHREKEIIQLTFYQN--LSQKQAGDIMGMSQ 235

Query: 267 ERVRQIEARAFKKVQESIQ-KQVELSS 292
             + +++ RA  K++E+++ +Q+E ++
Sbjct: 236 MHISRLQRRALGKLREALRVEQLETAT 262


>gi|154485092|ref|ZP_02027540.1| hypothetical protein EUBVEN_02815 [Eubacterium ventriosum ATCC
           27560]
 gi|149734045|gb|EDM50164.1| hypothetical protein EUBVEN_02815 [Eubacterium ventriosum ATCC
           27560]
          Length = 244

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 61/284 (21%), Positives = 112/284 (39%), Gaps = 66/284 (23%)

Query: 8   IIVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           +I+  E G+  YI     +P  L    E    K   E+ D  A   L+  +LRLVV IA 
Sbjct: 20  MIIKREGGI-HYIGGNDILPAPLSTDREGECIKNLIENNDEEAKSMLIEHNLRLVVYIAK 78

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            +   G+ + +++S G IGL++ +  F P++  +LATY+   I+  +  Y+ ++      
Sbjct: 79  KFDNTGVGVEDLISIGTIGLIKGINTFKPDKNIKLATYASRCIENEILMYLRKNNKT--- 135

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
                                                 KL VS  E ++++         
Sbjct: 136 --------------------------------------KLEVSIDEPLNVD--------- 148

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
                  D N     D L  D D    V+ +  E +  + +L +++  LN RE+ I E R
Sbjct: 149 ------WDGNELLLSDILGTDED----VISKGIESEVEKKLLYKAIEKLNHREKVIVEMR 198

Query: 247 RL----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                     +T + ++    +S+  + ++E +  K+++  I K
Sbjct: 199 YGLNNKDGEEMTQKEVADSLGISQSYISRLEKKIIKRLKREILK 242


>gi|256545958|ref|ZP_05473313.1| RNA polymerase sigma-B factor [Anaerococcus vaginalis ATCC 51170]
 gi|256398380|gb|EEU12002.1| RNA polymerase sigma-B factor [Anaerococcus vaginalis ATCC 51170]
          Length = 256

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 40/254 (15%), Positives = 111/254 (43%), Gaps = 17/254 (6%)

Query: 29  LEKQEEY-VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           LE+++E     +++ +  D    + L+  H+ +V  ++  Y G G+   ++    ++GL+
Sbjct: 8   LERKKEIKEKFEQFYKTRDKDLRNELIEDHMYIVDILSNKYVGKGIEKDDLYQVASLGLI 67

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
            A+ ++DP +G+  ++++   I   ++ Y      ++++      +R+    +++    +
Sbjct: 68  YAIDRYDPSKGYEFSSFATPTIMGELKRYFRDKGWVIRVP-----RRIQNLYKKINVAKK 122

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLV 205
            +     +   +  IA  L   E  ++      ++   +SL+         +S     ++
Sbjct: 123 ILPQELQRTPTIKDIAAYLGEDEETILETIEASKVYSPQSLDMKYQVQKGENSVDLSDMI 182

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            + D     +         ++++ +S   LN  E++I E R       T  +++++  +S
Sbjct: 183 GEDDKNFDSV-------ELKDLIDKSTERLNDLEKQILELRYY--EGRTQVDIANKLSIS 233

Query: 266 RERVRQIEARAFKK 279
           +  V +IE +  +K
Sbjct: 234 QMTVSRIEKKILQK 247


>gi|88809561|ref|ZP_01125068.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 7805]
 gi|88786311|gb|EAR17471.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 7805]
          Length = 211

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 54/212 (25%), Positives = 94/212 (44%), Gaps = 33/212 (15%)

Query: 15  GLSRYIHEIRKIPMLEKQEEY----------------VLA-------------KRYREHG 45
            LS ++ EI +  +L  ++E                 +LA             KR  + G
Sbjct: 4   SLSAFLGEIGRHQLLTPEQELTMGRKVQAMATLTERCMLAGGSGPACEYSEDEKRIIKRG 63

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
              A ++++T++LRLVV +A  Y+G GL + +++ EG +GL +AV+K+DP RG R +TY+
Sbjct: 64  -EKAKNQMITANLRLVVNLAKRYQGKGLDLLDLIQEGTLGLTRAVEKYDPTRGHRFSTYA 122

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
            WWI+  +   +      ++I    N+K     LR  K  L      +   EQ+      
Sbjct: 123 YWWIRQGLNRALSTQSRTIRIPVNVNEK--LTKLRASKARLMQRNGLSPSTEQLSDDMNL 180

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNS 197
                 +++    R +   SL  ++ S    S
Sbjct: 181 PISEVEDLLGCELR-SVTVSLQGVVKSKSDPS 211


>gi|118465934|ref|YP_882149.1| RNA polymerase sigma factor SigF [Mycobacterium avium 104]
 gi|118167221|gb|ABK68118.1| RNA polymerase sigma-F factor [Mycobacterium avium 104]
          Length = 269

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 45/243 (18%), Positives = 95/243 (39%), Gaps = 20/243 (8%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                R+V   L L   +A  +   G  + ++V    +GLM AV +FDP +G     +++
Sbjct: 43  RRQRERIVARCLPLADHVASHFARRGEGLDDLVQVARLGLMNAVNRFDPAKGPSFIGFAV 102

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +   ++ Y       +++     +  +     ++      +     +      +++ L
Sbjct: 103 PTMMGEVRRYFRDYSWGMRVPRRLRELHV-----QISRTTADLAQQLGRAPNAGELSQVL 157

Query: 167 NVSESEVISMNCRLAGD----ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
            V   E++   C +AGD    +SL+A   +    + +     V D D Q        E  
Sbjct: 158 EVPREEIVE--CLVAGDAYRLDSLDAPQGADSSGTPRSVADSVGDIDPQ-------IEHI 208

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             R  L   ++ L  RER +   R      +T   ++    VS+ +V +I A   + +++
Sbjct: 209 TNREALRVLVATLPHREREVLRMRFF--ESMTQSQIAERIGVSQMQVSRILANTLRCLRD 266

Query: 283 SIQ 285
            ++
Sbjct: 267 QLE 269


>gi|55274892|gb|AAV49248.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 190

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 53/200 (26%), Positives = 93/200 (46%), Gaps = 12/200 (6%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           +     +++      K L   LR  +     ++           IA++L+    +V  M 
Sbjct: 61  MNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRML 115

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                  S++  +    +     +  L    D +E    +  +  + +  + + +  LN 
Sbjct: 116 RLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNA 170

Query: 238 RERRIFEARR--LQENPVTL 255
           ++R +   R   L     TL
Sbjct: 171 KQREVLARRFGLLGYEAATL 190


>gi|256832234|ref|YP_003160961.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Jonesia denitrificans
           DSM 20603]
 gi|256685765|gb|ACV08658.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Jonesia denitrificans
           DSM 20603]
          Length = 283

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 47/255 (18%), Positives = 102/255 (40%), Gaps = 17/255 (6%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVK 91
             L   Y+ +        L+  +  LV  IA          +  +++VS G  GL+ A+ 
Sbjct: 34  RQLWDAYKANPTALGREELILHYAPLVTMIAGRVGMKLPNTVEAADLVSYGMFGLIDAID 93

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFDP R  +  TY+   ++ A+ + + R+   +     +  +        L+  L     
Sbjct: 94  KFDPSRDIKFETYASTRVRGAIIDEL-RALDWIPRSVRSRAREYDRACEHLENTLH---- 148

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHD 209
              +      IA+ L V E +V  +  +++     +L+ ++++ D+         V +  
Sbjct: 149 ---REPTSGEIAQHLGVPEKDVWQLQWQVSSGHVIALDEVVSTGDRVDQISAMDSVQETL 205

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
             +    +   +   R +L +++  LN RER +      +   +TL  +     V+  RV
Sbjct: 206 AVD--PAQSFAQGEMREILAQAVDHLNERERAVVTLYYFR--SMTLSEIGKLLGVTESRV 261

Query: 270 RQIEARAFKKVQESI 284
            Q+ +    K+++ +
Sbjct: 262 SQMHSAIIVKLRKQL 276


>gi|307717596|gb|ADN88851.1| RNA polymerase sigma-37 factor [Listeria innocua]
 gi|307717598|gb|ADN88852.1| RNA polymerase sigma-37 factor [Listeria innocua]
 gi|307717600|gb|ADN88853.1| RNA polymerase sigma-37 factor [Listeria innocua]
 gi|307717602|gb|ADN88854.1| RNA polymerase sigma-37 factor [Listeria innocua]
          Length = 220

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 53/237 (22%), Positives = 102/237 (43%), Gaps = 24/237 (10%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQENGDEDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G     +++  I   ++ ++      V +     +        ++K  ++ +T    
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQ 116

Query: 155 KPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +    
Sbjct: 117 SSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTD 173

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
           DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++S
Sbjct: 174 DGF--------ERVNQRMLLEKVLPVLDEREQKILQYTFIEN--RSQKETGELLDIS 220


>gi|41407572|ref|NP_960408.1| RNA polymerase sigma factor SigF [Mycobacterium avium subsp.
           paratuberculosis K-10]
 gi|41395925|gb|AAS03791.1| SigF_1 [Mycobacterium avium subsp. paratuberculosis K-10]
          Length = 269

 Score =  131 bits (330), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 45/243 (18%), Positives = 95/243 (39%), Gaps = 20/243 (8%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                R+V   L L   +A  +   G  + ++V    +GLM AV +FDP +G     +++
Sbjct: 43  RRQRERIVARCLPLADHVASHFARRGEGLDDLVQVARLGLMNAVNRFDPAKGPSFIGFAV 102

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +   ++ Y       +++     +  +     ++      +     +      +++ L
Sbjct: 103 PTMMGEVRRYFRDYSWGMRVPRRLRELHV-----QISRTTADLAQQLGRAPNAGELSQVL 157

Query: 167 NVSESEVISMNCRLAGD----ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
            V   E++   C +AGD    +SL+A   +    + +     V D D Q        E  
Sbjct: 158 EVPREEIVE--CLVAGDAYRLDSLDAPQGADSSGTPRSVADSVGDIDPQ-------IEHI 208

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             R  L   ++ L  RER +   R      +T   ++    VS+ +V +I A   + +++
Sbjct: 209 TNREALRVLVATLPHREREVLRMRFF--ESMTQSQIAERIGVSQMQVSRILANTLRCLRD 266

Query: 283 SIQ 285
            ++
Sbjct: 267 QLE 269


>gi|188011915|gb|ACD45254.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
          Length = 221

 Score =  131 bits (329), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 53/237 (22%), Positives = 102/237 (43%), Gaps = 24/237 (10%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 3   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 62

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G     +++  I   ++ ++      V +     +        ++K  ++ +T    
Sbjct: 63  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQ 117

Query: 155 KPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +    
Sbjct: 118 SSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTD 174

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
           DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++S
Sbjct: 175 DGF--------ERVNQRMLLEKVLPVLDEREQKILQYTFIEN--RSQKETGELLDIS 221


>gi|188011897|gb|ACD45245.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|188011901|gb|ACD45247.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|307717586|gb|ADN88846.1| RNA polymerase sigma-37 factor [Listeria seeligeri]
 gi|307717610|gb|ADN88858.1| RNA polymerase sigma-37 factor [Listeria seeligeri]
 gi|307717630|gb|ADN88868.1| RNA polymerase sigma-37 factor [Listeria seeligeri]
 gi|307717636|gb|ADN88871.1| RNA polymerase sigma-37 factor [Listeria ivanovii subsp. ivanovii]
 gi|307717638|gb|ADN88872.1| RNA polymerase sigma-37 factor [Listeria ivanovii subsp.
           londoniensis]
 gi|307717646|gb|ADN88876.1| RNA polymerase sigma-37 factor [Listeria ivanovii subsp. ivanovii]
          Length = 220

 Score =  131 bits (329), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 53/237 (22%), Positives = 102/237 (43%), Gaps = 24/237 (10%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G     +++  I   ++ ++      V +     +        ++K  ++ +T    
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQ 116

Query: 155 KPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +    
Sbjct: 117 SSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTD 173

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
           DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++S
Sbjct: 174 DGF--------ERVNQRMLLEKVLPVLDEREQKILQYTFIEN--RSQKETGELLDIS 220


>gi|85679195|gb|ABC72014.1| SigB [Listeria monocytogenes]
 gi|85679205|gb|ABC72019.1| SigB [Listeria monocytogenes]
 gi|85679211|gb|ABC72022.1| SigB [Listeria monocytogenes]
 gi|85679213|gb|ABC72023.1| SigB [Listeria monocytogenes]
 gi|307717608|gb|ADN88857.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|307717616|gb|ADN88861.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
          Length = 220

 Score =  131 bits (329), Expect = 1e-28,   Method: Composition-based stats.
 Identities = 53/237 (22%), Positives = 102/237 (43%), Gaps = 24/237 (10%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQENGDEDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G     +++  I   ++ ++      V +     +        ++K  ++ +T    
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQ 116

Query: 155 KPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +    
Sbjct: 117 SSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTD 173

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
           DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++S
Sbjct: 174 DGF--------ERVNQRMLLEKVLPVLDEREQKILQFTFIEN--RSQKETGELLDIS 220


>gi|307717606|gb|ADN88856.1| RNA polymerase sigma-37 factor [Listeria innocua]
          Length = 220

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 53/237 (22%), Positives = 103/237 (43%), Gaps = 24/237 (10%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQENGDEDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G     +++  I   ++ ++      V +     +        ++K  ++ +T    
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQ 116

Query: 155 KPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              Q+  IA+ + V+E EV+           L+ D S+ A    SD ++    D +    
Sbjct: 117 SSPQISDIAEFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTD 173

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
           DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++S
Sbjct: 174 DGF--------ERVNQRMLLEKVLPVLDEREQKILQYTFIEN--RSQKETGELLDIS 220


>gi|331269712|ref|YP_004396204.1| FliA/WhiG family RNA polymerase sigma 28 subunit [Clostridium
           botulinum BKT015925]
 gi|329126262|gb|AEB76207.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           botulinum BKT015925]
          Length = 249

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 61/264 (23%), Positives = 110/264 (41%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE  L  + R  GD S    L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 47  PPLSKEEEENLVAKIR-AGDDSVRTILIERNLRLVVYIARKFENSGVLVEDLISVGTIGL 105

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FDPE+  +LATY+   I+  +  Y+ R+                    ++K   
Sbjct: 106 IKAVNTFDPEKKIKLATYASRCIENEILMYLRRN-------------------NKVKAE- 145

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                            ++  E LN      D N     D L  
Sbjct: 146 ---------------------------------ISFYEPLNT---DWDGNKLLLSDILGT 169

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           ++D    ++ ++ +    + +L  +M  L+ RE+ I + R     +   T + ++    +
Sbjct: 170 ENDMVYNLIEDEVD----KQLLFIAMRKLSEREKEIIKLRFGLTGKGEKTQKQVADLLGI 225

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++ I K V
Sbjct: 226 SQSYISRLEKRIIKRLKKEINKMV 249


>gi|298243403|ref|ZP_06967210.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Ktedonobacter racemifer DSM 44963]
 gi|297556457|gb|EFH90321.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Ktedonobacter racemifer DSM 44963]
          Length = 294

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 57/258 (22%), Positives = 114/258 (44%), Gaps = 21/258 (8%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG----YGLPISEVVSEGNIGLMQAVK 91
            + +RY+EH      + L+T +  LV ++A+G  G      +   +++  G IGL+ A+ 
Sbjct: 9   EIWERYQEHKSSELRNELITMYAPLV-RLAVGRLGIPPTSIMDSEDLIGYGMIGLINAID 67

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           ++D  RG R   ++   I+ A+ + I +   L +   +         +R+++     +  
Sbjct: 68  RYDLSRGVRFEAFATPRIRGAVIDQIRQLNWLPRSSVS--------RIRQIERTHAELEQ 119

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSS--DKNSSQWQDWLVYDH 208
              +P      AK L+VS      M   ++    SL+A + SS  +  S+   D L    
Sbjct: 120 QLGRPATEAEAAKALDVSVERYRQMLTEMSVSVLSLDAPMGSSIQEDESASLGDML---E 176

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D  +Q   E  E +     L+ ++  L PRE+ +       +  +T++ +S    VS  R
Sbjct: 177 DESQQDPGEAVEHEELIQSLSAALQHLPPREQLLLSLYY--KEELTMKEISRIMNVSESR 234

Query: 269 VRQIEARAFKKVQESIQK 286
           V Q+  +A  +++ ++  
Sbjct: 235 VCQLRMQALVRLRSTLSA 252


>gi|239637364|ref|ZP_04678346.1| RNA polymerase sigma-B factor [Staphylococcus warneri L37603]
 gi|239596964|gb|EEQ79479.1| RNA polymerase sigma-B factor [Staphylococcus warneri L37603]
          Length = 256

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 47/263 (17%), Positives = 107/263 (40%), Gaps = 24/263 (9%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             ++     K ++E  +  A  +LV  + +L+  +A  Y        ++V  G +GL+ A
Sbjct: 12  SPEQINQWIKEHQEDQNSGAQDKLVRHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGA 71

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +FD     +   + +  +   ++ Y+      V +     +        R+K     +
Sbjct: 72  INRFDLSFDRKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIG-----PRIKKVSDEL 126

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNC------RLAGDESLNALINSSDKNSSQWQDW 203
           T+   +   +  IA +L V++ EV+           L+ D S+ A     D ++    D 
Sbjct: 127 TNELERSPSISEIAARLEVTDEEVLEAMEMGQSYNALSVDHSIEA---DKDGSTVTLLDI 183

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    D          +   +R +L R + +L+ RE+ I +   +    ++ +       
Sbjct: 184 MGQQDDNY--------DLTEKRMILERILPILSDREKEIIQCTFI--EGLSQKETGERIG 233

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+  V +++  A KK+QE+ ++
Sbjct: 234 LSQMHVSRLQRTAIKKLQEAAKQ 256


>gi|327439575|dbj|BAK15940.1| DNA-directed RNA polymerase specialized sigma subunit [Solibacillus
           silvestris StLB046]
          Length = 233

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 67/274 (24%), Positives = 102/274 (37%), Gaps = 65/274 (23%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+        L ++EE  +  R+ + GD SA   L+  ++RLV  +   +      
Sbjct: 17  ALLGYLKGQTFYKPLSREEEEEVINRFIK-GDESARVELIERNMRLVAHVVKKFHPSHDL 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + + +S G IGLM+AV  F PE+  RLATY+   I                      +  
Sbjct: 76  LDDYISIGTIGLMKAVSSFTPEKKTRLATYAARCI----------------------ENE 113

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS- 193
           +  +LR  K                                    +  D SL   I    
Sbjct: 114 ILMHLRAQKK-----------------------------------VQKDVSLFEPIGIDK 138

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--N 251
           D  S Q +D L  D        IEK ER+     L R +  L+PRE  I   R   +  +
Sbjct: 139 DGQSLQIRDLLQLDEPST----IEKIERQEDFAQLYRYLDTLDPRELEIISYRYGLQNFD 194

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           P T + ++    +SR  V +IE RA  K+ +  +
Sbjct: 195 PHTQKEIAKRLNISRSYVSRIEKRALIKLYQQFK 228


>gi|85679193|gb|ABC72013.1| SigB [Listeria monocytogenes]
 gi|85679197|gb|ABC72015.1| SigB [Listeria monocytogenes]
 gi|85679199|gb|ABC72016.1| SigB [Listeria monocytogenes]
 gi|85679201|gb|ABC72017.1| SigB [Listeria monocytogenes]
 gi|85679203|gb|ABC72018.1| SigB [Listeria monocytogenes]
 gi|85679207|gb|ABC72020.1| SigB [Listeria monocytogenes]
 gi|85679209|gb|ABC72021.1| SigB [Listeria monocytogenes]
 gi|85679215|gb|ABC72024.1| SigB [Listeria monocytogenes]
 gi|307717584|gb|ADN88845.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|307717618|gb|ADN88862.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
 gi|307717628|gb|ADN88867.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
          Length = 220

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 53/237 (22%), Positives = 102/237 (43%), Gaps = 24/237 (10%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G     +++  I   ++ ++      V +     +        ++K  ++ +T    
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQ 116

Query: 155 KPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +    
Sbjct: 117 SSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTD 173

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
           DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++S
Sbjct: 174 DGF--------ERVNQRMLLEKVLPVLDEREQKILQFTFIEN--RSQKETGELLDIS 220


>gi|325677679|ref|ZP_08157331.1| RNA polymerase sigma-K factor [Ruminococcus albus 8]
 gi|324110647|gb|EGC04811.1| RNA polymerase sigma-K factor [Ruminococcus albus 8]
          Length = 231

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 60/261 (22%), Positives = 97/261 (37%), Gaps = 65/261 (24%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L   EE    ++  + GD SA  RL++ +LRLV  I   Y        +++S G IGL+
Sbjct: 33  PLGASEERDCFEKMAQ-GDKSARDRLISHNLRLVAHIIKKYYAAASDQDDLISIGTIGLI 91

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV+ FD  +G R ATY    ++  +  +                               
Sbjct: 92  KAVQTFDYTKGTRFATYGSRCVENEILMHF------------------------------ 121

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                           + L  S S+V S+      D          D NS    D L   
Sbjct: 122 ----------------RALKKSASDV-SIEEPAQSD---------KDGNSLCLMDLLTDG 155

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSV-LNPRERRIFEARRL--QENPVTLENLSSEFEV 264
            D     + ++ E   R   L   +   L+ RER +   R      + +T   +S +  +
Sbjct: 156 ED-----VADRIELLMRAEQLYGILGDCLDDREREVVVMRYGLYGGSALTQREVSEKLCI 210

Query: 265 SRERVRQIEARAFKKVQESIQ 285
           SR  V +IE RA +K++E ++
Sbjct: 211 SRSYVSRIEKRALEKLRERLE 231


>gi|108799863|ref|YP_640060.1| RNA polymerase sigma factor SigF [Mycobacterium sp. MCS]
 gi|119868973|ref|YP_938925.1| RNA polymerase sigma factor SigF [Mycobacterium sp. KMS]
 gi|126435506|ref|YP_001071197.1| RNA polymerase sigma factor SigF [Mycobacterium sp. JLS]
 gi|108770282|gb|ABG09004.1| RNA polymerase, sigma 28 subunit [Mycobacterium sp. MCS]
 gi|119695062|gb|ABL92135.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Mycobacterium
           sp. KMS]
 gi|126235306|gb|ABN98706.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Mycobacterium
           sp. JLS]
          Length = 269

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 51/238 (21%), Positives = 104/238 (43%), Gaps = 19/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             R+VT  L L   IA  Y   G  + ++V    +GLM AV +FDPE G    ++++  +
Sbjct: 47  RERIVTRCLPLADHIAFRYHRKGENLDDLVQIARVGLMHAVNRFDPENGANFLSFAVPTM 106

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   + +      +RL     ++      +T +  +P     +A +L   
Sbjct: 107 LGEIRRHFRDNGWAMHVP-----RRLKDLHVQITRATPRLTQSLGRPPTPTDLAAELGAD 161

Query: 170 ESEVISMNCRLAGDE-SL--NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             EV+   C +AGD  SL       SS  ++++     + + DG+ + + +       R 
Sbjct: 162 RQEVVE--CLVAGDAYSLRSIDSPISSSDDTTRSLADTLGEVDGEMEHITD-------RE 212

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   ++ L  RER +   R      +T   ++    VS+ +V +I A+  +++++ +
Sbjct: 213 SLRPLLAALTERERTVISLRFFA--SMTQTQIAERIGVSQMQVSRILAKTLQQLRDGM 268


>gi|55274909|gb|AAV49256.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 193

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 53/203 (26%), Positives = 94/203 (46%), Gaps = 12/203 (5%)

Query: 55  TSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114
            S+LRLVVKIA  Y   GL + +++ EGN+ L++AV+KFDPERGFR +TY+ WWI+  ++
Sbjct: 1   ESNLRLVVKIARRYGNRGLALLDLIEEGNLVLIRAVEKFDPERGFRFSTYATWWIRQTIE 60

Query: 115 EYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVI 174
             I+     +++      K L   LR  +     ++           IA++L+    +V 
Sbjct: 61  RAIMNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVS 115

Query: 175 SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV 234
            M        S++  +    +     +  L    D +E    +  +  + +  + + +  
Sbjct: 116 RMLRLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWLFE 170

Query: 235 LNPRERRIFEARR--LQENPVTL 255
           LN ++R +   R   L     TL
Sbjct: 171 LNAKQREVLARRFGLLGYEAATL 193


>gi|318060086|ref|ZP_07978809.1| sigma factor [Streptomyces sp. SA3_actG]
 gi|318076269|ref|ZP_07983601.1| sigma factor [Streptomyces sp. SA3_actF]
          Length = 286

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 52/243 (21%), Positives = 104/243 (42%), Gaps = 15/243 (6%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+  ++ LV   A  +R  G  + +VV  G IGL++A+ +F+  R     T+++
Sbjct: 56  QDARNTLIEMNMSLVRFAARRFRSRGDDMEDVVQVGTIGLIKAIDRFELSREVEFTTFAV 115

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            +I   ++ +   +   V +     + R+      L    + ++    +  +V  +A  +
Sbjct: 116 PYIVGEIKRFFRDTTWAVHVPRRLQEARV-----ELAKANEELSTRLGRAPKVSELAALM 170

Query: 167 NVSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           ++SE +V+       G    SL+A I   D    +     + D  G E   +E  E    
Sbjct: 171 SLSEQQVVEAQIAANGYSSSSLDATIGGEDSGEGEAA---LSDFIGAEDPGMELVED--- 224

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + L   ++ L PR+R+I E R  QE  +T   +     VS+  V ++  R    ++  +
Sbjct: 225 LHALAPLLAGLEPRDRQILELRFGQE--LTQAQIGERLGVSQMHVSRLLNRTLGTLRAGL 282

Query: 285 QKQ 287
             +
Sbjct: 283 MSE 285


>gi|86609923|ref|YP_478685.1| RNA polymerase sigma factor SigF [Synechococcus sp.
           JA-2-3B'a(2-13)]
 gi|86558465|gb|ABD03422.1| RNA polymerase sigma factor, group 3 [Synechococcus sp.
           JA-2-3B'a(2-13)]
          Length = 293

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 48/254 (18%), Positives = 107/254 (42%), Gaps = 13/254 (5%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVKKFD 94
            L + Y ++ D +  +RLV  +L LV K A  +R        ++V  G +GL+QA+++FD
Sbjct: 51  ELLRLYHQNRDPALRNRLVEMNLGLVRKEAHHWRNQCNEGYDDLVQVGCLGLIQAIERFD 110

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             RG   +++++ +I+  +Q Y+      ++I      +R     R+ K  +  +     
Sbjct: 111 ISRGLAFSSFALPYIRGEIQHYLRDKSPTMRIP-----RRWTTLQRQAKKVIARLRQELG 165

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +      + + L ++E E   +         L+       +  S     +V D   +   
Sbjct: 166 RSPSEAEVREALQLTEQEWRELELAQQNSLLLSLDAPIQTEEDSVALGEVVPDQRYRSFQ 225

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
           L E++     R  L  +++ L  R R+I E     +  +T +  +    +S   V +   
Sbjct: 226 LAEED-----RIRLQHALAQLEERTRKILEFVFFYD--LTQKETAERLGISAVTVSRQVK 278

Query: 275 RAFKKVQESIQKQV 288
           +  +++ + + + +
Sbjct: 279 KGLERLAKLLNQDI 292


>gi|149183156|ref|ZP_01861605.1| SpoIIIC [Bacillus sp. SG-1]
 gi|148849139|gb|EDL63340.1| SpoIIIC [Bacillus sp. SG-1]
          Length = 238

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 56/267 (20%), Positives = 98/267 (36%), Gaps = 63/267 (23%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+        L  QEE    ++   +GD  A + L+  +LRLV  I   +   G   
Sbjct: 18  LVSYVKNNAFPQPLSSQEEKKYLRKMA-NGDEDARNILIEHNLRLVAHIVKKFENTGEDP 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++S G IGL++A++ +   +G +LATY+   I+  +                      
Sbjct: 77  EDLISIGTIGLIKAIESYSEGKGTKLATYAARCIENEI---------------------- 114

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
             +LR LK                            + +S++  +  D          + 
Sbjct: 115 LMHLRALKKT-------------------------KKDVSLHDPIGQD---------KEG 140

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPV 253
           N     D L  D D     +IE  +       + + + VL+ RE+ +   R   +     
Sbjct: 141 NEISLIDILKSDADD----VIETIQLSMELEKVRKYICVLDDREKEVIIGRFGLDMKEEK 196

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKV 280
           T   ++ E  +SR  V +IE RA  K+
Sbjct: 197 TQREIAKELGISRSYVSRIEKRALMKM 223


>gi|304404273|ref|ZP_07385935.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
 gi|304347251|gb|EFM13083.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
          Length = 262

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 55/267 (20%), Positives = 109/267 (40%), Gaps = 23/267 (8%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSE 81
           K P L         ++++   D+ A  +L+  +L LV  +           +   ++ S 
Sbjct: 5   KTPHLSN---IEKWRKWKTEKDIEAKKQLIEQYLPLVDYVTSRMAIGLPKTVSKDDLYSN 61

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           G +GL+ A++KFD ERG +  TY+ W I+  + + + R    V        K       R
Sbjct: 62  GVMGLIDAIEKFDYERGLQFETYASWRIRGGIIDGL-RQGDWVPRSVRDKAK-------R 113

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQ 199
           ++   Q +    L+      I+  LNVSE E   +   +A     SL   I   ++ S  
Sbjct: 114 IEEAYQLLEQKYLRSVTDAEISDYLNVSEKEFTGILQEIAVTTICSLEDPIR--EEESET 171

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
               LV +        + +      +  L + +  L  +ER +      +E  ++L  ++
Sbjct: 172 RLSLLVDEKAKNPDYKVHEFYL---KESLVKGIERLTEKERTVVSLFYYEE--LSLSEIA 226

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQK 286
               +S  R+ Q+ ++A  +++ ++ K
Sbjct: 227 EVMSLSPSRISQLHSKAILRLRGALAK 253


>gi|331090616|ref|ZP_08339467.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium 2_1_46FAA]
 gi|330401056|gb|EGG80651.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium 2_1_46FAA]
          Length = 246

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 56/272 (20%), Positives = 109/272 (40%), Gaps = 65/272 (23%)

Query: 18  RYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
            YI     +P  LE +EE  + ++     D  A   L+  +LRLVV IA  +   G+ + 
Sbjct: 31  HYIGGSDVLPAPLETEEETAVIEKLGTETDDVAKKTLIEHNLRLVVYIAKKFDNTGVGVE 90

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++S G IGL++A+  F+P +  +LATY+   I+  +  Y+ R+                
Sbjct: 91  DLISIGTIGLIKAINTFNPMKNIKLATYASRCIENEILMYLRRNNKT------------- 137

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
                                       +L VS  E ++++                D N
Sbjct: 138 ----------------------------RLEVSIDEPLNVD---------------WDGN 154

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL----QENP 252
                D L  + D   + L  + ERK    +L ++++ L+ RE+ I + R          
Sbjct: 155 ELLLSDILGTEEDTIYRDLETEVERK----LLMKAINRLSSREKTIVQMRFGIGTKDGEE 210

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            T + ++    +S+  + ++E +  ++++  I
Sbjct: 211 KTQKEVADILGISQSYISRLEKKIMQRLKREI 242


>gi|325478815|gb|EGC81925.1| putative RNA polymerase sigma-F factor [Anaerococcus prevotii
           ACS-065-V-Col13]
          Length = 255

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 39/244 (15%), Positives = 102/244 (41%), Gaps = 16/244 (6%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
            + Y +  D      L+  H+ +V  ++  Y G G+   ++    ++GL+ A+ +FDP +
Sbjct: 17  FEEYYKTRDKKLRDELIEEHMYIVDILSNKYVGKGIEKDDLYQVASLGLIYAIDRFDPTK 76

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G+  ++++   I   ++ Y      ++++      +R+    +++    + +     +  
Sbjct: 77  GYAFSSFATPTIMGELKRYFRDKGWVIRVP-----RRIQNLYKKINTAKKILPQELQRTP 131

Query: 158 QVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
            V  IA  L   E  ++      ++   +SL+         ++     ++ + D     +
Sbjct: 132 TVADIADYLGEDEETILETMEASKVYAPQSLDMKYQVQKGENAIDLSEMIGEEDKNFDSI 191

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
                    ++++ +S   LN  E+ I E R       T  ++++  ++S+  V +IE +
Sbjct: 192 -------ELKDLIDKSKERLNDLEKEILELRYY--EGRTQVDIANTLDISQMTVSRIEKK 242

Query: 276 AFKK 279
             +K
Sbjct: 243 IIQK 246


>gi|317132580|ref|YP_004091894.1| RNA polymerase, sigma 28 subunit, SigE [Ethanoligenens harbinense
           YUAN-3]
 gi|315470559|gb|ADU27163.1| RNA polymerase, sigma 28 subunit, SigE [Ethanoligenens harbinense
           YUAN-3]
          Length = 242

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 62/272 (22%), Positives = 113/272 (41%), Gaps = 66/272 (24%)

Query: 19  YIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           YI+    +P  L  ++E    +   E G+  A +RL+  +LRLVV IA  +   G+ + +
Sbjct: 31  YINGPDTLPAPLGAEDEAACLRGL-EAGEKDAKNRLIEHNLRLVVYIAKKFENTGVGVED 89

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +VS G IGL++AV  F P RG +LATY+   I+  +  ++ +         T NQK    
Sbjct: 90  LVSIGTIGLIKAVNTFCPSRGIKLATYASRCIENEILMFLRK---------TQNQKN--- 137

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN-SSDKN 196
                                                        + S++  ++   D N
Sbjct: 138 ---------------------------------------------EVSIDEPLHVDWDGN 152

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVT 254
                D L  D D    V+    E+   +++L  ++S L+ RER I E R         T
Sbjct: 153 ELLLSDVLGTDSD----VVHHNIEKDVDKSLLAAAISHLSKRERVIMEMRFGLRGGPGRT 208

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + ++    +S+  + ++E R  +++++ I++
Sbjct: 209 QKEVADSLGISQSYISRLEKRIIQRLKKEIER 240


>gi|303282119|ref|XP_003060351.1| predicted protein [Micromonas pusilla CCMP1545]
 gi|226457822|gb|EEH55120.1| predicted protein [Micromonas pusilla CCMP1545]
          Length = 425

 Score =  131 bits (329), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 51/261 (19%), Positives = 96/261 (36%), Gaps = 27/261 (10%)

Query: 47  LSAAHRLVTSHLRLVVKIAMG-YRGYGL------PISEVVSEGNIGLMQAVKKFDPERGF 99
            +A  +LV  ++ L   IA   +            +S++  EG  GL QA  KFDP RG+
Sbjct: 63  QNARRQLVVKNVGLAYSIARDVFEKLNHADRGLLSVSDLAQEGCAGLAQAADKFDPSRGY 122

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY+  W +  +   I  +   +++    ++      ++R K   + +T  + +    
Sbjct: 123 KFSTYAYNWTRKYVVNAIQNNGRTIRLPIHMHEI-----MQRAKKATRELTQKHGRAPTD 177

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD------------ 207
             +++ L V  S V  +N       SL+        +        + D            
Sbjct: 178 EEMSRTLGVPVSRVQEINDWARSTLSLDVGGGGRSSDDGDGGAEGMMDGIVFALGSKDGK 237

Query: 208 --HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
                  +      E    R  L  + + L PRE  +   R       +   L +   VS
Sbjct: 238 DGMLSPHEAAEADMEADLLRRDLEEAFATLLPREAFVLRHRFGLAAAAS-TALGTLLGVS 296

Query: 266 RERVRQIEARAFKKVQESIQK 286
            E +R  E RA +K+++  + 
Sbjct: 297 HETIRTYERRALEKLKQPSRA 317


>gi|295094809|emb|CBK83900.1| RNA polymerase, sigma 29 subunit, SigE [Coprococcus sp. ART55/1]
          Length = 245

 Score =  130 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 66/274 (24%), Positives = 106/274 (38%), Gaps = 65/274 (23%)

Query: 19  YIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           YI     +P  LE  EE V+      +   SA   L+  +LRLVV IA  +   G+ I +
Sbjct: 31  YIGGTEVLPAPLEPHEEAVVINELTNNQSDSAKKMLIERNLRLVVYIAKKFDNTGVGIED 90

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++S G IGL++A+  F  ++  +LATY+   I+  +  ++ R+                 
Sbjct: 91  LISIGTIGLIKAINTFKNDKNIKLATYASRCIENEILMFLRRNS---------------- 134

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            LR                   V+I + LNV                         D N 
Sbjct: 135 KLR-----------------TEVSIDEPLNV-----------------------DWDGNE 154

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL----QENPV 253
               D L  D D    V+    E +   N+L  ++S L  +ER I E R           
Sbjct: 155 LLLSDILGTDED----VVYRDLETEVDYNLLDNAISKLCEKERTIIELRYGINTIGGVEK 210

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           T + ++    +S+  + ++E R  KK++  I KQ
Sbjct: 211 TQKEVADLLGISQSYISRLEKRIIKKLRREIMKQ 244


>gi|225017509|ref|ZP_03706701.1| hypothetical protein CLOSTMETH_01436 [Clostridium methylpentosum
           DSM 5476]
 gi|224949748|gb|EEG30957.1| hypothetical protein CLOSTMETH_01436 [Clostridium methylpentosum
           DSM 5476]
          Length = 231

 Score =  130 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 56/263 (21%), Positives = 102/263 (38%), Gaps = 67/263 (25%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L  ++E    +  ++ GD +A  RL+  +LRLV  IA  Y        +++S G IGL+
Sbjct: 29  PLTLKQEKESFELMKQ-GDSAARDRLIEHNLRLVAHIAKKYYSVTNEQDDLISIGTIGLI 87

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV  FD  +G R ATY+   I                      +  +  + R +K    
Sbjct: 88  KAVGTFDYTKGTRFATYASRCI----------------------ENEILMHFRNVKKT-- 123

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS-DKNSSQWQDWLVY 206
                                            AGD  +N  I++  D NS    D +  
Sbjct: 124 ---------------------------------AGDVYINDTIDTDKDGNSISLIDVIAD 150

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVL-NPRERRIFEARRLQEN--PVTLENLSSEFE 263
           + +     +++  + K +   L +S+  L   RE+ I   R       P+T   ++   +
Sbjct: 151 ETN-----IVDTIDLKLKSEQLHKSIKNLLTEREQMIVILRYGLNGHRPMTQREVADRLK 205

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +SR  V +IE ++ ++++  I +
Sbjct: 206 ISRSYVSRIEKKSLEQLKTVIDR 228


>gi|302517710|ref|ZP_07270052.1| RNA polymerase sigma-B factor [Streptomyces sp. SPB78]
 gi|302426605|gb|EFK98420.1| RNA polymerase sigma-B factor [Streptomyces sp. SPB78]
          Length = 286

 Score =  130 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 52/243 (21%), Positives = 104/243 (42%), Gaps = 15/243 (6%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+  ++ LV   A  +R  G  + +VV  G IGL++A+ +F+  R     T+++
Sbjct: 56  QDARNTLIEMNMSLVRFAARRFRSRGDDMEDVVQVGTIGLIKAIDRFELSREVEFTTFAV 115

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            +I   ++ +   +   V +     + R+      L    + ++    +  +V  +A  +
Sbjct: 116 PYIVGEIKRFFRDTTWAVHVPRRLQEARV-----ELAKANEELSTRLGRAPKVSELAALM 170

Query: 167 NVSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           ++SE +V+       G    SL+A I   D    +     + D  G E   +E  E    
Sbjct: 171 SLSEQQVVEAQIAANGYSSSSLDATIGGEDSGEGEAA---LSDFIGAEDPGMELVED--- 224

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + L   ++ L PR+R+I E R  QE  +T   +     VS+  V ++  R    ++  +
Sbjct: 225 LHALAPLLADLEPRDRQILELRFGQE--LTQAQIGERLGVSQMHVSRLLNRTLGTLRAGL 282

Query: 285 QKQ 287
             +
Sbjct: 283 MSE 285


>gi|229165937|ref|ZP_04293702.1| RNA polymerase sigma-B factor [Bacillus cereus AH621]
 gi|228617490|gb|EEK74550.1| RNA polymerase sigma-B factor [Bacillus cereus AH621]
          Length = 224

 Score =  130 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 46/233 (19%), Positives = 106/233 (45%), Gaps = 16/233 (6%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           +V  +  LV  IA  Y   G    +++  G +GL+ A++++D   G     +++  I   
Sbjct: 1   MVNHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGE 60

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +++Y+      V +      +R+     ++K  ++ +TD+  +  +++ IA  L +SE E
Sbjct: 61  IKKYLRDKTWGVHVP-----RRIKDLGGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEE 115

Query: 173 VISMN--CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           V+ +          SL+ ++ +S   SS  +   V +       + +  E+  RR +L  
Sbjct: 116 VLEIMDAKNNYQVSSLDDVVENSSDGSSVARIESVGE-------VEQGYEQTERRLVLDD 168

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +VLN  E+ +      +   +  ++      +S+  V +I+ +A  K++++
Sbjct: 169 IFNVLNDTEKSVIHYIFGEN--LNQKDTGERLGISQMHVSRIKRQAISKLKQA 219


>gi|239827809|ref|YP_002950433.1| sporulation sigma factor SigK [Geobacillus sp. WCH70]
 gi|239808102|gb|ACS25167.1| RNA polymerase, sigma 28 subunit, SigK [Geobacillus sp. WCH70]
          Length = 236

 Score =  130 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 56/268 (20%), Positives = 98/268 (36%), Gaps = 65/268 (24%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI        L  +EE    +   + GD  A + L+  +LRLV  I   +   G   
Sbjct: 18  LVSYIKNNAFPQPLSAKEEEKYLQLMAK-GDEQARNILIEHNLRLVAHIVKKFENTGEDA 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++S G IGL++A++ + P +G +LATY+   I+  +                      
Sbjct: 77  EDLISIGTIGLIKAIESYSPGKGTKLATYAARCIENEI---------------------- 114

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS-D 194
             +LR LK                                       D SL+  I    +
Sbjct: 115 LMHLRSLKKT-----------------------------------RKDVSLHEPIGQDKE 139

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NP 252
            N     D L  + +     +I++ +       + + + VL+ RE+ +  +R   +    
Sbjct: 140 GNEISLIDVLKSEGND----IIDEIQLNMELEQVKKYIDVLDEREKEVIISRFGLDMQQE 195

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKV 280
            T   ++ E  +SR  V +IE RA  K+
Sbjct: 196 KTQREIAKELGISRSYVSRIEKRALMKM 223


>gi|229010401|ref|ZP_04167605.1| RNA polymerase sigma-B factor [Bacillus mycoides DSM 2048]
 gi|228750821|gb|EEM00643.1| RNA polymerase sigma-B factor [Bacillus mycoides DSM 2048]
          Length = 224

 Score =  130 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 45/233 (19%), Positives = 106/233 (45%), Gaps = 16/233 (6%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           +V  +  LV  IA  Y   G    +++  G +GL+ A++++D   G     +++  I   
Sbjct: 1   MVNHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGE 60

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +++Y+      + +      +R+     ++K  ++ +TD+  +  +++ IA  L +SE E
Sbjct: 61  IKKYLRDKTWGIHVP-----RRIKDLGGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEE 115

Query: 173 VISMN--CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           V+ +          SL+ ++ +S   SS  +   V +       + +  E+  RR +L  
Sbjct: 116 VLEIMDAKNNYQVSSLDDVVENSSDGSSVARIESVGE-------VEQGYEQTERRLVLDD 168

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +VLN  E+ +      +   +  ++      +S+  V +I+ +A  K++++
Sbjct: 169 IFNVLNDTEKSVIHYIFGEN--LNQKDTGERLGISQMHVSRIKRQAISKLKQA 219


>gi|57996878|emb|CAI45887.1| negative response regulator [Escherichia coli]
          Length = 191

 Score =  130 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 54/201 (26%), Positives = 93/201 (46%), Gaps = 12/201 (5%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL + +++ EGN+GL +AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLNRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           +     +++      K L   LR  +     ++           IA++L+    +V  M 
Sbjct: 61  MNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRML 115

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                  S++  +    +     +  L    D +E    +  +  + +  + + +  LN 
Sbjct: 116 RLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNA 170

Query: 238 RERRIFEARR--LQENPVTLE 256
           ++R +   R   L     TLE
Sbjct: 171 KQREVLARRFGLLGYEAATLE 191


>gi|225028516|ref|ZP_03717708.1| hypothetical protein EUBHAL_02795 [Eubacterium hallii DSM 3353]
 gi|224954159|gb|EEG35368.1| hypothetical protein EUBHAL_02795 [Eubacterium hallii DSM 3353]
          Length = 209

 Score =  130 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 61/264 (23%), Positives = 103/264 (39%), Gaps = 64/264 (24%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L+ +EE    K YR+ GD  A  +L+  +LRLV  I   Y      + +++S G IGL+
Sbjct: 7   PLKAEEERYYLKMYRD-GDEKAKEKLIEHNLRLVAHIVKKYNSPDRDLDDLISIGTIGLI 65

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV  FD  +G RL TY+   I                      +  L   +R+ K  L+
Sbjct: 66  KAVNTFDLNKGGRLVTYAARCI----------------------ENELLMMIRQEKKILR 103

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                                                SL   I +  + +      L+  
Sbjct: 104 E-----------------------------------VSLYEPIGTDQEGN---HISLLDI 125

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVL-NPRERRIFEARRL--QENPVTLENLSSEFEV 264
              +E  LIE+   K   + L + + +L + RER I   R       P T + +++   +
Sbjct: 126 ISTEEAELIEQYLHKYYLSRLEQEVFLLTDDREREIILKRYGLCGNEPHTQKEVAAMMGI 185

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           SR  V +IE +A +K++ S ++ +
Sbjct: 186 SRSYVSRIEKKALEKLRSSYEQYM 209


>gi|307717588|gb|ADN88847.1| RNA polymerase sigma-37 factor [Listeria seeligeri]
 gi|307717632|gb|ADN88869.1| RNA polymerase sigma-37 factor [Listeria seeligeri]
          Length = 220

 Score =  130 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 53/237 (22%), Positives = 103/237 (43%), Gaps = 24/237 (10%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  + +LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQENGDQDAQYNLVVHYKKLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G     +++  I   ++ ++      V +     +        ++K  ++ +T    
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQ 116

Query: 155 KPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +    
Sbjct: 117 SSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTD 173

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
           DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++S
Sbjct: 174 DGF--------ERVNQRMLLEKVLPVLDEREQKILQYTFIEN--RSQKETGELLDIS 220


>gi|302527791|ref|ZP_07280133.1| RNA polymerase sigma-F factor [Streptomyces sp. AA4]
 gi|302436686|gb|EFL08502.1| RNA polymerase sigma-F factor [Streptomyces sp. AA4]
          Length = 243

 Score =  130 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 47/233 (20%), Positives = 91/233 (39%), Gaps = 18/233 (7%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           VT  L +   IA  + G G P  ++V    IGL+ A+ +F P+RG    ++++  I   +
Sbjct: 23  VTEFLPVAEHIATRFTGRGEPREDLVQVARIGLINAIDRFTPDRGPDFLSFAVPTIMGEI 82

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
           + Y   +   V++      K L  +L R    L         P     +A+ L +  SEV
Sbjct: 83  RRYFRDTGWSVRVPRRL--KELHLSLSRGSATLSQTLGRAPTP---TELAEHLGLELSEV 137

Query: 174 IS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
               +        S++  ++  D       D L  D          + E       L   
Sbjct: 138 HEGLVAGHAYQTLSVDKPVHD-DAEPLLLADTLGSDDP--------EIEHIENHEALQPL 188

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +  L  RER I   R      +T   ++ +  +S+  V ++ ++  +++++ +
Sbjct: 189 LRELPKRERAILVMRFFGG--LTQTQIAEQVGISQMHVSRLLSQTLEQLRDKL 239


>gi|307717642|gb|ADN88874.1| RNA polymerase sigma-37 factor [Listeria ivanovii subsp.
           londoniensis]
          Length = 220

 Score =  130 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 53/237 (22%), Positives = 101/237 (42%), Gaps = 24/237 (10%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQEDGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G     +++  I   ++ ++      V +     +        ++K  ++ +T    
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQ 116

Query: 155 KPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +    
Sbjct: 117 SSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTD 173

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
           DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++S
Sbjct: 174 DGF--------ERVNQRMLLEKVLPVLDEREQKILQYTFIEN--RSQKETGELLDIS 220


>gi|295835999|ref|ZP_06822932.1| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
 gi|295825822|gb|EFG64505.1| RNA polymerase sigma-F factor [Streptomyces sp. SPB74]
          Length = 297

 Score =  130 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 53/240 (22%), Positives = 100/240 (41%), Gaps = 8/240 (3%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + L+  +  LV   A  +R  G   + +++  G +GL++A+ +FD  R     ++++ 
Sbjct: 64  ARNTLIEMNQSLVRFAARRFRNRGNGDMEDILQVGTVGLIKAIDRFDLTREAEFTSFAIP 123

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +I   ++ Y   S   V +     + R+  +L R K  L    D +     V  +A +L 
Sbjct: 124 YIVGEIKRYFRDSTWAVHVPRRLQELRV--DLARAKERLAVDLDRDPG---VKELAAELG 178

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +SE EVI       G  S +  + +    S +        +           E       
Sbjct: 179 ISEDEVIDGLIAANGYMSDSLDLPADSTTSGKPDQKTATTYADFLGDWDPAMELVEDFTA 238

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   +  L+ RER + E R  QE  +T   + +E  VS+  V ++ +R   K++E +  +
Sbjct: 239 LRPLLGTLDDRERYLLELRFGQE--LTQAQIGAELGVSQMHVSRLLSRTLGKLREGLLSE 296


>gi|307717644|gb|ADN88875.1| RNA polymerase sigma-37 factor [Listeria ivanovii subsp.
           londoniensis]
          Length = 220

 Score =  130 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 53/237 (22%), Positives = 101/237 (42%), Gaps = 24/237 (10%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQEDGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G     +++  I   ++ ++      V +     +        ++K  ++ +T    
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQ 116

Query: 155 KPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +    
Sbjct: 117 SSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSMEA---DSDGSTITLLDVVGGTD 173

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
           DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++S
Sbjct: 174 DGF--------ERVNQRMLLEKVLPVLDEREQKILQYTFIEN--RSQKETGELLDIS 220


>gi|271964601|ref|YP_003338797.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Streptosporangium roseum DSM 43021]
 gi|270507776|gb|ACZ86054.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Streptosporangium roseum DSM 43021]
          Length = 258

 Score =  130 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 51/261 (19%), Positives = 109/261 (41%), Gaps = 18/261 (6%)

Query: 30  EKQE---EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
             +E   E VL +   E+       R+V  H  L ++IA  YR  G P+ +++    +GL
Sbjct: 12  TAEELLAEMVLPE-ISEYRAERLRERIVEMHRPLAMEIARRYRYRGEPLEDLLQAAYVGL 70

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+A+  FDP  G     Y++  +   ++ +       +++     ++R       L   +
Sbjct: 71  MKAINGFDPTLGHAFRGYAVVTMTGEVKRHFRDRTWAIRVPRVYQERRA-----ELNRLV 125

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
             ++ +  +   V  +A K+ +SE +V+      A   +L+        + +     ++ 
Sbjct: 126 ADLSQDLGRAPTVAELAVKMRISEEDVLLTLDASAAYSALSLDAPLGADDDAAALGDIIP 185

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           D D    VL++       R  +   +  L  RE+ I   R      +T   +++EF +S+
Sbjct: 186 DEDDALGVLVD-------REAVKPLIDKLPTREKNILLLRFFGN--MTQAEIAAEFGISQ 236

Query: 267 ERVRQIEARAFKKVQESIQKQ 287
             V +I  +   +++E +  +
Sbjct: 237 MHVSRILRKVLDQLREELVAE 257


>gi|54022121|ref|YP_116363.1| putative sigma factor [Nocardia farcinica IFM 10152]
 gi|54013629|dbj|BAD54999.1| putative sigma factor [Nocardia farcinica IFM 10152]
          Length = 266

 Score =  130 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 44/237 (18%), Positives = 97/237 (40%), Gaps = 14/237 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +    L+   L L   IA  + G G    +++    +G++ AV +FDP +G     +++
Sbjct: 38  RALREELIERCLPLAEHIARKFSGRGENFEDLLQIARVGMVAAVDRFDPTQGAPFLGFAV 97

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I   ++ +       V++     + +       L   ++ +T    +  +   +A++L
Sbjct: 98  PTIMGEVRRHFRDHTWSVRVPRRLKELQAT-----LNPAIETLTQRLGRMPKARELAEEL 152

Query: 167 NVSESEV-ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
            V  +EV  ++  R A   S    I+ S  +  +     + D  G E       E     
Sbjct: 153 GVDIAEVTQALVARNAYQTS---SIDGSSGDDGESSAPALADTLGAEDPEFGTVENYL-- 207

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             +   ++ L  RE+R+   R    + ++ E ++ +   S+ +V +I +R  K ++E
Sbjct: 208 -AVKPLIAALPEREQRVLVMRFF--HSMSQEQIAQQIGCSQMQVSRILSRTLKSLRE 261


>gi|330684827|gb|EGG96520.1| RNA polymerase sigma-B factor [Staphylococcus epidermidis VCU121]
          Length = 256

 Score =  130 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 47/263 (17%), Positives = 107/263 (40%), Gaps = 24/263 (9%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             ++     K ++E  +  A  +LV  + +L+  +A  Y        ++V  G +GL+ A
Sbjct: 12  SPEQINQWIKEHQEDQNSGAQDKLVRHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGA 71

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +FD     +   + +  +   ++ Y+      V +     +        R+K     +
Sbjct: 72  INRFDLSFDRKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIG-----PRIKKVSDEL 126

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNC------RLAGDESLNALINSSDKNSSQWQDW 203
           T+   +   +  IA +L V++ EV+           L+ D S+ A     D ++    D 
Sbjct: 127 TNELERSPSISEIAARLEVTDEEVLEAIEMGQSYNALSVDHSIEA---DKDGSTVTLLDI 183

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    D          +   +R +L R + +L+ RE+ I +   +    ++ +       
Sbjct: 184 MGQQDDNY--------DLTEKRMILERILPILSDREKEIIQCTFI--EGLSQKETGERIG 233

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+  V +++  A KK+QE+ ++
Sbjct: 234 LSQMHVSRLQRTAIKKLQEAAKQ 256


>gi|307717590|gb|ADN88848.1| RNA polymerase sigma-37 factor [Listeria welshimeri]
 gi|307717592|gb|ADN88849.1| RNA polymerase sigma-37 factor [Listeria welshimeri]
 gi|307717624|gb|ADN88865.1| RNA polymerase sigma-37 factor [Listeria welshimeri]
 gi|307717626|gb|ADN88866.1| RNA polymerase sigma-37 factor [Listeria welshimeri]
          Length = 220

 Score =  130 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 53/237 (22%), Positives = 101/237 (42%), Gaps = 24/237 (10%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G     +++  I   ++ ++      V +     +        ++K  ++ +T    
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQ 116

Query: 155 KPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +    
Sbjct: 117 SSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTD 173

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
           DG         ER N+R +L + + VL+ RE+ I +   ++    + +      ++S
Sbjct: 174 DGF--------ERVNQRMLLEKVLPVLDEREQMILQYTFIEN--RSQKETGELLDIS 220


>gi|83589646|ref|YP_429655.1| sigma 28 (flagella/sporulation) [Moorella thermoacetica ATCC 39073]
 gi|83572560|gb|ABC19112.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Moorella
           thermoacetica ATCC 39073]
          Length = 255

 Score =  130 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 48/251 (19%), Positives = 92/251 (36%), Gaps = 13/251 (5%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKF 93
           L   Y    D      LV  +L LV              L   +++  G +GL++AV ++
Sbjct: 8   LWTSYMAGRDALRRQELVLKYLPLVKYHVNRLAVKPPPHLDQEDLLGYGIVGLLEAVDRY 67

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           DP RG    T++   I+ A+ + + R             + L   LRR     + +    
Sbjct: 68  DPSRGVNFETFASQRIRGAILDALRR--------AHWAPRSLIEKLRRASQVYRQLEQEQ 119

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
                  A+A+ L ++E+E+  +  R +    L+      D+   +         D    
Sbjct: 120 GGEVSDGAVARALGITEAELRELMERGSQMAILSLEDFLLDQEGEEGTTRGELLADPGSP 179

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
             +   E+   R  L  ++  L  ++R +          +TL+ +     +S  RV Q+ 
Sbjct: 180 DPVGIYEQGELRRALAAALENLKEKDRLVLTLYYY--EGLTLKEIGKVLGISESRVCQLH 237

Query: 274 ARAFKKVQESI 284
            RA   ++  +
Sbjct: 238 GRAILNLRRQL 248


>gi|326204596|ref|ZP_08194452.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           papyrosolvens DSM 2782]
 gi|325985163|gb|EGD46003.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           papyrosolvens DSM 2782]
          Length = 254

 Score =  130 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 44/251 (17%), Positives = 109/251 (43%), Gaps = 17/251 (6%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKF 93
           L K+Y E+ + +A  +L+  +  L+  +A     Y G  +   ++V  G  GL+ A++K+
Sbjct: 9   LWKQYIENKEAAAKEKLIIQYAYLIKYVAGRLSIYFGSNVEFDDLVGYGAFGLIDAIEKY 68

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D  +G +  TY+   I+ ++ + I     +  +  +  QK      + L+     I +  
Sbjct: 69  DLAKGVKFETYASLRIRGSIIDSIRD---MDWVPRSLRQKN-----KELEKVYAEIENEK 120

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
                   +A+K+ +   +   +      D +++++++  +     ++  L    +  E 
Sbjct: 121 GHTATDKEVAEKMGLGMDDFYKLL----NDVNVSSMMSLDEFMEQNYERGLEIFSESTED 176

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
                 E    + +L  S+  L  +E+ +      +E  +TL+ +S+   V+  R+ Q+ 
Sbjct: 177 KPEASLEFNEMKQLLADSIDKLPEKEKAVITFYYFEE--LTLKEISAIMSVTESRISQLH 234

Query: 274 ARAFKKVQESI 284
            +A  +++  +
Sbjct: 235 TKALLRMKGKL 245


>gi|302810520|ref|XP_002986951.1| hypothetical protein SELMODRAFT_43614 [Selaginella moellendorffii]
 gi|300145356|gb|EFJ12033.1| hypothetical protein SELMODRAFT_43614 [Selaginella moellendorffii]
          Length = 326

 Score =  130 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 57/251 (22%), Positives = 106/251 (42%), Gaps = 16/251 (6%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGY--RGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           +R  + G  +A ++++  +LRLV   A  Y      L + ++  EG  GLM AV KFDP+
Sbjct: 79  RRLLQSG-QAARNKMIKHNLRLVAHQARKYFKEELSLSLLDLCQEGVPGLMSAVDKFDPK 137

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +G+R +TY+++W+K ++     R   +V++      +++   ++R +  L    D     
Sbjct: 138 KGYRFSTYAVYWVKNSILRAQTRLGHIVRVPYNVAAQKM--TIQRKRAQLSLELDREPTH 195

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           E+V+    +L +       +    A   SLNA    + +         + D D  E    
Sbjct: 196 EEVI---TELKMDSRRYFEVLRTGAPRRSLNARSKVTGEE----LIHSISDPDENEAQYY 248

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEA 274
                   R  +   +  L P+E  I   R   +     +   +     +SRE VR+ E 
Sbjct: 249 NA--GAQLRLGMDDVLDSLKPKESLIIRQRYGLDGKGERSFTEIGRNLNLSREMVRKYEI 306

Query: 275 RAFKKVQESIQ 285
           R   K++   +
Sbjct: 307 RGMMKLKHPTR 317


>gi|118134194|gb|ABK61238.1| RNA polymerase sigma-E factor [Clostridium novyi NT]
          Length = 230

 Score =  130 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 61/264 (23%), Positives = 110/264 (41%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE  L  + R  GD S    L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 28  PPLSKEEEENLVNKIR-AGDDSVRTILIERNLRLVVYIARKFENSGILVEDLISVGTIGL 86

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FDPE+  +LATY+   I+  +  Y+ R+                    ++K   
Sbjct: 87  IKAVNTFDPEKKIKLATYASRCIENEILMYLRRN-------------------NKVKAE- 126

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                            ++  E LN      D N     D L  
Sbjct: 127 ---------------------------------ISFYEPLNT---DWDGNKLLLSDILGT 150

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           ++D    ++ ++ +    + +L  +M  L+ RE+ I + R     +   T + ++    +
Sbjct: 151 ENDMVYNLIEDEVD----KQLLFIAMRKLSDREKEIIKLRFGLTGKGEKTQKQVADLLGI 206

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++ I K V
Sbjct: 207 SQSYISRLEKRIIKRLKKEISKMV 230


>gi|152967736|ref|YP_001363520.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Kineococcus
           radiotolerans SRS30216]
 gi|151362253|gb|ABS05256.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Kineococcus
           radiotolerans SRS30216]
          Length = 326

 Score =  130 bits (328), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 46/239 (19%), Positives = 96/239 (40%), Gaps = 19/239 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L   HL L   +A  + G G P  ++V    IGL++A+ +FDP RG     Y++  +
Sbjct: 106 REELTRRHLPLADHLAARFLGRGEPQDDLVQVATIGLLKALDRFDPSRGVPFGAYAVPTM 165

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +       +++      +R+    R L    +A+T    +   V  +A++    
Sbjct: 166 LGEIKRHFRDRGWAMRVP-----RRIQEAGRALGDAREALTHELGRAPTVAELAERTGYD 220

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             +V+ +        +L         + +     L  D D  + V          R  L 
Sbjct: 221 PEDVVDVLESANAYSTL----PLDTGSPTSLVASLGADDDALQNV--------ENREALR 268

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
             ++ L  RERRI   R ++   ++   +++E  +S+  V ++  R   +++E +  + 
Sbjct: 269 PLLAGLPARERRILALRFVRG--MSQSQIAAEVGISQMHVSRLLTRTLAQLREGLGDEA 325


>gi|307717634|gb|ADN88870.1| RNA polymerase sigma-37 factor [Listeria seeligeri]
          Length = 220

 Score =  130 bits (327), Expect = 2e-28,   Method: Composition-based stats.
 Identities = 53/237 (22%), Positives = 103/237 (43%), Gaps = 24/237 (10%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV ++  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQENGDQDAQYNLVVNYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G     +++  I   ++ ++      V +     +        ++K  ++ +T    
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQ 116

Query: 155 KPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +    
Sbjct: 117 SSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTD 173

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
           DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++S
Sbjct: 174 DGF--------ERVNQRMLLEKVLPVLDEREQKILQYTFIEN--RSQKETGELLDIS 220


>gi|188586278|ref|YP_001917823.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|179350965|gb|ACB85235.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 253

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 46/250 (18%), Positives = 105/250 (42%), Gaps = 15/250 (6%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             L K++++ GD  A   ++  ++ LV  +   + G G+   ++   G +GL++A+ KFD
Sbjct: 16  IELIKKWQQKGDREARKIIIEENINLVKSVVKRFVGSGIEEEDLTQLGLMGLIKAIDKFD 75

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +  R +TY++  I   ++ ++      +K+      + L     R K   + +T    
Sbjct: 76  YRKEVRFSTYAVPLIIGEIKTFLRDD-HPIKVS-----RNLKELFNRSKEVKRWLTLKLR 129

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +   +  +A +L VS+ E+ +         SL+  ++    + S+ +  +    D     
Sbjct: 130 REPTISEVADELEVSKEELATAEEANQELISLDKPVSDEHNHESE-KALIDTIPDNSFDA 188

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
            I  E        +   +  L+ ++RR+   R   E   + +       +S+ +V ++E 
Sbjct: 189 KIHNELT------IQELLKKLDQKKRRLIVLRYFLE--KSQQETGVILGMSQVQVSRMER 240

Query: 275 RAFKKVQESI 284
           R    +Q  +
Sbjct: 241 RILNNLQRDL 250


>gi|229131899|ref|ZP_04260765.1| RNA polymerase sigma-B factor [Bacillus cereus BDRD-ST196]
 gi|228651574|gb|EEL07543.1| RNA polymerase sigma-B factor [Bacillus cereus BDRD-ST196]
          Length = 224

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 47/233 (20%), Positives = 106/233 (45%), Gaps = 16/233 (6%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           +V  +  LV  IA  Y   G    ++V  G +GL+ A++++D   G     +++  I   
Sbjct: 1   MVNHYKNLVYSIAYRYSKGGPMHEDIVQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGE 60

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +++Y+      V +      +R+     ++K  ++ +TD+  +  +++ IA  L +SE E
Sbjct: 61  IKKYLRDKTWGVHVP-----RRIKDLGGKIKLAIEELTDHLQRSPKIIEIANHLGLSEEE 115

Query: 173 VISMN--CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           V+ +          SL+ ++ +S   SS  +   V +       + +  E+  RR +L  
Sbjct: 116 VLEIMDAKNNYQVSSLDDVVENSSDGSSVARIESVGE-------VEQGYEQTERRLVLKD 168

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +VLN  E+ +      +   +  ++      +S+  V +I+ +A  K++++
Sbjct: 169 IFNVLNDTEKSVIHYIFGEN--LNQKDTGERLGISQMHVSRIKRQAISKLKQA 219


>gi|154484618|ref|ZP_02027066.1| hypothetical protein EUBVEN_02334 [Eubacterium ventriosum ATCC
           27560]
 gi|149734466|gb|EDM50383.1| hypothetical protein EUBVEN_02334 [Eubacterium ventriosum ATCC
           27560]
          Length = 237

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 44/246 (17%), Positives = 106/246 (43%), Gaps = 18/246 (7%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L  R  + GD  A  +++  +  L+  I   +   G    ++   G IG+++A+ +FD E
Sbjct: 6   LINRAHQ-GDKLARDKILIENTGLIWSIVRRFLNRGHEGEDLFQIGCIGMLKAIDRFDTE 64

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
                +TY++  I   ++ +I     +VKI     + ++     ++    +   +   + 
Sbjct: 65  FDVAFSTYAVPMIAGEIRRFIRDDG-IVKISRKIKENQM-----KIMHQREIYINEKKQE 118

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
             +  + K  ++++ E++         ES++  + S D ++    D    D + +E VL 
Sbjct: 119 PTIEELEKVCDLTKEEIVMAMDASRNVESIDKEMYSKD-SAYTLMDLAEDDTNIEETVL- 176

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
                   + M+ + M +L  +ER+I   R  +    T   ++ E  +++ +V ++E + 
Sbjct: 177 -------NKIMVQQLMDMLESKERKIINLRYFKN--KTQSQVAKEMGMTQVQVSRLEKKI 227

Query: 277 FKKVQE 282
              ++ 
Sbjct: 228 LNSMRN 233


>gi|51893096|ref|YP_075787.1| sporulation sigma factor SigK [Symbiobacterium thermophilum IAM
           14863]
 gi|51856785|dbj|BAD40943.1| RNA polymerase sigma factor similar to B. subtilis SigK
           [Symbiobacterium thermophilum IAM 14863]
          Length = 236

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 63/276 (22%), Positives = 104/276 (37%), Gaps = 66/276 (23%)

Query: 9   IVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           IV   + L+ ++      P  L ++EE     R + +GD  A   L+  +LRLV  I   
Sbjct: 12  IVRSMLLLAGFVANSGTFPQPLSEEEEAKYLSRLQ-NGDEEARAVLIERNLRLVAHIVKK 70

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           +   G  + +++S G +GL++A+  F PERG RLATY+   I+  +              
Sbjct: 71  FDNTGEDVDDLISIGTVGLIKAIGTFKPERGTRLATYAARCIENEI-------------- 116

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
                     +LR LK                                   R+ G+ SL 
Sbjct: 117 --------LMHLRSLK-----------------------------------RVRGEVSLY 133

Query: 188 ALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
             I    + N     D L  D D    ++ ++ +    R  L +    L  +ER++ E R
Sbjct: 134 DPIGVDREGNEITLIDVLGSDPDVVPDLVGKRLDESKLREKLKK----LGGKERQVLELR 189

Query: 247 RL--QENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                    T   ++    +SR  V +IE +A  K+
Sbjct: 190 YGIAGGPRKTQREIARMLGISRSYVSRIEKKAVMKL 225


>gi|310643126|ref|YP_003947884.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
 gi|309248076|gb|ADO57643.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
          Length = 233

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 57/275 (20%), Positives = 107/275 (38%), Gaps = 64/275 (23%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+        L ++EE    K + E G+  + + L+  +LRLV  I   +   G  +
Sbjct: 18  LVSYVKNNAFPQPLTEKEEARHLKLFAE-GNAHSRNTLIEHNLRLVAHIVKKFDNTGEDL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++S G IGL++A++ F   +G +LAT++   I+  +                      
Sbjct: 77  EDLISIGTIGLIKAIESFQTGKGTKLATFAARCIENEI---------------------- 114

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
             +LR LK                            + +S++  +  D          + 
Sbjct: 115 LMHLRSLKKT-------------------------RKDVSLHDPIGTD---------KEG 140

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE---NP 252
           N     D L  + D     +++K + K  ++ + R++ +L+ RE+ +   R   E     
Sbjct: 141 NEITLIDILGSEADD----IVDKVQLKIEKSKIYRNLDILDEREKEVVIGRFGLEAGGEE 196

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            T   ++ E  +SR  V +IE RA  K+     KQ
Sbjct: 197 RTQREIARELGISRSYVSRIEKRALMKLYHEFYKQ 231


>gi|300854412|ref|YP_003779396.1| putative RNA polymerase sigma-K factor [Clostridium ljungdahlii DSM
           13528]
 gi|300434527|gb|ADK14294.1| predicted RNA polymerase sigma-K factor precursor [Clostridium
           ljungdahlii DSM 13528]
          Length = 233

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 63/280 (22%), Positives = 108/280 (38%), Gaps = 65/280 (23%)

Query: 9   IVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           I+   + ++ Y+      P  L  +EE    K+  E GDL A   LV  +LRLV  I   
Sbjct: 10  ILGNVVFMTAYVTNSSSFPQPLSDEEEEYYLKKL-EQGDLLAKSILVERNLRLVAHIVKK 68

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y      + E++S G +GL++A+  FD  +G RLATY+   I+  +   I  +       
Sbjct: 69  YSYPSKEVDELISIGTVGLIKAIDSFDMSKGTRLATYAAKCIENEILMLIRNN------- 121

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
                       ++++                              + +   +  D    
Sbjct: 122 ------------KKIRNE----------------------------VYLEDPIGVD---- 137

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV-LNPRERRIFEAR 246
                 + N     D L  D    E  +IE  E+K +   L   ++  L+ RE+ + E R
Sbjct: 138 -----KEGNEISLMDVLSSD----EGSIIEIVEQKLQVKKLYSKINTCLSEREKSVVEMR 188

Query: 247 R--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              L+  P T   ++    +SR  V +IE +A KK+ + +
Sbjct: 189 YGLLEGKPRTQREIAKLLGISRSYVSRIEKKALKKLYKEL 228


>gi|323705419|ref|ZP_08116994.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
 gi|323535321|gb|EGB25097.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
          Length = 246

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 44/254 (17%), Positives = 106/254 (41%), Gaps = 19/254 (7%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAV 90
           E  L  +Y +  D S+   ++  ++ LV  I               +++S+G IGL+ AV
Sbjct: 5   EQDLWDKYEKQKDGSSKEDIIIKYMPLVKHIVKRICLSELSKEDTDDLISQGMIGLIDAV 64

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
            K+D  +G +  TY+   IK  + +Y+ +   +         + L    + ++  ++ + 
Sbjct: 65  NKYDVSKGVKFETYASIRIKGEIIDYLRKKDWI--------PRSLKKRYKSIEKTIEQLE 116

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
               +   +  I +   +S+++V+     +      NA   SS     +    +    D 
Sbjct: 117 QEYKREPTIEEIMEATKLSKNDVLKTLSYM------NAGYISSLDEVIENNLKITSITDN 170

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
           +      +    + +  +++++  L  +ER I      ++  +  + +S    ++  R+ 
Sbjct: 171 EVTNPENEVMMFDLKQNISKAIDTLQEKERLIISLYYYED--LNYKEISKIMGLTESRIS 228

Query: 271 QIEARAFKKVQESI 284
           QI ++A KK++E +
Sbjct: 229 QIHSKAIKKLKEKL 242


>gi|325844829|ref|ZP_08168281.1| RNA polymerase sigma-K factor [Turicibacter sp. HGF1]
 gi|325489016|gb|EGC91404.1| RNA polymerase sigma-K factor [Turicibacter sp. HGF1]
          Length = 229

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 53/262 (20%), Positives = 103/262 (39%), Gaps = 65/262 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  ++EE+ L      +GD +A  +L+  +LRLV  I   Y+       +++S G IGL
Sbjct: 29  PLSPEEEEHYLT--LMANGDKNAREKLIEHNLRLVAHIVKKYQNQTDDKEDLISIGTIGL 86

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+  F P++G +LATY+   I   +                     LF + ++++   
Sbjct: 87  IKAIDSFSPDKGTKLATYAARCIDNEILM-------------------LFRSTKKMRND- 126

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                      +S+   +             + N     D +  
Sbjct: 127 ---------------------------VSLYDPIG---------YDKEGNEICLIDVVKD 150

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEV 264
           ++     ++I++         + +++  L  RER I   R   EN    T + ++  + +
Sbjct: 151 ENKDLNDIIIQQLAF----EKIEKNLKSLTQRERDIIVRRFGLENHEEETQQEIAKSYGI 206

Query: 265 SRERVRQIEARAFKKV-QESIQ 285
           SR  V +IE RA  K+ +E I+
Sbjct: 207 SRSYVSRIEKRALMKLYREFIK 228


>gi|162139704|ref|YP_878335.2| sporulation sigma factor SigE [Clostridium novyi NT]
          Length = 235

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 61/264 (23%), Positives = 110/264 (41%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE  L  + R  GD S    L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 33  PPLSKEEEENLVNKIR-AGDDSVRTILIERNLRLVVYIARKFENSGILVEDLISVGTIGL 91

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FDPE+  +LATY+   I+  +  Y+ R+                    ++K   
Sbjct: 92  IKAVNTFDPEKKIKLATYASRCIENEILMYLRRN-------------------NKVKAE- 131

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                            ++  E LN      D N     D L  
Sbjct: 132 ---------------------------------ISFYEPLNT---DWDGNKLLLSDILGT 155

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           ++D    ++ ++ +    + +L  +M  L+ RE+ I + R     +   T + ++    +
Sbjct: 156 ENDMVYNLIEDEVD----KQLLFIAMRKLSDREKEIIKLRFGLTGKGEKTQKQVADLLGI 211

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++ I K V
Sbjct: 212 SQSYISRLEKRIIKRLKKEISKMV 235


>gi|138896107|ref|YP_001126560.1| sporulation sigma factor SigK [Geobacillus thermodenitrificans
           NG80-2]
 gi|196249000|ref|ZP_03147700.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
 gi|134267620|gb|ABO67815.1| RNA polymerase sigma-K factor [Geobacillus thermodenitrificans
           NG80-2]
 gi|196211876|gb|EDY06635.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
          Length = 237

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 60/282 (21%), Positives = 103/282 (36%), Gaps = 65/282 (23%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI        L  +EE    +   + GD  A +RL+  +LRLV  I   +   G  +
Sbjct: 18  LVSYIKNNAFPQPLSPKEEEKYLELMAK-GDEQARNRLIEHNLRLVAHIVKKFENTGEEV 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++S G IGL++A++ + P +G +LATY+   I+  +                      
Sbjct: 77  EDLISIGTIGLIKAIESYSPNKGTKLATYAARCIENEI---------------------- 114

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS-D 194
             +LR LK                                       D SL+  I    +
Sbjct: 115 LMHLRSLKKT-----------------------------------RKDVSLHEPIGQDKE 139

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--P 252
            N     D L  +     Q ++++ +       + + +SVL+ RE+ +   R        
Sbjct: 140 GNEISLLDILKSEG----QDIVDEIQLNMELEQVKKYISVLDEREKEVIVNRFGLGRQRE 195

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSP 294
            T   ++ E  +SR  V +IE RA  K+     +Q +    P
Sbjct: 196 KTQREIAKELGISRSYVSRIEKRALMKMFHEFYRQEKEKRRP 237


>gi|291436144|ref|ZP_06575534.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291339039|gb|EFE65995.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 282

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 47/243 (19%), Positives = 105/243 (43%), Gaps = 19/243 (7%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +    +V + L +  ++A  +R  G    ++     +GL++AV ++DPE G    +Y++ 
Sbjct: 51  ALRGEIVEAWLPMADRLAGRFRSRGESFDDLRQVAALGLVKAVDRYDPELGNAFESYAVP 110

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT-DNNLKPEQVVAIAKKL 166
            I   ++ +       + +     + R      R++   Q ++   + +P  V  IA+  
Sbjct: 111 TITGEIKRHFRDHMWTLHVPRRVQELR-----NRVRSASQDLSLSGSGRPPTVAEIAEHA 165

Query: 167 NVSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           ++SE +V +    L      SL+A + S D   S   D L       + V+         
Sbjct: 166 DLSEEDVRTGQGALDSFTALSLDAELTSGDDGYS-LGDTLGAPDPALDTVV--------D 216

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  +   ++ L  RE+ I   R   +  +T  ++++E  +S+  V ++ +R   +++E +
Sbjct: 217 REAVRERLAALPEREQAILYMRFFGD--MTQSSIAAELGISQMHVSRLISRCCGRIREQV 274

Query: 285 QKQ 287
            + 
Sbjct: 275 MRD 277


>gi|160895319|ref|ZP_02076090.1| hypothetical protein CLOL250_02878 [Clostridium sp. L2-50]
 gi|156863012|gb|EDO56443.1| hypothetical protein CLOL250_02878 [Clostridium sp. L2-50]
          Length = 225

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 41/230 (17%), Positives = 91/230 (39%), Gaps = 28/230 (12%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            ++GD  A  +L+  +L LV  +A  + G G  I ++   G IGL++ + KF  E   + 
Sbjct: 11  AKNGDDHAKEKLIEQNLGLVWSVARRFTGRGYDIEDLFQIGCIGLIKCIDKFSFEYDVKF 70

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY++  I+  ++ ++ R    +K+  +  +  +     +++ + Q I        ++  
Sbjct: 71  STYAVPLIQGEIRRFL-RDSGAIKVSRSLKEMNM-----KVEQYRQKIKKEKGYEPEITE 124

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           IA  L+    +++         ESL+     S                       E  + 
Sbjct: 125 IAAALSFDAGDIVMAMEASMEIESLDTPGVLSKTE--------------------EYSQD 164

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
                 L++ +  L+P E+ +   R  ++   T         +S+ +V +
Sbjct: 165 IVDHITLSQLLDRLDPDEQMLIRLRYFED--RTQTETGKALGLSQVQVSR 212


>gi|160914280|ref|ZP_02076501.1| hypothetical protein EUBDOL_00290 [Eubacterium dolichum DSM 3991]
 gi|158433907|gb|EDP12196.1| hypothetical protein EUBDOL_00290 [Eubacterium dolichum DSM 3991]
          Length = 233

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 64/271 (23%), Positives = 114/271 (42%), Gaps = 63/271 (23%)

Query: 19  YIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           YI     +P  LEK+EE   A    EHGD  A + L+  +LRLVV IA  Y    + + +
Sbjct: 22  YIQGSDVLPKPLEKEEEQA-ALIALEHGDEEARNTLIEHNLRLVVYIAKRYETNPIFMED 80

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++S G+IGL++AV  F   +  +L TY+   I+  +  ++ +                  
Sbjct: 81  LISIGSIGLIKAVNTFKRNKNIKLVTYASRCIENEILMFLRKKSR--------------- 125

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
                                     +KL VS  E ++++                D N 
Sbjct: 126 --------------------------RKLEVSFDEPLNIDY---------------DGNE 144

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE-NPVTLE 256
               D L  D D    V+ ++ ER+  +  L ++M  L  RER+I + R   E   +T +
Sbjct: 145 LLLSDILGTDDD----VVTKQFEREENKRELLKAMRGLKDRERQILQMRYGIEHEELTQK 200

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +++    +S+  + ++E R   K++  +++Q
Sbjct: 201 DIAKRLGISQSYISRLEKRIIHKLKLQMKQQ 231


>gi|161898885|gb|ABX80432.1| SigB [Listeria monocytogenes]
          Length = 217

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 52/231 (22%), Positives = 100/231 (43%), Gaps = 24/231 (10%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D   G  
Sbjct: 5   YQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKS 64

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
              +++  I   ++ ++      V +     +        ++K  ++ +T       Q+ 
Sbjct: 65  FEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQSSPQIS 119

Query: 161 AIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            IA  + V+E EV+           L+ D S+ A    SD ++    D +    DG    
Sbjct: 120 DIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTDDGF--- 173

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
                ER N+R +L + + VL+ RE++I +   ++    + +      ++S
Sbjct: 174 -----ERVNQRMLLEKVLPVLDEREQKILQFTFIEN--RSQKETGELLDIS 217


>gi|239944630|ref|ZP_04696567.1| RNA polymerase sigma factor WhiG [Streptomyces roseosporus NRRL
           15998]
 gi|239991094|ref|ZP_04711758.1| RNA polymerase sigma factor WhiG [Streptomyces roseosporus NRRL
           11379]
          Length = 247

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 47/252 (18%), Positives = 104/252 (41%), Gaps = 16/252 (6%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFD 94
            + Y+  GD     +L+  +  LV  +A          +  ++ VS G  GL+ A++KFD
Sbjct: 2   WRSYKTTGDERLREQLILHYSPLVKYVAGRVSVGLPSNVEQADFVSSGVFGLIDAIEKFD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
            ER  +  TY++  I+ AM + + R+   +        + +      L+   +       
Sbjct: 62  IERAIKFETYAITRIRGAMIDEL-RALDWIPRSVRQKARNVERAYATLEAQFR------- 113

Query: 155 KPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +      +A ++ ++  E+ ++     LA   +L  L++   +   +    +    D   
Sbjct: 114 RTPSEAEVASEMGIALEELHAVFSQLSLANVVALEELLHVGGEGGDRL-SLMDTLEDTAA 172

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
              +E  E +  R +L R+++ L  RE+ +          +TL  + +   V+  RV QI
Sbjct: 173 DNPVEVAEDRELRRLLARAINTLPDREKTVVTLYYY--EGLTLAEIGNVLGVTESRVSQI 230

Query: 273 EARAFKKVQESI 284
             ++  +++  +
Sbjct: 231 HTKSVLQLRAKL 242


>gi|291542453|emb|CBL15563.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Ruminococcus bromii
           L2-63]
          Length = 231

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 53/266 (19%), Positives = 101/266 (37%), Gaps = 66/266 (24%)

Query: 24  RKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
              P  L +++E    ++   +GD++A + LV  +LRLV  I   Y G      ++VS G
Sbjct: 23  GSFPKPLTEKQERECLEK-SANGDIAARNMLVEHNLRLVAHIIKKYYGTQSEQDDLVSIG 81

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            IGL++A+  FD  +  +L++Y+   I+  +                        + R  
Sbjct: 82  TIGLIKAINTFDMNKNIKLSSYASRCIENEI----------------------LMHFRNA 119

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
           K   Q I+ N                                    +    D N     D
Sbjct: 120 KKSAQDISLNE----------------------------------TIDTDKDGNPLTLLD 145

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQENP--VTLENLS 259
            +  D +     +I+  + K     L + +   LN RE++I   R   +    +T ++++
Sbjct: 146 IMSVDDN-----IIDNLDLKLNSKKLGQFIKEELNEREQKIIVLRYGLDGKEALTQKSVA 200

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQ 285
               +SR  V +IE +A K++++  +
Sbjct: 201 KMLGISRSYVSRIETKALKQLRKRFE 226


>gi|226323679|ref|ZP_03799197.1| hypothetical protein COPCOM_01454 [Coprococcus comes ATCC 27758]
 gi|225207863|gb|EEG90217.1| hypothetical protein COPCOM_01454 [Coprococcus comes ATCC 27758]
          Length = 247

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 55/272 (20%), Positives = 105/272 (38%), Gaps = 65/272 (23%)

Query: 18  RYIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
            YI     +P+ L  +EE           D      L+  +LRLVV IA  +   G+ + 
Sbjct: 31  HYIGGTDILPLPLSSEEEGHAISLLGGGQDEEGKKLLIEHNLRLVVYIAKKFDNTGVGVE 90

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++S G IGL++A+  F+PE+  +LATY+   I+  +  Y+ R+                
Sbjct: 91  DLISIGTIGLIKAINTFNPEKNIKLATYASRCIENEILMYLRRNNKT------------- 137

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
                                       KL VS  E ++++                D N
Sbjct: 138 ----------------------------KLEVSIDEPLNVD---------------WDGN 154

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP---- 252
                D L  + D   + +  + E K    +L +++  L+ RER I + R     P    
Sbjct: 155 ELLLSDILGTEEDTIYRDMETEAEHK----LLGKAIGRLSNRERVIVQMRFGLGTPDGEE 210

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            T + ++    +S+  + ++E +  ++++  +
Sbjct: 211 KTQKEVADLLGISQSYISRLEKKIMQRLRREM 242


>gi|251798285|ref|YP_003013016.1| sporulation sigma factor SigK [Paenibacillus sp. JDR-2]
 gi|247545911|gb|ACT02930.1| RNA polymerase, sigma 28 subunit, SigK [Paenibacillus sp. JDR-2]
          Length = 232

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 55/275 (20%), Positives = 106/275 (38%), Gaps = 66/275 (24%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+        L ++EE    +   E G+  + + L+  +LRLV  I   +   G  +
Sbjct: 17  LVSYVKNNAFPQPLHEEEEMKHLQLMAE-GNAHSRNLLIEHNLRLVAHIVKKFDNTGEDL 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++S G IGL++A++ F   +G +LAT++   I+  +                      
Sbjct: 76  EDLISIGTIGLIKAIESFQTGKGTKLATFAARCIENEI---------------------- 113

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS-D 194
             +LR LK   +                                   D SL+  I +  +
Sbjct: 114 LMHLRSLKKTRK-----------------------------------DVSLHDPIGTDKE 138

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE---N 251
            N     D L  + D     ++++ + K  ++ + R++ +L+ RE+ +   R   +   +
Sbjct: 139 GNEITLIDILGTEADD----VVDRVQLKIEKSKIYRNLDILDEREQEVIRGRFGLDHGGD 194

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             T   ++ E  +SR  V +IE RA  K+     K
Sbjct: 195 ERTQREIAKELGISRSYVSRIEKRALMKLYHEFYK 229


>gi|284992377|ref|YP_003410931.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geodermatophilus
           obscurus DSM 43160]
 gi|284065622|gb|ADB76560.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geodermatophilus
           obscurus DSM 43160]
          Length = 266

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 50/255 (19%), Positives = 104/255 (40%), Gaps = 20/255 (7%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVVSEGNIGLMQAVK 91
            L   Y          RL+  +  LV  +A    G GLP     +++VS G  GL+ A+ 
Sbjct: 22  ELWAGYVADRAPELRDRLILHYAPLVKYVAGR-VGSGLPAHVEQADLVSYGTFGLIDAIT 80

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           ++ P R  +  +Y+M  I+ A+ + + RS   +        ++    +  L+  LQ    
Sbjct: 81  RYQPSREVKFESYAMARIRGAIIDEL-RSTDWIPRSVRMKARQFERTVALLESRLQ---- 135

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHD 209
              +      +A ++++   +V     +L+     +L+ L++  +  + +  D L     
Sbjct: 136 ---RSPSEEEVAAEMDMDVEDVRKFLGQLSLVNVVALDELLSDDEGGAPRLVDTLQDTSA 192

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
              Q + E  E    R +L R++  L  RE+ +          +TL ++     V+  R+
Sbjct: 193 LDPQAMAEHSEA---RQLLARAVEQLPEREKVVVSLYYF--EGLTLADIGRVLGVTESRI 247

Query: 270 RQIEARAFKKVQESI 284
            Q+  +A   ++  +
Sbjct: 248 CQLHTKAVLHLRTKL 262


>gi|255525679|ref|ZP_05392612.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium carboxidivorans
           P7]
 gi|296185437|ref|ZP_06853847.1| RNA polymerase sigma-E factor [Clostridium carboxidivorans P7]
 gi|255510665|gb|EET86972.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium carboxidivorans
           P7]
 gi|296050271|gb|EFG89695.1| RNA polymerase sigma-E factor [Clostridium carboxidivorans P7]
          Length = 235

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 61/265 (23%), Positives = 104/265 (39%), Gaps = 65/265 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE  L  +  + G+      L+  +LRLVV IA  +   G+ + ++VS G IGL
Sbjct: 33  PPLSKKEEDDLVSKL-DGGEEKVRSTLIERNLRLVVYIARKFENTGVNVEDLVSVGTIGL 91

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FDP +  +LATY+   I+  +                         LRR     
Sbjct: 92  IKAVNTFDPSKKIKLATYASRCIENEI----------------------LMYLRR----- 124

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS-DKNSSQWQDWLV 205
                                         N ++  + S    +N   D N     D L 
Sbjct: 125 ------------------------------NSKVKAEISFYEPLNIDWDGNELLLSDILG 154

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFE 263
            D+D    V+    E +  + +L  +M  LN RE+ I   R     +   T + ++    
Sbjct: 155 TDND----VVYNLIEDEVDKQLLMVAMKKLNDREKEIVNLRFGLNGQGEKTQKEVADMLG 210

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           +S+  + ++E R  K++++ I K +
Sbjct: 211 ISQSYISRLEKRIIKRLKKEINKML 235


>gi|307717612|gb|ADN88859.1| RNA polymerase sigma-37 factor [Listeria welshimeri]
          Length = 220

 Score =  130 bits (327), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 53/237 (22%), Positives = 101/237 (42%), Gaps = 24/237 (10%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G     +++  I   ++ ++      V +     +        ++K  ++ +T    
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQ 116

Query: 155 KPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +    
Sbjct: 117 SSPQISDIAYFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTD 173

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
           DG         ER N+R +L + + VL+ RE+ I +   ++    + +      ++S
Sbjct: 174 DGF--------ERVNQRMLLEKVLPVLDEREQMILQYTFIEN--RSQKETGELLDIS 220


>gi|72161738|ref|YP_289395.1| RNA polymerase sigma factor [Thermobifida fusca YX]
 gi|71915470|gb|AAZ55372.1| RNA polymerase sigma factor [Thermobifida fusca YX]
          Length = 308

 Score =  129 bits (326), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 50/261 (19%), Positives = 99/261 (37%), Gaps = 22/261 (8%)

Query: 30  EKQEEYVLAKRYREHGDLS----AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
             Q E +LA       D          LV  ++ LV + A  YR  G P+ ++   G +G
Sbjct: 62  TGQAERLLAALADHQDDEETSARIRDELVRLYMPLVRREARRYRNRGEPMDDLYQVGMLG 121

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           LM+A+K FDP  G     Y +  +   ++ +   +   V++     ++R       L   
Sbjct: 122 LMKAIKGFDPSYGKPFVAYLLPMVTGELKRHFRDTTWAVRVPRVHQERR-----SELNRV 176

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDW 203
           +   T  + +      IA  L +     I +    +     SL+     ++  S+     
Sbjct: 177 IAEFTQKHGRTPTTREIADALEMDLESAIELIDASSAYSALSLDTPFGDTEDESALGDTL 236

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
            V D D          E    +  L  ++  L  RERR+   R       T   ++++  
Sbjct: 237 GVADGD---------LETVVDKTSLKDALDRLPERERRVILLRFFGN--KTQSEIAADVG 285

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S+  V ++ ++  ++++  +
Sbjct: 286 LSQMHVSRLLSQTLRQLRREL 306


>gi|307717594|gb|ADN88850.1| RNA polymerase sigma-37 factor [Listeria innocua]
 gi|307717604|gb|ADN88855.1| RNA polymerase sigma-37 factor [Listeria innocua]
 gi|307717614|gb|ADN88860.1| RNA polymerase sigma-37 factor [Listeria innocua]
 gi|307717620|gb|ADN88863.1| RNA polymerase sigma-37 factor [Listeria innocua]
 gi|307717622|gb|ADN88864.1| RNA polymerase sigma-37 factor [Listeria innocua]
          Length = 220

 Score =  129 bits (326), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 53/237 (22%), Positives = 101/237 (42%), Gaps = 24/237 (10%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQEDGDEDAQYNLVIHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G     +++  I   ++ ++      V +     +        ++K  ++ +T    
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQ 116

Query: 155 KPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +    
Sbjct: 117 SSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTD 173

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
           DG         ER N+R +L + + VL+ RE++I +   ++    + +      ++S
Sbjct: 174 DGF--------ERVNQRMLLEKVLPVLDEREQKILQYTFIEN--RSQKETGELLDIS 220


>gi|308070013|ref|YP_003871618.1| RNA polymerase sigma-28 factor precursor [Paenibacillus polymyxa
           E681]
 gi|305859292|gb|ADM71080.1| RNA polymerase sigma-28 factor precursor [Paenibacillus polymyxa
           E681]
          Length = 233

 Score =  129 bits (326), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 57/275 (20%), Positives = 107/275 (38%), Gaps = 64/275 (23%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+        L ++EE    K + E G+  + + L+  +LRLV  I   +   G  +
Sbjct: 18  LVSYVKNNAFPQPLTEKEEARHLKLFAE-GNAHSRNTLIEHNLRLVAHIVKKFDNTGEDL 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++S G IGL++A++ F   +G +LAT++   I+  +                      
Sbjct: 77  EDLISIGTIGLIKAIESFQTGKGTKLATFAARCIENEI---------------------- 114

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
             +LR LK                            + +S++  +  D          + 
Sbjct: 115 LMHLRSLKKT-------------------------RKDVSLHDPIGTD---------KEG 140

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE---NP 252
           N     D L  + D     +++K + K  ++ + R++ +L+ RE+ +   R   E     
Sbjct: 141 NEITLIDILGTEADD----IVDKVQLKIEKSKIYRNLDILDEREKEVVIGRFGLEAGGEE 196

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            T   ++ E  +SR  V +IE RA  K+     KQ
Sbjct: 197 RTQREIARELGISRSYVSRIEKRALMKLYHEFYKQ 231


>gi|311069177|ref|YP_003974100.1| sporulation sigma factor SigK [Bacillus atrophaeus 1942]
 gi|310869694|gb|ADP33169.1| sporulation sigma factor SigK [Bacillus atrophaeus 1942]
          Length = 242

 Score =  129 bits (326), Expect = 3e-28,   Method: Composition-based stats.
 Identities = 51/279 (18%), Positives = 98/279 (35%), Gaps = 63/279 (22%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
             +  +V   + L  Y+        L   EE    +   + GD  A + L+  +LRLV  
Sbjct: 7   TALGFVVKELVFLVSYVKNNAFPQPLSGSEEKKYLELMAK-GDEHARNMLIEHNLRLVAH 65

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           I   +   G    +++S G IGL++ ++ +   +G +LATY+   I+  +          
Sbjct: 66  IVKKFENTGEDAEDLISIGTIGLIKGIESYSAGKGTKLATYAARCIENEI---------- 115

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
                         +LR LK                                       D
Sbjct: 116 ------------LMHLRALKKT-----------------------------------KKD 128

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SL+  I    + +   +  L+     + + +I+  +       + + + +L+ RE+ + 
Sbjct: 129 VSLHDPIGQDKEGN---EISLIDVLKSESEDVIDTIQLNMELEKVKKYIDILDDREKEVI 185

Query: 244 EARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             R   +     T   ++ E  +SR  V +IE RA  K+
Sbjct: 186 VGRFGLDLKKEKTQREIAKELGISRSYVSRIEKRALMKM 224


>gi|55274907|gb|AAV49255.1| RNA polymerase subunit sigma-38 [Escherichia albertii]
          Length = 189

 Score =  129 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 48/199 (24%), Positives = 90/199 (45%), Gaps = 12/199 (6%)

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +
Sbjct: 1   ARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTI 60

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           ++      K L   LR  +     ++           IA++L+    +V  M        
Sbjct: 61  RLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERIT 115

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           S++  +    +     +  L    D +E    +  +  + +  + + +  LN ++R +  
Sbjct: 116 SVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVLA 170

Query: 245 ARR--LQENPVTLENLSSE 261
            R   L     TLE++  E
Sbjct: 171 RRFGLLGYEAATLEDVGRE 189


>gi|256751991|ref|ZP_05492860.1| RNA polymerase, sigma 28 subunit, SigE [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|256749101|gb|EEU62136.1| RNA polymerase, sigma 28 subunit, SigE [Thermoanaerobacter
           ethanolicus CCSD1]
          Length = 236

 Score =  129 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 54/247 (21%), Positives = 98/247 (39%), Gaps = 63/247 (25%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L  +EE  L  +  E GD  A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 39  PPLSVEEEMYLISKM-EKGDNEAKTVLIERNLRLVVYIAKKFENTGVGIEDLISIGTIGL 97

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+  F+P++  +LATY+   I+  +  Y+ R+                          
Sbjct: 98  IKAINTFNPKKKIKLATYASRCIENEILMYLRRNSKT----------------------- 134

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                             KL VS  E ++++                D N     D L  
Sbjct: 135 ------------------KLEVSFEEPLNVD---------------WDGNELLLSDILGT 161

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEV 264
           D++   + + ++ E    + +LT ++  L  RE++I   R         T + ++    +
Sbjct: 162 DNETVYKYIEDEVE----KELLTSALKKLPDREKKIIGLRFGLGGGVEKTQKEVADMLGI 217

Query: 265 SRERVRQ 271
           S+  + +
Sbjct: 218 SQSYISR 224


>gi|256396292|ref|YP_003117856.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Catenulispora acidiphila DSM 44928]
 gi|256362518|gb|ACU76015.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Catenulispora acidiphila DSM 44928]
          Length = 263

 Score =  129 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 40/238 (16%), Positives = 100/238 (42%), Gaps = 17/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              ++  ++     +A  +R  G   +++     +GL++AV  FDP+ G    TY+   I
Sbjct: 38  REFVIGEYMSYARYVAGKFRQRGESQADLEQVAYLGLVKAVDNFDPDYGAAFLTYATPMI 97

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V +     +  L      ++   + +T           IA++L++S
Sbjct: 98  AGEVRRHFRDTTWDVHVPRRVQENALA-----VRAAERELTQQLGHAPSAAQIAERLDLS 152

Query: 170 ESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
             EV       A     SL+  +  +D + +   + +  +  G E V+         R  
Sbjct: 153 ADEVAEAYEASAAHHTASLDVPVAMADGDGASMGELMGDEDPGFELVV--------DREA 204

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L   ++ L+ R++RI   +  +   ++   + +E  VS+ +V ++ ++   ++++ ++
Sbjct: 205 LKPLLAELSTRDKRILLMKFFRN--MSQAQIGAELGVSQMQVSRLLSQILGRLRDQLE 260


>gi|253682372|ref|ZP_04863169.1| RNA polymerase sigma-E factor [Clostridium botulinum D str. 1873]
 gi|253562084|gb|EES91536.1| RNA polymerase sigma-E factor [Clostridium botulinum D str. 1873]
          Length = 235

 Score =  129 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 61/264 (23%), Positives = 110/264 (41%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE  L  + R  GD S    L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 33  PPLSKEEEENLVAKIR-AGDDSVRTILIERNLRLVVYIARKFENSGVLVEDLISVGTIGL 91

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FDPE+  +LATY+   I+  +  Y+ R+                    ++K   
Sbjct: 92  IKAVNTFDPEKKIKLATYASRCIENEILMYLRRN-------------------NKVKAE- 131

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                            ++  E LN      D N     D L  
Sbjct: 132 ---------------------------------ISFYEPLNT---DWDGNKLLLSDILGT 155

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           ++D    ++ ++ +    + +L  +M  L+ RE+ I + R     +   T + ++    +
Sbjct: 156 ENDMVYNLIEDEVD----KQLLFIAMRKLSEREKEIIKLRFGLTGKGEKTQKQVADLLGI 211

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++ I K V
Sbjct: 212 SQSYISRLEKRIIKRLKKEINKMV 235


>gi|167767678|ref|ZP_02439731.1| hypothetical protein CLOSS21_02213 [Clostridium sp. SS2/1]
 gi|167710695|gb|EDS21274.1| hypothetical protein CLOSS21_02213 [Clostridium sp. SS2/1]
 gi|291560812|emb|CBL39612.1| RNA polymerase, sigma 29 subunit, SigE [butyrate-producing
           bacterium SSC/2]
          Length = 240

 Score =  129 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 57/275 (20%), Positives = 111/275 (40%), Gaps = 67/275 (24%)

Query: 18  RYIH--EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
            YI   EI   P+   +E+ +         + +A   L+  +LRLVV IA  +   G+ +
Sbjct: 23  HYIGGTEILPAPLDTAEEQKM-IHMLGTVNEETARSMLIERNLRLVVYIAKKFDNTGIGV 81

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++S G IGL++A+  F+P +  +LATY+   I+  +  Y+ R+               
Sbjct: 82  EDLISIGTIGLIKAINTFNPAKKIKLATYASRCIENEILMYLRRNNKT------------ 129

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
                                        K+ VS  E ++++                D 
Sbjct: 130 -----------------------------KMEVSIDEPLNVD---------------WDG 145

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL----QEN 251
           N     D L  D D    ++ +  E +  + +LTR+M++L  RE+ I E R      +  
Sbjct: 146 NELLLSDILGTDED----IIYKDLEHEVDKKLLTRAMTILTDREKMIIELRFGINQKEGK 201

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             T + ++    +S+  + ++E +  K+++  + K
Sbjct: 202 EKTQKEVADMLGISQSYISRLEKKIIKRLKREMIK 236


>gi|148380498|ref|YP_001255039.1| sporulation sigma factor SigK [Clostridium botulinum A str. ATCC
           3502]
 gi|170759231|ref|YP_001787857.1| sporulation sigma factor SigK [Clostridium botulinum A3 str. Loch
           Maree]
 gi|226949896|ref|YP_002804987.1| RNA polymerase sigma-K factor [Clostridium botulinum A2 str. Kyoto]
 gi|237795980|ref|YP_002863532.1| RNA polymerase sigma-K factor [Clostridium botulinum Ba4 str. 657]
 gi|148289982|emb|CAL84095.1| RNA polymerase sigma-28 factor [Clostridium botulinum A str. ATCC
           3502]
 gi|169406220|gb|ACA54631.1| RNA polymerase sigma-70 factor family [Clostridium botulinum A3
           str. Loch Maree]
 gi|226844119|gb|ACO86785.1| RNA polymerase sigma-K factor [Clostridium botulinum A2 str. Kyoto]
 gi|229261319|gb|ACQ52352.1| RNA polymerase sigma-K factor [Clostridium botulinum Ba4 str. 657]
          Length = 234

 Score =  129 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 60/279 (21%), Positives = 105/279 (37%), Gaps = 63/279 (22%)

Query: 9   IVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++   + L+ Y+      P  L  +EE     R ++ GD  A   LV  +LRLV  I   
Sbjct: 10  VLGSALFLTGYVTGNTSFPKPLSDEEEKYYLDRLKK-GDALAKDILVERNLRLVAHIVKK 68

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y   G  I +++S G +GL++A+  FD  +G RLATY+   I+  +   I  +       
Sbjct: 69  YSYPGKDIDDLISIGTVGLIKAIDSFDNSKGTRLATYAARCIENEILMLIRNNKKT---- 124

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
                                                K  V   + I ++     + SL 
Sbjct: 125 -------------------------------------KGEVYLQDPIGVDKE-GNEISLM 146

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
            +++S              D D   +++  K E K     +    + L  RE+++ + R 
Sbjct: 147 DILSS--------------DEDSIIEIVSTKIEVKKLYGKID---TCLRGREKKVIQMRY 189

Query: 248 L--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                 P T   ++    +SR  V +IE +A KK+ + +
Sbjct: 190 GLKDGRPRTQREIAGILNISRSYVSRIEKKALKKLYKEL 228


>gi|42566462|gb|AAS21043.1| major sigma factor 70 [Deinococcus grandis]
 gi|42566464|gb|AAS21044.1| major sigma factor 70 [Deinococcus proteolyticus]
          Length = 168

 Score =  129 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 42/176 (23%), Positives = 69/176 (39%), Gaps = 10/176 (5%)

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I     +      L R    LQ         E++   
Sbjct: 1   TYATWWIRQAINRAIADQARTIRIPVHMVE--TINKLTRTARQLQQELSREATYEEIAE- 57

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A       ++V  +        SL   I   D+  S + D++    D      +E   + 
Sbjct: 58  AMGPGWDAAKVEEVQKVSQEPVSLETPI--GDEKDSFYGDFIP---DENLDSPVENAAKT 112

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARA 276
                L +++S L  RE  + + R+        TLE +   F V+RER+RQIE +A
Sbjct: 113 LLSEELEKALSKLTEREAMVLKFRKGLVDGREHTLEEVGQRFSVTRERIRQIENKA 168


>gi|254519401|ref|ZP_05131457.1| RNA polymerase [Clostridium sp. 7_2_43FAA]
 gi|226913150|gb|EEH98351.1| RNA polymerase [Clostridium sp. 7_2_43FAA]
          Length = 241

 Score =  129 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 53/242 (21%), Positives = 107/242 (44%), Gaps = 19/242 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             ++V  ++ LV  +A      +   +   ++VS G +GL+ A+ ++D  +G + ++Y+ 
Sbjct: 10  KEQIVEKYIPLVKYLASRVMLGKTKYIEYEDLVSYGIVGLLDAINRYDSTKGMKFSSYAT 69

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             IK AM + I R    +        K     L +    ++ + +  ++   +  IA +L
Sbjct: 70  LRIKGAMIDEI-RKCRPIS-------KGAMDKLAKYNECVEKLQNRYMREPSLQEIALEL 121

Query: 167 NVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           N+SE EV  +   +      SL ++I S D + +     +    D       E  E K +
Sbjct: 122 NISEEEVSQVENYINYMSIISLESIIYSDDDDVT----IMETLEDKNSISPEESLEDKEK 177

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             +L  ++  L  +++ I          +TL+ +    EVS  RV Q+ +RA + ++  +
Sbjct: 178 LEILAEAIEKLKDKDKLILNLYYY--EKLTLKEIGQILEVSESRVCQLHSRAIRNLRAVM 235

Query: 285 QK 286
           QK
Sbjct: 236 QK 237


>gi|126649719|ref|ZP_01721955.1| sporulation sigma factor SigE [Bacillus sp. B14905]
 gi|126593438|gb|EAZ87383.1| sporulation sigma factor SigE [Bacillus sp. B14905]
          Length = 227

 Score =  129 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 56/269 (20%), Positives = 116/269 (43%), Gaps = 64/269 (23%)

Query: 19  YIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           YI     +P+ L ++EE  +   + + GDL A   L+  +LRLVV IA  +   G PI +
Sbjct: 15  YIGGNDSLPVPLSREEEVTVIASFMK-GDLRARDTLIERNLRLVVYIARRFDNTGTPIED 73

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++S G+IGL++A++ F+ ++  +LATY+   I                      +  +  
Sbjct: 74  LISIGSIGLIKAIETFNTDKNIKLATYASRCI----------------------ENEILM 111

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
           +LR+                                     R+ G+ SL+  +NS    +
Sbjct: 112 HLRK-----------------------------------TSRMKGEVSLDEPLNSDADGN 136

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTL 255
                 ++     +E ++++  E+K  R  +  ++++L  RER I E R        +T 
Sbjct: 137 ELLLSDILG---TEEHIILDNVEKKIERQHMFHAINLLGARERYIMECRFGLNGKVEMTQ 193

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + ++    +S+  + ++E +  + ++E++
Sbjct: 194 KEVADHLGISQSYISRLEKKIIQDLRENL 222


>gi|56963382|ref|YP_175113.1| sporulation sigma factor SigK [Bacillus clausii KSM-K16]
 gi|56909625|dbj|BAD64152.1| DNA-directed RNA polymerase sigma-27 factor sigma-K [Bacillus
           clausii KSM-K16]
          Length = 235

 Score =  129 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 58/265 (21%), Positives = 98/265 (36%), Gaps = 63/265 (23%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
            Y+        L K++E     R  E GD SA + L+  +LRLV  I   +      + +
Sbjct: 20  SYVKNNAFPQPLSKEDEKKYLARMAE-GDASARNMLIEHNLRLVAHIVKKFENTREDVED 78

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++S G IGL++A++ +   +G +LATY+   I+  +                        
Sbjct: 79  LISIGTIGLIKAIESYSEGKGTKLATYAARCIENEI----------------------LM 116

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
           +LR LK                            + +S++  +  D          + N 
Sbjct: 117 HLRALKK-------------------------VKKDVSLHDPIGTD---------KEGNE 142

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
               D L  D +    VL  + E+K     +     VL+ RE+ +   R     E   T 
Sbjct: 143 ITLIDILKDDGEDIVDVLQTEMEKKQIYEYIH----VLDEREKEVIIGRFGLNMEEERTQ 198

Query: 256 ENLSSEFEVSRERVRQIEARAFKKV 280
             ++ E  +SR  V +IE RA  K+
Sbjct: 199 REIAKELNISRSYVSRIEKRALMKL 223


>gi|300787087|ref|YP_003767378.1| RNA polymerase sigma factor [Amycolatopsis mediterranei U32]
 gi|299796601|gb|ADJ46976.1| RNA polymerase sigma factor [Amycolatopsis mediterranei U32]
          Length = 263

 Score =  129 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 44/237 (18%), Positives = 89/237 (37%), Gaps = 18/237 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             +LVT  L L   IA  + G G P  ++V    IGL+ AV +FDP RG    ++++  I
Sbjct: 39  RSKLVTELLPLAEHIATRFSGRGEPREDLVQVARIGLINAVDRFDPARGHDFLSFAVPTI 98

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     +  L      L      ++    +      +A+ LN+ 
Sbjct: 99  MGEVRRHFRDTGWSVRVPRRLKELHLS-----LSQGSAVLSQRLGRAPTPTELAEHLNLD 153

Query: 170 ESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
             EV    +        S++  ++   +  S        DH+                  
Sbjct: 154 VDEVREGLLAGNAYQALSVDKPVHDDAEALSLADTMGEPDHEMA---------MVENHEA 204

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   +  L  RER I   R      +T   ++    +S+  V ++ ++  ++++  +
Sbjct: 205 LQPLLQELPKRERAILVMRFFGG--LTQTQIADRVGISQMHVSRLLSQTLEQLRGKL 259


>gi|229492054|ref|ZP_04385868.1| RNA polymerase sigma-F factor [Rhodococcus erythropolis SK121]
 gi|229321078|gb|EEN86885.1| RNA polymerase sigma-F factor [Rhodococcus erythropolis SK121]
          Length = 259

 Score =  129 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 51/244 (20%), Positives = 104/244 (42%), Gaps = 22/244 (9%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           +        +++   L L   IA+ YRG G  + ++V   ++GL+ AV +FD  +G    
Sbjct: 23  DARCERLRTQIIELCLPLTRHIALRYRGRGQALDDLVQAASVGLVSAVNRFDLAKGKDFL 82

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
            +++  +   ++++       V++  +  +  L  N  R      A+T +  +   V  +
Sbjct: 83  AFAIPTMMGEVRKHFRDRGWDVRVPRSLQENCLALNKART-----ALTQDLGREPTVPEL 137

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE--- 219
           AK+L V  +EV  +   +A  +S +A         +      V D       L E +   
Sbjct: 138 AKELGVEPAEVAEI---VAAGDSYHA---------ASLDAAAVGDGRSIADALGEFDAAL 185

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           +  + +  L  ++  L  RER I   R   E  +T   ++ +  VS+  V ++ A++  K
Sbjct: 186 DGIDNQETLRPALLALPERERIIVIYRFFGE--LTQAEIAEKIGVSQMHVSRLLAQSLAK 243

Query: 280 VQES 283
           ++ S
Sbjct: 244 LRAS 247


>gi|168335365|ref|ZP_02693459.1| sporulation sigma factor SigE [Epulopiscium sp. 'N.t. morphotype
           B']
          Length = 246

 Score =  129 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 61/287 (21%), Positives = 111/287 (38%), Gaps = 69/287 (24%)

Query: 9   IVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDL-----SAAHRLVTSHLRLVV 62
           I+  +IG   YI     +P  L K+EE  L  +  E+ D           L+  +LRLVV
Sbjct: 18  ILKNQIGQIHYIGGSEVLPAPLSKEEENELLMQMIEYPDDDEKINEIKKILIERNLRLVV 77

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            IA  +      + +++S G+IGL++A+  F P++  +LATY+   I+  +   I R+  
Sbjct: 78  YIAKKFENTNKGMEDLISIGSIGLIKAINTFKPDKKIKLATYASRCIENEILMDIRRT-- 135

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
                             +LK                                    ++ 
Sbjct: 136 -----------------NKLKVE----------------------------------VSI 144

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
           DE LN      D N     D L  D D     +    E +  + +L  ++  L+ RER I
Sbjct: 145 DEPLNT---DWDGNELLLSDILGTDFDS----VYRNIEDEVDKALLNTALGQLSTREREI 197

Query: 243 FEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            E R     +    T + ++    +S+  + ++E +   ++++ ++K
Sbjct: 198 VELRYGFKNEGKEKTQKEVADMLGISQSYISRLEKKIIGRLKKEMKK 244


>gi|108762696|ref|YP_629049.1| RNA polymerase sigma-32 factor family protein [Myxococcus xanthus
           DK 1622]
 gi|108466576|gb|ABF91761.1| RNA polymerase sigma-32 factor family protein [Myxococcus xanthus
           DK 1622]
          Length = 273

 Score =  129 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 76/237 (32%), Positives = 121/237 (51%), Gaps = 8/237 (3%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
             A   V  HL+LV ++A  YR  GL + E+V+EGN+GLM+A  +F+ ERG   A Y+  
Sbjct: 29  EVAEARVREHLKLVRRLAWKYRWTGLSMEELVAEGNVGLMEAAGRFE-ERGVPFAAYASQ 87

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+A ++ Y+ R+WS+           + F LRR +  L+A       PE    +A+ L 
Sbjct: 88  WIRARIRAYVGRNWSM----AGGRAPWVVFQLRRERSRLEARWG-EGHPEVEKRLAEALG 142

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
             E EV      L+ D SL+A ++    + +   + L+ D D QE  +   +  +  R  
Sbjct: 143 KREDEVALAMEALSRDVSLDAPVSP--DSEATRLEGLMADADSQEDQVDRAKWARRLRAS 200

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +  +   L+ RER + E R L E+ V+ E L+  F V+  R+RQIE     K++  +
Sbjct: 201 VDAAWPELDARERALVEERMLAEDGVSAELLARRFGVTAVRIRQIEQGLRVKLRHRL 257


>gi|168186813|ref|ZP_02621448.1| RNA polymerase sigma-E factor [Clostridium botulinum C str. Eklund]
 gi|169295137|gb|EDS77270.1| RNA polymerase sigma-E factor [Clostridium botulinum C str. Eklund]
          Length = 235

 Score =  129 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 61/264 (23%), Positives = 110/264 (41%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE  L  + R  GD S    L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 33  PPLSKEEEESLVAKIR-AGDDSVRTILIERNLRLVVYIARKFENSGVLVEDLISVGTIGL 91

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FDPE+  +LATY+   I+  +  Y+ R+                    ++K   
Sbjct: 92  IKAVNTFDPEKKIKLATYASRCIENEILMYLRRN-------------------NKVKAE- 131

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                            ++  E LN      D N     D L  
Sbjct: 132 ---------------------------------ISFYEPLNT---DWDGNKLLLSDILGT 155

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           ++D    ++ ++ +    + +L  +M  L+ RE+ I + R     +   T + ++    +
Sbjct: 156 ENDMVYNLIEDEVD----KQLLFIAMRKLSDREKEIIKLRFGLTGKGEKTQKQVADLLGI 211

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++ I K V
Sbjct: 212 SQSYISRLEKRIIKRLKKEISKMV 235


>gi|293374267|ref|ZP_06620595.1| RNA polymerase sigma-K factor [Turicibacter sanguinis PC909]
 gi|292647100|gb|EFF65082.1| RNA polymerase sigma-K factor [Turicibacter sanguinis PC909]
          Length = 229

 Score =  129 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 53/262 (20%), Positives = 103/262 (39%), Gaps = 65/262 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+  ++EE+ L      +GD +A  +L+  +LRLV  I   Y+       +++S G IGL
Sbjct: 29  PLSAEEEEHYLT--LMANGDKNAREKLIEHNLRLVAHIVKKYQNQTDDKEDLISIGTIGL 86

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+  F P++G +LATY+   I   +                     LF + ++++   
Sbjct: 87  IKAIDSFSPDKGTKLATYAARCIDNEILM-------------------LFRSTKKMRND- 126

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                      +S+   +             + N     D +  
Sbjct: 127 ---------------------------VSLYDPIG---------YDKEGNEICLIDVVKD 150

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEV 264
           ++     ++I++         + +++  L  RER I   R   EN    T + ++  + +
Sbjct: 151 ENKDLNDIIIQQLAF----EKIEKNLKSLTQRERDIIVRRFGLENHEEETQQEIAKSYGI 206

Query: 265 SRERVRQIEARAFKKV-QESIQ 285
           SR  V +IE RA  K+ +E I+
Sbjct: 207 SRSYVSRIEKRALMKLYREFIK 228


>gi|57996884|emb|CAI45890.1| negative response regulator [Escherichia coli]
          Length = 191

 Score =  129 bits (326), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 54/201 (26%), Positives = 93/201 (46%), Gaps = 12/201 (5%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           +     +++      K L   LR  +     ++           IA++L+    +V  M 
Sbjct: 61  MNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRML 115

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                  S++  +    + +      L    D +E    +  +  + +  + +    LN 
Sbjct: 116 RLNERITSVDTPLGGDSEKA-----LLDILADEKENGPEDTTQDDDMKQSIVKWRFELNA 170

Query: 238 RERRIFEARR--LQENPVTLE 256
           ++R +   R   L     TLE
Sbjct: 171 KQREVLARRFGLLGYEAATLE 191


>gi|305675234|ref|YP_003866906.1| sporulation sigma factor SigmaK [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|161168469|dbj|BAF93933.1| RNA polymerase sigma factor [Bacillus subtilis subsp. natto]
 gi|291485028|dbj|BAI86103.1| hypothetical protein BSNT_03833 [Bacillus subtilis subsp. natto
           BEST195]
 gi|305413478|gb|ADM38597.1| sporulation sigma factor SigmaK [Bacillus subtilis subsp.
           spizizenii str. W23]
          Length = 242

 Score =  129 bits (325), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 53/278 (19%), Positives = 98/278 (35%), Gaps = 65/278 (23%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +  +V   + L  Y+        L   EE    +   + GD  A + L+  +LRLV  I 
Sbjct: 9   LGFVVKELVFLVSYVKNNAFPQPLSSSEEKKYLELMAK-GDEHARNMLIEHNLRLVAHIV 67

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             +   G    +++S G IGL++ ++ +   +G +LATY+   I+  +            
Sbjct: 68  KKFENTGEDAEDLISIGTIGLIKGIESYSAGKGTKLATYAARCIENEI------------ 115

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
                       +LR LK                                       D S
Sbjct: 116 ----------LMHLRALKKT-----------------------------------KKDVS 130

Query: 186 LNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           L+  I    + N     D L  ++    + +I+  +       + + + +L+ RE+ +  
Sbjct: 131 LHDPIGQDKEGNEISLIDVLKSEN----EDVIDTIQLNMELEKVKQYIDILDDREKEVIV 186

Query: 245 ARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            R   +     T   ++ E  +SR  V +IE RA  K+
Sbjct: 187 GRFGLDLKKEKTQREIAKELGISRSYVSRIEKRALMKM 224


>gi|311900244|dbj|BAJ32652.1| putative RNA polymerase sigma factor [Kitasatospora setae KM-6054]
          Length = 310

 Score =  129 bits (325), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 49/255 (19%), Positives = 103/255 (40%), Gaps = 19/255 (7%)

Query: 35  YVLAKRYR--EHGDLS---AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
            VL +R    E G          L+  +L LV      +     P  +++  G++GL++A
Sbjct: 66  KVLLRRLAGLEEGTREFSYVRTTLIELNLTLVRFAIRRFGHSKEPYEDLLQVGSVGLIKA 125

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +FDP  G    TY++  I   ++ +   +   V +     + RL  +L + +  L   
Sbjct: 126 IDRFDPSLGVEFTTYAVPTIIGEIRRHFRDTTWSVHVPRRLQELRL--DLAKAQDALAQT 183

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
            D       V  +A+ L++SE EVI          + +  + S  +   Q     +   D
Sbjct: 184 LDRE---PTVADLAEYLSISEEEVIEGLAAANAHTAGSLDLTSPGEGDGQQPAERLGRVD 240

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
           G+  ++            L   ++ L  R+R+I   R  ++  +T   + +   +S+  V
Sbjct: 241 GRFALVENLV-------ALKPLIAQLPERDRQILAMRFSED--LTQSQIGARLGLSQMHV 291

Query: 270 RQIEARAFKKVQESI 284
            ++ +R   +++  +
Sbjct: 292 SRLLSRTLARLRTGL 306


>gi|297196321|ref|ZP_06913719.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
 gi|197722899|gb|EDY66807.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
          Length = 307

 Score =  129 bits (325), Expect = 4e-28,   Method: Composition-based stats.
 Identities = 53/249 (21%), Positives = 109/249 (43%), Gaps = 21/249 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            + LV  +L LV   A+ +     P+ +++  G IGL++A+ +FD ER    A++++  +
Sbjct: 76  RNTLVELNLSLVKFAALRFANRAEPMEDIIQVGTIGLIKAINRFDLEREVEFASFALPTV 135

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   S   V++     + R+      L   L  +     +      +A  L VS
Sbjct: 136 IGEIKRFFRDSSWSVRVPRRLQELRID-----LAKALDVLEQRLGRRPTTAELAAYLGVS 190

Query: 170 ESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E EV+       G   +SL+A +N  D +++  +   + D            +  +    
Sbjct: 191 EEEVVEGERASNGYTAQSLDATVNDEDASNAVNRRLGIDDP---------AFDIIDSLEA 241

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L   ++ L+ R+R I   R  +E  +T   +     +S+  V ++ AR  +K++  I   
Sbjct: 242 LKPLIATLDERDRLILSLRFREE--LTQSEIGERLGISQMHVSRLLARILEKLRAGI--- 296

Query: 288 VELSSSPPL 296
           ++ SS+ P+
Sbjct: 297 MDDSSAVPV 305


>gi|239982580|ref|ZP_04705104.1| RNA polymerase sigma factor WhiG [Streptomyces albus J1074]
          Length = 259

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 54/256 (21%), Positives = 107/256 (41%), Gaps = 15/256 (5%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
            L   Y+  GD     +L+  +  LV  +A          +  ++ VS G  GL+ A++K
Sbjct: 11  ELWSSYKATGDARLREQLILHYSPLVKYVAGRVSVGLPPNVEQADFVSSGIFGLIDAIEK 70

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FDPER  +  TY++  I+ AM + +    +L  I  +  QK    N+ R    L+A    
Sbjct: 71  FDPERSIKFETYAITRIRGAMIDELR---ALDWIPRSVRQKA--RNVERAYASLEAELHR 125

Query: 153 NLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
                    +A ++ ++  ++ ++     LA   +L  L++   +        +    D 
Sbjct: 126 ---TPTEAEVAAEMGIAVEDLHAVFSQLSLANVVALEELLHGGGEGGGDRLSIMDTLEDT 182

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                +E  E +  R +L R++++L  RE+ +          +TL  +     V+  RV 
Sbjct: 183 SADNPVELAEDRELRRLLARAINLLPEREKTVVTLYYY--EGLTLAEIGHVLGVTESRVS 240

Query: 271 QIEARAFKKVQESIQK 286
           QI  ++  +++  +  
Sbjct: 241 QIHTKSVLQLRAKLSS 256


>gi|229490177|ref|ZP_04384024.1| RNA polymerase sigma-F factor [Rhodococcus erythropolis SK121]
 gi|229322925|gb|EEN88699.1| RNA polymerase sigma-F factor [Rhodococcus erythropolis SK121]
          Length = 264

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 45/238 (18%), Positives = 92/238 (38%), Gaps = 14/238 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                 L+T  L L   IA  + G G    ++V    +GL+ AV +FD  RG    ++++
Sbjct: 40  ERVRTALITRCLPLAEHIARRFDGRGEAHDDLVQVARLGLVNAVDRFDSTRGSDFVSFAV 99

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +   ++ +   +   +++      K L F L +    +  ++        V  +A+ L
Sbjct: 100 PTVMGEVRRHFRDTGWALRVPRRM--KELHFQLGQA---ISELSQQLGHAPTVDELAETL 154

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   EV      +AG+      ++     S+   D  + +  G     +E  E      
Sbjct: 155 GIEREEV--AQALIAGNA--YQTVSVDGAASNHTDDLPLVETLGDYDAALENVE---NHE 207

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L  RER +   R      +T   ++ +  VS+  V ++ A+    ++E +
Sbjct: 208 ALRPLLDKLPERERTVLMLRFFGN--LTQTQIAEKVGVSQMHVSRLLAKTLSNLREQL 263


>gi|228919826|ref|ZP_04083184.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228839842|gb|EEM85125.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
          Length = 224

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 45/233 (19%), Positives = 104/233 (44%), Gaps = 16/233 (6%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           +V  +  LV  IA  Y   G    +++  G +GL+ A++++D   G     +++  I   
Sbjct: 1   MVNHYKNLVYSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGE 60

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +++Y+      + +      +R+     ++K  ++ +TD   +  +++ IA  L +SE E
Sbjct: 61  IKKYLRDKTWGIHVP-----RRIKDLGGKIKLAIEELTDRLQRSPKIIEIADHLGLSEEE 115

Query: 173 VISMN--CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           V+ +          SL+ ++ +S   SS  +   V +       + +  E   RR +L  
Sbjct: 116 VLEIMDAKNNYRVSSLDDVVENSSDGSSVARIESVGE-------VEQGYEETERRLVLKD 168

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +VLN  E+ +      +   +  ++      +S+  V +I+ +A  K++++
Sbjct: 169 IFNVLNETEKSVIHYIFGEN--LNQKDTGERLGISQMHVSRIKRQAISKLKQA 219


>gi|261418447|ref|YP_003252129.1| sporulation sigma factor SigK [Geobacillus sp. Y412MC61]
 gi|319767593|ref|YP_004133094.1| RNA polymerase, sigma 28 subunit, SigK [Geobacillus sp. Y412MC52]
 gi|261374904|gb|ACX77647.1| RNA polymerase, sigma 28 subunit, SigK [Geobacillus sp. Y412MC61]
 gi|317112459|gb|ADU94951.1| RNA polymerase, sigma 28 subunit, SigK [Geobacillus sp. Y412MC52]
          Length = 245

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 58/275 (21%), Positives = 102/275 (37%), Gaps = 65/275 (23%)

Query: 16  LSRYIHEIRKIPMLEK-QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           L  YI        L   +EE  LA      GD  A +RL+  +LRLV  I   +   G  
Sbjct: 26  LVSYIKNNAFPQPLSAQEEEKYLA--LMAKGDEQARNRLIEHNLRLVAHIVKKFENTGEE 83

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++S G IGL++A++ + P +G +LATY+   I+  +                     
Sbjct: 84  VEDLISIGTIGLIKAIESYSPGKGTKLATYAARCIENEI--------------------- 122

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
              +LR LK                            + +S++  +  D          +
Sbjct: 123 -LMHLRSLKKT-------------------------RKDVSLHEPIGQD---------KE 147

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NP 252
            N     D L  + +     ++++         + + +SVL+ RE+ +   R        
Sbjct: 148 GNEISLLDILKAEGED----IVDEIHLNMELEQVKQYISVLDEREKEVIINRFGLGRQRE 203

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            T   ++ E  +SR  V +IE RA  K+     +Q
Sbjct: 204 KTQREIAKELGISRSYVSRIEKRALMKMFHEFYRQ 238


>gi|302792318|ref|XP_002977925.1| hypothetical protein SELMODRAFT_53596 [Selaginella moellendorffii]
 gi|300154628|gb|EFJ21263.1| hypothetical protein SELMODRAFT_53596 [Selaginella moellendorffii]
          Length = 326

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 57/251 (22%), Positives = 106/251 (42%), Gaps = 16/251 (6%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGY--RGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           +R  + G  +A ++++  +LRLV   A  Y      L + ++  EG  GLM AV KFDP+
Sbjct: 79  RRLLQLG-QAARNKMIKHNLRLVAHQARKYFKEELSLSLLDLCQEGVPGLMSAVDKFDPK 137

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +G+R +TY+++W+K ++     R   +V++      +++   ++R +  L    D     
Sbjct: 138 KGYRFSTYAVYWVKNSILRAQTRLGHIVRVPYNVAAQKM--TIQRKRAQLSLELDREPTH 195

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           E+V+    +L +       +    A   SLNA    + +         + D D  E    
Sbjct: 196 EEVI---TELKMDSRRYFEVLRTGAPRRSLNARSKVTGEE----LIHSISDPDENEAQYF 248

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEA 274
                   R  +   +  L P+E  I   R   +     +   +     +SRE VR+ E 
Sbjct: 249 NA--GAQLRLGMDDVLDSLKPKESLIIRQRYGLDGKGERSFTEIGRNLNLSREMVRKYEI 306

Query: 275 RAFKKVQESIQ 285
           R   K++   +
Sbjct: 307 RGMMKLKHPTR 317


>gi|229016304|ref|ZP_04173251.1| RNA polymerase sigma-B factor [Bacillus cereus AH1273]
 gi|229022543|ref|ZP_04179074.1| RNA polymerase sigma-B factor [Bacillus cereus AH1272]
 gi|228738763|gb|EEL89228.1| RNA polymerase sigma-B factor [Bacillus cereus AH1272]
 gi|228744996|gb|EEL95051.1| RNA polymerase sigma-B factor [Bacillus cereus AH1273]
          Length = 224

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 45/233 (19%), Positives = 105/233 (45%), Gaps = 16/233 (6%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           +V  +  LV  IA  Y   G    +++  G +GL+ A++++D   G     +++  I   
Sbjct: 1   MVDHYKNLVHSIAYRYSKGGPMHEDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGE 60

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +++Y+      + +      +R+     ++K  ++ +TD   +  +++ IA  L +SE E
Sbjct: 61  IKKYLRDKTWGIHVP-----RRIKDLGGKIKLAIEELTDRLQRSPKIIEIADHLGLSEEE 115

Query: 173 VISMN--CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           V+ +          SL+ ++ +S   SS  +   V +       + +  E+  RR +L  
Sbjct: 116 VLEIMDAKNNYRVSSLDDVVENSSDGSSVARIESVGE-------VEQGYEQTERRLILDD 168

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +VLN  E+ +      +   +  ++      +S+  V +I+ +A  K++++
Sbjct: 169 IFNVLNDTEKSVIHYIFGEN--LNQKDTGERLGISQMHVSRIKRQAISKLKQA 219


>gi|56964116|ref|YP_175847.1| sporulation sigma factor SigE [Bacillus clausii KSM-K16]
 gi|56910359|dbj|BAD64886.1| DNA-directed RNA polymerase sigma-29 factor sigma-E [Bacillus
           clausii KSM-K16]
          Length = 237

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 63/264 (23%), Positives = 106/264 (40%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE  L  +    GD +    L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 35  PPLSKEEEAELLGKL-PSGDKAVRSVLIERNLRLVVYIARKFENTGINIEDLISIGTIGL 93

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I                      +  +   LRR     
Sbjct: 94  IKAVNTFNPEKKIKLATYASRCI----------------------ENEILMYLRRNNKTR 131

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                            ++ DE LN      D N     D L  
Sbjct: 132 SE-------------------------------VSFDEPLN---IDWDGNELLLSDVLGT 157

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           + D    ++    E +  R +L +++  L+ RE++I E R     E   T ++++    +
Sbjct: 158 EED----IITRGIEERVDRRLLVKALHTLSEREKQIMELRFGLAGEEEKTQKDVADMLGI 213

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++Q+   K V
Sbjct: 214 SQSYISRLEKRIIKRLQKEFSKMV 237


>gi|226305067|ref|YP_002765025.1| RNA polymerase sigma factor SigF [Rhodococcus erythropolis PR4]
 gi|226184182|dbj|BAH32286.1| RNA polymerase sigma factor SigF [Rhodococcus erythropolis PR4]
          Length = 264

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 45/238 (18%), Positives = 92/238 (38%), Gaps = 14/238 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                 L+T  L L   IA  + G G    ++V    +GL+ AV +FD  RG    ++++
Sbjct: 40  ERVRTALITRCLPLAEHIARRFDGRGEAHDDLVQVARLGLVNAVDRFDSTRGSDFVSFAV 99

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +   ++ +   +   +++      K L F L +    +  ++        V  +A+ L
Sbjct: 100 PTVMGEVRRHFRDTGWALRVPRRM--KELHFQLGQA---ISELSQQLGHAPTVDELAETL 154

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   EV      +AG+      ++     S+   D  + +  G     +E  E      
Sbjct: 155 GIEREEV--AQALIAGNA--YQTVSVDGAASNHTDDLPLVETLGDYDAALENVE---NHE 207

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L   +  L  RER +   R      +T   ++ +  VS+  V ++ A+    ++E +
Sbjct: 208 ALRPLLDKLPERERTVLMLRFFGN--LTQTQIAEKVGVSQMHVSRLLAKTLSNLREQL 263


>gi|167037640|ref|YP_001665218.1| RNA polymerase sigma-28 subunit FliA/WhiG [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|167040301|ref|YP_001663286.1| RNA polymerase sigma-28 subunit FliA/WhiG [Thermoanaerobacter sp.
           X514]
 gi|256750769|ref|ZP_05491654.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|300914385|ref|ZP_07131701.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X561]
 gi|307724379|ref|YP_003904130.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter sp. X513]
 gi|320116055|ref|YP_004186214.1| FliA/WhiG family RNA polymerase sigma factor [Thermoanaerobacter
           brockii subsp. finnii Ako-1]
 gi|166854541|gb|ABY92950.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermoanaerobacter sp.
           X514]
 gi|166856474|gb|ABY94882.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|256750352|gb|EEU63371.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|300889320|gb|EFK84466.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X561]
 gi|307581440|gb|ADN54839.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter sp. X513]
 gi|319929146|gb|ADV79831.1| RNA polymerase sigma factor, FliA/WhiG family [Thermoanaerobacter
           brockii subsp. finnii Ako-1]
          Length = 246

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 42/254 (16%), Positives = 109/254 (42%), Gaps = 19/254 (7%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLMQAV 90
           E  + K Y  + D +  + ++  ++ LV  I               +++++G IGL+ A+
Sbjct: 5   EEDIWKTYNSNKDPNLRNEIIIKYMPLVKHIVKKLIISDITQSEYEDLINQGVIGLIDAI 64

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +K+ P +G +  TY+   I+  + +Y+ +   +         + L    R+++  ++ + 
Sbjct: 65  EKYQPSKGVKFETYATLRIRGEIIDYLRKKDWM--------PRSLKKKYRKIEETVETLQ 116

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
               +   V  I +   ++E++V+     +      N    +S + + +    L    D 
Sbjct: 117 QKYNREPTVEEITEACGLNETDVLKTLSYI------NVSNINSLEEAIENNFKLHAISDV 170

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
           + +   E+   K  +  L  ++  L  +ER +      ++  +  +++S    ++  R+ 
Sbjct: 171 ELKNPEEEVLYKELKRKLANAIENLPDKERLVITLYYYED--LNYKDISKILNLTESRIS 228

Query: 271 QIEARAFKKVQESI 284
           QI  +A K+++E +
Sbjct: 229 QIHTKAIKRIREIL 242


>gi|317499143|ref|ZP_07957420.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium 5_1_63FAA]
 gi|316893556|gb|EFV15761.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 231

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 57/275 (20%), Positives = 111/275 (40%), Gaps = 67/275 (24%)

Query: 18  RYIH--EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
            YI   EI   P+   +E+ +         + +A   L+  +LRLVV IA  +   G+ +
Sbjct: 14  HYIGGTEILPAPLDTAEEQKM-IHMLGTVNEETARSMLIERNLRLVVYIAKKFDNTGIGV 72

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++S G IGL++A+  F+P +  +LATY+   I+  +  Y+ R+               
Sbjct: 73  EDLISIGTIGLIKAINTFNPAKKIKLATYASRCIENEILMYLRRNNKT------------ 120

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
                                        K+ VS  E ++++                D 
Sbjct: 121 -----------------------------KMEVSIDEPLNVD---------------WDG 136

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL----QEN 251
           N     D L  D D    ++ +  E +  + +LTR+M++L  RE+ I E R      +  
Sbjct: 137 NELLLSDILGTDED----IIYKDLEHEVDKKLLTRAMTILTDREKMIIELRFGINQKEGK 192

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             T + ++    +S+  + ++E +  K+++  + K
Sbjct: 193 EKTQKEVADMLGISQSYISRLEKKIIKRLKREMIK 227


>gi|296333262|ref|ZP_06875715.1| sporulation sigma factor SigK [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|296149460|gb|EFG90356.1| sporulation sigma factor SigK [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
          Length = 241

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 53/278 (19%), Positives = 98/278 (35%), Gaps = 65/278 (23%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +  +V   + L  Y+        L   EE    +   + GD  A + L+  +LRLV  I 
Sbjct: 8   LGFVVKELVFLVSYVKNNAFPQPLSSSEEKKYLELMAK-GDEHARNMLIEHNLRLVAHIV 66

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             +   G    +++S G IGL++ ++ +   +G +LATY+   I+  +            
Sbjct: 67  KKFENTGEDAEDLISIGTIGLIKGIESYSAGKGTKLATYAARCIENEI------------ 114

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
                       +LR LK                                       D S
Sbjct: 115 ----------LMHLRALKKT-----------------------------------KKDVS 129

Query: 186 LNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           L+  I    + N     D L  ++    + +I+  +       + + + +L+ RE+ +  
Sbjct: 130 LHDPIGQDKEGNEISLIDVLKSEN----EDVIDTIQLNMELEKVKQYIDILDDREKEVIV 185

Query: 245 ARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            R   +     T   ++ E  +SR  V +IE RA  K+
Sbjct: 186 GRFGLDLKKEKTQREIAKELGISRSYVSRIEKRALMKM 223


>gi|328554314|gb|AEB24806.1| sporulation sigma factor SigK [Bacillus amyloliquefaciens TA208]
          Length = 241

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 53/277 (19%), Positives = 97/277 (35%), Gaps = 63/277 (22%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +  IV   + L  Y+        L   EE        E GD  A + L+  +LRLV  I 
Sbjct: 8   LGFIVKELVFLVSYVKNNAFPQPLSNNEEKKYLDLMAE-GDEHARNMLIEHNLRLVAHIV 66

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             +   G    +++S G IGL++ ++ +   +G +LATY+   I+  +            
Sbjct: 67  KKFENTGEDAEDLISIGTIGLIKGIESYSAGKGTKLATYAARCIENEI------------ 114

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
                       +LR LK                                       D S
Sbjct: 115 ----------LMHLRALKKT-----------------------------------KKDVS 129

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L+  I    + +   +  L+     + + +I+  +       + + + +L+ RE+ +   
Sbjct: 130 LHDPIGQDKEGN---EISLIDVLKSESEDVIDTIQLNMELEKVKKYIDILDDREKEVIVG 186

Query: 246 RRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           R   +     T   ++ E  +SR  V +IE RA  K+
Sbjct: 187 RFGLDLKKEKTQREIAKELGISRSYVSRIEKRALMKM 223


>gi|163814130|ref|ZP_02205522.1| hypothetical protein COPEUT_00283 [Coprococcus eutactus ATCC 27759]
 gi|158450579|gb|EDP27574.1| hypothetical protein COPEUT_00283 [Coprococcus eutactus ATCC 27759]
          Length = 245

 Score =  129 bits (325), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 58/274 (21%), Positives = 104/274 (37%), Gaps = 65/274 (23%)

Query: 18  RYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
            YI     +P  LE  EE ++     +     A   L+  +LRLVV IA  +   G+ I 
Sbjct: 30  HYIGGAEILPAPLEPHEEAIVIDELTQKQSEEAKKMLIERNLRLVVYIARKFDNTGVGIE 89

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++S G IGL++A+  F  ++  +LATY+   I+  +  ++ R+  L             
Sbjct: 90  DLISIGTIGLIKAINTFKNDKNIKLATYASRCIENEILMFLRRNNRL------------- 136

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
                                       +  VS  E ++++                D N
Sbjct: 137 ----------------------------RTEVSIDEPLNVD---------------WDGN 153

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL----QENP 252
                D L  D D    ++    E +   N+L  ++S L  +ER I E R          
Sbjct: 154 ELLLSDILGTDED----IVYRDLETEVDHNLLDAAISKLGEKERTIIELRYGINTIGGVE 209

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            T + ++    +S+  + ++E +  KK++  I K
Sbjct: 210 KTQKEVADILGISQSYISRLEKKIIKKLRREIMK 243


>gi|291060074|gb|ADD72809.1| RNA polymerase sigma factor WhiG [Treponema pallidum subsp.
           pallidum str. Chicago]
          Length = 262

 Score =  129 bits (324), Expect = 5e-28,   Method: Composition-based stats.
 Identities = 53/261 (20%), Positives = 111/261 (42%), Gaps = 19/261 (7%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGL 86
           E+Q E  L   YR           V  +  LV  +A      +   +   ++VS G  GL
Sbjct: 7   EQQSEEELWLEYRRTRSAKIREYFVVQYAPLVKYVASKIAVGKPGNVEFDDLVSYGIFGL 66

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
             A+ K+DPE+  R  TY++  I+ A+ + +    S+  +  +  Q       R+++  +
Sbjct: 67  FDAIDKYDPEKNIRFNTYAVTRIRGAIFDELR---SIDWVPRSVRQ-----QTRQIEEAI 118

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SL-NALINSSDKNSSQWQDW 203
             +     +      IA  LN+   E   +  +++G    SL ++     +++     D 
Sbjct: 119 ADLEARLGRAATDTEIACALNIELEEYHQLLLKVSGTSVISLADSKFGGDERDHVSVGDS 178

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +         V++E+EE    + ++  ++  L+ RE+++      +E  +TL+ +    +
Sbjct: 179 IEAPASLNPDVIVEREE---IKRIIAEAIRELSQREQQVLILYYYEE--MTLKEIGKVLK 233

Query: 264 VSRERVRQIEARAFKKVQESI 284
           V+  R+ QI   A  K++  +
Sbjct: 234 VTESRISQIHTSANLKLKAKL 254


>gi|168186818|ref|ZP_02621453.1| RNA polymerase sigma-K factor [Clostridium botulinum C str. Eklund]
 gi|169295229|gb|EDS77362.1| RNA polymerase sigma-K factor [Clostridium botulinum C str. Eklund]
          Length = 235

 Score =  129 bits (324), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 62/275 (22%), Positives = 105/275 (38%), Gaps = 63/275 (22%)

Query: 9   IVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           +++G   L+ Y+      P  L ++EE    ++++E GD  A   L+  +LRLV  I   
Sbjct: 10  MIDGMTFLTAYVSNGTSFPQPLNEKEEKYYLQQFKE-GDALAKGILIERNLRLVAHIVKK 68

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y      I +++S G +GL++A+  FD ++G RLATY+   I+  +   I  S       
Sbjct: 69  YSYPNKDIDDLISIGTVGLIKAIDSFDVDKGTRLATYAARCIENEILMLIRNS------- 121

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
                       +++K                              + +   +  D    
Sbjct: 122 ------------KKIKSE----------------------------VYLQDPIGVD---- 137

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
                 + N     D L  D D   +V+   E R   R +  +    L  RE+ I + R 
Sbjct: 138 -----KEGNEISLMDVLSSDEDSVIEVV---ENRMEVRKLYDKIEKCLTEREKIIIKMRY 189

Query: 248 L--QENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                   T   ++S   +SR  V +IE RA KK+
Sbjct: 190 GLVDGKSKTQREIASFLNISRSYVSRIEKRALKKI 224


>gi|3249733|gb|AAC26669.1| RNA polymerase sigma-like factor [Streptomyces peucetius]
          Length = 162

 Score =  129 bits (324), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 37/172 (21%), Positives = 68/172 (39%), Gaps = 12/172 (6%)

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI+ A+   I      ++I            L R+   +         PE    + 
Sbjct: 1   YATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPTPE---ELG 55

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           +++ + E ++  +        S+   I   D   S   D++    D   Q  I+    ++
Sbjct: 56  ERMEMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDSTMQSPIDVATVES 110

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIE 273
            +      +S L  RE ++   R   +     TLE +  +F+V+RER+RQIE
Sbjct: 111 LKEATRDVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 162


>gi|331092383|ref|ZP_08341209.1| RNA polymerase sigma-F factor [Lachnospiraceae bacterium 2_1_46FAA]
 gi|330401407|gb|EGG80993.1| RNA polymerase sigma-F factor [Lachnospiraceae bacterium 2_1_46FAA]
          Length = 237

 Score =  129 bits (324), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 50/250 (20%), Positives = 103/250 (41%), Gaps = 17/250 (6%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             L KR  + GD  A  +LV  ++ LV  +   + G G    ++   G+IGL++A+ KFD
Sbjct: 5   IALIKRSHK-GDEKARTQLVEENVGLVWCVVKRFYGRGTEPEDLFQIGSIGLLKAIDKFD 63

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
                + +TY++  I   ++ ++     ++K+  +  +      L +     + + +   
Sbjct: 64  LSYDVKFSTYAVPMISGEIKRFLRDDG-MIKVSRSLKELAYKAYLAK-----EEMKERLN 117

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +   V  +A+KL V + E+          ESL+  I   D N  Q  D L    + +E++
Sbjct: 118 REPTVEELAEKLEVEKEELALALESGGEVESLHKPIYQKDGNEIQLMDKLEEKEEQEEKI 177

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
           L     ++    +            R++   R       T   +     +S+ +V ++E 
Sbjct: 178 LNHMLLQQLLEQLKKEE--------RQLIYMRYFAN--KTQSEIGKTMGISQVQVSRLEK 227

Query: 275 RAFKKVQESI 284
           +    ++E I
Sbjct: 228 KILGYLREKI 237


>gi|28203259|gb|AAO35702.1| RNA polymerase sigma-E factor [Clostridium tetani E88]
          Length = 261

 Score =  129 bits (324), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 67/264 (25%), Positives = 115/264 (43%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L ++EE  L ++   +GD S    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 59  PPLTREEEENLVEKL-NYGDESIRSILIERNLRLVVYIARKFENTGIGIEDLVSVGTIGL 117

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FDP +  +LATY+   I+  +  Y+ R+                    ++K   
Sbjct: 118 IKAVNTFDPSKKIKLATYASRCIENEILMYLRRN-------------------NKIKSE- 157

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                        ++  + LNV             G+E L + I  +D +       +VY
Sbjct: 158 -------------ISFYEPLNVDWD----------GNELLLSDILGTDTD-------IVY 187

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEV 264
           D        IE+E  K    +L  +M  LN RE++I   R         T + ++    +
Sbjct: 188 D-------YIEEEVDKE---LLLIAMDKLNNREKQIVNLRFGLGGKTEKTQKEVADMLGI 237

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++ I K +
Sbjct: 238 SQSYISRLEKRIIKRLKKEINKMI 261


>gi|313624456|gb|EFR94462.1| RNA polymerase sigma-B factor [Listeria innocua FSL J1-023]
          Length = 215

 Score =  129 bits (324), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 50/230 (21%), Positives = 103/230 (44%), Gaps = 24/230 (10%)

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y        ++V  GNIGL+ A++++D   G     +++  I   ++ ++      
Sbjct: 1   IARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWS 60

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN------ 177
           V +     +        ++K  ++ +T       Q+  IA  + V+E EV+         
Sbjct: 61  VHVPRRIKELG-----PKIKNAVEELTRELQSSPQISDIADFIGVTEEEVLEAMEMGKSY 115

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
             L+ D S+ A    SD ++    D +    DG         ER N+R +L + + VL+ 
Sbjct: 116 QALSVDHSIEA---DSDGSTITLLDVVGGTDDGF--------ERVNQRMLLEKVLPVLDE 164

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           RE++I +   ++    + +      ++S+  V +I+ +A KK++E++Q +
Sbjct: 165 REQKILQYTFIEN--RSQKETGELLDISQMHVSRIQRQAIKKLREALQNE 212


>gi|302544852|ref|ZP_07297194.1| putative RNA polymerase sigma factor [Streptomyces hygroscopicus
           ATCC 53653]
 gi|302462470|gb|EFL25563.1| putative RNA polymerase sigma factor [Streptomyces himastatinicus
           ATCC 53653]
          Length = 315

 Score =  129 bits (324), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 47/221 (21%), Positives = 91/221 (41%), Gaps = 16/221 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            + LV  +L LV   A  +R    P+ ++V  G IGL++A+ +F+P RG    T++M  I
Sbjct: 91  RNTLVELNLALVKFAASRFRSRSEPMEDIVQVGTIGLIKAIDRFEPGRGVEFPTFAMPTI 150

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +   V  +A++L+++
Sbjct: 151 VGEIKRFFRDTSWSVRVPRRLQELRLD-----LAKAGDELAQRLDRAPTVHELAQRLDIT 205

Query: 170 ESEVIS-MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            +EV+  M    A   S        D +     D + Y+  G E +             L
Sbjct: 206 TAEVVEGMAASNAYTASSLDAQPEEDDSEGALADRIGYEDHGLEGI--------EYVESL 257

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
              ++ L  R+++I   R +    +T   +  E  +S+  V
Sbjct: 258 KPLIADLPARDKQILSLRFVAN--MTQSEIGEELGISQMHV 296


>gi|187778862|ref|ZP_02995335.1| hypothetical protein CLOSPO_02457 [Clostridium sporogenes ATCC
           15579]
 gi|187772487|gb|EDU36289.1| hypothetical protein CLOSPO_02457 [Clostridium sporogenes ATCC
           15579]
          Length = 234

 Score =  129 bits (324), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 60/279 (21%), Positives = 105/279 (37%), Gaps = 63/279 (22%)

Query: 9   IVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++   + L+ Y+      P  L  +EE     R ++ GD  A   LV  +LRLV  I   
Sbjct: 10  VLGSALFLTGYVTGNTSFPKPLSDEEEKYYLDRLKK-GDALAKDILVERNLRLVAHIVKK 68

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y   G  I +++S G +GL++A+  FD  +G RLATY+   I+  +   I  +       
Sbjct: 69  YSYPGKDIDDLISIGTVGLIKAIDSFDNSKGTRLATYAARCIENEILMLIRNNKKT---- 124

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
                                                K  V   + I ++     + SL 
Sbjct: 125 -------------------------------------KGEVYLQDPIGVDKE-GNEISLM 146

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
            +++S              D D   +++  K E K     +    + L  RE+++ + R 
Sbjct: 147 DILSS--------------DEDSIIEIVSTKIEVKKLYGKIE---TCLRGREKKVIQMRY 189

Query: 248 L--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                 P T   ++    +SR  V +IE +A KK+ + +
Sbjct: 190 GLKDGRPRTQREIAGILNISRSYVSRIEKKALKKLYKEL 228


>gi|58696753|ref|ZP_00372293.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of
           Drosophila simulans]
 gi|58537061|gb|EAL60191.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of
           Drosophila simulans]
          Length = 183

 Score =  129 bits (324), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 38/182 (20%), Positives = 75/182 (41%), Gaps = 13/182 (7%)

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           W++ ++   I     +V+I     +      + ++   L+ +T    +   +  ++ +L 
Sbjct: 5   WVRQSITRAIPEQSKVVRIPLHMVEI-----ISKINRALRKMTHEMGREPTLEELSVELT 59

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +    +  +        SL A     D  SS + D +    D +     +     + R +
Sbjct: 60  MPLERIRKVMKIARDPVSLEAPTGKDD--SSTFGDCI---EDKRVSRPEDAAILADLRGI 114

Query: 228 LTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            T  ++ L P+E RI   R          TLE +   F V+RER+RQIEA+A +K++   
Sbjct: 115 TTNVLATLTPKEERILRMRFGLGKDGKEHTLEEVGKIFNVTRERIRQIEAKALRKLKHPS 174

Query: 285 QK 286
           + 
Sbjct: 175 RA 176


>gi|284042121|ref|YP_003392461.1| RNA polymerase, sigma 32 subunit, RpoH [Conexibacter woesei DSM
           14684]
 gi|283946342|gb|ADB49086.1| RNA polymerase, sigma 32 subunit, RpoH [Conexibacter woesei DSM
           14684]
          Length = 300

 Score =  129 bits (324), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 58/244 (23%), Positives = 107/244 (43%), Gaps = 8/244 (3%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRG-YGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
            + G+  A   LV   + L+  +A  YRG   +  +E++  G +GL+ A+++FDP R   
Sbjct: 60  AQGGETGARDELVDVFMPLIGSVARLYRGVTSVHRAELMQAGVVGLLTALERFDPSRRAP 119

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
             TY+ WW++ AMQ+ +      V +       R    L R++   +  T  +      V
Sbjct: 120 FWTYASWWVRQAMQQVVAELARPVVMSD-----RGLRELARMRAARRDFTRLHDAGPSSV 174

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A    ++   + ++       E+L +    SD++    +     +  G E+      +
Sbjct: 175 RLAAATGLTRERIETLLALELVPETLESEPAWSDEDDLARRSGHPLEDPGAEEAFDRVLD 234

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKK 279
           R     +L R +  L  RER I  AR   +    TL  ++    +S ERVRQ+E  A  +
Sbjct: 235 RVECDRLL-RLIGDLRQRERVILHARFGLDGQERTLREVARMVGLSAERVRQLEHEALDE 293

Query: 280 VQES 283
           ++ +
Sbjct: 294 LRAA 297


>gi|323701301|ref|ZP_08112976.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
 gi|323533903|gb|EGB23767.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
          Length = 243

 Score =  129 bits (324), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 67/263 (25%), Positives = 109/263 (41%), Gaps = 63/263 (23%)

Query: 27  PMLEKQEEYVLAKRYREHG-DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           P L   EE  L  R  E   D S    L+  +LRLVV IA  +   G+ I ++VS G IG
Sbjct: 39  PPLTSDEENDLIGRLGEGDIDGSIKSVLIERNLRLVVYIARKFENTGVGIEDLVSIGTIG 98

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++AV  FDP +  +LATY+   I+  +  Y+ R+                         
Sbjct: 99  LIKAVNTFDPNKKIKLATYASRCIENEILMYLRRN------------------------- 133

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
                                N + SEV       + DE LN      D N     D L 
Sbjct: 134 ---------------------NKTRSEV-------SFDEPLN---IDWDGNELLLSDVLG 162

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFE 263
            ++D    ++ +  E +  + +L +++  L+ RERRI E R    N    T + ++    
Sbjct: 163 TEND----IIYKNIEEEVDKKLLHQALLKLSGRERRIMELRFGLNNGTEKTQKEVADMLG 218

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+  + ++E R  K++++ I +
Sbjct: 219 ISQSYISRLEKRIIKRLKKEIHR 241


>gi|323449639|gb|EGB05525.1| hypothetical protein AURANDRAFT_60247 [Aureococcus anophagefferens]
          Length = 399

 Score =  129 bits (324), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 54/261 (20%), Positives = 106/261 (40%), Gaps = 29/261 (11%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGY--------------GLPISEVVSEGNIGLMQAVK 91
              A   ++ S++RLVV +A   +                   + ++V+EG +GL +AV 
Sbjct: 134 CREAREVMMLSNMRLVVAMARRMQRSLPQASRLAVDRDGGSYALDDLVAEGTLGLAKAVD 193

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           +F+P+RGFR +TY+ WW++ A+Q  I R   +V +     Q       ++ +   Q + D
Sbjct: 194 RFEPDRGFRFSTYATWWVRQAIQRAIRRRA-VVAVPVHVQQLA-----KKCENATQELRD 247

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN------SSQWQDWLV 205
              +P     +A ++  SE  +           SL+  ++++                L 
Sbjct: 248 EYGRPPTSAELAARVGASEKRLKLAGRAALATFSLDVPLSAARGGKGSHVADFAEAATLN 307

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQENP--VTLENLSSEF 262
              +  E    E       R+ +  +M + L P ER +   R   ++    T   +    
Sbjct: 308 EIVESDEPAPEEAATFHELRDAIDYAMHANLQPSERDVLRLRLGLDDGETRTRRQVGEIC 367

Query: 263 EVSRERVRQIEARAFKKVQES 283
             + +++R IE  A  K++ +
Sbjct: 368 GQTEKKIRAIERAALTKLRHT 388


>gi|229093408|ref|ZP_04224513.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock3-42]
 gi|228690002|gb|EEL43805.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock3-42]
          Length = 258

 Score =  129 bits (324), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 49/265 (18%), Positives = 92/265 (34%), Gaps = 63/265 (23%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
            Y+        L   +E    +   E GD  A + L+  +LRLV  I   +   G    +
Sbjct: 22  SYVKNNAFPQPLSSDDERKYLELM-EQGDAQARNLLIEHNLRLVAHIVKKFENTGEDAED 80

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++S G IGL++A++ +   +G +LATY+   I                      +  +  
Sbjct: 81  LISIGTIGLIKAIESYSAGKGTKLATYAARCI----------------------ENEILM 118

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
           +LR LK                                       D SL+  I    + +
Sbjct: 119 HLRVLKKT-----------------------------------KKDVSLHDPIGQDKEGN 143

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTL 255
              +  L+     + + +I+  +       +   + +L+ RE+ +   R     +   T 
Sbjct: 144 ---EISLIDILKSESEDVIDMIQLSMELEKIKEYIDILDEREKEVIVKRFGLGLDKEKTQ 200

Query: 256 ENLSSEFEVSRERVRQIEARAFKKV 280
             ++    +SR  V +IE RA  K+
Sbjct: 201 REIAKALGISRSYVSRIEKRALMKM 225


>gi|291548178|emb|CBL21286.1| RNA polymerase, sigma 29 subunit, SigE [Ruminococcus sp. SR1/5]
          Length = 241

 Score =  129 bits (324), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 54/263 (20%), Positives = 101/263 (38%), Gaps = 64/263 (24%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L  + E  + +      +      L+  +LRLVV IA  +   G+ + +++S G IGL+
Sbjct: 37  PLSAEREAEVIEMLGTEKEKEGKSVLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGLI 96

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +A+  FDP +  +LATY+   I+  +  Y+ R+                           
Sbjct: 97  KAINTFDPVKNIKLATYASRCIENEILMYLRRNSKT------------------------ 132

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                            K+ VS  E ++++                D N     D L  D
Sbjct: 133 -----------------KMEVSIDEPLNVD---------------WDGNELLLSDILGTD 160

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN----PVTLENLSSEFE 263
            D   + L ++ E      +L +++S L  RE+ I   R    N      T + ++    
Sbjct: 161 DDVISRRLEDEVEIA----LLGKAISKLTKREQMIIRLRFGIGNREGSEKTQKEVADLLG 216

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+  + ++E R  K++++ I K
Sbjct: 217 ISQSYISRLEKRIMKRLRKEIVK 239


>gi|121534479|ref|ZP_01666302.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
 gi|121306972|gb|EAX47891.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
          Length = 234

 Score =  129 bits (324), Expect = 6e-28,   Method: Composition-based stats.
 Identities = 58/281 (20%), Positives = 108/281 (38%), Gaps = 65/281 (23%)

Query: 7   SIIVNGEIGLSRYIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           + ++ G   L  YI      P+ L ++EE +  +R +  GD  A + L+  +LRLV  I 
Sbjct: 10  ASVLKGIALLVSYITN-NTFPLPLSEKEEQIYLERLK-AGDEKAKNVLIERNLRLVAHIV 67

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             +   G  + +++S G IGL++A+  FD  +  RLATY+   I                
Sbjct: 68  KKFDNTGEDVDDLISIGTIGLIKAINTFDQAKKIRLATYAARCI---------------- 111

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
                 +  +  +LR  +                                   R+  + S
Sbjct: 112 ------ENEILMHLRSTR-----------------------------------RIRSEVS 130

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L   I    + +   +  L+        V+ E  E +     L++ +  L+ RE+ + E 
Sbjct: 131 LYDPIGVDKEGN---EITLIDVLGTAPDVVAEAVENQCETERLSKEIHRLSKREKWVLEM 187

Query: 246 RRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R      +  T  +++    +SR  V +IE RA  K+ +++
Sbjct: 188 RFGMPDGSRKTQRDIAKLLGISRSYVSRIEKRAISKLSKNL 228


>gi|15639696|ref|NP_219146.1| RNA polymerase sigma factor WhiG [Treponema pallidum subsp.
           pallidum str. Nichols]
 gi|189025934|ref|YP_001933706.1| RNA polymerase sigma factor WhiG [Treponema pallidum subsp.
           pallidum SS14]
 gi|3323011|gb|AAC65675.1| RNA polymerase sigma-28 factor [Treponema pallidum subsp. pallidum
           str. Nichols]
 gi|189018509|gb|ACD71127.1| RNA polymerase sigma-28 factor [Treponema pallidum subsp. pallidum
           SS14]
          Length = 262

 Score =  129 bits (324), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 53/261 (20%), Positives = 111/261 (42%), Gaps = 19/261 (7%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGL 86
           E+Q E  L   YR           V  +  LV  +A      +   +   ++VS G  GL
Sbjct: 7   EQQSEEELWLEYRRTRSAKIREYFVVQYAPLVKYVASKIAVGKPGNVEFDDLVSYGIFGL 66

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
             A+ K+DPE+  R  TY++  I+ A+ + +    S+  +  +  Q       R+++  +
Sbjct: 67  FDAIDKYDPEKNIRFNTYAVTRIRGAIFDELR---SIDWVPRSVRQ-----QTRQIEEAI 118

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SL-NALINSSDKNSSQWQDW 203
             +     +      IA  LN+   E   +  +++G    SL ++     +++     D 
Sbjct: 119 ADLEARLGRXATDTEIACALNIELEEYHQLLLKVSGTSVISLADSKFGGDERDHVSVGDS 178

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +         V++E+EE    + ++  ++  L+ RE+++      +E  +TL+ +    +
Sbjct: 179 IEAPASLNPDVIVEREE---IKRIIAEAIRELSQREQQVLILYYYEE--MTLKEIGKVLK 233

Query: 264 VSRERVRQIEARAFKKVQESI 284
           V+  R+ QI   A  K++  +
Sbjct: 234 VTESRISQIHTSANLKLKAKL 254


>gi|188011951|gb|ACD45272.1| RNA polymerase sigma-37 factor [Listeria monocytogenes]
          Length = 222

 Score =  129 bits (324), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 52/240 (21%), Positives = 103/240 (42%), Gaps = 24/240 (10%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           ++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++
Sbjct: 1   EKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIR 60

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           ++D   G     +++  I   ++ ++      V +     +        ++K  ++ +T 
Sbjct: 61  RYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTR 115

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLV 205
                 Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D + 
Sbjct: 116 ELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVG 172

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
               G         ER N+R +L + + VL+ RE++I +   ++    + +      ++S
Sbjct: 173 GTDYGF--------ERVNQRMLLEKVLPVLDEREQKILQFTFIEN--RSQKETGELLDIS 222


>gi|153938998|ref|YP_001391838.1| sporulation sigma factor SigK [Clostridium botulinum F str.
           Langeland]
 gi|168180573|ref|ZP_02615237.1| RNA polymerase sigma-70 factor family [Clostridium botulinum NCTC
           2916]
 gi|152934894|gb|ABS40392.1| RNA polymerase sigma-70 factor family [Clostridium botulinum F str.
           Langeland]
 gi|182668432|gb|EDT80411.1| RNA polymerase sigma-70 factor family [Clostridium botulinum NCTC
           2916]
 gi|295319864|gb|ADG00242.1| RNA polymerase sigma-70 factor family [Clostridium botulinum F str.
           230613]
          Length = 234

 Score =  129 bits (324), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 60/279 (21%), Positives = 106/279 (37%), Gaps = 63/279 (22%)

Query: 9   IVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++   + L+ Y+      P  L  +EE     R ++ GD  A   LV  +LRLV  I   
Sbjct: 10  VLGSALFLTGYVTGNTSFPKPLSDEEEKYYLDRLKK-GDALAKDILVERNLRLVAHIVKK 68

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y   G  I +++S G +GL++A+  FD  +G RLATY+   I+  +   I  +       
Sbjct: 69  YSYPGKDIDDLISIGTVGLIKAIDSFDNSKGTRLATYAARCIENEILMLIRNNKKT---- 124

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
                                                K  V   + I ++     + SL 
Sbjct: 125 -------------------------------------KGEVYLQDPIGVDKE-GNEISLM 146

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
            +++S              D D   +++  K E K     +    + L  RE+++ + R 
Sbjct: 147 DILSS--------------DEDSIIEIVSTKIEVKKLYGKID---TCLRGREKKVIQMRY 189

Query: 248 L--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                 P T   ++   ++SR  V +IE +A KK+ + +
Sbjct: 190 GLKDGRPRTQREIAGILDISRSYVSRIEKKALKKLYKEL 228


>gi|306021726|gb|ADM80299.1| RNA-polymerase sigma subunit [Geobacillus pallidus]
          Length = 256

 Score =  129 bits (324), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 47/259 (18%), Positives = 111/259 (42%), Gaps = 19/259 (7%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQA 89
           +E V   ++  H D  A + LV  ++ LV              +   +++S G +GL  A
Sbjct: 9   DERVYWDKWFRHRDQDAGNMLVKKYMPLVRYHVSRISVGLPKNVDKDDLISFGLMGLYDA 68

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           ++KFDP R  +  TY+ + I+ A+ + + +   L         +      ++++  ++ +
Sbjct: 69  LEKFDPTRDLKFDTYASFRIRGAILDGLRKEDWL--------PRSFREKAKKVEAAIERL 120

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                +      +A++L ++  EV+ +      A   S++  ++  ++         +  
Sbjct: 121 EQKYHRNVTPNEVAEELGMTPEEVVHVVNENFFANVLSIDEQLHDQEEGE----QMNIVL 176

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            D +     E   ++     LT+ +S LN +E+ +       +  +TL  + +   +S  
Sbjct: 177 KDDKTLTPEEHLLKEELFEHLTKLISQLNDKEQLVLSLFY--KEELTLTEIGNVLNLSTS 234

Query: 268 RVRQIEARAFKKVQESIQK 286
           R+ QI ++A  K++ ++ K
Sbjct: 235 RISQIHSKALYKLKGTLVK 253


>gi|37362432|gb|AAO23112.1| sigma factor S [Vibrio vulnificus]
          Length = 167

 Score =  129 bits (324), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 49/159 (30%), Positives = 82/159 (51%), Gaps = 5/159 (3%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L  R    GD +A  R++ S+LRLVVKI+  Y   GL + +++ EGN+GL++AV+KFDPE
Sbjct: 1   LYARRALRGDEAARKRMIESNLRLVVKISRRYSNRGLALLDLIEEGNLGLIRAVEKFDPE 60

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RGFR +TY+ WWI+  ++  ++     +++      K L   LR  +     ++      
Sbjct: 61  RGFRFSTYATWWIRQTIERALMNQTRTIRLPIHVV-KELNIYLRTAR----ELSQKLDHE 115

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
                IA +L++   +V  M        S++  I    +
Sbjct: 116 PTAEEIAAQLDIPVDDVGKMLRLNERISSVDTPIGGDGE 154


>gi|225375611|ref|ZP_03752832.1| hypothetical protein ROSEINA2194_01236 [Roseburia inulinivorans DSM
           16841]
 gi|225212590|gb|EEG94944.1| hypothetical protein ROSEINA2194_01236 [Roseburia inulinivorans DSM
           16841]
          Length = 244

 Score =  128 bits (323), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 54/262 (20%), Positives = 99/262 (37%), Gaps = 64/262 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P LE + E    +         A   L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 39  PPLEGEREAYCIRMLDGVHAERARKELIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIGL 98

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++ +  F+P++  +LATY+   I+  +  Y+ R+                          
Sbjct: 99  IKGINTFNPDKNIKLATYASRCIENEILMYLRRNSKT----------------------- 135

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                             KL VS  E ++++                D N     D L  
Sbjct: 136 ------------------KLEVSIDEPLNVD---------------WDGNELLLSDILGT 162

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL----QENPVTLENLSSEF 262
           D D    V+ +  E    R +L  ++  L+ RER I E R           T + ++   
Sbjct: 163 DED----VVGKDMETDVERKLLKTAIEKLSGRERMIIELRFGLNTSDGEEKTQKEVADML 218

Query: 263 EVSRERVRQIEARAFKKVQESI 284
            +S+  + ++E +   ++++ I
Sbjct: 219 GISQSYISRLEKKIMGRLKKEI 240


>gi|254775435|ref|ZP_05216951.1| RNA polymerase sigma factor SigF [Mycobacterium avium subsp. avium
           ATCC 25291]
          Length = 242

 Score =  128 bits (323), Expect = 7e-28,   Method: Composition-based stats.
 Identities = 45/243 (18%), Positives = 95/243 (39%), Gaps = 20/243 (8%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                R+V   L L   +A  +   G  + ++V    +GLM AV +FDP +G     +++
Sbjct: 16  RRQRERIVARCLPLADHVASHFARRGEGLDDLVQVARLGLMNAVNRFDPAKGPSFIGFAV 75

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +   ++ Y       +++     +  +     ++      +     +      +++ L
Sbjct: 76  PTMMGEVRRYFRDYSWGMRVPRRLRELHV-----QISRTTADLAQQLGRAPNAGELSQVL 130

Query: 167 NVSESEVISMNCRLAGD----ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
            V   E++   C +AGD    +SL+A   +    + +     V D D Q        E  
Sbjct: 131 EVPREEIVE--CLVAGDAYRLDSLDAPQGADSSGTPRSVADSVGDIDPQ-------IEHI 181

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             R  L   ++ L  RER +   R      +T   ++    VS+ +V +I A   + +++
Sbjct: 182 TNREALRVLVATLPHREREVLRMRFF--ESMTQSQIAERIGVSQMQVSRILANTLRCLRD 239

Query: 283 SIQ 285
            ++
Sbjct: 240 QLE 242


>gi|317128262|ref|YP_004094544.1| RNA polymerase, sigma 28 subunit, SigK [Bacillus cellulosilyticus
           DSM 2522]
 gi|315473210|gb|ADU29813.1| RNA polymerase, sigma 28 subunit, SigK [Bacillus cellulosilyticus
           DSM 2522]
          Length = 238

 Score =  128 bits (323), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 52/255 (20%), Positives = 96/255 (37%), Gaps = 63/255 (24%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L  +EE    +R  E GD  A + L+  +LRLV  I   +        +++S G IGL+
Sbjct: 30  PLNAKEEREYIRRMNE-GDDEARNLLIEHNLRLVAHIVKKFENTREENEDLISIGTIGLI 88

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +A++ + P +G +LATY+   I+  +                        +LR LK    
Sbjct: 89  KAIESYSPGKGTKLATYAARCIENEI----------------------LMHLRALKK--- 123

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                                   + +S++  +  D          + N     D L  +
Sbjct: 124 ----------------------VRKDVSLHDPIGQD---------KEGNEISLIDVLQAE 152

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVS 265
                + ++E  +    +  + + + VL+ RE+ +   R   +     T   ++ E  +S
Sbjct: 153 ----TEDVVETIQLNMEKKQIYQYIHVLDEREKEVVVGRFGLDMNKERTQREIAKELGIS 208

Query: 266 RERVRQIEARAFKKV 280
           R  V +IE RA  K+
Sbjct: 209 RSYVSRIEKRALMKL 223


>gi|218515736|ref|ZP_03512576.1| RNA polymerase sigma factor RpoD [Rhizobium etli 8C-3]
          Length = 191

 Score =  128 bits (323), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 44/191 (23%), Positives = 79/191 (41%), Gaps = 11/191 (5%)

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G+++  Y+ WW+ +     + R     +     +       + R    +         PE
Sbjct: 1   GYKVLDYATWWMPSG-DHPLDRRTRPARSAFRVHMIETINKIVRTSRQMLHEIGREPTPE 59

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A+KL +   +V  +        SL   +   D+  S   D++    D    + I+
Sbjct: 60  ---ELAEKLAMPLEKVRKVLKIAKEPISLETPV--GDEEDSHLGDFI---EDKNALLPID 111

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEAR 275
              + N R   TR ++ L PRE R+   R         TLE +  +F V+RER+RQIEA+
Sbjct: 112 AAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGQQFSVTRERIRQIEAK 171

Query: 276 AFKKVQESIQK 286
           A +K++   + 
Sbjct: 172 ALRKLKHPSRS 182


>gi|325662349|ref|ZP_08150958.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium 4_1_37FAA]
 gi|331086152|ref|ZP_08335234.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|325471351|gb|EGC74574.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium 4_1_37FAA]
 gi|330406311|gb|EGG85825.1| RNA polymerase sigma-E factor [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 247

 Score =  128 bits (323), Expect = 8e-28,   Method: Composition-based stats.
 Identities = 59/272 (21%), Positives = 110/272 (40%), Gaps = 65/272 (23%)

Query: 18  RYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
            YI     +P  LE +EE  + K      +  A   L+  +LRLVV IA  +   G+ + 
Sbjct: 31  HYIGGSEVLPAPLEMEEESAVIKELATEYNEKAKKVLIEHNLRLVVYIAKKFDNTGIGVE 90

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++S G IGL++A+  F+P +  +LATY+   I+  +  Y+ R+                
Sbjct: 91  DLISIGTIGLIKAINTFNPTKKIKLATYASRCIENEILMYLRRNNKT------------- 137

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
                                       KL VS  E ++++                D N
Sbjct: 138 ----------------------------KLEVSIDEPLNVD---------------WDGN 154

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL----QENP 252
                D L  + D   + L  + E+K    ML +++  L+PRE+ I E R      +   
Sbjct: 155 ELLLSDILGTEEDTIYRDLETEAEQK----MLRKAIEKLSPREKTIVEMRFGINRSEGEE 210

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            T + ++    +S+  + ++E +  +++++ I
Sbjct: 211 KTQKEVADLLGISQSYISRLEKKIMQRLKKEI 242


>gi|308174363|ref|YP_003921068.1| RNA polymerase sporulation-specific sigma-K factor [Bacillus
           amyloliquefaciens DSM 7]
 gi|307607227|emb|CBI43598.1| RNA polymerase sporulation-specific sigma-K factor precursor
           (Sigma-27) (C-terminal fragment) [Bacillus
           amyloliquefaciens DSM 7]
          Length = 240

 Score =  128 bits (323), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 53/277 (19%), Positives = 97/277 (35%), Gaps = 63/277 (22%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +  IV   + L  Y+        L   EE        E GD  A + L+  +LRLV  I 
Sbjct: 8   LGFIVKELVFLVSYVKNNAFPQPLSNSEEKKYLDLMAE-GDEHARNMLIEHNLRLVAHIV 66

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             +   G    +++S G IGL++ ++ +   +G +LATY+   I+  +            
Sbjct: 67  KKFENTGEDAEDLISIGTIGLIKGIESYSAGKGTKLATYAARCIENEI------------ 114

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
                       +LR LK                                       D S
Sbjct: 115 ----------LMHLRALKKT-----------------------------------KKDVS 129

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L+  I    + +   +  L+     + + +I+  +       + + + +L+ RE+ +   
Sbjct: 130 LHDPIGQDKEGN---EISLIDVLKSESEDVIDTIQLNMELEKVKKYIDILDDREKEVIVG 186

Query: 246 RRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           R   +     T   ++ E  +SR  V +IE RA  K+
Sbjct: 187 RFGLDLKKEKTQREIAKELGISRSYVSRIEKRALMKM 223


>gi|121535239|ref|ZP_01667053.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
 gi|121306124|gb|EAX47052.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
          Length = 234

 Score =  128 bits (323), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 63/264 (23%), Positives = 106/264 (40%), Gaps = 66/264 (25%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EE  L  R ++ GD +     +  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 31  PPLTSDEEVFLLSRLQK-GDKAVKSIFIERNLRLVVYIARKFENTGVGIEDLVSIGTIGL 89

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FDP +  +LATY+   I+  +                         LRR     
Sbjct: 90  IKAVNTFDPIKRIKLATYASRCIENEI----------------------LMYLRR----- 122

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS-DKNSSQWQDWLV 205
                                         N +   + S +  +N   D N     D L 
Sbjct: 123 ------------------------------NSKTRAEVSFDEPLNIDWDGNELLLSDVLG 152

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN---PVTLENLSSEF 262
            D+D    ++ +  E +  +N+L  +M+ L+ RERRI E R          T + ++   
Sbjct: 153 TDND----IIYKSVEEEVDKNLLYAAMNKLSGRERRIMELRFGLNGDGMERTQKEVADML 208

Query: 263 EVSRERVRQIEARAFKKVQESIQK 286
            +S+  + ++E R  K++++ I +
Sbjct: 209 GISQSYISRLEKRIIKRLRKEISR 232


>gi|56752504|ref|YP_173205.1| RNA polymerase sigma factor SigF [Synechococcus elongatus PCC 6301]
 gi|81300319|ref|YP_400527.1| RNA polymerase sigma factor SigF [Synechococcus elongatus PCC 7942]
 gi|56687463|dbj|BAD80685.1| group3 RNA polymerase sigma factor SigF1 [Synechococcus elongatus
           PCC 6301]
 gi|81169200|gb|ABB57540.1| group3 RNA polymerase sigma factor SigF [Synechococcus elongatus
           PCC 7942]
          Length = 259

 Score =  128 bits (323), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 49/251 (19%), Positives = 108/251 (43%), Gaps = 12/251 (4%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVKKFDP 95
           L ++Y++  D    +RLV  +L LV + A  +         E+V  G++GL+ A+ +F+ 
Sbjct: 16  LLRQYQQTRDHRIRNRLVELNLGLVRQEAYRWVQRCPESFEELVQIGSLGLIAAIDRFEL 75

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           ERG   +++++ +I+  +Q Y+      V++     +  L   +  L+  LQ     +  
Sbjct: 76  ERGKAFSSFAVPYIRGEIQHYLRDRSGTVRVPRRWAE--LHQQIDPLRHKLQRELGRSPT 133

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
            E++      L+  E + + +  R     SL+  + + ++  +   D +        Q+ 
Sbjct: 134 EEELRQ-GLGLDAEEWQEVRLIGRNRTTLSLDQPLYADEEQVTSLGDSIADPKYRSFQLA 192

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
            E       R  L ++M +L  R R I E     +  +T   ++ +  +S   V +   +
Sbjct: 193 EED------RIRLQQAMQLLEQRTREILEFVFFYD--LTQREVAEKLGLSAVTVSRQVKK 244

Query: 276 AFKKVQESIQK 286
             K ++  ++ 
Sbjct: 245 GLKHLKSILRS 255


>gi|296129329|ref|YP_003636579.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Cellulomonas flavigena
           DSM 20109]
 gi|296021144|gb|ADG74380.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Cellulomonas flavigena
           DSM 20109]
          Length = 328

 Score =  128 bits (322), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 45/253 (17%), Positives = 100/253 (39%), Gaps = 16/253 (6%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFD 94
             R+       A   L+  ++ LV  +A          +  +++VS G  GL+ A++K+ 
Sbjct: 82  WSRFTASRCAKAREVLILHYVPLVTAVAGRIGMRLPSTVEHADLVSYGMFGLIDAIEKYC 141

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
            +R  +  +Y+   I+ A+ + + R+   V        + +      L+  L        
Sbjct: 142 TDRAVKFESYASSRIRGAIIDEL-RAMDWVPRSVRTKARAVDRAYGELEATLH------- 193

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +      +A++L +  SE+ ++  +LA     +L+ ++  SD              D + 
Sbjct: 194 RAPTEAEVAQRLELPVSELRAVYSQLASVNIAALDEMLAGSDDRPGAAT-LADTLGDRRA 252

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
                  E +  + +L+R++  L  RER +          +TL  +     V+  R+ QI
Sbjct: 253 DDPAGSVEAQETKYLLSRAIECLGERERLVVVLYYY--ESMTLAEIGRVLGVTESRISQI 310

Query: 273 EARAFKKVQESIQ 285
              A  +++  ++
Sbjct: 311 HTAAMGRLRTRLR 323


>gi|15894966|ref|NP_348315.1| sporulation sigma factor SigK [Clostridium acetobutylicum ATCC 824]
 gi|15024653|gb|AAK79655.1|AE007679_1 DNA-dependent RNA polymerase sigma subunit [Clostridium
           acetobutylicum ATCC 824]
 gi|528974|gb|AAB94775.1| SigK [Clostridium acetobutylicum]
 gi|325509103|gb|ADZ20739.1| sporulation sigma factor SigK [Clostridium acetobutylicum EA 2018]
          Length = 234

 Score =  128 bits (322), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 60/275 (21%), Positives = 98/275 (35%), Gaps = 63/275 (22%)

Query: 9   IVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           IV        YI      P  L + EE    K+ +E GD  A + L+  +LRLV  I   
Sbjct: 10  IVGSITFFVAYIGNGASFPQPLSESEEKYYLKKLKE-GDPLAKNILIERNLRLVAHIVKK 68

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y   G  + +++S G IGL++A+  ++  +G RLATY+   I+  +   I  +       
Sbjct: 69  YSYSGKEVDDLISIGTIGLIKAIDSYNVSKGTRLATYAARCIENEILMLIRNNKK----- 123

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
                                                K  V   + I ++     + SL 
Sbjct: 124 ------------------------------------SKNEVYLQDPIGVDKE-GNEISLI 146

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
            +++S D +  +                   E R     +      VL  RE+ I + R 
Sbjct: 147 DILSSDDDSVIEIV-----------------ENRIQIGKLYVEINRVLKGREKAIIKMRY 189

Query: 248 LQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
              +  P     ++    +SR  V +IE RA KK+
Sbjct: 190 GLGDGKPRNQREIAQILGISRSYVSRIEKRALKKL 224


>gi|223975681|gb|ACN32028.1| unknown [Zea mays]
          Length = 565

 Score =  128 bits (322), Expect = 9e-28,   Method: Composition-based stats.
 Identities = 54/252 (21%), Positives = 104/252 (41%), Gaps = 14/252 (5%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E  L  R +         RL+ +   LV  IA  Y G G  + +++  G +G++   +K
Sbjct: 314 DEAELVSRLQAGYC--CRDRLLVTTEWLVRCIARTYTGMGTALDDLLQAGKMGVLDGAEK 371

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G R +TY  +WI+  M   +  +      G T    R+   +R++K   + I   
Sbjct: 372 FDSRKGCRFSTYVKYWIRKGMLALLAENS-----GVTLLPARMESIMRKVKEARRGIRYR 426

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      +A  + VS + V           SL + +        ++ + +  +    +
Sbjct: 427 QGRNPSDSEVAAAVGVSVANVRLARKCSRRAVSLYSEVAIG--QDVKFAEVIPDESASPD 484

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +  +    R   R  L   +  L  RE R+   R   E+    +LE +   + VS+E +R
Sbjct: 485 EAAL---FRGQLRERLLLVLGRLPAREGRVLRLRHGLEDGRCRSLEEIGGIYGVSKEWIR 541

Query: 271 QIEARAFKKVQE 282
           +IE  A  ++++
Sbjct: 542 KIEKSAMARLRD 553


>gi|45128589|gb|AAS55058.1| RpoD [Vibrio parahaemolyticus]
          Length = 492

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 44/157 (28%), Positives = 71/157 (45%), Gaps = 14/157 (8%)

Query: 21  HEIRKIPMLEKQEEYVL--------AKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
             I K+ M+  +EE  L        ++R    E     A   +V ++LRLV+ IA  Y  
Sbjct: 338 RSIAKLKMI--EEETSLNVQNIKDISRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTN 395

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            GL   +++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I    
Sbjct: 396 RGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM 455

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
                   L R+   +         PE++    +   
Sbjct: 456 --IETINKLNRISRQMLQEMGREPLPEELAERMQMPE 490


>gi|311894139|dbj|BAJ26547.1| putative RNA polymerase sigma factor [Kitasatospora setae KM-6054]
          Length = 281

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 50/238 (21%), Positives = 99/238 (41%), Gaps = 16/238 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              ++  ++ LV  +A  +R     + ++V  G +GL++AV  FDP+RG    TY++  I
Sbjct: 31  RGTVIELNMPLVRFVASRFRHRPEELDDIVQVGTVGLIKAVDGFDPDRGVEFVTYAIPTI 90

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   +++  +  ++ L     R    L+              +A +L+V+
Sbjct: 91  SGEIKRFFRDTSWPLRVPRSVQERYL--AAVRASDRLEQALGRL---PDTAELAAELHVT 145

Query: 170 ESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E E        RL   +SL++L +    ++       +   D        + E    R M
Sbjct: 146 EDEAAEGLEAGRLCRCDSLDSLRDDGSDDAGSALINRLGGCDP-------ELEVAELRVM 198

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            T  +S L  RER +   R      +T   +++   VS+  V +I A     ++E I+
Sbjct: 199 ATPFLSRLPERERTVLLLRFWGG--LTQSEIAARIGVSQMHVSRILAATLAGLRERIE 254


>gi|261419446|ref|YP_003253128.1| RNA polymerase sigma factor SigD [Geobacillus sp. Y412MC61]
 gi|319766261|ref|YP_004131762.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacillus sp.
           Y412MC52]
 gi|261375903|gb|ACX78646.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacillus sp.
           Y412MC61]
 gi|317111127|gb|ADU93619.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacillus sp.
           Y412MC52]
          Length = 251

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 53/260 (20%), Positives = 108/260 (41%), Gaps = 22/260 (8%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQA 89
           EE      +    D  AA  LV  ++ LV              +P  E+VS G +GL  A
Sbjct: 8   EERKYWDEWIHGRDRHAAEELVQRYMPLVFYHVQRLSATLPSSVPKDELVSLGLVGLYDA 67

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           ++KFDP R  +  TY+ + I+ A+ + + +   L         + +    ++++G ++ +
Sbjct: 68  LEKFDPSRDLKFDTYASFRIRGAILDGLRKEDWL--------PRSMRDKAKKIEGAIERL 119

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
              +++      IA +L ++E EV +       +    L       D+        L+  
Sbjct: 120 EQRHMRSVTAKEIAAELGMTEEEVQAAASETFFSHWLPLGQTTVDEDEG-------LLSV 172

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            D +  +  E+  ++     L  ++  LN +E+ +       +  +T   + S   +S  
Sbjct: 173 RDDRAPLPEEQIVKQEMIEKLAEAIGQLNEKEQLVISLFY--KEELTFTEIGSLLHLSTS 230

Query: 268 RVRQIEARAFKKVQESIQKQ 287
           R+ QI A+A  K++   +K+
Sbjct: 231 RISQIHAKALWKLRRFFEKE 250


>gi|154686834|ref|YP_001421995.1| sporulation sigma factor SigK [Bacillus amyloliquefaciens FZB42]
 gi|154352685|gb|ABS74764.1| SpoIIIC [Bacillus amyloliquefaciens FZB42]
          Length = 240

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 53/277 (19%), Positives = 97/277 (35%), Gaps = 63/277 (22%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +  IV   + L  Y+        L   EE        E GD  A + L+  +LRLV  I 
Sbjct: 8   LGFIVKELVFLVSYVKNNAFPQPLSNNEEKKYLDLMAE-GDEHARNMLIEHNLRLVAHIV 66

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             +   G    +++S G IGL++ ++ +   +G +LATY+   I+  +            
Sbjct: 67  KKFENTGEDAEDLISIGTIGLIKGIESYSAGKGTKLATYAARCIENEI------------ 114

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
                       +LR LK                                       D S
Sbjct: 115 ----------LMHLRALKKT-----------------------------------KKDVS 129

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L+  I    + +   +  L+     + + +I+  +       + + + +L+ RE+ +   
Sbjct: 130 LHDPIGQDKEGN---EISLIDVLKSESEDVIDTIQLNMELEKVKKYIDILDDREKEVIVG 186

Query: 246 RRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           R   +     T   ++ E  +SR  V +IE RA  K+
Sbjct: 187 RFGLDLKKEKTQREIAKELGISRSYVSRIEKRALMKM 223


>gi|297197353|ref|ZP_06914750.1| RNA polymerase sigma-B factor [Streptomyces sviceus ATCC 29083]
 gi|197714848|gb|EDY58882.1| RNA polymerase sigma-B factor [Streptomyces sviceus ATCC 29083]
          Length = 263

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 43/238 (18%), Positives = 96/238 (40%), Gaps = 15/238 (6%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +    LV   L +  +IA+ +RG G  + ++     +GL++AV  +DP RG     Y++
Sbjct: 35  KALRDELVELWLPMAERIAVRFRGRGESLEDLYQVAALGLVKAVDHYDPARGSAFEAYAV 94

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +   ++ +       + +       R      R++   + ++    +   V  IA++ 
Sbjct: 95  PTVTGEIKRHFRDHMWTLHVPRRVQDLR-----NRVRQASKELSQTPGRAPTVAEIAERA 149

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++E EV +    L    +L+        +     D L     G + V+         R 
Sbjct: 150 HLTEDEVRAGAEALECFSALSLEAEMPGTDGYALGDALGVPDPGYDVVV--------DRV 201

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +   +  L  RER I   R  +   +T   ++ E  +S+  V ++ +  F ++++ +
Sbjct: 202 AVGPCLKALPERERTILYLRFFRG--MTQSCIAEELGISQMHVSRLLSTCFAQLRDEV 257


>gi|312110136|ref|YP_003988452.1| RNA polymerase, sigma 28 subunit, SigK [Geobacillus sp. Y4.1MC1]
 gi|311215237|gb|ADP73841.1| RNA polymerase, sigma 28 subunit, SigK [Geobacillus sp. Y4.1MC1]
          Length = 236

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 55/268 (20%), Positives = 97/268 (36%), Gaps = 65/268 (24%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI        L  +EE    +   + GD  A + L+  +LRLV  I   +   G  +
Sbjct: 18  LVSYIKNNAFPQPLSAKEEEKYLQLMAK-GDEQARNILIEHNLRLVAHIVKKFENTGEDV 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++S G IGL++A++ +   +G +LATY+   I+  +                      
Sbjct: 77  EDLISIGTIGLIKAIESYSSNKGTKLATYAARCIENEI---------------------- 114

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS-D 194
             +LR LK                                       D SL+  I    +
Sbjct: 115 LMHLRSLKKT-----------------------------------RKDVSLHEPIGQDKE 139

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NP 252
            N     D L  + +     +I++ +       + + + VL+ RE+ +   R   +    
Sbjct: 140 GNEISLIDVLKSEGND----IIDEIQLNMELEQVKKYIDVLDEREKEVIINRFGLDMQQE 195

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKV 280
            T   ++ E  +SR  V +IE RA  K+
Sbjct: 196 KTQREIAKELGISRSYVSRIEKRALMKM 223


>gi|45128577|gb|AAS55057.1| RpoD [Vibrio parahaemolyticus]
          Length = 492

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 36/127 (28%), Positives = 58/127 (45%), Gaps = 2/127 (1%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   G    +++ EGNIGLM+AV KF+  RG++
Sbjct: 366 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGXQFLDLIQEGNIGLMKAVDKFEYRRGYK 425

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE++ 
Sbjct: 426 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPLPEELA 483

Query: 161 AIAKKLN 167
              +   
Sbjct: 484 ERMQMPE 490


>gi|303239292|ref|ZP_07325820.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302593078|gb|EFL62798.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 236

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 55/275 (20%), Positives = 100/275 (36%), Gaps = 63/275 (22%)

Query: 16  LSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           L  Y+  +   P  L   EE    K  +E GD  A + L+  +LRLV  I   Y      
Sbjct: 19  LFGYVSNVNSFPQPLSPDEEQHYIKLLKE-GDEEARNILIERNLRLVAHIVKKYNATIGD 77

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
             +++S G IGL++A+  F+ E+G RLATY+   I+  +   I  S              
Sbjct: 78  CDDLISIGTIGLIKAIATFNHEKGTRLATYAARCIENEILMQIRSS-------------- 123

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
                ++++                              +S+   +  D          +
Sbjct: 124 -----KKIQSE----------------------------VSLQDPIGVDR---------E 141

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENP 252
            N     D +  + +   + +  K + K   N +   +     RE+ + E R        
Sbjct: 142 GNEIALIDVIGNEAESVVEEVELKMQVKRLYNKMKVVLKS---REKVVLELRYGLLNGTS 198

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            T   ++    +SR  V +IE +A KK+ + ++ +
Sbjct: 199 KTQREIAKMLGISRSYVSRIEKKAIKKLGKELKAE 233


>gi|240144184|ref|ZP_04742785.1| RNA polymerase sigma-E factor [Roseburia intestinalis L1-82]
 gi|257203788|gb|EEV02073.1| RNA polymerase sigma-E factor [Roseburia intestinalis L1-82]
 gi|291536439|emb|CBL09551.1| RNA polymerase, sigma 29 subunit, SigE [Roseburia intestinalis
           M50/1]
 gi|291538693|emb|CBL11804.1| RNA polymerase, sigma 29 subunit, SigE [Roseburia intestinalis
           XB6B4]
          Length = 243

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 52/263 (19%), Positives = 100/263 (38%), Gaps = 65/263 (24%)

Query: 27  PMLEKQEEYVLAKRY-REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           P L  ++E V  +    +     A  +L+  +LRLVV IA  +   G+ + +++S G IG
Sbjct: 37  PPLAGEDEAVCIEMLTSDESGQLARKQLIEHNLRLVVYIAKKFDNTGVGVEDLISIGTIG 96

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A+  F+P +  +LATY+   I+  +  Y+ R+                         
Sbjct: 97  LIKAINTFNPGKNIKLATYASRCIENEILMYLRRNSKT---------------------- 134

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
                              ++ VS  E ++++                D N     D L 
Sbjct: 135 -------------------RMEVSIDEPLNVD---------------WDGNELLLSDILG 160

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL----QENPVTLENLSSE 261
            D D    V+    E      +L  ++  L+ RER I E R           T + ++  
Sbjct: 161 TDED----VIYHDIETDVEHRLLKTAIGKLSGRERMIIELRFGLNSIDGEEKTQKEVADM 216

Query: 262 FEVSRERVRQIEARAFKKVQESI 284
             +S+  + ++E +   ++++ I
Sbjct: 217 LGISQSYISRLEKKIMGRLKKEI 239


>gi|52081127|ref|YP_079918.1| sporulation sigma factor SigK [Bacillus licheniformis ATCC 14580]
 gi|52786504|ref|YP_092333.1| sporulation sigma factor SigK [Bacillus licheniformis ATCC 14580]
 gi|52004338|gb|AAU24280.1| RNA polymerase sporulation-specific sigma factor [Bacillus
           licheniformis ATCC 14580]
 gi|52349006|gb|AAU41640.1| SpoIIIC [Bacillus licheniformis ATCC 14580]
          Length = 241

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 51/257 (19%), Positives = 92/257 (35%), Gaps = 66/257 (25%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+    E+  L       GD  A + L+  +LRLV  I   +   G    +++S G IGL
Sbjct: 30  PLSSSDEKKYL--ELMAQGDEHARNMLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGL 87

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A++ +   +G +LATY+   I+  +                        +LR LK   
Sbjct: 88  IKAIESYSAGKGTKLATYAARCIENEI----------------------LMHLRALKKT- 124

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS-DKNSSQWQDWLV 205
                                               D SL+  I    + N     D L 
Sbjct: 125 ----------------------------------KKDVSLHDPIGQDKEGNEISLIDVLK 150

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFE 263
            ++    + +I+  +       + + + +L+ RE+ +   R   +     T   ++ E  
Sbjct: 151 SEN----EDVIDTIQLNMELEKVKKYIDILDGREKEVIVGRFGLDLKKEKTQREIAKELG 206

Query: 264 VSRERVRQIEARAFKKV 280
           +SR  V +IE RA  K+
Sbjct: 207 ISRSYVSRIEKRALMKM 223


>gi|111019111|ref|YP_702083.1| RNA polymerase sigma factor SigF [Rhodococcus jostii RHA1]
 gi|110818641|gb|ABG93925.1| sigma factor, sigma 70 type, group 3 [Rhodococcus jostii RHA1]
          Length = 265

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 41/235 (17%), Positives = 91/235 (38%), Gaps = 14/235 (5%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              +VT  L L   IA  + G G    ++V    +GL+ +V +FD ERG    ++++  I
Sbjct: 42  RDAVVTRCLPLAEHIARRFDGRGEAHDDLVQVARLGLVNSVDRFDVERGSDFVSFAVPTI 101

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     +  L      L   +  ++ +      V  +A+ L++ 
Sbjct: 102 MGEVRRHFRDTGWAVRVPRRMKELHLA-----LSQAVAELSQSLGHAPTVSELAEHLDLE 156

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           + EV          ++++    SSD+         + D+D     +            L 
Sbjct: 157 QEEVAQGLLAGNAYQTVSVDNTSSDRTGELSMVETLGDYDAAMDDV-------ENHETLR 209

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             +  L  RER +   R      +T   ++    +S+  V ++ A+    +++ +
Sbjct: 210 PLLQSLPERERTVLMLRFFGN--MTQTQIADRVGISQMHVSRLLAKTLASLRDQL 262


>gi|258515964|ref|YP_003192186.1| RNA polymerase, sigma 28 subunit, SigK [Desulfotomaculum
           acetoxidans DSM 771]
 gi|257779669|gb|ACV63563.1| RNA polymerase, sigma 28 subunit, SigK [Desulfotomaculum
           acetoxidans DSM 771]
          Length = 234

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 60/274 (21%), Positives = 102/274 (37%), Gaps = 63/274 (22%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +VNG + L  YI        L ++EE    +   E GD  A + L   +LRLV  I   +
Sbjct: 13  VVNGLLLLVSYIANNTFPQPLSEEEEAKYLQLLFE-GDEHARNVLTERNLRLVAHIVKKF 71

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
                   +++S G IGL++AV  ++PE+G +LATY+   I                   
Sbjct: 72  DKTVGDTDDLISIGTIGLIKAVNTYNPEKGTKLATYAARCI------------------- 112

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
              +  +  +LR +K                                    +  + SL  
Sbjct: 113 ---ENEILMHLRFMKK-----------------------------------VRAEVSLYD 134

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            I    + +      ++  H    +V+ E  E    +  L   + +L+ RE+++ E R  
Sbjct: 135 PIGVDKEGNEITLIDILGTHS---EVVAEIVENSFEQKRLGDKVKLLSRREKKVLELRFG 191

Query: 249 QE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            E     T   ++    +SR  V +IE RA  K+
Sbjct: 192 LEGRQRKTQREIAKFLGISRSYVSRIEKRALTKL 225


>gi|166154282|ref|YP_001654400.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis 434/Bu]
 gi|166155157|ref|YP_001653412.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis
           L2b/UCH-1/proctitis]
 gi|301335533|ref|ZP_07223777.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis L2tet1]
 gi|165930270|emb|CAP03756.1| RNA polymerase sigma factor [Chlamydia trachomatis 434/Bu]
 gi|165931145|emb|CAP06710.1| RNA polymerase sigma factor [Chlamydia trachomatis
           L2b/UCH-1/proctitis]
          Length = 253

 Score =  128 bits (322), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 52/254 (20%), Positives = 113/254 (44%), Gaps = 17/254 (6%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFD 94
            + Y    ++     L+ S+L LV  +A            + ++ + G  GL++AV++FD
Sbjct: 10  WQLYWSTKEIHHRDVLIESYLPLVKNVAHRLASGMPSHVKMEDLYALGVEGLIRAVERFD 69

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           PE+  R  +Y+++ IKAA+ + + +      +  +  Q+       RL   + ++     
Sbjct: 70  PEKSKRFESYALFIIKAAIIDGLRKQDW---VPRSVYQRA-----NRLADAMDSLRQTLG 121

Query: 155 KPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           K      + + LN+S+ E+     + R A   SLN   +  D +     +  + D   + 
Sbjct: 122 KEPTDGELCEYLNISQQELSHWFSSSRPALVLSLNDDFSCQDDDEGLALEERIADE--RA 179

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           +   +   +K   ++LT ++  L+ +ER++       +  + L+ +     VS  RV QI
Sbjct: 180 ETGYDVIRKKEAISILTEALLALDEKERQVMALYYYDD--LVLKEIGKILGVSESRVSQI 237

Query: 273 EARAFKKVQESIQK 286
            ++A  K++ ++  
Sbjct: 238 HSKALLKLRGTLSS 251


>gi|323703189|ref|ZP_08114842.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
 gi|323531848|gb|EGB21734.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
          Length = 251

 Score =  128 bits (321), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 54/258 (20%), Positives = 103/258 (39%), Gaps = 18/258 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKK 92
            L   Y    D  A  +L+  +L LV  +A              ++   G IGLM+A+ K
Sbjct: 5   ELWDTYITSRDERARQQLILHYLPLVKHLAGRLAVKLPSFIQREDLEGYGVIGLMEALDK 64

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD   G     Y+   I+ A+ + + R   L         +  +  L+ LK   + +   
Sbjct: 65  FDHTMGNSFDAYAYHRIRGAILDQVRRQNWL--------PRTAWQKLQHLKQTRERLERE 116

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYDHDG 210
                    +A+++ +S  E+  +          SL+  +  SD +  +  D +    D 
Sbjct: 117 LGGAVPDEILAREMGISVDELNHLASSAGKMYLMSLDEEVPGSDGSVVRKLDLV---EDT 173

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                +   E K  R +L R++  L  R++ I          +TL+ +    EVS  RV 
Sbjct: 174 GSPDPLSIVEEKENRKLLARAIEKLGQRDQLILSLYYT--EGLTLKEIGQVLEVSESRVC 231

Query: 271 QIEARAFKKVQESIQKQV 288
           Q+  +  +K+++++Q+ +
Sbjct: 232 QLHGQVMRKLRKTLQEML 249


>gi|332981462|ref|YP_004462903.1| RNA polymerase sigma-28 subunit FliA/WhiG [Mahella australiensis
           50-1 BON]
 gi|332699140|gb|AEE96081.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Mahella australiensis
           50-1 BON]
          Length = 247

 Score =  128 bits (321), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 47/254 (18%), Positives = 112/254 (44%), Gaps = 27/254 (10%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR--GYGLPISEVVSEGNIGLMQAVKKFD 94
           L + Y++   +   ++L   +  ++  IA        G  + +++  G  GL+ A++++D
Sbjct: 11  LWQEYKKTSSIEYRNKLAEHYAPMIKYIASRLMVYNTGDDLDDLIGYGVFGLLDAIERYD 70

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P R  +  TY+   I+ A+ + + R   ++        K L      +   L+A +D   
Sbjct: 71  PSRDVKFETYASHRIRGAIIDNL-RKKDVIPRSVRDKVKHLDA----VYKQLEATSD--- 122

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           KP     + + L +S  ++ ++   +      SL+ +            +W + D +  E
Sbjct: 123 KPVSDEDVCRYLGISIEQLDALYADINRFNCISLDEIFVD---------EWNIGDTESSE 173

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
            V     +R   + +L+ ++S L+ RE+++ +      + +TL+ +     +S  RV Q+
Sbjct: 174 SVY----DRIELKQVLSEAVSKLSDREKQLLQLYYY--DGLTLKEIGKVLGISESRVSQL 227

Query: 273 EARAFKKVQESIQK 286
             +A  +++  ++K
Sbjct: 228 HTKALLQLRSRLRK 241


>gi|307330561|ref|ZP_07609702.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306883810|gb|EFN14855.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 315

 Score =  128 bits (321), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 49/221 (22%), Positives = 92/221 (41%), Gaps = 16/221 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            + LV  +L LV   A  +R    P+ ++V  G IGL++A+ +F+  RG    T++M  I
Sbjct: 91  RNTLVELNLALVKFAASRFRSRSEPMEDIVQVGTIGLIKAIDRFETGRGVEFPTFAMPTI 150

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      +     +   V  +A++L++S
Sbjct: 151 VGEIKRFFRDTSWSVRVPRRLQELRLD-----LAKAGDELAQRLDRAPTVSELAQRLDIS 205

Query: 170 ESEVIS-MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +SEV+  M    A   S        D +     D + Y+  G E +             L
Sbjct: 206 QSEVVEGMAASNAYTASSLDAQPEEDDSEGALADRIGYEDHGLEGI--------EYVESL 257

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
              ++ L+ R+R+I   R +    +T   +  E  +S+  V
Sbjct: 258 KPLIADLSARDRKILSLRFVAN--MTQSEIGEELGISQMHV 296


>gi|254383401|ref|ZP_04998753.1| RNA polymerase sigma factor [Streptomyces sp. Mg1]
 gi|194342298|gb|EDX23264.1| RNA polymerase sigma factor [Streptomyces sp. Mg1]
          Length = 311

 Score =  128 bits (321), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 63/302 (20%), Positives = 115/302 (38%), Gaps = 39/302 (12%)

Query: 1   MNRKNMSIIVNGEI-GLSRYIHEIRKIPMLEKQEEYVLAKRYRE--HGDLS---AAHRLV 54
           MNR +++ +  GE   LS                   L +R  E   G        + LV
Sbjct: 20  MNRTDLTAVDTGEARALSA-----------------TLFRRLAELHEGSPEYSYVRNTLV 62

Query: 55  TSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114
             +L LV   A  +R    P+ ++V  G IGL++A+ +FDP RG    +++M  I   ++
Sbjct: 63  ELNLSLVRYAARRFRARSEPMEDIVQVGTIGLIKAINRFDPGRGVEFTSFAMPTITGEIK 122

Query: 115 EYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVI 174
            +   +   VK+     + R+            A+  +  +P   V +A +L+VS  E+ 
Sbjct: 123 RFFRDTSWAVKVPRRLQELRID-----AAKAHDALEQDLGRPPSDVELAGRLHVSPEELA 177

Query: 175 SMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
                  G    SL+A        +S      + + +          +R      L   +
Sbjct: 178 EGQKAAHGYSARSLDAPSQEEGDLASYSGAPAIGEEEPAY-------DRIECLESLKPIL 230

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
           + L  RER +   R  QE  +T   +     +S+  V ++ +R   +++  +    E   
Sbjct: 231 AALPDRERTLLSLRFGQE--LTQAEIGDRLGLSQMHVSRLLSRTLARLRTGLLTDPEHED 288

Query: 293 SP 294
            P
Sbjct: 289 PP 290


>gi|291538524|emb|CBL11635.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Roseburia
           intestinalis XB6B4]
          Length = 254

 Score =  128 bits (321), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 54/257 (21%), Positives = 116/257 (45%), Gaps = 21/257 (8%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQA 89
           E+  L + Y+++       +++  +  LV  +A     Y GY +   ++VS G  GL+ A
Sbjct: 5   EKERLWEEYQKNPSAELREKIIIEYAPLVRVVAGRLSMYLGYNVEYEDLVSYGIFGLIDA 64

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + KFD  +  +  TY+   I+ ++ + I +   +  I  T  QKR     ++++  ++ I
Sbjct: 65  IDKFDRGKDVKFETYASLRIRGSILDQIRK---MDWIPRTVRQKR-----KKIEEAIKQI 116

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYD 207
                +      IA++L + E E+     +L      SLN  +    +        +   
Sbjct: 117 ETKTGRNASDEEIAQELGIGEEELNDWQTQLNVTNVISLNEFVEQGGEP------VMDAK 170

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           ++       E  + +  + +L  S+ +L  +E+++      ++  +TL+ +SS  EVS  
Sbjct: 171 NNSHFIQPEESVQEEELKKVLMESLELLTEKEKKVILLYYYED--MTLKEISSILEVSES 228

Query: 268 RVRQIEARAFKKVQESI 284
           RV Q+  +A  K+++ +
Sbjct: 229 RVSQLHTKALLKMRKRM 245


>gi|16078710|ref|NP_389529.1| RNA polymerase sigma factor SigD [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221309525|ref|ZP_03591372.1| RNA polymerase sigma factor SigD [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221313849|ref|ZP_03595654.1| RNA polymerase sigma factor SigD [Bacillus subtilis subsp. subtilis
           str. NCIB 3610]
 gi|221318772|ref|ZP_03600066.1| RNA polymerase sigma factor SigD [Bacillus subtilis subsp. subtilis
           str. JH642]
 gi|221323044|ref|ZP_03604338.1| RNA polymerase sigma factor SigD [Bacillus subtilis subsp. subtilis
           str. SMY]
 gi|296330862|ref|ZP_06873337.1| RNA polymerase sigma factor SigD [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305674380|ref|YP_003866052.1| RNA polymerase sigma factor sigma-D [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|321315414|ref|YP_004207701.1| RNA polymerase sigma factor SigD [Bacillus subtilis BSn5]
 gi|1350863|sp|P10726|RPSD_BACSU RecName: Full=RNA polymerase sigma-D factor; AltName: Full=Sigma-28
 gi|289304|gb|AAA61470.1| sigma factor 28 [Bacillus subtilis]
 gi|2634019|emb|CAB13520.1| RNA polymerase sigma-28 factor (sigma-D) [Bacillus subtilis subsp.
           subtilis str. 168]
 gi|291484202|dbj|BAI85277.1| RNA polymerase sigma factor SigD [Bacillus subtilis subsp. natto
           BEST195]
 gi|296151867|gb|EFG92741.1| RNA polymerase sigma factor SigD [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305412624|gb|ADM37743.1| RNA polymerase sigma factor sigma-D [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|320021688|gb|ADV96674.1| RNA polymerase sigma factor SigD [Bacillus subtilis BSn5]
          Length = 254

 Score =  128 bits (321), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 51/262 (19%), Positives = 114/262 (43%), Gaps = 19/262 (7%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQA 89
           E+ VL  R++E  D  A   L+  ++ LV              +   +++S G +GL  A
Sbjct: 7   EDQVLWTRWKEWKDPKAGDDLMRRYMPLVTYHVGRISVGLPKSVHKDDLMSLGMLGLYDA 66

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           ++KFDP R  +  TY+ + I+ A+ + + +      +  T+ +K      ++++  ++ +
Sbjct: 67  LEKFDPSRDLKFDTYASFRIRGAIIDGLRKEDW---LPRTSREKT-----KKVEAAIEKL 118

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCR--LAGDESLNALINSSDKNSSQWQDWLVYD 207
               L+      IA++L ++  +V+S       A   S++  ++  D       +  V  
Sbjct: 119 EQRYLRNVSPAEIAEELGMTVQDVVSTMNEGFFANLLSIDEKLHDQDDGE----NIQVMI 174

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            D +     EK  +      L   +  L+ +E+ +       +  +TL  +     +S  
Sbjct: 175 RDDKNVPPEEKIMKDELIAQLAEKIHELSEKEQLVVSLFY--KEELTLTEIGQVLNLSTS 232

Query: 268 RVRQIEARAFKKVQESIQKQVE 289
           R+ QI ++A  K++  ++K ++
Sbjct: 233 RISQIHSKALFKLKNLLEKVIQ 254


>gi|240145473|ref|ZP_04744074.1| RNA polymerase sigma-27 factor [Roseburia intestinalis L1-82]
 gi|257202447|gb|EEV00732.1| RNA polymerase sigma-27 factor [Roseburia intestinalis L1-82]
 gi|291536032|emb|CBL09144.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Roseburia
           intestinalis M50/1]
          Length = 254

 Score =  128 bits (321), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 54/257 (21%), Positives = 116/257 (45%), Gaps = 21/257 (8%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQA 89
           E+  L + Y+++       +++  +  LV  +A     Y GY +   ++VS G  GL+ A
Sbjct: 5   EKEKLWEEYQKNPSAELREKIIIEYAPLVRVVAGRLSMYLGYNVEYEDLVSYGIFGLIDA 64

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + KFD  +  +  TY+   I+ ++ + I +   +  I  T  QKR     ++++  ++ I
Sbjct: 65  IDKFDRGKDVKFETYASLRIRGSILDQIRK---MDWIPRTVRQKR-----KKIEEAIKQI 116

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYD 207
                +      IA++L + E E+     +L      SLN  +    +        +   
Sbjct: 117 ETKTGRNASDEEIAQELGIGEEELNDWQTQLNVTNVISLNEFVEQGGEP------VMDAK 170

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           ++       E  + +  + +L  S+ +L  +E+++      ++  +TL+ +SS  EVS  
Sbjct: 171 NNSHFIQPEESVQEEELKKVLMESLELLTEKEKKVILLYYYED--LTLKEISSILEVSES 228

Query: 268 RVRQIEARAFKKVQESI 284
           RV Q+  +A  K+++ +
Sbjct: 229 RVSQLHTKALLKMRKKM 245


>gi|118442872|ref|YP_878340.1| sporulation sigma factor SigK [Clostridium novyi NT]
 gi|118133328|gb|ABK60372.1| DNA-dependent RNA polymerase sigma subunit [Clostridium novyi NT]
          Length = 225

 Score =  128 bits (321), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 60/275 (21%), Positives = 105/275 (38%), Gaps = 63/275 (22%)

Query: 9   IVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           +++G   L+ Y+      P  L ++EE    +++++ GD  A   L+  +LRLV  I   
Sbjct: 1   MIDGMTFLTAYVSNGTSFPQPLNEKEEKYYLQQFKQ-GDALAKGILIERNLRLVAHIVKK 59

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y      + +++S G +GL++A+  FD ++G RLATY+   I+  +   I  S       
Sbjct: 60  YSYPNKDVDDLISIGTVGLIKAIDSFDVDKGTRLATYAARCIENEILMLIRNS------- 112

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
                       +++K                              + +   +  D    
Sbjct: 113 ------------KKIKSE----------------------------VYLQDPIGVD---- 128

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
                 + N     D L  D D   +V+   E R   R +  +    L  RE+ I + R 
Sbjct: 129 -----KEGNEISLMDILSSDEDSVIEVV---ENRMEVRKLYDKIEKCLTEREKIIIKMRY 180

Query: 248 L--QENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                   T   ++S   +SR  V +IE RA KK+
Sbjct: 181 GLVDGKSKTQREIASLLNISRSYVSRIEKRALKKI 215


>gi|309778066|ref|ZP_07673005.1| RNA polymerase sigma-E factor [Erysipelotrichaceae bacterium
           3_1_53]
 gi|313901138|ref|ZP_07834626.1| RNA polymerase sigma-E factor [Clostridium sp. HGF2]
 gi|308914160|gb|EFP59961.1| RNA polymerase sigma-E factor [Erysipelotrichaceae bacterium
           3_1_53]
 gi|312954096|gb|EFR35776.1| RNA polymerase sigma-E factor [Clostridium sp. HGF2]
          Length = 234

 Score =  128 bits (321), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 61/269 (22%), Positives = 113/269 (42%), Gaps = 63/269 (23%)

Query: 19  YIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           YI     +P  L+K+EE   A    E+GD  A + L+  +LRLVV IA  Y    + + +
Sbjct: 24  YIQGNDVLPKPLDKEEELA-ALIALENGDEEARNTLIEHNLRLVVYIAKRYETNPIFMED 82

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++S G+IGL++AV  F  ++  +L TY+   I+  +  ++ +                  
Sbjct: 83  LISIGSIGLIKAVNTFKRDKNIKLVTYASRCIENEILMFLRKKSR--------------- 127

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
                                     +K+ VS  E ++++                D N 
Sbjct: 128 --------------------------RKVEVSFDEPLNIDY---------------DGNE 146

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL-QENPVTLE 256
               D L  D D    V+ ++ E+K  +  L  +MS L  RER+I + R   Q   +T +
Sbjct: 147 LLLSDILGTDDD----VVTKEFEKKENKRELLEAMSTLKERERQILQMRYGIQHEELTQK 202

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           +++    +S+  + ++E R   K++  ++
Sbjct: 203 DIAKRLGISQSYISRLEKRIIAKLKVQMK 231


>gi|254478789|ref|ZP_05092157.1| RNA polymerase sigma-E factor [Carboxydibrachium pacificum DSM
           12653]
 gi|214035301|gb|EEB76007.1| RNA polymerase sigma-E factor [Carboxydibrachium pacificum DSM
           12653]
          Length = 244

 Score =  128 bits (321), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 58/262 (22%), Positives = 107/262 (40%), Gaps = 63/262 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L  +EE  L  +  E GD  A   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 42  PPLSVEEESYLISKM-EKGDNEAKSILIERNLRLVVYIAKKFENTGVGIEDLISIGTIGL 100

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+  F+P +  +LATY+   I+  +  Y+ R+                          
Sbjct: 101 IKAINTFNPRKKIKLATYASRCIENEILMYLRRNNKT----------------------- 137

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                             +L VS  E ++++    G+E L + I  +D  +        Y
Sbjct: 138 ------------------RLEVSFDEPLNVD--WDGNELLLSDILGTDNET-----VYKY 172

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEV 264
             D  E+ L+    +K            L  RE++I   R   E     T + ++    +
Sbjct: 173 IEDEVERELLTSALKK------------LPDREKKIIRLRFGLEGGTEKTQKEVADMLGI 220

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+  + ++E +  K++++ + +
Sbjct: 221 SQSYISRLEKKILKRLKKEMNR 242


>gi|302531661|ref|ZP_07284003.1| RNA polymerase sigma-B factor [Streptomyces sp. AA4]
 gi|302440556|gb|EFL12372.1| RNA polymerase sigma-B factor [Streptomyces sp. AA4]
          Length = 258

 Score =  128 bits (321), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 95/240 (39%), Gaps = 23/240 (9%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                 LV  HL L   +A  +R     + ++V    +GL+ AV ++DP +G     +++
Sbjct: 31  EEIRDILVREHLELARNLARKFRNRDEAMDDLVQIATVGLIHAVDRYDPTQGTDFLAFAV 90

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I   ++ +   +   V++     +         +    + +T    +  +   IA+ L
Sbjct: 91  PTISGELRHHFRDNSWSVRVPRRLKELNAT-----ISAAREELTVRLSRAPKPSEIARHL 145

Query: 167 NVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +V   +V        G    SL+ L+    +NS+  +      + GQ ++          
Sbjct: 146 DVPIEDVYEGLRAGQGRYGASLDNLL----ENSAHTRFGAPDANLGQAEL---------- 191

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L   +  L  RER+I   R      ++  +++    VS+ +V ++ A   KK++  +
Sbjct: 192 REALRPMLDSLPERERKIVALRFGSG--MSQSDIARRVGVSQMQVSRLLAATLKKLRTGL 249


>gi|295092920|emb|CBK82011.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Coprococcus sp.
           ART55/1]
          Length = 206

 Score =  128 bits (321), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 53/261 (20%), Positives = 98/261 (37%), Gaps = 66/261 (25%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L  +EE          GD +A   L+  +LRLV  I+  Y        +++S G IGL+
Sbjct: 7   PLTPEEEKKYI-ALCLSGDKAARSILIEYNLRLVAHISRKYNSAVRDPEDLLSIGTIGLI 65

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +A+  + P++G +L+ Y+   I                      +  L   LR  K    
Sbjct: 66  KAIDSYKPDKGCKLSGYAAKCI----------------------ENELLMTLRHEKKK-- 101

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                                            A + S+   I +  + +    + ++ D
Sbjct: 102 ---------------------------------AREVSIYDPIGTDKEGN----EIVILD 124

Query: 208 HDGQEQV-LIEKEERKNRRNMLTRSMSV-LNPRERRIFEARRLQEN--PVTLENLSSEFE 263
             G E V +++K  + +   +L   +S  L+ RER I   R   +   P+T + ++    
Sbjct: 125 IIGSENVNVLDKMIQDDHLCLLPSCISSLLSSREREIICMRYGLDGQSPLTQKEVARMLG 184

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +SR  V +IE +A  K++  +
Sbjct: 185 ISRSYVSRIEKKALGKLRGCL 205


>gi|282861223|ref|ZP_06270288.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
 gi|282563881|gb|EFB69418.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           sp. ACTE]
          Length = 296

 Score =  128 bits (321), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 47/237 (19%), Positives = 102/237 (43%), Gaps = 11/237 (4%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + L+  ++ LV   A  +R  G   + ++   G +GL++A+ +F+  R    AT+++ 
Sbjct: 68  ARNTLIEMNISLVRFAARRFRNRGSGDMEDITQVGIVGLIKAIDRFELSREVEFATFAVP 127

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +I   ++ +   +   V +     + R+      L    + +     +   V  +A+ L 
Sbjct: 128 YIVGEIKRFFRDTTWAVHVPRRLQELRV-----ELAKAKEELAVRLDRDPTVKELAEYLG 182

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++E EV+       G  + +  + +    ++        D  G+    +E  E     + 
Sbjct: 183 LTEDEVVEGIVASNGYTAGSLDLPTDANEATATATRTFADILGEPDAAMETVE---NLHA 239

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   +  L+ RERRI E R  QE  +T   + +E  +S+  V ++ +R   K++  +
Sbjct: 240 LAPLLEELDDRERRIIEMRFGQE--MTQAQIGAELGISQMHVSRLLSRTLGKLRTGM 294


>gi|187932801|ref|YP_001885388.1| sporulation sigma factor SigE [Clostridium botulinum B str. Eklund
           17B]
 gi|187720954|gb|ACD22175.1| RNA polymerase sigma-E factor [Clostridium botulinum B str. Eklund
           17B]
          Length = 235

 Score =  128 bits (321), Expect = 1e-27,   Method: Composition-based stats.
 Identities = 58/265 (21%), Positives = 103/265 (38%), Gaps = 65/265 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K EE  L      HGD S    L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 33  PPLSKDEEETLVNNLM-HGDESIRSTLIERNLRLVVYIARKFENTGVHVEDLISVGTIGL 91

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I                      +  +   LRR     
Sbjct: 92  IKAVNTFNPEKKIKLATYASRCI----------------------ENEILMYLRR----- 124

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS-DKNSSQWQDWLV 205
                                         N ++  + S    +N   D N     D L 
Sbjct: 125 ------------------------------NSKIKAEISFYEPLNIDWDGNELLLSDILG 154

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFE 263
            ++D     +    E +  + +L  ++ +LN RE+ I   R         T + ++    
Sbjct: 155 TEND----EVYNLIEDEVDKQLLLMALRILNDREKEIVRLRFGLNGTREKTQKEVADMLG 210

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           +S+  + ++E +  +++++ I K +
Sbjct: 211 ISQSYISRLEKKIIRRLKKEISKMI 235


>gi|300871802|ref|YP_003786675.1| RNA polymerase sigma factor [Brachyspira pilosicoli 95/1000]
 gi|300689503|gb|ADK32174.1| RNA polymerase sigma factor [Brachyspira pilosicoli 95/1000]
          Length = 270

 Score =  128 bits (321), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 48/270 (17%), Positives = 109/270 (40%), Gaps = 19/270 (7%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG-----YRGYGLPISEV 78
             IP +    E      Y++         LV  +  LV  +A            +   ++
Sbjct: 7   GIIPNITDDNEQEYWIEYKKTLSPHIKEALVIKYSNLVKYVANQINFNMKATRDIEFDDL 66

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           V  G +GL+ A++K+DP +  +  TY+   IK ++ + + +   + K+  +   +R   +
Sbjct: 67  VGYGALGLIDAIEKYDPNKEVKFKTYATTRIKGSIYDELRK---IDKLPRSI--RREIKD 121

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL--AGDESLNALINSSDKN 196
           +   +  L++    N+       IA  + +  S++         A   SL+ +    D +
Sbjct: 122 IEIAREFLESKLGRNVNS---QEIADTMGIPLSKINETMRYSIEASTTSLSEVWYHGDDS 178

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
                   +   D      +   ERK+ +  +  ++  L  +ER +      ++  +TL+
Sbjct: 179 DEISIMDTLKASDKNNPEYL--AERKDVQKKIVEALDKLPEKERSVLILYYYED--LTLK 234

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +    +VS  RV Q+  +A ++++ S+ +
Sbjct: 235 EIGKVLDVSESRVSQLHTKAVQQLRYSLSE 264


>gi|229543758|ref|ZP_04432818.1| RNA polymerase, sigma 28 subunit, SigK [Bacillus coagulans 36D1]
 gi|229328178|gb|EEN93853.1| RNA polymerase, sigma 28 subunit, SigK [Bacillus coagulans 36D1]
          Length = 241

 Score =  128 bits (321), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 53/267 (19%), Positives = 95/267 (35%), Gaps = 63/267 (23%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+        L   EE    KR  E GD  A + L+  +LRLV  I   +   G   
Sbjct: 18  LVSYVKNNAFPQPLSASEERKYLKRMAE-GDADARNILIEHNLRLVAHIVKKFENTGEDT 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++S G IGL++A++ +   +G +LATY+   I+  +                      
Sbjct: 77  EDLISIGTIGLIKAIESYSEGKGTKLATYAARCIENEI---------------------- 114

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
             +LR LK                            + +S++  +  D          + 
Sbjct: 115 LMHLRALKKT-------------------------KKDVSLHDPIGQD---------KEG 140

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPV 253
           N     D L  +     + + +  +       + +   +L+ RE+++   R         
Sbjct: 141 NEISLIDVLQSE----AEDVFDTIQLNMELEKVKQFFDILDEREKQVIIGRFGLNLKKEK 196

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKV 280
           T   ++ E  +SR  V +IE RA  K+
Sbjct: 197 TQREIAKELGISRSYVSRIEKRALMKM 223


>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 =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 36/116 (31%), Positives = 56/116 (48%), Gaps = 2/116 (1%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 571 ERRAREAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 630

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           TY+ WWI+ A+   I      ++I            + R+   +   T N   P  
Sbjct: 631 TYATWWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGNEPDPAT 684


>gi|284053375|ref|ZP_06383585.1| RNA polymerase sigma factor SigC [Arthrospira platensis str.
           Paraca]
          Length = 183

 Score =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 38/183 (20%), Positives = 84/183 (45%), Gaps = 13/183 (7%)

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
            WWI+  +   I      +++     +K     L ++K   + I+    +   +  IA +
Sbjct: 1   YWWIRQGITRAIATQSRTIRLPVHITEK-----LNKIKKAQRKISQEKSRTATIDDIATE 55

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           L ++  ++  +  R+    SL   +       ++  D L  +    E++L+    R++  
Sbjct: 56  LKMTPDQIREVLLRVPRSVSLETKV--GTDKDTELGDLLETEESTPEELLM----RESLY 109

Query: 226 NMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             L   ++ L+ +ER + + R      +P +L  +    ++SRERVRQIEA+A +K+++ 
Sbjct: 110 RELQHILADLSGKERAVIQMRYGLGDGHPYSLAEIGRALDLSRERVRQIEAKALQKLRQP 169

Query: 284 IQK 286
            ++
Sbjct: 170 KRR 172


>gi|157826499|ref|YP_001495563.1| RNA polymerase sigma factor RpoD [Rickettsia bellii OSU 85-389]
 gi|157801803|gb|ABV78526.1| RNA polymerase sigma factor RpoD [Rickettsia bellii OSU 85-389]
          Length = 514

 Score =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 37/134 (27%), Positives = 67/134 (50%), Gaps = 5/134 (3%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E   L A   ++ ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 382 ERQTLQAKKDMIEANLRLVISIAKKYANRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 441

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+ WWI+ A+   I      ++I        +   + ++    + + +          I
Sbjct: 442 TYATWWIRQAITRAIADQARTIRIPVH-----MIETINKIIRTSRQMLNELGYEPTPAEI 496

Query: 163 AKKLNVSESEVISM 176
           A +L++   +V  +
Sbjct: 497 AARLSMPIDKVRKV 510



 Score = 35.6 bits (81), Expect = 9.5,   Method: Composition-based stats.
 Identities = 13/68 (19%), Positives = 28/68 (41%), Gaps = 8/68 (11%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM-GYR 69
             +  +  Y+ ++  + +L ++ E  +AKR  E         L+ +  R    IAM  +R
Sbjct: 99  TTDDPVRLYLKDMGGVDLLTRENEVEIAKRIEEG-----RKTLIAALCRSP--IAMDKFR 151

Query: 70  GYGLPISE 77
            +   +  
Sbjct: 152 KWYADLVN 159


>gi|226361251|ref|YP_002779029.1| RNA polymerase sigma factor SigF [Rhodococcus opacus B4]
 gi|226239736|dbj|BAH50084.1| RNA polymerase sigma factor SigF [Rhodococcus opacus B4]
          Length = 265

 Score =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 41/235 (17%), Positives = 91/235 (38%), Gaps = 14/235 (5%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              +VT  L L   IA  + G G    ++V    +GL+ +V +FD ERG    ++++  I
Sbjct: 42  RDAVVTRCLPLAEHIARRFDGRGEAHDDLVQVARLGLVNSVDRFDVERGSDFVSFAVPTI 101

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     +  L      L   +  ++ +      V  +A+ L++ 
Sbjct: 102 MGEVRRHFRDTGWAVRVPRRMKELHLA-----LSQAVAELSQSLGHAPTVSELAEHLDLE 156

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           + EV          ++++    SSD+         + D+D     +            L 
Sbjct: 157 QEEVAQGLLAGNAYQTVSVDNTSSDRAGELSMVETLGDYDAAMDDV-------ENHETLR 209

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             +  L  RER +   R      +T   ++    +S+  V ++ A+    +++ +
Sbjct: 210 PLLQSLPERERTVLMLRFFGN--MTQTQIADRVGISQMHVSRLLAKTLASLRDQL 262


>gi|167628365|ref|YP_001678864.1| RNA polymerase sigma-k factor, putative [Heliobacterium
           modesticaldum Ice1]
 gi|167591105|gb|ABZ82853.1| RNA polymerase sigma-k factor, putative [Heliobacterium
           modesticaldum Ice1]
          Length = 233

 Score =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 60/282 (21%), Positives = 98/282 (34%), Gaps = 65/282 (23%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           + G   L  YI        L   EE     R +E GD  A ++L+  +LRLV  +   + 
Sbjct: 14  IKGITALLSYISNNAFPQPLSDTEEAYCLARLKE-GDEQARNKLIEHNLRLVAHLVKKFD 72

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           G G    +++S G IGL++A+  FD  +G +LATY+   I+  +                
Sbjct: 73  GTGENNDDLISIGTIGLIKAINTFDASKGTKLATYAARCIENEI---------------- 116

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
                   +LR +K                                    + G+ SL   
Sbjct: 117 ------LMHLRAMKK-----------------------------------MRGEVSLYDP 135

Query: 190 INSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
           I    + N     D L  D +    ++    E+    + L +       RER + E R  
Sbjct: 136 IGVDKEGNEITLIDILGTDPEAVSDIVENALEQARLLSKLKKLSK----RERYVIELRYG 191

Query: 249 Q--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
                  T   ++    +SR  V +IE RA  K+   +  + 
Sbjct: 192 LLSGCRQTQREIAKNLGISRSYVSRIEKRAIMKLMSDLASKA 233


>gi|269795656|ref|YP_003315111.1| RNA polymerase sigma-28 subunit SigD/FliA/WhiG [Sanguibacter
           keddieii DSM 10542]
 gi|269097841|gb|ACZ22277.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Sanguibacter
           keddieii DSM 10542]
          Length = 345

 Score =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 45/252 (17%), Positives = 101/252 (40%), Gaps = 13/252 (5%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFD 94
            + Y+   D     RL+  +  LV  +A          +  +++VS G  GL+ A++KF+
Sbjct: 100 WREYKACADAPTRERLILHYAPLVTSVASRVGMKLPSTVEHADLVSYGMFGLIDAIEKFE 159

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
            +R  +  TY+   I+ A+ + + R+   V     +  + +      L+  L        
Sbjct: 160 LDREIKFETYATSRIRGAILDEL-RANDWVPRSVRSKARAVDRAHAELEARLH------- 211

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +      IA+ + ++ SE+ S+   ++    +         +  +    L   H  +   
Sbjct: 212 RAPTDPEIAEHMEIALSELRSIRHLVSTVNLVALDEVFGAGDQVEPVGHLDTGHGARSTD 271

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
                E K  + +L+++M  L  RE+ +          +TL  + +   V+  R+ Q+  
Sbjct: 272 PARTFESKETKFLLSQAMDQLGEREKIMLVLYYY--EGMTLAEIGAVLGVTESRISQMHT 329

Query: 275 RAFKKVQESIQK 286
            A  +++E + +
Sbjct: 330 AAMGRLREKLSR 341


>gi|303238907|ref|ZP_07325438.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302593540|gb|EFL63257.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 244

 Score =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 56/265 (21%), Positives = 102/265 (38%), Gaps = 64/265 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EE  L  +  E  D      L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 41  PPLSNDEESYLLNKL-EKNDYGVKTILIERNLRLVVYIARKFENTGVGVEDLISIGTIGL 99

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+  F+P +  +LATY+   I+  +                         LRR     
Sbjct: 100 IKAINTFNPSKNIKLATYASRCIENEI----------------------LMYLRRNNR-- 135

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                        M   ++ DE LN      D N     D L  
Sbjct: 136 -----------------------------MKTEISIDEPLN---IDWDGNELLLSDILGT 163

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN---PVTLENLSSEFE 263
           ++D    ++    E +  + +L  +M  L+ RE++I E R    N     T + ++    
Sbjct: 164 END----LIHRSIEDEVDKELLNTAMKKLSMREKKIMELRFGLSNGGMEKTQKEVADMLG 219

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           +S+  + ++E +   ++++ I + +
Sbjct: 220 ISQSYISRLEKKIICRLKKEISRMI 244


>gi|89100825|ref|ZP_01173677.1| SpoIIIC [Bacillus sp. NRRL B-14911]
 gi|89084471|gb|EAR63620.1| SpoIIIC [Bacillus sp. NRRL B-14911]
          Length = 240

 Score =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 52/267 (19%), Positives = 93/267 (34%), Gaps = 63/267 (23%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+        L   +E    +   E GD  A + L+  +LRLV  I   +   G   
Sbjct: 18  LVSYVKNNAFPQPLSAADERKYLRLMAE-GDAHARNMLIEHNLRLVAHIVKKFENTGEDS 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++S G IGL++A++ +   +G +LATY+   I+  +                      
Sbjct: 77  EDLISIGTIGLIKAIESYSEGKGTKLATYAARCIENEI---------------------- 114

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
             +LR LK                                       D SL+  I    +
Sbjct: 115 LMHLRALKKT-----------------------------------KKDVSLHDPIGQDKE 139

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPV 253
            +   +  L+     + + +I   +       +   + VL+ RE+ +   R   +     
Sbjct: 140 GN---EISLIDVLKSESEDVINTIQLNMELEKVKEYIDVLDDREKEVIIGRFGLDLKKEK 196

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKV 280
           T   ++ E  +SR  V +IE RA  K+
Sbjct: 197 TQREIAKELGISRSYVSRIEKRALMKM 223


>gi|160880817|ref|YP_001559785.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           phytofermentans ISDg]
 gi|160429483|gb|ABX43046.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Clostridium
           phytofermentans ISDg]
          Length = 254

 Score =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 51/258 (19%), Positives = 113/258 (43%), Gaps = 18/258 (6%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGL 86
             + +  L   Y +        +++  +  LV  +A     Y GY +   ++V  G  GL
Sbjct: 2   SAETKQKLWGEYGKKRTPDIREKIIIEYANLVKIVAGRLSIYLGYNVEYDDLVGYGTFGL 61

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           + A+ KFD E+G +  TY+   I+ A+ + I R    +       QKRL    ++    L
Sbjct: 62  IDAIDKFDCEKGAKFETYASLRIRGAILDQI-RKMDWIPRTLRQKQKRLDAAYQK----L 116

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           + +       E+V    +          +   +++   SL+  +   +       + +  
Sbjct: 117 ETMYGRQATDEEVAKELEITTEELETWQN-QTKISNLVSLDEYMEQGE----VKVESIAS 171

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           +   Q + ++EK+E    + ML +++  L  +E+++      ++  +TL+ +S+  EVS 
Sbjct: 172 EDYAQPEKVMEKQEL---KAMLVKALEYLTEKEKKVIVLYYYED--LTLKEISAVLEVSE 226

Query: 267 ERVRQIEARAFKKVQESI 284
            R+ Q+  +A +K+++ +
Sbjct: 227 SRISQLHTKALQKMRQKL 244


>gi|218289600|ref|ZP_03493820.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
 gi|218240250|gb|EED07433.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
          Length = 222

 Score =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 51/220 (23%), Positives = 91/220 (41%), Gaps = 17/220 (7%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           H + +   L  +E   L +R   +GD  A  RL+  + RLV  +   + G G    ++  
Sbjct: 11  HHVDEYEKLSDEEVRELLER-SHNGDAEARERLIVHNQRLVWAVVQRFLGRGYEAEDLFQ 69

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
            G IGLM+AV KFD     + +TY++  I   +Q ++    S VK+  +   K     +R
Sbjct: 70  IGCIGLMKAVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDD-STVKVSRSL--KETAKQIR 126

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
            ++  L        +   +  IA+ + +  SE++     L    S++  +  +D +    
Sbjct: 127 HVRDRL---AKELGRQPHITEIAEAMGMEPSEIVFAQEALRAPASIHETVYENDGDPIYL 183

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            D +            E+ E K  +  L   +  L  RER
Sbjct: 184 MDQIAD----------EETEGKFDKVELHEIIGRLPERER 213


>gi|15604780|ref|NP_219564.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis
           D/UW-3/CX]
 gi|76788774|ref|YP_327860.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis
           A/HAR-13]
 gi|237802495|ref|YP_002887689.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis
           B/Jali20/OT]
 gi|237804410|ref|YP_002888564.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis
           B/TZ1A828/OT]
 gi|255310863|ref|ZP_05353433.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis 6276]
 gi|255317163|ref|ZP_05358409.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis 6276s]
 gi|255348424|ref|ZP_05380431.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis 70]
 gi|255502966|ref|ZP_05381356.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis 70s]
 gi|255506635|ref|ZP_05382274.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis
           D(s)2923]
 gi|3328455|gb|AAC67652.1| Sigma-28/WhiG Family [Chlamydia trachomatis D/UW-3/CX]
 gi|76167304|gb|AAX50312.1| FliA [Chlamydia trachomatis A/HAR-13]
 gi|231272710|emb|CAX09614.1| RNA polymerase sigma factor [Chlamydia trachomatis B/TZ1A828/OT]
 gi|231273729|emb|CAX10508.1| RNA polymerase sigma factor [Chlamydia trachomatis B/Jali20/OT]
 gi|289525106|emb|CBJ14577.1| RNA polymerase sigma factor [Chlamydia trachomatis Sweden2]
 gi|296434648|gb|ADH16826.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis E/150]
 gi|296435578|gb|ADH17752.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis G/9768]
 gi|296436502|gb|ADH18672.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis
           G/11222]
 gi|296437438|gb|ADH19599.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis
           G/11074]
 gi|296438365|gb|ADH20518.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis
           E/11023]
 gi|297139937|gb|ADH96695.1| RNA polymerase sigma factor sigma-28 [Chlamydia trachomatis G/9301]
 gi|297748191|gb|ADI50737.1| FliA [Chlamydia trachomatis D-EC]
 gi|297749071|gb|ADI51749.1| FliA [Chlamydia trachomatis D-LC]
          Length = 253

 Score =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 51/254 (20%), Positives = 113/254 (44%), Gaps = 17/254 (6%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFD 94
            + Y    ++     L+ S+L LV  +A            + ++ + G  GL++AV++FD
Sbjct: 10  WQLYWSTKEIHHRDVLIESYLPLVKNVAHRLASGMPSHVKMEDLYALGVEGLIRAVERFD 69

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           PE+  R  +Y+++ IKAA+ + + +      +  +  Q+       RL   + ++     
Sbjct: 70  PEKSKRFESYALFIIKAAIIDGLRKQDW---VPRSVYQRA-----NRLADAMDSLRQTLG 121

Query: 155 KPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           K      + + LN+S+ E+     + R A   SL+   +  D +     +  + D   + 
Sbjct: 122 KEPTDGELCEYLNISQQELSHWFSSSRPALVLSLHDDFSCQDDDEGLALEERIADE--RA 179

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           +   +   +K   ++LT ++  L+ +ER++       +  + L+ +     VS  RV QI
Sbjct: 180 ETGYDVIRKKEAISILTEALLALDEKERQVMALYYYDD--LVLKEIGKILGVSESRVSQI 237

Query: 273 EARAFKKVQESIQK 286
            ++A  K++ ++  
Sbjct: 238 HSKALLKLRGTLSS 251


>gi|328912710|gb|AEB64306.1| RNA polymerase sigma factor [Bacillus amyloliquefaciens LL3]
          Length = 242

 Score =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 55/278 (19%), Positives = 96/278 (34%), Gaps = 65/278 (23%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +  IV   + L  Y+        L   EE        E GD  A + L+  +LRLV  I 
Sbjct: 9   LGFIVKELVFLVSYVKNNAFPQPLSNNEEKKYLDLMAE-GDEHARNMLIEHNLRLVAHIV 67

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             +   G    +++S G IGL++ ++ +   +G +LATY+   I+  +            
Sbjct: 68  KKFENTGEDAEDLISIGTIGLIKGIESYSAGKGTKLATYAARCIENEI------------ 115

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
                       +LR LK                                       D S
Sbjct: 116 ----------LMHLRALKKT-----------------------------------KKDVS 130

Query: 186 LNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           L+  I    + N     D L  +     + +I+  +       + + + +L+ RE+ +  
Sbjct: 131 LHDPIGQDKEGNEISRIDVLKSES----EDVIDTIQLNMELEKVKKYIDILDDREKEVIV 186

Query: 245 ARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            R   +     T   ++ E  +SR  V +IE RA  K+
Sbjct: 187 GRFGLDLKKEKTQREIAKELGISRSYVSRIEKRALMKM 224


>gi|297530579|ref|YP_003671854.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
 gi|297253831|gb|ADI27277.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
          Length = 251

 Score =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 52/260 (20%), Positives = 107/260 (41%), Gaps = 22/260 (8%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQA 89
           EE      +    D  AA  LV  ++ LV              +P  E+VS G +GL  A
Sbjct: 8   EERKYWDEWIHGRDRHAAEELVQRYMPLVFYHVQRLSATLPSSVPKDELVSLGLVGLYDA 67

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           ++KFDP R  +  TY+ + I+ A+ + + +   L         + +    ++++  ++ +
Sbjct: 68  LEKFDPSRDLKFDTYASFRIRGAILDGLRKEDWL--------PRSMRDKAKKIEEAIERL 119

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
              +++      IA +L ++E EV +       +    L       D+        L+  
Sbjct: 120 EQRHMRSVTAKEIAAELGMTEEEVQAAASETFFSHWLPLGQTTVDEDEG-------LLSV 172

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            D +  +  E+  ++     L  ++  LN +E+ +       +  +T   + S   +S  
Sbjct: 173 RDDRAPLPEEQIVKQEMIEKLAEAIGQLNEKEQLVISLFY--KEELTFTEIGSLLHLSTS 230

Query: 268 RVRQIEARAFKKVQESIQKQ 287
           R+ QI A+A  K++   +K+
Sbjct: 231 RISQIHAKALWKLRRFFEKE 250


>gi|168182618|ref|ZP_02617282.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           Bf]
 gi|182674200|gb|EDT86161.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           Bf]
          Length = 234

 Score =  127 bits (320), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 59/279 (21%), Positives = 106/279 (37%), Gaps = 63/279 (22%)

Query: 9   IVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++   + L+ Y+      P  L  +EE     R ++ GD  A   LV  +LRLV  I   
Sbjct: 10  VLGSALFLTGYVTGNTSFPKPLSDEEEKYYLDRLKK-GDALAKDILVERNLRLVAHIVKK 68

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           Y   G  I +++S G +GL++A+  FD  +G RLATY+   I+  +   I  +       
Sbjct: 69  YSYPGKDIDDLISIGTVGLIKAIDSFDNSKGTRLATYAARCIENEILMLIRNNKKT---- 124

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
                                                K  V   + I ++     + SL 
Sbjct: 125 -------------------------------------KGEVYLQDPIGVDKE-GNEISLM 146

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
            +++S              D D   +++  K E K     +    + L  RE+++ + R 
Sbjct: 147 DILSS--------------DEDSIIEIVSTKIEVKKLYGKID---TCLRGREKKVIQMRY 189

Query: 248 LQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             ++    T   ++    +SR  V +IE +A KK+ + +
Sbjct: 190 GLKDGRHRTQREIAGILNISRSYVSRIEKKALKKLYKEL 228


>gi|188587739|ref|YP_001920535.1| sporulation sigma factor SigE [Clostridium botulinum E3 str. Alaska
           E43]
 gi|251779018|ref|ZP_04821938.1| RNA polymerase sigma-E factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
 gi|188498020|gb|ACD51156.1| RNA polymerase sigma-E factor [Clostridium botulinum E3 str. Alaska
           E43]
 gi|243083333|gb|EES49223.1| RNA polymerase sigma-E factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
          Length = 235

 Score =  127 bits (319), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 58/265 (21%), Positives = 103/265 (38%), Gaps = 65/265 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K EE  L      HGD S    L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 33  PPLSKDEEETLVNNLM-HGDESIRSTLIERNLRLVVYIARKFENTGVHVEDLISVGTIGL 91

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I                      +  +   LRR     
Sbjct: 92  IKAVNTFNPEKKIKLATYASRCI----------------------ENEILMYLRR----- 124

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS-DKNSSQWQDWLV 205
                                         N ++  + S    +N   D N     D L 
Sbjct: 125 ------------------------------NSKIKAEISFYEPLNIDWDGNELLLSDILG 154

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFE 263
            ++D     +    E +  + +L  ++ +LN RE+ I   R         T + ++    
Sbjct: 155 TEND----EVYNLIEDEVDKQLLLMALRILNDREKEIVRLRFGLNGTREKTQKEVADMLG 210

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           +S+  + ++E +  +++++ I K +
Sbjct: 211 ISQSYISRLEKKIIRRLKKEISKMI 235


>gi|319651643|ref|ZP_08005770.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
 gi|317396710|gb|EFV77421.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
          Length = 239

 Score =  127 bits (319), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 52/267 (19%), Positives = 92/267 (34%), Gaps = 63/267 (23%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+        L   +E     R    GD  A + L+  +LRLV  I   +   G   
Sbjct: 18  LVSYVKNNAFPQPLSPADEKKYL-RLMAAGDAHARNMLIEHNLRLVAHIVKKFENTGEDS 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++S G IGL++A++ +   +G +LATY+   I+  +                      
Sbjct: 77  EDLISIGTIGLIKAIESYSEGKGTKLATYAARCIENEI---------------------- 114

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
             +LR LK                                       D SL+  I    +
Sbjct: 115 LMHLRALKKT-----------------------------------KKDVSLHDPIGQDKE 139

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPV 253
            +   +  L+     + + +I   +       +   + VL+ RE+ +   R   +     
Sbjct: 140 GN---EISLIDVLKSESEDVINTIQLNMELEKVKEYIDVLDDREKEVIVGRFGLDLQKEK 196

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKV 280
           T   ++ E  +SR  V +IE RA  K+
Sbjct: 197 TQREIAKELGISRSYVSRIEKRALMKM 223


>gi|172057862|ref|YP_001814322.1| RNA polymerase sigma factor SigD [Exiguobacterium sibiricum 255-15]
 gi|171990383|gb|ACB61305.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Exiguobacterium
           sibiricum 255-15]
          Length = 257

 Score =  127 bits (319), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 47/259 (18%), Positives = 111/259 (42%), Gaps = 19/259 (7%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLM 87
           ++E   L  ++    D++ A RL+ ++  LV              +   E+ S G +GL 
Sbjct: 2   REELQQLWNQWLSTRDIAVADRLLQNYEPLVHYHVQRLSATLPKSVDRDELKSLGMMGLY 61

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
            A++KFD     +  TY+ + I+ A+ + + +   L         + L    +R++  ++
Sbjct: 62  DALQKFDQNHNNKFDTYAAFRIRGAILDGLRKIDWL--------PRSLREKSKRVEAAVE 113

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLV 205
            +  +  +   +  ++  +++S  EV +       A   S++  +   D+  +    +L 
Sbjct: 114 ILEQSLQRTPTIDEVSSIVDMSPEEVKTALAESYFANILSIDEAVTLQDEGKAMAVSYLD 173

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            D    E  L+ +E        L   +  L+ +E+ +      +E  +TL  +     +S
Sbjct: 174 PDTATPEDTLLMRELIS----KLAEEVEQLSEKEQYVVSLFYFEE--LTLTEIGEVLGLS 227

Query: 266 RERVRQIEARAFKKVQESI 284
             R+ QI ++A +K+++++
Sbjct: 228 TSRISQIHSKALRKLKQAL 246


>gi|255505283|ref|ZP_05345211.3| RNA polymerase sigma-E factor [Bryantella formatexigens DSM 14469]
 gi|255268593|gb|EET61798.1| RNA polymerase sigma-E factor [Bryantella formatexigens DSM 14469]
          Length = 249

 Score =  127 bits (319), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 54/274 (19%), Positives = 103/274 (37%), Gaps = 65/274 (23%)

Query: 18  RYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
            YI     +P  LE   E  + ++        A   L+  +LRLVV IA  +   G+ + 
Sbjct: 34  HYIGGSEVLPSPLEPGREAEVIEQLGGRESGEAKSLLIEHNLRLVVYIAKKFDNTGVGVE 93

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++S G IGL++A+  F+P +  +LATY+   I+  +  Y+ R+                
Sbjct: 94  DLISIGTIGLIKAINTFNPGKNIKLATYASRCIENEILMYLRRTSKT------------- 140

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
                                       K+ VS  E ++++                D N
Sbjct: 141 ----------------------------KMEVSFDEPLNVD---------------WDGN 157

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL----QENP 252
                D L  D D    V+    E +    +L  ++  L+ RER I + R          
Sbjct: 158 ELLLSDILGTDED----VIYRDMETEVEYKLLMHAIDKLSDRERMIIQLRFGIGRNDGEE 213

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            T + ++    +S+  + ++E +   ++++ I +
Sbjct: 214 KTQKEVADMLGISQSYISRLEKKIIGRLKKEIAR 247


>gi|45128597|gb|AAS55059.1| RpoD [Vibrio parahaemolyticus]
          Length = 492

 Score =  127 bits (319), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 37/127 (29%), Positives = 59/127 (46%), Gaps = 2/127 (1%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 366 IGEAKAXRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 425

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ WWI+ A+   I      ++I            L R+   +         PE++ 
Sbjct: 426 FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMLQEMGREPLPEELA 483

Query: 161 AIAKKLN 167
              +   
Sbjct: 484 ERMQMPE 490


>gi|331696322|ref|YP_004332561.1| SigB/F/G subfamily RNA polymerase sigma-28 subunit [Pseudonocardia
           dioxanivorans CB1190]
 gi|326951011|gb|AEA24708.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Pseudonocardia dioxanivorans CB1190]
          Length = 283

 Score =  127 bits (319), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 51/242 (21%), Positives = 99/242 (40%), Gaps = 18/242 (7%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYR-GYGLPISEVVSEGNIGLMQAVKKFDPER-GFRLATYS 105
           +    L+ + L +V  +A+ +  GY     ++V  G +GL+ A+ ++DP+R G  L  Y 
Sbjct: 57  ALRSELILAFLPIVRHLALRHSAGYPGGYDDLVQVGTVGLISAIDRWDPDRAGADLLGYL 116

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
           +  ++  M  Y       V++      K L   + +  G L        +P     +A  
Sbjct: 117 VPCVRGEMLRYFRDRTWAVRVPRRL--KDLAVAINKATGPLSQQLGRAPRP---SELAAH 171

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           L V  SEV+      AG  S    +   D  + +     + + DG       + +    R
Sbjct: 172 LGVDVSEVVEALTAKAGHHS--DPLEPVDPETGESSHERLGELDG-------ELDHVEYR 222

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + L   +  L  RER I   R  ++  +T   ++ E  +S+  V ++ AR+   ++  + 
Sbjct: 223 HALRPLLESLPERERTILMLRFFRD--MTQTQIAEEIGISQMHVSRLLARSLTTLRAGLA 280

Query: 286 KQ 287
            +
Sbjct: 281 AE 282


>gi|154686064|ref|YP_001421225.1| RNA polymerase sigma factor SigD [Bacillus amyloliquefaciens FZB42]
 gi|308173610|ref|YP_003920315.1| RNA polymerase sigma-28 factor sigma-D [Bacillus amyloliquefaciens
           DSM 7]
 gi|154351915|gb|ABS73994.1| SigD [Bacillus amyloliquefaciens FZB42]
 gi|307606474|emb|CBI42845.1| RNA polymerase sigma-28 factor (sigma-D) [Bacillus
           amyloliquefaciens DSM 7]
 gi|328553458|gb|AEB23950.1| RNA polymerase sigma factor SigD [Bacillus amyloliquefaciens TA208]
 gi|328911751|gb|AEB63347.1| RNA polymerase sigma factor [Bacillus amyloliquefaciens LL3]
          Length = 254

 Score =  127 bits (319), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 52/262 (19%), Positives = 115/262 (43%), Gaps = 19/262 (7%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQA 89
           E+ VL  R++E  D  A   L+  ++ LV              +   +++S G +GL  A
Sbjct: 7   EDQVLWSRWKEWKDPKAGDDLMRRYMPLVTYHVGRISVGLPKSVHKDDLMSLGMLGLYDA 66

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           ++KFDP R  +  TY+ + I+ A+ + + +      +  T+ +K      ++++  ++ +
Sbjct: 67  LEKFDPGRDLKFDTYASFRIRGAIIDGLRKEDW---LPRTSREKT-----KKVEAAIEKL 118

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCR--LAGDESLNALINSSDKNSSQWQDWLVYD 207
               L+      IA++L ++E +V+S       A   S++  ++  D       +  V  
Sbjct: 119 EQRYLRNVTPSEIAEELGMTEQDVVSTMNEGFFANLLSIDEKLHDQDDGE----NIQVMI 174

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            D +     EK  +      L   +  L+ +E+ +       +  +TL  +     +S  
Sbjct: 175 RDDKNVPPEEKIMKDELIAQLAGKIHELSEKEQLVVSLFY--KEELTLTEIGQVLNLSTS 232

Query: 268 RVRQIEARAFKKVQESIQKQVE 289
           R+ QI ++A  K++  ++K ++
Sbjct: 233 RISQIHSKALFKLKHLLEKVIQ 254


>gi|239826640|ref|YP_002949264.1| RNA polymerase sigma factor SigD [Geobacillus sp. WCH70]
 gi|239806933|gb|ACS23998.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacillus sp. WCH70]
          Length = 254

 Score =  127 bits (319), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 46/259 (17%), Positives = 109/259 (42%), Gaps = 19/259 (7%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQA 89
           EE     R+  H D  A  +LV +++ LV              +   E++S G +GL  A
Sbjct: 8   EERKYWDRWIYHRDPQAGDKLVQTYMPLVHYHVQRIAASLPKTISKQELISLGLMGLYDA 67

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           ++KFDP R  +  TY+ + I+ A+ + + +      +  +  +K      ++++  ++ +
Sbjct: 68  LEKFDPSRDLKFDTYASFRIRGAIFDGLRKEDW---LPRSVREKA-----KKIEETIEKL 119

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
               ++      +A +L ++E EV         A   S   +I  + +      + L+  
Sbjct: 120 EQRYMRSVTAKEVADELGITEEEVYMAVNENFFANVLSFQHVITENKEEE----NALLAI 175

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            D +     E+  ++     L   +  L+ +E+ +       +  +T   +     +S  
Sbjct: 176 RDEKTPSPEEEVLKQELYEKLAEVIQQLSEKEQLVISLFY--KEELTFTEIGEILGLSTS 233

Query: 268 RVRQIEARAFKKVQESIQK 286
           R+ Q+ ++A  K+++ +++
Sbjct: 234 RISQLHSKAIFKLRKILEQ 252


>gi|260438776|ref|ZP_05792592.1| RNA polymerase sigma-27 factor [Butyrivibrio crossotus DSM 2876]
 gi|292808765|gb|EFF67970.1| RNA polymerase sigma-27 factor [Butyrivibrio crossotus DSM 2876]
          Length = 255

 Score =  127 bits (319), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 56/260 (21%), Positives = 114/260 (43%), Gaps = 17/260 (6%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKF 93
           L   Y ++       +++  +  LV  +A     Y GY +   ++VS G  GL+ A+ KF
Sbjct: 9   LWMSYSKNRTPELREQIIIEYAPLVKLVAGRLSMYLGYNVEYEDLVSYGIFGLIDAIDKF 68

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D  +  +  TY+   I+  + + I R    +       QK++       +  L+     N
Sbjct: 69  DYGKNVKFETYASLRIRGEILDQI-RKMDWIPRSVREKQKKIDS----ARTRLETENGKN 123

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
              E++ A A  L++ E        +++   SL+  +    + S    +     H  Q +
Sbjct: 124 ATDEELAA-ALDLSLDELNNWQGQTKVSNLVSLDEFVEQGSELS---METAGNSHFEQPE 179

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
            ++EKEE   +   ++ ++S L  +E+ +      +E  +TL+ +S+  EVS  RV Q+ 
Sbjct: 180 RVVEKEELAVK---ISEALSHLTEKEKMVVTLYYYEE--MTLKEISNVMEVSESRVSQLH 234

Query: 274 ARAFKKVQESIQKQVELSSS 293
            +A  K+++S+   + +   
Sbjct: 235 TKALVKLKKSLGNYMNIFDE 254


>gi|299535876|ref|ZP_07049196.1| RNA polymerase sigma-35 factor precursor [Lysinibacillus fusiformis
           ZC1]
 gi|298728628|gb|EFI69183.1| RNA polymerase sigma-35 factor precursor [Lysinibacillus fusiformis
           ZC1]
          Length = 206

 Score =  127 bits (319), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 53/259 (20%), Positives = 111/259 (42%), Gaps = 63/259 (24%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L ++EE  +   +  +GDL A   L+  +LRLVV IA  +   G PI +++S G+IGL+
Sbjct: 4   PLSREEEVTVIASFM-NGDLRARDTLIERNLRLVVYIARRFDNTGTPIEDLISIGSIGLI 62

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +A++ F+ ++  +LATY+   I                      +  +  +LR+      
Sbjct: 63  KAIETFNTDKNIKLATYASRCI----------------------ENEILMHLRK------ 94

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                                          R+ G+ SL+  +NS    +      ++  
Sbjct: 95  -----------------------------TSRMKGEVSLDEPLNSDADGNELLLSDILG- 124

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVS 265
              +E ++++  E+K  R  +  ++++L  RER I E R        +T + ++    +S
Sbjct: 125 --TEEHIILDNVEKKIERQHMFHAINLLGARERYIMECRFGLNGKVEMTQKEVADHLGIS 182

Query: 266 RERVRQIEARAFKKVQESI 284
           +  + ++E +  + ++E++
Sbjct: 183 QSYISRLEKKIIQDLRENL 201


>gi|162463525|ref|NP_001105185.1| sigma factor protein [Zea mays]
 gi|20159761|gb|AAM12034.1| sigma factor protein [Zea mays]
          Length = 568

 Score =  127 bits (319), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 54/252 (21%), Positives = 104/252 (41%), Gaps = 14/252 (5%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E  L  R +         RL+ +   LV  IA  Y G G  + +++  G +G++   +K
Sbjct: 317 DEAELVSRLQAGYC--CRDRLLVTTEWLVRCIARTYTGMGTALDDLLQAGKMGVLDGAEK 374

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G R +TY  +WI+  M   +  +      G T    R+   +R++K   + I   
Sbjct: 375 FDSRKGCRFSTYVKYWIRKGMLALLAENS-----GVTLLPARMESIMRKVKEARRGIRYR 429

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      +A  + VS + V           SL + +        ++ + +  +    +
Sbjct: 430 QGRNPSDSEVAAAVGVSVANVRLARKCSRRAVSLYSEVAIG--QDVKFAEVIPDESASPD 487

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
           +  +    R   R  L   +  L  RE R+   R   E+    +LE +   + VS+E +R
Sbjct: 488 EAAL---FRGQLRERLLLVLGRLPAREGRVLRLRHGLEDGRCRSLEEIGGIYGVSKEWIR 544

Query: 271 QIEARAFKKVQE 282
           +IE  A  ++++
Sbjct: 545 KIEKSAMARLRD 556


>gi|56419781|ref|YP_147099.1| RNA polymerase sigma factor SigD [Geobacillus kaustophilus HTA426]
 gi|56379623|dbj|BAD75531.1| DNA-directed RNA polymerase sigma-28 factor (sigma-D) [Geobacillus
           kaustophilus HTA426]
          Length = 251

 Score =  127 bits (319), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 52/260 (20%), Positives = 107/260 (41%), Gaps = 22/260 (8%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQA 89
           EE      +    D  AA  LV  ++ LV              +P  E+VS G +GL  A
Sbjct: 8   EERKYWDEWIHGRDRHAAEELVQRYMPLVFYHVQRLSATLPSSVPKDELVSLGLVGLYDA 67

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           ++KFDP R  +  TY+ + I+ A+ + + +   L         + +    ++++  ++ +
Sbjct: 68  LEKFDPSRDLKFDTYASFRIRGAILDGLRKEDWL--------PRSMRDKAKKIEEAIERL 119

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
              +++      IA +L ++E EV +       +    L       D+        L+  
Sbjct: 120 EQRHMRSVTAKEIAAELGMTEEEVQAAASETFFSHWLPLGQTTVDEDEG-------LLAV 172

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            D +  +  E+  ++     L  ++  LN +E+ +       +  +T   + S   +S  
Sbjct: 173 RDDRAPLPEEQIVKQEMIEKLAEAIGQLNEKEQLVISLFY--KEELTFTEIGSLLHLSTS 230

Query: 268 RVRQIEARAFKKVQESIQKQ 287
           R+ QI A+A  K++   +K+
Sbjct: 231 RISQIHAKALWKLRRFFEKE 250


>gi|289578405|ref|YP_003477032.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter italicus Ab9]
 gi|297544681|ref|YP_003676983.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
 gi|289528118|gb|ADD02470.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter italicus Ab9]
 gi|296842456|gb|ADH60972.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
          Length = 246

 Score =  127 bits (319), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 40/254 (15%), Positives = 108/254 (42%), Gaps = 19/254 (7%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLMQAV 90
           E  + K Y    D +  + ++  ++ LV  I               +++++G +GL+ A+
Sbjct: 5   EEDIWKTYNSSKDPNLRNEIIIKYMPLVKHIVKKLIISDVTQSEYEDLINQGVLGLIDAI 64

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +K+ P +G +  TY+   I+  + +Y+ +   +         + L    ++++  ++ + 
Sbjct: 65  EKYQPSKGVKFETYATLRIRGEIIDYLRKKDWM--------PRSLKKKYKKIEETVETLQ 116

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
               +   V  I +   ++E++V+     +      N    +S + + +    L    D 
Sbjct: 117 QKYNREPTVEEITEACGLNETDVLKTLSYI------NVSNINSLEEAIENNFKLHAISDV 170

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
           + +   E+   K  +  L  ++  L  +ER +      ++  +  +++S    ++  R+ 
Sbjct: 171 ELKNPEEEVLYKELKRKLANAIKNLPDKERLVITLYYYED--LNYKDISKILNLTESRIS 228

Query: 271 QIEARAFKKVQESI 284
           QI  +A K+++E +
Sbjct: 229 QIHTKAIKRIREML 242


>gi|291531057|emb|CBK96642.1| RNA polymerase, sigma 29 subunit, SigE [Eubacterium siraeum 70/3]
          Length = 239

 Score =  127 bits (319), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 59/263 (22%), Positives = 105/263 (39%), Gaps = 65/263 (24%)

Query: 27  PMLEKQEE-YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           P L K+EE   LAK        +A   L+  +LRLVV IA  +   G+ I +++S G IG
Sbjct: 36  PPLSKEEEAKTLAKL--NTDFENARETLIVHNLRLVVYIAKKFESTGIGIEDLISIGTIG 93

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++AV  F  E+  +LATY+   I+  +  Y+ ++                         
Sbjct: 94  LIKAVNTFSVEKNIKLATYASRCIENEILMYLRKTNP----------------------- 130

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
                             +K+ VS  E ++++                D N     D L 
Sbjct: 131 ------------------QKMEVSIDEPLNVD---------------WDGNELLLSDILG 157

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFE 263
            D D     +  + E    + ML  ++  L+ RE+ I E R    N    T + ++    
Sbjct: 158 TDDDTVSVDIESEAE----KRMLLEAVEKLDEREKLIMELRFGLNNRPEKTQKEVADMIG 213

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+  + ++E R  K++++ ++ 
Sbjct: 214 ISQSYISRLEKRIIKRLKKEMES 236


>gi|206900763|ref|YP_002250593.1| SigF [Dictyoglomus thermophilum H-6-12]
 gi|206739866|gb|ACI18924.1| SigF [Dictyoglomus thermophilum H-6-12]
          Length = 235

 Score =  127 bits (319), Expect = 2e-27,   Method: Composition-based stats.
 Identities = 49/249 (19%), Positives = 111/249 (44%), Gaps = 20/249 (8%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L  +YRE GD      L+     L+   A  +  YG P+ ++V  G +G ++AV+ +DP
Sbjct: 7   ELWLKYRETGDKKVLEELLEVFDDLIYYWASKFTSYGEPLEDLVQIGYLGFLKAVENYDP 66

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           E+G  L+TY   ++   ++ ++      +KI  +         + ++   ++ + +   +
Sbjct: 67  EKG-DLSTYISHYVLGEIRHHLRDKIDKIKIPRSVK-----GLINKMDNFIKEVWEKENR 120

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
                 IAK LN++   V  +           A++  S ++     D +  +     ++ 
Sbjct: 121 SPSCEEIAKHLNITVESVEELFKIK------EAMMTVSLEDLEIEMDRIRAEKLESFKLP 174

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
           IE       +  L ++++ L   +R++ E    Q+  +T   ++   ++S+ +V +I   
Sbjct: 175 IED------KIALEQALAKLPDIQRKVIEYIFYQD--LTQTEVAKILKISQSQVSRILRS 226

Query: 276 AFKKVQESI 284
           A +K++E +
Sbjct: 227 ALEKLKEML 235


>gi|167749813|ref|ZP_02421940.1| hypothetical protein EUBSIR_00781 [Eubacterium siraeum DSM 15702]
 gi|167657125|gb|EDS01255.1| hypothetical protein EUBSIR_00781 [Eubacterium siraeum DSM 15702]
 gi|291557474|emb|CBL34591.1| RNA polymerase, sigma 29 subunit, SigE [Eubacterium siraeum
           V10Sc8a]
          Length = 239

 Score =  127 bits (319), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 59/263 (22%), Positives = 105/263 (39%), Gaps = 65/263 (24%)

Query: 27  PMLEKQEE-YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           P L K+EE   LAK        +A   L+  +LRLVV IA  +   G+ I +++S G IG
Sbjct: 36  PPLSKEEEAKTLAKL--NTDFENARETLIVHNLRLVVYIAKKFESTGIGIEDLISIGTIG 93

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++AV  F  E+  +LATY+   I+  +  Y+ ++                         
Sbjct: 94  LIKAVNTFSVEKNIKLATYASRCIENEILMYLRKTNP----------------------- 130

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
                             +K+ VS  E ++++                D N     D L 
Sbjct: 131 ------------------QKMEVSIDEPLNVD---------------WDGNELLLSDILG 157

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFE 263
            D D     +  + E    + ML  ++  L+ RE+ I E R    N    T + ++    
Sbjct: 158 TDDDTVSVDIESEAE----KRMLLEAVEKLDEREKLIMELRFGLNNRPEKTQKEVADMIG 213

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+  + ++E R  K++++ ++ 
Sbjct: 214 ISQSYISRLEKRIIKRLKKEMES 236


>gi|3249719|gb|AAC26662.1| RNA polymerase sigma-like factor [Streptomyces lividans TK24]
          Length = 162

 Score =  127 bits (319), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 41/172 (23%), Positives = 72/172 (41%), Gaps = 12/172 (6%)

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI+ AM   +      +++     +  L   + R++  +         P++V A  
Sbjct: 1   YATWWIRQAMSRALADQARTIRVPVHVVE--LINRVVRVQRRMLQERGCEPTPQEVAA-- 56

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
             L+++   V  +        SL+A +   +++     D +    DG     +E      
Sbjct: 57  -HLDLAPERVGEVLRLAQEPVSLHAPV--GEEDDVALGDLI---EDGDAASPVESAAFLL 110

Query: 224 RRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIE 273
            R  L   +S L  RER++ + R       P TLE +   F V+RER+RQIE
Sbjct: 111 LRQHLEAVLSTLGERERKVVQLRYGLADGRPRTLEEIGRLFGVTRERIRQIE 162


>gi|125972968|ref|YP_001036878.1| sporulation sigma factor SigE [Clostridium thermocellum ATCC 27405]
 gi|256004765|ref|ZP_05429740.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium thermocellum
           DSM 2360]
 gi|281417179|ref|ZP_06248199.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium thermocellum
           JW20]
 gi|125713193|gb|ABN51685.1| RNA polymerase, sigma 29 subunit, SigE [Clostridium thermocellum
           ATCC 27405]
 gi|255991215|gb|EEU01322.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium thermocellum
           DSM 2360]
 gi|281408581|gb|EFB38839.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium thermocellum
           JW20]
 gi|316940796|gb|ADU74830.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium thermocellum
           DSM 1313]
          Length = 244

 Score =  127 bits (319), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 59/265 (22%), Positives = 102/265 (38%), Gaps = 64/265 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EE  L  +  E  D      L+  +LRLVV IA  +   G+ + ++VS G IGL
Sbjct: 41  PPLTNDEENYLLSKL-EKRDFGVKSILIERNLRLVVYIARKFENTGVGVEDLVSIGTIGL 99

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+  FDP +  +LATY+   I+  +                         LRR     
Sbjct: 100 IKAINTFDPNKNIKLATYASRCIENEI----------------------LMYLRRNNR-- 135

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                        M   ++ DE LN      D N     D L  
Sbjct: 136 -----------------------------MKTEISIDEPLN---VDWDGNELLLSDILGT 163

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN---PVTLENLSSEFE 263
           ++D    ++    E +  + +L  +M  L+ RE++I E R    N     T + ++    
Sbjct: 164 END----LIHRSIEDEIDKELLAMAMKKLSVREKKIMELRFGLTNGGVEKTQKEVADMLG 219

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           +S+  + ++E +   ++++ I + V
Sbjct: 220 ISQSYISRLEKKIISRLRKEISRMV 244


>gi|261886011|ref|ZP_06010050.1| RNA polymerase sigma factor RpoD [Campylobacter fetus subsp.
           venerealis str. Azul-94]
          Length = 190

 Score =  127 bits (319), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 41/185 (22%), Positives = 74/185 (40%), Gaps = 13/185 (7%)

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +       + AM   I      ++I        +   + R+   ++       K   V  
Sbjct: 3   SAACSLRARQAMCRAIADQALTIRIPIH-----MIETINRINKFIENFFQKKGKGPDVAF 57

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           I  ++ +S  +V  +        SL A I S D    ++ D++    D      +E+  +
Sbjct: 58  IPGEVGLSIDKVKQVIKITKEPISLEAPIGSEDD--GKYGDFV---EDKTNLSPMEQILK 112

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFK 278
            + +  +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQIE+ A K
Sbjct: 113 GDLKEQIDEVLDQLNDREKAVIRMRFGLLEDESDRTLEEIGKELNVTRERVRQIESSAIK 172

Query: 279 KVQES 283
           K++  
Sbjct: 173 KLKHP 177


>gi|311068169|ref|YP_003973092.1| RNA polymerase sigma factor SigD [Bacillus atrophaeus 1942]
 gi|310868686|gb|ADP32161.1| RNA polymerase sigma factor SigD [Bacillus atrophaeus 1942]
          Length = 254

 Score =  127 bits (319), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 51/262 (19%), Positives = 111/262 (42%), Gaps = 19/262 (7%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQA 89
           E+ VL  R++E  D  A   L+  ++ LV              +   +++S G +GL  A
Sbjct: 7   EDQVLWSRWKEWKDPKAGDDLMRRYMPLVTYHVGRISVGLPKSVHKDDLMSLGMLGLYDA 66

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           ++KFDP R  +  TY+ + I+ A+ + + +   L +              ++++  ++ +
Sbjct: 67  LEKFDPSRDLKFDTYASFRIRGAIIDGLRKEDWLPRTSR--------EKTKKVEAAIEKL 118

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCR--LAGDESLNALINSSDKNSSQWQDWLVYD 207
               L+      IA++L ++E +V+S       A   S++  ++  D       +  V  
Sbjct: 119 EQRYLRNVSPAEIAEELGMTEQDVVSTMNEGFFANLLSIDEKLHDQDDGE----NIQVMI 174

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            D +     EK  +      L   +  L+ +E+ +       +  +TL  +     +S  
Sbjct: 175 RDDKNVPPEEKIMKDELIAQLAEKIHELSEKEQLVVSLFY--KEELTLTEIGQVLSLSTS 232

Query: 268 RVRQIEARAFKKVQESIQKQVE 289
           R+ QI ++A  K++  + K ++
Sbjct: 233 RISQIHSKALFKLKHLLDKVIQ 254


>gi|326204637|ref|ZP_08194493.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium papyrosolvens
           DSM 2782]
 gi|325985204|gb|EGD46044.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium papyrosolvens
           DSM 2782]
          Length = 243

 Score =  127 bits (319), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 56/263 (21%), Positives = 104/263 (39%), Gaps = 65/263 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EE  L  +  E  D      L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 41  PPLTLDEETYLLNKL-EQSDYGVKSILIERNLRLVVYIARKFENTGVGVEDLISIGTIGL 99

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+  F+P +  +LATY+   I+  +                         LRR     
Sbjct: 100 IKAINTFNPSKNIKLATYASRCIENEI----------------------LMYLRR----- 132

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS-DKNSSQWQDWLV 205
                                         N R+  + S++  +N   D N     D L 
Sbjct: 133 ------------------------------NNRVKAEISIDEPLNIDWDGNELLLSDILG 162

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFE 263
            D+D   + + ++ +    + +L  +M  L+ RE++I E R    N    T + ++    
Sbjct: 163 TDNDMIHRSIEDEVD----KELLAAAMKKLSVREKKIMELRFGLSNGVEKTQKEVADMLG 218

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+  + ++E R   ++++ I +
Sbjct: 219 ISQSYISRLEKRIISRLKKEISR 241


>gi|114566068|ref|YP_753222.1| sporulation sigma factor SigK [Syntrophomonas wolfei subsp. wolfei
           str. Goettingen]
 gi|114337003|gb|ABI67851.1| sigma 28 (flagella/sporulation) [Syntrophomonas wolfei subsp.
           wolfei str. Goettingen]
          Length = 244

 Score =  126 bits (318), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 58/274 (21%), Positives = 110/274 (40%), Gaps = 64/274 (23%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           I+ G + L  Y++       L +++E    +  +  G   A + L+  +LRLV  +   Y
Sbjct: 13  ILKGSLCLFAYLNNQVFPQPLSEEDERKCLQEMQ-RGGEEARNILIEHNLRLVAHVVKKY 71

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
              G  + +++S G IGL++A++ ++ ERG RLATY+   I                   
Sbjct: 72  ESSGEDLEDLISIGTIGLIKAIRTYNFERGVRLATYAARCIDN----------------- 114

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
                 +  +LR  K   Q                          +S+   +  D     
Sbjct: 115 -----EVLMHLRSSKKQKQE-------------------------VSLYDPIGHD----- 139

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
                + N     D L  D++     +++  E K +   +   +++L+ RER++ E R  
Sbjct: 140 ----KEGNEISLIDILTNDNE-----IVDLVEAKMQEEKIKEKINLLSRRERQVIEMRYG 190

Query: 249 QENPV--TLENLSSEFEVSRERVRQIEARAFKKV 280
             N +  T  +++ +  +SR  V +IE +A KK+
Sbjct: 191 LFNGLKETQRDIAKKLGISRSYVSRIEKKAIKKL 224


>gi|323705323|ref|ZP_08116898.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
 gi|323535225|gb|EGB25001.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
          Length = 247

 Score =  126 bits (318), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 51/241 (21%), Positives = 102/241 (42%), Gaps = 18/241 (7%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           ++   L ++  ++ D S+  +L+  +  L+  I   +   G    ++   G IG ++A+ 
Sbjct: 10  EDVNELIRK-SKNNDKSSMEKLLKENSGLIWSIVKKFSYRGYEAEDLYQIGCIGFVKAIN 68

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD     +L+TY++  I   ++ ++     L+K+  +   K L      +K  L+   +
Sbjct: 69  KFDESYNVKLSTYAVPIIIGEIKRFLRDDG-LIKVSRSL--KELSNKAYFMKDKLEKELN 125

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
                  +  IA KL+VS  EV       A  E L      ++ ++    + +  D    
Sbjct: 126 RE---PTIQEIASKLDVSAEEVAMAFESTATAEYLYDNSQHNEDDNLLLIEKIGID---- 178

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
                E+E     +  L   +  LN RER+I   R  ++  +T   +S    +S+ +V +
Sbjct: 179 -----EQEYEIEDKLALRMVLKNLNSRERQIIVLRYFKD--MTQTEVSKILGISQVQVSR 231

Query: 272 I 272
           I
Sbjct: 232 I 232


>gi|114566372|ref|YP_753526.1| sporulation sigma factor SigE [Syntrophomonas wolfei subsp. wolfei
           str. Goettingen]
 gi|114337307|gb|ABI68155.1| sporulation sigma factor SigE [Syntrophomonas wolfei subsp. wolfei
           str. Goettingen]
          Length = 240

 Score =  126 bits (318), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 66/277 (23%), Positives = 119/277 (42%), Gaps = 67/277 (24%)

Query: 16  LSRYIHEIRKIPMLEK----QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
           L R+IH I    +L      QEE  L  +  + G +S    L+  +LRLVV IA  +   
Sbjct: 23  LPRFIHYIGSTEVLPAPLREQEEMALISQL-DQGIMSVKATLIEHNLRLVVYIAKKFENT 81

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           G+ I ++VS G IGL++AV  F+P++  +LATY+   I+  +  Y+ R+           
Sbjct: 82  GINIEDLVSIGTIGLIKAVNTFEPKKNIKLATYASRCIENEILMYLRRN----------- 130

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
                     +K  ++                                ++ DE LN    
Sbjct: 131 ----------IKNRVE--------------------------------ISLDEPLN---V 145

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--Q 249
             D N     D L  ++D    ++ ++ E +  +++L ++M  LN RE+ I + R     
Sbjct: 146 DWDGNELLLSDVLGTEND----MIYKQIEGEVEKSLLWKAMHKLNNREKTIIQLRFGLAD 201

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  T + ++    +S+  + ++E R  K++Q  I+K
Sbjct: 202 GDEKTQKEVADILGISQSYISRLEKRILKRLQREIRK 238


>gi|290962882|ref|YP_003494064.1| sigma factor [Streptomyces scabiei 87.22]
 gi|260652408|emb|CBG75541.1| probable sigma factor [Streptomyces scabiei 87.22]
          Length = 280

 Score =  126 bits (318), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 48/246 (19%), Positives = 105/246 (42%), Gaps = 17/246 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              LV + L +  +IA  +R  G  + ++     +GL++AV +F+PERG    +Y++  I
Sbjct: 51  RDELVRAWLPMAHRIASRFRNRGESLEDLRQVAAMGLVKAVDRFEPERG-AFESYAVPTI 109

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +       +++      + L   +R  +  L   +  + +P  V  IA    ++
Sbjct: 110 TGEIKRHFRDRMWTLRVPRRV--QDLRNKVRVARRELSQTSGGSAEP-SVADIAALAGLT 166

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E EV +    L    +L+     +  +        +   D    V+++       R  + 
Sbjct: 167 EEEVHAGMEALDSFSALSLDAEMASGDDGYNLADTLGAPDAAYDVVVD-------RESVK 219

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           + +S L  RER I   R  ++  +T   ++    +S+  V ++ +R+  +V+E    +  
Sbjct: 220 QGLSRLPERERAILYMRFFED--MTQNRIADRLGISQMHVSRLISRSCARVRE----EAL 273

Query: 290 LSSSPP 295
             ++PP
Sbjct: 274 GRTAPP 279


>gi|152965379|ref|YP_001361163.1| RNA polymerase sigma factor WhiG [Kineococcus radiotolerans
           SRS30216]
 gi|151359896|gb|ABS02899.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Kineococcus
           radiotolerans SRS30216]
          Length = 312

 Score =  126 bits (318), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 53/265 (20%), Positives = 115/265 (43%), Gaps = 20/265 (7%)

Query: 30  EKQEE------YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP----ISEVV 79
             ++E        + + Y+  GD     +L+  +  LV  +A    G GLP     +++V
Sbjct: 54  TPEQEQAEAALRAMWEEYKASGDGVVREKLIMHYSPLVKYVAGR-VGVGLPPNIEQADLV 112

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
           S G  GL+ A++KFD ER  +  TY++  I+ A+ + + RS   +     +  + +    
Sbjct: 113 SYGIFGLIDAIEKFDIERAIKFETYAISRIRGAIIDEL-RSIDWIPRSVRSKAREV---- 167

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
            R    L+A         +V A   ++ +SE   I          +L+ L++ S +   +
Sbjct: 168 ERTYAALEAELHRTPTEVEVAA-RMEIKLSELHHIFSQVSYVNVVALDELLSVSGEKGDK 226

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
               +    D + +  ++  E++  + +L+R+++ L  RE+ +          +TL  + 
Sbjct: 227 L-SLVDTLEDTKAEDPVQSFEKEETKFLLSRAINQLPEREKIVVTLYYY--EGLTLAEIG 283

Query: 260 SEFEVSRERVRQIEARAFKKVQESI 284
               V+  R+ Q+  +A  +++  +
Sbjct: 284 RVLGVTESRICQMHTKAVLQLRGKL 308


>gi|160933251|ref|ZP_02080640.1| hypothetical protein CLOLEP_02097 [Clostridium leptum DSM 753]
 gi|156868325|gb|EDO61697.1| hypothetical protein CLOLEP_02097 [Clostridium leptum DSM 753]
          Length = 230

 Score =  126 bits (318), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 59/262 (22%), Positives = 113/262 (43%), Gaps = 63/262 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L ++EE  + +R R  G+ +A   L+T +LRLVV IA  +   G  + +++S G IGL
Sbjct: 28  PPLSREEEDEVMERVR-RGEKNAREPLITHNLRLVVYIAKKFDSNGASVEDLISIGTIGL 86

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F PER  +LATY+   I+  +  ++ +S                          
Sbjct: 87  IKAVNTFCPERNIKLATYASRCIENEILMFLRKSS------------------------- 121

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                        +   ++ DE LN      D N     D L  
Sbjct: 122 ----------------------------QLKNEISIDEPLN---VDWDGNELLLSDILGS 150

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           D+D    ++    E++   +++ +++S L PRER+I E R     +   T + ++    +
Sbjct: 151 DND----IVNRDIEKEVECSLVLQAVSRLAPRERQIMELRFGLCGQKEHTQKQVADVLGI 206

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+  + ++E R  +++++ +++
Sbjct: 207 SQSYISRLEKRIIERLKKDLER 228


>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 =  126 bits (318), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 41/142 (28%), Positives = 66/142 (46%), Gaps = 5/142 (3%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +  ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 563 RQAKREMTEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 622

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I            + R+   +   T     P     +A+K+
Sbjct: 623 WWIRQAITRSIADQARTIRIPVHM--IETINKMNRISRQILQETGLEPDPAT---LAEKM 677

Query: 167 NVSESEVISMNCRLAGDESLNA 188
            + E+       R   D   NA
Sbjct: 678 EMPETRSADHEDREGADLDGNA 699


>gi|49484290|ref|YP_041514.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus MRSA252]
 gi|82751667|ref|YP_417408.1| RNA polymerase sigma factor SigB [Staphylococcus aureus RF122]
 gi|257426202|ref|ZP_05602617.1| SigB protein [Staphylococcus aureus subsp. aureus 55/2053]
 gi|257428861|ref|ZP_05605255.1| SigB protein [Staphylococcus aureus subsp. aureus 65-1322]
 gi|257431471|ref|ZP_05607844.1| SigB protein [Staphylococcus aureus subsp. aureus 68-397]
 gi|257434181|ref|ZP_05610531.1| SigB protein [Staphylococcus aureus subsp. aureus E1410]
 gi|257437094|ref|ZP_05613134.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           M876]
 gi|258422934|ref|ZP_05685834.1| RNA polymerase sigma factor SigB [Staphylococcus aureus A9635]
 gi|282904730|ref|ZP_06312604.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           C160]
 gi|282906409|ref|ZP_06314260.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           Btn1260]
 gi|282909377|ref|ZP_06317192.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           WW2703/97]
 gi|282911631|ref|ZP_06319430.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           WBG10049]
 gi|282914909|ref|ZP_06322689.1| RNA polymerase sigma-37 factor [Staphylococcus aureus subsp. aureus
           M899]
 gi|282917412|ref|ZP_06325165.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           D139]
 gi|282920240|ref|ZP_06327964.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           C427]
 gi|282925452|ref|ZP_06333106.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           C101]
 gi|283771232|ref|ZP_06344121.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           H19]
 gi|283958843|ref|ZP_06376288.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           A017934/97]
 gi|293508983|ref|ZP_06667770.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           58-424]
 gi|293510895|ref|ZP_06669594.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           M809]
 gi|293547495|ref|ZP_06672170.1| RNA polymerase sigma-37 factor [Staphylococcus aureus subsp. aureus
           M1015]
 gi|295428651|ref|ZP_06821277.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           EMRSA16]
 gi|297589872|ref|ZP_06948512.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           MN8]
 gi|49242419|emb|CAG41133.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           MRSA252]
 gi|61889366|emb|CAI72514.1| SigB protein [Staphylococcus aureus]
 gi|82657198|emb|CAI81638.1| RNA polymerase sigma factor B [Staphylococcus aureus RF122]
 gi|257270907|gb|EEV03080.1| SigB protein [Staphylococcus aureus subsp. aureus 55/2053]
 gi|257274203|gb|EEV05720.1| SigB protein [Staphylococcus aureus subsp. aureus 65-1322]
 gi|257277712|gb|EEV08382.1| SigB protein [Staphylococcus aureus subsp. aureus 68-397]
 gi|257280820|gb|EEV10965.1| SigB protein [Staphylococcus aureus subsp. aureus E1410]
 gi|257283487|gb|EEV13614.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           M876]
 gi|257846958|gb|EEV70972.1| RNA polymerase sigma factor SigB [Staphylococcus aureus A9635]
 gi|282312853|gb|EFB43254.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           C101]
 gi|282316100|gb|EFB46481.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           C427]
 gi|282318614|gb|EFB48971.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           D139]
 gi|282321112|gb|EFB51443.1| RNA polymerase sigma-37 factor [Staphylococcus aureus subsp. aureus
           M899]
 gi|282324396|gb|EFB54709.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           WBG10049]
 gi|282326647|gb|EFB56945.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           WW2703/97]
 gi|282330359|gb|EFB59877.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           Btn1260]
 gi|282594763|gb|EFB99740.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           C160]
 gi|283459437|gb|EFC06530.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           H19]
 gi|283471280|emb|CAQ50491.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           ST398]
 gi|283789561|gb|EFC28384.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           A017934/97]
 gi|290919615|gb|EFD96688.1| RNA polymerase sigma-37 factor [Staphylococcus aureus subsp. aureus
           M1015]
 gi|291094687|gb|EFE24959.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           58-424]
 gi|291466180|gb|EFF08707.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           M809]
 gi|295127321|gb|EFG56961.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           EMRSA16]
 gi|297577000|gb|EFH95714.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           MN8]
 gi|298695339|gb|ADI98561.1| RNA polymerase sigma factor B [Staphylococcus aureus subsp. aureus
           ED133]
 gi|302333711|gb|ADL23904.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus JKD6159]
 gi|312437522|gb|ADQ76593.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           TCH60]
 gi|315193223|gb|EFU23621.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus CGS00]
 gi|323439220|gb|EGA96947.1| RNA polymerase sigma factor SigB [Staphylococcus aureus O11]
 gi|323442402|gb|EGB00031.1| RNA polymerase sigma factor SigB [Staphylococcus aureus O46]
 gi|329729290|gb|EGG65698.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           21193]
          Length = 256

 Score =  126 bits (318), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 44/260 (16%), Positives = 104/260 (40%), Gaps = 18/260 (6%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             ++     K ++E+ +  A  +LV  + +L+  +A  Y        ++V  G +GL+ A
Sbjct: 12  SPEQINQWIKEHQENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGA 71

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +FD     +   + +  +   ++ Y+      V +      K +   ++++   L A 
Sbjct: 72  INRFDMSFERKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRI--KEIGPRIKKVSDELTAE 129

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNC---RLAGDESLNALINSSDKNSSQWQDWLVY 206
            + +    ++    +       E + M      L+ D S+ A     D ++    D +  
Sbjct: 130 LERSPSISEIADRLEVSEEEVLEAMEMGQSYNALSVDHSIEA---DKDGSTVTLLDIMGQ 186

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
             D          +   +R +L + + +L+ RER I +   +    ++ +       +S+
Sbjct: 187 QDDHY--------DLTEKRMILEKILPILSDREREIIQCTFI--EGLSQKETGERIGLSQ 236

Query: 267 ERVRQIEARAFKKVQESIQK 286
             V +++  A KK+QE+  K
Sbjct: 237 MHVSRLQRTAIKKLQEAAHK 256


>gi|145224453|ref|YP_001135131.1| FliA/WhiG family RNA polymerase sigma factor [Mycobacterium gilvum
           PYR-GCK]
 gi|145216939|gb|ABP46343.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Mycobacterium
           gilvum PYR-GCK]
          Length = 342

 Score =  126 bits (318), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 43/244 (17%), Positives = 90/244 (36%), Gaps = 18/244 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                 ++   L L   IA  +RG G    ++V    +GL+ AV +FD +       +++
Sbjct: 109 RRQREAIIARCLPLADHIARRFRGRGEGHEDLVQVARVGLLNAVNRFDVDSANDFLAFAV 168

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +   ++ Y       +K+     +  +     RL      +T    +      +AK L
Sbjct: 169 PTMMGEVRRYFRDHGWSLKVPRRLKELNV-----RLNAARADLTQELNRAPTPSELAKYL 223

Query: 167 NVSESEVIS--MNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
            +   EV+   +        S       S D      QD      D  ++V+        
Sbjct: 224 GIDREEVVEGLVAANAYSTRSTEQPTTFSGDGEGLSLQDTFGAPDDNIQKVI-------- 275

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             N +   ++ L  R+R + + R  ++   T   ++ +  VS+  V ++ ARA   +++ 
Sbjct: 276 DVNTVQPLLAALPERDRLVLKLRFFED--RTQSQIAEQIGVSQMHVSRLLARALATLRDQ 333

Query: 284 IQKQ 287
           +  +
Sbjct: 334 VGDE 337


>gi|322381761|ref|ZP_08055715.1| sporulation sigma factor SigF-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321154149|gb|EFX46471.1| sporulation sigma factor SigF-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 200

 Score =  126 bits (318), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 39/216 (18%), Positives = 89/216 (41%), Gaps = 18/216 (8%)

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
              G    ++   G IGL+++V KF+     + +TY++  I   +Q ++      +K+  
Sbjct: 1   MNRGYEADDLFQIGCIGLLKSVDKFNLSYEVKFSTYAVPMIIGEIQRFLRDDG-TLKVSR 59

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           +   K L   +R+ K  L    +       +  +A  L ++  EV+          S++ 
Sbjct: 60  SL--KELANKVRKTKDELSKNLERL---PTLKEVANALGITPEEVVFAQEANKPLSSIHE 114

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +  +D +     D +  D           +E+   +  L  ++  L+ RER I   R  
Sbjct: 115 TVFENDWDPITLMDQIADD----------SQEKWFDKLALNEAIEGLSERERLIVYLRYF 164

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++   T   +++   +S+ +V ++E +  + ++  I
Sbjct: 165 KDQ--TQSEVANRLGISQVQVSRLEKKILQSIRNQI 198


>gi|15618277|ref|NP_224562.1| RNA polymerase sigma factor sigma-28 [Chlamydophila pneumoniae
           CWL029]
 gi|15835895|ref|NP_300419.1| RNA polymerase sigma factor sigma-28 [Chlamydophila pneumoniae
           J138]
 gi|16752677|ref|NP_444944.1| RNA polymerase sigma factor sigma-28 [Chlamydophila pneumoniae
           AR39]
 gi|33241705|ref|NP_876646.1| RNA polymerase sigma factor sigma-28 [Chlamydophila pneumoniae
           TW-183]
 gi|4376638|gb|AAD18506.1| Sigma-28/WhiG Family [Chlamydophila pneumoniae CWL029]
 gi|7189319|gb|AAF38240.1| RNA polymerase sigma factor, sigma-70 family [Chlamydophila
           pneumoniae AR39]
 gi|8978734|dbj|BAA98570.1| sigma-28/WhiG family [Chlamydophila pneumoniae J138]
 gi|33236214|gb|AAP98303.1| transcription initiation factor sigmaD protein [Chlamydophila
           pneumoniae TW-183]
 gi|269303237|gb|ACZ33337.1| RNA polymerase sigma factor, FliA [Chlamydophila pneumoniae LPCoLN]
          Length = 257

 Score =  126 bits (318), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 51/259 (19%), Positives = 113/259 (43%), Gaps = 20/259 (7%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVK 91
             +   Y E  ++     L+  +L LV  +               ++ + G  GL++AV+
Sbjct: 10  IEVWNFYWETQEIEYRDSLIEFYLPLVKSVVHRLISGMPSHVKTEDLYASGVEGLVRAVE 69

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           +++PER  R   Y+++ IKAA+ + + +      +  + +QK       +L G + ++  
Sbjct: 70  RYNPERSRRFEGYAVFLIKAAIIDDLRKQDW---VPRSVHQKA-----NKLSGAMDSLRQ 121

Query: 152 NNLKPEQVVAIAKKLNVSESEV--ISMNCRLAGDESLNA--LINSSDKNSSQWQDWLVYD 207
           +  K    + + + LN+S+ E+    ++ R A   SLN      S +      ++ +  +
Sbjct: 122 SLGKEPTDLELCEYLNISQQELSGWFVSARPALIVSLNEEWPSQSDEGAGMALEERIPDE 181

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
                  +++K+E       L  ++  L  +ER++      +E  + L+ +     VS  
Sbjct: 182 RAETGYDVVDKQEFSLC---LANAIQELEEKERKVMALYYYEE--LVLKEIGKVLGVSES 236

Query: 268 RVRQIEARAFKKVQESIQK 286
           RV QI ++A  K++ ++  
Sbjct: 237 RVSQIHSKALLKLRAALSA 255


>gi|284028883|ref|YP_003378814.1| B/F/G subfamily RNA polymerase sigma-28 subunit [Kribbella flavida
           DSM 17836]
 gi|283808176|gb|ADB30015.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Kribbella
           flavida DSM 17836]
          Length = 287

 Score =  126 bits (318), Expect = 3e-27,   Method: Composition-based stats.
 Identities = 40/242 (16%), Positives = 87/242 (35%), Gaps = 15/242 (6%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E        +++  +  +   IA  YR  G+   ++     +GL++A   + P       
Sbjct: 54  EARRQELLDQVILLNSPIARSIASRYRSKGVDSDDLEQVAYLGLVKAANGYRPSESTAFL 113

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
            Y++  I+  ++ Y       V+      + +       +      +T            
Sbjct: 114 AYAVPTIRGELKRYFRDCAWTVRPPRRVQEMQ-----GSIAAAEPELTQKLGHLPTDRET 168

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+ L     E+       A   +L+     S +  +   D +    DG + V        
Sbjct: 169 AEALGTEPGEIAEATAVRACFSTLSLDAPGSGEGGASLMDTVADAEDGYDLV-------- 220

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              + LT +++ L+ R+RRI + R    +  T E +  E  VS+ +V ++      +++E
Sbjct: 221 ENVHTLTPAVADLDDRDRRILQLRF--CHGYTQEEIGQELGVSQMQVSRLLRGILDRLRE 278

Query: 283 SI 284
            +
Sbjct: 279 EL 280


>gi|312282679|dbj|BAJ34205.1| unnamed protein product [Thellungiella halophila]
          Length = 511

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 58/252 (23%), Positives = 105/252 (41%), Gaps = 18/252 (7%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDP 95
           KR  E G  +A ++L+  +LRLV+ +   Y      G    ++   G  GL+ A+ +F+P
Sbjct: 264 KRKIEIG-RAARNKLIKHNLRLVLFVMNKYFQDFTNGPKFQDLCQAGMRGLITAIDRFEP 322

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           +R FRL+TY ++WI+ A+   +  S    ++       R+   + + K  L         
Sbjct: 323 KRKFRLSTYGLFWIRHAIIRSMTTSNFT-RVPFGLESVRV--EIYKTKMELLFELGRLPT 379

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
            ++VV   K       EV+     +    S +++      N     D +  D+  Q  +L
Sbjct: 380 EDEVVERLKISPERYREVLRAAKPVFSLNSKHSVTQEEFINGITDVDGVGADNRRQPAIL 439

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIE 273
                    R  L   +  L P+E  +   R   +     TL  ++    +SRE VR+ E
Sbjct: 440 ---------RLALDDVLDSLKPKESLVIRQRYGLDGKGDRTLGEIAGNLNISREMVRKHE 490

Query: 274 ARAFKKVQESIQ 285
            +A  K++   +
Sbjct: 491 VKALMKLKHQAR 502


>gi|253731099|ref|ZP_04865264.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus USA300_TCH959]
 gi|253733102|ref|ZP_04867267.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus TCH130]
 gi|253725174|gb|EES93903.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus USA300_TCH959]
 gi|253728935|gb|EES97664.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus TCH130]
          Length = 256

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 44/261 (16%), Positives = 105/261 (40%), Gaps = 18/261 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           +  ++     K ++E+ +  A  +LV  + +L+  +A  Y        ++V  G +GL+ 
Sbjct: 11  ISPEQINQWIKEHQENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIG 70

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A+ +FD     +   + +  +   ++ Y+      V +      K +   ++++   L A
Sbjct: 71  AINRFDMSFERKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRI--KEIGPRIKKVSDELTA 128

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNC---RLAGDESLNALINSSDKNSSQWQDWLV 205
             + +    ++    +       E + M      L+ D S+ A     D ++    D + 
Sbjct: 129 ELERSPSISEIADRLEVSEEEVLEAMEMGQSYNALSVDHSIEA---DKDGSTVTLLDIMG 185

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
              D          +   +R +L + + +L+ RER I +   +    ++ +       +S
Sbjct: 186 QQDDHY--------DLTEKRMILEKILPILSDREREIIQCTFI--EGLSQKETGERIGLS 235

Query: 266 RERVRQIEARAFKKVQESIQK 286
           +  V +++  A KK+QE+  K
Sbjct: 236 QMHVSRLQRTAIKKLQEAAHK 256


>gi|164415557|gb|ABY53195.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415559|gb|ABY53196.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415561|gb|ABY53197.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415563|gb|ABY53198.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415565|gb|ABY53199.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415567|gb|ABY53200.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415569|gb|ABY53201.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415571|gb|ABY53202.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415573|gb|ABY53203.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415575|gb|ABY53204.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415577|gb|ABY53205.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415579|gb|ABY53206.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415581|gb|ABY53207.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415583|gb|ABY53208.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415585|gb|ABY53209.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415587|gb|ABY53210.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415589|gb|ABY53211.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415591|gb|ABY53212.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
 gi|164415593|gb|ABY53213.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
          Length = 166

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 35/167 (20%), Positives = 71/167 (42%), Gaps = 12/167 (7%)

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            ++I     +      L R+   +         PE    +AK++++ E ++  +      
Sbjct: 1   TIRIPVHMME--TINKLNRISRQMLQQFGREATPE---ELAKEMDMPEDKIRKVMKVAKE 55

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
             S+   I   D   S   D++    D   +  ++     N    +   ++ L PRE ++
Sbjct: 56  PISMETPI--GDDEDSHLGDFI---EDPNVESPVDTTTNVNLSETVREVLAGLTPREAKV 110

Query: 243 FEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              R   +     TLE +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 111 LRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 157


>gi|291165879|gb|EFE27926.1| RNA polymerase sigma-B factor [Filifactor alocis ATCC 35896]
          Length = 273

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 41/256 (16%), Positives = 108/256 (42%), Gaps = 17/256 (6%)

Query: 34  EYVLAKRYREHG-DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           E  L   Y E   +    + L+  +L +   ++  Y   G+   ++    ++GL+ A+++
Sbjct: 27  EKELFLLYNEDKQNRELRNELIQKNLYIAEILSKKYLNKGIEYDDIFQVASLGLILAIER 86

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           +D  +GF+ ++++   I   +++Y       +++     +       +++    + + + 
Sbjct: 87  YDVTKGFKFSSFATPTIIGEIKKYFRDKGWSIRVPRKIQELS-----KKVTQAREYLQNE 141

Query: 153 NLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
                +V  IA+ L +SE EV+ +    ++   +SL+    +  ++       ++ D D 
Sbjct: 142 KGAIPEVKDIAEYLEISEEEVMEVMEASQVYHLKSLDVTYENGGEDKEVSLIDVLGDEDK 201

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
               +         R+   +    L+  ER I   R  ++   T   ++ E  +S+  V 
Sbjct: 202 SFSEI-------ENRDFFEKMFQKLDDVEREIIIGRFFKQ--KTQMKIAEELNISQMTVS 252

Query: 271 QIEARAFKKVQESIQK 286
           +IE +   K+++  ++
Sbjct: 253 RIEKKVLSKIKKEYER 268


>gi|319644916|ref|ZP_07999149.1| RNA polymerase sigma factor [Bacillus sp. BT1B_CT2]
 gi|317392725|gb|EFV73519.1| RNA polymerase sigma factor [Bacillus sp. BT1B_CT2]
          Length = 241

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 51/257 (19%), Positives = 92/257 (35%), Gaps = 66/257 (25%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+    E+  L       GD  A + L+  +LRLV  I   +   G    +++S G IGL
Sbjct: 30  PLSSSDEKKYL--ELMAQGDEHARNMLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGL 87

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A++ +   +G +LATY+   I+  +                        +LR LK   
Sbjct: 88  IKAIESYSAGKGTKLATYAARCIENEI----------------------LMHLRALKKT- 124

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS-DKNSSQWQDWLV 205
                                               D SL+  I    + N     D L 
Sbjct: 125 ----------------------------------KKDVSLHDPIGQDKEGNEISLIDVLK 150

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFE 263
            ++    + +I+  +       + + + +L+ RE+ +   R   +     T   ++ E  
Sbjct: 151 SEN----EDVIDTIQLNMELEKVKKYIDILDGREKEVIVGRFGLDLKKEKTQREIAKELG 206

Query: 264 VSRERVRQIEARAFKKV 280
           +SR  V +IE RA  K+
Sbjct: 207 ISRSYVSRIEKRALMKM 223


>gi|302871379|ref|YP_003840015.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
 gi|302574238|gb|ADL42029.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
          Length = 262

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 51/254 (20%), Positives = 97/254 (38%), Gaps = 62/254 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EE  +  R    G+      L+  +LRLVV IA  +    + + ++VS G IGL
Sbjct: 41  PPLTPDEEAQILYRIHYQGEEGLKKLLIERNLRLVVYIARRFENTKVNLEDLVSIGTIGL 100

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+  ++P +  +LATY+   I+  +  ++ R+ +                        
Sbjct: 101 IKAINTYNPNKNIKLATYASKCIENEILMFLRRNSN------------------------ 136

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                            KKL +S  E ++++                D N     D L  
Sbjct: 137 -----------------KKLELSIDEPLNVD---------------WDGNELLLSDVLGT 164

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEV 264
           D     + +  + E    +  L +++  L  RE++I E R     E   T + ++    +
Sbjct: 165 D----TEEIYNRIESNVEKEALLQAIQKLPSREKKIVELRFGFGDEGEKTQKEVADMLGI 220

Query: 265 SRERVRQIEARAFK 278
           S+  + ++E R  +
Sbjct: 221 SQSYISRLEKRLLQ 234


>gi|303240258|ref|ZP_07326777.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302592168|gb|EFL61897.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 256

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 47/255 (18%), Positives = 109/255 (42%), Gaps = 17/255 (6%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVK 91
             + ++Y +  D +   +L+  +  ++  +A     Y G  +   +++  G  GL+ A+ 
Sbjct: 9   QEMWRQYSDTKDPAIKEKLIIEYSHIIKYVAGRLSIYFGSNVEYDDLIGYGVFGLIDAIN 68

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD  +G +  TY+   I+ A+ + I     L  +  +  QK     L R+   ++   +
Sbjct: 69  KFDINKGVKFETYASLRIRGAIIDSIRE---LDWVPRSLRQK--NKELERVYTEVE---N 120

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
                     +A+KL VS  E   +      + +L++LI+  +     ++  +      +
Sbjct: 121 ELGHSATDQEVAQKLGVSVDEFYKLL----NEVNLSSLISLEEFLEQNYEAGVNIAGGCK 176

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E       E    R +L  ++  L  +E+ +      ++  +TL+ +S   +VS  R+ Q
Sbjct: 177 EDRPEGYMEITELREILVDAIGKLPEKEKTVVSFYYFED--LTLKEISEIMKVSESRISQ 234

Query: 272 IEARAFKKVQESIQK 286
           +  +A  +++  + +
Sbjct: 235 LHTKAILRLRGKLAR 249


>gi|320012666|gb|ADW07516.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 294

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 55/239 (23%), Positives = 106/239 (44%), Gaps = 15/239 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + LV  ++ LV   A  +R  G   + ++   G IGL++A+ +F+  R    AT+++ 
Sbjct: 66  ARNTLVEMNISLVRFAARRFRNRGSGDMEDITQVGTIGLIKAIDRFELSREVEFATFAVP 125

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +I   ++ +   +   V +     + R+   L + K  L    D +     V  +A  L+
Sbjct: 126 YIVGEIKRFFRDTTWAVHVPRRLQELRV--ELAKAKDELAVRLDRD---PTVKELAAHLD 180

Query: 168 VSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
            +E EVI       G    SL+   ++ +   +  + +   D  G+    +E  E     
Sbjct: 181 RTEDEVIEGIIASNGYTAGSLDMPTDTGETTGTASRTF--ADILGEPDSAMETVE---NL 235

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + L   +  L+ RERR+ E R  QE  +T   + +E +VS+  V ++  R   K++  +
Sbjct: 236 HALAPLLEQLDDRERRLIEMRFGQE--MTQSQIGAELDVSQMHVSRLLTRTLGKLRAGM 292


>gi|326389454|ref|ZP_08211021.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermoanaerobacter
           ethanolicus JW 200]
 gi|325994459|gb|EGD52884.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermoanaerobacter
           ethanolicus JW 200]
          Length = 246

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 43/256 (16%), Positives = 109/256 (42%), Gaps = 23/256 (8%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLMQAV 90
           E  + K Y  + D +  + ++  ++ LV  I               +++++G IGL+ A+
Sbjct: 5   EEDIWKTYNSNKDPNLRNEIIIKYMPLVKHIVKKLIISDITQSEYEDLINQGVIGLIDAI 64

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +K+ P +G +  TY+   I+  + +Y+ R   +         + L    ++++  ++ + 
Sbjct: 65  EKYQPSKGVKFETYATLRIRGEIIDYLRRKDWM--------PRSLKKKYKKIEETVETLQ 116

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDH 208
               +   V  I +   ++E +V+     +  +   SL   I ++ K        L    
Sbjct: 117 QKYNREPTVEEITEACGLNEIDVLKTLSYINVSNVNSLEEAIENNFK--------LHAIS 168

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           + + +   E+   K  +  L  ++  L  +ER +      ++  +  +++S    ++  R
Sbjct: 169 NVELKNPEEEVLYKELKRKLASAIESLPDKERLVITLYYYED--LNYKDISKILNLTESR 226

Query: 269 VRQIEARAFKKVQESI 284
           + QI  +A K+++E +
Sbjct: 227 ISQIHTKAIKRIREML 242


>gi|54401904|gb|AAV34637.1| RNA polymerase subunit sigma-38 [Escherichia coli]
          Length = 183

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 47/190 (24%), Positives = 87/190 (45%), Gaps = 10/190 (5%)

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           LVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+ 
Sbjct: 1   LVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMN 60

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
               +++      K L   LR  +     ++            A++L+    +V  M   
Sbjct: 61  QTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEESAEQLDKPVDDVSRMLRL 115

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
                S++  +    +     +  L    D +E    +  +  + +  + + +  LN ++
Sbjct: 116 NERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQ 170

Query: 240 RRIFEARRLQ 249
           R +   R   
Sbjct: 171 REVLARRFGL 180


>gi|15927639|ref|NP_375172.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus N315]
 gi|148268516|ref|YP_001247459.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus JH9]
 gi|150394579|ref|YP_001317254.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus JH1]
 gi|253315694|ref|ZP_04838907.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus str. CF-Marseille]
 gi|257794514|ref|ZP_05643493.1| RNA polymerase sigma-B factor [Staphylococcus aureus A9781]
 gi|258411256|ref|ZP_05681534.1| RNA polymerase sigma factor SigB [Staphylococcus aureus A9763]
 gi|258419772|ref|ZP_05682738.1| RNA polymerase sigma-B factor [Staphylococcus aureus A9719]
 gi|258438079|ref|ZP_05689458.1| sigma factor B [Staphylococcus aureus A9299]
 gi|258441327|ref|ZP_05690812.1| sigma factor B [Staphylococcus aureus A8115]
 gi|258446979|ref|ZP_05695131.1| sigma factor B [Staphylococcus aureus A6300]
 gi|258449788|ref|ZP_05697888.1| sigma factor B [Staphylococcus aureus A6224]
 gi|258453474|ref|ZP_05701453.1| sigma factor B [Staphylococcus aureus A5937]
 gi|269203699|ref|YP_003282968.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus ED98]
 gi|282895212|ref|ZP_06303428.1| RNA polymerase sigma-B factor [Staphylococcus aureus A8117]
 gi|295407610|ref|ZP_06817401.1| RNA polymerase sigma-B factor [Staphylococcus aureus A8819]
 gi|296275695|ref|ZP_06858202.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus MR1]
 gi|297246607|ref|ZP_06930438.1| RNA polymerase sigma-B factor [Staphylococcus aureus A8796]
 gi|13701859|dbj|BAB43151.1| sigma factor B [Staphylococcus aureus subsp. aureus N315]
 gi|147741585|gb|ABQ49883.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Staphylococcus
           aureus subsp. aureus JH9]
 gi|149947031|gb|ABR52967.1| RNA polymerase sigma-B type [Staphylococcus aureus subsp. aureus
           JH1]
 gi|257788486|gb|EEV26826.1| RNA polymerase sigma-B factor [Staphylococcus aureus A9781]
 gi|257840011|gb|EEV64477.1| RNA polymerase sigma factor SigB [Staphylococcus aureus A9763]
 gi|257844254|gb|EEV68637.1| RNA polymerase sigma-B factor [Staphylococcus aureus A9719]
 gi|257848496|gb|EEV72486.1| sigma factor B [Staphylococcus aureus A9299]
 gi|257852371|gb|EEV76296.1| sigma factor B [Staphylococcus aureus A8115]
 gi|257854212|gb|EEV77163.1| sigma factor B [Staphylococcus aureus A6300]
 gi|257856962|gb|EEV79863.1| sigma factor B [Staphylococcus aureus A6224]
 gi|257864346|gb|EEV87095.1| sigma factor B [Staphylococcus aureus A5937]
 gi|262075989|gb|ACY11962.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus ED98]
 gi|282762402|gb|EFC02546.1| RNA polymerase sigma-B factor [Staphylococcus aureus A8117]
 gi|285817729|gb|ADC38216.1| RNA polymerase sigma factor SigB [Staphylococcus aureus 04-02981]
 gi|294967508|gb|EFG43546.1| RNA polymerase sigma-B factor [Staphylococcus aureus A8819]
 gi|297176507|gb|EFH35773.1| RNA polymerase sigma-B factor [Staphylococcus aureus A8796]
 gi|312830416|emb|CBX35258.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           ECT-R 2]
 gi|315128403|gb|EFT84412.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus CGS03]
 gi|329727790|gb|EGG64242.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           21172]
          Length = 256

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 44/260 (16%), Positives = 104/260 (40%), Gaps = 18/260 (6%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             ++     K ++E+ +  A  +LV  + +L+  +A  Y        ++V  G +GL+ A
Sbjct: 12  SPEQINQWIKEHQENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGA 71

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +FD     +   + +  +   ++ Y+      V +      K +   ++++   L A 
Sbjct: 72  INRFDMSFERKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRI--KEIGPRIKKVSDELTAE 129

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNC---RLAGDESLNALINSSDKNSSQWQDWLVY 206
            + +    ++    +       E + M      L+ D S+ A     D ++    D +  
Sbjct: 130 LERSPSISEIANRLEVSEEEVLEAMEMGQSYNALSVDHSIEA---DKDGSTVTLLDIMGQ 186

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
             D          +   +R +L + + +L+ RER I +   +    ++ +       +S+
Sbjct: 187 QDDHY--------DLTEKRMILEKILPILSDREREIIQCTFI--EGLSQKETGERIGLSQ 236

Query: 267 ERVRQIEARAFKKVQESIQK 286
             V +++  A KK+QE+  K
Sbjct: 237 MHVSRLQRTAIKKLQEAAHK 256


>gi|3249725|gb|AAC26665.1| RNA polymerase sigma-like factor [Streptomyces glauceuces]
          Length = 162

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 42/172 (24%), Positives = 72/172 (41%), Gaps = 12/172 (6%)

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI+ AM   +      +++     +  L   + R++  L          E    I 
Sbjct: 1   YATWWIRQAMSRALADQADTIRVPVHVVE--LINRVVRVQRRLLQERGVEPTAED---IG 55

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
             L+++   V  +        SL+A +   +++   + D +    DG     +E      
Sbjct: 56  VDLDLTPERVTDILRLGQEPVSLHAPV--GEEDDVSFGDLI---EDGDAASPVESAVFLL 110

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIE 273
            R  L   +S L  RER++ + R   E+  P TLE +   F V+RER+RQIE
Sbjct: 111 LREHLEAVLSTLGERERKVVQLRYGLEDGRPRTLEEIGRIFGVTRERIRQIE 162


>gi|20151056|pdb|1KU2|A Chain A, Crystal Structure Of Thermus Aquaticus Rna Polymerase
           Sigma Subunit Fragment Containing Regions 1.2 To 3.1
 gi|20151057|pdb|1KU2|B Chain B, Crystal Structure Of Thermus Aquaticus Rna Polymerase
           Sigma Subunit Fragment Containing Regions 1.2 To 3.1
          Length = 241

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 41/140 (29%), Positives = 63/140 (45%), Gaps = 3/140 (2%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +A   L+ ++LRLVV IA  Y G GL   +++ EGN GL++AV+KF+ +R F+ +TY+ 
Sbjct: 105 EAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYAT 164

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           WWI+ A+   I      ++I     +      L R    LQ         E++   A   
Sbjct: 165 WWIRQAINRAIADQARTIRIPVHMVE--TINKLSRTARQLQQELGREPSYEEIAE-AMGP 221

Query: 167 NVSESEVISMNCRLAGDESL 186
                 V           SL
Sbjct: 222 GWDAKRVEETLKIAQEPVSL 241



 Score = 42.5 bits (99), Expect = 0.075,   Method: Composition-based stats.
 Identities = 13/45 (28%), Positives = 25/45 (55%), Gaps = 2/45 (4%)

Query: 12 GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTS 56
              + +Y+HEI ++P+L  +EE  LA++  E   + A  +L  +
Sbjct: 1  TSDPVRQYLHEIGQVPLLTLEEEIDLARKVEEG--MEAIKKLSEA 43


>gi|225175485|ref|ZP_03729479.1| RNA polymerase, sigma 28 subunit, SigE [Dethiobacter alkaliphilus
           AHT 1]
 gi|225168814|gb|EEG77614.1| RNA polymerase, sigma 28 subunit, SigE [Dethiobacter alkaliphilus
           AHT 1]
          Length = 243

 Score =  126 bits (317), Expect = 4e-27,   Method: Composition-based stats.
 Identities = 65/262 (24%), Positives = 113/262 (43%), Gaps = 63/262 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L + EE  L ++ +  GD +    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 41  PPLSQDEEGFLLEKLK-TGDYAVKAVLIERNLRLVVYIARKFENTGILIDDLVSIGTIGL 99

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FDP +  +LATY+   I+  +  ++ R+                    ++K   
Sbjct: 100 IKAVNTFDPHKNIKLATYASKCIENEILMFLRRN-------------------NKVKAE- 139

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                            ++ DE LN      D N     D L  
Sbjct: 140 ---------------------------------VSFDEPLN---VDWDGNELLLSDVLGT 163

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEV 264
           ++D    ++I+  E +  R +L  ++  LN RE+RI E R   L +   T + ++    +
Sbjct: 164 END----LVIKGIEAEVERKLLYNAIEKLNRREKRIMELRFGLLGQEEKTQKEVAVMLGI 219

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+  + ++E R  K++Q+ I+K
Sbjct: 220 SQSYISRLEKRIIKRLQKEIRK 241


>gi|114765238|ref|ZP_01444370.1| RNA polymerase sigma factor protein (sigma-70) [Pelagibaca
           bermudensis HTCC2601]
 gi|114542373|gb|EAU45401.1| RNA polymerase sigma factor protein (sigma-70) [Roseovarius sp.
           HTCC2601]
          Length = 249

 Score =  126 bits (317), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 53/269 (19%), Positives = 117/269 (43%), Gaps = 32/269 (11%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +S   H   + P+L  ++E      +++ GD +A   L+ SH R     A  +    + +
Sbjct: 2   MSMSYHSAMREPLLSFEQERAAISGWQDRGDRAALEVLLRSHARQAWSHAARFTDNPVHL 61

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++ +EG +GL++A   FD  +  R ATY+ WW++ A+   + R  +++ I +       
Sbjct: 62  EDLAAEGVMGLLRAADSFDRAQDVRFATYAAWWVRNAVSSALSRIKAVIDIPSRTYLDAQ 121

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              L                             S+ +V  +     G  +L+     + +
Sbjct: 122 MGKL-----------------------------SDEDVFIVQLATRGTLALDTHQEDAGR 152

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
           + +Q    LV      E+    + +R+    ++  +++ + P E  +   RRL   P TL
Sbjct: 153 DPAQL---LVSSEPDPEEHASLQSQRRMLLRLIDDALARMEPEEVAVIRRRRLAPEPETL 209

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +++++  ++++R+RQ+E RA  +++  +
Sbjct: 210 ADIAADLGITQDRLRQVERRAMMRLRRVL 238


>gi|302556917|ref|ZP_07309259.1| stress response/stationary phase sigma factor SigF [Streptomyces
           griseoflavus Tu4000]
 gi|302474535|gb|EFL37628.1| stress response/stationary phase sigma factor SigF [Streptomyces
           griseoflavus Tu4000]
          Length = 263

 Score =  126 bits (317), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 46/239 (19%), Positives = 95/239 (39%), Gaps = 14/239 (5%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              LVT+ L +  +IA+ +RG G  + ++     +GL++AV  +DP RG     Y++  +
Sbjct: 38  RDELVTAWLPMAERIAVRFRGRGEALEDLYQVAALGLVKAVDHYDPARGNAFEAYAVPTV 97

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +       + +      + L   +R+    L   T    +   V  IA    ++
Sbjct: 98  TGEIKRHFRDHMWTLHVPRRV--QDLRNRVRQSAKELAQTT--PGRAPTVAEIAAHARLT 153

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E EV +    L    +L+        +     D L     G + V+         R  + 
Sbjct: 154 EDEVRTGMEALECFTALSLDAEMPGTDGYALGDALGGPDPGYDTVV--------DRVAVR 205

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
             +  L  RER I   R  +   +T   ++ +  +S+  V ++ +  F +++E +  + 
Sbjct: 206 PCLEALPERERLILYLRFFRG--MTQSGIAEQLGISQMHVSRLLSGCFARLREELLAEA 262


>gi|256784015|ref|ZP_05522446.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
          Length = 266

 Score =  126 bits (317), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 48/238 (20%), Positives = 99/238 (41%), Gaps = 15/238 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
               R+V + L +  ++A  +R  G    ++     +GL++AV ++DPERG    +Y++ 
Sbjct: 35  ELRDRIVEAWLPMAERLAGRFRSRGESFEDLRQVAALGLVKAVDRYDPERGNAFESYAVP 94

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKPEQVVAIAKKL 166
            I   ++ +       + +     + R      R++   Q ++     +   V  IA++ 
Sbjct: 95  TITGEIKRHFRDHMWTLHVPRRVQELR-----NRVRFAGQDLSQTIPGRRPTVAEIAERA 149

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +SE +V      L   ES  AL   ++   S+    L       +  L    +    R 
Sbjct: 150 ELSEEDVR---VGLEALESFTALSLDAELPGSEDGYSLGDALGAPDPAL----DTVVDRE 202

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +   ++ L PRER I   R   +  +T   ++ +  +S+  V ++  R   +V+E +
Sbjct: 203 AVKDRLAALPPRERAILYMRFFDD--MTQSRIAEQLGISQMHVSRLITRCCDRVREQV 258


>gi|300782223|ref|YP_003762514.1| RNA polymerase sigma factor [Amycolatopsis mediterranei U32]
 gi|299791737|gb|ADJ42112.1| RNA polymerase sigma factor [Amycolatopsis mediterranei U32]
          Length = 259

 Score =  126 bits (316), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 40/240 (16%), Positives = 86/240 (35%), Gaps = 19/240 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                 LV +HL L   +A  +R     + ++V    +GL+ AV +FDP +G     +++
Sbjct: 32  ERIRDTLVRTHLELARNLARKFRNRDEAMEDLVQIATVGLIHAVDRFDPAQGTDFLAFAV 91

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I   ++ +   +   V++     +         +    + +T    +  +   IA +L
Sbjct: 92  PTISGELRHHFRDNSWSVRVPRRLKELNAN-----ISAAREELTVQLSRAPKPSEIAARL 146

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            V   +V        G               +     L      +      +  +   R 
Sbjct: 147 GVPIEDVYEGLRAGQGR------------YGASLDHLLENAAHTRFGAPDAELGQAELRE 194

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L   +  L  RER+I   R      ++  +++    VS+ +V ++ A   KK++  + +
Sbjct: 195 ALRPMLESLPERERKIVALRFGSG--MSQSDIARRVGVSQMQVSRLLAATLKKLRSGLDE 252


>gi|301165903|emb|CBW25476.1| RNA polymerase sigma factor WhiG [Bacteriovorax marinus SJ]
          Length = 260

 Score =  126 bits (316), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 44/250 (17%), Positives = 98/250 (39%), Gaps = 15/250 (6%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDP 95
           K YR   D      ++  +  L+  IA          + + +++S G IGLM A++KFDP
Sbjct: 12  KDYRSTVDPKVKDEIIIEYAPLIKYIAQRIASRLPSNVELDDLISCGVIGLMDAIEKFDP 71

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            R  +  TY+ + I+ ++ + +      V        K +     +++           +
Sbjct: 72  SRDNKFKTYAEFRIRGSILDELRAQ-DWVPRSVREKAKLVERAYAKIEAA-------EGR 123

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
           P     +  +L V++ E   +  +      LN  I+ S   +   +  +    D +    
Sbjct: 124 PATDEEMCAELGVNQEEFYDLLNKAKSVSVLN--IDDSASFNKGDKKLIAGLEDNRNSNP 181

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
                 K  R+ +   ++ L  ++R +      ++  + L+ +     V+  RV Q+  +
Sbjct: 182 FHAVANKGSRDKIKEGIAQLPEKQRLVLSLYYYED--LNLKEIGQVLNVTESRVSQLHTQ 239

Query: 276 AFKKVQESIQ 285
           A  K++  ++
Sbjct: 240 AIMKLKVKLK 249


>gi|15237896|ref|NP_197800.1| SIGE (SIGMA FACTOR E); DNA binding / DNA-directed RNA polymerase/
           sigma factor/ transcription factor [Arabidopsis
           thaliana]
 gi|4033838|emb|CAA77213.1| sigma-like factor [Arabidopsis thaliana]
 gi|4972299|dbj|BAA78109.1| RNA polymerase sigma subunit SigE [Arabidopsis thaliana]
 gi|10178160|dbj|BAB11572.1| sigma-like factor [Arabidopsis thaliana]
 gi|222423237|dbj|BAH19595.1| AT5G24120 [Arabidopsis thaliana]
 gi|332005876|gb|AED93259.1| RNA polymerase sigma factor [Arabidopsis thaliana]
          Length = 517

 Score =  126 bits (316), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 53/244 (21%), Positives = 101/244 (41%), Gaps = 17/244 (6%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            +A ++L+  +LRLV+ +   Y      G    ++   G  GL+ A+ +F+P+R FRL+T
Sbjct: 277 RAARNKLIKHNLRLVLFVMNKYFHEFTNGPKFQDLCQAGMRGLITAIDRFEPKRKFRLST 336

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y ++WI+ A+   +  S    ++       R+   + + K  L          ++VV   
Sbjct: 337 YGLFWIRHAIIRSMTTSNFT-RVPFGLESVRV--EIYKAKTELWFEMGRPPTEDEVVERL 393

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           K       EV+     +    S +++      N     D +  ++  Q  +L        
Sbjct: 394 KITPERYREVLRAAKPVLSLNSKHSVTQEEFINGITDVDGVGANNSRQPALL-------- 445

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R  L   +  L P+E  +   R   +     TL  ++    +SRE VR+ E +A  K++
Sbjct: 446 -RLALDDVLDSLKPKESLVIRQRYGLDGKGDRTLGEIAGNLNISREMVRKHEVKALMKLK 504

Query: 282 ESIQ 285
              +
Sbjct: 505 HQAR 508


>gi|302389525|ref|YP_003825346.1| RNA polymerase, sigma 29 subunit, SigE [Thermosediminibacter oceani
           DSM 16646]
 gi|302200153|gb|ADL07723.1| RNA polymerase, sigma 29 subunit, SigE [Thermosediminibacter oceani
           DSM 16646]
          Length = 239

 Score =  126 bits (316), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 61/265 (23%), Positives = 105/265 (39%), Gaps = 65/265 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L  +EE +L  + +  GD    + L+  +LRLVV IA  +   G  I +++S G IGL
Sbjct: 37  PPLSSEEEAMLLDKLQ-MGDNGVRNVLIERNLRLVVYIARKFENTGAGIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+  FDP +  +LATY+   I+  +                         LRR     
Sbjct: 96  IKAINTFDPHKKIKLATYASRCIENEI----------------------LMYLRR----- 128

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS-DKNSSQWQDWLV 205
                                         N R   + S +  +N   D N     D L 
Sbjct: 129 ------------------------------NNRNRAEVSFDEPLNIDWDGNELLLSDILG 158

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFE 263
            D D   + + E+ E    + +L  +M  L+ RER I E R    +    T + ++    
Sbjct: 159 TDSDMIYKCIEEEVE----KELLDTAMKRLSKRERCIMELRFGLNDGKEKTQKEVAELLG 214

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           +S+  + ++E R  K++++ I + +
Sbjct: 215 ISQSYISRLEKRIIKRLRKEIVRMM 239


>gi|297812573|ref|XP_002874170.1| hypothetical protein ARALYDRAFT_489269 [Arabidopsis lyrata subsp.
           lyrata]
 gi|297320007|gb|EFH50429.1| hypothetical protein ARALYDRAFT_489269 [Arabidopsis lyrata subsp.
           lyrata]
          Length = 517

 Score =  126 bits (316), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 53/244 (21%), Positives = 101/244 (41%), Gaps = 17/244 (6%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            +A ++L+  +LRLV+ +   Y      G    ++   G  GL+ A+ +F+P+R FRL+T
Sbjct: 277 RAARNKLIKHNLRLVLFVMNKYFHDFTNGPKFQDLCQAGMRGLITAIDRFEPKRKFRLST 336

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y ++WI+ A+   +  S    ++       R+   + + K  L          ++VV   
Sbjct: 337 YGLFWIRHAIIRSMTTSNFT-RVPFGLESVRV--EIFKTKTELLFELGRLPTEDEVVERL 393

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           K       EV+     +    S +++      N     D +  ++  Q  +L        
Sbjct: 394 KITPERYREVLRAAKPVLSLNSKHSVTQEEFINGITDVDGVGANNSRQPALL-------- 445

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R  L   +  L P+E  +   R   +     TL  ++    +SRE VR+ E +A  K++
Sbjct: 446 -RLALDDVLDSLKPKESLVIRQRYGLDGKGDRTLGEIAGNLNISREMVRKHEVKALMKLK 504

Query: 282 ESIQ 285
              +
Sbjct: 505 HQAR 508


>gi|317133468|ref|YP_004092782.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Ethanoligenens
           harbinense YUAN-3]
 gi|315471447|gb|ADU28051.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Ethanoligenens
           harbinense YUAN-3]
          Length = 248

 Score =  126 bits (316), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 52/262 (19%), Positives = 106/262 (40%), Gaps = 23/262 (8%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGL 86
            ++E   L + YRE     A +RLV  +  LV  I        G      ++ S G IGL
Sbjct: 5   TQEESEPLWQVYRETRSREARNRLVLHYGWLVRAIVHRVMSVSGSYAESDDLTSCGTIGL 64

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A++KFD ++G + +T++ + I+  + +++ R    V  G              ++   
Sbjct: 65  IKAIEKFDSDKGVQFSTFATYRIRGEILDFVRR-SDWVPRGVRKRVLE-------MESAE 116

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
             +  +  +      + ++L V +              S+      S +   +     + 
Sbjct: 117 SELASSLGRRPSDSELCERLGVPDR------VLAKTRASMERFNVISFEEMLRDAARDMA 170

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
             D  E  L E E       +LT+++  L  R+R +      ++  +TL  +S    V+ 
Sbjct: 171 GDDSPENALQESELL----EVLTKAVEDLPERDRLVITLYYYED--LTLREISEVIGVTE 224

Query: 267 ERVRQIEARAFKKVQESIQKQV 288
            RV QI +RA  +++ ++   +
Sbjct: 225 SRVSQIHSRAVGRMKAAMGAYI 246


>gi|295399836|ref|ZP_06809817.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|312111652|ref|YP_003989968.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacillus sp.
           Y4.1MC1]
 gi|294978239|gb|EFG53836.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|311216753|gb|ADP75357.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacillus sp.
           Y4.1MC1]
          Length = 254

 Score =  126 bits (316), Expect = 5e-27,   Method: Composition-based stats.
 Identities = 45/259 (17%), Positives = 111/259 (42%), Gaps = 19/259 (7%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQA 89
           EE     R+    D  A ++LV +++ LV              +   E++S G +GL  A
Sbjct: 8   EERKYWDRWIYDRDPQAGNKLVQTYMPLVHYHVQRIAASLPKNISKQELISLGLVGLYDA 67

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           ++KFDP R  +  TY+ + I+ A+ + + +   L         + +    ++++  ++ +
Sbjct: 68  LEKFDPSRDLKFDTYASFRIRGAIFDGLRKEDWL--------PRSIREKAKKIEETIEKL 119

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
               ++      +A +L ++E+EV ++      A   S   +   +D+      + L+  
Sbjct: 120 EQRYMRSVTAKEVADELGITEAEVYTVVNEHFFANVLSFQHVATENDEEE----NALLAI 175

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            D +     E+  ++     L   +  L+ +E+ +       +  +T   +     +S  
Sbjct: 176 RDEKTLSPEEEVLKQELYEKLAEVIQQLSEKEQLVISLFY--KEELTFTEIGEILGLSTS 233

Query: 268 RVRQIEARAFKKVQESIQK 286
           R+ Q+ ++A  K+++ +++
Sbjct: 234 RISQLHSKAIFKLRKILEQ 252


>gi|307243397|ref|ZP_07525554.1| putative RNA polymerase sigma-B factor [Peptostreptococcus stomatis
           DSM 17678]
 gi|306493207|gb|EFM65203.1| putative RNA polymerase sigma-B factor [Peptostreptococcus stomatis
           DSM 17678]
          Length = 257

 Score =  126 bits (316), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 95/240 (39%), Gaps = 17/240 (7%)

Query: 35  YVLAKRYREHGDLSA-AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
             L K + +    +A  + L+  HL L   ++  Y   G+   ++    ++ L+ A+ ++
Sbjct: 15  KELFKIFSDDKTNAAVRNILIEKHLYLAKILSRKYMNKGVDYEDLYQVASLALIYAIDRY 74

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D  +GF  ++++   I   +++Y       +++     +  L   +   K +L+     +
Sbjct: 75  DISKGFEFSSFATPTIVGEIKKYFRDKVWTLRVPRRIQE--LSKKISNAKVYLEQELRRS 132

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQ 211
             P     IA  L+++E EV+       G    SL+        + S+ +D  + D  G 
Sbjct: 133 PTP---SEIAGYLDITEEEVLEAMEASYGYQPVSLDTP----SNDDSEDKDMTLGDRVGT 185

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E+      E  +    +   M  LN  E +I   R       T   ++ E  +S+  V +
Sbjct: 186 EEKNFRHIEEMDF---INHFMKTLNELEVQIIRGRFFDN--KTQSVIAEELGISQMTVSR 240


>gi|317502438|ref|ZP_07960602.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|331090300|ref|ZP_08339184.1| hypothetical protein HMPREF1025_02767 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|316896176|gb|EFV18283.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|330401435|gb|EGG81020.1| hypothetical protein HMPREF1025_02767 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 206

 Score =  126 bits (316), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 56/259 (21%), Positives = 99/259 (38%), Gaps = 62/259 (23%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L   EE    ++Y E GDL A H L+  +LRLV  +   Y+       +++S G IGL+
Sbjct: 7   PLTPSEEKYYIRKYTE-GDLEAKHILIERNLRLVAHVIKKYQNSEEDPEDLISIGTIGLI 65

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV  F+P++G RLA Y+   I+  +  Y+                              
Sbjct: 66  KAVVTFNPDKGNRLAAYASRCIENEILMYLRSK--------------------------- 98

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                                  ++ IS+   +  D          + N  +  D +  D
Sbjct: 99  --------------------KKAAKEISLYEPIGTDR---------EGNEIKLYDIIETD 129

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVS 265
               E+V  +   ++N + +  +    L+ RER I + R         T   ++ +  +S
Sbjct: 130 E---EEVAEKIHLKENIQTLYEKVEKELSQRERIILKMRYGLYNGEEYTQREIARQLGIS 186

Query: 266 RERVRQIEARAFKKVQESI 284
           R  V +IE  A +K+++S 
Sbjct: 187 RSYVSRIEKGAVEKLRKSF 205


>gi|307717640|gb|ADN88873.1| RNA polymerase sigma-37 factor [Listeria ivanovii subsp. ivanovii]
          Length = 220

 Score =  126 bits (316), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 52/231 (22%), Positives = 99/231 (42%), Gaps = 24/231 (10%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D
Sbjct: 2   YIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
              G     +++  I   ++ ++      V +     +        ++K  ++ +T    
Sbjct: 62  ATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQ 116

Query: 155 KPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +    
Sbjct: 117 SSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTD 173

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
           DG         ER N+R +L + + VL+ RE++I +   ++    + +   
Sbjct: 174 DGF--------ERVNQRMLLEKVLPVLDEREQKILQYTFIEN--RSQKETG 214


>gi|224992874|gb|ACN76152.1| SigB [Listeria monocytogenes]
 gi|224992886|gb|ACN76158.1| SigB [Listeria monocytogenes]
 gi|224992898|gb|ACN76164.1| SigB [Listeria monocytogenes]
 gi|224992902|gb|ACN76166.1| SigB [Listeria monocytogenes]
          Length = 214

 Score =  126 bits (316), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 51/229 (22%), Positives = 98/229 (42%), Gaps = 24/229 (10%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D   G  
Sbjct: 4   YQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKS 63

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
              +++  I   ++ ++      V +     +        ++K  ++ +T       Q+ 
Sbjct: 64  FEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQSSPQIS 118

Query: 161 AIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            IA  + V+E EV+           L+ D S+ A    SD ++    D +    DG    
Sbjct: 119 DIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTDDGF--- 172

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
                ER N+R +L + + VL+ RE++I +   ++    + +      +
Sbjct: 173 -----ERVNQRMLLEKVLPVLDEREQKILQYTFIEN--RSQKETGELLD 214


>gi|51894120|ref|YP_076811.1| RNA polymerase sigma factor related to flagellar biosynthesis
           [Symbiobacterium thermophilum IAM 14863]
 gi|51857809|dbj|BAD41967.1| RNA polymerase sigma factor related to flagellar biosynthesis
           [Symbiobacterium thermophilum IAM 14863]
          Length = 253

 Score =  126 bits (316), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 51/255 (20%), Positives = 111/255 (43%), Gaps = 17/255 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKK 92
            L +R+R+  D +A   LV  +L LV  +A              +V   G  GL++A+ +
Sbjct: 5   ELWQRWRQSHDTAARDALVQHYLWLVRYVAGRLMVGMPDHVDQGDVEGHGCFGLLEAIAR 64

Query: 93  FDPERGFRLATYSMWWIKAAMQEYI-LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           +DP+RG R  T+++ WI+ A  E +    W+          +R    L R++  L A+  
Sbjct: 65  YDPDRGVRFETFAIPWIRGACLEGLRAMQWAP-------ALRRRVRQLERVRDELMAVLG 117

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
                 ++      ++V E+E            SL+  +   D  ++   D +  +    
Sbjct: 118 REPSAAELAEQ-MGISVEEAERRLQEAGTLAVLSLDEALAFDDGETTALADRVADEEAVD 176

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
            ++  ++ ER   R +L R+++ L  +E+ +       +  +  + +S    +S+ R+ Q
Sbjct: 177 PELESQRAER---REVLARAIASLTEQEQLVIALIY--QEGLIAKEVSEILGLSQARISQ 231

Query: 272 IEARAFKKVQESIQK 286
           + ++A  +++  + +
Sbjct: 232 VHSKAILRLRGKLSR 246


>gi|169827019|ref|YP_001697177.1| RNA polymerase sigma-35 factor [Lysinibacillus sphaericus C3-41]
 gi|168991507|gb|ACA39047.1| RNA polymerase sigma-35 factor precursor [Lysinibacillus sphaericus
           C3-41]
          Length = 204

 Score =  126 bits (316), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 53/259 (20%), Positives = 111/259 (42%), Gaps = 63/259 (24%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L ++EE  +   + + GDL A   L+  +LRLVV IA  +   G PI +++S G+IGL+
Sbjct: 2   PLSREEEVTVIASFMK-GDLRARDTLIERNLRLVVYIARRFDNTGTPIEDLISIGSIGLI 60

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +A++ F+ ++  +LATY+   I                      +  +  +LR+      
Sbjct: 61  KAIETFNTDKNIKLATYASRCI----------------------ENEILMHLRK------ 92

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                                          R+ G+ SL+  +NS    +      ++  
Sbjct: 93  -----------------------------TSRMKGEVSLDEPLNSDADGNELLLSDILG- 122

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVS 265
              +E ++++  E+K  R  +  ++++L  RER I E R        +T + ++    +S
Sbjct: 123 --TEEHIILDNVEKKIERQHMFHAINLLGARERYIMECRFGLNGKVEMTQKEVADHLGIS 180

Query: 266 RERVRQIEARAFKKVQESI 284
           +  + ++E +  + ++E++
Sbjct: 181 QSYISRLEKKIIQDLRENL 199


>gi|15834951|ref|NP_296710.1| RNA polymerase sigma factor sigma-28 [Chlamydia muridarum Nigg]
 gi|270285123|ref|ZP_06194517.1| RNA polymerase sigma factor sigma-28 [Chlamydia muridarum Nigg]
 gi|270289144|ref|ZP_06195446.1| RNA polymerase sigma factor sigma-28 [Chlamydia muridarum Weiss]
 gi|301336518|ref|ZP_07224720.1| RNA polymerase sigma factor sigma-28 [Chlamydia muridarum
           MopnTet14]
 gi|7190373|gb|AAF39194.1| RNA polymerase sigma factor, sigma-70 family [Chlamydia muridarum
           Nigg]
          Length = 253

 Score =  126 bits (316), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 53/254 (20%), Positives = 114/254 (44%), Gaps = 17/254 (6%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFD 94
            + Y    ++     L+ ++L LV  +A            I ++ + G  GL++AV++FD
Sbjct: 10  WQLYWSTKEIHHRDFLIEAYLPLVKNVAHRLASGMPSHVKIEDLYASGVEGLVRAVERFD 69

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           PE+  R  +Y+++ IKAA+ + + +      +  +  Q+       RL   + A+     
Sbjct: 70  PEKSKRFESYALFIIKAAIIDDLRKQDW---VPRSVYQRA-----NRLADAMDALRQTLG 121

Query: 155 KPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           K      + + LN+S+ E+     + R A   SLN   +  D++     +  + D   + 
Sbjct: 122 KEPTDGDLCEYLNISQQELSHWFSSSRPALVLSLNDDFSCQDEDEGLALEERIADE--RA 179

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           +   +   +K   ++LT ++  L+ +ER++       +  + L+ +     VS  RV QI
Sbjct: 180 ENGYDVIRKKEAISILTEALLSLDEKERQVMALYYYDD--LVLKEIGKILGVSESRVSQI 237

Query: 273 EARAFKKVQESIQK 286
            ++A  K++ ++  
Sbjct: 238 HSKALLKLRGTLSS 251


>gi|224992792|gb|ACN76111.1| SigB [Listeria innocua]
 gi|224992796|gb|ACN76113.1| SigB [Listeria innocua]
 gi|224992810|gb|ACN76120.1| SigB [Listeria innocua]
 gi|224992814|gb|ACN76122.1| SigB [Listeria innocua]
 gi|224992832|gb|ACN76131.1| SigB [Listeria innocua]
 gi|224992834|gb|ACN76132.1| SigB [Listeria innocua]
 gi|224992848|gb|ACN76139.1| SigB [Listeria innocua]
 gi|224992850|gb|ACN76140.1| SigB [Listeria innocua]
 gi|224992856|gb|ACN76143.1| SigB [Listeria innocua]
          Length = 214

 Score =  126 bits (316), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 51/229 (22%), Positives = 98/229 (42%), Gaps = 24/229 (10%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D   G  
Sbjct: 4   YQENGDEDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKS 63

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
              +++  I   ++ ++      V +     +        ++K  ++ +T       Q+ 
Sbjct: 64  FEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQSSPQIS 118

Query: 161 AIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            IA  + V+E EV+           L+ D S+ A    SD ++    D +    DG    
Sbjct: 119 DIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTDDGF--- 172

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
                ER N+R +L + + VL+ RE++I +   ++    + +      +
Sbjct: 173 -----ERVNQRMLLEKVLPVLDEREQKILQYTFIEN--RSQKETGELLD 214


>gi|206895926|ref|YP_002247112.1| RNA polymerase sigma-37 factor [Coprothermobacter proteolyticus DSM
           5265]
 gi|206738543|gb|ACI17621.1| RNA polymerase sigma-37 factor [Coprothermobacter proteolyticus DSM
           5265]
          Length = 243

 Score =  125 bits (315), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 46/251 (18%), Positives = 101/251 (40%), Gaps = 22/251 (8%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L +RY E  D      L   +  L   +   +  Y +   ++  E    L+ A+ +F+P
Sbjct: 11  ELLERYAETRDPRIRDTLFLMYKPLADSVVNRFAPYQIDKDDLRQEAYRALVDAIDRFNP 70

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
             G    T+++  I   ++ Y+      + +      + +      ++  L  I +    
Sbjct: 71  SYGNLFETFAIPTIVGNLKRYLRDYGWAISVP-----RSMVDMAYSIQKKLPEIAEKLGH 125

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
              +  IA++L + E +V  +   +A     S+++ I      + +    L+ D D +++
Sbjct: 126 EPTIKEIAEELELDEEQVSEVLAIMAVKNTSSIDSKITDESDTTGEELLGLLSDRDLEDE 185

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
            L+E             ++S L   ER I E R      ++   ++    +S+ +V + E
Sbjct: 186 ALLEI------------AVSELPEPERFIIEKRL---EGLSQSEIAKLLNISQAQVSRFE 230

Query: 274 ARAFKKVQESI 284
            +A  K++E+I
Sbjct: 231 RKAITKLKEAI 241


>gi|167636574|ref|ZP_02394868.1| RNA polymerase sigma-G factor (Stage III sporulation protein G)
           [Bacillus anthracis str. A0442]
 gi|167527997|gb|EDR90803.1| RNA polymerase sigma-G factor (Stage III sporulation protein G)
           [Bacillus anthracis str. A0442]
          Length = 211

 Score =  125 bits (315), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 44/203 (21%), Positives = 94/203 (46%), Gaps = 7/203 (3%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+  E   L +  +  G++SA  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKNDEMRKLFREMQ-SGEISAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+++  FD  +  + +TY++  I   ++ Y+  +   +++  +   + + +   +++ 
Sbjct: 74  GLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSL--RDIAYKALQVRE 130

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L A    N K    + IAK L V+  E++     +    SL   I +   +     D L
Sbjct: 131 KLIA---ENSKEPTAMDIAKVLEVTHEEIVFALDAIQDPVSLFEPIYNDGGDPIFVMDQL 187

Query: 205 VYDHDGQEQVLIEKEERKNRRNM 227
             +    EQ + E     + +++
Sbjct: 188 SDEKQKDEQWVEELALNIDGKSI 210


>gi|291522682|emb|CBK80975.1| RNA polymerase, sigma 29 subunit, SigE [Coprococcus catus GD/7]
          Length = 245

 Score =  125 bits (315), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 59/280 (21%), Positives = 116/280 (41%), Gaps = 69/280 (24%)

Query: 11  NGEIGLSRYIH--EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           NGEI    YI   ++  +P+  ++E+  +A    E       + L+  +LRLVV IA  +
Sbjct: 23  NGEI---HYISGTDVLPVPLEGEEEKNAIAMLATEAEREHGRNILIEHNLRLVVYIARKF 79

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
              G  + +++S G IGL++A+  ++P++  +LATY+   I+  +  Y+ RS  L     
Sbjct: 80  DNTGAGMEDLISIGTIGLIKAINSYNPDKNIKLATYASRCIENEILMYLRRSSKL----- 134

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
                                               K+ VS  E ++++           
Sbjct: 135 ------------------------------------KMEVSIDEPLNVD----------- 147

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
                D N     D L  D    E V+  K E +   ++L ++++ L+PRE+ I + R  
Sbjct: 148 ----WDGNELLLSDILGTD----ENVIYNKMEEEVNYHLLYKALAKLSPREKTIIQLRFG 199

Query: 249 ----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                    T + ++    +S+  + ++E +   ++++ I
Sbjct: 200 IRTADGEEKTQKEVADFLGISQSYISRLEKKIIGRLKKDI 239


>gi|145224387|ref|YP_001135065.1| FliA/WhiG family RNA polymerase sigma factor [Mycobacterium gilvum
           PYR-GCK]
 gi|145216873|gb|ABP46277.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Mycobacterium
           gilvum PYR-GCK]
          Length = 301

 Score =  125 bits (315), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 41/236 (17%), Positives = 101/236 (42%), Gaps = 18/236 (7%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
             ++T  L L   IA  + G G P  +++    IGL+++V ++ P++G R   +++  I+
Sbjct: 75  QHIITECLPLADHIACRFAGRGEPSDDLIQVARIGLVKSVDRYVPDKG-RFMAFAVPTIR 133

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
             ++ +   S   +++      +++     R++   + ++    +      IA++L V +
Sbjct: 134 GEVRRHFRDSTWSMRVP-----RKIQDTQLRMRHAAEELSQRLKRAPTDREIARELGVDD 188

Query: 171 SEVISMNCR--LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            EV   +         SL+A    +++  +   +    D  G + V            +L
Sbjct: 189 GEVSRCHSAHWAYRPVSLDAPRGDAEQECAGIGELRGADDPGFDSV--------EDLIVL 240

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +  ++ L+PR R I   R      +T   ++    VS+ +V ++      ++++ +
Sbjct: 241 SGVIAELDPRRRAILGMRFYDC--LTQREIALRLNVSQVQVSRLLDSTLARLRQRM 294


>gi|331091330|ref|ZP_08340170.1| hypothetical protein HMPREF9477_00813 [Lachnospiraceae bacterium
           2_1_46FAA]
 gi|330404491|gb|EGG84035.1| hypothetical protein HMPREF9477_00813 [Lachnospiraceae bacterium
           2_1_46FAA]
          Length = 206

 Score =  125 bits (315), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 57/256 (22%), Positives = 96/256 (37%), Gaps = 62/256 (24%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L   EE    ++Y E GDL A H L+  +LRLV  I   Y+       +++S G IGL+
Sbjct: 7   PLTASEERYYLQKYTE-GDLEAKHILIERNLRLVAHIVKKYQHLDEDPEDLLSIGTIGLI 65

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV  F+ E+G RLATY+   I+  +   +                              
Sbjct: 66  KAVSTFNLEKGNRLATYAARCIENEILMMLRGKKKT------------------------ 101

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                                  S+ +S+   +  D          + N  Q  D +  D
Sbjct: 102 -----------------------SKEVSLYEPIGTDR---------EGNEIQLFDVIESD 129

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVS 265
            +     +  K++ K     ++   S L+PRER + + R         T   ++ +  +S
Sbjct: 130 EEDAPSKVALKDDIKMLYEKVS---SELSPRERLVLKMRYGLYEGEEYTQREIARQLGIS 186

Query: 266 RERVRQIEARAFKKVQ 281
           R  V +IE  A +K++
Sbjct: 187 RSYVSRIEKSAIEKLR 202


>gi|224992858|gb|ACN76144.1| SigB [Listeria monocytogenes]
 gi|224992860|gb|ACN76145.1| SigB [Listeria monocytogenes]
 gi|224992862|gb|ACN76146.1| SigB [Listeria monocytogenes]
 gi|224992864|gb|ACN76147.1| SigB [Listeria monocytogenes]
 gi|224992866|gb|ACN76148.1| SigB [Listeria monocytogenes]
 gi|224992868|gb|ACN76149.1| SigB [Listeria monocytogenes]
 gi|224992870|gb|ACN76150.1| SigB [Listeria monocytogenes]
 gi|224992872|gb|ACN76151.1| SigB [Listeria monocytogenes]
 gi|224992876|gb|ACN76153.1| SigB [Listeria monocytogenes]
 gi|224992878|gb|ACN76154.1| SigB [Listeria monocytogenes]
 gi|224992880|gb|ACN76155.1| SigB [Listeria monocytogenes]
 gi|224992882|gb|ACN76156.1| SigB [Listeria monocytogenes]
 gi|224992884|gb|ACN76157.1| SigB [Listeria monocytogenes]
 gi|224992888|gb|ACN76159.1| SigB [Listeria monocytogenes]
 gi|224992890|gb|ACN76160.1| SigB [Listeria monocytogenes]
 gi|224992892|gb|ACN76161.1| SigB [Listeria monocytogenes]
 gi|224992894|gb|ACN76162.1| SigB [Listeria monocytogenes]
 gi|224992896|gb|ACN76163.1| SigB [Listeria monocytogenes]
 gi|224992900|gb|ACN76165.1| SigB [Listeria monocytogenes]
          Length = 214

 Score =  125 bits (315), Expect = 6e-27,   Method: Composition-based stats.
 Identities = 51/229 (22%), Positives = 98/229 (42%), Gaps = 24/229 (10%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D   G  
Sbjct: 4   YQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKS 63

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
              +++  I   ++ ++      V +     +        ++K  ++ +T       Q+ 
Sbjct: 64  FEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQSSPQIS 118

Query: 161 AIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            IA  + V+E EV+           L+ D S+ A    SD ++    D +    DG    
Sbjct: 119 DIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTDDGF--- 172

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
                ER N+R +L + + VL+ RE++I +   ++    + +      +
Sbjct: 173 -----ERVNQRMLLEKVLPVLDEREQKILQFTFIEN--RSQKETGELLD 214


>gi|307264896|ref|ZP_07546458.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|306920154|gb|EFN50366.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
          Length = 246

 Score =  125 bits (315), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 41/254 (16%), Positives = 109/254 (42%), Gaps = 19/254 (7%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLMQAV 90
           E  + K Y  + D +  + ++  ++ LV  I               +++++G IGL+ A+
Sbjct: 5   EEDIWKTYNSNKDPNLRNEIIIKYMPLVKHIVKKLIISDITQSEYEDLINQGVIGLIDAI 64

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +K+ P +G +  TY+   I+  + +Y+ R   +         + L    ++++  ++ + 
Sbjct: 65  EKYQPSKGVKFETYATLRIRGEIIDYLRRKDWM--------PRSLKKKYKKIEETVETLQ 116

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
               +   V  I +   ++E++V+     +      N    +S + + +    L    + 
Sbjct: 117 QKYNREPTVEEITEACGLNETDVLKTLSYI------NVSNINSLEEAIENNLKLHAISNV 170

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
           + +   E+   K  +  L  ++  L  +ER +      ++  +  +++S    ++  R+ 
Sbjct: 171 ELKNPEEEVLYKELKRKLASAIESLPDKERLVITLYYYED--LNYKDISKILNLTESRIS 228

Query: 271 QIEARAFKKVQESI 284
           QI  +A K+++E +
Sbjct: 229 QIHTKAIKRIREML 242


>gi|324997618|ref|ZP_08118730.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily protein
           [Pseudonocardia sp. P1]
          Length = 277

 Score =  125 bits (315), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 51/249 (20%), Positives = 97/249 (38%), Gaps = 16/249 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +   +L      +V  IA  YR  G P  ++   G IGL+ A+ +FDPE+G     Y++ 
Sbjct: 41  ALREQLARGFHPVVRHIAGRYRHRGEPADDLEQVGAIGLLNALDRFDPEQGTPFLAYAVP 100

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I   ++ +       +++      +RL     R+    + +   + +  +V  +A+ L 
Sbjct: 101 TITGEIRRHFRDRTWSMRVP-----RRLKDFQTRMTRAQEELAVRHGRAPKVSELAEHLG 155

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
            S  EVI          S ++L   +    S   + +     G   V          R  
Sbjct: 156 TSREEVIEGLQAQDSYRS-DSLDRLAGDTESPLGEIVGGADAGIGTV--------EDREA 206

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L  ++  L  RER I   R       T   ++ E  +S+  V ++ AR+   ++  + ++
Sbjct: 207 LRPALRRLPERERTILLLRFFGN--RTQTQIAEEVGLSQMHVSRLLARSLATLRRHLVEE 264

Query: 288 VELSSSPPL 296
               S  P+
Sbjct: 265 PGGDSVSPM 273


>gi|150390631|ref|YP_001320680.1| sporulation sigma factor SigE [Alkaliphilus metalliredigens QYMF]
 gi|149950493|gb|ABR49021.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           metalliredigens QYMF]
          Length = 244

 Score =  125 bits (315), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 55/264 (20%), Positives = 108/264 (40%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EE  L  + +   + +    L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 42  PPLSHDEERFLINKLKND-ESTVRTILIERNLRLVVYIARKFENTGIGVEDLISIGTIGL 100

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+P++  +LATY+   I+  +  Y+ R+  +                       
Sbjct: 101 IKAVNTFNPDKNIKLATYASRCIENEILMYLRRNSKV----------------------- 137

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                             K+ VS  E ++++                D N     D L  
Sbjct: 138 ------------------KMEVSFDEPLNID---------------WDGNELLLSDILGT 164

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEV 264
           D+D   + L E+ +    + +L  ++  L+ RER+I E R         T + ++    +
Sbjct: 165 DNDIIYKFLEEEVD----KELLKFALKKLSKRERKIMELRFGLQTGKERTQKEVADLLGI 220

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R   ++++ I + +
Sbjct: 221 SQSYISRLEKRIIIRLKKEINRLI 244


>gi|304316787|ref|YP_003851932.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
 gi|302778289|gb|ADL68848.1| RNA polymerase, sigma 28 subunit, SigF [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
          Length = 247

 Score =  125 bits (315), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 48/241 (19%), Positives = 100/241 (41%), Gaps = 18/241 (7%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           ++   L ++  ++ D  +  +L+  +  L+  I   +   G    ++   G IG ++A+ 
Sbjct: 10  EDVNELIRK-SKNNDKLSLEKLLKENSGLIWSIVKKFSNRGYEAEDLYQIGCIGFVKAIN 68

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFD     +L+TY++  I   ++ ++     L+K+  +   K L      +K  L+   +
Sbjct: 69  KFDESYNVKLSTYAVPIILGEIKRFLRDDG-LIKVSRSL--KELSNKAYYIKDELEKELN 125

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
                  +  IA KLNVS  E+       A  E L      S+ ++    + +  +    
Sbjct: 126 RE---PTIQEIASKLNVSAEEIAMAFESTATAEYLYDNSQHSEDDNMLLIEKIGSE---- 178

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
                + E     +  L   +  L+ RER+I   R  ++  +T   +S    +S+ +V +
Sbjct: 179 -----DNEYDIEDKLALRMVLKKLDSRERQIIVLRYFKD--MTQTEVSKILGISQVQVSR 231

Query: 272 I 272
           I
Sbjct: 232 I 232


>gi|302549049|ref|ZP_07301391.1| RNA polymerase sigma-B factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302466667|gb|EFL29760.1| RNA polymerase sigma-B factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 263

 Score =  125 bits (315), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 45/251 (17%), Positives = 100/251 (39%), Gaps = 17/251 (6%)

Query: 40  RYREHGDLSA-AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           R  E  +  A    LV + L +  +IA+ +RG G  + ++     +GL++AV  +DP RG
Sbjct: 27  RLPEGPERKALRDELVEAWLPMAERIAVRFRGRGEALEDLYQVAALGLVKAVDHYDPARG 86

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL-KPE 157
                Y++  +   ++ +       + +       R      R++  ++ ++   L +  
Sbjct: 87  NAFEAYAVPTVTGEIKRHFRDHMWTLHVPRRVQDLR-----NRVRHAVKELSQTTLGRAP 141

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
            V  IA+  +++E EV +    L    +L+        +     D +       + V+  
Sbjct: 142 TVAEIAEYAHLTEGEVRTGTEALECFSALSLEAEMPGTDGYALGDAIGGPDPAFDTVV-- 199

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
                  R  +   +  L  RER I   R  +   +T   ++ +  +S+  V ++ +  F
Sbjct: 200 ------NRVAVKPCLEALPERERIILYLRFFKG--MTQSRIAEQLGISQMHVSRLLSSCF 251

Query: 278 KKVQESIQKQV 288
             ++E +  + 
Sbjct: 252 AHLREELLTEA 262


>gi|302391216|ref|YP_003827036.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Acetohalobium
           arabaticum DSM 5501]
 gi|302203293|gb|ADL11971.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Acetohalobium
           arabaticum DSM 5501]
          Length = 235

 Score =  125 bits (315), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 55/277 (19%), Positives = 106/277 (38%), Gaps = 64/277 (23%)

Query: 7   SIIVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           S + +G + L  YI      P  L+ +EE     RY E GD  A   L+  ++RLV  I 
Sbjct: 11  SSLADGILVLISYIANNNIFPQPLDDEEEKKYLTRYLE-GDEEAKEVLIEHNMRLVAHIV 69

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             Y    +   +++S G+IGL++A++ +DP +  +LATY+   I+  +  +  ++    +
Sbjct: 70  KKYNNSNVDKEDLISIGSIGLIKAIETYDPSKKVKLATYASRCIENEILMHFRQNKKTNR 129

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
                           +K H    +D       ++ + +    +  E + M         
Sbjct: 130 ---------------EVKLHDPLSSDKEGNEMTLMDVYETDEEAVLEKVEMAL------- 167

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
                                     E+ L +K E  + R              +++ + 
Sbjct: 168 -------------------------AEERLYDKIEGLSERE-------------QKVVKM 189

Query: 246 RRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
           R    N   +T   ++++  +SR  V +IE RA +K+
Sbjct: 190 RYGLNNVEELTQREIANKLGISRSYVSRIEKRALQKL 226


>gi|21224822|ref|NP_630601.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
 gi|3559995|emb|CAA20617.1| putative RNA polymerase sigma factor [Streptomyces coelicolor
           A3(2)]
          Length = 266

 Score =  125 bits (315), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 48/238 (20%), Positives = 99/238 (41%), Gaps = 15/238 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
               R+V + L +  ++A  +R  G    ++     +GL++AV ++DPERG    +Y++ 
Sbjct: 35  ELRDRIVEAWLPMAERLAGRFRSRGESFEDLRQVAALGLVKAVDRYDPERGNAFESYAVP 94

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKPEQVVAIAKKL 166
            I   ++ +       + +     + R      R++   Q ++     +   V  IA++ 
Sbjct: 95  TITGEIKRHFRDHMWTLHVPRRVQELR-----NRVRFAGQDLSQTIPGRRPTVAEIAERA 149

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +SE +V      L   ES  AL   ++   S+    L       +  L    +    R 
Sbjct: 150 ELSEEDVR---VGLEALESFTALSLDAELPGSEDGYSLGDALGAPDPAL----DTVVDRE 202

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +   ++ L PRER I   R   +  +T   ++ +  +S+  V ++  R   +V+E +
Sbjct: 203 AVKDRLAALPPRERAILYMRFFND--MTQSRIAEQLGISQMHVSRLITRCCDRVREQV 258


>gi|54024680|ref|YP_118922.1| putative sigma factor [Nocardia farcinica IFM 10152]
 gi|54016188|dbj|BAD57558.1| putative sigma factor [Nocardia farcinica IFM 10152]
          Length = 261

 Score =  125 bits (315), Expect = 7e-27,   Method: Composition-based stats.
 Identities = 35/237 (14%), Positives = 87/237 (36%), Gaps = 16/237 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +    ++   L L   IA  + G G    +++    +GL+QA  +FD  RG     +++ 
Sbjct: 34  ALRAEVIDRALPLAEHIARRFAGRGESFDDLLQVARLGLVQAADRFDVGRGSSFLAFAVP 93

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I   ++ +   +   V++     + +       +   ++ ++    +  +   IA +L 
Sbjct: 94  TIMGEVRRHFRDNTWAVRVPRRTKEIQ-----GSIGATVEELSQRLGRMPRAREIAAELG 148

Query: 168 VSESEVISMNCR--LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           +   EV             SL++      +N+       +   +   + + +        
Sbjct: 149 IDVVEVTQALIAGNAYQSSSLDSTAGDDGENTPLPLSESLGAEEPSFEFVDDYL------ 202

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             +   ++ L  RER++   R       T   ++    VS+  V +I ++    ++E
Sbjct: 203 -AVRPLIAELPERERQVLVMRFF--EGKTQTQIADVLGVSQMHVSRILSKTLHALRE 256


>gi|157692327|ref|YP_001486789.1| RNA polymerase sigma factor SigD [Bacillus pumilus SAFR-032]
 gi|157681085|gb|ABV62229.1| DNA-directed RNA polymerase sigma subunit D [Bacillus pumilus
           SAFR-032]
          Length = 255

 Score =  125 bits (315), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 49/262 (18%), Positives = 112/262 (42%), Gaps = 19/262 (7%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQA 89
           E+  L  R++E  D +A   L+  ++ LV              +   +++S G +GL  A
Sbjct: 7   EDQALWARWKEWKDPAAGDDLMRRYMPLVTYHVGRISIGLPKSVHKEDLISLGMLGLYDA 66

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           ++KFDP R  +  TY+ + I+ A+ + + +   L +              ++++  ++ +
Sbjct: 67  LEKFDPGRDLKFDTYASFRIRGAIIDGLRKEDWLPRTSR--------EKTKKVEAAIEKL 118

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCR--LAGDESLNALINSSDKNSSQWQDWLVYD 207
               L+      +A++L +SE +V++       A   S++  ++  +       +  V  
Sbjct: 119 EQRYLRNVTPTEVAEELGMSEQDVVTTMNEGFFANLLSIDEKLHDQEDGE----NVQVMI 174

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            D +     EK  +      L   M+ L+ +E+ +       +  +TL  +     +S  
Sbjct: 175 RDEKTVTPEEKMLKDELIEQLAEKMTELSEKEKLVISLFY--KEELTLTEIGHVLNLSTS 232

Query: 268 RVRQIEARAFKKVQESIQKQVE 289
           R+ QI ++A  K++  + K ++
Sbjct: 233 RISQIHSKALFKLKHLLDKAIQ 254


>gi|325262838|ref|ZP_08129574.1| RNA polymerase sigma-K factor [Clostridium sp. D5]
 gi|324031932|gb|EGB93211.1| RNA polymerase sigma-K factor [Clostridium sp. D5]
          Length = 212

 Score =  125 bits (315), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 55/257 (21%), Positives = 97/257 (37%), Gaps = 62/257 (24%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L   EE    ++Y E GDL A H L+  +LRLV  +   Y+       +++S G IGL+
Sbjct: 14  PLTPSEEKYYMQKYTE-GDLQAKHVLIERNLRLVAHVIKKYQYLDEDPEDLISIGTIGLI 72

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV  F+P++G RLA Y+   ++  +  Y+                       R K    
Sbjct: 73  KAVVTFNPDKGNRLAAYASKCVENEILMYL-----------------------RAKKKTS 109

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                                     IS+   +  D          + N  +  D +  D
Sbjct: 110 KE------------------------ISLYEPIGTDR---------EGNEIKLYDIIETD 136

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVS 265
                 V  +   ++N + +  +  + L+ RER + + R         T   ++ +  +S
Sbjct: 137 E---ADVPEKIHLKENIQKLYDKVENELSQRERLVLKMRYGLYNGEEYTQREIARQLGIS 193

Query: 266 RERVRQIEARAFKKVQE 282
           R  V +IE  A +K++E
Sbjct: 194 RSYVSRIEKSAVEKLRE 210


>gi|160915288|ref|ZP_02077501.1| hypothetical protein EUBDOL_01297 [Eubacterium dolichum DSM 3991]
 gi|158433087|gb|EDP11376.1| hypothetical protein EUBDOL_01297 [Eubacterium dolichum DSM 3991]
          Length = 239

 Score =  125 bits (315), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 63/280 (22%), Positives = 104/280 (37%), Gaps = 62/280 (22%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           I++  +G   Y+H       L+K+ E        + G+ +A  +L+  +LRLV  I   Y
Sbjct: 10  ILSNALGYVGYVHNNTFAQPLDKESETKYIAALAK-GNQTARDKLIEHNLRLVAHIVKKY 68

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
                   +++S G IGL++AV  F PE+G +L TY+   I+  +  Y+  S        
Sbjct: 69  DFKKEATEDLISIGTIGLIKAVDSFKPEKGHKLTTYASKCIENEILMYLRSS-------- 120

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
               K  F N                                   +S+N  +A D     
Sbjct: 121 ----KNYFQN-----------------------------------VSLNEPIATD----- 136

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
                D +     D +    D     +I+     +    L + M VL+ RE  I   R  
Sbjct: 137 ----KDGSEIMLIDAIASPCDTS---IIDDMLVADNIVKLKQYMHVLDARELEIITKRFG 189

Query: 249 --QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +   T   ++ +  +SR  V +IE RAF K+    +K
Sbjct: 190 LFGQKEATQREIAKQLHISRSYVSRIEKRAFMKLYREFKK 229


>gi|21283717|ref|NP_646805.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus MW2]
 gi|49486858|ref|YP_044079.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus MSSA476]
 gi|297210116|ref|ZP_06926509.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           ATCC 51811]
 gi|300910479|ref|ZP_07127931.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           TCH70]
 gi|21205159|dbj|BAB95853.1| sigma factor B [Staphylococcus aureus subsp. aureus MW2]
 gi|49245301|emb|CAG43776.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           MSSA476]
 gi|296885316|gb|EFH24256.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           ATCC 51811]
 gi|300888321|gb|EFK83512.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           TCH70]
          Length = 256

 Score =  125 bits (315), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 43/257 (16%), Positives = 103/257 (40%), Gaps = 18/257 (7%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             ++     K ++E+ +  A  +LV  + +L+  +A  Y        ++V  G +GL+ A
Sbjct: 12  SPEQINQWIKEHQENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGA 71

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +FD     +   + +  +   ++ Y+      V +      K +   ++++   L A 
Sbjct: 72  INRFDMSFERKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRI--KEIGPRIKKVSDELTAE 129

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNC---RLAGDESLNALINSSDKNSSQWQDWLVY 206
            + +    ++    +       E + M      L+ D S+ A     D ++    D +  
Sbjct: 130 LERSPSISEIADRLEVSEEEVLEAMEMGQSYNALSVDHSIEA---DKDGSTVTLLDIMGQ 186

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
             D          +   +R +L + + +L+ RER I +   +    ++ +       +S+
Sbjct: 187 QDDHY--------DLTEKRMILEKILPILSDREREIIQCTFI--EGLSQKETGERIGLSQ 236

Query: 267 ERVRQIEARAFKKVQES 283
             V +++  A KK+QE+
Sbjct: 237 MHVSRLQRTAIKKLQEA 253


>gi|289805026|ref|ZP_06535655.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. AG3]
          Length = 196

 Score =  125 bits (314), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 38/135 (28%), Positives = 64/135 (47%), Gaps = 4/135 (2%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 64  LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 123

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 124 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 181

Query: 138 NLRRLKGHLQAITDN 152
            L R+   +      
Sbjct: 182 KLNRISRQMLQEMGR 196


>gi|148273835|ref|YP_001223396.1| putative RNA polymerase sigma factor SigF [Clavibacter
           michiganensis subsp. michiganensis NCPPB 382]
 gi|147831765|emb|CAN02734.1| putative RNA polymerase sigma factor, SigF-homolog (stress
           response/stationary phase sigma factor) [Clavibacter
           michiganensis subsp. michiganensis NCPPB 382]
          Length = 335

 Score =  125 bits (314), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 42/240 (17%), Positives = 95/240 (39%), Gaps = 15/240 (6%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                ++V  HL L  ++A  + G     S++   G +GL++A +++DP  G    ++++
Sbjct: 83  RRLHDQIVLDHLELADQLARQHSGRAHDWSDLRQVGYLGLVKAARRYDPGFGAPFVSFAI 142

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I   ++ ++  +  +V+      + R       L   + A+T    +      +A   
Sbjct: 143 PTISGEIKRHLRDNGWVVRPPRHVQELRHA-----LLAVVPALTQRLGRTPTDAELAAHT 197

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             +  EV+      +     +      +       D +  D  G          R  R  
Sbjct: 198 GHAREEVVEALAAHSSLRPASLDFTVHEDEGISLADTIGADDPGYA--------RAERTV 249

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +L  +  VL+ R+RRI   R + E   +   +++E  V++ +V ++ AR    ++  + +
Sbjct: 250 LLDAARGVLSDRDRRILHLRFVDE--CSQSEIAAELGVTQMQVSRLLARILGALRAELTR 307


>gi|284045933|ref|YP_003396273.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
 gi|283950154|gb|ADB52898.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Conexibacter
           woesei DSM 14684]
          Length = 263

 Score =  125 bits (314), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 55/253 (21%), Positives = 105/253 (41%), Gaps = 18/253 (7%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
            +LA R R +GD  A   L+  HL L   +A  YR     + ++V   ++GL++AV +FD
Sbjct: 27  RMLATRAR-NGDGRAREALIAEHLPLARALARRYRRGSESLDDLVQVASVGLIKAVDRFD 85

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P+RG   +T++   I   +  +   +   V +     +  L     +++   +AI     
Sbjct: 86  PDRGHSFSTFAQPTIVGELLRHFRDTGWGVHVARGTQELAL-----KVRSAAEAIETETG 140

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQE 212
                  IA++       V+     LA     SL       D+  +   D L        
Sbjct: 141 AVATPRQIAERTGAELEAVVEALGALANRTALSLATPAGHDDEGDATIADTLGD------ 194

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
             + E       R +L  ++  L  RE+RI   R + +  +T   +++E  VS+ ++ ++
Sbjct: 195 --VEEGYRAAEARALLGPALRHLPEREQRIIRMRFVDD--LTQSEIATEIGVSQMQISRL 250

Query: 273 EARAFKKVQESIQ 285
             ++  K+ E  +
Sbjct: 251 LRQSLDKLHELTR 263


>gi|319937328|ref|ZP_08011735.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
 gi|319807694|gb|EFW04287.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
          Length = 227

 Score =  125 bits (314), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 54/257 (21%), Positives = 100/257 (38%), Gaps = 63/257 (24%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L  QEE  L ++Y + GD  A ++L+  +LRLV  IA  Y        +++S G IGL++
Sbjct: 27  LTPQEENDLLEKYFQ-GDQEARNQLIEHNLRLVAHIAKKYESTKDLQEDLISIGTIGLIK 85

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           AV  + P +  +L TY+   I+  +  ++  +                            
Sbjct: 86  AVDSYKPTKATKLGTYAAKCIENEILMHMRGNKKT------------------------- 120

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                            L+VS +E++ ++                D       D L  D 
Sbjct: 121 ----------------ALDVSLNEILGVDK---------------DGGEMTLLDILPSDQ 149

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSR 266
               + +I++ + +++   L     +L PRE+ I   R         T + ++S   +SR
Sbjct: 150 ----KEIIDQIDTEDQIKKLQEYFLLLTPREQEILIYRYGLNKHKVYTQKEIASTMHISR 205

Query: 267 ERVRQIEARAFKKVQES 283
             V ++E RA  K+ ++
Sbjct: 206 SYVSRLEKRALIKLLKA 222


>gi|297194001|ref|ZP_06911399.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
 gi|297152057|gb|EFH31507.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
          Length = 305

 Score =  125 bits (314), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 46/221 (20%), Positives = 90/221 (40%), Gaps = 16/221 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            + LV  +L LV   A  +R    P+ +++  G IGL++A+ +F+  RG    T++M  I
Sbjct: 81  RNTLVELNLALVKFAASRFRTRSEPMEDIIQVGTIGLIKAIDRFELSRGVEFPTFAMPTI 140

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V++     + RL      L      ++    +   V  +A++L++ 
Sbjct: 141 IGEIKRFFRDTSWSVRVPRRLQELRLD-----LAKAGDELSQQLDRAPTVDELAQRLDIG 195

Query: 170 ESEVIS-MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
             EV+  M    A   S        D +     + + Y+  G E +             L
Sbjct: 196 RDEVVEGMAASNAYTASSLDAQPEEDDSEGALANRIGYEDHGLEGI--------EYIESL 247

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
              ++ L PR+R+I   R +    +T   +  E  +S+  V
Sbjct: 248 RPMIASLPPRDRKILSLRFVAN--MTQSEIGEELGISQMHV 286


>gi|289767896|ref|ZP_06527274.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
 gi|289698095|gb|EFD65524.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
          Length = 270

 Score =  125 bits (314), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 48/238 (20%), Positives = 99/238 (41%), Gaps = 15/238 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
               R+V + L +  ++A  +R  G    ++     +GL++AV ++DPERG    +Y++ 
Sbjct: 39  ELRDRIVEAWLPMAERLAGRFRSRGESFEDLRQVAALGLVKAVDRYDPERGNAFESYAVP 98

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKPEQVVAIAKKL 166
            I   ++ +       + +     + R      R++   Q ++     +   V  IA++ 
Sbjct: 99  TITGEIKRHFRDHMWTLHVPRRVQELR-----NRVRFAGQDLSQTIPGRRPTVAEIAERA 153

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +SE +V      L   ES  AL   ++   S+    L       +  L    +    R 
Sbjct: 154 ELSEEDVR---VGLEALESFTALSLDAELPGSEDGYSLGDALGAPDPAL----DTVVDRE 206

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +   ++ L PRER I   R   +  +T   ++ +  +S+  V ++  R   +V+E +
Sbjct: 207 AVKDRLAALPPRERAILYMRFFDD--MTQSRIAEQLGISQMHVSRLITRCCDRVREQV 262


>gi|29828415|ref|NP_823049.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29605518|dbj|BAC69584.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 264

 Score =  125 bits (314), Expect = 8e-27,   Method: Composition-based stats.
 Identities = 46/240 (19%), Positives = 99/240 (41%), Gaps = 15/240 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              +V + L +  ++A  +R  G    ++    ++GL++AV ++DPE G    +Y++  I
Sbjct: 38  REEIVEAWLPMAERLAGRFRNRGENYEDLRQVASLGLVKAVDRYDPELGNAFESYAVPTI 97

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKPEQVVAIAKKLNV 168
              ++ +       + +       R      R++   Q ++   + +   V  IA+  N+
Sbjct: 98  TGEIKRHFRDHMWTLHVPRRVQDLR-----NRVRFASQDLSQTISGRRPTVAEIAEHANM 152

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SE +V +    L   ES  AL   ++   S+    L       +  L    +    R  +
Sbjct: 153 SEEDVRAGLEAL---ESFTALSLDAELPGSEDGYSLSDALGSADPAL----DIVVDREAV 205

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
              +  L  RER I   R   +  +T   ++ +  +S+  V +I +R   +++E + +  
Sbjct: 206 KPRLQALPERERDILYMRFFGD--MTQSRIAEQLGISQMHVSRIISRCCDRLREQVMRDA 263


>gi|57650736|ref|YP_186870.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus COL]
 gi|87160164|ref|YP_494668.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus USA300_FPR3757]
 gi|88195964|ref|YP_500776.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus NCTC 8325]
 gi|151222182|ref|YP_001333004.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus str. Newman]
 gi|161510276|ref|YP_001575935.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus USA300_TCH1516]
 gi|221141586|ref|ZP_03566079.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus str. JKD6009]
 gi|258453225|ref|ZP_05701216.1| RNA polymerase sigma-B factor [Staphylococcus aureus A5948]
 gi|262049235|ref|ZP_06022110.1| sigma factor B [Staphylococcus aureus D30]
 gi|262052481|ref|ZP_06024679.1| sigma factor B [Staphylococcus aureus 930918-3]
 gi|282923053|ref|ZP_06330738.1| RNA polymerase sigma-B factor [Staphylococcus aureus A9765]
 gi|284025100|ref|ZP_06379498.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus 132]
 gi|294850549|ref|ZP_06791276.1| RNA polymerase sigma-B factor [Staphylococcus aureus A9754]
 gi|304379245|ref|ZP_07361984.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           ATCC BAA-39]
 gi|1729797|emb|CAA71068.1| sigma-B [Staphylococcus aureus subsp. aureus COL]
 gi|1934991|emb|CAA68932.1| sigma factor B [Staphylococcus aureus]
 gi|37781588|gb|AAP42796.1| SigB [Staphylococcus aureus]
 gi|57284922|gb|AAW37016.1| RNA polymerase sigma-37 factor [Staphylococcus aureus subsp. aureus
           COL]
 gi|87126138|gb|ABD20652.1| RNA polymerase sigma-37 factor [Staphylococcus aureus subsp. aureus
           USA300_FPR3757]
 gi|87203522|gb|ABD31332.1| sigma factor B, putative [Staphylococcus aureus subsp. aureus NCTC
           8325]
 gi|150374982|dbj|BAF68242.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           str. Newman]
 gi|160369085|gb|ABX30056.1| DNA-directed RNA polymerase sigma subunit FliA [Staphylococcus
           aureus subsp. aureus USA300_TCH1516]
 gi|257859171|gb|EEV82028.1| RNA polymerase sigma-B factor [Staphylococcus aureus A5948]
 gi|259159602|gb|EEW44648.1| sigma factor B [Staphylococcus aureus 930918-3]
 gi|259162600|gb|EEW47167.1| sigma factor B [Staphylococcus aureus D30]
 gi|269941665|emb|CBI50072.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           TW20]
 gi|282593244|gb|EFB98241.1| RNA polymerase sigma-B factor [Staphylococcus aureus A9765]
 gi|294822569|gb|EFG39011.1| RNA polymerase sigma-B factor [Staphylococcus aureus A9754]
 gi|302751946|gb|ADL66123.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus str. JKD6008]
 gi|304342104|gb|EFM08004.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           ATCC BAA-39]
 gi|315197004|gb|EFU27346.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus CGS01]
 gi|320140765|gb|EFW32617.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           MRSA131]
 gi|320143740|gb|EFW35517.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           MRSA177]
 gi|329314750|gb|AEB89163.1| RNA polymerase sigma factor [Staphylococcus aureus subsp. aureus
           T0131]
 gi|329724065|gb|EGG60589.1| RNA polymerase sigma-B factor [Staphylococcus aureus subsp. aureus
           21189]
          Length = 256

 Score =  125 bits (314), Expect = 9e-27,   Method: Composition-based stats.
 Identities = 43/258 (16%), Positives = 104/258 (40%), Gaps = 18/258 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           +  ++     K ++E+ +  A  +LV  + +L+  +A  Y        ++V  G +GL+ 
Sbjct: 11  ISPEQINQWIKEHQENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIG 70

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A+ +FD     +   + +  +   ++ Y+      V +      K +   ++++   L A
Sbjct: 71  AINRFDMSFERKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRI--KEIGPRIKKVSDELTA 128

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNC---RLAGDESLNALINSSDKNSSQWQDWLV 205
             + +    ++    +       E + M      L+ D S+ A     D ++    D + 
Sbjct: 129 ELERSPSISEIADRLEVSEEEVLEAMEMGQSYNALSVDHSIEA---DKDGSTVTLLDIMG 185

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
              D          +   +R +L + + +L+ RER I +   +    ++ +       +S
Sbjct: 186 QQDDHY--------DLTEKRMILEKILPILSDREREIIQCTFI--EGLSQKETGERIGLS 235

Query: 266 RERVRQIEARAFKKVQES 283
           +  V +++  A KK+QE+
Sbjct: 236 QMHVSRLQRTAIKKLQEA 253


>gi|307327205|ref|ZP_07606393.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306887096|gb|EFN18094.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 272

 Score =  125 bits (314), Expect = 9e-27,   Method: Composition-based stats.
 Identities = 46/239 (19%), Positives = 106/239 (44%), Gaps = 19/239 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +   R+V + + +  ++A  YR  G  + ++     +GL++AVK++DPE G   A +++
Sbjct: 43  EALRRRVVEAWMPMAERLARQYRNRGESLEDLEQVAALGLVKAVKRYDPEHGTAFAGFAV 102

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKPEQVVAIAKK 165
             I   ++ +      ++ +       R      R++   + ++ + + +P +   IA++
Sbjct: 103 PTIVGEIKRHFRDHLWVLHVPRRVQDLR-----NRVRAAHRELSHSADDRPPRTQDIAER 157

Query: 166 LNVSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
             ++E EV +    +      SL+A +  SD   S      + D  G ++   +   R  
Sbjct: 158 TGLTEKEVRAGMEAMGSFTPLSLDAQLTGSDDGYS------LADTLGAQEAAYD---RVV 208

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            R  +   +S L  RER+I   R   +  +T   ++ +  +S+  V ++  R    +++
Sbjct: 209 DREAVRPGLSRLPERERQILYMRFFCD--MTQSRIAEQLGISQMHVSRLINRTCSTLRD 265


>gi|238924602|ref|YP_002938118.1| sporulation sigma factor SigE [Eubacterium rectale ATCC 33656]
 gi|238876277|gb|ACR75984.1| sporulation sigma factor SigE [Eubacterium rectale ATCC 33656]
          Length = 244

 Score =  125 bits (314), Expect = 9e-27,   Method: Composition-based stats.
 Identities = 59/271 (21%), Positives = 107/271 (39%), Gaps = 70/271 (25%)

Query: 27  PMLEKQEE----YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           P LE  EE      L  +        A  +L+  +LRLVV +A  +   G+ + +++S G
Sbjct: 35  PPLETDEEKCCLIALVDKNVAMSKEQAKKQLIEHNLRLVVYLAKKFENTGVCVEDLISIG 94

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            IGL++ +  F+PE+  +LATY+   I                      +  +   LRR 
Sbjct: 95  TIGLIKGINTFNPEKKIKLATYASRCI----------------------ENEILMYLRR- 131

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN-SSDKNSSQWQ 201
                                             N R+  + S +  +N   D N     
Sbjct: 132 ----------------------------------NNRVKLEVSFDEPLNTDWDGNELLLS 157

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL----QENPVTLEN 257
           D L  D D    V+ +  E +   ++L ++M  LN RER+I E R      +   +T + 
Sbjct: 158 DILGTDED----VIYKDLETEVEISLLKKAMLSLNERERQIIELRFGVNRVENKELTQKE 213

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           ++    +S+  + ++E +  +++++ IQK  
Sbjct: 214 VADILGISQSYISRLEKKIMERLKKEIQKMA 244


>gi|261883762|ref|ZP_06007801.1| RNA polymerase factor sigma-32 [Campylobacter fetus subsp.
           venerealis str. Azul-94]
          Length = 165

 Score =  125 bits (314), Expect = 9e-27,   Method: Composition-based stats.
 Identities = 67/156 (42%), Positives = 97/156 (62%), Gaps = 1/156 (0%)

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           +MQ+YILR+WS+V+ GT++ QK LFFNLRRL+  L    DN  K E    I+ +L VS S
Sbjct: 1   SMQDYILRNWSIVRGGTSSAQKALFFNLRRLRSKLAQTDDNMTKAEIYREISDQLGVSTS 60

Query: 172 EVISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           +V  M+ RL+G D SL+A +N  +  +S+  D+LV DH  Q+++     + + R   LTR
Sbjct: 61  DVEFMDSRLSGPDSSLSAPMNGEETGASRRMDFLVDDHPLQDEIAESSIDMERRNRWLTR 120

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           ++  LN RE  I   RRL ++ VTLE L  +  +SR
Sbjct: 121 ALDTLNERELHIIRERRLDDDGVTLEALGEKLGISR 156


>gi|210621718|ref|ZP_03292767.1| hypothetical protein CLOHIR_00712 [Clostridium hiranonis DSM 13275]
 gi|210154600|gb|EEA85606.1| hypothetical protein CLOHIR_00712 [Clostridium hiranonis DSM 13275]
          Length = 252

 Score =  125 bits (314), Expect = 9e-27,   Method: Composition-based stats.
 Identities = 47/242 (19%), Positives = 106/242 (43%), Gaps = 18/242 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             + GDL + ++L+  ++ LV K    +    L   ++   G IGL++A+++FDP  G  
Sbjct: 25  LAQKGDLKSKNKLIKLNIGLVKKAVSKFSFSSLDNDDLYQLGCIGLVKAIERFDPNLGNM 84

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            ++Y++  I+  ++ ++     ++KI      K + +  ++ K      T    K   + 
Sbjct: 85  FSSYAVPLIEGEIKRFLRDDG-IIKISREL--KTIGWKAKKYKTQYFKKTG---KEASLQ 138

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
           A++K+LN+   ++ S    L+  E  N   + S+       + ++ +       LIE   
Sbjct: 139 ALSKELNIPIEKIQSALIALSPVEYFNIYESDSEYTQLDLSNNIIMEDSIPYTELIE--- 195

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                  L   +  L   E+++ + R  ++   T         +S+ +V +IE +A   +
Sbjct: 196 -------LNEIIDELPDLEKKVMKLRYFED--FTQAKTGEILGISQVQVSRIERKALMLL 246

Query: 281 QE 282
           ++
Sbjct: 247 KK 248


>gi|169351192|ref|ZP_02868130.1| hypothetical protein CLOSPI_01971 [Clostridium spiroforme DSM 1552]
 gi|169292254|gb|EDS74387.1| hypothetical protein CLOSPI_01971 [Clostridium spiroforme DSM 1552]
          Length = 231

 Score =  125 bits (314), Expect = 9e-27,   Method: Composition-based stats.
 Identities = 53/275 (19%), Positives = 108/275 (39%), Gaps = 68/275 (24%)

Query: 17  SRYIHEIRKI----PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGY 71
           ++Y++ + +     P L   EE    ++  + GD  A   L+  +LRLVV +A  Y    
Sbjct: 12  TKYLYYVGRHDVLPPPLNAFEEKEALEKLAK-GDNDARDLLIEHNLRLVVYVAKRYDTNQ 70

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
              I +++S G IGL++A+  F  ++  +LATY+   I+  +  ++ ++           
Sbjct: 71  NGGIEDLISIGTIGLVKAINTFKTDKNIKLATYASRCIENEILMFLRKN----------- 119

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
                  LR                                       ++ DE LN    
Sbjct: 120 -----NKLRHE-------------------------------------ISLDEPLN---I 134

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ-- 249
             D N     D +  D D    ++  + E+ ++R M   +   L+ RE+ I   R     
Sbjct: 135 DYDGNELLLSDIIGTDSD----IVKNELEQSDQRTMFYEAFKDLSKREKEILMLRYGLMN 190

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + +T ++++    +S+  + ++E +  KK++  +
Sbjct: 191 YDELTQKDVAKMMGISQSYISRLEKKIIKKLRNKL 225


>gi|262204122|ref|YP_003275330.1| RNA polymerase sigma-70 factor, sigma-B/F/G subfamily [Gordonia
           bronchialis DSM 43247]
 gi|262087469|gb|ACY23437.1| RNA polymerase sigma-70 factor, sigma-B/F/G subfamily [Gordonia
           bronchialis DSM 43247]
          Length = 276

 Score =  125 bits (314), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 38/235 (16%), Positives = 90/235 (38%), Gaps = 15/235 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              ++   L L   +A  +   G P  +++    IG++ AV +FD ERG    ++++  +
Sbjct: 48  RDNIIERCLPLAEHVAWRFSDRGEPFDDLLQVARIGVVNAVDRFDGERGDSFLSFAVPTV 107

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   S   +++   A +  L      +      +     +  +   +A  L + 
Sbjct: 108 MGEVRRHFRDSMWAIRVPRRAKETSLS-----IGKATDELVQRLGRSPRPSELAAHLGLP 162

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             EVI      +  ++ +      D +    +D L  D     Q+        +    L 
Sbjct: 163 VDEVIDGLLARSAYQARSIDATPEDDDGRSIRDTLGDDDARLAQI--------DEFVTLR 214

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             +  L  RER I   R    + ++   +++   +S+  V ++ +R  + ++E +
Sbjct: 215 PVLDQLPDREREIVTLRFF--HAMSQSEIAARVGISQMHVSRLLSRTLETLREQL 267


>gi|37781598|gb|AAP42804.1| SigB [Staphylococcus aureus]
          Length = 256

 Score =  125 bits (314), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 44/261 (16%), Positives = 105/261 (40%), Gaps = 18/261 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           +  ++     K ++E+ +  A  +LV  + +L+  +A  Y        ++V  G +GL+ 
Sbjct: 11  ISPEQINQWIKEHQENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIG 70

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A+ +FD     +   + +  +   ++ Y+      V +      K +   ++++   L A
Sbjct: 71  AINRFDMSLERKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRI--KEIGPRIKKVSDELTA 128

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNC---RLAGDESLNALINSSDKNSSQWQDWLV 205
             + +    ++    +       E + M      L+ D S+ A     D ++    D + 
Sbjct: 129 ELERSPSISEIANRLEVSEEEVLEAMEMGQSYNALSVDHSIEA---DKDGSTVTLLDIMG 185

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
              D          +   +R +L + + +L+ RER I +   +    ++ +       +S
Sbjct: 186 QQDDHY--------DLTEKRMILEKILPILSDREREIIQCTFI--EGLSQKETGERIGLS 235

Query: 266 RERVRQIEARAFKKVQESIQK 286
           +  V +++  A KK+QE+  K
Sbjct: 236 QMHVSRLQRTAIKKLQEAAHK 256


>gi|321309572|ref|YP_004191901.1| RNA polymerase sigma factor rpoD [Mycoplasma haemofelis str.
           Langford 1]
 gi|319801416|emb|CBY92062.1| RNA polymerase sigma factor rpoD [Mycoplasma haemofelis str.
           Langford 1]
          Length = 461

 Score =  125 bits (314), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 59/235 (25%), Positives = 102/235 (43%), Gaps = 12/235 (5%)

Query: 29  LEKQEEYVLAKRYREHGDLS-AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           L  +EE  L+K        S A  +L  S+LRLV  +A  Y  YG P+ ++V EG  GLM
Sbjct: 154 LTLEEETALSKLMENPKTRSFAIKQLTISNLRLVQSVAKKYLNYGFPMEDLVQEGFFGLM 213

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV+KF+   G + +TY+ WWI+ A+   I   + ++++     +  +     ++   L 
Sbjct: 214 KAVQKFNYNLGNKFSTYATWWIRQAIVRSIAEKYRVIRVPVHLQE--IIKRFNKVSMTLM 271

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
           A        + +V + K     + E I+   +L+ D  L +L    D          + D
Sbjct: 272 AEKGEPSLQDILVEMQKYYPNFDLEKITNIKQLSKD--LLSLDGVLDSEEFFPLSGAIRD 329

Query: 208 HDGQEQVLIEKEERKNRR-NMLTRSMS-VLNPRERRIFEARR--LQENPVTLENL 258
            D  +    E+   K  R  ML   +   L P E  + + R   L+    ++  +
Sbjct: 330 EDMMD---AEELSFKAYRVEMLNDMLENELKPDEISLVKLRYGFLEYGKHSVREI 381


>gi|300864899|ref|ZP_07109744.1| RNA polymerase sigma factor SigF [Oscillatoria sp. PCC 6506]
 gi|300337103|emb|CBN54894.1| RNA polymerase sigma factor SigF [Oscillatoria sp. PCC 6506]
          Length = 292

 Score =  125 bits (314), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 47/257 (18%), Positives = 108/257 (42%), Gaps = 16/257 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVK 91
           E   L + Y++       + LV  ++ LV K    +         +++  G+IGL++A++
Sbjct: 49  ESLQLLREYQQAPSNEVRNELVKLNIGLVRKEVHHWLHQCTESYDDLLQVGSIGLIRAIE 108

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           +FD  +G   +++++ +I+  +Q Y+      V++             R+    ++ +  
Sbjct: 109 RFDMSKGNAFSSFAIPYIRGEIQHYLRDKSPSVRVPRHWLTLE-----RQSSSIVKDLQV 163

Query: 152 NNLKPEQVVAIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
              +    + +A  LN+S  E   I + CR     SL+A +   ++ ++   + +  +  
Sbjct: 164 RLNRHPTDIEVATALNISVGEWQEIKLACRNRSPLSLDAPLQDEEEGATCLGELVPDNRY 223

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
              Q+  E       R  L ++++ L  R R I E   L +  +T +  +    +S   V
Sbjct: 224 RSFQLAQED------RIRLQQALAKLEERTREILEFVFLYD--LTQKETAERLGISAVTV 275

Query: 270 RQIEARAFKKVQESIQK 286
            +   +    ++E + K
Sbjct: 276 SRRVKKGLDSLKEMMTK 292


>gi|169831890|ref|YP_001717872.1| FliA/WhiG family RNA polymerase sigma factor [Candidatus
           Desulforudis audaxviator MP104C]
 gi|169638734|gb|ACA60240.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Candidatus
           Desulforudis audaxviator MP104C]
          Length = 257

 Score =  124 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 51/259 (19%), Positives = 104/259 (40%), Gaps = 18/259 (6%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVK 91
             + +RYR+  +     +L+  HL LV  IA              ++   G  GL++AV+
Sbjct: 3   IEIWRRYRDTRNSGLREQLIVEHLPLVRLIAGRLAVRPPSFIAQEDLEGWGIFGLIEAVE 62

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           K+DP  G    T++   I+ A+ + + R   L         + L+  L+ +      +  
Sbjct: 63  KYDPNHGTDFRTFAYHRIRGAILDEVRRQSWL--------PRSLWHKLQEINEARARLER 114

Query: 152 NNLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
                     +A  L +++ E   +  + R     SL+ +  + +  +  W   +    D
Sbjct: 115 ETGASVTDAEVAASLGMTDLEFHRLANHFRSVSVMSLDDVRTTRNGEAVPWGSLI---ED 171

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
                 +E+   +     L  +++ L  ++R +       +  +TL+ L    EV+  R 
Sbjct: 172 TGSPDPLEQVLEEEDHQTLVAAITQLEEKDRLVLALYY--QEGLTLKELGRVLEVTESRA 229

Query: 270 RQIEARAFKKVQESIQKQV 288
            Q+ ARA  +++E I + V
Sbjct: 230 CQLHARAIARLREKIAQAV 248


>gi|158320542|ref|YP_001513049.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Alkaliphilus
           oremlandii OhILAs]
 gi|158140741|gb|ABW19053.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Alkaliphilus
           oremlandii OhILAs]
          Length = 245

 Score =  124 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 55/260 (21%), Positives = 114/260 (43%), Gaps = 25/260 (9%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG-YRGYGLPIS--EVVSEGNIGLMQ 88
           ++   L   Y+ + D  A   L+  ++RLV  IA   Y  YG  I   ++VS G  GL+ 
Sbjct: 2   EDIKTLWHNYKNNNDSQAKALLIEEYIRLVKFIAGRLYISYGSNIEYDDLVSYGIFGLID 61

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++KFD  +  +  TY+   I+ A+ + +    SL  +  +  QK      ++++    +
Sbjct: 62  AIEKFDLNKQVKFETYAQIRIRGAIIDSLR---SLDWVPRSIRQKS-----KKIEEAYSS 113

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVY 206
           + +   +    V +++ L++S  E+  +    A     SL  +I              + 
Sbjct: 114 LENKLGRSATDVEVSEALDISVKELQEILLNTASFNVISLEEVIFEVG----------LI 163

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
            +  +EQ+  +   R+   N L  ++  L  RER++        N +T + +    ++S 
Sbjct: 164 GNTAEEQLTEDLICRRETYNNLKDTIVQLPERERQVISLYYY--NNLTYKEIGKVLDISE 221

Query: 267 ERVRQIEARAFKKVQESIQK 286
            RV Q+ ++A  +++  +  
Sbjct: 222 SRVSQLHSKAISRLKSKLTS 241


>gi|315444719|ref|YP_004077598.1| RNA polymerase sigma factor, sigma-70 family [Mycobacterium sp.
           Spyr1]
 gi|315263022|gb|ADT99763.1| RNA polymerase sigma factor, sigma-70 family [Mycobacterium sp.
           Spyr1]
          Length = 275

 Score =  124 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 41/236 (17%), Positives = 102/236 (43%), Gaps = 18/236 (7%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
             ++T  L L   IA  + G G P  +++    IGL+++V ++ P++G R   +++  I+
Sbjct: 49  QHIITECLPLADHIACRFAGRGEPSDDLIQVARIGLVKSVDRYVPDKG-RFMAFAVPTIR 107

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
             ++ +   S   +++      +++     R++   + ++    +      IA++L V +
Sbjct: 108 GEVRRHFRDSTWSMRVP-----RKIQDTQLRMRHAAEELSQRLKRAPTDREIARELGVDD 162

Query: 171 SEVISMNCR--LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            EV   +         SL+A    +++  +   +    D  G + V            +L
Sbjct: 163 GEVSRCHSAHWAYRPVSLDAPRGDAEQECAGIGELRGADDPGFDSV--------EDLIVL 214

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +  ++ L+PR R I   R    + +T   ++    VS+ +V ++      ++++ +
Sbjct: 215 SGVIAELDPRRRAILGMRFY--DCLTQREIALRLNVSQVQVSRLLDSTLARLRQRM 268


>gi|118479504|ref|YP_896655.1| sporulation sigma factor SigK [Bacillus thuringiensis str. Al
           Hakam]
 gi|118418729|gb|ABK87148.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Bacillus
           thuringiensis str. Al Hakam]
          Length = 271

 Score =  124 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 49/265 (18%), Positives = 92/265 (34%), Gaps = 63/265 (23%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
            Y+        L   +E    +   E GD  A + L+  +LRLV  I   +   G    +
Sbjct: 53  SYVKNNAFPQPLSSDDERKYLELM-EQGDAQARNLLIEHNLRLVAHIVKKFENTGEDAED 111

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++S G IGL++A++ +   +G +LATY+   I                      +  +  
Sbjct: 112 LISIGTIGLIKAIESYSAGKGTKLATYAARCI----------------------ENEILM 149

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
           +LR LK                                       D SL+  I    + +
Sbjct: 150 HLRVLKKT-----------------------------------KKDVSLHDPIGQDKEGN 174

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTL 255
              +  L+     + + +I+  +       +   + +L+ RE+ +   R     +   T 
Sbjct: 175 ---EISLIDILKSESEDVIDMIQLSMELEKIKEYIDILDEREKEVIVKRFGLGLDKEKTQ 231

Query: 256 ENLSSEFEVSRERVRQIEARAFKKV 280
             ++    +SR  V +IE RA  K+
Sbjct: 232 REIAKALGISRSYVSRIEKRALMKM 256


>gi|15614994|ref|NP_243297.1| RNA polymerase sigma factor SigD [Bacillus halodurans C-125]
 gi|10175051|dbj|BAB06150.1| RNA polymerase sigma-D factor [Bacillus halodurans C-125]
          Length = 256

 Score =  124 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 46/254 (18%), Positives = 116/254 (45%), Gaps = 18/254 (7%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFD 94
              +       A   L+  +L LV              +   +++S G +GL+ A++KF+
Sbjct: 13  WTEWLTERSQEACDALIRQYLPLVHYHVQRISVGLPRSVSKDDLISHGMLGLLDALEKFN 72

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P+R  +  TY+ + ++ A+ + + +   L         + +   +++++   + +     
Sbjct: 73  PDRDLKFDTYASFRVRGAILDGLRKEDWL--------PRSMREKIKKIEAATEKLEQKLG 124

Query: 155 KPEQVVAIAKKLNVSESEVISMNCR--LAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +   V  +AK++ +SE+EV        +A   S++   N SD+  +     +       E
Sbjct: 125 RNVSVEEVAKEVGISENEVSQTMTESLVANLLSMDEKTNDSDREETYTATIIDKQSLSPE 184

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           + L+E+ +++    ++    ++LN +E+ +      +E  +TL  +    ++S  R+ QI
Sbjct: 185 EKLLEEAQKEELSQLIA---NILNEKEQLVIGLFYFEE--LTLTEIGQILKLSTSRISQI 239

Query: 273 EARAFKKVQESIQK 286
            ++A  ++Q++++K
Sbjct: 240 HSKALFRLQQALKK 253


>gi|323702739|ref|ZP_08114399.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
 gi|323532256|gb|EGB22135.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
          Length = 232

 Score =  124 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 59/275 (21%), Positives = 102/275 (37%), Gaps = 65/275 (23%)

Query: 9   IVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++NG I L  Y+    ++P  L  +EE  L  R ++ GD  A   LV  +LRLV  IA  
Sbjct: 13  LINGLIFLVSYLSS-GRLPDPLSAEEEQELLSRLQQ-GDQLARSVLVERNLRLVATIANK 70

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           ++  G+   ++   G IGL++AV  F+P R  + ATY+   I+  M+  + ++       
Sbjct: 71  HKDRGIDKQDLFQVGVIGLIKAVNTFNPARTNKFATYAGVCIENEMRMMLRKN------- 123

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
                 +  +    L   L    + N    Q   +A  + V E  V ++           
Sbjct: 124 ------KDEYRCLSLSEPLDYDKEGNPLELQDTLMADDVPVDEQVVHNLET--------- 168

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
                                                   L  +M  L PRER +   R 
Sbjct: 169 --------------------------------------ERLGAAMQKLTPRERVVINLRF 190

Query: 248 L--QENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                  +T   +  +  +SR  + +IE+++  K+
Sbjct: 191 GLNGGRELTQREVGKQLNISRSFISRIESKSISKL 225


>gi|294634080|ref|ZP_06712635.1| RNA polymerase sigma factor [Streptomyces sp. e14]
 gi|292829894|gb|EFF88248.1| RNA polymerase sigma factor [Streptomyces sp. e14]
          Length = 311

 Score =  124 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 53/257 (20%), Positives = 110/257 (42%), Gaps = 20/257 (7%)

Query: 36  VLAKRYREHGD----LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            L +R  +  D     SA   LVT+ L +  +IA  +R  G  I ++     +GL++A+ 
Sbjct: 56  ALFRRLADLPDGPERDSARDELVTAWLPMAHRIAGRFRDRGESIEDLRQVAALGLVKAID 115

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           +FDP+RG    +Y++  I   ++ +       +++     + R      +++   + +T 
Sbjct: 116 RFDPDRG-AFESYAVPTITGEVKRHFRDRMWALRVPRRVQELR-----NKVRVARRELTQ 169

Query: 152 NNLKPE-QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
           N   PE  V A+A    ++E EV +    L    +L+     S           +   D 
Sbjct: 170 NPGSPEPSVAAVAAHTGLTEDEVNTGMEALDSFSTLSLDAEMSTGADGYSLADTLGAADS 229

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
              V++++E  K         +  L  RER I   R  ++  +T   ++    +S+  V 
Sbjct: 230 SYDVVVDRESAK-------EGLRRLPERERAILYMRFFED--MTQSRIADRLGISQMHVS 280

Query: 271 QIEARAFKKVQESIQKQ 287
           ++ +R+  +V++ +  +
Sbjct: 281 RLISRSCARVRDEVLAE 297


>gi|61889360|emb|CAI72509.1| SigB protein [Staphylococcus aureus]
          Length = 256

 Score =  124 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 44/260 (16%), Positives = 104/260 (40%), Gaps = 18/260 (6%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             ++     K ++E+ +  A  +LV  + +L+  +A  Y        ++V  G +GL+ A
Sbjct: 12  SPEQINQWIKEHQENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGA 71

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +FD     +   + +  +   ++ Y+      V +      K +   ++++   L A 
Sbjct: 72  INRFDMSFERKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRI--KEIGPRIKKVSDELTAE 129

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNC---RLAGDESLNALINSSDKNSSQWQDWLVY 206
            + +    ++    +       E + M      L+ D S+ A     D ++    D +  
Sbjct: 130 LERSPSISEIADRLEVSEEEVLEAMEMGQSYNALSVDHSIEA---DKDGSTVTLLDIMGQ 186

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
             D          +   +R +L + + +L+ RER I +   +    ++ +       +S+
Sbjct: 187 QDDHY--------DLTEKRMILEKILPILSNREREIIQCTFI--EGLSQKETGERIGLSQ 236

Query: 267 ERVRQIEARAFKKVQESIQK 286
             V +++  A KK+QE+  K
Sbjct: 237 MHVSRLQRTAIKKLQEAAHK 256


>gi|311031586|ref|ZP_07709676.1| sporulation sigma factor SigK [Bacillus sp. m3-13]
          Length = 237

 Score =  124 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 54/267 (20%), Positives = 96/267 (35%), Gaps = 63/267 (23%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+        L   +E    K   E G+  A + L+  +LRLV  I   +   G   
Sbjct: 18  LVSYVKNNAFPQPLSSGDEAKYLKLMAE-GNEEARNLLIEHNLRLVAHIVKKFENTGEDS 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++S G IGL++A++ F   +G +LATY+   I+  +                      
Sbjct: 77  EDLISIGTIGLIKAIESFHSGKGTKLATYAARCIENEI---------------------- 114

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
             +LR LK                            + +S++  +  D          + 
Sbjct: 115 LMHLRALKKT-------------------------KKDVSLHDPIGQD---------KEG 140

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPV 253
           N     D L  +     + +I+  +       +   + VL+ RER +   R   +  +  
Sbjct: 141 NEISLIDVLKSES----EDVIDTIQLNMELEKIKVYIDVLDEREREVIVGRFGLDLKDEK 196

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKV 280
           T   ++ E  +SR  V +IE RA  K+
Sbjct: 197 TQREIAKELGISRSYVSRIEKRALMKM 223


>gi|302528260|ref|ZP_07280602.1| RNA polymerase sigma-B factor [Streptomyces sp. AA4]
 gi|302437155|gb|EFL08971.1| RNA polymerase sigma-B factor [Streptomyces sp. AA4]
          Length = 261

 Score =  124 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 49/254 (19%), Positives = 92/254 (36%), Gaps = 18/254 (7%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           +E   LA+   EH       RL+  HL L   IA  +   G P  +++    IGL+ AV 
Sbjct: 17  EEISHLAEDTDEH--SRLRRRLIEEHLPLAEHIARRFARRGQPTEDLLQVARIGLINAVD 74

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           ++DP R      +++  +   ++ Y       V++     +  L      +      +  
Sbjct: 75  RYDPARQTDFVAFAVPTVMGEVRRYFRDHTWSVRVPRRLKELHLT-----VGQAATELGQ 129

Query: 152 NNLKPEQVVAIAKKLNVSESEVIS-MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
              +      +A  L++   EV   ++   A   S        D  S    D L  +   
Sbjct: 130 RLGRAPTARELADHLDLDLDEVAEALHAGNAYQASSIDYPAHDDSGSVALADTLGDEDP- 188

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                  + E+   R  L   +  L  RER I   R      +T   ++    +S+ +V 
Sbjct: 189 -------EIEKLEDRETLKPLLRSLPERERAILVMRFFSN--MTQSQIAERVGLSQMQVS 239

Query: 271 QIEARAFKKVQESI 284
           ++ AR    +++ +
Sbjct: 240 RLLARTLSTLRDQL 253


>gi|329937639|ref|ZP_08287158.1| RNA polymerase sigma factor sig8 [Streptomyces griseoaurantiacus
           M045]
 gi|329303038|gb|EGG46926.1| RNA polymerase sigma factor sig8 [Streptomyces griseoaurantiacus
           M045]
          Length = 287

 Score =  124 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 44/236 (18%), Positives = 99/236 (41%), Gaps = 12/236 (5%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
            + L+  +L LV   A  +R  G   + ++V  G IGL++A+ +F+  R     ++++ +
Sbjct: 59  RNTLIEMNLSLVRYAASRFRSRGADEMEDIVQVGTIGLIKAIDRFELTREVEFTSFAVPY 118

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I   ++ +   +   V +     + R+      L    + ++    +   V  ++  +++
Sbjct: 119 IVGEIKRFFRDTSWAVHVPRRLQEARV-----ELARATEELSRRTGRQPTVRELSALMSL 173

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E EVI          S ++L  S   +     +  + D  G E+  +E  E     + L
Sbjct: 174 PEEEVIEARKASNAYRS-SSLDASLSGDGGLDGESALADFIGVEERGLELIED---LHSL 229

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              ++ L  R+R I   R ++E  +T   +     +S+  V ++  R    ++E +
Sbjct: 230 APLVAGLPERDRTILHLRFVEE--LTQAQIGERLGISQMHVSRLLNRIVTGLREGL 283


>gi|302389895|ref|YP_003825716.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK
           [Thermosediminibacter oceani DSM 16646]
 gi|302200523|gb|ADL08093.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK
           [Thermosediminibacter oceani DSM 16646]
          Length = 239

 Score =  124 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 53/240 (22%), Positives = 89/240 (37%), Gaps = 63/240 (26%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           +GD  A + L+  +LRLV  I   +   G  + +++S G IGL++A+  F+  +G RLAT
Sbjct: 50  NGDEEARNILIERNLRLVAHIVKKFANTGEDMDDLISIGTIGLIKAITTFNKTKGNRLAT 109

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   I+  +                        NLR  K                    
Sbjct: 110 YAARCIENEI----------------------LMNLRTTKK------------------- 128

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
                           +  + SL   I    + N     D L  + D   + +  K ++K
Sbjct: 129 ----------------IKAEVSLQDPIGVDKEGNEISLMDILGTESDAIIEEISNKFQQK 172

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
              + +    +VL  RE+++ E R         T   ++    +SR  V +IE RA KK+
Sbjct: 173 KLYDKIR---TVLKGREKKVIELRYGLLNGKARTQREIAKLLGISRSYVSRIEKRAIKKL 229


>gi|42783467|ref|NP_980714.1| sporulation sigma factor SigK [Bacillus cereus ATCC 10987]
 gi|42739396|gb|AAS43322.1| RNA polymerase sigma-27 factor [Bacillus cereus ATCC 10987]
          Length = 265

 Score =  124 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 49/265 (18%), Positives = 92/265 (34%), Gaps = 63/265 (23%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
            Y+        L   +E    +   E GD  A + L+  +LRLV  I   +   G    +
Sbjct: 47  SYVKNNAFPQPLSSDDERKYLELM-EQGDAQARNLLIEHNLRLVAHIVKKFENTGEDAED 105

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++S G IGL++A++ +   +G +LATY+   I                      +  +  
Sbjct: 106 LISIGTIGLIKAIESYSAGKGTKLATYAARCI----------------------ENEILM 143

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
           +LR LK                                       D SL+  I    + +
Sbjct: 144 HLRVLKKT-----------------------------------KKDVSLHDPIGQDKEGN 168

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTL 255
              +  L+     + + +I+  +       +   + +L+ RE+ +   R     +   T 
Sbjct: 169 ---EISLIDILKSESEDVIDMIQLSMELEKIKEYIDILDEREKEVIVKRFGLGLDKEKTQ 225

Query: 256 ENLSSEFEVSRERVRQIEARAFKKV 280
             ++    +SR  V +IE RA  K+
Sbjct: 226 REIAKALGISRSYVSRIEKRALMKM 250


>gi|70725968|ref|YP_252882.1| RNA polymerase sigma factor SigB [Staphylococcus haemolyticus
           JCSC1435]
 gi|68446692|dbj|BAE04276.1| sigma factor B [Staphylococcus haemolyticus JCSC1435]
          Length = 256

 Score =  124 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 49/263 (18%), Positives = 108/263 (41%), Gaps = 24/263 (9%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             ++     K ++++ +  A  RLV  + +L+  +A  Y        ++V  G +GL+ A
Sbjct: 12  SPEQINQWIKEHQDNANTEAQDRLVNHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGA 71

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +FD     +   + +  +   ++ Y+      V +     +        R+K     +
Sbjct: 72  INRFDLSFDRKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIG-----PRIKKVSDEL 126

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNC------RLAGDESLNALINSSDKNSSQWQDW 203
           T+   +   +  IA +L VSE EV+           L+ D S+ A     D ++    D 
Sbjct: 127 TNELERSPSIAEIADRLEVSEEEVLEAMEMGQSYNALSVDHSIEA---DKDGSTVTLLDI 183

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    D          +   +R +L R + +L+ RER I +   +    ++ +       
Sbjct: 184 MGQKDDNY--------DLTEKRMILERILPILSDREREIIQCTFI--EGLSQKETGERIG 233

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+  V +++  A KK+Q++ ++
Sbjct: 234 LSQMHVSRLQRTAIKKLQQAAKQ 256


>gi|22298280|ref|NP_681527.1| RNA polymerase sigma factor SigF [Thermosynechococcus elongatus
           BP-1]
 gi|22294459|dbj|BAC08289.1| group 3 RNA polymerase sigma factor [Thermosynechococcus elongatus
           BP-1]
          Length = 261

 Score =  124 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 51/253 (20%), Positives = 109/253 (43%), Gaps = 18/253 (7%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKKFDP 95
           L + YR++      +RLV  ++ LV K A  + +       +++  G +GL++A+++FDP
Sbjct: 17  LLQAYRDNPAPELRNRLVELNIGLVRKEAHRWVQCTQESFDDLMQVGTLGLIRAIERFDP 76

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            +G   +++++ +I+  +Q Y+      +++      +R      + K  +Q +     +
Sbjct: 77  TKGVAFSSFAIPYIRGEIQHYLRDKSPQIRLP-----RRWQTLQSQGKRVIQELRQQLER 131

Query: 156 PEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
           P     IA+ L+V   E  +           SL+A     ++ S    D L        Q
Sbjct: 132 PPTDSEIAQALDVPLEEWQAAKFASYHTTPVSLDAPTFEGEEESVALGDILPDQRYQSFQ 191

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV-RQI 272
           +  E       R  L + +  L  R  +I E   L++  ++ +  +    +S   V RQI
Sbjct: 192 LAEED------RIRLQQCLRKLEARTCQILEFVFLRD--LSQKETAELLGLSAVTVSRQI 243

Query: 273 EARAFKKVQESIQ 285
             +  + +Q+ ++
Sbjct: 244 -KKGLQALQQMMR 255


>gi|284050443|ref|ZP_06380653.1| RNA polymerase sigma factor SigF [Arthrospira platensis str.
           Paraca]
 gi|291567732|dbj|BAI90004.1| group 3 RNA polymerase sigma factor SigF [Arthrospira platensis
           NIES-39]
          Length = 261

 Score =  124 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 49/257 (19%), Positives = 108/257 (42%), Gaps = 16/257 (6%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQA 89
           K E   L + Y+     S  ++LV  ++ LV K    +         +++  G IGL++A
Sbjct: 10  KSESLELLREYQHSPSNSIRNQLVQINIGLVRKEVHHWLNQCTESYDDLLQVGCIGLIRA 69

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +++FD  +G   +++++ +I+  +Q Y+      V++      ++    LR+    +Q +
Sbjct: 70  IERFDMSKGHAFSSFAIPYIRGEIQHYLRDKSPSVRVP-----RQWLTLLRKATPCIQEL 124

Query: 150 TDNNLKPEQVVAIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                +    V IA  L +S  E   + +  +     SL+A I   ++ S+   D +   
Sbjct: 125 QVKLGRKPTDVEIASALEISVEEWNQVKLASQNRSLLSLDAPIQDEEEGSTSLGDLVPDT 184

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
                Q+  E + R      L +++  L    R++ E   L +  +T +  + +  +S  
Sbjct: 185 RYRSFQLAQEDQIR------LQQALGHLEDGTRKVLEFVFLYD--LTQKETAEKLGISAV 236

Query: 268 RVRQIEARAFKKVQESI 284
            V +   R    ++  +
Sbjct: 237 TVSRRVKRGLSLLKTMM 253


>gi|75761264|ref|ZP_00741246.1| RNA polymerase sigma-K factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|74491246|gb|EAO54480.1| RNA polymerase sigma-K factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
          Length = 271

 Score =  124 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 49/265 (18%), Positives = 92/265 (34%), Gaps = 63/265 (23%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
            Y+        L   +E    +   E GD  A + L+  +LRLV  I   +   G    +
Sbjct: 53  SYVKNNAFPQPLSSDDERKYLELM-EQGDAQARNLLIEHNLRLVAHIVKKFENTGEDAED 111

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++S G IGL++A++ +   +G +LATY+   I                      +  +  
Sbjct: 112 LISIGTIGLIKAIESYSAGKGTKLATYAARCI----------------------ENEILM 149

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
           +LR LK                                       D SL+  I    + +
Sbjct: 150 HLRVLKKT-----------------------------------KKDVSLHDPIGQDKEGN 174

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTL 255
              +  L+     + + +I+  +       +   + +L+ RE+ +   R     +   T 
Sbjct: 175 ---EISLIDILKSESEDVIDMIQLSMELEKIKEYIDILDEREKEVIVKRFGLGLDKEKTQ 231

Query: 256 ENLSSEFEVSRERVRQIEARAFKKV 280
             ++    +SR  V +IE RA  K+
Sbjct: 232 REIAKALGISRSYVSRIEKRALMKM 256


>gi|223984440|ref|ZP_03634576.1| hypothetical protein HOLDEFILI_01870 [Holdemania filiformis DSM
           12042]
 gi|223963596|gb|EEF67972.1| hypothetical protein HOLDEFILI_01870 [Holdemania filiformis DSM
           12042]
          Length = 232

 Score =  124 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 54/268 (20%), Positives = 106/268 (39%), Gaps = 63/268 (23%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           +++   P+   +EE  L     E+GD  A   L+  +LRLVV IA  Y    + + +++S
Sbjct: 26  NDVLPHPLARDEEEAALI--ALENGDQQARDTLIEHNLRLVVYIAKRYETNPIFMEDLIS 83

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
            G IGL++AV  F  ++  +L TY+   I+  +  ++ +                     
Sbjct: 84  IGTIGLIKAVNTFKRDKNIKLVTYASRCIENEILMFLRKKSR------------------ 125

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
                                  +K  +S  E ++++                D N    
Sbjct: 126 -----------------------RKTEISFDEPLNVDY---------------DGNELLL 147

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE-NPVTLENLS 259
            D L  + D    ++ E    +  +  L ++MS L   ER I E R       +T ++++
Sbjct: 148 SDILGTEGD----IVAESFYAEEDKRQLLKAMSKLKENERMILEMRYGINHEELTQKDIA 203

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +  +S+  + ++E R  +K++  + KQ
Sbjct: 204 DQLGISQSYISRLEKRIIQKLRNQLIKQ 231


>gi|226323675|ref|ZP_03799193.1| hypothetical protein COPCOM_01450 [Coprococcus comes ATCC 27758]
 gi|225207859|gb|EEG90213.1| hypothetical protein COPCOM_01450 [Coprococcus comes ATCC 27758]
          Length = 205

 Score =  124 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 45/213 (21%), Positives = 93/213 (43%), Gaps = 15/213 (7%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           +L ++ +  GD  A  + +  +LRLV+ +   + G      ++   G IGL++A+  F+P
Sbjct: 1   MLFEKIK-AGDEEAKEQYIKGNLRLVLSVIKRFSGSSENPDDLFQIGCIGLIKAINNFNP 59

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           E   + +TY++  I   ++ +I  + S +++      + L     +     +     N K
Sbjct: 60  ELEVKFSTYAVPMIIGEIRRFIRDNNS-IRVS-----RSLRDTAYKAIYAKENYVKVNQK 113

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
              V  IA+++ +++ E++     +    SLN  +  +D   + +    + D   +E   
Sbjct: 114 EPTVQEIAEEIGIAKEEIVYALDAIQMPVSLNEPVY-NDNGDAMYVMDQISDKRNKEDRW 172

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
           +EK         L  +M  L  RE+ I   R L
Sbjct: 173 VEKLS-------LQAAMDRLGKREKYIIRLRFL 198


>gi|224992794|gb|ACN76112.1| SigB [Listeria innocua]
 gi|224992800|gb|ACN76115.1| SigB [Listeria innocua]
 gi|224992802|gb|ACN76116.1| SigB [Listeria innocua]
 gi|224992804|gb|ACN76117.1| SigB [Listeria innocua]
 gi|224992806|gb|ACN76118.1| SigB [Listeria innocua]
 gi|224992808|gb|ACN76119.1| SigB [Listeria innocua]
 gi|224992812|gb|ACN76121.1| SigB [Listeria innocua]
 gi|224992816|gb|ACN76123.1| SigB [Listeria innocua]
 gi|224992818|gb|ACN76124.1| SigB [Listeria innocua]
 gi|224992820|gb|ACN76125.1| SigB [Listeria innocua]
 gi|224992822|gb|ACN76126.1| SigB [Listeria innocua]
 gi|224992824|gb|ACN76127.1| SigB [Listeria innocua]
 gi|224992826|gb|ACN76128.1| SigB [Listeria innocua]
 gi|224992828|gb|ACN76129.1| SigB [Listeria innocua]
 gi|224992830|gb|ACN76130.1| SigB [Listeria innocua]
 gi|224992836|gb|ACN76133.1| SigB [Listeria innocua]
 gi|224992838|gb|ACN76134.1| SigB [Listeria innocua]
 gi|224992840|gb|ACN76135.1| SigB [Listeria innocua]
 gi|224992842|gb|ACN76136.1| SigB [Listeria innocua]
 gi|224992844|gb|ACN76137.1| SigB [Listeria innocua]
 gi|224992846|gb|ACN76138.1| SigB [Listeria innocua]
 gi|224992852|gb|ACN76141.1| SigB [Listeria innocua]
 gi|224992854|gb|ACN76142.1| SigB [Listeria innocua]
          Length = 214

 Score =  124 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 51/229 (22%), Positives = 97/229 (42%), Gaps = 24/229 (10%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y+E GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D   G  
Sbjct: 4   YQEDGDEDAQYNLVIHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKS 63

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
              +++  I   ++ ++      V +     +        ++K  ++ +T       Q+ 
Sbjct: 64  FEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELTRELQSSPQIS 118

Query: 161 AIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            IA  + V+E EV+           L+ D S+ A    SD ++    D +    DG    
Sbjct: 119 DIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTDDGF--- 172

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
                ER N+R +L + + VL+ RE++I +   ++    + +      +
Sbjct: 173 -----ERVNQRMLLEKVLPVLDEREQKILQYTFIEN--RSQKETGELLD 214


>gi|254454176|ref|ZP_05067613.1| RNA polymerase sigma factor SigA [Octadecabacter antarcticus 238]
 gi|198268582|gb|EDY92852.1| RNA polymerase sigma factor SigA [Octadecabacter antarcticus 238]
          Length = 715

 Score =  124 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 53/254 (20%), Positives = 107/254 (42%), Gaps = 26/254 (10%)

Query: 40  RYREHGDLSAAHRLVT----SHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           R +    +S    L+     S L  + ++A  +   GL   ++  EG  GL ++V+ F  
Sbjct: 476 RMKLQESVSLRRSLIEAASISQLTQLRRLATRFPTEGLEEDDLFQEGYFGLTRSVEMFHA 535

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            RG RL TYS + I+  +   +    S+V+I      K     +R ++   + ++ N  +
Sbjct: 536 GRGNRLTTYSQYRIRQTIARAVDDHRSVVRIPVHFASK-----VRLIERFGERVSGNISR 590

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
            +   A+ K   +  +E+  +                    S ++ + L  D D  E   
Sbjct: 591 SDYHCALGKAFQIELAEIQKIENIPRL--------------SIEFDENLYSDAD-IELEP 635

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIE 273
            ++   + R+ ++   +  L  R   I   R   +  + +TLE     + V+RER+RQ+E
Sbjct: 636 FQRVLEQQRQAIIKDFLEDLPERHADIIVRRFGLDGNDEMTLEQCGQVYGVTRERIRQLE 695

Query: 274 ARAFKKVQESIQKQ 287
           A+A   ++  ++ +
Sbjct: 696 AKAIDWLRHPVRAK 709


>gi|3249723|gb|AAC26664.1| RNA polymerase sigma-like factor [Micromonospora olivasterospora]
          Length = 162

 Score =  124 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 37/172 (21%), Positives = 74/172 (43%), Gaps = 12/172 (6%)

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI+ A+   +      ++I     +  +   L R++            PE    +A
Sbjct: 1   YATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQREFFQDLGREPTPE---ELA 55

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           K+++++  +V+ +        SL+  I   D+  S   D++    D +  V ++      
Sbjct: 56  KEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSSLGDFI---EDSEAVVAVDAVSFSL 110

Query: 224 RRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIE 273
            ++ L + +  L+ RE  +   R       P TL+ +   + V+RER+RQIE
Sbjct: 111 LQDQLQQVLQTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIRQIE 162


>gi|294998208|gb|ADF57908.1| sporulation specific sigma factor K [Bacillus thuringiensis serovar
           aizawai]
 gi|308154182|gb|ADF57907.2| sporulation specific sigma factor K [Bacillus thuringiensis serovar
           aizawai]
          Length = 271

 Score =  124 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 49/265 (18%), Positives = 92/265 (34%), Gaps = 63/265 (23%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
            Y+        L   +E    +   E GD  A + L+  +LRLV  I   +   G    +
Sbjct: 53  SYVKNNAFPQPLSSDDERKYLELM-EQGDAQARNLLIEHNLRLVAHIVKKFENTGEDAED 111

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++S G IGL++A++ +   +G +LATY+   I                      +  +  
Sbjct: 112 LISIGTIGLIKAIESYSAGKGTKLATYAARCI----------------------ENEILM 149

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
           +LR LK                                       D SL+  I    + +
Sbjct: 150 HLRVLKKT-----------------------------------KKDVSLHDPIGQDKEGN 174

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTL 255
              +  L+     + + +I+  +       +   + +L+ RE+ +   R     +   T 
Sbjct: 175 ---EISLIDILKSESEDVIDMIQLSMELEKIKEYIDILDEREKEVIVKRFGLGLDKEKTQ 231

Query: 256 ENLSSEFEVSRERVRQIEARAFKKV 280
             ++    +SR  V +IE RA  K+
Sbjct: 232 REIAKALGISRSYVSRIEKRALMKM 256


>gi|222097784|ref|YP_002531841.1| sporulation sigma factor sigk [Bacillus cereus Q1]
 gi|221241842|gb|ACM14552.1| RNA polymerase sigma-27 factor [Bacillus cereus Q1]
          Length = 263

 Score =  124 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 49/265 (18%), Positives = 92/265 (34%), Gaps = 63/265 (23%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
            Y+        L   +E    +   E GD  A + L+  +LRLV  I   +   G    +
Sbjct: 45  SYVKNNAFPQPLSSDDERKYLELM-EQGDAQARNLLIEHNLRLVAHIVKKFENTGEDAED 103

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++S G IGL++A++ +   +G +LATY+   I                      +  +  
Sbjct: 104 LISIGTIGLIKAIESYSAGKGTKLATYAARCI----------------------ENEILM 141

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
           +LR LK                                       D SL+  I    + +
Sbjct: 142 HLRVLKKT-----------------------------------KKDVSLHDPIGQDKEGN 166

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTL 255
              +  L+     + + +I+  +       +   + +L+ RE+ +   R     +   T 
Sbjct: 167 ---EISLIDILKSESEDVIDMIQLSMELEKIKEYIDILDEREKEVIVKRFGLGLDKEKTQ 223

Query: 256 ENLSSEFEVSRERVRQIEARAFKKV 280
             ++    +SR  V +IE RA  K+
Sbjct: 224 REIAKALGISRSYVSRIEKRALMKM 248


>gi|213418760|ref|ZP_03351826.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
          Length = 162

 Score =  124 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 42/157 (26%), Positives = 75/157 (47%), Gaps = 7/157 (4%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 10  LRQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 69

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I      ++I           
Sbjct: 70  LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETIN 127

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVI 174
            L R+   +         PE    +A+++ + E ++ 
Sbjct: 128 KLNRISRQMLQEMGREPTPE---ELAERMLMPEDKIR 161


>gi|290956233|ref|YP_003487415.1| sigma factor [Streptomyces scabiei 87.22]
 gi|260645759|emb|CBG68850.1| putative sigma factor [Streptomyces scabiei 87.22]
          Length = 262

 Score =  124 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 47/260 (18%), Positives = 105/260 (40%), Gaps = 15/260 (5%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             ++   LA         +   R++ + L +  ++A  +R  G    ++    ++GL++A
Sbjct: 16  TAEDFRTLAALPPGQQRDTLRDRIIEAWLPMAERLAGRFRSRGESYEDLRQVASLGLVKA 75

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V ++DPE G    +Y++  I   ++ +       + +       R      R++   Q +
Sbjct: 76  VDRYDPELGNAFESYAVPTITGEIKRHFRDHMWTLHVPRRVQDLR-----NRVRFATQDL 130

Query: 150 TDN-NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           +   + +   V  IA+  N+SE +V      L   ES  AL   ++   S+    L    
Sbjct: 131 SQTISGRRPTVAEIAEHANMSEEDVR---VGLEALESFTALSLDAELPGSEDGYSLSDAL 187

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
              +  L    +    R  +   ++ L  RER I   R   +  +T   ++ E  +S+  
Sbjct: 188 GSADPAL----DTVVDREAVKPRLAALPERERAILYMRFFGD--MTQSRIADELGISQMH 241

Query: 269 VRQIEARAFKKVQESIQKQV 288
           V ++ +R   ++++ + +  
Sbjct: 242 VSRLISRCCDRLRDQVMRDA 261


>gi|20807860|ref|NP_623031.1| DNA-directed RNA polymerase specialized sigma subunit
           [Thermoanaerobacter tengcongensis MB4]
 gi|254478885|ref|ZP_05092249.1| RNA polymerase sigma factor, FliA/WhiG family [Carboxydibrachium
           pacificum DSM 12653]
 gi|20516424|gb|AAM24635.1| DNA-directed RNA polymerase specialized sigma subunit
           [Thermoanaerobacter tengcongensis MB4]
 gi|214035198|gb|EEB75908.1| RNA polymerase sigma factor, FliA/WhiG family [Carboxydibrachium
           pacificum DSM 12653]
          Length = 246

 Score =  124 bits (313), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 45/256 (17%), Positives = 110/256 (42%), Gaps = 23/256 (8%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL---PISEVVSEGNIGLMQAV 90
           E  + K Y    D  A + ++  +L LV  I        +      +++ +G +GL+ A+
Sbjct: 5   EEDVWKVYNLQKDPDARNEIIVKYLPLVKHIVKKLVISDIAQSEYEDLIHQGILGLIDAI 64

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +K+ P++G +  TY+   I+  + +Y+ +   +         + L    ++++  ++ + 
Sbjct: 65  EKYQPDKGVKFETYATLRIRGEIIDYLRKRDWM--------PRSLKKKYKKIEETVEKLQ 116

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDH 208
               +   V  I +   + E +V+     +  +   SL   I ++ K  S  +  L    
Sbjct: 117 QRYNREPTVEEITEACGLEEEDVLKTLSYINVSNINSLEEAIENNLKIHSISEIDL---- 172

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
               +   E+   K  +  L  ++  L+ +ER +      ++  +  +++S    ++  R
Sbjct: 173 ----KNPEEELLYKELKKKLAHAIEKLSEKERLVITLYYYED--LNYKDISKILNLTESR 226

Query: 269 VRQIEARAFKKVQESI 284
           + QI ++A KK++E +
Sbjct: 227 ISQIHSKAIKKIREML 242


>gi|332670026|ref|YP_004453034.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit [Cellulomonas
           fimi ATCC 484]
 gi|332339064|gb|AEE45647.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cellulomonas
           fimi ATCC 484]
          Length = 296

 Score =  124 bits (312), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 42/249 (16%), Positives = 99/249 (39%), Gaps = 16/249 (6%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           ++  G  +A   L+  +  LV  +A          +  +++VS G  GL+ A++K++ +R
Sbjct: 53  FKSTGSRAAREHLILHYAPLVAAVAGRVGMRLPSTVEQADLVSYGMFGLIDAIEKYETDR 112

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
             +  +Y+   I+ A+ + + R+   V        + +      L+  L        +  
Sbjct: 113 AVKFESYASSRIRGAIIDEL-RAMDWVPRSVRTKARSVDRAYAELEATLH-------RAP 164

Query: 158 QVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
               +A+ L +S  E+ +   +L+     +L+ L+   +   +     +    D + Q  
Sbjct: 165 TEAEVARHLEISVGELRATFSQLSTVNIAALDELLGGGEDRQA-GVCLVDTLGDERTQDP 223

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
               +    + +L R++  L  RER +          +TL  +     V+  R+ Q+   
Sbjct: 224 AGSLDAAETKYLLARAIEQLGDRERMVVVLYYY--EGMTLAEIGRVLGVTESRISQMHTA 281

Query: 276 AFKKVQESI 284
           A  +++  +
Sbjct: 282 AMLRLRTRL 290


>gi|138894662|ref|YP_001125115.1| sporulation sigma factor SigE [Geobacillus thermodenitrificans
           NG80-2]
 gi|196247723|ref|ZP_03146425.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
 gi|134266175|gb|ABO66370.1| RNA polymerase sigma-E factor [Geobacillus thermodenitrificans
           NG80-2]
 gi|196212507|gb|EDY07264.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
          Length = 239

 Score =  124 bits (312), Expect = 1e-26,   Method: Composition-based stats.
 Identities = 55/246 (22%), Positives = 101/246 (41%), Gaps = 62/246 (25%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD +A   L+  +LRLVV IA  +   G+ I +++S G IGL++AV  F+PE+  +LATY
Sbjct: 54  GDKTARSLLIERNLRLVVYIARKFENTGIHIEDLISIGTIGLIKAVNTFNPEKKIKLATY 113

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +   I+  +  Y+ R+                    +++                     
Sbjct: 114 ASRCIENEILMYLRRN-------------------NKVRAE------------------- 135

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
                          ++ DE LN      D N     D L  + D    V+ +  E    
Sbjct: 136 ---------------VSFDEPLN---IDWDGNELLLSDVLGTEDD----VITKDLEADVD 173

Query: 225 RNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           R +L  ++  L+ RE++I E R         T ++++    +S+  + ++E R  K++++
Sbjct: 174 RRLLLNALRQLSDREKQIMELRFGLSGGEEKTQKDVADLLGISQSYISRLEKRIIKRLRK 233

Query: 283 SIQKQV 288
              K +
Sbjct: 234 EFNKMM 239


>gi|225848018|ref|YP_002728181.1| RNA polymerase sigma-D factor (Sigma-28) [Sulfurihydrogenibium
           azorense Az-Fu1]
 gi|225644246|gb|ACN99296.1| RNA polymerase sigma-D factor (Sigma-28) [Sulfurihydrogenibium
           azorense Az-Fu1]
          Length = 240

 Score =  124 bits (312), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 45/246 (18%), Positives = 112/246 (45%), Gaps = 19/246 (7%)

Query: 50  AHRLVTSHLRLVVKIAM--GYRG--YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
            + ++  +L  +  I     +      +   +++  G +GL  A++K+DP +G +L+TY+
Sbjct: 8   KNEIIIEYLPKIKYIVKALKHENLPPIVDEEDLIQVGVLGLYDALEKYDPSKGIKLSTYA 67

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
              I+  + +++ R    V     +  K L   + +L+  L        +  +   IA  
Sbjct: 68  EIRIRGYIIDHL-RQLDWVPRSVRSKIKNLENKIAQLEAQL-------GRQAKTEEIANY 119

Query: 166 LNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           L ++  E ++    LA     SL++ ++  D  S    + +  + D  ++V+ EK+ ++ 
Sbjct: 120 LGMTVEEYMTYAEVLANKVLISLDSDVSKDDDESLHLWEVISSNDDTPDKVVEEKQLKEI 179

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +++   ++ L+ RER +      +E  + ++ ++    ++  RV Q+  +   K++  
Sbjct: 180 LSDII---LNHLDERERLLISLYYYEE--LNMKEIADILGITESRVSQLHTKIMLKLKNL 234

Query: 284 IQKQVE 289
           + K +E
Sbjct: 235 VMKYLE 240


>gi|239933042|ref|ZP_04689995.1| RNA polymerase secondary sigma factor [Streptomyces ghanaensis ATCC
           14672]
 gi|291441393|ref|ZP_06580783.1| conserved hypothetical protein [Streptomyces ghanaensis ATCC 14672]
 gi|291344288|gb|EFE71244.1| conserved hypothetical protein [Streptomyces ghanaensis ATCC 14672]
          Length = 263

 Score =  124 bits (312), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 48/261 (18%), Positives = 99/261 (37%), Gaps = 18/261 (6%)

Query: 30  EKQEEYVLAKRYREHGDLSA-AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
             +    LA R  E  +  A    LV + L +  +IA+ +RG G  + ++     +GL++
Sbjct: 18  TAEAFARLA-RLPEGPERRALRDDLVQAWLPMAERIAVRFRGRGEALEDLYQVAALGLVK 76

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           AV  +DP RG     Y++  I   ++ +       + +       R      R++   + 
Sbjct: 77  AVDHYDPVRGNAFEAYAVPTITGEIKRHFRDHMWTLHVPRRVQDLR-----NRVRHAARE 131

Query: 149 ITDNN-LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
           +      +   V  IA    ++ESEV +    L    +L+        +     D +   
Sbjct: 132 LAQTTVGRAPTVPEIAAYARLTESEVRTGMEALECFSALSLEAEMPGTDGYALGDSVGGP 191

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
               + V+         R  +   +  L  RER I   R  +   +T   ++    +S+ 
Sbjct: 192 DPAFDTVV--------DRVTVRPFLEALPERERLILYLRFFRG--MTQSTIAEHLGISQM 241

Query: 268 RVRQIEARAFKKVQESIQKQV 288
            V ++ +  F +++E +  + 
Sbjct: 242 HVSRLLSSCFAQLREELLTEA 262


>gi|258514353|ref|YP_003190575.1| sporulation sigma factor SigE [Desulfotomaculum acetoxidans DSM
           771]
 gi|257778058|gb|ACV61952.1| RNA polymerase, sigma 28 subunit, SigE [Desulfotomaculum
           acetoxidans DSM 771]
          Length = 241

 Score =  124 bits (312), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 66/262 (25%), Positives = 105/262 (40%), Gaps = 63/262 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EE +L  R  E GD +    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 39  PPLSIDEESILINRL-ETGDGAVRGVLIERNLRLVVYIARKFENTGISIEDLVSIGTIGL 97

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FDP +  +LATY+   I+  +                         LRR     
Sbjct: 98  IKAVNTFDPAKKIKLATYASRCIENEI----------------------LMYLRRNNKTR 135

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                            ++ DE LN      D N     D L  
Sbjct: 136 SE-------------------------------VSFDEPLN---IDWDGNELLLSDVLGT 161

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEV 264
           ++D   + + E+ +RK    +L  ++  L+ RERRI E R    N    T + ++    +
Sbjct: 162 ENDVIYKYIEEEVDRK----LLHLALQKLSGRERRIMELRFGLNNGSEKTQKEVADMLGI 217

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+  + ++E R  K+++  I +
Sbjct: 218 SQSYISRLEKRIIKRLKREIHR 239


>gi|220929479|ref|YP_002506388.1| sporulation sigma factor SigE [Clostridium cellulolyticum H10]
 gi|219999807|gb|ACL76408.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium cellulolyticum
           H10]
          Length = 243

 Score =  124 bits (312), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 55/263 (20%), Positives = 104/263 (39%), Gaps = 65/263 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EE  L  +  E  D      L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 41  PPLTLDEETYLLNKL-EQSDYGVKSILIERNLRLVVYIARKFENTGVGVEDLISIGTIGL 99

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+  F+P +  +LATY+   I+  +                         LRR     
Sbjct: 100 IKAINTFNPSKNIKLATYASRCIENEI----------------------LMYLRR----- 132

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS-DKNSSQWQDWLV 205
                                         N R+  + S++  +N   D N     D L 
Sbjct: 133 ------------------------------NNRVKAEISIDEPLNIDWDGNELLLSDILG 162

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFE 263
            ++D   + + ++ +    + +L  +M  L+ RE++I E R    N    T + ++    
Sbjct: 163 TENDMIHRSIEDEVD----KELLATAMKKLSVREKKIMELRFGLSNGVEKTQKEVADMLG 218

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+  + ++E R   ++++ I +
Sbjct: 219 ISQSYISRLEKRIISRLKKEISR 241


>gi|253998499|ref|YP_003050562.1| flagellar biosynthesis sigma factor [Methylovorus sp. SIP3-4]
 gi|313200585|ref|YP_004039243.1| RNA polymerase sigma-28 subunit FliA/WhiG [Methylovorus sp. MP688]
 gi|253985178|gb|ACT50035.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Methylovorus sp.
           SIP3-4]
 gi|312439901|gb|ADQ84007.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Methylovorus sp.
           MP688]
          Length = 244

 Score =  124 bits (312), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 51/251 (20%), Positives = 104/251 (41%), Gaps = 16/251 (6%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPER 97
           Y   G  +    L+  H  LV K+A   +    P   + ++V  G +GL+ A+ +++   
Sbjct: 2   YTATGKPNQKDSLLHQHATLVKKLAYQLKAKLPPSVELDDLVQAGMMGLLDAINRYEDTH 61

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G +  TY+   I+ AM + + R+   +      N + +   + +L+  L        +P 
Sbjct: 62  GAQFETYAAQRIRGAMIDEL-RNADWLPRSIRKNMRDVEGAINQLEQVL-------GRPP 113

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +AK+L +S  +   M    +G + L        +    + D  + D  G     I+
Sbjct: 114 TEGEVAKQLKMSLDDYYDMLGECSGHQLLYYEDFHESEGGDHFLDRFLQDDSGN---PIK 170

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
                N R  L  ++  L  RE+         E  + L+ + +   VS  RV Q+ ++A 
Sbjct: 171 GLLDSNFRETLIEAIENLPEREQ--ILMGLYYEQELNLKEIGAVMNVSESRVCQLHSQAI 228

Query: 278 KKVQESIQKQV 288
            +++  +++Q+
Sbjct: 229 ARLRAYMKEQL 239


>gi|15925054|ref|NP_372588.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus Mu50]
 gi|156980380|ref|YP_001442639.1| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus Mu3]
 gi|255006853|ref|ZP_05145454.2| RNA polymerase sigma factor SigB [Staphylococcus aureus subsp.
           aureus Mu50-omega]
 gi|14247837|dbj|BAB58226.1| sigma factor B [Staphylococcus aureus subsp. aureus Mu50]
 gi|156722515|dbj|BAF78932.1| sigma factor B [Staphylococcus aureus subsp. aureus Mu3]
          Length = 256

 Score =  124 bits (312), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 44/260 (16%), Positives = 104/260 (40%), Gaps = 18/260 (6%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             ++     K ++E+ +  A  +LV  + +L+  +A  Y        ++V  G +GL+ A
Sbjct: 12  SPEQINQWIKEHQENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGA 71

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +FD     +   + +  +   ++ Y+      V +      K +   ++++   L A 
Sbjct: 72  INRFDMSFERKFEAFLVPTVIGEIKRYLRDKTWSVHVARRI--KEIGPRIKKVSDELTAE 129

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNC---RLAGDESLNALINSSDKNSSQWQDWLVY 206
            + +    ++    +       E + M      L+ D S+ A     D ++    D +  
Sbjct: 130 LERSPSISEIANRLEVSEEEVLEAMEMGQSYNALSVDHSIEA---DKDGSTVTLLDIMGQ 186

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
             D          +   +R +L + + +L+ RER I +   +    ++ +       +S+
Sbjct: 187 QDDHY--------DLTEKRMILEKILPILSDREREIIQCTFI--EGLSQKETGERIGLSQ 236

Query: 267 ERVRQIEARAFKKVQESIQK 286
             V +++  A KK+QE+  K
Sbjct: 237 MHVSRLQRTAIKKLQEAAHK 256


>gi|168334573|ref|ZP_02692729.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Epulopiscium sp. 'N.t.
           morphotype B']
          Length = 247

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 52/252 (20%), Positives = 108/252 (42%), Gaps = 22/252 (8%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFD 94
             +Y++        +L+  +  LV  +A     Y    L + +++  G IGL+ A+ K+D
Sbjct: 8   WDKYKKTKSRELKEQLIEHYAPLVKIVAGRLGIYLNSYLELDDLLGFGVIGLIDAIDKYD 67

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
            ++  +  TY+   I+ A+ + I R    V       QK       R++  +        
Sbjct: 68  YDKKIKFETYASLRIRGAIIDEI-RKLDWVPRSIRQKQKEYIRAYERVEAKI-------G 119

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
                  + K+LN++ESE      +L  D +++ L++  +    ++        D   + 
Sbjct: 120 HSPTDTDVRKELNINESEY----NKLVHDTNISTLVSIDESELYEFNI-----EDITTKN 170

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
             ++ E K    +L   +  L  RE+ + +    +E  +TL+ +S   E+S  RV QI +
Sbjct: 171 PYQELENKEALEILEHEILALTEREQLLIKLYYYEE--LTLKEISLILEISESRVSQIHS 228

Query: 275 RAFKKVQESIQK 286
           +   K++  ++K
Sbjct: 229 KLMVKLRNKLKK 240


>gi|159029418|emb|CAO90794.1| unnamed protein product [Microcystis aeruginosa PCC 7806]
          Length = 258

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 50/259 (19%), Positives = 115/259 (44%), Gaps = 16/259 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVK 91
           E   L K+Y++ G+     +++  +L LV + A  +         ++V  G +GL++A+K
Sbjct: 12  ETLTLFKKYQKTGENQLRDQIIRLNLGLVRREAHHWVNQCHENYEDLVQVGCMGLIRAIK 71

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           +FD  +G   +++++ +I+  +Q Y+      V+I      +R     R+     +    
Sbjct: 72  RFDSSKGHAFSSFAIPYIRGEIQHYLRDKGYTVRIP-----RRWLDLGRQAANMRRDFQT 126

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHD 209
            + +      I+  LN+S  E   +       E  SL+A +N+ + N++  +D +     
Sbjct: 127 IHNRQPNDTEISLALNISLEEWQEVKLAFQNREPLSLDATVNNDEDNNTCLKDIVPDPGY 186

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
              Q+  E       R  L ++++ L  + R I E   L++  +T    + +  +S   V
Sbjct: 187 RSFQLCQED------RIRLQQALAQLEEKTRYILEFVFLKD--LTQRETAEQLGISIVTV 238

Query: 270 RQIEARAFKKVQESIQKQV 288
            +   +  + ++E++ ++ 
Sbjct: 239 SRRVKKGLEMLKETMLQEA 257


>gi|293400805|ref|ZP_06644950.1| RNA polymerase sigma-K factor [Erysipelotrichaceae bacterium
           5_2_54FAA]
 gi|291305831|gb|EFE47075.1| RNA polymerase sigma-K factor [Erysipelotrichaceae bacterium
           5_2_54FAA]
          Length = 247

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 64/281 (22%), Positives = 105/281 (37%), Gaps = 62/281 (22%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           I++  +G   YI     +  L+K+EE           D    ++L+  +LRLV  I   Y
Sbjct: 11  ILSSALGYVGYIRSNSFLQPLDKEEEAHCIAGLSLQ-DEECRNKLIEHNLRLVAHIVKKY 69

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
                   +++S G IGL++A+  F PE+G +L TY+   I+  +  Y+  S        
Sbjct: 70  DIKKEQTEDLISIGTIGLIKAIDSFKPEKGHKLTTYASRCIENEILMYLRSS-------- 121

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
               K  F N                                   +S+N  +A D     
Sbjct: 122 ----KNYFQN-----------------------------------VSLNDPIATD----- 137

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
                D +     D +      QE  +IE    ++  + L + + VL+ RE  I   R  
Sbjct: 138 ----KDGSEITLIDAI---SSPQETSIIEDMVVEDNISKLKQFLHVLDSRELEIITKRFG 190

Query: 249 QE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
                  T   ++ +  +SR  V +IE RAF K+    QK+
Sbjct: 191 LYGVEEETQREIAKQLHISRSYVSRIEKRAFMKLYREFQKE 231


>gi|223986127|ref|ZP_03636150.1| hypothetical protein HOLDEFILI_03458 [Holdemania filiformis DSM
           12042]
 gi|223961932|gb|EEF66421.1| hypothetical protein HOLDEFILI_03458 [Holdemania filiformis DSM
           12042]
          Length = 241

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 42/247 (17%), Positives = 96/247 (38%), Gaps = 19/247 (7%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + GD  A  + V  ++ LV  I   +        ++   G +GLM+A+  FD       
Sbjct: 14  AQQGDEQAREQCVLRNVGLVWSIVNRF-KTHSSAQDLFQIGCLGLMKAINNFDTSYNVMF 72

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY++  I   ++ Y      + KI  +  ++ L     +++   + +     +      
Sbjct: 73  STYAVPIILGEIKRYFRDEGQM-KISRSLKERYL-----QVQKSRERLAQKLQREPTYRE 126

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           I + L V E++V+          S++      D ++ + +D +   H           E 
Sbjct: 127 IGEDLGVEENDVMLAMEANQFLASMDEAFYQKDGSTIKLEDKVEDRHG----------ED 176

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +  L + +  L  RE+ +   R   E     E ++ +  +S+ +V ++E +   K++
Sbjct: 177 VPMKLALKKEIGHLEQREQYLIYLRYELE--YNQEAIAKKMGISQVQVSRLEKKILNKLK 234

Query: 282 ESIQKQV 288
             + +  
Sbjct: 235 CKLTEDA 241


>gi|304407606|ref|ZP_07389258.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
 gi|304343557|gb|EFM09399.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
          Length = 232

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 55/274 (20%), Positives = 105/274 (38%), Gaps = 64/274 (23%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+        L +++E    +   E G+  + + L+  +LRLV  I   +   G  +
Sbjct: 17  LVSYVKNNAFPQPLHEEDEMKHLQLMAE-GNQHSRNMLIEHNLRLVAHIVKKFDNTGEDL 75

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++S G IGL++A++ F   +G +LAT++   I+  +                      
Sbjct: 76  EDLISIGTIGLIKAIESFQVGKGTKLATFAARCIENEI---------------------- 113

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
             +LR LK                            + +S++  +  D          + 
Sbjct: 114 LMHLRSLKKT-------------------------RKDVSLHDPIGTD---------KEG 139

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE---NP 252
           N     D L  + D     ++EK + K  ++ + R++ +L+ RE+ +   R   E     
Sbjct: 140 NEITLIDILGSEADD----IVEKVQLKIEKSKIYRNLDILDDREKEVVVGRFGLEHGGEE 195

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            T   ++ E  +SR  V +IE RA  K+     K
Sbjct: 196 RTQREIAKELGISRSYVSRIEKRALMKLYHEFYK 229


>gi|238916778|ref|YP_002930295.1| phosphatidylserine decarboxylase [Eubacterium eligens ATCC 27750]
 gi|238872138|gb|ACR71848.1| phosphatidylserine decarboxylase [Eubacterium eligens ATCC 27750]
          Length = 252

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 50/251 (19%), Positives = 107/251 (42%), Gaps = 17/251 (6%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKF 93
           L K Y           L+  + +LV  +A     Y GY +   ++V  G  GL+ A+ KF
Sbjct: 9   LWKNYISTHSNEYRDELIVEYAQLVKLVAGRLNMYLGYNVEYDDLVGYGIFGLIDAIDKF 68

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D  +  +  TY+   I+ A+ + I R    +       QKR+   + +++     I  + 
Sbjct: 69  DYGKNVKFETYASLRIRGAILDQI-RKMDWIPRSLRQKQKRIEAAMTKIESETGHIASDE 127

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
                   +A +L +++ E+     ++      + LI+  +   +  +  +    +    
Sbjct: 128 -------ELAAELGITQDELSDWQGKMKA----SNLISLDEYTEAGSEVKMESVGNSHFD 176

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
              +  E++  + M+ +++  L  +ER +      +E  +TL+ +S   EVS  RV Q+ 
Sbjct: 177 QPEDAMEKEELKKMMVKAIDSLTEKERSVVVLYYYEE--MTLKEISLTLEVSESRVSQLH 234

Query: 274 ARAFKKVQESI 284
            +A  K+++ +
Sbjct: 235 TKALNKMKKLL 245


>gi|291542628|emb|CBL15738.1| RNA polymerase, sigma 29 subunit, SigE [Ruminococcus bromii L2-63]
          Length = 233

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 54/264 (20%), Positives = 102/264 (38%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L ++EE  + +   + GD  A   L+  +LRLVV IA  +        +++S G IGL
Sbjct: 31  PPLTREEEQHIMENIAK-GDSKAREPLIVHNLRLVVYIAKKFETPNASAEDLISIGTIGL 89

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F PE+  +LATY+   I+  +  ++ +S                          
Sbjct: 90  IKAVNTFSPEKNIKLATYASRCIENEILMFLRKSS------------------------- 124

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                        +   ++ DE LN      D N     D L  
Sbjct: 125 ----------------------------QLKNEVSIDEPLNT---DWDGNELLLCDVLGS 153

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEV 264
           D D     +    E +  ++++ +++S L  RE  I E R         T + ++ +  +
Sbjct: 154 DPD----TVNRNIECELEKSLVLQAVSKLRDRECLIMELRFGLNGQKEHTQKQVADKLGI 209

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E +  ++++  + K V
Sbjct: 210 SQSYISRLEKKIIRQLKIELDKAV 233


>gi|268610009|ref|ZP_06143736.1| sporulation sigma factor SigK [Ruminococcus flavefaciens FD-1]
          Length = 227

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 64/258 (24%), Positives = 93/258 (36%), Gaps = 65/258 (25%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L K EE+ L +R    GD  A  +L+  +LRLV  I   Y        E++S G IGL+
Sbjct: 25  PLPKSEEHELFER-SSCGDEYARKKLIEHNLRLVAHIVKKYTSSFDEQDELISIGTIGLI 83

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV  FD  +G + ATY+   I+  +                        + R  K    
Sbjct: 84  KAVSSFDHTKGSKFATYASRCIENEI----------------------LMHFRSAKKSAS 121

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
            +                          MN  +  D+  NAL            D L   
Sbjct: 122 DLY-------------------------MNEPVETDKDGNALT---------IMDLLDDG 147

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSV-LNPRERRIFEARRLQEN--PVTLENLSSEFEV 264
            D  EQV     +   R  ML R +   L+PRE  I   R       P T    + +  +
Sbjct: 148 SDINEQV-----DLLIRSKMLYRFIEQCLDPRETDIMIYRYGLYGTSPHTQSETAEKLGI 202

Query: 265 SRERVRQIEARAFKKVQE 282
           SR  V +IE +A  K+++
Sbjct: 203 SRSYVSRIEKKAVGKLKK 220


>gi|224992798|gb|ACN76114.1| SigB [Listeria innocua]
          Length = 214

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 51/229 (22%), Positives = 97/229 (42%), Gaps = 24/229 (10%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y+E GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A++++D   G  
Sbjct: 4   YQEDGDEDAQYNLVIHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAIRRYDATFGKS 63

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
              +++  I   ++ ++      V +     +        ++K  ++ +T       Q+ 
Sbjct: 64  FEAFAVPTIVGEIKRFLRDKKWSVHVPRRIKELG-----PKIKNAVEELTRELQSSPQIS 118

Query: 161 AIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            IA  + V+E EV+           L+ D S+ A    SD ++    D +    DG    
Sbjct: 119 DIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVVGGTDDGF--- 172

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
                ER N+R +L + + VL+ RE++I +   ++    + +      +
Sbjct: 173 -----ERVNQRMLLEKVLPVLDEREQKILQYTFIEN--RSQKETGELLD 214


>gi|189916717|gb|ACE62869.1| RNA polymerase sigma 70 factor [Xylella fastidiosa]
          Length = 161

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 35/160 (21%), Positives = 69/160 (43%), Gaps = 10/160 (6%)

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
            + K     L R+   +         PE    +AK++++ E ++  +        S+   
Sbjct: 1   VHMKETINKLNRISRQMLQQFGREATPE---ELAKEMDMPEDKIRKVMKIAKEPISMETP 57

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   D   S   D++    D   +  ++     N    +   ++ L PRE ++   R   
Sbjct: 58  I--GDDEDSHLGDFI---EDPNVESPVDTTTNVNLSETVREVLAGLTPREAKVLRMRFGI 112

Query: 250 E--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +     TLE +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 113 DMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 152


>gi|302871341|ref|YP_003839977.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
 gi|302574200|gb|ADL41991.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor obsidiansis OB47]
          Length = 242

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 61/262 (23%), Positives = 102/262 (38%), Gaps = 64/262 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI-SEVVSEGNIG 85
           PM  ++EE  L K +   G   A + LV  +LRLV  IA  Y      +  +++S G IG
Sbjct: 36  PMSSEEEEMYLNKMW--EGCKEARNILVEKNLRLVAHIAKKYTFSFPNLTDDIISVGTIG 93

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A++ +  ++  +L+TY+   I+  +  Y                      LR+ K  
Sbjct: 94  LIKAIETYSKDKSTKLSTYAAKCIENEILMY----------------------LRQNKKF 131

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           L  +                         S+   +  D          D N     D L 
Sbjct: 132 LSQL-------------------------SLENPIGSD---------KDGNEITLMDVLQ 157

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFE 263
            D D  ++ +  K + KN    L + +     RE++I E R   +N    T   ++S   
Sbjct: 158 NDQDDIDEQVDLKIQIKNLLKKLDKILKG---REKKIIELRYGLKNGIERTQMEVASLLG 214

Query: 264 VSRERVRQIEARAFKKVQESIQ 285
           +SR  V +IE +A KK+   +Q
Sbjct: 215 ISRSYVSRIEKKALKKLYGELQ 236


>gi|225174854|ref|ZP_03728851.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Dethiobacter
           alkaliphilus AHT 1]
 gi|225169494|gb|EEG78291.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Dethiobacter
           alkaliphilus AHT 1]
          Length = 219

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 46/228 (20%), Positives = 91/228 (39%), Gaps = 23/228 (10%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
              HL LV  +   Y+G      ++   G IGL++A+KKFDP RG   ATY++  I   +
Sbjct: 8   FEKHLPLVHSLVKRYQGEYAESDDLFQVGCIGLLKALKKFDPARGNAFATYAVPVIAGEI 67

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
           + Y+    ++         + L     R+K     +     +   +  +A    +   E+
Sbjct: 68  KMYLRGQGAM------KFSRSLVTQAGRIKRVQNELEQALGRQPTLGELAAASGLGREEL 121

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
           +     +    SL+A +        +  +  V   +  E V          R  L  +++
Sbjct: 122 LMALDAVRSPVSLDAAV------PGETAELAVTQAETDEVV---------DRVALREALT 166

Query: 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L  RERRI   R  +    + + ++    +S+  V ++E +   +++
Sbjct: 167 DLPERERRIVLYRFFRH--KSQQEVAEILGISQMHVSRLEKKVLARLK 212


>gi|209524790|ref|ZP_03273336.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Arthrospira
           maxima CS-328]
 gi|209494669|gb|EDZ94978.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Arthrospira
           maxima CS-328]
          Length = 255

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 48/257 (18%), Positives = 107/257 (41%), Gaps = 16/257 (6%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQA 89
           K E   L + Y+     S  ++LV  ++ LV K    +         +++  G IGL++A
Sbjct: 10  KSESLELLREYQHSPSNSVRNQLVQINIGLVRKEVHHWLNQCTESYDDLLQVGCIGLIRA 69

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +++FD  +G   +++++ +I+  +Q Y+      V++      ++    LR+    +Q +
Sbjct: 70  IERFDMSKGHAFSSFAIPYIRGEIQHYLRDKSPSVRVP-----RQWLTLLRKATPCIQDL 124

Query: 150 TDNNLKPEQVVAIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                +      IA  L +S  E   + +  +     SL+A I   ++ S+   D +   
Sbjct: 125 QVKLGRKPTDAEIASALEISVEEWNQVKLASQNRSLLSLDAPIQDEEEGSTSLGDLVPDT 184

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
                Q+  E + R      L +++  L    R++ E   L +  +T +  + +  +S  
Sbjct: 185 RYRSFQLAQEDQIR------LQQALGHLEDGTRKVLEFVFLYD--LTQKETAEKLGISAV 236

Query: 268 RVRQIEARAFKKVQESI 284
            V +   R    ++  +
Sbjct: 237 TVSRRVKRGLSLLKTMM 253


>gi|294811026|ref|ZP_06769669.1| Putative RNA polymerase sigma factor [Streptomyces clavuligerus
           ATCC 27064]
 gi|326439632|ref|ZP_08214366.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|294323625|gb|EFG05268.1| Putative RNA polymerase sigma factor [Streptomyces clavuligerus
           ATCC 27064]
          Length = 277

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 37/243 (15%), Positives = 96/243 (39%), Gaps = 15/243 (6%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +    LV + L +  ++A  +R  G  + ++     +GL++AV ++DP RG   A++++
Sbjct: 48  EALRQELVNAWLPMSERLARRFRDRGESLEDLRQVAALGLVKAVDRYDPARGCAFASFAV 107

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKPEQVVAIAKK 165
             I   ++ +       + +      +R      R++   Q +      +      IA++
Sbjct: 108 PTITGEVKRHFRDHMWTLHVPRRVQDQR-----NRVRAAQQELAQTVTGRAPTEAEIAER 162

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
             ++ ++       +    +L+    +            +   D    V+I+       R
Sbjct: 163 AGLTPAQTREGLAAIGSYRTLSLDAEAPGDGDGCTMADALGGPDPALDVVID-------R 215

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             +   +  L  RERRI   R  +   +T   ++ +  +S+  V ++ + +  ++++ I 
Sbjct: 216 EAVRPRLRELPERERRILYMRFFRG--MTQSRIAEDLGISQMHVSRLISHSCDRLRQEIM 273

Query: 286 KQV 288
           +  
Sbjct: 274 RDA 276


>gi|289550312|ref|YP_003471216.1| RNA polymerase sigma factor SigB [Staphylococcus lugdunensis
           HKU09-01]
 gi|315660227|ref|ZP_07913082.1| RNA polymerase sigma-B factor [Staphylococcus lugdunensis M23590]
 gi|289179844|gb|ADC87089.1| RNA polymerase sigma factor SigB [Staphylococcus lugdunensis
           HKU09-01]
 gi|315494654|gb|EFU82994.1| RNA polymerase sigma-B factor [Staphylococcus lugdunensis M23590]
          Length = 256

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 48/263 (18%), Positives = 106/263 (40%), Gaps = 24/263 (9%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             ++     K ++E     A  +LV  + +L+  +A  Y        ++V  G +GL+ A
Sbjct: 12  SPEQINQWIKEHQEDKSTEAQDKLVKHYRKLIESLAYKYSKGQSHHEDLVQVGMVGLIGA 71

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +FD     +   + +  +   ++ Y+      V +     +        R+K     +
Sbjct: 72  INRFDISFDRKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIG-----PRIKKVSDEL 126

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNC------RLAGDESLNALINSSDKNSSQWQDW 203
           T+   +   +  IA +L V+E EV+           L+ D S+ A     D ++    D 
Sbjct: 127 TNELERSPSITEIANRLEVTEEEVLEAMEMGQSYNALSVDHSIEA---DKDGSTVTLLDI 183

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    D          +   +R +L R + +L+ RER I +   +    ++ +       
Sbjct: 184 MGQQDDNY--------DLTEKRMILERILPILSEREREIIQCTFI--EGLSQKETGERIG 233

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+  V +++  A KK+Q++ ++
Sbjct: 234 LSQMHVSRLQRTAIKKLQQAAKQ 256


>gi|3249731|gb|AAC26668.1| RNA polymerase sigma-like factor [Streptomyces spectabilis]
          Length = 161

 Score =  124 bits (311), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 42/172 (24%), Positives = 71/172 (41%), Gaps = 13/172 (7%)

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI+ AM   +      +++     +  L   + R++  +         PE+V A  
Sbjct: 1   YATWWIRQAMSRAMADQARTIRVPVHVVE--LINRVVRVQRRMLQERGYEPSPEEVAA-- 56

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
             L++    V  +        SL+A +   +++     D +    DG     +E      
Sbjct: 57  -HLDLPHERVRGLRL-AQEPVSLHAPV--GEEDDVALGDLI---EDGDAASPVESAAFLL 109

Query: 224 RRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIE 273
            R  L   +S L  RER++ + R       P TLE +   F V+RER+RQIE
Sbjct: 110 LREHLEAVLSTLGERERKVVQLRYGLADGRPRTLEEIGRIFGVTRERIRQIE 161


>gi|37781593|gb|AAP42800.1| SigB [Staphylococcus aureus]
          Length = 256

 Score =  123 bits (310), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 43/261 (16%), Positives = 105/261 (40%), Gaps = 18/261 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           +  ++     K ++E+ +  A  +LV  + +L+  +A  Y        ++V  G +GL+ 
Sbjct: 11  ISPEQINQWIKEHQENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIG 70

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A+ +FD     +   + +  +   ++ Y+      V +      K +   ++++   L A
Sbjct: 71  AINRFDMSFERKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRI--KEIGPRIKKVSDELTA 128

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNC---RLAGDESLNALINSSDKNSSQWQDWLV 205
             + +    ++    +       E + M      L+ D S+ A     + ++    D + 
Sbjct: 129 ELERSPSISEIADRLEVSEEEVLEAMEMGQSYNALSVDHSIEA---DKEGSTVTLLDIMG 185

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
              D          +   +R +L + + +L+ RER I +   +    ++ +       +S
Sbjct: 186 QQDDHY--------DLTEKRMILEKILPILSDREREIIQCTFI--EGLSQKETGGRIGLS 235

Query: 266 RERVRQIEARAFKKVQESIQK 286
           +  V +++  A KK+QE+  K
Sbjct: 236 QMHVSRLQRTAIKKLQEAAHK 256


>gi|297196439|ref|ZP_06913837.1| sigma factor [Streptomyces pristinaespiralis ATCC 25486]
 gi|197722266|gb|EDY66174.1| sigma factor [Streptomyces pristinaespiralis ATCC 25486]
          Length = 292

 Score =  123 bits (310), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 36/222 (16%), Positives = 87/222 (39%), Gaps = 12/222 (5%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A + L+  ++ LV  +A  +R       ++V  G IGL++A+ +FD  R    AT+++ +
Sbjct: 67  ARNTLIEMNISLVRYVARRFRNRAESDEDIVQVGTIGLIKAIDRFDLSREVEFATFAVPY 126

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I   ++ +   +   V +     + RL      L   +  ++    +      +++ L +
Sbjct: 127 ILGEIKRFFRDTSWAVHVPRRLQELRL-----ELVQAVNELSGKLHRAPTAAELSEHLEI 181

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              EV      + G  + +  + +++   +    +     D    + + ++ +      L
Sbjct: 182 PVEEVTEGLVAMNGYVASSFDVPNTEGGPNAEAPFAERFGDLDPALGLVEDLQA-----L 236

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
              +  L+ R+R I   R   E       +     +S+ +V 
Sbjct: 237 KPLIEELDDRDRLILRLRFGDELK--QAEIGERLGISQMQVS 276


>gi|228474927|ref|ZP_04059656.1| RNA polymerase sigma-B factor [Staphylococcus hominis SK119]
 gi|228271159|gb|EEK12539.1| RNA polymerase sigma-B factor [Staphylococcus hominis SK119]
          Length = 256

 Score =  123 bits (310), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 47/272 (17%), Positives = 113/272 (41%), Gaps = 24/272 (8%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
            E + +  +  ++     K ++++ +  A  +LV  + +L+  +A  Y        ++V 
Sbjct: 3   KESKSVNEISPEQINQWIKEHQDNINPYAQDKLVKHYRKLIESLAYKYSKGQSHHEDLVQ 62

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
            G +GL+ A+ +FD     +   + +  +   ++ Y+      V +     +        
Sbjct: 63  VGMVGLIGAINRFDISFDRKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIG-----P 117

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC------RLAGDESLNALINSSD 194
           R+K     +T+   +   ++ IA +L V+E EV+           L+ D S+ A     D
Sbjct: 118 RIKKVGDELTNELGRSPSILEIANRLEVNEEEVLEAMEMGQSYNALSVDHSIEA---DKD 174

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
            ++    D +    D          +   +R +L R + +L+ RER I +   +    ++
Sbjct: 175 GSTVTLLDIMGQQDDNY--------DLTEKRMILERILPILSDREREIIQCTFI--EGLS 224

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +       +S+  V +++  A +K+Q++ ++
Sbjct: 225 QKETGERIGLSQMHVSRLQRTAIRKLQQAARQ 256


>gi|37781579|gb|AAP42789.1| SigB [Staphylococcus aureus]
          Length = 256

 Score =  123 bits (310), Expect = 2e-26,   Method: Composition-based stats.
 Identities = 42/258 (16%), Positives = 104/258 (40%), Gaps = 18/258 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           +  ++     K ++E+ +  A  +LV  + +L+  +A  Y        ++V  G +GL+ 
Sbjct: 11  ISPEQINQWIKEHQENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIG 70

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A+ +FD     +   + +  +   ++ Y+      V +      K +   ++++   L A
Sbjct: 71  AINRFDMSFERKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRI--KEIGPRIKKVSDELTA 128

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNC---RLAGDESLNALINSSDKNSSQWQDWLV 205
             + +    ++    +       E + M      L+ D S+ A     + ++    D + 
Sbjct: 129 ELERSPSISEIADRLEVSEEEVLEAMEMGQSYNALSVDHSIEA---DKEGSTVTLLDIMG 185

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
              D          +   +R +L + + +L+ RER I +   +    ++ +       +S
Sbjct: 186 QQDDHY--------DLTEKRMILEKILPILSDREREIIQCTFI--EGLSQKETGERIGLS 235

Query: 266 RERVRQIEARAFKKVQES 283
           +  V +++  A KK+QE+
Sbjct: 236 QMHVSRLQRTAIKKLQEA 253


>gi|110799358|ref|YP_696454.1| sporulation sigma factor SigK [Clostridium perfringens ATCC 13124]
 gi|110674005|gb|ABG82992.1| RNA polymerase sigma-70 factor family [Clostridium perfringens ATCC
           13124]
          Length = 233

 Score =  123 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 67/283 (23%), Positives = 112/283 (39%), Gaps = 66/283 (23%)

Query: 9   IVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           +V  +I L+ Y+      P  L ++EE +  +R ++ GD+ A   LV  +LRLV  I   
Sbjct: 10  LVGSKIFLTGYVTGNSTFPKPLNEKEEKIYLERLKD-GDVEAKRVLVERNLRLVAHIVKK 68

Query: 68  YRGYGL---PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           Y         + +++S G IGL++A+  FD  +G RLATY+   I   +  +        
Sbjct: 69  YSSNYQNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATYAAKCIDNEILMF-------- 120

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
                      F N ++ KG                             + +   +  D+
Sbjct: 121 -----------FRNTKKTKGE----------------------------VFLQDPIGVDK 141

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
             N  I   D  SS     L    +  E  L  KE  K   ++L       +PRE+ I +
Sbjct: 142 EGNE-ICLIDILSSDSDSVL----EAVENSLQVKELYKKMSDIL-------SPREKEIIK 189

Query: 245 ARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            R   L  +  T   +++   +SR  V +IE +A KK+ +  +
Sbjct: 190 MRYGLLDGDIKTQREIAAILGISRSYVSRIEKKALKKLNKEFK 232


>gi|325288837|ref|YP_004265018.1| RNA polymerase, sigma 29 subunit, SigE [Syntrophobotulus glycolicus
           DSM 8271]
 gi|324964238|gb|ADY55017.1| RNA polymerase, sigma 29 subunit, SigE [Syntrophobotulus glycolicus
           DSM 8271]
          Length = 250

 Score =  123 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 55/240 (22%), Positives = 101/240 (42%), Gaps = 62/240 (25%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GDLS    L+  +LRLVV I+  +   G+ I ++VS G IGL++AV  FDP +  +LATY
Sbjct: 65  GDLSVKGTLIERNLRLVVYISRKFENTGISIEDLVSIGTIGLIKAVNTFDPTKKIKLATY 124

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +   I+  +  Y+ R+                    +++                     
Sbjct: 125 ASRCIENEILMYLRRN-------------------NKIRSE------------------- 146

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
                          ++ DE LN      D N     D L  ++D   + + E+ +    
Sbjct: 147 ---------------VSFDEPLN---IDWDGNELLLSDVLGTENDIISKPIEEEVD---- 184

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           R +L ++MS L+ RE+ I E R         T + ++ +  +S+  + ++E +  K++++
Sbjct: 185 RQLLAQAMSSLSEREQLIMELRFGMGGKEEKTQKEVADKLGISQSYISRLEKKIIKRLRK 244


>gi|319788967|ref|YP_004090282.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Ruminococcus
           albus 7]
 gi|315450834|gb|ADU24396.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Ruminococcus
           albus 7]
          Length = 234

 Score =  123 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 57/262 (21%), Positives = 101/262 (38%), Gaps = 63/262 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K EE   A +     +  A   L+  +LRLVV I+  +   G  I +++S G+IGL
Sbjct: 32  PPLTKDEEAK-AFQLFATDEKKARELLIVHNLRLVVYISKKFESTGAGIEDLISIGSIGL 90

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F P++  +LATY+   I+  +  +                      LR+     
Sbjct: 91  IKAVNTFRPDKNIKLATYASRCIENEILMF----------------------LRKASQRR 128

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                            ++ DE LN      D N     D L  
Sbjct: 129 SE-------------------------------ISIDEPLNT---DWDGNELLLSDILGT 154

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEV 264
           D D     + +  E +  + +L R +  L  RE+ I E R        +T + ++    +
Sbjct: 155 DED----TVHKGIESEVEKTLLRREIDKLGEREKMIMEMRFGLNGKSEMTQKEVAQTVGI 210

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+  + ++E +  K ++E+++K
Sbjct: 211 SQSYISRLEKKTLKAIRENLEK 232


>gi|115378523|ref|ZP_01465679.1| sigma-D factor [Stigmatella aurantiaca DW4/3-1]
 gi|115364445|gb|EAU63524.1| sigma-D factor [Stigmatella aurantiaca DW4/3-1]
          Length = 171

 Score =  123 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 43/111 (38%), Positives = 70/111 (63%), Gaps = 1/111 (0%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           GLS Y+  +     L +++EY LA+  R+ GD SA   L TS+L  VV +A  +   G  
Sbjct: 11  GLSHYLRHLGGHHQLTREQEYELARAARK-GDESARQTLATSNLAFVVAVAKKFANRGAR 69

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
           + +++ EGN+GLM+A++ FDP++  R ATY++WWI+A +  Y+  + S V+
Sbjct: 70  LDDLIQEGNVGLMKAIEHFDPKKNVRFATYAVWWIRAYITRYLKDNRSQVR 120


>gi|282929291|ref|ZP_06336862.1| RNA polymerase sigma-B factor [Staphylococcus aureus A10102]
 gi|282589101|gb|EFB94200.1| RNA polymerase sigma-B factor [Staphylococcus aureus A10102]
          Length = 256

 Score =  123 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 43/260 (16%), Positives = 103/260 (39%), Gaps = 18/260 (6%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             ++     K ++E+ +  A  +LV  + +L+  +A  Y        ++V  G +GL+ A
Sbjct: 12  SPEQINQWIKEHQENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGA 71

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +FD     +   + +  +   ++ Y+        +      K +   ++++   L A 
Sbjct: 72  INRFDMSFERKFEAFLVPTVIGEIKRYLRDKTWSAHVPRRI--KEIGPRIKKVSDELTAE 129

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNC---RLAGDESLNALINSSDKNSSQWQDWLVY 206
            + +    ++    +       E + M      L+ D S+ A     D ++    D +  
Sbjct: 130 LERSPSISEIANRLEVSEEEVLEAMEMGQSYNALSVDHSIEA---DKDGSTVTLLDIMGQ 186

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
             D          +   +R +L + + +L+ RER I +   +    ++ +       +S+
Sbjct: 187 QDDHY--------DLTEKRMILEKILPILSDREREIIQCTFI--EGLSQKETGERIGLSQ 236

Query: 267 ERVRQIEARAFKKVQESIQK 286
             V +++  A KK+QE+  K
Sbjct: 237 MHVSRLQRTAIKKLQEAAHK 256


>gi|119715356|ref|YP_922321.1| FliA/WhiG family RNA polymerase sigma factor [Nocardioides sp.
           JS614]
 gi|119536017|gb|ABL80634.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Nocardioides sp.
           JS614]
          Length = 244

 Score =  123 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 52/251 (20%), Positives = 103/251 (41%), Gaps = 26/251 (10%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKF 93
           L +R+++ GD  A  RLV  +  LV  +A   R    P    +++VS+G IGL+ A+ KF
Sbjct: 12  LWERFKQDGDREARDRLVVHYSPLVKFVAGRVRSGLPPAVEHADLVSDGVIGLLDALDKF 71

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           DPERG +  TY++  I+ AM + + R+   V              +R +      +    
Sbjct: 72  DPERGLQFQTYAVSRIRGAMVDGL-RAADWVPRSVR-------EKIRDINTAQTELERRL 123

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            +  +   +A +L +S  ++  +  + A    ++      ++++ +    L    D    
Sbjct: 124 GRAPKDAEVADRLGISVGDLRKIYSQTAHTSVVSFETVLDEEDTPRATTDLPGADDDIPP 183

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
             +              ++  L  R++ +          +TL  +     VS  RV Q+ 
Sbjct: 184 GFL-------------AAVRELPERDQVVVALYYW--ERLTLAEIGQVLGVSESRVSQLH 228

Query: 274 ARAFKKVQESI 284
           +RA   ++  +
Sbjct: 229 SRATLALRRKL 239


>gi|167755748|ref|ZP_02427875.1| hypothetical protein CLORAM_01263 [Clostridium ramosum DSM 1402]
 gi|237734714|ref|ZP_04565195.1| sporulation sigma factor sigE [Mollicutes bacterium D7]
 gi|167704687|gb|EDS19266.1| hypothetical protein CLORAM_01263 [Clostridium ramosum DSM 1402]
 gi|229382042|gb|EEO32133.1| sporulation sigma factor sigE [Coprobacillus sp. D7]
          Length = 231

 Score =  123 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 54/275 (19%), Positives = 109/275 (39%), Gaps = 68/275 (24%)

Query: 17  SRYIHEIRKI----PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY- 71
           ++Y++ I +     P L+  EE    ++    GD  A   L+  +LRLVV +A  Y    
Sbjct: 12  TKYLYYIGRHDILPPPLKGIEEKEALEKLG-AGDNDARDLLIEHNLRLVVYVAKRYDTTQ 70

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
              I +++S G IGL++A+  F P++  +LATY+   I+  +  ++ ++           
Sbjct: 71  NGGIEDLISIGTIGLVKAINTFKPDKNIKLATYASRCIENEILMFLRKN----------- 119

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
                  LR                                       ++ DE LN    
Sbjct: 120 -----NKLRHE-------------------------------------ISLDEPLN---I 134

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ-- 249
             D N     D +  D D    ++  + E+ +++ M   +   L+ RE+ I   R     
Sbjct: 135 DYDGNELLLSDIIGTDSD----IVKNELEQSDQKAMFYEAFKDLSKREKEILMFRYGLMN 190

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + +T ++++    +S+  + ++E +  KK++  +
Sbjct: 191 YDELTQKDVAKMMGISQSYISRLEKKIIKKLRNKL 225


>gi|167757711|ref|ZP_02429838.1| hypothetical protein CLOSCI_00041 [Clostridium scindens ATCC 35704]
 gi|167664593|gb|EDS08723.1| hypothetical protein CLOSCI_00041 [Clostridium scindens ATCC 35704]
          Length = 208

 Score =  123 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 62/259 (23%), Positives = 101/259 (38%), Gaps = 62/259 (23%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L   EE    ++Y E GDL A H L+  +LRLV  I   Y+ +     +++S G IGL+
Sbjct: 10  PLTAAEERYYMQKYTE-GDLEAKHILIERNLRLVAHIVKKYQSFEEDTEDLLSIGTIGLI 68

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV  F+P++  RL TY+   I+  +                        +LR  K   +
Sbjct: 69  KAVVTFNPDKCVRLGTYAARCIENEI----------------------LMHLRAKKKSSR 106

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                                     IS+   +  D          + N  Q  D +  +
Sbjct: 107 E-------------------------ISLYEPIGTDR---------EGNEIQLFDIIETE 132

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVS 265
            D   + +   E R + R +  R  S L+PRER + + R     E   T   ++ +  +S
Sbjct: 133 EDDAHKKV---ELRDDIRMLYYRVESELSPRERLVLKMRYGLYNEEEYTQREIAKQLGIS 189

Query: 266 RERVRQIEARAFKKVQESI 284
           R  V +IE  A +K++E  
Sbjct: 190 RSYVSRIEKSAIEKLREYF 208


>gi|315444786|ref|YP_004077665.1| RNA polymerase sigma factor, sigma-70 family [Mycobacterium sp.
           Spyr1]
 gi|315263089|gb|ADT99830.1| RNA polymerase sigma factor, sigma-70 family [Mycobacterium sp.
           Spyr1]
          Length = 284

 Score =  123 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 43/244 (17%), Positives = 90/244 (36%), Gaps = 18/244 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                 ++   L L   IA  +RG G    ++V    +GL+ AV +FD +       +++
Sbjct: 51  RRQREAIIARCLPLADHIARRFRGRGEGHEDLVQVARVGLLNAVNRFDVDSANDFLAFAV 110

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +   ++ Y       +K+     +  +     RL      +T    +      +AK L
Sbjct: 111 PTMMGEVRRYFRDHGWSLKVPRRLKELNV-----RLNAARADLTQELNRAPTPSELAKYL 165

Query: 167 NVSESEVIS--MNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
            +   EV+   +        S       S D      QD      D  ++V+        
Sbjct: 166 GIDREEVVEGLVAANAYSTRSTEQPTTFSGDGEGLSLQDTFGAPDDNIQKVI-------- 217

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             N +   ++ L  R+R + + R  ++   T   ++ +  VS+  V ++ ARA   +++ 
Sbjct: 218 DVNTVQPLLAALPERDRLVLKLRFFED--RTQSQIAEQIGVSQMHVSRLLARALATLRDQ 275

Query: 284 IQKQ 287
           +  +
Sbjct: 276 VGDE 279


>gi|304316881|ref|YP_003852026.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
 gi|302778383|gb|ADL68942.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermoanaerobacterium
           thermosaccharolyticum DSM 571]
          Length = 246

 Score =  123 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 43/254 (16%), Positives = 106/254 (41%), Gaps = 19/254 (7%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAV 90
           E  L  +Y +  D S+   ++  ++ LV  I             + +++S+G IGL+ AV
Sbjct: 5   EQDLWDKYEKLKDGSSKEDIIIKYMPLVKHIVKRICLSEISKEDVDDLISQGMIGLIDAV 64

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
            K+D  +G +  TY+   IK  + +Y+ +   +         + L    + ++  ++ + 
Sbjct: 65  NKYDISKGVKFETYASIRIKGEIIDYLRKKDWI--------PRSLKKRYKSIEKTIERLE 116

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
               +   +  I     +S+++V+     +      NA   SS     +    +    + 
Sbjct: 117 QEYKREPTIEEIMDATKLSKNDVLKTLSYM------NAGYISSLDEVIENNLKISSITES 170

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
           +      +    + +  + +++ +L  +ER I      ++  +  + +S    ++  R+ 
Sbjct: 171 EITNPENEVLMYDLKQNIAKAIDMLQEKERLIISLYYYED--LNYKEISKIMGLTESRIS 228

Query: 271 QIEARAFKKVQESI 284
           QI ++A KK++E +
Sbjct: 229 QIHSKAIKKLKEKL 242


>gi|30022417|ref|NP_834048.1| sporulation sigma factor SigK [Bacillus cereus ATCC 14579]
 gi|228902866|ref|ZP_04067008.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis IBL 4222]
 gi|228910177|ref|ZP_04073996.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis IBL 200]
 gi|228916971|ref|ZP_04080532.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228929384|ref|ZP_04092407.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228935660|ref|ZP_04098474.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228941506|ref|ZP_04104056.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228954625|ref|ZP_04116649.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228960610|ref|ZP_04122256.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228974436|ref|ZP_04135004.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228981030|ref|ZP_04141332.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis Bt407]
 gi|229025805|ref|ZP_04182204.1| RNA polymerase sigma-28 factor [Bacillus cereus AH1272]
 gi|229031990|ref|ZP_04187975.1| RNA polymerase sigma-28 factor [Bacillus cereus AH1271]
 gi|229048046|ref|ZP_04193621.1| RNA polymerase sigma-28 factor [Bacillus cereus AH676]
 gi|229062038|ref|ZP_04199363.1| RNA polymerase sigma-28 factor [Bacillus cereus AH603]
 gi|229071846|ref|ZP_04205059.1| RNA polymerase sigma-28 factor [Bacillus cereus F65185]
 gi|229076014|ref|ZP_04208987.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock4-18]
 gi|229098811|ref|ZP_04229749.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock3-29]
 gi|229104971|ref|ZP_04235627.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock3-28]
 gi|229111812|ref|ZP_04241358.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock1-15]
 gi|229117837|ref|ZP_04247201.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock1-3]
 gi|229123878|ref|ZP_04253071.1| RNA polymerase sigma-28 factor [Bacillus cereus 95/8201]
 gi|229129620|ref|ZP_04258588.1| RNA polymerase sigma-28 factor [Bacillus cereus BDRD-Cer4]
 gi|229141077|ref|ZP_04269619.1| RNA polymerase sigma-28 factor [Bacillus cereus BDRD-ST26]
 gi|229157954|ref|ZP_04286026.1| RNA polymerase sigma-28 factor [Bacillus cereus ATCC 4342]
 gi|229163288|ref|ZP_04291242.1| RNA polymerase sigma-28 factor [Bacillus cereus R309803]
 gi|229169087|ref|ZP_04296802.1| RNA polymerase sigma-28 factor [Bacillus cereus AH621]
 gi|229175013|ref|ZP_04302532.1| RNA polymerase sigma-28 factor [Bacillus cereus MM3]
 gi|229180616|ref|ZP_04307957.1| RNA polymerase sigma-28 factor [Bacillus cereus 172560W]
 gi|229192552|ref|ZP_04319513.1| RNA polymerase sigma-28 factor [Bacillus cereus ATCC 10876]
 gi|229198467|ref|ZP_04325171.1| RNA polymerase sigma-28 factor [Bacillus cereus m1293]
 gi|29897975|gb|AAP11249.1| RNA polymerase sigma-K factor [Bacillus cereus ATCC 14579]
 gi|228584970|gb|EEK43084.1| RNA polymerase sigma-28 factor [Bacillus cereus m1293]
 gi|228590859|gb|EEK48717.1| RNA polymerase sigma-28 factor [Bacillus cereus ATCC 10876]
 gi|228602859|gb|EEK60339.1| RNA polymerase sigma-28 factor [Bacillus cereus 172560W]
 gi|228608474|gb|EEK65777.1| RNA polymerase sigma-28 factor [Bacillus cereus MM3]
 gi|228614315|gb|EEK71425.1| RNA polymerase sigma-28 factor [Bacillus cereus AH621]
 gi|228620195|gb|EEK77067.1| RNA polymerase sigma-28 factor [Bacillus cereus R309803]
 gi|228625514|gb|EEK82269.1| RNA polymerase sigma-28 factor [Bacillus cereus ATCC 4342]
 gi|228642355|gb|EEK98644.1| RNA polymerase sigma-28 factor [Bacillus cereus BDRD-ST26]
 gi|228653737|gb|EEL09607.1| RNA polymerase sigma-28 factor [Bacillus cereus BDRD-Cer4]
 gi|228659592|gb|EEL15239.1| RNA polymerase sigma-28 factor [Bacillus cereus 95/8201]
 gi|228665634|gb|EEL21112.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock1-3]
 gi|228671568|gb|EEL26866.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock1-15]
 gi|228678465|gb|EEL32686.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock3-28]
 gi|228684655|gb|EEL38595.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock3-29]
 gi|228707126|gb|EEL59326.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock4-18]
 gi|228711276|gb|EEL63238.1| RNA polymerase sigma-28 factor [Bacillus cereus F65185]
 gi|228717190|gb|EEL68865.1| RNA polymerase sigma-28 factor [Bacillus cereus AH603]
 gi|228723290|gb|EEL74660.1| RNA polymerase sigma-28 factor [Bacillus cereus AH676]
 gi|228729345|gb|EEL80337.1| RNA polymerase sigma-28 factor [Bacillus cereus AH1271]
 gi|228735513|gb|EEL86109.1| RNA polymerase sigma-28 factor [Bacillus cereus AH1272]
 gi|228778690|gb|EEM26955.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis Bt407]
 gi|228785272|gb|EEM33283.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228799038|gb|EEM46009.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228805071|gb|EEM51666.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228818156|gb|EEM64231.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228824020|gb|EEM69838.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228830290|gb|EEM75904.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228842692|gb|EEM87779.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228849460|gb|EEM94295.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis IBL 200]
 gi|228856740|gb|EEN01258.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis IBL 4222]
          Length = 240

 Score =  123 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 49/265 (18%), Positives = 92/265 (34%), Gaps = 63/265 (23%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
            Y+        L   +E    +   E GD  A + L+  +LRLV  I   +   G    +
Sbjct: 22  SYVKNNAFPQPLSSDDERKYLELM-EQGDAQARNLLIEHNLRLVAHIVKKFENTGEDAED 80

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++S G IGL++A++ +   +G +LATY+   I                      +  +  
Sbjct: 81  LISIGTIGLIKAIESYSAGKGTKLATYAARCI----------------------ENEILM 118

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
           +LR LK                                       D SL+  I    + +
Sbjct: 119 HLRVLKKT-----------------------------------KKDVSLHDPIGQDKEGN 143

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTL 255
              +  L+     + + +I+  +       +   + +L+ RE+ +   R     +   T 
Sbjct: 144 ---EISLIDILKSESEDVIDMIQLSMELEKIKEYIDILDEREKEVIVKRFGLGLDKEKTQ 200

Query: 256 ENLSSEFEVSRERVRQIEARAFKKV 280
             ++    +SR  V +IE RA  K+
Sbjct: 201 REIAKALGISRSYVSRIEKRALMKM 225


>gi|310659013|ref|YP_003936734.1| RNA polymerase sigma-28 factor (sigma-d) [Clostridium sticklandii
           DSM 519]
 gi|308825791|emb|CBH21829.1| RNA polymerase sigma-28 factor (sigma-D) [Clostridium sticklandii]
          Length = 247

 Score =  123 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 54/232 (23%), Positives = 100/232 (43%), Gaps = 19/232 (8%)

Query: 57  HLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           ++ LV  IA     Y    +   +++S G IGL+ A+ K+DP +  +  TY+   I+ ++
Sbjct: 31  YINLVKIIAGKLYNYYASNIEYDDLMSYGVIGLIDAIDKYDPTKNIKFETYASIRIRGSI 90

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
            + I     L  I  +  QK        LK   +A+     +      IAK L  SE EV
Sbjct: 91  IDQIRN---LDWIPRSIRQKSKI-----LKDANEALESKYGREASYQEIAKYLGKSEQEV 142

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
           +++      + S+  +++  D  +  ++  L  +    E    +     +    L R++S
Sbjct: 143 LTLI----EETSVYNVLSIEDDFNESFKIQLKDE--SLESSPEDLTVYNDTVKELERTIS 196

Query: 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            LN RE+ I          +T + +     +S  RV QI ++A  K+++  Q
Sbjct: 197 ELNEREQLIINLYYY--EGLTYKEIGEILNISESRVSQIHSKAISKMRKQFQ 246


>gi|170780849|ref|YP_001709181.1| putative sigma factor [Clavibacter michiganensis subsp.
           sepedonicus]
 gi|169155417|emb|CAQ00524.1| putative sigma factor [Clavibacter michiganensis subsp.
           sepedonicus]
          Length = 337

 Score =  123 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 46/242 (19%), Positives = 99/242 (40%), Gaps = 19/242 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                ++V  HL L  ++A  + G     S++   G +GL++A +++DP  G    ++++
Sbjct: 85  RRLHDQIVLDHLELADQLARQHSGRAHDWSDLRQVGYLGLVKAARRYDPGFGAPFVSFAI 144

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I   ++ ++  +  +V+      + R       L   + A+T    +      +A   
Sbjct: 145 PTISGEIKRHLRDNGWMVRPPRQIQELRHA-----LLAVVPALTQRLGRTPTDAELAAHT 199

Query: 167 NVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
                EV+      +     SL+  ++  +  S    D L  D  G          R  R
Sbjct: 200 GHPREEVMEALAAHSSLRPASLDHTVHEHEGIS--LADTLGADDPGYA--------RAER 249

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             +L  +  VL+ R+RRI   R + E   +   +++E  V++ +V ++ AR    ++  +
Sbjct: 250 TVLLDAARGVLSERDRRILHLRFVDE--CSQSEIAAELGVTQMQVSRLLARILGALRAEL 307

Query: 285 QK 286
            +
Sbjct: 308 TR 309


>gi|256783362|ref|ZP_05521793.1| RNA polymerase secondary sigma factor [Streptomyces lividans TK24]
 gi|289767236|ref|ZP_06526614.1| RNA polymerase secondary sigma factor [Streptomyces lividans TK24]
 gi|289697435|gb|EFD64864.1| RNA polymerase secondary sigma factor [Streptomyces lividans TK24]
          Length = 263

 Score =  123 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 44/242 (18%), Positives = 93/242 (38%), Gaps = 14/242 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +    L+   L +  +IA+ +RG G  + ++     +GL++AV  +DPERG     Y++
Sbjct: 35  KALRDNLIRVWLPMAERIAVRFRGRGENLEDLYQVAALGLVKAVDHYDPERGHAFEAYAV 94

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +   ++ +       + +      + L   +R+    L   T    +   V  IA+  
Sbjct: 95  PTVTGEIKRHFRDHMWTLHVPRRI--QDLRNRVRKSAKELAQTT--PGRAPTVEEIAEHA 150

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++ +EV +    L    +L+        +     D L       + V+         R 
Sbjct: 151 QLTTAEVRTGMEALECFSALSLEAEMPGTDGYALGDALGGPDPAFDAVV--------DRV 202

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +   +  L  RER I   R      +T   ++ +  +S+  V ++    F +++E I  
Sbjct: 203 AVRPCLEALPERERTILYLRFFGG--MTQSRIAQQLGISQMHVSRLLTGCFDRIREEILA 260

Query: 287 QV 288
           + 
Sbjct: 261 EA 262


>gi|65321710|ref|ZP_00394669.1| COG1191: DNA-directed RNA polymerase specialized sigma subunit
           [Bacillus anthracis str. A2012]
 gi|228923092|ref|ZP_04086384.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228948053|ref|ZP_04110338.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228987592|ref|ZP_04147708.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|229013560|ref|ZP_04170693.1| RNA polymerase sigma-28 factor [Bacillus mycoides DSM 2048]
 gi|229019564|ref|ZP_04176380.1| RNA polymerase sigma-28 factor [Bacillus cereus AH1273]
 gi|229081603|ref|ZP_04214099.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock4-2]
 gi|229135165|ref|ZP_04263965.1| RNA polymerase sigma-28 factor [Bacillus cereus BDRD-ST196]
 gi|229146910|ref|ZP_04275274.1| RNA polymerase sigma-28 factor [Bacillus cereus BDRD-ST24]
 gi|229152543|ref|ZP_04280733.1| RNA polymerase sigma-28 factor [Bacillus cereus m1550]
 gi|229186579|ref|ZP_04313740.1| RNA polymerase sigma-28 factor [Bacillus cereus BGSC 6E1]
 gi|228596838|gb|EEK54497.1| RNA polymerase sigma-28 factor [Bacillus cereus BGSC 6E1]
 gi|228630909|gb|EEK87548.1| RNA polymerase sigma-28 factor [Bacillus cereus m1550]
 gi|228636509|gb|EEK92975.1| RNA polymerase sigma-28 factor [Bacillus cereus BDRD-ST24]
 gi|228648293|gb|EEL04328.1| RNA polymerase sigma-28 factor [Bacillus cereus BDRD-ST196]
 gi|228701709|gb|EEL54199.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock4-2]
 gi|228741730|gb|EEL91914.1| RNA polymerase sigma-28 factor [Bacillus cereus AH1273]
 gi|228747720|gb|EEL97590.1| RNA polymerase sigma-28 factor [Bacillus mycoides DSM 2048]
 gi|228772133|gb|EEM20583.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228811639|gb|EEM57975.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228836590|gb|EEM81939.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
          Length = 243

 Score =  123 bits (310), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 49/265 (18%), Positives = 92/265 (34%), Gaps = 63/265 (23%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
            Y+        L   +E    +   E GD  A + L+  +LRLV  I   +   G    +
Sbjct: 25  SYVKNNAFPQPLSSDDERKYLELM-EQGDAQARNLLIEHNLRLVAHIVKKFENTGEDAED 83

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++S G IGL++A++ +   +G +LATY+   I                      +  +  
Sbjct: 84  LISIGTIGLIKAIESYSAGKGTKLATYAARCI----------------------ENEILM 121

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
           +LR LK                                       D SL+  I    + +
Sbjct: 122 HLRVLKKT-----------------------------------KKDVSLHDPIGQDKEGN 146

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTL 255
              +  L+     + + +I+  +       +   + +L+ RE+ +   R     +   T 
Sbjct: 147 ---EISLIDILKSESEDVIDMIQLSMELEKIKEYIDILDEREKEVIVKRFGLGLDKEKTQ 203

Query: 256 ENLSSEFEVSRERVRQIEARAFKKV 280
             ++    +SR  V +IE RA  K+
Sbjct: 204 REIAKALGISRSYVSRIEKRALMKM 228


>gi|314935979|ref|ZP_07843329.1| RNA polymerase sigma-B factor [Staphylococcus hominis subsp.
           hominis C80]
 gi|313655985|gb|EFS19727.1| RNA polymerase sigma-B factor [Staphylococcus hominis subsp.
           hominis C80]
          Length = 256

 Score =  123 bits (309), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 47/272 (17%), Positives = 113/272 (41%), Gaps = 24/272 (8%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
            E + +  +  ++     K ++++ +  A  +LV  + +L+  +A  Y        ++V 
Sbjct: 3   KESKSVNEISPEQINQWIKEHQDNINPHAQDKLVKHYRKLIESLAYKYSKGQSHHEDLVQ 62

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
            G +GL+ A+ +FD     +   + +  +   ++ Y+      V +     +        
Sbjct: 63  VGMVGLIGAINRFDISFDRKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIG-----P 117

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC------RLAGDESLNALINSSD 194
           R+K     +T+   +   ++ IA +L V+E EV+           L+ D S+ A     D
Sbjct: 118 RIKKVGDELTNELGRSPSILEIANRLEVNEEEVLEAMEMGQSYNALSVDHSIEA---DKD 174

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
            ++    D +    D          +   +R +L R + +L+ RER I +   +    ++
Sbjct: 175 GSTVTLLDIMGQQDDNY--------DLTEKRMILERILPILSDREREIIQCTFI--EGLS 224

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +       +S+  V +++  A +K+Q++ ++
Sbjct: 225 QKETGERIGLSQMHVSRLQRTAIRKLQQAARQ 256


>gi|217968787|ref|YP_002354021.1| sigma-70 region 2 domain protein [Thauera sp. MZ1T]
 gi|217506114|gb|ACK53125.1| sigma-70 region 2 domain protein [Thauera sp. MZ1T]
          Length = 590

 Score =  123 bits (309), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 36/109 (33%), Positives = 61/109 (55%), Gaps = 5/109 (4%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           L   +R++ S+LRLV+ IA  Y   G P  +++ EGN+GLM+AV+KFD  RGF+ +TY+ 
Sbjct: 473 LDHRNRMIKSNLRLVISIAKKYTHTGFPFLDLIQEGNLGLMKAVEKFDYRRGFKFSTYAT 532

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           WWI+ A+   I     LV++     +      + ++   L+ +     +
Sbjct: 533 WWIRQAITRGIADQQRLVRVPVHMVES-----INKVSRVLRELEGRAPR 576


>gi|218133693|ref|ZP_03462497.1| hypothetical protein BACPEC_01562 [Bacteroides pectinophilus ATCC
           43243]
 gi|217991068|gb|EEC57074.1| hypothetical protein BACPEC_01562 [Bacteroides pectinophilus ATCC
           43243]
          Length = 254

 Score =  123 bits (309), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 49/251 (19%), Positives = 105/251 (41%), Gaps = 16/251 (6%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKF 93
           L   Y      +   +L+  + +LV  +A     Y GY +   ++   G  GL+ A+ KF
Sbjct: 9   LWSEYSRTRSTALRDQLIIEYSQLVKLVAGRLGMYLGYSVEYDDLCGYGIFGLIDAIDKF 68

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D  +  +  TY+   I+ A+ + I R    +       QK++   + +++          
Sbjct: 69  DCNKNVKFETYASLRIRGAILDQI-RKMDWIPRSLRQKQKKIDAAMSKIEAQ-------K 120

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
                   +A++L ++  E      +      ++    +  + +    D +      Q +
Sbjct: 121 GSVATDEELAQELGITLDEFNDWQGKTKATNLISLDEYTETQGTEAKMDSVTNARFDQPE 180

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
            ++EKEE    + M+  ++S+L  +ER +      +E  +TL+ +S   +VS  RV Q+ 
Sbjct: 181 DVVEKEEL---KKMIVEAISLLTDKERSVVTLYYYEE--MTLKEISLVLDVSESRVSQLH 235

Query: 274 ARAFKKVQESI 284
            +A  K++  +
Sbjct: 236 TKALLKMKSKL 246


>gi|165973130|gb|ABY76244.1| sigma-K factor [Bacillus thuringiensis]
          Length = 237

 Score =  123 bits (309), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 49/265 (18%), Positives = 92/265 (34%), Gaps = 63/265 (23%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
            Y+        L   +E    +   E GD  A + L+  +LRLV  I   +   G    +
Sbjct: 19  SYVKNNAFPQPLSSDDERKYLELM-EQGDAQARNLLIEHNLRLVAHIVKKFENTGEDAED 77

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++S G IGL++A++ +   +G +LATY+   I                      +  +  
Sbjct: 78  LISIGTIGLIKAIESYSAGKGTKLATYAARCI----------------------ENEILM 115

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
           +LR LK                                       D SL+  I    + +
Sbjct: 116 HLRVLKKT-----------------------------------KKDVSLHDPIGQDKEGN 140

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTL 255
              +  L+     + + +I+  +       +   + +L+ RE+ +   R     +   T 
Sbjct: 141 ---EISLIDILKSESEDVIDMIQLSMELEKIKEYIDILDEREKEVIVKRFGLGLDKEKTQ 197

Query: 256 ENLSSEFEVSRERVRQIEARAFKKV 280
             ++    +SR  V +IE RA  K+
Sbjct: 198 REIAKALGISRSYVSRIEKRALMKM 222


>gi|302392368|ref|YP_003828188.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Acetohalobium arabaticum DSM 5501]
 gi|302204445|gb|ADL13123.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Acetohalobium arabaticum DSM 5501]
          Length = 260

 Score =  123 bits (309), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 46/261 (17%), Positives = 109/261 (41%), Gaps = 18/261 (6%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAV 90
           E  L   ++EH +  A   L+   + LV  +A              ++ + G IGL+ A+
Sbjct: 9   EQKLWIEFKEHNNQQAKEELMLRFMPLVKYVANRVAINLPDKFEFEDLQNYGIIGLIDAI 68

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           ++FD  RG + +TY++  I+ ++ + +     L  + TT          +++      + 
Sbjct: 69  ERFDHRRGMKFSTYAISRIRGSIIDQLR---RLDWVPTTIR-----RKAKQVAEINSELA 120

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCR--LAGDESLNALINSSDKNSSQWQDWLVYDH 208
           +   +      I ++L++   E   +     +  + SL++ INS   +     + +  + 
Sbjct: 121 NKLGRLPTDEEIRQELDLDSDEYSQLMSEINIPQETSLDSFINSRQADGVTLIEVIADED 180

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
             + +     EE    + +L  ++  L P+ER++          + L  +    EV+  R
Sbjct: 181 AARPEQTFRYEE---IKRILGEAIEKLKPQERKVVTLYYY--EGLNLTEIGEVLEVTTAR 235

Query: 269 VRQIEARAFKKVQESIQKQVE 289
           + Q+  +A  +++  + ++ E
Sbjct: 236 ISQLHTKAIYRLRGYLSRKKE 256


>gi|311900799|dbj|BAJ33207.1| putative RNA polymerase sigma factor [Kitasatospora setae KM-6054]
          Length = 296

 Score =  123 bits (309), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 42/239 (17%), Positives = 92/239 (38%), Gaps = 17/239 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              LV  +L LV      +  +     +++  G +GL++A+ +F+ ERG    T+++  I
Sbjct: 72  RASLVELNLSLVRFALRRFGSHRESTEDLMQVGAVGLIKAIDRFETERGLEFTTFAIPTI 131

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   V +     + RL   L + +  L    D   +   V  +++ L ++
Sbjct: 132 LGELRRHFRDTTWAVHVPRRLQELRL--ALVKAQDALSQALD---RAPTVAELSEHLGIT 186

Query: 170 ESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + EVI           +SL+      D         +            E+         
Sbjct: 187 QEEVIEGLQAANAHSTDSLDLPAGPDDDGPGALAAKIGGTD--------ERLGMVEDLVS 238

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           L   ++ L  R+R I   R  +E  +T   +     +S+  V ++ +R   K+++ ++ 
Sbjct: 239 LQPLIAALPERDRLILSMRFTEE--LTQSQIGERLGLSQMHVSRLLSRTLAKLRQGLEA 295


>gi|312134632|ref|YP_004001970.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|311774683|gb|ADQ04170.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor owensensis OL]
          Length = 242

 Score =  123 bits (309), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 57/262 (21%), Positives = 101/262 (38%), Gaps = 64/262 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI-SEVVSEGNIG 85
           PM  ++EE  L K +   G   A + L+  +LRLV  IA  Y      +  +++S G IG
Sbjct: 36  PMSSEEEEMYLNKMW--EGCKEARNILIEKNLRLVAHIAKKYTFSFPNLTDDIISVGTIG 93

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A++ +   +  +L+TY+   I+  +  Y                      LR+ K  
Sbjct: 94  LIKAIETYSTAKCTKLSTYAAKCIENEILMY----------------------LRQNKKF 131

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           L  +                         S+   +  D          D N     D L 
Sbjct: 132 LSQL-------------------------SLENPIGSD---------KDGNEITLMDVLQ 157

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFE 263
            + D  ++ +  K + KN    L + +     RE++I E R   +N    T   +++   
Sbjct: 158 NNQDDIDEQVDLKIQIKNLLKKLDKILKG---REKKIIELRYGLKNGIERTQMEVANLLG 214

Query: 264 VSRERVRQIEARAFKKVQESIQ 285
           +SR  V +IE +A +K+   +Q
Sbjct: 215 ISRSYVSRIEKKALQKLYGELQ 236


>gi|158340672|ref|YP_001521840.1| RNA polymerase sigma factor [Acaryochloris marina MBIC11017]
 gi|158310913|gb|ABW32526.1| RNA polymerase sigma factor [Acaryochloris marina MBIC11017]
          Length = 440

 Score =  123 bits (309), Expect = 3e-26,   Method: Composition-based stats.
 Identities = 57/279 (20%), Positives = 124/279 (44%), Gaps = 24/279 (8%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           I  + + P L  + E  L  +  ++GD  A   ++ S+L  +      +   G+   E++
Sbjct: 14  IATMARYPDLSPEREAELIIK-AQNGDYEARQTVIYSNLAWICSRGGQFSRKGIDDGELI 72

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
           +EG  GL +A+ ++DP +G  L TYS   I     E I R  + +++      K  +  L
Sbjct: 73  NEGYWGLNRAIDQWDPTKGANLRTYSERKIYKFQSEAI-RQKNHIRLP-----KSTYEQL 126

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
            +LK   +++ ++      V  +A++  + E  +  +   ++   SLN++    ++ + +
Sbjct: 127 SKLKKATESLGED----ATVAQLAEETEIKEKRIRKLQE-ISQPVSLNSVT--GERENLE 179

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
             D    D  G     +  E        L   +  L+PR+R I      +E  ++ + +S
Sbjct: 180 LLDQQADDSLGSLDPALSSE--------LLDLVDKLHPRQREILHLYHWEE--LSFQKIS 229

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQ 298
               +  ++VR++  +A   +++ +Q ++      PLL+
Sbjct: 230 DYLGLPAKQVRKLYKKALDLLRKFLQGEINEFPPLPLLE 268


>gi|147678181|ref|YP_001212396.1| sporulation sigma factor SigE [Pelotomaculum thermopropionicum SI]
 gi|146274278|dbj|BAF60027.1| DNA-directed RNA polymerase specialized sigma subunit
           [Pelotomaculum thermopropionicum SI]
          Length = 243

 Score =  123 bits (309), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 65/262 (24%), Positives = 106/262 (40%), Gaps = 63/262 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EE  L  R  E GD +    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 41  PPLTTDEESFLISRL-ESGDGAVRSVLIERNLRLVVYIARKFENTGVGIEDLVSIGTIGL 99

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FDP +  +LATY+   I                      +  +   LRR     
Sbjct: 100 IKAVNTFDPAKKIKLATYASRCI----------------------ENEILMYLRRS---- 133

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                      +     ++ DE LN      D N     D L  
Sbjct: 134 ---------------------------VKNRAEVSFDEPLN---IDWDGNELLLSDVLGT 163

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEV 264
           ++D   + + ++ E+K    +L  ++  L+ RERRI E R    N    T + ++    +
Sbjct: 164 ENDIIYKFIEDEIEKK----LLHLALQKLSGRERRIMELRFGLNNGTEKTQKEVADLLGI 219

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+  + ++E R  K++++ I +
Sbjct: 220 SQSYISRLEKRIIKRLKKEIHR 241


>gi|21225616|ref|NP_631395.1| RNA polymerase secondary sigma factor [Streptomyces coelicolor
           A3(2)]
 gi|2687404|gb|AAC01582.1| putative RNA polymerase secondary sigma factor [Streptomyces
           coelicolor A3(2)]
 gi|8246836|emb|CAB92887.1| putative RNA polymerase secondary sigma factor [Streptomyces
           coelicolor A3(2)]
          Length = 263

 Score =  123 bits (309), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 44/242 (18%), Positives = 93/242 (38%), Gaps = 14/242 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +    L+   L +  +IA+ +RG G  + ++     +GL++AV  +DPERG     Y++
Sbjct: 35  KALRDDLIRVWLPMAERIAVRFRGRGENLEDLYQVAALGLVKAVDHYDPERGHAFEAYAV 94

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +   ++ +       + +      + L   +R+    L   T    +   V  IA+  
Sbjct: 95  PTVTGEIKRHFRDHMWTLHVPRRI--QDLRNRVRKSAKELAQTT--PGRAPTVEEIAEHA 150

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++ +EV +    L    +L+        +     D L       + V+         R 
Sbjct: 151 QLTTAEVRTGMEALECFSALSLEAEMPGTDGYALGDALGGPDPAFDAVV--------DRV 202

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +   +  L  RER I   R      +T   ++ +  +S+  V ++    F +++E I  
Sbjct: 203 AVRPCLEALPERERTILYLRFFGG--MTQSRIAQQLGISQMHVSRLLTGCFDRIREEILA 260

Query: 287 QV 288
           + 
Sbjct: 261 EA 262


>gi|30264411|ref|NP_846788.1| sporulation sigma factor SigK [Bacillus anthracis str. Ames]
 gi|47529862|ref|YP_021211.1| sporulation sigma factor SigK [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49187232|ref|YP_030484.1| sporulation sigma factor SigK [Bacillus anthracis str. Sterne]
 gi|49481469|ref|YP_038392.1| sporulation sigma factor SigK [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|52141167|ref|YP_085663.1| sporulation sigma factor SigK [Bacillus cereus E33L]
 gi|163942095|ref|YP_001646979.1| sporulation sigma factor SigK [Bacillus weihenstephanensis KBAB4]
 gi|165873242|ref|ZP_02217852.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0488]
 gi|167634588|ref|ZP_02392908.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0442]
 gi|167638535|ref|ZP_02396811.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0193]
 gi|170687349|ref|ZP_02878566.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0465]
 gi|170707389|ref|ZP_02897843.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0389]
 gi|177653302|ref|ZP_02935554.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0174]
 gi|190566875|ref|ZP_03019791.1| RNA polymerase sigma-27 factor [Bacillus anthracis Tsiankovskii-I]
 gi|196034403|ref|ZP_03101812.1| RNA polymerase sigma-27 factor [Bacillus cereus W]
 gi|196039171|ref|ZP_03106477.1| RNA polymerase sigma-27 factor [Bacillus cereus NVH0597-99]
 gi|196044956|ref|ZP_03112190.1| RNA polymerase sigma-27 factor [Bacillus cereus 03BB108]
 gi|206969450|ref|ZP_03230404.1| RNA polymerase sigma-27 factor [Bacillus cereus AH1134]
 gi|217961829|ref|YP_002340399.1| sporulation sigma factor SigK [Bacillus cereus AH187]
 gi|218231149|ref|YP_002369149.1| sporulation sigma factor SigK [Bacillus cereus B4264]
 gi|218899507|ref|YP_002447918.1| RNA polymerase sigma-27 factor [Bacillus cereus G9842]
 gi|225866320|ref|YP_002751698.1| RNA polymerase sigma-27 factor [Bacillus cereus 03BB102]
 gi|227817116|ref|YP_002817125.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. CDC 684]
 gi|229603939|ref|YP_002868629.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0248]
 gi|254684096|ref|ZP_05147956.1| sporulation sigma factor SigK [Bacillus anthracis str. CNEVA-9066]
 gi|254721930|ref|ZP_05183719.1| sporulation sigma factor SigK [Bacillus anthracis str. A1055]
 gi|254736444|ref|ZP_05194150.1| sporulation sigma factor SigK [Bacillus anthracis str. Western
           North America USA6153]
 gi|254741481|ref|ZP_05199168.1| sporulation sigma factor SigK [Bacillus anthracis str. Kruger B]
 gi|254750920|ref|ZP_05202959.1| sporulation sigma factor SigK [Bacillus anthracis str. Vollum]
 gi|254757752|ref|ZP_05209779.1| sporulation sigma factor SigK [Bacillus anthracis str. Australia
           94]
 gi|300118668|ref|ZP_07056396.1| sporulation sigma factor SigK [Bacillus cereus SJ1]
 gi|49065844|sp|P62180|RP28_BACCR RecName: Full=RNA polymerase sigma-28 factor; Flags: Precursor
 gi|49065845|sp|P62181|RP28_BACTK RecName: Full=RNA polymerase sigma-28 factor; Flags: Precursor
 gi|49065846|sp|P62182|RP28_BACAN RecName: Full=RNA polymerase sigma-28 factor; Flags: Precursor
 gi|580953|emb|CAA40024.1| sigma factor 28 [Bacillus thuringiensis serovar kurstaki]
 gi|19918928|gb|AAL99379.1| sigma factor 28 [Bacillus thuringiensis serovar israelensis]
 gi|30259069|gb|AAP28274.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. Ames]
 gi|47505010|gb|AAT33686.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49181159|gb|AAT56535.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. Sterne]
 gi|49333025|gb|AAT63671.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|51974636|gb|AAU16186.1| RNA polymerase sigma-28 factor [Bacillus cereus E33L]
 gi|163864292|gb|ABY45351.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           weihenstephanensis KBAB4]
 gi|164711001|gb|EDR16568.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0488]
 gi|167513383|gb|EDR88753.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0193]
 gi|167530040|gb|EDR92775.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0442]
 gi|170127633|gb|EDS96506.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0389]
 gi|170668544|gb|EDT19290.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0465]
 gi|172081584|gb|EDT66656.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0174]
 gi|190561866|gb|EDV15835.1| RNA polymerase sigma-27 factor [Bacillus anthracis Tsiankovskii-I]
 gi|195992945|gb|EDX56904.1| RNA polymerase sigma-27 factor [Bacillus cereus W]
 gi|196024444|gb|EDX63117.1| RNA polymerase sigma-27 factor [Bacillus cereus 03BB108]
 gi|196029798|gb|EDX68399.1| RNA polymerase sigma-27 factor [Bacillus cereus NVH0597-99]
 gi|206735138|gb|EDZ52306.1| RNA polymerase sigma-27 factor [Bacillus cereus AH1134]
 gi|217066768|gb|ACJ81018.1| RNA polymerase sigma-27 factor [Bacillus cereus AH187]
 gi|218159106|gb|ACK59098.1| RNA polymerase sigma-27 factor [Bacillus cereus B4264]
 gi|218543613|gb|ACK96007.1| RNA polymerase sigma-27 factor [Bacillus cereus G9842]
 gi|225788740|gb|ACO28957.1| RNA polymerase sigma-27 factor [Bacillus cereus 03BB102]
 gi|227007199|gb|ACP16942.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. CDC 684]
 gi|229268347|gb|ACQ49984.1| RNA polymerase sigma-27 factor [Bacillus anthracis str. A0248]
 gi|298723917|gb|EFI64631.1| sporulation sigma factor SigK [Bacillus cereus SJ1]
 gi|324328243|gb|ADY23503.1| sporulation sigma factor SigK [Bacillus thuringiensis serovar
           finitimus YBT-020]
 gi|326942122|gb|AEA18018.1| sporulation sigma factor SigK [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 237

 Score =  123 bits (309), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 49/265 (18%), Positives = 92/265 (34%), Gaps = 63/265 (23%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
            Y+        L   +E    +   E GD  A + L+  +LRLV  I   +   G    +
Sbjct: 19  SYVKNNAFPQPLSSDDERKYLELM-EQGDAQARNLLIEHNLRLVAHIVKKFENTGEDAED 77

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++S G IGL++A++ +   +G +LATY+   I                      +  +  
Sbjct: 78  LISIGTIGLIKAIESYSAGKGTKLATYAARCI----------------------ENEILM 115

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
           +LR LK                                       D SL+  I    + +
Sbjct: 116 HLRVLKKT-----------------------------------KKDVSLHDPIGQDKEGN 140

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTL 255
              +  L+     + + +I+  +       +   + +L+ RE+ +   R     +   T 
Sbjct: 141 ---EISLIDILKSESEDVIDMIQLSMELEKIKEYIDILDEREKEVIVKRFGLGLDKEKTQ 197

Query: 256 ENLSSEFEVSRERVRQIEARAFKKV 280
             ++    +SR  V +IE RA  K+
Sbjct: 198 REIAKALGISRSYVSRIEKRALMKM 222


>gi|325290052|ref|YP_004266233.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Syntrophobotulus
           glycolicus DSM 8271]
 gi|324965453|gb|ADY56232.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Syntrophobotulus
           glycolicus DSM 8271]
          Length = 248

 Score =  123 bits (309), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 60/291 (20%), Positives = 108/291 (37%), Gaps = 73/291 (25%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL-----------SAAHRLVTSH 57
           I+ G   L  YI+       L + EE    K   E               +A ++L+  +
Sbjct: 14  ILKGITLLVSYINNNAFPQPLSEAEEAQNLKILAESKGEPANKPTEIEVENARNKLIEHN 73

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLV  +   Y G G    +++S G IGL++ +  F+ ++G RLATY+   I+  +  Y+
Sbjct: 74  LRLVAHLVKKYDGTGEDSDDLISIGTIGLIKGINTFNTDKGTRLATYAARCIENEILMYL 133

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
                                L++ +G                             +SM 
Sbjct: 134 -------------------RTLKKTRGE----------------------------VSMY 146

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
             +  D          + NS    D L  D D     + ++ E +  + ++   +  L  
Sbjct: 147 DPIGTD---------KEGNSINLIDILGTDPDA----ISDQVESEFEQRIVLEKLKCLTK 193

Query: 238 RERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           RER + + R    N    T   ++    +SR  V +IE +A +K+ E +++
Sbjct: 194 RERMVLQLRFGLLNSPKKTQREIARMLGISRSYVSRIEKKAVQKLTEEMKE 244


>gi|205373400|ref|ZP_03226204.1| RNA polymerase sigma factor SigD [Bacillus coahuilensis m4-4]
          Length = 257

 Score =  123 bits (309), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 58/264 (21%), Positives = 118/264 (44%), Gaps = 20/264 (7%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGL 86
             Q+E VL K + E+ +  A   LV  ++ LV              +   ++ S G +GL
Sbjct: 5   TTQDELVLWKSWIENRNEEAGDLLVKKYMHLVSFHVQRISSTLPKNISKDDLKSLGMMGL 64

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           + A++KFD ER  +  TY+ + I+ ++ + + +   L +     N +     + +    L
Sbjct: 65  LDALQKFDIERDLKFDTYASFRIRGSIIDGLRKEDWLPR-----NTRDKAKKIEKTISRL 119

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCR--LAGDESLNALINSSDKNSSQWQDWL 204
           +      + PE V   AK+L++S  EVI +      A   S++ +    +K+S ++Q   
Sbjct: 120 EQTLMRKIVPEDV---AKELDMSADEVIQIMNEHFFANVLSMDEMTREEEKDSPKFQM-- 174

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               D + +   E+  +  +   L + +  LN +E+ +       +  +TL  +    ++
Sbjct: 175 ---QDEKSRSPEEELVKSEQIRDLEQHIRGLNEKEQLVLSLFY--QEELTLTEIGEVLQL 229

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S  R+ QI ++A  K+++ I  Q 
Sbjct: 230 STSRISQIHSKALFKLRKFISTQA 253


>gi|18310750|ref|NP_562684.1| sporulation sigma factor SigK [Clostridium perfringens str. 13]
 gi|168214245|ref|ZP_02639870.1| RNA polymerase sigma-70 factor family [Clostridium perfringens CPE
           str. F4969]
 gi|169343581|ref|ZP_02864580.1| RNA polymerase sigma-70 factor family [Clostridium perfringens C
           str. JGS1495]
 gi|170764185|ref|ZP_02633869.2| RNA polymerase sigma-70 factor family [Clostridium perfringens E
           str. JGS1987]
 gi|182420555|ref|ZP_02643878.2| RNA polymerase sigma-70 factor family [Clostridium perfringens NCTC
           8239]
 gi|182625679|ref|ZP_02953448.1| RNA polymerase sigma-70 factor family [Clostridium perfringens D
           str. JGS1721]
 gi|18145431|dbj|BAB81474.1| probable transcription initiation factor sigma K [Clostridium
           perfringens str. 13]
 gi|169298141|gb|EDS80231.1| RNA polymerase sigma-70 factor family [Clostridium perfringens C
           str. JGS1495]
 gi|170660828|gb|EDT13511.1| RNA polymerase sigma-70 factor family [Clostridium perfringens E
           str. JGS1987]
 gi|170714308|gb|EDT26490.1| RNA polymerase sigma-70 factor family [Clostridium perfringens CPE
           str. F4969]
 gi|177909081|gb|EDT71556.1| RNA polymerase sigma-70 factor family [Clostridium perfringens D
           str. JGS1721]
 gi|182379749|gb|EDT77228.1| RNA polymerase sigma-70 factor family [Clostridium perfringens NCTC
           8239]
          Length = 233

 Score =  123 bits (309), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 67/283 (23%), Positives = 111/283 (39%), Gaps = 66/283 (23%)

Query: 9   IVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           +V  +I L+ Y+      P  L ++EE +  +R ++ GD+ A   LV  +LRLV  I   
Sbjct: 10  LVGSKIFLTGYVTGNSTFPKPLNEKEEKIYLERLKD-GDVEAKRVLVERNLRLVAHIVKK 68

Query: 68  YRGYGL---PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           Y         + +++S G IGL++A+  FD  +G RLATY+   I   +  +        
Sbjct: 69  YSSNYQNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATYAAKCIDNEILMF-------- 120

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
                      F N ++ KG                             + +   +  D+
Sbjct: 121 -----------FRNTKKTKGE----------------------------VFLQDPIGVDK 141

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
             N  I   D  SS     L    +  E  L  KE  K   ++L       +PRE+ I +
Sbjct: 142 EGNE-ICLIDILSSDSDSVL----EAVENSLQVKELYKKMSDVL-------SPREKEIIQ 189

Query: 245 ARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            R   L  +  T   ++    +SR  V +IE +A KK+ +  +
Sbjct: 190 MRYGLLDGDIKTQREIAGILGISRSYVSRIEKKALKKLNKEFK 232


>gi|317129180|ref|YP_004095462.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus
           cellulosilyticus DSM 2522]
 gi|315474128|gb|ADU30731.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus
           cellulosilyticus DSM 2522]
          Length = 254

 Score =  123 bits (309), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 52/255 (20%), Positives = 104/255 (40%), Gaps = 19/255 (7%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFD 94
             R+ E  D  A  RLV ++L LV              + + ++ S G +GL  A++KFD
Sbjct: 14  WSRWSEDRDEVACDRLVQAYLPLVDYHVQRIGANLPRNVQLDDLRSNGMLGLYDALEKFD 73

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
            +R  +  TY+ + I+ A+ + + R      +  +  +K      +++    + +     
Sbjct: 74  EKRELKFDTYASFRIRGAIIDGL-RQMDW--LPRSVREKT-----KKIDQATEKLEQQYG 125

Query: 155 KPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +      +A  L ++E +V        LA   S++     S+K  S    +     D + 
Sbjct: 126 RYVNPKEVADYLGMNEEDVYKTINESYLAHQLSIDEPAQDSEKEDS----FTATIMDEKT 181

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
               +  ++K +   L   +   N +E+ I      +E  +TL  +     VS  RV QI
Sbjct: 182 LTPEQHIDKKGQMEELAEIIKTFNEKEQLIISLFYFEE--LTLTEIGEILNVSTSRVSQI 239

Query: 273 EARAFKKVQESIQKQ 287
            ++   K+Q+ +  +
Sbjct: 240 HSKTIFKLQQKLLSK 254


>gi|55274905|gb|AAV49254.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 182

 Score =  122 bits (308), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 44/186 (23%), Positives = 84/186 (45%), Gaps = 10/186 (5%)

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     
Sbjct: 1   IARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRT 60

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           +++      K L   LR  +     ++           IA++L+    +V  M       
Sbjct: 61  IRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERI 115

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            S++  +    +     +  L    D +E    +  +  + +  + + +  LN ++R + 
Sbjct: 116 TSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVL 170

Query: 244 EARRLQ 249
             R   
Sbjct: 171 ARRFGL 176


>gi|326791235|ref|YP_004309056.1| RNA polymerase, sigma 28 subunit, SigK [Clostridium lentocellum DSM
           5427]
 gi|326541999|gb|ADZ83858.1| RNA polymerase, sigma 28 subunit, SigK [Clostridium lentocellum DSM
           5427]
          Length = 220

 Score =  122 bits (308), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 54/262 (20%), Positives = 96/262 (36%), Gaps = 62/262 (23%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L  +EE    + Y++ GD +A + L+  +LRLV  I   Y      + +++S G IGL+
Sbjct: 19  PLSAEEEKHYLECYQD-GDEAAKNILIERNLRLVAHIVKKYNNINNDVDDLISIGTIGLI 77

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           + +  FDP +  RLATY+   I+  +   I                              
Sbjct: 78  KGISSFDPNKCTRLATYAARCIENEILMSIR----------------------------- 108

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                  + E                 S++  +  D+         + N     D L  +
Sbjct: 109 --AGRKQRYET----------------SLHAPIGMDQ---------EGNEISLLDILCTE 141

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVS 265
           +D     +    E +     +   +    PRE+ I   R    N    T   ++ +  +S
Sbjct: 142 NDTIFDQVDLDIEVRKLYQHIRILLK---PREKEILLLRYGLNNQEEKTQREIAEQMGIS 198

Query: 266 RERVRQIEARAFKKVQESIQKQ 287
           R  V +IE +A KK+ + +QK+
Sbjct: 199 RSYVSRIEKKALKKLCKELQKK 220


>gi|89098615|ref|ZP_01171497.1| sigma factor SigD [Bacillus sp. NRRL B-14911]
 gi|89086577|gb|EAR65696.1| sigma factor SigD [Bacillus sp. NRRL B-14911]
          Length = 253

 Score =  122 bits (308), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 47/257 (18%), Positives = 109/257 (42%), Gaps = 15/257 (5%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQA 89
           +E      +++  D  A + LV  ++ LV              +   E+ S G +GL  A
Sbjct: 7   DEQAYWALWQQSRDAEAGNSLVKRYMPLVSYHVQRISAGLPKNVSRDELRSLGLMGLYDA 66

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           ++KFDP R  +  TY+ + I+ ++ + + +   L         +      ++++   + +
Sbjct: 67  LEKFDPTRDLKFDTYASFRIRGSIIDGLRKEDWL--------PRSTREKAKKIEAAAERL 118

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
             + ++      I K++++ E EV ++         L+      D++      +++ DH 
Sbjct: 119 EQHLMRKATAAEIGKEVDLHEDEVQTVMSEHFFANVLSMDEQPQDQDEKDGATYILKDH- 177

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
            +  V  EK  +    + +  ++S LN +E+ +       +  +TL  +     +S  R+
Sbjct: 178 -RAVVPEEKVAKDELLSEMADAVSCLNEKEQLVISLFY--KEELTLTEIGQVMGLSTSRI 234

Query: 270 RQIEARAFKKVQESIQK 286
            QI  +A   ++ ++QK
Sbjct: 235 SQIHTKAIFSLRHTLQK 251


>gi|270668763|ref|ZP_06222551.1| RNA polymerase sigma factor RpoD [Haemophilus influenzae HK1212]
 gi|270316653|gb|EFA28454.1| RNA polymerase sigma factor RpoD [Haemophilus influenzae HK1212]
          Length = 151

 Score =  122 bits (308), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 38/115 (33%), Positives = 56/115 (48%), Gaps = 2/115 (1%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +
Sbjct: 39  EQKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFS 98

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           TY+ WWI+ A+   I      ++I            L R+   L         PE
Sbjct: 99  TYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQLLQEMGREATPE 151


>gi|126348048|emb|CAJ89768.1| putative RNA polymerase secondary sigma factor [Streptomyces
           ambofaciens ATCC 23877]
          Length = 264

 Score =  122 bits (308), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 42/242 (17%), Positives = 93/242 (38%), Gaps = 14/242 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +    L+   L +  +IA+ +RG G  + ++     +GL++AV  +DP RG     Y++
Sbjct: 36  KALRDELIQVWLPMSERIAVRFRGRGENLEDLYQVAALGLVKAVDHYDPRRGHAFEAYAV 95

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +   ++ +       + +      + L   +R+    L  +T    +   V  IA   
Sbjct: 96  PTVTGEIKRHFRDHMWTLHVPRRI--QDLRNRVRKSAKELAQVT--PGRAPTVEEIADHA 151

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  EV +    L    +L+        +     D L       + V+         R 
Sbjct: 152 HLTTVEVRTGMEALECFSALSLEAEMPGTDGYALGDALGGPDPAFDAVV--------DRV 203

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +   +  L  RER I   R      +T   ++ +  +S+  V ++ +  F ++++ I  
Sbjct: 204 AVRPCLEALPERERTILYLRFFGG--MTQSRIAQQLGISQMHVSRLLSGCFDRIRDEILA 261

Query: 287 QV 288
           + 
Sbjct: 262 EA 263


>gi|111021699|ref|YP_704671.1| sigma factor, sigma 70 type, group 3 [Rhodococcus jostii RHA1]
 gi|110821229|gb|ABG96513.1| sigma factor, sigma 70 type, group 3 [Rhodococcus jostii RHA1]
          Length = 249

 Score =  122 bits (308), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 37/232 (15%), Positives = 86/232 (37%), Gaps = 16/232 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             RL+   L L   IA  + G G P+ +++    +GL++AV +FD   G    +Y++  I
Sbjct: 22  RQRLIERCLPLAEHIARRFHGRGEPLDDLIQVARLGLVKAVDRFDARCGANFVSYAVPTI 81

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   +++  +  +  L             +T    +      +A+ + + 
Sbjct: 82  TGEVRRHFRDTGWAMRVPRSMQELHLSLT-----NATTELTTTLGRAPTASELAEAVGID 136

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           + EV+    R+A   S  +      +N     + +         V            +L 
Sbjct: 137 KDEVVQ-GLRVADAYSTLSTDFPLGENERPLSETIGDVDPALAHV--------EDHVVLA 187

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             +  L   ER +   R      +T   +++   VS+ +V ++  +    ++
Sbjct: 188 PLLESLPDLERTVLVLRFFGN--MTQSQIAARVGVSQMQVSRLLTKTLADLR 237


>gi|194014777|ref|ZP_03053394.1| RNA polymerase sigma-D factor (Sigma-28) [Bacillus pumilus ATCC
           7061]
 gi|194013803|gb|EDW23368.1| RNA polymerase sigma-D factor (Sigma-28) [Bacillus pumilus ATCC
           7061]
          Length = 255

 Score =  122 bits (308), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 49/262 (18%), Positives = 112/262 (42%), Gaps = 19/262 (7%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQA 89
           E+  L  R++E  D +A   L+  ++ LV              +   +++S G +GL  A
Sbjct: 7   EDQALWARWKEWKDPAAGDDLMRRYMPLVTYHVGRISIGLPKSVHKEDLISLGMLGLYDA 66

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           ++KFDP R  +  TY+ + I+ A+ + + +   L +              ++++  ++ +
Sbjct: 67  LEKFDPGRDLKFDTYASFRIRGAIIDGLRKEDWLPRTSR--------EKTKKVEAAIEKL 118

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCR--LAGDESLNALINSSDKNSSQWQDWLVYD 207
               L+      +A++L +SE +V++       A   S++  ++  +       +  V  
Sbjct: 119 EQRYLRNVTPTEVAEELGMSEQDVVTTMNEGFFANLLSIDEKLHDQEDGE----NVQVMI 174

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            D +     EK  +      L   M+ L+ +E+ +       +  +TL  +     +S  
Sbjct: 175 RDEKTVTPEEKMLKDELIEQLAEKMTELSEKEKLVISLFY--KEELTLTEIGHVLNLSTS 232

Query: 268 RVRQIEARAFKKVQESIQKQVE 289
           R+ QI ++A  K++  + K ++
Sbjct: 233 RISQIHSKALFKLKYLLDKAIQ 254


>gi|186684907|ref|YP_001868103.1| RNA polymerase sigma factor SigF [Nostoc punctiforme PCC 73102]
 gi|186467359|gb|ACC83160.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Nostoc
           punctiforme PCC 73102]
          Length = 269

 Score =  122 bits (308), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 50/258 (19%), Positives = 113/258 (43%), Gaps = 18/258 (6%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQA 89
           K E + L + Y++    +  ++LV  +  LV K A  +         +++  G +GL++A
Sbjct: 21  KHEIWQLLREYQQSRSENVRNKLVKLNFGLVRKEAHYWTNQCHETYDDLLQVGCLGLIRA 80

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT---ANQKRLFFNLRRLKGHL 146
           ++KF+  +G   ++Y++ +I+  +Q Y+      V+I        Q+ +  +    + H 
Sbjct: 81  IEKFELSKGHAFSSYALPYIRGEIQHYLRDKGVTVRIPRKWLALQQQAIGVSRSWREKHN 140

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +  TD  L      A A +++ +E + I +        SL+  I   ++ S+   + +  
Sbjct: 141 RQPTDTEL------AAALEISPNEWQEIKLAWINRAPLSLDVPIQDGEEGSTCLGELVPD 194

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
            H    Q+  E + R      L +++  L  R R + E   LQ+  +T + ++    +S 
Sbjct: 195 PHYRSFQLAQEDQLR------LQQALVQLEQRTRDVLECVFLQD--LTQKQVAEHLGISV 246

Query: 267 ERVRQIEARAFKKVQESI 284
             V +   +    +++ +
Sbjct: 247 VTVSRRVKKGLDLMKQLM 264


>gi|110803132|ref|YP_699053.1| sporulation sigma factor SigK [Clostridium perfringens SM101]
 gi|6715486|gb|AAF26431.1|AF218835_2 RNA polymerase sigma factor SigK [Clostridium perfringens]
 gi|110683633|gb|ABG87003.1| RNA polymerase sigma-70 factor family [Clostridium perfringens
           SM101]
          Length = 233

 Score =  122 bits (308), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 67/283 (23%), Positives = 111/283 (39%), Gaps = 66/283 (23%)

Query: 9   IVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           +V  +I L+ Y+      P  L ++EE +   R ++ GD+ A   LV  +LRLV  I   
Sbjct: 10  LVGSKIFLTGYVTGNSTFPKPLNEKEEKIYLDRLKD-GDVEAKRVLVERNLRLVAHIVKK 68

Query: 68  YRGYGL---PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           Y         + +++S G IGL++A+  FD  +G RLATY+   I   +  +        
Sbjct: 69  YSSNYQNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATYAAKCIDNEILMF-------- 120

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
                      F N ++ KG                             + +   +  D+
Sbjct: 121 -----------FRNTKKTKGE----------------------------VFLQDPIGVDK 141

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
             N  I   D  SS     L    +  E  L  KE  K   ++L       +PRE+ I +
Sbjct: 142 EGNE-ICLIDILSSDSDSVL----EAVENSLQVKELYKKMSDIL-------SPREKEIIK 189

Query: 245 ARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            R   L  +  T   +++   +SR  V +IE +A KK+ +  +
Sbjct: 190 MRYGLLDGDIKTQREIAAILGISRSYVSRIEKKALKKLNKEFK 232


>gi|330961077|gb|EGH61337.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv.
           maculicola str. ES4326]
          Length = 167

 Score =  122 bits (308), Expect = 4e-26,   Method: Composition-based stats.
 Identities = 34/169 (20%), Positives = 68/169 (40%), Gaps = 12/169 (7%)

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++I            L R+   +         PE    + +++ + E ++  +    
Sbjct: 1   ARTIRIPVHM--IETINKLNRISRQMLQEMGREPTPE---ELGERMEMPEDKIRKVLKIA 55

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               S+   I   D   S   D++    D   Q  I+    ++ +      +S L  RE 
Sbjct: 56  KEPISMETPI--GDDEDSHLGDFI---EDSTMQSPIDVATVESLKEATREVLSGLTAREA 110

Query: 241 RIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 111 KVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPTRSE 159


>gi|189916711|gb|ACE62866.1| RNA polymerase sigma 70 factor [Xylella fastidiosa]
 gi|189916713|gb|ACE62867.1| RNA polymerase sigma 70 factor [Xylella fastidiosa]
 gi|189916715|gb|ACE62868.1| RNA polymerase sigma 70 factor [Xylella fastidiosa]
          Length = 161

 Score =  122 bits (308), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 34/160 (21%), Positives = 68/160 (42%), Gaps = 10/160 (6%)

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
            +       L R+   +         PE    +AK++++ E ++  +        S+   
Sbjct: 1   VHMIETINKLNRISRQMLQQFGREATPE---ELAKEMDMPEDKIRKVMKIAKEPISMETP 57

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   D   S   D++    D   +  ++     N    +   ++ L PRE ++   R   
Sbjct: 58  I--GDDEDSHLGDFI---EDPNVESPVDTTTNVNLSETVREVLAGLTPREAKVLRMRFGI 112

Query: 250 E--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +     TLE +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 113 DMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 152


>gi|229086911|ref|ZP_04219070.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock3-44]
 gi|228696421|gb|EEL49247.1| RNA polymerase sigma-28 factor [Bacillus cereus Rock3-44]
          Length = 228

 Score =  122 bits (308), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 49/256 (19%), Positives = 91/256 (35%), Gaps = 64/256 (25%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+    E+  L     E GD  A + L+  +LRLV  I   +   G    +++S G IGL
Sbjct: 20  PLSSDDEKKYL--ELMEQGDAHARNLLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGL 77

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A++ +   +G +LATY+   I                      +  +  +LR LK   
Sbjct: 78  IKAIESYSAGKGTKLATYAARCI----------------------ENEILMHLRVLKKT- 114

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                               D SL+  I    + +   +  L+ 
Sbjct: 115 ----------------------------------KKDVSLHDPIGQDKEGN---EISLID 137

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEV 264
               + + +I+  +       +   + +L+ RE+ +   R     +   T   ++    +
Sbjct: 138 ILKSESEDVIDMIQLSMELEKIKEYIDILDEREKEVIVKRFGLGLDKEKTQREIAKALGI 197

Query: 265 SRERVRQIEARAFKKV 280
           SR  V +IE RA  K+
Sbjct: 198 SRSYVSRIEKRALMKM 213


>gi|160939772|ref|ZP_02087119.1| hypothetical protein CLOBOL_04663 [Clostridium bolteae ATCC
           BAA-613]
 gi|158437206|gb|EDP14971.1| hypothetical protein CLOBOL_04663 [Clostridium bolteae ATCC
           BAA-613]
          Length = 209

 Score =  122 bits (308), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 52/261 (19%), Positives = 93/261 (35%), Gaps = 62/261 (23%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L   EE    +R +E GD SA   L+  ++RLV  +   Y+G    + +++S G IGL+
Sbjct: 7   PLSAGEEKEYLERCKE-GDQSARDMLIEHNMRLVAHVVKKYQGSDYDMEDLLSVGTIGLI 65

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV  F+ ++G RLATY+   ++  +                     L    R+      
Sbjct: 66  KAVNTFNVDKGSRLATYAARCVENEILM-------------------LLRASRKYSKE-- 104

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                                     +S+   +  D          D  +    D +  D
Sbjct: 105 --------------------------VSLFEPIGVD---------KDGETVSLVDVIEMD 129

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVS 265
           +      +I K++ K          S L   E+ +   R         T   ++ +  +S
Sbjct: 130 NKETLDTMILKQDVKELYEAFE---SCLTETEKTVLGMRYGLYRGKEHTQREIAGKLGIS 186

Query: 266 RERVRQIEARAFKKVQESIQK 286
           R  V +IE +A +K++    K
Sbjct: 187 RSYVSRIEKKAIEKIRTEFAK 207


>gi|167770197|ref|ZP_02442250.1| hypothetical protein ANACOL_01540 [Anaerotruncus colihominis DSM
           17241]
 gi|167667519|gb|EDS11649.1| hypothetical protein ANACOL_01540 [Anaerotruncus colihominis DSM
           17241]
          Length = 257

 Score =  122 bits (308), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 49/257 (19%), Positives = 111/257 (43%), Gaps = 16/257 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL---PISEVVSEGNIGLMQAVKK 92
            L + Y+E G     +R+V  +  +   +A+           I E+V++G I L+ +V +
Sbjct: 13  ELMRLYKETGSQELRNRIVMHYSYIAKSVAIEMNNMFHKYATIEEMVNQGVIALIDSVDR 72

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FDP+ G + +TY+   +K A+ +Y+ +   L +               R+      +   
Sbjct: 73  FDPDHGVKFSTYAFTKVKGAIIDYVRKQDWLPRRVRHNAI--------RVNNAYNDLPMK 124

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      +AK+L++SE E       ++G+   +     +D   +Q   W +       
Sbjct: 125 LGRNPTRSEMAKQLDMSEREFDQCIYEMSGESIFSYESLLADGPQNQNMLWPMEGEIVNP 184

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           +  ++ +E    R  L  ++  LN +ER +      +   +T++ +     VS +R+ QI
Sbjct: 185 EGCVDAKEL---REQLGMAIDSLNEQERHVLSLYYYEN--LTMKEIGGVLGVSEQRIGQI 239

Query: 273 EARAFKKVQESIQKQVE 289
             +  +K++  +++ ++
Sbjct: 240 NRKLIQKLRNKLEQYMK 256


>gi|288573001|ref|ZP_06391358.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Dethiosulfovibrio
           peptidovorans DSM 11002]
 gi|288568742|gb|EFC90299.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Dethiosulfovibrio
           peptidovorans DSM 11002]
          Length = 248

 Score =  122 bits (308), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 57/260 (21%), Positives = 120/260 (46%), Gaps = 24/260 (9%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGL 86
            K++E  L +RYR +        +V+ ++ LV  +          GL   +++S G +GL
Sbjct: 4   SKEDE-ALWQRYRSNPSE--KDEIVSRYIPLVKYVVARMTVTPPPGLDYEDLISFGLMGL 60

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           + A+ +F+ ERGF   T+++  I+ A+ + + +     + G           L+RL+   
Sbjct: 61  LDAIDRFEIERGFSFQTFAVPRIRGAVLDELRKCDWFSRTGR--------EKLQRLERAT 112

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWL 204
           + +    + P+   ++ ++++V +     M    +     SL+  + S D+   Q  D L
Sbjct: 113 ERLMIQGITPDD-ESLKREMDVDDKTYREMLSLASRGYVVSLDE-VMSLDEGDVQKGDLL 170

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
            Y     ++ L  +EE    R+++  +++ L+ RER +     L+E  +TL+ +     V
Sbjct: 171 SYTGASAQEFLENREE----RDLVVGALNRLSERERLVLSMYYLEE--MTLKEIGLVLGV 224

Query: 265 SRERVRQIEARAFKKVQESI 284
           +  RV QI  +A   ++  +
Sbjct: 225 TESRVSQIHGKAIVSLKARL 244


>gi|159137617|gb|ABW88899.1| HrdB [Streptomyces cacaoi subsp. asoensis]
          Length = 133

 Score =  122 bits (308), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 40/133 (30%), Positives = 68/133 (51%), Gaps = 28/133 (21%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRY---------------------------REHGDLSAAH 51
           Y+ +I K+P+L  ++E  LAKR                             E G   A +
Sbjct: 2   YLKQIGKVPLLNAEQEVELAKRIEAGLFAEDKLANADKLAPKLKRELEIIAEDG-RRAKN 60

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +G++ +TY+ WWI+ 
Sbjct: 61  HLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGYKFSTYATWWIRQ 120

Query: 112 AMQEYILRSWSLV 124
           A+   +      +
Sbjct: 121 AITRAMADQARTI 133


>gi|119715629|ref|YP_922594.1| sigma-70 region 4 domain-containing protein [Nocardioides sp.
           JS614]
 gi|119536290|gb|ABL80907.1| sigma-70 region 4 domain protein [Nocardioides sp. JS614]
          Length = 260

 Score =  122 bits (308), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 44/256 (17%), Positives = 99/256 (38%), Gaps = 23/256 (8%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                 +V  ++ +    A  YR  G+   ++     +GL++AV+ F+P RG    ++++
Sbjct: 24  RRIRDEIVRLNMGVASDCARRYRQRGIATEDLDQVAYLGLVKAVRGFEPGRGHDFLSFAV 83

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+  ++ +       ++   +  + +      R+      ++    +  +   +A+ L
Sbjct: 84  PTIRGEVRRHFRDLGWALRPPRSIQELQ-----SRIHAAEGDLSQELGRSPRPSDLARHL 138

Query: 167 NVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            V   +V+            SL+ +    D +        + D  G      ++ E    
Sbjct: 139 GVDLEQVLDALGATGCFAPASLDVVGADGDDS--------LGDRLGTADPAFDQAEA--- 187

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L   +  L PRERRI E R       T   + ++  V++ +V ++  R   +++E +
Sbjct: 188 RITLAAVLRGLTPRERRILELRFFGN--HTQAEIGADIGVTQMQVSRLLNRILARLRERM 245

Query: 285 QKQVELSSSPPLLQKP 300
              +  S   P+   P
Sbjct: 246 ---LAASDEAPVSSGP 258


>gi|37522237|ref|NP_925614.1| RNA polymerase sigma factor SigF [Gloeobacter violaceus PCC 7421]
 gi|35213237|dbj|BAC90609.1| glr2668 [Gloeobacter violaceus PCC 7421]
          Length = 254

 Score =  122 bits (307), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 57/240 (23%), Positives = 96/240 (40%), Gaps = 17/240 (7%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKKF 93
            +L + Y E    +  + LV  +L LV KIA    RG   P+ ++V  G IGLM+AV++F
Sbjct: 12  RLLLRAYGESPSTALRNELVCRNLGLVRKIAHQLARGSSEPLEDLVQVGAIGLMRAVERF 71

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           DP  G   ++++   I+ AMQ Y+      V++      +RL     R +    A++  +
Sbjct: 72  DPSLGHAFSSFATPCIRGAMQHYLRDHGHSVRLP-----RRLLELDSRARRAAHALSQRH 126

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYDHDGQ 211
                   +A  L++S  E + M    A     SL+A         +     L+   D  
Sbjct: 127 GCTPSERQVASALDISAEEWLQMRLARANRTLVSLDAPAGPH--PDTPPLVELLPGPDTP 184

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E     +E     R  L R+++ L    + +           T    +    VS   V +
Sbjct: 185 EVSPEGQE-----RAHLARALAQLEAATQVVVRQVYF--EKRTQSETARRLGVSPMTVSR 237


>gi|75908065|ref|YP_322361.1| RNA polymerase sigma factor SigF [Anabaena variabilis ATCC 29413]
 gi|75701790|gb|ABA21466.1| Sigma 32 (RpoH) [Anabaena variabilis ATCC 29413]
          Length = 258

 Score =  122 bits (307), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 45/255 (17%), Positives = 110/255 (43%), Gaps = 16/255 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVK 91
           E + L + Y++    +  ++LV  +L LV K A  +         ++V  G +GL++A++
Sbjct: 12  EIWQLLREYQQSRSETVRNQLVKLNLGLVRKEAHYWMNQCRENYDDLVQVGCLGLIRAIE 71

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           +F+  +G   +++++ +I+  +Q Y+      V+I      +R     +R  G  +++ +
Sbjct: 72  RFEIAKGHAFSSFAIPYIRGEIQHYLRDKGVTVRIP-----RRYLAIQQRAIGVSRSLRE 126

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHD 209
              +      +A  L++S  E   +          SL+  +   ++ ++   + +   H 
Sbjct: 127 QYNRQPTDSELATALDISPDEWQEIKLAWVNRAPLSLDVPVQDGEEGATSLGELVPDHHY 186

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
              Q+  E + R      L +++  L  R R + E   LQ+  +T + ++    +S   V
Sbjct: 187 RSFQLAQEDQIR------LQQALFQLEQRTREVLECVFLQD--LTQKQVAEHLGISVVTV 238

Query: 270 RQIEARAFKKVQESI 284
            +   +    ++  +
Sbjct: 239 SRRVKKGLDLLKHLM 253


>gi|189916709|gb|ACE62865.1| RNA polymerase sigma 70 factor [Xylella fastidiosa]
          Length = 161

 Score =  122 bits (307), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 34/160 (21%), Positives = 68/160 (42%), Gaps = 10/160 (6%)

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
            +       L R+   +         PE    +AK++++ E ++  +        S+   
Sbjct: 1   VHMIETINKLNRISRQMLQQFGREATPE---ELAKEMDMPEDKIRKVMKVAKEPISMETP 57

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I   D   S   D++    D   +  ++     N    +   ++ L PRE ++   R   
Sbjct: 58  I--GDDEDSHLGDFI---EDPNVESPVDTTTNVNLSETVREVLAGLTPREAKVLRMRFGI 112

Query: 250 E--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +     TLE +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 113 DMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 152


>gi|333022810|ref|ZP_08450874.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
 gi|332742662|gb|EGJ73103.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
          Length = 275

 Score =  122 bits (307), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 46/241 (19%), Positives = 96/241 (39%), Gaps = 16/241 (6%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                RLV + L +  +IA  YR  G  + ++     +GL++AV +FDPE      +Y++
Sbjct: 37  ERQRSRLVETWLPMAHRIAGRYRERGENLEDLCQVAALGLVKAVDRFDPEVSDAFESYAV 96

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN-LKPEQVVAIAKK 165
             I+  ++ +   +   V +     + R       ++  LQ +      +   V  +A+ 
Sbjct: 97  PTIRGELKRHFRDNTWGVHVPRRVQELR-----NAVRTALQELAPRTAPRTPSVAELAES 151

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
             + E EV      L     ++     + +     +D L  D      V+         R
Sbjct: 152 AKLGEEEVRRGLEALDSYRPVSLDGTPTPEGEHPLRDRLGADDPAYAIVV--------DR 203

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             +  +++ L  RER I   R    +  T   +++E  +S+  V ++  +A  +V+  ++
Sbjct: 204 ESVRPALAELPERERYILYLRFF--HARTQRAIAAELGLSQMHVSRLITQACAQVKHRVE 261

Query: 286 K 286
            
Sbjct: 262 A 262


>gi|167949416|ref|ZP_02536490.1| RNA polymerase sigma factor RpoD [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 134

 Score =  122 bits (307), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 36/116 (31%), Positives = 55/116 (47%), Gaps = 2/116 (1%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 3   IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 62

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
            +TY+ WWI+ A+   I      ++I            L R+   +         P
Sbjct: 63  FSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQMIQEMGREGYP 116


>gi|281421843|ref|ZP_06252842.1| RNA polymerase sigma-70 factor [Prevotella copri DSM 18205]
 gi|281404085|gb|EFB34765.1| RNA polymerase sigma-70 factor [Prevotella copri DSM 18205]
          Length = 136

 Score =  122 bits (307), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 40/113 (35%), Positives = 71/113 (62%), Gaps = 2/113 (1%)

Query: 17  SRYIHEIRKIPMLEKQEEYVLAKRYREHG--DLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            RY+ +I + P+L   EE  LA++ R+ G     A  +L+ ++LR VV +A  Y+  GL 
Sbjct: 16  ERYLMKIGREPLLSHDEELELARKIRKGGSEGERAKEKLIRANLRFVVSVAKRYQHRGLA 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           +++++ EGNIGL++AV++FD  RGF+   Y++WWI+ ++ + I     + +I 
Sbjct: 76  LTDLIDEGNIGLIKAVERFDETRGFKFIQYAIWWIRQSILQAIAEQNHITRIS 128


>gi|168986243|dbj|BAG11803.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H7]
 gi|168986245|dbj|BAG11804.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H7]
 gi|168986247|dbj|BAG11805.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H7]
 gi|168986249|dbj|BAG11806.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H7]
 gi|168986251|dbj|BAG11807.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H7]
 gi|168986253|dbj|BAG11808.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H7]
 gi|168986255|dbj|BAG11809.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H7]
 gi|168986259|dbj|BAG11811.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H6]
 gi|168986261|dbj|BAG11812.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H6]
 gi|258642983|gb|ACV86055.1| RNA polymerase sigma factor [Shigella flexneri]
          Length = 177

 Score =  122 bits (307), Expect = 6e-26,   Method: Composition-based stats.
 Identities = 44/186 (23%), Positives = 84/186 (45%), Gaps = 10/186 (5%)

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     
Sbjct: 1   IARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRT 60

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           +++      K L   LR  +     ++           IA++L+    +V  M       
Sbjct: 61  IRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERI 115

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            S++  +    +     +  L    D +E    +  +  + +  + + +  LN ++R + 
Sbjct: 116 TSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVL 170

Query: 244 EARRLQ 249
             R   
Sbjct: 171 ARRFGL 176


>gi|291532045|emb|CBK97630.1| RNA polymerase sigma factor, FliA/WhiG family/RNA polymerase sigma
           factor, sigma-70 family [Eubacterium siraeum 70/3]
          Length = 251

 Score =  122 bits (307), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 51/264 (19%), Positives = 119/264 (45%), Gaps = 24/264 (9%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGL 86
            K+    L ++YR  GD++  + +V  ++ LV  IA+  R          ++++EG I L
Sbjct: 5   SKERLNELLEKYRLTGDMNVRNEIVLMYMDLVKMIAVSMRNIYTGYAESDDIINEGVIAL 64

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ--KRLFFNLRRLKG 144
           M A+  FDPE+  +  TY+   IK A+ +Y+ +   L ++  T  +  K+L  N  RL  
Sbjct: 65  MAAIDGFDPEKNVKFETYAGIRIKGAVIDYLRK---LDRVPRTLRKLSKQLDDNFARLNS 121

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L        +      +A+ +N++ +++  +    AG  +L+            ++D L
Sbjct: 122 EL-------CRTPTDEELAESMNMTTAQLSKLMANTAGMITLSF-------EELLYEDNL 167

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             +     +    K   + ++ ++  +++ L  +E+++      +    +   ++    +
Sbjct: 168 DENISASSETADAKMYEREKKQVIADAVATLPEKEKQVVTMYYYERLKYS--EIAKVMSI 225

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           ++ RV QI ++A   ++  ++  +
Sbjct: 226 TQSRVCQIHSKAMLTLKNKLESYI 249


>gi|225850934|ref|YP_002731168.1| RNA polymerase sigma-D factor (Sigma-28) [Persephonella marina
           EX-H1]
 gi|225645790|gb|ACO03976.1| RNA polymerase sigma-D factor (Sigma-28) [Persephonella marina
           EX-H1]
          Length = 241

 Score =  122 bits (306), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 44/245 (17%), Positives = 111/245 (45%), Gaps = 20/245 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
            + ++   L  +  I    +   LP      ++++ G +GL+ A+ K+DP +G +L+TY+
Sbjct: 8   RNEIIMEFLPKINYIVQSLKQENLPPTVTEEDLINTGVLGLIDAINKYDPSKGVKLSTYA 67

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
              I+  + + + +   L  +     QK      R ++  +  +     +      IA+ 
Sbjct: 68  EIRIRGQIIDSLRK---LDWVPRNVRQKA-----RHIEAAILEVEQKLGREATPEEIAEY 119

Query: 166 LNVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           L +   E +    ++  +G  S++  + S +  +++    +  + D  ++ + E+E +K 
Sbjct: 120 LGMDVEEYMKYAEKISNSGLISIDTTVGSDEDANTKLWQIISINDDTPDKYVEEEELKK- 178

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
              +++  +S LN RER +      +E  ++++ +     ++  R+ QI  +   K++  
Sbjct: 179 ---IISDIISKLNERERLVITLYYYEE--LSMKEIGEVLGLTESRISQIHTKTMMKIKSM 233

Query: 284 IQKQV 288
           I+K +
Sbjct: 234 IKKYI 238


>gi|167750707|ref|ZP_02422834.1| hypothetical protein EUBSIR_01685 [Eubacterium siraeum DSM 15702]
 gi|167656386|gb|EDS00516.1| hypothetical protein EUBSIR_01685 [Eubacterium siraeum DSM 15702]
          Length = 251

 Score =  122 bits (306), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 51/265 (19%), Positives = 120/265 (45%), Gaps = 24/265 (9%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGL 86
            K+    L ++YR  GD++  + +V  ++ LV  IA+  R          ++++EG I L
Sbjct: 5   SKERLNELLEKYRLTGDMNVRNEIVLMYMDLVKMIAVSMRNIYTGYAESDDIINEGVIAL 64

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ--KRLFFNLRRLKG 144
           M A+  FDPE+  +  TY+   IK A+ +Y+ +   L ++  T  +  K+L  N  RL  
Sbjct: 65  MAAIDGFDPEKNVKFETYAGIRIKGAVIDYLRK---LDRVPRTLRKLSKQLDDNFARLNS 121

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L        +      +A+ +N++ +++  +    AG  +L+            ++D L
Sbjct: 122 EL-------CRTPTDEELAESMNMTTAQLSKLMANTAGMITLSF-------EELLYEDNL 167

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             +     +    K   + ++ ++  +++ L  +E+++      +    +   ++    +
Sbjct: 168 DENISASSETADAKMYEREKKQVIADAVATLPEKEKQVVTMYYYERLKYS--EIAKVMSI 225

Query: 265 SRERVRQIEARAFKKVQESIQKQVE 289
           ++ RV QI ++A   ++  ++  ++
Sbjct: 226 TQSRVCQIHSKAMLTLKNKLESYIK 250


>gi|312128148|ref|YP_003993022.1| RNA polymerase, sigma 28 subunit, flia/whig subfamily
           [Caldicellulosiruptor hydrothermalis 108]
 gi|311778167|gb|ADQ07653.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor hydrothermalis 108]
          Length = 219

 Score =  122 bits (306), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 57/257 (22%), Positives = 99/257 (38%), Gaps = 64/257 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI-SEVVSEGNIG 85
           PM  ++EE  L K +   G   A + L+  +LRLV  IA  Y      +  +++S G IG
Sbjct: 13  PMSSEEEEMYLNKMW--EGCKEARNILIEKNLRLVAHIAKKYTFSFPNLTDDIISVGTIG 70

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A++ +   +  +L+TY+   I+  +  Y                      LR+ K  
Sbjct: 71  LIKAIETYSTAKCTKLSTYAAKCIENEILMY----------------------LRQNKKF 108

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           L  +                         S+   +  D          D N     D L 
Sbjct: 109 LSQL-------------------------SLENPIGSD---------KDGNEITLMDVLQ 134

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFE 263
            D D  ++ +  K + KN    L + +     RE++I E R   +N    T   +++   
Sbjct: 135 NDQDDIDEQVDLKIQIKNLLKKLDKILKG---REKKIIELRYGLKNGIERTQMEVANLLG 191

Query: 264 VSRERVRQIEARAFKKV 280
           +SR  V +IE +A +K+
Sbjct: 192 ISRSYVSRIEKKALQKL 208


>gi|228993082|ref|ZP_04153005.1| RNA polymerase sigma-28 factor [Bacillus pseudomycoides DSM 12442]
 gi|228999132|ref|ZP_04158714.1| RNA polymerase sigma-28 factor [Bacillus mycoides Rock3-17]
 gi|229006680|ref|ZP_04164314.1| RNA polymerase sigma-28 factor [Bacillus mycoides Rock1-4]
 gi|228754541|gb|EEM03952.1| RNA polymerase sigma-28 factor [Bacillus mycoides Rock1-4]
 gi|228760749|gb|EEM09713.1| RNA polymerase sigma-28 factor [Bacillus mycoides Rock3-17]
 gi|228766730|gb|EEM15370.1| RNA polymerase sigma-28 factor [Bacillus pseudomycoides DSM 12442]
          Length = 228

 Score =  122 bits (306), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 49/256 (19%), Positives = 91/256 (35%), Gaps = 64/256 (25%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+    E+  L     E GD  A + L+  +LRLV  I   +   G    +++S G IGL
Sbjct: 20  PLSSDDEKKYL--ELMEQGDAHARNLLIEHNLRLVAHIVKKFENTGEDSEDLISIGTIGL 77

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A++ +   +G +LATY+   I                      +  +  +LR LK   
Sbjct: 78  IKAIESYSAGKGTKLATYAARCI----------------------ENEILMHLRVLKKT- 114

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                               D SL+  I    + +   +  L+ 
Sbjct: 115 ----------------------------------KKDVSLHDPIGQDKEGN---EISLID 137

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEV 264
               + + +I+  +       +   + +L+ RE+ +   R     +   T   ++    +
Sbjct: 138 ILKSESEDVIDMIQLSMELEKIKEYIDILDEREKEVIVKRFGLGLDKEKTQREIAKALGI 197

Query: 265 SRERVRQIEARAFKKV 280
           SR  V +IE RA  K+
Sbjct: 198 SRSYVSRIEKRALMKM 213


>gi|23099454|ref|NP_692920.1| sporulation sigma factor SigK [Oceanobacillus iheyensis HTE831]
 gi|22777683|dbj|BAC13955.1| RNA polymerase sigma 28 (sigam K) factor [Oceanobacillus iheyensis
           HTE831]
          Length = 234

 Score =  122 bits (306), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 55/276 (19%), Positives = 105/276 (38%), Gaps = 63/276 (22%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           + +I+   +    Y+        L   +E    +  +E GD  A ++L+  +LRLV  I 
Sbjct: 8   LGLIIKEALFFVSYVKNHSFPQPLPPDKESKYLQLMQE-GDEVARNKLIEHNLRLVAHIV 66

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             +   G  + +++S G IGL++ V+ F  ++G +LATY+   I+  +            
Sbjct: 67  KKFENTGEDMEDLISIGTIGLIKGVESFSTDKGTKLATYAARCIENEI------------ 114

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
                       +LR LK                            + +S++  +  D  
Sbjct: 115 ----------LMHLRALKK-------------------------VKKDVSLHDPIGQD-- 137

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
                   + N     D L  +++     +IE  +     + + +  SVL+ RER +   
Sbjct: 138 -------KEGNEISLIDILEAENEN----VIEYIQLNMEISKMQKYFSVLDKREREVIVY 186

Query: 246 RRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKK 279
           R    +   +T   ++ +  +SR  V +IE RA  K
Sbjct: 187 RYGLNDREEMTQREIAKKLNISRSYVSRIEKRALMK 222


>gi|297203565|ref|ZP_06920962.1| RNA polymerase sigma-B factor [Streptomyces sviceus ATCC 29083]
 gi|297148443|gb|EFH28990.1| RNA polymerase sigma-B factor [Streptomyces sviceus ATCC 29083]
          Length = 265

 Score =  122 bits (306), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 44/236 (18%), Positives = 97/236 (41%), Gaps = 15/236 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             ++V + L +  ++A  +R  G    ++     +GL++AV ++DP  G    +Y++  I
Sbjct: 38  RGQVVEAWLPMADRLAGRFRSRGESFDDLRQVAALGLVKAVDRYDPALGHAFESYAVPTI 97

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKPEQVVAIAKKLNV 168
              ++ +       + +       R      R++   Q +      +   V  IA+  ++
Sbjct: 98  TGEIKRHFRDHMWTLHVPRRVQDLR-----NRVRIASQDLAQTIPGRRPTVAEIAEHASM 152

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SE +V+     L   ES +AL   ++   S+    L       +  L    +    R  +
Sbjct: 153 SEEDVL---VGLEALESFSALSLDAELPGSEDGYSLADALGSFDPAL----DTVVDRESV 205

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              ++ L  RER I   R   +  +T   ++ +  +S+  V ++ +R   +++E I
Sbjct: 206 KPRLAALPERERAILYMRFFGD--MTQSRIAEQLGISQMHVSRLISRCCGRMREQI 259


>gi|220931430|ref|YP_002508338.1| sporulation sigma factor SigK [Halothermothrix orenii H 168]
 gi|219992740|gb|ACL69343.1| sporulation sigma factor SigK [Halothermothrix orenii H 168]
          Length = 232

 Score =  122 bits (306), Expect = 7e-26,   Method: Composition-based stats.
 Identities = 54/268 (20%), Positives = 104/268 (38%), Gaps = 64/268 (23%)

Query: 16  LSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           L  YI   +  P  L  +EE    KR R+ GD  A + L+  +LRLV  I   Y      
Sbjct: 15  LVSYIRNGKVFPQPLSPEEEEKYIKRMRQ-GDEEARNILIEHNLRLVAHIVKKYNSVYTD 73

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
             +++S G IGL++ +  +D  +  +LATY+   I+  +  ++                 
Sbjct: 74  NEDLISIGTIGLIKGINTYDETKKTKLATYAARCIENEILMHL----------------- 116

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
                      ++ +++  L  E + +     +++  +V+        D  +N +  S D
Sbjct: 117 ---------RSVKKLSNETLLQESIGSDKDGNDITLMDVLD----TREDSVINKVEKSID 163

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENP 252
           +                                L   +  L+PRE+++ E R   L    
Sbjct: 164 EE------------------------------QLYNKLGELSPREKKVLELRYGLLDGKR 193

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKV 280
           +T + ++S   +SR  V +IE +A +++
Sbjct: 194 LTQKEVASILGISRSYVSRIEKKAIQEL 221


>gi|170078529|ref|YP_001735167.1| RNA polymerase sigma factor SigF [Synechococcus sp. PCC 7002]
 gi|5359699|gb|AAD42767.1|AF121848_2 SigF [Synechococcus sp. PCC 7002]
 gi|169886198|gb|ACA99911.1| SigF [Synechococcus sp. PCC 7002]
          Length = 259

 Score =  122 bits (306), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 50/253 (19%), Positives = 113/253 (44%), Gaps = 18/253 (7%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG-LPISEVVSEGNIGLMQAVKKFD 94
            L + YR+  D+   +++V+ ++ LV K A  +         +++  G++GL++A+++F 
Sbjct: 18  ELLQEYRQSQDVKIRNQIVSLNIGLVRKEAHHWSRQCSENFDDLMQVGSLGLLRAIERFT 77

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
            ERG   ++++  +I+  +Q Y+    S V+I     Q R     ++    +      + 
Sbjct: 78  LERGNAFSSFANPYIRGEIQHYLRDKSSTVRIPRRMLQLR-----QQSNRFIHTFRQEHN 132

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +    + IA+ LN+S +E  S+N         SL+  + +    ++   D +        
Sbjct: 133 RQPSAIEIAEHLNISVTEWQSINLAYQNRDPVSLDVSVKADQGENTSLGDLVPDPGYKSF 192

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV-RQ 271
           Q+ IE + R      + + ++ L    R++ E   L +  +T +  +    VS   V R+
Sbjct: 193 QLAIEDQIR------IQQGLAQLEEHTRKVLEFVFLHD--LTQKEAADLLGVSVITVSRR 244

Query: 272 IEARAFKKVQESI 284
           I  +    +++ +
Sbjct: 245 I-KKGINSLKKIL 256


>gi|253580726|ref|ZP_04857990.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251848097|gb|EES76063.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 209

 Score =  122 bits (306), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 52/256 (20%), Positives = 95/256 (37%), Gaps = 62/256 (24%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L   +E    ++Y+E GD  A + L+  +LRLV  +   Y+G G    +++S G IGL+
Sbjct: 7   PLSISQEKYYLQKYQE-GDSQAKNILIEHNLRLVAHVVKKYQGTGEDTDDLISIGTIGLI 65

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV  F+P++  RL+TY+   I                      +  L    R  K H +
Sbjct: 66  KAVTTFNPQKASRLSTYAARCI----------------------ENELLMYFRAKKKHSK 103

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                                     +S+   +  D          + N     D +   
Sbjct: 104 E-------------------------VSLYEPIGTD---------KEGNEINLLDVI--- 126

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVS 265
                 ++ +   R+N   +L     VL+ +E ++   R         T   ++ +  +S
Sbjct: 127 ESAPVDIVEDCYIRENTDYLLRSLKKVLSDKEYQVICCRYGLFGMEEETQREIARKLCIS 186

Query: 266 RERVRQIEARAFKKVQ 281
           R  V +IE  A +K++
Sbjct: 187 RSYVSRIEKTALQKLR 202


>gi|150390456|ref|YP_001320505.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Alkaliphilus
           metalliredigens QYMF]
 gi|149950318|gb|ABR48846.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Alkaliphilus
           metalliredigens QYMF]
          Length = 243

 Score =  122 bits (306), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 56/258 (21%), Positives = 114/258 (44%), Gaps = 23/258 (8%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG-YRGYG--LPISEVVSEGNIGLMQA 89
           E   L + Y+++ DL   + L+  ++ LV  IA   Y  YG  +   ++VS G  GL+ A
Sbjct: 2   EHQSLWQHYKQNHDLQTKNELIEKYIALVKIIAGRLYTSYGSNVDYDDLVSYGIFGLIDA 61

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           ++KFD  +  +  TY+   I+ A+ + + R+   V        K++     + +  L   
Sbjct: 62  IEKFDINKNVKFETYAQIRIRGAIIDQL-RNLDWVPRSIRQKSKKIEDAYAKAENRL--- 117

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYD 207
                +      +A++L +S  +      ++      SL   ++ +  N    Q  +  +
Sbjct: 118 ----GRSVLDFEVAQELEMSIGDFHRTLQQINSFNIVSLEERLSDTHHN----QIPIGDE 169

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           +D  EQ++  KEE    R +L  S+  L+ RE+ +           T + +    +VS  
Sbjct: 170 NDLPEQIICNKEE----RLLLRSSIESLSEREKTVVTLYYY--EGFTYKEIGQVLDVSES 223

Query: 268 RVRQIEARAFKKVQESIQ 285
           RV Q+ ++A  +++  ++
Sbjct: 224 RVSQLHSKAIVRLKGVLK 241


>gi|326773500|ref|ZP_08232783.1| RNA polymerase sigma (70) factor RpoD [Actinomyces viscosus C505]
 gi|326636730|gb|EGE37633.1| RNA polymerase sigma (70) factor RpoD [Actinomyces viscosus C505]
          Length = 311

 Score =  122 bits (306), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 40/132 (30%), Positives = 68/132 (51%), Gaps = 27/132 (20%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY----------REHGD----------------- 46
             +  Y+ +I K+ +L  ++E  LAKR            E G+                 
Sbjct: 162 DPVKDYLKQIGKVALLNAEQEVELAKRIEAGLYAEHRLAEEGNDLPAKLRRELHWVAQDG 221

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+KFD  +GF+ +TY+ 
Sbjct: 222 QRAKNHLLEANLRLVVSLAKRYTGRGMLFLDLIQEGNLGLIRAVEKFDYTKGFKFSTYAT 281

Query: 107 WWIKAAMQEYIL 118
           WWI+ A+   + 
Sbjct: 282 WWIRQAITRAMA 293


>gi|83590422|ref|YP_430431.1| sporulation sigma factor SigK [Moorella thermoacetica ATCC 39073]
 gi|83573336|gb|ABC19888.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Moorella
           thermoacetica ATCC 39073]
          Length = 226

 Score =  122 bits (306), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 57/270 (21%), Positives = 100/270 (37%), Gaps = 64/270 (23%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           ++ G   L  YI        L ++EE    + + + GD  A + L+  +LRLV  I   +
Sbjct: 13  VLKGISLLLSYISNNAFPQPLSEEEEQKYLELWLQ-GDQKARNILIEHNLRLVAHITKKF 71

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
              G    +++S G +GL++A+  ++  +G +LATY+   I+  +               
Sbjct: 72  ENTGEDTEDLISIGTVGLIKAINTYNKAKGTKLATYAARCIENEI--------------- 116

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
                    +LR LK     I                                   SL  
Sbjct: 117 -------LMHLRTLKKTRGEI-----------------------------------SLYD 134

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            I        +  +  + D  G EQ + E  E    +  + + +S L PRER++ E R  
Sbjct: 135 PIGV----DREGNEIALIDILGSEQDVAEMVESSYEQQRVRQKISTLTPRERKVLEMRYG 190

Query: 249 QENP--VTLENLSSEFEVSRERVRQIEARA 276
             +    T  +++ +  +SR  V +IE  A
Sbjct: 191 LWHGLRRTQRDIARKMGISRSYVSRIEKPA 220


>gi|117926317|ref|YP_866934.1| FliA/WhiG family RNA polymerase sigma factor [Magnetococcus sp.
           MC-1]
 gi|117610073|gb|ABK45528.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Magnetococcus sp.
           MC-1]
          Length = 260

 Score =  122 bits (306), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 44/240 (18%), Positives = 102/240 (42%), Gaps = 14/240 (5%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              ++  +  LV  +A          + + ++   G +GL+ AV KFDP+RG +  TY+ 
Sbjct: 26  REEIILKYAPLVRYVAGRISMKLPQSVDLDDLYQVGVMGLIDAVSKFDPDRGIKFQTYAE 85

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           + I+ A+ + +               ++L  N  +++     +     +P + V +A+ L
Sbjct: 86  FRIRGAILDELR--------AIDWVPRQLRQNASQMQEAYNQLEAKFGRPAEDVEVAEHL 137

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +S +E      ++ G  S+ +  +    N  +  D L    D   Q  +E       R+
Sbjct: 138 GISLNEYHEQIDQVRG-ISIVSFEDIRPNNDDEEWDVLEVLADPSVQDPVEAIGLMELRH 196

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  +ER +      +E  +T+  +     ++  R+ Q+ ++A  +++  I++
Sbjct: 197 AMADAIETLPEKERLVVTLYYFEE--LTMSEIGEVLGLTESRISQLHSKAALRMRARIKR 254


>gi|78044674|ref|YP_359860.1| RNA polymerase sigma factor for flagellar operon [Carboxydothermus
           hydrogenoformans Z-2901]
 gi|77996789|gb|ABB15688.1| RNA polymerase sigma factor for flagellar operon [Carboxydothermus
           hydrogenoformans Z-2901]
          Length = 254

 Score =  122 bits (306), Expect = 8e-26,   Method: Composition-based stats.
 Identities = 52/251 (20%), Positives = 116/251 (46%), Gaps = 16/251 (6%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKF 93
           L + YR +  L   + L+  +L LV K++          L   ++   G IGL++AV+ +
Sbjct: 11  LWREYRRNKSLQLRNELLEYYLPLVRKVSAAMSLKLPTHLSREDIEGYGIIGLIEAVETY 70

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D  RG +  +Y+   I+AA+ + + +   L         + ++  ++++    + + +  
Sbjct: 71  DQNRGVKFESYASLKIRAAIIDELRKQNFL--------PRSVWDKIKKVTTSEEMLLNAL 122

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            +   V  +A++L VS S+V+ +   +A    L+       + S      L  D     +
Sbjct: 123 GEEVPVEKVAEQLGVSVSDVLKIKTLIALKNHLSLDEIIDPEGSVDRFAGLADDEKYSPE 182

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
               K  ++     L  ++  L+ RER I +   ++E  ++L+ +++  ++S  RV QI 
Sbjct: 183 ---NKFLKRVEIEELREALKRLSDRERLILQLFYVEE--LSLKEIAAVLDISTSRVSQIA 237

Query: 274 ARAFKKVQESI 284
           ++A  K+++ +
Sbjct: 238 SKALGKLRKLL 248


>gi|289751356|ref|ZP_06510734.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis T92]
 gi|289691943|gb|EFD59372.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis T92]
          Length = 470

 Score =  121 bits (305), Expect = 9e-26,   Method: Composition-based stats.
 Identities = 42/143 (29%), Positives = 73/143 (51%), Gaps = 31/143 (21%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------REHGDL- 47
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+  
Sbjct: 215 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSERGEKL 273

Query: 48  ----------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++AV+
Sbjct: 274 PAAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRAVE 333

Query: 92  KFDPERGFRLATYSMWWIKAAMQ 114
           KFD  +G++ +TY+ WWI+ A+ 
Sbjct: 334 KFDYTKGYKFSTYATWWIRQAIT 356


>gi|29833942|ref|NP_828576.1| RNA polymerase sigma factor [Streptomyces avermitilis MA-4680]
 gi|29611067|dbj|BAC75111.1| putative RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
          Length = 264

 Score =  121 bits (305), Expect = 9e-26,   Method: Composition-based stats.
 Identities = 49/241 (20%), Positives = 101/241 (41%), Gaps = 23/241 (9%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +    +V + L +  +IA  YRG G    ++     +GL++AV ++DP RG    +Y++
Sbjct: 35  QALRDEIVRAWLPMAERIAWRYRGRGESTEDLCQVAAVGLVKAVDRYDPARGNAFESYAV 94

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKPEQVVAIAKK 165
             I   ++ +      ++ +       R      R++   + ++         V  IA+ 
Sbjct: 95  PTITGEIKRHFRDHMWVLHVPRRVQDLR-----NRVRVAAKELSQTVPGHEPTVTEIAEH 149

Query: 166 LNVSESEVI----SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
             +SE +V     +M+   A   SL+A +  SD   +   D L     G + V+      
Sbjct: 150 AQLSEDDVQIGLEAMDTFTA--LSLDAELPGSDDGYA-LSDALGGPDSGYDLVV------ 200

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              R  +  S+  L  RER I   R  +   +T  +++ +  +S+  V ++ +    +++
Sbjct: 201 --DREAVKPSLRALPERERTILYLRYFRG--MTQSSIAEQLGISQMHVSRLISGCCARMR 256

Query: 282 E 282
           E
Sbjct: 257 E 257


>gi|206975995|ref|ZP_03236905.1| RNA polymerase sigma-27 factor [Bacillus cereus H3081.97]
 gi|206745747|gb|EDZ57144.1| RNA polymerase sigma-27 factor [Bacillus cereus H3081.97]
          Length = 237

 Score =  121 bits (305), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 49/265 (18%), Positives = 92/265 (34%), Gaps = 63/265 (23%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
            Y+        L   +E    +   E GD  A + L+  +LRLV  I   +   G    +
Sbjct: 19  SYVKNNAFPQPLSSDDERKYLELM-EQGDAQARNLLIEHNLRLVAHIVKKFENTGEDAED 77

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++S G IGL++A++ +   +G +LATY+   I                      +  +  
Sbjct: 78  LISIGTIGLIKAIESYSAGKGTKLATYAARCI----------------------ENEILM 115

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
           +LR LK                                       D SL+  I    + +
Sbjct: 116 HLRVLKKT-----------------------------------KKDVSLHDPIGQDKEGN 140

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTL 255
              +  L+     + + +I+  +       +   + +L+ RE+ +   R     +   T 
Sbjct: 141 ---EISLIDILKSESEDVIDMIQLSMELEKIKEYIDILDEREKEVIVKRFGLGLDKEETQ 197

Query: 256 ENLSSEFEVSRERVRQIEARAFKKV 280
             ++    +SR  V +IE RA  K+
Sbjct: 198 REIAKALGISRSYVSRIEKRALMKM 222


>gi|119718035|ref|YP_925000.1| sigma-70 region 2 domain-containing protein [Nocardioides sp.
           JS614]
 gi|119538696|gb|ABL83313.1| sigma-70 region 2 domain protein [Nocardioides sp. JS614]
          Length = 257

 Score =  121 bits (305), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 40/239 (16%), Positives = 93/239 (38%), Gaps = 19/239 (7%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
               +L+  ++ + V     +RG G+   ++     +GL++AVK FDP+RG    ++++ 
Sbjct: 30  EIEDQLIRLNMAVAVDATRRFRGRGIATDDLEQVAYVGLVKAVKGFDPDRGHDFLSFAIP 89

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+  ++ +       V+   +  + +      ++      +     +  +   IA+ L 
Sbjct: 90  TIRGEVRRHFRDLGWTVRPPRSIQEAQT-----KIIACEGELYQQLGRAPRPSEIAEHLG 144

Query: 168 VSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           +    V+            SL+A  +  D +    +               E  +    R
Sbjct: 145 LDRDLVVEALGASGCFAPASLDAPAHEGDDDPIGRRLGFTD----------EGFDVAEAR 194

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +L   ++ L+ RER I E R  +    T   +     V++ +V ++  R   +++E +
Sbjct: 195 AVLAPVLAKLSKRERIIVEMRFFRG--CTQAQIGEAIGVTQMQVSRLLTRLMARLREEL 251


>gi|17231345|ref|NP_487893.1| RNA polymerase sigma factor SigF [Nostoc sp. PCC 7120]
 gi|17132987|dbj|BAB75552.1| group 3 sigma 37-type sigma factor [Nostoc sp. PCC 7120]
          Length = 258

 Score =  121 bits (305), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 45/255 (17%), Positives = 109/255 (42%), Gaps = 16/255 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVK 91
           E + L + Y++    +  ++LV  +L LV K A  +         ++V  G +GL++A++
Sbjct: 12  EIWQLLREYQQSRSETVRNQLVKLNLGLVRKEAHYWMNQCRENYDDLVQVGCLGLIRAIE 71

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           +F+  +G   +++++ +I+  +Q Y+      V+I      +R     +R  G  +++ +
Sbjct: 72  RFEIAKGHAFSSFAIPYIRGEIQHYLRDKGVTVRIP-----RRYLAIQQRAIGVSRSLRE 126

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHD 209
              +      +A  L +S  E   +          SL+  +   ++ ++   + +   H 
Sbjct: 127 QYNRQPTDSELATALEISPDEWQEIKLAWVNRAPLSLDVPVQDGEEGATSLGELVPDHHY 186

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
              Q+  E + R      L +++  L  R R + E   LQ+  +T + ++    +S   V
Sbjct: 187 RSFQLAQEDQIR------LQQALFQLEQRTREVLECVFLQD--LTQKQVAEHLGISVVTV 238

Query: 270 RQIEARAFKKVQESI 284
            +   +    ++  +
Sbjct: 239 SRRVKKGLDLLKHLM 253


>gi|143615|gb|AAA22791.1| sporulation protein [Bacillus subtilis]
          Length = 195

 Score =  121 bits (305), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 42/177 (23%), Positives = 74/177 (41%), Gaps = 7/177 (3%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K   L+  E   L K+  ++GD  A   L+  ++RLV  +   +   G    ++   G 
Sbjct: 9   GKNAQLKDHEVKELIKQ-SQNGDQQARDLLIEKNMRLVWSVVQRFLNRGYEPDDLFQIGC 67

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL+++V KFD     R +TY++  I   +Q +I      VK+  +   K L   +RR K
Sbjct: 68  IGLLKSVDKFDLTYDVRFSTYAVPMIIGEIQRFIRDDG-TVKVSRSL--KELGNKIRRAK 124

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
             L        +   V  IA  L +   +V+     +    S++  +  +D +    
Sbjct: 125 DELSKTLG---RVPTVQEIADHLEIEAEDVVLAQEAVRAPSSIHETVYENDGDPITL 178


>gi|54025772|ref|YP_120014.1| putative sigma factor [Nocardia farcinica IFM 10152]
 gi|54017280|dbj|BAD58650.1| putative sigma factor [Nocardia farcinica IFM 10152]
          Length = 281

 Score =  121 bits (305), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 43/238 (18%), Positives = 92/238 (38%), Gaps = 16/238 (6%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +    ++   L L   IA  + G G    ++     +GL+QAV +FD  RG     +++
Sbjct: 47  RALREHIIGLCLPLADHIARRFSGRGEAFDDLHQTARLGLVQAVDRFDVRRGSSFLAFAV 106

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I   ++ +       +++   A + +       +    + ++  + +      IA +L
Sbjct: 107 PTIMGEVRRHFRDHTWALRVPRRAKELQAM-----IGPATEKLSQRHGRMPTAREIAAEL 161

Query: 167 NVSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +V   EV    +        +L+A+    D N        + D  G E+      E    
Sbjct: 162 DVELVEVTRALVAANAYSTNTLHAVGRDDDGNVG----LSIGDSLGTEEPCYRLMEDAM- 216

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              +   ++ L  RER++   R    + +T   ++    VS+ +V +I  R   +++E
Sbjct: 217 --AVRPLIAALPERERQVLIWRFY--DSLTQSQIAERLGVSQMQVSRILNRTLTRLRE 270


>gi|325679635|ref|ZP_08159210.1| RNA polymerase sigma-E factor [Ruminococcus albus 8]
 gi|324108665|gb|EGC02906.1| RNA polymerase sigma-E factor [Ruminococcus albus 8]
          Length = 235

 Score =  121 bits (305), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 58/271 (21%), Positives = 108/271 (39%), Gaps = 64/271 (23%)

Query: 19  YIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           YI+   K+P  L K+EE    + +    +  A   L+  +LRLVV I+  +   G+ + +
Sbjct: 24  YINGADKLPPPLTKEEERKAFELFA-TDEKKAKELLIVHNLRLVVYISRKFENAGVGLED 82

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++S G+IGL++AV  F P++  +LATY+   I+  +  +                     
Sbjct: 83  LISIGSIGLIKAVNTFRPDKNIKLATYASRCIENEILMF--------------------- 121

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            LR+                                      ++ DE LN      D N 
Sbjct: 122 -LRKASQRR-------------------------------TEISIDEPLNT---DHDGNE 146

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTL 255
               D L  D D     + +  E +  + +L R +  L  RER I E R      + +T 
Sbjct: 147 LLLSDILGTDED----TVHKGIESEVEKTLLRREIDKLGERERMIMEMRFGLNGRHEMTQ 202

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           + ++    +S+  + ++E +  K ++ +++K
Sbjct: 203 KEVAQTVGISQSYISRLEKKTLKAIRANLEK 233


>gi|146295930|ref|YP_001179701.1| sporulation sigma factor SigK [Caldicellulosiruptor saccharolyticus
           DSM 8903]
 gi|145409506|gb|ABP66510.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK
           [Caldicellulosiruptor saccharolyticus DSM 8903]
          Length = 220

 Score =  121 bits (305), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 65/272 (23%), Positives = 105/272 (38%), Gaps = 64/272 (23%)

Query: 19  YIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI-S 76
           YI      P  L  +EE +  K+  E G + A + L+  +LRLV  IA  Y      +  
Sbjct: 3   YIENANSFPHPLSDEEEEMHLKKMWE-GAIEARNILIEKNLRLVAHIAKKYTLSFPNLTD 61

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++S G IGL++A++ +  E+  RL+TY+   I+  +  Y                    
Sbjct: 62  DIISVGTIGLIKAIETYSQEKNTRLSTYAAKCIENEILMY-------------------- 101

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
             LR+ K  L                           IS+   +  D          D N
Sbjct: 102 --LRQNKKFLSQ-------------------------ISLENPIGSD---------KDGN 125

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVT 254
                D L  D D  +  +  K      +N+L +   +L  RE+ I E R   +N    T
Sbjct: 126 EITLIDVLQSDQDDIDDQVNVKI---QIKNLLRKLDKILKGREKHIIELRYGLKNGKERT 182

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +++   +SR  V +IE +A KK+   +QK
Sbjct: 183 QMEVANLLGISRSYVSRIEKKALKKLYNELQK 214


>gi|239626528|ref|ZP_04669559.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47_FAA]
 gi|239516674|gb|EEQ56540.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47FAA]
          Length = 209

 Score =  121 bits (305), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 51/261 (19%), Positives = 91/261 (34%), Gaps = 62/261 (23%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L   EE    +R +E GD SA   L+  ++RLV  +   Y+G    + +++S G IGL+
Sbjct: 7   PLSAGEEKEYLERCKE-GDQSARDMLIEHNMRLVAHVVKKYQGSDYDMEDLLSVGTIGLI 65

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV  F+ ++G RLATY+   ++  +                         L R      
Sbjct: 66  KAVNTFNADKGSRLATYAARCVENEILM-----------------------LLRASKKFS 102

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                                     +S+   +  D          D  +    D +  D
Sbjct: 103 KE------------------------VSLFEPIGVD---------KDGETVSLVDVIEMD 129

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVS 265
           +      +I K++ K          S L   E+ +   R         T   ++    +S
Sbjct: 130 NKETLDTMILKQDVKELYEAFE---SCLTETEKTVLGMRYGLYRGKEHTQREIAGNLGIS 186

Query: 266 RERVRQIEARAFKKVQESIQK 286
           R  V +IE +A +K++    +
Sbjct: 187 RSYVSRIEKKAIEKIRAEFSR 207


>gi|158340157|ref|YP_001521327.1| sigma-28 subunit [Acaryochloris marina MBIC11017]
 gi|158310398|gb|ABW32013.1| sigma-28 subunit [Acaryochloris marina MBIC11017]
          Length = 421

 Score =  121 bits (305), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 56/258 (21%), Positives = 110/258 (42%), Gaps = 21/258 (8%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             + GD     R +  + RLV K A  YRG     +++V+ GN GL +A++KFD  +G +
Sbjct: 28  LAQAGDRRTEDRFIRKNQRLVFKEANRYRGL-DDWNDLVTAGNWGLARAIEKFDVSKGCK 86

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            ++Y++  I+  +Q+++     L         K +  +L+ +K   Q +     +   + 
Sbjct: 87  FSSYAVKVIRTEIQQFLNDQRGL--------SKEIAKHLKDIKQASQKLEWELERQPTLE 138

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            ++++   S+  + S   R    E+ +  I   +   ++  D +  D D     L +  E
Sbjct: 139 ELSERTGYSQRIITSTLDRARVVETSSLNIPVGENLKAEQIDLVEGDDD-----LWDYAE 193

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             + +  + +    L  R   I  ARR   +  +   +   F +S ER+RQ+   A   +
Sbjct: 194 NIDEKEYIAQ----LPERYNVIVRARR---DGHSYRAIGRMFGLSGERIRQLFKEALAYL 246

Query: 281 QESIQKQVELSSSPPLLQ 298
           +  +     L   P  LQ
Sbjct: 247 KHLVTYGACLVRFPQPLQ 264


>gi|291558216|emb|CBL35333.1| RNA polymerase sigma factor, FliA/WhiG family/RNA polymerase sigma
           factor, sigma-70 family [Eubacterium siraeum V10Sc8a]
          Length = 251

 Score =  121 bits (305), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 51/264 (19%), Positives = 118/264 (44%), Gaps = 24/264 (9%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGL 86
            K+    L ++YR  GD++  + +V  ++ LV  IA+  R          ++++EG I L
Sbjct: 5   SKERLNELLEKYRLTGDMNVRNEIVLMYMDLVKMIAVSMRNIYTGYAESDDIINEGVIAL 64

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ--KRLFFNLRRLKG 144
           M A+  FDPE+  +  TY+   IK A+ +Y+ +   L ++  T  +  K+L  N  RL  
Sbjct: 65  MAAIDGFDPEKNVKFETYAGIRIKGAVIDYLRK---LDRVPRTLRKLSKQLDDNFARLNS 121

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L        +      +A+ +N++ +++  +    AG  +L+            ++D L
Sbjct: 122 EL-------CRTPTDEELAESMNMTTAQLSKLMANTAGMITLSF-------EELLYEDNL 167

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
                   +    K   + ++ ++  +++ L  +E+++      +    +   ++    +
Sbjct: 168 DESISASSETADAKMYEREKKQVIANAVATLPEKEKQVVTMYYYERLKYS--EIAKVMSI 225

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           ++ RV QI ++A   ++  ++  +
Sbjct: 226 TQSRVCQIHSKAMLTLKNKLESYI 249


>gi|212639538|ref|YP_002316058.1| RNA polymerase sigma factor SigD [Anoxybacillus flavithermus WK1]
 gi|212561018|gb|ACJ34073.1| DNA-directed RNA polymerase specialized sigma subunit
           [Anoxybacillus flavithermus WK1]
          Length = 243

 Score =  121 bits (305), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 47/256 (18%), Positives = 106/256 (41%), Gaps = 20/256 (7%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFD 94
            +++ +  D  A  +L+  ++ LV              +   ++ S   +GL  A++KFD
Sbjct: 3   WQKWIDTRDREAGDQLIEKYMPLVDYHVQRIASSLPKSVKKEDLKSLALLGLYDALEKFD 62

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P R  +  TY+ + I+ A+ + + +      +  +  +K      ++++  ++ +   ++
Sbjct: 63  PSRDLKFDTYASFRIRGAILDGLRKEDW---LPRSVREKA-----KKIEATIERLQQMHM 114

Query: 155 KPEQVVAIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +      +A  LN+SE EV  +      A   SL+      D +   +        D   
Sbjct: 115 RDVSAKEVADALNISEDEVYAVMNEQFFANVLSLDERPFDDDDDQPSFTI-----RDDHS 169

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
               E   R+ +   L + +  LN +E+ +       +  +T   +     +S  R+ QI
Sbjct: 170 PSPEEHMLREEQIAQLAQVIQQLNEKEQLVISLFY--KEELTFTEIGHIMGLSTSRISQI 227

Query: 273 EARAFKKVQESIQKQV 288
            A+A  K+++ I++ V
Sbjct: 228 HAKALFKMRKLIEQAV 243


>gi|47569335|ref|ZP_00240019.1| RNA polymerase sigma-K factor [Bacillus cereus G9241]
 gi|228967406|ref|ZP_04128439.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           sotto str. T04001]
 gi|47554006|gb|EAL12373.1| RNA polymerase sigma-K factor [Bacillus cereus G9241]
 gi|228792294|gb|EEM39863.1| RNA polymerase sigma-28 factor [Bacillus thuringiensis serovar
           sotto str. T04001]
          Length = 228

 Score =  121 bits (305), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 49/265 (18%), Positives = 92/265 (34%), Gaps = 63/265 (23%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
            Y+        L   +E    +   E GD  A + L+  +LRLV  I   +   G    +
Sbjct: 10  SYVKNNAFPQPLSSDDERKYLELM-EQGDAQARNLLIEHNLRLVAHIVKKFENTGEDAED 68

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++S G IGL++A++ +   +G +LATY+   I                      +  +  
Sbjct: 69  LISIGTIGLIKAIESYSAGKGTKLATYAARCI----------------------ENEILM 106

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
           +LR LK                                       D SL+  I    + +
Sbjct: 107 HLRVLKKT-----------------------------------KKDVSLHDPIGQDKEGN 131

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTL 255
              +  L+     + + +I+  +       +   + +L+ RE+ +   R     +   T 
Sbjct: 132 ---EISLIDILKSESEDVIDMIQLSMELEKIKEYIDILDEREKEVIVKRFGLGLDKEKTQ 188

Query: 256 ENLSSEFEVSRERVRQIEARAFKKV 280
             ++    +SR  V +IE RA  K+
Sbjct: 189 REIAKALGISRSYVSRIEKRALMKM 213


>gi|325678908|ref|ZP_08158506.1| putative RNA polymerase sigma-F factor [Ruminococcus albus 8]
 gi|324109412|gb|EGC03630.1| putative RNA polymerase sigma-F factor [Ruminococcus albus 8]
          Length = 217

 Score =  121 bits (304), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 52/238 (21%), Positives = 97/238 (40%), Gaps = 22/238 (9%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           +SA   L   +L LV   A  +RG G+   ++   G IGL++A K FD  RG + +TY++
Sbjct: 1   MSAESHLPEDNLGLVHLCANRFRGRGIEYDDLYGAGCIGLLKASKAFDSGRGVKFSTYAV 60

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I   ++  + R    VK+  +  +  L     RL G  Q     N +   V  +AK +
Sbjct: 61  PVILGEIKR-LFRDGGTVKVSRSLKELSL-----RLTGEAQVFAHKNGREPTVEELAKIV 114

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
                +VI          SL       D+N +Q         +     L           
Sbjct: 115 GTPVEDVIEALNAAQPVISL---TVGDDENETQADLPAPAPDEDITDRLA---------- 161

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L + ++ L+ ++R++ E R  Q   +T    ++   +++ +V + E +    ++  +
Sbjct: 162 -LRQVLTELDDKDRQLIELRYFQG--MTQSAAAAVLGMTQVQVSRKEKKLLLYMRSKL 216


>gi|119716157|ref|YP_923122.1| sigma-70 region 4 domain-containing protein [Nocardioides sp.
           JS614]
 gi|119536818|gb|ABL81435.1| sigma-70 region 4 domain protein [Nocardioides sp. JS614]
          Length = 282

 Score =  121 bits (304), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 44/243 (18%), Positives = 93/243 (38%), Gaps = 21/243 (8%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                R+V  +  +   +A  +R  G+P  ++      GL +AV +FDPE    L TY++
Sbjct: 56  EEVLGRVVVINRGVADAVAARFRNRGIPQEDLRQVAYEGLTKAVHRFDPELRNDLLTYAV 115

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+  +Q Y       V+      + +      R+   ++ +T    +      IA +L
Sbjct: 116 PTIRGELQRYFRDQGWTVRPPRRIQELQW-----RVNQVIERLTQERGREPSEDEIAAEL 170

Query: 167 NVSESEVISMNCRLA--GDESLNALI-NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + +  E              SL+  + +  +    +       D    E           
Sbjct: 171 DTTVEEYRDAASAFGCFQPTSLDQPVGHEGETPVGELIAGADADGPATEA---------- 220

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            R +L   +  L  R RRI   R  ++  +T E +  +  V++ +V ++ +R    +++ 
Sbjct: 221 -RMLLAPVVRRLPERHRRILYLRFFED--LTQEEIGRDLGVTQMQVSRLLSRILGDLRDE 277

Query: 284 IQK 286
           +++
Sbjct: 278 LKE 280


>gi|332653441|ref|ZP_08419186.1| RNA polymerase sigma-E factor [Ruminococcaceae bacterium D16]
 gi|332518587|gb|EGJ48190.1| RNA polymerase sigma-E factor [Ruminococcaceae bacterium D16]
          Length = 239

 Score =  121 bits (304), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 60/270 (22%), Positives = 109/270 (40%), Gaps = 64/270 (23%)

Query: 18  RYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
            YI     +P  L ++EE  L +R ++ GD  A   L+  +LRLVV IA  +   G+ I 
Sbjct: 27  MYIGGSDTLPTPLSREEEGELMERLQQ-GDQRARQTLIEHNLRLVVYIARRFENTGINIE 85

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++S G IGL++AV  + P R  +LATY+   I+  +  Y+ ++ S              
Sbjct: 86  DLISIGTIGLIKAVGTYQPARSIKLATYASRCIENEILMYLRKTSS-------------- 131

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
                                      +K  +S  E   +N    G+E L + I  +D  
Sbjct: 132 ---------------------------QKTELSFDEP--LNTDWDGNELLLSDILGTDG- 161

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVT 254
                       D   + +    +R+  R  L +    L+ RER I   R         T
Sbjct: 162 ------------DLVMRPIEADVDRQLLRQALEK----LDERERTIISLRFGLGGGEEQT 205

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + ++    +S+  + ++E R  +++++ +
Sbjct: 206 QKEVADRMGISQSYISRLEKRIIQRLKKEM 235


>gi|56964009|ref|YP_175740.1| RNA polymerase sigma factor SigD [Bacillus clausii KSM-K16]
 gi|56910252|dbj|BAD64779.1| DNA-directed RNA polymerase sigma-28 factor sigma-D [Bacillus
           clausii KSM-K16]
          Length = 254

 Score =  121 bits (304), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 53/255 (20%), Positives = 107/255 (41%), Gaps = 13/255 (5%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKK 92
            L K++ +     AA  L+  ++ LV              +   E+ S    GL+ A+ K
Sbjct: 6   ELWKQWDDEHSEVAAEALIEHYMPLVAYHVQRISNGLPSSISKDELKSHALSGLLDAIAK 65

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD +R  +  TY+ + I+ A+ + + +     ++  T   K     L ++   L+     
Sbjct: 66  FDSKRALKFDTYASFRIRGAIIDGLRKED---RLPRTIRDK--VKKLEQITEQLEQEKGR 120

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           ++ P +V A A  L   E E +      +   SL+ +++ +D        +   D   Q 
Sbjct: 121 SVLPGEVAA-AMGLPEKEIEALKREQFASHTLSLDDVMHMNDHLDPSAVAYQFEDE--QA 177

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
            +  +K   ++ R  L   +  L   E+ + +    +E  ++L  +     +S  R+ QI
Sbjct: 178 IMPDDKLVEEDTRKELAEMIKELGRNEQLVIQLSYYEE--LSLTEIGRILNLSTSRISQI 235

Query: 273 EARAFKKVQESIQKQ 287
            ARA  K+++ +QK+
Sbjct: 236 HARAIAKLRKGLQKK 250


>gi|167630135|ref|YP_001680634.1| RNA polymerase sigma-e factor [Heliobacterium modesticaldum Ice1]
 gi|167592875|gb|ABZ84623.1| RNA polymerase sigma-e factor [Heliobacterium modesticaldum Ice1]
          Length = 235

 Score =  121 bits (304), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 66/262 (25%), Positives = 107/262 (40%), Gaps = 63/262 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EEY L ++  E GDL+    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 33  PPLSNDEEYRLLEQL-EQGDLTVKSILIERNLRLVVYIARKFENTGVGIEDLVSIGTIGL 91

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FDP +  +LATY+   I+  +                         LRR     
Sbjct: 92  IKAVNTFDPLKKIKLATYASRCIENEI----------------------LMYLRRNNKTR 129

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                            ++ DE LN      D N     D L  
Sbjct: 130 SE-------------------------------VSFDEPLN---IDWDGNELLLSDVLGT 155

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEV 264
           ++D    ++ +  E +  R +L  +MS L  RERRI E R    +    T + ++    +
Sbjct: 156 END----IIYKSIEEEVDRKLLQAAMSKLTSRERRIVELRFGLRDSREKTQKEVADMLGI 211

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+  + ++E R  K++++ + +
Sbjct: 212 SQSYISRLEKRIIKRLRKEMNR 233


>gi|288553039|ref|YP_003424974.1| RNA polymerase sigma factor SigD [Bacillus pseudofirmus OF4]
 gi|288544199|gb|ADC48082.1| RNA polymerase sigma factor SigD [Bacillus pseudofirmus OF4]
          Length = 257

 Score =  121 bits (304), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 49/260 (18%), Positives = 107/260 (41%), Gaps = 16/260 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQA 89
           E   +  ++    DL A   L+  ++ +V              +   ++ S G +GL  A
Sbjct: 8   ENQKIWDKWLTSRDLDACDELIRLYMPIVNYHVQRISVGLPKNVSKDDLTSHGMLGLYDA 67

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           ++KF+P R  +  TY+ + ++ A+ + + +   L         + +   ++R++  +Q +
Sbjct: 68  LEKFNPNRDLKFDTYASFRVRGAIIDGLRKEDWL--------PRSMREKIKRVEACIQQL 119

Query: 150 TDNNLKPEQVVAIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                +      +  KL++ E EV  I     L+   S++   N SD++ S         
Sbjct: 120 EQEFGRNVSAKEVGVKLDMPEEEVYQIMNEHYLSNLLSIDERTNDSDRSDSNNSASYSAT 179

Query: 208 H-DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
             D Q +   E    +  +  L + ++ L+  E+ +       E  +TL  +     +S 
Sbjct: 180 LIDKQTKTPEESLMFEAVKEELIKGINRLSENEKLVISLFYFDE--LTLTEIGHILNLST 237

Query: 267 ERVRQIEARAFKKVQESIQK 286
            R+ QI ++A  ++ + I K
Sbjct: 238 SRISQIHSKALFRMNQLINK 257


>gi|154499842|ref|ZP_02037880.1| hypothetical protein BACCAP_03499 [Bacteroides capillosus ATCC
           29799]
 gi|150271440|gb|EDM98697.1| hypothetical protein BACCAP_03499 [Bacteroides capillosus ATCC
           29799]
          Length = 235

 Score =  121 bits (304), Expect = 1e-25,   Method: Composition-based stats.
 Identities = 48/243 (19%), Positives = 104/243 (42%), Gaps = 21/243 (8%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GD  A  R++  +  L+  I   Y G G+   ++   G +G ++AV+ FDP  G + +T
Sbjct: 14  QGDNDACARMMEENSGLIWSIVRRYYGRGVDPEDLYQLGCMGFLKAVRGFDPAFGCQFST 73

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y++  I   ++ ++      VK+     ++    ++R  +  LQA          +  +A
Sbjct: 74  YAVPKIAGEIRRFLRDDG-AVKVSRGLKERA--GSIRTARDRLQADLGRE---PTLSELA 127

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           ++  +   E+ +     A   SL           S          +G E+ ++E      
Sbjct: 128 EETGLEPEEIAAAEEANAPVASLQMETGDGFTLESVLG------TEGMEEGIVE------ 175

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            R  L  ++S L  RER++   R  +   +T +  +    VS+ ++ ++E +A + ++  
Sbjct: 176 -REALRSAVSSLPDRERQVIVLRYFRG--LTQDRTARIMGVSQVQISRVEKKAMEYLRRR 232

Query: 284 IQK 286
           +++
Sbjct: 233 LEE 235


>gi|218778853|ref|YP_002430171.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfatibacillum
           alkenivorans AK-01]
 gi|218760237|gb|ACL02703.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfatibacillum
           alkenivorans AK-01]
          Length = 252

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 53/252 (21%), Positives = 113/252 (44%), Gaps = 21/252 (8%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGF 99
           +  + +    L+T +  L    A        P   + +++S G +GL+ A+ K+D  RG 
Sbjct: 11  KSKERAKRDELITKYAYLAKLCAHRLAMRLPPSVNVDDLISAGIMGLLDALDKYDEGRGV 70

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           +  TY+ + I+ AM + + R+   V        + +   + R++           +P   
Sbjct: 71  KFRTYAEFRIRGAMLDEL-RAMDWVPRSVRKKVQEIEQAVNRVEK-------RESRPADA 122

Query: 160 VAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSD--KNSSQWQDWLVYDHDGQEQVL 215
             IA +L V      +M  +  G E  SL+  + S+D  K+  +    L+ D+   ++ L
Sbjct: 123 EEIANELGVDMDTYQNMLSKAGGIELVSLDEPLWSNDNTKDGRRTHVDLLEDNANPDRDL 182

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
           ++ E     + +L +S+S L P+E++I       ++ +TL+ +     ++  R+ QI  +
Sbjct: 183 MDSE----FKKILAQSISSLTPKEQQILSLYY--QDELTLKEVGEVMGLTESRICQIHTQ 236

Query: 276 AFKKVQESIQKQ 287
              K++  ++ Q
Sbjct: 237 CMIKLRSKLKTQ 248


>gi|239927803|ref|ZP_04684756.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 220

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 45/231 (19%), Positives = 100/231 (43%), Gaps = 19/231 (8%)

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           +  ++A  +R  G    ++     +GL++AV ++DPE G    +Y++  I   ++ +   
Sbjct: 1   MADRLAGRFRSRGESFDDLRQVAALGLVKAVDRYDPELGNAFESYAVPTITGEIKRHFRD 60

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAIT-DNNLKPEQVVAIAKKLNVSESEVISMNC 178
               + +     + R      R++   Q ++   + +P  V  IA+  ++SE +V +   
Sbjct: 61  HMWTLHVPRRVQELR-----NRVRSASQDLSLSGSGRPPTVAEIAEHADLSEEDVRTGQG 115

Query: 179 RLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
            L      SL+A + S D   S   D L       + V+         R  +   ++ L 
Sbjct: 116 ALDSFTALSLDAELTSGDDGYS-LGDTLGAPDPALDTVV--------DREAVRERLAALP 166

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            RE+ I   R   +  +T  ++++E  +S+  V ++ +R   +++E + + 
Sbjct: 167 EREQAILYMRFFGD--MTQSSIAAELGISQMHVSRLISRCCGRIREQVMRD 215


>gi|302557289|ref|ZP_07309631.1| RNA polymerase sigma-F factor [Streptomyces griseoflavus Tu4000]
 gi|302474907|gb|EFL38000.1| RNA polymerase sigma-F factor [Streptomyces griseoflavus Tu4000]
          Length = 269

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 48/246 (19%), Positives = 101/246 (41%), Gaps = 19/246 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +    +V + L +  ++A  +R  G    ++     +GL++AV ++D E G    +Y++
Sbjct: 39  EALRDEIVEAWLPMADRLAGRFRSRGESFDDLRQVAALGLVKAVDRYDSELGNAFESYAV 98

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL-KPEQVVAIAKK 165
             I   ++ +       + +     + R      R++   Q ++     +   V  IA+ 
Sbjct: 99  PTITGEIKRHFRDHMWTLHVPRRVQELR-----NRVRYASQDLSGTTPGRRPTVTEIAEH 153

Query: 166 LNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
            ++SE +V +    L      SL+A +  SD   S   D L       + V+        
Sbjct: 154 AHLSEEDVRTGQEALESFSALSLDAELPGSDDGYS-LGDALGAPDPALDTVV-------- 204

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            R  +   ++ L  RER I   R   +   T  +++ E  +S+  V ++ +R   +V+E 
Sbjct: 205 DREAVKERLAELPERERAILYMRFFDD--RTQSSIAEELGISQMHVSRLISRCCGRVREQ 262

Query: 284 IQKQVE 289
           + +  E
Sbjct: 263 VMRDQE 268


>gi|302556940|ref|ZP_07309282.1| RNA polymerase sigma factor [Streptomyces griseoflavus Tu4000]
 gi|302474558|gb|EFL37651.1| RNA polymerase sigma factor [Streptomyces griseoflavus Tu4000]
          Length = 285

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 51/251 (20%), Positives = 106/251 (42%), Gaps = 20/251 (7%)

Query: 36  VLAKRYREHGD----LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            L  R  E  D     +    LVT+ L +  +IA  +R  G  + ++     +GL++A+ 
Sbjct: 30  ALFTRMAELQDGPERDAVRDELVTAWLPMAHRIAGRFRDRGEAVEDLRQVAALGLVKAID 89

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           +FDP RG    +Y++  I   ++ +       +++     + R      +++   + +T 
Sbjct: 90  RFDPSRG-AFESYAVPTITGEVKRHFRDRMWALRVPRRVQELR-----NKVRVARRELTQ 143

Query: 152 NNLKPE-QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
           +   PE  V AIA    ++E EV +    L    +L+     S  +        +   D 
Sbjct: 144 SPGSPEPSVAAIAAHTGLTEDEVGAGMEALESFSTLSLDAELSSDDDGYSLADTLGASDS 203

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
              V++++E  K         +  L  RER I   R  ++  +T   ++ +  +S+  V 
Sbjct: 204 SYDVVVDRESAK-------EGLRRLPERERAILYMRFFED--MTQSRIADQLGISQMHVS 254

Query: 271 QIEARAFKKVQ 281
           ++ +R+  +V+
Sbjct: 255 RLISRSCARVR 265


>gi|307265198|ref|ZP_07546757.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
 gi|306919820|gb|EFN50035.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter wiegelii Rt8.B1]
          Length = 230

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 60/248 (24%), Positives = 91/248 (36%), Gaps = 66/248 (26%)

Query: 39  KRYRE---HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           K+Y E   +GD  A + L+  +LRLV  +   Y G G  I +++S G IGL++A+  FD 
Sbjct: 37  KKYLEAYRNGDEEARNILIERNLRLVAHVVKKYSGTGKDIDDLISIGTIGLIKAISTFDS 96

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            +G  LATY+   I+  +   I                                      
Sbjct: 97  SKGTHLATYAARCIENEILMSIR------------------------------------- 119

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
                    K  V   + I ++                + N     D L  + D     +
Sbjct: 120 ----AEKKMKGEVFLQDPIGVDK---------------EGNEISLMDVLGTEED----EI 156

Query: 216 IEKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQI 272
            E+ E+K +   L   M SVL  RER I E R    N    T   ++    +SR  V +I
Sbjct: 157 SEQVEKKLQIKKLYSKMNSVLKNRERLIIEMRYGLYNGKVRTQREIAKMLGISRSYVSRI 216

Query: 273 EARAFKKV 280
           E +A  K+
Sbjct: 217 EKKALNKL 224


>gi|166368033|ref|YP_001660306.1| RNA polymerase sigma factor SigF [Microcystis aeruginosa NIES-843]
 gi|166090406|dbj|BAG05114.1| group 3 RNA polymerase sigma factor [Microcystis aeruginosa
           NIES-843]
          Length = 258

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 47/259 (18%), Positives = 115/259 (44%), Gaps = 16/259 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVK 91
           E   L ++Y++  D     +++  +L LV + A  +         ++V  G++GL++A++
Sbjct: 12  ETLTLFQKYQKTADNKLRDQIMELNLGLVRREAHHWVNQCHENYEDLVQVGSMGLIRAIE 71

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           +FD  +G   +++++ +I+  +Q ++      V+I      +R     R+     +    
Sbjct: 72  RFDSSKGHAFSSFAIPYIRGEIQHHLRDKSYTVRIP-----RRWLDLGRQATNVRRDFQT 126

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHD 209
            + +      I++ LN+S  E   +       E  SL+  +N+ + N++  +D +     
Sbjct: 127 IHNRQPNDTEISRALNISSEEWQEVKLAFQNREPLSLDVTVNNDEDNNTCLKDLVPDPRY 186

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
              Q+  E       R  L ++++ L  + R I E   L++  +T    + +  +S   V
Sbjct: 187 RSFQLCQED------RIRLQQALAQLEEKTRHIIEFVFLKD--LTQRETAEQLGISVVTV 238

Query: 270 RQIEARAFKKVQESIQKQV 288
            +   +  + ++E++ K+ 
Sbjct: 239 SRRVKKGLEMIKETMVKEA 257


>gi|297584063|ref|YP_003699843.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus
           selenitireducens MLS10]
 gi|297142520|gb|ADH99277.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus
           selenitireducens MLS10]
          Length = 253

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 50/254 (19%), Positives = 108/254 (42%), Gaps = 19/254 (7%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFD 94
            + + E  D SA  RL+ + L LV         +    +   ++ S G +GL  A++KFD
Sbjct: 14  WELWEEKRDRSAGDRLIEAFLPLVDYHVHRIGVHLPKNVSSDDLRSHGLMGLFDALEKFD 73

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
            +R  +  TY+ + I+ A+ + + +   L         + L    ++++   +++     
Sbjct: 74  RKRELKFDTYASFRIRGAIIDGLRQEDWL--------PRTLRDKAKKIEQVTESLEQQLG 125

Query: 155 KPEQVVAIAKKLNVSESEVI--SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +      IA +  ++E++VI  S     +   S++      D+  +    +     D Q 
Sbjct: 126 RNVSPKEIADEAGLTEADVIKTSNENFFSHLLSIDEPTQEGDQTET----YASSIADQQT 181

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
               E   ++   + L  ++  LN +E+ +      +E  +TL  +     +S  R+ QI
Sbjct: 182 LTPAESLSKQADYDELADAIQNLNEKEQLVISLFYYEE--LTLTEIGEALSLSTSRISQI 239

Query: 273 EARAFKKVQESIQK 286
            ++A  K+Q+ + K
Sbjct: 240 HSKAVYKLQQQLHK 253


>gi|10834759|gb|AAG23813.1|AF274004_5 SigB [Staphylococcus epidermidis]
          Length = 246

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 44/247 (17%), Positives = 98/247 (39%), Gaps = 24/247 (9%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             ++     K+++E+ D  A  +LV  + +L+  +A  Y        ++V  G +GL+ A
Sbjct: 12  SPEQINQWIKQHQENEDSQAQDKLVKHYRKLIESLAYRYSKGQSHHEDLVQVGMVGLIGA 71

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +FD     +   + +  +   ++ Y+      V +     +        R+K     +
Sbjct: 72  INRFDLSFDRKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIG-----PRIKKVSDEL 126

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNC------RLAGDESLNALINSSDKNSSQWQDW 203
           T+   +   +  IA++L VS+ EV+           L+ D S+ A     D ++    D 
Sbjct: 127 TNELERSPSISEIAQRLEVSDEEVLEAMEMGQSYNALSVDHSIEA---DKDGSTVTLLDI 183

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +    D          +   +R +L   + +L+ RER+I +   +    ++ +       
Sbjct: 184 MGQQDDNY--------DLTEKRMILECILPILSERERQIIQCTFI--EGLSQKETGERIG 233

Query: 264 VSRERVR 270
           +S+  V 
Sbjct: 234 LSQMHVS 240


>gi|220909315|ref|YP_002484626.1| RNA polymerase sigma factor SigF [Cyanothece sp. PCC 7425]
 gi|219865926|gb|ACL46265.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cyanothece
           sp. PCC 7425]
          Length = 262

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 52/250 (20%), Positives = 107/250 (42%), Gaps = 19/250 (7%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVKKFDP 95
           L + Y+++   S  +RLV  +L LV K A  +  Y      ++V  G++GL++A+++FD 
Sbjct: 20  LLQAYQKNPAPSLRNRLVQMNLGLVRKEAHRWLSYSTETYEDLVQVGSLGLIRAIERFDI 79

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            +G   ++++M +I+  +Q Y+      V+I      +R     ++     Q + +   +
Sbjct: 80  TKGHAFSSFAMPYIRGEIQHYLRDKSPQVRIP-----RRWQVLQKQASLVAQELREQLHR 134

Query: 156 PEQVVAIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
                 +A  L +   E   + ++       SL+A +   D  S+   + +        Q
Sbjct: 135 VPTDDEMALALGIGLQEWQQVKLSSYNRSPLSLDAPVGEDDFGSTCLGEMVPDQRYRSFQ 194

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV-RQI 272
           +  E       R  L +++  L  R   I E   L +  +T +  +    +S   V RQ+
Sbjct: 195 LAQED------RLRLQQALQTLESRTCEILEFVFLHD--LTQKETAELLGISAVTVSRQV 246

Query: 273 EA--RAFKKV 280
           +    A +K+
Sbjct: 247 KKGLIALRKL 256


>gi|153006912|ref|YP_001381237.1| RNA polymerase sigma-32 subunit RpoH [Anaeromyxobacter sp. Fw109-5]
 gi|152030485|gb|ABS28253.1| RNA polymerase, sigma 32 subunit, RpoH [Anaeromyxobacter sp.
           Fw109-5]
          Length = 238

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 69/259 (26%), Positives = 108/259 (41%), Gaps = 51/259 (19%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L+ Y+   R    L ++ E  LA R R  GD  A   LV  +L LVV +A       L 
Sbjct: 7   SLAPYLEAARGRKPLTREAERALALRAR-RGDARAKDELVRHNLALVVMVARKQSRGALR 65

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + E+V EG +GL++A++KFDP  G R +TY++WWI+A + +Y+ ++ S V+         
Sbjct: 66  LEELVQEGMLGLLRAIEKFDPNAGTRFSTYAVWWIRAYVWKYLKQARSSVR--------- 116

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
                                  +  A+A                 A D SL+  +   +
Sbjct: 117 ----------------------PRSGAVA-----------------AADLSLDTAV--DE 135

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
           +    + D L  +     +     E  +  R  L +    +      I   R  Q+ P T
Sbjct: 136 EGDVSFLDRLEDEGASPLERYERVESGERLRASLEKVRKRIGDLGWDIVHTRLQQDPPDT 195

Query: 255 LENLSSEFEVSRERVRQIE 273
           LE +   + VSRERVRQ+E
Sbjct: 196 LEQIGQRWGVSRERVRQVE 214


>gi|297154338|gb|ADI04050.1| RNA polymerase sigma factor [Streptomyces bingchenggensis BCW-1]
          Length = 268

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 44/250 (17%), Positives = 105/250 (42%), Gaps = 23/250 (9%)

Query: 38  AKRYREHGD----LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
            +R  E  D     +   ++V + + +  ++A  YR  G  + ++     +GL++AV ++
Sbjct: 26  FERIAELPDGPQKEALRQQVVEAWIPMADRLAGQYRNRGESLEDLRQVAALGLVKAVNRY 85

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN- 152
           DP RG    ++++  +   ++ +       + +     + R      R++   + ++ + 
Sbjct: 86  DPGRGSAFESFAVPTVVGEIKRHFRDHLWALHVPRRVQELR-----NRVRTAHRELSHSL 140

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDG 210
           + +   V  IA +  +SE +V +    L      SL+A +  +D   +  +D L      
Sbjct: 141 DDRAPDVEEIADRTGLSEEDVRTGVAALDSFAPLSLDAPLTGTDDGYA-LRDTLGEQEPA 199

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
            ++V+         R  +   +  L  RERRI   R   +  +T   ++ +  +S+  V 
Sbjct: 200 YDRVV--------DREAVRSGLCRLPERERRILYMRFFCD--MTQSRIAEQLGISQMHVS 249

Query: 271 QIEARAFKKV 280
           ++  R   ++
Sbjct: 250 RLINRTCSRL 259


>gi|161486847|ref|NP_781765.2| sporulation sigma factor SigE [Clostridium tetani E88]
          Length = 235

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 61/264 (23%), Positives = 113/264 (42%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L ++EE  L ++   +GD S    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 33  PPLTREEEENLVEKL-NYGDESIRSILIERNLRLVVYIARKFENTGIGIEDLVSVGTIGL 91

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FDP +  +LATY+   I+  +  Y+ R+                    ++K   
Sbjct: 92  IKAVNTFDPSKKIKLATYASRCIENEILMYLRRN-------------------NKIKSE- 131

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                        ++  + LNV             G+E L + I  +D +       +VY
Sbjct: 132 -------------ISFYEPLNVDWD----------GNELLLSDILGTDTD-------IVY 161

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEV 264
           D       + E+ +++     + +     N RE++I   R         T + ++    +
Sbjct: 162 D------YIEEEVDKELLLIAMDKL----NNREKQIVNLRFGLGGKTEKTQKEVADMLGI 211

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R  K++++ I K +
Sbjct: 212 SQSYISRLEKRIIKRLKKEINKMI 235


>gi|172058807|ref|YP_001815267.1| RNA polymerase sigma factor SigB [Exiguobacterium sibiricum 255-15]
 gi|171991328|gb|ACB62250.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Exiguobacterium
           sibiricum 255-15]
          Length = 265

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 48/257 (18%), Positives = 106/257 (41%), Gaps = 13/257 (5%)

Query: 30  EKQEEYVLAKRYREH-GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
              E   L   Y++   D      L+  +  LV  +A  +        ++V  G IGL+ 
Sbjct: 11  SDDEVLRLIDLYQQDDQDEEVHAALLARYSDLVEALARKFSRGRPIHDDLVQVGMIGLLA 70

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A+++FD E G    ++++  I   ++ +I      V +      K L   +++    L  
Sbjct: 71  ALRRFDKEFGRSFESFAVPTIIGEIKRFIRDKTWSVHVPRRI--KELGPKIKKAVEELTT 128

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
               + + +++ A  +       E + M        S+++ I +  + S+     LV + 
Sbjct: 129 ELQRSPRIDEIAARLEVSEEEVLETLEMGKSYQA-LSVDSSIEADQEGSTVTLLDLVGNQ 187

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           +     + +K        +L ++ +VL  RER I E    +   ++ +       +S+  
Sbjct: 188 ENGYDSVDQKL-------ILEKAFAVLTDRERSILECAYYRN--MSQKETGELLGISQMH 238

Query: 269 VRQIEARAFKKVQESIQ 285
           V +++ RA +K++E+I+
Sbjct: 239 VSRLQRRALQKLREAIK 255


>gi|299535719|ref|ZP_07049040.1| RNA polymerase sigma-28 factor precursor [Lysinibacillus fusiformis
           ZC1]
 gi|298728919|gb|EFI69473.1| RNA polymerase sigma-28 factor precursor [Lysinibacillus fusiformis
           ZC1]
          Length = 235

 Score =  121 bits (303), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 56/268 (20%), Positives = 97/268 (36%), Gaps = 63/268 (23%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+          K+EE    +R+   GD  A   L+  ++RLV  +   +      
Sbjct: 17  ALLGYLKGQTFHKPFSKEEEAACIERFL-GGDEQARLDLIERNMRLVAHVVKKFHPKHEQ 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + + +S G IGLM+AV+ + P++  RLATY+   I+  +  ++                 
Sbjct: 76  LDDYISIGTIGLMKAVESYTPDKKTRLATYAARCIENEILMHLRTQ-------------- 121

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
                                                + +S+   +  D          D
Sbjct: 122 ---------------------------------KKVQKDVSLFEPIGTD---------KD 139

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NP 252
            N+ Q +D L  D    E+   EK E K     L   + +L+ RE  I   R      + 
Sbjct: 140 GNALQIRDLLQCD----EESATEKLEHKEHVAQLYHYLHMLDERELEIVTLRYGLNQQDA 195

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKV 280
           +T + +++   +SR  V +IE RA  K+
Sbjct: 196 LTQKEIAARLNISRSYVSRIEKRALIKL 223


>gi|325662152|ref|ZP_08150770.1| hypothetical protein HMPREF0490_01508 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|325471601|gb|EGC74821.1| hypothetical protein HMPREF0490_01508 [Lachnospiraceae bacterium
           4_1_37FAA]
          Length = 211

 Score =  120 bits (302), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 58/256 (22%), Positives = 96/256 (37%), Gaps = 62/256 (24%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L   EE    ++Y E GDL A H L+  +LRLV  I   Y+       +++S G +GL+
Sbjct: 10  PLTSAEEQYYMQKYTE-GDLEAKHILIEHNLRLVAHIVKKYQRPEEDNEDLISIGTVGLI 68

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV  F+PE+G RL+TY+   I+  +                         LR  K   +
Sbjct: 69  KAVITFNPEKGNRLSTYAARCIENEI----------------------LMMLRSRKKSSR 106

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                                     IS+   +  D          + N  Q  D +   
Sbjct: 107 E-------------------------ISLYEPIGTDR---------EGNEIQLFDVM--- 129

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVS 265
               E +  +   + + R +  +  S L+ RER + + R     E   T   ++    +S
Sbjct: 130 ETTDEDIHEKINLKDDVRTLYEKVESELSDRERLVLKMRYGLYNEEEYTQREIAKRLGIS 189

Query: 266 RERVRQIEARAFKKVQ 281
           R  V +IE  A +K++
Sbjct: 190 RSYVSRIEKSAVEKLR 205


>gi|134300490|ref|YP_001113986.1| sporulation sigma factor SigK [Desulfotomaculum reducens MI-1]
 gi|134053190|gb|ABO51161.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Desulfotomaculum reducens MI-1]
          Length = 232

 Score =  120 bits (302), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 60/276 (21%), Positives = 99/276 (35%), Gaps = 65/276 (23%)

Query: 8   IIVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
            I+NG   L  YI     +P  L  +EE  L  +    GD  A   L+  +LRLV KIA 
Sbjct: 12  TILNGIAILVSYISS-GSLPDPLSPEEERELLLKMA-TGDKLAKTILIERNLRLVAKIAN 69

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
             +  G+   ++   G IGL++ V  FD ++  + +TY+   I+  M   + +       
Sbjct: 70  KLKDSGVDKQDLFQVGVIGLIKGVDTFDIKKARKFSTYAGVCIQNEMLMMLRKQ------ 123

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
                                                     SE   IS++  L      
Sbjct: 124 -----------------------------------------KSERNTISISEPL------ 136

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
                  D +  + QD L       E  + E  E+      L +++  LNPRE+ + + R
Sbjct: 137 ---DFDKDGSPLELQDTLA----NNEIPVDELVEKSLDVERLEKALQTLNPREKIVIKLR 189

Query: 247 RLQENPV--TLENLSSEFEVSRERVRQIEARAFKKV 280
              E     T   +    ++SR  + +IE+    K+
Sbjct: 190 YGLEGERELTQREVGKRLDISRSFISRIESSTINKL 225


>gi|126653890|ref|ZP_01725737.1| DNA-directed RNA polymerase sigma-27 factor sigma-K [Bacillus sp.
           B14905]
 gi|126589615|gb|EAZ83754.1| DNA-directed RNA polymerase sigma-27 factor sigma-K [Bacillus sp.
           B14905]
          Length = 235

 Score =  120 bits (302), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 56/268 (20%), Positives = 97/268 (36%), Gaps = 63/268 (23%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+          K+EE    +R+   GD  A   L+  ++RLV  +   +      
Sbjct: 17  ALLGYLKGQTFHKPFSKEEEAACIERFL-GGDEQARLDLIERNMRLVAHVVKKFHPKHEQ 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + + +S G IGLM+AV+ + P++  RLATY+   I+  +  ++                 
Sbjct: 76  LDDYISIGTIGLMKAVESYTPDKKTRLATYAARCIENEILMHLRTQ-------------- 121

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
                                                + +S+   +  D          D
Sbjct: 122 ---------------------------------KKVQKDVSLFEPIGTD---------KD 139

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NP 252
            N+ Q +D L  D    E+   EK E K     L   + +L+ RE  I   R      + 
Sbjct: 140 GNALQIRDLLQCD----EESATEKIEHKEHVAQLYHYLHMLDERELEIVTLRYGLNQQDA 195

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKV 280
           +T + +++   +SR  V +IE RA  K+
Sbjct: 196 LTQKEIAARLNISRSYVSRIEKRALIKL 223


>gi|326385162|ref|ZP_08206830.1| putative sigma factor [Gordonia neofelifaecis NRRL B-59395]
 gi|326196127|gb|EGD53333.1| putative sigma factor [Gordonia neofelifaecis NRRL B-59395]
          Length = 250

 Score =  120 bits (302), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 95/249 (38%), Gaps = 18/249 (7%)

Query: 39  KRYREHGDLS---AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           + YR  GD          + + L L   IA  YR  G P  ++     +GL+ AV +FDP
Sbjct: 16  RAYRPPGDPRRTILRDEAIVACLPLARHIAQRYRERGEPFDDLEQVARLGLVHAVDRFDP 75

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            +G    ++++  I   ++ +     + +++  +A + R      R++   + +   + +
Sbjct: 76  TQGNDFLSFAVPTIIGEVRRHFRDRTASIRLPRSAIELR-----GRIREAEEQLEQTHGR 130

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
                 IA  L  S   ++          +++    + D   +   + L  D  G     
Sbjct: 131 TPDDDEIAAFLGESPDAIVRARAADIAQSAVSLDAGAGDDERALLLELLGADDPGYA--- 187

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
                R  R   L  ++  L  R+R I   R       T  +++    +S+  V ++ A 
Sbjct: 188 -----RVERCLALRPAVLRLPERDRTIIGMRFY--EQRTQSDIACRMGISQMHVSRLLAA 240

Query: 276 AFKKVQESI 284
           +  +++  +
Sbjct: 241 SLGQLRAQL 249


>gi|311030102|ref|ZP_07708192.1| RNA polymerase sigma factor SigD [Bacillus sp. m3-13]
          Length = 254

 Score =  120 bits (302), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 45/255 (17%), Positives = 102/255 (40%), Gaps = 21/255 (8%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVK 91
                ++   D  A   LV  ++ LV          GLP      E+ S   +GL  A++
Sbjct: 11  AYWDLWKTKKDPDAGDFLVKKYMPLVHYHVQR-ISTGLPKSVKREELKSLAFVGLFDAIE 69

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KFDP R  +  TY+ + I+ ++ + + +      +  +  +K      +R++  L+ +  
Sbjct: 70  KFDPSRDLKFDTYASFRIRGSIIDGLRKEDW---LPRSVREKA-----KRIESTLENLEQ 121

Query: 152 NNLKPEQVVAIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
             ++   +  +A  L++ E EV  +      +   S++ +   +D+ S           D
Sbjct: 122 KLMRNATLEEVAAHLDMPEEEVSTVMHEVFYSNILSMDEMPKENDEQS----HGAYVLKD 177

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
            +     E+  +     +L   +  L   E+ +       +  +TL  +     ++  R+
Sbjct: 178 EKVISPEEELIKSELIQLLGEQIENLTENEQIVISLFY--KEELTLTEIGQVLGLTTSRI 235

Query: 270 RQIEARAFKKVQESI 284
            QI ++A  K+++ +
Sbjct: 236 SQIHSKAIFKLRKQL 250


>gi|331696199|ref|YP_004332438.1| SigB/F/G subfamily RNA polymerase sigma-28 subunit [Pseudonocardia
           dioxanivorans CB1190]
 gi|326950888|gb|AEA24585.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Pseudonocardia dioxanivorans CB1190]
          Length = 303

 Score =  120 bits (302), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 46/241 (19%), Positives = 88/241 (36%), Gaps = 20/241 (8%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRG--YGLPISEVVSEGNIGLMQAVKKFDPER-GFRLAT 103
                +LV S L +V  +A  Y          ++V  G +GL+ A+ ++DPER       
Sbjct: 70  ERIREQLVLSFLPVVEHLARRYGNGYRVAAYDDLVQTGTVGLITAIDRWDPERAKGEFLG 129

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y +  ++  +  Y       +++      K L   + +  G L        +P     +A
Sbjct: 130 YLIPCVRGEILRYFRDRTWSMRVPRRL--KDLGVAIGKASGPLTQELGRAPRP---SELA 184

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
             L V   EVI      A   +      + D ++ + +   V           +  +   
Sbjct: 185 AHLGVDREEVIEALAAAADRRATPLFPVTHDDDAPEERVGTVE----------KAYDHVE 234

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               L   +  L  RER I   R   +   T   +++   VS+  V ++ AR  ++++E 
Sbjct: 235 YAIALKPLIEQLPERERLILTLRFFGDQ--TQSQIAARVGVSQMHVSRLLARTLERLREG 292

Query: 284 I 284
           +
Sbjct: 293 L 293


>gi|166031221|ref|ZP_02234050.1| hypothetical protein DORFOR_00908 [Dorea formicigenerans ATCC
           27755]
 gi|166029068|gb|EDR47825.1| hypothetical protein DORFOR_00908 [Dorea formicigenerans ATCC
           27755]
          Length = 227

 Score =  120 bits (302), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 57/259 (22%), Positives = 96/259 (37%), Gaps = 63/259 (24%)

Query: 26  IPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
            P+ L   EE    ++Y E GDL+A H L+  +LRLV  I   Y+       +++S G I
Sbjct: 26  FPLPLTASEEQYYLQKYIE-GDLNAKHILIEHNLRLVAHIVKKYQANVEEAEDLLSIGTI 84

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL++AV  F+P +  RL TY+   I+  +                        +LR  K 
Sbjct: 85  GLIKAVVTFNPGKNVRLGTYAARCIENEI----------------------LMHLRARKK 122

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
             +                          +S+   +  D          + N  Q  D +
Sbjct: 123 TSRE-------------------------VSLYEPIGTDR---------EGNEIQLFDVI 148

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEF 262
             D     + + EK++       +   +S    RER + + R     E   T   ++   
Sbjct: 149 ETDDQEAHRKIEEKDDILKLYQHVESKLST---RERLVLKMRYGLYNEEEYTQREIAKLL 205

Query: 263 EVSRERVRQIEARAFKKVQ 281
            +SR  V +IE  A +K++
Sbjct: 206 GISRSYVSRIEKSAIEKLR 224


>gi|309775717|ref|ZP_07670714.1| RNA polymerase sigma-K factor [Erysipelotrichaceae bacterium
           3_1_53]
 gi|308916522|gb|EFP62265.1| RNA polymerase sigma-K factor [Erysipelotrichaceae bacterium
           3_1_53]
          Length = 249

 Score =  120 bits (302), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 64/271 (23%), Positives = 100/271 (36%), Gaps = 62/271 (22%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           YI        L+K+EE        EH D  A ++L+  +LRLV  I   Y        ++
Sbjct: 18  YIRSNSFQQPLDKEEEARCISLLSEH-DEEARNKLIEHNLRLVAHIVKKYDIKKEQTEDL 76

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           +S G IGL++ V  F PE+G +L TY+   I+  +  Y+  S            K  F N
Sbjct: 77  ISIGTIGLIKGVDSFKPEKGHKLTTYASKCIENEILMYLRSS------------KNYFQN 124

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
                                              +S+N  +A D          D +  
Sbjct: 125 -----------------------------------VSLNEPIATD---------KDGSEI 140

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
              D +    D     +I+    ++    L R + VL+ RE  I   R     +   T  
Sbjct: 141 TLIDAIASPEDTS---IIDDMIVEDNIARLKRFIHVLDARELEIITKRFGLYGQEEETQR 197

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            ++ +  +SR  V +IE RAF K+    QK+
Sbjct: 198 EIARQLHISRSYVSRIEKRAFMKIYREFQKE 228


>gi|223984205|ref|ZP_03634353.1| hypothetical protein HOLDEFILI_01646 [Holdemania filiformis DSM
           12042]
 gi|223963820|gb|EEF68184.1| hypothetical protein HOLDEFILI_01646 [Holdemania filiformis DSM
           12042]
          Length = 234

 Score =  120 bits (302), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 52/262 (19%), Positives = 94/262 (35%), Gaps = 62/262 (23%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L  +EE    +R  + GD+ A   L+  +LRLV  I   +        +++S G IGL+
Sbjct: 28  PLTAEEEQDALQRMAK-GDVEARADLIEHNLRLVAHIVKKFDIRREQTEDLISIGTIGLI 86

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           + +  F  ++G +LATY    I+  +  ++                              
Sbjct: 87  KGIDTFKVDKGHKLATYVSRCIENEILMHLRN---------------------------- 118

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                              N    +  S++  +  D          D +     D +   
Sbjct: 119 -------------------NKHAFQTRSLDDAIGQD---------KDGSELTLIDVIPAP 150

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVS 265
                   I+K   +  +  LT+ M +L+ RE  I   R   E    +T  +++ +  +S
Sbjct: 151 DQPD---PIDKLMLEENKRKLTQFMGLLDEREHSIIVRRYGLEGHQEMTQRDIARQEHIS 207

Query: 266 RERVRQIEARAFKKVQESIQKQ 287
           R  V +IE RAF K+  +  K+
Sbjct: 208 RSYVSRIEKRAFMKLLRAFMKE 229


>gi|291563982|emb|CBL42798.1| RNA polymerase, sigma 29 subunit, SigE [butyrate-producing
           bacterium SS3/4]
          Length = 246

 Score =  120 bits (302), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 59/284 (20%), Positives = 116/284 (40%), Gaps = 65/284 (22%)

Query: 8   IIVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
            ++  E G   YI     +P  L  +EE     ++    +  A   L+  +LRLVV IA 
Sbjct: 21  TMIRPERGEIHYIGGADILPAPLSLKEETEALNKFGTEEEKEAKAELIEHNLRLVVYIAK 80

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            +    + + +++S G IGL++A+  F+P +  +LATY+   I+  +  Y+ R+  +   
Sbjct: 81  KFDNTSVGVEDLISIGTIGLIKAINTFNPTKNIKLATYASRCIENEILMYLRRTSKM--- 137

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
                                                 KL VS  E ++++         
Sbjct: 138 --------------------------------------KLEVSIDEPLNVD--------- 150

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
                  D N     D L  + D    V+ +  E +  +++L +++S L+PRER+I E R
Sbjct: 151 ------WDGNELLLSDILGTEED----VIYKDMEDEVEKDLLKKAVSRLSPRERKIVELR 200

Query: 247 RL----QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                     +T + ++    +S+  + ++E +   ++++ I K
Sbjct: 201 YGLKRRDGAEMTQKEVADLMGISQSYISRLEKKIMMRLKKEIVK 244


>gi|329940311|ref|ZP_08289592.1| putative RNA polymerase sigma factor [Streptomyces
           griseoaurantiacus M045]
 gi|329300372|gb|EGG44269.1| putative RNA polymerase sigma factor [Streptomyces
           griseoaurantiacus M045]
          Length = 270

 Score =  120 bits (302), Expect = 2e-25,   Method: Composition-based stats.
 Identities = 44/247 (17%), Positives = 102/247 (41%), Gaps = 15/247 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +   R+V + L +  ++A  +R  G    ++     +GL++AV +++P+ G    +Y++ 
Sbjct: 36  ALRSRVVEAWLPMAERLAGRFRNRGESYEDLRQVAALGLVKAVDRYEPDLGNAFESYAVP 95

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKPEQVVAIAKKL 166
            +   ++ +       + +       R      R++   Q ++   + +   V  IA   
Sbjct: 96  TVTGEIKRHFRDHMWTLHVPRRVQDLR-----NRVRFATQDLSQTISGRRPTVAEIAAHA 150

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++SE +V +    L   ES  AL   ++   S+    L       +  L    +    R 
Sbjct: 151 HLSEEDVKAGQEAL---ESFTALSLDAELPGSEDGYSLSDALGSADPAL----DTVVDRE 203

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +   ++ L  RER I   R   +  +T   ++ +  +S+  V ++ +R   +++E I +
Sbjct: 204 SVKPRLAALPERERAILYMRFFGD--MTQSRIAEQLGISQMHVSRLISRCCARLREQILR 261

Query: 287 QVELSSS 293
                +S
Sbjct: 262 DARTDTS 268


>gi|326332872|ref|ZP_08199129.1| RNA polymerase sigma-F factor [Nocardioidaceae bacterium Broad-1]
 gi|325949230|gb|EGD41313.1| RNA polymerase sigma-F factor [Nocardioidaceae bacterium Broad-1]
          Length = 265

 Score =  120 bits (301), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 51/240 (21%), Positives = 101/240 (42%), Gaps = 17/240 (7%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A   LV  ++ LV   A  + G G P  ++V  G +GL+ AV ++D  R    +TY++ 
Sbjct: 43  AAREELVHLNMALVEYCASQFYGRGEPHEDLVQVGVVGLLNAVDRYDLARDVEFSTYAVP 102

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I   ++ Y   S   V +      + L  NLR     L   +    +      +A +L 
Sbjct: 103 TILGEIKRYFRDSRWAVSVPRRL--RDLQQNLRDATAEL---SQELGRSPTARDLATRLG 157

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           VS   V+       G ES NA    S  + S     ++      +  L + E     R  
Sbjct: 158 VSLETVVE------GLESSNAYAALSLDSESDETAPMLDSLTAHDLRLDDVE----VRES 207

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +   +  L+  E+++   +  +    T   ++ E  VS+ +V ++  R+  ++++++++ 
Sbjct: 208 IKPVLDSLSAHEKQVLMLKFFRN--KTQTEIAGELGVSQMQVSRLLNRSLAQLRKALEED 265


>gi|217967265|ref|YP_002352771.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Dictyoglomus
           turgidum DSM 6724]
 gi|217336364|gb|ACK42157.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Dictyoglomus
           turgidum DSM 6724]
          Length = 235

 Score =  120 bits (301), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 45/249 (18%), Positives = 112/249 (44%), Gaps = 20/249 (8%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L  +Y+E GD      L+     L+   A  +  YG P+ +++  G +G ++A++ +DP
Sbjct: 7   DLWLKYKETGDKKFLEELLNVFDDLIHYWASKFTSYGEPLEDLIQIGYLGFLKAIENYDP 66

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           ++G  L+TY   ++   ++ ++      +KI  +         + ++   ++ + +   +
Sbjct: 67  KKG-ELSTYISHYVLGEIRHHLRDKIDKIKIPRSVKIL-----INKMDNFIKEVWEKENR 120

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
                 IAK LN++   V  +           A++  S ++     D +  +     ++ 
Sbjct: 121 SPSCEEIAKHLNITVESVDELFKIK------EAMMTVSIEDLEIEVDRIRTERLESFKLP 174

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
           IE+      +  L +++S L   +++I E    Q+  +T   ++   ++S+ +V ++   
Sbjct: 175 IEE------KIALEQAISKLPEIQKKIIEYIFYQD--LTQTEVAKILKISQTQVSRLLKS 226

Query: 276 AFKKVQESI 284
           A +K++E +
Sbjct: 227 ALEKLREML 235


>gi|138897001|ref|YP_001127454.1| sigma-B general stress transcription factor [Geobacillus
           thermodenitrificans NG80-2]
 gi|134268514|gb|ABO68709.1| Sigma-B general stress transcription factor [Geobacillus
           thermodenitrificans NG80-2]
          Length = 258

 Score =  120 bits (301), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 47/261 (18%), Positives = 107/261 (40%), Gaps = 18/261 (6%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI-SEVVSEGNIG 85
           P L K +   L   Y++     AA  L+     L+   A            ++   G + 
Sbjct: 8   PPLSKSKLDALISAYQQTKTEEAATALLVRFEPLIAAAAKKMARSRPDFYEDLFQVGRLS 67

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
            ++ ++ +DP +G    +Y+M  +   M+ Y+      +++     +     N  +++  
Sbjct: 68  FLRLLEHYDPNQGTSFESYAMKSLIGYMKNYLRDKAWYIQVPRRVKE-----NGSKVQKA 122

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDW 203
           +  +T    +   +  IA  L +S  E I +          S++A +   +K+++   ++
Sbjct: 123 IDELTVTLERSPNIEEIANHLGLSVEETIEILAGRDHYQAISIDAPVQDGEKDATTIGEF 182

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L  D +  E ++         R  L  ++  L+ +ER + EA   +    T  +L+    
Sbjct: 183 LADDTNEVEALIE--------RLDLQEAIGKLSEQERIVIEAVFRRGE--TQRSLAKRLG 232

Query: 264 VSRERVRQIEARAFKKVQESI 284
           VS+  + +I+ RA +K++  +
Sbjct: 233 VSQMTISRIQKRAIEKLKRQL 253


>gi|226225717|ref|YP_002759823.1| RNA polymerase sigma factor for flagellar operon [Gemmatimonas
           aurantiaca T-27]
 gi|226088908|dbj|BAH37353.1| RNA polymerase sigma factor for flagellar operon [Gemmatimonas
           aurantiaca T-27]
          Length = 251

 Score =  120 bits (301), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 53/258 (20%), Positives = 107/258 (41%), Gaps = 18/258 (6%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKF 93
           L + Y+  G+ SA  RL+  HL LV  +A              E+VS G IGLM A++ F
Sbjct: 5   LWQSYQ-AGNPSARDRLLEEHLGLVHHVARQVSRTLAVRADFDELVSAGTIGLMTALEGF 63

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D  RG   +T++   I+ A+ + + +   +         + +    R +    +A    +
Sbjct: 64  DASRGLAFSTFAAPRIRGAILDELRKQDHV--------PRSIRRKTREITAAREAFQRAS 115

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            +  +   +A++LNV    +      + G   +  L  +  +  +           G+E 
Sbjct: 116 GRAPEDRELAEQLNVDLETLWRWQADVEGAHHI-PLDRAPGERENTTPVPAEVLTSGEES 174

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
            + +    +   + L  ++  L  +ER +      +E    L  ++   E++  RV QI 
Sbjct: 175 GVEDSLTHEQEVSHLKDAILRLKEQERIVLSLYYFEELK--LHEIAKVLELTESRVSQIR 232

Query: 274 ARAFKKVQ---ESIQKQV 288
           ++A  K++   + ++ QV
Sbjct: 233 SKALSKLRVELKPLRDQV 250


>gi|289523542|ref|ZP_06440396.1| RNA polymerase sigma factor [Anaerobaculum hydrogeniformans ATCC
           BAA-1850]
 gi|289503234|gb|EFD24398.1| RNA polymerase sigma factor [Anaerobaculum hydrogeniformans ATCC
           BAA-1850]
          Length = 251

 Score =  120 bits (301), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 49/256 (19%), Positives = 105/256 (41%), Gaps = 21/256 (8%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
            + ++Y +    +    +V   L LV  +          GL   +++S G +GL+ A+ +
Sbjct: 12  EIWRKYVDTRSEAIKEEIVGLFLPLVRYVVGRMSIVIPPGLSQDDLLSFGAMGLLDAIDR 71

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           +DP RG    T++   I+ A+ + + R   L +             ++RL+  +  + + 
Sbjct: 72  YDPSRGVSFNTFAFSRIRGAILDELRRYDWLSRGAR--------DKIQRLEKAIAEMNEQ 123

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYDHDG 210
            LK      + +KL + E E+  +   ++     SL+ +I+  + +  +    LV D   
Sbjct: 124 GLKA-NDEMLMEKLQMDEKELRWLYELMSRSYVVSLDEVISLDEGDVER--SALVPDTSP 180

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
             +  +E  E  +    L  ++  L  RE+ +          +T + +     V+  RV 
Sbjct: 181 NPEEYMEAMEDCDT---LKGALEKLEEREQLVLSLYYY--EGLTFKEIGEVLGVTESRVS 235

Query: 271 QIEARAFKKVQESIQK 286
           QI  +A   ++  + K
Sbjct: 236 QIHGKALAMLKTLLGK 251


>gi|196249822|ref|ZP_03148518.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
 gi|196210698|gb|EDY05461.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
          Length = 256

 Score =  120 bits (301), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 47/261 (18%), Positives = 107/261 (40%), Gaps = 18/261 (6%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI-SEVVSEGNIG 85
           P L K +   L   Y++     AA  L+     L+   A            ++   G + 
Sbjct: 6   PPLSKSKLDALISAYQQTKTEEAATALLVRFEPLIAAAAKKMARSRPDFYEDLFQVGRLS 65

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
            ++ ++ +DP +G    +Y+M  +   M+ Y+      +++     +     N  +++  
Sbjct: 66  FLRLLEHYDPNQGTSFESYAMKSLIGYMKNYLRDKAWYIQVPRRVKE-----NGSKVQKA 120

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDW 203
           +  +T    +   +  IA  L +S  E I +          S++A +   +K+++   ++
Sbjct: 121 IDELTVTLERSPNIEEIANHLGLSVEETIEILAGRDHYQAISIDAPVQDGEKDATTIGEF 180

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L  D +  E ++         R  L  ++  L+ +ER + EA   +    T  +L+    
Sbjct: 181 LADDTNEVEALIE--------RLDLQEAIGKLSEQERIVIEAVFRRGE--TQRSLAKRLG 230

Query: 264 VSRERVRQIEARAFKKVQESI 284
           VS+  + +I+ RA +K++  +
Sbjct: 231 VSQMTISRIQKRAIEKLKRQL 251


>gi|154482592|ref|ZP_02025040.1| hypothetical protein EUBVEN_00259 [Eubacterium ventriosum ATCC
           27560]
 gi|149736617|gb|EDM52503.1| hypothetical protein EUBVEN_00259 [Eubacterium ventriosum ATCC
           27560]
          Length = 192

 Score =  120 bits (301), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 53/242 (21%), Positives = 92/242 (38%), Gaps = 61/242 (25%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A   L+  +LRLV  +   Y        +++S G +GL++AV  ++P++G RL TY
Sbjct: 4   GDKKAKDILIERNLRLVAHVVKKYYDENRENQDLISIGIVGLIKAVNTYNPDKGNRLVTY 63

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +   I                      +  L   LR  K                     
Sbjct: 64  AAKCI----------------------ENELLMMLRAEKKR------------------- 82

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
                           + D SLN  I +  + ++     +V + +      IEK E  N 
Sbjct: 83  ----------------SKDVSLNEPIGTDKEGNTISLIDVVENDEMDTLEQIEKAE--NI 124

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             +      +LN RE+ I   R   +   P+T + +  +  +SR  V +IE RA +K+++
Sbjct: 125 SLVQKYVAQILNEREKEIIVWRYGLDGKKPMTQKKVGEKLGISRSYVSRIEKRALEKLKK 184

Query: 283 SI 284
           ++
Sbjct: 185 AL 186


>gi|226364233|ref|YP_002782015.1| RNA polymerase sigma factor [Rhodococcus opacus B4]
 gi|226242722|dbj|BAH53070.1| RNA polymerase sigma factor [Rhodococcus opacus B4]
          Length = 285

 Score =  120 bits (301), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 36/235 (15%), Positives = 87/235 (37%), Gaps = 16/235 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             RL+   L L   IA  + G G P+ +++    +GL++AV +FD   G    +Y++  I
Sbjct: 59  RQRLIERCLPLAEHIARRFLGRGEPLDDLIQVARLGLVKAVDRFDARCGASFVSYAVPTI 118

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ +   +   + +  +  +  L             +T    +      +A+ L + 
Sbjct: 119 TGEVRRHFRDTGWAMHVPRSMQELHLSLT-----NATTELTTTLGRAPTASELAEALGID 173

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           + EV     R++   S  ++     ++     + +         V            +L 
Sbjct: 174 KDEVAR-GLRVSDAYSTLSVDFPLGEDERPLSETIGDVDPSLAHV--------EDHVVLE 224

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             +  L   ER +   R      +T   +++   VS+ +V ++ ++    ++  +
Sbjct: 225 PLLGSLPDLERTVLVLRFFGN--MTQSQIAARVGVSQMQVSRLLSKTLADLRGKL 277


>gi|297531625|ref|YP_003672900.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
 gi|297254877|gb|ADI28323.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. C56-T3]
          Length = 256

 Score =  120 bits (301), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 45/261 (17%), Positives = 106/261 (40%), Gaps = 18/261 (6%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI-SEVVSEGNIG 85
           P L K +   L   Y++     AA  L+     L+   A            ++   G + 
Sbjct: 6   PPLSKSKLDALISAYQQTKTEEAATALLVRFEPLIAAAAKKMARSRPDFYEDLFQIGRLS 65

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
            ++ +  +DP++G    +Y+M  +   M+ Y+      +++     +K       +++  
Sbjct: 66  FLRLLDHYDPKQGTSFESYAMKSLIGYMKNYLRDKAWYIQVPRKVKEKG-----SKVQQA 120

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDW 203
           +  +T    +   +  IA  L +S  E I +          SL+A +   +K+++   D+
Sbjct: 121 IDELTVKLERSPTLDEIAGHLGLSVEETIEILAGRDHYQAVSLDAPVQDGEKDATTIGDF 180

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  + +  E ++         R  L +++  L+ +E+ + +A   +    T   L+    
Sbjct: 181 VADEANEIESLIE--------RMDLEQAIGKLSEQEQIVIDAIFRRGE--TQRALAERLG 230

Query: 264 VSRERVRQIEARAFKKVQESI 284
           VS+  + +I+ RA  K++  +
Sbjct: 231 VSQMTISRIQKRAIAKLKREL 251


>gi|225418674|ref|ZP_03761863.1| hypothetical protein CLOSTASPAR_05898 [Clostridium asparagiforme
           DSM 15981]
 gi|225041795|gb|EEG52041.1| hypothetical protein CLOSTASPAR_05898 [Clostridium asparagiforme
           DSM 15981]
          Length = 216

 Score =  119 bits (300), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 53/262 (20%), Positives = 91/262 (34%), Gaps = 64/262 (24%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L  +EE    +R  E GD  A   L+  ++RLV  +   Y+     I +++S G IGL+
Sbjct: 13  PLSAREEKEYLERCNE-GDQLARDVLIERNMRLVAHVVKKYQSPDYDIEDLLSVGTIGLI 71

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV  F  ++G RLATY+   ++  +                         L R    L 
Sbjct: 72  KAVNTFKVDKGSRLATYAAKCVENEILM-----------------------LFRASKKLS 108

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS-DKNSSQWQDWLVY 206
                                                SL   I    D  +    D +  
Sbjct: 109 KE----------------------------------VSLFEPIGVDKDGEAVSLVDIIEM 134

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEV 264
           ++      +I K++ K          S L+  E+ +   R         T   ++++  +
Sbjct: 135 ENKETIDTMILKQDVKELYEAFD---SCLSDTEKTVIRMRYGLFRGKEHTQREIAAQLGI 191

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           SR  V +IE +A +K++   QK
Sbjct: 192 SRSYVSRIEKKALEKLKGEFQK 213


>gi|210610056|ref|ZP_03288235.1| hypothetical protein CLONEX_00421 [Clostridium nexile DSM 1787]
 gi|210152667|gb|EEA83673.1| hypothetical protein CLONEX_00421 [Clostridium nexile DSM 1787]
          Length = 208

 Score =  119 bits (300), Expect = 3e-25,   Method: Composition-based stats.
 Identities = 60/257 (23%), Positives = 99/257 (38%), Gaps = 62/257 (24%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L   EE    ++Y E GDL A H L+  +LRLV  +   Y+       +++S G IGL+
Sbjct: 10  PLTAAEEQYYIQKYIE-GDLEAKHILIERNLRLVAHVIKKYQYLDDDPEDLISIGTIGLI 68

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV  F+P +  RL TY+   I+  +   +                              
Sbjct: 69  KAVATFNPSKNNRLGTYAARCIENEILMMLRSK--------------------------- 101

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                                  S+ IS+   +  D          + N  Q  D +  D
Sbjct: 102 --------------------KKVSKEISLYEPIGTDR---------EGNEIQLFDIIEAD 132

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVS 265
            D  +  +  KE+ K    + T+  S L+PRER + + R     E   T   ++++  +S
Sbjct: 133 DDDAQTKVALKEDIKM---LYTKVESELSPRERLVLKMRYGLYDEEEYTQREIAAQLGIS 189

Query: 266 RERVRQIEARAFKKVQE 282
           R  V +IE  A +K++E
Sbjct: 190 RSYVSRIEKSAIEKLRE 206


>gi|242089037|ref|XP_002440351.1| hypothetical protein SORBIDRAFT_09g030110 [Sorghum bicolor]
 gi|241945636|gb|EES18781.1| hypothetical protein SORBIDRAFT_09g030110 [Sorghum bicolor]
          Length = 501

 Score =  119 bits (300), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 50/247 (20%), Positives = 101/247 (40%), Gaps = 22/247 (8%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            +A ++L+  +LRLV      Y    G      ++   G  GL+ A+ +F+P+RGFR++T
Sbjct: 261 RAARNKLIKHNLRLVPYAINKYYPDMGTDERFDDLCQAGANGLITAIDRFEPKRGFRIST 320

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+++WI+ ++   +  S    +       +R     + +    + +     +P     + 
Sbjct: 321 YALFWIRHSIVRAMTLSSFT-RFPFAMESER-----QEIGKAREELAFELGRPATDEEVR 374

Query: 164 KKLNVSESEVISMNCRLAGDESLNA---LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
           +K+ +S      +        SL+A   +      N     D +  D  G+   L+    
Sbjct: 375 RKVGISPQRYRDVLRMTRPTYSLHARNRVTQEELINEVTDDDAIGVDAGGRHNTLL---- 430

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
               R  +   +  L P+E  +   R   +     TL  ++    +SRE VR+ E +A  
Sbjct: 431 ----RLAIDDLLDSLKPKESLVIRQRFGLDGRGKRTLSEIAGNLSISREMVRKYELKALM 486

Query: 279 KVQESIQ 285
           K++   +
Sbjct: 487 KLKHPTR 493


>gi|152980386|ref|YP_001353773.1| RNA polymerase sigma factor for flagellar operon [Janthinobacterium
           sp. Marseille]
 gi|151280463|gb|ABR88873.1| RNA polymerase sigma factor for flagellar operon [Janthinobacterium
           sp. Marseille]
          Length = 243

 Score =  119 bits (300), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 42/242 (17%), Positives = 103/242 (42%), Gaps = 16/242 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + LV  H  LV K+A   +    P   + +++  G IGL+ AV +++   G +  TY++
Sbjct: 10  KNHLVGEHAPLVKKLAHQMKAKLPPSVEVDDLIQAGMIGLLDAVSRYEETHGAQFETYAV 69

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +  S  +         + +  N+R+++  +  +     +P     +AK+L
Sbjct: 70  QRIRGAMLDELRSSDWM--------PRSMRQNMRKIEVAMNTLQQRLGRPPNESEVAKQL 121

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +S ++   +     G + +        +++  + D    D        ++       R 
Sbjct: 122 KLSLADYQDLLSDGGGHQLVYYEDFHDSEDNEHFLDRYCTDESPD---PLQNLMNTGFRA 178

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+         E  + L+ + +   V+  RV Q+ ++A  +++ ++++
Sbjct: 179 AVIEAIQALPEREK--ILMGLYYEQEMNLKEIGAVMGVTESRVSQLHSQAIARMRANLRE 236

Query: 287 QV 288
           + 
Sbjct: 237 KA 238


>gi|91223562|ref|ZP_01258827.1| flagellar biosynthesis sigma factor [Vibrio alginolyticus 12G01]
 gi|269965686|ref|ZP_06179799.1| flagellar biosynthesis sigma factor FliA [Vibrio alginolyticus 40B]
 gi|91191648|gb|EAS77912.1| flagellar biosynthesis sigma factor [Vibrio alginolyticus 12G01]
 gi|269829754|gb|EEZ83990.1| flagellar biosynthesis sigma factor FliA [Vibrio alginolyticus 40B]
          Length = 244

 Score =  119 bits (300), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 50/252 (19%), Positives = 100/252 (39%), Gaps = 19/252 (7%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFD 94
           A  Y +HG  ++    +  +  LV +IA    G   P   + +++  G IGL++A + +D
Sbjct: 4   AITYDQHGKFNSQQAFIERYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLIEAQQNYD 63

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +G    TY+   I+ AM +  +R    V      N + +   +  L+G L        
Sbjct: 64  GSKGASFETYAGIRIRGAMLDD-MRKGDWVPRSVHKNNREINQAIAELEGELN------- 115

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +      +A  L ++  +  S       D + + L+   D   S   D +    +  +  
Sbjct: 116 RDPTDSEVATHLGMTLDQYHSALT----DINCSKLVGIEDLGVS--DDVISPADETDDSN 169

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
             +    ++ R  L  S+  L  RE  +       +  + L+ +     VS  RV QI +
Sbjct: 170 PFKGVVDESFRKALVESIKQLPEREALVLSLYY--DEELNLKEIGDVLGVSESRVSQILS 227

Query: 275 RAFKKVQESIQK 286
           +A ++++  +  
Sbjct: 228 QAMQRLRTKLSA 239


>gi|260893856|ref|YP_003239953.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Ammonifex degensii
           KC4]
 gi|260865997|gb|ACX53103.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Ammonifex degensii
           KC4]
          Length = 252

 Score =  119 bits (300), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 51/253 (20%), Positives = 105/253 (41%), Gaps = 16/253 (6%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFD 94
            + Y++ G+ ++   LV  +L LV  +         P   + ++   G +GL+ A++++D
Sbjct: 7   WRAYKQRGNTTSKEELVRRYLPLVKYLVGRLAVRLPPWVSLEDIEGAGILGLLAAMERYD 66

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P +G    +Y+ + I  AM + + R     +      Q  L    R  +           
Sbjct: 67  PSQGVEFESYARYRIWGAMLDEVRRWARFSRRTWQQMQAVLKVQERWEREK--------G 118

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
              +V  +A++L    ++V  +    A   S +     S +  S W+++L    D + Q 
Sbjct: 119 CRPKVEDVAQELGWEPAQVDRLGRYFAAFNSFSLEEVRSAEGRSPWEEFLA---DPKGQD 175

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
            +E+   K     L  ++  L  R + I       +  +TL  +     +S  RV Q+ +
Sbjct: 176 PLEELLEKEDLGRLAEAIGRLEERLQLILALYY--QEGLTLREIGEVLGISESRVCQLHS 233

Query: 275 RAFKKVQESIQKQ 287
           RA  K++E + ++
Sbjct: 234 RALTKLREILAEE 246


>gi|255094683|ref|ZP_05324161.1| RNA polymerase sigma-B factor [Clostridium difficile CIP 107932]
          Length = 252

 Score =  119 bits (300), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 45/237 (18%), Positives = 105/237 (44%), Gaps = 12/237 (5%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             L   Y ++ ++   + L+  HL L   +A  Y   G+   ++    ++ L+ A+ ++D
Sbjct: 16  KELFNLYNKNKNVDIRNILIERHLYLARLLAKKYINKGVDFEDIYQVASLALIYAIDRYD 75

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
            E+GF  ++++   I   +++Y       +++     +       +++      +   N 
Sbjct: 76  VEKGFEFSSFATPTIVGEIKKYFRDKVWTLRVPRRIQELS-----KKISDAKIKLEQENK 130

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           K  +V  IA  + VSE +V+       G + +   ++SS  + S+ +D  + D  G+E+ 
Sbjct: 131 KHPKVKDIADYIGVSEEDVLEAMEASYGYQPM--SLDSSSNDDSEDKDITLIDKIGKEEG 188

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
                E ++    + + +  LN  E +IF+ R   +   T  +++ E  +S+  V +
Sbjct: 189 NFGSIEYEDF---INKFIETLNELEVKIFKDRFFFD--KTQSSIAKELGISQMTVSR 240


>gi|169350469|ref|ZP_02867407.1| hypothetical protein CLOSPI_01237 [Clostridium spiroforme DSM 1552]
 gi|169292789|gb|EDS74922.1| hypothetical protein CLOSPI_01237 [Clostridium spiroforme DSM 1552]
          Length = 228

 Score =  119 bits (300), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 58/290 (20%), Positives = 110/290 (37%), Gaps = 66/290 (22%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M    +S++ NG      YI        L  +EE    +R+  +GD  A + L+  +LRL
Sbjct: 1   MFSTLLSLLTNG--FFLSYIKSKSFEIPLTPKEEAKYLERFF-NGDQEARNVLIERNLRL 57

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           V  IA  Y        +++S G IGL++AV  +      +LATY+   I+  +  ++  +
Sbjct: 58  VAHIAKKYENNKDLQEDLISIGTIGLIKAVDSYKQNHKTKLATYASRCIENEILMHLRAN 117

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
                                                        L+VS +E I ++   
Sbjct: 118 KKTN-----------------------------------------LDVSLNETIGIDK-- 134

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
                        D +     D +    D      I+  ++K+  N LT   ++L+PRE+
Sbjct: 135 -------------DGSEIVLGDTIAIKQD----EFIDIIDKKDTLNRLTTYFNILDPREK 177

Query: 241 RIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKK-VQESIQKQ 287
                     N    + + ++ +  +SR  V ++E RA  K +++ ++++
Sbjct: 178 ETLIMHYGLNNTKKYSQKEIAKKLNISRSYVSRLEKRALIKLLKKHMEEK 227


>gi|255280061|ref|ZP_05344616.1| RNA polymerase sigma-E factor [Bryantella formatexigens DSM 14469]
 gi|255269152|gb|EET62357.1| RNA polymerase sigma-E factor [Bryantella formatexigens DSM 14469]
          Length = 243

 Score =  119 bits (300), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 57/260 (21%), Positives = 101/260 (38%), Gaps = 64/260 (24%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L  +EE    ++Y+E GDL A   L+  +LRLV  +A  Y+  G    E+++ G IGL+
Sbjct: 42  PLTPEEEAWFLQKYKE-GDLEAKKILIERNLRLVAHVAKKYQKQGEDGEELIAVGTIGLI 100

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV  F+  R  +LATY+   ++  +                     LF + +++     
Sbjct: 101 KAVSTFNHARTNKLATYAARCVENELLM-------------------LFRSRKKISRE-- 139

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                                     +S+N  +  D          + N     D +   
Sbjct: 140 --------------------------VSLNEPIGTD---------KEGNEISLIDVI--- 161

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMS-VLNPRERRIFEARRLQENP--VTLENLSSEFEV 264
            +G+   +IE+ E       L R +  VL  RE+ I + R        +T   ++ +  +
Sbjct: 162 -EGENIDVIERMELDRNTRTLYRLLENVLTEREKEILKLRYGLYGKSEMTQREIADKMGI 220

Query: 265 SRERVRQIEARAFKKVQESI 284
           SR  V +IE  A  K+++  
Sbjct: 221 SRSYVSRIEKSAVAKLRQHF 240


>gi|155061095|gb|ABS90485.1| RNA polymerase sigma factor [Streptomyces albus]
          Length = 282

 Score =  119 bits (300), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 44/232 (18%), Positives = 100/232 (43%), Gaps = 15/232 (6%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            +V + L +  +IA  +R  G  + ++     +GL++AV +++P RG    +Y++  I  
Sbjct: 48  EIVEAWLPMAHRIAGRFRNKGESLEDLQQVAAMGLVKAVNRYEPGRG-AFESYAVPTITG 106

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            ++ +       V++     +  L   +R  +  L      + +   +  I ++  ++E+
Sbjct: 107 ELRRHFRDRMWDVRVPRRVQE--LRNKVRAARRELLDRPGGSGREPTLAEIGEQAELTEA 164

Query: 172 EVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           EV      + G    SL+A ++S++ +     D L       + +        N R    
Sbjct: 165 EVRDGMEAMEGYSALSLDAEVSSAEPDGFSLADTLGAPDPAYDHI--------NDREAAK 216

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             +  L  RER I   R  ++  +T   ++ E  +S+  V ++ +R+  +V+
Sbjct: 217 AGLRRLPERERTILYLRYFED--MTQSRIAEELGISQMHVSRLISRSCARVR 266


>gi|312622956|ref|YP_004024569.1| RNA polymerase, sigma 28 subunit, sigk [Caldicellulosiruptor
           kronotskyensis 2002]
 gi|312203423|gb|ADQ46750.1| RNA polymerase, sigma 28 subunit, SigK [Caldicellulosiruptor
           kronotskyensis 2002]
          Length = 219

 Score =  119 bits (300), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 58/263 (22%), Positives = 102/263 (38%), Gaps = 64/263 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI-SEVVSEGNIG 85
           PM  ++EE  L K +   G   A + L+  +LRLV  IA  Y      +  +++S G IG
Sbjct: 13  PMSPEEEEMYLNKMW--EGCKEARNILIEKNLRLVAHIAKKYTFSFPNLTDDIISVGTIG 70

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A++ +   +  +L+TY+   I+  +  Y                      LR+ K  
Sbjct: 71  LIKAIETYSSAKCTKLSTYAAKCIENEILMY----------------------LRQNKKF 108

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           L  +                         S+   +  D          D N     D L 
Sbjct: 109 LSQL-------------------------SLENPIGSD---------KDGNEITLMDVLQ 134

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFE 263
            D +  ++ +  K + KN    L + +     RE++I E R   +N    T   +++   
Sbjct: 135 NDQNDIDEQVDLKIQIKNLLKKLDKILKG---REKKIIELRYGLKNGIERTQMEVANLLG 191

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +SR  V +IE +A +K+   +QK
Sbjct: 192 ISRSYVSRIEKKALQKLYGELQK 214


>gi|332654157|ref|ZP_08419901.1| RNA polymerase sigma-F factor [Ruminococcaceae bacterium D16]
 gi|332517243|gb|EGJ46848.1| RNA polymerase sigma-F factor [Ruminococcaceae bacterium D16]
          Length = 239

 Score =  119 bits (300), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 48/249 (19%), Positives = 103/249 (41%), Gaps = 21/249 (8%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L +  RE GD  A  +++  +  L+  +   Y G G+   ++   G +G ++AV+ FDP
Sbjct: 9   ELLQAARE-GDNRACEQVLEENNGLIWSVVRRYYGRGVEPDDLYQLGCLGFLKAVRGFDP 67

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
             G + +TY++  I   ++ ++      VK+     ++        ++G    +     +
Sbjct: 68  AFGTQFSTYAVPKIAGEIRRFLRDDG-AVKVSRGLKEQGAL-----IRGVRSQLWSTLGR 121

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
              +  +A+   ++  E+ +         SL A     +          V    G E+ L
Sbjct: 122 EPALSELAQATGLTPEEIAAAETAADPVVSLQA-----ETGEGGLTLEGVLSAGGMEEGL 176

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
           +E       R  L  ++  L  RER +   R  +   +T  N +    VS+ ++ ++E R
Sbjct: 177 VE-------RIALRGALEQLPEREREVLLLRYYKG--LTQTNTARVLGVSQVQISRLERR 227

Query: 276 AFKKVQESI 284
           A  ++++ +
Sbjct: 228 AVDRLRQVL 236


>gi|126700257|ref|YP_001089154.1| sporulation sigma factor SigE [Clostridium difficile 630]
 gi|254976236|ref|ZP_05272708.1| sporulation sigma factor SigE [Clostridium difficile QCD-66c26]
 gi|255093623|ref|ZP_05323101.1| sporulation sigma factor SigE [Clostridium difficile CIP 107932]
 gi|255101811|ref|ZP_05330788.1| sporulation sigma factor SigE [Clostridium difficile QCD-63q42]
 gi|255307678|ref|ZP_05351849.1| sporulation sigma factor SigE [Clostridium difficile ATCC 43255]
 gi|255518036|ref|ZP_05385712.1| sporulation sigma factor SigE [Clostridium difficile QCD-97b34]
 gi|255651152|ref|ZP_05398054.1| sporulation sigma factor SigE [Clostridium difficile QCD-37x79]
 gi|255656620|ref|ZP_05402029.1| sporulation sigma factor SigE [Clostridium difficile QCD-23m63]
 gi|260684218|ref|YP_003215503.1| sporulation sigma factor SigE [Clostridium difficile CD196]
 gi|260687877|ref|YP_003219011.1| sporulation sigma factor SigE [Clostridium difficile R20291]
 gi|296449924|ref|ZP_06891688.1| RNA polymerase sigma-E factor [Clostridium difficile NAP08]
 gi|296878306|ref|ZP_06902314.1| RNA polymerase sigma-E factor [Clostridium difficile NAP07]
 gi|306521002|ref|ZP_07407349.1| sporulation sigma factor SigE [Clostridium difficile QCD-32g58]
 gi|115251694|emb|CAJ69529.1| RNA polymerase sigma-E factor [Clostridium difficile]
 gi|260210381|emb|CBA64762.1| RNA polymerase sigma-E factor [Clostridium difficile CD196]
 gi|260213894|emb|CBE05927.1| RNA polymerase sigma-E factor [Clostridium difficile R20291]
 gi|296261194|gb|EFH08025.1| RNA polymerase sigma-E factor [Clostridium difficile NAP08]
 gi|296430604|gb|EFH16443.1| RNA polymerase sigma-E factor [Clostridium difficile NAP07]
          Length = 240

 Score =  119 bits (300), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 53/263 (20%), Positives = 109/263 (41%), Gaps = 65/263 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L+ +EE  L ++     D S    L+  +LRLVV I+  +   G+ + +++S G IGL
Sbjct: 38  PPLKPEEEMELLQKL--ETDESVKSILIERNLRLVVYISRKFENTGIDVEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F   +  +LATY+   I+  +  Y+ ++                          
Sbjct: 96  IKAVNTFKLNKNIKLATYASRCIENEILMYLRKNNK------------------------ 131

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                            KK  VS  E ++++                D N     D L  
Sbjct: 132 -----------------KKTEVSFDEPLNIDL---------------DGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP---VTLENLSSEFE 263
           ++D   +++ E+ +    R++L  ++  L+ RE++I E R    +     T + ++    
Sbjct: 160 ENDEIYKIIEEEID----RDLLVMALDRLSDREKQIMELRFGLIDKGIEKTQKEVAGMLG 215

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+  + ++E +   ++Q+ ++K
Sbjct: 216 ISQSYISRLEKKIISRLQKEMKK 238


>gi|319649539|ref|ZP_08003695.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
 gi|317398701|gb|EFV79383.1| RNA polymerase sigma factor [Bacillus sp. 2_A_57_CT2]
          Length = 251

 Score =  119 bits (300), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 51/260 (19%), Positives = 109/260 (41%), Gaps = 19/260 (7%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQA 89
           EE     ++ +  D  A + LV  +L LV              +   ++ S G +GL  A
Sbjct: 7   EESTYWAKWVDSRDAQAGNFLVKKYLPLVSYHVQRISATLPKNVSRDDIRSLGLMGLYDA 66

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           ++KFDP R  +  TY+ + I+ A+ + + +   L         +      +++   ++ +
Sbjct: 67  LEKFDPARDLKFDTYASFRIRGAILDGLRKEDWL--------PRSTRDKAKKIDAAIEKL 118

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK-NSSQWQDWLVYDH 208
               ++   V  IA++  + E EV S+      +E   A I S D+   +  +D      
Sbjct: 119 EQRLMRNATVHEIAEEAEMQEDEVYSVM-----NEHFYANILSIDEQPDADEKDGSYSIK 173

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D +  +  EK  +      +   +  LN +E+ +       +  +TL  +     +S  R
Sbjct: 174 DEKAIIPEEKVLKNELLEEMAEKILQLNEKEQMVLSLFY--KEELTLTEIGEVMGLSTSR 231

Query: 269 VRQIEARAFKKVQESIQKQV 288
           + QI +++  K+++ ++K +
Sbjct: 232 ISQIHSKSIFKLRQLLEKAI 251


>gi|302539934|ref|ZP_07292276.1| stress response/stationary phase sigma factor SigF [Streptomyces
           hygroscopicus ATCC 53653]
 gi|302457552|gb|EFL20645.1| stress response/stationary phase sigma factor SigF [Streptomyces
           himastatinicus ATCC 53653]
          Length = 274

 Score =  119 bits (300), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 51/256 (19%), Positives = 107/256 (41%), Gaps = 21/256 (8%)

Query: 30  EKQEEYVLAKRYREHGDLSA-AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
              E   +A R  E  +  A   R+V + + +  ++A  YR  G  + ++     +GL++
Sbjct: 26  TDAEFREMA-RLPEGPEKEALRQRVVEAWMPMAQRLARQYRNRGESLEDLEQVAALGLVK 84

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           AVK++DPE G   A +++  +   ++ +      ++ +     + R      R++   + 
Sbjct: 85  AVKRYDPEHGTAFAGFAVPTVVGEIKRHFRDHLWVLHVPRRVQELR-----NRVRAAHRE 139

Query: 149 ITDN-NLKPEQVVAIAKKLNVSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLV 205
           ++ + +       AIA++  +SE EV      +      SL+A +  +D   S     L 
Sbjct: 140 LSHSLDDATVPTEAIAERTGLSEKEVRIGMEAMGSFTPLSLDAQLTGADDGYS-----LA 194

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
               GQE       +R   R  +   +  L  RER+I   R   +  +T   ++ +  +S
Sbjct: 195 DTLGGQEPAY----DRVVDREAVRPGLGRLPARERQILYMRFFCD--MTQSRIAEQLGIS 248

Query: 266 RERVRQIEARAFKKVQ 281
           +  V ++  R    ++
Sbjct: 249 QMHVSRLINRTCSTLR 264


>gi|167756988|ref|ZP_02429115.1| hypothetical protein CLORAM_02537 [Clostridium ramosum DSM 1402]
 gi|167703163|gb|EDS17742.1| hypothetical protein CLORAM_02537 [Clostridium ramosum DSM 1402]
          Length = 228

 Score =  119 bits (300), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 54/265 (20%), Positives = 104/265 (39%), Gaps = 65/265 (24%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+  K+EE  L + +  +GD  A + L+  +LRLV  IA  Y        +++S G IG
Sbjct: 25  LPLTAKEEERYLEQFF--NGDKEARNVLIERNLRLVAHIAKKYENNKDMQEDLISIGTIG 82

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++AV  +      +LATY+   I+  +  ++  +                         
Sbjct: 83  LIKAVDSYKQNHKTKLATYASRCIENEILMHLRTNKKTN--------------------- 121

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
                               L++S +E I ++                D +     D + 
Sbjct: 122 --------------------LDISLNETIGIDK---------------DGSEIVLGDIIA 146

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFE 263
              +      I+  ++K+  +  T   SVL PRE+     R    N    T ++++ +  
Sbjct: 147 AKQE----EFIDIVDKKDTLDKFTTYFSVLEPREKDTLIMRYGLNNTKKYTQKDIAKKLN 202

Query: 264 VSRERVRQIEARAFKK-VQESIQKQ 287
           +SR  V ++E RA  K ++E ++++
Sbjct: 203 ISRSYVSRLEKRALIKLLREHMKEK 227


>gi|257469126|ref|ZP_05633220.1| RpoD family RNA polymerase sigma factor [Fusobacterium ulcerans
           ATCC 49185]
          Length = 116

 Score =  119 bits (300), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 46/111 (41%), Positives = 75/111 (67%), Gaps = 1/111 (0%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +S Y+ +IRK  +L+K EE  L  + +  GD  A ++L+ S+LRLVV IA GY   GL  
Sbjct: 7   ISLYLADIRKYKILDKDEELNLLIKAK-AGDEEAKNQLILSNLRLVVNIAKGYINKGLSF 65

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            +++SEGN+GL+ A++KFD  +GFR +TY++WWIK ++ + ++     ++I
Sbjct: 66  IDLISEGNLGLIYAIEKFDITKGFRFSTYAVWWIKQSISKAVIVKGREIRI 116


>gi|302555286|ref|ZP_07307628.1| RNA polymerase sigma-B factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302472904|gb|EFL35997.1| RNA polymerase sigma-B factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 264

 Score =  119 bits (300), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 45/242 (18%), Positives = 101/242 (41%), Gaps = 15/242 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +    +V + L +  ++A  +R  G    ++     +GL++AV ++DPE G    +Y++ 
Sbjct: 36  ALRDEIVEAWLPMADRLAGRFRSRGESFEDLRQVAALGLVKAVDRYDPELGNAFESYAVP 95

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKPEQVVAIAKKL 166
            +   ++ +       + +       R      R++   Q ++   + +   +  IA+  
Sbjct: 96  TVTGEIKRHFRDHMWTLHVPRRVQDLR-----NRVRVASQDLSQTISGRRPTIAEIAEHA 150

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +SE +V +    L   ES  AL   ++   S+    L       +  L    +    R 
Sbjct: 151 KMSEDDVKAGLEAL---ESFTALSLDAELPGSEDGYSLSDALGSVDPAL----DTVVDRE 203

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +   ++ L  RER I   R   +  +T   ++ E  +S+  V ++ +R+  +V+E + +
Sbjct: 204 SVKARLAALPERERAILYMRFFGD--MTQSRIAEELGISQMHVSRLISRSCGRVREQVMR 261

Query: 287 QV 288
            V
Sbjct: 262 DV 263


>gi|168986257|dbj|BAG11810.1| RNA polymerase, sigma S (sigma 38) factor [Escherichia coli O55:H6]
          Length = 177

 Score =  119 bits (300), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 43/186 (23%), Positives = 83/186 (44%), Gaps = 10/186 (5%)

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y   GL + +++ EGN+GL++AV+KFDPERGF  +TY+ WWI+  ++  I+     
Sbjct: 1   IARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFLFSTYATWWIRQTIERAIMNQTRT 60

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           +++      K L   LR  +     ++           IA++L+    +V  M       
Sbjct: 61  IRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERI 115

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            S++  +    +     +  L    D +E    +  +  + +  + + +  LN ++R + 
Sbjct: 116 TSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNAKQREVL 170

Query: 244 EARRLQ 249
             R   
Sbjct: 171 ARRFGL 176


>gi|126697577|ref|YP_001086474.1| RNA polymerase sigma-B factor [Clostridium difficile 630]
 gi|254977353|ref|ZP_05273825.1| RNA polymerase sigma-B factor [Clostridium difficile QCD-66c26]
 gi|255102910|ref|ZP_05331887.1| RNA polymerase sigma-B factor [Clostridium difficile QCD-63q42]
 gi|255308730|ref|ZP_05352901.1| RNA polymerase sigma-B factor [Clostridium difficile ATCC 43255]
 gi|255316437|ref|ZP_05358020.1| RNA polymerase sigma-B factor [Clostridium difficile QCD-76w55]
 gi|255519098|ref|ZP_05386774.1| RNA polymerase sigma-B factor [Clostridium difficile QCD-97b34]
 gi|255652280|ref|ZP_05399182.1| RNA polymerase sigma-B factor [Clostridium difficile QCD-37x79]
 gi|260681780|ref|YP_003213065.1| RNA polymerase sigma-B factor [Clostridium difficile CD196]
 gi|260685377|ref|YP_003216510.1| RNA polymerase sigma-B factor [Clostridium difficile R20291]
 gi|296452670|ref|ZP_06894361.1| RNA polymerase sigma-B factor [Clostridium difficile NAP08]
 gi|296880077|ref|ZP_06904046.1| RNA polymerase sigma-B factor [Clostridium difficile NAP07]
 gi|306521994|ref|ZP_07408341.1| RNA polymerase sigma-B factor [Clostridium difficile QCD-32g58]
 gi|115249014|emb|CAJ66825.1| RNA polymerase sigma-B factor (Sigma-37) [Clostridium difficile]
 gi|260207943|emb|CBA60060.1| RNA polymerase sigma-B factor [Clostridium difficile CD196]
 gi|260211393|emb|CBE01463.1| RNA polymerase sigma-B factor [Clostridium difficile R20291]
 gi|296258452|gb|EFH05356.1| RNA polymerase sigma-B factor [Clostridium difficile NAP08]
 gi|296428944|gb|EFH14822.1| RNA polymerase sigma-B factor [Clostridium difficile NAP07]
          Length = 257

 Score =  119 bits (300), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 45/237 (18%), Positives = 105/237 (44%), Gaps = 12/237 (5%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             L   Y ++ ++   + L+  HL L   +A  Y   G+   ++    ++ L+ A+ ++D
Sbjct: 16  KELFNLYNKNKNVDIRNILIERHLYLARLLAKKYINKGVDFEDIYQVASLALIYAIDRYD 75

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
            E+GF  ++++   I   +++Y       +++     +       +++      +   N 
Sbjct: 76  VEKGFEFSSFATPTIVGEIKKYFRDKVWTLRVPRRIQELS-----KKISDAKIKLEQENK 130

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           K  +V  IA  + VSE +V+       G + ++   +SS  + S+ +D  + D  G+E+ 
Sbjct: 131 KHPKVKDIADYIGVSEEDVLEAMEASYGYQPMSL--DSSSNDDSEDKDITLIDKIGKEEG 188

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
                E ++    + + +  LN  E +IF+ R   +   T  +++ E  +S+  V +
Sbjct: 189 NFGSIEYEDF---INKFIETLNELEVKIFKDRFFFD--KTQSSIAKELGISQMTVSR 240


>gi|255315371|ref|ZP_05356954.1| sporulation sigma factor SigE [Clostridium difficile QCD-76w55]
          Length = 240

 Score =  119 bits (300), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 52/263 (19%), Positives = 109/263 (41%), Gaps = 65/263 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L+ +EE  L ++     D +    L+  +LRLVV I+  +   G+ + +++S G IGL
Sbjct: 38  PPLKPEEEMELLQKL--ETDENVKSILIERNLRLVVYISRKFENTGIDVEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F   +  +LATY+   I+  +  Y+ ++                          
Sbjct: 96  IKAVNTFKLNKNIKLATYASRCIENEILMYLRKNNK------------------------ 131

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                            KK  VS  E ++++                D N     D L  
Sbjct: 132 -----------------KKTEVSFDEPLNIDL---------------DGNELLLSDVLGT 159

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP---VTLENLSSEFE 263
           ++D   +++ E+ +    R++L  ++  L+ RE++I E R    +     T + ++    
Sbjct: 160 ENDEIYKIIEEEID----RDLLVMALDRLSDREKQIMELRFGLIDKGIEKTQKEVAGMLG 215

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+  + ++E +   ++Q+ ++K
Sbjct: 216 ISQSYISRLEKKIISRLQKEMKK 238


>gi|302547278|ref|ZP_07299620.1| stress response/stationary phase sigma factor SigF [Streptomyces
           hygroscopicus ATCC 53653]
 gi|302464896|gb|EFL27989.1| stress response/stationary phase sigma factor SigF [Streptomyces
           himastatinicus ATCC 53653]
          Length = 264

 Score =  119 bits (300), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 45/241 (18%), Positives = 102/241 (42%), Gaps = 15/241 (6%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +    +V + + +  ++A  +R  G    ++     +GL++AVK+++P+RG   A++++
Sbjct: 35  EALRQDVVRAWMPMAERLARQFRNRGESAEDLRQVAMLGLVKAVKRYEPDRGSAFASFAV 94

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKPEQVVAIAKK 165
             +   ++ +       V +     + R      R++   Q +T   + +   V AI + 
Sbjct: 95  PTVVGEIKRHFRDHMWGVHVPRRVQELR-----NRVRAAAQELTRTPDDRSPSVSAIVEH 149

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
             +SE +V+     +   ES +AL   ++   ++    L       E       +R  +R
Sbjct: 150 TGMSEEDVL---LGMEAMESFSALSLDAELPGAEDGYSLADTLGAPEPSY----DRVIQR 202

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             L   +  L  RER I   R  +E   T   ++ +  +S+  V ++  R   ++ + I+
Sbjct: 203 EALKPRLRALPERERHILYLRFFREE--TQGRIAEQLGISQMHVSRLINRTCARLHDQIE 260

Query: 286 K 286
            
Sbjct: 261 A 261


>gi|312794136|ref|YP_004027059.1| RNA polymerase, sigma 28 subunit, sigk [Caldicellulosiruptor
           kristjanssonii 177R1B]
 gi|312181276|gb|ADQ41446.1| RNA polymerase, sigma 28 subunit, SigK [Caldicellulosiruptor
           kristjanssonii 177R1B]
          Length = 219

 Score =  119 bits (299), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 57/257 (22%), Positives = 99/257 (38%), Gaps = 64/257 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI-SEVVSEGNIG 85
           PM  ++EE  L K +   G   A + L+  +LRLV  IA  Y      +  +++S G IG
Sbjct: 13  PMSSEEEEMYLNKMW--EGCKEARNILIEKNLRLVAHIAKKYTFSFPNLTDDIISVGTIG 70

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A++ +   +  +L+TY+   I+  +  Y                      LR+ K  
Sbjct: 71  LIKAIETYSKAKSTKLSTYAAKCIENEILMY----------------------LRQNKKF 108

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           L  +                         S+   +  D          D N     D L 
Sbjct: 109 LSQL-------------------------SLENPIGSD---------KDGNEITLMDVLQ 134

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFE 263
            D D  ++ +  K + KN    L + +     RE++I E R   +N    T   +++   
Sbjct: 135 NDQDDIDEQVNLKIQIKNLLKKLDKILKG---REKKIIELRYGLKNGIERTQMEVANLLG 191

Query: 264 VSRERVRQIEARAFKKV 280
           +SR  V +IE +A +K+
Sbjct: 192 ISRSYVSRIEKKALQKL 208


>gi|302037625|ref|YP_003797947.1| flagellar-specific RNA polymerase sigma 28 factor [Candidatus
           Nitrospira defluvii]
 gi|300605689|emb|CBK42022.1| Flagellar-specific RNA polymerase sigma 28 factor [Candidatus
           Nitrospira defluvii]
          Length = 247

 Score =  119 bits (299), Expect = 4e-25,   Method: Composition-based stats.
 Identities = 45/242 (18%), Positives = 101/242 (41%), Gaps = 15/242 (6%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            +   R++     +V  +A          +   +++S G +GLM A+ K+DP R  +  T
Sbjct: 14  EADRERVIQEFTHVVKAMAHRLAFRLPAYMDAEDLISVGIMGLMDAMDKYDPTREAKFKT 73

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ + I+ AM + I    S+  I  + +++        L+     +     +P     + 
Sbjct: 74  YAEFRIRGAMLDEIR---SMDWIPRSVHERITL-----LQKTYSELLHRLGRPPTDQEVG 125

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           K+L +S  E+     R  G   ++                ++ D +  + + +   ER  
Sbjct: 126 KELKMSAEELDEFLTRSRGAVVISLDDLGVQDADGHKIISVLTDSNQPDPLSVLVNERA- 184

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            R++L  ++  L  +ER +      +E  +T++ +    +V+  RV QI ++A   ++  
Sbjct: 185 -RHVLEAAIHDLPEKERLVLSLYYFEE--LTMKEIGQALKVTESRVCQIHSKAILHLKAR 241

Query: 284 IQ 285
           ++
Sbjct: 242 LE 243


>gi|261420836|ref|YP_003254518.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. Y412MC61]
 gi|319768505|ref|YP_004134006.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. Y412MC52]
 gi|261377293|gb|ACX80036.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. Y412MC61]
 gi|317113371|gb|ADU95863.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           sp. Y412MC52]
          Length = 256

 Score =  119 bits (299), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 44/261 (16%), Positives = 107/261 (40%), Gaps = 18/261 (6%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI-SEVVSEGNIG 85
           P L K +   L   Y++     AA  L+     L+   A            ++   G + 
Sbjct: 6   PPLSKSKLDALISAYQQTKTEEAATALLVRFEPLIAAAAKKMARSRPDFYEDLFQIGRLS 65

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
            ++ +  +DP++G    +Y+M  +   M+ Y+      +++     +K       +++  
Sbjct: 66  FLRLLDHYDPKQGTSFESYAMKSLIGYMKNYLRDKAWYIQVPRKVKEKG-----SKVQQA 120

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDW 203
           +  +T    +   +  IA  L +S  E I +          SL+A +   +K+++   ++
Sbjct: 121 IDELTVKLERSPTIDEIAGHLGLSVEETIEILAGRDHYQAVSLDAPVQDGEKDATTIGEF 180

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  + +  E ++         R  L +++  L+ +E+ + +A   +    T  +L+    
Sbjct: 181 VADEANEIESLIE--------RMDLEQAIGKLSEQEQIVIDAIFRRGE--TQRSLAERLG 230

Query: 264 VSRERVRQIEARAFKKVQESI 284
           VS+  + +I+ RA  K++  +
Sbjct: 231 VSQMTISRIQKRAIAKLKRQL 251


>gi|125553511|gb|EAY99220.1| hypothetical protein OsI_21178 [Oryza sativa Indica Group]
          Length = 500

 Score =  119 bits (299), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 50/252 (19%), Positives = 104/252 (41%), Gaps = 18/252 (7%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDP 95
           +R+ E G  +A ++L+  +LRLV+     Y           ++   G  GL+ A+ +F+P
Sbjct: 254 RRHLEVG-RAARNKLIKHNLRLVLYTINKYYPDMSNDERFDDICQAGANGLITAIDRFEP 312

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           +RGFR++TY+++WI+ ++   I  S    +       +R     + +    + +     +
Sbjct: 313 KRGFRISTYALFWIRHSIVRAITLSNFT-RFPFAMESER-----QEIHRAREELAFELGR 366

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
                 + KK+ +S +    +        SL+A      +N    ++ +    D     +
Sbjct: 367 APTEEEVMKKVGLSPARYRDVVRMTRPTYSLHA------RNRVTQEELINEVTDDDAIGV 420

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIE 273
                    R  +   +  L P+E  +   R   +     TL  ++    +SRE VR+ E
Sbjct: 421 DTSSHNTLLRLAIDDLLDSLKPKESVVIRQRFGLDGRGKRTLSEIAGNLNISREMVRKYE 480

Query: 274 ARAFKKVQESIQ 285
            +A  K++   +
Sbjct: 481 LKALMKLKHPTR 492


>gi|317063372|ref|ZP_07927857.1| RNA polymerase [Fusobacterium ulcerans ATCC 49185]
 gi|313689048|gb|EFS25883.1| RNA polymerase [Fusobacterium ulcerans ATCC 49185]
          Length = 118

 Score =  119 bits (299), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 46/111 (41%), Positives = 75/111 (67%), Gaps = 1/111 (0%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +S Y+ +IRK  +L+K EE  L  + +  GD  A ++L+ S+LRLVV IA GY   GL  
Sbjct: 9   ISLYLADIRKYKILDKDEELNLLIKAK-AGDEEAKNQLILSNLRLVVNIAKGYINKGLSF 67

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            +++SEGN+GL+ A++KFD  +GFR +TY++WWIK ++ + ++     ++I
Sbjct: 68  IDLISEGNLGLIYAIEKFDITKGFRFSTYAVWWIKQSISKAVIVKGREIRI 118


>gi|291300290|ref|YP_003511568.1| Sig B/F/G subfamily RNA polymerase sigma-28 subunit [Stackebrandtia
           nassauensis DSM 44728]
 gi|290569510|gb|ADD42475.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Stackebrandtia nassauensis DSM 44728]
          Length = 267

 Score =  119 bits (299), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 41/238 (17%), Positives = 94/238 (39%), Gaps = 15/238 (6%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +  + +V   L L  ++A  +   G P+ ++     +GL+ AV  F   RG     +++
Sbjct: 43  RALRNTVVQRALPLADRLARRFEHRGQPLEDLTQVARLGLINAVDNFKCGRGGGFTHFAV 102

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I   ++ +      LV++     + RL FN        + ++    +   +   A+ L
Sbjct: 103 PSILGELKRHFRDKGWLVRVPRRLQETRLAFN-----EASKDLSQRLGRSPTLEDYAEYL 157

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   +V +    +   E ++    +  ++S +  D L                    R 
Sbjct: 158 SMPVEQVRAGINCVGAYEGVSLHTPAHRESSEELIDSLGGSDPAMAS--------AEARM 209

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +L  ++  L PRE RI   R + +   +   ++ E  +S+  V ++  +   K++E +
Sbjct: 210 LLRPAIKELTPRECRILSLRFVDDLHQS--EIAREVGLSQMHVSRLLRQTLTKLRERL 265


>gi|298715063|emb|CBJ27770.1| RNA polymerase sigma factor, cyanobacterial RpoD-like family
           [Ectocarpus siliculosus]
          Length = 737

 Score =  119 bits (299), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 52/255 (20%), Positives = 104/255 (40%), Gaps = 29/255 (11%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           + A  +LV  +L LVV +A  Y+        +  ++ EG IGL++A +++DP +GFR  T
Sbjct: 477 MEARQKLVVCNLALVVSLANKYKRSHFDCGCLQTLIQEGTIGLIRAAERYDPSKGFRFTT 536

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y++WWI+A ++  +      + +      K  +  + R    L+         E++ A  
Sbjct: 537 YAIWWIEARLRVSVQTEERFIHVPMWV--KNQYNTVHRSVPKLRKSLGREPTSEELAAQV 594

Query: 164 K-----KLNVSESEVISMNCRLA---GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
           +     K+ V+   V  +   ++     ESL+  +  S          +       +   
Sbjct: 595 EIDTNSKVVVTPKRVEELETWVSFHRKHESLDVPLEVS-TPVPADCSTIEDGVKAPDPST 653

Query: 216 IEKEERKNRRNMLTRSM-SVLNPRERRIFEAR--RLQENPVTLENLSSEFE------VSR 266
               E + +R+ L   +   L+  +R+I   +     E     + +S   +      +S 
Sbjct: 654 ESTSELEIQRDFLESCLCQDLSKIQRKILRMKVGLGGEKGKNRQEISRALKMPFNNVISE 713

Query: 267 ERVRQIEARAFKKVQ 281
           ER      +AF K++
Sbjct: 714 ER------KAFYKLR 722


>gi|160895354|ref|ZP_02076125.1| hypothetical protein CLOL250_02913 [Clostridium sp. L2-50]
 gi|156863047|gb|EDO56478.1| hypothetical protein CLOL250_02913 [Clostridium sp. L2-50]
          Length = 226

 Score =  119 bits (299), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 56/261 (21%), Positives = 96/261 (36%), Gaps = 65/261 (24%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L  +EE    K  +E GD  A   L+  ++RLV  IA  Y G      +++S G IGL+
Sbjct: 27  PLSPKEEAYFLKLCKE-GDPRARKTLIEYNMRLVAHIAKKYNGSHEN-DDLISAGTIGLI 84

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +A+  +D ++G RL TY+   I                      +  L   LR+ + H  
Sbjct: 85  KAIDTYDSKKGKRLVTYASRCI----------------------ENELLMLLRQNRKH-- 120

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS-DKNSSQWQDWLVY 206
                                            A + SL   I +  + N     D +  
Sbjct: 121 ---------------------------------AREVSLFEPIGTDKEGNEISLMDIISP 147

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           D       ++      N + +    +  L  +E  +   R     E P T + ++S   +
Sbjct: 148 DTPSILDSMVHD---YNLKQLPDCMLHHLTKQEMVLLSRRYGLSGEAPCTQKEIASAMGI 204

Query: 265 SRERVRQIEARAFKKVQESIQ 285
           SR  V +IE RA  K++++++
Sbjct: 205 SRSYVSRIEKRALLKLRKALE 225


>gi|153835421|ref|ZP_01988088.1| RNA polymerase sigma factor for flagellar operon [Vibrio harveyi
           HY01]
 gi|156975413|ref|YP_001446320.1| flagellar biosynthesis sigma factor [Vibrio harveyi ATCC BAA-1116]
 gi|148868042|gb|EDL67225.1| RNA polymerase sigma factor for flagellar operon [Vibrio harveyi
           HY01]
 gi|156527007|gb|ABU72093.1| hypothetical protein VIBHAR_03144 [Vibrio harveyi ATCC BAA-1116]
          Length = 244

 Score =  119 bits (299), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 49/249 (19%), Positives = 99/249 (39%), Gaps = 19/249 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPER 97
           Y +HG  ++    +  +  LV +IA    G   P   + +++  G IGL++A + +D  +
Sbjct: 7   YDQHGKFNSQQAFIERYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLIEAQQNYDGSK 66

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G    TY+   I+ AM + I R    V      N + +   +  L+G L        +  
Sbjct: 67  GASFETYAGIRIRGAMLDDI-RKGDWVPRSVHKNNREINQAIAELEGVLN-------RDP 118

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A  L ++  +  S       D + + L+   D   S   D +    +  +    +
Sbjct: 119 SDSEVAAHLGMTLDQYHSALT----DINCSKLVGIEDLGVS--DDVISPADETDDSNPFK 172

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
               ++ +  L  S+  L  RE  +       +  + L+ +     VS  RV QI ++A 
Sbjct: 173 GVADESFKKALVESIKQLPEREALVLSLYY--DEELNLKEIGDVLGVSESRVSQILSQAM 230

Query: 278 KKVQESIQK 286
           ++++  +  
Sbjct: 231 QRLRTKLSA 239


>gi|115465727|ref|NP_001056463.1| Os05g0586600 [Oryza sativa Japonica Group]
 gi|30698488|dbj|BAC76601.1| Sig5 [Oryza sativa Japonica Group]
 gi|30698518|dbj|BAC76607.1| plastid sigma factor SIG5 [Oryza sativa Japonica Group]
 gi|113580014|dbj|BAF18377.1| Os05g0586600 [Oryza sativa Japonica Group]
          Length = 500

 Score =  119 bits (299), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 50/252 (19%), Positives = 104/252 (41%), Gaps = 18/252 (7%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDP 95
           +R+ E G  +A ++L+  +LRLV+     Y           ++   G  GL+ A+ +F+P
Sbjct: 254 RRHLEVG-RAARNKLIKHNLRLVLYTINKYYPDMSNDERFDDICQAGANGLITAIDRFEP 312

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           +RGFR++TY+++WI+ ++   I  S    +       +R     + +    + +     +
Sbjct: 313 KRGFRISTYALFWIRHSIVRAITLSNFT-RFPFAMESER-----QEIHRAREELAFELGR 366

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
                 + KK+ +S +    +        SL+A      +N    ++ +    D     +
Sbjct: 367 APTEEEVMKKVGLSPARYRDVVRMTRPTYSLHA------RNRVTQEELINEVTDDDAIGV 420

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIE 273
                    R  +   +  L P+E  +   R   +     TL  ++    +SRE VR+ E
Sbjct: 421 DTSSHNTLLRLAIDDLLDSLKPKESVVIRQRFGLDGRGKRTLSEIAGNLNISREMVRKYE 480

Query: 274 ARAFKKVQESIQ 285
            +A  K++   +
Sbjct: 481 LKALMKLKHPTR 492


>gi|330946768|gb|EGH47674.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. pisi
           str. 1704B]
          Length = 184

 Score =  119 bits (299), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 38/128 (29%), Positives = 60/128 (46%), Gaps = 4/128 (3%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L+  E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 59  LKIAEIKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 118

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M+AV KF+  RG++ +TY+ WWI+ A+   I      ++I            L R+   +
Sbjct: 119 MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHM--IETINKLNRISRQM 176

Query: 147 QAITDNNL 154
                   
Sbjct: 177 LQEMGREP 184


>gi|302548084|ref|ZP_07300426.1| stress response/stationary phase sigma factor SigF [Streptomyces
           hygroscopicus ATCC 53653]
 gi|302465702|gb|EFL28795.1| stress response/stationary phase sigma factor SigF [Streptomyces
           himastatinicus ATCC 53653]
          Length = 264

 Score =  119 bits (299), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 45/241 (18%), Positives = 102/241 (42%), Gaps = 15/241 (6%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +    +V + + +  ++A  +R  G    ++     +GL++AVK+++P+RG   A++++
Sbjct: 35  EALRQDVVRAWMPMAERLARQFRNRGESAEDLRQVAMLGLVKAVKRYEPDRGSAFASFAV 94

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKPEQVVAIAKK 165
             +   ++ +       V +     + R      R++   Q +T   + +   V AI + 
Sbjct: 95  PTVVGEIKRHFRDHMWGVHVPRRVQELR-----NRVRAAAQELTRTPDDRSPSVSAIVEH 149

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
             +SE +V+     +   ES +AL   ++   ++    L       E       +R  +R
Sbjct: 150 TGMSEEDVL---LGMEAMESFSALSLDAELPGAEDGYSLADTLGAPEPSY----DRVIQR 202

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             L   +  L  RER I   R  +E   T   ++ +  +S+  V ++  R   ++ + I+
Sbjct: 203 EALKPRLRALPERERHILYLRFFREE--TQGRIAEQLGISQMHVSRLINRTCARLHDQIE 260

Query: 286 K 286
            
Sbjct: 261 A 261


>gi|225375354|ref|ZP_03752575.1| hypothetical protein ROSEINA2194_00979 [Roseburia inulinivorans DSM
           16841]
 gi|225212843|gb|EEG95197.1| hypothetical protein ROSEINA2194_00979 [Roseburia inulinivorans DSM
           16841]
          Length = 256

 Score =  119 bits (299), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 55/253 (21%), Positives = 110/253 (43%), Gaps = 21/253 (8%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKF 93
           L + Y++        +L+  +  LV  +A     Y GY +   ++VS G  GL+ A+ KF
Sbjct: 9   LWEEYQKKKTPELREKLIIEYSPLVKLVAGRLSMYLGYNVEYDDLVSYGIFGLIDAIDKF 68

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D  +  +  TY+   I+  + + I R    +       QK++   +++++          
Sbjct: 69  DLGKEVKFETYASLRIRGTILDQI-RKMDWIPRTVRQKQKKIDEAIKQVEM-------RT 120

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
            K      IA++L +SE E+ +   +L      SLN  +    +        +    +  
Sbjct: 121 GKNASDEEIAQELGLSEDELTTWQSQLKVTNIVSLNEYLEQGAEP------VMDARRNSH 174

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
                +K E +  +  L  S+ VL  +ER++      ++  +TL+ +SS  EVS  R+ Q
Sbjct: 175 FIQPEDKVEEEELKQKLEESLEVLTEKERKVILLYYYED--LTLKEISSILEVSESRISQ 232

Query: 272 IEARAFKKVQESI 284
           +  +A  K+++ +
Sbjct: 233 LHTKALLKMRKKL 245


>gi|224116898|ref|XP_002331841.1| predicted protein [Populus trichocarpa]
 gi|222875079|gb|EEF12210.1| predicted protein [Populus trichocarpa]
          Length = 512

 Score =  119 bits (299), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 58/267 (21%), Positives = 110/267 (41%), Gaps = 27/267 (10%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNI 84
           + E  +  VL  R +     +A ++L+  +LRLV+ +   Y      G    ++   G  
Sbjct: 255 LAEATDMDVLQVRKQIEVGRAARNKLIKHNLRLVLFVINKYFQDYANGPRYQDLCQAGVK 314

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM A+ +F+P+R FRL+TY ++WI+ A+   +  S             R+ F L  ++ 
Sbjct: 315 GLMTAIDRFEPKRRFRLSTYGLFWIRHAIIRSMTLSSFT----------RVSFGLESIRS 364

Query: 145 HLQAITDNN----LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
            +Q          L+      I +K+ +S      +        SL++   ++ +     
Sbjct: 365 EIQKAKLELWFQLLRKPTGEEIIEKVGISIERYHEVMRASKPVLSLHSRHKTTQEELISG 424

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENL 258
              +    D ++  L+        R  L   +  L P+E  +   R   +     TL  +
Sbjct: 425 VADVNGGDDRRQSALL--------RLALDDVLDSLKPKESLVVRQRFGLDGKGDRTLGEI 476

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQ 285
           +    +SRE VR+ EA+A  K++   +
Sbjct: 477 AGNLNISREMVRKHEAKALMKLKHPTR 503


>gi|296133648|ref|YP_003640895.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           sp. JR]
 gi|296032226|gb|ADG82994.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           potens JR]
          Length = 242

 Score =  119 bits (299), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 63/263 (23%), Positives = 100/263 (38%), Gaps = 65/263 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EE  L  +    GD +    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 40  PPLSNAEENYLISKLA-TGDAAVRSVLIERNLRLVVYIARKFENTGVGIEDLVSIGTIGL 98

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FDP +  +LATY+   I+  +                         LRR     
Sbjct: 99  IKAVNTFDPAKKIKLATYASRCIENEI----------------------LMYLRR----- 131

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS-DKNSSQWQDWLV 205
                                         N +   + S +  IN   D N     D + 
Sbjct: 132 ------------------------------NNKTRAEVSFDEPINIDWDGNELLLSDVMG 161

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFE 263
            + D   + + E+ +RK     L +     N RERRI E R         T + ++    
Sbjct: 162 TESDIIYKFIEEEVDRKLLALALQKL----NGRERRIMELRFGLIDGTEKTQKEVADMLG 217

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+  + ++E R  K++++ I K
Sbjct: 218 ISQSYISRLEKRILKRLRKEIHK 240


>gi|302549077|ref|ZP_07301419.1| RNA polymerase sigma-G factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302466695|gb|EFL29788.1| RNA polymerase sigma-G factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 287

 Score =  119 bits (299), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 50/249 (20%), Positives = 103/249 (41%), Gaps = 16/249 (6%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +    LV   L +  +IA  +R  G  I ++     +GL++AV +FDP RG    +Y++
Sbjct: 47  EAVRDELVALWLPMAHRIAGRFRDRGESIEDLRQVAALGLVKAVDRFDPSRG-AFESYAV 105

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE-QVVAIAKK 165
             I   ++ +       +++     + R      +++   + +T N   PE  V A+A  
Sbjct: 106 PTITGEVKRHFRDRMWALRVPRRVQELR-----NKVRVARRELTQNPGSPEPSVPALAAH 160

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
             ++E EV +    L    +L+     S  +        +   D    V++++E  K   
Sbjct: 161 TGLTEEEVNAGLEALDSFSTLSLDAELSADDDGYSLADTLGASDTSYDVVVDRESAK--- 217

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
                 +  L  RER I   R  ++  +T   ++ +  +S+  V ++  R+  +V++ + 
Sbjct: 218 ----EGLRRLPERERAILYMRFFED--MTQSRIADQLGISQMHVSRLITRSCARVRDEVL 271

Query: 286 KQVELSSSP 294
            Q      P
Sbjct: 272 GQRGAGRGP 280


>gi|318061849|ref|ZP_07980570.1| sigma factor [Streptomyces sp. SA3_actG]
          Length = 295

 Score =  119 bits (299), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 49/241 (20%), Positives = 100/241 (41%), Gaps = 16/241 (6%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                 LV + L +  +IA  YRG G  + ++     +GL++AV +FDPE      TY++
Sbjct: 35  ERQRALLVEAWLPMAHRIAGRYRGRGESLEDLCQVAALGLLRAVDRFDPEVSDAFETYAV 94

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN-LKPEQVVAIAKK 165
             ++  ++ +   +   V +     + R       ++  LQ +     L+   V  +A+ 
Sbjct: 95  PTMQGELKRHFRDNTWGVHVPRRVQELR-----SAVRAALQELAPRPALRAPSVGELARC 149

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
             +SE+EV      L    S++    +  +     +D L  +    E V+         R
Sbjct: 150 AKLSEAEVRQGLEALDSYRSVSLDSAAPSEGEHPLRDRLGAEDPAYETVV--------DR 201

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             +  +++ L  RER I   R    +  T   +++E  +S+  V ++   A  +V+  ++
Sbjct: 202 ESVRPALAELPERERYILYLRFF--HARTQRAIAAELGLSQMHVSRLITHACAQVRHRVE 259

Query: 286 K 286
            
Sbjct: 260 A 260


>gi|193222293|emb|CAL61487.2| RNA polymerase sigma factor for flagellar operon (Sigma-F factor)
           (Sigma-27) (Sigma-28) [Herminiimonas arsenicoxydans]
          Length = 243

 Score =  119 bits (298), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 42/242 (17%), Positives = 105/242 (43%), Gaps = 16/242 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              LV+ H  LV K+A   +    P   + +++  G IGL+ AV +++   G +  TY++
Sbjct: 10  RDHLVSEHAPLVKKLAHQMKAKLPPSVEVDDLIQAGMIGLLDAVGRYEETHGAQFETYAV 69

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +  S  +         + +  N+R+++  + ++     +P     +AK+L
Sbjct: 70  QRIRGAMLDELRSSDWM--------PRSMRQNMRKIEVAMNSLQQKLGRPPNESEVAKQL 121

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +S ++   +     G + +        +++  + D    D        ++       R+
Sbjct: 122 KLSLADYQDLLSDGGGHQLVYYEDFHDSEDNEHFLDRYCTDESPD---PLQNLMNTGFRS 178

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+         E  + L+ + +   V+  RV Q+ ++A  +++ ++++
Sbjct: 179 AVIAAIEALPEREK--ILMSLYYEQEMNLKEIGAVMGVTESRVSQLHSQAIARMRANLRE 236

Query: 287 QV 288
           + 
Sbjct: 237 KA 238


>gi|169829306|ref|YP_001699464.1| RNA polymerase sigma-28 factor [Lysinibacillus sphaericus C3-41]
 gi|168993794|gb|ACA41334.1| RNA polymerase sigma-28 factor precursor [Lysinibacillus sphaericus
           C3-41]
          Length = 228

 Score =  119 bits (298), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 56/268 (20%), Positives = 97/268 (36%), Gaps = 63/268 (23%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
            L  Y+          K+EE    +R+   GD  A   L+  ++RLV  +   +      
Sbjct: 10  ALLGYLKGQTFHKPFSKEEEAACIERFL-GGDEQARLDLIERNMRLVAHVVKKFHPKHEQ 68

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + + +S G IGLM+AV+ + P++  RLATY+   I+  +  ++                 
Sbjct: 69  LDDYISIGTIGLMKAVESYTPDKKTRLATYAARCIENEILMHLRTQ-------------- 114

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
                                                + +S+   +  D          D
Sbjct: 115 ---------------------------------KKVQKDVSLFEPIGTD---------KD 132

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NP 252
            N+ Q +D L  D    E+   EK E K     L   + +L+ RE  I   R      + 
Sbjct: 133 GNALQIRDLLQCD----EESATEKIEHKEHVAQLYHYLHMLDERELEIVTLRYGLNQQDA 188

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKV 280
           +T + +++   +SR  V +IE RA  K+
Sbjct: 189 LTQKEIAARLNISRSYVSRIEKRALIKL 216


>gi|291545019|emb|CBL18128.1| RNA polymerase sigma factor, sigma-70 family [Ruminococcus sp.
           18P13]
          Length = 220

 Score =  119 bits (298), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 55/230 (23%), Positives = 96/230 (41%), Gaps = 22/230 (9%)

Query: 55  TSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114
             +L LV   A  +RG G+   ++ S G IGLM+AV  FD ERG R +TY++  I   ++
Sbjct: 11  EENLGLVHLCANRFRGRGVEYDDLYSAGCIGLMKAVNAFDTERGVRFSTYAVPVILGEIK 70

Query: 115 EYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVI 174
             + R    VK+  +   K L   + RL+  L+     + K   V  +A+++ V E+E++
Sbjct: 71  R-LFRDGGTVKVSRSM--KELSMRVVRLRDELRM---QSGKEPTVQQLAREMGVEEAEIV 124

Query: 175 SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV 234
              C      SL       +    Q    +         VL            L + M  
Sbjct: 125 QALCVSVPPVSLTDP---GESGEGQLDIPVPPPDTEIGDVLA-----------LRQIMQT 170

Query: 235 LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L+ R+R +   R  Q    T    +    +++ +V + E +    ++E +
Sbjct: 171 LSERDRMLLTMRYYQN--KTQSQTAQALGMTQVQVSRREKKLLLTMREEL 218


>gi|15419944|gb|AAK97216.1|AF300644_1 sigma factor RpoD [Lactobacillus acidophilus]
          Length = 162

 Score =  119 bits (298), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 36/164 (21%), Positives = 67/164 (40%), Gaps = 12/164 (7%)

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I     +      L R++  L         PE++ A   ++N+  ++V  +        
Sbjct: 1   RIPVHMVE--TINKLIRIQRQLLQDLGREPTPEEIGA---EMNMPTNKVRDILRIAQERV 55

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL   I   +++ S   D++    D       +    +  +  L + +  L  RE  +  
Sbjct: 56  SLETPI--GEEDDSHLGDFI---EDKDATSPEQHASYEMLKEQLEQVLETLTDREENVLR 110

Query: 245 ARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R   E     TLE +   F V+RER+RQIEA+A +K++   + 
Sbjct: 111 LRFGLEYGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRS 154


>gi|239628979|ref|ZP_04672010.1| DNA-directed RNA polymerase specialized sigma subunit
           [Clostridiales bacterium 1_7_47_FAA]
 gi|239519125|gb|EEQ58991.1| DNA-directed RNA polymerase specialized sigma subunit
           [Clostridiales bacterium 1_7_47FAA]
          Length = 244

 Score =  119 bits (298), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 52/254 (20%), Positives = 107/254 (42%), Gaps = 17/254 (6%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFDP 95
           + YR++G     ++LV  +L +V   A+  R   G  L   ++  +G + LM+ + ++DP
Sbjct: 2   EAYRKNGSQELRNKLVLHYLPIVRSAAVQLRTMAGSLLEQEDLTDQGVLALMECLDRYDP 61

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            +G R  TY+   ++ AM +YI      V       QK++             ++   + 
Sbjct: 62  GKGARFETYAFVRVRGAMIDYIRSQ-DWVPHRARNFQKKVD-------EAFSILSHEKMG 113

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY-DHDGQEQV 214
              V  +A  L++   +V +    +     L+      D  +   +  L   D DG+ + 
Sbjct: 114 EPDVKDVAGYLDMPVEKVENHIKYMNHASVLSFEAALQDMTAIFAKGELEAGDMDGKPE- 172

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
             E    +    MLT ++  L  +ER +      +E   +   ++    + + RV QI  
Sbjct: 173 --ESLFYREMMEMLTAAIDGLGEKERLVITLYYYEELKYS--EIAEVMGIGQSRVCQIHT 228

Query: 275 RAFKKVQESIQKQV 288
           +A +K++ S++  +
Sbjct: 229 KAIRKLKSSLEDYM 242


>gi|138894766|ref|YP_001125219.1| RNA polymerase sigma factor SigD [Geobacillus thermodenitrificans
           NG80-2]
 gi|196247611|ref|ZP_03146313.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacillus sp.
           G11MC16]
 gi|134266279|gb|ABO66474.1| RNA polymerase sigma-28 factor (sigma-D) [Geobacillus
           thermodenitrificans NG80-2]
 gi|196212395|gb|EDY07152.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacillus sp.
           G11MC16]
          Length = 253

 Score =  119 bits (298), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 49/260 (18%), Positives = 104/260 (40%), Gaps = 22/260 (8%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQA 89
           +E      +    D  AA  LV  ++ LV              +P  E+VS G +GL  A
Sbjct: 10  DEQKYWDDWVNGRDRHAAEELVQRYMPLVSYHVQRLSATLPSSVPKEELVSLGLVGLYDA 69

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           ++KFDP R  +  TY+ + I+ A+ + + +   L         + +   +++++   + +
Sbjct: 70  LEKFDPSRDLKFDTYASFRIRGAILDGLRKEDWL--------PRSVRDKVKKIEETAERL 121

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
               ++      +A +L ++E EV +       +   SL       D          +  
Sbjct: 122 EQRYMRSVTAKEVAAELGMTEEEVQAAVNETFFSNWLSLGQTACEEDDEP-------LAI 174

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            D +  +  E+  ++     L   +  LN +E+ +       +  +T   + S  ++S  
Sbjct: 175 RDDRAVLPEEQVVKQEMIEKLAVGIGQLNEKEQLVISLFY--KEELTFTEIGSILQLSTS 232

Query: 268 RVRQIEARAFKKVQESIQKQ 287
           R+ QI A+A  K++    ++
Sbjct: 233 RISQIHAKALWKLRRFFAEE 252


>gi|121533733|ref|ZP_01665560.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
 gi|121307724|gb|EAX48639.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Thermosinus
           carboxydivorans Nor1]
          Length = 252

 Score =  119 bits (298), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 46/264 (17%), Positives = 111/264 (42%), Gaps = 28/264 (10%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNI 84
           + +  E   L   Y+         +L+  +L LV  +A          +   +++S G  
Sbjct: 6   LTQANEVAWLWAEYQASKKPELREKLIEKYLPLVKMVAGRVAIGLPQHIDKEDLISYGFF 65

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GL+ A+++FDP R  +  TY++  I+ ++ + I        +  +  QK      R L+ 
Sbjct: 66  GLLDAIERFDPSRNIKFETYAVARIRGSIFDAIRVQDW---LPASLRQKG-----RLLER 117

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            +  + ++  +      IA+ +N +  +             L+ LIN  + ++    +  
Sbjct: 118 TVAELENSLGRSATDAEIAQAMNFTVEQ-------------LHQLINQLNASTLIPLEEF 164

Query: 205 VYDH--DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
           V +   +     L ++ E++  +  L +++  L  +ER +          +TL+ +S   
Sbjct: 165 VQNETVNQASPNLAQEIEQEEVKKTLAKAIDRLPEKERLVISLYYY--EGLTLKEISLIL 222

Query: 263 EVSRERVRQIEARAFKKVQESIQK 286
           ++S  R+ Q+  +A  +++ ++ +
Sbjct: 223 KLSEARISQLHTKAIFRLRGALSR 246


>gi|239933011|ref|ZP_04689964.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
 gi|291441364|ref|ZP_06580754.1| conserved hypothetical protein [Streptomyces ghanaensis ATCC 14672]
 gi|291344259|gb|EFE71215.1| conserved hypothetical protein [Streptomyces ghanaensis ATCC 14672]
          Length = 287

 Score =  119 bits (298), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 48/235 (20%), Positives = 100/235 (42%), Gaps = 16/235 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +    LVT+ L +  +IA  +R  G  I ++     +GL++A+ +FDP RG    +Y++ 
Sbjct: 48  AVRDELVTAWLPMAHRIAGRFRDRGESIEDLRQVAALGLVKAIDRFDPGRG-AFESYAVP 106

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE-QVVAIAKKL 166
            I   ++ +       +++     + R      +++   + +T N   PE  V  IA   
Sbjct: 107 TITGEVKRHFRDRMWALRVPRRVQELR-----NKVRVARRELTQNPGSPEPSVADIAAHT 161

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++E EV +    L    +L+     S  +        +   D    ++I++E  K    
Sbjct: 162 GLTEEEVGAGMEALESFSTLSLDAELSADDDGYSLADTLGASDASYDIVIDRESAK---- 217

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                +  L  RER I   R  ++  +T   ++    +S+  V ++ +R+  +V+
Sbjct: 218 ---EGLRRLPERERAILYMRFFED--MTQSRIADRLGISQMHVSRLISRSCARVR 267


>gi|220934511|ref|YP_002513410.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thioalkalivibrio sp.
           HL-EbGR7]
 gi|219995821|gb|ACL72423.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thioalkalivibrio sp.
           HL-EbGR7]
          Length = 241

 Score =  119 bits (298), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 54/238 (22%), Positives = 102/238 (42%), Gaps = 19/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +RLV +H+ LV +IA    G     + + +++  G +GL++A +++D  +G    TY+ 
Sbjct: 9   RNRLVDAHVPLVKRIAYHLLGRLPSSVQVDDLIQAGVVGLLEAAQQYDATQGASFETYAG 68

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS            + +  N RR+   ++ + +   +  Q   +A +L
Sbjct: 69  IRIRGAMLDEVRRSDWT--------PRSVHRNARRVSEAMRLVENRLGREAQPAEVAAEL 120

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            VS  E   M    A  + L+       +  S+ +D L  D    E    E  +    R 
Sbjct: 121 GVSLDEYQHMVSDAASCKVLS--FEDIFEPDSEGEDLLPGD----EPSPFEALQSDGFRA 174

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L R +  L  RER +       ++ + L  +     VS  RV Q+  +A  +++  +
Sbjct: 175 ALAREVGALPERERLVMSLYY--DDELNLREIGEVLGVSESRVCQLHGQALVRLRARM 230


>gi|258511987|ref|YP_003185421.1| RNA polymerase, sigma 28 subunit, SigK [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
 gi|257478713|gb|ACV59032.1| RNA polymerase, sigma 28 subunit, SigK [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
          Length = 239

 Score =  119 bits (298), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 55/284 (19%), Positives = 104/284 (36%), Gaps = 65/284 (22%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           ++++         Y+ +    P  L  +EE    + Y   GD  A +RL+  +LRLV  +
Sbjct: 8   LALVFKDVSLFVSYVKQ-GAFPHPLSPEEEERAIRDYL-AGDADARNRLIEHNLRLVAHL 65

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y   G  + +++S G IGL++AV+ + P++G +LATY+   I+  +  Y+  S    
Sbjct: 66  AKKYESSGEEMDDLISIGTIGLIKAVESYRPDKGTKLATYAARCIENEILMYLRSSKKHR 125

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +    ++      +   +                   +A  L     +VI          
Sbjct: 126 RDAFLSDPVGTDKDGNEMT------------------LADLLGSDPDDVI---------- 157

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
             +A+  S +K        L+                                RE  +  
Sbjct: 158 --DAVDMSWEKQKMFECLPLLAPR----------------------------ERE--VLC 185

Query: 245 ARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R         T   ++ E  +SR  V +IE +A  K+ E++++
Sbjct: 186 KRFGLPDGEERTQREIAKELGISRSYVSRIEQKAIVKLYENMRQ 229


>gi|260886663|ref|ZP_05897926.1| RNA polymerase sigma-27 factor [Selenomonas sputigena ATCC 35185]
 gi|330839507|ref|YP_004414087.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Selenomonas sputigena
           ATCC 35185]
 gi|260863515|gb|EEX78015.1| RNA polymerase sigma-27 factor [Selenomonas sputigena ATCC 35185]
 gi|329747271|gb|AEC00628.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Selenomonas sputigena
           ATCC 35185]
          Length = 252

 Score =  119 bits (298), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 55/260 (21%), Positives = 107/260 (41%), Gaps = 28/260 (10%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQ 88
            E   L   YRE        ++V  +L LV  IA          +   ++VS G  GL+ 
Sbjct: 9   AEIQDLWALYRETRAPEVRDKIVEKYLPLVNIIAGRVVVGLPAHVDRDDLVSSGFFGLLD 68

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++++D ERG +  TY    I+ AM +Y+    ++  I  +  QK     +RR +  +  
Sbjct: 69  AIERYDVERGNKFETYGGVRIRGAMLDYLR---TMDWIPVSKRQK-----IRRYEQAVTT 120

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +     +      +A +L +S+ E+  +     +A    L   + +   +S         
Sbjct: 121 LEGRLGRSATDDELAAELKISKKELHDLVSQTNIATVIPLEEYVRTESPSS--------- 171

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
               Q     E  E+   R+ L  ++  L  +ER +      +E  +TL+ +S    +S 
Sbjct: 172 ----QTIDPEENAEKNELRDTLAEAIDQLPEKERTVVSLYYYEE--LTLKEISLILHLSE 225

Query: 267 ERVRQIEARAFKKVQESIQK 286
            R+ Q+  +A  +++  + +
Sbjct: 226 ARISQLHTKAVFRLRGFLAR 245


>gi|326773499|ref|ZP_08232782.1| RNA polymerase sigma (70) factor RpoD [Actinomyces viscosus C505]
 gi|326636729|gb|EGE37632.1| RNA polymerase sigma (70) factor RpoD [Actinomyces viscosus C505]
          Length = 147

 Score =  119 bits (298), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 28/144 (19%), Positives = 62/144 (43%), Gaps = 7/144 (4%)

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           + +  +  +      +A +L+++  +V+ +        SL+  +   +   S++ D +  
Sbjct: 3   RQMLQDLGREPTPEELAVELDMTPEKVVEVQKYGREPISLHTPL--GEDGDSEFGDLI-- 58

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
             D +  V  +       +  L   +  L+ RE  +   R       P TL+ +   + V
Sbjct: 59  -EDSEAVVPADAVSFTLLQEQLHAVLDTLSEREAGVVSMRFGLTDGQPKTLDEIGKVYGV 117

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           +RER+RQIE++   K++   + QV
Sbjct: 118 TRERIRQIESKTMSKLRHPSRSQV 141


>gi|74317198|ref|YP_314938.1| RNA polymerase sigma-70 factor [Thiobacillus denitrificans ATCC
           25259]
 gi|74056693|gb|AAZ97133.1| RNA polymerase sigma-70 factor [Thiobacillus denitrificans ATCC
           25259]
          Length = 236

 Score =  119 bits (298), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 51/244 (20%), Positives = 104/244 (42%), Gaps = 17/244 (6%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
           G  S+    +T +  LV +IA          + + +++  G IGLM AV +FD  +G + 
Sbjct: 3   GKPSSQDEQITKYAPLVKRIAYHMMARLPASVEVDDLIQVGLIGLMDAVSRFDGTQGAQF 62

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
            +Y+   I+ AM + +  +     +     QK      R+++  +  +   + K      
Sbjct: 63  ESYATQRIRGAMLDELREADW---LPRHVRQKS-----RQIEAAIHKLEQRHGKAPSESE 114

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           I+ +L +   +  SM   +   + L     S + ++S  + +LV   +    VL    E 
Sbjct: 115 ISAELGIPIDQYQSMLGDVKCSQLLYYEDFSDEDSASFLERYLVDGSNDPLAVL----ED 170

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +  R  L  ++  L  RER +       E  + L+ + +   VS  RV Q+ ++A  +++
Sbjct: 171 EGFRASLIAAIHHLPERERSMMGMYY--EQDMNLKEIGAVLGVSESRVCQLHSQAVARLR 228

Query: 282 ESIQ 285
             ++
Sbjct: 229 AQLK 232


>gi|327441149|dbj|BAK17514.1| DNA-directed RNA polymerase specialized sigma subunit [Solibacillus
           silvestris StLB046]
          Length = 236

 Score =  118 bits (297), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 48/243 (19%), Positives = 98/243 (40%), Gaps = 62/243 (25%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           +GDL A   L+  +LRLVV IA  +     PI +++S G+IGL++A++ F+ ++  +LAT
Sbjct: 49  NGDLHARDMLIERNLRLVVYIARRFDNTSTPIEDLISIGSIGLIKAIETFNLDKNIKLAT 108

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   I                      +  +  +LR+                      
Sbjct: 109 YASRCI----------------------ENEILMHLRK---------------------- 124

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
                          R+ G+ S +  +N+    +      ++     +E ++    ERK 
Sbjct: 125 -------------TSRMKGEVSFDEPLNADADGNELLLSDILG---TEEHIITLDVERKI 168

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R  +  +++ L PRE+ I E R        +T + ++    +S+  + ++E +    ++
Sbjct: 169 ERQHMFNAINQLTPREKYIMECRFGLNGKEEMTQKEVADHLGISQSYISRLEKKIIMDLR 228

Query: 282 ESI 284
           E +
Sbjct: 229 EFL 231


>gi|313901762|ref|ZP_07835188.1| RNA polymerase, sigma 29 subunit, SigE [Thermaerobacter
           subterraneus DSM 13965]
 gi|313467968|gb|EFR63456.1| RNA polymerase, sigma 29 subunit, SigE [Thermaerobacter
           subterraneus DSM 13965]
          Length = 244

 Score =  118 bits (297), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 55/242 (22%), Positives = 102/242 (42%), Gaps = 61/242 (25%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +  H L+  +LRLVV IA  +   G+PI ++VS G IGL++AV  FDP +  +LATY+ 
Sbjct: 60  PAVRHTLIERNLRLVVYIARKFDNTGIPIEDLVSIGTIGLIKAVNTFDPSKRIKLATYAS 119

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+  +  ++ R+                                            + 
Sbjct: 120 KCIENEILMHLRRTSRT-----------------------------------------RY 138

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            VS  E ++++     +  L+ +I ++D +                 V+    E K  R+
Sbjct: 139 EVSLDEPLNVDWE-GNELLLSDVIPATDGD-----------------VIYRDLEAKVDRH 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +L R+++ L PRER I E R    +    T + ++    +S+  + ++E R   +++  I
Sbjct: 181 LLHRALARLTPRERLIMELRFGLVDGIERTQKQVADHLGISQSYISRLEKRIINRLRREI 240

Query: 285 QK 286
           +K
Sbjct: 241 RK 242


>gi|224826337|ref|ZP_03699439.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Lutiella nitroferrum
           2002]
 gi|224601438|gb|EEG07619.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Lutiella nitroferrum
           2002]
          Length = 248

 Score =  118 bits (297), Expect = 7e-25,   Method: Composition-based stats.
 Identities = 50/246 (20%), Positives = 102/246 (41%), Gaps = 19/246 (7%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAM---GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           HGD+      V  H  LV KIA          + + ++   G IGL++A ++FDP +G +
Sbjct: 17  HGDID-----VELHAPLVKKIAKLLIAKLPASVELDDLAQVGIIGLIEAARQFDPTQGVQ 71

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
             T++   I+ AM + + R   L         ++   + ++++  +  +     +P Q  
Sbjct: 72  FETFASQRIRGAMLDELRREDWL--------PRQARRHSKQIEDAIHQLEQREGRPPQES 123

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            IA  L +  +E  +M     G  SL    +  D++    +  +    D           
Sbjct: 124 EIADFLGLPLAEYQTMLGECKG-VSLQHFSDFDDEDGVGAEAAVANVADDNAVDPFASLA 182

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             + R  L  ++  L  R++ +       E  + L+ + +   VS  RV Q+ ++A  +V
Sbjct: 183 DGDFRGALVDAIKALPERDQLVMALYY--EQELNLKEIGAVLGVSESRVSQLHSQAIARV 240

Query: 281 QESIQK 286
           +  +++
Sbjct: 241 RSKLRE 246


>gi|313115572|ref|ZP_07801031.1| RNA polymerase sigma-E factor [Faecalibacterium cf. prausnitzii
           KLE1255]
 gi|310622087|gb|EFQ05583.1| RNA polymerase sigma-E factor [Faecalibacterium cf. prausnitzii
           KLE1255]
          Length = 234

 Score =  118 bits (297), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 65/263 (24%), Positives = 102/263 (38%), Gaps = 63/263 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L  ++E VL  R       +A   L+T +LRLVV +A  Y   G+P  +++S G IGL
Sbjct: 33  PPLTPEQEKVLLSRMAAGD-AAARDDLITHNLRLVVYLAKKYESSGVPAEDMISIGTIGL 91

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F PER  +LATY+   I   +  Y                      LR+     
Sbjct: 92  IKAVNTFTPERSIKLATYASRCIGNEILMY----------------------LRKSSNRR 129

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           Q                                 + DE LN      D N     D L  
Sbjct: 130 QEA-------------------------------SIDEPLN---VDGDGNELLLSDILGS 155

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEV 264
           D +   Q L +  E    R +L R++  L+PRER+I E R    +    T +  +    +
Sbjct: 156 DENQISQRLEQDAE----RAVLRRAVDSLSPRERQIMELRFGLADGIERTQKEAADALGI 211

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           S+  + ++E R    ++  ++ +
Sbjct: 212 SQSYISRLEKRIIHTLKVQLENE 234


>gi|253996640|ref|YP_003048704.1| flagellar biosynthesis sigma factor [Methylotenera mobilis JLW8]
 gi|253983319|gb|ACT48177.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Methylotenera mobilis
           JLW8]
          Length = 244

 Score =  118 bits (297), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 52/250 (20%), Positives = 106/250 (42%), Gaps = 16/250 (6%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPER 97
           Y  HG       L+  H  LV K+A   +    P   + +++  G +GL+ AV +++   
Sbjct: 2   YTAHGKKDQKDVLLDQHAILVKKLAYQLKAKLPPSVELDDLIQAGMMGLLDAVNRYEDTH 61

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G +  TY+   I+ AM + + RS   +      N + +   + +L+  L           
Sbjct: 62  GAQFETYAAQRIRGAMLDEL-RSSDWLPRSIRKNMRDVENAISQLEQQLGQ-------SP 113

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +AKKLN+S +E   M    +G + +         +   + D    DHD      I+
Sbjct: 114 TENDVAKKLNMSLAEYHEMLGDCSGHQLIYYEDFHEADSGEHFLDRFQTDHDND---PIK 170

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
                + ++ L  ++  L  RE+ +       E  + L+ + +   VS  RV Q+ ++A 
Sbjct: 171 GLLIGDFKDALIGAIDSLPEREKILLGLYY--EQELNLKEIGAVMSVSESRVCQLHSQAV 228

Query: 278 KKVQESIQKQ 287
            +++ +++++
Sbjct: 229 ARLRANLREK 238


>gi|163801862|ref|ZP_02195759.1| flagellar biosynthesis sigma factor FliA [Vibrio sp. AND4]
 gi|159174370|gb|EDP59174.1| flagellar biosynthesis sigma factor FliA [Vibrio sp. AND4]
          Length = 244

 Score =  118 bits (297), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 48/252 (19%), Positives = 98/252 (38%), Gaps = 19/252 (7%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFD 94
           A  Y +HG  ++    +  +  LV +IA    G   P   + +++  G IGL++A + +D
Sbjct: 4   AITYDQHGKFNSQQAFIERYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLIEAKQNYD 63

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +G    TY+   I+ AM + I R    V      N        R++   +  +     
Sbjct: 64  GSKGASFETYAGIRIRGAMLDDI-RKGDWVPRSVHKNN-------RQINQAIAELEGALN 115

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +      +A+ L ++  +  S       D + + L+   D   S   D +    +  +  
Sbjct: 116 RDPFDSEVAEHLGMTLDQYHSALT----DINCSKLVGIEDLGVS--DDVISPADETDDSN 169

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
             +     + +  L  S+  L  RE  +       +  + L+ +     VS  RV QI +
Sbjct: 170 PFKGVADDSFKKALVESIKQLPEREALVLSLYY--DEELNLKEIGDVLGVSESRVSQILS 227

Query: 275 RAFKKVQESIQK 286
           +A ++++  +  
Sbjct: 228 QAMQRLRTKLSA 239


>gi|255545052|ref|XP_002513587.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
 gi|223547495|gb|EEF48990.1| RNA polymerase sigma factor rpoD, putative [Ricinus communis]
          Length = 501

 Score =  118 bits (297), Expect = 8e-25,   Method: Composition-based stats.
 Identities = 48/244 (19%), Positives = 102/244 (41%), Gaps = 19/244 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            +A ++L+  +LRLV+ +   Y      G    ++   G  GL+ A+ +F+P+R F+L+T
Sbjct: 263 RAARNKLIKHNLRLVMFVMNKYFQDFANGPRFQDLCQAGVKGLITAIDRFEPQRRFQLST 322

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           YS++WI+ A+   +  S        +   + +   +++ K  L          E+++   
Sbjct: 323 YSLFWIRHAIIRSMTLSSFT---KVSFGLESVRTEIQKAKLELLIELQRRPTEEEIIE-- 377

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
            ++ +S      +        SL+A    + +        +    + ++  L+       
Sbjct: 378 -RVGISAERYHEVIRAAKPALSLHARHAVTQEEFINGITDIDGGDNRRQPALL------- 429

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R  L   +  L P+E  +   R   +     TL  ++    +SRE VR+ E +A  K++
Sbjct: 430 -RLALDDVLDSLKPKESLVIRQRYGLDGKGDRTLGEIAGNLNISREMVRKYEVKALMKLK 488

Query: 282 ESIQ 285
              +
Sbjct: 489 HPAR 492


>gi|89094438|ref|ZP_01167378.1| flagellar biosynthesis sigma factor FliA [Oceanospirillum sp.
           MED92]
 gi|89081330|gb|EAR60562.1| flagellar biosynthesis sigma factor FliA [Oceanospirillum sp.
           MED92]
          Length = 236

 Score =  118 bits (297), Expect = 9e-25,   Method: Composition-based stats.
 Identities = 44/239 (18%), Positives = 99/239 (41%), Gaps = 18/239 (7%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
             L+  +  LV +IA            + +++  G IGL++A  K+D  +G    TY+  
Sbjct: 11  EELIEQYAPLVKRIAHHLLARLPSTVLLDDLIQAGMIGLLEAASKYDASKGASFETYAGI 70

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+ ++ + + R             + +  N RR+   +Q I     +      +AK+L 
Sbjct: 71  RIRGSIIDEVRRGDWT--------PRSVHRNSRRVTEAIQQIEARTGRDASDSEVAKELG 122

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  E  ++       +SL++ + S ++  +   +         +    +  ER+     
Sbjct: 123 ISVDEYHNLLK-----DSLDSRLFSFEEMLNPEHEGPGESFANDDPGPNKHIEREAFLKA 177

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           L+ +++ L  RE+ +       +  + L+ +     VS  RV QI ++A  +++  + +
Sbjct: 178 LSEAINNLPEREKLVLALYY--DEELNLKEIGQVLGVSESRVSQIHSQAALRLRSRLSE 234


>gi|295798118|emb|CAX68947.1| RNA polymerase sigma factor 70 [uncultured bacterium]
          Length = 259

 Score =  118 bits (297), Expect = 9e-25,   Method: Composition-based stats.
 Identities = 43/254 (16%), Positives = 102/254 (40%), Gaps = 13/254 (5%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKF 93
           L K+Y++         +V  ++ LV  +A          +  +++VS G +GL  A++K+
Sbjct: 8   LWKKYKQRRTKLLREEIVRKYMYLVKYVAGRVAIGLPSNVEFNDLVSYGLLGLFDAIEKY 67

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D  +G +  TY++  I+ A+ + + +     ++        L    R ++   + + D  
Sbjct: 68  DVMQGNKFETYAVSRIRGAIMDELRKLDWAPRL--------LRKRAREIEKKSRELEDQF 119

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            +      +A+ L +S  ++  +   L     L+      + + ++    L    D    
Sbjct: 120 GRMATDDELAQSLGMSVEDLNGIYSELNSTTFLSLDEVWQNDDGNKPISRLQTVEDSLIT 179

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
                  +   + +L  S+ +L  +E+ +      +   +TL  +     VS  RV QI 
Sbjct: 180 NQFNYVNQNEVKQLLAESIDLLPEKEKLVVVLYYYEN--LTLREIGDVLNVSESRVCQIH 237

Query: 274 ARAFKKVQESIQKQ 287
            +   +++  + K+
Sbjct: 238 TKVVSRLRSHLMKK 251


>gi|237732926|ref|ZP_04563407.1| sporulation sigma factor sigK [Mollicutes bacterium D7]
 gi|229383995|gb|EEO34086.1| sporulation sigma factor sigK [Coprobacillus sp. D7]
          Length = 223

 Score =  118 bits (297), Expect = 9e-25,   Method: Composition-based stats.
 Identities = 58/280 (20%), Positives = 108/280 (38%), Gaps = 67/280 (23%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIR-KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLR 59
           M    +S++ NG      YI     ++P+  K+EE  L + +  +GD  A + L+  +LR
Sbjct: 1   MFSTLLSLLTNG--FFVSYIKSKSFELPLTAKEEERYLEQFF--NGDKEARNVLIERNLR 56

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           LV  IA  Y        +++S G IGL++AV  +      +LATY+   I+  +  ++  
Sbjct: 57  LVAHIAKKYENNKDMQEDLISIGTIGLIKAVDSYKQNHKTKLATYASRCIENEILMHLRT 116

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
           +                                             L++S +E I ++  
Sbjct: 117 NKKTN-----------------------------------------LDISLNETIGIDK- 134

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
                         D +     D +      +++  I+  ++K+  +  T   SVL PRE
Sbjct: 135 --------------DGSEIVLGDIIA----AKQEEFIDIVDKKDTLDKFTTYFSVLEPRE 176

Query: 240 RRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAF 277
           +     R    N    T ++++ +  +SR  V ++E RA 
Sbjct: 177 KDTLIMRYGLNNTKKYTQKDIAKKLNISRSYVSRLEKRAL 216


>gi|86146119|ref|ZP_01064445.1| flagellar biosynthesis sigma factor FliA [Vibrio sp. MED222]
 gi|218708840|ref|YP_002416461.1| flagellar biosynthesis sigma factor [Vibrio splendidus LGP32]
 gi|85836066|gb|EAQ54198.1| flagellar biosynthesis sigma factor FliA [Vibrio sp. MED222]
 gi|218321859|emb|CAV17839.1| RNA polymerase sigma factor for flagellar operon [Vibrio splendidus
           LGP32]
          Length = 244

 Score =  118 bits (297), Expect = 9e-25,   Method: Composition-based stats.
 Identities = 49/249 (19%), Positives = 98/249 (39%), Gaps = 19/249 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPER 97
           Y +H + ++       +  LV +IA    G   P   + +++  G IGL++A + +D  +
Sbjct: 7   YDQHANHNSQQAFFEKYSVLVKRIAHHLLGRLPPNVLVDDLIQAGMIGLIEAQQNYDGTK 66

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G    TY+   I+ AM + I R    V      N        R +   +  +     +  
Sbjct: 67  GASFETYAGIRIRGAMLDDIRR-GDWVPRSVHKNN-------REISSAIAELEGTLNRDP 118

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +AK + +S  +  S       D + + L+   D   S   D +  + D Q+    +
Sbjct: 119 SDAEVAKHMGLSLDQYHSALT----DINCSKLVGIEDLGVS--DDVISPNEDSQDNTPFQ 172

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
               ++ R  L  S+  L  RE  +       +  + L+ +     VS  RV QI +++ 
Sbjct: 173 GVADESFRQALIDSIKQLPEREGLVLSLYY--DEELNLKEIGEVLGVSESRVSQILSQSM 230

Query: 278 KKVQESIQK 286
           ++++  +  
Sbjct: 231 QRLRTKLSA 239


>gi|238916719|ref|YP_002930236.1| RNA polymerase sporulation-specific sigma factor [Eubacterium
           eligens ATCC 27750]
 gi|238872079|gb|ACR71789.1| RNA polymerase sporulation-specific sigma factor [Eubacterium
           eligens ATCC 27750]
          Length = 223

 Score =  118 bits (297), Expect = 9e-25,   Method: Composition-based stats.
 Identities = 58/263 (22%), Positives = 91/263 (34%), Gaps = 64/263 (24%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI--SEVVSEGNIG 85
            L  QEE  L  + RE GD +A + L+  ++RLV  I   Y          +++S G IG
Sbjct: 13  PLSAQEEKELLIKLRE-GDSAARNALIEKNMRLVAHIVKKYTSTERDYINEDLISVGTIG 71

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++AV  FD ER  R +TY+   I   +                          R+ K  
Sbjct: 72  LIKAVDSFDIERNVRFSTYAAKCIDNEI----------------------LMLFRQDKKK 109

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI-NSSDKNSSQWQDWL 204
            +                                     SLN  I    + N    +D +
Sbjct: 110 ERE-----------------------------------VSLNEPIGKDKEGNEISLKDII 134

Query: 205 VYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSE 261
             D +  Q   + +    +  + +      VL PRE  I + R         T   L+  
Sbjct: 135 GEDSEKKQPDAVEDYMFYEQIKCIYGNIEKVLAPREIEILKYRYGLFGAKECTQNELADR 194

Query: 262 FEVSRERVRQIEARAFKKVQESI 284
             +SR  V +IE +A  K++E +
Sbjct: 195 LGISRSYVSRIEKKALGKLREVL 217


>gi|266624394|ref|ZP_06117329.1| RNA polymerase sigma-E factor [Clostridium hathewayi DSM 13479]
 gi|288863758|gb|EFC96056.1| RNA polymerase sigma-E factor [Clostridium hathewayi DSM 13479]
          Length = 216

 Score =  118 bits (297), Expect = 9e-25,   Method: Composition-based stats.
 Identities = 49/261 (18%), Positives = 94/261 (36%), Gaps = 62/261 (23%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L  +EE     RY+E GD  A   L+  ++RLV  +A  Y+     + +++S G IGL+
Sbjct: 7   PLTAREERECLDRYQE-GDQEARATLIERNMRLVAHVAKKYQNTDYDMEDLLSVGTIGLI 65

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV  F  +RG RLATY+   ++  +                                  
Sbjct: 66  KAVNTFHTDRGSRLATYAAKCVENEIL--------------------------------- 92

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                         +  + N   S+ +S+   +  D          D  +    D +  +
Sbjct: 93  --------------MLLRANKKYSKEVSLFEPIGVD---------KDGETVSLVDVIEME 129

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVS 265
               ++ L      ++ R +       L   E+++   R         T   ++    +S
Sbjct: 130 ---NKEALETIILSQDIRELYDAFDHCLRDTEKKVIGMRYGLYGGKEHTQREIADMLGIS 186

Query: 266 RERVRQIEARAFKKVQESIQK 286
           R  V +IE ++ +K++   +K
Sbjct: 187 RSYVSRIEKKSIEKLRMEFEK 207


>gi|293400808|ref|ZP_06644953.1| RNA polymerase sigma-F factor [Erysipelotrichaceae bacterium
           5_2_54FAA]
 gi|291305834|gb|EFE47078.1| RNA polymerase sigma-F factor [Erysipelotrichaceae bacterium
           5_2_54FAA]
          Length = 241

 Score =  118 bits (296), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 42/235 (17%), Positives = 94/235 (40%), Gaps = 19/235 (8%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L +R ++ GD  A    V  +  LV  I   +    + + ++   G +GLM+A+  FD 
Sbjct: 9   ELIQRIKD-GDEEAKSIFVEKNSPLVYSIVRRFSRQRIAMDDLFQIGCVGLMKALNNFDT 67

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
               + +TY++  I   ++ +     ++ +I  +  +  L     ++    + +     +
Sbjct: 68  SYQVKFSTYAVPIIMGEIKRFFRDDGNM-RISRSLKEGYL-----QMSKKKEELLQKLNR 121

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
                 IA  L++  ++VI          SL+  I  +D +    +D +           
Sbjct: 122 EPTYQEIADALSMDVADVILAFEANQFVYSLDETIYENDGSPILLEDKVSN--------- 172

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
             KEE    +  L   ++ L  RE+ +   R   +  +  E ++ + ++S+ +V 
Sbjct: 173 -RKEEDVVMKVSLQNEIAHLEQREQLLLHYRY--DLGMKQEEIAKKLQISQVQVS 224


>gi|257062124|ref|YP_003140012.1| RNA polymerase sigma factor SigF [Cyanothece sp. PCC 8802]
 gi|256592290|gb|ACV03177.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cyanothece
           sp. PCC 8802]
          Length = 258

 Score =  118 bits (296), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 45/256 (17%), Positives = 112/256 (43%), Gaps = 16/256 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVKKFD 94
            L   Y++ G +   ++++  +  LV K A  +  +      +++  G++GL++A+++F+
Sbjct: 15  RLFLDYQKTGSIQLRNQILELNFGLVRKEAYHWVNHCSESYEDLLQVGSLGLIRAIERFN 74

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
            E+G   +++++ +I+  +Q Y+      V+I      +R     +++K   Q   +   
Sbjct: 75  SEKGHAFSSFALPYIRGEIQHYLRDKGYTVRIP-----RRWLEIGQQVKSIKQDFRERFN 129

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +      IA+ L +   E   +       E  SL+  + +     +   D +   +    
Sbjct: 130 RQPTDSEIAQILEIPLKEWQEIQLAFQNREPLSLDLKVGNDSDGQTSLADLVPDPNYRSF 189

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           Q+  E + R      L + ++ L  R RRI E   LQ+  +T    + +  +S   V + 
Sbjct: 190 QLSQEDQIR------LQQGLAQLEERTRRILEFVFLQD--LTQRETAEQLGISVVTVSRR 241

Query: 273 EARAFKKVQESIQKQV 288
             +  + +++++  ++
Sbjct: 242 VKKGLEILKQTMTAEI 257


>gi|218249036|ref|YP_002374407.1| RNA polymerase sigma factor SigF [Cyanothece sp. PCC 8801]
 gi|218169514|gb|ACK68251.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cyanothece
           sp. PCC 8801]
          Length = 258

 Score =  118 bits (296), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 45/256 (17%), Positives = 112/256 (43%), Gaps = 16/256 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVKKFD 94
            L   Y++ G +   ++++  +  LV K A  +  +      +++  G++GL++A+++F+
Sbjct: 15  RLFLDYQKTGSIQLRNQILELNFGLVRKEAYHWVNHCSESYEDLLQVGSLGLIRAIERFN 74

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
            E+G   +++++ +I+  +Q Y+      V+I      +R     +++K   Q   +   
Sbjct: 75  SEKGHAFSSFALPYIRGEIQHYLRDKGYTVRIP-----RRWLEIGQQVKSIKQDFRERFN 129

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +      IA+ L +   E   +       E  SL+  + +     +   D +   +    
Sbjct: 130 RQPTDSEIAQILEIPLKEWQEIQLAFQNREPLSLDLKVGNDSDGQTSLADLVPDPNYRSF 189

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           Q+  E + R      L + ++ L  R RRI E   LQ+  +T    + +  +S   V + 
Sbjct: 190 QLSQEDQIR------LQQGLAQLEERTRRILEFVFLQD--LTQRETAEQLGISVVTVSRR 241

Query: 273 EARAFKKVQESIQKQV 288
             +  + +++++  ++
Sbjct: 242 VKKGLEILKQTMTAEI 257


>gi|126348076|emb|CAJ89797.1| putative RNA polymerase sigma factor [Streptomyces ambofaciens ATCC
           23877]
          Length = 289

 Score =  118 bits (296), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 50/236 (21%), Positives = 103/236 (43%), Gaps = 16/236 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +    LVT+ L +  +IA  +R  G  I ++     +GL++A+ +FDPERG    +Y++ 
Sbjct: 51  AVRDELVTAWLPMAHRIAGRFRDRGESIEDLRQVAALGLVKAIDRFDPERG-AFESYAVP 109

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE-QVVAIAKKL 166
            I   ++ +       +++     + R      +++   + +T N   PE  V A+A   
Sbjct: 110 TITGEVKRHFRDRMWALRVPRRVQELR-----NKVRVARRELTQNPGSPEPSVAALAAHT 164

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++E EV +    L    +L+     S  +        +   DG    +I++E  K    
Sbjct: 165 GLTEDEVSAGMEALESFSTLSLDAELSAGDDGYSLADTLGAADGSYDTVIDRESAK---- 220

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
                +  L  RER I   R  ++  +T   ++    +S+  V ++ +R+  +V++
Sbjct: 221 ---EGLRRLPERERAILYMRFFED--MTQSRIADRLGISQMHVSRLISRSCARVRD 271


>gi|160939653|ref|ZP_02087001.1| hypothetical protein CLOBOL_04545 [Clostridium bolteae ATCC
           BAA-613]
 gi|158437444|gb|EDP15208.1| hypothetical protein CLOBOL_04545 [Clostridium bolteae ATCC
           BAA-613]
          Length = 258

 Score =  118 bits (296), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 48/262 (18%), Positives = 109/262 (41%), Gaps = 15/262 (5%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGL 86
           + ++   + + YR++G     +RL+  +L +V   A       G  L   E++ +G + L
Sbjct: 7   DSEDMVRVLEEYRKNGSQELRNRLIMHYLPIVRSAAVQLRSMAGSLLEQEELIDQGVLAL 66

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++ ++++DP+RG R  T++   ++ AM +YI     +          R     ++++   
Sbjct: 67  IECLERYDPDRGARFETFAFMRVRGAMIDYIRSQDWVPH--------RARNFQKKVEEAC 118

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
             ++   ++   V  +A  L++   +V +    +     L+      D  +   +  L  
Sbjct: 119 SILSHKQMREPDVNEVADYLDLPVEKVENHIKYMNHANLLSFESVLQDMTAIVAKGELES 178

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
                E    E    K     LT ++  L  +ER +      +E   +   ++    + +
Sbjct: 179 GD--IEGKPEENLFYKELMGTLTSAIDGLGEKERLVITLYYYEELKYS--EIAQVMGIGQ 234

Query: 267 ERVRQIEARAFKKVQESIQKQV 288
            RV QI  RA +K++ S++  +
Sbjct: 235 SRVCQIHTRAIQKLKASLEDYM 256


>gi|289805024|ref|ZP_06535653.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. AG3]
          Length = 145

 Score =  118 bits (296), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 53/106 (50%), Positives = 77/106 (72%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             RL+ SHLR VV IA  Y GYGLP ++++ EGNIGLM+AV++F+PE G RL ++++ WI
Sbjct: 38  LKRLILSHLRFVVHIARNYAGYGLPQADLIQEGNIGLMKAVRRFNPEVGVRLVSFAVHWI 97

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           KA + EY+LR+W +VK+ TT  Q++LFFNLR+ K  L     + ++
Sbjct: 98  KAEIHEYVLRNWRIVKVATTKAQRKLFFNLRKTKQRLGWFNQDEVE 143


>gi|222528742|ref|YP_002572624.1| sporulation sigma factor SigK [Caldicellulosiruptor bescii DSM
           6725]
 gi|222455589|gb|ACM59851.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor bescii DSM 6725]
          Length = 219

 Score =  118 bits (296), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 58/272 (21%), Positives = 104/272 (38%), Gaps = 64/272 (23%)

Query: 19  YIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI-S 76
           YI      P  +  +EE +   + RE G   A + L+  +LRLV  IA  Y      +  
Sbjct: 3   YIENQSSFPQPMSPEEEEMYLNKMRE-GCKEARNILIEKNLRLVAHIAKKYTFSFPNLTD 61

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++S G IGL++A++ +   +  +L+TY+   I+  +  Y                    
Sbjct: 62  DIISVGTIGLIKAIETYSSAKCTKLSTYAAKCIENEILMY-------------------- 101

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
             LR+ K  L  +                         S+   +  D          D N
Sbjct: 102 --LRQNKKFLSQL-------------------------SLENPIGSD---------KDGN 125

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVT 254
                D +  D +  ++ +  K + KN    L + +     RE++I E R   +N    T
Sbjct: 126 EITLMDVMQNDQEDIDEQVDLKIQIKNLLKKLDKILKG---REKKIIELRYGLKNGIERT 182

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +++   +SR  V +IE +A +K+   +QK
Sbjct: 183 QMEVANLLGISRSYVSRIEKKALQKLYGELQK 214


>gi|167465670|ref|ZP_02330759.1| sporulation sigma factor SigE [Paenibacillus larvae subsp. larvae
           BRL-230010]
          Length = 196

 Score =  118 bits (296), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 63/259 (24%), Positives = 106/259 (40%), Gaps = 66/259 (25%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EEY+L K     GD +    L+  +LRLVV IA  +   G+ I ++VS G IGL++AV  
Sbjct: 1   EEYLLGKL--PSGDAAIRAMLIERNLRLVVYIARKFENTGINIEDLVSIGAIGLIKAVNT 58

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FDPE+  +LATY+   I                      +  +   LRR           
Sbjct: 59  FDPEKKIKLATYASRCI----------------------ENEILMYLRR----------- 85

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS-DKNSSQWQDWLVYDHDGQ 211
                                   N ++  + S +  +N   D N     D L  ++D  
Sbjct: 86  ------------------------NSKIRTEVSFDEPLNIDWDGNELLLSDVLGTENDTI 121

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
            + + E+ +RK    +L +++  L  RER I E R         T ++++    +S+  +
Sbjct: 122 YRNIEEQVDRK----LLHKALDKLTERERVIMELRFGLQDGEEKTQKDVADLLGISQSYI 177

Query: 270 RQIEARAFKKVQESIQKQV 288
            ++E R  K++++   K V
Sbjct: 178 SRLEKRIIKRLRKEFNKMV 196


>gi|218133504|ref|ZP_03462308.1| hypothetical protein BACPEC_01371 [Bacteroides pectinophilus ATCC
           43243]
 gi|217990879|gb|EEC56885.1| hypothetical protein BACPEC_01371 [Bacteroides pectinophilus ATCC
           43243]
          Length = 238

 Score =  118 bits (296), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 50/233 (21%), Positives = 91/233 (39%), Gaps = 64/233 (27%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+  +LRLVV IA  +   G+ + +++S G IGL++A+  ++P++  +LATY+ 
Sbjct: 61  EQARSVLIEHNLRLVVYIAKRFDNTGIGVEDLISIGTIGLIKAIHSYNPDKSIKLATYAS 120

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+  +  Y+ R+                                            K 
Sbjct: 121 RCIENEILMYLRRNSKT-----------------------------------------KA 139

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            VS  E ++++                D N     D L  D D    V+ +  E +  R 
Sbjct: 140 EVSIDEPLNVD---------------WDGNELLLSDILGTDED----VIYKDIENQAERL 180

Query: 227 MLTRSMSVLNPRERRIFEARRL----QENPVTLENLSSEFEVSRERVRQIEAR 275
           ML ++M  L+ RER I   R       E  +T + ++    +S+  + ++E +
Sbjct: 181 MLGKAMEKLSDRERLIVNLRYGLTSPDEREMTQKEVADYLGISQSYISRLEKK 233


>gi|296132610|ref|YP_003639857.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           sp. JR]
 gi|296031188|gb|ADG81956.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           potens JR]
          Length = 245

 Score =  118 bits (296), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 51/272 (18%), Positives = 98/272 (36%), Gaps = 63/272 (23%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
            YI        L ++EE    +   E GD  A + L+  +LRLV  I   + G      +
Sbjct: 32  SYISNNTFPQPLSEEEEQKYLELL-EKGDEEARNVLIERNLRLVAHIVKKFDGALDDNDD 90

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++S G IGL++A+  F+  +G RLATY+   I+                           
Sbjct: 91  LISIGTIGLIKAINTFNRYKGTRLATYAARCIEN-------------------------- 124

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
                                   I   L  ++   + ++         +++    + N 
Sbjct: 125 -----------------------EILMHLRATKKNRVEVSLY-------DSIGVDKEGNE 154

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTL 255
               D L  +     +++++  E    +  L   +  L+ RE+ + + R    N    T 
Sbjct: 155 ITLIDVLGTES----EIVLDTVESLFEQRRLLEKVKKLSYREKNVLQLRFGLVNGIRKTQ 210

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             ++ +  +SR  V +IE RA  K+ +  + +
Sbjct: 211 REIARKLGISRSYVSRIEKRALNKLTKDFKAE 242


>gi|172037479|ref|YP_001803980.1| RNA polymerase sigma factor SigF [Cyanothece sp. ATCC 51142]
 gi|171698933|gb|ACB51914.1| group 3 sigma-70 RNA polymerase sigma factor F [Cyanothece sp. ATCC
           51142]
          Length = 269

 Score =  117 bits (295), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 44/259 (16%), Positives = 110/259 (42%), Gaps = 16/259 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVK 91
           E   L + Y++       ++++  +  LV K A  +         ++V  G++GL++A++
Sbjct: 23  ETLKLFQEYQKTPKTKLRNQILELNFGLVRKEAHHWVHQCPESYEDLVQVGSLGLIRAIE 82

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           +F  ++G   +++++ +I+  +Q Y+      V+I      +R     R+     Q   +
Sbjct: 83  RFSIDKGNAFSSFAIPYIRGEIQHYLRDKKYTVRIP-----RRWLELGRQSMNVRQEFRE 137

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHD 209
              +      IA+ L +S  E   +          SL+  +++  +  +   D +   + 
Sbjct: 138 KFNRQPTDSEIAQVLEISLKEWQEIKLAFQNREPVSLDVKVSNDGEGQTSLGDLVPDANY 197

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
              Q+  E + R      L +++  L  R R I E   L++  +T    + +  +S   V
Sbjct: 198 RSFQLAQEDQIR------LQQALEQLEERTRHILEFVFLKD--LTQRETAEQLGISVVTV 249

Query: 270 RQIEARAFKKVQESIQKQV 288
            +   +  + +++++ K++
Sbjct: 250 SRRVKKGLEVLKKNMNKEL 268


>gi|89895149|ref|YP_518636.1| sporulation sigma factor SigK [Desulfitobacterium hafniense Y51]
 gi|89334597|dbj|BAE84192.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 248

 Score =  117 bits (295), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 58/292 (19%), Positives = 102/292 (34%), Gaps = 75/292 (25%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSA-----------AHRLVTS 56
            ++ G   L  YI+       L +Q+E    K  R      A            ++LV  
Sbjct: 12  TVLKGVTLLVSYINNNAFPHPLNEQDEAHYLKVLRASKSPEATPKDLTKAEYARNKLVEH 71

Query: 57  HLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           +LRLV  +   + G G    +++S G IGL++ +  FDP +G +LATY+   I+  +   
Sbjct: 72  NLRLVAHLVKKFDGTGEDSDDLISIGTIGLIKGIDTFDPGKGTKLATYAARCIENEI--- 128

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
                                +LR LK                                 
Sbjct: 129 -------------------LMHLRSLKKSRGE---------------------------- 141

Query: 177 NCRLAGDESLNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
                   S+   I    + N     D L  +     + + ++ E +  + +L   +  L
Sbjct: 142 -------VSIYDPIGVDKEGNEISLMDVLASEG----EAISDRIENEFEQRVLLDKVKNL 190

Query: 236 NPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             RER + + R    N    T   ++    +SR  V +IE +A +K+ E ++
Sbjct: 191 TRRERLVLQLRYGLMNSPRRTQREIAKALGISRSYVSRIEKKAIQKLMEQME 242


>gi|302389688|ref|YP_003825509.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermosediminibacter oceani DSM 16646]
 gi|302200316|gb|ADL07886.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermosediminibacter oceani DSM 16646]
          Length = 245

 Score =  117 bits (295), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 54/256 (21%), Positives = 114/256 (44%), Gaps = 30/256 (11%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKF 93
           L   Y+  GD +   RL+  ++ LV  IA          +   ++VS G IGL+QA++++
Sbjct: 10  LWIEYKNTGDSNLKERLIEEYIPLVKHIAARLAINLPPCVDYDDLVSAGIIGLLQAIERY 69

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D  +G R  T++   I+ AM + +     L  I     +K     L+     ++   + N
Sbjct: 70  DVGKGVRFETFAYTRIRGAMLDELR---RLNWIPQKTMEKAKL--LQDAYSQMEQELNGN 124

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYDHDGQ 211
           +K E    IA+KLN++ +E+      LA     SL  + + + +++ +            
Sbjct: 125 VKDED---IARKLNITIAELHQTYKELAATNLVSLEEIFSVAVEDNGE------------ 169

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
               +   E++  + +L  ++  L P+E+ +          + L+ +S    +S  R+ Q
Sbjct: 170 ---PVSHVEKEEIKRILGEAIDRLPPKEKLVIALYYY--EGLNLKEISVVLNLSPARISQ 224

Query: 272 IEARAFKKVQESIQKQ 287
           +  +A  +++ S+ ++
Sbjct: 225 LHTKAILRLRGSLSRK 240


>gi|6952813|gb|AAF32414.1| flagellar-specific RNA polymerase sigma factor FliA [Vibrio
           parahaemolyticus]
          Length = 245

 Score =  117 bits (295), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 50/249 (20%), Positives = 99/249 (39%), Gaps = 19/249 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPER 97
           Y +HG  ++    +  +  LV +IA    G   P   + +++  G IGL++A + +D  +
Sbjct: 8   YDQHGKFNSQQAFIERYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLIEAQQNYDGSK 67

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G    TY+   I+ AM +  +R    V      N + +   +  L+G L        +  
Sbjct: 68  GASFETYAGIRIRGAMLDD-MRKGDWVPRSVHKNNREINQAVAELEGVLN-------RDP 119

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A  L +S  +  S       D + + L+   D   S   D +    +  +    +
Sbjct: 120 TDSEVAAHLGMSLDQYHSALT----DINCSRLVGIEDLGVS--DDVISPADETDDSNPFK 173

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
               ++ R  L  S+  L  RE  +       +  + L+ +     VS  RV QI ++A 
Sbjct: 174 GVADESFRKALVESIKQLPEREALVLSLYY--DEELNLKEIGDVLGVSESRVSQILSQAM 231

Query: 278 KKVQESIQK 286
           ++++  +  
Sbjct: 232 QRLRTKLSA 240


>gi|225181965|ref|ZP_03735398.1| RNA polymerase, sigma 28 subunit, SigK [Dethiobacter alkaliphilus
           AHT 1]
 gi|225167327|gb|EEG76145.1| RNA polymerase, sigma 28 subunit, SigK [Dethiobacter alkaliphilus
           AHT 1]
          Length = 234

 Score =  117 bits (295), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 52/277 (18%), Positives = 98/277 (35%), Gaps = 65/277 (23%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y++       L+ QEE        + GD  A   L+  +LRLV  +   +   G   
Sbjct: 18  LVSYLNNNSFPQPLKPQEEKKYLALMAK-GDEEARSILIERNLRLVAHVIKKFENTGEDQ 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++S G +GL++A+  F+  +G RLATY+   I                      +  +
Sbjct: 77  EDLISIGTVGLIKAIDSFNNNKGTRLATYAARCI----------------------ENEI 114

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS-D 194
             ++R +      +                                    L+  I +  +
Sbjct: 115 LMHIRVITKRKAEVL-----------------------------------LHDPIGTDKE 139

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENP 252
            N     D L  D    E++++ + +RK     L   +  L  RER +   R        
Sbjct: 140 GNEITLLDVLGSD----EELVLNEVDRKMLEAKLYEVIKKLKLRERTVLAMRFGLPMGRR 195

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
            T + ++    +SR  V +IE +   K+ E  +++ +
Sbjct: 196 KTQKEIAKSLGISRSYVSRIEKKVIAKIAEEFRQERQ 232


>gi|146344354|ref|YP_001202210.1| putative RNA polymerase sigma factor [Pseudomonas fluorescens
           SBW25]
 gi|146188166|emb|CAM96497.1| putative RNA polymerase sigma factor [Pseudomonas fluorescens
           SBW25]
          Length = 533

 Score =  117 bits (295), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 54/240 (22%), Positives = 104/240 (43%), Gaps = 19/240 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              A     +++RLV +    +R     I+   S  N+GL +AV +F PE GFR +T ++
Sbjct: 297 EKCADIFTNANVRLVEQQIGRFRFADKEIA--RSAANMGLTRAVYRFAPEMGFRFSTIAL 354

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            WI  ++   +    S +++             RR+  ++      +     + ++A+  
Sbjct: 355 TWINVSISRDLADQES-IRLP------EGMHKHRRMISNML----RDQPNVSINSLAEAT 403

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +  V  +     G  S++     +D + +     L+ D +      IE +   + R 
Sbjct: 404 KLEQDVVRDLVHFAGGQRSIDTAFQGTDSSDADGLHELLADTNNDFMSEIEDD---SMRQ 460

Query: 227 MLTRSM-SVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +  ++  VL  RE  +   R    +    TL  LS E  +S+ERVRQ+E +A  K+++S
Sbjct: 461 FVESALGDVLTQREIFVIVNRFGMGDAREKTLAELSVEMNLSKERVRQLEIQALSKIRDS 520


>gi|219669565|ref|YP_002460000.1| sporulation sigma factor SigK [Desulfitobacterium hafniense DCB-2]
 gi|219539825|gb|ACL21564.1| RNA polymerase, sigma 28 subunit, SigK [Desulfitobacterium
           hafniense DCB-2]
          Length = 249

 Score =  117 bits (295), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 58/292 (19%), Positives = 102/292 (34%), Gaps = 75/292 (25%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSA-----------AHRLVTS 56
            ++ G   L  YI+       L +Q+E    K  R      A            ++LV  
Sbjct: 13  TVLKGVTLLVSYINNNAFPHPLNEQDEAHYLKVLRASKSPEATPKDLTKAEYARNKLVEH 72

Query: 57  HLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           +LRLV  +   + G G    +++S G IGL++ +  FDP +G +LATY+   I+  +   
Sbjct: 73  NLRLVAHLVKKFDGTGEDSDDLISIGTIGLIKGIDTFDPGKGTKLATYAARCIENEI--- 129

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
                                +LR LK                                 
Sbjct: 130 -------------------LMHLRSLKKSRGE---------------------------- 142

Query: 177 NCRLAGDESLNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
                   S+   I    + N     D L  +     + + ++ E +  + +L   +  L
Sbjct: 143 -------VSIYDPIGVDKEGNEISLMDVLASEG----EAISDRIENEFEQRVLLDKVKNL 191

Query: 236 NPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             RER + + R    N    T   ++    +SR  V +IE +A +K+ E ++
Sbjct: 192 TRRERLVLQLRYGLMNSPRRTQREIAKALGISRSYVSRIEKKAIQKLMEQME 243


>gi|291442923|ref|ZP_06582313.1| RNA polymerase sigma factor [Streptomyces roseosporus NRRL 15998]
 gi|291345870|gb|EFE72774.1| RNA polymerase sigma factor [Streptomyces roseosporus NRRL 15998]
          Length = 265

 Score =  117 bits (295), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 46/237 (19%), Positives = 95/237 (40%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +     + S L +  +IA  +R  G  + ++     +GL++AV ++DPERG    TY++ 
Sbjct: 37  ALRDETIRSWLPMAHRIATRFRNRGEAMDDLRQVAAMGLVKAVDRYDPERGKAFETYAVP 96

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +   ++ +       V +      + L   +R  +  L   +           IA    
Sbjct: 97  TVTGELKRHFRDHTWDVHVPRRV--QDLRNRVRVARRELAQTSGGG--SPTCAEIASATG 152

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + E +V+     L   ES +AL   ++    +    LV      +  L    +    R  
Sbjct: 153 LGEEDVL---LGLEALESYSALSLDAEPAGVEGGSPLVDRLGSCDAALDTAVD----REA 205

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +   +  L  RER I   R  Q+  +T   ++    +S+  V ++ +R+ ++V+  +
Sbjct: 206 VKPELRGLPERERTILYLRYFQD--MTQVRIAERLGISQMHVSRLLSRSCERVRAGV 260


>gi|315179524|gb|ADT86438.1| RNA polymerase sigma factor for flagellar operon [Vibrio furnissii
           NCTC 11218]
          Length = 244

 Score =  117 bits (295), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 49/249 (19%), Positives = 101/249 (40%), Gaps = 19/249 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPER 97
           Y ++G++++    +  +  LV +IA    G   P   I +++  G +GL++A K +D  +
Sbjct: 7   YDQYGNMNSQKLFLDKYSVLVKRIAHHLIGRLPPSVLIEDLIQAGMVGLLEAQKNYDGSK 66

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G    TY+   I+ AM + I R    V      + + +   +  L+G L        +  
Sbjct: 67  GASFETYAGIRIRGAMLDDIRR-GDWVPRSVHKHNREIGQAIAVLEGELN-------RDP 118

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +AK L +S  +  S+         +N       ++     D +    D ++    +
Sbjct: 119 TDSEVAKHLGMSLDQYHSVLT------DINCSRIVGIEDLGVTDDAISPVDDDEDNSPFK 172

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
               ++ R  L  S+  L  RE  +       +  + L+ +     VS  RV QI ++A 
Sbjct: 173 GVADESFRKALVESIKSLPEREALVLSLYY--DEELNLKEIGEVLGVSESRVSQILSQAM 230

Query: 278 KKVQESIQK 286
           ++++  +  
Sbjct: 231 QRLRTKLSS 239


>gi|332994104|gb|AEF04159.1| flagellar biosynthesis sigma factor [Alteromonas sp. SN2]
          Length = 243

 Score =  117 bits (295), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 50/252 (19%), Positives = 100/252 (39%), Gaps = 22/252 (8%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFD 94
           A  Y++  D     +LV  H  LV +IA            + +++  G IGL++A + FD
Sbjct: 5   AAAYQQQTD---KSQLVERHASLVKRIAHHLMARLPASVLVDDLIQSGMIGLLEAARNFD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +G    T++   I+ AM + I +             + +  N R +   +  +     
Sbjct: 62  GSKGASFETFAGIRIRGAMLDEIRKGDWT--------PRSVHKNGRAITEAISQVEGETG 113

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +  + V IA K+NVS  +   M   +      NA      ++    +D +  + +     
Sbjct: 114 RDARDVDIAAKMNVSMQDYHQMLNEV------NAGKLVGIEDLGVSEDVISTEKNRGSDA 167

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
            +E   +   +  L  +++ L  RE  +       +  + L  +    +VS  RV QI +
Sbjct: 168 PLEDLMQGAFQKALAHAITTLPEREAIVLSLYY--DEELNLREIGEVLDVSESRVSQIHS 225

Query: 275 RAFKKVQESIQK 286
           +A  K++  ++ 
Sbjct: 226 QAMLKLKSRMKS 237


>gi|258592481|emb|CBE68790.1| RNA polymerase sigma factor whiG (modular protein) [NC10 bacterium
           'Dutch sediment']
          Length = 459

 Score =  117 bits (295), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 52/252 (20%), Positives = 104/252 (41%), Gaps = 17/252 (6%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFD 94
            K YR+  D     RL+T+++ LV ++A          + + ++ S G +GL+ AV+ +D
Sbjct: 8   WKAYRQTKDPGLRDRLITANISLVRQVAGRLSLQLPSCVELDDLESAGAVGLVSAVEHYD 67

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P++    ATY+ + I+ A+ + +               + L    R ++  L  +  +  
Sbjct: 68  PDQPSEFATYAQYRIRGAILDDLRAQ--------DFAPRSLRAKAREIQQTLVRLEVDLG 119

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +      +A  L +           + G    SL+     +D   S    W + D  G++
Sbjct: 120 REPSDDEVAAALGMDRETYWRTLGEIRGMVLVSLDEPGVEADGTESDRLIWELPDRAGRD 179

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
                +  R+ R  +L   +  L  +ER +      +E  +T++ +    EVS  RV QI
Sbjct: 180 --PSTEAARRERVRLLGGIIEALPAQERLVLTLYYFEE--LTMKEIGRVLEVSESRVSQI 235

Query: 273 EARAFKKVQESI 284
              A  +++  +
Sbjct: 236 HTSAILRMRARL 247


>gi|56421959|ref|YP_149277.1| DNA-directed RNA polymerase sigma-37 factor [Geobacillus
           kaustophilus HTA426]
 gi|56381801|dbj|BAD77709.1| DNA-directed RNA polymerase sigma-37 factor (sigma-B) [Geobacillus
           kaustophilus HTA426]
          Length = 256

 Score =  117 bits (295), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 44/261 (16%), Positives = 106/261 (40%), Gaps = 18/261 (6%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI-SEVVSEGNIG 85
           P L K +   L   Y++     AA  L+     L+   A            ++   G + 
Sbjct: 6   PPLSKSKLDALISAYQQTKTEEAATALLVRFEPLIAAAAKKMARSRPDFYEDLFQIGRLS 65

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
            ++ +  +DP +G    +Y+M  +   M+ Y+      +++     +K       +++  
Sbjct: 66  FLRLLDHYDPSQGASFESYAMKSLIGYMKNYLRDKAWYIQVPRKVKEKG-----SKVQQA 120

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDW 203
           +  +T    +   +  IA  L +S  E I +          SL+A +   +K+++   ++
Sbjct: 121 IDELTVKLERSPNIDEIAAHLGLSVEETIEILAGRDHYQAISLDAPVQDGEKDATTIGEF 180

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  + +  E ++         R  L +++  L+ +E+ + +A   +    T  +L+    
Sbjct: 181 VADEANEIESLIE--------RMDLEQAIGKLSEQEQIVIDAVFRRGE--TQRSLAERLG 230

Query: 264 VSRERVRQIEARAFKKVQESI 284
           VS+  + +I+ RA  K++  +
Sbjct: 231 VSQMTISRIQKRAIAKLKRQL 251


>gi|284053747|ref|ZP_06383957.1| RNA polymerase sigma factor [Arthrospira platensis str. Paraca]
          Length = 179

 Score =  117 bits (295), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 36/179 (20%), Positives = 78/179 (43%), Gaps = 13/179 (7%)

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
            WWI+ A+   I ++   +++     +K     L ++K   + +     +      IAK 
Sbjct: 1   YWWIRQAITRAIAQNSRTIRLPIHITEK-----LNKIKRVQRELFQQYGRNATPTEIAKA 55

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           L++  S++           SL+  +   D   ++ QD L  +    +  + ++  R++  
Sbjct: 56  LDLEPSQIRDYLLASRHPVSLD--LRVGDNQDTELQDLLEDESASADSYVTQQLLRQD-- 111

Query: 226 NMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             L   M+ L P++R +   R    +   ++L  +  +  +SRERVRQ+E +A   ++ 
Sbjct: 112 --LKDMMADLTPQQREVLTLRYGLNDGKEMSLSKVGVQMNISRERVRQLENQALNHLRR 168


>gi|90579944|ref|ZP_01235752.1| flagellar biosynthesis sigma factor FliA [Vibrio angustum S14]
 gi|90438829|gb|EAS64012.1| flagellar biosynthesis sigma factor FliA [Vibrio angustum S14]
          Length = 240

 Score =  117 bits (295), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 44/237 (18%), Positives = 97/237 (40%), Gaps = 19/237 (8%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              +  +  LV +IA        P   + +++  G IGL++A + +DP +G    T++  
Sbjct: 15  QAFIERYSSLVKRIAHHLMVRLPPSVLVEDLIQAGMIGLLEAQQNYDPTKGASFETFAGI 74

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+ AM + I R    V        + ++ N R++   +  + +   +      IA+ L+
Sbjct: 75  RIRGAMLDDIRR-GDWVP-------RSVYKNSRKISEAISHLENELGRDPNDQEIAQYLD 126

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +   +          D +   L+  SD   ++  D +  +    E   ++     N R  
Sbjct: 127 MPLEQYHQAL----NDVNCGRLVGISDLGVAE--DTVANEESIGENTPLQGVVDDNFRAS 180

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L  ++  L  RE  +       +  + L+ + +   VS  R+ QI ++A ++++  +
Sbjct: 181 LAEAIETLPEREALVLSLYY--DEELNLKEIGAVIGVSESRICQIHSQAMQRLRAKL 235


>gi|28899006|ref|NP_798611.1| flagellar biosynthesis sigma factor [Vibrio parahaemolyticus RIMD
           2210633]
 gi|153836996|ref|ZP_01989663.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus AQ3810]
 gi|260365248|ref|ZP_05777805.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus K5030]
 gi|260878798|ref|ZP_05891153.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus AN-5034]
 gi|260899951|ref|ZP_05908346.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus AQ4037]
 gi|28807225|dbj|BAC60495.1| flagellar-specific RNA polymerase sigma factor FliA [Vibrio
           parahaemolyticus RIMD 2210633]
 gi|149749769|gb|EDM60514.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus AQ3810]
 gi|308094185|gb|EFO43880.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus AN-5034]
 gi|308107226|gb|EFO44766.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus AQ4037]
 gi|308115412|gb|EFO52952.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus K5030]
 gi|328474457|gb|EGF45262.1| flagellar biosynthesis sigma factor [Vibrio parahaemolyticus 10329]
          Length = 244

 Score =  117 bits (295), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 51/252 (20%), Positives = 100/252 (39%), Gaps = 19/252 (7%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFD 94
           A  Y +HG  ++    +  +  LV +IA    G   P   + +++  G IGL++A + +D
Sbjct: 4   AITYDQHGKFNSQQAFIERYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLIEAQQNYD 63

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +G    TY+   I+ AM +  +R    V      N + +   +  L+G L        
Sbjct: 64  GSKGASFETYAGIRIRGAMLDD-MRKGDWVPRSVHKNNREINQAVAELEGVLN------- 115

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +      +A  L +S  +  S       D + + L+   D   S   D +    +  +  
Sbjct: 116 RDPTDSEVAAHLGMSLDQYHSALT----DINCSRLVGIEDLGVS--DDVISPADETDDSN 169

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
             +    ++ R  L  S+  L  RE  +       +  + L+ +     VS  RV QI +
Sbjct: 170 PFKGVADESFRKALVESIKQLPEREALVLSLYY--DEELNLKEIGDVLGVSESRVSQILS 227

Query: 275 RAFKKVQESIQK 286
           +A ++++  +  
Sbjct: 228 QAMQRLRTKLSA 239


>gi|160933635|ref|ZP_02081023.1| hypothetical protein CLOLEP_02489 [Clostridium leptum DSM 753]
 gi|156867512|gb|EDO60884.1| hypothetical protein CLOLEP_02489 [Clostridium leptum DSM 753]
          Length = 217

 Score =  117 bits (295), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 48/236 (20%), Positives = 98/236 (41%), Gaps = 24/236 (10%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             + + S++ LV   A  +RG G+   ++V  G +GL++AV  FD  RG + +TY++  I
Sbjct: 4   REQAIESNMGLVHACAKRFRGRGIEYDDLVQAGCLGLVKAVDHFDEGRGLQFSTYAVPVI 63

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              M+  + R    +K+G    +  L     +        +    +   +  +A++L V 
Sbjct: 64  LGEMRR-LFRDGGAIKVGRALKELSL-----KAARACNEFSLREGRQPTISELAEQLGVE 117

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK-EERKNRRNML 228
            +E            SL+A     ++N             GQ  V  E  EE+ +    L
Sbjct: 118 PAEASQALGASQQPLSLSA----DEENGG-----------GQIDVPTEAPEEKISELIAL 162

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + +  L+PR+R +   R       T    +    +++ +V + E +  ++++  +
Sbjct: 163 KQVVGELDPRDRSLIVMRFF--KSRTQTQTAEVLGMTQVQVSRREKKILQELKTKL 216


>gi|172038499|ref|YP_001805000.1| RNA polymerase sigma factor SigF [Cyanothece sp. ATCC 51142]
 gi|171699953|gb|ACB52934.1| group 3 sigma-70 RNA polymerase sigma factor J [Cyanothece sp. ATCC
           51142]
          Length = 282

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 54/256 (21%), Positives = 107/256 (41%), Gaps = 16/256 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG-LPISEVVSEGNIGLMQAVKKFD 94
            L   Y  +  L   ++LV  +L LV ++A         P  ++   G +GL++A+++FD
Sbjct: 39  ELLSAYARNPSLELRNQLVERNLGLVRQVAHRISRQCSEPYEDLEQIGYLGLIRAIERFD 98

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P++G   +++++ +I+  M  Y+    S+++I     +        + K   + +T +  
Sbjct: 99  PQQGCAFSSFAIPYIRGEMLHYLRDKGSVMRIPRRWQEL-----YNKAKKIRKQLTVSLK 153

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +P     IA  L V   E       L      SL+A I+ +   S  + D L       +
Sbjct: 154 RPPSDWEIADALGVPLEEWNECQLALQNRLLVSLDATISHNVDCSISFGDTLPDQEYQAK 213

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           Q L E       R  L R++  L  + +   E   L E P   +  + +  +S   V + 
Sbjct: 214 QKLEED------RLQLQRALGQLEEKTKAAIECVFLHELPR--KEAAKQIGISPMTVTRH 265

Query: 273 EARAFKKVQESIQKQV 288
             +  +++   ++ QV
Sbjct: 266 LKKGIQQLGSLLEPQV 281


>gi|239939493|ref|ZP_04691430.1| putative RNA polymerase sigma factor [Streptomyces roseosporus NRRL
           15998]
 gi|239985982|ref|ZP_04706646.1| putative RNA polymerase sigma factor [Streptomyces roseosporus NRRL
           11379]
          Length = 262

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 46/237 (19%), Positives = 95/237 (40%), Gaps = 13/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +     + S L +  +IA  +R  G  + ++     +GL++AV ++DPERG    TY++ 
Sbjct: 34  ALRDETIRSWLPMAHRIATRFRNRGEAMDDLRQVAAMGLVKAVDRYDPERGKAFETYAVP 93

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +   ++ +       V +      + L   +R  +  L   +           IA    
Sbjct: 94  TVTGELKRHFRDHTWDVHVPRRV--QDLRNRVRVARRELAQTSGGG--SPTCAEIASATG 149

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + E +V+     L   ES +AL   ++    +    LV      +  L    +    R  
Sbjct: 150 LGEEDVL---LGLEALESYSALSLDAEPAGVEGGSPLVDRLGSCDAALDTAVD----REA 202

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +   +  L  RER I   R  Q+  +T   ++    +S+  V ++ +R+ ++V+  +
Sbjct: 203 VKPELRGLPERERTILYLRYFQD--MTQVRIAERLGISQMHVSRLLSRSCERVRAGV 257


>gi|331006368|ref|ZP_08329678.1| RNA polymerase sigma factor for flagellar operon [gamma
           proteobacterium IMCC1989]
 gi|330419828|gb|EGG94184.1| RNA polymerase sigma factor for flagellar operon [gamma
           proteobacterium IMCC1989]
          Length = 251

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 46/241 (19%), Positives = 102/241 (42%), Gaps = 18/241 (7%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           ++A   V  +  LV +IA            + +++  G IGL++A KK+D  RG    TY
Sbjct: 21  ASADICVEDYADLVKRIAQHMVAKMPASVQVDDLIQSGMIGLLEAAKKYDGSRGASFETY 80

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +   I+ A+ + I R    V      N + +   + +L+  L        +  +   IA+
Sbjct: 81  AGIRIRGAIVDEI-RKGDWVPRSVHRNSRLISNTIHQLEASL-------GRDAKDSEIAE 132

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            + V   E  +M    + D S ++ + S D++    +  +  + +       +  + +  
Sbjct: 133 AMGVDIDEYYAM----SRDAS-SSRLFSIDESFESDESVISNEKNSPFVDPHDGAQHQAL 187

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++ L  ++  L  RE+ +       +  + L+ +     V+  RV QI ++A  +++  +
Sbjct: 188 KSSLVTAIDKLPEREKLVLSLYY--DEELNLKEIGQILGVTESRVSQIHSQAALRLKSKL 245

Query: 285 Q 285
           +
Sbjct: 246 K 246


>gi|318075206|ref|ZP_07982538.1| sigma factor [Streptomyces sp. SA3_actF]
          Length = 293

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 49/241 (20%), Positives = 100/241 (41%), Gaps = 16/241 (6%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                 LV + L +  +IA  YRG G  + ++     +GL++AV +FDPE      TY++
Sbjct: 35  ERQRALLVEAWLPMAHRIAGRYRGRGESLEDLCQVAALGLLRAVDRFDPEVSDAFETYAV 94

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN-LKPEQVVAIAKK 165
             ++  ++ +   +   V +     + R       ++  LQ +     L+   V  +A+ 
Sbjct: 95  PTMQGELKRHFRDNTWGVHVPRRVQELR-----SAVRAALQELAPRPALRAPSVGELARC 149

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
             +SE+EV      L    S++    +  +     +D L  +    E V+         R
Sbjct: 150 AKLSEAEVRQGLEALDSYRSVSLDSAAPSEGEHPLRDRLGAEDPAYETVV--------DR 201

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             +  +++ L  RER I   R    +  T   +++E  +S+  V ++   A  +V+  ++
Sbjct: 202 ESVRPALAELPERERYILYLRFF--HARTQRAIAAELGLSQMHVSRLITHACAQVRHRVE 259

Query: 286 K 286
            
Sbjct: 260 A 260


>gi|154249080|ref|YP_001409905.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Fervidobacterium
           nodosum Rt17-B1]
 gi|154153016|gb|ABS60248.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Fervidobacterium
           nodosum Rt17-B1]
          Length = 233

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 48/239 (20%), Positives = 106/239 (44%), Gaps = 17/239 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              ++  ++ +V KIA   +    Y + I +++ EG I L+QA +K+DP  G    T++ 
Sbjct: 4   KEMVIQEYIPMVTKIARDLKINLPYNVEIDDLIQEGVIALLQAAEKYDPRYGATFKTFAY 63

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +K AM +Y+ +   L         K +  ++++    L    + N +      +++ L
Sbjct: 64  TRVKGAMIDYLRKLDYL--------PKNVRQDIKKFDRELLNFYEQNKRLPTYDEMSEIL 115

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   EV  +   LA  +SLN      + + + +    +      E+ + E   +     
Sbjct: 116 GIDVEEVEEIYRELALKQSLNLDQYLFESDENSYGSIDI----KSEENVKENAWKSILHE 171

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            L  +++ L+ +E+ I   R   E+ ++L+ ++    V+  RV QI      K+++ ++
Sbjct: 172 QLVEAINKLDEKEKIILSMRF--EHELSLKEIAEVLGVTESRVSQILGVILSKLRKMLR 228


>gi|304404017|ref|ZP_07385679.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
 gi|304346995|gb|EFM12827.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
          Length = 240

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 58/247 (23%), Positives = 99/247 (40%), Gaps = 64/247 (25%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD +    L+  +LRLVV IA  +   G+ I ++VS G IGL++AV  FDPE+  +LATY
Sbjct: 55  GDTAIRAMLIERNLRLVVYIARKFENTGIHIEDLVSIGAIGLIKAVNTFDPEKKIKLATY 114

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +   I                      +  +   LRR                       
Sbjct: 115 ASRCI----------------------ENEILMYLRR----------------------- 129

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
                       N +   + S +  +N   D N     D L  ++D   + + E+ +RK 
Sbjct: 130 ------------NSKTRTEVSFDEPLNIDWDGNELLLSDVLGTENDTIYRNIEEQVDRK- 176

Query: 224 RRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +L +++  L  RER I E R         T ++++    +S+  + ++E R  K+++
Sbjct: 177 ---LLHKALDKLTERERIIMELRFGLADGEEKTQKDVADLLGISQSYISRLEKRIIKRLR 233

Query: 282 ESIQKQV 288
           +   K V
Sbjct: 234 KEFNKMV 240


>gi|220932500|ref|YP_002509408.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Halothermothrix orenii
           H 168]
 gi|219993810|gb|ACL70413.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Halothermothrix orenii
           H 168]
          Length = 254

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 56/260 (21%), Positives = 110/260 (42%), Gaps = 32/260 (12%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKK 92
            L + Y+  G   A   L+ ++L LV       +          ++ S G IGL+ A++K
Sbjct: 12  DLWEAYKGKGSQEARKELILNYLPLVKYQVERVKMIIPDFIEEDDLESYGIIGLIDAIEK 71

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD- 151
           +D   G +  TY+   I+ ++ +++ +               L  +LRR    LQ + D 
Sbjct: 72  YDYRLGIKFNTYASRRIRGSIIDHLRKLDW------------LPHSLRREGKELQKVADK 119

Query: 152 ---NNLKPEQVVAIAKKLNVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVY 206
                 +   V  +A K N+S  +V  +  +L  A   SL       D   S   +++  
Sbjct: 120 LAKELGRKPTVAELANKTNISREKVTKIYSKLNSAKWVSLY-----EDWGESTVFNFIKG 174

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           D    +++L    ++K R  +L R++  L+  ER +      +E  +T + ++    +S 
Sbjct: 175 DCLPPDRIL----DKKERIKLLARAIDRLSESERTVISLYYYEE--LTQKEIAEVMGLSP 228

Query: 267 ERVRQIEARAFKKVQESIQK 286
            R+ QI  RA  +++  + +
Sbjct: 229 ARISQIHKRAVYRLRGYLAR 248


>gi|291562040|emb|CBL40856.1| RNA polymerase sigma factor, sigma-70 family [butyrate-producing
           bacterium SS3/4]
          Length = 265

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 46/260 (17%), Positives = 107/260 (41%), Gaps = 22/260 (8%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAV 90
           E  L   Y++  D      +   +L +    A          + + + V+EG + +++ +
Sbjct: 9   EKELFALYKKTKDPEIKKEITMQYLYIARTTATKLYDLYSTTMQMEDAVNEGVVAIIKGI 68

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
             +DP++  + +TY    ++ AM +Y+ +   +         +  +  L  ++   + + 
Sbjct: 69  DMYDPDKNIKFSTYITTRVRGAMLDYVRKQEWM--------PRGFYKQLGIIESACEDMK 120

Query: 151 DNNLKPEQVVAIAKKLNVSE---SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
               +   V  +AK L + +     +ISM  R    +SL+ L+    +N +      + +
Sbjct: 121 RELGRTPTVDELAKHLGIEKKRCQRIISMKNR-RNIQSLDFLL----ENQNTSNGLQITN 175

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           +D Q Q   E    +    +L   ++ LN +E++      ++   +  E +     VS+ 
Sbjct: 176 NDTQVQ-PEEACLWEEDMRVLAEGIAQLNEKEQKTLALHYMEGLKM--EQVGRVIGVSQP 232

Query: 268 RVRQIEARAFKKVQESIQKQ 287
           R  QI   A +K++  I+ +
Sbjct: 233 RASQIHTIALRKLRHFIETK 252


>gi|313901033|ref|ZP_07834521.1| RNA polymerase sigma-K factor [Clostridium sp. HGF2]
 gi|312953991|gb|EFR35671.1| RNA polymerase sigma-K factor [Clostridium sp. HGF2]
          Length = 242

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 64/271 (23%), Positives = 100/271 (36%), Gaps = 62/271 (22%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           YI        L+K+EE        E  D  A ++L+  +LRLV  I   Y        ++
Sbjct: 18  YIRSNSFQQPLDKEEEARCISLLSER-DEEARNKLIEHNLRLVAHIVKKYDIKKEQTEDL 76

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           +S G IGL++AV  F PE+G +L TY+   I+  +  Y+  S            K  F N
Sbjct: 77  ISIGTIGLIKAVDSFKPEKGHKLTTYASKCIENEILMYLRSS------------KNYFQN 124

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
                                              +S+N  +A D          D +  
Sbjct: 125 -----------------------------------VSLNEPIATD---------KDGSEI 140

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLE 256
              D +    D     +I+    ++    L R + VL+ RE  I   R     +   T  
Sbjct: 141 TLIDAISSPEDSS---IIDDMIVEDNIARLKRYIHVLDARELEIITKRFGLYGQEEETQR 197

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            ++ +  +SR  V +IE RAF K+    QK+
Sbjct: 198 EIARQLHISRSYVSRIEKRAFMKIYREFQKE 228


>gi|54023854|ref|YP_118096.1| putative sigma factor [Nocardia farcinica IFM 10152]
 gi|54015362|dbj|BAD56732.1| putative sigma factor [Nocardia farcinica IFM 10152]
          Length = 273

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 41/235 (17%), Positives = 84/235 (35%), Gaps = 16/235 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              ++   L L   IA  +   G+   +++    +GL+ AV +FD E G     +++  I
Sbjct: 43  REEILHRCLPLAHNIARRFTNRGVEFEDLLQIARLGLVHAVDRFDLEHGDSFLGFAVPTI 102

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ Y       V++      K L   L      L   T    +      +A +L V 
Sbjct: 103 MGEVRRYFRDHGWAVRVPRRM--KELHQLLGPATDRL---THQLGRQPTARELASELGVE 157

Query: 170 ESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
            +EV    +       ESL+    + ++  +      +   +    +L +          
Sbjct: 158 LTEVTQALVARNAFTTESLDGGERTGEEGGALPIADRLGAVEPCYGLLEDAM-------A 210

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +   ++ L  RER++   R       T   +      S+ +V +I A+    ++E
Sbjct: 211 VRPLIAALPERERQVLILRFYDN--KTQAEIGRLLGCSQMQVSRILAKTLTMLRE 263


>gi|254228448|ref|ZP_04921874.1| RNA polymerase sigma factor, FliA/WhiG family [Vibrio sp. Ex25]
 gi|262393605|ref|YP_003285459.1| RNA polymerase sigma factor for flagellar operon [Vibrio sp. Ex25]
 gi|151939036|gb|EDN57868.1| RNA polymerase sigma factor, FliA/WhiG family [Vibrio sp. Ex25]
 gi|262337199|gb|ACY50994.1| RNA polymerase sigma factor for flagellar operon [Vibrio sp. Ex25]
          Length = 244

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 49/252 (19%), Positives = 100/252 (39%), Gaps = 19/252 (7%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFD 94
           A  Y +HG  ++    +  +  LV +IA    G   P   + +++  G IGL++A + +D
Sbjct: 4   AITYDQHGKFNSQQAFIERYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLIEAQQNYD 63

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +G    TY+   I+ AM +  +R    V      N + +   +  L+G L        
Sbjct: 64  GSKGASFETYAGIRIRGAMLDD-MRKGDWVPRSVHKNNREINQAIAELEGELN------- 115

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +      +A  L ++  +  S       D + + L+   D   S   D +    +  +  
Sbjct: 116 RDPTDSEVATHLGMTLDQYHSALT----DINCSKLVGIEDLGVS--DDVISPADETDDSN 169

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
             +    ++ R  L  S+  +  RE  +       +  + L+ +     VS  RV QI +
Sbjct: 170 PFKGVADESFRKALVESIKQIPEREALVLSLYY--DEELNLKEIGDVLGVSESRVSQILS 227

Query: 275 RAFKKVQESIQK 286
           +A ++++  +  
Sbjct: 228 QAMQRLRTKLSA 239


>gi|192362157|ref|YP_001982606.1| FliA [Cellvibrio japonicus Ueda107]
 gi|190688322|gb|ACE86000.1| FliA [Cellvibrio japonicus Ueda107]
          Length = 247

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 48/234 (20%), Positives = 96/234 (41%), Gaps = 17/234 (7%)

Query: 54  VTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           V  +  LV +IA            + +++  G IGL++A +K+D  RG    TY+   I+
Sbjct: 22  VEDYAPLVKRIAYHMMLRMPASVQVEDLIQAGMIGLIEASQKYDASRGASFETYAGIRIR 81

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            A+ + + R             + +  N RR+   + A+     +      IA +L+V  
Sbjct: 82  GAIVDEMRRGDW--------APRSVHRNGRRISQAMAAVEARTGRDASDTEIAAELDVGL 133

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            E   M      D S + L +  +    +  +    DH       +E  +R   +  L  
Sbjct: 134 DEYYQMLQ----DSSGSRLFSYEETFGEEDSNIDGSDHSSVFASPLESIQRDGLKRALAD 189

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++++L  RER +       +  + L+ +     VS  R+ QI ++A  ++++ +
Sbjct: 190 AIALLPERERLVLALYY--DEELNLKEIGLVLGVSESRISQIHSQAAARLRQKM 241


>gi|42524687|ref|NP_970067.1| RNA polymerase sigma factor for flagellar operon [Bdellovibrio
           bacteriovorus HD100]
 gi|39576897|emb|CAE78126.1| RNA polymerase sigma factor for flagellar operon [Bdellovibrio
           bacteriovorus HD100]
          Length = 261

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 49/259 (18%), Positives = 108/259 (41%), Gaps = 17/259 (6%)

Query: 36  VLAKRYREHGDLSA---AHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQA 89
            L K+Y+E     A      L+  +  L+  IA          + + +++S G IGLM A
Sbjct: 6   ALLKKYKEEPRKLAPTQKDDLIREYAPLIKFIAQKIAVRLPSNIELDDLISAGVIGLMDA 65

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           ++K+D  R  +  TY+ + I+ A+ + +      V        K L   + +L+  L   
Sbjct: 66  IEKYDSTRDNKFKTYAEFRIRGAILDELRAQ-DWVPRSIRDKAKLLDKTMVQLEADL--- 121

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
                +      +AK LNVS  E   +  ++    SL  +  ++  +++  +  +     
Sbjct: 122 ----GRTPSDEEVAKALNVSIDEFHDLVNQV-RPVSLLPIDQATSFSNTDKKSIMDILEG 176

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
            +      +   KN + ++ +++  L  R+R +      ++  + L+ +     V+  RV
Sbjct: 177 SRTNSPFNQLNVKNIKEVVAQAIEELPERQRLVLSLYYYED--LNLKEIGQVLRVTESRV 234

Query: 270 RQIEARAFKKVQESIQKQV 288
            Q+ A+A  +++  +   +
Sbjct: 235 SQLHAQAVARLRAKLAATI 253


>gi|239995147|ref|ZP_04715671.1| flagellar biosynthesis sigma factor [Alteromonas macleodii ATCC
           27126]
          Length = 243

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 50/252 (19%), Positives = 100/252 (39%), Gaps = 22/252 (8%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFD 94
           A  Y++  D +   +LV  H  LV +IA            + +++  G IGL++A + FD
Sbjct: 5   AAAYQQQTDKA---QLVERHAPLVKRIAHHLIARLPASVLVDDLIQSGMIGLLEAARNFD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +G    T++   I+ AM + I +             + +  N R +   +  +     
Sbjct: 62  GSKGASFETFAGIRIRGAMLDEIRKGDWT--------PRSVHRNGRAITEAISQVESETG 113

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +  +   IA KLNVS  +   M   +      NA      ++    +D +  + +     
Sbjct: 114 RDARDSDIADKLNVSLQDYHQMLNEV------NAGKLVGIEDLGVSEDVISTEQNRGSDA 167

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
            +E   +   +  L  +++ L  RE  +       +  + L  +    +VS  RV QI +
Sbjct: 168 PLEDLMQGAFQKALAHAITTLPEREAIVLSLYY--DEELNLREIGEVLDVSESRVSQIHS 225

Query: 275 RAFKKVQESIQK 286
           +A  K++  ++ 
Sbjct: 226 QAMLKLKSRMKS 237


>gi|224110206|ref|XP_002333134.1| predicted protein [Populus trichocarpa]
 gi|222834948|gb|EEE73397.1| predicted protein [Populus trichocarpa]
          Length = 512

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 51/248 (20%), Positives = 100/248 (40%), Gaps = 27/248 (10%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            +A ++L+  +LRLV+ +   Y      G    +    G  GL+ A+ +F+P+R FRL+T
Sbjct: 274 RAARNKLIKHNLRLVLFVIKKYFQDFANGTKFQDFCQAGVKGLITAIDRFEPKRRFRLST 333

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL----KPEQV 159
           Y ++WI+ A+   +  S             R+ F L  ++  +Q           +    
Sbjct: 334 YGLFWIRHAIIRSMTLSSFT----------RVSFGLESIRSEIQKAKLELWFQLKRQPME 383

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I +K+ +S      +        SL++   ++ +        +    D ++  L+   
Sbjct: 384 DEIIEKVRISPERYHEVTRASKPVLSLHSRHKTTQEEFIGGIADVDGGDDRRQSALL--- 440

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAF 277
                R  L   +  L P+E  +   R   +     TL  ++    +SRE VR+ E +A 
Sbjct: 441 -----RLALDDVLDSLKPKESLVVRQRYGLDGKGDRTLGEIAGNLNISREMVRKHEVKAL 495

Query: 278 KKVQESIQ 285
            K++   +
Sbjct: 496 MKLKHPTR 503


>gi|153854402|ref|ZP_01995680.1| hypothetical protein DORLON_01675 [Dorea longicatena DSM 13814]
 gi|149752928|gb|EDM62859.1| hypothetical protein DORLON_01675 [Dorea longicatena DSM 13814]
          Length = 230

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 62/256 (24%), Positives = 99/256 (38%), Gaps = 62/256 (24%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L   EE    ++Y E GDL A H L+  +LRLV  I   Y+     + +++S G IGLM
Sbjct: 30  PLTAAEEKYYVQKYTE-GDLEAKHILIERNLRLVAHIVKKYQPPPEEMEDLLSIGTIGLM 88

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV  FDPE+  RLATY+   I                      +  L  + R  K   +
Sbjct: 89  KAVVTFDPEKSARLATYAARCI----------------------ENELLMHFRGKKKSSK 126

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                                     +S+   +  D          + N  Q  D +   
Sbjct: 127 E-------------------------VSLYEPIGTDR---------EGNEIQLFDVI--- 149

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVS 265
             G+E V    E++++   +  +  S L+ RER + + R     E   T   ++    +S
Sbjct: 150 EMGEEDVHHRLEKKEDVIRLYQKVESELSARERIVLKLRYGLYNEEEYTQREIAKMLGIS 209

Query: 266 RERVRQIEARAFKKVQ 281
           R  V +IE  A +K++
Sbjct: 210 RSYVSRIEKSAIEKLR 225


>gi|30250410|ref|NP_842480.1| RNA polymerase sigma-70 factor family protein [Nitrosomonas
           europaea ATCC 19718]
 gi|30181205|emb|CAD86403.1| Sigma-70 factor family [Nitrosomonas europaea ATCC 19718]
          Length = 236

 Score =  117 bits (294), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 43/241 (17%), Positives = 97/241 (40%), Gaps = 17/241 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             + +T    LV +IA          + + +++  G IGL+ A+ +++   G +  +Y+ 
Sbjct: 10  KDQFITEFTPLVKRIAHHMMARLPASVQVDDLIQAGMIGLLDAINRYEGSYGRQFESYAA 69

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ ++ + +  +  L         + L   +R+++  ++A+      P     IA ++
Sbjct: 70  QRIRGSILDELREADWL--------PRSLRRKMRQIETAMRALEQRLGYPPSEQEIANEM 121

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           N+   E   M     G      LI   D    +   +L      Q    +++   KN R 
Sbjct: 122 NLPLVEYQEMLQEAGG----GQLIYYEDFQEDEEDHFLDRLRGDQSNEPLDRLLEKNLRE 177

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +L  ++  L  +E+ +       E  + L  +     VS  RV Q+  +A  +++  ++ 
Sbjct: 178 LLVAAIEKLPAKEKLVMGMYY--EQEMNLREIGKVLGVSESRVCQLHTQAISRLRTHLRD 235

Query: 287 Q 287
           +
Sbjct: 236 K 236


>gi|330445383|ref|ZP_08309035.1| RNA polymerase sigma factor, FliA/WhiG family protein
           [Photobacterium leiognathi subsp. mandapamensis
           svers.1.1.]
 gi|328489574|dbj|GAA03532.1| RNA polymerase sigma factor, FliA/WhiG family protein
           [Photobacterium leiognathi subsp. mandapamensis
           svers.1.1.]
          Length = 240

 Score =  117 bits (293), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 43/237 (18%), Positives = 97/237 (40%), Gaps = 19/237 (8%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              +  +  LV +IA        P   + +++  G IGL++A + +DP +G    T++  
Sbjct: 15  QAFIERYSSLVKRIAHHLMVRLPPSVLVEDLIQSGMIGLLEAQQNYDPTKGASFETFAGI 74

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+ AM + I R    V        + ++ N R++   +  + +   +      IA+ L+
Sbjct: 75  RIRGAMLDDIRR-GDWVP-------RSVYKNSRKISEAISHLENELGRDPNDQEIAQYLD 126

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +   +          D +   L+  SD   ++  D +  +   +E    +     + R  
Sbjct: 127 MPLEQYHQAL----NDVNCGRLVGISDLGVAE--DSVANEESIEENAPFQDVADDSFRAS 180

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L  ++  L  RE  +       +  + L+ + +   VS  R+ QI ++A ++++  +
Sbjct: 181 LAEAIKTLPEREALVLSLYY--DEELNLKEIGAVIGVSESRICQIHSQAMQRLRAKL 235


>gi|330444437|ref|YP_004377423.1| RNA polymerase sigma factor [Chlamydophila pecorum E58]
 gi|328807547|gb|AEB41720.1| RNA polymerase sigma factor [Chlamydophila pecorum E58]
          Length = 256

 Score =  117 bits (293), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 52/258 (20%), Positives = 109/258 (42%), Gaps = 21/258 (8%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKK 92
            L   Y E  D+     L+ S+L LV            P     ++ + G  GL++AV++
Sbjct: 11  ELWNLYWETQDIQYRDSLIESYLHLVKSAVHRLIVGMPPHIKTQDLYASGVEGLVRAVER 70

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           ++PER  R   ++++ IKAA+ + + +      +  +  QK       +L   +  +  +
Sbjct: 71  YNPER-SRFEGFAIFLIKAAIIDDLRKQDW---VPRSVYQKA-----NKLTEAMDTLRQS 121

Query: 153 NLKPEQVVAIAKKLNVSESEVIS--MNCRLAGDESLNA--LINSSDKNSSQWQDWLVYDH 208
             K    + + + LN+S  E+     + R A   SLN     +S +      ++ +    
Sbjct: 122 LGKEPTDLELCEYLNISLHELSQWFASSRPALIISLNTDWPSHSCEGEGIALEERIP--- 178

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D + +   +  ++K   + L  ++  L  +ER++          + L+ +     VS  R
Sbjct: 179 DERAETGYDVVDKKEFCSFLALAIQGLEEKERQVMALYYY--EGLVLKEIGKILGVSESR 236

Query: 269 VRQIEARAFKKVQESIQK 286
           V QI ++A  K++ ++  
Sbjct: 237 VSQIHSKALIKLRVALSA 254


>gi|222632729|gb|EEE64861.1| hypothetical protein OsJ_19718 [Oryza sativa Japonica Group]
          Length = 457

 Score =  117 bits (293), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 50/255 (19%), Positives = 102/255 (40%), Gaps = 17/255 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKK 92
           VL  R       +A ++L+  +LRLV+     Y           ++   G  GL+ A+ +
Sbjct: 207 VLQMRRHLEVGRAARNKLIKHNLRLVLYTINKYYPDMSNDERFDDICQAGANGLITAIDR 266

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+P+RGFR++TY+++WI+ ++   I  S    +       +R     + +    + +   
Sbjct: 267 FEPKRGFRISTYALFWIRHSIVRAITLSNFT-RFPFAMESER-----QEIHRAREELAFE 320

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      + KK+ +S +    +        SL+A      +N    ++ +    D   
Sbjct: 321 LGRAPTEEEVMKKVGLSPARYRDVVRMTRPTYSLHA------RNRVTQEELINEVTDDDA 374

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVR 270
             +         R  +   +  L P+E  +   R   +     TL  ++    +SRE VR
Sbjct: 375 IGVDTSSHNTLLRLAIDDLLDSLKPKESVVIRQRFGLDGRGKRTLSEIAGNLNISREMVR 434

Query: 271 QIEARAFKKVQESIQ 285
           + E +A  K++   +
Sbjct: 435 KYELKALMKLKHPTR 449


>gi|89073430|ref|ZP_01159953.1| flagellar biosynthesis sigma factor FliA [Photobacterium sp. SKA34]
 gi|89050694|gb|EAR56175.1| flagellar biosynthesis sigma factor FliA [Photobacterium sp. SKA34]
          Length = 240

 Score =  117 bits (293), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 44/237 (18%), Positives = 96/237 (40%), Gaps = 19/237 (8%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              +  +  LV +IA        P   + +++  G IGL++A + +DP +G    T++  
Sbjct: 15  QAFIERYSSLVKRIAHHLMVRLPPSVLVEDLIQSGMIGLLEAQQNYDPTKGASFETFAGI 74

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+ AM + I R    V        + ++ N R++   +  + +   +      IA+ L+
Sbjct: 75  RIRGAMLDDIRR-GDWVP-------RSVYKNSRKISEAISHLENELGRDPNDQEIAQYLD 126

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +   +          D +   L+  SD   ++  D +  +    E    +     N R  
Sbjct: 127 MPLEQYHQAL----NDVNCGRLVGISDLGVAE--DTVANEESIGENSPFQGVVDDNFRAS 180

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L  ++  L  RE  +       +  + L+ + +   VS  R+ QI ++A ++++  +
Sbjct: 181 LAEAIKTLPEREALVLSLYY--DEELNLKEIGAVIGVSESRICQIHSQAMQRLRAKL 235


>gi|218288661|ref|ZP_03492938.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
 gi|218241318|gb|EED08493.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
          Length = 239

 Score =  117 bits (293), Expect = 2e-24,   Method: Composition-based stats.
 Identities = 55/284 (19%), Positives = 103/284 (36%), Gaps = 65/284 (22%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           ++++         Y+ +    P  L   EE    + Y   GD  A +RL+  +LRLV  +
Sbjct: 8   LALVFKDVSLFVSYVKQ-GAFPHPLSPDEEERAIRDYL-AGDGDARNRLIEHNLRLVAHL 65

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  Y   G  + +++S G IGL++AV+ + P++G +LATY+   I+  +  Y+  S    
Sbjct: 66  AKKYESSGEEMDDLISIGTIGLIKAVESYRPDKGTKLATYAARCIENEILMYLRSSKKHR 125

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +    ++      +   +                   +A  L     +VI          
Sbjct: 126 RDAFLSDPVGTDKDGNEMT------------------LADLLGSDPDDVI---------- 157

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
             +A+  S +K        L+                                RE  +  
Sbjct: 158 --DAVDMSWEKQKMFECLPLLAPR----------------------------ERE--VLC 185

Query: 245 ARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            R         T   ++ E  +SR  V +IE +A  K+ E++++
Sbjct: 186 KRFGLPDGEERTQREIAKELGISRSYVSRIEQKAIVKLYENMRQ 229


>gi|317121712|ref|YP_004101715.1| RNA polymerase, sigma 29 subunit, SigE [Thermaerobacter marianensis
           DSM 12885]
 gi|315591692|gb|ADU50988.1| RNA polymerase, sigma 29 subunit, SigE [Thermaerobacter marianensis
           DSM 12885]
          Length = 245

 Score =  117 bits (293), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 55/242 (22%), Positives = 103/242 (42%), Gaps = 61/242 (25%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +  H L+  +LRLVV IA  +   G+PI ++VS G IGL++AV  FDP +  +LATY+ 
Sbjct: 61  PAVRHTLIERNLRLVVYIARKFDNTGIPIEDLVSIGTIGLIKAVNTFDPSKRIKLATYAS 120

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+  +  ++ R+                                            + 
Sbjct: 121 KCIENEILMHLRRTSRT-----------------------------------------RY 139

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            VS  E ++++     +  L+ +I ++D +                 V+    E K  R+
Sbjct: 140 EVSLDEPLNVDWE-GNELLLSDVIPATDGD-----------------VIYRDLEAKVDRH 181

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +L R+++ L+PRER I E R    +    T + ++    +S+  + ++E R   +++  I
Sbjct: 182 LLYRALARLSPRERLIMELRFGLVDGIERTQKQVADRLGISQSYISRLEKRIINRLRREI 241

Query: 285 QK 286
           +K
Sbjct: 242 RK 243


>gi|148976430|ref|ZP_01813136.1| flagellar biosynthesis sigma factor [Vibrionales bacterium SWAT-3]
 gi|145964253|gb|EDK29509.1| flagellar biosynthesis sigma factor [Vibrionales bacterium SWAT-3]
          Length = 244

 Score =  117 bits (293), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 50/249 (20%), Positives = 100/249 (40%), Gaps = 19/249 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPER 97
           Y +H + ++       +  LV +IA    G   P   + +++  G IGL++A + +D  +
Sbjct: 7   YDQHANHNSQQAFFEKYSVLVKRIAHHLLGRLPPNVLVDDLIQAGMIGLIEAQQNYDGTK 66

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G    TY+   I+ AM + I R    V      N + +   +  L+  L        +  
Sbjct: 67  GASFETYAGIRIRGAMLDDIRR-GDWVPRSVHKNNREISSAIAELESTLN-------RDP 118

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +AK + +S  +  S       D + + L+   D   S   D +  + D Q+    +
Sbjct: 119 SDAEVAKHMGLSLEQYHSALT----DINCSRLVGIEDLGVS--DDVISPNEDSQDNAPFQ 172

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
               ++ R  L  S+  L  RE  +       +  + L+ +     VS  RV QI +++ 
Sbjct: 173 GVADESFRQALIDSIKQLPEREGLVLSLYY--DEELNLKEIGEVLGVSESRVSQILSQSM 230

Query: 278 KKVQESIQK 286
           ++++  +  
Sbjct: 231 QRLRTKLSA 239


>gi|126698826|ref|YP_001087723.1| sporulation sigma factor SigK [Clostridium difficile 630]
 gi|26000675|gb|AAN75197.1| sigma K [Clostridium difficile]
 gi|26000677|gb|AAN75198.1| sigma K [Clostridium difficile]
          Length = 213

 Score =  116 bits (292), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 48/247 (19%), Positives = 89/247 (36%), Gaps = 61/247 (24%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L  +EE     +++   D SA   L+  ++RLV  IA  Y        +++S G IGL+
Sbjct: 10  PLTPEEEIEYLTKFKIENDKSAKDTLIERNMRLVAYIAKKYNNSTEDQDDLISIGTIGLI 69

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +A++ ++ ++G RLATY+   I+  +   I  +                    + +    
Sbjct: 70  KAIETYNIDKGTRLATYASRCIENEILMNIRSN-----------------KKNKTQ---- 108

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                                     +S+   +  D          + N     D L  +
Sbjct: 109 --------------------------VSLQDPIGTD---------KEGNEISLLDILGTE 133

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVS 265
            +    VL E E +     +  +   +L PRER I + R         T   ++ + ++S
Sbjct: 134 ANY---VLDEVELKVQVGKLYEQLNKILTPREREIVQLRYGLTPYGYKTQREIAQKLDIS 190

Query: 266 RERVRQI 272
           R  V +I
Sbjct: 191 RSYVSRI 197


>gi|307153354|ref|YP_003888738.1| FliA/WhiG subfamily RNA polymerase sigma-28 factor [Cyanothece sp.
           PCC 7822]
 gi|306983582|gb|ADN15463.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cyanothece
           sp. PCC 7822]
          Length = 258

 Score =  116 bits (292), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 46/259 (17%), Positives = 106/259 (40%), Gaps = 16/259 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVK 91
           E   L + Y++       ++++  +  LV + A  +         +++  G +GL++A++
Sbjct: 12  ESLRLFQDYQKSPSTELRNQILELNFGLVRREAYHWVSQCNENYEDLLQVGCLGLIRAIE 71

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           +F+  +G   +++++ +I+  +Q Y+      V+I      +R     R+     +    
Sbjct: 72  RFETGKGHAFSSFAIPYIRGEIQHYLRDKGYSVRIP-----RRWLDLGRQAMTIRRDFQT 126

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHD 209
              +      IA+ L +S  E   +       E  SL+  IN  D   +   D +     
Sbjct: 127 RLNRQPSDEEIAEILEISAKEWQEIKLAFQNREPLSLDVSINHDDDGQTSLGDLVPDPKY 186

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
              Q        ++ R  L ++++ L  R RR+ E   L +  +T    + +  +S   V
Sbjct: 187 RSFQ------LSEDDRIRLQQALAQLEERTRRVLEFVFLYD--LTQRETAEQLGISVVTV 238

Query: 270 RQIEARAFKKVQESIQKQV 288
            +   +    ++E++ K+V
Sbjct: 239 SRRVKKGLDLLKETMTKEV 257


>gi|270659580|ref|ZP_06222335.1| RNA polymerase sigma-32 factor [Haemophilus influenzae HK1212]
 gi|270316998|gb|EFA28670.1| RNA polymerase sigma-32 factor [Haemophilus influenzae HK1212]
          Length = 147

 Score =  116 bits (292), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 42/150 (28%), Positives = 75/150 (50%), Gaps = 6/150 (4%)

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSD 194
           FFNLR+ K  L    +N     +V  +A +L VS+ +VI M  R++G D   +   + ++
Sbjct: 1   FFNLRKTKQRLGWFNEN-----EVDMVANELGVSKEDVIEMESRMSGADVGFDLPTDDAE 55

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
             +     +L          L  +         L  ++  L+ R + I +AR L +N  T
Sbjct: 56  TETYSPALYLEDKSSNFAAELENENFESQATEQLGAALQSLDARSQDIIKARWLDDNKAT 115

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L +L++++ VS ER+RQ+E  A KK++ ++
Sbjct: 116 LHDLAAKYNVSAERIRQLETNALKKLKSAV 145


>gi|54308132|ref|YP_129152.1| flagellar biosynthesis sigma factor [Photobacterium profundum SS9]
 gi|46912558|emb|CAG19350.1| Putative flagellar-specific RNA polymerase sigma factor, FliA
           [Photobacterium profundum SS9]
          Length = 240

 Score =  116 bits (292), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 46/241 (19%), Positives = 95/241 (39%), Gaps = 19/241 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
             +    +  +  LV +IA    G   P   + +++  G IGL++A + +DP +G    T
Sbjct: 11  KESPQAFIERYSSLVKRIAYHLMGRLPPSVQVEDLIQSGMIGLLEAQQNYDPTKGASFET 70

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           ++   I+ AM + I R    V      N        RR+   +  + +   +      IA
Sbjct: 71  FAGIRIRGAMLDDIRR-GDWVPRSVYKNN-------RRITEAMAQLENKLGRDPTDTEIA 122

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + L ++  +          D +   L+   D   S+  D +  +   +E +  +     N
Sbjct: 123 EHLEMTLDQYHQAL----NDVNCGRLVGMDDLGVSE--DAVTTEASREENLPFQGVVDDN 176

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            R  L  ++  L  RE  +       +  + L+ +     VS  R+ QI ++A ++++  
Sbjct: 177 FRQSLADAIKTLPEREALVLSLYY--DEELNLKEIGVVVGVSESRICQIHSQAMQRLRSK 234

Query: 284 I 284
           +
Sbjct: 235 L 235


>gi|269103161|ref|ZP_06155858.1| RNA polymerase sigma factor for flagellar operon [Photobacterium
           damselae subsp. damselae CIP 102761]
 gi|268163059|gb|EEZ41555.1| RNA polymerase sigma factor for flagellar operon [Photobacterium
           damselae subsp. damselae CIP 102761]
          Length = 240

 Score =  116 bits (292), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 47/243 (19%), Positives = 97/243 (39%), Gaps = 19/243 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
             +    +  H  LV +IA        P   I +++  G IGL++A + +DP +G    T
Sbjct: 11  QESPQAFIARHSSLVKRIAHHLMARLPPNILIEDLIQAGMIGLLEAQQNYDPTKGASFET 70

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           ++   I+ AM + I R    V        + ++ N RR+   +  +     +      +A
Sbjct: 71  FAGIRIRGAMLDDIRR-GDWVP-------RSVYKNSRRISEAMAQLEHELGRDPNDHEVA 122

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + L +S  +          D +   L+   D   S+  D +  D   +E +  +     +
Sbjct: 123 EHLEMSLEQYHQAL----NDVNCGRLVGIDDLGISE--DAVANDELLEENLPFQGVVDDS 176

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            R  L  ++  L  RE  +       +  + L+ + +   VS  R+ QI  +A ++++  
Sbjct: 177 FRQALAEAIKTLPEREALVLSLYY--DEELNLKEIGAVIGVSESRICQIHTQAMQRLKAK 234

Query: 284 IQK 286
           ++ 
Sbjct: 235 LKA 237


>gi|255994576|ref|ZP_05427711.1| RNA polymerase sigma-B factor [Eubacterium saphenum ATCC 49989]
 gi|255993289|gb|EEU03378.1| RNA polymerase sigma-B factor [Eubacterium saphenum ATCC 49989]
          Length = 249

 Score =  116 bits (292), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 45/239 (18%), Positives = 101/239 (42%), Gaps = 11/239 (4%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           ++    ++Y +  D++  + +V  +L +V  +   Y   G+   ++   G + L+ AV++
Sbjct: 2   QDRERFEKYAKTRDINERNAIVEDYLYIVDILVRKYLNKGVEYDDLYQVGAMALIMAVER 61

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  RGF  ++++   I   +++Y       +K+  +  +         ++   +++   
Sbjct: 62  FDASRGFEFSSFATPTILGEIKKYFRDKEWKLKVPRSVKEANAA-----IQSARESLFAK 116

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +   V  IA++ N+ E EV  +        +L+  +   D  S    D  V  ++   
Sbjct: 117 LQRDPTVKEIAEEKNMKEEEVAKLIDSSMAYNTLSLDVTFDDSGS----DSGVSRYEKYM 172

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
            V     E      M+   +SVL+ + R IF+ R L     T   ++ +  VS+  + +
Sbjct: 173 AVEGSGIESLEYEEMIESILSVLSEKNRYIFKKRFL--EGKTQSEIAEKLGVSQMTISR 229


>gi|167770367|ref|ZP_02442420.1| hypothetical protein ANACOL_01710 [Anaerotruncus colihominis DSM
           17241]
 gi|167667689|gb|EDS11819.1| hypothetical protein ANACOL_01710 [Anaerotruncus colihominis DSM
           17241]
          Length = 225

 Score =  116 bits (292), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 46/235 (19%), Positives = 97/235 (41%), Gaps = 22/235 (9%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             + ++ ++ LV   A  ++G G+   ++   G +GL +AV  FDP+RG +L+TY++  I
Sbjct: 12  REQTISENIGLVHSCAHRFKGRGIEYDDLFQAGCMGLCKAVDAFDPQRGVKLSTYAVPVI 71

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              M+  + R    VK+  T  +  L     R+    + +     +   V  +A+ + + 
Sbjct: 72  LGEMRR-LFRDGGAVKVSRTLKELSL-----RIGRAREQLALALGREPSVSELAQAMELP 125

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E +V+   C  A   SL     S +    Q         D    V+            L 
Sbjct: 126 EEQVVEALCAAAPPLSL---TESDEDGGGQIDLPADSPEDQLADVI-----------SLN 171

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + +  L  ++R + E R      +T    ++   +++ +V + E +    +++ +
Sbjct: 172 QVVEKLEDKDRALIELRYYSG--MTQVQTAARLGMTQVQVSRREKKILGILRQQL 224


>gi|324999864|ref|ZP_08120976.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily protein
           [Pseudonocardia sp. P1]
          Length = 271

 Score =  116 bits (292), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 42/239 (17%), Positives = 88/239 (36%), Gaps = 23/239 (9%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER--GFRLATYSMW 107
             R++ + L L   ++  Y        +V     +GL++AV ++DP+   G  L  Y + 
Sbjct: 50  RDRVICAFLPLARNLSRRYVTGVHSADDVEQAATLGLIKAVDRYDPDVATGGPL-GYLVP 108

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            ++  +  Y+      +++     ++ +      L      +T    +  +   +A +L+
Sbjct: 109 CVRGELMRYLRDHSWALRVPRDLKERSVG-----LNRAAVTLTQRLGRAPRPSELASELD 163

Query: 168 VSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           V  SEV+     +      SL+      +   +   + L  D    E   +        R
Sbjct: 164 VDTSEVVEALGAMESYNAVSLDEPGPDGE---TTLGERLGEDDGALEGAPV--------R 212

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             L   +  L  RERRI   R       T   ++ +  VS+  V ++  R    ++  +
Sbjct: 213 TELRERIGELPERERRILLLRFYGN--RTQSEIAEDIGVSQMHVSRLLTRTVATLRHDL 269


>gi|269961637|ref|ZP_06175999.1| flagellar biosynthesis sigma factor FliA [Vibrio harveyi 1DA3]
 gi|269833678|gb|EEZ87775.1| flagellar biosynthesis sigma factor FliA [Vibrio harveyi 1DA3]
          Length = 244

 Score =  116 bits (292), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 48/249 (19%), Positives = 99/249 (39%), Gaps = 19/249 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPER 97
           Y +HG  ++    +  +  LV +IA    G   P   + +++  G IGL++A + +D  +
Sbjct: 7   YDQHGKFNSQQAFIERYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLIEAQQNYDGSK 66

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G    TY+   I+ AM + I R    V      N + +   +  L+G L        +  
Sbjct: 67  GASFETYAGIRIRGAMLDDI-RKGDWVPRSVHKNNREINQAIAELEGVLN-------RDP 118

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A  L ++  +  S       D + + L+   D   S   D +    +  +    +
Sbjct: 119 SDSEVAAHLGMTLDQYHSALT----DINCSKLVGIEDLGVS--DDVISPADETDDSNPFK 172

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
               ++ +  L  S+  L  RE  +       +  + L+ +     VS  RV QI +++ 
Sbjct: 173 GVADESFKKALVESIKQLPEREALVLSLYY--DEELNLKEIGDVLGVSESRVSQILSQSM 230

Query: 278 KKVQESIQK 286
           ++++  +  
Sbjct: 231 QRLRTKLSA 239


>gi|114332399|ref|YP_748621.1| RNA polymerase, sigma 28 subunit [Nitrosomonas eutropha C91]
 gi|114309413|gb|ABI60656.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Nitrosomonas
           eutropha C91]
          Length = 236

 Score =  116 bits (292), Expect = 3e-24,   Method: Composition-based stats.
 Identities = 46/250 (18%), Positives = 102/250 (40%), Gaps = 18/250 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPER 97
           Y E G +    + V     LV +IA          + + +++  G IGL+ A+ +++   
Sbjct: 2   YTEAGTID-KDQFVIEFTPLVKRIAYHMMARLPASVQVDDLIQAGMIGLLDAINRYEGSY 60

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G +  +Y+   I+ +M + +  +  L         + L   +R+++  ++ +      P 
Sbjct: 61  GRQFESYAAQRIRGSMLDELREADWL--------PRSLRRKMRQIETAMRTLEQRLGCPP 112

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               IA +LN+  +E   M     G      LI   D    +   +L +  + Q    ++
Sbjct: 113 SEQEIADELNLPLAEYQEMLQEAGG----GQLIYYEDFQVDEEDHFLDHLCNDQGNEPLD 168

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
           +   KN R +L  ++  L  +E+ +       E  + L  +     VS  R+ Q+  +A 
Sbjct: 169 QLLEKNLRELLVAAIEKLPAKEKLVMGMYY--EQEMNLREIGDVLGVSESRICQLHTQAI 226

Query: 278 KKVQESIQKQ 287
            +++  ++ +
Sbjct: 227 SRLRTRLRDK 236


>gi|323490161|ref|ZP_08095381.1| RNA polymerase sigma-D factor (Sigma-28) [Planococcus donghaensis
           MPA1U2]
 gi|323396209|gb|EGA89035.1| RNA polymerase sigma-D factor (Sigma-28) [Planococcus donghaensis
           MPA1U2]
          Length = 252

 Score =  116 bits (292), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 54/255 (21%), Positives = 110/255 (43%), Gaps = 21/255 (8%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQA 89
           EE V    +++H D  A   LV  +L LV  +   +       +   +V S    GL+ A
Sbjct: 9   EELVCWSDWQQHRDPDAGEYLVEQYLPLVDYVIQRFMISLPKTVEKDDVRSYAYEGLLDA 68

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + KF+ ER  +  TY+ W IK A+ + + +S  L         + +   +++++     +
Sbjct: 69  LSKFNIERDLKFETYASWRIKGAIIDGLRQSDWL--------PRSVRDKVKKIEKAFLLL 120

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
              +        ++  L ++++E      +   + +L+ +I+  D N  +    + Y  D
Sbjct: 121 EQQSGVSVSDEEVSSYLGITKAE----LNKTVSEAALSTMISMDDDNFEEQGKLVNYHVD 176

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
             E+ L E    + R+  L R++  L  +E+        +E  +T   ++    VS  RV
Sbjct: 177 SPERHLSE----QMRKESLVRAIERLPEKEKITVSLCYFEEMKLT--EIAEILNVSVSRV 230

Query: 270 RQIEARAFKKVQESI 284
            Q+ ++A  ++  SI
Sbjct: 231 SQLHSKAMLRLHASI 245


>gi|188997568|ref|YP_001931819.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Sulfurihydrogenibium
           sp. YO3AOP1]
 gi|188932635|gb|ACD67265.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Sulfurihydrogenibium
           sp. YO3AOP1]
          Length = 242

 Score =  116 bits (292), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 46/248 (18%), Positives = 106/248 (42%), Gaps = 19/248 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAM--GYRG--YGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
                 ++   L  +  I     ++     +   ++   G +GL  A++KFDP +G + +
Sbjct: 5   KEEKTNIIKEFLPKINYIVKALKHQNLPPIVDEEDLFQVGVLGLYDALEKFDPAKGVKFS 64

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+   ++  + +++ R    +        K L   +  L+  L        KPE    I
Sbjct: 65  TYAEIRVRGYILDHL-RQLDWIPRNIRNKVKNLENKIVELETKL----GREAKPE---EI 116

Query: 163 AKKLNVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
           A+ L +S  E +    +       SL++ ++  D  S    + +  + D  E+ + EK+ 
Sbjct: 117 AEYLGMSLEEYMIYAEKAVNKILISLDSDVSKDDDESLHLWEVISTNDDTPEKYVEEKQL 176

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           ++   +++   M+ L+ RE+ I      ++  + ++ ++     +  RV Q+  +   K+
Sbjct: 177 KEILSDII---MNKLDEREKLIVTLYYYED--LNMKEIAEILGCTESRVSQLHTKIMLKI 231

Query: 281 QESIQKQV 288
           ++ I+K V
Sbjct: 232 RKLIEKYV 239


>gi|254422308|ref|ZP_05036026.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp. PCC
           7335]
 gi|196189797|gb|EDX84761.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp. PCC
           7335]
          Length = 259

 Score =  116 bits (292), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 50/253 (19%), Positives = 113/253 (44%), Gaps = 16/253 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY-GLPISEVVSEGNIGLMQAVKKFD 94
            L   Y++   L   +RLV  ++ LV + A  + GY G    +++  G++GL+ A+++FD
Sbjct: 15  ELLSLYQKDRSLQLRNRLVQLNIGLVRQEAYRWLGYSGETFDDLMQIGSLGLINAIERFD 74

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
            E+G+  +++++ +I+  +Q Y+    ++V+I      ++      +    ++ + +   
Sbjct: 75  LEKGYAFSSFAIPYIRGEIQHYLRDKGTVVRIP-----RKWQALQNQAAQAIRHLQNELN 129

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +      +A +LNV+  E   +    +     SL+A I      +S   + L        
Sbjct: 130 RKPNDYEVAARLNVTVEEWQQVKLASSNRHLLSLDAPIREDRNGASSLGELLPDARYRSF 189

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           Q+  E       R  L +++  L  R R + E   LQ+  +T +  + +  +S   V + 
Sbjct: 190 QLAQED------RIRLQQALEQLEKRTREVLEFVFLQD--LTQKETAKKLGISSVTVSRR 241

Query: 273 EARAFKKVQESIQ 285
             +  + +Q  ++
Sbjct: 242 VRKGLQHLQAIMR 254


>gi|302541605|ref|ZP_07293947.1| RNA polymerase sigma-F factor [Streptomyces hygroscopicus ATCC
           53653]
 gi|302459223|gb|EFL22316.1| RNA polymerase sigma-F factor [Streptomyces himastatinicus ATCC
           53653]
          Length = 292

 Score =  116 bits (291), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 46/243 (18%), Positives = 103/243 (42%), Gaps = 15/243 (6%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +    +V + + +  ++A  +R  G    ++     +GL++AV ++DP+RG    +Y++
Sbjct: 63  EALRQDVVRAWMPMAERLAGQFRNRGESAEDLRQVAMLGLVKAVNRYDPDRGTAFESYAV 122

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKPEQVVAIAKK 165
             +   ++ +       + +     + R      R++  +Q +T   + +   V  +A+ 
Sbjct: 123 PTVVGEVKRHFRDHLWGLHVPRRVQELR-----NRVRTAVQDLTRTPDGRTPSVADVAEH 177

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
             +SE EV S    L   ES + L   ++   +     LV      E       +R  +R
Sbjct: 178 TGLSEEEVRSGMEAL---ESYSTLSLDAELRGADDGYALVDTLGSPEPSY----DRVVQR 230

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             L   ++ L  RERRI   R   +   T   ++    +S+  V ++ +R  +++ E + 
Sbjct: 231 EALKPCLAALPERERRILYLRFFCDE--TQGRIADRMGISQMHVSRLISRTCERLGEEVD 288

Query: 286 KQV 288
           ++ 
Sbjct: 289 REA 291


>gi|317497563|ref|ZP_07955881.1| sigma-70 region 2 [Lachnospiraceae bacterium 5_1_63FAA]
 gi|316895122|gb|EFV17286.1| sigma-70 region 2 [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 215

 Score =  116 bits (291), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 39/181 (21%), Positives = 81/181 (44%), Gaps = 7/181 (3%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +P+L ++E+  L +R  E GDL A    +  +LRLV+ I   + G      ++   G IG
Sbjct: 29  LPLLSEEEKEDLFERI-EQGDLLAREHYIKGNLRLVLSIIQRFSGSSENADDLFQVGCIG 87

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           LM+A+  FD     + +TY++  I   ++ Y+  + S+ ++      + L     +    
Sbjct: 88  LMKAIDNFDRNLNVKFSTYAVPMIIGEVKRYLRDNHSM-RVS-----RSLRDTAYKAINA 141

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            + +T        +  IAK++++ + +V+     +A   SL   +     ++    D + 
Sbjct: 142 REVLTKKLNHEPTIDVIAKEIDMKKEDVLFALDAIATPLSLYEPVYQDGGDTLYLMDQVK 201

Query: 206 Y 206
            
Sbjct: 202 D 202


>gi|317471864|ref|ZP_07931199.1| sigma-70 family RNA polymerase sigma factor [Anaerostipes sp.
           3_2_56FAA]
 gi|316900637|gb|EFV22616.1| sigma-70 family RNA polymerase sigma factor [Anaerostipes sp.
           3_2_56FAA]
          Length = 207

 Score =  116 bits (291), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 58/263 (22%), Positives = 98/263 (37%), Gaps = 64/263 (24%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +  L ++EE    K+ R  GD+ A + LV  +LRLV  I   Y  +     +++S G IG
Sbjct: 5   LEPLSQEEEQYYLKKSRL-GDMEARNILVEHNLRLVAHIVKKYNNFDRDKDDLISVGTIG 63

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A+  ++ E+G RL TY+   I                      +  L   LR+ +  
Sbjct: 64  LIKAINTYNMEKGHRLVTYASRCI----------------------ENELLMMLRQERKS 101

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS-DKNSSQWQDWL 204
                                              A D SL   I    + N     D L
Sbjct: 102 -----------------------------------AKDTSLYEPIGIDKEGNEINLLDVL 126

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEF 262
             D +     L  KE+ ++   M+         RE+     R       P+T + ++ E 
Sbjct: 127 GADENDIVDELDLKEKIRDLYKMVDEME---PSREKTTLIMRYGLYGKKPMTQKEVAKEL 183

Query: 263 EVSRERVRQIEARAFKKVQESIQ 285
            +SR  V +IE +A +K++  ++
Sbjct: 184 HISRSYVSRIEKKAVEKIKRRLK 206


>gi|2832900|emb|CAA04387.1| Sigma A [Lysinibacillus sphaericus]
          Length = 140

 Score =  116 bits (291), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 29/138 (21%), Positives = 61/138 (44%), Gaps = 7/138 (5%)

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
           +  +      I ++++++  +V  +        SL   I   +++ S   D++    D +
Sbjct: 1   DLGREPSPEEIGEEMDLTPEKVREILKIAQEPVSLETPI--GEEDDSHLGDFI---EDSE 55

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT--LENLSSEFEVSRERV 269
            Q   +    +  +  L   +  L  RE  +   R   ++  T  LE +   F V+RER+
Sbjct: 56  AQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERI 115

Query: 270 RQIEARAFKKVQESIQKQ 287
           RQIEA+A +K++   + +
Sbjct: 116 RQIEAKALRKLRHPSRSK 133


>gi|292669753|ref|ZP_06603179.1| DNA-directed RNA polymerase sigma subunit FliA [Selenomonas noxia
           ATCC 43541]
 gi|292648550|gb|EFF66522.1| DNA-directed RNA polymerase sigma subunit FliA [Selenomonas noxia
           ATCC 43541]
          Length = 251

 Score =  116 bits (291), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 45/261 (17%), Positives = 110/261 (42%), Gaps = 26/261 (9%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGL 86
             ++  +L + Y     ++  +R+   +L LV  +A          +   +++S G  GL
Sbjct: 8   TAEDIDMLWRAYETEKTVAVRNRIAEHYLPLVRLVAGRIAISLPQHVDREDLLSSGFFGL 67

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           + A+++++  RG +  TY+   ++ AM +++ R+   + +    N K+        +  +
Sbjct: 68  LDAIERYELARGNKFETYAGVRVRGAMLDHL-RAKDWIPVSVRQNIKKY-------EKAV 119

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
             +     +      +A++L+++    I     L G  S   +I          +++L  
Sbjct: 120 AHLEGELGRTATDEELAEELDLT----IEGLHHLEGQVSAATVI--------PLEEYLRT 167

Query: 207 DHDGQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
           D     E   +E  E    +  L  ++  L  +ER +       E  +TL+ +++   +S
Sbjct: 168 DSPTSLEDGPVEHAEWTEVKETLAAAIEKLPEKERTVITLYYYDE--MTLKEIAAILHLS 225

Query: 266 RERVRQIEARAFKKVQESIQK 286
             R+ Q+  +A  +++ S+ +
Sbjct: 226 EARISQLHTKAIFRMRGSLAR 246


>gi|229076790|ref|ZP_04209702.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock4-18]
 gi|228706352|gb|EEL58613.1| RNA polymerase sigma-43 factor [Bacillus cereus Rock4-18]
          Length = 252

 Score =  116 bits (291), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 47/235 (20%), Positives = 102/235 (43%), Gaps = 12/235 (5%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLP--ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           +   ++ LV+ IA  Y+         ++V EGN G+++A++ FDP+ G+  +TY+  WIK
Sbjct: 1   MFHVNIGLVLSIARKYKKKHPEIEFDDLVQEGNEGMLRAIEDFDPDLGYCFSTYAYCWIK 60

Query: 111 AAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
            +M  +I  +     KI    NQ  + +               + +   V  + K+L+V+
Sbjct: 61  KSMLGFICKKKSGPFKIPNYVNQFNVKYV-----EIEDKYLQMHNRIPTVEEVVKELDVT 115

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             +V+  N       ++   I++ +++      +   D+           E  N    + 
Sbjct: 116 REKVVRHNVYYNRVTTMTLDIDTINEDIGILNSFC-NDNSAIPSTNEMIMEDLNYEIWII 174

Query: 230 RSMSVLNPRERRIFEARR-LQENPVTLE-NLSSEFEVSRERVRQIEARAFKKVQE 282
               VLNP+++ +      L +  + L   ++    ++ ERV Q++  A  ++++
Sbjct: 175 FD-EVLNPKQKMVLNLCFGLLDGEIHLHKEIAKALMITTERVSQLKDEAINRLKK 228


>gi|332708995|ref|ZP_08428965.1| RNA polymerase sigma factor, sigma-70 family [Lyngbya majuscula 3L]
 gi|332352184|gb|EGJ31754.1| RNA polymerase sigma factor, sigma-70 family [Lyngbya majuscula 3L]
          Length = 258

 Score =  116 bits (291), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 114/249 (45%), Gaps = 12/249 (4%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVKKFDP 95
           L ++Y+++ D    ++LV  +L LV + A  +         +++  G IGL+ A+++FD 
Sbjct: 16  LLQKYQQYPDPELRNQLVALNLGLVRREAHHWVKQCNESYEDLLQVGCIGLIVAIERFDS 75

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            +G   +++++ +I+  +Q Y+      ++I        L      +  +L+A  +    
Sbjct: 76  TKGIAFSSFAIPYIRGEIQHYLRDRGYSIRIPRR--WLALRQKSVEITQNLRATLNRQPT 133

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
            E++ A A  +++ E + I++  +     SL+  +  S+  ++   + +        Q+ 
Sbjct: 134 EEEIAA-ALNISLEEWQEITLAHQNREPLSLDTPVGDSEDRNTSLGELVPDPRYRSFQLA 192

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
            E + R      + ++++ L  R R + E   L +  +T + ++   ++S   V +   +
Sbjct: 193 QEDQIR------IQQALAHLEKRTREVLEFVFLHD--LTQKEVAQRLDISVVTVSRRVKK 244

Query: 276 AFKKVQESI 284
             + +Q+ +
Sbjct: 245 GLEALQKLM 253


>gi|255085668|ref|XP_002505265.1| predicted protein [Micromonas sp. RCC299]
 gi|226520534|gb|ACO66523.1| predicted protein [Micromonas sp. RCC299]
          Length = 477

 Score =  116 bits (291), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 59/314 (18%), Positives = 103/314 (32%), Gaps = 70/314 (22%)

Query: 35  YVLAK--------RYREHGD--LSAAHRLVTSHLRLVVKIAMGYRGYGLPIS-------E 77
             LA+        + +E  D    A   LVT ++ L   +A                  +
Sbjct: 61  RELARAMGFTSPAQLKERVDAGQEARRVLVTRNVGLARTVAADIHAKLNDADRGLLSVSD 120

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++ EG  GL  A  KFDP+RG+R +TY+ +WIK A+ + +  S   +++    N+     
Sbjct: 121 LMQEGCAGLATAADKFDPQRGYRFSTYAFFWIKKAVIDCVGNSGRTIRLPIHVNE----- 175

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSSDK- 195
           N++++K   + + +  ++      +A +L  S  ++  M         S++A        
Sbjct: 176 NIQKMKKATRELKEIKVRDPTEDELADRLGWSVVKLRQMKVWAFRTPVSMDATTAKKGDP 235

Query: 196 --------------NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
                         N++          +          +    R  L    S L PRE  
Sbjct: 236 WEDADDAVAEAASLNAAMQSSDFGTGLNAPSDTAEADVDADLLRMALEEVFSTLLPREAF 295

Query: 242 IFEARRLQENPVTLEN--------------------------------LSSEFEVSRERV 269
           I   R       T                                   L +   VS E V
Sbjct: 296 ILRHRFGLAAASTAMEGGDWLKASRAEVLSALRDDEGMGTRGGANFKTLGNLLGVSSESV 355

Query: 270 RQIEARAFKKVQES 283
           R  E RA  K+++ 
Sbjct: 356 RTYERRALAKLKQP 369


>gi|160942608|ref|ZP_02089853.1| hypothetical protein FAEPRAM212_00082 [Faecalibacterium prausnitzii
           M21/2]
 gi|158446087|gb|EDP23090.1| hypothetical protein FAEPRAM212_00082 [Faecalibacterium prausnitzii
           M21/2]
          Length = 234

 Score =  116 bits (291), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 56/258 (21%), Positives = 92/258 (35%), Gaps = 65/258 (25%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L  +EE          GD +A  +L+  +LRLV  I   Y        ++VS G IGLM
Sbjct: 35  PLTAREEAAAFSALH-AGDAAAREKLIRHNLRLVAHIVKKYYALPGDQEDLVSIGTIGLM 93

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV  FD  R  R +TY+   I+  ++                         RR +   Q
Sbjct: 94  KAVDTFDATRKARFSTYASRCIENEIR----------------------MQFRRERKSGQ 131

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                                           ++  ESL A     D +S+     ++ D
Sbjct: 132 T-------------------------------VSLQESLEA-----DGDSALTLADVIQD 155

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVS 265
               E    +  ER+     L + +  L  RER+I   R     + P+T    +    +S
Sbjct: 156 GFCME----DSCERQEDVRRLRQLLDTLPARERQILLLRYGLAGQPPLTQLETAGLLGIS 211

Query: 266 RERVRQIEARAFKKVQES 283
           R  V ++E  A + ++++
Sbjct: 212 RSYVSRLETHALELLRQA 229


>gi|91776300|ref|YP_546056.1| flagellar biosynthesis sigma factor [Methylobacillus flagellatus
           KT]
 gi|91710287|gb|ABE50215.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Methylobacillus
           flagellatus KT]
          Length = 244

 Score =  116 bits (291), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 49/251 (19%), Positives = 106/251 (42%), Gaps = 16/251 (6%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPER 97
           Y  HG  S    L+  H  LV KIA   +      + I +++  G +GL+ A  +++   
Sbjct: 2   YTLHGKTSPKEELLKQHASLVKKIAYQLKAKLPASVDIDDLIQAGMMGLLDASNRYEDNH 61

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G +  TY+   I+ +M + + R+  L         + +  N+R ++  +  +     +P 
Sbjct: 62  GAQFETYAAQRIRGSMIDELRRADWL--------PRSVRKNMRDVESAVHLLEQKLGRPP 113

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A++LN+S  +   M    +G + +     S   +   + D    D  G     ++
Sbjct: 114 TEGELARELNLSMDDFQGMLDDCSGHQLIYYEDFSEQDSGDHFLDRYQSDDSGD---PLK 170

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
                + R  L  ++  L  RE+         E  + L+++ +   VS  RV Q+  +A 
Sbjct: 171 ALLSSDFREALIEAIEALPEREK--ILMGLYYEQEMNLKDIGAIMSVSESRVCQLHTQAV 228

Query: 278 KKVQESIQKQV 288
            +++  +++++
Sbjct: 229 ARLRAKLKEKL 239


>gi|224009562|ref|XP_002293739.1| RNA polymerase [Thalassiosira pseudonana CCMP1335]
 gi|220970411|gb|EED88748.1| RNA polymerase [Thalassiosira pseudonana CCMP1335]
          Length = 316

 Score =  116 bits (291), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 58/250 (23%), Positives = 113/250 (45%), Gaps = 23/250 (9%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRG----YGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
            SA   LV S++ LV  +   Y       G+ I E+V EG++GL++A + FDP +G R +
Sbjct: 63  RSAKQELVASNMGLVHAVVKNYSRKAYYRGITIDELVQEGSLGLIRAAELFDPAKGLRFS 122

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+  WIK  +    +    LV       +++++  +R +   +               I
Sbjct: 123 TYATIWIKGVLSNSRVDEMVLV----PQRERQIWNKIREVSKDVDDEDGRL----STDMI 174

Query: 163 AKKLNVSESEVISMNCRLAGDE---SLN----ALINSSDKNSSQWQDWLVYDHDGQEQVL 215
           AKKL + +S V     R++      SL+    +   S + + S+  + L+ D  G +  L
Sbjct: 175 AKKLGLDKSSVEQNIQRMSSVNNMLSLDYQYASTTRSGETDGSKPFEALMADKSGSDADL 234

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIE 273
            E+ + K   +++   +  LN RE ++        +    ++++ +    ++RE  R + 
Sbjct: 235 AERAQFKA--DLVAGLVRNLNEREIQLIRLMYGMHDGHEYSVKDSAKIMGINRETARLLH 292

Query: 274 ARAFKKVQES 283
               KK++E+
Sbjct: 293 HACLKKLREA 302


>gi|154500630|ref|ZP_02038668.1| hypothetical protein BACCAP_04303 [Bacteroides capillosus ATCC
           29799]
 gi|150270519|gb|EDM97828.1| hypothetical protein BACCAP_04303 [Bacteroides capillosus ATCC
           29799]
          Length = 221

 Score =  116 bits (291), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 53/251 (21%), Positives = 88/251 (35%), Gaps = 64/251 (25%)

Query: 24  RKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
              P  L+ +EE +  +R    GDL A + L+  +LRLV  I   Y        +++S G
Sbjct: 30  GSFPRPLKAEEERMYLERCA-AGDLEARNILIEHNLRLVAHIIKKYYTQTDDQDDLISIG 88

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            IGL++ +  F P++  RLATY+   I+  +  +                        R 
Sbjct: 89  TIGLIKGISTFKPDKNVRLATYASRCIENEILMHF-----------------------RS 125

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
           +  LQ                                  G+ SL+  + +    SS    
Sbjct: 126 RKKLQ----------------------------------GEVSLSDTLEADGDGSSLSLM 151

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSS 260
            ++   D     L  +E     R  +      LN RE  I   R      NP+T   +++
Sbjct: 152 DVISVDDDMLDNLDARESCIKVRQCVK---DCLNEREAMIIGLRYGLGGQNPLTQREIAA 208

Query: 261 EFEVSRERVRQ 271
           +  +SR  V +
Sbjct: 209 QCGISRSYVSR 219


>gi|326780902|ref|ZP_08240167.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
 gi|326661235|gb|EGE46081.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily [Streptomyces
           cf. griseus XylebKG-1]
          Length = 264

 Score =  116 bits (291), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 39/241 (16%), Positives = 96/241 (39%), Gaps = 13/241 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +     + + L +  +IA  +R  G  + ++     +GL++AV ++DP+RG    +Y++ 
Sbjct: 36  ALRDETICAWLPMAHRIATRFRDRGEAMDDLRQVAAMGLVKAVDRYDPDRGKAFESYAVP 95

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +   ++ +       V +      + L   +R  +  L   +           IA    
Sbjct: 96  TVTGELKRHFRDHTWDVHVPRRV--QDLRNRVRVARRELAQSSG--GAAPTCADIASATG 151

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + E +V+     L    +L+     +           +   DG   V I+       R  
Sbjct: 152 LGEEDVLLGLEALESYSALSLDAGPAGVEGGSPLADRLGSCDGALDVAID-------REA 204

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +   +  L  RER I   R  ++  +T   ++ +  +S+  V ++ +++ ++V++ + ++
Sbjct: 205 VKPGLRGLPERERTILYLRYFRD--MTQSRIAEQLGISQMHVSRLLSQSCERVRDGVLQE 262

Query: 288 V 288
            
Sbjct: 263 A 263


>gi|148645064|gb|ABR01057.1| RpoD [uncultured Geobacter sp.]
          Length = 102

 Score =  116 bits (291), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 36/104 (34%), Positives = 52/104 (50%), Gaps = 2/104 (1%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVV IA  Y   GL   +++ EGNIGLM+AV KF+ +RG++ +TY+ WWI+ A+   I
Sbjct: 1   LRLVVSIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYQRGYKFSTYATWWIRQAITRAI 60

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
                 ++I            L R    L         PE++  
Sbjct: 61  ADQARTIRIPVHM--IETINKLIRTSRQLVQEIGREPSPEEIAE 102


>gi|154498128|ref|ZP_02036506.1| hypothetical protein BACCAP_02109 [Bacteroides capillosus ATCC
           29799]
 gi|150273118|gb|EDN00275.1| hypothetical protein BACCAP_02109 [Bacteroides capillosus ATCC
           29799]
          Length = 240

 Score =  116 bits (291), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 52/264 (19%), Positives = 101/264 (38%), Gaps = 63/264 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K EE  L  R  + G+ +   +L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 38  PPLSKGEEAELIARL-DEGEETVKSQLIERNLRLVVYIARRFENTGVGIEDLISIGTIGL 96

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+  + P +  +LATY+   I+  +  ++ ++                          
Sbjct: 97  IKAINTYKPAKNIKLATYASRCIENEILMHLRKTS------------------------- 131

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                      +S +  L  D   N L+ S    +         
Sbjct: 132 ----------------------CLKSEVSFDEPLNTDWDGNELLLSDILGTENDVVMKPI 169

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEV 264
           + D   Q+L+E  E+             L+ RE++I   R   +     T + ++    +
Sbjct: 170 EDDVDRQLLLEAMEK-------------LDGREKQIITMRFGLDGRPERTQKEVADLLGI 216

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S+  + ++E R   ++++ I K +
Sbjct: 217 SQSYISRLEKRIISRLKKEILKML 240


>gi|298490935|ref|YP_003721112.1| FliA/WhiG subfamily RNA polymerase sigma 28 subunit ['Nostoc
           azollae' 0708]
 gi|298232853|gb|ADI63989.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily ['Nostoc
           azollae' 0708]
          Length = 265

 Score =  116 bits (291), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 46/246 (18%), Positives = 104/246 (42%), Gaps = 12/246 (4%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVKKFDP 95
           L + Y++       ++LV  +  LV K A  +         +++  G +GL++A++KF+ 
Sbjct: 23  LLREYQQCPSERLRNQLVKVNFGLVRKEAHYWINQCQESYDDLIQVGCLGLIRAIEKFEL 82

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            +G   ++Y++ +I+  +Q Y+      ++I        L      L   L+   +    
Sbjct: 83  SKGNAFSSYAIPYIRGEIQHYLRDKGVTMRIPRR--WLALQQQAIGLSRSLREKYNRQPT 140

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
             ++ A+   +++SE E I +        SL+  I   ++ +S   + +   H    Q+ 
Sbjct: 141 DAELAAVL-AISLSEWEEIKLAWMNRSPLSLDVPIKDGEEGASCLGELVPDPHYRSFQLA 199

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
            E + R      L +++  L  R R + E   LQ+  +T + ++    +S   V +   +
Sbjct: 200 QEDQIR------LQQALVQLENRTREVLECVFLQD--LTQKQVAEHLGISVVTVSRRVKK 251

Query: 276 AFKKVQ 281
               ++
Sbjct: 252 GLDLLK 257


>gi|317051537|ref|YP_004112653.1| FliA/WhiG family RNA polymerase sigma factor [Desulfurispirillum
           indicum S5]
 gi|316946621|gb|ADU66097.1| RNA polymerase sigma factor, FliA/WhiG family [Desulfurispirillum
           indicum S5]
          Length = 250

 Score =  116 bits (291), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 43/243 (17%), Positives = 103/243 (42%), Gaps = 13/243 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            +  ++++  +  L+  IA          + + +++S G +GL+ A+ KFD  RG    T
Sbjct: 17  PAIRNQIIEEYAPLIKYIATRIHAGLPSNIELDDLISIGALGLIDAIDKFDMNRGVLFKT 76

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   I+  + + + +   L         + L    + L      +  N  +      +A
Sbjct: 77  YAESRIRGKILDELRKLDWL--------PRGLRQKNKALDRAYSKLGINEGREVSDGELA 128

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
            +L + E+EV     +  G   L+      D++ S+         D +     E  E   
Sbjct: 129 AELGIDEAEVQQYISQAGGYTMLSLDEQMYDRDGSESGTLSDLIPDRENAGPEEHLEITQ 188

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +  L + + +L+ +E+++      +E  +T++ + +   ++  RV QI ++A  K++++
Sbjct: 189 NQEFLKKHIRLLSEKEQQMLALYYYEE--LTMKEIGTVLGITESRVSQIHSQALFKLKKA 246

Query: 284 IQK 286
           + +
Sbjct: 247 MGR 249


>gi|317501595|ref|ZP_07959789.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|316897012|gb|EFV19089.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
          Length = 239

 Score =  116 bits (290), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 39/243 (16%), Positives = 99/243 (40%), Gaps = 16/243 (6%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R    GD +A  +LV  ++ LV  +   +   G    ++   G+IGL++A+ KFD     
Sbjct: 9   RKSHSGDKAAREQLVKENVGLVHCVVKRFLERGAEREDLFQIGSIGLLKAIDKFDLTYNV 68

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY++  I   ++ ++     ++K+  +  +        R +     +  +  +   +
Sbjct: 69  KFSTYAVPLISGEIKRFLRDDG-MIKVSRSLKEIAYKSVQARER-----LISSLGREPTI 122

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +++++ V   E++         ES+   ++  + +  +  D L  + + +E  +++  
Sbjct: 123 EELSEEVGVEREELVQAMEAGCEIESIYRPVHQKEGSEIRLLDKL-EEKEKREDKILDLI 181

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
             K     L      L          R   +   T  ++     +S+ +V + E R  +K
Sbjct: 182 VLKELLETLDEEEKQL-------IFLRYFAD--RTQSDVGKIMGISQVQVSRSEKRIIEK 232

Query: 280 VQE 282
           +++
Sbjct: 233 LRK 235


>gi|332140599|ref|YP_004426337.1| flagellar biosynthesis sigma factor [Alteromonas macleodii str.
           'Deep ecotype']
 gi|327550621|gb|AEA97339.1| flagellar biosynthesis sigma factor [Alteromonas macleodii str.
           'Deep ecotype']
          Length = 243

 Score =  116 bits (290), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 51/252 (20%), Positives = 98/252 (38%), Gaps = 22/252 (8%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFD 94
           A  YR+  D     +LV  H  LV +IA            + +++  G IGL++A + FD
Sbjct: 5   AAAYRQQTD---KSQLVERHASLVKRIAHHLIARLPASVLVDDLIQSGMIGLLEAARNFD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +G    T++   I+ AM + I +             + +  N R +   +  +     
Sbjct: 62  GSKGASFETFAGIRIRGAMLDEIRKGDWT--------PRSVHRNGRAITEAISQVESETG 113

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +  +   IA KLNVS  +   M   +      NA      ++    +D +  +       
Sbjct: 114 RDARDSDIADKLNVSLQDYHQMLNEV------NAGKLVGIEDLGVSEDVITTEQSRGSDA 167

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
            +E   +   +  L  +++ L  RE  +       +  + L  +    +VS  RV QI +
Sbjct: 168 PLEDLMQGAFQKALAHAITTLPEREAIVLSLYY--DEELNLREIGEVLDVSESRVSQIHS 225

Query: 275 RAFKKVQESIQK 286
           +A  K++  ++ 
Sbjct: 226 QAMLKLKSRMKS 237


>gi|300311345|ref|YP_003775437.1| flagellar operon RNA polymerase sigma factor [Herbaspirillum
           seropedicae SmR1]
 gi|300074130|gb|ADJ63529.1| RNA polymerase sigma factor for flagellar operon (sigma-F factor)
           protein [Herbaspirillum seropedicae SmR1]
          Length = 244

 Score =  116 bits (290), Expect = 5e-24,   Method: Composition-based stats.
 Identities = 42/240 (17%), Positives = 98/240 (40%), Gaps = 15/240 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L+  H  LV K+A   +    P   + +++  G +GL+ AV +++   G +  TY++
Sbjct: 10  KNDLLEQHAPLVKKLAHQLKAKLPPSVEVDDLIQAGMMGLLDAVNRYEETHGAQFETYAV 69

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +  S  L         + +  N R+++  +Q +     +  +   +A+ +
Sbjct: 70  QRIRGAMLDELRSSDWL--------PRSIRQNARKVEEAMQTLLQQLGRQPKEAELAQHM 121

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +S  +  S+     G + +       D    +   +L           ++       R 
Sbjct: 122 QISLEDYQSLLSECGGHQLIYYEDFHDDDGGHE--HFLDRHQTSDSDDPLQNLINGGFRE 179

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  S+  L  RE+         E  + L+ + +   VS  RV Q+ ++A  +++  +++
Sbjct: 180 AVVDSIKALPEREQ--ILMALYYEQEMNLKEIGAVMGVSESRVCQLHSQAISRMRSYLRE 237


>gi|332305676|ref|YP_004433527.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Glaciecola agarilytica
           4H-3-7+YE-5]
 gi|332173005|gb|AEE22259.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Glaciecola agarilytica
           4H-3-7+YE-5]
          Length = 242

 Score =  116 bits (290), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 52/251 (20%), Positives = 100/251 (39%), Gaps = 22/251 (8%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFD 94
           A  Y++  D +A   LV  H  LV +IA            + +++  G IGL++A + FD
Sbjct: 5   AAAYQQLDDRNA---LVERHAPLVKRIAHHLIARLPASVLVDDLIQAGMIGLLEASRNFD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +G    T++   I+ +M + I R           N + +   + +++           
Sbjct: 62  GSKGASFETFAGIRIRGSMLDEI-RKGDWTPRSVHKNGRAITDAINKVER-------ETG 113

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +  + V IAKKL VS  +   M   +      NA      ++    +D +  +       
Sbjct: 114 RDARDVDIAKKLEVSIEQYHQMLSEV------NAGKIIGMEDLGVTEDVVTTEQTKGSDT 167

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
             E   + + +  L  +++ L  RE  +       +  + L  +    +VS  RV QI +
Sbjct: 168 PFEDLLQGSFQKALAHAITTLPEREAIVLSLYY--DEELNLREIGEVLDVSESRVSQIHS 225

Query: 275 RAFKKVQESIQ 285
           +A  K++  +Q
Sbjct: 226 QAMLKLKSKMQ 236


>gi|225028118|ref|ZP_03717310.1| hypothetical protein EUBHAL_02388 [Eubacterium hallii DSM 3353]
 gi|224954588|gb|EEG35797.1| hypothetical protein EUBHAL_02388 [Eubacterium hallii DSM 3353]
          Length = 247

 Score =  116 bits (290), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 49/244 (20%), Positives = 94/244 (38%), Gaps = 64/244 (26%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   L+  +LRLVV IA  +   G+ + +++S G IGL++A++ F  ++  +LATY+ 
Sbjct: 62  EEAKALLIERNLRLVVYIAKKFENTGIGVEDLISIGTIGLIKAIQTFKLDKKIKLATYAS 121

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+  +  Y+ R+                                            K+
Sbjct: 122 RCIENEILMYLRRTNKT-----------------------------------------KM 140

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            VS  E ++++                D N     D L  D D    V+ +  E +  R 
Sbjct: 141 EVSIDEPLNVD---------------WDGNELLLSDILGTDSD----VISKDIEDEIDRK 181

Query: 227 MLTRSMSVLNPRERRIFEARRLQE----NPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           ML ++M  L+ RE+ I   R           T + ++    +S+  + ++E +   +++ 
Sbjct: 182 MLNKAMETLSDREKLIIRLRFGIGGEESEEKTQKEVADLLGISQSYISRLEKKIIHRLKR 241

Query: 283 SIQK 286
            + K
Sbjct: 242 EMIK 245


>gi|158341383|ref|YP_001522549.1| RNA polymerase sigma-24 subunit [Acaryochloris marina MBIC11017]
 gi|158311624|gb|ABW33234.1| RNA polymerase sigma-24 subunit [Acaryochloris marina MBIC11017]
          Length = 423

 Score =  115 bits (289), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 53/245 (21%), Positives = 107/245 (43%), Gaps = 23/245 (9%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + GD  A  R +  + RLV K A  YRG  +   ++V+ G +GL  A++KFD  RGF+ 
Sbjct: 29  AQAGDRRAEDRFIRKNQRLVFKEAKRYRGL-VDWDDLVNAGTLGLSIAIQKFDLSRGFQF 87

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY++  I+  +++ I     L +         +  +L+++    Q +     +   +  
Sbjct: 88  STYAVKPIRTEIRQLICEQRGLSR--------EITKHLKKIDEAEQDLELELERKPTLDE 139

Query: 162 IAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           +A++   S   + +     R+    SLN  + +  +   +  D++            E  
Sbjct: 140 LAERTGYSHRVITNAWNKARVVDTSSLN--VLTGTEQGIECLDFVEDFEQLDSWDFAESI 197

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
             K+        ++ L  RE  I  ARR   +  +   + +  ++S ER+RQ+  +A + 
Sbjct: 198 NMKDY-------IAQLPDRESFIVRARR---DGHSYREIGTMLKLSGERIRQLYQKALEY 247

Query: 280 VQESI 284
           ++  I
Sbjct: 248 LKHLI 252


>gi|225462725|ref|XP_002268709.1| PREDICTED: hypothetical protein [Vitis vinifera]
 gi|302143685|emb|CBI22546.3| unnamed protein product [Vitis vinifera]
          Length = 518

 Score =  115 bits (289), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 58/260 (22%), Positives = 109/260 (41%), Gaps = 34/260 (13%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFDP 95
           +R+ E G  +A ++L+  +LRLV+ +   Y      G    ++   G  GL+ A+ +F+P
Sbjct: 271 RRHMEVG-QAARNKLIKHNLRLVLFVINKYFQEFANGPKFQDLCQAGVKGLITAIDRFEP 329

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSL--------VKIGTTANQKRLFFNLRRLKGHLQ 147
           +R FRL+TY ++WI+ A+   +  S           V++     +  L F L+RL    +
Sbjct: 330 KRSFRLSTYGLFWIRHAIMRSMTLSSFTRVSFGLESVRVEIQRAKLELLFKLQRLPTEEE 389

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
            I    + PE+   + +    +   V+S++ R       +A       N     + +  D
Sbjct: 390 IIEKVGISPERYHEVMR----ASKSVLSLHAR-------HATTQEEYINGITDVEGVGGD 438

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVS 265
              Q  +L                +  L P+E  +   R   +     TL  ++    +S
Sbjct: 439 RGRQLALLRLAL---------DDVLDSLKPKESLVMRQRYGLDGKGDRTLGEIAGNLSIS 489

Query: 266 RERVRQIEARAFKKVQESIQ 285
           RE VR+ E +A  K++   +
Sbjct: 490 REMVRKHEVKALMKLKHPAR 509


>gi|57996880|emb|CAI45888.1| negative response regulator [Escherichia coli]
          Length = 158

 Score =  115 bits (289), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 46/165 (27%), Positives = 80/165 (48%), Gaps = 7/165 (4%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 60

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           +     +++      K L   LR  +     ++           IA++L+    +V  M 
Sbjct: 61  MNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRML 115

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
                  S++  +     +     D L  + +   +   + ++ K
Sbjct: 116 RLNERITSVDTPL--GGDSEKALLDILADEKENGPEDTTQDDDMK 158


>gi|29840191|ref|NP_829297.1| RNA polymerase sigma factor sigma-28 [Chlamydophila caviae GPIC]
 gi|29834539|gb|AAP05175.1| RNA polymerase sigma factor, sigma-70 family [Chlamydophila caviae
           GPIC]
          Length = 257

 Score =  115 bits (289), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 51/257 (19%), Positives = 111/257 (43%), Gaps = 18/257 (7%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKK 92
            + + Y E  ++     L+  +L LV  +               ++ + G  GL++AV++
Sbjct: 11  EIWELYWETQEIEYRDTLIDFYLHLVKCVVHRLISGMPSHVKTEDLYASGVEGLVRAVER 70

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FDPE+  R   Y+++ IKAA+ + + +      +  + +QK       +L   +  +  +
Sbjct: 71  FDPEKSRRFEGYALFLIKAAIIDDLRKQDW---VPRSVHQKA-----NKLSEAMDTLRQS 122

Query: 153 NLKPEQVVAIAKKLNVSESEV--ISMNCRLAGDESLNALINS-SDKNSSQWQDWLVYDHD 209
             +      + +   +S+ E+    ++ R A   SLN    S SD  S    +  + D  
Sbjct: 123 LGREPTDGDLCEYFQISQQELSGWFISARPALIISLNEERPSLSDGESGVALEERIPDE- 181

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
            + +   +  ++K   + L  ++  L  +ER++      +E  + L+ +     VS  RV
Sbjct: 182 -RAETGYDIVDKKEFSSFLANAIEGLEEKERKVMALYYYEE--LVLKEIGKILGVSESRV 238

Query: 270 RQIEARAFKKVQESIQK 286
            QI ++A  K++ ++  
Sbjct: 239 SQIHSKALIKLRAALSA 255


>gi|225574871|ref|ZP_03783481.1| hypothetical protein RUMHYD_02949 [Blautia hydrogenotrophica DSM
           10507]
 gi|225037945|gb|EEG48191.1| hypothetical protein RUMHYD_02949 [Blautia hydrogenotrophica DSM
           10507]
          Length = 230

 Score =  115 bits (289), Expect = 6e-24,   Method: Composition-based stats.
 Identities = 53/257 (20%), Positives = 93/257 (36%), Gaps = 62/257 (24%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L  +EE    K+++E GDL A   L+  +LRLV  +   Y+G    + +++S G IGL+
Sbjct: 29  PLTVEEERYYLKKFQE-GDLKAKDILIERNLRLVAHVVKKYQGLEEDLDDLISIGTIGLI 87

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV  FD ++  RL+TY+   I                         L   LR  K +  
Sbjct: 88  KAVSTFDSKKSNRLSTYAARCIDN----------------------ELLMMLRARKKY-- 123

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                                  S  +S+   +  D          + N     D +   
Sbjct: 124 -----------------------SRDVSLYEPIGTD---------KEGNEINLLDII--- 148

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVS 265
               E V+     +++ +  +    + L+ +E  +   R     E   T   ++    +S
Sbjct: 149 ESPPEDVVENYSVKQDIQKAMHLLSTCLSHKEYEVIRLRFGLFGEKEYTQREIAKRLNIS 208

Query: 266 RERVRQIEARAFKKVQE 282
           R  V +IE  A  K++ 
Sbjct: 209 RSYVSRIEKNALLKLRR 225


>gi|327441027|dbj|BAK17392.1| DNA-directed RNA polymerase specialized sigma subunit [Solibacillus
           silvestris StLB046]
          Length = 256

 Score =  115 bits (289), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 45/261 (17%), Positives = 111/261 (42%), Gaps = 20/261 (7%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQA 89
           +E  L  R+ ++ D  A   L+     LV              +   +++S G +GL  A
Sbjct: 8   DEQSLWVRWTKNRDPEAGDLLIKKFKPLVSYHVQRIAVGLPKNISRDDLMSLGMMGLFDA 67

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + KFD  R  +  TY+ + ++ A+ + + +      +  +A +K      ++L+  ++++
Sbjct: 68  LNKFDINRDLKFDTYASFRVRGAILDGLRKEDW---LPRSAREKA-----KKLESQIESL 119

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
               ++      +A  +N+   EV         +   S+N  +   D+  S+ + +++ D
Sbjct: 120 EQKLMRHATAEEVAAHMNLPVEEVYQTFQEHFFSNVLSINEQL---DQEESEGKSFVIRD 176

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            +   +   +          L  ++  LN +E+ +      +E  +TL  +    ++S  
Sbjct: 177 DNT--KTPEQHSVHVELLGDLAENIKKLNEKEQLVISLFYSEE--LTLTEIGEILDLSTS 232

Query: 268 RVRQIEARAFKKVQESIQKQV 288
           R+ QI ++A  K+++ +  ++
Sbjct: 233 RISQIHSKALFKLRKLLSSEM 253


>gi|3249721|gb|AAC26663.1| RNA polymerase sigma-like factor [Micromonospora echinospora]
          Length = 161

 Score =  115 bits (289), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 39/172 (22%), Positives = 77/172 (44%), Gaps = 13/172 (7%)

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI+ A+   +      ++I     +  +   L R++  L         PE    +A
Sbjct: 1   YATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLGREPTPE---ELA 55

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           K+++++  +V+ +        SL+  I   D+  SQ  D++    D +  V ++      
Sbjct: 56  KEMDITPEKVLEIQQYAREPISLDQTI--GDEGDSQLGDFI---EDSEAVVAVDAVSFSL 110

Query: 224 RRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIE 273
            ++ L + +   +P  RR++  R       P TL+ +   + V+RER+RQIE
Sbjct: 111 LQDQLQQVLQG-SPSVRRVWSMRFGLTDGQPRTLDEIGQVYGVTRERIRQIE 161


>gi|229544420|ref|ZP_04433478.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus coagulans
           36D1]
 gi|229324905|gb|EEN90582.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus coagulans
           36D1]
          Length = 257

 Score =  115 bits (289), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 49/261 (18%), Positives = 107/261 (40%), Gaps = 18/261 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQA 89
           EE      + +  D  A + LV  ++ LV              +   ++ S G  GL+ +
Sbjct: 9   EEQKDWDLWLKSRDPEAGNALVKRYMPLVSFHVQRIAAGLPRNVSKEDLKSLGMFGLLDS 68

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + KFDP R  R  TY+ + I+ A+ + + +   L +              ++++  ++++
Sbjct: 69  LNKFDPSRELRFDTYASFRIRGAILDGLRKEDWLSR--------GTREKAKKIESAIESL 120

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVI--SMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
               L+      +A +L + E+EV         A   S+      +D+  +  +      
Sbjct: 121 EQKYLRTVSPKEVALELGMEETEVCTTMNEQFFANVLSIEETGTDNDEPEAASRFVSGDR 180

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           + GQ +  +EK   K     L  ++  L+ +E+ +       +   TL  +     +S  
Sbjct: 181 NAGQPESELEK---KETVKELAEAIRALSEKEQLVLSLFY--QEECTLTEIGEVMGLSTS 235

Query: 268 RVRQIEARAFKKVQESIQKQV 288
           R+ QI ++A  K++  ++K++
Sbjct: 236 RISQIHSKAIYKLRNILEKRL 256


>gi|116748823|ref|YP_845510.1| FliA/WhiG family RNA polymerase sigma factor [Syntrophobacter
           fumaroxidans MPOB]
 gi|116697887|gb|ABK17075.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Syntrophobacter
           fumaroxidans MPOB]
          Length = 279

 Score =  115 bits (289), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 45/251 (17%), Positives = 97/251 (38%), Gaps = 18/251 (7%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
                ++  H  LV  +A+           I +++S G IGL+ AV K+D  +G     Y
Sbjct: 30  ETKELVILKHSDLVKHMALRLFSRLPDHVSIDDLISAGVIGLIDAVDKYDSGQGIPFKFY 89

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +   I+ AM + I    ++  +  +  QK        L+    A+     +      +A 
Sbjct: 90  AKIRIRGAMLDEIR---AMDWVPRSLRQKGNV-----LERTFSALEQKLGRCPSDEQVAG 141

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +LN+   +   +   + G   L       + N +  ++          + L +   R+  
Sbjct: 142 ELNIGIEDYHRLLDEIKGISFL-----PENINEALLENGESGSLASDSEELFQHAYRQEI 196

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +  L  ++  L  +E+ +       E  +T++ + +    +  R+ QI  +A  K++  +
Sbjct: 197 QRHLADAIRTLTEKEQLVLSLYYYDE--LTMKEVGTALGYTESRISQIHTKAIIKLRSRL 254

Query: 285 QKQVELSSSPP 295
            K++     PP
Sbjct: 255 AKRLTADDLPP 265


>gi|52080250|ref|YP_079041.1| RNA polymerase sigma factor SigD [Bacillus licheniformis ATCC
           14580]
 gi|52785627|ref|YP_091456.1| RNA polymerase sigma factor SigD [Bacillus licheniformis ATCC
           14580]
 gi|319645970|ref|ZP_08000200.1| RNA polymerase sigma factor [Bacillus sp. BT1B_CT2]
 gi|52003461|gb|AAU23403.1| RNA polymerase sigma-28 factor (sigma-D) [Bacillus licheniformis
           ATCC 14580]
 gi|52348129|gb|AAU40763.1| SigD [Bacillus licheniformis ATCC 14580]
 gi|317391720|gb|EFV72517.1| RNA polymerase sigma factor [Bacillus sp. BT1B_CT2]
          Length = 254

 Score =  115 bits (289), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 51/248 (20%), Positives = 109/248 (43%), Gaps = 21/248 (8%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVK----IAMGYRGYGLPISEVVSEGNIGLMQ 88
           E+ +L  R++E  D  A   L+  ++ LV      IA+G         ++VS G +GL  
Sbjct: 7   EDQMLWSRWKEWKDPQAGDDLIRRYMPLVTYHVGRIAVGLPKSVH-KDDLVSLGMLGLYD 65

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++KFDP R  +  TY+ + I+ A+ + + +      +  T+ +K      ++++  ++ 
Sbjct: 66  ALEKFDPGRDLKFDTYASFRIRGAIIDGLRKEDW---LPRTSREKT-----KKVEAAIEK 117

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +    L+      IA +L +SE +V++       A   S++  ++  +       +  V 
Sbjct: 118 LEQRYLRNVSPSEIAAELGMSEQDVVTTINEGFFANLLSIDEKLHDHEDGE----NVQVM 173

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
             D +     EK  +    + L   ++ L+ +E+ +       +  +TL  +     +S 
Sbjct: 174 IRDDKTSTPEEKMLKDELISQLAEKINELSEKEQLVISLFY--KEELTLTEIGQVLNLST 231

Query: 267 ERVRQIEA 274
            R+ QI +
Sbjct: 232 SRISQIHS 239


>gi|254412979|ref|ZP_05026751.1| RNA polymerase sigma factor, sigma-70 family [Microcoleus
           chthonoplastes PCC 7420]
 gi|196180143|gb|EDX75135.1| RNA polymerase sigma factor, sigma-70 family [Microcoleus
           chthonoplastes PCC 7420]
          Length = 260

 Score =  115 bits (289), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 44/259 (16%), Positives = 109/259 (42%), Gaps = 20/259 (7%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQA 89
           K E   L + Y++       ++LV  ++ LV + A  +         +++  G +GL++A
Sbjct: 12  KHESLRLLRDYQQSKSAETRNQLVYLNIGLVRREAHYWVNQCTESYEDLLQVGCLGLIRA 71

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT--ANQKRLFFNLRRLKGHLQ 147
           +++F P +G   +++++ +I+  +Q Y+      ++I     A Q++    +R+L+  L 
Sbjct: 72  IERFAPSKGNAFSSFAIPYIRGEIQHYLRDRGGCIRIPRRWLALQQQSIAIIRQLRAQLN 131

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
                  +      +A+ L +  +E   I +  +     SL+  +   +  ++   D + 
Sbjct: 132 -------RQPTDAEVAEALEIPLAEWQEIKLAHQNREPLSLDTPVGDEEDGTTSLGDIVP 184

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
                  Q+  E + R      L +++  L  R R + E   L +  +T + ++    +S
Sbjct: 185 DPQYRSFQLAQEDQIR------LQQALVHLEQRTREVLEFVFLHD--LTQKEVAELLNIS 236

Query: 266 RERVRQIEARAFKKVQESI 284
              V +   +    ++  +
Sbjct: 237 VVTVSRRMKKGLNAMKNIM 255


>gi|46204564|ref|ZP_00049813.2| COG0568: DNA-directed RNA polymerase, sigma subunit
           (sigma70/sigma32) [Magnetospirillum magnetotacticum
           MS-1]
          Length = 132

 Score =  115 bits (289), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 69/127 (54%), Positives = 92/127 (72%), Gaps = 2/127 (1%)

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + E +VI MN RL+GD SLNA +   ++   +WQDWLV +   QE VL  +EE +NR + 
Sbjct: 1   MPEQDVIDMNRRLSGDTSLNAPLR--EEGEGEWQDWLVDNSPSQETVLAREEEGRNRLSA 58

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L  ++ VLNPRERRIFEARRL ++P+TLE+LS EF VSRERVRQIE RAF+KVQE++++ 
Sbjct: 59  LRDALGVLNPRERRIFEARRLADDPITLEDLSGEFGVSRERVRQIEVRAFEKVQEAVKRN 118

Query: 288 VELSSSP 294
           +     P
Sbjct: 119 LATRELP 125


>gi|331088539|ref|ZP_08337452.1| hypothetical protein HMPREF1025_01035 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|330407801|gb|EGG87295.1| hypothetical protein HMPREF1025_01035 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 239

 Score =  115 bits (289), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 39/243 (16%), Positives = 99/243 (40%), Gaps = 16/243 (6%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R    GD +A  +LV  ++ LV  +   +   G    ++   G+IGL++A+ KFD     
Sbjct: 9   RKSHSGDKAAREQLVKENVGLVHCVVKRFLERGAEREDLFQIGSIGLLKAIDKFDLTYNV 68

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY++  I   ++ ++     ++K+  +  +        R +     +  +  +   +
Sbjct: 69  KFSTYAVPLISGEIKRFLRDDG-MIKVSRSLKEIAYKSVQARER-----LISSLGRDPTI 122

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +++++ V   E++         ES+   ++  + +  +  D L  + + +E  +++  
Sbjct: 123 EELSEEVGVEREELVQAMEAGCEIESIYRPVHQKEGSEIRLLDKL-EEKEKREDKILDLI 181

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
             K     L      L          R   +   T  ++     +S+ +V + E R  +K
Sbjct: 182 VLKELLETLDEEEKQL-------IFLRYFAD--RTQSDVGKIMGISQVQVSRSEKRIIEK 232

Query: 280 VQE 282
           +++
Sbjct: 233 LRK 235


>gi|126659553|ref|ZP_01730685.1| sigma factor SigF [Cyanothece sp. CCY0110]
 gi|126619192|gb|EAZ89929.1| sigma factor SigF [Cyanothece sp. CCY0110]
          Length = 258

 Score =  115 bits (289), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 45/259 (17%), Positives = 111/259 (42%), Gaps = 16/259 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVK 91
           E   L + Y++    +  ++++  +  LV K A  +         ++V  G++GL++A++
Sbjct: 12  ETLNLFQAYQKTPKPTLRNKILELNFGLVRKEAHHWVHQCPESYEDLVQVGSLGLIRAIE 71

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           +F  E+G   +++++ +I+  +Q Y+      V+I      +R     R+     +   +
Sbjct: 72  RFSIEKGHAFSSFAIPYIRGEIQHYLRDKKYTVRIP-----RRWLELGRQSMNVRREFRE 126

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHD 209
              +      IA+ L +S  E   +          SL+  ++S  +  +   D +   + 
Sbjct: 127 KFNRQPTDSEIAQVLEISLKEWQEIKLAFQNREPVSLDVKVSSEGEGQTSLGDLVPDANY 186

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
              Q+  E + R      L +++  L  R R I E   L++  +T    + +  +S   V
Sbjct: 187 RSFQLAQEDQIR------LQQALEQLEERTRNILEFVFLKD--LTQRETAEQLGISVVTV 238

Query: 270 RQIEARAFKKVQESIQKQV 288
            +   +  + +++++ K++
Sbjct: 239 SRRVKKGLEILKQNMHKEI 257


>gi|260776433|ref|ZP_05885328.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           coralliilyticus ATCC BAA-450]
 gi|260607656|gb|EEX33921.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           coralliilyticus ATCC BAA-450]
          Length = 244

 Score =  115 bits (289), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 52/247 (21%), Positives = 104/247 (42%), Gaps = 19/247 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPER 97
           Y ++ +  +    +  +  LV +IA    G   P   + +++  G IGL++A K +D  +
Sbjct: 7   YDQYANQDSQRAFLEKYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLLEAQKNYDGSK 66

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G    TY+   I+ AM + I R    V      N + +   + +L+G L        +  
Sbjct: 67  GASFETYAGIRIRGAMLDDIRR-GDWVPRSVHKNSREISQAIAQLEGELN-------RDP 118

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +AK+L +S  +  S       D + + LI   D   S+  D + ++   +E +  +
Sbjct: 119 TDAEVAKRLEMSLEQYHSALT----DINSSRLIGIDDLGVSE--DAISHEDADEENIPFQ 172

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
               +  R  L  S+  L  RE  +       +  + L+ +     VS  RV QI +++ 
Sbjct: 173 GVADEYFRTALVESIKSLPEREALVLSLYY--DEELNLKEIGEVIGVSESRVSQILSQSM 230

Query: 278 KKVQESI 284
           ++++  +
Sbjct: 231 QRLRTKL 237


>gi|119897398|ref|YP_932611.1| RNA polymerase sigma factor [Azoarcus sp. BH72]
 gi|119669811|emb|CAL93724.1| RNA polymerase sigma factor [Azoarcus sp. BH72]
          Length = 256

 Score =  115 bits (289), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 46/238 (19%), Positives = 99/238 (41%), Gaps = 17/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              LV ++  LV +IA          + + +++  G +GL+ A+ +++   G +  TY++
Sbjct: 10  KDHLVVAYAPLVKRIAFQLMAKLPASVEVEDLIQNGMMGLLDAIGRYEEGLGAQFETYAV 69

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             ++ AM + +  +  L         + L  ++RR++  +  +   + +P     +A+ L
Sbjct: 70  QRVRGAMLDGLRENDWL--------PRSLRRDMRRIESAIHVLEQQHGRPPSETELAESL 121

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            V   E   M     G    + L+   D    + +D+L       E    E  E  + R 
Sbjct: 122 GVPLPEYQRMLQDARG----HQLVYFEDFTDGEGEDFLDRHLGAHESNPAELLEDADMRA 177

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L R++  L  RE+ +       E  + L  +     V+  RV Q+ ++A  +++  +
Sbjct: 178 NLIRAIDDLPEREKLVMALYY--EEELNLREIGEVLGVTESRVCQLHSQAVARLRARV 233


>gi|84388128|ref|ZP_00991024.1| flagellar biosynthesis sigma factor FliA [Vibrio splendidus 12B01]
 gi|84377195|gb|EAP94065.1| flagellar biosynthesis sigma factor FliA [Vibrio splendidus 12B01]
          Length = 244

 Score =  115 bits (289), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 47/249 (18%), Positives = 98/249 (39%), Gaps = 19/249 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPER 97
           Y +H + ++       +  LV +IA    G   P   + +++  G IGL++A + +D  +
Sbjct: 7   YDQHANHNSQQAFFEKYSVLVKRIAHHLLGRLPPNVLVDDLIQAGMIGLIEAQQNYDGTK 66

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G    TY+   I+ AM + I R    V      N + +   +  L+G L        +  
Sbjct: 67  GASFETYAGIRIRGAMLDDIRR-GDWVPRSVHKNNREISSAIAELEGALN-------RDP 118

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +AK +       +S++        +N       ++     D +  + D Q+    +
Sbjct: 119 SDAEVAKHMG------LSLDQYHNALTDINCSRLVGIEDLGVSDDVISPNEDSQDNTPFQ 172

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
               ++ R  L  S+  L  RE  +       +  + L+ +     VS  RV QI +++ 
Sbjct: 173 GVADESFRQALIDSIKQLPEREGLVLSLYY--DEELNLKEIGEVLGVSESRVSQILSQSM 230

Query: 278 KKVQESIQK 286
           ++++  +  
Sbjct: 231 QRLRTKLSA 239


>gi|169827282|ref|YP_001697440.1| RNA polymerase sigma-F factor [Lysinibacillus sphaericus C3-41]
 gi|168991770|gb|ACA39310.1| RNA polymerase sigma-F factor (Stage II sporulation protein AC)
           (Sporulation sigma factor) [Lysinibacillus sphaericus
           C3-41]
          Length = 195

 Score =  115 bits (289), Expect = 7e-24,   Method: Composition-based stats.
 Identities = 36/198 (18%), Positives = 83/198 (41%), Gaps = 18/198 (9%)

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           M++V KFD     + +TY++  I   +Q ++     +VK+  +  +        +++   
Sbjct: 1   MKSVDKFDLSYDVKFSTYAVPMIIGEIQRFLRDDG-MVKVSRSIRELNF-----KIRHAT 54

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                 N  P  +  +A+ L V+  E+++ +  L    SL+  +  S+ +S    D +  
Sbjct: 55  DEFIKRNEHPPTIQELAQVLGVTTEEIVTASDALRDPASLHEQLYESEGDSITLMDQMKD 114

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           +   Q    I           L   ++ L PRE+ I   R   +   T   +++   +S+
Sbjct: 115 EKSEQPFDYIP----------LKEVLTRLEPREQSIIYLRYFSD--CTQTEIANRLGISQ 162

Query: 267 ERVRQIEARAFKKVQESI 284
            +V ++E +   +++  +
Sbjct: 163 VQVSRLEKKILAQLKSWM 180


>gi|164686361|ref|ZP_02210391.1| hypothetical protein CLOBAR_02799 [Clostridium bartlettii DSM
           16795]
 gi|164601963|gb|EDQ95428.1| hypothetical protein CLOBAR_02799 [Clostridium bartlettii DSM
           16795]
          Length = 231

 Score =  115 bits (289), Expect = 8e-24,   Method: Composition-based stats.
 Identities = 49/244 (20%), Positives = 102/244 (41%), Gaps = 63/244 (25%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           D +    L+  +LRLVV I+  +   G+ + +++S G IGL++AV  F+ ++  +LATY+
Sbjct: 46  DENVKTILIERNLRLVVYISRKFENTGIDMEDLISIGTIGLIKAVNTFNLDKNIKLATYA 105

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
              I+  +   + ++                                             
Sbjct: 106 SRCIENEILMCLRKN--------------------------------------------- 120

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
            N  +SEV       + DE LN      D N     D L  D+D   +++ E+ +    +
Sbjct: 121 -NKKKSEV-------SFDEPLN---VDLDGNELLLSDVLGTDNDEIYKIIEEEID----K 165

Query: 226 NMLTRSMSVLNPRERRIFEARRLQ---ENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           N+L  ++  L+ RE++I E R          T + +++   +S+  + ++E +   ++++
Sbjct: 166 NLLFMALDKLSYREKQIMELRFGLSTKGKEKTQKEVANILGISQSYISRLEKKIIFRLKK 225

Query: 283 SIQK 286
            ++K
Sbjct: 226 EMKK 229


>gi|94500298|ref|ZP_01306831.1| flagellar biosynthesis sigma factor [Oceanobacter sp. RED65]
 gi|94427597|gb|EAT12574.1| flagellar biosynthesis sigma factor [Oceanobacter sp. RED65]
          Length = 245

 Score =  115 bits (289), Expect = 8e-24,   Method: Composition-based stats.
 Identities = 50/242 (20%), Positives = 109/242 (45%), Gaps = 18/242 (7%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           + LV  +  LV +IA   +G       + +++  G IGL++A +K++P +G    TY+  
Sbjct: 17  NTLVEEYASLVKRIAHHLKGRLPDSVQVDDLIQSGMIGLIEAAQKYEPSKGASFETYAGI 76

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+ +M + I +             + +  N RR+   ++ +     +  Q   +AK L 
Sbjct: 77  RIRGSMLDEIRKGDW--------APRSVHRNSRRISEAIRYVESQTGRDAQDQEVAKALG 128

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +   E        AG   L +  +  ++   Q  D++ +D     +  ++  + ++ +  
Sbjct: 129 MELEEYHQHLQDGAGSR-LFSFEDLLEQRGEQESDFMGHDD----ESPLQDLQSEHFQQQ 183

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L +++S L  RE+ +       +  + L+ + +  EVS  RV QI ++A  +++  +Q+ 
Sbjct: 184 LAKAISQLPEREQLVLALYY--DEELNLKEIGAVLEVSESRVSQIHSQAAHRLRARLQEW 241

Query: 288 VE 289
            E
Sbjct: 242 AE 243


>gi|291522735|emb|CBK81028.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Coprococcus catus
           GD/7]
          Length = 206

 Score =  115 bits (289), Expect = 8e-24,   Method: Composition-based stats.
 Identities = 54/257 (21%), Positives = 100/257 (38%), Gaps = 64/257 (24%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L   +E V  ++Y+ +GD+ A   L+  +LRLV  I   Y   G    E++S G +GL+
Sbjct: 7   PLSAAQETVYLRQYQ-NGDMHARDILIERNLRLVAHIVKKYMNSGKETDEMISVGIVGLV 65

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV  ++ E+G RLATY+   I   +                                  
Sbjct: 66  KAVNTYNFEKGSRLATYAARCIDNELL--------------------------------- 92

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                         +  + +   S  +S+   +  D          + N       L ++
Sbjct: 93  --------------MLMRGDRKLSREVSLYDPIGTD---------KEGNEITLLSILEHE 129

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMS-VLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
                + +I++ ++K     L++ +S VL PRE  +   R      +  T   L+ +  +
Sbjct: 130 D----EDIIDQLDKKQSLRKLSKILSKVLTPREYFVVIRRYGLYGHHETTQRELAEQLNI 185

Query: 265 SRERVRQIEARAFKKVQ 281
           SR  V +IE +A +K++
Sbjct: 186 SRSYVSRIEKKALEKLR 202


>gi|288942618|ref|YP_003444858.1| RNA polymerase sigma-28 subunit FliA/WhiG [Allochromatium vinosum
           DSM 180]
 gi|288897990|gb|ADC63826.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Allochromatium vinosum
           DSM 180]
          Length = 248

 Score =  115 bits (289), Expect = 8e-24,   Method: Composition-based stats.
 Identities = 50/247 (20%), Positives = 100/247 (40%), Gaps = 21/247 (8%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPER 97
           Y   GD +A   LV+ H+ LV +IA          + + +++  G +GL++A ++F   +
Sbjct: 10  YASAGDEAAR--LVSEHVDLVRRIAHHLVARLPASVQVEDLIQSGMVGLIEAARQFQTGQ 67

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G   ATY+   ++ AM + + R+            + +  N RR+   +  +     +  
Sbjct: 68  GATFATYAGIRVRGAMIDELRRADWT--------PRSVHRNSRRIAEAIHQVESREGRAA 119

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               IA+ L V+  +   M    A  + L       +   S           G      E
Sbjct: 120 SDREIAETLGVTLDDYHGMLQDTASCQILGLEDLFGEDADSDRF------LPGAGTAPTE 173

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
           + ER+     L  +++ L  RER +       +  + L  + +  +V+  RV QI ++A 
Sbjct: 174 QLEREQFAQALAEALADLPERERLVLALYY--DEELNLREIGAVLDVTESRVSQIRSQAL 231

Query: 278 KKVQESI 284
            +++  +
Sbjct: 232 HRLRGRL 238


>gi|89898386|ref|YP_515496.1| RNA polymerase sigma factor sigma-28 [Chlamydophila felis Fe/C-56]
 gi|89331758|dbj|BAE81351.1| DNA-directed RNA polymerase sigma 28 [Chlamydophila felis Fe/C-56]
          Length = 257

 Score =  115 bits (289), Expect = 8e-24,   Method: Composition-based stats.
 Identities = 49/258 (18%), Positives = 111/258 (43%), Gaps = 20/258 (7%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKK 92
            + + Y E   +     L+  +L LV  +               ++ + G  GL++AV++
Sbjct: 11  EIWELYWETQKIEYRDTLIDLYLHLVKCVVHRLISGMPSHIKTEDLYASGVEGLVRAVER 70

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+PE+  R   Y+++ IKAA+ + + +      +  + +QK       +L   +  +  +
Sbjct: 71  FNPEKSRRFEGYALFLIKAAIIDDLRKQDW---VPRSVHQKA-----NKLSDAMDTLRQS 122

Query: 153 NLKPEQVVAIAKKLNVSESEV--ISMNCRLAGDESLNA--LINSSDKNSSQWQDWLVYDH 208
             +      + +   +S+ E+    ++ R A   SLN    + S  ++    ++ +    
Sbjct: 123 LGREPTDGDLCEYFQISQQELSGWFVSARPALIISLNEERPLLSDGESGVALEERIP--- 179

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D + +   +  +RK   + L  ++  L  +ER++      +E  + L+ +     VS  R
Sbjct: 180 DERAETGYDIVDRKEFSSFLANAIEGLEEKERKVMALYYYEE--LVLKEIGKILGVSESR 237

Query: 269 VRQIEARAFKKVQESIQK 286
           V QI ++A  K++ S+  
Sbjct: 238 VSQIHSKALIKLRASLSA 255


>gi|153803716|ref|ZP_01958302.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           MZO-3]
 gi|124120749|gb|EAY39492.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           MZO-3]
          Length = 242

 Score =  115 bits (288), Expect = 9e-24,   Method: Composition-based stats.
 Identities = 52/249 (20%), Positives = 105/249 (42%), Gaps = 19/249 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPER 97
           Y ++G+L++    +  +  LV +IA    G   P   I +++  G +GL++A K +D  +
Sbjct: 7   YDQYGNLNSQQLFLEKYSVLVKRIAHHLIGRLPPSVLIEDLIQAGMVGLLEAQKNYDGSK 66

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G    TY+   I+ AM + I R    V      + + +   +  L+G L        +  
Sbjct: 67  GASFETYAGIRIRGAMLDDIRR-GDWVPRSVHKHNREISQAIAVLEGELN-------RDP 118

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +AK LN+S  +  S+      D + + ++   D   S   D +    +G++     
Sbjct: 119 TDAEVAKFLNMSLEQYHSVLM----DINCSRIVGIEDLGVS--DDAISPFEEGEDNSPFH 172

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
               ++ R  L  S+  L  RE  +       +  + L+ +     VS  RV QI +++ 
Sbjct: 173 GVAEESFRKALVESIKSLPEREALVLSLYY--DEELNLKEIGEVLGVSESRVSQILSQSM 230

Query: 278 KKVQESIQK 286
           ++++  +  
Sbjct: 231 QRLRTKLSS 239


>gi|14994233|gb|AAK73284.1| RNA polymerase sigma-70 factor [Xylella fastidiosa]
          Length = 144

 Score =  115 bits (288), Expect = 9e-24,   Method: Composition-based stats.
 Identities = 30/140 (21%), Positives = 62/140 (44%), Gaps = 7/140 (5%)

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
                +      +AK++++ E ++  +        S+   I   D   S   D++    D
Sbjct: 1   LQQFGREATPEELAKEMDMPEDKIRKVMKIAKEPISMETPI--GDDEDSHLGDFI---ED 55

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRE 267
              +  ++     N    +   ++ L PRE ++   R   +     TLE +  +F+V+RE
Sbjct: 56  PNVESPVDTTTNVNLSETVREVLAGLTPREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRE 115

Query: 268 RVRQIEARAFKKVQESIQKQ 287
           R+RQIEA+A +K++   + +
Sbjct: 116 RIRQIEAKALRKLRHPSRSE 135


>gi|251795840|ref|YP_003010571.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus sp. JDR-2]
 gi|247543466|gb|ACT00485.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus sp. JDR-2]
          Length = 258

 Score =  115 bits (288), Expect = 9e-24,   Method: Composition-based stats.
 Identities = 46/259 (17%), Positives = 107/259 (41%), Gaps = 19/259 (7%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI-SEVVSEGNIGLM 87
           L++Q+   L +RY+E     AA  L+     LV             +  ++   G + ++
Sbjct: 8   LDQQQIADLLQRYKEMSCNDAATALLQHFESLVRMAVSKISRNRPDLYEDLYQVGQMSML 67

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +  K++D ++G     Y+M  +   ++ Y+      +++     +K L      ++  + 
Sbjct: 68  RLFKQYDSDKGVPFEGYAMKSVIGQLKNYLRDKSWYIQVPRNMKEKGLL-----IQKAID 122

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLV 205
            +T    +  ++  IA  L +S  E I +          SL+  + SS+ +S+   D + 
Sbjct: 123 ELTTKLERSPKMDEIAAYLGLSVEETIEVLSSRESYQYVSLDTPL-SSEGDSATIGDVIS 181

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
              D    V        + +  L+ +M+ L   ER++       ++  +   ++ +  VS
Sbjct: 182 DHSDKYSHV--------DNQIALSDAMAQLKEEERKVLVLVY--QHGQSQREIADQLGVS 231

Query: 266 RERVRQIEARAFKKVQESI 284
           +  V + + RA  K+++ +
Sbjct: 232 QMSVSRFQKRALDKLRQLL 250


>gi|3249727|gb|AAC26666.1| RNA polymerase sigma-like factor [Pseudonocardia autotrophica]
          Length = 152

 Score =  115 bits (288), Expect = 9e-24,   Method: Composition-based stats.
 Identities = 30/162 (18%), Positives = 63/162 (38%), Gaps = 12/162 (7%)

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WWI+ A+   +      ++I     +  +   L R++  L         PE    +A
Sbjct: 1   YATWWIRQAITRAMADQARTIRIPVHMVE--VINKLGRIQRELLQDLGREPTPE---ELA 55

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           K+++++  +V+          SL+  I   D+  SQ  D++    D +     +      
Sbjct: 56  KEMDITPEKVLETQQYAREPISLDQTI--GDEGDSQLGDFI---EDSEAASPSDAVSFTL 110

Query: 224 RRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFE 263
            ++ L  ++  L+ RE  +   R       P TL+ +   + 
Sbjct: 111 LQDQLQSTLGTLSEREAGVVRLRFGLTDGRPRTLDEIGQVYG 152


>gi|109899335|ref|YP_662590.1| flagellar biosynthesis sigma factor [Pseudoalteromonas atlantica
           T6c]
 gi|109701616|gb|ABG41536.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Pseudoalteromonas
           atlantica T6c]
          Length = 242

 Score =  115 bits (288), Expect = 9e-24,   Method: Composition-based stats.
 Identities = 52/251 (20%), Positives = 100/251 (39%), Gaps = 22/251 (8%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFD 94
           A  Y++  D +A   LV  H  LV +IA            + +++  G IGL++A + FD
Sbjct: 5   AAAYQQLDDRNA---LVERHAPLVKRIAHHLIARLPASVLVDDLIQAGMIGLLEASRNFD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +G    T++   I+ +M + I R           N + +   + +++           
Sbjct: 62  GTKGASFETFAGIRIRGSMLDEI-RKGDWTPRSVHKNGRAITDAINKVER-------ETG 113

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +  + V IAKKL VS  +   M   +      NA      ++    +D +  +       
Sbjct: 114 RDARDVDIAKKLEVSIEQYHQMLGEV------NAGKIIGMEDLGVSEDVVTTEQTKGSDT 167

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
             E   + + +  L  +++ L  RE  +       +  + L  +    +VS  RV QI +
Sbjct: 168 PFEDLLQGSFQKALAHAITTLPEREAIVLSLYY--DEELNLREIGEVLDVSESRVSQIHS 225

Query: 275 RAFKKVQESIQ 285
           +A  K++  +Q
Sbjct: 226 QAMLKLKSKMQ 236


>gi|317123623|ref|YP_004097735.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Intrasporangium calvum DSM 43043]
 gi|315587711|gb|ADU47008.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Intrasporangium calvum DSM 43043]
          Length = 282

 Score =  115 bits (288), Expect = 9e-24,   Method: Composition-based stats.
 Identities = 40/234 (17%), Positives = 90/234 (38%), Gaps = 15/234 (6%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
             +V  HL L   +A  Y G  +P  ++V    + L+ A+K++ P  G     Y++  I 
Sbjct: 51  DEIVRLHLDLCDGVAARYAGRSIPTEDLVQVARLALLVAIKRYQPGPGSSFIGYALPTIS 110

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
             ++ +      +V+      +  L   LR  + H +     +        +A+++ V  
Sbjct: 111 GELKRHFRDHGWMVRPPRRLQE--LGPVLRLAREHWEQ---EHGTSPTTQDLAEEVGVDP 165

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            +V            L+  +   D  S    + L    D        + E    R  L  
Sbjct: 166 EQVSECLSAEHSYHPLSLDLTFGDDESRSLAESLAEPQD--------ELESAADRVSLGT 217

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++S L+ ++R + + R +  + +T + +     VS+ +V ++      +++  +
Sbjct: 218 ALSSLSQKDRELLQMRFV--DGMTQKEIGLALGVSQMQVSRLVRAVLDRLRTQM 269


>gi|90411040|ref|ZP_01219054.1| flagellar biosynthesis sigma factor FliA [Photobacterium profundum
           3TCK]
 gi|90328253|gb|EAS44564.1| flagellar biosynthesis sigma factor FliA [Photobacterium profundum
           3TCK]
          Length = 240

 Score =  115 bits (288), Expect = 9e-24,   Method: Composition-based stats.
 Identities = 45/241 (18%), Positives = 96/241 (39%), Gaps = 19/241 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
             +    +  +  LV +IA    G     + + +++  G IGL++A + +DP +G    T
Sbjct: 11  KESPQAFIERYSSLVKRIAYHLMGRLPSSVQVEDLIQSGMIGLLEAQQNYDPTKGASFET 70

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           ++   I+ AM + I R    V      N        RR+   +  + +   +      IA
Sbjct: 71  FAGIRIRGAMLDDIRR-GDWVPRSVYKNN-------RRITEAMALLENKLGRDPTDTEIA 122

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + L ++  +          D +   L+   D   S+  D +  +   +E +  +     N
Sbjct: 123 EHLEMTLDQYHQAL----NDVNCGRLVGMDDLGVSE--DAVTTEASREENLPFQGVVDDN 176

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            R  L  ++  L  RE  +       +  + L+ + +   VS  R+ QI ++A ++++  
Sbjct: 177 FRQSLADAIKTLPEREALVLSLYY--DEELNLKEIGAVVGVSESRICQIHSQAMQRLRSK 234

Query: 284 I 284
           +
Sbjct: 235 L 235


>gi|62185044|ref|YP_219829.1| RNA polymerase sigma factor sigma-28 [Chlamydophila abortus S26/3]
 gi|62148111|emb|CAH63868.1| putative RNA polymerase sigma factor [Chlamydophila abortus S26/3]
          Length = 257

 Score =  115 bits (288), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 51/257 (19%), Positives = 112/257 (43%), Gaps = 18/257 (7%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKK 92
            + + Y +  ++     L+  +L LV  +A              ++ + G  GL++AV++
Sbjct: 11  EIWELYWQTQEIEYRDTLIDFYLHLVKCVAHRLISGMPSHVKTEDLYASGVEGLVRAVER 70

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+PE+  R   Y+++ IKAA+ + + +      +  + +QK       +L   + A+  +
Sbjct: 71  FNPEKSRRFEGYALFLIKAAIIDDLRKQDW---VPRSVHQKA-----NKLADAMDALRLS 122

Query: 153 NLKPEQVVAIAKKLNVSESEV--ISMNCRLAGDESLNALINS-SDKNSSQWQDWLVYDHD 209
             +      + +   +S+ E+     + R A   SLN    S SD  S    +  + D  
Sbjct: 123 LGREPTDGDLCEYFQISQQELSGWFASARPALIISLNEERPSLSDGESGVALEERIADE- 181

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
            + +   +  ++K   + L  ++  L  +ER++      +E  + L+ +     VS  RV
Sbjct: 182 -RAETGYDIVDKKEFSSFLASAIESLEEKERKVMALYYYEE--LVLKEIGKILGVSESRV 238

Query: 270 RQIEARAFKKVQESIQK 286
            QI ++A  K++ ++  
Sbjct: 239 SQIHSKALIKLRAALSA 255


>gi|330959578|gb|EGH59838.1| putative RNA polymerase sigma factor [Pseudomonas syringae pv.
           maculicola str. ES4326]
          Length = 532

 Score =  115 bits (288), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 54/240 (22%), Positives = 104/240 (43%), Gaps = 19/240 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              A     +++RLV +    +R     I+   S  N+GL +AV +F PE GFR +T ++
Sbjct: 296 EKCADIFTNANVRLVEQQIGRFRFADKEIA--RSAANMGLTRAVYRFAPEMGFRFSTIAL 353

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            WI  ++   +    S +++             RR+  ++      +     +  +A+  
Sbjct: 354 TWINVSISRDLADQES-IRLP------EGMHKHRRMIANML----RDHPNVSIKTLAEAT 402

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + +  V  +     G  S++     +D + +     L+ D +      I + E  + R 
Sbjct: 403 KLEQDVVRDLVHFAGGQRSIDTAFQGTDSSEADGLHELLADTNND---FISEIEDDSMRQ 459

Query: 227 MLTRSM-SVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +  ++  VL  RE  +   R    +    TL  LS E ++S+ERVRQ+E +A  K+++S
Sbjct: 460 FVESALGDVLTQREIFVLVNRFGMGDAREKTLAELSIEMKLSKERVRQLEIQALGKIRDS 519


>gi|297538886|ref|YP_003674655.1| FliA/WhiG subfamily RNA polymerase sigma-28 factor [Methylotenera
           sp. 301]
 gi|297258233|gb|ADI30078.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Methylotenera sp. 301]
          Length = 244

 Score =  115 bits (288), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 53/251 (21%), Positives = 109/251 (43%), Gaps = 18/251 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPER 97
           Y  HG       L+  H  LV K+A   +    P   + +++  G +GL+ A+ +++   
Sbjct: 2   YTIHGKKDQKDELLNKHAVLVKKLAYQLKAKLPPSVELDDLIQAGMMGLLDAINRYEDTH 61

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G +  TY+   I+ +M + + RS   +      + + +   + +L+  L        KP 
Sbjct: 62  GAQFETYAAQRIRGSMLDEL-RSADWLPRSVRKSMRDVEIAISQLEQQL-------GKPP 113

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ-VLI 216
               +AKKL +S S+   M     GD S + LI   D + S+  +  +   +       I
Sbjct: 114 TENEVAKKLQLSLSDYYDML----GDCSGHQLIYYEDFHESENGEHFLDRFNADTTGDPI 169

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           +     + R  L  +++ L  RE+         E  + L+ + +   VS  RV Q+ ++A
Sbjct: 170 KSLLEGDFREALVGAITALPEREK--ILMGLYYEQELNLKEIGAVMNVSESRVCQLHSQA 227

Query: 277 FKKVQESIQKQ 287
             +++ +++++
Sbjct: 228 VARLRSNLKEK 238


>gi|62550939|emb|CAI79314.1| putative RNA polymerase sigma-32 [Aeromonas caviae]
          Length = 100

 Score =  115 bits (288), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 48/96 (50%), Positives = 66/96 (68%), Gaps = 2/96 (2%)

Query: 3  RKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVV 62
          ++ M++I  G   L  YI  +  IP+L  +E+  LA+R ++ GDL AA +LV SHLR VV
Sbjct: 6  QRTMALIPQG--SLEGYIQAVNSIPVLSAEEKRELAERLQQDGDLEAARQLVMSHLRFVV 63

Query: 63 KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           +A  Y GYGLP +++V EGNIGLM+AVK+FDP  G
Sbjct: 64 HVAKSYSGYGLPQADLVQEGNIGLMKAVKRFDPSVG 99


>gi|21225590|ref|NP_631369.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
 gi|8347047|emb|CAB93752.1| probable RNA polymerase sigma factor [Streptomyces coelicolor
           A3(2)]
          Length = 299

 Score =  115 bits (288), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 49/241 (20%), Positives = 102/241 (42%), Gaps = 16/241 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +    LVT+ L +  +IA  +R  G  I ++     +GL++A+ +FDPERG    +Y++ 
Sbjct: 51  AVRDELVTAWLPMAHRIAGRFRDRGESIEDLRQVAALGLVKAIDRFDPERG-AFESYAVP 109

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE-QVVAIAKKL 166
            I   ++ +       +++     + R      +++   + +  +   PE  V A+A   
Sbjct: 110 TITGEVKRHFRDRMWALRVPRRVQELR-----NKVRVARRELAQSPGSPEPSVAALAAHT 164

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +SE EV +    L    +L+     S  +        +   D     +I++E  K    
Sbjct: 165 GLSEDEVGAGMEALESFSTLSLDAELSAGDDGYSLADTLGAADTSYDTVIDRESAK---- 220

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                +  L  RER I   R  ++  +T   ++    +S+  V ++ +R+  +V++    
Sbjct: 221 ---EGLRRLPERERAILYMRFFED--MTQSRIADCLGISQMHVSRLISRSCARVRDEAMG 275

Query: 287 Q 287
           Q
Sbjct: 276 Q 276


>gi|93007303|gb|ABE97152.1| Sigma-70 [Pasteuria ramosa]
          Length = 241

 Score =  115 bits (288), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 51/241 (21%), Positives = 96/241 (39%), Gaps = 62/241 (25%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+  +LRLVV IA  +   G+ I ++VS G IGL++AV  FDPE+  +LATY+   I
Sbjct: 61  RACLIERNLRLVVYIARKFENTGIHIEDLVSTGTIGLIKAVNTFDPEKKIKLATYASRCI 120

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           +  +  ++ R+                    +++                          
Sbjct: 121 ENEILMFLRRN-------------------NKIRSE------------------------ 137

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
                     ++ DE LN      D N     D L  ++D     +    E +  + +L 
Sbjct: 138 ----------ISFDEPLN---IDWDGNELLLSDVLGTEND----TIYRDIEDEVDKEILR 180

Query: 230 RSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            ++S+L+ RERRI   R         T ++++    +S+  + ++E +   ++++   K 
Sbjct: 181 TALSMLSDRERRIVILRFGLGGGEEKTQKDVADLLGISQSYISRLEKKVIGRLRKEFNKM 240

Query: 288 V 288
            
Sbjct: 241 A 241


>gi|256783387|ref|ZP_05521818.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
 gi|289767263|ref|ZP_06526641.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
 gi|289697462|gb|EFD64891.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
          Length = 287

 Score =  114 bits (287), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 49/241 (20%), Positives = 102/241 (42%), Gaps = 16/241 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +    LVT+ L +  +IA  +R  G  I ++     +GL++A+ +FDPERG    +Y++ 
Sbjct: 51  AVRDELVTAWLPMAHRIAGRFRDRGESIEDLRQVAALGLVKAIDRFDPERG-AFESYAVP 109

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE-QVVAIAKKL 166
            I   ++ +       +++     + R      +++   + +  +   PE  V A+A   
Sbjct: 110 TITGEVKRHFRDRMWALRVPRRVQELR-----NKVRVARRELAQSPGSPEPSVAALAAHT 164

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +SE EV +    L    +L+     S  +        +   D     +I++E  K    
Sbjct: 165 GLSEDEVGAGMEALESFSTLSLDAELSAGDDGYSLADTLGAADTSYDTVIDRESAK---- 220

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                +  L  RER I   R  ++  +T   ++    +S+  V ++ +R+  +V++    
Sbjct: 221 ---EGLRRLPERERAILYMRFFED--MTQSRIADCLGISQMHVSRLISRSCARVRDEAMG 275

Query: 287 Q 287
           Q
Sbjct: 276 Q 276


>gi|257438786|ref|ZP_05614541.1| RNA polymerase sigma-E factor [Faecalibacterium prausnitzii A2-165]
 gi|257198754|gb|EEU97038.1| RNA polymerase sigma-E factor [Faecalibacterium prausnitzii A2-165]
          Length = 188

 Score =  114 bits (287), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 61/246 (24%), Positives = 96/246 (39%), Gaps = 62/246 (25%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GD +A   L+T +LRLVV +A  Y   G+P  +++S G IGL++AV  F P R  +LAT
Sbjct: 3   AGDAAARDDLITHNLRLVVYLAKKYENSGVPQEDMISIGTIGLIKAVNTFTPARNIKLAT 62

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   I   +  Y                      LR+     Q                
Sbjct: 63  YASRCIGNEILMY----------------------LRKSSNRRQEA-------------- 86

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
                            + DE LN      D N     D L  D +     L +  E   
Sbjct: 87  -----------------SIDEPLNT---DGDGNELLLSDVLGSDENLVGLQLEQAAE--- 123

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R  L RS+  L PRER+I E R    +    T +  +    +S+  + ++E R  ++++
Sbjct: 124 -RATLRRSVEQLAPRERQIMELRFGLVDGVEHTQKEAADALGISQSYISRLEKRIIRQLK 182

Query: 282 ESIQKQ 287
           E ++++
Sbjct: 183 EVLERE 188


>gi|308803162|ref|XP_003078894.1| RNA-polymerase sigma factor (ISS) [Ostreococcus tauri]
 gi|116057347|emb|CAL51774.1| RNA-polymerase sigma factor (ISS) [Ostreococcus tauri]
          Length = 485

 Score =  114 bits (287), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 52/272 (19%), Positives = 107/272 (39%), Gaps = 29/272 (10%)

Query: 34  EYVLAKRYREHGD-----------LSAAHRLVTSHLRLVVKIAMGYRGYGLPIS------ 76
           E  LA+R     D             A  +LV++++ L  K+A        P+       
Sbjct: 154 EQALARRAGFGEDSTKMRAVMRQGKIARQKLVSANIELAAKVATDVFHTFSPMERRSISR 213

Query: 77  -EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EG  GL++A +KFDP  G   +TY+  W K A+   +L +   +++      +R 
Sbjct: 214 QDMIHEGVTGLVRASEKFDPALGCAFSTYAYNWTKQAVTRGVLNNGRTIRVPEQVLYER- 272

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
                 L   ++          ++ A ++K +V   + + +   +A    L+  I     
Sbjct: 273 -REAHELSKRMEIELGRRPTLHEIAARSQKFSV---DKLQLLVGIAKQHPLSLDILGVGD 328

Query: 196 NSSQWQDWLV----YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--Q 249
                 +  +     +  G    +    E +  R+ + ++++ L+  E  + + R     
Sbjct: 329 EERDGDETGLSGTWENEMGSTDEITRTIELEFLRDDIKKTLNELSSDEAYVLKHRFGLVG 388

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              +T   + S    S E VR IE RA ++++
Sbjct: 389 GEFMTNAEIGSRIGKSAEGVRYIEKRALERLK 420


>gi|329942781|ref|ZP_08291560.1| RNA polymerase sigma factor, FliA/WhiG family protein
           [Chlamydophila psittaci Cal10]
 gi|332287373|ref|YP_004422274.1| RNA polymerase sigma factor [Chlamydophila psittaci 6BC]
 gi|313847955|emb|CBY16951.1| putative RNA polymerase sigma factor [Chlamydophila psittaci RD1]
 gi|325507072|gb|ADZ18710.1| RNA polymerase sigma factor [Chlamydophila psittaci 6BC]
 gi|328815041|gb|EGF85030.1| RNA polymerase sigma factor, FliA/WhiG family protein
           [Chlamydophila psittaci Cal10]
 gi|328914621|gb|AEB55454.1| RNA polymerase sigma factor, sigma-70 family [Chlamydophila
           psittaci 6BC]
          Length = 257

 Score =  114 bits (287), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 51/257 (19%), Positives = 112/257 (43%), Gaps = 18/257 (7%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKK 92
            + + Y +  ++     L+  +L LV  +A              ++ + G  GL++AV++
Sbjct: 11  EIWELYWQTQEIKYRDTLIDFYLHLVKCVAHRLISGMPSHVKTEDLYASGVEGLVRAVER 70

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+PE+  R   Y+++ IKAA+ + + +      +  + +QK       +L   + A+  +
Sbjct: 71  FNPEKSRRFEGYALFLIKAAIIDDLRKQDW---VPRSVHQKA-----NKLADAMDALRLS 122

Query: 153 NLKPEQVVAIAKKLNVSESEV--ISMNCRLAGDESLNALINS-SDKNSSQWQDWLVYDHD 209
             +      + +   +S+ E+     + R A   SLN    S SD  S    +  + D  
Sbjct: 123 LGREPTDGDLCEYFQISQQELSGWFASARPALIISLNEERPSLSDGESGVALEERIADE- 181

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
            + +   +  ++K   + L  ++  L  +ER++      +E  + L+ +     VS  RV
Sbjct: 182 -RAETGYDIVDKKEFSSFLASAIEGLEEKERKVMALYYYEE--LVLKEIGKILGVSESRV 238

Query: 270 RQIEARAFKKVQESIQK 286
            QI ++A  K++ ++  
Sbjct: 239 SQIHSKALIKLRAALSA 255


>gi|15642066|ref|NP_231698.1| flagellar biosynthesis sigma factor [Vibrio cholerae O1 biovar El
           Tor str. N16961]
 gi|121586929|ref|ZP_01676709.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae 2740-80]
 gi|121727398|ref|ZP_01680537.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae V52]
 gi|147674794|ref|YP_001217593.1| flagellar biosynthesis sigma factor [Vibrio cholerae O395]
 gi|153213706|ref|ZP_01948958.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae 1587]
 gi|153821715|ref|ZP_01974382.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae B33]
 gi|153826072|ref|ZP_01978739.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae MZO-2]
 gi|153828895|ref|ZP_01981562.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae 623-39]
 gi|227082193|ref|YP_002810744.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae M66-2]
 gi|229507844|ref|ZP_04397349.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           BX 330286]
 gi|229511920|ref|ZP_04401399.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           B33]
 gi|229513722|ref|ZP_04403184.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           TMA 21]
 gi|229519056|ref|ZP_04408499.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           RC9]
 gi|229522025|ref|ZP_04411442.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           TM 11079-80]
 gi|229524074|ref|ZP_04413479.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           bv. albensis VL426]
 gi|229528916|ref|ZP_04418306.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           12129(1)]
 gi|229607389|ref|YP_002878037.1| flagellar biosynthesis sigma factor [Vibrio cholerae MJ-1236]
 gi|254226075|ref|ZP_04919673.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae V51]
 gi|254286814|ref|ZP_04961767.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae AM-19226]
 gi|254849153|ref|ZP_05238503.1| flagellar biosynthesis sigma factor [Vibrio cholerae MO10]
 gi|297579572|ref|ZP_06941500.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae RC385]
 gi|298497906|ref|ZP_07007713.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae MAK 757]
 gi|9656612|gb|AAF95212.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae O1 biovar El Tor str. N16961]
 gi|121548865|gb|EAX58908.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae 2740-80]
 gi|121630290|gb|EAX62688.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae V52]
 gi|124115767|gb|EAY34587.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae 1587]
 gi|125621387|gb|EAZ49723.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae V51]
 gi|126520813|gb|EAZ78036.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae B33]
 gi|146316677|gb|ABQ21216.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae O395]
 gi|148875601|gb|EDL73736.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae 623-39]
 gi|149740189|gb|EDM54342.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae MZO-2]
 gi|150423105|gb|EDN15053.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae AM-19226]
 gi|227010081|gb|ACP06293.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae M66-2]
 gi|227013963|gb|ACP10173.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae O395]
 gi|229332690|gb|EEN98176.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           12129(1)]
 gi|229337655|gb|EEO02672.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           bv. albensis VL426]
 gi|229340950|gb|EEO05955.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           TM 11079-80]
 gi|229343745|gb|EEO08720.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           RC9]
 gi|229348903|gb|EEO13860.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           TMA 21]
 gi|229351885|gb|EEO16826.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           B33]
 gi|229355349|gb|EEO20270.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           BX 330286]
 gi|229370044|gb|ACQ60467.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           MJ-1236]
 gi|254844858|gb|EET23272.1| flagellar biosynthesis sigma factor [Vibrio cholerae MO10]
 gi|297537166|gb|EFH75999.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae RC385]
 gi|297542239|gb|EFH78289.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae MAK 757]
 gi|327484600|gb|AEA79007.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           LMA3894-4]
          Length = 244

 Score =  114 bits (287), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 52/249 (20%), Positives = 105/249 (42%), Gaps = 19/249 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPER 97
           Y ++G+L++    +  +  LV +IA    G   P   I +++  G +GL++A K +D  +
Sbjct: 7   YDQYGNLNSQQLFLEKYSVLVKRIAHHLIGRLPPSVLIEDLIQAGMVGLLEAQKNYDGSK 66

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G    TY+   I+ AM + I R    V      + + +   +  L+G L        +  
Sbjct: 67  GASFETYAGIRIRGAMLDDIRR-GDWVPRSVHKHNREISQAIAVLEGELN-------RDP 118

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +AK LN+S  +  S+      D + + ++   D   S   D +    +G++     
Sbjct: 119 TDAEVAKFLNMSLEQYHSVLM----DINCSRIVGIEDLGVS--DDAISPFEEGEDNSPFH 172

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
               ++ R  L  S+  L  RE  +       +  + L+ +     VS  RV QI +++ 
Sbjct: 173 GVAEESFRKALVESIKSLPEREALVLSLYY--DEELNLKEIGEVLGVSESRVSQILSQSM 230

Query: 278 KKVQESIQK 286
           ++++  +  
Sbjct: 231 QRLRTKLSS 239


>gi|120403519|ref|YP_953348.1| FliA/WhiG family RNA polymerase sigma factor [Mycobacterium
           vanbaalenii PYR-1]
 gi|119956337|gb|ABM13342.1| RNA polymerase, sigma 37 subunit, RpsB/SigB [Mycobacterium
           vanbaalenii PYR-1]
          Length = 242

 Score =  114 bits (287), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 39/241 (16%), Positives = 86/241 (35%), Gaps = 18/241 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                 ++   L L   IA  +RG G    ++V    +GL+ AV +FD +       +++
Sbjct: 16  RRQRDAIIERCLPLADHIARRFRGRGEAHEDLVQVARVGLLNAVNRFDVDSANDFLAFAV 75

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +   ++ Y       +K+     +  +     RL      +T    +      +A+ L
Sbjct: 76  PTMMGEVRRYFRDHGWSLKVPRRLKELNV-----RLNSARSELTHQLNRAPTPSELAEFL 130

Query: 167 NVSESEVIS---MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
            +   E++         +   +    + + D +     D +            E  +R  
Sbjct: 131 GMERDEIVEGLVAANAYSTRSTEQETMRTGDGDGLTLLDTIGG--------PDEGIQRVI 182

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               +   ++ L  R+R + + R      +T   ++    VS+  V ++ ARA   ++E 
Sbjct: 183 DIQTVQPLLAKLPARDRLVLQLRFFDN--LTQSQIAERIGVSQMHVSRLLARALATLREQ 240

Query: 284 I 284
           I
Sbjct: 241 I 241


>gi|23099037|ref|NP_692503.1| RNA polymerase sigma factor SigD [Oceanobacillus iheyensis HTE831]
 gi|22777265|dbj|BAC13538.1| RNA polymerase sigma-D factor [Oceanobacillus iheyensis HTE831]
          Length = 258

 Score =  114 bits (287), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 44/259 (16%), Positives = 107/259 (41%), Gaps = 19/259 (7%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVK----IAMGYRGYGLPISEVVSEGNIGLMQA 89
           E  L  +++ H D  AA++L+ +++ LV      IA       +   ++ S G +GL  A
Sbjct: 9   EQKLWDKWKNHQDGEAANQLINNYMYLVNYHTERIASHLPNNVV-KDDIRSFGILGLYDA 67

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +KKFDP R  +  TY+ + IK ++ + + +   L         + +    ++++  ++  
Sbjct: 68  LKKFDPSRDLKFDTYASFRIKGSIMDGLRKEDWL--------PRSIREKTKKVEQAMEEY 119

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVI--SMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
             +  +      IA    ++  EV     +   +   S+      +     +   + + D
Sbjct: 120 EQSYQREANSSEIANLTGMTTEEVETTMKDALFSNILSIEEKPKGNSDQLKEGIGYSISD 179

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
              +  +       +  +  L + + +LN +E+ +          +T   +     ++  
Sbjct: 180 E--RAILPENHIVNEELKEELIQGIKLLNEKEQLVVSLFY--NEELTFTEIGQVVGLTTS 235

Query: 268 RVRQIEARAFKKVQESIQK 286
           R+ QI  R+  K++++++K
Sbjct: 236 RISQIHKRSIFKLKKTLEK 254


>gi|308048769|ref|YP_003912335.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Ferrimonas
           balearica DSM 9799]
 gi|307630959|gb|ADN75261.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Ferrimonas
           balearica DSM 9799]
          Length = 237

 Score =  114 bits (287), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 45/243 (18%), Positives = 91/243 (37%), Gaps = 21/243 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              LV  H  LV +IA          + + +++  G +GL++A + FD  +G    T++ 
Sbjct: 13  RAALVERHTPLVKRIAHHLLARLPASVQLDDLLQSGMVGLLEAARNFDGSKGASFETFAG 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + I R             + +  N RR+   ++ +     +      +A  L
Sbjct: 73  IRIRGAMLDEIRRGDWT--------PRSVHRNSRRVTDAMEQLERQLGRDPTGTEVADYL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +S  E       +  D S   L+   D   S+       +       L +       ++
Sbjct: 125 ELSVDEYH----HILHDVSAGKLVGLDDLGVSEDAIGPGEESSEHFDHLADG----RFQS 176

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L  ++  L  RE  +       +  + L+ +     VS  RV QI +++  +++  ++ 
Sbjct: 177 ALVEAIKTLPEREALVLSLYY--DEELNLKEIGQVLGVSESRVSQIHSQSMVRLKTKLRA 234

Query: 287 QVE 289
             E
Sbjct: 235 WRE 237


>gi|182440239|ref|YP_001827958.1| putative RNA polymerase sigma factor [Streptomyces griseus subsp.
           griseus NBRC 13350]
 gi|178468755|dbj|BAG23275.1| putative RNA polymerase sigma factor [Streptomyces griseus subsp.
           griseus NBRC 13350]
          Length = 264

 Score =  114 bits (287), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 39/241 (16%), Positives = 96/241 (39%), Gaps = 13/241 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +     + + L +  +IA  +R  G  + ++     +GL++AV ++DP+RG    +Y++ 
Sbjct: 36  ALRDETICAWLPMAHRIATRFRDRGEAMDDLRQVAAMGLVKAVDRYDPDRGKAFESYAVP 95

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +   ++ +       V +      + L   +R  +  L   +           IA    
Sbjct: 96  TVTGELKRHFRDHTWDVHVPRRV--QDLRNRVRVARRELAQSSG--GAAPTCADIASATG 151

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + E +V+     L    +L+     +           +   DG   V I+       R  
Sbjct: 152 LGEEDVLLGLEALESYSALSLDAGPAGVEGGSPLADRLGSCDGALDVAID-------REA 204

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +   +  L  RER I   R  ++  +T   ++ +  +S+  V ++ +++ ++V++ + ++
Sbjct: 205 VKPGLRGLPERERTILYLRYFRD--MTQSRIAEQLGISQMHVSRLLSQSCERVRDGVLQK 262

Query: 288 V 288
            
Sbjct: 263 A 263


>gi|320107038|ref|YP_004182628.1| RNA polymerase sigma 28 subunit FliA/WhiG [Terriglobus saanensis
           SP1PR4]
 gi|319925559|gb|ADV82634.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Terriglobus saanensis
           SP1PR4]
          Length = 294

 Score =  114 bits (287), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 57/297 (19%), Positives = 116/297 (39%), Gaps = 27/297 (9%)

Query: 1   MNRKNMSIIVN---GEIGLSRYIHEIRKIPMLEKQE---EYVLAKRYREHG---DLSAAH 51
           M   N S       G I  S  + E+  + +L  +E           +  G     +   
Sbjct: 1   MATANASPAAPYAVGGIEFSDDLKELGDLSLLAGEEAPSSTTYGAESQSAGRTLSDAERD 60

Query: 52  RLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           +L+  H   V  +A          + + ++++ G IGL+ A  KFD  +  +  +Y+ + 
Sbjct: 61  QLLVEHFPTVRYVARRIHERLPQHMELDDLIAAGMIGLIDAFSKFDHSKKVQFKSYAQFR 120

Query: 109 IKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           I+ A+ + +    WS          + L    R ++  ++A+T           IA+++N
Sbjct: 121 IRGAILDSLRTLDWSP---------RELRRKGRAVEEAIRAVTQRFGCVPAEQEIAREMN 171

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S SE   +   L G   L      +++     ++ L Y     E   + +  +   +  
Sbjct: 172 LSLSEYQGLLGELKG---LEIGSLHAERGEDSGEEELAYVPGSPEDGPLFRCLKGELKQH 228

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L  ++  L  RER +      +E  +T++ +     V   RV QI + A  +++ S+
Sbjct: 229 LMEAIDDLPERERMVLTLYYYEE--LTMKEVGLTLGVVESRVSQIHSSAVARLRVSL 283


>gi|307109682|gb|EFN57919.1| hypothetical protein CHLNCDRAFT_141989 [Chlorella variabilis]
          Length = 509

 Score =  114 bits (287), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 44/243 (18%), Positives = 98/243 (40%), Gaps = 13/243 (5%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L   EE  LA+     GD  AA  L  ++  LV  +A  + G GL   ++V+EG + L +
Sbjct: 50  LTAAEEAQLAE-LAVGGDHRAAAMLAHANRPLVTWLAAKFAGRGLAKEDLVAEGMLALER 108

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A   F P+R  R  T++   I  A+   I R   +++I  T      + ++  ++  +  
Sbjct: 109 AAGSFHPDREARFGTFAAAAISNALSRAIRRQSRVIRIPET-----HYRDMAVVRQAMAE 163

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           ++    +P +   IA+   ++    + +   +                +++  D +    
Sbjct: 164 LSAELGRPPRCEEIAQSCVLTVKHTLHLLRAMGT-----QQQQGGGSEAAEEYDVVDDSL 218

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSR 266
           + +E    ++E +   R  L+  ++ L+ ++  I   R    +    + + +    + + 
Sbjct: 219 EEEECSFAQEERQGMLRQELSSRLAQLDSKQALIVSLRHGLHDGRAWSCKEIGERLDCTA 278

Query: 267 ERV 269
             V
Sbjct: 279 AWV 281


>gi|307323818|ref|ZP_07603027.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306890267|gb|EFN21244.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 268

 Score =  114 bits (287), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 48/250 (19%), Positives = 104/250 (41%), Gaps = 23/250 (9%)

Query: 38  AKRYREHGD----LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
            +R  E  D     +    +V + + +  +IA  YR  G    ++     +GL++AVK++
Sbjct: 26  FRRIAELPDGSEKEALREEVVRAWMPMAERIASQYRNRGETHEDLRQVAMVGLVKAVKRY 85

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN- 152
           +P+RG    +Y++  +   ++ +       + +     + R      R++  +Q +T + 
Sbjct: 86  EPDRGSAFESYAVPTVVGEVKRHFRDHMWGLHVPRRVQELR-----NRVRTAVQELTRSP 140

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDG 210
           + +   V  IA+   ++E +V+     L      SL+A +  +D   +   D L      
Sbjct: 141 DDRSPSVRDIARHTGMAEEDVLLGMEALESFRTLSLDAALRGADDGYA-LVDTLGSTESS 199

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
            E+V+        +R  L   +  L  RER I   R   +   T   ++    +S+  V 
Sbjct: 200 YERVV--------QRESLKPCLRRLPEREREILYLRFFCDE--TQSRIADRLGISQMHVS 249

Query: 271 QIEARAFKKV 280
           ++ +R   ++
Sbjct: 250 RLISRTCARL 259


>gi|55274889|gb|AAV49247.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 180

 Score =  114 bits (287), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 47/192 (24%), Positives = 84/192 (43%), Gaps = 18/192 (9%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           LRLVVKIA  Y   GL +        +GL++AV+KFDPERGFR +TY+ WWI+  ++  I
Sbjct: 1   LRLVVKIARRYGNRGLAL--------LGLIRAVEKFDPERGFRFSTYATWWIRQTIERAI 52

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           +     +++      K L   LR  +     ++           IA++L+    +V  M 
Sbjct: 53  MNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRML 107

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                  S++  +    +     +  L    D +E    +  +  + +  + + +  LN 
Sbjct: 108 RLNERITSVDTPLGGDSE-----KALLDILADEKENGPEDTTQDDDMKQSIVKWLFELNA 162

Query: 238 RERRIFEARRLQ 249
           ++R +   R   
Sbjct: 163 KQREVLARRFGL 174


>gi|241763670|ref|ZP_04761720.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Acidovorax delafieldii
           2AN]
 gi|241367145|gb|EER61511.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Acidovorax delafieldii
           2AN]
          Length = 246

 Score =  114 bits (287), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 44/242 (18%), Positives = 103/242 (42%), Gaps = 19/242 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L+  H+ LV +IA          + + +++  G +GL  A+ +++  +G +  T++ 
Sbjct: 18  RDALIRQHVPLVRRIAHHMIAKLPPNVELDDLIQVGMMGLADALSRYEATQGVQFETFAT 77

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + R    +   +  +QK +  +LRRL+  L        +P     IA  +
Sbjct: 78  QRIRGAMLDEL-REGDWMSRSSRKSQKDIEHSLRRLEQKL-------GRPPLESEIAADM 129

Query: 167 NVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            +S +E  S+  ++ G     L  + +  + +       +           +E       
Sbjct: 130 GMSLAEYQSLLGKVRGTQLVYLEDMTHGDEGDEGFLDRHVAD----SSADPLELLRDHRL 185

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L +++  L  RE+ I       E+ + L+ +++   V+  RV Q+ +++  +++  +
Sbjct: 186 RASLVQAIQSLPEREQHIMGMYY--EHDMNLKEIAAVLGVTESRVCQLHSQSIARLRAKM 243

Query: 285 QK 286
           + 
Sbjct: 244 RS 245


>gi|218441823|ref|YP_002380152.1| RNA polymerase sigma factor SigF [Cyanothece sp. PCC 7424]
 gi|218174551|gb|ACK73284.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cyanothece
           sp. PCC 7424]
          Length = 258

 Score =  114 bits (287), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 47/259 (18%), Positives = 109/259 (42%), Gaps = 16/259 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR-GYGLPISEVVSEGNIGLMQAVK 91
           E   L + Y++       ++++  +  LV + A  +         +++  G +GL++A++
Sbjct: 12  ETLRLFQDYQKTSTPELRNQILELNFGLVRREAHHWTTQCNENYEDLLQVGCLGLIRAIE 71

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           +F+  +G   +++++ +I+  +Q Y+      V+I      +R     R+     +    
Sbjct: 72  RFELGKGHAFSSFAIPYIRGEIQHYLRDKGYSVRIP-----RRWLDLGRQAMIIRREFQT 126

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHD 209
              +      IA  L VS  E   +       E  SL+  IN  ++  +   D +     
Sbjct: 127 QFNRQPTDTEIAYGLEVSLKEWQEIKLAFQNREPLSLDVSINHDEEGQTSLADLVPDPKY 186

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
              Q+  + + R      L +++S L  R RR+ E   LQ+  +T    + +  +S   V
Sbjct: 187 RSFQLSQDDQIR------LQQALSQLEERTRRVLEFVFLQD--LTQREAAEQLGISVVTV 238

Query: 270 RQIEARAFKKVQESIQKQV 288
            +   +    ++E+++K++
Sbjct: 239 SRRVKKGLDFLKETMKKEI 257


>gi|238927435|ref|ZP_04659195.1| DNA-directed RNA polymerase sigma subunit D [Selenomonas flueggei
           ATCC 43531]
 gi|238884717|gb|EEQ48355.1| DNA-directed RNA polymerase sigma subunit D [Selenomonas flueggei
           ATCC 43531]
          Length = 252

 Score =  114 bits (287), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 44/261 (16%), Positives = 109/261 (41%), Gaps = 25/261 (9%)

Query: 30  EKQEEYV-LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIG 85
            ++E    L + Y     ++  +R+   +L LV  +A          +   +++S G  G
Sbjct: 8   TEEENIEALWQEYEREKTVAVRNRIAEYYLPLVRLVAGRIAISLPQHVDREDLLSSGFFG 67

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L+ A+++++  RG +  TY+   ++ AM +++ R+   V +    N K+        +  
Sbjct: 68  LLDAIERYELARGNKFETYAGVRVRGAMLDHL-RAKDWVPVSVRQNIKKY-------EKT 119

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           +  +     +      +A++LN+S  E+  +  +++      A +   ++          
Sbjct: 120 VAQLEGELGRAATDKELAEELNLSIEELHHLESQVSA-----ATVIPLEE------YLRA 168

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
                 E   +E  E    +  L  ++  L  +ER +       E  +TL+ +++   +S
Sbjct: 169 DTQASLEDGPVEHAEWTEVKETLAAAIEKLPEKERTVIALYYYDE--MTLKEIAAILHLS 226

Query: 266 RERVRQIEARAFKKVQESIQK 286
             R+ Q+  +A  +++ S+ +
Sbjct: 227 EARISQLHTKAIFRMRGSLAR 247


>gi|108804004|ref|YP_643941.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108765247|gb|ABG04129.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 257

 Score =  114 bits (286), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 51/262 (19%), Positives = 102/262 (38%), Gaps = 26/262 (9%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY-GLPISEVVSEGNIGLMQAVKKFD 94
            L   YR+ GD  A  RL  SH  L+  IA  Y G  G P  +++  G +GLM+AV  +D
Sbjct: 17  ELVAAYRDGGDRRALERLFASHGALLKSIARRYAGSSGEPYEDLLQAGYVGLMKAVNGYD 76

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P  G   ++Y+   ++  +  + LR   LV+       +       R+      +T    
Sbjct: 77  PSSGAAFSSYAYSMMEGEI-RHHLRDSGLVRRP-----RWASGLYARVSEATAHLTRELG 130

Query: 155 KPEQVVAIAKKLNVSESEVISMNC--RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +P     +A++ N++   +  +          SL+   +     S  ++ + +   D   
Sbjct: 131 RPPLPEEVAREANITPEGIRELMKVYLATSVSSLDEEPDLGAIRSLHYESFSLPVED--- 187

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
                       R  L  ++  L+  +R+       ++  ++   +     + + +V ++
Sbjct: 188 ------------RIWLEEALESLSELQRKAVYLFFYKD--LSQTEIGRRLGLPQRKVSRL 233

Query: 273 EARAFKKVQESIQKQVELSSSP 294
            A A K +   +  + E   SP
Sbjct: 234 VASAVKSLARKLGPEGEQDYSP 255


>gi|256379404|ref|YP_003103064.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Actinosynnema mirum DSM 43827]
 gi|255923707|gb|ACU39218.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Actinosynnema mirum DSM 43827]
          Length = 243

 Score =  114 bits (286), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 47/253 (18%), Positives = 101/253 (39%), Gaps = 23/253 (9%)

Query: 35  YVLAK-RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
             LA+ + R         +LVT +L +   IA  +   G  + ++     +GL+ AV +F
Sbjct: 12  RELAEAQSRVERRQELRDQLVTEYLPVAWHIADRFAERGESVEDLRQVAAVGLIHAVDRF 71

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D +RG     +++  I   ++ ++      V++     +  L  +  R+      +   +
Sbjct: 72  DVQRGIDFLAFAVPTITGEVRRHLRDQGWAVRVPRRLKELCLAIDAARV-----ELARAS 126

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            +      +A+ LN+S +EV       + +  ++     SD         L  D    E 
Sbjct: 127 GRTPTPSEVARHLNLSLAEVYEGLHATSANHMVSLDEVDSD-------HRLGVDDPALEV 179

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
           V ++          L   +  L  RERRI   R  +   +T   ++    VS+  V ++ 
Sbjct: 180 VELQHA--------LDPMLRGLPKRERRIVLLRFFRN--MTQSQIADSVGVSQMHVSRLL 229

Query: 274 ARAFKKVQESIQK 286
           +R+  ++++ + +
Sbjct: 230 SRSLARLRDLLDE 242


>gi|302874716|ref|YP_003843349.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           cellulovorans 743B]
 gi|307690671|ref|ZP_07633117.1| sporulation sigma factor SigK [Clostridium cellulovorans 743B]
 gi|302577573|gb|ADL51585.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           cellulovorans 743B]
          Length = 233

 Score =  114 bits (286), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 69/282 (24%), Positives = 115/282 (40%), Gaps = 64/282 (22%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           M++IVN  + LS YI      P  LE++EE    ++ +E GDL +   LV  +LRLV  I
Sbjct: 7   MNLIVNMTM-LSGYISNGNSFPKPLEEEEEKYHLQKLKE-GDLLSKSILVERNLRLVAHI 64

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
              Y G G    E++S G +GL++A+  F+ ++G RLATY+   I+  +   I  S    
Sbjct: 65  VKKYSGVGKDSDELISIGTVGLIKAIDSFNVDKGTRLATYAARCIENELLMLIRNSKKT- 123

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
                                                   K  V   + I ++     + 
Sbjct: 124 ----------------------------------------KGEVYLQDPIGVDKE-GNEI 142

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL  +++S + +  +     + +++ Q   L E+ E              L  RE+ I +
Sbjct: 143 SLMDVLSSEEDSVIE-----IVENNMQIAKLYEEIE------------KCLKGREKTIIQ 185

Query: 245 ARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            R       P T   ++    +SR  V +IE RA KK+ + +
Sbjct: 186 MRYGLINGKPKTQREIALLLGISRSYVSRIEKRALKKLYKYL 227


>gi|89335089|dbj|BAE84684.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 238

 Score =  114 bits (286), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 57/239 (23%), Positives = 97/239 (40%), Gaps = 62/239 (25%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           D+S    L+  +LRLVV IA  +   G+ I ++VS G IGL++AV  FDP++  +LATY+
Sbjct: 54  DVSVRDVLIERNLRLVVYIARKFENTGVGIEDLVSIGTIGLIKAVNTFDPQKKIKLATYA 113

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
              I+  +                        +LRR                        
Sbjct: 114 SRCIENEI----------------------LMHLRRNNKTR------------------- 132

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
                         ++ DE LN      D N     D L  ++D   + L EK +    R
Sbjct: 133 ------------TEVSFDEPLN---IDWDGNELLLSDVLGTENDIISRPLEEKVD----R 173

Query: 226 NMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            +L  +M+ L  RE+ I E R   +N    T + ++    +S+  + ++E R  +++++
Sbjct: 174 QLLHLAMARLTDREKLIMELRFGLDNGEEKTQKEVADRLGISQSYISRLEKRIIRRLRK 232


>gi|119775415|ref|YP_928155.1| flagellar biosynthesis sigma factor [Shewanella amazonensis SB2B]
 gi|119767915|gb|ABM00486.1| RNA polymerase sigma factor, FliA/WhiG [Shewanella amazonensis
           SB2B]
          Length = 239

 Score =  114 bits (286), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 50/242 (20%), Positives = 102/242 (42%), Gaps = 20/242 (8%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           + +   +V  +  LV +IA          + + +++  G IGL++A  KFD  +G +  T
Sbjct: 10  MESKTSIVEQYAPLVKRIAHHMLARLPASVQLDDLLQAGMIGLLEASAKFDGGKGAKFET 69

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           ++   I+ AM + I R    V      NQ       RR+   +  +     +  +   IA
Sbjct: 70  FAGIRIRGAMLDEI-RKGDWVPRSVHRNQ-------RRVAQVIDELEQELGRDARDTEIA 121

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           ++L++S  E       +  D S+  +I   D   S   D LV D +    +  +   +  
Sbjct: 122 ERLDMSMEEYH----HILNDVSVGKIIGIEDLGVS--HDVLVPDGEQTNDIYDDLA-QSQ 174

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +  L  ++  L  R+  +       +  + L+ + +  +VS  RV QI ++A  +++  
Sbjct: 175 FQQALADAIRQLPERDALVLSLYY--DEALNLKEIGAILDVSESRVCQIHSQAMLRLKGK 232

Query: 284 IQ 285
           ++
Sbjct: 233 LK 234


>gi|239827399|ref|YP_002950023.1| RNA polymerase, sigma 70 family subunit [Geobacillus sp. WCH70]
 gi|239807692|gb|ACS24757.1| putative RNA polymerase, sigma 70 family subunit [Geobacillus sp.
           WCH70]
          Length = 831

 Score =  114 bits (286), Expect = 1e-23,   Method: Composition-based stats.
 Identities = 54/236 (22%), Positives = 94/236 (39%), Gaps = 18/236 (7%)

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           A  +    +P+ ++  E    L +A +K++PE G     Y    + A +Q Y   + SL+
Sbjct: 587 AKKFSCETVPMEDLYQEAYFALHKAYEKYNPELGGSFYHYFRRHLFARLQRYKSDNLSLI 646

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I T   +  +  +    K  +     N    +    + K   +S  E+ S+    AGDE
Sbjct: 647 RIPTHRIETLMKNDQIFEKQLITNEKTNINLLDSDYILFKTNYISFEELYSLYDDNAGDE 706

Query: 185 S-------LNALINSSDKNSSQWQDWLVYDHDGQEQVLI----EKEERKNRRNMLTRSMS 233
           +        N           Q      Y  + +E   +      EE    R +   ++ 
Sbjct: 707 ARARIYCYFNHPFYEDTSLKRQVFIDYSYIEEPEECDWLLSEERYEEEIENRVLAESAID 766

Query: 234 VL-----NPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            L     NPR+ +I   R        +TL+ +   F VSRER+RQIE +A K +++
Sbjct: 767 YLRNIIKNPRDWKIILYRFGFMTGEEMTLQEIGELFGVSRERIRQIENKALKHLKK 822


>gi|322421664|ref|YP_004200887.1| RNA polymerase sigma 28 subunit FliA/WhiG [Geobacter sp. M18]
 gi|320128051|gb|ADW15611.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacter sp. M18]
          Length = 250

 Score =  114 bits (286), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 41/250 (16%), Positives = 94/250 (37%), Gaps = 18/250 (7%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKKFDPERG 98
            + G   +   LV SHL LV  I         P     ++ S   IGL+ A ++FDP RG
Sbjct: 12  AQRGVPMSRDELVVSHLPLVKFIVDRIASSLPPHLDRDDLRSAAVIGLISAAERFDPSRG 71

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
            +  T++   I+  + + +     L +         L    ++L+     +     +   
Sbjct: 72  VQFKTFAEQRIRGTIMDELRAQDWLTR--------SLRDKFKKLEKEFSQLEQRLGRNPS 123

Query: 159 VVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
              +A  + +   +   +   +      SL+   +  D       D L    D   +   
Sbjct: 124 SDEVATAMGLELKDYFRLLEEIHLLSFVSLDDAWHDEDGAPFGLLDVL---EDKGTESPQ 180

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
            +   +     L  ++  L  +ER +      +E  + L+ + +  +++  R+ Q+ ++A
Sbjct: 181 NQLIARQTVERLAEAIDTLPEKERIVITLYYYEE--LNLKEIGAVLDLTESRISQLHSQA 238

Query: 277 FKKVQESIQK 286
             +++  +++
Sbjct: 239 IIRLRGKMKR 248


>gi|224370767|ref|YP_002604931.1| FliA [Desulfobacterium autotrophicum HRM2]
 gi|223693484|gb|ACN16767.1| FliA [Desulfobacterium autotrophicum HRM2]
          Length = 238

 Score =  114 bits (286), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 53/246 (21%), Positives = 104/246 (42%), Gaps = 17/246 (6%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           ++  +  LV +IA  +           E+VS G++GL+ AV KFD  +   L TY+ + I
Sbjct: 1   MIVEYAFLVRQIASRFARRLPSSVLFDELVSAGSLGLIDAVDKFDSGKHVSLKTYAQYRI 60

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           K A+ + +               + +   ++ +   ++AI D    P     +AK L V 
Sbjct: 61  KGAILDELR--------SMDTYSRSMRKKIQDISRAVKAIEDKKKGPASDNEVAKLLEVP 112

Query: 170 ESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
                 M   + G    SL+A I + D ++S    +        E    +  +R+  + +
Sbjct: 113 LESYYDMLTDIHGAAILSLDAFIRTGDNDTSSMTRFQA--GIKGEHTPADLLDREELKGV 170

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L R+++ L  +E+ +      +E  +TL+ +     ++  R+ QI      K++  I+  
Sbjct: 171 LARAVTTLTEKEQLVVSLYYYEE--LTLKEIGEVLTLTESRICQIHTAILIKLKVKIKDY 228

Query: 288 VELSSS 293
              S+S
Sbjct: 229 YGSSTS 234


>gi|218289913|ref|ZP_03494103.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
 gi|218240053|gb|EED07239.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
          Length = 179

 Score =  114 bits (286), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 57/239 (23%), Positives = 93/239 (38%), Gaps = 64/239 (26%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L+  +LRLVV IA  +   G+ I ++VS G IGL++AV  FDP +  +LATY+   I+  
Sbjct: 2   LIERNLRLVVYIARKFENTGVNIEDLVSIGTIGLIKAVNTFDPSKKIKLATYASRCIENE 61

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +                         LRR                               
Sbjct: 62  I----------------------LMYLRR------------------------------- 68

Query: 173 VISMNCRLAGDESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
               N +L  + SL+  +N   D N     D L  D D     +    E +  R +L  +
Sbjct: 69  ----NNKLRAEVSLDEPLNVDWDGNELLLSDVLGTDSD----TIYRNLEDEVDRELLYDA 120

Query: 232 MSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +  L+ RER I E R        +T ++++    +S+  + ++E R  K++Q    K +
Sbjct: 121 LDKLSERERTIMELRFGLGTGQEMTQKDVADLLGISQSYISRLEKRILKRLQREFNKMM 179


>gi|304438454|ref|ZP_07398394.1| DNA-directed RNA polymerase sigma subunit FliA [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
 gi|304368537|gb|EFM22222.1| DNA-directed RNA polymerase sigma subunit FliA [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
          Length = 256

 Score =  114 bits (286), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 43/260 (16%), Positives = 109/260 (41%), Gaps = 27/260 (10%)

Query: 32  QEEYV-LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLM 87
           +E+   L K Y     +   +R+   +L LV  +A          +   +++S G  GL+
Sbjct: 14  EEDIEALWKAYETEKTIEVRNRIAEYYLPLVRLVAGRIAISLPQHVDREDLLSSGFFGLL 73

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
            A+++++  RG +  TY+   ++ A+ +++ R+   + +    N K       R +  + 
Sbjct: 74  DAIERYELTRGNKFETYAGVRVRGAILDHL-RAKDWIPVSVRQNIK-------RYEKAVA 125

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
            +     +      +A+++++S  E+  +  +++                   +++L  D
Sbjct: 126 HLEGTLGRTATDQELAEEMDLSIEELHRLESQVSA------------ATVIPLEEYLRTD 173

Query: 208 -HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
                E   +E  E    +  L  ++  L  +ER +       E  +TL+ +++   +S 
Sbjct: 174 AQASLEDGPVEHAEWTEIKETLAAAIEKLPEKERTVVALYYYDE--MTLKEIAAVLHLSE 231

Query: 267 ERVRQIEARAFKKVQESIQK 286
            R+ Q+  +A  +++ S+ +
Sbjct: 232 ARISQLHTKAIFRMRGSLAR 251


>gi|242089059|ref|XP_002440362.1| hypothetical protein SORBIDRAFT_09g030350 [Sorghum bicolor]
 gi|241945647|gb|EES18792.1| hypothetical protein SORBIDRAFT_09g030350 [Sorghum bicolor]
          Length = 529

 Score =  114 bits (286), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 55/248 (22%), Positives = 97/248 (39%), Gaps = 10/248 (4%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E  L  R +         RL+ +   LV  IA  Y G G  + +++  G +G++   +K
Sbjct: 273 DEAELMSRLQTGYC--CRERLLVTTEWLVRCIARSYTGMGTALDDLLQAGKMGVLDGAEK 330

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G R +TY  +WI+  M   +  +      G T    R+   +R++K   + I  +
Sbjct: 331 FDTRKGCRFSTYVKYWIRKGMLALLAENS-----GVTLLPARMESIMRKVKEARRGIRYS 385

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      +A  + VS + V           SL + I    +++   +          E
Sbjct: 386 EGRNPSDSEVAAAVGVSVANVRLARKCSRRPVSLYSEIGIG-QHAKFAEVIPDEAAAAAE 444

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVR 270
                   R   R  L   +  L  RE  +   R   E+    +LE +   + VS+E +R
Sbjct: 445 APDEAALFRGQLRERLLLVLGRLPAREGHVLRLRHGLEDGRCRSLEEIGGMYRVSKEWIR 504

Query: 271 QIEARAFK 278
           +IE  A  
Sbjct: 505 KIEKSAMA 512


>gi|91792701|ref|YP_562352.1| flagellar biosynthesis sigma factor [Shewanella denitrificans
           OS217]
 gi|91714703|gb|ABE54629.1| RNA polymerase sigma factor, FliA/WhiG [Shewanella denitrificans
           OS217]
          Length = 239

 Score =  114 bits (286), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 51/235 (21%), Positives = 102/235 (43%), Gaps = 20/235 (8%)

Query: 54  VTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           +  +  LV KIA          + + +++  G +GL++A  KFD  +G +  T++   I+
Sbjct: 17  IEQYAPLVKKIAHHMLARLPASVQLDDLLQAGMMGLLEAASKFDGTKGAKFETFAGIRIR 76

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            AM + I R    V      NQ       RR+   +  +  +  +  +   IA+KL++S 
Sbjct: 77  GAMIDEIRR-GDWVPRSVHRNQ-------RRVAQVIDELEQHFGRDARDTEIAEKLDMSL 128

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            E       +  D S+  +I   D   SQ  D ++ +    ++   E  E    ++ L  
Sbjct: 129 DEYH----HILNDVSVGKIIGIEDLGVSQ--DVIITEETSMDESFDELVE-TQFQSALVE 181

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           ++  L  R+  +       +  + L+ + +  EVS  RV QI ++A  +++  ++
Sbjct: 182 AIKTLPERDALVLSLYY--DEALNLKEIGAILEVSESRVSQILSQAMLRLKAKLK 234


>gi|296504831|ref|YP_003666531.1| sporulation sigma factor SigK [Bacillus thuringiensis BMB171]
 gi|296325883|gb|ADH08811.1| sporulation sigma factor SigK [Bacillus thuringiensis BMB171]
          Length = 196

 Score =  114 bits (286), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 46/240 (19%), Positives = 86/240 (35%), Gaps = 62/240 (25%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E GD  A + L+  +LRLV  I   +   G    +++S G IGL++A++ +   +G +LA
Sbjct: 2   EQGDAQARNLLIEHNLRLVAHIVKKFENTGEDAEDLISIGTIGLIKAIESYSAGKGTKLA 61

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+   I                      +  +  +LR LK                   
Sbjct: 62  TYAARCI----------------------ENEILMHLRVLKKT----------------- 82

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
                               D SL+  I    + +   +  L+     + + +I+  +  
Sbjct: 83  ------------------KKDVSLHDPIGQDKEGN---EISLIDILKSESEDVIDMIQLS 121

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                +   + +L+ RE+ +   R     +   T   ++    +SR  V +IE RA  K+
Sbjct: 122 MELEKIKEYIDILDEREKEVIVKRFGLGLDKEKTQREIAKALGISRSYVSRIEKRALMKM 181


>gi|269836601|ref|YP_003318829.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Sphaerobacter
           thermophilus DSM 20745]
 gi|269785864|gb|ACZ38007.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Sphaerobacter
           thermophilus DSM 20745]
          Length = 264

 Score =  114 bits (286), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 56/254 (22%), Positives = 106/254 (41%), Gaps = 18/254 (7%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
            L +RY    D S    L+  +  LV  +    R      L   +++  G IGL++A+ +
Sbjct: 16  ALWRRYAIERDGSTREALIRQYAPLVKYVVDRLRVALTATLDRDDLLGYGTIGLIEAIDR 75

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FDPERG +  T+++  I+ A+ + +    +L  +  TA Q+     + +    + A T  
Sbjct: 76  FDPERGVKFETFAIQRIRGAIIDAVR---TLDLVPRTARQRA--RAIEQAYREIFAATGR 130

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
               E+V A    L ++           A   ++  L  S        +D L    D Q 
Sbjct: 131 MPPEEEVAA---HLGMTIDAFRQALQDAAC--AILPLQQSDRDGEGTLEDTLP---DAQA 182

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
              ++   R +  + L  ++  L  R+R I      +E  +TL  +S    ++  RV Q+
Sbjct: 183 TEPLDAAVRSDLVHRLAAALERLPERDRLIVTLYYYEE--LTLREISEVLGITESRVSQL 240

Query: 273 EARAFKKVQESIQK 286
            +RA  +++  + +
Sbjct: 241 LSRARLQLRALLHE 254


>gi|331698492|ref|YP_004334731.1| RNA polymerase sigma 28 subunit FliA/WhiG [Pseudonocardia
           dioxanivorans CB1190]
 gi|326953181|gb|AEA26878.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pseudonocardia
           dioxanivorans CB1190]
          Length = 429

 Score =  114 bits (286), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 52/258 (20%), Positives = 102/258 (39%), Gaps = 24/258 (9%)

Query: 37  LAKRYREHG---DLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAV 90
           LA  + + G   D +    LV  +  LV  +A          + +S++V  G  GL+ A+
Sbjct: 188 LAALWLDRGGPRDRTVRDLLVAHYGPLVRAVAARMAVGLPASVEVSDLVQAGVFGLLDAI 247

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
            +FDP RG R  TY+   I+ AM + +        +  T   +     +R ++   + + 
Sbjct: 248 ARFDPTRGIRFETYAAQRIRGAMLDELRAQDW---VPRTVRSR-----IREIERTREQLE 299

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
               +      IA +L +   E++    R     S+ AL  S+   +    D    D   
Sbjct: 300 RRLGRAPDRREIAAELGLPLRELVRAGQR-RRLVSVEALAESASSVAESVVDESAPD--- 355

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                 E    +     L  ++ +L+ R+R + +   ++    TL  +     V+  RV 
Sbjct: 356 ----PAEVFALQETHRELAAAVRLLDERDRLVVQLYYVEN--RTLAEIGRLLGVTESRVC 409

Query: 271 QIEARAFKKVQESIQKQV 288
           Q+ AR   +++  ++ + 
Sbjct: 410 QLHARMVVRLRGRLEDRA 427


>gi|295706259|ref|YP_003599334.1| RNA polymerase sigma-D factor [Bacillus megaterium DSM 319]
 gi|294803918|gb|ADF40984.1| RNA polymerase sigma-D factor [Bacillus megaterium DSM 319]
          Length = 253

 Score =  114 bits (286), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 52/259 (20%), Positives = 107/259 (41%), Gaps = 20/259 (7%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQA 89
           EE+ + + +RE  D  A + LV  ++ LV              +   E+ S G IGL  A
Sbjct: 8   EEHKIWQEWRETRDSHAGNMLVKKYMPLVNYHVQRISVGLPKNIHKEELRSLGLIGLYDA 67

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           ++KFD  R  +  TY+ + I+ A+ + + +   L +              +R++   +A+
Sbjct: 68  LEKFDYGRDLKFDTYASFRIRGAIIDGLRKEDWLSR--------SAREKTKRIEQATEAL 119

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVI--SMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
               L+      +AK++ ++E++V+       LA   S+       +    ++       
Sbjct: 120 EQRYLRRVAPSEVAKEVGMTEADVVHTMNEGFLANVLSMEEQPKEYEDGEQKYTI----- 174

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            D +     E+     R   L   +  LN +E+ +       +  +T   ++    +S  
Sbjct: 175 KDEKTLSPEEELINDERYQELAEVIEQLNEKEQLVVSLFY--KEELTFTEIAQLLGLSTS 232

Query: 268 RVRQIEARAFKKVQESIQK 286
           R+ QI ++A  K++ S+ K
Sbjct: 233 RISQIHSKALFKMRTSLSK 251


>gi|188586048|ref|YP_001917593.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|179350735|gb|ACB85005.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 250

 Score =  114 bits (285), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 49/254 (19%), Positives = 108/254 (42%), Gaps = 15/254 (5%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMG--YRG-YGLPISEVVSEGNIGLMQAVKKF 93
           L   Y++ GD     +L++ +  LV K      Y    GL   +++S G IGL+ A+KKF
Sbjct: 5   LITSYQDSGDRQQLEKLISEYSYLVKKQVDKVNYPSISGLNRDDLISFGVIGLIDAIKKF 64

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D  R      Y+   I+ A+ + + R +  V        K L    R+L+  L       
Sbjct: 65  DINRNVPFEAYANIRIRGAILDGL-RKFDFVPRNLREEMKTLHSEYRKLEQKL------- 116

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            +      +A ++++SE+E+  +                + +      + +  D +  + 
Sbjct: 117 GRTPTNNELAYQMSISEAELDKLWQATNCVIPSYLSDYITAEEGELTLEDIYPDSNSPD- 175

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
               + + K  +  L +++  L  +E+ +      +E  +TL+ ++   E++  R+ Q+ 
Sbjct: 176 -PQSRIDEKTTKQELGQAIDTLPQKEKLVLSLYYYEE--LTLKEIAKILELTESRISQLH 232

Query: 274 ARAFKKVQESIQKQ 287
           ++A  +++  + K+
Sbjct: 233 SKAVLRLRGKLAKK 246


>gi|158338094|ref|YP_001519270.1| RNA polymerase sigma factor SigF [Acaryochloris marina MBIC11017]
 gi|158308335|gb|ABW29952.1| RNA polymerase sigma factor, group3 [Acaryochloris marina
           MBIC11017]
          Length = 266

 Score =  114 bits (285), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 51/253 (20%), Positives = 108/253 (42%), Gaps = 9/253 (3%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG-LPISEVVSEGNIGLMQAVKKFD 94
            L   YR+   +   +RLV  ++ LV K+A         P  ++   G +GL+ A+++FD
Sbjct: 13  ELLVAYRQKPSVQLRNRLVRLNMGLVRKVAHRLTHQCAEPYEDLEQCGFLGLITAIERFD 72

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P +G+  +++++ +I+  +  ++    + V+I     Q       R      QA+T    
Sbjct: 73  PSQGYAFSSFAVPYIRGEILHFLRDRANTVRIPRRWQQLS-----RDAAKARQALTMELG 127

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +      IA  L++S  E  S+         L+     S  +S       + D       
Sbjct: 128 RQPNDQEIADALSLSMQEWRSVKLATTNRVPLSLNARVSSGHSQSDSAMTLGDTLMDVHS 187

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
            I +  +++ R  L ++++ L  R R + E+   Q+  ++ + ++    VS   V +   
Sbjct: 188 QILQANQED-RIELQQALNQLEDRTRIMIESVFFQQ--LSRQEVAKRIGVSSVTVTRNMK 244

Query: 275 RAFKKVQESIQKQ 287
           +   K+ + +Q+Q
Sbjct: 245 KGIDKLIDLLQQQ 257


>gi|240145516|ref|ZP_04744117.1| RNA polymerase sigma-E factor [Roseburia intestinalis L1-82]
 gi|257202333|gb|EEV00618.1| RNA polymerase sigma-E factor [Roseburia intestinalis L1-82]
          Length = 207

 Score =  114 bits (285), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 52/259 (20%), Positives = 90/259 (34%), Gaps = 62/259 (23%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L  ++E    K+ ++ G L A + L   ++RLV  +A  Y+     + +++S G IGLM
Sbjct: 7   PLTPEQENECLKKLKK-GSLEARNELTLHNMRLVAHVAKKYQNSEEDMEDLISIGTIGLM 65

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +A+  +  + G RLATY+   I   +  Y                        R K    
Sbjct: 66  KAIATYKEDYGSRLATYAARCIDNELLMYF-----------------------RAKKK-- 100

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                                  S  +S+   +             + N     D +  +
Sbjct: 101 ----------------------VSREVSLYEPIG---------MDKEGNQIHLLDIVESE 129

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVS 265
                 V+   E  +    +L     VL  RE  I   R        +T   ++S   +S
Sbjct: 130 E---PDVVEMMERTRQIEKLLGLVPKVLQERELYIVVHRYGLFGNKAMTQREIASAVGIS 186

Query: 266 RERVRQIEARAFKKVQESI 284
           R  V +IE +A  K+++S 
Sbjct: 187 RSYVSRIEKKALDKLKKSF 205


>gi|108743436|dbj|BAE95539.1| putative RNA polymerase sigma factor [Streptomyces kanamyceticus]
          Length = 278

 Score =  114 bits (285), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 41/240 (17%), Positives = 96/240 (40%), Gaps = 15/240 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              +V   L +  ++A  +R  G  + ++     +GL++AV ++DP RG    +Y++  +
Sbjct: 52  RQEVVEVWLPMSERLAGRFRNRGESLDDLRQVAALGLVKAVDRYDPRRGTAFESYAVPTV 111

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN-NLKPEQVVAIAKKLNV 168
              ++ +       + +       R      R++   Q +    + +      IA++  +
Sbjct: 112 TGEIKRHFRDHMWTLHVPRRVQDLR-----NRVRFARQDLAQTVSGRAPTTAEIAERAQM 166

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SE +       L   +S  AL   ++   S+    L     G +  L    +    R  +
Sbjct: 167 SEED---AKAGLEALDSFTALSLDAELPGSEDGYSLSDALGGPDPAL----DVVIDRESV 219

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
              ++ L  RER I   R   +  +T   ++ E  +S+  V ++ +R   ++++ + +  
Sbjct: 220 KPRIAQLPERERTILYMRFFGD--MTQSRIADEMGISQMHVSRLISRCCDRLRDQVMRDA 277


>gi|71906382|ref|YP_283969.1| sigma-70 region 4 [Dechloromonas aromatica RCB]
 gi|71846003|gb|AAZ45499.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Dechloromonas
           aromatica RCB]
          Length = 248

 Score =  114 bits (285), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 44/242 (18%), Positives = 94/242 (38%), Gaps = 17/242 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             +LV   + LV +IA        P     ++V  G IGL+ A+ +F    G +  TY+ 
Sbjct: 10  REQLVQRFVPLVKRIAYHLMARLPPSVQFDDLVQNGMIGLLDAIDRFQEGFGAQFETYAT 69

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +  +  L         + L   LRR++  +  +   + +      +A+ L
Sbjct: 70  QRIRGAMLDGLRENDWL--------PRNLRRELRRIETAINQLEHEHGRVPSEKELAEAL 121

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +S ++         G + +     + + +    +     +      +L    E K+ + 
Sbjct: 122 GMSLADYQKTLQDARGHQLVYFDDLAGEGDEGFLERHFTDNAADPAAIL----EDKSVKA 177

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L  ++  L  RE+ +       E  + L  +     V+  RV Q+  +A  +++  I  
Sbjct: 178 TLITAIGELPEREKMMMALYY--EQDLNLREIGEVMGVTESRVCQLHTQAIARLRSQIVG 235

Query: 287 QV 288
           ++
Sbjct: 236 EI 237


>gi|302343749|ref|YP_003808278.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfarculus baarsii DSM 2075]
 gi|301640362|gb|ADK85684.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfarculus baarsii DSM 2075]
          Length = 260

 Score =  114 bits (285), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 38/251 (15%), Positives = 101/251 (40%), Gaps = 13/251 (5%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFD 94
           A++ +     +   RL+  +  ++  +A          + + +++  G +GL+ AV KFD
Sbjct: 14  ARQNKAGFSAAERERLILEYAPMIRYVAGRIAMRLPAHVSMEDLIGAGVLGLIDAVDKFD 73

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           PE+  +  TY+ + ++ A+ + + R+   V          L   + RL+  L        
Sbjct: 74  PEKNVKFKTYAEFRVRGAILDEL-RAMDWVPRSVRKKSSDLEDAIGRLQNRL-------G 125

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +P +   IA++L +   ++  +   ++G   L+     S   +   +  +        + 
Sbjct: 126 RPAEDEEIAQELGIGLDDLHRLLDEVSGVNLLSLDDADSPLGNLDSEQVMEAMGREGLED 185

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
            +        R ++  ++  L  +E+ +       E  +T+  +      +  R+ Q+  
Sbjct: 186 PLVMLGLVELRRVIASAIEGLPEKEKLVVSLYYYDE--LTMREIGEVLGYTESRISQMHT 243

Query: 275 RAFKKVQESIQ 285
           +A  +++  ++
Sbjct: 244 KAILRLRARLR 254


>gi|284041500|ref|YP_003391840.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Conexibacter woesei
           DSM 14684]
 gi|283945721|gb|ADB48465.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Conexibacter woesei
           DSM 14684]
          Length = 270

 Score =  114 bits (285), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 51/266 (19%), Positives = 109/266 (40%), Gaps = 17/266 (6%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG---YGLPISEVVS 80
           R+   +  ++   L ++Y+E GD +   RLV +   +V  I             + + +S
Sbjct: 6   RRHNRISAEDALALWRQYKESGDRAVRDRLVLTFAPMVKYIVYKKVREIPARCEVEDFIS 65

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
            G   L+ +++++DPE+G  L  +S   I  A+ + + R     +     + +R   ++ 
Sbjct: 66  CGLEALIHSIERYDPEKGATLEQFSWTRIHGAVLDELRRQDWAPR-----SLRRWERDIN 120

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL--AGDESLNALINSSDKNSS 198
           + + H       + +      +A  L  + +E+ +    +  +   SLN L+ S D+ + 
Sbjct: 121 QAREH---FIGVHSRRPSREELAGALGTTPAELRAREDEIVASDVTSLNTLVLSDDETAI 177

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           +  D LV +    +        R   +     +   L  RER +     ++   +TL  +
Sbjct: 178 ERIDTLVSEDRFAD--PEHHTARDQAKMRFREAFERLPRREREVAVLLYVKN--LTLREI 233

Query: 259 SSEFEVSRERVRQIEARAFKKVQESI 284
                VS  RV QI  +  + ++E +
Sbjct: 234 GGILGVSESRVCQIHGQLKRMLKEEL 259


>gi|160892593|ref|ZP_02073383.1| hypothetical protein CLOL250_00123 [Clostridium sp. L2-50]
 gi|156865634|gb|EDO59065.1| hypothetical protein CLOL250_00123 [Clostridium sp. L2-50]
          Length = 245

 Score =  114 bits (285), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 52/259 (20%), Positives = 94/259 (36%), Gaps = 65/259 (25%)

Query: 18  RYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
            YI     +P  LE  EE  +        D      L+  +LRLVV IA  +   G+ + 
Sbjct: 30  HYIGGCDVLPAPLEPYEESAMVAGLGNGDDQEIKKILIERNLRLVVYIAKKFDNTGIGVE 89

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++S G IGL++A+  F  ++  +LATY+   I+  +  Y+ R+  L             
Sbjct: 90  DLISIGTIGLIKAINTFKCDKNIKLATYASRCIENEILMYLRRNSKL------------- 136

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
                                       ++ +S  E ++++                D N
Sbjct: 137 ----------------------------RMEISIDEPLNVD---------------WDGN 153

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN----P 252
                D L  D D     +    E +   ++L  ++S L+ RER I E R          
Sbjct: 154 ELLLSDILGTDED----TVYRNMETEMDHSLLETAVSHLSERERTIIELRYGINTINGIE 209

Query: 253 VTLENLSSEFEVSRERVRQ 271
            T + ++    +S+  + +
Sbjct: 210 RTQKEVADLLGISQSYISR 228


>gi|153814969|ref|ZP_01967637.1| hypothetical protein RUMTOR_01184 [Ruminococcus torques ATCC 27756]
 gi|145847537|gb|EDK24455.1| hypothetical protein RUMTOR_01184 [Ruminococcus torques ATCC 27756]
          Length = 243

 Score =  114 bits (285), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 39/243 (16%), Positives = 99/243 (40%), Gaps = 16/243 (6%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R    GD +A  +LV  ++ LV  +   +   G    ++   G+IGL++A+ KFD     
Sbjct: 9   RKSHSGDKAAREQLVKENVGLVHCVVKRFLERGAEREDLFQIGSIGLLKAIDKFDLTYNV 68

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +TY++  I   ++ ++     ++K+  +  +        R +     +  +  +   +
Sbjct: 69  KFSTYAVPLISGEIKRFLRDDG-MIKVSRSLKEIAYKSVQARER-----LISSLGRDPTI 122

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +++++ V   E++         ES+   ++  + +  +  D L  + + +E  +++  
Sbjct: 123 EELSEEVGVEREELVQAMEAGCEIESIYRPVHQKEGSEIRLLDKL-EEKEKREDKILDLI 181

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
             K     L      L          R   +   T  ++     +S+ +V + E R  +K
Sbjct: 182 VLKELLETLDEEEKQL-------IFLRYFAD--RTQSDVGKIMGISQVQVSRSEKRIIEK 232

Query: 280 VQE 282
           +++
Sbjct: 233 LRK 235


>gi|262276378|ref|ZP_06054187.1| RNA polymerase sigma factor for flagellar operon [Grimontia
           hollisae CIP 101886]
 gi|262220186|gb|EEY71502.1| RNA polymerase sigma factor for flagellar operon [Grimontia
           hollisae CIP 101886]
          Length = 224

 Score =  114 bits (285), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 44/237 (18%), Positives = 93/237 (39%), Gaps = 19/237 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           +   +  LV +IA        P   + +++  G +GL++A + +D  +G    TY+   I
Sbjct: 1   MFEQYATLVKRIAHHLVARLPPNVQVEDLIQAGMVGLLEAQQNYDASKGASFETYAGIRI 60

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + AM + I R    V      N        R++   +  +     +  +   IAK+L + 
Sbjct: 61  RGAMLDDI-RKGDWVPRSVHKNN-------RQISEVIAQLEGELGRDPKDKEIAKRLGM- 111

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
                S+         +NA       +    +D  V +    E +  E+    + ++ L 
Sbjct: 112 -----SLEQYHQAQNDINAGRLIGIVDLGVSEDAFVTESHRDENLPFEEVAGDSFKSHLA 166

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            ++  L  RE  +       +  + L+ + +   VS  RV QI+ +A ++++  +  
Sbjct: 167 NAIRGLPEREALVLSLYY--DEELNLKEIGAIIGVSESRVCQIQNQAMQRLRTKLSA 221


>gi|121596110|ref|YP_988006.1| FliA/WhiG family RNA polymerase sigma factor [Acidovorax sp. JS42]
 gi|222112265|ref|YP_002554529.1| RNA polymerase, sigma 28 subunit, flia/whig [Acidovorax ebreus
           TPSY]
 gi|120608190|gb|ABM43930.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Acidovorax sp.
           JS42]
 gi|221731709|gb|ACM34529.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Acidovorax ebreus
           TPSY]
          Length = 237

 Score =  114 bits (285), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 44/239 (18%), Positives = 100/239 (41%), Gaps = 16/239 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L   H+ LV +IA          + + +++  G IGL  A+ +++  +G +  T++ 
Sbjct: 10  RDALFHQHVPLVRRIAHHMIAKLPPNVELDDLIQVGMIGLNDALSRYEVAQGVQFETFAS 69

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + R    +   +  +QK +   L R++  L        +      IA +L
Sbjct: 70  QRIRGAMLDEL-REGDWMSRSSRKSQKDIEHALHRVEQRL-------GRSPIESEIAAEL 121

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +S  +  ++  ++ G + +       D     + D  V D       ++  +     R 
Sbjct: 122 GMSLEDYQALLSKVRGTQLVYLEDFHHDDEDEGFLDRHVADEGADPMAVLRDQRL---RA 178

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            L  ++  L  RE+ I       E+ + L+ +++   V+  RV Q+ ++A  +++  ++
Sbjct: 179 SLVEAIKALPEREQYIMGMYY--EHDMNLKEIAAVLGVTESRVCQLHSQAIARLRTKMR 235


>gi|284041831|ref|YP_003392171.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Conexibacter woesei
           DSM 14684]
 gi|283946052|gb|ADB48796.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Conexibacter woesei
           DSM 14684]
          Length = 262

 Score =  114 bits (285), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 47/252 (18%), Positives = 100/252 (39%), Gaps = 16/252 (6%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL---PISEVVSEGNIGLMQAVKKFD 94
            +RY+  G+ +A   LV ++  +V  +A            +++++S+G  GL+ AV++F+
Sbjct: 14  WRRYKGTGERAARDDLVLAYSPIVKYVAGRVAARMPAHVDVADLISDGFKGLLDAVERFE 73

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P RG R   Y+   I+ A+ + + RS   V     A  + +      L   LQ       
Sbjct: 74  PVRGVRFEAYADTRIRGAIFDGL-RSLDWVPRAVRAEAREIERATAELAMRLQ------- 125

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +      +A  L++S  ++ +   R++     +L+           +    L    D   
Sbjct: 126 RMPTDPELAGALSMSRRQLAASLQRVSDSRIVALDEP-WGPVLADGRPVALLDTLPDLDA 184

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
                  +   R   +  ++  L  RE+ +   R    + +TL  +     +S  R  Q+
Sbjct: 185 VDPAADSDETERSERIGAAVRQLPAREQVVLGLRY--HHDLTLLQIGEVLGISESRTSQL 242

Query: 273 EARAFKKVQESI 284
             +A  +++  +
Sbjct: 243 HTKAALQLKAVL 254


>gi|260589068|ref|ZP_05854981.1| RNA polymerase sigma-E factor [Blautia hansenii DSM 20583]
 gi|331082498|ref|ZP_08331623.1| hypothetical protein HMPREF0992_00547 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|260540488|gb|EEX21057.1| RNA polymerase sigma-E factor [Blautia hansenii DSM 20583]
 gi|330400476|gb|EGG80106.1| hypothetical protein HMPREF0992_00547 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 208

 Score =  114 bits (285), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 52/256 (20%), Positives = 94/256 (36%), Gaps = 62/256 (24%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L  +EE    + Y++ G+L A + L+  +LRLV  I   Y+G    + +++S G IGL+
Sbjct: 7   PLTSEEESYYLQEYKQ-GNLEAKNILIERNLRLVAHIVKKYQGAPEEMDDLISIGTIGLI 65

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +A+  FD ++  RL+TY+   I                         L   LR  K   +
Sbjct: 66  KAIHTFDAQKASRLSTYAARCIDN----------------------ELLMLLRSKKKSNR 103

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                                     +S+   +  D          + N     D +  +
Sbjct: 104 E-------------------------VSLYDPIGTD---------KEGNEISLLDIIETE 129

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVS 265
                +    K++      +L + ++    RER I + R     E  +T   ++    +S
Sbjct: 130 PVDVVKNYSLKQDIARLYQLLPKVLTT---REREIIKLRYGLYGEQELTQREIAKRLNIS 186

Query: 266 RERVRQIEARAFKKVQ 281
           R  V +IE  A  K++
Sbjct: 187 RSYVSRIEKNAILKLR 202


>gi|94968665|ref|YP_590713.1| sigma 28 [Candidatus Koribacter versatilis Ellin345]
 gi|94550715|gb|ABF40639.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Candidatus
           Koribacter versatilis Ellin345]
          Length = 262

 Score =  114 bits (285), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 48/243 (19%), Positives = 98/243 (40%), Gaps = 18/243 (7%)

Query: 48  SAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
               RLV   +  V  IA          +PI ++++ G +GL+ A  K+D E+  +  +Y
Sbjct: 16  EHRDRLVMEQMSQVKYIARRIHERLPRHVPIEDLINAGILGLIDAAGKYDSEKNVQFQSY 75

Query: 105 SMWWIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           + + I+ A+ + +    WS          + L    R L+     +T     P     +A
Sbjct: 76  AKFRIRGAILDSLRDLDWSP---------RDLRRKARALEAAELRLTSETGHPPLEDELA 126

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           ++L +       +   L G    +       +   + ++ +V  H   E+  ++   R  
Sbjct: 127 RELGMDLDGFRELTRELEGLGISSLQEGLPAEGFGEEREVVVESH---EESPLDAFLRSE 183

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
              +L  ++  L  RER++      +E  +T++ +     V   RV QI ++A  +V+  
Sbjct: 184 NHELLVEAIEQLPARERQVLALYYFEE--LTMKEVGDVLGVGESRVSQIHSQALTRVRAR 241

Query: 284 IQK 286
           +Q 
Sbjct: 242 LQS 244


>gi|94264039|ref|ZP_01287839.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
 gi|94266375|ref|ZP_01290074.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
 gi|93453027|gb|EAT03515.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
 gi|93455550|gb|EAT05737.1| Sigma-70-like protein [delta proteobacterium MLMS-1]
          Length = 256

 Score =  114 bits (285), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 48/254 (18%), Positives = 105/254 (41%), Gaps = 22/254 (8%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGF 99
           E  D +    L+ ++  L+  IA        P   + +++S G +GL+ A+ KFDP +  
Sbjct: 17  EQFDPARRDELILTYTPLIKYIASRLASRLPPQVAVDDLISCGIVGLIDAINKFDPAKNV 76

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           +  TY+ + IK AM + + R+   V        +R    L ++ G L++      +P   
Sbjct: 77  QFKTYAEFRIKGAMLDEL-RALDWVPRSV----RRKITELEKISGELES---KLGRPPDD 128

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD----HDGQEQVL 215
              A  L +  ++   +      DE+ +      D   S+  D +  D        ++  
Sbjct: 129 EETAAALGIELADFHRLL-----DETKSVTFLDIDYLRSKVPDEIEGDVGEIFARDDKDP 183

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
                    RN+L +++  L  +E+            +T++ +      +  R+ Q+ ++
Sbjct: 184 FTALNLGETRNLLAKAIGELPEKEKLTVALYY--HEELTMKEIGEVLGYTESRISQMHSK 241

Query: 276 AFKKVQESIQKQVE 289
           A  +++  ++KQ++
Sbjct: 242 AMLRLRAKLKKQLD 255


>gi|113477360|ref|YP_723421.1| RNA polymerase sigma factor SigF [Trichodesmium erythraeum IMS101]
 gi|110168408|gb|ABG52948.1| RNA polymerase, sigma 28 subunit [Trichodesmium erythraeum IMS101]
          Length = 254

 Score =  114 bits (285), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 49/258 (18%), Positives = 105/258 (40%), Gaps = 16/258 (6%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQA 89
           K E   L ++Y++       ++LV  ++ LV K A  +         +++  G IGL+ A
Sbjct: 10  KSETIKLLQQYQQFPSYELRNKLVQLNVGLVRKEAYHWLNKCSETYDDLLQVGYIGLILA 69

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +++FD  +    ++++  +I+  ++ Y+      V+I      +      R+    +Q +
Sbjct: 70  IERFDVSKARAFSSFATPYIRGEIKHYLRDKSPSVRIP-----RNWLAIDRQATKVIQDL 124

Query: 150 TDNNLKPEQVVAIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                +      +A  L +S  +   I M CR     SL+A +      S+   + +   
Sbjct: 125 RMKFQRKPTDQEVASALGISLDQWHKIQMACRNLAPLSLDAPVQDQAYGSTSLGELVPDS 184

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
                Q+  E + R      L +++S L    R++ E   L +  +T +  +    +S  
Sbjct: 185 QYRSFQLAQEDQIR------LQQALSKLEESTRKVLEFVFLCD--LTQKETAERMGISAV 236

Query: 268 RVRQIEARAFKKVQESIQ 285
            V +      K +Q+ +Q
Sbjct: 237 TVSRRVKNGLKCLQKIMQ 254


>gi|163789630|ref|ZP_02184068.1| Sigma factor of SigD/WhiG family protein [Carnobacterium sp. AT7]
 gi|159875162|gb|EDP69228.1| Sigma factor of SigD/WhiG family protein [Carnobacterium sp. AT7]
          Length = 238

 Score =  113 bits (284), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 58/246 (23%), Positives = 113/246 (45%), Gaps = 15/246 (6%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGY--RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
            +   + +  +L LV KI      +       ++ + G IGLM A++KFD  +      Y
Sbjct: 4   ENDREKEIIKYLPLVEKIVNRIDIKRSEYDRDDLYNIGVIGLMDALEKFDKSKKVPFEGY 63

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +   IK  + + I ++        +  +        R K  L+A        +++ A  K
Sbjct: 64  AYIRIKGTIIDEIRKTA-----PVSRTRMGKLNEYYRGKEKLEAELMRTPTEKEICAELK 118

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKN 223
               S +++      LA   SL  ++ S D NS +  D+L   H+ G E  L++KE    
Sbjct: 119 IDEKSLAKIHETVHNLAS-VSLEKVMFSDDGNSIELLDFLEDTHETGSEDTLLDKE---- 173

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           R+++LT+ +  L+ RE+ I     ++E  ++L+ ++  F++S  RV QI  +   K++ S
Sbjct: 174 RQHLLTKHVGQLDKREQTILNLIYVEE--LSLKEIAYIFDISVPRVSQIHGKMILKLKGS 231

Query: 284 IQKQVE 289
           + ++ +
Sbjct: 232 MGREYD 237


>gi|197335206|ref|YP_002156660.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-28) [Vibrio fischeri MJ11]
 gi|197316696|gb|ACH66143.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-28) [Vibrio fischeri MJ11]
          Length = 243

 Score =  113 bits (284), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 98/249 (39%), Gaps = 19/249 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPER 97
           Y   G++++    +  +  LV +IA            + +++  G IGL++A + +D  +
Sbjct: 7   YDHKGNVNSQKAFLERYSDLVKRIAHHLMARLPASVLVDDLIQAGMIGLLEAQQNYDGSK 66

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G    TY+   I+ +M + I R    V      N + +   +R L+  L        +  
Sbjct: 67  GASFETYAGIRIRGSMLDEIRR-GDWVPRSVHKNSRMINSAIRELEAKLS-------RDP 118

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               IA  L +   +      ++  D +   L+   D   S   D +  +    + +  +
Sbjct: 119 TDKEIADYLELPLDQY----YQILNDVNCGKLVGMEDLGVS--DDVIATEEQADDNIPFQ 172

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
               ++ R  L  ++  L  RE  +       +  + L+ + +   VS  RV QI +++ 
Sbjct: 173 GVADEHFRVALVEAIKTLPEREALVLSLYY--DEELNLKEIGAVIGVSESRVSQIHSQSM 230

Query: 278 KKVQESIQK 286
           ++++  +  
Sbjct: 231 QRLRAKLSS 239


>gi|158341591|ref|YP_001522756.1| RNA polymerase sigma-24 subunit [Acaryochloris marina MBIC11017]
 gi|158311832|gb|ABW33441.1| RNA polymerase sigma-24 subunit [Acaryochloris marina MBIC11017]
          Length = 423

 Score =  113 bits (284), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 48/243 (19%), Positives = 105/243 (43%), Gaps = 19/243 (7%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + GD  A  R +  + RLV   A  YRG  +   ++V+ G +GL  A++KFD  RGF+ 
Sbjct: 29  AQAGDRRAEDRFIRKNQRLVFNEAKRYRGL-VDWDDLVNAGTLGLSIAIQKFDLSRGFQF 87

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY++  I+  +++ I     L +         +  +L+++    Q +     +   +  
Sbjct: 88  STYAVKPIRTEIRQLICEQRGLSR--------EITKHLKKIDEAEQDLKLELERKPTLDE 139

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           +A++   S   + +   +    ++ +  + +  +   +  D++            E    
Sbjct: 140 LAERTGYSHRVITNAWSKARVVDTSSLNVLTGTEQGIECLDFVEDLEQLDSWDFAESINM 199

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           K+        ++ L  RE  I  ARR   +  +   + +  ++S ER+RQ+  +A + ++
Sbjct: 200 KDY-------IAQLPDRESFIVRARR---DGHSYREIGTMLKLSGERIRQLYQKALEYLK 249

Query: 282 ESI 284
             I
Sbjct: 250 HLI 252


>gi|126659593|ref|ZP_01730724.1| sigma factor SigF [Cyanothece sp. CCY0110]
 gi|126619136|gb|EAZ89874.1| sigma factor SigF [Cyanothece sp. CCY0110]
          Length = 245

 Score =  113 bits (284), Expect = 2e-23,   Method: Composition-based stats.
 Identities = 55/256 (21%), Positives = 107/256 (41%), Gaps = 16/256 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG-LPISEVVSEGNIGLMQAVKKFD 94
            L   Y  +  L   +RLV  +L LV ++A         P  ++   G +GL++A+++FD
Sbjct: 2   ELLIAYARNPSLELRNRLVERNLGLVRQVAHRISRQCSEPYEDLEQIGYLGLIRAIERFD 61

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P++G   +++++ +I+  M  Y+    S+++I     +        + K   + +T +  
Sbjct: 62  PQQGCAFSSFAIPYIRGEMLHYLRDKGSVMRIPRRWQELH-----NKAKKIRKQLTVSLK 116

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +P     IA  L V   E       L      SL+A I+ +   S  + D L       +
Sbjct: 117 RPPTDQEIANALEVPLKEWNECQLALQNRLLVSLDATISQNVDCSISFGDTLPDQDYQAK 176

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           Q L E       R  L R++  L  + +   E   L E P   +  + +  +S   V + 
Sbjct: 177 QKLEED------RLQLQRALGQLEEKTKAAIECVFLNELPR--KEAAKQIGISPMTVTRH 228

Query: 273 EARAFKKVQESIQKQV 288
             +  +++   ++ QV
Sbjct: 229 LKKGIQQLGSLLETQV 244


>gi|226324647|ref|ZP_03800165.1| hypothetical protein COPCOM_02432 [Coprococcus comes ATCC 27758]
 gi|225207095|gb|EEG89449.1| hypothetical protein COPCOM_02432 [Coprococcus comes ATCC 27758]
          Length = 222

 Score =  113 bits (284), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 54/250 (21%), Positives = 89/250 (35%), Gaps = 62/250 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L  +EE  L +R  +  D  A H L+  +LRLV  +   Y+       +++S G IGL
Sbjct: 6   PPLTPKEESELLRRSADS-DNEARHILIERNLRLVAHVIKKYQHLEDDTEDLLSIGTIGL 64

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+P++  RLATY+   I                      +  L   LR  +   
Sbjct: 65  IKAVSTFNPDKKARLATYACRCI----------------------ENELLMMLRTKRKSN 102

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +                           S+   +  D          + N  +  D +  
Sbjct: 103 RET-------------------------SLYEPIGTDR---------EGNEIRLYDVIES 128

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           D +     L  K +       L    SVL  RE+ + + R     E   T + +++   +
Sbjct: 129 DEEDACMQLALKNDISLLYEKLE---SVLTDREQLVLKKRYGLYGEKEYTQKEVAASLGI 185

Query: 265 SRERVRQIEA 274
           SR  V +IE 
Sbjct: 186 SRSYVSRIEK 195


>gi|72161291|ref|YP_288948.1| RNA polymerase sigma-B factor [Thermobifida fusca YX]
 gi|71915023|gb|AAZ54925.1| RNA polymerase sigma-B factor [Thermobifida fusca YX]
          Length = 307

 Score =  113 bits (284), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 51/273 (18%), Positives = 100/273 (36%), Gaps = 30/273 (10%)

Query: 17  SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHR----LVTSHLRLVVKIAMGYRGYG 72
             Y+ E R++          LA+  R   D  A  R    L   H  +  +IA  YR  G
Sbjct: 56  EAYLRETREL----------LAELDRVRDDPKARERIYLKLTELHAPVARRIARQYRNRG 105

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
            P  ++     +GL  A++ FDP  G    +Y++  +   ++ +       +++     +
Sbjct: 106 EPEEDLRQVAMVGLYNAIRNFDPAYGKEFISYALPMMTGEVKRHFRDRTWAIRVPRKYQE 165

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
           KR       L       T  + +   V  +A+ L + E + + +        +L+  +  
Sbjct: 166 KRA-----ELNRVTAEFTQRHGRSPTVRELAELLEMDEEQTLELIDAARAYSTLSLDVPF 220

Query: 193 S-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             D + +   D L    D  E+V+     R     +        +PR+RRI   R   + 
Sbjct: 221 GPDDDGATLGDTLGGLDDALERVVDHAALRPALAAL--------SPRDRRILLLRFAGD- 271

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             T   ++    +S+  V +  A     ++  +
Sbjct: 272 -KTQAQIAEIVGLSQMHVSRRLAAILTTLRRQL 303


>gi|311695193|gb|ADP98066.1| flagellar biosynthesis sigma factor FliA [marine bacterium HP15]
          Length = 247

 Score =  113 bits (284), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 49/238 (20%), Positives = 96/238 (40%), Gaps = 24/238 (10%)

Query: 52  RLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           +L+  H  LV KIA+         + + +++  G IGL++A +++   +G    TY+   
Sbjct: 20  QLIEQHAPLVKKIALHLMARLPASVQLEDLMQAGMIGLLEAAQRYSSTKGATFETYAGIR 79

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ AM + I R    V             N RR+   ++A+ D   +      +A++L +
Sbjct: 80  IRGAMVDEI-RKGDWVPRSVH-------RNARRISQAIKAVEDRLGREAHDQEVAEELGM 131

Query: 169 SESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
              E  S   +       SL+ L  S +         L  +    +   +E       R 
Sbjct: 132 GLPEYHSYLSDSNSGRLFSLDELNESGE---------LPIEQTETQDNPLEGLSSDAFRR 182

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L  ++  L  RE+ +       +  + L+ + +   VS  RV QI ++A  +++  +
Sbjct: 183 SLAEAIEDLPEREKLVLSLYY--QEELNLKEIGAVLGVSESRVSQIHSQAALRLRGRL 238


>gi|328958265|ref|YP_004375651.1| RNA polymerase sigma factor SigD [Carnobacterium sp. 17-4]
 gi|328674589|gb|AEB30635.1| RNA polymerase sigma factor SigD [Carnobacterium sp. 17-4]
          Length = 238

 Score =  113 bits (284), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 57/246 (23%), Positives = 115/246 (46%), Gaps = 15/246 (6%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGY--RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
            +   + +  +L LV KI      +       ++ + G IGLM A++KFD  +      Y
Sbjct: 4   ENDREKEIIKYLPLVEKIVNRIDVKRSEYDRDDLYNIGVIGLMDALEKFDKSKKVPFEGY 63

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +   IK ++ + I ++        +  +        R K  L+A        +++    K
Sbjct: 64  AYIRIKGSIIDEIRKTA-----PVSRTRMGKLNEYYRAKEKLEATLMRTPTEKEICEELK 118

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKN 223
               + +++      LA   SL  ++ S D NS +  D+L   H+ G E  L++KE    
Sbjct: 119 IDEKALTKIHETVHNLAS-ISLEKVMFSDDGNSIELIDFLEDKHETGSEDTLLDKE---- 173

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           R+ +LT+++S L+ RE+ I     ++E  ++L+ ++  F++S  RV QI  +   K++E 
Sbjct: 174 RQQLLTKNVSKLDKREQTILNLYYVEE--LSLKEIAYIFDISVPRVSQIHGKMILKLKEL 231

Query: 284 IQKQVE 289
           ++++ +
Sbjct: 232 MRREYD 237


>gi|119485331|ref|ZP_01619659.1| sigma factor SigF [Lyngbya sp. PCC 8106]
 gi|119457087|gb|EAW38213.1| sigma factor SigF [Lyngbya sp. PCC 8106]
          Length = 259

 Score =  113 bits (284), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 46/255 (18%), Positives = 104/255 (40%), Gaps = 16/255 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG-YGLPISEVVSEGNIGLMQAVK 91
           E   L + Y+        ++LV  ++ LV K    +         +++  G IGL++A++
Sbjct: 12  ETLELLRDYQCSNSKELRNQLVQLNIGLVRKEVHHWVNQCTENYDDLLQVGCIGLIRAIE 71

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           +FD  +G   +++++ +I+  +Q Y+      +++        L     +L   LQ    
Sbjct: 72  RFDLSKGHAFSSFAIPYIRGEIQHYLRDKSLPLRVPRH--WLTLQRQGMKLAQELQVKLK 129

Query: 152 NNLKPEQVVAIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
                     IA+ LN+SE+E   + +        SL+A +   ++ ++   + +  +  
Sbjct: 130 RQ---PTDTEIARGLNISETEWSQVKLAGYNRSLLSLDAPVQDENEGTTCLGELVPDNRY 186

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
              Q+  E + R      L + +S L    R++ E   L +  +T +  +    +S   V
Sbjct: 187 RSFQLAQEDQIR------LQQGLSKLEEGTRKVLEFVFLYD--LTQKETAERLGISAVTV 238

Query: 270 RQIEARAFKKVQESI 284
            +   +    +Q  +
Sbjct: 239 SRRVKKGLNLLQRIM 253


>gi|332294870|ref|YP_004436793.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermodesulfobium
           narugense DSM 14796]
 gi|332177973|gb|AEE13662.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermodesulfobium
           narugense DSM 14796]
          Length = 223

 Score =  113 bits (284), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 48/256 (18%), Positives = 108/256 (42%), Gaps = 41/256 (16%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG-YR--GYGLPISEVVSEGNIGLMQA 89
           +E  L  +YR +      + L  ++L LV +IA   Y      +   E+++ G  GL+ +
Sbjct: 3   DEKALWIKYRNNSTQENRNLLALNYLPLVKRIAAKIYTTIQGKVEFEELLNYGIFGLLTS 62

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +++F+  R  +  T++   I+ A+ + + R    +K GT +  K++   +  LK  L   
Sbjct: 63  IERFEESRNLKFETFATHRIRGAILDGL-RQIDPLKRGTRSKVKKIDRAINELKSSL--- 118

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
                K      +A  LN+++ E   +    A  ++L+   +    +   + D       
Sbjct: 119 ----GKDPSDKDVADYLNITKEE---LLNWYAEIDALSTFQSDFSDSEKSYID------- 164

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
                             L+ ++  L  RE+++ +    ++  ++L+ ++    +S  RV
Sbjct: 165 ------------------LSMAIEKLEEREKQVIDLYYYED--LSLDEIAKILNISVSRV 204

Query: 270 RQIEARAFKKVQESIQ 285
            QI  +A  K++  ++
Sbjct: 205 SQIHGKALIKLKSQLE 220


>gi|302387774|ref|YP_003823596.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           saccharolyticum WM1]
 gi|302198402|gb|ADL05973.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           saccharolyticum WM1]
          Length = 258

 Score =  113 bits (284), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 47/254 (18%), Positives = 109/254 (42%), Gaps = 19/254 (7%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKK 92
            L  +Y+   D+   H LV  ++ +V  I++  R   L      ++V+EG + +M  ++K
Sbjct: 12  DLLIKYKRTKDIHIKHELVMRYMYMVRSISIQMRDVYLSFAQVEDIVNEGVLTIMSGIEK 71

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FDPE   +  TY    I+  + + + R    +      N K L          +  + + 
Sbjct: 72  FDPEMNVKFETYISKRIRGMIID-MARKQDWIPRSVRKNAKELDN-------AVMELCNR 123

Query: 153 NLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
             +       A+ +N+S  +         +    SL+ ++ + + N    Q   V +++ 
Sbjct: 124 LGRFPSPRETAEYMNISLEKYQEALGKTNVYSVLSLDMVLEAGNDNKKTVQLPAVNENEQ 183

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
            E   +++E     + +L ++++ L   E+++     + E  + ++ ++    VS  R+ 
Sbjct: 184 PEDHYLQEE----FKQILVQAINNLKENEQKVISLYYMDE--LNMKEIAQVMNVSEPRIS 237

Query: 271 QIEARAFKKVQESI 284
           QI + A +K++  +
Sbjct: 238 QIHSNAIQKLKLYL 251


>gi|325288800|ref|YP_004264981.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Syntrophobotulus
           glycolicus DSM 8271]
 gi|324964201|gb|ADY54980.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Syntrophobotulus
           glycolicus DSM 8271]
          Length = 254

 Score =  113 bits (284), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 45/242 (18%), Positives = 114/242 (47%), Gaps = 17/242 (7%)

Query: 51  HRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              +  +L LV ++A          +   +++  G  GL+ A++K++P RG +  TY+  
Sbjct: 20  EEYIDQYLPLVKRLAGRLAMSLPSHIEEEDLIGYGVFGLIDALQKYEPSRGVKFETYASL 79

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+ AM + +    S+  +  +A QK     +++++     + +   +   +  +A  L 
Sbjct: 80  RIRGAMIDGLR---SMDWVPHSARQK-----VKKVRQAYIDLENLQGRTPSIEEVAGFLE 131

Query: 168 VSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           +   E+ +  ++ +     S++ L++    +S      L+ D + QE       E++ ++
Sbjct: 132 IQLEELHTTLLHGQYMTLVSMDQLLDGHSGDSGISPVDLIIDAEAQESF--NNIEKEEQK 189

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            +L R +  L+ +E+ +      +E  +TL+ +++   +S  R+ QI ++A  +++  + 
Sbjct: 190 QILAREIEKLSEKEKLVIAMYYREE--MTLKEIAAVMNLSESRISQIHSQAILRLRGYLG 247

Query: 286 KQ 287
           +Q
Sbjct: 248 RQ 249


>gi|323154963|gb|EFZ41155.1| RNA polymerase sigma factor rpoS domain protein [Escherichia coli
           EPECa14]
          Length = 148

 Score =  113 bits (283), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 43/89 (48%), Positives = 63/89 (70%), Gaps = 1/89 (1%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           + EGN+GL++AV+KFDPERGFR +TY+ W
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYATW 148


>gi|78221650|ref|YP_383397.1| sigma 28 (flagella/sporulation) [Geobacter metallireducens GS-15]
 gi|78192905|gb|ABB30672.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Geobacter
           metallireducens GS-15]
          Length = 250

 Score =  113 bits (283), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 42/241 (17%), Positives = 95/241 (39%), Gaps = 14/241 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
            +   L+ +HL LV  +           L   +++S   IGL+ A ++FDP RG +  T+
Sbjct: 18  QSRDELIVTHLPLVKFLVGRIATQLPPHLDQDDLMSAAVIGLITAAERFDPSRGVQFKTF 77

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +   I+  + + +     L +         L    ++L+     +     +      +AK
Sbjct: 78  AEQRIRGTIIDELRSQDWLTR--------SLRDKFKKLEREFVMLEHRLGRNPTSEEVAK 129

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            L +S  +   M   +    S  +L  S +         L    D   +    +   +  
Sbjct: 130 SLEISVDDYHHMLEEI-HLLSFVSLDESWEDEDGSPFGLLDILEDKGVENPQSQLMARQM 188

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + LT ++  L  +ER +      +E  + L+ + +  ++S  R+ Q+ ++A  +++  +
Sbjct: 189 LDTLTEAIEGLPEKERLVITFYYYEE--LNLKEIGAVLDLSESRISQLHSQAIVRLRAKM 246

Query: 285 Q 285
           +
Sbjct: 247 K 247


>gi|313895821|ref|ZP_07829375.1| RNA polymerase sigma factor, FliA/WhiG family [Selenomonas sp. oral
           taxon 137 str. F0430]
 gi|320529404|ref|ZP_08030492.1| putative RNA polymerase sigma factor WhiG [Selenomonas artemidis
           F0399]
 gi|312975246|gb|EFR40707.1| RNA polymerase sigma factor, FliA/WhiG family [Selenomonas sp. oral
           taxon 137 str. F0430]
 gi|320138370|gb|EFW30264.1| putative RNA polymerase sigma factor WhiG [Selenomonas artemidis
           F0399]
          Length = 246

 Score =  113 bits (283), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 41/259 (15%), Positives = 106/259 (40%), Gaps = 26/259 (10%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQ 88
           ++   L + Y     +   +R+   +L LV  +A          +   +++S G  GL+ 
Sbjct: 5   EDIEALWQAYGTEKTVEVRNRIAEYYLPLVRLVAGRIAISLPQHVDREDLLSSGFFGLLD 64

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A+++++  RG +  TY+   ++ AM +++ RS   + +    N K+        +  + +
Sbjct: 65  AIERYELTRGNKFETYAGVRVRGAMLDHL-RSKDWIPVSVRQNIKKY-------EKAVAS 116

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           +     +      +A +L ++   +  +  +++                   +++L  D 
Sbjct: 117 LEGKLGRTATDEELAAELGLTREGLRHLESQVSA------------ATVIPLEEYLRTDS 164

Query: 209 D-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
               E   +E  E    +  L  ++  L  +ER +       E  +TL+ +++   +S  
Sbjct: 165 PVSLEDGPVEHAEWTEVKETLAAAIENLPEKERTVVALYYYDE--MTLKEIAAILHLSEA 222

Query: 268 RVRQIEARAFKKVQESIQK 286
           R+ Q+  +A  +++ S+ +
Sbjct: 223 RISQLHTKAIFRMRGSLAR 241


>gi|332799203|ref|YP_004460702.1| RNA polymerase sigma-28 subunit FliA/WhiG [Tepidanaerobacter sp.
           Re1]
 gi|332696938|gb|AEE91395.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Tepidanaerobacter sp.
           Re1]
          Length = 246

 Score =  113 bits (283), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 43/257 (16%), Positives = 105/257 (40%), Gaps = 29/257 (11%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKKF 93
           L   Y    D     +LV  ++ L+  I         P     +++S G  GLMQA++++
Sbjct: 9   LWMNYNNTKDKYVKGQLVEKYVPLIKHIVNRMNINLPPYLEYEDLISYGVFGLMQAIERY 68

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D ++G +  TY+   IK ++ + + +        T    + +   ++ L+     +    
Sbjct: 69  DTKKGIKFETYAYTRIKGSIIDELRK--------TDMIPQDIRKKIKMLQNAFSEMEQIL 120

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLA---GDESLNALINSSDKNSSQWQDWLVYDHDG 210
                   I+  L +S+ ++  +   ++   G  S + LI   D   +  Q  +      
Sbjct: 121 GHSANDDDISNYLGISKKDLYKIYKEISAAYGVLSFDELIEYEDVGQASGQPDI------ 174

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                  + E++  + +L  +++ L P+E+ +          +  + ++   E+S+ R+ 
Sbjct: 175 -------QAEKEEVKEILGNAINQLPPQEKLVITLYYY--EGLNFKEIAEVLELSQGRIS 225

Query: 271 QIEARAFKKVQESIQKQ 287
           QI  +A  +++  + ++
Sbjct: 226 QIHTKAILRLRGHLSRK 242


>gi|258621167|ref|ZP_05716201.1| flagellar biosynthesis sigma factor FliA [Vibrio mimicus VM573]
 gi|258626709|ref|ZP_05721533.1| flagellar biosynthesis sigma factor FliA [Vibrio mimicus VM603]
 gi|258581005|gb|EEW05930.1| flagellar biosynthesis sigma factor FliA [Vibrio mimicus VM603]
 gi|258586555|gb|EEW11270.1| flagellar biosynthesis sigma factor FliA [Vibrio mimicus VM573]
          Length = 244

 Score =  113 bits (283), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 51/249 (20%), Positives = 104/249 (41%), Gaps = 19/249 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPER 97
           Y ++G+L++    +  +  LV +IA    G   P   I +++  G +GL++A K +D  +
Sbjct: 7   YDQYGNLNSQQLFLEKYSVLVKRIAHHLIGRLPPSVLIEDLIQAGMVGLLEAQKNYDGSK 66

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G    TY+   I+ AM + I R    V      + + +   +  L+G L        +  
Sbjct: 67  GASFETYAGIRIRGAMLDDIRR-GDWVPRSVHKHNREISQAIAVLEGELN-------RDP 118

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +AK L +S  +  S+      D + + ++   D   S   D +    +G++     
Sbjct: 119 TDAEVAKFLEMSLEQYHSVLM----DINCSRIVGIEDLGVS--DDAISPFEEGEDNSPFH 172

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
               ++ R  L  S+  L  RE  +       +  + L+ +     VS  RV QI +++ 
Sbjct: 173 GVAEESFRKALVESIKSLPEREALVLSLYY--DEELNLKEIGEVLGVSESRVSQILSQSM 230

Query: 278 KKVQESIQK 286
           ++++  +  
Sbjct: 231 QRLRTKLSS 239


>gi|59712441|ref|YP_205217.1| flagellar biosynthesis sigma factor [Vibrio fischeri ES114]
 gi|59480542|gb|AAW86329.1| RNA polymerase, sigma-28 (sigma-F, FliA) factor [Vibrio fischeri
           ES114]
          Length = 243

 Score =  113 bits (283), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 98/249 (39%), Gaps = 19/249 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPER 97
           Y   G++++    +  +  LV +IA            + +++  G IGL++A + +D  +
Sbjct: 7   YDHKGNVNSQKAFLERYSDLVKRIAHHLMARLPASVLVDDLIQAGMIGLLEAQQNYDGSK 66

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G    TY+   I+ +M + I R    V      N + +   +R L+  L        +  
Sbjct: 67  GASFETYAGIRIRGSMLDEIRR-GDWVPRSVHKNSRMINSAIRELEAKLS-------RDP 118

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               IA  L +   +      ++  D +   L+   D   S   D +  +    + +  +
Sbjct: 119 TDKEIADYLELPLDQY----YQILNDVNCGKLVGMEDLGVS--DDVIATEEQADDNLPFQ 172

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
               ++ R  L  ++  L  RE  +       +  + L+ + +   VS  RV QI +++ 
Sbjct: 173 GVADEHFRVALVEAIKTLPEREALVLSLYY--DEELNLKEIGAVIGVSESRVSQIHSQSM 230

Query: 278 KKVQESIQK 286
           ++++  +  
Sbjct: 231 QRLRAKLSS 239


>gi|161353798|ref|YP_519128.2| sporulation sigma factor SigE [Desulfitobacterium hafniense Y51]
 gi|219670065|ref|YP_002460500.1| sporulation sigma factor SigE [Desulfitobacterium hafniense DCB-2]
 gi|219540325|gb|ACL22064.1| RNA polymerase, sigma 28 subunit, SigE [Desulfitobacterium
           hafniense DCB-2]
          Length = 249

 Score =  113 bits (283), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 57/239 (23%), Positives = 97/239 (40%), Gaps = 62/239 (25%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           D+S    L+  +LRLVV IA  +   G+ I ++VS G IGL++AV  FDP++  +LATY+
Sbjct: 65  DVSVRDVLIERNLRLVVYIARKFENTGVGIEDLVSIGTIGLIKAVNTFDPQKKIKLATYA 124

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
              I+  +                        +LRR                        
Sbjct: 125 SRCIENEI----------------------LMHLRRNNKTR------------------- 143

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
                         ++ DE LN      D N     D L  ++D   + L EK +    R
Sbjct: 144 ------------TEVSFDEPLN---IDWDGNELLLSDVLGTENDIISRPLEEKVD----R 184

Query: 226 NMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            +L  +M+ L  RE+ I E R   +N    T + ++    +S+  + ++E R  +++++
Sbjct: 185 QLLHLAMARLTDREKLIMELRFGLDNGEEKTQKEVADRLGISQSYISRLEKRIIRRLRK 243


>gi|126664990|ref|ZP_01735973.1| flagellar biosynthesis sigma factor FliA [Marinobacter sp. ELB17]
 gi|126630360|gb|EBA00975.1| flagellar biosynthesis sigma factor FliA [Marinobacter sp. ELB17]
          Length = 246

 Score =  113 bits (283), Expect = 3e-23,   Method: Composition-based stats.
 Identities = 53/249 (21%), Positives = 102/249 (40%), Gaps = 25/249 (10%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPER 97
           Y+  G   A   L+  H  LV KIA+         + + +++  G IGL++A +++   +
Sbjct: 10  YQRSGASDA-SWLIEEHAPLVKKIALHLLARLPSSVQLEDLMQAGMIGLLEASQRYTTGK 68

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G    TY+   I+ AM + I R    V      N        RR+   ++A+     +  
Sbjct: 69  GATFETYAGIRIRGAMVDEI-RKGDWVPRSVHRNS-------RRISSAIKAVEGREGRES 120

Query: 158 QVVAIAKKLNVSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
             V +A +L+++ SE  S   +       SL+ L +S +         L  +    +   
Sbjct: 121 HDVEVAAELDMTLSEYHSCLADSNSGRLFSLDELNDSGE---------LPIEQSETDDNP 171

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
           +        RN L  ++  L  RE+ +       +  + L  + +  +VS  RV QI ++
Sbjct: 172 LHGVSEFAFRNSLAAAIETLPEREKLVLSLYY--QEELNLREIGAVLDVSESRVSQIHSQ 229

Query: 276 AFKKVQESI 284
           A  +++  +
Sbjct: 230 AALRLRSRL 238


>gi|306820145|ref|ZP_07453793.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Eubacterium yurii
           subsp. margaretiae ATCC 43715]
 gi|304551923|gb|EFM39866.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Eubacterium yurii
           subsp. margaretiae ATCC 43715]
          Length = 247

 Score =  113 bits (283), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 48/259 (18%), Positives = 101/259 (38%), Gaps = 23/259 (8%)

Query: 33  EEYVLAKRYREHGD----LSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIG 85
           E   + K Y E  +          ++T ++ LV  ++     Y    +   +++  G IG
Sbjct: 4   ESADIWKLYAEEKNPDKKRKIKEEIITKYVSLVKIVSGKLFNYYAQKIEYDDLMGYGIIG 63

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L+ A+ KFD  +  +  TY+   I+ A+ + I      V  G     K L          
Sbjct: 64  LIDAIDKFDYSKNIKFETYASIRIRGAIIDEIRSQ-DWVPRGIRKKMKTL-------NTA 115

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           ++ + +   +      +++ L +S  EV  +      DE+    I S +   S+     +
Sbjct: 116 MEELENKLGREATRHELSEHLGISLKEVDELF-----DETATFNIVSIEDELSENVKIQI 170

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            D    E    ++    +  N L +++  L  +E+ I      +   +T + +S    +S
Sbjct: 171 PDT-KVENSPEQQLIYTDTVNDLAKAIDTLKEKEKIIINLYYYEN--LTYKEISEIIGIS 227

Query: 266 RERVRQIEARAFKKVQESI 284
             R+ QI +    K+++ +
Sbjct: 228 ESRISQIISACLTKLRKLM 246


>gi|127512314|ref|YP_001093511.1| flagellar biosynthesis sigma factor [Shewanella loihica PV-4]
 gi|126637609|gb|ABO23252.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Shewanella
           loihica PV-4]
          Length = 239

 Score =  113 bits (283), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 45/236 (19%), Positives = 95/236 (40%), Gaps = 20/236 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           +V  +  LV +IA          + + +++  G +GL++A  KFD  +G +  T++   I
Sbjct: 16  IVEQYAPLVKRIAHHLLARLPASVQLDDLLQAGMMGLLEASAKFDGSKGAKFETFAGIRI 75

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + +M + I R    V      NQ       RR+   +  +     +  +   IA +L+++
Sbjct: 76  RGSMLDEIRR-GDWVPRSVHRNQ-------RRIAQVIDELEQELGRDAKDNEIADRLDMT 127

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             E       +  D S+  ++   D   S        DH   +    E          L 
Sbjct: 128 LDEYH----HILNDVSVGKVVGIEDLGVSVDVVRQEDDH---QDDAFESLAETQFHEALV 180

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            ++ +L  R+  +       +  + L+ + +  +VS  RV QI ++A  +++  ++
Sbjct: 181 EAIKLLPERDGLVLSLYY--DEALNLKEIGAVLDVSESRVSQIHSQAMLRLKAKLK 234


>gi|330828816|ref|YP_004391768.1| RNA polymerase sigma factor [Aeromonas veronii B565]
 gi|328803952|gb|AEB49151.1| RNA polymerase sigma factor [Aeromonas veronii B565]
          Length = 225

 Score =  113 bits (283), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 48/236 (20%), Positives = 94/236 (39%), Gaps = 19/236 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           LV  H  LV +IA            + +++  G IGL++A + FD  +G    TY+   I
Sbjct: 2   LVERHAPLVKRIAQHLLARLPSSVLLDDLIQAGMIGLLEASRNFDGSKGASFETYAGIRI 61

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + AM + I R    V      N        R +   ++ +   + +  +   +A ++ VS
Sbjct: 62  RGAMLDEIRR-GDWVPRSVHRNS-------RAIAEAIENVEQTHGRDARDTEVAAEMGVS 113

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
            ++  +M      D S   +I   D   S+  D + +  D       ++   +  +  L+
Sbjct: 114 IADYHAMLQ----DVSCGKIIGIEDLGVSE--DVIGHPDDAPSGSGFDELAAERFQIQLS 167

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             +  L  RE  +       +  + L  +     VS  RV QI ++A  +++  ++
Sbjct: 168 EQIGRLPEREALVLSLYY--DEELNLREIGEVLNVSESRVSQIHSQAMHRLRARLR 221


>gi|289808389|ref|ZP_06539018.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. AG3]
          Length = 148

 Score =  113 bits (283), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 30/147 (20%), Positives = 66/147 (44%), Gaps = 7/147 (4%)

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           + +     +      +A+++ + E ++  +        S+   I   D   S   D++  
Sbjct: 3   RQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPI--GDDEDSHLGDFI-- 58

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
             D   ++ ++    ++ R      ++ L  RE ++   R   +     TLE +  +F+V
Sbjct: 59  -EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDV 117

Query: 265 SRERVRQIEARAFKKVQESIQKQVELS 291
           +RER+RQIEA+A +K++   + +V  S
Sbjct: 118 TRERIRQIEAKALRKLRHPSRSEVLRS 144


>gi|56460225|ref|YP_155506.1| flagellar biosynthesis sigma factor [Idiomarina loihiensis L2TR]
 gi|56179235|gb|AAV81957.1| DNA-directed RNA polymerase specialized sigma 28 subunit
           [Idiomarina loihiensis L2TR]
          Length = 241

 Score =  113 bits (283), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 49/243 (20%), Positives = 96/243 (39%), Gaps = 18/243 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + ++  H  LV +IA          + + +++  G IGL++A + FD  +G    T++ 
Sbjct: 14  RNAIIEQHTGLVKRIAHHMMARLPASVQVDDLIQAGMIGLLEAARNFDNSKGASFETFAG 73

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + I R             + +  N RR+   ++ + +   +  +   +A KL
Sbjct: 74  IRIRGAMLDEIRRGDW--------APRSVHRNHRRVLEAIRQVENETGRDAKDTEVAAKL 125

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           N+   E       +  D S   ++   D   S+    +     G      +  E      
Sbjct: 126 NMGMDEYH----HILRDVSTGRIVGIEDLGVSE-DAIMPEQVTGSAYEPQKDVENAAFHK 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L  ++S L  RE  +       +  + L+ +     VS  RV QI ++A  +++  +Q 
Sbjct: 181 ALVSTISSLPEREALVLSLYY--DEELNLKEIGEVLSVSESRVSQIHSQAMLRLKSRMQN 238

Query: 287 QVE 289
            VE
Sbjct: 239 WVE 241


>gi|283797733|ref|ZP_06346886.1| RNA polymerase sigma-E factor [Clostridium sp. M62/1]
 gi|291074630|gb|EFE11994.1| RNA polymerase sigma-E factor [Clostridium sp. M62/1]
          Length = 205

 Score =  113 bits (283), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 50/261 (19%), Positives = 93/261 (35%), Gaps = 66/261 (25%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L  +EE    KR RE GD  A   L+  +LRLV  +   Y+       +++S G IGL+
Sbjct: 7   PLTAEEEREYLKRCRE-GDEEAKAVLIERNLRLVAHVIKKYQYTDYETEDLLSVGTIGLI 65

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV  F  E+G RLATY+   ++  +                                  
Sbjct: 66  KAVNTFKAEKGSRLATYAAKCVENEIL--------------------------------- 92

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA--LINSSDKNSSQWQDWLV 205
                         +  +     +  +S+   +  D+      L++  +   +Q  D ++
Sbjct: 93  --------------MLFRAGKKRARDVSLYDSIGVDKDGETVSLMDVLEAEETQVLDTII 138

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFE 263
            + D               R +       L   E+++   R         T   +++   
Sbjct: 139 MEQD--------------VRELYEAYAKCLKDMEKKVVCMRYGLFGTKEHTQREIAAVLG 184

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +SR  V +IE +A +K++E+ 
Sbjct: 185 ISRSYVSRIEKKAIEKLREAF 205


>gi|95929871|ref|ZP_01312612.1| RNA polymerase, sigma 28 subunit [Desulfuromonas acetoxidans DSM
           684]
 gi|95134167|gb|EAT15825.1| RNA polymerase, sigma 28 subunit [Desulfuromonas acetoxidans DSM
           684]
          Length = 243

 Score =  113 bits (283), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 47/242 (19%), Positives = 99/242 (40%), Gaps = 20/242 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + LV SH+ LV  +    R          ++ S   +GLM A  +FDP RG    T++ 
Sbjct: 15  KNELVKSHMSLVHLVVDRMRAQVPGFVTKDDMTSAAMMGLMDAATRFDPSRGIMFKTFAE 74

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ A+ + I +             + L     R+   +  +     +  +   +A+ +
Sbjct: 75  RRIRGAIYDEIRK--------MDWFSRSLREKQGRIGKTITQMEHRLGRTPEEEEVAEAM 126

Query: 167 NVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +++  E   M  ++   G  SLN  ++  D     + D L  D    +Q + E E     
Sbjct: 127 DMTLDEYRHMLGQVCHLGCVSLNETLDDRDDG-RNFLDLLTDDSPSVQQRIEESELASE- 184

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              L   +  L+ +ER +      +E  +T + ++   +++  R+ Q+ ++A  K++  +
Sbjct: 185 ---LAGQLDKLSEKERLVISLYYYEE--LTQKEIAEVLDLTEGRISQLHSQALVKLKVKL 239

Query: 285 QK 286
            +
Sbjct: 240 SR 241


>gi|227873530|ref|ZP_03991775.1| possible DNA-directed RNA polymerase sigma subunit D [Oribacterium
           sinus F0268]
 gi|227840620|gb|EEJ51005.1| possible DNA-directed RNA polymerase sigma subunit D [Oribacterium
           sinus F0268]
          Length = 259

 Score =  112 bits (282), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 46/264 (17%), Positives = 112/264 (42%), Gaps = 17/264 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIG 85
           LE++    L   Y+E G       L   ++ +V  IA   R          ++V+EG I 
Sbjct: 9   LEEKSNEELFALYKETGSQEVKQELTMRYVYIVRSIAYQMREMYHDFMQTDDIVNEGVIE 68

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           +M+A++++D  +  +  T+    I+  + + + ++  L         +    + R ++  
Sbjct: 69  IMRAIERYDESKDNKFETFISRRIRGMVIDMMRKNDWL--------PRNFHKDSRSIETA 120

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
              + +   +      +A  LN++  ++  +  R++   ++ +L  + D+ +        
Sbjct: 121 TVELNNRLGRAPTDEELADYLNMNVKKLQKIQ-RMSNMVNVLSLDMTYDEGNETLLQIPS 179

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            DH  Q +       +K     LT ++  L  +E+ +     ++E  +    ++   EVS
Sbjct: 180 EDHSTQPEF---SFMQKENVRALTEAIESLQEKEKLVISLYYVEELNMN--QIAEVMEVS 234

Query: 266 RERVRQIEARAFKKVQESIQKQVE 289
           + RV Q+ + A +K+++ + +  E
Sbjct: 235 QPRVSQLHSIAIRKLRKYMGEHGE 258


>gi|150015999|ref|YP_001308253.1| sporulation sigma factor SigK [Clostridium beijerinckii NCIMB 8052]
 gi|149902464|gb|ABR33297.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           beijerinckii NCIMB 8052]
          Length = 232

 Score =  112 bits (282), Expect = 4e-23,   Method: Composition-based stats.
 Identities = 56/260 (21%), Positives = 94/260 (36%), Gaps = 63/260 (24%)

Query: 16  LSRYIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           L+ Y+      P+ L++ EE +  K+++E GD +A   L+  +LRLV  I   Y      
Sbjct: 17  LTGYVTNNNTFPLPLDETEEQMYLKKFKE-GDKNAKSILIERNLRLVAHIVKKYSFPNKD 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + E++S G +GL++A+  FD  +G RLATY+   I+  +                     
Sbjct: 76  VDELISIGTVGLIKAIDSFDAGKGTRLATYASRCIENEILM------------------- 116

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           LF N ++ K                              + +   +  D          +
Sbjct: 117 LFRNSKKQKSE----------------------------VYLQDPIGVD---------KE 139

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENP 252
            N     D L  + D    VL + E     R +  + +  L  RE  I   R        
Sbjct: 140 GNEFCLMDILSSEKDS---VLEKVESNLQVRALYKKLIESLTKRESAIIIMRYGLIDGKC 196

Query: 253 VTLENLSSEFEVSRERVRQI 272
            T   ++    +SR  V +I
Sbjct: 197 KTQREIAVNLGISRSYVSRI 216


>gi|325981885|ref|YP_004294287.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Nitrosomonas sp.
           AL212]
 gi|325531404|gb|ADZ26125.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Nitrosomonas sp.
           AL212]
          Length = 238

 Score =  112 bits (282), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 40/239 (16%), Positives = 93/239 (38%), Gaps = 17/239 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             + +     LV +IA          + + +++  G IGL+ A+ +++   G +  +Y+ 
Sbjct: 12  KDQFIAEFTPLVKRIAYHMMTRLPASVQVDDLIQAGMIGLLDAINRYEGSYGRQFESYAA 71

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ ++ + +  +  L         + +   +RR++  +  +   N      + +AK+L
Sbjct: 72  QRIRGSILDELREADWL--------PRSIRKKMRRIEAAVNLLEQRNGCAPNELDLAKEL 123

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++S  E         G + +       D          +      E   +     +N RN
Sbjct: 124 DMSLDEYHETLQSARGAQLIYYEDFQQDDEEPFLDRLFID----SEGDPLNALLDENFRN 179

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            L  ++  L PRE+++       E  + L  +     VS  RV Q+  +A  +++  ++
Sbjct: 180 QLIAAIDNLPPREKQMMGMHY--EQEMNLREIGEVLGVSESRVCQLHTQAVARLRSRLR 236


>gi|226313414|ref|YP_002773308.1| sporulation sigma factor SigE [Brevibacillus brevis NBRC 100599]
 gi|226096362|dbj|BAH44804.1| RNA polymerase sigma-E factor precursor [Brevibacillus brevis NBRC
           100599]
          Length = 240

 Score =  112 bits (282), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 56/246 (22%), Positives = 101/246 (41%), Gaps = 62/246 (25%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD +    L+  +LRLVV IA  +   G+ I ++VS G IGL++AV  FDP++  +LATY
Sbjct: 55  GDPAVRGMLIERNLRLVVYIARKFENTGINIEDLVSIGTIGLIKAVNTFDPDKNIKLATY 114

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +   I+  +  Y+ R+                    +++                     
Sbjct: 115 ASRCIENEILMYLRRN-------------------NKIRSE------------------- 136

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
                          ++ DE LN      D N     D L  ++D   + + ++ +RK  
Sbjct: 137 ---------------VSFDEPLN---IDWDGNELLLSDVLGTENDTIYKNIEDQVDRKLL 178

Query: 225 RNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +  L +     + RER I E R     E   T ++++    +S+  + ++E R  K++++
Sbjct: 179 KKALDKL----SDRERIIMELRFGLAGEEEKTQKDVADLLGISQSYISRLEKRIIKRLRK 234

Query: 283 SIQKQV 288
              K V
Sbjct: 235 EFNKMV 240


>gi|91200244|emb|CAJ73289.1| strongly similar to RNA polymerase sigma factor for flagellar
           operon [Candidatus Kuenenia stuttgartiensis]
          Length = 259

 Score =  112 bits (282), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 102/240 (42%), Gaps = 13/240 (5%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             +LVT +L LV  +   +  Y        +++  G IGL++A ++FDP    +  T+++
Sbjct: 26  REKLVTENLSLVKYVVNKFIIYLPSFVDKEDLIEYGVIGLLEASERFDPCMDTKFGTFAV 85

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ A+ +++        +  +  +K      R     L+   + +  PE++ A   K+
Sbjct: 86  SRIRGAILDHLRAQDW---LPRSVREK--VSLAREAYATLEQKLNRHPLPEEIAA-ELKI 139

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           + +E E + +        SL  +   S+  + +    L  D    +   +   E +  + 
Sbjct: 140 DTAEWEKLLVEINFGMFLSLEEMNAKSEDGNKEAVGMLFADSKIGD--PLSNIETEEEKE 197

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +L  ++  L  RE+ +      ++  + L  +S   ++S  RV QI  +    ++  ++K
Sbjct: 198 LLVAAIKELPAREKLVITLYYYED--LMLREISQMLDISESRVSQIHHQGLFMLRSKVRK 255


>gi|120554892|ref|YP_959243.1| FliA/WhiG family RNA polymerase sigma factor [Marinobacter
           aquaeolei VT8]
 gi|120324741|gb|ABM19056.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Marinobacter
           aquaeolei VT8]
          Length = 247

 Score =  112 bits (282), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 47/237 (19%), Positives = 94/237 (39%), Gaps = 24/237 (10%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           L+  H  LV KIA+       P   + +++  G IGL++A +++   +G    TY+   I
Sbjct: 21  LIEEHAPLVKKIALHLMARLPPSVQLEDLMQAGMIGLLEAAQRYSSGKGATFETYAGIRI 80

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + AM + I R    V             N RR+   ++ + D   +  Q   +A++L + 
Sbjct: 81  RGAMVDEI-RKGDWVPRSVH-------RNARRIASAIKQVEDRTGREAQDAEVAEELGIG 132

Query: 170 ESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
             E  +   +       SL+ L  S +         L  +        ++       +  
Sbjct: 133 LDEYHASLADANSGRIFSLDELNESGE---------LPIEEAEASDNPLDGIASGAFQRS 183

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L  ++  L  RE+ +       +  + L+ + +   VS  RV QI ++A  +++  +
Sbjct: 184 LADAIEQLPEREKLVLSLYY--QEELNLKEIGAVLGVSESRVSQIHSQAALRLRSRL 238


>gi|85859187|ref|YP_461389.1| RNA polymerase flagellar sigma factor [Syntrophus aciditrophicus
           SB]
 gi|85722278|gb|ABC77221.1| RNA polymerase flagellar sigma factor [Syntrophus aciditrophicus
           SB]
          Length = 261

 Score =  112 bits (281), Expect = 5e-23,   Method: Composition-based stats.
 Identities = 46/254 (18%), Positives = 102/254 (40%), Gaps = 20/254 (7%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL----PISEVVSEGNIGLMQAVKKFD 94
           K +  + D      L+  +L  V  +                +++  G IGLM A++K+D
Sbjct: 19  KSWVMNADKKDREALILKYLPFVKAVVGRMASKIPIDAGDKEDLIHVGIIGLMSAIEKYD 78

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             R  R  TY+   I+ A+ + + R+   V     +    +   +  L+  L+       
Sbjct: 79  TRRNVRFETYAGIRIRGAVLDEL-RARDWVPRAVRSRDNEITKAISSLQKILR------- 130

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQE 212
           +      I++ L +S  E   +      D    +LI+S D        +   D     ++
Sbjct: 131 RAPDDHEISEYLGLSIEEYFKLL----DDSRCISLISSEDLPGDYLDRYSCSDVIRAVEQ 186

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
              ++       R  L ++M +L  +ER +      +E  +T++ +    +++  RV Q+
Sbjct: 187 GSALDLITDHEFRMQLKKAMELLPDKERLVLTLYYYEE--LTMKEIGKVLDLTESRVCQL 244

Query: 273 EARAFKKVQESIQK 286
            ++A  +++ +++K
Sbjct: 245 HSQAIFRLRAAVKK 258


>gi|237653596|ref|YP_002889910.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thauera sp. MZ1T]
 gi|237624843|gb|ACR01533.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thauera sp. MZ1T]
          Length = 257

 Score =  112 bits (281), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 39/235 (16%), Positives = 98/235 (41%), Gaps = 17/235 (7%)

Query: 53  LVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           LV ++  LV +IA          + + +++  G +GL+ A+ +++   G +  TY++  I
Sbjct: 13  LVENYAPLVKRIAYQLMSRLPASVDVDDLIQNGMMGLLDALGRYEQGLGAQFETYAVQRI 72

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + AM + +  +  L         + L  ++RR++  + ++   N +P     +A  L++ 
Sbjct: 73  RGAMLDGLRENDWL--------PRSLRRDMRRIEAAIHSLEQQNGRPPSESELAAALDLP 124

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             +   M     G + +     + +++       L  + +      +   E  + R  L 
Sbjct: 125 LEDYQRMLQDARGHQLVYLEDFNREEDDDYLDRHLAQEGND----PLTLLEDTDLRRRLV 180

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            ++  L  RE+ +       +  + L  +     V+  RV Q+ ++A  +++  +
Sbjct: 181 GAIEHLPEREQLVMALYY--DEELNLREIGEVLGVTESRVCQLHSQAVARLRACV 233


>gi|39998144|ref|NP_954095.1| RNA polymerase sigma factor for flagellar operon [Geobacter
           sulfurreducens PCA]
 gi|39985090|gb|AAR36445.1| RNA polymerase sigma factor for flagellar operon [Geobacter
           sulfurreducens PCA]
          Length = 250

 Score =  112 bits (281), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 44/239 (18%), Positives = 94/239 (39%), Gaps = 14/239 (5%)

Query: 50  AHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L+ +HL LV  +           L   +++S   IGL+ A ++FDP RG +  T++ 
Sbjct: 20  RDELIVNHLPLVKFLVGRIASQLPPHLDQEDLMSAAIIGLITAAERFDPTRGVQFKTFAE 79

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+  + + +     L +         L    ++L+     +     +      +A  L
Sbjct: 80  QRIRGTIIDELRSQDWLTR--------SLRDKFKKLEKEFVLLEHQLGRNPTSEEVATAL 131

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +S  E   M   +    S  +L  S + +       L    D   +    +   +   +
Sbjct: 132 KMSVDEYYQMLEEI-HLLSFVSLDESWEDDDGSPFGLLDILADTSIENPQSQLMARQMLD 190

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            LT S+  L  +ER +      +E  + L+ + +  E+S  R+ Q+ ++A  +++  ++
Sbjct: 191 SLTESIESLPEKERLVITLYYYEE--LNLKEIGAVLELSESRISQLHSQAIVRLRAKMK 247


>gi|167749234|ref|ZP_02421361.1| hypothetical protein EUBSIR_00185 [Eubacterium siraeum DSM 15702]
 gi|167657809|gb|EDS01939.1| hypothetical protein EUBSIR_00185 [Eubacterium siraeum DSM 15702]
          Length = 250

 Score =  112 bits (281), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 50/265 (18%), Positives = 93/265 (35%), Gaps = 68/265 (25%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L  +EE    ++  + GDL+A  +L+  +LRLV  I   +        +++S G IGL++
Sbjct: 45  LSAKEERECLEKAAQ-GDLAARDKLINHNLRLVAYIVKKHYPDSKEADDLISIGIIGLIR 103

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A + FD  +    +TY+   I   ++ Y  +        T   Q  ++ N          
Sbjct: 104 AAETFDYRKNISFSTYAGKCINNQIRMYFRK--------TKHQQTEIYMN---------- 145

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                                                 + +    D N+    D      
Sbjct: 146 --------------------------------------DPMDCDKDGNAVTLADIFKDGT 167

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ-------ENPVTLENLSSE 261
           D  E+  +  E  K  R +       L+ RE+ I   R          +  +T   ++ E
Sbjct: 168 DVAEEAALNIELDKMYRYIDEE----LDEREKEILTKRYGLSKTSYRTDRIMTQREVADE 223

Query: 262 FEVSRERVRQIEARAFKKVQESIQK 286
             +SR  + +IE +A +K++   +K
Sbjct: 224 LGISRSYISRIEKKALEKLRSRFEK 248


>gi|34496477|ref|NP_900692.1| RNA polymerase sigma factor for flagellar operon [Chromobacterium
           violaceum ATCC 12472]
 gi|34102331|gb|AAQ58697.1| RNA polymerase sigma factor for flagellar operon [Chromobacterium
           violaceum ATCC 12472]
          Length = 248

 Score =  112 bits (281), Expect = 6e-23,   Method: Composition-based stats.
 Identities = 44/236 (18%), Positives = 96/236 (40%), Gaps = 16/236 (6%)

Query: 54  VTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           V ++  LV K+A          + + ++V  G IGL++A ++FDP +G +  T++   I+
Sbjct: 22  VEAYAPLVRKLASIMIARLPASVELGDLVQVGMIGLIEAARQFDPAQGVQFETFASQRIR 81

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            AM + + R   L         ++   N R+++  +  +     +      IA ++ V  
Sbjct: 82  GAMLDELRREDWL--------PRQARRNSRQIEEAISKLEQRLGRAPLESEIAAEMGVEL 133

Query: 171 SEVISMNCRLAGDESLNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
            +   M     G   L+       D   S      + D D  +   +      + R  L 
Sbjct: 134 EQYQDMLGDCKGTTLLHFEDFGGGDDEGSHNPVTNIADDDSPD--PLAALSDDSFRRQLV 191

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            ++  L  R++ +       E  + L+ + +   V+  RV Q+ ++A  +++  ++
Sbjct: 192 SAIKFLPERDQLVMALYY--EQELNLKEIGAVLGVTESRVCQLHSQAIARLRAKLK 245


>gi|74055051|gb|AAZ95856.1| FliA [Aeromonas hydrophila]
          Length = 239

 Score =  112 bits (281), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 52/251 (20%), Positives = 97/251 (38%), Gaps = 22/251 (8%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFD 94
           A+ Y  H D      LV  H  LV +IA            + +++  G IGL++A + FD
Sbjct: 4   AQAYLRHQDSYV---LVERHAPLVKRIAQHLLARLPSSVLLDDLIQAGMIGLLEASRNFD 60

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +G    TY+   I+ +M + I R    V             N R +   ++ +   + 
Sbjct: 61  GSKGASFETYAGIRIRGSMLDEIRR-GDWVPRSVH-------RNSRSIAEAIENVEQAHG 112

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +  +   +A ++ VS  E  +M      D S   +I   D   S+  D + +  D     
Sbjct: 113 RDARDTEVAAQMGVSLGEYHTMLQ----DVSCGKIIGIEDLGVSE--DVIGHPDDAASNS 166

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
             ++   +  +  L   +  L  RE  +       +  + L  +     VS  RV QI +
Sbjct: 167 GFDELAAERFQGALAEHIGRLPEREALVLSLYY--DEELNLREIGEVLNVSESRVSQIHS 224

Query: 275 RAFKKVQESIQ 285
           +A  +++  ++
Sbjct: 225 QAMHRLRARLR 235


>gi|260438492|ref|ZP_05792308.1| RNA polymerase sigma-E factor [Butyrivibrio crossotus DSM 2876]
 gi|292809081|gb|EFF68286.1| RNA polymerase sigma-E factor [Butyrivibrio crossotus DSM 2876]
          Length = 207

 Score =  112 bits (281), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 61/261 (23%), Positives = 93/261 (35%), Gaps = 62/261 (23%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L   EE    KRY+ +GD  A + L+  +LRLV  I   Y      I E +S G IGL+
Sbjct: 7   PLTPSEEQEYLKRYK-NGDEEAGNVLILRNLRLVAHIVKHYNFDEKDIEEYLSIGTIGLI 65

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +A+K FD  +G RLATY+   I                         L   LR  K   +
Sbjct: 66  KAIKTFDCSKGNRLATYASKCIDN----------------------ELLMALRSEKKKNK 103

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                                              D SL   +    + +      ++  
Sbjct: 104 -----------------------------------DISLQETVGIDKEGNEINIIDIIDT 128

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVS 265
             G++  L     + N + +      VL  RE+ I   R   L+ + +T   L+    +S
Sbjct: 129 --GEKDFLDCYILKYNIKKLYEGIEKVLTEREKNIIIKRYGLLRNDEITQRELADGMGIS 186

Query: 266 RERVRQIEARAFKKVQESIQK 286
           R  V +IE  A  K++  I +
Sbjct: 187 RSYVSRIEKEALNKLKNYINR 207


>gi|56752318|ref|YP_173019.1| RNA polymerase sigma factor SigF [Synechococcus elongatus PCC 6301]
 gi|56687277|dbj|BAD80499.1| group3 RNA polymerase sigma factor SigF2 [Synechococcus elongatus
           PCC 6301]
          Length = 275

 Score =  112 bits (281), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 53/255 (20%), Positives = 116/255 (45%), Gaps = 14/255 (5%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG-LPISEVVSEGNIGLMQAVKKFD 94
            L   Y E   ++  +++V  +L LV KIA         P  ++   G +GL++A+++F 
Sbjct: 28  ELLVAYAETPSIALRNQIVQLNLGLVRKIAHRLSRQCSEPYEDLEQIGFMGLIRAIERFQ 87

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P +G   +++++ +I+  +  ++  S   ++I     +  L    ++L+  L+       
Sbjct: 88  PHQGCAFSSFAVPYIRGEILHFLRDSCHSIRIPRRWQE--LQRQGQQLREVLRHEWGRAP 145

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
             EQ +A A  L+++E + I +  R     SL+A ++ +  +S    + L       +Q 
Sbjct: 146 T-EQELAFALNLSMTEWQEIHLARRNRMPMSLDATLSQAGDSSVTLVETLPDTSQQWQQA 204

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV-RQIE 273
            +E+      R  L  ++  L  + R   E+  L+   +T +  + +F +S   + R+I 
Sbjct: 205 ALEE------RQQLVEAIGQLEEKARTAIESVYLRG--LTRKEAAQQFGISPMTITRRI- 255

Query: 274 ARAFKKVQESIQKQV 288
            R  +K+ E + +  
Sbjct: 256 NRGVQKIAEHLDRMA 270


>gi|326503440|dbj|BAJ86226.1| predicted protein [Hordeum vulgare subsp. vulgare]
 gi|326503904|dbj|BAK02738.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 496

 Score =  112 bits (281), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 52/252 (20%), Positives = 102/252 (40%), Gaps = 18/252 (7%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDP 95
           +R R+ G  +A ++L+  +LRLV+     Y          +++   G  GL+ A+ +F+P
Sbjct: 250 RRLRDVG-RAARNKLIKHNLRLVLYAINKYYPDMTGDERFADLCQAGANGLITAIDRFEP 308

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           +RGFR++TY+++WI+ ++   +  S    +       +R    + R +  L         
Sbjct: 309 KRGFRISTYALFWIRHSVVRAMTLSSFT-RFPFAMESER--QEINRAREELSFELGRTPT 365

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
            E+ +           +V+ M        S N +      N     D +  D     ++L
Sbjct: 366 DEETMKKVGLSPARYRDVVRMTRPAYSLHSRNRVTQEELINEVTDVDAIGVDTHKHNRLL 425

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIE 273
                    R  +   +  L P+E  +   R   +     TL  ++    +SRE VR+ E
Sbjct: 426 ---------RLAIDDLLDSLKPKESVVIRQRFGLDGRGRRTLSEIAGNLRISREMVRKYE 476

Query: 274 ARAFKKVQESIQ 285
            +A  K++   +
Sbjct: 477 LKALMKLKHPTR 488


>gi|294500913|ref|YP_003564613.1| RNA polymerase sigma-D factor [Bacillus megaterium QM B1551]
 gi|294350850|gb|ADE71179.1| RNA polymerase sigma-D factor [Bacillus megaterium QM B1551]
          Length = 253

 Score =  112 bits (280), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 51/259 (19%), Positives = 106/259 (40%), Gaps = 20/259 (7%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQA 89
           EE+ + + + E  D  A + LV  ++ LV              +   E+ S G IGL  A
Sbjct: 8   EEHKIWQEWIETRDSHAGNMLVKKYMPLVNYHVQRISVGLPKNIHKEELRSLGLIGLYDA 67

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           ++KFD  R  +  TY+ + I+ A+ + + +   L +              +R++   +A+
Sbjct: 68  LEKFDYGRDLKFDTYASFRIRGAIIDGLRKEDWLSR--------SAREKTKRIEQATEAL 119

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVI--SMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
               L+      +AK++ ++E++V+       LA   S+       +    ++       
Sbjct: 120 EQRYLRRVAPSEVAKEVGMTEADVVHTMNEGFLANVLSMEEQPKEYEDGEQKYTI----- 174

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            D +     E+     R   L   +  LN +E+ +       +  +T   ++    +S  
Sbjct: 175 KDEKTLSPEEELINDERYQELAEVIEQLNEKEQLVVSLFY--KEELTFTEIAQLLGLSTS 232

Query: 268 RVRQIEARAFKKVQESIQK 286
           R+ QI ++A  K++ S+ K
Sbjct: 233 RISQIHSKALFKMRTSLSK 251


>gi|124268265|ref|YP_001022269.1| DNA-directed RNA polymerase specialized sigma subunit [Methylibium
           petroleiphilum PM1]
 gi|124261040|gb|ABM96034.1| DNA-directed RNA polymerase specialized sigma subunit [Methylibium
           petroleiphilum PM1]
          Length = 237

 Score =  112 bits (280), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 43/238 (18%), Positives = 103/238 (43%), Gaps = 16/238 (6%)

Query: 51  HRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           + ++  +  LV ++A          + I +++  G IGL  A+ +FD  +G +  T++  
Sbjct: 11  NAMIKQYSPLVRRLAHQMIAKLPANVEIDDLIQVGLIGLTDAMSRFDSAQGVQFETFATQ 70

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+ AM + + R    +  G    Q+ +   + +L+  L        +      IAK++ 
Sbjct: 71  RIRGAMLDEL-RGSDWMSRGNRKQQREIEVAVHKLQQQL-------GRAPAESEIAKQMG 122

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S ++   +  ++ G + +     S D   + + D  V D +     L++       R  
Sbjct: 123 LSLADYQELLGKVRGTQLVYLEDMSGDDGDNDFLDRHVADENENPVALLQDH---RMRLA 179

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L  ++  L  RE+ +       E  + L+ +++   V+  RV Q+ +++  +++  ++
Sbjct: 180 LIEAIKTLPEREQFVMGMYY--EQDMNLKEIAAVLGVTESRVCQLHSQSIARLRAKLR 235


>gi|182418945|ref|ZP_02950202.1| RNA polymerase sigma-E factor [Clostridium butyricum 5521]
 gi|237668989|ref|ZP_04528973.1| RNA polymerase sigma-E factor [Clostridium butyricum E4 str. BoNT E
           BL5262]
 gi|182377228|gb|EDT74796.1| RNA polymerase sigma-E factor [Clostridium butyricum 5521]
 gi|237657337|gb|EEP54893.1| RNA polymerase sigma-E factor [Clostridium butyricum E4 str. BoNT E
           BL5262]
          Length = 235

 Score =  112 bits (280), Expect = 7e-23,   Method: Composition-based stats.
 Identities = 52/262 (19%), Positives = 108/262 (41%), Gaps = 59/262 (22%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K EE  L K+   +GD      L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 33  PPLSKDEEEELLKKL-NNGDEKIRSTLIERNLRLVVYIARKFENTGVYVEDLISVGTIGL 91

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+                    ++K   
Sbjct: 92  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRNS-------------------KVKAE- 131

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                        ++  + LN+             G+E L + I  ++ ++    + +  
Sbjct: 132 -------------ISFYEPLNIDWD----------GNELLLSDILGTENDTVY--NLIED 166

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           + D Q   +  K      + ++     +   RE+             T + ++    +S+
Sbjct: 167 EVDKQLLFMALKSLNDREKEIVRLRFGLNGAREK-------------TQKEVADMLGISQ 213

Query: 267 ERVRQIEARAFKKVQESIQKQV 288
             + ++E +  K++++ I + +
Sbjct: 214 SYISRLEKKIIKRLKKEINRMI 235


>gi|160896045|ref|YP_001561627.1| RNA polymerase sigma 28 subunit FliA/WhiG [Delftia acidovorans
           SPH-1]
 gi|160361629|gb|ABX33242.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Delftia acidovorans
           SPH-1]
          Length = 237

 Score =  112 bits (280), Expect = 8e-23,   Method: Composition-based stats.
 Identities = 48/240 (20%), Positives = 102/240 (42%), Gaps = 16/240 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L+  H+ LV +IA+       P   + +++  G IGL +A+ +F+ E+G +  T++ 
Sbjct: 10  RDALIRRHVPLVRRIALHMIAKLPPNVELDDLIQVGMIGLAEALSRFESEQGVQFETFAS 69

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + R    +   +  +QK +   L RL+  L        +      IA +L
Sbjct: 70  QRIRGAMLDEL-REGDWMSRSSRKSQKDIEHALHRLEQRL-------GRTPLESEIADEL 121

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +  S+  ++ G + +     S       + +  V D       L+        R 
Sbjct: 122 GMDLDDYQSLLGKVRGTQLVYLEDMSGGDEGEDFLERHVADSGADPFALLRDHRL---RV 178

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L  ++  L  RE+ I       E+ + L+ +++   V+  RV Q+ ++A  +++  ++ 
Sbjct: 179 ALVEAIKALPEREQYIMGMYY--EHDMNLKEIAAVLGVTESRVCQLHSQAIARLRTKMRA 236


>gi|83647839|ref|YP_436274.1| flagellar biosynthesis sigma factor FliA [Hahella chejuensis KCTC
           2396]
 gi|83635882|gb|ABC31849.1| flagellar biosynthesis sigma factor FliA [Hahella chejuensis KCTC
           2396]
          Length = 275

 Score =  112 bits (280), Expect = 8e-23,   Method: Composition-based stats.
 Identities = 47/249 (18%), Positives = 92/249 (36%), Gaps = 24/249 (9%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPER 97
           Y E     A   LV  +  LV +IA          + + +++  G IGL++A +K+D  +
Sbjct: 40  YSETRAERA-DTLVRQYAPLVKRIAHHLIARLPASVQVEDLIQAGMIGLLEAAQKYDAGK 98

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G +  TY+   I+ AM + I R    V      N + +   +  ++           +  
Sbjct: 99  GAKFETYAGIRIRGAMVDEI-RKGDWVPRSVHRNARNIAEAIHTIEA-------RTGRDA 150

Query: 158 QVVAIAKKLNVSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
               +A +L V   +  +   +       SL  L    +  S         D        
Sbjct: 151 SDAEVAAELGVPLEQYHASLRDASSGKLFSLEELGFHGEGGS--------DDETLTADNP 202

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
           +   E+      L+ ++  L  RE+ +       +  + L+ +     VS  RV QI ++
Sbjct: 203 LSDIEQNAFLEKLSAAIDGLPEREKLVLSLYY--DEELNLKEIGQVLSVSESRVSQIHSQ 260

Query: 276 AFKKVQESI 284
           A  +++  +
Sbjct: 261 ATLRLRSRL 269


>gi|212634384|ref|YP_002310909.1| flagellar biosynthesis sigma factor [Shewanella piezotolerans WP3]
 gi|212555868|gb|ACJ28322.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4 [Shewanella
           piezotolerans WP3]
          Length = 239

 Score =  112 bits (280), Expect = 8e-23,   Method: Composition-based stats.
 Identities = 48/239 (20%), Positives = 100/239 (41%), Gaps = 20/239 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              +V  +  LV +IA          + + +++  G +GL++A  KFD  +G +  T++ 
Sbjct: 13  KTSIVEQYAPLVKRIAHHLLARLPASVQLDDLLQAGMMGLLEASSKFDGSKGAKFETFAG 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ +M + I R    V      NQ+R+   +      L+     + +      IA++L
Sbjct: 73  IRIRGSMLDEIRR-GDWVPRSVHRNQRRVAQVI----DELEQELGRDARDP---EIAERL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +S  E  S+      D S+  ++   D   +     +V   D  + V  E        +
Sbjct: 125 EMSLDEYYSIL----NDVSVGKVVGIEDLGVA---VDVVNHEDNHDDVAYESLAEVEFHS 177

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            L  ++ +L  R+  +       +  + L+ + +  EVS  RV QI ++A  +++  ++
Sbjct: 178 ALVAAIKLLPERDALVLSLYY--DEALNLKEIGAILEVSESRVSQIHSQAMLRLKGKLK 234


>gi|298507081|gb|ADI85804.1| RNA polymerase sigma-28 factor for flagellar operon [Geobacter
           sulfurreducens KN400]
          Length = 250

 Score =  112 bits (280), Expect = 9e-23,   Method: Composition-based stats.
 Identities = 44/239 (18%), Positives = 94/239 (39%), Gaps = 14/239 (5%)

Query: 50  AHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L+ +HL LV  +           L   +++S   IGL+ A ++FDP RG +  T++ 
Sbjct: 20  RDELIVNHLPLVKFLVGRIASQLPPHLDQEDLMSAAIIGLITAAERFDPTRGVQFKTFAE 79

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+  + + +     L +         L    ++L+     +     +      +A  L
Sbjct: 80  QRIRGTIIDELRSQDWLTR--------SLRDKFKKLEKEFVLLEHQLGRNPTSDEVATAL 131

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +S  E   M   +    S  +L  S + +       L    D   +    +   +   +
Sbjct: 132 KMSVDEYYRMLEEI-HLLSFVSLDESWEDDDGSPFGLLDILADTSIENPQSQLMARQMLD 190

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            LT S+  L  +ER +      +E  + L+ + +  E+S  R+ Q+ ++A  +++  ++
Sbjct: 191 SLTESIESLPEKERLVITLYYYEE--LNLKEIGAVLELSESRISQLHSQAIVRLRAKMK 247


>gi|256532384|gb|ACU81350.1| RpoH [Rhizobium leguminosarum bv. trifolii]
 gi|256532396|gb|ACU81356.1| RpoH [Rhizobium leguminosarum bv. trifolii]
          Length = 148

 Score =  112 bits (280), Expect = 9e-23,   Method: Composition-based stats.
 Identities = 61/148 (41%), Positives = 88/148 (59%), Gaps = 1/148 (0%)

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFFNLRRL+  L      
Sbjct: 1   FEPERDVRFSTYASWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRAKLAKGDTQ 60

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQ 211
                    IA  L VS S+V +M+ RL+G D SL A   S D  S++  D+LV D    
Sbjct: 61  LTLQSIHQEIAAALGVSLSDVQTMDARLSGNDASLQAPSVSGDAESAEKMDFLVSDDPLP 120

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           ++ +    + + RR  L  ++  LN RE
Sbjct: 121 DEQVSNMIDGERRRVWLASALKHLNERE 148


>gi|323341369|ref|ZP_08081613.1| DNA-directed RNA polymerase sigma subunit FliA [Lactobacillus
           ruminis ATCC 25644]
 gi|323091246|gb|EFZ33874.1| DNA-directed RNA polymerase sigma subunit FliA [Lactobacillus
           ruminis ATCC 25644]
          Length = 250

 Score =  112 bits (280), Expect = 9e-23,   Method: Composition-based stats.
 Identities = 47/241 (19%), Positives = 101/241 (41%), Gaps = 17/241 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYR--GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
             + +  +L LV ++A             ++ + G IGL+ A++KFD  +      Y+  
Sbjct: 19  REQEILKYLPLVERVANRISIKNTEYEYDDLYNIGVIGLIDAMQKFDSSKKVPFENYAAI 78

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+ A+ + + R   + +            N+       Q +     +      I KK+ 
Sbjct: 79  RIRGAIIDEVRRHSKISRY--------KMGNVNSFYQAKQELEQEMKREVTDKEIMKKMG 130

Query: 168 VSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           ++ S++  +   +      SL + + S++  +   QD L    D +     ++  ++ R+
Sbjct: 131 ITSSQLGDIYDSIQYLSSVSLESTLYSNNDETVMVQDTL---RDSKAPSGEKELMKQERK 187

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             L  ++  L+ RE+ +       E   TL+ +++  +VS  RV QI  RA  K++  I+
Sbjct: 188 KELIEAIKRLSEREQLVLSLYY--EEDATLKEIAAILDVSIARVSQIHGRAIAKIRGYIE 245

Query: 286 K 286
           +
Sbjct: 246 E 246


>gi|323499559|ref|ZP_08104529.1| flagellar biosynthesis sigma factor [Vibrio sinaloensis DSM 21326]
 gi|323315432|gb|EGA68473.1| flagellar biosynthesis sigma factor [Vibrio sinaloensis DSM 21326]
          Length = 244

 Score =  112 bits (280), Expect = 9e-23,   Method: Composition-based stats.
 Identities = 49/249 (19%), Positives = 102/249 (40%), Gaps = 19/249 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPER 97
           Y ++ + ++    +  +  LV +IA    G   P   + +++  G IGL++A K +D  +
Sbjct: 7   YDQYANQNSQRAFLEKYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLLEAQKNYDGSK 66

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G    TY+   I+ AM + I R    V      + + +   +  L+G L        +  
Sbjct: 67  GASFETYAGIRIRGAMLDDIRR-GDWVPRSVHKHNREISQAISVLEGELN-------RDP 118

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A+ L +S ++  S       D + + L+   D   S+  D +  + D +     +
Sbjct: 119 TDAEVAQHLGMSLAQYHSALA----DINCSRLVGIEDLGVSE--DVISPEDDDEANTPFQ 172

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
               +  R  L  S+  L  RE  +       +  + L+ +     VS  RV QI +++ 
Sbjct: 173 GVADEYFRKALVDSIKALPEREALVLSLYY--DEELNLKEIGDVIGVSESRVSQILSQSM 230

Query: 278 KKVQESIQK 286
           ++++  +  
Sbjct: 231 QRLRTKLSA 239


>gi|326384337|ref|ZP_08206018.1| putative sigma factor [Gordonia neofelifaecis NRRL B-59395]
 gi|326196935|gb|EGD54128.1| putative sigma factor [Gordonia neofelifaecis NRRL B-59395]
          Length = 215

 Score =  111 bits (279), Expect = 9e-23,   Method: Composition-based stats.
 Identities = 40/226 (17%), Positives = 87/226 (38%), Gaps = 16/226 (7%)

Query: 55  TSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114
            + L L   IA  YR  G    ++     +GL+ AV +FDP +G    ++++  +   ++
Sbjct: 1   MACLPLAKHIAQRYRERGEAFDDLEQVARLGLVHAVDRFDPTQGTDFLSFAIPTVMGEVK 60

Query: 115 EYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVI 174
            +     + +++  +A + R      R++   +     + +      +AK L  + + V 
Sbjct: 61  RHFRDHSASIRMPRSAGELR-----SRIRLAEEQFEQKHGRSPDDTEVAKILGETPTAVS 115

Query: 175 SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV 234
                     S++ L  S   +     D L  D  G   V        +R   L  ++  
Sbjct: 116 RARAAAIAQASVS-LDGSGSDDERALLDVLGSDDPGYAHV--------DRALALRPAVRR 166

Query: 235 LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           L  R+R+I   R       T  +++    +S+  V ++   +  ++
Sbjct: 167 LPERDRKILGMRFF--EQRTQSDIARRMGISQMHVSRLLTASLGQL 210


>gi|297196315|ref|ZP_06913713.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
 gi|197722893|gb|EDY66801.1| RNA polymerase sigma factor [Streptomyces pristinaespiralis ATCC
           25486]
          Length = 272

 Score =  111 bits (279), Expect = 9e-23,   Method: Composition-based stats.
 Identities = 43/261 (16%), Positives = 101/261 (38%), Gaps = 20/261 (7%)

Query: 38  AKRYREHGD----LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
            +R  E  D          +V++ L +  +IA  +R  G  I ++     +GL++AV ++
Sbjct: 21  FRRLAELDDGPERQEVRQEIVSAWLPMAERIAGRFRNRGESIEDLQQVAALGLVKAVDRY 80

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN- 152
           DP RG    ++++  +   ++ +       + +       R      R++   Q +    
Sbjct: 81  DPSRG-AFESFAVPTVVGEVKRHFRDHMWALHVPRRVQDLR-----NRVRFARQDLVQTV 134

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           + +   V  IA++  VSE + +     L    +L+        +        +   D   
Sbjct: 135 SGRAPTVAEIAERAGVSEEDALVGLEALESFTALSLDAELPGADDGYSLSDTLGSADPAI 194

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
            VL++       R  +   +  L  RE+ I   R  ++  +T  +++    +S+  V ++
Sbjct: 195 DVLVD-------REAVKPGLRKLPEREQNILYMRFFRD--MTQSSIAQTLGISQMHVSRL 245

Query: 273 EARAFKKVQESIQKQVELSSS 293
            +R   +++  + +   L   
Sbjct: 246 ISRCCDQLRNEVMRDEALRED 266


>gi|117619369|ref|YP_855921.1| flagellar biosynthesis sigma factor [Aeromonas hydrophila subsp.
           hydrophila ATCC 7966]
 gi|117560776|gb|ABK37724.1| RNA polymerase sigma factor for flagellar operon [Aeromonas
           hydrophila subsp. hydrophila ATCC 7966]
          Length = 239

 Score =  111 bits (279), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 54/251 (21%), Positives = 94/251 (37%), Gaps = 22/251 (8%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFD 94
           A+ Y  H D      LV  H  LV +IA            + +++  G IGL++A + FD
Sbjct: 4   AQAYLRHQDSYV---LVERHAPLVKRIAQHLLARLPSSVLLDDLIQAGMIGLLEASRNFD 60

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +G    TY+   I+ +M + I R    V             N R +   ++ +   + 
Sbjct: 61  GSKGASFETYAGIRIRGSMLDEIRR-GDWVPRSVH-------RNSRTIAEAIENVEQAHG 112

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +  +   +A ++ VS  E  +M      D S   +I   D   S+       D  G    
Sbjct: 113 RDARDSEVAAQMGVSLGEYHTMLQ----DVSCGKIIGIEDLGVSEDVIGHPDDEPGSNGF 168

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
                ER   +  L   +  L  RE  +       +  + L  +     VS  RV QI +
Sbjct: 169 DELAAER--FQGALAEHIGRLPEREALVLSLYY--DEELNLREIGEVLNVSESRVSQIHS 224

Query: 275 RAFKKVQESIQ 285
           +A  +++  ++
Sbjct: 225 QAMHRLRARLR 235


>gi|313901053|ref|ZP_07834541.1| RNA polymerase sigma-F factor [Clostridium sp. HGF2]
 gi|312954011|gb|EFR35691.1| RNA polymerase sigma-F factor [Clostridium sp. HGF2]
          Length = 241

 Score =  111 bits (279), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 43/236 (18%), Positives = 91/236 (38%), Gaps = 19/236 (8%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L +R R  GD  A    V  +  LV  I   +    +   ++   G +GLM+A+  FD 
Sbjct: 9   ELIERIRL-GDEEAKSCFVQQNSALVYSIIRRFSRQRISNEDLFQIGCVGLMKALNNFDT 67

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
               + +TY++  I   ++ +     S ++I  +  +  L     ++    + +      
Sbjct: 68  SYEVKFSTYAVPIIMGEIKRFFRDDGS-IRISRSLKEGYL-----QMVKAKEVLLQKLNH 121

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
                 IA  + +  ++VI          SL+  I  +D +    +D +           
Sbjct: 122 EPTYQEIADAMELDVADVILAFEANQFIYSLDETIYENDGSPILLEDKVSN--------- 172

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
            +KEE    +  L   +  L+ RE+ +   R   +  +  E ++ +  +S+ +V +
Sbjct: 173 -KKEEDVVMKVSLRDEIQKLDQREQLLLHYRY--DLSMKQEEIARKLNISQVQVSR 225


>gi|218458675|ref|ZP_03498766.1| RNA polymerase factor sigma-32 [Rhizobium etli Kim 5]
          Length = 138

 Score =  111 bits (279), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 48/108 (44%), Positives = 79/108 (73%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           R I      P L +QEE+ LA R+++H D  A +++  +H+RLV+ +A  +R +GLP+S+
Sbjct: 30  RMIKIAMAAPYLARQEEHDLATRWKDHDDRGARNQIAMAHMRLVISMAGKFRNFGLPMSD 89

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
           +V EG +GL++A  +F+PER  R +TY+ WWI+A++Q+YILR+WS+V+
Sbjct: 90  LVQEGYVGLLEAAARFEPERDVRFSTYASWWIRASIQDYILRNWSIVR 137


>gi|329904712|ref|ZP_08273913.1| RNA polymerase sigma factor for flagellar operon [Oxalobacteraceae
           bacterium IMCC9480]
 gi|327547856|gb|EGF32614.1| RNA polymerase sigma factor for flagellar operon [Oxalobacteraceae
           bacterium IMCC9480]
          Length = 244

 Score =  111 bits (279), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 42/243 (17%), Positives = 105/243 (43%), Gaps = 19/243 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L+  H  LV ++A   +    P   + +++  G IGL  A+ +++   G +  TY++
Sbjct: 10  KNHLLVQHAPLVKRLAHQMKAKLPPSVEVDDLIQAGMIGLFDAINRYEDTHGAQFETYAV 69

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ +M + +  S  L         + +  N+R+++  +QA+     +      +AK +
Sbjct: 70  QRIRGSMLDELRSSDWL--------PRSMRQNMRKIEVAMQALQQKLGRAPLEAEVAKHM 121

Query: 167 NVSESEVISMNCRLAGDESL--NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            +S +E  ++     G + +      +SS+ N      +     D      ++       
Sbjct: 122 KLSLAEYQNLLGEGGGHQLVYYEDFHDSSEGNEHFLDRYCTDLSDN----PLQSLLNAGF 177

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R+ + R++  L  RE+         E  + L+ + +   V+  R+ Q+ ++A  +++  +
Sbjct: 178 RDAVIRAIEALPEREK--ILMGLYYEQEMNLKEIGAVLGVTESRISQLHSQAIARMRAFL 235

Query: 285 QKQ 287
           +++
Sbjct: 236 REK 238


>gi|209695722|ref|YP_002263652.1| flagellar biosynthesis sigma factor [Aliivibrio salmonicida
           LFI1238]
 gi|208009675|emb|CAQ79974.1| RNA polymerase sigma factor for flagellar regulon FliA [Aliivibrio
           salmonicida LFI1238]
          Length = 243

 Score =  111 bits (279), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 43/247 (17%), Positives = 100/247 (40%), Gaps = 19/247 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPER 97
           Y   G++++    +  +  LV +IA            + +++  G IGL++A + +D  +
Sbjct: 7   YDHKGNVNSQKAFLERYSELVKRIAHHLMARLPASVLVDDLIQSGMIGLLEAQQNYDGSK 66

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G    TY+   I+ +M + I R    V      N + +   ++ L+  L        +  
Sbjct: 67  GASFETYAGIRIRGSMLDEIRR-GDWVPRSVHKNSRMVNAAIKALEAKLS-------REP 118

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               IA+ L +   +      ++  D +   L+   D   S+  D +  +    + +  +
Sbjct: 119 TDKEIAEHLELPLDQY----YQILNDVNCGKLVGMEDLGVSE--DVITTEEHADDNIPFQ 172

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
               ++ R  L  ++  L  RE  +       +  + L+ + +   VS  RV QI +++ 
Sbjct: 173 GVVDEHFRVALVEAIKTLPEREALVLSLYY--DEELNLKEIGAVIGVSESRVSQIHSQSM 230

Query: 278 KKVQESI 284
           ++++  +
Sbjct: 231 QRLRAKL 237


>gi|152964789|ref|YP_001360573.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Kineococcus
           radiotolerans SRS30216]
 gi|151359306|gb|ABS02309.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Kineococcus
           radiotolerans SRS30216]
          Length = 267

 Score =  111 bits (279), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 52/222 (23%), Positives = 90/222 (40%), Gaps = 28/222 (12%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
             LV  HL L   +A  YR  G P  ++V    +GL++A ++FDP+ G R A Y+   I 
Sbjct: 16  EDLVLEHLPLARSVAAHYRNRGEPYDDLVQVAYLGLVKAAQRFDPDTGHRFAAYAAPTIT 75

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
             ++ +       V+      + R            + + ++   PE+V  +A++L+ + 
Sbjct: 76  GEVRRHFRDHGWNVRPPRRLQELRA-----------RLLAEDADTPEEV--LAQRLDATV 122

Query: 171 SEVISMNCR--LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +EV +           SL+A     D    +       D    +  L            L
Sbjct: 123 AEVRAARQASNAYSAVSLDAAHGPEDVPLCELLADDADDTAAVDDALT-----------L 171

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
            R  + L+ RERRI   R  +E   T   +++E  VS+ +V 
Sbjct: 172 RRITAGLDERERRILHLRFYRE--ATQSEIAAEIGVSQMQVS 211


>gi|225569957|ref|ZP_03778982.1| hypothetical protein CLOHYLEM_06052 [Clostridium hylemonae DSM
           15053]
 gi|225161427|gb|EEG74046.1| hypothetical protein CLOHYLEM_06052 [Clostridium hylemonae DSM
           15053]
          Length = 274

 Score =  111 bits (279), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 47/263 (17%), Positives = 110/263 (41%), Gaps = 19/263 (7%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKK 92
            L + YR+ G L     +   +L +V  IA+  R          ++V+EG I LM+A+ K
Sbjct: 18  ELLELYRKTGSLEVKQEIALRYLYIVKSIAVQMRNVYAGFSQVEDIVNEGVIMLMKAIDK 77

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           ++ ++  +  TY    I+  + + I R    +        + +  + R +K         
Sbjct: 78  YEADKNAKFETYVSKRIRGMIID-IARKQDWIP-------RTVRKSYRDIKEASAVFYSE 129

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDG 210
           + +  +   +++ L++   +   +  + +     SL+ ++    + + +    +    D 
Sbjct: 130 HGREPEAEELSELLHMDIEKFRDIMGKASLFSVLSLDMVL----EETKEQYRSIQIPSDK 185

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
           +E+        K  R+ML   +  L   E+ +     ++E  + ++ ++    VS  R+ 
Sbjct: 186 KEEQPEAHLMDKEFRHMLADGIRSLKENEQTVISLYYMEE--LNMKEIAGILHVSEPRIS 243

Query: 271 QIEARAFKKVQESIQKQVELSSS 293
           QI A A +K++E   ++ +L   
Sbjct: 244 QIHAGAIRKLREYFTEKTKLERE 266


>gi|167747049|ref|ZP_02419176.1| hypothetical protein ANACAC_01761 [Anaerostipes caccae DSM 14662]
 gi|167654009|gb|EDR98138.1| hypothetical protein ANACAC_01761 [Anaerostipes caccae DSM 14662]
          Length = 200

 Score =  111 bits (279), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 56/257 (21%), Positives = 93/257 (36%), Gaps = 64/257 (24%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +  L ++EE    K+ R  GD+ A + LV  +LRLV  I   Y  +     +++S G IG
Sbjct: 5   LEPLSQEEEQYYLKKSRL-GDMEARNILVEHNLRLVAHIVKKYNNFDRDKDDLISVGTIG 63

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A+  ++ E+G RL TY+   I                      +  L   LR+ +  
Sbjct: 64  LIKAINTYNLEKGHRLVTYASRCI----------------------ENELLMMLRQERKS 101

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS-DKNSSQWQDWL 204
                                              A D SL   I    + N     D L
Sbjct: 102 -----------------------------------AKDTSLYEPIGIDKEGNEINLLDVL 126

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEF 262
             D +     L  KE+ ++   M+         RE+     R       P+T + ++ E 
Sbjct: 127 GADENDIVDELDLKEKIRDLYKMVDEME---PSREKTTLIMRYGLYGKKPMTQKEVAKEL 183

Query: 263 EVSRERVRQIEARAFKK 279
            +SR  V +IE +  ++
Sbjct: 184 HISRSYVSRIEKKLLRR 200


>gi|149201624|ref|ZP_01878598.1| sigma factor FliA (Sigma-28 group, flagellar) [Roseovarius sp.
           TM1035]
 gi|149144672|gb|EDM32701.1| sigma factor FliA (Sigma-28 group, flagellar) [Roseovarius sp.
           TM1035]
          Length = 242

 Score =  111 bits (279), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 45/247 (18%), Positives = 110/247 (44%), Gaps = 26/247 (10%)

Query: 52  RLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           RLV  H+ LV ++A  + G     + I +++  G +GL+ A +++    G   A Y+   
Sbjct: 16  RLVEQHMPLVQRLAWHFHGRVGRFIEIDDLLQAGYLGLIDASQRYSVCDGVSFAAYATIR 75

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ ++ +++ R+ +L +   T  QK        ++   + ++    +  +V  +A+ L +
Sbjct: 76  IRGSIIDHLRRNSNLCRNSITMRQK--------IEATRRKLSQKLGREPEVPELAQSLEL 127

Query: 169 SESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           S  E      R   +  +SL+ +              L  DH        ++ E    + 
Sbjct: 128 STEEFQDWENRFQTNQLQSLDEVYTD--------HSLLFSDHGS---TPEDEVEHIQLKA 176

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +L  ++  L  R   + +   ++E  + +  +++  +V+  RV QI+  A  ++++ +Q 
Sbjct: 177 LLQSALQDLPERSALVLQLYYVEE--LNVYEIAAILDVTTGRVSQIKKAAIGQLRDLMQA 234

Query: 287 QVELSSS 293
           ++  +++
Sbjct: 235 RLHNTAA 241


>gi|85712287|ref|ZP_01043338.1| flagellar biosynthesis sigma factor FliA [Idiomarina baltica OS145]
 gi|85693914|gb|EAQ31861.1| flagellar biosynthesis sigma factor FliA [Idiomarina baltica OS145]
          Length = 241

 Score =  111 bits (279), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 49/243 (20%), Positives = 97/243 (39%), Gaps = 18/243 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              ++  H  LV +IA          + + +++  G IGL++A + FD  +G    T++ 
Sbjct: 14  RQAIIEQHTGLVKRIAHHMMARLPASVQVDDLIQSGMIGLLEAARNFDNSKGASFETFAG 73

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + I R             + +  N RR+   ++ + +   +  + V +A+KL
Sbjct: 74  IRIRGAMLDEIRRGDW--------APRSVHRNHRRVLEAIRQVENETGRDAKDVEVAEKL 125

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   E  ++      D +   +I   D   S+    +     G      +  E      
Sbjct: 126 EMPLEEYHAIL----RDVNSGRIIGIEDLGVSE-DAIMPEQVTGANYEPQKDVENDAFHR 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L  ++S L  RE  +       +  + L+ +     VS  RV QI ++A  +++  +Q 
Sbjct: 181 ALVETISGLPEREALVLSLYY--DEELNLKEIGEVLSVSESRVSQIHSQAMMRLKTRMQS 238

Query: 287 QVE 289
            VE
Sbjct: 239 WVE 241


>gi|309775720|ref|ZP_07670717.1| RNA polymerase sigma-F factor [Erysipelotrichaceae bacterium
           3_1_53]
 gi|308916525|gb|EFP62268.1| RNA polymerase sigma-F factor [Erysipelotrichaceae bacterium
           3_1_53]
          Length = 241

 Score =  111 bits (279), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 43/236 (18%), Positives = 92/236 (38%), Gaps = 19/236 (8%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L +R R  GD  A    V  +  LV  I   +    +   ++   G +GLM+A+  FD 
Sbjct: 9   ELIERIRL-GDEEAKSCFVQQNSALVYSIIRRFSRQRISNEDLFQIGCVGLMKALNNFDT 67

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
               + +TY++  I   ++ +     S ++I  +  +  L     ++    + +      
Sbjct: 68  SYEVKFSTYAVPIIMGEIKRFFRDDGS-IRISRSLKEGYL-----QMVKTKEMLLQKLNH 121

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
                 IA  + +  ++VI          SL+  I  +D +    +D +           
Sbjct: 122 EPTYQEIADAMELDVADVILAFEANQFIYSLDETIYENDGSPILLEDKVSN--------- 172

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
            +KEE    +  L   +  L+ RE+ +   R   +  +  E+++ +  +S+ +V +
Sbjct: 173 -KKEEDVVMKVSLRDEIQKLDQREQLLLHYRY--DLSMKQEDIAKKLNISQVQVSR 225


>gi|256532386|gb|ACU81351.1| RpoH [Rhizobium leguminosarum bv. trifolii]
 gi|256532388|gb|ACU81352.1| RpoH [Rhizobium leguminosarum bv. trifolii]
 gi|256532392|gb|ACU81354.1| RpoH [Rhizobium leguminosarum bv. trifolii]
 gi|256532394|gb|ACU81355.1| RpoH [Rhizobium leguminosarum bv. trifolii]
 gi|256532398|gb|ACU81357.1| RpoH [Rhizobium leguminosarum bv. trifolii]
 gi|256532400|gb|ACU81358.1| RpoH [Rhizobium leguminosarum bv. trifolii]
 gi|256532402|gb|ACU81359.1| RpoH [Rhizobium leguminosarum bv. trifolii]
 gi|256532404|gb|ACU81360.1| RpoH [Rhizobium leguminosarum bv. trifolii]
 gi|256532406|gb|ACU81361.1| RpoH [Rhizobium leguminosarum bv. trifolii]
          Length = 148

 Score =  111 bits (279), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 60/148 (40%), Positives = 88/148 (59%), Gaps = 1/148 (0%)

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFFNLRRL+  L      
Sbjct: 1   FEPERDVRFSTYASWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRAKLAKGDTQ 60

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQ 211
                    IA  L VS ++V +M+ RL+G D SL A   S D  S++  D+LV D    
Sbjct: 61  LTLQSIHQEIAAALGVSLADVQTMDARLSGNDASLQAPSVSGDAESAEKMDFLVSDDPLP 120

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           ++ +    + + RR  L  ++  LN RE
Sbjct: 121 DEQVSNMIDGERRRVWLASALKHLNERE 148


>gi|326490962|dbj|BAJ90342.1| predicted protein [Hordeum vulgare subsp. vulgare]
          Length = 496

 Score =  111 bits (278), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 52/252 (20%), Positives = 101/252 (40%), Gaps = 18/252 (7%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDP 95
           +R R+ G  +A ++L+  +LRLV+     Y          +++   G  GL+ A+ +F+P
Sbjct: 250 RRLRDVG-RAARNKLIKHNLRLVLYAINKYYPDMTGDERFADLCQAGANGLITAIDRFEP 308

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           +RGFR++TY++ WI+ ++   +  S    +       +R    + R +  L         
Sbjct: 309 KRGFRISTYALSWIRHSVVRAMTLSSFT-RFPFAMESER--QEINRAREELSFELGRTPT 365

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
            E+ +           +V+ M        S N +      N     D +  D     ++L
Sbjct: 366 DEETMKKVGLSPARYRDVVRMTRPAYSLHSRNRVTQEELINEVTDVDAIGVDTHKHNRLL 425

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIE 273
                    R  +   +  L P+E  +   R   +     TL  ++    +SRE VR+ E
Sbjct: 426 ---------RLAIDDLLDSLKPKESVVIRQRFGLDGRGRRTLSEIAGNLRISREMVRKYE 476

Query: 274 ARAFKKVQESIQ 285
            +A  K++   +
Sbjct: 477 LKALMKLKHPTR 488


>gi|152997431|ref|YP_001342266.1| RNA polymerase sigma-28 subunit FliA/WhiG [Marinomonas sp. MWYL1]
 gi|150838355|gb|ABR72331.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Marinomonas sp. MWYL1]
          Length = 245

 Score =  111 bits (278), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 42/237 (17%), Positives = 94/237 (39%), Gaps = 18/237 (7%)

Query: 51  HRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
             +V  +  LV KIA          + + +++  G +GL++A K+F+  +G    TY+  
Sbjct: 19  DAIVEQYGYLVKKIAYHLLARLPDSVDVDDLIQAGMMGLIEAYKRFESTKGASFETYAGI 78

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+ ++ + + +        T    + +  N R +   ++ +     +    + +A  +N
Sbjct: 79  RIRGSIMDEVRK--------TDWAPRSVRRNGRAVATAIKELEAKLGREVSDMEVASHMN 130

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  E   M        S++  + S ++      + L       E       E    +N 
Sbjct: 131 ISMDEYHEMI-----HSSMSTQLFSYEEMLDSDTNNLDSIESEVENAPYSLVEEGGFQNQ 185

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L + +  L  RE+ +          + L+ + +   VS  RV QI ++A  +++  +
Sbjct: 186 LAKEIDDLPEREKLVLSLYY--NEELNLKEIGAVLGVSESRVSQIHSQAAMRLRARL 240


>gi|284029882|ref|YP_003379813.1| FliA/WhiG subfamily RNA polymerase sigma 28 subunit [Kribbella
           flavida DSM 17836]
 gi|283809175|gb|ADB31014.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Kribbella
           flavida DSM 17836]
          Length = 272

 Score =  111 bits (278), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 44/252 (17%), Positives = 89/252 (35%), Gaps = 18/252 (7%)

Query: 37  LAKRYREHGDLSAAHRL----VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           L +R     D     +L    V  ++ +   IA  +RG G    ++     +GL++A   
Sbjct: 28  LLERRAASTDDEERQQLLEEVVELNIEMARGIARRFRGRGAEADDLEQVAYLGLVKAAHH 87

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           +  +       +++  I+  ++ Y       V+I      +RL      +   L  +   
Sbjct: 88  YRLDADTPFIGFAIPTIRGEVKRYFRDCAWTVRIP-----RRLQEMQGTIAAKLPYLEQL 142

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      IA  L V  SEV            L+        +     D  +   D   
Sbjct: 143 LNREPTPAEIADHLGVELSEVEQALAAKGCFNVLSL-------DRPAEADADLTLADVVA 195

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
                  ++    +ML   ++ L  RERRI + R +     T   + ++  VS+ +V ++
Sbjct: 196 DDDDATIDQLEAVDMLQPVLADLGERERRILQLRFV--EGWTQSEIGADIGVSQMQVSRV 253

Query: 273 EARAFKKVQESI 284
             R    +++ +
Sbjct: 254 LRRILDDLRDKL 265


>gi|225019367|ref|ZP_03708559.1| hypothetical protein CLOSTMETH_03320 [Clostridium methylpentosum
           DSM 5476]
 gi|224947998|gb|EEG29207.1| hypothetical protein CLOSTMETH_03320 [Clostridium methylpentosum
           DSM 5476]
          Length = 221

 Score =  111 bits (278), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 44/239 (18%), Positives = 89/239 (37%), Gaps = 22/239 (9%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                  V  +L LV   A  + G G+   ++ S G +GL++A   FD +RG + +TY++
Sbjct: 5   KQDRDSFVKQNLGLVHSCAHRFTGKGIEYDDLFSAGCMGLVKATDAFDEDRGVKFSTYAV 64

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I   ++  + R    VK+  +  +  +     R     +       +   V  +A  L
Sbjct: 65  PVILGEIRR-LFRDGGSVKVSRSLKELSM-----RATKERERFMLKTGREPTVSELADLL 118

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            V+  + I          SL       D+      D  V   D          E+     
Sbjct: 119 EVTPEQAIEALEVSVPPMSLTT----DDEEGGGQLDIRVDSPD----------EQLTDSI 164

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            +   ++ L+  +R++   R  Q    T    + E  +++ +V + E +    ++E ++
Sbjct: 165 SIKEVVNSLDEPDRKLILLRYFQY--KTQMETAKELGMTQVQVSRREKKILGFLREKLE 221


>gi|323484320|ref|ZP_08089687.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323694680|ref|ZP_08108842.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
 gi|323402314|gb|EGA94645.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14163]
 gi|323501272|gb|EGB17172.1| RNA polymerase sigma factor [Clostridium symbiosum WAL-14673]
          Length = 209

 Score =  111 bits (278), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 48/262 (18%), Positives = 85/262 (32%), Gaps = 64/262 (24%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L   EE    KR +E GD  A   L+  +LRLV  +   Y+     + +++S G IGL+
Sbjct: 7   PLTASEEREYLKRCKE-GDEEAKAVLIERNLRLVAHVIKKYQYTDYEMEDLLSVGTIGLI 65

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV  F  +                      R   L        +  +    R  K H  
Sbjct: 66  KAVNTFKMD----------------------RGSRLATYAAKCVENEILMLFRAGKKH-- 101

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS-DKNSSQWQDWLVY 206
                                            + D SL   I    D  +    D +  
Sbjct: 102 ---------------------------------SKDVSLYDPIGVDKDGETVNLIDVIEA 128

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           D     + +I +++     +   + +      E+ +   R     E   T   ++ +  +
Sbjct: 129 DDKAALETIILEQDVSELYDAYRKCLKN---TEQEVLSMRYGLFGEQERTQREIAGKMGI 185

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           SR  V +IE +A +K++   +K
Sbjct: 186 SRSYVSRIEKKALEKLRLEFEK 207


>gi|264676583|ref|YP_003276489.1| RNA polymerase, sigma 28 subunit [Comamonas testosteroni CNB-2]
 gi|262207095|gb|ACY31193.1| RNA polymerase, sigma 28 subunit [Comamonas testosteroni CNB-2]
          Length = 239

 Score =  111 bits (278), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 48/242 (19%), Positives = 106/242 (43%), Gaps = 18/242 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L+  H+ LV +IA+       P   + +++  G IGL +A+ +F+ E+G +  T++ 
Sbjct: 10  RDALIRQHVPLVRRIALHMIAKLPPNVELDDLIQVGMIGLAEALSRFESEQGVQFDTFAS 69

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + R    +   +  +QK +   L RL+  L        +P     IA +L
Sbjct: 70  QRIRGAMLDEL-REGDWMSRSSRKSQKEIEQALNRLEQRL-------GRPPLESEIAAEL 121

Query: 167 NVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            ++  +  S+  ++ G     L  +      +   + +  V D       L+     +  
Sbjct: 122 GMALDDYQSLLGKVRGTQLVYLEDIGGGDGDDGDDYLERHVADSGADPFALLRD---QRM 178

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R+ L  ++  L  RE+ +       E+ + L+ +++   V+  RV Q+ ++A  +++  +
Sbjct: 179 RSALVEAIKTLPEREQYVMGMYY--EHDMNLKEIAAVLGVTESRVCQLHSQAIARLRTKM 236

Query: 285 QK 286
           + 
Sbjct: 237 RS 238


>gi|320102910|ref|YP_004178501.1| RNA polymerase sigma-28 subunit SigD/FliA/WhiG [Isosphaera pallida
           ATCC 43644]
 gi|319750192|gb|ADV61952.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Isosphaera
           pallida ATCC 43644]
          Length = 273

 Score =  111 bits (278), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 58/254 (22%), Positives = 112/254 (44%), Gaps = 20/254 (7%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKK 92
            L + ++     S  +RLV  +L LV   A         G+ + +++S G  GLM A+  
Sbjct: 26  ELWRDFKAQPTTSLRNRLVERYLPLVKYNAERIWQRLPDGVDLDDLISAGTFGLMDAIDA 85

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  RG +  TY +  I+ AM + +     + ++  + +         R++   +A+   
Sbjct: 86  FDLSRGVKFETYCVPRIRGAMLDELRTMDWVPRLVRSKH--------SRMEEARKALEAI 137

Query: 153 NLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
           + +P     IA++L V+  E   M       G  SLN     +D      +  ++ D  G
Sbjct: 138 HGRPPTDAEIAERLGVTPEEFEKMALESNAVGLVSLNKKWYETDSYKDVREIDILEDKKG 197

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
           ++     + +RK+   M+TR    LN  ER I      +E  +T++ + +  ++S  RV 
Sbjct: 198 ED--PTRRLQRKDLMRMVTR---GLNRNERLIIILYYYEE--LTMKEIGATLDLSESRVS 250

Query: 271 QIEARAFKKVQESI 284
           Q+ +   +++Q  +
Sbjct: 251 QMHSSIIQRLQSQL 264


>gi|145298363|ref|YP_001141204.1| flagellar biosynthesis sigma factor [Aeromonas salmonicida subsp.
           salmonicida A449]
 gi|142851135|gb|ABO89456.1| RNA polymerase sigma-27 factor [Aeromonas salmonicida subsp.
           salmonicida A449]
          Length = 239

 Score =  111 bits (278), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 54/251 (21%), Positives = 94/251 (37%), Gaps = 22/251 (8%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFD 94
           A+ Y  H D      LV  H  LV +IA            + +++  G IGL++A + FD
Sbjct: 4   AQAYLRHQDSYV---LVERHAPLVKRIAQHLLARLPSSVLLDDLIQAGMIGLLEASRNFD 60

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +G    TY+   I+ +M + I R    V      N        R +   ++ +   + 
Sbjct: 61  GSKGASFETYAGIRIRGSMLDEIRR-GDWVPRSVHRNS-------RAIAEAIENVEQAHG 112

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +  +   +A ++ VS  E  +M      D S   +I   D   S+       D  G    
Sbjct: 113 RDARDTEVAVQMGVSLGEYHTMLQ----DVSCGKIIGIEDLGVSEDVIGHPDDAGGNSGF 168

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
                ER   +  L   +  L  RE  +       +  + L  +     VS  RV QI +
Sbjct: 169 DELAAER--FQGALAEHIGRLPEREALVLSLYY--DEELNLREIGEVLNVSESRVSQIHS 224

Query: 275 RAFKKVQESIQ 285
           +A  +++  ++
Sbjct: 225 QAMHRLRARLR 235


>gi|304406109|ref|ZP_07387766.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
 gi|304344693|gb|EFM10530.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus curdlanolyticus YK9]
          Length = 257

 Score =  111 bits (278), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 45/258 (17%), Positives = 110/258 (42%), Gaps = 19/258 (7%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAV 90
           Q+   L   Y++  D   A  L+  H  +V   A    R       ++V  G + L++  
Sbjct: 10  QDSTALIADYQQSPDNDKATILIERHAPMVRMAAGKIARNRPDLFEDLVQVGQMSLLKLF 69

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
            ++DP  G +   Y+M  I   M+ Y+      +++     +K +      ++  +  +T
Sbjct: 70  HQYDPSVGVQFEPYAMKSIIGHMKNYLRDKSWYIQVPRRIKEKGIA-----VQQAIDELT 124

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
               +  +V  IA+++ ++  E + +     L    SL+  I S +++++   + +    
Sbjct: 125 VKLERSPRVEEIAERMELTVEETVEILGGRDLYHYVSLDTPI-SEEESTTTLGELIGS-- 181

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
                  ++     +++  +  +M+ L P ER++ +       P     ++ +  VS+  
Sbjct: 182 ------PLDDFGLIDKKLDIEAAMAALKPEERQVLKLVFEDGEP--QRVIAEQLGVSQMS 233

Query: 269 VRQIEARAFKKVQESIQK 286
           + +I+ RA +K++ S+ +
Sbjct: 234 ISRIQRRAIEKLKRSLSE 251


>gi|168182610|ref|ZP_02617274.1| RNA polymerase sigma-E factor [Clostridium botulinum Bf]
 gi|170759960|ref|YP_001787849.1| sporulation sigma factor SigE [Clostridium botulinum A3 str. Loch
           Maree]
 gi|237795972|ref|YP_002863524.1| sporulation sigma factor SigE [Clostridium botulinum Ba4 str. 657]
 gi|169406949|gb|ACA55360.1| RNA polymerase sigma-E factor [Clostridium botulinum A3 str. Loch
           Maree]
 gi|182674165|gb|EDT86126.1| RNA polymerase sigma-E factor [Clostridium botulinum Bf]
 gi|229261167|gb|ACQ52200.1| RNA polymerase sigma-E factor [Clostridium botulinum Ba4 str. 657]
          Length = 235

 Score =  111 bits (278), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 57/262 (21%), Positives = 109/262 (41%), Gaps = 59/262 (22%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE    +R   +GD      L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 33  PPLSKEEEEYFVQRLI-NGDEKVRSVLIERNLRLVVYIARKFENTGICIEDLVSVGTIGL 91

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F P++  +LATY+   I+  +  Y+ R+                    ++K   
Sbjct: 92  IKAVNTFKPDKKIKLATYASRCIENEILMYLRRNS-------------------KVKAE- 131

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                        ++  + LN+             G+E L + I  +D +  +  + +  
Sbjct: 132 -------------ISFYEPLNIDWD----------GNELLLSDILGTDND--EVYNLIED 166

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           + D Q  +L  K+  +  + ++     +   RE+             T + ++    +S+
Sbjct: 167 EVDKQLLLLAMKKLNEREKEIVRLRFGLNGKREK-------------TQKEVADMLGISQ 213

Query: 267 ERVRQIEARAFKKVQESIQKQV 288
             + ++E R  K +++ I K V
Sbjct: 214 SYISRLEKRIIKTLKKEINKMV 235


>gi|292493580|ref|YP_003529019.1| RNA polymerase sigma factor, FliA/WhiG family [Nitrosococcus
           halophilus Nc4]
 gi|291582175|gb|ADE16632.1| RNA polymerase sigma factor, FliA/WhiG family [Nitrosococcus
           halophilus Nc4]
          Length = 241

 Score =  111 bits (278), Expect = 1e-22,   Method: Composition-based stats.
 Identities = 42/239 (17%), Positives = 98/239 (41%), Gaps = 21/239 (8%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
             LV  +  LV +IA        P   + +++  G IGL++A + ++  +G    TY+  
Sbjct: 18  DELVIQYAPLVKRIAYHLLTRLPPSVQLDDLIQAGMIGLLEAARNYNASQGASFETYAGI 77

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+ A+ + I R+            + +    R++   ++ I +   +  +   +AK+L 
Sbjct: 78  RIRGAILDEIRRNDW--------APRSVHRKARQVAEVMREIENREGRDARDHEVAKELG 129

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S ++   +     G    +    +  + +      L        Q   +  + ++ R+ 
Sbjct: 130 LSLNDYHRLLQDAGGYRVFSLDEFNEGEETEPLTTPL--------QGPFDGLQDQSFRSA 181

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           L  ++  L  RER +     +++  + L  +     VS  RV QI ++A  +++  + +
Sbjct: 182 LVGAIDGLPERERLVMSLYYVED--LNLREIGEVLGVSESRVSQIHSQAVLRLRARLSE 238


>gi|300113620|ref|YP_003760195.1| FliA/WhiG subfamily RNA polymerase sigma 28 subunit [Nitrosococcus
           watsonii C-113]
 gi|299539557|gb|ADJ27874.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Nitrosococcus watsonii C-113]
          Length = 241

 Score =  111 bits (278), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 42/237 (17%), Positives = 96/237 (40%), Gaps = 21/237 (8%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
             LVT +  LV +IA        P   + +++  G IGL++AV+ ++  +G    TY+  
Sbjct: 18  DELVTQYAPLVKRIAYHLLTRLPPSVQLDDLIQAGMIGLLEAVRNYNASQGASFETYAGI 77

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+ A+ + I R+            + +    R++   ++ + +   +  +   + ++L 
Sbjct: 78  RIRGAILDEIRRNDW--------APRSVHRKARQVAEVMREVENREGRDARDYEVVEELG 129

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +  +E   +     G    +    +  + +      L        +   E  + +N R  
Sbjct: 130 LPLNEYHRLLQDAGGYRVFSLDEFNEGEEAEPLSAPL--------KGPYEGLQDQNFRGA 181

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L  ++  L  RER +     +++  + L  +     VS  RV QI ++A  +++  +
Sbjct: 182 LVEAIEGLPERERLVMSLYYVED--LNLREIGEVLGVSESRVSQIHSQAVLRLRSRL 236


>gi|330721193|gb|EGG99303.1| RNA polymerase sigma factor for flagellar operon [gamma
           proteobacterium IMCC2047]
          Length = 246

 Score =  111 bits (278), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 44/235 (18%), Positives = 96/235 (40%), Gaps = 19/235 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           LV  H  LV +IA          + ++++V  G +GL++A +KFD  +G    T++   +
Sbjct: 22  LVEQHAPLVKRIAHHLMARLPSTVQLNDLVQSGMVGLLEAAQKFDASKGASFETFAGIRV 81

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + AM + + +             + +  N RR+   ++A+     +      +A ++ + 
Sbjct: 82  RGAMLDDVRKDDW--------APRSVHRNARRVSEAIKAVEGRTGRDASDQEVAAEMGIP 133

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             +  +     AG          S    ++  D  +           E  +R+  ++ L 
Sbjct: 134 LEDYYAYLQDSAGTR------LFSYDEVTEQDDSSILLAASATPTPHENVQRQAFKDNLA 187

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +++  L  RER +       +  + L+ + S   VS  RV QI ++A  +++  +
Sbjct: 188 QAIEALPERERMVLALYY--QEELNLKEIGSVLGVSESRVSQIHSQAALRLRSRL 240


>gi|323493327|ref|ZP_08098450.1| flagellar biosynthesis sigma factor [Vibrio brasiliensis LMG 20546]
 gi|323312413|gb|EGA65554.1| flagellar biosynthesis sigma factor [Vibrio brasiliensis LMG 20546]
          Length = 244

 Score =  111 bits (277), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 48/249 (19%), Positives = 103/249 (41%), Gaps = 19/249 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPER 97
           Y ++ + ++    +  +  LV +IA    G   P   + +++  G IGL++A K +D  +
Sbjct: 7   YEQYANQNSQRAFLEKYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLLEAQKNYDGSK 66

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G    TY+   I+ AM + I R    V      + + +   +  L+G L        +  
Sbjct: 67  GASFETYAGIRIRGAMLDDIRR-GDWVPRSVHKHNREVSQAISELEGQLN-------RDP 118

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A+ + +S  +  ++      D + + L+   D   S+  D +  D   +E +  +
Sbjct: 119 SDAEVAQHMGISLEQYHTILT----DINCSRLVGIEDLGVSE--DVISPDDRDEENLPFQ 172

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
               +  R  L  S+  L  RE  +       +  + L+ +     VS  RV QI +++ 
Sbjct: 173 GVADEYFRKALIDSIKSLPEREALVLSLYY--DEELNLKEIGEVIGVSESRVSQILSQSM 230

Query: 278 KKVQESIQK 286
           ++++  +  
Sbjct: 231 QRLRTKLSA 239


>gi|254387242|ref|ZP_05002505.1| sigma factor [Streptomyces sp. Mg1]
 gi|194346050|gb|EDX27016.1| sigma factor [Streptomyces sp. Mg1]
          Length = 272

 Score =  111 bits (277), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 54/256 (21%), Positives = 106/256 (41%), Gaps = 22/256 (8%)

Query: 40  RYREHGDLS---AAHRLVTSHLRLVVKIAMGYRGYG----LPISEVVSEGNIGLMQAVKK 92
           R  E G      A + L+  +L LV   A  +R       + + ++V  G IGL++A+ +
Sbjct: 24  RVLEEGTREYQYARNTLIEMNLSLVQFAARRFRARAFGGGIDMDDIVQVGTIGLIKAIDR 83

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           +DPER    +T ++ +I   ++ +   +   V +     + R       L    +++TD 
Sbjct: 84  YDPEREVEFSTLALPYITGEIKRHFRDTTWAVHVPRRLQELRT-----ELAKAQESLTDV 138

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN----SSQWQDWLVYDH 208
             +   V  IA+ L + E E+I       G  S +     S+ +    SS+    L    
Sbjct: 139 LGRAPTVKEIAQHLELPEEEIIEGLVAANGYTSGSLDTAGSEGDNQSTSSRGTRPLAEKI 198

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
              +  +   EE     + L   +  L+ R+  I   R  +E   T   + +E  +S+ +
Sbjct: 199 GDNDPAMELFEEF----HTLAPLLEKLDERDLLILRMRFGEE--KTQAEIGAELGISQMQ 252

Query: 269 VRQIEARAFKKVQESI 284
           V +I +R   +++  +
Sbjct: 253 VSRILSRTLTRLRAGM 268


>gi|328951994|ref|YP_004369328.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfobacca
           acetoxidans DSM 11109]
 gi|328452318|gb|AEB08147.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfobacca
           acetoxidans DSM 11109]
          Length = 258

 Score =  111 bits (277), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 46/243 (18%), Positives = 95/243 (39%), Gaps = 13/243 (5%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           + E  D     RLV  +  ++  IA          + + +++S G IGL+ A+KKFDP++
Sbjct: 18  WPEKIDPETHERLVLQYAPMIKYIAARLALRLPSHISLDDLISSGMIGLLDAIKKFDPQK 77

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
                TY+ + IK A+ + + R+   +         +L     +L+  L        +P 
Sbjct: 78  NISFKTYAEFRIKGAILDEL-RALDWIPRSIRKKTSQLEKAYTKLEKEL-------GRPA 129

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           +   +A  + +S  E   +     G   L+      + N     +      D   +    
Sbjct: 130 EAEEVAHSMGLSMEEFYHLIDETKGVSLLDIDAVRRNLNEFSEAELYEILQDESSRSPFI 189

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
                  R++L R++  L  +E+ +      +E  +T++ +      +  R+ QI  +A 
Sbjct: 190 SVHFAELRDLLMRALEDLPDKEKLLISLYYYEE--LTMKEIGEIMGYTESRISQIHTQAI 247

Query: 278 KKV 280
             +
Sbjct: 248 FHL 250


>gi|331085949|ref|ZP_08335032.1| hypothetical protein HMPREF0987_01335 [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|330406872|gb|EGG86377.1| hypothetical protein HMPREF0987_01335 [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 192

 Score =  111 bits (277), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 53/240 (22%), Positives = 89/240 (37%), Gaps = 61/240 (25%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GDL A H L+  +LRLV  I   Y+       +++S G +GL++AV  F+PE+G RL+T
Sbjct: 6   EGDLEAKHILIEHNLRLVAHIVKKYQRPEEDNEDLISIGTVGLIKAVITFNPEKGNRLST 65

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   I+  +                         LR  K   +                
Sbjct: 66  YAARCIENEI----------------------LMMLRSRKKSSRE--------------- 88

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
                     IS+   +  D          + N  Q  D +       E +  +   + +
Sbjct: 89  ----------ISLYEPIGTDR---------EGNEIQLFDVM---ETTDEDIHEKINLKDD 126

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R +  +  S L+ RER + + R     E   T   ++    +SR  V +IE  A +K++
Sbjct: 127 VRTLYEKVESELSDRERLVLKMRYGLYNEEEYTQREIAKRLGISRSYVSRIEKSAVEKLR 186


>gi|148380490|ref|YP_001255031.1| RNA polymerase sigma-E factor [Clostridium botulinum A str. ATCC
           3502]
 gi|153932419|ref|YP_001384713.1| sporulation sigma factor SigE [Clostridium botulinum A str. ATCC
           19397]
 gi|153937804|ref|YP_001388234.1| sporulation sigma factor SigE [Clostridium botulinum A str. Hall]
 gi|153940530|ref|YP_001391830.1| sporulation sigma factor SigE [Clostridium botulinum F str.
           Langeland]
 gi|168180581|ref|ZP_02615245.1| RNA polymerase sigma-E factor [Clostridium botulinum NCTC 2916]
 gi|170756639|ref|YP_001782077.1| sporulation sigma factor SigE [Clostridium botulinum B1 str. Okra]
 gi|187778871|ref|ZP_02995344.1| hypothetical protein CLOSPO_02466 [Clostridium sporogenes ATCC
           15579]
 gi|226949888|ref|YP_002804979.1| RNA polymerase sigma-E factor [Clostridium botulinum A2 str. Kyoto]
 gi|148289974|emb|CAL84087.1| RNA polymerase sigma-E factor [Clostridium botulinum A str. ATCC
           3502]
 gi|152928463|gb|ABS33963.1| RNA polymerase sigma-E factor [Clostridium botulinum A str. ATCC
           19397]
 gi|152933718|gb|ABS39217.1| RNA polymerase sigma-E factor [Clostridium botulinum A str. Hall]
 gi|152936426|gb|ABS41924.1| RNA polymerase sigma-E factor [Clostridium botulinum F str.
           Langeland]
 gi|169121851|gb|ACA45687.1| RNA polymerase sigma-E factor [Clostridium botulinum B1 str. Okra]
 gi|182668430|gb|EDT80409.1| RNA polymerase sigma-E factor [Clostridium botulinum NCTC 2916]
 gi|187772496|gb|EDU36298.1| hypothetical protein CLOSPO_02466 [Clostridium sporogenes ATCC
           15579]
 gi|226843077|gb|ACO85743.1| RNA polymerase sigma-E factor [Clostridium botulinum A2 str. Kyoto]
 gi|295319856|gb|ADG00234.1| RNA polymerase sigma-E factor [Clostridium botulinum F str. 230613]
 gi|322806803|emb|CBZ04372.1| RNA polymerase sporulation specific sigma factor SigE [Clostridium
           botulinum H04402 065]
          Length = 235

 Score =  111 bits (277), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 57/262 (21%), Positives = 109/262 (41%), Gaps = 59/262 (22%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE    +R   +GD      L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 33  PPLSKEEEEYFVQRLI-NGDEKVRSVLIERNLRLVVYIARKFENTGICIEDLVSVGTIGL 91

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F P++  +LATY+   I+  +  Y+ R+                    ++K   
Sbjct: 92  IKAVNTFKPDKKIKLATYASRCIENEILMYLRRNS-------------------KVKAE- 131

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                        ++  + LN+             G+E L + I  +D +  +  + +  
Sbjct: 132 -------------ISFYEPLNIDWD----------GNELLLSDILGTDND--EVYNLIED 166

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           + D Q  +L  K+  +  + ++     +   RE+             T + ++    +S+
Sbjct: 167 EVDKQLLLLAMKKLNEREKEIVRLRFGLNGKREK-------------TQKEVADMLGISQ 213

Query: 267 ERVRQIEARAFKKVQESIQKQV 288
             + ++E R  K +++ I K V
Sbjct: 214 SYISRLEKRIIKTLKKEINKMV 235


>gi|309388843|gb|ADO76723.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Halanaerobium praevalens DSM 2228]
          Length = 251

 Score =  111 bits (277), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 58/259 (22%), Positives = 115/259 (44%), Gaps = 22/259 (8%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQAVKK 92
           L K+Y+   +  A   ++  +L LV   A+G     LP      ++ S G IGL++A++ 
Sbjct: 7   LWKKYKVDDNQQAREEIILKNLGLVRY-AVGRINIMLPEHIEDQDLESYGIIGLIEAIEN 65

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+ +RG + +T+++  IK  + +Y+       K     N +R    +   K   +A T  
Sbjct: 66  FNYQRGVKFSTFALPRIKGEIYDYLRS-----KDWLPDNMRRELKKVDEQKRSYKAKTGK 120

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
               +++  +   +  S  E I  + +LA   SL     S D + ++  + +  D     
Sbjct: 121 KPDQKELSKL-TGIKKSRLEKIERHSQLANWISL-----SHDFDGTELIELVAADFKQAV 174

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
             L EKE      + L + + +L+ +E+ +      +E  +T   ++   E+S  RV QI
Sbjct: 175 DRLTEKEAV----DFLAKKIDLLSEKEKLVLSLYYYEE--LTQVEIAEIIELSAARVSQI 228

Query: 273 EARAFKKVQESIQKQVELS 291
             RA ++++  + +  E  
Sbjct: 229 HGRAIRRLRGMLSRAKEYF 247


>gi|261366886|ref|ZP_05979769.1| RNA polymerase sigma-E factor [Subdoligranulum variabile DSM 15176]
 gi|282571000|gb|EFB76535.1| RNA polymerase sigma-E factor [Subdoligranulum variabile DSM 15176]
          Length = 237

 Score =  111 bits (277), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 62/271 (22%), Positives = 104/271 (38%), Gaps = 64/271 (23%)

Query: 18  RYIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
            YI+    +P  L+ Q+E   A      G  SA   L+T +LRLVV IA  +      I 
Sbjct: 25  HYINGADTLPPPLDPQQEQQ-ALEGLSAGKGSARDLLITHNLRLVVYIAKKFETPSAGIE 83

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++S G IGL++AV  F+P +  +LATY+   I+  +  Y+ +S                
Sbjct: 84  DMISIGTIGLIKAVNTFEPSKNIKLATYASRCIENEILMYLRKSS--------------- 128

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
                                           +  +  S++  L  D   N L+      
Sbjct: 129 --------------------------------NRRQDASIDEPLNTDNDGNELLLMD--- 153

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVT 254
                  L  D     + L    E    R  L  ++  L PRERRI E R     E+  T
Sbjct: 154 ------VLTSDQPQVGEELERSAE----RAALRLAVGRLAPRERRIMELRFGLNHESEHT 203

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            + ++    +S+  + ++E R  K+++  ++
Sbjct: 204 QKEVADALGISQSYISRLEKRIIKRLRRELE 234


>gi|71281710|ref|YP_268261.1| flagellar biosynthesis sigma factor [Colwellia psychrerythraea 34H]
 gi|71147450|gb|AAZ27923.1| motility sigma factor FliA [Colwellia psychrerythraea 34H]
          Length = 239

 Score =  111 bits (277), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 49/249 (19%), Positives = 101/249 (40%), Gaps = 22/249 (8%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPER 97
           Y    D +A   L+     LV +IA          + + +++  G IGL +A   FD  +
Sbjct: 7   YNNQIDKAA---LLEQQTVLVKRIAYHLLARLPASVQVDDLIQSGMIGLFEAANNFDNTK 63

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G    T++   I+ AM + I R     +     N + +   +++L+  L        +  
Sbjct: 64  GASFETFAGIRIRGAMLDEIRRGDWTPR-SVHKNSRMISEAIKQLEAQL-------GRDV 115

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
             V +A+KL++S  +   +   ++  + L       ++++ +  D  + D         +
Sbjct: 116 SDVEVAEKLDISLKDYHQILSEVSTGKILGIDDLGVNEDAIKPSDDYIGDD------PYQ 169

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
             ER   +  LT+ +  L  RE  +       +  + L  +    +VS  RV QI ++A 
Sbjct: 170 SIERIAFKKGLTQCIKSLPEREALVLSLYY--DEELNLREIGQVLDVSESRVSQIHSQAM 227

Query: 278 KKVQESIQK 286
            +++  +Q 
Sbjct: 228 HRLKARMQS 236


>gi|88798984|ref|ZP_01114565.1| flagellar biosynthesis sigma factor FliA [Reinekea sp. MED297]
 gi|88778211|gb|EAR09405.1| flagellar biosynthesis sigma factor FliA [Reinekea sp. MED297]
          Length = 238

 Score =  111 bits (277), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 45/239 (18%), Positives = 91/239 (38%), Gaps = 18/239 (7%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            +L+  +  LV +IA            + +++  G IGL +A   +D  +G    TY+  
Sbjct: 11  EQLIEDYGVLVKRIAHHLLARLPDSVHVEDLIQSGMIGLFEAAANYDQSKGASFETYAGI 70

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+ +M + I R    +             N RR+   +  +     +  Q   +A++L 
Sbjct: 71  RIRGSMLDEI-RKGDWIPRSVH-------RNSRRISDAIHTVEMREGRDAQDHEVAQELG 122

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE-QVLIEKEERKNRRN 226
           VS  E  ++     G    + L +  +   +   D      D  E        +     +
Sbjct: 123 VSLDEYYTLMKDTQG----SRLFSFEELVDNSPSDHHENRPDASEGMAPHSGHQSSQMND 178

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            L  ++  L  RE+ +       E  + L+ + +   VS  RV QI ++A  +++  ++
Sbjct: 179 QLVEAIKALPEREQIVLSLYY--EEELNLKEIGAVLGVSESRVSQIHSQATLRLRSKMR 235


>gi|256532390|gb|ACU81353.1| RpoH [Rhizobium leguminosarum bv. trifolii]
          Length = 148

 Score =  110 bits (276), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 60/148 (40%), Positives = 89/148 (60%), Gaps = 1/148 (0%)

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F+PER  R +TY+ WWI+A++Q+YILR+WS+V+ GT++ QK LFFNLRRL+  L      
Sbjct: 1   FEPERDVRFSTYASWWIRASIQDYILRNWSIVRGGTSSAQKALFFNLRRLRAKLAKGDTQ 60

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLNALINSSDKNSSQWQDWLVYDHDGQ 211
                    IA  L VS ++V +M+ RL+G D SL A   S D  S++  D+LV D    
Sbjct: 61  LTLQSIHQEIAAALGVSLADVQTMDARLSGNDASLQAPSVSGDAESAEKMDFLVSDDPLP 120

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           ++ +    + + RR +L  ++  LN RE
Sbjct: 121 DEQVSNMIDGERRRVLLASALKHLNERE 148


>gi|291524907|emb|CBK90494.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Eubacterium rectale
           DSM 17629]
          Length = 230

 Score =  110 bits (276), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 53/261 (20%), Positives = 97/261 (37%), Gaps = 64/261 (24%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L  + E    K+  ++ D  A   L+  ++RLV  +   Y      + E++S G IGL+
Sbjct: 31  PLSLERETECLKKVAQN-DKEAKDELILHNMRLVAHVTKKYAVSEDEMEELISIGTIGLI 89

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV  F  + G R AT+++  I+                    N+  + F  R+      
Sbjct: 90  KAVSSFKADYGNRFATFAIRCIE--------------------NEILMHFRSRK------ 123

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS-DKNSSQWQDWLVY 206
                                          +  GD S+   I +  + N     D +  
Sbjct: 124 -------------------------------KSRGDVSIFDPIGTDKEGNQIHLVDVI-- 150

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
             +GQ  V+ + E  ++ + +     SVL+ RE  I   R     E  +T   ++    +
Sbjct: 151 -ENGQSDVVSDIEVSESLKILRQNMRSVLSDREYYIITKRFGLDGEKELTQRQIAKTLSI 209

Query: 265 SRERVRQIEARAFKKVQESIQ 285
           SR  V +IE    KK+++ ++
Sbjct: 210 SRSYVSRIEKAGLKKLRKLLE 230


>gi|119476300|ref|ZP_01616651.1| RNA polymerase sigma factor for flagellar operon [marine gamma
           proteobacterium HTCC2143]
 gi|119450164|gb|EAW31399.1| RNA polymerase sigma factor for flagellar operon [marine gamma
           proteobacterium HTCC2143]
          Length = 240

 Score =  110 bits (276), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 48/239 (20%), Positives = 93/239 (38%), Gaps = 23/239 (9%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
             +V  +  LV +IA            + ++V  G IGL++A + +D  +G    TY+  
Sbjct: 11  DEMVERYAPLVKRIAHHLMARMPSSVQVEDLVQAGLIGLLEAARNYDASKGASFETYAGI 70

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+ +M + + R             + +  N RR+   L+ +     +      +A +L+
Sbjct: 71  RIRGSMIDDVRRGDW--------APRSIHRNSRRVSEALKIVESRLGRDATDQEVAAELS 122

Query: 168 VSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           VS  +   M    A  +  S + + +  DK   Q         DG +   +        R
Sbjct: 123 VSLDDYYRMLQDSASSKLFSFDEITSGEDKPEEQLPSSTASPFDGIQANAL--------R 174

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             L  ++  L  RER +       +  + L+ +     VS  RV QI ++A  +++  +
Sbjct: 175 QGLADAIGTLPERERLVLALYY--DEELNLKEIGLILGVSESRVSQIHSQAATRLRGRM 231


>gi|329937662|ref|ZP_08287181.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
 gi|329303061|gb|EGG46949.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
          Length = 327

 Score =  110 bits (276), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 42/237 (17%), Positives = 99/237 (41%), Gaps = 16/237 (6%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +    LVT+ L +  +IA  +R  G  + ++     +GL++A+ ++D ERG    +Y++
Sbjct: 87  EALRDELVTAWLPMAHRIAGRFRDRGESLEDLRQVAALGLVKAIDRYDCERG-AFESYAV 145

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE-QVVAIAKK 165
             I   ++ +       +++     + R      +++   + +  +   PE     +A+ 
Sbjct: 146 PTITGEIKRHFRDRMWALRVPRRVQELR-----NKVRVARRELMQSPGSPEPSAADVARH 200

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
             ++E EV +    L    +L+     S  + +      +   +    V+++       R
Sbjct: 201 TGLTEEEVGTGMEALESFSTLSLDAAMSADDDAYSLADTLGVAEASYDVVVD-------R 253

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
                 +  L  RER I   R  Q+  +T   ++    +S+  V ++ +R+  +V+E
Sbjct: 254 EAAKEGLRRLPERERAILYMRFFQD--MTQNRIADRLGISQMHVSRLISRSCARVRE 308


>gi|113969642|ref|YP_733435.1| flagellar biosynthesis sigma factor [Shewanella sp. MR-4]
 gi|114046872|ref|YP_737422.1| flagellar biosynthesis sigma factor [Shewanella sp. MR-7]
 gi|113884326|gb|ABI38378.1| RNA polymerase, sigma 28 subunit [Shewanella sp. MR-4]
 gi|113888314|gb|ABI42365.1| RNA polymerase, sigma 28 subunit [Shewanella sp. MR-7]
          Length = 237

 Score =  110 bits (276), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 49/243 (20%), Positives = 101/243 (41%), Gaps = 20/243 (8%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
            L +   +V  +  LV +IA          + + +++  G +GL++A  KFD  +G +  
Sbjct: 9   CLDSKTSIVEQYAPLVKRIAHHLLARLPASVQLDDLLQAGMMGLLEASSKFDGGKGAKFE 68

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           T++   I+ AM + I R    V      N +R+   +      L+ +   + +      I
Sbjct: 69  TFAGIRIRGAMLDEIRR-GDWVPRSVHRNNRRVAQAI----DELEQVLGRDAR---DTEI 120

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+KL+++  E       +  D S+  +I   D   SQ    ++   D       E     
Sbjct: 121 AEKLDMTLDEYH----HILNDVSVGKIIGIEDLGVSQ---DILTPSDNVSDGTFEALAET 173

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              + L  ++ +L  R+  +       +  + L+ + +  EVS  RV QI ++A  +++ 
Sbjct: 174 QFHSALVEAIKLLPERDALVLSLYY--DEALNLKEIGAILEVSESRVSQILSQAMLRLKG 231

Query: 283 SIQ 285
            ++
Sbjct: 232 KLK 234


>gi|308273536|emb|CBX30138.1| RNA polymerase sigma factor whiG [uncultured Desulfobacterium sp.]
          Length = 255

 Score =  110 bits (276), Expect = 2e-22,   Method: Composition-based stats.
 Identities = 38/240 (15%), Positives = 96/240 (40%), Gaps = 18/240 (7%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           L+  +  LV  I+              ++ S G IGL  A++ FD  RG +  TY+ + I
Sbjct: 30  LILKYAPLVKYISDRLANRMPSHISRDDLNSAGIIGLFDAIENFDSSRGIKFETYASYRI 89

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + A+ +  +R    +             ++++++  + A      +  +   IA++L V+
Sbjct: 90  RGAILDE-MRKLDWIPRSVRK-------DIQKVETAVTAAQTKLGRTPEDHEIAEELGVN 141

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             +   +  R      L+      D+ +       V   +      ++K ++     ++ 
Sbjct: 142 LEDFYKIIDRTHNVNLLSL-----DEPALGTSVTTVNRLESDNPSPLDKVKKSEIEKVIA 196

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
            +++ L  + + +       E  +TL+ ++    ++  R+ QI ++A   ++  ++   E
Sbjct: 197 SALANLPEKVQMVISLYYYDE--MTLKEIAEIMGLTESRISQIHSKAIIILRSKLKAYFE 254


>gi|261416067|ref|YP_003249750.1| putative RNA polymerase, sigma 70 family subunit [Fibrobacter
           succinogenes subsp. succinogenes S85]
 gi|261372523|gb|ACX75268.1| putative RNA polymerase, sigma 70 family subunit [Fibrobacter
           succinogenes subsp. succinogenes S85]
 gi|302327561|gb|ADL26762.1| sigma-70 factor family protein [Fibrobacter succinogenes subsp.
           succinogenes S85]
          Length = 376

 Score =  110 bits (275), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 66/291 (22%), Positives = 115/291 (39%), Gaps = 29/291 (9%)

Query: 1   MNRKNMSIIVNGEIG----LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTS 56
           +N K+ S I +  I     L  +I  +RKI   +K+E   +  +  E G   A  R +  
Sbjct: 70  VNYKDFSCIFDAVIAAEPLLENFIEYVRKIQPADKKEMVRIQYQLFE-GHEYARKRAIEG 128

Query: 57  HLRLVVKIAMG-YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQE 115
           +LR+ V +A      Y   I + + E  + L+ A   + P+     A+Y    I  A+ +
Sbjct: 129 NLRIAVILAYRESVAYNKNIVDCIGEACLALVSACNSYKPDEHQTFASY----ISIAVFD 184

Query: 116 YILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
           Y+ R+  +       N   L   L +   +     +   K + ++ +             
Sbjct: 185 YLARTIGVPFFSIPVNIVNLCRKLYKDIKY-----NRLGKKDALLYVCSCYG-------- 231

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE---ERKNRRNMLTRSM 232
           +    +        +   D++        VY     E  L + E   ERKN + ++ R +
Sbjct: 232 LEEYWSNVLYDILHVFFLDEDVLDNVLDNVYSESCYENFLTDVENDIERKNVQILINRCL 291

Query: 233 SV-LNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           +  L  RE  + E R      +  +L  L S   VSRER+RQIE +A  K+
Sbjct: 292 NECLTDREYNVVEHRYGLNGKDSHSLVELGSHQVVSRERIRQIEKKALTKL 342


>gi|219125233|ref|XP_002182890.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217405684|gb|EEC45626.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 312

 Score =  110 bits (275), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 57/252 (22%), Positives = 103/252 (40%), Gaps = 18/252 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRG-----YGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
             A H LVT++L LV  +     G      G+   E++ EG++GL++A + FDPERG R 
Sbjct: 58  RRAKHDLVTANLGLVHAVVNQQYGSLKTHTGITKEELIQEGSLGLLRAAELFDPERGLRF 117

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY++ WIK  +    L    LV++      K       +++   + +   N     V  
Sbjct: 118 STYAVVWIKGVLSNSHLPE--LVRLPAREKTK-----WNKIQTIQREVETANGVVPTVEE 170

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           +A    ++  EV+    R+    S+ +L      +S    D          Q   E  + 
Sbjct: 171 LATLTGMTVQEVVQTTRRMQQARSILSLDFEYSSHSRSGADTATSSAALANQECPEDAKL 230

Query: 222 KNRRNMLTRSMS----VLNPRERRIFEARRLQENPVT--LENLSSEFEVSRERVRQIEAR 275
             R  +    ++     L+ RE R+   R    +  T  L   +    +S  R +QI   
Sbjct: 231 AARTQLQADVIAAMARNLDAREARLLRLRYGLADGQTRSLAECADAMGLSPTRTQQIAQT 290

Query: 276 AFKKVQESIQKQ 287
              K++++ + +
Sbjct: 291 CLSKLRQAAEAE 302


>gi|225181587|ref|ZP_03735028.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Dethiobacter
           alkaliphilus AHT 1]
 gi|225167695|gb|EEG76505.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Dethiobacter
           alkaliphilus AHT 1]
          Length = 239

 Score =  110 bits (275), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 48/253 (18%), Positives = 105/253 (41%), Gaps = 23/253 (9%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFD 94
             +Y+E  +      LV  +L LV   A          +   +++  G +GL++A+++FD
Sbjct: 7   WVKYQETKEEGLQETLVEKYLPLVRLHAGRLALGLPAHVNRDDLLQAGMLGLLEALQRFD 66

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P RG +  +++   I+ AM + +     L  +  +         +R +   +Q +     
Sbjct: 67  PTRGVKFESFAALRIRGAMLDELR---RLCWVPRSV-----VREMREMDRAVQELATQLG 118

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +      IA+K+ ++  ++  +            +INSS   S +     V   DG E  
Sbjct: 119 REPAEEEIAEKMGITIPQLRKITG----------MINSSSLLSLEDTLLAVPAVDGPEVE 168

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
            +++      R  L  ++  L  R +++       +  +TL+ +     V+  RV Q+ A
Sbjct: 169 ALDRLIAAEDRQRLAEAIGQLPERHQQLLALYY--QEDLTLKEVGLVLGVTESRVCQLHA 226

Query: 275 RAFKKVQESIQKQ 287
           R   +++ ++Q +
Sbjct: 227 RIIARLRTALQDE 239


>gi|326789987|ref|YP_004307808.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium lentocellum DSM
           5427]
 gi|326540751|gb|ADZ82610.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium lentocellum DSM
           5427]
          Length = 274

 Score =  110 bits (275), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 49/247 (19%), Positives = 94/247 (38%), Gaps = 61/247 (24%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           +  + GD  A  RL+ ++  L+ K++M +   R   +   ++V EG IGL+ A +K+D  
Sbjct: 8   KLYQCGDSKALERLLEANKGLIYKVSMKFYTERDNAIDQDDLVQEGRIGLIVAAEKYDIN 67

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
                A+Y+ +WI   M  ++    +++K                               
Sbjct: 68  GDVPFASYAYYWIYQKMHRFMYPKRNMIK------------------------------- 96

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
                       S  + +S+N  +  D  +       ++               +   + 
Sbjct: 97  ------------SSLKFVSLNTPIGEDGEMELGDTLGEEQE-------------EFCSVE 131

Query: 217 EKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEA 274
           +    +     L ++M   L  ++R++   R   E N  TLE    E  V+RERVRQIE 
Sbjct: 132 DSIYHQELAEELRQAMNDNLTLQQRQVLLFRFGFECNVHTLEETGKEIGVTRERVRQIEV 191

Query: 275 RAFKKVQ 281
            + +K++
Sbjct: 192 NSLRKLR 198


>gi|167630813|ref|YP_001681312.1| RNA polymerase, sigma-70 factor family [Heliobacterium
           modesticaldum Ice1]
 gi|167593553|gb|ABZ85301.1| RNA polymerase, sigma-70 factor family [Heliobacterium
           modesticaldum Ice1]
          Length = 252

 Score =  110 bits (275), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 51/262 (19%), Positives = 92/262 (35%), Gaps = 63/262 (24%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L  +EE     R    GD  A  +L+T +LRLV  I   Y      I +++S G IGL+
Sbjct: 32  PLSAEEEAEYIAR-TTGGDAEAREKLITHNLRLVAHICKKYYSNDEEIEDLISIGTIGLI 90

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +A+  F  E+  RL+TY+   I+  +  ++       ++ +      +  +  R+     
Sbjct: 91  KAINTFKAEKQVRLSTYASRCIENEILMHLRNKKRDSRVVSFEESVGIDKDGNRMT---- 146

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                          +  L      V  +  R +  E L                     
Sbjct: 147 --------------YSDILGTDGDTVAELVERSSEIEDL--------------------- 171

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVS 265
                            +N + R ++    RE  I   R       P T + ++    +S
Sbjct: 172 -----------------QNKVRRRLNK-KERE--ILTLRYGLSDGTPKTQQTVADLLNIS 211

Query: 266 RERVRQIEARAFKKV-QESIQK 286
           R  V +IE R  +K+ +E +++
Sbjct: 212 RSYVSRIEGRGIRKLMKEYLRE 233


>gi|269792915|ref|YP_003317819.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermanaerovibrio
           acidaminovorans DSM 6589]
 gi|269100550|gb|ACZ19537.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermanaerovibrio
           acidaminovorans DSM 6589]
          Length = 245

 Score =  110 bits (275), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 51/253 (20%), Positives = 103/253 (40%), Gaps = 21/253 (8%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKF 93
           L + Y +        R+V  ++ LV  +A         GL   +++S G +GL+ A+ +F
Sbjct: 8   LWEAYAKEPTGENRERIVKRYIPLVKYVAGRMAVTPPPGLDYDDILSFGVMGLLDAMDRF 67

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           DP RGF   T+++  I+ A+ + + R   + + G    Q+                    
Sbjct: 68  DPSRGFCFQTFAVPRIRGAILDELRRYDWISRTGRDKLQRLERA---------MEEAAAE 118

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYDHDGQ 211
                  A+ ++L ++E     +    +     SL+ ++   D    +  D L+ D    
Sbjct: 119 GTLLDDEALMERLGMNEKSYRELLEIASRSYVVSLDEVLGLEDGEVKR--DGLLEDPSPS 176

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
            Q   E+ ER+    ++ R++  L  RER +       +  +TL+ + +   V+  R  Q
Sbjct: 177 PQ---EEVERREELALVRRALEELPERERLLLSLYY--QEGLTLKEVGAVLGVTESRASQ 231

Query: 272 IEARAFKKVQESI 284
           +  RA   ++  +
Sbjct: 232 LHGRAIAMLRSKL 244


>gi|119963836|ref|YP_945938.1| RNA polymerase sigma (70) factor [Arthrobacter aurescens TC1]
 gi|119950695|gb|ABM09606.1| putative RNA polymerase sigma (70) factor [Arthrobacter aurescens
           TC1]
          Length = 258

 Score =  110 bits (275), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 45/250 (18%), Positives = 92/250 (36%), Gaps = 23/250 (9%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              LV  HL L   IA  Y  +   + +V     +GL++A + +D  +G     Y+   I
Sbjct: 27  QDSLVLDHLNLAKSIAARYSAHTHDLDDVRQVAYMGLIKASRGYDEAKGVSFPAYAAPTI 86

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++ Y+     +V+   T    R     R++    + +T    +      +A+ LN+ 
Sbjct: 87  AGEVKRYLRDHCWVVRPPRTIQDVR-----RQVLARTEEMTQTLQRTPSPEEVAEDLNLE 141

Query: 170 ESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
             +V    M       +SL+A  +                 D  E VL            
Sbjct: 142 PCQVREALMAGTSKRPDSLDAPASDGRDGLQGSLSAFGCPTDRLEDVLA----------- 190

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI--- 284
           L  ++  L+  +R +   R  +E   T   ++    +S+ +V +  ++    +Q  +   
Sbjct: 191 LRNAIRGLSAEDRHLLYRRYYREE--TQSTIAEALGMSQMQVSRKLSKILVSLQTQLLDE 248

Query: 285 QKQVELSSSP 294
           + Q+   ++P
Sbjct: 249 EAQLLDGTAP 258


>gi|150016004|ref|YP_001308258.1| sporulation sigma factor SigE [Clostridium beijerinckii NCIMB 8052]
 gi|149902469|gb|ABR33302.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           beijerinckii NCIMB 8052]
          Length = 235

 Score =  110 bits (275), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 52/262 (19%), Positives = 108/262 (41%), Gaps = 59/262 (22%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K EE  L  +    GD +    L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 33  PPLSKDEEEDLVNKL-NGGDENIRSTLIERNLRLVVYIARKFENTGVYVEDLISVGTIGL 91

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+                    ++K   
Sbjct: 92  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRNS-------------------KIKAE- 131

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                        ++  + LN+             G+E L + I  ++ ++    + +  
Sbjct: 132 -------------ISFYEPLNIDWD----------GNELLLSDILGTENDTVY--NLIED 166

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           + D Q  V+  K      + ++     +   RE+             T + ++    +S+
Sbjct: 167 EVDKQLLVMALKSLNDREKEIVRLRFGLNGTREK-------------TQKEVADMLGISQ 213

Query: 267 ERVRQIEARAFKKVQESIQKQV 288
             + ++E +  K++++ I + +
Sbjct: 214 SYISRLEKKIIKRLKKEISRMI 235


>gi|315649479|ref|ZP_07902564.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily protein
           [Paenibacillus vortex V453]
 gi|315274952|gb|EFU38327.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily protein
           [Paenibacillus vortex V453]
          Length = 256

 Score =  110 bits (275), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 41/262 (15%), Positives = 106/262 (40%), Gaps = 19/262 (7%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI-SEVVSEGNI 84
            P   + E   L ++Y++  D   A  L+  +  +V   A         +  ++   G +
Sbjct: 6   TPPESRDEAVHLIQQYQQTKDNDIATVLIKKYEPMVKMAAGKIARNRPDLYEDLYQVGQM 65

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
            L++ ++++D   G     Y+M  +   M+ ++      +++     +K        ++ 
Sbjct: 66  ALIRLLQQYDISLGIPFEPYAMKSMIGHMKNFLRDKSWYIQVPRRIKEKGAL-----VQQ 120

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC--RLAGDESLNALINSSDKNSSQWQD 202
            +  +     +   V  IA  L++S  E + +          SL++ + S ++  +   +
Sbjct: 121 AIDELMVKLERSPDVNEIAAYLDLSVEETVEVLAGRECYHYVSLDSPL-SQEETGATLGE 179

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
            +  D +  + V         +R  L ++MS L  +E+++       +   +   ++   
Sbjct: 180 LISSDVNDFDSV--------EKRMDLQQAMSQLKEQEQKVLLLAF--QEGQSQRAIAQRL 229

Query: 263 EVSRERVRQIEARAFKKVQESI 284
            VS+  V +I+ RA +K+++ +
Sbjct: 230 GVSQMSVSRIQKRATEKLKQIM 251


>gi|326319090|ref|YP_004236762.1| RNA polymerase sigma-28 subunit FliA/WhiG [Acidovorax avenae subsp.
           avenae ATCC 19860]
 gi|323375926|gb|ADX48195.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Acidovorax avenae
           subsp. avenae ATCC 19860]
          Length = 237

 Score =  110 bits (275), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 43/240 (17%), Positives = 104/240 (43%), Gaps = 16/240 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L+  H  LV +IA          + + +++  G IGL +A+ +++  +G +  T++ 
Sbjct: 10  RDALIRQHAPLVRRIAHHMIAKLPPNVELDDLIQVGMIGLSEALSRYEVTQGVQFETFAS 69

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + R    +   +  +QK +   + RL+  L        +      IA +L
Sbjct: 70  QRIRGAMLDEL-REGDWMSRSSRKSQKEIEHAVTRLEQKL-------GRSPLESEIATEL 121

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +S +E  S+  ++ G + +     +   +   + D  V D       ++  +     R 
Sbjct: 122 ELSLAEYQSLLSKVRGTQLVYLEDMTHGDDDDGFLDRHVADSAADPMAMLRDQRL---RA 178

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L  ++  L  RE++I       E+ + L+ +++   V+  R+ Q+ +++  +++  ++ 
Sbjct: 179 SLVAAIKALPEREQQIMGMYY--EHDMNLKEIAAVLGVTESRICQLHSQSIARLRAKMRS 236


>gi|6175924|gb|AAF05338.1|AF182104_2 truncated RNA polymerase sigma subunit [Escherichia coli]
          Length = 147

 Score =  110 bits (275), Expect = 3e-22,   Method: Composition-based stats.
 Identities = 42/88 (47%), Positives = 62/88 (70%), Gaps = 1/88 (1%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSM 106
           + EGN+GL++AV+KFDPERGFR +TY+ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYAT 147


>gi|317055657|ref|YP_004104124.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit [Ruminococcus
           albus 7]
 gi|315447926|gb|ADU21490.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Ruminococcus
           albus 7]
          Length = 218

 Score =  109 bits (274), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 43/230 (18%), Positives = 89/230 (38%), Gaps = 22/230 (9%)

Query: 55  TSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114
             +L LV   A  +RG G+   ++   G +GL++A + FD  RG + +TY++  I   ++
Sbjct: 10  EDNLGLVHLCANRFRGRGIEYDDLYGAGCMGLVKASRAFDASRGVKFSTYAVPVILGEIK 69

Query: 115 EYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVI 174
             + R    VK+  +  +  L     ++    Q     N +   V  ++        +VI
Sbjct: 70  R-LFRDGGTVKVSRSLKELSL-----KITRASQTFAHKNGREPTVSELSDITGADPDDVI 123

Query: 175 SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV 234
                     SL   I   D  S         D D  +            R  L + +S 
Sbjct: 124 EALNASQPTVSL--TIGDEDGESQTDLPTEPPDEDITD------------RLALRQVLSE 169

Query: 235 LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L+  +R++ + R  +   +T    + +  +++ +V + E +    ++  +
Sbjct: 170 LSADDRKLIDLRYFKG--MTQTAAAEKLGMTQVQVSRREKKLLTYMRTKL 217


>gi|16332163|ref|NP_442891.1| RNA polymerase sigma factor SigF [Synechocystis sp. PCC 6803]
 gi|1653792|dbj|BAA18703.1| RNA polymerase sigma-37 [Synechocystis sp. PCC 6803]
          Length = 258

 Score =  109 bits (274), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 53/260 (20%), Positives = 109/260 (41%), Gaps = 18/260 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVK 91
           E   L K Y E  D+   +R++  +L LV K A  +         ++   G +GL++A++
Sbjct: 12  ETLRLFKIYAESHDIGVRNRIMEVNLGLVRKEAHHWTAQCNESFEDLSQVGCLGLIRAIE 71

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           +FD  +G   +++++ +++  +Q ++    + V+I      +R     R+     Q    
Sbjct: 72  RFDVSKGNAFSSFAIPYVRGEIQHFLRDKSNCVRIP-----RRWLDLGRQAIAVQQEFRL 126

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHD 209
              +      IA+ L V  ++       L   E  SL+  +N  D+      D L +   
Sbjct: 127 KYDRAATDEEIAQILAVPLADWQETKLALQNRELVSLDTKVNGDDEGQVNLGDCLAHHEF 186

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
              Q+  E + R      L ++++ L  R RRI E   L +     +  +    VS   V
Sbjct: 187 RSFQLSQEDQIR------LQQALAGLEERTRRIVEFVFLHDFTH--KEAAEMMGVSVITV 238

Query: 270 -RQIEARAFKKVQESIQKQV 288
            R+I  +    +++++  ++
Sbjct: 239 SRRI-KQGIGALKKALNTEI 257


>gi|81300593|ref|YP_400801.1| RNA polymerase sigma factor SigF [Synechococcus elongatus PCC 7942]
 gi|81169474|gb|ABB57814.1| group3 RNA polymerase sigma factor SigF [Synechococcus elongatus
           PCC 7942]
          Length = 260

 Score =  109 bits (274), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 53/255 (20%), Positives = 116/255 (45%), Gaps = 14/255 (5%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG-LPISEVVSEGNIGLMQAVKKFD 94
            L   Y E   ++  +++V  +L LV KIA         P  ++   G +GL++A+++F 
Sbjct: 13  ELLVAYAETPSIALRNQIVQLNLGLVRKIAHRLSRQCSEPYEDLEQIGFMGLIRAIERFQ 72

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P +G   +++++ +I+  +  ++  S   ++I     +  L    ++L+  L+       
Sbjct: 73  PHQGCAFSSFAVPYIRGEILHFLRDSCHSIRIPRRWQE--LQRQGQQLREVLRHEWGRAP 130

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
             EQ +A A  L+++E + I +  R     SL+A ++ +  +S    + L       +Q 
Sbjct: 131 T-EQELAFALNLSMTEWQEIHLARRNRMPMSLDATLSQAGDSSVTLVETLPDTSQQWQQA 189

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV-RQIE 273
            +E+      R  L  ++  L  + R   E+  L+   +T +  + +F +S   + R+I 
Sbjct: 190 ALEE------RQQLVEAIGQLEEKARTAIESVYLRG--LTRKEAAQQFGISPMTITRRI- 240

Query: 274 ARAFKKVQESIQKQV 288
            R  +K+ E + +  
Sbjct: 241 NRGVQKIAEHLDRMA 255


>gi|114562377|ref|YP_749890.1| flagellar biosynthesis sigma factor [Shewanella frigidimarina NCIMB
           400]
 gi|114333670|gb|ABI71052.1| RNA polymerase, sigma 28 subunit [Shewanella frigidimarina NCIMB
           400]
          Length = 239

 Score =  109 bits (274), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 49/239 (20%), Positives = 101/239 (42%), Gaps = 20/239 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              +V  +  LV +IA          + + +++  G +GL++A  KFD  +G +  T++ 
Sbjct: 13  KTSIVEQYAPLVKRIAHHMLARLPASVQLDDLLQAGMMGLLEASSKFDNSKGAKFETFAG 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + I R    V      N + +   +         +     +      IA+KL
Sbjct: 73  IRIRGAMIDEIRR-GDWVPRSVHRNNRLVAHAI-------DELGQLLGRDANDTEIAEKL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++S  E       +  D S+  +I   D   SQ  D L+ D++  ++      E +  ++
Sbjct: 125 DMSLDEYH----HILNDVSVGKIIGIEDLGVSQ--DVLITDNESPDETFDSLAEIQ-FQS 177

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            L  ++  L  R+  +       +  + L+ + +  EVS  RV QI ++A  +++  ++
Sbjct: 178 ALVEAIKTLPERDALVLSLYY--DEALNLKEIGAILEVSESRVSQILSQAMLRLKAKLK 234


>gi|221069309|ref|ZP_03545414.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Comamonas testosteroni
           KF-1]
 gi|220714332|gb|EED69700.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Comamonas testosteroni
           KF-1]
          Length = 239

 Score =  109 bits (274), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 48/242 (19%), Positives = 106/242 (43%), Gaps = 18/242 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L+  H+ LV +IA+       P   + +++  G IGL +A+ +F+ E+G +  T++ 
Sbjct: 10  RDALIRQHVPLVRRIALHMIAKLPPNVELDDLIQVGMIGLAEALSRFESEQGVQFDTFAS 69

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + R    +   +  +QK +   L RL+  L        +P     IA +L
Sbjct: 70  QRIRGAMLDEL-REGDWMSRSSRKSQKEIEQALNRLEQRL-------GRPPLESEIAAEL 121

Query: 167 NVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            ++  +  S+  ++ G     L  +      +   + +  V D       L+     +  
Sbjct: 122 GMALDDYQSLLGKVRGTQLVYLEDIGGGDGDDGDDYLERHVADSGADPFALLRD---QRM 178

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R+ L  ++  L  RE+ +       E+ + L+ +++   V+  RV Q+ ++A  +++  +
Sbjct: 179 RSALVEAIKALPEREQYVMGMYY--EHDMNLKEIAAVLGVTESRVCQLHSQAIARLRTKM 236

Query: 285 QK 286
           + 
Sbjct: 237 RS 238


>gi|317132447|ref|YP_004091761.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Ethanoligenens harbinense YUAN-3]
 gi|315470426|gb|ADU27030.1| RNA polymerase, sigma 28 subunit, Sig B/F/G subfamily
           [Ethanoligenens harbinense YUAN-3]
          Length = 237

 Score =  109 bits (274), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 47/241 (19%), Positives = 97/241 (40%), Gaps = 23/241 (9%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD +A  +LV  +L LV   A  + G G+   ++   G +GL++AV  FD  RG + +TY
Sbjct: 17  GDAAAQTQLVEENLGLVHAAARHFNGKGIEYDDLYQAGCMGLVKAVTGFDITRGVQFSTY 76

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           ++  I   M+  + R    VK+  +  +  L     +     + ++    +   +  +A 
Sbjct: 77  AVPVIMGEMRR-LFRDDGPVKVSRSLKELSL-----KAMRAREKLSARLCREPTLSELAA 130

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L    +E        A   SL +                  + +GQ  + ++ EE    
Sbjct: 131 ELETDPAEAAQALEAAAAPLSLTS--------------SREDEENGQTDIPVDSEEDALV 176

Query: 225 RNM-LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            ++ L  ++  L   +R +   R  Q    T    +S   +++ +V + E +    ++  
Sbjct: 177 DHLALKDALGSLPADDRLLILLRYFQG--KTQTETASVLHMTQVQVSRREKKILALLRNR 234

Query: 284 I 284
           +
Sbjct: 235 L 235


>gi|261342189|ref|ZP_05970047.1| RNA polymerase sigma factor [Enterobacter cancerogenus ATCC 35316]
 gi|288315522|gb|EFC54460.1| RNA polymerase sigma factor [Enterobacter cancerogenus ATCC 35316]
          Length = 147

 Score =  109 bits (274), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 42/88 (47%), Positives = 62/88 (70%), Gaps = 1/88 (1%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSM 106
           + EGN+GL++AV+KFDPERGFR +TY+ 
Sbjct: 120 IEEGNLGLIRAVEKFDPERGFRFSTYAT 147


>gi|117919807|ref|YP_868999.1| flagellar biosynthesis sigma factor [Shewanella sp. ANA-3]
 gi|117612139|gb|ABK47593.1| RNA polymerase, sigma 28 subunit [Shewanella sp. ANA-3]
          Length = 237

 Score =  109 bits (274), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 49/243 (20%), Positives = 101/243 (41%), Gaps = 20/243 (8%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
            L +   +V  +  LV +IA          + + +++  G +GL++A  KFD  +G +  
Sbjct: 9   CLDSKTSIVEQYAPLVKRIAHHLLARLPASVQLDDLLQAGMMGLLEASSKFDGGKGAKFE 68

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           T++   I+ AM + I R    V      N +R+   +      L+ +   + +      I
Sbjct: 69  TFAGIRIRGAMLDEIRR-GDWVPRSVHRNNRRVAQAI----DELEQVLGRDAR---DTEI 120

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+KL+++  E       +  D S+  +I   D   SQ    ++   D       E     
Sbjct: 121 AEKLDMTLDEYH----HILNDVSVGKIIGIEDLGVSQ---DILTSSDNVSDGTYEALAET 173

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              + L  ++ +L  R+  +       +  + L+ + +  EVS  RV QI ++A  +++ 
Sbjct: 174 QFHSALVEAIKLLPERDALVLSLYY--DEALNLKEIGAILEVSESRVSQILSQAMLRLKG 231

Query: 283 SIQ 285
            ++
Sbjct: 232 KLK 234


>gi|222053730|ref|YP_002536092.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacter sp. FRC-32]
 gi|221563019|gb|ACM18991.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacter sp. FRC-32]
          Length = 251

 Score =  109 bits (274), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 49/255 (19%), Positives = 97/255 (38%), Gaps = 17/255 (6%)

Query: 37  LAKRYREHGDLSA---AHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAV 90
           L K Y +    +A      LV SHL LV  +           L   ++ S   IGL+ A 
Sbjct: 4   LLKAYEQEAQRTAIPDRDELVVSHLPLVKFLVDRIASALPPHLDRDDLRSAAVIGLISAA 63

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           ++FDP RG    T++   I+  + + +     L +     + +  F  L R    L+   
Sbjct: 64  ERFDPTRGVMFKTFAEQRIRGTIMDELRSQDWLTR-----SLRDKFKRLEREFSALEQRL 118

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
             N   ++V A A  L++     +          SL+      D +     D L    D 
Sbjct: 119 GRNPSSDEVAA-AMGLDLEAYFHLLEEIHFLSFVSLDDAWMDEDGSPLGLLDVL---EDK 174

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
             +    +   +     L  ++  L  +ER +      +E  + L+ + +   ++  R+ 
Sbjct: 175 GIESPQNQLIARQTVENLAEAIDNLPEKERIVITLYYYEE--MNLKEIGAVLHLTESRIS 232

Query: 271 QIEARAFKKVQESIQ 285
           Q+ ++A  +++  ++
Sbjct: 233 QLHSQALLRLRGRMK 247


>gi|238924178|ref|YP_002937694.1| sporulation sigma factor SigK [Eubacterium rectale ATCC 33656]
 gi|238875853|gb|ACR75560.1| sporulation sigma factor SigK [Eubacterium rectale ATCC 33656]
 gi|291529048|emb|CBK94634.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Eubacterium rectale
           M104/1]
          Length = 230

 Score =  109 bits (274), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 53/261 (20%), Positives = 97/261 (37%), Gaps = 64/261 (24%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L  + E    K+  ++ D  A   L+  ++RLV  +   Y      + E++S G IGL+
Sbjct: 31  PLSLERETECLKKVAQN-DKEAKDELILHNMRLVAHVTKKYAVSEDEMEELISIGTIGLI 89

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV  F  + G R AT+++  I+                    N+  + F  R+      
Sbjct: 90  KAVSSFKADYGNRFATFAIRCIE--------------------NEILMHFRSRK------ 123

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS-DKNSSQWQDWLVY 206
                                          +  GD S+   I +  + N     D +  
Sbjct: 124 -------------------------------KSRGDVSIFEPIGTDKEGNQIHLVDVI-- 150

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
             +GQ  V+ + E  ++ + +     SVL+ RE  I   R     E  +T   ++    +
Sbjct: 151 -ENGQSDVVSDIEVSESLKILRQNMRSVLSDREYYIITKRFGLDGEKELTQRQIAKTLSI 209

Query: 265 SRERVRQIEARAFKKVQESIQ 285
           SR  V +IE    KK+++ ++
Sbjct: 210 SRSYVSRIEKAGLKKLRKLLE 230


>gi|220907105|ref|YP_002482416.1| RNA polymerase sigma factor SigF [Cyanothece sp. PCC 7425]
 gi|219863716|gb|ACL44055.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cyanothece
           sp. PCC 7425]
          Length = 263

 Score =  109 bits (274), Expect = 4e-22,   Method: Composition-based stats.
 Identities = 57/260 (21%), Positives = 119/260 (45%), Gaps = 16/260 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKKFD 94
            L   Y ++  ++  ++LV  HL LV K+A    R    P  ++V  G +GL+ A+++FD
Sbjct: 13  RLLLTYHQNPTIAVRNQLVRLHLGLVRKVAHRLARQCKEPYEDLVQCGCLGLIAAIERFD 72

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P +G+  +++++ +I+  +  ++     ++KI     Q  L  + ++++  L  + D   
Sbjct: 73  PSQGYAFSSFAVPYIRGEILHFLRDRAYMLKIPRRWQQ--LNQDGQKVRQELAKVLDRPP 130

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
             EQV   A +L VS  E  S+   +     L+     S    +      + D     Q 
Sbjct: 131 TEEQV---ASQLQVSPEEWRSVRLAMRNRTPLSINTTLSSSAQAAGMALTLADLLVDAQE 187

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
            + + + ++    L ++++ L  R R++ E   L  + +T + ++S   VS   V     
Sbjct: 188 EVRQSQTEDSLE-LYQALAQLEERTRQMIEEVFL--HHLTRQEVASRKGVSPITVS---- 240

Query: 275 RAFKKVQESIQKQVELSSSP 294
              + +Q+ I++ + L  SP
Sbjct: 241 ---RHIQKGIEQLMNLLQSP 257


>gi|218669755|gb|ACL00354.1| Bcp26 [Bacillus phage Bcp1]
          Length = 256

 Score =  109 bits (273), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 56/259 (21%), Positives = 111/259 (42%), Gaps = 31/259 (11%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           +L K+E Y L +R  + G+  A   LV  + RLV  +            ++   G IGL+
Sbjct: 16  VLTKEETYELIER-SQAGEEEATESLVEHNARLVTYVVRRKNNPYHEYDDLFQLGMIGLI 74

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
            A+ KFD  +G + +TY++ WI A +  Y+    S++K+              +LK    
Sbjct: 75  TAIAKFDTSKGLQFSTYAVRWIDAEIGNYLKNRTSILKVPREIGAIVNKILAVKLKNEEP 134

Query: 148 AITDNNLKPE--QVVAIAKKLNVSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDW 203
           AI    LK +  Q+  +   L +  +EVIS++ +     D+SL++++   D N   +   
Sbjct: 135 AIIMEKLKLDASQLDNVTIALEIIHNEVISLDKQTGEEKDDSLSSIVGQ-DVNQDWFSGL 193

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
             YD                        +  L+ +E+ +   + + +  ++   +++ F 
Sbjct: 194 AFYD-----------------------IIRFLDDKEQSVLTLKYVHD--MSSNKIATLFG 228

Query: 264 VSRERVRQIEARAFKKVQE 282
               ++ ++E  A  K++E
Sbjct: 229 TYANKISRLEKVALDKLRE 247


>gi|197120125|ref|YP_002140552.1| RNA polymerase sigma-28 factor for flagellar operon [Geobacter
           bemidjiensis Bem]
 gi|253702434|ref|YP_003023623.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacter sp. M21]
 gi|197089485|gb|ACH40756.1| RNA polymerase sigma-28 factor for flagellar operon [Geobacter
           bemidjiensis Bem]
 gi|251777284|gb|ACT19865.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacter sp. M21]
          Length = 250

 Score =  109 bits (273), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 47/248 (18%), Positives = 99/248 (39%), Gaps = 14/248 (5%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKKFDPERG 98
            + G   +   LV +HL LV  I         P     ++ S   IGL+ A ++FDP RG
Sbjct: 12  AQRGVPMSRDELVVTHLPLVKFIVDRIASSLPPHLDRDDLRSAAVIGLISAAERFDPARG 71

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
            +  T++   I+  + + +     L +     + +  F  L R    L+     N   ++
Sbjct: 72  VQFKTFAEQRIRGTIMDELRAQDWLTR-----SLRDKFKKLEREFSQLEQRLGRNPSSDE 126

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           V A+A  L + +   +     L    SL+   +  D       D L    D   +    +
Sbjct: 127 V-ALAMGLELKDYFRLLEEIHLLSFVSLDDAWHDEDGAPFGLLDVL---EDKGTESPQSQ 182

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
              +     L  ++  L  +ER +      +E  + L+ + +  +++  R+ Q+ ++A  
Sbjct: 183 LIARQTVERLAEAIDALPEKERIVVTLYYYEE--LNLKEIGAVLDLTESRISQLHSQAII 240

Query: 279 KVQESIQK 286
           +++  +++
Sbjct: 241 RLRGKMKR 248


>gi|67922879|ref|ZP_00516377.1| Helix-turn-helix, Fis-type [Crocosphaera watsonii WH 8501]
 gi|67855303|gb|EAM50564.1| Helix-turn-helix, Fis-type [Crocosphaera watsonii WH 8501]
          Length = 260

 Score =  109 bits (273), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 52/257 (20%), Positives = 107/257 (41%), Gaps = 16/257 (6%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG-LPISEVVSEGNIGLMQAVKKF 93
             L   Y  +  L   ++LV  +L LV ++A         P  ++   G +G ++A+++F
Sbjct: 16  IELLSAYARNPSLELRNQLVECNLGLVRQVAHRISNQCSEPYEDLEQIGYLGFIRAIERF 75

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           +P++G   +++ + +I+  M  Y+    S+++I     +  L    ++++  L A    +
Sbjct: 76  NPQQGCAFSSFDIPYIRGEMLHYLRDKGSVMRIPRRWQE--LHNKGKKIRKQLTASLKRS 133

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYDHDGQ 211
                   IA+ L +   E       L      SL+A I+ +   S  + D L   H   
Sbjct: 134 PF---DWEIAEALMIPLEEWNECQLALQNRLLVSLDATISHNMDCSLSFGDTLPDQHYQA 190

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           +Q L E       R  L R++  L  + +   E   L E P   +  + +  +S   V +
Sbjct: 191 KQRLEED------RLQLQRALGQLEDKTKAAIECVFLNELPR--KEAAKQIGISPMTVTR 242

Query: 272 IEARAFKKVQESIQKQV 288
              +  +++   ++ QV
Sbjct: 243 HLKKGIQQLGSLLEPQV 259


>gi|332531601|ref|ZP_08407498.1| RNA polymerase sigma-28 subunit FliA/WhiG [Hylemonella gracilis
           ATCC 19624]
 gi|332038964|gb|EGI75393.1| RNA polymerase sigma-28 subunit FliA/WhiG [Hylemonella gracilis
           ATCC 19624]
          Length = 245

 Score =  109 bits (273), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 42/240 (17%), Positives = 106/240 (44%), Gaps = 16/240 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L+  ++ LV ++A        P   + +++  G IGL +A+ +++  +G +  T++ 
Sbjct: 18  RDALIRQYVPLVRRLAHHMMAKLPPSIQVDDLIQVGLIGLSEALTRYEATQGVQFETFAT 77

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +  +  + + G+  +QK +   L RL+  L        +      IA++L
Sbjct: 78  QRIRGAMIDELRENDWMSR-GSRKSQKEIESALTRLEHQL-------GRSPSESEIAEEL 129

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +  +E  ++  ++ G + +     S   +   + D  + D +     L+  +     R 
Sbjct: 130 GMELAEYQALLYKVKGTQLVYLEDMSGGDDEEGFLDRHMVDGESDPMALLRNQRL---RA 186

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L  ++  L  RE+ +       E  + L+ +++   V+  RV Q+ +++  +++  ++ 
Sbjct: 187 SLVDAIKALPEREQYVMSMYY--EQDMNLKEIAAVLGVTESRVCQLHSQSIARLRAKMRS 244


>gi|299531273|ref|ZP_07044683.1| RNA polymerase, sigma 28 subunit [Comamonas testosteroni S44]
 gi|298720680|gb|EFI61627.1| RNA polymerase, sigma 28 subunit [Comamonas testosteroni S44]
          Length = 239

 Score =  109 bits (273), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 48/242 (19%), Positives = 105/242 (43%), Gaps = 18/242 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L+  H+ LV +IA+       P   + +++  G IGL +A+ +F+ E+G +  T++ 
Sbjct: 10  RDALIRQHVPLVRRIALHMIAKLPPNVELDDLIQVGMIGLAEALSRFESEQGVQFDTFAS 69

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + R    +   +  +QK +   L RL+  L        +P     IA +L
Sbjct: 70  QRIRGAMLDEL-REGDWMSRSSRKSQKEIEQALNRLEQRL-------GRPPLESEIAAEL 121

Query: 167 NVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            ++  +  S+  ++ G     L  +      +   + +  V D       L+        
Sbjct: 122 GMALDDYQSLLGKVRGTQLVYLEDIGGGDGDDGDDYLERHVADSGADPFALLRDH---RM 178

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R+ L  ++  L  RE+ +       E+ + L+ +++   V+  RV Q+ ++A  +++  +
Sbjct: 179 RSALVEAIKALPEREQYVMGMYY--EHDMNLKEIAAVLGVTESRVCQLHSQAIARLRTKM 236

Query: 285 QK 286
           + 
Sbjct: 237 RS 238


>gi|157961206|ref|YP_001501240.1| flagellar biosynthesis sigma factor [Shewanella pealeana ATCC
           700345]
 gi|157846206|gb|ABV86705.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella pealeana
           ATCC 700345]
          Length = 239

 Score =  109 bits (273), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 47/239 (19%), Positives = 97/239 (40%), Gaps = 20/239 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              +V  +  LV +IA          + + +++  G +GL++A   FD  +G +  T++ 
Sbjct: 13  KTSIVEQYAPLVKRIAHHLLARLPASVQLDDLLQAGMMGLLEASSNFDGSKGAKFETFAG 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ +M + I R    V      NQ       RR+   +  +     +  +   IA++L
Sbjct: 73  IRIRGSMLDEIRR-GDWVPRSVHRNQ-------RRVAQVIDELEQELGRDARDGEIAERL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            VS  E  ++      D S+  ++   D   +      +   DG E    E        +
Sbjct: 125 EVSLEEYHAIL----NDVSVGKVVGIEDLGVAADG---INPEDGHEDDAYESLAEVEFHS 177

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            L  ++ +L  R+  +       +  + L+ + +  EVS  RV QI ++A  +++  ++
Sbjct: 178 ALVAAIKLLPERDALVLSLYY--DEALNLKEIGAILEVSESRVSQIHSQAMLRLKGKLK 234


>gi|327481248|gb|AEA84558.1| flagellar biosynthesis sigma factor [Pseudomonas stutzeri DSM 4166]
          Length = 241

 Score =  109 bits (273), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 48/247 (19%), Positives = 97/247 (39%), Gaps = 17/247 (6%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPER 97
           Y +     A +RL+  +  LV +IA          + + +++  G IGL++A KK+D  +
Sbjct: 3   YSKAQAKDAQYRLIDQYAPLVKRIAYHLLARLPASVQVDDLIQAGMIGLLEAAKKYDAGK 62

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G    TY+   I+  M + + R           N + +   +R +    +A T  + K  
Sbjct: 63  GASFETYAGIRIRGTMLDEV-RKGDWAPRSVHRNSRMVSEAIRAI----EAKTGRDAKDH 117

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           +V A   KL++ E   I  +   +   S + L+   +         L  D          
Sbjct: 118 EVAA-ELKLSLDEYYAILGDTLGSRLFSFDDLLQEGEHGE------LQEDASSTHPEPFR 170

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
             E +  +  L  ++  L  RE+ +       +  + L+ +     VS  RV Q+ ++  
Sbjct: 171 DLEDERFQQALADAIGNLPEREKLVLSLYY--DEELNLKEIGQVLGVSESRVSQLHSQCA 228

Query: 278 KKVQESI 284
            +++  +
Sbjct: 229 ARLRARL 235


>gi|320354339|ref|YP_004195678.1| RNA polymerase sigma-28 subunit SigD/FliA/WhiG [Desulfobulbus
           propionicus DSM 2032]
 gi|320122841|gb|ADW18387.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Desulfobulbus
           propionicus DSM 2032]
          Length = 244

 Score =  109 bits (273), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 44/240 (18%), Positives = 101/240 (42%), Gaps = 19/240 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           L    +L+  ++ LV  +               +++S   +GL+ A  KFDP +G +  T
Sbjct: 8   LDDRSQLIRENMPLVELVVQRMTPQVPSFMTKEDMISAAMVGLVDAANKFDPTKGVKFKT 67

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           ++ + ++ A+ +  +R            Q  L   + RL+  L        +  +   +A
Sbjct: 68  FAEYRVRGAIFDE-MRKLDWFSRSMRDKQNTLTQTMLRLERQL-------GRSPEEEEMA 119

Query: 164 KKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           +++ +S  E   +   ++  G  SL+  ++ ++   S    +L    D    V  +  E+
Sbjct: 120 REMALSIDEYRDLLAEVSHLGCVSLHETLDHTEDGRS----FLDSLEDIGGPVPDDLLEK 175

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +    ++   +  L+ +ER +      +E  +T + ++    VS  RV Q+ ++A  K++
Sbjct: 176 EEMTRVMAEILEELSEKERLVIALYYYEE--LTQKEIAEVLSVSEGRVSQLHSQALLKLR 233


>gi|163782183|ref|ZP_02177182.1| RNA polymerase sigma factor FliA [Hydrogenivirga sp. 128-5-R1-1]
 gi|159882715|gb|EDP76220.1| RNA polymerase sigma factor FliA [Hydrogenivirga sp. 128-5-R1-1]
          Length = 235

 Score =  109 bits (273), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 47/243 (19%), Positives = 105/243 (43%), Gaps = 20/243 (8%)

Query: 46  DLSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           +      LV  +L LV  IA          + + +++  G IGLM+A++K D ++     
Sbjct: 8   EEKEREELVLKYLPLVKSIAFTIKRQIPPTIDVRDLIGHGIIGLMKALEKLDTQKNP--E 65

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           +Y    I+ A+ +Y+               +R+    R+++  L+ +T+   +      I
Sbjct: 66  SYLKIRIRGAIYDYLR--------SLDFGSRRIREKERKIREALRELTEKLGREPTDEEI 117

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+ L      +     R++    LN     +++  S  +       D +++++     +K
Sbjct: 118 AEYLGEDLGTLQHDLSRISFSYILNLEDIFTEERRSYEEVIGSKRVDVEDEIV-----KK 172

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +    L  ++  L+ RE+ + +    +E P  L+ ++     S  RV QI+A A +K+++
Sbjct: 173 DLIEKLKEAIEALDEREKLVIQLIFYEELP--LKEIAQILNCSISRVSQIKAEAIEKLKK 230

Query: 283 SIQ 285
            ++
Sbjct: 231 FMK 233


>gi|294856637|gb|ADF45256.1| RNA polymerase sigma S factor [Escherichia sp. B1147]
          Length = 157

 Score =  109 bits (273), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 40/160 (25%), Positives = 74/160 (46%), Gaps = 7/160 (4%)

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     
Sbjct: 1   IARRYGNRGLALLDLIKEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRT 60

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           +++      K L   LR  +     ++           IA++L+    +V  M       
Sbjct: 61  IRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERI 115

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
            S++  +     +     D L  + +   +   + ++ K 
Sbjct: 116 TSVDTPL--GGDSEKALLDILADEKENGPEDTTQDDDMKQ 153


>gi|294856621|gb|ADF45248.1| RNA polymerase sigma S factor [Escherichia sp. B827]
 gi|294856623|gb|ADF45249.1| RNA polymerase sigma S factor [Escherichia sp. E1492]
 gi|294856625|gb|ADF45250.1| RNA polymerase sigma S factor [Escherichia sp. E807]
 gi|294856627|gb|ADF45251.1| RNA polymerase sigma S factor [Escherichia sp. H442]
 gi|294856629|gb|ADF45252.1| RNA polymerase sigma S factor [Escherichia sp. M863]
 gi|294856631|gb|ADF45253.1| RNA polymerase sigma S factor [Escherichia sp. TW10509]
 gi|294856633|gb|ADF45254.1| RNA polymerase sigma S factor [Escherichia sp. TW11930]
 gi|294856635|gb|ADF45255.1| RNA polymerase sigma S factor [Escherichia sp. TW11966]
 gi|294856639|gb|ADF45257.1| RNA polymerase sigma S factor [Escherichia sp. TW09231]
 gi|294856641|gb|ADF45258.1| RNA polymerase sigma S factor [Escherichia sp. TW09276]
 gi|294856643|gb|ADF45259.1| RNA polymerase sigma S factor [Escherichia sp. TW09254]
 gi|294856645|gb|ADF45260.1| RNA polymerase sigma S factor [Escherichia sp. TW09266]
 gi|294856647|gb|ADF45261.1| RNA polymerase sigma S factor [Escherichia sp. TA04]
 gi|294856649|gb|ADF45262.1| RNA polymerase sigma S factor [Escherichia sp. B685]
 gi|294856651|gb|ADF45263.1| RNA polymerase sigma S factor [Escherichia sp. TW14182]
 gi|294856653|gb|ADF45264.1| RNA polymerase sigma S factor [Escherichia albertii TW11588]
 gi|294856655|gb|ADF45265.1| RNA polymerase sigma S factor [Escherichia sp. H605]
 gi|294856657|gb|ADF45266.1| RNA polymerase sigma S factor [Escherichia sp. B49]
 gi|294856659|gb|ADF45267.1| RNA polymerase sigma S factor [Escherichia sp. TW09308]
 gi|294856661|gb|ADF45268.1| RNA polymerase sigma S factor [Escherichia sp. B1225]
 gi|294856663|gb|ADF45269.1| RNA polymerase sigma S factor [Escherichia sp. B646]
 gi|294856665|gb|ADF45270.1| RNA polymerase sigma S factor [Escherichia sp. E1118]
 gi|294856667|gb|ADF45271.1| RNA polymerase sigma S factor [Escherichia sp. E1195]
 gi|294856669|gb|ADF45272.1| RNA polymerase sigma S factor [Escherichia sp. E1196]
 gi|294856671|gb|ADF45273.1| RNA polymerase sigma S factor [Escherichia sp. E471]
 gi|294856673|gb|ADF45274.1| RNA polymerase sigma S factor [Escherichia sp. E472]
 gi|294856675|gb|ADF45275.1| RNA polymerase sigma S factor [Escherichia sp. E620]
 gi|294856677|gb|ADF45276.1| RNA polymerase sigma S factor [Escherichia sp. M1108]
 gi|294856679|gb|ADF45277.1| RNA polymerase sigma S factor [Escherichia sp. TA290]
 gi|294856681|gb|ADF45278.1| RNA polymerase sigma S factor [Escherichia sp. TW14263]
 gi|294856683|gb|ADF45279.1| RNA polymerase sigma S factor [Escherichia sp. TW14264]
 gi|294856685|gb|ADF45280.1| RNA polymerase sigma S factor [Escherichia sp. TW14265]
 gi|294856687|gb|ADF45281.1| RNA polymerase sigma S factor [Escherichia sp. TW14266]
 gi|294856689|gb|ADF45282.1| RNA polymerase sigma S factor [Escherichia sp. TW14267]
 gi|294856691|gb|ADF45283.1| RNA polymerase sigma S factor [Escherichia sp. RL325/96]
 gi|294856693|gb|ADF45284.1| RNA polymerase sigma S factor [Escherichia sp. Z205]
 gi|294856695|gb|ADF45285.1| RNA polymerase sigma S factor [Escherichia albertii]
 gi|294856697|gb|ADF45286.1| RNA polymerase sigma S factor [Escherichia albertii]
 gi|294856699|gb|ADF45287.1| RNA polymerase sigma S factor [Escherichia albertii]
 gi|294856701|gb|ADF45288.1| RNA polymerase sigma S factor [Escherichia albertii]
 gi|294856703|gb|ADF45289.1| RNA polymerase sigma S factor [Escherichia albertii]
 gi|294856705|gb|ADF45290.1| RNA polymerase sigma S factor [Escherichia albertii]
 gi|294856707|gb|ADF45291.1| RNA polymerase sigma S factor [Escherichia albertii]
 gi|294856709|gb|ADF45292.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|294856711|gb|ADF45293.1| RNA polymerase sigma S factor [Escherichia coli]
 gi|294856713|gb|ADF45294.1| RNA polymerase sigma S factor [Escherichia fergusonii]
 gi|294856715|gb|ADF45295.1| RNA polymerase sigma S factor [Escherichia fergusonii]
 gi|294856717|gb|ADF45296.1| RNA polymerase sigma S factor [Escherichia fergusonii]
          Length = 157

 Score =  109 bits (273), Expect = 5e-22,   Method: Composition-based stats.
 Identities = 40/160 (25%), Positives = 74/160 (46%), Gaps = 7/160 (4%)

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y   GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     
Sbjct: 1   IARRYGNRGLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRT 60

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           +++      K L   LR  +     ++           IA++L+    +V  M       
Sbjct: 61  IRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERI 115

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
            S++  +     +     D L  + +   +   + ++ K 
Sbjct: 116 TSVDTPL--GGDSEKALLDILADEKENGPEDTTQDDDMKQ 153


>gi|226939710|ref|YP_002794783.1| FliA1 [Laribacter hongkongensis HLHK9]
 gi|226714636|gb|ACO73774.1| FliA1 [Laribacter hongkongensis HLHK9]
          Length = 247

 Score =  109 bits (273), Expect = 6e-22,   Method: Composition-based stats.
 Identities = 46/238 (19%), Positives = 98/238 (41%), Gaps = 13/238 (5%)

Query: 54  VTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           +T HL LV K+A          + + ++V  G IGL++A ++FDP +G    T++   I+
Sbjct: 19  ITEHLTLVRKLASMMISRLPASVELDDLVQVGMIGLIEAAQQFDPAQGVLFETFASQRIR 78

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            AM + + R   L         ++   N ++++  +  +  +   P     IA +L +S 
Sbjct: 79  GAMLDELRRLDWL--------PRQARRNAKQIEEAMAQLEQSLGHPPGEGEIAARLGLSV 130

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            E  +M     G + +       D +       +    D       E       R+ L  
Sbjct: 131 DEYQTMLFECKGHQLVYFEDFGHDDDEGSSTRMVEQVADQGMVNPFEILGESRFRSHLVA 190

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           ++  L  R++ +       E  + L+ + +   V+  RV Q+ ++A  +++  ++  +
Sbjct: 191 AIKELPERDQLVMSLYY--EQELNLKEIGAVLNVTESRVCQLHSQAVARLRTKLKAWI 246


>gi|220932606|ref|YP_002509514.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Halothermothrix
           orenii H 168]
 gi|219993916|gb|ACL70519.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Halothermothrix
           orenii H 168]
          Length = 209

 Score =  109 bits (273), Expect = 6e-22,   Method: Composition-based stats.
 Identities = 50/269 (18%), Positives = 107/269 (39%), Gaps = 70/269 (26%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           ++ Y+ ++ KI +LE +EE  L  +Y+++ D  A  RL+TS+  LV KI   Y      +
Sbjct: 2   INDYLKQLGKIKILEAEEEKELWIKYKDYNDTEARQRLITSYQPLVFKIVRQYARDNEVV 61

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EG +GL+ A+  +D +RG   ++Y++++I+  +  Y                   
Sbjct: 62  MDLIQEGTLGLIDAIDSYDHKRGKSFSSYALYYIRGRVINY------------------- 102

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
                                         L  + +  I    R AG E L  L+   D 
Sbjct: 103 ------------------------------LKKAPACSIPAELRAAGSEFLEQLVTEGDD 132

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
                              L ++ E+    + + +++  L  RE  I     L++     
Sbjct: 133 -------------------LEDRVEKNLVMDRIKKAVGSLPSREGYIIREIYLKDKKP-- 171

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + ++ E  +S   + +++ +A ++++  +
Sbjct: 172 KKVAGEMGISLSYLHRLKKKAVRRLRGKL 200


>gi|146293655|ref|YP_001184079.1| flagellar biosynthesis sigma factor [Shewanella putrefaciens CN-32]
 gi|145565345|gb|ABP76280.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Shewanella
           putrefaciens CN-32]
 gi|319427054|gb|ADV55128.1| RNA polymerase sigma-28 factor for flagellar operon, FliA
           [Shewanella putrefaciens 200]
          Length = 237

 Score =  109 bits (273), Expect = 6e-22,   Method: Composition-based stats.
 Identities = 49/243 (20%), Positives = 99/243 (40%), Gaps = 20/243 (8%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
            L     +V  +  LV +IA          + + +++  G +GL++A  KFD  +G +  
Sbjct: 9   CLDNKSSIVEQYAPLVKRIAHHLLARLPASVQLDDLLQAGMMGLLEASSKFDGGKGAKFE 68

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           T++   I+ AM + I R    V      N        RR+   +  +     +  +   I
Sbjct: 69  TFAGIRIRGAMLDEIRR-GDWVPRSVHRNN-------RRVAQAIDELEQELGRDARDTEI 120

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+KL+++  E       +  D S+  +I   D   SQ    ++   D  +    E     
Sbjct: 121 AEKLDMTLDEYH----HILNDVSVGKIIGIEDLGVSQ---DILTLSDRSDDGSFEALAET 173

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              + L  ++ +L  R+  +       +  + L+ + +  EVS  RV QI ++A  +++ 
Sbjct: 174 QFHSALVEAIKLLPERDALVLSLYY--DEALNLKEIGAILEVSESRVSQILSQAMLRLKA 231

Query: 283 SIQ 285
            ++
Sbjct: 232 KLK 234


>gi|37680648|ref|NP_935257.1| flagellar biosynthesis sigma factor [Vibrio vulnificus YJ016]
 gi|37199396|dbj|BAC95228.1| polar Flagellar-specific RNA polymerase sigma factor FliA [Vibrio
           vulnificus YJ016]
          Length = 245

 Score =  109 bits (272), Expect = 6e-22,   Method: Composition-based stats.
 Identities = 43/249 (17%), Positives = 93/249 (37%), Gaps = 19/249 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPER 97
           Y +H ++++    +  +  LV +IA    G   P   + +++  G IGL++A + +D  +
Sbjct: 8   YDQHANVNSQKLFIERYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLIEAQQNYDASK 67

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G    TY+   I+ AM + I R    V      +        R +   +  +     +  
Sbjct: 68  GASFETYAGIRIRGAMLDDIRR-GDWVPRSVHKSN-------REISQAIAELEGLLNRDP 119

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +AK +       +S+         +N       ++     D +    D +     +
Sbjct: 120 TDAEVAKHMG------LSLEQYHGALTDINCSRLIGIEDLGVSDDVITSVEDSENNTPFK 173

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
               +  R  L  S+  L  RE  +       +  + L+ +     VS  RV QI +++ 
Sbjct: 174 GVADEYFRKALVESIKQLPEREALVLSLYY--DEELNLKEIGEILSVSESRVSQILSQSM 231

Query: 278 KKVQESIQK 286
           ++++  +  
Sbjct: 232 QRLRTKLSA 240


>gi|167623396|ref|YP_001673690.1| flagellar biosynthesis sigma factor [Shewanella halifaxensis
           HAW-EB4]
 gi|167353418|gb|ABZ76031.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella
           halifaxensis HAW-EB4]
          Length = 239

 Score =  109 bits (272), Expect = 6e-22,   Method: Composition-based stats.
 Identities = 46/239 (19%), Positives = 96/239 (40%), Gaps = 20/239 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              +V  +  LV +IA          + + +++  G +GL++A   FD  +G +  T++ 
Sbjct: 13  KTSIVEQYAPLVKRIAHHLLARLPASVQLDDLLQAGMMGLLEASSNFDGSKGAKFETFAG 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ +M + I R    V      NQ       RR+   +  +     +  +   IA++L
Sbjct: 73  IRIRGSMLDEIRR-GDWVPRSVHRNQ-------RRVAQVIDELEQELGRDARDGEIAERL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   E  S+      D S+  ++   D   +      +   DG E    E        +
Sbjct: 125 EMPLDEYYSIL----NDVSVGKVVGIEDLGVAVEG---LNQDDGHEDDAYESLAEVEFHS 177

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            L  ++ +L  R+  +       +  + L+ + +  EVS  RV QI ++A  +++  ++
Sbjct: 178 ALVAAIKLLPERDALVLSLYY--DEALNLKEIGAILEVSESRVSQIHSQAMLRLKGKLK 234


>gi|312879616|ref|ZP_07739416.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Aminomonas
           paucivorans DSM 12260]
 gi|310782907|gb|EFQ23305.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Aminomonas
           paucivorans DSM 12260]
          Length = 247

 Score =  109 bits (272), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 51/246 (20%), Positives = 103/246 (41%), Gaps = 21/246 (8%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQA 89
           E+  L + YR+        RLV  +L LV  +A         GL   +++S G +GL+ A
Sbjct: 4   EDNQLWEDYRKEPSPELKERLVRRYLPLVRYVAGRMAVSPPPGLDFEDLLSFGAMGLLDA 63

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +++FD +RGF   T+++  I+ A+ + + R   + + G           L++L+  ++  
Sbjct: 64  IERFDLDRGFCFQTFAVPRIRGAILDELRRYDWISRTGR--------EKLQKLERTVERF 115

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYD 207
                 P+    +   L ++E     +    +     SL+ ++   D +  Q +  L  D
Sbjct: 116 ARTQGNPDD-ETLMDALGMNEKAYKELLEIASRSYVVSLDEVLALEDGD-VQREGILEDD 173

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
                   +++ E+K   + +   +S L  RER +          +TL+ +     V+  
Sbjct: 174 ----APSPLDRMEQKEEVDRVLAGLSELPERERLLISLYYY--EGLTLKEIGGVLGVTES 227

Query: 268 RVRQIE 273
           R  Q+ 
Sbjct: 228 RASQLH 233


>gi|261409324|ref|YP_003245565.1| FliA/WhiG subfamily RNA polymerase sigma-28 factor [Paenibacillus
           sp. Y412MC10]
 gi|329928598|ref|ZP_08282465.1| putative RNA polymerase sigma factor SigB [Paenibacillus sp. HGF5]
 gi|261285787|gb|ACX67758.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus sp. Y412MC10]
 gi|328937714|gb|EGG34123.1| putative RNA polymerase sigma factor SigB [Paenibacillus sp. HGF5]
          Length = 256

 Score =  109 bits (272), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 41/262 (15%), Positives = 106/262 (40%), Gaps = 19/262 (7%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI-SEVVSEGNI 84
            P   + E   L ++Y++  D   A  L+  +  +V   A         +  ++   G +
Sbjct: 6   TPQESRDEAVHLIEQYQQTKDNDIATVLIKKYEPMVKMAAGKIARNRPDLYEDLYQVGQM 65

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
            L++ ++++D   G     Y+M  +   M+ ++      +++     +K        ++ 
Sbjct: 66  ALIRLLQQYDISLGIPFEPYAMKSMIGHMKNFLRDKSWYIQVPRRIKEKGAL-----VQQ 120

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC--RLAGDESLNALINSSDKNSSQWQD 202
            +  +     +   V  IA  L++S  E + +          SL++ + S ++  +   +
Sbjct: 121 AIDELMVKLERSPDVNEIASYLDLSVEETVEVLAGRECYHYVSLDSPL-SQEETGATLGE 179

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
            +  D +  + V         +R  L ++MS L  +E+++       +   +   ++   
Sbjct: 180 LISSDVNDFDSV--------EKRMDLQQAMSQLKEQEQKVLLLAF--QEGQSQRAIAQRL 229

Query: 263 EVSRERVRQIEARAFKKVQESI 284
            VS+  V +I+ RA +K+++ +
Sbjct: 230 GVSQMSVSRIQKRATEKLKQIM 251


>gi|332527910|ref|ZP_08403946.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Rubrivivax
           benzoatilyticus JA2]
 gi|332112486|gb|EGJ12279.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Rubrivivax
           benzoatilyticus JA2]
          Length = 237

 Score =  109 bits (272), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 46/249 (18%), Positives = 113/249 (45%), Gaps = 17/249 (6%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPER 97
           Y   G L A + L+  +  LV ++A          + + +++  G IGL  A+ +FD  +
Sbjct: 2   YTAKGQLDA-NALLRQYSPLVRRLAHQMIAKLPANVELDDLIQVGMIGLSDALSRFDAAQ 60

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G +  T++   I+ AM + +  +  + + G   +Q+ +   + +L+  L        +  
Sbjct: 61  GVQFETFATQRIRGAMLDELRGNDWMSR-GDRRHQRSIEAAVHKLEQKLH-------RAP 112

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               IAK++ +S +E   +  ++ G + +     S D     + D  V+D +      + 
Sbjct: 113 NESEIAKEMGLSLAEYQELLTKVRGTQLIYLEDMSGDDGDEDYLDRHVHDDEAN---PLG 169

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
           + + +  R  L  ++  L  RE+ +       E+ + L+ +++  +V+  RV Q+ +++ 
Sbjct: 170 RLQDQRMRQALVDAIKNLPEREQYVMSMYY--EHDMNLKEIAAVLKVTESRVCQLHSQSI 227

Query: 278 KKVQESIQK 286
            +++  +++
Sbjct: 228 ARLRTRLRE 236


>gi|124516296|gb|EAY57804.1| putative RNA polymerase sigma 28 subunit, FliA/WhiG [Leptospirillum
           rubarum]
          Length = 251

 Score =  109 bits (272), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 46/229 (20%), Positives = 96/229 (41%), Gaps = 18/229 (7%)

Query: 61  VVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           V   A+ Y       L + +++S G  GL+ A ++FDP RG +  T +   I+ AM + I
Sbjct: 17  VKFFALRYSHRLPPELDVDDLISAGMGGLLDAARRFDPSRGIKFKTLAEHRIRGAMLDEI 76

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV--IS 175
             +  +     +  +K       +       +     +      IA +++++E E   +S
Sbjct: 77  RAADWM---PRSVREKLTHVQQVKT-----ELIARYKREPTRQEIAARMDMTEEEFDRLS 128

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
           ++       SL  L++  D +S    D L    +G     +    +      L +++  L
Sbjct: 129 VDIEPHHLVSLEDLMDPEDGDSPSLLDRLSAPQEGD---PLASLLQSEVSEKLCQALDRL 185

Query: 236 NPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             ++R +      +E  +T++ ++    VS  RV QI  +A   +++S+
Sbjct: 186 PEKQRLVLSLYYYEE--LTMKEVARVVGVSESRVSQIHGQALAALKQSL 232


>gi|157833814|pdb|1SIG|A Chain A, Crystal Structure Of A Sigma70 Subunit Fragment From
           Escherichia Coli Rna Polymerase
          Length = 339

 Score =  109 bits (272), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 35/105 (33%), Positives = 57/105 (54%), Gaps = 2/105 (1%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + +I +   L  ++   + +R    E     A   +V ++LRLV+ IA  Y   GL   +
Sbjct: 235 LQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLD 294

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           ++ EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+   I     
Sbjct: 295 LIQEGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQAR 339


>gi|119491111|ref|ZP_01623269.1| Sigma 32 (RpoH) [Lyngbya sp. PCC 8106]
 gi|119453656|gb|EAW34816.1| Sigma 32 (RpoH) [Lyngbya sp. PCC 8106]
          Length = 304

 Score =  109 bits (272), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 38/253 (15%), Positives = 103/253 (40%), Gaps = 24/253 (9%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVKKFD 94
            L + Y++    S  +++V  ++ LV +    +         ++   G IGL+QA+++FD
Sbjct: 58  ELLQEYKQFPCQSIRNQIVQLNMGLVRQEVHHWVKKCPESYDDLFQIGCIGLIQAIERFD 117

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +G   +++++ +I+  +  Y+     L+++    +Q +     +     +  + +   
Sbjct: 118 LTKGCAFSSFAVPYIRGEILHYLRDKSLLIRVPRRCSQLK-----QEAAKLVILLQEKLH 172

Query: 155 KPEQVVAIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +    + IA  L +S  +   + +  + +   SL+  +N          + +V  +    
Sbjct: 173 RKPTDLEIANSLGISIEKWNQVKLTVKNSSVLSLDIPLNDEFNEKHCLGELIVDSNPNAS 232

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
               EK +       L  ++  L    R I E    +   +T + ++ +  +S   V   
Sbjct: 233 MSQEEKID-------LEMALLKLKAENRDILELVFFKN--LTYKEVAKQMNISVMTVS-- 281

Query: 273 EARAFKKVQESIQ 285
                +++++S++
Sbjct: 282 -----RRLKQSLR 289


>gi|27365297|ref|NP_760825.1| flagellar biosynthesis sigma factor [Vibrio vulnificus CMCP6]
 gi|320155681|ref|YP_004188060.1| RNA polymerase sigma factor for flagellar operon [Vibrio vulnificus
           MO6-24/O]
 gi|27361444|gb|AAO10352.1| RNA polymerase sigma factor for flagellar operon [Vibrio vulnificus
           CMCP6]
 gi|319930993|gb|ADV85857.1| RNA polymerase sigma factor for flagellar operon [Vibrio vulnificus
           MO6-24/O]
          Length = 244

 Score =  109 bits (272), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 43/249 (17%), Positives = 93/249 (37%), Gaps = 19/249 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPER 97
           Y +H ++++    +  +  LV +IA    G   P   + +++  G IGL++A + +D  +
Sbjct: 7   YDQHANVNSQKLFIERYSVLVKRIAHHLLGRLPPSVQVEDLIQAGMIGLIEAQQNYDASK 66

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G    TY+   I+ AM + I R    V      +        R +   +  +     +  
Sbjct: 67  GASFETYAGIRIRGAMLDDIRR-GDWVPRSVHKSN-------REISQAIAELEGLLNRDP 118

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +AK +       +S+         +N       ++     D +    D +     +
Sbjct: 119 TDAEVAKHMG------LSLEQYHGALTDINCSRLIGIEDLGVSDDVITSVEDSENNTPFK 172

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
               +  R  L  S+  L  RE  +       +  + L+ +     VS  RV QI +++ 
Sbjct: 173 GVADEYFRKALVESIKQLPEREALVLSLYY--DEELNLKEIGEILSVSESRVSQILSQSM 230

Query: 278 KKVQESIQK 286
           ++++  +  
Sbjct: 231 QRLRTKLSA 239


>gi|24374722|ref|NP_718765.1| flagellar biosynthesis sigma factor [Shewanella oneidensis MR-1]
 gi|24349382|gb|AAN56209.1|AE015759_1 RNA polymerase sigma-27 factor [Shewanella oneidensis MR-1]
          Length = 237

 Score =  109 bits (272), Expect = 7e-22,   Method: Composition-based stats.
 Identities = 48/244 (19%), Positives = 99/244 (40%), Gaps = 20/244 (8%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
            L     +V  +  LV +IA          + + +++  G +GL++A  KFD  +G +  
Sbjct: 9   CLDNKTSIVEQYAPLVKRIAHHLLARLPASVQLDDLLQAGMMGLLEASSKFDGGKGAKFE 68

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           T++   I+ AM + I R    V      N        RR+   +  +     +  +   I
Sbjct: 69  TFAGIRIRGAMLDEIRR-GDWVPRSVHRNN-------RRIAQAIDELEQVLGRDARDTEI 120

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+KL+++  E       +  D S+  +I   D   S+    ++   D       E     
Sbjct: 121 AEKLDMTLDEYH----HILNDVSVGKIIGIEDLGVSE---DILTTSDNVSDGTFEVLAET 173

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              + L  ++ +L  R+  +       +  + L+ + +  EVS  RV QI ++A  +++ 
Sbjct: 174 QFHSALVEAIKILPERDALVLSLYY--DEALNLKEIGAILEVSESRVSQILSQAMLRLKG 231

Query: 283 SIQK 286
            +++
Sbjct: 232 KLKQ 235


>gi|49082218|gb|AAT50509.1| PA1455 [synthetic construct]
          Length = 248

 Score =  108 bits (271), Expect = 8e-22,   Method: Composition-based stats.
 Identities = 44/251 (17%), Positives = 99/251 (39%), Gaps = 22/251 (8%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDP 95
           + Y +    ++  +L+  +  LV +IA    G     + + +++  G IGL++A KK+D 
Sbjct: 8   RMYSKAQAQNSQEQLIQRYAPLVKRIAYHLLGRLPASVQVEDLMQAGMIGLLEAAKKYDA 67

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            +G    TY+   I+ AM + + R           N + +   +R ++           +
Sbjct: 68  GKGASFETYAGIRIRGAMLDEV-RKGDWAPRSVHRNTRMVTDAIRAIEA-------RTGR 119

Query: 156 PEQVVAIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
             +   +A +L +S  +   I  + + +   S + L+   +         L  D      
Sbjct: 120 DAKDHEVAAELQLSLEDYYGILSDTQGSRLYSFDDLLQDGE-------HGLPEDTSLSHN 172

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
             I     +  +  L  +++ L  RER +       +  + L+ +     VS  RV Q+ 
Sbjct: 173 EPIHGLLDERFQAALADAIAKLPERERLVLALYY--DEELNLKEIGEVLGVSESRVSQLH 230

Query: 274 ARAFKKVQESI 284
           ++   +++  +
Sbjct: 231 SQCAARLRARL 241


>gi|169334386|ref|ZP_02861579.1| hypothetical protein ANASTE_00786 [Anaerofustis stercorihominis DSM
           17244]
 gi|169259103|gb|EDS73069.1| hypothetical protein ANASTE_00786 [Anaerofustis stercorihominis DSM
           17244]
          Length = 233

 Score =  108 bits (271), Expect = 8e-22,   Method: Composition-based stats.
 Identities = 51/262 (19%), Positives = 98/262 (37%), Gaps = 62/262 (23%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE  + K        +    L+  +LRLVV IA  +      + +++S G IGL
Sbjct: 29  PPLTKEEEQEVLKNLESDETNTTKTILIERNLRLVVYIAKKFDTSSASVEDLISIGTIGL 88

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AVK F  E+  +LATY+   I+  +  ++                     + R++G  
Sbjct: 89  IKAVKTFKVEKNIKLATYASKCIENEILMHL-------------------RKVNRIRGE- 128

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                            ++ DE LN      D N     D L  
Sbjct: 129 ---------------------------------ISLDEPLN---VDYDGNELLLSDILGT 152

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
           + D     + +K ++   + ++  ++  L   E+ I   R         T + L++   +
Sbjct: 153 NGDP----VKDKIDKDVNKEIMLLAVDRLKESEKEIINYRFGLNGKEKKTQKELANMLNI 208

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+  + ++E R    +++ + K
Sbjct: 209 SQSYISRLEKRIISNLKKEVNK 230


>gi|319944142|ref|ZP_08018420.1| DNA-directed RNA polymerase sigma subunit FliA [Lautropia mirabilis
           ATCC 51599]
 gi|319742636|gb|EFV95045.1| DNA-directed RNA polymerase sigma subunit FliA [Lautropia mirabilis
           ATCC 51599]
          Length = 241

 Score =  108 bits (271), Expect = 8e-22,   Method: Composition-based stats.
 Identities = 44/238 (18%), Positives = 102/238 (42%), Gaps = 16/238 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              ++  + ++V ++A+         + + +++  G IGL+ AV +FD   G +  T++M
Sbjct: 13  RDSVIERYGKMVRRVAVQMAARLPSSIELDDLIQAGLIGLVDAVSRFDAAMGVQFDTFAM 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             ++ AM + + R+   +      +Q       R ++  + A+     +P Q   IA +L
Sbjct: 73  QRVRGAMLDEL-RNADWMPRSVRKSQ-------RSIEQAIHAVEQRLGRPAQEREIADEL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            V   E   +     G + L    ++S+ +     + ++ D          + E    R 
Sbjct: 125 QVPLEEYQRLLSSAKGSQLLYFEDSASEDDDESRIEQMLPDD---APTPDRRLEDARFRE 181

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L  ++  L  RE+ +     ++E  +TL+ +     V+  RV Q+ ++A  +++  +
Sbjct: 182 SLVAAIDGLPEREKLLMNLYYVEE--LTLKEIGEVLGVTESRVSQLHSQAVARLRAKL 237


>gi|158341138|ref|YP_001522305.1| hypothetical protein AM1_E0222 [Acaryochloris marina MBIC11017]
 gi|158311379|gb|ABW32991.1| hypothetical protein AM1_E0222 [Acaryochloris marina MBIC11017]
          Length = 427

 Score =  108 bits (271), Expect = 8e-22,   Method: Composition-based stats.
 Identities = 50/243 (20%), Positives = 108/243 (44%), Gaps = 21/243 (8%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + GDL A  R +  +  LV + A  +RG      ++V+ GN+GL  A++KFD  +G++ 
Sbjct: 29  AQAGDLRARDRFIRQNEGLVFQQAHKFRGL-ADWDDLVNAGNLGLAIAIQKFDVAKGYKF 87

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           ++Y++  I+  ++  I     +           +  +L+ ++   QAI  +  +   +  
Sbjct: 88  SSYAVKVIRTEIRRLIHEFKGI--------SIEISLHLKEIEQASQAIRMDLDREPTITE 139

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           ++ +   S+  + +   +    E+ +  I  +D    +  D +  D    E    E  ++
Sbjct: 140 LSDETGYSQQVIFNAWNKANVVETASLNIPLNDDQGCEQLDVIGVDDRTWEFT--ETLDQ 197

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           KN        ++ L  RE  I  A+R   +  + + + +   +S ERVRQ+  +A   ++
Sbjct: 198 KNY-------IAQLPDREAFIVRAKR---DGFSNKEIGTMLSLSGERVRQLLKQARAFLK 247

Query: 282 ESI 284
             +
Sbjct: 248 HLM 250


>gi|149917001|ref|ZP_01905502.1| DNA-directed RNA polymerase sigma subunit (RpoD) [Plesiocystis
           pacifica SIR-1]
 gi|149822279|gb|EDM81670.1| DNA-directed RNA polymerase sigma subunit (RpoD) [Plesiocystis
           pacifica SIR-1]
          Length = 411

 Score =  108 bits (271), Expect = 8e-22,   Method: Composition-based stats.
 Identities = 61/266 (22%), Positives = 110/266 (41%), Gaps = 34/266 (12%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             RL    LRLV+ +   YR + +  +  +  G +GL +A+ +F+PERG++ +TY+ WWI
Sbjct: 162 RRRLFADSLRLVISLVHRYRKH-MDFATGMLRGALGLDKAIDRFEPERGWQFSTYATWWI 220

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA------ 163
           +  +    +   + +++   A ++   F +  ++  L + T      E+V+  A      
Sbjct: 221 RQNITRSSMDFATALRVPVHAAEQTTRFWM--VQQELWSQTGVRPTDEEVLNQANFKFSI 278

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD------WLVYDHDGQEQVLIE 217
           ++L        +    L   + L A     D +     +      W+    D     + +
Sbjct: 279 ERLGDYRRHART--AHLTRRDQLGAAEAILDSDIPSLLEGNPASGWVRAAIDHATAQVDD 336

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEAR 275
           KE  +  R                IF  R L +     TL  L  EF+++RER+RQ EA+
Sbjct: 337 KEHSRPSRGRWHA-----------IFSRRILGDQIQNNTLRELGEEFDITRERIRQNEAK 385

Query: 276 AFKKV-QESIQKQVELSSSPPLLQKP 300
               + +   + Q  L   PPL   P
Sbjct: 386 LIDFLARRLFRGQEHL---PPLAWGP 408


>gi|294084434|ref|YP_003551192.1| RNA polymerase sigma 28 subunit FliA/WhiG [Candidatus
           Puniceispirillum marinum IMCC1322]
 gi|292664007|gb|ADE39108.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Candidatus
           Puniceispirillum marinum IMCC1322]
          Length = 241

 Score =  108 bits (271), Expect = 8e-22,   Method: Composition-based stats.
 Identities = 38/237 (16%), Positives = 101/237 (42%), Gaps = 22/237 (9%)

Query: 53  LVTSHLRLVVKIAMGYRGYGL---PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           L+  H+ LV +IA    G       I ++V  G  GL+ A + +  + G   ++Y+   I
Sbjct: 15  LIRDHMELVRQIAWHIHGRVHASAEIEDLVQIGYYGLVMAAQNYTVQEGATFSSYASIRI 74

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + ++ +++ ++ +L +              ++ +   + +     +   +  +A  L+++
Sbjct: 75  RGSIVDHLRKNSNLCR--------TTIQMQKKARQSEEILRQKLGRDPSIDEVASDLDIA 126

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             E+         +        S D    ++  W V + +  E  + + E     R++L 
Sbjct: 127 PEEMREWEQAFQANVH-----QSLDNVYDEFSIWFVSNENTPEDNISDNEL----RDVLK 177

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +++ L  RE  + +   ++E  + +  ++   +V+  RV QI+  A  +++  +++
Sbjct: 178 DALTTLPEREALVIQLYYVEE--LNVYEIAEILDVTTGRVSQIKKAAIARLRGYMEQ 232


>gi|293376227|ref|ZP_06622470.1| RNA polymerase sigma-E factor [Turicibacter sanguinis PC909]
 gi|325845158|ref|ZP_08168467.1| RNA polymerase sigma-E factor [Turicibacter sp. HGF1]
 gi|292645119|gb|EFF63186.1| RNA polymerase sigma-E factor [Turicibacter sanguinis PC909]
 gi|325488823|gb|EGC91223.1| RNA polymerase sigma-E factor [Turicibacter sp. HGF1]
          Length = 236

 Score =  108 bits (271), Expect = 8e-22,   Method: Composition-based stats.
 Identities = 53/271 (19%), Positives = 111/271 (40%), Gaps = 64/271 (23%)

Query: 19  YIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           YI     +P  L K EE+ +  R++  GD  A   L+  +LRLVV IA  +   G+ + +
Sbjct: 25  YIRGNETLPEPLSKDEEFNVLTRFQ-GGDERARQTLIEHNLRLVVYIAKKFESSGVNLED 83

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++S G +GL++ V+ F  ++  +LATY+   I+  +  ++ ++  +              
Sbjct: 84  LISIGTLGLIKGVQTFKMDKNIKLATYASRCIENEILMHLRKTNRI-------------- 129

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
                                               +S++  L  D   N L+ S    +
Sbjct: 130 ---------------------------------RNEVSLDEPLNVDWDGNELLLSDILGT 156

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
            + + +   + D + Q++ +   R  RR            RE  I   R     E+P+T 
Sbjct: 157 EENEVYKDIEEDVERQLVFDAINRLKRRE-----------RE--IMYMRFGLCGEDPLTQ 203

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           + ++ + ++S+  + ++E +   K+++ + K
Sbjct: 204 KEVAQKLDISQSYISRLEKKIIDKIRKEVLK 234


>gi|298708236|emb|CBJ48299.1| rpoD [Ectocarpus siliculosus]
          Length = 381

 Score =  108 bits (271), Expect = 8e-22,   Method: Composition-based stats.
 Identities = 58/268 (21%), Positives = 106/268 (39%), Gaps = 24/268 (8%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYR--GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
             A   L   H  LV  +A  Y+     L + ++  EGN+GL++AV+KFD  +G R ++Y
Sbjct: 111 RKAQRTLALCHQGLVRSVAYRYKQVSRNLSLDDLTQEGNVGLLEAVEKFDSTKGTRFSSY 170

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +++ IKA++   I     LV++   A    +   +      LQ  +  ++  +  +A+A 
Sbjct: 171 AVFRIKASVLRAIADKDRLVRVPVHAQDAAM--RILAASHALQLESGGDVPTDAQLAVAL 228

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKN----SSQWQDWLVYDHDGQEQVLIEKEE 220
            +  +   +   +        L+     S       S       +    G EQ   E  +
Sbjct: 229 GMPEASVALYRKSLLPQNIADLDNPALPSSPQGRGGSGAAGGGSLGGRVGGEQWPWEASQ 288

Query: 221 RKN----RRNMLTRSMSVLNPRERRIFEARRL------------QENPVTLENLSSEFEV 264
                  RR+M+    + L+P E R    R                  +T + +    E+
Sbjct: 289 LAQAHVVRRDMMRAMQACLSPTEERALRLRFGLGGAEKEGAVADGGGALTFKEIGRTMEL 348

Query: 265 SRERVRQIEARAFKKVQESIQKQVELSS 292
           S E +R++  R+  K+Q S +    L S
Sbjct: 349 SAEGIRKMVFRSIAKLQASDEANGLLLS 376


>gi|206890966|ref|YP_002249859.1| RNA polymerase sigma factor for flagellar operon
           [Thermodesulfovibrio yellowstonii DSM 11347]
 gi|206742904|gb|ACI21961.1| RNA polymerase sigma factor for flagellar operon
           [Thermodesulfovibrio yellowstonii DSM 11347]
          Length = 236

 Score =  108 bits (271), Expect = 9e-22,   Method: Composition-based stats.
 Identities = 41/248 (16%), Positives = 106/248 (42%), Gaps = 21/248 (8%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
                 L+   L  +   A+ Y       L + +++S G  GL++A+ K++P     L  
Sbjct: 5   EDDKESLIKQFLPKIKHYALRYHHIVQSVLELEDLISAGIKGLLEALNKYNPSLNVPLVA 64

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           +  + I+ A+ + I      V +  +   ++   N+++   +L+     + K      +A
Sbjct: 65  FIDYRIRGAILDEI----RSVDV-FSKEFRKKVENVKKTYKNLKQ----SGKDPTDEELA 115

Query: 164 KKLNVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
             LN+++ E+  +   +  +   SL++ +   + +     + +  + +     + E  + 
Sbjct: 116 NYLNITQEELQEVYQSITASDIVSLDSFVVGENGDKLNLLEVISDEKN-----IFEDIKF 170

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +  +  LT ++  L+  E+ I      +E  + ++ ++    +S  RV QI  +   K++
Sbjct: 171 RELKEKLTSAIENLSETEKLIISLYYYEE--LNMKEIAQVLGISLSRVSQIHGKTLLKLK 228

Query: 282 ESIQKQVE 289
             + K+V+
Sbjct: 229 NFLAKEVD 236


>gi|134094539|ref|YP_001099614.1| sigma F (sigma 28) factor of RNA polymerase, transcription of late
           flagellar genes (class 3a and 3b operons) [Herminiimonas
           arsenicoxydans]
          Length = 216

 Score =  108 bits (271), Expect = 9e-22,   Method: Composition-based stats.
 Identities = 34/215 (15%), Positives = 94/215 (43%), Gaps = 13/215 (6%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++  G IGL+ AV +++   G +  TY++  I+ AM + +  S  +         +
Sbjct: 10  EVDDLIQAGMIGLLDAVGRYEETHGAQFETYAVQRIRGAMLDELRSSDWM--------PR 61

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            +  N+R+++  + ++     +P     +AK+L +S ++   +     G + +       
Sbjct: 62  SMRQNMRKIEVAMNSLQQKLGRPPNESEVAKQLKLSLADYQDLLSDGGGHQLVYYEDFHD 121

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
            +++  + D    D        ++       R+ +  ++  L  RE+         E  +
Sbjct: 122 SEDNEHFLDRYCTDESPD---PLQNLMNTGFRSAVIAAIEALPEREK--ILMSLYYEQEM 176

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            L+ + +   V+  RV Q+ ++A  +++ +++++ 
Sbjct: 177 NLKEIGAVMGVTESRVSQLHSQAIARMRANLREKA 211


>gi|56421070|ref|YP_148388.1| sporulation sigma factor SigK [Geobacillus kaustophilus HTA426]
 gi|56380912|dbj|BAD76820.1| sporulation mother cell-specific RNA polymerase sigma-27 factor
           precursor (sigma K) (stage IV sporulation protein CB)
           [Geobacillus kaustophilus HTA426]
          Length = 237

 Score =  108 bits (271), Expect = 9e-22,   Method: Composition-based stats.
 Identities = 57/273 (20%), Positives = 101/273 (36%), Gaps = 61/273 (22%)

Query: 16  LSRYIHEIRKIPMLEK-QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           L  YI        L   +EE  LA      GD  A +RL+  +LRLV  I   +   G  
Sbjct: 18  LVSYIKNNAFPQPLSAQEEEKYLA--LMAKGDEQARNRLIEHNLRLVAHIVKKFENTGEE 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++S G IGL++A++ + P +G +LATY+   I+  +                     
Sbjct: 76  VEDLISIGTIGLIKAIESYSPGKGTKLATYAARCIENEI--------------------- 114

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
              +LR LK   +                   +VS  E I  +        L+ L    +
Sbjct: 115 -LMHLRSLKKTRK-------------------DVSLHEPIGQDKEGNEISLLDILKAEGE 154

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
             + +    +  +   Q   ++++ E    + ++     +   RE+             T
Sbjct: 155 DIADEIHLNMELEQVKQYISVLDERE----KEVIINRFGLGRQREK-------------T 197

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              ++ E  +SR  V +IE RA  K+     +Q
Sbjct: 198 QREIAKELGISRSYVSRIEKRALMKMFHEFYRQ 230


>gi|146282908|ref|YP_001173061.1| flagellar biosynthesis sigma factor [Pseudomonas stutzeri A1501]
 gi|145571113|gb|ABP80219.1| flagellar biosynthesis sigma factor FliA [Pseudomonas stutzeri
           A1501]
          Length = 241

 Score =  108 bits (270), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 48/247 (19%), Positives = 98/247 (39%), Gaps = 17/247 (6%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPER 97
           Y +     A +RL+  +  LV +IA          + + +++  G IGL++A KK+D  +
Sbjct: 3   YSKAQAKDAQYRLIDQYAPLVKRIAYHLLARLPASVQVDDLIQAGMIGLLEAAKKYDAGK 62

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G    TY+   I+  M + + R           N + +   +R +    +A T  + K  
Sbjct: 63  GASFETYAGIRIRGTMLDEV-RKGDWAPRSVHRNSRMVSEAIRAI----EAKTGRDAKDH 117

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           +V A   KL++ E   I  +   +   S + L+   +         L  D          
Sbjct: 118 EVAA-ELKLSLDEYYGILGDTLGSRLFSFDDLLQEGEHGD------LQEDAGSTHPEPFR 170

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
             E +  +  L  +++ L  RE+ +       +  + L+ +     VS  RV Q+ ++  
Sbjct: 171 DLEDERFQQALADAIANLPEREKLVLSLYY--DEELNLKEIGQVLGVSESRVSQLHSQCA 228

Query: 278 KKVQESI 284
            +++  +
Sbjct: 229 ARLRARL 235


>gi|120598267|ref|YP_962841.1| flagellar biosynthesis sigma factor [Shewanella sp. W3-18-1]
 gi|120558360|gb|ABM24287.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Shewanella sp.
           W3-18-1]
          Length = 237

 Score =  108 bits (270), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 49/243 (20%), Positives = 99/243 (40%), Gaps = 20/243 (8%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
            L     +V  +  LV +IA          + + +++  G +GL++A  KFD  +G +  
Sbjct: 9   CLDNKSSIVEQYAPLVKRIAHHLLARLPASVQLDDLLQAGMMGLLEASSKFDGGKGAKFE 68

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           T++   I+ AM + I R    V      N        RR+   +  +     +  +   I
Sbjct: 69  TFAGIRIRGAMLDEIRR-GDWVPRSVHRNN-------RRVAQAIDELEKELGRDARDTEI 120

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+KL+++  E       +  D S+  +I   D   SQ    ++   D  +    E     
Sbjct: 121 AEKLDMTLDEYH----HILNDVSVGKIIGIEDLGVSQ---DILTLSDRSDDGSFEALAET 173

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              + L  ++ +L  R+  +       +  + L+ + +  EVS  RV QI ++A  +++ 
Sbjct: 174 QFHSALVEAIKLLPERDALVLSLYY--DEALNLKEIGAILEVSESRVSQILSQAMLRLKA 231

Query: 283 SIQ 285
            ++
Sbjct: 232 KLK 234


>gi|126175111|ref|YP_001051260.1| flagellar biosynthesis sigma factor [Shewanella baltica OS155]
 gi|153001435|ref|YP_001367116.1| flagellar biosynthesis sigma factor [Shewanella baltica OS185]
 gi|160876160|ref|YP_001555476.1| flagellar biosynthesis sigma factor [Shewanella baltica OS195]
 gi|217972633|ref|YP_002357384.1| flagellar biosynthesis sigma factor [Shewanella baltica OS223]
 gi|304409942|ref|ZP_07391561.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Shewanella
           baltica OS183]
 gi|307302345|ref|ZP_07582103.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Shewanella
           baltica BA175]
 gi|125998316|gb|ABN62391.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Shewanella
           baltica OS155]
 gi|151366053|gb|ABS09053.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella baltica
           OS185]
 gi|160861682|gb|ABX50216.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella baltica
           OS195]
 gi|217497768|gb|ACK45961.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella baltica
           OS223]
 gi|304351351|gb|EFM15750.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Shewanella
           baltica OS183]
 gi|306914383|gb|EFN44804.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Shewanella
           baltica BA175]
 gi|315268356|gb|ADT95209.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella baltica
           OS678]
          Length = 237

 Score =  108 bits (270), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 48/243 (19%), Positives = 100/243 (41%), Gaps = 20/243 (8%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
            L     +V  +  LV +IA          + + +++  G +GL++A  KFD  +G +  
Sbjct: 9   CLDNKSSIVEQYAPLVKRIAHHLLARLPASVQLDDLLQAGMMGLLEASSKFDGGKGAKFE 68

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           T++   I+ AM + I R    V      N +++   +      L+     + +      I
Sbjct: 69  TFAGIRIRGAMLDEIRR-GDWVPRSVHRNNRKVAHAI----DELEQALGRDAR---DTEI 120

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+KL+++  E       +  D S+  +I   D   SQ    ++   D  +    E     
Sbjct: 121 AEKLDMTLDEYH----HILNDVSVGKIIGIEDLGVSQ---DILTVSDRSDDDSFEALAEN 173

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              + L  ++ +L  R+  +       +  + L+ + +  EVS  RV QI ++A  +++ 
Sbjct: 174 QFHSALVEAIKLLPERDALVLSLYY--DEALNLKEIGAILEVSESRVSQILSQAMLRLKA 231

Query: 283 SIQ 285
            ++
Sbjct: 232 KLK 234


>gi|254239804|ref|ZP_04933126.1| sigma factor FliA [Pseudomonas aeruginosa 2192]
 gi|126193182|gb|EAZ57245.1| sigma factor FliA [Pseudomonas aeruginosa 2192]
          Length = 247

 Score =  108 bits (270), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 44/251 (17%), Positives = 99/251 (39%), Gaps = 22/251 (8%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDP 95
           + Y +    ++  +L+  +  LV +IA    G     + + +++  G IGL++A KK+D 
Sbjct: 8   RMYSKAQAQNSQEQLIQRYAPLVKRIAYHLLGRLPASVQVEDLMQAGMIGLLEAAKKYDA 67

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            +G    TY+   I+ AM + + R           N + +   +R ++           +
Sbjct: 68  GKGASFETYAGIRIRGAMLDEV-RKGDWAPRSVHRNTRMVTDAIRTIEA-------RTGR 119

Query: 156 PEQVVAIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
             +   +A +L +S  +   I  + + +   S + L+   +         L  D      
Sbjct: 120 DAKDHEVAAELQLSLEDYYGILSDTQGSRLYSFDDLLQDGE-------HGLPEDTSLSHN 172

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
             I     +  +  L  +++ L  RER +       +  + L+ +     VS  RV Q+ 
Sbjct: 173 EPIHGLLDERFQAALADAIAKLPERERLVLALYY--DEELNLKEIGEVLGVSESRVSQLH 230

Query: 274 ARAFKKVQESI 284
           ++   +++  +
Sbjct: 231 SQCAARLRARL 241


>gi|15596652|ref|NP_250146.1| flagellar biosynthesis sigma factor [Pseudomonas aeruginosa PAO1]
 gi|116049400|ref|YP_791797.1| flagellar biosynthesis sigma factor [Pseudomonas aeruginosa
           UCBPP-PA14]
 gi|218892672|ref|YP_002441541.1| flagellar biosynthesis sigma factor [Pseudomonas aeruginosa LESB58]
 gi|254234554|ref|ZP_04927877.1| sigma factor FliA [Pseudomonas aeruginosa C3719]
 gi|296390178|ref|ZP_06879653.1| flagellar biosynthesis sigma factor [Pseudomonas aeruginosa PAb1]
 gi|120310|sp|P29248|FLIA_PSEAE RecName: Full=RNA polymerase sigma factor for flagellar operon;
           AltName: Full=Sigma-28; AltName: Full=Sigma-F factor
 gi|9947407|gb|AAG04844.1|AE004575_3 sigma factor FliA [Pseudomonas aeruginosa PAO1]
 gi|45322|emb|CAA43548.1| sigma-28 class sigma factor [Pseudomonas aeruginosa]
 gi|115584621|gb|ABJ10636.1| motility sigma factor FliA [Pseudomonas aeruginosa UCBPP-PA14]
 gi|126166485|gb|EAZ51996.1| sigma factor FliA [Pseudomonas aeruginosa C3719]
 gi|218772900|emb|CAW28712.1| sigma factor FliA [Pseudomonas aeruginosa LESB58]
          Length = 247

 Score =  108 bits (270), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 44/251 (17%), Positives = 99/251 (39%), Gaps = 22/251 (8%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDP 95
           + Y +    ++  +L+  +  LV +IA    G     + + +++  G IGL++A KK+D 
Sbjct: 8   RMYSKAQAQNSQEQLIQRYAPLVKRIAYHLLGRLPASVQVEDLMQAGMIGLLEAAKKYDA 67

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            +G    TY+   I+ AM + + R           N + +   +R ++           +
Sbjct: 68  GKGASFETYAGIRIRGAMLDEV-RKGDWAPRSVHRNTRMVTDAIRAIEA-------RTGR 119

Query: 156 PEQVVAIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
             +   +A +L +S  +   I  + + +   S + L+   +         L  D      
Sbjct: 120 DAKDHEVAAELQLSLEDYYGILSDTQGSRLYSFDDLLQDGE-------HGLPEDTSLSHN 172

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
             I     +  +  L  +++ L  RER +       +  + L+ +     VS  RV Q+ 
Sbjct: 173 EPIHGLLDERFQAALADAIAKLPERERLVLALYY--DEELNLKEIGEVLGVSESRVSQLH 230

Query: 274 ARAFKKVQESI 284
           ++   +++  +
Sbjct: 231 SQCAARLRARL 241


>gi|313905149|ref|ZP_07838518.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Eubacterium
           cellulosolvens 6]
 gi|313470052|gb|EFR65385.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Eubacterium
           cellulosolvens 6]
          Length = 258

 Score =  108 bits (270), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 39/259 (15%), Positives = 106/259 (40%), Gaps = 18/259 (6%)

Query: 30  EKQEEYVLAKRYREHGDLSA-AHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIG 85
             +E + L +   +  D       L   +L +V  IA   R   +      ++++EG + 
Sbjct: 10  TNEELFYLYRNATDDNDRKILRQELTMRYLYIVKAIAYQMRDMYIGFAQPDDIINEGVLE 69

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           +M+ + ++DP+R  +  T+    I+  + + + ++  +         +    + R ++  
Sbjct: 70  IMKGIDRYDPDRDNKFDTFISRRIRGMVIDLMRKNDWM--------PRNFHRDRRTIEDT 121

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           +Q +++   +       A KL +   ++  +         L+  +   + + +  Q    
Sbjct: 122 VQELSEKLGRTPTDEETAHKLGIEVKKLQKVRTMTTMVNVLSLDMTYDENDEAVLQVPTE 181

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
                 E+  +    R     +L  +++ L  +E+ I     +    ++   ++S  ++S
Sbjct: 182 DISVQPERNFM----RGETVRILADAINSLQEKEKMIISLYYVDNLNMS--QIASVMDIS 235

Query: 266 RERVRQIEARAFKKVQESI 284
           + RV Q+ A+A KK+++ +
Sbjct: 236 QPRVSQLHAQAVKKLRKIM 254


>gi|268316324|ref|YP_003290043.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Rhodothermus marinus
           DSM 4252]
 gi|262333858|gb|ACY47655.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Rhodothermus marinus
           DSM 4252]
          Length = 253

 Score =  108 bits (270), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 41/255 (16%), Positives = 98/255 (38%), Gaps = 16/255 (6%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVK 91
             L ++Y      +    +V + + LV  +         P+    ++ + G +GL+QA+ 
Sbjct: 6   QRLVEQYVADPSSANREAVVLAAVPLVRSMVGRLSVPDHPLVTREDLENVGLMGLLQALD 65

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
            +DPERG    +Y+   I+ A+ +Y+            A  +     L  L+  ++ +  
Sbjct: 66  SYDPERGTPFVSYAYGRIRGALVDYLR--------SIDALPRERRRKLAELQQAIETLRQ 117

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
                 +   +A  L +S  E  ++        +L+      +       + +  +    
Sbjct: 118 TLGGEPEDQDVADYLGISLQEYYTLLTDAQRRFALSLQETVGEDGDQSVLETIPNED--- 174

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
            +  +E  +R +    +T+ +  L  RE+ I      +   +TL  ++    ++  R+ Q
Sbjct: 175 AEKQLEDIDRASLIEYVTKLIQRLPEREQNILALYYYEN--LTLREIAQLLGLTEARISQ 232

Query: 272 IEARAFKKVQESIQK 286
           I  +    ++  +Q+
Sbjct: 233 ILGKTLLTLRTELQR 247


>gi|223700510|gb|ACN20374.1| truncated RNA polymerase sigma factor SigB [Listeria monocytogenes]
          Length = 188

 Score =  108 bits (270), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 42/185 (22%), Positives = 79/185 (42%), Gaps = 14/185 (7%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++ Y+    Y+E+GD  A + LV  +  LV  IA  Y        ++V  GNIGL+ A+
Sbjct: 12  KEKVYIWIAAYQENGDQDAQYNLVVHYKNLVESIARKYSQGKSFHEDLVQVGNIGLLGAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +++D   G     +++  I   ++ ++      V +     +        ++K  ++ +T
Sbjct: 72  RRYDATFGKSFEAFAVPTIVGEIKRFLRDKTWSVHVPRRIKELG-----PKIKNAVEELT 126

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMN------CRLAGDESLNALINSSDKNSSQWQDWL 204
                  Q+  IA  + V+E EV+           L+ D S+ A    SD ++    D +
Sbjct: 127 RELQSSPQISDIADFIGVTEEEVLEAMEMGKSYQALSVDHSIEA---DSDGSTITLLDVV 183

Query: 205 VYDHD 209
               D
Sbjct: 184 GGTDD 188


>gi|206603135|gb|EDZ39615.1| Putative RNA polymerase sigma 28 subunit [Leptospirillum sp. Group
           II '5-way CG']
          Length = 251

 Score =  108 bits (270), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 48/227 (21%), Positives = 100/227 (44%), Gaps = 14/227 (6%)

Query: 61  VVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           V   A+ Y       L I +++S G  GL+ A ++FDP RG +  T +   I+ AM + I
Sbjct: 17  VKFFALRYSHRLPPELDIDDLISAGMGGLLDAARRFDPARGIKFKTLAEHRIRGAMLDEI 76

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
             +  +     +  +K    +++++K  L A        +++ A   ++   E + +S++
Sbjct: 77  RAADWM---PRSVREK--LTHVQQVKTELIARYKREPTRQEIAAR-MEMTEEEFDRLSVD 130

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                  SL  L++  D +S    D L    +G     +    +      L +++  L  
Sbjct: 131 IEPHHLVSLEDLMDPEDGDSPSLLDRLSAPQEGD---PLASLLQNEVSEKLCQALDRLPE 187

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++R +      +E  +T++ ++    VS  RV QI  +A   +++S+
Sbjct: 188 KQRLVLSLYYYEE--LTMKEVARVVGVSESRVSQIHGQALAALKQSL 232


>gi|291437789|ref|ZP_06577179.1| RNA polymerase sigma factor sig8 [Streptomyces ghanaensis ATCC
           14672]
 gi|291340684|gb|EFE67640.1| RNA polymerase sigma factor sig8 [Streptomyces ghanaensis ATCC
           14672]
          Length = 285

 Score =  108 bits (270), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 44/205 (21%), Positives = 89/205 (43%), Gaps = 16/205 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + L+  ++ LV   A  +R  G   + ++V  G IGL++A+ +F+  R     ++++ 
Sbjct: 91  ARNTLIEMNMSLVRFAAGRFRSRGPEEMEDIVQVGMIGLIKAIDRFELSREVEFTSFAIP 150

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +I   M+ +   +   V +     + R+     +L    + +     +      +A+ ++
Sbjct: 151 YIVGEMKRFFRDTSWSVHVPRRLQEARV-----QLARATEELRTRLGRTPTTRELAQLMS 205

Query: 168 VSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           ++E EV        G    SL+A I S     S   D++     G E   +E  E  +  
Sbjct: 206 LTEEEVNEARIAANGYNSASLDAAIGSEPDGESVLADFI-----GSEDAALELVEDFH-- 258

Query: 226 NMLTRSMSVLNPRERRIFEARRLQE 250
             L   ++ L+ RER+I   R ++E
Sbjct: 259 -ALAPMIAELDERERKIIHWRFVEE 282


>gi|18310744|ref|NP_562678.1| sporulation sigma factor SigE [Clostridium perfringens str. 13]
 gi|110798939|ref|YP_696448.1| sporulation sigma factor SigE [Clostridium perfringens ATCC 13124]
 gi|110801836|ref|YP_699048.1| sporulation sigma factor SigE [Clostridium perfringens SM101]
 gi|168207289|ref|ZP_02633294.1| RNA polymerase sigma-E factor [Clostridium perfringens E str.
           JGS1987]
 gi|168210605|ref|ZP_02636230.1| RNA polymerase sigma-E factor [Clostridium perfringens B str. ATCC
           3626]
 gi|168217049|ref|ZP_02642674.1| RNA polymerase sigma-E factor [Clostridium perfringens NCTC 8239]
 gi|169342673|ref|ZP_02863714.1| RNA polymerase sigma-E factor [Clostridium perfringens C str.
           JGS1495]
 gi|182625822|ref|ZP_02953588.1| RNA polymerase sigma-E factor [Clostridium perfringens D str.
           JGS1721]
 gi|18145425|dbj|BAB81468.1| probable transcription initiation factor sigma E [Clostridium
           perfringens str. 13]
 gi|110673586|gb|ABG82573.1| RNA polymerase sigma-E factor [Clostridium perfringens ATCC 13124]
 gi|110682337|gb|ABG85707.1| RNA polymerase sigma-E factor [Clostridium perfringens SM101]
 gi|169299179|gb|EDS81249.1| RNA polymerase sigma-E factor [Clostridium perfringens C str.
           JGS1495]
 gi|170661363|gb|EDT14046.1| RNA polymerase sigma-E factor [Clostridium perfringens E str.
           JGS1987]
 gi|170711254|gb|EDT23436.1| RNA polymerase sigma-E factor [Clostridium perfringens B str. ATCC
           3626]
 gi|177908856|gb|EDT71348.1| RNA polymerase sigma-E factor [Clostridium perfringens D str.
           JGS1721]
 gi|182380960|gb|EDT78439.1| RNA polymerase sigma-E factor [Clostridium perfringens NCTC 8239]
          Length = 235

 Score =  108 bits (270), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 53/263 (20%), Positives = 104/263 (39%), Gaps = 63/263 (23%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L K+EE  L  +  E+ D +    L+  +LRLVV IA  +   G+ + +++S G IGL+
Sbjct: 34  PLSKEEEEELVNKLGEN-DEAIRSILIERNLRLVVYIARKFENTGVGVEDLISVGTIGLI 92

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV  F+PE+  +LATY+   I+  +  Y+ R+                    ++K    
Sbjct: 93  KAVNTFNPEKKIKLATYASRCIENEILMYLRRNS-------------------KVKAE-- 131

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                       ++  + LN+             G+E L + I  +D +       L+ D
Sbjct: 132 ------------ISFYEPLNIDWD----------GNELLLSDILGTDDD---IVYNLIED 166

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVS 265
              +E +    +   NR   +                 R         T + ++    +S
Sbjct: 167 EVDKELLFTAMKNLSNREKEIVE--------------LRFGLCGYKEKTQKEVADMLGIS 212

Query: 266 RERVRQIEARAFKKVQESIQKQV 288
           +  + ++E +  K++++ I K +
Sbjct: 213 QSYISRLEKKIIKRLKKEINKMI 235


>gi|149188102|ref|ZP_01866397.1| flagellar biosynthesis sigma factor [Vibrio shilonii AK1]
 gi|148838090|gb|EDL55032.1| flagellar biosynthesis sigma factor [Vibrio shilonii AK1]
          Length = 243

 Score =  108 bits (270), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 49/249 (19%), Positives = 95/249 (38%), Gaps = 20/249 (8%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPER 97
           Y +H +LS     +  +  LV +IA    G   P   + +++  G IGL++A K +D  +
Sbjct: 7   YDQHANLSGQQAFLEKYSVLVKRIAHHLIGRLPPNVLVEDLIQAGMIGLIEAQKNYDGSK 66

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G    TY+   I+ AM + I R    V      + + +   +  L+  L        +  
Sbjct: 67  GASFETYAGIRIRGAMLDDIRR-GDWVPRSVHKHSRDISQAISVLEVELN-------RDP 118

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +A  L +S ++          D + + L+   D   S+    +  + D       +
Sbjct: 119 TDSEVANYLGLSLAQYHKALT----DINCSKLVGIEDLGVSEDSVSVSDEEDN---TPFQ 171

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
                  R  L  S+  L  RE          +  + L+ +     VS  RV QI +++ 
Sbjct: 172 GVADDAFREALIESIKSLPEREALTLSLYY--DEELNLKEIGEVLGVSESRVSQILSQSM 229

Query: 278 KKVQESIQK 286
           ++++  +  
Sbjct: 230 QRLRTKLSA 238


>gi|229074589|ref|ZP_04207614.1| RNA polymerase sigma-B factor [Bacillus cereus Rock4-18]
 gi|229095607|ref|ZP_04226590.1| RNA polymerase sigma-B factor [Bacillus cereus Rock3-29]
 gi|229114558|ref|ZP_04243973.1| RNA polymerase sigma-B factor [Bacillus cereus Rock1-3]
 gi|228668908|gb|EEL24335.1| RNA polymerase sigma-B factor [Bacillus cereus Rock1-3]
 gi|228687817|gb|EEL41712.1| RNA polymerase sigma-B factor [Bacillus cereus Rock3-29]
 gi|228708547|gb|EEL60695.1| RNA polymerase sigma-B factor [Bacillus cereus Rock4-18]
          Length = 203

 Score =  107 bits (269), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 38/210 (18%), Positives = 97/210 (46%), Gaps = 16/210 (7%)

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++  G +GL+ A++++D   G     +++  I   +++Y+      + +      +R+
Sbjct: 3   EDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRI 57

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSS 193
                ++K  ++ +TD+  +  +++ IA  L +SE EV+ +          SL+ ++ +S
Sbjct: 58  KDLGGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENS 117

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
              SS  +   V +       + +  E+  RR +L    +VLN  E+ +      +   +
Sbjct: 118 SDGSSVARIESVGE-------VEQGYEQTERRLVLEDIFNVLNETEKSVIHYIFGEN--L 168

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQES 283
             ++      +S+  V +I+ +A  K++++
Sbjct: 169 NQKDTGERLGISQMHVSRIKRQAISKLKQA 198


>gi|299472120|emb|CBN77105.1| RNA polymerase sigma factor [Ectocarpus siliculosus]
          Length = 555

 Score =  107 bits (269), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 50/284 (17%), Positives = 104/284 (36%), Gaps = 63/284 (22%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYR----GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            A  R+V +++ L+V +A  +       G   S+V+ EG++ +++A + FDP  G+R +T
Sbjct: 239 RAQERIVGANVGLIVVMARRHHPATMARGTITSDVIQEGSLAVLRAAETFDPRLGYRFST 298

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ WW++  +   + +   ++++    +  R     R       A+     +      IA
Sbjct: 299 YAGWWVRDRVTRCVTQQARIIRLPQYVHNFR-----RTASMTEAALLKELGRRPTYDEIA 353

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG------------- 210
           +++ V    V  +         +N     S  ++      +V D  G             
Sbjct: 354 ERMRVDVERVTRL---------MNCPDAFSLDDAPPPSARIVRDRIGLSGGGGKGGGGGG 404

Query: 211 ------------------------------QEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
                                               ++ E     + L + +SVL+  ER
Sbjct: 405 SGGGGGGGAAKAGGGKAAPGAGYRHERVACSMVNPEQRAEVGLFESKLDKLLSVLSEDER 464

Query: 241 RIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            + + R       P T   +++    ++ RVR +E RA  K++ 
Sbjct: 465 LVVKLRYGLGGASPTTWGEVAARAGSTKHRVRMVETRALNKLRR 508


>gi|299066547|emb|CBJ37737.1| putative RNA polymerase sigma factor [Ralstonia solanacearum CMR15]
          Length = 272

 Score =  107 bits (269), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 50/259 (19%), Positives = 100/259 (38%), Gaps = 33/259 (12%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVK-IAMGYRGYGLP---ISEVVSEGNIGLMQA 89
           E  L +  REHGD +A   L+  +L       AM Y           E      +GLM++
Sbjct: 37  EATLWRALREHGDTAARDALIARYLPYAKAQAAMLYARRTHDAFEFEEYHQFAVVGLMES 96

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           ++++DP++G +  TY    I  +M   + R         +  Q+++    R       ++
Sbjct: 97  LERYDPQQGAQFKTYVTPRIVGSMLNGLER--------LSEQQQQIGLRRRLAAERAASL 148

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
               L       + ++L             +    +L  L+        +    +V   +
Sbjct: 149 ASEPLSEGNPQKLLRELG-----------EIGLGIALGILL--------EGTGMVVGQDE 189

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
           G       + E +  R+ +   +  L  RER +      Q+ P   + +++E  V++ RV
Sbjct: 190 GLPDNAYSRTELRQLRHQIWHMVQHLTDRERDVIRLHYQQQKP--FDEVAAELGVTKGRV 247

Query: 270 RQIEARAFKKVQESIQKQV 288
            Q+  +A +++Q  + KQ 
Sbjct: 248 SQLHQQALRRLQTLVAKQA 266


>gi|260222460|emb|CBA32046.1| RNA polymerase sigma factor for flagellar operon [Curvibacter
           putative symbiont of Hydra magnipapillata]
          Length = 273

 Score =  107 bits (269), Expect = 1e-21,   Method: Composition-based stats.
 Identities = 43/242 (17%), Positives = 105/242 (43%), Gaps = 19/242 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L+  +  LV ++A        P   + +++  G IGL  A+ +++  +G +  T++ 
Sbjct: 45  RSALIKQYQPLVRRLAHHMMAKLPPSVEVDDLIQVGLIGLSDALSRYEASQGVQFETFAT 104

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +  +  + + G+  +QK +   LR+L+  L        +      IA +L
Sbjct: 105 QRIRGAMLDELRENDWMSR-GSRKSQKEIETALRKLEHKL-------GRSPAESEIATEL 156

Query: 167 NVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            +S S+  S+  ++ G     L  +   ++ + +     +      Q+   +     +  
Sbjct: 157 GMSLSDYQSLLGKVRGTQLVYLEDMARRNEDDDTYLDRHVAD----QDADPLNMLRDQRL 212

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L  ++  L  RE+ I       E  + L+ +++  +V+  RV Q+ +++  +++  +
Sbjct: 213 RQSLVDAIKCLPEREQYIMSMYY--EQDMNLKEIAAVLDVTESRVCQLHSQSIARLRAKM 270

Query: 285 QK 286
           + 
Sbjct: 271 RS 272


>gi|67921068|ref|ZP_00514587.1| Sigma-70 region 3:Sigma-70 region 4 [Crocosphaera watsonii WH 8501]
 gi|67857185|gb|EAM52425.1| Sigma-70 region 3:Sigma-70 region 4 [Crocosphaera watsonii WH 8501]
          Length = 179

 Score =  107 bits (269), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 33/177 (18%), Positives = 80/177 (45%), Gaps = 13/177 (7%)

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           +    I     ++++     +K     L ++K   + I+ +  +   +  I ++L ++ +
Sbjct: 3   SCTRAIATQSRIIRLPVHVTEK-----LNKIKQVQRKISQSKNRNASLEEIGQELGMTAA 57

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           +V  +  ++    SL   +    +  ++  D L  +    E+ L      ++ R  +   
Sbjct: 58  QVREVLMKIPRSVSLE--VKVGKEKDTELVDLLESEDISPEENLA----VESLRRDIGVL 111

Query: 232 MSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +  L  RE+++ + R   E+    +L  +    E+SRERVRQIEA+  +K+++  ++
Sbjct: 112 LKDLTEREQQVIKLRYGFEDGVAYSLAGIGRVLELSRERVRQIEAKTLQKLRQPRRR 168


>gi|157376181|ref|YP_001474781.1| flagellar biosynthesis sigma factor [Shewanella sediminis HAW-EB3]
 gi|157318555|gb|ABV37653.1| Phosphatidylserine decarboxylase [Shewanella sediminis HAW-EB3]
          Length = 239

 Score =  107 bits (269), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 48/236 (20%), Positives = 98/236 (41%), Gaps = 20/236 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           +V  +  LV KIA          + + +++  G +GL++A  KFD  +G +  T++   I
Sbjct: 16  IVEQYAPLVKKIAHHLLARLPASVQLDDLLQAGMMGLLEASSKFDGSKGAKFETFAGIRI 75

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + +M + I R    V      NQ       RR+   +  +     +      IA++L++S
Sbjct: 76  RGSMLDEIRR-GDWVPRSVHRNQ-------RRVAQVIDELGQELGRDAVDSEIAQRLDMS 127

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             E       +  D S+  ++   D   S     +V   + Q+  + E          L 
Sbjct: 128 LDEYH----HILNDVSVGKVVGIEDLGVS---VDVVSHEEVQQDDIFESIADVEFHKALV 180

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            ++ +L  R+  +       +  + L+ + +  EVS  RV QI ++A  +++  ++
Sbjct: 181 EAIKLLPERDGLVLSLYY--DEALNLKEIGAILEVSESRVSQILSQAMLRLKAKLK 234


>gi|326791410|ref|YP_004309231.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium lentocellum DSM
           5427]
 gi|326542174|gb|ADZ84033.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium lentocellum DSM
           5427]
          Length = 251

 Score =  107 bits (269), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 53/268 (19%), Positives = 104/268 (38%), Gaps = 68/268 (25%)

Query: 27  PMLEKQEEYVLAKRY-----REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           P L + EE +L ++      +E    +    L+  +LRLVV IA  +   G+ + +++S 
Sbjct: 42  PPLSRDEEEILIQKLIEFAEQEEEIKAIKTTLIERNLRLVVYIARKFENTGIYMEDLISI 101

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           G IGL++++  F P +  +LATY+   I+  +  ++ R+                    +
Sbjct: 102 GTIGLIKSINTFKPCKKIKLATYASRCIENEILMFLRRT-------------------NK 142

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           LK                                    ++ DE LN      D N     
Sbjct: 143 LKTE----------------------------------VSIDEPLN---VDWDGNELLLS 165

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENL 258
           D L  + D   + + E+ ++K  +  L +       RER I E R     Q    T + +
Sbjct: 166 DILGTEPDIIYRNIEEEVDKKLLKQALLKL----TDREREIVELRFGFTPQGKEKTQKEV 221

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQK 286
           +    +S+  + ++E +   ++++ I +
Sbjct: 222 ADLLGISQSYISRLEKKIILRLKKEINR 249


>gi|304311117|ref|YP_003810715.1| RNA polymerase sigma factor for flagellar operon (Sigma-F factor)
           [gamma proteobacterium HdN1]
 gi|301796850|emb|CBL45062.1| RNA polymerase sigma factor for flagellar operon (Sigma-F factor)
           [gamma proteobacterium HdN1]
          Length = 244

 Score =  107 bits (269), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 46/241 (19%), Positives = 96/241 (39%), Gaps = 18/241 (7%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           ++   LV  HL LV +IA    G       + +++  G IGL+ A++K+D  +G    TY
Sbjct: 16  ASLDTLVEQHLPLVRRIAHHMIGRLPSNVIVDDLIQAGVIGLIDALQKYDTGKGASFETY 75

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +   I+ AM + I R           N + +   +R ++  +Q       +      +A+
Sbjct: 76  AGIRIRGAMIDEIRR-GEWAPRSVHRNARAIQDAIRNVEARVQ-------RDATDREVAE 127

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L V      +M       +S+   + S ++ ++        D            +R   
Sbjct: 128 ELGVPLDAYHAM-----AQDSMATRLFSMEELTAPESIIDRGDLQQAHDNPASHFQRDMM 182

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              +  ++  L  RE+ +       +  + L+ +     VS  RV QI ++A  +++  +
Sbjct: 183 LTSMANAIKDLPEREQLVLSLYY--DEELNLKEIGEVLGVSESRVCQIHSQATHRLRARL 240

Query: 285 Q 285
           +
Sbjct: 241 R 241


>gi|228906737|ref|ZP_04070609.1| RNA polymerase sigma-B factor [Bacillus thuringiensis IBL 200]
 gi|228964059|ref|ZP_04125186.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228795629|gb|EEM43109.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228852914|gb|EEM97696.1| RNA polymerase sigma-B factor [Bacillus thuringiensis IBL 200]
          Length = 203

 Score =  107 bits (269), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 38/210 (18%), Positives = 97/210 (46%), Gaps = 16/210 (7%)

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++  G +GL+ A++++D   G     +++  I   +++Y+      + +      +R+
Sbjct: 3   EDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRI 57

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSS 193
                ++K  ++ +TD+  +  +++ IA  L +SE EV+ +          SL+ ++ +S
Sbjct: 58  KDLGGKIKLAIEELTDHLQRSPKIIEIANHLGLSEEEVLEIMDAKNNYRVSSLDDVVENS 117

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
              SS  +   V +       + +  E+  RR +L    +VLN  E+ +      +   +
Sbjct: 118 SDGSSVARIESVGE-------VEQGYEQTERRLVLEDIFNVLNDTEKSVIHYIFGEN--L 168

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQES 283
             ++      +S+  V +I+ +A  K++++
Sbjct: 169 NQKDTGERLGISQMHVSRIKRQAISKLKQA 198


>gi|268612026|ref|ZP_06145753.1| anti-sigma F factor [Ruminococcus flavefaciens FD-1]
          Length = 219

 Score =  107 bits (268), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 48/232 (20%), Positives = 97/232 (41%), Gaps = 23/232 (9%)

Query: 55  TSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114
             +L LV   A  +R  G+   E+ S G +GL++AVK FDP+RG + +TY++  I   ++
Sbjct: 11  EENLGLVHLCANRFRNRGIEYEELYSAGCVGLLKAVKAFDPDRGAQFSTYAVPVILGEIR 70

Query: 115 EYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVI 174
             + R    +++  +  +  +     R++          ++   +  +A     SE++V 
Sbjct: 71  R-LFRDGGAIRVSRSLKELSM-----RIQKMCTDFRQREMREPTISELAVISGESEADVS 124

Query: 175 SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV 234
              C      SL A     D +  Q         +    VL            L + MS 
Sbjct: 125 EALCVSQPMLSLTA----GDDDEGQIDIPTDAPDEAIVDVLA-----------LRQIMSG 169

Query: 235 LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           L+ R+R + E R  +   +T    +    +++ +V + E +   ++++ + K
Sbjct: 170 LDSRDRALLELRYFRC--LTQTKTAQALGMTQVQVSRREKKLLAEMRKELLK 219


>gi|229101713|ref|ZP_04232430.1| RNA polymerase sigma-B factor [Bacillus cereus Rock3-28]
 gi|228681661|gb|EEL35821.1| RNA polymerase sigma-B factor [Bacillus cereus Rock3-28]
          Length = 203

 Score =  107 bits (268), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 37/210 (17%), Positives = 97/210 (46%), Gaps = 16/210 (7%)

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++  G +GL+ A++++D   G     +++  I   +++Y+      + +      +R+
Sbjct: 3   EDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRI 57

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSS 193
                ++K  ++ +TD+  +  +++ IA  L +SE EV+ +          SL+ ++ ++
Sbjct: 58  KDLGGKIKLAIEELTDHLQRSPKIIEIANHLGLSEEEVLEIMDAKNNYRVSSLDDVVENA 117

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
              SS  +   V +       + +  E+  RR +L    +VLN  E+ +      +   +
Sbjct: 118 SDGSSVARIESVGE-------VEQGYEQTERRLVLNDIFNVLNETEKSVIHYIFGEN--L 168

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQES 283
             ++      +S+  V +I+ +A  K++++
Sbjct: 169 NQKDTGERLGISQMHVSRIKRQAINKLKQA 198


>gi|254411015|ref|ZP_05024793.1| RNA polymerase sigma factor, sigma-70 family [Microcoleus
           chthonoplastes PCC 7420]
 gi|196182370|gb|EDX77356.1| RNA polymerase sigma factor, sigma-70 family [Microcoleus
           chthonoplastes PCC 7420]
          Length = 260

 Score =  107 bits (268), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 49/237 (20%), Positives = 101/237 (42%), Gaps = 16/237 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKKFD 94
            L   Y ++  +   ++LV  +  LV KIA    +    P  ++V  G +GL++A+++F 
Sbjct: 12  ELLMAYSQNPSIELRNQLVRLNSGLVKKIAYRVSQQCSEPYDDLVQLGYLGLIRAIERFK 71

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P++G+  +++++ +I+  M  ++    ++VKI     +  L    +R+   L   T    
Sbjct: 72  PDQGYAFSSFAVPFIRGEMLHFLRDKGNIVKIPRRWQE--LQQEGQRVSKRL---TATLG 126

Query: 155 KPEQVVAIAKKLNVSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +P +   IA+ LN+S  E     +  +     SL+  +  +  +     D L   +D   
Sbjct: 127 RPPKEAEIAQALNISMQEWQESKLASKNRLPLSLDLTVGHNVDHPVTLGDMLPDSYDQTL 186

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
           Q   E       R  L  +++ L  + +   E    ++ P   +  +    VS   V
Sbjct: 187 QHWEED------RQQLQGAIAQLETKTQAAIEFVFFRDLPR--KEAAKHIGVSPMTV 235


>gi|219670137|ref|YP_002460572.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfitobacterium
           hafniense DCB-2]
 gi|219540397|gb|ACL22136.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfitobacterium
           hafniense DCB-2]
          Length = 248

 Score =  107 bits (268), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 39/237 (16%), Positives = 102/237 (43%), Gaps = 14/237 (5%)

Query: 54  VTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           +  +L LV +I+          +   +++  G  GL+ A+++FDP RG +  TY+   I+
Sbjct: 18  IEKYLPLVKRISGRLLISLPQHVDEDDLIGYGVFGLLDALERFDPVRGVKFETYATLRIR 77

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            A+ + +    ++  +  +A QK     ++R++     +   + +P     +A  L +  
Sbjct: 78  GAIIDGLR---TMDWVPHSARQK-----IKRIQDAFAEVEARHGRPASNEEVAVLLEMEP 129

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            + +          +L +L   +     +         D   Q   ++ E   ++ +L  
Sbjct: 130 RD-LEAALHQGQMLTLTSLDEVAVGEEGEAYTPRTQLTDPIAQEAFQEVELDEQKKILAD 188

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  L  +E+ +       +  +TL+ ++   ++S  R+ Q+ ++A  +++  + +Q
Sbjct: 189 AIEKLPEKEKLVVALYY--QEDLTLKEIAVIMKLSESRISQLHSQAILRLRGRLSRQ 243


>gi|228957370|ref|ZP_04119129.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|229028783|ref|ZP_04184888.1| RNA polymerase sigma-B factor [Bacillus cereus AH1271]
 gi|228732530|gb|EEL83407.1| RNA polymerase sigma-B factor [Bacillus cereus AH1271]
 gi|228802319|gb|EEM49177.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
          Length = 203

 Score =  107 bits (268), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 38/210 (18%), Positives = 96/210 (45%), Gaps = 16/210 (7%)

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++  G +GL+ A++++D   G     +++  I   +++Y+      + +      +R+
Sbjct: 3   EDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRI 57

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSS 193
                ++K  ++ +TD+  +  +++ IA  L +SE EV+ +          SL+ ++ +S
Sbjct: 58  KDLGGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENS 117

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
              SS  +   V +       + +  E   RR +L    +VLN  E+ +      +   +
Sbjct: 118 SDGSSVARIESVGE-------VEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGEN--L 168

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQES 283
             ++      +S+  V +I+ +A  K++++
Sbjct: 169 NQKDTGERLGISQMHVSRIKRQAISKLKQA 198


>gi|229918653|ref|YP_002887299.1| RNA polymerase sigma factor SigD [Exiguobacterium sp. AT1b]
 gi|229470082|gb|ACQ71854.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Exiguobacterium sp.
           AT1b]
          Length = 256

 Score =  107 bits (268), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 47/253 (18%), Positives = 104/253 (41%), Gaps = 15/253 (5%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKF 93
           L  R+    D+  A+ L+  +  L+              +   E+ S G +GL  A+ K+
Sbjct: 8   LWDRWNMDRDMDTANELLAHYEFLIHYHVQRMIVTLPKSVERDELKSLGYMGLYDALMKY 67

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           DPE   +  TY+ + I+ A+ + + +   +  +  +  +K     +  +   L+      
Sbjct: 68  DPEHNNKFDTYAAFRIRGAIIDGLRK---VDWLPRSVREK--VKKIDHVAEQLEQSLHRA 122

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
               ++ + A  L +SE E        A   S++  +   ++       +   D +  E 
Sbjct: 123 PTKSELAS-ACDLPISEIERTMAEGYFANMLSIDEAVTLQEEGKVMSVTYFDPDSEKPED 181

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
            L+++E      ++L   +  L+ +ER +       E  +TL  +    E+S  R+ QI 
Sbjct: 182 TLLQRELI----DVLAAEVDHLSEKERLVVSLFYFDE--LTLTEIGEVLELSTSRISQIH 235

Query: 274 ARAFKKVQESIQK 286
           ++A K ++ ++ +
Sbjct: 236 SKALKTLKHALGR 248


>gi|77359758|ref|YP_339333.1| flagellar biosynthesis sigma factor [Pseudoalteromonas haloplanktis
           TAC125]
 gi|76874669|emb|CAI85890.1| Polar Flagellar-specific RNA polymerase sigma factor FliA (sigma F)
           [Pseudoalteromonas haloplanktis TAC125]
          Length = 236

 Score =  107 bits (268), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 43/238 (18%), Positives = 90/238 (37%), Gaps = 18/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + +V  H  LV K+A        P   + +++  G IGL++A K FD  +G    T++ 
Sbjct: 9   LNMIVEKHASLVKKVACHLIARLPPSVQLDDLIQSGMIGLIEASKNFDATKGASFETFAG 68

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + R             + +    R++   + A+  +  +      +A+KL
Sbjct: 69  IRIRGAMLDEMRRGDW--------APRSVHRKSRQVIEAISALESSLNREPTDSEVAQKL 120

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++  +   +   +   + L       D++           HD          + +    
Sbjct: 121 EITLEQYHHILTDVNSSKILGIEDLGIDEDVITPVG-----HDLALDKPFNNVKNERFNE 175

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L  ++  L  R+  +        + + L+ +    +VS  RV QI  +A  K++  I
Sbjct: 176 SLLSAIKSLPERDAMVLSLYY--NDEMNLKEIGQILDVSESRVSQIHGQAMIKLKAKI 231


>gi|228943728|ref|ZP_04106130.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228976238|ref|ZP_04136717.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228977712|ref|ZP_04138098.1| RNA polymerase sigma-B factor [Bacillus thuringiensis Bt407]
 gi|229042834|ref|ZP_04190570.1| RNA polymerase sigma-B factor [Bacillus cereus AH676]
 gi|229143711|ref|ZP_04272133.1| RNA polymerase sigma-B factor [Bacillus cereus BDRD-ST24]
 gi|228639767|gb|EEK96175.1| RNA polymerase sigma-B factor [Bacillus cereus BDRD-ST24]
 gi|228726494|gb|EEL77715.1| RNA polymerase sigma-B factor [Bacillus cereus AH676]
 gi|228782010|gb|EEM30202.1| RNA polymerase sigma-B factor [Bacillus thuringiensis Bt407]
 gi|228783483|gb|EEM31583.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228815947|gb|EEM62170.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
          Length = 203

 Score =  107 bits (268), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 38/210 (18%), Positives = 96/210 (45%), Gaps = 16/210 (7%)

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++  G +GL+ A++++D   G     +++  I   +++Y+      + +      +R+
Sbjct: 3   EDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRI 57

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSS 193
                ++K  ++ +TD+  +  +++ IA  L +SE EV+ +          SL+ ++ +S
Sbjct: 58  KDLGGKIKLAIEELTDHLQRSPKIIEIANHLGLSEEEVLEIMDAKNNYRVSSLDDVVENS 117

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
              SS  +   V +       + +  E   RR +L    +VLN  E+ +      +   +
Sbjct: 118 SDGSSVARIESVGE-------VEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGEN--L 168

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQES 283
             ++      +S+  V +I+ +A  K++++
Sbjct: 169 NQKDTGERLGISQMHVSRIKRQAISKLKQA 198


>gi|291557292|emb|CBL34409.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Eubacterium siraeum
           V10Sc8a]
          Length = 250

 Score =  107 bits (268), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 50/265 (18%), Positives = 94/265 (35%), Gaps = 68/265 (25%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L  +EE    ++  + GDL+A  +L+  +LRLV  I   +        +++S G IGL++
Sbjct: 45  LSAKEERECLEKAAQ-GDLAARDKLINHNLRLVAYIVKKHYPDSKEADDLISIGIIGLIR 103

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A + FD  +    +TY+   I   ++ Y  ++                            
Sbjct: 104 AAETFDYRKNISFSTYAGKCINNQIRMYFRKT---------------------------- 135

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                                +   + MN  +  D+  NA+            D      
Sbjct: 136 -------------------KHQQTEVYMNDPMDCDKDGNAVT---------LSDIFKDGT 167

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ-------ENPVTLENLSSE 261
           D  E+  +  E  K  R +       L+ RE+ I   R          +  +T   ++ E
Sbjct: 168 DVAEEAALNIELDKMYRYIDEE----LDEREKEILTKRYGLSKTSYRTDRIMTQREVADE 223

Query: 262 FEVSRERVRQIEARAFKKVQESIQK 286
             +SR  + +IE +A +K++   +K
Sbjct: 224 LGISRSYISRIEKKALEKLRSRFEK 248


>gi|297569692|ref|YP_003691036.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfurivibrio alkaliphilus AHT2]
 gi|296925607|gb|ADH86417.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfurivibrio alkaliphilus AHT2]
          Length = 262

 Score =  107 bits (268), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 42/251 (16%), Positives = 95/251 (37%), Gaps = 14/251 (5%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERG 98
           RE  D +    L+ ++  L+  IA        P   + +++S G +GL+ A+ KFDP + 
Sbjct: 22  REQLDPAKREELILNYTPLIKYIASRLASRLPPQVAVDDLISCGIVGLIDAINKFDPAKN 81

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
            +  TY+ + IK AM + + R+   V          L      L+  L        +P  
Sbjct: 82  VQFKTYAEFRIKGAMLDEL-RALDWVPRSIRRKVTELEQVCSELEVKL-------GRPAT 133

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
               A  L +   E   +        S   +     +  ++ +  L       ++     
Sbjct: 134 DEETATALGIGLEEYHRLLDE-TKSVSFLDIEYLRRQAPAEVEGNLAEVFASDDKDPFAA 192

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                 + +L ++++ L  +E+            +T+  +      +  R+ Q+ ++A  
Sbjct: 193 LNLGETKALLAKAINELPEKEKLTVALYY--HEELTMREIGEVLGYTESRISQMHSKAML 250

Query: 279 KVQESIQKQVE 289
           +++  ++K ++
Sbjct: 251 RLRGKLKKSLD 261


>gi|146277655|ref|YP_001167814.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Rhodobacter
           sphaeroides ATCC 17025]
 gi|145555896|gb|ABP70509.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Rhodobacter
           sphaeroides ATCC 17025]
          Length = 239

 Score =  107 bits (268), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 48/237 (20%), Positives = 107/237 (45%), Gaps = 22/237 (9%)

Query: 51  HRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            RLV +H+ LV +IA       G  + I +++  G +GL+ A ++++P  G   A Y+  
Sbjct: 15  ERLVRAHMDLVRRIAWNLHARIGRKVEIDDLIQIGYMGLVDASRRYEPRDGVTFAAYAAI 74

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+ ++ +++  + +L +      QK        +K  +Q +    ++  +   +A +L 
Sbjct: 75  RIRGSIMDFLRSNSALCRTTILMQQK--------VKAAVQRLESRLMRAPETPEVAAELG 126

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +   E      + AG ++ + L    D  SS +Q        G E    ++ +    R +
Sbjct: 127 MPVGEYQDWLAQFAGSQTAS-LDEVYDDQSSLFQ--------GSEPSAEDRLQATQMRGL 177

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L +++  +  RE  + +   ++E  + +  ++    V+  RV QI+  A ++++  I
Sbjct: 178 LRQALGKMPEREALLLQLIFVEE--MNVYEVAEILGVTTGRVSQIKKAAIERLRGFI 232


>gi|119511848|ref|ZP_01630948.1| sigma factor SigF [Nodularia spumigena CCY9414]
 gi|119463490|gb|EAW44427.1| sigma factor SigF [Nodularia spumigena CCY9414]
          Length = 258

 Score =  107 bits (267), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 42/255 (16%), Positives = 106/255 (41%), Gaps = 16/255 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVK 91
           E + L + Y +    +  ++LV  +  LV K A  +         ++V  G +GL++A++
Sbjct: 12  EIWQLLREYEQSRSDTIRNKLVKLNFGLVRKEAHYWMNQCRENYDDLVQVGYLGLIRAIE 71

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           KF+  +G   +++++ +I+  +Q Y+      V+I      +R     ++  G  + + +
Sbjct: 72  KFEISKGHAFSSFAIPYIRGEIQHYLRDKGVTVRIP-----RRYLALQQQAIGVSRDLCE 126

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHD 209
              +      +A  L +S +E   +          SL+  +  S++ ++   + +     
Sbjct: 127 KYNRQPTDSELAAALAISLNEWQEIKLAWVNRSPLSLDVPVLDSEEGTTSLGELVPDPKY 186

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
              Q+  E + R      L +++  L    R + E    Q+  +T + ++    +S   V
Sbjct: 187 RSFQLAQEDQIR------LQQALFELEKCTREVLECVFFQD--LTQKQVAEHLGISVVTV 238

Query: 270 RQIEARAFKKVQESI 284
            +   +    +++ +
Sbjct: 239 SRRVKKGLGLLKKMM 253


>gi|89895713|ref|YP_519200.1| hypothetical protein DSY2967 [Desulfitobacterium hafniense Y51]
 gi|89335161|dbj|BAE84756.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 248

 Score =  107 bits (267), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 39/237 (16%), Positives = 102/237 (43%), Gaps = 14/237 (5%)

Query: 54  VTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           +  +L LV +I+          +   +++  G  GL+ A+++FDP RG +  TY+   I+
Sbjct: 18  IEKYLPLVKRISGRLLISLPQHVDEDDLIGYGVFGLLDALERFDPVRGVKFETYATLRIR 77

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            A+ + +    ++  +  +A QK     ++R++     +   + +P     +A  L +  
Sbjct: 78  GAIIDGLR---TMDWVPHSARQK-----IKRIQDAFAEVEARHGRPASNEEVAVLLQMEP 129

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            + +          +L +L   +     +         D   Q   ++ E   ++ +L  
Sbjct: 130 RD-LEAALHQGQMLTLTSLDEVAVGEEGEAYTPRTQLADPIAQEAFQEVELDEQKKILAD 188

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  L  +E+ +       +  +TL+ ++   ++S  R+ Q+ ++A  +++  + +Q
Sbjct: 189 AIEKLPEKEKLVVALYY--QEDLTLKEIAVIMKLSESRISQLHSQAILRLRGRLSRQ 243


>gi|291532029|emb|CBK97614.1| RNA polymerase sigma factor, sigma-70 family [Eubacterium siraeum
           70/3]
          Length = 221

 Score =  107 bits (267), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 52/232 (22%), Positives = 103/232 (44%), Gaps = 23/232 (9%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           +T H  LV  IA  +R  G+   E+ S G +GL++A   FD  RG + +TY++  I   +
Sbjct: 10  ITEHFALVHSIAGRFRNRGIEYDELFSAGCVGLVKAGNNFDESRGLKFSTYAVPVIMGEI 69

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
           ++ + R    VK+  +   K L   + RL+  L      N +   +  +A+KL ++  E 
Sbjct: 70  KQ-LFRDGGTVKVSRSL--KELSLKICRLRDELIK----NGEEPHISVLAEKLGITPEEA 122

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSM 232
                      SL++     ++N            +G   + +E E+ +   R  L + +
Sbjct: 123 SLALGASLPPVSLSS--YDDEEND-----------EGSFDLPVEPEQPKALDRMALRQLV 169

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           S L P +RR+   R  +E   T    +    +++ +V + E +  + +++ +
Sbjct: 170 SRLEPIDRRLIILRYSEE--CTQSRTAEILGMTQVQVSRREKKILEGLRKQL 219


>gi|294140220|ref|YP_003556198.1| RNA polymerase sigma-27 factor [Shewanella violacea DSS12]
 gi|293326689|dbj|BAJ01420.1| RNA polymerase sigma-27 factor [Shewanella violacea DSS12]
          Length = 239

 Score =  107 bits (267), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 49/236 (20%), Positives = 101/236 (42%), Gaps = 20/236 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           +V  +  LV KIA          + I +++  G +GL++A  KFD  +G +  T++   I
Sbjct: 16  IVEQYAPLVKKIAHHLLARLPASVQIDDLLQAGMMGLLEASSKFDGNKGAKFETFAGIRI 75

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + +M + I R    V      NQ       RR+   +  +     +  +   IA++L+++
Sbjct: 76  RGSMLDEIRR-GDWVPRSVHRNQ-------RRVAQVIDELEQELGRDAKDAEIAQRLDMT 127

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
            +E       +  D S+  +I   D   S   D + +D+   +       E +     L 
Sbjct: 128 LNEYH----HILNDVSVGKVIGIEDLGVS--VDVISHDNGVNDDTFESIAEGEFHL-ALV 180

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            ++ +L  R+  +       +  + L+ + +  EVS  RV QI ++A  +++  ++
Sbjct: 181 AAIKLLPERDGLVLSLYY--DEALNLKEIGAILEVSESRVSQILSQAMLRLKAKLK 234


>gi|254425398|ref|ZP_05039116.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp. PCC
           7335]
 gi|196192887|gb|EDX87851.1| RNA polymerase sigma factor, sigma-70 family [Synechococcus sp. PCC
           7335]
          Length = 246

 Score =  107 bits (267), Expect = 2e-21,   Method: Composition-based stats.
 Identities = 51/240 (21%), Positives = 104/240 (43%), Gaps = 19/240 (7%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG-LPISEVVSEGNIGLMQAVKKFDPERG 98
           +Y+    +   ++LV  +  LV KIA         P  ++   G IGL++++++FDP +G
Sbjct: 2   QYKVDRSVKLRNQLVRLNAGLVRKIAHRVSHQCAEPYEDLEQIGYIGLIRSIERFDPGQG 61

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL-KGHLQAITDNNLKPE 157
              +++++ +I+  M  ++    + VKI       R + +L++  +     +     +  
Sbjct: 62  CAFSSFAVPYIRGEMLHFLRDRGTTVKIP------RRWQDLQKEGQKRQSELIRRYGRQP 115

Query: 158 QVVAIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
             + +A+ L VS  E   + +  +     SL+A +     +S    D L   H    Q+L
Sbjct: 116 SDIEMAEALTVSVQEWRQVKLANKNRMPLSLDATVCHQIDSSITLGDTLPDVHYQLTQIL 175

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV-RQIEA 274
            E       R  + R+MS L  + R   E    +   ++ + ++    VS   V R+I+ 
Sbjct: 176 EED------RQQIQRAMSQLEEKTRSAIEFVFFKG--LSRKEVAERIGVSPMTVTRRIQR 227


>gi|167750689|ref|ZP_02422816.1| hypothetical protein EUBSIR_01667 [Eubacterium siraeum DSM 15702]
 gi|167656368|gb|EDS00498.1| hypothetical protein EUBSIR_01667 [Eubacterium siraeum DSM 15702]
 gi|291558233|emb|CBL35350.1| RNA polymerase sigma factor, sigma-70 family [Eubacterium siraeum
           V10Sc8a]
          Length = 221

 Score =  107 bits (267), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 52/232 (22%), Positives = 103/232 (44%), Gaps = 23/232 (9%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           +T H  LV  IA  +R  G+   E+ S G +GL++A   FD  RG + +TY++  I   +
Sbjct: 10  ITEHFALVHSIAGRFRNRGIEYDELFSAGCVGLVKAGNNFDESRGLKFSTYAVPVIMGEI 69

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
           ++ + R    VK+  +   K L   + RL+  L      N +   +  +A+KL ++  E 
Sbjct: 70  KQ-LFRDGGTVKVSRSL--KELSLKICRLRDELIK----NGEEPHISVLAEKLGITPEEA 122

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRNMLTRSM 232
                      SL++     ++N            +G   + +E E+ +   R  L + +
Sbjct: 123 SLALGASLPPVSLSS--YDDEEND-----------EGSFDLPVEPEQPKALDRMALRQLV 169

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           S L P +RR+   R  +E   T    +    +++ +V + E +  + +++ +
Sbjct: 170 SRLEPLDRRLIILRYSEE--CTQSRTAEILGMTQVQVSRREKKILEGLRKQL 219


>gi|9368549|emb|CAB98133.1| unnamed protein product [Mycoplasma genitalium]
          Length = 100

 Score =  107 bits (267), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 34/84 (40%), Positives = 52/84 (61%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           E     A ++LVTS+LRLVV IA  +   GL  ++++ EGN+GL++A+ KF+   G + +
Sbjct: 17  EESRKYAINQLVTSNLRLVVSIAKKHLERGLDFNDLIQEGNLGLLKAISKFNWSLGNKFS 76

Query: 103 TYSMWWIKAAMQEYILRSWSLVKI 126
           TY+ WWIK A+   I      V+I
Sbjct: 77  TYATWWIKQAITRAIADQARTVRI 100


>gi|229189193|ref|ZP_04316217.1| RNA polymerase sigma-B factor [Bacillus cereus ATCC 10876]
 gi|228594237|gb|EEK52032.1| RNA polymerase sigma-B factor [Bacillus cereus ATCC 10876]
          Length = 203

 Score =  107 bits (267), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 38/210 (18%), Positives = 95/210 (45%), Gaps = 16/210 (7%)

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++  G IGL+ A++++D   G     +++  I   +++Y+      + +      +R+
Sbjct: 3   EDIIQVGMIGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRI 57

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSS 193
                +++  ++ +TD   +  +++ IA  L +SE EV+ +          SL+ ++ +S
Sbjct: 58  KDLGGKIRLAIEELTDRLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENS 117

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
              SS  +   V +       + +  E   RR +L    +VLN  E+ +      +   +
Sbjct: 118 SDGSSVARIESVGE-------VEQGYEETERRLVLKDIFNVLNETEKSVIHYIFGEN--L 168

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQES 283
             ++      +S+  V +I+ +A  K++++
Sbjct: 169 NQKDTGERLGISQMHVSRIKRQAISKLKQA 198


>gi|107100889|ref|ZP_01364807.1| hypothetical protein PaerPA_01001919 [Pseudomonas aeruginosa PACS2]
 gi|152986686|ref|YP_001349226.1| flagellar biosynthesis sigma factor [Pseudomonas aeruginosa PA7]
 gi|313106454|ref|ZP_07792685.1| motility sigma factor FliA [Pseudomonas aeruginosa 39016]
 gi|150961844|gb|ABR83869.1| sigma factor FliA [Pseudomonas aeruginosa PA7]
 gi|310879187|gb|EFQ37781.1| motility sigma factor FliA [Pseudomonas aeruginosa 39016]
          Length = 239

 Score =  107 bits (267), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 44/249 (17%), Positives = 98/249 (39%), Gaps = 22/249 (8%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPER 97
           Y +    ++  +L+  +  LV +IA    G     + + +++  G IGL++A KK+D  +
Sbjct: 2   YSKAQAQNSQEQLIQRYAPLVKRIAYHLLGRLPASVQVEDLMQAGMIGLLEAAKKYDAGK 61

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G    TY+   I+ AM + + R           N + +   +R ++           +  
Sbjct: 62  GASFETYAGIRIRGAMLDEV-RKGDWAPRSVHRNTRMVTDAIRAIEA-------RTGRDA 113

Query: 158 QVVAIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
           +   +A +L +S  +   I  + + +   S + L+   +         L  D        
Sbjct: 114 KDHEVAAELQLSLEDYYGILSDTQGSRLYSFDDLLQDGE-------HGLPEDTSLSHNEP 166

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
           I     +  +  L  +++ L  RER +       +  + L+ +     VS  RV Q+ ++
Sbjct: 167 IHGLLDERFQAALADAIAKLPERERLVLALYY--DEELNLKEIGEVLGVSESRVSQLHSQ 224

Query: 276 AFKKVQESI 284
              +++  +
Sbjct: 225 CAARLRARL 233


>gi|171058305|ref|YP_001790654.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Leptothrix cholodnii
           SP-6]
 gi|170775750|gb|ACB33889.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Leptothrix cholodnii
           SP-6]
          Length = 238

 Score =  107 bits (267), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 44/238 (18%), Positives = 100/238 (42%), Gaps = 15/238 (6%)

Query: 51  HRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           + L+  +  LV ++A          + I +++  G IGL  A+ +FD  +G    T++  
Sbjct: 11  NSLLKQYSPLVRRLAHQMIAKLPANVEIDDLIQVGMIGLTDALSRFDIGQGVMFETFATQ 70

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+ AM + + R    +  G   +Q+ +   + RL+  L        +  Q   IAK++ 
Sbjct: 71  RIRGAMLDEL-RGSDWMSRGNRKHQRDIEGAVHRLEQKL-------GRTPQESEIAKEMG 122

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++  E   +  R+ G + +           + + D  V    G +   + +      R  
Sbjct: 123 ITLLEYQDLLNRVRGTQLIYLEDMGGADGDNDYLDRHVAADTGGD--PLARLNDHRMRQA 180

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L  ++  L  RE+ +       E  + L+ +++   V+  RV Q+ +++  +++  ++
Sbjct: 181 LVDAIKNLPEREQYVMSMYY--EEDMNLKEIAAVLGVTESRVCQLHSQSIARLRAKLR 236


>gi|330984347|gb|EGH82450.1| putative alternative sigma factor RpoH [Pseudomonas syringae pv.
           lachrymans str. M301315]
          Length = 263

 Score =  107 bits (267), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 58/263 (22%), Positives = 118/263 (44%), Gaps = 16/263 (6%)

Query: 23  IRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           + KI +   QE     + ++  G   A    VT+ L +V  +A+   G    + ++  +G
Sbjct: 14  LNKIQIPSIQEMDNNIRIFKSTGCRKAHDACVTALLPMVYGLAVANAGR-AEVDDMFQQG 72

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            + +M A++KFDP+    + +++  ++  A+    +    L+++  T   +  +  +   
Sbjct: 73  ALAVMDALRKFDPDDELNILSWTKLYVSRAINSLCVFGTKLIRVPDTKTIRLCYRRMG-- 130

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD--ESLNALINSSDKNSSQW 200
                 + D  +   +   +A +L VS  +      ++A D   S    + S      Q 
Sbjct: 131 ----LFLKDGPINEARSKILANELGVSLEDF-----KIARDLYSSCYEPVLSCGDEPWQG 181

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
            D  +   +  E+ +I ++E  +   ++ R M+VLNP+E  +   R LQE PV L  +  
Sbjct: 182 HD--IKTSETLEEAIIVEDEAAHVTRVVGRLMTVLNPKEAEVIRLRCLQEEPVQLRLVGE 239

Query: 261 EFEVSRERVRQIEARAFKKVQES 283
           +   S ER RQ+E  A  K++++
Sbjct: 240 QLGFSTERARQVENIAKDKMRKA 262


>gi|326332680|ref|ZP_08198943.1| hypothetical protein NBCG_04120 [Nocardioidaceae bacterium Broad-1]
 gi|325949508|gb|EGD41585.1| hypothetical protein NBCG_04120 [Nocardioidaceae bacterium Broad-1]
          Length = 264

 Score =  107 bits (267), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 48/237 (20%), Positives = 97/237 (40%), Gaps = 19/237 (8%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
             ++  +  +   IA  Y G G+P +++     I L++A K F P+R     TY++  I+
Sbjct: 39  EEVILLNAAVARSIAHRYTGRGIPRADLEQVAYIALVRAAKSFHPDRADDFLTYAVPTIR 98

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
             ++ +       V+      +  L   L R+          NL   ++  IA+   V E
Sbjct: 99  GEVKRWFRDHGWTVRPPRPIQE--LQSTLLRIGSE-----RGNLPTSELAEIAE---VPE 148

Query: 171 SEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            +V             SL+A + S D  SS  +  +     G +  L + E     R  L
Sbjct: 149 QKVREALDARGCFTPSSLDAPLRSGDSQSS-GEATIGDMLPGVDGGLSDCE----TRLAL 203

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            +++  L PR++ +   R L++   +   +     V++ +V +I  R   +++  ++
Sbjct: 204 EQAIHALCPRDQLVVRLRFLED--RSQAEIGEAIGVTQTQVSRILTRIIDELRVQLE 258


>gi|148266118|ref|YP_001232824.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacter
           uraniireducens Rf4]
 gi|146399618|gb|ABQ28251.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Geobacter
           uraniireducens Rf4]
          Length = 251

 Score =  107 bits (267), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 47/239 (19%), Positives = 90/239 (37%), Gaps = 14/239 (5%)

Query: 50  AHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              LV SHL LV  +           L   ++ S   IGL+ A ++FDP RG    T++ 
Sbjct: 20  RDELVVSHLPLVKFLVDRIASALPPHLDRDDLRSAAVIGLISAAERFDPSRGVMFKTFAE 79

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+  + + +     L +     + +  F  L R    L+     N   E+V A A  L
Sbjct: 80  QRIRGTIMDELRSQDWLTR-----SLRDKFKRLEREFSCLEQRLGRNPTSEEVAA-AMGL 133

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +     +          SL+      D +     D L    D   +    +   +    
Sbjct: 134 ELEGYFHLLEEIHFLSFVSLDDAWMDEDGSPLGLLDVL---EDKGVESPQNQLIARQTVE 190

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            L  ++  L  +ER +      +E  + L+ + S   ++  R+ Q+ ++A  +++  ++
Sbjct: 191 NLAEAIDGLPEKERIVITLYYYEE--LNLKEIGSVLSLTESRISQLHSQALLRLRGRMK 247


>gi|229068653|ref|ZP_04201951.1| RNA polymerase sigma-B factor [Bacillus cereus F65185]
 gi|229078304|ref|ZP_04210868.1| RNA polymerase sigma-B factor [Bacillus cereus Rock4-2]
 gi|229177534|ref|ZP_04304912.1| RNA polymerase sigma-B factor [Bacillus cereus 172560W]
 gi|228605896|gb|EEK63339.1| RNA polymerase sigma-B factor [Bacillus cereus 172560W]
 gi|228704979|gb|EEL57401.1| RNA polymerase sigma-B factor [Bacillus cereus Rock4-2]
 gi|228714400|gb|EEL66277.1| RNA polymerase sigma-B factor [Bacillus cereus F65185]
          Length = 203

 Score =  107 bits (267), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 38/210 (18%), Positives = 95/210 (45%), Gaps = 16/210 (7%)

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++  G +GL+ A++++D   G     +++  I   +++Y+      + +      +R+
Sbjct: 3   EDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRI 57

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSS 193
                ++K  ++ +TD   +  +++ IA  L +SE EV+ +          SL+ ++ +S
Sbjct: 58  KDLGGKIKLAIEELTDRFQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENS 117

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
              SS  +   V +       + +  E   RR +L    +VLN  E+ +      +   +
Sbjct: 118 SDGSSVARIESVGE-------VEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGEN--L 168

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQES 283
             ++      +S+  V +I+ +A  K++++
Sbjct: 169 NQKDTGERLGISQMHVSRIKRQAISKLKQA 198


>gi|228932399|ref|ZP_04095281.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228984185|ref|ZP_04144367.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|229183301|ref|ZP_04310530.1| RNA polymerase sigma-B factor [Bacillus cereus BGSC 6E1]
 gi|228600171|gb|EEK57762.1| RNA polymerase sigma-B factor [Bacillus cereus BGSC 6E1]
 gi|228775472|gb|EEM23856.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228827335|gb|EEM73087.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
          Length = 203

 Score =  106 bits (266), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 38/210 (18%), Positives = 97/210 (46%), Gaps = 16/210 (7%)

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++  G +GL+ A++++D   G     +++  I   +++Y+      + +      +R+
Sbjct: 3   EDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRI 57

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSS 193
                ++K  ++ +TD+  +  +++ IA  L +SE EV+ +          SL+ ++ ++
Sbjct: 58  KDLGGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENA 117

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
              SS  +   V +       + +  E   RR +L    +VLN  E+ +     + E  +
Sbjct: 118 SDGSSVARIESVGE-------VEQGYEETERRLVLKDIFNVLNETEKSVIH--YIFEENL 168

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQES 283
             ++      +S+  V +I+ +A  K++++
Sbjct: 169 NQKDTGERLGISQMHVSRIKRQAISKLKQA 198


>gi|254506869|ref|ZP_05119008.1| flagellar biosynthesis sigma factor FliA [Vibrio parahaemolyticus
           16]
 gi|219550154|gb|EED27140.1| flagellar biosynthesis sigma factor FliA [Vibrio parahaemolyticus
           16]
          Length = 220

 Score =  106 bits (266), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 48/230 (20%), Positives = 94/230 (40%), Gaps = 19/230 (8%)

Query: 60  LVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           LV +IA    G   P   + +++  G IGL++A K +D  +G    TY+   I+ AM + 
Sbjct: 2   LVKRIAHHLLGRLPPSVQVEDLIQAGMIGLLEAQKNYDGTKGASFETYAGIRIRGAMLDD 61

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
           I R    V      + + +   +  L+G L        +      +A+ L +S ++  + 
Sbjct: 62  IRR-GDWVPRSVHKHSREISQAISVLEGELN-------RDPTDAEVAQHLGLSLTQYHTA 113

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
                 D + + L+   D   S+  D +  D D +     +    +  R  L  S+  L 
Sbjct: 114 LT----DINCSRLVGIEDLGVSE--DVITPDGDEEANTPFQGVADEYFRKALIDSIKSLP 167

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            RE  +       +  + L+ +     VS  RV QI +++ ++++  +  
Sbjct: 168 EREALVLSLYY--DEELNLKEIGDVIGVSESRVSQILSQSMQRLRTKLSA 215


>gi|114320145|ref|YP_741828.1| RNA polymerase, sigma 28 subunit [Alkalilimnicola ehrlichii MLHE-1]
 gi|114226539|gb|ABI56338.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Alkalilimnicola
           ehrlichii MLHE-1]
          Length = 242

 Score =  106 bits (266), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 45/239 (18%), Positives = 99/239 (41%), Gaps = 20/239 (8%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           + L+  H  LV +IA    G   P   + +++  G +GL++A ++FDP +G    TY+  
Sbjct: 16  NDLLVQHASLVKRIAHHLAGRLPPSVQLDDLIQAGMVGLLEAARQFDPGQGASFQTYAGI 75

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+ AM + I R             + +    R +   ++A+     +  +   +A++L 
Sbjct: 76  RIRGAMLDEIRRLDWT--------PRSVHRKGRSVAEAIRAVEHRTGRDARDHEVAQELG 127

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++  E   +      D S + + +   ++ +  +   +    G       +   +  +  
Sbjct: 128 ITLDEYHQILQ----DVSTSRIFSIDQEDPATGEPHQL---PGDHPEPFAEITDEGFQRA 180

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           L  ++  L  RE+ I       +  + L  +     V+  RV QI  R   K++E++++
Sbjct: 181 LAEAIRRLPEREQLIMALYY--DEELNLREIGEVLNVTESRVSQIHGRIVVKLREALKE 237


>gi|325001881|ref|ZP_08122993.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pseudonocardia sp. P1]
          Length = 258

 Score =  106 bits (266), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 43/252 (17%), Positives = 91/252 (36%), Gaps = 21/252 (8%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKF 93
           L + +           LV  H  LV  I           + +++++  G  GL+ AV +F
Sbjct: 20  LWRAHLAVRSADTRRLLVEHHAPLVRGIGAKLATRLPSSIELADLLQSGTFGLIDAVDRF 79

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           DP RG R   Y+   ++ AM + +        +  T   +      R ++   +A+    
Sbjct: 80  DPARGVRFEGYAAQRVRGAMLDELRAQDW---VPRTVRSRS-----REIERAREAVQSKV 131

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            +P     +A +L +   ++              AL+ S+D                   
Sbjct: 132 GRPASDRELAAELGIGLRDLRQAVRP--------ALLVSADDLDGNAAPGPAALAAADTA 183

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
             +    R+     L  +++ L  R+R +     +++   TL  + +   V+  RV Q+ 
Sbjct: 184 DPVATAVRRETGAELRAAIAQLGERDRTVLRLYYVED--HTLAEIGALLGVTESRVCQLH 241

Query: 274 ARAFKKVQESIQ 285
            R   +++  ++
Sbjct: 242 TRMLTRLRTRME 253


>gi|310643955|ref|YP_003948713.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
 gi|309248905|gb|ADO58472.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
          Length = 257

 Score =  106 bits (266), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 42/262 (16%), Positives = 108/262 (41%), Gaps = 19/262 (7%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI-SEVVSEGNI 84
            P     E   L   Y++  D   A  L+  +  +V   A         +  ++   G +
Sbjct: 6   TPPESMDEAVGLIWEYQQTKDNEIATVLIRKYEPMVKMAAGKISRNRPDLYEDLYQTGQM 65

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
            L++ ++++D   G     Y+M  +   M+ Y+      +++     +K        ++ 
Sbjct: 66  ALIRLLQQYDISLGIPFEPYAMKSMLGHMKNYLRDKSWYIQVPRRIKEKGAL-----VQH 120

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC--RLAGDESLNALINSSDKNSSQWQD 202
            +  +T    +   V  IA+ L+++  E I +          SL++ + S +++++   +
Sbjct: 121 AIDELTVKLERSPNVNEIAEYLDLTVEETIEVLAGRECYHYVSLDSPL-SQEESAATLGE 179

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
            +  D +  + V         +R  L +++S L  +E+++       ++  +   ++   
Sbjct: 180 LISSDANDFDTV--------EKRMDLQQALSQLKEQEQKVLLLAF--QDGQSQRAIAQTL 229

Query: 263 EVSRERVRQIEARAFKKVQESI 284
            VS+  V +I+ RA +K+++ +
Sbjct: 230 GVSQMSVSRIQKRATEKLKQIM 251


>gi|77918763|ref|YP_356578.1| flagellar biosynthesis protein, alternative sigma factor 28
           [Pelobacter carbinolicus DSM 2380]
 gi|77544846|gb|ABA88408.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Pelobacter
           carbinolicus DSM 2380]
          Length = 255

 Score =  106 bits (266), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 46/242 (19%), Positives = 95/242 (39%), Gaps = 19/242 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             RL+ SHL +V  +A              ++ S   +GL+ A  +F P  G    T++ 
Sbjct: 15  KDRLIKSHLHMVSFLAERMVSQVPAFMTREDISSAAMVGLVDAANRFKPSMGVLFKTFAE 74

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             ++ A+ + + R             + L     R+   ++A+     +P +   +A +L
Sbjct: 75  KRMRGAVLDEVRR--------MDWFSRSLRQKQSRIAKTMEALEKRLGRPPEEHEMAAEL 126

Query: 167 NVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            +           ++  G  SL+  I    +++      L    D      +E  E    
Sbjct: 127 EMDLESYRQALGEVSYLGCVSLHETI----EDTPDGPTMLDNIEDQNSPSAVEMLENSEL 182

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              L R +  L  +ER +      +E  ++ + ++   E+S  RV Q+ ++A  K++ SI
Sbjct: 183 TQELARQIDRLTDKERLVVSLYYYEE--LSQKEIAEVLELSEGRVSQLHSQALIKLKTSI 240

Query: 285 QK 286
           ++
Sbjct: 241 KR 242


>gi|308070731|ref|YP_003872336.1| DNA-directed RNA polymerase specialized sigma subunit
           [Paenibacillus polymyxa E681]
 gi|305860010|gb|ADM71798.1| DNA-directed RNA polymerase specialized sigma subunit
           [Paenibacillus polymyxa E681]
          Length = 257

 Score =  106 bits (266), Expect = 3e-21,   Method: Composition-based stats.
 Identities = 42/262 (16%), Positives = 107/262 (40%), Gaps = 19/262 (7%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI-SEVVSEGNI 84
            P     E   L   Y++  D   A  L+  +  +V   A         +  ++   G +
Sbjct: 6   TPPESMDEAVGLIWEYQQTKDNEIATVLIRKYEPMVKMAAGKISRNRPDLYEDLYQTGQM 65

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
            L++ ++++D   G     Y+M  +   M+ Y+      +++     +K        ++ 
Sbjct: 66  ALIRLLQQYDISLGIPFEPYAMKSMLGHMKNYLRDKSWYIQVPRRIKEKGAL-----VQH 120

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC--RLAGDESLNALINSSDKNSSQWQD 202
            +  +T    +   V  IA  L+++  E I +          SL++ + S +++++   +
Sbjct: 121 AIDELTVKLERSPNVDEIATYLDLTVEETIEVLAGRECYHYVSLDSPL-SQEESAATLGE 179

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
            +  D +  + V         +R  L +++S L  +E+++       ++  +   ++   
Sbjct: 180 LISSDANDYDTV--------EKRMDLQQALSQLKEQEQKVLLLAF--QDGQSQRAIAQTL 229

Query: 263 EVSRERVRQIEARAFKKVQESI 284
            VS+  V +I+ RA +K+++ +
Sbjct: 230 GVSQMSVSRIQKRATEKLKQIM 251


>gi|229126412|ref|ZP_04255427.1| RNA polymerase sigma-B factor [Bacillus cereus BDRD-Cer4]
 gi|228656992|gb|EEL12815.1| RNA polymerase sigma-B factor [Bacillus cereus BDRD-Cer4]
          Length = 203

 Score =  106 bits (266), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 38/210 (18%), Positives = 96/210 (45%), Gaps = 16/210 (7%)

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++  G +GL+ A++++D   G     +++  I   +++Y+      + +      +R+
Sbjct: 3   EDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRI 57

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSS 193
                ++K  ++ +TD+  +  +++ IA  L +SE EV+ +          SL+ ++ +S
Sbjct: 58  KDLGGKIKLAIEELTDHLQRSPRIIEIANHLGLSEEEVLEIMDAKNNYRVSSLDDVVENS 117

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
              SS  +   V +       + +  E   RR +L    +VLN  E+ +      +   +
Sbjct: 118 SDGSSVARIESVGE-------VEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGEN--L 168

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQES 283
             ++      +S+  V +I+ +A  K++++
Sbjct: 169 NQKDTGERLGISQMHVSRIKRQAISKLKQA 198


>gi|168214239|ref|ZP_02639864.1| RNA polymerase sigma-E factor [Clostridium perfringens CPE str.
           F4969]
 gi|170714290|gb|EDT26472.1| RNA polymerase sigma-E factor [Clostridium perfringens CPE str.
           F4969]
          Length = 235

 Score =  106 bits (266), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 52/261 (19%), Positives = 104/261 (39%), Gaps = 59/261 (22%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L K+EE  L  +  E+ D +    L+  +LRLVV IA  +   G+ + +++S G IGL+
Sbjct: 34  PLSKEEEEELVNKLGEN-DEAIRSILIERNLRLVVYIARKFENTGVGVEDLISVGTIGLI 92

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV  F+PE+  +LATY+   I+  +  Y+ R+                    ++K    
Sbjct: 93  KAVNTFNPEKKIKLATYASRCIENEILMYLRRNS-------------------KVKAE-- 131

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                       ++  + LN+             G+E L + I  +D +       ++ D
Sbjct: 132 ------------ISFYEPLNIDWD----------GNELLLSDILGTDDD---IVYNMIED 166

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
              +E +    +   NR   +      L                  T + ++    +S+ 
Sbjct: 167 EVDKELLFTAMKNLSNREKEIVELRFGL------------CGYKEKTQKEVADMLGISQS 214

Query: 268 RVRQIEARAFKKVQESIQKQV 288
            + ++E +  K++++ I K +
Sbjct: 215 YISRLEKKIIKRLKKEINKMI 235


>gi|229149313|ref|ZP_04277550.1| RNA polymerase sigma-B factor [Bacillus cereus m1550]
 gi|229154668|ref|ZP_04282783.1| RNA polymerase sigma-B factor [Bacillus cereus ATCC 4342]
 gi|228628616|gb|EEK85328.1| RNA polymerase sigma-B factor [Bacillus cereus ATCC 4342]
 gi|228634127|gb|EEK90719.1| RNA polymerase sigma-B factor [Bacillus cereus m1550]
          Length = 203

 Score =  106 bits (266), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 37/210 (17%), Positives = 96/210 (45%), Gaps = 16/210 (7%)

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++  G +GL+ A++++D   G     +++  I   +++Y+      + +      +R+
Sbjct: 3   EDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRI 57

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSS 193
                ++K  ++ +TD+  +  +++ IA  L +SE EV+ +          SL+ ++ ++
Sbjct: 58  KDLGGKIKLAIEELTDHLQRSPKIIEIANHLGLSEEEVLEIMDAKNNYRVSSLDDVVENA 117

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
              SS  +   V +       + +  E   RR +L    +VLN  E+ +      +   +
Sbjct: 118 SDGSSVARIESVGE-------VEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGEN--L 168

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQES 283
             ++      +S+  V +I+ +A  K++++
Sbjct: 169 NQKDTGERLGISQMHVSRIKRQAISKLKQA 198


>gi|229171759|ref|ZP_04299331.1| RNA polymerase sigma-B factor [Bacillus cereus MM3]
 gi|228611656|gb|EEK68906.1| RNA polymerase sigma-B factor [Bacillus cereus MM3]
          Length = 203

 Score =  106 bits (266), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 38/210 (18%), Positives = 96/210 (45%), Gaps = 16/210 (7%)

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++  G +GL+ A++++D   G     +++  I   +++Y+      + +      +R+
Sbjct: 3   EDIIQVGMLGLLGAIRRYDCSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRI 57

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSS 193
                ++K  ++ +TD+  +  +++ IA  L +SE EV+ +          SL+ ++ +S
Sbjct: 58  KDLGGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENS 117

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
              SS  +   V +       + +  E   RR +L    +VLN  E+ +      +   +
Sbjct: 118 SDGSSVARIESVGE-------VEQGYEETERRLVLKDIFNVLNETEKSVIHYIFGEN--L 168

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQES 283
             ++      +S+  V +I+ +A  K++++
Sbjct: 169 NQKDTGERLGISQMHVSRIKRQAISKLKQA 198


>gi|289208354|ref|YP_003460420.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thioalkalivibrio sp. K90mix]
 gi|288943985|gb|ADC71684.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thioalkalivibrio sp. K90mix]
          Length = 253

 Score =  106 bits (266), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 55/246 (22%), Positives = 105/246 (42%), Gaps = 19/246 (7%)

Query: 51  HRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            + V  H+ LV +IA          + + +++  G IGL++A ++F+  +G   ATY+  
Sbjct: 20  EQRVAEHIELVHRIAHHLMARLPSSVQVDDLIQAGMIGLLEAARQFEGGQGATFATYAGI 79

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+ AM + + RS            + +  N R++   +Q +     +  + V +A++L 
Sbjct: 80  RIRGAMIDELRRSDWT--------PRSVHRNSRKIAEAIQTVEAREGRAARGVEVAEELE 131

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           V   E  SM    AG   L AL +    +    +       +GQE       E    R  
Sbjct: 132 VPIDEYYSMLQDHAG-AHLFALDDLGGTDGDADRVI-----EGQEASPSRTIEAGEFREE 185

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L  ++  L  RER +     ++E  + L  + +   V+  RV QI ++A  +++  +   
Sbjct: 186 LAAALGDLPERERLVLSLYYIEE--LNLREIGAVLGVTESRVSQIRSQAVIRLRARLGSW 243

Query: 288 VELSSS 293
           +E   +
Sbjct: 244 LEDGEA 249


>gi|319764532|ref|YP_004128469.1| RNA polymerase sigma factor, flia/whig family [Alicycliphilus
           denitrificans BC]
 gi|330826748|ref|YP_004390051.1| RNA polymerase sigma 28 subunit FliA/WhiG [Alicycliphilus
           denitrificans K601]
 gi|317119093|gb|ADV01582.1| RNA polymerase sigma factor, FliA/WhiG family [Alicycliphilus
           denitrificans BC]
 gi|329312120|gb|AEB86535.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Alicycliphilus
           denitrificans K601]
          Length = 238

 Score =  106 bits (265), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 44/241 (18%), Positives = 100/241 (41%), Gaps = 19/241 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L   HL LV +IA          + + ++V  G IGL  A+ +++  +G +  T++ 
Sbjct: 10  RDALFHQHLPLVRRIAHHMIAKLPPNVELDDLVQVGMIGLTDALSRYEAAQGVQFETFAS 69

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +     + + G   +QK +   L R++  L        +      IA +L
Sbjct: 70  QRIRGAMLDELRDGDWMSR-GARKSQKEIEQALHRVEQRL-------GRSPMESEIAAEL 121

Query: 167 NVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            +  ++  ++  ++ G     L  +    +         +  +      VL ++  R + 
Sbjct: 122 GMDLADYQALLGKVRGTQLVYLEDMGGGEEGEEGFLDRHVADEGADPMAVLRDQRLRTS- 180

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              L  ++  L  RE+ I       E+ + L+ +++   V+  RV Q+ ++A  +++  +
Sbjct: 181 ---LVAAIKQLPEREQHIMGMYY--EHDMNLKEIAAVLGVTESRVCQLHSQAIARLRTKM 235

Query: 285 Q 285
           +
Sbjct: 236 R 236


>gi|294673112|ref|YP_003573728.1| sigma factor [Prevotella ruminicola 23]
 gi|294471705|gb|ADE81094.1| putative sigma factor [Prevotella ruminicola 23]
          Length = 238

 Score =  106 bits (265), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 60/258 (23%), Positives = 106/258 (41%), Gaps = 57/258 (22%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  ++  IR +  L++++E  LA+R +  GD  A  +++ S+L+LVV IA  YR   + +
Sbjct: 14  LESFMARIRGVKALDEEQEVYLAQRIK-AGDTKAEEQMIKSNLKLVVSIANSYR-PMMSM 71

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++  GNIGL++AV++F+PE G+R   Y+   I+  +   I     +V           
Sbjct: 72  EDLIQNGNIGLIKAVREFNPELGYRFVFYASMMIRKYIIMGIRNDSGIVHSSDY------ 125

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
                                                           ESL+   +   K
Sbjct: 126 -----------------------------------------EQAFISSESLDVPGSGGYK 144

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF-EARRLQENPVT 254
           ++S+  D LV D D      +E +      ++     SVL+P    I  +   L   P+ 
Sbjct: 145 DTSK-ADMLVGDMD------VESDLDSLSADLKRAMCSVLSPCAVDIVCKVMGLGCTPMY 197

Query: 255 LENLSSEFEVSRERVRQI 272
            E++  E  + + RVR+I
Sbjct: 198 TESIGKELNMPKSRVRKI 215


>gi|221133291|ref|ZP_03559596.1| flagellar biosynthesis sigma factor [Glaciecola sp. HTCC2999]
          Length = 243

 Score =  106 bits (265), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 46/245 (18%), Positives = 96/245 (39%), Gaps = 20/245 (8%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
             LV  H  LV +IA        P   + +++  G +GL++A K F+  +G    T++  
Sbjct: 15  EELVEKHTILVKRIAHHLLARLPPNILVDDLIQAGMLGLLEAAKNFNSTKGASFETFAGI 74

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+ +M + I +             + +  N R +   + ++ +      +   IAK+L 
Sbjct: 75  RIRGSMLDDIRKGDWT--------PRSVHKNSRAITQAISSVENEMNSDAKDSDIAKRLG 126

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +   +   M      + ++  L+   D   S+  D +            ++      +  
Sbjct: 127 IELPQYHKML----NEVNIGKLVGIEDLGISE--DVIATPDFKSTNTPYDELVHGCFQKA 180

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK- 286
           L +++  L  RE  +       +  ++L  +     VS  RV QI ++A  K++  +   
Sbjct: 181 LAKAIVSLPEREAIVLSLYY--DEDLSLREIGQALNVSESRVSQIHSQAKSKLKIKLSSW 238

Query: 287 QVELS 291
           Q EL+
Sbjct: 239 QQELA 243


>gi|258655075|ref|YP_003204231.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nakamurella
           multipartita DSM 44233]
 gi|258558300|gb|ACV81242.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Nakamurella
           multipartita DSM 44233]
          Length = 308

 Score =  106 bits (265), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 39/240 (16%), Positives = 90/240 (37%), Gaps = 17/240 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
                ++VT ++ +   +A  Y G G+  S++     +GL++AV+++ P R      +++
Sbjct: 86  RRCQQQVVTEYIPVARSLAARYSGRGVERSDLEQLAYMGLIKAVQRWRPGRSDDFLQFAV 145

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I   ++ Y      LV+      + R       +    Q+    + +      +AK  
Sbjct: 146 PTIVGEIKRYFRDHSWLVRPPRRIQELRAA-----ISEAEQSQRHQDGRAPSDAELAKAT 200

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             + +++       A     +        +  Q     +    G+E   + + E    R 
Sbjct: 201 GATVTDIDEARAAAACCRPRSL-------DEEQGPGLALALSWGEEDAELRRVED---RA 250

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + R +  L  RER +   R   +N  +   +  E  VS+ +V +      +K+   +++
Sbjct: 251 TVERLLDALTDRERDVVHMRF--DNGWSQSRIGREIGVSQMQVSRWLRSITEKLASCVER 308


>gi|281420137|ref|ZP_06251136.1| RNA polymerase sigma-43 factor [Prevotella copri DSM 18205]
 gi|281405937|gb|EFB36617.1| RNA polymerase sigma-43 factor [Prevotella copri DSM 18205]
          Length = 205

 Score =  106 bits (265), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 45/239 (18%), Positives = 92/239 (38%), Gaps = 48/239 (20%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           +++V+ +L  V  +A  Y+G G+   ++VSEG + ++ A +KF  +RG     Y+  ++ 
Sbjct: 7   NKIVSENLNYVKSVANQYKGKGVEFDDLVSEGTLAMLMAARKFQADRGTDFVAYAGPFVH 66

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            A+ + I +   L ++                                     K    + 
Sbjct: 67  KAISQAIDKQSGLYRLPKDQK--------------------------------KFAPRNA 94

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            + +S++  L+ +     L   +D +     D L                 +  +  +  
Sbjct: 95  DKAVSVDAPLSANNPYTLLDILNDPDVKIADDTL---------------NIEMMKKKMAE 139

Query: 231 SMSVLNPRERRIFEARRLQENPV-TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           S++ L PRE+ I         P  T+  ++ +  + RERVRQI     +++  SI+ Q 
Sbjct: 140 SIADLLPREKEIITKFYGIGVPKETMAEIAEDMGLKRERVRQIRNLTIRRLNRSIRHQA 198


>gi|228951468|ref|ZP_04113574.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228808175|gb|EEM54688.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
          Length = 203

 Score =  106 bits (265), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 38/210 (18%), Positives = 94/210 (44%), Gaps = 16/210 (7%)

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++  G +GL+ A++++D   G     +++  I   +++Y+      + +      +R+
Sbjct: 3   EDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRI 57

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSS 193
                ++K  ++ +TD   +  ++  IA  L +SE EV+ +          SL+ ++ +S
Sbjct: 58  KDLGGKIKLAIEELTDRFQRSPKIKEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENS 117

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
              SS  +   V +       + +  E   RR +L    +VLN  E+ +      +   +
Sbjct: 118 SDGSSVARIESVGE-------VEQGYEEAERRLVLKDIFNVLNDTEKSVIHYIFGEN--L 168

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQES 283
             ++      +S+  V +I+ +A  K++++
Sbjct: 169 NQKDTGERLGISQMHVSRIKRQAISKLKQA 198


>gi|163750532|ref|ZP_02157770.1| flagellar biosynthesis sigma factor FliA [Shewanella benthica KT99]
 gi|161329687|gb|EDQ00676.1| flagellar biosynthesis sigma factor FliA [Shewanella benthica KT99]
          Length = 246

 Score =  106 bits (265), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 47/236 (19%), Positives = 97/236 (41%), Gaps = 20/236 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           +V  +  LV KIA          + + +++  G +GL++A  KFD  +G +  T++   I
Sbjct: 16  IVEQYASLVKKIAHHLLARLPASVQLDDLLQAGMMGLLEASAKFDANKGAKFETFAGIRI 75

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + +M + I R    V      NQ       RR+   +  +     +  +   IA++L ++
Sbjct: 76  RGSMLDDIRR-GDWVPRSVHRNQ-------RRVAQVIDELEQELGRDAKDDEIAQRLEMT 127

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             E       +  + S+  +I   D   S     ++   DG +    E          L 
Sbjct: 128 LDEYH----HILNNVSVGKIIGIEDLGVS---VDVISHDDGVKDDTYESIAEDKFHAALV 180

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            ++ +L  R+  +       +  + L+ + +  EVS  RV QI ++A  +++  ++
Sbjct: 181 AAIKLLPERDGLVLSLYY--DEALNLKEIGAILEVSESRVSQILSQAMLRLKAKLK 234


>gi|56551522|ref|YP_162361.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Zymomonas mobilis
           subsp. mobilis ZM4]
 gi|56543096|gb|AAV89250.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Zymomonas mobilis
           subsp. mobilis ZM4]
          Length = 247

 Score =  106 bits (265), Expect = 4e-21,   Method: Composition-based stats.
 Identities = 54/237 (22%), Positives = 104/237 (43%), Gaps = 23/237 (9%)

Query: 51  HRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
             L+ +HL+LV KIA    G     + + +++  G + L++A   F+  RGF  ATY+  
Sbjct: 26  EALIKTHLQLVRKIAWHVHGRVSSAIEVEDLIQIGMVALIEAANAFE-NRGFAFATYASM 84

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+ AM +Y+ +  +  +  + A QK L           + ++    +  +   IA+KLN
Sbjct: 85  RIRGAMIDYMRQHAATAR-SSIARQKTLN-------KAREELSATLGRRPEDAEIAEKLN 136

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S SE          D ++N    S D   S        D+  Q   +    ER+  ++ 
Sbjct: 137 MSPSEYREW-----ADGAINIRQESLDDVYSDHSSIFTDDNADQASEM----EREALQSA 187

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   +  L  RE  + +   ++E  + L+ +    ++   R+ QI+  A   +++ +
Sbjct: 188 LAEQIKTLPEREALVLQLYYVEE--LNLKEIGEVLDLGTARISQIKKSAVDHLRQKM 242


>gi|15022434|dbj|BAB62255.1| RNA polymerase sigma 70 factor [Treponema medium]
          Length = 155

 Score =  106 bits (265), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 32/150 (21%), Positives = 61/150 (40%), Gaps = 7/150 (4%)

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           + ++    + +     +      IA +L  +   V  +        SL   I   ++  S
Sbjct: 2   INKVTRESRQLMQKFGREPTDEEIAAQLGWNVERVKQVKNVAREPISLETPI--GEEEDS 59

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLE 256
              D++    D   +      E    +  L   +S L  RE+ + + R   +    +TLE
Sbjct: 60  SLGDFI---EDKDVENPSNLTEYILLQEQLRGVLSCLPLREQEVLKMRFGLDEGYALTLE 116

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +   F V+RER+RQIEA+A ++++   Q 
Sbjct: 117 EVGLYFNVTRERIRQIEAKALRRLRHPKQS 146


>gi|254491912|ref|ZP_05105091.1| RNA polymerase sigma factor, FliA/WhiG family [Methylophaga
           thiooxidans DMS010]
 gi|224463390|gb|EEF79660.1| RNA polymerase sigma factor, FliA/WhiG family [Methylophaga
           thiooxydans DMS010]
          Length = 234

 Score =  106 bits (265), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 46/245 (18%), Positives = 94/245 (38%), Gaps = 19/245 (7%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
            +   LV  +  LV +IA          + + +++  G IGL+ A  +FD  +G    TY
Sbjct: 6   QSKSELVEQNAALVKRIAYHLIARLPASVDVEDLIQAGMIGLLDASHQFDSSQGASFETY 65

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +   I+ AM + I R+            + +    R +   +Q I     +      +A+
Sbjct: 66  AGIRIRGAMLDEIRRNDW--------APRSVHRKAREISSTMQVIEQQKGRNASDAEVAQ 117

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            + +  SE         G + L +L   SD +    +               E+ ++ + 
Sbjct: 118 AMGLDISEYHQQLQDSTGHQ-LFSLDEFSDNDEVHARPI-----SSGPAAPEEEVQQDDF 171

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +  + R++  L  RER +        + + L+ +     VS  RV QI ++   +++  +
Sbjct: 172 QQAMVRAIDSLPERERLLMSLYY--NDELNLKEIGEVLGVSESRVSQIHSQTVIRLRSKL 229

Query: 285 QKQVE 289
           +  V 
Sbjct: 230 RDWVM 234


>gi|88858091|ref|ZP_01132733.1| flagellar biosynthesis sigma factor FliA [Pseudoalteromonas
           tunicata D2]
 gi|88819708|gb|EAR29521.1| flagellar biosynthesis sigma factor FliA [Pseudoalteromonas
           tunicata D2]
          Length = 227

 Score =  106 bits (265), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 50/235 (21%), Positives = 91/235 (38%), Gaps = 18/235 (7%)

Query: 53  LVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           L+  H+ LV +IA          + + ++   G IGL++A K FD  +G    TY+   I
Sbjct: 4   LIERHVSLVKRIAYHLLARLPASVQLDDLTQSGMIGLIEAAKNFDGTKGASFETYAGIRI 63

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + AM + I R    V      N +     + +    L+A     +K    V +A+KL+++
Sbjct: 64  RGAMLDEI-RKGDWVPRSVHKNAR----MVAQATAELEAELGREVK---DVEVAEKLDIT 115

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
            +E   +      D +   +I   D    +       D            + +     L 
Sbjct: 116 LNEYHDIL----NDVNSGRIIGIEDLGVDE-DVLHSDDQVHAFDSPFNHTQTEKFNLSLV 170

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            ++  L  R+  +        + + L+ +    EVS  RV QI  +A  K++  I
Sbjct: 171 EAIKSLPERDALVLSLYY--NDEMNLKEIGLILEVSESRVSQIHGQAMVKLKAKI 223


>gi|253577386|ref|ZP_04854702.1| RNA polymerase sigma factor [Paenibacillus sp. oral taxon 786 str.
           D14]
 gi|251843186|gb|EES71218.1| RNA polymerase sigma factor [Paenibacillus sp. oral taxon 786 str.
           D14]
          Length = 257

 Score =  106 bits (265), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 42/264 (15%), Positives = 110/264 (41%), Gaps = 19/264 (7%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI-SEVVSEG 82
           R  P    QE   L ++Y++  D   A +L+  +  +V   A         +  ++   G
Sbjct: 4   RAAPQASFQESTRLIQQYQQTRDNEIATQLIQKYDSMVKMAAGKIARNRPDLYEDLYQVG 63

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            + L++ ++++D + G     Y+M  +   M+ Y+      +++     +K        +
Sbjct: 64  EMALVRLLQQYDSDLGIPFEPYAMKSMIGHMKNYLRDKSWYIQVPRRIKEKGAL-----V 118

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC--RLAGDESLNALINSSDKNSSQW 200
           +  +  +T    +   V  IA+ L +S  E + +          SL++ + S D+++   
Sbjct: 119 QQAIDELTLKLERSPNVQEIAEYLELSVEETVEVLAGRDCYHYVSLDSPL-SPDESAVTL 177

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
            + +  D D  + +          R  L +++  L  +E+++       +   +   ++ 
Sbjct: 178 GEVISADADDYDAL--------ENRMDLQQALGQLKAQEQQVLLMAY--QEGQSQRAIAR 227

Query: 261 EFEVSRERVRQIEARAFKKVQESI 284
           +  +S+  V +I+ RA +++++ +
Sbjct: 228 KLGISQMSVSRIQKRATERLKQIM 251


>gi|46371303|gb|AAS90418.1| stationary phase sigma factor [Azotobacter chroococcum]
          Length = 172

 Score =  106 bits (264), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 36/179 (20%), Positives = 68/179 (37%), Gaps = 12/179 (6%)

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
           I+     +++      K L   LR  +     +T           IA  L    +EV  M
Sbjct: 1   IMNQTGTIRLPIHVV-KELNVYLRAAR----ELTQKLDHEPSAEEIANLLEKPVAEVKRM 55

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
                   S++  ++    +     D L  D       L++ ++       + + +  L 
Sbjct: 56  LGLNERVTSVD--VSLGPDSDRTLLDVLTEDRPSDPCDLLQDDDLSQS---IDQWLFDLT 110

Query: 237 PRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
            ++R +   R         TLE +  E  ++RERVRQI+  A K+++E ++K    S +
Sbjct: 111 DKQREVVVRRFGLRGHESCTLEEVGQEIGLTRERVRQIQVEALKRLREILEKNGLSSDA 169


>gi|158337871|ref|YP_001519047.1| RNA polymerase sigma factor SigF [Acaryochloris marina MBIC11017]
 gi|158308112|gb|ABW29729.1| RNA polymerase sigma factor, group 3 [Acaryochloris marina
           MBIC11017]
          Length = 265

 Score =  106 bits (264), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 45/236 (19%), Positives = 104/236 (44%), Gaps = 9/236 (3%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG-LPISEVVSEGNIGLMQAVKKFDPERGF 99
           YR+   +   +RLV  ++ LV K+A         P  ++   G +GL+ A+++FDP +G+
Sbjct: 18  YRQKPSVQLRNRLVRLNMGLVRKVAHRLAHQCAEPYEDLEQCGFLGLITAIERFDPTQGY 77

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
             +++++ +I+  +  ++    + V+I     Q  L  +  +++   QA+T    +    
Sbjct: 78  AFSSFAVPYIRGEILHFLRDRANTVRIPRRWQQ--LSRDGAKVR---QALTMELGRHPSD 132

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IA +L++S  E  ++    +    L+     S  +  Q    +       +      +
Sbjct: 133 QEIADELDLSMQEWRAVKLAASNRVPLSLNARVSSGHHQQSDSMMTLGDTLMDARCQIMQ 192

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV-RQIEA 274
             +  R  L +++  L  R R + E+  +  + ++ + ++    VS   V R+I+ 
Sbjct: 193 TNQEDRLELQQALDQLEDRTREMIESVFV--HQLSRQEVAQRIGVSPVTVTRRIKK 246


>gi|77463598|ref|YP_353102.1| sigma factor FliA (sigma-28 group, flagellar) [Rhodobacter
           sphaeroides 2.4.1]
 gi|126462430|ref|YP_001043544.1| FliA/WhiG family RNA polymerase sigma factor [Rhodobacter
           sphaeroides ATCC 17029]
 gi|332558454|ref|ZP_08412776.1| FliA/WhiG family RNA polymerase sigma factor [Rhodobacter
           sphaeroides WS8N]
 gi|77388016|gb|ABA79201.1| sigma factor FliA (Sigma-28 group, flagellar) [Rhodobacter
           sphaeroides 2.4.1]
 gi|126104094|gb|ABN76772.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Rhodobacter
           sphaeroides ATCC 17029]
 gi|332276166|gb|EGJ21481.1| FliA/WhiG family RNA polymerase sigma factor [Rhodobacter
           sphaeroides WS8N]
          Length = 239

 Score =  106 bits (264), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 44/236 (18%), Positives = 103/236 (43%), Gaps = 26/236 (11%)

Query: 51  HRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            RLV +H+ LV +IA       G  + I +++  G +GL+ A ++++P  G   A Y+  
Sbjct: 15  ERLVRAHMDLVRRIAWNLHARIGRKVEIDDLIQVGYMGLVDASRRYEPREGVSFAAYAAI 74

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+ ++ +++  + +L +      QK        +K  +Q +    ++  +   +A +L+
Sbjct: 75  RIRGSIMDFLRSNSALCRTTILMQQK--------VKAAVQRLEGRLMRAPETPEVAAELS 126

Query: 168 VSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           +   E      + AG    SL+           +  D      +G +    ++ +    R
Sbjct: 127 MPVGEYQDWLAQFAGSQTASLD-----------EVYDDQSALFEGHDPSAEDRLQASQMR 175

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +L +++  +  RE  + +   ++E  + +  +     V+  RV QI+  A ++++
Sbjct: 176 GLLRQALGRMPEREALLLQLIFVEE--LNVYEVGEILGVTTGRVSQIKKAAIERLR 229


>gi|319937135|ref|ZP_08011542.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
 gi|319807501|gb|EFW04094.1| RNA polymerase sigma factor [Coprobacillus sp. 29_1]
          Length = 230

 Score =  106 bits (264), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 52/267 (19%), Positives = 101/267 (37%), Gaps = 65/267 (24%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG-YGLPISEVV 79
           H++ K P+  K+E   L K   + GD  A   L+  +LRLVV +A  Y       I +++
Sbjct: 22  HDVLKAPLKGKEEADALVKL--QQGDAQARDLLIEHNLRLVVYVAKKYDSVQNGSIEDLI 79

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
           S G IGL++AV  F  ++  +LATY+   I+  +  ++ ++                  L
Sbjct: 80  SIGTIGLVKAVNTFKMDKNIKLATYASRCIENEILMFLRKN----------------NKL 123

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
           R+                                IS++  L  D   N L+ S    + +
Sbjct: 124 RQE-------------------------------ISLDEPLNVDYDGNELLLSDIIGTDK 152

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLEN 257
                  +H+ Q++         N R              + I   R      + +T ++
Sbjct: 153 DIVQDEIEHNDQKEKFYRALHHLNERE-------------QEILMMRYGLVGHDELTQKD 199

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESI 284
           ++    +S+  + ++E +  KK++  +
Sbjct: 200 VAEVLGISQSYISRLEKKIIKKLRNKL 226


>gi|291613029|ref|YP_003523186.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Sideroxydans
           lithotrophicus ES-1]
 gi|291583141|gb|ADE10799.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Sideroxydans
           lithotrophicus ES-1]
          Length = 247

 Score =  106 bits (264), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 48/239 (20%), Positives = 98/239 (41%), Gaps = 17/239 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
               +  +  LV +IA          + + +++  G +GL+ A  ++D  RG +  TY+ 
Sbjct: 21  KEECLKEYAPLVKRIAHHMMLKLPGSVEVDDLIQAGMMGLLDAASRYDELRGAQFETYAA 80

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +         G     + L  ++RR++  +  +     K      IA++L
Sbjct: 81  QRIRGAMLDELR--------GADWLPRSLRRDMRRIETAVSRLQQQMGKTPNETEIAREL 132

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            VS  E   M     G +    L+   D +  + +D+        +   +E  + +  R 
Sbjct: 133 GVSLHEYQQMLQEGRGAQ----LLYYEDFHGEEGEDFFERFEFSGDSNPLELLQDERFRE 188

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            L  ++  L  RER++       E  + L  +     VS  RV Q+ ++A  +++ S++
Sbjct: 189 ALIHAIERLPERERQMMGMHY--EQDMNLREIGEVMGVSESRVCQLHSQAVARLRASMK 245


>gi|302874723|ref|YP_003843356.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium cellulovorans
           743B]
 gi|307690664|ref|ZP_07633110.1| sporulation sigma factor SigE [Clostridium cellulovorans 743B]
 gi|302577580|gb|ADL51592.1| RNA polymerase, sigma 28 subunit, SigE [Clostridium cellulovorans
           743B]
          Length = 235

 Score =  106 bits (264), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 55/262 (20%), Positives = 105/262 (40%), Gaps = 59/262 (22%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE  L  +    G  +    L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 33  PPLTKEEEEELVGKLS-TGKEAVRSVLIERNLRLVVYIARKFENTGVGVEDLISVGTIGL 91

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FDPE+  +LATY+   I+  +  Y+ R+                    ++K   
Sbjct: 92  IKAVNTFDPEKKIKLATYASRCIENEILMYLRRNS-------------------KVKAE- 131

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                        ++  + LN+             G+E L + I  S+ ++         
Sbjct: 132 -------------ISFYEPLNIDWD----------GNELLLSDILGSENDNIYNLLEDEV 168

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           D       L +  ER+ +   L   ++  N +               T + ++    +S+
Sbjct: 169 DRQLLSIALRKLNEREKQIVELRYGLNGCNEK---------------TQKEVADMLGISQ 213

Query: 267 ERVRQIEARAFKKVQESIQKQV 288
             + ++E R  +++++ I K V
Sbjct: 214 SYISRLEKRIIRRLKKEINKMV 235


>gi|228950124|ref|ZP_04112308.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|229120608|ref|ZP_04249853.1| RNA polymerase sigma-B factor [Bacillus cereus 95/8201]
 gi|228662893|gb|EEL18488.1| RNA polymerase sigma-B factor [Bacillus cereus 95/8201]
 gi|228809547|gb|EEM55984.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
          Length = 203

 Score =  106 bits (264), Expect = 5e-21,   Method: Composition-based stats.
 Identities = 38/210 (18%), Positives = 97/210 (46%), Gaps = 16/210 (7%)

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++  G +GL+ A++++D   G     +++  I   +++Y+      + +      +R+
Sbjct: 3   EDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRI 57

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSS 193
                ++K  ++ +TD+  +  +++ IA  L +SE EV+ +          SL+ ++ ++
Sbjct: 58  KDLGGKIKLAIEELTDHLQRSPKIIEIANHLGLSEEEVLEIMDAKNNYRVSSLDDVVENA 117

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
              SS  +   V +       + +  E   RR +L    +VLN  E+ +     + E  +
Sbjct: 118 SDGSSVARIESVGE-------VEKGYEETERRLVLKDIFNVLNETEKSVIH--YIFEENL 168

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQES 283
             ++      +S+  V +I+ +A  K++++
Sbjct: 169 NQKDTGERLGISQMHVSRIKRQAISKLKQA 198


>gi|88856926|ref|ZP_01131577.1| RNA polymerase sigma-70 factor [marine actinobacterium PHSC20C1]
 gi|88813802|gb|EAR23673.1| RNA polymerase sigma-70 factor [marine actinobacterium PHSC20C1]
          Length = 244

 Score =  106 bits (264), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 57/258 (22%), Positives = 100/258 (38%), Gaps = 35/258 (13%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             + E  LA R   +G++ A H L  S       ++  + G G+ + ++ SE   GL++A
Sbjct: 14  TPEREAALAARIS-NGEMEAVHELAMSGYAWAKSLSHKFTGRGVDLDDLNSEAYFGLVEA 72

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
            K FDP RG R A YS  +++ A+ + I  S   V I   A    L  N  R+     A 
Sbjct: 73  AKTFDPTRG-RFAGYSTAFVQGAIWKAIRLSGRSVSIPKHAFDAELVGNRDRISERYAA- 130

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
                      A       +      ++  L+ D                  D L+ D  
Sbjct: 131 ----------NAALASEASAWHFPTQLDAPLSSDAP------------GTAADVLISDAR 168

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT---LENLSSEFEVSR 266
           G EQ ++E+         L   +S +   ER +  AR       +      +S+   + +
Sbjct: 169 GVEQTVVEQI-------FLDGMLSEIPRIEREVLLARFELPGACSAPGQAAISAALNIDQ 221

Query: 267 ERVRQIEARAFKKVQESI 284
            R+ +IE +A  +++ ++
Sbjct: 222 RRISEIEKKALARLRNAV 239


>gi|300854418|ref|YP_003779402.1| RNA polymerase sigma-E factor [Clostridium ljungdahlii DSM 13528]
 gi|300434533|gb|ADK14300.1| RNA polymerase sigma-E factor precursor [Clostridium ljungdahlii
           DSM 13528]
          Length = 241

 Score =  106 bits (264), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 56/262 (21%), Positives = 108/262 (41%), Gaps = 59/262 (22%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE  L  +    GD      L+  +LRLVV IA  +   G+ + ++VS G IGL
Sbjct: 39  PPLSKKEEEDLVLKLV-SGDEKVRSTLIERNLRLVVYIARKFENTGVNVEDLVSVGTIGL 97

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+                          
Sbjct: 98  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRNSKT----------------------- 134

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                             K  +S  E ++++    G+E L + I  +D +     +++  
Sbjct: 135 ------------------KAEISFYEPLNID--WDGNELLLSDILGTDNDVVY--NFIED 172

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           + D Q  +L  K+     + ++      LN +  +            T + ++    +S+
Sbjct: 173 EVDKQLLMLAMKKLSDREKEIVNLRFG-LNGKSEK------------TQKEVADLLGISQ 219

Query: 267 ERVRQIEARAFKKVQESIQKQV 288
             + ++E R  K++++ I K +
Sbjct: 220 SYISRLEKRIIKRLRKEINKML 241


>gi|158341129|ref|YP_001522296.1| RNA polymerase sigma factor domain-containing protein
           [Acaryochloris marina MBIC11017]
 gi|158311370|gb|ABW32982.1| RNA polymerase sigma factor domain protein [Acaryochloris marina
           MBIC11017]
          Length = 476

 Score =  106 bits (264), Expect = 6e-21,   Method: Composition-based stats.
 Identities = 54/279 (19%), Positives = 120/279 (43%), Gaps = 24/279 (8%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           I  I + P L  ++E  L  + ++ GD  A   ++ S+L  +  +       G+   E++
Sbjct: 14  IATIARHPNLSPEQEAELILKAQD-GDNDARQTVIYSNLAWICSMGGSLSRKGIEDGELI 72

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
           SEG  GL +A+ ++  E+G  + T+S   I     E + +    +++      K  +  L
Sbjct: 73  SEGYFGLNKAIDQWSSEKGANIRTFSRDKIYKFQSEAVHQKNH-IRLP-----KSTYEQL 126

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
            +LK     + ++      V  +A+   + E  + ++   ++   SLN++  + +    +
Sbjct: 127 SKLKKATAVLGED----ATVAQLAEGTEIKEKRIRTLQE-ISQPVSLNSVTGTREN--LE 179

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
             D    D  G     +  E        L   +  L+PR+R I      +E  ++ + +S
Sbjct: 180 LLDQQADDCQGSLDPALSSE--------LLDLVDKLHPRQREILHLYHWEE--LSFQKIS 229

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQ 298
               +  ++VR++  +A   +++ +Q ++      PLL+
Sbjct: 230 DYLGLPAKKVRKLYKQALDLLRKFLQGEINEFPPLPLLE 268


>gi|307824496|ref|ZP_07654721.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Methylobacter tundripaludum SV96]
 gi|307734480|gb|EFO05332.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Methylobacter tundripaludum SV96]
          Length = 237

 Score =  105 bits (263), Expect = 7e-21,   Method: Composition-based stats.
 Identities = 46/236 (19%), Positives = 94/236 (39%), Gaps = 23/236 (9%)

Query: 54  VTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           V  H  LV +IA    G       + +++  G +GL++A+K +D  +G    TY+   I+
Sbjct: 14  VMQHAPLVKRIAYHLLGRLPDSVQVDDLIQAGMLGLLEAIKNYDASQGASFDTYAGIRIR 73

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            +M + + RS        + ++K      R +   ++ I +   +  + V +AK L ++ 
Sbjct: 74  GSMLDEVRRSDWT---PRSVHKKS-----RMVSDAIRTIENKTGREARDVDVAKYLGIAI 125

Query: 171 SEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E   I  +       S+  L    D          + +    E+  ++   R+  +  L
Sbjct: 126 DEYNHILQDSSSCRVFSVEELAQDGD--------HYMDETLSHEEGPVDGLSREGFQQAL 177

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             ++  L  RER +       +    L  +     +S  RV QI  +A  +++  +
Sbjct: 178 ANAIMGLPERERLVISLYY--DEEFNLREIGEVLNISESRVSQICTQAVLRLRSRL 231


>gi|143621|gb|AAA22794.1| sporulation protein [Bacillus subtilis]
          Length = 239

 Score =  105 bits (263), Expect = 7e-21,   Method: Composition-based stats.
 Identities = 57/262 (21%), Positives = 107/262 (40%), Gaps = 59/262 (22%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K EE VL  +   +GD +A   L+   LRLVV IA  +   G+ I +++S G IGL
Sbjct: 37  PPLSKDEEQVLLMKL-PNGDQAARAILIERILRLVVYIARKFENTGINIEDLISIGTIGL 95

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+                    +++   
Sbjct: 96  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRN-------------------NKIRSE- 135

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                        V+  + LN+             G+E L + +  +D +          
Sbjct: 136 -------------VSFYEPLNIDWD----------GNELLLSDVLGTDDDIITKDIEANV 172

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           D    ++ L +  ER+ +   L   +               + E   T ++++    +S+
Sbjct: 173 DKKLLKKALEQLNEREKQIMELRFGL---------------VGEEEKTQKDVADMMGISQ 217

Query: 267 ERVRQIEARAFKKVQESIQKQV 288
             + ++E R  K++++   K V
Sbjct: 218 SYISRLEKRIIKRLRKEFNKMV 239


>gi|239929464|ref|ZP_04686417.1| RNA polymerase sigma factor sig8 [Streptomyces ghanaensis ATCC
           14672]
          Length = 245

 Score =  105 bits (263), Expect = 7e-21,   Method: Composition-based stats.
 Identities = 44/205 (21%), Positives = 89/205 (43%), Gaps = 16/205 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A + L+  ++ LV   A  +R  G   + ++V  G IGL++A+ +F+  R     ++++ 
Sbjct: 51  ARNTLIEMNMSLVRFAAGRFRSRGPEEMEDIVQVGMIGLIKAIDRFELSREVEFTSFAIP 110

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           +I   M+ +   +   V +     + R+     +L    + +     +      +A+ ++
Sbjct: 111 YIVGEMKRFFRDTSWSVHVPRRLQEARV-----QLARATEELRTRLGRTPTTRELAQLMS 165

Query: 168 VSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           ++E EV        G    SL+A I S     S   D++     G E   +E  E  +  
Sbjct: 166 LTEEEVNEARIAANGYNSASLDAAIGSEPDGESVLADFI-----GSEDAALELVEDFH-- 218

Query: 226 NMLTRSMSVLNPRERRIFEARRLQE 250
             L   ++ L+ RER+I   R ++E
Sbjct: 219 -ALAPMIAELDERERKIIHWRFVEE 242


>gi|251772425|gb|EES52992.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Leptospirillum
           ferrodiazotrophum]
          Length = 250

 Score =  105 bits (263), Expect = 7e-21,   Method: Composition-based stats.
 Identities = 41/247 (16%), Positives = 107/247 (43%), Gaps = 18/247 (7%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            +++      +   AM Y     P   + +++S G   L+++ ++FDP RG +  T +  
Sbjct: 7   DQMIKEFAGTIKYHAMRYAHRLPPELGVEDLISVGLHSLVESARRFDPSRGLKFKTMAEH 66

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+ AM + I    S+  +  +  +K+    + R     +++     +  +   +A +L 
Sbjct: 67  RIRGAMLDEIR---SMDWVPRSVREKQADVQMAR-----ESLERELGRHPEDAELAARLG 118

Query: 168 VSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           +S  ++ ++   +      SL+ +    +       D L        +  + +  +    
Sbjct: 119 LSLEDLETLLWEIDPHPVLSLDEVFGPDESEGESLGDHLPGPKG---EDPLSRLLQGEAL 175

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + L  ++  L  ++R +      +E  +T++ ++   +VS  RV QI ++A + ++  ++
Sbjct: 176 DALAGALDALPEKQRLVLTLYYYEE--LTMKEVAQVLDVSESRVSQIHSQALRGIRALLE 233

Query: 286 KQVELSS 292
           ++ + SS
Sbjct: 234 ERRQTSS 240


>gi|4378867|gb|AAD19735.1| sigma-F factor [Zymomonas mobilis subsp. mobilis ZM4]
          Length = 244

 Score =  105 bits (263), Expect = 7e-21,   Method: Composition-based stats.
 Identities = 54/237 (22%), Positives = 104/237 (43%), Gaps = 23/237 (9%)

Query: 51  HRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
             L+ +HL+LV KIA    G     + + +++  G + L++A   F+  RGF  ATY+  
Sbjct: 23  EALIKTHLQLVRKIAWHVHGRVSSAIEVEDLIQIGMVALIEAANAFE-NRGFAFATYASM 81

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+ AM +Y+ +  +  +  + A QK L           + ++    +  +   IA+KLN
Sbjct: 82  RIRGAMIDYMRQHAATAR-SSIARQKTLN-------KAREELSATLGRRPEDAEIAEKLN 133

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S SE          D ++N    S D   S        D+  Q   +    ER+  ++ 
Sbjct: 134 MSPSEYREW-----ADGAINIRQESLDDVYSDHSSIFTDDNADQASEM----EREALQSA 184

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   +  L  RE  + +   ++E  + L+ +    ++   R+ QI+  A   +++ +
Sbjct: 185 LAEQIKTLPEREALVLQLYYVEE--LNLKEIGEVLDLGTARISQIKKSAVDHLRQKM 239


>gi|221639440|ref|YP_002525702.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Rhodobacter
           sphaeroides KD131]
 gi|221160221|gb|ACM01201.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Rhodobacter
           sphaeroides KD131]
          Length = 239

 Score =  105 bits (263), Expect = 7e-21,   Method: Composition-based stats.
 Identities = 45/239 (18%), Positives = 104/239 (43%), Gaps = 26/239 (10%)

Query: 51  HRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            RLV +H+ LV +IA       G  + I +++  G +GL+ A ++++P  G   A Y+  
Sbjct: 15  ERLVRAHMDLVRRIAWNLHARIGRKVEIDDLIQVGYMGLVDASRRYEPREGVTFAAYAAI 74

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+ ++ +++  + +L +      QK        +K  +Q +    ++  +   +A +L+
Sbjct: 75  RIRGSIMDFLRSNSALCRTTILMQQK--------VKAAVQRLEGRLMRAPETPEVAAELS 126

Query: 168 VSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           +   E      + AG    SL+           +  D      +G +    ++ +    R
Sbjct: 127 MPVGEYQDWLAQFAGSQTASLD-----------EVYDDQSALFEGHDPSAEDRLQASQMR 175

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +L +++  +  RE  + +   ++E  + +  +     V+  RV QI+  A ++++  I
Sbjct: 176 GLLRQALGRMPEREALLLQLIFVEE--LNVYEVGEILGVTTGRVSQIKKAAIERLRSLI 232


>gi|52629120|gb|AAU27861.1| flagellar biosynthesis sigma factor FliA [Legionella pneumophila
           subsp. pneumophila str. Philadelphia 1]
          Length = 262

 Score =  105 bits (263), Expect = 8e-21,   Method: Composition-based stats.
 Identities = 49/239 (20%), Positives = 104/239 (43%), Gaps = 21/239 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              LV +H  LV +IA    G     + + +++  G +GL++A + +D  +G    TY+ 
Sbjct: 39  QEALVKTHATLVKRIAHHLLGRLPQSVQLDDLIQSGMLGLLEAARHYDSSKGASFETYAG 98

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+  M + + R+  +         + ++ N R +   ++ +     +  +   IA++L
Sbjct: 99  IRIRGHMLDEVRRNDWV--------PRSVYRNSRMISDAVRILEHKLGREAKDNEIAEEL 150

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRR 225
            VS  +   M       +S+++ +   D       D +++DH+G           R +  
Sbjct: 151 GVSLDDYHDMLQ-----DSISSHLYGFDDLGVT--DDVLFDHEGNGSTEPHRNVMRSDMM 203

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           N LT+ +  L  +ER +       E  + L+ +    EVS  R+ QI ++A  +++  +
Sbjct: 204 NRLTQVIDSLPRKERLVLSLYY--EQDLNLKEIGEILEVSESRISQILSQATHRIRSRL 260


>gi|311105912|ref|YP_003978765.1| RNA polymerase sigma factor for flagellar operon [Achromobacter
           xylosoxidans A8]
 gi|310760601|gb|ADP16050.1| RNA polymerase sigma factor for flagellar operon [Achromobacter
           xylosoxidans A8]
          Length = 259

 Score =  105 bits (263), Expect = 8e-21,   Method: Composition-based stats.
 Identities = 42/245 (17%), Positives = 104/245 (42%), Gaps = 16/245 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           A   LV  +  LV K+A+         + + +++  G IGL+ AV+++      +  TY+
Sbjct: 12  ADDSLVE-YAPLVRKLALQLLARLPASVELDDLIQAGMIGLLDAVRRYQETADAQFETYA 70

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
              I+ AM + +     L         + +    R+++  +Q +    ++      IA++
Sbjct: 71  TTRIRGAMLDELRGQDWL--------PRSVRAKARKIEQAIQQLEQRLMRAPSEAEIAQQ 122

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW--LVYDHDGQEQVLIEKEERKN 223
           L++   +  S+     G + ++    +++ +S+  Q       +H       ++     +
Sbjct: 123 LDMPLGDYQSLLHDAQGVQIVHYEDFATEPDSASGQSDWAATLNHGAAGGNPLDSLLAGD 182

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            R  L  ++  L  RE+ +       E  + L+ + +   V+  RV Q+ ++A  +++  
Sbjct: 183 FRQALVHAIDSLPEREKLLLSLCY--EQGLNLKEIGAILNVTEARVCQLRSQATARIRVK 240

Query: 284 IQKQV 288
           +++Q 
Sbjct: 241 LKEQA 245


>gi|108804234|ref|YP_644171.1| RNA polymerase sigma-28 subunit [Rubrobacter xylanophilus DSM 9941]
 gi|108765477|gb|ABG04359.1| RNA polymerase, sigma 28 subunit [Rubrobacter xylanophilus DSM
           9941]
          Length = 264

 Score =  105 bits (263), Expect = 8e-21,   Method: Composition-based stats.
 Identities = 55/250 (22%), Positives = 103/250 (41%), Gaps = 27/250 (10%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPE 96
           R  E        RLV ++  LV  +A         G+   ++VS G +GL++AV+ FDP 
Sbjct: 34  RRAERRVGQLRDRLVVNYSPLVKYVAGRMAARIPGGVEQEDLVSWGVVGLLKAVETFDPA 93

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RG +  TY++  I+ A+ + + ++  L         +R+   +R  +    A+T    + 
Sbjct: 94  RGAKFETYAISKIRWAILDELRKADPL--------PRRVRRRVRETQRAASALTQTLRRA 145

Query: 157 EQVVAIAKKLNVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
                IA+++ V  +E      R   A   SL  L++   +   +              V
Sbjct: 146 PTEAEIAREVGVGLAEHRETLERYHRARTWSLEELLSGMGEGGREL------------SV 193

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
                E    R  L  ++  L+ RER +      Q   +TL  +     ++  R+ QI  
Sbjct: 194 SDPTAETAELRERLAEALESLSERERVVITFYYYQG--LTLREIGRALNLTEGRISQILR 251

Query: 275 RAFKKVQESI 284
           RA +++++ +
Sbjct: 252 RALQRLRDRL 261


>gi|325523156|gb|EGD01548.1| RpoD family RNA polymerase sigma factor [Burkholderia sp. TJI49]
          Length = 206

 Score =  105 bits (263), Expect = 8e-21,   Method: Composition-based stats.
 Identities = 40/122 (32%), Positives = 62/122 (50%), Gaps = 4/122 (3%)

Query: 25  KIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           + P L       L  R    E     A  +LV S+LRLVV IA  Y   GLP+ +++ EG
Sbjct: 78  RSPDLPPDTIAALDARIERIERATRPARTKLVKSNLRLVVSIAKRYPDRGLPLPDLIQEG 137

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
           NIGL++AV+++D  RGF+ +TY+ WWI+ A+   +      +++            L R+
Sbjct: 138 NIGLLKAVERYDHRRGFKFSTYATWWIRQAITHALADLGRTIRVPAHT--VDAVNKLARI 195

Query: 143 KG 144
             
Sbjct: 196 AR 197


>gi|291543210|emb|CBL16319.1| RNA polymerase, sigma 29 subunit, SigE [Ruminococcus sp. 18P13]
          Length = 232

 Score =  105 bits (263), Expect = 8e-21,   Method: Composition-based stats.
 Identities = 50/260 (19%), Positives = 100/260 (38%), Gaps = 58/260 (22%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+ E     R       SA   L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 30  PPLSKEAEAEAFARLGTGDAESARQTLIVHNLRLVVYIAKKFESTGIGIEDLISIGTIGL 89

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F PE+  +LATY+   I+  +  +                      LR+   + 
Sbjct: 90  IKAVNTFCPEKNIKLATYASRCIENEILMF----------------------LRKTSQYR 127

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
             I+ +                       +N    G+E L + +  +D++          
Sbjct: 128 SEISIDEP---------------------LNIDWDGNELLLSDVLGTDEDIVNRGIEAEA 166

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           +     Q +   E R+  + ++     +L  RE+             T + ++ E  +S+
Sbjct: 167 EKSVLRQAVDGLEPRE--KRIMQMRFGLLGGREK-------------TQKEVADEIGISQ 211

Query: 267 ERVRQIEARAFKKVQESIQK 286
             + ++E +  ++++  + +
Sbjct: 212 SYISRLEKKIIRRLKTEMDR 231


>gi|149376625|ref|ZP_01894385.1| flagellar biosynthesis sigma factor FliA [Marinobacter algicola
           DG893]
 gi|149359143|gb|EDM47607.1| flagellar biosynthesis sigma factor FliA [Marinobacter algicola
           DG893]
          Length = 207

 Score =  105 bits (263), Expect = 8e-21,   Method: Composition-based stats.
 Identities = 43/210 (20%), Positives = 85/210 (40%), Gaps = 17/210 (8%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G IGL++A +++  ++G    TY+   I+ AM + I R    V      N   
Sbjct: 10  LDDLMQAGMIGLLEAAQRYSSDKGATFETYAGIRIRGAMVDEI-RKGDWVPRSVHRNS-- 66

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
                RR+   ++A+ D   +  Q   +A++L +   E  S    L+   S         
Sbjct: 67  -----RRIAKAIKAVEDRLGREAQDSEVAEELGLDLDEYYS---SLSDANSGRLFSLDEL 118

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
             S +       D D      ++     N R  L  ++  L  RE+ +       +  + 
Sbjct: 119 NESGELPIEETEDSDN----PLDGLASDNFRKSLATAIGDLPEREKLVLSLYY--QEELN 172

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L+ + +   VS  RV QI ++A  +++  +
Sbjct: 173 LKEIGAVLGVSESRVSQIHSQAALRLRGRL 202


>gi|299472548|emb|CBN77333.1| RNA polymerase sigma factor SigD [Ectocarpus siliculosus]
          Length = 825

 Score =  105 bits (263), Expect = 8e-21,   Method: Composition-based stats.
 Identities = 54/271 (19%), Positives = 106/271 (39%), Gaps = 22/271 (8%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG----LPISEVVSEGNIGL 86
             E     ++  + G   A   LV  +L LV  I   Y G          ++  +  +GL
Sbjct: 93  AMESVESLRQALDEG-EKAKQELVLDNLNLVDIIVKNYVGTFAYGRFTEKDLTQDATVGL 151

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV+KFDPE+GF  ATY  WW++  + E +     +V+I  +A  +     ++R++  L
Sbjct: 152 IRAVEKFDPEKGFFFATYGRWWVRKYLHEGVQNHNRMVRIPNSAAYR--IAKVKRVRDEL 209

Query: 147 QAITDNNLKPEQ--------VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           +          +        V  +   L      +  ++  +     +   + +S     
Sbjct: 210 EGELGRAPTKPEIALETDLTVQQVEACLEQDSFRIERLDGYMGHGFGMADTVFASHFGEG 269

Query: 199 QWQDWLVYDHDGQEQVLI---EKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQENPVT 254
                 +  H G+        EK  + + R  L+ +   +L+  ER     R    + VT
Sbjct: 270 FLYGSDMLTHPGETPAPTVEGEKVIQSSLRGDLSSAFVRLLDATERECLVLRYGLHDGVT 329

Query: 255 --LENLSSEFE-VSRERVRQIEARAFKKVQE 282
             +E  ++  +    + VR I  +A  K+++
Sbjct: 330 NSIEQTAAIMDFCDPDDVRIITTQAMAKLRD 360


>gi|90021809|ref|YP_527636.1| flagellar protein FliS [Saccharophagus degradans 2-40]
 gi|89951409|gb|ABD81424.1| RNA polymerase sigma factor, FliA/WhiG [Saccharophagus degradans
           2-40]
          Length = 250

 Score =  105 bits (262), Expect = 9e-21,   Method: Composition-based stats.
 Identities = 50/246 (20%), Positives = 99/246 (40%), Gaps = 20/246 (8%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGF 99
           + GD       V  +  LV +IA            I +++  G +GL++A +K+D  +G 
Sbjct: 16  KEGDQEIK---VEDYAYLVKRIAHHMMARMPSCVQIEDLIQAGMLGLLEAAQKYDASKGA 72

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
              TYS   I+ A+ + + R             + +  N RR+   +  +   + +  + 
Sbjct: 73  SFETYSGIRIRGAIVDEMRRGDW--------APRSVHRNSRRVAEAIATVEARHGRDARD 124

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IA+++ +S  E  +M    A D +   L +  +   +    +  Y+     +   E+ 
Sbjct: 125 HEIAEEMGLSLDEYYAM----ARDSASTRLFSYEETYENDESRFDEYEPSDGLRGPSEQV 180

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
            R      L  ++  L  RER +       E  + L+ +     VS  RV QI ++A  +
Sbjct: 181 HRNALYTDLVAAIGKLPERERLVLSLYY--EQEMNLKEIGLVLGVSESRVSQIHSQAALR 238

Query: 280 VQESIQ 285
           ++  +Q
Sbjct: 239 LKSRMQ 244


>gi|302878264|ref|YP_003846828.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Gallionella
           capsiferriformans ES-2]
 gi|302581053|gb|ADL55064.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Gallionella
           capsiferriformans ES-2]
          Length = 236

 Score =  105 bits (262), Expect = 9e-21,   Method: Composition-based stats.
 Identities = 50/239 (20%), Positives = 100/239 (41%), Gaps = 17/239 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            ++ +  +  LV +IA        Y + I +++  G +GL+ A  ++D   G +  TY+ 
Sbjct: 10  KNQCLRDYAPLVKRIAHQMMSKLPYSVQIDDIIQAGMMGLLDAATRYDEIHGAQFETYAT 69

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +  +  L         + L  ++RR++  +  +     +      IAK+L
Sbjct: 70  QRIRGAMLDELRSADWL--------PRSLRRDMRRIEQGVSRLQQKLGRAPNETEIAKEL 121

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            VS  E   M     G +    LI   D      +D+        +   +   +    ++
Sbjct: 122 EVSLVEYQQMLQESRGAQ----LIYYEDFQDEDHEDFFERFEFANDTDPLALLQDDRFKS 177

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            L R++ VL  RER +       E  + L  +   F VS  R+ Q+ ++A  +++ S++
Sbjct: 178 ELARAIDVLPERERLLMALIY--EQELNLREVGEVFGVSESRISQLHSQAVLRLRGSLK 234


>gi|33592168|ref|NP_879812.1| RNA polymerase sigma factor for flagellar operon [Bordetella
           pertussis Tohama I]
 gi|33601519|ref|NP_889079.1| RNA polymerase sigma factor for flagellar operon [Bordetella
           bronchiseptica RB50]
 gi|33571813|emb|CAE41322.1| RNA polymerase sigma factor for flagellar operon [Bordetella
           pertussis Tohama I]
 gi|33575955|emb|CAE33034.1| RNA polymerase sigma factor for flagellar operon [Bordetella
           bronchiseptica RB50]
 gi|332381584|gb|AEE66431.1| RNA polymerase sigma factor for flagellar operon [Bordetella
           pertussis CS]
          Length = 245

 Score =  105 bits (262), Expect = 9e-21,   Method: Composition-based stats.
 Identities = 44/235 (18%), Positives = 97/235 (41%), Gaps = 17/235 (7%)

Query: 57  HLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           +  LV K+A+         + + ++V  G IGL+ AV+++      +  TY+   I+ AM
Sbjct: 11  YAPLVRKLALQLLARLPSSVQLDDLVQAGMIGLLDAVRRYQESPDAQFETYATARIRGAM 70

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
            + +     L         + +    RR++  +Q      ++      IA++L V  +E 
Sbjct: 71  LDELRSQDWL--------PRSVRSKSRRIETAIQRKEQELMRAPSEGEIAEELGVPLAEY 122

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             M     G + L+    ++D +S         +   +    ++     + R  L  ++ 
Sbjct: 123 QGMLADAQGVQILHYEDFNTDGDSDSPW----AESSAEHADPLDALLAGDLRRALIDAID 178

Query: 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            L  RE+ +       E  + L+ + +   V+  RV Q+ A+A  +++  +++Q 
Sbjct: 179 GLPEREKLLLSLCY--EQGLNLKEIGAVLNVTEARVCQLRAQATARIRARLKEQA 231


>gi|99034132|ref|ZP_01314232.1| hypothetical protein Wendoof_01000979 [Wolbachia endosymbiont of
           Drosophila willistoni TSC#14030-0811.24]
          Length = 148

 Score =  105 bits (262), Expect = 9e-21,   Method: Composition-based stats.
 Identities = 52/138 (37%), Positives = 82/138 (59%), Gaps = 1/138 (0%)

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLA-GDESLNALINSSDKNSSQWQDWLVYDHD 209
              L  E++ AI+ +L+VSE +V+ MN R+A  D+SLN  I   D +  + QD +  +  
Sbjct: 3   RETLNNEEIKAISNELSVSEGDVLQMNYRMACKDQSLNDCIKIGDDSKRELQDMIPCNLV 62

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
            QE      EE++ +  +L  +++ LN R R IF +R L EN  TL+ LS ++ VSRER+
Sbjct: 63  SQEVTYQNHEEKELKETILNNALASLNERARDIFISRYLSENIQTLDELSKKYCVSRERI 122

Query: 270 RQIEARAFKKVQESIQKQ 287
           RQ+  +A  KV++ IQ +
Sbjct: 123 RQLAEQAMAKVKQYIQSE 140


>gi|121488749|emb|CAJ18259.1| sigma 70-type sigma factor [Pelodictyon luteolum]
          Length = 165

 Score =  105 bits (262), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 39/174 (22%), Positives = 78/174 (44%), Gaps = 11/174 (6%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + +     +V++    N+    
Sbjct: 1   DLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLP--LNRVGTL 58

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
             + +    L+   + +        +A  L++   +V           S++A     D N
Sbjct: 59  NKISKAYSQLEQEFERD---PNTKELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDN 115

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +  D L  D    +  L     R +    + RS+SVL PRE  +  +     
Sbjct: 116 --RLLDVLQNDGHMPDHSL----NRDSLTLEVERSLSVLAPREADVIRSYFGIG 163


>gi|312882106|ref|ZP_07741856.1| flagellar biosynthesis sigma factor [Vibrio caribbenthicus ATCC
           BAA-2122]
 gi|309370242|gb|EFP97744.1| flagellar biosynthesis sigma factor [Vibrio caribbenthicus ATCC
           BAA-2122]
          Length = 244

 Score =  105 bits (262), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 50/249 (20%), Positives = 100/249 (40%), Gaps = 19/249 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPER 97
           Y ++    +    +  +  LV +IA    G   P   + +++  G IGL++A K +D  +
Sbjct: 7   YEQYTKQDSQRDFLEKYSVLVRRIAHHLLGRLPPSVQVEDLIQAGMIGLLEAQKNYDGNK 66

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G    TY+   I+ AM + I R    V      + + +   +  L+G L        +  
Sbjct: 67  GASFETYAGIRIRGAMLDDIRR-GDWVPRSVHKHNREVSQAIATLEGILN-------RDP 118

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +AKKL +   +  ++      D + + LI   D   S+  D +      +E +  +
Sbjct: 119 TDAEVAKKLGLELDQYHNILT----DINCSRLIGIEDLGVSE--DTITMGGCDEENLPFQ 172

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
               +  R  L  S+  L  RE  +       +  + L+ +     VS  RV QI +++ 
Sbjct: 173 GVSDEFFRKALVDSIKSLPERESLVLSLYY--DEELNLKEIGEVIGVSESRVSQILSQSM 230

Query: 278 KKVQESIQK 286
           ++++  +  
Sbjct: 231 QRLRTKLSA 239


>gi|188592109|ref|YP_001796707.1| RNA polymerase sigma factor for flagellar operon; sigma-70 factor
           family; sigma-f factor; sigma-27; sigma-28 [Cupriavidus
           taiwanensis LMG 19424]
 gi|170938483|emb|CAP63470.1| RNA polymerase sigma factor for flagellar operon; sigma-70 factor
           family; Sigma-F factor; Sigma-27; Sigma-28 [Cupriavidus
           taiwanensis LMG 19424]
          Length = 238

 Score =  105 bits (262), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 43/235 (18%), Positives = 91/235 (38%), Gaps = 16/235 (6%)

Query: 54  VTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           V +H  LV +IA+         + I +++  G IGL+ A K+++   G R  TY+   I+
Sbjct: 14  VKAHAPLVRRIALQLAARLPASVQIDDLIQAGMIGLLDAAKRYEDTHGARFETYASQRIR 73

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            AM + +  +            + L    RR++   + +     +      +A+ + +  
Sbjct: 74  GAMLDEVRANDW--------QSRSLRQFTRRIERTQRNLEQKLGRTPIDSEVAEAMEMPL 125

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            E   +   + G + L+                L    DG    ++        R  L R
Sbjct: 126 DEYQLLLNEVYGCQLLHYEDFERSGEEDFLDRHLGGSDDGNPLTVL---MESGMREALVR 182

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           ++  L  RE+ +       +  + L  + +  +V+  RV QI  +A  +++  ++
Sbjct: 183 AIERLPEREKLVLSLCY--DQELNLREIGAVLDVTESRVCQIRGQAINRLRTQLR 235


>gi|332533108|ref|ZP_08408977.1| RNA polymerase sigma factor for flagellar operon [Pseudoalteromonas
           haloplanktis ANT/505]
 gi|332037390|gb|EGI73844.1| RNA polymerase sigma factor for flagellar operon [Pseudoalteromonas
           haloplanktis ANT/505]
          Length = 236

 Score =  105 bits (262), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 43/238 (18%), Positives = 89/238 (37%), Gaps = 18/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + +V  H  LV K+A        P   + +++  G IGL++A K FD  +G    T++ 
Sbjct: 9   LNVIVEKHASLVKKVACHLIARLPPSVQLDDLIQSGMIGLIEASKNFDATKGASFETFAG 68

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + R             + +    R++   +  +  +  +    + +A+KL
Sbjct: 69  IRIRGAMLDEMRRGDW--------APRSVHRKNRQVAEAITELESSLNREPTDIEVAEKL 120

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +S +E   +       + L       D++            D  +       +      
Sbjct: 121 EISLNEYHHILNDANTSKILGIEDLGVDEDVITPVG-----QDLAQDKPFNNVKNDRFNE 175

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L  ++  L  R+  +        + + L+ +    +VS  RV QI  +A  K++  I
Sbjct: 176 SLLSAIKSLPERDAMVLSLYY--NDEMNLKEIGHILDVSESRVSQIHGQAMIKLKAKI 231


>gi|170725990|ref|YP_001760016.1| flagellar biosynthesis sigma factor [Shewanella woodyi ATCC 51908]
 gi|169811337|gb|ACA85921.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella woodyi ATCC
           51908]
          Length = 242

 Score =  105 bits (262), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 48/236 (20%), Positives = 98/236 (41%), Gaps = 20/236 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           +V  +  LV KIA          + I +++  G +GL++A   FD  +G +  T++   I
Sbjct: 16  IVEQYAPLVKKIAHHLLARLPASVQIDDLLQAGMMGLLEASTNFDGSKGAKFETFAGIRI 75

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + +M + I R    V      NQ       RR+   +  +     +  +   IA++L++S
Sbjct: 76  RGSMLDEIRR-GDWVPRSVHRNQ-------RRVAQVIDELEQELGRDAKDTEIAQRLDIS 127

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
            +E       +  D S+  ++   D   S     +V   + ++    E          L 
Sbjct: 128 LNEYH----HILNDVSVGKVVGIEDLGVSL---DVVGQAEERKDDTFESIADVEFHTALV 180

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            ++ +L  R+  +       +  + L+ + S  EVS  RV QI ++A  +++  ++
Sbjct: 181 EAIKLLPERDGLVLSLYY--DEALNLKEIGSILEVSESRVSQILSQAMLRLKAKLK 234


>gi|121997280|ref|YP_001002067.1| FliA/WhiG family RNA polymerase sigma factor [Halorhodospira
           halophila SL1]
 gi|121588685|gb|ABM61265.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Halorhodospira
           halophila SL1]
          Length = 247

 Score =  105 bits (262), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 49/247 (19%), Positives = 99/247 (40%), Gaps = 24/247 (9%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPER 97
             + GD      LVT H  LV +IA        P   + +++  G IGL++A +++D  +
Sbjct: 10  VAQQGDED----LVTRHASLVKRIAHHLASRLPPSVQLEDLIQAGMIGLLEAARQYDSSQ 65

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G    TY+   I+ AM + + R             + +    R +   ++ I     +  
Sbjct: 66  GASFQTYAGIRIRGAMLDEMRRLDWT--------PRSVHRKGREVAEAIRTIEHQTGRDA 117

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           +   +A+ L +S +E  ++   ++     +A + S D+      +   ++  G E   + 
Sbjct: 118 RDHEVAEALGISVAEYHNILQDVS-----SAKVFSIDQEDPGTGEP--HEPAGHEPGPLA 170

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
             + +  +  L  ++  L  RER +       +  + L  +     VS  RV QI  R  
Sbjct: 171 MLQDEAFQGELAEAIRELPERERLVMALYY--DEELNLREIGEVLGVSESRVSQIHGRIM 228

Query: 278 KKVQESI 284
            K++  +
Sbjct: 229 LKLRNRL 235


>gi|121488735|emb|CAJ18251.1| sigma 70-type sigma factor [Chlorobium chlorovibrioides]
          Length = 165

 Score =  105 bits (262), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 39/174 (22%), Positives = 78/174 (44%), Gaps = 11/174 (6%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + +     +V++    N+    
Sbjct: 1   DLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLP--LNRVGTL 58

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
             + +    L+   + +        +A  L++   +V           S++A     D N
Sbjct: 59  NKISKAYSQLEQEYERD---PNTKELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDN 115

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +  D L  D    +  L     R +    + RS+SVL PRE  +  +     
Sbjct: 116 --RLLDVLQNDGHMPDHTL----NRDSLTLEVERSLSVLAPREADVIRSYFGIG 163


>gi|121488773|emb|CAJ18271.1| sigma 70-type sigma factor [Chlorobium phaeobacteroides]
          Length = 165

 Score =  104 bits (261), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 38/177 (21%), Positives = 76/177 (42%), Gaps = 17/177 (9%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + +     +V++    N+    
Sbjct: 1   DLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLP--LNRVGTL 58

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
             + +    L+   + +        +A  L++   +V           S++A     D N
Sbjct: 59  NKISKAYSQLEQEFERD---PNTRELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDN 115

Query: 197 ---SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
                   D  + DH   +  L  + ER          +SVL PRE  +  +     
Sbjct: 116 RLLDVLQNDGHLPDHGLNKDSLTLEVERS---------LSVLXPREADVIRSYFGIG 163


>gi|322432980|ref|YP_004210229.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Acidobacterium sp.
           MP5ACTX9]
 gi|321165207|gb|ADW70911.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Acidobacterium sp.
           MP5ACTX9]
          Length = 278

 Score =  104 bits (261), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 46/262 (17%), Positives = 101/262 (38%), Gaps = 15/262 (5%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGF 99
           E G     + L+   L  V  IA          + + ++V  G IGL++A + FD  +  
Sbjct: 14  EEGGFEERNELILQELPQVHYIASRMMERLPQHVELGDLVHAGVIGLLEAYRTFDNTKNA 73

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           +  T++ + IK A+ + +               + +    R +      +     +    
Sbjct: 74  QFKTFAKFRIKGAILDSLR--------ALDWGSRGIRRKAREIAEATLKLEGALGRSPSK 125

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             I+ +L ++ +++  +  +L G   +   + SS +  +     L+           E  
Sbjct: 126 EEISAELGLTIADLNEIQTQLNGLHLVGQEVTSSFEGET--AHDLIESAPSSWDNPFEMY 183

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
            +   +  L R++S L+ RE+ I      +E  +T++ ++    ++  RV QI +    K
Sbjct: 184 AKAESKAHLIRAISELSEREQLILSLYYREE--LTMKEVAEVVGLAVSRVSQIHSAVLAK 241

Query: 280 VQESIQKQVELSSSPPLLQKPR 301
           ++ ++        S P    PR
Sbjct: 242 LKAALGHLAPEDVSKPKGVGPR 263


>gi|291278833|ref|YP_003495668.1| RNA polymerase sigma factor for flagellar operon FliA
           [Deferribacter desulfuricans SSM1]
 gi|290753535|dbj|BAI79912.1| RNA polymerase sigma factor for flagellar operon FliA
           [Deferribacter desulfuricans SSM1]
          Length = 243

 Score =  104 bits (261), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 46/212 (21%), Positives = 92/212 (43%), Gaps = 14/212 (6%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + E+ S    G ++A+K++D  R      Y+   +K A+ + +LR   ++        K
Sbjct: 43  DMDEIYSAACFGFVEALKRYDKSRNIDFKYYAEKRVKGAILD-VLRKMDILSRNVRTKIK 101

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            L   + RL   L        +      IAK+ N+   EV  +   L   + ++  I   
Sbjct: 102 DLEDKIARLSSKL-------GRKPHPSEIAKEYNLDIDEVNKLLELLENSDQVSLDITFG 154

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           + +SS   +++  D    E    E  E+K    +L + +  LN +ER +      ++  +
Sbjct: 155 EDDSSSLINFIKSDILTPE----ESIEKKELIEVLGKEIEKLNEKERLVITLYYYED--L 208

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           T++ + S   +S  RV Q+   A KK+++ ++
Sbjct: 209 TMKEIGSVLGISESRVSQLHNSAVKKLKKRME 240


>gi|325107978|ref|YP_004269046.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Planctomyces
           brasiliensis DSM 5305]
 gi|324968246|gb|ADY59024.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Planctomyces
           brasiliensis DSM 5305]
          Length = 259

 Score =  104 bits (261), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 55/264 (20%), Positives = 111/264 (42%), Gaps = 21/264 (7%)

Query: 29  LEKQEEYVLAKRYREHG-DLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNI 84
           L  +E   + + Y++   +    +RL+  +L LV   A         G+ +++++S G  
Sbjct: 5   LSPEEVLEIWEAYKKDQTNQHLRNRLIERYLPLVRYNAERVWAKLPDGVDLNDLMSAGVF 64

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM A+  FD ERG +  TY +  I+ AM + + R+   V     +   +L    + ++ 
Sbjct: 65  GLMDAIDAFDMERGVKFETYCVPRIRGAMLDEL-RTMDWVPRLVRSKASKLAAASKAVEA 123

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQD 202
                     +P   V +A K+ +S  E   +       G  SLN     +D      + 
Sbjct: 124 -------ETGRPPTDVEVAAKMELSLEEFEKLKSEAAAVGLVSLNKKWYETDSYKDVREV 176

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
            ++ D  G++           +R+++      LN  ER I      +E  +T++ +    
Sbjct: 177 DILEDGKGEDPT-----NGIQKRDIMKLVTKGLNRNERLIMILYYYEE--LTMKEIGMTL 229

Query: 263 EVSRERVRQIEARAFKKVQESIQK 286
            +S  RV Q+ +    ++++ ++K
Sbjct: 230 GLSESRVSQMHSSIVNRLKDQLRK 253


>gi|229108567|ref|ZP_04238180.1| RNA polymerase sigma-B factor [Bacillus cereus Rock1-15]
 gi|228674898|gb|EEL30129.1| RNA polymerase sigma-B factor [Bacillus cereus Rock1-15]
          Length = 203

 Score =  104 bits (261), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 38/210 (18%), Positives = 96/210 (45%), Gaps = 16/210 (7%)

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++  G +GL+ A++++D   G     +++  I   +++Y+      + +      +R+
Sbjct: 3   EDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRI 57

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSS 193
                ++K  ++ +TD+  +  +++ IA  L +SE EV+ +          SL+ ++ +S
Sbjct: 58  KDLGGKIKLAIEELTDHLQRSPKIIEIANHLGLSEEEVLEIMDAKNNYRVSSLDDVVENS 117

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
              SS  +   V +       + +  E   RR +L    +VLN  E+ +     +    +
Sbjct: 118 SDGSSVARIESVGE-------VEQGYEETERRLVLKDIFNVLNDTEKSVIH--YIFRENL 168

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQES 283
             ++      +S+  V +I+ +A  K++++
Sbjct: 169 NQKDTGERLGISQMHVSRIKRQAISKLKQA 198


>gi|220911344|ref|YP_002486653.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Arthrobacter
           chlorophenolicus A6]
 gi|219858222|gb|ACL38564.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Arthrobacter
           chlorophenolicus A6]
          Length = 310

 Score =  104 bits (261), Expect = 1e-20,   Method: Composition-based stats.
 Identities = 54/278 (19%), Positives = 100/278 (35%), Gaps = 38/278 (13%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAA---------HRLVTSHLRLVVKIAMGYR 69
           YIHE++  P           ++     D  A          + LV  +L L   +A  + 
Sbjct: 14  YIHEVQSTP----------IQKTASPHDSQARSGQLRETFENDLVLGYLDLAEALAARFE 63

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
             G   +++     +GL++A + FD  +G     Y+   I   ++ Y+     +V+    
Sbjct: 64  ARGRERADLNQVAYLGLVKAARGFDRSKGESFPAYAAPTITGELKRYLRDRTWVVRPPRN 123

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG--DESLN 187
               R      RL      +T    +   V  +A +L    + V       +    +SL+
Sbjct: 124 IQDLRT-----RLFRAEPELTQALGRSPSVEELAGELETDPAAVQEAMSASSSMHPDSLD 178

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           A+  +SD  S       + D        +E+ E       L  +M  L P +R +   R 
Sbjct: 179 AVNPNSDAPS-------IGDMLACPDTPLERLEELAC---LRDAMHDLAPADRELLYRRY 228

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             E   T   L     +S+ +V +  AR   ++Q  ++
Sbjct: 229 FCEE--TQVQLGKRLGMSQMQVSRRLARVLVELQHRLE 264


>gi|251798274|ref|YP_003013005.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus sp. JDR-2]
 gi|247545900|gb|ACT02919.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Paenibacillus sp. JDR-2]
          Length = 184

 Score =  104 bits (260), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 42/228 (18%), Positives = 83/228 (36%), Gaps = 65/228 (28%)

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
                +   G  + +++S G IGL++A++ F   +G +LAT++   I+  +         
Sbjct: 15  HNVKKFDNTGEDLEDLISIGTIGLIKAIESFQTGKGTKLATFAARCIENEI--------- 65

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
                          +LR LK                                       
Sbjct: 66  -------------LMHLRSLKKT-----------------------------------RK 77

Query: 183 DESLNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           D SL+  I +  + N     D L  + D     ++++ + K  ++ + R++ +L+ RE+ 
Sbjct: 78  DVSLHDPIGTDKEGNEITLIDILGTEADD----VVDRVQLKIEKSKIYRNLDILDEREQE 133

Query: 242 IFEARRLQE---NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +   R   +   +  T   ++ E  +SR  V +IE RA  K+     K
Sbjct: 134 VIRGRFGLDHGGDERTQREIAKELGISRSYVSRIEKRALMKLYHEFYK 181


>gi|121488745|emb|CAJ18257.1| sigma 70-type sigma factor [Chlorobaculum thiosulfatiphilum]
          Length = 165

 Score =  104 bits (260), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 39/174 (22%), Positives = 78/174 (44%), Gaps = 11/174 (6%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + +     +V++    N+    
Sbjct: 1   DLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLP--LNRVGTL 58

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
             + +    L+   + +        +A  L++   +V           S++A     D N
Sbjct: 59  NKISKAYSQLEQEFERD---PNTKELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDN 115

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +  D L  D    +  L     R +    + RS+SVL PRE  +  +     
Sbjct: 116 --RLLDVLQNDGHMPDHGL----NRDSLTLEVERSLSVLAPREADVIRSYFGIG 163


>gi|125973016|ref|YP_001036926.1| RNA polymerase, sigma 28 subunit [Clostridium thermocellum ATCC
           27405]
 gi|125713241|gb|ABN51733.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Clostridium
           thermocellum ATCC 27405]
          Length = 218

 Score =  104 bits (260), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 40/218 (18%), Positives = 92/218 (42%), Gaps = 15/218 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKK 92
            L K+Y +  + +   +L+  +  +V  IA     Y G  +   +++  G  GL+ A++K
Sbjct: 10  ELWKQYADTKNPAIKEQLIIEYSNIVKYIAGRLSIYFGSNVEYDDLIGYGIFGLIDAIEK 69

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G +  TY+   I+ ++ + I     L  +  +  QK      + L+     I + 
Sbjct: 70  FDINKGVKFETYASLRIRGSIIDSIRE---LDWVPRSLRQKN-----KELEKVYAEIENE 121

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +      +A KL ++  E      +L  + +L+++I+  +     ++  +    + ++
Sbjct: 122 LGRSASDKEVADKLGITVDE----LNKLLNEVNLSSMISLEEFLEQNYEIGVTTAPESRD 177

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           +      E    R +L  ++S L  +E+ +       E
Sbjct: 178 EKPEGYIEMAELREILADAISKLPEKEKMVITLYYFGE 215


>gi|318040135|ref|ZP_07972091.1| RNA polymerase sigma factor, sigma-70 family protein [Synechococcus
           sp. CB0101]
          Length = 310

 Score =  104 bits (260), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 60/268 (22%), Positives = 112/268 (41%), Gaps = 26/268 (9%)

Query: 38  AKRYREHGD-------------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV----VS 80
            +R+++H D             L A  +LV  +L LV      +R       +     + 
Sbjct: 37  IQRWQQHPDGPSHAPKPVRRSALRAREQLVRHNLGLVAHTWGRHRCSLPAHDDTTADALQ 96

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           E  + L++A +KFDP +G+R +TY+ +W++    E+  R+   ++    A +  +     
Sbjct: 97  EAALNLVRAAEKFDPAKGYRFSTYATFWVRRGFTEFEQRAKRAIRFP--AEKAAVVLKAL 154

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE----SLNALINSSDKN 196
           RL    QA T +    E + A  K    + S           D     SL+      D+ 
Sbjct: 155 RLSQQHQATTGDEPALEWLAAQLKFDGKAMSAEQLAEFIRQWDATRTGSLDGAEEEGDEK 214

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
               +  L       EQ L ++ + ++    L + MS L+ +E R+   R L+  P++  
Sbjct: 215 GGCSRLDLASLQQAAEQQLTQEPDPQHAS--LPQLMSCLDEQEHRLIRNRYLRRPPLSPC 272

Query: 257 NLSSEF-EVSRERVRQIEARAFKKVQES 283
            L      + RE++ Q+EA A  K++++
Sbjct: 273 QLRRSMGGMQREQLEQLEATALDKLRQA 300


>gi|158339684|ref|YP_001520691.1| RNA polymerase sigma factor domain-containing protein
           [Acaryochloris marina MBIC11017]
 gi|158309925|gb|ABW31541.1| RNA polymerase sigma factor domain protein [Acaryochloris marina
           MBIC11017]
          Length = 400

 Score =  104 bits (260), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 46/224 (20%), Positives = 96/224 (42%), Gaps = 12/224 (5%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEI-RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLR 59
           M   ++S   +  I L  Y+ ++  + P+   +EE  L ++ +  G  ++   L+  H+R
Sbjct: 1   MTAASISSPFSEGIRLPDYLTQLLHRFPVPNPEEELDLIRKAKL-GHETSLSWLMIGHVR 59

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           LV K+A  Y        +++ EG +G+  AV+KFD  +G + +TY+  WI+  ++ +  +
Sbjct: 60  LVSKLAKQYAWTLDDAQDLIQEGMLGIRHAVRKFDSTKGCKFSTYARGWIRGYIRRFCYK 119

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGH-----LQAITDNNLKPEQVVAIAKKLNVSESEVI 174
           +    ++     ++     + RL+       L+ I        + +        S  E+ 
Sbjct: 120 N-RPKQLRLPEKKQVHLDRVYRLQNQFPDANLEEIAQKANLKLEYIEDLLYWGRSFQEIP 178

Query: 175 SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
             +     DES      + D+   ++ D+ V        VLI+ 
Sbjct: 179 DWHEFTINDESF----YTDDEEYDEYFDFEVVSETKTNLVLIKA 218


>gi|153953966|ref|YP_001394731.1| sporulation sigma factor SigE [Clostridium kluyveri DSM 555]
 gi|219854580|ref|YP_002471702.1| hypothetical protein CKR_1237 [Clostridium kluyveri NBRC 12016]
 gi|146346847|gb|EDK33383.1| SigE2 [Clostridium kluyveri DSM 555]
 gi|219568304|dbj|BAH06288.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 235

 Score =  104 bits (260), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 54/262 (20%), Positives = 105/262 (40%), Gaps = 59/262 (22%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K+EE  L  R    G+      L+  +LRLVV IA  +   G+ + ++VS G IGL
Sbjct: 33  PPLSKKEEEDLVSRLV-SGNEKVRATLIERNLRLVVYIARKFENTGVNVEDLVSVGTIGL 91

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+                    ++K   
Sbjct: 92  IKAVNTFNPEKKIKLATYASRCIENEILMYLRRNS-------------------KVKAE- 131

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                        ++  + LNV             G+E L + I  +D +      ++  
Sbjct: 132 -------------ISFYEPLNVDWD----------GNELLLSDILGTDNDVVY--SFIED 166

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           + D Q  V+  K+     + ++                     +   T + ++    +S+
Sbjct: 167 EVDKQLLVIAMKKLSDREKEIVN-------------LRFGLNGKKEKTQKEVADLLGISQ 213

Query: 267 ERVRQIEARAFKKVQESIQKQV 288
             + ++E R  +++++ I K +
Sbjct: 214 SYISRLEKRIIRRLRKEINKML 235


>gi|307152337|ref|YP_003887721.1| FliA/WhiG subfamily RNA polymerase sigma-28 factor [Cyanothece sp.
           PCC 7822]
 gi|306982565|gb|ADN14446.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cyanothece
           sp. PCC 7822]
          Length = 257

 Score =  104 bits (260), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 50/251 (19%), Positives = 105/251 (41%), Gaps = 16/251 (6%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGF 99
           Y  +  L   ++LV  +  LV ++A         P  ++   G +GL++A+++F+P++G 
Sbjct: 19  YSRNPSLKLRNQLVELNAGLVRQVAHRISRQCCEPYEDLEQVGYLGLIRAIERFNPQQGC 78

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
             +++++ +++  +  Y+    S+++I      + L+   ++L+  L        K    
Sbjct: 79  AFSSFAIPYVRGEILHYLRDRGSVMRIPRR--WQDLYTKGKKLRKQLAQTLGRQPKE--- 133

Query: 160 VAIAKKLNVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
             IA+ L VS  E       L      SL+A IN        + D L       +Q + E
Sbjct: 134 SEIAQALGVSYQEWNECQLALQNRLLVSLDATINQVHDGVITFGDTLPDPKSQGQQRMQE 193

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
                  R  L R+MS L  + +   E   L + P   +  + +  +S   V +   +  
Sbjct: 194 D------RLQLQRAMSQLEDKTKAAIECVFLWDLPR--KEAAKQIGISPMTVTRHLQKGL 245

Query: 278 KKVQESIQKQV 288
           +++   ++ Q 
Sbjct: 246 EQLIALLRPQA 256


>gi|299069774|emb|CBJ41053.1| RNA polymerase sigma factor for flagellar operon [Ralstonia
           solanacearum CMR15]
          Length = 253

 Score =  104 bits (260), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 41/241 (17%), Positives = 100/241 (41%), Gaps = 17/241 (7%)

Query: 56  SHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++  LV +IA          + + +++  G +GL+ A+ +++  +G +   Y+   I+ A
Sbjct: 26  AYAPLVRRIANQMMVKLPASVELDDLIQAGMMGLLDALSRYEETQGVQFEFYAAQRIRGA 85

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           + + +  S  L         + L  N R ++  +Q +     +      IA  LN+S ++
Sbjct: 86  ILDELRGSDWL--------PRGLRRNARTIEQAIQKLQQQKGRAPTETEIAAFLNMSLAD 137

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
              +   L G    + L+   D +      ++       +   +++    + R  +  ++
Sbjct: 138 YQKLLVELQG----SQLLYYEDFDREDADAFIENRAPENDATPLDQLLDHDLRESVVAAI 193

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
             L  RE+ +       E  + L  + +   VS  RV QI ++A  +++  ++++  L +
Sbjct: 194 EALPEREKLMMSLYY--EQDLNLREIGAVMGVSESRVCQIHSQAIARIRSRLRERAWLPT 251

Query: 293 S 293
            
Sbjct: 252 P 252


>gi|121488769|emb|CAJ18269.1| sigma 70-type sigma factor [Chlorobium limicola]
 gi|121488771|emb|CAJ18270.1| sigma 70-type sigma factor [Chlorobium phaeobacteroides]
          Length = 165

 Score =  104 bits (260), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 38/177 (21%), Positives = 76/177 (42%), Gaps = 17/177 (9%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + +     +V++    N+    
Sbjct: 1   DLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLP--LNRVGTL 58

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
             + +    L+   + +        +A  L++   +V           S++A     D N
Sbjct: 59  NKISKAYSQLEQEFERD---PNTRELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDN 115

Query: 197 ---SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
                   D  + DH   +  L  + ER          +SVL PRE  +  +     
Sbjct: 116 RLLDVLQNDGHLPDHGLNKDSLTLEVERS---------LSVLAPREADVIRSYFGIG 163


>gi|261366790|ref|ZP_05979673.1| RNA polymerase sigma-F factor [Subdoligranulum variabile DSM 15176]
 gi|282571621|gb|EFB77156.1| RNA polymerase sigma-F factor [Subdoligranulum variabile DSM 15176]
          Length = 232

 Score =  104 bits (260), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 41/235 (17%), Positives = 93/235 (39%), Gaps = 21/235 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
               +  +L LV   A  ++G G+   E+ + G +GL++A   FD  RG   +TY++  I
Sbjct: 11  RAEFIEKNLGLVHACAGRFKGRGIEYEELYAAGCLGLVKACDGFDTSRGVCFSTYAVPVI 70

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              +++ + R    VK+  +  +  L     ++    +       +   V  +A+ L  +
Sbjct: 71  LGEIKK-LFRDGGTVKVSRSLKELSL-----KINAERERCLKKTGQEPGVTQLAEILQTT 124

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             + I++  R +    ++      +    +W   +    D  E+ L +       R  L 
Sbjct: 125 PEQ-IALAIRASLPA-ISLTPTDEEDGQREWDVPV----DSPEESLSD-------RIGLA 171

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             M  L+P +R++   R       T    +     ++ ++ + E +  K ++  +
Sbjct: 172 EVMEKLSPTDRQMIRLRFFGG--RTQSETARVLGTTQVQISRRERKVLKWMRAEL 224


>gi|17549609|ref|NP_522949.1| flagellar biosynthesis sigma factor [Ralstonia solanacearum
           GMI1000]
 gi|17431863|emb|CAD18541.1| probable rna polymerase sigma factor for flagellar operon (sigma-f
           factor) transcription regulator protein [Ralstonia
           solanacearum GMI1000]
          Length = 253

 Score =  104 bits (260), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 41/241 (17%), Positives = 100/241 (41%), Gaps = 17/241 (7%)

Query: 56  SHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++  LV +IA          + + +++  G +GL+ A+ +++  +G +   Y+   I+ A
Sbjct: 26  AYAPLVRRIANQMMVKLPASVELDDLIQAGMMGLLDALSRYEETQGVQFEFYAAQRIRGA 85

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           + + +  S  L         + L  N R ++  +Q +     +      IA  LN+S ++
Sbjct: 86  ILDELRGSDWL--------PRGLRRNARTIEQAIQKLQQQKGRAPTETEIAAALNMSLAD 137

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
              +   L G    + L+   D +      ++       +   +++    + R  +  ++
Sbjct: 138 YQKLLVELQG----SQLLYYEDFDREDADAFIENRAPENDATPLDQLLDHDLRESVVAAI 193

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
             L  RE+ +       E  + L  + +   VS  RV QI ++A  +++  ++++  L +
Sbjct: 194 EALPEREKLMMSLYY--EQDLNLREIGAVMGVSESRVCQIHSQAIARIRSRLRERAWLPT 251

Query: 293 S 293
            
Sbjct: 252 P 252


>gi|291535996|emb|CBL09108.1| RNA polymerase, sigma 27/28 subunit, RpsK/SigK [Roseburia
           intestinalis M50/1]
          Length = 192

 Score =  104 bits (259), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 49/244 (20%), Positives = 83/244 (34%), Gaps = 61/244 (25%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + G L A + L   ++RLV  +A  Y+     + +++S G IGLM+A+  +  + G RLA
Sbjct: 6   KKGSLEARNELTLHNMRLVAHVAKKYQNSEEDMEDLISIGTIGLMKAIATYKEDYGSRLA 65

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+   I   +  Y                        R K                   
Sbjct: 66  TYAARCIDNELLMYF-----------------------RAKKK----------------- 85

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
                   S  +S+   +             + N     D +  +      V+   E  +
Sbjct: 86  -------VSREVSLYEPIG---------MDKEGNQIHLLDIVESEE---PDVVEMMERTR 126

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
               +L     VL  RE  I   R        +T   ++S   +SR  V +IE +A  K+
Sbjct: 127 QIEKLLGLVPKVLQERELYIIVHRYGLFGNKAMTQREIASAVGISRSYVSRIEKKALDKL 186

Query: 281 QESI 284
           ++S 
Sbjct: 187 KKSF 190


>gi|121488781|emb|CAJ18275.1| sigma 70-type sigma factor [Chlorobium phaeovibrioides]
          Length = 165

 Score =  104 bits (259), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 38/172 (22%), Positives = 79/172 (45%), Gaps = 11/172 (6%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + +     +V++    N+    
Sbjct: 1   DLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLP--LNRVGTL 58

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
             + +    L+   + +        +A +L++   +V           S++A     D N
Sbjct: 59  NKISKAYSQLEQEYERD---PNTKELANQLDMDSQDVADTLKIAGRHVSVDAPFAQGDDN 115

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
             +  D L  D      +      R +    + RS+SVL PRE  + ++   
Sbjct: 116 --RLLDVLQNDG----HLPDHGLNRDSLTLEVERSLSVLAPREADVIKSYFG 161


>gi|82776398|ref|YP_402747.1| flagellar biosynthesis sigma factor [Shigella dysenteriae Sd197]
 gi|81240546|gb|ABB61256.1| alternative sigma factor 28 [Shigella dysenteriae Sd197]
          Length = 239

 Score =  104 bits (259), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 46/240 (19%), Positives = 103/240 (42%), Gaps = 17/240 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   + +L+  L        +      +A++L
Sbjct: 73  QCIRGAMLDEL-RSRDWVPRSVRRNAREVAQAIGQLEQEL-------GRNATETEVAERL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +  ++   M      D + + L +  +          +   D Q +  +++    N R 
Sbjct: 125 GIDIADYRQMLL----DTNNSQLFSYDEWREEHGDSIELVTDDYQRENPLQQLLDSNLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +E EV   RV Q+ ++A K+++  + K
Sbjct: 181 RVMEAIETLPEREKLVLTLYY--QEELNLKEIGAELEVGESRVSQLHSQAIKRLRTKLGK 238


>gi|116668918|ref|YP_829851.1| RNA polymerase, sigma 28 subunit [Arthrobacter sp. FB24]
 gi|116609027|gb|ABK01751.1| RNA polymerase, sigma 28 subunit [Arthrobacter sp. FB24]
          Length = 275

 Score =  104 bits (259), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 48/237 (20%), Positives = 91/237 (38%), Gaps = 19/237 (8%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           + LV  +L L   +A  ++  G   +++     +GL++A + FD  RG     Y+   I 
Sbjct: 29  NHLVLDYLDLAEALAARFQARGRDRADLNQVAYLGLVKAARGFDEARGASFPAYAAPTIT 88

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
             ++ Y+     +V+        R       L     A+  +  +P     +A++L VS 
Sbjct: 89  GELKRYLRDRCWMVRPPRHVQDLR-----SELLRAEPALAQSLGRPPSAAELARELAVSP 143

Query: 171 SEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
             V       A    +SL+A+  ++D         L       E  L   EE       L
Sbjct: 144 EAVNEATAAAASLHPDSLDAVDANTD------TAPLAETLSSGEDPLARLEEL----ICL 193

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            +++  L   ++ +   R   E   +   L   F VS+ +V +  +R   ++Q  +Q
Sbjct: 194 NQAIHELTAEDQELLYRRYFCEE--SQAELGRRFGVSQMQVSRRLSRVLVQLQRLLQ 248


>gi|78485092|ref|YP_391017.1| sigma 28 (flagella/sporulation) [Thiomicrospira crunogena XCL-2]
 gi|78363378|gb|ABB41343.1| sigma 28 (Flagella/Sporulation) [Thiomicrospira crunogena XCL-2]
          Length = 241

 Score =  104 bits (259), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 46/235 (19%), Positives = 97/235 (41%), Gaps = 20/235 (8%)

Query: 54  VTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           + + L LV +IA   +G       + +++  G IGL+++ +KFD  +G    TY+   I+
Sbjct: 21  IEAFLPLVKRIAYHLKGRLPDSVMVDDLIQSGIIGLIESSQKFDATQGASFETYAGIRIR 80

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            AM + I +             + ++   R +   +  +     +  +   IA+ + VS 
Sbjct: 81  GAMLDEIRKGDWT--------PRSVYRKSREVSEAILKVESEKGREARDEEIAEVMGVSL 132

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            E   +   L    S   L      +    +D +V    G  +  I +    + +  L  
Sbjct: 133 DEYYHI---LQDTNSAQLLSIDEPDHDELAEDRMV----GTIKTPITELVESDFQGALAE 185

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            ++ L  +E+ +       +  + L+ +    EVS  RV QI ++A K+++  ++
Sbjct: 186 QINELPEKEKLVMALYY--DEELNLKEIGEVLEVSESRVSQIHSQAIKRLKSRLR 238


>gi|333003010|gb|EGK22564.1| RNA polymerase sigma factor for flagellar operon [Shigella flexneri
           VA-6]
          Length = 239

 Score =  104 bits (259), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 102/240 (42%), Gaps = 17/240 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KHSLWQRYVPLVCHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   + +L+  L        +      +A++L
Sbjct: 73  QRIRGAMLDEL-RSRDWVPRSVRRNAREVAQAIGQLEQEL-------GRNATETEVAERL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +  ++   M      D + + L +  +          +   D Q +  +++    N R 
Sbjct: 125 GIDIADYRQMLL----DTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 181 RVMEAIETLPEREKLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 238


>gi|270157125|ref|ZP_06185782.1| RNA polymerase sigma-28 factor FliA [Legionella longbeachae D-4968]
 gi|289164470|ref|YP_003454608.1| sigma factor 28 [Legionella longbeachae NSW150]
 gi|269989150|gb|EEZ95404.1| RNA polymerase sigma-28 factor FliA [Legionella longbeachae D-4968]
 gi|288857643|emb|CBJ11483.1| sigma factor 28 [Legionella longbeachae NSW150]
          Length = 238

 Score =  104 bits (259), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 48/242 (19%), Positives = 96/242 (39%), Gaps = 19/242 (7%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           +      LV +H  LV +IA    G    G+ + +++  G +GL++A + +D  +G    
Sbjct: 11  NQQIQETLVKNHALLVKRIAHHLLGRLPQGIQLDDLIQAGMLGLLEAARHYDSSKGASFE 70

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+   I+  M + + R+   V             N R +   ++ +     +  +   I
Sbjct: 71  TYAGIRIRGYMLDEVRRN-DWVPRSVH-------RNSRLISEAVKYVEHRLGREAKDSEI 122

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A +L VS +E   M       +S+++ +   D       D L  D+              
Sbjct: 123 AAELGVSLAEYHEMLQ-----DSVSSHLYGFDDLGVT-DDALQTDNQSASTEPHVNVFHS 176

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +    L+  +  L  +ER +       E+ + L+ +     VS  RV QI ++A  +++ 
Sbjct: 177 DLMRRLSEVIRGLPHKERMVLSLYY--EHDLNLKEIGEVIGVSESRVSQILSQATHRIKS 234

Query: 283 SI 284
            +
Sbjct: 235 RL 236


>gi|241761164|ref|ZP_04759253.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Zymomonas mobilis
           subsp. mobilis ATCC 10988]
 gi|241374783|gb|EER64244.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Zymomonas mobilis
           subsp. mobilis ATCC 10988]
          Length = 247

 Score =  104 bits (259), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 53/234 (22%), Positives = 101/234 (43%), Gaps = 23/234 (9%)

Query: 51  HRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
             L+ +HL+LV KIA    G     + + +++  G + L++A   F+  RGF  ATY+  
Sbjct: 26  EALIKTHLQLVRKIAWHVHGRVSSAIEVEDLIQIGMVALIEAANAFE-NRGFAFATYASM 84

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+ AM +Y+ +  +  +  +   QK L           + ++    +  +   IA+KLN
Sbjct: 85  RIRGAMIDYMRQHAATAR-SSIVRQKTLN-------KAREELSATLGRRPEEAEIAEKLN 136

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S SE          D ++N    S D   S        D+  Q   +    ER+  ++ 
Sbjct: 137 MSPSEYREW-----ADGAINIRQESLDDVYSDHSSIFTDDNADQASEM----EREALQSA 187

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           L   +  L  RE  + +   ++E  + L+ +    ++   R+ QI+  A   ++
Sbjct: 188 LAEQIKTLPEREALVLQLYYVEE--LNLKEIGEVLDLGTARISQIKKSAVDHLR 239


>gi|296121398|ref|YP_003629176.1| RNA polymerase sigma factor, FliA/WhiG family [Planctomyces
           limnophilus DSM 3776]
 gi|296013738|gb|ADG66977.1| RNA polymerase sigma factor, FliA/WhiG family [Planctomyces
           limnophilus DSM 3776]
          Length = 259

 Score =  104 bits (259), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 56/255 (21%), Positives = 108/255 (42%), Gaps = 21/255 (8%)

Query: 38  AKRYREHGDLSA-AHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKF 93
              Y++     A  +RL+ ++L LV   A         G+ I++++S G  GLM A++ F
Sbjct: 13  WNAYKQDQSSKALRNRLMENYLPLVRYNAERVWSKLPDGVDINDLISAGVFGLMDAIEAF 72

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D ERG +  TY +  I+ AM + + R+   V     +   +L    ++ +  L       
Sbjct: 73  DMERGVKFETYCVPRIRGAMLDEL-RTMDWVPRLVRSKASKLESARKQAEAEL------- 124

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYDHDGQ 211
            +P     +A K+ V   E   +    +     SLN     +D      +  ++ D  G+
Sbjct: 125 GRPPADNEVAAKMGVPLDEYEKLKSEASAVNLVSLNKKWYETDSYKDVREIDIIEDTKGE 184

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           +  L        +R+++      LN  ER I      +E  +T++ + S   +S  RV Q
Sbjct: 185 DPTL-----SIQKRDLMKLVTKGLNRNERLIIILYYYEE--LTMKEIGSTLGLSESRVSQ 237

Query: 272 IEARAFKKVQESIQK 286
           + +    +++E + +
Sbjct: 238 MHSSIVNRLKEQLGR 252


>gi|225568718|ref|ZP_03777743.1| hypothetical protein CLOHYLEM_04797 [Clostridium hylemonae DSM
           15053]
 gi|225162217|gb|EEG74836.1| hypothetical protein CLOHYLEM_04797 [Clostridium hylemonae DSM
           15053]
          Length = 189

 Score =  104 bits (259), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 50/243 (20%), Positives = 89/243 (36%), Gaps = 61/243 (25%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GDL A H L+  +LRLV  I   Y+       +++S G IGL++AV  F+P++  RL T
Sbjct: 6   EGDLEAKHVLIERNLRLVAHIVKKYQSLEEDNEDLLSIGTIGLIKAVVTFNPDKCVRLGT 65

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   I+  +  Y+               +    + + +  +    TD      Q+  I 
Sbjct: 66  YAARCIENEILMYL---------------RSKKKSSKEVSLYEPIGTDREGNEIQLFDII 110

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           +                            +D++ +  +  L  D                
Sbjct: 111 E----------------------------TDEDDAHRKVALKDD---------------- 126

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            R +  +    L+ RER + + R     E   T   ++    +SR  V +IE  A +K++
Sbjct: 127 IRLLYEKVEGELSQRERLVLKMRYGLYNEEEYTQREIARRLGISRSYVSRIEKSAIEKLR 186

Query: 282 ESI 284
           E  
Sbjct: 187 EYF 189


>gi|167461107|ref|ZP_02326196.1| SpoIIIC [Paenibacillus larvae subsp. larvae BRL-230010]
 gi|322384941|ref|ZP_08058597.1| sporulation sigma factor SigE-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321150238|gb|EFX43745.1| sporulation sigma factor SigE-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 181

 Score =  104 bits (259), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 45/228 (19%), Positives = 84/228 (36%), Gaps = 65/228 (28%)

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
                +   G  + +++S G IGL++A++ F P +G +LAT++   I+  +         
Sbjct: 12  HNIKKFDNTGEDLEDLISIGTIGLIKAIESFSPNKGTKLATFAARCIENEI--------- 62

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
                          +LR LK                                       
Sbjct: 63  -------------LMHLRSLKKT-----------------------------------RK 74

Query: 183 DESLNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           D SL+  I +  + N     D L  + D     +++K + K  ++ + R++ +L+ RE+ 
Sbjct: 75  DVSLHDPIGTDKEGNEITLIDILGTEVD----EVVDKVQLKIEKSKIYRNLDILDEREQE 130

Query: 242 IFEARRLQE---NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           + + R   E      T   ++ E  +SR  V +IE RA  K+     K
Sbjct: 131 VIKGRFGLEYGGEERTQREIACELGISRSYVSRIEKRALMKLYHEFYK 178


>gi|94312634|ref|YP_585843.1| RNA polymerase sigma 28 (sigma F) factor [Cupriavidus metallidurans
           CH34]
 gi|93356486|gb|ABF10574.1| RNA polymerase sigma 28 (sigma F) factor [Cupriavidus metallidurans
           CH34]
          Length = 238

 Score =  104 bits (259), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 44/235 (18%), Positives = 93/235 (39%), Gaps = 16/235 (6%)

Query: 54  VTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           V SH  LV +IA+         + I +++  G IGL+ A K+++   G R  TY+   I+
Sbjct: 14  VKSHAPLVRRIALQLAAKLPASVQIDDLIQAGMIGLLDAAKRYEDNHGARFETYASQRIR 73

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            AM + +  +            + L    R+++   + +     +      +AK+L +  
Sbjct: 74  GAMLDEVRANDW--------QSRSLRQFTRKIERTQRQLEQKLGRSPIDSEVAKELEMGL 125

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            E   +   + G + L+                L    +     ++        R+ L R
Sbjct: 126 EEYQELLNEVHGCQLLHYEDFERSGEEDFLDRHLGVTDEANPLTVL---MESGMRDALIR 182

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           ++  L  RE+ +       +  + L  + +  EV+  RV QI ++A  +++  ++
Sbjct: 183 AIEKLPEREKLVLSLCY--DQELNLREIGAVLEVTESRVCQIRSQAITRLRNQLR 235


>gi|167949417|ref|ZP_02536491.1| RNA polymerase sigma factor RpoD [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 128

 Score =  103 bits (258), Expect = 2e-20,   Method: Composition-based stats.
 Identities = 30/128 (23%), Positives = 55/128 (42%), Gaps = 7/128 (5%)

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           + + E +V  +        S+   I   D   S   D++    D      ++    +  R
Sbjct: 1   MEMPEDKVRKVLKIAKEPISMETPI--GDDEDSHLGDFI---EDSGVVSPVDSATSEGLR 55

Query: 226 NMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
                 +S L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++  
Sbjct: 56  EATQNMLSGLTSREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHP 115

Query: 284 IQKQVELS 291
            + +   S
Sbjct: 116 SRSERMRS 123


>gi|187935345|ref|YP_001885383.1| sporulation sigma factor SigK [Clostridium botulinum B str. Eklund
           17B]
 gi|187723498|gb|ACD24719.1| RNA polymerase sigma-K factor [Clostridium botulinum B str. Eklund
           17B]
          Length = 232

 Score =  103 bits (258), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 61/260 (23%), Positives = 94/260 (36%), Gaps = 63/260 (24%)

Query: 16  LSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           L+ YI      P  L + EE    KR ++ GD +A   L+  +LRLV  I   Y      
Sbjct: 17  LTGYISSGNTFPNPLNESEEEEYLKRLKD-GDKTAKGVLIERNLRLVAHIVKKYSFPNKD 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + E++S G +GL++A+  FD  +G RLATY+   I+  +                     
Sbjct: 76  VDELISIGTVGLIKAIDSFDSGKGTRLATYASRCIENEILM------------------- 116

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           LF N ++ K                              + +   +  D+  N  I   D
Sbjct: 117 LFRNNKKQKSE----------------------------VYLQDPIGVDKEGNE-ICLID 147

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENP 252
             SS     L    +  E  L  K+  K  ++ LT+       RE  I   R      N 
Sbjct: 148 ILSSDNDSVL----EKVESNLQIKDLYKKIKDSLTK-------RESTILIMRYGLIDGNR 196

Query: 253 VTLENLSSEFEVSRERVRQI 272
            T   ++    +SR  V +I
Sbjct: 197 KTQREIAGTLGISRSYVSRI 216


>gi|87119467|ref|ZP_01075364.1| flagellar biosynthesis sigma factor FliA [Marinomonas sp. MED121]
 gi|86164943|gb|EAQ66211.1| flagellar biosynthesis sigma factor FliA [Marinomonas sp. MED121]
          Length = 244

 Score =  103 bits (258), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 40/237 (16%), Positives = 94/237 (39%), Gaps = 19/237 (8%)

Query: 51  HRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            +++  +  LV KIA          + + +++  G +GL++A K+F+  +G    TY+  
Sbjct: 19  DQIIDEYGFLVKKIAYHLLARLPSSVELDDLIQAGMMGLIEAFKRFESTKGASFETYAGI 78

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+ ++ + + +S            + +  N R +   ++ +     +    + I++ ++
Sbjct: 79  RIRGSIMDEVRKSDW--------APRSVRRNGRAIASAIKELEAKLGREASDLEISQAMD 130

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S +E   M   L    S          +S         + D      +E       +  
Sbjct: 131 ISLNEYHEM---LQSSMSTQLFSFEELLDSEGLNIETDSEEDSAPYSFVEDL---GFQTQ 184

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L + +  L  RE+ +        + + L+ + S   VS  RV QI ++A  +++  +
Sbjct: 185 LAQEIDSLPEREKLVLSLYY--NDELNLKEIGSVLGVSESRVSQIHSQAAMRLKARL 239


>gi|237757202|ref|ZP_04585618.1| RNA polymerase sigma-D factor [Sulfurihydrogenibium yellowstonense
           SS-5]
 gi|237690638|gb|EEP59830.1| RNA polymerase sigma-D factor [Sulfurihydrogenibium yellowstonense
           SS-5]
          Length = 242

 Score =  103 bits (258), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 45/248 (18%), Positives = 106/248 (42%), Gaps = 19/248 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAM--GYRG--YGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
                 ++   L  +  I     ++     +   ++   G +GL  A++KFDP +G + +
Sbjct: 5   KEERESIIREFLPKINYIVKSLKHQNLPPIVDEEDLFQVGVLGLYDALEKFDPSKGVKFS 64

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+   ++  + +++ R    V        K L   +  L+  L        +  ++  I
Sbjct: 65  TYAEIRVRGYILDHL-RQLDWVPRNIRNKVKNLENKIVELETKL-------GREAKLEEI 116

Query: 163 AKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
           A+ L +S  E +    +       S+++ I+  D  S    + +  D D  E+ + EK+ 
Sbjct: 117 AEYLGMSLEEYMIYAEKAVNKILISIDSDISKDDDESLHLWEVISTDDDTPEKYVEEKQL 176

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           ++   +++   M+ L+ RER I      ++  + ++ ++     +  RV Q+  +   K+
Sbjct: 177 KEILSDII---MNKLDERERLIVTLYYYED--LNMKEIAEILGYTESRVSQLHTKIMLKI 231

Query: 281 QESIQKQV 288
           ++ I+K +
Sbjct: 232 RKLIEKYL 239


>gi|167034905|ref|YP_001670136.1| flagellar biosynthesis sigma factor [Pseudomonas putida GB-1]
 gi|166861393|gb|ABY99800.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pseudomonas putida
           GB-1]
          Length = 246

 Score =  103 bits (258), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 42/243 (17%), Positives = 96/243 (39%), Gaps = 21/243 (8%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
             A + L+  +  LV +IA          + + +++  G IGL++   K+D  +G    T
Sbjct: 14  KDAQYELIERYAPLVKRIAYHLLARLPANVQVEDLIQAGMIGLLEVANKYDASKGASFET 73

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   I+ AM + + +             + +  N R +   ++A+     +  +   +A
Sbjct: 74  YAGIRIRGAMLDEVRKGDW--------APRSVHRNTRMVSDAMRAVEARTGRDAKDHEVA 125

Query: 164 KKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
            +L +S  +   I  +   +   S + L+   +       + L  D    +       E 
Sbjct: 126 AELQLSLDDYYGILNDTLGSRLFSFDDLLQDGE------HEGLHEDGASGQVEPARGLED 179

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +  +  LT +++ L  RER +       +  + L+ +     VS  RV Q+ ++   +++
Sbjct: 180 ERFQVALTEAIANLPERERLVLALYY--DEELNLKEIGEVLGVSESRVSQLHSQCAARLR 237

Query: 282 ESI 284
             +
Sbjct: 238 SRL 240


>gi|121488727|emb|CAJ18247.1| sigma 70-type sigma factor [Chlorobium limicola]
          Length = 165

 Score =  103 bits (258), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 39/174 (22%), Positives = 77/174 (44%), Gaps = 11/174 (6%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           ++++EGN+GL +A K+FD  RGF+  +Y++WWI+ ++ + +     +V++    N+    
Sbjct: 1   DLINEGNLGLXKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLP--LNRVGTL 58

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
             + +    L+   + +        +A  L++   +V           S++A     D N
Sbjct: 59  NKISKAYSQLEQEYERD---PNTKELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDN 115

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +  D L  D    +  L     R +    + RS+SVL PRE  +  +     
Sbjct: 116 --RLLDVLQNDGHMPDHTL----NRDSLTLEVERSLSVLAPREADVIRSYFGIG 163


>gi|26991031|ref|NP_746456.1| flagellar biosynthesis sigma factor [Pseudomonas putida KT2440]
 gi|148546765|ref|YP_001266867.1| flagellar biosynthesis sigma factor [Pseudomonas putida F1]
 gi|24986061|gb|AAN69920.1|AE016630_11 flagellar biosynthesis sigma factor FliA [Pseudomonas putida
           KT2440]
 gi|148510823|gb|ABQ77683.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pseudomonas putida F1]
 gi|313497816|gb|ADR59182.1| FliA [Pseudomonas putida BIRD-1]
          Length = 246

 Score =  103 bits (258), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 42/243 (17%), Positives = 96/243 (39%), Gaps = 21/243 (8%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
             A + L+  +  LV +IA          + + +++  G IGL++   K+D  +G    T
Sbjct: 14  KDAQYELIERYAPLVKRIAYHLLARLPANVQVEDLIQAGMIGLLEVANKYDASKGASFET 73

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   I+ AM + + +             + +  N R +   ++A+     +  +   +A
Sbjct: 74  YAGIRIRGAMLDEVRKGDW--------APRSVHRNTRMVSDAMRAVEARTGRDAKDHEVA 125

Query: 164 KKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
            +L +S  +   I  +   +   S + L+   +       + L  D    +       E 
Sbjct: 126 AELQLSLDDYYGILNDTLGSRLFSFDDLLQDGE------HEGLHEDGASGQVEPARGLEE 179

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +  +  LT +++ L  RER +       +  + L+ +     VS  RV Q+ ++   +++
Sbjct: 180 ERFQAALTEAIANLPERERLVLALYY--DEELNLKEIGEVLGVSESRVSQLHSQCAARLR 237

Query: 282 ESI 284
             +
Sbjct: 238 SRL 240


>gi|104782801|ref|YP_609299.1| flagellar biosynthesis sigma factor [Pseudomonas entomophila L48]
 gi|95111788|emb|CAK16512.1| sigma factor FliA [Pseudomonas entomophila L48]
          Length = 246

 Score =  103 bits (258), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 42/243 (17%), Positives = 94/243 (38%), Gaps = 21/243 (8%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
             A + LV  +  LV +IA          + + +++  G IGL++   K+D  +G    T
Sbjct: 14  KDAQYELVERYAPLVKRIAYHLLARLPANVQVEDLIQAGMIGLLEVANKYDASKGASFET 73

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   I+ AM + + R           N + +   +R ++           +  +   +A
Sbjct: 74  YAGIRIRGAMLDEV-RKGDWAPRSVHRNTRMVSDAIRSVEA-------RTGRDAKDHEVA 125

Query: 164 KKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
            +L +S  +   I  +   +   S + L+   +       + L  D    +       E 
Sbjct: 126 AELQLSLDDYYGILNDTLGSRLFSFDDLLQDGE------HEGLHEDGASGQLEPSRDLED 179

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +  ++ L  +++ L  RER +       +  + L+ +     VS  RV Q+ ++   +++
Sbjct: 180 ERFQSALADAIANLPERERLVLALYY--DEELNLKEIGEVLGVSESRVSQLHSQCAARLR 237

Query: 282 ESI 284
             +
Sbjct: 238 SRL 240


>gi|167767366|ref|ZP_02439419.1| hypothetical protein CLOSS21_01885 [Clostridium sp. SS2/1]
 gi|317497448|ref|ZP_07955768.1| sigma-70 family RNA polymerase sigma factor [Lachnospiraceae
           bacterium 5_1_63FAA]
 gi|167711341|gb|EDS21920.1| hypothetical protein CLOSS21_01885 [Clostridium sp. SS2/1]
 gi|316895234|gb|EFV17396.1| sigma-70 family RNA polymerase sigma factor [Lachnospiraceae
           bacterium 5_1_63FAA]
          Length = 207

 Score =  103 bits (258), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 54/262 (20%), Positives = 98/262 (37%), Gaps = 65/262 (24%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+L ++E + L       GD++A + LV  +LRLV  I   Y        +++S G IGL
Sbjct: 7   PLLPEEERHYLI--LSRQGDMNARNLLVEHNLRLVAHIVKKYHNLDREKEDMISIGVIGL 64

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++A+  +D  +G RL TY+   I                      +  L   LR+ K   
Sbjct: 65  IKAINTYDISKGHRLVTYAARCI----------------------ENELLMMLRQEKKT- 101

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                             + + SL   I    + +   +  L+ 
Sbjct: 102 ----------------------------------SKNTSLYEPIGIDKEGN---EIHLLD 124

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNP-RERRIFEARRLQE--NPVTLENLSSEFE 263
               QE  LI+K E+K     +   +  +   +E++    R       P+T + ++ +  
Sbjct: 125 ILGTQETDLIKKIEQKENIKRIYEELEKMEMNKEKKTLIMRYGLYGREPMTQKEVAKKLH 184

Query: 264 VSRERVRQIEARAFKKVQESIQ 285
           +SR  V +IE +A   ++  I+
Sbjct: 185 ISRSYVSRIEKKALMLLKSKIK 206


>gi|330808235|ref|YP_004352697.1| RNA polymerase sigma factor for flagellar operon [Pseudomonas
           brassicacearum subsp. brassicacearum NFM421]
 gi|327376343|gb|AEA67693.1| RNA polymerase sigma factor for flagellar operon [Pseudomonas
           brassicacearum subsp. brassicacearum NFM421]
          Length = 247

 Score =  103 bits (257), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 44/241 (18%), Positives = 97/241 (40%), Gaps = 17/241 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
             A + L+  +  LV +IA          + + +++  G IGL++   K+D  +G    T
Sbjct: 15  RDAQYELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSNKYDASKGASFET 74

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   I+ AM + + R           N + +   +R +    +A T  + K  +V A  
Sbjct: 75  YAGIRIRGAMLDEV-RKGDWAPRSVHRNTRMVSDAIRAI----EAKTGRDAKDHEVAAEL 129

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + L++ +   I  +   +   S + L+   +       + L  D+           E + 
Sbjct: 130 Q-LSLDDYYGILNDTLGSRLFSFDDLLQDGE------HEGLHEDNASAHMEPSRDLEDER 182

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            ++ L  +++ L  RER +       +  + L+ +     VS  RV Q+ ++   +++  
Sbjct: 183 FQSALAEAIANLPERERLVLALYY--DEELNLKEIGEVLGVSESRVSQLHSQCAARLRGR 240

Query: 284 I 284
           +
Sbjct: 241 L 241


>gi|257876008|ref|ZP_05655661.1| RNA polymerase sigma factor whiG [Enterococcus casseliflavus EC20]
 gi|257810174|gb|EEV38994.1| RNA polymerase sigma factor whiG [Enterococcus casseliflavus EC20]
          Length = 235

 Score =  103 bits (257), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 47/243 (19%), Positives = 100/243 (41%), Gaps = 18/243 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPIS--EVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
               +  +L LV ++              ++ + G IGLM A++KFDP +     +Y+  
Sbjct: 6   REAEIIKYLPLVERVVQRLSIKTADYESGDLYNIGVIGLMDALRKFDPSKKVPFESYAAI 65

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            IK A+ + + +   + +             + +     Q +  +  +      I K+L 
Sbjct: 66  RIKGAIIDEVRKHAKISRY--------KMAAVNQFYQARQELEQSLKREATDTEICKQLG 117

Query: 168 VSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           +++S++  +   L      SL   + +  +     +D +    +  E  L+ +E    +R
Sbjct: 118 INQSQLADIYESLHYLASVSLEDTLFAYQEEGMTLKDMVRDPAENVEDTLVAEE----KR 173

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             L   +  L  RE+ I      +E  +TL+ ++   EVS  RV QI  +   K++  I+
Sbjct: 174 TALVACIKKLGEREQLILSLYYTEE--LTLKEIAEILEVSIPRVSQIHGKTIAKLRTLIE 231

Query: 286 KQV 288
           +++
Sbjct: 232 EEL 234


>gi|311741871|ref|ZP_07715682.1| DNA-directed RNA polymerase sigma subunit SigF [Aeromicrobium
           marinum DSM 15272]
 gi|311314877|gb|EFQ84783.1| DNA-directed RNA polymerase sigma subunit SigF [Aeromicrobium
           marinum DSM 15272]
          Length = 258

 Score =  103 bits (257), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 44/259 (16%), Positives = 101/259 (38%), Gaps = 27/259 (10%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           +L +  +   A+R +   D+      V SHL     +A  YR  GL + ++    N+ L+
Sbjct: 17  LLTRAADAEPAERAQLEDDV------VRSHLGFANSLASRYRNRGLELDDLRQVANLALV 70

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV++F  +RG   A+++   I   ++ +       ++   +  Q  L  +LR+ K   +
Sbjct: 71  KAVRRFRADRG-DFASFAAVTISGELKRHFRDHGWTIRPPRSIQQ--LQVDLRKAK---E 124

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLV 205
                +     +  +A +L+V    V   +         SL+    +S+   +     + 
Sbjct: 125 EAAHESSVEPTLDELAARLHVPREAVAEASAANGCFRTTSLDEPRGASEAPLADRLAAVG 184

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            D +  E+               T +   L   ++ + + R      +T   +     VS
Sbjct: 185 DDMEFVEEWCD-----------FTPAWEGLTDEDKELIKLRFF--EGLTQREIGEAVGVS 231

Query: 266 RERVRQIEARAFKKVQESI 284
           + ++ +  +R  + ++ S+
Sbjct: 232 QMQISRRLSRVLQSLRTSM 250


>gi|228913674|ref|ZP_04077301.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|229090035|ref|ZP_04221286.1| RNA polymerase sigma-B factor [Bacillus cereus Rock3-42]
 gi|228693265|gb|EEL46975.1| RNA polymerase sigma-B factor [Bacillus cereus Rock3-42]
 gi|228845962|gb|EEM90986.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
          Length = 196

 Score =  103 bits (257), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 38/204 (18%), Positives = 95/204 (46%), Gaps = 16/204 (7%)

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           G +GL+ A++++D   G     +++  I   +++Y+      + +      +R+     +
Sbjct: 2   GMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRIKDLGGK 56

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQ 199
           +K  ++ +TD+  +  +++ IA  L +SE EV+ +          SL+ ++ ++   SS 
Sbjct: 57  IKLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENASDGSSV 116

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
            +   V +       + +  E+  RR +L    +VLN  E+ +     + E  +  ++  
Sbjct: 117 ARIESVGE-------VEQGYEQTERRLVLKDIFNVLNETEKSVIH--YIFEENLNQKDTG 167

Query: 260 SEFEVSRERVRQIEARAFKKVQES 283
               +S+  V +I+ +A  K++++
Sbjct: 168 ERLGISQMHVSRIKRQAISKLKQA 191


>gi|225871941|ref|YP_002753395.1| flagellar operon sigma factor FliA [Acidobacterium capsulatum ATCC
           51196]
 gi|225792596|gb|ACO32686.1| flagellar operon sigma factor FliA [Acidobacterium capsulatum ATCC
           51196]
          Length = 336

 Score =  103 bits (257), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 46/239 (19%), Positives = 99/239 (41%), Gaps = 18/239 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             + +  HL  V  +A          + + ++VS G +GL+ A++KFDP +  +  +Y+ 
Sbjct: 77  QEQQLMEHLPTVRYLARRIHERLPHHVELDDLVSAGVVGLLDAMRKFDPAKKVQFRSYAQ 136

Query: 107 WWIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
           + I+ A+ + +    WS          + L    R ++  ++A+T    +  Q   +A +
Sbjct: 137 FRIRGAILDSLRMLDWSP---------RELRRKGRAVEEAIRAVTARLGRAPQESEVAGE 187

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           + +   E   +   L G E     +  S+ +  +   +L  D    E   + +  +   R
Sbjct: 188 MGLPLHEYQQLLGELKGLEIGTLHVERSEDSGEEELAFLPND---PEDDPLFRCLKGEMR 244

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             L  ++  L  RER +      +E  +T++ +     V   RV Q+ + A   ++  +
Sbjct: 245 ERLMAAIDALPERERLVMTLYYYEE--MTMKEIGLTLGVVESRVSQMHSSAVLHLRALL 301


>gi|74317267|ref|YP_315007.1| RNA polymerase sigma-70 factor [Thiobacillus denitrificans ATCC
           25259]
 gi|74056762|gb|AAZ97202.1| RNA polymerase sigma-70 factor [Thiobacillus denitrificans ATCC
           25259]
          Length = 246

 Score =  103 bits (257), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 42/241 (17%), Positives = 98/241 (40%), Gaps = 16/241 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L+  ++ +V ++A    G   P     ++V  G IGL+ AV ++D  +  +   Y++
Sbjct: 13  KNDLLEQYMPMVKRLAHHMMGRLPPSVEEDDLVQAGMIGLLDAVSRYDEAQSAQFEAYAI 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ +M + + +S  +     +A Q      +R+++  + A+     +      IA+ +
Sbjct: 73  QRIRGSMIDELRQSDWM---PRSARQS-----MRKIEQAIAALQHQLGRQPSEGEIAEAM 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +  ++  SM     G + L             + D    D      + + +    N R 
Sbjct: 125 KIPLADYQSMLGDARGHQLLYFEDFGESDEDDSFLDKQSADE---ATMPLPQLLDANLRA 181

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +   +  L  RE+ +       E  + L  ++  F VS  R+ Q+  +A  +++  +++
Sbjct: 182 CIIAGIENLPEREQLLMSLYY--EQELNLREIAEVFGVSESRICQLHGQAIARLRARLKE 239

Query: 287 Q 287
            
Sbjct: 240 D 240


>gi|313115504|ref|ZP_07800969.1| putative RNA polymerase sigma-F factor [Faecalibacterium cf.
           prausnitzii KLE1255]
 gi|310622214|gb|EFQ05704.1| putative RNA polymerase sigma-F factor [Faecalibacterium cf.
           prausnitzii KLE1255]
          Length = 223

 Score =  103 bits (257), Expect = 3e-20,   Method: Composition-based stats.
 Identities = 41/240 (17%), Positives = 89/240 (37%), Gaps = 24/240 (10%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           D +     +  +L LV   A  +RG G+   ++ S G +GL++A   FD  RG   +TY+
Sbjct: 4   DKTRRDAFIEQNLGLVHACAGRFRGRGIEYDDLYSAGCMGLVKACDNFDESRGVCFSTYA 63

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
           +  I   +++ + R    VK+  +  +  +     R++   +           +  +A++
Sbjct: 64  VPVILGEIKK-LFRDSGTVKVSRSLKELGM-----RVQAAREHHMKVCGTEPTLSQLAEE 117

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK-EERKNR 224
           LN     +           SL                    + D Q  + +E  EE    
Sbjct: 118 LNEPAENITLAIQAAQPAMSLTPE---------------NEEEDRQMDIPVESPEEALAE 162

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L   +  L  ++R++   R       T    +     ++ ++ + E +   +++  +
Sbjct: 163 RISLEEVLHALPEQDRQLIRLRFYGN--KTQSETAKVLHTTQVQISRRERKILVQLRRRL 220


>gi|148359326|ref|YP_001250533.1| flagellar biosynthesis sigma factor FliA [Legionella pneumophila
           str. Corby]
 gi|296107373|ref|YP_003619073.1| RNA polymerase sigma factor for flagellar operon FliA [Legionella
           pneumophila 2300/99 Alcoy]
 gi|148281099|gb|ABQ55187.1| flagellar biosynthesis sigma factor FliA [Legionella pneumophila
           str. Corby]
 gi|295649274|gb|ADG25121.1| RNA polymerase sigma factor for flagellar operon FliA [Legionella
           pneumophila 2300/99 Alcoy]
          Length = 238

 Score =  103 bits (257), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 48/238 (20%), Positives = 100/238 (42%), Gaps = 19/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              LV +H  LV +IA    G     + + +++  G +GL++A + +D  +G    TY+ 
Sbjct: 15  QEALVKTHATLVKRIAHHLLGRLPQSVQLDDLIQSGMLGLLEAARHYDSSKGASFETYAG 74

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+  M + + R+  +         + ++ N R +   ++ +     +  +   IA++L
Sbjct: 75  IRIRGHMLDEVRRNDWV--------PRSVYRNSRMISDAVRILEHKLGREAKDNEIAEEL 126

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            VS ++   M       +S+++ +   D       D L  D             R +  N
Sbjct: 127 GVSLNDYHDMLQ-----DSISSHLYGFDDLGVT-DDILFDDEGNGSTEPHRNVMRSDMMN 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            LT+ +  L  +ER +       E  + L+ +    EVS  R+ QI ++A  +++  +
Sbjct: 181 RLTQVIDSLPRKERLVLSLYY--EQDLNLKEIGEILEVSESRISQILSQATHRIRSRL 236


>gi|89068737|ref|ZP_01156123.1| sigma32-like factor [Oceanicola granulosus HTCC2516]
 gi|89045700|gb|EAR51762.1| sigma32-like factor [Oceanicola granulosus HTCC2516]
          Length = 241

 Score =  103 bits (257), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 61/263 (23%), Positives = 114/263 (43%), Gaps = 39/263 (14%)

Query: 22  EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           E  K P+L   +E    ++++  GD ++   L+ SH R     A  +      I ++V+E
Sbjct: 7   EALKEPLLGLDQERQAIEKWQGEGDRASLELLLRSHARQAYAQATRWTDNPSYIEDLVAE 66

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           G I LM+A ++FD  R  R +TY+ WW++ AM E   R  +++ +   A        L  
Sbjct: 67  GMIALMRAAERFDLTREVRFSTYAAWWLRTAMAEAYGRISAVIDVPVKA--------LAE 118

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
            +   +A+   N+                              +L+    +S+++     
Sbjct: 119 ARRAGEALAQRNV-----------------------------VALDGGARASEEDD--MS 147

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           D L       E  +I    R     +L  +++ L+  ER I   R+L + P  ++ L++E
Sbjct: 148 DRLACPEPTPEDRIIRDSSRDAAARLLHAALASLSETERTILARRKLSDRPAPVDALAAE 207

Query: 262 FEVSRERVRQIEARAFKKVQESI 284
             +S  R+RQIE RA  ++++ +
Sbjct: 208 LSMSPTRLRQIETRAMGRLRQRL 230


>gi|116694211|ref|YP_728422.1| DNA-directed RNA polymerase sigma subunit / flagellum specific
           [Ralstonia eutropha H16]
 gi|113528710|emb|CAJ95057.1| DNA-directed RNA polymerase sigma subunit / flagellum specific
           [Ralstonia eutropha H16]
          Length = 238

 Score =  103 bits (257), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 43/235 (18%), Positives = 93/235 (39%), Gaps = 16/235 (6%)

Query: 54  VTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           V +H +LV +IA+         + I +++  G IGL+ A K+++   G R  TY+   I+
Sbjct: 14  VKAHAQLVRRIALQLAARLPASVQIDDLIQAGMIGLLDAAKRYEDTHGARFETYASQRIR 73

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            AM + +  +            + L    RR++   + +     +      +A+ + ++ 
Sbjct: 74  GAMLDEVRANDW--------QSRSLRQFTRRIERTQRGLEQKLGRAPLDSEVAEAMEMAL 125

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            E   +   + G + L+                L    DG    ++        R  L R
Sbjct: 126 DEYQLLLNEVYGCQLLHYEDFERSGEEDFLDRHLGGSDDGNPLTVL---MESGMREALIR 182

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           ++  L  RE+ +       +  + L  + +  +V+  RV QI  +A  +++  ++
Sbjct: 183 AIDRLPEREKLVLSLCY--DQELNLREIGAVLDVTESRVCQIRGQAITRLRNQLR 235


>gi|218245540|ref|YP_002370911.1| RNA polymerase sigma factor SigF [Cyanothece sp. PCC 8801]
 gi|257058577|ref|YP_003136465.1| RNA polymerase sigma factor SigF [Cyanothece sp. PCC 8802]
 gi|218166018|gb|ACK64755.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cyanothece
           sp. PCC 8801]
 gi|256588743|gb|ACU99629.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cyanothece
           sp. PCC 8802]
          Length = 255

 Score =  103 bits (257), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 50/256 (19%), Positives = 111/256 (43%), Gaps = 16/256 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG-YGLPISEVVSEGNIGLMQAVKKFD 94
            L   Y  +  L+  ++LV  H  LV ++A         P  ++   G +GL+ A+++F+
Sbjct: 12  ELLITYSRNPSLALRNQLVELHTGLVRQVAHRISNQCTEPYEDLEQIGYLGLINAIERFN 71

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P +G   +++++ +I+  M  Y+    S+++I     +  L+   ++++     +T +  
Sbjct: 72  PHQGCAFSSFAIPYIRGEMLHYLRDKGSVMRIPRRWQE--LYNKGKKVRK---QLTTSLG 126

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +  +   +A  L VS  E       L      SL++ IN +  ++  + + L        
Sbjct: 127 RTPKDQELADALQVSLEEWHECELALQNRMLVSLDSTINQNTDSTVSFGETLPD------ 180

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
                K+ ++  R  L R+MS L  + +   E   ++E P   +  +    +S   V + 
Sbjct: 181 HRYQAKQSQEEDRLQLQRAMSQLEDKTKEAIECVFIKELPR--KEAAKRIGMSPMTVTRH 238

Query: 273 EARAFKKVQESIQKQV 288
             +  K++   ++ QV
Sbjct: 239 LHKGIKQLIILLESQV 254


>gi|326796449|ref|YP_004314269.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Marinomonas
           mediterranea MMB-1]
 gi|326547213|gb|ADZ92433.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Marinomonas
           mediterranea MMB-1]
          Length = 228

 Score =  103 bits (257), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 37/237 (15%), Positives = 91/237 (38%), Gaps = 18/237 (7%)

Query: 51  HRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
             ++  +  LV KIA          + + ++   G IGL++A K+F+  +G    TY+  
Sbjct: 2   DAIIQQYGYLVKKIAYHLLARLPNHVDVDDLTQAGMIGLIEAYKRFESTKGASFETYAGI 61

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+ A+ + + +S            + +  N R +   ++ +     +      +++ + 
Sbjct: 62  RIRGAIMDEMRKSDW--------APRSVRRNGRAVTEAIKELEGKLGRDVTDNEVSEHMG 113

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  E   +        S++  + S ++           + +  +    +  E    +  
Sbjct: 114 ISVDEYHEIMR-----SSMSTQLFSYEEMLESEHGSNEINIESDDSQPYDVVEEGGFQKQ 168

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   +  L  RE+ +          + L+ + +   VS  RV QI ++A  +++  +
Sbjct: 169 LAVEIDKLPEREKLVLSLYY--NEELNLKEIGAVLGVSESRVSQIHSQAAMRLRARL 223


>gi|47168808|pdb|1RP3|A Chain A, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma
           Complex, Sigma-28FLGM
 gi|47168810|pdb|1RP3|C Chain C, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma
           Complex, Sigma-28FLGM
 gi|47168812|pdb|1RP3|E Chain E, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma
           Complex, Sigma-28FLGM
 gi|47168814|pdb|1RP3|G Chain G, Cocrystal Structure Of The Flagellar SigmaANTI-Sigma
           Complex, Sigma-28FLGM
 gi|47169132|pdb|1SC5|A Chain A, Sigma-28(Flia)FLGM COMPLEX
          Length = 239

 Score =  103 bits (257), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 47/240 (19%), Positives = 101/240 (42%), Gaps = 23/240 (9%)

Query: 50  AHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L+  +L LV  IA     +    + I +++S G IGL++AV     E   R   Y  
Sbjct: 14  REELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIK 73

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             IK A+ +Y+               +++    RR+K  ++ + +   +      +AK+L
Sbjct: 74  LRIKGAIYDYLR--------SLDFGSRQVREKERRIKEVVEKLKEKLGREPTDEEVAKEL 125

Query: 167 NVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            +S  E+     ++  +   SL  +     ++ S+               + E+  ++  
Sbjct: 126 GISTEELFKTLDKINFSYILSLEEVFRDFARDYSELI--------PSSTNVEEEVIKREL 177

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              +  ++S L  RE+ + +    +E P   + ++   E S  RV Q++A+A ++++E +
Sbjct: 178 TEKVKEAVSKLPEREKLVIQLIFYEELPA--KEVAKILETSVSRVSQLKAKALERLREML 235


>gi|291542064|emb|CBL15174.1| RNA polymerase sigma factor, sigma-70 family [Ruminococcus bromii
           L2-63]
          Length = 219

 Score =  103 bits (257), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 44/235 (18%), Positives = 94/235 (40%), Gaps = 21/235 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            ++L   ++ LV      + G G+   E+ + G +GL +A+  FD  R  + +TY+   I
Sbjct: 4   KNKLADKNMGLVHACCKRFSGKGIEYEELFASGCLGLAKAINNFDESRNLQFSTYAFPVI 63

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
              ++  + R    +++  T   K L   + RL    +      L    V  +A++L+ S
Sbjct: 64  MGEIKR-LFRDGGAIRVSRTL--KELSLAISRLNNESKLKNGREL---TVSELAERLDTS 117

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           E ++I          SL A      +  S+    L    D  +  + E       R  L 
Sbjct: 118 EEKIIDALNSTRVPLSLTA------EYDSEGNPQLDVPTDDIQDEISE-------RLSLE 164

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            ++  L   +R+I + R  +    T    +    +++ ++ + E +    +++ +
Sbjct: 165 EAVKSLCETDRKIIQLRYYR--SKTQTQTAKILSMTQVQISRREKKILTAIRDKM 217


>gi|268611133|ref|ZP_06144860.1| sporulation sigma factor SigE [Ruminococcus flavefaciens FD-1]
          Length = 232

 Score =  103 bits (257), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 50/249 (20%), Positives = 92/249 (36%), Gaps = 63/249 (25%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L +QEE  +  +  E  D +A   L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 30  PPLTRQEEAEVFMKL-EANDPAARKYLIEHNLRLVVYIAKKFESSGVGIEDLVSIGTIGL 88

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F P +  +LATY+   I+  +  +                      LR+   + 
Sbjct: 89  IKAVNTFCPTKNIKLATYASRCIENEILMF----------------------LRKSSQYR 126

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
             ++ +                       +N    G+E L + +  +D++          
Sbjct: 127 NELSIDEP---------------------LNIDYDGNELLLSDVLGTDEDIVNKGIETEA 165

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           + +     + E  ER+                 R I E R         T + ++    +
Sbjct: 166 EREILRNAVSELSERE-----------------REIMEMRFGLVDGKEKTQKEVADSIGI 208

Query: 265 SRERVRQIE 273
           S+  + ++E
Sbjct: 209 SQSYISRLE 217


>gi|317969500|ref|ZP_07970890.1| RNA polymerase sigma factor, sigma-70 family protein [Synechococcus
           sp. CB0205]
          Length = 315

 Score =  103 bits (257), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 56/266 (21%), Positives = 109/266 (40%), Gaps = 22/266 (8%)

Query: 38  AKRYREHGD-------------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV----VS 80
            +R+++H D             L A  +LV  +L LV      +R       +     + 
Sbjct: 42  IQRWQQHPDGPSHAPKPLRRSALRAREQLVRHNLGLVAHTWGRHRCSLPAHDDTTADALQ 101

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           E  + L++A +KFDP +G+R +TY+ +W++    E+  R+   ++    A +  +     
Sbjct: 102 EAALNLVRAAEKFDPAKGYRFSTYATFWVRRGFTEFEQRAKRAIRFP--AEKAAVVLKAL 159

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLN--VSESEVISMNCRLAGDESLNALINSSDKNSS 198
           RL    QA T +    E + A  K     ++  ++     +     + +      D +  
Sbjct: 160 RLSQQQQATTGDEPSLEWLAAQLKFDGKAMNAEQLAEFIRQWDATRTGSLDGAEDDGDEK 219

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
                L      Q     + +E   +   L + MS L+ +E R+   R L+  P++   L
Sbjct: 220 GGCSRLDLASLQQAAEQQQTQEPDPQHAALPQLMSCLDEQEHRLIRNRYLRRPPLSPCQL 279

Query: 259 SSEF-EVSRERVRQIEARAFKKVQES 283
                 + RE++ Q+EA A  K+++S
Sbjct: 280 RRSMGGMQREQLEQLEATALNKLRQS 305


>gi|251797867|ref|YP_003012598.1| sporulation sigma factor SigE [Paenibacillus sp. JDR-2]
 gi|247545493|gb|ACT02512.1| RNA polymerase, sigma 28 subunit, SigE [Paenibacillus sp. JDR-2]
          Length = 240

 Score =  103 bits (257), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 54/262 (20%), Positives = 103/262 (39%), Gaps = 59/262 (22%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L ++EE  L  +    GD +    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 38  PPLTREEEEYLLDKL-PSGDTAIRAMLIERNLRLVVYIARKFENTGIHIEDLVSIGAIGL 96

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FDPE+  +LATY+   I+  +  Y+ R+                          
Sbjct: 97  IKAVNTFDPEKKIKLATYASRCIENEILMYLRRNSKT----------------------- 133

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                             +  VS  E ++++    G+E L + +  ++ ++         
Sbjct: 134 ------------------RTEVSFDEPLNID--WDGNELLLSDVLGTENDTIYRNIEEQV 173

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           D     + L +  ER+     L   ++                    T ++++    +S+
Sbjct: 174 DRKLLHKALDKLSERERIIMELRFGLA---------------DGEEKTQKDVADLLGISQ 218

Query: 267 ERVRQIEARAFKKVQESIQKQV 288
             + ++E R  K++++   K V
Sbjct: 219 SYISRLEKRIIKRLRKEFNKMV 240


>gi|149908440|ref|ZP_01897103.1| flagellar biosynthesis sigma factor FliA [Moritella sp. PE36]
 gi|149808603|gb|EDM68538.1| flagellar biosynthesis sigma factor FliA [Moritella sp. PE36]
          Length = 241

 Score =  102 bits (256), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 48/240 (20%), Positives = 88/240 (36%), Gaps = 19/240 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +  V     LV +IA        P   + +++  G IGL+ A + FD  +G    TY+ 
Sbjct: 14  QNHAVEQFGYLVKRIAHHLLLRLPPSVQLDDLIQSGMIGLLDAARNFDGSKGASFETYAG 73

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ +M + + R    V      N + +   + R++              +   IA +L
Sbjct: 74  IRIRGSMIDEMRR-GDWVPRSVHKNGRNIAAAIDRIEKQ-------TGTDAKDTDIAGEL 125

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            VS ++  SM      D +   ++   D   S    +  Y+           E+R   + 
Sbjct: 126 GVSLADYHSMLM----DVNSGHILAVEDLTVSNEDAYSAYEGKSSTPCAEFSEQR--FQQ 179

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L   +  L  RE  +       +  + L  +     VS  RV QI ++A  +V+  +  
Sbjct: 180 ALADCIKTLPERESLVLSLYY--DEELNLREIGEVLSVSESRVSQIHSQAMHRVKARMHA 237


>gi|309789348|ref|ZP_07683938.1| RNA polymerase sigma factor for flagellar operon [Shigella
           dysenteriae 1617]
 gi|308922742|gb|EFP68259.1| RNA polymerase sigma factor for flagellar operon [Shigella
           dysenteriae 1617]
          Length = 229

 Score =  102 bits (256), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 46/240 (19%), Positives = 103/240 (42%), Gaps = 17/240 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 3   KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 62

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   + +L+  L        +      +A++L
Sbjct: 63  QCIRGAMLDEL-RSRDWVPRSVRRNAREVAQAIGQLEQEL-------GRNATETEVAERL 114

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +  ++   M      D + + L +  +          +   D Q +  +++    N R 
Sbjct: 115 GIDIADYRQMLL----DTNNSQLFSYDEWREEHGDSIELVTDDYQRENPLQQLLDSNLRQ 170

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +E EV   RV Q+ ++A K+++  + K
Sbjct: 171 RVMEAIETLPEREKLVLTLYY--QEELNLKEIGAELEVGESRVSQLHSQAIKRLRTKLGK 228


>gi|257866395|ref|ZP_05646048.1| RNA polymerase sigma factor whiG [Enterococcus casseliflavus EC30]
 gi|257873089|ref|ZP_05652742.1| RNA polymerase sigma factor whiG [Enterococcus casseliflavus EC10]
 gi|257800353|gb|EEV29381.1| RNA polymerase sigma factor whiG [Enterococcus casseliflavus EC30]
 gi|257807253|gb|EEV36075.1| RNA polymerase sigma factor whiG [Enterococcus casseliflavus EC10]
          Length = 235

 Score =  102 bits (256), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 47/243 (19%), Positives = 101/243 (41%), Gaps = 18/243 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPIS--EVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
               +  +L LV ++              ++ + G IGLM A++KFDP +     +Y+  
Sbjct: 6   REAEIIKYLPLVERVVQRLSIKTADYESGDLYNIGVIGLMDALRKFDPSKKVPFESYAAI 65

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            IK A+ + + +   + +             + +     Q +  +  +      I K+L 
Sbjct: 66  RIKGAIIDEVRKHAKISRY--------KMAAVNQFYQARQELEQSLKREATDTEICKQLG 117

Query: 168 VSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           +++S++  +   L      SL   + +  +     +D +    +  E+ L+ +E    +R
Sbjct: 118 INQSQLADIYESLHYLASVSLEDTLFAYQEEGMTLKDMVRDPAENVEETLVAEE----KR 173

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             L   +  L  RE+ I      +E  +TL+ ++   EVS  RV QI  +   K++  I+
Sbjct: 174 TALVACIKKLGEREQLILSLYYTEE--LTLKEIAEILEVSIPRVSQIHGKTIAKLRTLIE 231

Query: 286 KQV 288
           +++
Sbjct: 232 EEL 234


>gi|169834796|ref|YP_001715634.1| RNA polymerase sigma-E factor [Clostridium botulinum A3 str. Loch
           Maree]
 gi|169408903|gb|ACA57313.1| RNA polymerase sigma-E factor [Clostridium botulinum A3 str. Loch
           Maree]
          Length = 296

 Score =  102 bits (256), Expect = 4e-20,   Method: Composition-based stats.
 Identities = 55/284 (19%), Positives = 125/284 (44%), Gaps = 48/284 (16%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHR-----------------LVTSHLRLVVKIAM 66
             I +LE +E+  L  +  +  D+ + ++                 L+  +  L+ K+A 
Sbjct: 44  SYIKLLEIKEDKELLIKSFDENDIDSINKYYVGKYKKTKDKKYLNSLIEKNQNLIFKVAN 103

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y+   + + ++  +G +G ++AV KFD  +  + +TY+ +WI+A +  +   +      
Sbjct: 104 KYKNKNIELQDLTQQGFLGFLKAVDKFDESKKVKFSTYAYYWIEAEISSFFNFN------ 157

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
              +      +  R+LKG+   I   +  PE V    +  N S               S+
Sbjct: 158 VDGSLSISSSYQHRKLKGYENGILSEDELPELVKNHIQLKNNS--------------ISV 203

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           +++++  +  +S   D+L+   D     +  K   KN       ++S L+ +E+ I  +R
Sbjct: 204 DSIVHGKENENS--ADYLLGKTDINYNNIESKIVMKN-------ALSGLSEKEKSIIISR 254

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
            + E     ++++ EF+VS + ++ +   A  K++ +I+K + +
Sbjct: 255 IIYEKKY--KDIAKEFKVSYQYIQYLYKNAIGKLKRTIKKDILV 296


>gi|68164561|gb|AAY87290.1| predicted flagellar-specific RNA polymerase sigma factor FliA
           [uncultured bacterium BAC17H8]
          Length = 240

 Score =  102 bits (256), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 50/239 (20%), Positives = 100/239 (41%), Gaps = 26/239 (10%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGL---PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
             L+TSH+ LV +IA    G       I +++  G  GL+ A + +    G   A+Y+  
Sbjct: 13  EELITSHMELVRQIAWHMHGRLHSSIEIEDLIQIGYFGLVTAAQNYTLREGATFASYAGI 72

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+ A+ +++ +S +L +  T   QK+     R L+  L        +      +A+ + 
Sbjct: 73  RIRGAIVDHLRKSSNLCRT-TIEMQKKANVAGRELRNRL-------GREPTSAEMAEHMC 124

Query: 168 VSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           +SE E+ +       +   SL+++            D      +  E    E    +  R
Sbjct: 125 ISEDEMHNWEHAFQANVHQSLDSV-----------YDEFSIWFESPENTPEENINEEELR 173

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           N+L  ++  L  RE  + +   ++E  + +  ++   EV+  RV QI+  A   ++  +
Sbjct: 174 NLLKEALRTLPEREALVIQLYYVEE--LNVYEIAEVLEVTTGRVSQIKKSAIGSLRHFL 230


>gi|160944585|ref|ZP_02091813.1| hypothetical protein FAEPRAM212_02099 [Faecalibacterium prausnitzii
           M21/2]
 gi|158444367|gb|EDP21371.1| hypothetical protein FAEPRAM212_02099 [Faecalibacterium prausnitzii
           M21/2]
 gi|295103334|emb|CBL00878.1| RNA polymerase sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii SL3/3]
          Length = 224

 Score =  102 bits (256), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 41/243 (16%), Positives = 92/243 (37%), Gaps = 23/243 (9%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           D +     +T +L LV   A  +RG G+   ++ S G +GL++A   FD  RG   +TY+
Sbjct: 4   DKTRREAFITQNLGLVHACAGRFRGRGMEYDDLYSAGCVGLIKAYDNFDESRGVCFSTYA 63

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
           +  I   +++ + R    VK+  +  +  +     R++   +           +  +A++
Sbjct: 64  VPVILGEIKK-LFRDGGTVKVSRSLKELGM-----RVQAAREHTMKLCGAEPTLQQLAEQ 117

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-R 224
           L+     V           SL                    D D Q  + +E  E +   
Sbjct: 118 LDEPIENVALAIQAAQPAMSLTPEGG--------------EDGDRQLDIPVESPEEELAD 163

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L   +  L  +++++   R       T    +     ++ ++ + E +   +++  +
Sbjct: 164 RISLAEVIEALPEQDKQLIRLRFYGN--RTQSETAKALHTTQVQISRRERKILIRLRARL 221

Query: 285 QKQ 287
            ++
Sbjct: 222 LEE 224


>gi|160880422|ref|YP_001559390.1| FliA/WhiG family RNA polymerase sigma factor [Clostridium
           phytofermentans ISDg]
 gi|160429088|gb|ABX42651.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           phytofermentans ISDg]
          Length = 207

 Score =  102 bits (256), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 50/248 (20%), Positives = 86/248 (34%), Gaps = 62/248 (25%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L  +EE  +  + +  G+  A   L+  +LRLV  I   Y        +++S G IGL+
Sbjct: 7   PLSAKEENEMLLQCK-AGNKVARDTLIERNLRLVAHIVKKYNTPDRETDDLISIGTIGLI 65

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +++  FD  +G RLATY+   I                         L   LR  K   +
Sbjct: 66  KSIDTFDSTKGIRLATYASRCIDN----------------------ELLMMLRSGKKQAR 103

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                                     + +   +  D          + N     D +   
Sbjct: 104 E-------------------------VYLYEPIGSD---------KEGNEINLLDVI--- 126

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVS 265
               E ++   E ++N + + T   + LN RE+ I   R     E  +T   ++ +  +S
Sbjct: 127 ESTDEDIVDIFEIQENIKRLYTFLNTALNEREQEIIIMRYGLSGEKEITQREIADKLGIS 186

Query: 266 RERVRQIE 273
           R  V +IE
Sbjct: 187 RSYVSRIE 194


>gi|51892359|ref|YP_075050.1| sporulation sigma factor SigE [Symbiobacterium thermophilum IAM
           14863]
 gi|51856048|dbj|BAD40206.1| RNA polymerase sigma factor similar to B. subtilis SigE
           [Symbiobacterium thermophilum IAM 14863]
          Length = 251

 Score =  102 bits (256), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 57/258 (22%), Positives = 105/258 (40%), Gaps = 59/258 (22%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L  +EE  L +R  + GD S  + L+  +LRLVV IA  +   G+ + ++VS G IGL
Sbjct: 49  PPLTGEEEAALLQRLTQ-GDESVKNTLIERNLRLVVYIARKFDNTGIWVEDLVSIGTIGL 107

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AVK FDP +  +LATY+   I+  +  Y+ R+                          
Sbjct: 108 IKAVKTFDPSKRIKLATYASKCIENEILMYLRRASRT----------------------- 144

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                             +  VS  E   +N    G+E L + +  +D + +     L  
Sbjct: 145 ------------------RSEVSFDEP--LNKDWEGNELLLSDVMGTDSDITY--RGLEE 182

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           + D         +     + ++     +++ RER             T + ++    +S+
Sbjct: 183 EVDRMLLRKAMAKLTGREKRIMELRFGLVDGRER-------------TQKEVADLLGISQ 229

Query: 267 ERVRQIEARAFKKVQESI 284
             + ++E R FK++++ I
Sbjct: 230 SYISRLEKRIFKRLKKEI 247


>gi|331696243|ref|YP_004332482.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit [Pseudonocardia
           dioxanivorans CB1190]
 gi|326950932|gb|AEA24629.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Pseudonocardia dioxanivorans CB1190]
          Length = 273

 Score =  102 bits (256), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 45/264 (17%), Positives = 94/264 (35%), Gaps = 30/264 (11%)

Query: 31  KQEEYVLAKRYREHGDL----SAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIG 85
             EE  L +      D     +    L+ + L +  ++   Y         ++    +  
Sbjct: 25  AAEEAQLRRLSTLPRDDPEHDALRTELILAFLPVAERLVGRYATSRPWSRDDIAQAASEA 84

Query: 86  LMQAVKKFDPER-GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           +++AV  +DP+R    +  Y +  ++ A+  +       +++      K L   +R+  G
Sbjct: 85  VVRAVDHWDPDRARGDVLGYLVPCVRGAILRWFRDQSWSLRVPRRV--KDLSVAIRQAVG 142

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L        +P     +A++L+V   E++               + + D + +   D  
Sbjct: 143 PLSQELGRAPRP---SELARRLDVDVDEIVEA-------------LYAEDNHQAATLDAP 186

Query: 205 VYDHDGQEQVLIEKEERKNRR----NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
             D D      I   + +  R      L   ++ L+ RERRI   R       T   +  
Sbjct: 187 AGDDDSSPGERIGDVDPRLGRVEDVETLRPLLAGLSERERRIVVLRFFCG--RTQSQIGE 244

Query: 261 EFEVSRERVRQIEARAFKKVQESI 284
           E  VS+  V ++ A    K++  +
Sbjct: 245 EIGVSQMHVSRLLAGTLAKLRAGM 268


>gi|157161393|ref|YP_001458711.1| flagellar biosynthesis sigma factor [Escherichia coli HS]
 gi|157067073|gb|ABV06328.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           HS]
          Length = 239

 Score =  102 bits (256), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 102/240 (42%), Gaps = 17/240 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   + +L+  L        +      +A++L
Sbjct: 73  QRIRGAMLDEL-RSRDWVPRSVRRNAREVVQAIGQLEQEL-------GRNATETEVAERL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +  ++   M      D + + L +  +          +   D Q +  +++    N R 
Sbjct: 125 GIDIADYRQMLL----DTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 181 RVMEAIETLPEREKLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 238


>gi|54294669|ref|YP_127084.1| flagellar biosynthesis sigma factor [Legionella pneumophila str.
           Lens]
 gi|53754501|emb|CAH15985.1| sigma factor 28 [Legionella pneumophila str. Lens]
          Length = 238

 Score =  102 bits (256), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 48/238 (20%), Positives = 100/238 (42%), Gaps = 19/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              LV +H  LV +IA    G     + + +++  G +GL++A + +D  +G    TY+ 
Sbjct: 15  QEALVKTHATLVKRIAHHLLGRLPQSVQLDDLIQSGMLGLLEAARHYDSSKGASFETYAG 74

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+  M + + R+  +         + ++ N R +   ++ +     +  +   IA++L
Sbjct: 75  IRIRGHMLDEVRRNDWV--------PRSVYRNSRMISDAVRILEHKFGREAKDNEIAEEL 126

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            VS ++   M       +S+++ +   D       D L  D             R +  N
Sbjct: 127 GVSLNDYHDMLQ-----DSISSHLYGFDDLGVT-DDVLFDDEGNGSTEPHRNVMRSDMMN 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            LT+ +  L  +ER +       E  + L+ +    EVS  R+ QI ++A  +++  +
Sbjct: 181 RLTQVIDSLPRKERLVLSLYY--EQDLNLKEIGEILEVSESRISQILSQATHRIRSRL 236


>gi|158340491|ref|YP_001521485.1| RNA polymerase sigma-2 subunit [Acaryochloris marina MBIC11017]
 gi|158310732|gb|ABW32346.1| RNA polymerase sigma-2 subunit domain protein [Acaryochloris marina
           MBIC11017]
          Length = 697

 Score =  102 bits (256), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 42/224 (18%), Positives = 93/224 (41%), Gaps = 12/224 (5%)

Query: 1   MNRKNMSIIVNGEIGLSRYI-HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLR 59
           M    ++   +  I L  Y+   + + P+ + ++E  L ++ +  G  ++   L+  H+R
Sbjct: 1   MTTTTIASPFSDGIRLPEYLVQFLHRFPIPDPEQELDLIRKAK-RGHETSLSWLMIGHVR 59

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           LV K+A  Y        +++ EG +G+  AV KFD  +G + +TY+  WI+  ++ +  +
Sbjct: 60  LVAKLAKQYAWTLDDAQDLIQEGMLGIRHAVGKFDSTKGCKFSTYARGWIRGYIRRFCYK 119

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGH-----LQAITDNNLKPEQVVAIAKKLNVSESEVI 174
           +    ++     ++     + RL+       L+ I        + +        S  E+ 
Sbjct: 120 N-RPKQLRLPEKKQVHLDRVYRLQNEFPDANLEEIARKANLKLEYIEDLLYWGRSFQEIP 178

Query: 175 SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
             +  +  D S      + D+   ++ D  +        VLI+ 
Sbjct: 179 DWHEFVIDDASF----YTDDEEYDEYFDIELEPETKTNLVLIKA 218


>gi|228899672|ref|ZP_04063925.1| RNA polymerase sigma-B factor [Bacillus thuringiensis IBL 4222]
 gi|228859981|gb|EEN04388.1| RNA polymerase sigma-B factor [Bacillus thuringiensis IBL 4222]
          Length = 203

 Score =  102 bits (256), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 38/210 (18%), Positives = 97/210 (46%), Gaps = 16/210 (7%)

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++  G +GL+ A++++D   G     +++  I   +++Y+      + +      +R+
Sbjct: 3   EDIIQVGMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRI 57

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSS 193
                ++K  ++ +TD+  +  +++ IA  L +SE EV+ +          SL+ ++ +S
Sbjct: 58  KDLGGKIKLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENS 117

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
              SS  +   V +       + +  E+  RR +L    +VLN  E+ +      +   +
Sbjct: 118 SDGSSVARIESVGE-------VEQGYEQTERRLVLEDIFNVLNDMEKSVIHYIFGEN--L 168

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQES 283
             ++      +S+  V +I+ +A  K++++
Sbjct: 169 NQKDTRERLGISQMHVSRIKRQAISKLKQA 198


>gi|315127302|ref|YP_004069305.1| flagellar biosynthesis sigma factor [Pseudoalteromonas sp. SM9913]
 gi|315015816|gb|ADT69154.1| flagellar biosynthesis sigma factor [Pseudoalteromonas sp. SM9913]
          Length = 236

 Score =  102 bits (256), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 43/238 (18%), Positives = 88/238 (36%), Gaps = 18/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + +V  H  LV K+A          + + +++  G IGL++A K FD  +G    T++ 
Sbjct: 9   LNMIVEKHASLVKKVACHLIARLPASVQLDDLIQSGMIGLIEASKNFDASKGASFETFAG 68

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + R    V        + +   +  L+  L        +  +   +A+KL
Sbjct: 69  IRIRGAMIDEMRR-GDWVPRSVHRKSRLVAETIVALENSLN-------REPKDSEVAEKL 120

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +S +E   +   +   + L       D +            D          + +    
Sbjct: 121 EISLNEYHHILNDVNVSKVLGIEDLGIDDDVITPHG-----QDLALDKPFNNVKNERFNE 175

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L  ++  L  ++  +        + + L+ +    +VS  RV QI  +A  K++  I
Sbjct: 176 SLLSAIKSLPEKDAMVLSLYY--NDEMNLKEIGHILDVSESRVSQIHGQAMIKLKAKI 231


>gi|331653330|ref|ZP_08354335.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli M718]
 gi|323174562|gb|EFZ60183.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           LT-68]
 gi|331049428|gb|EGI21500.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli M718]
          Length = 239

 Score =  102 bits (256), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 102/240 (42%), Gaps = 17/240 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KHSLWQRYIPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   + +L+  L        +      +A++L
Sbjct: 73  QRIRGAMLDEL-RSRDWVPRSVRRNAREVAQAIGQLEQEL-------GRNATETEVAERL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +  ++   M      D + + L +  +          +   D Q +  +++    N R 
Sbjct: 125 GIDIADYRQMLL----DTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 181 RVMEAIETLPEREKLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 238


>gi|260598417|ref|YP_003210988.1| flagellar biosynthesis sigma factor [Cronobacter turicensis z3032]
 gi|260217594|emb|CBA31853.1| RNA polymerase sigma factor for flagellar operon [Cronobacter
           turicensis z3032]
          Length = 239

 Score =  102 bits (256), Expect = 5e-20,   Method: Composition-based stats.
 Identities = 46/240 (19%), Positives = 102/240 (42%), Gaps = 17/240 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   + +L+  L        +    + +A++L
Sbjct: 73  QRIRGAMLDEL-RSRDWVPRSVRRNAREVAQAIGQLEQEL-------GRNATELEVAERL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   E   M      D + + L +  +          +   D Q +  + +    N R 
Sbjct: 125 SIPLEEYRQMLL----DTNNSQLFSYDEWREEHGDSIELVTEDNQNENPLHQLLEGNLRE 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 181 RVMEAIESLPEREQMVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 238


>gi|121488765|emb|CAJ18267.1| sigma 70-type sigma factor [Chlorobium phaeobacteroides]
          Length = 165

 Score =  102 bits (255), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 38/174 (21%), Positives = 76/174 (43%), Gaps = 17/174 (9%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + +     +V++    N+    
Sbjct: 1   DLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLP--LNRVGTL 58

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
             + +    L+   + +        +A  L++   +V           S++A     D N
Sbjct: 59  NKISKAYSQLEQEFERD---PNTRELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDN 115

Query: 197 ---SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
                   D  + DH   +  L  + ER          +SVL PRE  +  +  
Sbjct: 116 RLLDVLQNDGHLPDHGLNKDSLTLEVERS---------LSVLAPREADVIRSYF 160


>gi|218439022|ref|YP_002377351.1| RNA polymerase sigma factor SigF [Cyanothece sp. PCC 7424]
 gi|218171750|gb|ACK70483.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cyanothece
           sp. PCC 7424]
          Length = 257

 Score =  102 bits (255), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 47/251 (18%), Positives = 104/251 (41%), Gaps = 16/251 (6%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGF 99
           Y  +  L   ++LV  +  LV ++A         P  ++   G +GL++A+++F+P++G 
Sbjct: 19  YSRNPTLKLRNQLVELNAGLVRQVAHRISRQCCEPYEDLEQVGYLGLIRAIERFNPQQGS 78

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
             +++++ +I+  +  Y+    S+++I      + L+   ++L+  L        +    
Sbjct: 79  AFSSFAIPYIRGEILHYLRDRGSVMRIPRR--WQDLYTKGKKLRKELAQTLGRQPRE--- 133

Query: 160 VAIAKKLNVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
             IA+ L +S  E       L      SL+A +N +      + D L       +Q + E
Sbjct: 134 SEIAQALGISSQEWNECQLALQNRLLVSLDATVNQAHDGMISFGDTLPDPKSQGQQKIQE 193

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
                  R  L ++MS L  + +   E   L + P   +  +    +S   V +   +  
Sbjct: 194 D------RLQLQKAMSQLEDKTKAAIECVFLWDLPR--KEAAKRIGISPMTVTRHLQKGL 245

Query: 278 KKVQESIQKQV 288
            ++   ++ Q 
Sbjct: 246 DQLIALLRPQA 256


>gi|295102468|emb|CBL00013.1| RNA polymerase sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii L2-6]
          Length = 224

 Score =  102 bits (255), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 42/240 (17%), Positives = 90/240 (37%), Gaps = 23/240 (9%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           D +     +  +L LV   A  +RG G+   ++ S G +GL++A   FD  RG   +TY+
Sbjct: 4   DKTRRSAFIEQNLGLVHSCAGRFRGRGIEYDDLYSAGCMGLVKAYDGFDESRGVCFSTYA 63

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
           +  I   +++ + R    VK+  +  +  L     R+    +  +        +  +A++
Sbjct: 64  VPVILGEIKK-LFRDGGTVKVSRSLKELSL-----RINAAREHHSKLCGAEPTLSQLAEE 117

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN-R 224
           L  S   +           SL                    + D Q  + +E  E +   
Sbjct: 118 LGESVENITLAIQAAQPAVSLTPENR--------------EEGDRQMDIPVESPEEELAD 163

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +  L   +  L   +R I + R       T  + +     ++ ++ + E +  K +++ +
Sbjct: 164 KIGLAEVLKSLPEEDRLIIQLRFYGG--KTQSDTAKLLHTTQVQISRRERKILKVMRDRL 221


>gi|159901988|gb|ABX10718.1| RNA polymerase sigma factor [uncultured planctomycete 13FN]
          Length = 391

 Score =  102 bits (255), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 61/290 (21%), Positives = 108/290 (37%), Gaps = 102/290 (35%)

Query: 25  KIPMLEKQEEYVLAKRY-------------------------REHGDLS----AAHRLVT 55
           K  +L+ ++E  L +R                          R   DL         ++ 
Sbjct: 156 KTALLKPEQEQQLFRRMNFLKFRANAARSRLNSGRPNVRVMVRTEKDLDDARQVRDHIIQ 215

Query: 56  SHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQE 115
           ++LRLVV IA  +    + + E++S+GN+ LM+AV +F+   GFR +TY+          
Sbjct: 216 ANLRLVVSIARRFVTDFISLDELISDGNLILMKAVDRFNFSLGFRFSTYA---------- 265

Query: 116 YILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
                       T A Q+  + N +            N +  +V+ IA            
Sbjct: 266 ------------THAVQRDFYRNYK------------NGRRRRVMEIA------------ 289

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
                     L   + +SD                 EQ + +       + +L  +   L
Sbjct: 290 -----TDPAVLFGSVVASDD----------------EQQINDVHAVAYLKKLLVDA---L 325

Query: 236 NPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +PRE+ I + R      +   TL  +  +  +S+ERVRQ++ RA ++V+E
Sbjct: 326 SPREQTILDMRLGLKADDGGKTLREVGEKLSISKERVRQLQTRAIEQVRE 375


>gi|170722830|ref|YP_001750518.1| flagellar biosynthesis sigma factor [Pseudomonas putida W619]
 gi|169760833|gb|ACA74149.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pseudomonas putida
           W619]
          Length = 246

 Score =  102 bits (255), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 46/248 (18%), Positives = 98/248 (39%), Gaps = 17/248 (6%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPE 96
           +        A + LV  +  LV +IA          + + +++  G IGL++   K+D  
Sbjct: 7   KMYSKASKDAQYDLVERYAPLVKRIAYHLLARLPANVQVEDLIQAGMIGLLEVANKYDAS 66

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           +G    TY+   I+ AM + + R           N + +   +R     ++A T  + K 
Sbjct: 67  KGASFETYAGIRIRGAMLDEV-RKGDWAPRSVHRNTRMVSDAMR----AVEARTGRDAKD 121

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
            +V A   KL++ +   I  +   +   S + L+   +       + L  +    +    
Sbjct: 122 HEVAA-ELKLSLDDYYGILNDTLGSRLFSFDDLLQDGE------HEGLHEEGASGQVEPS 174

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
              E +  +  LT +++ L  RER +       +  + L+ +     VS  RV Q+ ++ 
Sbjct: 175 RDLEDERFQAALTDAIANLPERERLVLALYY--DEELNLKEIGEVLGVSESRVSQLHSQC 232

Query: 277 FKKVQESI 284
             +++  +
Sbjct: 233 AARLRSRL 240


>gi|83816261|ref|YP_446679.1| RNA polymerase sigma-28 factor [Salinibacter ruber DSM 13855]
 gi|294508614|ref|YP_003572673.1| RNA polymerase sigma factor for flagellar operon [Salinibacter
           ruber M8]
 gi|83757655|gb|ABC45768.1| RNA polymerase sigma-28 factor [Salinibacter ruber DSM 13855]
 gi|294344943|emb|CBH25721.1| RNA polymerase sigma factor for flagellar operon [Salinibacter
           ruber M8]
          Length = 248

 Score =  102 bits (255), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 43/256 (16%), Positives = 99/256 (38%), Gaps = 22/256 (8%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKKF 93
           L ++Y +    S    +V + L LV  I          +    ++ S G +GL++A+  +
Sbjct: 8   LVEQYLDDPTPSNREAVVMAALPLVRSIIGKISVPDHLLAAHEDLESVGIVGLLEALDNY 67

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           DPE+  + AT++   I+  + +Y+               +     +  ++  L ++    
Sbjct: 68  DPEQ-AQFATHAYRRIRGNIIDYLR--------SIDVLSREKRKKMGAVQEALSSLRQML 118

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            +      +A  + ++  E   +        SL+    S D + +        D      
Sbjct: 119 GEEPSDEDVADYMGMAVEEYHDLLRDAQCRFSLSLSRPSEDDDHTMLDVLPSDDGTEG-- 176

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
              E+ E+ + +  L   +  L  R++ I      ++  +TL+ +    ++S  R+ Q+ 
Sbjct: 177 --FEQFEKASTQKHLEDLIQTLPERQQTILGLYYTED--LTLQEIGEVLDLSAARISQL- 231

Query: 274 ARAFKKVQESIQKQVE 289
                K+Q ++Q + E
Sbjct: 232 ---LGKIQLTLQSKFE 244


>gi|15802357|ref|NP_288383.1| flagellar biosynthesis sigma factor [Escherichia coli O157:H7
           EDL933]
 gi|15831915|ref|NP_310688.1| flagellar biosynthesis sigma factor [Escherichia coli O157:H7 str.
           Sakai]
 gi|26248189|ref|NP_754229.1| flagellar biosynthesis sigma factor [Escherichia coli CFT073]
 gi|49176170|ref|NP_416432.3| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli str.
           K-12 substr. MG1655]
 gi|74311731|ref|YP_310150.1| flagellar biosynthesis sigma factor [Shigella sonnei Ss046]
 gi|89108757|ref|AP_002537.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli str.
           K-12 substr. W3110]
 gi|110642027|ref|YP_669757.1| flagellar biosynthesis sigma factor [Escherichia coli 536]
 gi|157158016|ref|YP_001463226.1| flagellar biosynthesis sigma factor [Escherichia coli E24377A]
 gi|170019740|ref|YP_001724694.1| flagellar biosynthesis sigma factor [Escherichia coli ATCC 8739]
 gi|170081570|ref|YP_001730890.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli str.
           K-12 substr. DH10B]
 gi|170684004|ref|YP_001743321.1| flagellar biosynthesis sigma factor [Escherichia coli SMS-3-5]
 gi|187776391|ref|ZP_02802353.2| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4196]
 gi|188025223|ref|ZP_02776870.2| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4113]
 gi|189010650|ref|ZP_02808323.2| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4076]
 gi|189402557|ref|ZP_02783240.2| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4401]
 gi|189403603|ref|ZP_02796533.2| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4486]
 gi|189404441|ref|ZP_02789463.2| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4501]
 gi|189405427|ref|ZP_02815329.2| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC869]
 gi|189406256|ref|ZP_02827273.2| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC508]
 gi|191168296|ref|ZP_03030089.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           B7A]
 gi|191173335|ref|ZP_03034865.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           F11]
 gi|193066383|ref|ZP_03047431.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           E22]
 gi|193071158|ref|ZP_03052082.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           E110019]
 gi|194429934|ref|ZP_03062444.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           B171]
 gi|194439580|ref|ZP_03071653.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           101-1]
 gi|208810387|ref|ZP_03252263.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4206]
 gi|209399914|ref|YP_002271036.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4115]
 gi|209919344|ref|YP_002293428.1| flagellar biosynthesis sigma factor [Escherichia coli SE11]
 gi|215487127|ref|YP_002329558.1| flagellar biosynthesis sigma factor [Escherichia coli O127:H6 str.
           E2348/69]
 gi|218554506|ref|YP_002387419.1| flagellar biosynthesis sigma factor [Escherichia coli IAI1]
 gi|218689915|ref|YP_002398127.1| flagellar biosynthesis sigma factor [Escherichia coli ED1a]
 gi|218695529|ref|YP_002403196.1| flagellar biosynthesis sigma factor [Escherichia coli 55989]
 gi|218699514|ref|YP_002407143.1| flagellar biosynthesis sigma factor [Escherichia coli IAI39]
 gi|218705417|ref|YP_002412936.1| flagellar biosynthesis sigma factor [Escherichia coli UMN026]
 gi|238901131|ref|YP_002926927.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli BW2952]
 gi|253773125|ref|YP_003035956.1| flagellar biosynthesis sigma factor [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254793572|ref|YP_003078409.1| flagellar biosynthesis sigma factor [Escherichia coli O157:H7 str.
           TW14359]
 gi|260844326|ref|YP_003222104.1| RNA polymerase, sigma 28 factor [Escherichia coli O103:H2 str.
           12009]
 gi|260855902|ref|YP_003229793.1| RNA polymerase, sigma 28 factor [Escherichia coli O26:H11 str.
           11368]
 gi|260868514|ref|YP_003234916.1| RNA polymerase, sigma 28 factor [Escherichia coli O111:H- str.
           11128]
 gi|291283099|ref|YP_003499917.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O55:H7 str. CB9615]
 gi|293405408|ref|ZP_06649400.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           FVEC1412]
 gi|293410281|ref|ZP_06653857.1| conserved hypothetical protein [Escherichia coli B354]
 gi|293446304|ref|ZP_06662726.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           B088]
 gi|298381052|ref|ZP_06990651.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           FVEC1302]
 gi|307314171|ref|ZP_07593781.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Escherichia
           coli W]
 gi|312967123|ref|ZP_07781341.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           2362-75]
 gi|312973866|ref|ZP_07788038.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           1827-70]
 gi|331642544|ref|ZP_08343679.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli H736]
 gi|331668616|ref|ZP_08369464.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli TA271]
 gi|331673440|ref|ZP_08374208.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli TA280]
 gi|331677807|ref|ZP_08378482.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli H591]
 gi|331683474|ref|ZP_08384075.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli H299]
 gi|332278907|ref|ZP_08391320.1| transcription initiation factor alternative sigma factor 28
           [Shigella sp. D9]
 gi|84028136|sp|P0AEM8|FLIA_ECO57 RecName: Full=RNA polymerase sigma factor for flagellar operon;
           AltName: Full=Sigma-27; AltName: Full=Sigma-28; AltName:
           Full=Sigma-F factor
 gi|84028137|sp|P0AEM7|FLIA_ECOL6 RecName: Full=RNA polymerase sigma factor for flagellar operon;
           AltName: Full=Sigma-27; AltName: Full=Sigma-28; AltName:
           Full=Sigma-F factor
 gi|84028138|sp|P0AEM6|FLIA_ECOLI RecName: Full=RNA polymerase sigma factor for flagellar operon;
           AltName: Full=Sigma-27; AltName: Full=Sigma-28; AltName:
           Full=Sigma-F factor
 gi|12516023|gb|AAG56937.1|AE005415_2 flagellar biosynthesis; alternative sigma factor 28; regulation of
           flagellar operons [Escherichia coli O157:H7 str. EDL933]
 gi|26108593|gb|AAN80796.1|AE016762_49 RNA polymerase sigma factor for flagellar operon [Escherichia coli
           CFT073]
 gi|556180|gb|AAC37011.1| sigma factor 28 [Escherichia coli]
 gi|687650|gb|AAC43543.1| sigma F [Escherichia coli]
 gi|1736581|dbj|BAA15742.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli str.
           K12 substr. W3110]
 gi|1788231|gb|AAC74989.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli str.
           K-12 substr. MG1655]
 gi|13362129|dbj|BAB36084.1| transcription initiation factor alternative sigma factor 28
           [Escherichia coli O157:H7 str. Sakai]
 gi|73855208|gb|AAZ87915.1| alternative sigma factor 28 [Shigella sonnei Ss046]
 gi|110343619|gb|ABG69856.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           536]
 gi|157080046|gb|ABV19754.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           E24377A]
 gi|169754668|gb|ACA77367.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Escherichia coli ATCC
           8739]
 gi|169889405|gb|ACB03112.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli str.
           K-12 substr. DH10B]
 gi|170521722|gb|ACB19900.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           SMS-3-5]
 gi|187767374|gb|EDU31218.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4196]
 gi|188014157|gb|EDU52279.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4113]
 gi|188999325|gb|EDU68311.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4076]
 gi|189354876|gb|EDU73295.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4401]
 gi|189359713|gb|EDU78132.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4486]
 gi|189365564|gb|EDU83980.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4501]
 gi|189370194|gb|EDU88610.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC869]
 gi|189375693|gb|EDU94109.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC508]
 gi|190901668|gb|EDV61424.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           B7A]
 gi|190906452|gb|EDV66061.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           F11]
 gi|192925968|gb|EDV80614.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           E22]
 gi|192955553|gb|EDV86032.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           E110019]
 gi|194412023|gb|EDX28335.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           B171]
 gi|194421489|gb|EDX37503.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           101-1]
 gi|208724903|gb|EDZ74610.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4206]
 gi|209161314|gb|ACI38747.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4115]
 gi|209748392|gb|ACI72503.1| transcription initiation factor alternative sigma factor 28
           [Escherichia coli]
 gi|209748394|gb|ACI72504.1| transcription initiation factor alternative sigma factor 28
           [Escherichia coli]
 gi|209748396|gb|ACI72505.1| transcription initiation factor alternative sigma factor 28
           [Escherichia coli]
 gi|209912603|dbj|BAG77677.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           SE11]
 gi|215265199|emb|CAS09588.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli O127:H6
           str. E2348/69]
 gi|218352261|emb|CAU98017.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli 55989]
 gi|218361274|emb|CAQ98858.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli IAI1]
 gi|218369500|emb|CAR17267.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli IAI39]
 gi|218427479|emb|CAR08375.2| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli ED1a]
 gi|218432514|emb|CAR13407.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli UMN026]
 gi|222033663|emb|CAP76404.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           LF82]
 gi|238863498|gb|ACR65496.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli BW2952]
 gi|253324169|gb|ACT28771.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Escherichia coli
           'BL21-Gold(DE3)pLysS AG']
 gi|254592972|gb|ACT72333.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli O157:H7
           str. TW14359]
 gi|257754551|dbj|BAI26053.1| RNA polymerase, sigma 28 factor [Escherichia coli O26:H11 str.
           11368]
 gi|257759473|dbj|BAI30970.1| RNA polymerase, sigma 28 factor [Escherichia coli O103:H2 str.
           12009]
 gi|257764870|dbj|BAI36365.1| RNA polymerase, sigma 28 factor [Escherichia coli O111:H- str.
           11128]
 gi|260448961|gb|ACX39383.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Escherichia coli DH1]
 gi|284921835|emb|CBG34908.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           042]
 gi|290762972|gb|ADD56933.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O55:H7 str. CB9615]
 gi|291323134|gb|EFE62562.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           B088]
 gi|291427616|gb|EFF00643.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           FVEC1412]
 gi|291470749|gb|EFF13233.1| conserved hypothetical protein [Escherichia coli B354]
 gi|298278494|gb|EFI20008.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           FVEC1302]
 gi|306906140|gb|EFN36658.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Escherichia
           coli W]
 gi|307553936|gb|ADN46711.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           ABU 83972]
 gi|309702217|emb|CBJ01534.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           ETEC H10407]
 gi|310332461|gb|EFP99696.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           1827-70]
 gi|312288587|gb|EFR16489.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           2362-75]
 gi|315061222|gb|ADT75549.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli W]
 gi|315617855|gb|EFU98453.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           3431]
 gi|320191897|gb|EFW66544.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC1212]
 gi|320194366|gb|EFW68997.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           WV_060327]
 gi|320198616|gb|EFW73216.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           EC4100B]
 gi|323158594|gb|EFZ44608.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           E128010]
 gi|323165278|gb|EFZ51066.1| RNA polymerase sigma factor for flagellar operon [Shigella sonnei
           53G]
 gi|323180827|gb|EFZ66367.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           1180]
 gi|323186802|gb|EFZ72122.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           RN587/1]
 gi|323378201|gb|ADX50469.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Escherichia coli KO11]
 gi|323937197|gb|EGB33477.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli E1520]
 gi|323940415|gb|EGB36606.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli E482]
 gi|323948197|gb|EGB44185.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli H120]
 gi|323961971|gb|EGB57570.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli H489]
 gi|323968339|gb|EGB63746.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli M863]
 gi|323972715|gb|EGB67916.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli TA007]
 gi|323977897|gb|EGB72983.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli TW10509]
 gi|324118976|gb|EGC12865.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli E1167]
 gi|326342331|gb|EGD66112.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. 1044]
 gi|326344837|gb|EGD68584.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. 1125]
 gi|327253053|gb|EGE64707.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           STEC_7v]
 gi|331039342|gb|EGI11562.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli H736]
 gi|331063810|gb|EGI35721.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli TA271]
 gi|331069638|gb|EGI41025.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli TA280]
 gi|331074267|gb|EGI45587.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli H591]
 gi|331079689|gb|EGI50886.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli H299]
 gi|332089656|gb|EGI94758.1| RNA polymerase sigma factor for flagellar operon [Shigella boydii
           5216-82]
 gi|332101259|gb|EGJ04605.1| transcription initiation factor alternative sigma factor 28
           [Shigella sp. D9]
 gi|332343648|gb|AEE56982.1| RNA polymerase sigma factor for flagellar operon protein
           [Escherichia coli UMNK88]
 gi|332756073|gb|EGJ86426.1| RNA polymerase sigma factor for flagellar operon [Shigella flexneri
           4343-70]
 gi|333003239|gb|EGK22785.1| RNA polymerase sigma factor for flagellar operon [Shigella flexneri
           K-218]
 gi|333004180|gb|EGK23712.1| RNA polymerase sigma factor for flagellar operon [Shigella flexneri
           K-272]
 gi|333017792|gb|EGK37099.1| RNA polymerase sigma factor for flagellar operon [Shigella flexneri
           K-227]
          Length = 239

 Score =  102 bits (255), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 102/240 (42%), Gaps = 17/240 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   + +L+  L        +      +A++L
Sbjct: 73  QRIRGAMLDEL-RSRDWVPRSVRRNAREVAQAIGQLEQEL-------GRNATETEVAERL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +  ++   M      D + + L +  +          +   D Q +  +++    N R 
Sbjct: 125 GIDIADYRQMLL----DTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 181 RVMEAIETLPEREKLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 238


>gi|15606452|ref|NP_213832.1| RNA polymerase sigma factor FliA [Aquifex aeolicus VF5]
 gi|2983663|gb|AAC07229.1| RNA polymerase sigma factor FliA [Aquifex aeolicus VF5]
          Length = 236

 Score =  102 bits (255), Expect = 6e-20,   Method: Composition-based stats.
 Identities = 47/240 (19%), Positives = 101/240 (42%), Gaps = 23/240 (9%)

Query: 50  AHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L+  +L LV  IA     +    + I +++S G IGL++AV     E   R   Y  
Sbjct: 11  REELILKYLPLVKAIATNIKKHLPEDVDIRDLISYGVIGLIKAVDNLSTENPKRAEAYIK 70

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             IK A+ +Y+               +++    RR+K  ++ + +   +      +AK+L
Sbjct: 71  LRIKGAIYDYLR--------SLDFGSRQVREKERRIKEVVEKLKEKLGREPTDEEVAKEL 122

Query: 167 NVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            +S  E+     ++  +   SL  +     ++ S+               + E+  ++  
Sbjct: 123 GISTEELFKTLDKINFSYILSLEEVFRDFARDYSELI--------PSSTNVEEEVIKREL 174

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              +  ++S L  RE+ + +    +E P   + ++   E S  RV Q++A+A ++++E +
Sbjct: 175 TEKVKEAVSKLPEREKLVIQLIFYEELPA--KEVAKILETSVSRVSQLKAKALERLREML 232


>gi|213419842|ref|ZP_03352908.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
          Length = 115

 Score =  102 bits (255), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 27/110 (24%), Positives = 53/110 (48%), Gaps = 5/110 (4%)

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           E ++      D   S   D++    D   ++ ++    ++ R      ++ L  RE ++ 
Sbjct: 5   EPISMETPIGDDEDSHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVL 61

Query: 244 EARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
             R   +     TLE +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 62  RMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 111


>gi|229137791|ref|ZP_04266393.1| RNA polymerase sigma-B factor [Bacillus cereus BDRD-ST26]
 gi|228645648|gb|EEL01880.1| RNA polymerase sigma-B factor [Bacillus cereus BDRD-ST26]
          Length = 196

 Score =  102 bits (255), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 37/204 (18%), Positives = 92/204 (45%), Gaps = 16/204 (7%)

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           G +GL+ A++++D   G     +++  I   +++Y+      + +      +R+     +
Sbjct: 2   GMLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRIKDLGGK 56

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQ 199
           +K  ++ +TD   +  +++ IA  L +SE EV+ +          SL+ ++ ++   SS 
Sbjct: 57  IKLAIEELTDRLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENASDGSSV 116

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
            +   V +       + +  E   RR +L    +VLN  E+ +      +   +  ++  
Sbjct: 117 ARIESVGE-------VEQGYEETERRLVLKDIFNVLNDTEKSVIHYIFGEN--LNQKDTG 167

Query: 260 SEFEVSRERVRQIEARAFKKVQES 283
               +S+  V +I+ +A  K++++
Sbjct: 168 ERLGISQMHVSRIKRQAISKLKQA 191


>gi|257871306|ref|ZP_05650959.1| RNA polymerase sigma-70 subunit [Enterococcus gallinarum EG2]
 gi|257805470|gb|EEV34292.1| RNA polymerase sigma-70 subunit [Enterococcus gallinarum EG2]
          Length = 235

 Score =  102 bits (255), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 46/243 (18%), Positives = 101/243 (41%), Gaps = 18/243 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPIS--EVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
               +  +L LV ++              ++ + G IGLM A++KFDP +     +Y++ 
Sbjct: 6   REAEIIKYLPLVERVVQRLSIKTADYESGDLYNIGVIGLMDALRKFDPSKKVPFESYAVI 65

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            IK A+ + + +   + +             + +     Q +  +  +      I K+L 
Sbjct: 66  RIKGAIIDEVRKHAKISRY--------KMAAVNQFYQARQELEQSLKREATDTEICKQLG 117

Query: 168 VSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           +++S++  +   L      SL   + +  +     +D +    +  E  L+ +E    +R
Sbjct: 118 INQSQLADIYESLHYLASVSLEDTLFAYQEEGMTIKDMVRDPAENVEDTLVAEE----KR 173

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             L   +  L  RE+ I      +E  +TL+ ++   E+S  RV QI  +   K++  I+
Sbjct: 174 TALVACIKKLGEREQIILSLYYTEE--LTLKEIAEILEISIPRVSQIHGKTIAKLRTLIE 231

Query: 286 KQV 288
           +++
Sbjct: 232 EEL 234


>gi|89902470|ref|YP_524941.1| sigma 28 (flagella/sporulation) [Rhodoferax ferrireducens T118]
 gi|89347207|gb|ABD71410.1| sigma 28 (Flagella/Sporulation) [Rhodoferax ferrireducens T118]
          Length = 238

 Score =  102 bits (255), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 42/242 (17%), Positives = 105/242 (43%), Gaps = 19/242 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + ++  +  LV ++A          + + +++  G IGL +A+ +++  +G +  T++ 
Sbjct: 10  RNAMIRQYQPLVRRLAHHMMAKLPANVEVDDLIQVGLIGLSEALTRYEAAQGVQFETFAT 69

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +  +  + + G+  +QK +   LRRL+  L        +      IA  L
Sbjct: 70  QRIRGAMLDELRGNDWMSR-GSRKSQKDIEQALRRLEHKL-------GRTPLESEIAADL 121

Query: 167 NVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            +S  +  ++  ++ G     L  +   +D+  S     +         VL +    +  
Sbjct: 122 GLSLVDYQTLLGKVRGTQLVYLEDMARGNDEEDSFLDRHVGDSDADPMNVLRD----QRL 177

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L  ++  L  RE+ I       E  + L+ +++  +V+  R+ Q+ +++  +++  +
Sbjct: 178 RQALVAAIKNLPEREQFIMSMYY--EQDMNLKEIAAVLDVTESRICQLHSQSIARLRAKM 235

Query: 285 QK 286
           + 
Sbjct: 236 RA 237


>gi|301029374|ref|ZP_07192470.1| flagellar biosynthesis sigma factor [Escherichia coli MS 196-1]
 gi|299877729|gb|EFI85940.1| flagellar biosynthesis sigma factor [Escherichia coli MS 196-1]
          Length = 239

 Score =  102 bits (255), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 102/240 (42%), Gaps = 17/240 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   + +L+  L        +      +A++L
Sbjct: 73  QRIRGAMLDEL-RSRDWVPRSVRRNAREVAQAIGQLEQEL-------GRNSTETEVAERL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +  ++   M      D + + L +  +          +   D Q +  +++    N R 
Sbjct: 125 GIDIADYRQMLL----DTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 181 RVMEAIETLPEREKLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 238


>gi|254246774|ref|ZP_04940095.1| Sigma-70 region 3 [Burkholderia cenocepacia PC184]
 gi|124871550|gb|EAY63266.1| Sigma-70 region 3 [Burkholderia cenocepacia PC184]
          Length = 306

 Score =  102 bits (255), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 42/215 (19%), Positives = 88/215 (40%), Gaps = 14/215 (6%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++  G IGLM A  ++  ++G +  TY+   I+ AM + +  +  L         +
Sbjct: 100 DLDDLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDELRSNDWL--------PR 151

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            L    R ++  +  +  +  +      IA+ LN+   E   M   L G + +       
Sbjct: 152 SLRKTSREVEHAVHQVEQHLGRSASETEIAQHLNMPLDEYQGMLQDLHGSQLIYYEDFDR 211

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
             +   + D    DH      L++     + R  L  ++  L  RE+ +       E  +
Sbjct: 212 AADDEPFLDRYRVDHADPLSALLDD----HLREALVEAIERLPEREKLLMSLYY--ERGL 265

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            L  + +  EVS  RV Q+ ++A  +++  +++Q 
Sbjct: 266 NLREIGAVLEVSESRVCQLHSQAVARLRARLREQA 300


>gi|2853597|gb|AAC08061.1| FliA [Pseudomonas putida]
          Length = 246

 Score =  102 bits (255), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 42/243 (17%), Positives = 95/243 (39%), Gaps = 21/243 (8%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
             A + L+  +  LV +IA          + + +++  G IGL++   K+D  +G    T
Sbjct: 14  KDAQYELIERYAPLVKRIAYHLLARLPANVQVEDLIQAGMIGLLEVSSKYDASKGASFET 73

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   I+ AM + + +             + +  N R +   ++A+     +  +   +A
Sbjct: 74  YAGIRIRGAMLDEVRKGDW--------APRSVHRNTRMVSDAMRAVEARTGRDAKDHEVA 125

Query: 164 KKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
            +L +S  +   I  +   +   S + L+   +       + L  D            E 
Sbjct: 126 AELQLSLDDYYGILNDTLGSRLFSFDDLLQDGE------HEGLHEDGASGHVEPARGLED 179

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +  +  LT +++ L  RER +       +  + L+ +     VS  RV Q+ ++   +++
Sbjct: 180 ERFQAALTEAIANLPERERLVLALYY--DEELNLKEIGEVLGVSESRVSQLHSQCAARLR 237

Query: 282 ESI 284
             +
Sbjct: 238 SRL 240


>gi|325567514|ref|ZP_08144181.1| DNA-directed RNA polymerase sigma subunit FliA [Enterococcus
           casseliflavus ATCC 12755]
 gi|325158947|gb|EGC71093.1| DNA-directed RNA polymerase sigma subunit FliA [Enterococcus
           casseliflavus ATCC 12755]
          Length = 235

 Score =  102 bits (255), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 47/243 (19%), Positives = 99/243 (40%), Gaps = 18/243 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPIS--EVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
               +  +L LV ++              ++ + G IGLM A++KFDP +     +Y+  
Sbjct: 6   REAEIIKYLPLVERVVQRLSIKTADYESGDLYNIGVIGLMDALRKFDPSKKVPFESYAAI 65

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            IK A+ + + +   + +             + +     Q +  +  +      I K+L 
Sbjct: 66  RIKGAIIDEVRKHAKISRY--------KMAAVNQFYQARQELEQSLKREATDTEICKQLG 117

Query: 168 VSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           +++S++  +   L      SL   + +  +     +D +    +  E  L+ +E    +R
Sbjct: 118 INQSQLADIYESLHYLASVSLEDTLFAYQEEGMTLKDMVRDPAENVEDTLVAEE----KR 173

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             L   +  L  RE+ I      +E  +TL+ ++   EVS  RV QI  +   K++  I 
Sbjct: 174 TALVACIKKLGEREQLILSLYYTEE--LTLKEIAEILEVSIPRVSQIHGKTIAKLRTLIG 231

Query: 286 KQV 288
           +++
Sbjct: 232 EEL 234


>gi|325273563|ref|ZP_08139791.1| flagellar biosynthesis sigma factor [Pseudomonas sp. TJI-51]
 gi|324101302|gb|EGB98920.1| flagellar biosynthesis sigma factor [Pseudomonas sp. TJI-51]
          Length = 246

 Score =  102 bits (255), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 45/241 (18%), Positives = 97/241 (40%), Gaps = 17/241 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
             A + L+  +  LV +IA          + + +++  G IGL++   K+D  +G    T
Sbjct: 14  KDAQYELIERYAPLVKRIAYHLLARLPANVQVEDLIQAGMIGLLEVANKYDASKGASFET 73

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   I+ AM + + R           N + +   +R     ++A T  + K  +V A  
Sbjct: 74  YAGIRIRGAMLDEV-RKGDWAPRSVHRNTRMVSDAMR----AVEARTGRDAKDHEVAAEL 128

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + L++ +   I  +   +   S + L+   +       + L  D    +       E + 
Sbjct: 129 Q-LSLDDYYAILNDTLGSRLFSFDDLLQDGE------HEGLHEDGASGQVEPARGLEEER 181

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +  LT +++ L  RER +       +  + L+ +     VS  RV Q+ ++   +++  
Sbjct: 182 FQLALTEAIANLPERERLVLALYY--DEELNLKEIGEVLGVSESRVSQLHSQCAARLRSR 239

Query: 284 I 284
           +
Sbjct: 240 L 240


>gi|307328384|ref|ZP_07607560.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306885957|gb|EFN16967.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 261

 Score =  102 bits (254), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 29/237 (12%), Positives = 92/237 (38%), Gaps = 14/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +    ++ + L +  ++A+ +R  G  + ++    ++ L++AV +++P+ G    +Y++ 
Sbjct: 35  ALRETIICAWLPVAKRLALRFRNKGENMEDLTQVASLALVKAVDRYNPDLGHAFPSYAIP 94

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I   ++ +       + I     + R     R  +  L+   +   +   +  I  +  
Sbjct: 95  VITGELKRHFRDYLWTLHIPRNIQEVR--SRTRSARDALEQ--ELGGRTPTIHEICLRTG 150

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + + +V++     A    L+              + +  D    E+V+         R  
Sbjct: 151 MPQEDVMAGLEASASCTPLSLNAAVQGAEERLLAETVGADDAAIERVV--------NREA 202

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   ++ L+ ++R +   R      ++   +      S+  + +  +R + ++++ +
Sbjct: 203 LRVLIAELSEQDRYVLYLRFFAG--LSQSQIGEILGFSQMHISRRLSRLYSELRQGL 257


>gi|116625262|ref|YP_827418.1| FliA/WhiG family RNA polymerase sigma factor [Candidatus Solibacter
           usitatus Ellin6076]
 gi|116228424|gb|ABJ87133.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Candidatus
           Solibacter usitatus Ellin6076]
          Length = 255

 Score =  102 bits (254), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 40/241 (16%), Positives = 91/241 (37%), Gaps = 18/241 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             ++V  HL LV  IA+         + + +++  G +GL  AV K+D ++     +Y+ 
Sbjct: 19  RDQIVLDHLPLVKAIAIRVHENLPVHVDLDDLIHAGVMGLFDAVTKYDGDKNVAFHSYAK 78

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             IK A+ + + R             + L    ++++   + +     +      IA+++
Sbjct: 79  HRIKGAILDSL-RQLDW-------ASRDLRRRQKQVESVTRDLGVKLGRSPHDSEIAEQM 130

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            V  +    M   +     ++A  N         +                  E++   +
Sbjct: 131 GVGLARWRQMQIEMRTVGLVSATPNPDQDRERAQEFPA-----KPNLQPDRMCEQRQLES 185

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L R++  L  R +++       +  +T++ +     V+  RV QI   A KK+   ++ 
Sbjct: 186 TLARAIGTLPLRYQKVVFLYYTND--LTMKEIGEVLGVNESRVSQIHKIALKKMAGVLES 243

Query: 287 Q 287
           +
Sbjct: 244 E 244


>gi|221635447|ref|YP_002523323.1| RNA polymerase sigma-D factor (Sigma-28) [Thermomicrobium roseum
           DSM 5159]
 gi|221157679|gb|ACM06797.1| RNA polymerase sigma-D factor (Sigma-28) [Thermomicrobium roseum
           DSM 5159]
          Length = 262

 Score =  102 bits (254), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 48/261 (18%), Positives = 110/261 (42%), Gaps = 21/261 (8%)

Query: 31  KQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIG 85
            ++E  L +R R  E  D     +LV  +  LV  +    R    P     +++  G IG
Sbjct: 5   ARQEGRLRQRLRRIEARD-DTRAQLVEQYAPLVKYVVDRLRLSLPPSVERDDLIGYGTIG 63

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A+ +FD  RG +  TY+   I+ A+ + +      + I   + + R     R+++  
Sbjct: 64  LLEALDRFDDTRGVKFETYAAMRIRGAILDAL----RTLDIVPRSARSRA----RQIEQA 115

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            +       +      +A  L ++ +E   +   ++    L   + +S+   +   +  +
Sbjct: 116 TREFFAEYGRMPSENELADHLGMTTTE---LQQAISDAACLFLPLQASEDPDTLTLEEQL 172

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            D +  E    E    ++ +  +  +++ L+ R+R I      ++  +T+  +S    +S
Sbjct: 173 ADPNALE--PGEVAAEEDLKQRIAAALATLSERDRLIVSLYYYED--LTMREISQLLGIS 228

Query: 266 RERVRQIEARAFKKVQESIQK 286
             RV QI  R   +++  +++
Sbjct: 229 ESRVSQILNRVRLQLRALLRE 249


>gi|188495466|ref|ZP_03002736.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           53638]
 gi|293415233|ref|ZP_06657876.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           B185]
 gi|331647515|ref|ZP_08348607.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli M605]
 gi|188490665|gb|EDU65768.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           53638]
 gi|281178984|dbj|BAI55314.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           SE15]
 gi|291432881|gb|EFF05860.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           B185]
 gi|330911730|gb|EGH40240.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           AA86]
 gi|331043239|gb|EGI15377.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli M605]
          Length = 239

 Score =  102 bits (254), Expect = 7e-20,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 102/240 (42%), Gaps = 17/240 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   + +L+  L        +      +A++L
Sbjct: 73  QRIRGAMLDEL-RSRDWVPRSVRRNAREVAQAIGQLEQEL-------GRNATETEVAERL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +  ++   M      D + + L +  +          +   D Q +  +++    N R 
Sbjct: 125 GIDIADYRQMLL----DTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDNNLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 181 RVMEAIETLPEREKLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 238


>gi|254446671|ref|ZP_05060147.1| RNA polymerase sigma factor, FliA/WhiG family [Verrucomicrobiae
           bacterium DG1235]
 gi|198260979|gb|EDY85287.1| RNA polymerase sigma factor, FliA/WhiG family [Verrucomicrobiae
           bacterium DG1235]
          Length = 269

 Score =  102 bits (254), Expect = 8e-20,   Method: Composition-based stats.
 Identities = 38/238 (15%), Positives = 91/238 (38%), Gaps = 13/238 (5%)

Query: 52  RLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
            L  +++ LV  I           +   ++ S G  GL+ A+KK+DP +     +Y+   
Sbjct: 38  ELFETYMPLVRSIVARIKINLPPHIDEQDLHSVGITGLIAALKKYDPAQKKSFGSYAAMR 97

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ ++ + + R   + +   T        N ++L+  ++ +     +P     I  +L +
Sbjct: 98  IRGSILDELRRMDWMPRNART--------NFKKLRATIEEVEQRLGRPATEEEIRAELGL 149

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +  E   +         L     ++  +  +  D      D     +  K E+     ++
Sbjct: 150 NRKEYDQLMAETRPVSFLPLDNAAAGGDDGEGADLYEVIPDDNVVPVTSKMEKDEVTRLV 209

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              ++ L    R++      Q+  + L  ++  F ++  R+ QI ++A   ++  I  
Sbjct: 210 AERINQLPETPRKVLAMYYFQD--MRLAEIAEVFGLTESRICQIHSQAIISLRSYITS 265


>gi|83749399|ref|ZP_00946393.1| RNA polymerase sigma-f factor for flagellar operon (fliA)
           [Ralstonia solanacearum UW551]
 gi|83723926|gb|EAP71110.1| RNA polymerase sigma-f factor for flagellar operon (fliA)
           [Ralstonia solanacearum UW551]
          Length = 253

 Score =  102 bits (254), Expect = 8e-20,   Method: Composition-based stats.
 Identities = 40/241 (16%), Positives = 99/241 (41%), Gaps = 17/241 (7%)

Query: 56  SHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++  LV +IA          + + +++  G +GL+ A+ +++  +G +   Y+   I+ A
Sbjct: 26  AYAPLVRRIANQMMVKLPASVELDDLIQAGMMGLLDALSRYEETQGVQFEFYAAQRIRGA 85

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           + + +  S  L         + L  N R ++  +Q +     +      IA  L +S ++
Sbjct: 86  ILDELRGSDWL--------PRGLRRNARTIEQAIQKLQQQKGRAPTETEIAAALEMSLAD 137

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
              +   L G    + L+   D +      ++       +   +++    + R  +  ++
Sbjct: 138 YQKLLVELQG----SQLLYYEDFDREDADAFIENRAAENDATPLDQLLDHDLRESVVAAI 193

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
             L  RE+ +       E  + L  + +   VS  RV QI ++A  +++  ++++  L +
Sbjct: 194 EALPEREKLMMSLYY--EQDLNLREIGAVMGVSESRVCQIHSQAIARIRARLRERAWLPT 251

Query: 293 S 293
            
Sbjct: 252 P 252


>gi|88813218|ref|ZP_01128458.1| flagellar biosynthesis sigma factor FliA [Nitrococcus mobilis
           Nb-231]
 gi|88789540|gb|EAR20667.1| flagellar biosynthesis sigma factor FliA [Nitrococcus mobilis
           Nb-231]
          Length = 240

 Score =  102 bits (254), Expect = 8e-20,   Method: Composition-based stats.
 Identities = 47/237 (19%), Positives = 94/237 (39%), Gaps = 20/237 (8%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
             LV  H  LV +IA    G       + +++  G IGL++A +++D  +G    TY+  
Sbjct: 17  DDLVVRHAPLVKRIAHHLAGRLPASVLVDDLIQAGMIGLLEAARQYDATQGASFQTYAAI 76

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+ AM + I R             + +    R +   +  I     +  +   + ++L 
Sbjct: 77  RIRGAMLDEIRRLDWT--------PRSVHRKAREVASAVAEIEHRTGREAKDWEVVQQLG 128

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +  ++   +    A      A I S D    +  +   ++  G E   +E  E+++ +  
Sbjct: 129 LDLNDYHQILQDAA-----TARIFSIDDQDPELGEP--HEIAGHEPTAMEILEQQDFQAA 181

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L  ++  L  RE+ + +        + L+ +     VS  RV QI  R   K++  +
Sbjct: 182 LIAAIRELPEREQLVMQLYY--NEELNLKEIGQVLGVSESRVSQIHGRIALKLRALL 236


>gi|319787083|ref|YP_004146558.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pseudoxanthomonas
           suwonensis 11-1]
 gi|317465595|gb|ADV27327.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pseudoxanthomonas
           suwonensis 11-1]
          Length = 248

 Score =  102 bits (254), Expect = 8e-20,   Method: Composition-based stats.
 Identities = 50/249 (20%), Positives = 98/249 (39%), Gaps = 21/249 (8%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPER 97
           YR     +++   V  H  LV +IA          + + +++  G IGL++A + +DPE+
Sbjct: 7   YRAVQQRASSDDAVVRHADLVRRIAHHLAARLPASVEVDDLIQAGMIGLIEASRSYDPEQ 66

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G    TY+   I+ +M + I R    V        +            ++  T     P+
Sbjct: 67  GASFETYASIRIRGSMIDEIRR-GDWVPRSVHRRARDAAAA----VREIEQATGRAAAPQ 121

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           +V A   KL++   E + +    +  + L+   +  D    Q         +       +
Sbjct: 122 EVAA---KLDMPLPEYLRLLEDASRGQVLSLDSHVEDHGDVQV--------NSNSPTPQQ 170

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
             ER +    L  ++S L  RE+ +       E  + L+ + +   VS  RV QI  +A 
Sbjct: 171 VLERGDFGRELATAISGLPEREQLVLSLYY--EQELNLKEIGAVLGVSESRVCQIHGQAV 228

Query: 278 KKVQESIQK 286
            +++  + +
Sbjct: 229 LRLRGRLSQ 237


>gi|146307827|ref|YP_001188292.1| flagellar biosynthesis sigma factor [Pseudomonas mendocina ymp]
 gi|145576028|gb|ABP85560.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Pseudomonas
           mendocina ymp]
          Length = 248

 Score =  102 bits (254), Expect = 8e-20,   Method: Composition-based stats.
 Identities = 42/251 (16%), Positives = 97/251 (38%), Gaps = 21/251 (8%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDP 95
           + Y +     + H+L+  +  LV +IA          + + +++  G IGL++A +K+D 
Sbjct: 8   RMYNKAQAQDSQHQLIERYAPLVKRIAYHLLARLPASVQVDDLIQAGMIGLLEASRKYDS 67

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            +G    T++   I+ AM + + R           N + +   +R ++           +
Sbjct: 68  GKGASFETFAGIRIRGAMLDEV-RKGDWAPRSVHRNSRMVSDAIRVVEA-------RTGR 119

Query: 156 PEQVVAIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
             +   +A +L +S  +   I  +   +   S + L+   +         L  D      
Sbjct: 120 DAKDHEVAAELQLSLEDYYGILGDTLGSRLFSFDDLLQDGE------HGGLHEDAGHTHL 173

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
                 E +  +  L  +++ L  RER +       +  + L+ +     VS  RV Q+ 
Sbjct: 174 EPSRDLEDERFQAALADAIAGLPERERLVLALYY--DEELNLKEIGEVLGVSESRVSQLH 231

Query: 274 ARAFKKVQESI 284
           ++   +++  +
Sbjct: 232 SQCAARLRSRL 242


>gi|331663420|ref|ZP_08364330.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli TA143]
 gi|331059219|gb|EGI31196.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli TA143]
          Length = 239

 Score =  102 bits (254), Expect = 9e-20,   Method: Composition-based stats.
 Identities = 46/240 (19%), Positives = 102/240 (42%), Gaps = 17/240 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   + +L+  L        +      +A++L
Sbjct: 73  QRIRGAMLDEL-RSRDWVPRSVRRNAREVAQAIGQLEQEL-------GRNATETEVAERL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +  ++   M      D + + L +  +          +   D Q +  +++    N R 
Sbjct: 125 GIDIADYRQMLL----DTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + S  EV   RV Q+ ++A K+++  + K
Sbjct: 181 RVMEAIETLPEREKLVLTLYY--QEELNLKEIGSVLEVGESRVSQLHSQAIKRLRTKLGK 238


>gi|161723249|ref|YP_095808.2| flagellar biosynthesis sigma factor [Legionella pneumophila subsp.
           pneumophila str. Philadelphia 1]
 gi|307610482|emb|CBX00054.1| sigma factor 28 [Legionella pneumophila 130b]
          Length = 238

 Score =  102 bits (254), Expect = 9e-20,   Method: Composition-based stats.
 Identities = 49/239 (20%), Positives = 104/239 (43%), Gaps = 21/239 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              LV +H  LV +IA    G     + + +++  G +GL++A + +D  +G    TY+ 
Sbjct: 15  QEALVKTHATLVKRIAHHLLGRLPQSVQLDDLIQSGMLGLLEAARHYDSSKGASFETYAG 74

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+  M + + R+  +         + ++ N R +   ++ +     +  +   IA++L
Sbjct: 75  IRIRGHMLDEVRRNDWV--------PRSVYRNSRMISDAVRILEHKLGREAKDNEIAEEL 126

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRR 225
            VS  +   M       +S+++ +   D       D +++DH+G           R +  
Sbjct: 127 GVSLDDYHDMLQ-----DSISSHLYGFDDLGVT--DDVLFDHEGNGSTEPHRNVMRSDMM 179

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           N LT+ +  L  +ER +       E  + L+ +    EVS  R+ QI ++A  +++  +
Sbjct: 180 NRLTQVIDSLPRKERLVLSLYY--EQDLNLKEIGEILEVSESRISQILSQATHRIRSRL 236


>gi|253576138|ref|ZP_04853470.1| RNA polymerase sigma-E factor [Paenibacillus sp. oral taxon 786
           str. D14]
 gi|251844481|gb|EES72497.1| RNA polymerase sigma-E factor [Paenibacillus sp. oral taxon 786
           str. D14]
          Length = 240

 Score =  102 bits (254), Expect = 9e-20,   Method: Composition-based stats.
 Identities = 55/262 (20%), Positives = 106/262 (40%), Gaps = 59/262 (22%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L ++EE  L +R    GD +    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 38  PPLTREEEEYLLQRL-PSGDSAIRAMLIERNLRLVVYIARKFENTGINIEDLVSIGAIGL 96

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FDPE+  +LATY+   I+  +  Y+ R+  +                       
Sbjct: 97  IKAVNTFDPEKKIKLATYASRCIENEILMYLRRNSKI----------------------- 133

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                             +  VS  E ++++    G+E L + +  ++ ++         
Sbjct: 134 ------------------RTEVSFDEPLNID--WDGNELLLSDVLGTENDTIYRNIEEQV 173

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           D     + L +  ER+     L   +   + +               T ++++    +S+
Sbjct: 174 DRKLLHKALDKLTERERMIMELRFGLVDGDEK---------------TQKDVADLLGISQ 218

Query: 267 ERVRQIEARAFKKVQESIQKQV 288
             + ++E R  K++++   K V
Sbjct: 219 SYISRLEKRIIKRLRKEFNKMV 240


>gi|83719422|ref|YP_443660.1| flagellar biosynthesis sigma factor [Burkholderia thailandensis
           E264]
 gi|167582695|ref|ZP_02375569.1| flagellar biosynthesis sigma factor [Burkholderia thailandensis
           TXDOH]
 gi|167620811|ref|ZP_02389442.1| flagellar biosynthesis sigma factor [Burkholderia thailandensis
           Bt4]
 gi|83653247|gb|ABC37310.1| RNA polymerase sigma factor for flagellar operon FliA [Burkholderia
           thailandensis E264]
          Length = 243

 Score =  102 bits (254), Expect = 9e-20,   Method: Composition-based stats.
 Identities = 40/215 (18%), Positives = 88/215 (40%), Gaps = 14/215 (6%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++  G IGL+ A  ++  ++G +  TY+   I+ AM + +  +  L         +
Sbjct: 37  DLDDLIQAGMIGLLDAASRYKEDQGAQFETYATQRIRGAMLDELRSNDWL--------PR 88

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            L    R ++  +  +     +      IA  L +   E  SM   L G    + L+   
Sbjct: 89  SLRKTSREVEHAVHQVEQRLGRSANETEIAAHLQMPLDEYQSMLQDLHG----SQLVYYE 144

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D + S   +  +  +       +     ++ R+ L  ++  L  RE+ +       E  +
Sbjct: 145 DFDRSADDEPFLDRYRADHSDPLSALLDEHLRSALVDAIEHLPEREKLLMSLYY--ERGL 202

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            L  + +  EVS  RV Q+ ++A  +++  +++Q 
Sbjct: 203 NLREIGAVLEVSESRVCQLHSQAVARLRAKLREQA 237


>gi|158320682|ref|YP_001513189.1| FliA/WhiG family RNA polymerase sigma factor [Alkaliphilus
           oremlandii OhILAs]
 gi|158140881|gb|ABW19193.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           oremlandii OhILAs]
          Length = 176

 Score =  102 bits (254), Expect = 9e-20,   Method: Composition-based stats.
 Identities = 38/120 (31%), Positives = 60/120 (50%), Gaps = 2/120 (1%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           +M + +   + L  YI      P  L  +EE +  +RY E GD  A + LV  +LRLV  
Sbjct: 7   SMLLTLKPILFLVSYISSTTSFPQPLTAEEESMYLERY-EQGDEEARNILVERNLRLVAH 65

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           I   Y   G  + +++S G IGL++ +  FD  +G RLATY+   I+  +   I  +  +
Sbjct: 66  IVKKYSNIGRDMDDLISIGTIGLIKGITTFDRSKGTRLATYAARCIENEILMTIRSNKKI 125


>gi|73539441|ref|YP_299808.1| sigma-70 region 4 [Ralstonia eutropha JMP134]
 gi|72122778|gb|AAZ64964.1| Sigma-70 region 4 [Ralstonia eutropha JMP134]
          Length = 238

 Score =  102 bits (254), Expect = 9e-20,   Method: Composition-based stats.
 Identities = 44/235 (18%), Positives = 94/235 (40%), Gaps = 16/235 (6%)

Query: 54  VTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           V +H +LV +IA+         + I +++  G IGL+ A K+++   G R  TY+   I+
Sbjct: 14  VKTHAQLVRRIALQLAAKLPASVQIDDLIQAGMIGLLDAAKRYEDTHGARFETYASQRIR 73

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            AM + +  +            + L    RR++   + +     +      +A++L +  
Sbjct: 74  GAMLDEVRANDW--------QSRSLRQFTRRIERTQRGLEQKLGRAPLDSEVAQELEMPL 125

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            E  ++   + G + L+                L    DG     + +      R  L R
Sbjct: 126 DEYQTLLNEVYGCQLLHYEDFERSGEEDFLDRHLGGSEDGN---PLTQLMENGMRAALIR 182

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           ++  L  RE+ +       +  + L  + +  +V+  RV QI  +A  +++  ++
Sbjct: 183 AIERLPEREKLVLSLCY--DQELNLREIGAVLDVTESRVCQIRGQAITRLRNQLR 235


>gi|186477706|ref|YP_001859176.1| flagellar biosynthesis sigma factor [Burkholderia phymatum STM815]
 gi|184194165|gb|ACC72130.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia phymatum
           STM815]
          Length = 244

 Score =  102 bits (254), Expect = 9e-20,   Method: Composition-based stats.
 Identities = 41/214 (19%), Positives = 89/214 (41%), Gaps = 14/214 (6%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++  G IGL+ A  ++  ++G +  TY+   I+ AM + +  +  L         +
Sbjct: 37  DLDDLIQAGMIGLLDAASRYKEDQGAQFETYASQRIRGAMLDELRSNDWL--------PR 88

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            L    R ++  +  +  +  +      IA+ L +   E  SM   L G + +       
Sbjct: 89  SLRRTSREVESAVHQVEQSLGRSASETEIAEHLKMPLDEYQSMLQDLHGSQLIYYEDFDR 148

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
             +   + D    DH      L++    ++ R  L  ++  L  RE+ +       E  +
Sbjct: 149 SADDEPFLDRYCVDHSDPLSALLD----ESLRGALVEAIDRLPEREKLLMSLYY--ERGL 202

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            L  + +  EVS  RV Q+ ++A  +++  +++Q
Sbjct: 203 NLREIGAVMEVSESRVCQLHSQAVARLRTRLREQ 236


>gi|157371179|ref|YP_001479168.1| flagellar biosynthesis sigma factor [Serratia proteamaculans 568]
 gi|157322943|gb|ABV42040.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Serratia
           proteamaculans 568]
          Length = 240

 Score =  102 bits (254), Expect = 9e-20,   Method: Composition-based stats.
 Identities = 45/241 (18%), Positives = 102/241 (42%), Gaps = 17/241 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KNSLWLRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDAMQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      + + +   +R+L+  L        +P   V +A+ L
Sbjct: 73  QRIRGAMLDEL-RSRDWVPRSVRRHAREVAQVMRQLEQQL-------GRPASEVEVAQTL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           N+S  E   +      D + + L +  +      +         +E   +      N R 
Sbjct: 125 NLSLDEYRQILL----DTNNSQLFSYDEWREEHGESAEPLLEGHEEANPLHHLLEGNLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  +V   RV Q+ ++A K+++  +  
Sbjct: 181 RVIDAIEALPEREKMVLTLYY--QEELNLKEIGAVLDVGESRVSQLHSQAIKRLRARLAS 238

Query: 287 Q 287
           +
Sbjct: 239 E 239


>gi|167838290|ref|ZP_02465149.1| flagellar biosynthesis sigma factor [Burkholderia thailandensis
           MSMB43]
          Length = 244

 Score =  101 bits (253), Expect = 9e-20,   Method: Composition-based stats.
 Identities = 40/215 (18%), Positives = 88/215 (40%), Gaps = 14/215 (6%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++  G IGL+ A  ++  ++G +  TY+   I+ AM + +  +  L         +
Sbjct: 38  DLDDLIQAGMIGLLDAASRYKEDQGAQFETYATQRIRGAMLDELRSNDWL--------PR 89

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            L    R ++  +  +     +      IA  L +   E  SM   L G    + L+   
Sbjct: 90  SLRKTSREVEHAVHQVEQRLGRSANETEIAAHLQMPLDEYQSMLQDLHG----SQLVYYE 145

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D + S   +  +  +       +     ++ R+ L  ++  L  RE+ +       E  +
Sbjct: 146 DFDRSADDEPFLDRYRADHSDPLSALLDEHLRDALVDAIEHLPEREKLLMSLYY--ERGL 203

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            L  + +  EVS  RV Q+ ++A  +++  +++Q 
Sbjct: 204 NLREIGAVLEVSESRVCQLHSQAVARLRAKLREQA 238


>gi|293604981|ref|ZP_06687378.1| DNA-directed RNA polymerase sigma subunit FliA [Achromobacter
           piechaudii ATCC 43553]
 gi|292816809|gb|EFF75893.1| DNA-directed RNA polymerase sigma subunit FliA [Achromobacter
           piechaudii ATCC 43553]
          Length = 251

 Score =  101 bits (253), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 43/243 (17%), Positives = 101/243 (41%), Gaps = 16/243 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           A   LV  +  LV K+A+         + + +++  G IGL+ AV+++      +  TY+
Sbjct: 4   ADDSLVE-YAPLVRKLALQLLARLPASVELDDLIQAGMIGLLDAVRRYQETADAQFETYA 62

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
              I+ AM + +     L +   T          R+++  +Q +    ++      IA +
Sbjct: 63  TTRIRGAMLDELRGQDWLPRSVRTKA--------RKIEQAIQQLEQRLMRAPTEAEIAAQ 114

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW--LVYDHDGQEQVLIEKEERKN 223
           L +   E  S+     G + ++    +++ +S+  Q       +H       ++     +
Sbjct: 115 LEMPIGEYQSLLHDAQGVQIVHYEDFTTEPDSASGQSDWTATLNHGSAGGNPLDALLAGD 174

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            R  L  ++  L  RE+ +       E  + L+ + +   V+  RV Q+ ++A  +++  
Sbjct: 175 FRQALVHAIDALPDREKLLLSLCY--EQGLNLKEIGAIMNVTEARVCQLRSQATARIRAK 232

Query: 284 IQK 286
           +++
Sbjct: 233 LKE 235


>gi|325961902|ref|YP_004239808.1| RNA polymerase sigma factor, sigma-70 family [Arthrobacter
           phenanthrenivorans Sphe3]
 gi|323467989|gb|ADX71674.1| RNA polymerase sigma factor, sigma-70 family [Arthrobacter
           phenanthrenivorans Sphe3]
          Length = 316

 Score =  101 bits (253), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 43/238 (18%), Positives = 89/238 (37%), Gaps = 19/238 (7%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           + LV  +L L   +A  +   G   +++     +GL++A + FD  +G     Y+   I 
Sbjct: 41  NDLVLGYLDLAEALAARFEARGRERADLNQVAYLGLVKAARGFDQSKGESFPAYAAPTIT 100

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
             ++ Y+     +V+        R      R+      +T +  +   V  +A  L+   
Sbjct: 101 GELKRYLRDRTWVVRPPRYIQDLRT-----RMFRAEPELTQSLGRNPSVAELAGALDEDP 155

Query: 171 SEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           + V       +    +SL+A+   SD  S       + +     +  +E+ E       L
Sbjct: 156 AAVQEAISASSSMHPDSLDAVNPHSDAPS-------IGEVLACPETPLERLEELAC---L 205

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             ++  L+  +R +   R   E   T   L     +S+ +V +  AR   ++Q  +  
Sbjct: 206 RDAIQDLDSADRELLYRRYFCEE--TQVQLGKRLGMSQMQVSRRLARVLVELQRRLAS 261


>gi|119470003|ref|ZP_01612808.1| flagellar biosynthesis sigma factor [Alteromonadales bacterium
           TW-7]
 gi|119446713|gb|EAW27986.1| flagellar biosynthesis sigma factor [Alteromonadales bacterium
           TW-7]
          Length = 240

 Score =  101 bits (253), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 43/238 (18%), Positives = 89/238 (37%), Gaps = 18/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + +V  H  LV K+A          + + +++  G IGL++A K FD  +G    T++ 
Sbjct: 13  LNVIVEKHASLVKKVACHLIARLPASVQLDDLIQSGMIGLIEASKSFDATKGASFETFAG 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + R             + +   +  L+  L        +    + +A+KL
Sbjct: 73  IRIRGAMLDEMRR-GDWAPRSVHRKSRLVAETIAFLEKSLN-------REPTDIEVAEKL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +S +E   +   +   + L       D+++           D          + +    
Sbjct: 125 EISLNEYHHILNDVNASKVLGIEDLGVDEDAISPVG-----QDLALDKPFNNVKNERFNE 179

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L  ++  L  R+  +        + + L+ +    +VS  RV QI  +A  K++  I
Sbjct: 180 SLLGAIKSLPERDAMVLSLYY--NDEMNLKEIGHILDVSESRVSQIHGQAMIKLKAKI 235


>gi|217077805|ref|YP_002335523.1| RNA polymerase sigma factor for flagellar operon [Thermosipho
           africanus TCF52B]
 gi|217037660|gb|ACJ76182.1| RNA polymerase sigma factor for flagellar operon [Thermosipho
           africanus TCF52B]
          Length = 226

 Score =  101 bits (253), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 47/238 (19%), Positives = 105/238 (44%), Gaps = 21/238 (8%)

Query: 50  AHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              LV+ +L  + KIA        + + + +++ EG +  +QA++KFDP++G +L +Y +
Sbjct: 4   KEALVSEYLPYIKKIAYDLKRNLPHNVEVDDLIQEGLVAFIQAIEKFDPKKGAKLRSYLL 63

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +K AM +Y+ +   +         K L  +++ ++  +  + +++        IAK  
Sbjct: 64  TRVKGAMYDYLRKIDWM--------PKNLRHDIKLVEDAIVNM-ESDTNDIDFEKIAKIT 114

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           N+    V      L   + L      SD   S+  D +  D +            +  + 
Sbjct: 115 NLPIENVKRAYNELTRKQLLMLDSYISDD--SELIDKIASDEN-----PYSYAINELLKE 167

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L  ++  L+ +E+ +   R   E+ ++L+ +     V+  RV Q+ A+   K+++ +
Sbjct: 168 QLIEAIKKLDDKEQLLLSLRF--EHELSLKEIGKVLNVTESRVSQLLAKTLAKLKKYL 223


>gi|323527722|ref|YP_004229875.1| RNA polymerase sigma-28 subunit FliA/WhiG [Burkholderia sp.
           CCGE1001]
 gi|323384724|gb|ADX56815.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia sp.
           CCGE1001]
          Length = 244

 Score =  101 bits (253), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 41/215 (19%), Positives = 89/215 (41%), Gaps = 14/215 (6%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++  G IGL+ A  ++  ++G +  TY+   I+ AM + +  +  L         +
Sbjct: 37  DLDDLIQAGMIGLLDAASRYKEDQGAQFETYASQRIRGAMLDELRSNDWL--------PR 88

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            L    R ++  +  +  N  +      IA+ L +   E  SM   L G + +       
Sbjct: 89  SLRRTSREVETAVHKVEQNLGRSASETEIAEHLQMPLDEYQSMLQDLHGSQLIYYEDFDR 148

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
             +   + D    DH      L++    ++ R+ L  ++  L  RE+ +       E  +
Sbjct: 149 SADDEPFLDRYCVDHSDPLSALLD----ESLRSALVEAIDRLPEREKLLMSLYY--ERGM 202

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            L  + +  EVS  RV Q+ ++A  +++  +++  
Sbjct: 203 NLREIGAVMEVSESRVCQLHSQAVARLRTRLREMA 237


>gi|207724998|ref|YP_002255395.1| rna polymerase sigma factor for flagellar operon (sigma-f factor)
           protein [Ralstonia solanacearum MolK2]
 gi|207738855|ref|YP_002257248.1| rna polymerase sigma factor for flagellar operon (sigma-f factor)
           protein [Ralstonia solanacearum IPO1609]
 gi|206590225|emb|CAQ37186.1| rna polymerase sigma factor for flagellar operon (sigma-f factor)
           protein [Ralstonia solanacearum MolK2]
 gi|206592225|emb|CAQ59131.1| rna polymerase sigma factor for flagellar operon (sigma-f factor)
           protein [Ralstonia solanacearum IPO1609]
          Length = 243

 Score =  101 bits (253), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 40/241 (16%), Positives = 99/241 (41%), Gaps = 17/241 (7%)

Query: 56  SHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++  LV +IA          + + +++  G +GL+ A+ +++  +G +   Y+   I+ A
Sbjct: 16  AYAPLVRRIANQMMVKLPASVELDDLIQAGMMGLLDALSRYEETQGVQFEFYAAQRIRGA 75

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           + + +  S  L         + L  N R ++  +Q +     +      IA  L +S ++
Sbjct: 76  ILDELRGSDWL--------PRGLRRNARTIEQAIQKLQQQKGRAPTETEIAAALEMSLAD 127

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
              +   L G    + L+   D +      ++       +   +++    + R  +  ++
Sbjct: 128 YQKLLVELQG----SQLLYYEDFDREDADAFIENRAAENDATPLDQLLDHDLRESVVAAI 183

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
             L  RE+ +       E  + L  + +   VS  RV QI ++A  +++  ++++  L +
Sbjct: 184 EALPEREKLMMSLYY--EQDLNLREIGAVMGVSESRVCQIHSQAIARIRARLRERAWLPT 241

Query: 293 S 293
            
Sbjct: 242 P 242


>gi|254250894|ref|ZP_04944212.1| DNA-directed RNA polymerase specialized sigma subunit [Burkholderia
           dolosa AUO158]
 gi|124893503|gb|EAY67383.1| DNA-directed RNA polymerase specialized sigma subunit [Burkholderia
           dolosa AUO158]
          Length = 369

 Score =  101 bits (253), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 41/215 (19%), Positives = 89/215 (41%), Gaps = 14/215 (6%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++  G IGLM A  ++  ++G +  TY+   I+ AM + +  +  L         +
Sbjct: 163 DLDDLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDELRSNDWL--------PR 214

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            L    R ++  +  +     +      IA+ LN+   E  +M   L G    + LI   
Sbjct: 215 SLRKTSREVEHAVHQVEQQLGRAASEAEIAQHLNMPLDEYQAMLQDLHG----SQLIYYE 270

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D + +   +  +          +     ++ R+ L  ++  L  RE+ +       E  +
Sbjct: 271 DFDRAADDEPFLDRFRVDHADPLSALLDEHLRDALVEAIERLPEREKLLMSLYY--ERGL 328

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            L  + +  EVS  RV Q+ ++A  +++  +++Q 
Sbjct: 329 NLREIGAVLEVSESRVCQLHSQAVARLRARLREQA 363


>gi|78064851|ref|YP_367620.1| flagellar biosynthesis sigma factor [Burkholderia sp. 383]
 gi|77965596|gb|ABB06976.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Burkholderia sp.
           383]
          Length = 244

 Score =  101 bits (253), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 43/215 (20%), Positives = 89/215 (41%), Gaps = 14/215 (6%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++  G IGLM A  ++  ++G +  TY+   I+ AM + +  +  L         +
Sbjct: 38  DLDDLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDELRSNDWL--------PR 89

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            L    R ++  +  +  N  +      IA+ LN+   E   M   L G + +       
Sbjct: 90  SLRKTSREVEHAVHQVEQNLGRSASETEIAQHLNMPLDEYQGMLQDLHGSQLIYYEDFDR 149

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
             +   + D    DH      L++    ++ R  L  ++  L  RE+ +       E  +
Sbjct: 150 AADDEPFLDRYRVDHADPLSALLD----EHLREALVEAIERLPEREKLLMSLYY--ERGL 203

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            L  + +  EVS  RV Q+ ++A  +++  +++Q 
Sbjct: 204 NLREIGAVLEVSESRVCQLHSQAVARLRARLREQA 238


>gi|152965591|ref|YP_001361375.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Kineococcus
           radiotolerans SRS30216]
 gi|151360108|gb|ABS03111.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Kineococcus
           radiotolerans SRS30216]
          Length = 286

 Score =  101 bits (253), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 59/238 (24%), Positives = 98/238 (41%), Gaps = 19/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H LV  +L LV  I   + G     +   ++ S G + L QA + +DP  G     Y+ 
Sbjct: 9   RHALVEKNLPLVGYITSEFIGRLPSHVSRDDLTSAGLMALFQASRGYDPNTGVPFNRYAN 68

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ A+ + + R       G  + Q       R+L      +T    +      +A  L
Sbjct: 69  TRIRGAILDDL-RGADWASRGVRSRQ-------RQLSRTEDQLTTELGRTPTSAELAASL 120

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            VSE E+ S          L+    +++  S    D L     G EQ L+ +E    R  
Sbjct: 121 GVSEKELASTRDEAQRSMVLSMQGFTAEGGS--IDDHLPTHAPGPEQELLHRE----RLG 174

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L  +++VL  R + + E   +QE P+    L+ E EVS  R+ Q+ A A   +++ +
Sbjct: 175 YLRSAIAVLPERLKHVIEGYFIQERPM--AELAEELEVSESRISQMRAEALALLRDGM 230


>gi|121488747|emb|CAJ18258.1| sigma 70-type sigma factor [Pelodictyon luteolum]
          Length = 165

 Score =  101 bits (253), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 38/174 (21%), Positives = 77/174 (44%), Gaps = 11/174 (6%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           ++++EGN+GL++  K+FD  RGF+  +Y++WWI+ ++ + +     +V++    N+    
Sbjct: 1   DLINEGNLGLIKXAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLP--LNRVGTL 58

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
             + +    L+   + +        +A  L++   +V           S++A     D N
Sbjct: 59  NKISKAYSQLEQEFERD---PNTKELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDN 115

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +  D L  D    +  L     R +    + RS+SVL PRE  +  +     
Sbjct: 116 --RLLDVLQNDGHMPDHSL----NRDSLTLEVERSLSVLAPREADVIRSYFGIG 163


>gi|227355968|ref|ZP_03840360.1| RNA polymerase sigma factor for flagellar operon [Proteus mirabilis
           ATCC 29906]
 gi|227163956|gb|EEI48858.1| RNA polymerase sigma factor for flagellar operon [Proteus mirabilis
           ATCC 29906]
          Length = 244

 Score =  101 bits (253), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 35/238 (14%), Positives = 96/238 (40%), Gaps = 17/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 17  KNSLWERYVPLVRHEALRLQVKLPASVELDDLLQAGGIGLLNAVERYDSMQGAAFTTYAV 76

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ +M + +               + +  N R +   +  +  +  +P     +A  L
Sbjct: 77  QRIRGSMLDELR--------SRDWAPRSVRRNAREVTQSIHQLEQDLGRPPSEQEVADHL 128

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +  +E   +      D + + L +  + +    +       +  +   ++     + R 
Sbjct: 129 QIELAEYRQILL----DTNNSQLFSYDEWHEIYGESCEPSQDEDHDDNPLQMLLESDIRQ 184

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  ++ +L  RE+ +       +  + L+ + +   V   RV Q+ ++A K+++  +
Sbjct: 185 RVIDAIELLPEREKMVLTLYY--QEELNLKEIGAVLNVGESRVSQLHSQAIKRLRARL 240


>gi|291280645|ref|YP_003497479.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Deferribacter
           desulfuricans SSM1]
 gi|290755347|dbj|BAI81723.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Deferribacter
           desulfuricans SSM1]
          Length = 255

 Score =  101 bits (253), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 46/245 (18%), Positives = 97/245 (39%), Gaps = 19/245 (7%)

Query: 50  AHRLVTSHLRLVVKIAMG-YRGY--GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L    L  +       Y      + I EV S    G ++A+ ++DP +      +  
Sbjct: 25  KEDLTKEFLPKIDIWVKKAYSKLPDHIDIDEVYSAACYGFVEALNRYDPSQNIDFKYFVE 84

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +K A+ + + R   L +   T         L+ L+  +Q ++    +      IA+K 
Sbjct: 85  KRVKGAILDVLRRLDLLSRTKRT--------KLKDLENKIQTLSKELGRQPTPEEIAEKY 136

Query: 167 NVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            +   E+ ++          SLN L++  D       D++  D    E    E+  ++  
Sbjct: 137 GIDTEEIYNLLELSDKTHIISLNTLLDKDDNEGHSLIDFIKSDLLTPE----EQVSKQEL 192

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            ++L + +  L  +ER +      +E  +T++ +     V+  RV QI  +  ++++E I
Sbjct: 193 IDILQKEIENLKEKERLVITLYYYEE--LTMKEIGEILGVTEARVCQIHNKVVEQLKEKI 250

Query: 285 QKQVE 289
            K ++
Sbjct: 251 LKMIK 255


>gi|224002653|ref|XP_002290998.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|220972774|gb|EED91105.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 345

 Score =  101 bits (253), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 53/258 (20%), Positives = 120/258 (46%), Gaps = 22/258 (8%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYG----LPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + A ++LV S+LR+V ++   Y   G        +++ +G + L++A +K++PERGFR +
Sbjct: 83  IEAKNQLVASNLRMVQRVVNLYIRNGLGSEYNAGDLMQDGTMALIRAAEKYEPERGFRFS 142

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+M+WI++A++        +V +    ++   +  + + +  L+     +    ++ A 
Sbjct: 143 TYAMYWIRSAVKRSQTMQSRIVNVPQRIHE--TYKRVTKTEARLRKELGRDPTKVELSAA 200

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDK-NSSQWQDWLVYD--HDGQEQVLIEKE 219
                V          + A   SL+A + ++ K N+S  +   +YD      ++   EK 
Sbjct: 201 CDITVVQLDRCRRAMQQAA--FSLDAEVQNTYKPNNSNSRKDTMYDLVASKVDETEYEKT 258

Query: 220 ERKNRRNMLTRSMSV-LNPRERRIFEARRLQEN----------PVTLENLSSEFEVSRER 268
           +R   +  L  ++   L+P E  +   R    +          P+T+  +S    +  ++
Sbjct: 259 QRLLMKEHLISTLRRYLSPHEVDLLLLRYGLMDERALPKGMSGPLTIAEVSKLVGLKPDK 318

Query: 269 VRQIEARAFKKVQESIQK 286
           VR+I   + K+++  +++
Sbjct: 319 VRRIIINSQKQLRHLMKE 336


>gi|187926255|ref|YP_001892600.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Ralstonia pickettii
           12J]
 gi|241665743|ref|YP_002984102.1| flagellar biosynthesis sigma factor [Ralstonia pickettii 12D]
 gi|309778948|ref|ZP_07673718.1| RNA polymerase sigma factor for flagellar operon [Ralstonia sp.
           5_7_47FAA]
 gi|187728009|gb|ACD29173.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Ralstonia pickettii
           12J]
 gi|240867770|gb|ACS65430.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Ralstonia pickettii
           12D]
 gi|308922295|gb|EFP67922.1| RNA polymerase sigma factor for flagellar operon [Ralstonia sp.
           5_7_47FAA]
          Length = 253

 Score =  101 bits (253), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 41/240 (17%), Positives = 96/240 (40%), Gaps = 17/240 (7%)

Query: 57  HLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           +  LV +IA          + + +++  G +GL+ A+ +++  +G +   Y+   I+ A+
Sbjct: 27  YAPLVRRIANQMMVKLPASVELDDLIQAGMMGLLDALSRYEETQGVQFEFYAAQRIRGAI 86

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
            + +  S  L         + L  N R ++  +Q +     +      IA  L +S +E 
Sbjct: 87  LDELRGSDWL--------PRGLRRNARTIEQAIQKLQQQKGRAPTETEIAVALGMSLAEY 138

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
                 L G    + L+   D +      ++       +   +++    + R  +  ++ 
Sbjct: 139 QKQLVDLQG----SQLLYYEDFDREDADAFIENRAPENDATPLDQLLDHDLRESVVAAIE 194

Query: 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
            L  RE+ +       E  + L  + +   VS  RV QI ++A  +++  ++ +  L + 
Sbjct: 195 GLPEREKLMMSLYY--EQDLNLREIGAVMGVSESRVCQIHSQAIARIRSRLRDRAWLPTP 252


>gi|120613052|ref|YP_972730.1| FliA/WhiG family RNA polymerase sigma factor [Acidovorax citrulli
           AAC00-1]
 gi|120591516|gb|ABM34956.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Acidovorax
           citrulli AAC00-1]
          Length = 238

 Score =  101 bits (253), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 44/241 (18%), Positives = 105/241 (43%), Gaps = 17/241 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L+  H  LV +IA          + + +++  G IGL +A+ +++  +G +  T++ 
Sbjct: 10  RDALIRQHAPLVRRIAHHMIAKLPPNVELDDLIQVGMIGLNEALSRYEVTQGVQFETFAS 69

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + R    +   +  +QK +   + RL+  L        +      IA +L
Sbjct: 70  QRIRGAMLDEL-REGDWMSRSSRKSQKEIEHAVTRLEQKL-------GRSPHESEIATEL 121

Query: 167 NVSESEVISMNCRLAGDESLNALINS-SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
            +S +E  S+  ++ G + +     +  D +   + D  V D       ++  +     R
Sbjct: 122 ELSLAEYQSLLSKVRGTQLVYLEDMTRGDDDDDGFLDRHVADSAADPMAMLRDQRL---R 178

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             L  ++  L  RE++I       E+ + L+ +++   V+  R+ Q+ +++  +++  ++
Sbjct: 179 ASLVAAIKALPEREQQIMGMYY--EHDMNLKEIAAVLGVTESRICQLHSQSIARLRAKMR 236

Query: 286 K 286
            
Sbjct: 237 S 237


>gi|226329392|ref|ZP_03804910.1| hypothetical protein PROPEN_03297 [Proteus penneri ATCC 35198]
 gi|225202578|gb|EEG84932.1| hypothetical protein PROPEN_03297 [Proteus penneri ATCC 35198]
          Length = 131

 Score =  101 bits (253), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 40/127 (31%), Positives = 70/127 (55%), Gaps = 3/127 (2%)

Query: 162 IAKKLNVSESEVISMNCRL-AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
           +A++L VSES+V  M  R+ A D + +   + SD +        + D        IE++ 
Sbjct: 4   VARELGVSESDVREMESRMSAQDMAFDMTADDSDDSHPIAPVLFLEDKSSDFADGIEEDN 63

Query: 221 RKNRR-NMLTRSMSVLNPRERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAFK 278
             N   + LT ++  L+ R + I  AR L ++   TL++L++++ VS ERVRQ+E  A K
Sbjct: 64  WDNHAADKLTSAIETLDERSQDIIRARWLDDDNKSTLQDLATKYGVSAERVRQLEKNAMK 123

Query: 279 KVQESIQ 285
           K++ +I+
Sbjct: 124 KLRLAIE 130


>gi|257095368|ref|YP_003169009.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Candidatus
           Accumulibacter phosphatis clade IIA str. UW-1]
 gi|257047892|gb|ACV37080.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Candidatus
           Accumulibacter phosphatis clade IIA str. UW-1]
          Length = 248

 Score =  101 bits (253), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 41/238 (17%), Positives = 98/238 (41%), Gaps = 17/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             +LV   + LV +IA          + + +++  G +GL+ A+ +F+   G +   Y+ 
Sbjct: 10  RDQLVQHFVPLVKRIACHLMARLPASVQVDDLIQNGMLGLLDAISRFEATMGAQFEAYAA 69

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             ++ AM + +  +  L         + L  + RR++  +  +   + +      +A  L
Sbjct: 70  QRVRGAMLDGLRENDWL--------PRSLRSDCRRIEVAIARLEQEHGRAPTEKELADSL 121

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++ ++   M     G + +      +++     +  LV D D     L+E+E     R 
Sbjct: 122 GMALADYQKMLQDARGHQLVYLEDMVAERGEDFLERHLV-DADADPSKLLEEE---TFRR 177

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +L +++  L  RER +       E  + +  +     V+  RV Q+ ++   +++  +
Sbjct: 178 LLVQAIDGLPERERLLMALYY--EQDLNMREIGEVMGVTESRVCQLHSQVVLRLRARL 233


>gi|154504525|ref|ZP_02041263.1| hypothetical protein RUMGNA_02029 [Ruminococcus gnavus ATCC 29149]
 gi|153795007|gb|EDN77427.1| hypothetical protein RUMGNA_02029 [Ruminococcus gnavus ATCC 29149]
          Length = 208

 Score =  101 bits (253), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 55/254 (21%), Positives = 99/254 (38%), Gaps = 58/254 (22%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L   EE    ++Y E GDL A H L+  +LRLV  +   Y+       +++S G IGL+
Sbjct: 7   PLTPSEEKEYIQKYTE-GDLQAKHILIERNLRLVAHVIKKYQYVDEDPEDLISIGTIGLI 65

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +A+  F+P +G RLA Y+   ++  +                        +LR  K   +
Sbjct: 66  KAIVTFNPSKGNRLAAYASKCVENEI----------------------LMHLRARKKTSK 103

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
            I                   S  E I  + R   +  L  +I + + +  +     V  
Sbjct: 104 EI-------------------SLYEPIGTD-REGNEIKLYDIIETDEDDIPER----VCL 139

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            +  +++  + E   ++R  L     VL  R    +     +E   T   ++ +  +SR 
Sbjct: 140 KENIQKLYEKVENELSQREKL-----VLKMR----YGLYGGEE--YTQREVAKQLGISRS 188

Query: 268 RVRQIEARAFKKVQ 281
            V +IE  A +K++
Sbjct: 189 YVSRIEKSAVEKLR 202


>gi|206558549|ref|YP_002229309.1| flagellar biosynthesis sigma factor [Burkholderia cenocepacia
           J2315]
 gi|198034586|emb|CAR50452.1| RNA polymerase sigma factor for flagellar regulon FliA
           [Burkholderia cenocepacia J2315]
          Length = 243

 Score =  101 bits (253), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 42/215 (19%), Positives = 89/215 (41%), Gaps = 14/215 (6%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++  G IGLM A  ++  ++G +  TY+   I+ AM + +  +  L         +
Sbjct: 37  DLDDLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDELRSNDWL--------PR 88

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            L    R ++  +  +  +  +      IA+ LN+   E   M   L G + +       
Sbjct: 89  SLRKTSREVEHAVHQVEQHLGRSASETEIAQHLNMPLDEYQGMLQDLHGSQLIYYEDFDR 148

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
             +   + D    DH      L++    ++ R  L  ++  L  RE+ +       E  +
Sbjct: 149 AADDEPFLDRYRVDHADPLSALLD----EHLREALVEAIERLPEREKLLMSLYY--ERGL 202

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            L  + +  EVS  RV Q+ ++A  +++  +++Q 
Sbjct: 203 NLREIGAVLEVSESRVCQLHSQAVARLRARLREQA 237


>gi|121607918|ref|YP_995725.1| FliA/WhiG family RNA polymerase sigma factor [Verminephrobacter
           eiseniae EF01-2]
 gi|121552558|gb|ABM56707.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Verminephrobacter eiseniae EF01-2]
          Length = 241

 Score =  101 bits (253), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 39/241 (16%), Positives = 100/241 (41%), Gaps = 14/241 (5%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L+  H+ LV KIA          + + +++  G +GL  A+ ++   +G +  T++ 
Sbjct: 10  RDALLRQHVPLVRKIAHHMIAKLPANVELDDLIQVGMMGLADALSRYQVAQGVQFETFAS 69

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + R    +      +QK +   + RL+  L        +      IA ++
Sbjct: 70  QRIRGAMLDQL-REGDWMSRSARKSQKEIEQAVHRLEQRL-------GRSPLESEIASEM 121

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH-DGQEQVLIEKEERKNRR 225
            +  +   S+  ++ G + +        ++  + +D  +  H        +E    +  +
Sbjct: 122 GLHLASYQSLLGKVRGTQLVYLEDMGQGRDEREAEDGFLERHIVDSAADPVELLRDQRLK 181

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             L  ++  L  RE+ I       E+ + L+ +++   ++  RV Q+ +++  +++  ++
Sbjct: 182 TSLVAAIQSLPEREQHIMGMYY--EHDMNLKEIAAVLGITESRVCQLHSQSIVRLRAKMR 239

Query: 286 K 286
            
Sbjct: 240 A 240


>gi|311279128|ref|YP_003941359.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Enterobacter cloacae
           SCF1]
 gi|308748323|gb|ADO48075.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Enterobacter cloacae
           SCF1]
          Length = 243

 Score =  101 bits (253), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 43/240 (17%), Positives = 102/240 (42%), Gaps = 17/240 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   + +L+  L        +      +A++L
Sbjct: 73  QRIRGAMLDEL-RSRDWVPRSVRRNAREVAQAMGQLEQEL-------GRNATETEVAQRL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++  E   M      D + + L +  +          +   + Q++  + +    N R 
Sbjct: 125 GIAVEEYRQMLL----DTNNSQLFSYDEWREEHGDSIELVTEENQQENPLHQLMESNLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  +V   RV Q+ ++A K+++  + +
Sbjct: 181 RVIEAIEALPEREQLVLTLYY--QEELNLKEIGAVLDVGESRVSQLHSQAIKRLRTKLGR 238


>gi|300697965|ref|YP_003748626.1| RNA polymerase sigma factor for flagellar operon [Ralstonia
           solanacearum CFBP2957]
 gi|299074689|emb|CBJ54246.1| RNA polymerase sigma factor for flagellar operon [Ralstonia
           solanacearum CFBP2957]
          Length = 245

 Score =  101 bits (253), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 41/241 (17%), Positives = 99/241 (41%), Gaps = 17/241 (7%)

Query: 56  SHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++  LV +IA          + + +++  G +GL+ A+ +++  +G +   Y+   I+ A
Sbjct: 18  AYAPLVRRIANQMMVKLPASVELDDLIQAGMMGLLDALSRYEETQGVQFEFYAAQRIRGA 77

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           + + +  S  L         + L  N R ++  +Q +     +      IA  L +S +E
Sbjct: 78  ILDELRGSDWL--------PRGLRRNARTIEQAIQKLQQQKGRAPTETEIAASLEMSLAE 129

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
              +   L G    + L+   D +      ++       +   +++    + R  +  ++
Sbjct: 130 YQKLLVELQG----SQLLYYEDFDREDADAFIENRAAENDATPLDQLLDHDLRESVVAAI 185

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
             L  RE+ +       E  + L  + +   VS  RV QI ++A  +++  ++++  L +
Sbjct: 186 EALPEREKLMMSLYY--EQDLNLREIGAVMGVSESRVCQIHSQAIARIRARLRERAWLPT 243

Query: 293 S 293
            
Sbjct: 244 P 244


>gi|167587836|ref|ZP_02380224.1| flagellar biosynthesis sigma factor [Burkholderia ubonensis Bu]
          Length = 244

 Score =  101 bits (253), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 42/215 (19%), Positives = 89/215 (41%), Gaps = 14/215 (6%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++  G IGLM A  ++  ++G +  TY+   I+ AM + +  +  L         +
Sbjct: 38  DLDDLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDELRSNDWL--------PR 89

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            L    R ++  +  +  +  +      IA+ LN+   E   M   L G + +       
Sbjct: 90  SLRKTSREVEHAVHQVEQHLGRAASEAEIAQHLNMPLDEYQGMLQDLHGSQLIYYEDFDR 149

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
             +   + D    DH      L++    ++ R  L  ++  L  RE+ +       E  +
Sbjct: 150 AADDEPFLDRYRVDHADPLSSLLD----EHLREALIEAIERLPEREKLLMSLYY--ERGL 203

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            L  + +  EVS  RV Q+ ++A  +++  +++Q 
Sbjct: 204 NLREIGAVLEVSESRVCQLHSQAVARLRARLREQA 238


>gi|156933482|ref|YP_001437398.1| flagellar biosynthesis sigma factor [Cronobacter sakazakii ATCC
           BAA-894]
 gi|156531736|gb|ABU76562.1| hypothetical protein ESA_01300 [Cronobacter sakazakii ATCC BAA-894]
          Length = 229

 Score =  101 bits (253), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 46/240 (19%), Positives = 102/240 (42%), Gaps = 17/240 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 3   KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 62

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   + +L+  L        +    + +A++L
Sbjct: 63  QRIRGAMLDEL-RSRDWVPRSVRRNAREVAQAIGQLEQEL-------GRNATELEVAERL 114

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   E   M      D + + L +  +          +   D Q +  + +    N R 
Sbjct: 115 SIPLEEYRQMLL----DTNNSQLFSYDEWREEHGDSIELVTEDNQNENPLHQLLESNLRE 170

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 171 RVMEAIESLPEREQMVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 228


>gi|270262372|ref|ZP_06190644.1| RNA polymerase sigma factor for flagellar operon [Serratia
           odorifera 4Rx13]
 gi|270044248|gb|EFA17340.1| RNA polymerase sigma factor for flagellar operon [Serratia
           odorifera 4Rx13]
          Length = 240

 Score =  101 bits (253), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 44/241 (18%), Positives = 101/241 (41%), Gaps = 17/241 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KNSLWLRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      + + +   +R+L+  L        +P   V +A+ L
Sbjct: 73  QRIRGAMLDEL-RSRDWVPRSVRRHAREVAQVMRQLEQRL-------GRPASEVEVAQTL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           N+   E   +      D + + L +  +      +         +E   +      N R 
Sbjct: 125 NIPLDEYRQILL----DTNNSQLFSYDEWREEHGESAEPLLEGHEEANPLHHLLEGNLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  +V   RV Q+ ++A K+++  +  
Sbjct: 181 RVIDAIDALPEREKMVLTLYY--QEELNLKEIGAVLDVGESRVSQLHSQAIKRLRARLAA 238

Query: 287 Q 287
           +
Sbjct: 239 E 239


>gi|91785643|ref|YP_560849.1| flagellar biosynthesis sigma factor [Burkholderia xenovorans LB400]
 gi|296157465|ref|ZP_06840300.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia sp.
           Ch1-1]
 gi|91689597|gb|ABE32797.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Burkholderia
           xenovorans LB400]
 gi|295892237|gb|EFG72020.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia sp.
           Ch1-1]
          Length = 244

 Score =  101 bits (253), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 41/215 (19%), Positives = 87/215 (40%), Gaps = 14/215 (6%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++  G IGL+ A  ++  ++G +  TY+   I+ AM + +  +  L         +
Sbjct: 37  DLDDLIQAGMIGLLDAASRYKEDQGAQFETYASQRIRGAMLDELRSNDWL--------PR 88

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            L    R ++  +  +  N  +      IA+ L +   E  SM   L G + +       
Sbjct: 89  SLRRTSREVETAVHKVEQNLGRSASETEIAEHLQMPLDEYQSMLQDLHGSQLIYYEDFDR 148

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
             +   + D    DH      L++       R+ L  ++  L  RE+ +       E  +
Sbjct: 149 SADDEPFLDRYCVDHSDPLSALLDDSL----RSALVEAIDRLPEREKLLMSLYY--ERGM 202

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            L  + +  EVS  RV Q+ ++A  +++  +++  
Sbjct: 203 NLREIGAVMEVSESRVCQLHSQAVARLRTRLREMA 237


>gi|307731372|ref|YP_003908596.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Burkholderia
           sp. CCGE1003]
 gi|307585907|gb|ADN59305.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Burkholderia
           sp. CCGE1003]
          Length = 244

 Score =  101 bits (252), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 41/215 (19%), Positives = 89/215 (41%), Gaps = 14/215 (6%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++  G IGL+ A  ++  ++G +  TY+   I+ AM + +  +  L         +
Sbjct: 37  DLDDLIQAGMIGLLDAASRYKEDQGAQFETYASQRIRGAMLDELRSNDWL--------PR 88

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            L    R ++  +  +  N  +      IA+ L +   E  SM   L G + +       
Sbjct: 89  SLRRTSREVETAVHKVEQNLGRSASETEIAEHLQMPLDEYQSMLQDLHGSQLIYYEDFDR 148

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
             +   + D    DH      L++    ++ R+ L  ++  L  RE+ +       E  +
Sbjct: 149 SADDEPFLDRYCVDHSDPLSALLD----ESLRSALVDAIDRLPEREKLLMSLYY--ERGM 202

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            L  + +  EVS  RV Q+ ++A  +++  +++  
Sbjct: 203 NLREIGAVMEVSESRVCQLHSQAVARLRTRLREMA 237


>gi|54297695|ref|YP_124064.1| flagellar biosynthesis sigma factor [Legionella pneumophila str.
           Paris]
 gi|53751480|emb|CAH12898.1| sigma factor 28 [Legionella pneumophila str. Paris]
          Length = 238

 Score =  101 bits (252), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 49/239 (20%), Positives = 104/239 (43%), Gaps = 21/239 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              LV +H  LV +IA    G     + + +++  G +GL++A + +D  +G    TY+ 
Sbjct: 15  QEALVKTHATLVKRIAHHLLGRLPQSVQLDDLIQSGMLGLLEAARHYDSSKGASFETYAG 74

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+  M + + R+  +         + ++ N R +   ++ +     +  +   IA++L
Sbjct: 75  IRIRGHMLDEVRRNDWV--------PRSVYRNSRMISDAVRILEHKFGREAKDNEIAEEL 126

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRR 225
            VS  +   M       +S+++ +   D       D +++DH+G           R +  
Sbjct: 127 GVSLDDYHDMLQ-----DSISSHLYGFDDLGVT--DDVLFDHEGNGSTEPHRNVMRSDMM 179

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           N LT+ +  L  +ER +       E  + L+ +    EVS  R+ QI ++A  +++  +
Sbjct: 180 NRLTQVIDSLPRKERLVLSLYY--EQDLNLKEIGEILEVSESRISQILSQATHRIRSRL 236


>gi|320647130|gb|EFX15963.1| flagellar biosynthesis sigma factor [Escherichia coli O157:H- str.
           493-89]
 gi|320652413|gb|EFX20711.1| flagellar biosynthesis sigma factor [Escherichia coli O157:H- str.
           H 2687]
          Length = 228

 Score =  101 bits (252), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 102/240 (42%), Gaps = 17/240 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 3   KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 62

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   + +L+  L        +      +A++L
Sbjct: 63  QRIRGAMLDEL-RSRDWVPRSVRRNAREVAQAIGQLEQEL-------GRNATETEVAERL 114

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +  ++   M      D + + L +  +          +   D Q +  +++    N R 
Sbjct: 115 GIDIADYRQMLL----DTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQ 170

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 171 RVMEAIETLPEREKLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 228


>gi|121488785|emb|CAJ18277.1| sigma 70-type sigma factor [Pelodictyon clathratiforme]
          Length = 165

 Score =  101 bits (252), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 38/174 (21%), Positives = 77/174 (44%), Gaps = 11/174 (6%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + +     +V++    N+    
Sbjct: 1   DLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLP--LNRVGTL 58

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
             + +    L+   + +        +A  L +   +V           S++A     D N
Sbjct: 59  NKISKAYSQLEQEFERD---PNTRELATLLEMDSQDVADTLKIAGRHVSVDAPFAQGDDN 115

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +  D L  D      +      R +    + RS+SVL PRE  + ++     
Sbjct: 116 --RLLDVLQNDG----HLPDYGLNRDSLTLEVERSLSVLAPREADVIKSYFGIG 163


>gi|168700558|ref|ZP_02732835.1| RNA polymerase sigma factor whiG [Gemmata obscuriglobus UQM 2246]
          Length = 260

 Score =  101 bits (252), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 54/254 (21%), Positives = 103/254 (40%), Gaps = 20/254 (7%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFD 94
              YRE   +   +RLV  +L LV   A         G+ + +++S G  GL+ A+  FD
Sbjct: 14  WLEYRERPTVELRNRLVERYLSLVKYNAERIWSRLPDGVELDDLISAGVFGLLDAIDAFD 73

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             RG +  TY +  I+ AM + +     + ++  +   K     +   +  L+A      
Sbjct: 74  LTRGVKFETYCVPRIRGAMLDELRTMDWVPRLVRSKASK-----MEAARKQLEAALGRPP 128

Query: 155 KPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           KPE    +++KL +   ++ S   +       SLN     +D      +  ++ D   + 
Sbjct: 129 KPE---ELSEKLGIPLEQLESYVGDATAVNLVSLNKKWYETDSYKDVREIDILEDKKAES 185

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
                   R   R+++      LN  ER I      +E  +T++ + +   +S  RV Q+
Sbjct: 186 PTG-----RLQNRDLMKLVTRGLNRNERLIVILYYYEE--MTMKEIGATLNLSESRVSQM 238

Query: 273 EARAFKKVQESIQK 286
            +    ++Q  + K
Sbjct: 239 HSSIVARLQSHLAK 252


>gi|110805895|ref|YP_689415.1| flagellar biosynthesis sigma factor [Shigella flexneri 5 str. 8401]
 gi|195939226|ref|ZP_03084608.1| flagellar biosynthesis sigma factor [Escherichia coli O157:H7 str.
           EC4024]
 gi|208816591|ref|ZP_03257711.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4045]
 gi|208820391|ref|ZP_03260711.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4042]
 gi|217328583|ref|ZP_03444664.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. TW14588]
 gi|227885651|ref|ZP_04003456.1| flagellar biosynthesis sigma factor [Escherichia coli 83972]
 gi|256017880|ref|ZP_05431745.1| flagellar biosynthesis sigma factor [Shigella sp. D9]
 gi|256022420|ref|ZP_05436285.1| flagellar biosynthesis sigma factor [Escherichia sp. 4_1_40B]
 gi|261227583|ref|ZP_05941864.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli O157:H7
           str. FRIK2000]
 gi|261255813|ref|ZP_05948346.1| RNA polymerase, sigma 28 factor [Escherichia coli O157:H7 str.
           FRIK966]
 gi|300818654|ref|ZP_07098862.1| flagellar biosynthesis sigma factor [Escherichia coli MS 107-1]
 gi|300822306|ref|ZP_07102447.1| flagellar biosynthesis sigma factor [Escherichia coli MS 119-7]
 gi|300899176|ref|ZP_07117454.1| flagellar biosynthesis sigma factor [Escherichia coli MS 198-1]
 gi|300904809|ref|ZP_07122636.1| flagellar biosynthesis sigma factor [Escherichia coli MS 84-1]
 gi|300917364|ref|ZP_07134033.1| flagellar biosynthesis sigma factor [Escherichia coli MS 115-1]
 gi|300925015|ref|ZP_07140938.1| flagellar biosynthesis sigma factor [Escherichia coli MS 182-1]
 gi|300951546|ref|ZP_07165380.1| flagellar biosynthesis sigma factor [Escherichia coli MS 116-1]
 gi|300956562|ref|ZP_07168843.1| flagellar biosynthesis sigma factor [Escherichia coli MS 175-1]
 gi|300982291|ref|ZP_07176001.1| flagellar biosynthesis sigma factor [Escherichia coli MS 200-1]
 gi|300993927|ref|ZP_07180602.1| flagellar biosynthesis sigma factor [Escherichia coli MS 45-1]
 gi|301018228|ref|ZP_07182743.1| flagellar biosynthesis sigma factor [Escherichia coli MS 69-1]
 gi|301050723|ref|ZP_07197582.1| flagellar biosynthesis sigma factor [Escherichia coli MS 185-1]
 gi|301305263|ref|ZP_07211360.1| flagellar biosynthesis sigma factor [Escherichia coli MS 124-1]
 gi|301327712|ref|ZP_07220918.1| flagellar biosynthesis sigma factor [Escherichia coli MS 78-1]
 gi|301645559|ref|ZP_07245489.1| flagellar biosynthesis sigma factor [Escherichia coli MS 146-1]
 gi|306814254|ref|ZP_07448420.1| flagellar biosynthesis sigma factor [Escherichia coli NC101]
 gi|307138589|ref|ZP_07497945.1| flagellar biosynthesis sigma factor [Escherichia coli H736]
 gi|309795968|ref|ZP_07690381.1| flagellar biosynthesis sigma factor [Escherichia coli MS 145-7]
 gi|110615443|gb|ABF04110.1| flagellar biosynthesis sigma factor FliA [Shigella flexneri 5 str.
           8401]
 gi|208730934|gb|EDZ79623.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4045]
 gi|208740514|gb|EDZ88196.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. EC4042]
 gi|217317930|gb|EEC26357.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           O157:H7 str. TW14588]
 gi|227837224|gb|EEJ47690.1| flagellar biosynthesis sigma factor [Escherichia coli 83972]
 gi|300297591|gb|EFJ53976.1| flagellar biosynthesis sigma factor [Escherichia coli MS 185-1]
 gi|300307268|gb|EFJ61788.1| flagellar biosynthesis sigma factor [Escherichia coli MS 200-1]
 gi|300316625|gb|EFJ66409.1| flagellar biosynthesis sigma factor [Escherichia coli MS 175-1]
 gi|300357213|gb|EFJ73083.1| flagellar biosynthesis sigma factor [Escherichia coli MS 198-1]
 gi|300399815|gb|EFJ83353.1| flagellar biosynthesis sigma factor [Escherichia coli MS 69-1]
 gi|300403277|gb|EFJ86815.1| flagellar biosynthesis sigma factor [Escherichia coli MS 84-1]
 gi|300406428|gb|EFJ89966.1| flagellar biosynthesis sigma factor [Escherichia coli MS 45-1]
 gi|300415410|gb|EFJ98720.1| flagellar biosynthesis sigma factor [Escherichia coli MS 115-1]
 gi|300418834|gb|EFK02145.1| flagellar biosynthesis sigma factor [Escherichia coli MS 182-1]
 gi|300449221|gb|EFK12841.1| flagellar biosynthesis sigma factor [Escherichia coli MS 116-1]
 gi|300525189|gb|EFK46258.1| flagellar biosynthesis sigma factor [Escherichia coli MS 119-7]
 gi|300528826|gb|EFK49888.1| flagellar biosynthesis sigma factor [Escherichia coli MS 107-1]
 gi|300839469|gb|EFK67229.1| flagellar biosynthesis sigma factor [Escherichia coli MS 124-1]
 gi|300845756|gb|EFK73516.1| flagellar biosynthesis sigma factor [Escherichia coli MS 78-1]
 gi|301076168|gb|EFK90974.1| flagellar biosynthesis sigma factor [Escherichia coli MS 146-1]
 gi|305852413|gb|EFM52864.1| flagellar biosynthesis sigma factor [Escherichia coli NC101]
 gi|308120418|gb|EFO57680.1| flagellar biosynthesis sigma factor [Escherichia coli MS 145-7]
 gi|312946514|gb|ADR27341.1| flagellar biosynthesis sigma factor [Escherichia coli O83:H1 str.
           NRG 857C]
 gi|315136559|dbj|BAJ43718.1| RNA polymerase sigma factor [Escherichia coli DH1]
 gi|315257247|gb|EFU37215.1| flagellar biosynthesis sigma factor [Escherichia coli MS 85-1]
 gi|315290288|gb|EFU49666.1| flagellar biosynthesis sigma factor [Escherichia coli MS 153-1]
 gi|315296505|gb|EFU55802.1| flagellar biosynthesis sigma factor [Escherichia coli MS 16-3]
 gi|320641770|gb|EFX11158.1| flagellar biosynthesis sigma factor [Escherichia coli O157:H7 str.
           G5101]
 gi|320658015|gb|EFX25777.1| flagellar biosynthesis sigma factor [Escherichia coli O55:H7 str.
           3256-97 TW 07815]
 gi|320658587|gb|EFX26281.1| flagellar biosynthesis sigma factor [Escherichia coli O55:H7 str.
           USDA 5905]
 gi|320668485|gb|EFX35312.1| flagellar biosynthesis sigma factor [Escherichia coli O157:H7 str.
           LSU-61]
 gi|323152745|gb|EFZ39017.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           EPECa14]
 gi|323186302|gb|EFZ71652.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           1357]
 gi|324007273|gb|EGB76492.1| flagellar biosynthesis sigma factor [Escherichia coli MS 57-2]
 gi|324013514|gb|EGB82733.1| flagellar biosynthesis sigma factor [Escherichia coli MS 60-1]
 gi|324017957|gb|EGB87176.1| flagellar biosynthesis sigma factor [Escherichia coli MS 117-3]
          Length = 229

 Score =  101 bits (252), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 102/240 (42%), Gaps = 17/240 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 3   KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 62

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   + +L+  L        +      +A++L
Sbjct: 63  QRIRGAMLDEL-RSRDWVPRSVRRNAREVAQAIGQLEQEL-------GRNATETEVAERL 114

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +  ++   M      D + + L +  +          +   D Q +  +++    N R 
Sbjct: 115 GIDIADYRQMLL----DTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQ 170

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 171 RVMEAIETLPEREKLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 228


>gi|107024379|ref|YP_622706.1| flagellar biosynthesis sigma factor [Burkholderia cenocepacia AU
           1054]
 gi|116688295|ref|YP_833918.1| flagellar biosynthesis sigma factor [Burkholderia cenocepacia
           HI2424]
 gi|170731608|ref|YP_001763555.1| flagellar biosynthesis sigma factor [Burkholderia cenocepacia
           MC0-3]
 gi|105894568|gb|ABF77733.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Burkholderia
           cenocepacia AU 1054]
 gi|116646384|gb|ABK07025.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Burkholderia
           cenocepacia HI2424]
 gi|169814850|gb|ACA89433.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia
           cenocepacia MC0-3]
          Length = 243

 Score =  101 bits (252), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 42/215 (19%), Positives = 88/215 (40%), Gaps = 14/215 (6%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++  G IGLM A  ++  ++G +  TY+   I+ AM + +  +  L         +
Sbjct: 37  DLDDLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDELRSNDWL--------PR 88

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            L    R ++  +  +  +  +      IA+ LN+   E   M   L G + +       
Sbjct: 89  SLRKTSREVEHAVHQVEQHLGRSASETEIAQHLNMPLDEYQGMLQDLHGSQLIYYEDFDR 148

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
             +   + D    DH      L++     + R  L  ++  L  RE+ +       E  +
Sbjct: 149 AADDEPFLDRYRVDHADPLSALLDD----HLREALVEAIERLPEREKLLMSLYY--ERGL 202

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            L  + +  EVS  RV Q+ ++A  +++  +++Q 
Sbjct: 203 NLREIGAVLEVSESRVCQLHSQAVARLRARLREQA 237


>gi|283785667|ref|YP_003365532.1| flagellar-specific Sigma F (Sigma 28) factor [Citrobacter rodentium
           ICC168]
 gi|282949121|emb|CBG88728.1| flagellar-specific Sigma F (Sigma 28) factor [Citrobacter rodentium
           ICC168]
          Length = 239

 Score =  101 bits (252), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 101/240 (42%), Gaps = 17/240 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV ++D  +G    TY++
Sbjct: 13  KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVDRYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   + +L+  L        +      +A++L
Sbjct: 73  QRIRGAMLDEL-RSRDWVPRSVRRNAREVAQAMGQLEQEL-------GRNATETEVAERL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   E   M      D + + L +  +          +   + Q++  +++    N R 
Sbjct: 125 GIPVEEYRQMLL----DTNNSQLFSYDEWREEHGDSIELVTEEHQQENPLQQLLESNLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 181 RVMDAIEALPEREQLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 238


>gi|83589703|ref|YP_429712.1| sporulation sigma factor SigE [Moorella thermoacetica ATCC 39073]
 gi|83572617|gb|ABC19169.1| RNA polymerase, sigma 29 subunit, SigE [Moorella thermoacetica ATCC
           39073]
          Length = 243

 Score =  101 bits (252), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 55/260 (21%), Positives = 105/260 (40%), Gaps = 59/260 (22%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EE  L  R  E GD +    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 41  PPLSSDEESDLLLRL-EDGDAAVKKVLIERNLRLVVYIARKFENTGVGIEDLVSIGTIGL 99

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FDP++  +LATY+   I+  +  Y+ R+                          
Sbjct: 100 IKAVNTFDPKKRIKLATYASRCIENEILMYLRRNNKT----------------------- 136

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                             +  VS  E ++++    G+E L + +  +D +       +  
Sbjct: 137 ------------------RAEVSFDEPLNID--WDGNELLLSDVLGTDND--IIYKSIEE 174

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           + D +   L  ++     R ++     +L+  E+             T + ++    +S+
Sbjct: 175 EVDHKLLQLAMRKLSSRERKIMEFRFGLLDGVEK-------------TQKEVADILGISQ 221

Query: 267 ERVRQIEARAFKKVQESIQK 286
             + ++E R  K++++ I +
Sbjct: 222 SYISRLEKRIIKRLRKEIAR 241


>gi|317403792|gb|EFV84272.1| RNA polymerase sigma factor for flagellar operon [Achromobacter
           xylosoxidans C54]
          Length = 253

 Score =  101 bits (252), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 39/247 (15%), Positives = 103/247 (41%), Gaps = 18/247 (7%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           A   LV  +  LV K+A+         + + +++  G IGL+ AV+++      +  TY+
Sbjct: 4   ADDSLVE-YAPLVRKLALQLLARLPASVELDDLIQAGMIGLLDAVRRYQETADAQFETYA 62

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
              I+ AM + +     L         + +    R+++  +Q++    ++      IA++
Sbjct: 63  TTRIRGAMLDELRGQDWL--------PRSVRAKARKIEQAIQSLEQRLMRAPTEAEIAQQ 114

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW----LVYDHDGQEQVLIEKEER 221
           + +  +E  ++     G + ++    +++ ++             +H       ++    
Sbjct: 115 MEIPLNEYQTLLHDAQGVQIVHYEDFATEPDTGSGSGQSDWTATLNHGAASGNPLDSLLA 174

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            + R  L  ++  L  RE+ +       E  + L+ + +   V+  RV Q+ ++A  +++
Sbjct: 175 GDFRQALIHAIDSLPDREKLLLSLCY--EQGLNLKEIGAIMNVTEARVCQLRSQATARIR 232

Query: 282 ESIQKQV 288
             +++Q 
Sbjct: 233 AKLREQA 239


>gi|296101730|ref|YP_003611876.1| flagellar biosynthesis sigma factor [Enterobacter cloacae subsp.
           cloacae ATCC 13047]
 gi|295056189|gb|ADF60927.1| flagellar biosynthesis sigma factor [Enterobacter cloacae subsp.
           cloacae ATCC 13047]
          Length = 239

 Score =  101 bits (252), Expect = 1e-19,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 99/240 (41%), Gaps = 17/240 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV ++D  +G    TY++
Sbjct: 13  KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVDRYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   + +L+  L        +      +A++L
Sbjct: 73  QRIRGAMLDEL-RSRDWVPRSVRRNAREVAHAMGQLEQEL-------GRNATETEVAERL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   E   M      D + + L +  +          +   + Q++  +      N R 
Sbjct: 125 GIPVEEYRQMLL----DTNNSQLFSYDEWREEHGDSIELVTDEHQQENPLHHLMEGNLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 181 RVMEAIEALPEREQLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 238


>gi|53720901|ref|YP_109887.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei
           K96243]
 gi|76811948|ref|YP_331475.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei
           1710b]
 gi|52211315|emb|CAH37304.1| RNA polymerase sigma factor for flagellar regulon FliA
           [Burkholderia pseudomallei K96243]
 gi|76581401|gb|ABA50876.1| RNA polymerase sigma factor for flagellar operon FliA [Burkholderia
           pseudomallei 1710b]
          Length = 243

 Score =  101 bits (252), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 40/215 (18%), Positives = 88/215 (40%), Gaps = 14/215 (6%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++  G IGL+ A  ++  ++G +  TY+   I+ AM + +  +  L         +
Sbjct: 37  DLDDLIQAGMIGLLDAASRYKEDQGAQFETYATQRIRGAMLDELRSNDWL--------PR 88

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            L    R ++  +  +     +      IA  L +   E  SM   L G    + L+   
Sbjct: 89  SLRKTSREVEHAVHQVEQRLGRSANETEIAAHLQMPLDEYQSMLQDLHG----SQLVYYE 144

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D + S   +  +  +       +     ++ R+ L  ++  L  RE+ +       E  +
Sbjct: 145 DFDRSADDEPFLDRYRADHSDPLSALLDEHLRSALVDAIERLPEREKLLMSLYY--ERGL 202

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            L  + +  EVS  RV Q+ ++A  +++  +++Q 
Sbjct: 203 NLREIGAVLEVSESRVCQLHSQAVARLRAKLREQA 237


>gi|300694351|ref|YP_003750324.1| RNA polymerase sigma factor for flagellar operon [Ralstonia
           solanacearum PSI07]
 gi|299076388|emb|CBJ35704.1| RNA polymerase sigma factor for flagellar operon [Ralstonia
           solanacearum PSI07]
          Length = 245

 Score =  101 bits (252), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 40/241 (16%), Positives = 99/241 (41%), Gaps = 17/241 (7%)

Query: 56  SHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++  LV +IA          + + +++  G +GL+ A+ +++  +G +   Y+   I+ A
Sbjct: 18  AYAPLVRRIANQMMVKLPASVELDDLIQAGMMGLLDALSRYEETQGVQFEFYAAQRIRGA 77

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           + + +  S  L         + L  N R ++  +Q +     +      IA  L++S ++
Sbjct: 78  ILDELRGSDWL--------PRGLRRNARTIEQAIQKLQQQKGRAPTETEIAAALDMSLAD 129

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
                  L G    + L+   D +      ++       +   +++    + R  +  ++
Sbjct: 130 YQRQLVELQG----SQLLYYEDFDREDADAFIENRAAENDATPLDQLLDHDLRESVVAAI 185

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
             L  RE+ +       E  + L  + +   VS  RV QI ++A  +++  ++++  L +
Sbjct: 186 EGLPEREKLMMSLYY--EQDLNLREIGAVMGVSESRVCQIHSQAIARIRARLRERAWLPT 243

Query: 293 S 293
            
Sbjct: 244 P 244


>gi|295678067|ref|YP_003606591.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Burkholderia
           sp. CCGE1002]
 gi|295437910|gb|ADG17080.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Burkholderia
           sp. CCGE1002]
          Length = 244

 Score =  101 bits (252), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 40/215 (18%), Positives = 87/215 (40%), Gaps = 14/215 (6%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++  G IGL+ A  ++  ++G +  TY+   I+ AM + +  +  L         +
Sbjct: 37  DLDDLIQAGMIGLLDAAGRYKEDQGAQFETYASQRIRGAMLDELRSNDWL--------PR 88

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            L    R ++  +  +  N  +      +A+ L +   E  SM   L G + +       
Sbjct: 89  SLRRTSREVETAVHKVEQNLGRSASEAEVAEHLQMPLDEYQSMLQDLHGSQLIYYEDFDR 148

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
             +   + D    DH      L++       R+ L  ++  L  RE+ +       E  +
Sbjct: 149 SADDEPFLDRYCVDHSDPLSALLDDSL----RSALIEAIDRLPEREKLLMSLYY--ERGM 202

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            L  + +  EVS  RV Q+ ++A  +++  +++  
Sbjct: 203 NLREIGAVMEVSESRVCQLHSQAVARLRARLREMA 237


>gi|146312155|ref|YP_001177229.1| flagellar biosynthesis sigma factor [Enterobacter sp. 638]
 gi|145319031|gb|ABP61178.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Enterobacter sp.
           638]
          Length = 239

 Score =  101 bits (251), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 44/240 (18%), Positives = 100/240 (41%), Gaps = 17/240 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV ++D  +G    TY++
Sbjct: 13  KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVDRYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   + +L+  L        +      +A++L
Sbjct: 73  QRIRGAMLDEL-RSRDWVPRSVRRNAREVAHAIGQLEQEL-------GRNATETEVAERL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++  +   M      D + + L +  +          +   + Q +  + +    N R 
Sbjct: 125 GIAVQDYRQMLL----DTNNSQLFSYDEWREEHGDSVELVTDENQHENPLHQLLEGNLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 181 RVMDAIEALPEREQLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 238


>gi|330502783|ref|YP_004379652.1| flagellar biosynthesis sigma factor [Pseudomonas mendocina NK-01]
 gi|328917069|gb|AEB57900.1| flagellar biosynthesis sigma factor [Pseudomonas mendocina NK-01]
          Length = 240

 Score =  101 bits (251), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 41/251 (16%), Positives = 97/251 (38%), Gaps = 21/251 (8%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPER 97
           Y +     + H+L+  +  LV +IA          + + +++  G IGL++A +K+D  +
Sbjct: 2   YNKAQAQDSQHQLIERYAPLVKRIAYHLLARLPASVQVDDLIQAGMIGLLEASRKYDSGK 61

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G    T++   I+ +M + + R           N + +   +R ++           +  
Sbjct: 62  GASFETFAGIRIRGSMLDEV-RKGDWAPRSVHRNSRMVSDAIRTVEA-------RTGRDA 113

Query: 158 QVVAIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
           +   +A +L +S  +   I  +   +   S + L+   +         L  D        
Sbjct: 114 KDHEVAAELQLSLEDYYGILGDTLGSRLFSFDDLLQDGE------HGGLHEDAGHTHLEP 167

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
               E +  +  L  +++ L  RER +       +  + L+ +     VS  RV Q+ ++
Sbjct: 168 SRDLEDERFQAALADAIAGLPERERLVLALYY--DEELNLKEIGEVLGVSESRVSQLHSQ 225

Query: 276 AFKKVQESIQK 286
              +++  + +
Sbjct: 226 CAARLRSRLSE 236


>gi|322833177|ref|YP_004213204.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Rahnella sp. Y9602]
 gi|321168378|gb|ADW74077.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Rahnella sp. Y9602]
          Length = 240

 Score =  101 bits (251), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 42/238 (17%), Positives = 95/238 (39%), Gaps = 17/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   ++ LV   A+  +      + + +++  G IGL+ AV++FD  +G    TY++
Sbjct: 13  KNSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERFDAMQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V             N R +   + +      +P     +A+ L
Sbjct: 73  QRIRGAMLDEL-RSRDWVPRSVR-------RNAREVSQAMHSAEQKLGRPPSEGEVAQVL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   E   +      D + + L +  +                +E   +      N R+
Sbjct: 125 DIPIEEYRQILM----DTNSSQLFSYDEWREEHGDTAEALMEGHEEANPLHHLLEGNLRH 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  ++  L  RE+ +       +  + L+ + +  +V   RV Q+ ++A K+++  +
Sbjct: 181 RVMEAIDALPEREKLVLTLYY--QEELNLKEIGAVLDVGESRVSQLHSQAIKRLRTRL 236


>gi|167470529|ref|ZP_02335233.1| alternative sigma factor RpoH [Yersinia pestis FV-1]
          Length = 127

 Score =  101 bits (251), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 33/127 (25%), Positives = 61/127 (48%), Gaps = 4/127 (3%)

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEE 220
           K+L V+  +V  M  R++  +         +    Q+   ++Y  D        + E   
Sbjct: 1   KELGVTSKDVREMESRMSAQDMTFDPSPDDEARDGQFMAPVLYLQDKTSDFADGIEEDNW 60

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKK 279
             +  + L+ ++  L+ R + I  AR L + N  TL+ L+ ++ VS ERVRQ+E  A KK
Sbjct: 61  DSHAADKLSYALEGLDERSQHIIRARWLDDENKSTLQELADQYGVSAERVRQLEKNAMKK 120

Query: 280 VQESIQK 286
           ++ +I+ 
Sbjct: 121 LRMAIEA 127


>gi|170694383|ref|ZP_02885537.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia graminis
           C4D1M]
 gi|170140806|gb|EDT08980.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia graminis
           C4D1M]
          Length = 244

 Score =  101 bits (251), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 40/215 (18%), Positives = 87/215 (40%), Gaps = 14/215 (6%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++  G IGL+ A  ++  ++G +  TY+   I+ AM + +  +  L         +
Sbjct: 37  DLDDLIQAGMIGLLDAASRYKEDQGAQFETYASQRIRGAMLDELRSNDWL--------PR 88

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            L    R ++  +  +  N  +      +A+ L +   E  SM   L G + +       
Sbjct: 89  SLRRTSREVETAVHKVEQNLGRSASETEVAEHLQMPLDEYQSMLQDLHGSQLIYYEDFDR 148

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
             +   + D    DH      L++       R+ L  ++  L  RE+ +       E  +
Sbjct: 149 SADDEPFLDRYCVDHSDPLSALLDDSL----RSALVEAIDRLPEREKLLMSLYY--ERGM 202

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            L  + +  EVS  RV Q+ ++A  +++  +++  
Sbjct: 203 NLREIGAVMEVSESRVCQLHSQAVARLRTRLREMA 237


>gi|297162318|gb|ADI12030.1| RNA polymerase sigma factor [Streptomyces bingchenggensis BCW-1]
          Length = 261

 Score =  101 bits (251), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 29/237 (12%), Positives = 93/237 (39%), Gaps = 14/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +    ++ + L +  ++A+ +R  G  + ++    ++ L++AV ++DP+ G    +Y++ 
Sbjct: 35  ALREAIICAWLPVAKRLALRFRNKGENMEDLTQVASLALVKAVDRYDPDLGHAFPSYAIP 94

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I   ++ +       + +     + R     R  +  L+   +   +   +  I+ +  
Sbjct: 95  VITGELKRHFRDYLWTLHVPRNIQEVR--SRTRSARDALEQ--ELGGRTPTITEISTRTG 150

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + + +V++     A    L+              + +  D    E+V+         R  
Sbjct: 151 MPKEDVMAGLEASASCTPLSLNAAVQGAEERLLAETVGADDAAIERVV--------NREA 202

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   ++ L+ ++R +   R      ++   +      S+  + +  +R + ++++ +
Sbjct: 203 LRALITHLSEQDRYVLYLRFFVG--LSQSQIGEILGFSQMHISRRLSRLYSELRQGL 257


>gi|134294347|ref|YP_001118082.1| flagellar biosynthesis sigma factor [Burkholderia vietnamiensis G4]
 gi|134137504|gb|ABO53247.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Burkholderia
           vietnamiensis G4]
          Length = 244

 Score =  101 bits (251), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 41/215 (19%), Positives = 86/215 (40%), Gaps = 14/215 (6%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++  G IGLM A  ++  ++G +  TY+   I+ AM + +  +  L         +
Sbjct: 38  DLDDLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDELRSNDWL--------PR 89

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            L    R ++  +  +     +      IA+ L +   E   M   L G + +       
Sbjct: 90  SLRKTSREVEHAVHQVEQQLGRSASEAEIAQHLKMPLDEYQEMLQDLHGSQLIYYEDFDR 149

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
             +   + D    DH      L++     + R  L  ++  L  RE+ +       E  +
Sbjct: 150 AADDEPFLDRYRVDHADPLSALLDD----HLRGALVDAIDRLPEREKLLMSLYY--ERGL 203

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            L  + +  EVS  RV Q+ ++A  +++  +++Q 
Sbjct: 204 NLREIGAVLEVSESRVCQLHSQAVARLRARLREQA 238


>gi|121488787|emb|CAJ18278.1| sigma 70-type sigma factor [Prosthecochloris aestuarii]
          Length = 165

 Score =  101 bits (251), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 38/174 (21%), Positives = 75/174 (43%), Gaps = 11/174 (6%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           ++  EGN+GL++A K+FD  RGF+  +Y++WWI+ +  + +     +V++    N+    
Sbjct: 1   DLXXEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSXLQALAEQSRIVRLP--LNRVGTL 58

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
             + +    L+   + +        +A  L++   +V           S++A     D N
Sbjct: 59  NKISKAYSQLEQEYERD---PNTKELANVLDMDSQDVADTLKIAGRHVSVDAPFAQGDDN 115

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +  D L +D    +  L +          + RS+SVL PRE  +  +     
Sbjct: 116 --RLLDVLQHDGQKPDYSLTKDSLTLE----VERSLSVLAPREADVIRSYFGIG 163


>gi|53724308|ref|YP_104354.1| flagellar biosynthesis sigma factor [Burkholderia mallei ATCC
           23344]
 gi|67639807|ref|ZP_00438640.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Burkholderia mallei GB8
           horse 4]
 gi|121601051|ref|YP_994697.1| flagellar biosynthesis sigma factor [Burkholderia mallei SAVP1]
 gi|124385599|ref|YP_001027679.1| flagellar biosynthesis sigma factor [Burkholderia mallei NCTC
           10229]
 gi|126442044|ref|YP_001060834.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei 668]
 gi|126450811|ref|YP_001082651.1| flagellar biosynthesis sigma factor [Burkholderia mallei NCTC
           10247]
 gi|126454531|ref|YP_001068141.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei
           1106a]
 gi|134281398|ref|ZP_01768106.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 305]
 gi|167002947|ref|ZP_02268737.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           mallei PRL-20]
 gi|167721669|ref|ZP_02404905.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei
           DM98]
 gi|167740651|ref|ZP_02413425.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei 14]
 gi|167817858|ref|ZP_02449538.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei 91]
 gi|167826237|ref|ZP_02457708.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei 9]
 gi|167847745|ref|ZP_02473253.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei
           B7210]
 gi|167896335|ref|ZP_02483737.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei
           7894]
 gi|167904709|ref|ZP_02491914.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei NCTC
           13177]
 gi|167912987|ref|ZP_02500078.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei 112]
 gi|167920926|ref|ZP_02508017.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei
           BCC215]
 gi|217423992|ref|ZP_03455492.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 576]
 gi|226193247|ref|ZP_03788857.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei Pakistan 9]
 gi|237814231|ref|YP_002898682.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-28) [Burkholderia pseudomallei MSHR346]
 gi|242316800|ref|ZP_04815816.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 1106b]
 gi|254174808|ref|ZP_04881469.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           mallei ATCC 10399]
 gi|254183872|ref|ZP_04890463.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 1655]
 gi|254186350|ref|ZP_04892867.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei Pasteur 52237]
 gi|254194761|ref|ZP_04901192.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei S13]
 gi|254201430|ref|ZP_04907794.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           mallei FMH]
 gi|254206772|ref|ZP_04913123.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           mallei JHU]
 gi|254261523|ref|ZP_04952577.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 1710a]
 gi|254298806|ref|ZP_04966257.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 406e]
 gi|254357205|ref|ZP_04973479.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           mallei 2002721280]
 gi|52427731|gb|AAU48324.1| RNA polymerase sigma factor for flagellar operon FliA [Burkholderia
           mallei ATCC 23344]
 gi|121229861|gb|ABM52379.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           mallei SAVP1]
 gi|124293619|gb|ABN02888.1| RNA polymerase sigma factor for flagellar operon FliA [Burkholderia
           mallei NCTC 10229]
 gi|126221537|gb|ABN85043.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 668]
 gi|126228173|gb|ABN91713.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 1106a]
 gi|126243681|gb|ABO06774.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           mallei NCTC 10247]
 gi|134247065|gb|EBA47151.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 305]
 gi|147747324|gb|EDK54400.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           mallei FMH]
 gi|147752314|gb|EDK59380.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           mallei JHU]
 gi|148026269|gb|EDK84354.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           mallei 2002721280]
 gi|157808491|gb|EDO85661.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 406e]
 gi|157934035|gb|EDO89705.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei Pasteur 52237]
 gi|160695853|gb|EDP85823.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           mallei ATCC 10399]
 gi|169651511|gb|EDS84204.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei S13]
 gi|184214404|gb|EDU11447.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 1655]
 gi|217393055|gb|EEC33077.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 576]
 gi|225934847|gb|EEH30824.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei Pakistan 9]
 gi|237506113|gb|ACQ98431.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-28) [Burkholderia pseudomallei MSHR346]
 gi|238520417|gb|EEP83877.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Burkholderia mallei GB8
           horse 4]
 gi|242140039|gb|EES26441.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 1106b]
 gi|243061438|gb|EES43624.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           mallei PRL-20]
 gi|254220212|gb|EET09596.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 1710a]
          Length = 244

 Score =  101 bits (251), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 40/215 (18%), Positives = 88/215 (40%), Gaps = 14/215 (6%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++  G IGL+ A  ++  ++G +  TY+   I+ AM + +  +  L         +
Sbjct: 38  DLDDLIQAGMIGLLDAASRYKEDQGAQFETYATQRIRGAMLDELRSNDWL--------PR 89

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            L    R ++  +  +     +      IA  L +   E  SM   L G    + L+   
Sbjct: 90  SLRKTSREVEHAVHQVEQRLGRSANETEIAAHLQMPLDEYQSMLQDLHG----SQLVYYE 145

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D + S   +  +  +       +     ++ R+ L  ++  L  RE+ +       E  +
Sbjct: 146 DFDRSADDEPFLDRYRADHSDPLSALLDEHLRSALVDAIERLPEREKLLMSLYY--ERGL 203

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            L  + +  EVS  RV Q+ ++A  +++  +++Q 
Sbjct: 204 NLREIGAVLEVSESRVCQLHSQAVARLRAKLREQA 238


>gi|91211141|ref|YP_541127.1| flagellar biosynthesis sigma factor [Escherichia coli UTI89]
 gi|117624064|ref|YP_852977.1| flagellar biosynthesis sigma factor [Escherichia coli APEC O1]
 gi|218558780|ref|YP_002391693.1| flagellar biosynthesis sigma factor [Escherichia coli S88]
 gi|237705878|ref|ZP_04536359.1| flagellar biosynthesis sigma factor FliA [Escherichia sp.
           3_2_53FAA]
 gi|91072715|gb|ABE07596.1| flagellar biosynthesis; alternative sigma factor 28; regulation of
           flagellar operons [Escherichia coli UTI89]
 gi|115513188|gb|ABJ01263.1| flagellar biosynthesis sigma factor FliA [Escherichia coli APEC O1]
 gi|218365549|emb|CAR03276.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli S88]
 gi|226900635|gb|EEH86894.1| flagellar biosynthesis sigma factor FliA [Escherichia sp.
           3_2_53FAA]
 gi|294492788|gb|ADE91544.1| flagellar operon sigma factor FliA [Escherichia coli IHE3034]
 gi|323952417|gb|EGB48290.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli H252]
 gi|323956319|gb|EGB52062.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli H263]
          Length = 239

 Score =  101 bits (251), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 102/240 (42%), Gaps = 17/240 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   + +L+  L        +      +A++L
Sbjct: 73  QRIRGAMLDEL-RSRDWVPRSVRRNAREVAQAIGQLEQEL-------GRNATETEVAERL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +  ++   M      D + + L +  +          +   D Q +  +++    N R 
Sbjct: 125 GIDIADYRQMLL----DTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 181 RVMETIETLPEREKLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 238


>gi|325527508|gb|EGD04836.1| flagellar biosynthesis sigma factor [Burkholderia sp. TJI49]
          Length = 243

 Score =  101 bits (251), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 42/215 (19%), Positives = 87/215 (40%), Gaps = 14/215 (6%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++  G IGLM A  ++  ++G +  TY+   I+ AM + +  +  L         +
Sbjct: 37  DLDDLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDELRSNDWL--------PR 88

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            L    R ++  +  +     +      IA+ LN+   E   M   L G + +       
Sbjct: 89  SLRKTSREVEHAVHQVEQQLGRAASEAEIAQHLNMPLDEYQGMLQDLHGSQLIYYEDFDR 148

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
             +   + D    DH      L++     + R  L  ++  L  RE+ +       E  +
Sbjct: 149 AADDEPFLDRYRVDHADPLSALLDD----HLRGALVEAIERLPEREKLLMSLYY--ERGL 202

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            L  + +  EVS  RV Q+ ++A  +++  +++Q 
Sbjct: 203 NLREIGAVLEVSESRVCQLHSQAVARLRARLREQA 237


>gi|229587526|ref|YP_002860564.1| putative DNA-directed RNA polymerase specialized sigma subunit
           [Clostridium botulinum Ba4 str. 657]
 gi|229260255|gb|ACQ51292.1| putative DNA-directed RNA polymerase specialized sigma subunit
           [Clostridium botulinum Ba4 str. 657]
          Length = 296

 Score =  101 bits (251), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 52/284 (18%), Positives = 126/284 (44%), Gaps = 48/284 (16%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHR-----------------LVTSHLRLVVKIAM 66
             I +LE +E+  L     +  D+ + ++                 L+  +  L+ K+A 
Sbjct: 44  SYIKLLEIKEDKELLIESYDENDIDSINKYYVGKYKKTKDKKYLNSLIEKNENLIFKVAN 103

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            Y+   + + ++  +G +G ++AV KFD  +  + +TY+ +WI+A +  +   +      
Sbjct: 104 KYKNKNIELQDLTQQGFLGFLKAVDKFDESKKVKFSTYAYYWIEAEISSFFNFN------ 157

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
              +      +  R+LKG+   I   +  P+ V    +  N S               S+
Sbjct: 158 VDGSLSISSSYQHRKLKGYENGILSEDELPKLVKNHIQLKNNS--------------ISV 203

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           +++++  +  +S   D+L+   D     +  K   +N       ++S L+ +E+ I  +R
Sbjct: 204 DSIVHGKENENS--ADYLLGKTDINYNNIESKIVMEN-------ALSGLSDKEKNIIISR 254

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
            + E     ++++ EF+VS + ++ +   A +K++++++K + +
Sbjct: 255 IIYEKKY--KDIAKEFKVSYQYIQYLYNNAIEKLRQTVKKDILV 296


>gi|212709528|ref|ZP_03317656.1| hypothetical protein PROVALCAL_00570 [Providencia alcalifaciens DSM
           30120]
 gi|212687866|gb|EEB47394.1| hypothetical protein PROVALCAL_00570 [Providencia alcalifaciens DSM
           30120]
          Length = 242

 Score =  101 bits (251), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 39/240 (16%), Positives = 96/240 (40%), Gaps = 17/240 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   +  L+   A+  +      + I +++  G IGL+ A+++FD   G   ATY++
Sbjct: 17  KNSLWERYYPLIRHEALKLQVRLPASVDIDDLIQAGGIGLLHALERFDASLGASFATYAV 76

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ +M + + RS   V               R +   +  +  +  +      IAK L
Sbjct: 77  QRIRGSMLDEL-RSRDWVPRSVR-------RQAREMTKAIGELEQSLGRSATEPEIAKAL 128

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++  +E   +      D + + L +  + +    +       +      +      + ++
Sbjct: 129 DIDLAEYRQVLL----DTNNSQLFSYDEWHEVHGESCEPSMDEDDGGNPLSLLMESSLKD 184

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  ++ 
Sbjct: 185 QIVAAIEQLPEREKMVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRSKLRS 242


>gi|150021309|ref|YP_001306663.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermosipho
           melanesiensis BI429]
 gi|149793830|gb|ABR31278.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermosipho
           melanesiensis BI429]
          Length = 226

 Score =  101 bits (251), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 45/243 (18%), Positives = 107/243 (44%), Gaps = 30/243 (12%)

Query: 50  AHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             +++  +L  + +IA        + + I +++ EG IGL+QA+++++P++G +L +Y +
Sbjct: 4   KEKIIQEYLPYIKRIAYDLKKNLPHNIEIDDLIQEGLIGLLQAIERYNPKKGAKLRSYIL 63

Query: 107 WWIKAAMQEYILRSWSLVK-----IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
             +K AM +Y+ +   + K     +    +      N  ++    +     NL  E V  
Sbjct: 64  TRVKGAMYDYLRKIDWMPKNLRHDVKVVEDAISKMENSGKIIDFNEISKITNLPLENVKR 123

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
              ++     + + ++  L  D  +N  I+SSD                      E   +
Sbjct: 124 AYNEM--VRKQFLMLDDYLTEDLEINETISSSD------------------YTPEETAFK 163

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +  +  L ++++ L+ +E+ I   R   E+ ++L+ +     ++  RV QI +    K++
Sbjct: 164 EIIKEELKKAINKLDEKEKIILNLRF--EHELSLKEIGKILNLTESRVSQILSSIILKLK 221

Query: 282 ESI 284
           + +
Sbjct: 222 KML 224


>gi|1419613|emb|CAA67397.1| signma factor 28 [Legionella pneumophila str. Corby]
          Length = 238

 Score =  101 bits (251), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 48/238 (20%), Positives = 100/238 (42%), Gaps = 19/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              LV +H  LV +I     G     + + +++  G +GL++A + +D  +G    TY+ 
Sbjct: 15  QEALVKTHATLVKRIRHHLLGRLPQSVQLDDLIQSGMLGLLEAARHYDSSKGASFETYAG 74

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+  M + + R+  +         + ++ N R +   ++ +     +  +   IA++L
Sbjct: 75  IRIRGHMLDEVRRNDWV--------PRSVYRNSRMISDAVRILEHKLGREAKDNEIAEEL 126

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            VS ++  SM       +S+++ +   D       D L  D             R +  N
Sbjct: 127 GVSLNDYHSMLQ-----DSISSHLYGFDDLGVT-DDILFDDEGNGSTEPHRNVMRSDMMN 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            LT+ +  L  +ER +       E  + L+ +    EVS  R+ QI ++A  +++  +
Sbjct: 181 RLTQVIDSLPRKERLVLSLYY--EQDLNLKEIGEILEVSESRISQILSQATHRIRSRL 236


>gi|237668235|ref|ZP_04528219.1| RNA polymerase sigma-K factor (Sigma-27) [Clostridium butyricum E4
           str. BoNT E BL5262]
 gi|237656583|gb|EEP54139.1| RNA polymerase sigma-K factor (Sigma-27) [Clostridium butyricum E4
           str. BoNT E BL5262]
          Length = 146

 Score =  101 bits (251), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 35/106 (33%), Positives = 58/106 (54%), Gaps = 2/106 (1%)

Query: 16  LSRYIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           L+ YI      P+ L+++EE +  K+++E GD SA   L+  +LRLV  I   Y      
Sbjct: 17  LTGYITNNNTFPLPLDEEEEQMYLKKFKE-GDKSAKSILIERNLRLVAHIVKKYSFPNKD 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           + E++S G +GL++A+  FD  +G RLATY+   I+  +      +
Sbjct: 76  VDELISIGTVGLIKAIDSFDSSKGTRLATYASRCIENEILMLFRNN 121


>gi|77457790|ref|YP_347295.1| flagellar biosynthesis sigma factor [Pseudomonas fluorescens Pf0-1]
 gi|77381793|gb|ABA73306.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Pseudomonas
           fluorescens Pf0-1]
          Length = 246

 Score =  100 bits (250), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 44/241 (18%), Positives = 95/241 (39%), Gaps = 17/241 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
             A + L+  +  LV +IA          + + +++  G IGL++   K+D  +G    T
Sbjct: 14  RDAQYELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDASKGASFET 73

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   I+ AM + + R           N + +   +R +    +A T  + K  +V A  
Sbjct: 74  YAGIRIRGAMLDEV-RKGDWAPRSVHRNTRMVSDAIRSI----EAKTGRDAKDHEVAAEL 128

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + L++ +   I  +   +   S + L+   +       + L  D            E + 
Sbjct: 129 Q-LSLDDYYGILNDTLGSRLFSFDDLLQDGE------HEGLHEDGASAHLEPSRDLEDER 181

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +  L  +++ L  RER +       +  + L+ +     VS  RV Q+ ++   +++  
Sbjct: 182 FQAALADAIANLPERERLVLALYY--DEELNLKEIGEVLGVSESRVSQLHSQCAARLRGR 239

Query: 284 I 284
           +
Sbjct: 240 L 240


>gi|302540326|ref|ZP_07292668.1| RNA polymerase sigma-F factor [Streptomyces hygroscopicus ATCC
           53653]
 gi|302457944|gb|EFL21037.1| RNA polymerase sigma-F factor [Streptomyces himastatinicus ATCC
           53653]
          Length = 263

 Score =  100 bits (250), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 30/237 (12%), Positives = 91/237 (38%), Gaps = 14/237 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +    ++   L +  ++A+ +R  G  + ++    ++ L++AV +++P+ G    +Y++ 
Sbjct: 37  ALREAIICEWLPVAKRLALRFRNKGENMEDLTQVASLALVKAVDRYNPDLGHAFPSYAIP 96

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I   ++ +       + I     + R     R  +  L+   +   +   V  I+ +  
Sbjct: 97  VITGELKRHFRDYLWTLHIPRNIQEVR--SRTRSARDALEQ--ELGGRTPTVGEISTRTG 152

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + + +V +     A    L+              + +  D    E+V+         R  
Sbjct: 153 MPQEDVRAGLEASASCTPLSLNAAVQGAEERLLAETVGADDAAIERVV--------NRES 204

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   ++ L+ ++R +   R      ++   +      S+  + +  +R + ++++ +
Sbjct: 205 LRVLIANLSEQDRYVLYLRFFAG--LSQSQIGEILGFSQMHISRRLSRLYSELRQGL 259


>gi|187925770|ref|YP_001897412.1| flagellar biosynthesis sigma factor [Burkholderia phytofirmans
           PsJN]
 gi|187716964|gb|ACD18188.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia
           phytofirmans PsJN]
          Length = 244

 Score =  100 bits (250), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 41/215 (19%), Positives = 87/215 (40%), Gaps = 14/215 (6%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++  G IGL+ A  ++  ++G +  TY+   I+ AM + +  +  L         +
Sbjct: 37  DLDDLIQAGMIGLLDAAGRYKEDQGAQFETYASQRIRGAMLDELRSNDWL--------PR 88

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            L    R ++  +  +  N  +      IA+ L +   E  SM   L G + +       
Sbjct: 89  SLRRTSREVETAVHKVEQNLGRSASETEIAEHLQMPLDEYQSMLQDLHGSQLIYYEDFDR 148

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
             +   + D    DH      L++       R+ L  ++  L  RE+ +       E  +
Sbjct: 149 SADDEPFLDRYCVDHSDPLSALLDDSL----RSALVEAIDRLPDREKLLMSLYY--ERGM 202

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            L  + +  EVS  RV Q+ ++A  +++  +++  
Sbjct: 203 NLREIGAVMEVSESRVCQLHSQAVARLRTRLREMA 237


>gi|212638647|ref|YP_002315167.1| RNA polymerase sporulation-specific sigma factor (sigma-K), SpoIVCB
           [Anoxybacillus flavithermus WK1]
 gi|212560127|gb|ACJ33182.1| RNA polymerase sporulation-specific sigma factor (sigma-K), SpoIVCB
           [Anoxybacillus flavithermus WK1]
          Length = 129

 Score =  100 bits (250), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 29/113 (25%), Positives = 60/113 (53%), Gaps = 1/113 (0%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +++ +   + L  Y+        L+ +EE +  K+  + GD +A ++L+  +LRLV  I 
Sbjct: 8   LALFIKELVFLVSYVKNNAFPQPLDAKEEAMYLKQMAK-GDENARNKLIEHNLRLVAHIV 66

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
             +   G    +++S G IGL++A++ +   +G +LATY+   I+  +   I+
Sbjct: 67  KKFENTGEDPEDLISIGTIGLIKAIESYSTGKGTKLATYAARCIENEIFMTIV 119


>gi|297580650|ref|ZP_06942576.1| RNA polymerase sigma factor RpoD [Vibrio cholerae RC385]
 gi|297535066|gb|EFH73901.1| RNA polymerase sigma factor RpoD [Vibrio cholerae RC385]
          Length = 477

 Score =  100 bits (250), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 34/105 (32%), Positives = 53/105 (50%), Gaps = 2/105 (1%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           +  I +   L  +    L++R    E     A   +V ++L LV+ IA  Y   GL   +
Sbjct: 373 LQMIEQETSLSVERIKDLSRRMSIGEAKARRANKEMVEANLPLVISIAKKYTNRGLQFLD 432

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           ++ EGNIGLM+AV K +  RG+  +TY+ WWI+ A+   I     
Sbjct: 433 LIQEGNIGLMKAVDKSEYRRGYNFSTYATWWIRQAITRSIADQSR 477


>gi|197285477|ref|YP_002151349.1| flagellar biosynthesis sigma factor [Proteus mirabilis HI4320]
 gi|6959882|gb|AAF33246.1|AF221596_2 FliA [Proteus mirabilis]
 gi|194682964|emb|CAR43378.1| RNA polymerase sigma factor for flagellar operon [Proteus mirabilis
           HI4320]
          Length = 240

 Score =  100 bits (250), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 35/238 (14%), Positives = 96/238 (40%), Gaps = 17/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KNSLWERYVPLVRHEALRLQVKLPASVELDDLLQAGGIGLLNAVERYDSMQGAAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ +M + +               + +  N R +   +  +  +  +P     +A  L
Sbjct: 73  QRIRGSMLDELR--------SRDWAPRSVRRNAREVTQSIHQLEQDLGRPPSEQEVADHL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +  +E   +      D + + L +  + +    +       +  +   ++     + R 
Sbjct: 125 QIELAEYRQILL----DTNNSQLFSYDEWHEIYGESCEPSQDEDHDDNPLQMLLESDIRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  ++ +L  RE+ +       +  + L+ + +   V   RV Q+ ++A K+++  +
Sbjct: 181 RVIDAIELLPEREKMVLTLYY--QEELNLKEIGAVLNVGESRVSQLHSQAIKRLRARL 236


>gi|228926137|ref|ZP_04089213.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228833502|gb|EEM79063.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
          Length = 194

 Score =  100 bits (250), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 37/203 (18%), Positives = 93/203 (45%), Gaps = 16/203 (7%)

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            +GL+ A++++D   G     +++  I   +++Y+      + +      +R+     ++
Sbjct: 1   MLGLLGAIRRYDYSIGNAFEPFAIPTIVGEIKKYLRDKTWGIHVP-----RRIKDLGGKI 55

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN--CRLAGDESLNALINSSDKNSSQW 200
           K  ++ +TD+  +  +++ IA  L +SE EV+ +          SL+ ++ ++   SS  
Sbjct: 56  KLAIEELTDHLQRSPKIIEIADHLGLSEEEVLEIMDAKNNYRVSSLDDVVENASDGSSVA 115

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
           +   V +       + +  E   RR +L    +VLN  E+ +     + E  +  ++   
Sbjct: 116 RIESVGE-------VEQGYEETERRLVLKDIFNVLNETEKSVIH--YIFEENLNQKDTGE 166

Query: 261 EFEVSRERVRQIEARAFKKVQES 283
              +S+  V +I+ +A  K++++
Sbjct: 167 RLGISQMHVSRIKRQAISKLKQA 189


>gi|326204040|ref|ZP_08193901.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           papyrosolvens DSM 2782]
 gi|325985807|gb|EGD46642.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           papyrosolvens DSM 2782]
          Length = 138

 Score =  100 bits (250), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 31/96 (32%), Positives = 53/96 (55%), Gaps = 2/96 (2%)

Query: 19  YIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           Y+  +   P  L+ +EE    + Y+ +G   A + L+  +LRLV  I   Y   G    +
Sbjct: 22  YVSNVNSFPQPLKPEEEQYYVEAYK-NGSEDARNILIERNLRLVAHIVKKYGSCGSDSDD 80

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           ++S G IGL++A+  F+ ++G RLATY+   I+ A+
Sbjct: 81  LISIGTIGLIKAISTFNMDKGTRLATYAARCIENAI 116


>gi|73662123|ref|YP_300904.1| RNA polymerase sigma-B factor [Staphylococcus saprophyticus subsp.
           saprophyticus ATCC 15305]
 gi|72494638|dbj|BAE17959.1| truncated RNA polymerase sigma-B factor [Staphylococcus
           saprophyticus subsp. saprophyticus ATCC 15305]
          Length = 192

 Score =  100 bits (250), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 38/210 (18%), Positives = 85/210 (40%), Gaps = 24/210 (11%)

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            +GL+ A+ +FD     +   + +  +   ++ Y+      V +     +        R+
Sbjct: 1   MVGLIGAINRFDLSFDRKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRIKEIG-----PRI 55

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC------RLAGDESLNALINSSDKN 196
           K     +T+   +   +  IA +L V+E +V+           L+ D S+ A     D +
Sbjct: 56  KKVTDELTNELERSPSITEIADRLEVNEEDVLEAMEMGQSYNALSVDHSIEA---DKDGS 112

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           +    D +    D          +   +R +L + + +L+ RER+I +   +    ++ +
Sbjct: 113 TVTLLDIMGQQDDNY--------DLTEKRMILEKILPILSERERQIIQCTFI--EGLSQK 162

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                  +S+  V +++  A KK+QE+  K
Sbjct: 163 ETGERIGLSQMHVSRLQRTAIKKLQEAANK 192


>gi|161523359|ref|YP_001578371.1| flagellar biosynthesis sigma factor [Burkholderia multivorans ATCC
           17616]
 gi|189351868|ref|YP_001947496.1| flagellar biosynthesis sigma factor [Burkholderia multivorans ATCC
           17616]
 gi|221202383|ref|ZP_03575416.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           multivorans CGD2M]
 gi|221208978|ref|ZP_03581974.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           multivorans CGD2]
 gi|221214209|ref|ZP_03587181.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           multivorans CGD1]
 gi|160340788|gb|ABX13874.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia
           multivorans ATCC 17616]
 gi|189335890|dbj|BAG44960.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           multivorans ATCC 17616]
 gi|221165864|gb|EED98338.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           multivorans CGD1]
 gi|221171100|gb|EEE03551.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           multivorans CGD2]
 gi|221177797|gb|EEE10211.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           multivorans CGD2M]
          Length = 244

 Score =  100 bits (250), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 42/215 (19%), Positives = 89/215 (41%), Gaps = 14/215 (6%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++  G IGLM A  ++  ++G +  TY+   I+ AM + +  +  L         +
Sbjct: 38  DLDDLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDELRSNDWL--------PR 89

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            L    R ++  +  +     +      IA+ LN+   E  +M   L G + +       
Sbjct: 90  SLRKTSREVELAVHQVEQRLGRAASEAEIAQHLNMPLDEYQAMLQDLHGSQLIYYEDFDR 149

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
             +   + D    DH      L++    ++ R  L  ++  L  RE+ +       E  +
Sbjct: 150 AADDEPFLDRYRVDHADPLSALLD----EHLRGALVEAIERLPEREKLLMSLYY--ERGL 203

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            L  + +  EVS  RV Q+ ++A  +++  +++Q 
Sbjct: 204 NLREIGAVLEVSESRVCQLHSQAVARLRARLREQA 238


>gi|114777586|ref|ZP_01452567.1| RNA polymerase sigma factor for flagellar operon [Mariprofundus
           ferrooxydans PV-1]
 gi|114552057|gb|EAU54574.1| RNA polymerase sigma factor for flagellar operon [Mariprofundus
           ferrooxydans PV-1]
          Length = 243

 Score =  100 bits (250), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 41/240 (17%), Positives = 96/240 (40%), Gaps = 19/240 (7%)

Query: 51  HRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
             L+  +L LV   A   M      +   ++++ G +GL+   ++FD  R  +  T+  +
Sbjct: 14  DELLEEYLPLVRYHADQLMRRTPDSIEFDDLINAGVLGLLDGAQRFDHSRDVQFKTFVSY 73

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            ++ AM +Y+ R++  +  G   + K        ++   Q +     +P +   IAK LN
Sbjct: 74  RVRGAMIDYL-RAFDWMPRGLRDHAKE-------MQTAFQQLEQVYGRPAEETEIAKHLN 125

Query: 168 VSESEVISMNCRLAGDESL---NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +S  E  +    +     +   +  +N+   +     + L  D          +      
Sbjct: 126 ISLDEYRTRLTNVRSMSIIHFDDLPVNNDFDDEISILETLAGD---PADTPEAQNSLMQF 182

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              L   +S L  RE+ +      +E  +T++ ++    ++  RV Q+ ++   +++  +
Sbjct: 183 VQQLADGISRLPAREQVLVTLYYYEE--LTMKEIALILGLTESRVSQLHSQMVVRLRGLM 240


>gi|312962254|ref|ZP_07776746.1| RNA polymerase sigma factor for flagellar operon FliA [Pseudomonas
           fluorescens WH6]
 gi|311283591|gb|EFQ62180.1| RNA polymerase sigma factor for flagellar operon FliA [Pseudomonas
           fluorescens WH6]
          Length = 246

 Score =  100 bits (250), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 44/241 (18%), Positives = 95/241 (39%), Gaps = 17/241 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
             +   L+  +  LV +IA    G     + + +++  G IGL++   K+D  +G    T
Sbjct: 14  RDSQGELIERYAPLVKRIAYHLLGRLPASVQVEDLIQAGMIGLLEVSTKYDASKGASFET 73

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   I+ AM + + R           N + +   +R +    +A T  + K  +V A  
Sbjct: 74  YAGIRIRGAMLDEV-RKGDWAPRSVHRNTRMVSDAIRAI----EAKTGRDAKDHEVAAEL 128

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + L++ +   I  +   +   S + L+   +       + L  D            E + 
Sbjct: 129 Q-LSLDDYYGILNDTLGSRLFSFDDLLQDGE------HEGLHEDGASAHMEPSRDLEDQR 181

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +  L  +++ L  RER +       +  + L+ +     VS  RV Q+ ++   +++  
Sbjct: 182 FQGALADAIANLPERERLVLALYY--DEELNLKEIGEVLGVSESRVSQLHSQCAARLRGR 239

Query: 284 I 284
           +
Sbjct: 240 L 240


>gi|253990087|ref|YP_003041443.1| flagellar biosynthesis sigma factor [Photorhabdus asymbiotica
           subsp. asymbiotica ATCC 43949]
 gi|253781537|emb|CAQ84700.1| rna polymerase sigma factor for flagellar operon (sigma-f factor
           (sigma-27) (sigma-28) [Photorhabdus asymbiotica]
          Length = 244

 Score =  100 bits (250), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 44/238 (18%), Positives = 102/238 (42%), Gaps = 17/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   ++ LV   A+  +      + + +++  G IGL+ AV++FD  +G    TY++
Sbjct: 17  KNSLWKRYVPLVRHEALRLQVRLPACVELDDLLQAGGIGLLNAVERFDSLQGTAFTTYAV 76

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS          N + +   +R+L+  L        +P     +AK+L
Sbjct: 77  QRIRGAMLDEL-RSRDWAPRSVRRNAREVTQTIRKLEQDL-------GRPASEQEVAKEL 128

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   E   +      D + + L +  + +    +       +G E   +++    + R 
Sbjct: 129 KIDLVEYRQILL----DTNNSQLFSYDEWHEMHGESCEPVIEEGHETNPLQQLLESDVRQ 184

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  ++  L  RE+ +       +  + L+ + +  EV   R+ Q+ ++A K+++  +
Sbjct: 185 RVIDAIDSLPEREKMVLTLYY--QEELNLKEIGAVLEVGESRISQLHSQAIKRLRARL 240


>gi|226326542|ref|ZP_03802060.1| hypothetical protein PROPEN_00392 [Proteus penneri ATCC 35198]
 gi|225205141|gb|EEG87495.1| hypothetical protein PROPEN_00392 [Proteus penneri ATCC 35198]
          Length = 244

 Score =  100 bits (250), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 35/238 (14%), Positives = 96/238 (40%), Gaps = 17/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 17  KNSLWERYVPLVRHEALRLQVKLPASVELDDLLQAGGIGLLNAVERYDSMQGAAFTTYAV 76

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ +M + +               + +  N R +   +  +  +  +P     +A  L
Sbjct: 77  QRIRGSMLDELR--------SRDWAPRSVRRNAREVTHSIHQLEQDLGRPPLEQEVADHL 128

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +  +E   +      D + + L +  + +    +       +  +   ++     + R 
Sbjct: 129 QIELAEYRQILL----DTNNSQLFSYDEWHEIYGESCEPSQDEDHDDNPLQMLLESDIRQ 184

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  ++ +L  RE+ +       +  + L+ + +   V   RV Q+ ++A K+++  +
Sbjct: 185 RVIDAIELLPEREKMVLTLYY--QEELNLKEIGAVLNVGESRVSQLHSQAIKRLRARL 240


>gi|290475011|ref|YP_003467895.1| sigma F (sigma 28) factor of RNA polymerase, transcription of late
           flagellar genes (class 3a and 3b operons) [Xenorhabdus
           bovienii SS-2004]
 gi|289174328|emb|CBJ81122.1| sigma F (sigma 28) factor of RNA polymerase, transcription of late
           flagellar genes (class 3a and 3b operons) [Xenorhabdus
           bovienii SS-2004]
          Length = 240

 Score =  100 bits (250), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 44/238 (18%), Positives = 100/238 (42%), Gaps = 17/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   ++ LV   A+  +      + + +++  G IGL+ AV++FD  +G    TY++
Sbjct: 13  KNSLWKRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERFDSLQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS          N + +   +R+L+  L        +P     +AK+L
Sbjct: 73  QRIRGAMLDEL-RSRDWAPRSVRRNAREVTQTIRKLEQEL-------GRPASEQEVAKEL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++  E   +      D + + L +  + +    +       D  E   +++    + R 
Sbjct: 125 KINLIEYRQILL----DTNNSQLFSYDEWHEIHGESCEPVIEDEHETNPLQQLLEGDLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +   +  L  RE+ +       +  + L+ + +   V   RV Q+ ++A K+++  +
Sbjct: 181 RVIDVIESLPEREKMVLTLYY--QEELNLKEIGAVLNVGESRVSQLHSQAIKRLRARL 236


>gi|154484272|ref|ZP_02026720.1| hypothetical protein EUBVEN_01984 [Eubacterium ventriosum ATCC
           27560]
 gi|149734749|gb|EDM50666.1| hypothetical protein EUBVEN_01984 [Eubacterium ventriosum ATCC
           27560]
          Length = 304

 Score =  100 bits (250), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 46/195 (23%), Positives = 88/195 (45%), Gaps = 7/195 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           +  Y+ E+  +P L K EE  L  +    GD S + ++V ++L LV KIA  +RG G+  
Sbjct: 101 IKMYMEEMEALPNLSKDEEADLIDKLL-AGDTSVSSKIVEANLSLVAKIAESHRGKGVNF 159

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+GLM AV  +    G    ++    I+ A+   +    +  +IG     K  
Sbjct: 160 GDLIQEGNVGLMLAVSDYTESVG-DFHSFISGRIEDAINNTVNVQINSDRIGQHLADK-- 216

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              L RL    + +++   +  ++  +AK +N+S+ E   +        S+N     +D 
Sbjct: 217 ---LNRLDEVTKNLSEKLGRVPELDELAKAMNISKDEASILLKTSLDTLSVNEDTQITDG 273

Query: 196 NSSQWQDWLVYDHDG 210
           + +      +   + 
Sbjct: 274 SEANGTSDGISTEEA 288


>gi|121488757|emb|CAJ18263.1| sigma 70-type sigma factor [Chlorobium phaeobacteroides]
          Length = 163

 Score =  100 bits (250), Expect = 2e-19,   Method: Composition-based stats.
 Identities = 38/173 (21%), Positives = 72/173 (41%), Gaps = 17/173 (9%)

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + +     +V++    N+      + 
Sbjct: 1   EGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLP--LNRVGTLNKIS 58

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN---S 197
           +    L+   + +        +A  L++   +V           S++A     D N    
Sbjct: 59  KAYSQLEQEFERD---PNTRELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDNRLLD 115

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
               D  + DH   +  L  + ER          +SVL PRE  +  +     
Sbjct: 116 VLQNDGHLPDHGLNKDSLTLEVERS---------LSVLAPREADVIRSYFGIG 159


>gi|332187909|ref|ZP_08389642.1| RNA polymerase sigma factor, FliA/WhiG family protein [Sphingomonas
           sp. S17]
 gi|332012070|gb|EGI54142.1| RNA polymerase sigma factor, FliA/WhiG family protein [Sphingomonas
           sp. S17]
          Length = 265

 Score =  100 bits (250), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 50/249 (20%), Positives = 103/249 (41%), Gaps = 24/249 (9%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKKFDPERG 98
           R  G + A   ++  HL LV +IA    G    +    ++V  G + L++A   F+ ERG
Sbjct: 37  RRRGGIEA-DAIIRQHLPLVRRIAWHVHGSMSSLIEVEDLVQVGLVALVEAAASFE-ERG 94

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
                Y    ++ AM + + R  +  +              R+    + A++    +   
Sbjct: 95  VEFGHYLKARLRGAMIDELRRQATTTR--------GAMRRRRQYHEAVTALSQVAGQVPT 146

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
             A+A+KL V+  ++ + + + A    +  +    D   +    W   D     + L E 
Sbjct: 147 DEAVAEKLGVTTEKLRT-DYKTAEAVRMEPI----DDVYADDLPWFADDTPDAFEQLAES 201

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           +     R+ L  +++ L  RE  + +   ++E  + LE +     V   RV QI++ A  
Sbjct: 202 DL----RDALIAAIASLPEREAMVIQLYYVEE--LNLEEIGQVLGVGAARVCQIKSAAHA 255

Query: 279 KVQESIQKQ 287
           ++++++  Q
Sbjct: 256 RLKKALSAQ 264


>gi|330862243|emb|CBX72404.1| RNA polymerase sigma factor rpoD [Yersinia enterocolitica W22703]
          Length = 113

 Score =  100 bits (249), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 26/103 (25%), Positives = 51/103 (49%), Gaps = 5/103 (4%)

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
              D   S   D++    D   ++ ++    ++ R+     ++ L  RE ++   R   +
Sbjct: 10  PIGDDEDSHLGDFI---EDTTLELPLDSATSESLRSATHDVLAGLTAREAKVLRMRFGID 66

Query: 251 --NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
                TLE +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 67  MNTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 109


>gi|331657967|ref|ZP_08358929.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli TA206]
 gi|331056215|gb|EGI28224.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) (Sigma-28) [Escherichia coli TA206]
          Length = 239

 Score =  100 bits (249), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 103/240 (42%), Gaps = 17/240 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   + +L+  L        +      +A++L
Sbjct: 73  QRIRGAMLDEL-RSRDWVPRSVRRNAREVAQAIGQLEQEL-------GRNATETEVAERL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +  ++   M      D + + L +  +          +   D Q +  +++    N R 
Sbjct: 125 GIDIADYRQMLL----DTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++ +L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 181 RVMEAIEMLPEREKLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 238


>gi|254497491|ref|ZP_05110284.1| flagellar biosynthesis sigma factor FliA [Legionella drancourtii
           LLAP12]
 gi|254353306|gb|EET12048.1| flagellar biosynthesis sigma factor FliA [Legionella drancourtii
           LLAP12]
          Length = 238

 Score =  100 bits (249), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 42/242 (17%), Positives = 93/242 (38%), Gaps = 19/242 (7%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           +      LV +H  LV +IA    G     + + +++  G +GL++A + +D  +G    
Sbjct: 11  NQQIQETLVKNHALLVKRIAHHLLGRLPQSVQLDDLIQAGMLGLLEATRHYDSSKGASFE 70

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+   I+  M + + R+  +         + ++ N R +   ++ +     +  +   I
Sbjct: 71  TYAGIRIRGYMLDEVRRNDWV--------PRSVYRNSRMISEAVKHVEHRLGREAKDFEI 122

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A ++ +S +E   M    A             ++     D L  +               
Sbjct: 123 AAEIGISLTEYHEMLQDSASSH------LYGFEDLGVTDDALHGEEGQSSTEPHANVFHS 176

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +  N L   +  L  +E+ +       E+ + L+ +     VS  RV QI ++A  +++ 
Sbjct: 177 DLMNRLAEVIKGLPHKEQMVLSLYY--EHDLNLKEIGEVLGVSESRVSQILSQATHRIKS 234

Query: 283 SI 284
            +
Sbjct: 235 RL 236


>gi|293375494|ref|ZP_06621773.1| putative RNA polymerase sigma-F factor [Turicibacter sanguinis
           PC909]
 gi|325844950|ref|ZP_08168315.1| RNA polymerase sigma-F factor [Turicibacter sp. HGF1]
 gi|292645894|gb|EFF63925.1| putative RNA polymerase sigma-F factor [Turicibacter sanguinis
           PC909]
 gi|325489000|gb|EGC91389.1| RNA polymerase sigma-F factor [Turicibacter sp. HGF1]
          Length = 236

 Score =  100 bits (249), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 50/242 (20%), Positives = 112/242 (46%), Gaps = 22/242 (9%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           +K++ + L  +  + GD  A   LVT+H+ LV  +   +    +   ++   G +GL+++
Sbjct: 2   DKKQIHELIAK-AQSGDEEARLTLVTNHMDLVWSVVHKFGHIEVEKDDLFQIGCMGLLKS 60

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +FD      L+TY++  I   ++ +I    S +KI  +   K     ++ +K HL  +
Sbjct: 61  INQFDSSYDTTLSTYAIPLIIGEIKAFIREQ-SPIKISRSI--KSNIHKIQEVKDHLNKV 117

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
            +       +  IA++  +SE ++I          +LNA IN +  ++ + +D  + +  
Sbjct: 118 LERE---PTIKEIAQETELSEEQII---------LALNAPINVTSLDNYEREDMPLIERI 165

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
              Q  +  E+    + +L + +S L+P E+ +   R   +   T   ++   E+++  V
Sbjct: 166 PNHQEGMGLEQ----KIVLKQLVSNLDPIEKLLIYLRF--DLGYTQSEVAKRLEINQVAV 219

Query: 270 RQ 271
            +
Sbjct: 220 SR 221


>gi|261252375|ref|ZP_05944948.1| RNA polymerase sigma factor for flagellar operon [Vibrio orientalis
           CIP 102891]
 gi|260935766|gb|EEX91755.1| RNA polymerase sigma factor for flagellar operon [Vibrio orientalis
           CIP 102891]
          Length = 203

 Score =  100 bits (249), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 39/214 (18%), Positives = 87/214 (40%), Gaps = 16/214 (7%)

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           + + +++  G IGL++A K +D  +G    TY+   I+ AM + I R    V      + 
Sbjct: 1   MQVEDLIQAGMIGLLEAQKNYDGTKGASFETYAGIRIRGAMLDDIRR-GDWVPRSVHKHN 59

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
           + +   +  L+G L        +      +A+++ +S  +   +      D + + L+  
Sbjct: 60  REVSQVIAILEGELN-------RDPTDAEVAQRMGISLEQYHVILT----DINCSRLVGI 108

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            D   S+  D +       + +  +    +  R  L  S+  L  RE  +       +  
Sbjct: 109 EDLGISE--DSISPGDSEDDNLPFKGVADEYFRKALVDSIKTLPEREALVLSLYY--DEE 164

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           + L+ +     VS  RV QI +++ ++++  +  
Sbjct: 165 LNLKEIGEVIGVSESRVSQILSQSMQRLRTKLSA 198


>gi|323702293|ref|ZP_08113959.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
 gi|323532783|gb|EGB22656.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
          Length = 121

 Score =  100 bits (249), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 36/105 (34%), Positives = 57/105 (54%), Gaps = 1/105 (0%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +VNG + L  YI        L ++EE    ++  + GD SA + LV  +LRLV  I   +
Sbjct: 13  VVNGALALVSYITNNTFPQPLTEEEEAYYLEQLAK-GDESARNVLVERNLRLVAHIVKKF 71

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
              G  + +++S G IGL++A+  F  ++G RLATY+   I+  M
Sbjct: 72  DQTGEDVDDLISIGAIGLIKAINTFKTDKGTRLATYAARCIENEM 116


>gi|254785490|ref|YP_003072919.1| RNA polymerase sigma factor for flagellar operon [Teredinibacter
           turnerae T7901]
 gi|237687129|gb|ACR14393.1| RNA polymerase sigma factor for flagellar operon [Teredinibacter
           turnerae T7901]
          Length = 235

 Score =  100 bits (249), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 44/234 (18%), Positives = 98/234 (41%), Gaps = 19/234 (8%)

Query: 54  VTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           V  ++ LV +IA            + +++  G IGL++A +K+D  +G    TY+   I+
Sbjct: 15  VEDYVPLVKRIAHHMMARMPSHVLVDDLMQAGMIGLLEAAQKYDAGKGASFETYAGIRIR 74

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            A+ + + R             + +  N RR+   +  +     +  +   IA++L +S 
Sbjct: 75  GAIVDEMRRGDW--------APRSVHRNARRVSEAIGNVEARLGRDARDGEIAEELQMSL 126

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            E   +       +S +  + S ++   + ++      +G ++   EK +    R  L  
Sbjct: 127 DEYHDILR-----DSTSTRLYSLEETFEENENQFSLGTEGLDE-PAEKVQIDAMRKALAG 180

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++  L  RE+ +       E  + L+ +     VS  R+ QI ++A  +++  +
Sbjct: 181 AIEGLPEREQLVLSLYY--EQEMNLKEIGLVLGVSESRISQIHSQAALRLKSKL 232


>gi|16760902|ref|NP_456519.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. CT18]
 gi|16765294|ref|NP_460909.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhimurium str. LT2]
 gi|29141406|ref|NP_804748.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. Ty2]
 gi|62180530|ref|YP_216947.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. SC-B67]
 gi|161936245|ref|YP_150204.2| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. ATCC 9150]
 gi|194736051|ref|YP_002114988.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Schwarzengrund str. CVM19633]
 gi|195873263|ref|ZP_02696436.2| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Newport str. SL317]
 gi|197263158|ref|ZP_03163232.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA23]
 gi|197301170|ref|ZP_02664251.2| RNA polymerase sigma factor for flagellar operon (Sigma-F factor)
           [Salmonella enterica subsp. enterica serovar
           Schwarzengrund str. SL480]
 gi|204931059|ref|ZP_03221885.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Javiana str.
           GA_MM04042433]
 gi|205357293|ref|ZP_02346566.2| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA29]
 gi|207856530|ref|YP_002243181.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Enteritidis str. P125109]
 gi|224583543|ref|YP_002637341.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Paratyphi C strain RKS4594]
 gi|289810757|ref|ZP_06541386.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. AG3]
 gi|61224055|sp|P0A2E8|FLIA_SALTY RecName: Full=RNA polymerase sigma factor for flagellar operon;
           AltName: Full=Sigma-27; AltName: Full=Sigma-28; AltName:
           Full=Sigma-F factor
 gi|61224057|sp|P0A2E9|FLIA_SALTI RecName: Full=RNA polymerase sigma factor for flagellar operon;
           AltName: Full=Sigma-27; AltName: Full=Sigma-28; AltName:
           Full=Sigma-F factor
 gi|25331353|pir||AF0750 RNA polymerase sigma transcription factor for flagellar operon fliA
           [imported] - Salmonella enterica subsp. enterica serovar
           Typhi (strain CT18)
 gi|556579|dbj|BAA00389.1| sigma factor [Salmonella enterica subsp. enterica serovar
           Typhimurium]
 gi|4115509|dbj|BAA36397.1| FliA [Salmonella enterica subsp. enterica serovar Typhimurium]
 gi|16420491|gb|AAL20868.1| sigma F (sigma 28) factor of RNA polymerase [Salmonella enterica
           subsp. enterica serovar Typhimurium str. LT2]
 gi|16503199|emb|CAD05705.1| RNA polymerase sigma transcription factor for flagellar operon
           [Salmonella enterica subsp. enterica serovar Typhi]
 gi|29137033|gb|AAO68597.1| RNA polymerase sigma transcription factor for flagellar operon
           [Salmonella enterica subsp. enterica serovar Typhi str.
           Ty2]
 gi|62128163|gb|AAX65866.1| sigma F (sigma 28) factor of RNA polymerase, transcription of late
           flagellar genes (class 3a and 3b operons) [Salmonella
           enterica subsp. enterica serovar Choleraesuis str.
           SC-B67]
 gi|194711553|gb|ACF90774.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Schwarzengrund str.
           CVM19633]
 gi|195634506|gb|EDX52858.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Newport str. SL317]
 gi|197241413|gb|EDY24033.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA23]
 gi|197288040|gb|EDY27427.1| RNA polymerase sigma factor for flagellar operon (Sigma-F factor)
           [Salmonella enterica subsp. enterica serovar
           Schwarzengrund str. SL480]
 gi|204320103|gb|EDZ05308.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Javiana str.
           GA_MM04042433]
 gi|205322652|gb|EDZ10491.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Saintpaul str. SARA29]
 gi|206708333|emb|CAR32636.1| RNA polymerase sigma transcription factor for flagellar operon
           [Salmonella enterica subsp. enterica serovar Enteritidis
           str. P125109]
 gi|224468070|gb|ACN45900.1| flagellar biosynthesis sigma factor FliA [Salmonella enterica
           subsp. enterica serovar Paratyphi C strain RKS4594]
 gi|261247122|emb|CBG24945.1| RNA polymerase sigma transcription factor for flagellar operon
           [Salmonella enterica subsp. enterica serovar Typhimurium
           str. D23580]
 gi|267993942|gb|ACY88827.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 14028S]
 gi|301158470|emb|CBW17980.1| RNA polymerase sigma transcription factor for flagellar operon
           [Salmonella enterica subsp. enterica serovar Typhimurium
           str. SL1344]
 gi|320085426|emb|CBY95207.1| RNA polymerase sigma factor rpoD Sigma-70 [Salmonella enterica
           subsp. enterica serovar Weltevreden str. 2007-60-3289-1]
 gi|322715006|gb|EFZ06577.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Choleraesuis str. A50]
 gi|323130234|gb|ADX17664.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhimurium str. 4/74]
 gi|323250213|gb|EGA34105.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2009159199]
 gi|332988845|gb|AEF07828.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhimurium str. UK-1]
          Length = 239

 Score =  100 bits (249), Expect = 3e-19,   Method: Composition-based stats.
 Identities = 44/240 (18%), Positives = 101/240 (42%), Gaps = 17/240 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV ++D  +G    TY++
Sbjct: 13  KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVDRYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   + +L+  L        +      +A++L
Sbjct: 73  QRIRGAMLDEL-RSRDWVPRSVRRNAREVAQAMGQLEQEL-------GRNATETEVAERL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +  +E   M      D + + L +  +          +   + Q++  + +    + R 
Sbjct: 125 GIPVAEYRQMLL----DTNNSQLFSYDEWREEHGDSIELVTEEHQQENPLHQLLEGDLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 181 RVMDAIESLPEREQLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 238


>gi|115350241|ref|YP_772080.1| flagellar biosynthesis sigma factor [Burkholderia ambifaria AMMD]
 gi|115280229|gb|ABI85746.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Burkholderia
           ambifaria AMMD]
          Length = 243

 Score =  100 bits (249), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 41/215 (19%), Positives = 86/215 (40%), Gaps = 14/215 (6%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++  G IGLM A  ++  ++G +  TY+   I+ AM + +  +  L         +
Sbjct: 37  DLDDLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDELRSNDWL--------PR 88

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            L    R ++  +  +     +      IA+ L +   E   M   L G + +       
Sbjct: 89  SLRKTSREVEYAVHQVEQQLGRSASETEIAEHLKMPLDEYQGMLQDLHGSQLIYYEDFDR 148

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
             +   + D    DH      L++     + R  L  ++  L  RE+ +       E  +
Sbjct: 149 AADDEPFLDRYRVDHADPLSALLDD----HLREALVDAIDRLPEREKLLMSLYY--ERGL 202

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            L  + +  EVS  RV Q+ ++A  +++  +++Q 
Sbjct: 203 NLREIGAVLEVSESRVCQLHSQAVARLRARLREQA 237


>gi|284007149|emb|CBA72430.1| flagellar biosynthesis sigma factor [Arsenophonus nasoniae]
          Length = 243

 Score =  100 bits (249), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 46/238 (19%), Positives = 93/238 (39%), Gaps = 17/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L   ++ LV   A+  +      + + ++V  G IGL+ A+++FD  +G    TY++
Sbjct: 16  KDVLWERYIPLVRHEALKLQVRLPASVELDDLVQAGGIGLLDALERFDASQGTAFTTYAV 75

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             ++ AM + + R+   V               R     +Q +     +P     IA KL
Sbjct: 76  QRVRGAMLDEL-RARDWVPRSVR-------RQAREATKVMQQLEQALGRPATEQEIADKL 127

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   E   +       +  +          S      V D     Q LI  + RKN   
Sbjct: 128 HIGLLEYQQLLQDTNNSQLCSYDEWHEVHGESCEPIIEVDDERNPLQTLIATDIRKN--- 184

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + +++  L  RE+ +       +  + L+ + +   V   RV Q+ ++A K+++  +
Sbjct: 185 -IIKAIECLPEREKMVLTLYY--QEDLNLKEIGAVLNVGESRVSQLHSQAIKRLRARL 239


>gi|205352349|ref|YP_002226150.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 287/91]
 gi|205272130|emb|CAR36983.1| RNA polymerase sigma transcription factor for flagellar operon
           [Salmonella enterica subsp. enterica serovar Gallinarum
           str. 287/91]
 gi|326627399|gb|EGE33742.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Gallinarum str. 9]
          Length = 239

 Score = 99.9 bits (248), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 44/240 (18%), Positives = 101/240 (42%), Gaps = 17/240 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV ++D  +G    TY++
Sbjct: 13  KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVDRYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   + +L+  L        +      +A++L
Sbjct: 73  QRIRGAMLDEL-RSRDWVPRSVRRNAREVAQAMGQLEQKL-------GRNATETEVAERL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +  +E   M      D + + L +  +          +   + Q++  + +    + R 
Sbjct: 125 GIPVAEYRQMLL----DTNNSQLFSYDEWREEHGDSIELVTEEHQQENPLHQLLEGDLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 181 RVMDAIESLPEREQLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 238


>gi|171320713|ref|ZP_02909726.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Burkholderia
           ambifaria MEX-5]
 gi|171094040|gb|EDT39138.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Burkholderia
           ambifaria MEX-5]
          Length = 266

 Score = 99.9 bits (248), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 41/257 (15%), Positives = 89/257 (34%), Gaps = 29/257 (11%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG-YRGYGLP---ISEVVSEGNIGLMQA 89
           E  L +R+    +      +   +L     IA   Y G         + V   +IGL+++
Sbjct: 23  ESELWRRWAAERNACNREAVFAHYLPYARAIAARLYAGRHRDDVEFRDFVQLASIGLLES 82

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +FDP RG    T+    ++ A+   +       K+     Q      +RR        
Sbjct: 83  IDRFDPARGVAFETFCTTRVRGAILTGVE------KLTDGQKQISFSRRVRR-------- 128

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS--SQWQDWLVYD 207
                  E+V ++   ++    +       +    +  A+    D     +Q  D +   
Sbjct: 129 -------ERVASLQADIDRPARQGRDALQAIGTLAAGLAIGFMLDGTGLVAQTTDGMPPG 181

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
                    +    +  +  L  ++  L  R R+I +      + +  E ++    VS+ 
Sbjct: 182 DPALPGAAYQGIAWRQTKTRLADAVRHLPERTRKIIQYHYF--HGLAFEQIADILGVSKG 239

Query: 268 RVRQIEARAFKKVQESI 284
           R+ Q+   A  +++E +
Sbjct: 240 RISQLHRAALAELRERL 256


>gi|300935898|ref|ZP_07150854.1| flagellar biosynthesis sigma factor [Escherichia coli MS 21-1]
 gi|300458917|gb|EFK22410.1| flagellar biosynthesis sigma factor [Escherichia coli MS 21-1]
 gi|307626601|gb|ADN70905.1| flagellar biosynthesis sigma factor [Escherichia coli UM146]
 gi|315286624|gb|EFU46057.1| flagellar biosynthesis sigma factor [Escherichia coli MS 110-3]
          Length = 229

 Score = 99.9 bits (248), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 102/240 (42%), Gaps = 17/240 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 3   KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 62

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   + +L+  L        +      +A++L
Sbjct: 63  QRIRGAMLDEL-RSRDWVPRSVRRNAREVAQAIGQLEQEL-------GRNATETEVAERL 114

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +  ++   M      D + + L +  +          +   D Q +  +++    N R 
Sbjct: 115 GIDIADYRQMLL----DTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQ 170

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 171 RVMETIETLPEREKLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 228


>gi|295095481|emb|CBK84571.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Enterobacter
           cloacae subsp. cloacae NCTC 9394]
          Length = 229

 Score = 99.9 bits (248), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 99/240 (41%), Gaps = 17/240 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV ++D  +G    TY++
Sbjct: 3   KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVDRYDALQGTAFTTYAV 62

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   + +L+  L        +      +A++L
Sbjct: 63  QRIRGAMLDEL-RSRDWVPRSVRRNAREVAHAMGQLEQEL-------GRNATETEVAERL 114

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   E   M      D + + L +  +          +   + Q++  +      N R 
Sbjct: 115 GIPVEEYRQMLL----DTNNSQLFSYDEWREEHGDSIELVTDEHQQENPLHHLLEGNLRQ 170

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 171 RVMEAIEALPEREQLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 228


>gi|148554202|ref|YP_001261784.1| RNA polymerase sigma 28 subunit FliA/WhiG [Sphingomonas wittichii
           RW1]
 gi|148499392|gb|ABQ67646.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Sphingomonas wittichii
           RW1]
          Length = 242

 Score = 99.9 bits (248), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 46/243 (18%), Positives = 99/243 (40%), Gaps = 31/243 (12%)

Query: 51  HRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
             LV +H++LV KIA    G     + + +++  G I L++A   ++ +RG   +TY+  
Sbjct: 22  EDLVRAHMQLVRKIAWHVHGRVSTAIDVEDLIQIGMIALVEAANGYE-DRGHAFSTYASM 80

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            ++ AM +++ R  +L +              R L          + +      +A+ L 
Sbjct: 81  RVRGAMIDHLRRQAALTR--------SAMAKRRALLTAKADFEKKHGRSPSESELAQALG 132

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +                + +AL++ +     +  D +  D       + E+ ++   R  
Sbjct: 133 L-------------DGAAFHALLDETAATYHESIDEVYSDQSMWFADVEERVDQTIEREE 179

Query: 228 LTRSM----SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           L  ++    S L  RE  + +   ++E  + LE +     +   RV QI+  A  K++ S
Sbjct: 180 LAGALAEHISELPEREAMVLQLYFVEE--MNLEEIGQTLGIGAARVCQIKKAALDKLRVS 237

Query: 284 IQK 286
           +++
Sbjct: 238 LRE 240


>gi|303326435|ref|ZP_07356878.1| flagellar biosynthesis protein FlhG [Desulfovibrio sp. 3_1_syn3]
 gi|302864351|gb|EFL87282.1| flagellar biosynthesis protein FlhG [Desulfovibrio sp. 3_1_syn3]
          Length = 555

 Score = 99.9 bits (248), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 42/249 (16%), Positives = 91/249 (36%), Gaps = 26/249 (10%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              +   +   +  +A+  +      + + E++  G +GL++A+  F PERG     Y+ 
Sbjct: 324 REVVARHYAPRIRPLALRLKARLPFHVELDELLGAGALGLVEALCNFRPERGVCFERYAE 383

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + R   L         + L   +RRL    + +     +      +    
Sbjct: 384 NRIRGAMLDELRRQDWL--------PRSLRRAMRRLDEARRMVERGRGRQATEEELLSMT 435

Query: 167 NVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            +    +      L   +  SL+A+           QD L  D  G           +  
Sbjct: 436 GLEPRTLRYAMEALEARQFFSLDAI-----------QDSLAADGPGGADEPCHTAVMREL 484

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              + R ++ L PRE+ +        + +T+   +    ++  RV Q+ A+A  +++  +
Sbjct: 485 AEHMERLLARLTPREKMVLSLYYT--DGLTMREAAEVMSITECRVSQLHAQALARLRTYL 542

Query: 285 QKQVELSSS 293
               E ++ 
Sbjct: 543 GSLYENATP 551


>gi|257440909|ref|ZP_05616664.1| RNA polymerase sigma-F factor [Faecalibacterium prausnitzii A2-165]
 gi|257196689|gb|EEU94973.1| RNA polymerase sigma-F factor [Faecalibacterium prausnitzii A2-165]
          Length = 222

 Score = 99.9 bits (248), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 42/239 (17%), Positives = 86/239 (35%), Gaps = 22/239 (9%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           D       +  +L LV   A  +RG G+   ++   G +GL++A   FD  RG   +TY+
Sbjct: 4   DKIRRSAFIEQNLGLVHACAGRFRGRGIEYDDLYGAGCMGLVKATDGFDEGRGVCFSTYA 63

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
           +  I   +++ + R    VK+  +   K L   +   + H + +         +  +A++
Sbjct: 64  VPVILGEIKK-LFREGGTVKVSRSL--KELGLRVNAAREHHRKLCG---TEPTLSQLAEE 117

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           L  S   +           SL       + N  Q    +              EE    +
Sbjct: 118 LGESVENITLAIQAAQPALSL---TPEGENNDRQIDIPVESP-----------EEELADK 163

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             L   +  L   +R +   R       T    +     ++ ++ + E +  +K++E +
Sbjct: 164 IGLAEVLESLPEEDRLLIRLRFYAN--RTQSETAKVLHTTQVQISRRERKILRKMRERL 220


>gi|171320641|ref|ZP_02909660.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia ambifaria
           MEX-5]
 gi|172059263|ref|YP_001806915.1| flagellar biosynthesis sigma factor [Burkholderia ambifaria MC40-6]
 gi|171094127|gb|EDT39215.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia ambifaria
           MEX-5]
 gi|171991780|gb|ACB62699.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia ambifaria
           MC40-6]
          Length = 244

 Score = 99.9 bits (248), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 41/215 (19%), Positives = 86/215 (40%), Gaps = 14/215 (6%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++  G IGLM A  ++  ++G +  TY+   I+ AM + +  +  L         +
Sbjct: 38  DLDDLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDELRSNDWL--------PR 89

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            L    R ++  +  +     +      IA+ L +   E   M   L G + +       
Sbjct: 90  SLRKTSREVEYAVHQVEQQLGRSASETEIAEHLKMPLDEYQGMLQDLHGSQLIYYEDFDR 149

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
             +   + D    DH      L++     + R  L  ++  L  RE+ +       E  +
Sbjct: 150 AADDEPFLDRYRVDHADPLSALLDD----HLREALVDAIDRLPEREKLLMSLYY--ERGL 203

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            L  + +  EVS  RV Q+ ++A  +++  +++Q 
Sbjct: 204 NLREIGAVLEVSESRVCQLHSQAVARLRARLREQA 238


>gi|83944156|ref|ZP_00956612.1| RNA polymerase sigma-32 factor [Sulfitobacter sp. EE-36]
 gi|83955144|ref|ZP_00963800.1| RNA polymerase sigma-32 factor [Sulfitobacter sp. NAS-14.1]
 gi|83840473|gb|EAP79646.1| RNA polymerase sigma-32 factor [Sulfitobacter sp. NAS-14.1]
 gi|83845023|gb|EAP82904.1| RNA polymerase sigma-32 factor [Sulfitobacter sp. EE-36]
          Length = 223

 Score = 99.9 bits (248), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 65/258 (25%), Positives = 106/258 (41%), Gaps = 57/258 (22%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           R  PML  ++E VL K ++   D  A   LV SH R+V   A           +++SEG 
Sbjct: 9   RNAPMLALEDERVLLKDWQVSKDKFALESLVLSHARIVFYWARKLSDDQAEREDLISEGI 68

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           +GL+ A   FD +R  R +TY+ WW+K A                              +
Sbjct: 69  LGLIHAADLFDLDRDVRFSTYAKWWVKNATMTA--------------------------R 102

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
            HL+AI +                 + + V         D+   AL+ S D N  +    
Sbjct: 103 NHLRAIVE-----------------TPAGVQKTVQHSIDDDDSFALLASEDPNPEE---- 141

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
                      +I +  +   R  L  +M  L P +R +  AR LQ+ P ++++L++  E
Sbjct: 142 ----------AVIAQSSQTLIRARLLEAMERLQPMDREVLRARTLQQPPESIQDLATRME 191

Query: 264 VSRERVRQIEARAFKKVQ 281
           V+  ++RQIE RA  +++
Sbjct: 192 VTPAKLRQIERRAMSRLK 209


>gi|239817113|ref|YP_002946023.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Variovorax paradoxus
           S110]
 gi|239803690|gb|ACS20757.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Variovorax paradoxus
           S110]
          Length = 243

 Score = 99.9 bits (248), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 38/241 (15%), Positives = 98/241 (40%), Gaps = 15/241 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L+  H  +V ++A+         + + +++  G IGL+ A  ++   RG +  T++ 
Sbjct: 10  KSHLLKQHQPMVRRMALQMLAKLPASVELDDLIQAGMIGLLDASTRYQDNRGAQFETFAS 69

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +          +    + L  + R+++  +QA+     +      IA++L
Sbjct: 70  QRIRGAMLDELR--------ASDWGSRGLRQSARKVEQAIQALEHRLGRSASEGEIAREL 121

Query: 167 NVSESEVISMNCRLAGDESL--NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            +   +  S+   + G + L         +  +   +     D        + +      
Sbjct: 122 KMELDDYQSLLQDIQGCQLLYVEDFAQDGEAENPWLERQAQADARLGGDDPLAQLLEAGF 181

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R+ L  +++ L  R++ +       E  + L  + +  EV++ RV Q+ ++A  +++  +
Sbjct: 182 RHELVDAIAALPERDQLLLNLYY--EEELNLREIGAILEVTQSRVCQLHSQAISRLRAKL 239

Query: 285 Q 285
           +
Sbjct: 240 K 240


>gi|284050754|ref|ZP_06380964.1| RNA polymerase sigma factor [Arthrospira platensis str. Paraca]
          Length = 159

 Score = 99.9 bits (248), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 34/137 (24%), Positives = 64/137 (46%), Gaps = 39/137 (28%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------------------ 43
             +  Y+HEI ++P+L ++EE +  K+ ++                              
Sbjct: 23  DAVRTYLHEIGRVPLLTREEEIIYGKKVQQMMNLLEVRDELTKELDRDPTPEEWSAKAGL 82

Query: 44  ---------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
                    +    A  +++ ++LRLVV IA  Y+   +   +++ EG +GL + V+KFD
Sbjct: 83  SESEMTDIINRGRRAKQKMIEANLRLVVSIAKKYQKRNMEFLDLIQEGTLGLERGVEKFD 142

Query: 95  PERGFRLATYSMWWIKA 111
           P RG++ +TY+ WWI+ 
Sbjct: 143 PMRGYKFSTYAYWWIRQ 159


>gi|307776476|pdb|3LES|A Chain A, 2f5 Epitope Scaffold Es2
 gi|307776477|pdb|3LES|B Chain B, 2f5 Epitope Scaffold Es2
 gi|307776478|pdb|3LEV|A Chain A, Hiv-1 Antibody 2f5 In Complex With Epitope Scaffold Es2
          Length = 179

 Score = 99.9 bits (248), Expect = 4e-19,   Method: Composition-based stats.
 Identities = 32/76 (42%), Positives = 48/76 (63%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +A   L+ ++LRLVV IA  Y G GL   +++ EGN GL++AV+KF+ +RGF  +TY+ 
Sbjct: 104 EAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRGFAFSTYAT 163

Query: 107 WWIKAAMQEYILRSWS 122
           WWI+ A+   I     
Sbjct: 164 WWIRQAINRAIADQAR 179


>gi|31747734|gb|AAO38358.1| Lfe160p1 [Leptospirillum ferrooxidans]
          Length = 218

 Score = 99.5 bits (247), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 49/224 (21%), Positives = 97/224 (43%), Gaps = 18/224 (8%)

Query: 66  MGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           M Y       + + ++VS G  GL+ A K+FDP RG +  T +   I+ AM + I RS  
Sbjct: 1   MRYAHRLPPEIDVDDLVSVGMTGLIDAAKRFDPSRGIKFKTMAEHRIRGAMLDEI-RSAD 59

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            V          +      L+  L       L+    + +AK L++S  E +++   +  
Sbjct: 60  WVPRSVREKASSVHAVREGLRAAL-------LREPDDMEMAKALSMSLDEYLTLENEIEP 112

Query: 183 DE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
               S+  L    +   S   D +V      E   + +  +    ++L +++  L  ++R
Sbjct: 113 HHLYSIEDLFEMEEGAGSSILDRMVVPG---EADPLSEFLKSEEASLLEKALDSLPEKQR 169

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +      +E  ++++ +++  EVS  RV QI   A K +++++
Sbjct: 170 LVLSLYYYEE--LSMKEVAAVLEVSESRVSQIHTLAIKNLKKAL 211


>gi|167564488|ref|ZP_02357404.1| flagellar biosynthesis sigma factor [Burkholderia oklahomensis
           EO147]
          Length = 244

 Score = 99.5 bits (247), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 39/215 (18%), Positives = 87/215 (40%), Gaps = 14/215 (6%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++  G IGL+ A  ++  ++G +  TY+   I+ AM + +  +  L         +
Sbjct: 38  DLDDLIQAGMIGLLDAASRYKEDQGAQFETYATQRIRGAMLDELRSNDWL--------PR 89

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            L    R ++  +  +     +      +A  L +   E  SM   L G    + L+   
Sbjct: 90  SLRKTSREVEHAIHQVEQRLGRSANETEVAAHLQMPLGEYQSMLQDLHG----SQLVYYE 145

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D + S   +  +  +       +      + R+ L  ++  L  RE+ +       E  +
Sbjct: 146 DFDRSADDEPFLDRYRADHADPLSALLDDHLRSALVDAIEHLPEREKLLMSLYY--ERGL 203

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            L  + +  EVS  RV Q+ ++A  +++  +++Q 
Sbjct: 204 NLREIGAVLEVSESRVCQLHSQAVARLRAKLREQA 238


>gi|152976769|ref|YP_001376286.1| sporulation sigma factor SigK [Bacillus cereus subsp. cytotoxis NVH
           391-98]
 gi|152025521|gb|ABS23291.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           cytotoxicus NVH 391-98]
          Length = 237

 Score = 99.5 bits (247), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 49/276 (17%), Positives = 97/276 (35%), Gaps = 60/276 (21%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
            Y+        L   +E    +   E GD  A + L+  +LRLV  I   +   G    +
Sbjct: 19  SYVKNNAFPQPLSPDDEKKYLELM-EQGDAQARNLLIEHNLRLVAHIVKKFENTGEDAED 77

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++S G IGL++A++ +   +G +LATY+   I+  +  ++               + L  
Sbjct: 78  LISIGTIGLIKAIESYSAGKGTKLATYAARCIENEILMHL---------------RVLKK 122

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
             + +  H     D       ++ I   L     +VI M       E +   I+  D+  
Sbjct: 123 TKKDVSLHDPIGQDKEGNEISLIDI---LKSESEDVIDMIQLSMELEKIKEYIDILDERE 179

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
                                      + ++ +   +   +E+             T   
Sbjct: 180 ---------------------------KEVIVKRFGLGLDKEK-------------TQRE 199

Query: 258 LSSEFEVSRERVRQIEARAFKKV-QESIQKQVELSS 292
           ++    +SR  V +IE RA  K+  E ++ + E+ +
Sbjct: 200 IAKALGISRSYVSRIEKRALMKMFHEFVRAEKEMKA 235


>gi|167571638|ref|ZP_02364512.1| flagellar biosynthesis sigma factor [Burkholderia oklahomensis
           C6786]
          Length = 244

 Score = 99.5 bits (247), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 39/215 (18%), Positives = 87/215 (40%), Gaps = 14/215 (6%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++  G IGL+ A  ++  ++G +  TY+   I+ AM + +  +  L         +
Sbjct: 38  DLDDLIQAGMIGLLDAASRYKEDQGAQFETYATQRIRGAMLDELRSNDWL--------PR 89

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            L    R ++  +  +     +      +A  L +   E  SM   L G    + L+   
Sbjct: 90  SLRKTSREVEHAVHQVEQRLGRSANETEVAAHLQMPLGEYQSMLQDLHG----SQLVYYE 145

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D + S   +  +  +       +      + R+ L  ++  L  RE+ +       E  +
Sbjct: 146 DFDRSADDEPFLDRYRADHADPLSALLDDHLRSALVDAIEHLPEREKLLMSLYY--ERGL 203

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            L  + +  EVS  RV Q+ ++A  +++  +++Q 
Sbjct: 204 NLREIGAVLEVSESRVCQLHSQAVARLRAKLREQA 238


>gi|307131576|ref|YP_003883592.1| RNA polymerase sigma-28 (sigma F) factor [Dickeya dadantii 3937]
 gi|306529105|gb|ADM99035.1| RNA polymerase, sigma 28 (sigma F) factor [Dickeya dadantii 3937]
          Length = 240

 Score = 99.5 bits (247), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 42/242 (17%), Positives = 96/242 (39%), Gaps = 17/242 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KNSLWKRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLSAVERYDSLQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +               + +  N R +   +Q    +  +      +A+ L
Sbjct: 73  QRIRGAMLDELR--------SRDWAPRSVRRNAREVAQAMQQAEQSLGRAPTEQEVAQTL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           N+S  E   +      D + + L +  +                +E   + +    N R 
Sbjct: 125 NISLEEYRQILL----DTNNSQLFSYDEWREEHGDSAEALLEGNEEANPLNQLMDVNLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  +  
Sbjct: 181 RVMDAIESLPEREKMVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRAKLMS 238

Query: 287 QV 288
            V
Sbjct: 239 DV 240


>gi|167461547|ref|ZP_02326636.1| RNA polymerase sigma factor [Paenibacillus larvae subsp. larvae
           BRL-230010]
          Length = 361

 Score = 99.5 bits (247), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 50/241 (20%), Positives = 96/241 (39%), Gaps = 40/241 (16%)

Query: 51  HRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFDPERGFR----LAT 103
             ++ ++ ++V  +A  YR   G GL   ++VS G IGL+QA + +DP+R  R     +T
Sbjct: 13  DEMIPAYEKMVHSVARKYRSCIGAGLDYDDLVSVGMIGLIQAFRNYDPDRFNRKVSSFST 72

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   IK ++Q ++      V++             R ++  L  I       E   +IA
Sbjct: 73  YAFNMIKWSIQRFLADKRFSVRVP------------RSIQNKLTVIWKQGWDQESAESIA 120

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE--KEER 221
           +K     +E+  +   LAG             + +     L  D   +E  +++      
Sbjct: 121 EKTGWKLAEIREVKRHLAG------------WSVASLDQALSSDKTDEEATMLDVLPAMT 168

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                 +   +  L P ER + E R       T + ++     ++  V +I     KK++
Sbjct: 169 DFTSVHVQDFLCALKPLERAVLELRL---QDQTQKEIAMHIGKTQMYVSRI----LKKIK 221

Query: 282 E 282
           +
Sbjct: 222 D 222


>gi|153932837|ref|YP_001384784.1| RNA polymerase sigma-K factor [Clostridium botulinum A str. ATCC
           19397]
 gi|170755199|ref|YP_001782157.1| RNA polymerase sigma-K factor [Clostridium botulinum B1 str. Okra]
 gi|152928881|gb|ABS34381.1| RNA polymerase sigma-K factor [Clostridium botulinum A str. ATCC
           19397]
 gi|169120411|gb|ACA44247.1| RNA polymerase sigma-K factor [Clostridium botulinum B1 str. Okra]
          Length = 144

 Score = 99.5 bits (247), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 35/116 (30%), Positives = 56/116 (48%), Gaps = 2/116 (1%)

Query: 9   IVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++   + L+ Y+      P  L  +EE     R ++ GD  A   LV  +LRLV  I   
Sbjct: 10  VLGSALFLTGYVTGNTSFPKPLSDEEEKYYLDRLKK-GDALAKDILVERNLRLVAHIVKK 68

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           Y   G  I +++S G +GL++A+  FD  +G RLATY+   I+  +   I  +   
Sbjct: 69  YSYPGKDIDDLISIGTVGLIKAIDSFDNSKGTRLATYAARCIENEILMLIRNNKKT 124


>gi|28210768|ref|NP_781712.1| RNA polymerase sigma factor [Clostridium tetani E88]
 gi|28203206|gb|AAO35649.1| RNA polymerase sigma factor [Clostridium tetani E88]
          Length = 182

 Score = 99.5 bits (247), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 38/116 (32%), Positives = 59/116 (50%), Gaps = 2/116 (1%)

Query: 9   IVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           I+   I L+ Y+      P  L+ +EE    K+  E GD+SA   L+  +LRLV  I   
Sbjct: 40  ILGSNILLTAYVTGNNSFPKPLKAEEEKYYLKQL-EKGDISAKGVLIERNLRLVAHIVKK 98

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           Y   G  + +++S G IGL++A+  F  +RG RLATY+   I+  +   I  +   
Sbjct: 99  YSFPGKDMDDLISIGTIGLIKAIDSFKIDRGTRLATYAAKCIENEILMLIRNNKKT 154


>gi|318040084|ref|ZP_07972040.1| RNA polymerase sigma factor, sigma-70 family protein [Synechococcus
           sp. CB0101]
          Length = 310

 Score = 99.5 bits (247), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 56/266 (21%), Positives = 108/266 (40%), Gaps = 22/266 (8%)

Query: 38  AKRYREHGD-------------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV----VS 80
            +R+++H D             L A  +LV  +L LV      +R       +     + 
Sbjct: 37  IQRWQQHPDGPSHAPKPVRRSALRAREQLVRHNLGLVAHTWGRHRCSLPAHDDTTADALQ 96

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           E  + L++A +KFDP +G+R +TY+ +W++    E+  R+   ++    A +  +     
Sbjct: 97  EAALNLVRAAEKFDPAKGYRFSTYATFWVRRGFTEFEQRAKRAIRFP--AEKAAVVLKAL 154

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLN--VSESEVISMNCRLAGDESLNALINSSDKNSS 198
           RL    QA T +    E + A  K     +S  ++     +     + +      D +  
Sbjct: 155 RLSQQHQASTGDEPSLEWLAAQLKFDGKAMSAEQLAEFIRQWDATRTGSLDGAEDDGDEK 214

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
                L      Q     + +E   +   L + MS L+ +E R+   R L+  P++   L
Sbjct: 215 GGCTRLDLASLQQAAEQQQTQEPDPQHAALPQLMSCLDEQEHRLIRNRYLRRPPLSPCQL 274

Query: 259 SSEF-EVSRERVRQIEARAFKKVQES 283
                 +  ER+ Q+EA A  K++++
Sbjct: 275 RRSMGGMQGERLEQLEATALDKLRQA 300


>gi|82543610|ref|YP_407557.1| flagellar biosynthesis sigma factor [Shigella boydii Sb227]
 gi|81245021|gb|ABB65729.1| alternative sigma factor 28 [Shigella boydii Sb227]
 gi|320176074|gb|EFW51142.1| RNA polymerase sigma factor for flagellar operon [Shigella
           dysenteriae CDC 74-1112]
 gi|320184751|gb|EFW59543.1| RNA polymerase sigma factor for flagellar operon [Shigella flexneri
           CDC 796-83]
          Length = 239

 Score = 99.5 bits (247), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 44/234 (18%), Positives = 99/234 (42%), Gaps = 17/234 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   + +L+  L        +      +A++L
Sbjct: 73  QRIRGAMLDEL-RSRDWVPRSVRRNAREVAQAIGQLEQEL-------GRNATETEVAERL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +  ++   M      D + + L +  +          +   D Q +  +++    N R 
Sbjct: 125 GIDIADYRQMLL----DTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K++
Sbjct: 181 RVMEAIETLPEREKLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRL 232


>gi|4972297|dbj|BAA78111.1| RNA polymerase sigma subunit SigD* [Arabidopsis thaliana]
 gi|16649075|gb|AAL24389.1| sigma-like factor [Arabidopsis thaliana]
 gi|21387209|gb|AAM48008.1| sigma-like factor [Arabidopsis thaliana]
          Length = 267

 Score = 99.5 bits (247), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 46/130 (35%), Positives = 70/130 (53%), Gaps = 15/130 (11%)

Query: 13  EIGLSRYIHEIRKIPML-EKQEEYV-----LA----KRYREHGD-----LSAAHRLVTSH 57
           E+ L  Y+ E  K+  L    EE       LA    K+ R   +       A  ++   +
Sbjct: 128 EVQLCLYLKEGAKLENLGTSVEENEMVSVLLASGRGKKKRSANEILCRRKEAREKITRCY 187

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
            RLVV IA GY+G GL + +++ EG+IGL++  ++FDP+RG++L+TY  WWIK A+   I
Sbjct: 188 RRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPDRGYKLSTYVYWWIKQAILRAI 247

Query: 118 LRSWSLVKIG 127
                LVK+ 
Sbjct: 248 AHKSRLVKLP 257


>gi|121488532|emb|CAJ18256.1| sigma 70-type sigma factor [Chlorobium limicola]
          Length = 165

 Score = 99.5 bits (247), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 38/174 (21%), Positives = 77/174 (44%), Gaps = 11/174 (6%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           ++++EGN+GL++A K+FD  RGF+  +Y++WWI+ ++ + +     +V++    N+    
Sbjct: 1   DLINEGNLGLIKAAKRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLP--LNRVGTL 58

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
             + +    L+   + +        +A  L++   +V           S++A     D N
Sbjct: 59  NKISKAYSQLEQEYERD---PNTKELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDN 115

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +  D L  D    +  L     R +    + RS+SVL P E  +  +     
Sbjct: 116 --RLLDVLQNDGHMPDHGL----NRDSLTLEVERSLSVLAPGEADVIRSXFGIG 163


>gi|291326349|ref|ZP_06124166.2| motility sigma factor FliA [Providencia rettgeri DSM 1131]
 gi|291314661|gb|EFE55114.1| motility sigma factor FliA [Providencia rettgeri DSM 1131]
          Length = 241

 Score = 99.5 bits (247), Expect = 5e-19,   Method: Composition-based stats.
 Identities = 41/239 (17%), Positives = 97/239 (40%), Gaps = 17/239 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   +  L+   A+  +      + I +++  G IGL+ A+++FD  +G   ATY++
Sbjct: 17  KNSLWERYYPLIRHEALKLQVRLPASVDIDDLIQAGGIGLLHALERFDVTQGASFATYAV 76

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ +M + + RS   V               R +   + A+  +  +      IAK L
Sbjct: 77  QRIRGSMLDEL-RSRDWVPRSVR-------RQAREMTKAIGALEQSLGRSATEPEIAKAL 128

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++  +E          D + + L +  + +    +       +      +      + R+
Sbjct: 129 DIDLAEYRQALL----DTNNSQLFSYDEWHEIHGESCEPQMDEDDGGNPLSLLLDSSLRD 184

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  ++
Sbjct: 185 QIAAAIEQLPEREKMVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRGRLR 241


>gi|255655251|ref|ZP_05400660.1| sporulation sigma factor SigK [Clostridium difficile QCD-23m63]
 gi|296451236|ref|ZP_06892976.1| RNA polymerase sigma-E factor [Clostridium difficile NAP08]
 gi|296880412|ref|ZP_06904375.1| RNA polymerase sigma-E factor [Clostridium difficile NAP07]
 gi|296259842|gb|EFH06697.1| RNA polymerase sigma-E factor [Clostridium difficile NAP08]
 gi|296428653|gb|EFH14537.1| RNA polymerase sigma-E factor [Clostridium difficile NAP07]
          Length = 138

 Score = 99.5 bits (247), Expect = 6e-19,   Method: Composition-based stats.
 Identities = 27/93 (29%), Positives = 49/93 (52%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L  +EE     +++   D SA   L+  ++RLV  IA  Y        +++S G IGL+
Sbjct: 10  PLTPEEEIEYLTKFKIENDKSAKDTLIERNMRLVAYIAKKYNNSTEDQDDLISIGTIGLI 69

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           +A++ ++ ++G RLATY+   I+  +   I  +
Sbjct: 70  KAIETYNIDKGTRLATYASRCIENEILMNIRSN 102


>gi|229591832|ref|YP_002873951.1| flagellar biosynthesis sigma factor [Pseudomonas fluorescens SBW25]
 gi|229363698|emb|CAY51076.1| RNA polymerase sigma factor for flagellar regulon FliA [Pseudomonas
           fluorescens SBW25]
          Length = 246

 Score = 99.5 bits (247), Expect = 6e-19,   Method: Composition-based stats.
 Identities = 43/241 (17%), Positives = 94/241 (39%), Gaps = 17/241 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
             +   L+  +  LV +IA          + + +++  G IGL++   K+D  +G    T
Sbjct: 14  RDSQGELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDASKGASFET 73

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   I+ AM + + R           N + +   +R +    +A T  + K  +V A  
Sbjct: 74  YAGIRIRGAMLDEV-RKGDWAPRSVHRNTRMVSDAIRAI----EAKTGRDAKDHEVAAEL 128

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + L++ +   I  +   +   S + L+   +       + L  D            E + 
Sbjct: 129 Q-LSLDDYYGILNDTLGSRLFSFDDLLQDGE------HEGLHEDGASAHMEPSRDLEDER 181

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +  L  +++ L  RER +       +  + L+ +     VS  RV Q+ ++   +++  
Sbjct: 182 FQGALADAIANLPERERLVLALYY--DEELNLKEIGEVLGVSESRVSQLHSQCAARLRGR 239

Query: 284 I 284
           +
Sbjct: 240 L 240


>gi|213610106|ref|ZP_03369932.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 103

 Score = 99.1 bits (246), Expect = 6e-19,   Method: Composition-based stats.
 Identities = 26/102 (25%), Positives = 50/102 (49%), Gaps = 5/102 (4%)

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE- 250
             D   S   D++    D   ++ ++    ++ R      ++ L  RE ++   R   + 
Sbjct: 1   IGDDEDSHLGDFI---EDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDM 57

Query: 251 -NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
               TLE +  +F+V+RER+RQIEA+A +K++   + +V  S
Sbjct: 58  NTDHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRS 99


>gi|7677125|gb|AAF67044.1|AF183382_4 motility sigma factor FliA [Pseudomonas putida]
          Length = 245

 Score = 99.1 bits (246), Expect = 6e-19,   Method: Composition-based stats.
 Identities = 42/241 (17%), Positives = 95/241 (39%), Gaps = 18/241 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
             A + L+  +  LV +IA          + + +++  G IGL++   K+D  +G    T
Sbjct: 14  KDAQYELIERYAPLVKRIAYHLLARLPANVQVEDLIQAGMIGLLEVSSKYDASKGASFET 73

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   I+ AM + + +             + +  N R +   ++A+     +  +   +A
Sbjct: 74  YAGIRIRGAMLDEVRKGDW--------APRSVHRNTRMVSDAMRAVEARTGRDAKDHEVA 125

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
            +L +S  +   +      +++L + + S D         L  D            E + 
Sbjct: 126 AELQLSLDDYYGIL-----NDTLGSRLFSFDDLLQTRARRLHEDGASGHVEPARGLEDER 180

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +  LT +++ L  RER +       +  + L+ +     VS  RV Q+ ++   +++  
Sbjct: 181 FQAALTEAIANLPERERLVLALYY--DEELNLKEIGEVLGVSESRVSQLHSQCAARLRSR 238

Query: 284 I 284
           +
Sbjct: 239 L 239


>gi|300928953|ref|ZP_07144457.1| flagellar biosynthesis sigma factor [Escherichia coli MS 187-1]
 gi|300463107|gb|EFK26600.1| flagellar biosynthesis sigma factor [Escherichia coli MS 187-1]
          Length = 229

 Score = 99.1 bits (246), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 103/240 (42%), Gaps = 17/240 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 3   KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 62

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   + +L+  L        +      +A++L
Sbjct: 63  QRIRGAMLDEL-RSRDWVPRSVRRNAREVAQAIGQLEQEL-------GRNATETEVAERL 114

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +  ++   M      D + + L +  +          +   D Q +  +++    N R 
Sbjct: 115 GIDIADYRQMLL----DTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQ 170

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++ +L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 171 RVMEAIEMLPEREKLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 228


>gi|37525878|ref|NP_929222.1| flagellar biosynthesis sigma factor [Photorhabdus luminescens
           subsp. laumondii TTO1]
 gi|36785307|emb|CAE14248.1| RNA polymerase sigma factor for flagellar operon (Sigma-F factor)
           (Sigma-27) (Sigma-28) [Photorhabdus luminescens subsp.
           laumondii TTO1]
          Length = 240

 Score = 99.1 bits (246), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 44/238 (18%), Positives = 102/238 (42%), Gaps = 17/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   ++ LV   A+  +      + + +++  G IGL+ AV++FD  +G    TY++
Sbjct: 13  KNSLWKRYVPLVRHEALRLQVRLPACVELDDLLQAGGIGLLNAVERFDSLQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS          N + +   +R+L+  L        +P     +AK+L
Sbjct: 73  QRIRGAMLDEL-RSRDWAPRSVRRNAREVTHIIRKLEQDL-------GRPASEQEVAKEL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   E   +      D + + L +  + +    +       +G E   +++    + R 
Sbjct: 125 KIDLVEYRQILL----DTNNSQLFSYDEWHEMHGESCEPVIEEGHETNPLQQLLESDVRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  ++  L  RE+ +       +  + L+ + +  EV   R+ Q+ ++A K+++  +
Sbjct: 181 RVIEAIDSLPEREKMVLTLYY--QEELNLKEIGAVLEVGESRISQLHSQAIKRLRARL 236


>gi|209522287|ref|ZP_03270915.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia sp. H160]
 gi|209497281|gb|EDZ97508.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia sp. H160]
          Length = 244

 Score = 99.1 bits (246), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 40/215 (18%), Positives = 87/215 (40%), Gaps = 14/215 (6%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++  G IGL+ A  ++  ++G +  TY+   I+ AM + +  +  L         +
Sbjct: 37  DLDDLIQAGMIGLLDAAGRYKEDQGAQFETYASQRIRGAMLDELRSNDWL--------PR 88

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            L    R ++  +  +  N  +      IA+ L +   E  SM   L G + +       
Sbjct: 89  SLRRTSREVETAVHRVEQNLGRSASEAEIAEHLQMPLDEYQSMLQDLHGSQLIYYEDFDR 148

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
             +   + D    DH      L++       R+ +  ++  L  RE+ +       E  +
Sbjct: 149 SADDEPFLDRYCVDHSDPLSALLDDSL----RSAVVDAIDRLPEREKLLMSLYY--ERGM 202

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            L  + +  EVS  RV Q+ ++A  +++  +++  
Sbjct: 203 NLREIGAVMEVSESRVCQLHSQAVARLRARLREMA 237


>gi|117929239|ref|YP_873790.1| RNA polymerase, sigma 28 subunit [Acidothermus cellulolyticus 11B]
 gi|117649702|gb|ABK53804.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Acidothermus
           cellulolyticus 11B]
          Length = 297

 Score = 99.1 bits (246), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 56/258 (21%), Positives = 104/258 (40%), Gaps = 31/258 (12%)

Query: 51  HRLVTSHLRLVVKI----AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +LV  HL LV  +    A    G+ +   ++ S G + L QA + +DP RG   A ++ 
Sbjct: 22  DQLVKDHLPLVGYLVAETASKLPGH-VNRDDLTSAGMMALAQAARTYDPSRGVPFARFAT 80

Query: 107 WWIKAAMQEYILRS---WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
             I+ A+ + +         V++             R+     + +     +      +A
Sbjct: 81  VRIRGAIIDELRSHDWASRSVRV-----------KARQRAAAEEELAAVLGRLPTQAELA 129

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + L VS  E+ S    +     L+        ++   +  L +   G E VL+ +E    
Sbjct: 130 EHLGVSVDELASTEGDVHRAVVLSL---QGFADAGTLEGMLPHQDPGPEDVLLNRE---- 182

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           R N L  +++ L PR R + E    QE P+    L+ E  V+  R+ Q+ A A   +++ 
Sbjct: 183 RVNYLLDAVAALPPRLRTVVEGYFFQERPM--AELAEELGVTESRISQMRAEALSLLRDG 240

Query: 284 IQKQVELSSSPPLLQKPR 301
           +   +     P   ++PR
Sbjct: 241 MTAMLAPEQLP---EEPR 255


>gi|330961240|gb|EGH61500.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           maculicola str. ES4326]
          Length = 246

 Score = 99.1 bits (246), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 44/241 (18%), Positives = 96/241 (39%), Gaps = 17/241 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            ++ + L+  +  LV +IA          + + +++  G IGL++   K+D  +G    T
Sbjct: 14  RNSQYELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDSTKGASFET 73

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   I+ AM + + R           N + +   +R +    +A T  + K  +V A  
Sbjct: 74  YAGIRIRGAMLDEV-RKGDWAPRSVHRNTRMVSDAIRAI----EAKTGRDAKDHEVAAEL 128

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + L++ +   I  +   +   S + L+   D       + L  D            E + 
Sbjct: 129 Q-LSLDDYYGILNDTLGSRLFSFDDLLQDGD------HEGLHEDGASGSLEPSRDLEDER 181

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +  L  +++ L  RER +       +  + L+ +     VS  RV Q+ ++   +++  
Sbjct: 182 FQAALADAIANLPERERLVLALYY--DEELNLKEIGEVLGVSESRVSQLHSQCAARLRGR 239

Query: 284 I 284
           +
Sbjct: 240 L 240


>gi|330876038|gb|EGH10187.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           morsprunorum str. M302280PT]
          Length = 246

 Score = 99.1 bits (246), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 44/241 (18%), Positives = 96/241 (39%), Gaps = 17/241 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            ++ + L+  +  LV +IA          + + +++  G IGL++   K+D  +G    T
Sbjct: 14  RNSQYELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDSTKGASFET 73

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   I+ AM + + R           N + +   +R +    +A T  + K  +V A  
Sbjct: 74  YAGIRIRGAMLDEV-RKGDWAPRSVHRNTRMVSDAIRAI----EAKTGRDAKDHEVAAEL 128

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + L++ +   I  +   +   S + L+   D       + L  D            E + 
Sbjct: 129 Q-LSLDDYYGILNDTLGSRLFSFDDLLQDGD------HEGLHEDGASGSLEPSRDLEDER 181

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +  L  +++ L  RER +       +  + L+ +     VS  RV Q+ ++   +++  
Sbjct: 182 FQAALADAIANLPERERLVLALYY--DEELNLKEIGEVLGVSESRVSQLHSQCAARLRGR 239

Query: 284 I 284
           +
Sbjct: 240 L 240


>gi|254517024|ref|ZP_05129082.1| flagellar biosynthesis sigma factor FliA [gamma proteobacterium
           NOR5-3]
 gi|219674529|gb|EED30897.1| flagellar biosynthesis sigma factor FliA [gamma proteobacterium
           NOR5-3]
          Length = 243

 Score = 99.1 bits (246), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 48/240 (20%), Positives = 102/240 (42%), Gaps = 24/240 (10%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           S+A  LV  +L LV KI +         + + +++  G IGL++A + +D  +G   +TY
Sbjct: 20  SSADALVREYLPLVKKIGLRLAAKLPAEIELDDLMQVGLIGLLRARESYDAAQGASFSTY 79

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +   IK AM + I     L         + +   LR++   +        +P     IA 
Sbjct: 80  AGIRIKGAMLDEIRSHDWL--------PRSVQSQLRQVSEAIDRADARLGRPANDAEIAG 131

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L++   E   ++ +LA          +  ++S + +  ++  H       +++   +  
Sbjct: 132 ELDMPLDEYQQLSGQLACAR------MTHIEDSVEAETAVLNTH-----TPLDEVGEEGF 180

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L  S++ L  +ER +          + L+ + +   VS  RV Q+  +A  +++ ++
Sbjct: 181 REALAESVTQLPEKERLMMSLYY--SEGLNLKEIGAVLGVSESRVSQLHGQALARLRVTL 238


>gi|28869183|ref|NP_791802.1| motility sigma factor FliA [Pseudomonas syringae pv. tomato str.
           DC3000]
 gi|66046666|ref|YP_236507.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           syringae B728a]
 gi|237799256|ref|ZP_04587717.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           oryzae str. 1_6]
 gi|28852423|gb|AAO55497.1| motility sigma factor FliA [Pseudomonas syringae pv. tomato str.
           DC3000]
 gi|63257373|gb|AAY38469.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4 [Pseudomonas
           syringae pv. syringae B728a]
 gi|330964675|gb|EGH64935.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           actinidiae str. M302091]
 gi|330972456|gb|EGH72522.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           aceris str. M302273PT]
 gi|331016985|gb|EGH97041.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           lachrymans str. M302278PT]
 gi|331022111|gb|EGI02168.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           oryzae str. 1_6]
          Length = 246

 Score = 99.1 bits (246), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 44/241 (18%), Positives = 96/241 (39%), Gaps = 17/241 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            ++ + L+  +  LV +IA          + + +++  G IGL++   K+D  +G    T
Sbjct: 14  RNSQYELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDSTKGASFET 73

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   I+ AM + + R           N + +   +R +    +A T  + K  +V A  
Sbjct: 74  YAGIRIRGAMLDEV-RKGDWAPRSVHRNTRMVSDAIRAI----EAKTGRDAKDHEVAAEL 128

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + L++ +   I  +   +   S + L+   D       + L  D            E + 
Sbjct: 129 Q-LSLDDYYGILNDTLGSRLFSFDDLLQDGD------HEGLHEDGASGSLEPSRDLEDER 181

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +  L  +++ L  RER +       +  + L+ +     VS  RV Q+ ++   +++  
Sbjct: 182 FQAALADAIANLPERERLVLALYY--DEELNLKEIGEVLGVSESRVSQLHSQCAARLRGR 239

Query: 284 I 284
           +
Sbjct: 240 L 240


>gi|158320420|ref|YP_001512927.1| sporulation sigma factor SigE [Alkaliphilus oremlandii OhILAs]
 gi|158140619|gb|ABW18931.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           oremlandii OhILAs]
          Length = 244

 Score = 99.1 bits (246), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 51/260 (19%), Positives = 103/260 (39%), Gaps = 59/260 (22%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EE +L  + +   + +    L+  +LRLVV IA  +   G+ I +++S G IGL
Sbjct: 42  PPLSNDEENLLISKLKSD-ESTVRTILIERNLRLVVYIARKFENTGIGIEDLISIGTIGL 100

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  F+PE+  +LATY+   I+  +  Y+ R+  +                       
Sbjct: 101 IKAVNTFNPEKNIKLATYASRCIENEILMYLRRNSKV----------------------- 137

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                             K+ VS  E ++++    G+E L + I  ++ +          
Sbjct: 138 ------------------KMEVSFDEPLNID--WDGNELLLSDILGTENDVIHKFLEEEV 177

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           D D  +  L +  +R+ +   L   ++                    T + ++    +S+
Sbjct: 178 DRDLLKIALEKLSKREKKIMELRFGLNT---------------GQEKTQKEVADILGISQ 222

Query: 267 ERVRQIEARAFKKVQESIQK 286
             + ++E R   ++Q+ I +
Sbjct: 223 SYISRLEKRIITRLQKEINR 242


>gi|261340320|ref|ZP_05968178.1| flagellar biosynthesis sigma factor FliA [Enterobacter cancerogenus
           ATCC 35316]
 gi|288317411|gb|EFC56349.1| flagellar biosynthesis sigma factor FliA [Enterobacter cancerogenus
           ATCC 35316]
          Length = 229

 Score = 99.1 bits (246), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 44/240 (18%), Positives = 100/240 (41%), Gaps = 17/240 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV ++D  +G    TY++
Sbjct: 3   KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVDRYDALQGTAFTTYAV 62

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   + +L+  L        +      +A++L
Sbjct: 63  QRIRGAMLDEL-RSRDWVPRSVRRNAREVAHAMGQLEQEL-------GRNATETEVAERL 114

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++  +   M      D + + L +  +          +   + Q++  +      N R 
Sbjct: 115 GIAVEDYRQMLL----DTNNSQLFSYDEWREEHGDSIELVTDEHQQENPLHHLMEGNLRQ 170

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 171 RVMEAIEALPEREQLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 228


>gi|289678962|ref|ZP_06499852.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           syringae FF5]
          Length = 239

 Score = 99.1 bits (246), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 44/238 (18%), Positives = 95/238 (39%), Gaps = 17/238 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            ++ + L+  +  LV +IA          + + +++  G IGL++   K+D  +G    T
Sbjct: 14  RNSQYELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDSTKGASFET 73

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   I+ AM + + R           N + +   +R +    +A T  + K  +V A  
Sbjct: 74  YAGIRIRGAMLDEV-RKGDWAPRSVHRNTRMVSDAIRSI----EAKTGRDAKDHEVAAEL 128

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + L++ +   I  +   +   S + L+   D       + L  D            E + 
Sbjct: 129 Q-LSLDDYYGILNDTLGSRLFSFDDLLQDGD------HEGLHEDGASGSLEPSRDLEDER 181

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +  L  +++ L  RER +       +  + L+ +     VS  RV Q+ ++   +++
Sbjct: 182 FQAALADAIANLPERERLVLALYY--DEELNLKEIGEVLGVSESRVSQLHSQCAARLR 237


>gi|257484896|ref|ZP_05638937.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           tabaci ATCC 11528]
 gi|289629013|ref|ZP_06461967.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           aesculi str. NCPPB3681]
 gi|289647088|ref|ZP_06478431.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           aesculi str. 2250]
 gi|298487813|ref|ZP_07005854.1| RNA polymerase sigma factor for flagellar operon [Pseudomonas
           savastanoi pv. savastanoi NCPPB 3335]
 gi|302185382|ref|ZP_07262055.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           syringae 642]
 gi|298157905|gb|EFH98984.1| RNA polymerase sigma factor for flagellar operon [Pseudomonas
           savastanoi pv. savastanoi NCPPB 3335]
 gi|320329393|gb|EFW85386.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           glycinea str. race 4]
 gi|330866465|gb|EGH01174.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           aesculi str. 0893_23]
 gi|330880595|gb|EGH14744.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           glycinea str. race 4]
 gi|330889039|gb|EGH21700.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv. mori
           str. 301020]
 gi|330953768|gb|EGH54028.1| flagellar biosynthesis sigma factor [Pseudomonas syringae Cit 7]
 gi|330986509|gb|EGH84612.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           lachrymans str. M301315]
          Length = 246

 Score = 99.1 bits (246), Expect = 7e-19,   Method: Composition-based stats.
 Identities = 44/241 (18%), Positives = 96/241 (39%), Gaps = 17/241 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            ++ + L+  +  LV +IA          + + +++  G IGL++   K+D  +G    T
Sbjct: 14  RNSQYELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDSTKGASFET 73

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   I+ AM + + R           N + +   +R +    +A T  + K  +V A  
Sbjct: 74  YAGIRIRGAMLDEV-RKGDWAPRSVHRNTRMVSDAIRAI----EAKTGRDAKDHEVAAEL 128

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + L++ +   I  +   +   S + L+   D       + L  D            E + 
Sbjct: 129 Q-LSLDDYYGILNDTLGSRLFSFDDLLQDGD------HEGLHEDGASGSLEPSRDLEDER 181

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +  L  +++ L  RER +       +  + L+ +     VS  RV Q+ ++   +++  
Sbjct: 182 FQAALADAIANLPERERLVLALYY--DEELNLKEIGEVLGVSESRVSQLHSQCAARLRGR 239

Query: 284 I 284
           +
Sbjct: 240 L 240


>gi|187478163|ref|YP_786187.1| RNA polymerase sigma factor for flagellar operon [Bordetella avium
           197N]
 gi|115422749|emb|CAJ49277.1| RNA polymerase sigma factor for flagellar operon [Bordetella avium
           197N]
          Length = 244

 Score = 99.1 bits (246), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 47/245 (19%), Positives = 101/245 (41%), Gaps = 19/245 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            +A   LV  +  LV K+A+         + + +++  G IGL+ AV+++      +  T
Sbjct: 2   PNAEESLVQ-YSPLVRKLALQLLARLPASVQLDDLIQAGMIGLLDAVRRYQKNPDAQFET 60

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   I+ AM + +     L         + +    RR++  +Q      ++P   + IA
Sbjct: 61  YATARIRGAMLDELRSQDWL--------PRSVRSKSRRIETAIQRQEQVLMRPPTEIEIA 112

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           ++L +   E  +M     G + L+     ++ +     DW     DG     +      +
Sbjct: 113 QELGLPLDEYQAMLSDAQGIQILHYENIDAEGDG----DWHEGAGDGGGN-PLNALLAAD 167

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            R  L +++  L  RE+ +       E  + L+ + +   V+  RV Q+  +A  +++  
Sbjct: 168 LRASLIQAIERLPEREQLLLSLYY--EQGLNLKEIGAVLNVTEARVCQLRTQATARLRSH 225

Query: 284 IQKQV 288
           +Q+  
Sbjct: 226 LQEMA 230


>gi|161613481|ref|YP_001587446.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|167993526|ref|ZP_02574620.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar 4,[5],12:i:- str.
           CVM23701]
 gi|168234127|ref|ZP_02659185.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Kentucky str. CDC 191]
 gi|168244804|ref|ZP_02669736.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL486]
 gi|168259759|ref|ZP_02681732.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Hadar str. RI_05P066]
 gi|168822997|ref|ZP_02834997.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Weltevreden str.
           HI_N05-537]
 gi|194445382|ref|YP_002041220.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Newport str. SL254]
 gi|194450090|ref|YP_002046006.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Heidelberg str. SL476]
 gi|194471287|ref|ZP_03077271.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Kentucky str. CVM29188]
 gi|197251137|ref|YP_002146068.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
 gi|197362055|ref|YP_002141692.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Paratyphi A str. AKU_12601]
 gi|198242943|ref|YP_002215131.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Dublin str. CT_02021853]
 gi|200390898|ref|ZP_03217509.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Virchow str. SL491]
 gi|213053507|ref|ZP_03346385.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. E00-7866]
 gi|213650343|ref|ZP_03380396.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. J185]
 gi|213855803|ref|ZP_03384043.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. M223]
 gi|238912471|ref|ZP_04656308.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Tennessee str. CDC07-0191]
 gi|289824078|ref|ZP_06543676.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-3139]
 gi|56127386|gb|AAV76892.1| RNA polymerase sigma transcription factor for flagellar operon
           [Salmonella enterica subsp. enterica serovar Paratyphi A
           str. ATCC 9150]
 gi|161362845|gb|ABX66613.1| hypothetical protein SPAB_01198 [Salmonella enterica subsp.
           enterica serovar Paratyphi B str. SPB7]
 gi|194404045|gb|ACF64267.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Newport str. SL254]
 gi|194408394|gb|ACF68613.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL476]
 gi|194457651|gb|EDX46490.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Kentucky str. CVM29188]
 gi|197093532|emb|CAR58994.1| RNA polymerase sigma transcription factor for flagellar operon
           [Salmonella enterica subsp. enterica serovar Paratyphi A
           str. AKU_12601]
 gi|197214840|gb|ACH52237.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Agona str. SL483]
 gi|197937459|gb|ACH74792.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Dublin str.
           CT_02021853]
 gi|199603343|gb|EDZ01889.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Virchow str. SL491]
 gi|205328422|gb|EDZ15186.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar 4,[5],12:i:- str.
           CVM23701]
 gi|205331884|gb|EDZ18648.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Kentucky str. CDC 191]
 gi|205336383|gb|EDZ23147.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Heidelberg str. SL486]
 gi|205340661|gb|EDZ27425.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Weltevreden str.
           HI_N05-537]
 gi|205350810|gb|EDZ37441.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Hadar str. RI_05P066]
 gi|312912946|dbj|BAJ36920.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhimurium str. T000240]
 gi|321224599|gb|EFX49662.1| RNA polymerase sigma factor for flagellar operon [Salmonella
           enterica subsp. enterica serovar Typhimurium str.
           TN061786]
 gi|322616949|gb|EFY13857.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315996572]
 gi|322618189|gb|EFY15081.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-1]
 gi|322625859|gb|EFY22678.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-3]
 gi|322626311|gb|EFY23121.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 495297-4]
 gi|322632726|gb|EFY29471.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-1]
 gi|322639068|gb|EFY35761.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 515920-2]
 gi|322640509|gb|EFY37162.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 531954]
 gi|322647255|gb|EFY43754.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. NC_MB110209-0054]
 gi|322649897|gb|EFY46318.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. OH_2009072675]
 gi|322655505|gb|EFY51813.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. CASC_09SCPH15965]
 gi|322660283|gb|EFY56521.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 19N]
 gi|322662964|gb|EFY59171.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 81038-01]
 gi|322668149|gb|EFY64308.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. MD_MDA09249507]
 gi|322674091|gb|EFY70185.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 414877]
 gi|322675556|gb|EFY71630.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 366867]
 gi|322683032|gb|EFY79048.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 413180]
 gi|322686726|gb|EFY82704.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 446600]
 gi|323195385|gb|EFZ80565.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609458-1]
 gi|323199276|gb|EFZ84371.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556150-1]
 gi|323204441|gb|EFZ89447.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 609460]
 gi|323207531|gb|EFZ92479.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 507440-20]
 gi|323211856|gb|EFZ96687.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 556152]
 gi|323217516|gb|EGA02235.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB101509-0077]
 gi|323219591|gb|EGA04075.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB102109-0047]
 gi|323223594|gb|EGA07909.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB110209-0055]
 gi|323231538|gb|EGA15651.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. MB111609-0052]
 gi|323235981|gb|EGA20060.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009083312]
 gi|323240551|gb|EGA24594.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 2009085258]
 gi|323245443|gb|EGA29443.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. 315731156]
 gi|323253976|gb|EGA37800.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008282]
 gi|323255497|gb|EGA39258.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008283]
 gi|323262094|gb|EGA45657.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008284]
 gi|323266217|gb|EGA49707.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008285]
 gi|323270674|gb|EGA54115.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Montevideo str. IA_2010008287]
 gi|326622879|gb|EGE29224.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Dublin str. 3246]
          Length = 229

 Score = 99.1 bits (246), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 44/240 (18%), Positives = 101/240 (42%), Gaps = 17/240 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV ++D  +G    TY++
Sbjct: 3   KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVDRYDALQGTAFTTYAV 62

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   + +L+  L        +      +A++L
Sbjct: 63  QRIRGAMLDEL-RSRDWVPRSVRRNAREVAQAMGQLEQEL-------GRNATETEVAERL 114

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +  +E   M      D + + L +  +          +   + Q++  + +    + R 
Sbjct: 115 GIPVAEYRQMLL----DTNNSQLFSYDEWREEHGDSIELVTEEHQQENPLHQLLEGDLRQ 170

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 171 RVMDAIESLPEREQLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 228


>gi|330899448|gb|EGH30867.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           japonica str. M301072PT]
 gi|330940686|gb|EGH43699.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv. pisi
           str. 1704B]
 gi|330976015|gb|EGH76081.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           aptata str. DSM 50252]
          Length = 246

 Score = 99.1 bits (246), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 44/241 (18%), Positives = 96/241 (39%), Gaps = 17/241 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            ++ + L+  +  LV +IA          + + +++  G IGL++   K+D  +G    T
Sbjct: 14  RNSQYELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDSTKGASFET 73

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   I+ AM + + R           N + +   +R +    +A T  + K  +V A  
Sbjct: 74  YAGIRIRGAMLDEV-RKGDWAPRSVHRNTRMVSDAIRSI----EAKTGRDAKDHEVAAEL 128

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + L++ +   I  +   +   S + L+   D       + L  D            E + 
Sbjct: 129 Q-LSLDDYYGILNDTLGSRLFSFDDLLQDGD------HEGLHEDGASGSLEPSRDLEDER 181

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +  L  +++ L  RER +       +  + L+ +     VS  RV Q+ ++   +++  
Sbjct: 182 FQAALADAIANLPERERLVLALYY--DEELNLKEIGEVLGVSESRVSQLHSQCAARLRGR 239

Query: 284 I 284
           +
Sbjct: 240 L 240


>gi|291527309|emb|CBK92895.1| RNA polymerase sigma factor, sigma-70 family [Eubacterium rectale
           M104/1]
          Length = 224

 Score = 99.1 bits (246), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 39/233 (16%), Positives = 101/233 (43%), Gaps = 17/233 (7%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RLVT ++ L+  +   +R  G+   ++   G +GL +A ++FD  +GF  +TY++  I  
Sbjct: 8   RLVTENINLIYLVMKRFRNRGVDREDLFQIGAVGLTKAAQRFDESKGFAFSTYAVPLIIG 67

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            +Q ++     +V I      +++  + R++    +    N      +  +     +S+ 
Sbjct: 68  EIQRFLRDDG-MVHIS-----RKILDDARKIAIIREKYRMNENSEISLEKMENISGMSKQ 121

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           ++I          ++ A  N+S   +    D+L      +      + ++      + ++
Sbjct: 122 DII---------IAMEADKNASSIENESVLDYLDNKMSAEASDKPSETDKVINHIAMQQA 172

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + L+  ERR+   R +Q+   T + ++     ++  + ++E     K++ ++
Sbjct: 173 FNSLDDSERRLIMLRYMQD--KTQKQVAEVLGRNQVAISRMEKNTLAKLRRAM 223


>gi|257063114|ref|YP_003142786.1| RNA polymerase sigma factor, sigma-70 family [Slackia
           heliotrinireducens DSM 20476]
 gi|256790767|gb|ACV21437.1| RNA polymerase sigma factor, sigma-70 family [Slackia
           heliotrinireducens DSM 20476]
          Length = 269

 Score = 99.1 bits (246), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 41/132 (31%), Positives = 62/132 (46%), Gaps = 32/132 (24%)

Query: 19  YIHEIRKIPMLEKQEEYVL-------------------------------AKRYREHGDL 47
           Y+ EI + P+L+ QEE  L                                 R +  GD 
Sbjct: 49  YLLEIDRFPLLDSQEEADLVAKIRAGAEAADQLRQASQDGVVLDDAEARRLARIQSDGD- 107

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +A  +LV + LRLV +IA  Y   G+   ++V EGN+GL++A ++FDP  G   + Y+ W
Sbjct: 108 AAKEQLVGASLRLVARIAKRYIFRGVSFMDLVHEGNMGLIRAAERFDPASGAAFSVYASW 167

Query: 108 WIKAAMQEYILR 119
           WI+AA+     R
Sbjct: 168 WIRAAISRATGR 179



 Score = 51.4 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 18/65 (27%), Positives = 29/65 (44%), Gaps = 10/65 (15%)

Query: 228 LTRSMSVLNPRERRIFEARRLQENP--VTLENLSSE--------FEVSRERVRQIEARAF 277
           +  ++S ++ RER     R   EN    T    + E          ++RER RQIEA+  
Sbjct: 198 IETALSSMSERERDYIRFRFGLENGSSRTFGESAPEPGVVCTLPSGITRERARQIEAKFL 257

Query: 278 KKVQE 282
            K++ 
Sbjct: 258 AKLRN 262


>gi|213967540|ref|ZP_03395688.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           tomato T1]
 gi|301382877|ref|ZP_07231295.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           tomato Max13]
 gi|302062797|ref|ZP_07254338.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           tomato K40]
 gi|302131296|ref|ZP_07257286.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           tomato NCPPB 1108]
 gi|213927841|gb|EEB61388.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           tomato T1]
          Length = 246

 Score = 99.1 bits (246), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 44/241 (18%), Positives = 96/241 (39%), Gaps = 17/241 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            ++ + L+  +  LV +IA          + + +++  G IGL++   K+D  +G    T
Sbjct: 14  RNSQYELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDSTKGASFET 73

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   I+ AM + + R           N + +   +R +    +A T  + K  +V A  
Sbjct: 74  YAGIRIRGAMLDEV-RKGDWAPRSVHRNTRMVSEAIRAI----EAKTGRDAKDHEVAAEL 128

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + L++ +   I  +   +   S + L+   D       + L  D            E + 
Sbjct: 129 Q-LSLDDYYGILNDTLGSRLFSFDDLLQDGD------HEGLHEDGASGSLEPSRDLEDER 181

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +  L  +++ L  RER +       +  + L+ +     VS  RV Q+ ++   +++  
Sbjct: 182 FQAALADAIANLPERERLVLALYY--DEELNLKEIGEVLGVSESRVSQLHSQCAARLRGR 239

Query: 284 I 284
           +
Sbjct: 240 L 240


>gi|157145286|ref|YP_001452605.1| flagellar biosynthesis sigma factor [Citrobacter koseri ATCC
           BAA-895]
 gi|157082491|gb|ABV12169.1| hypothetical protein CKO_01023 [Citrobacter koseri ATCC BAA-895]
          Length = 229

 Score = 99.1 bits (246), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 101/240 (42%), Gaps = 17/240 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV ++D  +G    TY++
Sbjct: 3   KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVDRYDALQGTAFTTYAV 62

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   + +L+  L        +      +A++L
Sbjct: 63  QRIRGAMLDEL-RSRDWVPRSVRRNAREVAQAMGQLEQEL-------GRNATETEVAERL 114

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   E   M      D + + L +  +          +   + Q++  +++    N R 
Sbjct: 115 AIPVEEYRQMLL----DTNNSQLFSYDEWREEHGDSIELVTEEHQQENPLQQLLESNLRQ 170

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 171 RVMDAIESLPEREQLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 228


>gi|226944861|ref|YP_002799934.1| motility sigma factor 28 [Azotobacter vinelandii DJ]
 gi|226719788|gb|ACO78959.1| motility sigma factor 28 [Azotobacter vinelandii DJ]
          Length = 231

 Score = 99.1 bits (246), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 48/247 (19%), Positives = 102/247 (41%), Gaps = 22/247 (8%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPER 97
           Y   G +     L+  +L LV + A+  +      + + +++  G IGL+ A+ ++D  +
Sbjct: 2   YTAQGKIRQRD-LLEEYLPLVRRQALNLQTRLPASVELDDLIQAGTIGLLDALSRYDAAQ 60

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G   AT++   ++ AM + + RS   V      N + L   LR+L+  L        +P 
Sbjct: 61  GASFATFASQRVRGAMLDEL-RSRDWVPRSVRRNARALEDTLRQLEQRL-------GRPA 112

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           +   IA  + +  +E   +      D + + L+   D    +     V  +      L E
Sbjct: 113 EEREIATSMGLDLAEYRQLLL----DSNGSQLVAIDDLGEDEVDAMSVGHYASPFVELAE 168

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
             +       L +++  L  RE+ +       +  + L+ + +   VS  RV Q+ ++A 
Sbjct: 169 GRDL----ERLVKAIEALPEREKLVLGLYY--QEDLNLKEIGAVLGVSESRVCQLHSQAV 222

Query: 278 KKVQESI 284
            +++  +
Sbjct: 223 ARLRNGL 229


>gi|213584001|ref|ZP_03365827.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. E98-0664]
          Length = 148

 Score = 99.1 bits (246), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 39/133 (29%), Positives = 65/133 (48%), Gaps = 3/133 (2%)

Query: 157 EQVVAIAKKLNVSESEVISMNCRLA-GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
           ++V  +A++L VS  +V  M  R+A  D + +   +    +        + D        
Sbjct: 16  DEVEMVARELGVSSKDVREMESRMAAQDMTFDMSSDDESDSQPMAPVLYLQDKSSNFADG 75

Query: 216 IEKE-ERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIE 273
           IE +   +   N LT +M  L+ R + I  AR L E+   TL+ L+  + VS ERVRQ+E
Sbjct: 76  IEDDNWEEQAANRLTDAMQGLDERSQDIIRARWLDEDNKSTLQELADRYGVSAERVRQLE 135

Query: 274 ARAFKKVQESIQK 286
             A KK++ +I+ 
Sbjct: 136 KNAMKKLRAAIEA 148


>gi|22596849|gb|AAN03367.1|AF481091_4 FliA [Pseudomonas fluorescens]
          Length = 246

 Score = 99.1 bits (246), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 43/241 (17%), Positives = 95/241 (39%), Gaps = 17/241 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
             +   L+  +  LV +IA          + + +++  G IGL++   K+D  +G    T
Sbjct: 14  RDSQGELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDASKGASFET 73

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   I+ AM + + R           N + +   +R +    +A T  + K  +V A  
Sbjct: 74  YAGIRIRGAMLDEV-RKGDWAPRSVHRNTRMVSDAIRAI----EAKTGRDAKDHEVAAEL 128

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + L++ +   I  +   +   S + L+   +       + L  D            E + 
Sbjct: 129 Q-LSLDDYYGILNDTLGSRLFSFDDLLQDGE------HEGLHEDGASAHLEPSRDLEDER 181

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            ++ L  +++ L  RER +       +  + L+ +     VS  RV Q+ ++   +++  
Sbjct: 182 FQSALAEAIANLPERERLVLALYY--DEELNLKEIGEVLGVSESRVSQLHSQCAARLRGR 239

Query: 284 I 284
           +
Sbjct: 240 L 240


>gi|238025872|ref|YP_002910103.1| flagellar biosynthesis sigma factor [Burkholderia glumae BGR1]
 gi|124695885|gb|ABN14279.1| FliA [Burkholderia glumae BGR1]
 gi|237875066|gb|ACR27399.1| FliA [Burkholderia glumae BGR1]
          Length = 241

 Score = 98.7 bits (245), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 38/215 (17%), Positives = 87/215 (40%), Gaps = 14/215 (6%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++  G IGL+ A  ++  ++G +  TY+   I+ AM + +  +  L         +
Sbjct: 35  DLDDLIQAGMIGLLDAASRYKEDQGAQFETYATQRIRGAMLDELRSNDWL--------PR 86

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            L    R ++  +  +     +      +A  L +   +  +M   L G + +       
Sbjct: 87  SLRKTSREVEQAIHQVEQRLGRSANESEVATHLEMPLDDYQAMLQDLHGSQLIYYEDFDR 146

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
             +   + D    DH      L++    ++ R  L  ++  L  RE+ +       E  +
Sbjct: 147 SADDEPFLDRYRVDHSDPLSALLD----EHLRAALVEAIDRLPEREKLLMSLYY--ERGL 200

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            L  + +  EVS  RV Q+ ++A  +++  +++Q 
Sbjct: 201 NLREIGAVLEVSESRVCQLHSQAVARLRARLREQA 235


>gi|188025882|ref|ZP_02960155.2| hypothetical protein PROSTU_02069 [Providencia stuartii ATCC 25827]
 gi|188020848|gb|EDU58888.1| hypothetical protein PROSTU_02069 [Providencia stuartii ATCC 25827]
          Length = 246

 Score = 98.7 bits (245), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 39/243 (16%), Positives = 95/243 (39%), Gaps = 17/243 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   +  L+   A+  +      + I +++  G IGL+ A+++FD  +G   ATY++
Sbjct: 17  KNSLWERYYPLIRHEALKLQVRLPASVDIDDLIQAGGIGLLHALERFDASQGASFATYAV 76

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ +M + +               + +    R +   +  +  +  +      IA+ L
Sbjct: 77  QRIRGSMLDELR--------SRDWAPRSVRRQAREMAKVIGELEQSLSRSATESEIAQAL 128

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           N+  +E          D + + L +  + +    +       +      +      N R 
Sbjct: 129 NIDVTEYRQALL----DTNNSQLYSYDEWHEIHGESCEPAIDESDGGNPLSLLMESNLRA 184

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  ++ 
Sbjct: 185 QIIEAIEQLPEREKLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRGRLKS 242

Query: 287 QVE 289
             E
Sbjct: 243 LTE 245


>gi|161502922|ref|YP_001570034.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:-- str. RSK2980]
 gi|160864269|gb|ABX20892.1| hypothetical protein SARI_00981 [Salmonella enterica subsp.
           arizonae serovar 62:z4,z23:--]
          Length = 229

 Score = 98.7 bits (245), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 44/240 (18%), Positives = 100/240 (41%), Gaps = 17/240 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV ++D  +G    TY++
Sbjct: 3   KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVDRYDALQGTAFTTYAV 62

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   + +L+  L        +      +A++L
Sbjct: 63  QRIRGAMLDEL-RSRDWVPRSVRRNAREVAQAMGQLEQEL-------GRNATETEVAERL 114

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   E   M      D + + L +  +          +   + Q++  + +    + R 
Sbjct: 115 GIPVEEYRQMLL----DTNNSQLFSYDEWREEHGDSIELVTEEHQKENPLHQLLESDLRQ 170

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 171 RVMGAIESLPEREQLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 228


>gi|254519267|ref|ZP_05131323.1| sporulation sigma factor SigE [Clostridium sp. 7_2_43FAA]
 gi|226913016|gb|EEH98217.1| sporulation sigma factor SigE [Clostridium sp. 7_2_43FAA]
          Length = 235

 Score = 98.7 bits (245), Expect = 8e-19,   Method: Composition-based stats.
 Identities = 44/245 (17%), Positives = 96/245 (39%), Gaps = 58/245 (23%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           HGD S    L+  +LRLVV IA  +   G+ + +++S G IGL++AV  F+PE+  +LAT
Sbjct: 49  HGDESIRDILIERNLRLVVYIARKFENTGVCVEDLISVGTIGLIKAVNTFNPEKKIKLAT 108

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   I+  +  Y+ R+                    ++K  +      N+  +    + 
Sbjct: 109 YASRCIENEILMYLRRNS-------------------KVKAEISFYEPLNIDWDGNELLL 149

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
             +  +E++++                           + +  + D Q   L  K     
Sbjct: 150 SDILGTENDIV--------------------------YNLIEDEVDRQLLFLALKHLNDR 183

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            + ++     +   RE+             T + ++    +S+  + ++E +   ++++ 
Sbjct: 184 EKEIVKLRFGLNGTREK-------------TQKEVADMLGISQSYISRLEKKIINRLKKE 230

Query: 284 IQKQV 288
           I K +
Sbjct: 231 INKMI 235


>gi|70729057|ref|YP_258793.1| flagellar biosynthesis sigma factor [Pseudomonas fluorescens Pf-5]
 gi|68343356|gb|AAY90962.1| motility sigma factor FliA [Pseudomonas fluorescens Pf-5]
          Length = 246

 Score = 98.7 bits (245), Expect = 9e-19,   Method: Composition-based stats.
 Identities = 43/241 (17%), Positives = 95/241 (39%), Gaps = 17/241 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
             + + L+  +  LV +IA          + + +++  G IGL++   K+D  +G    T
Sbjct: 14  RDSQYELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDASKGASFET 73

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   I+ AM + + R           N + +   +R +    +A T  + K  +V A  
Sbjct: 74  YAGIRIRGAMLDEV-RKGDWAPRSVHRNTRMVSDAIRAI----EAKTGRDAKDHEVAAEL 128

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + L++ +   I  +   +   S + L+   +       + L  D            E + 
Sbjct: 129 Q-LSLDDYYGILNDTLGSRLFSFDDLLQDGE------HEGLHEDGASAHLEPSRDLEDER 181

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +  L  +++ L  RER +       +  + L+ +     VS  RV Q+ ++   +++  
Sbjct: 182 FQAALADAIANLPERERLVLALYY--DEELNLKEIGEVLGVSESRVSQLHSQCAARLRGR 239

Query: 284 I 284
           +
Sbjct: 240 L 240


>gi|261855330|ref|YP_003262613.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Halothiobacillus
           neapolitanus c2]
 gi|261835799|gb|ACX95566.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Halothiobacillus
           neapolitanus c2]
          Length = 239

 Score = 98.7 bits (245), Expect = 9e-19,   Method: Composition-based stats.
 Identities = 46/240 (19%), Positives = 93/240 (38%), Gaps = 22/240 (9%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           A  +V  H  LV +IA              +++  G IGL++A   +D  +G    TY+ 
Sbjct: 15  AEAVVAEHAGLVKRIAFHLMNRLPDHIQAEDLIQAGMIGLLEASNHYDAAQGASFETYAG 74

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + R+            + +    R +   +  I        +   +   L
Sbjct: 75  IRIRGAMLDEVRRNDW--------APRSVHRRHREISQAVHEIETRTGCEAKDADVCALL 126

Query: 167 NVSESEVIS-MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
            +S  +    +N  +       A +++  ++ ++  D  V DH  Q    +     +   
Sbjct: 127 GISLDDYYEALNDSVQVRL---APLDAGGEDHNETID--VADHRDQPDQYL---SHERFH 178

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             L   +S L  RER +     + E  +  + + +   VS  RV QI+ +A  +++ S++
Sbjct: 179 EDLAEHISALPERERLVMSLYYVDE--LNQKEIGAVLGVSESRVCQIQNKAILRLKSSLK 236


>gi|331696172|ref|YP_004332411.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit [Pseudonocardia
           dioxanivorans CB1190]
 gi|326950861|gb|AEA24558.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Pseudonocardia dioxanivorans CB1190]
          Length = 270

 Score = 98.7 bits (245), Expect = 9e-19,   Method: Composition-based stats.
 Identities = 49/270 (18%), Positives = 98/270 (36%), Gaps = 30/270 (11%)

Query: 32  QEEYVLAKRYREHGDLSA-AHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQA 89
           +  + LA+   +     A    L+ + L +  +IA  +         ++    +  +++A
Sbjct: 24  ERLHRLARLPADDPARDALRDDLILTFLPVAERIAGRHASATPWSREDLRQAASEAVVRA 83

Query: 90  VKKFDPER-GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           V ++DPER       Y +  ++  +  +       V++      K L   +R   G +  
Sbjct: 84  VDRWDPERAQGDFLGYLVPCVRGEVLRWFRDQSWSVRVPRRL--KELSVAIRSAHGPMAQ 141

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
              +  +P     +A++L V   EV            L AL    +  ++        D 
Sbjct: 142 RLGSAPRP---SELARELGVDIEEV------------LEALHAEENHRAATLDAPAPGDE 186

Query: 209 DGQEQVLIE---KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
               + L E   + E       L   ++ L  RERRI   R       T   +  E  VS
Sbjct: 187 RLPGEQLGEIDRQLELVEDAETLRPLIAALPERERRILLLRFYGG--RTQSQIGEELGVS 244

Query: 266 RERVRQIEARAFKKVQESIQKQVELSSSPP 295
           +  V ++ +R   +++ ++     L  +PP
Sbjct: 245 QMHVSRLLSRTLARLRAAM-----LDDTPP 269


>gi|320325134|gb|EFW81203.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           glycinea str. B076]
          Length = 246

 Score = 98.7 bits (245), Expect = 9e-19,   Method: Composition-based stats.
 Identities = 44/241 (18%), Positives = 96/241 (39%), Gaps = 17/241 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            ++ + L+  +  LV +IA          + + +++  G IGL++   K+D  +G    T
Sbjct: 14  RNSQYELIERYAPLVKRIAYHLLARLPASVQVQDLIQAGMIGLLEVSTKYDSTKGASFET 73

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   I+ AM + + R           N + +   +R +    +A T  + K  +V A  
Sbjct: 74  YAGIRIRGAMLDEV-RKGDWAPRSVHRNTRMVSDAIRAI----EAKTGRDAKDHEVAAEL 128

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + L++ +   I  +   +   S + L+   D       + L  D            E + 
Sbjct: 129 Q-LSLDDYYGILNDTLGSRLFSFDDLLQDGD------HEGLHEDGASGSLEPSRDLEDER 181

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +  L  +++ L  RER +       +  + L+ +     VS  RV Q+ ++   +++  
Sbjct: 182 FQAALADAIANLPERERLVLALYY--DEELNLKEIGEVLGVSESRVSQLHSQCAARLRGR 239

Query: 284 I 284
           +
Sbjct: 240 L 240


>gi|170701719|ref|ZP_02892658.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia ambifaria
           IOP40-10]
 gi|170133382|gb|EDT01771.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia ambifaria
           IOP40-10]
          Length = 244

 Score = 98.7 bits (245), Expect = 9e-19,   Method: Composition-based stats.
 Identities = 40/215 (18%), Positives = 86/215 (40%), Gaps = 14/215 (6%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++  G IGLM A  ++  ++G +  TY+   I+ AM + +  +  L         +
Sbjct: 38  DLDDLIQAGMIGLMDAAGRYKEDQGAQFETYATQRIRGAMLDELRSNDWL--------PR 89

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            L    R ++  +  +     +      IA+ L +   E   M   L G    + LI   
Sbjct: 90  SLRKTSREVEYAVHQVEQQLGRSASETEIAEHLKMPLDEYQGMLQDLHG----SQLIYYE 145

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D + +   +  +  +       +      + R  L  ++  L  RE+ +       E  +
Sbjct: 146 DFDRAADDEPFLDRYRVDLADPLSALLDDHLREALVDAIDRLPEREKLLMSLYY--ERGL 203

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            L  + +  EVS  RV Q+ ++A  +++  +++Q 
Sbjct: 204 NLREIGAVLEVSESRVCQLHSQAVARLRARLREQA 238


>gi|169831583|ref|YP_001717565.1| sporulation sigma factor SigE [Candidatus Desulforudis audaxviator
           MP104C]
 gi|169638427|gb|ACA59933.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Candidatus
           Desulforudis audaxviator MP104C]
          Length = 241

 Score = 98.7 bits (245), Expect = 9e-19,   Method: Composition-based stats.
 Identities = 54/260 (20%), Positives = 102/260 (39%), Gaps = 59/260 (22%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L   EE  L  R  E GD      L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 39  PPLTVDEETGLISRL-EAGDHGVRSTLIERNLRLVVYIARKFESTGVGIEDMVSIGTIGL 97

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FDP +  +LATY+   I+  +  Y+ R+                    +++G  
Sbjct: 98  IKAVNTFDPRKRIKLATYASRCIENEILMYLRRNS-------------------KVRGE- 137

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                                +S  E ++++    G+E L + +  +D +       +  
Sbjct: 138 ---------------------ISFEEPLNID--WDGNELLLSDVLGTDSDIIYKDLEMEV 174

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           DH      L +  +R+ +   L   ++                    T + ++    +S+
Sbjct: 175 DHKLLRLALQKLSQRERKIMELRFGLN---------------NGEEKTQKEVADLLGISQ 219

Query: 267 ERVRQIEARAFKKVQESIQK 286
             + ++E R   ++++ I +
Sbjct: 220 SYISRLEKRIINRLKKEIYR 239


>gi|283781321|ref|YP_003372076.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pirellula staleyi DSM
           6068]
 gi|283439774|gb|ADB18216.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pirellula staleyi DSM
           6068]
          Length = 261

 Score = 98.7 bits (245), Expect = 9e-19,   Method: Composition-based stats.
 Identities = 57/256 (22%), Positives = 107/256 (41%), Gaps = 23/256 (8%)

Query: 38  AKRYREHGD-LSAAHRLVTSHLRLVVK---IAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
            K+Y+   +     + LV  +L LV             G+ + +++S G  GLM A+  F
Sbjct: 15  WKKYKHDPNQKELRNLLVEHYLPLVKYNGERIWARLPEGVELDDLISAGIFGLMDAIDAF 74

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D  RG +  TY +  I+ AM + + R+   V     +   +L    + L+  L       
Sbjct: 75  DMTRGVKFETYCVPRIRGAMLDEL-RTMDWVPRLVRSKASKLGEATKTLEARL------- 126

Query: 154 LKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
            +    V +A ++ +S  EV  M       G  SLN     +D      +  ++ D  G+
Sbjct: 127 GRHPTTVELAAQMEMSVPEVEKMVSEASAVGLISLNKKWYETDSYKDVREIDILEDKKGE 186

Query: 212 EQVLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
           +        R+ ++N L R +   LN  ER I      +E  +T++ + +  ++S  RV 
Sbjct: 187 DPT------RRIQKNDLMRLVTKGLNRNERLIIILYYYEE--LTMKEIGATLDLSESRVS 238

Query: 271 QIEARAFKKVQESIQK 286
           Q+ +    ++Q  + +
Sbjct: 239 QMHSSIVSRLQSQLGR 254


>gi|317492397|ref|ZP_07950826.1| FliA/WhiG family RNA polymerase sigma factor [Enterobacteriaceae
           bacterium 9_2_54FAA]
 gi|316919736|gb|EFV41066.1| FliA/WhiG family RNA polymerase sigma factor [Enterobacteriaceae
           bacterium 9_2_54FAA]
          Length = 240

 Score = 98.3 bits (244), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 43/241 (17%), Positives = 98/241 (40%), Gaps = 17/241 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   +  LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KNSLWQRYAPLVRHEALRLQVRLPASVELDDLLQAGGIGLLHAVERYDAMQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   ++R +  L        +      IA++L
Sbjct: 73  QRIRGAMLDEL-RSRDWVPRSVRRNAREVSAAMQRAEQRLH-------RAPTETEIAQEL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   E   +          +      +   S    +  ++     + L+E +     R 
Sbjct: 125 DMPLVEYQQILLDTNTSHLFSYDEWREEHGDSAEPVFQQHEDANPLKQLLEGDL----RQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  +  
Sbjct: 181 RVIAAIEALPEREKLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLAS 238

Query: 287 Q 287
           Q
Sbjct: 239 Q 239


>gi|300722632|ref|YP_003711922.1| sigma F (sigma 28) factor of RNA polymerase [Xenorhabdus
           nematophila ATCC 19061]
 gi|297629139|emb|CBJ89735.1| sigma F (sigma 28) factor of RNA polymerase, transcription of late
           flagellar genes (class 3a and 3b operons) [Xenorhabdus
           nematophila ATCC 19061]
          Length = 240

 Score = 98.3 bits (244), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 43/238 (18%), Positives = 100/238 (42%), Gaps = 17/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   ++ LV   A+  +      + + +++  G IGL+ AV++FD  +G    TY++
Sbjct: 13  KNSLWKRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERFDSMQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS          N + +   +R+L+  L        +P     +AK+L
Sbjct: 73  QRIRGAMLDEL-RSRDWAPRSVRRNAREVTQTIRKLEQEL-------GRPASEQEVAKEL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++  E   +      D + + L +  + +    +       +  E   +++    + R 
Sbjct: 125 KINLIEYRQILL----DTNNSQLFSYDEWHEIHGESCEPVIEEEHETNPLQQLLEGDLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +   +  L  RE+ +       +  + L+ + +   V   RV Q+ ++A K+++  +
Sbjct: 181 RVINIIESLPEREKMVLTLYY--QEELNLKEIGAVLNVGESRVSQLHSQAIKRLRARL 236


>gi|269139471|ref|YP_003296172.1| flagellar biosynthesis sigma factor [Edwardsiella tarda EIB202]
 gi|267985132|gb|ACY84961.1| flagellar biosynthesis sigma factor [Edwardsiella tarda EIB202]
          Length = 240

 Score = 98.3 bits (244), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 42/241 (17%), Positives = 97/241 (40%), Gaps = 17/241 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   +  LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KNTLWQRYAPLVRHEALRLQVRLPASVELDDLLQAGGIGLLHAVERYDAMQGTAFTTYAI 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   ++R +  L        +      IA+++
Sbjct: 73  QRIRGAMLDEL-RSRDWVPRSVRRNARGVSAAMQRAEQRL-------GRTPGDSEIAQEM 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   E   +      D + + L +  +                +E   + +    + R 
Sbjct: 125 GIPLEEYQQILL----DTNTSQLFSYDEWREDHGDSAEPVLEQSEEANPLRQLLESDLRG 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  +  
Sbjct: 181 RVIAAIEALPEREKLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTRLLS 238

Query: 287 Q 287
           Q
Sbjct: 239 Q 239


>gi|306410397|gb|ADM85820.1| RNA polymerase essential primary sigma 70 factor [Frankia alni]
 gi|306410399|gb|ADM85821.1| RNA polymerase essential primary sigma 70 factor [Frankia alni]
 gi|306410401|gb|ADM85822.1| RNA polymerase essential primary sigma 70 factor [Frankia alni]
 gi|306410403|gb|ADM85823.1| RNA polymerase essential primary sigma 70 factor [Frankia alni]
 gi|306410405|gb|ADM85824.1| RNA polymerase essential primary sigma 70 factor [Frankia sp. CcI3]
 gi|306410407|gb|ADM85825.1| RNA polymerase essential primary sigma 70 factor [Frankia sp. CpI1]
 gi|306410409|gb|ADM85826.1| RNA polymerase essential primary sigma 70 factor [Frankia sp.
           Cj1-82]
          Length = 106

 Score = 98.3 bits (244), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 28/111 (25%), Positives = 52/111 (46%), Gaps = 5/111 (4%)

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           +GL++AV+KFD  +G++ +TY+ WWI+ A+   I      ++I     +      L R++
Sbjct: 1   LGLIRAVEKFDYTKGYKFSTYATWWIRQAITRAIADQARTIRIPVHMVE--TINKLIRIQ 58

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
             L         PE    IAK+++++  +V  +        SL   I   +
Sbjct: 59  RQLLQDLGREPSPE---EIAKEMDLTPDKVREILKVSQEPVSLETPIGEEE 106


>gi|271500098|ref|YP_003333123.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit [Dickeya
           dadantii Ech586]
 gi|270343653|gb|ACZ76418.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Dickeya
           dadantii Ech586]
          Length = 240

 Score = 98.3 bits (244), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 41/242 (16%), Positives = 95/242 (39%), Gaps = 17/242 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KNSLWKRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLSAVERYDSLQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +               + +  N R +   +Q    +  +      +A+ L
Sbjct: 73  QRIRGAMLDELR--------SRDWAPRSVRRNAREVAQAMQQAEQSLGRAPTEQEVAQTL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           N+S  E   +      D + + L +  +                ++   +      N R 
Sbjct: 125 NISLEEYRQILL----DTNNSQLFSYDEWREEHGDSAEALLEGNEDANPLNLLMDVNLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  +  
Sbjct: 181 RVMDAIENLPEREKMVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRAKLMS 238

Query: 287 QV 288
            V
Sbjct: 239 DV 240


>gi|238924921|ref|YP_002938437.1| RNA polymerase sigma-F factor [Eubacterium rectale ATCC 33656]
 gi|238876596|gb|ACR76303.1| RNA polymerase sigma-F factor [Eubacterium rectale ATCC 33656]
          Length = 224

 Score = 98.3 bits (244), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 40/233 (17%), Positives = 104/233 (44%), Gaps = 17/233 (7%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RLVT ++ L+  +   +R  G+   ++   G +GL +A ++FD  +GF  +TY++  I  
Sbjct: 8   RLVTENINLIYLVMKRFRNRGVDREDLFQIGAVGLTKAAQRFDESKGFAFSTYAVPLIIG 67

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            +Q ++     +V I            + R K  +   ++ +L+  ++++      +S+ 
Sbjct: 68  EIQRFLRDDG-MVHISRKILDDARKIAIIREKYRMNENSEISLEKMEIIS-----GMSKQ 121

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           ++I          ++ A  N+S   +    D+L      +      + ++      + ++
Sbjct: 122 DII---------IAMEADKNASSIENESVLDYLDNKMSAEASDKPSETDKVINHIAMQQA 172

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + L+  ERR+   R +Q+   T + ++     ++  + ++E    +K++ ++
Sbjct: 173 FNSLDDSERRLIMLRYMQD--KTQKQVAEVLGRNQVAISRMEKNTLEKLRRAM 223


>gi|182418995|ref|ZP_02950251.1| RNA polymerase sigma-K factor [Clostridium butyricum 5521]
 gi|182377278|gb|EDT74846.1| RNA polymerase sigma-K factor [Clostridium butyricum 5521]
          Length = 232

 Score = 98.3 bits (244), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 35/106 (33%), Positives = 58/106 (54%), Gaps = 2/106 (1%)

Query: 16  LSRYIHEIRKIPM-LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           L+ YI      P+ L+++EE +  K+++E GD SA   L+  +LRLV  I   Y      
Sbjct: 17  LTGYITNNNTFPLPLDEEEEQMYLKKFKE-GDKSAKSILIERNLRLVAHIVKKYSFPNKD 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           + E++S G +GL++A+  FD  +G RLATY+   I+  +      +
Sbjct: 76  VDELISIGTVGLIKAIDSFDSSKGTRLATYASRCIENEILMLFRNN 121


>gi|332096706|gb|EGJ01697.1| RNA polymerase sigma factor for flagellar operon [Shigella boydii
           3594-74]
          Length = 229

 Score = 98.3 bits (244), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 44/234 (18%), Positives = 99/234 (42%), Gaps = 17/234 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 3   KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 62

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   + +L+  L        +      +A++L
Sbjct: 63  QRIRGAMLDEL-RSRDWVPRSVRRNAREVAQAIGQLEQEL-------GRNATETEVAERL 114

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +  ++   M      D + + L +  +          +   D Q +  +++    N R 
Sbjct: 115 GIDIADYRQMLL----DTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQ 170

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K++
Sbjct: 171 RVMEAIETLPEREKLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRL 222


>gi|322806877|emb|CBZ04447.1| RNA polymerase sporulation specific sigma factor SigK [Clostridium
           botulinum H04402 065]
          Length = 144

 Score = 98.3 bits (244), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 35/116 (30%), Positives = 56/116 (48%), Gaps = 2/116 (1%)

Query: 9   IVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++   + L+ Y+      P  L  +EE     R ++ GD  A   LV  +LRLV  I   
Sbjct: 10  VLGSALFLTGYVTANTSFPKPLSDEEEKYYLDRLKK-GDALAKDILVERNLRLVAHIVKK 68

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           Y   G  I +++S G +GL++A+  FD  +G RLATY+   I+  +   I  +   
Sbjct: 69  YSYPGKDIDDLISIGTVGLIKAIDSFDNSKGTRLATYAARCIENEILMLIRNNKKT 124


>gi|304559365|gb|ADM42029.1| RNA polymerase sigma factor for flagellar operon [Edwardsiella
           tarda FL6-60]
          Length = 237

 Score = 98.3 bits (244), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 42/241 (17%), Positives = 97/241 (40%), Gaps = 17/241 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   +  LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 10  KNTLWQRYAPLVRHEALRLQVRLPASVELDDLLQAGGIGLLHAVERYDAMQGTAFTTYAI 69

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   ++R +  L        +      IA+++
Sbjct: 70  QRIRGAMLDEL-RSRDWVPRSVRRNARGVSAAMQRAEQRL-------GRTPGDSEIAQEM 121

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   E   +      D + + L +  +                +E   + +    + R 
Sbjct: 122 GIPLEEYQQILL----DTNTSQLFSYDEWREDHGDSAEPVLEQSEEANPLRQLLESDLRG 177

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  +  
Sbjct: 178 RVIAAIEALPEREKLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTRLLS 235

Query: 287 Q 287
           Q
Sbjct: 236 Q 236


>gi|71736085|ref|YP_275521.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           phaseolicola 1448A]
 gi|71556638|gb|AAZ35849.1| RNA polymerase sigma factor for flagellar operon [Pseudomonas
           syringae pv. phaseolicola 1448A]
          Length = 239

 Score = 98.3 bits (244), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 44/241 (18%), Positives = 96/241 (39%), Gaps = 17/241 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            ++ + L+  +  LV +IA          + + +++  G IGL++   K+D  +G    T
Sbjct: 7   RNSQYELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDSTKGASFET 66

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   I+ AM + + R           N + +   +R +    +A T  + K  +V A  
Sbjct: 67  YAGIRIRGAMLDEV-RKGDWAPRSVHRNTRMVSDAIRAI----EAKTGRDAKDHEVAAEL 121

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + L++ +   I  +   +   S + L+   D       + L  D            E + 
Sbjct: 122 Q-LSLDDYYGILNDTLGSRLFSFDDLLQDGD------HEGLHEDGASGSLEPSRDLEDER 174

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +  L  +++ L  RER +       +  + L+ +     VS  RV Q+ ++   +++  
Sbjct: 175 FQAALADAIANLPERERLVLALYY--DEELNLKEIGEVLGVSESRVSQLHSQCAARLRGR 232

Query: 284 I 284
           +
Sbjct: 233 L 233


>gi|218548541|ref|YP_002382332.1| flagellar biosynthesis sigma factor [Escherichia fergusonii ATCC
           35469]
 gi|218356082|emb|CAQ88699.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia fergusonii
           ATCC 35469]
 gi|324113640|gb|EGC07615.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           fergusonii B253]
 gi|325496958|gb|EGC94817.1| flagellar biosynthesis sigma factor [Escherichia fergusonii ECD227]
          Length = 238

 Score = 98.3 bits (244), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 41/240 (17%), Positives = 96/240 (40%), Gaps = 17/240 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV ++D  +G    TY++
Sbjct: 13  KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVDRYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +               + +  N R +   +  +     +      +AK+L
Sbjct: 73  QRIRGAMLDELR--------SRDWAPRSVRRNAREVAQAIGQLEQELGRNASETEVAKRL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +S  E   M      D + + L +  +          +   + Q+   + +    + R 
Sbjct: 125 GISTEEYRQMLL----DTNNSQLFSYDEWREEHGDSAELITEEHQQANPLHQLLESDLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  + +
Sbjct: 181 QVMDAIERLPEREKLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRSKLGR 238


>gi|167462462|ref|ZP_02327551.1| DNA-directed RNA polymerase sigma-37 factor (sigma-B)
           [Paenibacillus larvae subsp. larvae BRL-230010]
 gi|322381881|ref|ZP_08055835.1| RNA polymerase sigma factor SigB-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321154269|gb|EFX46591.1| RNA polymerase sigma factor SigB-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 260

 Score = 98.3 bits (244), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 48/252 (19%), Positives = 99/252 (39%), Gaps = 19/252 (7%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI-SEVVSEGNIGLMQAVKKFDP 95
           L   Y++      A  L+      V   A         +  ++   G + L++  K+FDP
Sbjct: 16  LILEYQDSESNEIATTLLLQFESTVRMAAGKMSRNRPDLYEDLYQVGQMSLLKLFKQFDP 75

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
             G +   Y M  I   M+ Y+      +++     +K       +++  + ++T    +
Sbjct: 76  SHGVQFEAYMMKSIIGHMKNYLRDKSWYIQVPRRIKEKGF-----QIQQAIDSLTMKLER 130

Query: 156 PEQVVAIAKKLNVSESEVISMNC--RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
              V  IA +L +S  E I +          SL+  + S+++N S   D L    D    
Sbjct: 131 SPNVDEIANELGLSTEETIEILAGRECYHYVSLDMPL-STEENGSTIGDVLGIQED---- 185

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
               +    + R  L  +M  L P E++      +  +  +   ++ E ++S+  V +++
Sbjct: 186 ----EYLHVDNRLDLQEAMEHLKPEEKKALILAYI--DGYSQRTIAQELDISQMSVSRMQ 239

Query: 274 ARAFKKVQESIQ 285
            RA  K++E  +
Sbjct: 240 RRALSKLREYFK 251


>gi|254974785|ref|ZP_05271257.1| sporulation sigma factor SigK [Clostridium difficile QCD-66c26]
 gi|255100257|ref|ZP_05329234.1| sporulation sigma factor SigK [Clostridium difficile QCD-63q42]
 gi|255306197|ref|ZP_05350369.1| sporulation sigma factor SigK [Clostridium difficile ATCC 43255]
 gi|255313912|ref|ZP_05355495.1| sporulation sigma factor SigK [Clostridium difficile QCD-76w55]
 gi|255516591|ref|ZP_05384267.1| sporulation sigma factor SigK [Clostridium difficile QCD-97b34]
 gi|306519807|ref|ZP_07406154.1| sporulation sigma factor SigK [Clostridium difficile QCD-32g58]
          Length = 130

 Score = 98.3 bits (244), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 27/93 (29%), Positives = 49/93 (52%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L  +EE     +++   D SA   L+  ++RLV  IA  Y        +++S G IGL+
Sbjct: 10  PLTPEEEIEYLTKFKIENDKSAKDTLIERNMRLVAYIAKKYNNSTEDQDDLISIGTIGLI 69

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           +A++ ++ ++G RLATY+   I+  +   I  +
Sbjct: 70  KAIETYNIDKGTRLATYASRCIENEILMNIRSN 102


>gi|103488379|ref|YP_617940.1| RNA polymerase, sigma 28 subunit [Sphingopyxis alaskensis RB2256]
 gi|98978456|gb|ABF54607.1| RNA polymerase, sigma 28 subunit [Sphingopyxis alaskensis RB2256]
          Length = 248

 Score = 98.3 bits (244), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 49/254 (19%), Positives = 106/254 (41%), Gaps = 23/254 (9%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           +  R HG   +   LVT +  LV KIA            + +++  G I L++A + ++ 
Sbjct: 15  RALRPHGYGESVDALVTEYAPLVRKIAWQVFSRVSRTSELDDLIQTGLIALIEASRHYE- 73

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           ERGF  ATY+   I+ AM + + R   + +              +RL+    A+    L+
Sbjct: 74  ERGFAFATYASTRIRGAMIDQLRREADVGR--------SAMVAAKRLQATRAALEQQLLR 125

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
                 +A  L+++  +  ++        S +           +  D   +    ++ + 
Sbjct: 126 APTAAEMAVALDMAAEDYFALERNATHGRSTSL---------DELTDIGAFLAADEDALA 176

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
            ++ E+++    L + +  L+ RE+ + +    +E  + L  +    +VS  R+ QI+  
Sbjct: 177 DDRCEQEDLMGALRQCVGRLSEREQLVLQLYFFEE--LNLHEIGLTLDVSAARICQIKRE 234

Query: 276 AFKKVQESIQKQVE 289
           A  KV+  +++  +
Sbjct: 235 AMIKVERMMREMTD 248


>gi|92114133|ref|YP_574061.1| sigma 28 (flagella/sporulation) [Chromohalobacter salexigens DSM
           3043]
 gi|91797223|gb|ABE59362.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Chromohalobacter
           salexigens DSM 3043]
          Length = 232

 Score = 98.0 bits (243), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 40/238 (16%), Positives = 93/238 (39%), Gaps = 20/238 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L+  ++ LV + A+  +      + + +++  G +GL+ A+++FD  +G   +T++ 
Sbjct: 10  QHALLEQYMPLVRRHALALQVRLPASVELDDLIQAGMVGLLDALERFDATQGASFSTFAN 69

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             ++ AM + + RS   +      + + L   + +L+  L        +      IA  L
Sbjct: 70  QRVRGAMIDEL-RSRDWMPRSVRRSARALDQAVHKLEQTL-------GRAPDEREIANAL 121

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +S  E   +         L      S+              D       +   + + R 
Sbjct: 122 GMSVEEYHQLLLDANNGYLLGFDDVVSELGEPPGG-------DTAPATPHDALLQGDART 174

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L  ++  L  RE+ +       +  + L+ + +   VS  RV Q+ ++A  +++  +
Sbjct: 175 HLVAAIEHLPEREKLLLGLYY--QEELNLKEIGAVLGVSESRVCQLHSQAVARLRARL 230


>gi|149176711|ref|ZP_01855322.1| RNA polymerase sigma factor whiG [Planctomyces maris DSM 8797]
 gi|148844352|gb|EDL58704.1| RNA polymerase sigma factor whiG [Planctomyces maris DSM 8797]
          Length = 258

 Score = 98.0 bits (243), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 54/261 (20%), Positives = 108/261 (41%), Gaps = 21/261 (8%)

Query: 32  QEEYVLAKRYREHGDLSA-AHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLM 87
           +E   + K +++     A  + L+  ++ LV   A         G+ +++++S G  GLM
Sbjct: 7   EEIAEIWKVFKQDQSNQALRNMLIEQYVPLVRYNAERVWAKLPEGVDLNDLISAGVFGLM 66

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
            A+  FD ERG +  TY +  I+ AM + + R+   V     +   +L    +  +    
Sbjct: 67  DAINAFDLERGVKFETYCVPRIRGAMLDEL-RTMDWVPRLVRSKASKLEAARKAAEAEF- 124

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLV 205
                  +P     IA+K+ +S  E   +       G  SLN     +D      +  ++
Sbjct: 125 ------GRPPADEEIARKMQLSRKEFEKLKNEANAVGLVSLNKKWYETDSYKDVREVDIL 178

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            D  G++           +R+++      LN  ER I      +E  +T++ + S   +S
Sbjct: 179 EDAKGEDPTK-----SIQKRDLMRLVTKGLNRNERLIIILYYYEE--LTMKEIGSTLGLS 231

Query: 266 RERVRQIEARAFKKVQESIQK 286
             RV Q+ +    +++E + +
Sbjct: 232 ESRVSQMHSSIVNRLKEQLGR 252


>gi|119511138|ref|ZP_01630256.1| sigma factor SigF [Nodularia spumigena CCY9414]
 gi|119464233|gb|EAW45152.1| sigma factor SigF [Nodularia spumigena CCY9414]
          Length = 261

 Score = 98.0 bits (243), Expect = 1e-18,   Method: Composition-based stats.
 Identities = 46/218 (21%), Positives = 94/218 (43%), Gaps = 14/218 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFD 94
            L   Y ++  +   ++LV  H  LV KIA  +      P  ++   G  GL++A+++FD
Sbjct: 14  ELLHSYHQNPSIKLRNQLVQLHTGLVRKIAHKFSHQCHEPYEDLEQIGYFGLIRAIERFD 73

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P +G+  +++++ +I+  M  ++    SL+KI     +  L+ + ++++  L      + 
Sbjct: 74  PSQGYAFSSFAVPYIRGEMLHFLRDRSSLLKIPRRWQE--LYNDGQKVRKELAVSLGRSP 131

Query: 155 KPEQVVAIAKKLNVSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +      IA+KL VS  E     +  +     SL+A             + L        
Sbjct: 132 R---DAEIAQKLQVSVHEWQETKLAAQNRMPLSLDATAAHYVDCQITLGEALPCPRS--- 185

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
              I  +++   R  L  ++++L  + R   E   L+E
Sbjct: 186 ---IALQQQDEERQQLQGAINMLEDKPRMAVEMVFLKE 220


>gi|237731968|ref|ZP_04562449.1| flagellar biosynthesis sigma factor [Citrobacter sp. 30_2]
 gi|226907507|gb|EEH93425.1| flagellar biosynthesis sigma factor [Citrobacter sp. 30_2]
          Length = 239

 Score = 98.0 bits (243), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 100/240 (41%), Gaps = 17/240 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV ++D  +G    TY++
Sbjct: 13  KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVDRYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   + +L+  L        +      +A +L
Sbjct: 73  QRIRGAMLDEL-RSRDWVPRSVRRNAREVAQAMGQLEQEL-------GRNATETEVAARL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   E   M      D + + L +  +          +   + Q++  +++    N R 
Sbjct: 125 AIPVQEYRQMLL----DTNNSQLFSYDEWREEHGDSIELVTEEHQQENPLQQLLEGNLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 181 RVMDAIEALPEREKLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 238


>gi|291334306|gb|ADD93967.1| sigma factor FliA sigma 28 group flagellar [uncultured marine
           bacterium MedDCM-OCT-S09-C247]
          Length = 225

 Score = 98.0 bits (243), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 49/234 (20%), Positives = 101/234 (43%), Gaps = 22/234 (9%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYG---LPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
               +L+  +L +V KIA  Y G     + + +++  G +GL++A   + P+       Y
Sbjct: 10  DDKAQLINDNLDIVKKIAFFYVGRVGKVVEVDDLLQLGMVGLIEAAHNYTPQDDVSFVNY 69

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +   +K A+ +Y+ +S +L +      Q     +  R K  L+       +  +   IAK
Sbjct: 70  ARLRVKGAIVDYLRKSSNLCRGTIRRKQ-----DYERAKRKLEK---ELFRQPETHEIAK 121

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L V  S+++S     A  +       S ++ S  + D+L       E+ +   E     
Sbjct: 122 ELKVEVSDLLSWQHDFAASQH-----QSLEEASDAYGDFLFATDKSVEEKIFNGEL---- 172

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           +++L   +  LN ++  + +   ++E  + +  +     VS  RV QI++ A K
Sbjct: 173 KDILRTKLEDLNEQQLMVLQLYYVEE--LNVYEIGEILSVSTGRVSQIKSAAIK 224


>gi|32475302|ref|NP_868296.1| RNA polymerase sigma factor whiG [Rhodopirellula baltica SH 1]
 gi|32445843|emb|CAD78574.1| RNA polymerase sigma factor whiG [Rhodopirellula baltica SH 1]
 gi|327540927|gb|EGF27485.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Rhodopirellula baltica
           WH47]
          Length = 272

 Score = 98.0 bits (243), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 47/241 (19%), Positives = 101/241 (41%), Gaps = 22/241 (9%)

Query: 50  AHRLVTSHLRLVVK---IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            ++LV  +++LV             G+ + +++S G  GLM A+  +D ERG +  T+ +
Sbjct: 39  RNQLVERYMQLVRYNGERIWQRLPDGVELDDLISAGMFGLMDAIDAYDTERGVKFETFCV 98

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + +   + ++  +           +L    + +     +   V  ++  +
Sbjct: 99  PRIRGAMLDELRKMDWVPRLVRSKA--------SKLATATKTLEARFGRAPTVQELSAHM 150

Query: 167 NVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            +   EV  M       G  SLN     +D      +  ++ D  G++        R+ +
Sbjct: 151 EIDVKEVEKMQSEANAVGVVSLNKKWYETDSYKDVREIDILEDKKGEDPT------RRVQ 204

Query: 225 RNMLTRSM-SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +N L R +   LN  ER I      +E  +T++ + +  ++S  RV Q+      ++Q+ 
Sbjct: 205 KNDLMRLVTKGLNRNERLIIILYYYEE--LTMKEIGATLDLSESRVSQMHTAIVNRLQQQ 262

Query: 284 I 284
           +
Sbjct: 263 L 263


>gi|291525957|emb|CBK91544.1| RNA polymerase sigma factor, sigma-70 family [Eubacterium rectale
           DSM 17629]
          Length = 224

 Score = 98.0 bits (243), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 39/233 (16%), Positives = 101/233 (43%), Gaps = 17/233 (7%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           RLVT ++ L+  +   +R  G+   ++   G +GL +A ++FD  +GF  +TY++  I  
Sbjct: 8   RLVTENINLIYLVMKRFRNRGVDREDLFQIGAVGLTKAAQRFDESKGFAFSTYAVPLIIG 67

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            +Q ++     +V I      +++  + R++    +    N      +  +     +S+ 
Sbjct: 68  EIQRFLRDDG-MVHIS-----RKIRDDARKIAIIREKYRMNENSEISLEKMENISGMSKQ 121

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           ++I          ++ A  N+S   +    D+L      +      + ++      + ++
Sbjct: 122 DII---------IAMEADKNASSIENESVLDYLDNKMSAEASDKPSETDKVINHIAMQQA 172

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + L+  ERR+   R +Q+   T + ++     ++  + ++E     K++ ++
Sbjct: 173 FNSLDDSERRLIMLRYMQD--KTQKQVAEMLGRNQVAISRMEKNTLAKLRRAM 223


>gi|224005495|ref|XP_002291708.1| plastid RNA polymerase sigma factor [Thalassiosira pseudonana
           CCMP1335]
 gi|220972227|gb|EED90559.1| plastid RNA polymerase sigma factor [Thalassiosira pseudonana
           CCMP1335]
          Length = 541

 Score = 98.0 bits (243), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 64/291 (21%), Positives = 104/291 (35%), Gaps = 85/291 (29%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGL----------------------------------- 73
           A   L+  +++LV+ IA G+                                        
Sbjct: 251 ARETLMRKNVKLVMSIAKGWMKNSFTTENANLGGVDGAGGGSGSRNSGNKTSKKFLSQMY 310

Query: 74  -------PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
                   + E V EG +GL +AV K+DPERG R +TY+  WI                 
Sbjct: 311 EGSWDRPSLDEAVQEGMLGLARAVDKYDPERGLRFSTYATHWIT---------------- 354

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
            + A  K++      +K HLQ  T     P +  +IAK+L +SE  + +         S+
Sbjct: 355 -SYAAYKKI------IKDHLQLGT----TPPEQKSIAKELGISEQRLTTAIRATGSLVSV 403

Query: 187 NALINS-----------SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV- 234
           +A + S               S+  +  ++      E    ++ E    R  L  +M+  
Sbjct: 404 DAPVISPGSGSYKGSAAGGDGSNSQELLILDTLRCAEPKPEDQVEISFLRQCLENAMATE 463

Query: 235 LNPRERRIFEARRLQE--NPVTLENLSSEFE--VSRERVRQIEARAFKKVQ 281
           L P ER +   R   +     T+  +       V+   VR  E RAFKK++
Sbjct: 464 LTPYERDVLRLRLGLDSGEGKTVREVVEICGGSVTMSDVRSAERRAFKKLR 514


>gi|304399205|ref|ZP_07381072.1| sigma-70 region 3 domain protein [Pantoea sp. aB]
 gi|304353259|gb|EFM17639.1| sigma-70 region 3 domain protein [Pantoea sp. aB]
          Length = 172

 Score = 98.0 bits (243), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 32/172 (18%), Positives = 69/172 (40%), Gaps = 12/172 (6%)

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           +     +++      K L   LR  +     ++           IA++L+    +V  M 
Sbjct: 1   MNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRML 55

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                  S++  +     +     D L  + D   +   +  +  + +  + + +  LN 
Sbjct: 56  RLNERITSVDTPL--GGDSEKALLDILADEKDNGPE---DTTQDDDMKQSIVKWLFELNA 110

Query: 238 RERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++R +   R   L     TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 111 KQREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQAQ 162


>gi|153803628|ref|ZP_01958214.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae MZO-3]
 gi|124120837|gb|EAY39580.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae MZO-3]
          Length = 193

 Score = 97.6 bits (242), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 41/204 (20%), Positives = 83/204 (40%), Gaps = 16/204 (7%)

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            +GL++A K +D  +G    TY+   I+ AM + I R    V      + + +   +  L
Sbjct: 1   MVGLLEAQKNYDGSKGASFETYAGIRIRGAMLDDIRR-GDWVPRSVHKHNREISQAIAVL 59

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
           +G L        +      +AK LN+S  +  S+      D + + ++   D   S   D
Sbjct: 60  EGELN-------RDPTDAEVAKFLNMSLEQYHSVLM----DINCSRIVGIEDLGVS--DD 106

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
            +    +G++         ++ R  L  S+  L  RE  +       +  + L+ +    
Sbjct: 107 AISPFEEGEDNSPFHGVAEESFRKALVESIKSLPEREALVLSLYY--DEELNLKEIGEVL 164

Query: 263 EVSRERVRQIEARAFKKVQESIQK 286
            VS  RV QI +++ ++++  +  
Sbjct: 165 GVSESRVSQILSQSMQRLRTKLSS 188


>gi|332971253|gb|EGK10216.1| hypothetical protein HMPREF9374_2566 [Desmospora sp. 8437]
          Length = 188

 Score = 97.6 bits (242), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 50/239 (20%), Positives = 89/239 (37%), Gaps = 64/239 (26%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE-RGFRLATYS 105
                 LV  H RLV  +A  +R   +   ++V  G IGL++AV +++P  +  + +T++
Sbjct: 11  RDLREELVEQHQRLVYFVANQFRQSKMEWDDLVQIGFIGLIKAVDRYNPGIKKVKFSTFA 70

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
             +I+  +                         LR LK H  A                 
Sbjct: 71  FHYIRGEI----------------------LHELRALKRHNPA----------------- 91

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           + VS   V+                   + +  +  D L  D D       E E   + R
Sbjct: 92  MEVSVENVVE---------------GGGEDDEIRLMDTLGTDPD-------EVETTVSNR 129

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             L  SM+ L  +ER +   R  ++   T   ++  F+V  +R+R IE +A +K++  +
Sbjct: 130 VALEESMADLTDQEREVISFRFGKQ--WTQGEIAELFDVPEKRIRVIEQKAIRKLRRQM 186


>gi|150390238|ref|YP_001320287.1| FliA/WhiG family RNA polymerase sigma factor [Alkaliphilus
           metalliredigens QYMF]
 gi|149950100|gb|ABR48628.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           metalliredigens QYMF]
          Length = 149

 Score = 97.6 bits (242), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 38/139 (27%), Positives = 63/139 (45%), Gaps = 2/139 (1%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           + +I    +    YI      P  L  +EE +  +RY E GD  A + LV  +LRLV  +
Sbjct: 9   LPMIAKPLLFFVSYISSNTSFPQPLSPEEEAMYLERY-EQGDEEARNILVERNLRLVAHV 67

Query: 65  AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
              Y        +++S G IGL++A+  F+  +G RLATY+   I+ AM          +
Sbjct: 68  VKKYSNVNRDADDLISIGTIGLIKAITTFNRGKGTRLATYAARCIEKAMLPKCYMFNRCI 127

Query: 125 KIGTTANQKRLFFNLRRLK 143
              + ++       L +L+
Sbjct: 128 SRLSPSHTIFSIIPLIKLR 146


>gi|251789202|ref|YP_003003923.1| flagellar biosynthesis sigma factor [Dickeya zeae Ech1591]
 gi|247537823|gb|ACT06444.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Dickeya zeae Ech1591]
          Length = 240

 Score = 97.6 bits (242), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 40/242 (16%), Positives = 96/242 (39%), Gaps = 17/242 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KNSLWKRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLSAVERYDSLQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +               + +  N R +   +Q    +  +      +A+ L
Sbjct: 73  QRIRGAMLDELR--------SRDWAPRSVRRNAREVAQAMQQAEQSLGRAPSEQEVAQTL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           N+S  E   +      D + + L +  +                ++   + +    + R 
Sbjct: 125 NISLEEYRQILL----DTNNSQLFSYDEWREEHGDSAEALLEGNEDANPLNQLMDVSLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  +  
Sbjct: 181 RVMDAIENLPEREKMVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRAKLMS 238

Query: 287 QV 288
            V
Sbjct: 239 DV 240


>gi|5327289|emb|CAB46360.1| FliA, sigma 28 [Xenorhabdus nematophila]
 gi|139522465|gb|ABO77651.1| FliA [Xenorhabdus nematophila]
          Length = 230

 Score = 97.6 bits (242), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 43/238 (18%), Positives = 100/238 (42%), Gaps = 17/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   ++ LV   A+  +      + + +++  G IGL+ AV++FD  +G    TY++
Sbjct: 3   KNSLWKRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERFDSMQGTAFTTYAV 62

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS          N + +   +R+L+  L        +P     +AK+L
Sbjct: 63  QRIRGAMLDEL-RSRDWAPRSVRRNAREVTQTIRKLEQEL-------GRPASEQEVAKEL 114

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++  E   +      D + + L +  + +    +       +  E   +++    + R 
Sbjct: 115 KINLIEYRQILL----DTNNSQLFSYDEWHEIHGESCEPVIEEEHETNPLQQLLEGDLRQ 170

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +   +  L  RE+ +       +  + L+ + +   V   RV Q+ ++A K+++  +
Sbjct: 171 RVINIIESLPEREKMVLTLYY--QEELNLKEIGAVLNVGESRVSQLHSQAIKRLRARL 226


>gi|283832678|ref|ZP_06352419.1| flagellar biosynthesis sigma factor FliA [Citrobacter youngae ATCC
           29220]
 gi|291072353|gb|EFE10462.1| flagellar biosynthesis sigma factor FliA [Citrobacter youngae ATCC
           29220]
          Length = 229

 Score = 97.6 bits (242), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 101/240 (42%), Gaps = 17/240 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV ++D  +G    TY++
Sbjct: 3   KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVDRYDALQGTAFTTYAV 62

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   + +L+  L        +      +A++L
Sbjct: 63  QRIRGAMLDEL-RSRDWVPRSVRRNAREVAQAMGQLEQEL-------GRNATETEVAERL 114

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   E   M      D + + L +  +          +   + Q++  +++    N R 
Sbjct: 115 AIPVQEYRQMLL----DTNNSQLFSYDEWREEHGDSIELVTEEHQQENPLQQLLEGNLRQ 170

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 171 RVMDAIEALPEREKLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 228


>gi|256376481|ref|YP_003100141.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Actinosynnema mirum DSM 43827]
 gi|255920784|gb|ACU36295.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Actinosynnema mirum DSM 43827]
          Length = 294

 Score = 97.6 bits (242), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 49/256 (19%), Positives = 96/256 (37%), Gaps = 27/256 (10%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           A  L+  HL LV  +           +   E++S GN+ L+ A K FD  RG   A +++
Sbjct: 20  AEELIVKHLPLVGHLVREVLARVPVHVRREELMSAGNLALVAAAKSFDDSRGAPFAAFAV 79

Query: 107 WWIKAAMQEYILRS---WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
             ++ A+ + +         V++             R++          + +      IA
Sbjct: 80  VRVRGALMDELRGQDWASRSVRV-----------KARKMNAVQDEFVSKHGRTPTTAEIA 128

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
             + V   EV      +  D   +AL++         ++ +     G E+ L+ +E    
Sbjct: 129 GIMEVETREV----TAVQDDVQRSALLSLQGFTGGVLEEVVPERQPGPEETLLGRE---- 180

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           R   L  ++  L  R R +      +E P+    ++ E  V   RV Q+ A A   +++ 
Sbjct: 181 RIGYLHSAIDALPDRLRTVVRGYFFEERPM--AEIAEELGVHESRVSQLRAEAIALLRDG 238

Query: 284 IQKQVELSSSPPLLQK 299
           +  Q++    P   + 
Sbjct: 239 LNSQLDPERLPEPARP 254


>gi|238920292|ref|YP_002933807.1| flagellar biosynthesis sigma factor [Edwardsiella ictaluri 93-146]
 gi|238869861|gb|ACR69572.1| RNA polymerase sigma factor for flagellar operon [Edwardsiella
           ictaluri 93-146]
          Length = 240

 Score = 97.6 bits (242), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 43/241 (17%), Positives = 99/241 (41%), Gaps = 17/241 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   +  LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KNTLWQRYAPLVRHEALRLQVRLPASVELDDLLQAGGIGLLHAVERYDAMQGTAFTTYAI 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   ++R +  L        +      IA+++
Sbjct: 73  QRIRGAMLDEL-RSRDWVPRSVRRNARGVSAAMQRAEQRL-------GRVPGDSEIAQEM 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +S +E   +      D + + L +  +                +E   + +    + R 
Sbjct: 125 GISLAEYQQILL----DTNTSQLFSYDEWREEHGDSAEPVVEQSEESNPLHQLLESDLRG 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  +  
Sbjct: 181 RVIAAIEALPEREKLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRTRLLS 238

Query: 287 Q 287
           Q
Sbjct: 239 Q 239


>gi|259908158|ref|YP_002648514.1| flagellar biosynthesis sigma factor [Erwinia pyrifoliae Ep1/96]
 gi|224963780|emb|CAX55281.1| RNA polymerase sigma factor for flagellar operon [Erwinia
           pyrifoliae Ep1/96]
 gi|283478078|emb|CAY73994.1| RNA polymerase sigma factor FliA/RpoD [Erwinia pyrifoliae DSM
           12163]
 gi|310767931|gb|ADP12881.1| flagellar biosynthesis sigma factor [Erwinia sp. Ejp617]
          Length = 240

 Score = 97.6 bits (242), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 39/238 (16%), Positives = 97/238 (40%), Gaps = 17/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KHSLWQRYIPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDAMQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +               + +  N R + G +  +     +      +A +L
Sbjct: 73  QRIRGAMLDELR--------SRDWAPRSVRRNAREVAGAMHQVEQALGRTATEQEVAAQL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +V   E   +      D + + L +  +          +     +++  + +    + R+
Sbjct: 125 DVPLEEYRQILL----DTNNSQLFSFDEYREEHGDSAELVTEGHEQENPLHQLLEGDLRD 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  +
Sbjct: 181 RVIEAIDGLPEREKMVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRARL 236


>gi|163856407|ref|YP_001630705.1| flagellar-specific RNA polymerase sigma factor [Bordetella petrii
           DSM 12804]
 gi|163260135|emb|CAP42436.1| flagellar-specific RNA polymerase sigma factor [Bordetella petrii]
          Length = 246

 Score = 97.6 bits (242), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 44/243 (18%), Positives = 98/243 (40%), Gaps = 17/243 (6%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           A   LV  +  LV K+A+         + + +++  G IGL+ A +++      +  TY+
Sbjct: 4   ADDSLVR-YAPLVRKLALQLLARLPASVQLDDLIQAGMIGLLDAARRYQETPDAQFETYA 62

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
              I+ AM + +     L         + +    +R++  +Q      ++P     IA +
Sbjct: 63  TARIRGAMLDELRSQDWL--------PRSVRSKGKRIEAAIQRKEHELMRPPSESEIADE 114

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           L +   E  +M     G + L+     S+    +    +  D  G     ++     + R
Sbjct: 115 LELPLDEYQAMLNDARGIQILHYDDIGSNDPDERGWRDVPADSGGD---PLDALLTGDLR 171

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             L  ++  L  RE+ +       E  + L+ + +  EV+  RV Q+ ++A  +++  ++
Sbjct: 172 RALVNAIETLPEREKLVLSLCY--EQGLNLKEIGAVLEVTEARVCQLRSQATARIRARLK 229

Query: 286 KQV 288
           +  
Sbjct: 230 EDA 232


>gi|257469127|ref|ZP_05633221.1| RNA polymerase sigma factor RpoD [Fusobacterium ulcerans ATCC
           49185]
          Length = 157

 Score = 97.6 bits (242), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 33/153 (21%), Positives = 66/153 (43%), Gaps = 9/153 (5%)

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L ++  ++ +   +      V  IA +LN+   +V  +        SL+  I     +  
Sbjct: 8   LNKVNRYVMSRLKDEGNYPSVEEIAAELNIEADKVQDIIMDFQDPMSLSTQI----GDDI 63

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLE 256
             +D L    D   +   E+   +  R  +   ++ L  RE+ I + R   +     TLE
Sbjct: 64  YLEDTLAQQEDFSME---EEIFNEMGRKQVRDMVNQLEEREKEILKLRYGLDGYEIHTLE 120

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
            + +   ++RERVRQIE +  +K++    K+++
Sbjct: 121 EIGNTLNITRERVRQIEKKTLQKLRSKYTKELK 153


>gi|51246530|ref|YP_066414.1| RNA polymerase sigma factor (FliA) [Desulfotalea psychrophila
           LSv54]
 gi|50877567|emb|CAG37407.1| related to RNA polymerase sigma factor (FliA) [Desulfotalea
           psychrophila LSv54]
          Length = 245

 Score = 97.2 bits (241), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 43/243 (17%), Positives = 103/243 (42%), Gaps = 18/243 (7%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           ++LV  HL LV  +               ++ S G  GL  A KKFD  +     T++ +
Sbjct: 15  NQLVDDHLYLVDILVSRMVSQVPSFMSRDDMRSAGMFGLFDASKKFDASKNILFKTFAEY 74

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+ A+ + + +     +         L     ++   + A+     +  +   IA+ LN
Sbjct: 75  RIRGAIFDEMRKLDWFSR--------SLRDKHNKIGRAILALELKLGRDPEEFEIAQSLN 126

Query: 168 VSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           ++     ++  +++  G  SLN ++++S +  S     +    +      IE++E   + 
Sbjct: 127 MNLDAYHNLLGQVSHLGCVSLNEVLDNSQEGRSFLDSLVDKRKNNTPTAFIEQQELNIK- 185

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             +   +  L+ +E+ +      +E  ++ + ++    VS  R+ Q+ +++  K++  +Q
Sbjct: 186 --IAEILDQLSEKEKLVISLYYYEE--LSQKEIAEVIGVSEGRISQLHSQSLIKLKLKMQ 241

Query: 286 KQV 288
            Q+
Sbjct: 242 NQL 244


>gi|238758082|ref|ZP_04619262.1| RNA polymerase sigma factor for flagellar operon [Yersinia aldovae
           ATCC 35236]
 gi|238703620|gb|EEP96157.1| RNA polymerase sigma factor for flagellar operon [Yersinia aldovae
           ATCC 35236]
          Length = 240

 Score = 97.2 bits (241), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 39/238 (16%), Positives = 97/238 (40%), Gaps = 17/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KNSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +               + +  N R +   +Q +     +P     +A+ L
Sbjct: 73  QRIRGAMLDELR--------SRDWAPRSVRRNAREVATAMQKVEQRVGRPATEQEVAQTL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++  SE   +      D + + L +  +      +         ++   ++     N R 
Sbjct: 125 DIELSEYRQILL----DTNNSQLFSYDEWREEHGESVEPLLEGHEDANPLQHLLEGNLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  ++  L  RE+ +       +  + L+ + +  +V   RV Q+ ++A K+++  +
Sbjct: 181 RVIDAIEALPDREKMVLTLYY--QEELNLKEIGAVLDVGESRVSQLHSQAIKRLRARL 236


>gi|238784716|ref|ZP_04628720.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           bercovieri ATCC 43970]
 gi|238714395|gb|EEQ06403.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           bercovieri ATCC 43970]
          Length = 240

 Score = 97.2 bits (241), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 40/238 (16%), Positives = 97/238 (40%), Gaps = 17/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KNSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +               + +  N R +   +Q +     +P     +AK L
Sbjct: 73  QRIRGAMLDELR--------SRDWAPRSVRRNAREVASAMQQVEQRVGRPATEQEVAKIL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++  +E   +      D + + L +  +      +         ++   ++     N R 
Sbjct: 125 DIDLAEYRQILL----DTNNSQLFSYDEWREEHGESVEPLLEGHEDANPLQHLLEGNLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  +
Sbjct: 181 RVIEAIEALPEREKMVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRARL 236


>gi|312140062|ref|YP_004007398.1| sigma-70 factor [Rhodococcus equi 103S]
 gi|311889401|emb|CBH48717.1| sigma-70 factor [Rhodococcus equi 103S]
          Length = 289

 Score = 97.2 bits (241), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 41/234 (17%), Positives = 97/234 (41%), Gaps = 20/234 (8%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            RL  + L +  ++A  YR  G+P +E+     + L+ A ++FDP RG     Y++  ++
Sbjct: 65  DRLCVAALPMAYRVAGRYRNRGVPTAELRQVAALALVGAARRFDPSRGTDFIPYAVTSVR 124

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
             +++Y         +     +  L      ++  +++++    +  ++  +A  L +  
Sbjct: 125 GEIRKYFRDFTWSTHVPRRLQESHLA-----VRNRMESLSTELGRTVRLDEVAHSLGMPV 179

Query: 171 SEVISMNC--RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E         L   ESL+A     D +  +       D D           R   R++L
Sbjct: 180 EEAEEAERVGELYSCESLDAT--PVDGSVPRLHTTGDVDAD---------LSRVEHRHLL 228

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            R M+ L+ R+R +   R    + ++   ++ +  +S+  V ++  ++ + ++ 
Sbjct: 229 RRLMATLDERQRTLLWLRYF--HQMSQSEIAEQVGLSQMHVSRLLRQSLEHLRR 280


>gi|261342188|ref|ZP_05970046.1| RNA polymerase sigma factor [Enterobacter cancerogenus ATCC 35316]
 gi|288315521|gb|EFC54459.1| RNA polymerase sigma factor [Enterobacter cancerogenus ATCC 35316]
          Length = 172

 Score = 97.2 bits (241), Expect = 2e-18,   Method: Composition-based stats.
 Identities = 32/172 (18%), Positives = 69/172 (40%), Gaps = 12/172 (6%)

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           +     +++      K L   LR  +     ++           IA++L+    +V  M 
Sbjct: 1   MNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRML 55

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                  S++  +     +     D L  + D   +   +  +  + +  + + +  LN 
Sbjct: 56  RLNERITSVDTPL--GGDSEKALLDILADEKDNGPE---DTTQDDDMKQSIVKWLFELNA 110

Query: 238 RERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++R +   R   L     TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 111 KQREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQGQ 162


>gi|318066981|emb|CBY89105.1| RNA polymerase sigma70 factor [Halotalea alkalilenta]
          Length = 370

 Score = 97.2 bits (241), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 34/88 (38%), Positives = 51/88 (57%), Gaps = 2/88 (2%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L   E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 283 LTVAELKEVNRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 342

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQ 114
           M+AV KF+  RG++ +TY+ WWI+ A+ 
Sbjct: 343 MKAVDKFEYRRGYKFSTYATWWIRQAIT 370


>gi|269796407|ref|YP_003315862.1| RNA polymerase sigma-28 subunit SigD/FliA/WhiG [Sanguibacter
           keddieii DSM 10542]
 gi|269098592|gb|ACZ23028.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Sanguibacter
           keddieii DSM 10542]
          Length = 300

 Score = 97.2 bits (241), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 56/253 (22%), Positives = 95/253 (37%), Gaps = 23/253 (9%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +RLVT +L LV                  ++ S G + L+QA + +D   G     Y+ 
Sbjct: 5   QNRLVTENLPLVGYHVSEMLMRVPSHVSRDDLASAGALALVQAARAYDATTGVPFNRYAA 64

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             IK AM + + RS   V  G            R+L      +T +  +      IA  L
Sbjct: 65  IRIKGAMVDEL-RSMDWVSRGARQRA-------RKLTTVADELTADLGRAPTREEIAHAL 116

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            V  SEV +     A        + S +       + L     G E+ +I  E       
Sbjct: 117 GVDVSEVDTAREAAATR------VLSLEGYDGALAEVLPAREVGPEESVILDERLT---- 166

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L  ++S L  R R + E     +  VT  +++ +  V++ RV Q+ A A   +++ +  
Sbjct: 167 YLHAAVSTLPERLRTVVEQVFFHDRTVT--DIAKDMGVTQSRVSQLRAEAMVLLRDGLNT 224

Query: 287 QVELSSSPPLLQK 299
            ++ +  P   Q 
Sbjct: 225 HLDPAQVPAPAQP 237


>gi|219115846|ref|XP_002178718.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217409485|gb|EEC49416.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 217

 Score = 97.2 bits (241), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 46/214 (21%), Positives = 90/214 (42%), Gaps = 19/214 (8%)

Query: 49  AAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           A   L+ S++RLVV IA  + +       E V EG +GL +A  ++DPERG R ATY+ +
Sbjct: 10  ARDTLIASNVRLVVSIAKKWAKNAHKAARETVQEGILGLAKAADRYDPERGLRFATYATY 69

Query: 108 WIKAAMQEYILRSWSL--VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
           W+  ++  +  ++ S   +++    +  +      + K  ++   D       +  +A++
Sbjct: 70  WVTNSV-RFCFQTASTGCLRVPVGFHDTKT-----KFKRLVKEYYDEFGDAPGIDDLAEQ 123

Query: 166 LNVSESEVISMNCRLAGDESLNALINSS-------DKNSSQWQDWLVYDHDGQEQV--LI 216
           + ++   +  +        S++A + +          N     + L+ D    EQ     
Sbjct: 124 MGLTRPRLEVILRSTRPLVSIDAPLRTGAVTQAGKAGNDVSQTNLLLADLLTDEQALPPE 183

Query: 217 EKEERKNRRNMLTRSMSV-LNPRERRIFEARRLQ 249
           +  E    R  L  +M+  L P ER +   R   
Sbjct: 184 DLVELSFLRQNLENAMATELAPHERDVLRLRLGL 217


>gi|332975582|gb|EGK12472.1| DNA-directed RNA polymerase sigma subunit SigK [Desmospora sp.
           8437]
          Length = 160

 Score = 97.2 bits (241), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 28/92 (30%), Positives = 50/92 (54%), Gaps = 2/92 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ EK+EE  L  +    GD  A + L+  +LRLV  I   +        +++S G IGL
Sbjct: 30  PLNEKEEEKYL--KQMAGGDKEARNILIEHNLRLVAHIVKKFENTSEDNEDLISIGTIGL 87

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           ++A++ + P +G +LATY+   I+  +  ++ 
Sbjct: 88  IKAIESYQPNKGTKLATYAARCIENEILMHLR 119


>gi|258404724|ref|YP_003197466.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfohalobium
           retbaense DSM 5692]
 gi|257796951|gb|ACV67888.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfohalobium
           retbaense DSM 5692]
          Length = 241

 Score = 97.2 bits (241), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 46/249 (18%), Positives = 100/249 (40%), Gaps = 16/249 (6%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKKFDPER 97
           Y ++G   A  +L+  H+ +V                  E+ S    GL+ A  +FDP +
Sbjct: 5   YTQNG-EDARTQLIREHMNMVSYWVERMVTQVPAFMSRDEIRSAAMEGLINAANRFDPNQ 63

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G    T++   I+ A+ + + R             +RL   +R L+  L+   + N    
Sbjct: 64  GVLFKTFAEHRIRGAIFDEVRR-LDWFSRSMRDKHQRLAETIRELEISLERAPNEN---- 118

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
             VA A  ++++    +       G  SL  +++ SD   S        D    E+ + +
Sbjct: 119 -EVAAAMDMDLTGYHRMLGEVSHLGCMSLQEVLSDSDTGQSFLDVLEDTDGMPPEEAVEQ 177

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
            E  +    ML      L+ +E+++     L    ++ + ++    ++  R+ Q+ ++A 
Sbjct: 178 AELTREVAGMLHE----LSEKEQQVIAL--LYHEGLSQKEIADVLSLTEGRISQLHSQAL 231

Query: 278 KKVQESIQK 286
            K++  +++
Sbjct: 232 AKLRVKMER 240


>gi|291617817|ref|YP_003520559.1| FliA [Pantoea ananatis LMG 20103]
 gi|291152847|gb|ADD77431.1| FliA [Pantoea ananatis LMG 20103]
          Length = 240

 Score = 97.2 bits (241), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 41/238 (17%), Positives = 97/238 (40%), Gaps = 17/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +               + +  N R + G +  +     +      +A++L
Sbjct: 73  QRIRGAMLDELR--------SRDWAPRSVRRNAREVAGAMHQVEQMLGRAASEQEVAQQL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           NVS  E   +      D + + L +  +          +     +E   + +    + R 
Sbjct: 125 NVSIEEYRQILL----DTNNSQLFSYDEYREEHGDSAELVTEGHEEANPLHQLMEGSLRE 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  ++  L  RE+ +       +  + L+ + +  +V   RV Q+ ++A K+++  +
Sbjct: 181 RVIEAIEALPEREKMVLTLYY--QEELNLKEIGAVLDVGESRVSQLHSQAIKRLRARL 236


>gi|157363480|ref|YP_001470247.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermotoga lettingae
           TMO]
 gi|157314084|gb|ABV33183.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermotoga lettingae
           TMO]
          Length = 236

 Score = 97.2 bits (241), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 47/237 (19%), Positives = 106/237 (44%), Gaps = 19/237 (8%)

Query: 51  HRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
             ++   L  V +IAM         + + +++ EG + L+ A++++DP++G  + ++ + 
Sbjct: 7   EEIIKEMLPSVKRIAMDLLHTLPKNVEVDDLIQEGVLALLSAIRRYDPKKGVSMYSFVVK 66

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            IK AM +Y+ +   +         + L  N++ ++  +  + ++  K   +  IA    
Sbjct: 67  RIKGAMYDYLRKIDWM--------PRNLRKNVKEVEKAIHELENHLNKHPSIEEIALHTG 118

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S +EV     + A DE++   +   D+   +  D    D    +    E   R+     
Sbjct: 119 LSTNEV-----KRALDETVRKQLLRLDEFIYEGLDSF-SDIIKADDEPSENAFREIILEK 172

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +  ++  L+ RE+ +   R   E  ++L+ + +   VS  RV QI + +  K++  I
Sbjct: 173 VAEAIRTLSKREQLVLSLRF--EQDLSLKEIGTVIGVSESRVSQILSSSLIKIKRYI 227


>gi|33322911|gb|AAQ07192.1|AF496500_1 RNA polymerase sigma factor [Lactobacillus delbrueckii subsp.
           lactis]
          Length = 141

 Score = 97.2 bits (241), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 38/131 (29%), Positives = 63/131 (48%), Gaps = 9/131 (6%)

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
           PE++ A   +      E+I++  +    +SL+  +   ++  SQ  D L    D +    
Sbjct: 6   PEELAAEMNEPLQKXQEIITV-AKNQETDSLDKPV--GEEGDSQLGDLL---EDNKATNP 59

Query: 216 IEKEERKNRRNMLTRSMSV-LNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
            E    +  ++ L+  M   L  RE ++ + R   EN  P TLE +     V+RERVRQI
Sbjct: 60  EEYTAFEMLKDQLSSMMGEFLTDREAKVLKLRFGLENDEPHTLEEVGRSLGVTRERVRQI 119

Query: 273 EARAFKKVQES 283
           EA+A KK++  
Sbjct: 120 EAKAVKKLKHH 130


>gi|116626504|ref|YP_828660.1| FliA/WhiG family RNA polymerase sigma factor [Candidatus Solibacter
           usitatus Ellin6076]
 gi|116229666|gb|ABJ88375.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Candidatus
           Solibacter usitatus Ellin6076]
          Length = 251

 Score = 96.8 bits (240), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 46/246 (18%), Positives = 94/246 (38%), Gaps = 21/246 (8%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
                RL+  HL  V  IA   +      + + ++VS G +GL+ A+  FD     +L T
Sbjct: 12  EDERERLILEHLPQVRLIARRIQERLPESISLDDLVSTGVLGLISAIDNFDASHNVKLKT 71

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+ + I+ A+ + +         G     ++     ++++  +               IA
Sbjct: 72  YAEYKIRGAILDSLR--------GLDWAPRQKRRKSKQIEAAIAVAEQRLHASPGEEEIA 123

Query: 164 KKLNVSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
            +L ++  E       + G    SL          + Q +D L Y  DG + +     ER
Sbjct: 124 GELGITVDEYHEWLVEIRGLNVASLE------YAGNEQGRDLLHYIPDGSDNLPSTLLER 177

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                +L  S+  +   ER +          +TL  ++    +   R+ Q++++A  +++
Sbjct: 178 SELERLLASSIDGIPAIERTVLSLYF--HEELTLREIAQVVNLHESRISQLKSQAILRLR 235

Query: 282 ESIQKQ 287
             +  Q
Sbjct: 236 GQMASQ 241


>gi|330815163|ref|YP_004358868.1| FliA [Burkholderia gladioli BSR3]
 gi|327367556|gb|AEA58912.1| FliA [Burkholderia gladioli BSR3]
          Length = 254

 Score = 96.8 bits (240), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 39/215 (18%), Positives = 86/215 (40%), Gaps = 14/215 (6%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++  G IGL+ A  ++  ++G +  TY+   I+ AM + +  +  L         +
Sbjct: 48  DLDDLIQAGMIGLLDAASRYKEDQGAQFETYATQRIRGAMLDELRSNDWL--------PR 99

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            L    R ++  +  +     +      IA  L +   +  +M   L G + +       
Sbjct: 100 SLRKTSREVEQAVHRVEQQLGRSANESEIASHLEMPLPDYQAMLQDLHGSQLIYYEDFDR 159

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
             +   + D    DH      L++     + R  L  ++  L  RE+ +       E  +
Sbjct: 160 SADDEPFLDRYRVDHSDPLSALLDD----HLRAALVEAIERLPEREKLLMSLYY--ERGL 213

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            L  + +  EVS  RV Q+ ++A  +++  +++Q 
Sbjct: 214 NLREIGAVLEVSESRVCQLHSQAVARLRARLREQA 248


>gi|294636855|ref|ZP_06715188.1| flagellar biosynthesis sigma factor FliA [Edwardsiella tarda ATCC
           23685]
 gi|291089930|gb|EFE22491.1| flagellar biosynthesis sigma factor FliA [Edwardsiella tarda ATCC
           23685]
          Length = 240

 Score = 96.8 bits (240), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 41/241 (17%), Positives = 99/241 (41%), Gaps = 17/241 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   +  LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KNTLWQRYAPLVRHEALRLQVRLPASVELDDLLQAGGIGLLHAVERYDAMQGTAFTTYAI 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   ++R +  L        +      IA+++
Sbjct: 73  QRIRGAMLDEL-RSRDWVPRSVRRNARGVSAAMQRAEQRL-------GRVPSDGEIAQEM 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +  +E   +      D + + L +  +       +      + +    + +    + R 
Sbjct: 125 GIPLAEYQQILL----DTNSSQLFSYDEWREEHGDNAEPVWGEEESANPLRQLLESDLRG 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  +  
Sbjct: 181 RVIAAIEALPEREKLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRSRLLS 238

Query: 287 Q 287
           Q
Sbjct: 239 Q 239


>gi|282599758|ref|ZP_05971750.2| motility sigma factor FliA [Providencia rustigianii DSM 4541]
 gi|282567697|gb|EFB73232.1| motility sigma factor FliA [Providencia rustigianii DSM 4541]
          Length = 242

 Score = 96.8 bits (240), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 40/240 (16%), Positives = 94/240 (39%), Gaps = 17/240 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   +  L+   A+  +      + I +++  G IGL+ A+++FD   G   ATY++
Sbjct: 17  KNSLWERYYPLIRHEALKLQVRLPASVDIDDLIQAGGIGLLHALERFDASLGASFATYAV 76

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ +M + + RS   V               R +   +  +     +      IA+ L
Sbjct: 77  QRIRGSMLDEL-RSRDWVPRSVR-------RQAREMTKAIGELEQKLGRSASEPEIAQSL 128

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++  SE   +      D + + L +  + +    +       +      +      + R+
Sbjct: 129 DIELSEYRQVLL----DTNNSQLFSYDEWHEIHGESCEPSMDEDDGGNPLSLLMESSLRD 184

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE  +       +  + L+ + +  EV   RV Q+ ++A K+++  ++ 
Sbjct: 185 QIMGAIEQLPEREMLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRSKLKS 242


>gi|313672893|ref|YP_004051004.1| RNA polymerase, sigma 28 subunit, sigd/flia/whig [Calditerrivibrio
           nitroreducens DSM 19672]
 gi|312939649|gb|ADR18841.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Calditerrivibrio
           nitroreducens DSM 19672]
          Length = 242

 Score = 96.8 bits (240), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 41/248 (16%), Positives = 97/248 (39%), Gaps = 17/248 (6%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPER 97
           Y+   D      +V   L  +    +         +   E+ S   +GL+++++KFD  R
Sbjct: 6   YQGSLDRIEQEEIVKEFLPKIKVWVLRVSNRLPANVDNDELYSAACMGLVESLQKFDKGR 65

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
                +Y+   IK A+ + + +             + +   L++ +  LQ +T    +  
Sbjct: 66  SVDFYSYAERRIKGAILDALRQ--------MDFLPRNVRTKLKQFEEKLQELTVKLGRKP 117

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               I +  N+S+ +V +    +   +  +   +  +       D +    +G E   I+
Sbjct: 118 NTDEIVEYTNLSQEDVFNFLNLIETGQLTSLDTSLDEDGDISLLDTIKSFVEGPEDSAIK 177

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
           ++        L   +  L  +E+ +      +E  +T++ +    ++S  RV QI + A 
Sbjct: 178 EQLIS----KLGEIIDSLPDKEKLVITLYYYEE--LTMKEIGEVLKISESRVSQIHSEAV 231

Query: 278 KKVQESIQ 285
           KK++  ++
Sbjct: 232 KKLKRKLK 239


>gi|1378114|gb|AAB41955.1| whiG [Streptomyces sp.]
          Length = 209

 Score = 96.8 bits (240), Expect = 3e-18,   Method: Composition-based stats.
 Identities = 38/218 (17%), Positives = 88/218 (40%), Gaps = 16/218 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             +L+  +  LV  +A          +  ++ VS G  GL+ A++KFD +R  +  TY++
Sbjct: 3   REQLILHYSPLVKYVAGRVSVGLPPNVEQADFVSSGVFGLIDAIEKFDVDREIKFETYAI 62

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + R+   +        + +      L+   +       +      +A ++
Sbjct: 63  TRIRGAMIDEL-RALDWIPRSVRQKARNVERAYATLEAQFR-------RTPSEAEVASEM 114

Query: 167 NVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            ++  E+ ++     LA   +L  L+++  +   +    +    D      +E  E +  
Sbjct: 115 GIALEELHAVFSQLSLANVVALEELLHAGGEGGGRL-SLMDTLEDTAADNPVEVAEDREL 173

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
           R +L R+++ L  RE+ +          +TL  + +  
Sbjct: 174 RRLLARAINTLPDREKTVVTLYYY--EGLTLAEIGNVL 209


>gi|238798562|ref|ZP_04642039.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           mollaretii ATCC 43969]
 gi|238717582|gb|EEQ09421.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           mollaretii ATCC 43969]
          Length = 240

 Score = 96.8 bits (240), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 40/238 (16%), Positives = 96/238 (40%), Gaps = 17/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KNSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +               + +  N R +   +Q +     +P     +AK L
Sbjct: 73  QRIRGAMLDELR--------SRDWAPRSVRRNAREVASAMQQVEQRVGRPATEQEVAKIL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   E   +      D + + L +  +      +         ++   ++     N R 
Sbjct: 125 DIDLVEYRQILL----DTNNSQLFSYDEWREEHGESVEPLLEGHEDANPLQHLLEGNLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  +
Sbjct: 181 RVIEAIEALPEREKMVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRARL 236


>gi|327399094|ref|YP_004339963.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Hippea maritima DSM
           10411]
 gi|327181723|gb|AEA33904.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Hippea maritima DSM
           10411]
          Length = 238

 Score = 96.8 bits (240), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 37/248 (14%), Positives = 97/248 (39%), Gaps = 18/248 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFR-LATYS 105
              ++ S+  +V +I          G    + V  G +GL++A++ +D  +      +Y+
Sbjct: 4   KEEIIQSYYPIVRRIVKKTVVRMPEGYDEEDFVQIGMMGLLKAIENWDENKSLSEFKSYA 63

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
              I+     YIL     +    +   +     L+++    + +            IA++
Sbjct: 64  NTKIRG----YILDKLRSID-PVSRYARD---KLKKINMAYRQLMSEGNFNPTDDEIAER 115

Query: 166 LNVSESEVISMNCRLAGDESLN-ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            ++S  E   +  + +    L+     SSD       + +          ++E+EE K+ 
Sbjct: 116 ADMSIDEFNELLYKQSNSTMLSIDEAVSSDDGDMVLLEVIENKSSKSPLAILEEEELKD- 174

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             ++  ++  LN  E  +      ++  +  + ++S    +  R+ QI+ +A  K++  +
Sbjct: 175 --IVKEALKALNETEITVLSLYYYEDFNM--KEIASLIGKTESRISQIKTKALLKIRAYV 230

Query: 285 QKQVELSS 292
           + + ++  
Sbjct: 231 ENKTKMEG 238


>gi|262199287|ref|YP_003270496.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Haliangium
           ochraceum DSM 14365]
 gi|262082634|gb|ACY18603.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Haliangium
           ochraceum DSM 14365]
          Length = 244

 Score = 96.8 bits (240), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 48/253 (18%), Positives = 98/253 (38%), Gaps = 31/253 (12%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVK 91
              A R REH D      L+  H+ L + +A            + ++ S   +GL +A +
Sbjct: 19  VDAAARKREHCDE-----LIKEHIELALSMARRMARRLPASVCLDDIESAALLGLTEAAR 73

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           ++D +R      ++   I+ A+ + + RS  L + G  A         R++    ++   
Sbjct: 74  RYDDKRREPFMGFAAKRIRGAILDQLRRSDMLTRRGRRAA--------RQVAEAARSFEG 125

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
            + +P     +A +L VS+ E  S+   +      +  +   D   +   D         
Sbjct: 126 EHGRPATDSELADQLGVSDEEFHSVYASVR-----DVTVTGVDDADAILPD--------D 172

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
                   ER+  R  L R++  L+ R R +  A    ++ +TL  +     ++  RV Q
Sbjct: 173 AAATFACIERQQLRAALVRALEKLDDRARVVLAAYY--QDGLTLREIGQILGITESRVCQ 230

Query: 272 IEARAFKKVQESI 284
           I  +    +++ +
Sbjct: 231 IHTQTLALLRDQL 243


>gi|310642979|ref|YP_003947737.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
 gi|309247929|gb|ADO57496.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
          Length = 246

 Score = 96.8 bits (240), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 52/262 (19%), Positives = 102/262 (38%), Gaps = 59/262 (22%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L + EE  L  +    GD +    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 44  PPLTRDEEEYLLGKLS-SGDAAVRSMLIERNLRLVVYIARKFENTGINIEDLVSIGAIGL 102

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FDPE+  +LATY+   I+  +  Y+ R+                          
Sbjct: 103 IKAVNTFDPEKKIKLATYASRCIENEILMYLRRNSKT----------------------- 139

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                             +  VS  E ++++    G+E L + +  ++ ++         
Sbjct: 140 ------------------RTEVSFDEPLNID--WDGNELLLSDVMGTENDTIYRNIEEQV 179

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           D     + L +  +R+     L   +     + ++               +++    +S+
Sbjct: 180 DRKLLHKALDKLTDRERLIMELRFGLQDGEEKTQK---------------DVADLLGISQ 224

Query: 267 ERVRQIEARAFKKVQESIQKQV 288
             + ++E R  K++++   K V
Sbjct: 225 SYISRLEKRIIKRLRKEFNKMV 246


>gi|123442749|ref|YP_001006726.1| flagellar biosynthesis sigma factor [Yersinia enterocolitica subsp.
           enterocolitica 8081]
 gi|332161358|ref|YP_004297935.1| flagellar biosynthesis sigma factor [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|122089710|emb|CAL12562.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           enterocolitica subsp. enterocolitica 8081]
 gi|318605283|emb|CBY26781.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           enterocolitica subsp. palearctica Y11]
 gi|325665588|gb|ADZ42232.1| flagellar biosynthesis sigma factor [Yersinia enterocolitica subsp.
           palearctica 105.5R(r)]
 gi|330859514|emb|CBX69857.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           enterocolitica W22703]
          Length = 240

 Score = 96.4 bits (239), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 39/238 (16%), Positives = 97/238 (40%), Gaps = 17/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KNSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +               + +  N R +   +Q +     +P     +A+ L
Sbjct: 73  QRIRGAMLDELR--------SRDWAPRSVRRNAREVASAMQKVEQRLGRPATEQEVAQNL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++  +E   +      D + + L +  +      +         ++   ++     N R 
Sbjct: 125 DIDLTEYRQILL----DTNNSQLFSYDEWREEHGESVEPMLEGHEDANPLQHLLEGNLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  +
Sbjct: 181 RVIEAIEALPEREKMVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRARL 236


>gi|332701290|ref|ZP_08421378.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio
           africanus str. Walvis Bay]
 gi|332551439|gb|EGJ48483.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio
           africanus str. Walvis Bay]
          Length = 264

 Score = 96.4 bits (239), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 51/246 (20%), Positives = 104/246 (42%), Gaps = 21/246 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              +V  +   +  +A+  +      + + E++S G++GLM+A++KF+PE   +  TY+ 
Sbjct: 36  REEIVRHYGPKIKIMALRLKAKLPQTVELGELMSAGSLGLMEALQKFNPELRIKFETYAE 95

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             IK AM + + R             + L   LR ++  ++ I     +P  V  IAK+ 
Sbjct: 96  SRIKGAMLDELRR--------MDWYSRGLRQRLRLMEHTVREIEQETGRPATVQEIAKRT 147

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +SE +V      L     L+    S    S            G +    +    +   +
Sbjct: 148 GLSEKDVDMGLEMLQNQLCLSLDAISECVASVS--------DAGVDGDPYQSAAFQELID 199

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +T  +  L PRE+ +      +E  + +   ++  E++  RV Q+ ++A  K+++  + 
Sbjct: 200 KITLLIDELTPREKLVLSLYYGEE--LNMRETANVMEITEGRVSQLHSQALGKLRKLFKD 257

Query: 287 QVELSS 292
           Q  L +
Sbjct: 258 QYNLDA 263


>gi|26249145|ref|NP_755185.1| hypothetical protein c3306 [Escherichia coli CFT073]
 gi|289829787|ref|ZP_06547302.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-3139]
 gi|26109552|gb|AAN81755.1|AE016765_157 Hypothetical protein c3306 [Escherichia coli CFT073]
 gi|323154962|gb|EFZ41154.1| RNA polymerase sigma factor rpoS [Escherichia coli EPECa14]
          Length = 172

 Score = 96.4 bits (239), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 32/172 (18%), Positives = 69/172 (40%), Gaps = 12/172 (6%)

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           +     +++      K L   LR  +     ++           IA++L+    +V  M 
Sbjct: 1   MNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRML 55

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
                  S++  +    + +      L    D +E    +  +  + +  + + +  LN 
Sbjct: 56  RLNERITSVDTPLGGDSEKA-----LLDILADEKENGPEDTTQDDDMKQSIVKWLFELNA 110

Query: 238 RERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++R +   R   L     TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 111 KQREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 162


>gi|189426332|ref|YP_001953509.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacter lovleyi SZ]
 gi|189422591|gb|ACD96989.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Geobacter lovleyi SZ]
          Length = 250

 Score = 96.4 bits (239), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 35/242 (14%), Positives = 88/242 (36%), Gaps = 20/242 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              ++TSHL LV  +   +       +   ++ S   IGL+ A  ++DP RG +  T++ 
Sbjct: 19  RETMITSHLPLVRYLVNRFTAQLPSHIDPQDLASAAVIGLIHAADRYDPGRGVQFKTFAE 78

Query: 107 WWIKAAMQ---EYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
             I+ A+             ++      ++ +                   +      +A
Sbjct: 79  QHIRGAILDELRACDPLSRTMRDKCKMVEREMHRQ-----------EHQLGRNPTGREMA 127

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + L +S  +   +   +  + S  ++ +S D +            D + +    +     
Sbjct: 128 EALQISLDDYYGLLDEI-HEFSFISIDDSWDDDEGHPLSLADILGDDENKGPQCQVMAGQ 186

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               L  ++  L  +ER        +E  + L+ + +   ++  R+ QI ++A  +++  
Sbjct: 187 AAQALGSAIESLPEKERLAVTLYYYEE--LNLKEIGAVLGLTESRICQILSQAMIRLKGK 244

Query: 284 IQ 285
           ++
Sbjct: 245 LK 246


>gi|322384113|ref|ZP_08057831.1| sporulation sigma factor SigE-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321151193|gb|EFX44502.1| sporulation sigma factor SigE-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 233

 Score = 96.4 bits (239), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 53/262 (20%), Positives = 104/262 (39%), Gaps = 59/262 (22%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L ++EE  L  +    GD +    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 31  PPLTREEEEYLLGKL-PSGDAAIRAMLIERNLRLVVYIARKFENTGINIEDLVSIGAIGL 89

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FDPE+  +LATY+   I+  +  Y+ R+  +                       
Sbjct: 90  IKAVNTFDPEKKIKLATYASRCIENEILMYLRRNSKI----------------------- 126

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                             +  VS  E ++++    G+E L + +  ++ ++         
Sbjct: 127 ------------------RTEVSFDEPLNID--WDGNELLLSDVLGTENDTIYRNIEEQV 166

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           D     + L +  ER+     L   +     + ++               +++    +S+
Sbjct: 167 DRKLLHKALDKLTERERVIMELRFGLQDGEEKTQK---------------DVADLLGISQ 211

Query: 267 ERVRQIEARAFKKVQESIQKQV 288
             + ++E R  K++++   K V
Sbjct: 212 SYISRLEKRIIKRLRKEFNKMV 233


>gi|254523268|ref|ZP_05135323.1| RNA polymerase sigma factor [Stenotrophomonas sp. SKA14]
 gi|219720859|gb|EED39384.1| RNA polymerase sigma factor [Stenotrophomonas sp. SKA14]
          Length = 247

 Score = 96.4 bits (239), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 47/251 (18%), Positives = 99/251 (39%), Gaps = 21/251 (8%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFD 94
           A +YRE    SAA+ ++  H  LV +IA          + + +++  G +GL++A + +D
Sbjct: 4   AAQYREVQ-RSAANEVIAQHSDLVRRIAHHLAARLPASVEVDDLIQAGMMGLIEASRSYD 62

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
            ++G    TY+   I+ +M + I R    V        +     +RR       +  ++ 
Sbjct: 63  ADQGASFETYTSIRIRGSMIDEIRR-GDWVPRSVHRRARDAAATIRR-------LEQSSG 114

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +      +A  + +   E + +    A  + L+      D+         +         
Sbjct: 115 RAASATEVAAAMEMPLPEYLRLMEDAARGQVLSLESRIEDQGE-------LDTVAQGGPT 167

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
             +  ER      L +++  L  RE+ +       E  + L+ + +   VS  RV QI  
Sbjct: 168 PQQVLERGEFGRELGKAIGHLPEREQLVLSLYY--EQELNLKEIGAVLGVSESRVCQIHG 225

Query: 275 RAFKKVQESIQ 285
           +A  +++  ++
Sbjct: 226 QAVLRLRGRLK 236


>gi|238764885|ref|ZP_04625825.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           kristensenii ATCC 33638]
 gi|238696904|gb|EEP89681.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           kristensenii ATCC 33638]
          Length = 240

 Score = 96.4 bits (239), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 39/238 (16%), Positives = 97/238 (40%), Gaps = 17/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KNSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +               + +  N R +   +Q +     +P     +A+ L
Sbjct: 73  QRIRGAMLDELR--------SRDWAPRSVRRNAREVASAMQKVEQRLGRPATEQEVAQIL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++  +E   +      D + + L +  +      +         ++   ++     N R 
Sbjct: 125 DIDLAEYRQILL----DTNNSQLFSYDEWREEHGESVEPMLEGHEDANPLQHLLEGNLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  +
Sbjct: 181 RVIEAIEALPEREKMVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRSRL 236


>gi|194365639|ref|YP_002028249.1| RNA polymerase sigma-28 subunit, FliA/WhiG [Stenotrophomonas
           maltophilia R551-3]
 gi|194348443|gb|ACF51566.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Stenotrophomonas
           maltophilia R551-3]
          Length = 247

 Score = 96.4 bits (239), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 47/251 (18%), Positives = 99/251 (39%), Gaps = 21/251 (8%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFD 94
           A +YRE    SAA+ ++  H  LV +IA          + + +++  G +GL++A + +D
Sbjct: 4   AAQYREVQ-RSAANEVIAQHSDLVRRIAHHLAARLPASVEVDDLIQAGMMGLIEASRSYD 62

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
            ++G    TY+   I+ +M + I R    V        +     +RR       +  ++ 
Sbjct: 63  ADQGASFETYASIRIRGSMIDEIRR-GDWVPRSVHRRARDAAATIRR-------LEQSSG 114

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +      +A  + +   E + +    A  + L+      D+         +         
Sbjct: 115 RAASATEVAAAMEMPLPEYLRLMEDAARGQVLSLESRIEDQGE-------LDTVTQGGPT 167

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
             +  ER      L +++  L  RE+ +       E  + L+ + +   VS  RV QI  
Sbjct: 168 PQQVLERGEFGRELGKAIGHLPEREQLVLSLYY--EQELNLKEIGAVLGVSESRVCQIHG 225

Query: 275 RAFKKVQESIQ 285
           +A  +++  ++
Sbjct: 226 QAVLRLRGRLK 236


>gi|318066939|emb|CBY89084.1| RNA polymerase sigma70 factor [Halomonas elongata]
          Length = 367

 Score = 96.4 bits (239), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 46/74 (62%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 294 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 353

Query: 101 LATYSMWWIKAAMQ 114
            +TY+ WWI+ A+ 
Sbjct: 354 FSTYATWWIRQAIT 367


>gi|238788344|ref|ZP_04632138.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           frederiksenii ATCC 33641]
 gi|238723590|gb|EEQ15236.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           frederiksenii ATCC 33641]
          Length = 240

 Score = 96.4 bits (239), Expect = 4e-18,   Method: Composition-based stats.
 Identities = 39/238 (16%), Positives = 97/238 (40%), Gaps = 17/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KNSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +               + +  N R +   +Q +     +P     +A+ L
Sbjct: 73  QRIRGAMLDELR--------SRDWAPRSVRRNAREVASAMQKVEQRLGRPATEQEVAQIL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++  +E   +      D + + L +  +      +         ++   ++     N R 
Sbjct: 125 DIDLAEYRQILL----DTNNSQLFSYDEWREEHGESVEPLLEGHEDANPLQHLLEGNLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  +
Sbjct: 181 RVIEAIEALPEREKMVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRARL 236


>gi|292488613|ref|YP_003531497.1| RNA polymerase sigma factor FliA/RpoD [Erwinia amylovora CFBP1430]
 gi|292899773|ref|YP_003539142.1| RNA polymerase sigma factor for flagellar operon (sigma-F factor)
           [Erwinia amylovora ATCC 49946]
 gi|291199621|emb|CBJ46740.1| RNA polymerase sigma factor for flagellar operon (sigma-F factor)
           [Erwinia amylovora ATCC 49946]
 gi|291554044|emb|CBA21132.1| RNA polymerase sigma factor FliA/RpoD [Erwinia amylovora CFBP1430]
 gi|312172755|emb|CBX81011.1| RNA polymerase sigma factor FliA/RpoD [Erwinia amylovora ATCC
           BAA-2158]
          Length = 240

 Score = 96.4 bits (239), Expect = 5e-18,   Method: Composition-based stats.
 Identities = 39/238 (16%), Positives = 97/238 (40%), Gaps = 17/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KHSLWQRYIPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDAMQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +               + +  N R + G +  +     +      +A +L
Sbjct: 73  QRIRGAMLDELR--------SRDWAPRSVRRNAREVAGAMHQVEQALGRTATEQEVAAQL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +V   E   +      D + + L +  +          +     +++  + +    + R+
Sbjct: 125 DVPLEEYRQILL----DTNNSQLFSFDEYREEHGDSAELVTEGHEQENPLHQLLEGDLRD 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  +
Sbjct: 181 RVIEAIDGLPEREKMVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRARL 236


>gi|26000679|gb|AAN75199.1| sigma K [Clostridium difficile]
 gi|26000681|gb|AAN75200.1| sigma K [Clostridium difficile CD196]
 gi|26000696|gb|AAN75201.1| sigma K [Clostridium difficile]
 gi|26000698|gb|AAN75202.1| sigma K [Clostridium difficile]
 gi|26000700|gb|AAN75203.1| sigma K [Clostridium difficile]
          Length = 108

 Score = 96.4 bits (239), Expect = 5e-18,   Method: Composition-based stats.
 Identities = 27/93 (29%), Positives = 49/93 (52%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L  +EE     +++   D SA   L+  ++RLV  IA  Y        +++S G IGL+
Sbjct: 10  PLTPEEEIEYLTKFKIENDKSAKDTLIERNMRLVAYIAKKYNNSTEDQDDLISIGTIGLI 69

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           +A++ ++ ++G RLATY+   I+  +   I  +
Sbjct: 70  KAIETYNIDKGTRLATYASRCIENEILMNIRSN 102


>gi|255021389|ref|ZP_05293437.1| RNA polymerase sigma factor for flagellar operon [Acidithiobacillus
           caldus ATCC 51756]
 gi|254969252|gb|EET26766.1| RNA polymerase sigma factor for flagellar operon [Acidithiobacillus
           caldus ATCC 51756]
          Length = 241

 Score = 96.0 bits (238), Expect = 5e-18,   Method: Composition-based stats.
 Identities = 48/240 (20%), Positives = 93/240 (38%), Gaps = 20/240 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKF-DPERGFRLATYS 105
              LV  ++ LV +IA   R      + + +++  G IGL+  ++++ +P+       Y+
Sbjct: 13  RSALVARYVPLVQRIAQRLRARLPANVDLGDLIQAGLIGLLDVLEQYPEPDDSDAFLRYA 72

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
              I+ +M + +     L +      Q        ++   +  +     +P     +AK 
Sbjct: 73  TLRIRGSMIDELREQDWLPRRARAKEQ--------QVSRAMAQLEQQLGRPPSDQEVAKH 124

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           L     +         G   L  L + +  N S    +L   H    +VL   E      
Sbjct: 125 LGWDLDDYQKAIADSGGQ--LVYLEDLAADNDSFVGQYLRDRHADISEVLGSLE----FD 178

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             L  +++ L  RER +      +E  +TL  +    EV+  RV QI  +A  +++ S+Q
Sbjct: 179 RHLQEAITRLPERERLVLSLYYREE--LTLREIGEVLEVTESRVSQIVRQAVLRLRASLQ 236


>gi|118581847|ref|YP_903097.1| FliA/WhiG family RNA polymerase sigma factor [Pelobacter
           propionicus DSM 2379]
 gi|118504557|gb|ABL01040.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Pelobacter
           propionicus DSM 2379]
          Length = 250

 Score = 96.0 bits (238), Expect = 5e-18,   Method: Composition-based stats.
 Identities = 32/239 (13%), Positives = 87/239 (36%), Gaps = 14/239 (5%)

Query: 50  AHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L+  H+ +   +           L   +++S   IGL+ A  +FDP RG    T++ 
Sbjct: 19  REELIVKHMPMARYLVARISPQLPPHLDQQDLMSAAMIGLIHAADRFDPNRGVLFKTFAE 78

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+  + + +               + +    +RL   L ++     +      +A+ L
Sbjct: 79  QHIRGTIIDELR--------SYDVLSRTMRDKYKRLSRQLVSLEHQLGRNPTSEEVAESL 130

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   E   +   +    S  ++ +S D +            + + +   ++        
Sbjct: 131 GIGLEEYYELLDDVHA-YSFISIDDSWDDDEGNSLCLGDVLCESEAKSPQQQVMTMQLAE 189

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            L +++  L  ++R +       +  + L+ +     ++  R+ QI ++A  +++  ++
Sbjct: 190 ELGKAIDALPEKDRLVVTLYY--KEDLRLKEIGEAMGLTESRISQILSQAMVRLRSKLK 246


>gi|190574220|ref|YP_001972065.1| putative RNA polymerase sigma factor for flagellar regulon FliA
           [Stenotrophomonas maltophilia K279a]
 gi|190012142|emb|CAQ45765.1| putative RNA polymerase sigma factor for flagellar regulon FliA
           [Stenotrophomonas maltophilia K279a]
          Length = 247

 Score = 96.0 bits (238), Expect = 5e-18,   Method: Composition-based stats.
 Identities = 47/251 (18%), Positives = 99/251 (39%), Gaps = 21/251 (8%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFD 94
           A +YRE    SAA+ ++  H  LV +IA          + + +++  G +GL++A + +D
Sbjct: 4   AAQYREVQ-RSAANEVIAQHSDLVRRIAHHLAARLPASVEVDDLIQAGMMGLIEASRSYD 62

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
            ++G    TY+   I+ +M + I R    V        +     +RR       +  ++ 
Sbjct: 63  ADQGASFETYASIRIRGSMIDEIRR-GDWVPRSVHRRARDAAATIRR-------LEQSSG 114

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +      +A  + +   E + +    A  + L+      D+         +         
Sbjct: 115 RAASATEVAAAMEMPLPEYLRLMEDAARGQVLSLESRIEDQGE-------LDTVAQGGPT 167

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
             +  ER      L +++  L  RE+ +       E  + L+ + +   VS  RV QI  
Sbjct: 168 PQQVLERGEFGRELGKAIGHLPEREQLVLSLYY--EQELNLKEIGAVLGVSESRVCQIHG 225

Query: 275 RAFKKVQESIQ 285
           +A  +++  ++
Sbjct: 226 QAVLRLRGRLK 236


>gi|169827149|ref|YP_001697307.1| RNA polymerase sigma factor SigD [Lysinibacillus sphaericus C3-41]
 gi|168991637|gb|ACA39177.1| RNA polymerase sigma-D factor (Sigma-28) [Lysinibacillus sphaericus
           C3-41]
          Length = 271

 Score = 96.0 bits (238), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 44/246 (17%), Positives = 92/246 (37%), Gaps = 20/246 (8%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQA 89
           +E  L  R+    D  A   L+  ++ LV              +   ++ S G IGL  A
Sbjct: 23  DEQKLWNRWIHERDPDAGDLLIKKYISLVSYHVQRISAGLPKSVSRDDLTSLGMIGLFDA 82

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + KFD  R  +  TY+ + ++ A+ + + R    +        K+L   +       + +
Sbjct: 83  LNKFDINRDLKFDTYASFRVRGAIIDGL-RKEDWLPRSAREKAKKLDAQI-------EQL 134

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
               ++      +AK + V   +V         +   S+N      D+     + +++  
Sbjct: 135 EQKYMRHVTPEELAKHMEVPVEDVYQTVQEHFFSNVLSINE---QQDQEEVDGKSFVI-- 189

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            D   +   +   +    + L  ++  LN +E+ +      +E  +TL  +    E+S  
Sbjct: 190 RDDTTKTPEQSVVKSELLDDLAENIQKLNEKEQLVLSLFYTEE--LTLTEIGEMLELSTS 247

Query: 268 RVRQIE 273
           R+ QI 
Sbjct: 248 RISQIH 253


>gi|327394234|dbj|BAK11656.1| RNA polymerase sigma factor for flagellar operon FliA [Pantoea
           ananatis AJ13355]
          Length = 230

 Score = 96.0 bits (238), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 41/238 (17%), Positives = 97/238 (40%), Gaps = 17/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 3   KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 62

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +               + +  N R + G +  +     +      +A++L
Sbjct: 63  QRIRGAMLDELR--------SRDWAPRSVRRNAREVAGAMHQVEQMLGRAASEQEVAQQL 114

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           NVS  E   +      D + + L +  +          +     +E   + +    + R 
Sbjct: 115 NVSIEEYRQILL----DTNNSQLFSYDEYREEHGDSAELVTEGHEEANPLHQLMEGSLRE 170

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  ++  L  RE+ +       +  + L+ + +  +V   RV Q+ ++A K+++  +
Sbjct: 171 RVIEAIEALPEREKMVLTLYY--QEELNLKEIGAVLDVGESRVSQLHSQAIKRLRARL 226


>gi|298492777|ref|YP_003722954.1| FliA/WhiG subfamily RNA polymerase sigma 28 subunit ['Nostoc
           azollae' 0708]
 gi|298234695|gb|ADI65831.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily ['Nostoc
           azollae' 0708]
          Length = 263

 Score = 96.0 bits (238), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 48/239 (20%), Positives = 110/239 (46%), Gaps = 21/239 (8%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKKFD 94
            L   Y ++  +   ++LV  H  LV K+A  +      P  ++   G +GL++A+++F+
Sbjct: 14  ELIHLYHQNPSIKLRNQLVEVHKGLVRKMAYKFIHQCNEPYEDLEQIGYLGLIRAIERFN 73

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P + +  +++++ +I+  M  ++    +L+KI     +  L+   ++++      T +  
Sbjct: 74  PHQRYAFSSFAIPYIRGEMLHFLRDHSTLLKIPRRWQE--LYNAGQKIRK---QFTLSLG 128

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +P + + IA KLN+S  E       +      SL+A   +         D L        
Sbjct: 129 RPPREIDIATKLNISLQEWQECKLAVQNRIPLSLDATTANYVDYQITLGDILPCLR---- 184

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE-----VSR 266
             L++++E +  R  L  ++S+L+ + R + E   ++E  +T ++ + +       V+R
Sbjct: 185 TALLQQQEEE--RLQLQGAISMLDDKRRIVVELVLVKE--LTRKDAAKKIGTSPMTVTR 239


>gi|77165620|ref|YP_344145.1| Sigma28 (flagella) [Nitrosococcus oceani ATCC 19707]
 gi|76883934|gb|ABA58615.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Nitrosococcus
           oceani ATCC 19707]
          Length = 234

 Score = 96.0 bits (238), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 40/239 (16%), Positives = 93/239 (38%), Gaps = 28/239 (11%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
             LV  +  LV +IA        P   + +++  G IGL++A + ++  +G    TY+  
Sbjct: 18  DELVAQYAPLVKRIAYHLLTRLPPSVQLDDLIQAGMIGLLEAARNYNASQGASFETYAGI 77

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+ A+ + I R+            + +    R++   ++ + +   +  +   +A++L 
Sbjct: 78  RIRGAILDEIRRNDW--------APRSVHRKARQVAEVMREVENREGRDARDHEVAEELG 129

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +  +E   +     G    +    +  + S      L        +   E  + +N R  
Sbjct: 130 LPLNEYHRLLQDAGGYRVFSLDEFNEGEESEPLSASL--------KGPYEGLQDQNFRGA 181

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           L  ++  L  RER +     +++  + L  +     VS       E+RA  +++  + +
Sbjct: 182 LVEAIEGLPERERLVMSLYYVED--LNLREIGEVLGVS-------ESRAVLRLRARLSE 231


>gi|169334926|ref|ZP_02862119.1| hypothetical protein ANASTE_01332 [Anaerofustis stercorihominis DSM
           17244]
 gi|169257664|gb|EDS71630.1| hypothetical protein ANASTE_01332 [Anaerofustis stercorihominis DSM
           17244]
          Length = 233

 Score = 96.0 bits (238), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 54/273 (19%), Positives = 94/273 (34%), Gaps = 64/273 (23%)

Query: 19  YIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           Y       P  L+K++E     +++E  D+ A   L+  +LRLV  ++  Y    +   +
Sbjct: 20  YFSASESFPKPLKKEDETKYFVKFKEENDMHAKEMLINHNLRLVAHVSKKYSSSNITKED 79

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           ++S G IGL++ +  FD  +G + ATY    I   +   +                    
Sbjct: 80  LISIGIIGLIKGINSFDYNKGTKFATYGARCIDNEILMALRSETKTAS------------ 127

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
                                        NV   + IS +        L+ L    D  +
Sbjct: 128 -----------------------------NVFLEDYISFDEEGNNISLLDILATDEDDVN 158

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS-VLNPRERRIFEARRLQENPV--T 254
           S                   K   K     L + M  VL  RE+ I   R   +     T
Sbjct: 159 S-------------------KVNLKVESEFLYKIMDEVLEDREKEILYLRYGLKGKRSYT 199

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              ++  +++SR  V +IE +A +K+  S +K+
Sbjct: 200 QREIADMYDISRSYVSRIEKKAIEKIAISFKKK 232


>gi|317063374|ref|ZP_07927859.1| RNA polymerase [Fusobacterium ulcerans ATCC 49185]
 gi|313689050|gb|EFS25885.1| RNA polymerase [Fusobacterium ulcerans ATCC 49185]
          Length = 151

 Score = 96.0 bits (238), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 33/153 (21%), Positives = 66/153 (43%), Gaps = 9/153 (5%)

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           L ++  ++ +   +      V  IA +LN+   +V  +        SL+  I     +  
Sbjct: 2   LNKVNRYVMSRLKDEGNYPSVEEIAAELNIEADKVQDIIMDFQDPMSLSTQI----GDDI 57

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLE 256
             +D L    D   +   E+   +  R  +   ++ L  RE+ I + R   +     TLE
Sbjct: 58  YLEDTLAQQEDFSME---EEIFNEMGRKQVRDMVNQLEEREKEILKLRYGLDGYEIHTLE 114

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
            + +   ++RERVRQIE +  +K++    K+++
Sbjct: 115 EIGNTLNITRERVRQIEKKTLQKLRSKYTKELK 147


>gi|133481|sp|P26768|RPSX_BACTK RecName: Full=Putative RNA polymerase sigma-G factor; AltName:
           Full=ORF3
 gi|580955|emb|CAA40027.1| unnamed protein product [Bacillus thuringiensis serovar kurstaki]
          Length = 125

 Score = 96.0 bits (238), Expect = 6e-18,   Method: Composition-based stats.
 Identities = 26/107 (24%), Positives = 58/107 (54%), Gaps = 2/107 (1%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+L+ +E   L +  +  G++SA  +LV  +LRLV+ +   +   G  + ++   G I
Sbjct: 15  KLPVLKNEEMRKLFREMQ-SGEISAREKLVNGNLRLVLSVIQRFNNRGEYVDDLFQVGCI 73

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GLM+++  FD  +  + +TY++  I   ++ Y+  +   +++  +  
Sbjct: 74  GLMKSIDNFDLGQNVKFSTYAVPMIIGEIRRYLRDNN-PIRVSRSLR 119


>gi|50120672|ref|YP_049839.1| flagellar biosynthesis sigma factor [Pectobacterium atrosepticum
           SCRI1043]
 gi|49611198|emb|CAG74644.1| RNA polymerase sigma factor for flagellar operon [Pectobacterium
           atrosepticum SCRI1043]
          Length = 240

 Score = 96.0 bits (238), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 37/235 (15%), Positives = 94/235 (40%), Gaps = 17/235 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KNSLWKRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLSAVERYDSLQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ +M + +               + +  N R +   +Q       +      +A+ L
Sbjct: 73  QRIRGSMLDELR--------SRDWAPRSVRRNAREVAQAMQQTEQQLGRTPTEQEVAQTL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           N++  +   +      D + + L +  +                ++   + +    N R+
Sbjct: 125 NITLEDYRQILL----DTNNSQLFSYDEWREEHGDSAEALLEGNEDANPLHQLMEGNLRH 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++
Sbjct: 181 RVMDAIENLPEREKLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|322384374|ref|ZP_08058069.1| RNA polymerase sigma factor SigB-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321150809|gb|EFX44249.1| RNA polymerase sigma factor SigB-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 340

 Score = 96.0 bits (238), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 50/232 (21%), Positives = 91/232 (39%), Gaps = 40/232 (17%)

Query: 60  LVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFDPERGFR----LATYSMWWIKAA 112
           +V  +A  YR   G GL   ++VS G IGL+QA + +DP+R  R     +TY+   IK +
Sbjct: 1   MVHSVARKYRSCIGAGLDYDDLVSVGMIGLIQAFRNYDPDRLNRKVSSFSTYAFNMIKWS 60

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +Q ++      V++             R ++  L  I       E   +IA+K     +E
Sbjct: 61  IQRFLADKRFSVRVP------------RSIQNKLTVIWKQGWDQESAESIAEKTGWKLAE 108

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE--KEERKNRRNMLTR 230
           +  +   LAG             + +     L  D   +E  +++            +  
Sbjct: 109 IREVKRHLAG------------WSVASLDQALSSDKTDEEATMLDVLPAMTDFTSVHVQD 156

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            +  L P ER + E R       T + ++     ++  V +I     KK+++
Sbjct: 157 FLCALKPLERAVLELRL---QDQTQKEIAMHIGKTQMYVSRI----LKKIKD 201


>gi|88704270|ref|ZP_01101984.1| RNA polymerase sigma factor for flagellar operon [Congregibacter
           litoralis KT71]
 gi|88701321|gb|EAQ98426.1| RNA polymerase sigma factor for flagellar operon [Congregibacter
           litoralis KT71]
          Length = 236

 Score = 96.0 bits (238), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 51/240 (21%), Positives = 107/240 (44%), Gaps = 24/240 (10%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           S+A  LV   L LV KI +         + + +++  G IGL++A + +D  +G   ATY
Sbjct: 13  SSADALVREFLPLVKKIGLRLAAKLPAEIEVDDLMQVGLIGLLRARESYDASQGASFATY 72

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +   IK AM + I     L         + +   LR++   ++        P Q   IA 
Sbjct: 73  AGIRIKGAMLDEIRAHDWL--------PRSVQTQLRQVSVAIERADARLGHPAQDADIAA 124

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +L++  +E   ++ +LA          +  ++S++ ++ ++   +  ++V  E       
Sbjct: 125 ELDMPLAEYQQLSGQLACAR------MTHIEDSAEAENAVLNTVNPFDEVGEEG-----F 173

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L  S++ L  +ER +      ++  + L+ + +   VS  RV Q+  +A  +++ ++
Sbjct: 174 REALAESVAQLPEKERLMMSLYYAED--LNLKEIGAVLGVSESRVSQLHGQALARLRVTL 231


>gi|315654569|ref|ZP_07907475.1| DNA-directed RNA polymerase sigma subunit FliA [Mobiluncus curtisii
           ATCC 51333]
 gi|315491033|gb|EFU80652.1| DNA-directed RNA polymerase sigma subunit FliA [Mobiluncus curtisii
           ATCC 51333]
          Length = 433

 Score = 96.0 bits (238), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 46/248 (18%), Positives = 97/248 (39%), Gaps = 22/248 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L+ ++L LV                  ++ S G++ L+QA   +D   G     Y++
Sbjct: 10  RNELIENNLPLVGYQVAELLRRVPSFVQREDLASAGSLALVQAANSYDSATGVPFHRYAI 69

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           + I+ AM + +               +      ++L+     +T    +      +A  L
Sbjct: 70  YRIRGAMLDELR--------SMDWATRGARQRTKQLEEMTSTLTAAAGRAPTKEELASAL 121

Query: 167 NVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
            V    V S     A    S++A + S D+ S +  D    +    E  L++ E     R
Sbjct: 122 GVDVESVESAQQDAARRVVSMDAPVGSEDERSLELPD----ESPSPEDTLLDDERLVYLR 177

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             +      L  R R + E    +E P+  ++++ E  V++ RV Q+ + A   ++E + 
Sbjct: 178 ASVRA----LPQRLRYVVEQVFFEERPI--QDVADELGVTQSRVSQLRSEALTLMREGMN 231

Query: 286 KQVELSSS 293
           + ++  ++
Sbjct: 232 RHLDPETA 239


>gi|238752744|ref|ZP_04614214.1| RNA polymerase sigma factor for flagellar operon [Yersinia rohdei
           ATCC 43380]
 gi|238709075|gb|EEQ01323.1| RNA polymerase sigma factor for flagellar operon [Yersinia rohdei
           ATCC 43380]
          Length = 240

 Score = 95.7 bits (237), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 39/238 (16%), Positives = 96/238 (40%), Gaps = 17/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KNSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +               + +  N R +   +Q +     +P     +A+ L
Sbjct: 73  QRIRGAMLDELR--------SRDWAPRSVRRNAREVASAMQKVEQRLGRPATEQEVAQNL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +  +E   +      D + + L +  +      +         ++   ++     N R 
Sbjct: 125 EIDLAEYRQILL----DTNNSQLFSYDEWREEHGESVEPLLEGHEDANPLQHLLEGNLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  +
Sbjct: 181 RVIDAIEALPEREKMVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRARL 236


>gi|239815268|ref|YP_002944178.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Variovorax
           paradoxus S110]
 gi|239801845|gb|ACS18912.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Variovorax
           paradoxus S110]
          Length = 272

 Score = 95.7 bits (237), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 46/246 (18%), Positives = 92/246 (37%), Gaps = 17/246 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAM----GYRGYGLPISEVVSEGNIGLMQAVK 91
            L +R+RE GD  A  +L+  HL     +A           +  ++      +GL++AV 
Sbjct: 15  ALWRRWREEGDEGARAQLIEHHLPYARMMAAAAYGRRTHNEVEFADYHQLARLGLIEAVD 74

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK-GHLQAIT 150
           +FDP +G +  T++   ++ A+   +       ++     Q      LR  +   ++   
Sbjct: 75  RFDPAQGAQFKTFAAKRVQGAILNGLP------RLTEKNQQISTMMRLRHERLEAIKEAA 128

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD---ESLNALINSSDKNSSQWQDWLVYD 207
             +         A        +   +   LA      +L  L+  +    ++  D   + 
Sbjct: 129 SEDATSHSENESAPGGPAPSRDTDKLFRYLAEVGIGIALGVLLEETGMVDAEAFDSDAH- 187

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
               E     K E    RN+L   +  LN R++ +     LQE  ++   ++    ++R 
Sbjct: 188 SPSPEISYFRKSEIHQLRNVLRGLVDQLNDRQKTVIRYHYLQE--ISFSEIAIAMSLTRG 245

Query: 268 RVRQIE 273
           RV Q+ 
Sbjct: 246 RVSQLH 251


>gi|238794024|ref|ZP_04637642.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           intermedia ATCC 29909]
 gi|238726656|gb|EEQ18192.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           intermedia ATCC 29909]
          Length = 240

 Score = 95.7 bits (237), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 39/238 (16%), Positives = 97/238 (40%), Gaps = 17/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KNSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +               + +  N R +   +Q +     +P     +A+ L
Sbjct: 73  QRIRGAMLDELR--------SRDWAPRSVRRNAREVASAMQKVEQRVGRPATEQEVAQIL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++  +E   +      D + + L +  +      +         ++   ++     N R 
Sbjct: 125 DIDLAEYRQILL----DTNNSQLFSYDEWREEHGESVEPLLEGHEDANPLQHLLEGNLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  +
Sbjct: 181 RVIEAIEALPEREKMVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRARL 236


>gi|238019186|ref|ZP_04599612.1| hypothetical protein VEIDISOL_01050 [Veillonella dispar ATCC 17748]
 gi|237863885|gb|EEP65175.1| hypothetical protein VEIDISOL_01050 [Veillonella dispar ATCC 17748]
          Length = 261

 Score = 95.7 bits (237), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 52/260 (20%), Positives = 101/260 (38%), Gaps = 21/260 (8%)

Query: 29  LEKQEEYVLAKRYREH----GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           L K+EE  L K Y E             LV +    ++ IA  Y+     I ++  EG I
Sbjct: 13  LTKEEEKALFKEYHETPSLRRKKQIKEDLVLNQCGQIISIASIYKNV-DDIEDLFQEGMI 71

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
            ++++ + +D        TY    I   + +Y+ R+ +   IG           + + K 
Sbjct: 72  AVLESFENYDYTHEASFTTYMRRGIFRQICDYLRRNKT---IGLPQAAIEKLKKINKAK- 127

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
               + +   KP    AI+   N+ E  VI +   L+ +E L+ L N  +   S  +   
Sbjct: 128 ---ELLERLNKPITTEAISDITNIKEHNVIEILNTLSVEE-LDRLCNDGEGEVSILEHV- 182

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
               D Q     +          +   MS L+ RE+ +      +   ++L  ++    +
Sbjct: 183 ---EDKQASKAFDDVLDDMTEPTID--MSCLSDREKEVIILLYYKN--LSLHQIARRLHL 235

Query: 265 SRERVRQIEARAFKKVQESI 284
               +   ++RA KK+++++
Sbjct: 236 KITLISDAKSRALKKLRKAL 255


>gi|298345983|ref|YP_003718670.1| putative DNA-directed RNA polymerase sigma subunit D [Mobiluncus
           curtisii ATCC 43063]
 gi|304390259|ref|ZP_07372213.1| DNA-directed RNA polymerase sigma subunit FliA [Mobiluncus curtisii
           subsp. curtisii ATCC 35241]
 gi|315657524|ref|ZP_07910406.1| DNA-directed RNA polymerase sigma subunit FliA [Mobiluncus curtisii
           subsp. holmesii ATCC 35242]
 gi|298236044|gb|ADI67176.1| possible DNA-directed RNA polymerase sigma subunit D [Mobiluncus
           curtisii ATCC 43063]
 gi|304326741|gb|EFL93985.1| DNA-directed RNA polymerase sigma subunit FliA [Mobiluncus curtisii
           subsp. curtisii ATCC 35241]
 gi|315491996|gb|EFU81605.1| DNA-directed RNA polymerase sigma subunit FliA [Mobiluncus curtisii
           subsp. holmesii ATCC 35242]
          Length = 433

 Score = 95.7 bits (237), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 47/248 (18%), Positives = 98/248 (39%), Gaps = 22/248 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L+ ++L LV                  ++ S G++ L+QA   +D   G     Y++
Sbjct: 10  RNELIENNLPLVGYQVAELLRRVPSFVQREDLASAGSLALVQAANSYDSATGVPFHRYAI 69

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           + I+ AM + +               +      ++L+     +T    +      +A  L
Sbjct: 70  YRIRGAMLDELR--------SMDWATRGARQRTKQLEEMTSTLTAAAGRAPTKEELASAL 121

Query: 167 NVSESEVISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
            V    V S     A    S++A + S D+ S +  D    +    E  L++ E      
Sbjct: 122 GVDVESVESAQQDAARRVVSMDAPVGSEDERSLELPD----ESPSPEDTLLDDERLV--- 174

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             L  S+  L  R R + E    +E P+  ++++ E  V++ RV Q+ + A   ++E + 
Sbjct: 175 -YLHASVRALPQRLRYVVEQVFFEERPI--QDVADELGVTQSRVSQLRSEALTLMREGMN 231

Query: 286 KQVELSSS 293
           + ++  ++
Sbjct: 232 RHLDPETA 239


>gi|290968733|ref|ZP_06560271.1| sigma-70 region 2 [Megasphaera genomosp. type_1 str. 28L]
 gi|290781386|gb|EFD93976.1| sigma-70 region 2 [Megasphaera genomosp. type_1 str. 28L]
          Length = 217

 Score = 95.7 bits (237), Expect = 7e-18,   Method: Composition-based stats.
 Identities = 33/106 (31%), Positives = 61/106 (57%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+ E++KI +L ++EE  L + Y+E G++ A  RL+  +  LV K  M    +   I
Sbjct: 2   LTSYLEELKKITLLTREEEQTLWRAYKEQGNMQARARLIEQYQPLVFKEVMRLSMHSEWI 61

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            + + EG +GL++AV+ F  ++G   + Y++  I+  + EY+ R  
Sbjct: 62  PDAIQEGTVGLIEAVEHFRIQQGVAFSLYAVHRIRGEILEYLRREG 107


>gi|317048579|ref|YP_004116227.1| FliA/WhiG subfamily RNA polymerase sigma-28 factor [Pantoea sp.
           At-9b]
 gi|316950196|gb|ADU69671.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Pantoea sp.
           At-9b]
          Length = 240

 Score = 95.7 bits (237), Expect = 8e-18,   Method: Composition-based stats.
 Identities = 43/238 (18%), Positives = 96/238 (40%), Gaps = 17/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +               + +  N R + G +  +     +      +A +L
Sbjct: 73  QRIRGAMLDELR--------SRDWAPRSVRRNAREVAGAMHQVEQAMGRAATEQEVADQL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           NVS  E   +      D + + L +  +          +     +E   + +    N R 
Sbjct: 125 NVSLEEYRQILL----DTNNSQLFSYDEYREEHGDSAELVTEGHEEANPLHQLMEGNLRE 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  +
Sbjct: 181 RVIEAIEALPEREKLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRARL 236


>gi|242238998|ref|YP_002987179.1| flagellar biosynthesis sigma factor [Dickeya dadantii Ech703]
 gi|242131055|gb|ACS85357.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Dickeya dadantii
           Ech703]
          Length = 240

 Score = 95.7 bits (237), Expect = 8e-18,   Method: Composition-based stats.
 Identities = 40/235 (17%), Positives = 93/235 (39%), Gaps = 17/235 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KNSLWKRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLSAVERYDSLQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +               + +  N R +   ++       +      +A+ L
Sbjct: 73  QRIRGAMLDELR--------SRDWAPRSVRRNAREVAHAMRQAEQLLGRAPTEQEVAQSL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           N+S  E   +      D + + L +  +                +E   + +    N R 
Sbjct: 125 NISLEEYRQILL----DTNNSQLFSYDEWREEHGDSAEALLEGNEEANPLHQLMDVNLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++
Sbjct: 181 RVMEAIENLPEREKMVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|254698074|ref|ZP_05159902.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 2 str.
           86/8/59]
          Length = 118

 Score = 95.7 bits (237), Expect = 8e-18,   Method: Composition-based stats.
 Identities = 38/108 (35%), Positives = 64/108 (59%), Gaps = 3/108 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  ++          +   I      P LE++EE  LA R++E  D  A HR+ ++H+RL
Sbjct: 14  MAVRSFPAAAASSQSM---IRSAMSAPYLEREEERALAIRWKETKDQDALHRITSAHMRL 70

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           V+ +A  +R + LP+S+++ EG +GL++A  +FDP+R  R +TY+ WW
Sbjct: 71  VISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRDVRFSTYASWW 118


>gi|254459646|ref|ZP_05073062.1| flagellar-specific RNA polymerase sigma factor [Rhodobacterales
           bacterium HTCC2083]
 gi|206676235|gb|EDZ40722.1| flagellar-specific RNA polymerase sigma factor [Rhodobacteraceae
           bacterium HTCC2083]
          Length = 219

 Score = 95.7 bits (237), Expect = 8e-18,   Method: Composition-based stats.
 Identities = 41/236 (17%), Positives = 100/236 (42%), Gaps = 21/236 (8%)

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           R V           +   +++  G +GL++A +++  + G    +Y++  ++ A+ +++ 
Sbjct: 3   RKVAHHVHSRVRSIVEFDDLLQIGLMGLIEAAQRYTRQEGISFESYAVIRVRGAINDFLR 62

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
           ++ +L +     N+         +      +  +  +  +   +AK + +S  E  +   
Sbjct: 63  KNSALSRKSMKINK--------EVNEARNKLVHDLGRAPEGHEVAKAVGLSLDEFTAWEQ 114

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE-ERKNRRNMLTRSMSVLNP 237
            L  + S +  I       S W               IE+E +R   +  L  ++  L  
Sbjct: 115 TL--NSSYHNSIQDEYDEHSMWF--------ATADAPIEQELDRARLKEALLYALKTLPE 164

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           RE  + +   ++E  + L  +++  +V+  RV QI++ AFKK+Q  ++  ++ S +
Sbjct: 165 REALVLQLYYVEE--LNLFEIAAVLDVTSGRVSQIKSSAFKKMQPLLKDYIDNSQA 218


>gi|319790426|ref|YP_004152059.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermovibrio
           ammonificans HB-1]
 gi|317114928|gb|ADU97418.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermovibrio
           ammonificans HB-1]
          Length = 203

 Score = 95.7 bits (237), Expect = 8e-18,   Method: Composition-based stats.
 Identities = 51/240 (21%), Positives = 103/240 (42%), Gaps = 49/240 (20%)

Query: 50  AHRLVTSHLRLVVKIAMG-YRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
              LV  HL LV K+A   YR      +   E+V+ G IGL++A++++D  R  + +TY+
Sbjct: 6   RKELVLEHLPLVKKVANRIYRRIPEGAVEFEELVNTGVIGLIKAIERYDENR-AKFSTYA 64

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
              I+  + +Y+ +   L  +  +  +K    +L                          
Sbjct: 65  YIKIRGEILDYLRK---LDFLPRSVREKVKNGDL------------------------DD 97

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           L    +  IS+  +L            +D +    +D L    DG E    E+   ++ +
Sbjct: 98  LKEGVASFISIEEKL-----------FADSDRFTVKDTLASPDDGPE----ERMLLEDAK 142

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             LT ++  L+ +E+ + +   ++E    L+++     +S  RV QI++ A KK+++ ++
Sbjct: 143 EKLTEAIKKLSEKEQLVLQLIFVEELD--LKSIGEILGISVSRVSQIKSSALKKLRKFLE 200


>gi|318066917|emb|CBY89073.1| RNA polymerase sigma70 factor [Cobetia marina]
 gi|318066949|emb|CBY89089.1| RNA polymerase sigma70 factor [Halomonas halodurans]
          Length = 364

 Score = 95.7 bits (237), Expect = 8e-18,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 46/74 (62%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 291 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 350

Query: 101 LATYSMWWIKAAMQ 114
            +TY+ WWI+ A+ 
Sbjct: 351 FSTYATWWIRQAIT 364


>gi|195953358|ref|YP_002121648.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Hydrogenobaculum sp.
           Y04AAS1]
 gi|195932970|gb|ACG57670.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Hydrogenobaculum sp.
           Y04AAS1]
          Length = 245

 Score = 95.7 bits (237), Expect = 8e-18,   Method: Composition-based stats.
 Identities = 39/248 (15%), Positives = 103/248 (41%), Gaps = 22/248 (8%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
                + +  ++ LV KI           +  +++VS G IGL+ A+   D  +     +
Sbjct: 14  KEQREKKILEYIPLVKKICGKMSRNLPPSVDYNDLVSNGIIGLINAIDHLDELKNP--ES 71

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y    +K A+ +Y+               + +     ++K  ++   +   +      I+
Sbjct: 72  YIKIRVKGAIYDYLR--------SLDFGSRNIRDKEHKIKEIIRTFQNEYQREPTDEEIS 123

Query: 164 KKLNVSESEVISMNCRLAGD--ESLNALIN-SSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
             L  S  E  +   +++    +SL  ++   +++N S + ++++       +   E   
Sbjct: 124 SILGESLEEYQNSLYKISFSYLQSLEDMVYKITEENESSYDNFVI----SSIETPEEYAV 179

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           + +    L  ++  L  RE+ + +    +E  +  + ++    VS  RV QI+++A +K+
Sbjct: 180 KSDLAEKLKEAIDKLEEREKLVLQLLFYEEFGI--KEVAEILNVSLSRVSQIKSQALEKL 237

Query: 281 QESIQKQV 288
           ++ +++ +
Sbjct: 238 RKHLEEAI 245


>gi|87311163|ref|ZP_01093286.1| RNA polymerase sigma factor whiG [Blastopirellula marina DSM 3645]
 gi|87286071|gb|EAQ77982.1| RNA polymerase sigma factor whiG [Blastopirellula marina DSM 3645]
          Length = 261

 Score = 95.7 bits (237), Expect = 8e-18,   Method: Composition-based stats.
 Identities = 55/258 (21%), Positives = 109/258 (42%), Gaps = 23/258 (8%)

Query: 36  VLAKRYREHGD-LSAAHRLVTSHLRLVVK---IAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            + K Y+E        +RLV  +L LV             G+ + +++S G  GLM A+ 
Sbjct: 12  EVWKSYKEDQTRKELRNRLVERYLPLVKYNGERIWARLPEGVELDDLISAGVFGLMDAID 71

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
            FD  RG +  TY +  I+ AM + + R+   V     +   +L    ++L+        
Sbjct: 72  AFDMSRGVKFETYCVPRIRGAMLDEL-RTMDWVPRLVRSKASKLNEANKQLEAKF----- 125

Query: 152 NNLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
              +    + ++  + +S  E+  M  +    G  SLN     +D      +  ++ D  
Sbjct: 126 --GRQPTEIELSAHMGMSVKELEKMISDANAVGLISLNKKWYETDSYKDVREIDILEDIK 183

Query: 210 GQEQVLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           G++        R+ ++N L R +   LN  ER I      +E  +T++ + +  ++S  R
Sbjct: 184 GEDPT------RRIQKNDLMRLVTKGLNRNERLIIILYYYEE--LTMKEIGATLDLSESR 235

Query: 269 VRQIEARAFKKVQESIQK 286
           V Q+ +   +++Q  + +
Sbjct: 236 VSQMHSSIVQRLQSQLGR 253


>gi|308069873|ref|YP_003871478.1| RNA polymerase sigma-35 factor precursor [Paenibacillus polymyxa
           E681]
 gi|305859152|gb|ADM70940.1| RNA polymerase sigma-35 factor precursor [Paenibacillus polymyxa
           E681]
          Length = 246

 Score = 95.7 bits (237), Expect = 8e-18,   Method: Composition-based stats.
 Identities = 52/262 (19%), Positives = 102/262 (38%), Gaps = 59/262 (22%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L + EE  L  +    GD +    L+  +LRLVV IA  +   G+ I ++VS G IGL
Sbjct: 44  PPLTRDEEEYLLGKLS-SGDAAVRSMLIERNLRLVVYIARKFENTGINIEDLVSIGAIGL 102

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           ++AV  FDPE+  +LATY+   I+  +  Y+ R+                          
Sbjct: 103 IKAVNTFDPEKKIKLATYASRCIENEILMYLRRNSKT----------------------- 139

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
                             +  VS  E ++++    G+E L + +  ++ ++         
Sbjct: 140 ------------------RTEVSFDEPLNID--WDGNELLLSDVMGTENDTIYRNIEEQV 179

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           D     + L +  +R+     L   +     + ++               +++    +S+
Sbjct: 180 DRKLLHKALDKLTDRERLIMELRFGLQDGEEKTQK---------------DVADLLGISQ 224

Query: 267 ERVRQIEARAFKKVQESIQKQV 288
             + ++E R  K++++   K V
Sbjct: 225 SYISRLEKRIIKRLRKEFNKMV 246


>gi|318066901|emb|CBY89065.1| RNA polymerase sigma70 factor [Carnimonas nigrificans]
          Length = 371

 Score = 95.7 bits (237), Expect = 9e-18,   Method: Composition-based stats.
 Identities = 34/88 (38%), Positives = 51/88 (57%), Gaps = 2/88 (2%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L   E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 284 LSVAELKEINRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 343

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQ 114
           M+AV KF+  RG++ +TY+ WWI+ A+ 
Sbjct: 344 MKAVDKFEYRRGYKFSTYATWWIRQAIT 371


>gi|225018358|ref|ZP_03707550.1| hypothetical protein CLOSTMETH_02302 [Clostridium methylpentosum
           DSM 5476]
 gi|224948875|gb|EEG30084.1| hypothetical protein CLOSTMETH_02302 [Clostridium methylpentosum
           DSM 5476]
          Length = 245

 Score = 95.7 bits (237), Expect = 9e-18,   Method: Composition-based stats.
 Identities = 44/159 (27%), Positives = 79/159 (49%), Gaps = 10/159 (6%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P L K EE V+ ++  E  D  A  +L+  +LRLVV IA  +   G+ + +++S G IGL
Sbjct: 42  PPLTKDEERVVFQKLSEK-DPWARDQLIVHNLRLVVYIAKKFESTGIGVEDLISIGTIGL 100

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL---------VKIGTTANQKRLFF 137
           ++AV  F PE+  +LATY+   I+  +  ++ +S  +         +KI    N+  L  
Sbjct: 101 IKAVNTFSPEKNIKLATYASRCIENEILMHLRKSNPIKSEISIDEPLKIDWDGNELLLSD 160

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
            L      +    ++ ++ + +V+   KL   E  ++ M
Sbjct: 161 VLGTENDCVNRGIEDQVERDLIVSCVNKLGDRERSIMQM 199



 Score = 74.1 bits (181), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 27/142 (19%), Positives = 64/142 (45%), Gaps = 11/142 (7%)

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCR----LAGDESLNALINSS-DKNSSQWQDWLVY 206
           N   PE+ + +A   +      I M+ R    +  + S++  +    D N     D L  
Sbjct: 105 NTFSPEKNIKLATYASRCIENEILMHLRKSNPIKSEISIDEPLKIDWDGNELLLSDVLGT 164

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           ++D   + + ++ E    R+++   ++ L  RER I + R         T + ++ +  +
Sbjct: 165 ENDCVNRGIEDQVE----RDLIVSCVNKLGDRERSIMQMRFGMIDGKEHTQKEVADKIGI 220

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S+  + ++E R  K++++ I++
Sbjct: 221 SQSYISRLEKRIIKRLKKEIER 242


>gi|904172|gb|AAB38522.1| flagellin sigma factor [Yersinia enterocolitica (type O:8)]
          Length = 229

 Score = 95.7 bits (237), Expect = 9e-18,   Method: Composition-based stats.
 Identities = 42/238 (17%), Positives = 96/238 (40%), Gaps = 18/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 3   KNSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 62

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I   + E   R W           +RL  N R +   +Q +      P     +A+ L
Sbjct: 63  QRIAPMLDELRQRDW---------APRRLRRNAREVASAMQKVEQRLGAPATEQEVAQNL 113

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++  +E   +      D + + L +  +      +         ++   ++     N R 
Sbjct: 114 DIDLTEYRQILL----DTNNSQLFSYDEWREEHGRTVEPMLEGHEDANPLQHLLEGNLRQ 169

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  +
Sbjct: 170 RVIEAIEALPEREKMVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRARL 225


>gi|318066983|emb|CBY89106.1| RNA polymerase sigma70 factor [Kushneria aurantia]
          Length = 370

 Score = 95.7 bits (237), Expect = 9e-18,   Method: Composition-based stats.
 Identities = 35/91 (38%), Positives = 53/91 (58%), Gaps = 2/91 (2%)

Query: 26  IPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           + ML   E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGN
Sbjct: 280 LAMLPVAELKEINRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 339

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114
           IGLM+AV KF+  RG++ +TY+ WWI+ A+ 
Sbjct: 340 IGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 370


>gi|318066961|emb|CBY89095.1| RNA polymerase sigma70 factor [Halomonas muralis]
          Length = 367

 Score = 95.7 bits (237), Expect = 9e-18,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 46/74 (62%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 294 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 353

Query: 101 LATYSMWWIKAAMQ 114
            +TY+ WWI+ A+ 
Sbjct: 354 FSTYATWWIRQAIT 367


>gi|325264312|ref|ZP_08131043.1| putative RNA polymerase sigma factor RpoD [Clostridium sp. D5]
 gi|324030383|gb|EGB91667.1| putative RNA polymerase sigma factor RpoD [Clostridium sp. D5]
          Length = 288

 Score = 95.3 bits (236), Expect = 9e-18,   Method: Composition-based stats.
 Identities = 47/246 (19%), Positives = 99/246 (40%), Gaps = 13/246 (5%)

Query: 37  LAKRYREHGDL-SAAHRLVTSHLRLVVKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFD 94
           LA R +   D      +L   +   +  +   + G G   + +++ EG I L +AV+ FD
Sbjct: 6   LAARIQAGIDEAENMLQLWQQNEPFIRMMGRRFAGQGKAELDDLMQEGYIALCEAVRHFD 65

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
            E+      Y+ +WIK  M+ YI      V+I T A        +RR    +        
Sbjct: 66  SEQAVPFINYAAFWIKQGMKRYIENCCGTVRIPTHARDW-----VRRYGKIVAEYCKYYG 120

Query: 155 KPEQVVAIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              +   +   LN+S  ++  +  +  +    SLN  +   D +    ++++  + D + 
Sbjct: 121 SDPEDDVLCALLNISREKLQAVRKSEHMGKICSLNEPLGQEDGD-LNMEEFIASEEDLEG 179

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           +  + + + +N + ML  ++  L  ++  +   R L     TL        ++++ V   
Sbjct: 180 ET-VRRLDYQNMKEMLWEAVEGLEEKQAEVIRCRFLDH--KTLRETGELIGITKDAVVHQ 236

Query: 273 EARAFK 278
           +  A +
Sbjct: 237 QNNALR 242


>gi|295399263|ref|ZP_06809245.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|294978729|gb|EFG54325.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
          Length = 155

 Score = 95.3 bits (236), Expect = 9e-18,   Method: Composition-based stats.
 Identities = 29/110 (26%), Positives = 52/110 (47%), Gaps = 1/110 (0%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  YI        L  +EE    +   + GD  A + L+  +LRLV  I   +   G  +
Sbjct: 18  LVSYIKNNAFPQPLSAKEEEKYLQLMAK-GDEQARNILIEHNLRLVAHIVKKFENTGEDV 76

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            +++S G IGL++A++ +   +G +LATY+   I+  +  ++       K
Sbjct: 77  EDLISIGTIGLIKAIESYSSNKGTKLATYAARCIENEILMHLRSLKKTRK 126


>gi|299472406|emb|CBN77594.1| RpoD family RNA polymerase sigma factor [Ectocarpus siliculosus]
          Length = 242

 Score = 95.3 bits (236), Expect = 9e-18,   Method: Composition-based stats.
 Identities = 47/229 (20%), Positives = 93/229 (40%), Gaps = 29/229 (12%)

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EG I L  A +++DP+RG R  TY+ W ++AA +       + + I      +  
Sbjct: 14  MDLIQEGAIALHLAAERYDPQRGVRFFTYADWSLRAAFERAEASQATTIAIPRYVYVQ-- 71

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
                  K  L+AI   +  P+    +A  L +SE ++  +  R    +S+N ++ SS  
Sbjct: 72  -------KRRLKAILGQHCGPQTSQDLATSLGISERQLAKLLRRAKDCQSMNRVLVSSG- 123

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV-- 253
                    + +     Q   +   R +    L   +  L P+E  +   R         
Sbjct: 124 -------VALGEMIPGAQSCEDILRRLDAEASLVGLLGTLKPQEEEVIVHRYGLFGRRRK 176

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQKPRY 302
           +   +++   VSR+ V ++   A +K++ S +            Q+PR+
Sbjct: 177 STPAVAAVMGVSRQYVGRVHRSALEKMRASFEAD----------QQPRF 215


>gi|126653717|ref|ZP_01725635.1| sigma factor SigD [Bacillus sp. B14905]
 gi|126589681|gb|EAZ83817.1| sigma factor SigD [Bacillus sp. B14905]
          Length = 256

 Score = 95.3 bits (236), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 44/246 (17%), Positives = 92/246 (37%), Gaps = 20/246 (8%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQA 89
           +E  L  R+    D  A   L+  ++ LV              +   ++ S G IGL  A
Sbjct: 8   DEQKLWNRWIHERDPDAGDLLIKKYISLVSYHVQRISAGLPKSVSRDDLTSLGMIGLFDA 67

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + KFD  R  +  TY+ + ++ A+ + + R    +        K+L   +       + +
Sbjct: 68  LNKFDINRDLKFDTYASFRVRGAIIDGL-RKEDWLPRSAREKAKKLDAQI-------EQL 119

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
               ++      +AK + V   +V         +   S+N      D+     + +++  
Sbjct: 120 EQKYMRHVTPEELAKHMEVPVEDVYQTVQEHFFSNVLSINE---QQDQEEVDGKSFVI-- 174

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            D   +   +   +    + L  ++  LN +E+ +      +E  +TL  +    E+S  
Sbjct: 175 RDDTTKTPEQSVVKSELLDDLAENIQKLNEKEQLVLSLFYTEE--LTLTEIGEMLELSTS 232

Query: 268 RVRQIE 273
           R+ QI 
Sbjct: 233 RISQIH 238


>gi|304398826|ref|ZP_07380696.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Pantoea sp.
           aB]
 gi|308187260|ref|YP_003931391.1| RNA polymerase sigma factor for flagellar operon [Pantoea vagans
           C9-1]
 gi|304353530|gb|EFM17907.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Pantoea sp.
           aB]
 gi|308057770|gb|ADO09942.1| RNA polymerase sigma factor for flagellar operon [Pantoea vagans
           C9-1]
          Length = 240

 Score = 95.3 bits (236), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 43/238 (18%), Positives = 99/238 (41%), Gaps = 17/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS          N + +   + R++  L        +      +A++L
Sbjct: 73  QRIRGAMLDEL-RSRDWAPRSVRRNAREVAGAMHRVEQSL-------GRSASEQEVAQQL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           NVS  E   +      D + + L +  +          +     +E   + +    + R 
Sbjct: 125 NVSMEEYRQILL----DTNNSQLFSYDEYREEHGDSAELVTEGHEEANPLHQLLEGSLRE 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  ++  L  RE+ +       +  + L+ + +  +V   RV Q+ ++A K+++  +
Sbjct: 181 RVIEAIEALPDREKMVLTLYY--QEELNLKEIGAVLDVGESRVSQLHSQAIKRLRARL 236


>gi|121488737|emb|CAJ18252.1| sigma 70-type sigma factor [Chlorobium limicola]
          Length = 165

 Score = 95.3 bits (236), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 38/170 (22%), Positives = 74/170 (43%), Gaps = 11/170 (6%)

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           + +EGN+GL +A  +FD  RGF+  +Y++WWI+ ++ + +     +V++    N+     
Sbjct: 2   LXNEGNLGLXKAXXRFDETRGFKFISYAVWWIRQSILQALAEQSRIVRLP--LNRVGTLN 59

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            + +    L+   + +        +A  L++   +V           S++A     D N 
Sbjct: 60  KISKAYSQLEQEYERD---PNTKELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDN- 115

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
            +  D L  D    +  L     R +    + RS+SVL PRE  +  +  
Sbjct: 116 -RLLDVLQNDGHMPDHTL----NRDSLTLEVERSLSVLAPREADVIRSYF 160


>gi|213583576|ref|ZP_03365402.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-0664]
          Length = 201

 Score = 95.3 bits (236), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 39/214 (18%), Positives = 92/214 (42%), Gaps = 14/214 (6%)

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           + + +++  G IGL+ AV ++D  +G    TY++  I+ AM + + RS   V      N 
Sbjct: 1   MELDDLLQAGGIGLLNAVDRYDALQGTAFTTYAVQRIRGAMLDEL-RSRDWVPRSVRRNA 59

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
           + +   + +L+  L        +      +A++L +  +E   M      D + + L + 
Sbjct: 60  REVAQAMGQLEQEL-------GRNATETEVAERLGIPVAEYRQMLL----DTNNSQLFSY 108

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            +          +   + Q++  + +    + R  +  ++  L  RE+ +       +  
Sbjct: 109 DEWREEHGDSIELVTEEHQQENPLHQLLEGDLRQRVMDAIESLPEREQLVLTLYY--QEE 166

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 167 LNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 200


>gi|293395614|ref|ZP_06639897.1| DNA-directed RNA polymerase sigma subunit FliA [Serratia odorifera
           DSM 4582]
 gi|291421933|gb|EFE95179.1| DNA-directed RNA polymerase sigma subunit FliA [Serratia odorifera
           DSM 4582]
          Length = 240

 Score = 95.3 bits (236), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 44/238 (18%), Positives = 103/238 (43%), Gaps = 17/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KHSLWLRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      + + +   ++RL+  L        +P   + +A+ +
Sbjct: 73  QRIRGAMLDEL-RSRDWVPRSVRRHARDVAQAMQRLEQQL-------GRPAGELEVAQAM 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           N+S ++   +      D + + L +  +    Q +          E   + +    + R 
Sbjct: 125 NMSLADYRQILM----DTNNSQLFSYDEWREEQGESAEPLLEGHAEANPLHQLLEGSLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  +
Sbjct: 181 RVIDAIEALPEREKLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRARL 236


>gi|51596050|ref|YP_070241.1| flagellar biosynthesis sigma factor [Yersinia pseudotuberculosis IP
           32953]
 gi|153949581|ref|YP_001401249.1| flagellar biosynthesis sigma factor [Yersinia pseudotuberculosis IP
           31758]
 gi|170024605|ref|YP_001721110.1| flagellar biosynthesis sigma factor [Yersinia pseudotuberculosis
           YPIII]
 gi|186895155|ref|YP_001872267.1| flagellar biosynthesis sigma factor [Yersinia pseudotuberculosis
           PB1/+]
 gi|51589332|emb|CAH20954.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           pseudotuberculosis IP 32953]
 gi|152961076|gb|ABS48537.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           pseudotuberculosis IP 31758]
 gi|169751139|gb|ACA68657.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Yersinia
           pseudotuberculosis YPIII]
 gi|186698181|gb|ACC88810.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Yersinia
           pseudotuberculosis PB1/+]
          Length = 240

 Score = 95.3 bits (236), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 39/238 (16%), Positives = 96/238 (40%), Gaps = 17/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KNSLWKRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +               + +  N R +   +Q +     +P     +A+ L
Sbjct: 73  QRIRGAMLDELR--------SRDWAPRSVRRNAREVASAMQQVEQRVGRPATEQEVAQVL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   E   +      D + + L +  +      +         ++   ++     N R 
Sbjct: 125 DIGLVEYRQILL----DTNNSQLFSYDEWREEHGESVEPLLEGHEDANPLKHLLEGNLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  +
Sbjct: 181 RVIEAIEALPEREKMVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRARL 236


>gi|300717210|ref|YP_003742013.1| RNA polymerase sigma factor for flagellar operon [Erwinia
           billingiae Eb661]
 gi|299063046|emb|CAX60166.1| RNA polymerase sigma factor for flagellar operon [Erwinia
           billingiae Eb661]
          Length = 240

 Score = 95.3 bits (236), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 45/239 (18%), Positives = 101/239 (42%), Gaps = 19/239 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KNSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +               + +  N R + G +  +  +  +      +A  L
Sbjct: 73  QRIRGAMLDELR--------SRDWAPRSVRRNAREVAGAMHKVEQSLGRTATEQEVAASL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV-LIEKEERKNRR 225
           +VS  E   +       ++ N+ + S D+   +  D      DG E+   + +    N R
Sbjct: 125 DVSLQEYRQILL-----DTNNSQLFSYDEFREEHGDTAELVTDGHEEANPLHQLMEGNLR 179

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  +
Sbjct: 180 ERVIEAIEALPDREKMVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRARL 236


>gi|330946033|gb|EGH47317.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. pisi
           str. 1704B]
          Length = 166

 Score = 94.9 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 38/172 (22%), Positives = 73/172 (42%), Gaps = 14/172 (8%)

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-D 183
           ++      K L   LR  +   Q + D+   PE++  + +K       ++ +N R++  D
Sbjct: 3   RLPIHVV-KELNVYLRAARELTQKL-DHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVD 60

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SL         +     D L  D       L++ ++       + + +S L  ++R + 
Sbjct: 61  VSL------GPDSDKTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTEKQREVV 111

Query: 244 EARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
             R         TLE++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 112 IRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSSES 163


>gi|238756654|ref|ZP_04617944.1| RNA polymerase sigma factor for flagellar operon [Yersinia ruckeri
           ATCC 29473]
 gi|238705123|gb|EEP97550.1| RNA polymerase sigma factor for flagellar operon [Yersinia ruckeri
           ATCC 29473]
          Length = 240

 Score = 94.9 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 39/238 (16%), Positives = 97/238 (40%), Gaps = 17/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KNSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +               + +  N R +   ++ +     +P     +A+ L
Sbjct: 73  QRIRGAMLDELR--------SRDWAPRSVRRNAREVAQAMRQVEQKVGRPASEQEVAQIL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++S  E   +      D + + L +  +      +          +   +++    N R 
Sbjct: 125 DISLVEYRQILL----DTNNSQLFSYDEWREEHGESVEPVLDGLDDANPLQQLLEGNLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  +
Sbjct: 181 RVIEAIEALPEREKMVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRARL 236


>gi|299534757|ref|ZP_07048087.1| RNA polymerase sigma factor SigD [Lysinibacillus fusiformis ZC1]
 gi|298729845|gb|EFI70390.1| RNA polymerase sigma factor SigD [Lysinibacillus fusiformis ZC1]
          Length = 256

 Score = 94.9 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 47/247 (19%), Positives = 97/247 (39%), Gaps = 22/247 (8%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQ 88
           +E  L  R+    D  A   L+  ++ LV        G GLP      ++ S G +GL  
Sbjct: 8   DEQKLWNRWIHERDPDAGDLLIKKYISLVSYHVQR-IGAGLPKSVSRDDLTSLGMVGLFD 66

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A+ KFD  R  +  TY+ + ++ A+ + + R    +        K+L   +       + 
Sbjct: 67  ALNKFDINRDLKFDTYASFRVRGAIIDGL-RKEDWLPRSAREKAKKLDAQI-------EQ 118

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +    ++      +A+ + VS  +V         +   S+N      D+  +  + +++ 
Sbjct: 119 LEQKYMRHVTPEELAEHMEVSVEDVYQTVQEHFFSNVLSINE---QQDQEETDGKTFVI- 174

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
             D   +   +   +    + L  ++  LN +E+ +      +E  +TL  +    E+S 
Sbjct: 175 -RDDTTKTPEQAIIKSELLDDLAENIQKLNEKEQLVLSLFYTEE--LTLTEIGEMLELST 231

Query: 267 ERVRQIE 273
            R+ QI 
Sbjct: 232 SRISQIH 238


>gi|318066951|emb|CBY89090.1| RNA polymerase sigma70 factor [Halomonas hydrothermalis]
          Length = 370

 Score = 94.9 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 46/74 (62%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 297 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 356

Query: 101 LATYSMWWIKAAMQ 114
            +TY+ WWI+ A+ 
Sbjct: 357 FSTYATWWIRQAIT 370


>gi|1706832|sp|P52621|FLIA_YEREN RecName: Full=RNA polymerase sigma factor for flagellar operon;
           AltName: Full=Sigma-27; AltName: Full=Sigma-28; AltName:
           Full=Sigma-F factor
 gi|790557|gb|AAC43394.1| FliA [Yersinia enterocolitica (type O:9)]
          Length = 230

 Score = 94.9 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 39/238 (16%), Positives = 97/238 (40%), Gaps = 17/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 3   KNSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDRLQGTAFTTYAV 62

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +               + +  N R +   +Q +     +P     +A+ L
Sbjct: 63  QRIRGAMLDELR--------SRDWAPRSVRRNAREVASAMQKVEQRLGRPATEQEVAQNL 114

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++  +E   +      D + + L +  +      +         ++   ++     N R 
Sbjct: 115 DIDLTEYRQILL----DTNNSQLFSYDEWREEHGESVEPMLEGHEDANPLQHLLEGNLRQ 170

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  +
Sbjct: 171 RVIEAIEALPEREKMVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRARL 226


>gi|312282731|dbj|BAJ34231.1| unnamed protein product [Thellungiella halophila]
          Length = 269

 Score = 94.9 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 35/81 (43%), Positives = 53/81 (65%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A  ++   + RLVV IA GY+G GL + +++ EG+IGL++  ++FDPERG++L+TY  
Sbjct: 179 REAREKITRCYRRLVVSIATGYQGKGLNLQDLIQEGSIGLLRGAERFDPERGYKLSTYVY 238

Query: 107 WWIKAAMQEYILRSWSLVKIG 127
           WWIK A+   I     LVK+ 
Sbjct: 239 WWIKQAILRAIAHKSRLVKLP 259


>gi|82702442|ref|YP_412008.1| sigma 28 (flagella/sporulation) [Nitrosospira multiformis ATCC
           25196]
 gi|82410507|gb|ABB74616.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Nitrosospira
           multiformis ATCC 25196]
          Length = 242

 Score = 94.9 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 42/240 (17%), Positives = 97/240 (40%), Gaps = 17/240 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             + +     LV +IA          +   ++V  G IGLM+A+ +++   G +  TY+ 
Sbjct: 10  KQQHIVEFTPLVKRIANHMMARLPVSVEADDLVQVGMIGLMEALNRYEEMPGAQFETYAQ 69

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + +   L +             +R+++  +  +     +      IA++L
Sbjct: 70  QRIRGAMLDELRQLDWLPRGARRV--------MRQIESAINVLQHRLGRSPSERQIAEEL 121

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            VS      M     G +    LI+  D +  +  D+L  +        +      + R 
Sbjct: 122 GVSIESYQQMLFEAKGTQ----LIHYEDFSDDEDDDFLERNCADNTADPLAALLDGDLRR 177

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +L  ++ +L  RE+ +       E  +  + + +   VS  R+ Q+ ++A  +++  +++
Sbjct: 178 ILINAIEILPEREKTLMGLYY--EQELNFKEIGAVLGVSESRICQMHSQAIARLRVRLKE 235


>gi|318066979|emb|CBY89104.1| RNA polymerase sigma70 factor [Halomonas venusta]
          Length = 370

 Score = 94.9 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 46/74 (62%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 297 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 356

Query: 101 LATYSMWWIKAAMQ 114
            +TY+ WWI+ A+ 
Sbjct: 357 FSTYATWWIRQAIT 370


>gi|318066911|emb|CBY89070.1| RNA polymerase sigma70 factor [Chromohalobacter nigrandesensis]
          Length = 367

 Score = 94.9 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 46/74 (62%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 294 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 353

Query: 101 LATYSMWWIKAAMQ 114
            +TY+ WWI+ A+ 
Sbjct: 354 FSTYATWWIRQAIT 367


>gi|318066963|emb|CBY89096.1| RNA polymerase sigma70 factor [Halomonas neptunia]
          Length = 368

 Score = 94.9 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 46/74 (62%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 295 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 354

Query: 101 LATYSMWWIKAAMQ 114
            +TY+ WWI+ A+ 
Sbjct: 355 FSTYATWWIRQAIT 368


>gi|318066929|emb|CBY89079.1| RNA polymerase sigma70 factor [Halomonas boliviensis]
          Length = 368

 Score = 94.9 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 46/74 (62%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 295 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 354

Query: 101 LATYSMWWIKAAMQ 114
            +TY+ WWI+ A+ 
Sbjct: 355 FSTYATWWIRQAIT 368


>gi|318066971|emb|CBY89100.1| RNA polymerase sigma70 factor [Halomonas sulfidaeris]
          Length = 368

 Score = 94.9 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 46/74 (62%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 295 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 354

Query: 101 LATYSMWWIKAAMQ 114
            +TY+ WWI+ A+ 
Sbjct: 355 FSTYATWWIRQAIT 368


>gi|318066905|emb|CBY89067.1| RNA polymerase sigma70 factor [Chromohalobacter canadensis]
          Length = 367

 Score = 94.9 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 46/74 (62%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 294 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 353

Query: 101 LATYSMWWIKAAMQ 114
            +TY+ WWI+ A+ 
Sbjct: 354 FSTYATWWIRQAIT 367


>gi|325674464|ref|ZP_08154152.1| stress response/stationary phase sigma factor SigF [Rhodococcus
           equi ATCC 33707]
 gi|325554724|gb|EGD24398.1| stress response/stationary phase sigma factor SigF [Rhodococcus
           equi ATCC 33707]
          Length = 269

 Score = 94.9 bits (235), Expect = 1e-17,   Method: Composition-based stats.
 Identities = 41/234 (17%), Positives = 97/234 (41%), Gaps = 20/234 (8%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            RL  + L +  ++A  YR  G+P +E+     + L+ A ++FDP RG     Y++  ++
Sbjct: 45  DRLCVAALPMAYRVAGRYRNRGVPTAELRQVAALALVGAARRFDPSRGTDFIPYAVTSVR 104

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
             +++Y         +     +  L      ++  +++++    +  ++  +A  L +  
Sbjct: 105 GEIRKYFRDFTWSTHVPRRLQESHLA-----VRNRMESLSTELGRTVRLDEVAHSLGMPV 159

Query: 171 SEVISMNC--RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            E         L   ESL+A     D +  +       D D           R   R++L
Sbjct: 160 EEAEEAERVGELYSCESLDAT--PVDGSVPRLHTTGDVDAD---------LSRVEHRHLL 208

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            R M+ L+ R+R +   R    + ++   ++ +  +S+  V ++  ++ + ++ 
Sbjct: 209 RRLMATLDERQRTLLWLRYF--HQMSQSEIAEQVGLSQMHVSRLLRQSLEHLRR 260


>gi|28210822|ref|NP_781766.1| RNA polymerase sigma-G factor [Clostridium tetani E88]
 gi|28203260|gb|AAO35703.1| RNA polymerase sigma-G factor [Clostridium tetani E88]
          Length = 161

 Score = 94.5 bits (234), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 32/177 (18%), Positives = 72/177 (40%), Gaps = 16/177 (9%)

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I   ++ Y+  + S +++  +   + + +   +++  L A  D   K   V  IAK+L+
Sbjct: 1   MIIGEIRRYLRDNNS-IRVSRSL--RDIAYKALQVRDKLIAKND---KEPTVSEIAKELD 54

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +   +V+     +    SL   I     +S    D +    +  +  +            
Sbjct: 55  IPREDVVFALDAIQDPLSLFEPIYQDGGDSIYVMDQISDTKNLDDSWIENIA-------- 106

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +  +M  LN RE+ I   R    +  T   ++ E  +S+ +V ++E  A K +++ +
Sbjct: 107 IKEAMRNLNKREKLILSLRFF--DGRTQMEVADEIGISQAQVSRLEKTALKHMRKFV 161


>gi|318066993|emb|CBY89111.1| RNA polymerase sigma70 factor [Salinicola halophilus]
          Length = 368

 Score = 94.5 bits (234), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 46/74 (62%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 295 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 354

Query: 101 LATYSMWWIKAAMQ 114
            +TY+ WWI+ A+ 
Sbjct: 355 FSTYATWWIRQAIT 368


>gi|255092173|ref|ZP_05321651.1| sporulation sigma factor SigK [Clostridium difficile CIP 107932]
 gi|255649691|ref|ZP_05396593.1| sporulation sigma factor SigK [Clostridium difficile QCD-37x79]
          Length = 105

 Score = 94.5 bits (234), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 27/91 (29%), Positives = 48/91 (52%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L  +EE     +++   D SA   L+  ++RLV  IA  Y        +++S G IGL+
Sbjct: 10  PLTPEEEIEYLTKFKIENDKSAKDTLIERNMRLVAYIAKKYNNSTEDQDDLISIGTIGLI 69

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           +A++ ++ ++G RLATY+   I+  +   I 
Sbjct: 70  KAIETYNIDKGTRLATYASRCIENEILMNIR 100


>gi|318066975|emb|CBY89102.1| RNA polymerase sigma70 factor [Halomonas variabilis]
          Length = 368

 Score = 94.5 bits (234), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 46/74 (62%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 295 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 354

Query: 101 LATYSMWWIKAAMQ 114
            +TY+ WWI+ A+ 
Sbjct: 355 FSTYATWWIRQAIT 368


>gi|257438884|ref|ZP_05614639.1| RNA polymerase sigma-K factor [Faecalibacterium prausnitzii A2-165]
 gi|257198699|gb|EEU96983.1| RNA polymerase sigma-K factor [Faecalibacterium prausnitzii A2-165]
          Length = 153

 Score = 94.5 bits (234), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 39/125 (31%), Positives = 60/125 (48%), Gaps = 5/125 (4%)

Query: 22  EIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           E    P  L  +EE       R  GD SA  +++  +LRLV  +A  Y        +++S
Sbjct: 24  EAGSFPKPLSAREEIETFAALR-AGDRSAREKIIRHNLRLVAHVAKKYYAQPGDQEDLIS 82

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
            G IGLM+AV  FD  R  R ATY+   I+ A+   + R+ + ++IGT +    +   L 
Sbjct: 83  IGTIGLMKAVDTFDITRKARFATYASRCIENAI---LTRANAGLRIGTISTALGVVVVLF 139

Query: 141 RLKGH 145
           R+   
Sbjct: 140 RVYRE 144


>gi|318066903|emb|CBY89066.1| RNA polymerase sigma70 factor [Chromohalobacter beijerinckii]
          Length = 367

 Score = 94.5 bits (234), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 46/74 (62%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 294 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 353

Query: 101 LATYSMWWIKAAMQ 114
            +TY+ WWI+ A+ 
Sbjct: 354 FSTYATWWIRQAIT 367


>gi|318066907|emb|CBY89068.1| RNA polymerase sigma70 factor [Chromohalobacter israelensis]
 gi|318066913|emb|CBY89071.1| RNA polymerase sigma70 factor [Chromohalobacter salexigens]
          Length = 367

 Score = 94.5 bits (234), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 36/94 (38%), Positives = 53/94 (56%), Gaps = 11/94 (11%)

Query: 32  QEEYVLA---------KRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           +EE VL          +R    E     A   +V ++LRLV+ IA  Y   GL   +++ 
Sbjct: 274 EEEMVLLPVSHIKEVNRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 333

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114
           EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+ 
Sbjct: 334 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 367


>gi|317055222|ref|YP_004103689.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit [Ruminococcus
           albus 7]
 gi|315447491|gb|ADU21055.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Ruminococcus
           albus 7]
          Length = 127

 Score = 94.5 bits (234), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 30/87 (34%), Positives = 43/87 (49%), Gaps = 1/87 (1%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L   EE    ++  E GD  A   L+  +LRLV  I   Y        +++S G IGL+
Sbjct: 32  PLTAAEERDCFEKMSE-GDAGARDTLIRHNLRLVAHIIKKYYANSSDQDDLISIGTIGLI 90

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQ 114
           +AV+ FD  +G R ATY    ++ A Q
Sbjct: 91  KAVQTFDYTKGTRFATYGSRCVENATQ 117


>gi|219112653|ref|XP_002178078.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217410963|gb|EEC50892.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 358

 Score = 94.5 bits (234), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 53/261 (20%), Positives = 115/261 (44%), Gaps = 22/261 (8%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG----LPISEVVSEGNIGLMQAVKKF 93
           A R      L A ++LVTS+LR+V  +   Y   G        +++ EG I L++A +KF
Sbjct: 89  AIRQTIEEGLEAKNQLVTSNLRMVQSVVNTYIRNGLTAQYNAGDMMQEGIIALIRAAEKF 148

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           +P+RG++ +TY+M+W++A+++   +    ++ +      +RL  N +RL    + +  + 
Sbjct: 149 EPDRGWKFSTYAMYWVRASVKRSQIYQSRVITVP-----QRLHENHKRLLKVEREMEADL 203

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSS---DKNSSQWQDWLVYDHD 209
            +    + +  ++ +S+ +V      +    +SL+  +++S       +     +     
Sbjct: 204 GRKPSRIELGAEIGLSKLQVDRCFAAMEQRCQSLDQKLSNSKRPMSGDTSKDTLMEIIGS 263

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSV-LNPRERRIFEARRL--------QENPVTLENLSS 260
             E    +   R   R  L  ++   L+P E  +   R               T+  LS 
Sbjct: 264 KTEGNDFDSLNRIFLREDLIETLHRHLDPAEVELLLLRYGFKEVASSKLGGQPTIAELSR 323

Query: 261 EFEVSRERVRQIEARAFKKVQ 281
              +  ++VR++  R+ K ++
Sbjct: 324 TVGLKPDKVRRMINRSLKHLK 344


>gi|260762514|ref|ZP_05874851.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 2 str.
           86/8/59]
 gi|260672940|gb|EEX59761.1| RNA polymerase factor sigma-32 [Brucella abortus bv. 2 str.
           86/8/59]
          Length = 131

 Score = 94.1 bits (233), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 38/108 (35%), Positives = 64/108 (59%), Gaps = 3/108 (2%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
           M  ++          +   I      P LE++EE  LA R++E  D  A HR+ ++H+RL
Sbjct: 27  MAVRSFPAAAASSQSM---IRSAMSAPYLEREEERALAIRWKETKDQDALHRITSAHMRL 83

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           V+ +A  +R + LP+S+++ EG +GL++A  +FDP+R  R +TY+ WW
Sbjct: 84  VISMAGRFRKFKLPMSDLIQEGYVGLLEAAARFDPDRDVRFSTYASWW 131


>gi|239907027|ref|YP_002953768.1| RNA polymerase sigma factor for flagellar operon [Desulfovibrio
           magneticus RS-1]
 gi|239796893|dbj|BAH75882.1| RNA polymerase sigma factor for flagellar operon [Desulfovibrio
           magneticus RS-1]
          Length = 264

 Score = 94.1 bits (233), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 49/251 (19%), Positives = 101/251 (40%), Gaps = 21/251 (8%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           D      +V  +   +  +A   R    P   ++E++S G +GL++A+ +F PE G +  
Sbjct: 32  DARDRQEIVRHYSPKIKIVASRLRAKLPPSVELNELISAGAMGLLEALGRFRPELGIKFE 91

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+   IK AM + + R       G     + L    RR++       +++  P  +  +
Sbjct: 92  TYAESRIKGAMLDDLRR-MDWFSRGQRQRVRTLEEASRRIE-------NDSGGPASLEQL 143

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+   ++E EV      L     L+          +  ++   Y  +  E    +  E K
Sbjct: 144 AEATGLTEREVSMGLEALQNQLCLSL--------DAITENISSYQKNQLENEPYKSAEFK 195

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              + L   +  L PRE+ +      +E  + +   S    ++  RV Q+ ++A  ++++
Sbjct: 196 ELVDKLASLIDDLTPREKLVLSLYYGEE--LNMRETSEVMGITEGRVSQLHSQALARLRQ 253

Query: 283 SIQKQVELSSS 293
             + Q  +   
Sbjct: 254 KFKSQYNIEQH 264


>gi|313113343|ref|ZP_07798935.1| sigma-70 region 2 [Faecalibacterium cf. prausnitzii KLE1255]
 gi|310624319|gb|EFQ07682.1| sigma-70 region 2 [Faecalibacterium cf. prausnitzii KLE1255]
          Length = 167

 Score = 94.1 bits (233), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 32/93 (34%), Positives = 46/93 (49%), Gaps = 2/93 (2%)

Query: 22  EIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           E    P  L  +EE       R  GD +A  +L+  +LRLV  I   Y        +++S
Sbjct: 29  ESGSFPRPLSAREETEAFSALR-AGDPAAREKLIRHNLRLVAHIVKKYYALPGDQDDLIS 87

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
            G IGLM+AV  FD +R  R +TY+   I+ A+
Sbjct: 88  IGTIGLMKAVDTFDSDRRARFSTYASRCIENAI 120


>gi|147677461|ref|YP_001211676.1| hypothetical protein PTH_1126 [Pelotomaculum thermopropionicum SI]
 gi|146273558|dbj|BAF59307.1| hypothetical protein [Pelotomaculum thermopropionicum SI]
          Length = 127

 Score = 94.1 bits (233), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 35/105 (33%), Positives = 53/105 (50%), Gaps = 1/105 (0%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           +VNG + L  YI        L ++EE    K     G+  A + L   +LRLV  I   +
Sbjct: 13  LVNGLLLLVSYIANNTFPQPLSEEEEAKYLKLL-NMGNEEARNILTERNLRLVAHIVKKF 71

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
              G    +++S G IGL++A+  F+P +G RLATY+   I+  M
Sbjct: 72  DSTGEDSDDLISIGTIGLIKAINTFNPGKGTRLATYAAKCIENEM 116


>gi|254433106|ref|ZP_05046614.1| RNA polymerase sigma factor, FliA/WhiG family [Nitrosococcus oceani
           AFC27]
 gi|207089439|gb|EDZ66710.1| RNA polymerase sigma factor, FliA/WhiG family [Nitrosococcus oceani
           AFC27]
          Length = 189

 Score = 94.1 bits (233), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 34/204 (16%), Positives = 82/204 (40%), Gaps = 18/204 (8%)

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            IGL++A + ++  +G    TY+   I+ A+ + I R+            + +    R++
Sbjct: 1   MIGLLEAARNYNASQGASFETYAGIRIRGAILDEIRRNDW--------APRSVHRKARQV 52

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
              ++ + +   +  +   +A++L +  +E   +     G    +    +  + S     
Sbjct: 53  AEVMREVENREGRDARDHEVAEELGLPLNEYHRLLQDAGGYRVFSLDEFNEGEESEPLSA 112

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
            L        +   E  + +N R  L  ++  L  RER +     +++  + L  +    
Sbjct: 113 SL--------KGPYEGLQDQNFRGALVEAIEGLPERERLVMSLYYVED--LNLREIGEVL 162

Query: 263 EVSRERVRQIEARAFKKVQESIQK 286
            VS  RV QI ++A  +++  + +
Sbjct: 163 GVSESRVSQIHSQAVLRLRARLSE 186


>gi|318066955|emb|CBY89092.1| RNA polymerase sigma70 factor [Halomonas magadiensis]
          Length = 370

 Score = 94.1 bits (233), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 46/74 (62%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 297 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 356

Query: 101 LATYSMWWIKAAMQ 114
            +TY+ WWI+ A+ 
Sbjct: 357 FSTYATWWIRQAIT 370


>gi|318066925|emb|CBY89077.1| RNA polymerase sigma70 factor [Halomonas aquamarina]
 gi|318066927|emb|CBY89078.1| RNA polymerase sigma70 factor [Halomonas axialensis]
 gi|318066959|emb|CBY89094.1| RNA polymerase sigma70 factor [Halomonas meridiana]
          Length = 370

 Score = 94.1 bits (233), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 46/74 (62%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 297 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 356

Query: 101 LATYSMWWIKAAMQ 114
            +TY+ WWI+ A+ 
Sbjct: 357 FSTYATWWIRQAIT 370


>gi|318066995|emb|CBY89112.1| RNA polymerase sigma70 factor [Salinicola salarius]
          Length = 368

 Score = 94.1 bits (233), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 46/74 (62%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 295 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 354

Query: 101 LATYSMWWIKAAMQ 114
            +TY+ WWI+ A+ 
Sbjct: 355 FSTYATWWIRQAIT 368


>gi|318066915|emb|CBY89072.1| RNA polymerase sigma70 factor [Chromohalobacter sarecensis]
          Length = 369

 Score = 94.1 bits (233), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 46/74 (62%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 296 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 355

Query: 101 LATYSMWWIKAAMQ 114
            +TY+ WWI+ A+ 
Sbjct: 356 FSTYATWWIRQAIT 369


>gi|317970154|ref|ZP_07971544.1| RNA polymerase sigma factor SigF [Synechococcus sp. CB0205]
          Length = 253

 Score = 94.1 bits (233), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 55/237 (23%), Positives = 99/237 (41%), Gaps = 14/237 (5%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG-YRGYGLPISEVVSEGNIGLMQAV 90
            ++  L  RY +  + +  + +V ++L LV K+A       G    ++  EG  GL++AV
Sbjct: 5   DQQQWLLSRYLKDPNHAHRNAVVAANLPLVWKVARRESERSGHSFEDLAQEGVRGLIKAV 64

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           ++FDP  G+ L+T ++ WI+ AM+ Y+       +    +  + +   L+R     +   
Sbjct: 65  ERFDPSLGYTLSTAAVPWIRGAMRHYLRD-----RCRVFSGARNVIELLQRGAALQRRRE 119

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDH 208
              L P    ++A+ L  S+                SL+     SD  +      +    
Sbjct: 120 QQGLSPMNDSSLARALGCSQQRWQEAQALQTCLRVASLDQPGGGSDPETP----LVEQLS 175

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
           D Q        ER   R  L R +  L   +RR+  AR LQ+   T ++L +   +S
Sbjct: 176 DQQAPGQYGWLERCELRRQLWRGLKTLQASQRRLVLARVLQQ--RTWQDLGAMAGIS 230


>gi|225174918|ref|ZP_03728915.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Dethiobacter
           alkaliphilus AHT 1]
 gi|225169558|gb|EEG78355.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Dethiobacter
           alkaliphilus AHT 1]
          Length = 231

 Score = 94.1 bits (233), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 58/248 (23%), Positives = 108/248 (43%), Gaps = 31/248 (12%)

Query: 36  VLAKR---YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
            L KR   YR+ G      R+V +   L+   A  Y G      + V  G  GLM+AV++
Sbjct: 6   ELDKRFLEYRKSGKDEDLERVVEAGRSLIHHFARLYTGGFG--EDAVQAGMEGLMKAVQR 63

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           ++  +G   ATY+   +   ++ Y+ +  S  + G+    K L F + RL   +   T  
Sbjct: 64  YEVGKGTAFATYAAHCVMGEIRHYVRKESSYYRPGS---IKDLQFRVARLVDEVLKETGE 120

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
              P  V  IAK+LNV E  V+      AG  SL+ +            D +  +     
Sbjct: 121 ---PPGVSEIAKRLNVKEEGVVQAMR--AGLVSLDDV----------EVDKIRAEKYETF 165

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           ++ IE       R +L +++  LN  +RR+      ++  +T    + +  +S+ +V ++
Sbjct: 166 KLPIED------RLVLEQAIKKLNDLQRRVVYLLFYKD--LTQTQTAEKLGISQRKVSRV 217

Query: 273 EARAFKKV 280
             ++ +++
Sbjct: 218 LHKSLQEM 225


>gi|218289804|ref|ZP_03494004.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
 gi|218240095|gb|EED07280.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
          Length = 179

 Score = 94.1 bits (233), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 43/218 (19%), Positives = 75/218 (34%), Gaps = 64/218 (29%)

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
             +   G+   +++S G +GL++AV  + P +G + ATY+   I                
Sbjct: 2   KKFDTSGIDQDDLISIGTVGLIKAVDTYQPSKGTKFATYAARCI---------------- 45

Query: 126 IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
                 Q  +   LR  +                                       D S
Sbjct: 46  ------QNEILMQLRAQRKS-----------------------------------RKDVS 64

Query: 186 LNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           L + I +  + N     D L  + D  E  +  + E    R    + + VL+ RER++ E
Sbjct: 65  LYSPIGTDKEGNEITIGDILFSESDSTEDEVSRRMELNTMR----QLLDVLDERERKVIE 120

Query: 245 ARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKV 280
            R    +    T   ++   E+SR  V ++E RA  K+
Sbjct: 121 LRFGLADGREWTQNEVADSLEISRSYVSRLEKRALLKM 158


>gi|254255074|ref|ZP_04948391.1| DNA-directed RNA polymerase specialized sigma subunit [Burkholderia
           dolosa AUO158]
 gi|124899719|gb|EAY71562.1| DNA-directed RNA polymerase specialized sigma subunit [Burkholderia
           dolosa AUO158]
          Length = 241

 Score = 94.1 bits (233), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 42/236 (17%), Positives = 99/236 (41%), Gaps = 26/236 (11%)

Query: 54  VTSHLRLVVKIAMGYRGYG---LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           +  +  LV ++     G+G   +   ++   G +GL++A++++  E     A Y++  I+
Sbjct: 28  IAEYAPLVKRVVGKLAGHGAAGIDRDDLEQIGIMGLLEALRRYG-EPDDAFANYAVVRIR 86

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            A+ + + R             ++    LR  +  L++        + + A A  ++  E
Sbjct: 87  GAVLDELRRQD-----WRPRTARQGAHRLRSCERALRSKLGREPGKDDICA-ALGIDGVE 140

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            + I ++       SL+ LIN+      + Q                 E +   R  + +
Sbjct: 141 YDRIMLDDSANELMSLDELINAHGDVPGEAQAGP--------------EAQVLARRGIEQ 186

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ++ VL+ RE+R+ +     E  +TL  + +   ++  R+ Q+   A KK++  +++
Sbjct: 187 ALLVLDEREQRVIQLYY--EFDLTLPEIGAVLNLTTARICQLHRGALKKMRGYLER 240


>gi|318066957|emb|CBY89093.1| RNA polymerase sigma70 factor [Halomonas maura]
          Length = 365

 Score = 94.1 bits (233), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 36/94 (38%), Positives = 53/94 (56%), Gaps = 11/94 (11%)

Query: 32  QEEYVLA---------KRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           +EE VL          +R    E     A   +V ++LRLV+ IA  Y   GL   +++ 
Sbjct: 272 EEEMVLLPVTEIKEVNRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 331

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114
           EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+ 
Sbjct: 332 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 365


>gi|144971|gb|AAA23295.1| ORF1 [Corynebacterium diphtheriae]
 gi|144975|gb|AAA23298.1| open reading frame [Corynebacterium diphtheriae PW8]
          Length = 143

 Score = 94.1 bits (233), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 25/139 (17%), Positives = 60/139 (43%), Gaps = 7/139 (5%)

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
               +      +A++  + ES++  +  +     SL+  + + ++  +   D++      
Sbjct: 3   QQLGREATNEELAEESGIEESKIEMLLRQSRDPVSLDMPVGADEE--APLGDFIEDSEAT 60

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRER 268
             +  +    R    + +   +  L  RE+ +   R   ++  P TL+ +  +F +SRER
Sbjct: 61  DAESAVVASLR---HSDIRTVLDTLEQREQDVIRLRYGLDDGVPRTLDQIGRQFGLSRER 117

Query: 269 VRQIEARAFKKVQESIQKQ 287
           VRQIE     K+++  + +
Sbjct: 118 VRQIEREVMSKLRDGARAE 136


>gi|119503682|ref|ZP_01625765.1| flagellar biosynthesis sigma factor FliA [marine gamma
           proteobacterium HTCC2080]
 gi|119460744|gb|EAW41836.1| flagellar biosynthesis sigma factor FliA [marine gamma
           proteobacterium HTCC2080]
          Length = 237

 Score = 94.1 bits (233), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 45/252 (17%), Positives = 88/252 (34%), Gaps = 38/252 (15%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPER 97
           Y   G  S    LV +HL LV +IA          + + +++  G IGL++A      + 
Sbjct: 12  YGACGGASQGDALVRAHLPLVKRIAQQLLVRLPAHIEMDDLIQVGLIGLLKASDDHQADS 71

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G + +TY+   I+ AM + +     L         + +  +L R+   ++       +P 
Sbjct: 72  GAQFSTYAAIRIRGAMLDELRSRDWL--------PRSVQRDLGRVAAAIERAEQRVGRPA 123

Query: 158 QVVAIAKKLNVSESEVISMN-----CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
               IA +L +       ++      R+   E L+         S  +            
Sbjct: 124 TDQEIADQLEMDLDSYQQLSGELACARIGQLEELDVPTEVDATTSIVFD----------- 172

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
                      RR  +  ++  L  +E  +          + L+ +     VS  RV QI
Sbjct: 173 ---------SARREAVVEAIGRLPEKEGLMLSLYYT--EGLNLKEIGMVLNVSESRVSQI 221

Query: 273 EARAFKKVQESI 284
             +A  +++  +
Sbjct: 222 HGQAVARLRSKL 233


>gi|318066919|emb|CBY89074.1| RNA polymerase sigma70 factor [Halomonas alimentaria]
          Length = 362

 Score = 94.1 bits (233), Expect = 2e-17,   Method: Composition-based stats.
 Identities = 35/88 (39%), Positives = 52/88 (59%), Gaps = 2/88 (2%)

Query: 29  LEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L  QE   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGL
Sbjct: 275 LPVQEIKEVNRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL 334

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQ 114
           M+AV KF+  RG++ +TY+ WWI+ A+ 
Sbjct: 335 MKAVDKFEYRRGYKFSTYATWWIRQAIT 362


>gi|77020162|ref|YP_338218.1| RNA polymerase sigma factor, putative [Bacillus phage Gamma]
 gi|85701416|ref|YP_460001.1| putative RNA polymerase sigma subunit [Bacillus phage WBeta]
 gi|89152515|ref|YP_512346.1| sigma70 factor [Bacillus phage Fah]
 gi|196033415|ref|ZP_03100827.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus cereus
           W]
 gi|76445738|gb|ABA42728.1| sigma70 factor [Bacillus phage Fah]
 gi|76564064|gb|ABA46452.1| RNA polymerase sigma factor, putative [Bacillus phage Gamma]
 gi|83658652|gb|ABC40436.1| putative RNA polymerase sigma subunit [Bacillus phage WBeta]
 gi|83658705|gb|ABC40488.1| putative RNA polymerase sigma subunit [Bacillus phage Gamma isolate
           d'Herelle]
 gi|195993849|gb|EDX57805.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus cereus
           W]
          Length = 248

 Score = 93.7 bits (232), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 49/234 (20%), Positives = 94/234 (40%), Gaps = 30/234 (12%)

Query: 51  HRLVTSHLRLVVKIA-MGY--------RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
              +  + RLV       Y        R  GL I ++   G IGL++A   FD E G   
Sbjct: 20  DEFIEKYGRLVHHCVWKRYAKKKASIERDTGLDIEDLTQFGMIGLIKARDNFDLEFGCAF 79

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY++  I   +   I  +   +K+  T    +              I +  L  ++   
Sbjct: 80  STYAVPKIIGEIGRAIRDNQK-IKVQRTVYGVK------------GKILNQQLADKEPEE 126

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           IA  L+ S S V +        +SLN ++ +S  N     + ++ D   +     + EE 
Sbjct: 127 IADILDESVSLVKTALEYQPSTDSLNKVVYASGANEELTLERMIEDTKTE-----DIEET 181

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
              R ++    + L P+E  + + R      +T +N++++   S+ ++ +I A+
Sbjct: 182 TINRAVIREFKAALPPKEYIVLDMRL---QNMTQQNIANQMGYSQVQISRILAK 232


>gi|323698081|ref|ZP_08109993.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio sp.
           ND132]
 gi|323458013|gb|EGB13878.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio
           desulfuricans ND132]
          Length = 261

 Score = 93.7 bits (232), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 49/259 (18%), Positives = 108/259 (41%), Gaps = 22/259 (8%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAV 90
           E     R+ +         +V  +   +  +A+  +      + ++E++S G++GL+ A+
Sbjct: 20  ELEQGVRHWDDFSPRDRENIVRYYAPKIRILALRLKAKLPQSVELNELISAGSLGLLDAL 79

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
            KF+PE G +  TYS   IK AM + + R             + L   ++ L+  ++ I 
Sbjct: 80  GKFNPELGIKFDTYSENRIKGAMLDELRR--------MDWFSRGLRQKVKVLEDSMRQIE 131

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
                P     +     +S+ EV        G E+LN  +  S      +Q+ LV     
Sbjct: 132 HETGSPATTEQLCAHTGMSDREVQ------QGLEALNNQVCLSLD---SFQENLVGQKKM 182

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
            +    +    +   + +   +  L PRE+ +      +E  + ++  +   +++  RV 
Sbjct: 183 TDNEPFQSAAFQEIVDKVANLIEELTPREKLVISLYYGEE--LNMKETAEVMDITEGRVS 240

Query: 271 QIEARAFKKVQESIQKQVE 289
           Q+ ++A  K++++ + + E
Sbjct: 241 QLHSQALNKLRKTFRARYE 259


>gi|318066909|emb|CBY89069.1| RNA polymerase sigma70 factor [Chromohalobacter marismortui]
          Length = 367

 Score = 93.7 bits (232), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 46/74 (62%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 294 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 353

Query: 101 LATYSMWWIKAAMQ 114
            +TY+ WWI+ A+ 
Sbjct: 354 FSTYATWWIRQAIT 367


>gi|255658878|ref|ZP_05404287.1| sigma 70 family protein [Mitsuokella multacida DSM 20544]
 gi|260848826|gb|EEX68833.1| sigma 70 family protein [Mitsuokella multacida DSM 20544]
          Length = 208

 Score = 93.7 bits (232), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 31/106 (29%), Positives = 60/106 (56%), Gaps = 1/106 (0%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+ E+RK+  L+ +EE  L   ++E GD  A  RL+ S+  LV K A  +      +
Sbjct: 3   LADYLKELRKVKTLDLEEEQALWAAFKERGDEGARQRLIESYQPLVFKQAAPFAQLDCAL 62

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            +++ EG +GL++A +++D  RG   + +++  I+  M +++ R  
Sbjct: 63  -DLIQEGTVGLIEAAERYDHTRGVAFSLFAVHRIRGRMMDFLRREG 107



 Score = 38.3 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 12/70 (17%), Positives = 30/70 (42%), Gaps = 2/70 (2%)

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           E+ E     + L ++M+ L  +ER + E   L         ++    VS   + +++   
Sbjct: 136 EQAESHELAHRLHQAMARLPDKERAVLEGMYLSSEDA--AGMADALHVSASHIYRLQKNG 193

Query: 277 FKKVQESIQK 286
            ++V+  + +
Sbjct: 194 IRRVRGMLSR 203


>gi|318066973|emb|CBY89101.1| RNA polymerase sigma70 factor [Halomonas taeanensis]
          Length = 366

 Score = 93.7 bits (232), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 46/74 (62%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 293 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 352

Query: 101 LATYSMWWIKAAMQ 114
            +TY+ WWI+ A+ 
Sbjct: 353 FSTYATWWIRQAIT 366


>gi|330945998|gb|EGH47306.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. pisi
           str. 1704B]
          Length = 163

 Score = 93.7 bits (232), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 35/168 (20%), Positives = 68/168 (40%), Gaps = 12/168 (7%)

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG-DESLN 187
             +  +      R    L    D+   PE++  + +K       ++ +N R++  D SL 
Sbjct: 2   PIHVVKELNVYLRAARELTQKLDHEPSPEEIANLLEKPVGEVKRMLGLNERVSSVDVSL- 60

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
                   +     D L  D       L++ ++       + + +S L  ++R +   R 
Sbjct: 61  -----GPDSDKTLLDTLTDDRPTDPCELLQDDDLSQS---IDQWLSELTEKQREVVIRRF 112

Query: 248 L--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
                   TLE++  E  ++RERVRQI+    K+++E ++K    S S
Sbjct: 113 GLRGHESSTLEDVGLEIGLTRERVRQIQVEGLKRLREILEKNGLSSES 160


>gi|226311507|ref|YP_002771401.1| RNA polymerase sigma-K factor precursor [Brevibacillus brevis NBRC
           100599]
 gi|226094455|dbj|BAH42897.1| RNA polymerase sigma-K factor precursor [Brevibacillus brevis NBRC
           100599]
          Length = 119

 Score = 93.7 bits (232), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 27/87 (31%), Positives = 49/87 (56%), Gaps = 2/87 (2%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           P+ + +EE  L  R    GD  A ++L+  +LRLV  I   +   G    +++S G IGL
Sbjct: 30  PLQDTEEEKYL--RLMAKGDPYARNKLIEHNLRLVAHIVKKFENTGEDSEDLISIGTIGL 87

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAM 113
           ++A++ +  ++G +LATY+   I+  +
Sbjct: 88  IKAIESYQVDKGTKLATYAARCIENEI 114


>gi|149194332|ref|ZP_01871429.1| flagellar biosynthesis sigma factor [Caminibacter mediatlanticus
           TB-2]
 gi|149135507|gb|EDM23986.1| flagellar biosynthesis sigma factor [Caminibacter mediatlanticus
           TB-2]
          Length = 228

 Score = 93.7 bits (232), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 44/239 (18%), Positives = 89/239 (37%), Gaps = 30/239 (12%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L   ++  V  +A   +      +  +++VS G   L++  K++D         Y+ 
Sbjct: 15  RDSLAIDYMPAVKAMAARLKERLPSSVDFNDLVSIGYEELVKLAKRYDSSINDNFWGYAQ 74

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I  AM +++ RS   V  G     K +   + R          N+        IA  L
Sbjct: 75  KRINGAMLDFL-RSLDTVSRGDRKLIKEIDKIIER-------YMSNHGYEPDDEEIATIL 126

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +V  S+V                      ++  +    + D       + +K E+     
Sbjct: 127 DVDVSKVKKARQ-----------------SNEIYSVMPIEDQLNYFDDVSKKVEQDELIE 169

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            +   ++ L  +E+ I +    +E  ++L+ +S    V+  RV QI  +  KK++ES++
Sbjct: 170 KIEEILNDLGEKEQLIIQLYYFEE--MSLKEISEILGVTESRVSQIHKKVIKKLRESLK 226


>gi|318066989|emb|CBY89109.1| RNA polymerase sigma70 factor [Kushneria marisflavi]
          Length = 373

 Score = 93.7 bits (232), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 34/91 (37%), Positives = 53/91 (58%), Gaps = 2/91 (2%)

Query: 26  IPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           + +L   E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGN
Sbjct: 283 LALLPVSELKDINRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 342

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114
           IGLM+AV KF+  RG++ +TY+ WWI+ A+ 
Sbjct: 343 IGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 373


>gi|218132856|ref|ZP_03461660.1| hypothetical protein BACPEC_00717 [Bacteroides pectinophilus ATCC
           43243]
 gi|217991729|gb|EEC57733.1| hypothetical protein BACPEC_00717 [Bacteroides pectinophilus ATCC
           43243]
          Length = 205

 Score = 93.7 bits (232), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 50/250 (20%), Positives = 86/250 (34%), Gaps = 62/250 (24%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            L  +EE +  K+ RE GDL A ++L+  ++RLV  I   Y        +++S G IGL+
Sbjct: 14  PLSSEEEKIYLKKCRE-GDLEARNKLIEKNMRLVAHIVKKYACADRDTEDLLSVGTIGLI 72

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV  FD  +  RLATY+   I   +   +                      R +  +  
Sbjct: 73  KAVNTFDMNKSIRLATYAAKCIDNELLMLLRSDRR---------------KSREISIYEP 117

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
              D       ++ I   +  SE  V+                        + +  +   
Sbjct: 118 VGKDKEGNEINLIEI---IGTSEDTVVE---------------------DYELRQDVKKL 153

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVS 265
           +   E+ L ++E                  RE  I   R         T   ++ +  +S
Sbjct: 154 YSAVEKKLTDRE------------------RE--IIIMRYGLYGTQEITQREIAQKMNIS 193

Query: 266 RERVRQIEAR 275
           R  V +IE +
Sbjct: 194 RSYVSRIEKK 203


>gi|318066987|emb|CBY89108.1| RNA polymerase sigma70 factor [Kushneria indalinina]
          Length = 372

 Score = 93.3 bits (231), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 35/91 (38%), Positives = 53/91 (58%), Gaps = 2/91 (2%)

Query: 26  IPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           + ML   E   + +R    E     A   +V ++LRLV+ IA  Y   GL   +++ EGN
Sbjct: 282 LAMLPVSELKDINRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGN 341

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114
           IGLM+AV KF+  RG++ +TY+ WWI+ A+ 
Sbjct: 342 IGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 372


>gi|188586385|ref|YP_001917930.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|179351072|gb|ACB85342.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 114

 Score = 93.3 bits (231), Expect = 3e-17,   Method: Composition-based stats.
 Identities = 33/107 (30%), Positives = 52/107 (48%), Gaps = 1/107 (0%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +S+IV     L  YI        L  ++E    KR  E GD  A   L+  +LRLV  + 
Sbjct: 8   ISLIVKEISLLVSYISSNSFPQPLSAEDERKYLKRL-EQGDDKAREVLIERNLRLVAHVI 66

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
             +   G    +++S G IGL++A+  ++  +G RLATY+   I+  
Sbjct: 67  KKFENSGEDPEDLISIGTIGLIKAINTYNYRKGTRLATYAARCIENE 113


>gi|318066943|emb|CBY89086.1| RNA polymerase sigma70 factor [Halomonas halmophila]
          Length = 367

 Score = 93.3 bits (231), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 34/94 (36%), Positives = 51/94 (54%), Gaps = 10/94 (10%)

Query: 31  KQEEYVLA----------KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           ++E   LA              E     A   +V ++LRLV+ IA  Y   GL   +++ 
Sbjct: 274 EEEMVALAVTDLKEVNRKLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 333

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114
           EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+ 
Sbjct: 334 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 367


>gi|318066967|emb|CBY89098.1| RNA polymerase sigma70 factor [Halomonas pantelleriensis]
          Length = 363

 Score = 93.3 bits (231), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 46/74 (62%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 290 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 349

Query: 101 LATYSMWWIKAAMQ 114
            +TY+ WWI+ A+ 
Sbjct: 350 FSTYATWWIRQAIT 363


>gi|149916265|ref|ZP_01904786.1| RNA polymerase sigma factor [Roseobacter sp. AzwK-3b]
 gi|149809925|gb|EDM69776.1| RNA polymerase sigma factor [Roseobacter sp. AzwK-3b]
          Length = 80

 Score = 93.3 bits (231), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 50/79 (63%), Positives = 61/79 (77%), Gaps = 1/79 (1%)

Query: 2  NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
          N KN+    + E GL+RY+ EIRK P+LE +EEY+LAKR+ E  D  AAHR+VTSHLRL 
Sbjct: 3  NYKNLPAP-SPEGGLNRYLQEIRKFPLLEPEEEYMLAKRWVEKQDTEAAHRMVTSHLRLA 61

Query: 62 VKIAMGYRGYGLPISEVVS 80
           KIAMGYRGYGLP +EV+S
Sbjct: 62 AKIAMGYRGYGLPTAEVIS 80


>gi|318066965|emb|CBY89097.1| RNA polymerase sigma70 factor [Halomonas pacifica]
          Length = 362

 Score = 93.3 bits (231), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 46/74 (62%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 289 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 348

Query: 101 LATYSMWWIKAAMQ 114
            +TY+ WWI+ A+ 
Sbjct: 349 FSTYATWWIRQAIT 362


>gi|304570578|ref|YP_386879.2| sigma-70 factor [Desulfovibrio desulfuricans subsp. desulfuricans
           str. G20]
          Length = 265

 Score = 93.3 bits (231), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 43/243 (17%), Positives = 95/243 (39%), Gaps = 25/243 (10%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             ++V  +   +  +A+  +G     + ++E++S G +GLM+A  KF P+ G +  TY+ 
Sbjct: 36  QEQVVRHYAPKIKFLALRLKGKLPKSVELNELISAGTLGLMEAFGKFQPKLGIKFDTYAE 95

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +     L     +  Q+     +R L+  +  +     +      + K  
Sbjct: 96  NRIRGAMLDELR---RLDWFPRSLRQR-----VRLLEDTINRLEHEKGRRPSEEELQKAT 147

Query: 167 NVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            + E ++ S    L      SL+A+           + +     D  E         +  
Sbjct: 148 GLEEKDLRSGLEALQNHLCISLDAI----------QETFAADGRDHLEGEPFHSTATQEL 197

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              +   +  L PRE+ +       E  + +   +    V+  RV Q+ ++A  ++++  
Sbjct: 198 IERIASLIDQLTPREKLVLSLYYSDE--LNMRETAEVMGVTEGRVSQLHSQALNRLRKQF 255

Query: 285 QKQ 287
            +Q
Sbjct: 256 HEQ 258


>gi|318066947|emb|CBY89088.1| RNA polymerase sigma70 factor [Halomonas halodenitrificans]
          Length = 360

 Score = 93.3 bits (231), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 46/74 (62%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 287 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 346

Query: 101 LATYSMWWIKAAMQ 114
            +TY+ WWI+ A+ 
Sbjct: 347 FSTYATWWIRQAIT 360


>gi|318066941|emb|CBY89085.1| RNA polymerase sigma70 factor [Halomonas eurihalina]
          Length = 367

 Score = 93.3 bits (231), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 46/74 (62%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 294 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 353

Query: 101 LATYSMWWIKAAMQ 114
            +TY+ WWI+ A+ 
Sbjct: 354 FSTYATWWIRQAIT 367


>gi|295696140|ref|YP_003589378.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
 gi|295411742|gb|ADG06234.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
          Length = 242

 Score = 93.3 bits (231), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 42/224 (18%), Positives = 93/224 (41%), Gaps = 14/224 (6%)

Query: 54  VTSHLRLVVKIAMGYRGYGLP--ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +T +L +V  IA   +    P  + ++VS G +GL++A +++DP +      ++   I+ 
Sbjct: 13  ITLYLPMVENIARRLKSRFKPAAMEDLVSFGMLGLLEAARRYDPGQETPFEVFARLRIRG 72

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           AM + +       +       K++     RL    ++ +D  +  E  V     +   E 
Sbjct: 73  AMIDGVRAEGPASRR-RWERVKKVQEAYERLFSKGKSGSDEEMCKELGVDRGTFIGWLEE 131

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
                        SL+ +I++ D  S +  D +    D +     +   R+  R ML  +
Sbjct: 132 FERF------HPISLDRVIHTEDGESFRIADAIP---DPEGVDPAQTVSRQAVRQMLAEA 182

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
           ++ L  RE+ +     +    ++   +++   V+  RV Q+ ++
Sbjct: 183 ITALPEREKYVLSLHYI--EGLSFREVAAVLGVTPARVSQLHSK 224


>gi|318066923|emb|CBY89076.1| RNA polymerase sigma70 factor [Halomonas anticariensis]
          Length = 371

 Score = 93.3 bits (231), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 46/74 (62%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 298 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 357

Query: 101 LATYSMWWIKAAMQ 114
            +TY+ WWI+ A+ 
Sbjct: 358 FSTYATWWIRQAIT 371


>gi|218887101|ref|YP_002436422.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio vulgaris
           str. 'Miyazaki F']
 gi|218758055|gb|ACL08954.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio vulgaris
           str. 'Miyazaki F']
          Length = 265

 Score = 93.3 bits (231), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 40/239 (16%), Positives = 89/239 (37%), Gaps = 21/239 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             R+V  +   V  +A+  +      + ++E++S G +GLM+A+ KF P+ G R  TY+ 
Sbjct: 36  QERIVRHYAPKVRFLALRLKAKLPRNVELNELISAGTLGLMEALGKFRPQLGIRFETYAE 95

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +     L     +  Q+     +R+L   +Q I     +      +    
Sbjct: 96  SRIRGAMLDELR---RLDWFPRSLRQR-----VRQLDEAIQRIEHEKGRHPTEAELQDAT 147

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + + +V      L     L+          +             E    +    +    
Sbjct: 148 GLDQKDVRLGLEALQNQLCLSL--------DAIQDSLAPDTGVQGEGEPFQTTATQELIE 199

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            +   +  L PRE+ +       E  + +   +    ++  RV Q+ ++A  ++++  +
Sbjct: 200 RVAGLIDELTPREKLVLSLYYSDE--LNMRETAEVMGITEGRVSQLHSQALNRLRKEFR 256


>gi|121534953|ref|ZP_01666772.1| sigma-70 region 2 domain protein [Thermosinus carboxydivorans Nor1]
 gi|121306552|gb|EAX47475.1| sigma-70 region 2 domain protein [Thermosinus carboxydivorans Nor1]
          Length = 215

 Score = 93.0 bits (230), Expect = 4e-17,   Method: Composition-based stats.
 Identities = 36/106 (33%), Positives = 61/106 (57%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
            ++Y+ E++KI +LE  EE  L + ++  G L    RL+  +  LV K AM +R +   +
Sbjct: 3   FAQYLDELKKIRLLEPAEEAALWRGFKVDGCLDCRRRLIEHYQPLVFKEAMRWRAHEGVV 62

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            +++ EG +GL++AV+ FDPERG   + Y+   I+  M  Y+ R  
Sbjct: 63  MDLIQEGTVGLIEAVENFDPERGVAFSLYAPHRIRGRMLTYLEREG 108


>gi|75909293|ref|YP_323589.1| RNA polymerase sigma factor SigF [Anabaena variabilis ATCC 29413]
 gi|75703018|gb|ABA22694.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Anabaena
           variabilis ATCC 29413]
          Length = 261

 Score = 93.0 bits (230), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 36/156 (23%), Positives = 75/156 (48%), Gaps = 8/156 (5%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG-YGLPISEVVSEGNIGLMQAVKKFD 94
            L + Y  +  +   ++LV  H  LV K+A  +      P  ++   G  GL++A+++FD
Sbjct: 14  ELLRSYHHNPSIKLRNKLVQLHTGLVRKMAHKFSHQCNEPYEDLEQIGYFGLIRAIERFD 73

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P +G+  +++++ +I+  M  ++    +L+KI     +  L+   ++++  L     +  
Sbjct: 74  PSQGYAFSSFAVPYIRGEMLHFLRDRSTLLKIPRRWQE--LYNEGQKIRKELSI---SLG 128

Query: 155 KPEQVVAIAKKLNVSESEVIS--MNCRLAGDESLNA 188
           +P +   IAK L VS  E     +  +     SL+A
Sbjct: 129 RPPKDAEIAKHLKVSVQEWQETKLAAQNRMPLSLDA 164


>gi|318066991|emb|CBY89110.1| RNA polymerase sigma70 factor [Modicisalibacter tunisiensis]
          Length = 373

 Score = 93.0 bits (230), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 32/74 (43%), Positives = 46/74 (62%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 300 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 359

Query: 101 LATYSMWWIKAAMQ 114
            +TY+ WWI+ AM 
Sbjct: 360 FSTYATWWIRQAMT 373


>gi|94495423|ref|ZP_01302003.1| flagellar-specific RNA polymerase sigma factor [Sphingomonas sp.
           SKA58]
 gi|94424811|gb|EAT09832.1| flagellar-specific RNA polymerase sigma factor [Sphingomonas sp.
           SKA58]
          Length = 243

 Score = 93.0 bits (230), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 49/238 (20%), Positives = 101/238 (42%), Gaps = 23/238 (9%)

Query: 51  HRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            RL   ++ LV KIA    G     + + +++  G + L++A   F+ +RG   A Y+  
Sbjct: 22  ERLARQYMPLVRKIAWHVHGRVSTAIEVEDLLQIGMVALVEAANSFE-DRGLGFAAYAQL 80

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            ++ AM +++ R  +L +    A +K +     RL+  L        +      ++ ++ 
Sbjct: 81  RVRGAMIDHLRRQATLCR-SAMARRKEIAGVRNRLEQQL-------GRLPTEAEMSSEMG 132

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +  +        +   +       S D+  S    W     D  +QVL    ER++ +  
Sbjct: 133 LEPAAYREAADSVEMVQH-----TSMDEVYSDQSMWFADVEDRADQVL----ERESLKKA 183

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           +   +S L  RE  + +   ++E  + LE +    ++   RV QI+  A  K++E ++
Sbjct: 184 MAACISELPQREAMVLQLYFVEE--MNLEEIGQTLDIGAARVCQIKKAALDKLREKLR 239


>gi|332707787|ref|ZP_08427814.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Lyngbya majuscula
           3L]
 gi|332353490|gb|EGJ33003.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Lyngbya majuscula
           3L]
          Length = 260

 Score = 93.0 bits (230), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 54/256 (21%), Positives = 103/256 (40%), Gaps = 16/256 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAM-GYRGYGLPISEVVSEGNIGLMQAVKKFD 94
            L   Y  +  +   +++V  +  LV KIA    +    P  ++   G IGL++A+++FD
Sbjct: 12  ELLIAYYRNPSIQLRNQIVRLNAGLVRKIAHIVSQKCAEPYEDLEQMGYIGLIRAIERFD 71

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P +G   ++ ++ +I+  M  ++    SLVKI     +  L    +R+   L     N  
Sbjct: 72  PHQGCAFSSLAVPYIRGEMLHFLRDRGSLVKIPRRWQE--LQQAGKRVSKKL---ATNLG 126

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +  +   IAK L+VS  E       +      SL+A ++          + L   ++   
Sbjct: 127 RFPRDEEIAKALDVSLQEWQESKLAVQNRLPLSLDATVSQKVDQPMTLGETLPDYYEENL 186

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
               E       R  L  ++S L  + +   E   L+E P   +  +    VS   V + 
Sbjct: 187 HYWEED------RQQLQGALSQLEDKTQAAIEFVFLRELPR--KEAAKRIGVSPMTVTRH 238

Query: 273 EARAFKKVQESIQKQV 288
             R  +++   ++ Q 
Sbjct: 239 VKRGIQELVTLMKSQA 254


>gi|221319748|ref|ZP_03601042.1| RNA polymerase sporulation-specific sigma factor (sigma-K)
           (N-terminal half) [Bacillus subtilis subsp. subtilis
           str. JH642]
          Length = 160

 Score = 93.0 bits (230), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 27/108 (25%), Positives = 50/108 (46%), Gaps = 1/108 (0%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +  +V   + L  Y+        L   EE    +   + GD  A + L+  +LRLV  I 
Sbjct: 13  LGFVVKELVFLVSYVKNNAFPQPLSSSEEKKYLELMAK-GDEHARNMLIEHNLRLVAHIV 71

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
             +   G    +++S G IGL++ ++ +   +G +LATY+   I+  +
Sbjct: 72  KKFENTGEDAEDLISIGTIGLIKGIESYSAGKGTKLATYAARCIENEI 119


>gi|221310502|ref|ZP_03592349.1| RNA polymerase sporulation-specific sigma factor (sigma-K)
           (N-terminal half) [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221314826|ref|ZP_03596631.1| RNA polymerase sporulation-specific sigma factor (sigma-K)
           (N-terminal half) [Bacillus subtilis subsp. subtilis
           str. NCIB 3610]
 gi|221324026|ref|ZP_03605320.1| RNA polymerase sporulation-specific sigma factor (sigma-K)
           (N-terminal half) [Bacillus subtilis subsp. subtilis
           str. SMY]
 gi|321312063|ref|YP_004204350.1| sporulation sigma factor SigK [Bacillus subtilis BSn5]
 gi|143642|gb|AAA22804.1| spoIVCB peptide precursor [Bacillus subtilis]
 gi|320018337|gb|ADV93323.1| sporulation sigma factor SigK [Bacillus subtilis BSn5]
          Length = 155

 Score = 93.0 bits (230), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 27/108 (25%), Positives = 50/108 (46%), Gaps = 1/108 (0%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +  +V   + L  Y+        L   EE    +   + GD  A + L+  +LRLV  I 
Sbjct: 8   LGFVVKELVFLVSYVKNNAFPQPLSSSEEKKYLELMAK-GDEHARNMLIEHNLRLVAHIV 66

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
             +   G    +++S G IGL++ ++ +   +G +LATY+   I+  +
Sbjct: 67  KKFENTGEDAEDLISIGTIGLIKGIESYSAGKGTKLATYAARCIENEI 114


>gi|285018163|ref|YP_003375874.1| RNA polymerase sigma factor for flagellar operon (sigma-f factor)
           protein [Xanthomonas albilineans GPE PC73]
 gi|283473381|emb|CBA15886.1| probable rna polymerase sigma factor for flagellar operon (sigma-f
           factor) protein [Xanthomonas albilineans]
          Length = 249

 Score = 93.0 bits (230), Expect = 5e-17,   Method: Composition-based stats.
 Identities = 42/236 (17%), Positives = 89/236 (37%), Gaps = 20/236 (8%)

Query: 54  VTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           +  H  LV +IA          + I +++  G IGL++A + +D ++G    TY+   I+
Sbjct: 19  IAQHSDLVRRIAHHLAARLPASVEIDDLIQAGMIGLIEASRSYDADQGASFETYASIRIR 78

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            +M + I R    V        +     +R+++        N  +      +A  + +  
Sbjct: 79  GSMIDEIRR-GDWVPRSVHRRARDAASAIRKIE-------QNTGRAAAANEVAAAMEMPL 130

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            E + +    A  + L+      D          +           +  ER      L +
Sbjct: 131 PEYMRLMEDAARGQVLSLESRIEDHGE-------LDTIAKGGPNPQQMLERSEFGRELGK 183

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +++ L  RE+ +       E  + L+ + +   VS  RV QI  +A  +++  ++ 
Sbjct: 184 AIAQLPEREQLVLSLYY--EQELNLKEIGAVLGVSESRVCQIHGQATVRLRGRLKA 237


>gi|17227773|ref|NP_484321.1| RNA polymerase sigma factor SigF [Nostoc sp. PCC 7120]
 gi|17135255|dbj|BAB77801.1| RNA polymerase sigma-37 factor [Nostoc sp. PCC 7120]
          Length = 261

 Score = 92.6 bits (229), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 37/156 (23%), Positives = 75/156 (48%), Gaps = 8/156 (5%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG-YGLPISEVVSEGNIGLMQAVKKFD 94
            L + Y  +  +   +RLV  H  LV K+A  +      P  ++   G  GL++A+++FD
Sbjct: 14  ELLRSYHHNPSIKLRNRLVQLHTGLVRKMAHKFSHQCNEPYEDLEQIGYFGLIRAIERFD 73

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P +G+  +++++ +I+  M  ++    +L+KI     +  L+   ++++  L     +  
Sbjct: 74  PSQGYAFSSFAVPYIRGEMLHFLRDRSTLLKIPRRWQE--LYNEGQKVRKELSI---SLG 128

Query: 155 KPEQVVAIAKKLNVSESEVIS--MNCRLAGDESLNA 188
           +P +   IAK L VS  E     +  +     SL+A
Sbjct: 129 RPPKDAEIAKYLKVSVQEWQETKLAAQNRMPLSLDA 164


>gi|318066921|emb|CBY89075.1| RNA polymerase sigma70 factor [Halomonas almeriensis]
          Length = 366

 Score = 92.6 bits (229), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 34/94 (36%), Positives = 51/94 (54%), Gaps = 10/94 (10%)

Query: 31  KQEEYVLA----------KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
           ++E   LA              E     A   +V ++LRLV+ IA  Y   GL   +++ 
Sbjct: 273 EEEMVALAVTDLKEVNRKLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQ 332

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114
           EGNIGLM+AV KF+  RG++ +TY+ WWI+ A+ 
Sbjct: 333 EGNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 366


>gi|256833253|ref|YP_003161980.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Jonesia
           denitrificans DSM 20603]
 gi|256686784|gb|ACV09677.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Jonesia
           denitrificans DSM 20603]
          Length = 348

 Score = 92.6 bits (229), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 57/253 (22%), Positives = 92/253 (36%), Gaps = 23/253 (9%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             RLVT +L LV                  E+ S G   L+QA + FDP  G   A ++ 
Sbjct: 58  QERLVTENLHLVGYHVNDMLVRLPSHVTRDELSSAGQFALVQAARNFDPSSGVPFARFAA 117

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             IK A+ + + RS   V  G           +R L      +T    +      +A  L
Sbjct: 118 IRIKGALVDEL-RSMDWVSRGVRK-------KIRDLNQVSDTLTATLGRTPTRQELATAL 169

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            V  S++     + A        + S +       + L     G E  LI  E+      
Sbjct: 170 GVPLSDIDDARDQAA------TKVLSFEGYDGALAEVLPTREVGPEAALIASEQIV---- 219

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L  ++S L  R R I E    +E  VT   ++    V++ RV Q+ A A   +++ +  
Sbjct: 220 YLKSAVSALPERLRAIVEQIFFEEKSVT--EIAESLGVTQSRVSQLRAEAMVLLRDGMNA 277

Query: 287 QVELSSSPPLLQK 299
            +     P   ++
Sbjct: 278 HLNPDRVPTPERE 290


>gi|291288738|ref|YP_003505554.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Denitrovibrio
           acetiphilus DSM 12809]
 gi|290885898|gb|ADD69598.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Denitrovibrio
           acetiphilus DSM 12809]
          Length = 245

 Score = 92.6 bits (229), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 34/233 (14%), Positives = 92/233 (39%), Gaps = 17/233 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
                +++   +  +    +         + + ++ S   +GL++++++FD +R     T
Sbjct: 15  REEKDKIILEFMPRIKSWVLRISTTLPDTVDVDDLYSSACLGLIESLERFDKDRNVNFYT 74

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           +    IK A+ + +     L         + +   L++L+ H+        +   V  I 
Sbjct: 75  FGERRIKGAILDTLRNLDYL--------PRNVRTRLKQLERHIGNHYRTAGEKPTVEEII 126

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           +  + SE EV  +   +  D+ L+   +   +  +   D++       E    ++  +  
Sbjct: 127 ENSDFSEQEVYRLLELMENDKILSLDESVGPEGDTSLVDFIKSTGLTPE----DEALKTR 182

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
             + L   +  L+ +E+ +      +E  +T++ ++    ++  RV QI + A
Sbjct: 183 LVDTLGEEIENLSEKEKYVVSLYYYEE--LTMKEIAMVLGITESRVSQIHSAA 233


>gi|225164039|ref|ZP_03726324.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Opitutaceae bacterium TAV2]
 gi|224801345|gb|EEG19656.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Opitutaceae bacterium TAV2]
          Length = 274

 Score = 92.6 bits (229), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 41/247 (16%), Positives = 100/247 (40%), Gaps = 18/247 (7%)

Query: 46  DLSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           D      L+  +L LV  +           + + ++ S G  GL+ A++++DPE+G   A
Sbjct: 32  DRDDEQTLIERYLPLVRNVVDRIKMNLPAHVEVEDLYSVGVTGLLAAIQRYDPEQGNTFA 91

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
            Y+   I+ A+ + + R             +R     R++K  +  +   + +      +
Sbjct: 92  GYATLRIRGAVLDELRRLDWC--------PRRARAKARKIKDAIGELEQRHGRAVTDAEV 143

Query: 163 AKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH---DGQEQVLIE 217
           ++ L +S  +        R     +++   +  D  SS     +       D  +  + E
Sbjct: 144 SEHLGISLHDYAHWLEESRPVTFVAIDQPASGDDGGSSGGGSGVSLHEVIADKNDTPVRE 203

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
           + E++    ++ + ++ L   ++RI      +   + L  +++ F ++  R+ QI ++A 
Sbjct: 204 RMEKEEVWQLIAQRITELPDIQKRILAMYYFEN--MRLAEIAAVFRLTESRICQIHSQAV 261

Query: 278 KKVQESI 284
             ++  I
Sbjct: 262 LTLRAYI 268


>gi|270620051|ref|ZP_06221855.1| RNA polymerase sigma-32 factor [Haemophilus influenzae HK1212]
 gi|270317775|gb|EFA29151.1| RNA polymerase sigma-32 factor [Haemophilus influenzae HK1212]
          Length = 108

 Score = 92.6 bits (229), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 24/104 (23%), Positives = 48/104 (46%)

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
             D   +   + ++  +     +L          L  +         L  ++  L+ R +
Sbjct: 3   GADVGFDLPTDDAETETYSPALYLEDKSSNFAAELENENFESQATEQLGAALQSLDARSQ 62

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            I +AR L +N  TL +L++++ VS ER+RQ+E  A KK++ ++
Sbjct: 63  DIIKARWLDDNKATLHDLAAKYNVSAERIRQLETNALKKLKSAV 106


>gi|318066945|emb|CBY89087.1| RNA polymerase sigma70 factor [Halomonas halocynthiae]
          Length = 368

 Score = 92.6 bits (229), Expect = 6e-17,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 46/74 (62%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 295 IGEAKSRRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 354

Query: 101 LATYSMWWIKAAMQ 114
            +TY+ WWI+ A+ 
Sbjct: 355 FSTYATWWIRQAIT 368


>gi|254519270|ref|ZP_05131326.1| sporulation sigma factor SigK [Clostridium sp. 7_2_43FAA]
 gi|226913019|gb|EEH98220.1| sporulation sigma factor SigK [Clostridium sp. 7_2_43FAA]
          Length = 231

 Score = 92.6 bits (229), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 34/106 (32%), Positives = 53/106 (50%), Gaps = 2/106 (1%)

Query: 16  LSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           L+ YI      P  L+++EE    K  + +GD  A   L+  +LRLV  I   Y      
Sbjct: 17  LTGYISGNNTFPKPLDEEEEEQYLKLLK-NGDKEAKSILIERNLRLVAHIVKKYNFPNKD 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           I E++S G +GL++A+  FD  +G RLATY+   I+  +      +
Sbjct: 76  IDELISIGTVGLIKAIDSFDASKGTRLATYASRCIENEILMLFRNN 121



 Score = 51.4 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 21/91 (23%), Positives = 34/91 (37%), Gaps = 8/91 (8%)

Query: 186 LNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV-LNPRERRIF 243
           L   I    + N     D L  + D     ++EK E   +   L   + V L+ RE  I 
Sbjct: 130 LQDPIGVDKEGNEICLIDVLSSEKDS----VLEKVESNLQIKQLYNKICVSLSEREGEIV 185

Query: 244 EARRL--QENPVTLENLSSEFEVSRERVRQI 272
           + R         T   +++   +SR  V +I
Sbjct: 186 KMRYGLIDGRCRTQREIAALLGISRSYVSRI 216


>gi|225850277|ref|YP_002730511.1| RNA polymerase sigma factor for flagellar operon [Persephonella
           marina EX-H1]
 gi|225646527|gb|ACO04713.1| RNA polymerase sigma factor for flagellar operon [Persephonella
           marina EX-H1]
          Length = 209

 Score = 92.6 bits (229), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 48/242 (19%), Positives = 102/242 (42%), Gaps = 49/242 (20%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGY----GLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
           D     ++V  +L LV K+A           +   ++V+   IGLM+A+ ++D ++  + 
Sbjct: 6   DKKNKEQIVLENLSLVKKVASKIYSRLPKGDIEFDDLVNTWIIGLMKAIDRYDKDK-AKF 64

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY+   I+  + +Y+ RS  +V        K+            +        P    A
Sbjct: 65  STYAYIKIRGEILDYL-RSLDIVPRTVRDRIKK------------EKAEREEPMPLSTSA 111

Query: 162 IAKKLNVSESEVISMNCRLA-GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
           +           +S+   L+  DESL                 L+     +++   E+  
Sbjct: 112 VM----------VSIEKALSTKDESL----------------KLIDTLVSKKETPEEEVI 145

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKK 279
           + + ++ L + + +LN +E+R+ +    +E +  T   ++SE  +S  RV QI++ A +K
Sbjct: 146 KDDLKDRLIKVIDMLNEKEKRVLQMLYFEELDFKT---VASELNISVSRVSQIKSEALRK 202

Query: 280 VQ 281
           ++
Sbjct: 203 LK 204


>gi|318066977|emb|CBY89103.1| RNA polymerase sigma70 factor [Halomonas ventosae]
          Length = 366

 Score = 92.6 bits (229), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 46/74 (62%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 293 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 352

Query: 101 LATYSMWWIKAAMQ 114
            +TY+ WWI+ A+ 
Sbjct: 353 FSTYATWWIRQAIT 366


>gi|147677483|ref|YP_001211698.1| DNA-directed RNA polymerase specialized sigma subunit
           [Pelotomaculum thermopropionicum SI]
 gi|146273580|dbj|BAF59329.1| DNA-directed RNA polymerase specialized sigma subunit
           [Pelotomaculum thermopropionicum SI]
          Length = 243

 Score = 92.6 bits (229), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 44/244 (18%), Positives = 102/244 (41%), Gaps = 27/244 (11%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y + G   +  ++V +  RLV      Y   G    ++V  G  GL++A K++DP RG  
Sbjct: 25  YLQDGSAESLQKVVEAGTRLVHYFVGLY-APGHSREDLVQSGFEGLLKAAKRYDPGRGVS 83

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+   I   ++ +I +  S  + G  A  +       R+   L+   +   +   + 
Sbjct: 84  FSTYASHCIMGEVRHFIRKEASFSRPGWAAGLQE------RVNRFLEEYLNEKGELPTLD 137

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            IA  +N+ +  ++ +  R+         I+ S   S +++ + +   D           
Sbjct: 138 QIAGAVNIRKEGLLQV-MRVGWVAP--DEIDVSKIRSQRYESFQLPVED----------- 183

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
               R +L +++  L   +RR+      +   +T    + E  +++ +V ++  ++ K +
Sbjct: 184 ----RIVLRQAVEKLTELQRRVIAMLFFKN--MTQGEAAEELGITQRKVSRVLHKSLKLL 237

Query: 281 QESI 284
           ++ +
Sbjct: 238 RDIM 241


>gi|284032127|ref|YP_003382058.1| FliA/WhiG subfamily RNA polymerase sigma 28 subunit [Kribbella
           flavida DSM 17836]
 gi|283811420|gb|ADB33259.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Kribbella
           flavida DSM 17836]
          Length = 269

 Score = 92.2 bits (228), Expect = 7e-17,   Method: Composition-based stats.
 Identities = 35/243 (14%), Positives = 85/243 (34%), Gaps = 21/243 (8%)

Query: 34  EYVLAKRYREHGDL--SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           E +L     E G        + V   + +   +A  Y   G+   +++   ++GL++A  
Sbjct: 30  ERLLRLAAEETGARRTELIEQAVVEGVPMARTLAARYHRRGVDSDDLLQVASVGLVKAAH 89

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
            + P       +Y++  I+  ++ +      +V+       + L   +   +  L +   
Sbjct: 90  GYRPGPDTDFRSYAIPTIRGELRRHFRDQAWMVRPPRRI--QDLQTAINAAEADLASTLQ 147

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHD 209
           +    E    +A  + V   +++            SL+A +       +     ++ D  
Sbjct: 148 HWPTTED---LAAAIGVPVEDIVDAQRAQGCFRPASLDAKLT---GAPALSLGTVIADKT 201

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
              +++       +    L   +  L  R+R I   R +     T   +  E  VS+ +V
Sbjct: 202 NTYELV-------DHIETLRPVVEDLPARDRLILHRRFVDH--RTQAEIGEEIGVSQMQV 252

Query: 270 RQI 272
            ++
Sbjct: 253 SRL 255


>gi|318066935|emb|CBY89082.1| RNA polymerase sigma70 factor [Halomonas cupida]
          Length = 365

 Score = 92.2 bits (228), Expect = 8e-17,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 46/74 (62%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 292 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 351

Query: 101 LATYSMWWIKAAMQ 114
            +TY+ WWI+ A+ 
Sbjct: 352 FSTYATWWIRQAIT 365


>gi|238753169|ref|ZP_04614612.1| Lateral flagellar motor protein A (MotA-like) [Yersinia rohdei ATCC
           43380]
 gi|238708608|gb|EEQ00883.1| Lateral flagellar motor protein A (MotA-like) [Yersinia rohdei ATCC
           43380]
          Length = 525

 Score = 92.2 bits (228), Expect = 8e-17,   Method: Composition-based stats.
 Identities = 36/242 (14%), Positives = 103/242 (42%), Gaps = 34/242 (14%)

Query: 52  RLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKF-DPERGFRLATYSMW 107
           + +T++L LV +I           +   ++     +GL++A++++  P+   + A Y++ 
Sbjct: 19  QYLTAYLPLVKRIVRQLSFQVNSVIDREDMQQIALMGLLEALRRYGHPD--VQFAAYAVH 76

Query: 108 WIKAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            I+ A+ + +    W           +RL     ++   ++AI            I  +L
Sbjct: 77  RIRGAVLDQLREHDWRP---------RRLRQKTHKINEAIRAIMRKLGHEPSFEEITAEL 127

Query: 167 NVSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            ++  E     +    +  ESL+ ++      S +     +   + ++ +++E       
Sbjct: 128 KLTAEEYQEYLLLESASAMESLDDIL------SLETPTDALQSRNLEDSIIVE------- 174

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + L ++++ L  RE+ I      +E  ++++ ++   +++  R+ Q+  +  +K++   
Sbjct: 175 -DNLNQAIASLEEREQMILHLYYQKE--MSMKEIAEVLDLTEARICQLNKKIVQKIKSFF 231

Query: 285 QK 286
           +K
Sbjct: 232 KK 233


>gi|32453269|gb|AAP82767.1| sigma 70 [Hydrogenothermus marinus]
          Length = 369

 Score = 92.2 bits (228), Expect = 8e-17,   Method: Composition-based stats.
 Identities = 34/87 (39%), Positives = 52/87 (59%), Gaps = 5/87 (5%)

Query: 25  KIPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           ++P+    E   + KR    E    +A   +V ++LRLV+ IA  Y   GL   +++ EG
Sbjct: 285 RVPL---DELKDIFKRMSQGEAKMRAAKREMVEANLRLVISIAKKYTNRGLQFLDLIQEG 341

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWI 109
           NIGLM+AV KF+  RG++ +TY+ WWI
Sbjct: 342 NIGLMKAVDKFEYRRGYKFSTYATWWI 368


>gi|21231354|ref|NP_637271.1| RNA polymerase sigma factor [Xanthomonas campestris pv. campestris
           str. ATCC 33913]
 gi|66768593|ref|YP_243355.1| RNA polymerase sigma factor [Xanthomonas campestris pv. campestris
           str. 8004]
 gi|188991595|ref|YP_001903605.1| RNA polymerase sigma factor rpoD (Sigma-70). [Xanthomonas
           campestris pv. campestris str. B100]
 gi|21113015|gb|AAM41195.1| RNA polymerase sigma factor [Xanthomonas campestris pv. campestris
           str. ATCC 33913]
 gi|66573925|gb|AAY49335.1| RNA polymerase sigma factor [Xanthomonas campestris pv. campestris
           str. 8004]
 gi|167733355|emb|CAP51556.1| RNA polymerase sigma factor rpoD (Sigma-70) [Xanthomonas campestris
           pv. campestris]
          Length = 255

 Score = 92.2 bits (228), Expect = 8e-17,   Method: Composition-based stats.
 Identities = 43/239 (17%), Positives = 92/239 (38%), Gaps = 20/239 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           A+ +VT H  LV +IA          + + +++  G IGL++A + +D ++G    TY+ 
Sbjct: 21  ANDVVTQHADLVRRIAHHLAARLPASVEVDDLIQAGMIGLIEASRSYDSDQGASFETYAS 80

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ +M + I R    V        +     +R+++        N  +      +A  +
Sbjct: 81  IRIRGSMIDEIRR-GDWVPRSVHRRARDAAAAVRKIE-------QNTGRAAAATEVAAAM 132

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   + + +    A  + L+      D          +           +  ER     
Sbjct: 133 EMPLPDYLRLMEDAARGQVLSLESRIEDHGE-------LDTTAKGGPNPQQMMERGEFGR 185

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            L +++  L  RE+ +       E  + L+ + +   VS  RV QI  +A  +++  ++
Sbjct: 186 ELGKAIGQLPEREQLVLSLYY--EQELNLKEIGAVLGVSESRVCQIHGQAVVRLRGRLK 242


>gi|294013075|ref|YP_003546535.1| RNA polymerase sigma factor for flagellar operon FliA [Sphingobium
           japonicum UT26S]
 gi|292676405|dbj|BAI97923.1| RNA polymerase sigma factor for flagellar operon FliA [Sphingobium
           japonicum UT26S]
          Length = 245

 Score = 92.2 bits (228), Expect = 8e-17,   Method: Composition-based stats.
 Identities = 46/238 (19%), Positives = 103/238 (43%), Gaps = 23/238 (9%)

Query: 51  HRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            RL   ++ LV KIA    G     + I +++  G + L++A   F+ +RG   A+Y+  
Sbjct: 25  ERLARQYMPLVRKIAWHVHGRVSSAIEIEDLLQIGMVALVEAANGFE-DRGLGFASYAQM 83

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            ++ AM +++ R  ++ +   +  +      L  ++  L+          ++ A    L+
Sbjct: 84  RVRGAMIDHLRRHATMTRSAMSQRK-----QLAAIRNRLEQRLGRAPLEAEMSA-EMGLD 137

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
            +    ++  C +    S+       D+  S    W     D  + ++    ER++ +  
Sbjct: 138 AAAYREVADGCEMVQHTSM-------DEVYSDQSMWFADVEDRADDIM----ERESLKGA 186

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L + +  L  RE  + +   ++E  + LE + +  ++   RV QI+  A  K++E ++
Sbjct: 187 LAQYIGELPQREALVLQLYFVEE--LNLEEIGATLDIGAARVCQIKKAALDKLREKLR 242


>gi|90406802|ref|ZP_01214994.1| flagellar biosynthesis sigma factor FliA [Psychromonas sp. CNPT3]
 gi|90312039|gb|EAS40132.1| flagellar biosynthesis sigma factor FliA [Psychromonas sp. CNPT3]
          Length = 235

 Score = 92.2 bits (228), Expect = 8e-17,   Method: Composition-based stats.
 Identities = 50/239 (20%), Positives = 91/239 (38%), Gaps = 23/239 (9%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
            L+  H  LV KIA            + +++  G IGL++A + FD  +G    T+S   
Sbjct: 13  ELIEKHTGLVQKIAYHLMARLPASVLVDDLLQSGMIGLLEAARNFDGSKGASFETFSGIR 72

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ AM + + R    V      N        R +   + A+   N    +   IA +L V
Sbjct: 73  IRGAMLDEMRR-GDWVPRSVHKNS-------REISNAISAVEKRNAGDAKESEIASQLGV 124

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQ--WQDWLVYDHDGQEQVLIEKEERKNRRN 226
           + ++   M      D +   L+N  D   ++  +   +  + D     + E E       
Sbjct: 125 TLAKYQQML----RDVNCAKLVNYEDLGGAEATFSSSVNSEVDPTFNCVSESE----YSE 176

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            L   +  L  RE  +       +  + L+ +    E+   RV QI ++A  +++   Q
Sbjct: 177 QLLLMIKQLPEREALVLSLYY--DEELNLKEIGLVLELGESRVSQILSQALHRLKAKAQ 233


>gi|325917849|ref|ZP_08180027.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Xanthomonas
           vesicatoria ATCC 35937]
 gi|325535933|gb|EGD07751.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Xanthomonas
           vesicatoria ATCC 35937]
          Length = 255

 Score = 92.2 bits (228), Expect = 8e-17,   Method: Composition-based stats.
 Identities = 43/239 (17%), Positives = 92/239 (38%), Gaps = 20/239 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           A+ +VT H  LV +IA          + + +++  G IGL++A + +D ++G    TY+ 
Sbjct: 21  ANDVVTQHADLVRRIAHHLAARLPASVEVDDLIQAGMIGLIEASRSYDSDQGASFETYAS 80

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ +M + I R    V        +     +R+++        N  +      +A  +
Sbjct: 81  IRIRGSMIDEIRR-GDWVPRSVHRRARDAAAAVRKIE-------QNTGRAAAATEVAAAM 132

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   + + +    A  + L+      D          +           +  ER     
Sbjct: 133 EMPLPDYLRLMEDAARGQVLSLESRIEDHGE-------LDTTAKGGPNPQQMMERGEFGR 185

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            L +++  L  RE+ +       E  + L+ + +   VS  RV QI  +A  +++  ++
Sbjct: 186 ELGKAIGQLPEREQLVLSLYY--EQELNLKEIGAVLGVSESRVCQIHGQAVVRLRGRLK 242


>gi|167769451|ref|ZP_02441504.1| hypothetical protein ANACOL_00781 [Anaerotruncus colihominis DSM
           17241]
 gi|167668419|gb|EDS12549.1| hypothetical protein ANACOL_00781 [Anaerotruncus colihominis DSM
           17241]
          Length = 234

 Score = 92.2 bits (228), Expect = 9e-17,   Method: Composition-based stats.
 Identities = 51/273 (18%), Positives = 88/273 (32%), Gaps = 76/273 (27%)

Query: 24  RKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
              P  L  +EE    +     GD  A  RL+  +LRLV  I   Y              
Sbjct: 22  GSFPRPLSAKEERECLEGIA-RGDEEAKTRLIEHNLRLVAHIIKKYYS------------ 68

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
                                                   L+ IGT    K +       
Sbjct: 69  ---------------------------------AFKDQDDLISIGTIGLIKAV------- 88

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR----LAGDESLNALINSS-DKNS 197
                    +  KPE+    A   +      + M+ R     A D  ++  I++  D NS
Sbjct: 89  ---------STFKPEKGTRFATYASRCIENEVLMHFRNKKKSAQDVYISDPIDTDKDGNS 139

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV-LNPRERRIFEARRLQENPV--T 254
              QD +  D +     +++  + + +   L R +   L+ RER+I   R         T
Sbjct: 140 LTLQDIMAEDDN-----IVDCIDLRIKSEQLYRFIEGALDERERQIIIMRYGLGGTRSLT 194

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              ++ + ++SR  V +IE +A   ++   +K+
Sbjct: 195 QREVAKKLDISRSYVSRIEKKAISILRGKFEKE 227


>gi|283850718|ref|ZP_06368005.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio sp.
           FW1012B]
 gi|283573961|gb|EFC21934.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio sp.
           FW1012B]
          Length = 264

 Score = 92.2 bits (228), Expect = 9e-17,   Method: Composition-based stats.
 Identities = 47/251 (18%), Positives = 100/251 (39%), Gaps = 21/251 (8%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           D      +V  +   +  +A   +      + + E++S G +GL++A+ +F PE G +  
Sbjct: 32  DARDRQEIVRHYSPKIKIVASRLKAKLPQSVEMGELLSAGAMGLIEALGRFRPELGIKFE 91

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+   IK +M + + R       G     + L    RR++       +++ K   V  +
Sbjct: 92  TYAESRIKGSMLDDLRR-MDWFSRGQRHRVRTLEEASRRIE-------NDSGKAATVEQL 143

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+   ++E EV      L     L+          +  ++   Y  +  E    +  E K
Sbjct: 144 AEATGLTEREVTQGLEALQNQLCLSL--------DAITENISSYQKNQLENEPYKSAEFK 195

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              + L   +  L PRE+ +      +E  + +   S    ++  RV Q+ ++A  ++++
Sbjct: 196 ELVDKLASLIDDLTPREKLVLSLYYGEE--LNMRETSEVMGITEGRVSQLHSQALARLRQ 253

Query: 283 SIQKQVELSSS 293
             + Q  +   
Sbjct: 254 KFKAQYNIEQH 264


>gi|325520258|gb|EGC99421.1| RpoD family RNA polymerase sigma factor [Burkholderia sp. TJI49]
          Length = 167

 Score = 92.2 bits (228), Expect = 9e-17,   Method: Composition-based stats.
 Identities = 28/169 (16%), Positives = 61/169 (36%), Gaps = 13/169 (7%)

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              +++      ++     +R++ H         +      +A +  + E+ + ++    
Sbjct: 2   ARTIRVPVHVGDQQ-----QRVRRHALRFHQRTGRQPTPAELAAETGLDETRLRAVLALP 56

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           A   SL+  +  +D              D       E+      R  +T  +  + P E 
Sbjct: 57  AEPVSLDTPLPDADTGLVDLI------EDQSSASPFERLADTRMRECVTSLLRSVTPAEA 110

Query: 241 RIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   R       P T + ++ +  +SRERVRQIE RA   ++   + +
Sbjct: 111 DVLRRRFGLGGTEPDTYDAIAKDAGMSRERVRQIEKRALAALRTIAEAE 159


>gi|318066953|emb|CBY89091.1| RNA polymerase sigma70 factor [Halomonas koreensis]
          Length = 365

 Score = 92.2 bits (228), Expect = 9e-17,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 46/74 (62%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 292 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 351

Query: 101 LATYSMWWIKAAMQ 114
            +TY+ WWI+ A+ 
Sbjct: 352 FSTYATWWIRQAIT 365


>gi|238928124|ref|ZP_04659884.1| sigma-70 area 2 domain protein [Selenomonas flueggei ATCC 43531]
 gi|238884084|gb|EEQ47722.1| sigma-70 area 2 domain protein [Selenomonas flueggei ATCC 43531]
          Length = 208

 Score = 92.2 bits (228), Expect = 9e-17,   Method: Composition-based stats.
 Identities = 28/106 (26%), Positives = 58/106 (54%), Gaps = 1/106 (0%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
            S Y+ ++  +  L  +EE  L + Y++ GD +A  R++ ++  LV +    YR     +
Sbjct: 2   FSTYMKKLSAVKKLTPEEEKKLWRAYKDQGDAAARRRIIEAYQPLVFREVYPYRSLSAAM 61

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            + V EG IGL++AV+++DP  G   + Y++  ++  + +++ R  
Sbjct: 62  -DAVQEGTIGLIEAVERYDPHHGAAFSLYAVHRVRGRIHDFLRREG 106



 Score = 35.9 bits (82), Expect = 7.0,   Method: Composition-based stats.
 Identities = 12/93 (12%), Positives = 35/93 (37%), Gaps = 4/93 (4%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV- 253
           +  ++  +        +   + E  ER     +L  +M  L  RER + E   +      
Sbjct: 114 EAETEAHETAKERLVDECPSVAEVAERHALVGVLGDAMERLPARERMVLEGVTIGGAGAG 173

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           T+   +    V+   + +++    ++++  + +
Sbjct: 174 TM---ADALGVTPAHIYRLQKNGIRRIRGMLSR 203


>gi|318066933|emb|CBY89081.1| RNA polymerase sigma70 factor [Halomonas campisalis]
          Length = 367

 Score = 92.2 bits (228), Expect = 9e-17,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 46/74 (62%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 294 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 353

Query: 101 LATYSMWWIKAAMQ 114
            +TY+ WWI+ A+ 
Sbjct: 354 FSTYATWWIRQAIT 367


>gi|314918186|gb|EFS82017.1| sigma-70, region 4 [Propionibacterium acnes HL050PA1]
          Length = 270

 Score = 91.8 bits (227), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 51/255 (20%), Positives = 103/255 (40%), Gaps = 37/255 (14%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKK 92
           E  L +R  + G + A   L    L +V+  A      Y   + +++  G IGL +A+++
Sbjct: 47  EAEL-RRISDDG-VGARQTLWRQMLAIVLTQARQAAVSYRCSVEDLIQAGCIGLGEAIER 104

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           +D  RG R +T +  WI+  + E ++R          A  + +      +    + +T  
Sbjct: 105 YDVRRGARFSTVAWTWIRRRIGEEVVRLSG-------ARSRSVMREAAEVARIEEELTAR 157

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
                   AIA ++     +V+ +  R          +   +  +S ++   V      +
Sbjct: 158 WQSVPSSDAIAARMG---QDVMWVEKRR---------VECWEVETSFFEQVAVVQKSCDD 205

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPVTLENLSSEFEVSRERVRQ 271
                           +  + +L  +ERRI E R   +  P+T+  ++ E  +S   VR+
Sbjct: 206 PE--------------SGLIGLLTGQERRIVELRHGFEGEPMTITAVAHELGLSASNVRR 251

Query: 272 IEARAFKKVQESIQK 286
           IE RA  +++  +Q+
Sbjct: 252 IEQRALGRLRRHLQQ 266


>gi|318066931|emb|CBY89080.1| RNA polymerase sigma70 factor [Halomonas campaniensis]
          Length = 368

 Score = 91.8 bits (227), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 34/93 (36%), Positives = 55/93 (59%), Gaps = 1/93 (1%)

Query: 22  EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           E+ ++P+  + +E        E     A   +V ++LRLV+ IA  Y   GL   +++ E
Sbjct: 277 EMVRLPV-TEIKEVNRRLSIGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQE 335

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114
           GNIGLM+AV KF+  RG++ +TY+ WWI+ A+ 
Sbjct: 336 GNIGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 368


>gi|188533568|ref|YP_001907365.1| flagellar biosynthesis sigma factor [Erwinia tasmaniensis Et1/99]
 gi|188028610|emb|CAO96472.1| RNA polymerase sigma factor for flagellar operon [Erwinia
           tasmaniensis Et1/99]
          Length = 240

 Score = 91.8 bits (227), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 42/238 (17%), Positives = 100/238 (42%), Gaps = 17/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDAMQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS          N + +   + R++  L        +      +A +L
Sbjct: 73  QRIRGAMLDEL-RSRDWAPRSVRRNAREVAGAMHRVEQAL-------GRSASEQEVAAQL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +VS  E   +      D + + L +  +          +     +++  + +    + R+
Sbjct: 125 DVSLEEYRQILL----DTNNSQLFSFDEYREEHGDSAELVTEGHEQENPLHQLLEGDLRD 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  +
Sbjct: 181 RVIEAIEALPDREKMVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAVKRLRARL 236


>gi|292670483|ref|ZP_06603909.1| DNA-directed RNA polymerase sigma subunit RpoH [Selenomonas noxia
           ATCC 43541]
 gi|292647893|gb|EFF65865.1| DNA-directed RNA polymerase sigma subunit RpoH [Selenomonas noxia
           ATCC 43541]
          Length = 205

 Score = 91.8 bits (227), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 39/151 (25%), Positives = 79/151 (52%), Gaps = 6/151 (3%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L  +EE+ L + Y+E GD SA  R++ ++  LV +  M YR     + + V EG IGL++
Sbjct: 10  LTPEEEHALWRAYKEEGDESARRRIIEAYQPLVFREVMPYR-TMPVVMDAVQEGTIGLIE 68

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT----TANQKRLFFNLRRLKG 144
           AV+++DP RG   + Y++  ++  + +++ R  S V +      T  Q+     L   + 
Sbjct: 69  AVERYDPTRGVAFSLYAVHRVRGRILDFLRREGS-VDLPCLEAETEAQETAKELLVDERA 127

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
            +  + +++   + + A+ ++L + E  V+ 
Sbjct: 128 SVAELAEHHALVDLLGAVMERLPLRERLVLE 158


>gi|78047533|ref|YP_363708.1| RNA polymerase sigma factor for flagellar operon FliA [Xanthomonas
           campestris pv. vesicatoria str. 85-10]
 gi|325928018|ref|ZP_08189235.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Xanthomonas
           perforans 91-118]
 gi|78035963|emb|CAJ23654.1| RNA polymerase sigma factor for flagellar operon FliA [Xanthomonas
           campestris pv. vesicatoria str. 85-10]
 gi|325541614|gb|EGD13139.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Xanthomonas
           perforans 91-118]
          Length = 255

 Score = 91.8 bits (227), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 44/239 (18%), Positives = 92/239 (38%), Gaps = 20/239 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           A+ +VT H  LV +IA          + + +++  G IGL++A + +D E+G    TY+ 
Sbjct: 21  ANDVVTQHADLVRRIAHHLAARLPASVEVDDLIQAGMIGLIEASRSYDSEQGASFETYAS 80

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ +M + I R    V        +     +R+++        N  +      +A  +
Sbjct: 81  IRIRGSMIDEIRR-GDWVPRSVHRRARDAAAAVRKIE-------QNTGRAAAATEVAAAM 132

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   + + +    A  + L+      D          +           +  ER     
Sbjct: 133 EMPLPDYLRLMEDAARGQVLSLESRIEDHGE-------LDTTAKGGPNPQQMMERGEFGR 185

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            L +++  L  RE+ +       E  + L+ + +   VS  RV QI  +A  +++  ++
Sbjct: 186 ELGKAIGQLPEREQLVLSLYY--EQELNLKEIGAVLGVSESRVCQIHGQAVVRLRGRLK 242


>gi|327537603|gb|EGF24315.1| RNA polymerase ECF-type sigma factor [Rhodopirellula baltica WH47]
          Length = 340

 Score = 91.8 bits (227), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 69/316 (21%), Positives = 126/316 (39%), Gaps = 96/316 (30%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSA---------------- 49
           ++ I    + L  ++  + + P+L+ ++E +L +R       +A                
Sbjct: 89  IATIRRSGVDLPIHLGRLCEAPLLKPEQEKMLFERMNYLLQQAAIHRSVLNPERPSRHRL 148

Query: 50  -------------AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                          R+V ++LRLV  I   +        +++S+G + L++AV+KFD +
Sbjct: 149 ELIELFVALADWHRDRIVEANLRLVFSIVKKFVNPNNTFDDLLSDGIVALIRAVEKFDFD 208

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RGFR +TY       A Q     S+  V +     QK        ++G LQ +  +  + 
Sbjct: 209 RGFRFSTY-------ATQVVRRNSYRTVVLKQQERQK--------VQGGLQDMDIDVSEE 253

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           E+  AI      SE     +  RL+                      ++ D D +E+ +I
Sbjct: 254 ERSSAI------SEKRWHELRSRLS---------------------VMLGDLDRREKFII 286

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
                        R+   L P  R++           TL++L+    VS+ERVRQ+E RA
Sbjct: 287 -------------RARFSLGP-HRKV----------HTLQSLADRLGVSKERVRQLERRA 322

Query: 277 FKKVQESIQKQVELSS 292
             K++ ++   V+L+ 
Sbjct: 323 MDKLR-AMAGDVQLAE 337


>gi|289425371|ref|ZP_06427148.1| sigma-70, region 4 [Propionibacterium acnes SK187]
 gi|289427143|ref|ZP_06428859.1| sigma-70, region 4 [Propionibacterium acnes J165]
 gi|295130519|ref|YP_003581182.1| sigma-70, region 4 [Propionibacterium acnes SK137]
 gi|289154349|gb|EFD03037.1| sigma-70, region 4 [Propionibacterium acnes SK187]
 gi|289159612|gb|EFD07800.1| sigma-70, region 4 [Propionibacterium acnes J165]
 gi|291375175|gb|ADD99029.1| sigma-70, region 4 [Propionibacterium acnes SK137]
 gi|313764535|gb|EFS35899.1| sigma-70, region 4 [Propionibacterium acnes HL013PA1]
 gi|313772426|gb|EFS38392.1| sigma-70, region 4 [Propionibacterium acnes HL074PA1]
 gi|313792224|gb|EFS40325.1| sigma-70, region 4 [Propionibacterium acnes HL110PA1]
 gi|313801827|gb|EFS43061.1| sigma-70, region 4 [Propionibacterium acnes HL110PA2]
 gi|313807437|gb|EFS45924.1| sigma-70, region 4 [Propionibacterium acnes HL087PA2]
 gi|313809944|gb|EFS47665.1| sigma-70, region 4 [Propionibacterium acnes HL083PA1]
 gi|313813018|gb|EFS50732.1| sigma-70, region 4 [Propionibacterium acnes HL025PA1]
 gi|313816077|gb|EFS53791.1| sigma-70, region 4 [Propionibacterium acnes HL059PA1]
 gi|313818482|gb|EFS56196.1| sigma-70, region 4 [Propionibacterium acnes HL046PA2]
 gi|313825126|gb|EFS62840.1| sigma-70, region 4 [Propionibacterium acnes HL063PA1]
 gi|313827695|gb|EFS65409.1| sigma-70, region 4 [Propionibacterium acnes HL063PA2]
 gi|313830275|gb|EFS67989.1| sigma-70, region 4 [Propionibacterium acnes HL007PA1]
 gi|313834076|gb|EFS71790.1| sigma-70, region 4 [Propionibacterium acnes HL056PA1]
 gi|313838653|gb|EFS76367.1| sigma-70, region 4 [Propionibacterium acnes HL086PA1]
 gi|314915531|gb|EFS79362.1| sigma-70, region 4 [Propionibacterium acnes HL005PA4]
 gi|314920001|gb|EFS83832.1| sigma-70, region 4 [Propionibacterium acnes HL050PA3]
 gi|314932014|gb|EFS95845.1| sigma-70, region 4 [Propionibacterium acnes HL067PA1]
 gi|314955884|gb|EFT00284.1| sigma-70, region 4 [Propionibacterium acnes HL027PA1]
 gi|314958197|gb|EFT02300.1| sigma-70, region 4 [Propionibacterium acnes HL002PA1]
 gi|314960081|gb|EFT04183.1| sigma-70, region 4 [Propionibacterium acnes HL002PA2]
 gi|314962882|gb|EFT06982.1| sigma-70, region 4 [Propionibacterium acnes HL082PA1]
 gi|314967752|gb|EFT11851.1| sigma-70, region 4 [Propionibacterium acnes HL037PA1]
 gi|314973281|gb|EFT17377.1| sigma-70, region 4 [Propionibacterium acnes HL053PA1]
 gi|314975956|gb|EFT20051.1| sigma-70, region 4 [Propionibacterium acnes HL045PA1]
 gi|314978286|gb|EFT22380.1| sigma-70, region 4 [Propionibacterium acnes HL072PA2]
 gi|314984025|gb|EFT28117.1| sigma-70, region 4 [Propionibacterium acnes HL005PA1]
 gi|314988208|gb|EFT32299.1| sigma-70, region 4 [Propionibacterium acnes HL005PA2]
 gi|314990010|gb|EFT34101.1| sigma-70, region 4 [Propionibacterium acnes HL005PA3]
 gi|315078096|gb|EFT50147.1| sigma-70, region 4 [Propionibacterium acnes HL053PA2]
 gi|315080726|gb|EFT52702.1| sigma-70, region 4 [Propionibacterium acnes HL078PA1]
 gi|315084397|gb|EFT56373.1| sigma-70, region 4 [Propionibacterium acnes HL027PA2]
 gi|315085736|gb|EFT57712.1| sigma-70, region 4 [Propionibacterium acnes HL002PA3]
 gi|315088845|gb|EFT60821.1| sigma-70, region 4 [Propionibacterium acnes HL072PA1]
 gi|315096194|gb|EFT68170.1| sigma-70, region 4 [Propionibacterium acnes HL038PA1]
 gi|315098455|gb|EFT70431.1| sigma-70, region 4 [Propionibacterium acnes HL059PA2]
 gi|327326110|gb|EGE67900.1| RNA polymerase sigma factor [Propionibacterium acnes HL096PA2]
 gi|327332019|gb|EGE73756.1| RNA polymerase sigma factor [Propionibacterium acnes HL096PA3]
 gi|327443222|gb|EGE89876.1| sigma-70, region 4 [Propionibacterium acnes HL013PA2]
 gi|327446006|gb|EGE92660.1| sigma-70, region 4 [Propionibacterium acnes HL043PA2]
 gi|327448014|gb|EGE94668.1| sigma-70, region 4 [Propionibacterium acnes HL043PA1]
 gi|327450862|gb|EGE97516.1| sigma-70, region 4 [Propionibacterium acnes HL087PA3]
 gi|327453061|gb|EGE99715.1| sigma-70, region 4 [Propionibacterium acnes HL092PA1]
 gi|327453790|gb|EGF00445.1| sigma-70, region 4 [Propionibacterium acnes HL083PA2]
 gi|328753549|gb|EGF67165.1| sigma-70, region 4 [Propionibacterium acnes HL020PA1]
 gi|328754281|gb|EGF67897.1| sigma-70, region 4 [Propionibacterium acnes HL087PA1]
 gi|328754466|gb|EGF68082.1| sigma-70, region 4 [Propionibacterium acnes HL025PA2]
 gi|328760671|gb|EGF74238.1| RNA polymerase sigma factor [Propionibacterium acnes HL099PA1]
          Length = 270

 Score = 91.8 bits (227), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 51/255 (20%), Positives = 103/255 (40%), Gaps = 37/255 (14%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKK 92
           E  L +R  + G + A   L    L +V+  A      Y   + +++  G IGL +A+++
Sbjct: 47  EAEL-RRISDDG-VGARQTLWRQMLAIVLTQARQAAVSYRCSVEDLIQAGCIGLGEAIER 104

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           +D  RG R +T +  WI+  + E ++R          A  + +      +    + +T  
Sbjct: 105 YDVRRGARFSTVAWTWIRRRIGEEVVRLSG-------ARSRSVMREAAEVARIEEELTAR 157

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
                   AIA ++     +V+ +  R          +   +  +S ++   V      +
Sbjct: 158 WQSVPSSDAIAARMG---KDVMWVEKRR---------VECWEVETSFFEQVAVVQKSCDD 205

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPVTLENLSSEFEVSRERVRQ 271
                           +  + +L  +ERRI E R   +  P+T+  ++ E  +S   VR+
Sbjct: 206 PE--------------SGLIGLLTGQERRIVELRHGFEGEPMTITAVAHELGLSASNVRR 251

Query: 272 IEARAFKKVQESIQK 286
           IE RA  +++  +Q+
Sbjct: 252 IEQRALGRLRRHLQQ 266


>gi|134298861|ref|YP_001112357.1| sigma-70 region 2 domain-containing protein [Desulfotomaculum
           reducens MI-1]
 gi|134051561|gb|ABO49532.1| sigma-70 region 2 domain protein [Desulfotomaculum reducens MI-1]
          Length = 118

 Score = 91.8 bits (227), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 36/106 (33%), Positives = 56/106 (52%), Gaps = 3/106 (2%)

Query: 9   IVNGEIGLSRYI-HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           +VNG + L  YI +     P+ E +E   LA      GD  A + L   +LRLV  I   
Sbjct: 13  VVNGVMALVSYIANNTFPQPLKEVEEARYLA--LLAEGDEMARNILTERNLRLVAHIVKK 70

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           +   G  + +++S G IGL++A+  F  ++G RLATY+   I+ A+
Sbjct: 71  FDSTGEDVDDLISIGTIGLIKAINTFKADKGTRLATYAARCIENAI 116


>gi|21242677|ref|NP_642259.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. citri str.
           306]
 gi|294664736|ref|ZP_06730065.1| RNA polymerase sigma factor [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 10535]
 gi|21108148|gb|AAM36795.1| RNA polymerase sigma factor [Xanthomonas axonopodis pv. citri str.
           306]
 gi|292605490|gb|EFF48812.1| RNA polymerase sigma factor [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 10535]
          Length = 255

 Score = 91.8 bits (227), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 44/239 (18%), Positives = 92/239 (38%), Gaps = 20/239 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           A+ +VT H  LV +IA          + + +++  G IGL++A + +D E+G    TY+ 
Sbjct: 21  ANDVVTQHADLVRRIAHHLAARLPASVEVDDLIQAGMIGLIEASRSYDSEQGASFETYAS 80

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ +M + I R    V        +     +R+++        N  +      +A  +
Sbjct: 81  IRIRGSMIDEIRR-GDWVPRSVHRRARDAAAAVRKIE-------QNTGRAAAATEVAAAM 132

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   + + +    A  + L+      D          +           +  ER     
Sbjct: 133 EMPLPDYLRLMEDAARGQVLSLESRIEDHGE-------LDTTAKGGPNPQQMMERGEFGR 185

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            L +++  L  RE+ +       E  + L+ + +   VS  RV QI  +A  +++  ++
Sbjct: 186 ELGKAIGQLPEREQLVLSLYY--EQELNLKEIGAVLGVSESRVCQIHGQAVVRLRGRLK 242


>gi|301055830|ref|YP_003794041.1| RNA polymerase sigma-28 factor [Bacillus anthracis CI]
 gi|300377999|gb|ADK06903.1| RNA polymerase sigma-28 factor [Bacillus cereus biovar anthracis
           str. CI]
          Length = 181

 Score = 91.4 bits (226), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 36/220 (16%), Positives = 73/220 (33%), Gaps = 62/220 (28%)

Query: 63  KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
                +   G    +++S G IGL++A++ +   +G +LATY+   I             
Sbjct: 7   HNVKKFENTGEDAEDLISIGTIGLIKAIESYSAGKGTKLATYAARCI------------- 53

Query: 123 LVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
                    +  +  +LR LK                                       
Sbjct: 54  ---------ENEILMHLRVLKKT-----------------------------------KK 69

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
           D SL+  I    + +   +  L+     + + +I+  +       +   + +L+ RE+ +
Sbjct: 70  DVSLHDPIGQDKEGN---EISLIDILKSESEDVIDMIQLSMELEKIKEYIDILDEREKEV 126

Query: 243 FEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
              R     +   T   ++    +SR  V +IE RA  K+
Sbjct: 127 IVKRFGLGLDKEKTQREIAKALGISRSYVSRIEKRALMKM 166


>gi|455127|gb|AAA22315.1| RNA polymerase sigma-K subunit (cisB) [Bacillus subtilis]
 gi|1303780|dbj|BAA12436.1| SpoIVCB [Bacillus subtilis]
          Length = 156

 Score = 91.4 bits (226), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 26/108 (24%), Positives = 50/108 (46%), Gaps = 1/108 (0%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           +  +V   + L  Y+        L   EE    +   + GD  A + L+  +LRLV  I 
Sbjct: 9   LGFVVKELVFLVSYVKNNAFPQPLSSSEEKKYLELMAK-GDEHARNMLIEHNLRLVAHIV 67

Query: 66  MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
             +   G    +++S G IGL++ ++ +   +G ++ATY+   I+  +
Sbjct: 68  KKFENTGEDAEDLISIGTIGLIKGIESYSAGKGTKVATYAARCIENEI 115


>gi|315108409|gb|EFT80385.1| sigma-70, region 4 [Propionibacterium acnes HL030PA2]
          Length = 270

 Score = 91.4 bits (226), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 51/255 (20%), Positives = 103/255 (40%), Gaps = 37/255 (14%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKK 92
           E  L +R  + G + A   L    L +V+  A      Y   + +++  G IGL +A+++
Sbjct: 47  EAEL-RRISDDG-VGARQTLWRRMLAIVLTQARQAAVSYRCSVEDLIQAGCIGLGEAIER 104

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           +D  RG R +T +  WI+  + E ++R          A  + +      +    + +T  
Sbjct: 105 YDVRRGARFSTVAWTWIRRRIGEEVVRLSG-------ARSRSVMREAAEVARIEEELTAR 157

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
                   AIA ++     +V+ +  R          +   +  +S ++   V      +
Sbjct: 158 WQSVPSSDAIAARMG---KDVMWVEKRR---------VECWEVETSFFEQVAVVQKSCDD 205

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPVTLENLSSEFEVSRERVRQ 271
                           +  + +L  +ERRI E R   +  P+T+  ++ E  +S   VR+
Sbjct: 206 PE--------------SGLIGLLTGQERRIVELRHGFEGEPMTITAVAHELGLSASNVRR 251

Query: 272 IEARAFKKVQESIQK 286
           IE RA  +++  +Q+
Sbjct: 252 IEQRALGRLRRHLQQ 266


>gi|258645545|ref|ZP_05733014.1| RNA polymerase sigma-F factor [Dialister invisus DSM 15470]
 gi|260402901|gb|EEW96448.1| RNA polymerase sigma-F factor [Dialister invisus DSM 15470]
          Length = 205

 Score = 91.4 bits (226), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 45/160 (28%), Positives = 78/160 (48%), Gaps = 2/160 (1%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           LS YI  + K   L ++EE  L   Y+  G+L A  +L+  +  LV K A  Y      +
Sbjct: 2   LSEYISSLPKEGKLSREEEARLWDAYKNEGELEARQKLIEHYQLLVFKEATKYPVQETVL 61

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EG +GLM+A +KFD E+G   + Y++  I+  M +++ +  + + +G    +K  
Sbjct: 62  LDLIQEGTVGLMEAAEKFDIEQGVAFSLYAIHRIRGRMLDFLRKGQNDILMGEEQEEK-- 119

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
            F L+        +TD N     V     +L + E +VI 
Sbjct: 120 LFTLQVAPDTAFEVTDRNSLHSAVSMAVSRLPMKEQDVIR 159



 Score = 41.7 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 15/78 (19%), Positives = 38/78 (48%), Gaps = 2/78 (2%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
                E  +R +  + ++ ++S L  +E+ +  +  L+E   T+   ++E +VS   V +
Sbjct: 127 PDTAFEVTDRNSLHSAVSMAVSRLPMKEQDVIRSVYLKE--KTVAETANEMDVSTAYVYR 184

Query: 272 IEARAFKKVQESIQKQVE 289
           +E R   +++  + K + 
Sbjct: 185 LEKRGIHRLRGMLSKLMH 202


>gi|327330175|gb|EGE71924.1| RNA polymerase sigma factor [Propionibacterium acnes HL097PA1]
          Length = 270

 Score = 91.4 bits (226), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 49/250 (19%), Positives = 101/250 (40%), Gaps = 36/250 (14%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           +R  + G + A   L    L +V+  A      Y   + +++  G IGL +A++++D  R
Sbjct: 51  RRISDDG-VGARQTLWRQMLAIVLTQARQAAVSYRCSVEDLIQAGCIGLGEAIERYDVRR 109

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G R +T +  WI+  + E ++R          A  + +      +    + +T       
Sbjct: 110 GARFSTVAWTWIRRRIGEEVVRLSG-------ARSRSVMREAAEVARIEEELTARWQSVP 162

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
              AIA ++     +V+ +  R          +   +  +S ++   V      +     
Sbjct: 163 SSDAIAARMG---KDVMWVEKRR---------VECWEVETSFFEQVAVVQKSCDDPE--- 207

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPVTLENLSSEFEVSRERVRQIEARA 276
                      +  + +L  +ERRI E R   +  P+T+  ++ E  +S   VR+IE RA
Sbjct: 208 -----------SGLIGLLTGQERRIVELRHGFEGEPMTITAVAHELGLSASNVRRIEQRA 256

Query: 277 FKKVQESIQK 286
             +++  +Q+
Sbjct: 257 LGRLRRHLQQ 266


>gi|170737028|ref|YP_001778288.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia
           cenocepacia MC0-3]
 gi|169819216|gb|ACA93798.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Burkholderia
           cenocepacia MC0-3]
          Length = 242

 Score = 91.4 bits (226), Expect = 1e-16,   Method: Composition-based stats.
 Identities = 47/254 (18%), Positives = 107/254 (42%), Gaps = 25/254 (9%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAV 90
           EY  A+R  +    +   R +T +  LV +I        G  +   ++   G +GL++A+
Sbjct: 8   EYQSAQRENQTLSPADEARWMTQYAPLVKRIVRKLASQAGGAMEACDLEQLGLMGLLEAL 67

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           +++  E       ++++ ++ A+ + + R           + ++    LR  +  L+   
Sbjct: 68  RRYG-EPDDEFEHFALFRVRGAILDELRRQD-----WRPRSARQGAHRLRGTERALRREL 121

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
             +   E+V   A ++   E E + ++       S +AL+    +          Y+ D 
Sbjct: 122 GRDPTKEEVCN-ALEIGDDEYEQLQLDDCAQEFVSFDALLEEDAER---------YECDS 171

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
            + +    E R   R+ L +++ VL+ RE++I +     E  ++   + +   ++R RV 
Sbjct: 172 SDGI----EHRAMLRHSLEQALGVLDAREQQIIQLYY--EFDLSQAEIGAVLGLTRARVC 225

Query: 271 QIEARAFKKVQESI 284
           QI   A  K++  +
Sbjct: 226 QINKSALVKMRNRL 239


>gi|260221743|emb|CBA30612.1| hypothetical protein Csp_C24420 [Curvibacter putative symbiont of
           Hydra magnipapillata]
          Length = 264

 Score = 91.4 bits (226), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 41/254 (16%), Positives = 106/254 (41%), Gaps = 20/254 (7%)

Query: 51  HRLVTSHLRLVVKIAM---GYRGYGLPISEVVSEGNIGLMQAVKKF-DPERGFRLATYSM 106
            +LV  H  +V  +A          +  +++V +G +GLM+A+ ++     G     Y  
Sbjct: 13  RKLVEDHQPVVRSVANHVGRRLPPNVDRADLVQDGMLGLMEALLRWTKESSGTHFENYIA 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
              + AM + + R+   V        +++  ++RR++  LQ ++    +P     +AK+L
Sbjct: 73  LRAQGAMIDGL-RAADPVS-------RQVRKDMRRVEVALQQLSHRLGRPPTEGELAKQL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++  ++   +     G   ++    + D      +  L  + D      +   ER   R 
Sbjct: 125 DMPLADYQRLLQDAQGYVLISLQDLTGDSVDQYLKRCLEDNAD-----PLALLERAALRQ 179

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI-Q 285
            L  S+ +L  + + +       E+ + +  ++    +S  R+ Q+  ++  +++ S+  
Sbjct: 180 ALAESIQLLPRKSQILLTLYY--EHEMRMHEIAKHLGLSEARISQMHTQSIAQLRASLAD 237

Query: 286 KQVELSSSPPLLQK 299
           + ++   +P +  +
Sbjct: 238 RDIKRLLTPRMRPR 251


>gi|260752875|ref|YP_003225768.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Zymomonas mobilis
           subsp. mobilis NCIMB 11163]
 gi|258552238|gb|ACV75184.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Zymomonas mobilis
           subsp. mobilis NCIMB 11163]
          Length = 195

 Score = 91.4 bits (226), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 45/210 (21%), Positives = 91/210 (43%), Gaps = 20/210 (9%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           + +++  G + L++A   F+  RGF  ATY+   I+ AM +Y+ +  +  +  + A QK 
Sbjct: 1   MEDLIQIGMVALIEAANAFE-NRGFAFATYASMRIRGAMIDYMRQHAATAR-SSIARQKT 58

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           L           + ++    +  +   IA+KLN+S SE          D ++N    S D
Sbjct: 59  L-------NKAREELSATLGRRPEDAEIAEKLNMSPSEYREW-----ADGAINIRQESLD 106

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
              S        D+  Q   +    ER+  ++ L   +  L  RE  + +   ++E  + 
Sbjct: 107 DVYSDHSSIFTDDNADQASEM----EREALQSALAEQIKTLPEREALVLQLYYVEE--LN 160

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L+ +    ++   R+ QI+  A   +++ +
Sbjct: 161 LKEIGEVLDLGTARISQIKKSAVDHLRQKM 190


>gi|225075400|ref|ZP_03718599.1| hypothetical protein NEIFLAOT_00405 [Neisseria flavescens
           NRL30031/H210]
 gi|224953218|gb|EEG34427.1| hypothetical protein NEIFLAOT_00405 [Neisseria flavescens
           NRL30031/H210]
          Length = 113

 Score = 91.4 bits (226), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 30/98 (30%), Positives = 56/98 (57%), Gaps = 1/98 (1%)

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            D+++    DWL        + L ++     +   L  +++ L+ R  RI E+R LQ++ 
Sbjct: 14  DDEDNFAPIDWLADHDAEPSRQLSKQAHYALQTEGLQNALAQLDDRSHRIVESRWLQDDG 73

Query: 253 -VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
            +TL  L++E+ VS ER+RQIEA+A +K++  + ++ E
Sbjct: 74  GLTLHELAAEYGVSAERIRQIEAKAMQKLRGFLAEEAE 111


>gi|166712012|ref|ZP_02243219.1| RNA polymerase sigma factor [Xanthomonas oryzae pv. oryzicola
           BLS256]
 gi|289666124|ref|ZP_06487705.1| RNA polymerase sigma factor [Xanthomonas campestris pv. vasculorum
           NCPPB702]
          Length = 255

 Score = 91.4 bits (226), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 44/239 (18%), Positives = 92/239 (38%), Gaps = 20/239 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           A+ +VT H  LV +IA          + + +++  G IGL++A + +D E+G    TY+ 
Sbjct: 21  ANDVVTQHADLVRRIAHHLAARLPASVEVDDLIQAGMIGLIEASRSYDSEQGASFETYAS 80

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ +M + I R    V        +     +R+++        N  +      +A  +
Sbjct: 81  IRIRGSMIDEIRR-GDWVPRSVHRRARDAAAAVRKIE-------QNTGRAAAATEVAAAM 132

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   + + +    A  + L+      D          +           +  ER     
Sbjct: 133 EMPLPDYLRLMEDAARGQVLSLESRIEDHGE-------LDTTAKGGPNPQQMMERGEFGR 185

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            L +++  L  RE+ +       E  + L+ + +   VS  RV QI  +A  +++  ++
Sbjct: 186 ELGKAIGQLPEREQLVLSLYY--EQELNLKEIGAVLGVSESRVCQIHGQAVVRLRGRLK 242


>gi|160902849|ref|YP_001568430.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Petrotoga mobilis
           SJ95]
 gi|160360493|gb|ABX32107.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Petrotoga mobilis
           SJ95]
          Length = 231

 Score = 91.0 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 54/238 (22%), Positives = 108/238 (45%), Gaps = 20/238 (8%)

Query: 51  HRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            +LV   L  +  IA+  +      + + +++ EG IGL+Q+ K+++PE+G    TY++ 
Sbjct: 8   EQLVMEFLPKIKIIALNLKTTLPKNIELEDLIQEGIIGLLQSYKRYNPEKGTSFYTYALK 67

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            IK +M +Y+ R   L K   +  +K  + +L       + I DN        ++A+KL+
Sbjct: 68  RIKGSMYDYLRRIDWLPKDVRSLVKK--YEDLIYECKDNEYIDDN--------SVAEKLH 117

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + +++V  +   L+  + L       +     W + +  ++D           +    + 
Sbjct: 118 IEKNDVDKIKFSLSKRQILQLDEYFLNNEEDTWLEDIQEEND-----PEILAYKDMLHDK 172

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           LT S+  L  RE+ I          +T + + S  E+S  RV Q+ +    K+++ IQ
Sbjct: 173 LTESIEKLEEREKLILSLYY--NEGLTFKEIGSVLEISESRVSQLHSVILVKLKKMIQ 228


>gi|170764001|ref|ZP_02637018.2| RNA polymerase sigma-K factor [Clostridium perfringens B str. ATCC
           3626]
 gi|170710658|gb|EDT22840.1| RNA polymerase sigma-K factor [Clostridium perfringens B str. ATCC
           3626]
          Length = 152

 Score = 91.0 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 35/119 (29%), Positives = 59/119 (49%), Gaps = 5/119 (4%)

Query: 9   IVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           +V  +I L+ Y+      P  L ++EE +  +R ++ GD+ A   LV  +LRLV  I   
Sbjct: 10  LVGSKIFLTGYVTGNSTFPKPLNEKEEKIYLERLKD-GDVEAKRVLVERNLRLVAHIVKK 68

Query: 68  YRGYGL---PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           Y         + +++S G IGL++A+  FD  +G RLATY+   I   +  +   +   
Sbjct: 69  YSSNYQNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATYAAKCIDNEILMFFRNTKKT 127


>gi|332755592|gb|EGJ85955.1| RNA polymerase sigma factor rpoS domain protein [Shigella flexneri
           2747-71]
          Length = 133

 Score = 91.0 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 32/74 (43%), Positives = 50/74 (67%), Gaps = 1/74 (1%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKK 92
           + EGN+GL++AV+K
Sbjct: 120 IEEGNLGLIRAVEK 133


>gi|67921071|ref|ZP_00514590.1| Sigma-70 region 2:Sigma-70 region 1.2 [Crocosphaera watsonii WH
           8501]
 gi|67857188|gb|EAM52428.1| Sigma-70 region 2:Sigma-70 region 1.2 [Crocosphaera watsonii WH
           8501]
          Length = 250

 Score = 91.0 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 33/106 (31%), Positives = 60/106 (56%), Gaps = 7/106 (6%)

Query: 20  IHEI-----RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           + EI      +  +L   +   L +  ++ G + A   ++ ++LRLVV +A  Y+  GL 
Sbjct: 147 LKEILVQGKSQWAVLANMDVAEL-EEIQKSG-IKAKDEIIKANLRLVVSVAKKYQHRGLE 204

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           + +++ EG +GL +AV+KFDP +G+R +TY+ WWI+  +     R 
Sbjct: 205 LLDLIQEGTLGLEKAVEKFDPVKGYRFSTYAYWWIRQGITSAAWRK 250


>gi|289670573|ref|ZP_06491648.1| RNA polymerase sigma factor [Xanthomonas campestris pv. musacearum
           NCPPB4381]
          Length = 255

 Score = 91.0 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 44/239 (18%), Positives = 92/239 (38%), Gaps = 20/239 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           A+ +VT H  LV +IA          + + +++  G IGL++A + +D E+G    TY+ 
Sbjct: 21  ANDVVTQHADLVRRIAHHLAARLPASVEVDDLIQAGMIGLIEASRSYDSEQGASFETYAS 80

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ +M + I R    V        +     +R+++        N  +      +A  +
Sbjct: 81  IRIRGSMIDEIRR-GDWVPRSVHRRARDAAAAVRKIE-------QNTGRAAAATEVAAAM 132

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   + + +    A  + L+      D          +           +  ER     
Sbjct: 133 EMPLLDYLRLMEDAARGQVLSLESRIEDHGE-------LDTTAKGGPNPQQMMERGEFGR 185

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            L +++  L  RE+ +       E  + L+ + +   VS  RV QI  +A  +++  ++
Sbjct: 186 ELGKAIGQLPEREQLVLSLYY--EQELNLKEIGAVLGVSESRVCQIHGQAVVRLRGRLK 242


>gi|253688938|ref|YP_003018128.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pectobacterium
           carotovorum subsp. carotovorum PC1]
 gi|251755516|gb|ACT13592.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pectobacterium
           carotovorum subsp. carotovorum PC1]
          Length = 240

 Score = 91.0 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 37/235 (15%), Positives = 94/235 (40%), Gaps = 17/235 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KNSLWKRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLSAVERYDSLQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ +M + +               + +  N R +   +Q       +      +A+ L
Sbjct: 73  QRIRGSMLDELR--------SRDWAPRSVRRNAREVAQAMQQAEQQLGRTPTEQEVAQAL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           N++  +   +      D + + L +  +                ++   + +    N R+
Sbjct: 125 NITLEDYRQILL----DTNNSQLFSYDEWREEHGDSAEALLEGNEDANPLHQLMEGNLRH 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++
Sbjct: 181 RVMDAIESLPEREKLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 233


>gi|90415333|ref|ZP_01223267.1| flagellar biosynthesis sigma factor FliA [marine gamma
           proteobacterium HTCC2207]
 gi|90332656|gb|EAS47826.1| flagellar biosynthesis sigma factor FliA [marine gamma
           proteobacterium HTCC2207]
          Length = 240

 Score = 91.0 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 48/256 (18%), Positives = 96/256 (37%), Gaps = 26/256 (10%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           A+ Y E  +       +  ++ LV ++A    G     + + E++  G IGL++A K FD
Sbjct: 4   ARIYEEIQNADQQSTSLVDYIGLVKRVALHLKGRLPNFMELDELIQVGMIGLIEADKSFD 63

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +G     ++   I+ A+ + + +   L         +    ++R       A+T    
Sbjct: 64  STKGVDFEVFAKNRIRGAILDQVRKMSYL--------PRSAIVSIRDHNEASAALTGELG 115

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +      +A  +                    SL A        +S+  D    +    E
Sbjct: 116 RAPSQAELADFMGKDADTFQKERTHAHRFQTVSLEA-------QTSESVDLPTGNSSNPE 168

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           + L+E    +   + L  S+  L  R+R I     ++E  + L+ + +  +VS  RV QI
Sbjct: 169 KELVE----EQFMDALAASIGELPERDRTIVSLYYVEE--MNLKEIGAVLDVSESRVSQI 222

Query: 273 EARAFKKVQESIQKQV 288
            +   K ++  +   V
Sbjct: 223 LSACVKTLRVKMHNHV 238


>gi|219129831|ref|XP_002185083.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217403578|gb|EEC43530.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 435

 Score = 91.0 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 49/291 (16%), Positives = 106/291 (36%), Gaps = 63/291 (21%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGY--------GLPISEVVSEGNIGLMQAVKKFDPERGF 99
           ++   +VT ++ LV   A    G          L   +++ EG IGL +AV +++PE G 
Sbjct: 147 ASRETMVTRNMGLVHFCANDIVGTQARPSRLQTLSREDLIQEGAIGLARAVDRWNPEIGG 206

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL----- 154
           + +TY+++W++AA+   I     LV++    +       + R    L    D N      
Sbjct: 207 KFSTYAVYWVRAAILRCIAERDDLVRVPEHVS--AAVRKISRAARQLGIDIDGNDLISSV 264

Query: 155 --------KPEQVVAIAKKLNVSESEVISMN----CRLAGDESLNALINSSDKNSSQWQD 202
                   + +   A+A++  ++  +V         R  G  S  A +      ++    
Sbjct: 265 YSKDASWKEAQAAKALAEEAGLTPRQVSEAIKVKARRRGGMLSFEAWMQQGQDFATDLTP 324

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ------------- 249
            +  D+       +   E +  ++ L++    L P+E      R                
Sbjct: 325 VVADDN------PLASLETEQLKSTLSKF---LRPKEMEALSWRYGLQRDYVAEAEEELF 375

Query: 250 --------------ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                            ++   +  + +VS E  R++  +A  K++ + ++
Sbjct: 376 GRSPRAPITVKGRWGEAMSFTEVGKKMKVSAEYGRRLCHKALNKLRVAAEE 426


>gi|149927789|ref|ZP_01916040.1| sigma 28 (Flagella/Sporulation) [Limnobacter sp. MED105]
 gi|149823411|gb|EDM82642.1| sigma 28 (Flagella/Sporulation) [Limnobacter sp. MED105]
          Length = 238

 Score = 91.0 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 46/240 (19%), Positives = 97/240 (40%), Gaps = 15/240 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             + V  ++ LV ++A          + I +++  G IGLM A+ +F+  +G +  TY+ 
Sbjct: 10  KSKQVDQYIPLVRRLAHHLIAKLPASVQIDDLIQAGLIGLMDAITRFEEGQGAQFETYAS 69

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   +  G    Q+++     R +  L        +      IA  +
Sbjct: 70  QRIRGAMLDEL-RSADWMPRGVRQAQRKIETATLRAEQKL-------GRSASEKEIADVM 121

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            VS  E   M     G   +     + D +   + D  +   +  E   +E    +  R 
Sbjct: 122 GVSLDEYQDMLFDSRGASLVFYDDYADDGDGEGYLDRQIGGDE--EANPLEMLGDQRFRE 179

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L +++  L  RE+ +       E  +    +++   V+  RV Q+  +A  +++  +++
Sbjct: 180 NLIQAIEDLPEREKMLMGLYY--EQELNFREIAAVLGVTESRVCQLHTQAVSRLKAKLRE 237


>gi|58582244|ref|YP_201260.1| RNA polymerase sigma factor FliA [Xanthomonas oryzae pv. oryzae
           KACC10331]
 gi|84624137|ref|YP_451509.1| RNA polymerase sigma factor FliA [Xanthomonas oryzae pv. oryzae
           MAFF 311018]
 gi|188576807|ref|YP_001913736.1| RNA polymerase sigma factor FliA [Xanthomonas oryzae pv. oryzae
           PXO99A]
 gi|188577000|ref|YP_001913929.1| RNA polymerase sigma factor FliA [Xanthomonas oryzae pv. oryzae
           PXO99A]
 gi|6969595|gb|AAF33832.1|AF226282_6 RNA polymerase sigma factor FliA [Xanthomonas oryzae pv. oryzae]
 gi|58426838|gb|AAW75875.1| RNA polymerase sigma factor FliA [Xanthomonas oryzae pv. oryzae
           KACC10331]
 gi|84368077|dbj|BAE69235.1| RNA polymerase sigma factor FliA [Xanthomonas oryzae pv. oryzae
           MAFF 311018]
 gi|188521259|gb|ACD59204.1| RNA polymerase sigma factor FliA [Xanthomonas oryzae pv. oryzae
           PXO99A]
 gi|188521452|gb|ACD59397.1| RNA polymerase sigma factor FliA [Xanthomonas oryzae pv. oryzae
           PXO99A]
          Length = 251

 Score = 91.0 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 44/239 (18%), Positives = 91/239 (38%), Gaps = 20/239 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           A  +VT H  LV +IA          + + +++  G IGL++A + +D E+G    TY+ 
Sbjct: 17  ADNVVTQHADLVRRIAHHLAARLPASVEVDDLIQAGMIGLIEASRSYDSEQGASFETYAS 76

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ +M + I R    V        +     +R+++        N  +      +A  +
Sbjct: 77  IRIRGSMIDEIRR-GDWVPRSVHRRARDAAAAVRKIE-------QNTGRAAAAAEVAAAM 128

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   + + +    A  + L+      D          +           +  ER     
Sbjct: 129 EMPLPDYLRLMEDAARGQVLSLESRIEDHGE-------LDTTAKGGPNPQQMMERSEFGR 181

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            L +++  L  RE+ +       E  + L+ + +   VS  RV QI  +A  +++  ++
Sbjct: 182 ELGKAIGQLPEREQLVLSLYY--EQELNLKEIGAVLGVSESRVCQIHGQAVVRLRGRLK 238


>gi|318066937|emb|CBY89083.1| RNA polymerase sigma70 factor [Halomonas desiderata]
          Length = 375

 Score = 91.0 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 31/74 (41%), Positives = 46/74 (62%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++
Sbjct: 302 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYK 361

Query: 101 LATYSMWWIKAAMQ 114
            +TY+ WWI+ A+ 
Sbjct: 362 FSTYATWWIRQAIT 375


>gi|50842442|ref|YP_055669.1| RNA polymerase sigma factor [Propionibacterium acnes KPA171202]
 gi|50840044|gb|AAT82711.1| RNA polymerase sigma factor [Propionibacterium acnes KPA171202]
 gi|315105463|gb|EFT77439.1| sigma-70, region 4 [Propionibacterium acnes HL030PA1]
          Length = 270

 Score = 91.0 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 51/255 (20%), Positives = 103/255 (40%), Gaps = 37/255 (14%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKK 92
           E  L +R  + G + A   L    L +V+  A      Y   + +++  G IGL +A+++
Sbjct: 47  EAEL-RRISDDG-VGARQTLWRQMLAIVLTQARQAAVSYRCSVEDLIQAGCIGLGEAIER 104

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           +D  RG R +T +  WI+  + E ++R          A  + +      +    + +T  
Sbjct: 105 YDVRRGARFSTVAWTWIRRRIGEEVVRLSG-------ARSRSVMREAAEVARIEEELTAR 157

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
                   AIA ++     +V+ +  R          +   +  +S ++   V      +
Sbjct: 158 WQSVPSSDAIAARMG---KDVMWVEKRR---------VECWEVETSFFEQVAVVQKSCDD 205

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPVTLENLSSEFEVSRERVRQ 271
                           +  + +L  +ERRI E R   +  P+T+  ++ E  +S   VR+
Sbjct: 206 PE--------------SGLIGLLTGQERRIVELRHGFEGEPMTITAVAHELGLSASNVRR 251

Query: 272 IEARAFKKVQESIQK 286
           IE RA  +++  +Q+
Sbjct: 252 IEQRALGRLRRHLQQ 266


>gi|256825196|ref|YP_003149156.1| RNA polymerase sigma factor, sigma-70 family [Kytococcus
           sedentarius DSM 20547]
 gi|256688589|gb|ACV06391.1| RNA polymerase sigma factor, sigma-70 family [Kytococcus
           sedentarius DSM 20547]
          Length = 261

 Score = 91.0 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 33/231 (14%), Positives = 83/231 (35%), Gaps = 22/231 (9%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           +  H+    ++   +      + +      + L+ AV+++DP     L++Y+   I   +
Sbjct: 46  IADHIPFARRLGRRFAPTPSLVDDCEQVACMALVLAVQRWDPAFDANLSSYAQPTILGEL 105

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
           + ++  S   V+      +         ++   + +  +  +      IA+ +  S  EV
Sbjct: 106 RRFLRDSTWWVRPPRRIQELAAL-----VRSTEEELRHSTGREPTAQEIARAMGASPDEV 160

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
                  AG       + S D   ++    +           +           L   + 
Sbjct: 161 SEARVAAAGR-----YVASVDDEVTETARLVHPVQSPAVDEWV----------SLHPHIQ 205

Query: 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L+PR+R +   R L++   T  +++    +S+ +V +   RA   ++E +
Sbjct: 206 ALDPRDRCVLLRRYLEDE--TQASIARALGISQAQVSRRLKRALDTLREQV 254


>gi|77020206|ref|YP_338165.1| RNA polymerase sigma factor, putative [Bacillus phage Cherry]
 gi|76563996|gb|ABA46386.1| RNA polymerase sigma factor, putative [Bacillus phage Cherry]
          Length = 248

 Score = 91.0 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 48/234 (20%), Positives = 93/234 (39%), Gaps = 30/234 (12%)

Query: 51  HRLVTSHLRLVVKIA-MGY--------RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
              +  + RLV       Y        R  GL I ++     IGL++A   FD E G   
Sbjct: 20  DEFIEKYGRLVHHCVWKRYAKKKASIERDTGLDIEDLTQFXMIGLIKARDNFDLEFGCAF 79

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY++  I   +   I  +   +K+  T    +              I +  L  ++   
Sbjct: 80  STYAVPKIIGEIGRAIRDNQK-IKVQRTVYGVK------------GKILNQQLADKEPEE 126

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           IA  L+ S S V +        +SLN ++ +S  N     + ++ D   +     + EE 
Sbjct: 127 IADILDESVSLVKTALEYQPSTDSLNKVVYASGANEELTLERMIEDTKTE-----DIEET 181

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
              R ++    + L P+E  + + R      +T +N++++   S+ ++ +I A+
Sbjct: 182 TINRAVIREFKAALPPKEYIVLDMRL---QNMTQQNIANQMGYSQVQISRILAK 232


>gi|22126347|ref|NP_669770.1| flagellar biosynthesis sigma factor [Yersinia pestis KIM 10]
 gi|45441369|ref|NP_992908.1| flagellar biosynthesis sigma factor [Yersinia pestis biovar
           Microtus str. 91001]
 gi|108807215|ref|YP_651131.1| flagellar biosynthesis sigma factor [Yersinia pestis Antiqua]
 gi|108812441|ref|YP_648208.1| flagellar biosynthesis sigma factor [Yersinia pestis Nepal516]
 gi|145598571|ref|YP_001162647.1| flagellar biosynthesis sigma factor [Yersinia pestis Pestoides F]
 gi|149366211|ref|ZP_01888246.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           CA88-4125]
 gi|165925981|ref|ZP_02221813.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Orientalis str. F1991016]
 gi|165938720|ref|ZP_02227275.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Orientalis str. IP275]
 gi|166010831|ref|ZP_02231729.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Antiqua str. E1979001]
 gi|166210907|ref|ZP_02236942.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Antiqua str. B42003004]
 gi|167401029|ref|ZP_02306532.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Antiqua str. UG05-0454]
 gi|167420291|ref|ZP_02312044.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Orientalis str. MG05-1020]
 gi|167425870|ref|ZP_02317623.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Mediaevalis str. K1973002]
 gi|167470709|ref|ZP_02335413.1| flagellar biosynthesis sigma factor [Yersinia pestis FV-1]
 gi|218928962|ref|YP_002346837.1| flagellar biosynthesis sigma factor [Yersinia pestis CO92]
 gi|229896290|ref|ZP_04511460.1| RNA polymerase, sigma 28 (sigma F) factor [Yersinia pestis
           Pestoides A]
 gi|229897227|ref|ZP_04512383.1| RNA polymerase, sigma 28 (sigma F) factor [Yersinia pestis biovar
           Orientalis str. PEXU2]
 gi|229897954|ref|ZP_04513105.1| RNA polymerase, sigma 28 (sigma F) factor [Yersinia pestis biovar
           Orientalis str. India 195]
 gi|229902815|ref|ZP_04517932.1| RNA polymerase, sigma 28 (sigma F) factor [Yersinia pestis
           Nepal516]
 gi|270486604|ref|ZP_06203678.1| flagellar biosynthesis sigma factor [Yersinia pestis KIM D27]
 gi|294503994|ref|YP_003568056.1| flagellar biosynthesis sigma factor FliA [Yersinia pestis Z176003]
 gi|21959330|gb|AAM86021.1|AE013850_3 alternative sigma factor 28 [Yersinia pestis KIM 10]
 gi|45436229|gb|AAS61785.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Microtus str. 91001]
 gi|108776089|gb|ABG18608.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           Nepal516]
 gi|108779128|gb|ABG13186.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           Antiqua]
 gi|115347573|emb|CAL20483.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           CO92]
 gi|145210267|gb|ABP39674.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           Pestoides F]
 gi|149292624|gb|EDM42698.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           CA88-4125]
 gi|165913334|gb|EDR31956.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Orientalis str. IP275]
 gi|165922185|gb|EDR39362.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Orientalis str. F1991016]
 gi|165990175|gb|EDR42476.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Antiqua str. E1979001]
 gi|166208087|gb|EDR52567.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Antiqua str. B42003004]
 gi|166961986|gb|EDR58007.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Orientalis str. MG05-1020]
 gi|167049418|gb|EDR60826.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Antiqua str. UG05-0454]
 gi|167055269|gb|EDR65066.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Mediaevalis str. K1973002]
 gi|229680262|gb|EEO76361.1| RNA polymerase, sigma 28 (sigma F) factor [Yersinia pestis
           Nepal516]
 gi|229688995|gb|EEO81060.1| RNA polymerase, sigma 28 (sigma F) factor [Yersinia pestis biovar
           Orientalis str. India 195]
 gi|229693564|gb|EEO83613.1| RNA polymerase, sigma 28 (sigma F) factor [Yersinia pestis biovar
           Orientalis str. PEXU2]
 gi|229701213|gb|EEO89242.1| RNA polymerase, sigma 28 (sigma F) factor [Yersinia pestis
           Pestoides A]
 gi|262361821|gb|ACY58542.1| flagellar biosynthesis sigma factor FliA [Yersinia pestis D106004]
 gi|262366043|gb|ACY62600.1| flagellar biosynthesis sigma factor FliA [Yersinia pestis D182038]
 gi|270335108|gb|EFA45885.1| flagellar biosynthesis sigma factor [Yersinia pestis KIM D27]
 gi|294354453|gb|ADE64794.1| flagellar biosynthesis sigma factor FliA [Yersinia pestis Z176003]
 gi|320015417|gb|ADV98988.1| RNA polymerase sigma factor RpoD [Yersinia pestis biovar Medievalis
           str. Harbin 35]
          Length = 240

 Score = 91.0 bits (225), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 38/238 (15%), Positives = 95/238 (39%), Gaps = 17/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   ++ LV   A+  +      + + +++  G I L+ AV+++D  +G    TY++
Sbjct: 13  KNSLWKRYVPLVRHEALRLQVRLPASVELDDLLQAGGIDLLNAVERYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +               + +  N R +   +Q +     +P     +A+ L
Sbjct: 73  QRIRGAMLDELR--------SRDWAPRSVRRNAREVASAMQQVEQRVGRPATEQEVAQVL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   E   +      D + + L +  +      +         ++   ++     N R 
Sbjct: 125 DIGLVEYRQILL----DTNNSQLFSYDEWREEHGESVEPLLEGHEDANPLKHLLEGNLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  +
Sbjct: 181 RVIDAIEALPEREKMVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRARL 236


>gi|78217835|gb|ABB37184.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Desulfovibrio
           desulfuricans subsp. desulfuricans str. G20]
          Length = 227

 Score = 90.6 bits (224), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 43/240 (17%), Positives = 94/240 (39%), Gaps = 25/240 (10%)

Query: 53  LVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           +V  +   +  +A+  +G     + ++E++S G +GLM+A  KF P+ G +  TY+   I
Sbjct: 1   MVRHYAPKIKFLALRLKGKLPKSVELNELISAGTLGLMEAFGKFQPKLGIKFDTYAENRI 60

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + AM + +     L     +  Q+     +R L+  +  +     +      + K   + 
Sbjct: 61  RGAMLDELR---RLDWFPRSLRQR-----VRLLEDTINRLEHEKGRRPSEEELQKATGLE 112

Query: 170 ESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           E ++ S    L      SL+A+           + +     D  E         +     
Sbjct: 113 EKDLRSGLEALQNHLCISLDAI----------QETFAADGRDHLEGEPFHSTATQELIER 162

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +   +  L PRE+ +       E  + +   +    V+  RV Q+ ++A  ++++   +Q
Sbjct: 163 IASLIDQLTPREKLVLSLYYSDE--LNMRETAEVMGVTEGRVSQLHSQALNRLRKQFHEQ 220


>gi|167933077|ref|ZP_02520164.1| RNA polymerase, sigma 70 subunit, RpoD family protein [candidate
           division TM7 single-cell isolate TM7b]
          Length = 103

 Score = 90.6 bits (224), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 29/94 (30%), Positives = 47/94 (50%), Gaps = 5/94 (5%)

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             D+  S   D++    D       E    +  +  +   +S L+ RE++I + R   EN
Sbjct: 2   DGDEEDSVLGDFI---EDEDTATPEESASSQLLKEQVQGILSSLSDREQKIIKMRFGLEN 58

Query: 252 P--VTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               TLE +  EF V+RER+RQIEA+A  K+++ 
Sbjct: 59  GKSHTLEEVGQEFAVTRERIRQIEAKALAKLRKH 92


>gi|332669182|ref|YP_004452190.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit [Cellulomonas
           fimi ATCC 484]
 gi|332338220|gb|AEE44803.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Cellulomonas
           fimi ATCC 484]
          Length = 296

 Score = 90.6 bits (224), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 51/251 (20%), Positives = 94/251 (37%), Gaps = 27/251 (10%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
             LV +HL LV            P     E+ S G++ L+ A + +DP  G   A Y+  
Sbjct: 9   DELVLTHLPLVGYAVSEMLHRVPPTVSRDELASAGSLALVLAAQAYDPTTGVPFARYASL 68

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+ A+ + + RS      G     + L     RL   L+       +      +A+ + 
Sbjct: 69  RIRGALVDEL-RSMDWASRGARQRVRELAATTERLTAVLR-------RKPTRDELAEAMG 120

Query: 168 VSESEVISMNCRLAGDESLNAL--INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           V        + R   D + +A   + S D       D +V      E+ L+  E    R 
Sbjct: 121 V--------DVRAVDDAARDAERRVLSMDATEGTVADLVVDAEPTPEESLLNDE----RH 168

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             L  ++  L  R R +     L +   ++  L++E  V++ R+ Q+   A   +++ + 
Sbjct: 169 RWLRAAVETLPDRLRTVVVGLFLLD--RSVAELAAELGVTQSRISQLRTEALGLLRDGMN 226

Query: 286 KQVELSSSPPL 296
             ++    P  
Sbjct: 227 AGLDPDLVPTP 237


>gi|330948232|gb|EGH48492.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. pisi
           str. 1704B]
          Length = 95

 Score = 90.6 bits (224), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 26/97 (26%), Positives = 45/97 (46%), Gaps = 5/97 (5%)

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           E ++      D   S   D++    D   Q  I+    ++ +      +S L  RE ++ 
Sbjct: 2   EPISMETPIGDDEDSHLGDFI---EDSTMQSPIDVATVESLKEATREVLSGLTAREAKVL 58

Query: 244 EARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFK 278
             R   +     TLE +  +F+V+RER+RQIEA+A +
Sbjct: 59  RMRFGIDMNTDHTLEEVGKQFDVTRERIRQIEAKALR 95


>gi|260886518|ref|ZP_05897781.1| RNA polymerase sigma-70 factor [Selenomonas sputigena ATCC 35185]
 gi|330839639|ref|YP_004414219.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Selenomonas
           sputigena ATCC 35185]
 gi|260863661|gb|EEX78161.1| RNA polymerase sigma-70 factor [Selenomonas sputigena ATCC 35185]
 gi|329747403|gb|AEC00760.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Selenomonas
           sputigena ATCC 35185]
          Length = 208

 Score = 90.6 bits (224), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 48/190 (25%), Positives = 84/190 (44%), Gaps = 29/190 (15%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ E+ K+ +L  +EE  L + ++E G+ +A  RL+ S+  LV K A+ +R     I
Sbjct: 3   LEEYLQELEKVELLAPEEEQSLWQAFKERGERAARQRLIESYQPLVFKTALPWR-MSESI 61

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS------------- 122
            +++ EG +GL++A + FD +RG   + +++  I+  M  ++ +  S             
Sbjct: 62  MDIIQEGTVGLIEAAENFDWKRGVAFSLFAVHRIRGRMLNFLQKEGSRDVTCMDAPRADG 121

Query: 123 -------LVKIGTTANQKRLFFNLRRLKGHLQAITDNN--------LKPEQVVAIAKKLN 167
                       + A Q  L F  R L   L  +            LK E +  IA  L+
Sbjct: 122 RAPWELLPDTTPSVAEQAELGFMTRELHRALARLPQKERVVLESVYLKSETIPKIADVLD 181

Query: 168 VSESEVISMN 177
           VS S +  + 
Sbjct: 182 VSASHIYRLQ 191



 Score = 40.2 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 13/78 (16%), Positives = 35/78 (44%), Gaps = 2/78 (2%)

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
                 + E+ E       L R+++ L  +ER + E+  L+    T+  ++   +VS   
Sbjct: 129 PDTTPSVAEQAELGFMTRELHRALARLPQKERVVLESVYLKSE--TIPKIADVLDVSASH 186

Query: 269 VRQIEARAFKKVQESIQK 286
           + +++    ++V+  + +
Sbjct: 187 IYRLQKSGIRRVRGMLSR 204


>gi|224771307|dbj|BAH28595.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771319|dbj|BAH28601.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771321|dbj|BAH28602.1| sporulation sigma factor SigK [Clostridium perfringens]
          Length = 196

 Score = 90.6 bits (224), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 58/255 (22%), Positives = 95/255 (37%), Gaps = 66/255 (25%)

Query: 14  IGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           I L+ Y+      P  L ++EE +  +R ++ GD+ A   LV  +LRLV  I   Y    
Sbjct: 2   IFLTGYVTGNSTFPKPLNEKEEKIYLERLKD-GDVEAKRVLVERNLRLVAHIVKKYSSNY 60

Query: 73  L---PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
                + +++S G IGL++A+  FD  +G RLATY+   I   +  +             
Sbjct: 61  QNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATYAAKCIDNEILMF------------- 107

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
                 F N ++ KG                             + +   +  D+  N  
Sbjct: 108 ------FRNTKKTKGE----------------------------VFLQDPIGVDKEGNE- 132

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-- 247
           I   D  SS     L    +  E  L  KE  K   ++L       +PRE+ I + R   
Sbjct: 133 ICLIDILSSDSDSVL----EAVENSLQVKELYKKMSDIL-------SPREKEIIKMRYGL 181

Query: 248 LQENPVTLENLSSEF 262
           L  +  T   +++  
Sbjct: 182 LDGDIKTQREIAAIL 196


>gi|124265243|ref|YP_001019247.1| RNA polymerase sigma factor for flagellar operon [Methylibium
           petroleiphilum PM1]
 gi|124258018|gb|ABM93012.1| RNA polymerase sigma factor for flagellar operon [Methylibium
           petroleiphilum PM1]
          Length = 265

 Score = 90.6 bits (224), Expect = 2e-16,   Method: Composition-based stats.
 Identities = 48/242 (19%), Positives = 106/242 (43%), Gaps = 16/242 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +  +  H  LV +IA   R      + + E++  G IGL +A+ +F+   G    TY+ 
Sbjct: 32  RNEQLHQHGALVRRIAKRMRARLPANVEMDELLQAGLIGLNEAITRFEESFGASFDTYAS 91

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + R+   +     A+Q       R ++  +QA+    L+P + + +A +L
Sbjct: 92  RRIEGAMLDSL-RAADTLSRDARAHQ-------RAIRAAVQALEHRLLRPPRAMEVASEL 143

Query: 167 NVSESEV--ISMNCRLAGDESLNALINS-SDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
             S + +    +    AG  + +A ++  +D+ S++  +  ++         +   +R+ 
Sbjct: 144 GWSLARLHQRLVEAGAAGQRAGDAPLDGLADEASARGAEDDLHATADDHADPLAALQRRQ 203

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           R   L  +   L  RE+ + +    +      ++ +    VS  RV Q+ A   +K++  
Sbjct: 204 RTTALNAAFDTLEEREQLMMKMIYERGLDH--QDAAESLGVSPSRVSQMHAVVVQKLKRR 261

Query: 284 IQ 285
           ++
Sbjct: 262 LK 263


>gi|213028661|ref|ZP_03343108.1| RNA polymerase sigma factor RpoD [Salmonella enterica subsp.
           enterica serovar Typhi str. 404ty]
          Length = 88

 Score = 90.6 bits (224), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 22/81 (27%), Positives = 44/81 (54%), Gaps = 2/81 (2%)

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVR 270
           ++ ++    ++ R      ++ L  RE ++   R   +     TLE +  +F+V+RER+R
Sbjct: 4   ELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIR 63

Query: 271 QIEARAFKKVQESIQKQVELS 291
           QIEA+A +K++   + +V  S
Sbjct: 64  QIEAKALRKLRHPSRSEVLRS 84


>gi|261821180|ref|YP_003259286.1| flagellar biosynthesis sigma factor [Pectobacterium wasabiae
           WPP163]
 gi|261605193|gb|ACX87679.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pectobacterium
           wasabiae WPP163]
          Length = 240

 Score = 90.6 bits (224), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 39/242 (16%), Positives = 98/242 (40%), Gaps = 17/242 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KNSLWKRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLSAVERYDSLQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ +M + +               + +  N R +   +Q       +      +A+ L
Sbjct: 73  QRIRGSMLDELR--------SRDWAPRSVRRNAREVAQAMQQAEQQLGRTPTEQEVAQTL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           N++  +   +      +  L +     +++    +  L  + D      + +    N R+
Sbjct: 125 NITLEDYRQILLD-TNNTQLFSYDEWREEHGDSAEALLEGNEDAN---PLHQLMEGNLRH 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  +  
Sbjct: 181 RVMDAIESLPEREKLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRVKLMN 238

Query: 287 QV 288
            V
Sbjct: 239 DV 240


>gi|332284050|ref|YP_004415961.1| RNA polymerase sigma factor for flagellar operon [Pusillimonas sp.
           T7-7]
 gi|330428003|gb|AEC19337.1| RNA polymerase sigma factor for flagellar operon [Pusillimonas sp.
           T7-7]
          Length = 255

 Score = 90.3 bits (223), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 38/242 (15%), Positives = 94/242 (38%), Gaps = 18/242 (7%)

Query: 51  HRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            +LV  +  LV ++A+         + + +++  G +GL+ A++++      +  TY++ 
Sbjct: 6   DQLVGQYAPLVRRLALQLVAKLPASVEVDDLMQAGMMGLLDAIRRYQQTADAQFETYAVT 65

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+ AM + +     L         + +    R ++  +  +T   L+      IA+++ 
Sbjct: 66  RIRGAMLDELRSQDWL--------PRSVRSKTRNIEQAIHTLTHRLLRAPAESEIAEEMG 117

Query: 168 VSESEVISMNCRLAGDESL--NALINSSDKNSSQWQDWLVYDHDGQEQV---LIEKEERK 222
           V   E   +     G + L    L    +   S        +   Q       + +   K
Sbjct: 118 VPLPEYQQLLEEARGVQILHYEDLAGQGEDAGSSLDRSSEDESATQAAHWSNPLNQLVSK 177

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             R  L  ++  L  RE+ +   +   E  +  + +     ++  RV Q+ ++A  +++ 
Sbjct: 178 GLRRALVEAIKALPEREQLLLSLQF--EQDLNQKEIGLVMGITEGRVSQLRSQAVARIRA 235

Query: 283 SI 284
           ++
Sbjct: 236 AL 237


>gi|318066969|emb|CBY89099.1| RNA polymerase sigma70 factor [Halomonas salina]
          Length = 366

 Score = 90.3 bits (223), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 31/68 (45%), Positives = 45/68 (66%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             A   +V +HLRLV+ IA  Y   GLP  ++  EG+IGLM+AV KF+  RG++ +TY+ 
Sbjct: 299 RRAKKEMVEAHLRLVISIAQKYPHRGLPFLDLFQEGHIGLMKAVDKFEYRRGYKFSTYAT 358

Query: 107 WWIKAAMQ 114
           WWI+ A+ 
Sbjct: 359 WWIRQAIT 366


>gi|182412226|ref|YP_001817292.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Opitutus terrae
           PB90-1]
 gi|177839440|gb|ACB73692.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Opitutus terrae
           PB90-1]
          Length = 262

 Score = 90.3 bits (223), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 44/237 (18%), Positives = 94/237 (39%), Gaps = 14/237 (5%)

Query: 53  LVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           L+  HL LV  +           +   ++ S G  GL+ AV+KFDPE+G   A+Y+   I
Sbjct: 33  LIERHLYLVRNVVDRIKLNLPTHIDADDLYSVGVTGLIAAVRKFDPEQGCTFASYAAMRI 92

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + A+ + + R             +R     R+LK  +  +     +      I   L ++
Sbjct: 93  RGAVLDELRR--------MDWCPRRARARSRKLKETIIEVEQKLGRAASDEEICSALGLT 144

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
           + +        A   +  A+ + ++    +         D  +    E  E++    +LT
Sbjct: 145 QKDYAKW-VEDARPVTFLAIDHRNENEDGEGASLHELLKDETDVTGRENLEKRELLELLT 203

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           + +S L    ++I      +   + L  +++ F ++  R+ QI A+    ++  + +
Sbjct: 204 QRISELPDIPKKILAMYYFEN--MRLAEIAAVFNLTESRICQIHAQTILGLRGYLGR 258


>gi|162418642|ref|YP_001606497.1| flagellar biosynthesis sigma factor [Yersinia pestis Angola]
 gi|162351457|gb|ABX85405.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           Angola]
          Length = 240

 Score = 90.3 bits (223), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 38/238 (15%), Positives = 94/238 (39%), Gaps = 17/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   ++ LV   A+  +      + + +++  G I L+ AV+++D  +G    TY++
Sbjct: 13  KNSLWKRYVPLVRHEALRLQVRLPASVELDDLLQAGGIDLLNAVERYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +               + +  N R +   +Q +      P     +A+ L
Sbjct: 73  QRIRGAMLDELR--------SRDWAPRSVRRNAREVASAMQQVEQRVGSPATEQEVAQVL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++   E   +      D + + L +  +      +         ++   ++     N R 
Sbjct: 125 DIGLVEYRQILL----DTNNSQLFSYDEWREEHGESVEPLLEGHEDANPLKHLLEGNLRQ 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  +
Sbjct: 181 RVIDAIEALPEREKMVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRARL 236


>gi|32471396|ref|NP_864389.1| RNA polymerase sigma 70 [Rhodopirellula baltica SH 1]
 gi|32443237|emb|CAD72068.1| probable RNA polymerase sigma 70 [Rhodopirellula baltica SH 1]
          Length = 340

 Score = 90.3 bits (223), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 69/316 (21%), Positives = 126/316 (39%), Gaps = 96/316 (30%)

Query: 6   MSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSA---------------- 49
           ++ I    + L  ++  + + P+L+ ++E +L +R       +A                
Sbjct: 89  IATIRRSGVDLPIHLGRLCEAPLLKPEQEKMLFERMNYLLQQAAIHRSVLNPERPSRHRL 148

Query: 50  -------------AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
                          R+V ++LRLV  I   +        +++S+G + L++AV+KFD +
Sbjct: 149 ELIELFVALADWHRDRIVEANLRLVFSIVKKFVNPNNTFDDLLSDGIVALIRAVEKFDFD 208

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           RGFR +TY       A Q     S+  V +     QK        ++G LQ +  +  + 
Sbjct: 209 RGFRFSTY-------ATQVVRRNSYRTVVLKQQERQK--------VQGGLQDMDIDVSEE 253

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           E+  AI      SE     +  RL+                      ++ D D +E+ +I
Sbjct: 254 ERSSAI------SEKRWHELRSRLS---------------------VMLGDLDRREKFII 286

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
                        R+   L P  R++           TL++L+    VS+ERVRQ+E RA
Sbjct: 287 -------------RARFSLGP-HRKV----------HTLQSLADRLGVSKERVRQLERRA 322

Query: 277 FKKVQESIQKQVELSS 292
             K++ ++   V+L+ 
Sbjct: 323 MDKLR-AMAGDVQLAE 337


>gi|93007309|gb|ABE97157.1| SigF [Pasteuria ramosa]
          Length = 131

 Score = 90.3 bits (223), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 32/125 (25%), Positives = 58/125 (46%), Gaps = 4/125 (3%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           R+   L   E   L     + GD  A  RLV+ ++RLV  +   +   G    ++   G 
Sbjct: 9   RRYDHLTDTEVRELIIS-SQKGDTKARDRLVSHNIRLVWSVVQRFLNRGYESDDIFQIGC 67

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           IGL++AV KF+ E   + +TY++  I   +Q ++     +VK+  +   K +   +R+ +
Sbjct: 68  IGLLKAVDKFNLEYEVKFSTYAVPMILGEIQRFLRDDG-IVKVSRSL--KEMAHRVRKTR 124

Query: 144 GHLQA 148
             L  
Sbjct: 125 DELSK 129


>gi|224771305|dbj|BAH28594.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771309|dbj|BAH28596.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771311|dbj|BAH28597.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771313|dbj|BAH28598.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771315|dbj|BAH28599.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771317|dbj|BAH28600.1| sporulation sigma factor SigK [Clostridium perfringens CPE str.
           F4969]
 gi|224771323|dbj|BAH28603.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771325|dbj|BAH28604.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771327|dbj|BAH28605.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771329|dbj|BAH28606.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771335|dbj|BAH28609.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771339|dbj|BAH28611.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771341|dbj|BAH28612.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771343|dbj|BAH28613.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771345|dbj|BAH28614.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771347|dbj|BAH28615.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771351|dbj|BAH28617.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771353|dbj|BAH28618.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771355|dbj|BAH28619.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771359|dbj|BAH28621.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771361|dbj|BAH28622.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771365|dbj|BAH28624.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771369|dbj|BAH28626.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771373|dbj|BAH28628.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771375|dbj|BAH28629.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771379|dbj|BAH28631.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771381|dbj|BAH28632.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771383|dbj|BAH28633.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771393|dbj|BAH28638.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771395|dbj|BAH28639.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771397|dbj|BAH28640.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771399|dbj|BAH28641.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771401|dbj|BAH28642.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771403|dbj|BAH28643.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771405|dbj|BAH28644.1| sporulation sigma factor SigK [Clostridium perfringens]
          Length = 196

 Score = 90.3 bits (223), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 58/255 (22%), Positives = 94/255 (36%), Gaps = 66/255 (25%)

Query: 14  IGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           I L+ Y+      P  L ++EE +  +R ++ GD+ A   LV  +LRLV  I   Y    
Sbjct: 2   IFLTGYVTGNSTFPKPLNEKEEKIYLERLKD-GDVEAKRVLVERNLRLVAHIVKKYSSNY 60

Query: 73  L---PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
                + +++S G IGL++A+  FD  +G RLATY+   I   +  +             
Sbjct: 61  QNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATYAAKCIDNEILMF------------- 107

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
                 F N ++ KG                             + +   +  D+  N  
Sbjct: 108 ------FRNTKKTKGE----------------------------VFLQDPIGVDKEGNE- 132

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-- 247
           I   D  SS     L    +  E  L  KE  K   ++L       +PRE+ I + R   
Sbjct: 133 ICLIDILSSDSDSVL----EAVENSLQVKELYKKMSDVL-------SPREKEIIQMRYGL 181

Query: 248 LQENPVTLENLSSEF 262
           L  +  T   ++   
Sbjct: 182 LDGDIKTQREIAGIL 196


>gi|119715014|ref|YP_921979.1| FliA/WhiG family RNA polymerase sigma factor [Nocardioides sp.
           JS614]
 gi|119535675|gb|ABL80292.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Nocardioides sp.
           JS614]
          Length = 285

 Score = 90.3 bits (223), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 48/250 (19%), Positives = 91/250 (36%), Gaps = 21/250 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L+  H  LV  I           +   ++ S G + L+QA + FD ERG     Y+ 
Sbjct: 10  LEALILQHTALVGHIVRETMSRVPAHVDRDDLTSAGLLALVQAAQAFDAERGVPFNRYAA 69

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             ++ A+ + + R+            + L     RL   L        +P     +A   
Sbjct: 70  TRVRGAVVDELRRT-DWASRSVRRRARELDATRSRLATVL-------GRPATQAEVADTA 121

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +S  EV   +  +A  + L+          +   D +     G         E   R  
Sbjct: 122 GLSVDEVTGNDDDIARAQVLSL--------DASEDDGIGDTLVGNAPDPQGALEHGERLT 173

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            LT +++ L  R R + E   L E P+    +++   V+  R+ Q+ A A   +++++  
Sbjct: 174 YLTEAVAELPDRLRLVVEQYFLNERPM--AEIAATLGVTESRISQLRAEALVLLRDALNH 231

Query: 287 QVELSSSPPL 296
           +++    P  
Sbjct: 232 ELDPDLLPAP 241


>gi|26249146|ref|NP_755186.1| hypothetical protein c3307 [Escherichia coli CFT073]
 gi|26109553|gb|AAN81756.1|AE016765_158 Putative conserved protein [Escherichia coli CFT073]
          Length = 144

 Score = 90.3 bits (223), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 31/73 (42%), Positives = 49/73 (67%), Gaps = 1/73 (1%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 73  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 131

Query: 79  VSEGNIGLMQAVK 91
           + EGN+GL++AV+
Sbjct: 132 IEEGNLGLIRAVE 144


>gi|307690662|ref|ZP_07633108.1| sporulation sigma factor SigG [Clostridium cellulovorans 743B]
          Length = 139

 Score = 90.3 bits (223), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 33/146 (22%), Positives = 63/146 (43%), Gaps = 11/146 (7%)

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
            R L+   + +T+NN K   V  IAK+L+V++ EVI     +    SL   I     ++ 
Sbjct: 5   YRALQVRDKLLTENN-KEPTVYQIAKELDVAKEEVIFALDAIQEPVSLFEPIYHDGGDAI 63

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
              D +    +  E  L            +  +M  L+ RE+ I   R    +  T   +
Sbjct: 64  YVMDQISDSKNLDESWLENIA--------IKEAMKRLSDREKLILNMRFF--DGRTQMEV 113

Query: 259 SSEFEVSRERVRQIEARAFKKVQESI 284
           + E  +S+ +V ++E  A + +++ +
Sbjct: 114 ADEIGISQAQVSRLEKNALRHMRKHV 139


>gi|224771331|dbj|BAH28607.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771333|dbj|BAH28608.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771337|dbj|BAH28610.1| sporulation sigma factor SigK [Clostridium perfringens]
          Length = 196

 Score = 90.3 bits (223), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 58/255 (22%), Positives = 94/255 (36%), Gaps = 66/255 (25%)

Query: 14  IGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           I L+ Y+      P  L ++EE +  +R ++ GD+ A   LV  +LRLV  I   Y    
Sbjct: 2   IFLTGYVTGNSTFPKPLNEKEEKIYLERLKD-GDVEAKRVLVERNLRLVAHIVKKYSSSY 60

Query: 73  L---PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
                + +++S G IGL++A+  FD  +G RLATY+   I   +  +             
Sbjct: 61  QNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATYAAKCIDNEILMF------------- 107

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
                 F N ++ KG                             + +   +  D+  N  
Sbjct: 108 ------FRNTKKTKGE----------------------------VFLQDPIGVDKEGNE- 132

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-- 247
           I   D  SS     L    +  E  L  KE  K   ++L       +PRE+ I + R   
Sbjct: 133 ICLIDILSSDSDSVL----EAVENSLQVKELYKKMSDVL-------SPREKEIIQMRYGL 181

Query: 248 LQENPVTLENLSSEF 262
           L  +  T   ++   
Sbjct: 182 LDGDIKTQREIAGIL 196


>gi|224771367|dbj|BAH28625.1| sporulation sigma factor SigK [Clostridium perfringens]
          Length = 196

 Score = 90.3 bits (223), Expect = 3e-16,   Method: Composition-based stats.
 Identities = 58/255 (22%), Positives = 94/255 (36%), Gaps = 66/255 (25%)

Query: 14  IGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           I L+ Y+      P  L ++EE +  +R +  GD+ A   LV  +LRLV  I   Y    
Sbjct: 2   IFLTGYVTGNSTFPKPLNEKEEKIYLERLKY-GDVEAKRVLVERNLRLVAHIVKKYSSNY 60

Query: 73  L---PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
                + +++S G IGL++A+  FD  +G RLATY+   I   +  +             
Sbjct: 61  QNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATYAAKCIDNEILMF------------- 107

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
                 F N ++ KG                             + +   +  D+  N  
Sbjct: 108 ------FRNTKKTKGE----------------------------VFLQDPIGVDKEGNE- 132

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-- 247
           I   D  SS     L    +  E  L  KE  K   ++L       +PRE+ I + R   
Sbjct: 133 ICLIDILSSDSDSVL----EAVENSLQVKELYKKMSDIL-------SPREKEIIKMRYGL 181

Query: 248 LQENPVTLENLSSEF 262
           L  +  T   +++  
Sbjct: 182 LDGDIKTQREIAAIL 196


>gi|119714598|ref|YP_921563.1| sigma-70 region 4 domain-containing protein [Nocardioides sp.
           JS614]
 gi|119535259|gb|ABL79876.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Nocardioides sp.
           JS614]
          Length = 278

 Score = 90.3 bits (223), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 45/249 (18%), Positives = 94/249 (37%), Gaps = 21/249 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             +L   H+ LV  +           +  +++ S G + L+QA + FDPERG   A Y+ 
Sbjct: 6   RDQLAVQHVPLVAHLVRETMARVPSYMDRNDLHSAGLLALVQAARAFDPERGVPFAGYAS 65

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ A+ + +               + +    R ++     +     +     A+A+ L
Sbjct: 66  TRIRGALVDELR--------SVDWASRSVRRRAREIEAARARLAATLGQFPDDAAVAEAL 117

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++  E+   +  +A    L           +      V    G++    E+     R  
Sbjct: 118 GITPEEIGKADSEVARAVVLPL--------DAGPNAGFVESLAGRDPGPEEEALHAERAQ 169

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L  ++  L  R R +     + + P+    L++E  VS  R+ Q+ A A   +++++ +
Sbjct: 170 YLAAAIEELPERLRHVVRGYFVAQRPM--AELAAELGVSESRISQLRAEALVLLRDALAE 227

Query: 287 QVELSSSPP 295
             E   + P
Sbjct: 228 AFEPHLAAP 236


>gi|289548919|ref|YP_003473907.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermocrinis albus DSM
           14484]
 gi|289182536|gb|ADC89780.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermocrinis albus DSM
           14484]
          Length = 233

 Score = 90.3 bits (223), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 48/240 (20%), Positives = 102/240 (42%), Gaps = 25/240 (10%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
               V  +L LV  +A     +    + I++++  G + +M+++ + DP +    +TY  
Sbjct: 10  KDEDVLKYLPLVKSVAKKIHRHLPPSVDINDLIGYGILAVMESLSRIDPTKNP--STYLY 67

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +K AM +Y+               +R+    + ++  ++ +     +      I + L
Sbjct: 68  MRVKGAMYDYLR--------SLHLCSRRVREREKLIRRKMEELRQQLGRDPTDEEIGEAL 119

Query: 167 NVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
             +  ++     R A     SL+AL          +++ L    DG E    EK  R+ R
Sbjct: 120 GETPDKIYEDVQRAAFAQILSLDALFREG----RSYEELLAAAEDGPE----EKVLREER 171

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L  ++  L+ RE+ + +    +E P   + ++    VS  R+ QI+ +A +K++E +
Sbjct: 172 RRRLLEAIEKLSYREKLVLQLLFYEELPA--KTVAKLLGVSSARISQIKEQAIEKLKEEL 229


>gi|227112555|ref|ZP_03826211.1| flagellar biosynthesis sigma factor [Pectobacterium carotovorum
           subsp. brasiliensis PBR1692]
 gi|227329198|ref|ZP_03833222.1| flagellar biosynthesis sigma factor [Pectobacterium carotovorum
           subsp. carotovorum WPP14]
          Length = 230

 Score = 90.3 bits (223), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 37/235 (15%), Positives = 94/235 (40%), Gaps = 17/235 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 3   KNSLWKRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLSAVERYDSLQGTAFTTYAV 62

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ +M + +               + +  N R +   +Q       +      +A+ L
Sbjct: 63  QRIRGSMLDELR--------SRDWAPRSVRRNAREVAQAMQQAEQQLGRTPTEQEVAQTL 114

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           N++  +   +      D + + L +  +                ++   + +    N R+
Sbjct: 115 NITLEDYRQILL----DTNNSQLFSYDEWREEHGDSAEALLEGNEDANPLHQLMEGNLRH 170

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++
Sbjct: 171 RVMDAIESLPEREKLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLR 223


>gi|224771371|dbj|BAH28627.1| sporulation sigma factor SigK [Clostridium perfringens NCTC 8239]
 gi|224771377|dbj|BAH28630.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771385|dbj|BAH28634.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771387|dbj|BAH28635.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771389|dbj|BAH28636.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771391|dbj|BAH28637.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771407|dbj|BAH28645.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771409|dbj|BAH28646.1| sporulation sigma factor SigK [Clostridium perfringens]
 gi|224771411|dbj|BAH28647.1| sporulation sigma factor SigK [Clostridium perfringens]
          Length = 196

 Score = 89.9 bits (222), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 58/255 (22%), Positives = 94/255 (36%), Gaps = 66/255 (25%)

Query: 14  IGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           I L+ Y+      P  L ++EE +   R ++ GD+ A   LV  +LRLV  I   Y    
Sbjct: 2   IFLTGYVTGNSTFPKPLNEKEEKIYLDRLKD-GDVEAKRVLVERNLRLVAHIVKKYSSNY 60

Query: 73  L---PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
                + +++S G IGL++A+  FD  +G RLATY+   I   +  +             
Sbjct: 61  QNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATYAAKCIDNEILMF------------- 107

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
                 F N ++ KG                             + +   +  D+  N  
Sbjct: 108 ------FRNTKKTKGE----------------------------VFLQDPIGVDKEGNE- 132

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-- 247
           I   D  SS     L    +  E  L  KE  K   ++L       +PRE+ I + R   
Sbjct: 133 ICLIDILSSDSDSVL----EAVENSLQVKELYKKMSDIL-------SPREKEIIKMRYGL 181

Query: 248 LQENPVTLENLSSEF 262
           L  +  T   +++  
Sbjct: 182 LDGDIKTQREIAAIL 196


>gi|46581631|ref|YP_012439.1| RNA polymerase sigma factor for flagellar operon FliA
           [Desulfovibrio vulgaris str. Hildenborough]
 gi|120601210|ref|YP_965610.1| FliA/WhiG family RNA polymerase sigma factor [Desulfovibrio
           vulgaris DP4]
 gi|46451054|gb|AAS97699.1| RNA polymerase sigma factor for flagellar operon FliA
           [Desulfovibrio vulgaris str. Hildenborough]
 gi|120561439|gb|ABM27183.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Desulfovibrio
           vulgaris DP4]
 gi|311235273|gb|ADP88127.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfovibrio vulgaris RCH1]
          Length = 265

 Score = 89.9 bits (222), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 39/239 (16%), Positives = 87/239 (36%), Gaps = 21/239 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              +V  +   +  +A+  +      + + E++S G +GLM+A+ KF P+ G R  TY+ 
Sbjct: 36  KEAIVRHYAPKIRFLALRLKAKLPRNVELGELISAGTLGLMEALGKFKPQLGIRFETYAE 95

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +     L     +  Q+     +R+L   +Q I     +      + K  
Sbjct: 96  SRIRGAMLDELR---RLDWFPRSLRQR-----VRQLDEAMQRIEHETGRRATEEDLQKAT 147

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E +V      L     L+                        +   ++    +    
Sbjct: 148 GLDEKDVRLGLEALQNQLCLSLEAMQD--------SLAGEGGPQSDADPMQTAATQELIE 199

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            +   +  L PRE+ +       E  + +   +    ++  RV Q+ ++A  +++   +
Sbjct: 200 RVASLIDELTPREKLVLSLYYSDE--LNMRETAEVMGITEGRVSQLHSQALGRLRREFR 256


>gi|87302171|ref|ZP_01084996.1| RNA polymerase ECF-type (group 3) sigma-E factor [Synechococcus sp.
           WH 5701]
 gi|87283096|gb|EAQ75052.1| RNA polymerase ECF-type (group 3) sigma-E factor [Synechococcus sp.
           WH 5701]
          Length = 318

 Score = 89.9 bits (222), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 55/274 (20%), Positives = 103/274 (37%), Gaps = 22/274 (8%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFD 94
            L +R+   GD    +RLV  +L LV ++A+   G    P+ ++V  G +GL++A++ FD
Sbjct: 20  ELLQRFHSSGDHRLRNRLVELNLPLVRQVAVRQSGSTRVPLDDLVQLGCLGLIRAIEAFD 79

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P R   L+++++ +I+  MQ ++      ++      +       RR +  LQ      L
Sbjct: 80  PSRHTALSSFAVLYIRGEMQHHLRDHEQPLRCSRQLRELH-----RRGQALLQQRQHRQL 134

Query: 155 KPEQVVAIAKKLNVSESEVISMNC--RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
                  +A  L  S           +     SL+A  +  ++      + L        
Sbjct: 135 PALGEEELAAALGCSPQRWREALELHQALRLRSLDAPASDGEERGDTLLERLPARELPDP 194

Query: 213 QVLIEKEE----RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR-- 266
                + +        +  L R +  L+P  R++   R L               V +  
Sbjct: 195 CRADHEGDSLCCEGENQRWLKRRLERLDPSLRQLMLERVLHGASW------RRLGVDQGL 248

Query: 267 -ERVRQIEARAF-KKVQESIQKQVELSSSPPLLQ 298
             R  Q    A    ++E IQ+ V    +PP+  
Sbjct: 249 PARASQRRFDALVLLLREEIQQLVLARQAPPVWP 282


>gi|332675354|gb|AEE72170.1| RNA polymerase sigma factor [Propionibacterium acnes 266]
          Length = 266

 Score = 89.9 bits (222), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 52/255 (20%), Positives = 101/255 (39%), Gaps = 41/255 (16%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKK 92
           E  L +R  + G + A   L    L +V+  A      Y   + +++  G IGL +A+++
Sbjct: 47  EAEL-RRISDDG-VGARQTLWRQMLAIVLTQARQAAVSYRCSVEDLIQAGCIGLGEAIER 104

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           +D  RG R +T +  WI+  + E ++R          A  + +      +    + +T  
Sbjct: 105 YDVRRGARFSTVAWTWIRRRIGEEVVRLSG-------ARSRSVMREAAEVARIEEELTAR 157

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
                   AIA ++     +V+ +  R          +   +  +S ++   V      +
Sbjct: 158 WQSVPSSDAIAARMG---KDVMWVEKRR---------VECWEVETSFFEQVAVVQKSCDD 205

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPVTLENLSSEFEVSRERVRQ 271
                               S L  +ERRI E R   +  P+T+  ++ E  +S   VR+
Sbjct: 206 PE------------------SGLTGQERRIVELRHGFEGEPMTITAVAHELGLSASNVRR 247

Query: 272 IEARAFKKVQESIQK 286
           IE RA  +++  +Q+
Sbjct: 248 IEQRALGRLRRHLQQ 262


>gi|320529893|ref|ZP_08030970.1| sigma-70 region 2 [Selenomonas artemidis F0399]
 gi|320137911|gb|EFW29816.1| sigma-70 region 2 [Selenomonas artemidis F0399]
          Length = 208

 Score = 89.9 bits (222), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 36/164 (21%), Positives = 76/164 (46%), Gaps = 6/164 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
            + Y+ ++  +  L   EE  L + Y+E GD  A  R++ ++  LV +  M YR     +
Sbjct: 2   FADYVKKLSAVKKLRPDEERALWRAYKEKGDEGARRRIIEAYQPLVFREVMPYRAL-PAV 60

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            + V EG IGL++AV+++DP RG   + Y++  ++  + +++ R    V +        +
Sbjct: 61  MDAVQEGTIGLIEAVERYDPARGVAFSLYAVHRVRGCILDFLRREG-TVDLPCLEASDEM 119

Query: 136 FFNLRRLKGHLQ----AITDNNLKPEQVVAIAKKLNVSESEVIS 175
               + L   +Q     + +++     +     +L + E  V+ 
Sbjct: 120 HETAKELIAAVQPSVPELAEHHALVGVLGDAMARLPLQERRVLE 163


>gi|307293798|ref|ZP_07573642.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Sphingobium
           chlorophenolicum L-1]
 gi|306879949|gb|EFN11166.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Sphingobium
           chlorophenolicum L-1]
          Length = 245

 Score = 89.9 bits (222), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 46/238 (19%), Positives = 105/238 (44%), Gaps = 23/238 (9%)

Query: 51  HRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            RL   ++ LV K A    G     + I +++  G + L++A   F+ +RG   A+Y+  
Sbjct: 25  ERLARQYMPLVRKTAWHVHGRVSSAIEIEDLLQIGMVALVEAANGFE-DRGLGFASYAQM 83

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            ++ AM +++ R  ++ +  +   Q++    L  ++  L+      +  E  ++    L+
Sbjct: 84  RVRGAMIDHLRRHATMTR--SAMAQRK---QLAGIRNRLEQKLGR-IPLESEMSAEMGLD 137

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
            +    ++  C +    S+       D+  S    W     +  + V+    ER++ +  
Sbjct: 138 PAAYREVADGCEMVQHTSM-------DEVYSDQSMWFADVEERADDVM----ERESLKAA 186

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L + +  L  RE  + +   ++E  + LE + +  ++   RV QI+  A  K++E ++
Sbjct: 187 LAKCIGDLPQREALVLQLYFVEE--LNLEEIGATLDIGAARVCQIKKAALDKLREKLR 242


>gi|289754806|ref|ZP_06514184.1| predicted protein [Mycobacterium tuberculosis EAS054]
 gi|289695393|gb|EFD62822.1| predicted protein [Mycobacterium tuberculosis EAS054]
          Length = 84

 Score = 89.9 bits (222), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 20/78 (25%), Positives = 37/78 (47%), Gaps = 2/78 (2%)

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVR 270
            V ++       ++ L   +  L+ RE  +   R       P TL+ +   + V+RER+R
Sbjct: 1   MVAVDAVSFTLLQDQLQSVLDTLSEREAGVVRLRFGLTDGQPRTLDEIGQVYGVTRERIR 60

Query: 271 QIEARAFKKVQESIQKQV 288
           QIE++   K++   + QV
Sbjct: 61  QIESKTMSKLRHPSRSQV 78


>gi|313895463|ref|ZP_07829020.1| Sigma-70 region 2 [Selenomonas sp. oral taxon 137 str. F0430]
 gi|312976358|gb|EFR41816.1| Sigma-70 region 2 [Selenomonas sp. oral taxon 137 str. F0430]
          Length = 208

 Score = 89.9 bits (222), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 36/164 (21%), Positives = 76/164 (46%), Gaps = 6/164 (3%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
            + Y+ ++  +  L   EE  L + Y+E GD  A  R++ ++  LV +  M YR     +
Sbjct: 2   FADYVKKLSAVEKLRPDEERALWRAYKEKGDEGARRRIIEAYQPLVFREVMPYRAL-PAV 60

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            + V EG IGL++AV+++DP RG   + Y++  ++  + +++ R    V +        +
Sbjct: 61  MDAVQEGTIGLIEAVERYDPARGVAFSLYAVHRVRGCILDFLRREG-TVDLPCLEASDEM 119

Query: 136 FFNLRRLKGHLQ----AITDNNLKPEQVVAIAKKLNVSESEVIS 175
               + L   +Q     + +++     +     +L + E  V+ 
Sbjct: 120 HETAKELIAAVQPSVPELAEHHALVGVLGDAMARLPLQERRVLE 163


>gi|224553534|gb|ACN55005.1| RNA polymerase sigma factor [Escherichia coli]
          Length = 111

 Score = 89.9 bits (222), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 34/116 (29%), Positives = 59/116 (50%), Gaps = 5/116 (4%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  +   I+     +++     
Sbjct: 1   GLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIGRAIMNQTRTIRLPIHIV 60

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
            K L   LR  +     ++           IA++L+    +V  M        S++
Sbjct: 61  -KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVD 111


>gi|315101187|gb|EFT73163.1| sigma-70, region 4 [Propionibacterium acnes HL046PA1]
          Length = 270

 Score = 89.9 bits (222), Expect = 4e-16,   Method: Composition-based stats.
 Identities = 50/255 (19%), Positives = 102/255 (40%), Gaps = 37/255 (14%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKK 92
           E  L +R  + G + A   L    L +V+  A      Y   + +++  G IGL + +++
Sbjct: 47  EAEL-RRISDDG-VGARQTLWRQMLAIVLTQARQAAVSYRCSVEDLIQAGCIGLGETIER 104

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           +D  RG R +T +  WI+  + E ++R          A  + +      +    + +T  
Sbjct: 105 YDVRRGARFSTVAWTWIRRRIGEEVVRLSG-------ARSRSVMREAAEVARIEEELTAR 157

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
                   AIA ++     +V+ +  R          +   +  +S ++   V      +
Sbjct: 158 WQSVPSSDAIAARMG---KDVMWVEKRR---------VECWEVETSFFEQVAVVQKSCDD 205

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPVTLENLSSEFEVSRERVRQ 271
                           +  + +L  +ERRI E R   +  P+T+  ++ E  +S   VR+
Sbjct: 206 PE--------------SGLIGLLTGQERRIVELRHGFEGEPMTITAVAHELGLSASNVRR 251

Query: 272 IEARAFKKVQESIQK 286
           IE RA  +++  +Q+
Sbjct: 252 IEQRALGRLRRHLQQ 266


>gi|224553536|gb|ACN55006.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553538|gb|ACN55007.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553540|gb|ACN55008.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553542|gb|ACN55009.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553546|gb|ACN55011.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553548|gb|ACN55012.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553550|gb|ACN55013.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553552|gb|ACN55014.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553554|gb|ACN55015.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553556|gb|ACN55016.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553558|gb|ACN55017.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553560|gb|ACN55018.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553562|gb|ACN55019.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553564|gb|ACN55020.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553566|gb|ACN55021.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553568|gb|ACN55022.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553570|gb|ACN55023.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553572|gb|ACN55024.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553574|gb|ACN55025.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553576|gb|ACN55026.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553578|gb|ACN55027.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553580|gb|ACN55028.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553582|gb|ACN55029.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553584|gb|ACN55030.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553586|gb|ACN55031.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553588|gb|ACN55032.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553594|gb|ACN55035.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553596|gb|ACN55036.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553598|gb|ACN55037.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553600|gb|ACN55038.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553602|gb|ACN55039.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553604|gb|ACN55040.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553608|gb|ACN55042.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553610|gb|ACN55043.1| RNA polymerase sigma factor [Escherichia coli ETEC H10407]
 gi|224553612|gb|ACN55044.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553614|gb|ACN55045.1| RNA polymerase sigma factor [Escherichia coli]
 gi|224553616|gb|ACN55046.1| RNA polymerase sigma factor [Escherichia coli]
          Length = 111

 Score = 89.5 bits (221), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 34/116 (29%), Positives = 60/116 (51%), Gaps = 5/116 (4%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++     
Sbjct: 1   GLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV 60

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
            K L   LR  +     ++           IA++L+    +V  M        S++
Sbjct: 61  -KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVD 111


>gi|1588993|prf||2209422A fliA gene
          Length = 237

 Score = 89.5 bits (221), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 41/238 (17%), Positives = 95/238 (39%), Gaps = 19/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 12  KNSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 71

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I   + E   R W           +R+  N R +   +Q +      P     +A+ L
Sbjct: 72  QRIAPMLDELRQRDW---------APRRIRRNAREVASAMQKVEQRLGAPATEQEVAQNL 122

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ++  +E   +      D + + L +  +      +         ++   ++     N R 
Sbjct: 123 DIDLTEYRQILL----DTNNSQLFSYDEWREEHGRTVEPMLEGHEDANPLQHLLEGNLRQ 178

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +  +   L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+++  +
Sbjct: 179 RVIEA-EALPEREKMVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKRLRARL 233


>gi|225026956|ref|ZP_03716148.1| hypothetical protein EUBHAL_01212 [Eubacterium hallii DSM 3353]
 gi|224955721|gb|EEG36930.1| hypothetical protein EUBHAL_01212 [Eubacterium hallii DSM 3353]
          Length = 275

 Score = 89.5 bits (221), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 45/171 (26%), Positives = 83/171 (48%), Gaps = 11/171 (6%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ E+ K   L  ++E V+A++    GD +A + L+ ++L   V+IA  Y G GL +S++
Sbjct: 109 YLKEMEKANSLSGEQERVIARKLV-SGDDTARNLLIEANLSRAVEIAKEYEGRGLLLSDL 167

Query: 79  VSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           + EGNIGLM AV +F+P+       +S   I+  ++E +    S  +       +     
Sbjct: 168 IQEGNIGLMVAVNEFEPDIDKDFHAFSEKMIRKHLEETLEEYNSSTRSAVKMANR--VNE 225

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
           +  +        +   KP     IA+++ ++E EV  +        SL+A+
Sbjct: 226 MNDIATAFAKEYEREAKP---SEIAERMGITEEEVRELMK-----VSLDAI 268


>gi|251780405|ref|ZP_04823325.1| RNA polymerase sigma-K factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
 gi|243084720|gb|EES50610.1| RNA polymerase sigma-K factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
          Length = 232

 Score = 89.5 bits (221), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 34/106 (32%), Positives = 53/106 (50%), Gaps = 2/106 (1%)

Query: 16  LSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           L+ YI      P  L + EE    KR ++ GD +A   L+  +LRLV  I   Y      
Sbjct: 17  LTGYISSGNTFPSPLNESEEEEYLKRLKD-GDKTAKGVLIERNLRLVAHIVKKYSFPNKD 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           + E++S G +GL++A+  FD  +G RLATY+   I+  +      +
Sbjct: 76  VDELISIGTVGLIKAIDSFDSGKGTRLATYASRCIENEILMLFRNN 121



 Score = 72.5 bits (177), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 25/102 (24%), Positives = 40/102 (39%), Gaps = 6/102 (5%)

Query: 186 LNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           L   I    + N     D L  D D    VL + E     +++  +    L  RE  I  
Sbjct: 130 LQDPIGVDKEGNEICLIDILSSDSDS---VLEKVESNLQIKDLYIKIKDSLTKRESTILI 186

Query: 245 ARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            R      N  T   ++    +SR  V +IE +A KK+++ +
Sbjct: 187 MRYGLIDGNRKTQREIAGTLGISRSYVSRIEKKALKKLRKEL 228


>gi|218905533|ref|YP_002453367.1| RNA polymerase sigma-K factor [Bacillus cereus AH820]
 gi|218535778|gb|ACK88176.1| RNA polymerase sigma-K factor [Bacillus cereus AH820]
          Length = 149

 Score = 89.5 bits (221), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 26/101 (25%), Positives = 48/101 (47%), Gaps = 1/101 (0%)

Query: 18  RYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
            Y+        L   +E    +   E GD  A + L+  +LRLV  I   +   G    +
Sbjct: 19  SYVKNNAFPQPLSSDDERKYLELM-EQGDAQARNLLIEHNLRLVAHIVKKFENTGEDAED 77

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           ++S G IGL++A++ +   +G +LATY+   I+  +  ++ 
Sbjct: 78  LISIGTIGLIKAIESYSAGKGTKLATYAARCIENEILMHLR 118


>gi|76564105|gb|ABA46492.1| RNA polymerase sigma factor, putative [Bacillus phage Gamma]
          Length = 255

 Score = 89.5 bits (221), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 48/234 (20%), Positives = 93/234 (39%), Gaps = 30/234 (12%)

Query: 51  HRLVTSHLRLVVKIA-MGY--------RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
              +  + RLV       Y        R  GL I ++     IGL++A   FD E G   
Sbjct: 27  DEFIEKYGRLVHHCVWKRYAKKKASIERDTGLDIEDLTQFVMIGLIKARDNFDLEFGCAF 86

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY++  I   +   I  +   +K+  T    +              I +  L  ++   
Sbjct: 87  STYAVPKIIGEIGRAIRDNQK-IKVQRTVYGVK------------GKILNQQLADKEPEE 133

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           IA  L+ S S V +        +SLN ++ +S  N     + ++ D   +     + EE 
Sbjct: 134 IADILDESVSLVKTALEYQPSTDSLNKVVYASGANEELTLERMIEDTKTE-----DIEET 188

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
              R ++    + L P+E  + + R      +T +N++++   S+ ++ +I A+
Sbjct: 189 TINRAVIREFKAALPPKEYIVLDMRL---QNMTQQNIANQMGYSQVQISRILAK 239


>gi|318066985|emb|CBY89107.1| RNA polymerase sigma70 factor [Kushneria avicenniae]
          Length = 373

 Score = 89.1 bits (220), Expect = 6e-16,   Method: Composition-based stats.
 Identities = 35/91 (38%), Positives = 52/91 (57%), Gaps = 2/91 (2%)

Query: 26  IPMLEKQEEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           + ML   E   + +R    E     A   +V + LRLV+ IA  Y   GL   +++ EGN
Sbjct: 283 LAMLPVSELKDINRRLSIGEAKARRAKKEMVEAILRLVISIAKKYTNRGLQFLDLIQEGN 342

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114
           IGLM+AV KF+  RG++ +TY+ WWI+ A+ 
Sbjct: 343 IGLMKAVDKFEYRRGYKFSTYATWWIRQAIT 373


>gi|188588587|ref|YP_001920530.1| sporulation sigma factor SigK [Clostridium botulinum E3 str. Alaska
           E43]
 gi|188498868|gb|ACD52004.1| RNA polymerase sigma-K factor [Clostridium botulinum E3 str. Alaska
           E43]
          Length = 232

 Score = 89.1 bits (220), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 34/106 (32%), Positives = 53/106 (50%), Gaps = 2/106 (1%)

Query: 16  LSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           L+ YI      P  L + EE    KR ++ GD +A   L+  +LRLV  I   Y      
Sbjct: 17  LTGYISSGNTFPSPLNESEEEEYLKRLKD-GDKTAKGVLIERNLRLVAHIVKKYSFPNKD 75

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           + E++S G +GL++A+  FD  +G RLATY+   I+  +      +
Sbjct: 76  VDELISIGTVGLIKAIDSFDSGKGTRLATYASRCIENEILMLFRNN 121



 Score = 72.5 bits (177), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 25/102 (24%), Positives = 40/102 (39%), Gaps = 6/102 (5%)

Query: 186 LNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           L   I    + N     D L  D D    VL + E     +++  +    L  RE  I  
Sbjct: 130 LQDPIGVDKEGNEICLIDILSSDSDS---VLEKVESNLQIKDLYIKIKDSLTKRESTILI 186

Query: 245 ARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            R      N  T   ++    +SR  V +IE +A KK+++ +
Sbjct: 187 MRYGLIDGNRKTQREIAGALGISRSYVSRIEKKALKKLRKEL 228


>gi|289829788|ref|ZP_06547303.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-3139]
          Length = 158

 Score = 89.1 bits (220), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 31/80 (38%), Positives = 49/80 (61%), Gaps = 1/80 (1%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEV 78
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   GL + ++
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRGLALLDL 119

Query: 79  VSEGNIGLMQAVKKFDPERG 98
           + EGN+GL++A +      G
Sbjct: 120 IEEGNLGLIRASRSLTRNAG 139


>gi|224553590|gb|ACN55033.1| RNA polymerase sigma factor [Escherichia coli]
          Length = 111

 Score = 89.1 bits (220), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 33/116 (28%), Positives = 59/116 (50%), Gaps = 5/116 (4%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL + +++ EGN+GL++AV+KFDPERGF  +TY+ WWI+  ++  I+     +++     
Sbjct: 1   GLALLDLIEEGNLGLIRAVEKFDPERGFCFSTYATWWIRQTIERAIMNQTRTIRLPIHIV 60

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
            K L   LR  +     ++           IA++L+    +V  M        S++
Sbjct: 61  -KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVD 111


>gi|298528406|ref|ZP_07015810.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfonatronospira
           thiodismutans ASO3-1]
 gi|298512058|gb|EFI35960.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfonatronospira
           thiodismutans ASO3-1]
          Length = 261

 Score = 89.1 bits (220), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 42/245 (17%), Positives = 106/245 (43%), Gaps = 22/245 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + +V ++ + +   A   +      + +++++S G++GL++A+  FDP +G +L T++ 
Sbjct: 36  KNEIVRAYGQKIRITAARLKHKLPAHVDVNDLISAGSLGLIEALGNFDPTQGIKLETFAD 95

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             IK AM + + R             + L   +++L+  ++    N         + +  
Sbjct: 96  NRIKGAMLDELRR--------MDWFSRGLRKKVKKLEQSMREFEQNTGHSPSHSELKEIT 147

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             S  EV      L     L+      + +++  QD            L++K        
Sbjct: 148 GYSREEVEEGLLALQNQICLSLEAIQENFSATGTQDSDEPQLSVVFHDLVDK-------- 199

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +   +  L+ +E+ +      +E  +T++ ++   +V+  RV Q+ ++A KKV+++  +
Sbjct: 200 -VAAIIEKLSNKEQLVLSLYYTEE--LTMKEVAQVLDVTEGRVSQLHSQAIKKVKDNFAQ 256

Query: 287 QVELS 291
           + ++ 
Sbjct: 257 EHDVF 261


>gi|186681796|ref|YP_001864992.1| RNA polymerase sigma factor SigF [Nostoc punctiforme PCC 73102]
 gi|186464248|gb|ACC80049.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Nostoc
           punctiforme PCC 73102]
          Length = 261

 Score = 89.1 bits (220), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 34/157 (21%), Positives = 74/157 (47%), Gaps = 8/157 (5%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG-YGLPISEVVSEGNIGLMQAVKKF 93
             L   Y ++  +   ++LV  H  LV K+A  +      P  ++   G  GL++A+++F
Sbjct: 13  IELLHLYHQNPSIKLRNKLVQLHTGLVRKMAHKFSHQCNEPYEDLEQIGYFGLIRAIERF 72

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           DP +G+  +++++ +I+  M  ++    +L+KI     +  L+   ++++  L     + 
Sbjct: 73  DPSQGYAFSSFAVPYIRGEMLHFLRDRSTLLKIPRRWQE--LYNEGQKIRKDL---AMSL 127

Query: 154 LKPEQVVAIAKKLNVSESEVIS--MNCRLAGDESLNA 188
            +  +   IA +L VS  E     +  +     SL+A
Sbjct: 128 GRQPKDAEIASELRVSVQEWQETKLAAQNRMPLSLDA 164


>gi|259907643|ref|YP_002647999.1| RNA polymerase sigma factor [Erwinia pyrifoliae Ep1/96]
 gi|224963265|emb|CAX54749.1| RNA polymerase sigma factor [Erwinia pyrifoliae Ep1/96]
 gi|283477486|emb|CAY73402.1| RNA polymerase sigma factor FliA/RpoD [Erwinia pyrifoliae DSM
           12163]
          Length = 243

 Score = 89.1 bits (220), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 45/213 (21%), Positives = 95/213 (44%), Gaps = 18/213 (8%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQ 132
            + +++  G++G + A+  FDP +G  L+ +    I+ A+ + +  R W   ++   A  
Sbjct: 40  ELDDLIQAGSLGFLSAIDHFDPTKGVTLSAFLAQRIRWALMDELRERDWVPRRVRKHA-- 97

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                  R +   +Q +  N         IA ++ VS  E+  M   LA   S  + I S
Sbjct: 98  -------REVTAVIQQLEQNKGGEASEADIATEMGVSVGELQQM---LADTNS--SQIYS 145

Query: 193 SDKNSSQWQDWLVYDHDGQEQV-LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
            D+   Q+ D      +G E +  + +  ++N    +   +SV+  RE+RI +    Q+ 
Sbjct: 146 LDELQEQFADSYETIDEGNEALNPVHQAVQENLVGKIAEHISVIPEREQRILQLYYQQD- 204

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + +  + +   ++  RV Q+ + A K+++  +
Sbjct: 205 -LNMREIGAVLSLTETRVSQLHSLAIKRIRARM 236


>gi|224553592|gb|ACN55034.1| RNA polymerase sigma factor [Escherichia coli]
          Length = 111

 Score = 89.1 bits (220), Expect = 7e-16,   Method: Composition-based stats.
 Identities = 35/111 (31%), Positives = 60/111 (54%), Gaps = 2/111 (1%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++     
Sbjct: 1   GLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV 60

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            K L   LR  +  L    D+    E++     K     S ++ +N R+  
Sbjct: 61  -KELNVYLRTAR-ELSHKLDHEPSAEEITEQLDKPVDDVSRMLRLNERITS 109


>gi|46241492|gb|AAS82949.1| chloroplast RPOD [Chlamydomonas reinhardtii]
          Length = 182

 Score = 89.1 bits (220), Expect = 8e-16,   Method: Composition-based stats.
 Identities = 30/128 (23%), Positives = 56/128 (43%), Gaps = 7/128 (5%)

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
           P +   +AK   +  + V  +        SL+  I  ++   +  +D +  + +  ++  
Sbjct: 22  PSEDDLLAKAAGLPVTRVQMLMETARSAASLDTPIGGNELGPT-VKDSVEDEREAADEEF 80

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIE 273
                R +   ML      L  RE R+   R   ++    TLE +     V+RER+RQIE
Sbjct: 81  GSDSLRNDMEAMLLE----LPEREARVVRLRFGLDDGKEWTLEEIGEALNVTRERIRQIE 136

Query: 274 ARAFKKVQ 281
           A+A +K++
Sbjct: 137 AKALRKLR 144


>gi|282854097|ref|ZP_06263434.1| sigma-70, region 4 [Propionibacterium acnes J139]
 gi|282583550|gb|EFB88930.1| sigma-70, region 4 [Propionibacterium acnes J139]
 gi|314923070|gb|EFS86901.1| sigma-70, region 4 [Propionibacterium acnes HL001PA1]
 gi|314966840|gb|EFT10939.1| sigma-70, region 4 [Propionibacterium acnes HL082PA2]
 gi|314981182|gb|EFT25276.1| sigma-70, region 4 [Propionibacterium acnes HL110PA3]
 gi|315092002|gb|EFT63978.1| sigma-70, region 4 [Propionibacterium acnes HL110PA4]
 gi|315093239|gb|EFT65215.1| sigma-70, region 4 [Propionibacterium acnes HL060PA1]
 gi|315103504|gb|EFT75480.1| sigma-70, region 4 [Propionibacterium acnes HL050PA2]
 gi|327327666|gb|EGE69442.1| RNA polymerase sigma factor [Propionibacterium acnes HL103PA1]
          Length = 270

 Score = 89.1 bits (220), Expect = 8e-16,   Method: Composition-based stats.
 Identities = 50/255 (19%), Positives = 103/255 (40%), Gaps = 37/255 (14%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKK 92
           E  L +R  + G + A   L    L +V+  A      Y   + +++  G +GL +A+++
Sbjct: 47  EAEL-RRISDDG-VGARQTLWRQMLAIVLTHARQAAVSYRCSVEDLIQAGCVGLGEAIER 104

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           +D  RG R +T +  WI+  + E ++R          A  + +      +    + +T  
Sbjct: 105 YDVRRGARFSTVAWTWIRRRIGEEVVRLSG-------ARSRSVMREAAEVARIEEELTAR 157

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
                   AIA ++     +V+ +  R          +   +  +S ++   V      +
Sbjct: 158 WHSVPSSDAIAAQMG---KDVMWVEKRR---------VERWEVETSFFEQVAVVQKSCDD 205

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPVTLENLSSEFEVSRERVRQ 271
                           +  + +L  +ERRI E R   +  P+T+  ++ E  +S   VR+
Sbjct: 206 PE--------------SGLIGLLTGQERRIVELRHGFEGEPMTITAVAHELGLSASNVRR 251

Query: 272 IEARAFKKVQESIQK 286
           IE RA  +++  +Q+
Sbjct: 252 IEQRALGRLRRHLQQ 266


>gi|254729575|ref|YP_003084257.1| RNAP sigma factor [Cyanophage PSS2]
 gi|254211727|gb|ACT65675.1| RNAP sigma factor [Cyanophage PSS2]
 gi|265524923|gb|ACY75815.1| predicted protein [Cyanophage PSS2]
          Length = 284

 Score = 88.7 bits (219), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 54/244 (22%), Positives = 98/244 (40%), Gaps = 22/244 (9%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYR--------EHGDLSAAHRLVTSHLRLVVKI-AM 66
           ++ ++    + P+  ++E  V A+  +        E    +A  R+V  +LRLV  I   
Sbjct: 3   INDWLANAAQYPITSQEEVIVNARIVKNWKAGLVSERKGQAALQRIVKGNLRLVAAIWKK 62

Query: 67  GYRGYGLPIS---EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
            Y    +  +   E++ EG IGL  A  +FDP  G+R +T++ WWI  +M+EY   S  L
Sbjct: 63  RYLKRNIAPAHSLEILQEGAIGLNDAAMRFDPSSGYRFSTFASWWIIKSMKEYQRDSERL 122

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           V+        +   + + LK      T+      + +  A K+    +  ++M       
Sbjct: 123 VRF-------KGDMHWKALKAVKMLHTEKGQHSTEEIEKALKMPAKRAINLAMTFTQLHP 175

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           +SL+     S  ++S   +++           I   +R      L     V  PR R + 
Sbjct: 176 KSLDVPNQLSGNDASPLHEFIADPSTTTFDYEIPNADR--IAKYLFDQFDV-EPRMRELI 232

Query: 244 EARR 247
             R 
Sbjct: 233 LNRF 236


>gi|317153074|ref|YP_004121122.1| FliA/WhiG family RNA polymerase sigma factor [Desulfovibrio
           aespoeensis Aspo-2]
 gi|316943325|gb|ADU62376.1| RNA polymerase sigma factor, FliA/WhiG family [Desulfovibrio
           aespoeensis Aspo-2]
          Length = 261

 Score = 88.7 bits (219), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 39/216 (18%), Positives = 92/216 (42%), Gaps = 19/216 (8%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            ++E++S G++GL+ A+ K++ +RG +  TYS   IK AM + + R             +
Sbjct: 63  ELNELISAGSLGLLDALGKYNAQRGIKFDTYSENRIKGAMLDELRR--------MDWFSR 114

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            L   ++ L+   + +      P     +     +SE +V          + L AL N  
Sbjct: 115 GLRQKVKALEDAQRQVEHETGGPATTEQLQALTGMSEKDVR---------QGLEALHNQM 165

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
             +   + + ++      E    +    +   + +   +  L PRE+ +      +E  +
Sbjct: 166 CLSLDSFHENVIGRKAMTEDEPFQSTAFQEIVDKVASLIEELTPREKLVISLYYGEE--L 223

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
            ++  +   +++  RV Q+ ++A  K++++ + + E
Sbjct: 224 NMKETAEVMDITEGRVSQLHSQALTKLRKTFRARYE 259


>gi|303248004|ref|ZP_07334270.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfovibrio fructosovorans JJ]
 gi|302490561|gb|EFL50466.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfovibrio fructosovorans JJ]
          Length = 225

 Score = 88.7 bits (219), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 45/214 (21%), Positives = 89/214 (41%), Gaps = 18/214 (8%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + E++S G +GL++A+ +F PE G +  TY+   IK AM + + R       G     +
Sbjct: 24  ELGELLSAGAMGLLEALGRFRPELGIKFETYAESRIKGAMLDDLRR-MDWFSRGQRHRVR 82

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            L    RR++        ++ +   V  +A+   +SE EV      L     L+      
Sbjct: 83  TLEEASRRIES-------DSGRTPSVEQLAEATGLSEREVTQGLEALQNQLCLSL----- 130

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
               +  ++   Y  +  E    +  E K   + L   +  L PRE+ +      +E  +
Sbjct: 131 ---DAITENISSYQKNQLENEPYKSAEFKELVDKLASLIDDLTPREKLVLSLYYGEE--L 185

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +   S    ++  RV Q+ ++A  ++++  + Q
Sbjct: 186 NMRETSEVMGITEGRVSQLHSQALARLRQKFKAQ 219


>gi|317133668|ref|YP_004092982.1| RNA polymerase, sigma 28 subunit, SigK [Ethanoligenens harbinense
           YUAN-3]
 gi|315471647|gb|ADU28251.1| RNA polymerase, sigma 28 subunit, SigK [Ethanoligenens harbinense
           YUAN-3]
          Length = 228

 Score = 88.7 bits (219), Expect = 9e-16,   Method: Composition-based stats.
 Identities = 49/198 (24%), Positives = 75/198 (37%), Gaps = 39/198 (19%)

Query: 24  RKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
              P  L   EE     R +  GD  A   L+  +LRLV+ I   Y        +++S G
Sbjct: 24  GSFPKPLTAAEERECLARMQ-AGDTKAQDMLIEHNLRLVMHIIKKYYANARDQEDLLSVG 82

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQE------------YILRSWSLVK----- 125
            IGL++ V  F PE+G RLATY+   I+  +              YI       K     
Sbjct: 83  TIGLIKGVITFKPEKGTRLATYAARCIENEILMHFRSQKKSAQDVYISDPIDTDKDGNQL 142

Query: 126 ---------------IGTTANQKRLFFNLRRLKGHLQAITD-----NNLKPEQVVAIAKK 165
                          +      ++L   + +L    +AI +     +  KP+    +A K
Sbjct: 143 TLMDVVSCEDTILDDVDLKMKSEKLRAYIVKLPPRERAIIEMRYGLHGAKPQTQREVAGK 202

Query: 166 LNVSESEVISMNCRLAGD 183
           LN+S S V  +  R  G+
Sbjct: 203 LNISRSYVSRIEKRALGE 220



 Score = 74.5 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 29/129 (22%), Positives = 50/129 (38%), Gaps = 2/129 (1%)

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           KPE+   +A          I M+ R     + +  I+             + D    E  
Sbjct: 94  KPEKGTRLATYAARCIENEILMHFRSQKKSAQDVYISDPIDTDKDGNQLTLMDVVSCEDT 153

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
           +++  + K +   L   +  L PRER I E R       P T   ++ +  +SR  V +I
Sbjct: 154 ILDDVDLKMKSEKLRAYIVKLPPRERAIIEMRYGLHGAKPQTQREVAGKLNISRSYVSRI 213

Query: 273 EARAFKKVQ 281
           E RA  +++
Sbjct: 214 EKRALGELR 222


>gi|307546921|ref|YP_003899400.1| flagellar biosynthesis sigma factor [Halomonas elongata DSM 2581]
 gi|307218945|emb|CBV44215.1| flagellar biosynthesis sigma factor [Halomonas elongata DSM 2581]
          Length = 235

 Score = 88.7 bits (219), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 42/237 (17%), Positives = 99/237 (41%), Gaps = 19/237 (8%)

Query: 53  LVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           L+  +L LV + A+  +      + + +++  G +GL++A+ +FD  +G   +T++   I
Sbjct: 13  LLEEYLPLVRRQALALQVRLPASIELDDLIQAGTVGLLEALGRFDAAQGASFSTFASQRI 72

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + AM + + RS   +        +     +RRL+  L        +P +   IA+ L++ 
Sbjct: 73  RGAMLDEL-RSRDWLPRSVRRGARAADEAVRRLEQSL-------GRPPEEAEIAEALDMD 124

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
                 +       + L      S+    + +D      +   +  +       RR  LT
Sbjct: 125 IDAYRRLLSDTNSGQLLPFEDLMSEGGEGRLRD------NETAETPVSLLVDDERRRQLT 178

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             +  L  RE+ +       +  + L+ + +   V+  RV Q+ ++A  +++  +++
Sbjct: 179 AGIEALPEREKLLMALYY--QEELNLKEIGAVLGVTESRVCQLHSQAVSRLRGRLRE 233


>gi|304438393|ref|ZP_07398334.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
 gi|304368759|gb|EFM22443.1| deoxyuridine 5'-triphosphate nucleotidohydrolase [Selenomonas sp.
           oral taxon 149 str. 67H29BP]
          Length = 208

 Score = 88.7 bits (219), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 29/106 (27%), Positives = 62/106 (58%), Gaps = 1/106 (0%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
            S Y+ ++  +  L  +EE  L + Y+E+GD++A  R++ ++  LV +    YR     +
Sbjct: 2   FSAYMKKLSAVQKLAPEEERALWRAYKENGDMAARRRIIEAYQPLVFREVYPYRALPAAM 61

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            + V EG IGL++AV+++DP+ G   + Y++  ++  +++++ R  
Sbjct: 62  -DAVQEGTIGLIEAVERYDPDYGAAFSLYAVHRVRGRVRDFLRREG 106


>gi|303239104|ref|ZP_07325634.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302593442|gb|EFL63160.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 256

 Score = 88.7 bits (219), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 46/237 (19%), Positives = 88/237 (37%), Gaps = 26/237 (10%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           D S     +  + RLV  +      Y        +    G IGL+ A K+F PE G   +
Sbjct: 10  DESLLEEFIRENQRLVSMVIRKQFSYVYNTAEYEDYFQSGCIGLVNAAKRFKPEYGTAFS 69

Query: 103 TYSMWWIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           TY++  I   +  Y      S +        K   +   R +G  +A             
Sbjct: 70  TYAVSLIAGEIMRYRRDYCASGIHSSRNIKDKYYRYQALRNRGVAEA------------E 117

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
             ++L V  +E+  +   +    SL+A+I  +D  +      +  D    E+  ++  E 
Sbjct: 118 ACRELGVDSAELNKVINAMEPGYSLDAVIYDNDSGTPLTGGDITADDFNLEEEAMDWLEL 177

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE----RVRQIEA 274
           +    +L    ++L+  +R+IF          T   + +   +S+     R+R+I+ 
Sbjct: 178 E---EILRHVKNILSESDRKIFNLYL---QKKTQTQMKTMLGMSQANISRRIRKIKE 228


>gi|86148201|ref|ZP_01066499.1| RNA polymerase sigma factor [Vibrio sp. MED222]
 gi|85834048|gb|EAQ52208.1| RNA polymerase sigma factor [Vibrio sp. MED222]
          Length = 83

 Score = 88.7 bits (219), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 34/83 (40%), Positives = 47/83 (56%)

Query: 1  MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
          M  +   + +  +  L  YI      PML   EE  LA+R    G++ AA  L+ SHLR 
Sbjct: 1  MANQAYQMALVTQDSLDSYIRSANSYPMLTPDEERGLAERLHYKGEIDAAKGLILSHLRF 60

Query: 61 VVKIAMGYRGYGLPISEVVSEGN 83
          VV +A GY GYGLP++++V EGN
Sbjct: 61 VVHVARGYSGYGLPMADLVQEGN 83


>gi|119632740|gb|ABL84377.1| DNA directed RNA polymerase sigma 42 protein [Streptococcus suis]
          Length = 75

 Score = 88.7 bits (219), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 2/77 (2%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +++ EGN+GLM+AV KFD  +GF+ +TY+ WWI+ A+   I      ++I     +    
Sbjct: 1   DLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVE--TI 58

Query: 137 FNLRRLKGHLQAITDNN 153
             L R + +L      +
Sbjct: 59  NKLVREQRNLLQELGQD 75


>gi|152990367|ref|YP_001356089.1| RNA polymerase sigma factor for flagellar operon [Nitratiruptor sp.
           SB155-2]
 gi|151422228|dbj|BAF69732.1| RNA polymerase sigma factor for flagellar operon [Nitratiruptor sp.
           SB155-2]
          Length = 211

 Score = 88.3 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 50/242 (20%), Positives = 94/242 (38%), Gaps = 46/242 (19%)

Query: 50  AHRLVTSHLRLVVKIAMG-YRGYGLP----ISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
             ++V  +L LV K+A   Y            E+V+ G IGL +A++K++ ++  + +TY
Sbjct: 8   KQQIVLDNLALVKKVASKIYFKLPKDANIEFDELVNTGTIGLYKAIEKYNRDK-AQFSTY 66

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +   I+  + +Y+    SL  +  T           R K   +        P   +AI  
Sbjct: 67  AYIKIRGEILDYLR---SLHIVPRTM----------REKIKKEKEEGQKEIPLSNLAIMM 113

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
                     SM   L   E           N  +  D L+ +    E   I  E     
Sbjct: 114 ----------SMEKALGESE-----------NGPRLMDILISNEKSPEDYAISSE----I 148

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + +  ++  L+  ER+  +    +E     + +S    +S+ RV QI+++A  K++   
Sbjct: 149 HDKIVEALDSLSESERKTLQMLYFEEREP--KEISQILGISQSRVSQIKSKAIVKLKSVF 206

Query: 285 QK 286
           +K
Sbjct: 207 KK 208


>gi|226939286|ref|YP_002794357.1| RpoS [Laribacter hongkongensis HLHK9]
 gi|226714210|gb|ACO73348.1| RpoS [Laribacter hongkongensis HLHK9]
          Length = 170

 Score = 88.3 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 30/172 (17%), Positives = 66/172 (38%), Gaps = 12/172 (6%)

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           +     +++       +      R   HL++    +   +++  +  K       V+S+N
Sbjct: 1   MNQSRTIRLPVHV--IKELNVYLRASRHLESQIGRDPTIDEIAHLVGKPPEEVRRVMSLN 58

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
            R+A   SL+A ++                 D Q++    K         +   +  L  
Sbjct: 59  ERMA---SLDAPLDID-----PMLTIGESIPDEQQEEPDIKLHGMQVNRYVQTWLKQLTD 110

Query: 238 RERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++R + E R         TLE L+    ++RERVRQI+    + ++  ++++
Sbjct: 111 KQRLVIERRYGLNGYEICTLEELADSLSLTRERVRQIQIEGLESLRRILRRK 162


>gi|149177082|ref|ZP_01855690.1| sigma-70 factor [Planctomyces maris DSM 8797]
 gi|148844147|gb|EDL58502.1| sigma-70 factor [Planctomyces maris DSM 8797]
          Length = 556

 Score = 88.3 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 43/189 (22%), Positives = 83/189 (43%), Gaps = 29/189 (15%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKR----------YREHGDL----------------- 47
           GL  Y+  +  IP+L ++EE    ++           +E  D                  
Sbjct: 314 GLPPYLASLYSIPLLTREEEAYYFRKLNFLKYKAFQIQEQLDPNRPKARDMDQIEKLLDE 373

Query: 48  --SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
                + L+ S+LRLVV IA  +   G    E+VS+GN+ L++A++KFD  +G + +TY+
Sbjct: 374 STDVKNFLIRSNLRLVVSIAKRHIRPGGNFFEMVSDGNMSLIRAIEKFDYTKGNKFSTYA 433

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
            W I       I   + ++    T N++  F +    +   +    N  +   +++I  +
Sbjct: 434 SWAIMKNYARSIPAEYKVLDRFRTGNEELFFQSTDERESQYREELINQKQHAVIMSILDQ 493

Query: 166 LNVSESEVI 174
           L+  E +++
Sbjct: 494 LDGREKDIL 502



 Score = 81.8 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 27/104 (25%), Positives = 49/104 (47%), Gaps = 3/104 (2%)

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           S+ A     D+  +  ++      D +E    E+   + +  ++   +  L+ RE+ I  
Sbjct: 444 SIPAEYKVLDRFRTGNEELFFQSTDERESQYREELINQKQHAVIMSILDQLDGREKDILI 503

Query: 245 ARRLQE---NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            R        P TLE +   F V++ER+RQ+E+RA KK++   Q
Sbjct: 504 YRYGLNARNEPQTLEQVGDRFGVTKERIRQLESRALKKLRRITQ 547


>gi|325508641|gb|ADZ20277.1| RNA polymerase sigma factor [Clostridium acetobutylicum EA 2018]
          Length = 219

 Score = 88.3 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 44/238 (18%), Positives = 102/238 (42%), Gaps = 31/238 (13%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY--GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            +++V  ++ LV  IA  Y      L + ++V  G I ++ AV+ FD  +G + +TY+  
Sbjct: 9   RNKVVEKYMTLVKSIARKYINRSGTLELEDMVQSGAISMINAVENFDYNKGVKFSTYARH 68

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            ++  M+ Y  ++  L+ +     +     +LRR+K  L        K   +  I+ +L 
Sbjct: 69  CVEGGMKNYCKKNE-LIHLSEYQRK-----DLRRIKK-LFDEKQLENKDIDITEISAELG 121

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + + + I++ C L  D                 +   + D++ +     EKE   N   +
Sbjct: 122 IEKEKAINLICFLNKD-----------------KYIPIDDYEYKYGKSFEKEIVDNI--L 162

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           +   +  L   ++ +   R      ++  ++  ++ ++R+ V+Q   R   K++  ++
Sbjct: 163 IRSLIENLPKNQQNLIRERL---KDMSFTDIGKKYNITRQAVQQSVKRIINKMKRELE 217


>gi|168704081|ref|ZP_02736358.1| RNA polymerase sigma factor for flagellar operon [Gemmata
           obscuriglobus UQM 2246]
          Length = 247

 Score = 88.3 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 48/242 (19%), Positives = 96/242 (39%), Gaps = 26/242 (10%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFD 94
            + Y+   +      L+ SHL LV  +     G    G+ +  + S G +GL++A  KFD
Sbjct: 10  IQAYQRQAEQQRRDELIVSHLPLVKHVIGRLIGDVPPGVDVENLESAGVLGLVEAAAKFD 69

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P R  +  T++   I+ A+ + + R+     +    + +            ++       
Sbjct: 70  PARNAQFKTFAYLRIRGAIVDEMRRNS---PLPQHVHARLAL---------VRRACRTLP 117

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
            P  V AIA    +SE EV          ++L+A   +   +  Q  +    +  G  + 
Sbjct: 118 HPITVEAIAAATGLSEDEV---------TDTLSAERMAKTMSWEQASESTGLEPAGGGEE 168

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
              + ER      L  ++  L P+ER         +  + L+ ++   ++S  RV ++ +
Sbjct: 169 PGAEMERWESVQQLGDAIQELEPKERIAVTLYY--KEDLRLKEIAEVMKLSVSRVSRLLS 226

Query: 275 RA 276
           +A
Sbjct: 227 KA 228


>gi|292905274|ref|YP_003541145.1| sigma-70 region 2-containing protein [Anabaena variabilis ATCC
           29413]
 gi|75705012|gb|ABA24687.1| Sigma-70 region 2 [Anabaena variabilis ATCC 29413]
          Length = 240

 Score = 88.3 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 45/224 (20%), Positives = 90/224 (40%), Gaps = 14/224 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR-GYGLPISEVVSEGNIGLMQAVKKFD 94
            L + YR +       R+   H +L  +IA  YR     P+ +++    +G++ A+++FD
Sbjct: 4   ELFREYRNNPTRQLRDRIFNHHYKLACEIAHQYRICCDEPLEDLIQLAGVGMLTAIERFD 63

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P R    ++++  +IK  ++ Y+    S VKI  +   + L+   ++L G  + I     
Sbjct: 64  PSRSNAFSSFACPYIKGEIRHYLRDKASTVKIPRSL--QSLYQRGKKLHGTDEQIAKALG 121

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
             +Q    AK + V        N  L   ++L  L     +      D +          
Sbjct: 122 CTQQQWKEAKAIGV--------NRNLFNIDNLLTLTLEWSEGCG-GSDTVSMKRFLSALS 172

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
             E+  +     +   S+S L+   +++ E    Q  P  L+ +
Sbjct: 173 FQEQPVKPIATTIEPSSLSQLDEANQQLIEMFFFQNEP--LKEV 214


>gi|224553606|gb|ACN55041.1| RNA polymerase sigma factor [Escherichia coli]
          Length = 111

 Score = 88.3 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 35/111 (31%), Positives = 59/111 (53%), Gaps = 2/111 (1%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL + +++ EGN+GL++AV+KFDPERGFR +TY+ WWI+  ++  I+     +++     
Sbjct: 1   GLALLDLIEEGNLGLIRAVEKFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV 60

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            K L   LR  +  L    D+    E+      K     S ++ +N R+  
Sbjct: 61  -KELNVYLRTAR-ELSHKLDHEPSAEESAEQLDKPVDDVSRMLRLNERITS 109


>gi|15894509|ref|NP_347858.1| RNA polymerase sigma factor [Clostridium acetobutylicum ATCC 824]
 gi|15024150|gb|AAK79198.1|AE007635_12 RNA polymerase sigma factor [Clostridium acetobutylicum ATCC 824]
          Length = 227

 Score = 88.3 bits (218), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 44/238 (18%), Positives = 102/238 (42%), Gaps = 31/238 (13%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY--GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            +++V  ++ LV  IA  Y      L + ++V  G I ++ AV+ FD  +G + +TY+  
Sbjct: 17  RNKVVEKYMTLVKSIARKYINRSGTLELEDMVQSGAISMINAVENFDYNKGVKFSTYARH 76

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            ++  M+ Y  ++  L+ +     +     +LRR+K  L        K   +  I+ +L 
Sbjct: 77  CVEGGMKNYCKKNE-LIHLSEYQRK-----DLRRIKK-LFDEKQLENKDIDITEISAELG 129

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + + + I++ C L  D                 +   + D++ +     EKE   N   +
Sbjct: 130 IEKEKAINLICFLNKD-----------------KYIPIDDYEYKYGKSFEKEIVDNI--L 170

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           +   +  L   ++ +   R      ++  ++  ++ ++R+ V+Q   R   K++  ++
Sbjct: 171 IRSLIENLPKNQQNLIRERL---KDMSFTDIGKKYNITRQAVQQSVKRIINKMKRELE 225


>gi|225849143|ref|YP_002729307.1| RNA polymerase sigma factor for flagellar operon
           [Sulfurihydrogenibium azorense Az-Fu1]
 gi|225643617|gb|ACN98667.1| RNA polymerase sigma factor for flagellar operon
           [Sulfurihydrogenibium azorense Az-Fu1]
          Length = 225

 Score = 87.9 bits (217), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 45/239 (18%), Positives = 96/239 (40%), Gaps = 44/239 (18%)

Query: 50  AHRLVTSHLRLVVKIAMG--YR--GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
             RLV  +L LV K+A    YR     +   ++   G IGL++A + +  ++G + +TY+
Sbjct: 7   KKRLVEENLNLVKKVASKIYYRLPDCSIDFDDLFQVGVIGLIKATENYHQDKG-KFSTYA 65

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
              I+  + +++                            +   T+ +    +       
Sbjct: 66  YIRIRGEILDFLR------------------------SLEVFPHTEKDYITVEKAEPDDN 101

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           L  S + VI          SL+ +I+  D +S    D +V +    E+    KE+ +   
Sbjct: 102 LPYSNTAVI---------LSLDKIISIED-DSISLIDSIVSNSKTPEEEYALKEQIEKIS 151

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            ++ +    L+  E+++      +E     + +     +S  R+ QI+A+A +K++E +
Sbjct: 152 QIIEQ---YLDENEKKVINYLFFEEKDP--KEIQEIMGISLGRISQIKAKAVEKIREIM 205


>gi|302385749|ref|YP_003821571.1| sigma-70 region 3 domain protein [Clostridium saccharolyticum WM1]
 gi|302196377|gb|ADL03948.1| sigma-70 region 3 domain protein [Clostridium saccharolyticum WM1]
          Length = 203

 Score = 87.9 bits (217), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 47/203 (23%), Positives = 84/203 (41%), Gaps = 8/203 (3%)

Query: 17  SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
             Y+ E+  IP   + E+  L K   E G   A  RLV  +LR  ++ A  Y G G+ I+
Sbjct: 7   QMYLEEMGNIPPCTRDEQERLLKEAAE-GRKEAKKRLVEGNLRTALEYAREYDGRGVLIT 65

Query: 77  EVVSEGNIGLMQAVKKFDPERGFR--LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           ++V E N+ LM AV++F      R    +++   I+ A+   +    S  + G     + 
Sbjct: 66  DLVQEANMALMMAVEEFSAMENGRLAFDSFTGRKIREALTAAVEEQQSACQTG-----EE 120

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           L   +  L+   QA+     +   V  +A K+ +S  E+  +        S+NA     +
Sbjct: 121 LAARVNVLQKVSQALAGELGREATVEELADKMKMSVEEIKGIMKMAMDAMSMNAETMDLE 180

Query: 195 KNSSQWQDWLVYDHDGQEQVLIE 217
             +      +  D   ++    E
Sbjct: 181 ALAEVEGIEITEDEAAEDYDYEE 203


>gi|284052567|ref|ZP_06382777.1| RNA polymerase sigma factor SigC [Arthrospira platensis str.
           Paraca]
          Length = 232

 Score = 87.9 bits (217), Expect = 1e-15,   Method: Composition-based stats.
 Identities = 33/83 (39%), Positives = 53/83 (63%), Gaps = 5/83 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L  +E     K+ +  G + A   ++ ++LRLVV +A  Y+  GL + +++ EG +GL +
Sbjct: 155 LSVEE----LKQVQREG-IQAKDHMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLER 209

Query: 89  AVKKFDPERGFRLATYSMWWIKA 111
           AV+KFDP RG+R +TYS WWI+ 
Sbjct: 210 AVEKFDPTRGYRFSTYSYWWIRQ 232


>gi|312877884|ref|ZP_07737830.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
 gi|311795347|gb|EFR11730.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
          Length = 114

 Score = 87.9 bits (217), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 27/95 (28%), Positives = 51/95 (53%), Gaps = 3/95 (3%)

Query: 27  PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI-SEVVSEGNIG 85
           PM  ++EE  L K +   G   A + L+  +LRLV  IA  Y      +  +++S G IG
Sbjct: 13  PMSSEEEEMYLNKMW--EGCKEARNILIEKNLRLVAHIAKKYTFSFPNLTDDIISVGTIG 70

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           L++A++ +   +  +L+TY+   I+  +  Y+ ++
Sbjct: 71  LIKAIETYSKAKSTKLSTYAAKCIENEILMYLRQN 105


>gi|224771363|dbj|BAH28623.1| sporulation sigma factor SigK [Clostridium perfringens]
          Length = 196

 Score = 87.9 bits (217), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 57/255 (22%), Positives = 93/255 (36%), Gaps = 66/255 (25%)

Query: 14  IGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           I L+ Y+      P  L ++EE +  +R ++ GD+ A   LV  +LRLV  I   Y    
Sbjct: 2   IFLTGYVTGNSTFPKPLNEKEEKIYLERLKD-GDVEAKRVLVERNLRLVAHIVKKYSSNY 60

Query: 73  L---PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
                + +++S G IGL++A+  FD  +G RLATY+   I   +  +             
Sbjct: 61  QNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATYAAKCIDNEILMF------------- 107

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
                 F N ++ KG                             + +   +  D+  N  
Sbjct: 108 ------FRNTKKTKGE----------------------------VFLQDPIGVDKEGNE- 132

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-- 247
           I   D  SS     L    +  E  L  KE  K   ++L+        RE+ I + R   
Sbjct: 133 ICLIDILSSDSDSVL----EAVENSLQVKELYKKMSDVLSH-------REKEIIQMRYGL 181

Query: 248 LQENPVTLENLSSEF 262
           L  +  T   ++   
Sbjct: 182 LDGDIKTQREIAGIL 196


>gi|242280062|ref|YP_002992191.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio
           salexigens DSM 2638]
 gi|242122956|gb|ACS80652.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio
           salexigens DSM 2638]
          Length = 263

 Score = 87.9 bits (217), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 47/242 (19%), Positives = 96/242 (39%), Gaps = 23/242 (9%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              +V  +   +  IA+  +      + + E++S G++GL++++ KF PE   +  TY+ 
Sbjct: 36  QEAIVRHYSPKIRIIALRMKAKLPQNVELGELISAGSLGLVESLGKFRPELKIKFETYAE 95

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             IK AM + + R       G     K +   +R        I     +      + +  
Sbjct: 96  NRIKGAMLDELRR-MDWFSRGLRQKVKTIENCIR-------EIEHETGEKPTSAQLEEAT 147

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ-EQVLIEKEERKNRR 225
             S  EV          + L AL N    N   + D +  + D Q +    +    +   
Sbjct: 148 GFSAKEV---------QQGLEALQNQLCVNLDAFNDNIPSNKDSQLDDEPFQSAVFQETV 198

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           + +   +  L PRE+ +      +E  + ++  S   E++  RV Q+ ++A KK+++   
Sbjct: 199 DKVADLIDNLTPREKLVLSLYYGEE--LNMKETSEVMEITEGRVSQLHSQALKKLRKMFH 256

Query: 286 KQ 287
            +
Sbjct: 257 DK 258


>gi|87306557|ref|ZP_01088704.1| sigma-70 factor [Blastopirellula marina DSM 3645]
 gi|87290736|gb|EAQ82623.1| sigma-70 factor [Blastopirellula marina DSM 3645]
          Length = 556

 Score = 87.9 bits (217), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 49/225 (21%), Positives = 87/225 (38%), Gaps = 59/225 (26%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSA------------------------- 49
           GL  Y+  + + P+L +++EY L +++      +A                         
Sbjct: 313 GLPSYLASLYEAPLLTREQEYHLFRKFNYLKHHAAKLRESVETSKAKASVMDEIERLYEA 372

Query: 50  ----AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
                +++V S+LRLVV IA  + G      E+VS+GN+ L++AV+KFD  RG + +TY 
Sbjct: 373 AVEVKNQIVQSNLRLVVSIAKRHLGAADEFFELVSDGNMSLIRAVEKFDYSRGNKFSTYC 432

Query: 106 MWWIKAAMQEYI----------------LRSWSLVKIGTTANQKRL--------FFNLRR 141
            W I       I                L    +        Q+ +           L R
Sbjct: 433 SWAIMKNFARTIPVEFKHRDRFRTSLDELFQGRVDNRSDQYEQEAMQQQRERQIQRILNR 492

Query: 142 LKGHLQAI------TDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           L    Q I       D++ +P+ +  +  +L V++  +  +  R 
Sbjct: 493 LDEREQKIIIRRYGLDHDHEPQTLKEVGAELGVTKERIRQIEARA 537



 Score = 81.8 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 25/96 (26%), Positives = 50/96 (52%), Gaps = 3/96 (3%)

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--- 250
           D+  +   +      D +     ++  ++ R   + R ++ L+ RE++I   R   +   
Sbjct: 452 DRFRTSLDELFQGRVDNRSDQYEQEAMQQQRERQIQRILNRLDEREQKIIIRRYGLDHDH 511

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            P TL+ + +E  V++ER+RQIEARA  K++ + Q+
Sbjct: 512 EPQTLKEVGAELGVTKERIRQIEARALNKLRVAAQE 547


>gi|291544363|emb|CBL17472.1| DNA-directed RNA polymerase specialized sigma subunit [Ruminococcus
           sp. 18P13]
          Length = 118

 Score = 87.6 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 32/113 (28%), Positives = 54/113 (47%), Gaps = 2/113 (1%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLR 59
           M  + +S I++     + +++     P  L  +EE     R  + GD  A   L+  +LR
Sbjct: 1   MFLQFLSGILSNLFFFALHVNTAMAFPKPLSPKEEADCFARLAQ-GDSQARAMLIEHNLR 59

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  +   Y        E++S G +GL++AV  FD  +G + ATY+   I+ A
Sbjct: 60  LVAHMIKKYYANSKDQDELISIGTMGLIKAVNTFDAAKGSKFATYAGRCIEKA 112


>gi|253574829|ref|ZP_04852169.1| RNA polymerase sigma-K factor [Paenibacillus sp. oral taxon 786
           str. D14]
 gi|251845875|gb|EES73883.1| RNA polymerase sigma-K factor [Paenibacillus sp. oral taxon 786
           str. D14]
          Length = 110

 Score = 87.6 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 26/86 (30%), Positives = 45/86 (52%), Gaps = 1/86 (1%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+        L ++EE    +R  E GD  + + L+  +LRLV  I   +   G  +
Sbjct: 26  LVSYVKNNAFPQPLTEEEETKHLQRMAE-GDSESRNILIEHNLRLVAHIVKKFDNTGEDL 84

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRL 101
            +++S G IGL++A++ F P +G +L
Sbjct: 85  EDLISIGTIGLIKAIESFRPNKGTKL 110


>gi|292489124|ref|YP_003532011.1| RNA polymerase sigma factor FliA/RpoD [Erwinia amylovora CFBP1430]
 gi|292900243|ref|YP_003539612.1| RNA polymerase sigma factor for flagellar operon [Erwinia amylovora
           ATCC 49946]
 gi|291200091|emb|CBJ47217.1| RNA polymerase sigma factor for flagellar operon [Erwinia amylovora
           ATCC 49946]
 gi|291554558|emb|CBA22163.1| RNA polymerase sigma factor FliA/RpoD [Erwinia amylovora CFBP1430]
          Length = 243

 Score = 87.6 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 42/213 (19%), Positives = 92/213 (43%), Gaps = 18/213 (8%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQ 132
            + +++  G++G + A+  FDP +G  L+ +    I+ A+ + +  R W   ++   A  
Sbjct: 40  ELDDLIQAGSLGFLSAIDHFDPTKGVTLSAFLAQRIRWALMDELRERDWVPRRVRKHA-- 97

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                  R +   +Q +  N         IA ++ VS   V  +   LA   S  + I S
Sbjct: 98  -------REMTAVIQQLEQNKGGEASEADIATEMGVS---VCELQQMLADTNS--SQIYS 145

Query: 193 SDKNSSQWQDWLVY-DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
            D+   Q+ D     D + +    + +  ++N    +   +SV+  RE+ I +    Q+ 
Sbjct: 146 LDELQEQFADSYETIDEENEALNPVHQAVQENLVGKIAEHISVIPEREQVILQLYYQQD- 204

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + +  + +   ++  RV Q+ + A K+++  +
Sbjct: 205 -LNMREIGAVLSLTETRVSQLHSLAIKRIRARM 236


>gi|312173282|emb|CBX81537.1| RNA polymerase sigma factor FliA/RpoD [Erwinia amylovora ATCC
           BAA-2158]
          Length = 243

 Score = 87.6 bits (216), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 42/213 (19%), Positives = 92/213 (43%), Gaps = 18/213 (8%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQ 132
            + +++  G++G + A+  FDP +G  L+ +    I+ A+ + +  R W   ++   A  
Sbjct: 40  ELDDLIQAGSLGFLSAIDHFDPTKGVTLSAFLAQRIRWALMDELRERDWVPRRVRKHA-- 97

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                  R +   +Q +  N         IA ++ VS   V  +   LA   S  + I S
Sbjct: 98  -------REMTAVIQQLEQNKGGEASEADIATEMGVS---VCELQQMLADTNS--SQIYS 145

Query: 193 SDKNSSQWQDWLVY-DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
            D+   Q+ D     D + +    + +  ++N    +   +SV+  RE+ I +    Q+ 
Sbjct: 146 LDELQEQFADSYETIDEENEALNPVHQAVQENLVGKIAEHISVIPEREQVILQLYYQQD- 204

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + +  + +   ++  RV Q+ + A K+++  +
Sbjct: 205 -LNMREIGAVLSLTETRVSQLHSLAIKRIRSRM 236


>gi|327539462|gb|EGF26077.1| sigma-70 factor [Rhodopirellula baltica WH47]
          Length = 557

 Score = 87.2 bits (215), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 28/95 (29%), Positives = 52/95 (54%), Gaps = 3/95 (3%)

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--- 250
           D+  +   +  V   D +    +E+  +  R+  L R +  L+ RE++I  AR   +   
Sbjct: 452 DRFRATPDEMFVAHQDERLDPYLEETVQLQRQRELARILDRLDEREQKIITARFGLQRGV 511

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            P+TL+ +  E  V++ERVRQ+EARA  K++++ +
Sbjct: 512 EPLTLKEVGEEMGVTKERVRQLEARALSKLRDAAR 546



 Score = 83.7 bits (206), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 84/240 (35%), Gaps = 60/240 (25%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY----------------REH 44
           M     +  V     L  Y+  +  +P+L +++E  L ++                  + 
Sbjct: 298 MPVSETARKVRAPSELPSYLAALYDVPLLTREQEGHLFRKMNYLKHRANKLRQSLTDADR 357

Query: 45  GD--------------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
            D              +   +++V ++LRLVV IA  +         ++S+GN+ L++AV
Sbjct: 358 MDTAVMDQIQSLYEEAVKVKNKIVQANLRLVVSIAKRHVASAEDFFSLISDGNMSLIRAV 417

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILR--SWSLVKIGTT------------------- 129
           +KFD  RG + +TY+ W I       I            T                    
Sbjct: 418 EKFDYSRGNKFSTYASWAIMKNFARTIPNEFKHRDRFRATPDEMFVAHQDERLDPYLEET 477

Query: 130 ---ANQKRLFFNLRRLKGHLQAI------TDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
                Q+ L   L RL    Q I          ++P  +  + +++ V++  V  +  R 
Sbjct: 478 VQLQRQRELARILDRLDEREQKIITARFGLQRGVEPLTLKEVGEEMGVTKERVRQLEARA 537


>gi|227876732|ref|ZP_03994841.1| possible DNA-directed RNA polymerase sigma subunit D [Mobiluncus
           mulieris ATCC 35243]
 gi|269976259|ref|ZP_06183255.1| FliA/WhiG family RNA polymerase sigma factor [Mobiluncus mulieris
           28-1]
 gi|227842629|gb|EEJ52829.1| possible DNA-directed RNA polymerase sigma subunit D [Mobiluncus
           mulieris ATCC 35243]
 gi|269935588|gb|EEZ92126.1| FliA/WhiG family RNA polymerase sigma factor [Mobiluncus mulieris
           28-1]
          Length = 455

 Score = 87.2 bits (215), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 47/256 (18%), Positives = 99/256 (38%), Gaps = 22/256 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L+  +L LV                  ++ S G++ L+QA K ++PE G     Y++
Sbjct: 10  RDALIEKNLPLVGYQVAELLRRVPSFVQREDLASAGSLALVQAAKSYNPETGVPFHRYAV 69

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           + I+ AM + + R+      G+ +  K       +L+    A+T    +      +A  L
Sbjct: 70  FRIRGAMLDEL-RAMDWATRGSRSRTK-------QLEEMTAALTAAAGRAPTREELAVAL 121

Query: 167 NVSESEVISMNCRLAGD-ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
            +   +V +     +    S++   +  D  S +    +V D    E  ++  E      
Sbjct: 122 GIEVGQVEAAQLDASRRMVSIDVSYSEDDPRSIE----IVDDGLNPEDTVLTDERLV--- 174

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             L  ++  L  R R + E    +E  V    +++   V++ RV Q+   A   +++ + 
Sbjct: 175 -YLKAAVKALPQRLRYVVEQVFFEEKSVN--EVAASLGVTQSRVSQLRTEALSMIRDGMV 231

Query: 286 KQVELSSSPPLLQKPR 301
             +E   +     +P+
Sbjct: 232 HHLEPDDAAEAPHEPQ 247


>gi|228962768|ref|ZP_04124034.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228796921|gb|EEM44265.1| RNA polymerase sigma-B factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
          Length = 225

 Score = 87.2 bits (215), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 42/235 (17%), Positives = 96/235 (40%), Gaps = 16/235 (6%)

Query: 57  HLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           +  LV  +A  Y        + V  G +GL+ A++++D         + +  I   M++Y
Sbjct: 3   YTNLVHSLAYRYSKGNASHEDFVQIGMLGLLGAIRRYDTSLKKEFEAFLIPTIMGEMKKY 62

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA--KKLNVSESEVI 174
           +      V +      +R+      LK  ++ +T    +  Q+  IA   +L+  E   +
Sbjct: 63  LRDKTWDVHVP-----RRIKDKSSTLKKTIEILTSTLQRSPQIQEIAIHMELSEEEVLEL 117

Query: 175 SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV 234
               +     SL+A I    + +S+       +  G E+    K +R      L   ++ 
Sbjct: 118 MEAKQHYQTTSLDAEI----ETASEGAIGTKVEFVGVEEEGYGKVDRYLTLEKLLPLLTK 173

Query: 235 LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
              +E+ I     +++     ++  +   +S+  V +I+ RA +K++++   ++E
Sbjct: 174 ---QEKEILYYTFIKQ--YNQKDTGNLVGISQMHVSRIQRRALQKLRKASDSKLE 223


>gi|32474462|ref|NP_867456.1| sigma-70 factor [Rhodopirellula baltica SH 1]
 gi|32445000|emb|CAD75002.1| sigma-70 factor [Rhodopirellula baltica SH 1]
          Length = 557

 Score = 87.2 bits (215), Expect = 2e-15,   Method: Composition-based stats.
 Identities = 28/95 (29%), Positives = 52/95 (54%), Gaps = 3/95 (3%)

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--- 250
           D+  +   +  V   D +    +E+  +  R+  L R +  L+ RE++I  AR   +   
Sbjct: 452 DRFRATPDEMFVAHQDERLDPYLEETVQLQRQRELARILDRLDEREQKIITARFGLQRGV 511

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            P+TL+ +  E  V++ERVRQ+EARA  K++++ +
Sbjct: 512 EPLTLKEVGEEMGVTKERVRQLEARALSKLRDAAR 546



 Score = 83.7 bits (206), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 45/240 (18%), Positives = 84/240 (35%), Gaps = 60/240 (25%)

Query: 1   MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY----------------REH 44
           M     +  V     L  Y+  +  +P+L +++E  L ++                  + 
Sbjct: 298 MPVSETARKVRAPSELPSYLAALYDVPLLTREQEGHLFRKMNYLKHRANKLRQSLTDADR 357

Query: 45  GD--------------LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
            D              +   +++V ++LRLVV IA  +         ++S+GN+ L++AV
Sbjct: 358 MDTAVMDQIQSLYEEAVKVKNKIVQANLRLVVSIAKRHVASAEDFFSLISDGNMSLIRAV 417

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILR--SWSLVKIGTT------------------- 129
           +KFD  RG + +TY+ W I       I            T                    
Sbjct: 418 EKFDYSRGNKFSTYASWAIMKNFARTIPNEFKHRDRFRATPDEMFVAHQDERLDPYLEET 477

Query: 130 ---ANQKRLFFNLRRLKGHLQAI------TDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
                Q+ L   L RL    Q I          ++P  +  + +++ V++  V  +  R 
Sbjct: 478 VQLQRQRELARILDRLDEREQKIITARFGLQRGVEPLTLKEVGEEMGVTKERVRQLEARA 537


>gi|167574693|ref|ZP_02367567.1| flagellar biosynthesis sigma factor [Burkholderia oklahomensis
           C6786]
          Length = 236

 Score = 87.2 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 41/241 (17%), Positives = 100/241 (41%), Gaps = 36/241 (14%)

Query: 50  AHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L+  +  LV ++A          + + ++   G +GL++A++++        A Y+ 
Sbjct: 23  QRWLIE-YAPLVKRVARQLGSQANGAIALEDMEQIGLMGLLEALRRYG-SPDEAFAGYAA 80

Query: 107 WWIKAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
             ++ A+ + + R  W           + +     R +   +A+     +      ++  
Sbjct: 81  LRVRGAILDELRRHDWRP---------RAVRNAAHRARDCERALCRTLGRVPTAGEVSAS 131

Query: 166 LNVSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           L +   E     M  R     S + +++          DWL +D + + QV++       
Sbjct: 132 LGIGIDEYRENVMANRAEAMASFDEMLD---------ADWLAHDDNPERQVVL------- 175

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            R  L ++++ L+ RE+R+ +     E  ++L  +++  E++  RV QI   A +K++ +
Sbjct: 176 -RRCLEQALTSLDEREQRVIQLYY--EFDLSLREIAAVLELTEARVCQINKAALRKMRAA 232

Query: 284 I 284
           +
Sbjct: 233 L 233


>gi|56966075|pdb|1TLH|B Chain B, T4 Asia Bound To Sigma70 Region 4
          Length = 81

 Score = 87.2 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 22/77 (28%), Positives = 41/77 (53%), Gaps = 2/77 (2%)

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEA 274
           +    ++ R      ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA
Sbjct: 1   DSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEA 60

Query: 275 RAFKKVQESIQKQVELS 291
           +A +K++   + +V  S
Sbjct: 61  KALRKLRHPSRSEVLRS 77


>gi|299115565|emb|CBN75768.1| RNA polymerase, sigma 70 subunit, RpoD subfamily [Ectocarpus
           siliculosus]
          Length = 244

 Score = 87.2 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 33/79 (41%), Positives = 58/79 (73%), Gaps = 2/79 (2%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             L +  +  G  +A   +V +++R+V+ IA  Y+  G+P+++++ EG++GL++AV+KFD
Sbjct: 70  VELEESLKVGG--AAKKTMVEANMRMVISIARKYQHLGVPLTDLIQEGSLGLVRAVEKFD 127

Query: 95  PERGFRLATYSMWWIKAAM 113
           PERGF+L+TYS WWI+ A+
Sbjct: 128 PERGFKLSTYSAWWIQQAI 146


>gi|297605001|ref|NP_001056480.2| Os05g0589200 [Oryza sativa Japonica Group]
 gi|255676623|dbj|BAF18394.2| Os05g0589200 [Oryza sativa Japonica Group]
          Length = 464

 Score = 87.2 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 38/161 (23%), Positives = 71/161 (44%), Gaps = 7/161 (4%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E +L  R +E        RL+ +   LV  IA  Y G G    +++  G +G++   +K
Sbjct: 305 DEALLRSRLQEGYC--CRERLLVTTEWLVKYIAKTYAGMGTAFEDLLQAGKMGVLNGAEK 362

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD ++G + +TY  +WI+ AM   +  +  ++++       R+   +R+++   +AI  N
Sbjct: 363 FDSQKGCKFSTYVKYWIRKAMLALLAENSGVIQLP-----ARMEGIIRKVREARRAIRYN 417

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
             +      IA  + VS + V           SL   I   
Sbjct: 418 TGRNPPDAEIAALIGVSVANVRLARKCSRRVVSLYTEIGVG 458


>gi|224771349|dbj|BAH28616.1| sporulation sigma factor SigK [Clostridium perfringens]
          Length = 196

 Score = 87.2 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 57/255 (22%), Positives = 93/255 (36%), Gaps = 66/255 (25%)

Query: 14  IGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           I L+ Y+      P  L ++EE +  +R ++ GD+ A   LV  +LRLV  I   Y    
Sbjct: 2   IFLTGYVTGNSTFPKPLNEKEEKIYLERLKD-GDIEAKRVLVERNLRLVAHIVKKYSSSY 60

Query: 73  L---PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
                + +++S G IGL++A+  FD  +G RLATY+   I   +  +             
Sbjct: 61  QNSKEMDDLISIGTIGLIKAIDSFDTNKGIRLATYAAKCIDNEILMF------------- 107

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
                 F N ++ KG                             + +   +  D+  N  
Sbjct: 108 ------FRNTKKTKGE----------------------------VFLQDPIGVDKEGNE- 132

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-- 247
           I   D  SS     L    +  E  L  KE  K   ++L+        RE+ I + R   
Sbjct: 133 ICLIDILSSDSDSVL----EAVENSLQVKELYKKMSDVLST-------REKEIIQMRYGL 181

Query: 248 LQENPVTLENLSSEF 262
           L  +  T   ++   
Sbjct: 182 LDGDIKTQREIAGIL 196


>gi|307109683|gb|EFN57920.1| hypothetical protein CHLNCDRAFT_141990 [Chlorella variabilis]
          Length = 357

 Score = 87.2 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 43/234 (18%), Positives = 85/234 (36%), Gaps = 17/234 (7%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
              E+  LA R    GD  A   LV ++  LV  +A  + G GL   ++VSEG + L +A
Sbjct: 124 SAAEQRELA-RAAGAGDERAVAALVDANRALVHFLARRFLGKGLAREDLVSEGMLALERA 182

Query: 90  VKKFDPERGFR--LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH-L 146
            +++ P+ G      T++   I   M   +      V++         F ++ R++   L
Sbjct: 183 ARRYRPQPGRDASFGTFAAATILNGMSRALHTQSRDVRLPVH-----HFRDMARVRQATL 237

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +  T+   +P+  + + + +     +       L                + Q    L  
Sbjct: 238 ELATEQLRQPDYTLHLLRAMGSQVGQ-----SPLMQVLDQEMAAPMDQDPTQQGGVSLDG 292

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP---VTLEN 257
                E  +  +E  +     L   ++ L P++  + E R   +      T + 
Sbjct: 293 LEVLLEDEVAAEERSQLIEAELRSCLARLEPQQVSVVELRHGLDGEGLRRTWKE 346


>gi|167567742|ref|ZP_02360658.1| flagellar biosynthesis sigma factor [Burkholderia oklahomensis
           EO147]
          Length = 236

 Score = 87.2 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 41/241 (17%), Positives = 100/241 (41%), Gaps = 36/241 (14%)

Query: 50  AHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L+  +  LV ++A          + + ++   G +GL++A++++        A Y+ 
Sbjct: 23  QRWLIE-YAPLVKRVARQLGSQANGVIALEDMEQIGLMGLLEALRRYG-SPDEAFAGYAA 80

Query: 107 WWIKAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
             ++ A+ + + R  W           + +     R +   +A+     +      ++  
Sbjct: 81  LRVRGAILDELRRHDWRP---------RAVRNAAHRARDCERALCRTLGRVPTAGEVSAS 131

Query: 166 LNVSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           L +   E     M  R     S + +++          DWL +D + + QV++       
Sbjct: 132 LGIGIDEYRENVMANRAEAMASFDEMLD---------ADWLAHDDNPERQVVL------- 175

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            R  L ++++ L+ RE+R+ +     E  ++L  +++  E++  RV QI   A +K++ +
Sbjct: 176 -RRCLEQALTSLDEREQRVIQLYY--EFDLSLREIAAVLELTEARVCQINKAALRKMRAA 232

Query: 284 I 284
           +
Sbjct: 233 L 233


>gi|87303692|ref|ZP_01086467.1| group3 RNA polymerase sigma factor [Synechococcus sp. WH 5701]
 gi|87281797|gb|EAQ73762.1| group3 RNA polymerase sigma factor [Synechococcus sp. WH 5701]
          Length = 267

 Score = 87.2 bits (215), Expect = 3e-15,   Method: Composition-based stats.
 Identities = 50/272 (18%), Positives = 104/272 (38%), Gaps = 32/272 (11%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVKKFD 94
            L++R R+  D  A       HL LV  IA  Y         ++   G +GL++A + F 
Sbjct: 15  ALSRRLRQRNDRVAR------HLELVRPIAHHYSSLCREGRDDLTQVGLLGLLRAAELFQ 68

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
            ++G     ++   I+ A+  Y+     ++++     Q+ L   LRRL+           
Sbjct: 69  SDQGTPFEAFARHHIRGAILHYLRDQAPVIRLPRR--QRELEDRLRRLQQSQAGAAAEGC 126

Query: 155 KPEQVVA---IAKKLNVSESEVI--SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
             ++ +A   + + L +SE++        +L    SL+           + +D       
Sbjct: 127 HRQEALANSSLHQLLGLSEAQWQRFEQLRQLGRLVSLDGEEEKLAAAEPEPEDGPGGCEA 186

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
           G                 +   ++ L  R+R + +   L     +L   + + +VS   V
Sbjct: 187 G---------------ERIMALLAQLEHRQRTVVKEVVLAGQ--SLRGTARKMQVSPMTV 229

Query: 270 RQIEARAFKKVQESIQKQ-VELSSSPPLLQKP 300
            ++ ARA   +++ ++ + +  S +P     P
Sbjct: 230 HRLLARALDTLRQRLEGEGLGFSPAPGPHHGP 261


>gi|307699957|ref|ZP_07637008.1| RNA polymerase sigma factor, FliA/WhiG family [Mobiluncus mulieris
           FB024-16]
 gi|307614995|gb|EFN94213.1| RNA polymerase sigma factor, FliA/WhiG family [Mobiluncus mulieris
           FB024-16]
          Length = 455

 Score = 86.8 bits (214), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 47/256 (18%), Positives = 99/256 (38%), Gaps = 22/256 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L+  +L LV                  ++ S G++ L+QA K ++PE G     Y++
Sbjct: 10  RDALIEKNLPLVGYQVAELLRRVPSFVQREDLASAGSLALVQAAKSYNPETGVPFHRYAV 69

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           + I+ AM + + R+      G+ +  K       +L+    A+T    +      +A  L
Sbjct: 70  FRIRGAMLDEL-RAMDWATRGSRSRTK-------QLEEMTAALTAAAGRAPTREELAVAL 121

Query: 167 NVSESEVISMNCRLAGD-ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
            +   +V +     +    S++   +  D  S +    +V D    E  ++  E      
Sbjct: 122 GIEVGQVEAAQLDASRRMVSIDVSYSEDDPRSIE----IVDDGLNPEDTVLTDERLV--- 174

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             L  ++  L  R R + E    +E  V    +++   V++ RV Q+   A   +++ + 
Sbjct: 175 -YLKAAVKALPSRLRYVVEQVFFEEKSVN--EVAASLGVTQSRVSQLRTEALSMIRDGMV 231

Query: 286 KQVELSSSPPLLQKPR 301
             +E   +     +P+
Sbjct: 232 HHLEPDDAAEAPHEPQ 247


>gi|282856209|ref|ZP_06265492.1| RNA polymerase, sigma 28 subunit [Pyramidobacter piscolens W5455]
 gi|282585968|gb|EFB91253.1| RNA polymerase, sigma 28 subunit [Pyramidobacter piscolens W5455]
          Length = 196

 Score = 86.8 bits (214), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 37/156 (23%), Positives = 64/156 (41%), Gaps = 3/156 (1%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           ++E  L       GD  A  +L+ ++  LV  +A  +R  G   S++V EG + L++AV 
Sbjct: 10  EKEKKLWLAMS-SGDEEAREQLILAYRPLVYWVAKKFRVNGQRFSDLVQEGTLALIRAVD 68

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA--NQKRLFFNLRRLKGHLQAI 149
           KFD   G R  TY+ + I+  M  ++ R      I               R ++  +   
Sbjct: 69  KFDVSLGHRFTTYACYRIRGQMLNFLQRVEGKAPIPVDVECEDGDETAEFREVEEIIMLR 128

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
                 PE+   I ++L V       +   ++ D S
Sbjct: 129 EGLLQLPEREAHILRELVVECRNARELAEEMSLDVS 164


>gi|255039934|gb|ACT99724.1| putative sporulation sigma factor [Bacillus phage Wip4]
          Length = 248

 Score = 86.8 bits (214), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 46/234 (19%), Positives = 93/234 (39%), Gaps = 30/234 (12%)

Query: 51  HRLVTSHLRLVVKIA-MGYRG--------YGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
              +  + RLV       Y            L I ++   G IGL++A   F+PE G   
Sbjct: 20  DEFMEKYERLVHHCVWKRYAKKRPAIEHDTNLDIEDLTQFGMIGLIKARDNFNPEFGCAF 79

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY++  I   +   I  +   VK+     Q+ ++    ++    Q ++D          
Sbjct: 80  STYAVPKIIGEIGRAIRDNQK-VKV-----QRSVYSVKGKILN--QQLSDKGP-----EE 126

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           IA  LN   + V          +SLN ++ +S  N     + ++ D       + + EE 
Sbjct: 127 IADILNEPVTLVKMALKYQPSTDSLNKVVYASGSNEDVTLEKMLEDTK-----VEDIEET 181

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
              R ++    + L P+E  + +        +T +N++++   S+ ++ +I A+
Sbjct: 182 TINRAVIREFKAALAPKEYIVLDMHL---QNMTQQNIANQMGYSQVQISRILAK 232


>gi|224771357|dbj|BAH28620.1| sporulation sigma factor SigK [Clostridium perfringens]
          Length = 196

 Score = 86.8 bits (214), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 47/177 (26%), Positives = 78/177 (44%), Gaps = 15/177 (8%)

Query: 14  IGLSRYIHEIRKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           I L+ Y+      P  L ++EE +  +R ++ GD+ A   LV  +LRLV  I   Y    
Sbjct: 2   IFLTGYVTGNSTFPKPLNEKEEKIYLERLKD-GDVEAKRVLVERNLRLVAHIVKKYSSNY 60

Query: 73  L---PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL------ 123
                + +++S G IGL++A+  FD  +G RLATY+   I   +  +   S         
Sbjct: 61  QNSKEMDDLISIGTIGLIKAIDSFDTSKGIRLATYAAKCIDNEILMFFRNSKKTKGEVFL 120

Query: 124 ---VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP-EQVVAIAKKLNVSESEVISM 176
              + +    N+  L   L      +    +N+L+  E    I+  L+  E E+I M
Sbjct: 121 QDPIGVDKEGNEICLIDILSSDSDSVLETVENSLQVKELYKKISDVLSTREKEIIQM 177


>gi|296282290|ref|ZP_06860288.1| sigma 28 (flagella/sporulation) [Citromicrobium bathyomarinum
           JL354]
          Length = 240

 Score = 86.8 bits (214), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 49/239 (20%), Positives = 99/239 (41%), Gaps = 23/239 (9%)

Query: 54  VTSHLRLVVKIAMGYRGYG---LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           VT  L LV K+A  Y G+G   + + +++  G + L +A ++ D       A Y+   ++
Sbjct: 22  VTQFLPLVRKLAWYYEGHGSATVDVDDLMQVGMMALTEAAQRHDRPSDDGFAAYAKMRVR 81

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            AM + +           +A         R+     Q +     +      +A+ + +  
Sbjct: 82  GAMVDLLRGQS---HRPRSAAAWT-----RKRDVAEQTLRTELGRAPNAAEMAQAMEMPL 133

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
               SM  RLA   S  ++      + + + D    +    E  L+  E+      +L +
Sbjct: 134 DRYESM--RLAASTSATSIDECYSDSDTAFSD----NRPDPEANLLASEDS----GVLAQ 183

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           ++  L  R + + +   ++E  + L  +++   VS  RV Q++A A KK + ++  QVE
Sbjct: 184 AIGALPERLQLVLKLYFIEE--LNLNEIAAVLGVSVPRVHQLKADALKKARVAMVSQVE 240


>gi|296135638|ref|YP_003642880.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thiomonas
           intermedia K12]
 gi|295795760|gb|ADG30550.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thiomonas
           intermedia K12]
          Length = 250

 Score = 86.4 bits (213), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 43/257 (16%), Positives = 92/257 (35%), Gaps = 18/257 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
                  ++ HL +V +IA          +  S++   G IGL  A+ + + +   + AT
Sbjct: 9   PETREERLSKHLPMVRRIAGQMAAQLPASVDFSDLEQAGMIGLWDALDRGEMQSPAQFAT 68

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   I+ A+ + + +   L +              R+++   Q +T    +  +   +A
Sbjct: 69  YAAIRIRGAIYDELRKLDWLPRRSR--------AKERQIERAEQLLTQRLGRHPEDGELA 120

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
             L    +E        +       L+   D       D+     D    +  E  +   
Sbjct: 121 AHLGWELAEYYDALAETSM-----QLVYLEDLTHDDGGDYADRKADEASLLPEELLQDAQ 175

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               L  +++ L  RE+ +       +  + L+++    EVS  RV Q+  +A  +++  
Sbjct: 176 LERDLQAAIADLPEREKLVLSLYY--QEDLQLKDIGRVLEVSESRVSQLMKQAVMRLRAR 233

Query: 284 IQKQVELSSSPPLLQKP 300
           +Q     +S       P
Sbjct: 234 LQAHQHSASGAGRRAAP 250


>gi|310764851|gb|ADP09801.1| RNA polymerase sigma factor for flagellar operon [Erwinia sp.
           Ejp617]
          Length = 243

 Score = 86.4 bits (213), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 43/213 (20%), Positives = 93/213 (43%), Gaps = 18/213 (8%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQ 132
            + +++  G++G + A+  FDP +G  L+ +    I+ A+ + +  R W   ++   A  
Sbjct: 40  ELDDLIQAGSLGFLSAIDHFDPTKGVTLSAFLAQRIRWALMDELRERDWVPRRVRKHA-- 97

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
                  R +   +Q +  N         IA ++ VS  E+  M   LA   S  + I S
Sbjct: 98  -------REVTAVIQQLEQNKGGEASEADIATEMGVSVGELQQM---LADTNS--SQIYS 145

Query: 193 SDKNSSQWQDWLVY-DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
            D+   Q+ D     D + +    + +  ++N    +   +SV+  RE+ I +    Q+ 
Sbjct: 146 LDELQEQFADSYETIDEENEALNPVHQAVQENLVGKIAEHISVIPEREQVILQLYYQQD- 204

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + +  + +   ++  RV Q+ + A K+++  +
Sbjct: 205 -LNMREIGAVLSLTETRVSQLHSLAIKRIRARM 236


>gi|294339807|emb|CAZ88170.1| RNA polymerase sigma factor for flagellar operon (Sigma-F factor)
           (Sigma-27) (Sigma-28) [Thiomonas sp. 3As]
          Length = 250

 Score = 86.4 bits (213), Expect = 4e-15,   Method: Composition-based stats.
 Identities = 43/257 (16%), Positives = 92/257 (35%), Gaps = 18/257 (7%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
                  ++ HL +V +IA          +  S++   G IGL  A+ + + +   + AT
Sbjct: 9   PETREERLSKHLPMVRRIAGQMAAQLPASVDFSDLEQAGMIGLWDALDRGEMQSPAQFAT 68

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   I+ A+ + + +   L +              R+++   Q +T    +  +   +A
Sbjct: 69  YAAIRIRGAIYDELRKLDWLPRRSR--------AKERQIERAEQLLTQRLGRHPEDGELA 120

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
             L    +E        +       L+   D       D+     D    +  E  +   
Sbjct: 121 AHLGWELAEYYDALAETSM-----QLVYLEDLTHDDGGDYADRKADEASLLPEELLQDAQ 175

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               L  +++ L  RE+ +       +  + L+++    EVS  RV Q+  +A  +++  
Sbjct: 176 LERDLQAAIADLPEREKLVLSLYY--QEDLQLKDIGRVLEVSESRVSQLMKQAVMRLRAR 233

Query: 284 IQKQVELSSSPPLLQKP 300
           +Q     +S       P
Sbjct: 234 LQAHQHSASGAGRRTAP 250


>gi|306817679|ref|ZP_07451421.1| DNA-directed RNA polymerase sigma subunit FliA [Mobiluncus mulieris
           ATCC 35239]
 gi|304649493|gb|EFM46776.1| DNA-directed RNA polymerase sigma subunit FliA [Mobiluncus mulieris
           ATCC 35239]
          Length = 455

 Score = 86.4 bits (213), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 47/256 (18%), Positives = 99/256 (38%), Gaps = 22/256 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L+  +L LV                  ++ S G++ L+QA K ++PE G     Y++
Sbjct: 10  RDALIEKNLPLVGYQVAELLRRVPSFVQREDLASAGSLALVQAAKSYNPETGVPFHRYAV 69

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           + I+ AM + + R+      G+ +  K       +L+    A+T    +      +A  L
Sbjct: 70  FRIRGAMLDEL-RAMDWATRGSRSRTK-------QLEEMTAALTAAAGRAPTREELAVAL 121

Query: 167 NVSESEVISMNCRLAGD-ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
            +   +V +     +    S++   +  D  S +    +V D    E  ++  E      
Sbjct: 122 GIEVGQVEAAQLDASRRMVSIDVSYSEDDPRSIE----IVDDGLNPEDTVLTDERLV--- 174

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             L  ++  L  R R + E    +E  V    +++   V++ RV Q+   A   +++ + 
Sbjct: 175 -YLKAAVRALPQRLRYVVEQVFFEEKSVN--EVAASLGVTQSRVSQLRTEALSMIRDGMV 231

Query: 286 KQVELSSSPPLLQKPR 301
             +E   +     +P+
Sbjct: 232 HHLEPDDAAEAPHEPQ 247


>gi|289754805|ref|ZP_06514183.1| predicted protein [Mycobacterium tuberculosis EAS054]
 gi|289695392|gb|EFD62821.1| predicted protein [Mycobacterium tuberculosis EAS054]
          Length = 473

 Score = 86.4 bits (213), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 32/136 (23%), Positives = 59/136 (43%), Gaps = 32/136 (23%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------REHGDL- 47
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+  
Sbjct: 217 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSERGEKL 275

Query: 48  ----------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE-GNIGLMQAV 90
                            A + L+ ++LRLVV +A  Y G G+   +++     +GL++AV
Sbjct: 276 PAAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIPGKATLGLIRAV 335

Query: 91  KKFDPERGFRLATYSM 106
           +KF   +G ++     
Sbjct: 336 EKFRLHQGVQVLHLRY 351


>gi|84514822|ref|ZP_01002185.1| sigma factor FliA (Sigma-28 group, flagellar) [Loktanella
           vestfoldensis SKA53]
 gi|84510981|gb|EAQ07435.1| sigma factor FliA (Sigma-28 group, flagellar) [Loktanella
           vestfoldensis SKA53]
          Length = 239

 Score = 86.4 bits (213), Expect = 5e-15,   Method: Composition-based stats.
 Identities = 42/242 (17%), Positives = 106/242 (43%), Gaps = 22/242 (9%)

Query: 51  HRLVTSHLRLVVKI---AMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            +LV  H  LV ++           +   +++  G IGL++A +++    G     Y++ 
Sbjct: 12  EKLVREHEALVRRVSHHIHSRVRSIVEFDDLLQVGLIGLIEAAQRYTRREGVSFENYAVL 71

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            ++ A+ +Y+ ++ +L +        +     + +K     ++    +    V +A+ ++
Sbjct: 72  RVRGAIYDYLRKNSNLGR--------KTIATTKVVKFAQAELSQKLGRAPTRVELAEAVS 123

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++  E+ +         SLN+   +S ++     D        +E    +  +R   ++ 
Sbjct: 124 MTIGELNAWEQ------SLNSSYQNSLQDE---YDEYSMWFSAEEPPAEQLLDRGRLKDA 174

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L  ++  L  RE  + +   ++E  + +  +++  EV+  RV Q+++ AFKK+Q  ++  
Sbjct: 175 LLIALKSLPQREALVLQLYYVEE--LNIYEIAAILEVTPGRVSQLKSMAFKKMQPLLRDF 232

Query: 288 VE 289
            E
Sbjct: 233 AE 234


>gi|224553544|gb|ACN55010.1| RNA polymerase sigma factor [Escherichia coli]
          Length = 111

 Score = 86.0 bits (212), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 33/116 (28%), Positives = 59/116 (50%), Gaps = 5/116 (4%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           GL + +++ EGN+GL++AV+KFDPERGFR +T + WWI+  ++  I+     +++     
Sbjct: 1   GLALLDLIEEGNLGLIRAVEKFDPERGFRFSTSATWWIRQTIERAIMNQTRTIRLPIHIV 60

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
            K L   LR  +     ++           IA++L+    +V  M        S++
Sbjct: 61  -KELNVYLRTAR----ELSHKLDHEPSAEEIAEQLDKPVDDVSRMLRLNERITSVD 111


>gi|58699689|ref|ZP_00374359.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of
           Drosophila ananassae]
 gi|58533795|gb|EAL58124.1| RNA polymerase sigma factor RpoD [Wolbachia endosymbiont of
           Drosophila ananassae]
          Length = 256

 Score = 86.0 bits (212), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 32/74 (43%), Positives = 47/74 (63%), Gaps = 2/74 (2%)

Query: 32  QEEYVLAKRYREHGDL--SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           QE   L KR ++H      A   ++ ++LRLVV IA  Y   GL + +++ EGNIGLM+A
Sbjct: 118 QEFKELIKRIQKHEREVSEAKQEMIKANLRLVVSIAKKYSKRGLDLLDLIQEGNIGLMKA 177

Query: 90  VKKFDPERGFRLAT 103
           V KFD +RG++ +T
Sbjct: 178 VDKFDYKRGYKFST 191


>gi|254437394|ref|ZP_05050888.1| RNA polymerase sigma factor, sigma-70 family [Octadecabacter
           antarcticus 307]
 gi|198252840|gb|EDY77154.1| RNA polymerase sigma factor, sigma-70 family [Octadecabacter
           antarcticus 307]
          Length = 207

 Score = 86.0 bits (212), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 40/216 (18%), Positives = 96/216 (44%), Gaps = 19/216 (8%)

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
               + I +++  G IGL++A +++  + G    +Y++  I+ A+ +Y+ ++ +L +   
Sbjct: 1   MRSIVEIEDLLQVGLIGLIEAAQRYTRQEGVSFESYAVLRIRGAIYDYLRKNTNLGR--- 57

Query: 129 TANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNA 188
                +     + +K  L +++    +      +A+ L++S  E+      +  + S + 
Sbjct: 58  -----KAILTSKAVKAALASLSQKLGREPTQPELAEALSMSLQELSKWAQNV--NSSYHN 110

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +       S W           E       +R   ++ L  ++  L  RE  + +   +
Sbjct: 111 SLQDEYDEHSLWF-------SSNEPTTEHLVDRGRLKDALLAALVSLPKREALVLQLYYV 163

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +E  + L  +++  EV+  RV Q+++ AFKK+Q S+
Sbjct: 164 EE--LNLYEIAAVLEVTPGRVSQLKSAAFKKMQPSL 197


>gi|229073720|ref|ZP_04206833.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus cereus
           F65185]
 gi|228709429|gb|EEL61490.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus cereus
           F65185]
          Length = 236

 Score = 85.6 bits (211), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 45/238 (18%), Positives = 94/238 (39%), Gaps = 29/238 (12%)

Query: 51  HRLVTSHLRLVVKIAM-GY--------RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
                 + +LV K     Y           GL I +++  G IGL++A K FDP  G++ 
Sbjct: 7   DAFFKKYKKLVYKFVWEKYGSNLESIKSNTGLEIEDLIQCGMIGLLKARKDFDPAYGYKF 66

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +T ++  +       I+ +           + ++   +  LKG    I    L  E+   
Sbjct: 67  STLAIPKMHGETTRAIINN----------QKVKVTREIFYLKGR---IIREKLAEEKPEV 113

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           I++ L V+  +V           SL+ +  SS    +     L  +    ++    K E 
Sbjct: 114 ISQLLGVTVEDVEEALRYQQIPSSLHDVTFSSGSGDT----DLTLEQMLVDESSTRKTEE 169

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
            + + ++   ++ L  RE  I++      N ++ E++     V++ ++ +I  R  ++
Sbjct: 170 IDEKIVMRSFINTLPDRELMIWDMY---SNHMSQESIGERVGVTQTQISRILKRINRR 224


>gi|114566052|ref|YP_753206.1| sigma 28 (flagella/sporulation) [Syntrophomonas wolfei subsp.
           wolfei str. Goettingen]
 gi|114336987|gb|ABI67835.1| sigma 28 (flagella/sporulation) [Syntrophomonas wolfei subsp.
           wolfei str. Goettingen]
          Length = 126

 Score = 85.6 bits (211), Expect = 7e-15,   Method: Composition-based stats.
 Identities = 29/105 (27%), Positives = 54/105 (51%), Gaps = 1/105 (0%)

Query: 9   IVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
           I+ G + L  Y++       L +++E    +  +  G   A + L+  +LRLV  +   Y
Sbjct: 13  ILKGSLCLFAYLNNQVFPQPLSEEDERKCLQEMQ-RGGEEARNILIEHNLRLVAHVVKKY 71

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
              G  + +++S G IG ++A++ ++ ERG RLATY+   I   +
Sbjct: 72  ESSGEDLEDLISIGTIGPIKAIRTYNFERGVRLATYAARCIDNEV 116


>gi|188997549|ref|YP_001931800.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Sulfurihydrogenibium sp. YO3AOP1]
 gi|188932616|gb|ACD67246.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Sulfurihydrogenibium sp. YO3AOP1]
          Length = 213

 Score = 85.6 bits (211), Expect = 8e-15,   Method: Composition-based stats.
 Identities = 44/247 (17%), Positives = 99/247 (40%), Gaps = 43/247 (17%)

Query: 47  LSAAHRLVTSHLRLVVKIAMG--YR--GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
                ++V  ++ LV K+A    YR     +   ++V  G +GL++A++ ++ ++G + +
Sbjct: 5   KEQKKQIVEEYIGLVKKVASKIFYRLPDCEIEFDDLVQTGIVGLLKALENYNEDKG-KFS 63

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+   I+  + +++ +   +     T   K       +L   L                
Sbjct: 64  TYAYIRIRGEILDFLRQQDIM---PKTEKDKITIEYADKLGDEL---------------- 104

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
                      IS N  +    SL+ +I S D     + D         E+   +KE  +
Sbjct: 105 ----------PISKNAIM---LSLDKII-SEDGEEFSFIDLFASKSKTPEEEYAQKELLE 150

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
                + +    L+  E++I +    +E     + +S    +S  R+ Q+++RA +K+++
Sbjct: 151 KISEAIDK---YLDDIEKKIIQYLYFEEKDP--KEISEIMNISLGRISQLKSRAVEKLKK 205

Query: 283 SIQKQVE 289
            +   +E
Sbjct: 206 ILYDNIE 212


>gi|312898376|ref|ZP_07757766.1| sigma-70 region 2 [Megasphaera micronuciformis F0359]
 gi|310620295|gb|EFQ03865.1| sigma-70 region 2 [Megasphaera micronuciformis F0359]
          Length = 205

 Score = 85.6 bits (211), Expect = 8e-15,   Method: Composition-based stats.
 Identities = 38/159 (23%), Positives = 77/159 (48%), Gaps = 3/159 (1%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           + E++KI +L+  EE  L   Y++ G + +  RL+  +  LV + A+ +      +++V+
Sbjct: 1   MEELQKITLLKPDEEKRLWMAYKDEGCMDSRGRLIEQYQPLVFREALRWHVGEEHMADVL 60

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT---TANQKRLF 136
            EGN+GL++AV+++D + G   + Y++  I+  + +++ +      +       N   L 
Sbjct: 61  QEGNLGLIEAVERYDYKLGVAFSIYAVHRIRGEIVDWLKKEGKSANVSMDEPDENGLTLG 120

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
             L      L   T+  L  EQV A   +L   E  ++ 
Sbjct: 121 DMLSDNSEDLGDRTNRQLLLEQVGAFMARLPEKEQFIME 159



 Score = 35.9 bits (82), Expect = 7.5,   Method: Composition-based stats.
 Identities = 21/98 (21%), Positives = 46/98 (46%), Gaps = 8/98 (8%)

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           S N  ++  D+N     D L        + L ++  R+     +   M+ L  +E+ I E
Sbjct: 104 SANVSMDEPDENGLTLGDMLSD----NSEDLGDRTNRQLLLEQVGAFMARLPEKEQFIME 159

Query: 245 ARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           A  L++  P T   ++++ +VS   V +++ R  ++++
Sbjct: 160 AVYLKDRQPKT---VAADLDVSLPYVYRLQKRGVRRIR 194


>gi|320101986|ref|YP_004177577.1| RNA polymerase sigma-32 subunit RpoH [Isosphaera pallida ATCC
           43644]
 gi|319749268|gb|ADV61028.1| RNA polymerase, sigma 32 subunit, RpoH [Isosphaera pallida ATCC
           43644]
          Length = 565

 Score = 85.2 bits (210), Expect = 9e-15,   Method: Composition-based stats.
 Identities = 45/190 (23%), Positives = 82/190 (43%), Gaps = 31/190 (16%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRY------------------REHGDLS-------- 48
           GL  Y+  + ++P+L +++E  L ++                      GDL         
Sbjct: 325 GLPPYLASLYEVPLLSREQETHLFRKMNFLKYLAQKLRDQVDPARARAGDLDQIEALQEE 384

Query: 49  ---AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
                +++++++LRLVV IA  + G      ++VS+GN+ L++AV+KFD  RG + +TY+
Sbjct: 385 ALAVKNQIISANLRLVVSIAKRHVGPSNNFFDLVSDGNMSLIRAVEKFDFARGNKFSTYA 444

Query: 106 MWWIKAAMQEYI-LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
            W I       I   ++   +  T   +        R   H Q      ++ E V  +  
Sbjct: 445 SWAIMKNFARTIPEENYRRDRFVTGHEEMFEAAADNRSDEHEQESNQRRMR-EGVNGMLS 503

Query: 165 KLNVSESEVI 174
           KL   E ++I
Sbjct: 504 KLEPREQKII 513



 Score = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 27/96 (28%), Positives = 51/96 (53%), Gaps = 2/96 (2%)

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-- 251
           D+  +  ++      D +     ++  ++  R  +   +S L PRE++I  +R       
Sbjct: 464 DRFVTGHEEMFEAAADNRSDEHEQESNQRRMREGVNGMLSKLEPREQKIIVSRFGINGAK 523

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +TLE L  E  +++ERVRQIEARA +K+++  Q++
Sbjct: 524 EMTLEQLGKELGITKERVRQIEARAQQKLRKIAQEE 559


>gi|110626973|gb|ABG79025.1| RpoH [Wolbachia endosymbiont of Armadillidium vulgare]
 gi|110626982|gb|ABG79031.1| RpoH [Wolbachia endosymbiont of Armadillidium nasatum]
 gi|110626985|gb|ABG79033.1| RpoH [Wolbachia endosymbiont of Armadillidium album]
          Length = 78

 Score = 85.2 bits (210), Expect = 9e-15,   Method: Composition-based stats.
 Identities = 37/72 (51%), Positives = 54/72 (75%)

Query: 7  SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
          ++ VN    L +YI E+RK PML ++EE  LAK ++EH D+S+AH+L+TSHL LVVKIAM
Sbjct: 7  NLYVNSSTNLMQYIAEVRKFPMLSQEEEVRLAKNWQEHKDISSAHKLITSHLNLVVKIAM 66

Query: 67 GYRGYGLPISEV 78
           ++ YGL + ++
Sbjct: 67 KFKNYGLLLMDL 78


>gi|159163074|pdb|1TTY|A Chain A, Solution Structure Of Sigma A Region 4 From Thermotoga
           Maritima
          Length = 87

 Score = 85.2 bits (210), Expect = 9e-15,   Method: Composition-based stats.
 Identities = 24/72 (33%), Positives = 38/72 (52%), Gaps = 2/72 (2%)

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEAR 275
           +  R   R  L + +  L+PRE  +   R   L   P TLE +   F V+RER+RQIE +
Sbjct: 2   EAMRMLMREELEKVLKTLSPREAMVLRMRYGLLDGKPKTLEEVGQYFNVTRERIRQIEVK 61

Query: 276 AFKKVQESIQKQ 287
           A +K++   + +
Sbjct: 62  ALRKLRHPSRSK 73


>gi|256831228|ref|YP_003159956.1| RNA polymerase sigma-28 subunit FliA/WhiG [Desulfomicrobium
           baculatum DSM 4028]
 gi|256580404|gb|ACU91540.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfomicrobium
           baculatum DSM 4028]
          Length = 267

 Score = 85.2 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 35/216 (16%), Positives = 83/216 (38%), Gaps = 18/216 (8%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
            + +S+++S G +GLM+A+ KF PE   R  T++   I+ AM + + R            
Sbjct: 65  HIELSDLISAGTLGLMEALGKFQPELNIRFETFADSRIRGAMLDELRR--------MDWY 116

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
            + L   +++L+  ++     N        + +       E+ +    +     L+    
Sbjct: 117 SRGLRQRIKKLEQVIRGFEQENGHAPTRSELLELTGQDRQELEATLEAVNSQIILSLDAI 176

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
               N             G  +         +  + L   +  LN RE+ +      +E 
Sbjct: 177 QDQWNQP--------GDGGNHREPFAAVAFHDIIDKLGHLIDRLNEREKLVLSLYYTEEF 228

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +  + ++   +++  RV Q+ ++A  K+++   ++
Sbjct: 229 NM--KEVALALDITEGRVSQLHSQALGKLKKMFVRE 262


>gi|121488755|emb|CAJ18262.1| sigma 70-type sigma factor [Chlorobium phaeobacteroides]
          Length = 165

 Score = 85.2 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 33/174 (18%), Positives = 65/174 (37%), Gaps = 17/174 (9%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           +  +EG  G ++A K+ D  RGF+  +Y++WW + +  + +     +V++          
Sbjct: 1   DXXNEGXXGXIKAAKRXDETRGFKFISYAVWWXRQSXLQALAEQSRIVRLPLNR-----V 55

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
             L ++      +     +      +A  L++   +V           S++A     D N
Sbjct: 56  GTLNKISKAYXQLEQEFERDPNTRELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDN 115

Query: 197 ---SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
                   D  + DH   +  L  + ER          +SVL PRE  +  +  
Sbjct: 116 RLLDVLQNDGHLPDHGLNKDSLTLEVERS---------LSVLXPREADVIRSYF 160


>gi|283780334|ref|YP_003371089.1| RNA polymerase, sigma 32 subunit, RpoH [Pirellula staleyi DSM 6068]
 gi|283438787|gb|ADB17229.1| RNA polymerase, sigma 32 subunit, RpoH [Pirellula staleyi DSM 6068]
          Length = 556

 Score = 85.2 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 27/93 (29%), Positives = 51/93 (54%), Gaps = 3/93 (3%)

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--- 250
           D+  +   +  V   D +   L  +  ++ R+  + + +  L+ RE++I  +R   +   
Sbjct: 453 DRFRTSQDELFVAKQDNRSDQLGLEHVQQQRQLQVEKILEKLDEREQKIIISRFGLDHSH 512

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            P+TL+ +  E  V++ERVRQIEARA  K++E+
Sbjct: 513 EPLTLKEVGHELGVTKERVRQIEARALNKLREA 545



 Score = 82.6 bits (203), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 48/205 (23%), Positives = 81/205 (39%), Gaps = 31/205 (15%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR--------------------------E 43
           V    GL  Y+  + ++P+L +++EY L +++                           E
Sbjct: 309 VRTPSGLPPYLAALYEVPLLMREQEYHLFRKFNYLKFKATALRDKLDPASARTSVMDEIE 368

Query: 44  HGDLSA---AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           H    A    + +V ++LRLVV IA  +         +VS+GN+ L++A +KFD  RG +
Sbjct: 369 HLYEEAVAVKNSIVQANLRLVVSIAKRHVNGSEDFFGLVSDGNMSLIRAAEKFDFSRGNK 428

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +TY+ W I       I   +       T+  +            L        +  QV 
Sbjct: 429 FSTYASWAIMKNFARTIPEEFKHRDRFRTSQDELFVAKQDNRSDQLGLEHVQQQRQLQVE 488

Query: 161 AIAKKLNVSESEVISMNCRLAGDES 185
            I +KL+  E ++I    R   D S
Sbjct: 489 KILEKLDEREQKII--ISRFGLDHS 511


>gi|148242553|ref|YP_001227710.1| putative group 3 RNA polymerase sigma factor [Synechococcus sp.
           RCC307]
 gi|147850863|emb|CAK28357.1| Putative group 3 RNA polymerase sigma factor [Synechococcus sp.
           RCC307]
          Length = 259

 Score = 85.2 bits (210), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 49/232 (21%), Positives = 88/232 (37%), Gaps = 21/232 (9%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVK 91
           E   L +RY +   L   +RLV +HL LV + A  + +       ++  +G  GL+ AV+
Sbjct: 10  ELLALHRRYGQSRCLKLRNRLVEAHLNLVRQQAARFSQASSACYDDLFQQGCFGLLDAVQ 69

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           ++ P+RG+  +TY++  I+  MQ Y+     L++      Q  L     +L+   Q    
Sbjct: 70  RYQPQRGYAFSTYAVTLIRGQMQHYLRDRHHLIRSPWRLRQ--LLSRWDQLQNQRQQA-- 125

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
             L P      A+ L      V  +   L    +LN  + S D                 
Sbjct: 126 -GLPPLDRRGQARSLGC---RVERLQMALQMRAALN--LRSFDAAPEGIAFETADQRPTP 179

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           E  L E E        L   +   +P ++       +    ++   L+ + +
Sbjct: 180 EARLAEAE--------LEEWIEAQSPDDQ--LLLCGVMHQGLSQRQLARQLD 221


>gi|14346036|gb|AAK59987.1| RNA polymerase major sigma subunit [Corynebacterium ammoniagenes]
          Length = 145

 Score = 84.9 bits (209), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 19/155 (12%), Positives = 58/155 (37%), Gaps = 12/155 (7%)

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +      +++     ++     L R+K  +          E    +A++  + E++
Sbjct: 1   ITRGMADQSRTIRLPVHLVEQ--VNKLSRIKREMYQSLGREATNE---ELAEESGIEENK 55

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           +  +  +     SL+  + + ++  +   D++        +  +    R    + +   +
Sbjct: 56  IEMLLRQSRDPVSLDMPVGADEE--APLGDFIEDAEATDAETAVVASMR---HSDIRDVI 110

Query: 233 SVLNPRERRIFEARRLQEN--PVTLENLSSEFEVS 265
             L  RE+ +   R   ++  P TL+ +  +F +S
Sbjct: 111 GTLEQREQDVIRLRYGLDDGVPRTLDQIGRKFGLS 145


>gi|294673099|ref|YP_003573715.1| RNA polymerase sigma-70 factor family protein [Prevotella
           ruminicola 23]
 gi|294472548|gb|ADE81937.1| RNA polymerase sigma-70 factor family protein [Prevotella
           ruminicola 23]
          Length = 240

 Score = 84.9 bits (209), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 33/120 (27%), Positives = 60/120 (50%), Gaps = 1/120 (0%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG 67
           ++ N   G + Y+ +I     L  +EE  L +R    GD +A ++L+ ++LR V+  A+ 
Sbjct: 4   LLENHAEGFNVYLEQIENNQPLTMEEEQELGRRIM-AGDTTARNKLIEANLRFVLTCAID 62

Query: 68  YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
                +PI E+++ GN GL  A  +++P       +Y++  I+ A+ E I      VK  
Sbjct: 63  MATPFVPIEELIAAGNYGLTIAAARYNPSFDNHFCSYAVHHIRRAISEAIRTWTCSVKTP 122


>gi|313837242|gb|EFS74956.1| sigma-70, region 4 [Propionibacterium acnes HL037PA2]
 gi|314927738|gb|EFS91569.1| sigma-70, region 4 [Propionibacterium acnes HL044PA1]
 gi|314972014|gb|EFT16112.1| sigma-70, region 4 [Propionibacterium acnes HL037PA3]
 gi|328907208|gb|EGG26974.1| sigma-70, region 4 [Propionibacterium sp. P08]
          Length = 270

 Score = 84.9 bits (209), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 49/255 (19%), Positives = 105/255 (41%), Gaps = 37/255 (14%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKK 92
           E  L ++  + G ++A   L    L +V+  A      Y   + +++  G +GL +A+++
Sbjct: 47  EAEL-RKISDDG-VAARQALWRQMLAIVLTQARQAAVTYRCSVEDLIQSGCVGLGEAIER 104

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           +D  RG R +T +  WI+  + E ++R          A  + +      +    + +T  
Sbjct: 105 YDERRGARFSTVAWTWIRRRIGEEVVRLSG-------ARSRSVMREAAEVARIEEELTAR 157

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
             +     AIA ++     +V+ +  R          +   +  +S ++   V      +
Sbjct: 158 WQRVPSSDAIAAQMG---KDVMWVEKRR---------VECWEIETSFFEQVAVVQKCCDD 205

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR-RLQENPVTLENLSSEFEVSRERVRQ 271
                           +  +S+L  +ERRI E R   +  P+T+  ++ E  +S    R+
Sbjct: 206 PE--------------SGLISLLMGQERRIVELRHGFEGEPMTITAVADELGLSASNARR 251

Query: 272 IEARAFKKVQESIQK 286
           IE RA  +++  +Q+
Sbjct: 252 IEHRALARLRRYLQE 266


>gi|115377816|ref|ZP_01465004.1| RNA polymerase sigma factor for flagellar operon [Stigmatella
           aurantiaca DW4/3-1]
 gi|310820297|ref|YP_003952655.1| RNA polymerase sigma-70 factor [Stigmatella aurantiaca DW4/3-1]
 gi|115365148|gb|EAU64195.1| RNA polymerase sigma factor for flagellar operon [Stigmatella
           aurantiaca DW4/3-1]
 gi|309393369|gb|ADO70828.1| RNA polymerase sigma-70 factor [Stigmatella aurantiaca DW4/3-1]
          Length = 260

 Score = 84.9 bits (209), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 49/242 (20%), Positives = 103/242 (42%), Gaps = 22/242 (9%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           +R +           L + E+VS G IGL++A  +FDP+ G    T++ + IK A+ + +
Sbjct: 1   MRSLAATVRKQFNAQLELDELVSYGQIGLLEAADRFDPKVGANFLTFAHYRIKGAIFDGL 60

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
            R   +++ G      R  F   R   +L  ++D             +    + +V  ++
Sbjct: 61  -RKMGILRGGD----ARSAFVGERAAAYLGNLSDRE------QGGGNRGGSFDDDVNDIS 109

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
             +AG   + A       ++    + L  D         ++ E +  +  +  ++  L  
Sbjct: 110 NAVAGLAMVFATSLEGADSAGYSDESLPAD---------QRLEMEQLKRRVRAAIERLPD 160

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLL 297
           +ER++ +    Q    TLE   SE   S+    ++ ARA ++++E + ++   +SS  L 
Sbjct: 161 KERQLLQGYYFQG--RTLEEAGSEIGQSKSWASRLHARAIERLKEFLDEEEAPASSDELR 218

Query: 298 QK 299
           ++
Sbjct: 219 RQ 220


>gi|330984057|gb|EGH82160.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. lachrymans
           str. M301315]
          Length = 227

 Score = 84.9 bits (209), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 49/235 (20%), Positives = 100/235 (42%), Gaps = 22/235 (9%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            H+L  ++L++  ++   Y    +   + + E  + L +A   +          Y+   +
Sbjct: 7   QHQLWQANLQVAARLVNDYCYNPVLSQDALQEAQLALWEATFNWQESMEGTFTHYAWMHM 66

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           +  +  Y+ ++ S          +R    L  LK HL+A     +  + + A++++  ++
Sbjct: 67  RRKLLTYLTQTAS----DQPKLSRRERQVLNELKKHLRA--GELISCQLLEALSEETGIT 120

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
                           L+ L++   +NS           +  E +  E E   +    L 
Sbjct: 121 RFR-------------LSQLVSYWYQNSITISACSFQAFEELEAIEPEPETDIST---LE 164

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             ++ L  RE+ I  AR LQ+   TL +L+++F VS ERVRQ+E+ A KK++  +
Sbjct: 165 EGIANLPEREKLIVLARHLQDPRATLADLATKFGVSIERVRQLESSAIKKLRNHL 219


>gi|325679376|ref|ZP_08158961.1| putative RNA polymerase sigma-G factor [Ruminococcus albus 8]
 gi|324108973|gb|EGC03204.1| putative RNA polymerase sigma-G factor [Ruminococcus albus 8]
          Length = 162

 Score = 84.9 bits (209), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 26/179 (14%), Positives = 70/179 (39%), Gaps = 17/179 (9%)

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
           M  I   ++ Y +R +  +++  +   + L +   + K    A          +  IA+ 
Sbjct: 1   MPMILGEIKRY-MRDFRPIRVSRSM--RDLAYKAMQAKESFIAKHQRE---PSIDEIAEL 54

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
                +++++    +    S+   + +   ++    D +   +D  ++  +E+       
Sbjct: 55  TGEKRADIVTALESITDPVSIYEPVYTEGGDALYIVDQICDSND--DKSWLEELN----- 107

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             L  ++  L  RE+ I   R  +    T   ++ E  +S+ +V ++E  A  K++  +
Sbjct: 108 --LKEALKTLKDREKNILFLRFYKG--HTQMEVAKEIGISQAQVSRLEKNALDKIKSQL 162


>gi|258516390|ref|YP_003192612.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum acetoxidans DSM 771]
 gi|257780095|gb|ACV63989.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum acetoxidans DSM 771]
          Length = 239

 Score = 84.9 bits (209), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 48/246 (19%), Positives = 99/246 (40%), Gaps = 30/246 (12%)

Query: 35  YVLAKRYREH---GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
             L + ++E+    D     +++ S  RLV   A  Y   G    +++  G  GL++A+ 
Sbjct: 13  VDLNQAFQEYLVVKDEERLRQVMMSGSRLVRHFAKLY-ASGRQTEDLMQSGYEGLLKALG 71

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           +FD  RG   +TY+   I   ++ +I +  S       A    +     R+   +     
Sbjct: 72  RFDSSRGVLFSTYAAHCIMGEIRHHIRKEAS------YACPAAVAELQARINRFVDDYMK 125

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
            N +   +  IA+ +NV E  V+      AG  SL+  I      S +++ + +   D  
Sbjct: 126 ENGQIPSLSQIAEFVNVCEEGVVQAMR--AGFVSLDE-IELHKIQSLKYESFCLPIED-- 180

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
                        R +L +++  L   ++R+      ++  +T    +S+  +S+  V +
Sbjct: 181 -------------RIVLEQALYKLTELQQRVIHLLFYKD--MTQTEAASQLGISQRSVSR 225

Query: 272 IEARAF 277
           I  ++ 
Sbjct: 226 ILRKSL 231


>gi|324328848|gb|ADY24108.1| FliA/WhiG family RNA polymerase sigma factor [Bacillus
           thuringiensis serovar finitimus YBT-020]
          Length = 248

 Score = 84.9 bits (209), Expect = 1e-14,   Method: Composition-based stats.
 Identities = 49/233 (21%), Positives = 92/233 (39%), Gaps = 30/233 (12%)

Query: 52  RLVTSHLRLVVKIA-MGYRG--------YGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
             +  + RLV       Y           GL I ++   G IGL++A   F+ E G + +
Sbjct: 21  EFMKKYERLVHHCVWKRYAKKMKSIEHDTGLDIEDLTQFGMIGLIKARDNFNLEYGCKFS 80

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I   +   I              + ++  N+  +KG    I   NL+ E    I
Sbjct: 81  TYAVPKILGEIGRAIRDH----------QKVKVQRNVYSIKG---KILRQNLEDETPEEI 127

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A  L    S V +      G +SLN +++ S+ N     + ++ D   +       E+  
Sbjct: 128 ASILQEDVSVVSNALHYQPGAQSLNKVVHQSNGNEELTLESMLEDKKAE-----NVEDVS 182

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
             R ++    S L+ +E  + +         T +N+++E   S+ +V +I  +
Sbjct: 183 INRMVIQAFKSQLSHKEHIVLDM---SLQNRTQQNIANEIGCSQVQVSRILTK 232


>gi|153955577|ref|YP_001396342.1| RNA polymerase sigma factor-related protein [Clostridium kluyveri
           DSM 555]
 gi|146348435|gb|EDK34971.1| RNA polymerase sigma factor-related protein [Clostridium kluyveri
           DSM 555]
          Length = 235

 Score = 84.9 bits (209), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 48/261 (18%), Positives = 88/261 (33%), Gaps = 71/261 (27%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGL 86
             +E   L     + G+  A  +L+  +  +V K A  +   +   +   ++  EG +GL
Sbjct: 2   SNEELVQL----YQAGNKGALDKLIELNKGIVYKFANRFYTEKTNSIDKEDLKQEGFMGL 57

Query: 87  MQAVKKFDPE--RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           M A  K+     +  + +TY+++WI   M  +I    +                      
Sbjct: 58  MVAADKYKFNIEKPCKFSTYAVYWIYHKMNRFIKSKNT---------------------- 95

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
                                     +E  S+N   + D  +  +          +    
Sbjct: 96  --------------------------NEETSLNIPNSSDGDIEFMDCI---EGVDYGFEN 126

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEF 262
           V D    EQ+  E EE   R N L         +ER I + R   +N   +T   +   +
Sbjct: 127 VEDKIYNEQLHRELEEVMARYNTL---------KEREILKFRYGWDNYKCMTCGQIGEIY 177

Query: 263 EVSRERVRQIEARAFKKVQES 283
            V+R ++  IE  A  K++ S
Sbjct: 178 NVTRSKINNIEHTALGKIRRS 198


>gi|296120653|ref|YP_003628431.1| RNA polymerase sigma factor, sigma-70 family [Planctomyces
           limnophilus DSM 3776]
 gi|296012993|gb|ADG66232.1| RNA polymerase sigma factor, sigma-70 family [Planctomyces
           limnophilus DSM 3776]
          Length = 558

 Score = 84.9 bits (209), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 45/241 (18%), Positives = 87/241 (36%), Gaps = 66/241 (27%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKRYRE-----------------------------HG 45
           GL  Y+  +   P+L +++E+   ++                                  
Sbjct: 316 GLPPYLASLYATPLLTREQEHHYFRKMNYLKFAAENLRKTISLAQPRVKLMDEIESLLAR 375

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
                + L+ S+LRLVV IA  +        E++S+GN+ L++A++KFD  RGF+ +TY+
Sbjct: 376 STEIKNFLIRSNLRLVVSIAKKHSHPTANFFEMISDGNMSLIKAIEKFDYTRGFKFSTYA 435

Query: 106 MWWIKAAMQEYI-LRSWSLVKI-------------GTTANQKRLFFNLRRLKGHLQAITD 151
            W I       I   +  L +                T   +    N R+ +  +  +  
Sbjct: 436 SWAIMKNFARSIPAENTRLDRFRTGSEEVFVQSMDPRTDQFRDEIVNYRQREALMGILGQ 495

Query: 152 NNLK----------------PEQVVAIAKKLNVSESEVISMNC-------RLAGDESLNA 188
             L+                P+ +  +  +L V++  +  +         R+A DE L+ 
Sbjct: 496 LELRERDIIMHRYGLETGQQPQTLEQVGHRLGVTKERIRQIEARALKKLKRIATDERLDI 555

Query: 189 L 189
            
Sbjct: 556 P 556


>gi|206901181|ref|YP_002249992.1| SigD [Dictyoglomus thermophilum H-6-12]
 gi|206740284|gb|ACI19342.1| SigD [Dictyoglomus thermophilum H-6-12]
          Length = 171

 Score = 84.9 bits (209), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 28/99 (28%), Positives = 51/99 (51%), Gaps = 2/99 (2%)

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL- 248
           ++   +   +   + + D     + + E  E+ + R  + R++  L+ RER I + R   
Sbjct: 69  VSDHYEYFEEENIYAIQDLIEDPRSIEETIEQIDIRREIERALDALSEREREILKWRYGF 128

Query: 249 -QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
               P TLE +   F ++RERVRQIE RA +K++  +Q+
Sbjct: 129 KDGKPRTLEEVGKLFNITRERVRQIEERALRKLRHILQQ 167


>gi|228912145|ref|ZP_04075860.1| RNA polymerase sigma factor [Bacillus thuringiensis IBL 200]
 gi|228847482|gb|EEM92421.1| RNA polymerase sigma factor [Bacillus thuringiensis IBL 200]
          Length = 232

 Score = 84.5 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 49/233 (21%), Positives = 89/233 (38%), Gaps = 30/233 (12%)

Query: 52  RLVTSHLRLVVKIA-MGYRG--------YGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
             +  + RLV       Y           GL I ++   G IGL++A   FD E G + +
Sbjct: 5   EFMKKYGRLVHHCVWKRYAKKMKSIEHDTGLDIEDLTQFGMIGLIKARDNFDLEYGCKFS 64

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I   +   I      VK+  +    +              I   NL  E    I
Sbjct: 65  TYAVPKIIGEIGRAIRDHQK-VKVQRSVYSVK------------GKILRQNLGDEIPEEI 111

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A  LN   S V +      G +SLN +++ S+ N     + ++ D   +       E+  
Sbjct: 112 ASILNEDVSVVSNALHYQPGTQSLNKVVHQSNGNEELTLESMLEDKKAE-----NVEDVS 166

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
             R ++    S L+ +E  + +         T +N+++E   S+ ++ +I  +
Sbjct: 167 INRMVIQSFKSQLSHKEHIVLDM---SLQNRTQQNIANEVGCSQVQISRILTK 216


>gi|55274881|gb|AAV49243.1| RNA polymerase subunit sigma-38 [Shigella boydii]
          Length = 184

 Score = 84.5 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 26/152 (17%), Positives = 58/152 (38%), Gaps = 10/152 (6%)

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           GFR +TY+ WWI+  ++  I+     +++      K L   LR  +     ++       
Sbjct: 37  GFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV-KELNVYLRTAR----ELSHKLDHEP 91

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               IA++L+    +V  M        S++  +    + +      L    D +E    +
Sbjct: 92  SAEEIAEQLDKPVDDVSRMLRLNERITSVDTPLGGDSEKA-----LLDILADEKENGPED 146

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
             +  + +  + + +  LN ++R +   R   
Sbjct: 147 TTQDDDMKQSIVKWLFELNAKQREVLARRFGL 178


>gi|318041750|ref|ZP_07973706.1| Type II alternative RNA polymerase sigma factor, sigma-70 family
           protein [Synechococcus sp. CB0101]
          Length = 279

 Score = 84.5 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 54/240 (22%), Positives = 96/240 (40%), Gaps = 40/240 (16%)

Query: 53  LVTSHLRLVVKIAMGYRGYGL-----PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           ++  +LRLVV IA  Y            S+++  G IGL++AV+KFDP  G+  +TY+ W
Sbjct: 55  MIKENLRLVVCIAKPYHARIQRSSALEFSDLLQAGTIGLIRAVEKFDPALGYSFSTYASW 114

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+ A++  I  S S +++     Q RL  +                       +A+ L 
Sbjct: 115 WIRQAIRREIEASESSIRLSARQQQMRLKAHFA-------------PPGLSHDELAEYLG 161

Query: 168 VSESEVISMNC--RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           V   ++  +    R +  +SL+  I                D       L     R    
Sbjct: 162 VEPRQLKELQEAWRASQVDSLDRPIEMG------------NDQLKLSDSLAAPLNRSLDH 209

Query: 226 NMLTRSMSVLN---PRERRIFEARRLQENPVTLENLSSEFEVSRERV-RQIEARAFKKVQ 281
             L    +      P E  +F+ R  Q    +   ++    ++R+ + R++E RA K+++
Sbjct: 210 QDLQDVAARFRRKAPSEIAVFD-RLAQGESQS--EVARSMGITRQALNRRLE-RASKRLR 265


>gi|219855964|ref|YP_002473086.1| hypothetical protein CKR_2621 [Clostridium kluyveri NBRC 12016]
 gi|219569688|dbj|BAH07672.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 238

 Score = 84.5 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 48/261 (18%), Positives = 88/261 (33%), Gaps = 71/261 (27%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGL 86
             +E   L     + G+  A  +L+  +  +V K A  +   +   +   ++  EG +GL
Sbjct: 5   SNEELVQL----YQAGNKGALDKLIELNKGIVYKFANRFYTEKTNSIDKEDLKQEGFMGL 60

Query: 87  MQAVKKFDPE--RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           M A  K+     +  + +TY+++WI   M  +I    +                      
Sbjct: 61  MVAADKYKFNIEKPCKFSTYAVYWIYHKMNRFIKSKNT---------------------- 98

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
                                     +E  S+N   + D  +  +          +    
Sbjct: 99  --------------------------NEETSLNIPNSSDGDIEFMDCI---EGVDYGFEN 129

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEF 262
           V D    EQ+  E EE   R N L         +ER I + R   +N   +T   +   +
Sbjct: 130 VEDKIYNEQLHRELEEVMARYNTL---------KEREILKFRYGWDNYKCMTCGQIGEIY 180

Query: 263 EVSRERVRQIEARAFKKVQES 283
            V+R ++  IE  A  K++ S
Sbjct: 181 NVTRSKINNIEHTALGKIRRS 201


>gi|85058037|ref|YP_453739.1| flagellar biosynthesis sigma factor [Sodalis glossinidius str.
           'morsitans']
 gi|84778557|dbj|BAE73334.1| RNA polymerase sigma factor for flagellar operon FliA [Sodalis
           glossinidius str. 'morsitans']
          Length = 241

 Score = 84.5 bits (208), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 49/250 (19%), Positives = 94/250 (37%), Gaps = 21/250 (8%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPER 97
           Y   G L+    L   +  ++   A+  +      + + +++  G IGL+ A+  FD  +
Sbjct: 5   YNHQGRLADDRGLWQQYAPIIRHEALRLQVRLPASVELEDLIQAGMIGLLAAIDSFDAAQ 64

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G    TY+   I+  M + + R    V      N + +   ++RL+  L A T       
Sbjct: 65  GASFTTYARSRIRWGMLDEL-RERDWVPRSVRRNAREIAAAIQRLEQRLGANTSE----- 118

Query: 158 QVVAIAKKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
               IA +L VS +   +M      +   SL+ L+    + +               Q  
Sbjct: 119 --QQIADELGVSLTAYQTMLHETNCSQLFSLDELMAQEAQGTG------PALPADAGQDP 170

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
            +       R  +   +  L  RE+ +      QE  + L+ +     V   RV Q+ + 
Sbjct: 171 FQLLMAGGLRKQVKDEIGRLPEREQLLLNLYYHQE--LNLKEIGEVLGVGESRVSQLHSL 228

Query: 276 AFKKVQESIQ 285
           A K+++  +Q
Sbjct: 229 AIKRLRARLQ 238


>gi|228943596|ref|ZP_04106021.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228976443|ref|ZP_04136903.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228981654|ref|ZP_04141950.1| RNA polymerase sigma factor [Bacillus thuringiensis Bt407]
 gi|228778139|gb|EEM26410.1| RNA polymerase sigma factor [Bacillus thuringiensis Bt407]
 gi|228783244|gb|EEM31363.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228816045|gb|EEM62245.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
          Length = 232

 Score = 84.1 bits (207), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 49/233 (21%), Positives = 90/233 (38%), Gaps = 30/233 (12%)

Query: 52  RLVTSHLRLVVKIA-MGYRG--------YGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
             +  + RLV       Y           GL I ++   G IGL++A   FD E G + +
Sbjct: 5   EFMKKYGRLVHHCVWKRYAKKMKSIEHDTGLDIEDLTQFGMIGLIKARDNFDLEYGCKFS 64

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I   +   I      VK+  +    +              I   NL+ E    I
Sbjct: 65  TYAVPKIIGEIGRAIRDHQK-VKVQRSVYSIK------------GKILRQNLEYEIPEEI 111

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A  LN   S V +      G +SLN +++ S+ N     + ++ D   +       E+  
Sbjct: 112 ASILNEDVSVVSNALHYQPGTQSLNKVVHQSNGNEELTLESMLEDKKAE-----NVEDVS 166

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
             R ++    S L+ +E  + +         T +N+++E   S+ ++ +I  +
Sbjct: 167 INRMVIQAFKSQLSHKEHIVLDM---SLQNRTQQNIANEVGCSQVQISRILTK 216


>gi|288572993|ref|ZP_06391350.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Dethiosulfovibrio peptidovorans DSM 11002]
 gi|288568734|gb|EFC90291.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Dethiosulfovibrio peptidovorans DSM 11002]
          Length = 189

 Score = 84.1 bits (207), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 32/107 (29%), Positives = 52/107 (48%), Gaps = 1/107 (0%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L ++EE  L     E GD SA   L+ ++  LV  IA  +   G    +++ EG + L++
Sbjct: 6   LAEEEERRLWSSL-EDGDPSAREDLILAYRPLVFWIAKKFNVGGDIYPDLIQEGMMALIK 64

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +  FDP RGFR  TY  + I+  M  Y+ R  +   +   +  + L
Sbjct: 65  GIDSFDPSRGFRFTTYGYYRIRGQMLNYLQRKEAKAPLPMDSFDEEL 111


>gi|220903606|ref|YP_002478918.1| RNA polymerase sigma-28 subunit FliA/WhiG [Desulfovibrio
           desulfuricans subsp. desulfuricans str. ATCC 27774]
 gi|219867905|gb|ACL48240.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Desulfovibrio
           desulfuricans subsp. desulfuricans str. ATCC 27774]
          Length = 260

 Score = 84.1 bits (207), Expect = 2e-14,   Method: Composition-based stats.
 Identities = 41/238 (17%), Positives = 90/238 (37%), Gaps = 26/238 (10%)

Query: 50  AHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              +V  +   +  +A+  +      + + E++S G +GLM+A+ KF P+ G R  TY+ 
Sbjct: 32  QEAVVRHYAPKIRFLALRLKAKLPRSVELGELISSGTLGLMEALGKFRPQLGIRFETYAE 91

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +     L     +  Q+     +R L   ++ +   + +      +    
Sbjct: 92  SRIRGAMLDELR---RLDWFPRSLRQR-----VRTLDEAIRKVEHEHGRQATEEELQAIT 143

Query: 167 NVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            +   +V      L      SL+A+           QD +  D          K   +  
Sbjct: 144 GLPLRDVRQGLEALQNQLWLSLDAI-----------QDTISGDAQEPGGEPYRKTAFREL 192

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
              +   +  L PRE+ +       E  + +   +    ++  RV Q+ ++A  ++++
Sbjct: 193 VERVAPLIDRLTPREKLVLSLYYTDE--LNMRETAEVMGITEGRVSQLHSQALSRLRK 248


>gi|238782801|ref|ZP_04626830.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           bercovieri ATCC 43970]
 gi|238716224|gb|EEQ08207.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           bercovieri ATCC 43970]
          Length = 241

 Score = 84.1 bits (207), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 44/238 (18%), Positives = 101/238 (42%), Gaps = 17/238 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             +L   +  LV   A+  +      + + +++  G IGL+ A+  FDP++G  L+TY  
Sbjct: 13  KDQLWPKYGFLVRHEALRLQARLPASVELDDLIQAGAIGLLTAIDHFDPKKGIGLSTYIT 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             ++ AM + + R    V     +N + +   ++R++         ++  E  VA +  +
Sbjct: 73  QRVRWAMIDEL-RERDWVPRRVRSNAREIAVIIQRIEQE-----SGHVATEADVANSMGV 126

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            + E + +  +   +   SL+ L             +   D   +    + +  + N   
Sbjct: 127 TLPEYQKMLADTNSSQLYSLDEL------QEELADGFEQSDTQHEMLNPLHEIMKGNLTK 180

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            ++R +  L  RE+ +      QE  + ++ +S    V+  RV Q+ ++A K+++  +
Sbjct: 181 QISREIKALPEREQLLLNLYYQQE--LNMKEISVLLNVTETRVSQLHSQAIKRLRARL 236


>gi|150389709|ref|YP_001319758.1| FliA/WhiG family RNA polymerase sigma factor [Alkaliphilus
           metalliredigens QYMF]
 gi|150392068|ref|YP_001322117.1| FliA/WhiG family RNA polymerase sigma factor [Alkaliphilus
           metalliredigens QYMF]
 gi|149949571|gb|ABR48099.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           metalliredigens QYMF]
 gi|149951930|gb|ABR50458.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           metalliredigens QYMF]
          Length = 215

 Score = 83.7 bits (206), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 51/267 (19%), Positives = 99/267 (37%), Gaps = 55/267 (20%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           +H++     + ++E   L  ++RE  +      L+  +LRLV   A  Y+       ++ 
Sbjct: 2   LHKVNFKEPMTEEESKRLINQFRELNNEEIRKHLIERNLRLVAYEAYKYKN--QDSEDIF 59

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
           S G IGL++A+  +DP +  R  TY+   I+  +  YI               KRL    
Sbjct: 60  SVGCIGLIKAIDSYDPSKQTRFDTYANRCIQNEILLYI---------------KRLKKGS 104

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
           R     L                                  A + S +   +  +  +  
Sbjct: 105 RWTFVRLD---------------------------------AKNLSFDDGSSIYNFETLA 131

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
             + L     G+E+ LI +   K+  N++  S+   + + +     R      +T  ++S
Sbjct: 132 SDENLEESFIGREEKLIARSIIKD--NLIEESIEEQSTKRQMAIRLRY---QGLTQIDVS 186

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQK 286
               +S+  V +IE R   K+ + ++K
Sbjct: 187 QRLGISQSYVARIEKRYQDKLYQKLRK 213


>gi|330938480|gb|EGH42083.1| RNA polymerase sigma factor RpoD [Pseudomonas syringae pv. pisi
           str. 1704B]
          Length = 82

 Score = 83.7 bits (206), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 21/74 (28%), Positives = 40/74 (54%), Gaps = 2/74 (2%)

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIE 273
           I+    ++ +      +S L  RE ++   R   +     TLE +  +F+V+RER+RQIE
Sbjct: 1   IDVATVESLKEATREVLSGLTAREAKVLRMRFGIDMNTDHTLEEVGKQFDVTRERIRQIE 60

Query: 274 ARAFKKVQESIQKQ 287
           A+A +K++   + +
Sbjct: 61  AKALRKLRHPTRSE 74


>gi|317131781|ref|YP_004091095.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Ethanoligenens harbinense YUAN-3]
 gi|315469760|gb|ADU26364.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Ethanoligenens harbinense YUAN-3]
          Length = 256

 Score = 83.7 bits (206), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 44/240 (18%), Positives = 97/240 (40%), Gaps = 29/240 (12%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y      +A   +V +   LV   A  Y G G P+ +    G +GL++A+K +D      
Sbjct: 22  YTATPSDAALEAVVLAGRPLVYHFAALY-GVGCPLEDTAQTGMLGLVKAIKSYDGR--VL 78

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            +T++   I   +  +  R   + +     N+ +      + +  L+   ++   P +  
Sbjct: 79  FSTWASHCIIGEI-RHFARKERVYRRPGCLNRLQ-----EQAEKVLERTAEDGEPPPEED 132

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            +A +L +    V  +    AG  + + L      +S+Q Q + +   D           
Sbjct: 133 KLADELGIRPEGVREVLR--AGLVAFSDLD-IEKISSTQMQPFHLPLED----------- 178

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
               R  L ++M  L+  +RR+  A   +   +T E  ++E  +++ +V ++++   K +
Sbjct: 179 ----RLALAQAMEKLDELQRRVISALFFRG--LTQEQTAAELGLNQRKVSRVKSAGLKSL 232


>gi|61966525|emb|CAI72582.1| SigB protein [Staphylococcus aureus]
          Length = 186

 Score = 83.7 bits (206), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 28/179 (15%), Positives = 70/179 (39%), Gaps = 8/179 (4%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           +  ++     K ++E+ +  A  +LV  + +L+  +A  Y        ++V  G +GL+ 
Sbjct: 11  ISPEQINQWIKEHQENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIG 70

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A+ +FD     +   + +  +   ++ Y+      V +      K +   ++++   L A
Sbjct: 71  AINRFDMSFERKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRI--KEIGPRIKKVSDELTA 128

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNC---RLAGDESLNALINSSDKNSSQWQDWL 204
             + +    ++    +       E + M      L+ D S+ A     D ++    D +
Sbjct: 129 ELERSPSISEIADRLEVSEEEVLEAMEMGQSYNALSVDHSIEA---DKDGSTVTLLDIM 184


>gi|318041689|ref|ZP_07973645.1| RNA polymerase sigma factor SigF [Synechococcus sp. CB0101]
          Length = 263

 Score = 83.7 bits (206), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 40/192 (20%), Positives = 75/192 (39%), Gaps = 8/192 (4%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG-YRGYGLPISEVVSEGNIGLMQAVKKFD 94
            L   Y++    +  + ++ ++L LV ++A    +  G    ++  EG  GL++AV++FD
Sbjct: 16  ALLAAYQQCRTTANRNAVIHANLPLVWRVARQESQRSGHSFDDLTQEGCFGLIKAVERFD 75

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           P RG  L+T ++ WI+ A++ Y+      +          L    RR +   +      L
Sbjct: 76  PGRGHSLSTAAVPWIRGAIRHYLRDRSHPISGSHH-----LLELHRRGQALQKQRQQQGL 130

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAG--DESLNALINSSDKNSSQWQDWLVYDHDGQE 212
            P    A+A  L  S         R       SL       D + +   + L     G  
Sbjct: 131 APLSAGALATALGCSLERWQLALARRRSLQLASLEQPHLDDDGDLTPLVEQLRDSRAGDH 190

Query: 213 QVLIEKEERKNR 224
              + + E++  
Sbjct: 191 YARVIRWEQRRH 202


>gi|158340150|ref|YP_001521320.1| RNA polymerase sigma factor domain-containing protein
           [Acaryochloris marina MBIC11017]
 gi|158310391|gb|ABW32006.1| RNA polymerase sigma factor domain protein [Acaryochloris marina
           MBIC11017]
          Length = 508

 Score = 83.7 bits (206), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 47/248 (18%), Positives = 94/248 (37%), Gaps = 15/248 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L   +E  L ++ R  G+  A  +L+  +   +V  +  Y    +    +V  G   +  
Sbjct: 75  LTFDQELDLIQKVRV-GNPRALRQLIKEYKGFIVTASQRYDRS-IDRQALVCSGEAAVDI 132

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A KK+D  +G R  TY  W ++  +Q+       + +         +  N+  +      
Sbjct: 133 AAKKYDESKGHRFITYFSWVLRTEIQKRYCSEAGISR--------EVSRNVSAVNEAAAF 184

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           +T+   +   V  IA++ N++   V++        +SL+      + ++ Q++  LV DH
Sbjct: 185 LTNALGREPSVEEIAEQSNLTVQTVLNALMAKNFTQSLSLSGLIDEDSTIQYESALV-DH 243

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
                      E+ +    L  S   L  +      +R       + + +     V  ER
Sbjct: 244 SCDPWAYALSTEQADILQALEES-GRLESKHVDAVTSRI---EGYSAKEIGERHGVGPER 299

Query: 269 VRQIEARA 276
           VRQ   +A
Sbjct: 300 VRQFIKKA 307


>gi|110626976|gb|ABG79027.1| RpoH [Wolbachia endosymbiont of Armadillidium vulgare]
          Length = 78

 Score = 83.7 bits (206), Expect = 3e-14,   Method: Composition-based stats.
 Identities = 36/66 (54%), Positives = 50/66 (75%)

Query: 7  SIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
          ++ VN    L +YI E+RK PML ++EE  LAK ++EH D+S+AH+L+TSHL LVVKIAM
Sbjct: 7  NLYVNSSTNLMQYIAEVRKFPMLSQEEEVRLAKNWQEHKDISSAHKLITSHLNLVVKIAM 66

Query: 67 GYRGYG 72
           ++ YG
Sbjct: 67 KFKNYG 72


>gi|150388236|ref|YP_001318285.1| FliA/WhiG family RNA polymerase sigma factor [Alkaliphilus
           metalliredigens QYMF]
 gi|149948098|gb|ABR46626.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           metalliredigens QYMF]
          Length = 218

 Score = 83.3 bits (205), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 51/267 (19%), Positives = 99/267 (37%), Gaps = 55/267 (20%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           +H++     + ++E   L  ++RE  +      L+  +LRLV   A  Y+       ++ 
Sbjct: 5   LHKVNFKEPMTEEESKRLINQFRELNNEEIRKHLIERNLRLVAYEAYKYKN--QDSEDIF 62

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
           S G IGL++A+  +DP +  R  TY+   I+  +  YI               KRL    
Sbjct: 63  SVGCIGLIKAIDSYDPSKQTRFDTYANRCIQNEILLYI---------------KRLKKGS 107

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
           R     L                                  A + S +   +  +  +  
Sbjct: 108 RWTFVRLD---------------------------------AKNLSFDDGSSIYNFETLA 134

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
             + L     G+E+ LI +   K+  N++  S+   + + +     R      +T  ++S
Sbjct: 135 SDENLEESFIGREEKLIARSIIKD--NLIEESIEEQSTKRQMAIRLRY---QGLTQIDVS 189

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQK 286
               +S+  V +IE R   K+ + ++K
Sbjct: 190 QRLGISQSYVARIEKRYQDKLYQKLRK 216


>gi|149174362|ref|ZP_01852989.1| probable RNA polymerase sigma 70 [Planctomyces maris DSM 8797]
 gi|148846907|gb|EDL61243.1| probable RNA polymerase sigma 70 [Planctomyces maris DSM 8797]
          Length = 309

 Score = 83.3 bits (205), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 54/286 (18%), Positives = 92/286 (32%), Gaps = 95/286 (33%)

Query: 25  KIPMLEKQEEYVLAK----------RYREHGDLS-------------------AAHRLVT 55
           +  +L  +EE  L +          +YR   D                         ++ 
Sbjct: 73  RADVLSAEEEKKLFRSFNFLKYKANQYRSQLDPDWVTEDQLELIEQLLHRAQLVRDEILR 132

Query: 56  SHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQE 115
            ++RLV  I       G+   E+ S+G + +++A+ KFD  RGFR +TY+   I      
Sbjct: 133 RNMRLVASIVKKCTTTGVSFDELFSDGCLTMLKAIDKFDYSRGFRFSTYAYHAISNFAYR 192

Query: 116 YILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
            I                             +      L PEQ                S
Sbjct: 193 KIAN------------------------RKKERAKYKQLPPEQ----------------S 212

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
           M    A    L       +   S+  +  +   D +EQ++++       R  L +    L
Sbjct: 213 MEETGAVKNPLMGTDTWDEL--SELLNQSIDTLDEREQLIVKS------RFALGKHRKTL 264

Query: 236 NPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                             T + L+ +  +S+ERVRQ+E RA  K++
Sbjct: 265 ------------------TFQKLADQLGISKERVRQLEQRAVAKLK 292


>gi|149184196|ref|ZP_01862514.1| sigma 28 (Flagella/Sporulation) [Erythrobacter sp. SD-21]
 gi|148831516|gb|EDL49949.1| sigma 28 (Flagella/Sporulation) [Erythrobacter sp. SD-21]
          Length = 241

 Score = 83.3 bits (205), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 40/234 (17%), Positives = 96/234 (41%), Gaps = 23/234 (9%)

Query: 54  VTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           +   L +V K+A  Y    G  + + +++  G I L +  ++ +       A Y+   ++
Sbjct: 22  IGKFLPMVRKLAWYYESSCGSSIDVDDLLQAGMIALTECAQRHERPSEDGFAAYAKMRVR 81

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            AM + +  +   V+              R++      +     +      +A  L ++ 
Sbjct: 82  GAMIDLLRSNSHHVRGAAALR--------RKMDAATDELRRQFGRDPSGDEVALFLGMTP 133

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            +      R+A       +++  D  S     +   + D +EQ++ + +     +  L +
Sbjct: 134 EDYQKARNRVATR-----MVDLQDCYSDSDPAFATEEPDAEEQLVAQAD-----KTALAQ 183

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +++ L  R + + +   L+E  + L  +++  EVS  RV Q++A A  K++ S+
Sbjct: 184 AIANLPERLQLVIQLHFLEE--LNLTEIAAVLEVSVPRVHQLKANALDKLKISL 235


>gi|326942736|gb|AEA18632.1| sporulation sigma factor SigF [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 248

 Score = 83.3 bits (205), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 49/233 (21%), Positives = 90/233 (38%), Gaps = 30/233 (12%)

Query: 52  RLVTSHLRLVVKIA-MGYRG--------YGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
             +  + RLV       Y           GL I ++   G IGL++A   FD E G + +
Sbjct: 21  EFMKKYGRLVHHCVWKRYAKKMKSIEHDTGLDIEDLTQFGMIGLIKARDNFDLEYGCKFS 80

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I   +   I      VK+  +    +              I   NL+ E    I
Sbjct: 81  TYAVPKIIGEIGRAIRDHQK-VKVQRSVYSIK------------GKILRQNLEYEIPEEI 127

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A  LN   S V +      G +SLN +++ S+ N     + ++ D   +       E+  
Sbjct: 128 ASILNEDVSVVSNALHYQPGTQSLNKVVHQSNGNEELTLESMLEDKKAE-----NVEDVS 182

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
             R ++    S L+ +E  + +         T +N+++E   S+ ++ +I  +
Sbjct: 183 INRMVIQAFKSQLSHKEHIVLDM---SLQNRTQQNIANEVGCSQVQISRILTK 232


>gi|310830517|ref|YP_003965618.1| Sporulation sigma factor SigK [Paenibacillus polymyxa SC2]
 gi|309249984|gb|ADO59550.1| Sporulation sigma factor SigK [Paenibacillus polymyxa SC2]
          Length = 248

 Score = 83.3 bits (205), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 47/271 (17%), Positives = 98/271 (36%), Gaps = 75/271 (27%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K+P+ + +             D  A          LV  +   +   G+   E+VS   +
Sbjct: 47  KLPLTDAE------------KDKHARED-----ESLVFYVVKMFENSGVDYDELVSIAMV 89

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           G  +A+  FD  R  + +TYS+  IK  +                       F LR+ + 
Sbjct: 90  GFAKALHAFDKNRLVKFSTYSINCIKNEI----------------------LFFLRKERN 127

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
           H+                  K ++S + V+S++ +     SL   +++ DK+    +D +
Sbjct: 128 HV------------------KNSISMNCVLSVD-KNGNSLSLEDTVSTFDKDERSVEDDI 168

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEF 262
           V                 +   +L  ++S L+ +E+ I   R   +     T   ++   
Sbjct: 169 V---------------LSDEIKLLRSALSDLSDKEQYIITYRYGLDRGITKTQREIADAI 213

Query: 263 EVSRERVRQIEARAFKKVQESIQKQVELSSS 293
            +S+  V +IE     KV++ ++ +  ++  
Sbjct: 214 GMSQANVSKIEKNILDKVKKILKDRYHMTEE 244


>gi|113473821|ref|YP_718084.1| RNA polymerase sigma factor (RpoD) [Sphingomonas sp. KA1]
 gi|112821501|dbj|BAF03372.1| Probable RNA polymerase sigma factor (RpoD) [Sphingomonas sp. KA1]
          Length = 328

 Score = 83.3 bits (205), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 23/76 (30%), Positives = 41/76 (53%), Gaps = 5/76 (6%)

Query: 227 MLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +LT ++S L+ RE R+   R         TL+ +  EF V+ +R+RQIE +A ++++   
Sbjct: 53  VLTAALSCLSAREERVIRLRFGLGGHGEWTLQQIGDEFGVNPQRIRQIEMKALRRLRHQF 112

Query: 285 QKQVELSSSPPLLQKP 300
           +K+       P+  KP
Sbjct: 113 RKRY---GPLPMDPKP 125


>gi|153812846|ref|ZP_01965514.1| hypothetical protein RUMOBE_03253 [Ruminococcus obeum ATCC 29174]
 gi|149831058|gb|EDM86147.1| hypothetical protein RUMOBE_03253 [Ruminococcus obeum ATCC 29174]
          Length = 107

 Score = 83.3 bits (205), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 24/101 (23%), Positives = 49/101 (48%), Gaps = 2/101 (1%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             L  R  + GD  A   L   +  L+  +A  + G G  + ++   G+IGL++AV KFD
Sbjct: 6   VALIGRAHQ-GDKEARDILFHENTGLIYSVAHRFLGRGAEMEDLFQIGSIGLLKAVDKFD 64

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
                + +TY++  I   ++ ++     ++K+  +  +K +
Sbjct: 65  LSYDVKFSTYAVPMIAGEIKRFLRDDG-MLKVSRSIKRKSI 104


>gi|119718669|ref|YP_925634.1| sigma-70 region 4 domain-containing protein [Nocardioides sp.
           JS614]
 gi|119539330|gb|ABL83947.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Nocardioides sp.
           JS614]
          Length = 300

 Score = 83.3 bits (205), Expect = 4e-14,   Method: Composition-based stats.
 Identities = 41/228 (17%), Positives = 86/228 (37%), Gaps = 21/228 (9%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             +L   H+ LV  +           +  +++ S G + L+QA + FDPERG   A Y+ 
Sbjct: 14  RDQLAVEHVPLVAHLVRETMARVPSYMDRNDLHSAGLLALVQAARAFDPERGVPFAGYAS 73

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ A+ + +               + +    R ++     +     +     A+A+ L
Sbjct: 74  TRIRGALVDELR--------SVDWASRSVRRRAREIEAARARLAATLGQFPDDAAVAEAL 125

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++  E+   +  +A    L           +      V    G++    E+  R  R  
Sbjct: 126 GITPEEIGKADSEVARAVVLPL--------DAGPNAGFVESLAGRDPGPEEEALRAERAQ 177

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
            L  ++  L  R R +     + + P+    L++E  VS+ R+ +++ 
Sbjct: 178 YLAAAVEELPERLRHVVRGYFIAQRPM--AELAAELGVSKSRISRLQT 223


>gi|330447923|ref|ZP_08311571.1| RNA polymerase sigma factor, FliA/WhiG family protein
           [Photobacterium leiognathi subsp. mandapamensis
           svers.1.1.]
 gi|328492114|dbj|GAA06068.1| RNA polymerase sigma factor, FliA/WhiG family protein
           [Photobacterium leiognathi subsp. mandapamensis
           svers.1.1.]
          Length = 242

 Score = 82.9 bits (204), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 34/240 (14%), Positives = 91/240 (37%), Gaps = 31/240 (12%)

Query: 51  HRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           + L+  HL LV ++      +        ++   G IGL++A +++      +   +++ 
Sbjct: 26  NVLIKRHLNLVKRVVNQLRHHTSSHCSYEDMQQIGLIGLLEAARRYGDVDDPQFPAFAVC 85

Query: 108 WIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            I+ A+ + + R  W           ++       L    + +     +      I   L
Sbjct: 86  RIRGAILDELRRLDWRS---------RQTRQQAHELNDATRDLMKQLGRQPTEAEITHAL 136

Query: 167 NVSESEV-ISMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            +  ++    +   +A +  SL+ L+ +  +  + + D  +              E ++ 
Sbjct: 137 GIDNNDYHQRLQASMASEMQSLDQLLEAGKELETPFTDTSI--------------EHEHL 182

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  LT +++ L  RE+ +       ++ + L  ++    ++  R+ Q+  +A K +   +
Sbjct: 183 RRSLTYALTQLTKREQLLLTLFY--QHELNLHEIALVLNLTPPRICQLHKQALKSLNHYL 240


>gi|303326430|ref|ZP_07356873.1| RNA polymerase sigma factor for flagellar operon FliA
           [Desulfovibrio sp. 3_1_syn3]
 gi|302864346|gb|EFL87277.1| RNA polymerase sigma factor for flagellar operon FliA
           [Desulfovibrio sp. 3_1_syn3]
          Length = 260

 Score = 82.9 bits (204), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 41/242 (16%), Positives = 88/242 (36%), Gaps = 26/242 (10%)

Query: 50  AHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              +V  +   +  +A+  +      + + E++S G +GLM+A+ KF P+ G R  TY+ 
Sbjct: 32  QEEVVRHYAPKIRFLALRLKSKLPRSVELGEMISSGTLGLMEALGKFRPQLGIRFETYAE 91

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + +     L     +  Q+     +R L   ++ +     +      +    
Sbjct: 92  NRIRGAMLDELR---RLDWFPRSLRQR-----VRVLDEAMRKVEHEQGRQATEEELQDIT 143

Query: 167 NVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            +   +V      L      SL+A+           QD L  D              +  
Sbjct: 144 GLELRDVRQGLEALQNQLWLSLDAI-----------QDTLAGDGPESGGEPYSNTALREL 192

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              +   +  L PRE+ +       E  + +   +    ++  RV Q+ ++A  ++++  
Sbjct: 193 VERVAPLIERLTPREKLVLSLYYTDE--LNMRETAEIMGITEGRVSQLHSQALGRLRKEF 250

Query: 285 QK 286
             
Sbjct: 251 AS 252


>gi|224825766|ref|ZP_03698870.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Lutiella nitroferrum
           2002]
 gi|224601990|gb|EEG08169.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Lutiella nitroferrum
           2002]
          Length = 230

 Score = 82.9 bits (204), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 43/234 (18%), Positives = 98/234 (41%), Gaps = 30/234 (12%)

Query: 52  RLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           R ++    LV ++A          +   ++   G + L++A++++  E   R A Y++  
Sbjct: 17  RCLSDFAPLVKRVARQLNSQANGVIEREDMEQIGLMALLEALRRYG-EPDARFAGYAVLR 75

Query: 109 IKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           ++ A+ + + R  W           + L  +  RL+  L+ +T    +         +L 
Sbjct: 76  VRGAILDELRRLDWRP---------RALRQDAHRLRDGLRELTRRLGREPSEAEAVAQLG 126

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +  ++        + NA   +S           + D+  +  VL        +R  
Sbjct: 127 LSAEDYRALL------VAENAEAMASFDELVAAGIEPIDDNTPEASVL--------QRRT 172

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           L  ++S L+ RE+R+ +     E  ++L+ +++  +++  RV QI   A KK++
Sbjct: 173 LAAALSALDEREQRVIQLYY--EFELSLKEIAAVLDLTEARVCQINKSALKKMK 224


>gi|218661227|ref|ZP_03517157.1| RNA polymerase factor sigma-32 [Rhizobium etli IE4771]
          Length = 62

 Score = 82.9 bits (204), Expect = 5e-14,   Method: Composition-based stats.
 Identities = 41/61 (67%), Positives = 47/61 (77%)

Query: 1  MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
          M R  +  I  GE GL+RY+ EIRK PMLE Q+EY+LAKRY EHGD  AAH+LVTSHLRL
Sbjct: 1  MARNTLPSITAGEAGLNRYLDEIRKFPMLEPQQEYMLAKRYAEHGDRDAAHKLVTSHLRL 60

Query: 61 V 61
          V
Sbjct: 61 V 61


>gi|153818374|ref|ZP_01971041.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae NCTC 8457]
 gi|126511064|gb|EAZ73658.1| RNA polymerase sigma factor for flagellar operon FliA [Vibrio
           cholerae NCTC 8457]
          Length = 232

 Score = 82.9 bits (204), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 46/213 (21%), Positives = 88/213 (41%), Gaps = 17/213 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPER 97
           Y ++G+L++    +  +  LV +IA    G   P   I +++  G +GL++A K +D  +
Sbjct: 7   YDQYGNLNSQQLFLEKYSVLVKRIAHHLIGRLPPSVLIEDLIQAGMVGLLEAQKNYDGSK 66

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G    TY+   I+ AM + I R    V      + + +   +  L+G L        +  
Sbjct: 67  GASFETYAGIRIRGAMLDDIRR-GDWVPRSVHKHNREISQAIAVLEGELN-------RDP 118

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
               +AK LN+S  +  S+      D + + ++   D   S   D +    +G++     
Sbjct: 119 TDAEVAKFLNMSLEQYHSVLM----DINCSRIVGIEDLGVS--DDAISPFEEGEDNSPFH 172

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
               ++ R  L  S+  L  RE  +      +E
Sbjct: 173 GVAEESFRKALVESIKSLPEREALVLSLYYDEE 205


>gi|325111003|ref|YP_004272071.1| RNA polymerase, sigma 32 subunit, RpoH [Planctomyces brasiliensis
           DSM 5305]
 gi|324971271|gb|ADY62049.1| RNA polymerase, sigma 32 subunit, RpoH [Planctomyces brasiliensis
           DSM 5305]
          Length = 555

 Score = 82.9 bits (204), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 56/287 (19%), Positives = 110/287 (38%), Gaps = 54/287 (18%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAKR--YREHGDLSAAHRLVTS--HLRLVVKIAMGYRG 70
           GL  Y+  + ++P+L + +E    ++  Y +         L T     RL+ KI      
Sbjct: 313 GLPAYLASLYELPLLTRAQEQYYFRKMNYLKFKAQELREDLNTDRPSARLMTKI------ 366

Query: 71  YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
                 E++ E       AVK F      RL       + +  + +     +  ++ +  
Sbjct: 367 -----EELIREAV-----AVKNFLIRSNLRL-------VVSIAKRHFKPQANFFEMVSDG 409

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS-ESEVISMNCRLAGDESLNAL 189
           N       L R          N        AI K    S  +E+  ++    G + L + 
Sbjct: 410 NMS-----LIRAIEKFDYSQGNKFSTYATWAIMKNYARSIPTELKQLDRYRTGHDELFS- 463

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
                              D ++    ++  ++++ + +   +  L+PRER I   R   
Sbjct: 464 ----------------QSTDARDNPFRQELNQQHQHSAIMSILGQLDPRERDIILHRFGL 507

Query: 250 E---NPVTLENLSSEFEVSRERVRQIEARAFKKVQE-SIQKQVELSS 292
                P TLE +   F V++ER+RQIE+RA  K+++ ++++++E+  
Sbjct: 508 NKGTEPETLEQVGHRFGVTKERIRQIESRALSKLKKIAVEEKLEIPG 554


>gi|154499126|ref|ZP_02037504.1| hypothetical protein BACCAP_03120 [Bacteroides capillosus ATCC
           29799]
 gi|150271966|gb|EDM99192.1| hypothetical protein BACCAP_03120 [Bacteroides capillosus ATCC
           29799]
          Length = 340

 Score = 82.6 bits (203), Expect = 6e-14,   Method: Composition-based stats.
 Identities = 20/95 (21%), Positives = 38/95 (40%), Gaps = 4/95 (4%)

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            +  S    D  +YD         ++   +     +  ++S L  RE  +   R      
Sbjct: 74  CEDRSCSITDCTIYDD--AISAAEDQIWCEELSGAIESALSQLTTREEEVLRLRFF--EG 129

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +T      +F V+RER+ QIE  A +K++   + +
Sbjct: 130 LTGAECGKKFGVTRERIHQIEVTALRKLRHPSRSK 164


>gi|289444245|ref|ZP_06433989.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis T46]
 gi|289417164|gb|EFD14404.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis T46]
          Length = 375

 Score = 82.6 bits (203), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 30/118 (25%), Positives = 53/118 (44%), Gaps = 31/118 (26%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------REHGDL- 47
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+  
Sbjct: 215 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSERGEKL 273

Query: 48  ----------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN+GL++ 
Sbjct: 274 PAAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNLGLIRG 331


>gi|110626979|gb|ABG79029.1| RpoH [Wolbachia endosymbiont of Armadillidium vulgare]
          Length = 78

 Score = 82.6 bits (203), Expect = 7e-14,   Method: Composition-based stats.
 Identities = 36/72 (50%), Positives = 51/72 (70%)

Query: 1  MNRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRL 60
          M     ++ VN    L +YI E+RK PML ++EE  LAK ++E+ D+S+AH+L+TSHL L
Sbjct: 1  MLTSVANLCVNSSTNLMQYIAEVRKFPMLSQEEEVRLAKNWQEYKDISSAHKLITSHLNL 60

Query: 61 VVKIAMGYRGYG 72
          VVKIAM ++ YG
Sbjct: 61 VVKIAMKFKNYG 72


>gi|187935479|ref|YP_001884301.1| RNA polymerase sigma-F factor [Clostridium botulinum B str. Eklund
           17B]
 gi|187723632|gb|ACD24853.1| RNA polymerase sigma-F factor [Clostridium botulinum B str. Eklund
           17B]
          Length = 233

 Score = 82.2 bits (202), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 48/260 (18%), Positives = 90/260 (34%), Gaps = 70/260 (26%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGL 86
             +E   L     + GD  A ++L+ ++ +LV KI   +       + I ++  EG +GL
Sbjct: 2   SNEELVEL----YQEGDKQALNKLIENNKKLVFKIVNKFYINATNSIDIEDLEQEGYMGL 57

Query: 87  MQAVKKF--DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           + A KK+  + +     +TYS +WI   +  +I              QK         + 
Sbjct: 58  IMAAKKYNSNMDYHASFSTYSFYWIYQKINSFI-------------KQKNTND-----ET 99

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L    +   + E+V  I    N  E+                                 
Sbjct: 100 SLNIPLNEGEEKEKVDLIEYIDNGYEN--------------------------------- 126

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE-NPVTLENLSSEFE 263
           + +    EQ+  + E        L           R I +     +    T+  ++   E
Sbjct: 127 IEEKLYLEQLRSDLENLMEHNTTLRE---------RSILKLHYGWDCRECTMTYIAGMLE 177

Query: 264 VSRERVRQIEARAFKKVQES 283
           +S++RVRQIE    +K++ +
Sbjct: 178 ISQQRVRQIEKSTLRKLRRT 197


>gi|157826497|ref|YP_001495561.1| RNA polymerase sigma factor RpoD [Rickettsia bellii OSU 85-389]
 gi|157801801|gb|ABV78524.1| RNA polymerase sigma factor RpoD [Rickettsia bellii OSU 85-389]
          Length = 81

 Score = 82.2 bits (202), Expect = 8e-14,   Method: Composition-based stats.
 Identities = 22/58 (37%), Positives = 36/58 (62%), Gaps = 2/58 (3%)

Query: 232 MSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++ L PRE R+   R         TLE +  +F+V+RER+RQIE++A +K+Q  I+ +
Sbjct: 2   LATLTPREERVLRMRFGIGMNTDHTLEEVGQQFKVTRERIRQIESKALRKLQHPIRSK 59


>gi|325106726|ref|YP_004267794.1| RNA polymerase, sigma 32 subunit, RpoH [Planctomyces brasiliensis
           DSM 5305]
 gi|324966994|gb|ADY57772.1| RNA polymerase, sigma 32 subunit, RpoH [Planctomyces brasiliensis
           DSM 5305]
          Length = 332

 Score = 82.2 bits (202), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 47/226 (20%), Positives = 81/226 (35%), Gaps = 58/226 (25%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRY--------------------------REHG 45
            E  L  ++ ++   P+L  ++E    +R                            E  
Sbjct: 86  SEGSLPTHLSQLCGTPLLTPEQEVSSFRRMNYLKFRFNRIRSKLNAETATAEQVAEAEST 145

Query: 46  DLSA---AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
              A      L+ ++LRLVV +A  +    L   E+ S+G I LM AV+KFD +RG+R +
Sbjct: 146 LRQANSVRDLLIRANLRLVVSVARKFVTPQLTFDELFSDGVIALMNAVEKFDYDRGYRFS 205

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQK----------------------RLFFNLR 140
           TY+ + I  ++  +I       +I +   ++                       L   L 
Sbjct: 206 TYAYYSISRSLYRFIKVQ-RKNRIHSDVLEQVVEADDDGQSGWNQESWDFVNEELDSMLA 264

Query: 141 RLKGHLQAIT------DNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           +L    + I       D+  K      +A+KL V    V  +  R 
Sbjct: 265 QLDQRERWIIRQRYTFDSEGKAPTYKVLAEKLGVCNERVRQLEKRA 310



 Score = 62.9 bits (152), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 26/89 (29%), Positives = 40/89 (44%), Gaps = 5/89 (5%)

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP---V 253
           S   +  +  D DGQ     E  +  N    L   ++ L+ RER I   R   ++     
Sbjct: 230 SDVLEQVVEADDDGQSGWNQESWDFVN--EELDSMLAQLDQRERWIIRQRYTFDSEGKAP 287

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQE 282
           T + L+ +  V  ERVRQ+E RA  K++ 
Sbjct: 288 TYKVLAEKLGVCNERVRQLEKRALSKLRN 316


>gi|150019798|ref|YP_001312052.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium beijerinckii
           NCIMB 8052]
 gi|149906263|gb|ABR37096.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium beijerinckii
           NCIMB 8052]
          Length = 250

 Score = 82.2 bits (202), Expect = 9e-14,   Method: Composition-based stats.
 Identities = 53/260 (20%), Positives = 89/260 (34%), Gaps = 66/260 (25%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR--GYGLPISEVVSEGNIGLMQAV 90
           EE VL     + G++ A   L+ ++  +V K+A  +      +   ++V  G IGL+ A 
Sbjct: 4   EELVL---LYQQGNIKALESLIEANEGIVKKLANKFNGINKMIEFDDLVQAGIIGLINAA 60

Query: 91  KKFDPERGFR--LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
            K++ E   +    TY+  +IK  +   +                               
Sbjct: 61  NKYNNELENKASFITYAFQYIKREIFSCV------------------------------- 89

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                             N    + IS N       SL+  I   + N  Q +D +    
Sbjct: 90  ------------------NGRSEKEISNNKLYNSCVSLDVPIQ--EDNDIQLKDTIESID 129

Query: 209 DGQEQVLIEKEERKNRRNMLTRSM---SVLNPRERRIFEARRLQENPV--TLENLSSEFE 263
            G E V  EK   K  R  L  +M   + L  RE  I +           T + ++    
Sbjct: 130 YGFENV-EEKIYIKQLREELEDAMLDNNTLKERE--ILQLCYGWNYQKIFTYKEVAETLN 186

Query: 264 VSRERVRQIEARAFKKVQES 283
           +S   + QIE  A +K++ S
Sbjct: 187 ISINSIPQIEFNALRKLRNS 206


>gi|331027965|ref|YP_004421515.1| RNA polymerase sigma factor [Synechococcus phage S-CBS2]
 gi|294805578|gb|ADF42417.1| RNA polymerase sigma factor [Synechococcus phage S-CBS2]
          Length = 261

 Score = 82.2 bits (202), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 32/137 (23%), Positives = 67/137 (48%), Gaps = 13/137 (9%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYR--EHGDLS---AAHRLVTSHLRLVVKIAMGY 68
             ++ +++   +  +L  ++   L ++ +  E G        ++L   +LRLV K    Y
Sbjct: 3   DPITAWLNNAARYELLTAEQTIELGRKIQAAEEGSPERIKLVNKLCQHNLRLVAKFTRAY 62

Query: 69  R--------GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
                      G    +++ EG  GL +A  KFDPERG+  ATY+  W++ A+ +Y +  
Sbjct: 63  MKGGTRKLTWGGDETMDLLQEGYFGLRRAANKFDPERGYTFATYANAWVRQALGKYHVDK 122

Query: 121 WSLVKIGTTANQKRLFF 137
            SL+++  ++ ++  ++
Sbjct: 123 LSLIRVPESSAREIFYY 139


>gi|297197375|ref|ZP_06914772.1| RNA polymerase sigma-G factor [Streptomyces sviceus ATCC 29083]
 gi|297146698|gb|EDY58861.2| RNA polymerase sigma-G factor [Streptomyces sviceus ATCC 29083]
          Length = 294

 Score = 82.2 bits (202), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 32/154 (20%), Positives = 70/154 (45%), Gaps = 9/154 (5%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +    LV++ L +  +IA  +R  G  + ++     +GL++A+ +F+PERG    +Y++ 
Sbjct: 48  ALRDELVSAWLPMAHRIAGRFRDRGESLEDLRQVAALGLVKAIDRFEPERG-AFESYAVP 106

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE-QVVAIAKKL 166
            I   ++ +       +++     + R      +++   + +T N   PE     +A   
Sbjct: 107 TITGEVKRHFRDRMWALRVPRRVQELR-----NKVRVARRELTQNPGSPEPTTADLAAHT 161

Query: 167 NVSESEVISMNCRLA--GDESLNALINSSDKNSS 198
            ++E EV +    L      SL+A +++ D   S
Sbjct: 162 GLTEEEVTTGLEALESFSTLSLDAELSTGDDGYS 195


>gi|159795060|pdb|2P7V|B Chain B, Crystal Structure Of The Escherichia Coli Regulator Of
           Sigma 70, Rsd, In Complex With Sigma 70 Domain 4
          Length = 68

 Score = 81.8 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 21/64 (32%), Positives = 37/64 (57%), Gaps = 2/64 (3%)

Query: 230 RSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             ++ L  RE ++   R   +     TLE +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 1   DVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 60

Query: 288 VELS 291
           V  S
Sbjct: 61  VLRS 64


>gi|225575508|ref|ZP_03784118.1| hypothetical protein RUMHYD_03600 [Blautia hydrogenotrophica DSM
           10507]
 gi|225037258|gb|EEG47504.1| hypothetical protein RUMHYD_03600 [Blautia hydrogenotrophica DSM
           10507]
          Length = 286

 Score = 81.8 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 42/236 (17%), Positives = 96/236 (40%), Gaps = 14/236 (5%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           L   +   + K+A+ Y G    + ++  EG + L +AV+ +D  R     +Y+ +W+K  
Sbjct: 23  LWQQNEGFIGKLALIYAG-QAEMEDLKQEGYLALCEAVRGYDVTREVPFLSYASFWLKTR 81

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           M+ Y+      V++ +      L   +R+ +                  +   L V+E +
Sbjct: 82  MRRYV-DQNKPVRLPSY-----LGDEVRQYQKTKSDFLKRYGYEASDRELCGLLGVNEKK 135

Query: 173 VISMN--CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           +  +     +   +SLN L+  ++  + +     +   +  E+    + +R+  +  L R
Sbjct: 136 IRKLKRAASMGQIQSLNELLPGTEDFTLEES---IASEEDLEEEAAARLDRERMKEELWR 192

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           S+  L  R   +   R   +   TL  +     VS  R  Q+  +A + +++ + +
Sbjct: 193 SVDELPDRLPVVVRMRY--QEETTLNEVGERLGVSLSRAAQMNKQAMRTLRQRVHR 246


>gi|308205503|gb|ADO18993.1| RNA polymerase sigma factor [Nostoc flagelliforme str. Sunitezuoqi]
          Length = 158

 Score = 81.8 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 28/152 (18%), Positives = 61/152 (40%), Gaps = 8/152 (5%)

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
             +   L ++K   + ++ +  +   VV IA++L V   +            SL   +  
Sbjct: 3   IHINEKLNKIKKIQRELSQSLGRKPTVVEIAEELKVKPEQAREYIQADRKLVSLEMRV-- 60

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            ++  ++  + L  +        +E+      R  +   ++ L P +R +   R   EN 
Sbjct: 61  GNEQETELSELLADEK----ISPLEELNSSLMRQNIKELLASLAPIQREVLTLRFGLEND 116

Query: 253 V--TLENLSSEFEVSRERVRQIEARAFKKVQE 282
              +L  +     +SRER+RQ+E +A   ++ 
Sbjct: 117 HQLSLTQIGERLNLSRERIRQLEHKALSILRR 148


>gi|268678937|ref|YP_003303368.1| RNA polymerase sigma factor, FliA/WhiG family [Sulfurospirillum
           deleyianum DSM 6946]
 gi|268616968|gb|ACZ11333.1| RNA polymerase sigma factor, FliA/WhiG family [Sulfurospirillum
           deleyianum DSM 6946]
          Length = 237

 Score = 81.8 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 39/243 (16%), Positives = 88/243 (36%), Gaps = 32/243 (13%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
                 LV  +L  V  +A   R      + +++++S G   +++  +++D ++      
Sbjct: 17  KKEQDELVLQYLPAVRAMAYRLRERLPASVDVNDLISIGTEEMIKLSRRYDKDQNDSFWG 76

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y    +  +M +++        + T +   R    L  +   + A    +        +A
Sbjct: 77  YGKKRVYGSMLDFLRS------LDTMSRANRRLIKL--VDQEITAYLGEHGSEPDDAYLA 128

Query: 164 KKLNVSESEVISM--NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           K L     ++     +  +    SLN  +       +                  +K E+
Sbjct: 129 KVLGEDSEKIAEARNSAMIVSVMSLNEQVTILSGEDT-----------------AQKVEK 171

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
                M+   +S  N RE+ I +    +E  + L+ +S   E+S  R+ QI  +   K++
Sbjct: 172 DELMEMVQSILSTFNEREQMIIQLYYFEE--LNLKEISEILEISESRISQIHKKLLAKLK 229

Query: 282 ESI 284
           E +
Sbjct: 230 EQL 232


>gi|91794980|ref|YP_564631.1| flagellar biosynthesis sigma factor [Shewanella denitrificans
           OS217]
 gi|91716982|gb|ABE56908.1| RNA polymerase sigma factor, FliA/WhiG [Shewanella denitrificans
           OS217]
          Length = 236

 Score = 81.8 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 44/237 (18%), Positives = 89/237 (37%), Gaps = 27/237 (11%)

Query: 51  HRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            +L+  +L LV +       + G  L + ++   G + L+++ +++  E      +++  
Sbjct: 24  DQLIVQYLPLVKRAVLQLRSHCGAMLSLEDMEQIGMMALIESSRRYPGEFDNGFISFAGQ 83

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+ A+ + + R               L   +R L   L        +      +A  L 
Sbjct: 84  RIRGAILDELRRQ-DWRPRPVRQQAHILNDKVRELSRTL-------GREPTDTEVATGLG 135

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S           A  ESL A    S K+  +         D   +V     ER   +  
Sbjct: 136 LSPE---------AYRESLYATQAESMKSLDEMLTIGEQPADKHNEV-----ERFMLKKT 181

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L ++M+ LN RE+ I        + + L+ ++    ++  R+ Q+  +A  K+Q  I
Sbjct: 182 LIKAMTKLNEREQLILSLYY--HHELNLKEIALTLGLTETRICQLHKQAVAKLQSLI 236


>gi|86157781|ref|YP_464566.1| sigma 28 (flagella/sporulation) [Anaeromyxobacter dehalogenans
           2CP-C]
 gi|85774292|gb|ABC81129.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Anaeromyxobacter
           dehalogenans 2CP-C]
          Length = 232

 Score = 81.8 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 40/240 (16%), Positives = 88/240 (36%), Gaps = 32/240 (13%)

Query: 51  HRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
             L+  H  L+ + A       G+ +   ++ S G +GL++A +++D  +  R  T++  
Sbjct: 20  EALLRRHATLLDRCARRLAARTGHAVEPGDLWSAGAMGLLEAARRYDASQDVRFETFAEH 79

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            ++ AM + + R   L +       + L       +  L+        P   V IA+   
Sbjct: 80  RVRGAMLDELRRMDHLPRRLRADADRVLA-----ARARLEQALGREPDP---VEIAEAAG 131

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRN 226
           +   +V  +    +    +                    D      V  ++      RR 
Sbjct: 132 LPAEQVGELLLLASPPVPVE------------------DDVAPAPAVPADEALGAAERRG 173

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L R+++ L  R + +       +  +T   ++    VS  RV Q+ + A K+++  + +
Sbjct: 174 ALARAVAALPERLQVLLALYY--DEALTYREIAKVLGVSEPRVCQLHSEAAKRLRALMSE 231


>gi|331005480|ref|ZP_08328859.1| RNA polymerase sigma factor for flagellar operon [gamma
           proteobacterium IMCC1989]
 gi|330420756|gb|EGG95043.1| RNA polymerase sigma factor for flagellar operon [gamma
           proteobacterium IMCC1989]
          Length = 225

 Score = 81.8 bits (201), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 41/241 (17%), Positives = 83/241 (34%), Gaps = 45/241 (18%)

Query: 60  LVVKIA----MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQE 115
           LV KIA           L   +    G IGL++A KK+  ++G    TY+ + IK A+  
Sbjct: 22  LVTKIAASLYKKRFDNSLEFDDYKHYGFIGLLEAKKKYTSDQGASFDTYATYRIKGAILN 81

Query: 116 YILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
            I+++            +   +N RR K  L+++                          
Sbjct: 82  GIVKNS--------EKMQLYAYNSRREKDRLRSLKAPEPTNR------------------ 115

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSM 232
                     ++      +   +     L+ D    E  + E  E   +    + L   +
Sbjct: 116 ----------MDLFDLFIELTGNLAVASLLDDMSESEISVDECSETYYQSQMSSDLLLGV 165

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
             LN  E+ +             + ++   EV++ R+ Q+   A +K++ +++     S+
Sbjct: 166 EHLNGNEKLVVTYHYFGGLD--FQEVADILEVTKGRISQLHKSALEKLRITLENSSHYSA 223

Query: 293 S 293
            
Sbjct: 224 E 224


>gi|121488741|emb|CAJ18254.1| sigma 70-type sigma factor [Chlorobaculum limnaeum]
          Length = 149

 Score = 81.4 bits (200), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 32/158 (20%), Positives = 63/158 (39%), Gaps = 11/158 (6%)

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  RGF+  +Y++WWI+ ++ + +     +V++    N+      + +    L+   + 
Sbjct: 1   FDETRGFKFISYAVWWIRQSILQALAEQSRIVRLP--LNRVGTLNKISKAYSQLEQEYER 58

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +        +A  L++   +V           S++A     D N  +  D L  D    +
Sbjct: 59  D---PNTKELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDN--RLLDVLQNDGHMPD 113

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             L     R +    + RS+SVL PRE  +  +     
Sbjct: 114 HGL----NRDSLTLEVERSLSVLAPREADVIRSYFGIG 147


>gi|213027409|ref|ZP_03341856.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. 404ty]
          Length = 185

 Score = 81.4 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 35/198 (17%), Positives = 82/198 (41%), Gaps = 14/198 (7%)

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           AV ++D  +G    TY++  I+ AM + + RS   V      N + +   + +L+  L  
Sbjct: 1   AVDRYDALQGTAFTTYAVQRIRGAMLDEL-RSRDWVPRSVRRNAREVAQAMGQLEQEL-- 57

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                 +      +A++L +  +E   M      D + + L +  +          +   
Sbjct: 58  -----GRNATETEVAERLGIPVAEYRQMLL----DTNNSQLFSYDEWREEHGDSIELVTE 108

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           + Q++  + +    + R  +  ++  L  RE+ +       +  + L+ + +  EV   R
Sbjct: 109 EHQQENPLHQLLEGDLRQRVMDAIESLPEREQLVLTLYY--QEELNLKEIGAVLEVGESR 166

Query: 269 VRQIEARAFKKVQESIQK 286
           V Q+ ++A K+++  + K
Sbjct: 167 VSQLHSQAIKRLRTKLGK 184


>gi|237751751|ref|ZP_04582231.1| flagellar biosynthesis sigma factor [Helicobacter bilis ATCC 43879]
 gi|229373117|gb|EEO23508.1| flagellar biosynthesis sigma factor [Helicobacter bilis ATCC 43879]
          Length = 240

 Score = 81.4 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 39/240 (16%), Positives = 91/240 (37%), Gaps = 32/240 (13%)

Query: 50  AHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L   +L  V  +A          + ++++VS G   L++  +++D  +      Y+ 
Sbjct: 23  QDELALQYLPAVKAMAFRLKERLPSSVDMNDLVSIGTEELIKLARRYDSNKNDSFWGYAK 82

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +  AM +Y+ R+  +V   +    K +   + R     +              +AK L
Sbjct: 83  TRVNGAMLDYL-RTLDIVSRSSRKLIKAIEAEVSRYFNEFEE-------EPSNEYLAKVL 134

Query: 167 NVSESEVI--SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           N    ++    +   +     L+   N+ +                    +++  E+K  
Sbjct: 135 NEDIEKIHQARLASDIYAVVPLDEQFNALEDGD-----------------ILQYCEQKEL 177

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             ++ + ++ L  RE+ I +   L+E  ++L  +S   +++  R+ QI     KK++  I
Sbjct: 178 MEIIQKVLAKLTEREQLIIQLYYLEE--LSLSEISEVLDITESRISQISKEVIKKIRREI 235


>gi|224373368|ref|YP_002607740.1| flagellar biosynthesis sigma factor [Nautilia profundicola AmH]
 gi|223589587|gb|ACM93323.1| RNA polymerase sigma factor, sigma-F [Nautilia profundicola AmH]
          Length = 229

 Score = 81.4 bits (200), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 36/238 (15%), Positives = 90/238 (37%), Gaps = 30/238 (12%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L   ++  V  +A   +      +  +++VS G   L++  +++DP++      Y+ 
Sbjct: 17  RDELAVDYMPAVKAMAARLKERLPSSVEFNDLVSIGLEELVKLARRYDPKQNDNFWGYAQ 76

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I  +M +++ RS   V    + + +++  ++ ++    QA  D          IA  L
Sbjct: 77  KRIYGSMLDFL-RSLDTV----SRSDRKIIKDIEKIVESYQAEHDIE---PDDEYIADIL 128

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V                       S  +    + +       +  K E +    
Sbjct: 129 GIEVEKVRRAK-----------------NASEIYNVMPIEEQMNFFDNVSLKIEEEELIE 171

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + + +  +  +E+ I +    +E  ++L+ +S    V+  R+ QI     KK+++ +
Sbjct: 172 TIKKVLKTMTEKEQLIIQLYYFEE--LSLKEISEILGVTESRISQIHKNVIKKLRKEL 227


>gi|167464009|ref|ZP_02329098.1| RNA polymerase, sigma 28 subunit [Paenibacillus larvae subsp.
           larvae BRL-230010]
          Length = 175

 Score = 81.0 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 41/158 (25%), Positives = 73/158 (46%), Gaps = 21/158 (13%)

Query: 51  HRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFDPERGFR----LAT 103
            +++ ++ ++V  +A  YR   G GL   ++VS G IGL+QA + +DP+R  R     +T
Sbjct: 13  DQIIPAYEKMVHSVARKYRSCIGAGLDYDDLVSVGMIGLIQAFRNYDPDRLNRKVSSFST 72

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   IK ++Q ++      V++             R ++  L  I       E   +IA
Sbjct: 73  YAFNMIKWSIQRFLADKRFSVRVP------------RSIQNKLTVIWKQGWDQESAESIA 120

Query: 164 KKLNVSESEVISMNCRLAG--DESLNALINSSDKNSSQ 199
           +K      E+      +AG    SL+  ++SSDK   +
Sbjct: 121 EKTGWKLPEIREAQRHIAGWSVASLDQALSSSDKTDEE 158


>gi|89476431|gb|ABD73716.1| SigB [Staphylococcus aureus]
 gi|89476433|gb|ABD73717.1| SigB [Staphylococcus aureus]
 gi|89476435|gb|ABD73718.1| SigB [Staphylococcus aureus]
 gi|89476437|gb|ABD73719.1| SigB [Staphylococcus aureus]
 gi|89476439|gb|ABD73720.1| SigB [Staphylococcus aureus]
 gi|89476441|gb|ABD73721.1| SigB [Staphylococcus aureus]
 gi|89476443|gb|ABD73722.1| SigB [Staphylococcus aureus]
 gi|89476445|gb|ABD73723.1| SigB [Staphylococcus aureus]
 gi|89476447|gb|ABD73724.1| SigB [Staphylococcus aureus]
 gi|89476449|gb|ABD73725.1| SigB [Staphylococcus aureus]
 gi|89476451|gb|ABD73726.1| SigB [Staphylococcus aureus]
 gi|89476453|gb|ABD73727.1| SigB [Staphylococcus aureus]
 gi|89476455|gb|ABD73728.1| SigB [Staphylococcus aureus]
 gi|89476457|gb|ABD73729.1| SigB [Staphylococcus aureus]
 gi|89476459|gb|ABD73730.1| SigB [Staphylococcus aureus]
 gi|89476461|gb|ABD73731.1| SigB [Staphylococcus aureus]
 gi|89476463|gb|ABD73732.1| SigB [Staphylococcus aureus]
 gi|89476465|gb|ABD73733.1| SigB [Staphylococcus aureus]
 gi|89476467|gb|ABD73734.1| SigB [Staphylococcus aureus]
 gi|89476469|gb|ABD73735.1| SigB [Staphylococcus aureus]
 gi|89476471|gb|ABD73736.1| SigB [Staphylococcus aureus]
 gi|89476473|gb|ABD73737.1| SigB [Staphylococcus aureus]
 gi|89476475|gb|ABD73738.1| SigB [Staphylococcus aureus]
 gi|89476481|gb|ABD73741.1| SigB [Staphylococcus aureus]
 gi|89476483|gb|ABD73742.1| SigB [Staphylococcus aureus]
 gi|89476487|gb|ABD73744.1| SigB [Staphylococcus aureus]
          Length = 147

 Score = 81.0 bits (199), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 22/147 (14%), Positives = 58/147 (39%), Gaps = 2/147 (1%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             ++     K ++E+ +  A  +LV  + +L+  +A  Y        ++V  G +GL+ A
Sbjct: 1   SPEQINQWIKEHQENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGA 60

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +FD     +   + +  +   ++ Y+      V +      K +   ++++   L A 
Sbjct: 61  INRFDMSFERKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRI--KEIGPRIKKVSDELTAE 118

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISM 176
            + +    ++    +       E + M
Sbjct: 119 LERSPSISEIADRLEVSEEEVLEAMEM 145


>gi|296103602|ref|YP_003613748.1| RNA polymerase sigma factor for flagellar operon FliA [Enterobacter
           cloacae subsp. cloacae ATCC 13047]
 gi|295058061|gb|ADF62799.1| RNA polymerase sigma factor for flagellar operon FliA [Enterobacter
           cloacae subsp. cloacae ATCC 13047]
          Length = 241

 Score = 80.6 bits (198), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 40/237 (16%), Positives = 94/237 (39%), Gaps = 23/237 (9%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
               +  H RL   +          + +++  G+IG + AV+ FDP++G  L  +    +
Sbjct: 25  RQEALRLHKRLPASV---------ELDDLIQAGSIGFLSAVESFDPKKGVTLTAWISQRV 75

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           K A+ + +  S  +         +R+  + R +   +Q I            IA+++ VS
Sbjct: 76  KWALLDELRESDWV--------PRRVRTHTREIVALIQQIEQEKGGEATEAEIAERMGVS 127

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             E   M      D + + + +  +   +    W   D + ++   +    R+N    +T
Sbjct: 128 LQEFQQMLA----DNNASQMYSVDELQENYADSWETSDEENEQLNPLNDAVRQNLMERIT 183

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             + V+  RE+     +      + ++ +     ++  RV Q+ + A K+++  ++ 
Sbjct: 184 EHIQVIPEREQ--VLLQLYYLQDLNMKEIGLILGITETRVSQLHSLAVKRLRSRMES 238


>gi|126176138|ref|YP_001052287.1| flagellar biosynthesis sigma factor [Shewanella baltica OS155]
 gi|304412490|ref|ZP_07394096.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella baltica
           OS183]
 gi|307307149|ref|ZP_07586887.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella baltica
           BA175]
 gi|125999343|gb|ABN63418.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Shewanella
           baltica OS155]
 gi|304349132|gb|EFM13544.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella baltica
           OS183]
 gi|306910388|gb|EFN40819.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella baltica
           BA175]
          Length = 238

 Score = 80.6 bits (198), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 36/246 (14%), Positives = 93/246 (37%), Gaps = 31/246 (12%)

Query: 46  DLSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           +  +  +++  +L L+ +I      + G  L + ++   G + L+++ +++  E      
Sbjct: 19  ERQSEQQIIRQYLPLIKRIVSQMRSHCGVMLSLEDMEQIGMMALLESSRRYPGELDNGFI 78

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           +++   I+ A+ + + R               L   +RRL   +        +    + +
Sbjct: 79  SFAGQRIRGAILDELRRQ-DWRPRPVRQQAHELNDVVRRLSREM-------GREPSDLEV 130

Query: 163 AKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
           A  L +S  +          +   SL+ L+   ++   +  D                 E
Sbjct: 131 ASALGLSAEDYRERLYSTQAESMKSLDELLLGGEQPVDRSND----------------VE 174

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           R   +  L + +S LN RE+ I        + + L+ ++    ++  R+ Q+   A  ++
Sbjct: 175 RLMLKQTLIKVISKLNEREQLILSLYY--HHELNLKEIAMALGLTETRICQLHKSAISQL 232

Query: 281 QESIQK 286
           +  +Q+
Sbjct: 233 KTILQR 238


>gi|126442822|ref|YP_001061239.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei 668]
 gi|134280863|ref|ZP_01767573.1| RNA polymerase sigma factor for flagellar operon FliA [Burkholderia
           pseudomallei 305]
 gi|167725922|ref|ZP_02409158.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei
           DM98]
 gi|167905082|ref|ZP_02492287.1| flagellar biosynthesis sigma factor [Burkholderia pseudomallei NCTC
           13177]
 gi|254182899|ref|ZP_04889492.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 1655]
 gi|254299694|ref|ZP_04967143.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 406e]
 gi|125657228|gb|ABN48716.1| RNA polymerase sigma factor [Burkholderia pseudomallei]
 gi|126222313|gb|ABN85818.1| RNA polymerase sigma factor for flagellar operon FliA [Burkholderia
           pseudomallei 668]
 gi|134247885|gb|EBA47969.1| RNA polymerase sigma factor for flagellar operon FliA [Burkholderia
           pseudomallei 305]
 gi|157809669|gb|EDO86839.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 406e]
 gi|184213433|gb|EDU10476.1| RNA polymerase sigma factor for flagellar operon [Burkholderia
           pseudomallei 1655]
          Length = 236

 Score = 80.6 bits (198), Expect = 2e-13,   Method: Composition-based stats.
 Identities = 38/239 (15%), Positives = 96/239 (40%), Gaps = 29/239 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           A  R +  +  +V + A   +      L + ++   G +GL++A++++          Y+
Sbjct: 21  AEQRWLVEYAPIVKRAARQLKSQAVGMLTLDDIEQIGLMGLLEALRRYG-MPDAAFPCYA 79

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
              ++ A+ + + R             + +     R +   + +  +  +      ++  
Sbjct: 80  ATRVRGAILDELRRHDW--------RPRSVRLEAHRTRDCERELCRSLGREPTEAEVSDA 131

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           L +S +E                 + +++  +    D ++ D     +   E+E  +  R
Sbjct: 132 LGISTTEYRER-------------VMANNAEAMASFDSVLDDDALTHEESPEREIVR--R 176

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             L ++++ LN RE+R+ +     E  ++L  ++S   ++  RV QI   A KK++E +
Sbjct: 177 RCLEQALARLNEREQRVIQLYY--EFDLSLREIASVLGLTEARVCQINKAALKKMREVL 233


>gi|186896753|ref|YP_001873865.1| flagellar biosynthesis sigma factor [Yersinia pseudotuberculosis
           PB1/+]
 gi|186699779|gb|ACC90408.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Yersinia
           pseudotuberculosis PB1/+]
          Length = 231

 Score = 80.6 bits (198), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 36/235 (15%), Positives = 92/235 (39%), Gaps = 30/235 (12%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           + + ++L LV +I          +    ++     +GL++A++++    G + A Y++  
Sbjct: 19  KYLNAYLPLVKRIVRQLSFQADSVIGKEDMQQIALMGLLEALRRYGHPDG-QFAAYAVHR 77

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ ++ + +               +RL     +    ++ I            I+ +LN+
Sbjct: 78  IRGSILDQLREHDW--------RPRRLRQKTHKTNEAIRQIAKRLGHEPNFEEISAELNL 129

Query: 169 SESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +  E     +       ESL+ ++     N       L              EE     +
Sbjct: 130 TADEYQEYLLLENAGAMESLDEILALDAHNDILQSCDL--------------EENIIIED 175

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L +++S L+ RE+ I      QE  ++++ ++   +++  R+ Q+  +  +K++
Sbjct: 176 NLKQAISALDEREQMILHLYYQQE--LSMKEIAQVLDLTEARICQLNKKLVQKIK 228


>gi|154816043|emb|CAO85715.1| putative RNA polymerase sigma factor rpoD [Clostridium sp.]
          Length = 75

 Score = 80.6 bits (198), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 25/63 (39%), Positives = 37/63 (58%), Gaps = 3/63 (4%)

Query: 226 NMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           + L+  +S L+PRE RI   R          TLE +  EF ++RER+RQIEARA +K++ 
Sbjct: 4   DTLSNVLSTLSPREERIVRLRYGLVGDGESRTLEEIGREFNLTRERIRQIEARAIRKLRH 63

Query: 283 SIQ 285
             +
Sbjct: 64  PTR 66


>gi|89476477|gb|ABD73739.1| SigB [Staphylococcus aureus]
 gi|89476479|gb|ABD73740.1| SigB [Staphylococcus aureus]
 gi|89476485|gb|ABD73743.1| SigB [Staphylococcus aureus]
          Length = 147

 Score = 80.6 bits (198), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 22/147 (14%), Positives = 58/147 (39%), Gaps = 2/147 (1%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             ++     K ++E+ +  A  +LV  + +L+  +A  Y        ++V  G +GL+ A
Sbjct: 1   SPEQINQWIKEHQENKNTDAQDKLVKHYQKLIESLAYKYSKGQSHHEDLVQVGMVGLIGA 60

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +FD     +   + +  +   ++ Y+      V +      K +   ++++   L A 
Sbjct: 61  INRFDMSFERKFEAFLVPTVIGEIKRYLRDKTWSVHVPRRI--KEIGPRIKKVSDELTAE 118

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISM 176
            + +    ++    +       E + M
Sbjct: 119 LERSPSISEIANRLEVSEEEVLEAMEM 145


>gi|120597321|ref|YP_961895.1| flagellar biosynthesis sigma factor [Shewanella sp. W3-18-1]
 gi|146294534|ref|YP_001184958.1| flagellar biosynthesis sigma factor [Shewanella putrefaciens CN-32]
 gi|120557414|gb|ABM23341.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Shewanella sp.
           W3-18-1]
 gi|145566224|gb|ABP77159.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Shewanella
           putrefaciens CN-32]
          Length = 238

 Score = 80.6 bits (198), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 35/246 (14%), Positives = 92/246 (37%), Gaps = 31/246 (12%)

Query: 46  DLSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           +  +  +++  +L L+ +I      + G  L + ++   G + L+++ +++  E      
Sbjct: 19  ERQSEQQVIRQYLPLIKRIVSQMRSHCGVMLSLEDMEQIGMMALLESSRRYPGELDNGFI 78

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           +++   I+ A+ + + R               L   +RRL   +        +    + +
Sbjct: 79  SFAGQRIRGAILDELRRQ-DWRPRPVRQQAHELNDVVRRLSREM-------GREPSDLEV 130

Query: 163 AKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
           A  L +S  +          +   SL+ L+   +    +  D                 E
Sbjct: 131 ASALGLSAEDYRERLYSTQAESMKSLDELLLVGEHPVDRGND----------------VE 174

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           +   +  L + +S LN RE+ I        + + L+ ++    ++  R+ Q+   A  ++
Sbjct: 175 QLMLKQTLIKVISKLNEREQLILSLYY--HHELNLKEIAMALGLTETRICQLHKSAISQL 232

Query: 281 QESIQK 286
           +  +Q+
Sbjct: 233 KTILQR 238


>gi|218673042|ref|ZP_03522711.1| RNA polymerase factor sigma-32 [Rhizobium etli GR56]
          Length = 88

 Score = 80.6 bits (198), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 28/77 (36%), Positives = 47/77 (61%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
               ++ +    + + RR  L  ++  LN RE +I  ARRL E+  TLE L ++  +S+E
Sbjct: 1   DPLPDEQVSNMIDGERRRVWLASALKHLNEREMKIISARRLAEDGATLEELGADLGISKE 60

Query: 268 RVRQIEARAFKKVQESI 284
           RVRQIE+RA +K++ ++
Sbjct: 61  RVRQIESRAMEKLRSAL 77


>gi|45442811|ref|NP_994350.1| flagellar biosynthesis sigma factor [Yersinia pestis biovar
           Microtus str. 91001]
 gi|108809036|ref|YP_652952.1| flagellar biosynthesis sigma factor [Yersinia pestis Antiqua]
 gi|150260230|ref|ZP_01916958.1| lateral flagellar sigma factor 28 protein [Yersinia pestis
           CA88-4125]
 gi|162420360|ref|YP_001604825.1| flagellar biosynthesis sigma factor [Yersinia pestis Angola]
 gi|165925029|ref|ZP_02220861.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis biovar
           Orientalis str. F1991016]
 gi|165939031|ref|ZP_02227583.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis biovar
           Orientalis str. IP275]
 gi|166008912|ref|ZP_02229810.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis biovar
           Antiqua str. E1979001]
 gi|166212025|ref|ZP_02238060.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis biovar
           Antiqua str. B42003004]
 gi|167398583|ref|ZP_02304107.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis biovar
           Antiqua str. UG05-0454]
 gi|167418724|ref|ZP_02310477.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis biovar
           Orientalis str. MG05-1020]
 gi|167466317|ref|ZP_02331021.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis FV-1]
 gi|218927931|ref|YP_002345806.1| flagellar biosynthesis sigma factor [Yersinia pestis CO92]
 gi|229837430|ref|ZP_04457593.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           Pestoides A]
 gi|229840642|ref|ZP_04460801.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Orientalis str. PEXU2]
 gi|229842806|ref|ZP_04462958.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Orientalis str. India 195]
 gi|294502807|ref|YP_003566869.1| flagellar biosynthesis sigma factor FliA [Yersinia pestis Z176003]
 gi|45437677|gb|AAS63227.1| putative RNA polymerase sigma factor for flagellar operon [Yersinia
           pestis biovar Microtus str. 91001]
 gi|108780949|gb|ABG15007.1| putative RNA polymerase sigma factor for flagellar operon [Yersinia
           pestis Antiqua]
 gi|115346542|emb|CAL19419.1| putative RNA polymerase sigma factor for flagellar operon [Yersinia
           pestis CO92]
 gi|149289638|gb|EDM39715.1| lateral flagellar sigma factor 28 protein [Yersinia pestis
           CA88-4125]
 gi|162353175|gb|ABX87123.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis Angola]
 gi|165912987|gb|EDR31612.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis biovar
           Orientalis str. IP275]
 gi|165923229|gb|EDR40380.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis biovar
           Orientalis str. F1991016]
 gi|165992251|gb|EDR44552.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis biovar
           Antiqua str. E1979001]
 gi|166206771|gb|EDR51251.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis biovar
           Antiqua str. B42003004]
 gi|166962718|gb|EDR58739.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis biovar
           Orientalis str. MG05-1020]
 gi|167051087|gb|EDR62495.1| flagellar operon sigma factor , sigma-28 [Yersinia pestis biovar
           Antiqua str. UG05-0454]
 gi|229690073|gb|EEO82130.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Orientalis str. India 195]
 gi|229697008|gb|EEO87055.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           biovar Orientalis str. PEXU2]
 gi|229705553|gb|EEO91563.1| RNA polymerase sigma factor for flagellar operon [Yersinia pestis
           Pestoides A]
 gi|262360839|gb|ACY57560.1| flagellar biosynthesis sigma factor FliA [Yersinia pestis D106004]
 gi|262364784|gb|ACY61341.1| flagellar biosynthesis sigma factor FliA [Yersinia pestis D182038]
 gi|294353266|gb|ADE63607.1| flagellar biosynthesis sigma factor FliA [Yersinia pestis Z176003]
          Length = 231

 Score = 80.2 bits (197), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 36/235 (15%), Positives = 100/235 (42%), Gaps = 30/235 (12%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           + + ++L LV +I          +    ++     +GL++A++++    G + A Y++  
Sbjct: 19  KYLNAYLPLVKRIVRQLSFQADSVIGKEDMQQIALMGLLEALRRYGHPDG-QFAAYAVHR 77

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ ++ + +               +RL     +    ++ I            I+ +LN+
Sbjct: 78  IRGSILDQLREHDW--------RPRRLRQKTHKTNEAIRQIAKRLGHEPNFEEISAELNL 129

Query: 169 SESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +  E     +       ESL+ ++      + +  + ++   D +E ++IE        +
Sbjct: 130 TADEYQEYLLLENAGAMESLDEIL------ALEAHNDILQSRDLEENIIIE--------D 175

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L +++S L+ RE+ I      QE  ++++ ++   +++  R+ Q+  +  +K++
Sbjct: 176 NLKQAISTLDEREQMILHLYYQQE--LSMKEIAQVLDLTEARICQLNKKLVQKIK 228


>gi|228982422|ref|ZP_04142681.1| sporulation sigma factor SigK [Bacillus thuringiensis Bt407]
 gi|228776605|gb|EEM24913.1| sporulation sigma factor SigK [Bacillus thuringiensis Bt407]
          Length = 203

 Score = 80.2 bits (197), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 38/241 (15%), Positives = 88/241 (36%), Gaps = 59/241 (24%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              +   + RLV  +   +    +   E+V+ G +G  +A+  FD  R  + +TY++  I
Sbjct: 16  KEIIAVENERLVYYVVKMFENSQIDPDELVNAGMVGYAKALNAFDTTREVKFSTYAINCI 75

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           K  +                       F LR+ K H                        
Sbjct: 76  KNEI----------------------LFFLRKEKKHRL---------------------- 91

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
                        + SLN +++     +    + +V + +  E+ L ++    + + ++ 
Sbjct: 92  ------------NNVSLNTVLSVDKNGNGFHLEDIVAEKNNGEKSLEDRVVEDDHKRLIR 139

Query: 230 RSMSVLNPRERRIFEARRLQEN---PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            ++ +LNP E+ I   R   +      T + ++ +  +S+  V +I+     K++  I++
Sbjct: 140 EAIKMLNPEEQYIMTFRYGLDKNGTEKTQKQIAEDINMSQANVSKIQKHCLLKIKRLIKE 199

Query: 287 Q 287
           +
Sbjct: 200 E 200


>gi|295092950|emb|CBK82041.1| DNA-directed RNA polymerase specialized sigma subunit [Coprococcus
           sp. ART55/1]
          Length = 128

 Score = 80.2 bits (197), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 29/111 (26%), Positives = 60/111 (54%), Gaps = 3/111 (2%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             + GD  A  +LVT ++ LVV +A  Y G G  + +++  G IGL++A+ +FD +   +
Sbjct: 10  LAKDGDRDARDKLVTDNMGLVVSVARRYVGRGQELEDLIQIGLIGLVKAIDRFDMDYEVK 69

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           L+TY++  I+  ++ ++     +VK+    N K +++   R +  ++    
Sbjct: 70  LSTYAVPLIQGEIRRFLRDDG-MVKVSR--NLKTIYYRADRYRHEVEKTEG 117


>gi|87201086|ref|YP_498343.1| sigma 28 (flagella/sporulation) [Novosphingobium aromaticivorans
           DSM 12444]
 gi|87136767|gb|ABD27509.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Novosphingobium
           aromaticivorans DSM 12444]
          Length = 244

 Score = 80.2 bits (197), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 51/250 (20%), Positives = 105/250 (42%), Gaps = 26/250 (10%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL---PISEVVSEGNIGLMQAVKKFD 94
           A+ YR+  D +A    +   L +V ++A    G G     I +++  G + L +  ++ D
Sbjct: 11  AQAYRK--DETADR--IRRFLPMVKRLAWHVHGSGRSGIEIEDLIQAGLVALTECAQRHD 66

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
                  A Y+   ++ AM + + RS     +  +A ++R     R L+     +     
Sbjct: 67  GPTEDGFAAYAKLRVRGAMVDLVRRST---PLSRSATERR-----RVLREKTATLATELG 118

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +P     +A+ + ++E E   +  + A DE L     + D   S        D      +
Sbjct: 119 RPPSEAELARAVGLTERE---LADQRAADEPL--RFEAIDDAYSDSNSAFADDRPDSFDM 173

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
           L + E     R  +  +++ L  R + I +   ++E  + L  ++    VS  RV Q++A
Sbjct: 174 LADAE----MRGAVAAAIAGLPERLQLIIQLYFVEE--LNLAEIAEVLGVSIPRVHQLKA 227

Query: 275 RAFKKVQESI 284
           +A  K++ ++
Sbjct: 228 QAIDKLRMAL 237


>gi|57241943|ref|ZP_00369883.1| alternative transcription initiation factor, sigma-F (fliA)
           [Campylobacter upsaliensis RM3195]
 gi|57017135|gb|EAL53916.1| alternative transcription initiation factor, sigma-F (fliA)
           [Campylobacter upsaliensis RM3195]
          Length = 231

 Score = 80.2 bits (197), Expect = 3e-13,   Method: Composition-based stats.
 Identities = 41/241 (17%), Positives = 89/241 (36%), Gaps = 28/241 (11%)

Query: 47  LSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
                 LV S++  +  +A          + +++++S G   +++  +++D ++      
Sbjct: 15  KKEQDELVISYMPALRAMAFRLKERLPSSIDVNDLISVGIEEMIKLSRRYDKDQNDNFWG 74

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           ++   +  +M +Y+ R             +     L+ +   L      N        +A
Sbjct: 75  FARKRVNGSMLDYLRR--------LDVMSRNNRKILKDIDVILDEYFLENECEPDDEYLA 126

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           KKL +    V  +  R A   S     +   +  S             E   +EK ER  
Sbjct: 127 KKLEIDVERVREV--RAAHAISYTLPFDEQIEMYS-------------EDETLEKIERGE 171

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               +   +  L  R++ I +    +E  ++L+ +S    VS  R+ QI  +  KK++E 
Sbjct: 172 FLEHINEILDTLKERDQLIIQLYYYEE--LSLKEISEILNVSESRISQIHKKLLKKLRER 229

Query: 284 I 284
           +
Sbjct: 230 L 230


>gi|87125785|ref|ZP_01081628.1| putative type III sigma factor [Synechococcus sp. RS9917]
 gi|86166594|gb|EAQ67858.1| putative type III sigma factor [Synechococcus sp. RS9917]
          Length = 262

 Score = 79.9 bits (196), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 54/264 (20%), Positives = 103/264 (39%), Gaps = 26/264 (9%)

Query: 39  KRYREHGDLSAAHR--LVTSHLRLVVKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDP 95
           + +R     +  HR   + SHL L   +A      G     ++V E ++GL+ AV+ FD 
Sbjct: 17  REWRRSLPEAIRHRNGEIISHLGLAHHVAGRQSTRGHGDWDDLVQEASLGLIAAVEGFDS 76

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            RG +L++Y++      +  +     S ++I      + L+    RL+          L 
Sbjct: 77  SRGHQLSSYAVSRAHGQILHFRRDRQSTIRIPWRL--RSLYGRGMRLQEQQWQAHGAPLS 134

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
            E ++A+   L VS           A +E L+      D    +             +  
Sbjct: 135 EEALIAM---LEVSRERWRQAVQAHAQEEVLSL-----DGPGVEPG-----------EAF 175

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
            E      +R  L +++  L P +RR   A  +    V+L  L+    V    ++++ A 
Sbjct: 176 GEVAAEDPQRQWLHQALPQLQPEQRRWLLAHWV--EGVSLRALARREGVHPAMLKRVLAT 233

Query: 276 AFKKVQESIQKQVELSSSPPLLQK 299
           A ++++   Q + E S   P+  +
Sbjct: 234 ALEQLRSLAQVEAEPSRPSPIANR 257


>gi|51597620|ref|YP_071811.1| flagellar biosynthesis sigma factor [Yersinia pseudotuberculosis IP
           32953]
 gi|51590902|emb|CAH22558.1| Putative RNA polymerase sigma factor for flagellar operon [Yersinia
           pseudotuberculosis IP 32953]
          Length = 231

 Score = 79.9 bits (196), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 37/235 (15%), Positives = 98/235 (41%), Gaps = 30/235 (12%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           + + ++L LV +I          +    ++     +GL++A++++    G + A Y++  
Sbjct: 19  KYLNAYLPLVKRIVRQLSFQADSVIGKEDMQQIALMGLLEALRRYGHPDG-QFAAYAVHR 77

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ ++ + +               +RL     +    ++ I            I+ +LN+
Sbjct: 78  IRGSILDQLREHDW--------RPRRLRQKTHKTNEAIRQIAKRLGHEPNFEEISAELNL 129

Query: 169 SESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +  E     +       ESL+ ++     N       ++   D +E ++IE        +
Sbjct: 130 TADEYQEYLLLENAGAMESLDEILALDAHND------ILQSRDLEENIIIE--------D 175

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L +++S L+ RE+ I      QE  ++++ ++   +++  R+ Q+  +  +K++
Sbjct: 176 NLKQAISALDEREQMILHLYYQQE--LSMKEIAQVLDLTEARICQLNKKLVQKIK 228


>gi|330983153|gb|EGH81256.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv. aptata
           str. DSM 50252]
          Length = 70

 Score = 79.9 bits (196), Expect = 4e-13,   Method: Composition-based stats.
 Identities = 24/68 (35%), Positives = 38/68 (55%)

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           + +   N    L +++ VL+ R R I   R L E   TL +L+ ++ VS ER+RQ+E  A
Sbjct: 1   DSDWTDNSTANLHQALDVLDERSRDILYQRWLAEEKATLHDLAQKYNVSAERIRQLEKSA 60

Query: 277 FKKVQESI 284
             K++ SI
Sbjct: 61  MNKLKTSI 68


>gi|312794234|ref|YP_004027157.1| RNA polymerase, sigma 70 family subunit [Caldicellulosiruptor
           kristjanssonii 177R1B]
 gi|312181374|gb|ADQ41544.1| putative RNA polymerase, sigma 70 family subunit
           [Caldicellulosiruptor kristjanssonii 177R1B]
          Length = 206

 Score = 79.9 bits (196), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 46/251 (18%), Positives = 89/251 (35%), Gaps = 60/251 (23%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L   E+  L  R ++ GD  AA  L+ ++  L++ IA  Y    +   ++  EG + ++Q
Sbjct: 4   LSLDEQKELVCRIKQ-GDKKAAEELIRAYEPLIISIASKYNKPDI-FEDLKQEGAVAILQ 61

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A +KFD   G    T ++++IK      + R    ++                       
Sbjct: 62  AAQKFDESLGVSFITLAVYYIKRNTDRCVKR-SQTIRPP--------------------- 99

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                           K +    +VISM   +               N++ + D      
Sbjct: 100 --------------FNKFDAIVPQVISMESVI---------------NANSYADDEELKV 130

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS--- 265
               Q  I  EE+      L + +  L   E++I   R       +L+ ++ +  ++   
Sbjct: 131 KDTIQDTINVEEQVVHNEYLKKLVDKLTDEEKKILLLRI---KQYSLKEIAEKLGLTEKQ 187

Query: 266 -RERVRQIEAR 275
              RV++I A+
Sbjct: 188 VAARVQKIRAK 198


>gi|153947529|ref|YP_001399652.1| flagellar biosynthesis sigma factor [Yersinia pseudotuberculosis IP
           31758]
 gi|152959024|gb|ABS46485.1| flagellar operon sigma factor , sigma-28 [Yersinia
           pseudotuberculosis IP 31758]
          Length = 231

 Score = 79.5 bits (195), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 37/235 (15%), Positives = 98/235 (41%), Gaps = 30/235 (12%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           + + ++L LV +I          +    ++     +GL++A++++    G + A Y++  
Sbjct: 19  KYLNAYLPLVKRIVRQLSFQADSVIGKEDMQQIALMGLLEALRRYGHPDG-QFAAYAVHR 77

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ ++ + +               +RL     +    ++ I            I+ +LN+
Sbjct: 78  IRGSILDQLREHDW--------RPRRLRQKTHKTNEAIRQIAKRLGHEPNFEEISAELNL 129

Query: 169 SESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +  E     +       ESL+ ++     N       ++   D +E ++IE        +
Sbjct: 130 TADEYQEYLLLENAGAMESLDEILALDAHND------ILQSRDLEENIIIE--------D 175

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L +++S L+ RE+ I      QE  ++++ ++   +++  R+ Q+  +  +K++
Sbjct: 176 NLKQAISALDEREQMILHLYYQQE--LSMKEIAQVLDLTEARICQLNKKLVQKIK 228


>gi|220917697|ref|YP_002493001.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Anaeromyxobacter
           dehalogenans 2CP-1]
 gi|219955551|gb|ACL65935.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Anaeromyxobacter
           dehalogenans 2CP-1]
          Length = 232

 Score = 79.5 bits (195), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 38/238 (15%), Positives = 83/238 (34%), Gaps = 32/238 (13%)

Query: 51  HRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
             L+  H  L+ + A       G+ +   ++ S G +GL++A +++DP    R  T++  
Sbjct: 20  DALLRRHAPLLDRCARRLAARTGHAVEPGDLWSAGAMGLLEAARRYDPAHDVRFETFAEH 79

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            ++ AM + + R   L +       + L       +  L+        P +V   A+   
Sbjct: 80  RVRGAMLDELRRMDHLPRRLRADADRVLA-----ARARLEQSLGREPDPVEVAEAAE--- 131

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +   +V  +    +    +                    D      +  ++      R  
Sbjct: 132 LPAEQVGELLLLASPPVPVE------------------DDLAPTPALPADEALGAAERRR 173

Query: 228 LTRSM-SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
               M + L  R + +       +  +T   ++    VS  RV Q+ A A K+++  +
Sbjct: 174 ALARMVAALPERLQVLLALYY--DEALTYREIAKVLGVSEPRVCQLHAEAVKRLRALM 229


>gi|330874712|gb|EGH08861.1| RNA polymerase factor sigma-32 [Pseudomonas syringae pv.
           morsprunorum str. M302280PT]
          Length = 81

 Score = 79.5 bits (195), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 25/70 (35%), Positives = 39/70 (55%)

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
           L + +   N    L +++ VL+ R R I   R L E   TL +L+ ++ VS ER+RQ+E 
Sbjct: 10  LEDADWTDNSTANLHQALDVLDERSRDILYQRWLAEEKATLHDLAQKYNVSAERIRQLEK 69

Query: 275 RAFKKVQESI 284
            A  K++ SI
Sbjct: 70  SAMNKLKTSI 79


>gi|197122905|ref|YP_002134856.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Anaeromyxobacter sp.
           K]
 gi|196172754|gb|ACG73727.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Anaeromyxobacter sp.
           K]
          Length = 232

 Score = 79.5 bits (195), Expect = 5e-13,   Method: Composition-based stats.
 Identities = 41/238 (17%), Positives = 87/238 (36%), Gaps = 32/238 (13%)

Query: 51  HRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
             L+  H  L+ + A       G+ +   ++ S G +GL++A +++DP    R  T++  
Sbjct: 20  DALLRRHAPLLDRCARRLAARTGHAVEPGDLWSAGAMGLLEAARRYDPAHDVRFETFAEH 79

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            ++ AM + + R   L +       + L       +  L+        P +V   A+   
Sbjct: 80  RVRGAMLDELRRMDHLPRRLRADADRVLA-----ARARLEQSLGREPDPVEVAEAAE--- 131

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE-RKNRRN 226
           +   +V  +    +    +                    D      V  ++      RR 
Sbjct: 132 LPAEQVGELLLLASPPVPVE------------------DDLAPAPAVPADEALGAAERRR 173

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L R+++ L  R + +       +  +T   ++    VS  RV Q+ A A K+++  +
Sbjct: 174 ALARTVAALPERLQVLLALYY--DEALTYREIAKVLGVSEPRVCQLHAEAVKRLRALM 229


>gi|90577362|ref|ZP_01233173.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio angustum S14]
 gi|90440448|gb|EAS65628.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio angustum S14]
          Length = 242

 Score = 79.5 bits (195), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 32/240 (13%), Positives = 91/240 (37%), Gaps = 27/240 (11%)

Query: 51  HRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
             L+ +HL LV ++      +        ++   G IGL++A +++      +   +++ 
Sbjct: 26  DLLIRNHLVLVKRVVNQLRHHTSSHCSYEDMQQIGLIGLLEAARRYGDVEDPQFPAFAIC 85

Query: 108 WIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            I+ A+ + + R  W       + + ++    L  +   L           ++ + A  +
Sbjct: 86  RIRGAILDELRRLDWR------SRHTRQQAHELNDITRDLMKQLGRQPTEAEITS-ALGI 138

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +    ++       +  +SL+ L+ +  +  S  +                  E ++ R 
Sbjct: 139 DSENYQLRLQASMASEMQSLDQLLEAGKELDSPLEY--------------NGVEHEHMRR 184

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L  +++ L+ RE+ +       ++ + L  ++    ++  R+ Q+  +A K +   +  
Sbjct: 185 TLEYALTQLSKREQLLLTLFY--QHELNLHEIALVLNLTPPRICQLHKQALKSLNHYLSA 242


>gi|148747769|ref|YP_001285848.1| putative DNA-directed RNA polymerase specialized sigma subunit
           [Geobacillus virus E2]
 gi|113715711|gb|ABI36860.1| putative DNA-directed RNA polymerase specialized sigma subunit
           [Geobacillus virus E2]
          Length = 232

 Score = 79.5 bits (195), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 42/236 (17%), Positives = 86/236 (36%), Gaps = 36/236 (15%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI----SEVVSEGNIGLMQAVKKFDPERGF 99
           +G+     + +  H+RLV  +   Y      I     + +S G I L +A +KFD   G+
Sbjct: 8   NGEWLTLEQAIEKHIRLVHYVVRRYFRSLHEIRIEYDDAISVGVIALARAYQKFDDSHGY 67

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           R +TY++  I   +   + ++ S +   T      L    +++          +L     
Sbjct: 68  RFSTYAVPRIWGEITNCV-KNSSPIHFATRIKNLYLKAKNKQI----------DLSNPTK 116

Query: 160 VAIAKKLNVSESEVISMNCRLAG--DESLNALINSSD-KNSSQWQDWLVYDHDGQEQVLI 216
            +  K+L V+   V+ +   +      SL+ ++  ++ +  +  +D+L  + D       
Sbjct: 117 AS--KELGVTVDVVMEVKKYVDSFYMTSLSDVVFENEREKKTTIEDFLSTEEDFSSAY-- 172

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
                      +   +  L  R + +           T   +  E  V   RV QI
Sbjct: 173 -----------VRDFLDTLPNRHKMVLLM---VMAGYTHVQIGREIGVGSSRVGQI 214


>gi|304413523|ref|ZP_07394996.1| flagellar biosynthesis sigma factor [Candidatus Regiella
           insecticola LSR1]
 gi|304284366|gb|EFL92759.1| flagellar biosynthesis sigma factor [Candidatus Regiella
           insecticola LSR1]
          Length = 246

 Score = 79.5 bits (195), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 38/237 (16%), Positives = 98/237 (41%), Gaps = 32/237 (13%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKKF-DPERGFRLATYSMW 107
           + + ++L LV ++          +    ++     +GL++A++++  P++  + A Y++ 
Sbjct: 32  KYLDAYLPLVKRVVRQLSFQADSVLEREDMQQIALMGLLEALRRYGHPDQ--QFAAYAVH 89

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+ A+ + +               +RL     +    ++ +            IA +L+
Sbjct: 90  RIRGAILDQLREHDW--------RPRRLRQKTHKTNEAIRELGKRLGHEPNYDEIAAELS 141

Query: 168 VSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           ++  E     +       ESL+ L++    N +                  E EE+   +
Sbjct: 142 ITPQEYQEYLLLENAKAMESLDDLLSLETHNDALQSR--------------ELEEQMIIQ 187

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           + L +++  L+ RE+ I      QE  ++L+ ++   E++  RV Q+  +  +K+++
Sbjct: 188 DSLRQAIGTLDDREKLILSLYYQQE--LSLKEIALVLELTEARVCQLNKKIAEKIKK 242


>gi|238796912|ref|ZP_04640416.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           mollaretii ATCC 43969]
 gi|238719172|gb|EEQ10984.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           mollaretii ATCC 43969]
          Length = 241

 Score = 79.5 bits (195), Expect = 6e-13,   Method: Composition-based stats.
 Identities = 41/239 (17%), Positives = 101/239 (42%), Gaps = 19/239 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L   +  LV   A+  +      + + +++  G IGL+ A++ FDP++G  ++ Y  
Sbjct: 13  KDELWPKYGFLVRHEALRLQARLPASVELDDLIQAGAIGLLTAIEHFDPKKGIAISIYIT 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             ++ AM + +     +         +R+  N R +   +Q +   +        +A  +
Sbjct: 73  QKVRWAMIDELRERDWV--------PRRVRSNAREVAAVIQRVEQESGTVATEADVAAAM 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV-LIEKEERKNRR 225
            V+  E   M   LA   S  + + S D+   +  D +       E +  + +  ++N  
Sbjct: 125 GVTLREYQQM---LADTNS--SQLYSLDELQEELSDSIEQPDIQHEMLNPLHELMKENLT 179

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             +++ +  L  R++ +      Q+  + ++ +    E++  RV Q+ ++A K+++  +
Sbjct: 180 KHISQEIKALPERDQLLLNLYYQQD--LNMKEVGILLEITETRVSQLHSQAIKRLRARL 236


>gi|315638331|ref|ZP_07893511.1| DNA-directed RNA polymerase sigma subunit FliA [Campylobacter
           upsaliensis JV21]
 gi|315481598|gb|EFU72222.1| DNA-directed RNA polymerase sigma subunit FliA [Campylobacter
           upsaliensis JV21]
          Length = 231

 Score = 79.1 bits (194), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 40/241 (16%), Positives = 89/241 (36%), Gaps = 28/241 (11%)

Query: 47  LSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
                 LV S++  +  +A          + +++++  G   +++  +++D ++      
Sbjct: 15  KKEQDELVISYMPALRAMAFRLKERLPSSIDVNDLIGVGIEEMIKLSRRYDKDQNDNFWG 74

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           ++   +  +M +Y+ R             +     L+ +   L      N        +A
Sbjct: 75  FARKRVNGSMLDYLRR--------LDVMSRNNRKILKDIDVILDEYFLENECEPDDEYLA 126

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           KKL +    V  +  R A   S    ++   +  S             E   +EK ER  
Sbjct: 127 KKLEIDVERVREV--RAAHAISYTLPLDEQIEMYS-------------EDETLEKIERGE 171

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               +   +  L  R++ I +    +E  ++L+ +S    VS  R+ QI  +  KK++E 
Sbjct: 172 LLEHINEILDTLKERDQLIIQLYYYEE--LSLKEISEILNVSESRISQIHKKLLKKLRER 229

Query: 284 I 284
           +
Sbjct: 230 L 230


>gi|126215794|gb|ABN81017.1| putative sigma factor sigma 70 type group 3 [Rhodococcus opacus]
          Length = 139

 Score = 79.1 bits (194), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 22/114 (19%), Positives = 47/114 (41%), Gaps = 5/114 (4%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              ++T  L L   IA  + G G    ++     +GL++AV +FDP+RGF   +Y++  I
Sbjct: 30  RDEVITRCLPLADHIARRFGGRGEAHEDLRQVARLGLVKAVDRFDPDRGFDFVSYAVPTI 89

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
              ++ Y   +   +++     +         +   +  ++    +      IA
Sbjct: 90  MGEVRRYFRDTGWSMRVPRRMQELHAL-----ITKAVDDLSQELGRSPSASEIA 138


>gi|34733392|gb|AAP82769.1| sigma 70 [Hydrogenobacter hydrogenophilus]
          Length = 310

 Score = 79.1 bits (194), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 35/98 (35%), Positives = 54/98 (55%), Gaps = 3/98 (3%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDL--SAAHRLVTSHLRLVVKIAMGYRGY 71
           + L + + E+RK      +E   +    +E       A   +V  +LRLVV IA  Y   
Sbjct: 214 LSLEKEVKELRKEKGSFPEELDRVMHIIKEGRTKVTKAKQVMVKCNLRLVVSIAK-YVNR 272

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           GL   +++ EGNIGLM+AV K+D  +G++ +TY+ WWI
Sbjct: 273 GLHFLDLIQEGNIGLMKAVDKYDYRKGYKFSTYATWWI 310



 Score = 37.5 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 9/28 (32%), Positives = 19/28 (67%)

Query: 14 IGLSRYIHEIRKIPMLEKQEEYVLAKRY 41
            +  Y+ E+ +IP+L+++EE + AK+ 
Sbjct: 1  DPVKLYLREMGRIPLLKREEEIMYAKQI 28


>gi|213422468|ref|ZP_03355534.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. E01-6750]
          Length = 79

 Score = 79.1 bits (194), Expect = 7e-13,   Method: Composition-based stats.
 Identities = 26/76 (34%), Positives = 41/76 (53%), Gaps = 1/76 (1%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN-PVTLENLSSEFEVSRERVR 270
              + +    +   N LT +M  L+ R + I  AR L E+   TL+ L+  + VS ERVR
Sbjct: 4   ADGIEDDNWEEQAANRLTDAMQGLDERSQDIIRARWLDEDNKSTLQELADRYGVSAERVR 63

Query: 271 QIEARAFKKVQESIQK 286
           Q+E  A KK++ +I+ 
Sbjct: 64  QLEKNAMKKLRAAIEA 79


>gi|89072296|ref|ZP_01158875.1| flagellar-specific transcription initiation factor sigma, LafS
           [Photobacterium sp. SKA34]
 gi|89051828|gb|EAR57280.1| flagellar-specific transcription initiation factor sigma, LafS
           [Photobacterium sp. SKA34]
          Length = 242

 Score = 79.1 bits (194), Expect = 8e-13,   Method: Composition-based stats.
 Identities = 33/240 (13%), Positives = 94/240 (39%), Gaps = 27/240 (11%)

Query: 51  HRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
             L+ +HL LV ++      +        ++   G IGL++A +++      +   +++ 
Sbjct: 26  DLLIRNHLVLVKRVVNQLRHHTSSHCSYEDMQQIGLIGLLEAARRYGNVEDPQFPAFAVC 85

Query: 108 WIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            I+ A+ + + R  W       + + ++    L  +   L           ++ + A  +
Sbjct: 86  RIRGAILDELRRLDWR------SRHTRQQAHELNDITRDLMKQLGRQPTEAEITS-ALGI 138

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +    ++    C  +  +SL+ L+ +  +  +  +                  E ++ R 
Sbjct: 139 DSENYQLRLQACMASEMQSLDQLLEAGKELDAPLEY--------------NGVEHEHMRR 184

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L  +++ L+ RE+ +       ++ + L  ++   +++  R+ Q+  +A K +  S+  
Sbjct: 185 TLEYALTQLSRREQLLLTLFY--QHELNLHEIALVLDLTPPRICQLHKQALKSLNHSLSA 242


>gi|295097196|emb|CBK86286.1| RNA polymerase sigma factor, FliA/WhiG family/RNA polymerase sigma
           factor, sigma-70 family [Enterobacter cloacae subsp.
           cloacae NCTC 9394]
          Length = 259

 Score = 78.7 bits (193), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 34/213 (15%), Positives = 90/213 (42%), Gaps = 14/213 (6%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++  G++G + A+  FDP++G  L  +    +K A+ + +  S  +         +
Sbjct: 57  ELDDLIQAGSMGFLSAIDSFDPKKGVALNAWISQRVKWALMDELRESDWV--------PR 108

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
           R+  + R +   +Q I            IA+++ VS  E   M      D + + + +  
Sbjct: 109 RVRSHSREIVSLIQQIEQEKGGEATEADIAERMGVSLKEFQQMLA----DNNSSQMYSID 164

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           +   +    W   D +  +   + +  ++N    +   + ++  RE++I +     +  +
Sbjct: 165 ELQENYSDSWESNDGENAQLNPLNEAIQENLIANIAEHIRMIPRREQQILQ--FYYQQDL 222

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            ++ +     V+  RV Q+ + A K+++  + +
Sbjct: 223 NMKEIGLILGVTETRVSQLHSLAIKRLRSRMDR 255


>gi|83716542|ref|YP_438382.1| RNA polymerase sigma factor for flagellar operon FliA [Burkholderia
           thailandensis E264]
 gi|83650367|gb|ABC34431.1| RNA polymerase sigma factor for flagellar operon FliA [Burkholderia
           thailandensis E264]
          Length = 369

 Score = 78.7 bits (193), Expect = 9e-13,   Method: Composition-based stats.
 Identities = 40/240 (16%), Positives = 99/240 (41%), Gaps = 31/240 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           A  R +  +  +V + A   +      L + ++   G +GL++A++++          Y+
Sbjct: 154 AEQRWLVEYAPIVKRAARQLKSQAVGMLTLDDIEQIGLMGLLEALRRYG-MPDAAFPCYA 212

Query: 106 MWWIKAAMQEYILRS-WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
              ++ A+ + + R  W    +   A+         R +   + +  +  +      ++ 
Sbjct: 213 ATRVRGAILDELRRHDWRPRSVRLEAH---------RTRDCERELCRSLGREPTEAEVSS 263

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            L +S +E                 + +++  +    D ++ D     +   E++  +  
Sbjct: 264 ALGISTAEYRER-------------VMANNAEAMASFDSVLDDDALTHEESPERQIVR-- 308

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L ++++ LN RE+R+ +     E  ++L  ++S  E++  RV QI   A KK++E +
Sbjct: 309 RRCLEQALARLNEREQRVIQLYY--EFDLSLREIASVLELTEARVCQINKAALKKMREVL 366


>gi|257470879|ref|ZP_05634969.1| RNA polymerase sigma factor [Fusobacterium ulcerans ATCC 49185]
 gi|317065081|ref|ZP_07929566.1| RNA polymerase sigma factor rpoD [Fusobacterium ulcerans ATCC
           49185]
 gi|313690757|gb|EFS27592.1| RNA polymerase sigma factor rpoD [Fusobacterium ulcerans ATCC
           49185]
          Length = 284

 Score = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 39/181 (21%), Positives = 73/181 (40%), Gaps = 14/181 (7%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
            E  +  Y+ E+  + ++  ++E    K  RE    +   +++  +L  V  IA  Y   
Sbjct: 54  AEETVIDYLEELSNMEVISDEDENNYLKDLRE----ADKEKVIVKNLNEVASIAFNYVKN 109

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           G+   +VV EG +GL++AV  FDP+R      YS +WI   +  YI    + ++      
Sbjct: 110 GIAYMDVVQEGTVGLIKAVDYFDPDRNGDFKNYSKYWIAREIVLYIENKVADIRNEFKNF 169

Query: 132 QKRLFFNLRRLKGHLQAI----------TDNNLKPEQVVAIAKKLNVSESEVISMNCRLA 181
            K    N  +   H               ++ L   + +   +K+     +  S+  RL+
Sbjct: 170 FKNKKENFGKEHHHEHEEEMHHDEVYLKEEDLLPTVEAIEKREKMVEKRIDFFSLENRLS 229

Query: 182 G 182
            
Sbjct: 230 E 230


>gi|225375310|ref|ZP_03752531.1| hypothetical protein ROSEINA2194_00935 [Roseburia inulinivorans DSM
           16841]
 gi|225212799|gb|EEG95153.1| hypothetical protein ROSEINA2194_00935 [Roseburia inulinivorans DSM
           16841]
          Length = 196

 Score = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 27/94 (28%), Positives = 50/94 (53%), Gaps = 1/94 (1%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           ++E    K+ + +GDL A + L+  ++RLV  +A  Y+     + +++S G IGL++AV+
Sbjct: 2   EQESECLKKMK-NGDLEARNELIERNMRLVAHVAKKYQNPEDEMEDLISIGTIGLIKAVE 60

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            +  + G RLATY+   I   +  +        K
Sbjct: 61  TYKEDYGSRLATYAARCIDNELLMHFRAKKKTSK 94



 Score = 59.4 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 23/106 (21%), Positives = 46/106 (43%), Gaps = 4/106 (3%)

Query: 181 AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           + + SL   I +  + +      +V   D     L+E++ +  R N +      L+ RE 
Sbjct: 93  SKEVSLYEPIGTDKEGNQIQLLDVVVSEDEDVVELLEQDRKVRRLNEIIP--QTLSGREL 150

Query: 241 RIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            I   R        +T   ++ +  +SR  V +IE RA +K++++ 
Sbjct: 151 FIIINRYGLYGKKTMTQREIARKLGISRSYVSRIEKRAIEKLRQAF 196


>gi|327478799|gb|AEA82109.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pseudomonas stutzeri
           DSM 4166]
          Length = 256

 Score = 78.7 bits (193), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 42/236 (17%), Positives = 93/236 (39%), Gaps = 30/236 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           A  R +  +L LV +I           L   ++   G IGL++ ++++  E   +   ++
Sbjct: 24  AEQRWLMQYLPLVKRIVRQLSLQANQVLDREDMEQIGMIGLLEGLRRYG-EPDEQFGRFA 82

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
              I+ A+ + + R             +++     +++  ++ +T           I   
Sbjct: 83  ALRIRGAILDELRRQDW--------RPRQVRQQAHKVRDAIRELTRQLGHTPSDEEIKAF 134

Query: 166 LNVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
             + E +  +     + +  ESL+ L+ S               H+         EER  
Sbjct: 135 TGLDEKDYQAFLWADSSEAIESLDELLQSG--------------HEHFPDAAELFEERLL 180

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           +  +L +++S L+ RER +       ++ ++L+ ++   EVS  RV Q+  +A  K
Sbjct: 181 KERLLEQALSRLDERERLVLTLYY--QHELSLKEIALVLEVSDARVCQLSKQAIGK 234


>gi|15643664|ref|NP_228710.1| RNA polymerase sigma-28 factor, putative [Thermotoga maritima MSB8]
 gi|4981438|gb|AAD35983.1|AE001755_6 RNA polymerase sigma-28 factor, putative [Thermotoga maritima MSB8]
          Length = 220

 Score = 78.3 bits (192), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 39/238 (16%), Positives = 98/238 (41%), Gaps = 31/238 (13%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              ++ S L  + +IA        P   + +++ EG +  + +++++DP +     T+ M
Sbjct: 4   KESVIRSLLPFIKRIAEDLAQTLPPNVEVDDLIQEGIVAALSSLERYDPSK-ASFTTFIM 62

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +K AM +Y+ +   + +            NLR+    ++ +   + +      IA+K 
Sbjct: 63  KRVKGAMYDYLRKIDWMPR------------NLRKNVKMIERVIYESEEFPSDEEIARKT 110

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   EV+     +   + L               D +  +   + +   E   R+    
Sbjct: 111 GLELKEVVRARNEMMRKQLL-------------MIDAMEDEIVLKTEGPDENAYRELLVE 157

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + +++  L+ +E+ +   R   E  ++L+ ++    VS  RV QI +++  K+++ +
Sbjct: 158 EMKKAIEKLSDKEKLVLSLRF--EKGLSLKEIARVLGVSESRVSQIISKSLLKIKKEV 213


>gi|30263977|ref|NP_846354.1| prophage LambdaBa02, RNA polymerase sigma-F factor, putative
           [Bacillus anthracis str. Ames]
 gi|47529410|ref|YP_020759.1| prophage LambdaBa02, RNA polymerase sigma-F factor [Bacillus
           anthracis str. 'Ames Ancestor']
 gi|30258621|gb|AAP27840.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. Ames]
 gi|47504558|gb|AAT33234.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. 'Ames Ancestor']
          Length = 299

 Score = 78.3 bits (192), Expect = 1e-12,   Method: Composition-based stats.
 Identities = 46/238 (19%), Positives = 93/238 (39%), Gaps = 30/238 (12%)

Query: 51  HRLVTSHLRLVVKIAMGY---------RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
              +  + RLV      Y         +   L + +++  G +GL+ A + F  E GF+ 
Sbjct: 5   DDFMKKYSRLVYYYVNKYFSNIAKAIEQETNLNMDDLIQSGMLGLVTARRDFKTELGFKF 64

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
            T+++  I   +++ +  S    KI  T     +   + R+K          L  E+V +
Sbjct: 65  TTFAVPRILGYIRKAVRDSQ---KIRITNEVYEIKGKISRMK----------LHDEEVES 111

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           IAK L VS  +V +         SL   +N          +  + D      +     + 
Sbjct: 112 IAKLLEVSVRDVKTAKEFNPRTISLQTPLNKEVNKEKVTLENTLIDKKTSMTL-----DD 166

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
             ++ ++T  +S L  +E+ ++E   L    +T   +     V++ ++ +I    +KK
Sbjct: 167 VIKKMIITAFLSTLCSKEKFVWE---LHAKNMTQAAIGKRLGVTQTQISRILKGIYKK 221


>gi|330809249|ref|YP_004353711.1| RNA polymerase sigma factor for flagellar regulon FliA [Pseudomonas
           brassicacearum subsp. brassicacearum NFM421]
 gi|327377357|gb|AEA68707.1| Putative RNA polymerase sigma factor for flagellar regulon FliA
           [Pseudomonas brassicacearum subsp. brassicacearum
           NFM421]
          Length = 241

 Score = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 41/253 (16%), Positives = 92/253 (36%), Gaps = 43/253 (16%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA----MGYRGYGLPISEVVSEGNIGLMQ 88
           +E  L + + +    +A  RL   + + +  I       Y        + V+  +IGL+Q
Sbjct: 16  DEQALWRNWLDSKTEAARSRLFFFYGQWLRMIVGLLYSRYPHPLAEWGDYVNLASIGLLQ 75

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A+ +F+PE   R  +Y+  ++K  + + +              ++     L  + G +Q 
Sbjct: 76  AIDRFNPELNTRFQSYAEPYVKGNVLKGLS-------CYVGDRRRYYRERLESISG-MQE 127

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                   EQV  +A  L                                 + +  + D 
Sbjct: 128 EGRAESDLEQVANVAIGLAF-----------------------------GLFLESGIVDP 158

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           + ++   +   E +   + L   + +L+  E+R+ +        ++   +S    +S+ R
Sbjct: 159 EPKDNNPLSLYEVERESDTLEECVKLLSANEQRVIQGHY--HQHLSFTEISELMGISKSR 216

Query: 269 VRQIEARAFKKVQ 281
           V Q+ A+A K ++
Sbjct: 217 VSQLHAQALKNIR 229


>gi|167626171|ref|YP_001676465.1| flagellar biosynthesis sigma factor [Shewanella halifaxensis
           HAW-EB4]
 gi|167356193|gb|ABZ78806.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella
           halifaxensis HAW-EB4]
          Length = 240

 Score = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 42/240 (17%), Positives = 97/240 (40%), Gaps = 31/240 (12%)

Query: 52  RLVTSHLRLVV---KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           +++  +L LV         + G  L I ++   G + L++A +++  E      +++   
Sbjct: 24  KVMVQYLPLVKRSVSQLRSHCGSVLAIEDMEQIGMMALLEAARRYPGEYDNGFLSFAGQR 83

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+ + + R               L   +R+L   L+       +      +A+ + +
Sbjct: 84  IRGAILDELRRQ-DWRPRPVRQQAHELNDTIRKLTRLLE-------REPSDKEVAEAMGL 135

Query: 169 SESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +E E          +   SL+ LI+             V ++D  EQ         + + 
Sbjct: 136 NEVEYRERLFASQSESMRSLDELISEGGN--------FVDNNDMLEQF--------SAKE 179

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L +++S LN RE+ I       ++ + L+ +++   ++  R+ Q+  +A K++Q   Q+
Sbjct: 180 CLFQAISKLNKREQLILSLYY--QHELNLKEIAATLGLTETRICQLHKQAVKQLQNIYQQ 237


>gi|238762342|ref|ZP_04623313.1| Lateral flagellar sigma factor 28 protein (FliA-like) [Yersinia
           kristensenii ATCC 33638]
 gi|238699327|gb|EEP92073.1| Lateral flagellar sigma factor 28 protein (FliA-like) [Yersinia
           kristensenii ATCC 33638]
          Length = 231

 Score = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 37/235 (15%), Positives = 90/235 (38%), Gaps = 30/235 (12%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           + + ++L LV +I          +    ++     +GL++A++++    G + A Y++  
Sbjct: 19  KYLQAYLPLVKRIVRQLSFQADSVIGKEDMQQIALMGLLEALRRYGHPDG-QFAAYAVHR 77

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+ + +               +RL     +    ++ +            IA  L +
Sbjct: 78  IRGAVLDQLREHDW--------RPRRLRQKTHKTNEAIRQLAKKLGHEPSFEEIATALQL 129

Query: 169 SESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +  E     +    +G ESL+              + L  D         E EE     +
Sbjct: 130 TAEEYQEYLLLESASGMESLD--------------EILSLDTPTDALQSRELEESIIIED 175

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L  +++ L  RE+ I      QE  ++++ ++   +++  R+ Q+  +  +K++
Sbjct: 176 NLNHAIASLEKREQMILHLYYQQE--MSMKEIAQVLDLTEARICQLNKKLVQKIK 228


>gi|294102492|ref|YP_003554350.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Aminobacterium colombiense DSM 12261]
 gi|293617472|gb|ADE57626.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Aminobacterium colombiense DSM 12261]
          Length = 196

 Score = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 38/159 (23%), Positives = 68/159 (42%), Gaps = 4/159 (2%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L  ++E +L  R   H D  A   L+ S+  LV  +A  +        +++ EG + L++
Sbjct: 14  LSPEKEEMLWARC--HLDDDAREELIISYRPLVFWLAQKFYVSPSLYPDLIQEGMVALIK 71

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           +V KF+PER  +  TY+ + IK  M  ++ RS +   I       R+  N       L  
Sbjct: 72  SVDKFEPERQLKFTTYAFYRIKGQMVNFLQRSEAKAPIPMDDEDMRIQDNFSYETYDLLL 131

Query: 149 ITDNNLK--PEQVVAIAKKLNVSESEVISMNCRLAGDES 185
                +K  P++   I +++     E   +  +   D S
Sbjct: 132 TLSQEIKNLPDREGEIVREMFYKGREAKEVADKQDLDIS 170


>gi|312126664|ref|YP_003991538.1| RNA polymerase sigma factor, sigma-70 family [Caldicellulosiruptor
           hydrothermalis 108]
 gi|311776683|gb|ADQ06169.1| RNA polymerase sigma factor, sigma-70 family [Caldicellulosiruptor
           hydrothermalis 108]
          Length = 206

 Score = 77.9 bits (191), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 44/257 (17%), Positives = 96/257 (37%), Gaps = 60/257 (23%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L   E+  L  R ++ GD  AA  L+ ++  L++  A  Y    +   ++  EG   ++Q
Sbjct: 4   LSFDEQKELVCRIKQ-GDKKAAEELICAYEPLIISFAAKYNKPEI-FEDLKQEGYCAILQ 61

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A +KF+   G    T ++++IK  M   + R    ++                       
Sbjct: 62  AARKFNVSLGVSFITLAVYYIKRNMDRCVNRD-RTIRPP--------------------- 99

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                           K +    +VISM+  +               N++ + D  +   
Sbjct: 100 --------------FNKPSTEIPQVISMDAPV---------------NTNNYDDEELRVK 130

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D  +    + EE+      L + + +L+  ER+I   R       + + ++ +  ++   
Sbjct: 131 DTIQSSTADVEEKVMYNETLRKLVELLSNEERKILLLRL---KQYSYKEIAEKLGLTE-- 185

Query: 269 VRQIEARAFKKVQESIQ 285
            +Q+  +A +K++  +Q
Sbjct: 186 -KQVATKA-QKIRAKLQ 200


>gi|325523159|gb|EGD01550.1| RpoD family RNA polymerase sigma factor [Burkholderia sp. TJI49]
          Length = 126

 Score = 77.5 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 21/120 (17%), Positives = 49/120 (40%), Gaps = 7/120 (5%)

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           +++  ++V+ +   +    S +  ++           +     D    +  +       R
Sbjct: 1   MDLPLAKVLDLMAIVREPVSTDVPVSPDGD-----MTFGEVVPDQATPLPEDAAAATQLR 55

Query: 226 NMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +  ++  L  RE  +   R      + V+L ++  +  +S ERVRQIEA A ++++ S
Sbjct: 56  AAMAATLGGLPAREATVLRLRYGIGTADGVSLRDIGRQLNLSAERVRQIEASALERIRAS 115


>gi|237734715|ref|ZP_04565196.1| sporulation sigma factor sigG [Mollicutes bacterium D7]
 gi|229382043|gb|EEO32134.1| sporulation sigma factor sigG [Coprobacillus sp. D7]
          Length = 97

 Score = 77.5 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 21/79 (26%), Positives = 41/79 (51%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L   E Y L   Y+   + +   RLV  + +LV+ +A  + G    + ++   G IGL++
Sbjct: 18  LTTDETYKLIDEYQATKNEAIKDRLVNDNTKLVLSMARRFYGREDSMDDLFQVGMIGLIK 77

Query: 89  AVKKFDPERGFRLATYSMW 107
           A++ F+   G + +TY++ 
Sbjct: 78  AIENFNTSFGLKFSTYAVP 96


>gi|224437149|ref|ZP_03658130.1| flagellar biosynthesis sigma factor [Helicobacter cinaedi CCUG
           18818]
 gi|313143612|ref|ZP_07805805.1| flagellar biosynthesis sigma factor [Helicobacter cinaedi CCUG
           18818]
 gi|313128643|gb|EFR46260.1| flagellar biosynthesis sigma factor [Helicobacter cinaedi CCUG
           18818]
          Length = 235

 Score = 77.5 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 41/241 (17%), Positives = 96/241 (39%), Gaps = 28/241 (11%)

Query: 47  LSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
             A   L   +L  V  +A          + ++++VS G   L++  +++D         
Sbjct: 15  KYAQDELALQYLPAVKAMAFRLKERLPSSIEMADLVSIGTEELIKLARRYDSSLNDSFWG 74

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   +  AM +Y+ RS  ++   +    K + + + +     Q              +A
Sbjct: 75  YAKTRVNGAMLDYL-RSLDVLSRASRKLVKAIDYEISKYFNDYQE-------EPSDEYLA 126

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           K LN   +++     R+A D    AL+   ++ ++   + ++ D            ++  
Sbjct: 127 KILNEDVAKIKE--ARVASDV--YALVPIDEQYNAICGENILED-----------VQKDE 171

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
              ++   +  L  RE+ I +    +E  + L+ +S   E++  R+ QI     KK++++
Sbjct: 172 LMEIVHNVLKKLGKREQMIIQLYYFEE--LNLKEISEILEITESRISQITKEVIKKIRQA 229

Query: 284 I 284
           +
Sbjct: 230 L 230


>gi|222530382|ref|YP_002574264.1| putative RNA polymerase, sigma 70 family subunit
           [Caldicellulosiruptor bescii DSM 6725]
 gi|222457229|gb|ACM61491.1| putative RNA polymerase, sigma 70 family subunit
           [Caldicellulosiruptor bescii DSM 6725]
          Length = 210

 Score = 77.5 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 44/241 (18%), Positives = 83/241 (34%), Gaps = 56/241 (23%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L   E+  L  R ++ GD  AA  L+ ++  L++ +A  Y    +   ++  EG + ++Q
Sbjct: 8   LSFDEQKELIGRIKK-GDKEAAETLIMAYEPLIISLAAKYNKPDI-FEDLKQEGAVAILQ 65

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A +KFD   G    T ++++IK  M          ++                       
Sbjct: 66  AAQKFDESLGVSFVTLAIYYIKRNMDR-CTNKSRTIRPP--------------------- 103

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                           K N    +VISM   +               N++   D      
Sbjct: 104 --------------FNKPNTEIPQVISMESVI---------------NTNSHADDEELKV 134

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
               Q     EE+      L R + +L+  ER+I   R       + + ++ E  ++ ++
Sbjct: 135 KDTVQDTANVEEQAMYNETLQRLIKMLSDEERKILLLRL---KQYSFKEIAKELGLTEKQ 191

Query: 269 V 269
           V
Sbjct: 192 V 192


>gi|108756900|ref|YP_630657.1| FliA/WhiG family RNA polymerase sigma factor [Myxococcus xanthus DK
           1622]
 gi|108460780|gb|ABF85965.1| RNA polymerase sigma factor, FliA/WhiG/SigD family [Myxococcus
           xanthus DK 1622]
          Length = 278

 Score = 77.5 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 40/235 (17%), Positives = 90/235 (38%), Gaps = 25/235 (10%)

Query: 48  SAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
                ++  +   V  +A          L + E+++ G IGL++A ++FDP+ G    T+
Sbjct: 5   DDRQVILEKYGPYVRSLAATVRKQFNAQLELDELLAYGQIGLLEAAERFDPKVGANFLTF 64

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           + + IK A+ + + +   L       +  R  +   R   +L  ++D             
Sbjct: 65  AHYRIKGAIFDGLRKMGVL-----RGSDARNAYVGERAAAYLGNLSDRE------AGAGN 113

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           + +  + +V  ++  + G   + A        +    + L  D          + E++  
Sbjct: 114 RGSSFDDDVNDISDAVTGLAMVFATSIEGADTAGYTDESLPVDI---------RMEQEQL 164

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           +  +  ++  L  +ER++      Q    TLE   +E   S+    ++ ARA  +
Sbjct: 165 KTRVRAAIEKLPEKERKLLMGYYFQG--RTLEEAGAEIGQSKSWASRLHARAIDR 217


>gi|34557955|ref|NP_907770.1| flagellar biosynthesis sigma factor [Wolinella succinogenes DSM
           1740]
 gi|34483673|emb|CAE10670.1| RNA POLYMERASE SIGMA FACTOR [Wolinella succinogenes]
          Length = 235

 Score = 77.5 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 43/238 (18%), Positives = 96/238 (40%), Gaps = 28/238 (11%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L  S+L  V  +A   +      +  +++VS G   L++  ++++         ++ 
Sbjct: 18  QDELAVSYLPAVKAMAYRLKERLPSSIDTADLVSIGAEELIKLSRRYNEALNDSFWGFAK 77

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             ++ AM +Y+ RS  +V  G     K       ++   +    + +        +A+ L
Sbjct: 78  TRVQGAMLDYL-RSLDVVSRGNRKLIK-------QIDVEISHYMNEHSSEPSDEYLAEVL 129

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
                ++     ++A D  +   I          +D L   H+   +  IE+EE      
Sbjct: 130 GEDIKKIRE--AKIASDIYVLMPI----------EDQLSALHEEATEGRIEQEELV---G 174

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +++  +  L+ RE+ I +    +E  + L+ +S   E++  R+ QI     KK++E +
Sbjct: 175 IISEILESLSEREQLIIQLYYFEE--LNLKEISEVLEITESRISQIHKEVIKKIRERL 230


>gi|161546627|ref|NP_860677.2| flagellar biosynthesis sigma factor [Helicobacter hepaticus ATCC
           51449]
          Length = 235

 Score = 77.5 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 38/241 (15%), Positives = 92/241 (38%), Gaps = 28/241 (11%)

Query: 47  LSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
             A   L   +L  V  +A          + ++++VS G   L++  +++D         
Sbjct: 15  KYAQDELALQYLPAVKAMAFRLKERLPSSIEMADLVSIGTEELIKLARRYDSSLNDSFWG 74

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           ++   +  AM +Y+     L +      +   +   +    H +  +D  L       IA
Sbjct: 75  FAKTRVNGAMLDYLRSLDVLSRANRKLVKSIDYEVSKYFNEHQEEPSDEYLAKVLKEDIA 134

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           K              R+A D  + AL+   ++ ++              + ++E  ++  
Sbjct: 135 KI----------KEARMASD--IYALVPIDEQYNAI-----------CAENILEDVQKDE 171

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
              ++   +  L  RE+ I +    +E  ++L+ +S   +++  R+ QI     KK++++
Sbjct: 172 LMEIIFNVLKKLGKREQMIIQLYYFEE--LSLKEISEILDITESRISQITKEIVKKIRQA 229

Query: 284 I 284
           +
Sbjct: 230 L 230


>gi|13446369|gb|AAK20925.1| RNA polymerase sigma factor [Aeromonas hydrophila]
          Length = 237

 Score = 77.5 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 33/237 (13%), Positives = 90/237 (37%), Gaps = 29/237 (12%)

Query: 51  HRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
             ++T +L LV + A              ++   G +GL++A +++D E   +   Y+  
Sbjct: 22  QAILTRYLPLVKRAASHLRSQVSACFDQEDMEQVGMMGLLEAWRRYDSEPDPQFERYAFK 81

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+ AM + + R     ++ T   Q       +R       + +   +      +A  LN
Sbjct: 82  RIRGAMLDELRRLDW--RLPTLRQQVHSHNQAQR------ELYNRLGRSPTEQELAVSLN 133

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
            +  EV  +                +  + ++    L    +   +    + +  +    
Sbjct: 134 CTVEEVRQL----------------AYASQAEALQSLEEWLENGGKAPATESDDVDMAMT 177

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +++ ++ L+ RE+ +      QE  + ++ ++    ++  RV Q+  +   ++++ +
Sbjct: 178 ISKVLTSLDKREQLLLSLYYQQE--LNMKEIALVLGLTESRVCQLHKQCVLQLKQRL 232


>gi|49186821|ref|YP_030073.1| prophage LambdaBa02, RNA polymerase sigma-F factor [Bacillus
           anthracis str. Sterne]
 gi|65321304|ref|ZP_00394263.1| COG1191: DNA-directed RNA polymerase specialized sigma subunit
           [Bacillus anthracis str. A2012]
 gi|165872143|ref|ZP_02216782.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A0488]
 gi|167641041|ref|ZP_02399298.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A0193]
 gi|170688784|ref|ZP_02879988.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A0465]
 gi|170705857|ref|ZP_02896320.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A0389]
 gi|177654265|ref|ZP_02936194.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A0174]
 gi|190565820|ref|ZP_03018739.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis Tsiankovskii-I]
 gi|227813117|ref|YP_002813126.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. CDC 684]
 gi|229600567|ref|YP_002868208.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A0248]
 gi|254683672|ref|ZP_05147532.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. CNEVA-9066]
 gi|254721508|ref|ZP_05183297.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A1055]
 gi|254736016|ref|ZP_05193722.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. Western North America USA6153]
 gi|254754314|ref|ZP_05206349.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. Vollum]
 gi|254757995|ref|ZP_05210022.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. Australia 94]
 gi|49180748|gb|AAT56124.1| prophage LambdaBa02, RNA polymerase sigma-F factor, putative
           [Bacillus anthracis str. Sterne]
 gi|164712090|gb|EDR17628.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A0488]
 gi|167511091|gb|EDR86480.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A0193]
 gi|170129397|gb|EDS98261.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A0389]
 gi|170667300|gb|EDT18059.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A0465]
 gi|172080755|gb|EDT65836.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A0174]
 gi|190562739|gb|EDV16705.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis Tsiankovskii-I]
 gi|227006745|gb|ACP16488.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. CDC 684]
 gi|229264975|gb|ACQ46612.1| putative prophage LambdaBa02, RNA polymerase sigma-F factor
           [Bacillus anthracis str. A0248]
          Length = 314

 Score = 77.5 bits (190), Expect = 2e-12,   Method: Composition-based stats.
 Identities = 46/238 (19%), Positives = 93/238 (39%), Gaps = 30/238 (12%)

Query: 51  HRLVTSHLRLVVKIAMGY---------RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
              +  + RLV      Y         +   L + +++  G +GL+ A + F  E GF+ 
Sbjct: 20  DDFMKKYSRLVYYYVNKYFSNIAKAIEQETNLNMDDLIQSGMLGLVTARRDFKTELGFKF 79

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
            T+++  I   +++ +  S    KI  T     +   + R+K          L  E+V +
Sbjct: 80  TTFAVPRILGYIRKAVRDSQ---KIRITNEVYEIKGKISRMK----------LHDEEVES 126

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           IAK L VS  +V +         SL   +N          +  + D      +     + 
Sbjct: 127 IAKLLEVSVRDVKTAKEFNPRTISLQTPLNKEVNKEKVTLENTLIDKKTSMTL-----DD 181

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
             ++ ++T  +S L  +E+ ++E   L    +T   +     V++ ++ +I    +KK
Sbjct: 182 VIKKMIITAFLSTLCSKEKFVWE---LHAKNMTQAAIGKRLGVTQTQISRILKGIYKK 236


>gi|57168743|ref|ZP_00367874.1| probable RNA polymerase sigma factor for flagellar operon Cj0061c
           [Campylobacter coli RM2228]
 gi|305432515|ref|ZP_07401677.1| DNA-directed RNA polymerase sigma subunit FliA [Campylobacter coli
           JV20]
 gi|57019790|gb|EAL56473.1| probable RNA polymerase sigma factor for flagellar operon Cj0061c
           [Campylobacter coli RM2228]
 gi|304444554|gb|EFM37205.1| DNA-directed RNA polymerase sigma subunit FliA [Campylobacter coli
           JV20]
          Length = 230

 Score = 77.2 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 37/241 (15%), Positives = 92/241 (38%), Gaps = 28/241 (11%)

Query: 47  LSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
                +LV S++  +  +A          + +++++S G   +++  +++D E+      
Sbjct: 14  KDEQDQLVLSYMPALRAMAFRLKERLPSSIDVNDLISIGVEEMIKLSRRYDKEQNDSFWG 73

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           ++   +  AM +++     + +      +          + H +              +A
Sbjct: 74  FARKRVNGAMLDFLRSLDVMSRNNRKIIKDIDILIDEYFREHEEE--------PDDEYLA 125

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           KKL++   ++  +  R A   S    I+                    E   +EK E++ 
Sbjct: 126 KKLDLDVEKIKEV--RTAHAISYTLPIDD-------------QLELYNEDDTLEKLEKEQ 170

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               +   +  L  R++ I +    +E  ++L+ +S   E+S  R+ QI  +  KK++E 
Sbjct: 171 LLEKIHEVLEDLKERDQLIIQLYYYEE--LSLKEISEILEISESRISQIHKKLLKKLRER 228

Query: 284 I 284
           +
Sbjct: 229 L 229


>gi|306813287|ref|ZP_07447480.1| flagellar biosynthesis sigma factor [Escherichia coli NC101]
 gi|305854050|gb|EFM54489.1| flagellar biosynthesis sigma factor [Escherichia coli NC101]
          Length = 239

 Score = 77.2 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 41/268 (15%), Positives = 105/268 (39%), Gaps = 47/268 (17%)

Query: 22  EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEV 78
           E    P+L  Q+E    +                ++L LV K+           +   ++
Sbjct: 11  EFAAAPVLTPQQESHYLQ----------------AYLPLVRKVVRQLAPQCNCIIDRQDM 54

Query: 79  VSEGNIGLMQAVKKFD-PERGFRLATYSMWWIKAAMQEYI-LRSWSLVKIGTTANQKRLF 136
                +GL+ A++++  P+ G   A Y++  I+ A+ + +    W           ++L 
Sbjct: 55  EQTALMGLLNAIRRYGLPDEG--FAGYAVHRIRGAILDELRALDWRP---------RQLR 103

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
               ++K  ++          +   +A++  +S  + +    +L G E+L          
Sbjct: 104 QKYHQMKDLIRETRKKLGHEPEWQELAEE-GISHEDYLEYQ-QLEGAETL---------- 151

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
            +   + L  +  G      E E++   + ML  ++S L+ +E+ I       ++ + L+
Sbjct: 152 -ASLDELLNGEGPGIPLAGRELEDQFVTQQMLQHALSQLSEKEQLILSMYY--QHEMNLK 208

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
            ++    ++  R+ Q+  +  +K+++ +
Sbjct: 209 EIALVLGLTEARICQLNKQIAQKIRDFV 236


>gi|109947668|ref|YP_664896.1| flagellar biosynthesis sigma factor [Helicobacter acinonychis str.
           Sheeba]
 gi|109714889|emb|CAJ99897.1| putative RNA polymerase sigma factor for flagellar operon
           [Helicobacter acinonychis str. Sheeba]
          Length = 258

 Score = 77.2 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 49/271 (18%), Positives = 107/271 (39%), Gaps = 35/271 (12%)

Query: 21  HEIRKIPMLEKQE---EYVL-AKRYREHGDLSAAHRLVTSHLRLVVKIA---MGYRGYGL 73
            EI++    EK E   E VL A   ++H    A   L   +L  V  +A     +    +
Sbjct: 11  QEIQQTEPSEKSEKNKEKVLNAYDKQQHHHQDA---LAIQYLPAVRAMAFRLKEHLPGSI 67

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
             +++VS G   L++  ++++         Y+   +  AM +Y+ RS  +V   +    K
Sbjct: 68  DFNDLVSIGTEELIKLARRYESALNDSFWGYAKTRVNGAMLDYL-RSLDVVSRSSRKLIK 126

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            + F             + + K      +A+ L  +  ++            + AL+   
Sbjct: 127 SIDF-------ETTKYLNEHGKEPSDEYLAQALGENIEKIREAKTA----SDIYALVPID 175

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           ++ ++  QD +            +K E +     + + ++ ++ RE+ + +    +E  +
Sbjct: 176 EQFNAIEQDEI-----------TKKIEVEELLEHVQKVLNQMSEREQMLIQLYYFEE--L 222

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L  +     ++  R+ QI   A KKV++S+
Sbjct: 223 NLSEIKEILGITESRISQIIKEAIKKVRQSL 253


>gi|32490948|ref|NP_871202.1| flagellar biosynthesis sigma factor [Wigglesworthia glossinidia
           endosymbiont of Glossina brevipalpis]
 gi|25166154|dbj|BAC24345.1| fliA [Wigglesworthia glossinidia endosymbiont of Glossina
           brevipalpis]
          Length = 246

 Score = 77.2 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 44/217 (20%), Positives = 87/217 (40%), Gaps = 17/217 (7%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++  G IG + A+  FD  +G    TY+   ++ +M + + R    V      N +
Sbjct: 45  ELDDLIQAGMIGFLSAIDNFDINQGASFPTYARSRVRWSMLDEL-RERDWVPRSVRRNAR 103

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNALIN 191
            +   ++RL+  L               IAK+L +S  E   M          SL+ L N
Sbjct: 104 DIASAIQRLEQRL-------GSSASEKQIAKELKISLCEYQKMLQETNCGQIFSLDELNN 156

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
                S      + +  D  + +LI   ++K  + +       L  RE+ +      QE 
Sbjct: 157 QEIIGSFGMNIPIDHSKDPCQLLLINSLKKKIIKEI-----QKLPKREKILLNLYYQQE- 210

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            + L+ +     V   RV Q+ + A K+++  +++ +
Sbjct: 211 -LNLKEIGEVLGVGESRVSQLHSLAIKRLRSRLKENI 246


>gi|300936144|ref|ZP_07151083.1| RNA polymerase sigma factor, FliA/WhiG family [Escherichia coli MS
           21-1]
 gi|300458722|gb|EFK22215.1| RNA polymerase sigma factor, FliA/WhiG family [Escherichia coli MS
           21-1]
          Length = 239

 Score = 77.2 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 40/268 (14%), Positives = 105/268 (39%), Gaps = 47/268 (17%)

Query: 22  EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEV 78
           E    P+L  Q+E    +                ++L LV K+           +   ++
Sbjct: 11  EFAAAPVLTPQQESHYLQ----------------AYLPLVRKVVRQLAPQCNCIIDRQDM 54

Query: 79  VSEGNIGLMQAVKKFD-PERGFRLATYSMWWIKAAMQEYI-LRSWSLVKIGTTANQKRLF 136
                +GL+ A++++  P+ G   A Y++  I+ A+ + +    W           ++L 
Sbjct: 55  EQTALMGLLNAIRRYGLPDEG--FAGYAVHRIRGAILDELRALDWRP---------RQLR 103

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
               ++K  ++          +   +A++  +S  + +    +L G E+L          
Sbjct: 104 QKYHQMKDLIRETRKKLGHEPEWQELAEE-GISHEDYLEYQ-QLEGAETL---------- 151

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
            +   + L  +  G      + E++   + ML  ++S L+ +E+ I       ++ + L+
Sbjct: 152 -ASLDELLNGEGPGIPLAGRDLEDQFVTQQMLQHALSQLSEKEQLILSMYY--QHEMNLK 208

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
            ++    ++  R+ Q+  +  +K+++ +
Sbjct: 209 EIALVLGLTEARICQLNKQIAQKIRDFV 236


>gi|260853482|ref|YP_003227373.1| putative RNA polymerase, sigma 28 factor [Escherichia coli O26:H11
           str. 11368]
 gi|307313503|ref|ZP_07593124.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Escherichia
           coli W]
 gi|257752131|dbj|BAI23633.1| predicted RNA polymerase, sigma 28 factor [Escherichia coli O26:H11
           str. 11368]
 gi|306906671|gb|EFN37182.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Escherichia
           coli W]
 gi|315059558|gb|ADT73885.1| RNA polymerase, sigma 28 (sigma F) factor [Escherichia coli W]
 gi|323158087|gb|EFZ44186.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           EPECa14]
 gi|323379883|gb|ADX52151.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Escherichia coli KO11]
          Length = 238

 Score = 77.2 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 42/268 (15%), Positives = 106/268 (39%), Gaps = 47/268 (17%)

Query: 22  EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEV 78
           E    P+L  Q+E    +                ++L LV K+           +   ++
Sbjct: 10  EFAAAPVLTPQQESHYLQ----------------AYLPLVRKVVRQLAPQCNCIIDRQDM 53

Query: 79  VSEGNIGLMQAVKKFD-PERGFRLATYSMWWIKAAMQEYI-LRSWSLVKIGTTANQKRLF 136
                +GL+ A++++  P+ G   A Y++  I+ A+ + +    W           ++L 
Sbjct: 54  EQTALMGLLNAIRRYGLPDEG--FAGYAVHRIRGAILDELRALDWRP---------RQLR 102

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
               ++K  ++          +   +A +  +S  + +    +L G E+L          
Sbjct: 103 QKYHQMKDLIRETRKKLGHEPEWSELAVE-GISHEDYLEYQ-QLEGAETL---------- 150

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
            +   + L  +  G   V  E E++   + ML +++S L+ +E+ I       ++ + L+
Sbjct: 151 -ASLDELLNGEGPGIPLVGRELEDQFVTQQMLQQALSQLSEKEQLILSMYY--QHEMNLK 207

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
            ++    ++  R+ Q+  +  +K+++ +
Sbjct: 208 EIALVLGLTEARICQLNKQIAQKIRDFV 235


>gi|291277483|ref|YP_003517255.1| putative flagellar operon RNA polymerase sigma factor [Helicobacter
           mustelae 12198]
 gi|290964677|emb|CBG40532.1| putative RNA polymerase sigma factor for flagellar operon
           [Helicobacter mustelae 12198]
          Length = 231

 Score = 77.2 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 42/238 (17%), Positives = 94/238 (39%), Gaps = 28/238 (11%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L   +L  V  +A   +      + +++++S G   L++  +K+D +       Y+ 
Sbjct: 14  QDELAIQYLPAVRAMAYRMKERLPSSVDVNDLISIGTEELIKLARKYDSKLNDSFWGYAK 73

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +  A+ +Y+ RS  ++        K +   + R     Q              +A+ L
Sbjct: 74  TRVNGALLDYL-RSLDIISRANRKLIKSIDQEITRYYNQHQE-------EPSDAYLAQVL 125

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
              E ++     R+A D  L   I+       +  + +  D       ++EK E++    
Sbjct: 126 GEDEEKIRE--ARIASDIYLLVPID-------EQYNAIESDD------IVEKLEKEELVQ 170

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + + +S L+ RE+ I +    +E  + L  +    +++  R+ QI     KK+++ I
Sbjct: 171 KIKKILSGLSQREQMIMQMYFFEE--MNLNEIKEVLDITESRISQITKEVIKKIRKVI 226


>gi|260779335|ref|ZP_05888227.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           coralliilyticus ATCC BAA-450]
 gi|260605499|gb|EEX31794.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           coralliilyticus ATCC BAA-450]
          Length = 242

 Score = 77.2 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 43/242 (17%), Positives = 95/242 (39%), Gaps = 31/242 (12%)

Query: 51  HRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           ++L+  H  LV +I      +      I ++   G IGL++A +++          +++ 
Sbjct: 26  NKLLKQHQVLVNRIVNQLRAHATPHCSIEDMQQIGLIGLLEAGRRYGNVEDPNFPAFAVC 85

Query: 108 WIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            I+ ++ + + R  W           ++       L    + +  +  +      I K L
Sbjct: 86  RIRGSILDELRRLDWRS---------RKTRQQAHELNDVTRDLMRSLGRQPTDAEIIKAL 136

Query: 167 NVSESEVI-SMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
              E + +   N  LAG+  SL+ LI    +N  + Q   VYD    EQ           
Sbjct: 137 GTDEQDYLTRQNAALAGEMQSLDQLI----ENGIEAQSDAVYDGMSHEQT---------- 182

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L  +++ L  R++ +       ++ + L  ++   +++  R+ Q+  +A K++   +
Sbjct: 183 RRSLEFALNKLPKRDQLLLTLFY--QHELNLHEIALVLDLTPPRICQLHKQALKQLNHYL 240

Query: 285 QK 286
             
Sbjct: 241 SS 242


>gi|116074935|ref|ZP_01472196.1| putative type III sigma factor [Synechococcus sp. RS9916]
 gi|116068157|gb|EAU73910.1| putative type III sigma factor [Synechococcus sp. RS9916]
          Length = 248

 Score = 77.2 bits (189), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 39/236 (16%), Positives = 76/236 (32%), Gaps = 13/236 (5%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
            +  V  H  L         G G     +++ E  +GL+Q  ++F+  RG R ++Y+M  
Sbjct: 6   RNAQVLRHCGLAHLATHRQLGRGCGEHDDLLQEAYLGLIQGSERFEASRGNRFSSYAMRL 65

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
               +Q +       ++I    +         +     +        P     +A  L V
Sbjct: 66  ATGRIQHFRRDRVRCLRIPWRLDALHT-----QAIRLQEQRAHAQRPPFSDHQLASTLGV 120

Query: 169 SESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           S                 SL+   +     S    D  +        V     +   +R 
Sbjct: 121 SLERWRQALIGHQQHHLISLDQPRSRDRYPSDADGDIPLIQELSDMTV---SCDDDQQRE 177

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            L   +  L  R R   E   L       ++++ E   S   +R+I   + +K+++
Sbjct: 178 WLQEQLEQLPQRARSCIERHYLAGTSA--KDIAKEDGCSCSEIRRILRSSLEKLRQ 231


>gi|308205773|gb|ADO19206.1| RNA polymerase sigma factor [Nostoc flagelliforme str. Sunitezuoqi]
          Length = 124

 Score = 76.8 bits (188), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 31/72 (43%), Positives = 47/72 (65%), Gaps = 2/72 (2%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           E  L  +  E G L A H ++T++LRLVV +A  YR   L   +++ EG IGL +AV+KF
Sbjct: 32  EAEL-TQILEQGQL-AKHLMITANLRLVVAVAKKYRWSNLEFLDLIQEGAIGLQKAVEKF 89

Query: 94  DPERGFRLATYS 105
           +P RG++ +TY+
Sbjct: 90  EPNRGYKFSTYA 101


>gi|312879625|ref|ZP_07739425.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Aminomonas
           paucivorans DSM 12260]
 gi|310782916|gb|EFQ23314.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Aminomonas
           paucivorans DSM 12260]
          Length = 210

 Score = 76.8 bits (188), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 29/91 (31%), Positives = 46/91 (50%), Gaps = 1/91 (1%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           LE +EE  L  R  + GD  A  RL+ ++  LV  +A  +R       ++V EG + L+ 
Sbjct: 27  LEPEEEERLWSRCCQ-GDEEARERLILAYRPLVFWLAKRFRVPYGTYPDLVQEGMLALIF 85

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILR 119
           AV  FD  R  R  TY+ + ++  M  ++ R
Sbjct: 86  AVDHFDALRKNRFITYAYYRVRGRMINFLQR 116



 Score = 39.0 bits (90), Expect = 0.97,   Method: Composition-based stats.
 Identities = 15/84 (17%), Positives = 39/84 (46%), Gaps = 7/84 (8%)

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE--FE 263
            + D + +  +  E+ +  +  L   +  L  RE  +  +  ++       +++ E  F+
Sbjct: 126 DEEDLEREAPVAYEDLE-WKVDLADGLKGLPSREAEVITSLVVEGRRA--ADVAKEKGFD 182

Query: 264 VSRERVRQIEARAFKKVQESIQKQ 287
           VS   V +I+ +A +K++   Q++
Sbjct: 183 VS--HVYRIQRKALQKLRSWFQQE 204


>gi|207109684|ref|ZP_03243846.1| RNA polymerase sigma factor RpoD [Helicobacter pylori
           HPKX_438_CA4C1]
          Length = 84

 Score = 76.8 bits (188), Expect = 3e-12,   Method: Composition-based stats.
 Identities = 24/69 (34%), Positives = 38/69 (55%), Gaps = 3/69 (4%)

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRL---QENPVTLENLSSEFEVSRERVRQI 272
           I+   R++ +  +   +  LN RE+ +   R      E+  TLE +  E  V+RERVRQI
Sbjct: 2   IDHIMREDLKVQIESVLDQLNEREKAVIRMRFGLLDDESDRTLEEIGKELNVTRERVRQI 61

Query: 273 EARAFKKVQ 281
           E+ A KK++
Sbjct: 62  ESSAIKKLR 70


>gi|170021344|ref|YP_001726298.1| flagellar biosynthesis sigma factor [Escherichia coli ATCC 8739]
 gi|188494786|ref|ZP_03002056.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           53638]
 gi|169756272|gb|ACA78971.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Escherichia coli ATCC
           8739]
 gi|188489985|gb|EDU65088.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           53638]
          Length = 238

 Score = 76.8 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 41/268 (15%), Positives = 105/268 (39%), Gaps = 47/268 (17%)

Query: 22  EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEV 78
           E    P+L  Q+E    +                ++L LV K+           +   ++
Sbjct: 10  EFAAAPVLTPQQESHYLQ----------------AYLPLVRKVVRQLAPQCNCIIDRQDM 53

Query: 79  VSEGNIGLMQAVKKFD-PERGFRLATYSMWWIKAAMQEYI-LRSWSLVKIGTTANQKRLF 136
                +GL+ A++++  P+ G   A Y++  I+ A+ + +    W           ++L 
Sbjct: 54  EQTALMGLLNAIRRYGLPDEG--FAGYAVHRIRGAILDELRALDWRP---------RQLR 102

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
               ++K  ++          +   +A +  +S  + +    +L G E+L          
Sbjct: 103 QKYHQMKDLIRETRKKLGHEPEWSELAVE-GISHEDYLEYQ-QLEGAETL---------- 150

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
            +   + L  +  G      E E++   + ML +++S L+ +E+ I       ++ + L+
Sbjct: 151 -ASLDELLNSEGPGIPLAGRELEDQFVTQQMLQQALSQLSEKEQLILSMYY--QHEMNLK 207

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
            ++    ++  R+ Q+  +  +K+++ +
Sbjct: 208 EIALVLGLTEARICQLNKQIAQKIRDFV 235


>gi|295091014|emb|CBK77121.1| RNA polymerase sigma factor, sigma-70 family [Clostridium cf.
           saccharolyticum K10]
          Length = 292

 Score = 76.8 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 41/236 (17%), Positives = 95/236 (40%), Gaps = 9/236 (3%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
                L +     +  +A  YR     + ++  EG + L  AV+ + P++G     Y+ +
Sbjct: 18  ECMEELYSQVKAFIHMLACKYR-SASDVEDLEQEGFLALYDAVRGYQPDKG-AFLAYAAY 75

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           WI+A ++ +I +      +   A ++     L++ +   +        P+ V      L 
Sbjct: 76  WIEARIRRFIQKDSC---LHIPAGRQGQAKELQQFQEAYEKEYGQTP-PDAVSCCFLGLT 131

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + E +            SL+A I   +       D +      +E ++ + + ++ +R +
Sbjct: 132 LEEYQERKKTALTGRCLSLDAPITDQEGEGLTLGDTVAASGSLEEDIIGQIDCQELKR-L 190

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           L   ++ L   +  I  AR   +   ++  +++E   S E VR  +A+A + ++  
Sbjct: 191 LWGMVNSLPGMQPAIIRARY--QEGKSIREIAAEQGNSPEEVRGQQAKAIRTLRNP 244


>gi|307720637|ref|YP_003891777.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Sulfurimonas
           autotrophica DSM 16294]
 gi|306978730|gb|ADN08765.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Sulfurimonas
           autotrophica DSM 16294]
          Length = 228

 Score = 76.8 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 46/237 (19%), Positives = 91/237 (38%), Gaps = 28/237 (11%)

Query: 51  HRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
             L   +L  V  +A          +  S++ + G   L++  +++D +       Y+  
Sbjct: 15  DELAIQYLPAVKAMAFRLKERLPSSVDFSDLCAIGTEELIKLARRYDEKLNDSFWGYAKK 74

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +  AM +Y+     L +      +         +   +Q     + +      +A+ L+
Sbjct: 75  RVYGAMLDYLRSLDILSRASRKLVKA--------IDYAVQEYMLTHDEEPSDEELAQVLD 126

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
            S  ++              A I SS        D L    +G   V IEKEE      +
Sbjct: 127 ESVEKIHE------------ARIASSIYTVMPLHDQLQVGDEGAALVQIEKEEL---ITV 171

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + + +S    RE+ I +    +E  +TL+ +SS  +++  R+ QI     +K++ESI
Sbjct: 172 IKKVLSSYKEREQMIIQLYYFEE--LTLKEISSILDITESRISQIHKSVIQKIKESI 226


>gi|160933395|ref|ZP_02080783.1| hypothetical protein CLOLEP_02240 [Clostridium leptum DSM 753]
 gi|156867272|gb|EDO60644.1| hypothetical protein CLOLEP_02240 [Clostridium leptum DSM 753]
          Length = 149

 Score = 76.8 bits (188), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 26/111 (23%), Positives = 53/111 (47%), Gaps = 7/111 (6%)

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM-SVLNP 237
           + A D S+N  I++  + ++      + D    E  +++  + K +   L + +  VL P
Sbjct: 37  KSAQDVSMNEPIDTDKEGNT----LTLMDVMSTEDNIVDNLDIKIKSEQLKKYLVEVLTP 92

Query: 238 RERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           RER I E R       P+T   ++   ++SR  V +IE +A   +++  ++
Sbjct: 93  RERIIIELRYGLNGSRPLTQREVAQRLKISRSYVSRIEKKALLTLRKRFER 143


>gi|323976253|gb|EGB71346.1| FliA/WhiG family protein RNA polymerase sigma protein [Escherichia
           coli TW10509]
          Length = 238

 Score = 76.4 bits (187), Expect = 4e-12,   Method: Composition-based stats.
 Identities = 42/268 (15%), Positives = 105/268 (39%), Gaps = 47/268 (17%)

Query: 22  EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEV 78
           E    P+L  Q+E    +                ++L LV K+           +   ++
Sbjct: 10  EFAAAPVLTPQQESHYLQ----------------AYLPLVRKVVRQLAPQCNCIIDRQDM 53

Query: 79  VSEGNIGLMQAVKKFD-PERGFRLATYSMWWIKAAMQEYI-LRSWSLVKIGTTANQKRLF 136
                +GL+ A++++  P+ G   A Y++  I+ A+ + +    W           ++L 
Sbjct: 54  EQTALMGLLNAIRRYGLPDEG--FAGYAVHRIRGAILDELRALDWRP---------RQLR 102

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
               ++K  ++          +   +A +  +S  + +    +L G E+L          
Sbjct: 103 QKYHQMKDLIRETRKKLGHEPEWSELAVE-GISHEDYLEYQ-QLEGAETL---------- 150

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
            +   + L  +  G      E EE+   + ML +++S L+ +E+ I       ++ + L+
Sbjct: 151 -ASLDELLNGEGPGIPLAGRELEEQFITQQMLQQALSQLSEKEQLILSMYY--QHEMNLK 207

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
            ++    ++  R+ Q+  +  +K+++ +
Sbjct: 208 EIALVLGLTEARICQLNKQIAQKIRDFV 235


>gi|119714600|ref|YP_921565.1| FliA/WhiG family RNA polymerase sigma factor [Nocardioides sp.
           JS614]
 gi|119535261|gb|ABL79878.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Nocardioides sp.
           JS614]
          Length = 300

 Score = 76.4 bits (187), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 54/238 (22%), Positives = 91/238 (38%), Gaps = 21/238 (8%)

Query: 50  AHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           A RL   H+ LV  +           +  +++ S G + L+ A + FDPERG   A Y+M
Sbjct: 28  ADRLAVEHVPLVTHVVYETLARVPSYVDRNDLRSAGLLALVAAARSFDPERGVPFARYAM 87

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS            + +     RL   L              A+A  L
Sbjct: 88  PRIRGAMVDEL-RSVDWASRSVRRRAREIEEARARLAATLGEF-------PDDEAVAAAL 139

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            ++  EV  ++   A    L           +  Q  L      +E    E+     R  
Sbjct: 140 GMTLDEVNRVDSEAARGTVLPL--------DAGAQQGLAEILPVREAGPEERAVHLERVR 191

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L  ++  L  R R +     L+E P+    L++E  V+  RV Q+ A A   +++++
Sbjct: 192 YLADAVEELPERMRLVVRGYFLEERPM--AELAAELGVTESRVSQVRAEALALLRDAL 247


>gi|212637801|ref|YP_002314326.1| flagellar biosynthesis sigma factor [Shewanella piezotolerans WP3]
 gi|212559285|gb|ACJ31739.1| Sigma-70 region 3:Sigma-70 region 2:Sigma-70 region 4 [Shewanella
           piezotolerans WP3]
          Length = 240

 Score = 76.4 bits (187), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 42/238 (17%), Positives = 99/238 (41%), Gaps = 27/238 (11%)

Query: 52  RLVTSHLRLVV---KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           +++  +L LV         + G  L I ++   G + L+++ +++  E      +Y+   
Sbjct: 24  QVMMLYLPLVKRSVSQLRSHCGAVLAIEDMEQIGMMALLESARRYPGEYDNGFISYAGQR 83

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+ + + R               L   +R+L   L+       +      +A+ + +
Sbjct: 84  IRGAILDELRRQ-DWRPRPVRQQAHELNDTVRKLTKMLE-------RAPSDNEVAQAMGL 135

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S+ +      R     SL+  + S D+        L+ D    E    +  E+ + +  L
Sbjct: 136 SQDD-----YRKRLHASLSESMRSLDE--------LISDGGHFEDKQ-DVFEQISAKETL 181

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            +++S LN RE+ I       ++ + L+ +++   ++  R+ Q+  +A K++Q   Q+
Sbjct: 182 FQAISKLNKREQVILSLYY--QHELNLKEIAATLGLTETRICQLHKQAVKQLQNIYQQ 237


>gi|167614829|ref|ZP_02383464.1| flagellar biosynthesis sigma factor [Burkholderia thailandensis
           Bt4]
 gi|257141414|ref|ZP_05589676.1| RNA polymerase sigma factor for flagellar operon FliA [Burkholderia
           thailandensis E264]
          Length = 236

 Score = 76.4 bits (187), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 38/239 (15%), Positives = 97/239 (40%), Gaps = 29/239 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           A  R +  +  +V + A   +      L + ++   G +GL++A++++          Y+
Sbjct: 21  AEQRWLVEYAPIVKRAARQLKSQAVGMLTLDDIEQIGLMGLLEALRRYG-MPDAAFPCYA 79

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
              ++ A+ + + R             + +     R +   + +  +  +      ++  
Sbjct: 80  ATRVRGAILDELRRHDW--------RPRSVRLEAHRTRDCERELCRSLGREPTEAEVSSA 131

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           L +S +E                 + +++  +    D ++ D     +   E++  +  R
Sbjct: 132 LGISTAEYRER-------------VMANNAEAMASFDSVLDDDALTHEESPERQIVR--R 176

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             L ++++ LN RE+R+ +     E  ++L  ++S  E++  RV QI   A KK++E +
Sbjct: 177 RCLEQALARLNEREQRVIQLYY--EFDLSLREIASVLELTEARVCQINKAALKKMREVL 233


>gi|157959887|ref|YP_001499921.1| flagellar biosynthesis sigma factor [Shewanella pealeana ATCC
           700345]
 gi|157844887|gb|ABV85386.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Shewanella pealeana
           ATCC 700345]
          Length = 240

 Score = 76.4 bits (187), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 44/256 (17%), Positives = 101/256 (39%), Gaps = 36/256 (14%)

Query: 41  YREHGDLSAAHRLVTS-----HLRLVV---KIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           Y+E  +  A +RL  S     +L LV         + G  L I ++   G + L+++ ++
Sbjct: 8   YQEAAEEVAINRLAESQVMKQYLPLVKRSVSQLRSHCGIALAIEDMEQIGMMALLESARR 67

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           +  E      +++   I+ A+ + + R               L   +R+L   L+     
Sbjct: 68  YPGEYDNGFLSFAGQRIRGAILDELRRQ-DWRPRPVRQQAHELNDMVRKLTRSLK----- 121

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDG 210
             +    + +A+ + +S+ E          +   SL+ LI                   G
Sbjct: 122 --REPTDLEVAQSMGLSQVEYRERLFASQSESMRSLDELIGDG----------------G 163

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
             +   +  E+ + +  L +++  LN RE+ I       ++ + L+ +++   ++  R+ 
Sbjct: 164 HFEDKSDMLEQFSTKETLFQAILKLNKREQIILSLYY--QHELNLKEIAATLGLTETRIC 221

Query: 271 QIEARAFKKVQESIQK 286
           Q+   A K++Q+  Q+
Sbjct: 222 QLHKHAVKQLQQIYQE 237


>gi|323191388|gb|EFZ76650.1| RNA polymerase sigma factor, FliA/WhiG family protein [Escherichia
           coli RN587/1]
          Length = 239

 Score = 76.4 bits (187), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 40/267 (14%), Positives = 100/267 (37%), Gaps = 45/267 (16%)

Query: 22  EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEV 78
           E    P+L  Q+E    +                ++L LV K+           +   ++
Sbjct: 11  EFAAAPVLTPQQESHYLQ----------------AYLPLVRKVVRQLAPQCNCIIDRQDM 54

Query: 79  VSEGNIGLMQAVKKFD-PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
                +GL+ A++++  P+ G   A Y++  I+ A+ + +               + L +
Sbjct: 55  EQTALMGLLNAIRRYGLPDEG--FAGYAVHRIRGAILDEL---------------RALDW 97

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
             R+L+     + D       +    KKL             ++ ++ L        +  
Sbjct: 98  RPRQLRQKYHQMKDL------IRETRKKLGHEPEWPELAVEGISHEDYLEYQQLEGAETL 151

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           +   + L  +  G      E E++   + ML  ++S L+ +E+ I       ++ + L+ 
Sbjct: 152 ASLDELLNGEGPGIPLAGRELEDQFVTQQMLQHALSQLSEKEQLILSMYY--QHEMNLKE 209

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESI 284
           ++    ++  R+ Q+  +  +K+++ +
Sbjct: 210 IALVLGLTEARICQLNKQIAQKIRDFV 236


>gi|325509467|gb|ADZ21103.1| DNA-dependent RNA polymerase sigma subunit [Clostridium
           acetobutylicum EA 2018]
          Length = 246

 Score = 76.4 bits (187), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 51/258 (19%), Positives = 112/258 (43%), Gaps = 23/258 (8%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY--RGYGLPISEVVSEGNIGLMQAV 90
           E   L  R ++ G   A   L+ S ++ + KIA G+      L + +++ EG I +++A+
Sbjct: 5   EVKDLILRAKD-GSKDAKSFLIDSSMKYIKKIANGFCLNNKSLSLEDLMQEGIIAVIKAI 63

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
             +D ++  + +TY    I   +   I + +S  KI      K + F  R         +
Sbjct: 64  NSYDLDKNVKFSTYVYSMINFTLISEIKKKYSYFKIPEHQVSKIVKFKRR--------AS 115

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
           +  ++        +++ +S  +   M         L+ L N +  +  ++ D  V + D 
Sbjct: 116 ELKVEDTCYKYGCERIGLSYEQYADMM-------HLSKLNNVAYLDEKKYFDGKVSEEDK 168

Query: 211 ---QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
              ++      EE+ +   +L  +   L+  E+ I     +++  V  +N+S   ++S +
Sbjct: 169 FAYEDVNYKRVEEKIDLNVILKENADKLSQLEKYIIREILIKDQKV--KNISKITKMSTK 226

Query: 268 RVRQIEARAFKKVQESIQ 285
           ++  I+  A KK+Q S++
Sbjct: 227 KISNIKYSALKKIQNSLK 244


>gi|331666562|ref|ZP_08367436.1| sigma-70, region 4 subfamily [Escherichia coli TA271]
 gi|323181563|gb|EFZ66983.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           1357]
 gi|331065786|gb|EGI37670.1| sigma-70, region 4 subfamily [Escherichia coli TA271]
          Length = 238

 Score = 76.4 bits (187), Expect = 5e-12,   Method: Composition-based stats.
 Identities = 41/268 (15%), Positives = 104/268 (38%), Gaps = 47/268 (17%)

Query: 22  EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEV 78
           E    P+L  Q+E    +                ++L LV K+           +   ++
Sbjct: 10  EFAAAPVLTPQQESHYLQ----------------AYLPLVRKVVRQLAPQCNCIIDRQDM 53

Query: 79  VSEGNIGLMQAVKKFD-PERGFRLATYSMWWIKAAMQEYI-LRSWSLVKIGTTANQKRLF 136
                +GL+ A++++  P+ G   A Y++  I+ A+ + +    W           ++L 
Sbjct: 54  EQTALMGLLNAIRRYGLPDEG--FAGYAVHRIRGAILDELRALDWRP---------RQLR 102

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
               ++K  ++          +   +A +  +S  + +    +L G E+L          
Sbjct: 103 QKYHQMKDLIRETRKKLGHEPEWSELAVE-GISHEDYLEYQ-QLEGAETL---------- 150

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
            +   + L  +  G      E E++   + ML  ++S L+ +E+ I       ++ + L+
Sbjct: 151 -ASLDELLNGEGPGIPLAGRELEDQFVTQQMLQHALSQLSEKEQLILSMYY--QHEMNLK 207

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
            ++    ++  R+ Q+  +  +K+++ +
Sbjct: 208 EIALVLGLTEARICQLNKQIAQKIRDFV 235


>gi|170682912|ref|YP_001742389.1| flagellar biosynthesis sigma factor [Escherichia coli SMS-3-5]
 gi|170520630|gb|ACB18808.1| lateral flagellar sigma factor 28 protein LafS [Escherichia coli
           SMS-3-5]
          Length = 239

 Score = 76.0 bits (186), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 41/268 (15%), Positives = 104/268 (38%), Gaps = 47/268 (17%)

Query: 22  EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEV 78
           E    P+L  Q+E    +                ++L LV K+           +   ++
Sbjct: 11  EFAAAPVLTPQQESHYLQ----------------AYLPLVRKVVRQLAPQCNCIIDRQDM 54

Query: 79  VSEGNIGLMQAVKKFD-PERGFRLATYSMWWIKAAMQEYI-LRSWSLVKIGTTANQKRLF 136
                +GL+ A++++  P+ G   A Y++  I+ A+ + +    W           ++L 
Sbjct: 55  EQTALMGLLNAIRRYGLPDEG--FAGYAVHRIRGAILDELRALDWRP---------RQLR 103

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
               ++K  ++          +   +A +  +S  + +    +L G E+L          
Sbjct: 104 QKYHQMKDLIRETRKKLGHEPEWSELAVE-GISHEDYLEYQ-QLEGAETL---------- 151

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
            +   + L  +  G      E E++   + ML  ++S L+ +E+ I       ++ + L+
Sbjct: 152 -ASLDELLNGEGPGIPLAGRELEDQFVTQQMLQHALSQLSEKEQLILSMYY--QHEMNLK 208

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
            ++    ++  R+ Q+  +  +K+++ +
Sbjct: 209 EIALVLGLTEARICQLNKQIAQKIRDFV 236


>gi|167576654|ref|ZP_02369528.1| flagellar biosynthesis sigma factor [Burkholderia thailandensis
           TXDOH]
          Length = 236

 Score = 76.0 bits (186), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 37/239 (15%), Positives = 97/239 (40%), Gaps = 29/239 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           A  R +  +  +V + A   +      L + ++   G +GL++A++++          Y+
Sbjct: 21  AEQRWLVEYAPIVKRAARQLKSQAVGMLTLDDIEQIGLMGLLEALRRYG-MPDAAFPCYA 79

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
              ++ A+ + + R             + +     R +   + +  +  +      ++  
Sbjct: 80  ATRVRGAILDELRRHDW--------RPRSVRLEAHRTRDCERELCRSLGREPTEAEVSSA 131

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           L +S +E                 + +++  +    D ++ D     +   E++  +  R
Sbjct: 132 LGISTAEYRER-------------VMANNAEAMASFDSVLDDDALTHEESPERQIVR--R 176

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             L ++++ L+ RE+R+ +     E  ++L  ++S  E++  RV QI   A KK++E +
Sbjct: 177 RCLEQALARLDEREQRVIQLYY--EFDLSLREIASVLELTEARVCQINKAALKKMREVL 233


>gi|157373192|ref|YP_001471792.1| flagellar biosynthesis sigma factor [Shewanella sediminis HAW-EB3]
 gi|157315566|gb|ABV34664.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Shewanella
           sediminis HAW-EB3]
          Length = 240

 Score = 76.0 bits (186), Expect = 6e-12,   Method: Composition-based stats.
 Identities = 41/256 (16%), Positives = 96/256 (37%), Gaps = 36/256 (14%)

Query: 41  YREHGDLSAAHRLVTS-----HLRLVV---KIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           Y+E  D    +RL  +     +L LV         + G  L I ++   G + L+++ ++
Sbjct: 8   YQEASDEQVPNRLSENQVMSQYLPLVKRSISQLRSHCGTVLAIEDMEQIGMMALLESSRR 67

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           +  E      +Y+   I+ A+ + + R               L   +R+L   L      
Sbjct: 68  YPGEYDNGFISYAGQRIRGAILDELRRQ-DWRPRPVRQQAHELNDTVRKLTRLL------ 120

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDG 210
             +    + +A+ + ++  E          +   SL+ +++                   
Sbjct: 121 -GREPSDIEVAEAMGLNREEYRERLYASQSESMKSLDDMLSVG----------------A 163

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
                    E+ + +  L +++S L+ RE+ I       ++ + L+ ++    ++  R+ 
Sbjct: 164 HFPDKTNVIEQFSVQKTLIKAISKLSKREQLILSLYY--QHELNLKEIAGTLGLTETRIC 221

Query: 271 QIEARAFKKVQESIQK 286
           Q+  +A K +QE  Q+
Sbjct: 222 QLHKQAVKHLQEIYQQ 237


>gi|322378964|ref|ZP_08053378.1| flagellar biosynthesis sigma factor [Helicobacter suis HS1]
 gi|322379818|ref|ZP_08054115.1| flagellar biosynthesis sigma factor [Helicobacter suis HS5]
 gi|321147786|gb|EFX42389.1| flagellar biosynthesis sigma factor [Helicobacter suis HS5]
 gi|321148640|gb|EFX43126.1| flagellar biosynthesis sigma factor [Helicobacter suis HS1]
          Length = 236

 Score = 76.0 bits (186), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 35/241 (14%), Positives = 93/241 (38%), Gaps = 28/241 (11%)

Query: 47  LSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            ++ + L   +L  V  +A          +  +++VS G   L++  +++D         
Sbjct: 16  QNSQNELAIQYLPAVRSMAFRLKERLPSSVDFNDLVSAGTEELIKLSRRYDVALNDSFWG 75

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   +  AM +Y+ RS  +V   +    K +   + +         + + +      +A
Sbjct: 76  YAKTRVNGAMLDYL-RSLDVVSRSSRKLIKNIDHEISK-------YYNVHGQEPDDAYLA 127

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + L    S++   + ++A D  ++  I+                +  ++  + +K E + 
Sbjct: 128 EVLGEDISKIR--DAKVASDIYVHVPID-------------EQFNAIEQDTMTKKLEFEE 172

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
                   +  ++ RE+ + +    +E  + L  +     ++  R+ QI     KK+++S
Sbjct: 173 LVEATQMILKTMSDREQLVIQLYFFEE--LNLSEIREILGITESRISQIIKEVIKKIRKS 230

Query: 284 I 284
           +
Sbjct: 231 L 231


>gi|327254572|gb|EGE66188.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           STEC_7v]
          Length = 238

 Score = 76.0 bits (186), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 41/268 (15%), Positives = 105/268 (39%), Gaps = 47/268 (17%)

Query: 22  EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEV 78
           E    P+L  Q+E    +                ++L LV K+           +   ++
Sbjct: 10  EFAAAPVLTAQQESHYLQ----------------AYLPLVRKVVRQLAPQCNCIIDRQDM 53

Query: 79  VSEGNIGLMQAVKKFD-PERGFRLATYSMWWIKAAMQEYI-LRSWSLVKIGTTANQKRLF 136
                +GL+ A++++  P+ G   A Y++  I+ A+ + +    W           ++L 
Sbjct: 54  EQTALMGLLNAIRRYGLPDEG--FAGYAVHRIRGAILDELRALDWRP---------RQLR 102

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
               ++K  ++          +   +A +  +S  + +    +L G E+L          
Sbjct: 103 QKYHQMKDLIRETRKKLGHEPEWSELAVE-GISHEDYLEYQ-QLEGAETL---------- 150

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
            +   + L  +  G      E E++   + ML +++S L+ +E+ I       ++ + L+
Sbjct: 151 -ASLDELLNGEGPGIPLAGRELEDQFITQQMLQQALSQLSEKEQLILAMYY--QHEMNLK 207

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
            ++    ++  R+ Q+  +  +K+++ +
Sbjct: 208 EIALVLGLTEARICQLNKQIAQKIRDFV 235


>gi|331645434|ref|ZP_08346538.1| putative RNA polymerase sigma factor for flagellar operon
           [Escherichia coli M605]
 gi|331045596|gb|EGI17722.1| putative RNA polymerase sigma factor for flagellar operon
           [Escherichia coli M605]
          Length = 238

 Score = 75.6 bits (185), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 36/236 (15%), Positives = 98/236 (41%), Gaps = 31/236 (13%)

Query: 54  VTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFD-PERGFRLATYSMWWI 109
           + ++L LV K+           +   ++     +GL+ A++++  P+ G   A Y++  I
Sbjct: 26  LQAYLPLVRKVVRQLAPQCNCIIDRQDMEQTALMGLLNAIRRYGLPDEG--FAGYAVHRI 83

Query: 110 KAAMQEYI-LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           + A+ + +    W           ++L     ++K  ++          +   +A++  +
Sbjct: 84  RGAILDELRALDWRP---------RQLRQKYHQMKDLIRETRKKLGHEPEWQELAEE-GI 133

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S  + +    +L G E+L           +   + L  +  G      E E++   + ML
Sbjct: 134 SHEDYLEYQ-QLEGAETL-----------ASLDELLNGEGPGIPLAGRELEDQFVTQQML 181

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             ++S L+ +E+ I       ++ + L+ ++    ++  R+ Q+  +  +K+++ +
Sbjct: 182 QHALSQLSEKEQLILSMYY--QHEMNLKEIALVLGLTEARICQLNKQIAQKIRDFV 235


>gi|59889798|emb|CAH19154.1| Lateral flagellar sigma factor 28 protein (FliA-like) [Escherichia
           coli]
 gi|284920062|emb|CBG33119.1| lateral flagellar sigma factor 28 protein (FliA-like) [Escherichia
           coli 042]
          Length = 238

 Score = 75.6 bits (185), Expect = 7e-12,   Method: Composition-based stats.
 Identities = 41/268 (15%), Positives = 105/268 (39%), Gaps = 47/268 (17%)

Query: 22  EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEV 78
           E    P+L  Q+E    +                ++L LV K+           +   ++
Sbjct: 10  EFAAAPVLTPQQESHYLQ----------------AYLPLVRKVVRQLAPQCNCIIDRQDM 53

Query: 79  VSEGNIGLMQAVKKFD-PERGFRLATYSMWWIKAAMQEYI-LRSWSLVKIGTTANQKRLF 136
                +GL+ A++++  P+ G   A Y++  I+ A+ + +    W           ++L 
Sbjct: 54  EQTALMGLLNAIRRYGLPDEG--FAGYAVHRIRGAILDELRALDWRP---------RQLR 102

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
               ++K  ++          +   +A +  +S  + +    +L G E+L          
Sbjct: 103 QKYHQMKDLIRETRKKLGHEPEWSELAVE-GISHEDYLEYQ-QLEGAETL---------- 150

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
            +   + L  +  G      E E++   + ML  ++S+L+ +E+ I       ++ + L+
Sbjct: 151 -ASLDELLNGEGPGIPLAGRELEDQFVTQQMLQHALSLLSEKEQLILSMYY--QHEMNLK 207

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
            ++    ++  R+ Q+  +  +K+++ +
Sbjct: 208 EIALVLGLTEARICQLNKQIAQKIRDFV 235


>gi|58699678|ref|ZP_00374352.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Drosophila
           ananassae]
 gi|58533807|gb|EAL58132.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Drosophila
           ananassae]
          Length = 93

 Score = 75.6 bits (185), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 31/85 (36%), Positives = 50/85 (58%)

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
            +  +   QE      EE++ +  +L  +++ LN R R IF +R L EN  TL+ LS ++
Sbjct: 1   MIPCNLVSQEVTYQNHEEKELKEAILNNALASLNERARDIFISRYLSENIQTLDELSKKY 60

Query: 263 EVSRERVRQIEARAFKKVQESIQKQ 287
            VSRER+RQ+  +A  KV++ IQ +
Sbjct: 61  CVSRERIRQLAEQAMAKVKQYIQSE 85


>gi|253581342|ref|ZP_04858568.1| DNA-directed RNA polymerase sigma subunit RpoD [Fusobacterium
           varium ATCC 27725]
 gi|251836706|gb|EES65240.1| DNA-directed RNA polymerase sigma subunit RpoD [Fusobacterium
           varium ATCC 27725]
          Length = 286

 Score = 75.6 bits (185), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 28/109 (25%), Positives = 50/109 (45%), Gaps = 4/109 (3%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
            E  +  Y+ E+  + ++  +EE    K   +        +++  +L  V  IA  Y   
Sbjct: 54  AEETVIDYLEELSNMEVISDEEESNYLKNISDFD----KEKIIVKNLNEVASIAFYYVKT 109

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           G+   ++V EG +GL++AV  FDP++      YS +WI   +  YI   
Sbjct: 110 GIAYMDIVQEGTVGLIKAVDYFDPDKNGDFKNYSKYWIVREIVLYIENK 158


>gi|170287832|ref|YP_001738070.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermotoga sp. RQ2]
 gi|281411468|ref|YP_003345547.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermotoga
           naphthophila RKU-10]
 gi|170175335|gb|ACB08387.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermotoga sp. RQ2]
 gi|281372571|gb|ADA66133.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermotoga
           naphthophila RKU-10]
          Length = 220

 Score = 75.6 bits (185), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 38/238 (15%), Positives = 97/238 (40%), Gaps = 31/238 (13%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              ++ S L  + + A        P   + +++ EG +  + +++++DP +     T+ M
Sbjct: 4   KESMIRSLLPFIKRTAEDLAQTLPPNVEVDDLIQEGIVAALSSLERYDPSK-ASFTTFIM 62

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +K AM +Y+ +   + +            NLR+    ++     + +      IA+K 
Sbjct: 63  KRVKGAMYDYLRKIDWMPR------------NLRKNVKMIERAIYESEEFPSDEEIARKT 110

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   EV+     +   + L               D +  +   + +   E   R+    
Sbjct: 111 GLELKEVVRARNEMMRKQLL-------------MIDAMEDEIVLKTEGPDENAYRELLVE 157

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + +++  L+ +E+ +   R   E  ++L+ ++   +VS  RV QI +++  K+++ +
Sbjct: 158 EMKKAIEKLSDKEKLVLSLRF--EKDLSLKEIAKVLDVSESRVSQIISKSLLKIKKEV 213


>gi|229140635|ref|ZP_04269187.1| Prophage LambdaBa02, RNA polymerase sigma-F factor [Bacillus cereus
           BDRD-ST26]
 gi|228642831|gb|EEK99110.1| Prophage LambdaBa02, RNA polymerase sigma-F factor [Bacillus cereus
           BDRD-ST26]
          Length = 314

 Score = 75.6 bits (185), Expect = 8e-12,   Method: Composition-based stats.
 Identities = 46/238 (19%), Positives = 93/238 (39%), Gaps = 30/238 (12%)

Query: 51  HRLVTSHLRLVVKIAMGY---------RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
              +  + RLV      Y         +   L + +++  G +GL+ A + F  E GF+ 
Sbjct: 20  DDFMKKYSRLVYYYVNKYFSNIAKAIEQETNLNMDDLIQSGMLGLVTARRDFKTELGFKF 79

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
            T+++  I   +++ +  S    KI  T     +   + R+K          L  E+V +
Sbjct: 80  TTFAVPIILGYIRKAVRDSQ---KIRITNEVYEIKGKISRMK----------LHDEEVES 126

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           IAK L VS  +V +         SL   +N          +  + D      +     + 
Sbjct: 127 IAKLLEVSVRDVKTAKEFNPRTISLQTPLNKEVNKEKVTLENTLIDKKTSMTL-----DN 181

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
             ++ ++T  +S L  +E+ ++E   L    +T   +     V++ ++ +I    +KK
Sbjct: 182 VIKKMIITAFLSTLCSKEKFVWE---LHAKNMTQAAIGKRLGVTQTQISRILKGIYKK 236


>gi|148239819|ref|YP_001225206.1| putative group 3 RNA polymerase sigma factor [Synechococcus sp. WH
           7803]
 gi|147848358|emb|CAK23909.1| Putative group 3 RNA polymerase sigma factor [Synechococcus sp. WH
           7803]
          Length = 286

 Score = 75.6 bits (185), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 45/260 (17%), Positives = 89/260 (34%), Gaps = 19/260 (7%)

Query: 50  AHRLVTSHLRLVVKIA-MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
            + LV  HL L    A       G    ++  E  +GL++++ +F+P RG ++++Y++  
Sbjct: 33  RNGLVLQHLGLAHHAANQQLPRGGGEYDDLCQEARLGLVKSLDRFEPSRGHQVSSYAIPK 92

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
               +  Y       ++I      K L     RL+   +        P     +A  L V
Sbjct: 93  ATGQILHYRRDRLHTLRIPWRI--KDLHTRGMRLQ---EQRLQAGQAPFSDADLAAALGV 147

Query: 169 SESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +            G    SLNA +    +  +      +      E     + +   + +
Sbjct: 148 APQRWQLAKSTHQGQRLLSLNAPVPRGGRTDATEASERIDLLPSPES----EAQDDPQHH 203

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L  ++  L+P  RR   +  +   P  L  L+    + R  +  I     + ++     
Sbjct: 204 WLHEALQSLDPTHRRWLWSHWIDGIP--LGKLAEREGMDRRTLSTIMRNTLQHLRRRAAA 261

Query: 287 QV-----ELSSSPPLLQKPR 301
                  E+   P    +PR
Sbjct: 262 AFSAASPEVLPLPSPAAQPR 281


>gi|261341477|ref|ZP_05969335.1| RNA polymerase sigma factor [Enterobacter cancerogenus ATCC 35316]
 gi|288316273|gb|EFC55211.1| RNA polymerase sigma factor [Enterobacter cancerogenus ATCC 35316]
          Length = 233

 Score = 75.6 bits (185), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 38/242 (15%), Positives = 94/242 (38%), Gaps = 34/242 (14%)

Query: 52  RLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKF-DPERGFRLATYSMW 107
           + V++ L LV ++           +   ++     +GL+ A++++  P+   +   Y+  
Sbjct: 19  KYVSAWLPLVHRVVKQLAWQTSSVMDREDMEQIALMGLLTALRRYGHPD--EQFGAYAAQ 76

Query: 108 WIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            I+ A+ + +    W           +RL     +L   ++ +T    +      ++  L
Sbjct: 77  RIRGAVLDELRELDWRP---------RRLRQKSHKLNDAIREVTRKLGRTPSFEDLSTHL 127

Query: 167 NVSESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           +++  E     +       ESL+ L+     N +     L              E+    
Sbjct: 128 SITAEEYHEYLLLDCAKTLESLDELLGGDALNGTLNTCSL--------------EDEMVT 173

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              L  +++ L+ RE+ I       ++ ++L+ ++   +++  RV Q+  +  +K+Q   
Sbjct: 174 SGTLRAALASLDEREQLILSLYY--QHEMSLKEIALVLDLTEARVCQLNKKIAQKIQCFF 231

Query: 285 QK 286
           QK
Sbjct: 232 QK 233


>gi|251779245|ref|ZP_04822165.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium botulinum E1
           str. 'BoNT E Beluga']
 gi|243083560|gb|EES49450.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium botulinum E1
           str. 'BoNT E Beluga']
          Length = 234

 Score = 75.6 bits (185), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 49/257 (19%), Positives = 86/257 (33%), Gaps = 69/257 (26%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQA 89
           EE VL     + GD     +L+ ++ +L+ KI   +       + I ++  EG IGLM A
Sbjct: 4   EELVL---LYQQGDKKELEQLIENNKKLIYKIVNKFYVNETNSIDIEDLEQEGMIGLMIA 60

Query: 90  VKKFDPE--RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
            +K+        + +TY+++WI   + E+I               KR       L   + 
Sbjct: 61  AEKYKFNIENKAKFSTYAIYWIYGRITEFIN--------------KRNTNYETSLNTPIT 106

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
              +  LK + +  I  +    E  +     R                            
Sbjct: 107 EEGEKELK-DIIEYIDYEFENVEERIYIKELR---------------------------- 137

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP-VTLENLSSEFEVSR 266
                     +E  +  + +L      L  R+  I            T   +   F ++ 
Sbjct: 138 ----------RELEEVMKEIL-----TLRERQ--ILMFYYGWHTKECTFNYIGEIFNITS 180

Query: 267 ERVRQIEARAFKKVQES 283
            RVRQI  RA  K+++S
Sbjct: 181 SRVRQIHLRALSKIRKS 197


>gi|218703543|ref|YP_002411062.1| flagellar biosynthesis sigma factor [Escherichia coli UMN026]
 gi|293403374|ref|ZP_06647465.1| flagellar biosynthesis sigma factor [Escherichia coli FVEC1412]
 gi|298378986|ref|ZP_06988867.1| flagellar biosynthesis sigma factor [Escherichia coli FVEC1302]
 gi|300899471|ref|ZP_07117719.1| RNA polymerase sigma factor, FliA/WhiG family [Escherichia coli MS
           198-1]
 gi|218430640|emb|CAR11506.1| putative RNA polymerase sigma factor for flagellar operon
           (FliA/lafS-like) [Escherichia coli UMN026]
 gi|291429227|gb|EFF02247.1| flagellar biosynthesis sigma factor [Escherichia coli FVEC1412]
 gi|298280099|gb|EFI21603.1| flagellar biosynthesis sigma factor [Escherichia coli FVEC1302]
 gi|300356950|gb|EFJ72820.1| RNA polymerase sigma factor, FliA/WhiG family [Escherichia coli MS
           198-1]
          Length = 238

 Score = 75.6 bits (185), Expect = 9e-12,   Method: Composition-based stats.
 Identities = 41/268 (15%), Positives = 104/268 (38%), Gaps = 47/268 (17%)

Query: 22  EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEV 78
           E    P+L  Q+E    +                ++L LV K+           +   ++
Sbjct: 10  EFAAAPVLTPQQESHYLQ----------------AYLPLVRKVVRQLAPQCNCIIDRQDM 53

Query: 79  VSEGNIGLMQAVKKFD-PERGFRLATYSMWWIKAAMQEYI-LRSWSLVKIGTTANQKRLF 136
                +GL+ A++++  P+ G   A Y++  I+ A+ + +    W           ++L 
Sbjct: 54  EQTALMGLLNAIRRYGLPDEG--FAGYAVHRIRGAILDELRALDWRP---------RQLR 102

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
               ++K  ++          +   +A +  +S  + +    +L G E+L          
Sbjct: 103 QKYHQMKDLIRETRKKLGHEPEWSELAVE-GISHEDYLEYQ-QLEGAETL---------- 150

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
            +   + L  +  G      E E++   + ML  ++S L+ +E+ I       ++ + L+
Sbjct: 151 -ASLDELLNGEGPGIPLAGRELEDQFVTQQMLQYALSQLSEKEQLILSMYY--QHEMNLK 207

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
            ++    ++  R+ Q+  +  +K+++ +
Sbjct: 208 EIALVLGLTEARICQLNKQIAQKIRDFV 235


>gi|297379636|gb|ADI34523.1| RNA polymerase sigma factor, FliA/WhiG family [Helicobacter pylori
           v225d]
          Length = 250

 Score = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 36/238 (15%), Positives = 92/238 (38%), Gaps = 28/238 (11%)

Query: 50  AHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L   +L  V  +A          +  +++VS G   L++  ++++         Y+ 
Sbjct: 33  QDALAIQYLPAVRAMAFRLKERLPSSIDFNDLVSIGTEELIKLARRYESALNDSFWGYAK 92

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +  AM +Y+ RS  ++        K +   + +         + + K      +A+ L
Sbjct: 93  TRVNGAMLDYL-RSLDVISRSNRKLIKSIDIEITKH-------LNEHGKEPSDAYLAEVL 144

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             +  ++            + AL+   ++ ++  QD +            +K E +    
Sbjct: 145 GENIEKIKEAKTA----SDIYALVPIDEQFNAIEQDEI-----------TKKIEAEELLE 189

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + ++++ ++ RE+ + +    +E  + L  +     ++  R+ QI   A KKV++S+
Sbjct: 190 HVQKALNQMSEREQILIQLYYFEE--LNLSEIKEILGITESRISQIIKEAIKKVRKSL 245


>gi|87124483|ref|ZP_01080332.1| Possible type 3 alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9917]
 gi|86168055|gb|EAQ69313.1| Possible type 3 alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9917]
          Length = 213

 Score = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 45/221 (20%), Positives = 82/221 (37%), Gaps = 36/221 (16%)

Query: 50  AHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
            +R V  HLRLV  IA  Y +  G    +++  G +GL++A   +D  +G     ++   
Sbjct: 8   RNRRVEQHLRLVQPIARHYAQRSGEDRDDLLQVGCLGLIRAAGLYDGAKGVPFEAFARPH 67

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           ++ A+  Y+  S  LVK+     ++     L R           +   ++  A+A  L  
Sbjct: 68  VRGAILHYLRDSRGLVKLPRRLQERA--QRLNR---------GEDGTEQRGDALAMALYR 116

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           ++    S++ +    E   A+   +D   S                      ++  R  L
Sbjct: 117 NQGRWWSLDDQGRDVE---AMTPPADGGWSDL-------------------SQRETREQL 154

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
            R +  L   E+R   +  L    ++L     E  VS   V
Sbjct: 155 ARQLKRLPVVEQRSVRSVVL--EGLSLRQCGREQGVSAMTV 193


>gi|308050008|ref|YP_003913574.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Ferrimonas
           balearica DSM 9799]
 gi|307632198|gb|ADN76500.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Ferrimonas
           balearica DSM 9799]
          Length = 242

 Score = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 37/234 (15%), Positives = 89/234 (38%), Gaps = 27/234 (11%)

Query: 51  HRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +  +  +L LV +       + G  +   ++   G + L+ A++++  E       ++  
Sbjct: 23  NHYLRQYLPLVKRAMGQLRSHCGPMMGPEDMEQIGLMALLDALRRYPGEPDNGFIAFASL 82

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+ A+ + + R             ++L      L   ++ +T    +P     +A  L+
Sbjct: 83  RIRGAILDELRRQDW--------RPRQLRQQSHELNDTVRRLTRELGRPPHDQEVADALS 134

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +S  +        +  ESL +L       +S  Q+               + ER  R   
Sbjct: 135 LSLEQYRE-RLYASQAESLQSLDELLGAGASLEQEG-------------NETERFQRHRT 180

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           L  ++  LN RE+ +       ++ + L+ ++    ++  R+ Q+   A K+++
Sbjct: 181 LASALGKLNQREQLVLSLYY--QHELNLKEIALTLGLTESRICQLHKHAVKQLK 232


>gi|253681618|ref|ZP_04862415.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium botulinum D
           str. 1873]
 gi|253561330|gb|EES90782.1| RNA polymerase, sigma 32 subunit, RpoH [Clostridium botulinum D
           str. 1873]
          Length = 236

 Score = 75.2 bits (184), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 48/261 (18%), Positives = 94/261 (36%), Gaps = 71/261 (27%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY---RGYGLPISEVVSEGNIGL 86
             +E   L     + GD  A   L+  +  ++ K+   +   +   +   ++  EG IGL
Sbjct: 2   TNEELVEL----YQQGDKQALDSLIEQNKGIIYKLVNRFYVEKTNSIDREDLEQEGTIGL 57

Query: 87  MQAVKKFDPE--RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           + A +K+D    +  +  TY++ WI + +  YI             NQ+           
Sbjct: 58  IIAARKYDFNNEKKAKFITYAIHWIYSKINRYI-------------NQRNTN-------- 96

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
                                      +  S+N  +  DE    +    D + S      
Sbjct: 97  ---------------------------DETSLNIHIGEDEENELIDTIKDIDYSY----- 124

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEF 262
               +  E+ +  KE R+    ++    + L  RE  I + R   +  N + L ++    
Sbjct: 125 ----ENVEEKIYMKELRQEIEEVMKE-YNTLEERE--ILKLRHGWDSNNIMALSDIGELL 177

Query: 263 EVSRERVRQIEARAFKKVQES 283
            ++  RVR IE RA++K++ +
Sbjct: 178 NINVGRVRTIEDRAYRKLRRT 198


>gi|225629823|ref|ZP_03787747.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of
           Muscidifurax uniraptor]
 gi|225591324|gb|EEH12440.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of
           Muscidifurax uniraptor]
          Length = 95

 Score = 74.8 bits (183), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 33/87 (37%), Positives = 50/87 (57%)

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
           QD +  +   QE      EE + +  +L  +++ LN R R IF +R L EN  TL+ LS 
Sbjct: 1   QDMIPCNLVSQEVTYQNHEEEELKETILNNALASLNERARDIFISRYLSENIQTLDELSK 60

Query: 261 EFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++ VSRER+RQ+  +A  KV+  IQ +
Sbjct: 61  KYCVSRERIRQLAEQAMAKVKPYIQSE 87


>gi|78184703|ref|YP_377138.1| type 3 alternative RNA polymerase sigma factor [Synechococcus sp.
           CC9902]
 gi|78168997|gb|ABB26094.1| possible type 3 alternative RNA polymerase sigma factor
           [Synechococcus sp. CC9902]
          Length = 206

 Score = 74.8 bits (183), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 45/237 (18%), Positives = 91/237 (38%), Gaps = 44/237 (18%)

Query: 50  AHRLVTSHLRLVVKIAMGYRG-YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
            +  +  +L LV  IA  Y    G    ++   G +GL+QA ++F    G     ++   
Sbjct: 9   RNHRIQKYLSLVHPIARRYSYQSGCYCDDLTQVGYLGLIQASQRFKLTHGNSFPAFAKPH 68

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+  Y+    SLV++     ++ +     +++GH +   +N                
Sbjct: 69  IRGAILHYLRDHVSLVRLPRGVEERAI-----KIRGHNERTLNN---------------- 107

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
                            ++ LI  + K +S W++ L  D  G      +  E K +   +
Sbjct: 108 -----------------IDQLILQNYKFNSNWKE-LNEDCVGGTCNGSDDMEFKEQNRKI 149

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV-RQIEARAFKKVQESI 284
             +M  L   E+ I +    + N  +L       +VS   V R++  RA  ++++ +
Sbjct: 150 ELAMKKLAKNEQIIIQLVIFEGN--SLRKAGKIIDVSAMTVQRRL-KRARAQLRDLL 203


>gi|78776905|ref|YP_393220.1| flagellar biosynthesis sigma factor [Sulfurimonas denitrificans DSM
           1251]
 gi|78497445|gb|ABB43985.1| sigma 28 (Flagella/Sporulation) [Sulfurimonas denitrificans DSM
           1251]
          Length = 227

 Score = 74.8 bits (183), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 37/237 (15%), Positives = 91/237 (38%), Gaps = 28/237 (11%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG---LMQAVKKFDPERGFRLATYSMW 107
             L   +L  V  +A   +       + +    IG   L++  +++D         Y+  
Sbjct: 14  DELAIQYLPAVKAMAFRLKERLPSSVDYMDLSAIGTEELIKLARRYDESLNDSFWGYAKK 73

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +  AM +Y+ RS  +V   +    K + + +       +AI D     E++  I  + +
Sbjct: 74  RVYGAMLDYL-RSLDIVSRASRKLIKAIDYAI----EEHRAIHDEEPSDEELALIIGE-D 127

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           + +     +   +     L+  +   D+ +S                 +   E++   ++
Sbjct: 128 IEKIHEARIASSIYAVMPLHDQLQVGDEGAS-----------------LANIEKEELIDV 170

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +   + + + RE+ I +    +E  ++L+ +S    ++  R+ QI      K++ES+
Sbjct: 171 IKTVLGLYSEREQMIIQLYYFEE--LSLKEISDVLGITESRISQIHKSVIHKIKESV 225


>gi|148269170|ref|YP_001243630.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermotoga petrophila
           RKU-1]
 gi|147734714|gb|ABQ46054.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermotoga petrophila
           RKU-1]
          Length = 214

 Score = 74.8 bits (183), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 34/211 (16%), Positives = 89/211 (42%), Gaps = 28/211 (13%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++ EG +  + +++++DP +     T+ M  +K AM +Y+ +   + +        
Sbjct: 25  EVDDLIQEGIVAALSSLERYDPSK-ASFTTFIMKRVKGAMYDYLRKIDWMPR-------- 75

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
               NLR+    ++     + +      IA+K  +   EV+     +   + L       
Sbjct: 76  ----NLRKNVKMIERAIYESEEFPSDEEIARKTGLELKEVVRARNEMMRKQLL------- 124

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
                   D +  +   + +   E   R+     + +++  L+ +E+ +   R   E  +
Sbjct: 125 ------MIDAMEDEIVLKTEGPDENAYRELLVEEMKKAIEKLSDKEKLVLSLRF--EKDL 176

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +L+ ++   +VS  RV QI +++  K+++ +
Sbjct: 177 SLKEIAKVLDVSESRVSQIISKSLLKIKKEV 207


>gi|300817253|ref|ZP_07097471.1| RNA polymerase sigma factor, FliA/WhiG family [Escherichia coli MS
           107-1]
 gi|301643537|ref|ZP_07243580.1| RNA polymerase sigma factor, FliA/WhiG family [Escherichia coli MS
           146-1]
 gi|307136893|ref|ZP_07496249.1| flagellar biosynthesis sigma factor [Escherichia coli H736]
 gi|331640757|ref|ZP_08341892.1| sigma-70, region 4 subfamily [Escherichia coli H736]
 gi|300530229|gb|EFK51291.1| RNA polymerase sigma factor, FliA/WhiG family [Escherichia coli MS
           107-1]
 gi|301078088|gb|EFK92894.1| RNA polymerase sigma factor, FliA/WhiG family [Escherichia coli MS
           146-1]
 gi|315616809|gb|EFU97426.1| RNA polymerase sigma factor, FliA/WhiG family protein [Escherichia
           coli 3431]
 gi|323171082|gb|EFZ56731.1| RNA polymerase sigma factor, FliA/WhiG family protein [Escherichia
           coli LT-68]
 gi|331037555|gb|EGI09775.1| sigma-70, region 4 subfamily [Escherichia coli H736]
          Length = 238

 Score = 74.8 bits (183), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 41/268 (15%), Positives = 105/268 (39%), Gaps = 47/268 (17%)

Query: 22  EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEV 78
           E    P+L  Q+E    +                ++L LV K+           +   ++
Sbjct: 10  EFAAAPVLTPQQESHYLQ----------------AYLPLVRKVVRQLAPQCNCIIDRQDM 53

Query: 79  VSEGNIGLMQAVKKFD-PERGFRLATYSMWWIKAAMQEYI-LRSWSLVKIGTTANQKRLF 136
                +GL+ A++++  P+ G   A Y++  I+ A+ + +    W           ++L 
Sbjct: 54  EQTALMGLLNAIRRYGLPDEG--FAGYAVHRIRGAILDELRALDWRP---------RQLR 102

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
               ++K  ++          +   +A +  +S  + +    +L G E+L          
Sbjct: 103 QKYHQMKDLIRETRKKLGHEPEWSELAVE-GISHEDYLEYQ-QLEGAETL---------- 150

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
            +   + L  +  G      E E++   + ML +++S L+ +E+ I       ++ + L+
Sbjct: 151 -ASLDELLNGEGPGILLAGRELEDQFVTQQMLQQALSQLSEKEQLILSMYY--QHEMNLK 207

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
            ++    ++  R+ Q+  +  +K+++ +
Sbjct: 208 EIALVLGLTEARICQLNKQIAQKIRDFV 235


>gi|330501119|ref|YP_004377988.1| RNA polymerase sigma 28 subunit FliA/WhiG [Pseudomonas mendocina
           NK-01]
 gi|328915405|gb|AEB56236.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pseudomonas mendocina
           NK-01]
          Length = 244

 Score = 74.8 bits (183), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 38/236 (16%), Positives = 95/236 (40%), Gaps = 30/236 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           A  + +  +L LV +I           L   ++   G +GL++ ++++      +   ++
Sbjct: 25  AEQKWLLQYLPLVKRIVSQLALQANQVLDREDMEQIGLMGLLECLRRYG-TPDEQFGRFA 83

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
              I+ A+ + + R             +++     +++  ++ +     +  Q   I + 
Sbjct: 84  ALRIRGAILDELRRQDW--------RPRQVRQQTHKIRDAIRQLARQLGRAPQEEEILQA 135

Query: 166 LNVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
             ++  E        A +  ESL+ L+ +  +  +     +              EER  
Sbjct: 136 AGINAKEYQEFLQADACEAIESLDELLQNGHEGFACGGSAV--------------EERVL 181

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           +  +LT+++S L+ RER +       ++ ++L+ ++   E+S  RV Q+  +A  K
Sbjct: 182 KERLLTQALSQLSERERLVLTLYY--QHELSLKEIALVLELSDARVCQLSKQAIAK 235


>gi|54307284|ref|YP_128304.1| flagellar-specific transcription initiation factor sigma, LafS
           [Photobacterium profundum SS9]
 gi|46911704|emb|CAG18502.1| Hypothetical flagellar-specific transcription initiation factor
           sigma, LafS [Photobacterium profundum SS9]
          Length = 251

 Score = 74.8 bits (183), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 40/248 (16%), Positives = 101/248 (40%), Gaps = 30/248 (12%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDP 95
           ++  + G  +   RLV  H  LV ++           + + ++   G + L+  ++++  
Sbjct: 17  QKSHQLGQKAREQRLVNKHASLVKRVVRHLTAQVTTVMSLEDMEQIGLMALLDVIRRYSD 76

Query: 96  ERGFRLATYSMWWIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           E    L   ++  I+ A+ + + R  W   +    +++         L+   +A+     
Sbjct: 77  ENDASLERLAVQRIRGAILDELRRMDWRSRRSRQKSHE---------LRDTERALGRQLG 127

Query: 155 KPEQVVAIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
           +      +A +L++   +V    ++ +     S++AL     +   +    L +  +  E
Sbjct: 128 RMPTDQEVAAELDIELGDVKQRRVDTQAESLTSMDAL-----QEDGEQFFGLSFQCNSYE 182

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           +V ++K           ++++ L+ RE+         E+ + L+ +   FE++  RV QI
Sbjct: 183 RVALKKAM--------AQALARLSKREQ--VMLSFYYEHEMNLKEIGLVFELTEARVSQI 232

Query: 273 EARAFKKV 280
             +A K +
Sbjct: 233 HKKALKSL 240


>gi|332162882|ref|YP_004299459.1| putative RNA polymerase sigma factor for flagellar operon [Yersinia
           enterocolitica subsp. palearctica 105.5R(r)]
 gi|318604274|emb|CBY25772.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           enterocolitica subsp. palearctica Y11]
 gi|325667112|gb|ADZ43756.1| Putative RNA polymerase sigma factor for flagellar operon [Yersinia
           enterocolitica subsp. palearctica 105.5R(r)]
 gi|330863330|emb|CBX73453.1| RNA polymerase sigma factor for flagellar operon [Yersinia
           enterocolitica W22703]
          Length = 228

 Score = 74.8 bits (183), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 36/235 (15%), Positives = 88/235 (37%), Gaps = 30/235 (12%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           + + ++L LV +I          +    ++     +GL++A++++    G + A Y++  
Sbjct: 16  KYLEAYLPLVKRIVRQLSFQADSVIGKEDMQQIALMGLLEALRRYGHPDG-QFAAYAVHR 74

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+ + +               +RL     +    ++ +            IA +L +
Sbjct: 75  IRGAVLDQLREHDW--------RPRRLRQKTHKTNESIRQLAKKLGHEPSFEEIAAELQL 126

Query: 169 SESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +  E     +       ESL+              + L  D         E EE     +
Sbjct: 127 TAEEYQEYLLLESAGAMESLD--------------EILSLDTPTDALQSRELEESIITED 172

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L  +++ L  RE+ I      QE  ++++ ++   +++  R+ Q+     +K++
Sbjct: 173 NLNHAIASLEKREQMILHLYYQQE--MSMKEIAEVLDLTEARICQLNKILVQKIK 225


>gi|168703207|ref|ZP_02735484.1| sigma-70 factor [Gemmata obscuriglobus UQM 2246]
          Length = 566

 Score = 74.8 bits (183), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 43/190 (22%), Positives = 68/190 (35%), Gaps = 31/190 (16%)

Query: 27  PMLEKQEEYVLAKRY-----------------------------REHGDLSAAHRLVTSH 57
           P+L K++E  + ++                                 G       L+  +
Sbjct: 339 PLLTKEQEQHVFRKMNFLKHKLHQLQSAIDPARATVDELRRAEQLRQGVRDTRDVLINCN 398

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
            RLV   A      G  I ++VS+GN+ LM+AV+KFD  RG + +TY+ W I       I
Sbjct: 399 QRLVYAQAKQKLALGENIDDLVSDGNLSLMRAVEKFDYARGNKFSTYATWAIMKNFARSI 458

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQA-ITDNNLKPEQVVAIAKKLNVSESEVISM 176
                  K         LF     ++   Q  +   +    +V  +   L+    EVI M
Sbjct: 459 PD-AKTHKQRYMTGHDELFEAKADIRTDEQEVLALADQARARVNRLLDHLDARTREVIRM 517

Query: 177 NCRLAGDESL 186
              L G E +
Sbjct: 518 RTGLDGSEEM 527



 Score = 74.5 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 23/83 (27%), Positives = 40/83 (48%), Gaps = 4/83 (4%)

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEV 264
           D    EQ ++   ++   R  + R +  L+ R R +   R   +    +TLE +   F +
Sbjct: 481 DIRTDEQEVLALADQA--RARVNRLLDHLDARTREVIRMRTGLDGSEEMTLEQIGQHFGI 538

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           ++ERVRQI  R  K ++E   K+
Sbjct: 539 TKERVRQINVRGMKMLREWAAKE 561


>gi|153812847|ref|ZP_01965515.1| hypothetical protein RUMOBE_03254 [Ruminococcus obeum ATCC 29174]
 gi|149831059|gb|EDM86148.1| hypothetical protein RUMOBE_03254 [Ruminococcus obeum ATCC 29174]
          Length = 136

 Score = 74.8 bits (183), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 28/144 (19%), Positives = 64/144 (44%), Gaps = 10/144 (6%)

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           + +  N  +   V  +A++L ++  E+   +      ES+   I+  +    Q  D L  
Sbjct: 3   EKLEKNLGREPTVTELAEELGMTPEEIAMASDAATEVESIYRPIHQGEGTELQLLDKLPE 62

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
             + QE++L         +  L   +++L   ERR+   R   +  +T   ++    +S+
Sbjct: 63  KENRQERIL--------DKIFLEELLNILGTEERRLICMRYFCD--MTQTEVAKRLGISQ 112

Query: 267 ERVRQIEARAFKKVQESIQKQVEL 290
            +V ++E R   ++++ IQ + E+
Sbjct: 113 VQVSRMEKRILHRLKKEIQDKTEV 136


>gi|326386918|ref|ZP_08208532.1| sigma 28 (flagella/sporulation) [Novosphingobium nitrogenifigens
           DSM 19370]
 gi|326208598|gb|EGD59401.1| sigma 28 (flagella/sporulation) [Novosphingobium nitrogenifigens
           DSM 19370]
          Length = 243

 Score = 74.8 bits (183), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 46/250 (18%), Positives = 109/250 (43%), Gaps = 27/250 (10%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL---PISEVVSEGNIGLMQAVKKFD 94
           A+ YR+  D +     +   L +V ++A    G G     + +++  G + L +  +K  
Sbjct: 11  ARAYRD--DTADR---IRRFLPMVRRLAWHVHGSGRAGIDLEDLIQAGLVALTECSQKHT 65

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
            +     A Y+   ++ AM + I R+  + +   +A  +R     R L+ H ++++    
Sbjct: 66  GQTEDGFAAYAKLRVRGAMVDLIRRTAPMSR---SAADRR-----RTLRDHTESLSCALG 117

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +      +A+ + ++ +    +    A  E L     + D   S+       D      +
Sbjct: 118 RQPTEGELAEAMGLTLA---DLADLRAAAEPL--RFETIDDAYSESSMAFADDRPDSFAL 172

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
           L ++E     R+++  +++ L  R + + +   ++E  + L  +++  EVS  RV Q++A
Sbjct: 173 LADEE----TRHVVGAAIAALPERLQMVIQLYFVEE--LNLAEIAAVLEVSVPRVHQLKA 226

Query: 275 RAFKKVQESI 284
           +A  K++  +
Sbjct: 227 QALDKLRSLL 236


>gi|269792906|ref|YP_003317810.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermanaerovibrio acidaminovorans DSM 6589]
 gi|269100541|gb|ACZ19528.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermanaerovibrio acidaminovorans DSM 6589]
          Length = 187

 Score = 74.8 bits (183), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 29/96 (30%), Positives = 46/96 (47%), Gaps = 3/96 (3%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E  L  R  + GD  A   L+ ++  +V  +A           +VV EG +GL++AV  
Sbjct: 12  DEEALWARLAQ-GDQEAREELILAYRPMVFWLARRLGNRAY--QDVVQEGMLGLLEAVDN 68

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           FDP RG R +TY+ + I+  M  ++ R      I  
Sbjct: 69  FDPSRGHRFSTYAYYRIRGRMINFLSRVEGSSPIPV 104



 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 13/70 (18%), Positives = 31/70 (44%), Gaps = 2/70 (2%)

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
             +   R +    L  ++  L+ RE  +  +  L++  ++   L+ E  +    + +I  
Sbjct: 115 WEDGFSRLDWTMDLQLALGALSEREADVVRSLVLED--MSARELAEEKGLDVSYIHKIRR 172

Query: 275 RAFKKVQESI 284
           RA  K++E +
Sbjct: 173 RALAKLREVL 182


>gi|158327335|emb|CAM82841.1| sigma factor FliA [Yersinia enterocolitica W22703]
          Length = 231

 Score = 74.8 bits (183), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 36/235 (15%), Positives = 88/235 (37%), Gaps = 30/235 (12%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           + + ++L LV +I          +    ++     +GL++A++++    G + A Y++  
Sbjct: 19  KYLEAYLPLVKRIVRQLSFQADSVIGKEDMQQIALMGLLEALRRYGHPDG-QFAAYAVHR 77

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+ + +               +RL     +    ++ +            IA +L +
Sbjct: 78  IRGAVLDQLREHDW--------RPRRLRQKTHKTNESIRQLAKKLGHEPSFEEIAAELQL 129

Query: 169 SESEVIS--MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +  E     +       ESL+              + L  D         E EE     +
Sbjct: 130 TAEEYQEYLLLESAGAMESLD--------------EILSLDTPTDALQSRELEESIITED 175

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L  +++ L  RE+ I      QE  ++++ ++   +++  R+ Q+     +K++
Sbjct: 176 NLNHAIASLEKREQMILHLYYQQE--MSMKEIAEVLDLTEARICQLNKILVQKIK 228


>gi|260896280|ref|ZP_05904776.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-28) [Vibrio parahaemolyticus Peru-466]
 gi|308088782|gb|EFO38477.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-28) [Vibrio parahaemolyticus Peru-466]
          Length = 146

 Score = 74.8 bits (183), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 24/147 (16%), Positives = 53/147 (36%), Gaps = 8/147 (5%)

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQ 199
           R +   +  +     +      +A  L +S  +  S       D + + L+   D   S 
Sbjct: 3   REINQAVAELEGVLNRDPTDSEVAAHLGMSLDQYHSALT----DINCSRLVGIEDLGVS- 57

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
             D +    +  +    +    ++ R  L  S+  L  RE  +       +  + L+ + 
Sbjct: 58  -DDVISPADETDDSNPFKGVADESFRKALVESIKQLPEREALVLSLYY--DEELNLKEIG 114

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQK 286
               VS  RV QI ++A ++++  +  
Sbjct: 115 DVLGVSESRVSQILSQAMQRLRTKLSA 141


>gi|317010689|gb|ADU84436.1| flagellar biosynthesis sigma factor [Helicobacter pylori
           SouthAfrica7]
          Length = 255

 Score = 74.8 bits (183), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 37/238 (15%), Positives = 92/238 (38%), Gaps = 28/238 (11%)

Query: 50  AHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            + L   +L  V  +A          +  +++VS G   L++  ++++         Y+ 
Sbjct: 38  QNALAIQYLPAVRAMAFRLKERLPSSIDFNDLVSIGTEELIKLARRYESALNDSFWGYAK 97

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +  AM +Y+ RS  ++        K + F + +         + + K      +AK L
Sbjct: 98  TRVNGAMLDYL-RSLDVISRSNRKLIKSIDFEITK-------YLNEHGKEPSDEYLAKAL 149

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             +  ++            + AL+   ++ ++  QD +            +K E +    
Sbjct: 150 GENIEKIREAKTA----SDIYALVPIDEQFNAIEQDEI-----------TKKIEAEELLE 194

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + + ++ ++ RE+ + +    +E  + L  +     ++  R+ QI     KKV++S+
Sbjct: 195 HVQKVLNQMSEREQMLIQLYYFEE--LNLSEIKEILGITESRISQIIKEVIKKVRQSL 250


>gi|289575401|ref|ZP_06455628.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis K85]
 gi|289539832|gb|EFD44410.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis K85]
          Length = 470

 Score = 74.8 bits (183), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 29/114 (25%), Positives = 49/114 (42%), Gaps = 31/114 (27%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------REHGDL- 47
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+  
Sbjct: 215 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSERGEKL 273

Query: 48  ----------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
                            A + L+ ++LRLVV +A  Y G G+   +++ EGN G
Sbjct: 274 PAAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGNRG 327


>gi|157962130|ref|YP_001502164.1| sigma-70 region 4 domain-containing protein [Shewanella pealeana
           ATCC 700345]
 gi|157847130|gb|ABV87629.1| sigma-70 region 4 domain protein [Shewanella pealeana ATCC 700345]
          Length = 930

 Score = 74.8 bits (183), Expect = 1e-11,   Method: Composition-based stats.
 Identities = 19/52 (36%), Positives = 34/52 (65%), Gaps = 1/52 (1%)

Query: 225 RNMLTRSMSVLNPRERRIFEAR-RLQENPVTLENLSSEFEVSRERVRQIEAR 275
           +   T+++S+L  RE+ I E R     + +TLE + ++F V+RER+RQI+ +
Sbjct: 391 KEHFTQALSLLKDREKEIIELRMGFHGHILTLEEVGTKFGVTRERIRQIQKK 442


>gi|317012254|gb|ADU82862.1| flagellar biosynthesis sigma factor [Helicobacter pylori
           Lithuania75]
          Length = 255

 Score = 74.8 bits (183), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 37/238 (15%), Positives = 94/238 (39%), Gaps = 28/238 (11%)

Query: 50  AHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L   +L  V  +A          +  +++VS G   L++  ++++         Y+ 
Sbjct: 38  QDDLAIQYLPAVRAMAFRLKERLPSSIDFNDLVSIGTEELIKLARRYESALNDSFWGYAK 97

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +  AM +Y+      + + + +N+K +      +  HL    + + K      +A+ L
Sbjct: 98  TRVNGAMLDYL----RSLDVISRSNRKLIKSIDAEITKHL----NEHGKEPSDAYLAEVL 149

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             +  ++            + AL+   ++ ++  QD +            +K E +    
Sbjct: 150 GENIEKIREAKTA----SDIYALVPIDEQFNAIEQDEI-----------TKKIEAEELLE 194

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + + ++ ++ RE+ + +    +E  + L  +     ++  R+ QI   A KKV++S+
Sbjct: 195 HVQKVLNQMSEREQILIQLYYFEE--LNLSEIKEILGITESRISQIIKEAIKKVRKSL 250


>gi|256020244|ref|ZP_05434109.1| flagellar biosynthesis sigma factor [Shigella sp. D9]
 gi|332281406|ref|ZP_08393819.1| lateral flagellar sigma factor 28 protein [Shigella sp. D9]
 gi|332103758|gb|EGJ07104.1| lateral flagellar sigma factor 28 protein [Shigella sp. D9]
          Length = 238

 Score = 74.8 bits (183), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 41/268 (15%), Positives = 105/268 (39%), Gaps = 47/268 (17%)

Query: 22  EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEV 78
           E    P+L  Q+E    +                ++L LV K+           +   ++
Sbjct: 10  EFAAAPVLTPQQESHYLQ----------------AYLPLVRKVVRHLAPQCNCIIDRQDM 53

Query: 79  VSEGNIGLMQAVKKFD-PERGFRLATYSMWWIKAAMQEYI-LRSWSLVKIGTTANQKRLF 136
                +GL+ A++++  P+ G   A Y++  I+ A+ + +    W           ++L 
Sbjct: 54  EQTALMGLLNAIRRYGLPDEG--FAGYAVHRIRGAILDELRALDWRP---------RQLR 102

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
               ++K  ++          +   +A +  +S  + +    +L G E+L          
Sbjct: 103 QKYHQMKDLIRETRKKLGHEPEWSELAVE-GISHEDYLEYQ-QLEGAETL---------- 150

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
            +   + L  +  G      E E++   + ML +++S L+ +E+ I       ++ + L+
Sbjct: 151 -ASLDELLNGEGPGILLAGRELEDQFVTQQMLQQALSQLSEKEQLILSMYY--KHEMNLK 207

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
            ++    ++  R+ Q+  +  +K+++ +
Sbjct: 208 EIALVLGLTEARICQLNKQIAQKIRDFV 235


>gi|331671820|ref|ZP_08372616.1| putative RNA polymerase sigma factor for flagellar operon
           [Escherichia coli TA280]
 gi|331070809|gb|EGI42168.1| putative RNA polymerase sigma factor for flagellar operon
           [Escherichia coli TA280]
          Length = 238

 Score = 74.5 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 42/268 (15%), Positives = 104/268 (38%), Gaps = 47/268 (17%)

Query: 22  EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEV 78
           E    P+L  Q+E    +                ++L LV K+           +   ++
Sbjct: 10  EFAAAPILTPQQESHYLQ----------------AYLPLVRKVVRHLAPQCNCIIDRQDM 53

Query: 79  VSEGNIGLMQAVKKFD-PERGFRLATYSMWWIKAAMQEYI-LRSWSLVKIGTTANQKRLF 136
                IGL+ A++++  P+ G   A Y++  I+ A+ + +    W           ++L 
Sbjct: 54  EQTALIGLLNAIRRYGLPDEG--FAGYAVQRIRGAILDELRALDWRP---------RQLR 102

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
               ++K  ++          +   +A +  +S  + +    +L G E+L          
Sbjct: 103 QKYHQMKDLIRETRKKLGHEPEWSELAVE-GISHEDYLEYQ-QLEGAETL---------- 150

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
            +   + L  +  G      E E++   + ML  ++S L+ +E+ I       ++ + L+
Sbjct: 151 -ASLDELLNGEGPGIPLAGRELEDQFVTQQMLQHALSQLSEKEQLILSMYY--QHEMNLK 207

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
            ++    ++  R+ Q+  +  +K+++ +
Sbjct: 208 EIALVLGLTEARICQLNKQIAQKIRDFV 235


>gi|222100647|ref|YP_002535215.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermotoga neapolitana
           DSM 4359]
 gi|221573037|gb|ACM23849.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Thermotoga neapolitana
           DSM 4359]
          Length = 220

 Score = 74.5 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 42/238 (17%), Positives = 95/238 (39%), Gaps = 31/238 (13%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
             R + S L ++ +IA        P   + +++ EG +  + A +++DP +     T+ +
Sbjct: 4   KERAIKSLLPVIKRIAEDLVQTLPPNVEVEDLIQEGILAALSAFERYDPSK-ASFTTFVI 62

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +K AM +Y+ R   + +            NLR+    ++     + +      +A+K 
Sbjct: 63  KRVKGAMYDYLRRIDWMPR------------NLRKNVKLVEKAIHESEEFPSDEELARKT 110

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   EVI     +   + L               D    +   + +   E   R+  + 
Sbjct: 111 GLELKEVIRAKNEMMRRQIL-------------MIDAFDEELALKTEGPDETAYREILKE 157

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + +++  L+ +E+ +   R   E  ++L+ ++    VS  RV QI + A  K++  +
Sbjct: 158 KIKKAIEKLSEKEKLVLSLRF--EKELSLKEIARVLGVSESRVSQIVSLALLKIKREV 213


>gi|308205502|gb|ADO18992.1| RNA polymerase sigma 70 subunit [Nostoc flagelliforme str.
           Sunitezuoqi]
          Length = 165

 Score = 74.5 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 27/133 (20%), Positives = 48/133 (36%), Gaps = 39/133 (29%)

Query: 8   IIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE------------------------ 43
           +       +  Y+ EI + P+L  ++E   A+  ++                        
Sbjct: 1   MPSPTTDLVHSYLKEIGRYPLLTPEQEITNARLVQQMMAIEEQRSNLALQLNREPTTREL 60

Query: 44  ---------------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
                          H    A  ++VT++LRLVV IA  Y+   L   +++ EG +GL +
Sbjct: 61  ATSLGQSEAEVESILHQGERAKQKMVTANLRLVVAIAKKYQNRNLEFLDLIQEGTLGLYR 120

Query: 89  AVKKFDPERGFRL 101
            V+K    R    
Sbjct: 121 GVEKLIQTRATNF 133


>gi|312884823|ref|ZP_07744515.1| DNA-directed RNA polymerase sigma subunit/flagellum specific
           [Vibrio caribbenthicus ATCC BAA-2122]
 gi|309367475|gb|EFP95035.1| DNA-directed RNA polymerase sigma subunit/flagellum specific
           [Vibrio caribbenthicus ATCC BAA-2122]
          Length = 256

 Score = 74.5 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 34/241 (14%), Positives = 83/241 (34%), Gaps = 31/241 (12%)

Query: 52  RLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
            L+  H  LV +I      +      I ++   G IGL++A +++   +      +++  
Sbjct: 41  ELLNLHQILVKRIVNQLKVHASSHCSIEDMQQIGLIGLLEAGRRYGDIQDPNFPAFAVCR 100

Query: 109 IKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           I+ A+ + + R  W           ++       L    + +     +      I   L 
Sbjct: 101 IRGAILDELRRLDWRS---------RKTRQAAHELNDVTRDLMRTLGRQPNDNEIIAALG 151

Query: 168 VSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
             E + I+          +SL+ L+    +                     E    +  R
Sbjct: 152 TDEKDYIARQNATLAGEMQSLDQLLEHGGEGHIDGNY--------------EGMSHEQTR 197

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             L ++++ L  RE+ I       ++ + L  ++    ++  R+ Q+  +A +++   + 
Sbjct: 198 RTLEKALTKLAKREQLIMTLFY--QHELNLHEIALVLNLTPPRICQLHKKALEQLNRYLS 255

Query: 286 K 286
            
Sbjct: 256 S 256


>gi|260866428|ref|YP_003232830.1| putative RNA polymerase, sigma 28 factor [Escherichia coli O111:H-
           str. 11128]
 gi|257762784|dbj|BAI34279.1| predicted RNA polymerase, sigma 28 factor [Escherichia coli O111:H-
           str. 11128]
 gi|323178476|gb|EFZ64054.1| RNA polymerase sigma factor for flagellar operon [Escherichia coli
           1180]
          Length = 213

 Score = 74.5 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 37/235 (15%), Positives = 98/235 (41%), Gaps = 31/235 (13%)

Query: 55  TSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFD-PERGFRLATYSMWWIK 110
            ++L LV K+           +   ++     +GL+ A++++  P+ G   A Y++  I+
Sbjct: 2   QAYLPLVRKVVRQLAPQCNCIIDRQDMEQTALMGLLNAIRRYGLPDEG--FAGYAVHRIR 59

Query: 111 AAMQEYI-LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
            A+ + +    W           ++L     ++K  ++          +   +A +  +S
Sbjct: 60  GAILDELRALDWRP---------RQLRQKYHQMKDLIRETRKKLGHEPEWSELAVE-GIS 109

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             + +    +L G E+L           +   + L  +  G   V  E E++   + ML 
Sbjct: 110 HEDYLEYQ-QLEGAETL-----------ASLDELLNGEGPGIPLVGRELEDQFVTQQMLQ 157

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +++S L+ +E+ I       ++ + L+ ++    ++  R+ Q+  +  +K+++ +
Sbjct: 158 QALSQLSEKEQLILSMYY--QHEMNLKEIALVLGLTEARICQLNKQIAQKIRDFV 210


>gi|145297471|ref|YP_001140312.1| LafS [Aeromonas salmonicida subsp. salmonicida A449]
 gi|22758825|gb|AAN04223.1| LafS [Aeromonas salmonicida]
 gi|142850243|gb|ABO88564.1| LafS [Aeromonas salmonicida subsp. salmonicida A449]
          Length = 235

 Score = 74.5 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 32/238 (13%), Positives = 91/238 (38%), Gaps = 31/238 (13%)

Query: 51  HRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
             ++T +L LV + A              ++   G +GL++A +++D E   +  +Y+  
Sbjct: 20  RAILTRYLPLVKRAASHLRSQVSACFDQEDMEQVGMMGLLEAWRRYDSEPDPQFESYAFK 79

Query: 108 WIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            I+ AM + + R  W           ++L   +       + + +   +      +A  L
Sbjct: 80  RIRGAMLDELRRLDWRP---------RQLRQQVHSHNQAQRELYNRLGRAPTEQELAVSL 130

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           N +  EV  +                +  + ++    L    +   +    + +  +   
Sbjct: 131 NCTVEEVRQL----------------AYASQAEALQSLEEWLENGGKAPATESDDVDMAM 174

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +++ ++ L+ RE+ +      QE  + ++ ++    ++  RV Q+  +   ++++ +
Sbjct: 175 TISKVLTSLDKREQLLLSLYYQQE--LNMKEIALVLGLTESRVCQLHKQCVLQLKQRL 230


>gi|315453792|ref|YP_004074062.1| putative RNA polymerase sigma factor for flagellar operon
           [Helicobacter felis ATCC 49179]
 gi|315132844|emb|CBY83472.1| putative RNA polymerase sigma factor for flagellar operon
           [Helicobacter felis ATCC 49179]
          Length = 232

 Score = 74.5 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 33/238 (13%), Positives = 87/238 (36%), Gaps = 28/238 (11%)

Query: 47  LSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            S+   L   +L  V  +A          +  ++++S G   L++  +++D         
Sbjct: 12  QSSQDALAIQYLPAVRAMAFRLKERLPSCVDFNDLISVGTEELIKLARRYDTSLNDSFWG 71

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   +  AM +Y+               +     ++++   +    + + +      +A
Sbjct: 72  YAKTRVNGAMLDYLR--------SLDVVSRASRKLIKKIDHEVSKYYNEHGQEPDDAYLA 123

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           + L    S++   + ++A D  + A +   ++ ++  Q  +             K E + 
Sbjct: 124 EVLGEDISKIR--DAKMASD--IYASVPIDEQFNAIEQRNINA-----------KLEFEE 168

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
               +   +  ++ RE+ I +    +E  + L  +     V+  R+ QI     KK++
Sbjct: 169 LIAHIHAILKTMSEREQLIIQLYFFEE--LNLSEIREILGVTESRISQIIKEVIKKIR 224


>gi|182420443|ref|ZP_02641505.2| RNA polymerase sigma factor RpoD [Clostridium perfringens NCTC
           8239]
 gi|182382221|gb|EDT79700.1| RNA polymerase sigma factor RpoD [Clostridium perfringens NCTC
           8239]
          Length = 237

 Score = 74.5 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 49/268 (18%), Positives = 105/268 (39%), Gaps = 70/268 (26%)

Query: 23  IRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG---YGLPISEVV 79
           I+++  +  +E  VL     + G+  A   L+ ++ +L+ K+A  +       +   +++
Sbjct: 5   IKEVKAMTNEELVVL----YQQGEKKALDELLENNDKLIYKVASKFYSEKTSSIEFDDLL 60

Query: 80  SEGNIGLMQAVKKFD--PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
            EG IG + A  K+D    +  +  TY+ +WI   +  +I R                  
Sbjct: 61  QEGRIGFILACSKYDIEYIKSTKFITYAFYWIYQKIHRFITR------------------ 102

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
                                          + +E IS+N  ++  E+ + LINS + NS
Sbjct: 103 ------------------------------YNTNEEISLNTPVSE-ENKDELINSIESNS 131

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE-NPVTLE 256
           ++  D          +  +   + +     +    + LN RE  I +     +   +++E
Sbjct: 132 NEINDR---------EEELYLSDLRIELESIMDRYNTLNERE--ILKLYYGWDTEELSIE 180

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
            ++  FE S   V+ I+ +A +K++ S+
Sbjct: 181 QIADIFETSSNEVKSIKGKAIRKLRNSM 208


>gi|297626395|ref|YP_003688158.1| RNA polymerase principal sigma factor HrdD [Propionibacterium
           freudenreichii subsp. shermanii CIRM-BIA1]
 gi|296922160|emb|CBL56728.1| RNA polymerase principal sigma factor HrdD [Propionibacterium
           freudenreichii subsp. shermanii CIRM-BIA1]
          Length = 272

 Score = 74.5 bits (182), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 42/262 (16%), Positives = 96/262 (36%), Gaps = 39/262 (14%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG-YGLPISEVVSEGNIGLMQ 88
             +E     ++   HG+L A  +    ++ LV  +   +         ++V EG +GL++
Sbjct: 45  SAEE----LRQVVAHGEL-AWQKFFEGNISLVRCVVARWVPVTHPDSEDLVHEGCMGLVE 99

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A+ +FD   G+R +T + + +   +    + +      GT A+ +R+     R++     
Sbjct: 100 AIMRFDHALGWRFSTLAWYLVSQQVAIAAVGN-RSCGSGTVAHARRV----ARIERARSR 154

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
            + +   P     +A  +  S   V     +    E+   ++  +  +     D      
Sbjct: 155 ASASRGAPVSDREVADLVGRSVEAVRRDLGQARRVEADQDILEQTIPDERPVHDV----- 209

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSR 266
                                  +S L  +ERR+ E      N    TL  ++    +S 
Sbjct: 210 ---------------------SFLSELADQERRVLELNFGIRNGRAQTLVQIAEHMGMSV 248

Query: 267 ERVRQIEARAFKKVQESIQKQV 288
             V +++ RA ++ +  +  ++
Sbjct: 249 SAVSRLKQRALRRGRALVHAEL 270


>gi|323140910|ref|ZP_08075823.1| Sigma-70 region 2 [Phascolarctobacterium sp. YIT 12067]
 gi|322414648|gb|EFY05454.1| Sigma-70 region 2 [Phascolarctobacterium sp. YIT 12067]
          Length = 211

 Score = 74.1 bits (181), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 45/162 (27%), Positives = 82/162 (50%), Gaps = 4/162 (2%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ E+RK  +LE +EE  L +R    GD +A  RL+T++  LV KIA  +R      
Sbjct: 2   LQGYLEELRKTSLLEPEEELELWRR-DAAGDEAAHQRLMTAYQPLVFKIASSFRLPEADT 60

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            E++ EG +GL++A + +D +R    + ++ + I+ +M +Y+  S     +   +   + 
Sbjct: 61  MELIQEGMVGLLEAAESYDYKRQVAFSLFASYRIRGSMVDYLRHSTDKGMLYLDSELSKG 120

Query: 136 FFNLRRLKGHL---QAITDNNLKPEQVVAIAKKLNVSESEVI 174
           F     L   L     +T+ +L  E+V     +L + E +V+
Sbjct: 121 FTLSDALPSELASPSEVTEQHLLCEKVAQAMDRLPLKEQQVL 162



 Score = 36.7 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 11/86 (12%), Positives = 38/86 (44%), Gaps = 2/86 (2%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L      +     E  E+      + ++M  L  +E+++ +   L++ P   + ++   +
Sbjct: 123 LSDALPSELASPSEVTEQHLLCEKVAQAMDRLPLKEQQVLQGMYLEDRPA--QAVADAID 180

Query: 264 VSRERVRQIEARAFKKVQESIQKQVE 289
           VS   V +++ +  ++++  + + + 
Sbjct: 181 VSLGHVYRLQKQGVRRIRGMLSRFIH 206


>gi|254431663|ref|ZP_05045366.1| group3 RNA polymerase sigma factor SigF1 [Cyanobium sp. PCC 7001]
 gi|197626116|gb|EDY38675.1| group3 RNA polymerase sigma factor SigF1 [Cyanobium sp. PCC 7001]
          Length = 257

 Score = 74.1 bits (181), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 46/250 (18%), Positives = 91/250 (36%), Gaps = 22/250 (8%)

Query: 40  RYREHGD---LSAAHRLVTSHLRLVVKIAMGYRGYG-LPISEVVSEGNIGLMQAVKKFDP 95
           R   H D   + A +R V  +  LV  IA+ Y      P+ +++  G +GL++A + + P
Sbjct: 8   RLSSHQDCRAIQARNRRVEQYKALVRPIALHYHHRCSEPLDDLIQVGLMGLLRAAELYRP 67

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
                   ++   ++ A+  Y+      +++    +++RL   L RL+    A       
Sbjct: 68  STATPFEAFARPHVRGALLHYLRDVALPIRLPRRLDEQRL--QLARLRSSWLAAHHR-PA 124

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
            EQ +     L+ S    +    +L   +SL+  ++   +      +    D    E+  
Sbjct: 125 TEQELRQLLGLDQSHWNRLQAAEQLVRVQSLDFWLDDGGEPPCAETETGPADPCRGEEAS 184

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV-RQIEA 274
                       L + +      ER I           T    +S   VS   V R++  
Sbjct: 185 APAALLAGLEEPLRQVV------ERVILA---GWSYRRT----ASALNVSPMTVQRRLH- 230

Query: 275 RAFKKVQESI 284
           RA   ++  +
Sbjct: 231 RALALLRGCL 240


>gi|87310296|ref|ZP_01092427.1| sigma-70 factor [Blastopirellula marina DSM 3645]
 gi|87287045|gb|EAQ78948.1| sigma-70 factor [Blastopirellula marina DSM 3645]
          Length = 287

 Score = 74.1 bits (181), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 41/236 (17%), Positives = 77/236 (32%), Gaps = 71/236 (30%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
               ++  ++LRLV  I+           E ++E N  L+ A+ KFD  RG+R +TY+  
Sbjct: 106 ETREQIACANLRLVTSISQKLSLSRDEFEEFLAESNAILLNAIDKFDYARGYRFSTYA-- 163

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
                               T A Q+ LF  + +     +  +   +      A A    
Sbjct: 164 --------------------THAVQRNLFRVIEKRNKRRKLESCEEVALHAATAPAA--- 200

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
                                                        +    ++      ++
Sbjct: 201 -------------------------------------------NPEEPSGQDVLSAFESI 217

Query: 228 LTRSMSVLNPRERRIFEARRLQEN---PVTLENLSSEFEVSRERVRQIEARAFKKV 280
           ++R   VL+ RE+ I   R   +      +L  +  E  +S+ER RQ+  R+ +K+
Sbjct: 218 MSRIDQVLDSREQFIVRERFGLDGIGKGKSLREIGEELGISKERTRQLFQRSIEKL 273


>gi|284989565|ref|YP_003408119.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Geodermatophilus obscurus DSM 43160]
 gi|284062810|gb|ADB73748.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Geodermatophilus obscurus DSM 43160]
          Length = 333

 Score = 74.1 bits (181), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 47/241 (19%), Positives = 93/241 (38%), Gaps = 22/241 (9%)

Query: 51  HRLVTSHLRL----VVKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
             LVT HL L    V  +A            +++S   + L++  ++FDP  G   ATY+
Sbjct: 48  DALVTEHLPLAAFAVNAVASRISLPAHVSREDLLSCARVALVEVARRFDPSAGASFATYA 107

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
           +  ++ A+ + + RS            + +    RR      A+     +P     +A  
Sbjct: 108 LARLQGAVLDEL-RSGDW-------ASRSVRAAARRTDAAADALAIQLGRPPTREELAAS 159

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           L ++ S++ S+   +       A++ S D  +    D    D     +       R  R 
Sbjct: 160 LGMARSDLESLQVDVHR-----AVMVSIDAETG--PDGASLDLPDTGESPERALLRSERS 212

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             L  ++  L  R   + E        +T  +++++  V+  RV Q+ ARA   +  ++ 
Sbjct: 213 RYLHEAIRQLPDRLDEVVERNFFGGESLT--DIAADLGVTLSRVSQMRARALTLLHAAMS 270

Query: 286 K 286
           +
Sbjct: 271 E 271


>gi|118474443|ref|YP_892645.1| flagellar biosynthesis sigma factor [Campylobacter fetus subsp.
           fetus 82-40]
 gi|118413669|gb|ABK82089.1| flagellar biosynthesis sigma factor FliA [Campylobacter fetus
           subsp. fetus 82-40]
          Length = 234

 Score = 74.1 bits (181), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 40/241 (16%), Positives = 91/241 (37%), Gaps = 28/241 (11%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
             +   LV S++  +  +A   +      + +++++S G   +++  + +D E+      
Sbjct: 17  KKSQDELVLSYMPALRAMAFRLKSRLPSSIEVNDLISVGATAMVKLSRTYDKEQNDSFWG 76

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y    +  +M +Y+ R    +  G     K +   +       +              +A
Sbjct: 77  YVKQRVYGSMIDYL-RGLDFLSRGNRKLVKDIDNAINEYFNKFE-------CEPDDAYLA 128

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           K L   E+++     R   D S    I+         Q  L+ + D +      K E+  
Sbjct: 129 KILGEDEAKIRE--ARNLSDVSATFPIDE--------QSQLLSESDTES-----KIEKDE 173

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               +T  ++    RE+ I +    +E  ++L+ +S    ++  R+ QI  R   K++E 
Sbjct: 174 LIQKITDVLNEFGEREQMIIQLYYYEE--LSLKEISDILGITESRISQIHKRLITKIRER 231

Query: 284 I 284
           +
Sbjct: 232 L 232


>gi|323492324|ref|ZP_08097477.1| DNA-directed RNA polymerase sigma subunit/flagellum specific
           [Vibrio brasiliensis LMG 20546]
 gi|323313371|gb|EGA66482.1| DNA-directed RNA polymerase sigma subunit/flagellum specific
           [Vibrio brasiliensis LMG 20546]
          Length = 223

 Score = 74.1 bits (181), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 41/240 (17%), Positives = 91/240 (37%), Gaps = 31/240 (12%)

Query: 51  HRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           ++L+  H  LV +I      +      I ++   G IGL++A +++          +++ 
Sbjct: 7   NKLLAQHQVLVKRIVNQLRAHATSHCSIEDMQQIGLIGLLEAGRRYGNIDDPNFPAFAVC 66

Query: 108 WIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            I+ A+ + + R  W           ++       L    + +     +      I K L
Sbjct: 67  RIRGAILDELRRLDWRS---------RKTRQQAHELNDVTRDLMRKLGRQPSDAEIIKAL 117

Query: 167 NVSESEVI-SMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
              E + +   N  LAG+  SL+ LI    ++  +      YD    EQ           
Sbjct: 118 GTDEQDYLARQNASLAGEMQSLDQLI----ESGVESHIDASYDGMAHEQT---------- 163

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L  ++  +  RE+ +       ++ + L  ++    ++  R+ Q+  +A K++ + +
Sbjct: 164 RRSLQAALDKMPQREQLLLTLFY--QHELNLHEIALVLNLTPPRICQLHKQALKQLNQFL 221


>gi|293392778|ref|ZP_06637096.1| DNA-directed RNA polymerase sigma subunit RpoS [Serratia odorifera
           DSM 4582]
 gi|291424637|gb|EFE97848.1| DNA-directed RNA polymerase sigma subunit RpoS [Serratia odorifera
           DSM 4582]
          Length = 119

 Score = 74.1 bits (181), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 27/119 (22%), Positives = 52/119 (43%), Gaps = 17/119 (14%)

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
             + S++  L GD     L   +D+  +  +D    D               + +  + +
Sbjct: 6   ERITSVDTPLGGDSEKALLDILADEKDNGPEDTTQDD---------------DMKQSIVK 50

Query: 231 SMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +  LN ++R +   R   L     TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 51  WLFELNAKQREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQMQ 109


>gi|260767948|ref|ZP_05876882.1| RNA polymerase sigma factor for flagellar operon [Vibrio furnissii
           CIP 102972]
 gi|260615978|gb|EEX41163.1| RNA polymerase sigma factor for flagellar operon [Vibrio furnissii
           CIP 102972]
 gi|315179652|gb|ADT86566.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio furnissii NCTC 11218]
          Length = 242

 Score = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 39/261 (14%), Positives = 102/261 (39%), Gaps = 31/261 (11%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQ 88
           Q+EY +A            +RL++ +  LV +++     +      + ++   G IGL++
Sbjct: 7   QDEYAMADEVASPTQPIDENRLLSQYQHLVKRVSNQLRVHATTHCSLEDMQQIGLIGLLE 66

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           A +++          +++  I+ A+ + + R  W           ++       L    +
Sbjct: 67  AGRRYGNIDDPNFPAFAVCRIRGAILDELRRLDWRS---------RKTRQQAHELNDVTR 117

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVI-SMNCRLAGDE-SLNALINSSDKNSSQWQDWLV 205
            +T    +      I   L   E +    +N  LAG+  SL+ LI++  +  +       
Sbjct: 118 DLTRKLGRQPSDREIIAALGTDEQDYYARLNASLAGEMQSLDQLIDTGVEQFADGHY--- 174

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
                      +    ++ R  L +++  L+ R++ +       ++ + L  ++   +++
Sbjct: 175 -----------DGMTHEHIRRSLEQAVGQLSKRDQLLLTLFY--QHELNLHEIALVLDLT 221

Query: 266 RERVRQIEARAFKKVQESIQK 286
             R+ Q+  +A K++ + +  
Sbjct: 222 PPRICQLHKQALKQLNQYLSS 242


>gi|15611460|ref|NP_223111.1| flagellar biosynthesis sigma factor [Helicobacter pylori J99]
 gi|4154925|gb|AAD05973.1| RNA POLYMERASE SIGMA FACTOR (sigma 28) [Helicobacter pylori J99]
          Length = 255

 Score = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 46/268 (17%), Positives = 105/268 (39%), Gaps = 32/268 (11%)

Query: 21  HEIRKIPMLEKQEEYVL-AKRYREHGDLSAAHRLVTSHLRLVVKIA---MGYRGYGLPIS 76
            EI+K    EK  E VL A   ++H    A   L   +L  V  +A          +  +
Sbjct: 11  KEIQKTEASEKSIEKVLNAYDKQQHHHQDA---LAIQYLPAVRAMAFRLKERLPSSIDFN 67

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           ++VS G   L++  ++++         Y+   +  AM +Y+ RS  ++   +    K + 
Sbjct: 68  DLVSIGTEELIKLARRYESALNDSFWGYAKTRVNGAMLDYL-RSLDVISRSSRKLIKSID 126

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
             + +         + + K      +A+ L  +  ++            + AL+   ++ 
Sbjct: 127 IEITK-------YLNEHGKEPSDEHLAEALGENIEKIREAKTA----SDIYALVPIDEQF 175

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           ++  QD +            +K E +     + + ++ ++ RE+ + +    +E  + L 
Sbjct: 176 NAIEQDEI-----------TQKIEAEELLEHIQKVLNQMSEREQILIQLYYFEE--LNLS 222

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
            +     ++  R+ QI     KKV++S+
Sbjct: 223 EIKEILGITESRISQIIKEVIKKVRQSL 250


>gi|333024157|ref|ZP_08452221.1| putative RNA polymerase sigma factor WhiG [Streptomyces sp. Tu6071]
 gi|332744009|gb|EGJ74450.1| putative RNA polymerase sigma factor WhiG [Streptomyces sp. Tu6071]
          Length = 123

 Score = 74.1 bits (181), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 21/123 (17%), Positives = 48/123 (39%), Gaps = 3/123 (2%)

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
             + V +   +     LA   +L  L++   +   +    +    D      +E  E + 
Sbjct: 1   MGVGVEDLHAVFSQLSLANVVALEELLSVGSEGGGRL-SIMDTLEDTGADNPVEVAEGRE 59

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            R +L+R+++ L  RE+ +          +TL  +     V+  RV QI  ++  +++  
Sbjct: 60  LRQLLSRAINSLPDREKTVVMLYYY--EGLTLAEIGHVLGVTESRVSQIHTKSVLQLRAK 117

Query: 284 IQK 286
           +  
Sbjct: 118 LSS 120


>gi|313681607|ref|YP_004059345.1| RNA polymerase, sigma 28 subunit, sigd/flia/whig [Sulfuricurvum
           kujiense DSM 16994]
 gi|313154467|gb|ADR33145.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Sulfuricurvum
           kujiense DSM 16994]
          Length = 230

 Score = 73.7 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 33/216 (15%), Positives = 83/216 (38%), Gaps = 29/216 (13%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              ++ + G   L++  +++D  +      Y+   +  AM +Y+ RS  +V   +    K
Sbjct: 42  DYMDLCAIGTEELVKLARRYDESQNDSFWGYAKTRVYGAMLDYL-RSLDMVSRSSRRLIK 100

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            +   +       +    ++        ++  L + E +V     R+A D          
Sbjct: 101 EIDHAI-------EVYMADHDDEPSDSELSVILGIEEDKVRE--ARIASDI--------- 142

Query: 194 DKNSSQWQDWLVYDHDGQEQV--LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
                 +    + D  G  +   ++E+ E ++    +   +     RE+ I +    +E 
Sbjct: 143 ------YTVLPLDDQLGTPEEGGMLERMEHEDLIEAIQEVLMTFEEREQIIIQLYYFEE- 195

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            +TL+ +S    ++  R+ QI     ++++E++  Q
Sbjct: 196 -LTLKEISEIVNITESRISQIHKSVIRRIKEAVGGQ 230


>gi|146305232|ref|YP_001185697.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Pseudomonas mendocina
           ymp]
 gi|145573433|gb|ABP82965.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Pseudomonas
           mendocina ymp]
          Length = 244

 Score = 73.7 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 41/236 (17%), Positives = 92/236 (38%), Gaps = 30/236 (12%)

Query: 49  AAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           A  + +  +L LV +I           L   ++   G +GL++ ++++      +   ++
Sbjct: 25  AEQKWLLQYLPLVKRIVSQLALQANQVLDREDMEQIGLMGLLECLRRYG-TPDEQFGRFA 83

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
              I+ A+ + + R             +++     R++  ++ +     +  Q   I   
Sbjct: 84  ALRIRGAILDELRRQDW--------RPRQVRQQTHRIRDAIRQLARQLGRVPQEEEILAA 135

Query: 166 LNVSESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
             +            A +  ESL+ L+ S               H+G        EER  
Sbjct: 136 AGIDAKTYQEFLQADACEAIESLDELLQSG--------------HEGFVCGASAVEERVL 181

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           +  +LT+++S L+ RER +       ++ ++L+ ++   E+S  RV Q+  +A  K
Sbjct: 182 KERLLTQALSQLSERERLVLTLYY--QHELSLKEIALVLELSDARVCQLSKQAIAK 235


>gi|222112349|ref|YP_002554613.1| sigma-70 region 4 domain-containing protein [Acidovorax ebreus
           TPSY]
 gi|221731793|gb|ACM34613.1| sigma-70 region 4 domain protein [Acidovorax ebreus TPSY]
          Length = 893

 Score = 73.7 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 25/60 (41%), Positives = 36/60 (60%), Gaps = 1/60 (1%)

Query: 226 NMLTRSMSVLNPRERRIFEAR-RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + +  +   LN  ER IF AR   +  P TL+ +S +  VSRERVRQIE + FKK++  +
Sbjct: 339 DGIVEAAQCLNENERGIFAARLGFRCEPHTLQQISDQIGVSRERVRQIEVKIFKKIRRHL 398


>gi|329897641|ref|ZP_08272165.1| RNA polymerase sigma factor for flagellar operon [gamma
           proteobacterium IMCC3088]
 gi|328921090|gb|EGG28499.1| RNA polymerase sigma factor for flagellar operon [gamma
           proteobacterium IMCC3088]
          Length = 204

 Score = 73.7 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 36/212 (16%), Positives = 82/212 (38%), Gaps = 20/212 (9%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + E+V  G IGL++A K FD  +G  LA+++   I+ A+ + + R   L +      Q 
Sbjct: 12  ELEELVQIGMIGLLEAFKSFDESQGDDLASFATKRIRGAILDEVRRRSPLSR------QD 65

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            +    R  +  +        +    V I+ ++ V+  +      +           ++ 
Sbjct: 66  NIHAKTR--EAIIDDHLARTGRRPSAVEISSEMGVTLEDYHRSEMK----------THTY 113

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
             +S +      ++         E+ E      +L   +  L  R++ I       E  +
Sbjct: 114 QLSSYEVLTENGFEQAHDADSPDEEIEHSQTLGILETRIGQLEQRDQLILSLYY--EKEL 171

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            L+ + S   +S  RV Q+ ++   +++  ++
Sbjct: 172 NLKEIGSILNISESRVSQLLSKIVTQLRAEVR 203


>gi|229587513|ref|YP_002860551.1| putative sporulation sigma factor SigK [Clostridium botulinum Ba4
           str. 657]
 gi|229260138|gb|ACQ51175.1| putative sporulation sigma factor SigK [Clostridium botulinum Ba4
           str. 657]
          Length = 271

 Score = 73.7 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 44/243 (18%), Positives = 96/243 (39%), Gaps = 27/243 (11%)

Query: 50  AHRLVTSHLRLVVKIAMGYRG----YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
              L+  +  L+V+    Y       G+   +++ +  +G ++A++KFD  +G  L+TY+
Sbjct: 38  KEELLKRYEGLIVQWTNKYFKILNVQGMEFDDLLIDAKLGFLKALEKFDINKGNALSTYA 97

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
              ++  +   I  + +++K+ +    KR+     +L    +A   N             
Sbjct: 98  THCMRNYILNSIRVNNNMIKLSSREVNKRI-----KLSKKFKANILNKGN------YKFN 146

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
            N+        N RL            + +  S   +  +      E++ +EKE+++   
Sbjct: 147 YNIYNKIFSQHNVRL----------IDTHEYQSYLDNSSIEQEISSEEMFMEKEQKRFNT 196

Query: 226 NMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +  ++ +L+  E  I        N    TL  LS    +  E  R+I+ +A  K++  
Sbjct: 197 RQIISALKILDKTELFIIVHYFGLFNKKKRTLRELSKRLNIGYENTRKIKGKALSKIECY 256

Query: 284 IQK 286
            +K
Sbjct: 257 FKK 259


>gi|208434361|ref|YP_002266027.1| alternative transcription initiation factor, sigma-F [Helicobacter
           pylori G27]
 gi|208432290|gb|ACI27161.1| alternative transcription initiation factor, sigma-F [Helicobacter
           pylori G27]
          Length = 247

 Score = 73.7 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 36/238 (15%), Positives = 94/238 (39%), Gaps = 28/238 (11%)

Query: 50  AHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L   +L  V  +A          +  +++VS G   L++  ++++         Y+ 
Sbjct: 30  QDDLAIQYLPAVRAMAFRLKERLPSSIDFNDLVSIGTEELIKLARRYESALNDSFWGYAK 89

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +  AM +Y+      + + + +N+K +      +  HL    + + K      +A+ L
Sbjct: 90  TRVNGAMLDYL----RSLDVISRSNRKLIKSIDAEITKHL----NEHGKEPSDAYLAEAL 141

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             +  ++            + AL+   ++ ++  QD +            +K E +    
Sbjct: 142 GENIEKIREAKTA----SDIYALVPIDEQFNAIEQDEI-----------TKKIEAEELLE 186

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + ++++ ++ RE+ + +    +E  + L  +     ++  R+ QI     KKV++S+
Sbjct: 187 HVQKALNQMSEREQILIQLYYFEE--LNLSEIKEILGITESRISQIIKEVIKKVRKSL 242


>gi|124023188|ref|YP_001017495.1| hypothetical protein P9303_14841 [Prochlorococcus marinus str. MIT
           9303]
 gi|123963474|gb|ABM78230.1| Hypothetical protein P9303_14841 [Prochlorococcus marinus str. MIT
           9303]
          Length = 237

 Score = 73.7 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 45/232 (19%), Positives = 92/232 (39%), Gaps = 34/232 (14%)

Query: 50  AHRLVTSHLRLVVKIAMGYR-GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
            ++ +  HL+LV  IA+ Y    G    ++   G +GL++A + F   +    A ++   
Sbjct: 8   RNKQIEEHLQLVRPIALHYAFRTGQDKEDLTQVGMLGLIRAAQFFQSSKSVPFAAFAKPH 67

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+  Y+  S   VKI             RRL+   QA+   +       +  +KL+ 
Sbjct: 68  IRGAILHYLRDSLGPVKIP------------RRLEERAQALL-RDSTLMDSASFIEKLSA 114

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
            +   I    +      L+               ++  D D   +++      K R  ML
Sbjct: 115 VDRTAIESYKQKGRWYPLD-------------HQFITADKDQWSELV-----DKERNRML 156

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++  L+ +E  + +   L+    +L + +S   +S   V++   RA +++
Sbjct: 157 MNALEKLDCQEFAVVDHVVLRGE--SLRSTASYLGISCMTVQRRVKRALRRL 206


>gi|291519565|emb|CBK74786.1| RNA polymerase, sigma 28 subunit, SigD/FliA/WhiG [Butyrivibrio
           fibrisolvens 16/4]
          Length = 194

 Score = 73.7 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 34/171 (19%), Positives = 70/171 (40%), Gaps = 13/171 (7%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKF 93
           L  +Y+         +L+  +  LV  +A     Y G  +   ++ S G  GL+ A+ KF
Sbjct: 9   LWDKYKVTPTPELREQLILEYAPLVKIVAGRLCMYLGNTVEYEDLCSYGIFGLIDAIDKF 68

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D  +  +  TY+   I+ ++ + I +   +  I  T  Q++     R +   ++ +    
Sbjct: 69  DLAKDVKFETYASLRIRGSILDQIRK---MDWIPRTIRQRQ-----RMIDDAIKTVEART 120

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQD 202
                   IA +LN+S  E +    +L      SLN  + + ++   + + 
Sbjct: 121 GHSASDEDIAAELNISSDEFLKWQNQLNVTNVVSLNEFVEAGNEPVMEAEH 171


>gi|149189848|ref|ZP_01868128.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio shilonii AK1]
 gi|148836334|gb|EDL53291.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio shilonii AK1]
          Length = 242

 Score = 73.7 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 40/242 (16%), Positives = 94/242 (38%), Gaps = 31/242 (12%)

Query: 51  HRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           +RL++ H  LV ++    R        I ++   G IGL++A +++          +++ 
Sbjct: 26  NRLLSQHQILVKRVVNQLRNHATTHCSIEDMQQIGLIGLLEAGRRYGNIDDPNFPAFAVC 85

Query: 108 WIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            I+ ++ + + R  W           ++       L    + +T    +      I K L
Sbjct: 86  RIRGSILDELRRLDWRS---------RKTRQQAHELNDITRDLTKALKRMPTEQEIIKAL 136

Query: 167 NVSESEVI-SMNCRLAGDE-SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
              +++    ++  +AG+  SL+ LI    +              GQ     E    ++ 
Sbjct: 137 GTDQADYHTRLSASMAGEMQSLDQLIEKGLE--------------GQVDSAYEGMSHEHI 182

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L  +++ L  RE+         ++ + L  ++   E++  R+ Q+  +A K++ + +
Sbjct: 183 RRSLEVALAKLPKREQ--LLMTLFYQHELNLHEIALVLELTPPRICQLHKQALKQLNQLL 240

Query: 285 QK 286
             
Sbjct: 241 SS 242


>gi|255316500|ref|ZP_05358083.1| sporulation sigma factor SigK [Clostridium difficile QCD-76w55]
          Length = 215

 Score = 73.7 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 33/253 (13%), Positives = 85/253 (33%), Gaps = 58/253 (22%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           AK  +E        ++  ++ +L+  +            E+ S G +G  +A++ FD +R
Sbjct: 15  AKIEKEFYTKEEKEKVAYANNKLIHHVIKQLNTNVASHDELYSVGLVGYAKALESFDKKR 74

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
             + +TY++  I+  +                       + LR+   H +          
Sbjct: 75  NVKFSTYAINCIRNEI----------------------LYFLRKENNHNK---------- 102

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
                                      S N +++S     +   + ++ + +  ++   +
Sbjct: 103 ------------------------NTVSFNKILSSDKDGHNLELEDIISEDEISKKRFED 138

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEAR 275
               K  R  + +++  L   ER +   R    N   +T   +     +S+  + +I+  
Sbjct: 139 NLVDKEDRETILKALEFLKEEERIVIIYRFGLNNGIMMTQSEIGKMINMSQANISKIQKS 198

Query: 276 AFKKVQESIQKQV 288
           +  K++  + K +
Sbjct: 199 SIDKLRLILDKNI 211


>gi|327188541|gb|EGE55752.1| RNA polymerase sigma factor RpoD [Rhizobium etli CNPAF512]
          Length = 764

 Score = 73.7 bits (180), Expect = 3e-11,   Method: Composition-based stats.
 Identities = 20/60 (33%), Positives = 34/60 (56%), Gaps = 2/60 (3%)

Query: 228 LTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L   +   N R+R + E R    +    TLE + S++ V+RER+RQIE RA  +++  ++
Sbjct: 144 LDWLLGQCNARDRLVIERRFGLGSNARETLEEIGSDYGVTRERIRQIEKRALTRMRVRMR 203


>gi|307637111|gb|ADN79561.1| RNA polymerase sigma factor [Helicobacter pylori 908]
 gi|325995702|gb|ADZ51107.1| RNA polymerase sigma factor of flagellar operon [Helicobacter
           pylori 2018]
 gi|325997298|gb|ADZ49506.1| Flagellar biosynthesis sigma factor [Helicobacter pylori 2017]
          Length = 247

 Score = 73.7 bits (180), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 34/238 (14%), Positives = 91/238 (38%), Gaps = 28/238 (11%)

Query: 50  AHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L   +L  V  +A          +  +++VS G   L++  ++++         Y+ 
Sbjct: 30  QDALAIQYLPAVRAMAFRLKERLPSSIDFNDLVSIGTEELIKLARRYESALNDSFWGYAK 89

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +  AM +Y+ RS  ++   +    K +   + +         + + +      +A+ L
Sbjct: 90  TRVNGAMLDYL-RSLDVISRSSRKLIKSIDIEITK-------YLNEHGEEPSDAYLAEVL 141

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             +  ++            + AL+   ++ ++  QD +            +K E +    
Sbjct: 142 GENIEKIREAKTA----SDIYALVPIDEQFNAIEQDEI-----------TQKIEAEELLE 186

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + + ++ ++ RE+ + +    +E  + L  +     ++  R+ QI     KKV++S+
Sbjct: 187 HVQKVLNQMSEREQILIQLYYFEE--LNLSEIKEILGITESRISQIIKEVIKKVRQSL 242


>gi|169834851|ref|YP_001715950.1| putative sporulation sigma factor SigK [Clostridium botulinum A3
           str. Loch Maree]
 gi|169408958|gb|ACA57368.1| putative sporulation sigma factor SigK [Clostridium botulinum A3
           str. Loch Maree]
          Length = 271

 Score = 73.3 bits (179), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 44/243 (18%), Positives = 96/243 (39%), Gaps = 27/243 (11%)

Query: 50  AHRLVTSHLRLVVKIAMGYRG----YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
              L+  +  L+V+    Y       G+   +++ +  +G ++A++KFD  +G  L+TY+
Sbjct: 38  KEELLKRYEGLIVQWTNKYFKILNVQGMEFDDLLIDAKLGFLKALEKFDINKGNALSTYA 97

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
              ++  +   I  + +++K+ +    KR+     +L    +A   N             
Sbjct: 98  THCMRNYILNSIRVNNNMIKLSSREVNKRI-----KLSKKFKANILNKGN------YKFN 146

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
            N+        N RL            + +  S   +  +      E++ +EKE+++   
Sbjct: 147 YNIYNKIFSQHNVRL----------IDTHEYQSYLDNSSIEQEISSEEMFMEKEQKRFNT 196

Query: 226 NMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             +  ++ +L+  E  I        N    TL  LS    +  E  R+I+ +A  K++  
Sbjct: 197 RQIISALKILDKTELFIIVHYFGLFNKKKRTLRELSKRLNIGYENTRKIKGKALSKIECH 256

Query: 284 IQK 286
            +K
Sbjct: 257 FKK 259


>gi|317013857|gb|ADU81293.1| flagellar biosynthesis sigma factor [Helicobacter pylori
           Gambia94/24]
          Length = 255

 Score = 73.3 bits (179), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 46/268 (17%), Positives = 105/268 (39%), Gaps = 32/268 (11%)

Query: 21  HEIRKIPMLEKQEEYVL-AKRYREHGDLSAAHRLVTSHLRLVVKIA---MGYRGYGLPIS 76
            EI+K    EK  E VL A   ++H    A   L   +L  V  +A          +  +
Sbjct: 11  KEIQKTEASEKSIEKVLNAYDKQQHHHQDA---LAIQYLPAVRAMAFRLKERLPSSIDFN 67

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           ++VS G   L++  ++++         Y+   +  AM +Y+ RS  ++   +    K + 
Sbjct: 68  DLVSIGTEELIKLARRYESALNDSFWGYAKTRVNGAMLDYL-RSLDVISRSSRKLIKSID 126

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
             + +         + + K      +A+ L  +  ++            + AL+   ++ 
Sbjct: 127 IEITK-------YLNEHGKEPSDAYLAEALGENIEKIREAKTA----SDIYALVPIDEQF 175

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           ++  QD +            +K E +     + + ++ ++ RE+ + +    +E  + L 
Sbjct: 176 NAIEQDEI-----------TQKIEAEELLEHVQKVLNQMSEREQILIQLYYFEE--LNLS 222

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
            +     ++  R+ QI     KKV++S+
Sbjct: 223 EIKEILGITESRISQIIKEVIKKVRQSL 250


>gi|124023131|ref|YP_001017438.1| type III sigma factor [Prochlorococcus marinus str. MIT 9303]
 gi|123963417|gb|ABM78173.1| putative type III sigma factor [Prochlorococcus marinus str. MIT
           9303]
          Length = 269

 Score = 73.3 bits (179), Expect = 4e-11,   Method: Composition-based stats.
 Identities = 44/215 (20%), Positives = 92/215 (42%), Gaps = 15/215 (6%)

Query: 50  AHRLVTSHLRLVVKIA-MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
            ++ V  HL L    A       G  + +++ E  +GL+ A++KFD  RGF++++Y+M  
Sbjct: 39  RNQAVIEHLGLAHLAATRQATRGGEELDDLIQEARLGLIMAMEKFDANRGFKVSSYAMAR 98

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
               +  +      +V++      + L+    RL+   Q   ++ L P     +A +LNV
Sbjct: 99  ANGQILHFRRDRSQIVRVPWRL--RDLYTRGMRLQQMQQ---NDGLNPLTEEQLAAQLNV 153

Query: 169 SESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           S          +      SL+A   S+  N ++ +  L+      +Q      E   ++ 
Sbjct: 154 SSDRWHQAAEAVWQTNLVSLDAKETSTAGNHAEKRVSLLELLKSPKQK-----EPDLQQQ 208

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
            L +++  L P ++ +  A  + +  ++L  L+  
Sbjct: 209 WLKKAIERLTPHQQHLLYAHYIDD--ISLRQLAKR 241


>gi|317177227|dbj|BAJ55016.1| flagellar biosynthesis sigma factor [Helicobacter pylori F16]
          Length = 250

 Score = 72.9 bits (178), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 36/238 (15%), Positives = 94/238 (39%), Gaps = 28/238 (11%)

Query: 50  AHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L   +L  V  +A          +  +++VS G   L++  ++++         Y+ 
Sbjct: 33  QDALAIQYLPAVRAMAFRLKERLPSSIDFNDLVSIGTEELIKLARRYESALNDSFWGYAK 92

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +  AM +Y+      + + + +N+K +      +  HL    + + K      +A+ L
Sbjct: 93  TRVNGAMLDYL----RSLDVISRSNRKLIKSIDAEITKHL----NEHGKEPSDAYLAEVL 144

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             +  ++            + AL+   ++ ++  QD +            +K E +    
Sbjct: 145 GENIEKIKEAKTA----SDIYALVPIDEQFNAIEQDEI-----------TKKIEAEELLE 189

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + ++++ ++ RE+ + +    +E  + L  +     ++  R+ QI     KKV++S+
Sbjct: 190 HVQKALNQMSEREQILIQLYYFEE--LNLSEIKEILGITESRISQIIKEVIKKVRKSL 245


>gi|254779107|ref|YP_003057212.1| flagellar biosynthesis sigma factor [Helicobacter pylori B38]
 gi|254001018|emb|CAX28962.1| RNA polymerase sigma factor for flagellar operon (Sigma-F factor)
           (Sigma-27) (Sigma-28) [Helicobacter pylori B38]
          Length = 255

 Score = 72.9 bits (178), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 36/238 (15%), Positives = 94/238 (39%), Gaps = 28/238 (11%)

Query: 50  AHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L   +L  V  +A          +  +++VS G   L++  ++++         Y+ 
Sbjct: 38  QDALAIQYLPAVRAMAFRLKERLPSSIDFNDLVSIGTEELIKLARRYESALNDSFWGYAK 97

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +  AM +Y+      + + + +N+K +      +  HL    + + K      +A+ L
Sbjct: 98  TRVNGAMLDYL----RSLDVISRSNRKLIKSIDAEITKHL----NEHGKEPSDAYLAQTL 149

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             +  ++            + AL+   ++ ++  QD +            +K E +    
Sbjct: 150 GENIEKIREAKTA----SDIYALVPIDEQFNAIEQDEI-----------TKKIEAEELLE 194

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + ++++ ++ RE+ + +    +E  + L  +     ++  R+ QI     KKV++S+
Sbjct: 195 HVKKALNQMSEREQILIQLYYFEE--LNLSEIKEILGITESRISQIIKEVIKKVRKSL 250


>gi|308061767|gb|ADO03655.1| flagellar biosynthesis sigma factor [Helicobacter pylori Cuz20]
          Length = 258

 Score = 72.9 bits (178), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 36/238 (15%), Positives = 94/238 (39%), Gaps = 28/238 (11%)

Query: 50  AHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L   +L  V  +A          +  +++VS G   L++  ++++         Y+ 
Sbjct: 41  QDALAIQYLPAVRAMAFRLKERLPSSIDFNDLVSIGTEELIKLARRYESALNDSFWGYAK 100

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +  AM +Y+      + + + +N+K +      +  HL    + + K      +A+ L
Sbjct: 101 TRVNGAMLDYL----RSLDVISRSNRKLIKSIDNEITKHL----NEHGKEPSDAYLAEVL 152

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             +  ++            + AL+   ++ ++  QD +            +K E +    
Sbjct: 153 GENIEKIKEAKTA----SDIYALVPIDEQFNAIEQDEI-----------TKKIEAEELLE 197

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + ++++ ++ RE+ + +    +E  + L  +     ++  R+ QI     KKV++S+
Sbjct: 198 HVQKALNQMSEREQILIQLYYFEE--LNLSEIKEILGITESRISQIIKEVIKKVRKSL 253


>gi|289523531|ref|ZP_06440385.1| RNA polymerase sigma factor WhiG [Anaerobaculum hydrogeniformans
           ATCC BAA-1850]
 gi|289503223|gb|EFD24387.1| RNA polymerase sigma factor WhiG [Anaerobaculum hydrogeniformans
           ATCC BAA-1850]
          Length = 189

 Score = 72.9 bits (178), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 24/87 (27%), Positives = 46/87 (52%), Gaps = 1/87 (1%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           E  L +R +  GD  A   ++ S+  +V  +A  +        +++ EG + L++AV ++
Sbjct: 16  EENLWQRIK-FGDEKAREEVIISYRPMVFWLAKKFHVPSDSYQDLIQEGMVALIEAVDRY 74

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRS 120
           D +RG +  TY+ + IK  M  ++ RS
Sbjct: 75  DAKRGTKFITYAYYRIKGRMVNFLERS 101



 Score = 39.4 bits (91), Expect = 0.74,   Method: Composition-based stats.
 Identities = 13/80 (16%), Positives = 36/80 (45%), Gaps = 2/80 (2%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           V   D   +  +   + +     L  ++  L+ RE  I +A  +  N ++++ ++ +  V
Sbjct: 109 VDIDDHLYESNMASFDDEGWLIDLEAAIRSLSEREAEIVKA--VDLNGLSVKEVARKKGV 166

Query: 265 SRERVRQIEARAFKKVQESI 284
               + ++  RA  K+++ +
Sbjct: 167 DISYIYRLRRRAIAKLKKVL 186


>gi|160934631|ref|ZP_02082017.1| hypothetical protein CLOLEP_03504 [Clostridium leptum DSM 753]
 gi|156866084|gb|EDO59456.1| hypothetical protein CLOLEP_03504 [Clostridium leptum DSM 753]
          Length = 251

 Score = 72.9 bits (178), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 39/222 (17%), Positives = 91/222 (40%), Gaps = 26/222 (11%)

Query: 48  SAAHRLVTSHLRLVVKIAM-GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            A   ++  + + V  I    +  Y     ++   G  GL++A++ +DP       TY  
Sbjct: 23  EAKKAVIEDYSKFVSYIIKEKFYSYRKHWEDLFQCGICGLLKALENYDPHFSKP-TTYFY 81

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           ++I   + ++I +         +   K L  ++ +LK          +       +AK +
Sbjct: 82  YFIVQEINDFISKYIEGTNRYYSRKVKSLDESILKLKRS-------GIPEPSARELAKVM 134

Query: 167 NVSESEVISMNC--RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
           N+ E+   ++     ++   SL+ LI S+          L+ D+    +VL+EK   +  
Sbjct: 135 NLKETSARNLIRIKHISQPISLDYLIESN----------LLKDNQTYVEVLVEK---RML 181

Query: 225 RNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEV 264
           + +L +++  L   E+++ E +        +T + +S +  +
Sbjct: 182 KEILEKAVFSLPKNEKKVIERKFGLFGHTKMTNQEISVDTGI 223


>gi|317181757|dbj|BAJ59541.1| flagellar biosynthesis sigma factor [Helicobacter pylori F57]
          Length = 250

 Score = 72.9 bits (178), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 36/238 (15%), Positives = 94/238 (39%), Gaps = 28/238 (11%)

Query: 50  AHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L   +L  V  +A          +  +++VS G   L++  ++++         Y+ 
Sbjct: 33  QDALAIQYLPAVRAMAFRLKERLPSSIDFNDLVSIGTEELIKLARRYESALNDSFWGYAK 92

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +  AM +Y+      + + + +N+K +      +  HL    + + K      +A+ L
Sbjct: 93  TRVNGAMLDYL----RSLDVISRSNRKLIKSIDAEITKHL----NEHGKEPSDAYLAEVL 144

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             +  ++            + AL+   ++ ++  QD +            +K E +    
Sbjct: 145 GENIEKIKEAKTA----SDIYALVPIDEQFNAIEQDEI-----------TKKIEAEELLE 189

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + ++++ ++ RE+ + +    +E  + L  +     ++  R+ QI     KKV++S+
Sbjct: 190 HVQKALNQMSEREQILIQLYYFEE--LNLSEIKEILGITESRISQIIKEVIKKVRKSL 245


>gi|56964615|ref|YP_176346.1| DNA-directed RNA polymerase sigma factor [Bacillus clausii KSM-K16]
 gi|56910858|dbj|BAD65385.1| DNA-directed RNA polymerase sigma factor [Bacillus clausii KSM-K16]
          Length = 220

 Score = 72.9 bits (178), Expect = 5e-11,   Method: Composition-based stats.
 Identities = 41/226 (18%), Positives = 86/226 (38%), Gaps = 33/226 (14%)

Query: 50  AHRLVTSHLRLVVKIAMGY----RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
            + ++ S++ LV KIA       R      S+++S G IGL+ AV+ ++ ++G   A Y+
Sbjct: 7   QNEMILSNMGLVHKIAKDLKWSIRSSWFHYSDLISVGTIGLINAVENYENKKGITFAAYA 66

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
           +  I+ +M + + +  + + +        L   L+ L          N     V  +A  
Sbjct: 67  VPVIRRSMLKALNKQMAGLSVPDYI--IELVPRLKSL---------ENWGNLSVEEVASI 115

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           L +   +              N LI  +  +       +  D D  E      +      
Sbjct: 116 LGIPTKKAR------------NLLIAVNRPDLISMDSEVKEDRDYNEVFGARTDYGMIY- 162

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
             +   ++ L  R++ I EA+       + + ++S +  S + + Q
Sbjct: 163 --VNDFLNTLKERDKEILEAKLAG---YSQQEIASMYGTSPQAISQ 203


>gi|296121384|ref|YP_003629162.1| RNA polymerase sigma factor, sigma-70 family [Planctomyces
           limnophilus DSM 3776]
 gi|296013724|gb|ADG66963.1| RNA polymerase sigma factor, sigma-70 family [Planctomyces
           limnophilus DSM 3776]
          Length = 376

 Score = 72.9 bits (178), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 23/99 (23%), Positives = 47/99 (47%), Gaps = 4/99 (4%)

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIE-KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           ++  ++   + L    D +  V  +  E ++  +  LT  +  L+ RER +  AR   + 
Sbjct: 269 NEHTTAYIHEALEQFEDFRSPVETQPGESQEACQRELTSLLETLSDRERAVIAARFGLDG 328

Query: 252 ---PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
                +L  +S    +S+ERVRQI  +A  K++   +++
Sbjct: 329 QPRGQSLSEISGRIGLSKERVRQIVLKALDKLKLYAEQK 367



 Score = 64.8 bits (157), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 24/71 (33%), Positives = 44/71 (61%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A +++V ++LRLVV +A    G    ++E+VSEG + L+++V+ FD   G R +TY+ W 
Sbjct: 194 ARNQIVQANLRLVVALARKCCGSIEQLAELVSEGVMPLIRSVELFDISLGNRFSTYATWA 253

Query: 109 IKAAMQEYILR 119
           ++  M  +  +
Sbjct: 254 VRNQMHRHFKK 264


>gi|188527224|ref|YP_001909911.1| flagellar biosynthesis sigma factor [Helicobacter pylori Shi470]
 gi|188143464|gb|ACD47881.1| flagellar biosynthesis sigma factor [Helicobacter pylori Shi470]
 gi|317179191|dbj|BAJ56979.1| flagellar biosynthesis sigma factor [Helicobacter pylori F30]
          Length = 250

 Score = 72.5 bits (177), Expect = 6e-11,   Method: Composition-based stats.
 Identities = 35/238 (14%), Positives = 91/238 (38%), Gaps = 28/238 (11%)

Query: 50  AHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L   +L  V  +A          +  +++VS G   L++  ++++         Y+ 
Sbjct: 33  QDALAIQYLPAVRAMAFRLKERLPSSIDFNDLVSIGTEELIKLARRYESALNDSFWGYAK 92

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +  AM +Y+ RS  ++        K +   + +         + + K      +A+ L
Sbjct: 93  TRVNGAMLDYL-RSLDVISRSNRKLIKSIDIEITKH-------LNEHGKEPSDAYLAEVL 144

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             +  ++            + AL+   ++ ++  QD +            +K E +    
Sbjct: 145 GENIEKIKEAKTA----SDIYALVPIDEQFNAIEQDEI-----------TKKIEAEELLE 189

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + ++++ ++ RE+ + +    +E  + L  +     ++  R+ QI     KKV++S+
Sbjct: 190 HVQKALNQMSEREQILIQLYYFEE--LNLSEIKEILGITESRISQIIKEVIKKVRKSL 245


>gi|260653773|dbj|BAI44426.1| DNA-directed RNA polymerase sigma 32 subunit, RpoH subfamily
          [Monochamus alternatus]
          Length = 56

 Score = 72.5 bits (177), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 32/54 (59%), Positives = 43/54 (79%)

Query: 46 DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
          D+S+AH+L+TSHL LV KIAM ++ YGL   ++V EGN+GLM  VKKF+P+ GF
Sbjct: 3  DISSAHKLITSHLNLVXKIAMKFKNYGLLFMDLVMEGNMGLMHPVKKFNPDLGF 56


>gi|238789522|ref|ZP_04633307.1| RNA polymerase sigma factor [Yersinia frederiksenii ATCC 33641]
 gi|238722472|gb|EEQ14127.1| RNA polymerase sigma factor [Yersinia frederiksenii ATCC 33641]
          Length = 531

 Score = 72.5 bits (177), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 22/84 (26%), Positives = 42/84 (50%), Gaps = 2/84 (2%)

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN-PRERRIFEARRL-QENPVTLE 256
              +  + D     + L       +   +++ ++  L+  R+R I   R    E+P TL 
Sbjct: 132 TPDEKQITDFVPNTEFLDYVASESDVIMLVSAAVESLSKERDRDILLMRLGMDEHPHTLA 191

Query: 257 NLSSEFEVSRERVRQIEARAFKKV 280
            ++ +  +SRERVRQI+ RAF+++
Sbjct: 192 EIAIKLGISRERVRQIQERAFRRL 215


>gi|302669016|ref|YP_003832841.1| RNA polymerase sigma factor sigma-70 family protein [Butyrivibrio
           proteoclasticus B316]
 gi|302397356|gb|ADL36259.1| RNA polymerase sigma factor sigma-70 family [Butyrivibrio
           proteoclasticus B316]
          Length = 378

 Score = 72.5 bits (177), Expect = 7e-11,   Method: Composition-based stats.
 Identities = 45/274 (16%), Positives = 99/274 (36%), Gaps = 25/274 (9%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHR----LVTSHLRLVVKIAMGYRGYGL--PISEVVSEGN 83
             QE   L    ++  D     R     V S   LV+ +   Y    +     +++  G 
Sbjct: 71  TAQEWVRLYYDMKQEDDPELRERALTEFVESLQGLVLFVVNRYYKTYMKDYKDDLIGSGM 130

Query: 84  IGLMQAVKKFDP-----ERGFRL--ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           IGLM+ +K++DP      +G     +T     I+ A ++Y+    S++ + T    K + 
Sbjct: 131 IGLMEGIKRYDPYHNGGNKGEPFVPSTIVTRDIRHACRDYV---NSMI-LNTKTRYKTIE 186

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD---ESLNALINSS 193
             LR++    +  +        +  +  +L +S      +   +       SL+  +   
Sbjct: 187 DKLRQIIARKRDESGGEDIDIDIDDLVNELGISPKTAQGILANIQTRNNMVSLDE-VMQD 245

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI-FEARRLQENP 252
             NS+   +         E+  +EKE+      M+      L   +R +           
Sbjct: 246 SNNSTSRHELFASQTKTPEEEYLEKEKTIRINKMMY---DNLTDEQREVCMYHYGFYGEK 302

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            T   +S    +  ++V +I   +  +++ ++ +
Sbjct: 303 CTNTEISKIMGIPVQKVSKIINESELRMRRAMSR 336


>gi|159469913|ref|XP_001693104.1| predicted protein [Chlamydomonas reinhardtii]
 gi|158277362|gb|EDP03130.1| predicted protein [Chlamydomonas reinhardtii]
          Length = 525

 Score = 72.2 bits (176), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 38/164 (23%), Positives = 67/164 (40%), Gaps = 20/164 (12%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAM---------------GYRGYGLPISEVVSEG 82
           A R R      A   L   + RLVV  A                    Y L   + ++ G
Sbjct: 105 ALRLRLDAGNRARAILAQKNYRLVVACAKWACKNGVGGGGAGSGHDGSYELAFEDALTAG 164

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
             GLM+ + KF P+ G+RL+TY  WWI+ ++++ + R  + +++  +  Q        RL
Sbjct: 165 MEGLMRGIHKFRPDSGYRLSTYCTWWIRMSIRKTLSRQSTALQLPLSVLQSVEALVSARL 224

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
           +     +T     P    A+A +L  S + + + +       S+
Sbjct: 225 R-----LTKPGASPPTDEAVAAELGWSMTRIRNADAARRFATSI 263


>gi|182625388|ref|ZP_02953161.1| sigma factor [Clostridium perfringens D str. JGS1721]
 gi|177909385|gb|EDT71837.1| sigma factor [Clostridium perfringens D str. JGS1721]
          Length = 232

 Score = 72.2 bits (176), Expect = 8e-11,   Method: Composition-based stats.
 Identities = 38/191 (19%), Positives = 87/191 (45%), Gaps = 19/191 (9%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG---YGLPISEVVS 80
            ++ ++  +E  VL     +HGD  A  +L+ ++ +L+ K+A  +       +   +++ 
Sbjct: 1   MRVILMTNEELVVL----YQHGDKKALDKLLENNDKLIYKVASKFYSDKTSSIEFDDLLQ 56

Query: 81  EGNIGLMQAVKKFD--PERGFRLATYSMWWIKAAMQEYIL--RSWSLVKIGTTA---NQK 133
           EG IG + A  K+D    +  +  TY+ +WI   +  +I    +   + + T     NQ 
Sbjct: 57  EGRIGFILACSKYDIEYIKKTKFITYAFYWIYQKIHRFITTHNTNEEISLNTPVSEENQD 116

Query: 134 RLFFNL----RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNA 188
            L  ++      +K   + +  + L+ E    + K   ++E E++ +      DE S++ 
Sbjct: 117 ELINSIESHSNEIKDREEELYLSELRLELEAVMDKHNTLNEREILKLYYGWDTDELSIDQ 176

Query: 189 LINSSDKNSSQ 199
           + +  + +SS+
Sbjct: 177 IADIFETSSSE 187



 Score = 46.7 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 19/104 (18%), Positives = 46/104 (44%), Gaps = 3/104 (2%)

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
            + SLN  ++  +++          +     +  +   E +     +    + LN RE  
Sbjct: 102 EEISLNTPVSEENQDELINSIESHSNEIKDREEELYLSELRLELEAVMDKHNTLNERE-- 159

Query: 242 IFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           I +     + + ++++ ++  FE S   V+ I+ARA +K++ S+
Sbjct: 160 ILKLYYGWDTDELSIDQIADIFETSSSEVKNIKARAIRKLRNSM 203


>gi|213419681|ref|ZP_03352747.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
          Length = 174

 Score = 72.2 bits (176), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 31/187 (16%), Positives = 75/187 (40%), Gaps = 14/187 (7%)

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
              TY++  I+ AM + + RS   V      N + +   + +L+  L        +    
Sbjct: 1   AFTTYAVQRIRGAMLDEL-RSRDWVPRSVRRNAREVAQAMGQLEQEL-------GRNATE 52

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             +A++L +  +E   M      D + + L +  +          +   + Q++  + + 
Sbjct: 53  TEVAERLGIPVAEYRQMLL----DTNNSQLFSYDEWREEHGDSIELVTEEHQQENPLHQL 108

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
              + R  +  ++  L  RE+ +       +  + L+ + +  EV   RV Q+ ++A K+
Sbjct: 109 LEGDLRQRVMDAIESLPEREQLVLTLYY--QEELNLKEIGAVLEVGESRVSQLHSQAIKR 166

Query: 280 VQESIQK 286
           ++  + K
Sbjct: 167 LRTKLGK 173


>gi|254442345|ref|ZP_05055821.1| RNA polymerase sigma factor, sigma-70 family [Verrucomicrobiae
           bacterium DG1235]
 gi|198256653|gb|EDY80961.1| RNA polymerase sigma factor, sigma-70 family [Verrucomicrobiae
           bacterium DG1235]
          Length = 324

 Score = 72.2 bits (176), Expect = 9e-11,   Method: Composition-based stats.
 Identities = 48/267 (17%), Positives = 96/267 (35%), Gaps = 48/267 (17%)

Query: 23  IRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSH--LRLVVKIAMGYRGYGLPISEVVS 80
           IR+   L +     LA R++ +    A   L ++H  L L   +A           +   
Sbjct: 84  IRQWNALARAVSLRLATRHQLY--KEAQSALYSAHQGLPLACSLAA--CRKPSLREDACQ 139

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           E  + L++A+ + DPE+      Y+   IK  +Q YI++    VK             + 
Sbjct: 140 EARLALLEAIDRIDPEQ--PFEAYARQRIKRRIQNYIMKEAVPVKAP-----------IN 186

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
            +    ++  D NL  E+ +            V+ ++               +       
Sbjct: 187 LISKTFRSQPDGNLLLEKAIRDG---------VVRLD--------------DTHAGGPML 223

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN---PVTLEN 257
              L  D D     +    +       +  ++  L  ++R + E R    +   P +L  
Sbjct: 224 ARELHCDSDLAPDQIAVSADES---AKVAEALLQLTDKQREVIELRFGLNDSATPQSLSQ 280

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESI 284
           ++    +SR++V Q E RA +K+  ++
Sbjct: 281 IAQHTGISRQQVFQREKRALQKLSSAL 307


>gi|283784102|ref|YP_003363967.1| lateral flagellar sigma factor 28 protein [Citrobacter rodentium
           ICC168]
 gi|282947556|emb|CBG87109.1| lateral flagellar sigma factor 28 protein [Citrobacter rodentium
           ICC168]
          Length = 238

 Score = 72.2 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 43/272 (15%), Positives = 103/272 (37%), Gaps = 55/272 (20%)

Query: 22  EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEV 78
           E    P+L  Q+E    +                ++L LV K+           +   ++
Sbjct: 10  EFSATPVLTPQQESHYLQ----------------AYLPLVRKVVRQLAPQCTCVIDRQDM 53

Query: 79  VSEGNIGLMQAVKKFD-PERGFRLATYSMWWIKAAMQEYILR-SWSLVKIGTTANQ-KRL 135
                +GL+ A++++  P+ G   A Y++  I+ A+ + +    W    +    +Q K L
Sbjct: 54  EQTALLGLLNAIRRYGMPDEG--FAGYAIHRIRGAILDELRSLDWRPRLLRQKYHQIKDL 111

Query: 136 FFNLRR---LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
             ++R+    +   Q ++   L PE  +                  +L G E+L      
Sbjct: 112 IRDMRKQLGREPEWQELSQTGLTPEDYLEF---------------QQLEGAETL------ 150

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
                +   + L  +  G        EE+   + ML+ ++  L+ +E  +       ++ 
Sbjct: 151 -----ASLDELLSGEGHGALPEGRGLEEQFVNQEMLSYALGQLSEKEGLVLSMYY--QHD 203

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + L+ ++    ++  R+ Q+  +  +K+++ +
Sbjct: 204 MNLKEIALVLGLTEARICQMNKKITQKIRDCL 235


>gi|283834438|ref|ZP_06354179.1| RNA polymerase sigma factor [Citrobacter youngae ATCC 29220]
 gi|291069985|gb|EFE08094.1| RNA polymerase sigma factor [Citrobacter youngae ATCC 29220]
          Length = 238

 Score = 72.2 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 38/266 (14%), Positives = 97/266 (36%), Gaps = 47/266 (17%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVS 80
              P+L  ++E    +                ++L LV K+           +   ++  
Sbjct: 12  NATPVLTPKQESHYLQ----------------AYLPLVRKVVRQLAPQCTCVMDRQDMEQ 55

Query: 81  EGNIGLMQAVKKF-DPERGFRLATYSMWWIKAAMQEYILR-SWSLVKIGTTANQKRLFFN 138
              +GL+ A++++  P+ G   A Y++  I+ A+ + +    W           ++L   
Sbjct: 56  TALMGLLNAIRRYGQPDEG--FAGYAVHRIRGAILDELRSLDWRP---------RQLRQK 104

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
             ++K  ++                 +L +S  +      +L G E+L           +
Sbjct: 105 YHQIKDLIRDARTQLGHEPS-WEELSRLGLSSEDYQEYQ-QLEGAETL-----------A 151

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
              + L  D           EE+   + ML+ ++S L+ +E  +       ++ + L+ +
Sbjct: 152 SLDELLNGDMPIAPLEGRGLEEQFVTQEMLSYALSQLSEKEGLVLSMYY--QHDMNLKEI 209

Query: 259 SSEFEVSRERVRQIEARAFKKVQESI 284
           +    ++  R+ Q+  +   K+++ +
Sbjct: 210 ALVLGLTEARICQMNKKITHKIRDCL 235


>gi|217031645|ref|ZP_03437150.1| hypothetical protein HPB128_21g203 [Helicobacter pylori B128]
 gi|216946845|gb|EEC25441.1| hypothetical protein HPB128_21g203 [Helicobacter pylori B128]
          Length = 247

 Score = 72.2 bits (176), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 35/238 (14%), Positives = 91/238 (38%), Gaps = 28/238 (11%)

Query: 50  AHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L   +L  V  +A          +  +++VS G   L++  ++++         Y+ 
Sbjct: 30  QDALAIQYLPAVRAMAFRLKERLPSSIDFNDLVSIGTEELIKLARRYESALNDSFWGYAK 89

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +  AM +Y+ RS  ++        K +   + +         + + K      +A+ L
Sbjct: 90  TRVNGAMLDYL-RSLDVISRSNRKLIKSIDIEITKH-------LNEHGKEPSDAYLAEAL 141

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             +  ++            + AL+   ++ ++  QD +            +K E +    
Sbjct: 142 GENIEKIKEAKTA----SDIYALVPIDEQFNAIEQDEI-----------TKKIEAEELLE 186

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + ++++ ++ RE+ + +    +E  + L  +     ++  R+ QI     KKV++S+
Sbjct: 187 HVQKALNQMSEREQILIQLYYFEE--LNLSEIKEILGITESRISQIIKEVIKKVRKSL 242


>gi|226311518|ref|YP_002771412.1| RNA polymerase sigma-K factor precursor [Brevibacillus brevis NBRC
           100599]
 gi|226094466|dbj|BAH42908.1| RNA polymerase sigma-K factor precursor [Brevibacillus brevis NBRC
           100599]
          Length = 121

 Score = 71.8 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 24/101 (23%), Positives = 45/101 (44%), Gaps = 7/101 (6%)

Query: 183 DESLNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           D SL+  I +  + N     D L  + D     +++  + K   N + + + +L+ RE+ 
Sbjct: 12  DVSLHDPIGTDKEGNEITLIDVLGTETD----EVVDAVQLKLESNKIYQHIHILDEREKE 67

Query: 242 IFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
           +   R   +     T   ++ E  +SR  V +IE RA  K+
Sbjct: 68  VIIGRFGLDQDKEKTQREIARELGISRSYVSRIEKRALMKL 108


>gi|308184219|ref|YP_003928352.1| flagellar biosynthesis sigma factor [Helicobacter pylori SJM180]
 gi|308060139|gb|ADO02035.1| flagellar biosynthesis sigma factor [Helicobacter pylori SJM180]
          Length = 255

 Score = 71.8 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 35/238 (14%), Positives = 90/238 (37%), Gaps = 28/238 (11%)

Query: 50  AHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L   +L  V  +A          +  +++VS G   L++  ++++         Y+ 
Sbjct: 38  QDDLAIQYLPAVRAMAFRLKERLPSSIDFNDLVSIGTEELIKLARRYESALNDSFWGYAK 97

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +  AM +Y+ RS  ++        K +   + +         + + K      +A+ L
Sbjct: 98  TRVNGAMLDYL-RSLDVISRSNRKLIKSIDIEITKH-------LNEHGKEPSDAYLAEAL 149

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             +  ++            + AL+   ++ ++  QD +            +K E +    
Sbjct: 150 GENIEKIREAKTA----SDIYALVPIDEQFNAIEQDEI-----------TKKIEAEELLE 194

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + + ++ ++ RE+ + +    +E  + L  +     ++  R+ QI     KKV++S+
Sbjct: 195 HVQKVLNQMSEREQILIQLYYFEE--LNLSEIKEILGITESRISQIIKEVIKKVRQSL 250


>gi|317009060|gb|ADU79640.1| flagellar biosynthesis sigma factor [Helicobacter pylori India7]
          Length = 255

 Score = 71.8 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 36/238 (15%), Positives = 94/238 (39%), Gaps = 28/238 (11%)

Query: 50  AHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L   +L  V  +A          +  +++VS G   L++  ++++         Y+ 
Sbjct: 38  QDALAIQYLPAVRAMAFRLKERLPSSIDFNDLVSIGTEELIKLARRYESALNDSFWGYAK 97

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +  AM +Y+      + + + +N+K +      +  HL    + + K      +A+ L
Sbjct: 98  TRVNGAMLDYL----RSLDVVSRSNRKLIKSIDIEITKHL----NEHGKEPSDAYLAQTL 149

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             +  ++            + AL+   ++ ++  QD +            +K E +    
Sbjct: 150 GENIEKIKEAKTA----SDIYALVPIDEQFNAIEQDEI-----------TKKIEAEELLE 194

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + ++++ ++ RE+ + +    +E  + L  +     ++  R+ QI     KKV++S+
Sbjct: 195 HVQKALNQMSEREQILIQLYYFEE--LNLSEIKEILGITESRISQIIKEVIKKVRKSL 250


>gi|237734716|ref|ZP_04565197.1| sporulation sigma factor sigG [Mollicutes bacterium D7]
 gi|229382044|gb|EEO32135.1| sporulation sigma factor sigG [Coprobacillus sp. D7]
          Length = 128

 Score = 71.8 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 26/131 (19%), Positives = 52/131 (39%), Gaps = 10/131 (7%)

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
           +   +  +A +L V  S VI          SL   + + D N+ +  D +  D       
Sbjct: 8   REPTINELANELEVEPSAVIEALLSTNSVSSLQEEVKNDDGNNLKMIDSITDDKTV---- 63

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
                 R N    L  ++  LN +E R+ + R      ++   ++ E  +S+ +V +IE 
Sbjct: 64  ----VSRTNETIDLYDALKSLNQKEHRVIKQRYF--EGLSQSEIAKELFISQAQVSRIER 117

Query: 275 RAFKKVQESIQ 285
           +A   +   ++
Sbjct: 118 KALDNLHNYLK 128


>gi|171741952|ref|ZP_02917759.1| hypothetical protein BIFDEN_01055 [Bifidobacterium dentium ATCC
           27678]
 gi|283456904|ref|YP_003361468.1| RNA polymerase sigma factor [Bifidobacterium dentium Bd1]
 gi|171277566|gb|EDT45227.1| hypothetical protein BIFDEN_01055 [Bifidobacterium dentium ATCC
           27678]
 gi|283103538|gb|ADB10644.1| RNA polymerase sigma factor [Bifidobacterium dentium Bd1]
          Length = 596

 Score = 71.8 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 23/105 (21%), Positives = 47/105 (44%), Gaps = 10/105 (9%)

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM------LTRSMSVLNPRER 240
           + L       S++  + L    D       + +E +    +      L+ ++  L+ RE 
Sbjct: 69  DNLPMDEIGFSTELFESLEDLDDYIPIEDGDSDEDEEPIQLDNFPLALSSAICDLDEREY 128

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           +IF  R L E P + + +  +  ++RER+RQIE      +++ +Q
Sbjct: 129 KIFNERFLMEEPRSFKAIGGDLGITRERIRQIEKN----LRDRMQ 169


>gi|317180689|dbj|BAJ58475.1| flagellar biosynthesis sigma factor [Helicobacter pylori F32]
          Length = 247

 Score = 71.8 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 35/238 (14%), Positives = 91/238 (38%), Gaps = 28/238 (11%)

Query: 50  AHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L   +L  V  +A          +  +++VS G   L++  ++++         Y+ 
Sbjct: 30  QDALAIQYLPAVRAMAFRLKERLPSSIDFNDLVSIGTEELIKLARRYESALNDSFWGYAK 89

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +  AM +Y+ RS  ++        K +   + +         + + K      +A+ L
Sbjct: 90  TRVNGAMLDYL-RSLDVISRSNRKLIKSIDIEITKH-------LNEHGKEPSDAYLAQTL 141

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             +  ++            + AL+   ++ ++  QD +            +K E +    
Sbjct: 142 GENIEKIKEAKTA----SDIYALVPIDEQFNAIEQDEI-----------TKKIEAEELLE 186

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + ++++ ++ RE+ + +    +E  + L  +     ++  R+ QI     KKV++S+
Sbjct: 187 HVQKALNQMSEREQILIQLYYFEE--LNLSEIKEILGITESRISQIIKEVIKKVRKSL 242


>gi|58699437|ref|ZP_00374184.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Drosophila
           ananassae]
 gi|58534044|gb|EAL58296.1| heat shock sigma factor RpoH [Wolbachia endosymbiont of Drosophila
           ananassae]
          Length = 57

 Score = 71.8 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 32/57 (56%), Positives = 48/57 (84%)

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           M AVKKF+P+ GFR +TY++WWI+A+++++IL+SWS VKIG+T  Q+ L F+LR +K
Sbjct: 1   MHAVKKFNPDLGFRFSTYAVWWIEASIKDFILKSWSFVKIGSTQAQRILCFSLREIK 57


>gi|157147079|ref|YP_001454398.1| flagellar biosynthesis sigma factor [Citrobacter koseri ATCC
           BAA-895]
 gi|157084284|gb|ABV13962.1| hypothetical protein CKO_02856 [Citrobacter koseri ATCC BAA-895]
          Length = 231

 Score = 71.8 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 41/240 (17%), Positives = 92/240 (38%), Gaps = 30/240 (12%)

Query: 52  RLVTSHLRLVVKIAMG--YR-GYGLPISEVVSEGNIGLMQAVKKF-DPERGFRLATYSMW 107
           R V+++L LV K+     Y+    +   ++     +GL+ +++++  P+   + A Y++ 
Sbjct: 17  RYVSTYLPLVNKVVKQLAYQTSSVIDRDDMEQIALMGLLTSLRRYGHPD--EQFAAYAIQ 74

Query: 108 WIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            ++ A+ + +    W           +RL     +L   ++ I     +      I+  L
Sbjct: 75  RVRGAVLDELRLLDWRP---------RRLRQKTHKLNDAIREIARQLGRTPSFEDISHHL 125

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +++  E                L+    K      D L  D           EE      
Sbjct: 126 SITAEEYQEY------------LLLDCAKTLESLDDLLGNDVYAGALDSRPLEEEIIVSR 173

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L  +++ L+ RE+ I       ++ ++L+ ++    ++  RV Q+     +K+Q   QK
Sbjct: 174 TLRNALASLDEREQLILTLYY--QHEMSLKEIALVLNLTEARVCQLNKIIAQKIQSFFQK 231


>gi|308182585|ref|YP_003926712.1| flagellar biosynthesis sigma factor [Helicobacter pylori PeCan4]
 gi|308063276|gb|ADO05163.1| flagellar biosynthesis sigma factor [Helicobacter pylori Sat464]
 gi|308064770|gb|ADO06662.1| flagellar biosynthesis sigma factor [Helicobacter pylori PeCan4]
 gi|332673262|gb|AEE70079.1| DNA-directed RNA polymerase sigma subunit FliA [Helicobacter pylori
           83]
          Length = 258

 Score = 71.8 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 35/238 (14%), Positives = 91/238 (38%), Gaps = 28/238 (11%)

Query: 50  AHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L   +L  V  +A          +  +++VS G   L++  ++++         Y+ 
Sbjct: 41  QDALAIQYLPAVRAMAFRLKERLPSSIDFNDLVSIGTEELIKLARRYESALNDSFWGYAK 100

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +  AM +Y+ RS  ++        K +   + +         + + K      +A+ L
Sbjct: 101 TRVNGAMLDYL-RSLDVISRSNRKLIKSIDIEITKH-------LNEHGKEPSDAYLAEVL 152

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             +  ++            + AL+   ++ ++  QD +            +K E +    
Sbjct: 153 GENIEKIKEAKTA----SDIYALVPIDEQFNAIEQDEI-----------TKKIEAEELLE 197

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + ++++ ++ RE+ + +    +E  + L  +     ++  R+ QI     KKV++S+
Sbjct: 198 HVQKALNQMSEREQILIQLYYFEE--LNLSEIKEILGITESRISQIIKEVIKKVRKSL 253


>gi|317055256|ref|YP_004103723.1| sigma-70 region 4 domain-containing protein [Ruminococcus albus 7]
 gi|315447525|gb|ADU21089.1| sigma-70 region 4 domain protein [Ruminococcus albus 7]
          Length = 129

 Score = 71.8 bits (175), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 23/110 (20%), Positives = 44/110 (40%), Gaps = 5/110 (4%)

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
             + A D S+    +S    SS     ++ D +   + +      +     L +    L+
Sbjct: 22  LKKTANDVSMEEPSHSDKDGSSLSLMDMIADSEDVAERIELLVRAEQMYIDLDK---CLD 78

Query: 237 PRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            RER I   R        +T    + +  +SR  V +IE RA +K+++ +
Sbjct: 79  DREREIIVMRYGLFGKPALTQREAAKKLGISRSYVSRIEKRALEKLRKEL 128


>gi|229817514|ref|ZP_04447796.1| hypothetical protein BIFANG_02777 [Bifidobacterium angulatum DSM
           20098]
 gi|229785303|gb|EEP21417.1| hypothetical protein BIFANG_02777 [Bifidobacterium angulatum DSM
           20098]
          Length = 621

 Score = 71.4 bits (174), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 26/83 (31%), Positives = 37/83 (44%), Gaps = 2/83 (2%)

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
           N +   D     +   E   IE          LT  +   + RE  I   R + E P TL
Sbjct: 108 NETTANDGTAAANTANEFTPIESAPPSLA-ESLTMLLFSFDEREYAIATQRLMAEQPSTL 166

Query: 256 ENLSSEFEVSRERVRQIEARAFK 278
           + +  EF ++RERVRQIE +A +
Sbjct: 167 DEIGKEFNITRERVRQIE-KALR 188


>gi|283779412|ref|YP_003370167.1| RNA polymerase, sigma 32 subunit, RpoH [Pirellula staleyi DSM 6068]
 gi|283437865|gb|ADB16307.1| RNA polymerase, sigma 32 subunit, RpoH [Pirellula staleyi DSM 6068]
          Length = 374

 Score = 71.4 bits (174), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 30/109 (27%), Positives = 53/109 (48%), Gaps = 4/109 (3%)

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL  L+    +  +          + +    + +      R  L + +S L+PRER I  
Sbjct: 261 SLQQLMRDRTRFMNAETSLFEDTPEEERPGTMSEARFDELRRALAKMLSKLDPRERSIIR 320

Query: 245 ARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
            R   +      TL++L+ EF V +ERVRQ+E RA  K++ S+ ++++L
Sbjct: 321 CRFGLDRKEQVQTLQSLAGEFGVCKERVRQLEMRAISKLR-SMAEEIDL 368



 Score = 67.1 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 31/136 (22%), Positives = 58/136 (42%), Gaps = 29/136 (21%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRY---------------REHGDLSA----------- 49
           +  ++  + +  +L   EE  L +R                 +H D              
Sbjct: 132 MPAHLARMCETSLLSPTEERDLFRRMNFAKYTADVLRRKINTDHPDRELIVSIERLIAQA 191

Query: 50  ---AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
               +R+V ++LRLVV IA  +        +++SEG   L++AV+KFD +RGFR +TY+ 
Sbjct: 192 LADRNRIVRANLRLVVSIAKKFSDARNSFDDLLSEGITSLLRAVEKFDYDRGFRFSTYAT 251

Query: 107 WWIKAAMQEYILRSWS 122
             ++  +   + +   
Sbjct: 252 QAVRRTLCRSLQQLMR 267


>gi|150390243|ref|YP_001320292.1| FliA/WhiG family RNA polymerase sigma 28 subunit [Alkaliphilus
           metalliredigens QYMF]
 gi|149950105|gb|ABR48633.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alkaliphilus metalliredigens QYMF]
          Length = 117

 Score = 71.4 bits (174), Expect = 1e-10,   Method: Composition-based stats.
 Identities = 29/116 (25%), Positives = 47/116 (40%), Gaps = 6/116 (5%)

Query: 174 ISMNCRLAGDESLNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           I  N +   + SL   I    + N     D L  + DG   V+ E E +   R +  +  
Sbjct: 3   IRSNKKTKAEVSLQDPIGVDKEGNEISLLDILGTESDG---VVDEVELKIQIRKLYQKMS 59

Query: 233 SVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            VL  RE+ + E R         T   ++    +SR  V +IE RA  K+ ++ + 
Sbjct: 60  KVLKSREKMVIELRYGIAGCGSKTQREIAKMLGISRSYVSRIEKRAINKLHKAFES 115


>gi|168213645|ref|ZP_02639270.1| RNA polymerase sigma factor RpoD [Clostridium perfringens CPE str.
           F4969]
 gi|170714810|gb|EDT26992.1| RNA polymerase sigma factor RpoD [Clostridium perfringens CPE str.
           F4969]
          Length = 227

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 29/133 (21%), Positives = 60/133 (45%), Gaps = 11/133 (8%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGL 86
             +E  VL     + GD  A  +L+ ++ +L+ KIA  +       +   +++ EG IGL
Sbjct: 2   TNEELVVL----YQQGDKKALDKLLENNDKLIYKIANKFYSDKTSSIEFDDLLQEGRIGL 57

Query: 87  MQAVKKFD--PERGFRLATYSMWWIKAAMQEYILRSWS--LVKIGTTANQKRLFFNLRRL 142
           + A  K+D    +  +  TY+ +WI   +  +I +  +   + + T  +++     +  +
Sbjct: 58  ILACSKYDIEYIKRTKFITYAFYWIYQKIHRFITKYSTNEEISLNTPVSEENTDELINSI 117

Query: 143 KGHLQAITDNNLK 155
           + H   I D   K
Sbjct: 118 ESHSDEINDREEK 130



 Score = 41.3 bits (96), Expect = 0.15,   Method: Composition-based stats.
 Identities = 19/104 (18%), Positives = 43/104 (41%), Gaps = 3/104 (2%)

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
            + SLN  ++  + +          D     +  +   E +     +    + LN RE  
Sbjct: 97  EEISLNTPVSEENTDELINSIESHSDEINDREEKLYLSELRLELEAVMDKHNTLNERE-- 154

Query: 242 IFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           I +     + + + +E ++  FE S   ++  +ARA +K++ S+
Sbjct: 155 ILKLYYCWDTDELNIEQIADIFETSSSDIKNTKARAIRKLRNSM 198


>gi|76664996|emb|CAJ17940.1| DNA-directed RNA polymerase sigma subunit [Candidatus Phytoplasma
           solani]
          Length = 110

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 35/110 (31%), Positives = 50/110 (45%), Gaps = 30/110 (27%)

Query: 18  RYIHEIRKIPMLEKQEEYV---------LAKRY-------------REHGDLS------- 48
            Y+ EI +I +L   EE            A++              +E  DL        
Sbjct: 1   MYLKEIGRISLLSSSEELKRSIAVFVGKKARQLMDQFKAQEIILTEQEIKDLEFKIQQAQ 60

Query: 49  -AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
            A   LV S+ RLVV IA  Y G G+   +++ EGN+GLM+AV KFD ++
Sbjct: 61  LAKDSLVESNYRLVVSIAKRYIGRGILFLDLIQEGNMGLMRAVDKFDYQK 110


>gi|168069803|ref|XP_001786584.1| predicted protein [Physcomitrella patens subsp. patens]
 gi|162660945|gb|EDQ48604.1| predicted protein [Physcomitrella patens subsp. patens]
          Length = 406

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 49/234 (20%), Positives = 82/234 (35%), Gaps = 39/234 (16%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
               +T +LRLV   A  Y  Y     +VVSEG IGL+ A  ++  +     +T++  +I
Sbjct: 14  RDAFITQNLRLVHMCAKRY-AYNRGYDDVVSEGTIGLILAYDRYS-DATVAFSTFAATYI 71

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           +  ++ Y       V +      +R   N RR+          +  PE V   A+ L ++
Sbjct: 72  RGYIRNYFRSLRGTVSVP-----RRTLDNSRRI----AEAGLEDKAPETV---AEALGIA 119

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
                     LA  ES      S D +       +    D     +    ER+  +N   
Sbjct: 120 VKHAEDALYYLAVTES-----GSRDYDEEINAKSVHTFDDDTVPDVNAFIERQVPKNQ-- 172

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
                            RL  +  T    + +  VSR+   Q    A K+++  
Sbjct: 173 --------------RLLRLLMDEYTQTEAAEKLGVSRQAASQ----ALKRMRAP 208


>gi|261837848|gb|ACX97614.1| transcription initiation factor sigma-28 [Helicobacter pylori 51]
          Length = 258

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 35/238 (14%), Positives = 92/238 (38%), Gaps = 28/238 (11%)

Query: 50  AHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L   +L  V  +A          +  +++VS G   L++  ++++         Y+ 
Sbjct: 41  QDDLAIQYLPAVRAMAFRLKERLPSSIDFNDLVSIGTEELIKLARRYESALNDSFWGYAK 100

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +  AM +Y+ RS  ++   +    K +   + +         + + K      +A+ L
Sbjct: 101 TRVNGAMLDYL-RSLDVISRSSRKLIKSIDIEITKH-------LNEHGKEPSDAYLAEVL 152

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             +  ++            + AL+   ++ ++  QD +            +K E +    
Sbjct: 153 GENIEKIKEAKTA----SDIYALVPIDEQFNAIEQDEI-----------TKKIEAEELLE 197

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + ++++ ++ RE+ + +    +E  + L  +     ++  R+ QI     KKV++S+
Sbjct: 198 HVQKALNQMSEREQILIQLYYFEE--LNLSEIKEILGITESRISQIIKEVIKKVRKSL 253


>gi|315125999|ref|YP_004068002.1| LafS [Pseudoalteromonas sp. SM9913]
 gi|315014513|gb|ADT67851.1| LafS [Pseudoalteromonas sp. SM9913]
          Length = 239

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 40/239 (16%), Positives = 99/239 (41%), Gaps = 28/239 (11%)

Query: 52  RLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           +L++ +  LV + A   R   G  +   ++   G I L+ +++++  +   + A ++   
Sbjct: 24  QLLSQYAFLVNRAAAHMRTQVGVIVDNDDIYQIGIIALLSSIRRYGRDLDEKFAAFAFKR 83

Query: 109 IKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           I+ AM +   R  W   ++   ++Q      LR +   LQ     +        + + L 
Sbjct: 84  IRGAMLDEFRRVDWRPRQLRQQSHQ------LRDMSRSLQKKLGRD---ATDTEMCEALG 134

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           ++  E+I ++              S    +    + L+  +           E++     
Sbjct: 135 INHKELIQLH-------------YSEQAEAFDSLEALLEANPNLALTCAHTHEKEETAAT 181

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           L  +MS LN RE+ + +   + E  + ++ ++   +++  RV Q+  +A + + +++QK
Sbjct: 182 LKVAMSKLNTREKLLLQLYYMHE--MNMKEIALTLDLTEARVCQLHKQALEALTQTLQK 238


>gi|134298777|ref|YP_001112273.1| sigma-70 region 4 domain-containing protein [Desulfotomaculum
           reducens MI-1]
 gi|134051477|gb|ABO49448.1| sigma-70 region 4 domain protein [Desulfotomaculum reducens MI-1]
          Length = 118

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 26/105 (24%), Positives = 43/105 (40%), Gaps = 7/105 (6%)

Query: 179 RLAGDESLNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
           ++  + SL   I    + N     D L  D     +V+ +  E    +N L   ++ L  
Sbjct: 8   KVKAEVSLYDPIGVDKEGNEISLIDILGTD----PEVVADTVESTFEKNRLLEKITKLTT 63

Query: 238 RERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKV 280
           RE+R+ E R         T   ++    +SR  V +IE RA  K+
Sbjct: 64  REKRVLEMRFGLGTTARKTQREIARTLGISRSYVSRIEKRALNKL 108


>gi|21104386|dbj|BAB93463.1| putative rpoD gene [Variovorax sp. WFF52]
 gi|21104388|dbj|BAB93464.1| putative rpoD gene [Leptothrix discophora]
 gi|21104390|dbj|BAB93465.1| putative rpoD gene [Sphaerotilus natans]
          Length = 47

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 22/47 (46%), Positives = 32/47 (68%)

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           LV+ IA  Y   GL   +++ EGNIGLM+AV KF+  RG++ +TY+ 
Sbjct: 1   LVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYAT 47


>gi|15645646|ref|NP_207822.1| flagellar biosynthesis sigma factor [Helicobacter pylori 26695]
 gi|2314177|gb|AAD08076.1| alternative transcription initiation factor, sigma-F (fliA)
           [Helicobacter pylori 26695]
          Length = 255

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 35/238 (14%), Positives = 92/238 (38%), Gaps = 28/238 (11%)

Query: 50  AHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L   +L  V  +A          +  +++VS G   L++  ++++         Y+ 
Sbjct: 38  QDDLAIQYLPAVRAMAFRLKERLPSSIDFNDLVSIGTEELIKLARRYESALNDSFWGYAK 97

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +  AM +Y+ RS  ++   +    K +   + +         + + K      +A+ L
Sbjct: 98  TRVNGAMLDYL-RSLDVISRSSRKLIKSIDIEITKH-------LNEHGKEPSDAYLAQTL 149

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             +  ++            + AL+   ++ ++  QD +            +K E +    
Sbjct: 150 GENIEKIKEAKTA----SDIYALVPIDEQFNAIEQDEI-----------TKKIEAEELLE 194

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + ++++ ++ RE+ + +    +E  + L  +     ++  R+ QI     KKV++S+
Sbjct: 195 HVQKALNQMSEREQILIQLYYFEE--LNLSEIKEILGITESRISQIIKEVIKKVRKSL 250


>gi|261839263|gb|ACX99028.1| flagellar biosynthesis sigma factor [Helicobacter pylori 52]
          Length = 258

 Score = 71.4 bits (174), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 35/238 (14%), Positives = 91/238 (38%), Gaps = 28/238 (11%)

Query: 50  AHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L   +L  V  +A          +  +++VS G   L++  ++++         Y+ 
Sbjct: 41  QDALAIQYLPAVRAMAFRLKERLPSSIDFNDLVSIGTEELIKLARRYESALNDSFWGYAK 100

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +  AM +Y+ RS  ++        K +   + +         + + K      +A+ L
Sbjct: 101 TRVNGAMLDYL-RSLDVISRSNRKLIKSIDIEITKH-------LNEHGKEPSDAYLAQTL 152

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             +  ++            + AL+   ++ ++  QD +            +K E +    
Sbjct: 153 GENIEKIKEAKTA----SDIYALVPIDEQFNAIEQDEI-----------TKKIEAEELLE 197

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + ++++ ++ RE+ + +    +E  + L  +     ++  R+ QI     KKV++S+
Sbjct: 198 HVQKALNQMSEREQILIQLYYFEE--LNLSEIKEILGITESRISQIIKEVIKKVRKSL 253


>gi|298736645|ref|YP_003729171.1| RNA polymerase sigma factor for flagellar operon FliA [Helicobacter
           pylori B8]
 gi|298355835|emb|CBI66707.1| RNA polymerase sigma factor for flagellar operon FliA [Helicobacter
           pylori B8]
          Length = 255

 Score = 71.0 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 35/238 (14%), Positives = 91/238 (38%), Gaps = 28/238 (11%)

Query: 50  AHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L   +L  V  +A          +  +++VS G   L++  ++++         Y+ 
Sbjct: 38  QDALAIQYLPAVRAMAFRLKERLPSSIDFNDLVSIGTEELIKLARRYESALNDSFWGYAK 97

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +  AM +Y+ RS  ++        K +   + +         + + K      +A+ L
Sbjct: 98  TRVNGAMLDYL-RSLDVISRSNRKLIKSIDIEITKH-------LNEHGKEPSDAYLAEAL 149

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             +  ++            + AL+   ++ ++  QD +            +K E +    
Sbjct: 150 GENIEKIKEAKTA----SDIYALVPIDEQFNAIEQDEI-----------TKKIEAEELLE 194

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + ++++ ++ RE+ + +    +E  + L  +     ++  R+ QI     KKV++S+
Sbjct: 195 HVQKALNQMSEREQILIQLYYFEE--LNLSEIKEILGITESRISQIIKEVIKKVRKSL 250


>gi|315586407|gb|ADU40788.1| DNA-directed RNA polymerase sigma subunit FliA [Helicobacter pylori
           35A]
          Length = 258

 Score = 71.0 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 35/238 (14%), Positives = 90/238 (37%), Gaps = 28/238 (11%)

Query: 50  AHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L   +L  V  +A          +  +++VS G   L++  ++++         Y+ 
Sbjct: 41  QDALAIQYLPAVRAMAFRLKERLPSSIDFNDLVSIGTEELIKLARRYESALNDSFWGYAK 100

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +  AM +Y+ RS  ++        K +   + +         + + K      +A+ L
Sbjct: 101 TRVNGAMLDYL-RSLDVISRSNRKLIKSIDIEITKH-------LNEHGKEPSDAYLAEVL 152

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             +  ++            + AL+   ++ ++  QD +            +K E +    
Sbjct: 153 GENIEKIKEAKTA----SDIYALVPIDEQFNAIEQDEI-----------TKKIEAEELLE 197

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + + ++ ++ RE+ + +    +E  + L  +     ++  R+ QI     KKV++S+
Sbjct: 198 HVQKVLNQMSEREQILIQLYYFEE--LNLSEIKEILGITESRISQIIKEVIKKVRKSL 253


>gi|210134610|ref|YP_002301049.1| flagellar biosynthesis sigma factor [Helicobacter pylori P12]
 gi|210132578|gb|ACJ07569.1| alternative transcription initiation factor sigma-F [Helicobacter
           pylori P12]
          Length = 255

 Score = 71.0 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 36/238 (15%), Positives = 93/238 (39%), Gaps = 28/238 (11%)

Query: 50  AHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L   +L  V  +A          +  +++VS G   L++  ++++         Y+ 
Sbjct: 38  QDDLAIQYLPAVRAMAFRLKERLPSSIDFNDLVSIGTEELIKLARRYESALNDSFWGYAK 97

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +  AM +Y+      + + + +N+K +      +  HL    + + K      +A+ L
Sbjct: 98  TRVNGAMLDYL----RSLDVISRSNRKLIKSIDAEITKHL----NEHGKEPSDAYLAQTL 149

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             +  ++            + AL+   ++ ++  QD +            +K E +    
Sbjct: 150 GENIEKIKEAKTA----SDIYALVPIDEQFNAIEQDEI-----------TKKIEAEELLE 194

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + + ++ ++ RE+ + +    +E  + L  +     ++  R+ QI     KKV++S+
Sbjct: 195 HVQKVLNQMSEREQILIQLYYFEE--LNLSEIKEILGITESRISQIIKEVIKKVRKSL 250


>gi|182412871|ref|YP_001817937.1| FliA/WhiG family RNA polymerase sigma 28 subunit [Opitutus terrae
           PB90-1]
 gi|177840085|gb|ACB74337.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Opitutus terrae PB90-1]
          Length = 240

 Score = 71.0 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 40/207 (19%), Positives = 82/207 (39%), Gaps = 18/207 (8%)

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++ S G + L++A+ +FD     +L  Y    ++ A+ + + R         + + +  
Sbjct: 37  EDLASAGKLALVEAMLRFD-GPAEQLRGYCFARVRGALLDELRRLD-----PLSRHTRSQ 90

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              +RR    L+         +++V           E ++   RLA      A   S D+
Sbjct: 91  VTFVRRATAALEKELHRAPTRDEIVTA----TGYSHETLTQLERLAEA----AQACSIDE 142

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
             +   D  V + +          E  +  + +  +++ L      +     L +   TL
Sbjct: 143 TDAYGDDLHVIEDEAAC--PARTAESLDAHSSVHVALARLPANHAHVLRRYYLDD--ATL 198

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQE 282
           + ++ E  VS+ERVRQ+   A KK++E
Sbjct: 199 DVIAGELGVSKERVRQLREAAEKKLRE 225


>gi|148645062|gb|ABR01056.1| RpoD [uncultured Geobacter sp.]
          Length = 72

 Score = 71.0 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 18/73 (24%), Positives = 31/73 (42%), Gaps = 2/73 (2%)

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +AV KF+ +RG++ +TY  WWI+ A+   J      ++I            L R    L 
Sbjct: 1   KAVDKFEYQRGYKFSTYXTWWIRQAITRAJXDQARTIRIPVHM--IETINKLIRTSRQLV 58

Query: 148 AITDNNLKPEQVV 160
                   PE++ 
Sbjct: 59  QEIGREPMPEEIA 71


>gi|222823277|ref|YP_002574850.1| flagellar biosynthesis sigma factor, sigma-F [Campylobacter lari
           RM2100]
 gi|222538498|gb|ACM63599.1| flagellar biosynthesis sigma factor, sigma-F [Campylobacter lari
           RM2100]
          Length = 228

 Score = 71.0 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 39/241 (16%), Positives = 93/241 (38%), Gaps = 28/241 (11%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
                 LV S++  +  +A   +      + +++++S G   +++  +++D E+      
Sbjct: 12  KKEQDDLVISYMPALRAMAFRLKERLPASIDVNDLISIGVEEMIKLSRRYDKEQNDNFWG 71

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           ++   +  AM +Y+               +     ++ +   +      N K      +A
Sbjct: 72  FARKRVNGAMLDYLR--------SLDVMSRSNRKIIKDIDVIVDEYYQENEKEPDDEYLA 123

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           +KLN+   +V     R A   SL   +        Q   +        +  +IE+ E++ 
Sbjct: 124 QKLNLEVEKVKE--ARAAHAISLVMPL------DEQLNCF-------NDSNIIEQIEKEE 168

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               +   +     RE+ + +    +E  + L+ ++   E+S  R+ QI  R  KK++E 
Sbjct: 169 LIEKINAVLEEFKEREKLVIQLYYYEE--LNLKEIAEILEISESRISQIHKRLLKKIRER 226

Query: 284 I 284
           +
Sbjct: 227 L 227


>gi|307747021|gb|ADN90291.1| RNA polymerase sigma factor [Campylobacter jejuni subsp. jejuni M1]
          Length = 238

 Score = 71.0 bits (173), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 36/241 (14%), Positives = 91/241 (37%), Gaps = 28/241 (11%)

Query: 47  LSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
                 LV S++  +  +A          + +++++S G   +++  +++D E+      
Sbjct: 22  KKEQDELVLSYMPALRAMAFRLKERLPSSIDVNDLISIGVEEMIKLSRRYDKEQNNNFWG 81

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           ++   +  +M +Y+               +     ++ +   +      N        +A
Sbjct: 82  FARKRVNGSMLDYLR--------SLDVMSRNNRKIIKDIDAIMDEYFLENECEPDDEYLA 133

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           KKL++   ++  +  R A   S    I+                    E   +EK E++ 
Sbjct: 134 KKLDLDVEKIKEV--RTAHAISYTLPID-------------EQIELYNEDNTLEKIEKEE 178

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               +   +  L  R++ I +    +E  ++L+ +S   ++S  R+ QI  +  KK++E 
Sbjct: 179 LLEKIHEVLDDLKERDQLIIQLYYYEE--LSLKEISEILQISESRISQIHKKLLKKLRER 236

Query: 284 I 284
           +
Sbjct: 237 L 237


>gi|218669756|gb|ACL00355.1| Bcp25 [Bacillus phage Bcp1]
          Length = 250

 Score = 70.6 bits (172), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 45/260 (17%), Positives = 96/260 (36%), Gaps = 33/260 (12%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG-LPISEVVSEGNIGLM 87
           L ++E   L K  R  G   A  +++  +  +V  +A  +         ++  EG   L+
Sbjct: 11  LTREETIELVKEAR-AGSEEAKEKIILGYKGMVYTLAKRFSRSKQHEFEDMFQEGLTILL 69

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK---G 144
           + V KFD + G+  +TY+  ++   M   + + ++ +KI        +   +R+ K    
Sbjct: 70  EVVDKFDIDSGYAFSTYAYPFVFGKMNN-VRKRYNPIKISAHITD--IISRIRKYKLTDR 126

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSES-EVISMNCRLAGDESLN--ALINSSDKNSSQWQ 201
             + I +   K  ++  +   L      +V+S+    A DE  +  A +       +   
Sbjct: 127 SEKEIYEFLNKEYELKWVRAALEYMRRGKVLSLEKTFAEDEESDWAATLKEVVSKDANGD 186

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
             L+ D  G    L   E+     ++L   M                        +++ E
Sbjct: 187 WELMMDIKGCVPSLTSYEQYAFCEHILKDRM----------------------QSDIAEE 224

Query: 262 FEVSRERVRQIEARAFKKVQ 281
             V  + V +   +A +K++
Sbjct: 225 LGVKPQTVSKHVNKACRKIK 244


>gi|189219201|ref|YP_001939842.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Methylacidiphilum infernorum V4]
 gi|189186059|gb|ACD83244.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Methylacidiphilum infernorum V4]
          Length = 401

 Score = 70.6 bits (172), Expect = 2e-10,   Method: Composition-based stats.
 Identities = 44/258 (17%), Positives = 102/258 (39%), Gaps = 25/258 (9%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVK 91
           EE  + +  +   +  A   L    L +  ++A  Y  Y      +  + G  G++ A++
Sbjct: 130 EELPIIQSAKAA-EKKALEWLAIHSLPMRQQVARFYLPYLADQWPDAENVGWFGILDALE 188

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           K+D +   R   Y++  +K  ++ Y     + V+   +           R    ++   +
Sbjct: 189 KWDEQMQIRFFDYAIHHVKNRVRNYANACRTTVRRPNSV---------YREYRKIEKFLE 239

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
             L  E++ A+      S  ++  +    + D SL+      +++ + + D LVY     
Sbjct: 240 QGLTLEEITALY---GYSPYQLEKILQVYSLDISLH-FTAFDEESETCFLDLLVY----- 290

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN-----LSSEFEVSR 266
            +   +  ER+ R   L   +S L+   R+I       E     +      ++ + ++ R
Sbjct: 291 PENPDDSLEREERLRKLFTVLSHLDEISRKIVFFFFGIEEGTGAKGKPTAWIAHKLKIPR 350

Query: 267 ERVRQIEARAFKKVQESI 284
           ++V Q+   A K+++  +
Sbjct: 351 QKVMQMLEEALKQLKRDL 368


>gi|163784183|ref|ZP_02179117.1| DNA-directed RNA polymerase specialized sigma subunit
           [Hydrogenivirga sp. 128-5-R1-1]
 gi|159880543|gb|EDP74113.1| DNA-directed RNA polymerase specialized sigma subunit
           [Hydrogenivirga sp. 128-5-R1-1]
          Length = 102

 Score = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 16/100 (16%), Positives = 48/100 (48%), Gaps = 6/100 (6%)

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           + + + + ++    +  + D  ++ +    E+K  + +L  +++ L+ RER +      +
Sbjct: 4   VGNDEDSDTKLWQIIAINDDTPDKYV----EQKQLKKILADAIAKLDERERLVITLYYYE 59

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           E  ++++ +     ++  R+ QI  +   K+++ I K V 
Sbjct: 60  E--LSMKEIGEVLGLTESRISQIHTKTMLKLRKLISKYVH 97


>gi|223041126|ref|ZP_03611381.1| flagellar biosynthesis sigma factor FliA [Campylobacter rectus
           RM3267]
 gi|222877620|gb|EEF12746.1| flagellar biosynthesis sigma factor FliA [Campylobacter rectus
           RM3267]
          Length = 231

 Score = 70.6 bits (172), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 33/242 (13%), Positives = 90/242 (37%), Gaps = 28/242 (11%)

Query: 47  LSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
                 +V +++  +  +A          + +S+++  G   +++  +K+D E+      
Sbjct: 13  KKEQDDIVLAYMPALRAMAFRLKERLPSHIDVSDLIGAGLEEMVKLSRKYDKEQNDSFWG 72

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   +  AM +++ R   + +   T  +         ++  +    +          IA
Sbjct: 73  YAQKRVYGAMLDFLRRLDVVSRSDRTLVKS--------IETLVDEYFNKFEHEPDDAYIA 124

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
            KL +   +V       A    LN                        E+  +E+ E+++
Sbjct: 125 GKLGIDVEKVSEARNVSAVVAVLNIDDQM---------------ELMSEENTLEQVEKED 169

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               + + ++    R++ I +    +E  ++L+ +S    ++  R+ QI  R   K+++ 
Sbjct: 170 LIEKIAQILNEFEERDQLIVQLYYYEE--LSLKEISEILGITESRISQIHKRLMDKIRKK 227

Query: 284 IQ 285
           ++
Sbjct: 228 LE 229


>gi|320178177|gb|EFW53154.1| RNA polymerase sigma factor for flagellar operon [Shigella boydii
           ATCC 9905]
 gi|320182764|gb|EFW57648.1| RNA polymerase sigma factor for flagellar operon [Shigella boydii
           ATCC 9905]
          Length = 196

 Score = 70.2 bits (171), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 36/193 (18%), Positives = 79/193 (40%), Gaps = 15/193 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 72

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   + +L+  L        +      +A++L
Sbjct: 73  QRIRGAMLDEL-RSRDWVPRSVRRNAREVAQAIGQLEQEL-------GRNATETEVAERL 124

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +  ++   M      D + + L +  +          +   D Q +  +++    N R 
Sbjct: 125 GIDIADYRQMLL----DTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQ 180

Query: 227 MLTRSMSVLNPRE 239
            +  ++  L  RE
Sbjct: 181 RVMEAIETLPERE 193


>gi|291544355|emb|CBL17464.1| Sigma-70, region 4 [Ruminococcus sp. 18P13]
          Length = 116

 Score = 70.2 bits (171), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 26/108 (24%), Positives = 44/108 (40%), Gaps = 7/108 (6%)

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV-L 235
             + A D  ++  I++    ++     +V D       + E+ +   R   L R +   L
Sbjct: 6   QKKTANDVYIDEPIDTDKDGNTLTLMDIVADSSD----VFEQVDLTIRSKQLYRYLDKCL 61

Query: 236 NPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            PRE  I   R    N  P T   ++    +SR  V +IE RA  K++
Sbjct: 62  EPRELDIITRRYGLYNHMPQTQREVADRLGISRSYVSRIEKRALSKLK 109


>gi|257468173|ref|ZP_05632269.1| sporulation sigma factor SigG [Fusobacterium ulcerans ATCC 49185]
          Length = 239

 Score = 70.2 bits (171), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 44/247 (17%), Positives = 93/247 (37%), Gaps = 35/247 (14%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           R+ P + + E   L    +E GD+ A ++++  +LR +  +   Y        +      
Sbjct: 3   REYPAITEVEVQELLPLAQE-GDIEARNKIIVGYLRYITHLNNRYGNGS---EDCFQSAI 58

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
            G+++ ++ +    G + +TY  +WIK            + +     N       + R K
Sbjct: 59  FGVIEGIRNYK-NNGIKFSTYCYFWIKQ----------RINRTRDKENYDGNTSFIERRK 107

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
            + + I ++ L P++   + KKL +SES +  +        SL          + +  ++
Sbjct: 108 KYEKLIKNDPLLPKK--EVLKKLQISESTLRGIERSTYAKISL---------QNKRSWEF 156

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSV-LNPRERRIFEARRLQENPVTLENLSSEF 262
           L  D            E+   R  L + +      RE  I +    +E   T + L+  +
Sbjct: 157 LGTDAGTV------AIEQIVNREYLEQLIKKYCTKREATIIKLLYFEE--YTEQELAKIY 208

Query: 263 EVSRERV 269
            ++   V
Sbjct: 209 NITASGV 215


>gi|254459039|ref|ZP_05072462.1| sigma 28 [Campylobacterales bacterium GD 1]
 gi|207084310|gb|EDZ61599.1| sigma 28 [Campylobacterales bacterium GD 1]
          Length = 227

 Score = 70.2 bits (171), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 44/237 (18%), Positives = 87/237 (36%), Gaps = 28/237 (11%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG---LMQAVKKFDPERGFRLATYSMW 107
             L   +L  V  +A   +       + +    IG   L++  +++D +       Y+  
Sbjct: 14  DELAIQYLPAVKAMAFRLKERLPSSIDYMDLSAIGTEELIKLARRYDEKLNDSFWGYAKK 73

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            +  AM +Y+     L +      +         +   ++     + +      +A  L 
Sbjct: 74  RVYGAMLDYLRSLDILSRASRKLVKA--------IDYAVEEHRLTHEEEPTDAELALILG 125

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
            SE +V              A I S+        D L    +G    LIEKEE      +
Sbjct: 126 ESEEKVHE------------ARIASTIYTVMPLHDQLQVGDEGAALALIEKEEL---IAV 170

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           + + +S  N RE+ I +    +E  + L+ +S   +++  R+ QI      K++ES+
Sbjct: 171 IKKVLSGYNEREQLIIQFYYFEE--LNLKEISEILDITESRISQIHKSVIHKIKESV 225


>gi|307243701|ref|ZP_07525841.1| sigma-70, region 4 [Peptostreptococcus stomatis DSM 17678]
 gi|306492910|gb|EFM64923.1| sigma-70, region 4 [Peptostreptococcus stomatis DSM 17678]
          Length = 289

 Score = 70.2 bits (171), Expect = 3e-10,   Method: Composition-based stats.
 Identities = 42/251 (16%), Positives = 107/251 (42%), Gaps = 23/251 (9%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIA------MGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           +GD SA ++ + S +  + KI         ++  GL   ++   G +G++ A+ KFD   
Sbjct: 49  NGDRSARNKFILSKIDYIRKIVTCDNEIKSFKARGLDDDDLFQTGVMGVLCAIDKFDFRP 108

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G ++ TY    +K +++          +   + +  R   ++ ++      + ++ +   
Sbjct: 109 GVKVKTYINNNVKYSIKN-------TYRKYGSISVSREANSIYKICSSQMDLLEDKIDSR 161

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI- 216
           +++ I+++ N+  S    +   +   +S N        N       LV       +VL+ 
Sbjct: 162 KILKISRETNIPPSR---LEYGIMAVKSRNC--QYRYDNDGCLDTDLVSMEKYSRKVLMN 216

Query: 217 --EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
             ++ +RK    ++  ++S L  +E  + +   + +   T + ++ +   S   V  I+ 
Sbjct: 217 YNQEAKRKFNYWLVMEAISRLEGKENLVIKEIYIND--KTQKEVARQLGCSTTSVGNIKR 274

Query: 275 RAFKKVQESIQ 285
           RA +K++  ++
Sbjct: 275 RALEKIRYMMR 285


>gi|289758831|ref|ZP_06518209.1| predicted protein [Mycobacterium tuberculosis T85]
 gi|289714395|gb|EFD78407.1| predicted protein [Mycobacterium tuberculosis T85]
          Length = 330

 Score = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 28/114 (24%), Positives = 48/114 (42%), Gaps = 31/114 (27%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------REHGDL- 47
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+  
Sbjct: 217 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSERGEKL 275

Query: 48  ----------------SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
                            A + L+ ++LRLVV +A  Y G G+   +++ EG  G
Sbjct: 276 PAAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRGMAFLDLIQEGLPG 329


>gi|225018077|ref|ZP_03707269.1| hypothetical protein CLOSTMETH_02014 [Clostridium methylpentosum
           DSM 5476]
 gi|224949074|gb|EEG30283.1| hypothetical protein CLOSTMETH_02014 [Clostridium methylpentosum
           DSM 5476]
          Length = 267

 Score = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 36/223 (16%), Positives = 80/223 (35%), Gaps = 56/223 (25%)

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            +   G+   ++V E    +++AV+ FDPE   +  +Y  + I                 
Sbjct: 47  RFTRLGVDYDDLVQECYFAMVEAVEAFDPESELKFTSYLNFPI----------------- 89

Query: 127 GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
                           K  L AI++N    ++                  N       SL
Sbjct: 90  ----------------KKRLNAISNNRTSRQK------------------NDPTLSCTSL 115

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-RNMLTRSMSVLNPRERRIFEA 245
           +  I    +      + +     G    +IE+++     +  +   +  L   ++ +   
Sbjct: 116 D--IEVGAEGDCPLGELIPDKTAGIPFEVIEQQDWNRALQEAIETVLDTLTENQQEVIRL 173

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           R  ++   +L  +S E   SRER+RQI+ ++ K +++ + +++
Sbjct: 174 RFYED--KSLIEISEETGRSRERIRQIQGQSLKAMKKPLPRKI 214


>gi|152976319|ref|YP_001375836.1| FliA/WhiG family RNA polymerase sigma factor [Bacillus cereus
           subsp. cytotoxis NVH 391-98]
 gi|152025071|gb|ABS22841.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Bacillus
           cytotoxicus NVH 391-98]
          Length = 242

 Score = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 46/239 (19%), Positives = 83/239 (34%), Gaps = 33/239 (13%)

Query: 46  DLSAA--HRLVTSHLRLVVK-IAMGYRGY--------GLPISEVVSEGNIGLMQAVKKFD 94
           D+ A      +  + + V   I   Y           GL   ++V  G I L++A ++F 
Sbjct: 6   DVKALSDEEFIQKYEKFVFHFIHKKYGHRLQAIKDDTGLEFEDLVQCGMIALIKAREQFK 65

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
           PE GF+  T+++  I   +   I ++  L KI  T    +              I  N L
Sbjct: 66  PEMGFKFLTFAVPKIIGEIGNEIWKTQKL-KIERTVYYAK------------GKILKNKL 112

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV 214
             E V  I++ L++    V +      G  S++ +    D          +      E  
Sbjct: 113 SEESVDHISETLDIDPKLVEAAQDYQPGTFSIDKVFYPDDNGEG----GEITLEKQLEDE 168

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT-LENLSSEFEVSRERVRQI 272
            ++ E     + +L      L   E  +        +  T  EN+      S+ +V +I
Sbjct: 169 SVDVESTVENKVILHSFFDTLQHSELVV----WDMHSKGTRQENIGKRIGKSQVQVSRI 223


>gi|143644|gb|AAA22805.1| spoIIIC peptide [Bacillus subtilis]
 gi|1303719|dbj|BAA12375.1| SpoIIIC [Bacillus subtilis]
          Length = 138

 Score = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 20/100 (20%), Positives = 43/100 (43%), Gaps = 5/100 (5%)

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
           D SL+  I    + +   +  L+     + + +I+  +       + + + +L+ RE+ +
Sbjct: 24  DVSLHDPIGQDKEGN---EISLIDVLKSENEDVIDTIQLNMELEKVKQYIDILDDREKEV 80

Query: 243 FEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
              R   +     T   ++ E  +SR  V +IE RA  K+
Sbjct: 81  IVGRFGLDLKKEKTQREIAKELGISRSYVSRIEKRALMKM 120


>gi|317062458|ref|ZP_07926943.1| predicted protein [Fusobacterium ulcerans ATCC 49185]
 gi|313688134|gb|EFS24969.1| predicted protein [Fusobacterium ulcerans ATCC 49185]
          Length = 244

 Score = 70.2 bits (171), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 44/247 (17%), Positives = 93/247 (37%), Gaps = 35/247 (14%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           R+ P + + E   L    +E GD+ A ++++  +LR +  +   Y        +      
Sbjct: 8   REYPAITEVEVQELLPLAQE-GDIEARNKIIVGYLRYITHLNNRYGNGS---EDCFQSAI 63

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
            G+++ ++ +    G + +TY  +WIK            + +     N       + R K
Sbjct: 64  FGVIEGIRNYK-NNGIKFSTYCYFWIKQ----------RINRTRDKENYDGNTSFIERRK 112

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
            + + I ++ L P++   + KKL +SES +  +        SL          + +  ++
Sbjct: 113 KYEKLIKNDPLLPKK--EVLKKLQISESTLRGIERSTYAKISL---------QNKRSWEF 161

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSV-LNPRERRIFEARRLQENPVTLENLSSEF 262
           L  D            E+   R  L + +      RE  I +    +E   T + L+  +
Sbjct: 162 LGTDAGTV------AIEQIVNREYLEQLIKKYCTKREATIIKLLYFEE--YTEQELAKIY 213

Query: 263 EVSRERV 269
            ++   V
Sbjct: 214 NITASGV 220


>gi|20151058|pdb|1KU3|A Chain A, Crystal Structure Of Thermus Aquaticus Rna Polymerase
           Sigma Subunit Fragment, Region 4
 gi|20151059|pdb|1KU7|A Chain A, Crystal Structure Of Thermus Aquatics Rna Polymerase
           Sigmaa Subunit Region 4 Bound To-35 Element Dna
 gi|20151062|pdb|1KU7|D Chain D, Crystal Structure Of Thermus Aquatics Rna Polymerase
           Sigmaa Subunit Region 4 Bound To-35 Element Dna
          Length = 73

 Score = 69.8 bits (170), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 20/58 (34%), Positives = 35/58 (60%), Gaps = 2/58 (3%)

Query: 226 NMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             L +++S L+ RE  + + R+        TLE + + F V+RER+RQIE +A +K++
Sbjct: 2   EELEKALSKLSEREAMVLKMRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLK 59


>gi|34498445|ref|NP_902660.1| flagellar biosynthesis sigma factor [Chromobacterium violaceum ATCC
           12472]
 gi|34104300|gb|AAQ60659.1| RNA polymerase sigma factor for flagellar operon [Chromobacterium
           violaceum ATCC 12472]
          Length = 231

 Score = 69.8 bits (170), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 41/241 (17%), Positives = 95/241 (39%), Gaps = 31/241 (12%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
            A H  V  +  LV + A       G      ++   G + L+  ++++  E   R A +
Sbjct: 15  EARHLAV--YAPLVKRAARQLSSQAGGVFDREDMEQIGLMALLDCLRRYGGEPDERFAGF 72

Query: 105 SMWWIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           +M  I+ A+ + + R  W           + +     R++  L+ +     +        
Sbjct: 73  AMLRIRGAILDELRRLDWRP---------RSVRQEAHRVRDGLRELRRKLRREPTEAEAL 123

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
             L +                  +AL+  + +  + + + +    +   +   E   R  
Sbjct: 124 GLLGLDADAYR------------DALLAENAEAMASFDELVASGMELAAEGTPEA--RLE 169

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           R++ L R+++ LN RE+++ +     E  ++L+ +++  E++  R+ QI   A KK+Q  
Sbjct: 170 RQSELARALTALNEREQQVIQLYY--EFELSLKEIAAVLELTEARICQINKSALKKMQAC 227

Query: 284 I 284
           +
Sbjct: 228 L 228


>gi|32262696|gb|AAP77743.1| RNA polymerase sigma 28 factor [Helicobacter hepaticus ATCC 51449]
          Length = 190

 Score = 69.8 bits (170), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 33/210 (15%), Positives = 84/210 (40%), Gaps = 25/210 (11%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           ++++VS G   L++  +++D         ++   +  AM +Y+     L +      +  
Sbjct: 1   MADLVSIGTEELIKLARRYDSSLNDSFWGFAKTRVNGAMLDYLRSLDVLSRANRKLVKSI 60

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
            +   +    H +  +D  L       IAK              R+A D  + AL+   +
Sbjct: 61  DYEVSKYFNEHQEEPSDEYLAKVLKEDIAKI----------KEARMASD--IYALVPIDE 108

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
           + ++              + ++E  ++     ++   +  L  RE+ I +    +E  ++
Sbjct: 109 QYNAI-----------CAENILEDVQKDELMEIIFNVLKKLGKREQMIIQLYYFEE--LS 155

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L+ +S   +++  R+ QI     KK+++++
Sbjct: 156 LKEISEILDITESRISQITKEIVKKIRQAL 185


>gi|108562840|ref|YP_627156.1| flagellar biosynthesis sigma factor [Helicobacter pylori HPAG1]
 gi|107836613|gb|ABF84482.1| alternative transcription initiation factor, sigma-F [Helicobacter
           pylori HPAG1]
          Length = 255

 Score = 69.8 bits (170), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 35/238 (14%), Positives = 90/238 (37%), Gaps = 28/238 (11%)

Query: 50  AHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L   +L  V  +A          +  +++VS G   L++  ++++         Y+ 
Sbjct: 38  QDALAIQYLPAVRAMAFRLKERLPSSIDFNDLVSIGTEELIKLARRYESALNDSFWGYAK 97

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +  AM +Y+ RS  ++        K +   + +         + + K      +A+ L
Sbjct: 98  TRVNGAMLDYL-RSLDVISRSNRKLIKSIDIEITKH-------LNEHGKEPSDAYLAQTL 149

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
             +  ++            + AL+   ++ ++  QD +            +K E +    
Sbjct: 150 GENIEKIKEAKTA----SDIYALVPIDEQFNAIEQDEI-----------TKKIEAEELLE 194

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + + ++ ++ RE+ + +    +E  + L  +     ++  R+ QI     KKV++S+
Sbjct: 195 HVQKVLNQMSEREQILIQLYYFEE--LNLSEIKEILGITESRISQIIKEVIKKVRKSL 250


>gi|110678161|ref|YP_681168.1| RNA polymerase sigma factor, putative [Roseobacter denitrificans
           OCh 114]
 gi|109454277|gb|ABG30482.1| RNA polymerase sigma factor, putative [Roseobacter denitrificans
           OCh 114]
          Length = 1005

 Score = 69.8 bits (170), Expect = 4e-10,   Method: Composition-based stats.
 Identities = 24/85 (28%), Positives = 44/85 (51%), Gaps = 5/85 (5%)

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTL 255
           ++       D    E   IE+        ++   +S LN R++ I + R    +    TL
Sbjct: 436 TELGSIKPEDIKASESASIEEL---TVTEIIEGCISTLNDRQQDILQRRYGINRGQTETL 492

Query: 256 ENLSSEFEVSRERVRQIEARAFKKV 280
           E ++S+++V+RER+RQIE +A +K+
Sbjct: 493 EQVASDYDVTRERIRQIEKKAKQKL 517


>gi|220913709|ref|YP_002489018.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Arthrobacter
           chlorophenolicus A6]
 gi|219860587|gb|ACL40929.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Arthrobacter
           chlorophenolicus A6]
          Length = 264

 Score = 69.8 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 42/258 (16%), Positives = 87/258 (33%), Gaps = 25/258 (9%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLPI--SEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           +    + LV  HL LV  +          +   ++ S G+I L+ +   FDP  G     
Sbjct: 2   NREQRNGLVLQHLPLVGYLVSEVCAKASHLSRDDLASVGSIALITSADSFDPAMGVPFGA 61

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           ++   I  A  + +          T + +KR+   +    G  + +     +   V  +A
Sbjct: 62  FARRRIIGAFADEMRSQDW----ATRSARKRIKETM----GVEETLRGLLGRNPTVPEMA 113

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
             L V  S V              A +  + +  +   D +V  +  +            
Sbjct: 114 ATLGVERSVV-------------EAALADAARTLTPLDDVIVETYPAETASPEHSVLADE 160

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           R   L  +++ L  + R + E   L     T++ L+ E   +   V Q  + A + +++ 
Sbjct: 161 RVKYLRAAVTALPAKMRYVIEEIYLAG--RTVKELAEELGSTHAAVSQQRSEAIRLMRDG 218

Query: 284 IQKQVELSSSPPLLQKPR 301
           +        +     + R
Sbjct: 219 LAAHYADDPAAAYTPESR 236


>gi|56606829|gb|AAW02799.1| sigma factor [Nonomuraea sp. ATCC 39727]
          Length = 92

 Score = 69.8 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 20/96 (20%), Positives = 39/96 (40%), Gaps = 5/96 (5%)

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
           G++ +TY+ WWIK A+   +      ++I     +  L   + R++  +Q        PE
Sbjct: 1   GYKFSTYATWWIKQAITRAMADQARTIRIPVHMVE--LINKVARVQRRMQNELGREPTPE 58

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
               IA++  +    VI +        SL+  +   
Sbjct: 59  ---EIAQESELEVDRVIEVQRYGREPISLHTPLGEE 91


>gi|42543555|pdb|1RIO|H Chain H, Structure Of Bacteriophage Lambda Ci-Ntd In Complex With
           Sigma-Region4 Of Thermus Aquaticus Bound To Dna
          Length = 73

 Score = 69.8 bits (170), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 20/58 (34%), Positives = 35/58 (60%), Gaps = 2/58 (3%)

Query: 226 NMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             L +++S L+ RE  + + R+        TLE + + F V+RER+RQIE +A +K++
Sbjct: 2   EELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAYFGVTRERIRQIENKALRKLK 59


>gi|133722029|gb|ABO37133.1| SigF [Mycobacterium asiaticum]
          Length = 142

 Score = 69.5 bits (169), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 27/154 (17%), Positives = 51/154 (33%), Gaps = 13/154 (8%)

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
             +   VK+     +  L     RL      ++    +      +A +L +  +EV+   
Sbjct: 1   RDNSWSVKVPRRLKELHL-----RLGTATAELSQRLGRAPTATELAAELGMDRAEVVE-- 53

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
             L    S N L   S   +       + D  G     +++ E    R  L   +  L  
Sbjct: 54  -GLVAGSSYNTLSIDSGGGNEDDDARAIADTLGDVDAGLDRIE---NREALRPLLEALPE 109

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           RER +   R      +T   ++    +S+  V +
Sbjct: 110 RERMVLVLRFF--ESMTQTQIAERVGISQMHVSR 141


>gi|283955505|ref|ZP_06373000.1| RNA polymerase sigma factor for flagellar operon [Campylobacter
           jejuni subsp. jejuni 1336]
 gi|283792966|gb|EFC31740.1| RNA polymerase sigma factor for flagellar operon [Campylobacter
           jejuni subsp. jejuni 1336]
          Length = 238

 Score = 69.5 bits (169), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 36/241 (14%), Positives = 92/241 (38%), Gaps = 28/241 (11%)

Query: 47  LSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
                 LV S++  +  +A          + +++++S G   +++  +++D E+      
Sbjct: 22  KKEQDELVLSYMPALRAMAFRLKERLPSSIDVNDLISIGVEEMIKLSRRYDKEQNDNFWG 81

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           ++   +  +M +Y+               +     ++ +   +      N        +A
Sbjct: 82  FARKRVNGSMLDYLR--------SLDVMSRNNRKIIKDIDAIMDEYFLENECEPDDEYLA 133

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           KKL++   ++  +  R A   S    I+                    E   +EK E++ 
Sbjct: 134 KKLDLDVEKIKEV--RTAHAISYTLPID-------------EQIELYNEDNTLEKIEKEE 178

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               + + +  L  R++ I +    +E  ++L+ +S   ++S  R+ QI  +  KK++E 
Sbjct: 179 LLEKIHKVLDDLKERDQLIIQLYYYEE--LSLKEISEILQISESRISQIHKKLLKKLRER 236

Query: 284 I 284
           +
Sbjct: 237 L 237


>gi|116334961|ref|YP_802456.1| putative RNA polymerase sigma factor rpoD [Candidatus Carsonella
           ruddii PV]
 gi|116235242|dbj|BAF35090.1| putative RNA polymerase sigma factor rpoD [Candidatus Carsonella
           ruddii PV]
          Length = 320

 Score = 69.5 bits (169), Expect = 5e-10,   Method: Composition-based stats.
 Identities = 19/75 (25%), Positives = 37/75 (49%), Gaps = 2/75 (2%)

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQIE 273
           I + + +N  N++   +  L  +E+ I   R     P   TLE +   + +++ER+RQIE
Sbjct: 234 IREYDNRNLNNLIRLIILELPKKEQIIIRLRFGIGFPKSYTLEEIGLMYYLTKERIRQIE 293

Query: 274 ARAFKKVQESIQKQV 288
                K++   + +V
Sbjct: 294 LNVLFKLRHPTRSEV 308


>gi|251733353|emb|CAR82426.1| RNA polymerase sigma factor [Bradyrhizobium japonicum]
          Length = 205

 Score = 69.5 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 29/82 (35%), Positives = 43/82 (52%), Gaps = 5/82 (6%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAH---RLVTSHLRLVVKIAMGYRGYGLPI 75
           HE+ ++  L   E     K     + G+  A      +V ++LRLV+ IA  Y   GL  
Sbjct: 124 HEVHQLAALTGLEIVEFRKIVHSVQKGEREARQAKKEMVEANLRLVISIAKKYTNRGLQF 183

Query: 76  SEVVSEGNIGLMQAVKKFDPER 97
            +++ EGNIGLM+AV KF+  R
Sbjct: 184 LDLIQEGNIGLMKAVDKFEYRR 205


>gi|57237071|ref|YP_178083.1| flagellar biosynthesis sigma factor [Campylobacter jejuni RM1221]
 gi|86149716|ref|ZP_01067946.1| RNA polymerase sigma factor, sigma-F [Campylobacter jejuni subsp.
           jejuni CF93-6]
 gi|86151250|ref|ZP_01069465.1| RNA polymerase sigma factor, sigma-F [Campylobacter jejuni subsp.
           jejuni 260.94]
 gi|86154044|ref|ZP_01072245.1| RNA polymerase sigma factor, sigma-F [Campylobacter jejuni subsp.
           jejuni HB93-13]
 gi|88597726|ref|ZP_01100959.1| RNA polymerase sigma factor, sigma-F [Campylobacter jejuni subsp.
           jejuni 84-25]
 gi|121612660|ref|YP_999787.1| flagellar biosynthesis sigma factor [Campylobacter jejuni subsp.
           jejuni 81-176]
 gi|157414375|ref|YP_001481631.1| flagellar biosynthesis sigma factor [Campylobacter jejuni subsp.
           jejuni 81116]
 gi|167004762|ref|ZP_02270520.1| RNA polymerase sigma factor, sigma-F [Campylobacter jejuni subsp.
           jejuni 81-176]
 gi|315123666|ref|YP_004065670.1| flagellar biosynthesis sigma factor FliA [Campylobacter jejuni
           subsp. jejuni ICDCCJ07001]
 gi|57165875|gb|AAW34654.1| RNA polymerase sigma factor, sigma-F [Campylobacter jejuni RM1221]
 gi|85839984|gb|EAQ57243.1| RNA polymerase sigma factor, sigma-F [Campylobacter jejuni subsp.
           jejuni CF93-6]
 gi|85841597|gb|EAQ58844.1| RNA polymerase sigma factor, sigma-F [Campylobacter jejuni subsp.
           jejuni 260.94]
 gi|85842458|gb|EAQ59672.1| RNA polymerase sigma factor, sigma-F [Campylobacter jejuni subsp.
           jejuni HB93-13]
 gi|87248999|gb|EAQ71961.1| RNA polymerase sigma factor, sigma-F [Campylobacter jejuni subsp.
           jejuni 81-176]
 gi|88190030|gb|EAQ94006.1| RNA polymerase sigma factor, sigma-F [Campylobacter jejuni subsp.
           jejuni 84-25]
 gi|157385339|gb|ABV51654.1| RNA polymerase sigma factor, sigma-F [Campylobacter jejuni subsp.
           jejuni 81116]
 gi|284925357|gb|ADC27709.1| flagellar biosynthesis sigma factor [Campylobacter jejuni subsp.
           jejuni IA3902]
 gi|315017388|gb|ADT65481.1| flagellar biosynthesis sigma factor FliA [Campylobacter jejuni
           subsp. jejuni ICDCCJ07001]
 gi|315057502|gb|ADT71831.1| RNA polymerase sigma factor for flagellar operon [Campylobacter
           jejuni subsp. jejuni S3]
 gi|315927744|gb|EFV07071.1| RNA polymerase sigma factor, FliA/WhiG family protein
           [Campylobacter jejuni subsp. jejuni DFVF1099]
          Length = 230

 Score = 69.5 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 37/241 (15%), Positives = 100/241 (41%), Gaps = 28/241 (11%)

Query: 47  LSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
                 LV S++  +  +A          + +++++S G   +++  +++D E+      
Sbjct: 14  KKEQDELVLSYMPALRAMAFRLKERLPSSIDVNDLISIGVEEMIKLSRRYDKEQNDNFWG 73

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           ++   +  +M +Y+     + +     N +++  ++  +    +   ++  +P+    +A
Sbjct: 74  FARKRVNGSMLDYLRSLDVMSR-----NNRKIIKDIDAIMD--EYFLEHECEPDD-EYLA 125

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           KKL++   ++  +  R A   S    I+                    E   +EK E++ 
Sbjct: 126 KKLDLDVEKIKEV--RTAHAISYTLPID-------------EQIELYNEDNTLEKIEKEE 170

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               +   +  L  R++ I +    +E  ++L+ +S   ++S  R+ QI  +  KK++E 
Sbjct: 171 LLEKIHEVLDDLKERDQLIIQLYYYEE--LSLKEISEILQISESRISQIHKKLLKKLRER 228

Query: 284 I 284
           +
Sbjct: 229 L 229


>gi|261368117|ref|ZP_05981000.1| RNA polymerase sigma-27 factor [Subdoligranulum variabile DSM
           15176]
 gi|282569875|gb|EFB75410.1| RNA polymerase sigma-27 factor [Subdoligranulum variabile DSM
           15176]
          Length = 147

 Score = 69.5 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 20/64 (31%), Positives = 34/64 (53%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+  +LRLV  +   Y        +++S G IGL++AV  FDP R  + ++Y+   I
Sbjct: 55  RDLLIRHNLRLVAHVTKKYFAATASQDDLISIGTIGLIKAVDTFDPVRASKFSSYASRCI 114

Query: 110 KAAM 113
           + A+
Sbjct: 115 ENAI 118


>gi|256267|gb|AAC60414.1| RpoD1 [Synechococcus]
          Length = 48

 Score = 69.5 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 17/48 (35%), Positives = 32/48 (66%)

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
            +++ EG++GL++A +KFD E+G++ +TY+ WWI+ A+   I      
Sbjct: 1   QDLIQEGSLGLIRAAEKFDHEKGYKFSTYATWWIRQAITRAIADQSRT 48


>gi|310658943|ref|YP_003936664.1| RNA polymerase subunit alpha domain-containing protein [Clostridium
           sticklandii DSM 519]
 gi|308825721|emb|CBH21759.1| RNA polymerase, alpha subunit domain protein [Clostridium
           sticklandii]
          Length = 911

 Score = 69.5 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 26/91 (28%), Positives = 39/91 (42%), Gaps = 6/91 (6%)

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I S D       D L      +  ++ + +           +   LN RE  +   R   
Sbjct: 260 IKSLDNLYDSLNDLL---DSKKIDLVFDDKFIAIYDEFHEGAKEHLNEREYNVLLQRI-- 314

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
               TLE++  E  V+RER+RQIEA+A KK+
Sbjct: 315 -QGKTLEDVGLEMNVTRERIRQIEAKAIKKL 344


>gi|228970817|ref|ZP_04131457.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus thuringiensis
           serovar thuringiensis str. T01001]
 gi|228977391|ref|ZP_04137786.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus thuringiensis
           Bt407]
 gi|228782368|gb|EEM30551.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus thuringiensis
           Bt407]
 gi|228788942|gb|EEM36881.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus thuringiensis
           serovar thuringiensis str. T01001]
          Length = 234

 Score = 69.5 bits (169), Expect = 6e-10,   Method: Composition-based stats.
 Identities = 45/234 (19%), Positives = 93/234 (39%), Gaps = 28/234 (11%)

Query: 51  HRLVTSHLRLVVK-IAMGYR--------GYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
              ++ +  LV   I   Y+          GL I ++V  G IGL++A + F+ E G++ 
Sbjct: 4   EEFMSKYEDLVHHFIWKRYKGMLEIVKANTGLEIEDLVQYGMIGLIKARRDFNHELGYQF 63

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY++  I   + ++I+ +   +K+     Q R              +    L  E    
Sbjct: 64  STYAIPKIHGEVGKFIM-NSHKIKVPRALYQLR------------GKMMRQGLMEEDGET 110

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           I K+L V+  EV          +SL  ++ +S    S+    ++ +   ++  +IE+ E+
Sbjct: 111 ICKQLEVALPEVKEALQYQPNTKSLQDVMYTSAGGGSE---EILLEDMLEDTQVIEETEQ 167

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
                +L      L   E  +++         T + + +     + +V +I  R
Sbjct: 168 VENHMVLQSFYQTLEHPELIVWDMH---SKHKTQQEIGNRVGRCQVQVSRILKR 218


>gi|323356683|ref|YP_004223079.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Microbacterium testaceum StLB037]
 gi|323273054|dbj|BAJ73199.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Microbacterium testaceum StLB037]
          Length = 538

 Score = 69.1 bits (168), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 23/60 (38%), Positives = 34/60 (56%), Gaps = 5/60 (8%)

Query: 237 PRERRIFEAR-RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPP 295
           PRE++I   R   +  P TL  ++ EF++SRER+RQIE+RA    +  +  Q     SP 
Sbjct: 177 PREQKILRMRVGFEGAPRTLAEIAREFDLSRERIRQIESRA----RNILVHQARTPGSPG 232


>gi|256269|gb|AAC60415.1| RpoD2 [Synechococcus]
          Length = 48

 Score = 69.1 bits (168), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 17/47 (36%), Positives = 31/47 (65%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           +++ EG +GL + V+KFDP +G++ +TY+ WWI+ A+   I +    
Sbjct: 2   DLIQEGTLGLERGVEKFDPSKGYKFSTYAYWWIRQAITRAIAQQSRT 48


>gi|85859095|ref|YP_461297.1| putative cytoplasmic protein [Syntrophus aciditrophicus SB]
 gi|85722186|gb|ABC77129.1| hypothetical cytosolic protein [Syntrophus aciditrophicus SB]
          Length = 94

 Score = 69.1 bits (168), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 19/49 (38%), Positives = 29/49 (59%), Gaps = 1/49 (2%)

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK-QVELSSSPPLLQ 298
            P TLE +     V+RER+RQIEA+A KK+Q   ++ Q++  + P    
Sbjct: 43  GPFTLEEVGDMMGVTRERIRQIEAKALKKLQHKKRRDQLKDFALPSNEW 91


>gi|168206182|ref|ZP_02632187.1| sigma factor [Clostridium perfringens E str. JGS1987]
 gi|170662325|gb|EDT15008.1| sigma factor [Clostridium perfringens E str. JGS1987]
          Length = 227

 Score = 69.1 bits (168), Expect = 7e-10,   Method: Composition-based stats.
 Identities = 36/184 (19%), Positives = 80/184 (43%), Gaps = 19/184 (10%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG---YGLPISEVVSEGNIGL 86
             +E  VL     + GD  A  +L+ ++ +L+ KIA  +       +   +++ EG IG 
Sbjct: 2   TNEELVVL----YQQGDKRALDKLLENNDKLIYKIASKFYSEKINAIEFDDLLQEGRIGF 57

Query: 87  MQAVKKFDPE--RGFRLATYSMWWIKAAMQEYIL--RSWSLVKIGTTANQKR-------L 135
           + A  K+D E  +  +  TY+ +WI   +  +I    +   + + T  +++        +
Sbjct: 58  ILACNKYDCEYIKKTKFITYAFYWIYQKIHRFITGNNTNDEISLNTPVSEENKDELINGI 117

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE-SLNALINSSD 194
             N   +    + +  + L+ E    + K   ++E E++ +      DE S+  + +  +
Sbjct: 118 ESNRNEINDREEELYLSELRLELEAVMDKHNTLNEREILKLYYGWDTDELSIEQIADIFE 177

Query: 195 KNSS 198
            +SS
Sbjct: 178 TSSS 181



 Score = 41.0 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 19/103 (18%), Positives = 44/103 (42%), Gaps = 3/103 (2%)

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
            + SLN  ++  +K+          +     +  +   E +     +    + LN RE  
Sbjct: 97  DEISLNTPVSEENKDELINGIESNRNEINDREEELYLSELRLELEAVMDKHNTLNERE-- 154

Query: 242 IFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           I +     + + +++E ++  FE S   ++  +ARA +K++ S
Sbjct: 155 ILKLYYGWDTDELSIEQIADIFETSSSDIKNTKARAIRKLRGS 197


>gi|148926867|ref|ZP_01810545.1| putative RNA polymerase sigma factor for flagellar operon
           [Campylobacter jejuni subsp. jejuni CG8486]
 gi|205356444|ref|ZP_03223208.1| putative RNA polymerase sigma factor for flagellar operon
           [Campylobacter jejuni subsp. jejuni CG8421]
 gi|218561746|ref|YP_002343525.1| flagellar biosynthesis sigma factor [Campylobacter jejuni subsp.
           jejuni NCTC 11168]
 gi|112359452|emb|CAL34235.1| RNA polymerase sigma factor for flagellar operon [Campylobacter
           jejuni subsp. jejuni NCTC 11168]
 gi|145844444|gb|EDK21552.1| putative RNA polymerase sigma factor for flagellar operon
           [Campylobacter jejuni subsp. jejuni CG8486]
 gi|205345631|gb|EDZ32270.1| putative RNA polymerase sigma factor for flagellar operon
           [Campylobacter jejuni subsp. jejuni CG8421]
 gi|315929165|gb|EFV08390.1| RNA polymerase sigma factor, FliA/WhiG family protein
           [Campylobacter jejuni subsp. jejuni 305]
          Length = 238

 Score = 69.1 bits (168), Expect = 8e-10,   Method: Composition-based stats.
 Identities = 37/241 (15%), Positives = 100/241 (41%), Gaps = 28/241 (11%)

Query: 47  LSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
                 LV S++  +  +A          + +++++S G   +++  +++D E+      
Sbjct: 22  KKEQDELVLSYMPALRAMAFRLKERLPSSIDVNDLISIGVEEMIKLSRRYDKEQNDNFWG 81

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           ++   +  +M +Y+     + +     N +++  ++  +    +   ++  +P+    +A
Sbjct: 82  FARKRVNGSMLDYLRSLDVMSR-----NNRKIIKDIDAIMD--EYFLEHECEPDD-EYLA 133

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           KKL++   ++  +  R A   S    I+                    E   +EK E++ 
Sbjct: 134 KKLDLDVEKIKEV--RTAHAISYTLPID-------------EQIELYNEDNTLEKIEKEE 178

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               +   +  L  R++ I +    +E  ++L+ +S   ++S  R+ QI  +  KK++E 
Sbjct: 179 LLEKIHEVLDDLKERDQLIIQLYYYEE--LSLKEISEILQISESRISQIHKKLLKKLRER 236

Query: 284 I 284
           +
Sbjct: 237 L 237


>gi|207743453|ref|YP_002259845.1| hypothetical alternative rna sigma factor rpos (partial sequence)
           protein [Ralstonia solanacearum IPO1609]
 gi|206594850|emb|CAQ61777.1| hypothetical alternative rna sigma factor rpos (partial sequence)
           protein [Ralstonia solanacearum IPO1609]
          Length = 184

 Score = 69.1 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 26/76 (34%), Positives = 42/76 (55%), Gaps = 1/76 (1%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY 71
               +  Y++ I   P+L   EE   + R +  G+ +A   ++  +LRLVV IA GY   
Sbjct: 105 AADTVQHYLNRISIKPLLTPAEELHFSTRAK-AGEFAARQVMIERNLRLVVSIAKGYLKQ 163

Query: 72  GLPISEVVSEGNIGLM 87
           G+ + E++SEGN G+M
Sbjct: 164 GVRLMEMISEGNRGVM 179


>gi|321312139|ref|YP_004204426.1| sporulation sigma factor SigK [Bacillus subtilis BSn5]
 gi|320018413|gb|ADV93399.1| sporulation sigma factor SigK [Bacillus subtilis BSn5]
          Length = 126

 Score = 69.1 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 20/100 (20%), Positives = 43/100 (43%), Gaps = 5/100 (5%)

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
           D SL+  I    + +   +  L+     + + +I+  +       + + + +L+ RE+ +
Sbjct: 12  DVSLHDPIGQDKEGN---EISLIDVLKSENEDVIDTIQLNMELEKVKQYIDILDDREKEV 68

Query: 243 FEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
              R   +     T   ++ E  +SR  V +IE RA  K+
Sbjct: 69  IVGRFGLDLKKEKTQREIAKELGISRSYVSRIEKRALMKM 108


>gi|313637835|gb|EFS03172.1| RNA polymerase sigma factor RpoD [Listeria seeligeri FSL S4-171]
          Length = 56

 Score = 69.1 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 16/48 (33%), Positives = 28/48 (58%), Gaps = 2/48 (4%)

Query: 242 IFEARRLQENPVT--LENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +   R   ++  T  LE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 2   VLRLRFGLDDGRTRTLEEVGRVFGVTRERIRQIEAKALRKLRHPSRSK 49


>gi|228902053|ref|ZP_04066217.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus thuringiensis
           IBL 4222]
 gi|228857479|gb|EEN01975.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus thuringiensis
           IBL 4222]
          Length = 237

 Score = 69.1 bits (168), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 45/234 (19%), Positives = 93/234 (39%), Gaps = 28/234 (11%)

Query: 51  HRLVTSHLRLVVK-IAMGYR--------GYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
              ++ +  LV   I   Y+          GL I ++V  G IGL++A + F+ E G++ 
Sbjct: 7   EEFMSKYEDLVHHFIWKRYKGMLEIVKANTGLEIEDLVQYGMIGLIKARRDFNHELGYQF 66

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY++  I   + ++I+ +   +K+     Q R              +    L  E    
Sbjct: 67  STYAIPKIHGEVGKFIM-NSHKIKVPRALYQLR------------GKMMRQGLMEEDGET 113

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           I K+L V+  EV          +SL  ++ +S    S+    ++ +   ++  +IE+ E+
Sbjct: 114 ICKQLEVALPEVKEALQYQPNTKSLQDVMYTSAGGGSE---EILLEDMLEDTQVIEETEQ 170

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
                +L      L   E  +++         T + + +     + +V +I  R
Sbjct: 171 VENHMVLQSFYQTLEHPELIVWDMH---SKHKTQQEIGNRVGRCQVQVSRILKR 221


>gi|33863056|ref|NP_894616.1| putative type III sigma factor [Prochlorococcus marinus str. MIT
           9313]
 gi|33634973|emb|CAE20959.1| putative type III sigma factor [Prochlorococcus marinus str. MIT
           9313]
          Length = 269

 Score = 68.7 bits (167), Expect = 9e-10,   Method: Composition-based stats.
 Identities = 43/215 (20%), Positives = 87/215 (40%), Gaps = 15/215 (6%)

Query: 50  AHRLVTSHLRLVVKIA-MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
            +  V  HL L    A       G  + +++ E  +GL+ A++ FD   GF+ ++Y+M  
Sbjct: 39  RNEAVVEHLGLAHLAATRQATRGGEELDDLIQEARLGLIMAMENFDANLGFKASSYAMAR 98

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
               +  +      +V++      + L+    RLK   Q   ++ LKP     +A +LNV
Sbjct: 99  ANGQILHFRRDRSQIVRVPWRL--RDLYTRGMRLKQKQQ---NDGLKPFTEEQLAAQLNV 153

Query: 169 SESEVISMNCRLAGD--ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           S          +      SL+A  +S+  N  + +  L+      +Q      E   +  
Sbjct: 154 SSDRWHQAAEAIWQTHLVSLDAKESSTGGNHVEKRVPLLERLKSPKQK-----EPDLQYQ 208

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
            L +++  L   ++ +  A  + +  ++L  L+  
Sbjct: 209 WLKKAIQRLTSHQQHLLYAHYIDD--ISLRQLAKR 241


>gi|221310570|ref|ZP_03592417.1| RNA polymerase sporulation-specific sigma factor (sigma-K)
           (C-terminal half) [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221314894|ref|ZP_03596699.1| RNA polymerase sporulation-specific sigma factor (sigma-K)
           (C-terminal half) [Bacillus subtilis subsp. subtilis
           str. NCIB 3610]
 gi|221319816|ref|ZP_03601110.1| RNA polymerase sporulation-specific sigma factor (sigma-K)
           (C-terminal half) [Bacillus subtilis subsp. subtilis
           str. JH642]
 gi|221324095|ref|ZP_03605389.1| RNA polymerase sporulation-specific sigma factor (sigma-K)
           (C-terminal half) [Bacillus subtilis subsp. subtilis
           str. SMY]
          Length = 132

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 20/100 (20%), Positives = 43/100 (43%), Gaps = 5/100 (5%)

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
           D SL+  I    + +   +  L+     + + +I+  +       + + + +L+ RE+ +
Sbjct: 18  DVSLHDPIGQDKEGN---EISLIDVLKSENEDVIDTIQLNMELEKVKQYIDILDDREKEV 74

Query: 243 FEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
              R   +     T   ++ E  +SR  V +IE RA  K+
Sbjct: 75  IVGRFGLDLKKEKTQREIAKELGISRSYVSRIEKRALMKM 114


>gi|326938416|gb|AEA14312.1| sporulation sigma factor SigF [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 243

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 45/234 (19%), Positives = 93/234 (39%), Gaps = 28/234 (11%)

Query: 51  HRLVTSHLRLVVK-IAMGYR--------GYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
              ++ +  LV   I   Y+          GL I ++V  G IGL++A + F+ E G++ 
Sbjct: 13  EEFMSKYEDLVHHFIWKRYKGMLEIVKANTGLEIEDLVQYGMIGLIKARRDFNHELGYQF 72

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           +TY++  I   + ++I+ +   +K+     Q R              +    L  E    
Sbjct: 73  STYAIPKIHGEVGKFIM-NSHKIKVPRALYQLR------------GKMMRQGLMEEDGET 119

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           I K+L V+  EV          +SL  ++ +S    S+    ++ +   ++  +IE+ E+
Sbjct: 120 ICKQLEVALPEVKEALQYQPNTKSLQDVMYTSAGGGSE---EILLEDMLEDTQVIEETEQ 176

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
                +L      L   E  +++         T + + +     + +V +I  R
Sbjct: 177 VENHMVLQSFYQTLEHPELIVWDMH---SKHKTQQEIGNRVGRCQVQVSRILKR 227


>gi|226310246|ref|YP_002770140.1| RNA polymerase sigma factor [Brevibacillus brevis NBRC 100599]
 gi|226093194|dbj|BAH41636.1| RNA polymerase sigma factor [Brevibacillus brevis NBRC 100599]
          Length = 268

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 38/256 (14%), Positives = 99/256 (38%), Gaps = 26/256 (10%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG--------YGLPISEVVSEGNIGLMQA 89
            +R +E  D      ++ ++  L+      Y G        Y L  ++++  G +G+++A
Sbjct: 27  IRRCKE--DSEYLGEVILANEELIWHSVHKYIGKPETLVKQYCLEKADILQLGRMGIIKA 84

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +K FD  RG + +++++  I   +  ++  S ++V+   TA    +  ++ +++  L  +
Sbjct: 85  IKAFDIARGVKFSSFAVITIVREINCFLRDSGNIVRPTRTAT--TILHHISKIEADLGYL 142

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
                    +  ++  L  +  ++          + L      +  +S +    +    D
Sbjct: 143 -------PTIEELSLLLGENVEQIKKALDVGRPVKYLQEPFLKASASSHEAATAMDVLKD 195

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
               V     ++     +L +  + ++ +E ++ + R    N       +    VS+  V
Sbjct: 196 EGRDVEEYVLDKLYVTALLAQLQNQISLKEWQVLQLRMAGYN---QTQTAEFLNVSQMCV 252

Query: 270 RQIEARAFKKVQESIQ 285
                R  KK+Q   +
Sbjct: 253 S----RTMKKIQNISK 264


>gi|313650139|gb|EFS14552.1| RNA polymerase sigma factor for flagellar operon [Shigella flexneri
           2a str. 2457T]
 gi|332757220|gb|EGJ87557.1| RNA polymerase sigma factor for flagellar operon [Shigella flexneri
           2747-71]
 gi|332766654|gb|EGJ96858.1| RNA polymerase sigma factor, sigma-70 family protein [Shigella
           flexneri 2930-71]
          Length = 161

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 23/154 (14%), Positives = 61/154 (39%), Gaps = 6/154 (3%)

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
           + +  N R +   +  +     +      +A++L +  ++   M      D + + L + 
Sbjct: 13  RSVRRNAREVAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLL----DTNNSQLFSY 68

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            +          +   D Q +  +++    N R  +  ++  L  RE+ +       +  
Sbjct: 69  DEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQRVMEAIETLPEREKLVLTLYY--QEE 126

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           + L+ + +  EV   RV Q+ ++A K+++  + K
Sbjct: 127 LNLKEIGAVLEVGESRVSQLHSQAIKRLRTKLGK 160


>gi|154173651|ref|YP_001408770.1| flagellar biosynthesis sigma factor [Campylobacter curvus 525.92]
 gi|153792993|gb|EAT99591.2| flagellar biosynthesis sigma factor FliA [Campylobacter curvus
           525.92]
          Length = 234

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 32/241 (13%), Positives = 89/241 (36%), Gaps = 28/241 (11%)

Query: 47  LSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
                 +V  ++  +  +A          + +++++  G   +++  +K+D E+      
Sbjct: 17  KKEQDEIVLQYMPALRAMAFRLKERLPSSIDVNDLIGVGVEEMIKLSRKYDKEQNDSFWG 76

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y    I  AM +Y+         G     +     ++ +   + A  +   +      +A
Sbjct: 77  YGKKRIYGAMLDYLR--------GLDIMSRTNRKLVKAINSAIDAYFNEFEEEPDDEYLA 128

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           KKL     ++        G  S+  ++   D+     Q             + +  E+++
Sbjct: 129 KKLGEDIEKIRE----ARGVSSIITVLPIDDQMELFSQH-----------NVEQSVEKED 173

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               +   +   + R++ + +    +E  + L+ +S   ++S  R+ QI  R   ++++S
Sbjct: 174 LIQKIEAILENFDERDQMVIQLYYYEE--LNLKEISEIMQISESRISQIHKRLLDRLRKS 231

Query: 284 I 284
           +
Sbjct: 232 L 232


>gi|283955444|ref|ZP_06372942.1| RNA polymerase sigma factor, sigma-F [Campylobacter jejuni subsp.
           jejuni 414]
 gi|283793071|gb|EFC31842.1| RNA polymerase sigma factor, sigma-F [Campylobacter jejuni subsp.
           jejuni 414]
          Length = 230

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 38/241 (15%), Positives = 100/241 (41%), Gaps = 28/241 (11%)

Query: 47  LSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
                 LV S++  +  +A          + +++++S G   +++  +++D E+      
Sbjct: 14  KKEQDELVLSYMPALRAMAFRLKERLPSSIDVNDLISIGVEEMIKLSRRYDKEQNDNFWG 73

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           ++   +  +M +Y+     + +     N +++  ++  +    +   ++  +P+    +A
Sbjct: 74  FARKRVNGSMLDYLRSLDVMSR-----NNRKIIKDIDAIMD--EYFLEHECEPDD-EYLA 125

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           KKL++   ++  +  R A   S    I+                    E   +EK E++ 
Sbjct: 126 KKLDLDVEKIKEV--RTAHAISYTLPID-------------EQIELYNEDNTLEKIEKEE 170

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               +   +  L  R++ I +    +E  ++L+ +S   E+S  R+ QI  +  KK++E 
Sbjct: 171 LLEKIHEVLDDLKERDQLIIQLYYYEE--LSLKEISEILEISESRISQIHKKLLKKLRER 228

Query: 284 I 284
           +
Sbjct: 229 L 229


>gi|14646833|dbj|BAB62001.1| RNA polymerase sigma factor [Pseudomonas putida]
          Length = 79

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 19/76 (25%), Positives = 37/76 (48%), Gaps = 2/76 (2%)

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAF 277
           +  +    + + +  L  ++R +   R         TLE++  E  ++RERVRQI+    
Sbjct: 1   QDDDLSQSIDQWLGELTDKQREVVVRRFGLRGHESSTLEDVGLEIGLTRERVRQIQVEGL 60

Query: 278 KKVQESIQKQVELSSS 293
           K+++E ++K    S S
Sbjct: 61  KRLREILEKNGLSSES 76


>gi|6010734|gb|AAF01233.1|AF184102_1 mutant RpoS [Salmonella enterica subsp. enterica serovar
           Typhimurium str. LT2]
          Length = 119

 Score = 68.7 bits (167), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 23/54 (42%), Positives = 33/54 (61%), Gaps = 1/54 (1%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA  Y   G
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIARRYGNRG 113


>gi|303242138|ref|ZP_07328628.1| RNA polymerase, sigma 32 subunit, RpoH [Acetivibrio cellulolyticus
           CD2]
 gi|302590325|gb|EFL60083.1| RNA polymerase, sigma 32 subunit, RpoH [Acetivibrio cellulolyticus
           CD2]
          Length = 244

 Score = 68.3 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 46/262 (17%), Positives = 87/262 (33%), Gaps = 72/262 (27%)

Query: 33  EEYVLAKRYR--EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP-------ISEVVSEGN 83
           EE VLA +    +   + A + L  ++++L+   A    G  +          +++ E  
Sbjct: 4   EEIVLAYQTATTDTDKIKAINDLTEANIKLLHYFANRSGGTVISACGDVITYEDLIQESW 63

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           I L+ A K F P++G    T++  +IK                              R+K
Sbjct: 64  IALLGAAKSFKPDKGALFTTWASHYIK-----------------------------NRIK 94

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
            H+   T                   +   IS N  +  D  +       D         
Sbjct: 95  RHIGDYT------------------PKVTTISTNTPVEPDSDITYEDMIPDSE------- 129

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMS-VLNPRERRIFEARRLQEN-PVTLENLSSE 261
                   E+        K  R  L + MS  L  +++ I +          T  +++  
Sbjct: 130 -------AEKRFWNYIHNKELRFELEQVMSGHLTEQQQEIIKMFYGWNGYEYTFAHIAGI 182

Query: 262 FEVSRERVRQIEARAFKKVQES 283
           +  S E +RQI  +A +++++S
Sbjct: 183 YSCSSENIRQIHNKALRQIRKS 204


>gi|153812706|ref|ZP_01965374.1| hypothetical protein RUMOBE_03113 [Ruminococcus obeum ATCC 29174]
 gi|149831222|gb|EDM86311.1| hypothetical protein RUMOBE_03113 [Ruminococcus obeum ATCC 29174]
          Length = 114

 Score = 68.3 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 22/104 (21%), Positives = 45/104 (43%), Gaps = 6/104 (5%)

Query: 181 AGDESLNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           + + SL   I +  + N     D +         ++ E   R++ R + +    +L P+E
Sbjct: 10  SREVSLYEPIGTDKEGNEISLLDII---ESPPVDIVEEYSTRQDIRFLFSSMKDILTPKE 66

Query: 240 RRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            ++   R      N +T   ++ +  +SR  V +IE  A KK++
Sbjct: 67  YQVICCRYGLFENNEMTQREIADQLHISRSYVSRIEKNALKKLK 110


>gi|289422613|ref|ZP_06424455.1| RNA polymerase sigma factor, sigma-70 family [Peptostreptococcus
           anaerobius 653-L]
 gi|289156964|gb|EFD05587.1| RNA polymerase sigma factor, sigma-70 family [Peptostreptococcus
           anaerobius 653-L]
          Length = 289

 Score = 68.3 bits (166), Expect = 1e-09,   Method: Composition-based stats.
 Identities = 50/243 (20%), Positives = 97/243 (39%), Gaps = 21/243 (8%)

Query: 33  EEYVLAKRY----REHGDLSAAHRLVTSHLRLVVKIAMG------YRGYGLPISEVVSEG 82
           ++  LA R      + GDL A ++++    + V  I         Y+  GL   ++   G
Sbjct: 36  DKRELADRKLVKSAKEGDLVALNKVIEKKSKYVKGIIKNDYEIMAYKKRGLDQEDLFQSG 95

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            IGL+ AVKKFD   G +  TY    +K +++        L       +  R   ++   
Sbjct: 96  MIGLLNAVKKFDFRDGIKFDTYLAHNVKYSIKNDFRDYGGL-------SVSREASSIYSK 148

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
                   D NL  E +  +++KL V++ ++      +    ++       +   ++ Q 
Sbjct: 149 CSSSLYEYDGNLSDELLEELSEKLYVTKEKISKSILAVKIRNAMYTYTCDGEIE-AEEQI 207

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
              Y     E    + E+R   R +L + +  L+ +ER I E   +++   T  +++ E 
Sbjct: 208 LYKYKKQLVEDYESKFEKRMLYREILNQ-IKKLSDKERYILENLYIKD--RTQVSIAQEL 264

Query: 263 EVS 265
             S
Sbjct: 265 GCS 267


>gi|226949740|ref|YP_002804831.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           A2 str. Kyoto]
 gi|226840763|gb|ACO83429.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           A2 str. Kyoto]
          Length = 183

 Score = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 38/240 (15%), Positives = 75/240 (31%), Gaps = 68/240 (28%)

Query: 55  TSHLRLVVKIA-MGYR--GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
             HL LV  IA   Y    +     E+  EG +GLM+AV +FD  RG + +TY+  ++  
Sbjct: 5   EEHLNLVHSIASKRYSQFKHKYTYEELFQEGCLGLMKAVNRFDTSRGIKFSTYAYPYVDG 64

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           A+                A   + +   R+ +                            
Sbjct: 65  AIL-------------IMARDDKWYGKNRKERFEK------------------------- 86

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
                    +   SL+A I   +                    LI  ++    +  +   
Sbjct: 87  ---------SAPYSLDAAIKGLENEMPYIN-------------LIGNDDFNFEKIEVKML 124

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ---ESIQKQV 288
           +  L    + I     +     T   ++     S+  + +++  A   ++    SI+K++
Sbjct: 125 VDELPSDLKDIVNMIYI--EGFTQTEIAKIIGCSQISISRLKKEALDYLRFQVSSIKKEM 182


>gi|147677457|ref|YP_001211672.1| DNA-directed RNA polymerase, sigma subunit [Pelotomaculum
           thermopropionicum SI]
 gi|146273554|dbj|BAF59303.1| DNA-directed RNA polymerase, sigma subunit [Pelotomaculum
           thermopropionicum SI]
          Length = 118

 Score = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 22/106 (20%), Positives = 44/106 (41%), Gaps = 5/106 (4%)

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
             ++  + SL   I    + +      ++  H    +V+ E  E    +  L   +  L 
Sbjct: 6   MKKVKVEVSLYDPIGVDKEGNEITLIDILGTH---PEVVAEMVENNFEQKRLLEKVRQLT 62

Query: 237 PRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKV 280
            RE+++ E R   E+   +T   ++    +SR  V +IE +A  K+
Sbjct: 63  RREKKVLELRFGLEDGARMTQREIAKSLGISRSYVSRIEKKALNKL 108


>gi|260437950|ref|ZP_05791766.1| RNA polymerase sigma-H factor [Butyrivibrio crossotus DSM 2876]
 gi|292809701|gb|EFF68906.1| RNA polymerase sigma-H factor [Butyrivibrio crossotus DSM 2876]
          Length = 205

 Score = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 24/97 (24%), Positives = 44/97 (45%), Gaps = 4/97 (4%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
             +L  +E   L  +Y   GD  AA  L+  +  LV K    Y   G    +++ EG +G
Sbjct: 7   YKLLSDEE---LVAKYH-SGDEKAADYLIEKYKNLVRKNVRSYYLAGADNEDLLQEGMLG 62

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           L +A++ ++P+R     T++   +   ++  I R   
Sbjct: 63  LFKAIRDYNPDRDALFMTFASLCVSRHIRSTITRYNR 99


>gi|228937937|ref|ZP_04100564.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus thuringiensis
           serovar berliner ATCC 10792]
 gi|228821728|gb|EEM67729.1| RNA polymerase, sigma 28 subunit, FliA/WhiG [Bacillus thuringiensis
           serovar berliner ATCC 10792]
          Length = 210

 Score = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 41/206 (19%), Positives = 85/206 (41%), Gaps = 19/206 (9%)

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
             GL I ++V  G IGL++A + F+ E G++ +TY++  I   + ++I+ +   +K+   
Sbjct: 8   NTGLEIEDLVQYGMIGLIKARRDFNHELGYQFSTYAIPKIHGEVGKFIM-NSHKIKVPRA 66

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             Q R              +    L  E    I K+L V+  EV          +SL  +
Sbjct: 67  LYQLR------------GKMMRQGLMEEDGETICKQLEVALPEVKEALQYQPNTKSLQDV 114

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           + +S    S+    ++ +   ++  +IE+ E+     +L      L   E  +++     
Sbjct: 115 MYTSAGGGSE---EILLEDMLEDTQVIEETEQVENHMVLQSFYQTLEHPELIVWDMH--- 168

Query: 250 ENPVTLENLSSEFEVSRERVRQIEAR 275
               T + + +     + +V +I  R
Sbjct: 169 SKHKTQQEIGNRVGRCQVQVSRILKR 194


>gi|88809560|ref|ZP_01125067.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 7805]
 gi|88786310|gb|EAR17470.1| possible type II alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 7805]
          Length = 131

 Score = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 28/123 (22%), Positives = 53/123 (43%), Gaps = 8/123 (6%)

Query: 166 LNVSESEVISMN--CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           +N+  SEV  +      +   SL  ++ S   + S+  D L  +     +     E   +
Sbjct: 1   MNLPISEVEDLLGCELRSVTVSLQGVVKSK-SDPSELVDVLPSEEIPPLERAEIAERTAS 59

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENP---VTLENLSSEFEVSRERVRQIEARAFKKV 280
              +L +  S L P+ER +   R   +      TL  ++ +   SRE  RQ+  RA +K+
Sbjct: 60  AWKLLDK--SNLTPKERTVVMLRFGLDGSNEWRTLAEVARQMNCSREYCRQVVQRALRKL 117

Query: 281 QES 283
           +++
Sbjct: 118 RKT 120


>gi|188586354|ref|YP_001917899.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Natranaerobius thermophilus JW/NM-WN-LF]
 gi|179351041|gb|ACB85311.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Natranaerobius thermophilus JW/NM-WN-LF]
          Length = 113

 Score = 67.9 bits (165), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 24/98 (24%), Positives = 42/98 (42%), Gaps = 7/98 (7%)

Query: 186 LNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           L   I    + N     D L  D +    ++I++      ++ L R +  L PRE +I  
Sbjct: 15  LQDPIGVDKEGNEITLLDILGSDSN----MVIDQVTLSIDKDKLRRVIKTLKPREEKILR 70

Query: 245 ARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            R     E  +T + ++ +  +SR  V +IE R   K+
Sbjct: 71  WRFGLSNEKALTQKEVAEKLGISRSYVSRIEKRILNKM 108


>gi|225164110|ref|ZP_03726391.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Opitutaceae bacterium TAV2]
 gi|224801282|gb|EEG19597.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Opitutaceae bacterium TAV2]
          Length = 235

 Score = 67.5 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 45/225 (20%), Positives = 86/225 (38%), Gaps = 37/225 (16%)

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV--KKFDPERGFRLATYSMWWIKAAMQEY 116
           RL   IA           ++ S G + L+ A+  +  +P+    +  Y    ++ AM + 
Sbjct: 28  RLPANIAR---------DDLASVGKLALIAALGQRNGEPD---DVRAYCYVRVRGAMLDE 75

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
           + R         +  Q+     + R +    A+T    +   +  IA    ++++E+ S 
Sbjct: 76  LRRLD-----PLSRRQRNRISFIARART---ALTKRLGRLPTLDEIASATQLTKAELTS- 126

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
                   +++A   ++D    +W        D Q     E  E  + R  L  ++  L 
Sbjct: 127 --------AIDAATQATDTTEIEWDTI----PDTQLPSPAEVVELDDIRASLGVALDRLP 174

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             +      RR      TL+ ++ E  VSRER RQ+     KK++
Sbjct: 175 ANQA--LALRRYYLEDATLDAIAVELGVSRERARQVREAGEKKLR 217


>gi|149175161|ref|ZP_01853784.1| sigma-70 factor [Planctomyces maris DSM 8797]
 gi|148846139|gb|EDL60479.1| sigma-70 factor [Planctomyces maris DSM 8797]
          Length = 349

 Score = 67.5 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 20/70 (28%), Positives = 40/70 (57%), Gaps = 3/70 (4%)

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE---NLSSEFEVSRERVRQIEARAF 277
            +N  ++L + +  L+ RE+ I + R       T E    ++ +  VS ERVRQ+  R+ 
Sbjct: 269 HQNIDDVLQKVLHTLDEREQVILKRRFGLAQSDTPEKFREIAEDLGVSTERVRQLTIRSL 328

Query: 278 KKVQESIQKQ 287
           ++++E+I++Q
Sbjct: 329 QRMREAIEEQ 338



 Score = 66.0 bits (160), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 46/213 (21%), Positives = 81/213 (38%), Gaps = 59/213 (27%)

Query: 26  IPMLEKQEEYVL----------AKRYREHGDLSA-------------------AHRLVTS 56
           +P+L+K++E +L          A++ +   DL +                    + ++ +
Sbjct: 114 VPLLDKEQEVILFRGMNYLKYRAEKLKSQIDLKSPCIGLLDRIEQKLKDARRLRNYIIQA 173

Query: 57  HLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQE- 115
           +LRLVV IA           ++VS+G++ L++AV+ FD +RG R +TY  W ++  +   
Sbjct: 174 NLRLVVSIAKNLTDRANLFEDIVSDGHLPLIRAVEIFDVDRGNRFSTYGTWAVRNFLFRT 233

Query: 116 --------------------YILRSWSLVKIGTTANQKR---LFFNLRRLKGHLQAITDN 152
                                +    S ++   T +Q     L   L  L    Q I   
Sbjct: 234 TKKGRKYRKTFLNGAETLALGLSDIRSTMRSHETYHQNIDDVLQKVLHTLDEREQVILKR 293

Query: 153 NL------KPEQVVAIAKKLNVSESEVISMNCR 179
                    PE+   IA+ L VS   V  +  R
Sbjct: 294 RFGLAQSDTPEKFREIAEDLGVSTERVRQLTIR 326


>gi|224005601|ref|XP_002291761.1| RNA polymerase [Thalassiosira pseudonana CCMP1335]
 gi|220972280|gb|EED90612.1| RNA polymerase [Thalassiosira pseudonana CCMP1335]
          Length = 217

 Score = 67.5 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 29/226 (12%), Positives = 81/226 (35%), Gaps = 20/226 (8%)

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPER-----GFRLATYSMWWIKAAMQEYILRSWSL 123
           R   +   ++V EG I L+ A+  ++  +           Y+   I++++  ++  S   
Sbjct: 1   RKSSISYPDLVQEGMIALLHAISSYNSYKTHNKNDQSFEKYAQQTIQSSLLHFLAHSSRP 60

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           +++  +     L   L+        +     +   +  +AK++N+   +   +       
Sbjct: 61  IRLPFS-----LQTTLQSANEAAAKLRSALGREPTLTQVAKEVNIDAHQ---LALYPGAT 112

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           E  +  IN+ ++  +  +D L    +     L   +     + +       L   E  + 
Sbjct: 113 EEDDWEINNPERTVAPLRDILTDTEEINNP-LSYTQHYLLTQELDQFLYETLTHDELEVI 171

Query: 244 EARRL------QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           + R             +   +     + +E V +I + A +K++++
Sbjct: 172 QLRFGLLDSKYGGKGWSAGQIGERMNMDKEEVVKIASSALEKLRKA 217


>gi|332095502|gb|EGJ00518.1| RNA polymerase sigma factor for flagellar operon [Shigella
           dysenteriae 155-74]
          Length = 186

 Score = 67.5 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 35/193 (18%), Positives = 78/193 (40%), Gaps = 15/193 (7%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 3   KHSLWQRYVPLVRHEALRLQVRLLASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 62

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   + +L+  L        +      +A++L
Sbjct: 63  QRIRGAMLDEL-RSRDWVPRSVRRNAREVAQAIGQLEQEL-------GRNATETEVAERL 114

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +  ++   M      D + + L +  +          +   D Q +  +++    N   
Sbjct: 115 GIDIADYRQML----RDTNNSQLFSYDEWREEHGDSIELVTDDHQRENPLQQLLDSNLCQ 170

Query: 227 MLTRSMSVLNPRE 239
            +  ++  L  RE
Sbjct: 171 RVMEAIETLPERE 183


>gi|50954397|ref|YP_061685.1| RNA polymerase, sigma factor [Leifsonia xyli subsp. xyli str.
           CTCB07]
 gi|50950879|gb|AAT88580.1| RNA polymerase, sigma factor [Leifsonia xyli subsp. xyli str.
           CTCB07]
          Length = 272

 Score = 67.5 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 48/236 (20%), Positives = 84/236 (35%), Gaps = 40/236 (16%)

Query: 50  AHRLVTSHLRLVVKIAMG--YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
             RLVT HL LV  I      +   L   E+ S GN+ L +A   FDP++G   A+Y+  
Sbjct: 30  RDRLVTDHLPLVGYIVSDLCMKAAHLDRDELASAGNLALPRA---FDPDKGVTFASYART 86

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I  A+ + + RS   V  G     K         +     +     +      +A  L 
Sbjct: 87  RISGAISDEL-RSKDWVSRGMRKRIKA-------AQSARDDLAKTLGRTPTEDEVASLLG 138

Query: 168 VSESEVIS-MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           + +  +   M+ +  G  S + L                           E  E   R  
Sbjct: 139 IGKKALAEAMHHQATGPVSFDDL------------------------APDEAAEITERDV 174

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            L  ++  L  R R +      +E  V  +++++E  ++   V   ++ A + + E
Sbjct: 175 FLRTAVEALPDRLRLVVTRIFCEERQV--KDVAAELGITHAAVSMTKSEAVRMLHE 228


>gi|242309557|ref|ZP_04808712.1| flagellar biosynthesis sigma factor [Helicobacter pullorum MIT
           98-5489]
 gi|239524128|gb|EEQ63994.1| flagellar biosynthesis sigma factor [Helicobacter pullorum MIT
           98-5489]
          Length = 235

 Score = 67.5 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 34/240 (14%), Positives = 89/240 (37%), Gaps = 28/240 (11%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L   +L  +  +A   +      +  +++VS G   L++  +K+D         Y+ 
Sbjct: 16  QDNLALDYLPALKALAARLKERLPANVEFADLVSIGTEELIKLARKYDSTLNDSFWGYAK 75

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +  AM +Y+     + +   T  +         +   +    + + +      +++ L
Sbjct: 76  SRVHGAMLDYLRGLDCMSRYSRTLTKN--------IDREISKYYNEHQEEPDNAYLSQVL 127

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           N    ++     + A + S    I   D+  S  QD   Y+          K E++    
Sbjct: 128 NEDIEKI-----KDARNASEIYGILPLDEELSASQDDKTYN----------KVEKEELIE 172

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ++ + +      E+ + +    +E  +  + +    E++  RV QI     +K+++ +++
Sbjct: 173 IIQKILETSPQNEQLVIQLYYYEE--LNFKEIGEILEITESRVSQIHKAVIRKIKKYLEE 230


>gi|317063373|ref|ZP_07927858.1| RNA polymerase [Fusobacterium ulcerans ATCC 49185]
 gi|313689049|gb|EFS25884.1| RNA polymerase [Fusobacterium ulcerans ATCC 49185]
          Length = 54

 Score = 67.5 bits (164), Expect = 2e-09,   Method: Composition-based stats.
 Identities = 20/54 (37%), Positives = 39/54 (72%)

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           +   +++SEGN+GL+ A++KFD  +GFR +TY++WWIK ++ + ++     ++I
Sbjct: 1   MSFIDLISEGNLGLIYAIEKFDITKGFRFSTYAVWWIKQSISKAVIVKGREIRI 54


>gi|85710152|ref|ZP_01041217.1| flagellar-specific RNA polymerase sigma factor [Erythrobacter sp.
           NAP1]
 gi|85688862|gb|EAQ28866.1| flagellar-specific RNA polymerase sigma factor [Erythrobacter sp.
           NAP1]
          Length = 242

 Score = 67.1 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 48/238 (20%), Positives = 99/238 (41%), Gaps = 24/238 (10%)

Query: 54  VTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           V   L LV + A    G G     I +++  G + L +  ++ +       A Y+   ++
Sbjct: 26  VRRFLPLVRRAAWHIYGSGREGLEIEDLMQAGVVALTECAQRHEGPGEDGFAAYAKIRVR 85

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            AM + I +  +  +   TA +KR      +L   ++ + +   +      I + L +S+
Sbjct: 86  GAMFDQIRKLMNDTR---TARKKRA-----QLGEVVERLRNETGEEPSRARICETLGISD 137

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           +E++ +        S+       D+ S+ +      D     QVL   E+    R  L  
Sbjct: 138 AELLEIEASSVTVTSIAD---EYDETSTAF----ASDDPDPFQVLAGNED----RERLIA 186

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           +M  L  R + + +   ++E  + L  +++  EVS  RV Q+ A+A K ++  ++   
Sbjct: 187 AMVKLPDRLKLVLQLFFVEE--LNLTEIATVLEVSVPRVHQLRAKALKDLRALMEADA 242


>gi|91223192|ref|ZP_01258458.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio alginolyticus 12G01]
 gi|269967118|ref|ZP_06181185.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio alginolyticus 40B]
 gi|91192005|gb|EAS78268.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio alginolyticus 12G01]
 gi|269828255|gb|EEZ82522.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio alginolyticus 40B]
          Length = 242

 Score = 67.1 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 32/242 (13%), Positives = 88/242 (36%), Gaps = 31/242 (12%)

Query: 51  HRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           + L+  H  +V ++      +      I ++   G I L++A +++          +++ 
Sbjct: 26  NALLQRHQVMVKRVVNQLRVHATSHCSIEDMQQIGLIALVEAGRRYGDVDDPHFPAFAVC 85

Query: 108 WIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            ++ A+ + + R  W           ++       L    + +T    +      I + L
Sbjct: 86  RVRGAILDELRRLDWRS---------RKTRQQAHELNDVTRDLTRTLGRMPTDAEIIQAL 136

Query: 167 NVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
             +E +             +SL+ L+ SS  +    Q               +  E ++ 
Sbjct: 137 GTNEQDYYNRQNAALAGEMQSLDQLMESSGDSYIGGQY--------------DGMEHEHI 182

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L  ++  L  R++ +       ++ + L  ++   +++  R+ Q+  +A K++ + +
Sbjct: 183 RRSLDSALGKLPKRDQLLLTLFY--QHELNLHEIALVLDLTPPRICQLHKQALKQLNQLM 240

Query: 285 QK 286
             
Sbjct: 241 SS 242


>gi|156636391|gb|ABU92466.1| RpoD [Vibrio vulnificus]
          Length = 202

 Score = 67.1 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 24/57 (42%), Positives = 33/57 (57%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 146 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|162454470|ref|YP_001616837.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
 gi|161165052|emb|CAN96357.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
          Length = 321

 Score = 67.1 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 18/77 (23%), Positives = 34/77 (44%), Gaps = 2/77 (2%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           H   E   IE    +  R  L+ +++ L  RERR+      +     L+++ +E  +   
Sbjct: 244 HMSGEDDPIEAISAQATRRALSFAIARLPERERRVIGMYYFEGAK--LKDIGAELGIGEP 301

Query: 268 RVRQIEARAFKKVQESI 284
           RV Q+  RA   ++  +
Sbjct: 302 RVSQLHTRALGMLRGML 318


>gi|28901410|ref|NP_801065.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio parahaemolyticus RIMD 2210633]
 gi|153835911|ref|ZP_01988578.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus AQ3810]
 gi|260362964|ref|ZP_05775833.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus K5030]
 gi|260880251|ref|ZP_05892606.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus AN-5034]
 gi|260895368|ref|ZP_05903864.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) [Vibrio parahaemolyticus Peru-466]
 gi|260901193|ref|ZP_05909588.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus AQ4037]
 gi|417236|sp|Q03474|LAFS_VIBPA RecName: Full=RNA polymerase sigma factor for flagellar operon;
           AltName: Full=Sigma-27; AltName: Full=Sigma-F factor
 gi|677908|gb|AAA62353.1| LafS [Vibrio parahaemolyticus]
 gi|1518952|gb|AAB07356.1| lateral flagellar FliA [Vibrio parahaemolyticus]
 gi|28809957|dbj|BAC62898.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio parahaemolyticus RIMD 2210633]
 gi|149750665|gb|EDM61410.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus AQ3810]
 gi|308085610|gb|EFO35305.1| RNA polymerase sigma factor for flagellar operon (Sigma-F
           factor)(Sigma-27) [Vibrio parahaemolyticus Peru-466]
 gi|308092554|gb|EFO42249.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus AN-5034]
 gi|308109363|gb|EFO46903.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus AQ4037]
 gi|308112404|gb|EFO49944.1| RNA polymerase sigma factor for flagellar operon [Vibrio
           parahaemolyticus K5030]
 gi|328469344|gb|EGF40290.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio parahaemolyticus 10329]
          Length = 242

 Score = 67.1 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 34/242 (14%), Positives = 90/242 (37%), Gaps = 31/242 (12%)

Query: 51  HRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           + L+  H  +V ++      +      I ++   G I L++A +++          +++ 
Sbjct: 26  NALLQRHQVMVKRVVNQLRVHATSHCSIEDMQQIGLIALVEAGRRYGDIDDTHFPAFAVC 85

Query: 108 WIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            ++ A+ + + R  W           ++       L    + +T +  +      I K L
Sbjct: 86  RVRGAILDELRRLDWRS---------RKTRQQAHELNDVTRDLTRSLGRMPTDSEIIKAL 136

Query: 167 NVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
              E +             +SL+ L+    +NS+       YD            E ++ 
Sbjct: 137 GTDEQDYYNRQNAALAGEMQSLDQLM----ENSTDSHFGGQYD----------GMEHEHI 182

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L  ++  L+ R++ +       ++ + L  ++   +++  R+ Q+  +A K++ + +
Sbjct: 183 RRSLDSALGRLSKRDQLLLTLFY--QHELNLHEIALVLDLTPPRICQLHKQALKQLNQLM 240

Query: 285 QK 286
             
Sbjct: 241 SS 242


>gi|251733357|emb|CAR82428.1| RNA polymerase sigma factor [Rhizobium giardinii]
          Length = 202

 Score = 67.1 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 24/60 (40%), Positives = 35/60 (58%), Gaps = 3/60 (5%)

Query: 41  YREHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
             + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 143 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|21104384|dbj|BAB93462.1| rpoS like gene [Variovorax sp. WFF52]
          Length = 47

 Score = 67.1 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 26/47 (55%), Positives = 35/47 (74%)

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           LVV IA  Y   G+P S+++ EGN+GLM A+ KF+PERGFR +TY+ 
Sbjct: 1   LVVNIAKAYLNRGVPFSDLIEEGNLGLMHAITKFEPERGFRFSTYAT 47


>gi|156636431|gb|ABU92486.1| RpoD [Vibrio vulnificus]
          Length = 202

 Score = 67.1 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 24/57 (42%), Positives = 33/57 (57%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 146 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|254228817|ref|ZP_04922240.1| DNA-directed RNA polymerase specialized sigma subunit [Vibrio sp.
           Ex25]
 gi|262396464|ref|YP_003288317.1| RNA polymerase sigma factor for flagellar operon [Vibrio sp. Ex25]
 gi|151938764|gb|EDN57599.1| DNA-directed RNA polymerase specialized sigma subunit [Vibrio sp.
           Ex25]
 gi|262340058|gb|ACY53852.1| RNA polymerase sigma factor for flagellar operon [Vibrio sp. Ex25]
          Length = 242

 Score = 67.1 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 32/242 (13%), Positives = 89/242 (36%), Gaps = 31/242 (12%)

Query: 51  HRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           + L+  H  +V ++      +      I ++   G I L++A +++          +++ 
Sbjct: 26  NALLQRHQVMVKRVVNQLRVHATSHCSIEDMQQIGLIALVEAGRRYGDVDDPHFPAFAVC 85

Query: 108 WIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            ++ A+ + + R  W           ++       L    + +T +  +      I + L
Sbjct: 86  RVRGAILDELRRLDWRS---------RKTRQQAHELNDVTRDLTRSLGRMPTDAEIIQAL 136

Query: 167 NVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
             +E +             +SL+ L+ SS  +    Q               +  E ++ 
Sbjct: 137 GTNEQDYYNRQNAALAGEMQSLDQLMESSGDSYIGGQY--------------DGMEHEHI 182

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L  ++  L  R++ +       ++ + L  ++   +++  R+ Q+  +A K++ + +
Sbjct: 183 RRSLDSALGKLPKRDQLLLTLFY--QHELNLHEIALVLDLTPPRICQLHKQALKQLNQLM 240

Query: 285 QK 286
             
Sbjct: 241 SS 242


>gi|156636373|gb|ABU92457.1| RpoD [Vibrio vulnificus]
 gi|156636375|gb|ABU92458.1| RpoD [Vibrio vulnificus]
 gi|156636377|gb|ABU92459.1| RpoD [Vibrio vulnificus]
 gi|156636379|gb|ABU92460.1| RpoD [Vibrio vulnificus]
 gi|156636381|gb|ABU92461.1| RpoD [Vibrio vulnificus]
 gi|156636383|gb|ABU92462.1| RpoD [Vibrio vulnificus]
 gi|156636385|gb|ABU92463.1| RpoD [Vibrio vulnificus]
 gi|156636387|gb|ABU92464.1| RpoD [Vibrio vulnificus]
 gi|156636389|gb|ABU92465.1| RpoD [Vibrio vulnificus]
 gi|156636393|gb|ABU92467.1| RpoD [Vibrio vulnificus]
 gi|156636397|gb|ABU92469.1| RpoD [Vibrio vulnificus]
 gi|156636399|gb|ABU92470.1| RpoD [Vibrio vulnificus]
 gi|156636401|gb|ABU92471.1| RpoD [Vibrio vulnificus]
 gi|156636403|gb|ABU92472.1| RpoD [Vibrio vulnificus]
 gi|156636405|gb|ABU92473.1| RpoD [Vibrio vulnificus]
 gi|156636407|gb|ABU92474.1| RpoD [Vibrio vulnificus]
 gi|156636409|gb|ABU92475.1| RpoD [Vibrio vulnificus]
 gi|156636411|gb|ABU92476.1| RpoD [Vibrio vulnificus]
 gi|156636413|gb|ABU92477.1| RpoD [Vibrio vulnificus]
 gi|156636415|gb|ABU92478.1| RpoD [Vibrio vulnificus]
 gi|156636417|gb|ABU92479.1| RpoD [Vibrio vulnificus MO6-24/O]
 gi|156636419|gb|ABU92480.1| RpoD [Vibrio vulnificus]
 gi|156636421|gb|ABU92481.1| RpoD [Vibrio vulnificus]
 gi|156636423|gb|ABU92482.1| RpoD [Vibrio vulnificus]
 gi|156636425|gb|ABU92483.1| RpoD [Vibrio vulnificus]
 gi|156636427|gb|ABU92484.1| RpoD [Vibrio vulnificus]
 gi|156636429|gb|ABU92485.1| RpoD [Vibrio vulnificus]
 gi|156636435|gb|ABU92488.1| RpoD [Vibrio vulnificus]
 gi|156636437|gb|ABU92489.1| RpoD [Vibrio vulnificus]
 gi|156636439|gb|ABU92490.1| RpoD [Vibrio vulnificus]
 gi|156636441|gb|ABU92491.1| RpoD [Vibrio vulnificus]
 gi|156636443|gb|ABU92492.1| RpoD [Vibrio vulnificus]
 gi|156636445|gb|ABU92493.1| RpoD [Vibrio vulnificus]
 gi|156636447|gb|ABU92494.1| RpoD [Vibrio vulnificus]
          Length = 202

 Score = 67.1 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 24/57 (42%), Positives = 33/57 (57%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 146 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|156636395|gb|ABU92468.1| RpoD [Vibrio vulnificus]
 gi|156636449|gb|ABU92495.1| RpoD [Vibrio vulnificus]
 gi|156636451|gb|ABU92496.1| RpoD [Vibrio vulnificus]
 gi|156636453|gb|ABU92497.1| RpoD [Vibrio vulnificus]
 gi|156636459|gb|ABU92500.1| RpoD [Vibrio vulnificus]
 gi|156636463|gb|ABU92502.1| RpoD [Vibrio vulnificus]
 gi|156636465|gb|ABU92503.1| RpoD [Vibrio vulnificus]
 gi|156636467|gb|ABU92504.1| RpoD [Vibrio vulnificus]
 gi|156636469|gb|ABU92505.1| RpoD [Vibrio vulnificus]
 gi|156636471|gb|ABU92506.1| RpoD [Vibrio vulnificus]
 gi|156636473|gb|ABU92507.1| RpoD [Vibrio vulnificus]
 gi|156636477|gb|ABU92509.1| RpoD [Vibrio vulnificus]
 gi|156636479|gb|ABU92510.1| RpoD [Vibrio vulnificus]
 gi|156636481|gb|ABU92511.1| RpoD [Vibrio vulnificus]
 gi|156636483|gb|ABU92512.1| RpoD [Vibrio vulnificus]
 gi|156636485|gb|ABU92513.1| RpoD [Vibrio vulnificus]
 gi|156636487|gb|ABU92514.1| RpoD [Vibrio vulnificus]
 gi|156636489|gb|ABU92515.1| RpoD [Vibrio vulnificus]
 gi|156636491|gb|ABU92516.1| RpoD [Vibrio vulnificus]
 gi|156636493|gb|ABU92517.1| RpoD [Vibrio vulnificus]
          Length = 202

 Score = 67.1 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 24/57 (42%), Positives = 33/57 (57%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 146 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|156636433|gb|ABU92487.1| RpoD [Vibrio vulnificus]
 gi|156636455|gb|ABU92498.1| RpoD [Vibrio vulnificus]
 gi|156636457|gb|ABU92499.1| RpoD [Vibrio vulnificus]
 gi|156636461|gb|ABU92501.1| RpoD [Vibrio vulnificus]
 gi|156636475|gb|ABU92508.1| RpoD [Vibrio vulnificus]
 gi|156636495|gb|ABU92518.1| RpoD [Vibrio vulnificus]
 gi|156636497|gb|ABU92519.1| RpoD [Vibrio vulnificus]
 gi|156636499|gb|ABU92520.1| RpoD [Vibrio vulnificus]
 gi|156636501|gb|ABU92521.1| RpoD [Vibrio vulnificus]
          Length = 202

 Score = 67.1 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 24/57 (42%), Positives = 33/57 (57%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
             E     A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 146 IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|251733365|emb|CAR82432.1| RNA polymerase sigma factor [Agrobacterium rubi]
          Length = 202

 Score = 67.1 bits (163), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 24/60 (40%), Positives = 35/60 (58%), Gaps = 3/60 (5%)

Query: 41  YREHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
             + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 143 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|318041416|ref|ZP_07973372.1| type 3 alternative RNA polymerase sigma factor [Synechococcus sp.
           CB0101]
          Length = 233

 Score = 66.8 bits (162), Expect = 3e-09,   Method: Composition-based stats.
 Identities = 43/239 (17%), Positives = 91/239 (38%), Gaps = 30/239 (12%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPI-SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
            +R V  HL LV ++A  Y         ++   G +GL++A +++D       A ++   
Sbjct: 12  RNRQVAEHLFLVRRVANHYAACTAERRDDLQQVGALGLIRAAERYDDRSAVPFAAFARPH 71

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+ A+  Y+     L+++             RRL+     ++                  
Sbjct: 72  IRGAVLHYLRDVAPLLRLS------------RRLQERAFQLSRQCGSAA----------- 108

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR--- 225
             S+  S + R    ESL  L +       + Q+      +      +++ E  N+    
Sbjct: 109 -VSQQASHDSRQGELESLRCLQSVQLLPPWRLQEVQANSTNCWANPPVDRIEDANQEIES 167

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             +  ++S L  R+R++ EA  LQ    TL  ++    +S   V ++  +   +++  +
Sbjct: 168 ETVLAALSQLERRQRQVVEAVVLQGQ--TLRTVAERLGISAATVHRVLHQGLAELRRQL 224


>gi|262273680|ref|ZP_06051493.1| putative RNA polymerase sigma-38 factor [Grimontia hollisae CIP
           101886]
 gi|262222095|gb|EEY73407.1| putative RNA polymerase sigma-38 factor [Grimontia hollisae CIP
           101886]
          Length = 78

 Score = 66.8 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 18/66 (27%), Positives = 35/66 (53%), Gaps = 2/66 (3%)

Query: 224 RRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +  +   +  LNP++R +   R   L     TLE++  E  ++RERVRQI+    ++++
Sbjct: 1   MKKSIVHWLQELNPKQREVLARRFGLLGHEASTLEDVGREIGLTRERVRQIQVEGLRRLR 60

Query: 282 ESIQKQ 287
           + +  Q
Sbjct: 61  DMLTHQ 66


>gi|251733351|emb|CAR82425.1| RNA polymerase sigma factor [Mesorhizobium loti]
          Length = 202

 Score = 66.8 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 23/49 (46%), Positives = 32/49 (65%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 154 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|313647806|gb|EFS12252.1| RNA polymerase sigma factor rpoS domain protein [Shigella flexneri
           2a str. 2457T]
          Length = 76

 Score = 66.8 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 19/66 (28%), Positives = 36/66 (54%), Gaps = 2/66 (3%)

Query: 224 RRNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +  + + +  LN ++R +   R   L     TLE++  E  ++RERVRQI+    ++++
Sbjct: 1   MKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLR 60

Query: 282 ESIQKQ 287
           E +Q Q
Sbjct: 61  EILQTQ 66


>gi|149182533|ref|ZP_01861006.1| sigma factor SigD [Bacillus sp. SG-1]
 gi|148849793|gb|EDL63970.1| sigma factor SigD [Bacillus sp. SG-1]
          Length = 161

 Score = 66.8 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 27/147 (18%), Positives = 63/147 (42%), Gaps = 11/147 (7%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGL 86
              +E      +++  D  A   LV  +L LV              +   ++ S G +GL
Sbjct: 5   STADEQKYWDLWKKSKDPHAGDMLVKKYLPLVSYHVQRISVGLPKNVSREDLKSLGLMGL 64

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL 146
           + A++KFDP R  +  TY+ + ++ ++ + + +   L         +      ++++  +
Sbjct: 65  LDALEKFDPSRDLKFDTYASFRVRGSIIDGLRKEDWL--------PRSTRERAKKIEAKI 116

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEV 173
           +++    L+      IA+++ + E EV
Sbjct: 117 ESLEQELLRHVTPEEIAQEMQMEEGEV 143


>gi|251733405|emb|CAR82452.1| RNA polymerase sigma factor [Ensifer adhaerens]
 gi|251733407|emb|CAR82453.1| RNA polymerase sigma factor [Ensifer adhaerens]
 gi|251733425|emb|CAR82462.1| RNA polymerase sigma factor [Ensifer adhaerens]
 gi|251733427|emb|CAR82463.1| RNA polymerase sigma factor [Ensifer adhaerens]
 gi|251733429|emb|CAR82464.1| RNA polymerase sigma factor [Ensifer adhaerens]
 gi|251733431|emb|CAR82465.1| RNA polymerase sigma factor [Ensifer adhaerens]
 gi|251733433|emb|CAR82466.1| RNA polymerase sigma factor [Ensifer adhaerens]
 gi|251733435|emb|CAR82467.1| RNA polymerase sigma factor [Ensifer adhaerens]
 gi|251733437|emb|CAR82468.1| RNA polymerase sigma factor [Ensifer adhaerens]
          Length = 202

 Score = 66.8 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 23/49 (46%), Positives = 32/49 (65%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 154 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|257451779|ref|ZP_05617078.1| RpoS [Fusobacterium sp. 3_1_5R]
 gi|317058336|ref|ZP_07922821.1| predicted protein [Fusobacterium sp. 3_1_5R]
 gi|313684012|gb|EFS20847.1| predicted protein [Fusobacterium sp. 3_1_5R]
          Length = 201

 Score = 66.8 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 39/251 (15%), Positives = 86/251 (34%), Gaps = 68/251 (27%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           E   L  R  + G++ A + L+  ++ L+ KI   Y        +   EG +    A+ K
Sbjct: 5   ETLELI-RLAKLGNIQARNELIEKNINLIHKINRRYGSS----EDGFQEGVLAFCHAIDK 59

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +  +L++Y+  WI+  ++ Y  R     ++                          
Sbjct: 60  FDETKKVKLSSYAFHWIRQRIKRYRDREK--YRLPAH----------------------- 94

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
                    + +K+   E ++                            D+   D + ++
Sbjct: 95  ---------VIEKMTKEERKIR--------------------------IDFEYQDFNSED 119

Query: 213 QVLIEKEERKNRRNMLTRSMSV-LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           +   E+E     +  L + + +  + +E  I +           + ++ E  V R+RV  
Sbjct: 120 EKTTEEENSICLKTTLEQYIKLACDEKEALILKKIYF--ESYQQQEIAKEMGVCRQRVNA 177

Query: 272 IEARAFKKVQE 282
           I  R+ +K++ 
Sbjct: 178 IVKRSLQKLRR 188


>gi|251733363|emb|CAR82431.1| RNA polymerase sigma factor [Agrobacterium rhizogenes]
 gi|251733369|emb|CAR82434.1| RNA polymerase sigma factor [Rhizobium tropici]
 gi|251733371|emb|CAR82435.1| RNA polymerase sigma factor [Rhizobium tropici]
          Length = 202

 Score = 66.8 bits (162), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 23/49 (46%), Positives = 32/49 (65%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 154 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|251733367|emb|CAR82433.1| RNA polymerase sigma factor [Agrobacterium vitis]
          Length = 202

 Score = 66.4 bits (161), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 24/60 (40%), Positives = 35/60 (58%), Gaps = 3/60 (5%)

Query: 41  YREHGDLSAA---HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
             + G+  A      +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 143 MVQKGEREARIAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|251733349|emb|CAR82424.1| RNA polymerase sigma factor [Sinorhizobium americanum]
 gi|251733415|emb|CAR82457.1| RNA polymerase sigma factor [Sinorhizobium terangae]
 gi|251733417|emb|CAR82458.1| RNA polymerase sigma factor [Sinorhizobium terangae]
 gi|251733419|emb|CAR82459.1| RNA polymerase sigma factor [Sinorhizobium terangae]
          Length = 202

 Score = 66.4 bits (161), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 23/49 (46%), Positives = 32/49 (65%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 154 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|313810027|gb|EFS47748.1| conserved domain protein [Propionibacterium acnes HL083PA1]
          Length = 52

 Score = 66.4 bits (161), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 15/46 (32%), Positives = 25/46 (54%), Gaps = 2/46 (4%)

Query: 245 ARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            R       P TL+ +   + V+RER+RQIE++   K++   + QV
Sbjct: 1   MRFGLTDGQPKTLDEIGKVYGVTRERIRQIESKTMSKLRHPSRSQV 46


>gi|163785765|ref|ZP_02180266.1| RNA polymerase sigma factor RpoS [Hydrogenivirga sp. 128-5-R1-1]
 gi|159878964|gb|EDP72967.1| RNA polymerase sigma factor RpoS [Hydrogenivirga sp. 128-5-R1-1]
          Length = 64

 Score = 66.4 bits (161), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 22/49 (44%), Positives = 29/49 (59%), Gaps = 2/49 (4%)

Query: 235 LNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           L+ RER I + R     E P TL  +     +SRERVRQ+E RA KK++
Sbjct: 3   LDEREREIIKHRYGLEGEEPKTLNEVGEMLGISRERVRQLENRALKKLR 51


>gi|251733359|emb|CAR82429.1| RNA polymerase sigma factor [Rhizobium leguminosarum]
          Length = 202

 Score = 66.4 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 23/49 (46%), Positives = 32/49 (65%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 154 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|256271|gb|AAC60416.1| RpoD3 [Synechococcus]
          Length = 48

 Score = 66.4 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 18/47 (38%), Positives = 30/47 (63%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           +++ EG IG+ + V+KFDP +G+R +TY+ WWI+ A+   I      
Sbjct: 2   DLIQEGTIGMQRGVEKFDPTKGYRFSTYAYWWIRQAITRAIAEKART 48


>gi|325295407|ref|YP_004281921.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfurobacterium thermolithotrophum DSM 11699]
 gi|325065855|gb|ADY73862.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfurobacterium thermolithotrophum DSM 11699]
          Length = 204

 Score = 66.4 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 54/245 (22%), Positives = 101/245 (41%), Gaps = 48/245 (19%)

Query: 48  SAAHRLVTSHLRLVVKIAMG-YRG---YGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            +   L+  +L LV KIA   YR      +   E+V+ G IGL++A+  +D  +  + +T
Sbjct: 4   KSRKELIIENLPLVKKIANKIYRRLPENAVEFEELVNTGVIGLIKALDNYDKTK-AKFST 62

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   I+  + +Y+               ++L F  R  +                +   
Sbjct: 63  YAYIKIRGEILDYL---------------RKLDFLSRSARER--------------IKNT 93

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           +     + E+IS         SL   I  S     + +D L  D    E+ +I KE    
Sbjct: 94  EYYQDLKEEIISF-------VSLEENIFISSDK-VKIRDILSSDSKTPEEEVILKEA--- 142

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +  L  ++  L+ +E+ I +   ++E    L+++S    +S  RV QI+  A KK+ + 
Sbjct: 143 -KERLANALKRLSEKEQLILQLIFVEELD--LKSISEIIGISISRVSQIKGAAIKKLSKY 199

Query: 284 IQKQV 288
           ++  V
Sbjct: 200 LKDSV 204


>gi|251733379|emb|CAR82439.1| RNA polymerase sigma factor [Sinorhizobium fredii]
 gi|251733381|emb|CAR82440.1| RNA polymerase sigma factor [Sinorhizobium fredii]
 gi|251733383|emb|CAR82441.1| RNA polymerase sigma factor [Sinorhizobium fredii]
 gi|251733385|emb|CAR82442.1| RNA polymerase sigma factor [Sinorhizobium fredii]
 gi|251733421|emb|CAR82460.1| RNA polymerase sigma factor [Sinorhizobium xinjiangense]
 gi|251733423|emb|CAR82461.1| RNA polymerase sigma factor [Sinorhizobium xinjiangense]
          Length = 202

 Score = 66.4 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 23/49 (46%), Positives = 32/49 (65%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 154 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|145559057|gb|ABP73390.1| SigF [Mycobacterium aurum]
          Length = 140

 Score = 66.4 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 27/154 (17%), Positives = 54/154 (35%), Gaps = 15/154 (9%)

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
           +   VK+     +  L     RL      ++    +      +A++L +   EV+     
Sbjct: 1   NSWSVKVPRRLEELHL-----RLGSATAELSQRLGRAPTPTELAEELGMDRDEVVE--GP 53

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +AG  S    ++     S       + D  G   + +++ E    R  L   +  L  RE
Sbjct: 54  VAG--SSYNTLSIDSGGSGNEDAPAIADTLGDVDLTLDQIE---NREALRPLLESLPERE 108

Query: 240 RRIFE-ARRLQENPVTLENLSSEFEVSRERVRQI 272
           R +    R      +T   ++    VS+  V ++
Sbjct: 109 RTVVVPLRFF--ESLTQTQIAERIGVSQMHVSRL 140


>gi|133722027|gb|ABO37132.1| SigF [Mycobacterium simiae]
          Length = 142

 Score = 66.4 bits (161), Expect = 5e-09,   Method: Composition-based stats.
 Identities = 28/154 (18%), Positives = 52/154 (33%), Gaps = 13/154 (8%)

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
             +   VK+     +  L     RL      ++    +      +A +L++  +EV+   
Sbjct: 1   RDNSWSVKVPRRLKELHL-----RLGSATADLSQRLGRAPTATELAAELDMDRAEVVE-- 53

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
             L    S N L   S  +        + D  G     I++ E    R  L   +  L  
Sbjct: 54  -GLVAGSSYNTLSIDSGGSGDDDDVRAIADTLGDVDASIDRIED---REALRPLLGSLPE 109

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           RER +   R      +T   ++    +S+  V +
Sbjct: 110 RERTVLVLRFF--ESMTQTQIADRVGISQMHVSR 141


>gi|21104382|dbj|BAB93461.1| unnamed protein product [Roseateles depolymerans]
          Length = 47

 Score = 66.4 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 28/47 (59%), Positives = 37/47 (78%)

Query: 60  LVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           LVV IA  Y G GLP+S+++ EGN+GLM A+ KF+PERGFR +TY+ 
Sbjct: 1   LVVSIAKNYLGRGLPMSDLIEEGNLGLMHAIGKFEPERGFRFSTYAS 47


>gi|251733373|emb|CAR82436.1| RNA polymerase sigma factor [Sinorhizobium arboris LMG 14919]
 gi|251733375|emb|CAR82437.1| RNA polymerase sigma factor [Sinorhizobium arboris]
 gi|251733377|emb|CAR82438.1| RNA polymerase sigma factor [Sinorhizobium arboris]
 gi|251733393|emb|CAR82446.1| RNA polymerase sigma factor [Sinorhizobium medicae]
 gi|251733395|emb|CAR82447.1| RNA polymerase sigma factor [Sinorhizobium medicae]
 gi|251733397|emb|CAR82448.1| RNA polymerase sigma factor [Sinorhizobium medicae]
 gi|251733399|emb|CAR82449.1| RNA polymerase sigma factor [Sinorhizobium meliloti]
 gi|251733401|emb|CAR82450.1| RNA polymerase sigma factor [Sinorhizobium meliloti]
 gi|251733403|emb|CAR82451.1| RNA polymerase sigma factor [Sinorhizobium meliloti]
          Length = 202

 Score = 66.4 bits (161), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 23/49 (46%), Positives = 32/49 (65%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 154 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|148239620|ref|YP_001225007.1| DNA-directed RNA polymerase specialized sigma subunit
           [Synechococcus sp. WH 7803]
 gi|147848159|emb|CAK23710.1| Possible DNA-directed RNA polymerase specialized sigma subunit
           [Synechococcus sp. WH 7803]
          Length = 210

 Score = 66.0 bits (160), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 20/86 (23%), Positives = 43/86 (50%), Gaps = 1/86 (1%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY-GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
            ++ V  HL+LV  IA  Y    G+   ++   G +GL++A + F+ +R      ++   
Sbjct: 21  RNQRVNDHLQLVSPIARHYANRCGVECDDLNQVGLMGLLRAAENFNADRCIPFHAFARPH 80

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKR 134
           I+ A+  Y+  + S+V++     + +
Sbjct: 81  IRGAILHYLRDNASMVRMPRRWQESK 106


>gi|251733361|emb|CAR82430.1| RNA polymerase sigma factor [Agrobacterium tumefaciens]
          Length = 202

 Score = 66.0 bits (160), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 23/49 (46%), Positives = 32/49 (65%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 154 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|152965726|ref|YP_001361510.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Kineococcus
           radiotolerans SRS30216]
 gi|151360243|gb|ABS03246.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Kineococcus
           radiotolerans SRS30216]
          Length = 227

 Score = 66.0 bits (160), Expect = 6e-09,   Method: Composition-based stats.
 Identities = 49/261 (18%), Positives = 87/261 (33%), Gaps = 68/261 (26%)

Query: 49  AAHRLVTSHLRLVVKIAMGY--RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           A  R +  H  + + I              E  S  N+GL+QA + +DP RG  +A +  
Sbjct: 9   AEERFIADHGDIAMSITRRRLLDVAPSERDEAASAANLGLLQAARAWDPARG-EVAPHLW 67

Query: 107 WWIKAAMQE-YILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
             I  A+ + +  R       G+T ++                                 
Sbjct: 68  HRINGAITDDFRARHGRP---GSTRHKA-------------------------------- 92

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
                         +A   SL+  + +     S      + D        +   +R   R
Sbjct: 93  --------------MAAQVSLDMPLVTGGDRVSLTLGDTIQD-------PVNHIDRAMDR 131

Query: 226 NMLTRSMSVLNPRERRIFEARRLQE-NPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             LTR++  L  R+RR+ + R + E + +T   ++    V+  RV Q+E     +++  +
Sbjct: 132 IDLTRAIDHLTDRDRRLLQWRFVDELHLLT---IAGYLNVTESRVSQMEREVITRLRRFM 188

Query: 285 QKQVELSS----SPPLLQKPR 301
               E         PL  KPR
Sbjct: 189 NGDTEHRKCRYCGRPLTGKPR 209


>gi|251733409|emb|CAR82454.1| RNA polymerase sigma factor [Sinorhizobium saheli]
 gi|251733411|emb|CAR82455.1| RNA polymerase sigma factor [Sinorhizobium saheli]
 gi|251733413|emb|CAR82456.1| RNA polymerase sigma factor [Sinorhizobium saheli]
          Length = 202

 Score = 66.0 bits (160), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 23/49 (46%), Positives = 32/49 (65%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 154 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|251733355|emb|CAR82427.1| RNA polymerase sigma factor [Rhizobium galegae]
          Length = 202

 Score = 66.0 bits (160), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 23/49 (46%), Positives = 32/49 (65%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 154 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|251733387|emb|CAR82443.1| RNA polymerase sigma factor [Sinorhizobium kostiense]
 gi|251733389|emb|CAR82444.1| RNA polymerase sigma factor [Sinorhizobium kostiense]
 gi|251733391|emb|CAR82445.1| RNA polymerase sigma factor [Sinorhizobium kostiense]
          Length = 202

 Score = 66.0 bits (160), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 23/49 (46%), Positives = 32/49 (65%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A   +V ++LRLV+ IA  Y   GL   +++ EGNIGLM+AV KF+  R
Sbjct: 154 AKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRR 202


>gi|255322026|ref|ZP_05363176.1| flagellar biosynthesis sigma factor FliA [Campylobacter showae
           RM3277]
 gi|255301130|gb|EET80397.1| flagellar biosynthesis sigma factor FliA [Campylobacter showae
           RM3277]
          Length = 235

 Score = 66.0 bits (160), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 34/242 (14%), Positives = 93/242 (38%), Gaps = 28/242 (11%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
                 +V ++   +  +A   +      + +S+++  G   +++  +K+D E+      
Sbjct: 17  KKEQDEVVLAYTPALRAMAFRLKERLPAHIDVSDLIGAGLEEMVKLSRKYDKEQNDSFWG 76

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   +  AM +++         G     +     ++ ++  +    +        V IA
Sbjct: 77  YAQKRVYGAMLDFLR--------GLDVVSRSDRTLVKSIEALVNEYFNKFECEPDDVYIA 128

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
            KL +   +V       A    LN                        E+  +E+ E+++
Sbjct: 129 GKLGIDVEKVSEARNVSAVVAVLNIDDQM---------------ELMSEENTLERVEKED 173

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               +T+ ++    R++ I +    +E  ++L+ +S   +++  R+ QI  R  +K+++ 
Sbjct: 174 LIEKITQILNEFEERDQLIVQLYYYEE--LSLKEISEILQITESRISQIHKRLMEKIRKK 231

Query: 284 IQ 285
           ++
Sbjct: 232 LE 233


>gi|257463359|ref|ZP_05627755.1| RNA polymerase sigma factor RpoS [Fusobacterium sp. D12]
          Length = 155

 Score = 66.0 bits (160), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 31/145 (21%), Positives = 63/145 (43%), Gaps = 10/145 (6%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R  + GD+ A + L+  ++ LV KI   Y        +   EG +    A+ KFD  +  
Sbjct: 3   RLAKLGDIEARNELIEKNINLVHKINRMYGSS----EDGFQEGILAFCHAIDKFDETKNV 58

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           +L++Y+  WI+  ++ Y  R     ++     +K +    R+++   +     + K E  
Sbjct: 59  KLSSYAFHWIRQKIKRYREREK--YRLPAHVIEK-MSKEERKIRIDFEY---RDFKSEDE 112

Query: 160 VAIAKKLNVSESEVISMNCRLAGDE 184
             I ++ ++     +    +LA DE
Sbjct: 113 TTIEEESSICLKSTLEQYIKLACDE 137


>gi|168208009|ref|ZP_02634014.1| putative DNA-dependent RNA polymerase sigma subunit [Clostridium
           perfringens E str. JGS1987]
 gi|170660682|gb|EDT13365.1| putative DNA-dependent RNA polymerase sigma subunit [Clostridium
           perfringens E str. JGS1987]
          Length = 230

 Score = 65.6 bits (159), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 46/246 (18%), Positives = 83/246 (33%), Gaps = 58/246 (23%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGF-- 99
           ++GD  A ++L+  +  L+ KI   Y G       ++   G +G ++ +  +D  +    
Sbjct: 11  KNGDKKALNKLIEKNNGLIYKIINKYIGVKRAEEEDLYQSGVLGFIKGLNHYDINKNNKA 70

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           +L+TY  +WI+  +  Y L +    K       K L  N                     
Sbjct: 71  KLSTYVTYWIEREV--YSLVNGRTTK---DIENKELMNNC-------------------- 105

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
                                    SLN  I   D+  ++  + ++   D   +  IEKE
Sbjct: 106 ------------------------ISLNTPI---DEEGAELLE-VIEGVDYIFENTIEKE 137

Query: 220 ERKNRRNMLTRSMSV-LNPRERRIFEARRL-QENPVTLENLSSEFEVSRERVRQIEARAF 277
             K  R  L   M   LN  E+ +            T   L +   V+  R+  I   A 
Sbjct: 138 FFKKIRIELDEVMEKYLNEEEKVVLHYHFGWFGTTYTDVQLGNLLSVTNTRIGHIRTTAL 197

Query: 278 KKVQES 283
            +++ +
Sbjct: 198 MRIRRT 203


>gi|167945650|ref|ZP_02532724.1| flagellar biosynthesis sigma factor [Endoriftia persephone
           'Hot96_1+Hot96_2']
          Length = 104

 Score = 65.6 bits (159), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 20/102 (19%), Positives = 42/102 (41%), Gaps = 8/102 (7%)

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL+ L    + N +       Y+         E  ++   +N L  +++ L  RER +  
Sbjct: 3   SLDELTAVGEINITPATGKNTYEG------PFEGLQKDAFKNALAEAIAGLPERERLVIS 56

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                ++ + L  +     VS  RV QI ++A  +++  + +
Sbjct: 57  MYY--DDELNLREIGQVLGVSESRVCQIHSQATLRLRSRLSE 96


>gi|145952318|gb|ABP98982.1| sigma factor F [Mycobacterium gilvum]
          Length = 139

 Score = 65.6 bits (159), Expect = 8e-09,   Method: Composition-based stats.
 Identities = 28/153 (18%), Positives = 56/153 (36%), Gaps = 14/153 (9%)

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
           +   VK+     +  L     RL      ++    +      +A +L +   EVI     
Sbjct: 1   NSWSVKVPRRLKELHL-----RLGAATAELSQRLGRAPTATELAAELEMDRDEVIE---G 52

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           L    S N L   S ++ ++     + D  G   + +++ E    R  L   ++ L  RE
Sbjct: 53  LVAGSSYNTLSIDSGRHGNE-DAPAIADTLGDVDLTLDQIE---NREALRPLLAALPERE 108

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           R +   R      +T   ++    +S+  V ++
Sbjct: 109 RTVLVLRFF--ESMTQTQIAERVGISQMHVSRL 139


>gi|302390625|ref|YP_003826446.1| RNA polymerase, sigma 30 subunit, SigH [Thermosediminibacter oceani
           DSM 16646]
 gi|302201253|gb|ADL08823.1| RNA polymerase, sigma 30 subunit, SigH [Thermosediminibacter oceani
           DSM 16646]
          Length = 214

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 43/261 (16%), Positives = 83/261 (31%), Gaps = 66/261 (25%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           +E    A+R    G   A   L+  +   V   A  Y   G    +++ EG IGL +A++
Sbjct: 19  EEVVYEARR----GSREALEYLINKYKNFVKSKARSYFLIGADKEDIIQEGMIGLYKAIR 74

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
            F+P++      ++   I   +   I  +     I                         
Sbjct: 75  DFNPDKLSSFKAFAELCITRQIITAIKTATRQKHI------------------------- 109

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
                                       L    SLN  I   D   +             
Sbjct: 110 ---------------------------PLNSYISLNKPIYDEDSERTLLDVLSEVKITDP 142

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E+++I +EE ++    +   +S L   E  +  +     N  + + ++ E    R  V+ 
Sbjct: 143 EELIISREEVEDIEGKMGEILSKL---EWEVLISYL---NGKSYQEIAKEL---RRHVKS 193

Query: 272 IEARAFKKVQESIQKQVELSS 292
           I   A ++V+  ++K +E+  
Sbjct: 194 I-DNALQRVKRKLEKYLEVRD 213


>gi|255599375|ref|XP_002537218.1| RNA polymerase sigma factor for flagellar operon, putative [Ricinus
           communis]
 gi|223517098|gb|EEF25164.1| RNA polymerase sigma factor for flagellar operon, putative [Ricinus
           communis]
          Length = 124

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 20/121 (16%), Positives = 46/121 (38%), Gaps = 4/121 (3%)

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           + +S  E  SM     G + +       D +  +   +L      +    ++       R
Sbjct: 1   MKISLEEYQSMLADCGGHQLIYYEDFHDDDSGHE--HFLDRYQSTETDDPLQNLINGGFR 58

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             +  S+  L  RE+         E  + L+ + +   VS  RV Q+ ++A  +++  ++
Sbjct: 59  EAVVDSIRALPEREQ--ILMGLYYEQEMNLKEIGAVMGVSESRVCQLHSQAISRMRSYLR 116

Query: 286 K 286
           +
Sbjct: 117 E 117


>gi|237808347|ref|YP_002892787.1| sigma-70 region 4 domain-containing protein [Tolumonas auensis DSM
           9187]
 gi|237500608|gb|ACQ93201.1| sigma-70 region 4 domain protein [Tolumonas auensis DSM 9187]
          Length = 913

 Score = 65.2 bits (158), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 18/45 (40%), Positives = 26/45 (57%)

Query: 236 NPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           N +E      R L  N  TLE L + + V+RER+RQ+E+ A  K+
Sbjct: 403 NEKELATIVCRLLSNNKKTLEELGAIYGVTRERIRQLESLAIAKL 447


>gi|253795563|ref|YP_003038659.1| putative RNA polymerase sigma factor [Candidatus Hodgkinia
           cicadicola Dsem]
 gi|253739871|gb|ACT34206.1| putative RNA polymerase sigma factor [Candidatus Hodgkinia
           cicadicola Dsem]
          Length = 373

 Score = 64.8 bits (157), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 50/239 (20%), Positives = 81/239 (33%), Gaps = 49/239 (20%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +A   LV S   ++  +   Y         + S G  GLM +  +FD   G+R A YS 
Sbjct: 166 KAAKRSLVGSSASVIADVIKAYPSCDAQDPALASAGRDGLMASANRFDLVSGYRFAAYSK 225

Query: 107 WWIKAAMQEYI---LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           WW+K  +  ++    + W+      +A Q      L+RL                     
Sbjct: 226 WWVKHNVIAHVLAGAKGWA----AASAKQLAGAAKLKRLS-------------------- 261

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
                             G  SL+  +    +  S     ++       Q   E      
Sbjct: 262 -------------LDYCGGGASLHEAV----EGGSALAGGVLKPAARGAQPRFEARCDDY 304

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKV 280
               L  S+ +L PRE R+   R     P   +L  +  +  ++RERVRQ+   A  K+
Sbjct: 305 T---LISSLMLLAPREERVVRLRGRARAPFSWSLRRIGLDVGLTRERVRQLALSASTKL 360


>gi|237753387|ref|ZP_04583867.1| flagellar biosynthesis sigma factor [Helicobacter winghamensis ATCC
           BAA-430]
 gi|229375654|gb|EEO25745.1| flagellar biosynthesis sigma factor [Helicobacter winghamensis ATCC
           BAA-430]
          Length = 234

 Score = 64.8 bits (157), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 33/213 (15%), Positives = 88/213 (41%), Gaps = 26/213 (12%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
             S+++S G   L++  +K+D         Y+   ++ AM +Y+           + N +
Sbjct: 43  DFSDLISIGTEELIKLARKYDNSLNDSFWGYARPRVQGAMLDYLRSLD-----PLSRNMR 97

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            L    +R++  +    + + +      ++K L  +E ++     R+A +      I+  
Sbjct: 98  TLV---KRIEKEIAIYYNEHQEEPDNAYLSKLLGENEEKIKE--ARMASEIYSVLPIDDQ 152

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
                            Q++  +E  E++   +++ + +    P E+ + +    +E  +
Sbjct: 153 LGE--------------QKEGTLESIEKEELISVILQILEHATPNEQLVVQLYYYEE--L 196

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           + + +S   EVS  RV Q+     ++V++ +++
Sbjct: 197 SFKEISQVLEVSEARVSQLHRAVIRRVRQYLEE 229


>gi|158320673|ref|YP_001513180.1| FliA/WhiG family RNA polymerase sigma 28 subunit [Alkaliphilus
           oremlandii OhILAs]
 gi|158140872|gb|ABW19184.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alkaliphilus oremlandii OhILAs]
          Length = 88

 Score = 64.8 bits (157), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 2/75 (2%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERV 269
           ++VL E E +   + + ++  SVL  RER + E R         T   ++    +SR  V
Sbjct: 10  DEVLEEVELKMQIKKLYSKMASVLKTRERIVIELRYGICNGGSKTQREIAQMLGISRSYV 69

Query: 270 RQIEARAFKKVQESI 284
            +IE RA +K+ +++
Sbjct: 70  SRIEKRAIRKLNKAL 84


>gi|237736225|ref|ZP_04566706.1| RNA polymerase sigma factor [Fusobacterium mortiferum ATCC 9817]
 gi|229421778|gb|EEO36825.1| RNA polymerase sigma factor [Fusobacterium mortiferum ATCC 9817]
          Length = 232

 Score = 64.8 bits (157), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 35/186 (18%), Positives = 71/186 (38%), Gaps = 23/186 (12%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           ++  + + GE  +  Y+ EI  I   E  E                    +  +L LV  
Sbjct: 7   EDEDLDILGEESVIDYLEEIASITPNENPE----------------GEDFIVQNLPLVAS 50

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           IA  Y   G+   +VV EG +GL++ ++ ++ E+      Y  +WI   +  +I    + 
Sbjct: 51  IAFNYLREGVAYLDVVQEGTMGLIKGIENYNGEKHGDFENYKKYWIIREIVLFINNKITD 110

Query: 124 VK---IGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
           +K        +++  F  +      ++  T+  L  E ++     ++  E     +  +L
Sbjct: 111 IKNEFKSFFKDKRENFGKVGHEHEEVEDKTEVYLTEEDLLPSIDAIDKREK----LMEKL 166

Query: 181 AGDESL 186
               SL
Sbjct: 167 TEFSSL 172


>gi|295092257|emb|CBK78364.1| RNA polymerase sigma factor, sigma-70 family [Clostridium cf.
           saccharolyticum K10]
          Length = 220

 Score = 64.8 bits (157), Expect = 1e-08,   Method: Composition-based stats.
 Identities = 49/258 (18%), Positives = 92/258 (35%), Gaps = 67/258 (25%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAM-GYRGYG-------LPISEVVSEGNIGLMQAVKK 92
             + GD +A   L+ ++L  + KIA+  YR  G       + + ++V EG+IGL+ A+  
Sbjct: 12  LAQAGDTAARDILLENNLGFIRKIALEQYRSMGLDENDIGIDLDDLVQEGSIGLLNAIPL 71

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  RG +  TY+   I+ AM + I                         +  L      
Sbjct: 72  FDAGRGMKFLTYAAPAIRNAMTDCI-------------------------RAALAQFEQR 106

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
                    +  K N    + + ++  L+ DE                   +    D   
Sbjct: 107 ---------MVDKKNGPGFQRVYLDDILSDDE---------------RMLRIEAIADPHT 142

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR----LQENPVTLENLSS--EFEVSR 266
           Q   +   +K +   L  ++  L  RE+     R       E+P+    + +   F +S 
Sbjct: 143 QTPEQIYIQKEQLTELYAALDKLTAREQTYLLYRYGFTDGIEHPL----IGAALHFHLSE 198

Query: 267 ERVRQIEARAFKKVQESI 284
            R +++E  A   ++  +
Sbjct: 199 SRTKKVEGEAMDSLRGKL 216


>gi|15895322|ref|NP_348671.1| DNA-dependent RNA polymerase sigma subunit [Clostridium
           acetobutylicum ATCC 824]
 gi|15025038|gb|AAK80011.1|AE007708_7 DNA-dependent RNA polymerase sigma subunit [Clostridium
           acetobutylicum ATCC 824]
          Length = 237

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 43/229 (18%), Positives = 94/229 (41%), Gaps = 21/229 (9%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY--RGYGLPISEVVSEGNIGLM 87
           E +E   L  R ++ G   A   L+ S ++ + KIA G+      L + +++ EG I ++
Sbjct: 4   EDKEVKDLILRAKD-GSKDAKSFLIDSSMKYIKKIANGFCLNNKSLSLEDLMQEGIIAVI 62

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +A+  +D ++  + +TY    I   +   I + +S  KI      K + F  R       
Sbjct: 63  KAINSYDLDKNVKFSTYVYSMINFTLISEIKKKYSYFKIPEHQVSKIVKFKRR------- 115

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
             ++  ++        +++ +S  +   M         L+ L N +  +  ++ D  V +
Sbjct: 116 -ASELKVEDTCYKYGCERIGLSYEQYADMM-------HLSKLNNVAYLDEKKYFDGKVSE 167

Query: 208 HDG---QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
            D    ++      EE+ +   +L  +   L+  E+ I     +++  V
Sbjct: 168 EDKFAYEDVNYKRVEEKIDLNVILKENADKLSQLEKYIIREILIKDQKV 216


>gi|225389367|ref|ZP_03759091.1| hypothetical protein CLOSTASPAR_03114 [Clostridium asparagiforme
          DSM 15981]
 gi|225044546|gb|EEG54792.1| hypothetical protein CLOSTASPAR_03114 [Clostridium asparagiforme
          DSM 15981]
          Length = 384

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 25/78 (32%), Positives = 43/78 (55%), Gaps = 1/78 (1%)

Query: 17 SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
            Y+ E+ +I  +  +EE  + +R    G++ A  RLV  +L+ V+ IA  Y G  LP++
Sbjct: 7  EMYLEEMGQIAPMSAEEEARILER-TAAGEVQARKRLVEGNLQKVLSIAKEYEGSRLPMA 65

Query: 77 EVVSEGNIGLMQAVKKFD 94
          ++V E N  L  A  ++D
Sbjct: 66 DIVQEANTALTLAAVEYD 83


>gi|153933487|ref|YP_001384721.1| DNA-dependent RNA polymerase sigma subunit [Clostridium botulinum A
           str. ATCC 19397]
 gi|153936370|ref|YP_001388242.1| DNA-dependent RNA polymerase sigma subunit [Clostridium botulinum A
           str. Hall]
 gi|152929531|gb|ABS35031.1| DNA-dependent RNA polymerase sigma subunit [Clostridium botulinum A
           str. ATCC 19397]
 gi|152932284|gb|ABS37783.1| DNA-dependent RNA polymerase sigma subunit [Clostridium botulinum A
           str. Hall]
          Length = 96

 Score = 64.8 bits (157), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 22/92 (23%), Positives = 39/92 (42%), Gaps = 5/92 (5%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENP 252
            N     D L  D D   +++  K E K     +    + L  RE+++ + R       P
Sbjct: 2   GNEISLMDILSSDEDSIIEIVSTKIEVKKLYGKID---TCLRGREKKVIQMRYGLKDGRP 58

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            T   ++    +SR  V +IE +A KK+ + +
Sbjct: 59  RTQREIAGILNISRSYVSRIEKKALKKLYKEL 90


>gi|229073422|ref|ZP_04206558.1| RNA polymerase sigma factor [Bacillus cereus F65185]
 gi|228709729|gb|EEL61767.1| RNA polymerase sigma factor [Bacillus cereus F65185]
          Length = 301

 Score = 64.4 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 41/257 (15%), Positives = 91/257 (35%), Gaps = 41/257 (15%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY--------GLPISEVVSEGNIGLM 87
           +L K  +E  D      L+  +   +  I   Y+G          +   E++    I ++
Sbjct: 1   MLLKACQE--DPDLLSELLYENKEFLFSIIAHYKGSIESLKNKFNVDEEELLQHAYIAVI 58

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
            A++ FD  +G +  TY    I   + + +     LV++  +A           L   ++
Sbjct: 59  TAIRDFDFNKGIKFTTYIYRPIIWEINQLLYNDSRLVRLSRSAVD---------LLKQME 109

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
            + +      +   +AK L+V+   + ++    +   SLN+L +   ++ S   +  V D
Sbjct: 110 KVENELGYFPKAEELAKLLDVTVERIENVLRFASELTSLNSLESFEPEDYSIGYESKVMD 169

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
               E +L   +               L+  E ++        N      ++ +  V   
Sbjct: 170 KIYVENLLKNSD---------------LSEFETQVINLIMDGNNNS---QIAKKLNVYPM 211

Query: 268 RVRQIEARAFKKVQESI 284
            V     RA  +++  +
Sbjct: 212 TV----NRALNRIKNKL 224


>gi|15612678|ref|NP_240981.1| RNA polymerase factor sigma-70 [Bacillus halodurans C-125]
 gi|10172727|dbj|BAB03834.1| RNA polymerase sigma-H factor (sigma-30) [Bacillus halodurans
           C-125]
          Length = 217

 Score = 64.4 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 44/260 (16%), Positives = 88/260 (33%), Gaps = 63/260 (24%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           E+  L  R R +GD +A   L+  +   V   A  Y   G    ++V EG IGL +A++ 
Sbjct: 18  EDVGLVNRVR-NGDGAALEYLIHKYKNFVRAKARSYFLIGADHEDIVQEGMIGLYKAIRD 76

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F  ++      ++   I   +   I  +     I   +                      
Sbjct: 77  FKGDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSY--------------------- 115

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
                                +S++  L  +ES          + +             E
Sbjct: 116 ---------------------VSLDKPLYDEES----------DRTLLDVVCGSRVTDPE 144

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           ++LI +EE  +    +   +S L   ER++        +  + + +S+E       V+ I
Sbjct: 145 ELLINQEEFDDIEVKMGELLSDL---ERKVLMLYL---DGRSYQEISAELN---RHVKSI 195

Query: 273 EARAFKKVQESIQKQVELSS 292
              A ++V+  +++ +EL  
Sbjct: 196 -DNALQRVKRKLERYMELKG 214


>gi|271969632|ref|YP_003343828.1| hypothetical protein Sros_8441 [Streptosporangium roseum DSM 43021]
 gi|270512807|gb|ACZ91085.1| hypothetical protein Sros_8441 [Streptosporangium roseum DSM 43021]
          Length = 615

 Score = 64.4 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 19/72 (26%), Positives = 36/72 (50%), Gaps = 4/72 (5%)

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            ++    + L+ R+R I   R       TL++L+  F V+RER+RQIE      +++ + 
Sbjct: 129 ELIDEVFAALDDRQRAIARDRLYASQRATLDDLAQRFSVTRERIRQIERD----LRDHVD 184

Query: 286 KQVELSSSPPLL 297
             +    + PL+
Sbjct: 185 AWLASEDAAPLV 196


>gi|332757481|gb|EGJ87816.1| RNA polymerase sigma factor for flagellar operon [Shigella flexneri
           K-671]
 gi|333017677|gb|EGK36989.1| RNA polymerase sigma factor for flagellar operon [Shigella flexneri
           K-304]
          Length = 161

 Score = 64.4 bits (156), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 22/154 (14%), Positives = 60/154 (38%), Gaps = 6/154 (3%)

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
           + +  N R +   +  +     +      +A++L +  ++   M      D + + L + 
Sbjct: 13  RSVRRNAREVAQAIGQLEQELGRNATETEVAERLGIDIADYRQMLL----DTNNSQLFSY 68

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            +          +   D Q +  +++    N R  +  ++  L  RE+ +       +  
Sbjct: 69  DEWREEHGDSIELVTDDHQRENPLQQLLDSNLRQRVMEAIETLPEREKLVLTLYY--QEE 126

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           + L+ + +  EV   RV Q+ ++  K+++  + K
Sbjct: 127 LNLKEIGAVLEVGESRVSQLHSQDIKRLRTKLGK 160


>gi|262190809|ref|ZP_06049034.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           CT 5369-93]
 gi|262033330|gb|EEY51843.1| RNA polymerase sigma factor for flagellar operon [Vibrio cholerae
           CT 5369-93]
          Length = 116

 Score = 64.1 bits (155), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 17/113 (15%), Positives = 43/113 (38%), Gaps = 2/113 (1%)

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
           +S+    +    +N       ++     D +    +G++         ++ R  L  S+ 
Sbjct: 1   MSLEQYHSVLMDINCSRIVGIEDLGVSDDAISPFEEGEDNSPFHGVAEESFRKALVESIK 60

Query: 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            L  RE  +       +  + L+ +     VS  RV QI +++ ++++  +  
Sbjct: 61  SLPEREALVLSLYY--DEELNLKEIGEVLGVSESRVSQILSQSMQRLRTKLSS 111


>gi|153815652|ref|ZP_01968320.1| hypothetical protein RUMTOR_01888 [Ruminococcus torques ATCC 27756]
 gi|145847083|gb|EDK24001.1| hypothetical protein RUMTOR_01888 [Ruminococcus torques ATCC 27756]
          Length = 114

 Score = 64.1 bits (155), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 25/109 (22%), Positives = 49/109 (44%), Gaps = 6/109 (5%)

Query: 179 RLAGDESLNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
           + A + SL   I +  + N  +  D +  D    E+V  +   ++N + +  +    L+ 
Sbjct: 8   KAAKEISLYEPIGTDREGNEIKLYDIIETDE---EEVAEKIHLKENIQTLYEKVEKELSQ 64

Query: 238 RERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           RER I + R         T   ++ +  +SR  V +IE  A +K+++S 
Sbjct: 65  RERIILKMRYGLYNGEEYTQREIARQLGISRSYVSRIEKGAVEKLRKSF 113


>gi|317060933|ref|ZP_07925418.1| predicted protein [Fusobacterium sp. D12]
 gi|313686609|gb|EFS23444.1| predicted protein [Fusobacterium sp. D12]
          Length = 149

 Score = 64.1 bits (155), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 30/140 (21%), Positives = 61/140 (43%), Gaps = 10/140 (7%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD+ A + L+  ++ LV KI   Y        +   EG +    A+ KFD  +  +L++Y
Sbjct: 2   GDIEARNELIEKNINLVHKINRMYGSS----EDGFQEGILAFCHAIDKFDETKNVKLSSY 57

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +  WI+  ++ Y  R     ++     +K +    R+++   +     + K E    I +
Sbjct: 58  AFHWIRQKIKRYREREK--YRLPAHVIEK-MSKEERKIRIDFEY---RDFKSEDETTIEE 111

Query: 165 KLNVSESEVISMNCRLAGDE 184
           + ++     +    +LA DE
Sbjct: 112 ESSICLKSTLEQYIKLACDE 131


>gi|170755460|ref|YP_001782085.1| DNA-dependent RNA polymerase sigma subunit [Clostridium botulinum
           B1 str. Okra]
 gi|169120672|gb|ACA44508.1| DNA-dependent RNA polymerase sigma subunit [Clostridium botulinum
           B1 str. Okra]
          Length = 96

 Score = 64.1 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 22/92 (23%), Positives = 40/92 (43%), Gaps = 5/92 (5%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENP 252
            N     D L  D D   +++  K E K     +    + L  RE+++ + R       P
Sbjct: 2   GNEISLMDILSSDEDSIIEIVSTKIEVKKLYGKID---TCLRGREKKVIQMRYGLKDGRP 58

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            T   ++   ++SR  V +IE +A KK+ + +
Sbjct: 59  RTQREIAGILDISRSYVSRIEKKALKKLYKEL 90


>gi|163800115|ref|ZP_02194016.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio sp. AND4]
 gi|159175558|gb|EDP60352.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio sp. AND4]
          Length = 242

 Score = 64.1 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 33/263 (12%), Positives = 93/263 (35%), Gaps = 37/263 (14%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGL 86
            ++EE     R  +       + L+  H  +V ++      +      I ++   G I L
Sbjct: 11  TQEEEVNTPSRAIDE------NALLQRHQIMVKRVVNQLRAHATSHCSIEDMQQIGLIAL 64

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGH 145
           ++A +++          +++  ++ A+ + + R  W           ++       L   
Sbjct: 65  VEAGRRYGEVDDPHFPAFAVCRVRGAILDELRRLDWRS---------RKTRQKAHELNDV 115

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDW 203
            + +T    +      I K L   E +             +SL+ L+ +  ++    Q  
Sbjct: 116 TRDLTRALGRMPTDAEIIKALGTDEQDYYNRQNAALAGEMQSLDQLMEAGGESHFGGQY- 174

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
                        +  E ++ R  L  ++  +  R++ +       ++ + L  ++   +
Sbjct: 175 -------------DGMEHEHIRRSLDAALGKMPKRDQLLLTLFY--QHELNLHEIALVLD 219

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           ++  R+ Q+  +A K++ + +  
Sbjct: 220 LTPPRICQLHKQALKQLNQLMSS 242


>gi|153831527|ref|ZP_01984194.1| RNA polymerase sigma factor for flagellar operon [Vibrio harveyi
           HY01]
 gi|148872037|gb|EDL70854.1| RNA polymerase sigma factor for flagellar operon [Vibrio harveyi
           HY01]
          Length = 242

 Score = 64.1 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 30/242 (12%), Positives = 87/242 (35%), Gaps = 31/242 (12%)

Query: 51  HRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           + L+  H  +V ++      +      I ++   G I L++A +++          +++ 
Sbjct: 26  NALLQRHQVMVKRVVNQLRVHATSHCSIEDMQQIGLIALVEAGRRYGDVDDPHFPAFAVC 85

Query: 108 WIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            ++ A+ + + R  W           ++       L    + +T    +      I K L
Sbjct: 86  RVRGAILDELRRLDWRS---------RKTRQQAHELNDVTRDLTRALGRMPTDAEIIKAL 136

Query: 167 NVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
              E +             +SL+ L+ +   +    Q               +  E ++ 
Sbjct: 137 GTDEQDYYNRQNAALAGEMQSLDQLMETGGDSHFGGQY--------------DGMEHEHI 182

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L  ++  ++ R++ +       ++ + L  ++   +++  R+ Q+  +A K++ + +
Sbjct: 183 RRSLDTALGKMSKRDQLLLTLFY--QHELNLHEIALVLDLTPPRICQLHKQALKQLNQLM 240

Query: 285 QK 286
             
Sbjct: 241 SS 242


>gi|67920929|ref|ZP_00514448.1| Sigma-70 region 2 [Crocosphaera watsonii WH 8501]
 gi|67857046|gb|EAM52286.1| Sigma-70 region 2 [Crocosphaera watsonii WH 8501]
          Length = 110

 Score = 64.1 bits (155), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 16/89 (17%), Positives = 45/89 (50%), Gaps = 1/89 (1%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVK 91
           E   L + Y ++      ++++  +  LV + A  +         ++V  G++GL++A++
Sbjct: 12  ETLKLFQEYEKNPKTRLRNKILELNFGLVRREAHHWVHQCPESYEDLVQVGSLGLIRAIE 71

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRS 120
           +F   +G   +++++ +I+  +Q Y+   
Sbjct: 72  RFSIGKGHAFSSFAIPYIRGEIQHYLREK 100


>gi|256273|gb|AAC60417.1| RpoD4 [Synechococcus]
          Length = 48

 Score = 63.7 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 18/47 (38%), Positives = 31/47 (65%)

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           +++ EG++GL +AV+KFDP  G++ +TY+ WWI+ +M   I      
Sbjct: 2   DLIQEGSLGLERAVEKFDPALGYKFSTYAYWWIRQSMTRAIDNHART 48


>gi|295094135|emb|CBK83226.1| RNA polymerase sigma factor, sigma-70 family [Coprococcus sp.
           ART55/1]
          Length = 220

 Score = 63.7 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 48/259 (18%), Positives = 94/259 (36%), Gaps = 67/259 (25%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAM-GYRGYG-------LPISEVVSEGNIGLMQAVK 91
           R  + GD +A   L+  +L  + KIA+  YR  G       + + +++ EG+IGL+ A+ 
Sbjct: 11  RLAQKGDTAARDILLEKNLGFIRKIALEQYRNMGLDENDIGIDLDDLMQEGSIGLLNAIP 70

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
            FD  RG +  TY+   ++ AM + I                         +  L     
Sbjct: 71  LFDAGRGMKFLTYAAPALRNAMTDCI-------------------------RAALGLFEQ 105

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
             +  +      +   V   +V+S + R+   E++                      D  
Sbjct: 106 RMVDKKDAPGFQR---VYLDDVLSEDERMLRIEAI---------------------ADPH 141

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR----LQENPVTLENLSS--EFEVS 265
            Q   +   +K +   L  ++  L  RE+     R       E+P+    + +   F +S
Sbjct: 142 TQTPEQIYIQKEQLIELYAALDKLTAREQTYLLYRYGFTDGIEHPL----IGAALHFHLS 197

Query: 266 RERVRQIEARAFKKVQESI 284
             R +++E  A   ++  +
Sbjct: 198 ESRTKKVEGEAMDSLRGKL 216


>gi|237745256|ref|ZP_04575737.1| predicted protein [Fusobacterium sp. 7_1]
 gi|229432485|gb|EEO42697.1| predicted protein [Fusobacterium sp. 7_1]
          Length = 200

 Score = 63.7 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 41/255 (16%), Positives = 96/255 (37%), Gaps = 69/255 (27%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           E +E   L +  ++ G+  A  +L+  +L  + KI   +        +   EG +G+ QA
Sbjct: 2   ESKEVLELIREAKK-GNNEATEKLIERYLNTIRKINHKWGNT----DDGFQEGILGIYQA 56

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +K +D     +  T+  ++++A +++YI +     ++            +  +K   Q  
Sbjct: 57  IKTYDENYNTKFMTHLYFYVEAKIRKYIDKER--YRVPQYV--------IESIKKGEQER 106

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
                                                   +  S+  + + +D  + + +
Sbjct: 107 ----------------------------------------VYFSELENFEIEDANINNEN 126

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
            + +VLIE            + ++    +E+ +     L     T E ++ +  +SR+ V
Sbjct: 127 LENKVLIE------------KVLNYCTDQEKTVIN--YLFFEGYTGEEVAQKLGISRQWV 172

Query: 270 RQIEARAFKKVQESI 284
             I+ RAF+K++ +I
Sbjct: 173 HTIKHRAFEKIRNNI 187


>gi|156976180|ref|YP_001447086.1| DNA-directed RNA polymerase sigma subunit/flagellum specific
           [Vibrio harveyi ATCC BAA-1116]
 gi|156527774|gb|ABU72859.1| hypothetical protein VIBHAR_04951 [Vibrio harveyi ATCC BAA-1116]
          Length = 242

 Score = 63.7 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 30/242 (12%), Positives = 88/242 (36%), Gaps = 31/242 (12%)

Query: 51  HRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           + L+  H  +V ++      +      I ++   G I L++A +++          +++ 
Sbjct: 26  NALLQRHQVMVKRVVNQLRVHATSHCSIEDMQQIGLIALVEAGRRYGDVDDPHFPAFAVC 85

Query: 108 WIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            ++ A+ + + R  W           ++       L    + +T    +      I K L
Sbjct: 86  RVRGAILDELRRLDWRS---------RKTRQQAHELNDVTRDLTRALGRMPTDAEIIKAL 136

Query: 167 NVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
              E +             +SL+ L+ +  ++    Q               +  E ++ 
Sbjct: 137 GTDEQDYYNRQNAALAGEMQSLDQLMETGGESHFGGQY--------------DGMEHEHI 182

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L  ++  ++ R++ +       ++ + L  ++   +++  R+ Q+  +A K++ + +
Sbjct: 183 RRSLDTALGKMSKRDQLLLTLFY--QHELNLHEIALVLDLTPPRICQLHKQALKQLNQLM 240

Query: 285 QK 286
             
Sbjct: 241 SS 242


>gi|261368103|ref|ZP_05980986.1| RNA polymerase sigma-E factor [Subdoligranulum variabile DSM 15176]
 gi|282569861|gb|EFB75396.1| RNA polymerase sigma-E factor [Subdoligranulum variabile DSM 15176]
          Length = 118

 Score = 63.7 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 21/107 (19%), Positives = 44/107 (41%), Gaps = 4/107 (3%)

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
           M  R    E    L++  +          + D      V+ +  ER+     L + +  L
Sbjct: 1   MELRRTRRE--GTLLSLQEPLEGSEGQLTLADTLPDPAVMEDDCERRADAARLRKLLETL 58

Query: 236 NPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
            PRE+++   R   +   P T + ++ +  +SR  + ++E RA + +
Sbjct: 59  PPREQQVLTRRYGLDGRPPCTQQEIAGQMGISRSYISRLEKRALQAL 105


>gi|266621294|ref|ZP_06114229.1| DNA-directed RNA polymerase sigma subunit [Clostridium hathewayi
           DSM 13479]
 gi|288867054|gb|EFC99352.1| DNA-directed RNA polymerase sigma subunit [Clostridium hathewayi
           DSM 13479]
          Length = 188

 Score = 63.7 bits (154), Expect = 3e-08,   Method: Composition-based stats.
 Identities = 40/194 (20%), Positives = 77/194 (39%), Gaps = 7/194 (3%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           + E++ I    ++E   L       G+  A  RL+  +L   +K A  Y G G+ ++++V
Sbjct: 1   MEEMKAITPCTQEENTQLLNDAA-AGNEGAKKRLIEGNLEAALKCAKEYDGKGVLLTDLV 59

Query: 80  SEGNIGLMQAVKKFDPERG-FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
           +E N+ L  AV +F  + G      +    +KAA+   +    S          + L   
Sbjct: 60  AEANMALTMAVTEFLTDAGDGDFEGFLAARMKAALDLAVEEQQSA-----KQTGEELAAR 114

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           +  L+   Q +     +   V  +A K+ ++  EV  +        S+NA     +  + 
Sbjct: 115 VNVLQTVSQMLAKELGREATVEELADKMKMTAGEVKDIMKMAMDAMSMNAENADLEDLAE 174

Query: 199 QWQDWLVYDHDGQE 212
                +    DG+E
Sbjct: 175 VEGIEITGAEDGEE 188


>gi|269960144|ref|ZP_06174520.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio harveyi 1DA3]
 gi|269835115|gb|EEZ89198.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio harveyi 1DA3]
          Length = 242

 Score = 63.3 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 30/242 (12%), Positives = 87/242 (35%), Gaps = 31/242 (12%)

Query: 51  HRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           + L+  H  +V ++      +      I ++   G I L++A +++          +++ 
Sbjct: 26  NALLQRHQVMVKRVVNQLRVHATSHCSIEDMQQIGLIALVEAGRRYGDVDDPHFPAFAVC 85

Query: 108 WIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            ++ A+ + + R  W           ++       L    + +T    +      I K L
Sbjct: 86  RVRGAILDELRRLDWRS---------RKTRQQAHELNDVTRDLTRALGRMPSDAEIIKAL 136

Query: 167 NVSESEV--ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
              E +             +SL+ L+ +   +    Q               +  E ++ 
Sbjct: 137 GTDEQDFYNRQNAALAGEMQSLDQLMETGGDSHFGGQY--------------DGMEHEHI 182

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L  ++  ++ R++ +       ++ + L  ++   +++  R+ Q+  +A K++ + +
Sbjct: 183 RRSLDTALGKMSKRDQLLLTLFY--QHELNLHEIALVLDLTPPRICQLHKQALKQLNQLM 240

Query: 285 QK 286
             
Sbjct: 241 SS 242


>gi|258624678|ref|ZP_05719613.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio mimicus VM603]
 gi|258583070|gb|EEW07884.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio mimicus VM603]
          Length = 242

 Score = 63.3 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 30/242 (12%), Positives = 90/242 (37%), Gaps = 31/242 (12%)

Query: 51  HRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           ++L+  H  +V ++      +      I ++   G I L++A +++         T+++ 
Sbjct: 26  NQLLQRHKIMVKRVVNQLKVHATAYCSIDDMQQIGLIALIEAGRRYGDISDPNFPTFAVC 85

Query: 108 WIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            ++ A+ + + R  W           ++       L    + +     +        K L
Sbjct: 86  RVRGAILDELRRLDWRS---------RKTRQQAHELNDITRDLIRALGRQPTDAETIKAL 136

Query: 167 NVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
             +E +  +          +SL+ LI +  +N                    +  + ++ 
Sbjct: 137 GTNEQDYYARQSAALAGELQSLDQLIENGVENQLSGHY--------------DGLKHEHI 182

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L  +++ L+ R++ +       ++ + L  ++   +++  R+ Q+  +A K++ + +
Sbjct: 183 RRSLETALNKLSKRDQLLLTLFY--QHELNLNEIALILDLTSPRICQLHKQALKQLNQYL 240

Query: 285 QK 286
             
Sbjct: 241 SS 242


>gi|298708238|emb|CBJ48301.1| RNA polymerase sigma factor [Ectocarpus siliculosus]
          Length = 516

 Score = 63.3 bits (153), Expect = 4e-08,   Method: Composition-based stats.
 Identities = 52/317 (16%), Positives = 101/317 (31%), Gaps = 72/317 (22%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA-----MGYRGYGLPISEVVSEGNIGLMQ 88
           E     R  + G + A   LV  ++ +V+++         RG  +  ++++ EG   L  
Sbjct: 200 EVEDLPRVLQEG-IEAKQTLVERNMPMVIRMVEGQYRWRLRGGQVSFADLLQEGAYALGV 258

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG------TTANQKRLFFNLRRL 142
           A ++FDP    R  TY+++ ++  +   + R  S + +           ++ L   L R 
Sbjct: 259 AAERFDPTMPNRFLTYALYTVRDKLDVALARGNSAISVPATALKEVHRARRELTGRLGRT 318

Query: 143 KGHLQAI--------------------------------------TDNNLKPEQVVAIAK 164
               +                                             +       A 
Sbjct: 319 PSEAELANFFANGVVVVGDAEPAASAGDGGIRRGGADGDRGRSTAAGRRARAVTDGEFAV 378

Query: 165 KLNVSESEVISMN----------CRLAGDESLNALINSSDKNSS-QWQDWLVYD-HDGQE 212
           K   S+ E                 +    S++ LI +SD ++     D LV D  DGQ 
Sbjct: 379 KAASSDREARQQARTRRRRLNLLSAVQKVTSIDRLIRASDGSTMVPLVDTLVGDLEDGQP 438

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVR 270
           +           R        VL PR+  +           P+T+   S E  +S  R +
Sbjct: 439 RSAGGDIAELLPR--------VLTPRQASLVRMACGLSDGKPMTMAECSKELSLSVARTK 490

Query: 271 QIEARAFKKVQESIQKQ 287
            +   + +K++ + +  
Sbjct: 491 SLFDSSLQKLRAAAEAD 507


>gi|228969112|ref|ZP_04130026.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228790601|gb|EEM38288.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar sotto
           str. T04001]
          Length = 301

 Score = 63.3 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 41/257 (15%), Positives = 91/257 (35%), Gaps = 41/257 (15%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY--------GLPISEVVSEGNIGLM 87
           +L K  +E  D      L+  +   +  I   Y+G          +   E++    I ++
Sbjct: 1   MLLKACQE--DPDLLSELLYENKEFLFSIIAHYKGSIESLKNKFNVDEEELLQHAYIAVI 58

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
            A++ FD  +G +  TY    I   + + +     LV++  +A           L   ++
Sbjct: 59  TAIRDFDFNKGIKFTTYIYRPIIWEVNQLLYNDSRLVRLSRSAVD---------LLKQME 109

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
            + +      +   +AK L+V+   + ++    +   SLN+L +   ++ S   +  V D
Sbjct: 110 KVENELGYFPKAEELAKLLDVTVERIENVLRFASELTSLNSLESFEPEDYSIGYESKVMD 169

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
               E +L   +               L+  E ++        N      ++ +  V   
Sbjct: 170 KIYVENLLKNSD---------------LSEFETQVINLIMDGNNNS---QIAKKLNVYPM 211

Query: 268 RVRQIEARAFKKVQESI 284
            V     RA  +++  +
Sbjct: 212 TV----NRALNRIKNKL 224


>gi|168212152|ref|ZP_02637777.1| sporulation sigma factor SigK [Clostridium perfringens B str. ATCC
           3626]
 gi|170709952|gb|EDT22134.1| sporulation sigma factor SigK [Clostridium perfringens B str. ATCC
           3626]
          Length = 58

 Score = 63.3 bits (153), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 2/55 (3%)

Query: 233 SVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            VL+PRE+ I + R   L  +  T   ++    +SR  V +IE +A KK+ +  +
Sbjct: 3   DVLSPREKEIIQMRYGLLDGDIKTQREIAGILGISRSYVSRIEKKALKKLNKEFK 57


>gi|163785214|ref|ZP_02179892.1| RNA polymerase sigma factor for flagellar operon [Hydrogenivirga
           sp. 128-5-R1-1]
 gi|159879519|gb|EDP73345.1| RNA polymerase sigma factor for flagellar operon [Hydrogenivirga
           sp. 128-5-R1-1]
          Length = 177

 Score = 62.9 bits (152), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 34/210 (16%), Positives = 78/210 (37%), Gaps = 42/210 (20%)

Query: 47  LSAAHRLVTSHLRLVVKIAMG--YR--GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
               +++V  +L L+ K+A    YR     +   E+V+ G IGL++A+  ++ +   + +
Sbjct: 6   KEEKNKVVLDNLNLIKKVASKIYYRLPKGEIDFDELVNIGVIGLLKALDNYNEDL-AKFS 64

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY+   I+  + +Y+ RS  +V  G     K+                    + + V   
Sbjct: 65  TYAYIRIRGEILDYL-RSLDIVPRGIRDKIKK--------------------EEKPVDEQ 103

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
            +    S +  +S+   + G E L                  +     + +   E   + 
Sbjct: 104 MEIPLSSSAIFLSIEKAIGGTEDL----------------KFIDTLKSRMESPEEYAYKV 147

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENP 252
             R  +   +++L   E+++ +    +E  
Sbjct: 148 ELREKIEEKLNLLTENEKKVIQMIFFEEKD 177


>gi|167768028|ref|ZP_02440081.1| hypothetical protein CLOSS21_02571 [Clostridium sp. SS2/1]
 gi|317498378|ref|ZP_07956673.1| sigma-70 region 2 [Lachnospiraceae bacterium 5_1_63FAA]
 gi|167710357|gb|EDS20936.1| hypothetical protein CLOSS21_02571 [Clostridium sp. SS2/1]
 gi|291561028|emb|CBL39828.1| Sigma-70 region 3./Sigma-70 region 2 [butyrate-producing bacterium
           SSC/2]
 gi|316894272|gb|EFV16459.1| sigma-70 region 2 [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 256

 Score = 62.9 bits (152), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 37/189 (19%), Positives = 87/189 (46%), Gaps = 14/189 (7%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYR-EHGDLSAAHRLVTSHLRL 60
            ++   I    +  +  Y  E+ ++ +  ++E+  L   +  E GD  A   ++ S L  
Sbjct: 71  AKEKADISEEEQGAIRFYEEELEQMDLPGEEEQKELIHAWLVEKGDGEA---VIESFLPQ 127

Query: 61  VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           +++IA  + G G+   ++V EGNIGL++A+  +  +       ++   ++ ++ + I   
Sbjct: 128 ILEIARTHTGKGVLFGDLVQEGNIGLLEAMAIYQGKDAEGFLAHAKSAVEDSILDAIA-- 185

Query: 121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRL 180
              ++ G+ +  + +     RL      ++    +  ++  +AK L+++E EV  +    
Sbjct: 186 ---IQRGSDSVGEAMAIKANRLDDASTFLSKELGREPKIEELAKYLSMTEEEVKEVMK-- 240

Query: 181 AGDESLNAL 189
               SL+AL
Sbjct: 241 ---ISLDAL 246


>gi|157165349|ref|YP_001467213.1| flagellar biosynthesis sigma factor [Campylobacter concisus 13826]
 gi|112799934|gb|EAT97278.1| flagellar biosynthesis sigma factor FliA [Campylobacter concisus
           13826]
          Length = 234

 Score = 62.9 bits (152), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 37/242 (15%), Positives = 89/242 (36%), Gaps = 30/242 (12%)

Query: 47  LSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
                 +V  ++  +  +A          + +++++S G   +++  +K+D E+      
Sbjct: 17  KKEQDEIVLKYMPALRAMAFRLKERLPSSIDVNDLISVGVEEMIKLSRKYDKEQNDSFWG 76

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL-RRLKGHLQAITDNNLKPEQVVAI 162
           Y    I  +M +Y+ R+  +V        K +   +      H +  +D  L  +    I
Sbjct: 77  YGKKRIYGSMLDYL-RALDVVSRSDRKLVKSINTEIDNYFNTHEEEPSDEYLAEKLNEDI 135

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
            K        V  +   L  DE +  +  S  + S + +D ++                 
Sbjct: 136 EKI--REARGVSGIITILPIDEQMELIGQSDVEKSVEKEDLIL----------------- 176

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
                +  ++   + R++ I +    +E  + L+ +S    +S  R+ QI  R   +++ 
Sbjct: 177 ----KIESALKDFDERDQMIVQLYYYEE--LNLKEISEIMNISESRISQIHKRLLDRIRR 230

Query: 283 SI 284
           S+
Sbjct: 231 SL 232


>gi|323484667|ref|ZP_08090029.1| sigma-70 region 3 [Clostridium symbiosum WAL-14163]
 gi|323694798|ref|ZP_08108953.1| hypothetical protein HMPREF9475_03817 [Clostridium symbiosum
           WAL-14673]
 gi|323402050|gb|EGA94386.1| sigma-70 region 3 [Clostridium symbiosum WAL-14163]
 gi|323501114|gb|EGB17021.1| hypothetical protein HMPREF9475_03817 [Clostridium symbiosum
           WAL-14673]
          Length = 192

 Score = 62.9 bits (152), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 36/168 (21%), Positives = 76/168 (45%), Gaps = 9/168 (5%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
            +GE     Y+ E++ +P    +EE  L       G  SA  RLV   L   V++A  YR
Sbjct: 22  TSGEDFYQLYLEELKLVPPCSPEEEERLLDEI-LAGSQSAVKRLVEGKLGRAVRMAEEYR 80

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
             GL ++++V E NI L+   +++   +G    + S   I+  +++ +    +  K+   
Sbjct: 81  DRGLSMNDLVQEANIALLLTAQEY---KGGDFDSQSEERIRRMIEDALELQNTEYKV--- 134

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
             ++ +   +  LK     + +   +   V  +A+++ ++E E+  + 
Sbjct: 135 --EEEMLARVNVLKDISAGMAEELGREATVEELAERMKMTEQEIKDIM 180


>gi|73532520|dbj|BAE19818.1| RNA polymerase sigma factor for flagellar operon [Edwardsiella
           tarda]
          Length = 168

 Score = 62.9 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 29/169 (17%), Positives = 67/169 (39%), Gaps = 12/169 (7%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
            + +++  G IGL+ AV+++D  +G    TY++  I+ AM + + RS   V      N +
Sbjct: 12  ELDDLLQAGGIGLLHAVERYDAMQGTAFTTYAIQRIRGAMLDEL-RSRDWVPRSVRRNAR 70

Query: 134 RLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
            +   ++R +  L        +      IA+++ +   E   +      D + + L +  
Sbjct: 71  GVSAAMQRAEQRL-------GRTPGDSEIAQEMGIPLEEYQQILL----DTNTSQLFSYD 119

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
           +                +E   + +    + R  +  ++  L  RE+ +
Sbjct: 120 EWREDHGDSAEPVLEQSEEANPLRQLLESDLRGRVIAAIEALPEREKLV 168


>gi|197294375|ref|YP_001798916.1| RNA polymerase sigma factor [Candidatus Phytoplasma australiense]
 gi|171853702|emb|CAM11593.1| RNA polymerase sigma factor [Candidatus Phytoplasma australiense]
          Length = 151

 Score = 62.9 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 28/124 (22%), Positives = 59/124 (47%), Gaps = 9/124 (7%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI--SEVVSEGNIGLMQAVKKFDPERG 98
            +   +L+   +L+  H  LV KIA  ++ +   +   ++  EG +GL++++  ++ + G
Sbjct: 11  LKNKNNLAIRDQLIKMHFPLVKKIANKFKYFPKSLQREDLYQEGILGLIKSLDNYE-DLG 69

Query: 99  FRLATYSMWWIKAAMQEYIL---RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           +    Y+   IK  + E I     + + +K+     Q     N+   +   Q+I +NNL 
Sbjct: 70  YDFIAYATPTIKGEITELIRGLQTTSTPIKVFRKEKQ---TSNIPFEENQPQSINNNNLN 126

Query: 156 PEQV 159
           P Q+
Sbjct: 127 PHQI 130


>gi|116070637|ref|ZP_01467906.1| putative type III sigma factor [Synechococcus sp. BL107]
 gi|116066042|gb|EAU71799.1| putative type III sigma factor [Synechococcus sp. BL107]
          Length = 213

 Score = 62.9 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 31/124 (25%), Positives = 49/124 (39%), Gaps = 6/124 (4%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPI-SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
            ++ V  HL L   +A   R  G     +++ E  +GL+Q V+  +P RGFR ++Y M  
Sbjct: 48  RNQKVLQHLGLAHCVATRQRQRGPEERDDLLQEACLGLIQGVENLNPSRGFRPSSYLMSR 107

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
               +  Y      +V+I        +     + K      T   L P    +IA  L V
Sbjct: 108 ANGQVLHYRRDRSRMVRIPWRLQDLFVSGQRLQEKR-----TQRGLPPLNNRSIAAHLKV 162

Query: 169 SESE 172
           S   
Sbjct: 163 SPQR 166


>gi|312792353|ref|YP_004025276.1| RNA polymerase sigma factor, sigma-70 family [Caldicellulosiruptor
           kristjanssonii 177R1B]
 gi|312179493|gb|ADQ39663.1| RNA polymerase sigma factor, sigma-70 family [Caldicellulosiruptor
           kristjanssonii 177R1B]
          Length = 311

 Score = 62.9 bits (152), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 21/93 (22%), Positives = 47/93 (50%), Gaps = 6/93 (6%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGY----RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
           D +    L+  +L+LV  IA  +    +GY   + +++SEG  GL+ A + + PE G   
Sbjct: 10  DKAQRQLLIADNLKLVYHIANKFMPCPKGYMYEVDDLISEGYFGLIVAAQNYKPELGTPF 69

Query: 102 ATYSMWWIKAAMQEYI--LRSWSLVKIGTTANQ 132
            +Y+   I++ ++  +   +  S + + +  ++
Sbjct: 70  VSYACKVIESRIKRSLPKYKLSSTISLDSPVSK 102


>gi|228907496|ref|ZP_04071353.1| RNA polymerase sigma factor [Bacillus thuringiensis IBL 200]
 gi|228851988|gb|EEM96785.1| RNA polymerase sigma factor [Bacillus thuringiensis IBL 200]
          Length = 324

 Score = 62.5 bits (151), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 42/257 (16%), Positives = 90/257 (35%), Gaps = 41/257 (15%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY--------GLPISEVVSEGNIGLM 87
           VL K  +E  D      L+  +   +  I   Y+G          +   E++    I ++
Sbjct: 21  VLLKACQE--DPDLLSELLYENKEFLFSIIAHYKGSIESLKNKFNVDEEELLQHAYIAVI 78

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
            A++ FD  +G +  TY    I   + + +     LV++  +A           L   ++
Sbjct: 79  TAIRDFDFNKGIKFTTYIYRPIIWEINQLLYNDSRLVRLSRSAVD---------LLKQME 129

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
            + +      +   +A  L+V+   + ++    +   SLN+L N   ++ S   +  V D
Sbjct: 130 KVENELGYFPKAEELAILLDVTVERIENVLRFASELTSLNSLENFEPEDYSIGYESKVMD 189

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
               E +L   +               L+  E ++        N      ++ +  V   
Sbjct: 190 KIYVENLLKNSD---------------LSEFETQVINLIMDGNNNS---QIAKKLNVYPM 231

Query: 268 RVRQIEARAFKKVQESI 284
            V     RA  +++  +
Sbjct: 232 TV----NRALNRIKNKL 244


>gi|224419054|ref|ZP_03657060.1| flagellar biosynthesis sigma factor [Helicobacter canadensis MIT
           98-5491]
 gi|253827994|ref|ZP_04870879.1| flagellar biosynthesis sigma factor FliA [Helicobacter canadensis
           MIT 98-5491]
 gi|313142562|ref|ZP_07804755.1| flagellar biosynthesis sigma factor [Helicobacter canadensis MIT
           98-5491]
 gi|253511400|gb|EES90059.1| flagellar biosynthesis sigma factor FliA [Helicobacter canadensis
           MIT 98-5491]
 gi|313131593|gb|EFR49210.1| flagellar biosynthesis sigma factor [Helicobacter canadensis MIT
           98-5491]
          Length = 235

 Score = 62.5 bits (151), Expect = 6e-08,   Method: Composition-based stats.
 Identities = 34/243 (13%), Positives = 88/243 (36%), Gaps = 34/243 (13%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              L   +L  +  +A   +      +  +++VS G   L++  +K+D         Y+ 
Sbjct: 16  QDNLALDYLPALKALAARLKERLPANVEFADLVSIGTEELIKLARKYDQNLNDSFWGYAK 75

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             +  AM +Y+     + +   T         ++ +   +    +   +      ++K L
Sbjct: 76  SRVYGAMLDYLRGLDCMSRHTRTL--------IKSINKEISKYYNEYQEEPDNAYLSKVL 127

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD---GQEQVLIEKEERKN 223
           N    ++                     +N+S+    L  D +    QE     K E++ 
Sbjct: 128 NEDIEKIKEA------------------RNASEIYGILPLDEELSAAQEDKTYNKIEKQE 169

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
              ++   +   +  E+ + +    +E  ++ + +S   E+S  R+ QI     +K++  
Sbjct: 170 LIGIIQNILESASKNEQLVIQLYYYEE--LSFKEISEILEISESRISQIHKSVIRKIRAY 227

Query: 284 IQK 286
           +++
Sbjct: 228 LEE 230


>gi|332975577|gb|EGK12467.1| RNA polymerase sigma-K factor [Desmospora sp. 8437]
          Length = 86

 Score = 62.5 bits (151), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 16/70 (22%), Positives = 32/70 (45%), Gaps = 2/70 (2%)

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVR 270
             ++E  + K  ++ +   + +L+ RE+ +   R         T   ++ E  +SR  V 
Sbjct: 7   DEIVETVQLKIEKSKIYGYLHILDEREQDVIRNRFGLSGGKEKTQREIAKELGISRSYVS 66

Query: 271 QIEARAFKKV 280
           +IE RA  K+
Sbjct: 67  RIEKRALIKL 76


>gi|153938326|ref|YP_001391685.1| sigma-70 family RNA polymerase sigma factor [Clostridium botulinum
           F str. Langeland]
 gi|152934222|gb|ABS39720.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           F str. Langeland]
 gi|295319714|gb|ADG00092.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           F str. 230613]
          Length = 183

 Score = 62.5 bits (151), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 43/240 (17%), Positives = 81/240 (33%), Gaps = 68/240 (28%)

Query: 55  TSHLRLVVKIA-MGYR--GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
             HL +V  I    Y+   +     ++  EG +GLM+A  +FD  R  + +TY+  ++  
Sbjct: 5   EEHLGIVYLITNKRYKQFKHKYSYEDLFQEGCLGLMKAANRFDSSRRIKFSTYAYPYVDG 64

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            +   I              +   ++   R K  L+ I                      
Sbjct: 65  QILRMI--------------ESDKWYGKNR-KERLEGI---------------------- 87

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
                        SL+A I+  D   +        D  G   +  EK E       +   
Sbjct: 88  ----------VPYSLDAAIDGLDNEIAYI------DSIGNYDLNFEKIE-------IKTL 124

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ---ESIQKQV 288
           +  L  + + I E   +Q    T   ++ +   SR  V +++  A   ++    SI+K++
Sbjct: 125 IDSLPEKLKEIMEMYYMQ--SFTQAEIARKIGCSRSNVTRLKIEALDYLRFQVNSIKKEM 182


>gi|229917375|ref|YP_002886021.1| RNA polymerase factor sigma-70 [Exiguobacterium sp. AT1b]
 gi|229468804|gb|ACQ70576.1| transcriptional regulator, LuxR family [Exiguobacterium sp. AT1b]
          Length = 213

 Score = 62.5 bits (151), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 44/259 (16%), Positives = 86/259 (33%), Gaps = 64/259 (24%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            EE VL  R    GD  A   L+  +   V   A  Y   G    ++V EG IGL + V+
Sbjct: 14  DEELVLLAR--NEGDSDALEFLIERYRYFVRAKARSYFLIGADHEDIVQEGMIGLYKGVR 71

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
            +  ER     +++   I   M   I  +     I   +                     
Sbjct: 72  DYKDERLASFKSFAEMCITRQMITAIKTATRQKHIPLNSY-------------------- 111

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
                                 +S++  +  +ES                D ++  H   
Sbjct: 112 ----------------------VSLDKPIFDEES-----------DRTLLDVILPPHPTD 138

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
            Q LI  +E ++      +   +L+  ER++        +  + + +S + +     V+ 
Sbjct: 139 PQELIVTQEEQSFME--AKMDEILSDLERKVLRLYL---DGRSYQEISDDLD---RHVKS 190

Query: 272 IEARAFKKVQESIQKQVEL 290
           I   A ++V++  ++ V++
Sbjct: 191 I-DNALQRVKKKFERHVDV 208


>gi|323704017|ref|ZP_08115638.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
 gi|323531020|gb|EGB20938.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
          Length = 85

 Score = 62.5 bits (151), Expect = 8e-08,   Method: Composition-based stats.
 Identities = 18/73 (24%), Positives = 32/73 (43%), Gaps = 2/73 (2%)

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRE 267
              +V+ +  E    +N L   +  L+ RE+++ E R         T   ++    +SR 
Sbjct: 3   TDPEVVADMVENAFEKNRLLEKVHKLSRREKKVLEMRFGLGTSARKTQREIARALGISRS 62

Query: 268 RVRQIEARAFKKV 280
            V +IE RA  K+
Sbjct: 63  YVSRIEKRALNKL 75


>gi|302876551|ref|YP_003845184.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           cellulovorans 743B]
 gi|307687223|ref|ZP_07629669.1| RNA polymerase factor sigma-70 [Clostridium cellulovorans 743B]
 gi|302579408|gb|ADL53420.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           cellulovorans 743B]
          Length = 217

 Score = 62.1 bits (150), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 30/155 (19%), Positives = 57/155 (36%), Gaps = 9/155 (5%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            EE VL     + GD  A   L+  +   V   A  Y   G    ++  EG IGL +A++
Sbjct: 19  DEEIVL---VAKDGDSDALEYLINKYKGFVKSKAKSYFLIGADKEDIYQEGMIGLYKAIR 75

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR-LKGHLQAIT 150
            F P +      ++   I   +   I  +     I         + +L + +       T
Sbjct: 76  DFKPHKLASFKAFAEICITRQIITAIKTATRQKHIPL-----NTYISLNKPVYDEESDRT 130

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
             ++     V+  ++L +S  E+  +  ++    S
Sbjct: 131 LMDMLTTLKVSDPEELMISREEIQRIEKQIECVLS 165


>gi|261886377|ref|ZP_06010416.1| flagellar biosynthesis sigma factor [Campylobacter fetus subsp.
           venerealis str. Azul-94]
          Length = 234

 Score = 62.1 bits (150), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 38/241 (15%), Positives = 91/241 (37%), Gaps = 28/241 (11%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
             +   LV S++  +  +A   +      + +++++S G   +++  + +D E+      
Sbjct: 17  KKSQDELVLSYMPALRAMAFRLKSRLPSSIEVNDLISVGATAMVKLSRTYDKEQSDSFWG 76

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y    +  +M +Y+ R    +  G     K +   +       +              +A
Sbjct: 77  YVKQRVYGSMIDYL-RGLDFLSRGNRKLVKDIDSAINEYFNKFE-------CEPDDAYLA 128

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           K L   E+++     R   D S    I+         Q  L+ + D +      K E+  
Sbjct: 129 KILGEDEAKIRE--ARNLSDVSATFPIDE--------QSQLLSESDTES-----KIEKDE 173

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               +T  ++    RE+ I + +  +E  ++L+ +S    ++  R+  I  R   K+++ 
Sbjct: 174 LIQKITDVLNEFGEREQMIIQLKNYEE--LSLKEISDILGITESRISHIHRRLITKIRDR 231

Query: 284 I 284
           +
Sbjct: 232 L 232


>gi|322806811|emb|CBZ04380.1| RNA polymerase sporulation specific sigma factor SigK [Clostridium
           botulinum H04402 065]
          Length = 89

 Score = 62.1 bits (150), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 21/86 (24%), Positives = 38/86 (44%), Gaps = 5/86 (5%)

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENL 258
            D L  D D   +++  K E K     +    + L  RE+++ + R       P T   +
Sbjct: 1   MDILSSDEDSIIEIVSTKIEVKKLYGKID---TCLRGREKKVIQMRYGLKDGRPRTQREI 57

Query: 259 SSEFEVSRERVRQIEARAFKKVQESI 284
           +    +SR  V +IE +A KK+ + +
Sbjct: 58  AGILNISRSYVSRIEKKALKKLYKEL 83


>gi|317970333|ref|ZP_07971723.1| RNA polymerase sigma factor, sigma-70 family protein [Synechococcus
           sp. CB0205]
          Length = 202

 Score = 62.1 bits (150), Expect = 9e-08,   Method: Composition-based stats.
 Identities = 31/151 (20%), Positives = 59/151 (39%), Gaps = 22/151 (14%)

Query: 15  GLSRYIHEIRKIPMLEKQEEYVLAK---RYREH-------------GDLSAAHRLVTSHL 58
            + +++   R+   L ++    LA+   R+++H               L A  +LV  +L
Sbjct: 4   SVRQWLERSRRHAPLPERTVLELARTIQRWQQHPAGPTQAPRAIQKRGLRARDQLVRHNL 63

Query: 59  RLVVKIAMGYRGYGLPIS----EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114
            LV            P      + + E  + L++A +KFDP R +R +TY+ +WI+  + 
Sbjct: 64  ALVGFTWRKQHSGLSPEDAATADALQEAALNLLRAAEKFDPTRSYRFSTYASFWIRRGLL 123

Query: 115 EYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
            +  R    +       Q  L     +L   
Sbjct: 124 RFCQRDRRCIAFPR--EQAALVLKAEQLSEE 152


>gi|258622499|ref|ZP_05717521.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio mimicus VM573]
 gi|258585199|gb|EEW09926.1| flagellar-specific transcription initiation factor sigma, LafS
           [Vibrio mimicus VM573]
          Length = 242

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 29/242 (11%), Positives = 91/242 (37%), Gaps = 31/242 (12%)

Query: 51  HRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           ++L+  H  +V ++      +      I ++   G I L+++ +++         T+++ 
Sbjct: 26  NQLLQRHKIMVKRVVNQLKVHATAYCSIDDMQQIGLIALIESGRRYGDISDPNFPTFAVC 85

Query: 108 WIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            ++ A+ + + R  W           ++       L    + +     +        K L
Sbjct: 86  RVRGAILDELRRLDWRS---------RKTRQQAHELNDITRDLIRALGRQPTDAETIKAL 136

Query: 167 NVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
            ++E +  +          +SL+ LI +  +N                    +  + ++ 
Sbjct: 137 GINEQDYYARQSAALAGELQSLDQLIENGVENQLSGHY--------------DGLKHEHI 182

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L  +++ L+ R++ +       ++ + L  ++   +++  R+ Q+  +A K++ + +
Sbjct: 183 RRSLETALNKLSKRDQLLLTLFY--QHELNLNEIALILDLTSPRICQLHKQALKQLNQYL 240

Query: 285 QK 286
             
Sbjct: 241 SS 242


>gi|212637937|ref|YP_002314457.1| RNA polymerase factor sigma-70 [Anoxybacillus flavithermus WK1]
 gi|212559417|gb|ACJ32472.1| RNA polymerase sigma-30 factor, sigH [Anoxybacillus flavithermus
           WK1]
          Length = 223

 Score = 62.1 bits (150), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 45/259 (17%), Positives = 84/259 (32%), Gaps = 62/259 (23%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           E  +       GD  A   L+  +   V   A  Y   G    ++V EG IGL +A++ F
Sbjct: 24  EDEMIVELVHQGDSEALDYLIHKYKNFVRAKARSYFLVGADREDIVQEGMIGLYKAIRDF 83

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
             ++      ++   I   M   I  +     I                           
Sbjct: 84  KEDKQSSFKAFAELCITRQMITAIKMATRQKHIP-------------------------- 117

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
                       LN      +S++  +  D+S   L++                    E+
Sbjct: 118 ------------LNCY----VSLDKPIYEDDSARTLMDVLSGTKIT----------NPEE 151

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
           ++I +EE  +    +T  +S L   ER++           + + +S E       V+ I 
Sbjct: 152 LIINREEFNHIEEKMTELLSDL---ERKVLLLYL---EGRSYQEISEELN---RHVKSI- 201

Query: 274 ARAFKKVQESIQKQVELSS 292
             A ++V+  ++K VE+  
Sbjct: 202 DNALQRVKRKLEKYVEIQG 220


>gi|293375374|ref|ZP_06621655.1| putative RNA polymerase sigma-H factor [Turicibacter sanguinis
           PC909]
 gi|325844422|ref|ZP_08168149.1| putative RNA polymerase sigma-H factor [Turicibacter sp. HGF1]
 gi|292645927|gb|EFF63956.1| putative RNA polymerase sigma-H factor [Turicibacter sanguinis
           PC909]
 gi|325489096|gb|EGC91480.1| putative RNA polymerase sigma-H factor [Turicibacter sp. HGF1]
          Length = 200

 Score = 61.8 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 22/89 (24%), Positives = 38/89 (42%), Gaps = 1/89 (1%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y L    RE  +  A H ++  +  L+ KIA  Y G G    +   EG +  ++A+  FD
Sbjct: 8   YELVYLVREQ-NEEALHIIIEKYSPLIGKIASSYYGIGYDYQDFFQEGRMAFIKAIYSFD 66

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSL 123
               +   +Y+M  ++ A+     R    
Sbjct: 67  ENSNYSFYSYAMTCVRNAITTSYRRLKRT 95


>gi|237756227|ref|ZP_04584790.1| RNA polymerase sigma factor RpoD [Sulfurihydrogenibium
           yellowstonense SS-5]
 gi|237691619|gb|EEP60664.1| RNA polymerase sigma factor RpoD [Sulfurihydrogenibium
           yellowstonense SS-5]
          Length = 78

 Score = 61.8 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 20/57 (35%), Positives = 29/57 (50%), Gaps = 2/57 (3%)

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEAR 275
            +     L   + VL+ RE+ I + R     E   TLE +  +  +SRERVRQ+E R
Sbjct: 3   EETIHEELESMLDVLDEREKEIIKMRYGLNGEESRTLEEVGEKLGISRERVRQLEQR 59


>gi|88808533|ref|ZP_01124043.1| Possible type 3 alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 7805]
 gi|88787521|gb|EAR18678.1| Possible type 3 alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 7805]
          Length = 198

 Score = 61.8 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 21/93 (22%), Positives = 43/93 (46%), Gaps = 1/93 (1%)

Query: 50  AHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
            ++ V  HL+LV  IA  Y +  G+   ++   G +GL++A + F+ ER      ++   
Sbjct: 8   RNQRVKDHLQLVTPIARHYAQRCGIDADDLRQVGLMGLLRAAENFNTERCTPFKAFARPH 67

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           I+ A+  Y+  + S+V+        +      +
Sbjct: 68  IRGAILHYLRDNASVVRFPRRLQSDKEMNESGK 100


>gi|239825676|ref|YP_002948300.1| RNA polymerase factor sigma-70 [Geobacillus sp. WCH70]
 gi|239805969|gb|ACS23034.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Geobacillus sp.
           WCH70]
          Length = 216

 Score = 61.8 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 42/264 (15%), Positives = 84/264 (31%), Gaps = 66/264 (25%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           LE ++   L       GD  A   L+  +   V   A  Y   G    +++ EG IGL +
Sbjct: 16  LEDEQLVELV----HQGDGDALDFLIHKYQNFVRAKARSYFLVGADREDIIQEGMIGLYK 71

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           AV+ F  ++      ++   I   M   I  +     I                      
Sbjct: 72  AVRDFKGDKLSSFKAFAELCITRQMITAIKTATRQKHIP--------------------- 110

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                                      +N  ++    L+  I   + + +          
Sbjct: 111 ---------------------------LNSYIS----LDRPIYDDESDRTLMDVISGTKA 139

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
              E++++ +EE  +    +T  +S L   ER++        +  + + +S E       
Sbjct: 140 MDPEELIVNREEVDDIEVKMTELLSDL---ERKVLALYL---DGRSYQEISEELN---RH 190

Query: 269 VRQIEARAFKKVQESIQKQVELSS 292
           V+ I   A ++V+  ++K +E   
Sbjct: 191 VKSI-DNALQRVKRKLEKYLEYRE 213


>gi|313115853|ref|ZP_07801286.1| sporulation sigma factor SigK family protein [Faecalibacterium cf.
           prausnitzii KLE1255]
 gi|310621830|gb|EFQ05352.1| sporulation sigma factor SigK family protein [Faecalibacterium cf.
           prausnitzii KLE1255]
          Length = 150

 Score = 61.8 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 35/200 (17%), Positives = 63/200 (31%), Gaps = 64/200 (32%)

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
           GLM+AV  FD  R  R +TY+   I                      +  +    RR   
Sbjct: 1   GLMKAVDTFDSARRARFSTYASRCI----------------------ENEIRMQFRR--- 35

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
                                           N +  G  SL   + S   ++    D L
Sbjct: 36  --------------------------------NRKTGGTVSLQEALESDGDSALTLADVL 63

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEF 262
                     + +  E ++    + + +  L  RER+I   R     + P+T    +   
Sbjct: 64  QD-----SFCMEDTCETQDDIRRMRQLLDGLPARERQIILLRYGLSGQPPLTQLETAKLL 118

Query: 263 EVSRERVRQIEARAFKKVQE 282
           ++SR  V ++E  A + +++
Sbjct: 119 DISRSYVSRLETHALELLRQ 138


>gi|168207186|ref|ZP_02633191.1| RNA polymerase sigma-B factor [Clostridium perfringens E str.
           JGS1987]
 gi|170661420|gb|EDT14103.1| RNA polymerase sigma-B factor [Clostridium perfringens E str.
           JGS1987]
          Length = 184

 Score = 61.8 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 32/217 (14%), Positives = 84/217 (38%), Gaps = 56/217 (25%)

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ-EYILRSWSLVKIG 127
           +   +   EV+S   +GL++A  +FD ++GF+ +TY+M  ++  ++ +Y       ++  
Sbjct: 21  KNSSMNFEEVLSAAMLGLVKAANRFDEKKGFKFSTYAMSTMRGQIKNDYYHDKNRFIR-- 78

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
                KR                           I +K+++S               SLN
Sbjct: 79  -----KRNGNT----------------------EIYEKVSIS---------------SLN 96

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             +  + +   +  D L  + +   +++         +  L  ++S L   ++++ +   
Sbjct: 97  DTLPLNLEKDVELIDTLPSNFEIDNEIV---------KLDLKNAISKLPDLQKQVIKIIF 147

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            Q    T    +     ++ ++ +I+ RA + +++ +
Sbjct: 148 FQG--KTQNEAAKLLGTNQVQISRIKNRAIESLRKIL 182


>gi|317054637|ref|YP_004119704.1| hypothetical protein p3521_p048 [Escherichia coli]
 gi|284433167|gb|ADB84906.1| hypothetical protein [Escherichia coli]
          Length = 528

 Score = 61.8 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 16/61 (26%), Positives = 33/61 (54%), Gaps = 2/61 (3%)

Query: 219 EERKNRRNMLTRSMSVL-NPRERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARA 276
            +  +   ++  ++  L N R + I   R   ++ P +L +++ +  +SRERVRQ++ RA
Sbjct: 132 ADEHDVIMLIHSAIESLSNKRHQYILLMRLGTDDSPHSLADIAVKLGISRERVRQLQERA 191

Query: 277 F 277
            
Sbjct: 192 L 192


>gi|300857263|ref|YP_003782247.1| RNA polymerase sigma-H factor [Clostridium ljungdahlii DSM 13528]
 gi|300437378|gb|ADK17145.1| RNA polymerase sigma-H factor [Clostridium ljungdahlii DSM 13528]
          Length = 213

 Score = 61.8 bits (149), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 35/192 (18%), Positives = 80/192 (41%), Gaps = 7/192 (3%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + GD+SA   L+  +   V   +  Y   G    ++  EG IGL +A++ F P++    
Sbjct: 26  AKKGDVSAQEYLINKYGNFVKSKSKSYFLIGADKEDIYQEGMIGLYKAIRDFKPDKLSSF 85

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQAITDNNLK-PEQ 158
             ++   +   +   I  +     I   T  +  +  ++    +  L  +++  +  PE+
Sbjct: 86  KAFAELCVTRQIITAIKTATRQKHIPLNTYISLNKPIYDEESDRTLLDVLSETKVADPEE 145

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           +V   ++LN  +SE+  +   L     +  L++  D  S Q     +  H       +++
Sbjct: 146 LVIGREELNHIQSEIGEVLSNL----EMEVLMSYVDGKSYQEIACDLDRHAKSIDNALQR 201

Query: 219 EERKNRRNMLTR 230
            +RK  + ++ +
Sbjct: 202 VKRKLEKCLIHK 213


>gi|300973581|ref|ZP_07172278.1| sigma-70, region 4 [Escherichia coli MS 200-1]
 gi|301030086|ref|ZP_07193035.1| sigma-70, region 4 [Escherichia coli MS 196-1]
 gi|305667846|ref|YP_003864320.1| putative RNA polymerase sigma factor [Escherichia coli]
 gi|309783634|ref|ZP_07678284.1| sigma-70, region 4 family protein [Shigella dysenteriae 1617]
 gi|299877172|gb|EFI85383.1| sigma-70, region 4 [Escherichia coli MS 196-1]
 gi|300309083|gb|EFJ63603.1| sigma-70, region 4 [Escherichia coli MS 200-1]
 gi|304655595|emb|CBM42259.1| putative RNA polymerase sigma factor [Escherichia coli]
 gi|308928530|gb|EFP73987.1| sigma-70, region 4 family protein [Shigella dysenteriae 1617]
 gi|324010801|gb|EGB80020.1| sigma-70, region 4 [Escherichia coli MS 60-1]
          Length = 528

 Score = 61.4 bits (148), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 16/61 (26%), Positives = 33/61 (54%), Gaps = 2/61 (3%)

Query: 219 EERKNRRNMLTRSMSVL-NPRERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARA 276
            +  +   ++  ++  L N R + I   R   ++ P +L +++ +  +SRERVRQ++ RA
Sbjct: 132 ADEHDVIMLIHSAIESLSNKRHQYILLMRLGTDDSPHSLADIAVKLGISRERVRQLQERA 191

Query: 277 F 277
            
Sbjct: 192 L 192


>gi|237749638|ref|ZP_04580118.1| RNA polymerase sigma-K factor [Helicobacter bilis ATCC 43879]
 gi|229374766|gb|EEO25157.1| RNA polymerase sigma-K factor [Helicobacter bilis ATCC 43879]
          Length = 104

 Score = 61.4 bits (148), Expect = 1e-07,   Method: Composition-based stats.
 Identities = 16/79 (20%), Positives = 35/79 (44%), Gaps = 2/79 (2%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSE 261
           L+     + + +I+  +       + + + +L+ RE+ +   R   +     T   ++ E
Sbjct: 8   LLDVLKAENEDVIDTIQLNMELEKVKKYIDILDGREKEVIVGRFGLDLKKEKTQREIAKE 67

Query: 262 FEVSRERVRQIEARAFKKV 280
             +SR  V +IE RA  K+
Sbjct: 68  LGISRSYVSRIEKRALMKM 86


>gi|262173365|ref|ZP_06041042.1| RNA polymerase sigma factor for flagellar operon [Vibrio mimicus
           MB-451]
 gi|261890723|gb|EEY36710.1| RNA polymerase sigma factor for flagellar operon [Vibrio mimicus
           MB-451]
          Length = 242

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 29/242 (11%), Positives = 90/242 (37%), Gaps = 31/242 (12%)

Query: 51  HRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           ++L+  H  +V ++      +      I ++   G I L+++ +++         T+++ 
Sbjct: 26  NQLLQRHKIMVKRVVNQLKVHATAYCSIDDMQQIGLIALIESGRRYGDISDPNFPTFAVC 85

Query: 108 WIKAAMQEYILR-SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            ++ A+ + + R  W           ++       L    + +     +        K L
Sbjct: 86  RVRGAILDELRRLDWRS---------RKTRQQAHELNDITRDLIRALGRQPTDAETIKAL 136

Query: 167 NVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
             +E +  +          +SL+ LI +  +N                    +  + ++ 
Sbjct: 137 GTNEQDYYARQSAALAGELQSLDQLIENGVENQLSGHY--------------DGLKHEHI 182

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R  L  +++ L+ R++ +       ++ + L  ++   +++  R+ Q+  +A K++ + +
Sbjct: 183 RRSLETALNKLSKRDQLLLTLFY--QHELNLNEIALILDLTSPRICQLHKQALKQLNQYL 240

Query: 285 QK 286
             
Sbjct: 241 SS 242


>gi|226201088|ref|YP_002756700.1| hypothetical protein p026VIR_p149 [Escherichia coli]
 gi|219881717|gb|ACL52087.1| hypothetical protein [Escherichia coli]
          Length = 528

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 16/61 (26%), Positives = 33/61 (54%), Gaps = 2/61 (3%)

Query: 219 EERKNRRNMLTRSMSVL-NPRERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARA 276
            +  +   ++  ++  L N R + I   R   ++ P +L +++ +  +SRERVRQ++ RA
Sbjct: 132 ADEHDVIMLIHSAIESLSNKRHQYILLMRLGTDDSPHSLADIAVKLGISRERVRQLQERA 191

Query: 277 F 277
            
Sbjct: 192 L 192


>gi|289809217|ref|ZP_06539846.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. AG3]
          Length = 52

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 22/51 (43%), Positives = 30/51 (58%), Gaps = 1/51 (1%)

Query: 226 NMLTRSMSVLNPRERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEAR 275
           N LT +M  L+ R + I  AR L E+   TL+ L+  + VS ERVRQ+E  
Sbjct: 2   NRLTDAMQGLDERSQDIIRARWLDEDNKSTLQELADRYGVSAERVRQLEKN 52


>gi|297528465|ref|YP_003669740.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Geobacillus sp.
           C56-T3]
 gi|297251717|gb|ADI25163.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Geobacillus sp.
           C56-T3]
          Length = 227

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 41/249 (16%), Positives = 76/249 (30%), Gaps = 62/249 (24%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GD  A   L+  +   V   A  Y   G    ++V EG IGL +AV+ F  ++      
Sbjct: 38  EGDGEALDFLIHKYQNFVRAKARSYFLVGADREDIVQEGMIGLYKAVRDFKGDKLSSFKA 97

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           ++   I   M   I  +     I   +                                 
Sbjct: 98  FAELCITRQMITAIKTATRQKHIPLNSY-------------------------------- 125

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
                     +S++  +  DES                D L        + LI   E  +
Sbjct: 126 ----------VSLDKPIYDDES-----------DRTLMDVLSGTQVTDPEQLIVNREEVD 164

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
              +  +   +L+  ER++        +  + + +S E       V+ I   A ++V+  
Sbjct: 165 DIEL--KMAELLSDLERKVLALYL---DGRSYQEISEELN---RHVKSI-DNALQRVKRK 215

Query: 284 IQKQVELSS 292
           ++K +E   
Sbjct: 216 LEKYLEYRE 224


>gi|295401937|ref|ZP_06811900.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|312109244|ref|YP_003987560.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Geobacillus sp.
           Y4.1MC1]
 gi|294976067|gb|EFG51682.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|311214345|gb|ADP72949.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Geobacillus sp.
           Y4.1MC1]
          Length = 216

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 44/261 (16%), Positives = 87/261 (33%), Gaps = 66/261 (25%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           LE ++   L       GD  A   L+  +   V   A  Y   G    +++ EG IGL +
Sbjct: 16  LEDEQLVELV----HQGDGDALDFLIHKYQNFVRAKARSYFLVGADREDIIQEGMIGLYK 71

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           AV+ F  ++      ++   I   M   I  +     I   +                  
Sbjct: 72  AVRDFKGDKLSSFKAFAELCITRQMITAIKTATRQKHIPLNSY----------------- 114

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                                    +S++  +  DES   L++      +          
Sbjct: 115 -------------------------VSLDKPIYDDESDRTLMDVISGTKAT--------- 140

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
              E++++ +EE  +    +T  +S L   ER++        +  + + +S E       
Sbjct: 141 -DPEELIVNREEVDDIEVKMTELLSDL---ERKVLALYL---DGRSYQEISEELN---RH 190

Query: 269 VRQIEARAFKKVQESIQKQVE 289
           V+ I   A ++V+  ++K +E
Sbjct: 191 VKSI-DNALQRVKRKLEKYLE 210


>gi|295104067|emb|CBL01611.1| RNA polymerase sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii SL3/3]
          Length = 220

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 47/259 (18%), Positives = 93/259 (35%), Gaps = 67/259 (25%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAM-GYRGYG-------LPISEVVSEGNIGLMQAVK 91
           R  + GD +A   L+  +L  + KIA+  YR  G       + + +++ EG+IGL+ A+ 
Sbjct: 11  RLAQKGDTAARDILLEKNLGFIRKIALEQYRNMGLDENDIGIDLDDLMQEGSIGLLNAIP 70

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
            FD  RG +  TY+   ++ AM + I                         +  L     
Sbjct: 71  LFDAGRGMKFLTYAAPALRNAMTDCI-------------------------RAALGLFEQ 105

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
             +  +      +   V   +V+S + R+   E++                      D  
Sbjct: 106 RMVDKKDGPGFQR---VYLDDVLSEDERMLRIEAI---------------------ADPH 141

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR----LQENPVTLENLSS--EFEVS 265
            Q   +   +K +   L  ++  L  RE+     R       E+P+    + +   F +S
Sbjct: 142 TQTPEQIYIQKEQLIELYAALDNLTAREQTYLLYRYGFTDGIEHPL----IGAALHFHLS 197

Query: 266 RERVRQIEARAFKKVQESI 284
               +++E  A   ++  +
Sbjct: 198 ESWTKKVEGEAMDSLRGKL 216


>gi|295105020|emb|CBL02564.1| DNA-directed RNA polymerase specialized sigma subunit
           [Faecalibacterium prausnitzii SL3/3]
          Length = 157

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 26/90 (28%), Positives = 44/90 (48%), Gaps = 8/90 (8%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMG--------YRGYGLPISEVVSEGNIGLMQAVKKF 93
            + GD  A + LV ++LR + K A              G+ ++++V EG++GL+  +  F
Sbjct: 13  AQSGDKWAENALVENNLRFIRKTAYEIWSAQRELNVALGIELNDLVQEGSLGLLGCISSF 72

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSL 123
            P+ G +  TY+   I  AM +YI R    
Sbjct: 73  QPDYGNKFLTYAAPAIHNAMLDYIRRLNPT 102


>gi|197250155|ref|YP_002147819.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
 gi|197213858|gb|ACH51255.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Agona str. SL483]
          Length = 68

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 20/58 (34%), Positives = 33/58 (56%), Gaps = 2/58 (3%)

Query: 232 MSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           M  LN ++R +   R   L     TLE++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 1   MFELNAKQREVLARRFGLLGYEAATLEDVGREIGLTRERVRQIQVEGLRRLREILQTQ 58


>gi|51038841|gb|AAT94221.1| hypothetical protein [Escherichia coli]
          Length = 528

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 16/61 (26%), Positives = 33/61 (54%), Gaps = 2/61 (3%)

Query: 219 EERKNRRNMLTRSMSVL-NPRERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARA 276
            +  +   ++  ++  L N R + I   R   ++ P +L +++ +  +SRERVRQ++ RA
Sbjct: 132 ADEHDVIMLIHSAIESLSNKRHQYILLMRLGTDDSPHSLADIAVKLGISRERVRQLQERA 191

Query: 277 F 277
            
Sbjct: 192 L 192


>gi|300940820|ref|ZP_07155355.1| sigma-70, region 4 [Escherichia coli MS 21-1]
 gi|300454422|gb|EFK17915.1| sigma-70, region 4 [Escherichia coli MS 21-1]
          Length = 528

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 16/61 (26%), Positives = 33/61 (54%), Gaps = 2/61 (3%)

Query: 219 EERKNRRNMLTRSMSVL-NPRERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARA 276
            +  +   ++  ++  L N R + I   R   ++ P +L +++ +  +SRERVRQ++ RA
Sbjct: 132 ADEHDVIMLIHSAIESLSNKRHQYILLMRLGTDDSPHSLADIAVKLGISRERVRQLQERA 191

Query: 277 F 277
            
Sbjct: 192 L 192


>gi|11466545|ref|NP_044794.1| transcription initiation factor sigma [Reclinomonas americana]
 gi|2258375|gb|AAD11909.1| transcription initiation factor sigma [Reclinomonas americana]
          Length = 532

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 25/113 (22%), Positives = 54/113 (47%), Gaps = 3/113 (2%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR--GYGLPISEVVSEGNIGLMQAVKKFD 94
           L    RE+  ++  +R++ +++  +  I+  Y   GY    S+++ EG  G+  A +KF 
Sbjct: 340 LISILRENIKVTLKNRIIFNYMPYITTISKQYVKIGYQAQFSDLIQEGISGVSDAAEKFQ 399

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR-LFFNLRRLKGHL 146
             RG R  TY+ WW+   M +  ++    ++       ++ L   + +L+  +
Sbjct: 400 LGRGVRFLTYAYWWMHNYMMKATIKKKKKLRFNEHETPRKELLLKIEKLQTEI 452


>gi|85057474|ref|YP_456390.1| RNA polymerase sigma factor [Aster yellows witches'-broom
           phytoplasma AYWB]
 gi|84789579|gb|ABC65311.1| RNA polymerase sigma factor [Aster yellows witches'-broom
           phytoplasma AYWB]
          Length = 208

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 24/85 (28%), Positives = 45/85 (52%), Gaps = 3/85 (3%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI--SEVVSEGNIGLMQAVKKFDPERG 98
            +   +L   ++L+  HL LV K+A  ++ Y   +   ++  EG +GL++A+  +  + G
Sbjct: 11  LKNKKNLEIRNQLIELHLPLVKKLAYHFKYYPKVLTKEDLYQEGILGLIKALNNYQ-DLG 69

Query: 99  FRLATYSMWWIKAAMQEYILRSWSL 123
           +   TY+   IK A+ E I +S S 
Sbjct: 70  YDFVTYATPKIKFAINELIRKSHSP 94


>gi|283133054|dbj|BAI63821.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           tabaci]
          Length = 115

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 17/100 (17%), Positives = 37/100 (37%), Gaps = 8/100 (8%)

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           S + L+   D       + L  D            E +  +  L  +++ L  RER +  
Sbjct: 18  SFDDLLQDGD------HEGLHEDGASGSLEPSRDLEDERFQAALADAIANLPERERLVLA 71

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                +  + L+ +     VS  RV Q+ ++   +++  +
Sbjct: 72  LYY--DEELNLKEIGEVLGVSESRVSQLHSQCAARLRGRL 109


>gi|148243883|ref|YP_001220122.1| sigma-70 region 4 domain-containing protein [Acidiphilium cryptum
           JF-5]
 gi|146400446|gb|ABQ28980.1| sigma-70 region 4 domain protein [Acidiphilium cryptum JF-5]
          Length = 894

 Score = 61.4 bits (148), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 19/56 (33%), Positives = 34/56 (60%), Gaps = 2/56 (3%)

Query: 236 NPRERRIFEARRLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKV-QESIQKQVE 289
           N ++ +I   R    + P TL+ +S+   +++ERVRQIE  A K + +E  +++VE
Sbjct: 289 NEKQAQILAMRYGFFDKPATLDVVSNTVGITKERVRQIEVEAVKHLGREPSRQKVE 344


>gi|210611678|ref|ZP_03288975.1| hypothetical protein CLONEX_01165 [Clostridium nexile DSM 1787]
 gi|210151925|gb|EEA82932.1| hypothetical protein CLONEX_01165 [Clostridium nexile DSM 1787]
          Length = 254

 Score = 61.0 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 41/159 (25%), Positives = 72/159 (45%), Gaps = 10/159 (6%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ +I  I   +++E   L ++  E GD  A  RLV  +L  VV+IA       + +
Sbjct: 90  LKEYMKDIGGIREADEEEREALFEKVLE-GDALAKSRLVEIYLPEVVEIAKQLYHPEVFL 148

Query: 76  SEVVSEGNIGLMQAVKKF-DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++V EGN+GL+  V    D ++   +       I+ A+Q  I     L         K+
Sbjct: 149 GDLVQEGNVGLILGVDMIDDLDKAHDVIR---REIRQAIQMLIEEQTEL-----KNRDKK 200

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
           +   +  L   +QA+T+   +   +  +A  + +SE EV
Sbjct: 201 MVEKVNTLDESIQALTEELGRKVTIEELAVYMGMSEEEV 239


>gi|158319526|ref|YP_001512033.1| RNA polymerase factor sigma-70 [Alkaliphilus oremlandii OhILAs]
 gi|158139725|gb|ABW18037.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Alkaliphilus
           oremlandii OhILAs]
          Length = 213

 Score = 61.0 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 29/143 (20%), Positives = 58/143 (40%), Gaps = 3/143 (2%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             + GDL A   L+  +   V   A  Y   G    ++V EG IGL +A++ F P++   
Sbjct: 23  IAKEGDLEALEYLIKKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDFKPDKLSS 82

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQAITDNNLK-PE 157
              ++   I   +   I  +     I   +  +  +  ++    +  L  I+   +  PE
Sbjct: 83  FRAFAELCITRQIITAIKTATRQKHIPLNSYVSLNKPIYDEESDRTLLDVISGQKVTDPE 142

Query: 158 QVVAIAKKLNVSESEVISMNCRL 180
           ++V   ++L   E ++  +   L
Sbjct: 143 ELVVSREELGHIEDKIGEILSDL 165


>gi|297545332|ref|YP_003677634.1| ECF subfamily RNA polymerase sigma-24 subunit [Thermoanaerobacter
           mathranii subsp. mathranii str. A3]
 gi|296843107|gb|ADH61623.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermoanaerobacter
           mathranii subsp. mathranii str. A3]
          Length = 214

 Score = 61.0 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 39/262 (14%), Positives = 89/262 (33%), Gaps = 64/262 (24%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           +EE V+ +   + GD +A   L+  +   V   A  Y   G    +++ EG IGL +A++
Sbjct: 17  EEEEVVFR--AQKGDEAALEYLLERYKSFVKAKARAYFLVGADKEDIMQEGMIGLYKAIR 74

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
            +  ++      ++   +   +   I  +     I                         
Sbjct: 75  DYKSDKLSSFKAFAELCVTRQIITAIKTATRQKHIP------------------------ 110

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
                                   +N  ++    LN  I   + + +             
Sbjct: 111 ------------------------LNSYIS----LNKPIFDEESDRTLLDVVSTQCIADP 142

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E+++I KEE  N  N +   +S L   E  +  +     +  + + ++ +       V+ 
Sbjct: 143 EELIISKEEYVNIENKMEELLSGL---EWEVLVSYL---DGKSYQEIAEDLN---RHVKS 193

Query: 272 IEARAFKKVQESIQKQVELSSS 293
           I   A ++V+  +++ +E+ +S
Sbjct: 194 I-DNALQRVKRKLERYLEMRNS 214


>gi|237785799|ref|YP_002906504.1| hypothetical protein ckrop_1216 [Corynebacterium kroppenstedtii DSM
           44385]
 gi|237758711|gb|ACR17961.1| hypothetical protein ckrop_1216 [Corynebacterium kroppenstedtii DSM
           44385]
          Length = 655

 Score = 61.0 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 19/87 (21%), Positives = 33/87 (37%), Gaps = 6/87 (6%)

Query: 187 NALINSSDKNSSQWQDWL-VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           +A    ++   +     +   D         E+  R     +L       + RE+ I   
Sbjct: 96  DAPTYINEAVDNALASSVTASDSWAIGIPPAERAAR-----LLETIFVQFSDREQEILYR 150

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQI 272
           R    +  TLEN+     ++RER+RQI
Sbjct: 151 RYGDGHEETLENIGHAVGLTRERIRQI 177


>gi|39939186|ref|NP_950952.1| DNA-directed RNA polymerase specialized sigma subunit [Onion
           yellows phytoplasma OY-M]
 gi|39722295|dbj|BAD04785.1| DNA-directed RNA polymerase specialized sigma [Onion yellows
           phytoplasma OY-M]
          Length = 228

 Score = 61.0 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 21/85 (24%), Positives = 42/85 (49%), Gaps = 3/85 (3%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI--SEVVSEGNIGLMQAVKKFDPERG 98
            +   +     +L+  HL LV KI+  ++ Y   +   ++  EG +GL++A+  +  + G
Sbjct: 35  LKNKKNFEIRDQLIELHLPLVKKISSKFKYYPKLLTKEDLYQEGVLGLIKALDNYQ-DLG 93

Query: 99  FRLATYSMWWIKAAMQEYILRSWSL 123
           +    Y+   IK+ + E I +S S 
Sbjct: 94  YDFIAYATPTIKSTINELIRKSHSP 118


>gi|39939022|ref|NP_950788.1| DNA-directed RNA polymerase specialized sigma subunit [Onion
           yellows phytoplasma OY-M]
 gi|39722131|dbj|BAD04621.1| DNA-directed RNA polymerase specialized sigma [Onion yellows
           phytoplasma OY-M]
          Length = 228

 Score = 61.0 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 21/85 (24%), Positives = 42/85 (49%), Gaps = 3/85 (3%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI--SEVVSEGNIGLMQAVKKFDPERG 98
            +   +     +L+  HL LV KI+  ++ Y   +   ++  EG +GL++A+  +  + G
Sbjct: 35  LKNKKNFEIRDQLIELHLPLVKKISSKFKYYPKLLTKEDLYQEGILGLIKALDNYQ-DLG 93

Query: 99  FRLATYSMWWIKAAMQEYILRSWSL 123
           +    Y+   IK+ + E I +S S 
Sbjct: 94  YDFIAYATPTIKSTINELIRKSHSP 118


>gi|298243769|ref|ZP_06967576.1| RNA polymerase sigma factor, sigma-70 family [Ktedonobacter
           racemifer DSM 44963]
 gi|297556823|gb|EFH90687.1| RNA polymerase sigma factor, sigma-70 family [Ktedonobacter
           racemifer DSM 44963]
          Length = 453

 Score = 61.0 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 41/305 (13%), Positives = 97/305 (31%), Gaps = 73/305 (23%)

Query: 1   MNRKNMSIIVNGE--IGLSRYIHEIRKIPMLEKQEEYVLAKRYRE-----HGDLSAA--- 50
           M+   M +    +      +Y+ +I   P L   ++  L ++ +           A    
Sbjct: 1   MSTTTMILSAPEDCTDFYRQYLADISIHPPLVNNQDDRLVQQLKALRNDPTRQDEARAIV 60

Query: 51  HRLVTSHLRLVVKIAMGYRGYGL---------PISEVVSEGNIGLMQAVKKF--DPERGF 99
            +L+   LRLV+ +A  +  Y           P+ +++  GN+ L++   ++        
Sbjct: 61  QQLIEGSLRLVIFVAARFYRYYRALDGGRFRVPLMDLIQTGNMALVECAHRYLDREAEHT 120

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
             + Y+  +I+ A+++  +R  SL K+                +       +        
Sbjct: 121 DFSAYAASYIRFALRKSYIR-ASLFKVP---------------QAEWDEAAEQGR----- 159

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
                              +     SL+     SD+++    D L        +      
Sbjct: 160 -----------------LFQFYEVSSLDQPF--SDESTRSLLDCL--------ETPEPLS 192

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQE----NPVTLENLSSEFEVSRERVRQIEAR 275
           E           ++ +  RE+++   R   +       T + ++ +   S +    IE R
Sbjct: 193 ENTQACERAETLLARVPEREQQVVRLRYGLDPLDQRTHTYQEIADKIGASVQTCLNIEQR 252

Query: 276 AFKKV 280
             + +
Sbjct: 253 VLQAL 257


>gi|326566649|gb|EGE16790.1| RNA polymerase sigma factor 70 [Moraxella catarrhalis 12P80B1]
          Length = 48

 Score = 61.0 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 15/36 (41%), Positives = 26/36 (72%)

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             TLE +  +F+V+RER+RQIEA+A +K++   + +
Sbjct: 4   DHTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSE 39


>gi|325510557|gb|ADZ22193.1| RNA polymerase factor sigma-70 [Clostridium acetobutylicum EA 2018]
          Length = 212

 Score = 61.0 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 40/255 (15%), Positives = 82/255 (32%), Gaps = 65/255 (25%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            EE V+     + GD  +   L+  +   V   A  Y   G    ++  EG IGL +A++
Sbjct: 18  DEEIVM---MAKLGDEKSQEYLINKYSNFVKVKAKSYFLIGADKEDICQEGMIGLYKAIR 74

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
            F P +      ++   I   +   I  +     I                         
Sbjct: 75  DFKPSKLASFKAFAEICITRQIITAIKTATRQKHIP------------------------ 110

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
                                   +N  ++    LN  I   D + + +      +    
Sbjct: 111 ------------------------LNTYVS----LNKPIYDEDSDRTLFDVVSSVEVSDP 142

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E+++I KEE    R  + + +S L   E  + E+        + + ++ + +    R  +
Sbjct: 143 EELIISKEEVAKIRKNMLKVLSSL---EIEVLESYL---EGKSYQEIAKDLD----RCSK 192

Query: 272 IEARAFKKVQESIQK 286
               A ++V+  ++K
Sbjct: 193 SIDNALQRVKRKLEK 207


>gi|138893768|ref|YP_001124221.1| RNA polymerase factor sigma-70 [Geobacillus thermodenitrificans
           NG80-2]
 gi|196251121|ref|ZP_03149800.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Geobacillus sp.
           G11MC16]
 gi|134265281|gb|ABO65476.1| RNA polymerase sigma-30 factor [Geobacillus thermodenitrificans
           NG80-2]
 gi|196209362|gb|EDY04142.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Geobacillus sp.
           G11MC16]
          Length = 216

 Score = 61.0 bits (147), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 44/271 (16%), Positives = 83/271 (30%), Gaps = 66/271 (24%)

Query: 22  EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
            +R    L+ ++   L       GD  A   L+  +   V   A  Y   G    ++V E
Sbjct: 9   NVRDYQKLDDEQLVALV----HQGDGEALDFLIHKYQNFVRAKARSYFLVGADREDIVQE 64

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           G IGL +AV+ F  ++      ++   I   M   I  +     I   +           
Sbjct: 65  GMIGLYKAVRDFKGDKLSSFKAFAELCITRQMITAIKTATRQKHIPLNSY---------- 114

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
                                           +S++  +  DES                
Sbjct: 115 --------------------------------VSLDKPIYDDES-----------DRTLM 131

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           D L        + LI   E  +   +  +   +L+  ER++        +  + + +S E
Sbjct: 132 DVLSGTQATDPEELIVNREEVDDIEL--KMAELLSDLERKVLALYL---DGRSYQEISEE 186

Query: 262 FEVSRERVRQIEARAFKKVQESIQKQVELSS 292
                  V+ I   A ++V+  ++K +E   
Sbjct: 187 LN---RHVKSI-DNALQRVKRKLEKYLEYRE 213


>gi|284989337|ref|YP_003407891.1| sigma-70 region 4 domain-containing protein [Geodermatophilus
           obscurus DSM 43160]
 gi|284062582|gb|ADB73520.1| sigma-70 region 4 domain protein [Geodermatophilus obscurus DSM
           43160]
          Length = 896

 Score = 60.6 bits (146), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 24/117 (20%), Positives = 42/117 (35%), Gaps = 12/117 (10%)

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           L    SL  L   +           V D +     L      +   ++L  ++     + 
Sbjct: 381 LGRAASLGDLFEDAGPPDLTRLRRTVEDAEHILHWLKGFTLEEEAESVLRAALGKSADKW 440

Query: 240 RRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSP 294
                +R      +P TL+ +     V+RERVRQ++++A          Q  L S+P
Sbjct: 441 LEALGSRYGLAGADPQTLDEVGRTLGVTRERVRQVQSKA----------QAHLPSAP 487


>gi|239623611|ref|ZP_04666642.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47_FAA]
 gi|239521642|gb|EEQ61508.1| conserved hypothetical protein [Clostridiales bacterium 1_7_47FAA]
          Length = 197

 Score = 60.6 bits (146), Expect = 2e-07,   Method: Composition-based stats.
 Identities = 42/187 (22%), Positives = 81/187 (43%), Gaps = 12/187 (6%)

Query: 17  SRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS 76
             Y+ E+  I  L  QE+  L K   + G+  A +RLV   LR V+ +A  Y G  LP+S
Sbjct: 7   EMYLEEMGGIAPLTGQEKPELLKETAK-GNAGARNRLVEGSLRHVLNLAAEYEGRELPMS 65

Query: 77  EVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
           ++V E N  LM A  ++D    +   +     ++ A++  +    +  +I  T   +   
Sbjct: 66  DIVQEANTALMLAAIEYDGSEEWD--SLLARRVREAVELALEEQKAEAEIEETMAAR--- 120

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN----ALINS 192
             +  L+   Q +     +   +  +A K+ ++E E+  +        ++N    A +++
Sbjct: 121 --VNVLQTVSQMLARELGREATLQELAAKMKMTEDEIKDIMKLALDALTVNGEGQAFVDT 178

Query: 193 SDKNSSQ 199
            D   S 
Sbjct: 179 EDDTDSS 185


>gi|150392177|ref|YP_001322226.1| RNA polymerase factor sigma-70 [Alkaliphilus metalliredigens QYMF]
 gi|149952039|gb|ABR50567.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Alkaliphilus
           metalliredigens QYMF]
          Length = 213

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 28/142 (19%), Positives = 59/142 (41%), Gaps = 3/142 (2%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + GDL+A   L+  +   V   A  Y   G    ++V EG IGL +A++ F P++    
Sbjct: 24  AKDGDLAALEFLIKKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDFKPDKLSSF 83

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQAITDNNLK-PEQ 158
             ++   I   +   I  +     I   +  +  +  ++    +  L  I+   +  PE+
Sbjct: 84  RAFAELCITRQIITAIKTATRQKHIPLNSYVSLNKPIYDEESDRTLLDVISGQKVTDPEE 143

Query: 159 VVAIAKKLNVSESEVISMNCRL 180
           ++   ++L   E ++  +   L
Sbjct: 144 LIICREELGHIEGKIGEILSDL 165


>gi|113954672|ref|YP_730552.1| type 3 alternative RNA polymerase sigma factor [Synechococcus sp.
           CC9311]
 gi|113882023|gb|ABI46981.1| Possible type 3 alternative RNA polymerase sigma factor
           [Synechococcus sp. CC9311]
          Length = 218

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 43/241 (17%), Positives = 87/241 (36%), Gaps = 36/241 (14%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGY-GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           +  ++ +  HL+LV  IA  Y    GL   ++   G +GL++A + ++  +      Y+ 
Sbjct: 6   ALRNQRIERHLKLVDPIAGHYAKRSGLDRDDLKQVGMLGLLRAAEGYEQGQEKPFEVYAR 65

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ A+  Y+  S  LV++             RRL+   Q    N+    Q        
Sbjct: 66  PHIRGAILHYLRDSVGLVRLP------------RRLQEQAQNTIKNSTAEPQRRQAM--- 110

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
                             S    +N       Q  + L       +    +   R+ R  
Sbjct: 111 ------------------SAELELNVHAYRCRQTWEPLDEGRVAADVPGWQPLLRQERAK 152

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            + ++++ L P E+R      L     +L    ++  VS   +++   RA  ++++ +  
Sbjct: 153 RIWKAINRLAPSEKRALNEVVL--EGASLRGAGTKLGVSAMTMQRRLKRALAQLRQELAD 210

Query: 287 Q 287
           Q
Sbjct: 211 Q 211


>gi|150015027|ref|YP_001307281.1| RNA polymerase factor sigma-70 [Clostridium beijerinckii NCIMB
           8052]
 gi|149901492|gb|ABR32325.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           beijerinckii NCIMB 8052]
          Length = 223

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 36/198 (18%), Positives = 77/198 (38%), Gaps = 7/198 (3%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           +K +E ++AK   + G+  A   L++ +   V   A  Y   G    ++  EG IGL +A
Sbjct: 26  DKSDEEIVAK--AKSGNSRAQEYLISKYENFVKSKAKSYFLIGADKEDIYQEGMIGLYKA 83

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQ 147
           ++ F+ E+      ++   +   +   I  +     I   T  +  +  +     +  L 
Sbjct: 84  IRDFNAEKSTSFKAFAEICVIRQIITAIKTATRQKHIPLNTYVSLNKPIYEEESERTLLD 143

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
            +    +   + + I+K+      + IS   ++  D  L  L +  D  S Q     +  
Sbjct: 144 VLAGLKISDPEELMISKEQMDYIEKKIS---KVLSDLELEVLTSYLDGKSYQEIASDLER 200

Query: 208 HDGQEQVLIEKEERKNRR 225
           H       +++ +RK  +
Sbjct: 201 HSKSIDNALQRVKRKLEK 218


>gi|73853219|ref|YP_308715.1| hypothetical protein LH0044 [Escherichia coli]
 gi|33414081|gb|AAQ17636.1| hypothetical protein LH0044 [Escherichia coli]
          Length = 320

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 16/61 (26%), Positives = 33/61 (54%), Gaps = 2/61 (3%)

Query: 219 EERKNRRNMLTRSMSVL-NPRERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARA 276
            +  +   ++  ++  L N R + I   R   ++ P +L +++ +  +SRERVRQ++ RA
Sbjct: 132 ADEHDVIMLIHSAIESLSNKRHQYILLMRLGTDDSPHSLADIAVKLGISRERVRQLQERA 191

Query: 277 F 277
            
Sbjct: 192 L 192


>gi|332753464|gb|EGJ83844.1| RNA polymerase sigma factor rpoS domain protein [Shigella flexneri
           4343-70]
          Length = 114

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 21/47 (44%), Positives = 31/47 (65%), Gaps = 1/47 (2%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
           Y+ EI   P+L  +EE   A+R    GD+++  R++ S+LRLVVKIA
Sbjct: 61  YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRRMIESNLRLVVKIA 106


>gi|320120593|gb|EFE29148.2| RNA polymerase sigma-H factor [Filifactor alocis ATCC 35896]
          Length = 227

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 37/232 (15%), Positives = 76/232 (32%), Gaps = 62/232 (26%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           +++   LA++    GD  A   + T ++ LV   A  Y   G    ++V EG IGL +A+
Sbjct: 29  EEQIVHLAQK----GDSYAIDYIFTKYMGLVRSKAKLYFLVGADKEDIVQEGLIGLHKAI 84

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           + F+P++     +++   I   +   +  S     I   +                    
Sbjct: 85  RDFNPDKNRLFRSFADLCITRQLITAVKGSTRQKHIPLNSY------------------- 125

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
                                  IS+N RL             ++N +   D +  +   
Sbjct: 126 -----------------------ISLNRRL-----------YEEENDTTMLDLIENERVS 151

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
             + +   EE+      L     +L+  E ++ E        +T  +++   
Sbjct: 152 NPEDIFLNEEKGLYFRKLMA--EILSDLEAKVIEMYL---EGMTYHDIADVL 198


>gi|269925713|ref|YP_003322336.1| sigma-70 region 4 domain protein [Thermobaculum terrenum ATCC
           BAA-798]
 gi|269789373|gb|ACZ41514.1| sigma-70 region 4 domain protein [Thermobaculum terrenum ATCC
           BAA-798]
          Length = 785

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 21/86 (24%), Positives = 44/86 (51%), Gaps = 2/86 (2%)

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL-NPRERRIFEARRLQENP-VTLE 256
            + + L  + +   +   E          +T+ +  + +PR RR+ EAR       +TL+
Sbjct: 297 SYSEQLPAEVELSSETTQEDVSITELDKEITKLIQTIKSPRVRRVLEARFGVSGKILTLQ 356

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQE 282
            + +E ++S+ERVRQ+E R  + +++
Sbjct: 357 EIGAELKLSKERVRQLEERGLRLIRK 382


>gi|295849257|gb|ADG45292.1| sigma 70 factor-like protein [uncultured bacterium]
          Length = 173

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 30/125 (24%), Positives = 57/125 (45%), Gaps = 5/125 (4%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
            ++++ ++LRLVV IA  +    + + E+VSEG + LM+AV  FD  RG + +TY+   +
Sbjct: 22  KNQIIRANLRLVVSIARRHLRGSVSLMELVSEGTMTLMRAVDSFDAHRGHKFSTYATLAL 81

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
                  + +      +   +               +    D  L  EQV  + ++L+  
Sbjct: 82  MKGFARCVPQ-----MLWKRSAGGDPELLAEVADHRVTTAADRFLAREQVGELMRRLDAR 136

Query: 170 ESEVI 174
           E +V+
Sbjct: 137 ERDVL 141



 Score = 51.0 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 2/57 (3%)

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
             +R   R  +   M  L+ RER +        +  P T E L+    ++++R+RQI
Sbjct: 116 AADRFLAREQVGELMRRLDARERDVLLNHYGLGHRTPATYEQLAQRLGLTKQRIRQI 172


>gi|15643300|ref|NP_228344.1| RNA polymerase factor sigma-70 [Thermotoga maritima MSB8]
 gi|148269529|ref|YP_001243989.1| RNA polymerase factor sigma-70 [Thermotoga petrophila RKU-1]
 gi|170288204|ref|YP_001738442.1| ECF subfamily RNA polymerase sigma-24 factor [Thermotoga sp. RQ2]
 gi|281411753|ref|YP_003345832.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermotoga
           naphthophila RKU-10]
 gi|4981047|gb|AAD35619.1|AE001728_20 RNA polymerase sigma-H factor, putative [Thermotoga maritima MSB8]
 gi|147735073|gb|ABQ46413.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermotoga
           petrophila RKU-1]
 gi|170175707|gb|ACB08759.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermotoga sp.
           RQ2]
 gi|281372856|gb|ADA66418.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermotoga
           naphthophila RKU-10]
          Length = 193

 Score = 60.6 bits (146), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 38/232 (16%), Positives = 75/232 (32%), Gaps = 70/232 (30%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE V    Y + G   A   +V  +  +VVKIA  Y        ++V  G +GL++A+  
Sbjct: 12  EELV---EYAQAGFKEAIDLIVEKYYPMVVKIASQYFASWAEHEDIVQNGLVGLIKAIFY 68

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           +D  +     +++   + + ++ ++                     L R K  +      
Sbjct: 69  YDKTK-SSFTSFAWRSVDSEIKSFLT-------------------YLNRKKNRM------ 102

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
                  ++ A  ++  E E          D       + +D   S +   +        
Sbjct: 103 -------LSDAVNVDGMEKE--------EDDAPFEVPDSETDVARSAFSGII-------- 139

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
                          L   + +LN +E+ IF  R L     +   ++ E  V
Sbjct: 140 ---------------LETVLELLNEKEKEIF-LRWLDGCSYS--EIAKELGV 173


>gi|37595578|gb|AAQ94633.1| FliA [Phytoplasma sp. AY1]
 gi|47717362|gb|AAT37711.1| DNA-directed RNA polymerase sigma subunit [New Jersey aster yellows
           phytoplasma]
          Length = 150

 Score = 60.2 bits (145), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 24/85 (28%), Positives = 45/85 (52%), Gaps = 3/85 (3%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI--SEVVSEGNIGLMQAVKKFDPERG 98
            +   +L   ++L+  HL LV K+A  ++ Y   +   ++  EG +GL++A+  +  + G
Sbjct: 11  LKNKKNLEIRNQLIELHLPLVKKLAYHFKYYPKVLTKEDLYQEGILGLIKALNNYQ-DLG 69

Query: 99  FRLATYSMWWIKAAMQEYILRSWSL 123
           +   TY+   IK A+ E I +S S 
Sbjct: 70  YDFVTYATPKIKFAINELIRKSHSP 94


>gi|56418624|ref|YP_145942.1| RNA polymerase factor sigma-70 [Geobacillus kaustophilus HTA426]
 gi|56378466|dbj|BAD74374.1| DNA-directed RNA polymerase sigma-30 factor (sigma-H) [Geobacillus
           kaustophilus HTA426]
          Length = 216

 Score = 60.2 bits (145), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 41/249 (16%), Positives = 76/249 (30%), Gaps = 62/249 (24%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GD  A   L+  +   V   A  Y   G    ++V EG IGL +AV+ F  ++      
Sbjct: 27  EGDGEALDFLIHKYQNFVRAKARSYFLVGADREDIVQEGMIGLYKAVRDFKGDKLSSFKA 86

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           ++   I   M   I  +     I   +                                 
Sbjct: 87  FAELCITRQMITAIKTATRQKHIPLNSY-------------------------------- 114

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
                     +S++  +  DES                D L        + LI   E  +
Sbjct: 115 ----------VSLDKPIYDDES-----------DRTLMDVLSGTQVTDPEQLIVNREEVD 153

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
              +  +   +L+  ER++        +  + + +S E       V+ I   A ++V+  
Sbjct: 154 DIEL--KMAELLSDLERKVLALYL---DGRSYQEISEELN---RHVKSI-DNALQRVKRK 204

Query: 284 IQKQVELSS 292
           ++K +E   
Sbjct: 205 LEKYLEYRE 213


>gi|39938809|ref|NP_950575.1| DNA-directed RNA polymerase specialized sigma subunit [Onion
           yellows phytoplasma OY-M]
 gi|39938849|ref|NP_950615.1| DNA-directed RNA polymerase specialized sigma subunit [Onion
           yellows phytoplasma OY-M]
 gi|39721918|dbj|BAD04408.1| DNA-directed RNA polymerase specialized sigma [Onion yellows
           phytoplasma OY-M]
 gi|39721958|dbj|BAD04448.1| DNA-directed RNA polymerase specialized sigma [Onion yellows
           phytoplasma OY-M]
          Length = 206

 Score = 60.2 bits (145), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 29/121 (23%), Positives = 57/121 (47%), Gaps = 7/121 (5%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI--SEVVSEGNIGLMQAVKKFDPERG 98
            +   +L    +L+  HL LV KI+  ++ Y   +   ++  EG +GL++A+  ++ + G
Sbjct: 11  LKNKKNLEIRDQLIELHLPLVKKISSKFKYYPNFLTRDDLYQEGILGLIKALNNYE-DLG 69

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           +    Y+   IK+ ++E I +S S     +   +     NL   +   +    NNL P Q
Sbjct: 70  YDFIAYANPTIKSEIKELIRKSHS----PSVPQKNHKANNLSFREELYETYQKNNLNPHQ 125

Query: 159 V 159
           +
Sbjct: 126 L 126


>gi|289579162|ref|YP_003477789.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermoanaerobacter
           italicus Ab9]
 gi|289528875|gb|ADD03227.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermoanaerobacter
           italicus Ab9]
          Length = 214

 Score = 60.2 bits (145), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 39/262 (14%), Positives = 89/262 (33%), Gaps = 64/262 (24%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           +EE V+ +   + GD +A   L+  +   V   A  Y   G    +++ EG IGL +A++
Sbjct: 17  EEEEVVFR--AQKGDEAALEYLLERYKSFVKAKARAYFLVGADREDIMQEGMIGLYKAIR 74

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
            +  ++      ++   +   +   I  +     I                         
Sbjct: 75  DYKGDKLSSFKAFAELCVTRQIITAIKTATRQKHIP------------------------ 110

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
                                   +N  ++    LN  I   + + +             
Sbjct: 111 ------------------------LNSYIS----LNKPIFDEESDRTLLDVVSTQCIADP 142

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E+++I KEE  N  N +   +S L   E  +  +     +  + + ++ +       V+ 
Sbjct: 143 EELIISKEEYVNIENKMEELLSGL---EWEVLVSYL---DGKSYQEIAEDLN---RHVKS 193

Query: 272 IEARAFKKVQESIQKQVELSSS 293
           I   A ++V+  +++ +E+ +S
Sbjct: 194 I-DNALQRVKRKLERYLEMRNS 214


>gi|167745714|ref|ZP_02417841.1| hypothetical protein ANACAC_00407 [Anaerostipes caccae DSM 14662]
 gi|317472694|ref|ZP_07932009.1| RNA polymerase sigma-H factor [Anaerostipes sp. 3_2_56FAA]
 gi|167655026|gb|EDR99155.1| hypothetical protein ANACAC_00407 [Anaerostipes caccae DSM 14662]
 gi|316899871|gb|EFV21870.1| RNA polymerase sigma-H factor [Anaerostipes sp. 3_2_56FAA]
          Length = 192

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 31/145 (21%), Positives = 59/145 (40%), Gaps = 16/145 (11%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A   L+  +  LV + +  +   G    +++ EG IGL +AVK +D E+    +
Sbjct: 17  KSGDDRAMDFLLNRYGGLVRRESRKFFLAGADEEDLIQEGMIGLFKAVKNYDDEKNASFS 76

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-- 160
           T++   +K  +   +  S               + +L   +G      + +  PEQV+  
Sbjct: 77  TFASLCVKRQIYTTVTASKRKKHGPL-----NNYISLFNEQGEEDQFMEEDTNPEQVLIQ 131

Query: 161 ---------AIAKKLNVSESEVISM 176
                     I  KL+  E +V+ +
Sbjct: 132 KENISDYYKKIETKLSSFEKDVMEL 156


>gi|332970731|gb|EGK09711.1| DNA-directed RNA polymerase sigma subunit SigH [Desmospora sp.
           8437]
          Length = 217

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 39/262 (14%), Positives = 87/262 (33%), Gaps = 65/262 (24%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
             EE V    Y    D +A  +L+  +   V   A  Y   G    ++V EG IGL +A+
Sbjct: 18  ADEELV---EYVRADDGAALEQLINKYKNFVRAKARSYFLIGADHEDIVQEGMIGLFKAI 74

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           + F  ++      ++   I   +   I  +     I   +                    
Sbjct: 75  RDFRGDKLASFKAFAELCITRQIITAIKTATRQKHIPLNSY------------------- 115

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
                                  +S++            I   D + +            
Sbjct: 116 -----------------------VSLDK----------PIYDEDSDRTLMDILTGGRASD 142

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
            E++ I +EE  +  + +++ +S L   ER++        +  + + ++   ++ R  V+
Sbjct: 143 PEELYINQEEFDDIEDKMSQILSDL---ERQVLMLYL---DGRSYQEIA--IDLKR-HVK 193

Query: 271 QIEARAFKKVQESIQKQVELSS 292
            I   A ++V+  +++ +E+  
Sbjct: 194 SI-DNALQRVKRKLERYLEVRG 214


>gi|325479543|gb|EGC82639.1| sigma-70, region 4 [Anaerococcus prevotii ACS-065-V-Col13]
          Length = 242

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 22/90 (24%), Positives = 44/90 (48%), Gaps = 2/90 (2%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMG-YRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
            K YRE  D+   + +  +++ LV       Y  Y     E+  EG   L++A++K++P 
Sbjct: 7   FKEYRETKDIKLRNEIALNNMGLVHYALKEIYNKYYHDYEELEQEGAYFLLKAIEKYNPN 66

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
            G++ ++++  +I  A   Y L  +  + I
Sbjct: 67  LGYKFSSFAYKYILKA-SRYRLDYFKNISI 95


>gi|220932485|ref|YP_002509393.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Halothermothrix
           orenii H 168]
 gi|219993795|gb|ACL70398.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Halothermothrix
           orenii H 168]
          Length = 207

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 22/96 (22%), Positives = 44/96 (45%), Gaps = 3/96 (3%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           +EE +   R  ++ +  A   L+ S++ +V   A  +   GL   +V+ EG +GL +A++
Sbjct: 7   EEEII---RQAQNRNRRAIEYLINSNMDIVYAKAKYFFIKGLDKDDVIQEGMVGLFKAIR 63

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
            F  E+G     ++   +   +   I R+     I 
Sbjct: 64  DFKFEKGASFRGFAQLCVHRQLVSAIKRANRQKHIP 99


>gi|332800097|ref|YP_004461596.1| ECF subfamily RNA polymerase sigma-24 subunit SigH
           [Tepidanaerobacter sp. Re1]
 gi|332697832|gb|AEE92289.1| RNA polymerase, sigma-24 subunit, SigH, ECF subfamily
           [Tepidanaerobacter sp. Re1]
          Length = 215

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 41/270 (15%), Positives = 89/270 (32%), Gaps = 70/270 (25%)

Query: 31  KQEEYVLAKRYRE--------HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
            +EEY+L     +        +GD  A   L+  +   V   A  Y   G    +++ EG
Sbjct: 6   PKEEYLLFDDMTDEEIVCEATNGDHEALEYLINKYKNFVKSKARSYFLIGADREDIIQEG 65

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            IGL +A++ F+PER      ++   I   +   I  +     I   +            
Sbjct: 66  MIGLYKAIRDFNPERLSSFRAFAELCITRQIITAIKTATRQKHIPLNSY----------- 114

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
                                          +S+N            +   D + +    
Sbjct: 115 -------------------------------VSLNK----------PLYDEDSDRTLLDI 133

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
                    E+++I +EE +   + +   +S L   E ++  A        + + ++ + 
Sbjct: 134 LSGVKISDPEELIISQEEFEEIEDKMGEILSKL---EWQVLMAYLGG---KSYQEIAKDL 187

Query: 263 EVSRERVRQIEARAFKKVQESIQKQVELSS 292
              +  V+ I   A ++V+  +++ +E+  
Sbjct: 188 ---KRHVKSI-DNALQRVKRKLERFLEVRD 213


>gi|261417590|ref|YP_003251272.1| RNA polymerase factor sigma-70 [Geobacillus sp. Y412MC61]
 gi|319765248|ref|YP_004130749.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Geobacillus sp.
           Y412MC52]
 gi|261374047|gb|ACX76790.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Geobacillus sp.
           Y412MC61]
 gi|317110114|gb|ADU92606.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Geobacillus sp.
           Y412MC52]
          Length = 238

 Score = 60.2 bits (145), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 41/249 (16%), Positives = 76/249 (30%), Gaps = 62/249 (24%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GD  A   L+  +   V   A  Y   G    ++V EG IGL +AV+ F  ++      
Sbjct: 38  EGDGEALDFLIHKYQNFVRAKARSYFLVGADREDIVQEGMIGLYKAVRDFKGDKLSSFKA 97

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           ++   I   M   I  +     I   +                                 
Sbjct: 98  FAELCITRQMITAIKTATRQKHIPLNSY-------------------------------- 125

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
                     +S++  +  DES                D L        + LI   E  +
Sbjct: 126 ----------VSLDKPIYDDES-----------DRTLMDVLSGTQVTDPEQLIVNREEVD 164

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
              +  +   +L+  ER++        +  + + +S E       V+ I   A ++V+  
Sbjct: 165 DIEL--KMAELLSDLERKVLALYL---DGRSYQEISEELN---RHVKSI-DNALQRVKRK 215

Query: 284 IQKQVELSS 292
           ++K +E   
Sbjct: 216 LEKYLEYRE 224


>gi|295399303|ref|ZP_06809285.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Geobacillus thermoglucosidasius C56-YS93]
 gi|294978769|gb|EFG54365.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Geobacillus thermoglucosidasius C56-YS93]
          Length = 99

 Score = 59.8 bits (144), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 16/68 (23%), Positives = 32/68 (47%), Gaps = 2/68 (2%)

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQI 272
           +I++ +       + + + VL+ RE+ +   R   +     T   ++ E  +SR  V +I
Sbjct: 19  IIDEIQLNMELEQVKKYIDVLDEREKEVIINRFGLDMQQEKTQREIAKELGISRSYVSRI 78

Query: 273 EARAFKKV 280
           E RA  K+
Sbjct: 79  EKRALMKM 86


>gi|296270991|ref|YP_003653623.1| hypothetical protein Tbis_3033 [Thermobispora bispora DSM 43833]
 gi|296093778|gb|ADG89730.1| hypothetical protein Tbis_3033 [Thermobispora bispora DSM 43833]
          Length = 621

 Score = 59.8 bits (144), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 20/79 (25%), Positives = 37/79 (46%), Gaps = 12/79 (15%)

Query: 226 NMLTRSMSVLNPRERRIFEARRLQE--------NPVTLENLSSEFEVSRERVRQIEARAF 277
            ++    + L+ R+R I   R   +           TL+ L+  F V+RER+RQIE    
Sbjct: 130 EIIDEIFAELDDRQRAIARDRLYADPSQPGEAGQRATLDELAQRFSVTRERIRQIERD-- 187

Query: 278 KKVQESIQKQVELSSSPPL 296
             ++E +++ +    + PL
Sbjct: 188 --LREHVEQWLTTPQAAPL 204


>gi|291517908|emb|CBK73129.1| RNA polymerase sigma factor, sigma-70 family [Butyrivibrio
           fibrisolvens 16/4]
          Length = 233

 Score = 59.8 bits (144), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 42/253 (16%), Positives = 78/253 (30%), Gaps = 59/253 (23%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIA----MGYR-----GYGLPISEVVSEGNIGLMQAVKKF 93
           + GD +A   L+ ++  LV+  A      Y        G  I +++ EG + L+ A   F
Sbjct: 23  QSGDDNAKQLLILANKGLVIANAILVEKEYSLNSNPYGGWDIEDLIQEGYLALIDAALSF 82

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
            PE G + +TY+   I+  M++   R++                                
Sbjct: 83  SPEAGAKFSTYATEVIRNKMRDVGRRTFGTF----------------------------- 113

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
                             E  S++  L      +   N                   ++ 
Sbjct: 114 ------------------EKHSVDDGLTNIFLDDDPANGYRDEYIGQLTAEASVDSHRDP 155

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQ 271
                  R     ML R +  L    R++             TLE  +  F  S+E V+ 
Sbjct: 156 TGELAVHRTMLLKMLIR-LQDLPSDARKVLTYHYGFSLREGRTLEATARHFNKSKETVKG 214

Query: 272 IEARAFKKVQESI 284
           IE  + + ++ ++
Sbjct: 215 IEQSSLQHLRVAM 227


>gi|266621945|ref|ZP_06114880.1| flagellar biosynthesis sigma factor FliA [Clostridium hathewayi DSM
           13479]
 gi|288866379|gb|EFC98677.1| flagellar biosynthesis sigma factor FliA [Clostridium hathewayi DSM
           13479]
          Length = 103

 Score = 59.8 bits (144), Expect = 4e-07,   Method: Composition-based stats.
 Identities = 15/74 (20%), Positives = 34/74 (45%), Gaps = 2/74 (2%)

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
             E    ++ +  L  ++  L  +ER +      +E   +   ++    + + RV QI  
Sbjct: 30  PEESLFYRDLQRTLAEAVEALGDKERLVVSLYYYEELKYS--EIAEIMGIGQSRVCQIHT 87

Query: 275 RAFKKVQESIQKQV 288
           +A KK++ S+++ V
Sbjct: 88  KAMKKLKSSLEEYV 101


>gi|310828614|ref|YP_003960971.1| ECF subfamily RNA polymerase sigma-24 factor [Eubacterium limosum
           KIST612]
 gi|310828996|ref|YP_003961353.1| ECF subfamily RNA polymerase sigma-24 factor [Eubacterium limosum
           KIST612]
 gi|308740348|gb|ADO38008.1| ECF subfamily RNA polymerase sigma-24 factor [Eubacterium limosum
           KIST612]
 gi|308740730|gb|ADO38390.1| ECF subfamily RNA polymerase sigma-24 factor [Eubacterium limosum
           KIST612]
          Length = 210

 Score = 59.8 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 36/261 (13%), Positives = 81/261 (31%), Gaps = 69/261 (26%)

Query: 25  KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           K P    + E              A   L+ +   LV+ +   ++       +   +G +
Sbjct: 19  KYPPNSPERENA----------KVAGEMLIITFKPLVLSVMSRFQVPDEQFEDGFQDGLL 68

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
             M+ +++FDPERG     +    +         R W   +   +   K+          
Sbjct: 69  AFMKGLERFDPERGTAFNAFIRTHLCQYY-----RKWKSGRFNQSVTAKK---------- 113

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
                                          ++ +  G + L             + D L
Sbjct: 114 ------------------------------RLDDKAPGTQGL------------TFADTL 131

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             +  G E   I K+E +  +  L   +S L  +++ +          ++L  ++ +   
Sbjct: 132 ADEAPGPENGFIWKKENERHQRKLAEGLSRLTTKQKEVINDHYTLG--LSLREIADKQGK 189

Query: 265 SRERVRQIEARAFKKVQESIQ 285
           + + V +  A A KK+++  +
Sbjct: 190 AHQSVCETHAAALKKLKKFFE 210


>gi|75706611|gb|ABA25854.1| FliA [Phytoplasma sp. CPh]
          Length = 155

 Score = 59.8 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 29/121 (23%), Positives = 56/121 (46%), Gaps = 7/121 (5%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI--SEVVSEGNIGLMQAVKKFDPERG 98
            +   +L    +L+  HL LV KI+  ++ Y   +    +  EG +GL++A+  ++ + G
Sbjct: 11  LKNKKNLEIRDQLIELHLPLVKKISSKFKYYPNFLTRDVLYQEGILGLIKALNNYE-DFG 69

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           +    Y+   IK+ ++E I +S S     +   +     NL   +   +    NNL P Q
Sbjct: 70  YDFIAYANPTIKSEIKELIRKSHS----PSVPQKNHKANNLSFREELYETYQKNNLNPHQ 125

Query: 159 V 159
           +
Sbjct: 126 L 126


>gi|323183986|gb|EFZ69369.1| sigma-70, region 4 family protein [Escherichia coli 1357]
          Length = 390

 Score = 59.8 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 16/53 (30%), Positives = 31/53 (58%), Gaps = 2/53 (3%)

Query: 227 MLTRSMSVL-NPRERRIFEARRLQEN-PVTLENLSSEFEVSRERVRQIEARAF 277
           ++  ++  L N R + I   R   ++ P +L +++ +  +SRERVRQ++ RA 
Sbjct: 2   LIHSAIESLSNKRHQYILLMRLGTDDSPHSLADIAVKLGISRERVRQLQERAL 54


>gi|118595065|ref|ZP_01552412.1| hypothetical protein MB2181_05315 [Methylophilales bacterium
           HTCC2181]
 gi|118440843|gb|EAV47470.1| hypothetical protein MB2181_05315 [Methylophilales bacterium
           HTCC2181]
          Length = 808

 Score = 59.8 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 15/32 (46%), Positives = 22/32 (68%)

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
            L++ P TLE +  +  V+RER+RQIEA+  K
Sbjct: 244 GLRDKPKTLEEIGEKLGVTRERIRQIEAKVIK 275


>gi|85057639|ref|YP_456555.1| RNA polymerase sigma factor [Aster yellows witches'-broom
           phytoplasma AYWB]
 gi|84789744|gb|ABC65476.1| RNA polymerase sigma factor [Aster yellows witches'-broom
           phytoplasma AYWB]
          Length = 208

 Score = 59.8 bits (144), Expect = 5e-07,   Method: Composition-based stats.
 Identities = 24/85 (28%), Positives = 42/85 (49%), Gaps = 3/85 (3%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAM--GYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
            +   +L   ++L+  HL LV KI     Y    L   ++  EG +GL++A+  +  + G
Sbjct: 11  LKNKKNLEIRNQLIELHLPLVKKITYHFKYCPKVLTKEDLYQEGILGLIKALNNYQ-DLG 69

Query: 99  FRLATYSMWWIKAAMQEYILRSWSL 123
           +    Y+   IK+A+ E I +S S 
Sbjct: 70  YDFIAYATPTIKSAINELIRKSHSP 94


>gi|33865766|ref|NP_897325.1| type 3 alternative RNA polymerase sigma factor [Synechococcus sp.
           WH 8102]
 gi|33632936|emb|CAE07747.1| Possible type 3 alternative RNA polymerase sigma factor
           [Synechococcus sp. WH 8102]
          Length = 225

 Score = 59.4 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 36/233 (15%), Positives = 82/233 (35%), Gaps = 43/233 (18%)

Query: 50  AHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
            ++ V  HL L  ++A  + +  GL   ++     +GL++A K +  E       ++   
Sbjct: 25  RNQQVERHLYLAERLARSFSQRTGLDHDDLYQVAVLGLIKATKAYRSETNVPFEAFARVH 84

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
            + A+  Y+  S +LV++             RR++   Q ++  +          + L  
Sbjct: 85  ARGAILHYLRDSVALVRLP------------RRIEEEAQRLSQIHQPKNSREEWVQALYR 132

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S++  +                                +   Q    I       RR+ +
Sbjct: 133 SKNRWL----------------------------PCPEEQQAQSNSGITMMVNAERRDAI 164

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             + S L   E+   +A  +  +  +L N+ +   VS   V++   +  K+++
Sbjct: 165 QLAFSQLGDAEKHAVKAVVI--DGRSLRNVGTSLGVSAMTVQRRVKKGLKQLK 215


>gi|188588004|ref|YP_001919656.1| RNA polymerase factor sigma-70 [Clostridium botulinum E3 str.
           Alaska E43]
 gi|251778497|ref|ZP_04821417.1| RNA polymerase sigma-H factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
 gi|188498285|gb|ACD51421.1| RNA polymerase sigma-H factor [Clostridium botulinum E3 str. Alaska
           E43]
 gi|243082812|gb|EES48702.1| RNA polymerase sigma-H factor [Clostridium botulinum E1 str. 'BoNT
           E Beluga']
          Length = 206

 Score = 59.4 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 32/196 (16%), Positives = 73/196 (37%), Gaps = 8/196 (4%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            EE VL     ++G+  A   +++ +   V   A  Y   G    ++  EG IGL +A++
Sbjct: 12  DEEVVLE---AKNGNTRAQEYMISKYENFVKAKAKSYFLIGADREDIYQEGMIGLYKAIR 68

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQAI 149
            F  ++      ++   +   +   I  +     I   T  +  +  +     +  L  +
Sbjct: 69  DFKADKLTSFKAFAELCVTRQIITAIKTATRQKHIPLNTYVSLNKPIYEEESERTLLDVL 128

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
           +   +   + + I K+      ++ +   ++  D  L  L +  D  S Q     +  H 
Sbjct: 129 SGIKISDPEELLINKE---HMDDIEAAIAKVLSDLELEVLTSYLDGKSYQEIACDLDRHS 185

Query: 210 GQEQVLIEKEERKNRR 225
                 +++ +RK  +
Sbjct: 186 KSIDNALQRVKRKLEK 201


>gi|315931621|gb|EFV10586.1| RNA polymerase sigma factor [Campylobacter jejuni subsp. jejuni
           327]
          Length = 232

 Score = 59.4 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 34/235 (14%), Positives = 97/235 (41%), Gaps = 28/235 (11%)

Query: 47  LSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
                 LV S++  +  +A          + +++++S G   +++  +++D E+      
Sbjct: 22  KKEQDELVLSYMPALRAMAFRLKERLPSSIDVNDLISIGVEEMIKLSRRYDKEQNDNFWG 81

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           ++   +  +M +Y+     + +     N +++  ++  +    +   ++  +P+    +A
Sbjct: 82  FARKRVNGSMLDYLRSLDVMSR-----NNRKIIKDIDAIMD--EYFLEHECEPDD-EYLA 133

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           KKL++   ++  +  R A   S    I+   +         +Y+ D   + + ++E  + 
Sbjct: 134 KKLDLDVEKIKEV--RTAHAISYTLPIDEQIE---------LYNEDNTLEKIEKEELLEK 182

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
                   +  L  R++ I +    +E  ++L+ +S   ++S  R+ QI     K
Sbjct: 183 I----HEVLDDLKERDQLIIQLYYYEE--LSLKEISEILQISESRISQIHKNFLK 231


>gi|157364507|ref|YP_001471274.1| RNA polymerase factor sigma-70 [Thermotoga lettingae TMO]
 gi|157315111|gb|ABV34210.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermotoga
           lettingae TMO]
          Length = 206

 Score = 59.4 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 19/86 (22%), Positives = 41/86 (47%), Gaps = 5/86 (5%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           +E   LA    + G   A   LV     +VVKI+  Y        ++V  G +GL++AV 
Sbjct: 13  EELVNLA----QSGLKEALDLLVEKFYPMVVKISSKYYAPWAEFQDLVQNGLVGLIKAVY 68

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYI 117
            +  ++G    +++   +++ ++ ++
Sbjct: 69  YYQSDKGG-FTSFAWTSVESELKSFL 93


>gi|302391432|ref|YP_003827252.1| sigma-70 region 4 domain protein [Acetohalobium arabaticum DSM
           5501]
 gi|302203509|gb|ADL12187.1| sigma-70 region 4 domain protein [Acetohalobium arabaticum DSM
           5501]
          Length = 1154

 Score = 59.4 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 47/211 (22%), Positives = 82/211 (38%), Gaps = 12/211 (5%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
           I +++++G + L+    K + E  +    +S       +    L     + +    N + 
Sbjct: 300 IKDLLNDGPLCLVDLKMKLELEDNWYFCLFSA---LKKINNIGLNKKRKICLTNNLNARI 356

Query: 135 LFF---NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
            F     L ++K       DN +K    + I  +  +   E+      L  D SL  +  
Sbjct: 357 RFCINSALTKIKRLKNKKIDNLIKN---LFINLETPLLLKEIKKYLMFLNIDLSLEEIDE 413

Query: 192 SSDKN-SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI-FEARRLQ 249
               N   +  D   +  D  ++     EE K+    +  S    N RER I    +R+ 
Sbjct: 414 LLRNNADFKLIDVNKWSLDSWDEYPEFNEEFKSTWEQILSSFPEEN-RERDIDILNKRIF 472

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            N  TLE L  E  +SR+RVRQ+E    +K+
Sbjct: 473 SNDYTLEKLGEEHSISRQRVRQLEESGMRKL 503


>gi|294500560|ref|YP_003564260.1| RNA polymerase sigma-H factor [Bacillus megaterium QM B1551]
 gi|294350497|gb|ADE70826.1| RNA polymerase sigma-H factor [Bacillus megaterium QM B1551]
          Length = 216

 Score = 59.4 bits (143), Expect = 6e-07,   Method: Composition-based stats.
 Identities = 37/249 (14%), Positives = 78/249 (31%), Gaps = 62/249 (24%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  +   L+  +  LV   A  Y   G    ++V EG IGL +A++ F+ ++      +
Sbjct: 28  GDEKSLEYLINKYQNLVRGKARKYFLIGAEKEDIVQEGMIGLYKAIRDFNEDKLTSFKGF 87

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +   I   +   I  +         +                                  
Sbjct: 88  AELCITRQIITAIKTATRQKHGPLNSY--------------------------------- 114

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
                    IS++  L  +ES           +    D +  D     + ++  +E+   
Sbjct: 115 ---------ISLDKPLYDEES-----------NYTLMDMIPGDQIANPEAVLIHQEKVED 154

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R +  +    L+  ER+         +  +   +S E       V+ I   A ++++  +
Sbjct: 155 REL--KIAETLSELERKALTLY---MDGHSYAEISKELN---THVKSI-DNALQRIKRKL 205

Query: 285 QKQVELSSS 293
            + VE   +
Sbjct: 206 GRDVESRQA 214


>gi|39939142|ref|NP_950908.1| DNA-directed RNA polymerase specialized sigma subunit [Onion
           yellows phytoplasma OY-M]
 gi|39722251|dbj|BAD04741.1| DNA-directed RNA polymerase specialized sigma [Onion yellows
           phytoplasma OY-M]
          Length = 200

 Score = 59.4 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 28/122 (22%), Positives = 52/122 (42%), Gaps = 13/122 (10%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAM--GYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
            +   +L   ++L+T HL LV KI     Y    L   ++  EG +GL++A+  +  + G
Sbjct: 11  LKNKKNLEIRNQLITLHLPLVKKIVNQFKYYPRVLTKEDLYREGILGLIKALNHYQ-DLG 69

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF---------FNLRRLKGHLQAI 149
           +    Y+   IK+ + E I +S S   I    ++K            + + +L  H   +
Sbjct: 70  YDFIAYATPTIKSEINELIRKSHSP-SIPQKNHKKDNLSFREEFYEPYQINKLNPHQLWL 128

Query: 150 TD 151
             
Sbjct: 129 KQ 130


>gi|163938101|ref|YP_001642985.1| RNA polymerase factor sigma-70 [Bacillus weihenstephanensis KBAB4]
 gi|229009603|ref|ZP_04166829.1| RNA polymerase sigma-H factor [Bacillus mycoides DSM 2048]
 gi|229053940|ref|ZP_04195374.1| RNA polymerase sigma-H factor [Bacillus cereus AH603]
 gi|229131101|ref|ZP_04260013.1| RNA polymerase sigma-H factor [Bacillus cereus BDRD-ST196]
 gi|229165082|ref|ZP_04292877.1| RNA polymerase sigma-H factor [Bacillus cereus AH621]
 gi|163860298|gb|ABY41357.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Bacillus
           weihenstephanensis KBAB4]
 gi|228618345|gb|EEK75375.1| RNA polymerase sigma-H factor [Bacillus cereus AH621]
 gi|228652314|gb|EEL08239.1| RNA polymerase sigma-H factor [Bacillus cereus BDRD-ST196]
 gi|228721358|gb|EEL72879.1| RNA polymerase sigma-H factor [Bacillus cereus AH603]
 gi|228751625|gb|EEM01425.1| RNA polymerase sigma-H factor [Bacillus mycoides DSM 2048]
          Length = 219

 Score = 59.4 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 37/268 (13%), Positives = 88/268 (32%), Gaps = 66/268 (24%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           LE +    L ++    G+  A   L+  +   V   +  Y   G    ++V EG IGL +
Sbjct: 16  LEDEAIVELVRK----GNTDALEYLIHKYKNFVRAKSRSYFLVGADREDIVQEGMIGLFK 71

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++ +  ++      ++   I   +   I  +     I   +                  
Sbjct: 72  AIRDYKGDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSY----------------- 114

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                                    +S++            I   + + +          
Sbjct: 115 -------------------------VSLDK----------PIYDEESDRTLLDVISESKV 139

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
              E+++I +EE  +  + ++  +S L   ER++        +  + + +S +       
Sbjct: 140 TDPEEMIISQEEYTDIESKISELLSDL---ERKVLSLYL---DGRSYQEISEQLN---RH 190

Query: 269 VRQIEARAFKKVQESIQKQVELSSSPPL 296
           V+ I   A ++V+  +++ +E+  S  L
Sbjct: 191 VKSI-DNALQRVKRKLERYMEMRESTTL 217


>gi|238927910|ref|ZP_04659670.1| DNA-directed RNA polymerase sigma subunit SigH [Selenomonas
           flueggei ATCC 43531]
 gi|238884243|gb|EEQ47881.1| DNA-directed RNA polymerase sigma subunit SigH [Selenomonas
           flueggei ATCC 43531]
          Length = 266

 Score = 59.4 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 36/256 (14%), Positives = 79/256 (30%), Gaps = 66/256 (25%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L  R R      A   L+  +   V   A  Y   G    ++V EG IG  +A++ + P
Sbjct: 51  DLLNRIRGCDGDEALDYLINKYRNFVRSKARSYFLIGADREDIVQEGMIGFFKAIRDYRP 110

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           ++      ++   +   +   I  +     I   +                         
Sbjct: 111 DKLSSFRAFAELCVTRQIITAIKTATRQKHIPLNSY------------------------ 146

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
                             +S+N            I   D + +             E+++
Sbjct: 147 ------------------VSLNK----------PIYDEDSDRTLLDVLSGARISDPEELV 178

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA- 274
           I  EE  +    +   +S L   E R+  +     +  + + ++ +        RQ+++ 
Sbjct: 179 ISHEEFIDIEQKMEEILSDL---EWRVLMSYL---DGKSYQEIAVDLH------RQVKSI 226

Query: 275 -RAFKKVQESIQKQVE 289
             A ++V+  ++K +E
Sbjct: 227 DNALQRVKRKLEKYME 242


>gi|154248931|ref|YP_001409756.1| RNA polymerase factor sigma-70 [Fervidobacterium nodosum Rt17-B1]
 gi|154152867|gb|ABS60099.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Fervidobacterium
           nodosum Rt17-B1]
          Length = 207

 Score = 59.4 bits (143), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 18/91 (19%), Positives = 42/91 (46%), Gaps = 5/91 (5%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           ++   LA    + G   A   ++  +  +VV+IA  +        ++V  G IGL++A+ 
Sbjct: 12  EKLVELA----QSGLNDAVDLIIEKYYPMVVRIASQFYAPWAEFDDIVQNGLIGLIKAIY 67

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            F+  +    +T++   I++ ++ +I     
Sbjct: 68  YFEENK-SSFSTFAWRSIESEIKTFITYQNR 97


>gi|87303200|ref|ZP_01085998.1| sigma factor SigF [Synechococcus sp. WH 5701]
 gi|87282367|gb|EAQ74327.1| sigma factor SigF [Synechococcus sp. WH 5701]
          Length = 233

 Score = 59.1 bits (142), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 26/130 (20%), Positives = 54/130 (41%), Gaps = 14/130 (10%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYG-LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           +AA  L   H  L  KIA  +      P  +++    IGL++A +++DP RG     Y  
Sbjct: 103 AAADALALQHRDLAEKIAGNFARRTVHPREDLLQLAMIGLIKAARRYDPSRGP-FRPYGR 161

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
            +    +  ++  +  L+K+  T          R +    Q +  + +    V  + +++
Sbjct: 162 TYANGEITHFLRDNGFLLKVPPT---------WREIHARGQRLLTSGIG---VGEMLERI 209

Query: 167 NVSESEVISM 176
            +S  + I +
Sbjct: 210 GISREQWIEI 219


>gi|253584124|ref|ZP_04861322.1| RNA polymerase sigma-H factor [Fusobacterium varium ATCC 27725]
 gi|251834696|gb|EES63259.1| RNA polymerase sigma-H factor [Fusobacterium varium ATCC 27725]
          Length = 197

 Score = 59.1 bits (142), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 19/81 (23%), Positives = 38/81 (46%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + GD  A  ++  S  +L++     Y  +G    +V+ E  IGL++A+  +D  +    
Sbjct: 10  AQEGDEDAIQQIFESFKQLIIFKTKKYFFHGGDRDDVMQEAMIGLLKAINAYDENKNASF 69

Query: 102 ATYSMWWIKAAMQEYILRSWS 122
            T+++  IK  +   +  S S
Sbjct: 70  TTFALLCIKRQIITALKNSNS 90


>gi|326790455|ref|YP_004308276.1| LuxR family transcriptional regulator [Clostridium lentocellum DSM
           5427]
 gi|326541219|gb|ADZ83078.1| transcriptional regulator, LuxR family [Clostridium lentocellum DSM
           5427]
          Length = 216

 Score = 59.1 bits (142), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 39/267 (14%), Positives = 86/267 (32%), Gaps = 63/267 (23%)

Query: 21  HEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVS 80
            E + +  L  +E   L +RYR+ G   A   LV  + R V          G+   +++ 
Sbjct: 9   KENKNLEQLTDEE---LIQRYRD-GINEAIEVLVQRYKRFVRTKIKANYFIGVDKDDLIQ 64

Query: 81  EGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR 140
           EG IGL +A+  +D  +     +++   +   +            I              
Sbjct: 65  EGMIGLFKAICDYDAHKDTSFKSFATLCVTRQVSTAFKAVSRQKHIP------------- 111

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
                                              +N  ++    +N   N  D      
Sbjct: 112 -----------------------------------LNTSISLSIPINHKGNEEDDEGITL 136

Query: 201 QDWLVYDHDG-QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
            D +  +     E  +I KE  +   N + +++S L   E ++       +N    + ++
Sbjct: 137 LDTIKNNTSMTPEDEMISKENLEVLNNQIIKALSKL---EWQVLNLYISGKN---YQEIA 190

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQK 286
            E + S + +      A +++++ ++ 
Sbjct: 191 KELDKSPKSI----DNALQRIKKKLES 213


>gi|255606356|ref|XP_002538551.1| RNA polymerase sigma factor for flagellar operon, putative [Ricinus
           communis]
 gi|223511619|gb|EEF23833.1| RNA polymerase sigma factor for flagellar operon, putative [Ricinus
           communis]
          Length = 123

 Score = 59.1 bits (142), Expect = 7e-07,   Method: Composition-based stats.
 Identities = 29/125 (23%), Positives = 61/125 (48%), Gaps = 11/125 (8%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLP---ISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            +  + L+T H+ LV ++A   +    P   + ++V  G +GL+ A+ +++   G +  T
Sbjct: 7   KADKNSLLTEHMPLVKRLAHQMKAKLPPSVEVDDLVQAGMMGLLDAINRYEENHGAQFET 66

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y++  I+ AM + + RS   +   T AN       +R+++  + A+     +P     +A
Sbjct: 67  YAVLRIRGAMLDEL-RSSDWMPRSTRAN-------MRKVESAMAALQQQLGRPPSESEVA 118

Query: 164 KKLNV 168
           K L +
Sbjct: 119 KSLKL 123


>gi|304399206|ref|ZP_07381073.1| sigma-70 region 1.2 [Pantoea sp. aB]
 gi|304353260|gb|EFM17640.1| sigma-70 region 1.2 [Pantoea sp. aB]
          Length = 113

 Score = 59.1 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 21/48 (43%), Positives = 30/48 (62%), Gaps = 1/48 (2%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLVVKIA 
Sbjct: 61  YLGEIGYSPLLTAEEEVFFARR-ALRGDIPSRRRMIESNLRLVVKIAR 107


>gi|215404667|ref|ZP_03416848.1| RNA polymerase sigma factor [Mycobacterium tuberculosis 02_1987]
 gi|289746504|ref|ZP_06505882.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           02_1987]
 gi|289687032|gb|EFD54520.1| RNA polymerase sigma factor sigA [Mycobacterium tuberculosis
           02_1987]
 gi|326904317|gb|EGE51250.1| LOW QUALITY PROTEIN: RNA polymerase sigma factor [Mycobacterium
           tuberculosis W-148]
          Length = 316

 Score = 59.1 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 25/101 (24%), Positives = 41/101 (40%), Gaps = 31/101 (30%)

Query: 2   NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRY-------------REHGDL- 47
            RK+  +  + +  +  Y+ +I K+ +L  +EE  LAKR               E G+  
Sbjct: 217 ARKDAELTASAD-SVRAYLKQIGKVALLNAEEEVELAKRIEAGLYATQLMTELSERGEKL 275

Query: 48  ----------------SAAHRLVTSHLRLVVKIAMGYRGYG 72
                            A + L+ ++LRLVV +A  Y G G
Sbjct: 276 PAAQRRDMMWICRDGDRAKNHLLEANLRLVVSLAKRYTGRG 316


>gi|15896400|ref|NP_349749.1| RNA polymerase factor sigma-70 [Clostridium acetobutylicum ATCC
           824]
 gi|15026218|gb|AAK81089.1|AE007810_8 DNA-dependent RNA polymerase sigma subunit [Clostridium
           acetobutylicum ATCC 824]
          Length = 212

 Score = 59.1 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 40/255 (15%), Positives = 82/255 (32%), Gaps = 65/255 (25%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            EE V+     + GD  +   L+  +   V   A  Y   G    ++  EG IGL +A++
Sbjct: 18  DEEIVM---MAKLGDEKSQEYLINKYSNFVKVKAKSYFLIGADKEDICQEGMIGLYKAIR 74

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
            F P +      ++   I   +   I  +     I                         
Sbjct: 75  DFKPIKLASFKAFAEICITRQIITAIKTATRQKHIP------------------------ 110

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
                                   +N  ++    LN  I   D + + +      +    
Sbjct: 111 ------------------------LNTYVS----LNKPIYDEDSDRTLFDVVSSVEVSDP 142

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E+++I KEE    R  + + +S L   E  + E+        + + ++ + +    R  +
Sbjct: 143 EELIISKEEVAKIRKNMLKVLSSL---EIEVLESYL---EGKSYQEIAKDLD----RCSK 192

Query: 272 IEARAFKKVQESIQK 286
               A ++V+  ++K
Sbjct: 193 SIDNALQRVKRKLEK 207


>gi|237666438|ref|ZP_04526423.1| RNA polymerase sigma-H factor [Clostridium butyricum E4 str. BoNT E
           BL5262]
 gi|237657637|gb|EEP55192.1| RNA polymerase sigma-H factor [Clostridium butyricum E4 str. BoNT E
           BL5262]
          Length = 206

 Score = 59.1 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 24/136 (17%), Positives = 53/136 (38%), Gaps = 2/136 (1%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + G+  A   L++ +   V   A  Y   G    ++  EG IGL +A++ F+PE+    
Sbjct: 19  AKAGNNKAQEYLISKYENFVKAKAKSYFLIGADKEDIYQEGMIGLYKAIRDFNPEKSTSF 78

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
             ++   +   +   I  +     I   T  +  +  +     +  L  ++   +   + 
Sbjct: 79  KAFAEICVTRQIITAIKTATRQKHIPLNTYVSLNKPIYEEESERTLLDVLSGLKISDPEE 138

Query: 160 VAIAKKLNVSESEVIS 175
           + I+K+      + IS
Sbjct: 139 LMISKEQMHFIEDKIS 154


>gi|218905476|ref|YP_002453310.1| RNA polymerase sigma-K factor [Bacillus cereus AH820]
 gi|218536250|gb|ACK88648.1| RNA polymerase sigma-K factor [Bacillus cereus AH820]
          Length = 100

 Score = 59.1 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 15/79 (18%), Positives = 33/79 (41%), Gaps = 2/79 (2%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSE 261
           L+     + + +I+  +       +   + +L+ RE+ +   R     +   T   ++  
Sbjct: 7   LIDILKSESEDVIDMIQLSMELEKIKEYIDILDEREKEVIVKRFGLGLDKEKTQREIAKA 66

Query: 262 FEVSRERVRQIEARAFKKV 280
             +SR  V +IE RA  K+
Sbjct: 67  LGISRSYVSRIEKRALMKM 85


>gi|331268396|ref|YP_004394888.1| RNA polymerase sigma-H factor [Clostridium botulinum BKT015925]
 gi|329124946|gb|AEB74891.1| RNA polymerase sigma-H factor [Clostridium botulinum BKT015925]
          Length = 236

 Score = 59.1 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 25/146 (17%), Positives = 55/146 (37%), Gaps = 8/146 (5%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + GD+ A   L+  +   V   A  Y   G    ++  EG IGL +A++ F P++    
Sbjct: 45  AKQGDVEAQEYLINKYKNFVKAKAKSYFLIGADKEDIYQEGMIGLYKAIRDFKPDKLASF 104

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
             ++   +   +   I  +     I   T  +  +  ++    +  L  ++   +   + 
Sbjct: 105 KAFAELCVTRQIITAIKTATRQKHIPLNTYVSLNKPIYDEESDRTLLDILSTVKICDPE- 163

Query: 160 VAIAKKLNVSESEVISMNCRLAGDES 185
                +L +S  EV+ +   +    S
Sbjct: 164 -----ELVISREEVLKIESDIQEVLS 184


>gi|296329094|ref|ZP_06871599.1| hypothetical protein HMPREF0397_1792 [Fusobacterium nucleatum
           subsp. nucleatum ATCC 23726]
 gi|296153813|gb|EFG94626.1| hypothetical protein HMPREF0397_1792 [Fusobacterium nucleatum
           subsp. nucleatum ATCC 23726]
          Length = 979

 Score = 59.1 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 19/52 (36%), Positives = 27/52 (51%), Gaps = 3/52 (5%)

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
               + L   E +I  +R    +  TLE +     V+RER+RQIE R FKK+
Sbjct: 366 EEVHNYLKESEAKIILSRI---SGKTLEEIGEALNVTRERIRQIETRGFKKL 414


>gi|39938997|ref|NP_950763.1| DNA-directed RNA polymerase specialized sigma subunit [Onion
           yellows phytoplasma OY-M]
 gi|39722106|dbj|BAD04596.1| DNA-directed RNA polymerase specialized sigma [Onion yellows
           phytoplasma OY-M]
          Length = 201

 Score = 59.1 bits (142), Expect = 8e-07,   Method: Composition-based stats.
 Identities = 26/101 (25%), Positives = 49/101 (48%), Gaps = 5/101 (4%)

Query: 36  VLAKRY-REHGDLSAAHRLVTSHLRLVVKIAM--GYRGYGLPISEVVSEGNIGLMQAVKK 92
            L K + +   +L   ++L+  HL LV K+     Y    L   ++  EG +GL++A+  
Sbjct: 5   ELFKDFLKNKKNLEIRNQLIDLHLPLVNKLVKQFKYYPRVLQKEDLYQEGVLGLIKALNH 64

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           +  + G+    Y+   IK+ ++E I +S S   I    ++K
Sbjct: 65  YQ-DLGYDFIAYATPTIKSEIREIIRKSHSP-SIPQKNHKK 103


>gi|146295621|ref|YP_001179392.1| FliA/WhiG family RNA polymerase sigma factor [Caldicellulosiruptor
           saccharolyticus DSM 8903]
 gi|145409197|gb|ABP66201.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Caldicellulosiruptor saccharolyticus DSM 8903]
          Length = 310

 Score = 59.1 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 5/75 (6%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGY----RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
            S    L+  +L+LV  +A  +    +GY   + ++VSEG IGL+ A K +DP +G   +
Sbjct: 11  ESQRQLLIVDNLKLVYHVANKFMPCPKGYYYEVEDLVSEGYIGLVVAAKNYDPTKGS-FS 69

Query: 103 TYSMWWIKAAMQEYI 117
           TY+   I++ ++  +
Sbjct: 70  TYACKVIESKIKRSL 84


>gi|51245066|ref|YP_064950.1| RNA polymerase sigma factor for flagellar operon [Desulfotalea
           psychrophila LSv54]
 gi|50876103|emb|CAG35943.1| related to RNA polymerase sigma factor for flagellar operon
           [Desulfotalea psychrophila LSv54]
          Length = 242

 Score = 59.1 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 50/235 (21%), Positives = 97/235 (41%), Gaps = 27/235 (11%)

Query: 64  IAMG-YRGY--------GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114
           +A   Y  Y        G+ + +++  G IG ++A  + D E+G     +    +K    
Sbjct: 12  VARKLYHNYVAGSASEVGISVEDLIQTGIIGYLEAKSRLDKEKGDG-KAFIFMRMKGNQL 70

Query: 115 EYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
             I R   LV++   T A  K L    ++L+      TD  L        A++L  +  E
Sbjct: 71  SLIRRQA-LVRMPQKTYAKVKELLAVRKQLEASCVEATDQLL--------AERLGWTVKE 121

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           +  +   +    S + + ++ + +      +L        Q LI + E+K   +++   +
Sbjct: 122 IHQLLASVPRVFSSDDVTDNEESSDFYESHFLPG---QNPQPLISEMEKKEIADLIQGCL 178

Query: 233 SVL-NPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           + L NPR+R I  A+  +   V  + L+  F  SR  V   E +   ++Q  ++K
Sbjct: 179 ARLENPRQRLILVAKYFEGINV--KKLADRFGCSRYFVESEEQKGLGQMQTCLEK 231


>gi|78044583|ref|YP_361138.1| RNA polymerase factor sigma-70 [Carboxydothermus hydrogenoformans
           Z-2901]
 gi|77996698|gb|ABB15597.1| RNA polymerase sigma-H factor [Carboxydothermus hydrogenoformans
           Z-2901]
          Length = 217

 Score = 59.1 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 39/262 (14%), Positives = 81/262 (30%), Gaps = 65/262 (24%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            EE V    +   GD  A   ++  +   V   A  Y   G    +++ EG IGL +AV+
Sbjct: 20  DEEIV---EWARAGDEQALEYIINKYKNFVRSKARAYFLIGADREDIIQEGMIGLYKAVR 76

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
            F P++      ++   +   +   I  +     I   +                     
Sbjct: 77  DFRPDKLSSFRAFAELCVTRQIITAIKTATRQKHIPLNSY-------------------- 116

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
                                 +S+N            I   D + +             
Sbjct: 117 ----------------------VSLNK----------PIYDEDSDRTLMDVLSGVKVADP 144

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E+++I +EE  +    +   +S L   E ++           + + ++ E       V+ 
Sbjct: 145 EELIISREEFADIEGKMNEILSSL---EWKVLIYYL---EGKSYQEIACELN---RHVKS 195

Query: 272 IEARAFKKVQESIQKQVELSSS 293
           I   A ++V+  ++K +E   +
Sbjct: 196 I-DNALQRVKRKLEKYLECREA 216


>gi|20808677|ref|NP_623848.1| RNA polymerase factor sigma-70 [Thermoanaerobacter tengcongensis
           MB4]
 gi|20517313|gb|AAM25452.1| DNA-directed RNA polymerase specialized sigma subunits, sigma24
           homologs [Thermoanaerobacter tengcongensis MB4]
          Length = 219

 Score = 59.1 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 39/261 (14%), Positives = 85/261 (32%), Gaps = 63/261 (24%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE  +  R ++ GD  A   L+  +   V   A  Y   G    +++ EG IGL +A++ 
Sbjct: 22  EEEEIVSRAQQ-GDELALEYLIERYKNFVKAKARTYFLVGADKEDIIQEGMIGLYKAIRD 80

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           +   +      ++   +   +   I  +     I   +                      
Sbjct: 81  YKNNKLTSFKAFAELCVTRQIITAIKTATRQKHIPLNSY--------------------- 119

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
                                +S+N            I   + + +             E
Sbjct: 120 ---------------------VSLNKP----------IFDEESDRTLMDVVSTQCIADPE 148

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           +++I KEE  N  N +   +S L   E  +  A     +  + + ++ +       V+ I
Sbjct: 149 ELIISKEEYVNIENKMEELLSGL---EWEVLVAYL---DGKSYQEIAEDLN---RHVKSI 199

Query: 273 EARAFKKVQESIQKQVELSSS 293
              A ++V+  +++ +E+ +S
Sbjct: 200 -DNALQRVKRKLERYLEMRNS 219


>gi|42779174|ref|NP_976421.1| RNA polymerase factor sigma-70 [Bacillus cereus ATCC 10987]
 gi|218895229|ref|YP_002443640.1| RNA polymerase sigma-30 factor [Bacillus cereus G9842]
 gi|228898847|ref|ZP_04063129.1| RNA polymerase sigma-H factor [Bacillus thuringiensis IBL 4222]
 gi|228905891|ref|ZP_04069788.1| RNA polymerase sigma-H factor [Bacillus thuringiensis IBL 200]
 gi|228937396|ref|ZP_04100042.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228963194|ref|ZP_04124363.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228970282|ref|ZP_04130941.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228976852|ref|ZP_04137264.1| RNA polymerase sigma-H factor [Bacillus thuringiensis Bt407]
 gi|229027941|ref|ZP_04184094.1| RNA polymerase sigma-H factor [Bacillus cereus AH1271]
 gi|229074155|ref|ZP_04207201.1| RNA polymerase sigma-H factor [Bacillus cereus Rock4-18]
 gi|229094816|ref|ZP_04225821.1| RNA polymerase sigma-H factor [Bacillus cereus Rock3-29]
 gi|229100893|ref|ZP_04231697.1| RNA polymerase sigma-H factor [Bacillus cereus Rock3-28]
 gi|229113770|ref|ZP_04243205.1| RNA polymerase sigma-H factor [Bacillus cereus Rock1-3]
 gi|229159267|ref|ZP_04287291.1| RNA polymerase sigma-H factor [Bacillus cereus R309803]
 gi|229170945|ref|ZP_04298546.1| RNA polymerase sigma-H factor [Bacillus cereus MM3]
 gi|42735089|gb|AAS39029.1| RNA polymerase sigma-30 factor [Bacillus cereus ATCC 10987]
 gi|218544887|gb|ACK97281.1| RNA polymerase sigma-30 factor [Bacillus cereus G9842]
 gi|228612485|gb|EEK69706.1| RNA polymerase sigma-H factor [Bacillus cereus MM3]
 gi|228624159|gb|EEK80961.1| RNA polymerase sigma-H factor [Bacillus cereus R309803]
 gi|228669641|gb|EEL25048.1| RNA polymerase sigma-H factor [Bacillus cereus Rock1-3]
 gi|228682472|gb|EEL36545.1| RNA polymerase sigma-H factor [Bacillus cereus Rock3-28]
 gi|228688559|gb|EEL42432.1| RNA polymerase sigma-H factor [Bacillus cereus Rock3-29]
 gi|228708925|gb|EEL61052.1| RNA polymerase sigma-H factor [Bacillus cereus Rock4-18]
 gi|228733329|gb|EEL84158.1| RNA polymerase sigma-H factor [Bacillus cereus AH1271]
 gi|228782822|gb|EEM30988.1| RNA polymerase sigma-H factor [Bacillus thuringiensis Bt407]
 gi|228789391|gb|EEM37311.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228796452|gb|EEM43891.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar sotto
           str. T04001]
 gi|228822229|gb|EEM68211.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228853706|gb|EEM98466.1| RNA polymerase sigma-H factor [Bacillus thuringiensis IBL 200]
 gi|228860747|gb|EEN05125.1| RNA polymerase sigma-H factor [Bacillus thuringiensis IBL 4222]
 gi|324324083|gb|ADY19343.1| RNA polymerase factor sigma-70 [Bacillus thuringiensis serovar
           finitimus YBT-020]
 gi|326937887|gb|AEA13783.1| RNA polymerase factor sigma-70 [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 219

 Score = 59.1 bits (142), Expect = 9e-07,   Method: Composition-based stats.
 Identities = 37/268 (13%), Positives = 88/268 (32%), Gaps = 66/268 (24%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           LE +    L ++    G+  A   L+  +   V   +  Y   G    ++V EG IGL +
Sbjct: 16  LEDEAIVELVRK----GNTDALEYLIHKYKNFVRAKSRSYFLVGADREDIVQEGMIGLFK 71

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++ +  ++      ++   I   +   I  +     I   +                  
Sbjct: 72  AIRDYKEDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSY----------------- 114

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                                    +S++            I   + + +          
Sbjct: 115 -------------------------VSLDK----------PIYDEESDRTLLDVISEAKV 139

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
              E+++I +EE  +  + ++  +S L   ER++        +  + + +S +       
Sbjct: 140 TDPEEMIISQEEYTDIESKISELLSDL---ERKVLSLYL---DGRSYQEISEQLN---RH 190

Query: 269 VRQIEARAFKKVQESIQKQVELSSSPPL 296
           V+ I   A ++V+  +++ +E+  S  L
Sbjct: 191 VKSI-DNALQRVKRKLERYMEMRESTTL 217


>gi|219853509|ref|YP_002470631.1| hypothetical protein CKR_0166 [Clostridium kluyveri NBRC 12016]
 gi|219567233|dbj|BAH05217.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 213

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 33/202 (16%), Positives = 80/202 (39%), Gaps = 10/202 (4%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            EE V+     + GD+ A   ++  +   V   A  Y   G    ++  EG IGL +A++
Sbjct: 19  DEEVVIQ---AKEGDVRAQEYMINKYENFVKSKAKSYFLIGADKEDIYQEGMIGLYKAIR 75

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQAI 149
            F  ++      ++   +   +   I  +     I   T  +  +  ++    +  L  +
Sbjct: 76  DFKTDKLSSFKAFAELCVTRQIITAIKTATRQKHIPLNTYVSLNKPIYDEESDRTLLDVL 135

Query: 150 TDNNLK-PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           ++  +  PE+++   ++L    +E+  +   L     +  L++  D  S Q     +  H
Sbjct: 136 SEAKVADPEELIISREELKHIHNEIGEVLSSL----EMEVLMSYLDGKSYQEIACDLDRH 191

Query: 209 DGQEQVLIEKEERKNRRNMLTR 230
                  +++ +RK  + ++ +
Sbjct: 192 AKSIDNALQRVKRKLEKCLINK 213


>gi|87125755|ref|ZP_01081598.1| Sigma-70 region 2 [Synechococcus sp. RS9917]
 gi|86166564|gb|EAQ67828.1| Sigma-70 region 2 [Synechococcus sp. RS9917]
          Length = 233

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 20/88 (22%), Positives = 39/88 (44%), Gaps = 2/88 (2%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYG-LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           +AA  L   H  L  K+A  +      P  +++    IGL++A +++DP RG     Y  
Sbjct: 103 AAADALALQHRDLAEKVAGNFARRTVHPKEDLLQLAMIGLIKAARRYDPSRGP-FRPYGR 161

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKR 134
            +    +  ++  +  L+K+  T  +  
Sbjct: 162 TYANGEITHFLRDNGFLLKVPPTWREIH 189


>gi|295705913|ref|YP_003598988.1| RNA polymerase sigma-H factor [Bacillus megaterium DSM 319]
 gi|294803572|gb|ADF40638.1| RNA polymerase sigma-H factor [Bacillus megaterium DSM 319]
          Length = 216

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 37/249 (14%), Positives = 78/249 (31%), Gaps = 62/249 (24%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  +   L+  +  LV   A  Y   G    ++V EG IGL +A++ F+ ++      +
Sbjct: 28  GDEKSLEYLINKYQNLVRGKARKYFLIGAEKEDIVQEGMIGLYKAIRDFNEDKLTSFKGF 87

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +   I   +   I  +         +                                  
Sbjct: 88  AELCITRQIITAIKTATRQKHGPLNSY--------------------------------- 114

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
                    IS++  L  +ES           +    D +  D     + ++  +E+   
Sbjct: 115 ---------ISLDKPLYDEES-----------NYTLMDMIPGDQIANPEAVLIHQEKVED 154

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R +  +    L+  ER+         +  +   +S E       V+ I   A ++++  +
Sbjct: 155 REL--KIAETLSELERKALMLY---MDGHSYAEISKELN---THVKSI-DNALQRIKRKL 205

Query: 285 QKQVELSSS 293
            + VE   +
Sbjct: 206 GRDVESRQA 214


>gi|168187718|ref|ZP_02622353.1| RNA polymerase sigma-H factor [Clostridium botulinum C str. Eklund]
 gi|169294447|gb|EDS76580.1| RNA polymerase sigma-H factor [Clostridium botulinum C str. Eklund]
          Length = 219

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 25/146 (17%), Positives = 56/146 (38%), Gaps = 8/146 (5%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            ++GD+ A   L+  +   V   A  Y   G    ++  EG IGL +A++ F P++    
Sbjct: 28  AKNGDVEAQEYLINKYKNFVKAKAKSYFLIGADKEDIYQEGMIGLYKAIRDFKPDKLSSF 87

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
             ++   +   +   I  +     I   T  +  +  ++    +  L  ++   +   + 
Sbjct: 88  KAFAELCVTRQIITAIKTATRQKHIPLNTYISLNKPIYDEESDRTLLDILSTVKVCDPE- 146

Query: 160 VAIAKKLNVSESEVISMNCRLAGDES 185
                +L +S  EV+ +   +    S
Sbjct: 147 -----ELVISREEVLKIEKEIEQVLS 167


>gi|85057660|ref|YP_456576.1| RNA polymerase sigma factor [Aster yellows witches'-broom
           phytoplasma AYWB]
 gi|84789765|gb|ABC65497.1| RNA polymerase sigma factor [Aster yellows witches'-broom
           phytoplasma AYWB]
          Length = 144

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 21/85 (24%), Positives = 44/85 (51%), Gaps = 3/85 (3%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI--SEVVSEGNIGLMQAVKKFDPERG 98
            +   +L   ++L+  HL LV K+   ++ Y   +   ++  EG +GL++A+  +  + G
Sbjct: 11  LKNKKNLEIRNQLIDLHLPLVKKLVSKFKYYPCVLQKQDLYQEGVLGLIKALDNY-VDLG 69

Query: 99  FRLATYSMWWIKAAMQEYILRSWSL 123
           +    Y+   IK+ ++E I +S S 
Sbjct: 70  YDFIAYATPTIKSDIRESIRKSHSP 94


>gi|167629450|ref|YP_001679949.1| RNA polymerase sigma-70 factor [Heliobacterium modesticaldum Ice1]
 gi|167592190|gb|ABZ83938.1| RNA polymerase sigma-70 factor [Heliobacterium modesticaldum Ice1]
          Length = 247

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 22/102 (21%), Positives = 38/102 (37%), Gaps = 4/102 (3%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
              L  +E   +AK     GD  A   L+  +   V   A  Y   G    +++ EG IG
Sbjct: 18  FEQLVDEEVVEMAK----EGDEEALEYLINKYKNFVRAKARSYFLIGADREDIIQEGMIG 73

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           L +A++ F  ++      ++   I   +   I  +     I 
Sbjct: 74  LYKAIRDFRCDKLSSFRAFAELCITRQIITAIKTATRQKHIP 115


>gi|30018364|ref|NP_829995.1| RNA polymerase factor sigma-70 [Bacillus cereus ATCC 14579]
 gi|206972181|ref|ZP_03233128.1| RNA polymerase sigma-30 factor [Bacillus cereus AH1134]
 gi|218231038|ref|YP_002364943.1| RNA polymerase factor sigma-70 [Bacillus cereus B4264]
 gi|228950642|ref|ZP_04112776.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228956535|ref|ZP_04118331.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|229040999|ref|ZP_04189762.1| RNA polymerase sigma-H factor [Bacillus cereus AH676]
 gi|229067859|ref|ZP_04201176.1| RNA polymerase sigma-H factor [Bacillus cereus F65185]
 gi|229077389|ref|ZP_04210049.1| RNA polymerase sigma-H factor [Bacillus cereus Rock4-2]
 gi|229107780|ref|ZP_04237416.1| RNA polymerase sigma-H factor [Bacillus cereus Rock1-15]
 gi|229125611|ref|ZP_04254643.1| RNA polymerase sigma-H factor [Bacillus cereus BDRD-Cer4]
 gi|229142900|ref|ZP_04271341.1| RNA polymerase sigma-H factor [Bacillus cereus BDRD-ST24]
 gi|229148503|ref|ZP_04276759.1| RNA polymerase sigma-H factor [Bacillus cereus m1550]
 gi|229176694|ref|ZP_04304098.1| RNA polymerase sigma-H factor [Bacillus cereus 172560W]
 gi|229188379|ref|ZP_04315427.1| RNA polymerase sigma-H factor [Bacillus cereus ATCC 10876]
 gi|296500928|ref|YP_003662628.1| RNA polymerase factor sigma-70 [Bacillus thuringiensis BMB171]
 gi|29893904|gb|AAP07196.1| RNA polymerase sigma-H factor [Bacillus cereus ATCC 14579]
 gi|206732755|gb|EDZ49930.1| RNA polymerase sigma-30 factor [Bacillus cereus AH1134]
 gi|218158995|gb|ACK58987.1| RNA polymerase sigma-30 factor [Bacillus cereus B4264]
 gi|228595053|gb|EEK52824.1| RNA polymerase sigma-H factor [Bacillus cereus ATCC 10876]
 gi|228606737|gb|EEK64154.1| RNA polymerase sigma-H factor [Bacillus cereus 172560W]
 gi|228634919|gb|EEK91492.1| RNA polymerase sigma-H factor [Bacillus cereus m1550]
 gi|228640521|gb|EEK96910.1| RNA polymerase sigma-H factor [Bacillus cereus BDRD-ST24]
 gi|228657803|gb|EEL13609.1| RNA polymerase sigma-H factor [Bacillus cereus BDRD-Cer4]
 gi|228675629|gb|EEL30837.1| RNA polymerase sigma-H factor [Bacillus cereus Rock1-15]
 gi|228705923|gb|EEL58249.1| RNA polymerase sigma-H factor [Bacillus cereus Rock4-2]
 gi|228715218|gb|EEL67077.1| RNA polymerase sigma-H factor [Bacillus cereus F65185]
 gi|228727296|gb|EEL78490.1| RNA polymerase sigma-H factor [Bacillus cereus AH676]
 gi|228803100|gb|EEM49922.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228808993|gb|EEM55478.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|296321980|gb|ADH04908.1| RNA polymerase factor sigma-70 [Bacillus thuringiensis BMB171]
          Length = 219

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 37/268 (13%), Positives = 88/268 (32%), Gaps = 66/268 (24%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           LE +    L ++    G+  A   L+  +   V   +  Y   G    ++V EG IGL +
Sbjct: 16  LEDEAIVELVRK----GNTDALEYLIHKYKNFVRAKSRSYFLVGADREDIVQEGMIGLFK 71

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++ +  ++      ++   I   +   I  +     I   +                  
Sbjct: 72  AIRDYKEDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSY----------------- 114

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                                    +S++            I   + + +          
Sbjct: 115 -------------------------VSLDK----------PIYDEESDRTLLDVISEAKV 139

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
              E+++I +EE  +  + ++  +S L   ER++        +  + + +S +       
Sbjct: 140 TDPEEMIISQEEYTDIESKISELLSDL---ERKVLSLYL---DGRSYQEISEQLN---RH 190

Query: 269 VRQIEARAFKKVQESIQKQVELSSSPPL 296
           V+ I   A ++V+  +++ +E+  S  L
Sbjct: 191 VKSI-DNALQRVKRKLERYMEMRESTTL 217


>gi|228919044|ref|ZP_04082423.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228840569|gb|EEM85831.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
          Length = 219

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 38/268 (14%), Positives = 88/268 (32%), Gaps = 66/268 (24%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           LE +    L ++    G+  A   L+  +   V   +  Y   G    ++V EG IGL +
Sbjct: 16  LEDEAIVELVRK----GNTDALEYLIHKYKNFVRAKSRSYFLVGADREDIVQEGMIGLFK 71

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++ +  ++      ++   I   +   I  +     I   +                  
Sbjct: 72  AIRDYKEDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSY----------------- 114

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                                    +S++            I   + + +          
Sbjct: 115 -------------------------VSLDK----------PIYDEESDRTLLDVISEAKV 139

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
              E+++I +EE  +  + ++  +S L   ER++        N  + + +S +       
Sbjct: 140 TDPEEMIISQEEYTDIESKISELLSDL---ERKVLSLYL---NGRSYQEISEQLN---RH 190

Query: 269 VRQIEARAFKKVQESIQKQVELSSSPPL 296
           V+ I   A ++V+  +++ +E+  S  L
Sbjct: 191 VKSI-DNALQRVKRKLERYMEMRESTTL 217


>gi|153952844|ref|YP_001393609.1| RNA polymerase factor sigma-70 [Clostridium kluyveri DSM 555]
 gi|146345725|gb|EDK32261.1| RpoD1 [Clostridium kluyveri DSM 555]
          Length = 212

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 33/202 (16%), Positives = 80/202 (39%), Gaps = 10/202 (4%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            EE V+     + GD+ A   ++  +   V   A  Y   G    ++  EG IGL +A++
Sbjct: 18  DEEVVIQ---AKEGDVRAQEYMINKYENFVKSKAKSYFLIGADKEDIYQEGMIGLYKAIR 74

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQAI 149
            F  ++      ++   +   +   I  +     I   T  +  +  ++    +  L  +
Sbjct: 75  DFKTDKLSSFKAFAELCVTRQIITAIKTATRQKHIPLNTYVSLNKPIYDEESDRTLLDVL 134

Query: 150 TDNNLK-PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           ++  +  PE+++   ++L    +E+  +   L     +  L++  D  S Q     +  H
Sbjct: 135 SEAKVADPEELIISREELKHIHNEIGEVLSSL----EMEVLMSYLDGKSYQEIACDLDRH 190

Query: 209 DGQEQVLIEKEERKNRRNMLTR 230
                  +++ +RK  + ++ +
Sbjct: 191 AKSIDNALQRVKRKLEKCLINK 212


>gi|257469667|ref|ZP_05633759.1| RNA polymerase factor sigma-70 [Fusobacterium ulcerans ATCC 49185]
 gi|317063900|ref|ZP_07928385.1| RNA polymerase sigma-H factor [Fusobacterium ulcerans ATCC 49185]
 gi|313689576|gb|EFS26411.1| RNA polymerase sigma-H factor [Fusobacterium ulcerans ATCC 49185]
          Length = 197

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 19/81 (23%), Positives = 38/81 (46%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + GD  A  ++  S  +L++     Y  +G    +V+ E  IGL++A+  +D  +    
Sbjct: 10  AQEGDEDAIQQIFESFKQLMIFKTKKYFFHGGDREDVMQEAMIGLLKAINAYDENKNASF 69

Query: 102 ATYSMWWIKAAMQEYILRSWS 122
            T+++  IK  +   +  S S
Sbjct: 70  TTFALLCIKRQIITALKNSNS 90


>gi|172056123|ref|YP_001812583.1| RNA polymerase factor sigma-70 [Exiguobacterium sibiricum 255-15]
 gi|171988644|gb|ACB59566.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Exiguobacterium
           sibiricum 255-15]
          Length = 213

 Score = 58.7 bits (141), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 41/255 (16%), Positives = 84/255 (32%), Gaps = 64/255 (25%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L ++ +   +  A   L+  +   V   A  Y   G    +++ EG IGL +AV+ +  
Sbjct: 16  ALVEQAKVFDNSDALEFLIERYRNFVRAKARSYFLIGADREDIIQEGMIGLYKAVRDYRT 75

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           ++      ++   I   M   I  +     I   +                         
Sbjct: 76  DKLASFKGFAELCITRQMITAIKTATRQKHIPLNSY------------------------ 111

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
                             IS++  +  DES                D +        QVL
Sbjct: 112 ------------------ISLDKPIYDDES-----------ERTLLDIITSTAPSDPQVL 142

Query: 216 I-EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
           I  +EE  +  + +   +S L   ER++        +  T + +S + +     V+ I  
Sbjct: 143 IVNREEYADIESKMDEILSDL---ERKVLALYL---DGRTYQEISDDLD---RHVKSI-D 192

Query: 275 RAFKKVQESIQKQVE 289
            A ++V++ +++ +E
Sbjct: 193 NALQRVKKKLERYLE 207


>gi|222099110|ref|YP_002533678.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermotoga
           neapolitana DSM 4359]
 gi|221571500|gb|ACM22312.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermotoga
           neapolitana DSM 4359]
          Length = 193

 Score = 58.3 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 36/225 (16%), Positives = 72/225 (32%), Gaps = 67/225 (29%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y + G   A   ++  +  +VVKI+  Y        +V+  G +GL++A+  +D  +   
Sbjct: 17  YAQAGFKEAIDLIIEKYYPMVVKISSRYFASWAEQEDVIQNGLVGLIKAIFYYDSSK-SS 75

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
             +++   +++ ++ ++                     + R K                 
Sbjct: 76  FTSFAWRSVESEIKSFLT-------------------YMNRKKNR--------------- 101

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
                +     +V SM      D        S D   S   D +                
Sbjct: 102 -----MLSDAVKVESMEKE-EDDSPFEMPDASRDIAQSALSDII---------------- 139

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
                  L + +  LN  E+ IF  R L  +  + + ++ EF VS
Sbjct: 140 -------LEKVLENLNELEKNIF-LRWL--DGYSYKEIAEEFRVS 174


>gi|308070993|ref|YP_003872598.1| RNA polymerase sigma-H factor (Sigma-30) [Paenibacillus polymyxa
           E681]
 gi|305860272|gb|ADM72060.1| RNA polymerase sigma-H factor (Sigma-30) [Paenibacillus polymyxa
           E681]
          Length = 221

 Score = 58.3 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 34/250 (13%), Positives = 81/250 (32%), Gaps = 62/250 (24%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GD  A   L+  +   V   A  Y   G    +++ EG IGL ++++ F  ++      
Sbjct: 34  EGDGEALEFLINKYRNFVRAKARSYFLIGADREDIIQEGMIGLYKSIRDFKGDKLASFKA 93

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           ++   I   +   I  +     I   +                                 
Sbjct: 94  FAELCITRQIITAIKTATRQKHIPLNSY-------------------------------- 121

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
                     +S++            I   + + +             E+++I +EE   
Sbjct: 122 ----------VSLDK----------PIYDEESDRTLLDVICGTQVSDPEELIINQEEFVG 161

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             + ++  +S L   ER++        +  + + ++ + +     V+ I   A ++V+  
Sbjct: 162 LEDKMSEILSEL---ERKVLMLYL---DGRSYQEIAEDLD---RHVKSI-DNALQRVKRK 211

Query: 284 IQKQVELSSS 293
           ++K +E+  S
Sbjct: 212 LEKYLEVRDS 221


>gi|291558000|emb|CBL35117.1| DNA-directed RNA polymerase specialized sigma subunit [Eubacterium
           siraeum V10Sc8a]
          Length = 73

 Score = 58.3 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 13/57 (22%), Positives = 31/57 (54%), Gaps = 2/57 (3%)

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L  ++  L+ RE+ I + R  +    T   ++ E  +S+ +V ++E  A  K+++++
Sbjct: 19  LKEAIIGLDDREKNILKLRFFRG--KTQVEVAQEIGISQAQVSRLEKGALGKIKKAL 73


>gi|221312231|ref|ZP_03594036.1| RNA polymerase factor sigma-70 [Bacillus subtilis subsp. subtilis
           str. NCIB 3610]
 gi|221321428|ref|ZP_03602722.1| RNA polymerase factor sigma-70 [Bacillus subtilis subsp. subtilis
           str. SMY]
 gi|296333095|ref|ZP_06875549.1| RNA polymerase factor sigma-70 [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|305672797|ref|YP_003864468.1| RNA polymerase sigma factor H [Bacillus subtilis subsp. spizizenii
           str. W23]
 gi|321313769|ref|YP_004206056.1| RNA polymerase factor sigma-70 [Bacillus subtilis BSn5]
 gi|291482470|dbj|BAI83545.1| RNA polymerase factor sigma-70 [Bacillus subtilis subsp. natto
           BEST195]
 gi|296149711|gb|EFG90606.1| RNA polymerase factor sigma-70 [Bacillus subtilis subsp. spizizenii
           ATCC 6633]
 gi|305411040|gb|ADM36158.1| RNA polymerase sigma factor H [Bacillus subtilis subsp. spizizenii
           str. W23]
 gi|320020043|gb|ADV95029.1| RNA polymerase factor sigma-70 [Bacillus subtilis BSn5]
          Length = 218

 Score = 58.3 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 37/248 (14%), Positives = 79/248 (31%), Gaps = 62/248 (25%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A   L+T +   V   A  Y   G    ++V EG IGL ++++ F  ++      +
Sbjct: 30  GDSDALDYLITKYRNFVRAKARSYFLIGADREDIVQEGMIGLYKSIRDFKEDKLTSFKAF 89

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +   I   +   I  +     I   +                                  
Sbjct: 90  AELCITRQIITAIKTATRQKHIPLNSY--------------------------------- 116

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
                    +S++            I   + + +             E+++I +EE  + 
Sbjct: 117 ---------VSLDK----------PIFDEESDRTLLDVISGAKTLNPEEMIINQEEFDDI 157

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              +   +S L   ER++        +  + + +S E       V+ I   A ++V+  +
Sbjct: 158 EMKMGELLSDL---ERKVLVLYL---DGRSYQEISDELN---RHVKSI-DNALQRVKRKL 207

Query: 285 QKQVELSS 292
           +K +E+  
Sbjct: 208 EKYLEIRE 215


>gi|254431755|ref|ZP_05045458.1| SigH putative RNA polymerase sigma factor [Cyanobium sp. PCC 7001]
 gi|197626208|gb|EDY38767.1| SigH putative RNA polymerase sigma factor [Cyanobium sp. PCC 7001]
          Length = 206

 Score = 58.3 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 33/249 (13%), Positives = 71/249 (28%), Gaps = 57/249 (22%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGLMQAVKKFDPERG 98
           R   D  +   L+   L L    A  +      +    + +    + L+QA  +   ER 
Sbjct: 7   RSRRDAHSRDALIRRFLPLADARARRFHHRMPDLLEQDDCIQVARLALVQATARLREERT 66

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
                Y    I  A+  ++     +V++   A     + +L                   
Sbjct: 67  AP--AYLKRCIDGALSHHLRDRALMVRLPARARGHAPWRHL------------------- 105

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
                                     SL+A   S+  +S     WL             +
Sbjct: 106 --------------------------SLDAPATSAHSDSGPAPSWLDCLPAPAPIQPALE 139

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
            E+      + + +  L  R+  +     L  +  +L   +    +S   V +   R  +
Sbjct: 140 PEKP-----IVQLLKALPQRQAAVLRLTVL--DGRSLRQAAEFLGLSPMTVSRDRQRGLE 192

Query: 279 KVQESIQKQ 287
           ++++   +Q
Sbjct: 193 RLRQLFLEQ 201


>gi|39938894|ref|NP_950660.1| DNA-directed RNA polymerase sigma subunit [Onion yellows
           phytoplasma OY-M]
 gi|39722003|dbj|BAD04493.1| DNA-directed RNA polymerase sigma subunit [Onion yellows
           phytoplasma OY-M]
          Length = 199

 Score = 58.3 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 22/85 (25%), Positives = 44/85 (51%), Gaps = 3/85 (3%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL--PISEVVSEGNIGLMQAVKKFDPERG 98
            +   +L   ++L+  HL LV K+   ++ Y    P  ++  EG +GL++A+  +  + G
Sbjct: 11  LKSKKNLEMRNQLIDLHLSLVKKLVSKFKYYPCVLPKQDLYQEGVLGLIKALNNY-VDLG 69

Query: 99  FRLATYSMWWIKAAMQEYILRSWSL 123
           +    Y+   IK+ ++E I +S S 
Sbjct: 70  YDFIAYATPTIKSEIRELIRKSHSP 94


>gi|30260284|ref|NP_842661.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. Ames]
 gi|47525348|ref|YP_016697.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49183127|ref|YP_026379.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. Sterne]
 gi|49476711|ref|YP_034446.1| RNA polymerase factor sigma-70 [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|52145123|ref|YP_081705.1| RNA polymerase factor sigma-70 [Bacillus cereus E33L]
 gi|118475864|ref|YP_893015.1| RNA polymerase factor sigma-70 [Bacillus thuringiensis str. Al
           Hakam]
 gi|167635061|ref|ZP_02393378.1| RNA polymerase sigma-30 factor [Bacillus anthracis str. A0442]
 gi|170689558|ref|ZP_02880744.1| RNA polymerase sigma-30 factor [Bacillus anthracis str. A0465]
 gi|170707536|ref|ZP_02897989.1| RNA polymerase sigma-30 factor [Bacillus anthracis str. A0389]
 gi|177655592|ref|ZP_02936973.1| RNA polymerase sigma-30 factor [Bacillus anthracis str. A0174]
 gi|217957669|ref|YP_002336213.1| RNA polymerase factor sigma-70 [Bacillus cereus AH187]
 gi|218901296|ref|YP_002449130.1| RNA polymerase sigma-30 factor [Bacillus cereus AH820]
 gi|222093864|ref|YP_002527914.1| RNA polymerase factor sigma-70 [Bacillus cereus Q1]
 gi|225862146|ref|YP_002747524.1| RNA polymerase sigma-30 factor [Bacillus cereus 03BB102]
 gi|227812767|ref|YP_002812776.1| RNA polymerase sigma-30 factor [Bacillus anthracis str. CDC 684]
 gi|228912833|ref|ZP_04076480.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228925347|ref|ZP_04088443.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228931596|ref|ZP_04094502.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228943900|ref|ZP_04106285.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228983349|ref|ZP_04143562.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|229089225|ref|ZP_04220506.1| RNA polymerase sigma-H factor [Bacillus cereus Rock3-42]
 gi|229119756|ref|ZP_04249017.1| RNA polymerase sigma-H factor [Bacillus cereus 95/8201]
 gi|229136940|ref|ZP_04265567.1| RNA polymerase sigma-H factor [Bacillus cereus BDRD-ST26]
 gi|229153872|ref|ZP_04282002.1| RNA polymerase sigma-H factor [Bacillus cereus ATCC 4342]
 gi|229182488|ref|ZP_04309739.1| RNA polymerase sigma-H factor [Bacillus cereus BGSC 6E1]
 gi|229194484|ref|ZP_04321287.1| RNA polymerase sigma-H factor [Bacillus cereus m1293]
 gi|229601909|ref|YP_002864745.1| RNA polymerase sigma-30 factor [Bacillus anthracis str. A0248]
 gi|254684403|ref|ZP_05148263.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. CNEVA-9066]
 gi|254724234|ref|ZP_05186019.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. A1055]
 gi|254733752|ref|ZP_05191467.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. Western
           North America USA6153]
 gi|254756308|ref|ZP_05208337.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. Vollum]
 gi|300119596|ref|ZP_07057140.1| RNA polymerase factor sigma-70 [Bacillus cereus SJ1]
 gi|301051831|ref|YP_003790042.1| RNA polymerase sigma-70 factor [Bacillus anthracis CI]
 gi|30253605|gb|AAP24147.1| RNA polymerase sigma-30 factor [Bacillus anthracis str. Ames]
 gi|47500496|gb|AAT29172.1| RNA polymerase sigma-30 factor [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49177054|gb|AAT52430.1| RNA polymerase sigma-30 factor [Bacillus anthracis str. Sterne]
 gi|49328267|gb|AAT58913.1| RNA polymerase sigma-30 factor [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|51978592|gb|AAU20142.1| RNA polymerase sigma-30 factor [Bacillus cereus E33L]
 gi|118415089|gb|ABK83508.1| RNA polymerase, sigma 30 subunit, SigH [Bacillus thuringiensis str.
           Al Hakam]
 gi|167529535|gb|EDR92285.1| RNA polymerase sigma-30 factor [Bacillus anthracis str. A0442]
 gi|170127532|gb|EDS96406.1| RNA polymerase sigma-30 factor [Bacillus anthracis str. A0389]
 gi|170666471|gb|EDT17248.1| RNA polymerase sigma-30 factor [Bacillus anthracis str. A0465]
 gi|172080056|gb|EDT65154.1| RNA polymerase sigma-30 factor [Bacillus anthracis str. A0174]
 gi|217066749|gb|ACJ80999.1| RNA polymerase sigma-30 factor [Bacillus cereus AH187]
 gi|218535383|gb|ACK87781.1| RNA polymerase sigma-30 factor [Bacillus cereus AH820]
 gi|221237912|gb|ACM10622.1| RNA polymerase sigma-30 factor [Bacillus cereus Q1]
 gi|225786519|gb|ACO26736.1| RNA polymerase sigma-30 factor [Bacillus cereus 03BB102]
 gi|227007411|gb|ACP17154.1| RNA polymerase sigma-30 factor [Bacillus anthracis str. CDC 684]
 gi|228588950|gb|EEK46965.1| RNA polymerase sigma-H factor [Bacillus cereus m1293]
 gi|228600943|gb|EEK58512.1| RNA polymerase sigma-H factor [Bacillus cereus BGSC 6E1]
 gi|228629553|gb|EEK86250.1| RNA polymerase sigma-H factor [Bacillus cereus ATCC 4342]
 gi|228646478|gb|EEL02685.1| RNA polymerase sigma-H factor [Bacillus cereus BDRD-ST26]
 gi|228663657|gb|EEL19236.1| RNA polymerase sigma-H factor [Bacillus cereus 95/8201]
 gi|228694064|gb|EEL47746.1| RNA polymerase sigma-H factor [Bacillus cereus Rock3-42]
 gi|228776339|gb|EEM24692.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228815733|gb|EEM61969.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228828024|gb|EEM73752.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228834269|gb|EEM79810.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|228846769|gb|EEM91774.1| RNA polymerase sigma-H factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|229266317|gb|ACQ47954.1| RNA polymerase sigma-30 factor [Bacillus anthracis str. A0248]
 gi|298723068|gb|EFI63966.1| RNA polymerase factor sigma-70 [Bacillus cereus SJ1]
 gi|300374000|gb|ADK02904.1| RNA polymerase sigma-70 factor [Bacillus cereus biovar anthracis
           str. CI]
          Length = 218

 Score = 58.3 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 36/265 (13%), Positives = 87/265 (32%), Gaps = 66/265 (24%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           LE +    L ++    G+  A   L+  +   V   +  Y   G    ++V EG IGL +
Sbjct: 16  LEDEAIVELVRK----GNTDALEYLIHKYKNFVRAKSRSYFLVGADREDIVQEGMIGLFK 71

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++ +  ++      ++   I   +   I  +     I   +                  
Sbjct: 72  AIRDYKEDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSY----------------- 114

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                                    +S++            I   + + +          
Sbjct: 115 -------------------------VSLDK----------PIYDEESDRTLLDVISEAKV 139

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
              E+++I +EE  +  + ++  +S L   ER++        +  + + +S +       
Sbjct: 140 TDPEEMIISQEEYTDIESKISELLSDL---ERKVLSLYL---DGRSYQEISEQLN---RH 190

Query: 269 VRQIEARAFKKVQESIQKQVELSSS 293
           V+ I   A ++V+  +++ +E+  S
Sbjct: 191 VKSI-DNALQRVKRKLERYMEMRES 214


>gi|229015496|ref|ZP_04172494.1| RNA polymerase sigma-H factor [Bacillus cereus AH1273]
 gi|229021705|ref|ZP_04178287.1| RNA polymerase sigma-H factor [Bacillus cereus AH1272]
 gi|228739573|gb|EEL89987.1| RNA polymerase sigma-H factor [Bacillus cereus AH1272]
 gi|228745783|gb|EEL95787.1| RNA polymerase sigma-H factor [Bacillus cereus AH1273]
          Length = 219

 Score = 58.3 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 36/265 (13%), Positives = 87/265 (32%), Gaps = 66/265 (24%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           LE +    L ++    G+  A   L+  +   V   +  Y   G    ++V EG IGL +
Sbjct: 16  LEDEAIVELVRK----GNTDALEYLIHKYKNFVRAKSRSYFLVGADREDIVQEGMIGLFK 71

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++ +  ++      ++   I   +   I  +     I   +                  
Sbjct: 72  AIRDYKEDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSY----------------- 114

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                                    +S++            I   + + +          
Sbjct: 115 -------------------------VSLDK----------PIYDEESDRTLLDVISEAKV 139

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
              E+++I +EE  +  + ++  +S L   ER++        +  + + +S +       
Sbjct: 140 TDPEEMIISQEEYTDIESKISELLSDL---ERKVLSLYL---DGRSYQEISEQLN---RH 190

Query: 269 VRQIEARAFKKVQESIQKQVELSSS 293
           V+ I   A ++V+  +++ +E+  S
Sbjct: 191 VKSI-DNALQRVKRKLERYMEMRES 214


>gi|118443284|ref|YP_877182.1| RNA polymerase factor sigma-70 [Clostridium novyi NT]
 gi|118133740|gb|ABK60784.1| RNA polymerase sigma-H factor [Clostridium novyi NT]
          Length = 219

 Score = 58.3 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 26/146 (17%), Positives = 57/146 (39%), Gaps = 8/146 (5%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            ++GD+ A   L+  +   V   A  Y   G    ++  EG IGL +A++ F P++    
Sbjct: 28  AKNGDIKAQEYLINKYKNFVKAKAKSYFLVGADKEDIYQEGMIGLYKAIRDFKPDKLSSF 87

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
             ++   +   +   I  +     I   T  +  +  ++    +  L  ++   +   + 
Sbjct: 88  KAFAELCVTRQIITAIKTATRQKHIPLNTYISLNKPIYDEESDRTLLDILSTVKVCDPE- 146

Query: 160 VAIAKKLNVSESEVISMNCRLAGDES 185
                +L +S+ EVI +   +    S
Sbjct: 147 -----ELVISKEEVIKIEKEIEQVLS 167


>gi|288554708|ref|YP_003426643.1| RNA polymerase factor sigma-70 [Bacillus pseudofirmus OF4]
 gi|288545868|gb|ADC49751.1| RNA polymerase factor sigma-70 [Bacillus pseudofirmus OF4]
          Length = 215

 Score = 58.3 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 42/248 (16%), Positives = 81/248 (32%), Gaps = 62/248 (25%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A   L+  +   V   A  Y   G    ++V EG IGL +AV+ F  ++      +
Sbjct: 27  GDSGALEFLINKYKNFVRAKARSYFLIGADHEDIVQEGMIGLYKAVRDFKGDKLASFKAF 86

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +   I   +   I  +     I   +                                  
Sbjct: 87  AELCITRQIITAIKTATRQKHIPLNSY--------------------------------- 113

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
                    +S++  L  +ES          + +             E +LI +EE ++ 
Sbjct: 114 ---------VSLDKPLYDEES----------DRTLLDVICGSRVTNPEDLLINQEEFEDI 154

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              +   +S L   ER++     L  +  + + +S +       V+ I   A ++V+  +
Sbjct: 155 ELKMGEILSEL---ERQVL-MHYL--DGRSYQEISEDLN---RHVKSI-DNALQRVKRKL 204

Query: 285 QKQVELSS 292
           ++ VEL  
Sbjct: 205 ERYVELKG 212


>gi|310779951|ref|YP_003968283.1| RNA polymerase, sigma 30 subunit, SigH [Ilyobacter polytropus DSM
           2926]
 gi|309749274|gb|ADO83935.1| RNA polymerase, sigma 30 subunit, SigH [Ilyobacter polytropus DSM
           2926]
          Length = 203

 Score = 58.3 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 23/89 (25%), Positives = 40/89 (44%), Gaps = 1/89 (1%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           E  L K   + GD  A   +   +  LV+  +  Y   G    +++ EG IGL++A++ +
Sbjct: 2   EVNLVK-MAQEGDQEAVTEIFNKYRGLVLMKSKNYFLNGADRDDLLQEGMIGLLKAIRAY 60

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWS 122
           D  +     T++   IK  +   I  S S
Sbjct: 61  DEGKNTSFNTFASLCIKRQIITAIKNSNS 89


>gi|302872420|ref|YP_003841056.1| RNA polymerase sigma factor, sigma-70 family [Caldicellulosiruptor
           obsidiansis OB47]
 gi|302575279|gb|ADL43070.1| RNA polymerase sigma factor, sigma-70 family [Caldicellulosiruptor
           obsidiansis OB47]
          Length = 310

 Score = 58.3 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 18/72 (25%), Positives = 39/72 (54%), Gaps = 4/72 (5%)

Query: 50  AHRLVTSHLRLVVKIAMGY----RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
              L+ ++L+LV  +A  +    +GY   + +++SEG  GL+ A   + PE G   ++Y+
Sbjct: 14  RQLLIANNLKLVYHVANKFMPCPKGYMYEVDDLISEGYFGLVVAANNYKPELGTPFSSYA 73

Query: 106 MWWIKAAMQEYI 117
              I++ ++  +
Sbjct: 74  CKVIESKIKRSL 85


>gi|325677915|ref|ZP_08157557.1| putative RNA polymerase sigma-H factor [Ruminococcus albus 8]
 gi|324110469|gb|EGC04643.1| putative RNA polymerase sigma-H factor [Ruminococcus albus 8]
          Length = 194

 Score = 58.3 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 36/150 (24%), Positives = 61/150 (40%), Gaps = 8/150 (5%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEVVSEGNIG 85
           L  +E   LA       D +A   L+  ++ L   IA G     G    I ++V EG + 
Sbjct: 12  LSDEELVRLAV-----DDKAALTALLLRYVSLTEYIAAGLAPKAGREQMIKDLVQEGMMA 66

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++AV  + P+RG   ATY+   I+ +M  YI+             +     +       
Sbjct: 67  LLKAVNSYRPDRGAGFATYAGVCIRHSMLSYIMHDSRYSGSTLPEEELVKLTDRSIESDP 126

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
            + + D     E    IA++L+  E +V+ 
Sbjct: 127 ERLVIDREEYDELFKRIAEELSEKEWQVLR 156


>gi|256752506|ref|ZP_05493363.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermoanaerobacter
           ethanolicus CCSD1]
 gi|256748641|gb|EEU61688.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermoanaerobacter
           ethanolicus CCSD1]
          Length = 214

 Score = 58.3 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 37/264 (14%), Positives = 88/264 (33%), Gaps = 68/264 (25%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           +EE V+ +   + GD  A   L+  +   V   A  Y   G    +++ EG IGL +A++
Sbjct: 17  EEEEVVFR--AQKGDEIALEYLIERYKSFVKAKARAYFLVGADKEDIIQEGMIGLYKAIR 74

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
            +  ++      ++   +   +   I  +     I   +                     
Sbjct: 75  DYKSDKLTSFKAFAELCVTRQIITAIKTATRQKHIPLNSY-------------------- 114

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
                                 +S+N            I   + + +             
Sbjct: 115 ----------------------VSLNKP----------IFDEESDRTLMDVVSTQCIADP 142

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E+++I KEE  N  + +   +S L   E  +  +     +  + + ++ +        R 
Sbjct: 143 EELIISKEEYVNIESKMEELLSGL---EWEVLVSYL---DGKSYQEIAEDLN------RH 190

Query: 272 IEA--RAFKKVQESIQKQVELSSS 293
           +++   A ++V+  +++ +EL +S
Sbjct: 191 VKSVDNALQRVKRKLERYLELRNS 214


>gi|210623158|ref|ZP_03293612.1| hypothetical protein CLOHIR_01562 [Clostridium hiranonis DSM 13275]
 gi|210153791|gb|EEA84797.1| hypothetical protein CLOHIR_01562 [Clostridium hiranonis DSM 13275]
          Length = 216

 Score = 58.3 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 32/155 (20%), Positives = 65/155 (41%), Gaps = 4/155 (2%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EEY + KR   +GD  A   ++  +   V   A  Y   G    +++ EG IGL +A++ 
Sbjct: 19  EEYEIVKRAA-NGDRMALEYIMAKYKNFVRVKAKSYFLIGADREDIIQEGMIGLYKAIRD 77

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQAIT 150
           FD  +     +++   I   +   I  +     I   T  +  +  ++    +  L  IT
Sbjct: 78  FDETKAHSFRSFAEVCITRQIITAIKTATRQKHIPLNTYVSLSKPIYDEESERTLLDIIT 137

Query: 151 DNNLK-PEQVVAIAKKLNVSESEVISMNCRLAGDE 184
            + +  PE+++   ++L   E ++  +   L  + 
Sbjct: 138 ASMVTNPEELIISKEELKNIEDKINKLLSELEQEV 172


>gi|160901830|ref|YP_001567411.1| RNA polymerase factor sigma-70 [Petrotoga mobilis SJ95]
 gi|160359474|gb|ABX31088.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Petrotoga mobilis
           SJ95]
          Length = 212

 Score = 58.3 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 35/249 (14%), Positives = 89/249 (35%), Gaps = 70/249 (28%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             + GD  A   ++     +V  I   Y G  L   + +  G +GL+QAV  F  +   +
Sbjct: 19  LAQIGDNQALGIILEKFEPMVKSIVGKYYGTWLEFEDFLQIGLVGLIQAVYNFRKDANAK 78

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            ++++   I + ++ ++                     L R K  +              
Sbjct: 79  FSSFAYMNISSEIKSFVT-------------------YLNRNKHKVL------------- 106

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
                     +E +SM               ++D   ++  D+ +   D +++  +++  
Sbjct: 107 ----------TEAVSME--------------NTDDEFTENADYYIESVDSEKKDFLQE-- 140

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                  L++S+  L   ER I E   +  +  + + +  + +++ ++V        +K+
Sbjct: 141 -----YFLSKSLEQLECNEREIVEL-WI--DGYSYQEIGDKMKINTKKV----DNTIQKI 188

Query: 281 QESIQKQVE 289
           ++   + +E
Sbjct: 189 KKVFARNIE 197


>gi|326391114|ref|ZP_08212660.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermoanaerobacter
           ethanolicus JW 200]
 gi|325992813|gb|EGD51259.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermoanaerobacter
           ethanolicus JW 200]
          Length = 214

 Score = 58.3 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 38/262 (14%), Positives = 89/262 (33%), Gaps = 64/262 (24%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           +EE V+ +   + GD  A   L+  +   V   A  Y   G    +++ EG IGL +A++
Sbjct: 17  EEEEVVFR--AQKGDEVALEYLIERYKSFVKAKARAYFLVGADKEDIIQEGMIGLYKAIR 74

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
            +  ++      ++   +   +   I  +     I   +                     
Sbjct: 75  DYKSDKLTSFKAFAELCVTRQIITAIKTATRQKHIPLNSY-------------------- 114

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
                                 +S+N  +  +ES          + +             
Sbjct: 115 ----------------------VSLNKPIFDEES----------DRTLMDVVSTQCVADP 142

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E+++I KEE  N  + +   +S L   E  +  +     +  + + ++ +       V+ 
Sbjct: 143 EELIISKEEYVNIESKMEELLSGL---EWEVLVSYL---DGKSYQEIAEDLN---RHVKS 193

Query: 272 IEARAFKKVQESIQKQVELSSS 293
           I   A ++V+  +++ +E+ +S
Sbjct: 194 I-DNALQRVKRKLERYLEMRNS 214


>gi|295101345|emb|CBK98890.1| RNA polymerase sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii L2-6]
          Length = 221

 Score = 58.3 bits (140), Expect = 1e-06,   Method: Composition-based stats.
 Identities = 44/250 (17%), Positives = 85/250 (34%), Gaps = 58/250 (23%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL--------PISEVVSEGNIGLMQAVKK 92
             + GD +A   L+ ++   + K+A                   ++   GN+GL +AV K
Sbjct: 11  LAQKGDAAALDSLIDNNKSFIGKVANDLFRSMNLAQSGLNLDTDDLKQAGNLGLWKAVPK 70

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  RG +  TY+   I+ AM + +                              A    
Sbjct: 71  FDAARGMKFLTYAAPAIRNAMMDMVRD-------------------------AFAAFEQR 105

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
            +  ++     ++        +S++  L G+E L            Q  + +   +  Q 
Sbjct: 106 MVTEDKDGICYQR--------VSLDDVLPGEEQL------------QRIEAIADPYAMQP 145

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVR 270
           Q ++E +E    R  L   +  L  RE+     R          L   +  F +++ R +
Sbjct: 146 QSIMEDQES---RRELYDGLKRLTQREQTYLLYRYGFTDGKEHPLIGTAIYFHLTKGRAQ 202

Query: 271 QIEARAFKKV 280
           + E +A   +
Sbjct: 203 KTEEQAMDNL 212


>gi|160893355|ref|ZP_02074142.1| hypothetical protein CLOL250_00905 [Clostridium sp. L2-50]
 gi|156865047|gb|EDO58478.1| hypothetical protein CLOL250_00905 [Clostridium sp. L2-50]
          Length = 200

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 23/93 (24%), Positives = 43/93 (46%), Gaps = 3/93 (3%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             +E   L    RE  D +A   L+  ++ +V K +      G    +++ EG IGL++A
Sbjct: 8   TDEENIRL---IREENDNAAFEYLIKKYMGIVKKESRALYIIGAENEDIIQEGMIGLIKA 64

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           ++ FD  +G   +T++   IK  +   +  S  
Sbjct: 65  IRSFDGSKGASFSTFANLCIKRQLITAVKLSNR 97


>gi|39938806|ref|NP_950572.1| DNA-directed RNA polymerase specialized sigma subunit [Onion
           yellows phytoplasma OY-M]
 gi|39938846|ref|NP_950612.1| DNA-directed RNA polymerase specialized sigma subunit [Onion
           yellows phytoplasma OY-M]
 gi|39721915|dbj|BAD04405.1| DNA-directed RNA polymerase specialized sigma [Onion yellows
           phytoplasma OY-M]
 gi|39721955|dbj|BAD04445.1| DNA-directed RNA polymerase specialized sigma [Onion yellows
           phytoplasma OY-M]
          Length = 209

 Score = 58.3 bits (140), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 24/95 (25%), Positives = 45/95 (47%), Gaps = 4/95 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAM--GYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
            +   +L    +L+  HL L+ KI     Y    L   ++  EG +GL++A+  +  + G
Sbjct: 11  LKNKKNLEIRDQLIELHLPLIKKIVNQFKYYPRVLTKEDLYQEGILGLIKALNHYQ-DLG 69

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
           +    Y+   IK+ ++E I +S S   I    ++K
Sbjct: 70  YDFIAYANPTIKSEIKELIRKSHSP-SIPQKNHKK 103


>gi|310829596|ref|YP_003961953.1| RNA polymerase [Eubacterium limosum KIST612]
 gi|308741330|gb|ADO38990.1| RNA polymerase [Eubacterium limosum KIST612]
          Length = 191

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 31/249 (12%), Positives = 83/249 (33%), Gaps = 63/249 (25%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L K+  + GD  A   +V  +  +V + A  +   G    +++ EG I L+ A+  +  
Sbjct: 6   ELVKK-AQGGDKEAVVTIVEKYRCVVTQKARPFYYIGGDQEDLIQEGMIALLGAIWDYRE 64

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           +RG    T++   ++  ++  + ++                                   
Sbjct: 65  DRGTSFKTFAGLCVENRIKSVVTKAKRPKH------------------------------ 94

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
                                   +    SL + I+  D +++             ++ L
Sbjct: 95  ----------------------SPMGDTVSLYSPISEDDPDTTLLDLVASTAALDPDEEL 132

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
           + +E  ++   +   + S L+  E+++           + + +S +   S++ V      
Sbjct: 133 VTREAVEHFSQV---AKSELSELEKQVL---YFYLKGASHQEISDKIGRSKKAV----DN 182

Query: 276 AFKKVQESI 284
           A +++++ I
Sbjct: 183 AIQRIRKKI 191


>gi|291563180|emb|CBL41996.1| Sigma-70 region 3 [butyrate-producing bacterium SS3/4]
          Length = 203

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 31/178 (17%), Positives = 74/178 (41%), Gaps = 9/178 (5%)

Query: 10  VNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           ++ E     Y+ EI  IP   + E   L    R +G+ +A  RL+  +L+  +     Y 
Sbjct: 27  LSAEDIYRVYMEEIAAIPPCSEAENAKLLGEIR-NGNKAARERLIEGNLKNALFFVQDYI 85

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
             G+P+++++ E ++ LM    +                I+  M+E I        I   
Sbjct: 86  NKGVPMADLIQEASLELMMLADE---GFEGSFEKLLESRIRVRMEEIINDQKKEADI--- 139

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
             ++ +   +  L+   +++ +   +  ++  +A+++ ++E EV  +        S++
Sbjct: 140 --EEEMLARVNVLQEVSKSMAEELGREAKLSELAERMKMTEDEVREIMKVTMDALSMS 195


>gi|310644222|ref|YP_003948981.1| RNA polymerase sigma-h factor [Paenibacillus polymyxa SC2]
 gi|309249173|gb|ADO58740.1| RNA polymerase sigma-H factor [Paenibacillus polymyxa SC2]
          Length = 214

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 33/250 (13%), Positives = 81/250 (32%), Gaps = 62/250 (24%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GD  A   L+  +   V   A  Y   G    +++ EG IGL ++++ F  ++      
Sbjct: 27  EGDGEALEFLINKYRNFVRAKARSYFLIGADREDIIQEGMIGLYKSIRDFKGDKLASFKA 86

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           ++   I   +   I  +     I   +                                 
Sbjct: 87  FAELCITRQIITAIKTATRQKHIPLNSY-------------------------------- 114

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
                     +S++            I   + + +             E+++I +EE   
Sbjct: 115 ----------VSLDK----------PIYDEESDRTLLDVICGTQVSDPEELIINQEEFVG 154

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             + ++  ++ L   ER++        +  + + ++ + +     V+ I   A ++V+  
Sbjct: 155 LEDKMSEILNEL---ERKVLMLYL---DGRSYQEIAEDLD---RHVKSI-DNALQRVKRK 204

Query: 284 IQKQVELSSS 293
           ++K +E+  S
Sbjct: 205 LEKYLEVRDS 214


>gi|253580392|ref|ZP_04857658.1| RNA polymerase [Ruminococcus sp. 5_1_39B_FAA]
 gi|251848485|gb|EES76449.1| RNA polymerase [Ruminococcus sp. 5_1_39BFAA]
          Length = 178

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 26/96 (27%), Positives = 44/96 (45%), Gaps = 2/96 (2%)

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           DK +    + L      +E++  E   +  R   L +S+  L+ RER I   R   +   
Sbjct: 85  DKKTHYSLEILKQQTIPREKMPEEIVAKIMREETLRKSLEQLSDREREILLGRFYYQKSS 144

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           T   L  +  +S   VR I+ RA +K++  ++KQ E
Sbjct: 145 T--ELGRQMNLSPGNVRMIQKRALEKLRMIMEKQGE 178


>gi|323490597|ref|ZP_08095802.1| RNA polymerase factor sigma-70 [Planococcus donghaensis MPA1U2]
 gi|323395689|gb|EGA88530.1| RNA polymerase factor sigma-70 [Planococcus donghaensis MPA1U2]
          Length = 216

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 41/251 (16%), Positives = 84/251 (33%), Gaps = 64/251 (25%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           G+  A   L+T     V   A  Y   G    +++ EG IGL +A++ F  ++      +
Sbjct: 27  GNTEALDFLITKFRPFVRMKARSYFLIGADKEDIIQEGMIGLYKAIRDFKSDKLSSFRAF 86

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +   I   +   I  +     I   +                                  
Sbjct: 87  AELCIIRQIITAIKTATRQKHIPLNSY--------------------------------- 113

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
                    IS++  +  +ES   L++    N            D  E ++I  EE +  
Sbjct: 114 ---------ISLDKPIYDEESDRTLMDVLTGNGV----------DDPEDLIIHNEEFQYM 154

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER-VRQIEARAFKKVQES 283
              +   +S L   ER +        +  + + +S +     ER V+ I   A ++V+  
Sbjct: 155 EEKMGEVLSEL---EREVLALYL---DGQSYQEISEKL----ERHVKSI-DNALQRVKRK 203

Query: 284 IQKQVELSSSP 294
           +++ ++++  P
Sbjct: 204 LERHLQINEMP 214


>gi|332982726|ref|YP_004464167.1| RNA polymerase sigma-30 subunit SigH [Mahella australiensis 50-1
           BON]
 gi|332700404|gb|AEE97345.1| RNA polymerase, sigma 30 subunit, SigH [Mahella australiensis 50-1
           BON]
          Length = 216

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 27/148 (18%), Positives = 54/148 (36%), Gaps = 7/148 (4%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           E  L  R ++ GD  A   L+  +  ++   A  Y   G    +++ EG IGL +A+K +
Sbjct: 17  ERELVSRAKK-GDDVALECLIERYKSIIHNRAKTYFLKGSDREDIIQEGLIGLYKAIKNY 75

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG----TTANQKRLFFNLRRLKGHLQAI 149
             ++     +++   I   +   +  +     I      + N+        R    + A+
Sbjct: 76  REDKAVSFRSFADMCITRQIITAVKAATRQKHIPLNSYVSLNKTIYEDEAERQLMDVIAL 135

Query: 150 TDNNLKPEQV--VAIAKKLNVSESEVIS 175
                  E V     A +L     + +S
Sbjct: 136 EPQGDPEEMVISEESAMRLRSKIEQTLS 163


>gi|294509181|ref|YP_003566109.1| RNA polymerase sigma-H factor [Bacillus megaterium QM B1551]
 gi|294352105|gb|ADE72429.1| RNA polymerase sigma-H factor [Bacillus megaterium QM B1551]
          Length = 220

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 42/194 (21%), Positives = 68/194 (35%), Gaps = 23/194 (11%)

Query: 22  EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           EIR+  M    EE V   +  + GD    + LV  +  LV      Y   G    +++ E
Sbjct: 8   EIREKKMTLNDEEIV---QAFQKGDEDVFNVLVKKYEYLVWSKVKRYFLLGGDREDLLQE 64

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--------TTANQK 133
             +GL +AV+ F  E       ++   I   +   I  S                  N K
Sbjct: 65  ARLGLYKAVRDFKTEGMSSFRGFADLCITRQLITAIKASARQKHSPLNNALSLNIPKNSK 124

Query: 134 RLFFNLR--------RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM----NCRLA 181
           RL  +L         R     QA  +   K E+   + + L+  E +V ++       + 
Sbjct: 125 RLEDDLILMEMLPHPRAVSPEQATVEKENKREREQMLQEILSPIEQDVFTLYLKGQTYMQ 184

Query: 182 GDESLNALINSSDK 195
             ++LN    S D 
Sbjct: 185 ISQNLNLPQKSVDN 198


>gi|309390163|gb|ADO78043.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Halanaerobium
           praevalens DSM 2228]
          Length = 208

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 19/97 (19%), Positives = 43/97 (44%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K++E     +  + G+  A   L+  ++ +V   +  +   GL   +V+ EG +GL +A+
Sbjct: 3   KEKEEAEIIQMAQAGNDFAIEYLINQNMDIVYAKSRFFFIKGLDHDDVIQEGRVGLYKAI 62

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           + F  E+G     +S   +   +   I ++     + 
Sbjct: 63  RDFRAEKGASFRGFSQLCVHRQLISAIKKANRQKHVP 99


>gi|119716505|ref|YP_923470.1| sigma-70 region 4 domain-containing protein [Nocardioides sp.
           JS614]
 gi|119537166|gb|ABL81783.1| sigma-70 region 4 domain protein [Nocardioides sp. JS614]
          Length = 473

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 3/50 (6%)

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
           R  L  +   L  R R I   R   E   TL+ +     ++RERVRQ++ 
Sbjct: 41  RGWLDDAWVALPERSRDILRRRLAGE---TLDEIGLALNLTRERVRQVQK 87


>gi|295102717|emb|CBL00262.1| RNA polymerase sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii L2-6]
          Length = 221

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 42/250 (16%), Positives = 85/250 (34%), Gaps = 58/250 (23%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL--------PISEVVSEGNIGLMQAVKK 92
             + GD +A   L+ ++   + K+A                   ++   GN+GL +AV K
Sbjct: 11  LAQKGDAAALDSLIENNKSFIGKVANDLFRSMNLAQSGLNLDTDDLKQAGNLGLWKAVSK 70

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD   G +  TY+   I+ AM + +                              A    
Sbjct: 71  FDAACGMKFLTYAAPAIRNAMMDMVRD-------------------------AFAAFEQR 105

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
            +  ++     ++        +S++  L G+E L            +  + +   +  Q 
Sbjct: 106 MVTEDKDGVCYQR--------VSLDEVLPGEEQL------------RRIEAIADPYAMQP 145

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVR 270
           Q ++E++E    R  L   +  L  RE+     R          L   +  F +++ R +
Sbjct: 146 QSIMEEQES---RRELYDGLKRLTQREQTYLLYRYGFTDGEEHPLIGTAIYFHLTKGRAK 202

Query: 271 QIEARAFKKV 280
           + E +A   +
Sbjct: 203 KTEEQAMDNL 212


>gi|254756805|ref|ZP_05208833.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. Australia
           94]
          Length = 212

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 36/265 (13%), Positives = 87/265 (32%), Gaps = 66/265 (24%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           LE +    L ++    G+  A   L+  +   V   +  Y   G    ++V EG IGL +
Sbjct: 10  LEDEAIVELVRK----GNTDALEYLIHKYKNFVRAKSRSYFLVGADREDIVQEGMIGLFK 65

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++ +  ++      ++   I   +   I  +     I   +                  
Sbjct: 66  AIRDYKEDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSY----------------- 108

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                                    +S++            I   + + +          
Sbjct: 109 -------------------------VSLDK----------PIYDEESDRTLLDVISEAKV 133

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
              E+++I +EE  +  + ++  +S L   ER++        +  + + +S +       
Sbjct: 134 TDPEEMIISQEEYTDIESKISELLSDL---ERKVLSLYL---DGRSYQEISEQLN---RH 184

Query: 269 VRQIEARAFKKVQESIQKQVELSSS 293
           V+ I   A ++V+  +++ +E+  S
Sbjct: 185 VKSI-DNALQRVKRKLERYMEMRES 208


>gi|307266358|ref|ZP_07547896.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermoanaerobacter
           wiegelii Rt8.B1]
 gi|306918594|gb|EFN48830.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermoanaerobacter
           wiegelii Rt8.B1]
          Length = 214

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 38/262 (14%), Positives = 89/262 (33%), Gaps = 64/262 (24%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           +EE V+ +   + GD  A   L+  +   V   A  Y   G    +++ EG IGL +A++
Sbjct: 17  EEEEVVFR--AQKGDEVALEYLIERYKSFVKAKARAYFLVGADKEDIIQEGMIGLYKAIR 74

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
            +  ++      ++   +   +   I  +     I   +                     
Sbjct: 75  DYKSDKLTSFKAFAELCVTRQIITAIKTATRQKHIPLNSY-------------------- 114

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
                                 +S+N  +  +ES          + +             
Sbjct: 115 ----------------------VSLNKPIFDEES----------DRTLMDVVSTQCIADP 142

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E+++I KEE  N  + +   +S L   E  +  +     +  + + ++ +       V+ 
Sbjct: 143 EELIISKEEYVNIESKMEELLSGL---EWEVLVSYL---DGKSYQEIAEDLN---RHVKS 193

Query: 272 IEARAFKKVQESIQKQVELSSS 293
           I   A ++V+  +++ +E+ +S
Sbjct: 194 I-DNALQRVKRKLERYLEMRNS 214


>gi|261409537|ref|YP_003245778.1| RNA polymerase factor sigma-70 [Paenibacillus sp. Y412MC10]
 gi|315649720|ref|ZP_07902804.1| RNA polymerase factor sigma-70 [Paenibacillus vortex V453]
 gi|261286000|gb|ACX67971.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Paenibacillus sp.
           Y412MC10]
 gi|315274908|gb|EFU38284.1| RNA polymerase factor sigma-70 [Paenibacillus vortex V453]
          Length = 214

 Score = 57.9 bits (139), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 36/249 (14%), Positives = 80/249 (32%), Gaps = 62/249 (24%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GD  A   L+  +   V   A  Y   G    ++V EG IGL +A++ F  ++      
Sbjct: 27  EGDSGALEYLINKYRNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDFKGDKLSSFKA 86

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           ++   I   +   I  +     I   +                                 
Sbjct: 87  FAELCITRQIITAIKTATRQKHIPLNSY-------------------------------- 114

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
                     +S++            I   D + +             E+++I +EE   
Sbjct: 115 ----------VSLDK----------PIYDEDSDRTLLDVICGTAVSDPEELIINQEEFVG 154

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             + ++  +S L   ER++        +  + + ++ +    R  V+ I   A ++V+  
Sbjct: 155 LEDKMSEILSDL---ERKVLMLYL---DGRSYQEIAVDL---RRHVKSI-DNALQRVKRK 204

Query: 284 IQKQVELSS 292
           +++ +E+  
Sbjct: 205 LERYLEVRD 213


>gi|291531210|emb|CBK96795.1| DNA-directed RNA polymerase specialized sigma subunit [Eubacterium
           siraeum 70/3]
          Length = 97

 Score = 57.5 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 14/70 (20%), Positives = 36/70 (51%), Gaps = 2/70 (2%)

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
            +  +     L  ++  L+ RE+ I + R  +    T   ++ E  +S+ +V ++E  A 
Sbjct: 9   DDRNRLDEIALKEAIIGLDDREKNILKLRFFRG--KTQVEVAQEIGISQAQVSRLEKGAP 66

Query: 278 KKVQESIQKQ 287
            K+++++Q++
Sbjct: 67  GKIKKALQQK 76


>gi|266623350|ref|ZP_06116285.1| RNA polymerase sigma factor WhiG [Clostridium hathewayi DSM 13479]
 gi|288864870|gb|EFC97168.1| RNA polymerase sigma factor WhiG [Clostridium hathewayi DSM 13479]
          Length = 131

 Score = 57.5 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 23/109 (21%), Positives = 50/109 (45%), Gaps = 4/109 (3%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI---SEVVSEGNIGL 86
            ++E   +   Y ++G     ++L+   L +V   A   RG         +++ +G + L
Sbjct: 7   SREEGKTVLSVYLKNGSQELRNKLIVHFLPIVRSAAAQLRGMAGSFTEEEDLIDQGVLAL 66

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           M+ + ++D  +G +  TY+   ++ AM +YI      V     + QK++
Sbjct: 67  MECLDRYDASKGAQFETYAFIRVRGAMIDYIRSQ-DWVPHRARSFQKKV 114


>gi|187933087|ref|YP_001884458.1| RNA polymerase factor sigma-70 [Clostridium botulinum B str. Eklund
           17B]
 gi|187721240|gb|ACD22461.1| RNA polymerase sigma-H factor [Clostridium botulinum B str. Eklund
           17B]
          Length = 206

 Score = 57.5 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 32/196 (16%), Positives = 73/196 (37%), Gaps = 8/196 (4%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            EE VL     ++G+  A   +++ +   V   A  Y   G    ++  EG IGL +A++
Sbjct: 12  DEEVVLE---AKNGNTRAQEYMISKYENFVKAKAKSYFLIGADREDIYQEGMIGLYKAIR 68

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQAI 149
            F  ++      ++   +   +   I  +     I   T  +  +  +     +  L  +
Sbjct: 69  DFKADKLTSFKAFAELCVTRQIITAIKTATRQKHIPLNTYVSLNKPIYEEESERTLLDVL 128

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
           +   +   + + I K+       + +   ++  D  L  L++  D  S Q     +  H 
Sbjct: 129 SGIKISDPEELLINKE---HMDNIEAAIAKVLSDLELEVLMSYLDGKSYQEIACDLDRHS 185

Query: 210 GQEQVLIEKEERKNRR 225
                 +++ +RK  +
Sbjct: 186 KSIDNALQRVKRKLEK 201


>gi|56961915|ref|YP_173637.1| RNA polymerase factor sigma-70 [Bacillus clausii KSM-K16]
 gi|56908149|dbj|BAD62676.1| DNA-directed RNA polymerase sigma-30 factor sigma-H [Bacillus
           clausii KSM-K16]
          Length = 220

 Score = 57.5 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 49/263 (18%), Positives = 91/263 (34%), Gaps = 66/263 (25%)

Query: 33  EEYV---LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           EE+    L K  R  G+  A   L+  +   V   A  Y   G    ++V EG IGL +A
Sbjct: 18  EEWEDDSLIKEVR-TGNTLALEHLIGKYRNFVRAKARSYFLIGADHEDIVQEGMIGLYKA 76

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V+ F+ ++      ++   I   +   I  +     I   +                   
Sbjct: 77  VRDFNVDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSY------------------ 118

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
                                   +S++  L  +ES   L++    N     + L     
Sbjct: 119 ------------------------VSLDKPLYDEESDRTLMDVICGNKVTDPEAL----- 149

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
                LI +E+       ++  +S L   ER++        +  T + +S   ++ R  V
Sbjct: 150 -----LINQEDFAYIEGKMSEILSEL---ERQVLMLYL---DGRTYQEIS--IDLKR-HV 195

Query: 270 RQIEARAFKKVQESIQKQVELSS 292
           + I   A ++V+  +++ VEL S
Sbjct: 196 KSI-DNALQRVKRKLERYVELKS 217


>gi|262204446|ref|YP_003275654.1| sigma-70 region 4 domain-containing protein [Gordonia bronchialis
           DSM 43247]
 gi|262087793|gb|ACY23761.1| sigma-70 region 4 domain protein [Gordonia bronchialis DSM 43247]
          Length = 289

 Score = 57.5 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 19/73 (26%), Positives = 33/73 (45%)

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
              +    +   +  L+ R+R I E R L   P     L++   +SRERV QIE +   +
Sbjct: 151 MIADGLEAVADVIGSLDARDRLILEDRILALRPRRQSELAAMLGISRERVAQIERQLRAR 210

Query: 280 VQESIQKQVELSS 292
           ++E++     L  
Sbjct: 211 LRENVDTTAHLRG 223


>gi|257437879|ref|ZP_05613634.1| group2 RNA polymerase sigma factor RpoD6 [Faecalibacterium
           prausnitzii A2-165]
 gi|257199539|gb|EEU97823.1| group2 RNA polymerase sigma factor RpoD6 [Faecalibacterium
           prausnitzii A2-165]
          Length = 221

 Score = 57.5 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 43/250 (17%), Positives = 86/250 (34%), Gaps = 58/250 (23%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL--------PISEVVSEGNIGLMQAVKK 92
             + GD +A   L+ ++   + K+A                   ++   GN+GL +AV K
Sbjct: 11  LAQKGDAAALDSLIDNNKSFIGKVANDLFRSMNLAQAGLNLDTDDLKQAGNMGLWKAVPK 70

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  RG +  TY+   I+ AM + +                              A    
Sbjct: 71  FDAARGMKFLTYAAPAIRNAMMDMVRD-------------------------AFTAFEQR 105

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
            +  ++     ++        +S++  L G+E L            +  + +   +  Q 
Sbjct: 106 MVTEDKDGICCQR--------VSLDDVLPGEEQL------------RRIEAIADPYAMQP 145

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVR 270
           Q ++E++E    R  L   +  L  RE+     R          L   +  F +++ R +
Sbjct: 146 QTIMEEQEL---RRELYDGLKRLTQREQTYLLYRYGFTDGEEHPLIGTAIYFHLTKGRAQ 202

Query: 271 QIEARAFKKV 280
           + E +A   +
Sbjct: 203 KTEEQAMDNL 212


>gi|167036784|ref|YP_001664362.1| RNA polymerase factor sigma-70 [Thermoanaerobacter pseudethanolicus
           ATCC 33223]
 gi|167039504|ref|YP_001662489.1| RNA polymerase factor sigma-70 [Thermoanaerobacter sp. X514]
 gi|300915246|ref|ZP_07132561.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermoanaerobacter
           sp. X561]
 gi|307725170|ref|YP_003904921.1| ECF subfamily RNA polymerase sigma-24 subunit [Thermoanaerobacter
           sp. X513]
 gi|320115206|ref|YP_004185365.1| RNA polymerase sigma-H factor [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
 gi|166853744|gb|ABY92153.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermoanaerobacter
           sp. X514]
 gi|166855618|gb|ABY94026.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|300888970|gb|EFK84117.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermoanaerobacter
           sp. X561]
 gi|307582231|gb|ADN55630.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermoanaerobacter
           sp. X513]
 gi|319928297|gb|ADV78982.1| RNA polymerase sigma-H factor [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
          Length = 214

 Score = 57.5 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 27/155 (17%), Positives = 64/155 (41%), Gaps = 8/155 (5%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           +EE V+ +   + GD  A   L+  +   V   A  Y   G    +++ EG IGL +A++
Sbjct: 17  EEEEVVFR--AQKGDEIALEYLIERYKSFVKAKARAYFLVGADKEDIIQEGMIGLYKAIR 74

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR-LKGHLQAIT 150
            +  ++      ++   +   +   I  +     I   +     + +L + +       T
Sbjct: 75  DYKSDKLTSFKAFAELCVTRQIITAIKTATRQKHIPLNS-----YVSLNKPIFDEESDRT 129

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
             ++   Q +A  ++L +S+ E +++  ++    S
Sbjct: 130 LMDVVSTQCIADPEELIISKEEYVNIESKMEELLS 164


>gi|46371299|gb|AAS90415.1| stationary phase sigma factor [Azomonas macrocytogenes]
          Length = 55

 Score = 57.5 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 16/45 (35%), Positives = 26/45 (57%)

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
                TLE +  E  ++RERVRQI+  A K+++E ++K    S +
Sbjct: 8   GHESCTLEEVGQEIGLTRERVRQIQVEALKRLREILEKNGLSSDA 52


>gi|197301393|ref|ZP_03166474.1| hypothetical protein RUMLAC_00124 [Ruminococcus lactaris ATCC
           29176]
 gi|197299550|gb|EDY34069.1| hypothetical protein RUMLAC_00124 [Ruminococcus lactaris ATCC
           29176]
          Length = 206

 Score = 57.5 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 25/91 (27%), Positives = 44/91 (48%), Gaps = 1/91 (1%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L K +R +GD      L+  +  +V K A     +G    +++ EG IGL++AV+ +DP+
Sbjct: 12  LIKDFR-NGDREIMDHLMMKYKAMVRKKARAMYLFGGENEDLIQEGMIGLIKAVRDYDPD 70

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           +G   A+++   +   M   I  S     I 
Sbjct: 71  QGASFASFAELCVSRQMYSAIEASKRKKHIP 101


>gi|85057486|ref|YP_456402.1| hypothetical protein AYWB_206 [Aster yellows witches'-broom
           phytoplasma AYWB]
 gi|84789591|gb|ABC65323.1| conserved hypothetical protein [Aster yellows witches'-broom
           phytoplasma AYWB]
          Length = 120

 Score = 57.5 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 21/85 (24%), Positives = 44/85 (51%), Gaps = 3/85 (3%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS--EVVSEGNIGLMQAVKKFDPERG 98
            +   +L   ++L+  HL LV K+   ++ Y   +   ++  EG +GL++A+  +  + G
Sbjct: 11  LKSKKNLEMRNQLIDLHLPLVKKLVSKFKYYPCVLQKQDLYQEGFLGLIKALNNYQ-DLG 69

Query: 99  FRLATYSMWWIKAAMQEYILRSWSL 123
           +    Y+   IK+ ++E I +S S 
Sbjct: 70  YDFIAYAEPTIKSEIRELIRKSHSP 94


>gi|167767099|ref|ZP_02439152.1| hypothetical protein CLOSS21_01617 [Clostridium sp. SS2/1]
 gi|167711074|gb|EDS21653.1| hypothetical protein CLOSS21_01617 [Clostridium sp. SS2/1]
          Length = 1305

 Score = 57.5 bits (138), Expect = 2e-06,   Method: Composition-based stats.
 Identities = 36/217 (16%), Positives = 78/217 (35%), Gaps = 51/217 (23%)

Query: 71   YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            Y L I +V+SE   GL++AV K    +   L +     I   + EYI  +    +I    
Sbjct: 1139 YNLDIQDVISEAWCGLVEAVNKQSLRKNKNLVSD----IMKYVLEYISVNNYKNQISRLT 1194

Query: 131  NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
              K L ++   +                                        DE    +I
Sbjct: 1195 EIKCLVYDFAEI----------------------------------------DEVDGTVI 1214

Query: 191  NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +S         + + + +    +  E  +       L + +++L  +E++I       E
Sbjct: 1215 FNSRD------FYNINESEPDSIIYEENWDMICNIADLKKFLNILTKKEQKIICLYYGIE 1268

Query: 251  -NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             +   +  +++ + +S +RV QI  R  +K+++ +++
Sbjct: 1269 CDRRKIGEIANVYGISGQRVSQIIKRVLEKIKKYLRQ 1305


>gi|328551799|gb|AEB22291.1| RNA polymerase factor sigma-70 [Bacillus amyloliquefaciens TA208]
          Length = 218

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 36/248 (14%), Positives = 79/248 (31%), Gaps = 62/248 (25%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A   L+T +   V   A  Y   G    ++V EG IGL ++++ F  ++      +
Sbjct: 30  GDSDALDYLITKYRNFVRAKARSYFLIGADREDIVQEGMIGLYKSIRDFREDKLTSFKAF 89

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +   I   +   I  +     I   +                                  
Sbjct: 90  AELCITRQIITAIKTATRQKHIPLNSY--------------------------------- 116

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
                    +S++            I   + + +             E+++I +EE  + 
Sbjct: 117 ---------VSLDK----------PIFDEESDRTLLDVISGAKTLNPEEMIINQEEFDDI 157

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              +   +S L   ER++        +  + + +S +       V+ I   A ++V+  +
Sbjct: 158 EMKMGELLSDL---ERKVLVLYL---DGRSYQEISDDLN---RHVKSI-DNALQRVKRKL 207

Query: 285 QKQVELSS 292
           +K +E+  
Sbjct: 208 EKYLEIRE 215


>gi|154684616|ref|YP_001419777.1| RNA polymerase factor sigma-70 [Bacillus amyloliquefaciens FZB42]
 gi|126363077|emb|CAM35804.1| RNA polymerase sigma factor H [Bacillus amyloliquefaciens FZB42]
 gi|154350467|gb|ABS72546.1| SigH [Bacillus amyloliquefaciens FZB42]
          Length = 218

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 36/248 (14%), Positives = 79/248 (31%), Gaps = 62/248 (25%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A   L+T +   V   A  Y   G    ++V EG IGL ++++ F  ++      +
Sbjct: 30  GDSDALDYLITKYRNFVRAKARSYFLIGADREDIVQEGMIGLYKSIRDFREDKLTSFKAF 89

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +   I   +   I  +     I   +                                  
Sbjct: 90  AELCITRQIITAIKTATRQKHIPLNSY--------------------------------- 116

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
                    +S++            I   + + +             E+++I +EE  + 
Sbjct: 117 ---------VSLDK----------PIFDEESDRTLLDVISGAKTLNPEEMIINQEEFDDI 157

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              +   +S L   ER++        +  + + +S +       V+ I   A ++V+  +
Sbjct: 158 EMKMGELLSDL---ERKVLVLYL---DGRSYQEISDDLN---RHVKSI-DNALQRVKRKL 207

Query: 285 QKQVELSS 292
           +K +E+  
Sbjct: 208 EKYLEIRE 215


>gi|329925600|ref|ZP_08280441.1| RNA polymerase sigma-H factor [Paenibacillus sp. HGF5]
 gi|328939729|gb|EGG36071.1| RNA polymerase sigma-H factor [Paenibacillus sp. HGF5]
          Length = 212

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 36/249 (14%), Positives = 80/249 (32%), Gaps = 62/249 (24%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GD  A   L+  +   V   A  Y   G    ++V EG IGL +A++ F  ++      
Sbjct: 25  EGDSGALEYLINKYRNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDFKGDKLSSFKA 84

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           ++   I   +   I  +     I   +                                 
Sbjct: 85  FAELCITRQIITAIKTATRQKHIPLNSY-------------------------------- 112

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
                     +S++            I   D + +             E+++I +EE   
Sbjct: 113 ----------VSLDK----------PIYDEDSDRTLLDVICGTAVSDPEELIINQEEFVG 152

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             + ++  +S L   ER++        +  + + ++ +    R  V+ I   A ++V+  
Sbjct: 153 LEDKMSEILSDL---ERKVLMLYL---DGRSYQEIAVDL---RRHVKSI-DNALQRVKRK 202

Query: 284 IQKQVELSS 292
           +++ +E+  
Sbjct: 203 LERYLEVRD 211


>gi|260892313|ref|YP_003238410.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ammonifex degensii
           KC4]
 gi|260864454|gb|ACX51560.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ammonifex degensii
           KC4]
          Length = 215

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 27/152 (17%), Positives = 64/152 (42%), Gaps = 7/152 (4%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           +E    A++    GD+ A   L+  +   V   A  Y   G    +++ EG IGL +A++
Sbjct: 20  EEVVAYARK----GDVRAQEYLINKYKNFVRAKARAYFLVGADREDIIQEGMIGLYKAIR 75

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQAI 149
            F  ++      ++   I   +   I  +     I   +  +  +  ++    +  L  +
Sbjct: 76  DFRMDKLSSFRAFAELCITRQIITAIKTATRQKHIPLNSYVSLNKPIYDEDSDRTLLDVV 135

Query: 150 TDNNLK-PEQVVAIAKKLNVSESEVISMNCRL 180
           ++  +  PE+VV   ++ +  E+++  +  +L
Sbjct: 136 SEAKITDPEEVVISREEFDHIEAKMGEILSKL 167


>gi|317497564|ref|ZP_07955882.1| sigma-70 protein [Lachnospiraceae bacterium 5_1_63FAA]
 gi|316895123|gb|EFV17287.1| sigma-70 protein [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 61

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 14/57 (24%), Positives = 26/57 (45%), Gaps = 2/57 (3%)

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L  +M  L  RE  I + R       T   ++ E  +S+ +V ++E  A K ++  +
Sbjct: 6   LKEAMEHLPDREYDIIKMRFF--EGKTQTEVADEIAISQAQVSRLEKNALKHMKNHL 60


>gi|126215764|gb|ABN81002.1| putative RNA polymerase sigma-F factor [Rhodococcus opacus]
          Length = 130

 Score = 57.5 bits (138), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 21/139 (15%), Positives = 48/139 (34%), Gaps = 9/139 (6%)

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
           +R+      L   +  ++ +      V  +A+ L++ + EV          ++++    S
Sbjct: 1   RRMKELHLALSQAVAELSQSLGHAPTVSELAEHLDLEQEEVAQGLLAGNAYQTVSVDNTS 60

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
           SD+         + D+D     +            L   +  L  RER +   R      
Sbjct: 61  SDRTGELSMVETLGDYDAAMDDV-------ENHETLRPLLQSLPERERTVLMLRFFGN-- 111

Query: 253 VTLENLSSEFEVSRERVRQ 271
           +T   ++    +S+  V +
Sbjct: 112 MTQTQIADRVGISQMHVSR 130


>gi|222833283|gb|EEE71760.1| predicted protein [Populus trichocarpa]
          Length = 152

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 30/146 (20%), Positives = 58/146 (39%), Gaps = 11/146 (7%)

Query: 54  VTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           V SH  LV +IA+         + I +++  G IGL+ A K+++   G R  TY+   I+
Sbjct: 14  VKSHAPLVRRIALQLAAKLPASVQIDDLIQAGMIGLLDAAKRYEDNHGARFETYASQRIR 73

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
            AM + +  +            + L    R+++   + +     +      +AK+L +  
Sbjct: 74  GAMLDEVRANDW--------QSRSLRQFTRKIERTQRQLEQKLGRSPIDSEVAKELEMGL 125

Query: 171 SEVISMNCRLAGDESLNALINSSDKN 196
            E +  +       S +A       N
Sbjct: 126 EERLPGSAPWGDRRSESAHGADGIGN 151


>gi|207723155|ref|YP_002253554.1| alternative rna sigma factor rpos (partial sequence) protein
           [Ralstonia solanacearum MolK2]
 gi|206588349|emb|CAQ35312.1| alternative rna sigma factor rpos (partial sequence) protein
           [Ralstonia solanacearum MolK2]
          Length = 157

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 1/57 (1%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY 68
               +  Y++ I   P+L   EE   + R +  G+ +A   ++  +LRLVV IA GY
Sbjct: 100 AADTVQHYLNRISIKPLLTPAEELHFSTRAK-AGEFAARQVMIERNLRLVVSIAKGY 155


>gi|304437200|ref|ZP_07397161.1| RNA polymerase sigma-H factor [Selenomonas sp. oral taxon 149 str.
           67H29BP]
 gi|304369862|gb|EFM23526.1| RNA polymerase sigma-H factor [Selenomonas sp. oral taxon 149 str.
           67H29BP]
          Length = 279

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 39/259 (15%), Positives = 84/259 (32%), Gaps = 67/259 (25%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E +LA    E GD  A   L+  +   V   A  Y   G    ++V EG IG  +A++ 
Sbjct: 60  DEDLLAHIRGERGD-EALDYLINKYRNFVRSKARSYFLIGADREDIVQEGMIGFFKAIRD 118

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           + P++      ++   +   +   I  +     I   +                      
Sbjct: 119 YRPDKLSSFRAFAELCVTRQIITAIKTATRQKHIPLNSY--------------------- 157

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
                                +S+N            I   D + +             E
Sbjct: 158 ---------------------VSLNK----------PIYDEDSDRTLLDVLSGARISDPE 186

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           +++I  EE  +    +   +S L   E R+  +     +  + + ++ +        RQ+
Sbjct: 187 ELVISHEEFIDIEQKMEEILSDL---EWRVLMSYL---DGKSYQEIAVDLH------RQV 234

Query: 273 EA--RAFKKVQESIQKQVE 289
           ++   A ++V+  ++K +E
Sbjct: 235 KSIDNALQRVKRKLEKYME 253


>gi|319644909|ref|ZP_07999142.1| RNA polymerase sigma factor [Bacillus sp. BT1B_CT2]
 gi|319644913|ref|ZP_07999146.1| RNA polymerase sigma factor [Bacillus sp. BT1B_CT2]
 gi|317392718|gb|EFV73512.1| RNA polymerase sigma factor [Bacillus sp. BT1B_CT2]
 gi|317392722|gb|EFV73516.1| RNA polymerase sigma factor [Bacillus sp. BT1B_CT2]
          Length = 78

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 14/57 (24%), Positives = 27/57 (47%), Gaps = 2/57 (3%)

Query: 226 NMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             + + + +L+ RE+ +   R   +     T   ++ E  +SR  V +IE RA  K+
Sbjct: 4   EKVKKYIDILDGREKEVIVGRFGLDLKKEKTQREIAKELGISRSYVSRIEKRALMKM 60


>gi|313682837|ref|YP_004060575.1| sigma-70 region 4 domain protein [Sulfuricurvum kujiense DSM 16994]
 gi|313155697|gb|ADR34375.1| sigma-70 region 4 domain protein [Sulfuricurvum kujiense DSM 16994]
          Length = 83

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 16/41 (39%), Positives = 21/41 (51%)

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            +   L     TL  +     V+RERVRQIEA A KK++  
Sbjct: 31  LDRLGLHGCDFTLSEIGEVLHVTRERVRQIEASAIKKLKHP 71


>gi|28373140|ref|NP_783738.1| putative RNA polymerase sigma factor [Clostridium tetani E88]
 gi|28208724|gb|AAO37406.1|AF528097_10 putative RNA polymerase sigma factor [Clostridium tetani E88]
          Length = 179

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 26/134 (19%), Positives = 54/134 (40%), Gaps = 8/134 (5%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
            Y L   Y+  G+  A  +++ + + L++K A  Y+       ++V  G + +++A  K+
Sbjct: 1   MYKLLCEYK-RGNNKALEKIIENFIPLILKEASKYKIKCYDYEDLVQHGYLSVIKACNKY 59

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
               G     Y    I A    Y       +K      +    F L + K ++  + D  
Sbjct: 60  KGN-GDNFIPY---CINAIKNNYTALLKGEIK---HHREIPDEFILNKAKDYMFTLEDEV 112

Query: 154 LKPEQVVAIAKKLN 167
           +  E++  + K L+
Sbjct: 113 IAYEKIEELYKALD 126


>gi|292669227|ref|ZP_06602653.1| RNA polymerase, sigma-24 subunit, ECF subfamily protein
           [Selenomonas noxia ATCC 43541]
 gi|292649068|gb|EFF67040.1| RNA polymerase, sigma-24 subunit, ECF subfamily protein
           [Selenomonas noxia ATCC 43541]
          Length = 207

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 43/259 (16%), Positives = 83/259 (32%), Gaps = 69/259 (26%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM-GYRGYGLPISEVVSEG 82
            + P L K EE  L  R   HGD  AA  +   +  L+++ +   Y       ++  +  
Sbjct: 4   NEYPPLPKAEEDALIARAV-HGDAQAAAEMNARYRGLIIRESRASYLRNAALSADAENIA 62

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            +  ++A+  +DP+ G   A ++   I +A                      L+   RR 
Sbjct: 63  ALAFVEALHDYDPQHGAPFAAFAKTRIHSA----------------------LYTEFRRE 100

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
           +     + +    PEQ                                            
Sbjct: 101 RR----LWERTSHPEQDAEGRDVWERC--------------------------------- 123

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
                  G ++     + R   R +L R+M  L  RE++I       +  +TL  +++  
Sbjct: 124 ------GGTDEPTACADLRLLVRGILARAMHRLTEREKKILSLHYFSD--LTLRRIAALL 175

Query: 263 EVSRERVRQIEARAFKKVQ 281
             S   V + +A   +K++
Sbjct: 176 GTSAGAVSKSKANLLRKLR 194


>gi|39938883|ref|NP_950649.1| hypothetical protein PAM_397 [Onion yellows phytoplasma OY-M]
 gi|39721992|dbj|BAD04482.1| hypothetical protein [Onion yellows phytoplasma OY-M]
          Length = 131

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 26/105 (24%), Positives = 49/105 (46%), Gaps = 5/105 (4%)

Query: 35  YVLAKRY-REHGDLSAAHRLVTSHLRLVVKIAM--GYRGYGLPISEVVSEGNIGLMQAVK 91
             L K + +   +L   ++L+  HL LV K+     Y    L   ++  EG +GL++A+ 
Sbjct: 4   QELFKDFLKNKQNLEIRNQLIELHLPLVKKLVYQFKYYPRVLTKEDLYQEGILGLIKALN 63

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF 136
            +  + G+    Y+   IK+ ++E I +S S   I     ++  F
Sbjct: 64  HYQ-DLGYDFIAYATPTIKSEIRETIRKSHSP-SIPKKITKRDNF 106


>gi|317969864|ref|ZP_07971254.1| DNA-directed RNA polymerase specialized sigma subunit
           [Synechococcus sp. CB0205]
          Length = 227

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 38/229 (16%), Positives = 86/229 (37%), Gaps = 29/229 (12%)

Query: 54  VTSHLRLVVKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           V  H  LV+  A  Y      PI +++  G +G ++A  +F P     L  Y+  +++ A
Sbjct: 11  VKRHRGLVLGTARHYAQRCREPIDDLIQAGWVGFLRASARFQPGPDRSLGAYAKPFVRGA 70

Query: 113 MQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +  ++  +  LV++  +   +     L ++    +A T N       V + ++L  SE+ 
Sbjct: 71  ILRHLRDNSRLVRLPRSVQDR--LAQLNKI----EAATGNQAT----VGLGRRLGWSETA 120

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           +  +                      +  DWL  +       + ++ +    R M    +
Sbjct: 121 LRVLQQ----------------AEQLERLDWLDPERCEGIAAMDDETDPLLPRAMAQSWL 164

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           + +  R  ++ E   L     +L   +    +S   VR+      ++++
Sbjct: 165 ASIQQRHSQVVELVVL--EGYSLRRTAGLLGISSATVRRRLHAGLEELR 211


>gi|78184762|ref|YP_377197.1| putative type III sigma factor [Synechococcus sp. CC9902]
 gi|78169056|gb|ABB26153.1| putative type III sigma factor [Synechococcus sp. CC9902]
          Length = 124

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 24/83 (28%), Positives = 39/83 (46%), Gaps = 1/83 (1%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPI-SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
            ++ V  HL L   +AM  R  G     +++ E  +GL+Q ++KFDP RG R ++Y M  
Sbjct: 22  RNQKVLQHLGLAHCVAMRQRHRGPEERDDLLQEACLGLIQGLQKFDPSRGLRPSSYLMSR 81

Query: 109 IKAAMQEYILRSWSLVKIGTTAN 131
               +  Y      +V+I     
Sbjct: 82  ANGQVLHYRRDRSRMVRIPWRLQ 104


>gi|317126839|ref|YP_004093121.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Bacillus
           cellulosilyticus DSM 2522]
 gi|315471787|gb|ADU28390.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Bacillus
           cellulosilyticus DSM 2522]
          Length = 217

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 40/252 (15%), Positives = 83/252 (32%), Gaps = 62/252 (24%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           Y   GD SA   L+  +   V   A  Y   G    ++V EG IGL +A++ F  ++   
Sbjct: 25  YVREGDSSALEYLINKYKNFVRAKARSYFLIGADHEDIVQEGMIGLYKAIRDFKGDKLSS 84

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
              ++   I   +   I  +     I   +                              
Sbjct: 85  FKAFAELCITRQIITAIKTATRQKHIPLNSY----------------------------- 115

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
                        +S++            I   + + +     +       E++LI +EE
Sbjct: 116 -------------VSLDK----------PIYDEESDRTLLDVIVGSKISDPEELLINREE 152

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             +    ++  +S L   ER++        +  + + +S +    +  V+ I   A ++V
Sbjct: 153 FDDIELKMSEILSDL---ERKVLMQYL---DGRSYQEISVDL---KRHVKSI-DNALQRV 202

Query: 281 QESIQKQVELSS 292
           +  +++ VEL  
Sbjct: 203 KRKLERYVELKG 214


>gi|311070745|ref|YP_003975668.1| RNA polymerase factor sigma-70 [Bacillus atrophaeus 1942]
 gi|310871262|gb|ADP34737.1| RNA polymerase factor sigma-70 [Bacillus atrophaeus 1942]
          Length = 218

 Score = 57.1 bits (137), Expect = 3e-06,   Method: Composition-based stats.
 Identities = 36/248 (14%), Positives = 79/248 (31%), Gaps = 62/248 (25%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A   L+T +   V   A  Y   G    ++V EG IGL ++++ F  ++      +
Sbjct: 30  GDSDALDYLITKYRNFVRAKARSYFLIGADREDIVQEGMIGLYKSIRDFREDKLTSFKAF 89

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +   I   +   I  +     I   +                                  
Sbjct: 90  AELCITRQIITAIKTATRQKHIPLNSY--------------------------------- 116

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
                    +S++            I   + + +             E+++I +EE  + 
Sbjct: 117 ---------VSLDK----------PIFDEESDRTLLDVISGAKTLNPEEMIINQEEFDDI 157

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              +   +S L   ER++        +  + + +S +       V+ I   A ++V+  +
Sbjct: 158 EMKMGELLSDL---ERKVLVLYL---DGRSYQEISDDLN---RHVKSI-DNALQRVKRKL 207

Query: 285 QKQVELSS 292
           +K +E+  
Sbjct: 208 EKYLEIRE 215


>gi|168704991|ref|ZP_02737268.1| RNA polymerase sigma factor whiG [Gemmata obscuriglobus UQM 2246]
          Length = 169

 Score = 56.7 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 29/145 (20%), Positives = 60/145 (41%), Gaps = 10/145 (6%)

Query: 72  GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           G+ + +++S G  GL+ A+  FD  RG +  TY +  I+ AM + +     + ++  +  
Sbjct: 18  GVELDDLISAGVFGLLDAIDAFDLTRGVKFETYCVPRIRGAMLDELRTMDWVPRLVRSKA 77

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM--NCRLAGDESLNAL 189
            K     +   +  L+A      KPE    +++KL +   ++ S   +       SLN  
Sbjct: 78  SK-----MEAARKQLEAALGRPPKPE---ELSEKLGIPLEQLESYVGDATAVNLVSLNKK 129

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQV 214
              +D      +  ++ D   +   
Sbjct: 130 WYETDSYKDVREIDILEDKKAESPT 154


>gi|150019951|ref|YP_001305305.1| RNA polymerase factor sigma-70 [Thermosipho melanesiensis BI429]
 gi|149792472|gb|ABR29920.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermosipho
           melanesiensis BI429]
          Length = 206

 Score = 56.7 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 21/86 (24%), Positives = 43/86 (50%), Gaps = 5/86 (5%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           ++   LA    + G + A   ++  +  +VVKI+  Y        ++V  G IGL++AV 
Sbjct: 12  EKLVELA----QSGLMEALELIIERYYPMVVKISSKYYAPWAEFEDIVQNGLIGLIKAVF 67

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYI 117
            F+ E+     +++   I++ +Q +I
Sbjct: 68  YFNFEK-SSFNSFAWRSIESEIQTFI 92


>gi|306518735|ref|ZP_07405082.1| RNA polymerase factor sigma-70 [Clostridium difficile QCD-32g58]
          Length = 205

 Score = 56.7 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 25/96 (26%), Positives = 40/96 (41%), Gaps = 1/96 (1%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           Q+EY +  R  E GD  A   ++T +   V   A  Y   G    +++ EG IGL +AV+
Sbjct: 17  QDEYNIVLRASE-GDKIALEYIITKYRNFVKAKAKSYFLIGADKEDIIQEGMIGLYKAVR 75

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
            FD  +      ++   I   +   I  +     I 
Sbjct: 76  DFDGSKTNSFKCFAEICITRQIITAIKTATRQKHIP 111


>gi|294496966|ref|YP_003560666.1| RNA polymerase sigma-H factor [Bacillus megaterium QM B1551]
 gi|295702333|ref|YP_003595408.1| RNA polymerase sigma-H factor [Bacillus megaterium DSM 319]
 gi|39649|emb|CAA41793.1| sigma H factor [Bacillus megaterium]
 gi|294346903|gb|ADE67232.1| RNA polymerase sigma-H factor [Bacillus megaterium QM B1551]
 gi|294799992|gb|ADF37058.1| RNA polymerase sigma-H factor [Bacillus megaterium DSM 319]
          Length = 216

 Score = 56.7 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 37/262 (14%), Positives = 83/262 (31%), Gaps = 62/262 (23%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           +Q+E          GD+ A   L+  +   V   A  Y   G    ++V EG IGL +A+
Sbjct: 14  EQQEDETVVDLVHKGDIDALEYLIHKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKAI 73

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           + F  ++      ++   I   +   I  +     I   +                    
Sbjct: 74  RDFREDKLTSFKAFAELCITRQIITAIKTATRQKHIPLNSY------------------- 114

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
                                  +S++  +  +ES                D +      
Sbjct: 115 -----------------------VSLDKPIYDEES-----------DRTLMDVISGTKVA 140

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
             + L+   E+ +   +  +   +L+  ER++        +  + + +S E       V+
Sbjct: 141 NPEELLINREKFDDIEL--KMAELLSDLERKVLVLYL---DGQSYQEISEELN---RHVK 192

Query: 271 QIEARAFKKVQESIQKQVELSS 292
            I   A ++V+  +++ +E+  
Sbjct: 193 SI-DNALQRVKRKLERYLEIRE 213


>gi|258513623|ref|YP_003189845.1| RNA polymerase factor sigma-70 [Desulfotomaculum acetoxidans DSM
           771]
 gi|257777328|gb|ACV61222.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Desulfotomaculum
           acetoxidans DSM 771]
          Length = 214

 Score = 56.7 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 22/106 (20%), Positives = 40/106 (37%), Gaps = 4/106 (3%)

Query: 22  EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
           EI    +L  ++    A+     GD  A   L+  +   V   A  Y   G    +++ E
Sbjct: 9   EIAGFEVLIDEDVVEFAR----EGDDIALEYLINKYKNFVRAKARSYFLIGADREDIIQE 64

Query: 82  GNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           G IGL +A++ F  ++      ++   I   +   I  +     I 
Sbjct: 65  GMIGLYKAIRDFRMDKLSSFRAFAELCITRQIITAIKTATRQKHIP 110


>gi|213621148|ref|ZP_03373931.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 150

 Score = 56.7 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 28/132 (21%), Positives = 57/132 (43%), Gaps = 11/132 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV ++D  +G    TY++
Sbjct: 9   KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVDRYDALQGTAFTTYAV 68

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   + +L+  L        +      +A++L
Sbjct: 69  QRIRGAMLDEL-RSRDWVPRSVRRNAREVAQAMGQLEQEL-------GRNATETEVAERL 120

Query: 167 NVSESEVISMNC 178
            +  +E   M  
Sbjct: 121 GIPVAEYRQMLL 132


>gi|152973941|ref|YP_001373458.1| RNA polymerase factor sigma-70 [Bacillus cereus subsp. cytotoxis
           NVH 391-98]
 gi|152022693|gb|ABS20463.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Bacillus
           cytotoxicus NVH 391-98]
          Length = 220

 Score = 56.7 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 36/268 (13%), Positives = 88/268 (32%), Gaps = 66/268 (24%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           LE +    L ++    G++ A   L+  +   V   +  Y   G    ++V EG IGL +
Sbjct: 16  LEDEAIVELVRK----GNIDALEYLIHKYKNFVRAKSRSYFLVGADREDIVQEGMIGLFK 71

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++ +  ++      ++   I   +   I  +     I   +                  
Sbjct: 72  AIRDYKEDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSY----------------- 114

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                                    +S++            I   + + +          
Sbjct: 115 -------------------------VSLDK----------PIYDEESDRTLLDVISEAKV 139

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
              E+++I +EE  +    ++  +S L   ER++        +  + + +S +       
Sbjct: 140 TDPEEMIISQEEYSDIELKISELLSDL---ERKVLSLYL---DGRSYQEISEQLN---RH 190

Query: 269 VRQIEARAFKKVQESIQKQVELSSSPPL 296
           V+ I   A ++V+  +++ +E+  +  L
Sbjct: 191 VKSI-DNALQRVKRKLERYMEMRENTTL 217


>gi|228989302|ref|ZP_04149293.1| RNA polymerase sigma-H factor [Bacillus pseudomycoides DSM 12442]
 gi|228995485|ref|ZP_04155153.1| RNA polymerase sigma-H factor [Bacillus mycoides Rock3-17]
 gi|229003108|ref|ZP_04160957.1| RNA polymerase sigma-H factor [Bacillus mycoides Rock1-4]
 gi|228758144|gb|EEM07340.1| RNA polymerase sigma-H factor [Bacillus mycoides Rock1-4]
 gi|228764214|gb|EEM13093.1| RNA polymerase sigma-H factor [Bacillus mycoides Rock3-17]
 gi|228770380|gb|EEM18953.1| RNA polymerase sigma-H factor [Bacillus pseudomycoides DSM 12442]
          Length = 219

 Score = 56.7 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 36/268 (13%), Positives = 88/268 (32%), Gaps = 66/268 (24%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           LE +    L ++    G++ A   L+  +   V   +  Y   G    ++V EG IGL +
Sbjct: 16  LEDEAIVELVRK----GNIDALEYLIHKYKNFVRAKSRSYFLVGADREDIVQEGMIGLFK 71

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++ +  ++      ++   I   +   I  +     I   +                  
Sbjct: 72  AIRDYKEDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSY----------------- 114

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                                    +S++            I   + + +          
Sbjct: 115 -------------------------VSLDK----------PIYDEESDRTLLDVISEAKV 139

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
              E+++I +EE  +    ++  +S L   ER++        +  + + +S +       
Sbjct: 140 TDPEEMIISQEEYTDIELKISELLSDL---ERKVLSLYL---DGRSYQEISEQLN---RH 190

Query: 269 VRQIEARAFKKVQESIQKQVELSSSPPL 296
           V+ I   A ++V+  +++ +E+  +  L
Sbjct: 191 VKSI-DNALQRVKRKLERYMEMRENTTL 217


>gi|226309789|ref|YP_002769683.1| RNA polymerase factor sigma-70 [Brevibacillus brevis NBRC 100599]
 gi|226092737|dbj|BAH41179.1| RNA polymerase sigma-H factor [Brevibacillus brevis NBRC 100599]
          Length = 222

 Score = 56.7 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 37/272 (13%), Positives = 88/272 (32%), Gaps = 68/272 (25%)

Query: 20  IHEIR--KIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           + E++  +  ++  +E   L +      D  A   L+  +   V   A  Y   G    +
Sbjct: 11  LKELKHAQYELMTDEEVVDLVR----DNDAEALEYLINKYKNFVRAKARSYFLIGADRED 66

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           +V EG IGL ++++ F  ++      ++   I   +   I  +     I   +       
Sbjct: 67  IVQEGMIGLYKSIRDFRGDKLTSFKAFAELCITRQIITAIKTATRQKHIPLNSY------ 120

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
                                               +S++            I   D + 
Sbjct: 121 ------------------------------------VSLDK----------PIYDEDSDR 134

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           +             E++ I +EE  +    ++  +S L   ER++        +  + + 
Sbjct: 135 TLLDVISGTKVTDPEELFINREEFDDIEGKMSEILSDL---ERQVLMLYL---DGRSYQQ 188

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           ++ E    +  V+ I   A ++V+  +++ +E
Sbjct: 189 IAVEL---KRHVKSI-DNALQRVKRKLERYLE 216


>gi|242089065|ref|XP_002440365.1| hypothetical protein SORBIDRAFT_09g030380 [Sorghum bicolor]
 gi|241945650|gb|EES18795.1| hypothetical protein SORBIDRAFT_09g030380 [Sorghum bicolor]
          Length = 182

 Score = 56.7 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 19/66 (28%), Positives = 34/66 (51%)

Query: 59  RLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
            L   IA  Y G G  + +++  G IG++   +KFD  +G R +TY  +WI+  M   + 
Sbjct: 7   WLFSYIARTYTGMGTALDKLLQAGKIGVLDGSEKFDNRKGCRFSTYVKYWIRKGMLALLA 66

Query: 119 RSWSLV 124
            +  ++
Sbjct: 67  ENSGVI 72


>gi|255527271|ref|ZP_05394152.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           carboxidivorans P7]
 gi|296187250|ref|ZP_06855646.1| RNA polymerase sigma-H factor [Clostridium carboxidivorans P7]
 gi|255509056|gb|EET85415.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           carboxidivorans P7]
 gi|296048121|gb|EFG87559.1| RNA polymerase sigma-H factor [Clostridium carboxidivorans P7]
          Length = 213

 Score = 56.7 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 35/197 (17%), Positives = 78/197 (39%), Gaps = 10/197 (5%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            EE V+     + G+  A   L+  +   V   A  Y   G    ++  EG IGL +A++
Sbjct: 19  DEEIVIQ---AKKGETRAQEYLINKYENFVKAKAKSYFLIGADKEDIYQEGMIGLYKAIR 75

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQAI 149
            F P++      ++   +   +   I  +     I   T  +  +  ++    +  L  +
Sbjct: 76  DFKPDKLSSFKAFAELCVTRQIITAIKTATRQKHIPLNTYISLNKPIYDEESDRTLLDVL 135

Query: 150 TDNNLK-PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           ++  +  PE+++   ++LN   +E+  +   L     +  L++  D  S Q     +  H
Sbjct: 136 SEAKVADPEELIISREELNHIHAEIGEVLSSL----EMEVLMSYLDGKSYQEIACDLDRH 191

Query: 209 DGQEQVLIEKEERKNRR 225
                  +++ +RK  +
Sbjct: 192 AKSIDNALQRVKRKLEK 208


>gi|325288494|ref|YP_004264675.1| RNA polymerase, sigma 30 subunit, SigH [Syntrophobotulus glycolicus
           DSM 8271]
 gi|324963895|gb|ADY54674.1| RNA polymerase, sigma 30 subunit, SigH [Syntrophobotulus glycolicus
           DSM 8271]
          Length = 252

 Score = 56.7 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 21/98 (21%), Positives = 39/98 (39%), Gaps = 4/98 (4%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           + +E   LAK    +GD  +   L+  +   V   A  Y   G    +++ EG IGL +A
Sbjct: 56  DDEEMVELAK----NGDSISQEYLINKYKNFVRAKARSYFLIGADREDIIQEGMIGLYKA 111

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           ++ F  ++      ++   I   +   I  +     I 
Sbjct: 112 IRDFRGDKLSSFRAFAELCITRQIITAIKTATRQKHIP 149


>gi|296119762|ref|ZP_06838316.1| putative DNA polymerase III epsilon subunit [Corynebacterium
           ammoniagenes DSM 20306]
 gi|295966916|gb|EFG80187.1| putative DNA polymerase III epsilon subunit [Corynebacterium
           ammoniagenes DSM 20306]
          Length = 1149

 Score = 56.7 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 15/40 (37%), Positives = 25/40 (62%), Gaps = 2/40 (5%)

Query: 236 NPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
           + R+  I E R + +   TL+ L  +F ++RERVRQ+E +
Sbjct: 653 DARKLAIIEKRWVGDQ--TLDELGEQFGITRERVRQLEKQ 690


>gi|147676636|ref|YP_001210851.1| RNA polymerase factor sigma-70 [Pelotomaculum thermopropionicum SI]
 gi|146272733|dbj|BAF58482.1| DNA-directed RNA polymerase specialized sigma subunit, sigma24
           homolog [Pelotomaculum thermopropionicum SI]
          Length = 214

 Score = 56.7 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 21/104 (20%), Positives = 40/104 (38%), Gaps = 4/104 (3%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            +  +L  +E    A+     GD +A   L+  +   V   A  Y   G    +++ EG 
Sbjct: 11  NEYQVLVDEEIVEFAR----EGDDAALEYLINKYKNFVRAKARSYFLIGADREDIIQEGM 66

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           IGL +A++ F  ++      ++   I   +   I  +     I 
Sbjct: 67  IGLYKAIRDFRLDKLSSFRAFAELCITRQIITAIKTATRQKHIP 110


>gi|301060344|ref|ZP_07201207.1| bacterial RNA polymerase, alpha chain C-terminal domain protein
           [delta proteobacterium NaphS2]
 gi|300445540|gb|EFK09442.1| bacterial RNA polymerase, alpha chain C-terminal domain protein
           [delta proteobacterium NaphS2]
          Length = 772

 Score = 56.7 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 1/44 (2%)

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ-KQVE 289
              E   TLE +   F ++RERVRQI  +A K+ + +    Q+E
Sbjct: 247 FDSERSPTLEEIGQAFGITRERVRQIVKKAIKQFKHTANISQIE 290


>gi|52078593|ref|YP_077384.1| RNA polymerase factor sigma-70 [Bacillus licheniformis ATCC 14580]
 gi|52783954|ref|YP_089783.1| RNA polymerase factor sigma-70 [Bacillus licheniformis ATCC 14580]
 gi|319649133|ref|ZP_08003341.1| RNA polymerase sigma-H factor [Bacillus sp. BT1B_CT2]
 gi|133476|sp|P02964|RPSH_BACLI RecName: Full=RNA polymerase sigma-H factor; AltName: Full=Sigma-30
 gi|143542|gb|AAA22755.1| RNA polymerase sigma-30 factor [Bacillus licheniformis]
 gi|52001804|gb|AAU21746.1| RNA polymerase sigma-30 factor (sigma-H) [Bacillus licheniformis
           ATCC 14580]
 gi|52346456|gb|AAU39090.1| SigH [Bacillus licheniformis ATCC 14580]
 gi|317388833|gb|EFV69652.1| RNA polymerase sigma-H factor [Bacillus sp. BT1B_CT2]
          Length = 223

 Score = 56.7 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 38/248 (15%), Positives = 79/248 (31%), Gaps = 62/248 (25%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A   L+T +   V   A  Y   G    ++V EG IGL ++++ F  ++      +
Sbjct: 35  GDSDALDYLITKYRNFVRAKARSYFLIGADREDIVQEGMIGLYKSIRDFREDKLTSFKAF 94

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +   I   +   I  +     I   +                                  
Sbjct: 95  AELCITRQIITAIKTATRQKHIPLNSY--------------------------------- 121

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
                    +S++            I   + + +             E+++I +EE  + 
Sbjct: 122 ---------VSLDK----------PIYDEESDRTLLDVISGAKVMNPEELIINQEEFDDI 162

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              +   +S L   ER++        +  + + +S E       V+ I   A ++V+  +
Sbjct: 163 ELKMGELLSDL---ERKVLALYL---DGRSYQEISEELN---RHVKSI-DNALQRVKRKL 212

Query: 285 QKQVELSS 292
           +K +EL  
Sbjct: 213 EKYLELRE 220


>gi|229083413|ref|ZP_04215761.1| RNA polymerase sigma-H factor [Bacillus cereus Rock3-44]
 gi|228699846|gb|EEL52483.1| RNA polymerase sigma-H factor [Bacillus cereus Rock3-44]
          Length = 219

 Score = 56.7 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 36/268 (13%), Positives = 88/268 (32%), Gaps = 66/268 (24%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           LE +    L ++    G++ A   L+  +   V   +  Y   G    ++V EG IGL +
Sbjct: 16  LEDEAIVELVRK----GNIDALEYLIHKYKNFVRAKSRSYFLVGADREDIVQEGMIGLFK 71

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++ +  ++      ++   I   +   I  +     I   +                  
Sbjct: 72  AIRDYKEDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSY----------------- 114

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                                    +S++            I   + + +          
Sbjct: 115 -------------------------VSLDK----------PIYDEESDRTLLDVISETKV 139

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
              E+++I +EE  +    ++  +S L   ER++        +  + + +S +       
Sbjct: 140 TDPEEMIISQEEYTDIELKISELLSDL---ERKVLSLYL---DGRSYQEISEQLN---RH 190

Query: 269 VRQIEARAFKKVQESIQKQVELSSSPPL 296
           V+ I   A ++V+  +++ +E+  +  L
Sbjct: 191 VKSI-DNALQRVKRKLERYMEMRENTTL 217


>gi|255961255|ref|YP_003097813.1| DNA-directed RNA polymerase sigma subunit [Onion yellows
           phytoplasma OY-M]
 gi|162809325|dbj|BAF95570.1| DNA-directed RNA polymerase sigma subunit [Onion yellows
           phytoplasma OY-M]
          Length = 208

 Score = 56.7 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 24/85 (28%), Positives = 41/85 (48%), Gaps = 3/85 (3%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAM--GYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
            +   +L   + L+  HL LV K+     Y    L   ++  EG +GL++A+  +  + G
Sbjct: 11  LKNKKNLEIRNHLIELHLPLVKKLTYQFKYYPRVLTKEDLYQEGILGLIKALNNYQ-DLG 69

Query: 99  FRLATYSMWWIKAAMQEYILRSWSL 123
           +   TY+   IK A+ E I +S S 
Sbjct: 70  YDFVTYATPKIKFAINELIRKSHSP 94


>gi|307243396|ref|ZP_07525553.1| RNA polymerase sigma-H factor [Peptostreptococcus stomatis DSM
           17678]
 gi|306493206|gb|EFM65202.1| RNA polymerase sigma-H factor [Peptostreptococcus stomatis DSM
           17678]
          Length = 219

 Score = 56.7 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 28/159 (17%), Positives = 59/159 (37%), Gaps = 4/159 (2%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           LE ++E  +     + GD  A   ++  +  LV   A  Y   G    +++ EG IGL +
Sbjct: 14  LEAKDEIEIIN-LAKLGDSQAIECIIDRYSVLVKAKAKTYFLVGADKEDIIQEGLIGLYK 72

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHL 146
           A++ +D         ++   I   +   I  +     I   +  +  +  F     +   
Sbjct: 73  AIRDYDQSHTCSFKHFADICITRQIITAIKTATRQKHIPLNSYISLNKPVFEDESERSLF 132

Query: 147 QAITDN-NLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
             IT N +  PE++  + ++    E ++  +        
Sbjct: 133 DMITSNFDSDPEKMTILKEEYEYIEQKMAEVLSPFEEQV 171


>gi|163816512|ref|ZP_02207876.1| hypothetical protein COPEUT_02701 [Coprococcus eutactus ATCC 27759]
 gi|158448212|gb|EDP25207.1| hypothetical protein COPEUT_02701 [Coprococcus eutactus ATCC 27759]
          Length = 196

 Score = 56.7 bits (136), Expect = 4e-06,   Method: Composition-based stats.
 Identities = 21/129 (16%), Positives = 46/129 (35%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L +      +  A   L+  +  LV + +      G    +++ EG IGL++A+  + P
Sbjct: 9   ELLELIGTEKNNEAMETLIKRYGPLVTRQSRSLYIIGADEEDLIQEGMIGLIKAINDYKP 68

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           +RG    T++   ++  M   +  S S                       L  +    + 
Sbjct: 69  DRGASFKTFAFTCVRRQMLTAVSSSNSQKNTPLNHYISIYGDEKSEYMSPLDEMDSGVIT 128

Query: 156 PEQVVAIAK 164
             + + +A+
Sbjct: 129 NPEEIMMAR 137


>gi|23097558|ref|NP_691024.1| RNA polymerase factor sigma-70 [Oceanobacillus iheyensis HTE831]
 gi|22775781|dbj|BAC12059.1| RNA polymerase sigma-H factor (sigma-30) [Oceanobacillus iheyensis
           HTE831]
          Length = 217

 Score = 56.4 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 32/250 (12%), Positives = 83/250 (33%), Gaps = 62/250 (24%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           ++   G+  A   L+  ++  V   A  Y   G    +++ EG IGL +A++ +D ++  
Sbjct: 24  QFIRQGNSHALDLLIQRYISFVRAKARTYFLVGADKEDIIQEGMIGLYKAIRDYDVDKLS 83

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
               ++   +   +   I  +     I   +                             
Sbjct: 84  SFKAFAELCVTRQIITAIKTATRQKHIPLNSY---------------------------- 115

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
                         +S++            I   + + +             +++LI +E
Sbjct: 116 --------------VSLDK----------PIYDEESDRTLLDIIGGSIDVDPQELLISQE 151

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           +     + L++ +S L   E+++ +      +  T + +S         V+ I   A ++
Sbjct: 152 DYGTLEHKLSKLLSDL---EKKVLQLYL---DGRTYQEISEHLN---RHVKSI-DNALQR 201

Query: 280 VQESIQKQVE 289
           V+  +++ +E
Sbjct: 202 VKRKLEQLME 211


>gi|326332685|ref|ZP_08198948.1| putative stress response/stationary phase sigma factor SigF
           [Nocardioidaceae bacterium Broad-1]
 gi|325949513|gb|EGD41590.1| putative stress response/stationary phase sigma factor SigF
           [Nocardioidaceae bacterium Broad-1]
          Length = 176

 Score = 56.4 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 19/76 (25%), Positives = 37/76 (48%), Gaps = 1/76 (1%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              LV  HL +   +A  Y G G+ + ++     +GL++A +++DPE+G    +Y++   
Sbjct: 15  QEDLVVRHLPVARSLAARYSGRGIEVEDLRQAARMGLVKAARRYDPEQG-AFLSYAVPMA 73

Query: 110 KAAMQEYILRSWSLVK 125
           K  M+         V+
Sbjct: 74  KGEMRRCFRDLARCVR 89



 Score = 44.4 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 8/62 (12%), Positives = 26/62 (41%), Gaps = 2/62 (3%)

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           +R   R ++  ++  L+  +  +   R      +T   +      ++ +V +  AR  ++
Sbjct: 112 DRAEARVLVGEALEGLDETDLTVLRLRYA--EGLTQAEIGERIGATQAQVSRTLARILRQ 169

Query: 280 VQ 281
           ++
Sbjct: 170 MR 171


>gi|224120616|ref|XP_002318375.1| predicted protein [Populus trichocarpa]
 gi|222859048|gb|EEE96595.1| predicted protein [Populus trichocarpa]
          Length = 97

 Score = 56.4 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 2/56 (3%)

Query: 232 MSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           +  L P+E  +   R   +     TL  ++    +SRE VR+ E +A  K++   +
Sbjct: 33  LDSLKPKESLVVRQRYGLDGKGDRTLGEIAGNLNISREMVRKHEVKALMKLKHPTR 88


>gi|289422448|ref|ZP_06424291.1| RNA polymerase sigma-H factor [Peptostreptococcus anaerobius 653-L]
 gi|289157020|gb|EFD05642.1| RNA polymerase sigma-H factor [Peptostreptococcus anaerobius 653-L]
          Length = 217

 Score = 56.4 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 17/87 (19%), Positives = 37/87 (42%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             + GD  A ++L+  +  +V   A  Y   G    +++ EG IGL +A++ +D ++   
Sbjct: 24  MAKQGDKYAINKLIEKYSIMVKAKAKTYFLVGADKEDIIQEGLIGLYKAIRDYDEDKTCS 83

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIG 127
              ++   +   +   I  +     I 
Sbjct: 84  FRYFADICVTRQIITAIKTATRQKHIP 110


>gi|303242132|ref|ZP_07328622.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302590319|gb|EFL60077.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 261

 Score = 56.4 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 32/216 (14%), Positives = 70/216 (32%), Gaps = 61/216 (28%)

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
              + + ++V  G + L  A+K +DP+ G     Y  ++                     
Sbjct: 42  NTKVELDDLVQSGYLALCSAIKNYDPDAGCSFIGYLSFY--------------------- 80

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
                       L+   +           V+  A                    ESLN  
Sbjct: 81  ------------LRHQFRKEIGTRTSRRDVLLTA--------------------ESLNKP 108

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I+  +            + +     ++E+ E +   N++   M  L+PR R I     L+
Sbjct: 109 ISEDNDELHLIDAVPCPEAELAFDDMLEQLEHQRIMNIVFECMQRLSPRHRDILILAYLK 168

Query: 250 ENPVTLENLSSEFEV---SRERVRQIEARAFKKVQE 282
           +     + ++ +  +   S   VR+I+  A +++++
Sbjct: 169 QAK--QDEIAEQLGIVYGS---VRRIKKDALRELRK 199


>gi|227498999|ref|ZP_03929136.1| RNA polymerase [Acidaminococcus sp. D21]
 gi|226904448|gb|EEH90366.1| RNA polymerase [Acidaminococcus sp. D21]
          Length = 232

 Score = 56.4 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 29/154 (18%), Positives = 62/154 (40%), Gaps = 4/154 (2%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
              +E  L KR +E GD  A   L+  +  LV K    Y   G    ++V EG IGL +A
Sbjct: 9   SPSDEV-LLKRIQEEGDGKAQDILLARYKELVKKKTSLYYMAGAERDDIVQEGMIGLFKA 67

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQ 147
           ++ +  ++      ++   I   +   I  +         +  +  + F++  + +  + 
Sbjct: 68  IRDYRFDQKASFKVFAELCINRQIISAIKGANRQKHRPLNSYVSLDKPFYDDGKERTLMD 127

Query: 148 AITD-NNLKPEQVVAIAKKLNVSESEVISMNCRL 180
            +    ++ PE ++   +     E  V++M   +
Sbjct: 128 MLGGSRSVDPENLIVDQEAFKDIEKNVLAMLSAM 161


>gi|149920035|ref|ZP_01908509.1| RNA polymerase sigma factor, FliA/WhiG/SigD family protein
           [Plesiocystis pacifica SIR-1]
 gi|149819132|gb|EDM78568.1| RNA polymerase sigma factor, FliA/WhiG/SigD family protein
           [Plesiocystis pacifica SIR-1]
          Length = 229

 Score = 56.4 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 38/240 (15%), Positives = 89/240 (37%), Gaps = 21/240 (8%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRG--YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
            A    V +H +LV ++A         L + E+ S GN  L+ A  +FDP  G   +T++
Sbjct: 7   DAQAARVEAHTQLVERLARALSRQLRALSVEELESVGNEALVVAAMRFDPSAGASFSTFA 66

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
            + I+ AM + + +     +      ++R    L   +  ++   ++    ++     + 
Sbjct: 67  HYRIRGAMIDAVRK-----RSPGRRRKQRAIQRLEATQLLMRQAAEDRGA-KRAGGGRES 120

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           L         +  R          I  ++            D D       ++  +  + 
Sbjct: 121 LEQRVHAARELVYRAG------LAILIAEATHGGLAVAPSEDTD-----PEQRVLKARQI 169

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             L  +++ L P  R +     L  +  T   L+ +  VS   + +  +R  +++ ++++
Sbjct: 170 ERLRAAIAALEPESRELIV--GLYVHGKTGRELAEQLGVSAATLSRRHSRLLERLGQALR 227


>gi|39939188|ref|NP_950954.1| DNA-directed RNA polymerase sigma subunit [Onion yellows
           phytoplasma OY-M]
 gi|39722297|dbj|BAD04787.1| DNA-directed RNA polymerase sigma subunit [Onion yellows
           phytoplasma OY-M]
          Length = 208

 Score = 56.4 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 24/85 (28%), Positives = 41/85 (48%), Gaps = 3/85 (3%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAM--GYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
            +   +L   + L+  HL LV K+     Y    L   ++  EG +GL++A+  +  + G
Sbjct: 11  LKNKKNLEIRNHLIELHLPLVKKLTYQFKYYPRVLTKEDLYQEGILGLIKALNNYQ-DLG 69

Query: 99  FRLATYSMWWIKAAMQEYILRSWSL 123
           +   TY+   IK A+ E I +S S 
Sbjct: 70  YDFVTYATPKIKFAINELIRKSHSP 94


>gi|319654851|ref|ZP_08008926.1| RNA polymerase sigma-70 factor [Bacillus sp. 2_A_57_CT2]
 gi|317393414|gb|EFV74177.1| RNA polymerase sigma-70 factor [Bacillus sp. 2_A_57_CT2]
          Length = 218

 Score = 56.4 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 39/264 (14%), Positives = 85/264 (32%), Gaps = 66/264 (25%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           LE +E   L  +    G+  A   L+  +   V   A  Y   G    ++V EG IGL +
Sbjct: 18  LEDEEIVELVHK----GESEALDYLIHKYRNFVRAKARSYFLIGADKEDIVQEGMIGLYK 73

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++ F  ++      ++   I   +   I  +     I   +                  
Sbjct: 74  AIRDFKEDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSY----------------- 116

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                                    +S++            I   + + +          
Sbjct: 117 -------------------------VSLDK----------PIYDEESDRTLMDVISGAKV 141

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
              E+++I +EE  +    ++  +S L   ER++        +  + + +S E       
Sbjct: 142 MDPEELIINQEEFDHIEVKMSELLSDL---ERKVLALYL---DGQSYQEISEELN---RH 192

Query: 269 VRQIEARAFKKVQESIQKQVELSS 292
           V+ I   A ++V+  +++ +E+  
Sbjct: 193 VKSI-DNALQRVKRKLERYLEVRE 215


>gi|300856821|ref|YP_003781805.1| putative RNA polymerase sigma factor [Clostridium ljungdahlii DSM
           13528]
 gi|300436936|gb|ADK16703.1| predicted RNA polymerase sigma factor [Clostridium ljungdahlii DSM
           13528]
          Length = 187

 Score = 56.4 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 34/234 (14%), Positives = 70/234 (29%), Gaps = 64/234 (27%)

Query: 54  VTSHLRLVVKI-AMGYRG--YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
           V  ++ +V KI    Y    Y     ++   G +GLM+A K F+  +G + +TY+  +++
Sbjct: 13  VEDYIPMVHKITHKQYMKFKYRYSYDDMFQAGCVGLMRAAKNFNESKGRKFSTYAYKYVE 72

Query: 111 AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
             +          V                                              
Sbjct: 73  GHIINLARNDSWYV---------------------------------------------A 87

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
           + V           SL+ L+               Y  D     LI  +  +     L  
Sbjct: 88  NRVRDRTKESYAPVSLDQLVG--------------YQEDTPMVDLIMGDVSEYSNLDLRM 133

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++  L    ++I E R   +   T   +S    + +  + + +  A + +++ I
Sbjct: 134 ALGKLPGTLKKIIEMRYFYD--FTWREISKSINMPQSTLYKYKKEALETLRKEI 185


>gi|187776560|ref|ZP_02993033.1| hypothetical protein CLOSPO_00072 [Clostridium sporogenes ATCC
           15579]
 gi|187775219|gb|EDU39021.1| hypothetical protein CLOSPO_00072 [Clostridium sporogenes ATCC
           15579]
          Length = 223

 Score = 56.4 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 30/187 (16%), Positives = 74/187 (39%), Gaps = 7/187 (3%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + G+  A   ++  +   V   A  Y   G    ++  EG IGL +A++ F P++    
Sbjct: 36  AKAGNSRAQEYIIGKYENFVKAKAKSYFLIGADKEDIYQEGMIGLYKAIRDFKPDKLSSF 95

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQAITDNNLK-PEQ 158
             ++   +   +   I  +     I   T  +  +  ++    +  L  +++  +  PE+
Sbjct: 96  KAFAELCVTRQIITAIKTATRQKHIPLNTYVSLNKPIYDEESDRTLLDILSEAKVANPEE 155

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           ++   ++L   ++E+  +      D  +  L++  D  S Q     +  H       +++
Sbjct: 156 LIISREELKHIQNEIGEVLS----DLEMEVLMSYLDGKSYQEIACDLDRHAKSIDNALQR 211

Query: 219 EERKNRR 225
            +RK  +
Sbjct: 212 VKRKLEK 218


>gi|167771908|ref|ZP_02443961.1| hypothetical protein ANACOL_03281 [Anaerotruncus colihominis DSM
           17241]
 gi|167665706|gb|EDS09836.1| hypothetical protein ANACOL_03281 [Anaerotruncus colihominis DSM
           17241]
          Length = 202

 Score = 56.4 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 27/148 (18%), Positives = 55/148 (37%), Gaps = 4/148 (2%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           LA+R + +GD  A   L+  +  LV   A  Y    + + +V  EG I L++AV+ +  +
Sbjct: 17  LAQRAK-NGDDEALADLIERYTPLVCMRARAYARGVMDVDDVYQEGMIALLKAVRNYRED 75

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
                 T++   +   M   +            +    L  + R +   L A       P
Sbjct: 76  TAGSFRTFAAVCVNNKMLSAVTAHMRDKNAPMRSY---LSLSGREIPEDLLAAVSPETDP 132

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDE 184
           E++V  +++       + ++        
Sbjct: 133 EKLVIASEESAARNRRIENLLSPFERQV 160


>gi|328474969|gb|EGF45763.1| RNA polymerase sigma factor RpoD [Listeria monocytogenes 220]
          Length = 47

 Score = 56.4 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 14/33 (42%), Positives = 23/33 (69%)

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           LE +   F V+RER+RQIEA+A +K++   + +
Sbjct: 8   LEEVGRVFGVTRERIRQIEAKALRKLRHPSRSK 40


>gi|16077166|ref|NP_387979.1| RNA polymerase factor sigma-70 [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221307910|ref|ZP_03589757.1| RNA polymerase factor sigma-70 [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221317165|ref|ZP_03598459.1| RNA polymerase factor sigma-70 [Bacillus subtilis subsp. subtilis
           str. JH642]
 gi|133477|sp|P17869|RPSH_BACSU RecName: Full=RNA polymerase sigma-H factor; AltName:
           Full=Sigma-30; AltName: Full=Stage 0 sporulation protein
           H
 gi|143544|gb|AAA22756.1| RNA polymerase sigma-30 factor [Bacillus subtilis]
 gi|2632365|emb|CAB11874.1| RNA polymerase sigma-30 factor (sigma(H)) [Bacillus subtilis subsp.
           subtilis str. 168]
          Length = 218

 Score = 56.4 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 38/248 (15%), Positives = 80/248 (32%), Gaps = 62/248 (25%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A   L+T +   V   A  Y   G    ++V EG IGL ++++ F  ++      +
Sbjct: 30  GDSDALDYLITKYRNFVRAKARSYFLIGADREDIVQEGMIGLYKSIRDFKEDKLTSFKAF 89

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +   I   +   I  +     I   +                                  
Sbjct: 90  AELCITRQIITAIKTATRQKHIPLNSYA-------------------------------- 117

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
                     S++  +  +ES          + +             E+++I +EE  + 
Sbjct: 118 ----------SLDKPIFDEES----------DRTLLDVISGAKTLNPEEMIINQEEFDDI 157

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              +   +S L   ER++        +  + + +S E       V+ I   A ++V+  +
Sbjct: 158 EMKMGELLSDL---ERKVLVLYL---DGRSYQEISDELN---RHVKSI-DNALQRVKRKL 207

Query: 285 QKQVELSS 292
           +K +E+  
Sbjct: 208 EKYLEIRE 215


>gi|158321550|ref|YP_001514057.1| ECF subfamily RNA polymerase sigma-24 factor [Alkaliphilus
           oremlandii OhILAs]
 gi|158141749|gb|ABW20061.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Alkaliphilus
           oremlandii OhILAs]
          Length = 190

 Score = 56.4 bits (135), Expect = 5e-06,   Method: Composition-based stats.
 Identities = 43/258 (16%), Positives = 85/258 (32%), Gaps = 78/258 (30%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            E+  LA      GD SA   L+     L+V  +  Y G      E+  EG   +++A++
Sbjct: 6   DEKVALA----LEGDHSAKEWLIHQLKPLIVSYSRKYGGQVGWDEELYQEGAWQVLEALQ 61

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
            FD  +G     +                        T   K  + N RR +  L     
Sbjct: 62  DFDRSKGVPFLGF-----------------------VTVRLKHHYQNKRRKEKSL----- 93

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
                                            SL+  +   ++  +   D++V +    
Sbjct: 94  --------------------------------ISLDEPV--GEEQDTTLLDFIVDESVDI 119

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV---SRER 268
           E   ++ E        L  +M  L  +E ++ EA         L+ ++ E  V   +  +
Sbjct: 120 EGDYLKAESW----IALREAMGRLKEQEHQLIEAYYFNGRK--LKEIAEEAGVHYITAVK 173

Query: 269 VRQIEARAFKKVQESIQK 286
              ++A + +K+++ ++K
Sbjct: 174 ---LKAHSLEKLKKYLEK 188


>gi|160943408|ref|ZP_02090642.1| hypothetical protein FAEPRAM212_00899 [Faecalibacterium prausnitzii
           M21/2]
 gi|158445268|gb|EDP22271.1| hypothetical protein FAEPRAM212_00899 [Faecalibacterium prausnitzii
           M21/2]
          Length = 221

 Score = 56.4 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 42/250 (16%), Positives = 86/250 (34%), Gaps = 58/250 (23%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL--------PISEVVSEGNIGLMQAVKK 92
             + GD +A   L+ ++   + K+A                   ++   GN+GL +AV K
Sbjct: 11  LAQKGDAAALDSLIDNNKSFIGKVANDLFRSMNLAQSGLNLDTDDLKQAGNLGLWKAVPK 70

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  +G +  TY+   I+ AM + +                              A    
Sbjct: 71  FDAAQGMKFLTYAAPAIRNAMVDMVRD-------------------------AFAAFEQR 105

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
            +  ++     ++        +S++  L G+E L            +  + +   +  Q 
Sbjct: 106 MVTEDKDGICYQR--------VSLDDVLPGEEQL------------RRIEAIADPYAMQP 145

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVR 270
           Q ++E++E    R  L   +  L  RE+     R          L   +  F +++ R +
Sbjct: 146 QSIMEEQES---RRELYDGLKRLTQREQTYLLYRYGFTDGEEHPLIGTAIYFHLTKGRAK 202

Query: 271 QIEARAFKKV 280
           + E +A   +
Sbjct: 203 KTEEQAMDNL 212


>gi|65321232|ref|ZP_00394191.1| COG1191: DNA-directed RNA polymerase specialized sigma subunit
           [Bacillus anthracis str. A2012]
          Length = 76

 Score = 56.4 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 2/69 (2%)

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           +K+E+      L   M  LN RE+ I   R  Q    T   ++ E  +S+ +V ++E  A
Sbjct: 9   QKDEQWVEELALKEGMKRLNDREKMIIRKRFFQG--KTQMEVAEEIGISQAQVSRLEKSA 66

Query: 277 FKKVQESIQ 285
            K++ ++IQ
Sbjct: 67  IKQMNKTIQ 75


>gi|312621865|ref|YP_004023478.1| RNA polymerase sigma factor, sigma-70 family [Caldicellulosiruptor
           kronotskyensis 2002]
 gi|312202332|gb|ADQ45659.1| RNA polymerase sigma factor, sigma-70 family [Caldicellulosiruptor
           kronotskyensis 2002]
          Length = 302

 Score = 56.4 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 19/72 (26%), Positives = 41/72 (56%), Gaps = 5/72 (6%)

Query: 50  AHRLVTSHLRLVVKIAMGY----RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
              L+  +++LV  +A  +    +GY   + +++SEG IGL+ A K +DP +G   ++Y+
Sbjct: 10  RQMLIADNIKLVYHVANKFMPCPKGYCYEVDDLISEGYIGLVVAAKNYDPAKGS-FSSYA 68

Query: 106 MWWIKAAMQEYI 117
              I++ ++  +
Sbjct: 69  CKVIESRIKRSL 80


>gi|262273512|ref|ZP_06051326.1| RNA polymerase sigma factor for flagellar operon [Grimontia
           hollisae CIP 101886]
 gi|262222490|gb|EEY73801.1| RNA polymerase sigma factor for flagellar operon [Grimontia
           hollisae CIP 101886]
          Length = 246

 Score = 56.4 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 26/212 (12%), Positives = 82/212 (38%), Gaps = 27/212 (12%)

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILR-SWSLVKIGTTANQKR 134
            ++   G + L++ ++++  E    L   ++  I+ A+ + + R  W           ++
Sbjct: 53  DDMEQIGLMALLETIRRYPEEDEGGLKKLAVPRIRGALLDEMRRLDWRS---------RQ 103

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVI--SMNCRLAGDESLNALINS 192
           L     +L    + +     +      +A+ + +S S+V    ++       S  ++   
Sbjct: 104 LRQKTHQLCEKEREVAKTLGRAPTDPELAQAMEMSVSDVRQLRLDYEAERPHSFESM--- 160

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            + N +     +  DH  +E++ +  +                  RE+ +       E+ 
Sbjct: 161 QEDNIAIPGLAVYCDHIEKEKLAVALKAALATLT----------EREQIVLS--FYFEHE 208

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++++ ++   +++  R+ QI+ +A   + + +
Sbjct: 209 MSMKEIALVLDLTEARICQIQKKALATLNQKL 240


>gi|188584818|ref|YP_001916363.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|179349505|gb|ACB83775.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 213

 Score = 56.4 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 25/99 (25%), Positives = 39/99 (39%), Gaps = 3/99 (3%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L   EE   AKR RE G   A   L+  +   V   A  Y   G    +++ EG IGL +
Sbjct: 14  LNSDEEV--AKRARE-GCHEALEFLIGKYKNFVRAKARSYFLIGADREDIIQEGMIGLYK 70

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           A++ F  ++      ++   I   +   I  +     I 
Sbjct: 71  AIRDFRGDKLSSFKAFAELCITRQIITAIKTATRQKHIP 109


>gi|149183038|ref|ZP_01861492.1| possible RNA polymerase sigma-B factor (Sigma-37) (General stress
           protein84) (GSP84) [Bacillus sp. SG-1]
 gi|148849268|gb|EDL63464.1| possible RNA polymerase sigma-B factor (Sigma-37) (General stress
           protein84) (GSP84) [Bacillus sp. SG-1]
          Length = 191

 Score = 56.4 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 19/109 (17%), Positives = 39/109 (35%), Gaps = 2/109 (1%)

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
            R+  D  L  L              L+ D    +    +  E       L  +   L  
Sbjct: 81  TRMDRDRQLLTLDKPLGDEEEGTYKELIADTAAPDSYTEKSLEESISDARLMEAFQRLTH 140

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           R++ I     ++E   T   ++    VS++ V +   +  KK++ +++K
Sbjct: 141 RQKFILNLAYVEERSDT--EIADVLGVSQQAVSKTHKKVLKKLKNALEK 187


>gi|311029031|ref|ZP_07707121.1| RNA polymerase factor sigma-70 [Bacillus sp. m3-13]
          Length = 216

 Score = 56.4 bits (135), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 38/267 (14%), Positives = 85/267 (31%), Gaps = 66/267 (24%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           + ++E ++   L       GD  A   L+  +   V   A  Y   G    ++V EG IG
Sbjct: 13  LELMEDEQMVELVHL----GDSEALDYLINKYKNFVRAKARSYFLIGADREDIVQEGMIG 68

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L +A++ F  ++      ++   I   +   I  +     I   +               
Sbjct: 69  LYKAIRDFKEDKLTSFKAFAELCITRQIITAIKTATRQKHIPLNSY-------------- 114

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
                                       +S++            I   + + +       
Sbjct: 115 ----------------------------VSLDK----------PIYDEESDRTLMDVISG 136

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
                 E+++I +EE  +    +   +S L   ER++        +  + + +S +    
Sbjct: 137 AKVMDPEELIINQEEFDDIEVKMGELLSDL---ERKVLALYL---DGRSYQEISEDLN-- 188

Query: 266 RERVRQIEARAFKKVQESIQKQVELSS 292
              V+ I   A ++V+  +++ +EL  
Sbjct: 189 -RHVKSI-DNALQRVKRKLERYLELRE 213


>gi|37520799|ref|NP_924176.1| hypothetical protein glr1230 [Gloeobacter violaceus PCC 7421]
 gi|35211794|dbj|BAC89171.1| glr1230 [Gloeobacter violaceus PCC 7421]
          Length = 296

 Score = 56.0 bits (134), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 28/141 (19%), Positives = 53/141 (37%), Gaps = 11/141 (7%)

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
           G L    +++    ++  + + L V    ++  + RL    SLN  I   + N   +   
Sbjct: 155 GRLVQGLEDSQVRPELAKMRQMLGVGRKVILRRDPRLVPALSLNCPIRPGEGNEEYFDIA 214

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
                 G E+           R  L  S+  L   ER +             + L+ E  
Sbjct: 215 AAPRLAGMEEA---------CRQALHESLVHLTAGERLVVLGLFFANRSR--KELAEEAG 263

Query: 264 VSRERVRQIEARAFKKVQESI 284
           +S  RV Q+  +A+K+++E +
Sbjct: 264 ISTARVSQLLQQAYKRLREVL 284


>gi|218290032|ref|ZP_03494199.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Alicyclobacillus
           acidocaldarius LAA1]
 gi|258512687|ref|YP_003186121.1| RNA polymerase factor sigma-70 [Alicyclobacillus acidocaldarius
           subsp. acidocaldarius DSM 446]
 gi|218239866|gb|EED07054.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Alicyclobacillus
           acidocaldarius LAA1]
 gi|257479413|gb|ACV59732.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
          Length = 223

 Score = 56.0 bits (134), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 36/259 (13%), Positives = 80/259 (30%), Gaps = 66/259 (25%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             +E      R    GD  A   L+  +   V   A  Y   G    ++V EG IGL ++
Sbjct: 25  TDEELVEAVHR----GDTDALDYLIHKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKS 80

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           ++ F  ++      ++   I   +   I  +     I   +                   
Sbjct: 81  IRDFRGDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSY------------------ 122

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
                                   +S++            I   D + +           
Sbjct: 123 ------------------------VSLDK----------PIYDEDSDRTLLDVICTVRVA 148

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
             E+++I +EE  +    ++  +S L   ER++        +  + + ++ +       V
Sbjct: 149 DPEELIINQEEFDDIEGKMSELLSDL---ERQVLMLYL---DGRSYQEIAVDL---ARHV 199

Query: 270 RQIEARAFKKVQESIQKQV 288
           + I   A ++V+  ++K +
Sbjct: 200 KSI-DNALQRVKRKLEKYL 217


>gi|157690881|ref|YP_001485343.1| RNA polymerase factor sigma-70 [Bacillus pumilus SAFR-032]
 gi|194017543|ref|ZP_03056154.1| RNA polymerase sigma-H factor [Bacillus pumilus ATCC 7061]
 gi|157679639|gb|ABV60783.1| DNA-directed RNA polymerase sigma subunit SigH [Bacillus pumilus
           SAFR-032]
 gi|194010815|gb|EDW20386.1| RNA polymerase sigma-H factor [Bacillus pumilus ATCC 7061]
          Length = 218

 Score = 56.0 bits (134), Expect = 6e-06,   Method: Composition-based stats.
 Identities = 38/248 (15%), Positives = 78/248 (31%), Gaps = 62/248 (25%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A   L+T +   V   A  Y   G    ++V EG IGL ++++ F  ++      +
Sbjct: 30  GDSDALDYLITKYRNFVRAKARSYFLIGADREDIVQEGMIGLYKSIRDFREDKLTSFKAF 89

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +   I   +   I  +     I   +                                  
Sbjct: 90  AELCITRQIITAIKTATRQKHIPLNSY--------------------------------- 116

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
                    +S++            I   + + +             E ++I KEE  + 
Sbjct: 117 ---------VSLDK----------PIYDEESDRTLLDVISGAKALNPEDLIISKEEFDDI 157

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              +   +S L   ER++        +  + + +S +       V+ I   A ++V+  +
Sbjct: 158 EMKMGELLSEL---ERKVLVLYL---DGRSYQEISEDLN---RHVKSI-DNALQRVKRKL 207

Query: 285 QKQVELSS 292
           +K +EL  
Sbjct: 208 EKYLELRE 215


>gi|317497614|ref|ZP_07955932.1| RNA polymerase sigma-H factor [Lachnospiraceae bacterium 5_1_63FAA]
 gi|316895173|gb|EFV17337.1| RNA polymerase sigma-H factor [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 200

 Score = 56.0 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 24/136 (17%), Positives = 52/136 (38%), Gaps = 2/136 (1%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
              +E +L  R  + G+  A   L+  +  +V K A  +   G    +++ EG IGL +A
Sbjct: 6   TISDEKLL--RQIQSGNDDAMECLLERYRDMVRKEARSFFLAGGDEEDLIQEGMIGLFKA 63

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V  +  E+    +T++   ++  +   I        I             +  +  L  I
Sbjct: 64  VTSYQEEKNTSFSTFAYLCVQRQIYTTITAFNRKKHIPLNTAISLFEQKNQEEELSLDEI 123

Query: 150 TDNNLKPEQVVAIAKK 165
            +   +  + + + K+
Sbjct: 124 LETPEETPEEMMLRKE 139


>gi|223934543|ref|ZP_03626464.1| RNA polymerase, sigma-24 subunit, ECF subfamily [bacterium
           Ellin514]
 gi|223897006|gb|EEF63446.1| RNA polymerase, sigma-24 subunit, ECF subfamily [bacterium
           Ellin514]
          Length = 485

 Score = 56.0 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 21/94 (22%), Positives = 39/94 (41%), Gaps = 10/94 (10%)

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           S+ +  L  +     Q L    +  + +  L  +MS L P +R     R  ++   +L  
Sbjct: 86  SEQRRRLREETAVTMQALDSDSDAGHIKEHLEPAMSELEPDDRDTLVLRYFED--RSLRE 143

Query: 258 LSSEFEVS----RERVRQIEARAFKKVQESIQKQ 287
           +  EF +S    R RV     RA +K++    ++
Sbjct: 144 VGQEFGISEDAARMRV----NRALEKLRTIFNRK 173


>gi|299821037|ref|ZP_07052925.1| RNA polymerase factor sigma-70 [Listeria grayi DSM 20601]
 gi|299816702|gb|EFI83938.1| RNA polymerase factor sigma-70 [Listeria grayi DSM 20601]
          Length = 204

 Score = 56.0 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 35/250 (14%), Positives = 74/250 (29%), Gaps = 67/250 (26%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             ++GD  A       +  ++   A  Y   G    +++ E  IGL +A++ F P++   
Sbjct: 17  LAKNGDTEALDYFFQKYQPIMYWKATQYFLQGAERDDLLQEAMIGLFKAIRDFSPDKEAS 76

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
             T++   I   +   + RS                                        
Sbjct: 77  FRTFAEICINRQLLSAVKRSAR-------------------------------------- 98

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD-GQEQVLIEKE 219
                           N  L    SL+  +           D +        E  L++ E
Sbjct: 99  --------------QKNQPLNQSLSLDTPMTEEHGLDWTLLDVISEQAAQTPEDYLLKSE 144

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA--RAF 277
           +R +    L +  S   P E+ +           + + ++  F       + I+A   A 
Sbjct: 145 DRIDIAERLEKVTS---PFEKEVLRCYL---EGKSYQEMADHFG------KNIKAIDNAL 192

Query: 278 KKVQESIQKQ 287
           +++++ +  Q
Sbjct: 193 QRIKKKMGAQ 202


>gi|160944734|ref|ZP_02091961.1| hypothetical protein FAEPRAM212_02248 [Faecalibacterium prausnitzii
           M21/2]
 gi|158443918|gb|EDP20922.1| hypothetical protein FAEPRAM212_02248 [Faecalibacterium prausnitzii
           M21/2]
          Length = 221

 Score = 56.0 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 48/250 (19%), Positives = 88/250 (35%), Gaps = 58/250 (23%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL--------PISEVVSEGNIGLMQAVKK 92
             + GD +A   L+ ++   + K A                   ++   GN+GL +AV K
Sbjct: 11  LAQKGDAAALDSLIDNNKSFIGKAANDLFRSMNLAQSGLNLDTDDLKQAGNMGLWKAVPK 70

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  RG +  TY+   I  AM +       +V+   TA ++R+                 
Sbjct: 71  FDAARGMKFLTYAAPAIHNAMMD-------MVRDAFTAFEQRMVTE-------------- 109

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
                       K  +    V S++  L G+E L            +  + +   +  Q 
Sbjct: 110 -----------DKDGICYQRV-SLDDVLPGEEQL------------RRIEAIADPYAMQP 145

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVR 270
           Q ++E++E    R  L   +  L  RE+     R          L   +  F +++ R +
Sbjct: 146 QTIMEEQES---RRELYDGLKRLTQREQTYLLYRYGFTDGEEHPLIGTAIYFHLTKGRAK 202

Query: 271 QIEARAFKKV 280
           + E +A   +
Sbjct: 203 KTEEQAMDNL 212


>gi|115378971|ref|ZP_01466103.1| AsgB [Stigmatella aurantiaca DW4/3-1]
 gi|115364010|gb|EAU63113.1| AsgB [Stigmatella aurantiaca DW4/3-1]
          Length = 136

 Score = 56.0 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 14/42 (33%), Positives = 26/42 (61%)

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPP 295
           TLE +     ++RER+RQ+E R   K++E+ + +  +S+  P
Sbjct: 95  TLEEVGEIMNLTRERIRQVETRGLMKLREATEAEPPVSARKP 136


>gi|323705645|ref|ZP_08117219.1| RNA polymerase, sigma-24 subunit, ECF subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
 gi|323535122|gb|EGB24899.1| RNA polymerase, sigma-24 subunit, ECF subfamily
           [Thermoanaerobacterium xylanolyticum LX-11]
          Length = 214

 Score = 56.0 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 39/252 (15%), Positives = 85/252 (33%), Gaps = 62/252 (24%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + G+ +A   ++  +   V   A  Y   G    ++V EG IGL +A++ F  ++    
Sbjct: 25  AQRGNEAALEFIIDKYYSFVKAKARSYFLVGADKEDIVQEGMIGLYKAIRDFKSDKLSSF 84

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
             ++   I   M   I  +     I   +                               
Sbjct: 85  KAFAELCITRQMITAIKTATRQKHIPLNSY------------------------------ 114

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
                       +S+N  +  +ES          + +             E+++I +EE 
Sbjct: 115 ------------VSLNKPIFEEES----------DRTLMDVVSSECISDPEELIINREEY 152

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            N  N +   +S L   E  +  +     +  + + ++ E    R  V+ I   A ++V+
Sbjct: 153 VNIENKIGEMLSDL---EWEVLISYL---DGKSYQEIAVEL---RRHVKSI-DNALQRVK 202

Query: 282 ESIQKQVELSSS 293
             +++ +E+ +S
Sbjct: 203 RKLERYLEMRNS 214


>gi|237755445|ref|ZP_04584070.1| RNA polymerase sigma factor for flagellar operon
           [Sulfurihydrogenibium yellowstonense SS-5]
 gi|237692409|gb|EEP61392.1| RNA polymerase sigma factor for flagellar operon
           [Sulfurihydrogenibium yellowstonense SS-5]
          Length = 98

 Score = 56.0 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 17/78 (21%), Positives = 41/78 (52%), Gaps = 5/78 (6%)

Query: 47  LSAAHRLVTSHLRLVVKIAMG--YR--GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
                 +V  H+ LV K+A    YR     +   ++V  G +GL++A++ ++ ++G + +
Sbjct: 5   KEQKKEIVEEHIGLVKKVASKIFYRLPDCEIEFDDLVQTGIVGLLKALENYNEDKG-KFS 63

Query: 103 TYSMWWIKAAMQEYILRS 120
           TY+   I+  + +++ + 
Sbjct: 64  TYAYIRIRGEILDFLRQQ 81


>gi|291559860|emb|CBL38660.1| RNA polymerase sigma factor, sigma-70 family [butyrate-producing
           bacterium SSC/2]
          Length = 200

 Score = 56.0 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 24/136 (17%), Positives = 52/136 (38%), Gaps = 2/136 (1%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
              +E +L  R  + G+  A   L+  +  +V K A  +   G    +++ EG IGL +A
Sbjct: 6   TISDEKLL--RQIQSGNDDAMECLLERYRDMVRKEARSFFLAGGDEEDLIQEGMIGLFKA 63

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V  +  E+    +T++   ++  +   I        I             +  +  L  I
Sbjct: 64  VTSYQEEKNTSFSTFAYLCVQRQIYTTITAFNRKKHIPLNTAISLFEQKNQEEELSLDEI 123

Query: 150 TDNNLKPEQVVAIAKK 165
            +   +  + + + K+
Sbjct: 124 LETPEETPEEMMLRKE 139


>gi|254973714|ref|ZP_05270186.1| RNA polymerase factor sigma-70 [Clostridium difficile QCD-66c26]
 gi|255091104|ref|ZP_05320582.1| RNA polymerase factor sigma-70 [Clostridium difficile CIP 107932]
 gi|255099216|ref|ZP_05328193.1| RNA polymerase factor sigma-70 [Clostridium difficile QCD-63q42]
 gi|255304999|ref|ZP_05349171.1| RNA polymerase factor sigma-70 [Clostridium difficile ATCC 43255]
 gi|255312759|ref|ZP_05354342.1| RNA polymerase factor sigma-70 [Clostridium difficile QCD-76w55]
 gi|255515519|ref|ZP_05383195.1| RNA polymerase factor sigma-70 [Clostridium difficile QCD-97b34]
 gi|255648612|ref|ZP_05395514.1| RNA polymerase factor sigma-70 [Clostridium difficile QCD-37x79]
 gi|255654145|ref|ZP_05399554.1| RNA polymerase factor sigma-70 [Clostridium difficile QCD-23m63]
          Length = 215

 Score = 56.0 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 25/96 (26%), Positives = 40/96 (41%), Gaps = 1/96 (1%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           Q+EY +  R  E GD  A   ++T +   V   A  Y   G    +++ EG IGL +AV+
Sbjct: 17  QDEYNIVLRASE-GDKIALEYIITKYRNFVKAKAKSYFLIGADKEDIIQEGMIGLYKAVR 75

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
            FD  +      ++   I   +   I  +     I 
Sbjct: 76  DFDGSKTNSFKCFAEICITRQIITAIKTATRQKHIP 111


>gi|149908744|ref|ZP_01897405.1| RNA polymerase sigma factor for flagellar operon [Moritella sp.
           PE36]
 gi|149808286|gb|EDM68225.1| RNA polymerase sigma factor for flagellar operon [Moritella sp.
           PE36]
          Length = 238

 Score = 56.0 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 36/239 (15%), Positives = 94/239 (39%), Gaps = 31/239 (12%)

Query: 51  HRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
           + L+  ++ LV +         G      ++V  G +GL++A++++  E  +   +Y+  
Sbjct: 22  NALLIKYMHLVKRAVTHLRSQIGTLQSYEDLVQIGTMGLLEAIRRYGSEPDYGFESYAFQ 81

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
            I+  + + + R             ++   +L   +  L          ++++A    L 
Sbjct: 82  RIRGEILDELRRQD-----WRPRQARQQGHSLNHARRTLSRTLGREANEKELMAF---LE 133

Query: 168 VSESEVISMNCRLAGDE--SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           +   ++  M      +E  SL+ L+ +    + +  D   +D                 +
Sbjct: 134 IDAEQLQDMIFDSVSEEMQSLDELLQAGTDITDENSDIQKFD----------------IK 177

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             L +++S+L+ R++ +       E  + ++ +S   +++  RV Q+   A KK+   +
Sbjct: 178 RSLKQTLSLLDQRDQLLLTLYYQYE--LNMKEISLTLKITESRVCQLHQLALKKLHSHL 234


>gi|308171989|ref|YP_003918694.1| RNA polymerase sigma-30 factor sigma H [Bacillus amyloliquefaciens
           DSM 7]
 gi|307604853|emb|CBI41224.1| RNA polymerase sigma-30 factor (sigma(H)) [Bacillus
           amyloliquefaciens DSM 7]
          Length = 206

 Score = 56.0 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 36/248 (14%), Positives = 79/248 (31%), Gaps = 62/248 (25%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A   L+T +   V   A  Y   G    ++V EG IGL ++++ F  ++      +
Sbjct: 18  GDSDALDYLITKYRNFVRAKARSYFLIGADREDIVQEGMIGLYKSIRDFREDKLTSFKAF 77

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +   I   +   I  +     I   +                                  
Sbjct: 78  AELCITRQIITAIKTATRQKHIPLNSY--------------------------------- 104

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
                    +S++            I   + + +             E+++I +EE  + 
Sbjct: 105 ---------VSLDK----------PIFDEESDRTLLDVISGAKTLNPEEMIINQEEFDDI 145

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              +   +S L   ER++        +  + + +S +       V+ I   A ++V+  +
Sbjct: 146 EMKMGELLSDL---ERKVLVLYL---DGRSYQEISDDLN---RHVKSI-DNALQRVKRKL 195

Query: 285 QKQVELSS 292
           +K +E+  
Sbjct: 196 EKYLEIRE 203


>gi|227505453|ref|ZP_03935502.1| possible exonuclease, RNase T and DNA polymerase III
           [Corynebacterium striatum ATCC 6940]
 gi|227197946|gb|EEI77994.1| possible exonuclease, RNase T and DNA polymerase III
           [Corynebacterium striatum ATCC 6940]
          Length = 1118

 Score = 56.0 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 25/115 (21%), Positives = 50/115 (43%), Gaps = 5/115 (4%)

Query: 163 AKKLNVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
           A+ L  +  E+ +++      G   LN  +       S     +       E     +  
Sbjct: 559 AEFLGRTSEEIRALDQAALYIGWAQLNGAVVEVASLPSAVAAEVPIISAHLEHQSPVRAL 618

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
            +   + L R++   + R+R I  +R L E   TL+++ + F ++RER+RQ+E +
Sbjct: 619 FQRAVDELDRAIGG-DERKRGIANSRWLGE--ATLDSIGTAFGLTRERIRQLERQ 670


>gi|222529010|ref|YP_002572892.1| FliA/WhiG subfamily RNA polymerase sigma-28 factor
           [Caldicellulosiruptor bescii DSM 6725]
 gi|222455857|gb|ACM60119.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor bescii DSM 6725]
          Length = 310

 Score = 56.0 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 22/69 (31%), Positives = 41/69 (59%), Gaps = 5/69 (7%)

Query: 53  LVTSHLRLVVKIAMGY----RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           L+  +L+LV  +A  +    +GY   + ++VSEG IGL+ A K +DP +G   +TY+   
Sbjct: 17  LIVDNLKLVYHVANKFMPCPKGYYYEVDDLVSEGYIGLVVAAKNYDPAKGS-FSTYACKV 75

Query: 109 IKAAMQEYI 117
           I++ ++  +
Sbjct: 76  IESKIKRSL 84


>gi|126697623|ref|YP_001086520.1| RNA polymerase factor sigma-70 [Clostridium difficile 630]
 gi|260681829|ref|YP_003213114.1| RNA polymerase factor sigma-70 [Clostridium difficile CD196]
 gi|260685427|ref|YP_003216560.1| RNA polymerase factor sigma-70 [Clostridium difficile R20291]
 gi|296449816|ref|ZP_06891583.1| DNA-directed RNA polymerase sigma subunit SigH [Clostridium
           difficile NAP08]
 gi|296877880|ref|ZP_06901900.1| DNA-directed RNA polymerase sigma subunit SigH [Clostridium
           difficile NAP07]
 gi|115249060|emb|CAJ66871.1| RNA polymerase factor sigma-70 [Clostridium difficile]
 gi|260207992|emb|CBA60155.1| RNA polymerase sigma-H factor [Clostridium difficile CD196]
 gi|260211443|emb|CBE01550.1| RNA polymerase sigma-H factor [Clostridium difficile R20291]
 gi|296261303|gb|EFH08131.1| DNA-directed RNA polymerase sigma subunit SigH [Clostridium
           difficile NAP08]
 gi|296431077|gb|EFH16904.1| DNA-directed RNA polymerase sigma subunit SigH [Clostridium
           difficile NAP07]
          Length = 220

 Score = 56.0 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 25/96 (26%), Positives = 40/96 (41%), Gaps = 1/96 (1%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           Q+EY +  R  E GD  A   ++T +   V   A  Y   G    +++ EG IGL +AV+
Sbjct: 22  QDEYNIVLRASE-GDKIALEYIITKYRNFVKAKAKSYFLIGADKEDIIQEGMIGLYKAVR 80

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
            FD  +      ++   I   +   I  +     I 
Sbjct: 81  DFDGSKTNSFKCFAEICITRQIITAIKTATRQKHIP 116


>gi|284043155|ref|YP_003393495.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Conexibacter
           woesei DSM 14684]
 gi|283947376|gb|ADB50120.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Conexibacter
           woesei DSM 14684]
          Length = 216

 Score = 56.0 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 32/172 (18%), Positives = 64/172 (37%), Gaps = 9/172 (5%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             + G+  A  RLV  +   V   A  Y   G    +++ EG +GL +A++ +  +R   
Sbjct: 22  LAKQGNPDAYDRLVRRYYGFVRLKASSYFLAGGDADDLIQEGLVGLYKAIRDYRTDRESS 81

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
              ++   I   +          VK  T      L   +        A  D +   ++V+
Sbjct: 82  FRNFAELCITRQIITA-------VKTATRNKHTPLNQYVSFSASPASAAGDGDPTLDEVI 134

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS-SQWQDWLVYDHDGQ 211
                ++   ++VIS     A    L+ +++  +    S + D   Y+  G+
Sbjct: 135 P-GPTVHDPVNQVISSEELRALVACLSTVLSDLESRVLSLYLDGYSYESVGE 185


>gi|297582430|ref|YP_003698210.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Bacillus
           selenitireducens MLS10]
 gi|297140887|gb|ADH97644.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Bacillus
           selenitireducens MLS10]
          Length = 214

 Score = 56.0 bits (134), Expect = 7e-06,   Method: Composition-based stats.
 Identities = 19/99 (19%), Positives = 35/99 (35%), Gaps = 4/99 (4%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L  +E     +     GD  A   L+  +   V   +  Y   G    +++ EG IGL +
Sbjct: 12  LTDEEVVEYVR----EGDSQALEYLIEKYRNFVRAKSRSYFLIGADHEDILQEGMIGLYK 67

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           A++ F   +      ++   I   +   I  +     I 
Sbjct: 68  AIRDFKQGKESSFRAFAELCITRQIITAIKTATRQKHIP 106


>gi|89100740|ref|ZP_01173595.1| RNA polymerase sigma-70 factor [Bacillus sp. NRRL B-14911]
 gi|89084557|gb|EAR63703.1| RNA polymerase sigma-70 factor [Bacillus sp. NRRL B-14911]
          Length = 212

 Score = 56.0 bits (134), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 41/264 (15%), Positives = 85/264 (32%), Gaps = 66/264 (25%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           LE +E   L  R    G+  A   L+  +   V   A  Y   G    ++V EG IGL +
Sbjct: 12  LEDEEIIELVHR----GESEALDYLIQKYRNFVRAKARSYFLIGADKEDIVQEGMIGLYK 67

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++ F  ++      ++   I   +   I  +     I   +                  
Sbjct: 68  AIRDFKEDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSY----------------- 110

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                                    +S++            I   + + +          
Sbjct: 111 -------------------------VSLDK----------PIYDEESDRTLMDVISGAKV 135

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
              E+++I +EE  N    ++  +S L   ER++        +  + + +S E       
Sbjct: 136 MDPEELIINQEEFDNIEVKMSELLSDL---ERKVLALYL---DGQSYQEISEELN---RH 186

Query: 269 VRQIEARAFKKVQESIQKQVELSS 292
           V+ I   A ++V+  +++ +E+  
Sbjct: 187 VKSI-DNALQRVKRKLERYLEVRE 209


>gi|113954054|ref|YP_730869.1| type III sigma factor [Synechococcus sp. CC9311]
 gi|113881405|gb|ABI46363.1| putative type III sigma factor [Synechococcus sp. CC9311]
          Length = 271

 Score = 55.6 bits (133), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 39/182 (21%), Positives = 67/182 (36%), Gaps = 8/182 (4%)

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
            Y     ++V EG +GL+  +  FDP+RGFR++TY +  +   +  +       ++I   
Sbjct: 44  RYPGDPDDLVQEGCLGLINGMANFDPQRGFRISTYVLARVNGQILHFRRDRQHALRIPWR 103

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS-MNCRLAGDESLNA 188
              K L     RL+         +L P   + +A  LNVS       +     G      
Sbjct: 104 L--KDLHSRGVRLQA---QRLQQSLDPLDELGLAASLNVSPQRWREALIAHSFGHVDSLD 158

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
           +  S      + +  L+   +    V    EE       L  +M  L P++     AR +
Sbjct: 159 VAPSIQSVDGELRSSLINQIEDPSSVPALVEEPTL--RWLKDAMMSLEPQQCCWLLARYV 216

Query: 249 QE 250
             
Sbjct: 217 DN 218


>gi|253577162|ref|ZP_04854482.1| RNA polymerase sigma-H factor [Paenibacillus sp. oral taxon 786
           str. D14]
 gi|251843406|gb|EES71434.1| RNA polymerase sigma-H factor [Paenibacillus sp. oral taxon 786
           str. D14]
          Length = 217

 Score = 55.6 bits (133), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 32/249 (12%), Positives = 79/249 (31%), Gaps = 62/249 (24%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GD  A   L+  +   V   A  Y   G    +++ EG IGL ++++ F  ++      
Sbjct: 28  EGDSEALEYLINKYRSFVRAKARSYFLIGADREDIIQEGMIGLYKSIRDFRGDKLASFKA 87

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           ++   I   +   I  +     I   +                                 
Sbjct: 88  FAELCITRQIITAIKTATRQKHIPLNSY-------------------------------- 115

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
                     +S++            I   + + +             E+++I +EE   
Sbjct: 116 ----------VSLDK----------PIYDEESDRTLLDVICGSQVSDPEELIINQEEFTG 155

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             + ++  +S L   ER++        +  + + ++ +       V+ I   A ++V+  
Sbjct: 156 LEDKMSEILSDL---ERKVLMLYL---DGRSYQEIAVDLN---RHVKSI-DNALQRVKRK 205

Query: 284 IQKQVELSS 292
           +++ +E+  
Sbjct: 206 LERYLEVRD 214


>gi|134298076|ref|YP_001111572.1| RNA polymerase factor sigma-70 [Desulfotomaculum reducens MI-1]
 gi|134050776|gb|ABO48747.1| RNA polymerase, sigma 30 subunit, SigH [Desulfotomaculum reducens
           MI-1]
          Length = 214

 Score = 55.6 bits (133), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 35/258 (13%), Positives = 81/258 (31%), Gaps = 66/258 (25%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           ++    A+     GD +A   L+  +   V   A  Y   G    +++ EG IGL +A++
Sbjct: 19  EDVVEFAR----EGDNAALEYLINKYKNFVRAKARSYFLIGADREDIIQEGMIGLYKAIR 74

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
            F  ++      ++   I   +   I  +     I   +                     
Sbjct: 75  DFRLDKLSSFRAFAELCITRQIITAIKTATRQKHIPLNSY-------------------- 114

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
                                 +S+N            I   D + +             
Sbjct: 115 ----------------------VSLNK----------PIYDEDSDRTLLDVISGSKITDP 142

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E+++I +EE  +    +   +S L   E ++  +        + + ++ +       V+ 
Sbjct: 143 EELIISREEFDDIEEKMGEILSSL---EWKVLMSYL---EGKSYQEIAEDLN---RHVKS 193

Query: 272 IEARAFKKVQESIQKQVE 289
           I   A ++V+  +++ +E
Sbjct: 194 I-DNALQRVKRKLERYLE 210


>gi|65317554|ref|ZP_00390513.1| COG1595: DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog [Bacillus anthracis str. A2012]
          Length = 218

 Score = 55.6 bits (133), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 35/265 (13%), Positives = 86/265 (32%), Gaps = 66/265 (24%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           LE +    L ++    G+      L+  +   V   +  Y   G    ++V EG IGL +
Sbjct: 16  LEDEAIVELVRK----GNTDXLEYLIHKYKNFVRAKSRSYFLVGADREDIVQEGMIGLFK 71

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++ +  ++      ++   I   +   I  +     I   +                  
Sbjct: 72  AIRDYKEDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSY----------------- 114

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                                    +S++            I   + + +          
Sbjct: 115 -------------------------VSLDK----------PIYDEESDRTLLDVISEAKV 139

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
              E+++I +EE  +  + ++  +S L   ER++        +  + + +S +       
Sbjct: 140 TDPEEMIISQEEYTDIESKISELLSDL---ERKVLSLYL---DGRSYQEISEQLN---RH 190

Query: 269 VRQIEARAFKKVQESIQKQVELSSS 293
           V+ I   A ++V+  +++ +E+  S
Sbjct: 191 VKSI-DNALQRVKRKLERYMEMRES 214


>gi|325921797|ref|ZP_08183616.1| DNA-directed RNA polymerase specialized sigma subunit [Xanthomonas
           gardneri ATCC 19865]
 gi|325547729|gb|EGD18764.1| DNA-directed RNA polymerase specialized sigma subunit [Xanthomonas
           gardneri ATCC 19865]
          Length = 135

 Score = 55.6 bits (133), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 15/71 (21%), Positives = 31/71 (43%), Gaps = 2/71 (2%)

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
             +  ER      L +++  L  RE+ +       E  + L+ + +   VS  RV QI  
Sbjct: 54  PQQMMERGEFGRELGKAIGQLPEREQLVLSLYY--EQELNLKEIGAVLGVSESRVCQIHG 111

Query: 275 RAFKKVQESIQ 285
           +A  +++  ++
Sbjct: 112 QAVVRLRGRLK 122


>gi|257439708|ref|ZP_05615463.1| RNA polymerase sigma-E factor [Faecalibacterium prausnitzii A2-165]
 gi|257197848|gb|EEU96132.1| RNA polymerase sigma-E factor [Faecalibacterium prausnitzii A2-165]
          Length = 118

 Score = 55.6 bits (133), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 22/108 (20%), Positives = 46/108 (42%), Gaps = 6/108 (5%)

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
             R     SL   + +  ++S+     ++ D    E    +  ER++    L R +  L 
Sbjct: 6   ERRNGVVVSLQETLEAGKEDSALTLSDVLQDGFCME----DACERQDEARRLRRLIEGLP 61

Query: 237 PRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            RER++   R     + P+T    +   ++SR  V ++E  A  ++++
Sbjct: 62  ARERKLILLRYGLAGQPPLTQLETAQLLQISRSYVSRLETHALNQLRK 109


>gi|85057513|ref|YP_456429.1| RNA polymerase sigma factor [Aster yellows witches'-broom
           phytoplasma AYWB]
 gi|84789618|gb|ABC65350.1| RNA polymerase sigma factor [Aster yellows witches'-broom
           phytoplasma AYWB]
          Length = 201

 Score = 55.6 bits (133), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 23/121 (19%), Positives = 51/121 (42%), Gaps = 6/121 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS--EVVSEGNIGLMQAVKKFDPERG 98
            +   +L   ++L+  H  LV K+   ++ Y   +   ++  EG +GL++A+  +  + G
Sbjct: 11  LKSKKNLEIRNQLINLHEPLVKKLVSKFKYYPRVLQKQDLYQEGVLGLIKALNNY-VDLG 69

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           +    Y+   IK+ ++E I +S S           +      + + H     + N    Q
Sbjct: 70  YDFIAYATPTIKSEIRELIRKSHSP---SIPQKTHKTNSTSFQEEKHSLEKGNRNPNTHQ 126

Query: 159 V 159
           +
Sbjct: 127 I 127


>gi|291546870|emb|CBL19978.1| RNA polymerase, sigma 30 subunit, SigH [Ruminococcus sp. SR1/5]
          Length = 194

 Score = 55.6 bits (133), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 23/92 (25%), Positives = 38/92 (41%), Gaps = 1/92 (1%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L +R R  G+ + A  L+  +  LV K A      G    +++ EG IGL +AV+ + P
Sbjct: 11  ALIERLR-AGESAIADYLMEKYKGLVRKKARAMFLIGGDTDDLIQEGMIGLFKAVRDYQP 69

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           +R      ++   I   +   I  S       
Sbjct: 70  DRESSFQFFANICIDRQIYTAIKSSNRQKHQP 101


>gi|153930829|ref|YP_001385813.1| RNA polymerase factor sigma-70 [Clostridium botulinum A str. ATCC
           19397]
 gi|153937099|ref|YP_001389220.1| RNA polymerase factor sigma-70 [Clostridium botulinum A str. Hall]
 gi|153938469|ref|YP_001392851.1| RNA polymerase factor sigma-70 [Clostridium botulinum F str.
           Langeland]
 gi|168178815|ref|ZP_02613479.1| RNA polymerase sigma-H factor [Clostridium botulinum NCTC 2916]
 gi|168181847|ref|ZP_02616511.1| RNA polymerase sigma-H factor [Clostridium botulinum Bf]
 gi|170756449|ref|YP_001783138.1| RNA polymerase factor sigma-70 [Clostridium botulinum B1 str. Okra]
 gi|170758920|ref|YP_001788838.1| RNA polymerase factor sigma-70 [Clostridium botulinum A3 str. Loch
           Maree]
 gi|226950950|ref|YP_002806041.1| RNA polymerase sigma-H factor [Clostridium botulinum A2 str. Kyoto]
 gi|237796959|ref|YP_002864511.1| RNA polymerase sigma-H factor [Clostridium botulinum Ba4 str. 657]
 gi|152926873|gb|ABS32373.1| RNA polymerase sigma-H factor [Clostridium botulinum A str. ATCC
           19397]
 gi|152933013|gb|ABS38512.1| RNA polymerase sigma-H factor [Clostridium botulinum A str. Hall]
 gi|152934365|gb|ABS39863.1| RNA polymerase sigma-H factor [Clostridium botulinum F str.
           Langeland]
 gi|169121661|gb|ACA45497.1| RNA polymerase sigma-H factor [Clostridium botulinum B1 str. Okra]
 gi|169405909|gb|ACA54320.1| RNA polymerase sigma-H factor [Clostridium botulinum A3 str. Loch
           Maree]
 gi|182669996|gb|EDT81972.1| RNA polymerase sigma-H factor [Clostridium botulinum NCTC 2916]
 gi|182674901|gb|EDT86862.1| RNA polymerase sigma-H factor [Clostridium botulinum Bf]
 gi|226843434|gb|ACO86100.1| RNA polymerase sigma-H factor [Clostridium botulinum A2 str. Kyoto]
 gi|229260872|gb|ACQ51905.1| RNA polymerase sigma-H factor [Clostridium botulinum Ba4 str. 657]
 gi|295320829|gb|ADG01207.1| RNA polymerase sigma-H factor [Clostridium botulinum F str. 230613]
 gi|322807823|emb|CBZ05398.1| RNA polymerase sporulation specific sigma factor SigH [Clostridium
           botulinum H04402 065]
          Length = 213

 Score = 55.6 bits (133), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 30/187 (16%), Positives = 74/187 (39%), Gaps = 7/187 (3%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + G+  A   ++  +   V   A  Y   G    ++  EG IGL +A++ F P++    
Sbjct: 26  AKAGNSRAQEYIIGKYENFVKAKAKSYFLIGADKEDIYQEGMIGLYKAIRDFKPDKLSSF 85

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQAITDNNLK-PEQ 158
             ++   +   +   I  +     I   T  +  +  ++    +  L  +++  +  PE+
Sbjct: 86  KAFAELCVTRQIITAIKTATRQKHIPLNTYVSLNKPIYDEESDRTLLDILSEAKVANPEE 145

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           ++   ++L   ++E+  +      D  +  L++  D  S Q     +  H       +++
Sbjct: 146 LIISREELKHIQNEIGEVLS----DLEMEVLMSYLDGKSYQEIACDLDRHAKSIDNALQR 201

Query: 219 EERKNRR 225
            +RK  +
Sbjct: 202 VKRKLEK 208


>gi|295694818|ref|YP_003588056.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Bacillus tusciae
           DSM 2912]
 gi|295410420|gb|ADG04912.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Bacillus tusciae
           DSM 2912]
          Length = 221

 Score = 55.6 bits (133), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 36/257 (14%), Positives = 85/257 (33%), Gaps = 63/257 (24%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L  R R+ GD  A   L+  +   V   A  Y   G    ++V EG IGL ++++ F  
Sbjct: 22  DLVDRVRD-GDEEALEYLIHRYKNFVRAKARSYFLIGADREDIVQEGMIGLYKSIRDFRN 80

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           ++      ++   I   +   I  +     I                             
Sbjct: 81  DKLVSFRAFAELCITRQIITAIKTATRQKHIP---------------------------- 112

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
                               +N  ++    L+  I   + + +             E+++
Sbjct: 113 --------------------LNSYIS----LDKPIYDEESDRTLLDVLCGTRVADPEELI 148

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
           I +EE  +    +   +S L   E+++        +  + + ++ +    +  V+ I   
Sbjct: 149 INQEEFDDIEVKMGEILSDL---EQQVLMLYL---DGRSYQEIAVDL---KRHVKSI-DN 198

Query: 276 AFKKVQESIQKQVELSS 292
           A ++V+  +++ +E+ +
Sbjct: 199 ALQRVKRKLERYLEVRN 215


>gi|217076384|ref|YP_002334100.1| RNA polymerase factor sigma-70 [Thermosipho africanus TCF52B]
 gi|217036237|gb|ACJ74759.1| RNA polymerase sigma-H factor [Thermosipho africanus TCF52B]
          Length = 206

 Score = 55.6 bits (133), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 20/86 (23%), Positives = 41/86 (47%), Gaps = 5/86 (5%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           ++   LA    + G   A   ++  +  +V++I+  Y        ++V  G IGL++AV 
Sbjct: 12  EKLVELA----QSGLKEALELIIEKYYPMVIRISSKYYAPWAEFEDIVQNGLIGLIKAVF 67

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYI 117
            FD E+     +++   I+  +Q +I
Sbjct: 68  YFDNEK-SSFNSFAWKSIEGEVQTFI 92


>gi|18311404|ref|NP_563338.1| RNA polymerase factor sigma-70 [Clostridium perfringens str. 13]
 gi|110798736|ref|YP_697111.1| RNA polymerase factor sigma-70 [Clostridium perfringens ATCC 13124]
 gi|168211256|ref|ZP_02636881.1| RNA polymerase sigma-H factor [Clostridium perfringens B str. ATCC
           3626]
 gi|18146088|dbj|BAB82128.1| RNA polymerase sigma-H factor [Clostridium perfringens str. 13]
 gi|110673383|gb|ABG82370.1| RNA polymerase sigma-H factor [Clostridium perfringens ATCC 13124]
 gi|170710792|gb|EDT22974.1| RNA polymerase sigma-H factor [Clostridium perfringens B str. ATCC
           3626]
          Length = 215

 Score = 55.6 bits (133), Expect = 8e-06,   Method: Composition-based stats.
 Identities = 39/262 (14%), Positives = 90/262 (34%), Gaps = 74/262 (28%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L  +E  +LAK    +GD  A   +++ + + V   +  Y   G    ++  EG IGL +
Sbjct: 19  LTDKEVVMLAK----NGDNMAQEYVISKYEQFVKAKSKSYFLIGADKEDIYQEGMIGLYK 74

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++ F+P++     +++   +   +   I  +     I                      
Sbjct: 75  AIRDFNPDKFASFKSFAELCVTRQIITAIKTATRQKHIP--------------------- 113

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                                      +N  +    SL+  I   + + +     +    
Sbjct: 114 ---------------------------LNTYI----SLSKPIYEEESDRTLLDTVVGITI 142

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
              E ++I KEE +   + +   +S L   E  +  +     +  + + ++ + +     
Sbjct: 143 TDPESLVIGKEEVEKIESAINSVLSEL---ELEVLNSYL---DGKSYQEIACDLD----- 191

Query: 269 VRQIEAR----AFKKVQESIQK 286
            R  EA+    A ++V+  ++K
Sbjct: 192 -R--EAKSIDNALQRVKRKLEK 210


>gi|39938526|ref|NP_950292.1| DNA-directed RNA polymerase specialized sigma subunit [Onion
           yellows phytoplasma OY-M]
 gi|39721635|dbj|BAD04125.1| DNA-directed RNA polymerase specialized sigma [Onion yellows
           phytoplasma OY-M]
          Length = 201

 Score = 55.6 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 24/92 (26%), Positives = 45/92 (48%), Gaps = 4/92 (4%)

Query: 35  YVLAKRY-REHGDLSAAHRLVTSHLRLVVKIAM--GYRGYGLPISEVVSEGNIGLMQAVK 91
             L K + +   +L   ++L+  HL LV K+     Y    L   ++  EG +GL++A+ 
Sbjct: 4   QELFKDFLKNKQNLEIRNQLIELHLPLVKKLVYQFKYYPRVLTKKDLYQEGILGLIKALN 63

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
            +  + G+    Y+   IK+ ++E I +S S 
Sbjct: 64  HYQ-DLGYDFMAYATPTIKSEIREIIRKSHSP 94


>gi|297618401|ref|YP_003703560.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Syntrophothermus
           lipocalidus DSM 12680]
 gi|297146238|gb|ADI02995.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Syntrophothermus
           lipocalidus DSM 12680]
          Length = 217

 Score = 55.6 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 21/99 (21%), Positives = 38/99 (38%), Gaps = 4/99 (4%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L  +E   LA    + G+  A   LV  +   V   A  Y   G    +++ EG IGL +
Sbjct: 16  LSDEEIVELA----QEGEQLATEYLVDKYKNFVRAKARSYFLIGADKEDIIQEGMIGLFK 71

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           A++ +  ++      ++   I   +   I  +     I 
Sbjct: 72  AIRDYKGDKLTSFRAFAELCITRQIITAIKTATRQKHIP 110


>gi|323141399|ref|ZP_08076290.1| RNA polymerase sigma-H factor [Phascolarctobacterium sp. YIT 12067]
 gi|322414148|gb|EFY04976.1| RNA polymerase sigma-H factor [Phascolarctobacterium sp. YIT 12067]
          Length = 245

 Score = 55.6 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 37/259 (14%), Positives = 85/259 (32%), Gaps = 68/259 (26%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            EE VL    ++H ++ A   L+  +   V   A  Y   G    +++ EG IGL +A++
Sbjct: 23  DEEIVL--ESQQHDNVLAQEYLLHKYRNFVRAKARSYFLIGAEREDIIQEGMIGLYKAIR 80

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
            F  ++      ++   +   +   I  +     I   +                     
Sbjct: 81  DFRADKQASFRAFAELCVTRQIITAIKTATRQKHIPLNSY-------------------- 120

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
                                 +S+N            I   D + +             
Sbjct: 121 ----------------------VSLNK----------PIYEEDSDRTLLDVISGVKVANP 148

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E ++I +EE  +  + +   +S L   E ++  +     +  + + +++E        R 
Sbjct: 149 EDMIISREEFSDIESKMNDILSDL---EWKVLMSYL---DGKSYQEIAAELG------RH 196

Query: 272 IEA--RAFKKVQESIQKQV 288
           I++   A ++V+  ++K +
Sbjct: 197 IKSIDNALQRVKRKLEKYI 215


>gi|304315923|ref|YP_003851068.1| RNA polymerase, sigma-24 subunit, ECF subfamily
           [Thermoanaerobacterium thermosaccharolyticum DSM 571]
 gi|302777425|gb|ADL67984.1| RNA polymerase, sigma-24 subunit, ECF subfamily
           [Thermoanaerobacterium thermosaccharolyticum DSM 571]
          Length = 214

 Score = 55.6 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 40/253 (15%), Positives = 86/253 (33%), Gaps = 64/253 (25%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + G+ +A   ++  +   V   A  Y   G    ++V EG IGL +A++ F  ++    
Sbjct: 25  AQRGNQAALEFIIDKYYSFVKAKARSYFLVGADKEDIVQEGMIGLYKAIRDFKSDKLSSF 84

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
             ++   I   M   I  +     I   +                               
Sbjct: 85  KAFAELCITRQMITAIKTATRQKHIPLNSY------------------------------ 114

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH-DGQEQVLIEKEE 220
                       +S+N  +  +ES                D +  +     E+++I +EE
Sbjct: 115 ------------VSLNKPIFEEES-----------DRTLMDVVSSECISDPEELIINREE 151

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             N  N +   +S L   E  +  +     +  + + ++ E    R  V+ I   A ++V
Sbjct: 152 YVNIENKIGEMLSDL---EWEVLISYL---DGKSYQEIAVEL---RRHVKSI-DNALQRV 201

Query: 281 QESIQKQVELSSS 293
           +  +++ +E+ +S
Sbjct: 202 KRKLERYLEMRNS 214


>gi|167765724|ref|ZP_02437777.1| hypothetical protein CLOSS21_00212 [Clostridium sp. SS2/1]
 gi|167712597|gb|EDS23176.1| hypothetical protein CLOSS21_00212 [Clostridium sp. SS2/1]
          Length = 101

 Score = 55.6 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 20/88 (22%), Positives = 40/88 (45%), Gaps = 2/88 (2%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
              +E +L  R  + G+  A   L+  +  +V K A  +   G    +++ EG IGL +A
Sbjct: 6   TISDEKLL--RQIQSGNDDAMECLLERYRDMVRKEARSFFLAGGDEEDLIQEGMIGLFKA 63

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYI 117
           V  +  E+    +T++   ++  +   I
Sbjct: 64  VTSYQEEKNTSFSTFAYLCVQRQIYTTI 91


>gi|57908870|gb|AAW59363.1| stationary phase sigma factor [Azotobacter salinestris]
          Length = 55

 Score = 55.6 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 16/45 (35%), Positives = 25/45 (55%)

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
                TLE +  E  ++RERVRQI+  A K ++E ++K    S +
Sbjct: 8   GHESCTLEEVGQEIGLTRERVRQIQVEALKPLREILEKNGLSSDA 52


>gi|313902852|ref|ZP_07836249.1| RNA polymerase, sigma 30 subunit, SigH [Thermaerobacter
           subterraneus DSM 13965]
 gi|313466972|gb|EFR62489.1| RNA polymerase, sigma 30 subunit, SigH [Thermaerobacter
           subterraneus DSM 13965]
          Length = 224

 Score = 55.6 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 39/260 (15%), Positives = 83/260 (31%), Gaps = 66/260 (25%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           E +E   +A++    G+  A   L+  +   V   A  Y   G    +++ EG IGL +A
Sbjct: 19  EDEEIVEIARQ----GNPEALEYLIGKYKNFVRAKARSYFLVGADREDIIQEGMIGLYKA 74

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           ++ F  ++      ++   I   +   I  +     I   +                   
Sbjct: 75  IRDFRSDKLSSFRAFAELCITRQIITAIKTATRQKHIPLNSY------------------ 116

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
                                   +S+N            I   D + +           
Sbjct: 117 ------------------------VSLNK----------PIYDEDSDRTLLDIISGSRVT 142

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
             E++ I +EE  +    +   +S L   E R+  A     +  + + ++ E       V
Sbjct: 143 DPEELFISREEFGDIEQKMGEILSEL---EWRVLIAYL---DGKSYQEIADELN---RHV 193

Query: 270 RQIEARAFKKVQESIQKQVE 289
           + I   A ++V+  +++ +E
Sbjct: 194 KSI-DNALQRVKRKLERYIE 212


>gi|169830406|ref|YP_001716388.1| RNA polymerase factor sigma-70 [Candidatus Desulforudis audaxviator
           MP104C]
 gi|169637250|gb|ACA58756.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Candidatus
           Desulforudis audaxviator MP104C]
          Length = 216

 Score = 55.6 bits (133), Expect = 9e-06,   Method: Composition-based stats.
 Identities = 37/203 (18%), Positives = 79/203 (38%), Gaps = 7/203 (3%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           LE ++    A+     GD  A   L+  +   V   A  Y   G    +++ EG IGL +
Sbjct: 18  LEDEKIVEHAR----EGDSEALEFLINKYRHFVRAKARSYFLIGADREDIIQEGMIGLYK 73

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHL 146
           A++ F  ++      ++   I   +   I  +     I   +  +  +  ++    +  L
Sbjct: 74  AIRDFRLDKLSSFRAFAELCITRQIITAIKTATRQKHIPLNSYVSLNKPIYDEDSDRTLL 133

Query: 147 QAITDNNLK-PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
             I+ + +  PE++V   ++ +  E ++  +   L     ++ L   S +  ++  D  V
Sbjct: 134 DVISGSKITDPEELVISREEFDDIEEKIGELLSSLEWKVLMSYLEGKSYQEIAEDLDRHV 193

Query: 206 YDHDGQEQVLIEKEERKNRRNML 228
              D   Q +  K E+   R  +
Sbjct: 194 KSIDNALQRVKRKLEKYLERREI 216


>gi|313820245|gb|EFS57959.1| sigma-70 region 2 [Propionibacterium acnes HL036PA1]
 gi|313822945|gb|EFS60659.1| sigma-70 region 2 [Propionibacterium acnes HL036PA2]
 gi|314925132|gb|EFS88963.1| sigma-70 region 2 [Propionibacterium acnes HL036PA3]
          Length = 228

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 29/138 (21%), Positives = 56/138 (40%), Gaps = 10/138 (7%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKK 92
           E  L +R  + G + A   L    L +V+  A      Y   + +++  G IGL +A+++
Sbjct: 47  EAEL-RRISDDG-VGARQTLWRQMLAIVLTQARQAAVSYRCSVEDLIQAGCIGLGEAIER 104

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           +D  RG R +T +  WI+  + E ++R          A  + +      +    + +T  
Sbjct: 105 YDVRRGARFSTVAWTWIRRRIGEEVVRLSG-------ARSRSVMREAAEVARIEEELTAR 157

Query: 153 NLKPEQVVAIAKKLNVSE 170
                   AIA ++    
Sbjct: 158 WQSVPSSDAIAARMGKDV 175


>gi|164686510|ref|ZP_02210538.1| hypothetical protein CLOBAR_00075 [Clostridium bartlettii DSM
           16795]
 gi|164604521|gb|EDQ97986.1| hypothetical protein CLOBAR_00075 [Clostridium bartlettii DSM
           16795]
          Length = 220

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 22/98 (22%), Positives = 40/98 (40%), Gaps = 1/98 (1%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
            +Q+EY +  +    GD  A   +++ +   V   A  Y   G    +++ EG IGL +A
Sbjct: 20  SQQDEYNIVLK-ANKGDKLALEYIISKYKNFVKAKAKSYFLVGADKEDIIQEGMIGLYKA 78

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           V+ FD  +      ++   I   +   I  +     I 
Sbjct: 79  VRDFDGTKTNSFKCFAEICITRQIITAIKTATRQKHIP 116


>gi|222528749|ref|YP_002572631.1| FliA/WhiG subfamily RNA polymerase sigma-28 factor
           [Caldicellulosiruptor bescii DSM 6725]
 gi|222530717|ref|YP_002574606.1| FliA/WhiG subfamily RNA polymerase sigma-28 factor
           [Caldicellulosiruptor bescii DSM 6725]
 gi|222455596|gb|ACM59858.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor bescii DSM 6725]
 gi|222457564|gb|ACM61825.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor bescii DSM 6725]
          Length = 310

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 22/69 (31%), Positives = 41/69 (59%), Gaps = 5/69 (7%)

Query: 53  LVTSHLRLVVKIAMGY----RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           L+  +L+LV  +A  +    +GY   + ++VSEG IGL+ A K +DP +G   +TY+   
Sbjct: 17  LIVDNLKLVYHVANKFMPCPKGYYYEVDDLVSEGYIGLVVAAKNYDPAKGS-FSTYACKV 75

Query: 109 IKAAMQEYI 117
           I++ ++  +
Sbjct: 76  IESKIKRSL 84


>gi|300933403|ref|ZP_07148659.1| exonuclease, RNase T and DNA polymerase III [Corynebacterium
           resistens DSM 45100]
          Length = 1144

 Score = 55.6 bits (133), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 14/40 (35%), Positives = 21/40 (52%), Gaps = 2/40 (5%)

Query: 236 NPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
           + R+  I   R       TL+ L  +  V+RERVRQ+E +
Sbjct: 654 DDRKWLILMERWFGG--ATLDELGQKMGVTRERVRQLEKQ 691


>gi|313116074|ref|ZP_07801498.1| sigma-70 region 2 [Faecalibacterium cf. prausnitzii KLE1255]
 gi|310621671|gb|EFQ05202.1| sigma-70 region 2 [Faecalibacterium cf. prausnitzii KLE1255]
          Length = 221

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 43/250 (17%), Positives = 85/250 (34%), Gaps = 58/250 (23%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL--------PISEVVSEGNIGLMQAVKK 92
             + GD +A   L+ ++   + K+A                   ++   GN+G  +AV K
Sbjct: 11  LAQKGDATALDSLIENNKSFIGKVANDLFRSMDLAQSGLNLDTDDLKQAGNLGFWKAVPK 70

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  RG +  TY+   I+ AM + +                              A    
Sbjct: 71  FDAARGMKFLTYAAPAIRNAMMDMVRD-------------------------AFAAFEQR 105

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
            +  ++     ++        +S+N  L G+E L            +  + +   +  Q 
Sbjct: 106 MVTEDKDGICYQR--------VSLNDVLPGEEQL------------RRIEAIADPYAMQP 145

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVR 270
           Q ++E++E    R  L   +  L  RE+     R          L   +  F +++ R +
Sbjct: 146 QSIMEEQES---RRELYDGLKRLTQREQTYLLYRYGFTDGEEHPLIGTAIYFHLTKGRAQ 202

Query: 271 QIEARAFKKV 280
           + E +A   +
Sbjct: 203 KTEEQAMDNL 212


>gi|292669555|ref|ZP_06602981.1| RNA polymerase sigma-H factor [Selenomonas noxia ATCC 43541]
 gi|292648764|gb|EFF66736.1| RNA polymerase sigma-H factor [Selenomonas noxia ATCC 43541]
          Length = 269

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 38/259 (14%), Positives = 84/259 (32%), Gaps = 67/259 (25%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E +LA+     GD  A   L+  +   V   A  Y   G    ++V EG IG  +A++ 
Sbjct: 49  DEDLLARIRACQGD-DALDYLINKYRNFVRSKARSYFLIGADREDIVQEGMIGFFKAIRD 107

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F  ++      ++   +   +   I  +     I   +                      
Sbjct: 108 FREDKLSSFRAFAELCVTRQIITAIKTATRQKHIPLNSY--------------------- 146

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
                                +S+N            I   D + +             E
Sbjct: 147 ---------------------VSLNK----------PIYDEDSDRTLLDVLSGARISDPE 175

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           +++I +EE  +    +   +S L   E R+  +     +  + + ++ +        RQ+
Sbjct: 176 ELVISREEFVDIEQKMEEILSDL---EWRVLMSYL---DGKSYQEIAVDLH------RQV 223

Query: 273 EA--RAFKKVQESIQKQVE 289
           ++   A ++V+  ++K +E
Sbjct: 224 KSIDNALQRVKRKLEKYME 242


>gi|317057764|ref|YP_004106231.1| LuxR family transcriptional regulator [Ruminococcus albus 7]
 gi|315450033|gb|ADU23597.1| transcriptional regulator, LuxR family [Ruminococcus albus 7]
          Length = 195

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 40/243 (16%), Positives = 84/243 (34%), Gaps = 78/243 (32%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           D +A   L+  ++    +IA G     G    + ++V EG + L++AV  + P+RG   A
Sbjct: 24  DKAALSALLFRYMGTAERIAAGIAPGAGREQTVKDLVQEGMMALLRAVNSYRPDRGAGFA 83

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
            Y+   I+ +M  YI++                                           
Sbjct: 84  AYAGVCIRHSMLSYIMKDNR---------------------------------------- 103

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
                       S   R++ DE L+  ++ SD++  +       +HDG            
Sbjct: 104 -----------YSGENRISTDE-LDDDLSGSDEDIPENAVIAKEEHDG------------ 139

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
               +  R    L+ RE ++ +      N  +   ++ +  +S + V        ++V++
Sbjct: 140 ----LFGRIADELSEREWQVLQLFL---NGHSYRQIAEKMSISEKSV----NNTMQRVRK 188

Query: 283 SIQ 285
            ++
Sbjct: 189 KLR 191


>gi|255659336|ref|ZP_05404745.1| RNA polymerase sigma-H factor [Mitsuokella multacida DSM 20544]
 gi|260848418|gb|EEX68425.1| RNA polymerase sigma-H factor [Mitsuokella multacida DSM 20544]
          Length = 248

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 38/262 (14%), Positives = 83/262 (31%), Gaps = 64/262 (24%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            EE +L    +EH +  A   L+  +   V   A  Y   G    ++V EG IG  +A++
Sbjct: 22  DEEILL--DIKEHNNKVALDYLINKYRNFVRAKARSYFLIGADREDIVQEGMIGFYKAIR 79

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
            F  ++      ++   +   +   I  +     I   +                     
Sbjct: 80  DFRDDKLSSFRAFAELCVTRQIITAIKTATRQKHIPLNSY-------------------- 119

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
                                 +S+N            I   D + +             
Sbjct: 120 ----------------------VSLNK----------PIYDEDSDRTLLDIISGAKVSDP 147

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E+++I +EE  +    +   +S L   E ++  +     +  + + ++ +       V+ 
Sbjct: 148 EELVISQEEFVDIEKKMEEILSDL---EWKVLMSYL---DGKSYQEIAEDLG---RHVKS 198

Query: 272 IEARAFKKVQESIQKQVELSSS 293
           I   A ++V+  ++K +E  S 
Sbjct: 199 I-DNALQRVKRKLEKYMETRSD 219


>gi|167628189|ref|YP_001678688.1| hypothetical protein HM1_0052 [Heliobacterium modesticaldum Ice1]
 gi|167590929|gb|ABZ82677.1| hypothetical protein HM1_0052 [Heliobacterium modesticaldum Ice1]
          Length = 238

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 42/234 (17%), Positives = 72/234 (30%), Gaps = 63/234 (26%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY------GLPISEVVSEGNIGLMQA 89
            LA      GD  + H+L  +   L+ KI   Y  Y      G+   ++   G    + A
Sbjct: 5   ELAI-MAAQGDTESLHKLYFAVAPLIYKITSRYFKYCETNRKGVRPEDLTQCGYFAYLSA 63

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           +K++ PER  +  +Y  + +                                        
Sbjct: 64  LKQYSPERELKFTSYLDFCVARECWR---------------------------------- 89

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
                          +L +S      +  R     SL   I  SD       + ++ D D
Sbjct: 90  ---------------ELGISFQTGGKVLNREVETISLETPI--SDDEEGLTLEDIISDPD 132

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
                  E     + R ++ R +  L+PRE+ +        N  T+E L+ EF 
Sbjct: 133 ADTYSFCE---LNDMRLIVRREIERLSPREQCVIYGIFY--NNKTIEGLAQEFG 181


>gi|219666470|ref|YP_002456905.1| RNA polymerase factor sigma-70 [Desulfitobacterium hafniense DCB-2]
 gi|219536730|gb|ACL18469.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Desulfitobacterium
           hafniense DCB-2]
          Length = 217

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 18/87 (20%), Positives = 34/87 (39%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             ++GD  A   L+  +   V   A  Y   G    +++ EG IGL +A++ F  ++   
Sbjct: 27  LAKNGDAEAQEYLINKYKNFVRAKARSYFLIGADREDIIQEGMIGLYKAIRDFRGDKLSS 86

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIG 127
              ++   I   +   I  +     I 
Sbjct: 87  FRAFAELCITRQIITAIKTATRQKHIP 113


>gi|89893197|ref|YP_516684.1| RNA polymerase factor sigma-70 [Desulfitobacterium hafniense Y51]
 gi|89332645|dbj|BAE82240.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 208

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 18/87 (20%), Positives = 34/87 (39%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             ++GD  A   L+  +   V   A  Y   G    +++ EG IGL +A++ F  ++   
Sbjct: 18  LAKNGDAEAQEYLINKYKNFVRAKARSYFLIGADREDIIQEGMIGLYKAIRDFRGDKLSS 77

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIG 127
              ++   I   +   I  +     I 
Sbjct: 78  FRAFAELCITRQIITAIKTATRQKHIP 104


>gi|117924589|ref|YP_865206.1| sigma-70 region 4 domain-containing protein [Magnetococcus sp.
           MC-1]
 gi|117608345|gb|ABK43800.1| sigma-70 region 4 domain protein [Magnetococcus sp. MC-1]
          Length = 187

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 22/62 (35%), Positives = 38/62 (61%), Gaps = 3/62 (4%)

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R ML R+M  L+ RE ++   R      +  E+++   +++RERVR IEA+A KK++  I
Sbjct: 122 RIMLGRAMQHLSAREAQVVNMR---MENLRYEDVAKVMKITRERVRIIEAKASKKIKAVI 178

Query: 285 QK 286
           ++
Sbjct: 179 EQ 180


>gi|295104322|emb|CBL01866.1| RNA polymerase sigma factor, sigma-70 family [Faecalibacterium
           prausnitzii SL3/3]
          Length = 221

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 48/250 (19%), Positives = 87/250 (34%), Gaps = 58/250 (23%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGL--------PISEVVSEGNIGLMQAVKK 92
             + GD +A   L+ ++   + K A                   ++   GN+GL +AV K
Sbjct: 11  LAQKGDATALDSLIENNKSFIGKEANDLFRSMNLAQSGLNLDTDDLKQAGNLGLWKAVPK 70

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           FD  RG +  TY+   I  AM + +  +++                              
Sbjct: 71  FDAARGMKFLTYAAPAICNAMMDMVRDAFATF---------------------------- 102

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
               EQ + I  K  +    V S++  L G+E L            +  + +   +  Q 
Sbjct: 103 ----EQRMQIEDKDGICYQRV-SLDDVLPGEEQL------------RRIEAIADLYAMQP 145

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVR 270
           Q +IE++E    R  L   +  L  RE+     R          L   +  F +++ R +
Sbjct: 146 QSIIEEQES---RRELYDGLKRLTQREQTYLLYRYGFTDGEEHPLIGTAIYFHLAKSRAK 202

Query: 271 QIEARAFKKV 280
           + E +A   +
Sbjct: 203 KTEEQAMDNL 212


>gi|148381438|ref|YP_001255979.1| RNA polymerase sigma-H factor [Clostridium botulinum A str. ATCC
           3502]
 gi|148290922|emb|CAL85058.1| RNA polymerase sigma-H factor [Clostridium botulinum A str. ATCC
           3502]
 gi|164511636|emb|CAO86124.1| RNA polymerase sigma-H factor [Clostridium botulinum]
 gi|164511638|emb|CAO86125.1| RNA polymerase sigma-H factor [Clostridium botulinum]
 gi|164511640|emb|CAO86126.1| RNA polymerase sigma-H factor [Clostridium botulinum]
 gi|164511642|emb|CAO86127.1| RNA polymerase sigma-H factor [Clostridium botulinum]
 gi|164511644|emb|CAO86128.1| RNA polymerase sigma-H factor [Clostridium botulinum]
 gi|164511646|emb|CAO86129.1| RNA polymerase sigma-H factor [Clostridium botulinum]
 gi|164511648|emb|CAO86130.1| RNA polymerase sigma-H factor [Clostridium botulinum]
 gi|164511650|emb|CAO86131.1| RNA polymerase sigma-H factor [Clostridium botulinum]
          Length = 190

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 30/187 (16%), Positives = 74/187 (39%), Gaps = 7/187 (3%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + G+  A   ++  +   V   A  Y   G    ++  EG IGL +A++ F P++    
Sbjct: 3   AKAGNSRAQEYIIGKYENFVKAKAKSYFLIGADKEDIYQEGMIGLYKAIRDFKPDKLSSF 62

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQAITDNNLK-PEQ 158
             ++   +   +   I  +     I   T  +  +  ++    +  L  +++  +  PE+
Sbjct: 63  KAFAELCVTRQIITAIKTATRQKHIPLNTYVSLNKPIYDEESDRTLLDILSEAKVANPEE 122

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           ++   ++L   ++E+  +      D  +  L++  D  S Q     +  H       +++
Sbjct: 123 LIISREELKHIQNEIGEVLS----DLEMEVLMSYLDGKSYQEIACDLDRHAKSIDNALQR 178

Query: 219 EERKNRR 225
            +RK  +
Sbjct: 179 VKRKLEK 185


>gi|254744604|ref|ZP_05202283.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. Kruger B]
          Length = 191

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 30/235 (12%), Positives = 72/235 (30%), Gaps = 62/235 (26%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           LE +    L ++    G+  A   L+  +   V   +  Y   G    ++V EG IGL +
Sbjct: 16  LEDEAIVELVRK----GNTDALEYLIHKYKNFVRAKSRSYFLVGADREDIVQEGMIGLFK 71

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++ +  ++      ++   I   +   I  +     I   +                  
Sbjct: 72  AIRDYKEDKLSSFKAFAELCITRQIITAIKTATRQKHIPLNSY----------------- 114

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                                    +S++            I   + + +          
Sbjct: 115 -------------------------VSLDK----------PIYDEESDRTLLDVISEAKV 139

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
              E+++I +EE  +  + ++  +S L   ER++        +  + + +S +  
Sbjct: 140 TDPEEMIISQEEYTDIESKISELLSDL---ERKVLSLYL---DGRSYQEISEQLN 188


>gi|169835541|ref|ZP_02868729.1| hypothetical protein cdivTM_00208 [candidate division TM7
           single-cell isolate TM7a]
          Length = 45

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 13/39 (33%), Positives = 24/39 (61%)

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                 TL+ +  +  ++RERVRQIE +A  K++E +++
Sbjct: 2   YDNKIHTLKEIGEQMGITRERVRQIEKKAITKLKEHLEE 40


>gi|28212187|ref|NP_783131.1| RNA polymerase factor sigma-70 [Clostridium tetani E88]
 gi|28204631|gb|AAO37068.1| RNA polymerase sigma-H factor [Clostridium tetani E88]
          Length = 220

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 35/197 (17%), Positives = 77/197 (39%), Gaps = 10/197 (5%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            EE VL     + G+  A   L+  +   V   A  Y   G    ++  EG IGL +A++
Sbjct: 26  DEEVVLE---AKEGNTRAQEYLINKYKNFVKAKAKSYFLIGADREDIYQEGMIGLYKAIR 82

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQAI 149
            F  +R      ++   I   +   I  +     I   T  +  +  ++    +  +  +
Sbjct: 83  DFRADRLASFKAFAELCITRQIITAIKTATRQKHIPLNTYISLNKPIYDDESDRTLMDVL 142

Query: 150 TDNNLK-PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
           ++  +  PE++V   +++   ++E+  +   L     +  L++  D  S Q     +  H
Sbjct: 143 SEAKVSDPEELVISREEIGCIQNEMEEVLSAL----EMEVLMSYIDGKSYQEIACDLDRH 198

Query: 209 DGQEQVLIEKEERKNRR 225
                  +++ +RK  +
Sbjct: 199 AKSIDNALQRVKRKLEK 215


>gi|328910060|gb|AEB61656.1| RNA polymerase sigma-30 factor (sigma(H)) [Bacillus
           amyloliquefaciens LL3]
          Length = 201

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 36/248 (14%), Positives = 79/248 (31%), Gaps = 62/248 (25%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A   L+T +   V   A  Y   G    ++V EG IGL ++++ F  ++      +
Sbjct: 13  GDSDALDYLITKYRNFVRAKARSYFLIGADREDIVQEGMIGLYKSIRDFREDKLTSFKAF 72

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +   I   +   I  +     I   +                                  
Sbjct: 73  AELCITRQIITAIKTATRQKHIPLNSY--------------------------------- 99

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
                    +S++            I   + + +             E+++I +EE  + 
Sbjct: 100 ---------VSLDK----------PIFDEESDRTLLDVISGAKTLNPEEMIINQEEFDDI 140

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              +   +S L   ER++        +  + + +S +       V+ I   A ++V+  +
Sbjct: 141 EMKMGELLSDL---ERKVLVLYL---DGRSYQEISDDLN---RHVKSI-DNALQRVKRKL 190

Query: 285 QKQVELSS 292
           +K +E+  
Sbjct: 191 EKYLEIRE 198


>gi|310822428|ref|YP_003954786.1| RNA polymerase sigma factor [Stigmatella aurantiaca DW4/3-1]
 gi|309395500|gb|ADO72959.1| RNA polymerase sigma factor [Stigmatella aurantiaca DW4/3-1]
          Length = 163

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 14/42 (33%), Positives = 26/42 (61%)

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPP 295
           TLE +     ++RER+RQ+E R   K++E+ + +  +S+  P
Sbjct: 122 TLEEVGEIMNLTRERIRQVETRGLMKLREATEAEPPVSARKP 163


>gi|304405636|ref|ZP_07387295.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Paenibacillus
           curdlanolyticus YK9]
 gi|304345675|gb|EFM11510.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Paenibacillus
           curdlanolyticus YK9]
          Length = 216

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 34/249 (13%), Positives = 80/249 (32%), Gaps = 62/249 (24%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GD  A   L+  +   V   A  Y   G    ++V EG IGL ++++ F  ++      
Sbjct: 27  EGDSEALEYLINKYRNFVRAKARSYFLIGADREDIVQEGMIGLYKSIRDFKGDKLSSFKA 86

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           ++   I   +   I  +     I   +                                 
Sbjct: 87  FAELCITRQIITAIKTATRQKHIPLNSY-------------------------------- 114

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
                     +S++            I   D + +             E+++I +EE   
Sbjct: 115 ----------VSLDK----------PIYDEDSDRTLLDVICGTRVSDPEELIINQEEFVG 154

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             + ++  +S L   ER++        +  + + ++ + +     V+ I   A ++V+  
Sbjct: 155 LEDKMSEILSDL---ERKVLMLYL---DGRSYQEIAVDLD---RHVKSI-DNALQRVKRK 204

Query: 284 IQKQVELSS 292
           +++ +E+  
Sbjct: 205 LERYLEVRD 213


>gi|169823613|ref|YP_001691116.1| RNA polymerase sigma factor [Finegoldia magna ATCC 29328]
 gi|167832233|dbj|BAG09148.1| RNA polymerase sigma factor [Finegoldia magna ATCC 29328]
          Length = 288

 Score = 55.2 bits (132), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 26/130 (20%), Positives = 45/130 (34%), Gaps = 13/130 (10%)

Query: 29  LEKQEEYVLAKRYRE-HGDLSAAHRLVTSHL----RLVVKIAMGYRGY----GLPI---- 75
           + K++E    K Y     D +   +L  + L     LV      Y               
Sbjct: 33  ISKEDEENFFKAYNNPDIDENCRLKLANNFLKELIPLVYSYVNSYCHRKNYQNFDFSEIR 92

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++VSEG   + +    FDP +  R  TY+   I+  ++ Y          GT    + +
Sbjct: 93  DDLVSEGLTAVYRCFDTFDPSKKIRFTTYASSCIQGKIKNYCRDHHLRHFTGTRTLYENI 152

Query: 136 FFNLRRLKGH 145
             + R+ K  
Sbjct: 153 QKDYRKAKQK 162


>gi|295092949|emb|CBK82040.1| DNA-directed RNA polymerase specialized sigma subunit [Coprococcus
           sp. ART55/1]
          Length = 106

 Score = 54.8 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 15/75 (20%), Positives = 32/75 (42%), Gaps = 2/75 (2%)

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           D    E    E  +R   R  +++ +  L P ER++   R  Q+   T         +S+
Sbjct: 29  DDLHAEMCGTEDGDRIVDRLCVSQLLDTLTPDERKLVVLRYFQD--KTQGQTGQILGMSQ 86

Query: 267 ERVRQIEARAFKKVQ 281
            +V ++E +   +++
Sbjct: 87  VQVSRLEKKILGRLR 101


>gi|282882222|ref|ZP_06290861.1| putative sporulation sigma factor SigK [Peptoniphilus lacrimalis
           315-B]
 gi|281297987|gb|EFA90444.1| putative sporulation sigma factor SigK [Peptoniphilus lacrimalis
           315-B]
          Length = 256

 Score = 54.8 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 24/91 (26%), Positives = 45/91 (49%), Gaps = 4/91 (4%)

Query: 37  LAKRY-REHGDLSAAHRLVTSHLRLVVKIAMGYR---GYGLPISEVVSEGNIGLMQAVKK 92
           L +RY +   D+S  +++V  +L LV      Y           E++ +G I L++AV+ 
Sbjct: 7   LFERYSKNKNDISLRNKIVLDNLSLVPYTINHYHLFIDGVHDYEEMLQDGYIALIKAVES 66

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           FD   GF+ ++Y++  I +  +  I  +  L
Sbjct: 67  FDYRLGFKFSSYAIKCILSLTRTRIDYNKDL 97


>gi|197294264|ref|YP_001798805.1| RNA polymerase sigma factor [Candidatus Phytoplasma australiense]
 gi|171853591|emb|CAM11462.1| RNA polymerase sigma factor [Candidatus Phytoplasma australiense]
          Length = 124

 Score = 54.8 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 18/80 (22%), Positives = 36/80 (45%), Gaps = 3/80 (3%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI--SEVVSEGNIGLMQAVKKFDPERG 98
            +   +L+   +L+  H  LV KIA  ++ +   +   ++  EG +GL++ +  +    G
Sbjct: 11  LKNKNNLAIRDQLIKMHFPLVKKIANQFKYFPKALQREDLYQEGILGLIKVLNNYQY-LG 69

Query: 99  FRLATYSMWWIKAAMQEYIL 118
                Y+   IK  + E I 
Sbjct: 70  CDFIAYANPTIKGEITELIR 89


>gi|262196406|ref|YP_003267615.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Haliangium
           ochraceum DSM 14365]
 gi|262079753|gb|ACY15722.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Haliangium
           ochraceum DSM 14365]
          Length = 210

 Score = 54.8 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 29/238 (12%), Positives = 79/238 (33%), Gaps = 47/238 (19%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGL---PISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
              LV  ++ L   IA   +          ++++    GL++A  ++D         ++ 
Sbjct: 6   RRCLVEQNIGLARSIAGRLQRSMSLQVDFDDLLAHAQAGLIEASLRYDFAAETPFRMFAR 65

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
           + I+ A+ ++I R     + G  A                      +    +    A+++
Sbjct: 66  YRIRGAIFDWIRRMGYSRRAGRNA---------------------RSPAEGEGAEDAERV 104

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            +   +V+                       + +++          +       +K R  
Sbjct: 105 RLPVPQVVF---------------------QAAYEESGPQAARAPTESAEAALAQKLRDR 143

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + ++++ L  RE++       ++   T     +   +SR +  ++ ARA   ++E +
Sbjct: 144 FVAQALTRLPAREQQFLRQCYYED--KTRVAAGASLGLSRYQAFRLHARAVGMLREEL 199


>gi|317123113|ref|YP_004103116.1| RNA polymerase, sigma 30 subunit, SigH [Thermaerobacter marianensis
           DSM 12885]
 gi|315593093|gb|ADU52389.1| RNA polymerase, sigma 30 subunit, SigH [Thermaerobacter marianensis
           DSM 12885]
          Length = 224

 Score = 54.8 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 39/260 (15%), Positives = 83/260 (31%), Gaps = 66/260 (25%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           E +E   +A++    G+  A   L+  +   V   A  Y   G    +++ EG IGL +A
Sbjct: 19  EDEEIVEIARQ----GNAEALEYLIGKYKNFVRAKARSYFLVGADREDIIQEGMIGLYKA 74

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           ++ F  ++      ++   I   +   I  +     I   +                   
Sbjct: 75  IRDFRSDKLSSFRAFAELCITRQIITAIKTATRQKHIPLNSY------------------ 116

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
                                   +S+N            I   D + +           
Sbjct: 117 ------------------------VSLNK----------PIYDEDSDRTLLDIISGSRVT 142

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
             E++ I +EE  +    +   +S L   E R+  A     +  + + ++ E       V
Sbjct: 143 DPEELFISREEFGDIEQKMGEILSEL---EWRVLNAYL---DGKSYQEIADELN---RHV 193

Query: 270 RQIEARAFKKVQESIQKQVE 289
           + I   A ++V+  +++ +E
Sbjct: 194 KSI-DNALQRVKRKLERYIE 212


>gi|296131816|ref|YP_003639063.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermincola sp.
           JR]
 gi|296030394|gb|ADG81162.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermincola potens
           JR]
          Length = 214

 Score = 54.8 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 18/87 (20%), Positives = 35/87 (40%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           + + GD +A   L+  +   V   A  Y   G    +++ EG IGL +A++ F  ++   
Sbjct: 24  FAKEGDDAALEYLINKYKNFVRAKARSYFLIGADREDIIQEGMIGLYKAIRDFKSDKLSS 83

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIG 127
              ++   I   +   I  +     I 
Sbjct: 84  FRAFAELCITRQIITAIKTATRQKHIP 110


>gi|108762633|ref|YP_631124.1| DNA-binding protein AsgB [Myxococcus xanthus DK 1622]
 gi|401779|gb|AAB59069.1| The asgB coding sequence was deduced from the DNA sequence. A
           putative DNA-binding helix-turn-helix is present near
           the C-terminus [Myxococcus xanthus]
 gi|108466513|gb|ABF91698.1| DNA-binding protein AsgB [Myxococcus xanthus DK 1622]
          Length = 163

 Score = 54.8 bits (131), Expect = 1e-05,   Method: Composition-based stats.
 Identities = 14/42 (33%), Positives = 26/42 (61%)

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPP 295
           TLE +     ++RER+RQ+E R   K++E+ + +  +S+  P
Sbjct: 122 TLEEVGEIMNLTRERIRQVETRGLMKLREATEAEPPVSARKP 163


>gi|323703773|ref|ZP_08115411.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Desulfotomaculum
           nigrificans DSM 574]
 gi|323531242|gb|EGB21143.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Desulfotomaculum
           nigrificans DSM 574]
          Length = 199

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 19/96 (19%), Positives = 37/96 (38%), Gaps = 4/96 (4%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           ++    A+     GD +A   L+  +   V   A  Y   G    +++ EG IGL +A++
Sbjct: 4   EDVVEFAR----EGDDAALEYLINKYKNFVRAKARSYFLIGADREDIIQEGMIGLYKAIR 59

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
            F  ++      ++   I   +   I  +     I 
Sbjct: 60  DFRMDKLSSFRAFAELCITRQIITAIKTATRQKHIP 95


>gi|253682087|ref|ZP_04862884.1| RNA polymerase sigma-H factor [Clostridium botulinum D str. 1873]
 gi|253561799|gb|EES91251.1| RNA polymerase sigma-H factor [Clostridium botulinum D str. 1873]
          Length = 218

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 24/143 (16%), Positives = 54/143 (37%), Gaps = 8/143 (5%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           G++ A   L+  +   V   A  Y   G    ++  EG IGL +A++ F P++      +
Sbjct: 30  GNVEAQEYLINKYKNFVKAKAKSYFLIGADKEDIYQEGMIGLYKAIRDFKPDKLASFKAF 89

Query: 105 SMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           +   +   +   I  +     I   T  +  +  ++    +  L  ++   +   +    
Sbjct: 90  AELCVTRQIITAIKTATRQKHIPLNTYVSLNKPIYDEESDRTLLDILSTVKICDPE---- 145

Query: 163 AKKLNVSESEVISMNCRLAGDES 185
             +L +S  EV+ +   +    S
Sbjct: 146 --ELVISREEVLKIENDIQEVLS 166


>gi|283479514|emb|CAY75430.1| RNA polymerase sigma factor rpoS pseudogene [Erwinia pyrifoliae DSM
           12163]
          Length = 136

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 17/43 (39%), Positives = 26/43 (60%), Gaps = 1/43 (2%)

Query: 19  YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
           Y+ EI   P+L  +EE   A+R    GD+ +  R++ S+LRLV
Sbjct: 61  YLGEIGYSPLLTAEEEVFFARR-ALRGDVPSRRRMIESNLRLV 102


>gi|84687559|ref|ZP_01015435.1| RNA polymerase sigma factor [Maritimibacter alkaliphilus HTCC2654]
 gi|84664468|gb|EAQ10956.1| RNA polymerase sigma factor [Rhodobacterales bacterium HTCC2654]
          Length = 562

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 18/69 (26%), Positives = 29/69 (42%), Gaps = 2/69 (2%)

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIE 273
                      +    + V + R   +        ++ P TLE     + ++RERVRQI 
Sbjct: 79  EWHAHDTLESELFALLLEVEDERNAEMLSVFYGFNEDGPKTLEYSGQPYGLTRERVRQIA 138

Query: 274 ARAFKKVQE 282
           AR  KK++E
Sbjct: 139 ARTEKKLRE 147


>gi|317970612|ref|ZP_07972002.1| hypothetical protein SCB02_13859 [Synechococcus sp. CB0205]
          Length = 136

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 20/129 (15%), Positives = 50/129 (38%), Gaps = 12/129 (9%)

Query: 158 QVVAIAKKLNVSESEVISMNC--RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
            V  +A+ L+ S   ++        +   SL+  I S+D   +                 
Sbjct: 10  SVDEMARLLDESPQRLLHAINVHYRSNTLSLDQQIASADGAMTIL----------DTVTD 59

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
            E+ E  +    +   M  L+  E  + + R   E+  +   ++     ++++V+++E +
Sbjct: 60  KEEIEIHDDYAWMYSLMQHLSCPEADVIKLRYGAEDQPSFAEVARTIGRTKDQVQRLERK 119

Query: 276 AFKKVQESI 284
           A  K++  +
Sbjct: 120 ALAKLRTRL 128


>gi|114567859|ref|YP_755013.1| RNA polymerase factor sigma-70 [Syntrophomonas wolfei subsp. wolfei
           str. Goettingen]
 gi|114338794|gb|ABI69642.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Syntrophomonas
           wolfei subsp. wolfei str. Goettingen]
          Length = 216

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 26/155 (16%), Positives = 59/155 (38%), Gaps = 10/155 (6%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           +E   LA+     GD  A   L+  +   V   A  Y   G    +++ EG IGL +A++
Sbjct: 20  EEIVDLAQL----GDQFAIEFLMDKYKNFVRAKARSYFLIGADKEDIIQEGMIGLFKAIR 75

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR-LKGHLQAIT 150
            +  ++      ++   I   +   I  +     I   +     + +L + +       T
Sbjct: 76  DYKMDKLTSFRAFAELCITRQIITAIKTATRQKHIPLNS-----YVSLNKPIYDEESERT 130

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
             ++     ++  +++ +S  E I +  ++    S
Sbjct: 131 LMDILSTTRISNPEEIVISREEFIFIEKKIGEILS 165


>gi|328885789|emb|CCA59028.1| hypothetical protein SVEN_5742 [Streptomyces venezuelae ATCC 10712]
          Length = 750

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 20/42 (47%), Positives = 22/42 (52%)

Query: 236 NPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
           + RER I   R   E P T   L   FEVSRERVRQ+E    
Sbjct: 259 DERERTIAARRIFAEQPETFAALGDRFEVSRERVRQLERSIL 300


>gi|299541910|ref|ZP_07052233.1| RNA polymerase factor sigma-70 [Lysinibacillus fusiformis ZC1]
 gi|298725648|gb|EFI66289.1| RNA polymerase factor sigma-70 [Lysinibacillus fusiformis ZC1]
          Length = 215

 Score = 54.8 bits (131), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 40/204 (19%), Positives = 73/204 (35%), Gaps = 14/204 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L +   + G+  A   L+T +  LV   A  Y   G    ++V EG IGL +A++ F  
Sbjct: 20  ELIEMVHQ-GNTDALDYLITKYRLLVRAKARSYFLIGADKEDIVQEGMIGLYKAIRDFKG 78

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           ++      ++   I   +   I  +     I        L   +   K      +D  L 
Sbjct: 79  DKLASFRAFAELCITRQIITAIKTATRQKHIP-------LNSYISLDKPIFDEESDRTLM 131

Query: 156 PEQVVAIA---KKLNVSESEVISMNCRLAGDES---LNALINSSDKNSSQWQDWLVYDHD 209
                AI    ++L +   E   +  +++   S   L  L    D  S       +  H 
Sbjct: 132 DVLTGAIMDDPEELMIHREEFGYLEEKMSEILSELELQVLALYLDGQSYHEISAKLNRHV 191

Query: 210 GQEQVLIEKEERKNRRNMLTRSMS 233
                 +++ +RK  R+++   MS
Sbjct: 192 KSIDNALQRVKRKLERHLVLEEMS 215


>gi|162451917|ref|YP_001614284.1| hypothetical protein sce3644 [Sorangium cellulosum 'So ce 56']
 gi|161162499|emb|CAN93804.1| hypothetical protein predicted by Glimmer/Critica [Sorangium
           cellulosum 'So ce 56']
          Length = 258

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 13/42 (30%), Positives = 26/42 (61%), Gaps = 1/42 (2%)

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
              TLE++ +   ++RER+RQ+E +A  K+ E+++  + L  
Sbjct: 151 GGTTLEDVGAIMNLTRERIRQVEVKALAKL-EALKDMMALRD 191


>gi|110802727|ref|YP_699680.1| RNA polymerase factor sigma-70 [Clostridium perfringens SM101]
 gi|110683228|gb|ABG86598.1| RNA polymerase sigma-H factor [Clostridium perfringens SM101]
          Length = 215

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 39/262 (14%), Positives = 90/262 (34%), Gaps = 74/262 (28%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L  +E  +LAK    +GD  A   +++ + + V   +  Y   G    ++  EG IGL +
Sbjct: 19  LTDKEVVMLAK----NGDNMAQEYVISKYEQFVKAKSKSYFLIGADKEDIYQEGMIGLYK 74

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++ F+P++     +++   +   +   I  +     I                      
Sbjct: 75  AIRDFNPDKFASFRSFAELCVTRQIITAIKTATRQKHIP--------------------- 113

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                                      +N  +    SL+  I   + + +     +    
Sbjct: 114 ---------------------------LNTYI----SLSKPIYEEESDRTLLDTVVGITI 142

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
              E ++I KEE +   + +   +S L   E  +  +     +  + + ++ + +     
Sbjct: 143 TDPESLIIGKEEVEKIESAINSVLSEL---ELEVLNSYL---DGKSYQEIACDLD----- 191

Query: 269 VRQIEAR----AFKKVQESIQK 286
            R  EA+    A ++V+  ++K
Sbjct: 192 -R--EAKSIDNALQRVKRKLEK 210


>gi|85057634|ref|YP_456550.1| hypothetical protein AYWB_354 [Aster yellows witches'-broom
           phytoplasma AYWB]
 gi|84789739|gb|ABC65471.1| conserved hypothetical protein [Aster yellows witches'-broom
           phytoplasma AYWB]
          Length = 103

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 18/76 (23%), Positives = 39/76 (51%), Gaps = 3/76 (3%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI--SEVVSEGNIGLMQAVKKFDPERG 98
           ++   +L   ++L+  HL L+ K+A  ++ Y   +   ++  EG +GL++A+  +  + G
Sbjct: 11  FKNKKNLEIRNQLIELHLPLLKKLAYHFKYYPKVLTKEDLYQEGILGLIKALNNYQ-DLG 69

Query: 99  FRLATYSMWWIKAAMQ 114
           +    Y+   IK A  
Sbjct: 70  YDFIAYATPTIKKATH 85


>gi|262198088|ref|YP_003269297.1| hypothetical protein Hoch_4915 [Haliangium ochraceum DSM 14365]
 gi|262081435|gb|ACY17404.1| hypothetical protein Hoch_4915 [Haliangium ochraceum DSM 14365]
          Length = 246

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 14/42 (33%), Positives = 23/42 (54%)

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPP 295
           TLE +     ++RER+RQ+E R  +K++       EL +  P
Sbjct: 201 TLEEVGEIMNLTRERIRQVEVRGLRKLRARSPSPEELGAIEP 242


>gi|116074869|ref|ZP_01472130.1| Possible type 3 alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9916]
 gi|116068091|gb|EAU73844.1| Possible type 3 alternative RNA polymerase sigma factor
           [Synechococcus sp. RS9916]
          Length = 203

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 19/121 (15%), Positives = 47/121 (38%), Gaps = 3/121 (2%)

Query: 60  LVVKIAMGYRG-YGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYIL 118
           +V  IA+ Y         +++  G +GL++A   +        + ++   I+ A+  Y+ 
Sbjct: 1   MVTPIALHYARIARQDKDDLIQVGRLGLIKAAGLYQNAFQVPFSAFARPHIRGAILHYLR 60

Query: 119 RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
            S  LV++     ++     L + +G       + + P  +  +         + +S + 
Sbjct: 61  DSVGLVRLPRRVQERA--QRLLKQQGQTAQFLQHQVSPSDLQLVEDYRQRGGWQPLSESE 118

Query: 179 R 179
           R
Sbjct: 119 R 119


>gi|318042873|ref|ZP_07974829.1| RNA polymerase sigma factor, sigma-70 family protein [Synechococcus
           sp. CB0101]
          Length = 95

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 13/79 (16%), Positives = 31/79 (39%), Gaps = 8/79 (10%)

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--------ENPVTLENLSSEFEVSR 266
             E  + +  R+ +   +  L   + R+ + R           + P++L  +     +SR
Sbjct: 9   PEELVDGECLRSDMRDLLEQLPDLQCRVLKMRYGIPCADVPDPDEPMSLTGIGRILGMSR 68

Query: 267 ERVRQIEARAFKKVQESIQ 285
           +RVR +E      ++   +
Sbjct: 69  DRVRNLERDGLAGLRRLSE 87


>gi|309389949|gb|ADO77829.1| RNA polymerase, sigma 30 subunit, SigH [Halanaerobium praevalens
           DSM 2228]
          Length = 219

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 35/175 (20%), Positives = 64/175 (36%), Gaps = 14/175 (8%)

Query: 13  EIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG 72
           +I L  Y         +   E   L       GD+ A   L+  +   V+  +  Y   G
Sbjct: 12  DISLEEYQQ-------MSDDELVELV----HQGDMEAQETLIKRYKNFVLAKSRSYFLVG 60

Query: 73  LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--TTA 130
               ++V EG IGL +AV+ +  ER      ++   I   +   I  +         T  
Sbjct: 61  ADREDIVQEGMIGLYKAVRDYKIERLASFRAFAELCITRQIITAIKAATRQKHQPLNTYI 120

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK-LNVSESEVISMNCRLAGDE 184
           +  +  ++    +  L  +    L   + + I+ +  ++ ESE+ SM   L  D 
Sbjct: 121 SLNKPIYDEESDRTLLDILKGGKLSNPEALFISNETYDLIESEISSMLSDLEFDV 175


>gi|312135662|ref|YP_004003000.1| RNA polymerase sigma factor, sigma-70 family [Caldicellulosiruptor
           owensensis OL]
 gi|311775713|gb|ADQ05200.1| RNA polymerase sigma factor, sigma-70 family [Caldicellulosiruptor
           owensensis OL]
          Length = 302

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 22/71 (30%), Positives = 44/71 (61%), Gaps = 5/71 (7%)

Query: 51  HRLVTSHLRLVVKIAMGY----RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            +LV  +++LV  +A  +    +GY   + ++VSEG IGL+ A + +DPE+G   +TY+ 
Sbjct: 11  QKLVADNIKLVYHVANKFMPCPKGYCYEVDDLVSEGYIGLVVAARNYDPEKGS-FSTYAC 69

Query: 107 WWIKAAMQEYI 117
             I++ +++ +
Sbjct: 70  KVIESKIRKSL 80


>gi|70727086|ref|YP_254000.1| hypothetical protein SH2085 [Staphylococcus haemolyticus JCSC1435]
 gi|68447810|dbj|BAE05394.1| unnamed protein product [Staphylococcus haemolyticus JCSC1435]
          Length = 109

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 22/108 (20%), Positives = 41/108 (37%), Gaps = 4/108 (3%)

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM- 232
                +   D S      + +  ++   D+     + +   L E    +   N L + + 
Sbjct: 5   REAIKQFIRDYSKENHDTTYNDENTNIDDFFSLSDEAEPFSLNENTSNQVFFNELDQLIY 64

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           +V   RE  IF    L     ++  ++  F +SRER+RQI      K+
Sbjct: 65  AVGTRREYYIF---FLLCEGKSMNEIAKIFNLSRERIRQILNDLLDKL 109


>gi|169344130|ref|ZP_02865113.1| RNA polymerase sigma-H factor [Clostridium perfringens C str.
           JGS1495]
 gi|169297741|gb|EDS79840.1| RNA polymerase sigma-H factor [Clostridium perfringens C str.
           JGS1495]
          Length = 201

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 21/99 (21%), Positives = 44/99 (44%), Gaps = 4/99 (4%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L  +E  +LAK    +GD  A   +++ + + V   +  Y   G    ++  EG IGL +
Sbjct: 19  LTDKEIVMLAK----NGDNMAQEYVISKYEQFVKAKSKSYFLIGADKEDIYQEGMIGLYK 74

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           A++ F+P++     +++   +   +   I  +     I 
Sbjct: 75  AIRDFNPDKFASFKSFAELCVTRQIITAIKTATRQKHIP 113


>gi|160936421|ref|ZP_02083790.1| hypothetical protein CLOBOL_01313 [Clostridium bolteae ATCC
           BAA-613]
 gi|158440704|gb|EDP18442.1| hypothetical protein CLOBOL_01313 [Clostridium bolteae ATCC
           BAA-613]
          Length = 199

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 36/162 (22%), Positives = 67/162 (41%), Gaps = 8/162 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
              Y+ E+R I  LE+ E   + +     GD  A  RLV   L  V+++   Y    LP+
Sbjct: 7   FDMYLEEMRSITPLERDEMVSVLE-GTARGDAGARSRLVEGCLGEVLEMVREYGDSELPL 65

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           S++V E N  LM A  ++D              +K +++  +    +  +I  T   +  
Sbjct: 66  SDLVQEANTALMLAAIEYDGS--EPWNELMTRRVKESVELALEEQRTENQIEETMAAR-- 121

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
              +  L+   Q +     +   +  ++ K+ +SE EV  + 
Sbjct: 122 ---VNVLQTVSQVLAKELGREATLEELSAKMKMSEDEVRDIM 160


>gi|331011085|gb|EGH91141.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           tabaci ATCC 11528]
          Length = 83

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 13/79 (16%), Positives = 30/79 (37%), Gaps = 2/79 (2%)

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            D            E +  +  L  +++ L  RER +       +  + L+ +     VS
Sbjct: 1   EDGASGSLEPSRDLEDERFQAALADAIANLPERERLVLALYY--DEELNLKEIGEVLGVS 58

Query: 266 RERVRQIEARAFKKVQESI 284
             RV Q+ ++   +++  +
Sbjct: 59  ESRVSQLHSQCAARLRGRL 77


>gi|326202358|ref|ZP_08192227.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           papyrosolvens DSM 2782]
 gi|325987476|gb|EGD48303.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           papyrosolvens DSM 2782]
          Length = 214

 Score = 54.4 bits (130), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 26/167 (15%), Positives = 63/167 (37%), Gaps = 7/167 (4%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GD  A   L+  +   V   A  Y   G    +++ EG IGL +A++ +  ++      
Sbjct: 27  AGDQQALEYLINKYKSFVRAKARTYFLIGADREDIIQEGMIGLFKAIRDYKGDKLSSFRA 86

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR-LKGHLQAITDNNLKPEQVVAI 162
           ++   I   +   I  +     I   +     + +L + +       T  ++  E+ ++ 
Sbjct: 87  FAELCITRQIITAIKTATRQKHIPLNS-----YVSLNKPIFDEESDRTLMDIISEESISD 141

Query: 163 AKKLNVSESEVISMNCRLAGD-ESLNALINSSDKNSSQWQDWLVYDH 208
            ++L ++  E   +  ++     SL   + +S  +   +Q+      
Sbjct: 142 PEELIINREEFRGIENKMGEILSSLEWEVLTSYLDGKSYQEIAEDLD 188


>gi|238909186|ref|YP_002939653.1| hypothetical protein EUBELI_10082 [Eubacterium eligens ATCC 27750]
 gi|238873423|gb|ACR73132.1| Hypothetical protein EUBELI_10082 [Eubacterium eligens ATCC 27750]
          Length = 202

 Score = 54.0 bits (129), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 18/93 (19%), Positives = 41/93 (44%), Gaps = 2/93 (2%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY--GLPISEVVSEGNIGLMQAVKKF 93
            L K Y+E  D S    L+ ++  L+  +   Y        + ++ SE  I +++A++ +
Sbjct: 12  ELIKAYKESRDESYLKELIEANKGLINLLVSPYLTSIPNSELEDLTSESYIPMLRAIEDY 71

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           DPE+G   +T    +++  +      +    + 
Sbjct: 72  DPEQGVAFSTLLKVYVRQHLNRLYNEATRQKRF 104


>gi|167751712|ref|ZP_02423839.1| hypothetical protein EUBSIR_02721 [Eubacterium siraeum DSM 15702]
 gi|167655520|gb|EDR99649.1| hypothetical protein EUBSIR_02721 [Eubacterium siraeum DSM 15702]
          Length = 73

 Score = 54.0 bits (129), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 11/67 (16%), Positives = 33/67 (49%), Gaps = 2/67 (2%)

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
            +  +     L  ++  L+ RE+ I +    +    T   ++ +  +S+ +V ++E  A 
Sbjct: 9   DDRNRLDEIALKEAIIGLDYREKNILKLCFFRG--KTQVEVAQKIGISQAQVSRLEKGAL 66

Query: 278 KKVQESI 284
           +K+++++
Sbjct: 67  RKIKKAL 73


>gi|224004150|ref|XP_002295726.1| predicted protein [Thalassiosira pseudonana CCMP1335]
 gi|209585758|gb|ACI64443.1| predicted protein [Thalassiosira pseudonana CCMP1335]
          Length = 395

 Score = 54.0 bits (129), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 38/251 (15%), Positives = 74/251 (29%), Gaps = 55/251 (21%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPI----------------------------SEVVS 80
           A   L+  +L LV  I          +                             +++ 
Sbjct: 14  ARQTLLLHNLPLVQSIVTKTLRSRPHLLSGPAGGSGGGSASPSSSELQVGAALTKDDLLH 73

Query: 81  EGNIGLMQAVKKFDPE---------------RGFRLATYSMWWIKAAMQEYILRSWSLVK 125
           EG IGL +A+ K+D                 +G RL TY+ +WI+  +   I       +
Sbjct: 74  EGTIGLAEALDKYDFSYSDLSVTEHTSSTAPKGARLGTYATYWIRGRILRAIQSREHAFR 133

Query: 126 IGTTANQKRLFFNLRRLKGHLQ-------AITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
                 Q      L +    L         + D + K    VA+     +S   +     
Sbjct: 134 FPERVLQ--ASHRLVKAAKELGLEWSTVVELKDASKKNRLRVALCDAAGISTEFLFQEAI 191

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           R+                S   +       + +  + +E+   ++  + L++    L+ R
Sbjct: 192 RVRTISKSGMPTQLESWMSLSPKSVEQQQEEEELLLEMEEMGPQHTLDTLSKF---LDSR 248

Query: 239 ERRIFEARRLQ 249
           E ++   R   
Sbjct: 249 EVQVLSLRYGL 259


>gi|310829283|ref|YP_003961640.1| ECF subfamily RNA polymerase sigma-24 factor [Eubacterium limosum
           KIST612]
 gi|308741017|gb|ADO38677.1| ECF subfamily RNA polymerase sigma-24 factor [Eubacterium limosum
           KIST612]
          Length = 209

 Score = 54.0 bits (129), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 25/105 (23%), Positives = 45/105 (42%), Gaps = 4/105 (3%)

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +  D++L+  I   +       + +       E   IE+EE+ N +  L R +S L P  
Sbjct: 109 IKPDKTLDDPIPGREG--LTLAEVIPDKEINLEADYIEREEKSNDQKRLARGLSRLKPSY 166

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R + E         T   ++ +  VS + V Q   RA KK+++ +
Sbjct: 167 RSVLEKHYY--EGRTQTEIAEKEGVSLQAVNQRHDRALKKLKKVL 209


>gi|209972885|ref|YP_002300332.1| gp2.21 [Bacillus phage SPO1]
 gi|209871205|gb|ACI90961.1| gp2.21 [Bacillus phage SPO1]
          Length = 231

 Score = 54.0 bits (129), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 41/262 (15%), Positives = 73/262 (27%), Gaps = 77/262 (29%)

Query: 36  VLAKRYREHGDL----SAAHRLVTSHLRLVVKIAMGYRGYGLPI--------SEVVSEGN 83
              +   +  D         ++  +    V      Y      +         E  S   
Sbjct: 27  EYFQLIDQTEDELEKEKLREKIFMNTCLFVKHYIRKYVHGMNTLCQRSRTTPDEFYSVAY 86

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           + L  AV+ +D   G + +TY+   I+  + +YI+RS                  + RL 
Sbjct: 87  LALWVAVQSYDVNVGVKFSTYAYKIIQNRINKYIVRS------------------INRLS 128

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203
                                                 G  SL      +D++    +  
Sbjct: 129 --------------------------------------GVYSLQTPAYDTDESEPVSEQD 150

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L+ D       +   E       +L        P +  IF A  L+    T   ++ EF 
Sbjct: 151 LLVD---PVDYISSFENLTMVDTLLKDLSRKFTPEKADIFFAYTLRGG--TQTEIAKEFG 205

Query: 264 VSRERVRQIEARAFKKVQESIQ 285
            S+  V     R   K+QE ++
Sbjct: 206 CSQVYVS----RVVSKIQEYLR 223


>gi|331002428|ref|ZP_08325946.1| hypothetical protein HMPREF0491_00808 [Lachnospiraceae oral taxon
           107 str. F0167]
 gi|330410244|gb|EGG89678.1| hypothetical protein HMPREF0491_00808 [Lachnospiraceae oral taxon
           107 str. F0167]
          Length = 172

 Score = 54.0 bits (129), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 30/172 (17%), Positives = 69/172 (40%), Gaps = 9/172 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ +++ I  L++ ++  L K     GD +A +RL+ +H+    ++   + G G  +
Sbjct: 7   LEMYLEDMKNIKPLDEAKKDDLLKALC-TGDNNAKNRLIEAHMMYATELVQPFMGCGQEV 65

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++SE ++ L  AV ++   +   L       ++  + E I                 L
Sbjct: 66  MDLISESHLALTMAVTEY---KSGDLKAQIRQAVEKRLNEIIDEQNRAKHDS-----NEL 117

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
              L  L     A+ +   +      ++ +L + + EV  +        +L+
Sbjct: 118 TNRLNELMEISSALANEYGREATAKELSDRLLIPQDEVEELLKISLNAINLD 169


>gi|290968523|ref|ZP_06560062.1| RNA polymerase sigma-H factor [Megasphaera genomosp. type_1 str.
           28L]
 gi|290781519|gb|EFD94108.1| RNA polymerase sigma-H factor [Megasphaera genomosp. type_1 str.
           28L]
          Length = 229

 Score = 54.0 bits (129), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 23/136 (16%), Positives = 50/136 (36%), Gaps = 4/136 (2%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            EE VL    ++  D  A   +V  +   +   A  Y   G    +++ EG IGL +A +
Sbjct: 18  DEEVVLW--LQKTHDDRAMEYIVHKYKNFIKSKARTYFLVGADREDLIQEGMIGLYKATR 75

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQAI 149
            F  E+      ++   I   +   +  +     +   +  +  +  F     +   + I
Sbjct: 76  DFRAEKKVAFRVFAELCIMRQIITAVKTATRQKHVPLNSYISLSKPLFAEESERKLEETI 135

Query: 150 TDNNLKPEQVVAIAKK 165
           +   +   + V I+ +
Sbjct: 136 SALTVTDPEEVLISWE 151


>gi|68304088|gb|AAY89702.1| FliA [Escherichia coli LW1655F+]
          Length = 157

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 27/132 (20%), Positives = 58/132 (43%), Gaps = 11/132 (8%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 3   KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 62

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL 166
             I+ AM + + RS   V      N + +   + +L+  L        +      +A++L
Sbjct: 63  QRIRGAMLDEL-RSRDWVPRSVRRNAREVAQAIGQLEQEL-------GRNATETEVAERL 114

Query: 167 NVSESEVISMNC 178
            +  ++   M  
Sbjct: 115 GIDIADYRQMLL 126


>gi|149917779|ref|ZP_01906274.1| DNA-binding protein AsgB [Plesiocystis pacifica SIR-1]
 gi|149821299|gb|EDM80701.1| DNA-binding protein AsgB [Plesiocystis pacifica SIR-1]
          Length = 166

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 12/35 (34%), Positives = 23/35 (65%)

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           ++  +TLE +     ++RER+RQ+E R   K++E+
Sbjct: 120 EQGGITLEEVGEILNLTRERIRQVEVRGLMKLKEA 154


>gi|251799662|ref|YP_003014393.1| RNA polymerase factor sigma-70 [Paenibacillus sp. JDR-2]
 gi|247547288|gb|ACT04307.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Paenibacillus sp.
           JDR-2]
          Length = 216

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 38/263 (14%), Positives = 86/263 (32%), Gaps = 65/263 (24%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
              E+ V A R   +GD  A   L+  +   V   A  Y   G    ++V EG IGL ++
Sbjct: 16  SSDEDIVEAVR---NGDSLALEYLINKYKNFVRAKARSYFLIGADREDIVQEGMIGLYKS 72

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           ++ F  ++      ++   I   +   I  +     I   +                   
Sbjct: 73  IRDFKGDKLASFKAFAELCITRQIITAIKTATRQKHIPLNSY------------------ 114

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
                                   +S++            I   D + +           
Sbjct: 115 ------------------------VSLDK----------PIYDEDSDRTLLDVICGTRVS 140

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
             E+++I +EE     + ++  +S L   ER++        +  + + ++ + +     V
Sbjct: 141 DPEELIINQEEFVGLEDKMSEILSDL---ERKVLMLYL---DGRSYQEIAVDLD---RHV 191

Query: 270 RQIEARAFKKVQESIQKQVELSS 292
           + I   A ++V+  +++ +E+  
Sbjct: 192 KSI-DNALQRVKRKLERYLEVRD 213


>gi|51894248|ref|YP_076939.1| RNA polymerase factor sigma-70 [Symbiobacterium thermophilum IAM
           14863]
 gi|51857937|dbj|BAD42095.1| stage 0 sporulation protein H, RNA polymerase sigma factor
           [Symbiobacterium thermophilum IAM 14863]
          Length = 221

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 37/258 (14%), Positives = 77/258 (29%), Gaps = 66/258 (25%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           ++    A+     G   A   L+  +   V   A  Y   G    ++  EG IGL +A++
Sbjct: 19  EDIVEFAR----EGSTEALEYLINKYKNFVRAKARSYFLIGADRDDITQEGMIGLYKAIR 74

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
            F  ++      ++   I   +   I  +     I                         
Sbjct: 75  DFRADKLSSFRAFAELCITRQIITAIKTATRQKHI------------------------- 109

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
                                       L    SLN  I   D + +             
Sbjct: 110 ---------------------------PLNSYVSLNKPIYDDDSDRTLLDVISGSKVTDP 142

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E+++I +EE  +    +   +S L   E ++  +     +  +   ++ E       V+ 
Sbjct: 143 EELIISREEFGDIEGKMEEILSDL---EWKVLMSYL---DGKSYHEIAVELH---RHVKS 193

Query: 272 IEARAFKKVQESIQKQVE 289
           I   A ++V+  +++ +E
Sbjct: 194 I-DNALQRVKRKLERYLE 210


>gi|39939052|ref|NP_950818.1| hypothetical protein PAM_566 [Onion yellows phytoplasma OY-M]
 gi|39722161|dbj|BAD04651.1| hypothetical protein [Onion yellows phytoplasma OY-M]
          Length = 78

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 20/73 (27%), Positives = 40/73 (54%), Gaps = 3/73 (4%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPIS--EVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
            ++L+  HL LV K+   ++ Y   +   ++  EG +GL++A+  +  + G+    Y+  
Sbjct: 2   RNQLIDLHLSLVKKLVSKFKYYPCVLQKQDLYQEGVLGLIKALNNY-VDLGYDFIAYATP 60

Query: 108 WIKAAMQEYILRS 120
            IK+ ++E I RS
Sbjct: 61  TIKSEIRELIRRS 73


>gi|261367813|ref|ZP_05980696.1| putative RNA polymerase sigma-H factor [Subdoligranulum variabile
           DSM 15176]
 gi|282570611|gb|EFB76146.1| putative RNA polymerase sigma-H factor [Subdoligranulum variabile
           DSM 15176]
          Length = 180

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 25/75 (33%), Positives = 36/75 (48%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + GD +A   L+   +  + K A  YR  GL   + V EG IGL QAV+ +    G   
Sbjct: 12  AQQGDDTALAALIARMMPAIRKGAAVYRAPGLDFEDAVQEGLIGLFQAVRGYRSAAGTPF 71

Query: 102 ATYSMWWIKAAMQEY 116
           A+Y+   I  A Q+ 
Sbjct: 72  ASYAATCIHHAQQDA 86


>gi|330838634|ref|YP_004413214.1| RNA polymerase, sigma-24 subunit, SigH, ECF subfamily [Selenomonas
           sputigena ATCC 35185]
 gi|329746398|gb|AEB99754.1| RNA polymerase, sigma-24 subunit, SigH, ECF subfamily [Selenomonas
           sputigena ATCC 35185]
          Length = 244

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 39/261 (14%), Positives = 84/261 (32%), Gaps = 65/261 (24%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L  +E      R +E+    A   L+  +   V   A  Y   G    ++V EG IGL +
Sbjct: 16  LTDEEVIS---RIKENCSNIALDYLINKYRNFVRAKARSYFLIGADREDIVQEGMIGLYK 72

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++ F  +R      ++   +   +   I  +     I                      
Sbjct: 73  AIRDFRNDRLSSFRAFAELCVTRQIITAIKTATRQKHIP--------------------- 111

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                                      +N  ++    LN  I   D + +          
Sbjct: 112 ---------------------------LNSYIS----LNKPIYDEDSDRTLLDILPGARV 140

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
              E+++I +EE  +    +   +S L   E R+  +     +  + + ++ + +     
Sbjct: 141 SNPEELVISQEEFVDIEEKMEEILSDL---EWRVLMSYL---DGKSYQEIAVDLD---RH 191

Query: 269 VRQIEARAFKKVQESIQKQVE 289
           V+ I   A ++V+  +++ +E
Sbjct: 192 VKSI-DNALQRVKRKLERYME 211


>gi|312877883|ref|ZP_07737829.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
 gi|311795346|gb|EFR11729.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
          Length = 90

 Score = 54.0 bits (129), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 14/45 (31%), Positives = 25/45 (55%), Gaps = 2/45 (4%)

Query: 238 RERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQIEARAFKKV 280
           RE++I E R   +N    T   +++   +SR  V +IE +A +K+
Sbjct: 35  REKKIIELRYGLKNGIERTQMEVANLLGISRSYVSRIEKKALQKL 79


>gi|312126947|ref|YP_003991821.1| RNA polymerase, sigma-24 subunit, ecf subfamily
           [Caldicellulosiruptor hydrothermalis 108]
 gi|311776966|gb|ADQ06452.1| RNA polymerase, sigma-24 subunit, ECF subfamily
           [Caldicellulosiruptor hydrothermalis 108]
          Length = 244

 Score = 53.7 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 28/137 (20%), Positives = 49/137 (35%), Gaps = 5/137 (3%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
             EE V   +Y   G   A   L++ +   V      Y   G    ++  EG IGL +AV
Sbjct: 47  PDEELV---KYSREGVKEALEELLSRYQNFVKAKCRMYFLIGADKEDIYQEGMIGLFKAV 103

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQA 148
           + FD  +      ++   I   M   I  +     I   T  +  +  +     +  +  
Sbjct: 104 RDFDETKYPSFRLFAEMCITRQMITAIKTASRQKHIPLNTYISLNKPVYEENDERTLIDT 163

Query: 149 ITDNNLKPEQVVAIAKK 165
           + D  +   + V I K+
Sbjct: 164 LADTFISDPEEVMITKE 180


>gi|33865698|ref|NP_897257.1| hypothetical protein SYNW1164 [Synechococcus sp. WH 8102]
 gi|33632868|emb|CAE07679.1| conserved hypothetical protein [Synechococcus sp. WH 8102]
          Length = 238

 Score = 53.7 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 16/80 (20%), Positives = 34/80 (42%), Gaps = 1/80 (1%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGL-PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
            +  V +HL +   IA      G     ++  E  +GL++  ++FDP RG +L+T+    
Sbjct: 100 RNIKVLNHLGIAGMIASRQTRRGPKERDDLEQEARVGLIRGWERFDPRRGLKLSTFLSTA 159

Query: 109 IKAAMQEYILRSWSLVKIGT 128
               +  +       +++  
Sbjct: 160 TNGQVLHFRRDRAVTIRVPW 179


>gi|291519564|emb|CBK74785.1| DNA-directed RNA polymerase specialized sigma subunit [Butyrivibrio
           fibrisolvens 16/4]
          Length = 59

 Score = 53.7 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 32/54 (59%), Gaps = 2/54 (3%)

Query: 235 LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           L  +E+++      ++  +TL+ +S+  EVS  RV Q+  +A +K+++ + + +
Sbjct: 2   LTEKEKQVILLYYYED--MTLKEISAALEVSESRVSQLHTKALQKMRKVLGEYM 53


>gi|171058011|ref|YP_001790360.1| FliA/WhiG family RNA polymerase sigma 28 subunit [Leptothrix
           cholodnii SP-6]
 gi|170775456|gb|ACB33595.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Leptothrix cholodnii SP-6]
          Length = 321

 Score = 53.7 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 37/236 (15%), Positives = 83/236 (35%), Gaps = 30/236 (12%)

Query: 49  AAHRLVTSHLRLVVKIAM---GYRGYGLPISEVVSEGNIGLMQAVKKFDPE-------RG 98
           A   L+  +   V K A          +  ++++  G I + Q+   F  E         
Sbjct: 7   ATSALIARNESWVRKQASALVRRLPSNVEKADLIQVGLIAVAQSALGFKWEGDPDSEEAK 66

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
                Y+   +K AM + + +   L +      Q+R F  ++  +   +A    +     
Sbjct: 67  EAFVRYARMRVKGAMLDELRQMDHLGR-----AQRRKFKVIQIARERWRA---RHGSDPG 118

Query: 159 VVAIAKKLNVSESEVISMNCR--LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           +  +A    ++  E+  ++    +A  +SL+   +  ++  +                + 
Sbjct: 119 LAELAGVCGIAVDEISMLDQAALMAQAQSLDDDPDHENREPAHAA--------TPRDEVE 170

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
            + +       L +  + L  RER++ +A       ++   L+    VS  RV QI
Sbjct: 171 ARVDTAIVMRRLEKFFATLPDRERQVIDAYLGIG--MSPVELAGALRVSPSRVSQI 224


>gi|227501930|ref|ZP_03931979.1| possible exonuclease [Corynebacterium accolens ATCC 49725]
 gi|227077314|gb|EEI15277.1| possible exonuclease [Corynebacterium accolens ATCC 49725]
          Length = 1118

 Score = 53.7 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 19/63 (30%), Positives = 36/63 (57%), Gaps = 8/63 (12%)

Query: 219 EERKNRRNMLTRSMSVL------NPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           E++   R +  R++  L      + R+R I  +R L E   TL+++ + F ++RER+RQ+
Sbjct: 610 EQQSPVRTLFQRAVDELVRATGGDERKRGIACSRWLGE--ATLDSIGAAFGLTRERIRQL 667

Query: 273 EAR 275
           E +
Sbjct: 668 ERQ 670


>gi|169830054|ref|YP_001700212.1| RNA polymerase factor sigma-70 [Lysinibacillus sphaericus C3-41]
 gi|168994542|gb|ACA42082.1| RNA polymerase sigma-H factor (Sigma-30) [Lysinibacillus sphaericus
           C3-41]
          Length = 215

 Score = 53.7 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 41/204 (20%), Positives = 74/204 (36%), Gaps = 14/204 (6%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L +   + G+  A   L+T +  LV   A  Y   G    ++V EG IGL +A++ F  
Sbjct: 20  ELIEMVHQ-GNTDALDYLITKYRLLVRAKARSYFLIGADKEDIVQEGMIGLYKAIRDFKG 78

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           ++      ++   I   +   I  +     I        L   +   K  L   +D  L 
Sbjct: 79  DKLASFRAFAELCITRQIITAIKTATRQKHIP-------LNSYVSLDKPILDEESDRTLM 131

Query: 156 PEQVVAIA---KKLNVSESEVISMNCRLAGDES---LNALINSSDKNSSQWQDWLVYDHD 209
                AI    ++L +   E   +  +++   S   L  L    D  S       +  H 
Sbjct: 132 DVLTGAIMDDPEELIIHREEFGYLEEKMSEILSELELQVLALYLDGRSYHEISAKLNRHV 191

Query: 210 GQEQVLIEKEERKNRRNMLTRSMS 233
                 +++ +RK  R+++   MS
Sbjct: 192 KSIDNALQRVKRKLERHLVLEEMS 215


>gi|78212818|ref|YP_381597.1| DNA-directed RNA polymerase specialized sigma subunit-like
           [Synechococcus sp. CC9605]
 gi|78197277|gb|ABB35042.1| DNA-directed RNA polymerase specialized sigma subunit-like
           [Synechococcus sp. CC9605]
          Length = 183

 Score = 53.7 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 18/117 (15%), Positives = 48/117 (41%), Gaps = 1/117 (0%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLP-ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
            ++    HL L    A   +  G     +++ E  +GL++ V +FDP+R  + ++Y +  
Sbjct: 32  RNQQALEHLGLAHCAARRQQQRGPEEFDDLLQESRVGLIRGVDRFDPQRRVKPSSYLLSR 91

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
               +  Y      ++K+            ++R +      + ++L+    +++  +
Sbjct: 92  ATGQILHYRRDRSRMIKVHGGCVLYAAGMKIQREREQNTQPSLSDLELATALSVLPE 148


>gi|302872437|ref|YP_003841073.1| RNA polymerase, sigma-24 subunit, ECF subfamily
           [Caldicellulosiruptor obsidiansis OB47]
 gi|302575296|gb|ADL43087.1| RNA polymerase, sigma-24 subunit, ECF subfamily
           [Caldicellulosiruptor obsidiansis OB47]
          Length = 244

 Score = 53.7 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 29/137 (21%), Positives = 48/137 (35%), Gaps = 5/137 (3%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
             EE V   RY   G   A   L+  +   V      Y   G    ++  EG IGL +AV
Sbjct: 47  PDEELV---RYSREGIKEATEELLCRYQNFVKAKCRMYFLIGADKEDIYQEGMIGLFKAV 103

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQA 148
           + FD  +      ++   I   M   I  +     I   T  +  +  +     +  +  
Sbjct: 104 RDFDETKYPSFRLFAEMCITRQMITAIKTASRQKHIPLNTYISLNKPVYEENDERTLIDT 163

Query: 149 ITDNNLKPEQVVAIAKK 165
           + D  +   + V I K+
Sbjct: 164 LADTFISDPEEVMITKE 180


>gi|292492344|ref|YP_003527783.1| sigma-70 region 4 domain protein [Nitrosococcus halophilus Nc4]
 gi|291580939|gb|ADE15396.1| sigma-70 region 4 domain protein [Nitrosococcus halophilus Nc4]
          Length = 192

 Score = 53.7 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 16/43 (37%), Positives = 24/43 (55%), Gaps = 2/43 (4%)

Query: 237 PRERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEARAF 277
            R + I   R     E   TLE++   ++++RERVRQIEA+  
Sbjct: 131 ERNKDILCKRFNLEGEGEYTLEDIGIYYDLTRERVRQIEAKTI 173


>gi|291526282|emb|CBK91869.1| RNA polymerase sigma factor, sigma-70 family [Eubacterium rectale
           DSM 17629]
          Length = 202

 Score = 53.7 bits (128), Expect = 3e-05,   Method: Composition-based stats.
 Identities = 18/93 (19%), Positives = 41/93 (44%), Gaps = 2/93 (2%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY--GLPISEVVSEGNIGLMQAVKKF 93
            L K Y+E  D S    L+ ++  L+  +   Y        + ++ SE  I +++A++ +
Sbjct: 12  ELIKAYKESRDESYLKELIEANNGLINLLVSPYLTSIPNSELEDLTSESYIPMLRAIEDY 71

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           DPE+G   +T    +++  +      +    + 
Sbjct: 72  DPEQGVAFSTLLKVYVRQHLNRLYNEATRQKRF 104


>gi|260589560|ref|ZP_05855473.1| RNA polymerase sigma-H factor [Blautia hansenii DSM 20583]
 gi|331082987|ref|ZP_08332106.1| hypothetical protein HMPREF0992_01030 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|260540128|gb|EEX20697.1| RNA polymerase sigma-H factor [Blautia hansenii DSM 20583]
 gi|330399724|gb|EGG79385.1| hypothetical protein HMPREF0992_01030 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 197

 Score = 53.7 bits (128), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 33/167 (19%), Positives = 69/167 (41%), Gaps = 11/167 (6%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L+ +E + L  +    G       L+  +  +V+K A      G    +++ EG IGL +
Sbjct: 8   LKDEELFELLWQ----GQEGLEDYLINKYKGMVLKKAHAMFLIGGEQEDLIQEGMIGLFK 63

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           AV+ + P++    +T++   I+  M + I  S         +     + +L  ++G L  
Sbjct: 64  AVRGYHPDKNASFSTFANLCIERQMYKAIEISGRQKHKPLNS-----YISLSEMEGPLYN 118

Query: 149 ITD-NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
             D     PE++V   + ++    E+            L+A ++ +D
Sbjct: 119 AEDITQQNPEEIVIGKENVSRMMEEIKERLSPFENQV-LDAYLDGAD 164


>gi|303240979|ref|ZP_07327489.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302591404|gb|EFL61142.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 214

 Score = 53.3 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 36/247 (14%), Positives = 78/247 (31%), Gaps = 62/247 (25%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + G+L A   L+  +   V   A  Y   G    +++ EG IGL +A++ F  ++     
Sbjct: 26  KSGNLKALEYLINKYKGFVRAKARTYFLIGADREDIIQEGMIGLYKAIRDFREDKLSSFR 85

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
            ++   I   +   I  +     I                                    
Sbjct: 86  AFAELCITRQIITAIKTATRQKHIP----------------------------------- 110

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
                        +N  ++    LN  I   + + +          +  E+++I +EE  
Sbjct: 111 -------------LNSYIS----LNKPIFDDESDRTLMDIISEDTINDPEEMVINREEFS 153

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
                +   +S L   E  +           + + ++ E +     V+ I   A ++V+ 
Sbjct: 154 GIEEKMGEILSGL---ECEVLALYL---EGKSYQEIAIELD---RHVKSI-DNALQRVKR 203

Query: 283 SIQKQVE 289
            ++K +E
Sbjct: 204 KLEKYLE 210


>gi|253579508|ref|ZP_04856777.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251849009|gb|EES76970.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 199

 Score = 53.3 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 23/97 (23%), Positives = 41/97 (42%), Gaps = 3/97 (3%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K EE  L  R++ +G+      L+  +  +V K A      G    +++ EG IGL +AV
Sbjct: 8   KDEE--LISRFK-NGESEILDYLMEKYKNMVRKKARTMFLIGGENDDLIQEGMIGLFKAV 64

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           + + P+R     T++   +   +   I  S       
Sbjct: 65  RDYQPDRDAAFQTFASICVDRQIYNAIQSSNRQKHQP 101


>gi|150389913|ref|YP_001319962.1| RNA polymerase subunit alpha [Alkaliphilus metalliredigens QYMF]
 gi|149949775|gb|ABR48303.1| RNA polymerase, alpha subunit domain protein [Alkaliphilus
           metalliredigens QYMF]
          Length = 912

 Score = 53.3 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 16/46 (34%), Positives = 26/46 (56%), Gaps = 3/46 (6%)

Query: 235 LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           LN +E  +   R       TL ++    +VS++R+RQIE +A KK+
Sbjct: 303 LNDKEYDVIWQRI---QGKTLVDVGKTKDVSKQRIRQIEEKAIKKL 345


>gi|312144264|ref|YP_003995710.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Halanaerobium sp.
           'sapolanicus']
 gi|311904915|gb|ADQ15356.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Halanaerobium sp.
           'sapolanicus']
          Length = 219

 Score = 53.3 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 30/144 (20%), Positives = 57/144 (39%), Gaps = 3/144 (2%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GD+ A   L+  +   V+  +  Y   G    ++V EG IGL +AV+ +  ER      
Sbjct: 32  QGDMEAQETLIRRYKNFVLAKSRSYFLVGADREDIVQEGMIGLYKAVRDYKIERLASFRA 91

Query: 104 YSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           ++   I   +   I  +         T  +  +  ++    +  L  +    L   + + 
Sbjct: 92  FAELCITRQIITAIKAATRQKHQPLNTYISLNKPIYDEESDRTLLDVLKGGKLSNPESLF 151

Query: 162 IAKK-LNVSESEVISMNCRLAGDE 184
           I+ +  ++ ESE+ SM   L  D 
Sbjct: 152 ISNETYDLIESEISSMLSDLEFDV 175


>gi|260887693|ref|ZP_05898956.1| RNA polymerase sigma-H factor [Selenomonas sputigena ATCC 35185]
 gi|260862573|gb|EEX77073.1| RNA polymerase sigma-H factor [Selenomonas sputigena ATCC 35185]
          Length = 248

 Score = 53.3 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 39/261 (14%), Positives = 84/261 (32%), Gaps = 65/261 (24%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L  +E      R +E+    A   L+  +   V   A  Y   G    ++V EG IGL +
Sbjct: 20  LTDEEVIS---RIKENCSNIALDYLINKYRNFVRAKARSYFLIGADREDIVQEGMIGLYK 76

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++ F  +R      ++   +   +   I  +     I                      
Sbjct: 77  AIRDFRNDRLSSFRAFAELCVTRQIITAIKTATRQKHIP--------------------- 115

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                                      +N  ++    LN  I   D + +          
Sbjct: 116 ---------------------------LNSYIS----LNKPIYDEDSDRTLLDILPGARV 144

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
              E+++I +EE  +    +   +S L   E R+  +     +  + + ++ + +     
Sbjct: 145 SNPEELVISQEEFVDIEEKMEEILSDL---EWRVLMSYL---DGKSYQEIAVDLD---RH 195

Query: 269 VRQIEARAFKKVQESIQKQVE 289
           V+ I   A ++V+  +++ +E
Sbjct: 196 VKSI-DNALQRVKRKLERYME 215


>gi|296119760|ref|ZP_06838314.1| conserved hypothetical protein [Corynebacterium ammoniagenes DSM
           20306]
 gi|295966914|gb|EFG80185.1| conserved hypothetical protein [Corynebacterium ammoniagenes DSM
           20306]
          Length = 549

 Score = 53.3 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 16/73 (21%), Positives = 36/73 (49%), Gaps = 8/73 (10%)

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            +  + ++  +    + R+  I   R + +   TL++L ++F ++RERVRQ+E      +
Sbjct: 45  EEAIQELIDAARG--DERKFAIIAKRWIGD--ATLDDLGNQFGITRERVRQLEVE----L 96

Query: 281 QESIQKQVELSSS 293
           +E   K  +   +
Sbjct: 97  REDFNKSRDFYDA 109


>gi|83591295|ref|YP_431304.1| RNA polymerase factor sigma-70 [Moorella thermoacetica ATCC 39073]
 gi|83574209|gb|ABC20761.1| RNA polymerase, sigma 30 subunit, SigH [Moorella thermoacetica ATCC
           39073]
          Length = 217

 Score = 53.3 bits (127), Expect = 4e-05,   Method: Composition-based stats.
 Identities = 19/86 (22%), Positives = 33/86 (38%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + GD  A   L+  +   V   A  Y   G    ++V EG IGL +A++ F  ++    
Sbjct: 25  AQEGDEVAQEYLINKYRNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDFRGDKLSSF 84

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIG 127
             ++   I   +   I  +     I 
Sbjct: 85  RAFAELCITRQIITAIKTATRQKHIP 110


>gi|312142838|ref|YP_003994284.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Halanaerobium sp.
           'sapolanicus']
 gi|311903489|gb|ADQ13930.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Halanaerobium sp.
           'sapolanicus']
          Length = 208

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 16/87 (18%), Positives = 37/87 (42%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             + G+  A   L+  ++ +V   A  +   GL   +V+ EG +GL +A++ +   +G  
Sbjct: 13  MAQAGNDFAIEYLIDQNMDIVYAKARFFFIKGLDRDDVIQEGRVGLYKAIRDYREGKGAS 72

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIG 127
              +S   +   +   I ++     + 
Sbjct: 73  FRGFSQLCVHRQLVSAIKKANRQKHMP 99


>gi|327313254|ref|YP_004328691.1| RNA polymerase sigma factor, sigma-70 family [Prevotella denticola
           F0289]
 gi|326944626|gb|AEA20511.1| RNA polymerase sigma factor, sigma-70 family [Prevotella denticola
           F0289]
          Length = 208

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 16/74 (21%), Positives = 39/74 (52%), Gaps = 2/74 (2%)

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
             +I++EE+ + + ++   ++ L  R+R     R +Q   ++ E ++   ++S   VR++
Sbjct: 119 DTIIDEEEKSDIKEIVEDLLNTLTDRQREAIYLRYMQN--LSYEEIAELLDISPGSVRKL 176

Query: 273 EARAFKKVQESIQK 286
             RA   ++E  +K
Sbjct: 177 VYRAIMCLREESRK 190


>gi|258511073|ref|YP_003184507.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Alicyclobacillus acidocaldarius subsp. acidocaldarius
           DSM 446]
 gi|257477799|gb|ACV58118.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Alicyclobacillus acidocaldarius subsp. acidocaldarius
           DSM 446]
          Length = 176

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 19/70 (27%), Positives = 36/70 (51%), Gaps = 5/70 (7%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGY----GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           +A   LV  + RLV  +A  +R      G+   ++V+ G +GL +A + +DP R  + + 
Sbjct: 3   AAQEVLVVENQRLVYFVANRFRHRAVAAGIEFDDLVATGMLGLCKAARVYDPSR-AKFSV 61

Query: 104 YSMWWIKAAM 113
            ++  I+  M
Sbjct: 62  LAVRCIENEM 71


>gi|313895843|ref|ZP_07829397.1| RNA polymerase sigma-H factor [Selenomonas sp. oral taxon 137 str.
           F0430]
 gi|312975268|gb|EFR40729.1| RNA polymerase sigma-H factor [Selenomonas sp. oral taxon 137 str.
           F0430]
          Length = 285

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 37/256 (14%), Positives = 79/256 (30%), Gaps = 66/256 (25%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L    R H    A   LV  +   V   A  Y   G    ++V EG IG  +A++ F  
Sbjct: 69  ELLVHIRTHEGNEALDYLVNKYRNFVRSKARSYFLIGADREDIVQEGMIGFFKAIRDFRE 128

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           ++      ++   +   +   I  +     I   +                         
Sbjct: 129 DKLSSFRAFAELCVTRQIITAIKTATRQKHIPLNSY------------------------ 164

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
                             +S+N            I   D + +             E+++
Sbjct: 165 ------------------VSLNK----------PIYDEDSDRTLLDVLSGARISDPEELV 196

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA- 274
           I +EE  +    +   +S L   E R+  +     +  + + ++ +        RQ+++ 
Sbjct: 197 ISREEFVDIEKKMEEILSDL---EWRVLMSYL---DGKSYQEIAVDLH------RQVKSI 244

Query: 275 -RAFKKVQESIQKQVE 289
             A ++V+  ++K +E
Sbjct: 245 DNALQRVKRKLEKYME 260


>gi|160933813|ref|ZP_02081201.1| hypothetical protein CLOLEP_02674 [Clostridium leptum DSM 753]
 gi|156867690|gb|EDO61062.1| hypothetical protein CLOLEP_02674 [Clostridium leptum DSM 753]
          Length = 187

 Score = 53.3 bits (127), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 20/95 (21%), Positives = 39/95 (41%), Gaps = 1/95 (1%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L  R R+ G+  A   L++ +  L+     GYR  G+   +++ E  +GL+ +V  F  
Sbjct: 8   ELVARVRQ-GNQEAFSELISRYYGLLQWKISGYRKLGIDADDLLQEATLGLLDSVMSFQE 66

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
            +G    TY+   +   +      +     I   +
Sbjct: 67  GKGASFETYATVCVNNRLVTLYRAAARQKNIPFHS 101


>gi|295108535|emb|CBL22488.1| RNA polymerase, sigma 30 subunit, SigH [Ruminococcus obeum A2-162]
          Length = 202

 Score = 52.9 bits (126), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 20/92 (21%), Positives = 38/92 (41%), Gaps = 1/92 (1%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L  R R+ G+   +  L+  +   V K A      G    +++ EG IGL +A++ + P
Sbjct: 11  ELIFRLRQ-GETEISDYLMEKYKEFVRKKARAMFLIGGETDDLIQEGMIGLFKAIQNYQP 69

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           +R     T++   I   +   +  S     + 
Sbjct: 70  DREASFQTFAGLCIDRQLYSAVQNSNRQKHLP 101


>gi|206896523|ref|YP_002246663.1| RNA polymerase sigma factor for flagellar operon [Coprothermobacter
           proteolyticus DSM 5265]
 gi|206739140|gb|ACI18218.1| RNA polymerase sigma factor for flagellar operon [Coprothermobacter
           proteolyticus DSM 5265]
          Length = 199

 Score = 52.9 bits (126), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 36/242 (14%), Positives = 79/242 (32%), Gaps = 67/242 (27%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMG--YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           GD  A  +++ S  R++ + A    Y    L   ++++ G I   + +  ++ E      
Sbjct: 14  GDDKAREQVLMSLQRVIERQASQLTYYNISLEWDDLLAVGLIAANECIDLYNLESEIPFE 73

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
            ++   I+  M +Y+ R+         A  K+    L +                     
Sbjct: 74  AFASKVIRNKMVDYL-RTTGTFTKSDVAKYKQGQLTLNK--------------------- 111

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
                               + SL ALI    +   +    L                  
Sbjct: 112 -------------------EELSLEALIEQGIEEVGEQGIILE----------------- 135

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
                L  +++ L+ R +++ + R +    ++++ ++    VS  RV Q+   A   ++E
Sbjct: 136 -----LEEALNRLDLRHKQVLQFRYVDN--LSVKEVADILGVSPGRVSQLVNEALDLLRE 188

Query: 283 SI 284
            I
Sbjct: 189 DI 190


>gi|218291390|ref|ZP_03495333.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
 gi|218238745|gb|EED05961.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
          Length = 187

 Score = 52.9 bits (126), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 20/70 (28%), Positives = 35/70 (50%), Gaps = 5/70 (7%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGY----GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            A  RLV  + RLV  +A   R      G+   ++V+ G +GL +A + +DP R  + + 
Sbjct: 14  EAQERLVVENQRLVYFVANRLRHRAQEAGVEFEDLVATGMLGLCKAARVYDPSR-AKFSV 72

Query: 104 YSMWWIKAAM 113
            ++  I+  M
Sbjct: 73  LAVRCIENEM 82


>gi|291519019|emb|CBK74240.1| RNA polymerase sigma factor, sigma-70 family [Butyrivibrio
           fibrisolvens 16/4]
          Length = 195

 Score = 52.9 bits (126), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 37/228 (16%), Positives = 71/228 (31%), Gaps = 66/228 (28%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L K+Y++ GD +  + +   +  LV+K +  Y   G    +++ EG IGL  A+  +D 
Sbjct: 14  DLVKKYQD-GDQAVLNYICEKYKPLVLKTSKKYFLVGGENEDLIQEGMIGLFGAIGDYDT 72

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           +       ++   I   M + I  S                      K H          
Sbjct: 73  DSEVTFFRFAQLCIDRQMIKAIEASNR--------------------KKH---------- 102

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
                                   L    SL           S       Y  D   +++
Sbjct: 103 ----------------------SPLNAYVSLYDEDGGEIDEPS-------YTSDDPAELI 133

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           IE E   +    L ++   L+P E+++F+      +    + ++ +  
Sbjct: 134 IEAEANSDLIMRLKKA---LSPMEQQVFDLYMQDYD---YKEIAQKLG 175


>gi|302671184|ref|YP_003831144.1| RNA polymerase sigma factor sigma-70 family protein [Butyrivibrio
           proteoclasticus B316]
 gi|302395657|gb|ADL34562.1| RNA polymerase sigma factor sigma-70 family [Butyrivibrio
           proteoclasticus B316]
          Length = 207

 Score = 52.9 bits (126), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 35/158 (22%), Positives = 60/158 (37%), Gaps = 7/158 (4%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            EE +L+   R+  D  A   ++  +  LV K A      G    +++ EG IGL +AV+
Sbjct: 11  DEELILS--IRDGDDPGAVDHIMNKYKNLVRKKAASMFALGADKDDLIQEGMIGLFKAVR 68

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTA-----NQKRLFFNLRRLKGHL 146
            +D  R    AT++   I   M   I            +      ++    +   +    
Sbjct: 69  DYDCGRDASFATFAELCISRQMYSAIKAMARKKHAPLNSYISIYAKREDMGDDASVALEE 128

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
              +D+++ PEQ V   + L   E  + S    L G  
Sbjct: 129 LLESDSSMIPEQHVIDQENLKALEEAIESELSPLEGQV 166


>gi|153931605|ref|YP_001385116.1| sigma-70 family RNA polymerase sigma factor [Clostridium botulinum
           A str. ATCC 19397]
 gi|153936750|ref|YP_001388585.1| sigma-70 family RNA polymerase sigma factor [Clostridium botulinum
           A str. Hall]
 gi|152927649|gb|ABS33149.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           A str. ATCC 19397]
 gi|152932664|gb|ABS38163.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           A str. Hall]
          Length = 176

 Score = 52.9 bits (126), Expect = 5e-05,   Method: Composition-based stats.
 Identities = 27/140 (19%), Positives = 60/140 (42%), Gaps = 13/140 (9%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
            + L K+YRE GD  A  +++ + + L++K A  Y+       ++V  G + +++A   +
Sbjct: 1   MHQLIKKYRE-GDNKALQKIIDNFIPLILKEASKYKIKCYDYEDLVQHGYLSVIKAANMY 59

Query: 94  D-PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
              ++ F+      + IKA  Q Y       +K      +++  +       +   + D 
Sbjct: 60  KGEDKNFKF-----YCIKAIKQNYKALLKGEIKHHREIPEEKDIY------PYEFTLEDE 108

Query: 153 NLKPEQVVAIAKKLNVSESE 172
            L  E++  + K L+    +
Sbjct: 109 ILAYEKIKEVYKALDYLTQD 128


>gi|331011084|gb|EGH91140.1| flagellar biosynthesis sigma factor [Pseudomonas syringae pv.
           tabaci ATCC 11528]
          Length = 160

 Score = 52.9 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 30/153 (19%), Positives = 64/153 (41%), Gaps = 9/153 (5%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            ++ + L+  +  LV +IA          + + +++  G IGL++   K+D  +G    T
Sbjct: 14  RNSQYELIERYAPLVKRIAYHLLARLPASVQVEDLIQAGMIGLLEVSTKYDSTKGASFET 73

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           Y+   I+ AM + + R           N + +   +R +    +A T  + K  +V A  
Sbjct: 74  YAGIRIRGAMLDEV-RKGDWAPRSVHRNTRMVSDAIRAI----EAKTGRDAKDHEVAAEL 128

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
           + L++ +   I  +   +   S + L+   D  
Sbjct: 129 Q-LSLDDYYGILNDTLGSRLFSFDDLLQDGDHE 160


>gi|313893511|ref|ZP_07827081.1| sigma-70, region 4 [Veillonella sp. oral taxon 158 str. F0412]
 gi|313441954|gb|EFR60376.1| sigma-70, region 4 [Veillonella sp. oral taxon 158 str. F0412]
          Length = 296

 Score = 52.9 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 19/106 (17%), Positives = 47/106 (44%), Gaps = 2/106 (1%)

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           RL     ++    ++D         +    +    +++  +E +  R  L  ++  L+P 
Sbjct: 183 RLRNHREIHIPDRTTDDGDVAVGMDIFASGENIADMIMTADEEQRLRARLVWALGRLSPD 242

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +R +   RR+     +L ++S E   SR+ +++   RA +K++  +
Sbjct: 243 QRDLL--RRVYGECQSLVSVSEELNCSRQAIQRRHERAIRKLRRYL 286


>gi|310826509|ref|YP_003958866.1| putative RNA polymerase [Eubacterium limosum KIST612]
 gi|308738243|gb|ADO35903.1| putative RNA polymerase [Eubacterium limosum KIST612]
          Length = 198

 Score = 52.9 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 47/256 (18%), Positives = 93/256 (36%), Gaps = 67/256 (26%)

Query: 35  YVLAKRYR---EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           Y L   +    + GD  AA  L+ S   L++K+A    G      +   +G    ++AV+
Sbjct: 6   YELINTWAAEAQKGDKRAAELLLQSFRPLILKMAGRCFG-DSGFEDAYQDGTAAFLEAVR 64

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           ++DPE+      Y                           +K L F  R+ +        
Sbjct: 65  RYDPEKNHLFPGYI--------------------------RKYLDFYFRKRQE------- 91

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
                        + + S S V+S++   A D                    LV D +  
Sbjct: 92  ------------GRFDKSVSAVVSLDAPAAED--------------GTTLGQLVPDPNQP 125

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR- 270
            Q   E+ +RK+R   L  ++  L   +RR   A  L     + + ++++ ++S   V+ 
Sbjct: 126 IQACHEENDRKSRLEKLDWALKQLPGDQRRAITAYYLGGQ--SQKAIAADCQLSASAVKM 183

Query: 271 QIEARAFKKVQESIQK 286
           +I  R  ++++  +++
Sbjct: 184 RIH-RGLRRLRVLMEE 198


>gi|254729465|ref|YP_003084147.1| type III RNAP sigma factor [Cyanophage PSS2]
 gi|254211617|gb|ACT65565.1| type III RNAP sigma factor [Cyanophage PSS2]
 gi|265524818|gb|ACY75710.1| predicted protein [Cyanophage PSS2]
          Length = 213

 Score = 52.9 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 44/233 (18%), Positives = 80/233 (34%), Gaps = 43/233 (18%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLP-----ISEVVSEGNIGLMQAVKKFDPERGFRLA 102
            A       +L L  K A        P       ++ +   IGLM+A  +FD E G + +
Sbjct: 10  KAQQLKTEENLNLARKEAWRAFKRQSPRSRLPYDDLEAAAFIGLMKACFRFDEEFGCKFS 69

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           TY++  I+  +  +I     L+K+  T   +  +   +RL                 + I
Sbjct: 70  TYAVPKIRGEILHFIRDHTYLLKL--THRMRETWQRGKRLLDQGN----------SDIEI 117

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER- 221
           AK L       I +   L    + +       + +    D LV   D +   L+   +R 
Sbjct: 118 AKALE------IELEVWLDTRSACSGPPLELKEYAGLHGDELVAKEDDRLGPLLRAVDRA 171

Query: 222 -----KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE--NLSS-EFEVSR 266
                   +  L ++           F    L ++  + +   ++  EF VSR
Sbjct: 172 WELVGDKGQRHLAQA-----------FRFNHLLDHTYSQKLVQVAEAEFNVSR 213


>gi|167747162|ref|ZP_02419289.1| hypothetical protein ANACAC_01876 [Anaerostipes caccae DSM 14662]
 gi|317473634|ref|ZP_07932923.1| hypothetical protein HMPREF1011_03274 [Anaerostipes sp. 3_2_56FAA]
 gi|167654122|gb|EDR98251.1| hypothetical protein ANACAC_01876 [Anaerostipes caccae DSM 14662]
 gi|316898924|gb|EFV20949.1| hypothetical protein HMPREF1011_03274 [Anaerostipes sp. 3_2_56FAA]
          Length = 249

 Score = 52.9 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 31/155 (20%), Positives = 67/155 (43%), Gaps = 12/155 (7%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             L  R  +  D+   + L+ S L  V   A  Y G+G+ + +++ EGN+GL++AV +  
Sbjct: 97  RELIVRLADGEDVQ--NELIESMLADVALDARNYTGHGVLLGDLIQEGNMGLIEAVFELG 154

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
                    +     ++AM++ +    +   +G     +++     RL    + + ++  
Sbjct: 155 DREPKEAEKFLREAAESAMKKAVSEQMNTDSVG-----EQMARKANRLDEAARFLAEDLG 209

Query: 155 KPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
           +      +A  L ++E EV  +        SL+A+
Sbjct: 210 REATAGELADHLKMTEEEVKEIMK-----MSLDAI 239


>gi|322381141|ref|ZP_08055144.1| RNA polymerase factor sigma-70-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321154717|gb|EFX46988.1| RNA polymerase factor sigma-70-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 205

 Score = 52.9 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 33/249 (13%), Positives = 79/249 (31%), Gaps = 62/249 (24%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            G+  A   L+  +   V   A  Y   G    ++V EG +GL ++++ F  ++      
Sbjct: 18  AGNSEALEYLINKYKNFVRAKARSYFLIGADREDIVQEGMVGLYKSIRDFRGDKLASFKA 77

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           ++   I   +   I  +     I   +                                 
Sbjct: 78  FAELCITRQIITAIKTATRQKHIPLNSY-------------------------------- 105

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
                     +S++            I   D + +             E+++I +EE   
Sbjct: 106 ----------VSLDK----------PIYDEDSDRTLLDVICGSRVTDPEELIINQEEFSG 145

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             + +   +S L   ERR+        +  + + ++ + +     V+ I   A ++V+  
Sbjct: 146 LEDKMGEILSDL---ERRVLMLYL---DGRSYQEIAVDLDC---HVKSI-DNALQRVKRK 195

Query: 284 IQKQVELSS 292
           +++ +E+  
Sbjct: 196 LERYLEIRD 204


>gi|294783390|ref|ZP_06748714.1| RNA polymerase sigma-H factor [Fusobacterium sp. 1_1_41FAA]
 gi|294480268|gb|EFG28045.1| RNA polymerase sigma-H factor [Fusobacterium sp. 1_1_41FAA]
          Length = 196

 Score = 52.9 bits (126), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 17/88 (19%), Positives = 42/88 (47%), Gaps = 1/88 (1%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           +E   +  +  + GD  A   ++  + +++   A  Y   G    +++ EG +GL++A+K
Sbjct: 3   EENINIILKKAQTGDSEAIDWILKEYSKILSFNAQKYYLVGAEQEDLLQEGILGLLKAIK 62

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILR 119
            +D  +    ++++   I+  M   I +
Sbjct: 63  FYDETK-SSFSSFAFLCIRREMISAIRK 89


>gi|320530729|ref|ZP_08031773.1| RNA polymerase sigma-H factor [Selenomonas artemidis F0399]
 gi|320137016|gb|EFW28954.1| RNA polymerase sigma-H factor [Selenomonas artemidis F0399]
          Length = 266

 Score = 52.5 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 37/256 (14%), Positives = 79/256 (30%), Gaps = 66/256 (25%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L    R H    A   LV  +   V   A  Y   G    ++V EG IG  +A++ F  
Sbjct: 50  ELLVHIRTHEGNEALDYLVNKYRNFVRSKARSYFLIGADREDIVQEGMIGFFKAIRDFRE 109

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           ++      ++   +   +   I  +     I   +                         
Sbjct: 110 DKLSSFRAFAELCVTRQIITAIKTATRQKHIPLNSY------------------------ 145

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
                             +S+N            I   D + +             E+++
Sbjct: 146 ------------------VSLNK----------PIYDEDSDRTLLDVLSGARISDPEELV 177

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA- 274
           I +EE  +    +   +S L   E R+  +     +  + + ++ +        RQ+++ 
Sbjct: 178 ISREEFVDIEKKMEEILSDL---EWRVLMSYL---DGKSYQEIAVDLH------RQVKSI 225

Query: 275 -RAFKKVQESIQKQVE 289
             A ++V+  ++K +E
Sbjct: 226 DNALQRVKRKLEKYME 241


>gi|124514599|gb|EAY56111.1| putative RNA polymerase sigma-70 factor family [Leptospirillum
           rubarum]
          Length = 99

 Score = 52.5 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 2/60 (3%)

Query: 230 RSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           R +  L  R R++   R         TL+ +  EF ++RERVRQI   + +K+ +  +++
Sbjct: 34  RILQDLPDRSRKMVLLRYGIGTGISWTLQEIGLEFGLTRERVRQILRTSLEKLVKRQRRK 93


>gi|325678366|ref|ZP_08157986.1| RNA polymerase sigma factor, sigma-70 family [Ruminococcus albus 8]
 gi|324109867|gb|EGC04063.1| RNA polymerase sigma factor, sigma-70 family [Ruminococcus albus 8]
          Length = 265

 Score = 52.5 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 43/236 (18%), Positives = 85/236 (36%), Gaps = 29/236 (12%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM----GYRGYGLPISE-VVSEGNIGLM 87
           EE VL  R+ E+GD +A + L       +  I       +      + + +   G++ L+
Sbjct: 4   EELVL--RF-ENGDKTALNELYLQLDIFIKSIVKDVMKKFGISNEELEDELFQVGSVELI 60

Query: 88  QAVKK--FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           + V K  +DP +G    +Y   ++K AM  ++ +  + V I             R++   
Sbjct: 61  ELVYKRSYDPNKGI-FTSYIYPYLKYAMIRHVEKFITPVAIA--HRDMLAISKCRKMHRD 117

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
             A            +IA +L +S+  V          ES+   +N            L+
Sbjct: 118 GMA----------DESIANELGISKQLVARYLRFSFKTESIMLTLNDEYGEEYLENPKLI 167

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLS 259
                +E         K     L      L+P++++I  +         +T+E ++
Sbjct: 168 ----SKEPKPDHAAYVKICAERLKLLFDKLSPKQQQIIGSFFGAYGYEEMTIEKIA 219


>gi|229542221|ref|ZP_04431281.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Bacillus coagulans
           36D1]
 gi|229326641|gb|EEN92316.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Bacillus coagulans
           36D1]
          Length = 216

 Score = 52.5 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 35/257 (13%), Positives = 84/257 (32%), Gaps = 63/257 (24%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L  R   +G+  A   L+  +   V   A  Y   G    +++ EG IGL +A++ +  
Sbjct: 20  ELVGRIH-NGESEALDYLIQKYRNFVRAKARSYFIIGADREDIIQEGMIGLYKAIRDYRE 78

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           ++      ++   I   M   I  +     I                             
Sbjct: 79  DKLTSFKAFAELCINRQMITAIKTATRQKHIP---------------------------- 110

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
                               +N  ++    L+  I   + + +             E+++
Sbjct: 111 --------------------LNSYIS----LDKPIYDEESDRTLMDVITGAKISNPEELI 146

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
           + +E+  +    ++  +S L   ER++        +  + + +S E       V+ I   
Sbjct: 147 LIREKYVHIEVKISELLSDL---ERKVLALYL---DGQSYQEISEELN---RHVKSI-DN 196

Query: 276 AFKKVQESIQKQVELSS 292
           A ++V++ +++ +E+  
Sbjct: 197 ALQRVKKKLERLLEMRE 213


>gi|146296392|ref|YP_001180163.1| RNA polymerase factor sigma-70 [Caldicellulosiruptor
           saccharolyticus DSM 8903]
 gi|145409968|gb|ABP66972.1| RNA polymerase, sigma 30 subunit, SigH [Caldicellulosiruptor
           saccharolyticus DSM 8903]
          Length = 210

 Score = 52.5 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 29/136 (21%), Positives = 50/136 (36%), Gaps = 5/136 (3%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            EE V   +Y   G   A   L+  +  LV      Y   G    ++  EG IGL +AV+
Sbjct: 15  DEELV---KYSREGIKEATEELLNRYQNLVKAKCRMYFLIGAEKDDIYQEGMIGLFKAVR 71

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQAI 149
            FD  +      ++   I   +   I  +     I   T  +  +  +     +  L  I
Sbjct: 72  DFDETKYPAFKLFAELCITRQVITAIKTASRQKHIPLNTYISLNKPVYEENDERTLLDTI 131

Query: 150 TDNNLKPEQVVAIAKK 165
            ++ +   + V I K+
Sbjct: 132 ANSFISDPEEVMITKE 147


>gi|317134088|ref|YP_004089999.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Ruminococcus
           albus 7]
 gi|315450550|gb|ADU24113.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Ruminococcus
           albus 7]
          Length = 330

 Score = 52.5 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 34/232 (14%), Positives = 87/232 (37%), Gaps = 29/232 (12%)

Query: 28  MLEKQEEYVLAK------------RYREHGDLSAAHRLVTSHLRLVVKIAMGYR-GYGLP 74
           M+ ++E   L              ++ +     AA  L+  ++ L+      +       
Sbjct: 1   MITREEIIELTNEDIVRIYQDLESQFTKREKELAATVLIEKNIGLITSTLKHFTTNKRTS 60

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
             E++  G  G+  A K++    G +  T+++  IKAA+ + + ++ S        N+K+
Sbjct: 61  WDELMQAGRYGIFYAAKRYKFNEGTQFHTFAVSQIKAAILDELNKATSNSSNHYMINEKK 120

Query: 135 LFF---NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
           +     +++ +KG       + ++   +    + +  +  E   +  R    +SL+    
Sbjct: 121 IKMAIADIQAIKGANYYPNADEIRSCILANRGEDIPTTTIERCMVGSRQNEAQSLD---- 176

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
             D  +    D              E  +++  ++ + +++  L P ER + 
Sbjct: 177 -DDNFNHSIPDLTA--------TCEEIVDQQYMKSDVEKALDRLPPAERFVL 219


>gi|125974549|ref|YP_001038459.1| RNA polymerase factor sigma-70 [Clostridium thermocellum ATCC
           27405]
 gi|256004092|ref|ZP_05429077.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           thermocellum DSM 2360]
 gi|281419072|ref|ZP_06250089.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           thermocellum JW20]
 gi|125714774|gb|ABN53266.1| RNA polymerase, sigma 30 subunit, SigH [Clostridium thermocellum
           ATCC 27405]
 gi|255992015|gb|EEU02112.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           thermocellum DSM 2360]
 gi|281407221|gb|EFB37482.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           thermocellum JW20]
 gi|316941666|gb|ADU75700.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           thermocellum DSM 1313]
          Length = 214

 Score = 52.5 bits (125), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 23/143 (16%), Positives = 54/143 (37%), Gaps = 6/143 (4%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GD  A   L+  +   V   A  Y   G    +++ EG IGL +A++ F  ++      
Sbjct: 27  AGDDRALEYLINKYKGFVRAKARTYFLIGADREDIIQEGMIGLYKAIRDFRKDKLSSFRA 86

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR-LKGHLQAITDNNLKPEQVVAI 162
           ++   I   +   I  +     I   +     + +L + +       T  ++  E+ +  
Sbjct: 87  FAELCITRQIITAIKTATRQKHIPLNS-----YVSLNKPIFDEESDRTLMDIISEESIND 141

Query: 163 AKKLNVSESEVISMNCRLAGDES 185
            +++ ++  E   +  ++    S
Sbjct: 142 PEEMVINREEFSGIEAKMGEILS 164


>gi|310828140|ref|YP_003960497.1| ECF subfamily RNA polymerase sigma-24 factor [Eubacterium limosum
           KIST612]
 gi|308739874|gb|ADO37534.1| ECF subfamily RNA polymerase sigma-24 factor [Eubacterium limosum
           KIST612]
          Length = 209

 Score = 52.5 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 38/242 (15%), Positives = 78/242 (32%), Gaps = 62/242 (25%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD +A   L+ +   ++  +   Y      + +   E     ++ V+ F  +      
Sbjct: 30  QQGDKTAVEALLMAFKPMLWSVVSHYVYNREELEDAYQEACAVFIEGVRDFALDARIYFQ 89

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           T+                  LV            + L+R +G   A              
Sbjct: 90  TFM--------------QGRLVH-----------YFLKRREGRFSA-------------- 110

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
                            LAG  SL+  +  +D  +    + ++ +    E   +  E++K
Sbjct: 111 ----------------SLAGTLSLDRPVEGADG-AVALAELILDEKADVEGACVAAEQQK 153

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
                L R+   L+P +R +   + L     TL  L+++  VS   + Q   RA   ++ 
Sbjct: 154 ----ALLRAYRKLSPGQREVLRYQYL--EKGTLSELAAQKGVSPAAITQTHKRALAALKR 207

Query: 283 SI 284
            +
Sbjct: 208 HL 209


>gi|310777972|ref|YP_003966305.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ilyobacter
           polytropus DSM 2926]
 gi|309747295|gb|ADO81957.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ilyobacter
           polytropus DSM 2926]
          Length = 203

 Score = 52.5 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 20/76 (26%), Positives = 36/76 (47%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            ++GD  A  ++   +   V   A  Y   G    ++V EG IGL++A++ +D E+    
Sbjct: 14  AQNGDQEAVRKVFDYYKNFVFLKAKNYFLIGADRDDLVQEGMIGLLKAIRAYDTEKAASF 73

Query: 102 ATYSMWWIKAAMQEYI 117
            T++   IK  +   I
Sbjct: 74  KTFATICIKRQLITAI 89


>gi|254517456|ref|ZP_05129512.1| RNA polymerase sigma-H factor [Clostridium sp. 7_2_43FAA]
 gi|226911205|gb|EEH96406.1| RNA polymerase sigma-H factor [Clostridium sp. 7_2_43FAA]
          Length = 214

 Score = 52.5 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 38/257 (14%), Positives = 85/257 (33%), Gaps = 70/257 (27%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           +E    AK+    G+  A   L++ +   V   A  Y   G    ++  EG IGL +A++
Sbjct: 20  EEVVDEAKK----GNSRAQDYLISKYENFVKAKAKSYFLIGADKEDIYQEGMIGLYKAIR 75

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
            F  +R      ++   I   +   I  +     I                         
Sbjct: 76  DFKSDRLTSFKAFAELCITRQIITAIKTATRQKHIP------------------------ 111

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
                                   +N  ++    LN  I   + + +             
Sbjct: 112 ------------------------LNTYIS----LNKPIYEEESDRTLIDVLSGLKITNP 143

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E+++I KE+ K+    + + +S L   E  + ++     +  + + ++ + +      RQ
Sbjct: 144 EELIIGKEQLKHIEGEMAKVLSDL---EMEVLQSYL---DGKSYQEIACDLD------RQ 191

Query: 272 IEA--RAFKKVQESIQK 286
            ++   A ++V+  ++K
Sbjct: 192 AKSIDNALQRVKRKLEK 208


>gi|148378736|ref|YP_001253277.1| RNA polymerase sigma factor [Clostridium botulinum A str. ATCC
           3502]
 gi|153931118|ref|YP_001383122.1| sigma-70 family RNA polymerase sigma factor [Clostridium botulinum
           A str. ATCC 19397]
 gi|153937466|ref|YP_001386672.1| sigma-70 family RNA polymerase sigma factor [Clostridium botulinum
           A str. Hall]
 gi|148288220|emb|CAL82289.1| putative RNA polymerase sigma factor [Clostridium botulinum A str.
           ATCC 3502]
 gi|152927162|gb|ABS32662.1| RNA polymerase sigma-70 factor family [Clostridium botulinum A str.
           ATCC 19397]
 gi|152933380|gb|ABS38879.1| RNA polymerase sigma-70 factor family [Clostridium botulinum A str.
           Hall]
          Length = 179

 Score = 52.5 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 29/139 (20%), Positives = 58/139 (41%), Gaps = 8/139 (5%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
            Y L ++YR +GD+ A + ++ +   L++K A  +R  G    ++V  G + +++AV  F
Sbjct: 1   MYKLLEKYR-NGDIGALNEIIENFNPLILKEASRWRIGGYEYEDLVQHGYLSVIKAVNMF 59

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
             E     + +  + I A    Y       +K      +      L +   ++  I D  
Sbjct: 60  KGEE----SKFVPYCINAIKTNYKALLKGEIK---HHREIPDENILNKGNEYMFTIEDEI 112

Query: 154 LKPEQVVAIAKKLNVSESE 172
           +  E+   I + L+    E
Sbjct: 113 IAYEKTKEIYEALDKLTQE 131


>gi|225574360|ref|ZP_03782970.1| hypothetical protein RUMHYD_02427 [Blautia hydrogenotrophica DSM
           10507]
 gi|225038416|gb|EEG48662.1| hypothetical protein RUMHYD_02427 [Blautia hydrogenotrophica DSM
           10507]
          Length = 202

 Score = 52.5 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 25/140 (17%), Positives = 54/140 (38%), Gaps = 6/140 (4%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L ++ R+ G    A  L+  +  LV + A      G    +++ EG IGL +AV+ + P
Sbjct: 11  ELIEKLRD-GQEDVADYLMEKYKELVRQKARAMYLIGGETDDLIQEGMIGLFKAVRDYQP 69

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           ++     T++   I   + + I  S               + +L +     + +     +
Sbjct: 70  DKAASFQTFARLCIDRQLYKAISGSNRQKHQPL-----NTYVSLSQETEGERQLRSLWEQ 124

Query: 156 PEQVVAIAKKLNVSESEVIS 175
             + + IA++      + I 
Sbjct: 125 NPEAIVIARENVEDLEKRIE 144


>gi|284047634|ref|YP_003397973.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Acidaminococcus
           fermentans DSM 20731]
 gi|283951855|gb|ADB46658.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Acidaminococcus
           fermentans DSM 20731]
          Length = 244

 Score = 52.5 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 26/155 (16%), Positives = 57/155 (36%), Gaps = 6/155 (3%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L  +E   L +  ++  D  A   L+  +   +   A  Y   G    +++ EG IGL +
Sbjct: 12  LSDEE---LIQLIQDRDDRQAQDYLLDKYKEFIRLKATRYFLVGAEKEDIIQEGMIGLFK 68

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT--TANQKRLFFNLRRLKGHL 146
           A++ + P +      ++   +   +   I  +            +  +  F   + +  L
Sbjct: 69  AIRDYRPGKQASFKVFAEICVNRQIISAIKSATRQKHRPLNCYVSLDKPVFEEGKERTLL 128

Query: 147 QAITD-NNLKPEQVVAIAKKLNVSESEVISMNCRL 180
             +   + + PE ++   +  N  E  V +M   L
Sbjct: 129 DMLGGSHGVDPENLLVDQEAFNDIERNVSTMLSDL 163


>gi|222530009|ref|YP_002573891.1| RNA polymerase factor sigma-70 [Caldicellulosiruptor bescii DSM
           6725]
 gi|312621716|ref|YP_004023329.1| RNA polymerase, sigma-24 subunit, ecf subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
 gi|222456856|gb|ACM61118.1| RNA polymerase, sigma-24 subunit, ECF subfamily
           [Caldicellulosiruptor bescii DSM 6725]
 gi|312202183|gb|ADQ45510.1| RNA polymerase, sigma-24 subunit, ECF subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
          Length = 244

 Score = 52.5 bits (125), Expect = 8e-05,   Method: Composition-based stats.
 Identities = 28/136 (20%), Positives = 49/136 (36%), Gaps = 5/136 (3%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            EE V   +Y   G   A   L++ +   V      Y   G    ++  EG IGL +AV+
Sbjct: 48  DEELV---KYSREGVKEALEELLSRYQNFVKAKCRMYFLIGADKEDIYQEGMIGLFKAVR 104

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQAI 149
            FD  +      ++   I   M   I  +     I   T  +  +  +     +  +  +
Sbjct: 105 DFDETKYPSFRLFAEMCITRQMITAIKTASRQKHIPLNTYISLNKPVYEENDERTLIDTL 164

Query: 150 TDNNLKPEQVVAIAKK 165
            D  +   + V I K+
Sbjct: 165 ADAFISDPEEVMITKE 180


>gi|312876809|ref|ZP_07736787.1| RNA polymerase, sigma-24 subunit, ECF subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
 gi|311796428|gb|EFR12779.1| RNA polymerase, sigma-24 subunit, ECF subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
          Length = 211

 Score = 52.1 bits (124), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 28/136 (20%), Positives = 49/136 (36%), Gaps = 5/136 (3%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            EE V   +Y   G   A   L++ +   V      Y   G    ++  EG IGL +AV+
Sbjct: 15  DEELV---KYSREGVKEATEELLSRYQNFVKAKCRMYFLIGADKEDIFQEGMIGLFKAVR 71

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQAI 149
            FD  +      ++   I   M   I  +     I   T  +  +  +     +  +  +
Sbjct: 72  DFDETKYPSFRLFAEMCITRQMITAIKTASRQKHIPLNTYISLNKPVYEENDERTLIDTL 131

Query: 150 TDNNLKPEQVVAIAKK 165
            D  +   + V I K+
Sbjct: 132 ADTFISDPEEVMITKE 147


>gi|260589994|ref|ZP_05855907.1| sigma-70 region 2 family protein [Blautia hansenii DSM 20583]
 gi|260539801|gb|EEX20370.1| sigma-70 region 2 family protein [Blautia hansenii DSM 20583]
          Length = 261

 Score = 52.1 bits (124), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 31/174 (17%), Positives = 69/174 (39%), Gaps = 23/174 (13%)

Query: 26  IPMLEKQ----EEYVLA------------KRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           IP+  ++    EEY+L              R    G+     +L+ ++   +VK A    
Sbjct: 94  IPLTSEEKEFLEEYLLGFETEEELLKEELLRAFLAGNQECTEKLIRAYQDEIVKAAKKLN 153

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
              +   +++ EGN+GL+ A+++   +       + +  I++ M+ +I            
Sbjct: 154 REDIFFGDLLQEGNMGLLTALERLSEQENPD--EWIVREIESTMKLFIEEQAQ-----QK 206

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
                L   +R L+  ++ +T++      V  +A  L++   E+ S+      D
Sbjct: 207 KEDNILVEKVRDLEKKVKELTEDEDVKYSVEELAAFLDMDLEEMESVLRLTGDD 260


>gi|238916437|ref|YP_002929954.1| RNA polymerase sporulation-specific sigma factor [Eubacterium
           eligens ATCC 27750]
 gi|238871797|gb|ACR71507.1| RNA polymerase sporulation-specific sigma factor [Eubacterium
           eligens ATCC 27750]
          Length = 203

 Score = 52.1 bits (124), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 23/93 (24%), Positives = 39/93 (41%), Gaps = 4/93 (4%)

Query: 33  EEY---VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           EEY    L   YR  G+  A   +   +  +V K A      G    +++ EG IGL +A
Sbjct: 5   EEYPDEELIDMYR-AGNEQAIEYIFERYKYIVRKKAKAMFLAGGDSDDLIQEGMIGLYKA 63

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           V+ +D ++     T++   I   +   +  S  
Sbjct: 64  VRDYDKQKDASFMTFAGMCINRQILNAVTASNR 96


>gi|237736330|ref|ZP_04566811.1| RNA polymerase sigma-H factor [Fusobacterium mortiferum ATCC 9817]
 gi|229421678|gb|EEO36725.1| RNA polymerase sigma-H factor [Fusobacterium mortiferum ATCC 9817]
          Length = 205

 Score = 52.1 bits (124), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 16/81 (19%), Positives = 37/81 (45%), Gaps = 1/81 (1%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           +  ++GD  A   ++  + +L+      Y   G    +++ EG IGL++A+K +   +  
Sbjct: 19  KLAQNGDQEALDLILKEYKKLIYLNIRNYFLVGADQDDLLQEGTIGLLKAIKNYSEGK-A 77

Query: 100 RLATYSMWWIKAAMQEYILRS 120
              T++   I+  +   +  S
Sbjct: 78  SFKTFATLCIRRQILTAVRSS 98


>gi|205372085|ref|ZP_03224902.1| RNA polymerase factor sigma-70 [Bacillus coahuilensis m4-4]
          Length = 215

 Score = 52.1 bits (124), Expect = 9e-05,   Method: Composition-based stats.
 Identities = 32/249 (12%), Positives = 79/249 (31%), Gaps = 62/249 (24%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           +G+  A   L+  +   V   A  Y   G    ++V EG IGL +A++ +  ++      
Sbjct: 26  NGNSDALDFLIHKYRNFVRAKARSYFLIGADREDIVQEGMIGLYKAIRDYKGDKLASFKA 85

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           ++   I   +   I  +     I   +                                 
Sbjct: 86  FAELCITRQIITAIKTATRQKHIPLNSY-------------------------------- 113

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
                     +S++            I   + + +             +++++ +EE  N
Sbjct: 114 ----------VSLDK----------PIYDEESDRTLMDIITPAKTLDPQELIVSREEFSN 153

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             + +   +S L   ER +        +  + + +S   +     V+ I   A ++V+  
Sbjct: 154 MEDKMAEILSDL---EREVLALYL---DGQSYQEISELLD---RHVKSI-DNALQRVKRK 203

Query: 284 IQKQVELSS 292
           +++ +E+  
Sbjct: 204 LERYLEVRE 212


>gi|312792762|ref|YP_004025685.1| RNA polymerase, sigma-24 subunit, ecf subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
 gi|312179902|gb|ADQ40072.1| RNA polymerase, sigma-24 subunit, ECF subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
          Length = 211

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 28/136 (20%), Positives = 49/136 (36%), Gaps = 5/136 (3%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            EE V   +Y   G   A   L++ +   V      Y   G    ++  EG IGL +AV+
Sbjct: 15  DEELV---KYSREGIKEATEELLSRYQNFVKAKCRMYFLIGADKEDIYQEGMIGLFKAVR 71

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQAI 149
            FD  +      ++   I   M   I  +     I   T  +  +  +     +  +  +
Sbjct: 72  DFDETKYPSFRLFAEMCITRQMITAIKTASRQKHIPLNTYISLNKPVYEENDERTLIDTL 131

Query: 150 TDNNLKPEQVVAIAKK 165
            D  +   + V I K+
Sbjct: 132 ADTFISDPEEVMITKE 147


>gi|226324508|ref|ZP_03800026.1| hypothetical protein COPCOM_02291 [Coprococcus comes ATCC 27758]
 gi|225206956|gb|EEG89310.1| hypothetical protein COPCOM_02291 [Coprococcus comes ATCC 27758]
          Length = 212

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 20/98 (20%), Positives = 40/98 (40%), Gaps = 4/98 (4%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             ++   L +     G       L+  +  +V K A     +G    +++ EG IGL +A
Sbjct: 9   TDEQLIELLR----EGKTEITDYLMEKYKDMVRKQARAMYLWGGENDDLIQEGMIGLFKA 64

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           V+ +DP+ G   ++++   +   M   I  S     + 
Sbjct: 65  VQDYDPKEGASFSSFAGLCVSRQMYTAIKASQRKKHLP 102


>gi|269798881|ref|YP_003312781.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Veillonella
           parvula DSM 2008]
 gi|269095510|gb|ACZ25501.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Veillonella
           parvula DSM 2008]
          Length = 288

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 20/114 (17%), Positives = 49/114 (42%), Gaps = 2/114 (1%)

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           RL     ++    ++D     +   +    +    +++  +E    R  L  ++  L+P 
Sbjct: 175 RLRYRREIHIPDRTTDDGEVAFGMDIFASGENVADMVMSADEEHRLRARLVWALGRLSPD 234

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
           +R +   RR+     +L ++S E   SR+ +++   RA +K++  +    E+  
Sbjct: 235 QRDLL--RRVYGECQSLVSVSEELNCSRQAIQRRHERAIRKLRRYLSTDFEVLR 286


>gi|169836116|ref|ZP_02869304.1| hypothetical protein cdivTM_03213 [candidate division TM7
          single-cell isolate TM7a]
          Length = 54

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 21/46 (45%), Positives = 30/46 (65%)

Query: 16 LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLV 61
          +S Y+ +I+K  +L ++EEY L KR RE  D  A   L+ S+LRLV
Sbjct: 9  MSLYLSDIQKFDLLSREEEYELLKRIREDNDEQARQLLILSNLRLV 54


>gi|322805057|emb|CBZ02617.1| RNA polymerase sigma factor RpoD [Clostridium botulinum H04402 065]
          Length = 179

 Score = 52.1 bits (124), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 29/139 (20%), Positives = 57/139 (41%), Gaps = 8/139 (5%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
            Y L ++YR +GD+ A + ++ +   L++K A  +R       ++V  G + +++AV  F
Sbjct: 1   MYSLLEKYR-NGDVGALNEIIENFNPLILKEAARWRIRCYEYEDLVQHGYLSVIKAVNMF 59

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
             E     + +  + I A    Y       +K      +      L +   ++  I D  
Sbjct: 60  KGEE----SKFVPYCINAIKTNYKALLKGEIK---HHREIPDENILNKGNEYMFTIEDEI 112

Query: 154 LKPEQVVAIAKKLNVSESE 172
           +  E+   I K L+    E
Sbjct: 113 IAYEKTKEIYKALDKLTQE 131


>gi|329121465|ref|ZP_08250089.1| RNA polymerase subunit alpha [Dialister micraerophilus DSM 19965]
 gi|327469380|gb|EGF14850.1| RNA polymerase subunit alpha [Dialister micraerophilus DSM 19965]
          Length = 899

 Score = 51.7 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 15/40 (37%), Positives = 26/40 (65%), Gaps = 3/40 (7%)

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
           R + I  +R    +  TLE+++ EF+++RERVRQI ++  
Sbjct: 301 RTKEIVRSRF---SGKTLEDVAKEFDLTRERVRQIVSKVI 337


>gi|313891416|ref|ZP_07825032.1| RNA polymerase, alpha subunit C-terminal domain protein [Dialister
           microaerophilus UPII 345-E]
 gi|313120191|gb|EFR43367.1| RNA polymerase, alpha subunit C-terminal domain protein [Dialister
           microaerophilus UPII 345-E]
          Length = 897

 Score = 51.7 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 15/40 (37%), Positives = 26/40 (65%), Gaps = 3/40 (7%)

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
           R + I  +R    +  TLE+++ EF+++RERVRQI ++  
Sbjct: 299 RTKEIVRSRF---SGKTLEDVAKEFDLTRERVRQIVSKVI 335


>gi|156744109|ref|YP_001434238.1| FliA/WhiG family RNA polymerase sigma 28 subunit [Roseiflexus
           castenholzii DSM 13941]
 gi|156235437|gb|ABU60220.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Roseiflexus castenholzii DSM 13941]
          Length = 220

 Score = 51.7 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 18/101 (17%), Positives = 42/101 (41%), Gaps = 9/101 (8%)

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           ESL+A       +     + +    D     L E+ + +  R  L  +++ L   ER + 
Sbjct: 123 ESLDAPFG---DDGPPLHEVI---EDPTPARLAEEHDEEQVRKRLYEAIAALPEIERAVV 176

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             R  +   +   +++    +S   V +I  RA  ++++++
Sbjct: 177 THRLSEVRGI---DIAQMLGMSPANVSRIYKRAINRLRQAL 214


>gi|317132052|ref|YP_004091366.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ethanoligenens
           harbinense YUAN-3]
 gi|315470031|gb|ADU26635.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ethanoligenens
           harbinense YUAN-3]
          Length = 245

 Score = 51.7 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 25/84 (29%), Positives = 39/84 (46%), Gaps = 1/84 (1%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            LA R    GD  A   LV+S +  +   ++     GL   +++ EG +GL+ AV+ F P
Sbjct: 59  ELAAR-ACAGDRDAMADLVSSFVPFIRAHSVPVAAAGLEADDMMQEGMLGLLGAVRHFCP 117

Query: 96  ERGFRLATYSMWWIKAAMQEYILR 119
           + G     Y+   IK  M   + R
Sbjct: 118 QNGVPFRAYAHICIKRRMASAVRR 141


>gi|282849510|ref|ZP_06258894.1| sigma-70, region 4 [Veillonella parvula ATCC 17745]
 gi|282580447|gb|EFB85846.1| sigma-70, region 4 [Veillonella parvula ATCC 17745]
          Length = 288

 Score = 51.7 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 20/111 (18%), Positives = 48/111 (43%), Gaps = 2/111 (1%)

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           RL     ++    ++D     +   +    +    +++  +E    R  L  ++  L+P 
Sbjct: 175 RLRYRREIHIPDRTTDDGEVAFGMDIFASGENVADMVMSADEEHRLRARLVWALGRLSPD 234

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           +R +   RR+     +L ++S E   SR+ +++   RA +K++  +    E
Sbjct: 235 QRDLL--RRVYGECQSLVSVSEELNCSRQAIQRRHERAIRKLRRYLSTDFE 283


>gi|331084310|ref|ZP_08333415.1| hypothetical protein HMPREF0992_02339 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|330401845|gb|EGG81422.1| hypothetical protein HMPREF0992_02339 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 247

 Score = 51.7 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 31/174 (17%), Positives = 69/174 (39%), Gaps = 23/174 (13%)

Query: 26  IPMLEKQ----EEYVLA------------KRYREHGDLSAAHRLVTSHLRLVVKIAMGYR 69
           IP+  ++    EEY+L              R    G+     +L+ ++   +VK A    
Sbjct: 80  IPLTSEEKEFLEEYLLGFETEEELLKEELLRAFLAGNQECTEKLIRAYQDEIVKAAKKLN 139

Query: 70  GYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
              +   +++ EGN+GL+ A+++   +       + +  I++ M+ +I            
Sbjct: 140 REDIFFGDLLQEGNMGLLTALERLSEQENPD--EWIVREIESTMKLFIEEQAQ-----QK 192

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
                L   +R L+  ++ +T++      V  +A  L++   E+ S+      D
Sbjct: 193 KEDNILVEKVRDLEKKVKELTEDEDVKYSVEELAAFLDMDLEEMESVLRLTGDD 246


>gi|225181307|ref|ZP_03734752.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Dethiobacter
           alkaliphilus AHT 1]
 gi|225168087|gb|EEG76893.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Dethiobacter
           alkaliphilus AHT 1]
          Length = 219

 Score = 51.7 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 19/96 (19%), Positives = 35/96 (36%), Gaps = 3/96 (3%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            EE  +     + G   A   L+  +   V   A  Y   G    +++ EG IGL +A++
Sbjct: 23  DEEVAIQ---AKDGCEVALEYLINKYRNFVKAKARSYFLIGADREDIIQEGMIGLYKAIR 79

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
            F  ++      ++   I   +   I  +     I 
Sbjct: 80  DFKEDKLSSFRAFAELCITRQIITAIKTATRQKHIP 115


>gi|170759910|ref|YP_001786104.1| sigma-70 family RNA polymerase sigma factor [Clostridium botulinum
           A3 str. Loch Maree]
 gi|169406899|gb|ACA55310.1| RNA polymerase sigma-70 factor family [Clostridium botulinum A3
           str. Loch Maree]
          Length = 179

 Score = 51.7 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 28/139 (20%), Positives = 57/139 (41%), Gaps = 8/139 (5%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
            Y L ++YR +GD+ A + ++ +   L++K A  +R       ++V  G + +++AV  F
Sbjct: 1   MYNLLEKYR-NGDIGALNEIIENFNPLILKEASRWRIGCYEYEDLVQHGYLSVIKAVNMF 59

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
             E     + +  + I A    Y       +K      +      L +   ++  I D  
Sbjct: 60  KGEE----SKFVPYCINAIKTNYKALLKGEIK---HHREIPDENILNKGNEYMFTIEDEI 112

Query: 154 LKPEQVVAIAKKLNVSESE 172
           +  E+   I + L+    E
Sbjct: 113 IAYEKTKEIYEALDKLTQE 131


>gi|166031080|ref|ZP_02233909.1| hypothetical protein DORFOR_00762 [Dorea formicigenerans ATCC
           27755]
 gi|166028927|gb|EDR47684.1| hypothetical protein DORFOR_00762 [Dorea formicigenerans ATCC
           27755]
          Length = 202

 Score = 51.7 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 27/156 (17%), Positives = 57/156 (36%), Gaps = 7/156 (4%)

Query: 23  IRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           + +   +  ++   L ++ R+ GD      ++  +  LV K A      G    +++ EG
Sbjct: 1   MDRYEKMTDEQ---LIQKLRD-GDNRIVDYIMEKYKNLVRKEANAMYLLGGENEDLIQEG 56

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            IGL +AV+ ++P++     +++   I   +   I  S         +          + 
Sbjct: 57  MIGLFKAVQNYEPDQNSSFFSFAKLCISRQLYSAIEASRRKKHSPLNSYVSLYDMTEEKE 116

Query: 143 KGHLQAITDNNLKPEQV---VAIAKKLNVSESEVIS 175
                     N  PE++      A+ L     E +S
Sbjct: 117 PLINTMEAHKNSNPEELLVSQEYAELLESKLEESLS 152


>gi|225405814|ref|ZP_03761003.1| hypothetical protein CLOSTASPAR_05035 [Clostridium asparagiforme
           DSM 15981]
 gi|225042654|gb|EEG52900.1| hypothetical protein CLOSTASPAR_05035 [Clostridium asparagiforme
           DSM 15981]
          Length = 173

 Score = 51.7 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 18/83 (21%), Positives = 39/83 (46%), Gaps = 1/83 (1%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             +L+  ++ L   +    R   +  +E +S  N GL++A  +FDP+RG + +T+++  I
Sbjct: 5   RKKLIEENIALAGYVYGKMRYPPIDDTEKISAANYGLVKAAMQFDPDRGLKFSTFAVPVI 64

Query: 110 KAAMQEYILRSWSLVKIGTTANQ 132
           +  +     R         + N+
Sbjct: 65  RNVILHE-ARQARKNNRYISLNE 86


>gi|304316201|ref|YP_003851346.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium thermosaccharolyticum DSM 571]
 gi|302777703|gb|ADL68262.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacterium thermosaccharolyticum DSM 571]
          Length = 188

 Score = 51.7 bits (123), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 32/250 (12%), Positives = 83/250 (33%), Gaps = 77/250 (30%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + GD  +   ++     L++ +A  +       ++++ +G   L+ A+K+FD ++G   
Sbjct: 11  AKSGDEKSTVEILDKFNPLLISLAKKF--PYDDFNDMLQDGREVLILAIKEFDEKKGKEF 68

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
             Y+   +K                                                   
Sbjct: 69  IGYANMRLKFYF------------------------------------------------ 80

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
               ++  +   +S+N     DE              +  D +  D    E+   +    
Sbjct: 81  --MGMHRKKKPNLSLNSSAGDDED-------------EIIDLIESDGLSPEEEFFKCVSI 125

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV---SRERVRQIEARAFK 278
           KN    L  +++ L  +++RI      +    +L  +++E  +   S  +   ++ RA +
Sbjct: 126 KN----LKDALNSLTEKQKRIISLYFFRG--KSLVEIANEIGIGYQSAVK---LKNRAIE 176

Query: 279 KVQESIQKQV 288
           +++ +I+  +
Sbjct: 177 RLRFAIKNDI 186


>gi|33152994|ref|NP_874347.1| hypothetical protein HD2030 [Haemophilus ducreyi 35000HP]
 gi|33149219|gb|AAP96736.1| hypothetical protein HD_2030 [Haemophilus ducreyi 35000HP]
          Length = 705

 Score = 51.4 bits (122), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 15/38 (39%), Positives = 21/38 (55%), Gaps = 2/38 (5%)

Query: 237 PRERRIFEARRLQENPV--TLENLSSEFEVSRERVRQI 272
            R+R+I   R   E     TLE++     ++RERVRQI
Sbjct: 214 ERDRQILFRRYGLETHSIETLEHIGHSLGLTRERVRQI 251


>gi|153004264|ref|YP_001378589.1| sigma-70 region 4 domain-containing protein [Anaeromyxobacter sp.
           Fw109-5]
 gi|152027837|gb|ABS25605.1| sigma-70 region 4 domain protein [Anaeromyxobacter sp. Fw109-5]
          Length = 194

 Score = 51.4 bits (122), Expect = 1e-04,   Method: Composition-based stats.
 Identities = 15/42 (35%), Positives = 24/42 (57%), Gaps = 3/42 (7%)

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPP 295
           TLE + S   ++RER+RQ+E R   K++   + +     SPP
Sbjct: 148 TLEEVGSIMNLTRERIRQVETRGLAKLRTIAEDE---PRSPP 186


>gi|262066779|ref|ZP_06026391.1| RNA polymerase sigma-H factor [Fusobacterium periodonticum ATCC
           33693]
 gi|291379582|gb|EFE87100.1| RNA polymerase sigma-H factor [Fusobacterium periodonticum ATCC
           33693]
          Length = 195

 Score = 51.4 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 17/88 (19%), Positives = 41/88 (46%), Gaps = 1/88 (1%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           +E      +  + GD  A   ++  + +++   A  Y   G    +++ EG +GL++A+K
Sbjct: 2   EENINTILKKAQTGDSEAIDWILKEYSKILSFNAQKYYLIGAEQEDLLQEGILGLLKAIK 61

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILR 119
            +D  +    ++++   I+  M   I +
Sbjct: 62  FYDETK-SSFSSFAFLCIRREMISAIRK 88


>gi|149174254|ref|ZP_01852881.1| RNA polymerase ECF-type sigma factor [Planctomyces maris DSM 8797]
 gi|148846799|gb|EDL61135.1| RNA polymerase ECF-type sigma factor [Planctomyces maris DSM 8797]
          Length = 217

 Score = 51.4 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 16/83 (19%), Positives = 42/83 (50%), Gaps = 3/83 (3%)

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           D L + H+  +  +   EE+++    +    + L  +E+++     L    +T   ++ E
Sbjct: 134 DNLNHIHNLIDDSIETVEEKRDIAEGVIE-FAGLTDKEKQVLRLFFLSG--MTTREIAEE 190

Query: 262 FEVSRERVRQIEARAFKKVQESI 284
            + +   +RQI++RA +K+++ +
Sbjct: 191 LQTTTANIRQIQSRALRKIRDLL 213


>gi|153938798|ref|YP_001390098.1| sigma-70 family RNA polymerase sigma factor [Clostridium botulinum
           F str. Langeland]
 gi|152934694|gb|ABS40192.1| RNA polymerase sigma-70 factor family [Clostridium botulinum F str.
           Langeland]
 gi|295318191|gb|ADF98568.1| RNA polymerase sigma-70 factor family [Clostridium botulinum F str.
           230613]
          Length = 179

 Score = 51.4 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 28/139 (20%), Positives = 57/139 (41%), Gaps = 8/139 (5%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
            Y L ++YR +GD+ A + ++ +   L++K A  +R       ++V  G + +++AV  F
Sbjct: 1   MYNLLEKYR-NGDMGALNEIIENFNPLILKEASKWRIGCYEYEDLVQHGYLSVIKAVNMF 59

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
             E     + +  + I A    Y       +K      +      L +   ++  I D  
Sbjct: 60  KGEE----SKFVPYCINAIKTNYKALLKGEIK---HHREIPDENILNKGNEYMFTIEDEI 112

Query: 154 LKPEQVVAIAKKLNVSESE 172
           +  E+   I + L+    E
Sbjct: 113 IAYEKTKEIYEALDKLTQE 131


>gi|237739548|ref|ZP_04570029.1| RNA polymerase sigma-H factor [Fusobacterium sp. 2_1_31]
 gi|229423156|gb|EEO38203.1| RNA polymerase sigma-H factor [Fusobacterium sp. 2_1_31]
          Length = 196

 Score = 51.4 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 17/88 (19%), Positives = 41/88 (46%), Gaps = 1/88 (1%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           +E      +  + GD  A   ++  + +++   A  Y   G    +++ EG +GL++A+K
Sbjct: 3   EENINTILKKAQTGDSEAIDWILKEYSKILSFNAQKYYLIGAEQEDLLQEGILGLLKAIK 62

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILR 119
            +D  +    ++++   I+  M   I +
Sbjct: 63  FYDETK-SSFSSFAFLCIRREMISAIRK 89


>gi|187777857|ref|ZP_02994330.1| hypothetical protein CLOSPO_01449 [Clostridium sporogenes ATCC
           15579]
 gi|187774785|gb|EDU38587.1| hypothetical protein CLOSPO_01449 [Clostridium sporogenes ATCC
           15579]
          Length = 179

 Score = 51.4 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 28/141 (19%), Positives = 57/141 (40%), Gaps = 5/141 (3%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
            Y L ++YR +GD+SA + ++ +   L++K A  +R       ++V  G + +++AV  F
Sbjct: 1   MYNLLEKYR-NGDMSALNEIIENFNPLILKEASRWRIGCYEYEDLVQHGYLSVIKAVNMF 59

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
             E     + +  + I A    Y       +K       + +          ++      
Sbjct: 60  KGEE----SKFVPYCINAIKTNYKALLKGEIKHHREIPDENILNKGNEYMFTIEDEIIAY 115

Query: 154 LKPEQVVAIAKKLNVSESEVI 174
            K +++     KL   E +VI
Sbjct: 116 EKTKEIYEAIDKLTQEEKQVI 136


>gi|168178132|ref|ZP_02612796.1| RNA polymerase sigma-70 factor family [Clostridium botulinum NCTC
           2916]
 gi|182671478|gb|EDT83452.1| RNA polymerase sigma-70 factor family [Clostridium botulinum NCTC
           2916]
          Length = 179

 Score = 51.4 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 28/139 (20%), Positives = 57/139 (41%), Gaps = 8/139 (5%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
            Y L ++YR +GD+ A + ++ +   L++K A  +R       ++V  G + +++AV  F
Sbjct: 1   MYKLLEKYR-NGDIGALNEIIENFNPLILKEASRWRIGCYEYEDLVQHGYLSVIKAVNMF 59

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
             E     + +  + I A    Y       +K      +      L +   ++  I D  
Sbjct: 60  KGEE----SKFVPYCINAIKTNYKALLKGEIK---HHREIPDENILNKGNEYMFTIEDEI 112

Query: 154 LKPEQVVAIAKKLNVSESE 172
           +  E+   I + L+    E
Sbjct: 113 IAYEKTKEIYEALDKLTQE 131


>gi|154498065|ref|ZP_02036443.1| hypothetical protein BACCAP_02046 [Bacteroides capillosus ATCC
           29799]
 gi|150273055|gb|EDN00212.1| hypothetical protein BACCAP_02046 [Bacteroides capillosus ATCC
           29799]
          Length = 211

 Score = 51.4 bits (122), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 20/83 (24%), Positives = 35/83 (42%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A   LV  + RLV   A      G    +++ EG +GL+ A++ +D  +G    TY
Sbjct: 23  GDPLAEETLVIRYNRLVRVCARPLFLAGGDSEDLIQEGMVGLLSAIRVYDLSKGASFHTY 82

Query: 105 SMWWIKAAMQEYILRSWSLVKIG 127
           +   I+  +   +  +       
Sbjct: 83  AETCIRNRLLSAVKAASRDKHTP 105


>gi|255523582|ref|ZP_05390549.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           carboxidivorans P7]
 gi|255512637|gb|EET88910.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           carboxidivorans P7]
          Length = 194

 Score = 51.0 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 44/247 (17%), Positives = 88/247 (35%), Gaps = 68/247 (27%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + GD  +   ++ +    + K A      G  I +++    I L+ AV K++ E     
Sbjct: 14  AQDGDKLSLKAIIKNFEGFMYKTASSIYINGYEIEDLIQIEAIALINAVFKYNCEYKNAF 73

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
            TY+   IK A                             L+ +L        +      
Sbjct: 74  TTYATTAIKNA-------------------------ACNELRSYLNKKNGEKFE------ 102

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
                                  SLN   N+ D+++ ++ D L+ D + +E +L++++ R
Sbjct: 103 ----------------------FSLN---NTMDEDT-EFMDILLSDDNVEEDILLKEDVR 136

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV--SRERVRQIEARAFKK 279
                 L +++ +L    R I      +E   +L+  +    +  S  + R   ARA +K
Sbjct: 137 T-----LEKALKLLPDNFREIIYWHYFKE--KSLKEYAEFKNIKYSAAKKR--HARALEK 187

Query: 280 VQESIQK 286
           +++ I K
Sbjct: 188 LKQIINK 194


>gi|160881445|ref|YP_001560413.1| RNA polymerase factor sigma-70 [Clostridium phytofermentans ISDg]
 gi|160430111|gb|ABX43674.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           phytofermentans ISDg]
          Length = 213

 Score = 51.0 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 21/97 (21%), Positives = 40/97 (41%), Gaps = 4/97 (4%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           ++  M+  +E   L +      D  A   L+  +  LV K A      G    +++ EG 
Sbjct: 4   KQYEMISDEEIISLIR----GDDRLAMDYLIDKYKNLVRKKAKALYLIGGDREDLIQEGM 59

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           IGL +A++ +  ++     T++   +   M   I  S
Sbjct: 60  IGLYKAIRDYQKDKEASFLTFADLCVSRQMYTAIKNS 96


>gi|237743869|ref|ZP_04574350.1| RNA polymerase sigma-30 factor [Fusobacterium sp. 7_1]
 gi|256027520|ref|ZP_05441354.1| RNA polymerase factor sigma-70 [Fusobacterium sp. D11]
 gi|289765480|ref|ZP_06524858.1| RNA polymerase sigma-30 factor [Fusobacterium sp. D11]
 gi|229432900|gb|EEO43112.1| RNA polymerase sigma-30 factor [Fusobacterium sp. 7_1]
 gi|289717035|gb|EFD81047.1| RNA polymerase sigma-30 factor [Fusobacterium sp. D11]
          Length = 113

 Score = 51.0 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 18/78 (23%), Positives = 39/78 (50%), Gaps = 1/78 (1%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + GD  A + ++  + +L+   A  Y   G    ++V EG +GL++A+K +D  +    
Sbjct: 11  AQSGDSEAINLILKEYSKLLSFNAQKYYLIGAEKEDLVQEGILGLLKAIKFYDETK-SSF 69

Query: 102 ATYSMWWIKAAMQEYILR 119
           ++++   I+  M   I +
Sbjct: 70  SSFAFLCIRREMISAIRK 87


>gi|238018262|ref|ZP_04598688.1| hypothetical protein VEIDISOL_00086 [Veillonella dispar ATCC 17748]
 gi|237864733|gb|EEP66023.1| hypothetical protein VEIDISOL_00086 [Veillonella dispar ATCC 17748]
          Length = 304

 Score = 51.0 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 17/106 (16%), Positives = 46/106 (43%), Gaps = 2/106 (1%)

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           RL     ++     +D         +    +    +++  +E +  R  L  ++  L+  
Sbjct: 191 RLRNHREIHIPDRITDDGEVTVGMDIFASGENIADMIMTADEEQRLRARLVWALGRLSQD 250

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++ +   RR+  +  +L ++S E   SR+ +++   RA +K++  +
Sbjct: 251 QQDLL--RRVYGDCKSLVSVSEELNCSRQAIQRRHERALRKLRRYL 294


>gi|254758386|ref|ZP_05210413.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. Australia
           94]
          Length = 170

 Score = 51.0 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 19/99 (19%), Positives = 38/99 (38%), Gaps = 4/99 (4%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           LE +    L ++    G+  A   L+  +   V   +  Y   G    ++V EG IGL +
Sbjct: 16  LEDEAIVELVRK----GNTDALEYLIHKYKNFVRAKSRSYFLVGADREDIVQEGMIGLFK 71

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           A++ +  ++      ++   I   +   I  +     I 
Sbjct: 72  AIRDYKEDKLSSFKAFAELCITRQIITAIKTATRQKHIP 110


>gi|257419804|ref|ZP_05596798.1| predicted protein [Enterococcus faecalis T11]
 gi|257161632|gb|EEU91592.1| predicted protein [Enterococcus faecalis T11]
          Length = 1045

 Score = 51.0 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 16/51 (31%), Positives = 29/51 (56%), Gaps = 3/51 (5%)

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             +  L    ++I E R L +   TL+ ++ E +++RERVRQIE +   ++
Sbjct: 376 DHIEELPANRKQILEGRVLGD---TLQTIAMELDLTRERVRQIEVKILSEL 423


>gi|95930798|ref|ZP_01313530.1| sigma-70 region 4 [Desulfuromonas acetoxidans DSM 684]
 gi|95133146|gb|EAT14813.1| sigma-70 region 4 [Desulfuromonas acetoxidans DSM 684]
          Length = 251

 Score = 51.0 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 33/213 (15%), Positives = 89/213 (41%), Gaps = 18/213 (8%)

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            ++   G +GL++A   +D   G     ++   ++  M +++ R   +V++      +  
Sbjct: 40  EDLCHYGVVGLLEARVSYDERSGTPWLAFAALRVRGEMIDHL-RKLPMVRLPQAVQSR-- 96

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
              +++LK   +A+    ++ +    ++  L+ +  EV  +   L    +++  ++    
Sbjct: 97  ---VKQLKEARRALQTQQIEVDH-QHLSTALDWTLDEVREVEALLPRRVAVDDGVDQGGD 152

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
                   +  D    E   ++ E       ++ R +  L+ + R I   R L+   +  
Sbjct: 153 ELPSAV-TVTSDGPSPETQALQFELAM----LINRCLQRLSAQNRLIVVGRLLEGLKL-- 205

Query: 256 ENLSSEFEVSRE--RVRQIEARAFKKVQESIQK 286
           + L++    + E  RVRQ   ++ ++++  I+K
Sbjct: 206 KELAATLGYTAENIRVRQ--KKSQEQLKSCIEK 236


>gi|153814447|ref|ZP_01967115.1| hypothetical protein RUMTOR_00659 [Ruminococcus torques ATCC 27756]
 gi|317500161|ref|ZP_07958394.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|331087612|ref|ZP_08336540.1| hypothetical protein HMPREF1025_00123 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|145848843|gb|EDK25761.1| hypothetical protein RUMTOR_00659 [Ruminococcus torques ATCC 27756]
 gi|316898450|gb|EFV20488.1| RNA polymerase sigma factor [Lachnospiraceae bacterium 8_1_57FAA]
 gi|330399791|gb|EGG79451.1| hypothetical protein HMPREF1025_00123 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 208

 Score = 51.0 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 23/105 (21%), Positives = 42/105 (40%), Gaps = 4/105 (3%)

Query: 23  IRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           + +   L  ++   L ++    GD      L+  +  +V K A      G    +++ EG
Sbjct: 1   MEQYEKLTDEQ---LIEKLH-SGDRDVTDYLMEKYKMMVRKKARAMYLIGGETEDLIQEG 56

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
            IGL++AV+ FD   G   A ++   +   M   I  S     + 
Sbjct: 57  MIGLIKAVRNFDSGMGRSFAGFAETCVLRQMYTAIEASNRKKHMP 101


>gi|220930679|ref|YP_002507588.1| RNA polymerase factor sigma-70 [Clostridium cellulolyticum H10]
 gi|220001007|gb|ACL77608.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           cellulolyticum H10]
          Length = 214

 Score = 51.0 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 25/169 (14%), Positives = 64/169 (37%), Gaps = 7/169 (4%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + G+  A   L+  +   V   A  Y   G    +++ EG IGL +A++ +  ++    
Sbjct: 25  AKAGNTMALEYLINKYKSFVRAKARTYFLIGADREDIIQEGMIGLFKAIRDYKGDKLSSF 84

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR-LKGHLQAITDNNLKPEQVV 160
             ++   I   +   I  +     I   +     + +L + +       T  ++  E+ +
Sbjct: 85  RAFAELCITRQIITAIKTATRQKHIPLNS-----YVSLNKPIFDEESDRTLMDIISEESI 139

Query: 161 AIAKKLNVSESEVISMNCRLAGD-ESLNALINSSDKNSSQWQDWLVYDH 208
           +  ++L ++  E   +  ++     SL   + +S  +   +Q+      
Sbjct: 140 SDPEELIINREEFKGIESKMGEILSSLEWEVLTSYLDGKSYQEIAEDLD 188


>gi|51892300|ref|YP_074991.1| putative RNA polymerase sigma factor SigI [Symbiobacterium
           thermophilum IAM 14863]
 gi|51855989|dbj|BAD40147.1| RNA polymerase sigma factor [Symbiobacterium thermophilum IAM
           14863]
          Length = 251

 Score = 51.0 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 25/90 (27%), Positives = 44/90 (48%), Gaps = 6/90 (6%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAM----GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
            GD +A   L+ ++  LV+++       Y   G    E VS G I L +A+ KFDPERG 
Sbjct: 30  AGDKAAREELIRAYTPLVLRVGSQVTGRYLRVGRD--EEVSVGLIALNEAIDKFDPERGN 87

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
               ++   I+  + ++  R+   V++  +
Sbjct: 88  AFIPFAEMVIRRRLVDFYRRNAGRVEVPLS 117


>gi|317063890|ref|ZP_07928375.1| RNA polymerase sigma-H factor [Fusobacterium ulcerans ATCC 49185]
 gi|313689566|gb|EFS26401.1| RNA polymerase sigma-H factor [Fusobacterium ulcerans ATCC 49185]
          Length = 203

 Score = 51.0 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 20/87 (22%), Positives = 38/87 (43%), Gaps = 1/87 (1%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L ++ +  G   A   +  S   +++     Y  YG    +V+ E  IGL++A+  ++ 
Sbjct: 10  HLIEKAK-AGSEEAIQEIFKSFQGIMLLKTKKYFFYGGDKDDVLQEAMIGLLKAINGYEA 68

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWS 122
            R     T+++  IK  +   I  S S
Sbjct: 69  NRQASFKTFAILCIKRQLITAIKSSNS 95


>gi|257469656|ref|ZP_05633748.1| RNA polymerase factor sigma-70 [Fusobacterium ulcerans ATCC 49185]
          Length = 198

 Score = 51.0 bits (121), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 20/87 (22%), Positives = 38/87 (43%), Gaps = 1/87 (1%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L ++ +  G   A   +  S   +++     Y  YG    +V+ E  IGL++A+  ++ 
Sbjct: 5   HLIEKAK-AGSEEAIQEIFKSFQGIMLLKTKKYFFYGGDKDDVLQEAMIGLLKAINGYEA 63

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWS 122
            R     T+++  IK  +   I  S S
Sbjct: 64  NRQASFKTFAILCIKRQLITAIKSSNS 90


>gi|312135726|ref|YP_004003064.1| RNA polymerase, sigma-24 subunit, ecf subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|311775777|gb|ADQ05264.1| RNA polymerase, sigma-24 subunit, ECF subfamily
           [Caldicellulosiruptor owensensis OL]
          Length = 211

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 26/136 (19%), Positives = 49/136 (36%), Gaps = 5/136 (3%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            EE V   +Y   G   A   L++ +   V      Y   G    ++  EG IGL +AV+
Sbjct: 15  DEELV---KYSREGIKEATEELLSRYQNFVKAKCRMYFLIGADKEDIYQEGMIGLFKAVR 71

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQAI 149
            FD  +      ++   I   M   I  +     I   T  +  +  +     +  +  +
Sbjct: 72  DFDETKYPSFRLFAEMCITRQMITAIKTASRQKHIPLNTYISLNKPVYEENDERTLIDTL 131

Query: 150 TDNNLKPEQVVAIAKK 165
            +  +   + V I ++
Sbjct: 132 ANKFISDPEEVMITRE 147


>gi|116871626|ref|YP_848407.1| RNA polymerase factor sigma-70 [Listeria welshimeri serovar 6b str.
           SLCC5334]
 gi|116740504|emb|CAK19624.1| RNA polymerase sigma-30 factor [Listeria welshimeri serovar 6b str.
           SLCC5334]
          Length = 201

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 26/151 (17%), Positives = 58/151 (38%), Gaps = 12/151 (7%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           +E  +L       GD  A     + +  ++   +  Y   G    +++ E  IGL +A++
Sbjct: 8   EEMAML--ELARSGDTEALEYFFSKYQSVIYWKSTQYFLQGAERDDLIQEAMIGLFKAIR 65

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--------TTANQKRLFFNLRRLK 143
            +D  +     +++   I   +   + R+     I         T   +  + + L  + 
Sbjct: 66  DYDQTKEASFRSFAEMCINRQLLSAVKRASRQKNIPLNNSVSLDTPMAEDDVDWTLLDVI 125

Query: 144 GHLQAITDNN--LKPEQVVAIAKKLNVSESE 172
              +A T  +  +K E +  +A++L    SE
Sbjct: 126 SEKEAETPEDFLIKNEDLTHVARQLEEVTSE 156


>gi|78212878|ref|YP_381657.1| type 3 alternative RNA polymerase sigma factor [Synechococcus sp.
           CC9605]
 gi|78197337|gb|ABB35102.1| possible type 3 alternative RNA polymerase sigma factor
           [Synechococcus sp. CC9605]
          Length = 85

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 16/66 (24%), Positives = 35/66 (53%), Gaps = 1/66 (1%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
            L   +R +  +L +V  IA  Y +  GL   +++  G +GL++A  +++ +RG    ++
Sbjct: 20  CLKRRNRQIHDNLHMVRPIARHYAQQTGLESDDLLQVGCLGLIKAYNRYEAKRGAPFPSF 79

Query: 105 SMWWIK 110
           +   I+
Sbjct: 80  AKPHIR 85


>gi|237742620|ref|ZP_04573101.1| RNA polymerase sigma-H factor [Fusobacterium sp. 4_1_13]
 gi|229430268|gb|EEO40480.1| RNA polymerase sigma-H factor [Fusobacterium sp. 4_1_13]
          Length = 204

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 20/87 (22%), Positives = 41/87 (47%), Gaps = 1/87 (1%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE     +  + GD  A   ++  + +L+   A  Y   G    ++V EG +GL++A+K 
Sbjct: 2   EEINAILKKAQSGDSEAISLILKEYSKLLSFNAQKYYLVGAEKEDLVQEGILGLLKAIKF 61

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILR 119
           +D  +    ++++   I+  M   I +
Sbjct: 62  YDETK-SSFSSFAFLCIRREMISAIRK 87


>gi|291294889|ref|YP_003506287.1| sigma-70 region 4 domain-containing protein [Meiothermus ruber DSM
           1279]
 gi|290469848|gb|ADD27267.1| sigma-70 region 4 domain protein [Meiothermus ruber DSM 1279]
          Length = 222

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 20/57 (35%), Positives = 30/57 (52%), Gaps = 3/57 (5%)

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           + L   +  L P ER +  AR   E   TL  +    +++ E VRQ+E RA KK++E
Sbjct: 18  SQLADRLEQLYPLEREVLLARASGE---TLRAIGGRLDLTPEGVRQVEIRALKKLRE 71


>gi|153813243|ref|ZP_01965911.1| hypothetical protein RUMOBE_03659 [Ruminococcus obeum ATCC 29174]
 gi|149830656|gb|EDM85747.1| hypothetical protein RUMOBE_03659 [Ruminococcus obeum ATCC 29174]
          Length = 197

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 20/105 (19%), Positives = 40/105 (38%), Gaps = 4/105 (3%)

Query: 23  IRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           + +      +E   L  R RE G+   +  L+  +   V K A      G    +++ EG
Sbjct: 1   MGRYDQYSDEE---LIVRLRE-GETEISDYLMEKYKEFVRKKARAMFLIGGETDDLIQEG 56

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
            IGL +A++ +  ++     T++   I   +   +  S       
Sbjct: 57  MIGLFKAIQNYQADKETSFRTFASLCIDRQLYSAVQNSNRQKHQP 101


>gi|312898324|ref|ZP_07757714.1| RNA polymerase sigma-H factor [Megasphaera micronuciformis F0359]
 gi|310620243|gb|EFQ03813.1| RNA polymerase sigma-H factor [Megasphaera micronuciformis F0359]
          Length = 216

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 25/131 (19%), Positives = 50/131 (38%), Gaps = 6/131 (4%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
             L+  +  LV   A  Y   G    ++V EG IGL +A++ F P      + ++   I 
Sbjct: 30  DYLIQKYRNLVKSRAHAYFLVGADAEDLVQEGMIGLYKAIRDFKPHMHTIFSAFAEICIT 89

Query: 111 AAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQAITDN-NLKPEQV---VAIAK 164
             +   +  +         +  +  R  +     +     +T   +L PE++       K
Sbjct: 90  RQIISAVKTATRYKHAPLNSYVSIDRPVYADESERTLQDVLTGEKDLNPEELVINEEAYK 149

Query: 165 KLNVSESEVIS 175
            + +  +EV+S
Sbjct: 150 DMELRMNEVLS 160


>gi|207092362|ref|ZP_03240149.1| flagellar biosynthesis sigma factor [Helicobacter pylori
           HPKX_438_AG0C1]
          Length = 130

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 13/74 (17%), Positives = 37/74 (50%), Gaps = 2/74 (2%)

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
           ++  + +K E +     + ++++ ++ RE+ + +    +E  + L  +     ++  R+ 
Sbjct: 54  EQDEITKKIEAEELLEHVQKALNQMSEREQILIQLYYFEE--LNLSEIKEILGITESRIS 111

Query: 271 QIEARAFKKVQESI 284
           QI     KKV++S+
Sbjct: 112 QIIKEVIKKVRKSL 125


>gi|310829442|ref|YP_003961799.1| ECF subfamily RNA polymerase sigma-24 factor [Eubacterium limosum
           KIST612]
 gi|308741176|gb|ADO38836.1| ECF subfamily RNA polymerase sigma-24 factor [Eubacterium limosum
           KIST612]
          Length = 209

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 41/236 (17%), Positives = 77/236 (32%), Gaps = 59/236 (25%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A   LV +   L++        +     +   +G I  M+ +KKFDP RG     +    
Sbjct: 33  AGQLLVMAFRPLILATLSRSGIHDDQFEDAFQDGIIAFMEGLKKFDPRRGASFNAFI--- 89

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
                                  Q  L    R+ +                     + N 
Sbjct: 90  -----------------------QAHLRQYYRKWQH-------------------GQFNH 107

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S     +++ ++ G + L             + + L       E   I++EE+   +  L
Sbjct: 108 SVKPDTTLDDQVPGRQGL------------TYAEVLPDKATNLEADYIQREEKSASQKKL 155

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            R +S L+P  R + E        +T   ++    +S + V Q   RA KK+++ +
Sbjct: 156 ARGLSRLSPSYRSVLEKHYY--EGMTQTEIAETEGISPQAVNQRRDRALKKIKKVL 209


>gi|327438254|dbj|BAK14619.1| DNA-directed RNA polymerase specialized sigma subunit [Solibacillus
           silvestris StLB046]
          Length = 215

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 23/166 (13%), Positives = 59/166 (35%), Gaps = 8/166 (4%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           +  + +   L  +E   L ++    G+  A   L++ +   V   A  Y   G    +++
Sbjct: 7   LQMVLRFEHLTDEE---LVEQVHL-GNTDALDYLISKYRLFVKAKARSYFLIGADKEDII 62

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            EG IGL +A++ F  ++      ++   I   +   I  +     I   +         
Sbjct: 63  QEGMIGLYKAIRDFKEDKLASFRAFAELCITRQIITAIKTATRQKHIPLNS----YVSLD 118

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           + +       T  ++    +    + L ++  + + +  ++    S
Sbjct: 119 KPIYDEESERTLMDIITSPISDDPEYLMINREDYLYLEEKMGEVLS 164


>gi|228474706|ref|ZP_04059437.1| conserved hypothetical protein [Staphylococcus hominis SK119]
 gi|228271369|gb|EEK12737.1| conserved hypothetical protein [Staphylococcus hominis SK119]
          Length = 108

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 19/86 (22%), Positives = 36/86 (41%), Gaps = 4/86 (4%)

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQENPVT 254
           + +   D+     + +   L E    +   N L + + +V   RE  IF    L     +
Sbjct: 26  DDTDIDDFFSLSDEVEPFALNENTGNQVFFNELDQLIYAVGTRREYYIF---FLLCEGKS 82

Query: 255 LENLSSEFEVSRERVRQIEARAFKKV 280
           +  ++  F +SRER+RQ+      K+
Sbjct: 83  MNEIAKIFNLSRERIRQLLNGLLDKL 108


>gi|257469377|ref|ZP_05633470.1| RNA polymerase factor sigma-70 [Fusobacterium ulcerans ATCC 49185]
 gi|317063622|ref|ZP_07928107.1| RNA polymerase sigma-H factor [Fusobacterium ulcerans ATCC 49185]
 gi|313689298|gb|EFS26133.1| RNA polymerase sigma-H factor [Fusobacterium ulcerans ATCC 49185]
          Length = 197

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 20/81 (24%), Positives = 37/81 (45%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + G+ SA   + +S   ++      Y  YG    +V+ E  IGL++A+  +D  +    
Sbjct: 10  AKAGNESAIQEIFSSFKSILQLKTKNYFFYGGDKEDVLQEAMIGLLKAINAYDENKNASF 69

Query: 102 ATYSMWWIKAAMQEYILRSWS 122
            T+++  IK  +   I  S S
Sbjct: 70  TTFAILCIKRQIITAIKSSNS 90


>gi|313145503|ref|ZP_07807696.1| RNA polymerase ECF-type sigma factor [Bacteroides fragilis 3_1_12]
 gi|313134270|gb|EFR51630.1| RNA polymerase ECF-type sigma factor [Bacteroides fragilis 3_1_12]
          Length = 187

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 18/71 (25%), Positives = 33/71 (46%), Gaps = 2/71 (2%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E  +I  EE+      +   +SVL  R+R I   R +QE   + E ++   ++S    R+
Sbjct: 103 EDEMIAAEEQAEVSQKVDEILSVLTERQREIIYLRYMQE--CSYEEIAEIMQISVPACRK 160

Query: 272 IEARAFKKVQE 282
           +  R   K++ 
Sbjct: 161 LLYRTLLKLKH 171


>gi|255007798|ref|ZP_05279924.1| putative RNA polymerase ECF-type sigma factor [Bacteroides fragilis
           3_1_12]
          Length = 194

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 18/71 (25%), Positives = 33/71 (46%), Gaps = 2/71 (2%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E  +I  EE+      +   +SVL  R+R I   R +QE   + E ++   ++S    R+
Sbjct: 110 EDEMIAAEEQAEVSQKVDEILSVLTERQREIIYLRYMQE--CSYEEIAEIMQISVPACRK 167

Query: 272 IEARAFKKVQE 282
           +  R   K++ 
Sbjct: 168 LLYRTLLKLKH 178


>gi|293408384|ref|ZP_06652223.1| conserved hypothetical protein [Escherichia coli B354]
 gi|291471562|gb|EFF14045.1| conserved hypothetical protein [Escherichia coli B354]
          Length = 131

 Score = 50.6 bits (120), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 18/128 (14%), Positives = 52/128 (40%), Gaps = 2/128 (1%)

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
           + +    KKL             ++ ++ L        +  +   + L  +  G      
Sbjct: 3   DLIRETRKKLGHEPEWSELAVEGISHEDYLEYQQLEGAETLASLDELLNGEGPGIPLAGR 62

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           E E++   + ML  ++S L+ +E+ I       ++ + L+ ++    ++  R+ Q+  + 
Sbjct: 63  ELEDQFVTQQMLQYALSQLSEKEQLILSMYY--QHEMNLKEIALVLGLTEARICQLNKQI 120

Query: 277 FKKVQESI 284
            +K+++ +
Sbjct: 121 AQKIRDFV 128


>gi|314935723|ref|ZP_07843075.1| conserved hypothetical protein [Staphylococcus hominis subsp.
           hominis C80]
 gi|313656288|gb|EFS20028.1| conserved hypothetical protein [Staphylococcus hominis subsp.
           hominis C80]
          Length = 109

 Score = 50.2 bits (119), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 19/86 (22%), Positives = 36/86 (41%), Gaps = 4/86 (4%)

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARRLQENPVT 254
           + +   D+     + +   L E    +   N L + + +V   RE  IF    L     +
Sbjct: 27  DDTDIDDFFSLSDEVEPFALNENTGNQVFFNELDQLIYAVGTRREYYIF---FLLCEGKS 83

Query: 255 LENLSSEFEVSRERVRQIEARAFKKV 280
           +  ++  F +SRER+RQ+      K+
Sbjct: 84  MNEIAKIFNLSRERIRQLLNGLLDKL 109


>gi|225181958|ref|ZP_03735391.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Dethiobacter alkaliphilus AHT 1]
 gi|225167320|gb|EEG76138.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Dethiobacter alkaliphilus AHT 1]
          Length = 71

 Score = 50.2 bits (119), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 14/64 (21%), Positives = 27/64 (42%), Gaps = 2/64 (3%)

Query: 228 LTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L   +  L  RER +   R         T + ++    +SR  V +IE +   K+ E  +
Sbjct: 6   LYEVIKKLKLRERTVLAMRFGLPMGRRKTQKEIAKSLGISRSYVSRIEKKVIAKIAEEFR 65

Query: 286 KQVE 289
           ++ +
Sbjct: 66  QERQ 69


>gi|217033290|ref|ZP_03438721.1| hypothetical protein HP9810_9g43 [Helicobacter pylori 98-10]
 gi|216944231|gb|EEC23656.1| hypothetical protein HP9810_9g43 [Helicobacter pylori 98-10]
          Length = 143

 Score = 50.2 bits (119), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 20/135 (14%), Positives = 55/135 (40%), Gaps = 17/135 (12%)

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
            + + K      +A+ L  +  ++            + AL+   ++ ++  QD +     
Sbjct: 21  LNEHGKEPSDAYLAEVLGENIEKIKEAKTA----SDIYALVPIDEQFNAIEQDEI----- 71

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
                  +K E +     + ++++ ++ RE+ + +    +E  + L  +     ++  R+
Sbjct: 72  ------TKKIEAEELLEHVQKALNQMSEREQILIQLYYFEE--LNLSEIKEILGITESRI 123

Query: 270 RQIEARAFKKVQESI 284
            QI     KKV++S+
Sbjct: 124 SQIIKEVIKKVRKSL 138


>gi|218291391|ref|ZP_03495334.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
 gi|218238746|gb|EED05962.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alicyclobacillus acidocaldarius LAA1]
          Length = 177

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 26/77 (33%), Positives = 38/77 (49%), Gaps = 5/77 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGY----GLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            A   LVT ++ LV  IA  YR      G+   E+V+ G + L +A   + PE G R  T
Sbjct: 6   DAQRELVTRNIGLVYYIAQRYRTRAERLGVEFDELVASGFLALCRAALFYRPEVG-RFVT 64

Query: 104 YSMWWIKAAMQEYILRS 120
           ++   I   M+  ILR+
Sbjct: 65  FAAPTIAREMKRLILRT 81


>gi|319647795|ref|ZP_08002013.1| YvrI protein [Bacillus sp. BT1B_CT2]
 gi|317390136|gb|EFV70945.1| YvrI protein [Bacillus sp. BT1B_CT2]
          Length = 193

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 15/95 (15%), Positives = 39/95 (41%), Gaps = 2/95 (2%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
            +S    +    D         E      +  ML  +   L  +++++     +  + V+
Sbjct: 92  DDSPNLPEPPRGDLLDDVLEQEEDLSEHLQDPMLYEAFLQLTDKQKKVLAQIYI--HGVS 149

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           ++ ++     SR+ + +I  RA +K++E +  + E
Sbjct: 150 MQEIADSLGESRQNISRIHKRALEKIRELLNSKAE 184


>gi|213023552|ref|ZP_03337999.1| RNA polymerase factor sigma-32 [Salmonella enterica subsp. enterica
           serovar Typhi str. 404ty]
          Length = 33

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 15/33 (45%), Positives = 23/33 (69%)

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           TL+ L+  + VS ERVRQ+E  A KK++ +I+ 
Sbjct: 1   TLQELADRYGVSAERVRQLEKNAMKKLRAAIEA 33


>gi|223937031|ref|ZP_03628939.1| RNA polymerase, sigma-24 subunit, ECF subfamily [bacterium
           Ellin514]
 gi|223894312|gb|EEF60765.1| RNA polymerase, sigma-24 subunit, ECF subfamily [bacterium
           Ellin514]
          Length = 452

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 18/84 (21%), Positives = 34/84 (40%), Gaps = 11/84 (13%)

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS----RERV 269
                +  K    +L  +M  LN R+R     R    +  +L+ + +    S    + RV
Sbjct: 107 EPEADDAWKQIAPLLDMAMDALNERDRNAIVLRFF--DGKSLQEVGTVLGASEDAAKMRV 164

Query: 270 RQIEARAFKKVQE-SIQKQVELSS 292
                RA  K++   +++ V LS+
Sbjct: 165 ----NRALDKLRNFFVKRGVALSA 184


>gi|291544102|emb|CBL17211.1| RNA polymerase sigma factor, sigma-70 family [Ruminococcus sp.
           18P13]
          Length = 235

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 20/104 (19%), Positives = 41/104 (39%), Gaps = 6/104 (5%)

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
            L    SL+A   +  +  S + + L           +E++E     +     +   +P 
Sbjct: 103 PLNECSSLDAP--ADPEGESTFLELLPDPEALPIYTDLEEQEDAAAVHAAVERLK--SPV 158

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +RR+          ++ +       VS ERVRQI   A +++++
Sbjct: 159 QRRVICLCDFSG--MSQKAAGEALGVSGERVRQIRRAALRELRK 200


>gi|295091495|emb|CBK77602.1| DNA-directed RNA polymerase specialized sigma subunit [Clostridium
           cf. saccharolyticum K10]
          Length = 121

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 13/70 (18%), Positives = 33/70 (47%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
              L+ +++ L    A  +    L + ++ S   +GL++A ++FD  R    +T++   +
Sbjct: 6   QRELIENNIGLAKYTAKKFHTMPLEMDDIYSAAYLGLVKAAERFDEGRAVSFSTFACRVM 65

Query: 110 KAAMQEYILR 119
           +  ++    R
Sbjct: 66  ENEIKMLWRR 75


>gi|253583804|ref|ZP_04861002.1| DNA-directed RNA polymerase sigma subunit RpoE [Fusobacterium
           varium ATCC 27725]
 gi|251834376|gb|EES62939.1| DNA-directed RNA polymerase sigma subunit RpoE [Fusobacterium
           varium ATCC 27725]
          Length = 197

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 20/81 (24%), Positives = 37/81 (45%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + G+ SA   + +S   ++      Y  YG    +V+ E  IGL++A+  +D  +    
Sbjct: 10  AKAGNESAIQEIFSSFKSILQLKTKNYFFYGGDKEDVLQEAMIGLLKAINAYDETKNASF 69

Query: 102 ATYSMWWIKAAMQEYILRSWS 122
            T+++  IK  +   I  S S
Sbjct: 70  TTFAILCIKRQIITAIKSSNS 90


>gi|86158891|ref|YP_465676.1| hypothetical protein Adeh_2469 [Anaeromyxobacter dehalogenans
           2CP-C]
 gi|85775402|gb|ABC82239.1| hypothetical protein Adeh_2469 [Anaeromyxobacter dehalogenans
           2CP-C]
          Length = 142

 Score = 50.2 bits (119), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 12/34 (35%), Positives = 21/34 (61%)

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           TLE + S   ++RER+RQ+E R   K++   + +
Sbjct: 95  TLEEVGSIMNLTRERIRQVETRGLLKLRAIAEDE 128


>gi|257469599|ref|ZP_05633691.1| RNA polymerase factor sigma-70 [Fusobacterium ulcerans ATCC 49185]
 gi|317063835|ref|ZP_07928320.1| RNA polymerase factor sigma-70 [Fusobacterium ulcerans ATCC 49185]
 gi|313689511|gb|EFS26346.1| RNA polymerase factor sigma-70 [Fusobacterium ulcerans ATCC 49185]
          Length = 193

 Score = 49.8 bits (118), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 20/81 (24%), Positives = 37/81 (45%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            ++GD  A   +  S  R+++     Y  YG    +V+ E  IGL +A+  +D  +    
Sbjct: 9   AKNGDDKAFIEIFQSLKRIILYRTKKYFFYGGDKDDVMQEAMIGLFKAINAYDENKTASF 68

Query: 102 ATYSMWWIKAAMQEYILRSWS 122
            T+++  IK  +   +  S S
Sbjct: 69  KTFALLCIKRHLITVLKNSNS 89


>gi|67920930|ref|ZP_00514449.1| Helix-turn-helix, Fis-type [Crocosphaera watsonii WH 8501]
 gi|67857047|gb|EAM52287.1| Helix-turn-helix, Fis-type [Crocosphaera watsonii WH 8501]
          Length = 139

 Score = 49.8 bits (118), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 22/144 (15%), Positives = 56/144 (38%), Gaps = 10/144 (6%)

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWL 204
           Q   +   +      IA+ L +S  E   +          SL+  I++  +  +   + +
Sbjct: 3   QEFREKFNRQPTDSEIAQVLEISLKEWQEIKLAFQNREPVSLDVKISNGGEGQTSLGELV 62

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
              +    Q+  E + R      L +++  L  + R I E   L++  +T    + +  +
Sbjct: 63  PDINYRSFQLAQEDQIR------LQQALGQLEEKTRNILEFVFLKD--LTQRETAEQLGI 114

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S   V +   +  + ++ ++ K++
Sbjct: 115 SVVTVSRRVKKGLEVLKSNMGKEI 138


>gi|325263767|ref|ZP_08130500.1| RNA polymerase sigma-H factor [Clostridium sp. D5]
 gi|324030805|gb|EGB92087.1| RNA polymerase sigma-H factor [Clostridium sp. D5]
          Length = 205

 Score = 49.8 bits (118), Expect = 4e-04,   Method: Composition-based stats.
 Identities = 22/91 (24%), Positives = 40/91 (43%), Gaps = 1/91 (1%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L   +RE G+      L+  +  +V K A      G    +++ EG IGL++AV+ + P 
Sbjct: 13  LISEFRE-GNSDIMDYLMVKYKSMVRKKARAMYLIGGENEDLIQEGMIGLIKAVRDYSPS 71

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           +G   A+++   +   M   I  S     + 
Sbjct: 72  QGASFASFAELCVSRQMYTAIEASKRKKHMP 102


>gi|188588718|ref|YP_001921821.1| specialized sigma subunit of RNA polymerase [Clostridium botulinum
           E3 str. Alaska E43]
 gi|188498999|gb|ACD52135.1| specialized sigma subunit of RNA polymerase [Clostridium botulinum
           E3 str. Alaska E43]
          Length = 190

 Score = 49.8 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 18/84 (21%), Positives = 35/84 (41%), Gaps = 2/84 (2%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
            + D    +  L E    K   + L +++  LN RER +   +       T   ++   E
Sbjct: 104 YIIDMISPKPSLDELILTKENNSYLFQALGKLNERERSVVSLKYGAVLKNT--EIAKIME 161

Query: 264 VSRERVRQIEARAFKKVQESIQKQ 287
           +S   V  I  R+ KK+++ +  +
Sbjct: 162 LSESNVSVILCRSLKKLKKILVSE 185


>gi|220916592|ref|YP_002491896.1| hypothetical protein A2cp1_1486 [Anaeromyxobacter dehalogenans
           2CP-1]
 gi|219954446|gb|ACL64830.1| conserved hypothetical protein [Anaeromyxobacter dehalogenans
           2CP-1]
          Length = 189

 Score = 49.8 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 12/34 (35%), Positives = 21/34 (61%)

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           TLE + S   ++RER+RQ+E R   K++   + +
Sbjct: 143 TLEEVGSIMNLTRERIRQVETRGLLKLRAIAEDE 176


>gi|119947183|ref|YP_944863.1| sigma-28 (sigma F) factor [Psychromonas ingrahamii 37]
 gi|119865787|gb|ABM05264.1| predicted sigma-28 (sigma F) factor [Psychromonas ingrahamii 37]
          Length = 243

 Score = 49.8 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 36/236 (15%), Positives = 85/236 (36%), Gaps = 39/236 (16%)

Query: 53  LVTSHLRLVVKIAMG--YRGYGLPISEVVSEGNIGLMQAVKKFD-PERGFRLATYSMWWI 109
           LV  +L LV  +     Y        ++   G I L++ +++F   +        +   I
Sbjct: 28  LVNKYLYLVHAVIKKMGYINCISDNDDMKQVGLIALLKMIRRFPVMDDEKEFIRLTYIRI 87

Query: 110 KAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           + ++ + I  R W      +  ++K     L + K  +Q++     +      + +   +
Sbjct: 88  RGSILDEIRSRDWR-----SEESRKNASTFLAQEKALMQSL----GRLPNKSEMLENKVL 138

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           SE +     C + G               S+  D L+ D+     +  E     +    L
Sbjct: 139 SEQQYEEARCAINGKV------------FSELSDQLLKDNAQSVDICTEI----DNTQCL 182

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLS----SEFEVSRERVRQIEARAFKKV 280
           + ++  L   E  +     + E  ++ + ++    + F     R+ +I+  A +K+
Sbjct: 183 SVALKQLT--EEEVLILHLMYEKDMSFKEMALATNNNF----SRINKIQREAHRKL 232


>gi|253583909|ref|ZP_04861107.1| RNA polymerase sigma-H factor [Fusobacterium varium ATCC 27725]
 gi|251834481|gb|EES63044.1| RNA polymerase sigma-H factor [Fusobacterium varium ATCC 27725]
          Length = 193

 Score = 49.8 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 19/81 (23%), Positives = 37/81 (45%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            ++GD  A   +  S  ++++     Y  YG    +V+ E  IGL +A+  +D  +    
Sbjct: 9   AKNGDDKAFIEIFQSMKKIILYRTKKYFFYGGDKDDVMQEAMIGLFKAINAYDENKTASF 68

Query: 102 ATYSMWWIKAAMQEYILRSWS 122
            T+++  IK  +   +  S S
Sbjct: 69  KTFALLCIKRHLITTLKNSNS 89


>gi|197121799|ref|YP_002133750.1| hypothetical protein AnaeK_1390 [Anaeromyxobacter sp. K]
 gi|196171648|gb|ACG72621.1| hypothetical protein AnaeK_1390 [Anaeromyxobacter sp. K]
          Length = 189

 Score = 49.8 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 12/34 (35%), Positives = 21/34 (61%)

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           TLE + S   ++RER+RQ+E R   K++   + +
Sbjct: 143 TLEEVGSIMNLTRERIRQVETRGLLKLRAIAEDE 176


>gi|220930948|ref|YP_002507856.1| sporulation sigma factor SigH [Halothermothrix orenii H 168]
 gi|219992258|gb|ACL68861.1| sporulation sigma factor SigH [Halothermothrix orenii H 168]
          Length = 215

 Score = 49.8 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 28/155 (18%), Positives = 61/155 (39%), Gaps = 7/155 (4%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L  +E   L  +    GD  A   L+  +   V+  +  Y   G    ++V EG IGL +
Sbjct: 17  LGDEELVELVHK----GDKIAEETLIKRYKNFVLAKSRSYFLVGADREDIVQEGMIGLYK 72

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHL 146
           A++ +  +R      ++   I   +   I  +         +  +  R  ++    +  L
Sbjct: 73  AIRDYKVDRLASFRAFAELCITRQIITAIKAATRQKHQPLNSYVSLNRPIYDEESDRTLL 132

Query: 147 QAITDNNLKPEQVVAIAKK-LNVSESEVISMNCRL 180
             +    L   + + ++K+  N+ E+++  M  +L
Sbjct: 133 DVLNGGKLSDPEELFVSKETYNLIENKITEMLSQL 167


>gi|317968505|ref|ZP_07969895.1| RNA polymerase sigma factor, sigma-70 family protein [Synechococcus
           sp. CB0205]
          Length = 74

 Score = 49.8 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 12/63 (19%), Positives = 25/63 (39%), Gaps = 8/63 (12%)

Query: 231 SMSVLNPRERRIFEARRLQ--------ENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            +  L   + R+ + R           + P++L  +     +SR+RVR +E      ++ 
Sbjct: 4   LLDQLPDLQGRVLKMRYAIPCRDVPDPDEPMSLTGIGRVLGISRDRVRNLERDGLAGLRR 63

Query: 283 SIQ 285
             Q
Sbjct: 64  LSQ 66


>gi|291550112|emb|CBL26374.1| RNA polymerase, sigma 30 subunit, SigH [Ruminococcus torques L2-14]
          Length = 203

 Score = 49.8 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 18/85 (21%), Positives = 37/85 (43%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           ++G+      L+  +  +V K A      G    +++ EG IGL++AV+ FD  +    +
Sbjct: 17  KNGNQEIMDYLMVKYKSMVRKKARAMYLLGGENEDLIQEGMIGLIKAVRDFDVTQKTSFS 76

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIG 127
           +++   +   M   I  S     + 
Sbjct: 77  SFAELCVSRQMYSAIEASNRKKHLP 101


>gi|162449915|ref|YP_001612282.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
 gi|161160497|emb|CAN91802.1| RNA polymerase sigma factor [Sorangium cellulosum 'So ce 56']
          Length = 222

 Score = 49.8 bits (118), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 36/223 (16%), Positives = 80/223 (35%), Gaps = 24/223 (10%)

Query: 58  LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYI 117
           L+LV K      G  +P+ ++V+ G+  L++ V+  DP R      Y+   ++ A+ + +
Sbjct: 16  LQLVAKRIARRLGRRIPVEDLVALGHPALLEIVRTHDPSR-STFEAYAKRKLRWAIFDGV 74

Query: 118 LRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
            R         +A  +             +   D+   P    A A +L         + 
Sbjct: 75  RRETRW----RSAAARASALAASARFAEGRGADDDADAPATQEAYAARLG-------DLL 123

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
              A   +L  L +  D          V           E+  R      +  ++  L  
Sbjct: 124 AGHAAAMALGLLSSHGD----------VAAVPDAADDPEERASRAELAQAVRHAVRELPE 173

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           RER + E    ++     + ++ +  +S+    ++ ++A +++
Sbjct: 174 RERTLVERHYFEDER--FDQIAQDLGISKSWASRLHSQAIERL 214


>gi|313625371|gb|EFR95162.1| RNA polymerase sigma-H factor [Listeria innocua FSL J1-023]
          Length = 139

 Score = 49.4 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 16/96 (16%), Positives = 37/96 (38%), Gaps = 2/96 (2%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           +E  +L       GD  A     + +  ++   +  Y   G    +++ E  IGL +A++
Sbjct: 8   EEMAML--ELARSGDTEALEYFFSKYQSVIYWKSTQYFLQGAERDDLIQEAMIGLFKAIR 65

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
            +D  +     +++   I   +   + R+     I 
Sbjct: 66  DYDESKEASFRSFAEMCINRQLLSAVKRASRQKNIP 101


>gi|187779022|ref|ZP_02995495.1| hypothetical protein CLOSPO_02617 [Clostridium sporogenes ATCC
           15579]
 gi|187772647|gb|EDU36449.1| hypothetical protein CLOSPO_02617 [Clostridium sporogenes ATCC
           15579]
          Length = 176

 Score = 49.4 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 21/84 (25%), Positives = 42/84 (50%), Gaps = 7/84 (8%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
            + L K+YRE GD  A  +++ + + L++K A  Y+       ++V  G + +++A   +
Sbjct: 1   MHQLIKKYRE-GDNRALQKIIDNFIPLILKEASKYKIKCYDYEDLVQHGYLSVIKAANMY 59

Query: 94  D-PERGFRLATYSMWWIKAAMQEY 116
              ++ F+      + IKA  Q Y
Sbjct: 60  KGEDKNFKF-----YCIKAIKQNY 78


>gi|255022533|ref|ZP_05294519.1| RNA polymerase factor sigma-70 [Listeria monocytogenes FSL J1-208]
          Length = 191

 Score = 49.4 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 28/151 (18%), Positives = 60/151 (39%), Gaps = 11/151 (7%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           QEE  + +  R  GD  A     + +  ++   +  Y   G    +++ E  IGL +A++
Sbjct: 7   QEELAMLELAR-SGDTEALEYFFSKYQSVIYWKSTQYFLQGAERDDLIQEAMIGLFKAIR 65

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--------TTANQKRLFFNLRRLK 143
            +D  +     +++   I   +   + R+     I         T   +  + + L  + 
Sbjct: 66  DYDKTKEASFRSFAEMCINRQLLSAVKRASRQKNIPLNNSVSLDTPMAEDDVDWTLLDVI 125

Query: 144 GHLQAITDNN--LKPEQVVAIAKKLNVSESE 172
               A T  +  +K E ++ +A++L    SE
Sbjct: 126 SEKAAETPEDFLIKNEDLIHVARQLEKVTSE 156


>gi|332652978|ref|ZP_08418723.1| hypothetical protein HMPREF0866_00674 [Ruminococcaceae bacterium
           D16]
 gi|332518124|gb|EGJ47727.1| hypothetical protein HMPREF0866_00674 [Ruminococcaceae bacterium
           D16]
          Length = 291

 Score = 49.4 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 50/276 (18%), Positives = 87/276 (31%), Gaps = 47/276 (17%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLV----VKIAMGYRGYGLP------------ISEVV 79
            L +R   +G+ +A  +L   +  +V      IA  Y                  +SE+ 
Sbjct: 5   ELLERIA-NGEEAALTKLCLINTGIVKNRAWSIARQYHCLRQTKYGGLSDYAKETLSELE 63

Query: 80  SEGNIGLMQAVKK--FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFF 137
           S G + L++ V+   +D E+G R  TY   ++  AM+ ++ RS             R   
Sbjct: 64  SVGKLALVECVRAGGYDAEKG-RFTTYVTPFLDGAMRRHLERSMGT------LALDRDSM 116

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R    L       L       I   L +                S+  L    D   
Sbjct: 117 GLVRKAQRLYYQEGKEL-----CEICASLGIPFRTAARAITYPTHFFSVYDLQGPDDDGD 171

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTL 255
              +          E+ ++    R      L      L+ +E+ I              L
Sbjct: 172 IFERIASTRLSGSAEEAVV----RMVTMECLREEFLRLSKKEQDILGRYFGVYGFPKADL 227

Query: 256 ENLS-----SEFEVSRERVRQIEARAFKKVQESIQK 286
           + ++      E  V  ER    + +A K++Q+  Q 
Sbjct: 228 QEIAMRNLLKESGV--ERA---KDQAIKRLQDQCQS 258


>gi|296328928|ref|ZP_06871436.1| DNA-directed RNA polymerase sigma subunit RpoE [Fusobacterium
           nucleatum subsp. nucleatum ATCC 23726]
 gi|296153917|gb|EFG94727.1| DNA-directed RNA polymerase sigma subunit RpoE [Fusobacterium
           nucleatum subsp. nucleatum ATCC 23726]
          Length = 204

 Score = 49.4 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 18/78 (23%), Positives = 38/78 (48%), Gaps = 1/78 (1%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + GD  A   ++  + +L+   A  Y   G    ++V EG +GL++A+K +D  +    
Sbjct: 11  AQSGDNEAIDLILKEYSKLLSFNAQKYYLVGAEKEDLVQEGILGLLKAIKFYDETK-SSF 69

Query: 102 ATYSMWWIKAAMQEYILR 119
           ++++   I+  M   I +
Sbjct: 70  SSFAFLCIRREMISAIRK 87


>gi|226948021|ref|YP_002803112.1| RNA polymerase sigma-70 factor family [Clostridium botulinum A2
           str. Kyoto]
 gi|226842855|gb|ACO85521.1| RNA polymerase sigma-70 factor family [Clostridium botulinum A2
           str. Kyoto]
          Length = 179

 Score = 49.4 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 28/139 (20%), Positives = 57/139 (41%), Gaps = 8/139 (5%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
            Y L K+YR +GD+ + + ++ +   L++K A  +R       ++V  G + +++AV  F
Sbjct: 1   MYNLLKKYR-NGDMGSLNEIIENFNPLILKEASRWRIGCYEYEDLVQHGYLSVIKAVNIF 59

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
             E     + +  + I A    Y       +K      +      L +   ++  I D  
Sbjct: 60  KGEE----SKFVPYCINAIKTNYKALLKGEIK---HHREIPDENILNKGNEYMFTIEDEI 112

Query: 154 LKPEQVVAIAKKLNVSESE 172
           +  E+   I + L+    E
Sbjct: 113 IAYEKTKEIYEALDKLTQE 131


>gi|218134246|ref|ZP_03463050.1| hypothetical protein BACPEC_02138 [Bacteroides pectinophilus ATCC
           43243]
 gi|217991621|gb|EEC57627.1| hypothetical protein BACPEC_02138 [Bacteroides pectinophilus ATCC
           43243]
          Length = 228

 Score = 49.4 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 43/265 (16%), Positives = 94/265 (35%), Gaps = 64/265 (24%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L + YR+ G   +   L   +   V + A      G    +++ EG IGL +AV+ +D 
Sbjct: 17  ALIQMYRD-GSRDSIDELFERYKGCVRRKAHAMYIAGGDEEDLIQEGMIGLYKAVQDYDA 75

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
            R    AT++   I   M   + +S                          Q + ++   
Sbjct: 76  GREASFATFASMCINRNMCTAVAKSNR---------------------KKYQLLNES--- 111

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
                             +S++  +A DE       + D+  +   D +V       + +
Sbjct: 112 ------------------LSLDMPVAVDE------EAYDEPQTHLIDVVVASSAQDPENM 147

Query: 216 IEKEERKNRRNMLTRSMSV-LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
              +ER +   ++  ++   L+  E+++ +      + V    ++          +Q ++
Sbjct: 148 YIDKERVD---VIYEAIRTCLSEYEKQVLDLYIDGNDYV---AIARLLN------KQPKS 195

Query: 275 --RAFKKVQESIQKQVELSSSPPLL 297
              A ++++  I+K  E S +P L 
Sbjct: 196 VDNALQRIRSKIRKAAEGSRTPDLF 220


>gi|331090786|ref|ZP_08339633.1| hypothetical protein HMPREF9477_00276 [Lachnospiraceae bacterium
           2_1_46FAA]
 gi|330399894|gb|EGG79553.1| hypothetical protein HMPREF9477_00276 [Lachnospiraceae bacterium
           2_1_46FAA]
          Length = 202

 Score = 49.4 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 21/97 (21%), Positives = 38/97 (39%), Gaps = 3/97 (3%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
             EE +   R   +G+      ++  +  LV + A      G    +++ EG IGL +A+
Sbjct: 8   ADEELL---RCLRNGEKEITEYIINKYKNLVKEKAKAMFLLGGDNDDLIQEGMIGLFKAI 64

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           + +D E+      ++   I   M   I  S     I 
Sbjct: 65  RDYDEEQETSFYHFAELCISRQMYTAIEASKRQKHIP 101


>gi|298247626|ref|ZP_06971431.1| RNA polymerase, sigma 32 subunit, RpoH [Ktedonobacter racemifer DSM
           44963]
 gi|297550285|gb|EFH84151.1| RNA polymerase, sigma 32 subunit, RpoH [Ktedonobacter racemifer DSM
           44963]
          Length = 450

 Score = 49.4 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 24/128 (18%), Positives = 46/128 (35%), Gaps = 22/128 (17%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLS--------------------AAH 51
             + L+ Y+ ++   P L  ++E  LA +  +                         A +
Sbjct: 325 SALALADYLRDL--TPTLSPEQERQLAHKVTQAEREKKRAEYRSVQPDSQVIEEGKLAYY 382

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +L  +    V  I   Y   G  + +++   N GL  A+ KF  ++      Y+  WI  
Sbjct: 383 QLFMACQEQVFTIIKEYLAPGRDVGKLLDAANRGLTYAIYKFGLKQQVSFRAYASHWIHL 442

Query: 112 AMQEYILR 119
            + E +L 
Sbjct: 443 EIMELVLE 450



 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 16/75 (21%), Positives = 35/75 (46%), Gaps = 2/75 (2%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L  +   +  ++  + E+   +  + R +S+L  RER++   R +Q    T   +  E  
Sbjct: 90  LPLETLEEHAIIPHELEQGEAQVRVQRLLSLLPERERQVLLLRYMQG--YTAAEVGQELG 147

Query: 264 VSRERVRQIEARAFK 278
           ++   VR ++ RA +
Sbjct: 148 LTPGHVRVLQLRALR 162


>gi|291544496|emb|CBL17605.1| RNA polymerase sigma factor, sigma-70 family [Ruminococcus sp.
           18P13]
          Length = 204

 Score = 49.4 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 30/153 (19%), Positives = 55/153 (35%), Gaps = 10/153 (6%)

Query: 34  EYVLAKRYREHGDLSAA----------HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           E  L KR  E  D   A            L++ +++L+   A       +   ++  EG 
Sbjct: 6   EQDLGKRQTERSDEELALSAAKCSDSTAELISRYMKLIWVKANTMANAVVDAEDLAQEGM 65

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLK 143
           +GLM A+  FDP R  + +T++   I   M+  ++R+         A       N     
Sbjct: 66  LGLMNAIAHFDPNREIKFSTFADVCITNKMKSALIRTRHTALPVEDAESAAQVQNEVEDD 125

Query: 144 GHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
              + +       E    +   L+  E E+  +
Sbjct: 126 DPERILLRKERLHELYREMDLVLSKRELEIFKL 158


>gi|255030922|ref|ZP_05302873.1| RNA polymerase factor sigma-70 [Listeria monocytogenes LO28]
          Length = 117

 Score = 49.4 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 18/96 (18%), Positives = 39/96 (40%), Gaps = 1/96 (1%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           QEE  + +  R  GD  A     + +  ++   +  Y   G    +++ E  IGL +A++
Sbjct: 7   QEELAMLELAR-SGDTEALEYFFSKYQSVIYWKSTQYFLQGAERDDLIQEAMIGLFKAIR 65

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
            +D  +     +++   I   +   + R+     I 
Sbjct: 66  DYDKTKEASFRSFAEMCINRQLLSAVKRASRQKNIP 101


>gi|121535681|ref|ZP_01667485.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermosinus
           carboxydivorans Nor1]
 gi|121305712|gb|EAX46650.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermosinus
           carboxydivorans Nor1]
          Length = 243

 Score = 49.4 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 24/156 (15%), Positives = 60/156 (38%), Gaps = 10/156 (6%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            EE V+    +++ +  A   L+  +   V   A  Y   G    +++ EG IGL +A++
Sbjct: 18  DEEIVI--DAKDNDNAVAQEYLINKYRNFVRAKARSYFLIGADREDIIQEGMIGLYKAIR 75

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQAI 149
            F  ++      ++   +   +   I  +     I   +  +  +  ++    +  L  +
Sbjct: 76  DFRNDKLSSFRAFAELCVTRQIITAIKTATRQKHIPLNSYVSLNKPIYDEDSDRTLLDVL 135

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
           + + +   +      +L +S  E I +  ++    S
Sbjct: 136 SGSKISDPE------ELVISREEFIDIEAKMGQILS 165


>gi|19704850|ref|NP_602345.1| RNA polymerase factor sigma-70 [Fusobacterium nucleatum subsp.
           nucleatum ATCC 25586]
 gi|19712731|gb|AAL93644.1| RNA polymerase sigma-H factor [Fusobacterium nucleatum subsp.
           nucleatum ATCC 25586]
          Length = 204

 Score = 49.4 bits (117), Expect = 6e-04,   Method: Composition-based stats.
 Identities = 18/78 (23%), Positives = 38/78 (48%), Gaps = 1/78 (1%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + GD  A   ++  + +L+   A  Y   G    ++V EG +GL++A+K +D  +    
Sbjct: 11  AQSGDNEAIDLILKEYSKLLSFNAQKYYLVGAEKEDLVQEGILGLLKAIKFYDETK-SSF 69

Query: 102 ATYSMWWIKAAMQEYILR 119
           ++++   I+  M   I +
Sbjct: 70  SSFAFLCIRREMISAIRK 87


>gi|167758884|ref|ZP_02431011.1| hypothetical protein CLOSCI_01229 [Clostridium scindens ATCC 35704]
 gi|167663624|gb|EDS07754.1| hypothetical protein CLOSCI_01229 [Clostridium scindens ATCC 35704]
          Length = 203

 Score = 49.4 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 30/156 (19%), Positives = 54/156 (34%), Gaps = 7/156 (4%)

Query: 23  IRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           + K   +  ++   L  R R+ GD +    ++  +  LV K A      G    +++ EG
Sbjct: 1   MAKFEQMTDEQ---LICRLRD-GDKTVIDYVMEKYKNLVRKEANAMYLLGGENDDLIQEG 56

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
            IGL +AV+ +D  +     +++   I   M   I  S                 N  ++
Sbjct: 57  MIGLFKAVQDYDVRQETSFYSFAKLCITRQMYSAIEASKRKKHSPLNTYISLYEKNDEKV 116

Query: 143 KGHLQAITDNNLKPEQV---VAIAKKLNVSESEVIS 175
                        PE++      A  L     E +S
Sbjct: 117 SLIETMEAGGESNPEELLVSREYAMLLESKLEENLS 152


>gi|229063910|ref|ZP_04200211.1| RNA polymerase sigma factor [Bacillus cereus AH603]
 gi|228716380|gb|EEL68088.1| RNA polymerase sigma factor [Bacillus cereus AH603]
          Length = 156

 Score = 49.4 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 19/84 (22%), Positives = 40/84 (47%), Gaps = 2/84 (2%)

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           + +V +         E+ E ++        MSVL+ RER I   R      +    ++SE
Sbjct: 74  ECVVQERYVCTDEYEERFECEDAGTRAKDFMSVLDERERHIISERFFTGKNMG--EIASE 131

Query: 262 FEVSRERVRQIEARAFKKVQESIQ 285
             ++  +VR +  +A +K+++S++
Sbjct: 132 MGMTYYQVRWVYRQALEKMRDSVR 155


>gi|310659524|ref|YP_003937245.1| RNA polymerase factor sigma-70 [Clostridium sticklandii DSM 519]
 gi|308826302|emb|CBH22340.1| RNA polymerase factor sigma-70 [Clostridium sticklandii]
          Length = 229

 Score = 49.4 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 14/86 (16%), Positives = 35/86 (40%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + GD  + + ++  +   V   A  +   G    +++ EG IGL +A++ +D E+    
Sbjct: 41  AKAGDEKSLNHILKKYRNFVRSKAKPFFIVGADKEDILQEGMIGLFKAIRDYDEEKTVSF 100

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIG 127
             ++   +   +   +  +     I 
Sbjct: 101 RAFAELCVTRQIITAVKTATRQKHIP 126


>gi|310826848|ref|YP_003959205.1| putative RNA polymerase [Eubacterium limosum KIST612]
 gi|308738582|gb|ADO36242.1| putative RNA polymerase [Eubacterium limosum KIST612]
          Length = 195

 Score = 49.4 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 36/261 (13%), Positives = 81/261 (31%), Gaps = 76/261 (29%)

Query: 33  EEYVLAKRY---REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           E+Y L   +    ++ D +A  +L+ +   L++ +   Y        + + +G + +M+A
Sbjct: 3   EKYALIDTWVQEAKNNDKAAKEQLINTFKPLILSVMQKYIYDTDAYEDALQDGALVVMEA 62

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           V+ +DP+ G     Y                           + RLF +       ++  
Sbjct: 63  VQAYDPDLGVVFPFYL--------------------------KNRLFHHFVNAAKAIKKQ 96

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
            +N                                     +    ++     +       
Sbjct: 97  QENERA----------------------------------VTGGGEDGENSLEQYPDAGP 122

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR--- 266
             E+ ++ +E+      ML    +    R   +   R  +E   +L  ++   ++S    
Sbjct: 123 SPEKEMVRQEKNAVLEQMLAEIRA---ER-ADVIRLRYFEE--KSLNEIAQILDISPCLA 176

Query: 267 -ERV-RQIEARAFKKVQESIQ 285
              V R IE  A +K +  +Q
Sbjct: 177 GVHVHRGIE--ALRKNKHRLQ 195


>gi|53712284|ref|YP_098276.1| RNA polymerase ECF-type sigma factor [Bacteroides fragilis YCH46]
 gi|60680462|ref|YP_210606.1| putative RNA polymerase ECF-type sigma factor [Bacteroides fragilis
           NCTC 9343]
 gi|253563677|ref|ZP_04841134.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 3_2_5]
 gi|265762475|ref|ZP_06091043.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 2_1_16]
 gi|52215149|dbj|BAD47742.1| RNA polymerase ECF-type sigma factor [Bacteroides fragilis YCH46]
 gi|60491896|emb|CAH06655.1| putative RNA polymerase ECF-type sigma factor [Bacteroides fragilis
           NCTC 9343]
 gi|251947453|gb|EES87735.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 3_2_5]
 gi|263255083|gb|EEZ26429.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 2_1_16]
 gi|301161996|emb|CBW21540.1| putative RNA polymerase ECF-type sigma factor [Bacteroides fragilis
           638R]
          Length = 193

 Score = 49.4 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 17/71 (23%), Positives = 33/71 (46%), Gaps = 2/71 (2%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E  +I  EE+      +   +S+L  R+R I   R +QE   + E ++   ++S    R+
Sbjct: 109 EDEIIAAEEQAEVSQKVDEILSILTERQREIIYLRYMQE--CSYEEIAEIMQISVPACRK 166

Query: 272 IEARAFKKVQE 282
           +  R   K++ 
Sbjct: 167 LLYRTLLKLKH 177


>gi|46370560|gb|AAS90114.1| RNA polymerase sigma-G factor [Pasteuria penetrans]
          Length = 92

 Score = 49.4 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 14/56 (25%), Positives = 30/56 (53%), Gaps = 1/56 (1%)

Query: 26 IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
          +P+L+ QE  +L  + +  G++ A  +LV  +LRLV+ +   +   G  + ++   
Sbjct: 38 LPVLKNQEMRLLFTQLQ-SGEIWARQKLVHGNLRLVLSVIQRFHNRGESVDDLFQV 92


>gi|256763531|ref|ZP_05504111.1| predicted protein [Enterococcus faecalis T3]
 gi|307274364|ref|ZP_07555552.1| hypothetical protein HMPREF9514_03085 [Enterococcus faecalis
           TX0855]
 gi|307287484|ref|ZP_07567532.1| hypothetical protein HMPREF9505_00942 [Enterococcus faecalis
           TX0109]
 gi|256684782|gb|EEU24477.1| predicted protein [Enterococcus faecalis T3]
 gi|306501492|gb|EFM70793.1| hypothetical protein HMPREF9505_00942 [Enterococcus faecalis
           TX0109]
 gi|306508957|gb|EFM78039.1| hypothetical protein HMPREF9514_03085 [Enterococcus faecalis
           TX0855]
          Length = 864

 Score = 49.4 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 12/24 (50%), Positives = 14/24 (58%)

Query: 252 PVTLENLSSEFEVSRERVRQIEAR 275
             TLE +     VSRER+RQIE  
Sbjct: 282 GQTLEEIGQTMGVSRERIRQIEKN 305


>gi|89096017|ref|ZP_01168910.1| RNA polymerase sigma-70 factor [Bacillus sp. NRRL B-14911]
 gi|89088871|gb|EAR67979.1| RNA polymerase sigma-70 factor [Bacillus sp. NRRL B-14911]
          Length = 216

 Score = 49.4 bits (117), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 27/171 (15%), Positives = 59/171 (34%), Gaps = 18/171 (10%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           ++GD  A+  L+  +   V   A  +   G    ++  EG IGL +A++ F  ++     
Sbjct: 26  QNGDGMASEYLMKKYRHFVRAKASKFFLIGGDKDDLFQEGMIGLYKAIRDFKEDKLASFK 85

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ--------------A 148
            ++   I   +   +  +    ++   +              H                 
Sbjct: 86  VFAELCITRQIITAVKTATRQKQMPLNSYISLDKPIYEDESKHTLMDILPGTMVTDPAIL 145

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISM----NCRLAGDESLNALINSSDK 195
           I +     +    IA+KL+  E +V+ +    +  +   E L+  + S D 
Sbjct: 146 IVNQENTADIEEKIAEKLSDLERKVLDLYVAGHSYIEISEELDTHVKSIDN 196


>gi|152964709|ref|YP_001360493.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Kineococcus
           radiotolerans SRS30216]
 gi|151359226|gb|ABS02229.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Kineococcus
           radiotolerans SRS30216]
          Length = 227

 Score = 49.0 bits (116), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 18/90 (20%), Positives = 35/90 (38%), Gaps = 2/90 (2%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           V D    E    +          + R +  L P+ R I   R      ++ E      ++
Sbjct: 140 VPDAATTEPGPEQLALDTFDAETVGRLLDTLPPKLREIITLRVGAG--MSAEETGRALDM 197

Query: 265 SRERVRQIEARAFKKVQESIQKQVELSSSP 294
           +   VR  + RA +K++++  + V L  +P
Sbjct: 198 TAGAVRVAQHRAMQKLRKTAAEDVSLQVAP 227


>gi|313639756|gb|EFS04507.1| RNA polymerase sigma-H factor [Listeria seeligeri FSL S4-171]
          Length = 148

 Score = 49.0 bits (116), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 16/96 (16%), Positives = 37/96 (38%), Gaps = 2/96 (2%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           +E  +L       GD  A     + +  ++   +  Y   G    +++ E  IGL +A++
Sbjct: 8   EEMTML--ELARSGDTDALEYFFSKYQAVIYWKSTQYFLQGAERDDLIQEAMIGLFKAIR 65

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
            +D  +     +++   I   +   + R+     I 
Sbjct: 66  DYDKTKEASFRSFAEMCINRQLLSAVKRASRQKNIP 101


>gi|229105854|ref|ZP_04236481.1| RNA polymerase sigma factor [Bacillus cereus Rock3-28]
 gi|228677575|gb|EEL31825.1| RNA polymerase sigma factor [Bacillus cereus Rock3-28]
          Length = 156

 Score = 49.0 bits (116), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 19/69 (27%), Positives = 34/69 (49%), Gaps = 2/69 (2%)

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           E+ E +         MSVLN RER I   R      +    ++ E  ++  +VR I  +A
Sbjct: 89  EQFESEETGMRAQDFMSVLNKRERHIISERFFVGKKMG--EIACEMGMTYYQVRWIYRQA 146

Query: 277 FKKVQESIQ 285
            +K+++S++
Sbjct: 147 LEKMRDSVK 155


>gi|20065995|ref|NP_612861.1| putative sigma factor [Clostridium phage phi3626]
 gi|168211320|ref|ZP_02636945.1| putative sigma factor [Clostridium perfringens B str. ATCC 3626]
 gi|19908326|gb|AAL96802.1| putative sigma factor [Clostridium phage phi3626]
 gi|170710678|gb|EDT22860.1| putative sigma factor [Clostridium perfringens B str. ATCC 3626]
          Length = 181

 Score = 49.0 bits (116), Expect = 7e-04,   Method: Composition-based stats.
 Identities = 41/233 (17%), Positives = 88/233 (37%), Gaps = 59/233 (25%)

Query: 54  VTSHLRLVVKIAMGY--RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           V  ++    K+A  +  + + + I E+ S   +GL++A K+F+  +G    TY+M  I+ 
Sbjct: 4   VEDYIGAAYKVASKFYSKNWDMSIDEINSIAFLGLLKAKKRFEY-KGVEFVTYAMKTIEY 62

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            ++  + R  S  +                                       + N++  
Sbjct: 63  EIKNSLYRDRSKFR---------------------------------------RKNIAGK 83

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           +V     R+  D SL+  INS++    +  D LV + +  E V             L  +
Sbjct: 84  DVYE---RIYTD-SLDKEINSAEG--VKLIDCLVEESNTDEYV---------ENIDLKIA 128

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++ LN  +R+I +     E   T    +    V  + + + + +    ++E++
Sbjct: 129 INKLNTYQRKILKMLYFDE--KTQRETAKILSVHEKTISREKKKILNLLRETL 179


>gi|229118742|ref|ZP_04248093.1| RNA polymerase sigma factor [Bacillus cereus Rock1-3]
 gi|228664710|gb|EEL20201.1| RNA polymerase sigma factor [Bacillus cereus Rock1-3]
          Length = 156

 Score = 49.0 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 19/69 (27%), Positives = 34/69 (49%), Gaps = 2/69 (2%)

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           E+ E +         MSVLN RER I   R      +    ++ E  ++  +VR I  +A
Sbjct: 89  EQFESEETGMRAQDFMSVLNKRERHIISERFFVGKKMG--EIACEMGMTYYQVRWIYRQA 146

Query: 277 FKKVQESIQ 285
            +K+++S++
Sbjct: 147 LEKMRDSVK 155


>gi|302670826|ref|YP_003830786.1| RNA polymerase sigma factor sigma-70 family protein [Butyrivibrio
           proteoclasticus B316]
 gi|302395299|gb|ADL34204.1| RNA polymerase sigma factor sigma-70 family [Butyrivibrio
           proteoclasticus B316]
          Length = 258

 Score = 49.0 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 28/161 (17%), Positives = 65/161 (40%), Gaps = 7/161 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+  ++++P     E+    +     GD  A  +L+   L LVV +A  Y   G+ +
Sbjct: 81  LNDYLESLKELPEYTDGEKRA-IEMSAISGDKEAQSKLIECFLPLVVDVARMYTEQGVYL 139

Query: 76  SEVVSEGNIGLMQAVKKFDP-ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            +++ EGN  L + V   D       +  +    +  AM+  I  +     +   A +++
Sbjct: 140 EDLIGEGNFALTKGVTMLDAVGEPEEVEGFLYKLMLDAMEAVIESN-----LAEDAGEQK 194

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
           +   ++ +      +  +  +   V  +  +    E ++ S
Sbjct: 195 VLKLVQEVADKASELAQDLRRKVTVKELMDETGWDEDKIRS 235


>gi|289433597|ref|YP_003463469.1| RNA polymerase sigma-30 factor [Listeria seeligeri serovar 1/2b
           str. SLCC3954]
 gi|289169841|emb|CBH26379.1| RNA polymerase sigma-30 factor [Listeria seeligeri serovar 1/2b
           str. SLCC3954]
 gi|313635072|gb|EFS01422.1| RNA polymerase sigma-H factor [Listeria seeligeri FSL N1-067]
          Length = 201

 Score = 49.0 bits (116), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 26/151 (17%), Positives = 57/151 (37%), Gaps = 12/151 (7%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           +E  +L       GD  A     + +  ++   +  Y   G    +++ E  IGL +A++
Sbjct: 8   EEMTML--ELARSGDTDALEYFFSKYQSVIYWKSTQYFLQGAERDDLIQEAMIGLFKAIR 65

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--------TTANQKRLFFNLRRLK 143
            +D  +     +++   I   +   + R+     I         T   +  + + L  + 
Sbjct: 66  DYDKTKEASFRSFAEMCINRQLLSAVKRASRQKNIPLNNSVSLDTPMAEDDVDWTLLDVI 125

Query: 144 GHLQAITDNN--LKPEQVVAIAKKLNVSESE 172
               A T  +  +K E +  +A++L    SE
Sbjct: 126 SEKAAETPEDFLIKNEDLTHVARQLEEVTSE 156


>gi|253584047|ref|ZP_04861245.1| RNA polymerase sigma-H factor [Fusobacterium varium ATCC 27725]
 gi|251834619|gb|EES63182.1| RNA polymerase sigma-H factor [Fusobacterium varium ATCC 27725]
          Length = 203

 Score = 49.0 bits (116), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 19/86 (22%), Positives = 38/86 (44%), Gaps = 1/86 (1%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L K+ +  G   A   +  +   +++     Y  YG    +V+ E  IGL++A+  ++  
Sbjct: 11  LIKKAK-AGSEEAIQEIFKTFQGIMLLKTKKYFFYGGDKDDVLQEAMIGLLKAINGYEAG 69

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWS 122
           +     T+++  IK  +   I  S S
Sbjct: 70  KQASFKTFAILCIKRQLITAIKSSNS 95


>gi|313844183|ref|YP_004061846.1| hypothetical protein OlV1_214 [Ostreococcus lucimarinus virus OlV1]
 gi|312599568|gb|ADQ91590.1| hypothetical protein OlV1_214 [Ostreococcus lucimarinus virus OlV1]
          Length = 171

 Score = 49.0 bits (116), Expect = 9e-04,   Method: Composition-based stats.
 Identities = 21/78 (26%), Positives = 41/78 (52%), Gaps = 7/78 (8%)

Query: 50  AHRLVTSHLRLVVKIA-----MGY--RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
              L+ +H++L  K++       Y  +       ++ S G  GL++A +KF+PE GF+ +
Sbjct: 25  KKELIANHVKLAYKVSNDVYFKTYPRQRGIHTRKDINSVGLHGLVRAAQKFNPELGFKFS 84

Query: 103 TYSMWWIKAAMQEYILRS 120
           TY+  WI  + +  + R+
Sbjct: 85  TYAYPWIYWSCKNCLRRT 102


>gi|187933850|ref|YP_001886856.1| specialized sigma subunit of RNA polymerase [Clostridium botulinum
           B str. Eklund 17B]
 gi|187722003|gb|ACD23224.1| specialized sigma subunit of RNA polymerase [Clostridium botulinum
           B str. Eklund 17B]
          Length = 190

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 18/84 (21%), Positives = 35/84 (41%), Gaps = 2/84 (2%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
            + D    +  L E    K   + L +++  LN RER +   +       T   ++   E
Sbjct: 104 YIIDMVSPKPSLDELILTKENNSYLFQALGKLNERERSVVSLKYGAVLKNT--EIAKIME 161

Query: 264 VSRERVRQIEARAFKKVQESIQKQ 287
           +S   V  I  R+ KK+++ +  +
Sbjct: 162 LSESNVSVILYRSLKKLKKILVSE 185


>gi|284122984|ref|ZP_06386888.1| two component regulator propeller domain protein [Candidatus
           Poribacteria sp. WGA-A3]
 gi|283829313|gb|EFC33715.1| two component regulator propeller domain protein [Candidatus
           Poribacteria sp. WGA-A3]
          Length = 883

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 16/67 (23%), Positives = 31/67 (46%), Gaps = 4/67 (5%)

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV-RQIEAR 275
           E+E  +  R ++ + +  L   ER +     L E  +T + +     VS   +  ++  R
Sbjct: 26  EEEVNEQCRELVRKLLKKLPESERTVMTLYYLGE--MTTKEIGKFLGVSMNTITSRLH-R 82

Query: 276 AFKKVQE 282
           A K++QE
Sbjct: 83  ARKRLQE 89


>gi|160933364|ref|ZP_02080752.1| hypothetical protein CLOLEP_02209 [Clostridium leptum DSM 753]
 gi|156867241|gb|EDO60613.1| hypothetical protein CLOLEP_02209 [Clostridium leptum DSM 753]
          Length = 68

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 2/44 (4%)

Query: 24 RKIP-MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM 66
             P  L  +EE    +R++ +GD+ A  +L+  +LRLV  I  
Sbjct: 24 GSFPRPLTAKEEREYLERFQ-NGDMEARSKLIEHNLRLVAHIIK 66


>gi|169838533|ref|ZP_02871721.1| RNA polymerase factor sigma-32 [candidate division TM7 single-cell
           isolate TM7a]
          Length = 36

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 19/36 (52%), Positives = 27/36 (75%), Gaps = 1/36 (2%)

Query: 241 RIFEARRLQENP-VTLENLSSEFEVSRERVRQIEAR 275
           RI E R LQ++  +TL  L++E+ VS ER+RQIEA+
Sbjct: 1   RIVETRWLQDDGGLTLHELAAEYGVSAERIRQIEAK 36


>gi|153952569|ref|YP_001397326.1| flagellar biosynthesis sigma factor [Campylobacter jejuni subsp.
           doylei 269.97]
 gi|152940015|gb|ABS44756.1| RNA polymerase sigma factor, sigma-F [Campylobacter jejuni subsp.
           doylei 269.97]
          Length = 238

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 29/234 (12%), Positives = 90/234 (38%), Gaps = 36/234 (15%)

Query: 47  LSAAHRLVTSHLRLVVKIA---MGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
                 LV S++  +  +A          + +++++S G   +++  +++D E+      
Sbjct: 22  KKEQDELVLSYMPALRAMAFRLKERLPSSIDVNDLISIGVEEMIKLSRRYDKEQNDNFWG 81

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
           ++   +  +M +Y+     + +     N +++  ++  +    +   ++  +P+    +A
Sbjct: 82  FARKRVNGSMLDYLRSLDVMSR-----NNRKIIKDIDAIMD--EYFLEHECEPDD-EYLA 133

Query: 164 KKLNVSESEVISMNCRLAGDESL----NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
           KKL++   ++  +    A   +L       + + D    + +   + +            
Sbjct: 134 KKLDLDVEKIKEVRTAHAISYTLPIDEQIELYNEDNTLEKIEKEELLEKI---------- 183

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
                       +  L  R++ I +    +E  ++L+ +S   ++S  R+ QI 
Sbjct: 184 ---------HEVLYDLKERDQLIIQLYYYEE--LSLKEISEILQISESRISQIH 226


>gi|317121689|ref|YP_004101692.1| RNA polymerase, sigma 28 subunit, SigI [Thermaerobacter marianensis
           DSM 12885]
 gi|315591669|gb|ADU50965.1| RNA polymerase, sigma 28 subunit, SigI [Thermaerobacter marianensis
           DSM 12885]
          Length = 240

 Score = 49.0 bits (116), Expect = 0.001,   Method: Composition-based stats.
 Identities = 23/134 (17%), Positives = 54/134 (40%), Gaps = 3/134 (2%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP--ISEVVSEGNIGLMQAVKKFDPERGF 99
            + GD  A + L+ ++   V+K+A    G  L     E +S G +   +A+ +FD  RG 
Sbjct: 15  AKAGDDDARNELIRAYTPFVLKVASRVCGRFLHAGQDEEISIGLLAFNEAIDRFDATRGH 74

Query: 100 RLATYSMWWIKAAMQEYILRSWSLV-KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
               ++   I+  + ++  +  +    +  +  +          +  +QA  D +   E+
Sbjct: 75  NFIAFAETVIRRRLIDHFRKQSAARAAVPFSDLETEDDEGHPISQVDVQAALDRHALAEE 134

Query: 159 VVAIAKKLNVSESE 172
                +++   + E
Sbjct: 135 AWERRQEILRLQQE 148


>gi|302391036|ref|YP_003826856.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Acetohalobium
           arabaticum DSM 5501]
 gi|302203113|gb|ADL11791.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Acetohalobium
           arabaticum DSM 5501]
          Length = 222

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 20/104 (19%), Positives = 45/104 (43%), Gaps = 4/104 (3%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            K   + +QE   LA    ++GD  A   L+ +++ +V   +  +   GL   +V+ EG 
Sbjct: 10  SKYDEMPEQEVIDLA----QNGDKLAEEYLLDNNIDIVYAKSKLFYIKGLDKDDVIQEGL 65

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           +GL +A++ +  +R      ++   +   +   I  +     + 
Sbjct: 66  VGLYKAIRDYKEQRAASFRGFAHLCVSRQLISAIKTANRQKHMP 109


>gi|314055297|ref|YP_004063635.1| RNA-polymerase sigma factor-possible host origin [Ostreococcus
           tauri virus 2]
 gi|313575188|emb|CBI70201.1| RNA-polymerase sigma factor-possible host origin [Ostreococcus
           tauri virus 2]
          Length = 172

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 21/78 (26%), Positives = 41/78 (52%), Gaps = 7/78 (8%)

Query: 50  AHRLVTSHLRLVVKIA-----MGY--RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
              L+ +H++L  K++       Y  +       ++ S G  GL++A +KF+PE GF+ +
Sbjct: 25  KKELIANHVKLAYKVSNDVYFKTYPRQRGIHTRKDINSVGLHGLVRAAQKFNPELGFKFS 84

Query: 103 TYSMWWIKAAMQEYILRS 120
           TY+  WI  + +  + R+
Sbjct: 85  TYAYPWIYWSCKNCLRRT 102


>gi|291542179|emb|CBL15289.1| RNA polymerase sigma factor, sigma-70 family [Ruminococcus bromii
           L2-63]
          Length = 196

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 26/135 (19%), Positives = 53/135 (39%), Gaps = 3/135 (2%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A   LV  +L  +  IA  +   G   ++ V EG +GL+ + K FD   G    +Y
Sbjct: 23  GDDRAFDELVVRYLDTISIIARKFSAEGYEHNDFVQEGLVGLLCSCKAFDQNGGASFKSY 82

Query: 105 SMWWIKAAMQEYILR--SWSLVKIGTTANQKRLFFNLR-RLKGHLQAITDNNLKPEQVVA 161
               ++      I R     ++   +      +  ++    K   + +       + ++ 
Sbjct: 83  MSVVVERRFISIIRRGEQKKVIPSSSIVPMDDVGESIEDSAKTPEELLMCREQLDQLLLR 142

Query: 162 IAKKLNVSESEVISM 176
           +   L+ SE +V+ +
Sbjct: 143 LQSVLSKSEYDVLML 157


>gi|188585298|ref|YP_001916843.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|179349985|gb|ACB84255.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 266

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 25/139 (17%), Positives = 48/139 (34%), Gaps = 9/139 (6%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYG--LPISEVVSEGNIGLMQAVKKFDPERGF 99
            + GD  +   L+TS+   + +IA GY          + +S   + L +A+  +D     
Sbjct: 12  AQSGDEQSRELLITSYTSYIQEIASGYCNRKLVWENDDELSIALLALNEAIDSYDLNSNK 71

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           +   Y    +K+ + +Y         +        L  NL      L    DN ++ E  
Sbjct: 72  KFKNYLRMVVKSRLVDYFRTEKRHHHLP-------LSNNLEESNTELDEPPDNKIEDEAA 124

Query: 160 VAIAKKLNVSESEVISMNC 178
                +    +  V  M+ 
Sbjct: 125 WKQYHQQKEFQERVEEMSQ 143


>gi|163942935|ref|YP_001647819.1| RNA polymerase factor sigma-70 [Bacillus weihenstephanensis KBAB4]
 gi|163865132|gb|ABY46191.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Bacillus
           weihenstephanensis KBAB4]
          Length = 156

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 19/84 (22%), Positives = 40/84 (47%), Gaps = 2/84 (2%)

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           + +V +         E+ E ++        MSVL+ RER I   R      +    ++SE
Sbjct: 74  ECVVQERYVCTDEYKERFECEDAGTRAKDFMSVLDERERHIISERFFSGKNMG--EIASE 131

Query: 262 FEVSRERVRQIEARAFKKVQESIQ 285
             ++  +VR +  +A +K+++S++
Sbjct: 132 MGMTYYQVRWVYRQALEKMRDSVR 155


>gi|293400037|ref|ZP_06644183.1| RNA polymerase sigma factor, sigma-70 family [Erysipelotrichaceae
           bacterium 5_2_54FAA]
 gi|291306437|gb|EFE47680.1| RNA polymerase sigma factor, sigma-70 family [Erysipelotrichaceae
           bacterium 5_2_54FAA]
          Length = 262

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 40/257 (15%), Positives = 86/257 (33%), Gaps = 55/257 (21%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY----GLPISEVVSEGNIGLMQAV 90
             L  RYR +GD +A   L   + +L+  I   +            +++ E  I   + +
Sbjct: 4   IELIIRYR-NGDNTAFDYLFERNKKLIYFITRKHEWMIPYLHYDFDDILQESYIIFTKCI 62

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
             FD    ++  TY    I           W L K+  +A   + +              
Sbjct: 63  NDFDISSDYKFTTYLGNSIH----------WGLNKLFNSATNAKRYNKN----------- 101

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
                           + S  + IS+  +   D+ L   ++     +S+ +  L  + + 
Sbjct: 102 ----------------DDSIIQDISLEQKFNDDQDL---LSVLSDPNSEAEMKLFMEMEF 142

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNP---RERRIFEARRLQENP-VTLENLSSEFEVSR 266
            +Q       +K+ R +L +   V      R + I ++    +      + LS     S 
Sbjct: 143 NDQ------LKKDTRLLLNQVFDVQKDGVQRIKYIIQSNYGIDQEVKNAKELSILLNCSY 196

Query: 267 ERVRQIEARAFKKVQES 283
           + + Q+  +  + ++ S
Sbjct: 197 QNICQLRNKGIRMIRNS 213


>gi|229099677|ref|ZP_04230604.1| RNA polymerase sigma factor [Bacillus cereus Rock3-29]
 gi|228683747|gb|EEL37698.1| RNA polymerase sigma factor [Bacillus cereus Rock3-29]
          Length = 156

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 19/69 (27%), Positives = 34/69 (49%), Gaps = 2/69 (2%)

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           E+ E +         MSVLN RER I   R      +    ++ E  ++  +VR I  +A
Sbjct: 89  EQFESEETGMRAQDFMSVLNKRERYIISERFFVGKKMG--EIACEMGMTYYQVRWIYRQA 146

Query: 277 FKKVQESIQ 285
            +K+++S++
Sbjct: 147 LEKMRDSVK 155


>gi|226310285|ref|YP_002770179.1| hypothetical protein BBR47_06980 [Brevibacillus brevis NBRC 100599]
 gi|226093233|dbj|BAH41675.1| hypothetical protein [Brevibacillus brevis NBRC 100599]
          Length = 586

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 45/255 (17%), Positives = 78/255 (30%), Gaps = 57/255 (22%)

Query: 30  EKQE----EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
             +E    E        + GD  A   LV  H   V   A  Y        ++V +    
Sbjct: 10  THEEHTQIEDEALVEQAKAGDQEAFSELVRRHRSKVYGYARSYTQEAFLAEDIVQDA--- 66

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH 145
           L++A          R   +  W     +   +       ++     ++   F+    + H
Sbjct: 67  LIRAFLHLGTLVDSR--RFLPW-----LHRIVRNQAYT-RLSKGPQKRETVFSSMGKQTH 118

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
            Q   D     E + +I  +L  S S                                  
Sbjct: 119 EQEPAD----WEDLDSILHRLGRSWS---------------------------------- 140

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
             H  Q     E   R+     +   +  LNPRERRI E+       +    ++  F++S
Sbjct: 141 --HSAQNTNPEEVMVRRELFETIRSLLYCLNPRERRIVESHFFDH--LAPHEIAHMFQMS 196

Query: 266 RERVRQIEARAFKKV 280
           +  V Q+ +R+ KK+
Sbjct: 197 QANVYQVLSRSRKKL 211


>gi|217965669|ref|YP_002351347.1| RNA polymerase sigma-H factor (Sigma-30) [Listeria monocytogenes
           HCC23]
 gi|290892616|ref|ZP_06555609.1| RNA polymerase sigma-30 factor [Listeria monocytogenes FSL J2-071]
 gi|217334939|gb|ACK40733.1| RNA polymerase sigma-H factor (Sigma-30) [Listeria monocytogenes
           HCC23]
 gi|290557925|gb|EFD91446.1| RNA polymerase sigma-30 factor [Listeria monocytogenes FSL J2-071]
 gi|307569782|emb|CAR82961.1| RNA polymerase sigma-30 factor [Listeria monocytogenes L99]
          Length = 201

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 28/151 (18%), Positives = 60/151 (39%), Gaps = 11/151 (7%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           QEE  + +  R  GD  A     + +  ++   +  Y   G    +++ E  IGL +A++
Sbjct: 7   QEELAMLELAR-SGDTEALEYFFSKYQSVIYWKSTQYFLQGAERDDLIQEAMIGLFKAIR 65

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--------TTANQKRLFFNLRRLK 143
            +D  +     +++   I   +   + R+     I         T   +  + + L  + 
Sbjct: 66  DYDKTKEASFRSFAEMCINRQLLSAVKRASRQKNIPLNNSVSLDTPMAEDDVDWTLLDVI 125

Query: 144 GHLQAITDNN--LKPEQVVAIAKKLNVSESE 172
               A T  +  +K E ++ +A++L    SE
Sbjct: 126 SEKAAETPEDFLIKNEDLIHVARQLEQVTSE 156


>gi|153855858|ref|ZP_01996833.1| hypothetical protein DORLON_02855 [Dorea longicatena DSM 13814]
 gi|149751826|gb|EDM61757.1| hypothetical protein DORLON_02855 [Dorea longicatena DSM 13814]
          Length = 208

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 31/157 (19%), Positives = 59/157 (37%), Gaps = 11/157 (7%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L  +E   L +R R  G+      L+  +  LV K A      G    +++ EG IGL +
Sbjct: 14  LTDEE---LIRRLR-MGETGIIDYLMEKYKNLVRKEANAMYLLGGETDDLIQEGMIGLFK 69

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           AV+ +D ++     +++   +   +   I  S              L   +   +     
Sbjct: 70  AVQDYDVDQEASFFSFARLCVTRQLYSAIEASNR-------KKHSPLNSYISLYEREDGE 122

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES 185
            +  ++   +     ++L VS+    S+  RL  D S
Sbjct: 123 GSLIDMMESEHETNPEELLVSQEHAKSLEERLEKDLS 159


>gi|320104153|ref|YP_004179744.1| sigma-70 familyRNA polymerase sigma factor [Isosphaera pallida ATCC
           43644]
 gi|319751435|gb|ADV63195.1| RNA polymerase sigma factor, sigma-70 family [Isosphaera pallida
           ATCC 43644]
          Length = 304

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 41/259 (15%), Positives = 83/259 (32%), Gaps = 64/259 (24%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGY----GLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           A    V SH  + +++A GY       GL   E+ S     L++AV+   PERG  L   
Sbjct: 105 AQSERVASHAAMALRVARGYARGRRLAGLDQDELESTALWALIRAVRHHCPERGPFLPYA 164

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           +       ++                          R++  +         P        
Sbjct: 165 AS-----VIRHACANLAR--------------REGYRIERFVHWTPSGRHDPP------- 198

Query: 165 KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR 224
                                      SS   +     W       +E+   E+  R   
Sbjct: 199 ---------------------------SSRSQTRSAACWTSRHPHAREESSEERATRLED 231

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            + L  ++  L   +RR+ ++R   + P     ++    ++  +V ++  RA  +++   
Sbjct: 232 HDALRHAVERLPESQRRVIQSRLAGDPPR---VIAQTLGLTHRQVYRLYNRALIRLRREF 288

Query: 285 -QKQVELSSSPPLLQKPRY 302
            ++Q +   +PP   +PR+
Sbjct: 289 DERQPDQRPTPP---RPRF 304


>gi|46906476|ref|YP_012865.1| RNA polymerase factor sigma-70 [Listeria monocytogenes serotype 4b
           str. F2365]
 gi|226222872|ref|YP_002756979.1| RNA polymerase sigma-30 factor (sigma-H) [Listeria monocytogenes
           Clip81459]
 gi|254825713|ref|ZP_05230714.1| RNA polymerase sigma-30 factor [Listeria monocytogenes FSL J1-194]
 gi|254853490|ref|ZP_05242838.1| RNA polymerase sigma-30 factor [Listeria monocytogenes FSL R2-503]
 gi|254932462|ref|ZP_05265821.1| RNA polymerase sigma-30 factor [Listeria monocytogenes HPB2262]
 gi|254991757|ref|ZP_05273947.1| RNA polymerase factor sigma-70 [Listeria monocytogenes FSL J2-064]
 gi|255520313|ref|ZP_05387550.1| RNA polymerase factor sigma-70 [Listeria monocytogenes FSL J1-175]
 gi|300764632|ref|ZP_07074624.1| hypothetical protein LMHG_11122 [Listeria monocytogenes FSL N1-017]
 gi|46879740|gb|AAT03042.1| RNA polymerase sigma-30 factor [Listeria monocytogenes serotype 4b
           str. F2365]
 gi|225875334|emb|CAS04031.1| RNA polymerase sigma-30 factor (sigma-H) [Listeria monocytogenes
           serotype 4b str. CLIP 80459]
 gi|258606862|gb|EEW19470.1| RNA polymerase sigma-30 factor [Listeria monocytogenes FSL R2-503]
 gi|293584018|gb|EFF96050.1| RNA polymerase sigma-30 factor [Listeria monocytogenes HPB2262]
 gi|293594957|gb|EFG02718.1| RNA polymerase sigma-30 factor [Listeria monocytogenes FSL J1-194]
 gi|300514739|gb|EFK41794.1| hypothetical protein LMHG_11122 [Listeria monocytogenes FSL N1-017]
 gi|328467852|gb|EGF38892.1| RNA polymerase factor sigma-70 [Listeria monocytogenes 1816]
 gi|328476084|gb|EGF46793.1| RNA polymerase factor sigma-70 [Listeria monocytogenes 220]
 gi|332310654|gb|EGJ23749.1| RNA polymerase sigma-30 factor [Listeria monocytogenes str. Scott
           A]
          Length = 201

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 28/151 (18%), Positives = 59/151 (39%), Gaps = 11/151 (7%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           QEE  + +  R  GD  A     + +  ++   +  Y   G    +++ E  IGL +A++
Sbjct: 7   QEELAMLELAR-SGDTEALEYFFSKYQSVIYWKSTQYFLQGAERDDLIQEAMIGLFKAIR 65

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--------TTANQKRLFFNLRRLK 143
            +D  +     +++   I   +   + R+     I         T   +  + + L  + 
Sbjct: 66  DYDKTKEASFRSFAEMCINRQLLSAVKRASRQKNIPLNNSVSLDTPIAEDDMDWTLLDVI 125

Query: 144 GHLQAITDNN--LKPEQVVAIAKKLNVSESE 172
               A T  +  +K E +  +A++L    SE
Sbjct: 126 SEKAAETPEDFLIKNEDLTHVARQLEQVTSE 156


>gi|315274660|ref|ZP_07869500.1| RNA polymerase sigma-H factor [Listeria marthii FSL S4-120]
 gi|313615717|gb|EFR89005.1| RNA polymerase sigma-H factor [Listeria marthii FSL S4-120]
          Length = 201

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 26/151 (17%), Positives = 57/151 (37%), Gaps = 12/151 (7%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           +E  +L       GD  A     + +  ++   +  Y   G    +++ E  IGL +A++
Sbjct: 8   EEMTML--ELARSGDTEALEYFFSKYQSVIYWKSTQYFLQGAERDDLIQEAMIGLFKAIR 65

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--------TTANQKRLFFNLRRLK 143
            +D  +     +++   I   +   + R+     I         T   +  + + L  + 
Sbjct: 66  DYDKTKEASFRSFAEMCINRQLLSAVKRASRQKNIPLNNSVSLDTPMAEDDVDWTLLDVI 125

Query: 144 GHLQAITDNN--LKPEQVVAIAKKLNVSESE 172
               A T  +  +K E +  +A++L    SE
Sbjct: 126 SEKAAETPEDFLIKNEDLTHVARQLEQVTSE 156


>gi|251780547|ref|ZP_04823467.1| specialized sigma subunit of RNA polymerase [Clostridium botulinum
           E1 str. 'BoNT E Beluga']
 gi|243084862|gb|EES50752.1| specialized sigma subunit of RNA polymerase [Clostridium botulinum
           E1 str. 'BoNT E Beluga']
          Length = 190

 Score = 48.7 bits (115), Expect = 0.001,   Method: Composition-based stats.
 Identities = 27/142 (19%), Positives = 54/142 (38%), Gaps = 13/142 (9%)

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD-----------WLV 205
           +Q  A      + E  +I  +     D+SL++ I +  +N+                  +
Sbjct: 46  DQHEAEELCSKIFERIIIKYSSFGGNDDSLDSWIFTIARNTITDHYRSKNKRFHFSLDYI 105

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            D    +  L E    K   + L +++  LN RER +   +       T   ++   E+S
Sbjct: 106 IDMVSPKPSLDELILTKENNSYLFKALRKLNERERSVVSLKYGAALKNT--EIAKIMELS 163

Query: 266 RERVRQIEARAFKKVQESIQKQ 287
              V  I  R+ KK+++ +  +
Sbjct: 164 ESNVSVILCRSLKKLKKILVSE 185


>gi|229076462|ref|ZP_04209424.1| RNA polymerase sigma factor [Bacillus cereus Rock4-18]
 gi|228706648|gb|EEL58859.1| RNA polymerase sigma factor [Bacillus cereus Rock4-18]
          Length = 156

 Score = 48.3 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 19/69 (27%), Positives = 33/69 (47%), Gaps = 2/69 (2%)

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           E+ E +         MSVLN RER I   R      +    ++ E  ++  +VR I  +A
Sbjct: 89  EQFEFEETGMRAQDFMSVLNKRERHIISERFFVGKKMG--EIACEMGMTYYQVRWIYRQA 146

Query: 277 FKKVQESIQ 285
             K+++S++
Sbjct: 147 LGKMRDSVK 155


>gi|296130341|ref|YP_003637591.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Cellulomonas
           flavigena DSM 20109]
 gi|296022156|gb|ADG75392.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Cellulomonas
           flavigena DSM 20109]
          Length = 192

 Score = 48.3 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 15/70 (21%), Positives = 43/70 (61%), Gaps = 2/70 (2%)

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
           + + ++ +  R+ L R++++L PR+RR+   R +    +T + ++++  VS   V+   +
Sbjct: 106 VADGQDARADRDQLARALALLTPRQRRVVVLRHI--EGLTEKEVAADLGVSVGTVKSTAS 163

Query: 275 RAFKKVQESI 284
           RA +++++++
Sbjct: 164 RALRQLRDAL 173


>gi|313901949|ref|ZP_07835366.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermaerobacter subterraneus DSM 13965]
 gi|313467795|gb|EFR63292.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermaerobacter subterraneus DSM 13965]
          Length = 240

 Score = 48.3 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 19/84 (22%), Positives = 38/84 (45%), Gaps = 2/84 (2%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP--ISEVVSEGNIGLMQAVKKFDPERGF 99
            + GD  A + L+ ++   V+K+A    G  L     E +S G +   +A+ +FD  RG 
Sbjct: 15  AKAGDEHARNELIRAYTPFVLKVASRVCGRYLHAGQDEEISIGLLAFNEAIDRFDDTRGN 74

Query: 100 RLATYSMWWIKAAMQEYILRSWSL 123
               ++   IK  + ++  +  + 
Sbjct: 75  NFIAFAETVIKRRLIDHFRKQSAT 98


>gi|315652062|ref|ZP_07905063.1| hypothetical protein HMPREF0381_2057 [Eubacterium saburreum DSM
           3986]
 gi|315485709|gb|EFU76090.1| hypothetical protein HMPREF0381_2057 [Eubacterium saburreum DSM
           3986]
          Length = 171

 Score = 48.3 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 33/162 (20%), Positives = 70/162 (43%), Gaps = 9/162 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ +++ I  ++++E   L      HGD SA +RL+  H+   VK+   + G G  +
Sbjct: 7   LEMYLEDMKAIKEIDEKEIKELTDALL-HGDESARNRLIEGHMMYAVKLIKPFIGCGEEM 65

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
           S+++SE ++ L  AV ++       L +     ++  + E      S           +L
Sbjct: 66  SDLISESHLALTMAVMEYSH---GDLKSQIKSRVEKRLNEIADEEKS-----KKDASNKL 117

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
              +  L     A+  +  K   +  ++++L + + EV  + 
Sbjct: 118 ADRINELMDVSSALASDIGKEATLEELSERLQIPKDEVEELL 159


>gi|331088921|ref|ZP_08337830.1| hypothetical protein HMPREF1025_01413 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|330406519|gb|EGG86027.1| hypothetical protein HMPREF1025_01413 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 198

 Score = 48.3 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 27/154 (17%), Positives = 68/154 (44%), Gaps = 7/154 (4%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY--GLPISEVVSEGNIGLMQAVKKF 93
            L K Y+E  D +    L++ +  L+  +   Y        + ++VSE  I +++A++ F
Sbjct: 10  ELVKLYKESRDEAYLAELISQNTGLINILVSSYLSSIPNSELEDLVSESYIPMLKAIEDF 69

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKI-GTTANQKRLFFNLRRLKGHLQ----A 148
           D ++GF  +T    +++  +      +    +  G+T         + +  G        
Sbjct: 70  DEKQGFSFSTLLKAYVRQHLNRLYNEATRKKRFTGSTPVSYESLVEINKEGGSELDSSFT 129

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAG 182
           +   ++   + + + + LN+++ E +++N  +AG
Sbjct: 130 VELEDISSVEFMDLLRSLNLNDKEQVAVNVLMAG 163


>gi|323705058|ref|ZP_08116634.1| RNA polymerase sigma factor, sigma-70 family [Thermoanaerobacterium
           xylanolyticum LX-11]
 gi|323535484|gb|EGB25259.1| RNA polymerase sigma factor, sigma-70 family [Thermoanaerobacterium
           xylanolyticum LX-11]
          Length = 188

 Score = 48.3 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 18/95 (18%), Positives = 40/95 (42%), Gaps = 6/95 (6%)

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D+  ++  D +  D    E+       RK+    L  +++ L  +++ I           
Sbjct: 98  DEEENEIIDLIESDELTPEEKFFNDIMRKD----LKEALNGLTGKQKNIIMLYFF--ERK 151

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           TL  +S E  V  + V +++ RA  +++  I+  +
Sbjct: 152 TLVEISKELGVGYQSVVKLKDRALDRLRFLIKNDI 186


>gi|16802289|ref|NP_463774.1| RNA polymerase factor sigma-70 [Listeria monocytogenes EGD-e]
 gi|224502463|ref|ZP_03670770.1| RNA polymerase factor sigma-70 [Listeria monocytogenes FSL R2-561]
 gi|254828703|ref|ZP_05233390.1| RNA polymerase sigma-30 factor [Listeria monocytogenes FSL N3-165]
 gi|254831932|ref|ZP_05236587.1| RNA polymerase factor sigma-70 [Listeria monocytogenes 10403S]
 gi|254900576|ref|ZP_05260500.1| RNA polymerase factor sigma-70 [Listeria monocytogenes J0161]
 gi|254913473|ref|ZP_05263485.1| RNA polymerase factor sigma-70 [Listeria monocytogenes J2818]
 gi|254937946|ref|ZP_05269643.1| RNA polymerase sigma-30 factor [Listeria monocytogenes F6900]
 gi|284800538|ref|YP_003412403.1| RNA polymerase factor sigma-70 [Listeria monocytogenes 08-5578]
 gi|284993724|ref|YP_003415492.1| RNA polymerase factor sigma-70 [Listeria monocytogenes 08-5923]
 gi|16409608|emb|CAD00770.1| RNA polymerase sigma-30 factor (sigma-H) [Listeria monocytogenes
           EGD-e]
 gi|258601108|gb|EEW14433.1| RNA polymerase sigma-30 factor [Listeria monocytogenes FSL N3-165]
 gi|258610555|gb|EEW23163.1| RNA polymerase sigma-30 factor [Listeria monocytogenes F6900]
 gi|284056100|gb|ADB67041.1| RNA polymerase factor sigma-70 [Listeria monocytogenes 08-5578]
 gi|284059191|gb|ADB70130.1| RNA polymerase factor sigma-70 [Listeria monocytogenes 08-5923]
 gi|293591481|gb|EFF99815.1| RNA polymerase factor sigma-70 [Listeria monocytogenes J2818]
          Length = 201

 Score = 48.3 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 28/151 (18%), Positives = 59/151 (39%), Gaps = 11/151 (7%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           QEE  + +  R  GD  A     + +  ++   +  Y   G    +++ E  IGL +A++
Sbjct: 7   QEELAMLELAR-SGDTEALEYFFSKYQSVIYWKSTQYFLQGAERDDLIQEAMIGLFKAIR 65

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--------TTANQKRLFFNLRRLK 143
            +D  +     +++   I   +   + R+     I         T   +  + + L  + 
Sbjct: 66  DYDKTKEASFRSFAEMCINRQLLSAVKRASRQKNIPLNNSVSLDTPMAEDDVDWTLLDVI 125

Query: 144 GHLQAITDNN--LKPEQVVAIAKKLNVSESE 172
               A T  +  +K E +  +A++L    SE
Sbjct: 126 SEKAAETPEDFLIKNEDLTHVARQLEQVTSE 156


>gi|229169962|ref|ZP_04297655.1| RNA polymerase sigma factor [Bacillus cereus AH621]
 gi|228613480|gb|EEK70612.1| RNA polymerase sigma factor [Bacillus cereus AH621]
          Length = 156

 Score = 48.3 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 18/84 (21%), Positives = 40/84 (47%), Gaps = 2/84 (2%)

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           + +V +         E+ E ++        MSVL+ RE+ I   R      +    ++SE
Sbjct: 74  ECVVQERYVCTDEYEERFECEDAGTRAKDFMSVLDEREKHIISERFFTGKNMG--EIASE 131

Query: 262 FEVSRERVRQIEARAFKKVQESIQ 285
             ++  +VR +  +A +K+++S++
Sbjct: 132 MGMTYYQVRWVYRQALEKMRDSVR 155


>gi|313620925|gb|EFR92099.1| RNA polymerase sigma-H factor [Listeria innocua FSL S4-378]
          Length = 201

 Score = 48.3 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 26/151 (17%), Positives = 57/151 (37%), Gaps = 12/151 (7%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           +E  +L       GD  A     + +  ++   +  Y   G    +++ E  IGL +A++
Sbjct: 8   EEMAML--ELARSGDTDALEYFFSRYQSVIYWKSTQYFLQGAERDDLIQEAMIGLFKAIR 65

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--------TTANQKRLFFNLRRLK 143
            +D  +     +++   I   +   + R+     I         T   +  + + L  + 
Sbjct: 66  DYDESKEASFRSFAEMCINRQLLSAVKRASRQKNIPLNNSVSLDTPMAEDDVDWTLLDVI 125

Query: 144 GHLQAITDNN--LKPEQVVAIAKKLNVSESE 172
               A T  +  +K E +  +A++L    SE
Sbjct: 126 SEKAAETPEDFLIKNEDLTHVARQLEQVTSE 156


>gi|294792433|ref|ZP_06757580.1| RNA polymerase sigma factor rpoD1 [Veillonella sp. 6_1_27]
 gi|294456332|gb|EFG24695.1| RNA polymerase sigma factor rpoD1 [Veillonella sp. 6_1_27]
          Length = 130

 Score = 48.3 bits (114), Expect = 0.001,   Method: Composition-based stats.
 Identities = 19/106 (17%), Positives = 47/106 (44%), Gaps = 2/106 (1%)

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           RL     ++    ++D     +   +    +    +++  +E    R  L  ++  L+P 
Sbjct: 17  RLRYRREIHIPDRTTDDGEVAFGMDIFASGENVADMVMSADEEHRLRARLAWALGRLSPD 76

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +R +   RR+     +L ++S E   SR+ +++   RA +K++  +
Sbjct: 77  QRDLL--RRVYGECQSLVSVSEELNCSRQAIQRRHERAIRKLRRYL 120


>gi|52081877|ref|YP_080668.1| YvrI [Bacillus licheniformis ATCC 14580]
 gi|52787265|ref|YP_093094.1| YvrI [Bacillus licheniformis ATCC 14580]
 gi|52005088|gb|AAU25030.1| YvrI [Bacillus licheniformis ATCC 14580]
 gi|52349767|gb|AAU42401.1| YvrI [Bacillus licheniformis ATCC 14580]
          Length = 193

 Score = 48.3 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 15/95 (15%), Positives = 40/95 (42%), Gaps = 2/95 (2%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
            +S    +    D         E+     +  ML  +   L  +++++     +  + V+
Sbjct: 92  DDSPNLPEPPRGDLLDDVLEQEEELSEHLQDPMLYEAFLQLTDKQKKVLAQIYI--HGVS 149

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           ++ ++     SR+ + +I  RA +K++E +  + E
Sbjct: 150 MQEIADSLGESRQNISKIHKRALEKIRELLNSKAE 184


>gi|224498911|ref|ZP_03667260.1| RNA polymerase factor sigma-70 [Listeria monocytogenes Finland
           1988]
          Length = 201

 Score = 48.3 bits (114), Expect = 0.002,   Method: Composition-based stats.
 Identities = 28/151 (18%), Positives = 59/151 (39%), Gaps = 11/151 (7%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           QEE  + +  R  GD  A     + +  ++   +  Y   G    +++ E  IGL +A++
Sbjct: 7   QEELAMLELAR-SGDTEALEYFFSKYQSVIYWKSTQYFLQGAERDDLIQEAMIGLFKAIR 65

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--------TTANQKRLFFNLRRLK 143
            +D  +     +++   I   +   + R+     I         T   +  + + L  + 
Sbjct: 66  DYDKTKEASFRSFAEMCINRQLLSAVKRASRQKNIPLNNSVSLDTPMAEDDVDWTLLDVI 125

Query: 144 GHLQAITDNN--LKPEQVVAIAKKLNVSESE 172
               A T  +  +K E +  +A++L    SE
Sbjct: 126 SEKAAETPEDFLIKNEDLTHVARQLEQVTSE 156


>gi|255035489|ref|YP_003086110.1| RNA polymerase, sigma 32 subunit, RpoH [Dyadobacter fermentans DSM
           18053]
 gi|254948245|gb|ACT92945.1| RNA polymerase, sigma 32 subunit, RpoH [Dyadobacter fermentans DSM
           18053]
          Length = 201

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 18/86 (20%), Positives = 35/86 (40%), Gaps = 2/86 (2%)

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
            Q   ++       E  ++  EE   +   L+  +  L  R++ I   R  Q      + 
Sbjct: 102 PQDVQFVAGADISIESQIVLNEEETAQIRQLSAVLETLTTRQQEIVYLRFYQGLE--FDE 159

Query: 258 LSSEFEVSRERVRQIEARAFKKVQES 283
           +S    ++R+ V  +  R  KK++ES
Sbjct: 160 ISGIMGLTRQSVANLLHRTLKKLKES 185


>gi|225870575|ref|YP_002746522.1| DNA-binding protein [Streptococcus equi subsp. equi 4047]
 gi|213033092|emb|CAP20375.1| putative DNA-binding protein [Streptococcus equi subsp. equi]
 gi|225699979|emb|CAW93959.1| putative DNA-binding protein [Streptococcus equi subsp. equi 4047]
          Length = 133

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 14/82 (17%), Positives = 37/82 (45%), Gaps = 2/82 (2%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           + D       + +  E K     L  ++  LN  ER++ EA    +   TL  ++ + + 
Sbjct: 54  IVDIADNTVDVEKIIETKMLIEDLYYALDSLNDEERKLIEALYFDD--KTLTEVAKQRDT 111

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           +  ++ ++  +  +K+++ + K
Sbjct: 112 NPMKISRLRNKILEKLRKFLDK 133


>gi|254302087|ref|ZP_04969445.1| DNA-directed RNA polymerase sigma subunit RpoE [Fusobacterium
           nucleatum subsp. polymorphum ATCC 10953]
 gi|148322279|gb|EDK87529.1| DNA-directed RNA polymerase sigma subunit RpoE [Fusobacterium
           nucleatum subsp. polymorphum ATCC 10953]
          Length = 204

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 17/78 (21%), Positives = 38/78 (48%), Gaps = 1/78 (1%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + GD  A + ++  + +++   A  Y   G    ++V EG +GL++A+K +D  +    
Sbjct: 11  AQSGDNEAINLILEEYSKILSFNAQKYYLVGAEQEDLVQEGILGLLKAIKFYDETK-SSF 69

Query: 102 ATYSMWWIKAAMQEYILR 119
            +++   I+  M   I +
Sbjct: 70  NSFAFLCIRREMISAIRK 87


>gi|160880198|ref|YP_001559166.1| hypothetical protein Cphy_2059 [Clostridium phytofermentans ISDg]
 gi|160428864|gb|ABX42427.1| hypothetical protein Cphy_2059 [Clostridium phytofermentans ISDg]
          Length = 254

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 38/166 (22%), Positives = 72/166 (43%), Gaps = 11/166 (6%)

Query: 16  LSRYIHEIRKIPMLEKQ-EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLP 74
           L  Y+ +I+ +P L  + EE    +    +GD S +  +    L  VV++A  Y  Y + 
Sbjct: 87  LEMYLEDIKHLPRLTAELEERAYIRLI--NGDNSVSQSISDHWLSTVVELAKKYETYDVN 144

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLAT--YSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           + +++ EGNIGL+  +K+       ++    Y M  +  A + YI        I     +
Sbjct: 145 MEDLIQEGNIGLLGGLKQLLGS-NQKIEAKEYLMESVLKAFENYIDEV-----IDEDDME 198

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
             +   +  +   + A  ++N     V+ IA    +SE E+ S+  
Sbjct: 199 NSILSKITLINEAITAFAEDNGVTPTVMEIADYTKISEDEIASILR 244


>gi|271961816|ref|YP_003336012.1| ECF subfamily RNA polymerase sigma-24 subunit [Streptosporangium
           roseum DSM 43021]
 gi|270504991|gb|ACZ83269.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Streptosporangium
           roseum DSM 43021]
          Length = 170

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 15/63 (23%), Positives = 31/63 (49%), Gaps = 2/63 (3%)

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           ++R +    L + +  L P++R +   R  ++ P   + ++    +SR  VR   ARA  
Sbjct: 99  DDRLDGDVGLWKELEGLPPKQRAVLVLRYYEDLPD--QEIAELLGISRGTVRSQAARALD 156

Query: 279 KVQ 281
           K++
Sbjct: 157 KLR 159


>gi|16799352|ref|NP_469620.1| RNA polymerase factor sigma-70 [Listeria innocua Clip11262]
 gi|16412704|emb|CAC95508.1| RNA polymerase sigma-30 factor (sigma-H) [Listeria innocua
           Clip11262]
          Length = 201

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 26/151 (17%), Positives = 57/151 (37%), Gaps = 12/151 (7%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           +E  +L       GD  A     + +  ++   +  Y   G    +++ E  IGL +A++
Sbjct: 8   EEMAML--ELARSGDTDALEYFFSRYQSVIYWKSTQYFLQGAERDDLIQEAMIGLFKAIR 65

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--------TTANQKRLFFNLRRLK 143
            +D  +     +++   I   +   + R+     I         T   +  + + L  + 
Sbjct: 66  DYDESKEASFRSFAEMCINRQLLSAVKRASRQKNIPLNNSVSLDTPMAEDDVDWTLLDVI 125

Query: 144 GHLQAITDNN--LKPEQVVAIAKKLNVSESE 172
               A T  +  +K E +  +A++L    SE
Sbjct: 126 SEKAAETPEDFLIKNEDLTHVARQLEQVTSE 156


>gi|197294755|ref|YP_001799296.1| DNA-directed RNA polymerase specialized sigma subunit [Candidatus
           Phytoplasma australiense]
 gi|171854082|emb|CAM12057.1| DNA-directed RNA polymerase specialized sigma subunit [Candidatus
           Phytoplasma australiense]
          Length = 224

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 22/109 (20%), Positives = 49/109 (44%), Gaps = 7/109 (6%)

Query: 35  YVLAKRY-REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI--SEVVSEGNIGLMQAVK 91
             L + + +   +L   ++LV  +  LV KI   ++ +   +   ++  EG +GL+ A++
Sbjct: 9   KELFQEFLKNKKNLQIRNQLVELYYPLVNKIVSKFKYFPSILQRRDLFQEGVLGLINALE 68

Query: 92  KFDPERGF-RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
            +D +    +   Y++  IK A+ E I +  S          K++   +
Sbjct: 69  GYDFQVDIDQFIGYAIEHIKFAIHELIRKCQSA---SMPQKHKKIITKI 114


>gi|238019170|ref|ZP_04599596.1| hypothetical protein VEIDISOL_01033 [Veillonella dispar ATCC 17748]
 gi|237863869|gb|EEP65159.1| hypothetical protein VEIDISOL_01033 [Veillonella dispar ATCC 17748]
          Length = 238

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 34/229 (14%), Positives = 75/229 (32%), Gaps = 24/229 (10%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             ++  V+A   +E  +  A   +V  +   V   A  Y   G    +++ EG IGL +A
Sbjct: 31  TDEQVVVIA---QEEQNEFAIDYIVNKYKNFVRAKARSYFLVGADREDIIQEGMIGLYKA 87

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQ 147
            + F  ++      ++   I   +   I  +         +  +  +  +     +  ++
Sbjct: 88  TRDFKHDKLASFRAFAELCITRQIITAIKSATRQKHAPLNSYVSLNKPVYTEESERTLIE 147

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
            ++   +   +       L +S+ E+  +   +    S         +   +  +  +  
Sbjct: 148 MLSSAKVTNPED------LIISQEELDDIERNIGHILS---------ELEWEVLEGYLDG 192

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
              QE   +     K+  N L R    L     +  E R L     T E
Sbjct: 193 RSYQEMAEVTDRSVKSIDNALQRVKRKL----EKYLEHRVLDSPRATQE 237


>gi|119488697|ref|ZP_01621706.1| DNA-directed RNA polymerase ECF-type sigma factor (sigma-W)
           [Lyngbya sp. PCC 8106]
 gi|119455120|gb|EAW36261.1| DNA-directed RNA polymerase ECF-type sigma factor (sigma-W)
           [Lyngbya sp. PCC 8106]
          Length = 396

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 20/93 (21%), Positives = 39/93 (41%), Gaps = 10/93 (10%)

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS---- 265
            QE+       R+     L  ++  L PR R +F      +  ++ + ++    +S    
Sbjct: 122 SQEETPFLSATRRETAQFLRNAIENLPPRLREVFVL--FADQELSYQEIAQHLNISYDNV 179

Query: 266 RERVRQIEARAFKKVQESIQKQVELSSSPPLLQ 298
           R+R+ Q    A K ++E +Q+      S P L+
Sbjct: 180 RKRISQ----ARKTLREQLQEYEGGEQSVPSLK 208


>gi|294794237|ref|ZP_06759373.1| RNA polymerase sigma factor SigK (Sigma-K factor) [Veillonella sp.
           3_1_44]
 gi|294454567|gb|EFG22940.1| RNA polymerase sigma factor SigK (Sigma-K factor) [Veillonella sp.
           3_1_44]
          Length = 130

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 19/106 (17%), Positives = 47/106 (44%), Gaps = 2/106 (1%)

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           RL     ++    ++D     +   +    +    +++  +E    R  L  ++  L+P 
Sbjct: 17  RLRYRREIHIPDRTTDDGEVAFGMDIFASGENVADMVMSADEEHRLRARLVWALGRLSPD 76

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +R +   RR+     +L ++S E   SR+ +++   RA +K++  +
Sbjct: 77  QRDLL--RRVYGECQSLVSVSEELNCSRQAIQRRHERAIRKLRRYL 120


>gi|254974765|ref|ZP_05271237.1| sporulation sigma factor SigK [Clostridium difficile QCD-66c26]
 gi|255092154|ref|ZP_05321632.1| sporulation sigma factor SigK [Clostridium difficile CIP 107932]
 gi|255306134|ref|ZP_05350306.1| sporulation sigma factor SigK [Clostridium difficile ATCC 43255]
 gi|255313891|ref|ZP_05355474.1| sporulation sigma factor SigK [Clostridium difficile QCD-76w55]
 gi|255516572|ref|ZP_05384248.1| sporulation sigma factor SigK [Clostridium difficile QCD-97b34]
 gi|255649672|ref|ZP_05396574.1| sporulation sigma factor SigK [Clostridium difficile QCD-37x79]
 gi|255655236|ref|ZP_05400645.1| sporulation sigma factor SigK [Clostridium difficile QCD-23m63]
 gi|296451220|ref|ZP_06892961.1| RNA polymerase sigma-K factor [Clostridium difficile NAP08]
 gi|296880427|ref|ZP_06904390.1| RNA polymerase sigma-K factor [Clostridium difficile NAP07]
 gi|306519787|ref|ZP_07406134.1| sporulation sigma factor SigK [Clostridium difficile QCD-32g58]
 gi|296260041|gb|EFH06895.1| RNA polymerase sigma-K factor [Clostridium difficile NAP08]
 gi|296428668|gb|EFH14552.1| RNA polymerase sigma-K factor [Clostridium difficile NAP07]
          Length = 94

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 17/74 (22%), Positives = 34/74 (45%), Gaps = 3/74 (4%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMS-VLNPRERRIFEARRLQ--ENPVTLENLSS 260
           L+     +   ++++ E K +   L   ++ +L PRER I + R         T   ++ 
Sbjct: 7   LLDILGTEANYVLDEVELKVQVGKLYEQLNKILTPREREIVQLRYGLTPYGYKTQREIAQ 66

Query: 261 EFEVSRERVRQIEA 274
           + ++SR  V +IE 
Sbjct: 67  KLDISRSYVSRIEK 80


>gi|169342173|ref|ZP_02628013.2| bacteriocin UviA [Clostridium perfringens C str. JGS1495]
 gi|169299726|gb|EDS81781.1| bacteriocin UviA [Clostridium perfringens C str. JGS1495]
          Length = 185

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 11/57 (19%), Positives = 29/57 (50%), Gaps = 2/57 (3%)

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +   +  L  +E+++ + + L +       ++     SR+ + +I+  A KK++E+I
Sbjct: 131 IEDMLKCLTEKEQKVIKYKFLNDKSEV--EIAEIMGTSRQWINRIKNTALKKLKENI 185


>gi|302390283|ref|YP_003826104.1| RNA polymerase sigma factor, sigma-70 family [Thermosediminibacter
           oceani DSM 16646]
 gi|302200911|gb|ADL08481.1| RNA polymerase sigma factor, sigma-70 family [Thermosediminibacter
           oceani DSM 16646]
          Length = 141

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 27/145 (18%), Positives = 56/145 (38%), Gaps = 16/145 (11%)

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISM---NCRLAGDESL---NALINSSDKNSSQWQ 201
              + +L PE     A  L   + E   +     +L   E L   N +   +D  S +  
Sbjct: 6   KFYELDLDPEDARIAAWFLKGLKREARRLYLKQKKLKQHELLILNNRVDRDNDGESPELI 65

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           D L           I+   R   R  +  ++ +L  R++++  A        T + ++  
Sbjct: 66  DTLADG--------IDVLSRVEDRIFVREALMMLTARQQKVIMATVF--EGATEKEVAER 115

Query: 262 FEVSRERVRQIEARAFKKVQESIQK 286
             +S+  V +I+ RA  K+++ ++ 
Sbjct: 116 LGISQPAVNKIKNRALSKLKKYLRA 140


>gi|313894725|ref|ZP_07828286.1| sigma-70, region 4 [Selenomonas sp. oral taxon 137 str. F0430]
 gi|312976634|gb|EFR42088.1| sigma-70, region 4 [Selenomonas sp. oral taxon 137 str. F0430]
          Length = 186

 Score = 47.9 bits (113), Expect = 0.002,   Method: Composition-based stats.
 Identities = 16/72 (22%), Positives = 33/72 (45%), Gaps = 2/72 (2%)

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
           G     +  + R    ++LTR+M  L  RE++I       +  +TL  ++     S + V
Sbjct: 107 GMSDPSVNADRRLLLHDILTRAMHRLTEREKKILSLHYYGD--LTLRRIADVLGTSADAV 164

Query: 270 RQIEARAFKKVQ 281
            + +A   +K++
Sbjct: 165 SKGKANLLRKLR 176


>gi|182627195|ref|ZP_02954903.1| bacteriocin [Clostridium perfringens D str. JGS1721]
 gi|177907408|gb|EDT70094.1| bacteriocin [Clostridium perfringens D str. JGS1721]
          Length = 185

 Score = 47.5 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 11/57 (19%), Positives = 29/57 (50%), Gaps = 2/57 (3%)

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +   +  L  +E+++ + + L +       ++     SR+ + +I+  A KK++E+I
Sbjct: 131 IEDMLKCLTEKEQKVIKYKFLNDKSEV--EIAEIMGTSRQWINRIKNTALKKLKENI 185


>gi|60677324|ref|YP_209682.1| bacteriocin [Clostridium perfringens]
 gi|60417959|dbj|BAD90626.1| UviA protein [Clostridium perfringens]
          Length = 185

 Score = 47.5 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 11/57 (19%), Positives = 29/57 (50%), Gaps = 2/57 (3%)

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +   +  L  +E+++ + + L +       ++     SR+ + +I+  A KK++E+I
Sbjct: 131 IEDMLKCLTEKEQKVIKYKFLNDKSEV--EIAEIMGTSRQWINRIKNTALKKLKENI 185


>gi|326776074|ref|ZP_08235339.1| sigma-70 region 4 domain protein [Streptomyces cf. griseus
           XylebKG-1]
 gi|326656407|gb|EGE41253.1| sigma-70 region 4 domain protein [Streptomyces cf. griseus
           XylebKG-1]
          Length = 454

 Score = 47.5 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 20/49 (40%), Positives = 25/49 (51%), Gaps = 4/49 (8%)

Query: 225 RNMLTRSMSV-LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           R  LT++     + R R I EAR       TLE   + F V+RER RQI
Sbjct: 4   RGWLTKAWDTVFDERARGIIEAR---AAGCTLEEAGARFGVTRERARQI 49


>gi|303228975|ref|ZP_07315785.1| RNA polymerase sigma-H factor [Veillonella atypica ACS-134-V-Col7a]
 gi|302516389|gb|EFL58321.1| RNA polymerase sigma-H factor [Veillonella atypica ACS-134-V-Col7a]
          Length = 222

 Score = 47.5 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 22/147 (14%), Positives = 56/147 (38%), Gaps = 6/147 (4%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             ++  V+A   ++  +  A   +V  +   V   A  Y   G    +++ EG IGL +A
Sbjct: 17  TDEQVVVIA---QQEQNEFAIDYIVNKYKNFVRAKARTYFLVGADRDDIIQEGMIGLYKA 73

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQ 147
            + F  ++      ++   I   +   I  +         +  +  +  +     +  L+
Sbjct: 74  TRDFRHDKLASFRAFAELCITRQIITAIKSATRQKHAPLNSYISLNKPVYTEESERTLLE 133

Query: 148 AITD-NNLKPEQVVAIAKKLNVSESEV 173
            ++   +  PE ++   ++L+  E  +
Sbjct: 134 MLSSARSTNPEDLIISQEELDDIEKNI 160


>gi|303231496|ref|ZP_07318226.1| RNA polymerase sigma-H factor [Veillonella atypica ACS-049-V-Sch6]
 gi|302513839|gb|EFL55851.1| RNA polymerase sigma-H factor [Veillonella atypica ACS-049-V-Sch6]
          Length = 222

 Score = 47.5 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 22/147 (14%), Positives = 56/147 (38%), Gaps = 6/147 (4%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             ++  V+A   ++  +  A   +V  +   V   A  Y   G    +++ EG IGL +A
Sbjct: 17  TDEQVVVIA---QQEQNEFAIDYIVNKYKNFVRAKARTYFLVGADRDDIIQEGMIGLYKA 73

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQ 147
            + F  ++      ++   I   +   I  +         +  +  +  +     +  L+
Sbjct: 74  TRDFRHDKLASFRAFAELCITRQIITAIKSATRQKHAPLNSYISLNKPVYTEESERTLLE 133

Query: 148 AITD-NNLKPEQVVAIAKKLNVSESEV 173
            ++   +  PE ++   ++L+  E  +
Sbjct: 134 MLSSARSTNPEDLIISQEELDDIEKNI 160


>gi|34763277|ref|ZP_00144236.1| RNA polymerase sigma-H factor [Fusobacterium nucleatum subsp.
           vincentii ATCC 49256]
 gi|256846014|ref|ZP_05551472.1| RNA polymerase sigma-H factor [Fusobacterium sp. 3_1_36A2]
 gi|294784859|ref|ZP_06750147.1| RNA polymerase sigma-H factor [Fusobacterium sp. 3_1_27]
 gi|27887048|gb|EAA24160.1| RNA polymerase sigma-H factor [Fusobacterium nucleatum subsp.
           vincentii ATCC 49256]
 gi|256719573|gb|EEU33128.1| RNA polymerase sigma-H factor [Fusobacterium sp. 3_1_36A2]
 gi|294486573|gb|EFG33935.1| RNA polymerase sigma-H factor [Fusobacterium sp. 3_1_27]
          Length = 204

 Score = 47.5 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 18/78 (23%), Positives = 38/78 (48%), Gaps = 1/78 (1%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + GD  A   ++  + +L+   A  Y   G    ++V EG +GL++A+K +D  +    
Sbjct: 11  AQSGDSEAISLILKEYSKLLSFNAQKYYLVGAEKEDLVQEGILGLLKAIKFYDETK-SSF 69

Query: 102 ATYSMWWIKAAMQEYILR 119
           ++++   I+  M   I +
Sbjct: 70  SSFAFLCIRREMISAIRK 87


>gi|168211177|ref|ZP_02636802.1| UviA protein [Clostridium perfringens B str. ATCC 3626]
 gi|169344573|ref|ZP_02865539.1| UviA protein [Clostridium perfringens C str. JGS1495]
 gi|169297183|gb|EDS79295.1| UviA protein [Clostridium perfringens C str. JGS1495]
 gi|170710831|gb|EDT23013.1| UviA protein [Clostridium perfringens B str. ATCC 3626]
          Length = 188

 Score = 47.5 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 12/57 (21%), Positives = 28/57 (49%), Gaps = 2/57 (3%)

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             +  L+ +ER+I + + +         +      SR+ V QI+ RA K +++ +++
Sbjct: 134 DLIDKLSEKERKIIKYKYIHGKSDV--EIGKLLNYSRQHVNQIKNRALKNLKKFLEE 188


>gi|199599554|ref|ZP_03212940.1| ComX [Lactobacillus rhamnosus HN001]
 gi|229550809|ref|ZP_04439534.1| competence-specific sigma factor ComX [Lactobacillus rhamnosus
           LMS2-1]
 gi|258507818|ref|YP_003170569.1| hypothetical protein LGG_00823 [Lactobacillus rhamnosus GG]
 gi|258539008|ref|YP_003173507.1| hypothetical protein LC705_00817 [Lactobacillus rhamnosus Lc 705]
 gi|199589543|gb|EDY97663.1| ComX [Lactobacillus rhamnosus HN001]
 gi|229315836|gb|EEN81809.1| competence-specific sigma factor ComX [Lactobacillus rhamnosus
           LMS2-1]
 gi|257147745|emb|CAR86718.1| ComX [Lactobacillus rhamnosus GG]
 gi|257150684|emb|CAR89656.1| ComX [Lactobacillus rhamnosus Lc 705]
 gi|259649154|dbj|BAI41316.1| RNA polymerase factor sigma-70 [Lactobacillus rhamnosus GG]
          Length = 179

 Score = 47.5 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 21/89 (23%), Positives = 37/89 (41%), Gaps = 3/89 (3%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           K+EE  L +      D  A  +L   +  LV+K+   Y        + + E  I +++AV
Sbjct: 2   KKEELSLIREAVN--DSEAFRKLFEQYRPLVLKVLKPYNLREFSYEDWLQEARIAMIKAV 59

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILR 119
            ++D   G +   Y    +  +    ILR
Sbjct: 60  ARYDGSSGSQFGPY-YRMVLQSHLRSILR 87


>gi|223938038|ref|ZP_03629936.1| RNA polymerase, sigma-24 subunit, ECF subfamily [bacterium
           Ellin514]
 gi|223893252|gb|EEF59715.1| RNA polymerase, sigma-24 subunit, ECF subfamily [bacterium
           Ellin514]
          Length = 560

 Score = 47.5 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 17/74 (22%), Positives = 28/74 (37%), Gaps = 10/74 (13%)

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS----RERVRQIE 273
           + +    R+ L   M  LN  +R     R        L  +     +S    R+RV    
Sbjct: 112 ELDWTTLRHALDAVMHELNDADREAILLRYF--EHRQLAEIGERLGLSEDAARKRV---- 165

Query: 274 ARAFKKVQESIQKQ 287
            RA +K++E   K+
Sbjct: 166 DRALEKLREHFAKK 179


>gi|325922773|ref|ZP_08184506.1| DNA-directed RNA polymerase specialized sigma subunit [Xanthomonas
           gardneri ATCC 19865]
 gi|325546748|gb|EGD17869.1| DNA-directed RNA polymerase specialized sigma subunit [Xanthomonas
           gardneri ATCC 19865]
          Length = 128

 Score = 47.5 bits (112), Expect = 0.002,   Method: Composition-based stats.
 Identities = 24/98 (24%), Positives = 46/98 (46%), Gaps = 4/98 (4%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           A+ +VT H  LV +IA          + + +++  G IGL++A + +D E+G    TY+ 
Sbjct: 23  ANDIVTQHADLVRRIAHHLAARLPASVEVDDLIQAGMIGLIEASRSYDSEQGASFETYAS 82

Query: 107 WWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
             I+ +M + I R    V        +     +R+++ 
Sbjct: 83  IRIRGSMIDEIRR-GDWVPRSVHRRARDAAAAVRKIEQ 119


>gi|326800342|ref|YP_004318161.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Sphingobacterium
           sp. 21]
 gi|326551106|gb|ADZ79491.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Sphingobacterium
           sp. 21]
          Length = 198

 Score = 47.5 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 19/87 (21%), Positives = 40/87 (45%), Gaps = 2/87 (2%)

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           +  D+        E V I+KEE +     L + +  L  R+R +   +      ++ E +
Sbjct: 97  ERIDYSFDLEWSPETVWIKKEEDRQLVVKLQQLIKRLPARQREVIYLKF--NEELSYEEI 154

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQ 285
           +S  ++S    R +  RA K+++E ++
Sbjct: 155 ASMLDISIASCRTLIYRAIKQLREHVE 181


>gi|308175056|ref|YP_003921761.1| co-sigma factor [Bacillus amyloliquefaciens DSM 7]
 gi|307607920|emb|CBI44291.1| co-sigma factor with YvrHa [Bacillus amyloliquefaciens DSM 7]
 gi|328555025|gb|AEB25517.1| co-sigma factor with YvrHa [Bacillus amyloliquefaciens TA208]
 gi|328913381|gb|AEB64977.1| co-sigma factor with YvrHa [Bacillus amyloliquefaciens LL3]
          Length = 192

 Score = 47.5 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 14/96 (14%), Positives = 40/96 (41%), Gaps = 6/96 (6%)

Query: 196 NSSQWQDWLVYD--HDGQEQVLIEKEERKNR--RNMLTRSMSVLNPRERRIFEARRLQEN 251
           +  +  + L Y+   D  E+ L ++ +         L  ++  L  +++ +     L  +
Sbjct: 92  DQPEGGETLPYEMGKDAYEEFLRQQGDLSQHVQNRDLYEALQTLTDKQKSVLTNIYL--H 149

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             T++ ++     SR+ +  I  +    +++ + KQ
Sbjct: 150 GATMKEIAESLGESRQNISNIHKKGLGNLRKQLDKQ 185


>gi|300856419|ref|YP_003781403.1| RNA polymerase sigma factor rpoE-like protein [Clostridium
           ljungdahlii DSM 13528]
 gi|300436534|gb|ADK16301.1| RNA polymerase sigma factor rpoE related protein [Clostridium
           ljungdahlii DSM 13528]
          Length = 178

 Score = 47.5 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 18/93 (19%), Positives = 35/93 (37%), Gaps = 4/93 (4%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE V   R  + GD ++   ++      ++K A  Y        ++V  G + +++AVK 
Sbjct: 5   EELV---RKAKSGDKNSMDSIIAKFTCFIIKKAYKYNIPSYDFDDLVQHGYLSVIKAVKL 61

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
           +   +G    TY    I       +       +
Sbjct: 62  YKIGKGS-FTTYCTNSIVNNFNALLKGQIKHFR 93



 Score = 35.9 bits (82), Expect = 7.4,   Method: Composition-based stats.
 Identities = 15/100 (15%), Positives = 41/100 (41%), Gaps = 2/100 (2%)

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
            NAL+    K+  + QD  V      +  L ++    ++   +  ++  L   E ++ ++
Sbjct: 81  FNALLKGQIKHFREVQDEGVLSIQPYDFTLEDEVIAFDQAEKIKLALCKLQDIEIKVIKS 140

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             +     TL+  +    +      +I+  A  K+++ ++
Sbjct: 141 VYM--EGRTLKETAEMLNIKYRHAIEIKKSALNKLKKYLK 178


>gi|29347317|ref|NP_810820.1| putative RNA polymerase sigma factor RpoS [Bacteroides
           thetaiotaomicron VPI-5482]
 gi|29339216|gb|AAO77014.1| putative RNA polymerase sigma factor RpoS [Bacteroides
           thetaiotaomicron VPI-5482]
          Length = 405

 Score = 47.5 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 14/56 (25%), Positives = 26/56 (46%), Gaps = 13/56 (23%)

Query: 236 NPRERRIFEARRLQENPVTLENL------SSEFEVSRERVRQIEARAFKK---VQE 282
           + RE+ IF      E       +        +  +SRER+RQ++ + FKK   +++
Sbjct: 28  SDREQYIFSELYGLEGN----EIQNMISLGDKLGLSRERIRQLKVKVFKKFGILRK 79


>gi|268610544|ref|ZP_06144271.1| RNA polymerase factor sigma-70 [Ruminococcus flavefaciens FD-1]
          Length = 208

 Score = 47.5 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 19/93 (20%), Positives = 42/93 (45%), Gaps = 5/93 (5%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             +E   LAK      D +AA  +++ + +L++  +  Y        ++  EG + L++A
Sbjct: 18  TDEELVSLAK-----TDKAAASVILSRYSKLILIKSKIYANSDTDSEDLHQEGLMSLLKA 72

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           +  +DP  G + +T++   +   M+    R   
Sbjct: 73  INAYDPSMGAKFSTFAEKCVVNRMKTVSARMGR 105


>gi|229828824|ref|ZP_04454893.1| hypothetical protein GCWU000342_00907 [Shuttleworthia satelles DSM
           14600]
 gi|229791987|gb|EEP28101.1| hypothetical protein GCWU000342_00907 [Shuttleworthia satelles DSM
           14600]
          Length = 202

 Score = 47.5 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 31/157 (19%), Positives = 63/157 (40%), Gaps = 15/157 (9%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L + YR  G  ++   L++ +  LV++ A      G    +++ EG +G+  A+  +  
Sbjct: 8   ELLRAYR-GGHDASGEELLSRYKGLVLRNAKSLFLVGGDQDDLIQEGMMGVFSAMLTYRE 66

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT-------------ANQKRLFFNLRRL 142
           +RG    T++   I+  M + I  S +   +                  +  L   L   
Sbjct: 67  DRGASFRTFANLCIRRQMLKAIESSGTKKHMPLNTALSLNLTGEGEGVREADLPEALNPS 126

Query: 143 KG-HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC 178
               LQ + D+      ++ I K L+  E +V+S++ 
Sbjct: 127 PEDPLQILLDDEAVERLLMKIRKSLSPMEEQVLSLHL 163


>gi|9507366|ref|NP_040459.1| bacteriocin [Plasmid pIP404]
 gi|114875|sp|P15935|BCNA_CLOPE RecName: Full=Bacteriocin UviA
 gi|150747|gb|AAA98257.1| bacteriocin [Plasmid pIP404]
          Length = 185

 Score = 47.5 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 11/57 (19%), Positives = 29/57 (50%), Gaps = 2/57 (3%)

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +   +  L  +E+++ + + L +       ++     SR+ + +I+  A KK++E+I
Sbjct: 131 IEDMLKCLTEKEQKVIKYKFLNDKSEV--EIAEIMGTSRQWINRIKNTALKKLKENI 185


>gi|297568140|ref|YP_003689484.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Desulfurivibrio
           alkaliphilus AHT2]
 gi|296924055|gb|ADH84865.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Desulfurivibrio
           alkaliphilus AHT2]
          Length = 183

 Score = 47.5 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 15/56 (26%), Positives = 30/56 (53%), Gaps = 2/56 (3%)

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +  L+ R+RR  E R   E   +   +S+   +S    RQI +RA ++++++  +Q
Sbjct: 126 LDGLDARQRRALELRF--EQGFSFAEISARLGLSTVNARQIISRALRRLRQTFGEQ 179


>gi|319649849|ref|ZP_08004000.1| sigma factor SgiI [Bacillus sp. 2_A_57_CT2]
 gi|317398429|gb|EFV79116.1| sigma factor SgiI [Bacillus sp. 2_A_57_CT2]
          Length = 247

 Score = 47.5 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 21/96 (21%), Positives = 40/96 (41%), Gaps = 11/96 (11%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRL----VVKIAMGYRGYGLPISEVVSEGNIG 85
             +E   L     + GD +  + L+ S+       V  +   Y        +  S G I 
Sbjct: 14  TLEETVELI----QQGDTALNNELIESYKPFIAKTVSSVCKRYI---HESDDEFSIGLIA 66

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
             +A++K+ P++G  L ++S   IK  + +YI +  
Sbjct: 67  FNEAIQKYSPDKGSSLISFSEVLIKRRVIDYIRKQS 102


>gi|298253791|ref|ZP_06977380.1| hypothetical protein GV51_1079 [Gardnerella vaginalis 5-1]
 gi|297532127|gb|EFH71100.1| hypothetical protein GV51_1079 [Gardnerella vaginalis 5-1]
          Length = 159

 Score = 47.5 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 9/61 (14%), Positives = 27/61 (44%), Gaps = 2/61 (3%)

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
                +  + S L  ++R++     +     T   ++S   +S   V++   +A +K+++
Sbjct: 100 EWSEEMEHAFSTLTDKQRQVIRLMFI--EGYTQSEIASMLGISSAGVKKHLDKALEKLRK 157

Query: 283 S 283
           +
Sbjct: 158 T 158


>gi|168185356|ref|ZP_02619991.1| sigma-70 region 2 domain protein [Clostridium botulinum C str.
           Eklund]
 gi|169296292|gb|EDS78425.1| sigma-70 region 2 domain protein [Clostridium botulinum C str.
           Eklund]
          Length = 184

 Score = 47.5 bits (112), Expect = 0.003,   Method: Composition-based stats.
 Identities = 16/84 (19%), Positives = 33/84 (39%), Gaps = 1/84 (1%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             L K+  +  D  A   L+  +   ++K   G    G    +++  G + +++A++K+D
Sbjct: 4   KELIKK-SKAKDEEAIKILIEKYRPFILKTMQGVYIKGYDREDLIQMGYVSIIKAIEKYD 62

Query: 95  PERGFRLATYSMWWIKAAMQEYIL 118
                   +Y    IK      I 
Sbjct: 63  LNSKTPFTSYVCNAIKNNYYYKIR 86


>gi|328554318|gb|AEB24810.1| sporulation sigma factor SigK [Bacillus amyloliquefaciens TA208]
 gi|328912713|gb|AEB64309.1| RNA polymerase sporulation-specific sigma factor (sigma-K)
           (C-terminal half) [Bacillus amyloliquefaciens LL3]
          Length = 64

 Score = 47.1 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 11/40 (27%), Positives = 17/40 (42%), Gaps = 2/40 (5%)

Query: 243 FEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKV 280
              R   +     T   ++ E  +SR  V +IE RA  K+
Sbjct: 2   IVGRFGLDLKKEKTQRGIAKELGISRSYVSRIEKRALMKM 41


>gi|197294401|ref|YP_001798942.1| DNA-directed RNA polymerase,specialized sigma subunit [Candidatus
           Phytoplasma australiense]
 gi|197294480|ref|YP_001799021.1| Putative DNA-directed RNA polymerase,specialized sigma subunit
           [Candidatus Phytoplasma australiense]
 gi|197294806|ref|YP_001799347.1| DNA-directed RNA polymerase specialized sigma subunit [Candidatus
           Phytoplasma australiense]
 gi|171853728|emb|CAM11651.1| DNA-directed RNA polymerase,specialized sigma subunit [Candidatus
           Phytoplasma australiense]
 gi|171853807|emb|CAM11743.1| Putative DNA-directed RNA polymerase,specialized sigma subunit
           [Candidatus Phytoplasma australiense]
 gi|171854133|emb|CAM12124.1| DNA-directed RNA polymerase specialized sigma subunit [Candidatus
           Phytoplasma australiense]
          Length = 223

 Score = 47.1 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 18/89 (20%), Positives = 44/89 (49%), Gaps = 4/89 (4%)

Query: 35  YVLAKRY-REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI--SEVVSEGNIGLMQAVK 91
             L + + +   +L   ++LV  +  LV KI   ++ +   +   ++  EG +GL+ A++
Sbjct: 9   KELFQEFLKNKKNLQIRNQLVEIYYPLVNKIVSKFKYFPSILQRQDLFQEGVLGLINALE 68

Query: 92  KFDPERGF-RLATYSMWWIKAAMQEYILR 119
            +D +    +   Y+   IK+ +++ I +
Sbjct: 69  GYDFQVDIDQFIYYASKNIKSHIRDLIKK 97


>gi|313158401|gb|EFR57800.1| RNA polymerase sigma-70 factor [Alistipes sp. HGB5]
          Length = 178

 Score = 47.1 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 15/90 (16%), Positives = 37/90 (41%), Gaps = 8/90 (8%)

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           SQ    +   +D  +  ++ K    + R  L +++  L  + R IF  R  +   ++ + 
Sbjct: 93  SQIDRMVFDYYDPDKNPILAKIYDNDMRQQLRQAVDELPDKRREIFRMRFFEN--MSNKE 150

Query: 258 LSSEFEVSRERVRQIEAR---AFKKVQESI 284
           +     ++   V  +E     A K +++ +
Sbjct: 151 IGERLGLT---VSTVENHMYLALKNLRDKL 177


>gi|229136063|ref|ZP_04264819.1| RNA polymerase sigma factor [Bacillus cereus BDRD-ST196]
 gi|228647384|gb|EEL03463.1| RNA polymerase sigma factor [Bacillus cereus BDRD-ST196]
          Length = 156

 Score = 47.1 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 17/84 (20%), Positives = 40/84 (47%), Gaps = 2/84 (2%)

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           + +V +         E+ E ++        MSVL+ +E+ I   R      +    ++SE
Sbjct: 74  ECVVQERYVCTDEYEERFECEDVGTRAKDFMSVLDEKEKHIISERFFTGKNMG--EIASE 131

Query: 262 FEVSRERVRQIEARAFKKVQESIQ 285
             ++  +VR +  +A +K+++S++
Sbjct: 132 MGMTYYQVRWVYRQALEKMRDSVR 155


>gi|225377344|ref|ZP_03754565.1| hypothetical protein ROSEINA2194_02991 [Roseburia inulinivorans DSM
           16841]
 gi|225210875|gb|EEG93229.1| hypothetical protein ROSEINA2194_02991 [Roseburia inulinivorans DSM
           16841]
          Length = 235

 Score = 47.1 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 20/87 (22%), Positives = 36/87 (41%), Gaps = 1/87 (1%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L ++ R  GD +    ++  +  LV K A      G    +++ EG IGL +A++ +  
Sbjct: 42  ALLRQLR-AGDAAIMDYVLDKYKPLVRKKANAMFLIGGDTDDLIQEGMIGLFKAIRDYRE 100

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWS 122
           ER      ++   I   +   I  S  
Sbjct: 101 ERETSFFHFAELCITRQIYSAIEASNR 127


>gi|182416009|ref|YP_001821075.1| ECF subfamily RNA polymerase sigma-24 factor [Opitutus terrae
           PB90-1]
 gi|177843223|gb|ACB77475.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Opitutus terrae
           PB90-1]
          Length = 407

 Score = 47.1 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 17/79 (21%), Positives = 33/79 (41%), Gaps = 2/79 (2%)

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
             +    R++L  ++  L P E+     R       TL  + +   V+ E  R+   RA 
Sbjct: 118 NADFARLRSVLDDALVELKPDEQEAIVLRFF--EKHTLAEVGAVLRVTEEAARKRVDRAL 175

Query: 278 KKVQESIQKQVELSSSPPL 296
           +K+   + ++   S+S  L
Sbjct: 176 EKLHGVLTRRGITSTSVAL 194


>gi|323701219|ref|ZP_08112894.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
 gi|323533821|gb|EGB23685.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
          Length = 236

 Score = 47.1 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 19/143 (13%), Positives = 56/143 (39%), Gaps = 12/143 (8%)

Query: 36  VLAKRYREHGDLSAAHRLVTSH----LRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
            L +R + +GD  A   L+  H     R+  +I   +  +     + +S   +   +A+ 
Sbjct: 8   RLLQRAK-NGDEGAREELIRKHRDFIARVSSRICKRFLCWEND--DELSIALLAFNEAID 64

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL-----RRLKGHL 146
            +  +R    ++++   I   + +Y  ++ +  ++  +A+Q     ++     R+ +   
Sbjct: 65  SYHFDRRTSFSSFAYTVIHRRLTDYFRKNPAKYELLLSADQDDTEDSISSLLDRQAQDTY 124

Query: 147 QAITDNNLKPEQVVAIAKKLNVS 169
           +         E +    ++L+  
Sbjct: 125 RDQLQREKMAETIDLFRQRLSCY 147


>gi|154687438|ref|YP_001422599.1| YvrI [Bacillus amyloliquefaciens FZB42]
 gi|154353289|gb|ABS75368.1| YvrI [Bacillus amyloliquefaciens FZB42]
          Length = 192

 Score = 47.1 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 11/100 (11%), Positives = 40/100 (40%), Gaps = 3/100 (3%)

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARR 247
            +        +   + +     +E +  + +  ++ +N  L  ++  L  +++ +     
Sbjct: 88  PLTVDQPEGGEALPYEMGKDAYEEFLRKQGDLSQHVQNRDLYEALQTLTDKQKSVLTNIY 147

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L  +  T++ ++     SR+ +  I  +    +++ + KQ
Sbjct: 148 L--HGATMKEIAESLGESRQNISNIHKKGLDNLRKQLDKQ 185


>gi|110804015|ref|YP_699922.1| bacteriocin uviA [Clostridium perfringens SM101]
 gi|110684516|gb|ABG87884.1| bacteriocin uviA [Clostridium perfringens SM101]
          Length = 190

 Score = 47.1 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 11/57 (19%), Positives = 29/57 (50%), Gaps = 2/57 (3%)

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +   +  L  +E+++ + + L +       ++     SR+ + +I+  A KK++E+I
Sbjct: 136 IEDMLKCLTEKEQKVIKYKFLNDKSEV--EIAEIMGTSRQWINRIKNTALKKLKENI 190


>gi|313124316|ref|YP_004034575.1| comx [Lactobacillus delbrueckii subsp. bulgaricus ND02]
 gi|312280879|gb|ADQ61598.1| ComX [Lactobacillus delbrueckii subsp. bulgaricus ND02]
          Length = 212

 Score = 47.1 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 19/101 (18%), Positives = 35/101 (34%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K+ E +L  R ++  D  A   L  S L ++      Y        +   E  I   +
Sbjct: 26  LTKERERLLISRIQKDDDEQALKELYYSCLPVIGGTIKQYFVELYDSQDWEQEALILCYK 85

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
             K+FD ++G     +    +       I R     ++  +
Sbjct: 86  TAKRFDLKQGKPFVGFYKVSLHNRAINLIRRGKRKKRLAAS 126


>gi|154502840|ref|ZP_02039900.1| hypothetical protein RUMGNA_00655 [Ruminococcus gnavus ATCC 29149]
 gi|153796723|gb|EDN79143.1| hypothetical protein RUMGNA_00655 [Ruminococcus gnavus ATCC 29149]
          Length = 211

 Score = 47.1 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 21/104 (20%), Positives = 43/104 (41%), Gaps = 4/104 (3%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
            +  ML  +    L +  R  GD +    ++  +  +V K A      G    +++ EG 
Sbjct: 8   NRYEMLTDE---NLIEELR-GGDSAITDFIMNKYKPMVRKKARAMFLLGGENEDLIQEGM 63

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           IGL +A++ ++  +G   A+++   +   M   I  S     + 
Sbjct: 64  IGLFKAIRDYETRQGTSFASFAELCVSRQMYSAIEASQRKKHLP 107


>gi|325685665|gb|EGD27747.1| putative RNA polymerase sigma factor [Lactobacillus delbrueckii
           subsp. lactis DSM 20072]
          Length = 212

 Score = 47.1 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 19/101 (18%), Positives = 35/101 (34%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K+ E +L  R ++  D  A   L  S L ++      Y        +   E  I   +
Sbjct: 26  LTKERERLLISRIQKDDDEQALKELYYSCLPVIGGTIKQYFVELYDSQDWEQEALILCYK 85

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
             K+FD ++G     +    +       I R     ++  +
Sbjct: 86  TAKRFDLKQGKPFVGFYKVSLHNRAINLIRRGKRKKRLAAS 126


>gi|322421804|ref|YP_004201027.1| hypothetical protein GM18_4340 [Geobacter sp. M18]
 gi|320128191|gb|ADW15751.1| hypothetical protein GM18_4340 [Geobacter sp. M18]
          Length = 1030

 Score = 47.1 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 10/44 (22%), Positives = 22/44 (50%), Gaps = 2/44 (4%)

Query: 240 RRIFE--ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R++     R +  +   L  L   + V+ ER+RQ+E++    ++
Sbjct: 321 RQVLRSRLRLVDGSKCQLRELGRRYGVTGERIRQMESKVMAVLK 364


>gi|70727569|ref|YP_254485.1| hypothetical protein SH2570 [Staphylococcus haemolyticus JCSC1435]
 gi|68448295|dbj|BAE05879.1| unnamed protein product [Staphylococcus haemolyticus JCSC1435]
          Length = 112

 Score = 47.1 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 22/99 (22%), Positives = 41/99 (41%), Gaps = 4/99 (4%)

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM-SVLNPRERR 241
           D S      + +  ++   D+     + +   L E    +   N L + + +V   RE  
Sbjct: 14  DYSKENHDTTYNDKNTNIDDFFSLSDEVEPFELSENTSNQVFFNELDQLIYTVGTRREYY 73

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           IF    L     ++  ++  FE+SRER+RQ+      K+
Sbjct: 74  IF---FLLCEGKSINEIAKIFELSRERIRQLLNSLLDKL 109


>gi|150017104|ref|YP_001309358.1| ECF subfamily RNA polymerase sigma-24 factor [Clostridium
           beijerinckii NCIMB 8052]
 gi|149903569|gb|ABR34402.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           beijerinckii NCIMB 8052]
          Length = 190

 Score = 47.1 bits (111), Expect = 0.003,   Method: Composition-based stats.
 Identities = 17/83 (20%), Positives = 34/83 (40%), Gaps = 2/83 (2%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           ++ D  A  +L      L+  I+           +++ E    L ++V K++ E+  R  
Sbjct: 14  KNNDEDAKEKLAYEFRPLIYNISKRTFIDRYNFHDIIQECYHSLFKSVSKYNLEK-HRFV 72

Query: 103 TYSMWWIKAAMQEYILRSWSLVK 125
            Y+   IK  M + I R+    +
Sbjct: 73  AYATNAIKNNMNDLIKRT-RTRR 94


>gi|256425106|ref|YP_003125759.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Chitinophaga
           pinensis DSM 2588]
 gi|256040014|gb|ACU63558.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Chitinophaga
           pinensis DSM 2588]
          Length = 190

 Score = 47.1 bits (111), Expect = 0.004,   Method: Composition-based stats.
 Identities = 24/103 (23%), Positives = 41/103 (39%), Gaps = 8/103 (7%)

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L  LI      S Q  D       G +   IE EE       + +++S L  R+R I   
Sbjct: 80  LFRLIKEQQNTSYQEDDLSFSFELGFDARFIEGEEAAILSAQIRQALSKLTSRQREIIWF 139

Query: 246 RRLQENPVTLENLSSEFEVSRERVR---QIEARAFKKVQESIQ 285
           R       + E ++   +    +VR   ++ ARA   ++E ++
Sbjct: 140 RFF--EGRSFEEIAEIMD---MQVRATYKLSARALASLKEIME 177


>gi|168204769|ref|ZP_02630774.1| putative sigma factor [Clostridium perfringens E str. JGS1987]
 gi|170663697|gb|EDT16380.1| putative sigma factor [Clostridium perfringens E str. JGS1987]
          Length = 181

 Score = 47.1 bits (111), Expect = 0.004,   Method: Composition-based stats.
 Identities = 41/233 (17%), Positives = 84/233 (36%), Gaps = 59/233 (25%)

Query: 54  VTSHLRLVVKIAMGY--RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           V  ++    K+A  +  +   + I E+ S   +GL++A K+F+  +G    TY+M  I+ 
Sbjct: 4   VEDYIGAAYKVASKFYSKNLDMSIDEINSIAFLGLLKAKKRFEY-KGVEFVTYAMKTIEY 62

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            ++  + R  S  +    A +                                       
Sbjct: 63  EIKNSLYRDRSKFRRKIIAGK--------------------------------------- 83

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
               +  R+  D SL+  INS+D    +  D LV + +  E V             L  +
Sbjct: 84  ---DVYERIYTD-SLDKEINSADG--VKLIDCLVEEFNIDEYV---------ENIDLKIA 128

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           ++ LN  +R+I +     E   T    +    V  + + + + +    ++E++
Sbjct: 129 INKLNTYQRKILKMIYFDE--KTQRETAKILCVHEKTISREKKKILNLLRETL 179


>gi|225166763|ref|YP_002650748.1| putative RNA polymerase sigma factor [Clostridium botulinum]
 gi|253771350|ref|YP_003034243.1| RNA polymerase sigma-70 factor family [Clostridium botulinum D str.
           1873]
 gi|225007427|dbj|BAH29523.1| putative RNA polymerase sigma factor [Clostridium botulinum]
 gi|253721327|gb|ACT33620.1| RNA polymerase sigma-70 factor family [Clostridium botulinum D str.
           1873]
          Length = 182

 Score = 46.7 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 30/168 (17%), Positives = 65/168 (38%), Gaps = 30/168 (17%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L K+ +E GD ++   ++  +   + K A  Y   G    ++V  G + +++A+ K+   
Sbjct: 4   LIKKAKE-GDRASIISIIEKYKPFIFKCAHKYNIPGYDFQDLVQHGYLSVIKAIHKYTLG 62

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVK------------------------IGTTANQ 132
                 +Y+ ++I +    +       +K                        I      
Sbjct: 63  SN----SYNGYFINSISLNFKALLKGEIKHFREVPDDKIMDKDDYYDFTLDDEIIAYDEV 118

Query: 133 KRLFFNLRRLKGHLQAITDNN-LKPEQVVAIAKKLNVSESEVISMNCR 179
           ++L+ +L +L+   + I + + +K E    IA  L+V    VI +  R
Sbjct: 119 EKLYKSLNKLEPLEREIINRHYIKGESYSEIACSLDVKYDRVIYLKKR 166



 Score = 41.0 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 16/83 (19%), Positives = 37/83 (44%), Gaps = 2/83 (2%)

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
             D ++   D  +  L ++    +    L +S++ L P ER I     ++    +   ++
Sbjct: 93  PDDKIMDKDDYYDFTLDDEIIAYDEVEKLYKSLNKLEPLEREIINRHYIKGESYS--EIA 150

Query: 260 SEFEVSRERVRQIEARAFKKVQE 282
              +V  +RV  ++ R F K+++
Sbjct: 151 CSLDVKYDRVIYLKKRGFLKIRK 173


>gi|318040245|ref|ZP_07972201.1| RNA polymerase sigma factor, sigma-70 family protein [Synechococcus
           sp. CB0101]
          Length = 89

 Score = 46.7 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 18/81 (22%), Positives = 41/81 (50%), Gaps = 2/81 (2%)

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ--ENPVTLENLSSEFEVSRERVRQI 272
             E  + +  R+ +   +  L   + R+ + R     E P++L +++ E E+SR+R R +
Sbjct: 9   PEELVDGECLRSDMRDLLDQLPELQGRVLKMRYGIGIEEPMSLSSIARELEMSRDRARSL 68

Query: 273 EARAFKKVQESIQKQVELSSS 293
           E RA ++++   Q+     ++
Sbjct: 69  ERRAHEEMRRLSQQMGAYLAA 89


>gi|332524258|ref|ZP_08400482.1| FliA/WhiG family RNA polymerase sigma 28 subunit [Rubrivivax
           benzoatilyticus JA2]
 gi|332107591|gb|EGJ08815.1| FliA/WhiG family RNA polymerase sigma 28 subunit [Rubrivivax
           benzoatilyticus JA2]
          Length = 304

 Score = 46.7 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 34/238 (14%), Positives = 83/238 (34%), Gaps = 25/238 (10%)

Query: 53  LVTSHLRLVVKIAM---GYRGYGLPISEVVSEGNIGLMQAVKKFDPE-------RGFRLA 102
           LV  +   V + A     +    +  ++++  G I + QA   F  +            A
Sbjct: 11  LVARNQSWVRQQAQSLVRHLPANVEKADLIQVGLIAVAQASLSFVWDGDPDTAEAHEAFA 70

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
            Y+   +K AM + + R   +     T  Q+R    L+  +   ++          +  +
Sbjct: 71  RYARQRVKGAMIDEL-RQMDV----LTRAQRRKIKVLQIARERWRSTNGGEAG---LAEL 122

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           A+   +   EV  +       +  ++     +   ++           ++  +  + +  
Sbjct: 123 ARLCKMDLEEVALLEQLAQASQQRSSSGEDDEPEFTERHHPA-----TEKDEVEARVDTA 177

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                L    + L  RERR+ +A       ++   L++  +V+  RV Q+     +++
Sbjct: 178 IVLRHLETFFAQLPERERRVIDAYLGIG--MSPVELAASLKVTPSRVSQMYHGLLRRM 233


>gi|255525392|ref|ZP_05392331.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           carboxidivorans P7]
 gi|296188002|ref|ZP_06856394.1| sigma-70 region 2 [Clostridium carboxidivorans P7]
 gi|255510963|gb|EET87264.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           carboxidivorans P7]
 gi|296047128|gb|EFG86570.1| sigma-70 region 2 [Clostridium carboxidivorans P7]
          Length = 181

 Score = 46.7 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 16/90 (17%), Positives = 35/90 (38%), Gaps = 2/90 (2%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L K+ +  GD +A   ++      V+K A  Y        ++V  G + ++++V  ++ 
Sbjct: 7   ELVKKAK-SGDRAAVDEIIGKFKYFVIKQASKYSIPSYDFEDLVQHGYLSIIKSVHLYNT 65

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            RG    TY    +    +  +       +
Sbjct: 66  GRGS-FTTYCTNAVINNFKALLKGQIKHYR 94


>gi|210608926|ref|ZP_03288063.1| hypothetical protein CLONEX_00243 [Clostridium nexile DSM 1787]
 gi|210152843|gb|EEA83849.1| hypothetical protein CLONEX_00243 [Clostridium nexile DSM 1787]
          Length = 155

 Score = 46.7 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 21/84 (25%), Positives = 36/84 (42%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            G+      ++  +  LV K A      G    +++ EG IGL +AV+ +D E+G   A+
Sbjct: 18  AGEQEITDYVMDKYKFLVKKKAKEMYLLGGENDDLIQEGMIGLFKAVRDYDSEQGTSFAS 77

Query: 104 YSMWWIKAAMQEYILRSWSLVKIG 127
           ++   I   M   I  S     + 
Sbjct: 78  FADLCISRQMYSAIKASQRQKHMP 101


>gi|302390942|ref|YP_003826762.1| RNA polymerase, sigma 30 subunit, SigH [Acetohalobium arabaticum
           DSM 5501]
 gi|302203019|gb|ADL11697.1| RNA polymerase, sigma 30 subunit, SigH [Acetohalobium arabaticum
           DSM 5501]
          Length = 217

 Score = 46.7 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 21/102 (20%), Positives = 35/102 (34%), Gaps = 4/102 (3%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
              L   E    A    + G+  A   L+  +   V   A  Y   G    ++V EG IG
Sbjct: 16  YDQLTDDELVQFA----QDGNQLAMEYLLKKYKNFVRNRARSYFLIGAGRDDLVQEGMIG 71

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
           L +A+  +  ER     +++   I   +   I  +       
Sbjct: 72  LYKAICDYKVERLASFQSFAELCITRQLITAIKTATRQKHQP 113


>gi|224023371|ref|ZP_03641737.1| hypothetical protein BACCOPRO_00064 [Bacteroides coprophilus DSM
           18228]
 gi|224016593|gb|EEF74605.1| hypothetical protein BACCOPRO_00064 [Bacteroides coprophilus DSM
           18228]
          Length = 404

 Score = 46.7 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 2/47 (4%)

Query: 235 LNPRERRIFEARRLQENPVTL--ENLSSEFEVSRERVRQIEARAFKK 279
           L  RER +F +    +   T     +++E  + +ER+RQ+E + FKK
Sbjct: 28  LKERERMLFISLYGLDETDTRNHTEMAAELGLCKERIRQLEVKVFKK 74


>gi|160944373|ref|ZP_02091601.1| hypothetical protein FAEPRAM212_01883 [Faecalibacterium prausnitzii
           M21/2]
 gi|158444155|gb|EDP21159.1| hypothetical protein FAEPRAM212_01883 [Faecalibacterium prausnitzii
           M21/2]
          Length = 1010

 Score = 46.7 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 15/59 (25%), Positives = 29/59 (49%), Gaps = 4/59 (6%)

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           RK     +    S+ +P+E+     R    +   L+++   + ++RER+RQI  +  KK
Sbjct: 383 RKTLSEYIHNLESLDDPKEKM-LAERL---HGAALQDVGERYGLTRERIRQIAVKQLKK 437


>gi|228964014|ref|ZP_04125144.1| hypothetical protein bthur0004_8740 [Bacillus thuringiensis serovar
           sotto str. T04001]
 gi|228795666|gb|EEM43143.1| hypothetical protein bthur0004_8740 [Bacillus thuringiensis serovar
           sotto str. T04001]
          Length = 1430

 Score = 46.7 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 20/84 (23%), Positives = 37/84 (44%), Gaps = 8/84 (9%)

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR---LQENPVTLEN 257
            + + Y+ D  +++L +  E  +    L  S   L      I   R    L     TLE 
Sbjct: 724 DERMQYETDQLKEMLQDMLENGSIHTKLKISEKAL-----EIMRERYEGTLNGKRPTLEE 778

Query: 258 LSSEFEVSRERVRQIEARAFKKVQ 281
            +   +V+RER+RQI  ++  +++
Sbjct: 779 TAQNHDVTRERIRQIVKKSVGRIR 802


>gi|313904854|ref|ZP_07838226.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Eubacterium
           cellulosolvens 6]
 gi|313470287|gb|EFR65617.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Eubacterium
           cellulosolvens 6]
          Length = 195

 Score = 46.7 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 22/87 (25%), Positives = 40/87 (45%), Gaps = 1/87 (1%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L +R+R  G++     LV  +  LV   A      G    +++ EG IGL +AV+++D 
Sbjct: 14  ELIRRFR-AGEVQIGDYLVEKYKPLVKSKARELFLAGGDHEDLLQEGMIGLFRAVREYDE 72

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWS 122
           +R     T+++  +   M   I  +  
Sbjct: 73  DREASFRTFALLLVTRQMYSAIQGAQR 99


>gi|210610578|ref|ZP_03288504.1| hypothetical protein CLONEX_00694 [Clostridium nexile DSM 1787]
 gi|210152437|gb|EEA83443.1| hypothetical protein CLONEX_00694 [Clostridium nexile DSM 1787]
          Length = 211

 Score = 46.7 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 10/63 (15%), Positives = 26/63 (41%), Gaps = 2/63 (3%)

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           E   R+  +   + +L  R++ +           +   ++ +  VS   V +I  RA  +
Sbjct: 142 ETTIRKETMRELLGLLTDRQKEVIVQYFW--EQKSQSEIAEKLGVSHAAVSKILTRAINR 199

Query: 280 VQE 282
           +++
Sbjct: 200 LRK 202


>gi|163754805|ref|ZP_02161927.1| putative RNA polymerase sigma factor [Kordia algicida OT-1]
 gi|161325746|gb|EDP97073.1| putative RNA polymerase sigma factor [Kordia algicida OT-1]
          Length = 171

 Score = 46.7 bits (110), Expect = 0.004,   Method: Composition-based stats.
 Identities = 17/80 (21%), Positives = 35/80 (43%), Gaps = 8/80 (10%)

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D   Q      E    +  L  +++ L+ +ER +F   R++        ++   ++S++ 
Sbjct: 95  DRTNQDPAYIMEENEFKQKLQNAIADLDDKEREVFLLSRVEGKKY--REIAELLDISQKT 152

Query: 269 VRQIEAR---AFKKVQESIQ 285
           V   E R   A KK++  I+
Sbjct: 153 V---EKRMSLALKKLRAKIE 169


>gi|170754474|ref|YP_001780381.1| sigma-70 family RNA polymerase sigma factor [Clostridium botulinum
           B1 str. Okra]
 gi|169119686|gb|ACA43522.1| RNA polymerase sigma-70 factor family [Clostridium botulinum B1
           str. Okra]
          Length = 130

 Score = 46.7 bits (110), Expect = 0.005,   Method: Composition-based stats.
 Identities = 26/134 (19%), Positives = 55/134 (41%), Gaps = 8/134 (5%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
            Y L ++YR +GD+ A + ++ +   L++K A  +R       ++V  G + +++ V  F
Sbjct: 1   MYNLLEKYR-NGDMGALNEIIENFNPLILKEASKWRIGCYEYEDLVQHGYLSVIKVVNMF 59

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
             E     + +  + I A    Y       +K      +      L +   ++  I D  
Sbjct: 60  KGEE----SKFVPYCINAIKTNYKALLKGEIK---HHREIPDENILNKGNEYMFTIEDEI 112

Query: 154 LKPEQVVAIAKKLN 167
           +  E+   I + L+
Sbjct: 113 IAYEKTKEIYEALD 126


>gi|269125238|ref|YP_003298608.1| ECF subfamily RNA polymerase sigma-24 subunit [Thermomonospora
           curvata DSM 43183]
 gi|268310196|gb|ACY96570.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermomonospora
           curvata DSM 43183]
          Length = 173

 Score = 46.3 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 16/62 (25%), Positives = 30/62 (48%), Gaps = 2/62 (3%)

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           ER      L   ++ L  R+R +   R  ++  ++ E +++   +SR  VR   ARA  K
Sbjct: 98  ERAEHDPRLWDLLTALPRRQRAVLVLRYYED--MSDEEIAATLGISRGTVRSQAARALDK 155

Query: 280 VQ 281
           ++
Sbjct: 156 LR 157


>gi|119964667|gb|ABM17096.1| putative RNA polymerase sigma factor [Sulfobacillus acidophilus DSM
           10332]
          Length = 177

 Score = 46.3 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 12/70 (17%), Positives = 32/70 (45%), Gaps = 2/70 (2%)

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
              +  ++ +   + L  ++  L+ RERR+ +         T + +++ + V    V+ +
Sbjct: 99  DSPVVDDDGEEDHDWLQDALGQLSDRERRVLQLAYYYG--FTQKEIAALWGVPVGTVKSL 156

Query: 273 EARAFKKVQE 282
            +RA  K++ 
Sbjct: 157 ASRAIHKLRR 166


>gi|313888184|ref|ZP_07821858.1| sigma-70, region 4 [Peptoniphilus harei ACS-146-V-Sch2b]
 gi|312845874|gb|EFR33261.1| sigma-70, region 4 [Peptoniphilus harei ACS-146-V-Sch2b]
          Length = 246

 Score = 46.3 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 15/90 (16%), Positives = 35/90 (38%), Gaps = 3/90 (3%)

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRR-NMLTRSMSVLNPRERRIFEARRLQENPVT 254
           + +  ++ L         V IE +  +  R  +L  ++  L PR+  +          + 
Sbjct: 154 DDAPDEEGLSIFDSLDAGVDIESDFLEAERLGILKEALDSLTPRQALVVRLFFY--ERLG 211

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L  ++    +SR  V  ++  A   +++ I
Sbjct: 212 LSEIADFLGISRWTVVNLKRNAIANLRKFI 241


>gi|296130343|ref|YP_003637593.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Cellulomonas
           flavigena DSM 20109]
 gi|296022158|gb|ADG75394.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Cellulomonas
           flavigena DSM 20109]
          Length = 178

 Score = 46.3 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 17/85 (20%), Positives = 44/85 (51%), Gaps = 2/85 (2%)

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           + L       E+ +   +   + R+ L R+++ L PR+RR+   R L    ++ + ++ +
Sbjct: 82  EVLAAAEHLPERAVEGGQSLHDDRDQLARALATLTPRQRRVVVLRHL--EGLSEQEVADD 139

Query: 262 FEVSRERVRQIEARAFKKVQESIQK 286
             +S   V+   +RA ++++E++ +
Sbjct: 140 LGISVGTVKSTASRALRQLRETMDR 164


>gi|282850299|ref|ZP_06259678.1| RNA polymerase sigma-H factor [Veillonella parvula ATCC 17745]
 gi|294793807|ref|ZP_06758944.1| RNA polymerase sigma-H factor [Veillonella sp. 3_1_44]
 gi|282579792|gb|EFB85196.1| RNA polymerase sigma-H factor [Veillonella parvula ATCC 17745]
 gi|294455377|gb|EFG23749.1| RNA polymerase sigma-H factor [Veillonella sp. 3_1_44]
          Length = 224

 Score = 46.3 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 18/98 (18%), Positives = 36/98 (36%), Gaps = 3/98 (3%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             ++  V+A   +E  +  A   +V  +   V   A  Y   G    +++ EG IGL +A
Sbjct: 17  TDEQVVVIA---QEEQNEFAIDYIVNKYKNFVRAKARSYFLVGADREDIIQEGMIGLYKA 73

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
            + F  ++      ++   I   +   I  +       
Sbjct: 74  TRDFKHDKLASFRAFAELCITRQIITAIKSATRQKHAP 111


>gi|168205269|ref|ZP_02631274.1| RNA polymerase sigma factor, sigma-70 family [Clostridium
           perfringens E str. JGS1987]
 gi|170663095|gb|EDT15778.1| RNA polymerase sigma factor, sigma-70 family [Clostridium
           perfringens E str. JGS1987]
          Length = 205

 Score = 46.3 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 20/78 (25%), Positives = 37/78 (47%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + G+     +L+  +   + K    +    +   EV +   IGLM A+  F+  RG +L
Sbjct: 13  AQKGNKECLGQLINYYDGYIKKFIKLFNLTAVQEEEVYNSAIIGLMTALDNFNVSRGLKL 72

Query: 102 ATYSMWWIKAAMQEYILR 119
            TY+  +IK  + E+I +
Sbjct: 73  NTYATGFIKKEIVEFIKK 90


>gi|205374842|ref|ZP_03227635.1| hypothetical protein Bcoam_17560 [Bacillus coahuilensis m4-4]
          Length = 174

 Score = 46.3 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 22/100 (22%), Positives = 49/100 (49%), Gaps = 5/100 (5%)

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L+A I   D+N   +++W+V +     +  +   E    R  +  +M +L   ++R  E 
Sbjct: 78  LDAPIK--DENMETYKEWIVGETPSYYEHSL-HLEDVLDRQDVWEAMKLLTKNQKRTLEY 134

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             +++   T   ++SEF +S++ V +    A KK++  ++
Sbjct: 135 AYIKDMKDT--EIASEFGISQQAVSKTRQSALKKLRRRLK 172


>gi|89885916|ref|YP_516114.1| XRE family transcriptional regulator [Rhodoferax ferrireducens
           T118]
 gi|89347914|gb|ABD72116.1| transcriptional regulator, XRE family [Rhodoferax ferrireducens
           T118]
          Length = 887

 Score = 46.3 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 17/48 (35%), Positives = 23/48 (47%), Gaps = 5/48 (10%)

Query: 233 SVLNPRER---RIFEARRL--QENPVTLENLSSEFEVSRERVRQIEAR 275
            +L P E+    IF  R     E   TLE+      V+RER+RQI  +
Sbjct: 413 GLLTPTEKSWAEIFSVRYGVQGEGQSTLESGGKRVGVTRERIRQIVKK 460


>gi|225166748|ref|YP_002650733.1| putative RNA polymerase sigma factor [Clostridium botulinum]
 gi|253771400|ref|YP_003034227.1| RNA polymerase sigma-70 factor family [Clostridium botulinum D
          str. 1873]
 gi|225007412|dbj|BAH29508.1| putative RNA polymerase sigma factor [Clostridium botulinum]
 gi|253721377|gb|ACT33670.1| RNA polymerase sigma-70 factor family [Clostridium botulinum D
          str. 1873]
          Length = 146

 Score = 46.3 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 13/58 (22%), Positives = 29/58 (50%), Gaps = 1/58 (1%)

Query: 37 LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
          L K+ +E GD ++   ++  +   + K A  Y   G    ++V  G + +++A+ K+ 
Sbjct: 4  LIKKAKE-GDRASIISIIEKYKPFIFKCAHKYNIPGYDFEDLVQHGYLSVIKAIHKYT 60


>gi|22299523|ref|NP_682770.1| putative RNA polymerase sigma factor [Thermosynechococcus elongatus
           BP-1]
 gi|22295706|dbj|BAC09532.1| tll1980 [Thermosynechococcus elongatus BP-1]
          Length = 376

 Score = 46.3 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 40/219 (18%), Positives = 81/219 (36%), Gaps = 37/219 (16%)

Query: 93  FDPERGFRLATYSMWWIKAAMQEYI----------LRSWSLVKIGTTANQK----RLFFN 138
           FDP+RG RL+TY+   I   +   +          LR     ++ +    +        +
Sbjct: 115 FDPQRGTRLSTYAYRRIYDQVYAALVGVRQSDWGLLRDTGRRRLSSALKNQGYSEDKIVH 174

Query: 139 LRRLKGHLQAITDNNLKP-----EQVVAIAKKLNVSESEVIS------MNCRLAGDESLN 187
           +++L    Q + D    P     EQVV I  +       V S      +   ++   +  
Sbjct: 175 IQQLVHLWQELADQPTAPDQALLEQVVKIYHQCRPDLPCVTSREVGTLLRTAISALRAHG 234

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR--NMLTRSMSVLNPRERRIFEA 245
                +      W      ++   E +L ++E+   +R   +L  ++  L+   R++F  
Sbjct: 235 QPQVVNTAEERFWDILEGRENMPWEAILKQEEQETLKRVFEILKNAVETLDDASRQVFCL 294

Query: 246 RRLQENPVTLENLSSEFE------VSR--ERVRQIEARA 276
                  ++ + ++ +        VSR  ER+R   A+A
Sbjct: 295 YY--CEQLSQQQIAQDLGFEKQYKVSRALERIRSHLAKA 331


>gi|300811850|ref|ZP_07092316.1| RNA polymerase sigma factor, sigma-70 family [Lactobacillus
           delbrueckii subsp. bulgaricus PB2003/044-T3-4]
 gi|300497169|gb|EFK32225.1| RNA polymerase sigma factor, sigma-70 family [Lactobacillus
           delbrueckii subsp. bulgaricus PB2003/044-T3-4]
          Length = 189

 Score = 46.3 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 19/101 (18%), Positives = 35/101 (34%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K+ E +L  R ++  D  A   L  S L ++      Y        +   E  I   +
Sbjct: 3   LTKERERLLISRIQKDDDEQALKELYYSCLPVIGGTIKQYFVELYDNQDWEQEALILCYK 62

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
             K+FD ++G     +    +       I R     ++  +
Sbjct: 63  TAKRFDLKQGKPFVGFYKVSLHNRAINLIRRGKRKKRLAAS 103


>gi|269121539|ref|YP_003309716.1| RNA polymerase, sigma 32 subunit, RpoH [Sebaldella termitidis ATCC
           33386]
 gi|268615417|gb|ACZ09785.1| RNA polymerase, sigma 32 subunit, RpoH [Sebaldella termitidis ATCC
           33386]
          Length = 309

 Score = 46.3 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 43/254 (16%), Positives = 92/254 (36%), Gaps = 43/254 (16%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           D +   +LV  HL++V++ ++ Y   G    ++V E  IG++  ++K          +  
Sbjct: 92  DETDRDQLVNKHLKIVIRESLQYVKLGFSFLDLVQEATIGVINGIEKLKNS-----ESDI 146

Query: 106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKK 165
            +W+K    +YIL     +     A++      L      +Q   +N L  E++      
Sbjct: 147 EFWLKNFAIKYILEYQKKILKDFKASELAYILYL-----KVQLELNNGLSLEEI------ 195

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
                              S    I  +  N+ Q     + D       ++EK     R+
Sbjct: 196 -------------------SKQMNIELNYLNALQELFTKMDDMPENSYSIVEKVSHLTRK 236

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKV--- 280
            +L+     LN  + RI       ++    T + +S    +    +  +  +A  K+   
Sbjct: 237 YVLSNIPKKLNYLDERILMMHYGLDDKFYKT-KEISKILNIEESNINVLREKALTKLAFN 295

Query: 281 --QESIQKQVELSS 292
             +E +++ +E  +
Sbjct: 296 LNKEQMEENMEYLN 309


>gi|104774467|ref|YP_619447.1| putative RNA polymerase sigma factor [Lactobacillus delbrueckii
           subsp. bulgaricus ATCC 11842]
 gi|116514572|ref|YP_813478.1| ComX [Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365]
 gi|103423548|emb|CAI98466.1| Putative RNA polymerase sigma factor [Lactobacillus delbrueckii
           subsp. bulgaricus ATCC 11842]
 gi|116093887|gb|ABJ59040.1| ComX [Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-365]
 gi|325126285|gb|ADY85615.1| Hypothetical conserved protein [Lactobacillus delbrueckii subsp.
           bulgaricus 2038]
          Length = 189

 Score = 46.3 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 19/101 (18%), Positives = 35/101 (34%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L K+ E +L  R ++  D  A   L  S L ++      Y        +   E  I   +
Sbjct: 3   LTKERERLLISRIQKDDDEQALKELYYSCLPVIGGTIKQYFVELYDNQDWEQEALILCYK 62

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
             K+FD ++G     +    +       I R     ++  +
Sbjct: 63  TAKRFDLKQGKPFVGFYKVSLHNRAINLIRRGKRKKRLAAS 103


>gi|225568313|ref|ZP_03777338.1| hypothetical protein CLOHYLEM_04388 [Clostridium hylemonae DSM
           15053]
 gi|225162842|gb|EEG75461.1| hypothetical protein CLOHYLEM_04388 [Clostridium hylemonae DSM
           15053]
          Length = 203

 Score = 46.3 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 22/86 (25%), Positives = 37/86 (43%), Gaps = 1/86 (1%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L +  R  GD +    ++  +  LV K A      G    +++ EG IGL +AV+ +D E
Sbjct: 12  LIRNLR-AGDKAIVDYIMDKYKNLVRKEANAMYLLGGENDDLIQEGMIGLFKAVEDYDVE 70

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWS 122
           +     +++   I   M   I  S  
Sbjct: 71  QQASFFSFARLCITRQMYSAIEASRR 96


>gi|302670194|ref|YP_003830154.1| RNA polymerase sigma factor sigma-70 family protein [Butyrivibrio
           proteoclasticus B316]
 gi|302394667|gb|ADL33572.1| RNA polymerase sigma factor sigma-70 family [Butyrivibrio
           proteoclasticus B316]
          Length = 162

 Score = 46.3 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 12/90 (13%), Positives = 38/90 (42%), Gaps = 10/90 (11%)

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
                +  D   ++ ++ ++        +L +++  L   +R I   R  +   +TL+ +
Sbjct: 77  HIHSEIPEDLAEEKSLIEDEVLNNESLEILAKALKELPQEQRDIIVLRYYRG--LTLQEV 134

Query: 259 SSE----FEVSRERVRQIEARAFKKVQESI 284
           +++    + V++ R       A  ++++ I
Sbjct: 135 AAQMNLSYGVTKLR----HREALGRLKDLI 160


>gi|194365388|ref|YP_002027998.1| RNA polymerase sigma factor [Stenotrophomonas maltophilia R551-3]
 gi|194348192|gb|ACF51315.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Stenotrophomonas
           maltophilia R551-3]
          Length = 207

 Score = 46.3 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 19/89 (21%), Positives = 37/89 (41%), Gaps = 8/89 (8%)

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
            +  +   + D    E  L E E+    R  +  +M  L P +R + + R   +  ++LE
Sbjct: 124 DADLRLAAIEDGQTPEAELSEFEQ----RRRIQLAMEQLPPEQREVLQLR--LDQELSLE 177

Query: 257 NLSSEFEVSRERV-RQIEARAFKKVQESI 284
            +     V RE V  ++   A  K++  +
Sbjct: 178 EIGQITGVGRETVKSRL-RYAMDKLRAGL 205


>gi|304360723|ref|YP_003856854.1| putative RNA polymerase sigma factor [Clostridium phage phiCTP1]
 gi|302495582|gb|ADL40362.1| putative RNA polymerase sigma factor [Clostridium phage phiCTP1]
          Length = 178

 Score = 46.3 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 27/231 (11%), Positives = 61/231 (26%), Gaps = 64/231 (27%)

Query: 54  VTSHLRLVVKIAMGYRGY--GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           +  +L  +  +A           + E+   G +  ++A   + P +G  L T+S  ++  
Sbjct: 6   LEDNLGFIKSVAKKVMATTNYRDMEELFQTGCVAYLEAQNNYKPNKGASLLTFSYMYVFG 65

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            M  +                                                  N SE 
Sbjct: 66  RMMNFARHKSFTNH-----------------------------------------NHSEE 84

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
             I          SL+           ++      D+       + K E       L   
Sbjct: 85  PPI---------YSLD----------YEYDRQNSNDNKKFSMQTLLKTETFEDTATLRVL 125

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +S L   ++ I   +           +      ++ +V ++E +A + ++ 
Sbjct: 126 ISELPTVQKSIICYKYYFGLK--QREIGKLLGFTQTKVSRLENKALQALRR 174


>gi|310827577|ref|YP_003959934.1| ECF subfamily RNA polymerase sigma-24 factor [Eubacterium limosum
           KIST612]
 gi|308739311|gb|ADO36971.1| ECF subfamily RNA polymerase sigma-24 factor [Eubacterium limosum
           KIST612]
          Length = 192

 Score = 46.3 bits (109), Expect = 0.005,   Method: Composition-based stats.
 Identities = 17/92 (18%), Positives = 34/92 (36%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
             R    GD +A   L+ S   L+ K A  YR +   + + V  G + L++A   +    
Sbjct: 12  WVRMAGEGDQTAREMLLMSFKPLIYKQAAKYRHHHDSLEDAVQYGGVILLEATADYRAGS 71

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
                 +    ++    +   R+    ++ T 
Sbjct: 72  SQPFPAFLSARLRYRFADAGRRAARSGRMETR 103


>gi|294791943|ref|ZP_06757091.1| RNA polymerase sigma-H factor [Veillonella sp. 6_1_27]
 gi|294457173|gb|EFG25535.1| RNA polymerase sigma-H factor [Veillonella sp. 6_1_27]
          Length = 224

 Score = 46.3 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 18/98 (18%), Positives = 36/98 (36%), Gaps = 3/98 (3%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             ++  V+A   +E  +  A   +V  +   V   A  Y   G    +++ EG IGL +A
Sbjct: 17  TDEQVVVIA---QEEQNEFAIDYIVNKYKNFVRAKARSYFLVGADREDIIQEGMIGLYKA 73

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
            + F  ++      ++   I   +   I  +       
Sbjct: 74  TRDFKHDKLASFRAFAELCITRQIITAIKSATRQKHAP 111


>gi|229825691|ref|ZP_04451760.1| hypothetical protein GCWU000182_01054 [Abiotrophia defectiva ATCC
           49176]
 gi|229790254|gb|EEP26368.1| hypothetical protein GCWU000182_01054 [Abiotrophia defectiva ATCC
           49176]
          Length = 205

 Score = 46.3 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 22/82 (26%), Positives = 37/82 (45%), Gaps = 1/82 (1%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L ++ +E GD  A + L+  +  LV   A      G    +++ EG IGL  AV+ FD 
Sbjct: 10  ELCEKAKE-GDGKAENYLLNKYKNLVRGKAKTLYLLGGDREDLIQEGMIGLFMAVRDFDK 68

Query: 96  ERGFRLATYSMWWIKAAMQEYI 117
            +    +T++    +  M   I
Sbjct: 69  TKNASFSTFANLVCERRMYNAI 90


>gi|332662590|ref|YP_004445378.1| ECF subfamily RNA polymerase sigma-24 subunit [Haliscomenobacter
           hydrossis DSM 1100]
 gi|332331404|gb|AEE48505.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Haliscomenobacter
           hydrossis DSM 1100]
          Length = 181

 Score = 46.3 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 27/177 (15%), Positives = 68/177 (38%), Gaps = 24/177 (13%)

Query: 122 SLVKIGTTANQKRLFFNLRRLKGHLQAITD------NNLKPEQVVAIAKKLNVSESEVIS 175
           S V+  +    + +   +R  +     + D           ++V +++  L       I+
Sbjct: 9   STVRRYSNQLFRFIRGRVRSEEEAEDILQDVWVQLSRLSNLDEVESLSGWLYQVARNRIT 68

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
              R  G ESL+ L    ++ +   ++ L+ D    E        ++   + L  ++  L
Sbjct: 69  DTYRKKGTESLDDLTYEDEEGNLNVKEILLSDSQSPEDAFF----KEIFWDALMNALDEL 124

Query: 236 NPRERRIFEARRLQENPVTLENLSSEFE------VSRERVRQIEARAFKKVQESIQK 286
              +R++F     +   +TL+ ++ +        +SR+R       A + +++ +Q 
Sbjct: 125 PENQRQVFV--WNELEDLTLQEIADKTNENLITIISRKR------YAVQHLRQRLQA 173


>gi|150017679|ref|YP_001309933.1| RNA polymerase sigma factor SigI [Clostridium beijerinckii NCIMB
           8052]
 gi|149904144|gb|ABR34977.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Clostridium
           beijerinckii NCIMB 8052]
          Length = 250

 Score = 46.3 bits (109), Expect = 0.006,   Method: Composition-based stats.
 Identities = 19/88 (21%), Positives = 38/88 (43%), Gaps = 7/88 (7%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRL----VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
             +R R +GD+    +L+  +L      V K++  Y        ++ S G I   +A+  
Sbjct: 20  YIERIR-NGDVKLKDKLIKEYLPFIGKSVSKVSKKYEDIRYS--DIFSIGMIAFNEALDN 76

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRS 120
           +D  +G     Y    I++ + +Y  +S
Sbjct: 77  YDENKGKNFFAYCDMIIRSRIIDYYRKS 104


>gi|41019054|gb|AAR98498.1| putative sigma factor E [Pasteuria penetrans]
          Length = 106

 Score = 46.0 bits (108), Expect = 0.006,   Method: Composition-based stats.
 Identities = 17/86 (19%), Positives = 36/86 (41%), Gaps = 7/86 (8%)

Query: 177 NCRLAGDESLNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
           N ++  + S +  +N   D N     D L  + D     +    E +  + +L  +++ L
Sbjct: 25  NNKIRSEVSFDEPLNIDWDGNELLLSDVLGTESD----TIYRDIEDQVDKQVLRMALNTL 80

Query: 236 NPRERRIFEARR--LQENPVTLENLS 259
           + RER+I   R         T ++++
Sbjct: 81  SDRERKIVILRFGLGGGEEKTQKDVA 106


>gi|157691589|ref|YP_001486051.1| DNA-directed RNA polymerase sigma subunit FliA [Bacillus pumilus
           SAFR-032]
 gi|157680347|gb|ABV61491.1| possible DNA-directed RNA polymerase sigma subunit FliA [Bacillus
           pumilus SAFR-032]
          Length = 200

 Score = 46.0 bits (108), Expect = 0.006,   Method: Composition-based stats.
 Identities = 12/76 (15%), Positives = 32/76 (42%), Gaps = 4/76 (5%)

Query: 209 DGQEQVLIEKEERKNRRN--MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           D  E VL  +++         L ++   L  +++ +     +     T++ ++     +R
Sbjct: 106 DTYEAVLFNQQDLGEHLQDKRLYKAYQQLTDKQKMVLTHIYV--EGQTMKEIADRLGETR 163

Query: 267 ERVRQIEARAFKKVQE 282
           + +  I  +A  K++E
Sbjct: 164 QNISNIHKKALNKLKE 179


>gi|223986010|ref|ZP_03636040.1| hypothetical protein HOLDEFILI_03346 [Holdemania filiformis DSM
           12042]
 gi|223962010|gb|EEF66492.1| hypothetical protein HOLDEFILI_03346 [Holdemania filiformis DSM
           12042]
          Length = 143

 Score = 46.0 bits (108), Expect = 0.006,   Method: Composition-based stats.
 Identities = 19/108 (17%), Positives = 39/108 (36%), Gaps = 6/108 (5%)

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             M CR   + SL+A ++  D +     D    D         +         ++  + +
Sbjct: 31  REMKCRRDREVSLDA-VSPDDWDKLSTVDRYSCDSFTFSSHGYDLHIDN---ELVAEAFA 86

Query: 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L   E+ I   R + +  +T E +     +SR  V++      K ++
Sbjct: 87  SLPKDEQSILILRFVLD--LTDEEIGRLMGMSRSAVQRHRTSTLKDLR 132


>gi|254522376|ref|ZP_05134431.1| RNA polymerase sigma-70 factor [Stenotrophomonas sp. SKA14]
 gi|219719967|gb|EED38492.1| RNA polymerase sigma-70 factor [Stenotrophomonas sp. SKA14]
          Length = 207

 Score = 46.0 bits (108), Expect = 0.006,   Method: Composition-based stats.
 Identities = 19/89 (21%), Positives = 37/89 (41%), Gaps = 8/89 (8%)

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
            +  +   + D    E  L E E+    R  +  +M  L P +R + + R   +  ++LE
Sbjct: 124 DADLRLAAIEDGQTPEAELSEFEQ----RRRIQLAMEQLPPEQREVLQLR--LDQELSLE 177

Query: 257 NLSSEFEVSRERV-RQIEARAFKKVQESI 284
            +     V RE V  ++   A  K++  +
Sbjct: 178 EIGQITGVGRETVKSRL-RYAMDKLRAGL 205


>gi|190573973|ref|YP_001971818.1| RNA polymerase sigma factor [Stenotrophomonas maltophilia K279a]
 gi|190011895|emb|CAQ45516.1| putative ECF-type RNA polymerase sigma factor [Stenotrophomonas
           maltophilia K279a]
          Length = 230

 Score = 46.0 bits (108), Expect = 0.006,   Method: Composition-based stats.
 Identities = 19/89 (21%), Positives = 37/89 (41%), Gaps = 8/89 (8%)

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
            +  +   + D    E  L E E+    R  +  +M  L P +R + + R   +  ++LE
Sbjct: 147 DADLRLAAIEDGQTPEGELSEFEQ----RRRIQLAMEQLPPEQREVLQLR--LDQELSLE 200

Query: 257 NLSSEFEVSRERV-RQIEARAFKKVQESI 284
            +     V RE V  ++   A  K++  +
Sbjct: 201 EIGQITGVGRETVKSRL-RYAMDKLRAGL 228


>gi|282865779|ref|ZP_06274829.1| putative RNA polymerase, sigma 70 family subunit [Streptomyces sp.
           ACTE]
 gi|282559423|gb|EFB64975.1| putative RNA polymerase, sigma 70 family subunit [Streptomyces sp.
           ACTE]
          Length = 527

 Score = 46.0 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 25/101 (24%), Positives = 43/101 (42%), Gaps = 9/101 (8%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           E  L K  ++ GD  A  RLV+S+L L   I          + +VV E  + +++ +   
Sbjct: 6   ETALIKAAQQ-GDEQAQERLVSSYLPLAYNIVGRALNGHADVDDVVQESVLRMLRGLPGL 64

Query: 94  D-PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
             PE      ++  W++   M E I R W   + G  +  +
Sbjct: 65  RAPE------SFRSWFVAITMNE-IRRHWRERRTGEISADR 98


>gi|37522463|ref|NP_925840.1| hypothetical protein glr2894 [Gloeobacter violaceus PCC 7421]
 gi|35213464|dbj|BAC90835.1| glr2894 [Gloeobacter violaceus PCC 7421]
          Length = 669

 Score = 46.0 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 22/118 (18%), Positives = 46/118 (38%), Gaps = 8/118 (6%)

Query: 174 ISMNCRLAGDESLNALINSS--DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
             +   +    SL+A +  +  D       + +     G E  L+E +     R    R+
Sbjct: 183 RWLKRWVHAPLSLDAPVGDARQDGELPALGETVASGGGGPETQLLEDQ----CRERFLRA 238

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           +  L   ER + E   L+      + ++    ++  RV Q   RA  ++ E++++  E
Sbjct: 239 LERLAEAERVLIERVHLRGER--QQEVARSVGLTPGRVSQKLKRAAGRLAETLEESFE 294


>gi|197294829|ref|YP_001799370.1| DNA-directed RNA polymerase specialized sigma subunit [Candidatus
           Phytoplasma australiense]
 gi|171854156|emb|CAM12149.1| DNA-directed RNA polymerase specialized sigma subunit [Candidatus
           Phytoplasma australiense]
          Length = 223

 Score = 46.0 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 18/89 (20%), Positives = 43/89 (48%), Gaps = 4/89 (4%)

Query: 35  YVLAKRY-REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI--SEVVSEGNIGLMQAVK 91
             L + + +   +L   ++LV  +  LV KI   ++ +   +   ++  EG +GL+ A++
Sbjct: 9   KELFQEFLKNKKNLQIRNQLVEIYYPLVNKIVSKFKYFPSILQRQDLFQEGVLGLINALE 68

Query: 92  KFDPERGF-RLATYSMWWIKAAMQEYILR 119
            +D +    +   Y+   IK+ ++  I +
Sbjct: 69  GYDFQVDIDQFIYYASKNIKSHIRGLIKK 97


>gi|317970336|ref|ZP_07971726.1| RNA polymerase sigma factor SigF [Synechococcus sp. CB0205]
          Length = 138

 Score = 46.0 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 25/93 (26%), Positives = 46/93 (49%), Gaps = 3/93 (3%)

Query: 50  AHRLVTSHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
             R    HL L  + A  Y R +G+PI E++S    GL +   +FD  +G+R ++Y +  
Sbjct: 9   QRRFACQHLGLARQQAHRYARRWGIPIEELLSPAYEGLCKGAAQFDAAKGYRPSSYLVSK 68

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           +K  +  ++  +   V+I  +   + L+   RR
Sbjct: 69  VKGELLHHLRDTGFAVRI--SHRYRELWVKARR 99


>gi|315656941|ref|ZP_07909828.1| conserved hypothetical protein [Mobiluncus curtisii subsp. holmesii
           ATCC 35242]
 gi|315492896|gb|EFU82500.1| conserved hypothetical protein [Mobiluncus curtisii subsp. holmesii
           ATCC 35242]
          Length = 259

 Score = 46.0 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 18/114 (15%), Positives = 47/114 (41%), Gaps = 2/114 (1%)

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
             S++  +  D     +++ SD  S+  +D      D Q     +   +      L  ++
Sbjct: 120 PWSLDWFMEIDREPEFVVDKSDDPSAVVEDITASPED-QLIAAEDTTRKAREFQALREAI 178

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           + L  + +++ E   L +  +   +++    +SR RV Q+   A   ++ +++ 
Sbjct: 179 AGLEGKHKQVMELM-LADADMKQSDVARALGLSRARVSQLFKEAAAVLRAAVEA 231


>gi|269798072|ref|YP_003311972.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Veillonella
           parvula DSM 2008]
 gi|269094701|gb|ACZ24692.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Veillonella
           parvula DSM 2008]
          Length = 224

 Score = 46.0 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 17/98 (17%), Positives = 35/98 (35%), Gaps = 3/98 (3%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             ++   +A   +E  +  A   +V  +   V   A  Y   G    +++ EG IGL +A
Sbjct: 17  TDEQVVAIA---QEEQNEFAIDYIVNKYKNFVRAKARSYFLVGADREDIIQEGMIGLYKA 73

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
            + F  ++      ++   I   +   I  +       
Sbjct: 74  TRDFKHDKLASFRAFAELCITRQIITAIKSATRQKHAP 111


>gi|240146530|ref|ZP_04745131.1| RNA polymerase sigma-H factor [Roseburia intestinalis L1-82]
 gi|257201341|gb|EEU99625.1| RNA polymerase sigma-H factor [Roseburia intestinalis L1-82]
          Length = 208

 Score = 46.0 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 18/96 (18%), Positives = 37/96 (38%), Gaps = 5/96 (5%)

Query: 29  LEKQEEYVLAKRYREHGDLSAA--HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L  ++   L    +  GD        ++  +  LV K A      G    +++ EG IGL
Sbjct: 8   LTDEQ---LIAALKNSGDPDGKIMDYILDKYKPLVRKKANAVFLIGGETDDLIQEGMIGL 64

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A++ +D  +      ++   I   + + +  S  
Sbjct: 65  FKAIRDYDDTKETSFFHFAELCITRQLYKAVEASNR 100


>gi|255103059|ref|ZP_05332036.1| RNA polymerase sigma factor, sigma-70 family protein [Clostridium
           difficile QCD-63q42]
 gi|255313155|ref|ZP_05354738.1| RNA polymerase sigma factor, sigma-70 family protein [Clostridium
           difficile QCD-76w55]
 gi|255519160|ref|ZP_05386836.1| RNA polymerase sigma factor, sigma-70 family protein [Clostridium
           difficile QCD-97b34]
 gi|255652343|ref|ZP_05399245.1| RNA polymerase sigma factor, sigma-70 family protein [Clostridium
           difficile QCD-37x79]
          Length = 181

 Score = 46.0 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 18/75 (24%), Positives = 33/75 (44%), Gaps = 6/75 (8%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGY-----RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
           L   ++L   ++ LV  I   Y     R Y     ++  EG IGL +    FD  +G + 
Sbjct: 4   LEEKNKLFEDNINLVHFIINRYFKSFLRRYPYLKEDLFQEGYIGLYKTTCCFDESKG-KF 62

Query: 102 ATYSMWWIKAAMQEY 116
           +T +  +I   ++ +
Sbjct: 63  STIAFSYISGHLKRF 77


>gi|312197538|ref|YP_004017599.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Frankia sp. EuI1c]
 gi|311228874|gb|ADP81729.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Frankia sp. EuI1c]
          Length = 227

 Score = 46.0 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 16/68 (23%), Positives = 35/68 (51%), Gaps = 2/68 (2%)

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
           ++  +R ++R+ L R++  L PR+R +   R   + P    ++++    S   VR   +R
Sbjct: 106 LDHADRMSQRDGLVRALRTLPPRQRAVLVLRYFDDLPE--ADVAAALGCSVGSVRSQASR 163

Query: 276 AFKKVQES 283
              +++ES
Sbjct: 164 GLARLRES 171


>gi|269960387|ref|ZP_06174760.1| conserved hypothetical protein [Vibrio harveyi 1DA3]
 gi|269834814|gb|EEZ88900.1| conserved hypothetical protein [Vibrio harveyi 1DA3]
          Length = 91

 Score = 46.0 bits (108), Expect = 0.007,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 20/50 (40%), Gaps = 1/50 (2%)

Query: 2  NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAH 51
           R+              Y+ EI   P+L  +EE + A+R    GD +A  
Sbjct: 38 AREEFDASSKSLDATQLYLGEIGFSPLLTAEEEVLYARR-ALRGDEAARQ 86


>gi|258514844|ref|YP_003191066.1| putative RNA polymerase sigma factor SigI [Desulfotomaculum
           acetoxidans DSM 771]
 gi|257778549|gb|ACV62443.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum acetoxidans DSM 771]
          Length = 246

 Score = 46.0 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 18/100 (18%), Positives = 39/100 (39%), Gaps = 6/100 (6%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYG--LPISEVVSEGNIGLMQA 89
           +E   LAK+    GDL     L+ +H   + K++             + +S   +   +A
Sbjct: 7   EETLKLAKK----GDLGKREELIRNHKNFIAKVSSKICNRYLIWNNDDELSIAFLAFNEA 62

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTT 129
           +  F P  G    +++   I+  + +Y  +    + I  +
Sbjct: 63  IDNFKPSEGTAFHSFAQRIIRNRLIDYFRKESKHMHISLS 102


>gi|313893311|ref|ZP_07826886.1| RNA polymerase sigma-H factor [Veillonella sp. oral taxon 158 str.
           F0412]
 gi|313442207|gb|EFR60624.1| RNA polymerase sigma-H factor [Veillonella sp. oral taxon 158 str.
           F0412]
          Length = 224

 Score = 46.0 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 28/207 (13%), Positives = 72/207 (34%), Gaps = 8/207 (3%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
             ++  V+A   +E  ++ A   +V  +   V   A  Y   G    +++ EG IGL +A
Sbjct: 17  TDEQVVVIA---QEEQNVFAIDYIVNKYKNFVRAKARSYFLVGADREDIIQEGMIGLYKA 73

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG--TTANQKRLFFNLRRLKGHLQ 147
            + F  ++      ++   I   +   I  +         +  +  +  +     +  ++
Sbjct: 74  TRDFKHDKLASFRAFAELCITRQIITAIKSATRQKHAPLNSYISLNKPVYTEESERTLIE 133

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
            ++   +   + + I+K+      ++      +  D     L    D  S Q    +   
Sbjct: 134 MLSSAKVTNPEDLIISKE---ELDDIERNIGHILSDLEWEVLEGYLDGRSYQEMAEVTDR 190

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSV 234
                   +++ +RK  + +  R +  
Sbjct: 191 SVKSIDNALQRVKRKLEKYLEHRVLGS 217


>gi|152977451|ref|YP_001376968.1| RNA polymerase factor sigma-70 [Bacillus cereus subsp. cytotoxis
           NVH 391-98]
 gi|152026203|gb|ABS23973.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Bacillus
           cytotoxicus NVH 391-98]
          Length = 156

 Score = 46.0 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 29/54 (53%), Gaps = 2/54 (3%)

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +   MSVLN RE+ +           +++ ++ E  ++  +VR I  +AFKK++
Sbjct: 102 VHEYMSVLNEREKHVITESFFMG--KSIDEIAGEMGLTYYQVRWIYRQAFKKMR 153


>gi|227875072|ref|ZP_03993217.1| conserved hypothetical protein [Mobiluncus mulieris ATCC 35243]
 gi|304390315|ref|ZP_07372268.1| sigma-70 family protein [Mobiluncus curtisii subsp. curtisii ATCC
           35241]
 gi|306817359|ref|ZP_07451104.1| sigma-70 family protein [Mobiluncus mulieris ATCC 35239]
 gi|227844350|gb|EEJ54514.1| conserved hypothetical protein [Mobiluncus mulieris ATCC 35243]
 gi|304326071|gb|EFL93316.1| sigma-70 family protein [Mobiluncus curtisii subsp. curtisii ATCC
           35241]
 gi|304649800|gb|EFM47080.1| sigma-70 family protein [Mobiluncus mulieris ATCC 35239]
          Length = 229

 Score = 46.0 bits (108), Expect = 0.008,   Method: Composition-based stats.
 Identities = 16/82 (19%), Positives = 41/82 (50%), Gaps = 8/82 (9%)

Query: 210 GQEQVLIEKE---ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
             E  +IE+E   ER     ++   ++ L+P+ R +   R L  + +    ++ +  ++R
Sbjct: 123 SAEDQVIEREDSVERACDLEVMRDIIAGLDPQHREVMT-RLLATDKLNQAQVARDMGLTR 181

Query: 267 ERVRQI--EARAFKKVQESIQK 286
            RV Q+  E +    +++++++
Sbjct: 182 ARVSQLVAEVKPL--IRQAVEE 201


>gi|70730971|ref|YP_260712.1| RNA polymerase sigma-70 family protein [Pseudomonas fluorescens
           Pf-5]
 gi|68345270|gb|AAY92876.1| RNA polymerase sigma-70 family protein [Pseudomonas fluorescens
           Pf-5]
          Length = 172

 Score = 45.6 bits (107), Expect = 0.008,   Method: Composition-based stats.
 Identities = 19/96 (19%), Positives = 42/96 (43%), Gaps = 2/96 (2%)

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
            S  +    R+  + S + L  S+ +N       L+ +          +    ++  +L 
Sbjct: 57  PSNPVGYLYRIVRNLSFDLLRRSTLENRHPDGADLLNELPSSTPSPEHQALHSDQLRLLQ 116

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            ++++L  R RR F   RLQ   +T + +++E ++S
Sbjct: 117 DALALLPERTRRAFHMHRLQH--LTFQEIAAELKIS 150


>gi|168185132|ref|ZP_02619796.1| sigma-70 region 2 domain protein [Clostridium botulinum Bf]
 gi|182671806|gb|EDT83767.1| sigma-70 region 2 domain protein [Clostridium botulinum Bf]
          Length = 191

 Score = 45.6 bits (107), Expect = 0.008,   Method: Composition-based stats.
 Identities = 12/88 (13%), Positives = 33/88 (37%), Gaps = 1/88 (1%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           E+     +  + GD  A   ++      ++K+   +        +++    I L++A+ K
Sbjct: 4   EQIEHQVKLAKRGDTEAIITVLDVFKPFILKMIKDFNCSTNDFYDLLQICYIALIRAIDK 63

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRS 120
           +         +Y+   IK   + +   +
Sbjct: 64  YRLGSNV-FKSYAYSVIKNEFRRFTRDN 90


>gi|212702128|ref|ZP_03310256.1| hypothetical protein DESPIG_00138 [Desulfovibrio piger ATCC 29098]
 gi|212674435|gb|EEB34918.1| hypothetical protein DESPIG_00138 [Desulfovibrio piger ATCC 29098]
          Length = 252

 Score = 45.6 bits (107), Expect = 0.008,   Method: Composition-based stats.
 Identities = 27/208 (12%), Positives = 67/208 (32%), Gaps = 14/208 (6%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
             E+  L   Y+ +       +L+     ++      + G  +P   +++E  +   +A+
Sbjct: 14  ADEDMRLWHEYKRNPSSDNLGKLLDRFSGVINGQVNKWAGP-IPRDILLNEAKLLTKKAL 72

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
             ++P  G  LAT+    +   +   +    S V++      K   +N       +  +T
Sbjct: 73  DSYNPNSGAALATWVTNSLLP-LSRIVYTHQSTVRMPENITMKVNTYN-----TAVDQLT 126

Query: 151 DNNLKPEQVVAIAKKLNVSESEV-------ISMNCRLAGDESLNALINSSDKNSSQWQDW 203
               +      +  +L  + +E+                  S +      D +       
Sbjct: 127 TILGREPTTDELHDELGWTAAEITRFRDYNRRDLLESGPTVSGDFFSAQDDGDDDMLLSG 186

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           +  +    E+ L E     N   +L+ +
Sbjct: 187 IYMELSPDEKWLFEYTTGYNGAAVLSNA 214


>gi|309790037|ref|ZP_07684611.1| ECF subfamily RNA polymerase sigma-24 factor [Oscillochloris
           trichoides DG6]
 gi|308227892|gb|EFO81546.1| ECF subfamily RNA polymerase sigma-24 factor [Oscillochloris
           trichoides DG6]
          Length = 225

 Score = 45.6 bits (107), Expect = 0.008,   Method: Composition-based stats.
 Identities = 28/142 (19%), Positives = 58/142 (40%), Gaps = 9/142 (6%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           + + GD +A  +LV S  + V  IAM         +++  E  I L +A+ +++ E   R
Sbjct: 11  FAQQGDSAALTQLVISQQQYVYSIAMSVLKNPEDAADLTQEAFIRLFRALPQYNGE--SR 68

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR------RLKGHLQAITDNNL 154
             T+    +    ++ + R    V I    +++     +       R     QA+  + L
Sbjct: 69  FTTWLYRLVVNLCRDELRRRGRQVPITPPMDEEEEHDQIAGVADTDRWSDPAQALDSHEL 128

Query: 155 KPEQVVAIAKKLNVSESEVISM 176
           + +QV     +L      V+++
Sbjct: 129 R-DQVRRALDQLEAHYRLVLTL 149


>gi|7021510|gb|AAF35381.1| SpoIIGB [Bacillus megaterium]
          Length = 106

 Score = 45.6 bits (107), Expect = 0.008,   Method: Composition-based stats.
 Identities = 24/110 (21%), Positives = 46/110 (41%), Gaps = 11/110 (10%)

Query: 157 EQVVAIAKKLNVSESEVISMNCRL----AGDESLNALINSS-DKNSSQWQDWLVYDHDGQ 211
           E+ + +A   +      I M+ R       + S +  +N   D N     D L  D D  
Sbjct: 1   EKKIKLATYASRCIENEILMHLRRNNKNRSEVSFDEPLNIDWDGNELLLSDVLGTDDD-- 58

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL--QENPVTLENLS 259
             ++ +  E    R++L +++  LN RE++I E R         T ++++
Sbjct: 59  --IITKDLEATVDRHLLMKALHQLNDREKQIMELRFGLAGGEEKTQKDVA 106


>gi|125973787|ref|YP_001037697.1| putative RNA polymerase sigma factor SigI [Clostridium thermocellum
           ATCC 27405]
 gi|256004518|ref|ZP_05429497.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           thermocellum DSM 2360]
 gi|281417944|ref|ZP_06248964.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           thermocellum JW20]
 gi|125714012|gb|ABN52504.1| DNA-directed RNA polymerase sigma factor [Clostridium thermocellum
           ATCC 27405]
 gi|255991523|gb|EEU01626.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           thermocellum DSM 2360]
 gi|281409346|gb|EFB39604.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           thermocellum JW20]
 gi|316940020|gb|ADU74054.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           thermocellum DSM 1313]
          Length = 245

 Score = 45.6 bits (107), Expect = 0.008,   Method: Composition-based stats.
 Identities = 17/86 (19%), Positives = 39/86 (45%), Gaps = 3/86 (3%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM---QAVKKFDPERGF 99
           ++GD     + +  ++  ++ I   +        +   E +IGLM   +A++KFD  +  
Sbjct: 23  KNGDKHLKEKFIKDYIPFILNIVSSFYSSKTGDLKSSDEYSIGLMAFNEAIEKFDVNKSK 82

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVK 125
               ++   IK  M +Y  ++ S+ +
Sbjct: 83  SFLKFAEMVIKKRMIDYFRKTSSIGR 108


>gi|32487227|emb|CAD91194.1| hypothetical protein [Nonomuraea sp. ATCC 39727]
          Length = 170

 Score = 45.6 bits (107), Expect = 0.008,   Method: Composition-based stats.
 Identities = 14/70 (20%), Positives = 32/70 (45%), Gaps = 10/70 (14%)

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV----RQIE 273
             +  + R M+  ++  L PR+R I   R  ++   T   ++    +   RV     QI 
Sbjct: 96  HADGADLRVMMRAALGRLTPRQRTILVLRYFEDLSET--EIARVLGI---RVGSVRSQIH 150

Query: 274 ARAFKKVQES 283
            R+ ++++++
Sbjct: 151 -RSLERLKQT 159


>gi|150388552|ref|YP_001318601.1| ECF subfamily RNA polymerase sigma-24 factor [Alkaliphilus
           metalliredigens QYMF]
 gi|149948414|gb|ABR46942.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Alkaliphilus
           metalliredigens QYMF]
          Length = 190

 Score = 45.6 bits (107), Expect = 0.008,   Method: Composition-based stats.
 Identities = 33/223 (14%), Positives = 75/223 (33%), Gaps = 65/223 (29%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + G+  A   +V     LV+  +  Y G      + + +G + +++A++ FD E+G   
Sbjct: 12  AKAGNRQAKEWIVFKLNPLVISHSGRYGGCKGYDEDAIQDGRMKILEAIETFDLEKGVPF 71

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
             Y    ++                         F+  RR K  +               
Sbjct: 72  LGYVALAVQH------------------------FYQNRRRKQRIH-------------- 93

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
                       +S++  +             ++ +  W D +V +    E+ LI    R
Sbjct: 94  ------------LSLDSPIGNGV---------EEENGTWIDLIVDESVEIEEDLI----R 128

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           K     +  +MS L+  ++++        N  +L+ ++++  V
Sbjct: 129 KETHQWIHENMSCLSQGQQQVVRDFYF--NKHSLKTIAAKRGV 169


>gi|331091960|ref|ZP_08340792.1| hypothetical protein HMPREF9477_01435 [Lachnospiraceae bacterium
           2_1_46FAA]
 gi|330402859|gb|EGG82426.1| hypothetical protein HMPREF9477_01435 [Lachnospiraceae bacterium
           2_1_46FAA]
          Length = 205

 Score = 45.6 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 11/63 (17%), Positives = 27/63 (42%), Gaps = 2/63 (3%)

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           E   R+ M+   + +L  R++ +           +   ++ +  VS   V +I  RA  +
Sbjct: 136 ETAIRKEMIQELLGLLTERQKEVVFEYFW--EQKSQSEIAEKLGVSHAAVSKILTRAVTR 193

Query: 280 VQE 282
           +++
Sbjct: 194 LRK 196


>gi|256419405|ref|YP_003120058.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Chitinophaga
           pinensis DSM 2588]
 gi|256034313|gb|ACU57857.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Chitinophaga
           pinensis DSM 2588]
          Length = 182

 Score = 45.6 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 17/74 (22%), Positives = 34/74 (45%), Gaps = 2/74 (2%)

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           +  E++ I  EE   ++  L   MS L  R + +   R       + E ++   +++ + 
Sbjct: 108 ESIEELKIRTEEDLLQQQRLQYLMSKLPERHQEVIRLRFYDN--FSWEEIAGILQINEQS 165

Query: 269 VRQIEARAFKKVQE 282
           VR +  RA  K++E
Sbjct: 166 VRNLVQRAIVKLRE 179


>gi|194017897|ref|ZP_03056505.1| YvrI [Bacillus pumilus ATCC 7061]
 gi|194010363|gb|EDW19937.1| YvrI [Bacillus pumilus ATCC 7061]
          Length = 200

 Score = 45.6 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 11/90 (12%), Positives = 38/90 (42%), Gaps = 3/90 (3%)

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENP 252
           D   +Q     V     +  +  +++  ++ ++  L ++   L  +++ +     +    
Sbjct: 92  DHPDTQEVKDPVQTDTYEAVLFNQQDLGEHLQDQTLYKAYQQLTDKQKMVLTHIYV--EG 149

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            T++ ++     +R+ +  I  +A  K++E
Sbjct: 150 QTMKEIADRLGETRQNISNIHKKALNKIKE 179


>gi|330468975|ref|YP_004406718.1| RNA polymerase, sigma-24 subunit, ecf subfamily protein
           [Verrucosispora maris AB-18-032]
 gi|328811946|gb|AEB46118.1| RNA polymerase, sigma-24 subunit, ecf subfamily protein
           [Verrucosispora maris AB-18-032]
          Length = 167

 Score = 45.6 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 20/79 (25%), Positives = 40/79 (50%), Gaps = 5/79 (6%)

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           +  +    R  L  ++  L  R+R I   R L + P   + ++ E +VS   V+   +RA
Sbjct: 91  DVADEVTARRWLQLALGALTARQRAIVVLRYLFDLPE--QQVARELDVSLGTVKSTTSRA 148

Query: 277 FKKVQESIQKQVELSSSPP 295
            +K+++++   VEL ++P 
Sbjct: 149 LEKLRQTL---VELPTAPG 164


>gi|320531093|ref|ZP_08032122.1| sigma-70, region 4 [Selenomonas artemidis F0399]
 gi|320136675|gb|EFW28628.1| sigma-70, region 4 [Selenomonas artemidis F0399]
          Length = 217

 Score = 45.6 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 16/72 (22%), Positives = 33/72 (45%), Gaps = 2/72 (2%)

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
           G     +  + R    ++LTR+M  L  RE++I       +  +TL  ++     S + V
Sbjct: 138 GMSDPSVNADRRLLLHDILTRAMHRLTEREKKILSLHYYGD--LTLRRIADLLGTSADAV 195

Query: 270 RQIEARAFKKVQ 281
            + +A   +K++
Sbjct: 196 SKGKANLLRKLR 207



 Score = 35.9 bits (82), Expect = 6.4,   Method: Composition-based stats.
 Identities = 28/159 (17%), Positives = 57/159 (35%), Gaps = 6/159 (3%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAM-GYRGYGLPISEVVSEG 82
           R    L K EE  L  R    G+ +A   ++  +  L+V  +   Y        E  S  
Sbjct: 17  RAYQPLTKAEEDHLIVRAV-RGEAAALAEILGRYRGLIVNESRASYLRNTALAHEAESIA 75

Query: 83  NIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ----KRLFFN 138
            +  M+A+  +DP+ G   A +    +  A+     R   L +  +   Q    +  +  
Sbjct: 76  ELAFMEALHDYDPKHGAPFAGFVKSRVHMALYGAFRRERRLWERESHPEQDEGGRDAWER 135

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           +  +           L  + +     +L   E +++S++
Sbjct: 136 IGGMSDPSVNADRRLLLHDILTRAMHRLTEREKKILSLH 174


>gi|319955669|ref|YP_004166936.1| RNA polymerase, sigma-24 subunit, ecf subfamily [Cellulophaga
           algicola DSM 14237]
 gi|319424329|gb|ADV51438.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Cellulophaga
           algicola DSM 14237]
          Length = 191

 Score = 45.6 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 16/79 (20%), Positives = 44/79 (55%), Gaps = 2/79 (2%)

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
             E++ I++E    + + +T  ++ L+PRER +   +   E  +++  +++  ++S + V
Sbjct: 108 SPEELKIDQEISFAQTSSITLILNTLSPREREVIYLKYYGE--LSMSEIATTMDISYQSV 165

Query: 270 RQIEARAFKKVQESIQKQV 288
                +AF K++++I+  +
Sbjct: 166 LNTLQKAFSKIRKTIENNM 184


>gi|313905469|ref|ZP_07838833.1| hypothetical protein EubceDRAFT_1548 [Eubacterium cellulosolvens 6]
 gi|313469653|gb|EFR64991.1| hypothetical protein EubceDRAFT_1548 [Eubacterium cellulosolvens 6]
          Length = 269

 Score = 45.6 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 36/185 (19%), Positives = 70/185 (37%), Gaps = 9/185 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L  Y+ EI +IP     E   L +R R  GD +A  R+    L  +V  A      G+ +
Sbjct: 91  LDSYMEEICQIPRAGDGEWEALTQRLR-AGDPTAKRRIAELMLPAIVDEAKALYVPGVHL 149

Query: 76  SEVVSEGNIGLMQAVKKFDPER---GFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           S+V+ EG++ ++  + + D         + T+ M  I+  +   I               
Sbjct: 150 SDVIQEGSLQVVLGLDRMDASMVAGEADIRTHLMAQIRDCISAMIEEQKD-----VRTRD 204

Query: 133 KRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINS 192
           +R+   +  LK  +  + +   +   +  +A  +N++E E   +      D   +     
Sbjct: 205 QRMVEKVEELKDGVSTLKEEYGRKVYLDEVADFMNITEEEAQDILKLAGEDVPEDTEGID 264

Query: 193 SDKNS 197
               S
Sbjct: 265 GQPTS 269


>gi|317969496|ref|ZP_07970886.1| RNA polymerase sigma factor SigF [Synechococcus sp. CB0205]
          Length = 137

 Score = 45.6 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 18/87 (20%), Positives = 40/87 (45%), Gaps = 3/87 (3%)

Query: 56  SHLRLVVKIAMGY-RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQ 114
           +HL L  + A  + R + + + +++     GL +    FDP  G R ++Y +  +K  + 
Sbjct: 11  AHLGLAHQQAHRFARRWSMAVDDLIGPAYEGLCKGAIGFDPSLGHRPSSYLVPKVKGELL 70

Query: 115 EYILRSWSLVKIGTTANQKRLFFNLRR 141
            Y+  +   ++I      + L+   R+
Sbjct: 71  HYLRDTGFSLRISHRL--RELWIKARK 95


>gi|296130019|ref|YP_003637269.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Cellulomonas
           flavigena DSM 20109]
 gi|296021834|gb|ADG75070.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Cellulomonas
           flavigena DSM 20109]
          Length = 190

 Score = 45.6 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 17/90 (18%), Positives = 40/90 (44%), Gaps = 2/90 (2%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
               + +  ++   D    +   ++     R+ L R++  L PR+RR+   R L    ++
Sbjct: 94  DTWRRRRREVLSPPDELPDLAAPQDTTTEDRDQLDRALQRLTPRQRRVVVLRYLVG--LS 151

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESI 284
              ++ +  VS   V+   +RA   +++S+
Sbjct: 152 EREVADDLHVSVGTVKSTASRALASLRDSL 181


>gi|167749358|ref|ZP_02421485.1| hypothetical protein EUBSIR_00310 [Eubacterium siraeum DSM 15702]
 gi|167657639|gb|EDS01769.1| hypothetical protein EUBSIR_00310 [Eubacterium siraeum DSM 15702]
          Length = 249

 Score = 45.6 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 19/85 (22%), Positives = 40/85 (47%), Gaps = 2/85 (2%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLV--VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           L  R  + G    A  L+  ++ ++      M  R       ++ SEG +GL++A++ ++
Sbjct: 71  LVSRITQTGGEKYATVLIKRYIPVISAKSAKMSLRCPSADKDDLFSEGLLGLLKAIRLYN 130

Query: 95  PERGFRLATYSMWWIKAAMQEYILR 119
            E+G    T++     +AM+  I +
Sbjct: 131 SEKGASFVTFANLCTDSAMKTCISK 155


>gi|150002964|ref|YP_001297708.1| RNA polymerase ECF-type sigma factor [Bacteroides vulgatus ATCC
           8482]
 gi|254883608|ref|ZP_05256318.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 4_3_47FAA]
 gi|319642323|ref|ZP_07996981.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 3_1_40A]
 gi|149931388|gb|ABR38086.1| RNA polymerase ECF-type sigma factor [Bacteroides vulgatus ATCC
           8482]
 gi|254836401|gb|EET16710.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 4_3_47FAA]
 gi|317386046|gb|EFV66967.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 3_1_40A]
          Length = 200

 Score = 45.6 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 16/91 (17%), Positives = 41/91 (45%), Gaps = 10/91 (10%)

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           S   + L+         + +  E KN + ++ +++  L+PR+R IFE  R +      + 
Sbjct: 95  SVLYEKLMEQAIDYVDDVEKSLEEKNIKELIAQALEQLSPRQREIFELSRNRGLSH--KE 152

Query: 258 LSSEFEVS----RERVRQIEARAFKKVQESI 284
           ++ +  +S    ++ +      A +K++  +
Sbjct: 153 IAEQLGLSVYTVQDHI----KNALEKIRAYL 179


>gi|146301907|ref|YP_001196498.1| ECF subfamily RNA polymerase sigma-24 factor [Flavobacterium
           johnsoniae UW101]
 gi|146156325|gb|ABQ07179.1| ECF subfamily RNA polymerase sigma-24 subunit [Flavobacterium
           johnsoniae UW101]
          Length = 180

 Score = 45.6 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 16/87 (18%), Positives = 44/87 (50%), Gaps = 6/87 (6%)

Query: 208 HDGQEQVLIEKEERKNRR--NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            D  E  +I+     +    ++L   +  L  + + +    + Q+  ++++ ++ E  +S
Sbjct: 88  EDKFEDYIIDNFSTIDPEVTDLLYSLLDKLPEKRKEVLLMYKFQD--MSIDQIADELGIS 145

Query: 266 RERVR-QIEARAFKKVQESIQKQVELS 291
           ++ V+ QI + A K+++E ++  V L+
Sbjct: 146 KQTVKNQI-SSALKQLREGLKDLVWLA 171


>gi|291535117|emb|CBL08229.1| RNA polymerase, sigma 30 subunit, SigH [Roseburia intestinalis
           M50/1]
 gi|291539643|emb|CBL12754.1| RNA polymerase, sigma 30 subunit, SigH [Roseburia intestinalis
           XB6B4]
          Length = 208

 Score = 45.6 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 18/96 (18%), Positives = 37/96 (38%), Gaps = 5/96 (5%)

Query: 29  LEKQEEYVLAKRYREHGDLSAA--HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L  ++   L    +  GD        ++  +  LV K A      G    +++ EG IGL
Sbjct: 8   LTDEQ---LIVALKNSGDPDGKIMDYILDKYKPLVRKKANAVFLIGGETDDLIQEGMIGL 64

Query: 87  MQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +A++ +D  +      ++   I   + + +  S  
Sbjct: 65  FKAIRDYDDTKETSFFHFAELCITRQLYKAVEASNR 100


>gi|226307539|ref|YP_002767499.1| hypothetical protein RER_40520 [Rhodococcus erythropolis PR4]
 gi|226186656|dbj|BAH34760.1| hypothetical protein RER_40520 [Rhodococcus erythropolis PR4]
          Length = 711

 Score = 45.6 bits (107), Expect = 0.009,   Method: Composition-based stats.
 Identities = 24/133 (18%), Positives = 46/133 (34%), Gaps = 5/133 (3%)

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
              +  + P  + A+   L       ++M  R+ G +S   +    D  S      +   
Sbjct: 168 ETAEEAVAPPAITALLDDLAQ-----LAMWRRVRGQDSRPLVTVEIDDESPASIQEVAAR 222

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
                   +   +R +  + +    S L+ RE  +   R +   P     + ++  V   
Sbjct: 223 ISALTPNDLPDTDRTDAMDEIDNLFSQLDERESLVLRERIVARVPQRRGAIGAKLGVGSG 282

Query: 268 RVRQIEARAFKKV 280
           RV QIEA    K+
Sbjct: 283 RVGQIEADVKAKL 295


>gi|296134074|ref|YP_003641321.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           sp. JR]
 gi|296032652|gb|ADG83420.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           potens JR]
          Length = 240

 Score = 45.6 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 24/126 (19%), Positives = 52/126 (41%), Gaps = 4/126 (3%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMG--YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           ++GDL+A  +L+  +   V K+A     R     + + +S   I    A+  ++P +   
Sbjct: 17  KNGDLAARDQLLNEYRPFVWKVASSICKRSLTWGVDDELSVALIAFNDALDAYEPGKNVS 76

Query: 101 LATYSMWWIKAAMQEYILRSWSL-VKIG-TTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
             TYS   I   +++   +   L  ++   T  +    FNL   K   +   +  ++ E+
Sbjct: 77  FLTYSRVIILNRLKDLFRKQAKLSNEVPFETELENGEIFNLADTKAAWEEYQNKTIEDER 136

Query: 159 VVAIAK 164
              + +
Sbjct: 137 QEELER 142


>gi|304438813|ref|ZP_07398739.1| RNA polymerase sigma-F factor [Peptoniphilus duerdenii ATCC
           BAA-1640]
 gi|304372696|gb|EFM26276.1| RNA polymerase sigma-F factor [Peptoniphilus duerdenii ATCC
           BAA-1640]
          Length = 225

 Score = 45.6 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 15/82 (18%), Positives = 34/82 (41%), Gaps = 2/82 (2%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           V D+      L +   +      L  ++  L  RER +      +    +L  ++ E  +
Sbjct: 145 VEDYMAASDSLEDDFFKDKDYASLYNAIGSLKSREREVIFLNFYKG--FSLLEIARELGI 202

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           S   V +++  A  K++E +++
Sbjct: 203 SLRTVNRVKQVALDKMKEFLKE 224



 Score = 39.8 bits (92), Expect = 0.46,   Method: Composition-based stats.
 Identities = 15/71 (21%), Positives = 35/71 (49%), Gaps = 4/71 (5%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
            ++ ++  L++     +       S++ ++G + L++++  FDP RGF    Y    IK+
Sbjct: 68  EIIEAYRPLIISSIKRFCPISKEFSDLFNDGVVYLIESLSNFDPSRGFTFGAY----IKS 123

Query: 112 AMQEYILRSWS 122
            ++ Y L +  
Sbjct: 124 GLRIYYLDTLR 134


>gi|302531555|ref|ZP_07283897.1| RNA polymerase [Streptomyces sp. AA4]
 gi|302440450|gb|EFL12266.1| RNA polymerase [Streptomyces sp. AA4]
          Length = 165

 Score = 45.6 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 15/78 (19%), Positives = 31/78 (39%), Gaps = 2/78 (2%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
              +   +   + +       R  L+ +++ L  RER +   R   + P     ++ E  
Sbjct: 78  YATEEMPEPAKVPDISHAVTDREWLSDALARLTARERAVVVLRHFFDLPE--HQVAEELG 135

Query: 264 VSRERVRQIEARAFKKVQ 281
           VS   V+   +RA  K++
Sbjct: 136 VSVGTVKSTNSRALAKLR 153


>gi|226315173|ref|YP_002775069.1| hypothetical protein BBR47_55880 [Brevibacillus brevis NBRC 100599]
 gi|226098123|dbj|BAH46565.1| hypothetical protein [Brevibacillus brevis NBRC 100599]
          Length = 195

 Score = 45.6 bits (107), Expect = 0.010,   Method: Composition-based stats.
 Identities = 18/96 (18%), Positives = 37/96 (38%), Gaps = 2/96 (2%)

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           +        +  D LV D D  E+    + E       +  ++  L   E+ I     L+
Sbjct: 86  VCQPTDEIERVIDSLVSDPDKSEREDNSEWEDVLSDKRILDAVQALTENEQEILTLLYLR 145

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
                    +S   VS++ V + + RA  K+++ ++
Sbjct: 146 NLKE--AEAASLLGVSQQAVSKTKKRALLKLRKQLE 179


>gi|331085692|ref|ZP_08334775.1| hypothetical protein HMPREF0987_01078 [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|330406615|gb|EGG86120.1| hypothetical protein HMPREF0987_01078 [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 207

 Score = 45.2 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 20/83 (24%), Positives = 33/83 (39%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           G+      ++  +  LV K A      G    +++ EG IGL +AV+ +D       A++
Sbjct: 19  GESEIMDFIMEKYKYLVRKKAKAMFLLGGENDDLIQEGMIGLFKAVRDYDLALETSFASF 78

Query: 105 SMWWIKAAMQEYILRSWSLVKIG 127
           +   I   M   I  S     I 
Sbjct: 79  AELCISRQMYSAIEASKRKKHIP 101


>gi|251778808|ref|ZP_04821728.1| putative RNA polymerase sigma factor [Clostridium botulinum E1 str.
           'BoNT E Beluga']
 gi|243083123|gb|EES49013.1| putative RNA polymerase sigma factor [Clostridium botulinum E1 str.
           'BoNT E Beluga']
          Length = 201

 Score = 45.2 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 16/73 (21%), Positives = 30/73 (41%), Gaps = 1/73 (1%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            ++GD  +  +L+      + K A  +        ++V  G I L+ AV K+        
Sbjct: 13  AKNGDDESLLKLMVQFKPFIFKTANSFNIKDYDTYDLVQIGYIALINAVDKYKNGSNS-F 71

Query: 102 ATYSMWWIKAAMQ 114
           ++Y    IK  M+
Sbjct: 72  SSYVYTAIKNCMR 84


>gi|218263146|ref|ZP_03477365.1| hypothetical protein PRABACTJOHN_03046 [Parabacteroides johnsonii
           DSM 18315]
 gi|218222931|gb|EEC95581.1| hypothetical protein PRABACTJOHN_03046 [Parabacteroides johnsonii
           DSM 18315]
          Length = 184

 Score = 45.2 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 13/75 (17%), Positives = 35/75 (46%), Gaps = 2/75 (2%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
                  L+  E++      +   + +L  R++     R +QE     E +++  +++  
Sbjct: 109 EPSVLDELVANEDKAAIETEIKNLLEILTDRQKEAVYLRFIQELEY--EEVANLLDMTAP 166

Query: 268 RVRQIEARAFKKVQE 282
            VR++ +RA K++++
Sbjct: 167 AVRKLISRAIKRMRD 181


>gi|193215105|ref|YP_001996304.1| ECF subfamily RNA polymerase, sigma-24 subunit [Chloroherpeton
           thalassium ATCC 35110]
 gi|193088582|gb|ACF13857.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Chloroherpeton
           thalassium ATCC 35110]
          Length = 188

 Score = 45.2 bits (106), Expect = 0.011,   Method: Composition-based stats.
 Identities = 18/85 (21%), Positives = 42/85 (49%), Gaps = 3/85 (3%)

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           R+A +ES+N  + S     +   D L+ +  G+E    E  E+  +  ++  +++ L  +
Sbjct: 78  RIAANESIN-YMRSQKVRQAVGLDTLMSEPAGKESHPDEHLEKTEQSKLIEEAIARLPEK 136

Query: 239 ERRIFEARRLQENPVTLENLSSEFE 263
           +R++F  R  +E  ++ E ++    
Sbjct: 137 QRKVFVMRYYEE--LSYEEIAESLG 159


>gi|227513726|ref|ZP_03943775.1| ECF family DNA-directed RNA polymerase sigma subunit [Lactobacillus
           buchneri ATCC 11577]
 gi|227522457|ref|ZP_03952506.1| ECF family DNA-directed RNA polymerase sigma subunit [Lactobacillus
           hilgardii ATCC 8290]
 gi|227083045|gb|EEI18357.1| ECF family DNA-directed RNA polymerase sigma subunit [Lactobacillus
           buchneri ATCC 11577]
 gi|227090409|gb|EEI25721.1| ECF family DNA-directed RNA polymerase sigma subunit [Lactobacillus
           hilgardii ATCC 8290]
          Length = 187

 Score = 45.2 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 16/94 (17%), Positives = 38/94 (40%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R    GD  A  RL   +  +V K+       G+   ++  E ++ L++  +++  ER  
Sbjct: 11  RLVAKGDEQAFSRLFHKYYPIVRKLRRLCFIEGMDADDLDQEASLVLIRTAQRYKWERSV 70

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              T+    ++  + + I +  +  +      Q+
Sbjct: 71  SFGTFYSHNLRNRIYDLIRKYKAKKRAPQQPVQR 104


>gi|325661897|ref|ZP_08150518.1| hypothetical protein HMPREF0490_01256 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|325471875|gb|EGC75092.1| hypothetical protein HMPREF0490_01256 [Lachnospiraceae bacterium
           4_1_37FAA]
          Length = 207

 Score = 45.2 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 20/83 (24%), Positives = 33/83 (39%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           G+      ++  +  LV K A      G    +++ EG IGL +AV+ +D       A++
Sbjct: 19  GESEIMDFIMEKYKYLVRKKAKAMFLLGGENDDLIQEGMIGLFKAVRDYDLALETSFASF 78

Query: 105 SMWWIKAAMQEYILRSWSLVKIG 127
           +   I   M   I  S     I 
Sbjct: 79  AELCISRQMYSAIEASKRKKHIP 101


>gi|256390006|ref|YP_003111570.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Catenulispora
           acidiphila DSM 44928]
 gi|256356232|gb|ACU69729.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Catenulispora
           acidiphila DSM 44928]
          Length = 179

 Score = 45.2 bits (106), Expect = 0.012,   Method: Composition-based stats.
 Identities = 17/82 (20%), Positives = 34/82 (41%), Gaps = 2/82 (2%)

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
           +++   D      V     ER   R +L  +++ L  R+R++   R       T   ++ 
Sbjct: 86  EEYPASDELPDSAVWDLDTERVELRTVLHSALAALPHRDRQVLALRYYG--SYTDSEIAE 143

Query: 261 EFEVSRERVRQIEARAFKKVQE 282
              +S   V+    RA +K++E
Sbjct: 144 RLGMSVGTVKSTLWRALRKLRE 165


>gi|163787808|ref|ZP_02182255.1| RNA polymerase ECF-type sigma factor [Flavobacteriales bacterium
           ALC-1]
 gi|159877696|gb|EDP71753.1| RNA polymerase ECF-type sigma factor [Flavobacteriales bacterium
           ALC-1]
          Length = 173

 Score = 45.2 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 17/87 (19%), Positives = 45/87 (51%), Gaps = 8/87 (9%)

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           +     +    K E +  R  L  +++ L+P+E+ +F   R+++   T + ++    ++ 
Sbjct: 92  EKHTDYESPDFKIEMEEFRVKLKDAINSLSPKEKEVFLLSRVED--KTYKEIAEITGLT- 148

Query: 267 ERVRQIEA---RAFKKVQESIQKQVEL 290
             V+ IE    +A K+++E++ K +++
Sbjct: 149 --VKAIERRMSKALKELRETLGKHIKV 173


>gi|300118619|ref|ZP_07056357.1| type I restriction enzyme EcoKI subunit R [Bacillus cereus SJ1]
 gi|298724008|gb|EFI64712.1| type I restriction enzyme EcoKI subunit R [Bacillus cereus SJ1]
          Length = 1437

 Score = 45.2 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 21/84 (25%), Positives = 37/84 (44%), Gaps = 8/84 (9%)

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR---LQENPVTLEN 257
            + + Y+ D  +++L E  E  +    L      +N +   I   R    L     TLE 
Sbjct: 731 DERVQYETDQLKEMLQEMIETGSIHTKLK-----INEKALAIMRERYEGTLNGKRPTLEE 785

Query: 258 LSSEFEVSRERVRQIEARAFKKVQ 281
            +   +V+RER+RQI   +  K++
Sbjct: 786 TAQNHDVTRERIRQIVKNSVGKIK 809


>gi|116619510|ref|YP_821666.1| ECF subfamily RNA polymerase sigma-24 factor [Candidatus Solibacter
           usitatus Ellin6076]
 gi|116222672|gb|ABJ81381.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Candidatus
           Solibacter usitatus Ellin6076]
          Length = 182

 Score = 45.2 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 29/159 (18%), Positives = 67/159 (42%), Gaps = 6/159 (3%)

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
            + N +R+F  + R+ G++    D   +        ++    + +      ++A + +++
Sbjct: 27  VSDNMRRIFIQIYRIVGNVADAQDLTQEAFIKALQHQEQLKDDRKAAHWLSKIATNTAID 86

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
            L  S      +  +      +  EQ L+    R   R  L   + +L+PRER+    R 
Sbjct: 87  FLRRSGRATFCEIDEAPESQIESPEQTLL----RGEHREYLEDGLRLLSPRERQALLLRD 142

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +++ P   E ++   + S+  VR   A A  K++  +++
Sbjct: 143 VEDMPA--EEVARVLDCSKATVRSHIANARIKLRRYMER 179


>gi|229826254|ref|ZP_04452323.1| hypothetical protein GCWU000182_01626 [Abiotrophia defectiva ATCC
           49176]
 gi|229789124|gb|EEP25238.1| hypothetical protein GCWU000182_01626 [Abiotrophia defectiva ATCC
           49176]
          Length = 280

 Score = 45.2 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 37/158 (23%), Positives = 71/158 (44%), Gaps = 7/158 (4%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+ Y+ E+R I  +  +EE          GD  A    +   L  VV+IA G+       
Sbjct: 113 LNMYLEELRYIEKMTVKEEEK-LIELLLKGDEKAEASYIERKLHKVVEIARGFELTEDYF 171

Query: 76  SEVVSEGNIGLMQAVKKF-DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            E++SEGN+GL+  +K+  + ER  +   +    I++AMQ++I  S     +   +    
Sbjct: 172 KELISEGNVGLLIGLKELKNLERDDKPIEFIESRIESAMQDFIEES-----LEMESTANA 226

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESE 172
           +   +  +    + + + N     +  +A   N++E+E
Sbjct: 227 MVAKVNFVSDAAKKMKEMNGSSPTLKELASYTNLTEAE 264


>gi|225572790|ref|ZP_03781545.1| hypothetical protein RUMHYD_00981 [Blautia hydrogenotrophica DSM
           10507]
 gi|225039847|gb|EEG50093.1| hypothetical protein RUMHYD_00981 [Blautia hydrogenotrophica DSM
           10507]
          Length = 171

 Score = 45.2 bits (106), Expect = 0.013,   Method: Composition-based stats.
 Identities = 21/141 (14%), Positives = 53/141 (37%), Gaps = 2/141 (1%)

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                 L  +  + + K     E E  SM   +    +        D+      + +   
Sbjct: 28  QEDAEELTGDIFLNLYKNRGSYEKEKSSMETWIFAITNNRLKNYYRDRKDEILTNSVEIY 87

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
               E  + ++  ++  +  ++ ++  L+ RER+I   +  Q        ++ E +++  
Sbjct: 88  ESSCEISVEKEVFQRQMKEDISWALQRLSERERKILVKKYYQGKGA--REIAEEMQITEG 145

Query: 268 RVRQIEARAFKKVQESIQKQV 288
            VR I  R+  K++  I +++
Sbjct: 146 NVRVIAKRSLDKLKRIINERL 166


>gi|300728092|ref|ZP_07061465.1| RNA polymerase sigma factor, sigma-70 family [Prevotella bryantii
           B14]
 gi|299774694|gb|EFI71313.1| RNA polymerase sigma factor, sigma-70 family [Prevotella bryantii
           B14]
          Length = 186

 Score = 45.2 bits (106), Expect = 0.014,   Method: Composition-based stats.
 Identities = 15/51 (29%), Positives = 27/51 (52%), Gaps = 2/51 (3%)

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
           EE+   + ++      L+P E+ IF  R L+E  +T + ++    VSR+ V
Sbjct: 116 EEQMQMKELMRYVRKNLSPMEQEIFRLRYLRE--MTCQEVAEALNVSRQTV 164


>gi|288556436|ref|YP_003428371.1| hypothetical protein BpOF4_17190 [Bacillus pseudofirmus OF4]
 gi|288547596|gb|ADC51479.1| Protein with sigma70, rpoD and rpoS domains [Bacillus pseudofirmus
           OF4]
          Length = 820

 Score = 45.2 bits (106), Expect = 0.014,   Method: Composition-based stats.
 Identities = 12/43 (27%), Positives = 23/43 (53%), Gaps = 3/43 (6%)

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           +++ I   R   E   +L+ +     +SRER+RQ EA+   ++
Sbjct: 228 KDKEILIRRMKGE---SLQQIGDSLNLSRERIRQREAKLLNRL 267


>gi|257462509|ref|ZP_05626921.1| RNA polymerase factor sigma-70 [Fusobacterium sp. D12]
 gi|317060165|ref|ZP_07924650.1| DNA-directed RNA polymerase sigma subunit RpoE [Fusobacterium sp.
           D12]
 gi|313685841|gb|EFS22676.1| DNA-directed RNA polymerase sigma subunit RpoE [Fusobacterium sp.
           D12]
          Length = 197

 Score = 44.8 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 19/82 (23%), Positives = 41/82 (50%), Gaps = 2/82 (2%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L ++ + +GD  A   ++  +  ++   A  Y   G    +++ EG +GL++A+K +D 
Sbjct: 11  ELIEKAK-NGDQEAITFIIERYQNVISMSASHYYMVGAEKQDLLQEGMLGLLKALKAYDK 69

Query: 96  ERGFRLATYSMWWIKAAMQEYI 117
           ER     T+++  I+  +   I
Sbjct: 70  ER-SSFRTFAILCIRRQLISAI 90


>gi|118443493|ref|YP_877626.1| sigma-70 region 2 domain-containing protein [Clostridium novyi NT]
 gi|118133949|gb|ABK60993.1| Sigma-70 region 2 domain protein [Clostridium novyi NT]
          Length = 182

 Score = 44.8 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 15/84 (17%), Positives = 33/84 (39%), Gaps = 1/84 (1%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             L K+  +  D  A   L+  +   +++   G    G    +++  G + +++A++K+D
Sbjct: 4   KELIKK-SKAKDEEATKILIEKYRPFILRTMQGVYIKGYDREDLIQIGYVSVIKAIEKYD 62

Query: 95  PERGFRLATYSMWWIKAAMQEYIL 118
            +       Y    IK      I 
Sbjct: 63  LDSKTPFTAYVCNSIKNNYYYKIR 86


>gi|227510711|ref|ZP_03940760.1| possible RNA polymerase sigma-30 factor [Lactobacillus brevis
           subsp. gravesensis ATCC 27305]
 gi|227189832|gb|EEI69899.1| possible RNA polymerase sigma-30 factor [Lactobacillus brevis
           subsp. gravesensis ATCC 27305]
          Length = 187

 Score = 44.8 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 16/94 (17%), Positives = 38/94 (40%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R    GD  A  RL   +  +V K+       G+   ++  E ++ L++  +++  ER  
Sbjct: 11  RLVAKGDEQAFSRLFHKYYPIVRKLRRLCFIEGMDADDLDQEASLVLIRTAQRYRWERSV 70

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQK 133
              T+    ++  + + I +  +  +      Q+
Sbjct: 71  SFGTFYSHNLRNRIYDLIRKYKAKKRAPQQPVQR 104


>gi|228942390|ref|ZP_04104928.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
 gi|228975323|ref|ZP_04135879.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228981959|ref|ZP_04142253.1| RNA polymerase sigma factor [Bacillus thuringiensis Bt407]
 gi|228777720|gb|EEM25993.1| RNA polymerase sigma factor [Bacillus thuringiensis Bt407]
 gi|228784305|gb|EEM32328.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           thuringiensis str. T01001]
 gi|228817231|gb|EEM63318.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           berliner ATCC 10792]
          Length = 156

 Score = 44.8 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 16/64 (25%), Positives = 35/64 (54%), Gaps = 2/64 (3%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    +   MSVL+ +E+ I   R       T+  ++ E EV+  +VR +  +A +K++
Sbjct: 94  EDVEMKVKDFMSVLDEKEKYIIFERFFVG--KTMGEIALEMEVTYYQVRWMYRQALEKMR 151

Query: 282 ESIQ 285
           +S++
Sbjct: 152 DSVR 155


>gi|296448813|ref|ZP_06890658.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Methylosinus
           trichosporium OB3b]
 gi|296253682|gb|EFH00864.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Methylosinus
           trichosporium OB3b]
          Length = 166

 Score = 44.8 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 22/107 (20%), Positives = 43/107 (40%), Gaps = 2/107 (1%)

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           V A+  +   +  +  +   R+A + SL+ L     ++S         D    E    E 
Sbjct: 42  VRALRHERFDAVVDPPAFLQRIAVNLSLDFLRRRKTESSYLQYVDYFLDAPSPEATPEET 101

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
              K +   L  +++ L+PR R +F     ++ P+T   ++    VS
Sbjct: 102 LAHKRKSERLAAAIAALSPRCRDVFLMGVFEDIPMT--EIARRLGVS 146


>gi|229489292|ref|ZP_04383156.1| hypothetical protein RHOER0001_0591 [Rhodococcus erythropolis
           SK121]
 gi|229323785|gb|EEN89542.1| hypothetical protein RHOER0001_0591 [Rhodococcus erythropolis
           SK121]
          Length = 701

 Score = 44.8 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 24/133 (18%), Positives = 45/133 (33%), Gaps = 5/133 (3%)

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
              +  + P  + A+   L       ++M  R+ G  S   +    D  S      +   
Sbjct: 158 ETAEEAVAPPAITALLDDLAQ-----LAMWRRVRGQASKPLVTVEIDDESPASIQEVAAR 212

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
                   +   +R +  + +    S L+ RE  +   R +   P     + ++  V   
Sbjct: 213 ISALTPNDLPDTDRTDAIDEIDNLFSQLDERESLVLRERIVARVPQRRGAIGAKLGVGSG 272

Query: 268 RVRQIEARAFKKV 280
           RV QIEA    K+
Sbjct: 273 RVGQIEADVKAKL 285


>gi|237784938|ref|YP_002905643.1| ECF-family sigma factor D [Corynebacterium kroppenstedtii DSM
           44385]
 gi|237757850|gb|ACR17100.1| ECF-family sigma factor D [Corynebacterium kroppenstedtii DSM
           44385]
          Length = 203

 Score = 44.8 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 28/135 (20%), Positives = 50/135 (37%), Gaps = 5/135 (3%)

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHD 209
            +   E  +A+ K L+            + G  S  +     S  ++ SQ  D +  +  
Sbjct: 53  EDTAQEICMAVLKSLDRFVDRGTPFMSYVYGIASHKVKDGYRSMGRDRSQPTDEIP-ESI 111

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
                  E   + + RN L R + +L  R R I   R L     T E  +     +   V
Sbjct: 112 HDAAGPEELAIQSDGRNKLLRLLDILGERPREIIILRVL--EGYTSEETAKIIGSTPNAV 169

Query: 270 RQIEARAFKKVQESI 284
           R  + RA  K+++++
Sbjct: 170 RVAQFRAIAKLKKAM 184


>gi|237725230|ref|ZP_04555711.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D4]
 gi|265754258|ref|ZP_06089447.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 3_1_33FAA]
 gi|229436496|gb|EEO46573.1| RNA polymerase ECF-type sigma factor [Bacteroides dorei 5_1_36/D4]
 gi|263234967|gb|EEZ20522.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 3_1_33FAA]
          Length = 200

 Score = 44.8 bits (105), Expect = 0.014,   Method: Composition-based stats.
 Identities = 16/91 (17%), Positives = 41/91 (45%), Gaps = 10/91 (10%)

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           S   + L+         + +  E KN + ++ +++  L+PR+R IFE  R +      + 
Sbjct: 95  SVLYEKLMEQAIDYVDDVEKSLEEKNIQELIAQALEQLSPRQREIFELSRNRGLSH--KE 152

Query: 258 LSSEFEVS----RERVRQIEARAFKKVQESI 284
           ++ +  +S    ++ +      A +K++  +
Sbjct: 153 IAEQLGLSVYTVQDHI----KNALEKIRAYL 179


>gi|150017473|ref|YP_001309727.1| ECF subfamily RNA polymerase sigma-24 factor [Clostridium
           beijerinckii NCIMB 8052]
 gi|149903938|gb|ABR34771.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           beijerinckii NCIMB 8052]
          Length = 190

 Score = 44.8 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 17/78 (21%), Positives = 32/78 (41%), Gaps = 1/78 (1%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           +  D  A  +L      L+  I+      G    +++ E    L ++V ++  E+  R  
Sbjct: 14  KDNDEEAKEKLAYEFKPLIYNISKRTFIDGYNAHDIIQECYHSLFKSVSRYSSEK-HRFV 72

Query: 103 TYSMWWIKAAMQEYILRS 120
            Y+   IK  M + I R+
Sbjct: 73  AYATNAIKNNMNDLIKRT 90


>gi|52786517|ref|YP_092346.1| hypothetical protein BLi02782 [Bacillus licheniformis ATCC 14580]
 gi|52349019|gb|AAU41653.1| hypothetical protein BLi02782 [Bacillus licheniformis ATCC 14580]
          Length = 126

 Score = 44.8 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 21/98 (21%), Positives = 35/98 (35%), Gaps = 6/98 (6%)

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           +SLN L   S    S      +          ++ +  K  +N LT         +++  
Sbjct: 8   QSLNLLKPVSGIEISLIDALRIGKRRRHRHHSVQAQSLKKSKNSLTSW----TAEKKKFI 63

Query: 244 EARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKK 279
             R   +     T   ++ E  +SR  V +IE RA  K
Sbjct: 64  AGRFSLDLKKEKTQREIAKELGISRSYVSRIEKRALMK 101


>gi|138894489|ref|YP_001124942.1| putative RNA polymerase sigma factor SigI [Geobacillus
           thermodenitrificans NG80-2]
 gi|196247909|ref|ZP_03146611.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
 gi|134266002|gb|ABO66197.1| RNA polymerase sigma factor [Geobacillus thermodenitrificans
           NG80-2]
 gi|196212693|gb|EDY07450.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Geobacillus sp.
           G11MC16]
          Length = 246

 Score = 44.8 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 21/100 (21%), Positives = 45/100 (45%), Gaps = 7/100 (7%)

Query: 29  LEKQEEYVLAKRYRE--HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
           L K+ E  L +   E   G+ +  + L+  +   + K   G     +   +   E +IGL
Sbjct: 5   LLKKRERTLERTVAEIQQGNEALRNELIQQYKPFIAKTVSGVCKRFIHEED--DEASIGL 62

Query: 87  M---QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           +   +A++K+ P +G    +++   IK  + +YI +   +
Sbjct: 63  IAFNEAIEKYAPHKGGSFLSFAELLIKRRLIDYIRKEARI 102


>gi|227500472|ref|ZP_03930531.1| sigma factor [Anaerococcus tetradius ATCC 35098]
 gi|227217386|gb|EEI82711.1| sigma factor [Anaerococcus tetradius ATCC 35098]
          Length = 135

 Score = 44.8 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 10/67 (14%), Positives = 31/67 (46%), Gaps = 2/67 (2%)

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           E K     L  +++ LN  ER + +     +   TL  ++ +   +  ++ ++  +  +K
Sbjct: 71  ETKMLIEDLHCALNNLNEEERNLIKLLYFDD--KTLIEVAKQRNTNPMKISRLRNKILEK 128

Query: 280 VQESIQK 286
           +++ + +
Sbjct: 129 LRKLLDR 135


>gi|158334762|ref|YP_001515934.1| hypothetical protein AM1_1596 [Acaryochloris marina MBIC11017]
 gi|158305003|gb|ABW26620.1| hypothetical protein AM1_1596 [Acaryochloris marina MBIC11017]
          Length = 51

 Score = 44.8 bits (105), Expect = 0.015,   Method: Composition-based stats.
 Identities = 14/33 (42%), Positives = 23/33 (69%)

Query: 74  PISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
               ++ EG IGL ++V+KFDP +G+R +TY+ 
Sbjct: 19  EFLVLIQEGTIGLRRSVEKFDPTKGYRFSTYAY 51


>gi|297199464|ref|ZP_06916861.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces sviceus
           ATCC 29083]
 gi|197712993|gb|EDY57027.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces sviceus
           ATCC 29083]
          Length = 173

 Score = 44.8 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 13/77 (16%), Positives = 33/77 (42%), Gaps = 2/77 (2%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            D     + +  +   +R  +  ++  L  R+R +   R  ++ P   E +++   V++ 
Sbjct: 89  PDQPSAQVTDWADTVAQRQDIMAALRRLPKRQRAVIVLRYFEDRPD--EEIAAILGVAQG 146

Query: 268 RVRQIEARAFKKVQESI 284
            VR    +A   ++ S+
Sbjct: 147 TVRSQTHKALASLRTSL 163


>gi|303238959|ref|ZP_07325490.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302593592|gb|EFL63309.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 245

 Score = 44.8 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 16/86 (18%), Positives = 41/86 (47%), Gaps = 3/86 (3%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM---QAVKKFDPERGF 99
           ++GD     + +  ++  ++K+   +    +   +   E +IGLM   +A++K+D  +  
Sbjct: 23  KNGDKQLKEKFIEDYIPFILKVVSSFYTSKMVDLKSSDEYSIGLMAFDEAIEKYDSSKSR 82

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVK 125
               ++   IK  + +Y  ++ S+ K
Sbjct: 83  NFFKFAELVIKRRVIDYFKKTSSISK 108


>gi|237709626|ref|ZP_04540107.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 9_1_42FAA]
 gi|229456262|gb|EEO61983.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 9_1_42FAA]
          Length = 200

 Score = 44.8 bits (105), Expect = 0.016,   Method: Composition-based stats.
 Identities = 16/91 (17%), Positives = 41/91 (45%), Gaps = 10/91 (10%)

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           S   + L+         + +  E KN + ++ +++  L+PR+R IFE  R +      + 
Sbjct: 95  SVLYEKLMEQAIDYVDDVEKSLEEKNIQELIAQALEQLSPRQREIFELSRNRGLSH--KE 152

Query: 258 LSSEFEVS----RERVRQIEARAFKKVQESI 284
           ++ +  +S    ++ +      A +K++  +
Sbjct: 153 IAEQLGLSVYTVQDHI----KNALEKIRACL 179


>gi|291563737|emb|CBL42553.1| DNA-directed RNA polymerase specialized sigma subunit
           [butyrate-producing bacterium SS3/4]
          Length = 143

 Score = 44.8 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 20/108 (18%), Positives = 40/108 (37%), Gaps = 6/108 (5%)

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             M CR   + SL+AL + +D +     D    D         +         ++  + +
Sbjct: 31  REMKCRRDREVSLDAL-SPADWDKLSTVDRYSCDSFTFSSHGYDLHIDN---ELVAEAFA 86

Query: 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L   E+ I   R + +  +T E +     +SR  V++      K ++
Sbjct: 87  SLPKDEQSILILRFVLD--LTDEEIGRLMGMSRSAVQRHRTSTLKDLR 132


>gi|28377490|ref|NP_784382.1| DNA-directed RNA polymerase, sigma factor 30 [Lactobacillus
           plantarum WCFS1]
 gi|254555720|ref|YP_003062137.1| DNA-directed RNA polymerase, sigma factor 30 [Lactobacillus
           plantarum JDM1]
 gi|300769742|ref|ZP_07079624.1| DNA-directed RNA polymerase [Lactobacillus plantarum subsp.
           plantarum ATCC 14917]
 gi|308179701|ref|YP_003923829.1| DNA-directed RNA polymerase, sigma factor 30 [Lactobacillus
           plantarum subsp. plantarum ST-III]
 gi|28270322|emb|CAD63223.1| DNA-directed RNA polymerase, sigma factor 30 [Lactobacillus
           plantarum WCFS1]
 gi|254044647|gb|ACT61440.1| DNA-directed RNA polymerase, sigma factor 30 [Lactobacillus
           plantarum JDM1]
 gi|300492650|gb|EFK27836.1| DNA-directed RNA polymerase [Lactobacillus plantarum subsp.
           plantarum ATCC 14917]
 gi|308045192|gb|ADN97735.1| DNA-directed RNA polymerase, sigma factor 30 [Lactobacillus
           plantarum subsp. plantarum ST-III]
          Length = 200

 Score = 44.8 bits (105), Expect = 0.017,   Method: Composition-based stats.
 Identities = 16/87 (18%), Positives = 36/87 (41%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
               GD ++ + L   ++ +V ++   Y        + + EG I + +A KK+   R   
Sbjct: 22  LAADGDDASINALAQQYVPVVWRLRRQYYVRNFDEDDWLQEGRIAVYRAAKKYQRLRQCS 81

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIG 127
             TY    +   + ++I R+ +  +  
Sbjct: 82  FGTYYRVLLSNQIIDHIRRTQARKRRP 108


>gi|311748044|ref|ZP_07721829.1| RNA polymerase ECF-type sigma factor [Algoriphagus sp. PR1]
 gi|126575027|gb|EAZ79385.1| RNA polymerase ECF-type sigma factor [Algoriphagus sp. PR1]
          Length = 195

 Score = 44.8 bits (105), Expect = 0.018,   Method: Composition-based stats.
 Identities = 17/76 (22%), Positives = 34/76 (44%), Gaps = 2/76 (2%)

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           IN S K + +  D  +      E+ +IE +E  + ++ +  ++  ++ R+R I   R   
Sbjct: 103 INKSRKFTDEPTDTFLGSDLTIEEKIIESDESYSNKSKIKSALRKVSKRQREILILRFFH 162

Query: 250 ENPVTLENLSSEFEVS 265
               T   +SS   +S
Sbjct: 163 GMDYT--EISSMMGIS 176


>gi|298245362|ref|ZP_06969168.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297552843|gb|EFH86708.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 207

 Score = 44.8 bits (105), Expect = 0.018,   Method: Composition-based stats.
 Identities = 18/88 (20%), Positives = 32/88 (36%), Gaps = 6/88 (6%)

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
             R         L    + + + W   +  +H   +    E+ ERK+ R  L R++  L 
Sbjct: 104 ELRKRRPLLFCELDVPLEDDENSWPYTIADNHPQPD----EELERKDIRTALRRAILALP 159

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEV 264
           PR R I   R   +  +T   +     +
Sbjct: 160 PRFRSIVLLRY--QEELTFSEIGRILGM 185


>gi|255038698|ref|YP_003089319.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Dyadobacter
           fermentans DSM 18053]
 gi|254951454|gb|ACT96154.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Dyadobacter
           fermentans DSM 18053]
          Length = 182

 Score = 44.8 bits (105), Expect = 0.018,   Method: Composition-based stats.
 Identities = 21/139 (15%), Positives = 48/139 (34%), Gaps = 18/139 (12%)

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            + E +  ++  L       I    R    ESL       +     ++D L+ D    E 
Sbjct: 48  PEIEAIEQMSSWLYRVARNRIIDKYRKQKPESLEDFGYEDEDGEFHFKDILLADDHTPET 107

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE------VSRE 267
             +    +      L+ ++  L   +R++F     +    T + ++          +SR+
Sbjct: 108 AYL----KDLFWEQLSIALDELPENQRQVFI--WNELEDQTFQQIADRTGENIKTLISRK 161

Query: 268 RVRQIEARAFKKVQESIQK 286
           R       A + ++E ++ 
Sbjct: 162 R------YAVRHLRERLES 174


>gi|212690591|ref|ZP_03298719.1| hypothetical protein BACDOR_00077 [Bacteroides dorei DSM 17855]
 gi|212666837|gb|EEB27409.1| hypothetical protein BACDOR_00077 [Bacteroides dorei DSM 17855]
          Length = 200

 Score = 44.4 bits (104), Expect = 0.018,   Method: Composition-based stats.
 Identities = 16/91 (17%), Positives = 41/91 (45%), Gaps = 10/91 (10%)

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           S   + L+         + +  E KN + ++ +++  L+PR+R IFE  R +      + 
Sbjct: 95  SVLYEKLMEQAIDYVDDVEKSLEEKNIQELIAQALEQLSPRQREIFELSRNRGLSH--KE 152

Query: 258 LSSEFEVS----RERVRQIEARAFKKVQESI 284
           ++ +  +S    ++ +      A +K++  +
Sbjct: 153 IAEQLGLSVYTVQDHI----KNALEKIRACL 179


>gi|154499637|ref|ZP_02037675.1| hypothetical protein BACCAP_03294 [Bacteroides capillosus ATCC
           29799]
 gi|150271235|gb|EDM98492.1| hypothetical protein BACCAP_03294 [Bacteroides capillosus ATCC
           29799]
          Length = 177

 Score = 44.4 bits (104), Expect = 0.018,   Method: Composition-based stats.
 Identities = 14/74 (18%), Positives = 28/74 (37%), Gaps = 5/74 (6%)

Query: 54  VTSHLRLVVKIAMGY-----RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           V  ++ LV K+          G      ++   G +GL +A +   P      +TY+   
Sbjct: 13  VEENMGLVGKVIQDCVHTLGTGSMFDYDDLFQIGCLGLCKAAQTDKPGHTVAFSTYAYRL 72

Query: 109 IKAAMQEYILRSWS 122
           I+  +   + R+  
Sbjct: 73  IRNEIYTELERATR 86


>gi|219668837|ref|YP_002459272.1| RNA polymerase factor sigma-70 [Desulfitobacterium hafniense DCB-2]
 gi|219539097|gb|ACL20836.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Desulfitobacterium
           hafniense DCB-2]
          Length = 206

 Score = 44.4 bits (104), Expect = 0.018,   Method: Composition-based stats.
 Identities = 14/82 (17%), Positives = 32/82 (39%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           G+  + + L+  +   + KIA  Y        +++ EG I + +A+  +DP        +
Sbjct: 21  GNQDSLNWLIQYYEPEIRKIAYKYFLNRAEYDDLLQEGRIAIYKAIVSYDPSSEIPFLHF 80

Query: 105 SMWWIKAAMQEYILRSWSLVKI 126
               IK  + + +        +
Sbjct: 81  LRMVIKRKLIDSLRAHNRQKHL 102


>gi|315654974|ref|ZP_07907879.1| conserved hypothetical protein [Mobiluncus curtisii ATCC 51333]
 gi|315490935|gb|EFU80555.1| conserved hypothetical protein [Mobiluncus curtisii ATCC 51333]
          Length = 178

 Score = 44.4 bits (104), Expect = 0.018,   Method: Composition-based stats.
 Identities = 17/76 (22%), Positives = 37/76 (48%), Gaps = 2/76 (2%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           + D  G  +   +  +  + R  +  +++ L+ RER I    RL + P+T   +++E  +
Sbjct: 97  LVDQYGHMKAFDDPFDDVDTRLTVESALAGLDERERFIVIQNRLNQVPLT--VVAAELGI 154

Query: 265 SRERVRQIEARAFKKV 280
           ++ R  Q+   A  K+
Sbjct: 155 TQPRASQLLKSARAKI 170


>gi|210610554|ref|ZP_03288480.1| hypothetical protein CLONEX_00670 [Clostridium nexile DSM 1787]
 gi|210152413|gb|EEA83419.1| hypothetical protein CLONEX_00670 [Clostridium nexile DSM 1787]
          Length = 143

 Score = 44.4 bits (104), Expect = 0.018,   Method: Composition-based stats.
 Identities = 20/108 (18%), Positives = 40/108 (37%), Gaps = 6/108 (5%)

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             M CR   + SL+AL + +D +     D    D         +         ++  + +
Sbjct: 31  REMKCRRDREVSLDAL-SPADWDKLSTVDRYSCDSFTFSSHGYDLHIDN---ELVAEAFA 86

Query: 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L   E+ I   R + +  +T E +     +SR  V++      K ++
Sbjct: 87  SLPKDEQSILILRFVLD--LTDEEIGRLMGMSRSAVQRHRTSTLKDLR 132


>gi|210617631|ref|ZP_03291670.1| hypothetical protein CLONEX_03894 [Clostridium nexile DSM 1787]
 gi|210149231|gb|EEA80240.1| hypothetical protein CLONEX_03894 [Clostridium nexile DSM 1787]
          Length = 48

 Score = 44.4 bits (104), Expect = 0.018,   Method: Composition-based stats.
 Identities = 9/50 (18%), Positives = 22/50 (44%), Gaps = 2/50 (4%)

Query: 235 LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           L   ER++   R       T   +     +S+ +V ++E +  K +++ +
Sbjct: 1   LEKEERQLIYLRYFANQ--TQSQVGKTLGISQVQVSRLEKKILKNLRQKV 48


>gi|326943042|gb|AEA18938.1| RNA polymerase factor sigma-70 [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 145

 Score = 44.4 bits (104), Expect = 0.019,   Method: Composition-based stats.
 Identities = 16/64 (25%), Positives = 35/64 (54%), Gaps = 2/64 (3%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    +   MSVL+ +E+ I   R       T+  ++ E EV+  +VR +  +A +K++
Sbjct: 83  EDVEMKVKDFMSVLDEKEKYIIFERFFVG--KTMGEIALEMEVTYYQVRWMYRQALEKMR 140

Query: 282 ESIQ 285
           +S++
Sbjct: 141 DSVR 144


>gi|291485815|dbj|BAI86890.1| hypothetical protein BSNT_04952 [Bacillus subtilis subsp. natto
           BEST195]
          Length = 212

 Score = 44.4 bits (104), Expect = 0.019,   Method: Composition-based stats.
 Identities = 13/96 (13%), Positives = 40/96 (41%), Gaps = 6/96 (6%)

Query: 196 NSSQWQDWLVYD--HDGQEQVLIEKEERKNRRN--MLTRSMSVLNPRERRIFEARRLQEN 251
           +  +  D L  +   D  E+ L  +++         L +++  L  +++ +     L  +
Sbjct: 92  DHPEAGDRLPSETGSDAFEEFLDRQDDLSQHVQDYQLYQAIQKLTDKQKSVLTKVYL--H 149

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             T++ ++     SR+ +  I  +  + +++ +  Q
Sbjct: 150 GATMQEIADSLGESRQNISNIHKKGLENIRKQLAAQ 185


>gi|116492329|ref|YP_804064.1| hypothetical protein PEPE_0533 [Pediococcus pentosaceus ATCC 25745]
 gi|116102479|gb|ABJ67622.1| hypothetical protein PEPE_0533 [Pediococcus pentosaceus ATCC 25745]
          Length = 833

 Score = 44.4 bits (104), Expect = 0.019,   Method: Composition-based stats.
 Identities = 19/79 (24%), Positives = 34/79 (43%), Gaps = 7/79 (8%)

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           D        +++  + +    L   +  L+     I   R+   +  TLE ++    +SR
Sbjct: 212 DMKKNPSEAVKEYRKTSNLLDLEECLLNLDD---NIGTLRKRL-SGKTLEEIAKPLNLSR 267

Query: 267 ERVRQIEARAFK---KVQE 282
           ERVRQ +A+      K+QE
Sbjct: 268 ERVRQKQAKLILLFPKLQE 286


>gi|294054255|ref|YP_003547913.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Coraliomargarita
           akajimensis DSM 45221]
 gi|293613588|gb|ADE53743.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Coraliomargarita
           akajimensis DSM 45221]
          Length = 197

 Score = 44.4 bits (104), Expect = 0.019,   Method: Composition-based stats.
 Identities = 19/91 (20%), Positives = 40/91 (43%), Gaps = 1/91 (1%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y L +R ++ GD +A   LV  + R +  +    +     I ++  +  IGL + + K+D
Sbjct: 9   YTLLQRAQDLGDEAAWAELVEHYKRFIYHVLHRLKVPQDDIDDISQQVLIGLTRDLSKYD 68

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
            ++  R   +    I+ A   +  +  S  +
Sbjct: 69  RDK-SRFRNWLSTIIRNAAYSHFRQQKSQAR 98


>gi|83816830|ref|YP_446354.1| RNA polymerase ECF-type sigma factor, putative [Salinibacter ruber
           DSM 13855]
 gi|83758224|gb|ABC46337.1| RNA polymerase ECF-type sigma factor, putative [Salinibacter ruber
           DSM 13855]
          Length = 216

 Score = 44.4 bits (104), Expect = 0.019,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 2/97 (2%)

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
             QD      D       E  +    R++L R ++ L  R+R     RR ++     + +
Sbjct: 122 HEQDVRDAHPDASPPAPDETLDADLLRSLLERWIAELPDRQREALTLRRQKDLSH--DEI 179

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPP 295
           +   +VS   V     RA + ++E + +      S P
Sbjct: 180 AEIMDVSPNTVNNHIVRAMRTLRERLGEYRPDVRSEP 216


>gi|153811788|ref|ZP_01964456.1| hypothetical protein RUMOBE_02181 [Ruminococcus obeum ATCC 29174]
 gi|149832191|gb|EDM87276.1| hypothetical protein RUMOBE_02181 [Ruminococcus obeum ATCC 29174]
          Length = 158

 Score = 44.4 bits (104), Expect = 0.020,   Method: Composition-based stats.
 Identities = 20/122 (16%), Positives = 48/122 (39%), Gaps = 7/122 (5%)

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
            I +       +  +M  +    E L+  + S + +    QD         E ++I + E
Sbjct: 39  EIYRSKKWQPEDPETMTRKTKWTELLD-CVFSENTDGIGVQDLPDEGQRSVEDLVILQAE 97

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                  L ++++ L+  E+ I ++       +    L+    +S+ R+ Q  +   KK+
Sbjct: 98  SAE----LHQNIAKLSEHEQFIIKSIYF--EGMKQVELAKILGISKVRMSQKVSAILKKM 151

Query: 281 QE 282
           ++
Sbjct: 152 RK 153


>gi|296156806|ref|ZP_06839643.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Burkholderia sp.
           Ch1-1]
 gi|295892692|gb|EFG72473.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Burkholderia sp.
           Ch1-1]
          Length = 223

 Score = 44.4 bits (104), Expect = 0.020,   Method: Composition-based stats.
 Identities = 19/97 (19%), Positives = 40/97 (41%), Gaps = 2/97 (2%)

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             + ++   R+  + S++A    S +N+    +         E         ++    + 
Sbjct: 91  VRQPVAYVTRMVRNASIDAFRRQSLENTYHADEDDGLHVPSPEPSPEAALLVRDTLRHVY 150

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
            ++  L PR R  FE  RL+E   TL++ +   +VS+
Sbjct: 151 NALDQLPPRSRAAFEMVRLREE--TLQSTARALDVSQ 185


>gi|269976589|ref|ZP_06183574.1| putative sigma factor [Mobiluncus mulieris 28-1]
 gi|269935390|gb|EEZ91939.1| putative sigma factor [Mobiluncus mulieris 28-1]
          Length = 178

 Score = 44.4 bits (104), Expect = 0.020,   Method: Composition-based stats.
 Identities = 17/76 (22%), Positives = 37/76 (48%), Gaps = 2/76 (2%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           + D  G  +   +  +  + R  +  +++ L+ RER I    RL + P+T   +++E  +
Sbjct: 97  LVDQYGHLKAFDDPFDDVDTRLTVESALAGLDERERFIVIQNRLNQVPLT--AVAAELGI 154

Query: 265 SRERVRQIEARAFKKV 280
           ++ R  Q+   A  K+
Sbjct: 155 TQPRASQLLKSARAKI 170


>gi|54025688|ref|YP_119930.1| hypothetical protein nfa37180 [Nocardia farcinica IFM 10152]
 gi|54017196|dbj|BAD58566.1| hypothetical protein [Nocardia farcinica IFM 10152]
          Length = 417

 Score = 44.4 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 15/40 (37%), Positives = 23/40 (57%), Gaps = 2/40 (5%)

Query: 238 RERRIFEARRL--QENPVTLENLSSEFEVSRERVRQIEAR 275
           R+  I  AR     E P TL  + + F+++R+RVRQ+  R
Sbjct: 62  RDAEILAARLGIGGEPPQTLAAIGARFDLARDRVRQLHTR 101


>gi|229124759|ref|ZP_04253939.1| RNA polymerase sigma factor [Bacillus cereus 95/8201]
 gi|228658736|gb|EEL14396.1| RNA polymerase sigma factor [Bacillus cereus 95/8201]
          Length = 156

 Score = 44.4 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 16/64 (25%), Positives = 34/64 (53%), Gaps = 2/64 (3%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    +   MSVL+ +E+ I   R       T+  ++ E E++  +VR I  +A +K++
Sbjct: 94  EDIEMKVKDFMSVLDEKEKYIIFERFFVG--KTMGEIALETEMTYYQVRWIYRQALEKMR 151

Query: 282 ESIQ 285
            S++
Sbjct: 152 NSLR 155


>gi|218906428|ref|YP_002454262.1| putative sigma factor [Bacillus cereus AH820]
 gi|218538340|gb|ACK90738.1| putative sigma factor [Bacillus cereus AH820]
          Length = 156

 Score = 44.4 bits (104), Expect = 0.021,   Method: Composition-based stats.
 Identities = 17/64 (26%), Positives = 34/64 (53%), Gaps = 2/64 (3%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    +   MSVL+ +E+ I   R       T+  ++ E E+S  +VR I  +A +K++
Sbjct: 94  EDIEMKVKDFMSVLDEKEKYIIFERFFVG--KTMGEIALETEMSYYQVRWIYRQALEKMR 151

Query: 282 ESIQ 285
            S++
Sbjct: 152 NSLR 155


>gi|294508291|ref|YP_003572349.1| RNA polymerase sigma-E factor [Salinibacter ruber M8]
 gi|294344619|emb|CBH25397.1| RNA polymerase sigma-E factor [Salinibacter ruber M8]
          Length = 216

 Score = 44.4 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 2/97 (2%)

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
             QD      D       E  +    R++L R ++ L  R+R     RR ++     + +
Sbjct: 122 HEQDVRDAHPDASPPAPDETLDADLLRSLLERWIAELPDRQREALTLRRQKDLSH--DEI 179

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPP 295
           +   +VS   V     RA + ++E + +      S P
Sbjct: 180 AEIMDVSPNTVNNHIVRAMRTLRERLGEYRPDVRSEP 216


>gi|257470690|ref|ZP_05634780.1| RNA polymerase factor sigma-70 [Fusobacterium ulcerans ATCC 49185]
 gi|317064896|ref|ZP_07929381.1| RNA polymerase sigma-H factor [Fusobacterium ulcerans ATCC 49185]
 gi|313690572|gb|EFS27407.1| RNA polymerase sigma-H factor [Fusobacterium ulcerans ATCC 49185]
          Length = 204

 Score = 44.4 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 15/73 (20%), Positives = 34/73 (46%), Gaps = 1/73 (1%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  + + ++  +  L+      Y   G    +++ EG IGL++A+K +   +     T+
Sbjct: 17  GDQESINIILREYRNLIYLNVRNYFIIGAEQDDLLQEGTIGLLKALKAYQKGK-SSFKTF 75

Query: 105 SMWWIKAAMQEYI 117
           +M  I+  +   +
Sbjct: 76  AMICIRRQILTAV 88


>gi|108759609|ref|YP_629469.1| putative RNA polymerase sigma-70 factor [Myxococcus xanthus DK
           1622]
 gi|108463489|gb|ABF88674.1| putative RNA polymerase sigma-70 factor [Myxococcus xanthus DK
           1622]
          Length = 353

 Score = 44.4 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 33/214 (15%), Positives = 86/214 (40%), Gaps = 28/214 (13%)

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFR-LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
            ++     + +++AV K+D  RG +     + +  +AA ++Y     + V +    +++R
Sbjct: 164 DDLAQVAAMAMLRAVSKYDATRGRQSFGQVAYFRARAACEQYARLHGTDVHLSDGEHKRR 223

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
              ++R  +                         +   V  M+      +  +A  +  D
Sbjct: 224 TVRSIRSNER------------------------NVVRVHRMDIPSHFSDGASADDSWVD 259

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP-V 253
           +  S  ++    D D  E+    K     RR ++  ++  L P +R +         P  
Sbjct: 260 ELESALREMSCLDAD--EETPEAKLLAAERRALVFDAVRRLAPEQRELVSRVFGINRPAQ 317

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++ +++  ++  + R+ ++ ARA  +++E++ +Q
Sbjct: 318 SVRSVAEAWKAPKSRIDRMLARALAELREALVRQ 351


>gi|89894412|ref|YP_517899.1| RNA polymerase factor sigma-70 [Desulfitobacterium hafniense Y51]
 gi|89333860|dbj|BAE83455.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 208

 Score = 44.4 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 14/82 (17%), Positives = 32/82 (39%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           G+  + + L+  +   + KIA  Y        +++ EG I + +A+  +DP        +
Sbjct: 23  GNQDSLNWLIQYYEPEIRKIAYKYFLNRAEYDDLLQEGRIAIYKAIVSYDPSSEIPFLHF 82

Query: 105 SMWWIKAAMQEYILRSWSLVKI 126
               IK  + + +        +
Sbjct: 83  LRMVIKRKLIDSLRAHNRQKHL 104


>gi|307690663|ref|ZP_07633109.1| sporulation sigma factor SigG [Clostridium cellulovorans 743B]
          Length = 65

 Score = 44.4 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 12/54 (22%), Positives = 26/54 (48%), Gaps = 1/54 (1%)

Query: 24 RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           K+P+L++ E   L  + +  GD  +  + +  +LRLV+ +   +   G    +
Sbjct: 13 SKLPVLKEHEMRELLDKMK-AGDYISREKFIRGNLRLVLSVIQRFNNRGENADD 65


>gi|294674809|ref|YP_003575425.1| ECF family RNA polymerase sigma-70 factor [Prevotella ruminicola
           23]
 gi|294472013|gb|ADE81402.1| RNA polymerase sigma-70 factor, ECF family [Prevotella ruminicola
           23]
          Length = 162

 Score = 44.4 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 14/67 (20%), Positives = 31/67 (46%), Gaps = 2/67 (2%)

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
            E  ER      L  ++  L  R R IF     +++ +T   ++ E  +S + V    ++
Sbjct: 86  EEAAERSLHEAELWTAIDTLPERCRMIFLM--AKQDGMTYHEIAEELHISEKTVEHQLSK 143

Query: 276 AFKKVQE 282
           A +++++
Sbjct: 144 AIRQLRK 150


>gi|238923822|ref|YP_002937338.1| RNA polymerase factor sigma-70 [Eubacterium rectale ATCC 33656]
 gi|238875497|gb|ACR75204.1| RNA polymerase factor sigma-70 [Eubacterium rectale ATCC 33656]
          Length = 201

 Score = 44.4 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 39/257 (15%), Positives = 90/257 (35%), Gaps = 71/257 (27%)

Query: 36  VLAKRYR----EHGDL-SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
            L  R      +HGD       ++  +  LV K        G    +++ EG IGL +AV
Sbjct: 11  ELIMRIHNDKNDHGDNNEIMDYILEKYKPLVRKKTNALYLIGGENDDLIQEGMIGLFKAV 70

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           + +  ++     +++   I   +   +  S     +                        
Sbjct: 71  RDYKSDKEASFYSFAQLCITRQLSSALEASNRKKHMP----------------------- 107

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
                                    +N  ++  +S        D + +++++ L  D   
Sbjct: 108 -------------------------LNTYISFSQS--------DSDGTEFEEMLQDDIAS 134

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
            EQ+LIEKE+ K  +  L   +S +   E+++ +   L+ N  T  +++     S + + 
Sbjct: 135 PEQLLIEKEKFKEFKEQLWNKLSNM---EKKVLQL-YLEGNNYT--SIAHMLGKSDKSI- 187

Query: 271 QIEARAFKKVQESIQKQ 287
                A  ++++ ++++
Sbjct: 188 ---DNALSRIRQKLKRK 201


>gi|255035252|ref|YP_003085873.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Dyadobacter
           fermentans DSM 18053]
 gi|254948008|gb|ACT92708.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Dyadobacter
           fermentans DSM 18053]
          Length = 197

 Score = 44.4 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 15/75 (20%), Positives = 35/75 (46%), Gaps = 2/75 (2%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
              +E  +IE E+ + +++ L   +  L  R+  +   R  Q+   +   +S    ++ +
Sbjct: 109 ELSKESEIIESEQFQKQKDELDAWLKSLPGRQYEVLMLRYYQDFSYS--QISEMLTINEQ 166

Query: 268 RVRQIEARAFKKVQE 282
            VR +  RA  K+++
Sbjct: 167 SVRNLVQRAVSKLRQ 181


>gi|196036327|ref|ZP_03103725.1| putative sigma factor [Bacillus cereus W]
 gi|196045646|ref|ZP_03112876.1| putative sigma factor [Bacillus cereus 03BB108]
 gi|225867222|ref|YP_002752600.1| putative sigma factor [Bacillus cereus 03BB102]
 gi|228930254|ref|ZP_04093262.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|229187470|ref|ZP_04314612.1| RNA polymerase sigma factor [Bacillus cereus BGSC 6E1]
 gi|301056717|ref|YP_003794928.1| RNA polymerase sigma-70 factor [Bacillus anthracis CI]
 gi|195991119|gb|EDX55089.1| putative sigma factor [Bacillus cereus W]
 gi|196023477|gb|EDX62154.1| putative sigma factor [Bacillus cereus 03BB108]
 gi|225789005|gb|ACO29222.1| putative sigma factor [Bacillus cereus 03BB102]
 gi|228595991|gb|EEK53669.1| RNA polymerase sigma factor [Bacillus cereus BGSC 6E1]
 gi|228829395|gb|EEM75024.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           pondicheriensis BGSC 4BA1]
 gi|300378886|gb|ADK07790.1| RNA polymerase sigma-70 factor [Bacillus cereus biovar anthracis
           str. CI]
          Length = 156

 Score = 44.4 bits (104), Expect = 0.022,   Method: Composition-based stats.
 Identities = 16/64 (25%), Positives = 34/64 (53%), Gaps = 2/64 (3%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    +   MSVL+ +E+ I   R       T+  ++ E E++  +VR I  +A +K++
Sbjct: 94  EDIEMKVKDFMSVLDEKEKYIIFERFFVG--KTMGEIALETEMTYYQVRWIYRQALEKMR 151

Query: 282 ESIQ 285
            S++
Sbjct: 152 NSLR 155


>gi|302390178|ref|YP_003825999.1| Sigma-70 region 4 type 2 [Thermosediminibacter oceani DSM 16646]
 gi|302200806|gb|ADL08376.1| Sigma-70 region 4 type 2 [Thermosediminibacter oceani DSM 16646]
          Length = 144

 Score = 44.4 bits (104), Expect = 0.023,   Method: Composition-based stats.
 Identities = 17/99 (17%), Positives = 43/99 (43%), Gaps = 10/99 (10%)

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           LN  +N  D    +  + +    D   +V          +  + + +SVL  ++R++ E 
Sbjct: 51  LNDFVNPDDSKPVEMINTISDPTDPFSEV--------EDKIYIQQVLSVLTLQQRKVIEL 102

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              +   +T + ++ +  +S+  V +++ R   K++  I
Sbjct: 103 IIFKG--LTEKEIAKQLGISQPSVHRLKIRGLNKIKNII 139


>gi|237667676|ref|ZP_04527660.1| RNA polymerase sigma-K factor (Sigma-27) [Clostridium butyricum E4
           str. BoNT E BL5262]
 gi|237656024|gb|EEP53580.1| RNA polymerase sigma-K factor (Sigma-27) [Clostridium butyricum E4
           str. BoNT E BL5262]
          Length = 87

 Score = 44.4 bits (104), Expect = 0.023,   Method: Composition-based stats.
 Identities = 14/67 (20%), Positives = 26/67 (38%), Gaps = 3/67 (4%)

Query: 209 DGQEQVLIEKEERKNRRNMLTRSM-SVLNPRERRIFEARRL--QENPVTLENLSSEFEVS 265
             ++  +++K E   +   L + +   L  RE  I   R         T   ++S   +S
Sbjct: 5   SSEKDSVLDKVESNLQVRALYKKLGESLTSRESSILIMRYGLIDGKCKTQREIASNLGIS 64

Query: 266 RERVRQI 272
           R  V +I
Sbjct: 65  RSYVSRI 71


>gi|226314708|ref|YP_002774604.1| RNA polymerase ECF-type sigma factor [Brevibacillus brevis NBRC
           100599]
 gi|226097658|dbj|BAH46100.1| RNA polymerase ECF-type sigma factor [Brevibacillus brevis NBRC
           100599]
          Length = 218

 Score = 44.4 bits (104), Expect = 0.023,   Method: Composition-based stats.
 Identities = 21/94 (22%), Positives = 47/94 (50%), Gaps = 5/94 (5%)

Query: 198 SQWQDWLVYDHDGQEQVLIEKE-ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
               D L    D Q    +E+E   + +R  +   +  L P+ R++      ++  +++ 
Sbjct: 127 PTMDDHLGDLMDRQANNQVEEEILNRVKREEIVTYIQSLAPKYRQVILLHYYED--LSIA 184

Query: 257 NLSSEFEVSRERVR-QIEARAFKKVQESIQKQVE 289
            ++    VS+E VR ++  RA K+++E++ K+V+
Sbjct: 185 EVADILSVSQEVVRTRLH-RARKQLKETMSKEVQ 217


>gi|187779720|ref|ZP_02996193.1| hypothetical protein CLOSPO_03316 [Clostridium sporogenes ATCC
           15579]
 gi|187773345|gb|EDU37147.1| hypothetical protein CLOSPO_03316 [Clostridium sporogenes ATCC
           15579]
          Length = 183

 Score = 44.4 bits (104), Expect = 0.023,   Method: Composition-based stats.
 Identities = 17/80 (21%), Positives = 37/80 (46%), Gaps = 2/80 (2%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y L ++Y+E GD    ++++     +++K A  +R       ++V  G + +++A   F 
Sbjct: 6   YKLLEKYKE-GDTEVLNKIIAYFTPIILKEASKWRISCYEYEDLVQHGYLSVIKAANMFK 64

Query: 95  PERGFRLATYSMWWIKAAMQ 114
            E   +   Y +  IK   +
Sbjct: 65  GE-ESKFIPYCIKTIKTNYK 83



 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 22/100 (22%), Positives = 48/100 (48%), Gaps = 3/100 (3%)

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK-NRRNMLTRSMSVLNPRERRIFEAR 246
           AL+    K+  +  D  + D   +    IE E       N L +++  L   E+ +  + 
Sbjct: 84  ALLKGEIKHHREIPDENISDKGNEYFFTIEDEIIAYENINELYKALDKLTSEEKEVINSF 143

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            ++ N  +L+ +++  + S   VR I+ +A KK+Q+ +++
Sbjct: 144 YIKNN--SLQKVANSIDKSYNSVRYIKNKAIKKLQKILEE 181


>gi|229032872|ref|ZP_04188827.1| RNA polymerase sigma factor [Bacillus cereus AH1271]
 gi|228728417|gb|EEL79438.1| RNA polymerase sigma factor [Bacillus cereus AH1271]
          Length = 156

 Score = 44.0 bits (103), Expect = 0.023,   Method: Composition-based stats.
 Identities = 16/64 (25%), Positives = 34/64 (53%), Gaps = 2/64 (3%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++        MSVL+ +E+ I   R       T+  ++SE E++  +VR +  +A +K++
Sbjct: 94  EDIEMRAKDFMSVLDEKEKYIIFERFFVG--KTMGEIASEMEMTYYQVRWVYRQALEKMR 151

Query: 282 ESIQ 285
            S++
Sbjct: 152 NSLR 155


>gi|86606871|ref|YP_475634.1| RNA polymerase sigma factor [Synechococcus sp. JA-3-3Ab]
 gi|86555413|gb|ABD00371.1| RNA polymerase sigma factor, ECF family [Synechococcus sp.
           JA-3-3Ab]
          Length = 196

 Score = 44.0 bits (103), Expect = 0.023,   Method: Composition-based stats.
 Identities = 14/86 (16%), Positives = 37/86 (43%), Gaps = 10/86 (11%)

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS--- 265
           + +     E+   + RR  +  ++  L   +R++ E    Q   ++  +++    +    
Sbjct: 115 ENRAPAPFEQLSLEERRQAVQEALGQLPESQRQVLELIYYQG--LSQADVARHLGIPPAT 172

Query: 266 -RERVRQIEARAFKKVQESIQKQVEL 290
            + R RQ    A  K++ S++  +E+
Sbjct: 173 VKARARQ----ALCKLRGSLRALLEV 194


>gi|321312872|ref|YP_004205159.1| alternative sigma factor sigmaO [Bacillus subtilis BSn5]
 gi|320019146|gb|ADV94132.1| alternative sigma factor sigmaO [Bacillus subtilis BSn5]
          Length = 190

 Score = 44.0 bits (103), Expect = 0.023,   Method: Composition-based stats.
 Identities = 13/96 (13%), Positives = 40/96 (41%), Gaps = 6/96 (6%)

Query: 196 NSSQWQDWLVYD--HDGQEQVLIEKEERKNRRN--MLTRSMSVLNPRERRIFEARRLQEN 251
           +  +  D L  +   D  E+ L  +++         L +++  L  +++ +     L  +
Sbjct: 92  DHPEAGDRLPSETGSDAFEEFLDRQDDLSQHVQDYQLYQAIQKLTDKQKSVLTKVYL--H 149

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             T++ ++     SR+ +  I  +  + +++ +  Q
Sbjct: 150 GATMQEIADSLGESRQNISNIHKKGLENIRKQLAAQ 185


>gi|271967956|ref|YP_003342152.1| ECF subfamily RNA polymerase sigma-24 subunit [Streptosporangium
           roseum DSM 43021]
 gi|270511131|gb|ACZ89409.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Streptosporangium
           roseum DSM 43021]
          Length = 165

 Score = 44.0 bits (103), Expect = 0.024,   Method: Composition-based stats.
 Identities = 12/59 (20%), Positives = 26/59 (44%), Gaps = 6/59 (10%)

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R  + ++++ L  R+R +   R   +  +P     ++     S   VR   +RA  K++
Sbjct: 98  REAVRQALAGLPDRQRAVIVLRYFADLPDPR----IAEILGCSVATVRSQASRALAKLR 152


>gi|255767760|ref|NP_391203.2| alternative sigma factor [Bacillus subtilis subsp. subtilis str.
           168]
 gi|239977656|sp|O34843|SIGO_BACSU RecName: Full=RNA polymerase sigma factor sigO
 gi|225185388|emb|CAB15313.2| alternative sigma factor [Bacillus subtilis subsp. subtilis str.
           168]
          Length = 176

 Score = 44.0 bits (103), Expect = 0.024,   Method: Composition-based stats.
 Identities = 13/96 (13%), Positives = 40/96 (41%), Gaps = 6/96 (6%)

Query: 196 NSSQWQDWLVYD--HDGQEQVLIEKEERKNRRN--MLTRSMSVLNPRERRIFEARRLQEN 251
           +  +  D L  +   D  E+ L  +++         L +++  L  +++ +     L  +
Sbjct: 78  DHPEAGDRLSSETGSDAFEEFLDRQDDLSQHVQDYQLYQAIQKLTDKQKSVLTKVYL--H 135

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             T++ ++     SR+ +  I  +  + +++ +  Q
Sbjct: 136 GATMQEIADSLGESRQNISNIHKKGLENIRKQLAAQ 171


>gi|331086351|ref|ZP_08335431.1| hypothetical protein HMPREF0987_01734 [Lachnospiraceae bacterium
           9_1_43BFAA]
 gi|330406117|gb|EGG85640.1| hypothetical protein HMPREF0987_01734 [Lachnospiraceae bacterium
           9_1_43BFAA]
          Length = 246

 Score = 44.0 bits (103), Expect = 0.024,   Method: Composition-based stats.
 Identities = 34/158 (21%), Positives = 65/158 (41%), Gaps = 8/158 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+RY+ EI+ I   E  E   L       GD  A  RL+  +L  VV++A       + +
Sbjct: 88  LARYMEEIKTIKAEEAGERQKLF-AASIEGDALARGRLIELYLEKVVEVAKEMYHKEVFL 146

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+ LM A+ +                  A MQ  I     + +   T  +K  
Sbjct: 147 GDLIQEGNVSLMLALDELKSAEEAHGKIMEEVC--AGMQMLIEEQTEVKRRDHTLLEKYT 204

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
                 L  +++ + +   +   +  ++  L+++E E+
Sbjct: 205 D-----LDDNIKKLKEETGRDVTIEEVSAFLDMTEEEI 237


>gi|213621633|ref|ZP_03374416.1| flagellar biosynthesis sigma factor [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 79

 Score = 44.0 bits (103), Expect = 0.024,   Method: Composition-based stats.
 Identities = 12/70 (17%), Positives = 31/70 (44%), Gaps = 2/70 (2%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            + Q++  + +    + R  +  ++  L  RE+ +       +  + L+ + +  EV   
Sbjct: 12  EEHQQENPLHQLLEGDLRQRVMDAIESLPEREQLVLTLYY--QEELNLKEIGAVLEVGES 69

Query: 268 RVRQIEARAF 277
           RV Q+ ++A 
Sbjct: 70  RVSQLHSQAI 79


>gi|52140312|ref|YP_086517.1| RNA polymerase factor sigma-70 [Bacillus cereus E33L]
 gi|167636533|ref|ZP_02394829.1| putative sigma factor [Bacillus anthracis str. A0442]
 gi|170689408|ref|ZP_02880600.1| putative sigma factor [Bacillus anthracis str. A0465]
 gi|228917858|ref|ZP_04081395.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
 gi|228936536|ref|ZP_04099332.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228948972|ref|ZP_04111245.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|229094354|ref|ZP_04225428.1| RNA polymerase sigma factor [Bacillus cereus Rock3-42]
 gi|254686326|ref|ZP_05150185.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. CNEVA-9066]
 gi|254724322|ref|ZP_05186106.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. A1055]
 gi|254744385|ref|ZP_05202065.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. Kruger B]
 gi|51973781|gb|AAU15331.1| RNA polymerase, sigma-70 subunit [Bacillus cereus E33L]
 gi|167528065|gb|EDR90865.1| putative sigma factor [Bacillus anthracis str. A0442]
 gi|170666635|gb|EDT17406.1| putative sigma factor [Bacillus anthracis str. A0465]
 gi|228689032|gb|EEL42857.1| RNA polymerase sigma factor [Bacillus cereus Rock3-42]
 gi|228810728|gb|EEM57076.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           monterrey BGSC 4AJ1]
 gi|228823124|gb|EEM68960.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           andalousiensis BGSC 4AW1]
 gi|228841794|gb|EEM86904.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           pulsiensis BGSC 4CC1]
          Length = 156

 Score = 44.0 bits (103), Expect = 0.025,   Method: Composition-based stats.
 Identities = 16/64 (25%), Positives = 34/64 (53%), Gaps = 2/64 (3%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    +   MSVL+ +E+ I   R       T+  ++ E E++  +VR I  +A +K++
Sbjct: 94  EDIEMKVKDFMSVLDEKEKYIIFERFFVG--KTMGEIALETEMTYYQVRWIYRQALEKMR 151

Query: 282 ESIQ 285
            S++
Sbjct: 152 NSLR 155


>gi|255654691|ref|ZP_05400100.1| hypothetical protein CdifQCD-2_03122 [Clostridium difficile
           QCD-23m63]
 gi|309778268|ref|ZP_07673197.1| conserved hypothetical protein [Erysipelotrichaceae bacterium
           3_1_53]
 gi|291535238|emb|CBL08350.1| hypothetical protein ROI_11700 [Roseburia intestinalis M50/1]
 gi|308913956|gb|EFP59767.1| conserved hypothetical protein [Erysipelotrichaceae bacterium
           3_1_53]
          Length = 146

 Score = 44.0 bits (103), Expect = 0.025,   Method: Composition-based stats.
 Identities = 22/102 (21%), Positives = 42/102 (41%), Gaps = 4/102 (3%)

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           A I     NS   +D    D+    +V  EK   ++    L R++  +  R+R I     
Sbjct: 44  AEIMDDLLNSIGTEDTYSTDYVAVFEVCGEKVSIED--EQLARALKAIEERKRNIVLQYF 101

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
              +  T   +    + SR  V +   +A  K+++ I+++ E
Sbjct: 102 FIGDTDTY--IGKMLDCSRANVTKCRIQALDKLKQLIEEEKE 141


>gi|196039429|ref|ZP_03106734.1| putative sigma factor [Bacillus cereus NVH0597-99]
 gi|196029589|gb|EDX68191.1| putative sigma factor [Bacillus cereus NVH0597-99]
          Length = 156

 Score = 44.0 bits (103), Expect = 0.025,   Method: Composition-based stats.
 Identities = 16/64 (25%), Positives = 34/64 (53%), Gaps = 2/64 (3%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    +   MSVL+ +E+ I   R       T+  ++ E E++  +VR I  +A +K++
Sbjct: 94  EDIEMKVKDFMSVLDEKEKYIIFERFFVG--KTMGEIALETEMTYYQVRWIYRQALEKMR 151

Query: 282 ESIQ 285
            S++
Sbjct: 152 NSLR 155


>gi|187779209|ref|ZP_02995682.1| hypothetical protein CLOSPO_02804 [Clostridium sporogenes ATCC
           15579]
 gi|187772834|gb|EDU36636.1| hypothetical protein CLOSPO_02804 [Clostridium sporogenes ATCC
           15579]
          Length = 182

 Score = 44.0 bits (103), Expect = 0.026,   Method: Composition-based stats.
 Identities = 33/164 (20%), Positives = 66/164 (40%), Gaps = 25/164 (15%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
            Y L ++YR +GD+ A ++++ +   L++K A  +R       ++V  G + +++    F
Sbjct: 1   MYKLLEKYR-NGDMEALNKIIENFNPLILKEASKWRIQCYEYEDLVQHGYLSVIKVANIF 59

Query: 94  DPERGFRLATYSMWWIKAAMQ---------------EYILRSWSLVKIGTTANQKRLFFN 138
             E   +   Y +  IK   +               EYIL  +    + T  ++   +  
Sbjct: 60  QGE-ESKFVPYCINSIKTNYKALLKGEIKHHREMPDEYILDKYDDEYMFTIEDEILAYEK 118

Query: 139 LRRLKGHLQAITDNN--------LKPEQVVAIAKKLNVSESEVI 174
            + +   L A+T            K + +  IAK+ N S + V 
Sbjct: 119 TKEIYEALDALTSEEKNIINDFYFKEKTIDKIAKENNKSYNNVR 162


>gi|219850598|ref|YP_002465031.1| ECF subfamily RNA polymerase sigma-24 subunit [Chloroflexus
           aggregans DSM 9485]
 gi|219544857|gb|ACL26595.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Chloroflexus
           aggregans DSM 9485]
          Length = 180

 Score = 44.0 bits (103), Expect = 0.026,   Method: Composition-based stats.
 Identities = 16/81 (19%), Positives = 31/81 (38%), Gaps = 2/81 (2%)

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
               L      +E    E  ER      L R+++ L   +R +   R  Q  P+  + ++
Sbjct: 92  PHTTLDEKMVSREPSPDELAERAVMNEELRRAINQLTDDQRHVLALRFGQRMPI--QEVA 149

Query: 260 SEFEVSRERVRQIEARAFKKV 280
                +   V+Q++ RA   +
Sbjct: 150 RLLGKTEGAVKQLQLRALANL 170


>gi|206976937|ref|ZP_03237839.1| putative sigma factor [Bacillus cereus H3081.97]
 gi|217962737|ref|YP_002341313.1| RNA polymerase factor sigma-70 [Bacillus cereus AH187]
 gi|206744903|gb|EDZ56308.1| putative sigma factor [Bacillus cereus H3081.97]
 gi|217066793|gb|ACJ81043.1| putative sigma factor [Bacillus cereus AH187]
          Length = 156

 Score = 44.0 bits (103), Expect = 0.026,   Method: Composition-based stats.
 Identities = 16/64 (25%), Positives = 34/64 (53%), Gaps = 2/64 (3%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    +   MSVL+ +E+ I   R       T+  ++ E E++  +VR I  +A +K++
Sbjct: 94  EDIEMKVKDFMSVLDEKEKYIIFERFFVG--KTMGEIALETEMTYYQVRWIYRQALEKMR 151

Query: 282 ESIQ 285
            S++
Sbjct: 152 NSLR 155


>gi|86143166|ref|ZP_01061568.1| hypothetical protein MED217_08290 [Leeuwenhoekiella blandensis
           MED217]
 gi|85830071|gb|EAQ48531.1| hypothetical protein MED217_08290 [Leeuwenhoekiella blandensis
           MED217]
          Length = 508

 Score = 44.0 bits (103), Expect = 0.026,   Method: Composition-based stats.
 Identities = 10/34 (29%), Positives = 20/34 (58%)

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
              +  +TL+ ++ + ++SRERVRQI     + +
Sbjct: 4   FNNQKELTLDEIAEQVDLSRERVRQIRKIGLESL 37


>gi|270296318|ref|ZP_06202518.1| conserved hypothetical protein [Bacteroides sp. D20]
 gi|270273722|gb|EFA19584.1| conserved hypothetical protein [Bacteroides sp. D20]
          Length = 182

 Score = 44.0 bits (103), Expect = 0.027,   Method: Composition-based stats.
 Identities = 18/88 (20%), Positives = 38/88 (43%), Gaps = 1/88 (1%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE  LA+R R+ GD  A   L   +   ++ + + Y G      +++ +G + L  +  K
Sbjct: 2   EEQELAERCRQ-GDNLARKELYERYAGRMLSVCLRYAGDQETAQDLMHDGFLKLFDSFDK 60

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRS 120
           F       L  +    +   + +Y+ ++
Sbjct: 61  FTWRGEGSLRAWMERVMVNTVLQYLRKN 88


>gi|163815060|ref|ZP_02206447.1| hypothetical protein COPEUT_01216 [Coprococcus eutactus ATCC 27759]
 gi|166033464|ref|ZP_02236293.1| hypothetical protein DORFOR_03190 [Dorea formicigenerans ATCC
           27755]
 gi|158449743|gb|EDP26738.1| hypothetical protein COPEUT_01216 [Coprococcus eutactus ATCC 27759]
 gi|166026649|gb|EDR45406.1| hypothetical protein DORFOR_03190 [Dorea formicigenerans ATCC
           27755]
          Length = 217

 Score = 44.0 bits (103), Expect = 0.027,   Method: Composition-based stats.
 Identities = 16/115 (13%), Positives = 49/115 (42%), Gaps = 7/115 (6%)

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            E      +L    SL +L   +D   +   D++  +     + ++         + L  
Sbjct: 109 RERWRYLQKLDARNSLLSLDGFTDSEGNPL-DFIADEAADIAETVVNAVMV----DRLKA 163

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           ++ +L+  E+ + +A     + ++   + +   +++  V + +AR  +K+++ I+
Sbjct: 164 ALPLLSDSEQELIQAIFF--DGLSEREVGARLGITQSVVNKRKARILRKLRKIIE 216


>gi|298243844|ref|ZP_06967651.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297556898|gb|EFH90762.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 208

 Score = 44.0 bits (103), Expect = 0.027,   Method: Composition-based stats.
 Identities = 18/88 (20%), Positives = 31/88 (35%), Gaps = 6/88 (6%)

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
             R         L    + + + W   +   H     +  E+ ERK  R  L R++  L+
Sbjct: 104 ELRKRRPLLFCELDVPLEDDENAWPYTIADTH----PLPDEELERKEMRTALLRAILALS 159

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEV 264
           PR R I   R   +  +T   +     +
Sbjct: 160 PRFRSIVLLRY--QEELTFREIGRILGM 185


>gi|226310242|ref|YP_002770136.1| hypothetical protein BBR47_06550 [Brevibacillus brevis NBRC 100599]
 gi|226093190|dbj|BAH41632.1| hypothetical protein [Brevibacillus brevis NBRC 100599]
          Length = 184

 Score = 44.0 bits (103), Expect = 0.027,   Method: Composition-based stats.
 Identities = 21/91 (23%), Positives = 37/91 (40%), Gaps = 10/91 (10%)

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
           L++S D+N  +     +     +E    E E   +    +      L+ R++ I + R  
Sbjct: 99  LVSSGDENEEETMISRIA-APSEEFRYEEVEMMLDIMEYMK-----LSTRDKLILQMRSE 152

Query: 249 QENPVTLENLSSEFEVSRERVRQIEARAFKK 279
                  E +   F +S+ERV QI  +A  K
Sbjct: 153 GYYH---EEIGQRFNISKERVCQI-IKAILK 179


>gi|89099293|ref|ZP_01172170.1| sigma factor SgiI [Bacillus sp. NRRL B-14911]
 gi|89085902|gb|EAR65026.1| sigma factor SgiI [Bacillus sp. NRRL B-14911]
          Length = 247

 Score = 44.0 bits (103), Expect = 0.027,   Method: Composition-based stats.
 Identities = 21/81 (25%), Positives = 36/81 (44%), Gaps = 1/81 (1%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMG-YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
           + GD    + L+ S+   + K      R Y     +  S G I   +AV+K+ PE+G  L
Sbjct: 22  QQGDSRLLNELIESYKPFIAKTVSSVCRRYIHESDDEYSIGLIAFDEAVRKYSPEKGSSL 81

Query: 102 ATYSMWWIKAAMQEYILRSWS 122
             ++   IK  + +YI +   
Sbjct: 82  LGFAEIIIKRRVIDYIRQQAR 102


>gi|225166785|ref|YP_002650770.1| putative RNA polymerase sigma factor [Clostridium botulinum]
 gi|253771351|ref|YP_003034261.1| RNA polymerase sigma-70 factor family [Clostridium botulinum D
          str. 1873]
 gi|225007354|dbj|BAH29453.1| putative RNA polymerase sigma factor [Clostridium botulinum]
 gi|225007371|dbj|BAH29469.1| putative RNA polymerase sigma factor [Clostridium botulinum]
 gi|225007386|dbj|BAH29483.1| putative RNA polymerase sigma factor [Clostridium botulinum]
 gi|225007449|dbj|BAH29545.1| putative RNA polymerase sigma factor [Clostridium botulinum]
 gi|253721328|gb|ACT33621.1| RNA polymerase sigma-70 factor family [Clostridium botulinum D
          str. 1873]
          Length = 180

 Score = 44.0 bits (103), Expect = 0.028,   Method: Composition-based stats.
 Identities = 13/57 (22%), Positives = 29/57 (50%), Gaps = 1/57 (1%)

Query: 37 LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
          L K+ +E GD ++   ++  +   + K A  Y   G    ++V  G + +++A+ K+
Sbjct: 4  LIKKAKE-GDRASIIFIIEKYKPFIFKSASRYNIPGYDFEDLVQHGYLSIIKAIHKY 59


>gi|319757745|gb|ADV69687.1| hypothetical protein SSUJS14_0594 [Streptococcus suis JS14]
          Length = 211

 Score = 44.0 bits (103), Expect = 0.028,   Method: Composition-based stats.
 Identities = 16/115 (13%), Positives = 49/115 (42%), Gaps = 7/115 (6%)

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            E      +L    SL +L   +D   +   D++  +     + ++         + L  
Sbjct: 103 RERWRYLQKLDARNSLLSLDGFTDSEGNPL-DFIADEAADIAETVVNAVMV----DRLKA 157

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           ++ +L+  E+ + +A     + ++   + +   +++  V + +AR  +K+++ I+
Sbjct: 158 ALPLLSDSEQELIQAIFF--DGLSEREVGARLGITQSVVNKRKARILRKLRKIIE 210


>gi|258651450|ref|YP_003200606.1| LuxR family transcriptional regulator [Nakamurella multipartita DSM
           44233]
 gi|258554675|gb|ACV77617.1| transcriptional regulator, LuxR family [Nakamurella multipartita
           DSM 44233]
          Length = 202

 Score = 44.0 bits (103), Expect = 0.028,   Method: Composition-based stats.
 Identities = 15/88 (17%), Positives = 32/88 (36%), Gaps = 2/88 (2%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           V D    E          +   ++   +  L   +R I   R +    ++ E  +    +
Sbjct: 114 VPDAASTEGGPDHYVAASSTAAIVEELLEHLPETQREILRLRVVAG--LSAEETADALGM 171

Query: 265 SRERVRQIEARAFKKVQESIQKQVELSS 292
           +   VR  + RA  K+++ +  + EL  
Sbjct: 172 TAGAVRVAQHRALAKLRQRLSSRAELDE 199


>gi|115525243|ref|YP_782154.1| ECF subfamily RNA polymerase sigma-24 factor [Rhodopseudomonas
           palustris BisA53]
 gi|115519190|gb|ABJ07174.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Rhodopseudomonas
           palustris BisA53]
          Length = 213

 Score = 44.0 bits (103), Expect = 0.028,   Method: Composition-based stats.
 Identities = 23/122 (18%), Positives = 44/122 (36%), Gaps = 3/122 (2%)

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
            +    L+   V     +      +      R+A +  L  L+      +       +  
Sbjct: 60  ELAGEALQEAWVRLERHQPREPVRQPRPYLFRIAYNIGLKLLLRERRTVTLADTRIALDL 119

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            D     +   E+R +   +L R++  L PR+R I    RL+E   +L  L+    +S+ 
Sbjct: 120 IDETPDPMAVAEDRSDF-ELLKRALQELTPRQRDILLGSRLEE--RSLAELARRHGISQR 176

Query: 268 RV 269
            V
Sbjct: 177 WV 178


>gi|332523817|ref|ZP_08400069.1| sigma-70, region 4 [Streptococcus porcinus str. Jelinkova 176]
 gi|332315081|gb|EGJ28066.1| sigma-70, region 4 [Streptococcus porcinus str. Jelinkova 176]
          Length = 211

 Score = 44.0 bits (103), Expect = 0.028,   Method: Composition-based stats.
 Identities = 16/115 (13%), Positives = 49/115 (42%), Gaps = 7/115 (6%)

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            E      +L    SL +L   +D   +   D++  +     + ++         + L  
Sbjct: 103 RERWRYLQKLDARNSLLSLDGFTDSEGNPL-DFIADEAADIAETVVNAVMV----DRLKA 157

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           ++ +L+  E+ + +A     + ++   + +   +++  V + +AR  +K+++ I+
Sbjct: 158 ALPLLSDSEQELIQAIFF--DGLSEREVGARLGITQSVVNKRKARILRKLRKIIE 210


>gi|255262813|ref|ZP_05342155.1| transcriptional regulator, AraC family [Thalassiobium sp. R2A62]
 gi|255105148|gb|EET47822.1| transcriptional regulator, AraC family [Thalassiobium sp. R2A62]
          Length = 341

 Score = 44.0 bits (103), Expect = 0.028,   Method: Composition-based stats.
 Identities = 24/106 (22%), Positives = 47/106 (44%), Gaps = 8/106 (7%)

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
           +     G  +   +I+   K+  +     V D       +  + E+   R+ + +++S  
Sbjct: 181 LMTSGGGVAATEMMISVIAKDYGEDFAIAVSDMCLNGPDVTTRTEQ---RSSIAKAISSR 237

Query: 236 NPRERRIFEARRLQ-ENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           NPR   +  A     E P+TL  L++   +SR   RQIE + F+++
Sbjct: 238 NPRVLSVLRAMYDNVETPLTLSELAASAGISR---RQIERQ-FRQL 279


>gi|118578609|ref|YP_899859.1| sigma-70, region 4 type 2 [Pelobacter propionicus DSM 2379]
 gi|118501319|gb|ABK97801.1| Sigma-70, region 4 type 2 [Pelobacter propionicus DSM 2379]
          Length = 390

 Score = 44.0 bits (103), Expect = 0.028,   Method: Composition-based stats.
 Identities = 30/144 (20%), Positives = 51/144 (35%), Gaps = 16/144 (11%)

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG--------QEQVL 215
           ++LN   S   S+ C +  +  L             + + LV D           Q   L
Sbjct: 201 RELNRYVSGNYSLGCAVTTESQLTMPACEDGSQPFSFDEILVTDAQNDVLGSMGRQHPRL 260

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER-VRQIEA 274
                      +   ++S L  R+R I   R   E+  TL+ ++ E     ER    I  
Sbjct: 261 DCDIIETELEALAHDTLSELTERQRTIL-LR--VEDGATLDEIARELG---ERGASNIHY 314

Query: 275 RAFKKVQESIQKQVELSSSPPLLQ 298
              KK  ++++++  L   P L Q
Sbjct: 315 H-LKKAYQTMKRKWSLWGPPTLAQ 337


>gi|221311271|ref|ZP_03593118.1| hypothetical protein Bsubs1_18041 [Bacillus subtilis subsp.
           subtilis str. 168]
 gi|221315598|ref|ZP_03597403.1| hypothetical protein BsubsN3_17957 [Bacillus subtilis subsp.
           subtilis str. NCIB 3610]
 gi|221320514|ref|ZP_03601808.1| hypothetical protein BsubsJ_17925 [Bacillus subtilis subsp.
           subtilis str. JH642]
 gi|221324798|ref|ZP_03606092.1| hypothetical protein BsubsS_18076 [Bacillus subtilis subsp.
           subtilis str. SMY]
          Length = 190

 Score = 44.0 bits (103), Expect = 0.029,   Method: Composition-based stats.
 Identities = 13/96 (13%), Positives = 40/96 (41%), Gaps = 6/96 (6%)

Query: 196 NSSQWQDWLVYD--HDGQEQVLIEKEERKNRRN--MLTRSMSVLNPRERRIFEARRLQEN 251
           +  +  D L  +   D  E+ L  +++         L +++  L  +++ +     L  +
Sbjct: 92  DHPEAGDRLSSETGSDAFEEFLDRQDDLSQHVQDYQLYQAIQKLTDKQKSVLTKVYL--H 149

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             T++ ++     SR+ +  I  +  + +++ +  Q
Sbjct: 150 GATMQEIADSLGESRQNISNIHKKGLENIRKQLAAQ 185


>gi|152941015|gb|ABS44971.1| P188 [Bacillus megaterium]
          Length = 188

 Score = 44.0 bits (103), Expect = 0.029,   Method: Composition-based stats.
 Identities = 12/96 (12%), Positives = 37/96 (38%), Gaps = 4/96 (4%)

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L+  I   + + S  +D +V           +          L + +  L  ++ ++ E 
Sbjct: 94  LDQPI--GNDHESTIKDHIVDPQPQIPHEEGKSLSSLVENRALIKGLKTLTDKQLQVLEL 151

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             +++  +T   ++ +   + + V     +A +K++
Sbjct: 152 IYVKD--LTNAEIAKKMNSTTQNVCNTHRKAIRKLK 185


>gi|218884055|ref|YP_002428437.1| Putative transcriptional regulatory protein [Desulfurococcus
           kamchatkensis 1221n]
 gi|218765671|gb|ACL11070.1| Putative transcriptional regulatory protein [Desulfurococcus
           kamchatkensis 1221n]
          Length = 135

 Score = 44.0 bits (103), Expect = 0.029,   Method: Composition-based stats.
 Identities = 10/49 (20%), Positives = 23/49 (46%), Gaps = 3/49 (6%)

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            +L  ++  + + R      +T E ++    +SR  +  IE  A +K++
Sbjct: 4   GLLTEKQYLVLKYR---AQGLTQEEIARILGISRSTIAVIEKSALRKIR 49


>gi|291302602|ref|YP_003513880.1| LuxR family transcriptional regulator [Stackebrandtia nassauensis
           DSM 44728]
 gi|290571822|gb|ADD44787.1| transcriptional regulator, LuxR family [Stackebrandtia nassauensis
           DSM 44728]
          Length = 168

 Score = 44.0 bits (103), Expect = 0.030,   Method: Composition-based stats.
 Identities = 16/79 (20%), Positives = 32/79 (40%), Gaps = 2/79 (2%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           V D   +     +  +    R+ + R ++ L  R+R +   R  ++ P     ++     
Sbjct: 78  VADEMAKTASGTDTAQAIAERDAMWRVLATLPRRQRAVLVLRYYEDLPD--AQVAELLGC 135

Query: 265 SRERVRQIEARAFKKVQES 283
           S   VR   +RA  K++E 
Sbjct: 136 SAATVRVHVSRALAKLREH 154


>gi|166033031|ref|ZP_02235860.1| hypothetical protein DORFOR_02752 [Dorea formicigenerans ATCC
           27755]
 gi|166027388|gb|EDR46145.1| hypothetical protein DORFOR_02752 [Dorea formicigenerans ATCC
           27755]
          Length = 139

 Score = 44.0 bits (103), Expect = 0.030,   Method: Composition-based stats.
 Identities = 12/64 (18%), Positives = 28/64 (43%), Gaps = 2/64 (3%)

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             + L + +  L+ R R         +   T   ++    +SR  V Q    A K++++S
Sbjct: 77  YDDELAKVIKQLSDRYRENVLMYYFLDMSDT--EIAKLQNISRSGVFQNRHYALKQMKKS 134

Query: 284 IQKQ 287
           ++++
Sbjct: 135 LEEE 138


>gi|319901643|ref|YP_004161371.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Bacteroides
           helcogenes P 36-108]
 gi|319416674|gb|ADV43785.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Bacteroides
           helcogenes P 36-108]
          Length = 182

 Score = 43.6 bits (102), Expect = 0.030,   Method: Composition-based stats.
 Identities = 18/88 (20%), Positives = 37/88 (42%), Gaps = 1/88 (1%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE  LA+R R  GD  A   L   +   ++ + + Y G      +++ +G + L  +  K
Sbjct: 2   EEQELAERCRL-GDNLARKELYEHYAGRMLSVCLRYAGDRETAQDLMHDGFLKLFNSFDK 60

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRS 120
           F       L  +    +   + +Y+ ++
Sbjct: 61  FTWWGKGSLRAWMERVMVNTVLQYLRKN 88


>gi|124008999|ref|ZP_01693684.1| RNA polymerase ECF-type sigma factor [Microscilla marina ATCC
           23134]
 gi|123985425|gb|EAY25333.1| RNA polymerase ECF-type sigma factor [Microscilla marina ATCC
           23134]
          Length = 204

 Score = 43.6 bits (102), Expect = 0.030,   Method: Composition-based stats.
 Identities = 18/90 (20%), Positives = 44/90 (48%), Gaps = 5/90 (5%)

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           +V  EK E K     +  +++ L P+ R +F   R +E  ++ + ++ +  +S + V   
Sbjct: 114 EVATEKMEFKELELQVNEAINELPPKCREVFILSRYEE--LSYKEIAQQMGISPKTVENQ 171

Query: 273 EARAFKKVQESIQ---KQVELSSSPPLLQK 299
            ++A K +++ +    K + L  +P  + +
Sbjct: 172 MSKALKHLRKKLAAYIKNILLFLTPYAIWE 201


>gi|312888009|ref|ZP_07747593.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Mucilaginibacter
           paludis DSM 18603]
 gi|311299490|gb|EFQ76575.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Mucilaginibacter
           paludis DSM 18603]
          Length = 198

 Score = 43.6 bits (102), Expect = 0.031,   Method: Composition-based stats.
 Identities = 17/75 (22%), Positives = 36/75 (48%), Gaps = 2/75 (2%)

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           E+    +    L R +S L  R R IF   R  +   T E ++ +  +S+  V+     +
Sbjct: 115 ERLLEADYAAFLQRELSKLPERSREIFRLCR--QEYRTYEEVAQQLGISKSAVKSHMVSS 172

Query: 277 FKKVQESIQKQVELS 291
            K ++ S+++++ +S
Sbjct: 173 MKVLKTSVEQELGVS 187


>gi|163119564|ref|YP_079928.2| RNA polymerase sporulation-specific sigma factor (sigma-K)
           (C-terminal half) [Bacillus licheniformis ATCC 14580]
 gi|319644898|ref|ZP_07999131.1| RNA polymerase sporulation-specific sigma factor [Bacillus sp.
           BT1B_CT2]
 gi|145903073|gb|AAU24290.2| RNA polymerase sporulation-specific sigma factor (sigma-K)
           (C-terminal half) [Bacillus licheniformis ATCC 14580]
 gi|317392707|gb|EFV73501.1| RNA polymerase sporulation-specific sigma factor [Bacillus sp.
           BT1B_CT2]
          Length = 82

 Score = 43.6 bits (102), Expect = 0.031,   Method: Composition-based stats.
 Identities = 11/42 (26%), Positives = 18/42 (42%), Gaps = 2/42 (4%)

Query: 240 RRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKK 279
           ++    R   +     T   ++ E  +SR  V +IE RA  K
Sbjct: 16  KKFIAGRFSLDLKKEKTQREIAKELGISRSYVSRIEKRALMK 57


>gi|229175919|ref|ZP_04303416.1| RNA polymerase sigma factor [Bacillus cereus MM3]
 gi|228607513|gb|EEK64838.1| RNA polymerase sigma factor [Bacillus cereus MM3]
          Length = 156

 Score = 43.6 bits (102), Expect = 0.031,   Method: Composition-based stats.
 Identities = 15/65 (23%), Positives = 35/65 (53%), Gaps = 2/65 (3%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++        MSVL+ +E+ I   R       T+  +++E E++  +VR +  +A +K++
Sbjct: 94  EDIEMRAKDFMSVLDEKEKYIIFERFFVG--KTMGEIANEMEMTYYQVRWVYRQALEKMR 151

Query: 282 ESIQK 286
            S+++
Sbjct: 152 NSLRE 156


>gi|169346891|ref|ZP_02865839.1| RNA polymerase sigma factor, sigma-70 family [Clostridium
           perfringens C str. JGS1495]
 gi|169296950|gb|EDS79074.1| RNA polymerase sigma factor, sigma-70 family [Clostridium
           perfringens C str. JGS1495]
          Length = 197

 Score = 43.6 bits (102), Expect = 0.032,   Method: Composition-based stats.
 Identities = 18/74 (24%), Positives = 27/74 (36%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           E   L     + G+  A  +L   H  L+ K +  Y   G    ++   G I  M  VKK
Sbjct: 4   EMVDLLLIEGKKGNKEAMEKLFEIHKGLIYKYSTKYFIKGYDREDLEQIGWIEFMNGVKK 63

Query: 93  FDPERGFRLATYSM 106
           +D   G     +  
Sbjct: 64  YDGSFGIDFVAFIT 77


>gi|192358878|ref|YP_001981671.1| RNA polymerase sigma-24 factor [Cellvibrio japonicus Ueda107]
 gi|190685043|gb|ACE82721.1| RNA polymerase sigma-24 factor [Cellvibrio japonicus Ueda107]
          Length = 181

 Score = 43.6 bits (102), Expect = 0.032,   Method: Composition-based stats.
 Identities = 20/132 (15%), Positives = 50/132 (37%), Gaps = 11/132 (8%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           M    +E +L +R  + GD SA  +L+  +  L+ + A  + G      ++     + L 
Sbjct: 1   MSSPPDEQLLIRR-AQAGDASAFEQLLGHYYDLMFRFAFRWSGQRSDAEDITQNACLKLA 59

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW--------SLVKIGTTANQKRLFFNL 139
           +++ +F  E     +++    +    +++               V      +   +   L
Sbjct: 60  RSIGQFRFE--SAFSSWLYRLVINCAKDWYKSQGHARDAQPLDAVPEALCDDASHIPVYL 117

Query: 140 RRLKGHLQAITD 151
           R++   L+ + D
Sbjct: 118 RQVLQQLETLAD 129


>gi|256389890|ref|YP_003111454.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Catenulispora
           acidiphila DSM 44928]
 gi|256356116|gb|ACU69613.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Catenulispora
           acidiphila DSM 44928]
          Length = 171

 Score = 43.6 bits (102), Expect = 0.032,   Method: Composition-based stats.
 Identities = 25/151 (16%), Positives = 56/151 (37%), Gaps = 5/151 (3%)

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
           +  +  + D +   + V    ++       V +M+   A    + A + +          
Sbjct: 26  RTAVLIVGDRHAAEDLVQGALERAYRHWDRVAAMDAPEAYVRRILANLAADHHRRRGRGA 85

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
             + +HDG         +     + + R +S L PR R +   R   +  +T   ++   
Sbjct: 86  LPLMEHDGAAPDAYPDVDE---HDAVIRILSQLPPRMRAVLVLRYYDD--LTEAQIAEAL 140

Query: 263 EVSRERVRQIEARAFKKVQESIQKQVELSSS 293
            +S   V+   ARA  K++E++    E  ++
Sbjct: 141 GISVGTVKSQAARALAKLREAMAAHEEERTA 171


>gi|226326122|ref|ZP_03801640.1| hypothetical protein COPCOM_03940 [Coprococcus comes ATCC 27758]
 gi|225205664|gb|EEG88018.1| hypothetical protein COPCOM_03940 [Coprococcus comes ATCC 27758]
          Length = 139

 Score = 43.6 bits (102), Expect = 0.032,   Method: Composition-based stats.
 Identities = 12/64 (18%), Positives = 28/64 (43%), Gaps = 2/64 (3%)

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             + L + +  L+ R R         +   T   ++    +SR  V Q    A K++++S
Sbjct: 77  YDDELAKVIKQLSDRYRENVLMYYFLDMSDT--EIAKLQNISRSGVFQNRHYALKQMKKS 134

Query: 284 IQKQ 287
           ++++
Sbjct: 135 LEEE 138


>gi|116327030|ref|YP_796750.1| RNA polymerase sigma subunit [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116119774|gb|ABJ77817.1| RNA polymerase sigma subunit [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
          Length = 182

 Score = 43.6 bits (102), Expect = 0.032,   Method: Composition-based stats.
 Identities = 14/68 (20%), Positives = 33/68 (48%), Gaps = 2/68 (2%)

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
              E  ++EK ++ + +N++   + +++P  + +   R  Q+    LE +S    +S   
Sbjct: 98  PSPEFSVLEKIDQSDVKNIIDSLLDIISPEYKEVLLLRYQQDLK--LEEISKILGISISG 155

Query: 269 VRQIEARA 276
           V ++  RA
Sbjct: 156 VSRLIERA 163


>gi|302866519|ref|YP_003835156.1| RNA polymerase sigma-70 factor [Micromonospora aurantiaca ATCC
           27029]
 gi|315502929|ref|YP_004081816.1| RNA polymerase, sigma-24 subunit, ecf subfamily [Micromonospora sp.
           L5]
 gi|302569378|gb|ADL45580.1| RNA polymerase sigma-70 factor, sigma-E family [Micromonospora
           aurantiaca ATCC 27029]
 gi|315409548|gb|ADU07665.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Micromonospora sp.
           L5]
          Length = 167

 Score = 43.6 bits (102), Expect = 0.032,   Method: Composition-based stats.
 Identities = 18/76 (23%), Positives = 33/76 (43%), Gaps = 2/76 (2%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            D  E+   +  E    R  L  ++  L  RER +   R   + P     ++ E +VS  
Sbjct: 82  DDLPERRGGDMAEEVATRRWLVTALGTLTARERAVVVLRHYFDLPE--AQVARELDVSVG 139

Query: 268 RVRQIEARAFKKVQES 283
            V+   +RA +K++ +
Sbjct: 140 TVKSTSSRALEKLRTA 155


>gi|94970159|ref|YP_592207.1| ECF subfamily RNA polymerase sigma-24 factor [Candidatus Koribacter
           versatilis Ellin345]
 gi|94552209|gb|ABF42133.1| sigma-24, ECF subfamily [Candidatus Koribacter versatilis Ellin345]
          Length = 177

 Score = 43.6 bits (102), Expect = 0.032,   Method: Composition-based stats.
 Identities = 14/76 (18%), Positives = 38/76 (50%), Gaps = 2/76 (2%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E++    +E   RR +L + +  L   ++ +   R L  +  ++  ++ E   S   ++Q
Sbjct: 102 EEIDPSFDEGTERRALLMQLLDRLPSDQQLVISRRFL--DGRSIAEIAGELGRSEGAIKQ 159

Query: 272 IEARAFKKVQESIQKQ 287
           ++ RA + +++ ++ Q
Sbjct: 160 LQFRALQSLRQQMRSQ 175


>gi|120401797|ref|YP_951626.1| ECF subfamily RNA polymerase sigma-24 factor [Mycobacterium
           vanbaalenii PYR-1]
 gi|119954615|gb|ABM11620.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Mycobacterium
           vanbaalenii PYR-1]
          Length = 219

 Score = 43.6 bits (102), Expect = 0.033,   Method: Composition-based stats.
 Identities = 38/254 (14%), Positives = 67/254 (26%), Gaps = 68/254 (26%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
              +E  L    R   D  A  RLV  H   ++++A GY        EVV E  I L++ 
Sbjct: 12  TSADEADLIAALRAR-DEVAFARLVDQHTPAMLRVARGYVASHEVAEEVVQETWIALLKG 70

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
           + +F+     R   +++  I  A    +                                
Sbjct: 71  IDRFEGRSSLRTWLFTV-MINIAKTRGLRD------------------------------ 99

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
                + +  V IA     +                        D +      W   +  
Sbjct: 100 -----RTDADVQIAAYTGGTV-----------------DPKRFRDSDDPWPGHWKADEVP 137

Query: 210 GQ-EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS--- 265
                             +  R ++ L  R+R +   R + +       +S   ++S   
Sbjct: 138 SPFPDTPEGSVLGGELLAVTRRELAKLPERQRLVVTMRDVLDMDS--AEVSRLLDLSPAN 195

Query: 266 --------RERVRQ 271
                   R  VRQ
Sbjct: 196 QRVLLHRGRAAVRQ 209


>gi|296331196|ref|ZP_06873669.1| alternative sigma factor [Bacillus subtilis subsp. spizizenii ATCC
           6633]
 gi|305675926|ref|YP_003867598.1| alternative sigma factor sigmaO [Bacillus subtilis subsp.
           spizizenii str. W23]
 gi|296151647|gb|EFG92523.1| alternative sigma factor [Bacillus subtilis subsp. spizizenii ATCC
           6633]
 gi|305414170|gb|ADM39289.1| alternative sigma factor sigmaO [Bacillus subtilis subsp.
           spizizenii str. W23]
          Length = 192

 Score = 43.6 bits (102), Expect = 0.033,   Method: Composition-based stats.
 Identities = 11/82 (13%), Positives = 34/82 (41%), Gaps = 4/82 (4%)

Query: 208 HDGQEQVLIEKEERKNRRN--MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            D  E  L  +++         L +++  L  +++ +     L  +  T++ ++     S
Sbjct: 106 SDAFEAFLDMQDDLSQHVQDYQLYQAIQKLTDKQKSVLTKVYL--HGATMQEIADSLGES 163

Query: 266 RERVRQIEARAFKKVQESIQKQ 287
           R+ +  I  +  + +++ +  Q
Sbjct: 164 RQNISNIHKKGLENIRKQLAAQ 185


>gi|225573334|ref|ZP_03782089.1| hypothetical protein RUMHYD_01526 [Blautia hydrogenotrophica DSM
           10507]
 gi|225039247|gb|EEG49493.1| hypothetical protein RUMHYD_01526 [Blautia hydrogenotrophica DSM
           10507]
          Length = 143

 Score = 43.6 bits (102), Expect = 0.033,   Method: Composition-based stats.
 Identities = 20/108 (18%), Positives = 40/108 (37%), Gaps = 6/108 (5%)

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             M CR   + SL+AL + +D +     D    D         +         ++  + +
Sbjct: 31  REMKCRRDREVSLDAL-SPADWDKLSTVDRYSCDSFIFSSHGYDLHIDN---ELVAEAFA 86

Query: 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            L   E+ I   R + +  +T E +     +SR  V++      K ++
Sbjct: 87  SLPKDEQSILILRFVLD--LTDEEIGRLMGMSRSAVQRHRTSTLKDLR 132


>gi|169335254|ref|ZP_02862447.1| hypothetical protein ANASTE_01662 [Anaerofustis stercorihominis DSM
           17244]
 gi|169257992|gb|EDS71958.1| hypothetical protein ANASTE_01662 [Anaerofustis stercorihominis DSM
           17244]
          Length = 159

 Score = 43.6 bits (102), Expect = 0.033,   Method: Composition-based stats.
 Identities = 14/64 (21%), Positives = 30/64 (46%), Gaps = 2/64 (3%)

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           E +E+++    + +++  L   ER++   R  +   +T   +S     SRE   ++  RA
Sbjct: 74  ELKEKQSLVFEIEKALECLTDLERKVIVMRYFKMQRMT--EISDNLGYSREYGSRVRKRA 131

Query: 277 FKKV 280
             K+
Sbjct: 132 VNKI 135


>gi|284036346|ref|YP_003386276.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Spirosoma linguale
           DSM 74]
 gi|283815639|gb|ADB37477.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Spirosoma linguale
           DSM 74]
          Length = 201

 Score = 43.6 bits (102), Expect = 0.034,   Method: Composition-based stats.
 Identities = 16/81 (19%), Positives = 35/81 (43%), Gaps = 2/81 (2%)

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
            D  + +    E +LI +E      + +   ++ L  RER     R  +   +++  ++ 
Sbjct: 103 WDCSLAEDSNTETLLIRQESLAILSHTIQAQLATLPAREREALYLRYYEN--LSIPEIAE 160

Query: 261 EFEVSRERVRQIEARAFKKVQ 281
             EV+R+ V     +A  K++
Sbjct: 161 VMEVNRQSVSNFLQKALGKLR 181


>gi|317497321|ref|ZP_07955644.1| hypothetical protein HMPREF0996_00624 [Lachnospiraceae bacterium
           5_1_63FAA]
 gi|316895390|gb|EFV17549.1| hypothetical protein HMPREF0996_00624 [Lachnospiraceae bacterium
           5_1_63FAA]
          Length = 149

 Score = 43.6 bits (102), Expect = 0.035,   Method: Composition-based stats.
 Identities = 22/102 (21%), Positives = 42/102 (41%), Gaps = 4/102 (3%)

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           A I     NS   +D    D+    +V  EK   ++    L R++  +  R+R I     
Sbjct: 47  AEIMDDLLNSIGTEDTYSTDYVAVFEVCGEKVSIED--EQLARALKAIEERKRNIVLQYF 104

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
              +  T   +    + SR  V +   +A  K+++ I+++ E
Sbjct: 105 FIGDTDTY--IGKMLDCSRANVTKCRIQALDKLKQLIEEEKE 144


>gi|317498318|ref|ZP_07956616.1| sigma-70 protein [Lachnospiraceae bacterium 5_1_63FAA]
 gi|316894394|gb|EFV16578.1| sigma-70 protein [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 191

 Score = 43.6 bits (102), Expect = 0.035,   Method: Composition-based stats.
 Identities = 11/91 (12%), Positives = 42/91 (46%), Gaps = 6/91 (6%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
            +  +  D++  +     + ++         + L  ++ +L+  E+ + +A     + ++
Sbjct: 106 DSEGKPLDFIADEAADIAETVVNAVMV----DRLKAALPLLSDSEQELIQAIFF--DGLS 159

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              + + F +++  V + +AR  +K+++ I+
Sbjct: 160 EREVGARFGITQSVVNKRKARILRKLRKIIE 190


>gi|324329197|gb|ADY24457.1| RNA polymerase factor sigma-70 [Bacillus thuringiensis serovar
           finitimus YBT-020]
          Length = 156

 Score = 43.6 bits (102), Expect = 0.035,   Method: Composition-based stats.
 Identities = 16/64 (25%), Positives = 34/64 (53%), Gaps = 2/64 (3%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    +   MSVL+ +E+ I   R       T+  ++ E E++  +VR +  RA +K++
Sbjct: 94  EDIEMKVKDFMSVLDEKEKYIIFERFFVG--KTMGEIALETEMTYYQVRWLYRRALEKMR 151

Query: 282 ESIQ 285
            S++
Sbjct: 152 NSLR 155


>gi|33863005|ref|NP_894565.1| hypothetical protein PMT0733 [Prochlorococcus marinus str. MIT
           9313]
 gi|33634922|emb|CAE20908.1| conserved hypothetical protein [Prochlorococcus marinus str. MIT
           9313]
          Length = 80

 Score = 43.6 bits (102), Expect = 0.035,   Method: Composition-based stats.
 Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 1/53 (1%)

Query: 50  AHRLVTSHLRLVVKIAMGYR-GYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            ++ +  HL+LV  IA+ Y    G    ++   G +GL++A   F P   +  
Sbjct: 9   RNKQIEEHLQLVRPIALHYAFRTGQDKEDLTQVGMLGLIRAAHSFKPVNQYHF 61


>gi|329922405|ref|ZP_08278082.1| sigma-70, region 4 [Paenibacillus sp. HGF5]
 gi|328942268|gb|EGG38539.1| sigma-70, region 4 [Paenibacillus sp. HGF5]
          Length = 406

 Score = 43.6 bits (102), Expect = 0.036,   Method: Composition-based stats.
 Identities = 13/76 (17%), Positives = 35/76 (46%), Gaps = 12/76 (15%)

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE-----RVR 270
           ++     + R  +  ++  L+ R+++I   R   +   TL+ +S    + RE     R+ 
Sbjct: 108 LDFAGYVDIRIDIGAALKKLSERDQQIISLRFFVD--CTLQEISKIVGM-RESAVKNRL- 163

Query: 271 QIEARAFKKVQESIQK 286
               R+  K+++ +++
Sbjct: 164 ---YRSLAKLKKELRE 176


>gi|160892072|ref|ZP_02073075.1| hypothetical protein BACUNI_04533 [Bacteroides uniformis ATCC 8492]
 gi|317480489|ref|ZP_07939582.1| sigma-70 family RNA polymerase sigma factor [Bacteroides sp.
           4_1_36]
 gi|156858550|gb|EDO51981.1| hypothetical protein BACUNI_04533 [Bacteroides uniformis ATCC 8492]
 gi|316903334|gb|EFV25195.1| sigma-70 family RNA polymerase sigma factor [Bacteroides sp.
           4_1_36]
          Length = 182

 Score = 43.6 bits (102), Expect = 0.036,   Method: Composition-based stats.
 Identities = 18/88 (20%), Positives = 38/88 (43%), Gaps = 1/88 (1%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE  LA+R R+ GD  A   L   +   ++ + + Y G      +++ +G + L  +  K
Sbjct: 2   EEQELAERCRQ-GDNLARKELYERYAGRMLSVCLRYAGDRETAQDLMHDGFLKLFDSFDK 60

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRS 120
           F       L  +    +   + +Y+ ++
Sbjct: 61  FTWRGEGSLRAWMERVMVNTVLQYLRKN 88


>gi|291529655|emb|CBK95241.1| RNA polymerase sigma factor, sigma-70 family [Eubacterium rectale
           M104/1]
          Length = 231

 Score = 43.6 bits (102), Expect = 0.037,   Method: Composition-based stats.
 Identities = 20/108 (18%), Positives = 47/108 (43%), Gaps = 8/108 (7%)

Query: 183 DESLNALINSSDKNSS--QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
             SL+ +++    N +   +    +      E++ ++KE     R ++ +    LN  E+
Sbjct: 130 PASLDVMMDEKSNNDTNKTYSPKALATVKTPEEIAVDKETLAEAREVIKQ----LNDNEK 185

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           ++     +  N VT+   + E  +S+  V  I+  A  KV+ ++   +
Sbjct: 186 KVINLVVI--NGVTVRQAADEIGMSKSSVSYIKQTALNKVRAALDAAM 231


>gi|323703947|ref|ZP_08115576.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Desulfotomaculum
           nigrificans DSM 574]
 gi|323531082|gb|EGB20992.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Desulfotomaculum
           nigrificans DSM 574]
          Length = 198

 Score = 43.6 bits (102), Expect = 0.037,   Method: Composition-based stats.
 Identities = 24/145 (16%), Positives = 49/145 (33%), Gaps = 4/145 (2%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           E  L     + GD  A  +LV  +   V  IA    G     +++  E  I + QA+  F
Sbjct: 4   EDRLLVERSKKGDREAFEQLVQMYENKVYTIAYRLMGNHTDAADLAQEAFIKIYQALPNF 63

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWS--LVKIGTTANQKRLFFNLRRLKGHLQAITD 151
             +     +T+         ++ + +      V +  + +     + LR      +   D
Sbjct: 64  RGD--SSFSTWIYHITVNVCRDELRKRQRRPTVSLDDSPDNNTCTYELRSNMPTPEEELD 121

Query: 152 NNLKPEQVVAIAKKLNVSESEVISM 176
            +     V     +L+     ++ M
Sbjct: 122 RSETQAMVQQCLNELSDDYRIILVM 146



 Score = 40.6 bits (94), Expect = 0.33,   Method: Composition-based stats.
 Identities = 23/102 (22%), Positives = 44/102 (43%), Gaps = 10/102 (9%)

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
           + S   +   Y+         E+ +R   + M+ + ++ L+   R I   R +QE  +  
Sbjct: 97  DDSPDNNTCTYELRSNMPTPEEELDRSETQAMVQQCLNELSDDYRIILVMREIQE--MAY 154

Query: 256 ENLSSEFEVS----RERVRQIEARAFKKVQESIQKQVELSSS 293
           E ++     S    + R+     RA + ++E I KQ+EL S 
Sbjct: 155 EEIAENLGCSLGTVKSRLS----RARQALKEKISKQMELLSP 192


>gi|261406353|ref|YP_003242594.1| ECF subfamily RNA polymerase sigma-24 factor [Paenibacillus sp.
           Y412MC10]
 gi|261282816|gb|ACX64787.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Paenibacillus sp.
           Y412MC10]
          Length = 406

 Score = 43.6 bits (102), Expect = 0.037,   Method: Composition-based stats.
 Identities = 13/76 (17%), Positives = 35/76 (46%), Gaps = 12/76 (15%)

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE-----RVR 270
           ++     + R  +  ++  L+ R+++I   R   +   TL+ +S    + RE     R+ 
Sbjct: 108 LDFAGYVDIRIDIGAALKKLSERDQQIISLRFFVD--CTLQEISQIVGM-RESAVKNRL- 163

Query: 271 QIEARAFKKVQESIQK 286
               R+  K+++ +++
Sbjct: 164 ---YRSLAKLKKELRE 176


>gi|312196994|ref|YP_004017055.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Frankia sp. EuI1c]
 gi|311228330|gb|ADP81185.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Frankia sp. EuI1c]
          Length = 217

 Score = 43.6 bits (102), Expect = 0.038,   Method: Composition-based stats.
 Identities = 15/68 (22%), Positives = 32/68 (47%), Gaps = 2/68 (2%)

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
           I+  +R ++   L R++  L PR+R +   R  ++ P     +++    S   VR   +R
Sbjct: 101 IDHADRLSQHEDLVRALRSLPPRQRAVVVLRYFEDLPE--AEVAAALGCSVGSVRSQASR 158

Query: 276 AFKKVQES 283
              +++ S
Sbjct: 159 GLARLRGS 166


>gi|317127675|ref|YP_004093957.1| RNA polymerase, sigma 32 subunit, RpoH [Bacillus cellulosilyticus
           DSM 2522]
 gi|315472623|gb|ADU29226.1| RNA polymerase, sigma 32 subunit, RpoH [Bacillus cellulosilyticus
           DSM 2522]
          Length = 173

 Score = 43.6 bits (102), Expect = 0.038,   Method: Composition-based stats.
 Identities = 15/75 (20%), Positives = 34/75 (45%), Gaps = 3/75 (4%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            + +E +  E E+     + L + +  LN  E+ I   R  +E   TL+ +     +   
Sbjct: 92  REYEEFIPSESEDISLSIS-LKQLLDYLNEEEKSIIILRFYKE--YTLKEIGEVLNIPLG 148

Query: 268 RVRQIEARAFKKVQE 282
            V+ +  R+ +K+++
Sbjct: 149 TVKTLLYRSLEKLRK 163


>gi|91070518|gb|ABE11425.1| type II alternative RNA polymerase sigma factor, sigma-70 family
           [uncultured Prochlorococcus marinus clone HOT0M-3E5]
          Length = 109

 Score = 43.6 bits (102), Expect = 0.038,   Method: Composition-based stats.
 Identities = 12/55 (21%), Positives = 22/55 (40%), Gaps = 5/55 (9%)

Query: 12  GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSH-----LRLV 61
               +  Y+  I ++P+L   EE  LA   +   +     + +  +     LRLV
Sbjct: 49  ASDSIGHYLSSIGRVPLLTPAEEIELAHHVQNIKNCCKFRKKIEHNVIFIKLRLV 103


>gi|150392361|ref|YP_001322410.1| ECF subfamily RNA polymerase sigma-24 factor [Alkaliphilus
           metalliredigens QYMF]
 gi|149952223|gb|ABR50751.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Alkaliphilus
           metalliredigens QYMF]
          Length = 188

 Score = 43.6 bits (102), Expect = 0.038,   Method: Composition-based stats.
 Identities = 18/93 (19%), Positives = 41/93 (44%), Gaps = 4/93 (4%)

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           S +    + D    E ++IE  +++ ++  L  S+  L+P  + I   R    + +T E+
Sbjct: 94  SFYPMETLADDHMTEDIVIENMDKEEQKEKLRNSLEQLDPDAKEIITLRYY--HHLTYED 151

Query: 258 LSSEFEVSRERV-RQIEARAFKKVQESIQKQVE 289
           +     + +  V  ++  RA  K+ +    + E
Sbjct: 152 VGKALSLKQGTVKSRL-RRAKDKLIKIFNSEGE 183


>gi|237733518|ref|ZP_04563999.1| conjugative transposon protein [Mollicutes bacterium D7]
 gi|229383351|gb|EEO33442.1| conjugative transposon protein [Coprobacillus sp. D7]
          Length = 171

 Score = 43.6 bits (102), Expect = 0.039,   Method: Composition-based stats.
 Identities = 11/61 (18%), Positives = 30/61 (49%), Gaps = 2/61 (3%)

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             L  ++  L+ +ER +   R  Q   ++ + ++  + VSR  + +  +   KK++  ++
Sbjct: 111 EKLAVALYKLSSKERDVILLRYFQ--SMSDQEIAELYHVSRSAIYRRRSNGLKKLKTVLK 168

Query: 286 K 286
           +
Sbjct: 169 E 169


>gi|154489777|ref|ZP_02030038.1| hypothetical protein PARMER_00005 [Parabacteroides merdae ATCC
           43184]
 gi|154089502|gb|EDN88546.1| hypothetical protein PARMER_00005 [Parabacteroides merdae ATCC
           43184]
          Length = 178

 Score = 43.6 bits (102), Expect = 0.039,   Method: Composition-based stats.
 Identities = 14/75 (18%), Positives = 41/75 (54%), Gaps = 2/75 (2%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
               E ++ ++EER+N    +   +++L  ++R +   R +    ++++ +S    ++ +
Sbjct: 93  EVDAEALMEDEEERRNYEKEVESLLNLLTNKQREVIYLRFI--KALSIQEISEILNITPK 150

Query: 268 RVRQIEARAFKKVQE 282
            VR++  RA +++Q+
Sbjct: 151 SVRKMIYRAIERMQQ 165


>gi|49481227|ref|YP_039241.1| RNA polymerase factor sigma-70 [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|49332783|gb|AAT63429.1| RNA polymerase, sigma-70 subunit [Bacillus thuringiensis serovar
           konkukian str. 97-27]
          Length = 146

 Score = 43.6 bits (102), Expect = 0.039,   Method: Composition-based stats.
 Identities = 16/64 (25%), Positives = 34/64 (53%), Gaps = 2/64 (3%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    +   MSVL+ +E+ I   R       T+  ++ E E++  +VR I  +A +K++
Sbjct: 84  EDIEMKVKDFMSVLDEKEKYIIFERFFVG--KTMGEIALETEMTYYQVRWIYRQALEKMR 141

Query: 282 ESIQ 285
            S++
Sbjct: 142 NSLR 145


>gi|284029132|ref|YP_003379063.1| ECF subfamily RNA polymerase sigma-24 subunit [Kribbella flavida
           DSM 17836]
 gi|283808425|gb|ADB30264.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Kribbella flavida
           DSM 17836]
          Length = 300

 Score = 43.6 bits (102), Expect = 0.039,   Method: Composition-based stats.
 Identities = 25/107 (23%), Positives = 42/107 (39%), Gaps = 2/107 (1%)

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             E  +   R+A  ++LN L   S +      +WL         V  + E   +    + 
Sbjct: 57  VREPRAYLVRIATRQALNRLRTVSRRREDYVGEWLPEPLLTSPDVAEDVELADSVSIAMM 116

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
             +  L P ER +F  R + + P   + +++    S   VRQI  RA
Sbjct: 117 TVLETLGPIERAVFVLREVFDVPY--DEIAAAVGKSPAAVRQIAHRA 161


>gi|2832804|emb|CAA11728.1| putative sigma factor, YvrI [Bacillus subtilis]
          Length = 190

 Score = 43.6 bits (102), Expect = 0.039,   Method: Composition-based stats.
 Identities = 13/96 (13%), Positives = 40/96 (41%), Gaps = 6/96 (6%)

Query: 196 NSSQWQDWLVYD--HDGQEQVLIEKEERKNRRN--MLTRSMSVLNPRERRIFEARRLQEN 251
           +  +  D L  +   D  E+ L  +++         L +++  L  +++ +     L  +
Sbjct: 92  DHPEAGDRLSSETGSDAFEEFLDRQDDLSQHVQDYQLYQAIQKLTDKQKSVLTKVYL--H 149

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             T++ ++     SR+ +  I  +  + +++ +  Q
Sbjct: 150 GATMQEIADSLGESRQNISNIHKKGLENIRKQLAAQ 185


>gi|7021520|gb|AAF35386.1| SpoIIGB [Clostridium sporogenes]
          Length = 106

 Score = 43.6 bits (102), Expect = 0.039,   Method: Composition-based stats.
 Identities = 19/86 (22%), Positives = 33/86 (38%), Gaps = 7/86 (8%)

Query: 177 NCRLAGDESLNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
           N ++  + S    +N   D N     D L  D+D     +    E +  + +L  +M  L
Sbjct: 25  NSKIKAEISFYEPLNIDWDGNELLLSDILGTDND----EVYNLIEDEVDKQLLLLAMKKL 80

Query: 236 NPRERRIFEARRLQENP--VTLENLS 259
           N RE+ I   R         T + ++
Sbjct: 81  NEREKEIVRLRFGLNGKKEKTQKEVA 106


>gi|83590677|ref|YP_430686.1| sigma-24 (FecI-like) [Moorella thermoacetica ATCC 39073]
 gi|83573591|gb|ABC20143.1| RNA polymerase, sigma-24 subunit, RpoE [Moorella thermoacetica ATCC
           39073]
          Length = 204

 Score = 43.6 bits (102), Expect = 0.039,   Method: Composition-based stats.
 Identities = 21/93 (22%), Positives = 35/93 (37%), Gaps = 6/93 (6%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
             +E +LA+     GD  A   LV  + R++  IA  + G      +   E    L++A 
Sbjct: 2   PSDEELLAR--SRDGDAEAFALLVERYQRMLFTIAYRFLGNTEDAGDAAQEA---LVRAF 56

Query: 91  KKFDPERG-FRLATYSMWWIKAAMQEYILRSWS 122
           K     RG     T+    I    ++ + R   
Sbjct: 57  KNLAAFRGQCSFKTWLQHIIANVCRDELRRLKR 89


>gi|91779572|ref|YP_554780.1| extracytoplasmic-function sigma-70 factor PvdS [Burkholderia
           xenovorans LB400]
 gi|91692232|gb|ABE35430.1| Sigma-24 (FecI) [Burkholderia xenovorans LB400]
          Length = 223

 Score = 43.3 bits (101), Expect = 0.040,   Method: Composition-based stats.
 Identities = 19/97 (19%), Positives = 40/97 (41%), Gaps = 2/97 (2%)

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             + ++   R+  + S++A    S +N+    +         E         ++    + 
Sbjct: 91  VRQPVAYVTRMVRNASIDAFRRQSLENTYHADEDDGLHVPSPEPSPEAALLVRDTLRHVY 150

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
            ++  L PR R  FE  RL+E   TL++ +   +VS+
Sbjct: 151 NALDQLPPRSRAAFEMVRLREE--TLQSTARALDVSQ 185


>gi|229014749|ref|ZP_04171852.1| RNA polymerase sigma factor [Bacillus mycoides DSM 2048]
 gi|228746515|gb|EEL96415.1| RNA polymerase sigma factor [Bacillus mycoides DSM 2048]
          Length = 53

 Score = 43.3 bits (101), Expect = 0.040,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 31/54 (57%), Gaps = 2/54 (3%)

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           MSVL+ RE+ I   R      +    ++SE  ++  +VR +  +A +K+++S++
Sbjct: 1   MSVLDEREKHIISERFFTGKNMG--EIASEMGMTYYQVRWVYRQALEKMRDSVR 52


>gi|168211077|ref|ZP_02636702.1| RNA polymerase sigma factor, sigma-70 family [Clostridium
           perfringens B str. ATCC 3626]
 gi|170710864|gb|EDT23046.1| RNA polymerase sigma factor, sigma-70 family [Clostridium
           perfringens B str. ATCC 3626]
          Length = 197

 Score = 43.3 bits (101), Expect = 0.041,   Method: Composition-based stats.
 Identities = 18/74 (24%), Positives = 27/74 (36%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           E   L     + G+  A  +L   H  L+ K +  Y   G    ++   G I  M  VKK
Sbjct: 4   EMVDLLLIEGKKGNKEAMEKLFEIHKGLIYKYSTKYFIKGYDREDLEQIGWIEFMNGVKK 63

Query: 93  FDPERGFRLATYSM 106
           +D   G     +  
Sbjct: 64  YDGSFGIDFVAFIT 77


>gi|223938528|ref|ZP_03630420.1| RNA polymerase, sigma-24 subunit, ECF subfamily [bacterium
           Ellin514]
 gi|223892790|gb|EEF59259.1| RNA polymerase, sigma-24 subunit, ECF subfamily [bacterium
           Ellin514]
          Length = 535

 Score = 43.3 bits (101), Expect = 0.043,   Method: Composition-based stats.
 Identities = 14/71 (19%), Positives = 26/71 (36%), Gaps = 10/71 (14%)

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS----RERVRQIE 273
           + +      +L   M  L   +R     R  ++ P     + +   VS    R RV    
Sbjct: 105 EVDWSATSRVLDELMHQLKEGDREAILLRYFEDRP--FAEVGTSLGVSENAARMRV---- 158

Query: 274 ARAFKKVQESI 284
            RA +K++  +
Sbjct: 159 ERALEKLRNLL 169


>gi|260062065|ref|YP_003195145.1| putative RNA polymerase ECF-type sigma factor [Robiginitalea
           biformata HTCC2501]
 gi|88783627|gb|EAR14798.1| putative RNA polymerase ECF-type sigma factor [Robiginitalea
           biformata HTCC2501]
          Length = 172

 Score = 43.3 bits (101), Expect = 0.043,   Method: Composition-based stats.
 Identities = 16/92 (17%), Positives = 46/92 (50%), Gaps = 2/92 (2%)

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
             + N +++ D   +  +  E+V++ KE ++  R  L +++  L   +++  + R  Q+ 
Sbjct: 77  DDETNGARFLDQPGHFTESAEEVIVLKESQRGLRQSLHKALQTLTEHQKQAIQLRFTQD- 135

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             + E ++ + ++S    R +  R  K ++++
Sbjct: 136 -KSYEEIAKDLQLSVPSARTLVYRTLKAMRKA 166


>gi|213621938|ref|ZP_03374721.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. E98-2068]
          Length = 42

 Score = 43.3 bits (101), Expect = 0.043,   Method: Composition-based stats.
 Identities = 11/31 (35%), Positives = 21/31 (67%)

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++  E  ++RERVRQI+    ++++E +Q Q
Sbjct: 2   DVGREIGLTRERVRQIQVEGLRRLREILQTQ 32


>gi|148380330|ref|YP_001254871.1| RNA polymerase sigma factor [Clostridium botulinum A str. ATCC
           3502]
 gi|148289814|emb|CAL83922.1| putative RNA polymerase sigma factor [Clostridium botulinum A str.
           ATCC 3502]
          Length = 317

 Score = 43.3 bits (101), Expect = 0.043,   Method: Composition-based stats.
 Identities = 17/110 (15%), Positives = 45/110 (40%), Gaps = 13/110 (11%)

Query: 182 GDESLNALI--NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
             +SL+  I     D  +    D++    + +++ +     ++     +   +  LN R+
Sbjct: 80  DVDSLDKPILNQKQDNENLSLIDFISDKTNYEDKSIFNITCKE-----VAAIIENLNERD 134

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           ++I +      N  T + +  E  + +  + +I     KK+  +I+ + E
Sbjct: 135 KKIIKEFYF--NNKTQKQIGEEIGLKQSYISRI----LKKIPNTIKNKYE 178


>gi|284030361|ref|YP_003380292.1| ECF subfamily RNA polymerase sigma-24 subunit [Kribbella flavida
           DSM 17836]
 gi|283809654|gb|ADB31493.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Kribbella flavida
           DSM 17836]
          Length = 175

 Score = 43.3 bits (101), Expect = 0.044,   Method: Composition-based stats.
 Identities = 15/79 (18%), Positives = 34/79 (43%), Gaps = 2/79 (2%)

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
             E    +   R    + +  +M  L  R+R +   R   +  ++   ++    +SR  V
Sbjct: 99  PDEPSAEQAVLRTVETDRVIEAMRTLPERQRTVMVLRYYGD--LSEAEIADTMGISRGSV 156

Query: 270 RQIEARAFKKVQESIQKQV 288
           +   ARA K +++ +++ V
Sbjct: 157 KSHAARASKSLRQVLERNV 175


>gi|296132470|ref|YP_003639717.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermincola sp.
           JR]
 gi|296031048|gb|ADG81816.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermincola potens
           JR]
          Length = 199

 Score = 43.3 bits (101), Expect = 0.044,   Method: Composition-based stats.
 Identities = 27/148 (18%), Positives = 56/148 (37%), Gaps = 8/148 (5%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E ++A+   + GD+ A  +LV  +   V  IA  + G     S++  E  I + +++  
Sbjct: 5   DEVLIAQ--SKEGDVEAFTQLVAKYENKVYTIAYRFFGNHADASDIAQEAFIRVYKSLHS 62

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWS--LVKIGTTANQKR--LFFNLRRLKGHLQA 148
           F  +      T+    +    ++ + +      V IG   + K+         +    + 
Sbjct: 63  FRGD--SAFLTWMYRVVTNVCKDELRKRAREKTVSIGELMDNKKGSAMRKEGSISKLPED 120

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISM 176
                   ++V  I   L+V    VI M
Sbjct: 121 AVIRKEWQQEVQEILNSLSVEHRTVIIM 148


>gi|256392461|ref|YP_003114025.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Catenulispora
           acidiphila DSM 44928]
 gi|256358687|gb|ACU72184.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Catenulispora
           acidiphila DSM 44928]
          Length = 259

 Score = 43.3 bits (101), Expect = 0.044,   Method: Composition-based stats.
 Identities = 35/230 (15%), Positives = 69/230 (30%), Gaps = 54/230 (23%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            LA+R R  GD  A   ++ +    ++++A  +   G    EVV E  +G++Q +++F+ 
Sbjct: 12  ELAERLR-AGDEDAFRMVLEAWSPSMLRLARSFVSTGDSAEEVVQEAWLGVIQGIERFE- 69

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
                                 L++W + +I     + R     R L        D    
Sbjct: 70  ------------------GRSALKTW-VFRILVNIAKGRGVKESRTLPFSSLLPEDEGPS 110

Query: 156 PEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL 215
                       V  S   S +   AG                    W          + 
Sbjct: 111 ------------VDPSRFRSADDPYAGR-------------------WSPGQKPQTWALP 139

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
             +      R ++  ++  L  R R +   R ++      + +     +S
Sbjct: 140 ESEALDGEVRRVVADALDELPERHRTVVILRDVEGYAS--DEVCRLLNIS 187


>gi|322806592|emb|CBZ04161.1| RNA polymerase sporulation specific sigma factor SigE [Clostridium
           botulinum H04402 065]
          Length = 331

 Score = 43.3 bits (101), Expect = 0.045,   Method: Composition-based stats.
 Identities = 20/115 (17%), Positives = 48/115 (41%), Gaps = 13/115 (11%)

Query: 177 NCRLAGDESLNALINSS--DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV 234
             +    +SL+  I S   DK +    D +    + +++ +     ++     +T  +  
Sbjct: 89  EEKHVDVDSLDKPILSQKLDKENLSLIDLVADKTNYEDRSIFNVTYKE-----ITAIIEN 143

Query: 235 LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           LN R+++I +      N  T + +  E  + +  + +I     KK+  +I+ + E
Sbjct: 144 LNERDKKIIKEFYF--NNKTQKQIGEEIGLKQSYISRI----LKKIPNTIKNKYE 192


>gi|253582716|ref|ZP_04859937.1| RNA polymerase sigma-H factor [Fusobacterium varium ATCC 27725]
 gi|251835586|gb|EES64126.1| RNA polymerase sigma-H factor [Fusobacterium varium ATCC 27725]
          Length = 204

 Score = 43.3 bits (101), Expect = 0.045,   Method: Composition-based stats.
 Identities = 15/73 (20%), Positives = 34/73 (46%), Gaps = 1/73 (1%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  +   ++  +  L+      Y   G    +++ EG IGL++A+K ++  +     T+
Sbjct: 17  GDQESIDIILKEYKNLIYLNIRNYFIIGAEQDDLLQEGTIGLLKALKAYEKGK-SSFKTF 75

Query: 105 SMWWIKAAMQEYI 117
           +M  I+  +   +
Sbjct: 76  AMICIRRQILTAV 88


>gi|225378781|ref|ZP_03756002.1| hypothetical protein ROSEINA2194_04451 [Roseburia inulinivorans DSM
           16841]
 gi|225209373|gb|EEG91727.1| hypothetical protein ROSEINA2194_04451 [Roseburia inulinivorans DSM
           16841]
          Length = 167

 Score = 43.3 bits (101), Expect = 0.046,   Method: Composition-based stats.
 Identities = 13/78 (16%), Positives = 41/78 (52%), Gaps = 2/78 (2%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            +   Q ++E   ++ +  +L ++M+ L  R+R I   +      ++ + +++  +++ E
Sbjct: 85  QNTASQEVLEGILKEEKNRLLYQAMNELEERKREILLMQYFGG--LSQKEIAAILKMTPE 142

Query: 268 RVRQIEARAFKKVQESIQ 285
            VR +  RA ++++  ++
Sbjct: 143 NVRVLSYRAKRELRTYME 160


>gi|170761133|ref|YP_001787022.1| putative RNA polymerase sigma factor [Clostridium botulinum A3 str.
           Loch Maree]
 gi|169408122|gb|ACA56533.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           A3 str. Loch Maree]
          Length = 179

 Score = 43.3 bits (101), Expect = 0.046,   Method: Composition-based stats.
 Identities = 24/100 (24%), Positives = 48/100 (48%), Gaps = 5/100 (5%)

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE--ERKNRRNMLTRSMSVLNPRERRIFEA 245
           AL+    K+  +  D  + D   +    IE E    +N +  L +++  L P E+ + + 
Sbjct: 83  ALLKGEIKHHREIPDENISDKGNEYFFTIEDEIIAYENIKE-LYKALDKLTPEEKEVIDN 141

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             ++ N  +L+ ++S    S   VR I+ +A KK+Q  ++
Sbjct: 142 FYIKNN--SLQEIASYTNKSYNSVRYIKNKAIKKLQNMLE 179


>gi|258510244|ref|YP_003183678.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
 gi|257476970|gb|ACV57289.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Alicyclobacillus
           acidocaldarius subsp. acidocaldarius DSM 446]
          Length = 191

 Score = 43.3 bits (101), Expect = 0.046,   Method: Composition-based stats.
 Identities = 17/95 (17%), Positives = 40/95 (42%), Gaps = 13/95 (13%)

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
            S +    ++ DH      +    E+ + R+ + ++++ L   +R++ E    Q    T 
Sbjct: 97  ESGEELFPILPDHAPTPDRV---AEQSDLRSRIRQALAKLPEEQRQVVEWMYFQG--YTQ 151

Query: 256 ENLSSEFEVS----RERVRQIEARAFKKVQESIQK 286
             ++  F  S    + R R     A +K+++ +Q 
Sbjct: 152 NEIAERFGWSLGTVKSRARL----AMQKLRDELQS 182


>gi|300777141|ref|ZP_07086999.1| DNA-directed RNA polymerase sigma subunit FecI [Chryseobacterium
           gleum ATCC 35910]
 gi|300502651|gb|EFK33791.1| DNA-directed RNA polymerase sigma subunit FecI [Chryseobacterium
           gleum ATCC 35910]
          Length = 192

 Score = 43.3 bits (101), Expect = 0.047,   Method: Composition-based stats.
 Identities = 22/121 (18%), Positives = 47/121 (38%), Gaps = 17/121 (14%)

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           R    E+L   +   +      +D L+ D     +V + ++E       L  ++  L  +
Sbjct: 83  RKKKTENLEDFVYEDEDGEFSIKDILLMDESAGPEVKMFQDE---IWKKLFEALDELPEK 139

Query: 239 ERRIFEARRLQENPVTLENLSSEFE------VSRERVRQIEARAFKKVQESIQKQVELSS 292
           +R ++    L +   TL+ ++ E        +SR      +  A K ++  ++K  E   
Sbjct: 140 QRLVYVENELND--KTLQEIADEQGENIKTIISR------KNYAVKHLRNRLRKLYEDLK 191

Query: 293 S 293
           S
Sbjct: 192 S 192


>gi|225181935|ref|ZP_03735369.1| RNA polymerase, sigma 28 subunit, SigI [Dethiobacter alkaliphilus
           AHT 1]
 gi|225167375|gb|EEG76192.1| RNA polymerase, sigma 28 subunit, SigI [Dethiobacter alkaliphilus
           AHT 1]
          Length = 246

 Score = 43.3 bits (101), Expect = 0.047,   Method: Composition-based stats.
 Identities = 16/97 (16%), Positives = 39/97 (40%), Gaps = 5/97 (5%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI--SEVVSEGNIGLMQAV 90
           +EY L     + GD      L+ S+   V+++A  Y    +     E  S   +   +A+
Sbjct: 15  DEYAL---LAQQGDSQCRDYLLESYRPYVMRVASRYCRRYILAGTDEEFSVALLAFNEAI 71

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
             +   +G    +++   I+  + +Y  ++    ++ 
Sbjct: 72  DSYRSGQGKGFLSFARLVIERRLADYCRKNTRRREVP 108


>gi|88801775|ref|ZP_01117303.1| putative RNA polymerase ECF-type sigma factor [Polaribacter
           irgensii 23-P]
 gi|88782433|gb|EAR13610.1| putative RNA polymerase ECF-type sigma factor [Polaribacter
           irgensii 23-P]
          Length = 169

 Score = 43.3 bits (101), Expect = 0.047,   Method: Composition-based stats.
 Identities = 18/82 (21%), Positives = 38/82 (46%), Gaps = 11/82 (13%)

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
             +   +   + L+E+EE    ++ L  ++  L  +ER +F   R+       + ++   
Sbjct: 90  PYLDVDNQSPEYLLEEEE---FKDKLKSAILELTEKERSVFLMHRIDGKKY--KEIAVLL 144

Query: 263 EVSRERVRQIEAR---AFKKVQ 281
           E+S++ V   E R   A KK++
Sbjct: 145 EISQKAV---EKRMSAALKKLR 163


>gi|229112662|ref|ZP_04242198.1| RNA polymerase sigma factor [Bacillus cereus Rock1-15]
 gi|228670794|gb|EEL26102.1| RNA polymerase sigma factor [Bacillus cereus Rock1-15]
          Length = 156

 Score = 43.3 bits (101), Expect = 0.048,   Method: Composition-based stats.
 Identities = 15/64 (23%), Positives = 35/64 (54%), Gaps = 2/64 (3%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    +   MSVL+ +E+ I   R       T+  ++ E E++  +VR +  +A +K++
Sbjct: 94  EDVEIRVKDFMSVLDEKEKYIIFERFFVG--KTMGEIALEMEMTYYQVRWMYRQALEKMR 151

Query: 282 ESIQ 285
           +S++
Sbjct: 152 DSVR 155


>gi|325279404|ref|YP_004251946.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Odoribacter
           splanchnicus DSM 20712]
 gi|324311213|gb|ADY31766.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Odoribacter
           splanchnicus DSM 20712]
          Length = 185

 Score = 43.3 bits (101), Expect = 0.048,   Method: Composition-based stats.
 Identities = 8/64 (12%), Positives = 31/64 (48%), Gaps = 3/64 (4%)

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            + R  +L+ ++  L PR   +        + ++ E ++ +  ++   V+ +++   +K+
Sbjct: 114 EEERYRLLSEAIKQLPPRTATVI---GYSCDGLSQEEIARKMGITVATVKLLKSHGIQKL 170

Query: 281 QESI 284
           ++ +
Sbjct: 171 KKIL 174


>gi|255035576|ref|YP_003086197.1| transcriptional regulator, LuxR family [Dyadobacter fermentans DSM
           18053]
 gi|254948332|gb|ACT93032.1| transcriptional regulator, LuxR family [Dyadobacter fermentans DSM
           18053]
          Length = 203

 Score = 43.3 bits (101), Expect = 0.048,   Method: Composition-based stats.
 Identities = 12/90 (13%), Positives = 34/90 (37%), Gaps = 2/90 (2%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
                  + L       E   +  E    R + +++S+ +L+ RER +   +   +  + 
Sbjct: 101 DVEMDAMESLAETQASVETDWVTSETETQRSSRISQSLRLLSEREREVISLKYYSDLKI- 159

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESI 284
              ++    +  + +      A +K++ S+
Sbjct: 160 -REIAEMLNLKEQTIANTLQNALRKLRNSL 188


>gi|218264039|ref|ZP_03477956.1| hypothetical protein PRABACTJOHN_03646 [Parabacteroides johnsonii
           DSM 18315]
 gi|218222329|gb|EEC94979.1| hypothetical protein PRABACTJOHN_03646 [Parabacteroides johnsonii
           DSM 18315]
          Length = 214

 Score = 43.3 bits (101), Expect = 0.048,   Method: Composition-based stats.
 Identities = 23/133 (17%), Positives = 49/133 (36%), Gaps = 6/133 (4%)

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           N S+S+V +    +A  E  + L    +K   +     + D+     +  +       + 
Sbjct: 82  NASKSKVTTWMSNIAKHEMFDLLDVLKEKRIGEKTFVPLDDNLVVPDIKDDTNIETPEKK 141

Query: 227 MLTRSMSVLNPRERRIF--EARRLQENPVTLENLSS----EFEVSRERVRQIEARAFKKV 280
            L  ++  L+ RER +          N    + ++      +  +   +R+I+ R  +KV
Sbjct: 142 ALNEALQTLSERERDVLLTYMMYQDGNKHLPDEVTKLLCERYGTTSVNLRKIKQRTLEKV 201

Query: 281 QESIQKQVELSSS 293
           +  I     L  S
Sbjct: 202 KTHILHNTHLLKS 214


>gi|223983686|ref|ZP_03633862.1| hypothetical protein HOLDEFILI_01143 [Holdemania filiformis DSM
           12042]
 gi|225572813|ref|ZP_03781568.1| hypothetical protein RUMHYD_01004 [Blautia hydrogenotrophica DSM
           10507]
 gi|227824268|ref|ZP_03989100.1| conserved hypothetical protein [Acidaminococcus sp. D21]
 gi|229827137|ref|ZP_04453206.1| hypothetical protein GCWU000182_02522 [Abiotrophia defectiva ATCC
           49176]
 gi|291459466|ref|ZP_06598856.1| sigma-70, region 4 subfamily [Oribacterium sp. oral taxon 078 str.
           F0262]
 gi|331084541|ref|ZP_08333641.1| hypothetical protein HMPREF0992_02565 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|223964383|gb|EEF68719.1| hypothetical protein HOLDEFILI_01143 [Holdemania filiformis DSM
           12042]
 gi|225039870|gb|EEG50116.1| hypothetical protein RUMHYD_01004 [Blautia hydrogenotrophica DSM
           10507]
 gi|226904767|gb|EEH90685.1| conserved hypothetical protein [Acidaminococcus sp. D21]
 gi|229788755|gb|EEP24869.1| hypothetical protein GCWU000182_02522 [Abiotrophia defectiva ATCC
           49176]
 gi|291417923|gb|EFE91642.1| sigma-70, region 4 subfamily [Oribacterium sp. oral taxon 078 str.
           F0262]
 gi|291557363|emb|CBL34480.1| DNA-directed RNA polymerase specialized sigma subunit [Eubacterium
           siraeum V10Sc8a]
 gi|330401091|gb|EGG80685.1| hypothetical protein HMPREF0992_02565 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 148

 Score = 43.3 bits (101), Expect = 0.049,   Method: Composition-based stats.
 Identities = 12/63 (19%), Positives = 28/63 (44%), Gaps = 10/63 (15%)

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE----RVRQIEARAFKKVQE 282
           +L  ++S L+ RER +      +  P     +  ++  SR      +R    +A +++Q 
Sbjct: 86  LLAEALSRLDEREREMIYLSFFKRIP--QHEIGRQYGRSRSTAGYHIR----KALRQLQA 139

Query: 283 SIQ 285
            ++
Sbjct: 140 EME 142


>gi|325104249|ref|YP_004273903.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Pedobacter saltans
           DSM 12145]
 gi|324973097|gb|ADY52081.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Pedobacter saltans
           DSM 12145]
          Length = 196

 Score = 43.3 bits (101), Expect = 0.049,   Method: Composition-based stats.
 Identities = 18/78 (23%), Positives = 37/78 (47%), Gaps = 2/78 (2%)

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
            E+   K     L +++  L  R + IF   R  E   T E ++S   +S+  V+     
Sbjct: 113 EERLLDKEYLYYLNKALEELPERSKEIFRLCR--EQKKTYEEVASIMGISKNAVKNHMVF 170

Query: 276 AFKKVQESIQKQVELSSS 293
           + K ++++I+ ++ +S S
Sbjct: 171 SMKHLRKNIEGELGMSLS 188


>gi|86608074|ref|YP_476836.1| RNA polymerase sigma factor [Synechococcus sp. JA-2-3B'a(2-13)]
 gi|86556616|gb|ABD01573.1| RNA polymerase sigma factor, ECF family [Synechococcus sp.
           JA-2-3B'a(2-13)]
          Length = 207

 Score = 43.3 bits (101), Expect = 0.049,   Method: Composition-based stats.
 Identities = 14/78 (17%), Positives = 34/78 (43%), Gaps = 14/78 (17%)

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV------SRER 268
             E+   + RR  +  ++S L   +R+I E    Q   ++  +++ +  +      +R R
Sbjct: 131 PFEQVSIEERRQAVQAALSQLPENQRQILELLYYQG--LSQADIARQLGIPLGTVKTRSR 188

Query: 269 VRQIEARAFKKVQESIQK 286
                 +A  K++ S++ 
Sbjct: 189 ------QALCKLRGSLRA 200


>gi|193215824|ref|YP_001997023.1| ECF subfamily RNA polymerase, sigma-24 subunit [Chloroherpeton
           thalassium ATCC 35110]
 gi|193089301|gb|ACF14576.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Chloroherpeton
           thalassium ATCC 35110]
          Length = 224

 Score = 43.3 bits (101), Expect = 0.050,   Method: Composition-based stats.
 Identities = 14/69 (20%), Positives = 36/69 (52%), Gaps = 6/69 (8%)

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVT------LENLSSEFEVSRERVRQIEARAFKK 279
            ++  +++ L+P+E+ I         P T      +E L+ ++  + E +R+I +RA +K
Sbjct: 151 QLMKEALNTLSPKEQEIMRTIYQWYEPHTKLPSHIVEELTKQYNTTPENIRKIRSRARQK 210

Query: 280 VQESIQKQV 288
           ++  ++  +
Sbjct: 211 IEAYLKSHI 219


>gi|49477012|ref|YP_035202.1| RNA polymerase sigma-B factor (sigma-37) (general stress protein84)
           (GSP84) [Bacillus thuringiensis serovar konkukian str.
           97-27]
 gi|49328568|gb|AAT59214.1| possible RNA polymerase sigma-B factor (Sigma-37) (General stress
           protein84) (GSP84) [Bacillus thuringiensis serovar
           konkukian str. 97-27]
          Length = 199

 Score = 43.3 bits (101), Expect = 0.051,   Method: Composition-based stats.
 Identities = 20/103 (19%), Positives = 48/103 (46%), Gaps = 6/103 (5%)

Query: 186 LNALINSSDKNSSQWQDWLV---YDHDGQEQVLIEKEERKNRRN-MLTRSMSVLNPRERR 241
           L+  I++ + N++   D L     D    E   I+K+ +++  N +L  S+++L+ ++  
Sbjct: 93  LDTPISTEENNTTSKLDILTSSKEDLTYLEFENIQKDIKEHISNDILFASLNLLSDKQLE 152

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           I +   +       + ++     S + V     +A KK++ S+
Sbjct: 153 ILKLIYIVNYNN--KEVAKLLGESEQTVSYNHKKAIKKLRNSM 193


>gi|126698006|ref|YP_001086903.1| putative sigma factor [Clostridium difficile 630]
 gi|115249443|emb|CAJ67258.1| putative sigma factor Tn1549-like, CTn2-Orf31 [Clostridium
           difficile]
          Length = 161

 Score = 43.3 bits (101), Expect = 0.051,   Method: Composition-based stats.
 Identities = 20/100 (20%), Positives = 48/100 (48%), Gaps = 6/100 (6%)

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           + L  SS  +   + D ++ +    E+++    E +     +  ++S LN  ER I E  
Sbjct: 66  HLLFFSSLDHDGHFVDSIIDESVDVEKIV----ETQMMIEAVRNAISRLNAEERDIIERL 121

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +   TL +++ +  V+ + ++  + R  +K++E ++K
Sbjct: 122 YFNDE--TLSSVARDKGVTYQTIQWRKDRILRKLKEILEK 159


>gi|304439342|ref|ZP_07399254.1| sigma-70 family protein [Peptoniphilus duerdenii ATCC BAA-1640]
 gi|304372124|gb|EFM25718.1| sigma-70 family protein [Peptoniphilus duerdenii ATCC BAA-1640]
          Length = 157

 Score = 42.9 bits (100), Expect = 0.052,   Method: Composition-based stats.
 Identities = 14/82 (17%), Positives = 39/82 (47%), Gaps = 2/82 (2%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           V D       + +  E K R   L R++  LN  ER + ++   ++   TL  ++ + + 
Sbjct: 78  VVDIADNTVDVEKIIETKMRIEDLYRALDSLNDEERNLIKSLYFED--KTLTEVAKKEDT 135

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           +  ++ ++  +  +K+++ + +
Sbjct: 136 NPMKISRLRNKVLEKLRKLLDR 157


>gi|150392371|ref|YP_001322420.1| ECF subfamily RNA polymerase sigma-24 factor [Alkaliphilus
           metalliredigens QYMF]
 gi|149952233|gb|ABR50761.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Alkaliphilus
           metalliredigens QYMF]
          Length = 188

 Score = 42.9 bits (100), Expect = 0.052,   Method: Composition-based stats.
 Identities = 18/93 (19%), Positives = 41/93 (44%), Gaps = 4/93 (4%)

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           S +    + D    E ++IE  +++ ++  L  S+  L+P  + I   R    + +T E+
Sbjct: 94  SFYPMETLADDHITEDIVIENMDKEEQKEKLRNSLEQLDPDAKEIITLRYY--HHLTYED 151

Query: 258 LSSEFEVSRERV-RQIEARAFKKVQESIQKQVE 289
           +     + +  V  ++  RA  K+ +    + E
Sbjct: 152 VGKALSLKQGTVKSRL-RRAKDKLIKIFNSEGE 183


>gi|294146897|ref|YP_003559563.1| ECF-type sigma factor [Sphingobium japonicum UT26S]
 gi|292677314|dbj|BAI98831.1| ECF-type sigma factor [Sphingobium japonicum UT26S]
          Length = 244

 Score = 42.9 bits (100), Expect = 0.055,   Method: Composition-based stats.
 Identities = 15/59 (25%), Positives = 30/59 (50%), Gaps = 2/59 (3%)

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENP--VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              + R +++L P E+++   R        +TL   +    VS  R+ QIE +AF++++
Sbjct: 31  HRTVERLIAMLEPHEQQVVRLRIGLGPSPALTLAATAKIVGVSPSRIGQIEDKAFRRIR 89


>gi|237795772|ref|YP_002863324.1| hypothetical protein CLJ_B2561 [Clostridium botulinum Ba4 str. 657]
 gi|229262514|gb|ACQ53547.1| hypothetical protein CLJ_B2561 [Clostridium botulinum Ba4 str. 657]
          Length = 331

 Score = 42.9 bits (100), Expect = 0.055,   Method: Composition-based stats.
 Identities = 15/116 (12%), Positives = 45/116 (38%), Gaps = 9/116 (7%)

Query: 182 GDESLNALI--NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
             +SL+  I     D  +    D +    + +++ +     ++     +   +  LN R+
Sbjct: 94  DVDSLDKPILNQKQDNENLSLIDLISDKTNYEDRSIFNVTCKE-----IAAIIENLNERD 148

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPP 295
           ++I +      N  T + +  E  + +  + +I  +    ++   + + E+ +  P
Sbjct: 149 KKIIKEFYF--NNKTQKQIGEEIGLKQSYISRILKKIPNTIKNKYEGENEMFTKEP 202


>gi|182411906|ref|YP_001816972.1| ECF subfamily RNA polymerase sigma-24 factor [Opitutus terrae
           PB90-1]
 gi|177839120|gb|ACB73372.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Opitutus terrae
           PB90-1]
          Length = 564

 Score = 42.9 bits (100), Expect = 0.056,   Method: Composition-based stats.
 Identities = 18/79 (22%), Positives = 36/79 (45%), Gaps = 6/79 (7%)

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS--RERVRQIEARAF 277
           + +  R ++  ++  LN R+R     R  ++ P     +   F  S    RVR    RA 
Sbjct: 114 DWEKLRPVIDDAIGTLNERDREAVLMRFFEDRP--FAEIGDRFFTSEDAARVR--VNRAL 169

Query: 278 KKVQESIQKQVELSSSPPL 296
           +K+Q ++ ++   S++  L
Sbjct: 170 EKLQSALAQRGITSTATAL 188


>gi|300932937|ref|ZP_07148193.1| RNA polymerase sigma factor SigD [Corynebacterium resistens DSM
           45100]
          Length = 191

 Score = 42.9 bits (100), Expect = 0.057,   Method: Composition-based stats.
 Identities = 28/180 (15%), Positives = 65/180 (36%), Gaps = 5/180 (2%)

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I+AA+   I      ++         +    R   G  +  T +++  E  +A+A+ +  
Sbjct: 11  IQAAVTRAIAGEKRALQEVINLIHPPVVRYCRARVGSDKYPTADDIAQEVCLAVARAIPT 70

Query: 169 SESEVISMNCRLAGDES--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
            E + +     +    S  +     +  ++  Q  D +       +   +E  E      
Sbjct: 71  YEDKGLPFMAFVYRIASNKIVDGRRAHGRDQLQPTDEVPEVEVTHDTPELEILELDACNE 130

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ++ + + +L  + R I   R         E  +    +S   VR  + RA  K+++ I++
Sbjct: 131 VV-QLLDLLGEKAREIITLRVFSGYSA--EETAEIMNMSAGAVRVAQFRALAKLRKHIEQ 187


>gi|253568212|ref|ZP_04845623.1| ECF-type sigma factor [Bacteroides sp. 1_1_6]
 gi|251842285|gb|EES70365.1| ECF-type sigma factor [Bacteroides sp. 1_1_6]
          Length = 183

 Score = 42.9 bits (100), Expect = 0.058,   Method: Composition-based stats.
 Identities = 18/86 (20%), Positives = 40/86 (46%), Gaps = 2/86 (2%)

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
           + +  +D         E   +E+E+RKN  +++ R +  L+PR+R       ++E     
Sbjct: 96  SDTAIEDVNAVAPTDVEDDYMEEEQRKNEFSLVKRLLDQLSPRQREALTLYYIEEKKY-- 153

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           E++     ++ + VR +  R   K++
Sbjct: 154 EDICEIMNMNYQSVRNLMHRGLTKLR 179


>gi|317500623|ref|ZP_07958842.1| sigma-70 protein [Lachnospiraceae bacterium 8_1_57FAA]
 gi|316897941|gb|EFV19993.1| sigma-70 protein [Lachnospiraceae bacterium 8_1_57FAA]
          Length = 148

 Score = 42.9 bits (100), Expect = 0.059,   Method: Composition-based stats.
 Identities = 12/63 (19%), Positives = 28/63 (44%), Gaps = 10/63 (15%)

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE----RVRQIEARAFKKVQE 282
           +L  ++S L+ RER +      +  P     +  ++  SR      +R    +A +++Q 
Sbjct: 86  LLAEALSRLDEREREMIYLSFFKRIP--QHEIGRQYGRSRSTAGYHIR----KALRQLQA 139

Query: 283 SIQ 285
            ++
Sbjct: 140 EME 142


>gi|299145560|ref|ZP_07038628.1| ECF-type sigma factor [Bacteroides sp. 3_1_23]
 gi|298516051|gb|EFI39932.1| ECF-type sigma factor [Bacteroides sp. 3_1_23]
          Length = 183

 Score = 42.9 bits (100), Expect = 0.059,   Method: Composition-based stats.
 Identities = 17/86 (19%), Positives = 41/86 (47%), Gaps = 2/86 (2%)

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
           + +  ++  +      E   +E+E+RKN  +++ R +  L+PR+R       ++E     
Sbjct: 96  SDTAIEEVSISTPTDVEDDYMEEEQRKNEFSLVRRLLDQLSPRQREALTLYYIEEKKY-- 153

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           E++     ++ + VR +  R   K++
Sbjct: 154 EDICEIMNMNYQSVRNLMHRGLTKLR 179


>gi|158321693|ref|YP_001514200.1| putative RNA polymerase sigma factor SigI [Alkaliphilus oremlandii
           OhILAs]
 gi|158141892|gb|ABW20204.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           oremlandii OhILAs]
          Length = 250

 Score = 42.9 bits (100), Expect = 0.059,   Method: Composition-based stats.
 Identities = 25/149 (16%), Positives = 63/149 (42%), Gaps = 6/149 (4%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS--EVVSEGNIGLMQ 88
           KQE      ++ + GD    +RL+  ++  + K+   + G  + +   +  S G +   +
Sbjct: 10  KQETLEQRVKHIQAGDEEDKNRLIQEYIPFIKKVISNHIGAYVDVENHDAFSAGLMAFNE 69

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
           A++K+   +G    T++   IK+ + +   ++    K        +L  +L     H+ A
Sbjct: 70  AIEKYQEHKGN-FLTFASLVIKSRLIDAHRKASKTSK---EVFVSQLENDLETTAEHIMA 125

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMN 177
           +     + E  + + + +   E+  +S+ 
Sbjct: 126 VDGFESELEMKLDLRELIRSMEAFGVSLE 154


>gi|310826034|ref|YP_003958391.1| ECF subfamily RNA polymerase sigma-24 factor [Eubacterium limosum
           KIST612]
 gi|308737768|gb|ADO35428.1| ECF subfamily RNA polymerase sigma-24 factor [Eubacterium limosum
           KIST612]
          Length = 211

 Score = 42.9 bits (100), Expect = 0.060,   Method: Composition-based stats.
 Identities = 20/100 (20%), Positives = 47/100 (47%), Gaps = 8/100 (8%)

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L+A   SSD      ++ +  +    E   IE+E+++     L +S+  L+ R+ ++   
Sbjct: 116 LSAPAGSSDG--LTLEEVIADEAIDLEGCYIEREDQQ----RLWQSVHALSARQGKVLYQ 169

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
                   +L  +  E  V+ + VR++  +  K +++S++
Sbjct: 170 SF--HESKSLVQICKEMGVTHKAVRKLRDKGLKNLKKSLK 207


>gi|167464255|ref|ZP_02329344.1| hypothetical protein Plarl_17139 [Paenibacillus larvae subsp.
           larvae BRL-230010]
          Length = 197

 Score = 42.9 bits (100), Expect = 0.060,   Method: Composition-based stats.
 Identities = 21/104 (20%), Positives = 46/104 (44%), Gaps = 6/104 (5%)

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK---EERKNRRNMLTRSMSVLNPRERRI 242
           L+  + S DK ++  +D +   +     +L E     E     + L  S+  L  +ER +
Sbjct: 96  LDQPL-SEDKENTAIKDLIPAANSEPSSLLEEDCNTLEDLATTSALYNSIRSLTEKERSV 154

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
                +  + +T   ++ +  VS++ V + +  A KK++  +Q 
Sbjct: 155 LTWHFI--HGLTDTEIARKTGVSQQAVTKTKRNALKKLKRQLQA 196


>gi|62701715|gb|AAX92788.1| Sigma-70 region 3, putative [Oryza sativa Japonica Group]
          Length = 368

 Score = 42.9 bits (100), Expect = 0.060,   Method: Composition-based stats.
 Identities = 18/53 (33%), Positives = 32/53 (60%), Gaps = 2/53 (3%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           +E  L KR  +HG +   +R+VTS++RLV+ IA  + G G+ + +++     G
Sbjct: 309 DERTLRKRL-DHG-IYCKNRMVTSNVRLVISIAREFEGPGMELYDLIQVFITG 359


>gi|7021518|gb|AAF35385.1| SpoIIGB [Clostridium perfringens]
          Length = 106

 Score = 42.9 bits (100), Expect = 0.061,   Method: Composition-based stats.
 Identities = 19/86 (22%), Positives = 34/86 (39%), Gaps = 7/86 (8%)

Query: 177 NCRLAGDESLNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
           N ++  + S    +N   D N     D L  D D    ++    E +  + +L  +M  L
Sbjct: 25  NSKVKAEISFYEPLNIDWDGNELLLSDILGTDDD----IVYNLIEDEVDKELLFTAMKNL 80

Query: 236 NPRERRIFEARRL--QENPVTLENLS 259
           + RE+ I E R         T + ++
Sbjct: 81  SNREKEIVELRFGLCGYKEKTQKEVA 106


>gi|229050920|ref|ZP_04194471.1| RNA polymerase sigma factor [Bacillus cereus AH676]
 gi|228722465|gb|EEL73859.1| RNA polymerase sigma factor [Bacillus cereus AH676]
          Length = 156

 Score = 42.9 bits (100), Expect = 0.061,   Method: Composition-based stats.
 Identities = 15/64 (23%), Positives = 35/64 (54%), Gaps = 2/64 (3%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    +   MSVL+ +E+ I   R       T+  ++ E E++  +VR +  +A +K++
Sbjct: 94  EDVEIRVKDFMSVLDEKEKYIIFERFFVG--KTMGEIALEMEMTYYQVRWMYRQALEKMR 151

Query: 282 ESIQ 285
           +S++
Sbjct: 152 DSVK 155


>gi|298385715|ref|ZP_06995273.1| ECF-type sigma factor [Bacteroides sp. 1_1_14]
 gi|298261856|gb|EFI04722.1| ECF-type sigma factor [Bacteroides sp. 1_1_14]
          Length = 183

 Score = 42.9 bits (100), Expect = 0.062,   Method: Composition-based stats.
 Identities = 18/86 (20%), Positives = 40/86 (46%), Gaps = 2/86 (2%)

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
           + +  +D         E   +E+E+RKN  +++ R +  L+PR+R       ++E     
Sbjct: 96  SDTAIEDVNAVAPTDIEDDYMEEEQRKNEFSLVKRLLDQLSPRQREALTLYYIEEKKY-- 153

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           E++     ++ + VR +  R   K++
Sbjct: 154 EDICEIMNMNYQSVRNLMHRGLTKLR 179


>gi|295401257|ref|ZP_06811229.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|312111921|ref|YP_003990237.1| RNA polymerase, sigma 28 subunit, SigI [Geobacillus sp. Y4.1MC1]
 gi|294976664|gb|EFG52270.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|311217022|gb|ADP75626.1| RNA polymerase, sigma 28 subunit, SigI [Geobacillus sp. Y4.1MC1]
          Length = 245

 Score = 42.9 bits (100), Expect = 0.062,   Method: Composition-based stats.
 Identities = 26/159 (16%), Positives = 58/159 (36%), Gaps = 16/159 (10%)

Query: 43  EHGDLSAAHRLVTSHLRL----VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           + G+ +  ++L+  +       V  +   +   G    + +S G I   +A++K+ P +G
Sbjct: 22  QQGNKTLHNQLIQQYKPFIAKTVSSVCKRFIHEG---DDELSIGLIAFNEAIEKYAPHKG 78

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL------QAITDN 152
               +++   IK  + +YI +      I    ++         L   L      + I   
Sbjct: 79  GSFISFAELLIKRRLIDYIRKEAKCRNIVFHTDEDEENSAQTYLDTKLSMDEFYRQIEQQ 138

Query: 153 NLKPE--QVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
             + E      + K+  +   E++        D  LNA+
Sbjct: 139 QRREEILHYQQVLKEFGIHFHELVE-QSPKHKDARLNAI 176


>gi|256390610|ref|YP_003112174.1| sigma-70 region 4 domain-containing protein [Catenulispora
           acidiphila DSM 44928]
 gi|256356836|gb|ACU70333.1| sigma-70 region 4 domain-containing protein [Catenulispora
           acidiphila DSM 44928]
          Length = 428

 Score = 42.9 bits (100), Expect = 0.062,   Method: Composition-based stats.
 Identities = 13/42 (30%), Positives = 24/42 (57%), Gaps = 3/42 (7%)

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
               L+PR++    +RR      TL+++   + +SRER+RQ+
Sbjct: 3   LWKSLSPRDQA-LHSRRASGE--TLDSIGQSYGLSRERIRQL 41


>gi|7021514|gb|AAF35383.1| SpoIIGB [Clostridium bifermentans]
          Length = 107

 Score = 42.9 bits (100), Expect = 0.062,   Method: Composition-based stats.
 Identities = 16/80 (20%), Positives = 35/80 (43%), Gaps = 6/80 (7%)

Query: 183 DESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
           + S +  +N     +      ++   + +   LIE+E  K+   +L  ++  L+ RE++I
Sbjct: 31  EVSFDEPLNVDLDGNELLLSDILGTENDEIYKLIEEEIDKD---LLVMALDRLSDREKQI 87

Query: 243 FEARRLQ---ENPVTLENLS 259
            E R       N  T + ++
Sbjct: 88  MELRFGLASKGNERTQKEVA 107


>gi|300771490|ref|ZP_07081365.1| RNA polymerase sigma factor (possible RNA polymerase sigma-24
           factor) [Sphingobacterium spiritivorum ATCC 33861]
 gi|300761479|gb|EFK58300.1| RNA polymerase sigma factor (possible RNA polymerase sigma-24
           factor) [Sphingobacterium spiritivorum ATCC 33861]
          Length = 205

 Score = 42.9 bits (100), Expect = 0.063,   Method: Composition-based stats.
 Identities = 16/78 (20%), Positives = 41/78 (52%), Gaps = 4/78 (5%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           V        +++EK E+++ ++ +   +  L+PR + IF+  R +   ++ + ++ +  +
Sbjct: 112 VTTETSVSNLVLEKMEQEDIKSSVGDVLKKLSPRCQEIFQLSRFEN--LSNDEIAVKLGI 169

Query: 265 SRERVR-QIEARAFKKVQ 281
           S+  V  QI  +A K ++
Sbjct: 170 SKRSVENQI-TKALKHLR 186


>gi|160939951|ref|ZP_02087297.1| hypothetical protein CLOBOL_04841 [Clostridium bolteae ATCC
           BAA-613]
 gi|158437095|gb|EDP14861.1| hypothetical protein CLOBOL_04841 [Clostridium bolteae ATCC
           BAA-613]
          Length = 134

 Score = 42.9 bits (100), Expect = 0.063,   Method: Composition-based stats.
 Identities = 19/79 (24%), Positives = 37/79 (46%), Gaps = 6/79 (7%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE--VS 265
            D + + + E+ E    R++L  +M  L+PRE+ I   RR+     +L  +S E    V+
Sbjct: 59  QDTRAKPVDEQAEEALERSLLFEAMKDLDPREKDII--RRIYCYDQSLRQISRETGVPVT 116

Query: 266 RERVRQIEARAFKKVQESI 284
               R    +  +K++  +
Sbjct: 117 TLHYR--HGKILRKLRSLM 133


>gi|221057916|ref|XP_002261466.1| hypothetical protein, conserved in Plasmodium species [Plasmodium
           knowlesi strain H]
 gi|194247471|emb|CAQ40871.1| hypothetical protein, conserved in Plasmodium species [Plasmodium
           knowlesi strain H]
          Length = 792

 Score = 42.9 bits (100), Expect = 0.065,   Method: Composition-based stats.
 Identities = 28/190 (14%), Positives = 63/190 (33%), Gaps = 20/190 (10%)

Query: 24  RKIPMLEKQEEYVLAKRY-------REHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGL 73
            + P+L   EE   A  Y       +    +  + +L+   + L+  I           L
Sbjct: 483 NRPPLL---EEVAFAYNYDKDIFIQKLEVKIKLSQKLLIYFIPLINNIIRKAESNFSSNL 539

Query: 74  PISEVVSEGNIGLMQAVKKFDPER-GFR-LATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
              + +      +    +++D E+ G + L  Y   W K +   Y  +  S V +     
Sbjct: 540 SEDDFLLVSLDAVKNGFRRYDVEKLGIKNLTKYVYIWAKNSTYNYYQKHKSFVSVSPH-- 597

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
               + +  ++K   ++  + + +   +  IA  L+++   V                I 
Sbjct: 598 ---TYKDYNKIKKFEESFEEKHERKPSIKEIADGLSMTMERVQKALSSAVNVIDAEKPIM 654

Query: 192 SSDKNSSQWQ 201
             + NS   +
Sbjct: 655 YQNNNSDHPE 664


>gi|326333950|ref|ZP_08200180.1| RNA polymerase sigma-E factor [Nocardioidaceae bacterium Broad-1]
 gi|325948229|gb|EGD40339.1| RNA polymerase sigma-E factor [Nocardioidaceae bacterium Broad-1]
          Length = 167

 Score = 42.9 bits (100), Expect = 0.066,   Method: Composition-based stats.
 Identities = 16/73 (21%), Positives = 35/73 (47%), Gaps = 2/73 (2%)

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D  E+   ++ E    R++L + +  L PR+R +   R  ++  +T  +++    ++   
Sbjct: 82  DLPERAGDDETETVGVRHLLWQRIGALPPRQRAVVVLRYYED--LTDADIAEALGIATAT 139

Query: 269 VRQIEARAFKKVQ 281
           VR    RA  K++
Sbjct: 140 VRSTAMRALTKLR 152


>gi|89893570|ref|YP_517057.1| putative RNA polymerase sigma factor SigI [Desulfitobacterium
           hafniense Y51]
 gi|89333018|dbj|BAE82613.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 243

 Score = 42.9 bits (100), Expect = 0.067,   Method: Composition-based stats.
 Identities = 22/141 (15%), Positives = 53/141 (37%), Gaps = 7/141 (4%)

Query: 42  REHGDLSAAHRLVTSHLRLVVK----IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
            ++GD  A   ++ SH   + K    I   Y        + +S   +   +A+  FDP+ 
Sbjct: 16  AQNGDTLAREEIIESHKNFIAKVSSTICKRYL--TWDNDDELSIALMAFNEAIDSFDPQG 73

Query: 98  GFRLATYSMWWIKAAMQEYILRSWSLVKIG-TTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           G    +++   I+  + +Y  +      +  +  N +    ++  +    +     N   
Sbjct: 74  GAAFESFAHTVIRRRLVDYFRKEGKHKYLSLSPMNPEDEELSIYDINNSQEQYQRENSNT 133

Query: 157 EQVVAIAKKLNVSESEVISMN 177
           +   A+ K + V     +S++
Sbjct: 134 QFAEAMEKYIKVLSEYGVSID 154


>gi|150390876|ref|YP_001320925.1| ECF subfamily RNA polymerase sigma-24 factor [Alkaliphilus
           metalliredigens QYMF]
 gi|149950738|gb|ABR49266.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Alkaliphilus
           metalliredigens QYMF]
          Length = 201

 Score = 42.9 bits (100), Expect = 0.067,   Method: Composition-based stats.
 Identities = 16/92 (17%), Positives = 38/92 (41%), Gaps = 3/92 (3%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           Q+E  L ++  + GD  +  +L+  H +    IA    G     ++V  E  +   +A+ 
Sbjct: 6   QQEATLIEK-SKDGDSESFEKLILQHQKKAFNIAYRMLGNLEDANDVTQEALLKAYRAIN 64

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           +F  +     +T+    +     ++I ++   
Sbjct: 65  RFQEK--SSFSTWLYTIVTNTCVDFIRKNRKT 94


>gi|169826111|ref|YP_001696269.1| RNA polymerase sigma-B factor [Lysinibacillus sphaericus C3-41]
 gi|168990599|gb|ACA38139.1| possible RNA polymerase sigma-B factor (sigma-37) (general stress
           protein84) (GSP84) [Lysinibacillus sphaericus C3-41]
          Length = 168

 Score = 42.5 bits (99), Expect = 0.068,   Method: Composition-based stats.
 Identities = 11/76 (14%), Positives = 37/76 (48%), Gaps = 2/76 (2%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           ++++ E          L +S+  L  ++ +I E     +   +++ ++   + + + +  
Sbjct: 93  DEIIQEGLLDAVENEELFQSLKSLTDKQLQILEMIYAHD--YSIKAVAETLQTTPQNISN 150

Query: 272 IEARAFKKVQESIQKQ 287
           +  +A KK+Q+ ++K+
Sbjct: 151 LHRKALKKLQQKLRKE 166


>gi|260172353|ref|ZP_05758765.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D2]
 gi|315920652|ref|ZP_07916892.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D2]
 gi|313694527|gb|EFS31362.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D2]
          Length = 190

 Score = 42.5 bits (99), Expect = 0.069,   Method: Composition-based stats.
 Identities = 18/93 (19%), Positives = 44/93 (47%), Gaps = 2/93 (2%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
               + +D +       E + I  E+ K  +  +   MSVL  R+R I   R ++E  ++
Sbjct: 100 DEIGEREDTVDNSPSTPETIYINNEQEKLVQTTVHSMMSVLTDRQREIIYYRYIKE--MS 157

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++ +S   +++ + V     RA  ++++  +++
Sbjct: 158 IDEISEVTDMNNQSVSNSIQRALGRIRDLFKRK 190


>gi|189522303|ref|XP_001343753.2| PREDICTED: centrosome-associated protein 350 [Danio rerio]
          Length = 3043

 Score = 42.5 bits (99), Expect = 0.069,   Method: Composition-based stats.
 Identities = 31/184 (16%), Positives = 66/184 (35%), Gaps = 17/184 (9%)

Query: 108  WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA---- 163
            W++   +    +            Q+ L   L++ +  ++ + + N    +   +     
Sbjct: 1644 WLEHQKRRLRDKGEDDKMPPLRKKQRGLIMKLQQEQAEIKRLQEANKAARRERQLLLKQQ 1703

Query: 164  KKLNVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE--KE 219
            +++       + +  RL  AGD  + + + S    SS     +V D D +    +     
Sbjct: 1704 EEIERMRHTTLKLKERLKTAGDTKMESPV-SGVAESSAPPSVIVTDADTRSPSPMSVSGS 1762

Query: 220  ERKNRRNMLTRSMSV-----LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
            E  +    L +  S      L  RE+++ + RR  E    L       +V    VR++E 
Sbjct: 1763 ETSSIMQKLKKMRSHMDEKFLTKREQQLMQRRRHAEE---LLEWRQRLDVEEAEVRRMEK 1819

Query: 275  RAFK 278
            +A  
Sbjct: 1820 QALA 1823


>gi|329961317|ref|ZP_08299463.1| Sigma-70 region 2 [Bacteroides fluxus YIT 12057]
 gi|328531923|gb|EGF58743.1| Sigma-70 region 2 [Bacteroides fluxus YIT 12057]
          Length = 182

 Score = 42.5 bits (99), Expect = 0.070,   Method: Composition-based stats.
 Identities = 17/88 (19%), Positives = 38/88 (43%), Gaps = 1/88 (1%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE  LA+R R+ GD  A   L   +   ++ + + Y G      +++ +G + L  +  K
Sbjct: 2   EELELAERCRQ-GDNLARKELYERYAGRMLSVCLRYAGDREIAQDLMHDGFLKLFDSFDK 60

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRS 120
           F       L  +    +   + +++ ++
Sbjct: 61  FTWRGEGSLRAWMERVMVNTVLQFLRKN 88


>gi|284041391|ref|YP_003391321.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Spirosoma linguale
           DSM 74]
 gi|283820684|gb|ADB42522.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Spirosoma linguale
           DSM 74]
          Length = 196

 Score = 42.5 bits (99), Expect = 0.070,   Method: Composition-based stats.
 Identities = 25/113 (22%), Positives = 47/113 (41%), Gaps = 8/113 (7%)

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
            S+  ++    + +    ++D N +        D    E  LIE EE +     L +S +
Sbjct: 77  RSLRNKITKTRNRDLFFQAADINDA----PTAVDDFIIENTLIEGEEVQRINQQLLKSFA 132

Query: 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVS-RERVRQIEARAFKKVQESIQ 285
           +L PR++     R  Q      E ++    V+ +   R I A A K ++E ++
Sbjct: 133 LLTPRQQEALNLRFYQHFSN--EEIAQIMGVNYQSACRFIYA-ALKTLREVVR 182


>gi|237720729|ref|ZP_04551210.1| ECF-type sigma factor [Bacteroides sp. 2_2_4]
 gi|262408058|ref|ZP_06084606.1| ECF-type sigma factor [Bacteroides sp. 2_1_22]
 gi|298481264|ref|ZP_06999457.1| ECF-type sigma factor [Bacteroides sp. D22]
 gi|229449564|gb|EEO55355.1| ECF-type sigma factor [Bacteroides sp. 2_2_4]
 gi|262354866|gb|EEZ03958.1| ECF-type sigma factor [Bacteroides sp. 2_1_22]
 gi|298272468|gb|EFI14036.1| ECF-type sigma factor [Bacteroides sp. D22]
          Length = 182

 Score = 42.5 bits (99), Expect = 0.070,   Method: Composition-based stats.
 Identities = 17/86 (19%), Positives = 41/86 (47%), Gaps = 2/86 (2%)

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
           + +  ++  +      E   +E+E+RKN  +++ R +  L+PR+R       ++E     
Sbjct: 95  SDTAVEEVSISTPTDVEDDYMEEEQRKNEFSLVRRLLDQLSPRQREALTLYYIEEKKY-- 152

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           E++     ++ + VR +  R   K++
Sbjct: 153 EDICEIMNMNYQSVRNLMHRGLTKLR 178


>gi|148658606|ref|YP_001278811.1| ECF subfamily RNA polymerase sigma-24 factor [Roseiflexus sp. RS-1]
 gi|148570716|gb|ABQ92861.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Roseiflexus sp.
           RS-1]
          Length = 224

 Score = 42.5 bits (99), Expect = 0.070,   Method: Composition-based stats.
 Identities = 32/237 (13%), Positives = 68/237 (28%), Gaps = 75/237 (31%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
            +    L +R  + GD  A   LV S  + +  IAM         +++  E  I L +A+
Sbjct: 2   AEPSAELIRR-AQAGDPEALTHLVLSQQQYIYSIAMSVLKNPDDAADLTQEAFIRLFRAL 60

Query: 91  KKFDPERGFRLATYSMWWIKA---AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
            +++ E   R  T+    +            R   LV +  +                  
Sbjct: 61  PQYNGE--SRFTTWLYRLVVNLGRDELRRRGRQAPLVSVPES------------------ 100

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
                                              DE  +A+   +D +           
Sbjct: 101 -----------------------------------DEDFDAIGTIADDD----------- 114

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
                +V ++ +E    R  + R++  L    R +      ++   T  +++   ++
Sbjct: 115 RWSDPEVALDSQEL---RQEVRRALDQLEEHYRLVLTLYYFEDMKYT--DIAEILDL 166


>gi|7021512|gb|AAF35382.1| SpoIIGB [Paenibacillus polymyxa]
          Length = 106

 Score = 42.5 bits (99), Expect = 0.070,   Method: Composition-based stats.
 Identities = 19/86 (22%), Positives = 38/86 (44%), Gaps = 7/86 (8%)

Query: 177 NCRLAGDESLNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
           N +   + S +  +N   D N     D +  ++D   + + E+ +RK    +L +++  L
Sbjct: 25  NSKTRTEVSFDEPLNIDWDGNELLLSDVMGTENDTIYRNIEEQVDRK----LLHKALDKL 80

Query: 236 NPRERRIFEARRL--QENPVTLENLS 259
             RER I E R         T ++++
Sbjct: 81  TDRERLIMELRFGLQDGEEKTQKDVA 106


>gi|312887700|ref|ZP_07747289.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Mucilaginibacter
           paludis DSM 18603]
 gi|311299795|gb|EFQ76875.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Mucilaginibacter
           paludis DSM 18603]
          Length = 200

 Score = 42.5 bits (99), Expect = 0.071,   Method: Composition-based stats.
 Identities = 15/93 (16%), Positives = 37/93 (39%), Gaps = 2/93 (2%)

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
           N +       YD         +         M+  ++S L    +R    R  +E  ++L
Sbjct: 96  NDANLVKKAAYDRAEWSTNTEDTIAFNESLAMINSAVSELP--SQRQLIYRLSREEGLSL 153

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           E ++   ++SR  V+     A + +++ ++++ 
Sbjct: 154 EEIADRLDISRSTVKNQLGHALRSIRDFLERRA 186


>gi|284033654|ref|YP_003383585.1| ECF subfamily RNA polymerase sigma-24 subunit [Kribbella flavida
           DSM 17836]
 gi|283812947|gb|ADB34786.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Kribbella flavida
           DSM 17836]
          Length = 164

 Score = 42.5 bits (99), Expect = 0.071,   Method: Composition-based stats.
 Identities = 15/88 (17%), Positives = 36/88 (40%), Gaps = 4/88 (4%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE-NPVTLENLSSEFEVSR 266
               ++ + +        + L R+++ L+ RER +   R  Q+ +  T   ++    +  
Sbjct: 80  DLDPDRTVPDPATDIVNSDDLWRALATLSARERVVLVLRYYQDLDDRT---IADLLGIKP 136

Query: 267 ERVRQIEARAFKKVQESIQKQVELSSSP 294
             VR + +RA   ++++ Q        P
Sbjct: 137 SSVRSVASRALASLRKARQSHRVDERLP 164


>gi|213422923|ref|ZP_03355949.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
           enterica serovar Typhi str. E01-6750]
          Length = 36

 Score = 42.5 bits (99), Expect = 0.071,   Method: Composition-based stats.
 Identities = 12/28 (42%), Positives = 17/28 (60%)

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEAR 275
           L     TLE++  E  ++RERVRQI+  
Sbjct: 8   LGYEAATLEDVGREIGLTRERVRQIQVE 35


>gi|317129443|ref|YP_004095725.1| hypothetical protein Bcell_2739 [Bacillus cellulosilyticus DSM
           2522]
 gi|315474391|gb|ADU30994.1| hypothetical protein Bcell_2739 [Bacillus cellulosilyticus DSM
           2522]
          Length = 290

 Score = 42.5 bits (99), Expect = 0.072,   Method: Composition-based stats.
 Identities = 17/68 (25%), Positives = 28/68 (41%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMW 107
              H LV  +  +V  IA  YR     I ++   G +GL+ A+  F+      L   +  
Sbjct: 5   EEKHDLVLRYQYIVYDIAYHYRFLDRDIEDIRGWGYVGLVNAINDFEKCSDIDLKVMAYP 64

Query: 108 WIKAAMQE 115
            IK  + +
Sbjct: 65  RIKREILK 72


>gi|289524474|ref|ZP_06441328.1| RNA polymerase sigma factor [Anaerobaculum hydrogeniformans ATCC
           BAA-1850]
 gi|289502286|gb|EFD23450.1| RNA polymerase sigma factor [Anaerobaculum hydrogeniformans ATCC
           BAA-1850]
          Length = 100

 Score = 42.5 bits (99), Expect = 0.073,   Method: Composition-based stats.
 Identities = 18/64 (28%), Positives = 34/64 (53%), Gaps = 2/64 (3%)

Query: 58  LRLVVKIAMGYRGYGLPI-SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           + LV+K+A         +  ++V EG IGL  A++K+D  RG     ++   ++ AM  Y
Sbjct: 1   MPLVLKMASMLSNGDPHLKEDLVQEGYIGLYHAIRKYDENRGH-FPAFARTCVRNAMISY 59

Query: 117 ILRS 120
           + ++
Sbjct: 60  LRKN 63


>gi|156740052|ref|YP_001430181.1| ECF subfamily RNA polymerase sigma-24 factor [Roseiflexus
           castenholzii DSM 13941]
 gi|156231380|gb|ABU56163.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Roseiflexus
           castenholzii DSM 13941]
          Length = 224

 Score = 42.5 bits (99), Expect = 0.073,   Method: Composition-based stats.
 Identities = 26/131 (19%), Positives = 52/131 (39%), Gaps = 8/131 (6%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R  + GD  A  +LV S  + V  IAM         +++  E  I L +A+ +++ E   
Sbjct: 10  RRAQAGDPEALTQLVLSQQQYVYSIAMSVLKNPDDAADLTQEAFIRLFRALPQYNGE--S 67

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTA------NQKRLFFNLRRLKGHLQAITDNN 153
           R  T+    +    ++ + R      + + A      +   +  +  R     +A+    
Sbjct: 68  RFTTWLYRLVVNLGRDELRRRGRQAPLASPADGDEELDAIDVIADDDRWSDPEEALDSRE 127

Query: 154 LKPEQVVAIAK 164
           L+ E   A+A+
Sbjct: 128 LRSEVRRALAQ 138


>gi|320161961|ref|YP_004175186.1| RNA polymerase ECF-type sigma factor [Anaerolinea thermophila
           UNI-1]
 gi|319995815|dbj|BAJ64586.1| RNA polymerase ECF-type sigma factor [Anaerolinea thermophila
           UNI-1]
          Length = 185

 Score = 42.5 bits (99), Expect = 0.074,   Method: Composition-based stats.
 Identities = 15/89 (16%), Positives = 37/89 (41%), Gaps = 2/89 (2%)

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           S  Q+ L  +H    +   E  + +++   L  ++  L   +R +   R L   P  L  
Sbjct: 93  SHPQENLSENHQAVNETPEETVQSRSQVQELYIALQRLPEDQRDVLVLRFLNGLP--LAE 150

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ++     S + ++ ++ R    ++E ++ 
Sbjct: 151 VARILHRSEDAIKGLQRRGLIALREEMKS 179


>gi|307324447|ref|ZP_07603655.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306890178|gb|EFN21156.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 189

 Score = 42.5 bits (99), Expect = 0.074,   Method: Composition-based stats.
 Identities = 19/97 (19%), Positives = 40/97 (41%), Gaps = 6/97 (6%)

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
            + +   G+  V  ++  R + R+ L R++  L  R R +   R   +  ++   ++++ 
Sbjct: 94  MVPHQDSGERAVAGDEYGRIDSRDQLVRALQCLPMRMRTVVVLRYFHD--LSDAEIAADL 151

Query: 263 EVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQK 299
            +S   VR   +R   K++     Q    S P   Q 
Sbjct: 152 GISPGTVRSQLSRGMDKLR----SQFPALSGPSPRQP 184


>gi|115379607|ref|ZP_01466693.1| myxococcus probable DNA-binding regulatory protein, putative
           [Stigmatella aurantiaca DW4/3-1]
 gi|115363387|gb|EAU62536.1| myxococcus probable DNA-binding regulatory protein, putative
           [Stigmatella aurantiaca DW4/3-1]
          Length = 355

 Score = 42.5 bits (99), Expect = 0.074,   Method: Composition-based stats.
 Identities = 32/167 (19%), Positives = 55/167 (32%), Gaps = 26/167 (15%)

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
           T     R+F      +   + +     +P +++  A K  +     +     +A  E+LN
Sbjct: 168 THLRPDRVFVEEVHQRLRQKLLLSREGRPPKLLEYAGKGPL-----VQWLRAVALREALN 222

Query: 188 ALINSSDK---NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
            L          S      L       E  L++       +  L  ++  L  RER    
Sbjct: 223 LLAQQRAGAPLESGTVLPELAAPGPDPELTLLKHRYAPEFKAALEAALRGLPARERNFLR 282

Query: 245 ARRLQENPVTLENLSSEFE-----VS------RERV-----RQIEAR 275
              L    +T+E ++         VS      RERV     RQ++ R
Sbjct: 283 LFFL--ESLTVEQIARMDGTHKSTVSRRMASARERVLTGMRRQLQER 327


>gi|51895595|gb|AAU13829.1| SigE [Pasteuria ramosa]
          Length = 99

 Score = 42.5 bits (99), Expect = 0.074,   Method: Composition-based stats.
 Identities = 19/85 (22%), Positives = 37/85 (43%), Gaps = 7/85 (8%)

Query: 177 NCRLAGDESLNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
           N ++  + S +  +N   D N     D L  ++D     +    E +  + +L  ++S+L
Sbjct: 19  NNKIRSEISFDEPLNIDWDGNELLLSDVLGTEND----TIYRDIEDEVDKEILRTALSML 74

Query: 236 NPRERRIFEARR--LQENPVTLENL 258
           + RERRI   R         T +++
Sbjct: 75  SDRERRIVILRFGLGGGEEKTQKDV 99


>gi|325262960|ref|ZP_08129696.1| RNA polymerase sigma factor RpoD [Clostridium sp. D5]
 gi|324032054|gb|EGB93333.1| RNA polymerase sigma factor RpoD [Clostridium sp. D5]
          Length = 75

 Score = 42.5 bits (99), Expect = 0.075,   Method: Composition-based stats.
 Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 1/52 (1%)

Query: 2  NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRL 53
           + NM         +  Y+ +  K  +L K++EY LA R ++ GD  A ++L
Sbjct: 10 TKVNMVEDSEEMDTVKHYLKQAGKAKLLNKKDEYALAVRAKQ-GDDEAKNKL 60


>gi|300786258|ref|YP_003766549.1| RNA polymerase sigma-70 factor, ECF subfamily [Amycolatopsis
           mediterranei U32]
 gi|299795772|gb|ADJ46147.1| RNA polymerase sigma-70 factor, ECF subfamily [Amycolatopsis
           mediterranei U32]
          Length = 208

 Score = 42.5 bits (99), Expect = 0.075,   Method: Composition-based stats.
 Identities = 19/79 (24%), Positives = 32/79 (40%), Gaps = 7/79 (8%)

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV---SRERVRQIE 273
           E  ER    +  +  +  L PR+R I   R +    +T E  ++   +      RV Q  
Sbjct: 134 EAAERSAALDWSSGLLDTLPPRQREILVLRIILG--MTAEETAAAVGLGSPGAVRVAQ-- 189

Query: 274 ARAFKKVQESIQKQVELSS 292
            RA   ++ S+    E +S
Sbjct: 190 HRALATLRRSLADHREAAS 208


>gi|306519584|ref|ZP_07405931.1| hypothetical protein CdifQ_05397 [Clostridium difficile QCD-32g58]
          Length = 164

 Score = 42.5 bits (99), Expect = 0.075,   Method: Composition-based stats.
 Identities = 18/72 (25%), Positives = 33/72 (45%), Gaps = 6/72 (8%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLP-----ISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           +LV ++L LV      +    +        E   EG IGL +A   +D  RG + +T ++
Sbjct: 8   KLVENNLNLVHFSINRFFKSYVEQHPYLYEEFYQEGCIGLYKAALNYDSNRG-KFSTVAV 66

Query: 107 WWIKAAMQEYIL 118
            +I+  M + + 
Sbjct: 67  SYIRIEMFKALR 78


>gi|284042902|ref|YP_003393242.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Conexibacter
           woesei DSM 14684]
 gi|283947123|gb|ADB49867.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Conexibacter
           woesei DSM 14684]
          Length = 510

 Score = 42.5 bits (99), Expect = 0.075,   Method: Composition-based stats.
 Identities = 22/113 (19%), Positives = 46/113 (40%), Gaps = 8/113 (7%)

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
           +   +V +   + A +++L+    +  + S +  + L  +    E    E          
Sbjct: 83  MRPQQVRAYLTQTALNKALDEGKRARRRTSVELDEGL--EVAAGEPTADELLSESWDGAR 140

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV--RQIEARAFK 278
           L   ++ L  R++ I + R   +   T E +     V+ ERV  R++E RA +
Sbjct: 141 LREIVAELPERQQAIVKLRFFFD--RTPEEIQRYLGVT-ERVYRRELE-RAMR 189


>gi|224539027|ref|ZP_03679566.1| hypothetical protein BACCELL_03926 [Bacteroides cellulosilyticus
           DSM 14838]
 gi|224519355|gb|EEF88460.1| hypothetical protein BACCELL_03926 [Bacteroides cellulosilyticus
           DSM 14838]
          Length = 182

 Score = 42.5 bits (99), Expect = 0.075,   Method: Composition-based stats.
 Identities = 18/88 (20%), Positives = 36/88 (40%), Gaps = 1/88 (1%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE  LA R R+ GD  A   L   +   ++ + + Y G      +++ +G + L  +  K
Sbjct: 2   EEQELAGRCRQ-GDNLARKELYERYAGRMLSVCLRYAGDRDTAEDLMHDGFLKLFDSFDK 60

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRS 120
           F       L  +    +     +Y+ ++
Sbjct: 61  FTWRGDGSLRAWMERVMVNTALQYLRKN 88


>gi|160882822|ref|ZP_02063825.1| hypothetical protein BACOVA_00784 [Bacteroides ovatus ATCC 8483]
 gi|237716460|ref|ZP_04546941.1| ECF-type sigma factor [Bacteroides sp. D1]
 gi|260170290|ref|ZP_05756702.1| ECF-type sigma factor [Bacteroides sp. D2]
 gi|293370750|ref|ZP_06617297.1| sigma-70, region 4 [Bacteroides ovatus SD CMC 3f]
 gi|294645051|ref|ZP_06722777.1| sigma-70, region 4 [Bacteroides ovatus SD CC 2a]
 gi|294809908|ref|ZP_06768583.1| sigma-70, region 4 [Bacteroides xylanisolvens SD CC 1b]
 gi|315918651|ref|ZP_07914891.1| ECF-type sigma factor [Bacteroides sp. D2]
 gi|156111846|gb|EDO13591.1| hypothetical protein BACOVA_00784 [Bacteroides ovatus ATCC 8483]
 gi|229444107|gb|EEO49898.1| ECF-type sigma factor [Bacteroides sp. D1]
 gi|292634183|gb|EFF52725.1| sigma-70, region 4 [Bacteroides ovatus SD CMC 3f]
 gi|292639557|gb|EFF57849.1| sigma-70, region 4 [Bacteroides ovatus SD CC 2a]
 gi|294442899|gb|EFG11691.1| sigma-70, region 4 [Bacteroides xylanisolvens SD CC 1b]
 gi|295084149|emb|CBK65672.1| RNA polymerase sigma factor, sigma-70 family [Bacteroides
           xylanisolvens XB1A]
 gi|313692526|gb|EFS29361.1| ECF-type sigma factor [Bacteroides sp. D2]
          Length = 183

 Score = 42.5 bits (99), Expect = 0.076,   Method: Composition-based stats.
 Identities = 17/86 (19%), Positives = 41/86 (47%), Gaps = 2/86 (2%)

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
           + +  ++  +      E   +E+E+RKN  +++ R +  L+PR+R       ++E     
Sbjct: 96  SDTAVEEVSISTPTDVEDDYMEEEQRKNEFSLVRRLLDQLSPRQREALTLYYIEEKKY-- 153

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           E++     ++ + VR +  R   K++
Sbjct: 154 EDICEIMNMNYQSVRNLMHRGLTKLR 179


>gi|255027365|ref|ZP_05299351.1| RNA polymerase factor sigma-70 [Listeria monocytogenes FSL J2-003]
          Length = 83

 Score = 42.5 bits (99), Expect = 0.077,   Method: Composition-based stats.
 Identities = 16/78 (20%), Positives = 34/78 (43%), Gaps = 1/78 (1%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           QEE  + +  R  GD  A     + +  ++   +  Y   G    +++ E  IGL +A++
Sbjct: 7   QEELAMLELAR-SGDTEALEYFFSKYQSVIYWKSTQYFLQGAERDDLIQEAMIGLFKAIR 65

Query: 92  KFDPERGFRLATYSMWWI 109
            +D  +     +++   I
Sbjct: 66  DYDKTKEASFRSFAEMCI 83


>gi|160883163|ref|ZP_02064166.1| hypothetical protein BACOVA_01132 [Bacteroides ovatus ATCC 8483]
 gi|237719125|ref|ZP_04549606.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 2_2_4]
 gi|156111388|gb|EDO13133.1| hypothetical protein BACOVA_01132 [Bacteroides ovatus ATCC 8483]
 gi|229451504|gb|EEO57295.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 2_2_4]
 gi|295086516|emb|CBK68039.1| RNA polymerase sigma factor, sigma-70 family [Bacteroides
           xylanisolvens XB1A]
          Length = 196

 Score = 42.5 bits (99), Expect = 0.077,   Method: Composition-based stats.
 Identities = 20/119 (16%), Positives = 51/119 (42%), Gaps = 2/119 (1%)

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           ++L + E ++     R   ++ ++      D +S + ++         E+  I  EE   
Sbjct: 58  ERLCIDEKKIKFYLLRSVRNQLIDWERTKKDTSSIEEEERSFKLSVSVEESFISDEEDLL 117

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            +  + R + +L   +R I     ++E P   E ++   ++  + VR    +A +K+++
Sbjct: 118 LKKRVNRILDLLTDHQREIVYLHFIEEMPY--EEIAVMLDMKIQTVRGQVFKAMEKLRK 174


>gi|296446714|ref|ZP_06888653.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Methylosinus
           trichosporium OB3b]
 gi|296255717|gb|EFH02805.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Methylosinus
           trichosporium OB3b]
          Length = 165

 Score = 42.5 bits (99), Expect = 0.078,   Method: Composition-based stats.
 Identities = 15/84 (17%), Positives = 39/84 (46%), Gaps = 2/84 (2%)

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
            +    +    E  + +  E  +R  +L ++++ L P+ R +F  R  +E P   + ++ 
Sbjct: 83  PEDSAPETPAPEISVEQSLEAGHRAELLAQAIATLPPKCREVFVMRMHEELP--QDEIAR 140

Query: 261 EFEVSRERVRQIEARAFKKVQESI 284
              +SR  V +    A ++ ++++
Sbjct: 141 RLGISRNMVDRHLRIAIRRCRQAV 164


>gi|313906563|ref|ZP_07839891.1| RNA polymerase alpha subunit domain protein [Eubacterium
           cellulosolvens 6]
 gi|313468593|gb|EFR63967.1| RNA polymerase alpha subunit domain protein [Eubacterium
           cellulosolvens 6]
          Length = 976

 Score = 42.5 bits (99), Expect = 0.079,   Method: Composition-based stats.
 Identities = 16/52 (30%), Positives = 29/52 (55%), Gaps = 3/52 (5%)

Query: 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           V++ R +   + R   E   TLE ++ +  ++RERVRQ+   + KKV+   +
Sbjct: 359 VIDDRSKTFIQRRLQGE---TLEAIALDTGLTRERVRQVVKASIKKVKNQYR 407


>gi|189467297|ref|ZP_03016082.1| hypothetical protein BACINT_03684 [Bacteroides intestinalis DSM
           17393]
 gi|189435561|gb|EDV04546.1| hypothetical protein BACINT_03684 [Bacteroides intestinalis DSM
           17393]
          Length = 182

 Score = 42.5 bits (99), Expect = 0.079,   Method: Composition-based stats.
 Identities = 18/88 (20%), Positives = 36/88 (40%), Gaps = 1/88 (1%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE  LA R R+ GD  A   L   +   ++ + + Y G      +++ +G + L  +  K
Sbjct: 2   EEQELAGRCRQ-GDNLARKELYERYAGRMLSVCLRYAGDRETAEDLMHDGFLKLFDSFDK 60

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRS 120
           F       L  +    +     +Y+ ++
Sbjct: 61  FTWRGDGSLRAWMERVMVNTALQYLRKN 88


>gi|219666176|ref|YP_002456611.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Desulfitobacterium
           hafniense DCB-2]
 gi|219536436|gb|ACL18175.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Desulfitobacterium
           hafniense DCB-2]
          Length = 200

 Score = 42.5 bits (99), Expect = 0.079,   Method: Composition-based stats.
 Identities = 15/86 (17%), Positives = 37/86 (43%), Gaps = 2/86 (2%)

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           D    D   +E   +E  E    ++ L ++++ L+ RE+ I   +   +  ++   ++  
Sbjct: 111 DGYTRDIVAREPEPVEIVELNELQHHLLKAIASLSQREQEIIALKFWSD--LSNREIAKL 168

Query: 262 FEVSRERVRQIEARAFKKVQESIQKQ 287
             +S      I  RA ++++  +  Q
Sbjct: 169 VGISESNTGVILFRAMRQLRLILASQ 194


>gi|311068891|ref|YP_003973814.1| hypothetical protein BATR1942_09750 [Bacillus atrophaeus 1942]
 gi|310869408|gb|ADP32883.1| hypothetical protein BATR1942_09750 [Bacillus atrophaeus 1942]
          Length = 247

 Score = 42.5 bits (99), Expect = 0.080,   Method: Composition-based stats.
 Identities = 19/97 (19%), Positives = 43/97 (44%), Gaps = 4/97 (4%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGY----RGYGLPISEVVSEGNI 84
           L   E   LA  Y+   + +  + L+++   L   +A  +    RG  +P  + V E  +
Sbjct: 9   LTNIEINALAMEYKATREEAVFNTLMSAVKDLAENLAYKFYNNSRGLNVPEDDFVQEAYL 68

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
            +  ++  +D E+G     +    ++  +Q+ I++S 
Sbjct: 69  AVYSSIDSYDVEKGSYFTAHLKRCVEWKIQDNIIKSS 105


>gi|323342431|ref|ZP_08082663.1| sigma-70 region 2 subfamily protein [Erysipelothrix rhusiopathiae
           ATCC 19414]
 gi|322463543|gb|EFY08737.1| sigma-70 region 2 subfamily protein [Erysipelothrix rhusiopathiae
           ATCC 19414]
          Length = 203

 Score = 42.5 bits (99), Expect = 0.080,   Method: Composition-based stats.
 Identities = 32/223 (14%), Positives = 68/223 (30%), Gaps = 63/223 (28%)

Query: 47  LSAAHRLVTSHLRLVVKIAMG-YRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
             A   ++    RL+ K A   Y      G+ I ++  EG +G   A+  F   +    A
Sbjct: 16  EDALDIVMGKFKRLLWKRAYELYTQQKPIGISIEDLFQEGFLGFYDAIYTFKEIKDVGFA 75

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
            Y    + + M+                        LR+ +     + D+          
Sbjct: 76  YYVNLCVISTMRTA----------------------LRKCRSQSYKLLDSKW-------- 105

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
                                 SL+  +  ++  S    D +       + V++     +
Sbjct: 106 ----------------------SLDLFV--TEDKSVYLADMIESQDITSDPVVV--AHYQ 139

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
           + R +  + +  ++ +ER I+  R   E       ++  F +S
Sbjct: 140 DARKIERKVLETISEKERVIYTMR---EEGFGYREIAERFNIS 179


>gi|94313162|ref|YP_586371.1| two component LuxR family transcriptional regulator [Cupriavidus
           metallidurans CH34]
 gi|93357014|gb|ABF11102.1| two component transcriptional regulator, LuxR family [Cupriavidus
           metallidurans CH34]
          Length = 215

 Score = 42.5 bits (99), Expect = 0.080,   Method: Composition-based stats.
 Identities = 25/144 (17%), Positives = 50/144 (34%), Gaps = 6/144 (4%)

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
           F+L      LQ I         V  I   +N S   V  M   +A   S         ++
Sbjct: 58  FSLNEAGDGLQLIGRIKRMRPDVAVIVFSMNASPPAVRDM---IAAGASAFVSKTCGTRD 114

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
            ++    ++          +     ++       ++  L+PRER +     L    ++L 
Sbjct: 115 VAEACRVVLAGRKFVAPASLAHLLDQDDGGTPQAALQRLSPREREVLR---LLAQGLSLR 171

Query: 257 NLSSEFEVSRERVRQIEARAFKKV 280
            +++ F  SR+ +   +  A  K+
Sbjct: 172 EIAARFNRSRKTISVQKCAAMAKL 195


>gi|294785122|ref|ZP_06750410.1| RNA polymerase sigma factor [Fusobacterium sp. 3_1_27]
 gi|294486836|gb|EFG34198.1| RNA polymerase sigma factor [Fusobacterium sp. 3_1_27]
          Length = 274

 Score = 42.5 bits (99), Expect = 0.081,   Method: Composition-based stats.
 Identities = 28/127 (22%), Positives = 51/127 (40%), Gaps = 5/127 (3%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V  +L+ V ++A+     G+   ++  EG IGL++A + F+ ++ F+L  Y  ++I   +
Sbjct: 84  VEKNLKKVYEMALYMLREGISYDDLTQEGIIGLIKAHELFEEDKDFKL--YKDYYIAREI 141

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
             YI    +  K       K        LK  L+   D N   E      +       E+
Sbjct: 142 FNYINNYANYRKSAFKDYAKHEIHKNNHLKVSLK---DRNKSEELKKLEKENKEKHIEEI 198

Query: 174 ISMNCRL 180
             +  R 
Sbjct: 199 KQLEKRA 205


>gi|116332311|ref|YP_802029.1| RNA polymerase sigma subunit [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
 gi|116126000|gb|ABJ77271.1| RNA polymerase sigma subunit [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
          Length = 196

 Score = 42.5 bits (99), Expect = 0.081,   Method: Composition-based stats.
 Identities = 14/68 (20%), Positives = 32/68 (47%), Gaps = 2/68 (2%)

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
              E  ++EK ++ + +N++   + +++P  + +   R  Q     LE +S    +S   
Sbjct: 112 PSPEFSVLEKIDQSDVKNIIDSLLDIISPEYKEVLLLRYQQNLK--LEEISKILGISISG 169

Query: 269 VRQIEARA 276
           V ++  RA
Sbjct: 170 VSRLIERA 177


>gi|82523834|emb|CAI78576.1| RNA polymerase sigma-E factor [uncultured candidate division OP8
           bacterium]
          Length = 239

 Score = 42.5 bits (99), Expect = 0.082,   Method: Composition-based stats.
 Identities = 16/87 (18%), Positives = 32/87 (36%), Gaps = 1/87 (1%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
             + GD +A  +L   H   V  +A+ Y  +     +VV E  + +   ++ FD E    
Sbjct: 65  IAKEGDPAALEQLFMRHAARVFHLALRYVCFREDAEDVVQETFLKVHDGIRSFDLELSAG 124

Query: 101 LATYSMW-WIKAAMQEYILRSWSLVKI 126
            + +     I  A+           ++
Sbjct: 125 FSAWINRICIHCAIDYLRAGKRRGRRM 151


>gi|239625074|ref|ZP_04668105.1| LOW QUALITY PROTEIN: RNA polymerase sigma-B factor [Clostridiales
           bacterium 1_7_47_FAA]
 gi|239521460|gb|EEQ61326.1| LOW QUALITY PROTEIN: RNA polymerase sigma-B factor [Clostridiales
           bacterium 1_7_47FAA]
          Length = 180

 Score = 42.5 bits (99), Expect = 0.083,   Method: Composition-based stats.
 Identities = 11/91 (12%), Positives = 42/91 (46%), Gaps = 6/91 (6%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
            +  +  D++  +     + ++         + L  ++ +L+  E+ + +A     + ++
Sbjct: 95  DSEGKPLDFIADEAADIAETVVNAVMV----DRLKAALPLLSDSEQELIQAIFF--DGLS 148

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              + + F +++  V + +AR  +K+++ I+
Sbjct: 149 EREVGARFGITQSVVNKRKARILRKLRKIIE 179


>gi|260171948|ref|ZP_05758360.1| putative RNA polymerase ECF-type sigma factor [Bacteroides sp. D2]
          Length = 196

 Score = 42.5 bits (99), Expect = 0.083,   Method: Composition-based stats.
 Identities = 20/119 (16%), Positives = 51/119 (42%), Gaps = 2/119 (1%)

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           ++L + E ++     R   ++ ++      D +S + ++         E+  I  EE   
Sbjct: 58  ERLCIDEKKIKFYLLRSVRNQLIDWERTKKDTSSIEEEERSFKLSVSVEESFISDEEDLL 117

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            +  + R + +L   +R I     ++E P   E ++   ++  + VR    +A +K+++
Sbjct: 118 LKKRVNRILDLLTDHQREIVYLHFIEEMPY--EEIAVMLDMKIQTVRGQVFKAMEKLRK 174


>gi|300782138|ref|YP_003762429.1| RNA polymerase ECF sigma factor [Amycolatopsis mediterranei U32]
 gi|299791652|gb|ADJ42027.1| RNA polymerase ECF sigma factor [Amycolatopsis mediterranei U32]
          Length = 170

 Score = 42.5 bits (99), Expect = 0.084,   Method: Composition-based stats.
 Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 2/58 (3%)

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +R  LT  +  L  RER +   R   + P    +++ E  VS   V+   +RA  K++
Sbjct: 99  QRAWLTAVLKTLTARERAVVVLRHFFDLPE--ADVARELGVSLGTVKSTNSRALAKLR 154


>gi|116669094|ref|YP_830027.1| ECF subfamily RNA polymerase sigma-24 factor [Arthrobacter sp.
           FB24]
 gi|116609203|gb|ABK01927.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Arthrobacter sp.
           FB24]
          Length = 184

 Score = 42.5 bits (99), Expect = 0.084,   Method: Composition-based stats.
 Identities = 11/54 (20%), Positives = 27/54 (50%), Gaps = 2/54 (3%)

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
             + VL   ++ +   R + +  +T+E ++     S   V+Q++ RA  +++E 
Sbjct: 124 ELLDVLGEDQKEVLTLRIIAD--LTVEQVAEIMGKSAGAVKQLQRRALDRLREH 175


>gi|332668463|ref|YP_004451479.1| ECF subfamily RNA polymerase sigma-24 subunit [Haliscomenobacter
           hydrossis DSM 1100]
 gi|332337508|gb|AEE54606.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Haliscomenobacter
           hydrossis DSM 1100]
          Length = 193

 Score = 42.5 bits (99), Expect = 0.085,   Method: Composition-based stats.
 Identities = 14/76 (18%), Positives = 34/76 (44%), Gaps = 2/76 (2%)

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
                 E+ LI +E+ +  + +L++ + +L  R+ +    R           ++    ++
Sbjct: 107 DAEASIEESLIAQEQSEEYKQILSKGLVLLPQRQLQAVHLRFFDNLDTG--EIAEIMGMN 164

Query: 266 RERVRQIEARAFKKVQ 281
            + VR I +RA  K++
Sbjct: 165 EQSVRNIISRALHKLR 180


>gi|331701826|ref|YP_004398785.1| RNA polymerase sigma factor, sigma-70 family [Lactobacillus
           buchneri NRRL B-30929]
 gi|329129169|gb|AEB73722.1| RNA polymerase sigma factor, sigma-70 family [Lactobacillus
           buchneri NRRL B-30929]
          Length = 185

 Score = 42.5 bits (99), Expect = 0.085,   Method: Composition-based stats.
 Identities = 13/93 (13%), Positives = 36/93 (38%), Gaps = 1/93 (1%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L ++  +  +  A  +L   +  +V K    Y   G    ++  E  + L ++  +F+ 
Sbjct: 8   ELIRQTAKR-NEEAFAQLFHQYYPIVRKYKRQYYINGYDKDDLDQEARMVLFRSACRFES 66

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
            R     T+    ++  + + I  + +  ++  
Sbjct: 67  ARKVSFGTFFSHNLRNRLFDLIRTNNAQKRVPV 99


>gi|169158283|emb|CAQ15556.1| novel protein similar to vertebrate centrosomal protein 350kDa
           (CEP350) [Danio rerio]
          Length = 1800

 Score = 42.5 bits (99), Expect = 0.086,   Method: Composition-based stats.
 Identities = 31/184 (16%), Positives = 66/184 (35%), Gaps = 17/184 (9%)

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA---- 163
           W++   +    +            Q+ L   L++ +  ++ + + N    +   +     
Sbjct: 401 WLEHQKRRLRDKGEDDKMPPLRKKQRGLIMKLQQEQAEIKRLQEANKAARRERQLLLKQQ 460

Query: 164 KKLNVSESEVISMNCRL--AGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE--KE 219
           +++       + +  RL  AGD  + + + S    SS     +V D D +    +     
Sbjct: 461 EEIERMRHTTLKLKERLKTAGDTKMESPV-SGVAESSAPPSVIVTDADTRSPSPMSVSGS 519

Query: 220 ERKNRRNMLTRSMSV-----LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
           E  +    L +  S      L  RE+++ + RR  E    L       +V    VR++E 
Sbjct: 520 ETSSIMQKLKKMRSHMDEKFLTKREQQLMQRRRHAEE---LLEWRQRLDVEEAEVRRMEK 576

Query: 275 RAFK 278
           +A  
Sbjct: 577 QALA 580


>gi|65317222|ref|ZP_00390181.1| COG1595: DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog [Bacillus anthracis str. A2012]
 gi|165870076|ref|ZP_02214733.1| putative sigma factor [Bacillus anthracis str. A0488]
 gi|167641819|ref|ZP_02400060.1| putative sigma factor [Bacillus anthracis str. A0193]
 gi|170708957|ref|ZP_02899389.1| putative sigma factor [Bacillus anthracis str. A0389]
 gi|177654050|ref|ZP_02936060.1| putative sigma factor [Bacillus anthracis str. A0174]
 gi|227818013|ref|YP_002818022.1| putative sigma factor [Bacillus anthracis str. CDC 684]
 gi|229603576|ref|YP_002869467.1| putative sigma factor [Bacillus anthracis str. A0248]
 gi|254735179|ref|ZP_05192888.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. Western
           North America USA6153]
 gi|254755687|ref|ZP_05207720.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. Vollum]
 gi|254759582|ref|ZP_05211607.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. Australia
           94]
 gi|164714399|gb|EDR19919.1| putative sigma factor [Bacillus anthracis str. A0488]
 gi|167510231|gb|EDR85636.1| putative sigma factor [Bacillus anthracis str. A0193]
 gi|170126122|gb|EDS95017.1| putative sigma factor [Bacillus anthracis str. A0389]
 gi|172080933|gb|EDT66012.1| putative sigma factor [Bacillus anthracis str. A0174]
 gi|227002542|gb|ACP12285.1| putative sigma factor [Bacillus anthracis str. CDC 684]
 gi|229267984|gb|ACQ49621.1| putative sigma factor [Bacillus anthracis str. A0248]
          Length = 156

 Score = 42.5 bits (99), Expect = 0.086,   Method: Composition-based stats.
 Identities = 16/64 (25%), Positives = 33/64 (51%), Gaps = 2/64 (3%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++        MSVL+ +E+ I   R       T+  ++ E E++  +VR I  +A +K++
Sbjct: 94  EDIEMKAKDFMSVLDEKEKYIIFERFFVG--KTMGEIALETEMTYYQVRWIYRQALEKMR 151

Query: 282 ESIQ 285
            S++
Sbjct: 152 NSLR 155


>gi|94313156|ref|YP_586365.1| two component LuxR family transcriptional regulator [Cupriavidus
           metallidurans CH34]
 gi|93357008|gb|ABF11096.1| Two component transcriptional regulator, Signal receiver domain
           LuxR family [Cupriavidus metallidurans CH34]
          Length = 215

 Score = 42.1 bits (98), Expect = 0.088,   Method: Composition-based stats.
 Identities = 25/144 (17%), Positives = 50/144 (34%), Gaps = 6/144 (4%)

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
           F+L      LQ I         V  I   +N S   V  M   +A   S         ++
Sbjct: 58  FSLNEAGDGLQLIGRIKRMRPDVAVIVFSMNASPPAVRDM---IAAGASAFVSKTCGTRD 114

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
            ++    ++          +     ++       ++  L+PRER +     L    ++L 
Sbjct: 115 VAEACRVVLAGRKFVAPASLAHLLDQDDGGTPQAALQRLSPREREVLR---LLAQGLSLR 171

Query: 257 NLSSEFEVSRERVRQIEARAFKKV 280
            +++ F  SR+ +   +  A  K+
Sbjct: 172 EIAARFNRSRKTISVQKCAAMAKL 195


>gi|221195040|ref|ZP_03568096.1| RNA polymerase sigma factor, sigma-70 family [Atopobium rimae ATCC
           49626]
 gi|221184943|gb|EEE17334.1| RNA polymerase sigma factor, sigma-70 family [Atopobium rimae ATCC
           49626]
          Length = 622

 Score = 42.1 bits (98), Expect = 0.089,   Method: Composition-based stats.
 Identities = 24/103 (23%), Positives = 48/103 (46%), Gaps = 6/103 (5%)

Query: 185 SLNALINSSD--KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
           S NA I ++D   ++S   D++    D   ++  +  E  + + ++   +  L   +++ 
Sbjct: 132 SDNAPILNTDYTNDTSDSSDYIESLADDTLELPEDVVENTSTQQIIRGFIQELPKDQQKF 191

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVR-QIEARAFKKVQESI 284
             AR   E  +    ++  F +    VR Q+ +RA K +QESI
Sbjct: 192 LVARYFAE--MNAAQIAETFGIPAGTVRSQL-SRARKTLQESI 231


>gi|294643366|ref|ZP_06721186.1| sigma-70, region 4 [Bacteroides ovatus SD CC 2a]
 gi|294810470|ref|ZP_06769125.1| sigma-70, region 4 [Bacteroides xylanisolvens SD CC 1b]
 gi|292641303|gb|EFF59501.1| sigma-70, region 4 [Bacteroides ovatus SD CC 2a]
 gi|294442316|gb|EFG11128.1| sigma-70, region 4 [Bacteroides xylanisolvens SD CC 1b]
          Length = 204

 Score = 42.1 bits (98), Expect = 0.090,   Method: Composition-based stats.
 Identities = 17/93 (18%), Positives = 44/93 (47%), Gaps = 2/93 (2%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
               + ++ +       E + I  E+ K  +  +   MSVL  R+R I   R ++E  ++
Sbjct: 114 DEIGEREETVDESPSTPETIYINNEQEKQVQATVHTMMSVLTDRQREIIYYRYIKE--MS 171

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++ +S   +++ + V     RA  ++++  +++
Sbjct: 172 IDEISKVTDMNNQSVSNSIQRALGRIRDLFKRK 204


>gi|150018495|ref|YP_001310749.1| RNA polymerase factor sigma-70 [Clostridium beijerinckii NCIMB
           8052]
 gi|149904960|gb|ABR35793.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           beijerinckii NCIMB 8052]
          Length = 181

 Score = 42.1 bits (98), Expect = 0.090,   Method: Composition-based stats.
 Identities = 16/90 (17%), Positives = 39/90 (43%), Gaps = 10/90 (11%)

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
               +  +     +++ E+  +   RN L   ++ L P +R IF  +         E+++
Sbjct: 96  LHVSIEDEEISTNELVEEEIIKLEERNELINLINTLEPMDRDIFIMKFFLGEKS--EDIA 153

Query: 260 SEFEVSRE----RVRQIEARAFKKVQESIQ 285
            +F ++R     R+     R  KK++ +++
Sbjct: 154 RKFGLTRAALDNRI----YRGKKKLRLNLE 179


>gi|258514229|ref|YP_003190451.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Desulfotomaculum
           acetoxidans DSM 771]
 gi|257777934|gb|ACV61828.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Desulfotomaculum
           acetoxidans DSM 771]
          Length = 180

 Score = 42.1 bits (98), Expect = 0.091,   Method: Composition-based stats.
 Identities = 17/72 (23%), Positives = 31/72 (43%), Gaps = 6/72 (8%)

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQI 272
             E      RR  L +++S LN R+R I   +      N      +S    ++R  V  I
Sbjct: 109 PEEAAICNERREELFQALSCLNDRQRNIISLKFAFGLNNK----EISEITGLTRSNVAVI 164

Query: 273 EARAFKKVQESI 284
             RA ++++ ++
Sbjct: 165 IYRALQRMRSNL 176


>gi|167747614|ref|ZP_02419741.1| hypothetical protein ANACAC_02335 [Anaerostipes caccae DSM 14662]
 gi|167652976|gb|EDR97105.1| hypothetical protein ANACAC_02335 [Anaerostipes caccae DSM 14662]
          Length = 135

 Score = 42.1 bits (98), Expect = 0.092,   Method: Composition-based stats.
 Identities = 11/91 (12%), Positives = 42/91 (46%), Gaps = 6/91 (6%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
            +  +  D++  +     + ++         + L  ++ +L+  E+ + +A     + ++
Sbjct: 50  DSEGKPLDFIADEAADIAETVVNAVMV----DRLKAALPLLSDSEQELIQAIFF--DGLS 103

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              + + F +++  V + +AR  +K+++ I+
Sbjct: 104 EREVGARFGITQSVVNKRKARILRKLRKIIE 134


>gi|83748017|ref|ZP_00945047.1| hypothetical protein RRSL_02545 [Ralstonia solanacearum UW551]
 gi|207742058|ref|YP_002258450.1| extracytoplasmic function sigma factor protein [Ralstonia
           solanacearum IPO1609]
 gi|83725319|gb|EAP72467.1| hypothetical protein RRSL_02545 [Ralstonia solanacearum UW551]
 gi|206593445|emb|CAQ60372.1| extracytoplasmic function sigma factor protein [Ralstonia
           solanacearum IPO1609]
          Length = 196

 Score = 42.1 bits (98), Expect = 0.092,   Method: Composition-based stats.
 Identities = 22/98 (22%), Positives = 41/98 (41%), Gaps = 2/98 (2%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           V D    E    +      +   L  +++ L PR R++F   RL +  +T E ++    +
Sbjct: 90  VPDLHCHEMDGAKHVHLTQQIEALRVAINNLPPRCRQVFLLHRLHD--MTQEGVAQALGI 147

Query: 265 SRERVRQIEARAFKKVQESIQKQVELSSSPPLLQKPRY 302
           SR  V +  ARA + ++  +       +S P    P +
Sbjct: 148 SRNMVARHVARAMQDLRPLLNGGARADASVPAYGTPAF 185


>gi|221135438|ref|ZP_03561741.1| RNA polymerase sigma factor RpoE [Glaciecola sp. HTCC2999]
          Length = 193

 Score = 42.1 bits (98), Expect = 0.093,   Method: Composition-based stats.
 Identities = 21/132 (15%), Positives = 43/132 (32%), Gaps = 2/132 (1%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A + LV  +   V  I   Y      +++V  E  I   +A+  F  +      
Sbjct: 15  KEGDKKAFNLLVLKYQNRVTNIVSRYIKNNGDVADVTQEAFIKAYRALPNFRGD--SAFY 72

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           T+       + + Y++             Q+  F+        + +     L  E   A+
Sbjct: 73  TWLYRIAVNSAKNYLVSQSRKPPASDVDAQEAEFYEGADALREVASPESKLLTKEIETAL 132

Query: 163 AKKLNVSESEVI 174
            + +     E+ 
Sbjct: 133 LRAIERLPDELR 144


>gi|107022705|ref|YP_621032.1| extracytoplasmic-function sigma-70 factor [Burkholderia cenocepacia
           AU 1054]
 gi|116689654|ref|YP_835277.1| extracytoplasmic-function sigma-70 factor PvdS [Burkholderia
           cenocepacia HI2424]
 gi|170732955|ref|YP_001764902.1| extracytoplasmic-function sigma-70 factor [Burkholderia cenocepacia
           MC0-3]
 gi|254245473|ref|ZP_04938794.1| Sigma-70 region 2 [Burkholderia cenocepacia PC184]
 gi|105892894|gb|ABF76059.1| RNA polymerase, sigma-24 subunit, RpoE [Burkholderia cenocepacia AU
           1054]
 gi|116647743|gb|ABK08384.1| RNA polymerase, sigma-24 subunit, RpoE [Burkholderia cenocepacia
           HI2424]
 gi|124870249|gb|EAY61965.1| Sigma-70 region 2 [Burkholderia cenocepacia PC184]
 gi|169816197|gb|ACA90780.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Burkholderia
           cenocepacia MC0-3]
          Length = 222

 Score = 42.1 bits (98), Expect = 0.093,   Method: Composition-based stats.
 Identities = 19/97 (19%), Positives = 39/97 (40%), Gaps = 2/97 (2%)

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             + ++   R+  + S++A    S +N    ++   +D    E         ++    + 
Sbjct: 90  VRQPVAYVTRMVRNASIDACRRQSLENVYHTEEDDGFDVPSPEPTPEAALMTRDTLRRVW 149

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
            ++  L  R R  FE  RL+E   TL+  +    VS+
Sbjct: 150 AALDDLPARSRAAFEMVRLREE--TLQTAARALNVSQ 184


>gi|228994359|ref|ZP_04154243.1| RNA polymerase sigma factor [Bacillus pseudomycoides DSM 12442]
 gi|228765376|gb|EEM14046.1| RNA polymerase sigma factor [Bacillus pseudomycoides DSM 12442]
          Length = 157

 Score = 42.1 bits (98), Expect = 0.094,   Method: Composition-based stats.
 Identities = 15/74 (20%), Positives = 35/74 (47%), Gaps = 2/74 (2%)

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           Q +++        +     MS+L+ +E+ I   R      +    ++ E E++  +VR +
Sbjct: 86  QEMLQNVCGAEVSSETQDYMSLLDEKEKHIIYERFYAGKKI--HEIAEEMEMTYHQVRWV 143

Query: 273 EARAFKKVQESIQK 286
             +A  K++ SI++
Sbjct: 144 YRQALGKMRSSIRE 157


>gi|284109795|ref|ZP_06386501.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Candidatus
           Poribacteria sp. WGA-A3]
 gi|283829801|gb|EFC34101.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Candidatus
           Poribacteria sp. WGA-A3]
          Length = 969

 Score = 42.1 bits (98), Expect = 0.095,   Method: Composition-based stats.
 Identities = 20/99 (20%), Positives = 39/99 (39%), Gaps = 10/99 (10%)

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I S D   +   + L Y     E+  +E    + RR ++   +  L   ER +     L 
Sbjct: 93  IKSLDAMPTAQLEELCYTQ--YERNHLEAAAIEQRRELVKSLLKKLPESERTVVTLFYLA 150

Query: 250 ENPVTLENLSSEFEVSRERVR-QIEARAFKKVQESIQKQ 287
           E  ++   +S    VS   VR ++        ++ ++K+
Sbjct: 151 E--MSGAEISQFLGVSPNTVRSRLHRA-----RQRLEKE 182


>gi|134295684|ref|YP_001119419.1| extracytoplasmic-function sigma-70 factor [Burkholderia
           vietnamiensis G4]
 gi|134138841|gb|ABO54584.1| RNA polymerase, sigma-24 subunit, RpoE [Burkholderia vietnamiensis
           G4]
          Length = 221

 Score = 42.1 bits (98), Expect = 0.095,   Method: Composition-based stats.
 Identities = 19/97 (19%), Positives = 39/97 (40%), Gaps = 2/97 (2%)

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             + ++   R+  + S++AL   S ++     +   +D    E         ++    + 
Sbjct: 89  VRQPVAYVTRMVRNASIDALRRQSFESIHHTDEDDGFDVPSPEPTPEAALMTRDALRRVC 148

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
            ++  L  R R  FE  RL+E   TL+  +    VS+
Sbjct: 149 AALDDLPARSRAAFEMVRLREE--TLQTAARALNVSQ 183


>gi|227536386|ref|ZP_03966435.1| RNA polymerase sigma factor (possible RNA polymerase sigma-24
           factor) [Sphingobacterium spiritivorum ATCC 33300]
 gi|227243762|gb|EEI93777.1| RNA polymerase sigma factor (possible RNA polymerase sigma-24
           factor) [Sphingobacterium spiritivorum ATCC 33300]
          Length = 205

 Score = 42.1 bits (98), Expect = 0.096,   Method: Composition-based stats.
 Identities = 15/79 (18%), Positives = 40/79 (50%), Gaps = 4/79 (5%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
                 +++EK E+++ ++ +   +  L PR + IF+  R     ++ + ++ +  +S+ 
Sbjct: 115 ETSVSNLVLEKMEQEDIKSSVDDVLKELPPRCQEIFQLSRF--EHLSNDEIAIKLGISKR 172

Query: 268 RVR-QIEARAFKKVQESIQ 285
            V  QI  +A K ++ + +
Sbjct: 173 SVENQI-TKALKHLRIAFR 190


>gi|54261990|emb|CAD65853.1| Flagellin A [Escherichia coli]
 gi|54261993|emb|CAD65855.1| Flagellin A [Escherichia coli]
 gi|54261996|emb|CAD65857.1| Flagellin A [Escherichia coli]
 gi|54261999|emb|CAD65859.1| Flagellin A [Escherichia coli]
 gi|54262002|emb|CAD65861.1| Flagellin A [Escherichia coli]
 gi|54262005|emb|CAD65863.1| Flagellin A [Escherichia coli]
 gi|54262008|emb|CAD65865.1| Flagellin A [Escherichia coli]
 gi|54262011|emb|CAD65867.1| Flagellin A [Escherichia coli]
          Length = 77

 Score = 42.1 bits (98), Expect = 0.097,   Method: Composition-based stats.
 Identities = 16/65 (24%), Positives = 33/65 (50%), Gaps = 3/65 (4%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 72

Query: 107 WWIKA 111
             I+ 
Sbjct: 73  QRIRG 77


>gi|323702979|ref|ZP_08114636.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Desulfotomaculum
           nigrificans DSM 574]
 gi|323532110|gb|EGB21992.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Desulfotomaculum
           nigrificans DSM 574]
          Length = 183

 Score = 42.1 bits (98), Expect = 0.098,   Method: Composition-based stats.
 Identities = 14/80 (17%), Positives = 28/80 (35%), Gaps = 2/80 (2%)

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           D L+      E    E+  +      L + +  L P  R +   R   +       ++  
Sbjct: 91  DVLLELAATSEGGPEEQILQGEELRKLRQLLRDLAPDYRDVVALRYAGDLK--FAQIAQV 148

Query: 262 FEVSRERVRQIEARAFKKVQ 281
              +   VR +  RA K+++
Sbjct: 149 LGKTESAVRMLHHRALKQLR 168


>gi|29346388|ref|NP_809891.1| ECF-type sigma factor [Bacteroides thetaiotaomicron VPI-5482]
 gi|29338283|gb|AAO76085.1| ECF-type sigma factor [Bacteroides thetaiotaomicron VPI-5482]
          Length = 163

 Score = 42.1 bits (98), Expect = 0.098,   Method: Composition-based stats.
 Identities = 18/86 (20%), Positives = 40/86 (46%), Gaps = 2/86 (2%)

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
           + +  +D         E   +E+E+RKN  +++ R +  L+PR+R       ++E     
Sbjct: 76  SDTAIEDVNAVAPTDVEDDYMEEEQRKNEFSLVKRLLDQLSPRQREALTLYYIEEKKY-- 133

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQ 281
           E++     ++ + VR +  R   K++
Sbjct: 134 EDICEIMNMNYQSVRNLMHRGLTKLR 159


>gi|315499393|ref|YP_004088196.1| RNA polymerase, sigma-24 subunit, ecf subfamily [Asticcacaulis
           excentricus CB 48]
 gi|315417405|gb|ADU14045.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Asticcacaulis
           excentricus CB 48]
          Length = 177

 Score = 42.1 bits (98), Expect = 0.099,   Method: Composition-based stats.
 Identities = 15/78 (19%), Positives = 33/78 (42%), Gaps = 6/78 (7%)

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
            ++ +SD++       L  D    E  L+ ++        L +++  L PR + I   RR
Sbjct: 83  DIVRASDRHDDVTGLSLATDAPSAEDSLVSRQRLA----RLIKALDTLPPRAQAIVMLRR 138

Query: 248 LQENPVTLENLSSEFEVS 265
            +E  ++   +  +  +S
Sbjct: 139 FEE--MSYAEIGKKLGIS 154


>gi|225573002|ref|ZP_03781757.1| hypothetical protein RUMHYD_01193 [Blautia hydrogenotrophica DSM
           10507]
 gi|225039653|gb|EEG49899.1| hypothetical protein RUMHYD_01193 [Blautia hydrogenotrophica DSM
           10507]
          Length = 245

 Score = 42.1 bits (98), Expect = 0.10,   Method: Composition-based stats.
 Identities = 34/155 (21%), Positives = 66/155 (42%), Gaps = 11/155 (7%)

Query: 33  EEYVLAKRYRE--HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           E   L K Y+    G   A  RL    L  VV+IA         + +++ EGN+ LM A+
Sbjct: 99  ETRELEKLYQAMSAGKTQAQSRLAQLFLPEVVEIAKRLHTEEGYLGDMIQEGNVALMSAL 158

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
            ++ P+       +    I++ +   + +S              L   +R+L+  ++ +T
Sbjct: 159 NQWRPDGEP--GEWLRRRIESGICGMVSQSER-----QKFEDDILVEKVRKLEAAVRELT 211

Query: 151 DNNLKPE-QVVAIAKKLNVSESEVISMNCRLAGDE 184
           + N + +  V  ++  L++   E+  +  RL GD 
Sbjct: 212 EENEEKKFSVEELSILLDMDIDEIRDI-LRLTGDA 245


>gi|149277362|ref|ZP_01883504.1| RNA polymerase ECF-type sigma factor [Pedobacter sp. BAL39]
 gi|149232239|gb|EDM37616.1| RNA polymerase ECF-type sigma factor [Pedobacter sp. BAL39]
          Length = 194

 Score = 42.1 bits (98), Expect = 0.10,   Method: Composition-based stats.
 Identities = 11/52 (21%), Positives = 26/52 (50%), Gaps = 2/52 (3%)

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
             E +LI  +E +  +  L  +M  L+PR++ I + R      ++ + ++ +
Sbjct: 114 SYESILIASQEDEQLKKRLQHAMESLSPRQKEIVKMRYF--ECLSFKEIAEK 163


>gi|315920259|ref|ZP_07916499.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D2]
 gi|313694134|gb|EFS30969.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D2]
          Length = 181

 Score = 42.1 bits (98), Expect = 0.10,   Method: Composition-based stats.
 Identities = 20/119 (16%), Positives = 51/119 (42%), Gaps = 2/119 (1%)

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           ++L + E ++     R   ++ ++      D +S + ++         E+  I  EE   
Sbjct: 43  ERLCIDEKKIKFYLLRSVRNQLIDWERTKKDTSSIEEEERSFKLSVSVEESFISDEEDLL 102

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
            +  + R + +L   +R I     ++E P   E ++   ++  + VR    +A +K+++
Sbjct: 103 LKKRVNRILDLLTDHQREIVYLHFIEEMPY--EEIAVMLDMKIQTVRGQVFKAMEKLRK 159


>gi|300782080|ref|YP_003762371.1| RNA polymerase ECF sigma factor [Amycolatopsis mediterranei U32]
 gi|299791594|gb|ADJ41969.1| RNA polymerase ECF sigma factor [Amycolatopsis mediterranei U32]
          Length = 170

 Score = 42.1 bits (98), Expect = 0.10,   Method: Composition-based stats.
 Identities = 12/86 (13%), Positives = 34/86 (39%), Gaps = 6/86 (6%)

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
           ++ +    D    V  +  E       L R++  L PR+R +   R      ++   ++ 
Sbjct: 80  ENLVADLPDTSPHVPADPFE----HEPLWRALRTLPPRQRAVMVLRYY--EGLSEAEIAG 133

Query: 261 EFEVSRERVRQIEARAFKKVQESIQK 286
              +++  V+   ++A   ++  ++ 
Sbjct: 134 VLGITQGTVKSQASKAIASLRMKLKS 159


>gi|171320152|ref|ZP_02909215.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Burkholderia
           ambifaria MEX-5]
 gi|171094596|gb|EDT39647.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Burkholderia
           ambifaria MEX-5]
          Length = 222

 Score = 42.1 bits (98), Expect = 0.10,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 39/97 (40%), Gaps = 2/97 (2%)

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             + I+   R+  + S++A    S +N    ++   +D    E         ++    + 
Sbjct: 90  VRQPIAYVTRMVRNASIDACRRQSLENVYHTEEDDGFDVPSPEPTPEAALMTRDTLRRVW 149

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
            ++  L  R R  FE  RL+E   TL+  +    VS+
Sbjct: 150 AALDDLPARSRAAFEMVRLREE--TLQTAARALNVSQ 184


>gi|227822379|ref|YP_002826351.1| putative RNA polymerase sigma factor [Sinorhizobium fredii NGR234]
 gi|227341380|gb|ACP25598.1| putative RNA polymerase sigma factor [Sinorhizobium fredii NGR234]
          Length = 175

 Score = 42.1 bits (98), Expect = 0.10,   Method: Composition-based stats.
 Identities = 17/78 (21%), Positives = 29/78 (37%), Gaps = 2/78 (2%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A  RL+  H   V  +A  + G      ++  +  I L  A++ F      R  T+
Sbjct: 12  GDREAFGRLIERHYDFVHAVAWRWSGSEADAEDIAQDVCIRLGSAIRGFRGT--SRFRTW 69

Query: 105 SMWWIKAAMQEYILRSWS 122
                  A +++  R   
Sbjct: 70  LYTLTLNAARDHCRRQAR 87


>gi|313822944|gb|EFS60658.1| hypothetical protein HMPREF9605_02054 [Propionibacterium acnes
           HL036PA2]
 gi|314925133|gb|EFS88964.1| hypothetical protein HMPREF9606_01838 [Propionibacterium acnes
           HL036PA3]
          Length = 49

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 11/40 (27%), Positives = 23/40 (57%)

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             +  P+T+  ++ E  +S   VR+IE RA  +++  +Q+
Sbjct: 6   GFEGEPMTITAVAHELGLSASNVRRIEQRALGRLRRHLQQ 45


>gi|310818180|ref|YP_003950538.1| RNA polymerase sigma-70 factor [Stigmatella aurantiaca DW4/3-1]
 gi|309391252|gb|ADO68711.1| RNA polymerase sigma-70 factor [Stigmatella aurantiaca DW4/3-1]
          Length = 282

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 43/266 (16%), Positives = 99/266 (37%), Gaps = 36/266 (13%)

Query: 32  QEEYVLAKRY---REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE------VVSEG 82
           +++  L  R    RE GD  A   L    L  V  I         P ++      +    
Sbjct: 41  EQQAALVARIMFARETGDTVAERALSAELLASVCPIIKSVVNCSKPFADSPLSKDLEQVA 100

Query: 83  NIGLMQAVKKFDPERGFR-LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           +I +++ + K+DP RG +     + +  + A +++     S V +   A++ R       
Sbjct: 101 SIAVLRTICKYDPTRGGQSFGEVAYFRARTACEQFARMHASDVHLSDWAHKGRT------ 154

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
              H      + ++ E   A+A                 + + S  +      + + +  
Sbjct: 155 --SHSAHGESDTIRVESTDALA---------------PASDEPSGQSRGAVEFEAAFRAF 197

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
                + +  EQ L+ +E R +  N + R   V   RE  +     + ++  ++ +++  
Sbjct: 198 TSREAEAESPEQALLAEERRVHVFNAVRRLAPV--KRE-LVSRVYGINQSAQSVRSVAEA 254

Query: 262 FEVSRERVRQIEARAFKKVQESIQKQ 287
           + V + RV ++   +  +++E +  Q
Sbjct: 255 WGVPKSRVDRMLVLSLAELRELLTTQ 280


>gi|332798751|ref|YP_004460250.1| ECF subfamily RNA polymerase sigma-24 subunit [Tepidanaerobacter
           sp. Re1]
 gi|332696486|gb|AEE90943.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Tepidanaerobacter
           sp. Re1]
          Length = 186

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 15/75 (20%), Positives = 33/75 (44%), Gaps = 6/75 (8%)

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE--NLSSEFEVSRERVRQ 271
              +  E     + L +++S+L+ RER I   +        L+   +S    ++   V  
Sbjct: 114 TPEDIVEIAETNDELLKALSILDERERSIVALKFGAG----LKNVEISKLLGLTENNVGV 169

Query: 272 IEARAFKKVQESIQK 286
           I  R  KK+++ +++
Sbjct: 170 ILFRTMKKLKKELER 184


>gi|269124421|ref|YP_003297791.1| LuxR family transcriptional regulator [Thermomonospora curvata DSM
           43183]
 gi|268309379|gb|ACY95753.1| transcriptional regulator, LuxR family [Thermomonospora curvata DSM
           43183]
          Length = 197

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 17/90 (18%), Positives = 39/90 (43%), Gaps = 3/90 (3%)

Query: 205 VYDHDGQEQVLIEKEER-KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +Y  D      ++   R     + L+R+++ L  R+R     R  ++ P     ++    
Sbjct: 81  IYPTDVLPDRPVDDHTRRSEMHDALSRALARLPERQRLAVILRYYEDLPE--PEIAKVLG 138

Query: 264 VSRERVRQIEARAFKKVQESIQKQVELSSS 293
           VS   V+   +RA  K++E +  + + ++ 
Sbjct: 139 VSVGTVKSTVSRAMAKLREDVDLEHDFTAP 168


>gi|170701615|ref|ZP_02892560.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Burkholderia
           ambifaria IOP40-10]
 gi|170133469|gb|EDT01852.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Burkholderia
           ambifaria IOP40-10]
          Length = 222

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 19/97 (19%), Positives = 39/97 (40%), Gaps = 2/97 (2%)

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             + ++   R+  + S++A    S +N    ++   +D    E         ++    + 
Sbjct: 90  VRQPVAYVTRMVRNASIDACRRQSLENVYHTEEDDGFDVPSPEPTPEAALMTRDTLRRVW 149

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
            ++  L  R R  FE  RL+E   TL+  +    VS+
Sbjct: 150 AALDDLPARSRAAFEMVRLREE--TLQTAARALNVSQ 184


>gi|325662599|ref|ZP_08151199.1| hypothetical protein HMPREF0490_01939 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|325471096|gb|EGC74322.1| hypothetical protein HMPREF0490_01939 [Lachnospiraceae bacterium
           4_1_37FAA]
          Length = 246

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 34/158 (21%), Positives = 66/158 (41%), Gaps = 8/158 (5%)

Query: 16  LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI 75
           L+RY+ EI+ I   E  E   L       GD  A  RL+  +L  VV+ A       + +
Sbjct: 88  LARYMEEIKTIKAEEAGERQKLF-AASIEGDALARGRLIELYLEKVVEAAKEMYHKEVFL 146

Query: 76  SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL 135
            +++ EGN+ LM A+ + +              ++A MQ  I     + +   T  +K  
Sbjct: 147 GDLIQEGNVSLMLALDELESVEEAHGKIMEE--VRAGMQMLIEEQTEVKRRDHTLLEKYT 204

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
                 L  +++ + +   +   +  ++  L++ E E+
Sbjct: 205 D-----LDDNIKKLKEETGRDVTIEEVSAFLDMPEEEI 237


>gi|160895826|ref|YP_001561408.1| two component LuxR family transcriptional regulator [Delftia
           acidovorans SPH-1]
 gi|160361410|gb|ABX33023.1| two component transcriptional regulator, LuxR family [Delftia
           acidovorans SPH-1]
          Length = 245

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 3/55 (5%)

Query: 235 LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           L+ RE  +     L     TL+ ++ +  VSR  VR    R + K+Q S + Q+ 
Sbjct: 180 LSARELEVLR---LVARGHTLDEVARQLGVSRHTVRTFVRRIYGKLQVSSRTQMM 231


>gi|111018675|ref|YP_701647.1| DNA repair helicase [Rhodococcus jostii RHA1]
 gi|110818205|gb|ABG93489.1| possible DNA repair helicase [Rhodococcus jostii RHA1]
          Length = 574

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 30/191 (15%), Positives = 73/191 (38%), Gaps = 21/191 (10%)

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
           ++ I R   +++               +       +  +    EQ+  IA +L   +++ 
Sbjct: 374 RQMIQRMGRIIRPKQDGRHASFLVLFAKGSAEDPELGAHGTFLEQLTGIASELITVDADQ 433

Query: 174 ISMNCR--LAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQVLI-------------- 216
            +   R  L G ES + L ++SSD    +  + LV + D  E   +              
Sbjct: 434 AADVLRDWLGGVESFDGLSVDSSDAVYRETAERLVGEADSVEPAAVTLGSAGSELRAVLS 493

Query: 217 --EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN--PVTLENLSSEFEVSRERVRQI 272
              +  R +  +++   +SVL P +  +   R       P++   +++   ++   V ++
Sbjct: 494 RVAENPRADDLDIVLTGLSVLEPDQVGVVILRFGLGGHRPMSQTEVAATLALTAVDVGRM 553

Query: 273 EARAFKKVQES 283
           E+ A  ++++ 
Sbjct: 554 ESTAMSRLEKP 564


>gi|271968480|ref|YP_003342676.1| ECF subfamily RNA polymerase sigma-24 subunit [Streptosporangium
           roseum DSM 43021]
 gi|270511655|gb|ACZ89933.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Streptosporangium
           roseum DSM 43021]
          Length = 295

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 22/113 (19%), Positives = 37/113 (32%), Gaps = 2/113 (1%)

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             +  +   R+    S++ L     +  S    WL         V    E   +    L 
Sbjct: 46  VEDDRAYLIRVTTRLSIDRLRRVKARRESYVGPWLPELVGAVPDVAEHAELTASIELALL 105

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             +  L+P ER +F  R     P     +      +    RQ+  RA + V+E
Sbjct: 106 VVLETLSPLERAVFVLREAFALPY--AEIGEIIGRTEATARQLARRAKQHVRE 156


>gi|150008317|ref|YP_001303060.1| RNA polymerase ECF-type sigma factor [Parabacteroides distasonis
           ATCC 8503]
 gi|301309175|ref|ZP_07215119.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 20_3]
 gi|149936741|gb|ABR43438.1| RNA polymerase ECF-type sigma factor [Parabacteroides distasonis
           ATCC 8503]
 gi|300832857|gb|EFK63483.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 20_3]
          Length = 237

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 14/95 (14%), Positives = 37/95 (38%), Gaps = 2/95 (2%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
               + +D +            +     +   +L +++  L P+++R+F+  R       
Sbjct: 138 DRELELRDKIRSASLDSTNETEDSVLDTDLNALLDKALETLTPQQKRVFDMSRKDMKSH- 196

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
            + ++    +S   V+Q  + A K ++  + K  E
Sbjct: 197 -KEIADSLGISVYTVQQHISTALKVIRAFLAKYAE 230


>gi|260886272|ref|ZP_05897535.1| DNA-directed RNA polymerase general stress sigma factor sigma-B
           [Selenomonas sputigena ATCC 35185]
 gi|330839743|ref|YP_004414323.1| RNA polymerase sigma factor, sigma-70 family [Selenomonas sputigena
           ATCC 35185]
 gi|260863991|gb|EEX78491.1| DNA-directed RNA polymerase general stress sigma factor sigma-B
           [Selenomonas sputigena ATCC 35185]
 gi|329747507|gb|AEC00864.1| RNA polymerase sigma factor, sigma-70 family [Selenomonas sputigena
           ATCC 35185]
          Length = 183

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 11/77 (14%), Positives = 35/77 (45%), Gaps = 2/77 (2%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
              +++   +       ++ L  +M  L+ RE+ +     L +   +L+  +++  +S  
Sbjct: 108 ESVEDETASDASMHFALKDALFAAMRTLSEREKELLSLVYLAD--WSLKEAAAKLGLSAA 165

Query: 268 RVRQIEARAFKKVQESI 284
               ++ RA +K+++ +
Sbjct: 166 YAAVVKRRALQKLKKLL 182


>gi|210614501|ref|ZP_03290201.1| hypothetical protein CLONEX_02415 [Clostridium nexile DSM 1787]
 gi|210150685|gb|EEA81694.1| hypothetical protein CLONEX_02415 [Clostridium nexile DSM 1787]
          Length = 158

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 11/91 (12%), Positives = 42/91 (46%), Gaps = 6/91 (6%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
            +  +  D++  +     + ++         + L  ++ +L+  E+ + +A     + ++
Sbjct: 73  DSEGKPLDFIADEAADIAETVVNAVMV----DRLKAALPLLSDSEQELIQAIFF--DGLS 126

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              + + F +++  V + +AR  +K+++ I+
Sbjct: 127 EREVGARFGITQSVVNKRKARILRKLRKIIE 157


>gi|223937206|ref|ZP_03629113.1| RNA polymerase, sigma-24 subunit, ECF subfamily [bacterium
           Ellin514]
 gi|223894228|gb|EEF60682.1| RNA polymerase, sigma-24 subunit, ECF subfamily [bacterium
           Ellin514]
          Length = 498

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 14/64 (21%), Positives = 29/64 (45%), Gaps = 10/64 (15%)

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS----RERVRQIEARAFKKVQE 282
           +L  +M  L  ++R     R  +E   +L  ++   +V+    + RV     RA +K+++
Sbjct: 121 LLDEAMGRLGKKDREAVVLRFFKE--KSLNEVAEAMKVTEAAAQSRV----HRAMEKLRK 174

Query: 283 SIQK 286
              K
Sbjct: 175 HFMK 178



 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 17/60 (28%), Positives = 23/60 (38%)

Query: 36 VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           L + Y + G   A   LV  H+ LV   A  + G G    E+     I L +   K  P
Sbjct: 8  ELLRDYDQQGSEEAFAELVRRHVHLVYSAAYRHVGSGAHAEEITQAVFIILARKAGKLRP 67


>gi|150002717|ref|YP_001297461.1| RNA polymerase ECF-type sigma factor [Bacteroides vulgatus ATCC
           8482]
 gi|149931141|gb|ABR37839.1| RNA polymerase ECF-type sigma factor [Bacteroides vulgatus ATCC
           8482]
          Length = 198

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 12/70 (17%), Positives = 36/70 (51%), Gaps = 2/70 (2%)

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
           + ++    + +  + R +  L PR++ +F+  R  +  +T + +++   +S + V +   
Sbjct: 123 MEDELSAADLKEFIKRMVGELPPRQQEVFKMSR--DEHLTYKEIATRLNISEKTVERHIN 180

Query: 275 RAFKKVQESI 284
            A K ++++I
Sbjct: 181 EAIKFLKKNI 190


>gi|332969693|gb|EGK08709.1| DNA-directed RNA polymerase sigma subunit SigI [Desmospora sp.
           8437]
          Length = 265

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 16/143 (11%), Positives = 54/143 (37%), Gaps = 4/143 (2%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMG-YRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           +  +   D +    L+  +   ++K+A            +  S   +G  +A+  +  ++
Sbjct: 22  RLLKARNDPAVREELIDENQTYILKVASKICIRNITRQDDEYSVALLGFNEAINSYRSDQ 81

Query: 98  GFRLATYSMWWIKAAMQEYIL---RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
             +  +++   I+  + +Y     R ++ V + +  ++         ++   +   D  L
Sbjct: 82  STKFHSFAFTVIRRRLTDYFRSETRHFNQVPLVSADSKDNEPTYPEVIRKAFEEHHDREL 141

Query: 155 KPEQVVAIAKKLNVSESEVISMN 177
           + ++   + +     +   IS+N
Sbjct: 142 EEKRRSDLEEFAKHLQRFKISLN 164


>gi|227888792|ref|ZP_04006597.1| sigma factor 30 RNA polymerase [Lactobacillus johnsonii ATCC 33200]
 gi|227850629|gb|EEJ60715.1| sigma factor 30 RNA polymerase [Lactobacillus johnsonii ATCC 33200]
          Length = 185

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 27/149 (18%), Positives = 47/149 (31%), Gaps = 2/149 (1%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           E  L +R +E  D+ A H LV  +  L+    + +        +   E  I   Q+   +
Sbjct: 6   EVYLIRRVKEEQDMEALHELVERYRPLINGAKLSFFIRNFDHDDWEQEALIMCYQSCCTY 65

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D +R      Y        ++  +    +  +   T          + L           
Sbjct: 66  DEKRANSFGAYYRTKFYNHLRSLLRYELAQKRTSFTKAISYDNVVHKNLIKEEVEEMQIT 125

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            + E       KL  SE EVI++   L  
Sbjct: 126 PRKEMYQKFINKL--SEKEVIALKVFLGE 152


>gi|254975140|ref|ZP_05271612.1| RNA polymerase sigma factor, sigma-70 family protein [Clostridium
           difficile QCD-66c26]
 gi|255092530|ref|ZP_05322008.1| RNA polymerase sigma factor, sigma-70 family protein [Clostridium
           difficile CIP 107932]
 gi|255306557|ref|ZP_05350728.1| RNA polymerase sigma factor, sigma-70 family protein [Clostridium
           difficile ATCC 43255]
 gi|255314267|ref|ZP_05355850.1| RNA polymerase sigma factor, sigma-70 family protein [Clostridium
           difficile QCD-76w55]
 gi|255516947|ref|ZP_05384623.1| RNA polymerase sigma factor, sigma-70 family protein [Clostridium
           difficile QCD-97b34]
 gi|255650049|ref|ZP_05396951.1| RNA polymerase sigma factor, sigma-70 family protein [Clostridium
           difficile QCD-37x79]
 gi|260683190|ref|YP_003214475.1| hypothetical protein CD196_1447 [Clostridium difficile CD196]
 gi|260686786|ref|YP_003217919.1| hypothetical protein CDR20291_1422 [Clostridium difficile R20291]
 gi|260209353|emb|CBA62781.1| hypothetical protein CD196_1447 [Clostridium difficile CD196]
 gi|260212802|emb|CBE03967.1| hypothetical protein CDR20291_1422 [Clostridium difficile R20291]
          Length = 190

 Score = 42.1 bits (98), Expect = 0.11,   Method: Composition-based stats.
 Identities = 18/72 (25%), Positives = 33/72 (45%), Gaps = 6/72 (8%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLP-----ISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
           +LV ++L LV      +    +        E   EG IGL +A   +D  RG + +T ++
Sbjct: 8   KLVENNLNLVHFSINRFFKSYVEQHPYLYEEFYQEGCIGLYKAALNYDSNRG-KFSTVAV 66

Query: 107 WWIKAAMQEYIL 118
            +I+  M + + 
Sbjct: 67  SYIRIEMFKALR 78


>gi|85711489|ref|ZP_01042547.1| DNA-directed RNA polymerase specialized sigma factor [Idiomarina
           baltica OS145]
 gi|85694641|gb|EAQ32581.1| DNA-directed RNA polymerase specialized sigma factor [Idiomarina
           baltica OS145]
          Length = 359

 Score = 41.7 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 11/78 (14%), Positives = 35/78 (44%), Gaps = 2/78 (2%)

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
            ++        + ++ ++  ++  L  + R +      ++     E+++    ++ E VR
Sbjct: 114 SDESPEASLSEQQQQAIIYHALDKLPEQSRDVVLLYYREQQSA--EHVADLLGITPEAVR 171

Query: 271 QIEARAFKKVQESIQKQV 288
           Q  +RA K++ + +  +V
Sbjct: 172 QRLSRARKQLAQQLLSRV 189


>gi|30265276|ref|NP_847653.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. Ames]
 gi|47530811|ref|YP_022160.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49188088|ref|YP_031341.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. Sterne]
 gi|254737058|ref|ZP_05194763.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. Western
           North America USA6153]
 gi|30259954|gb|AAP29139.1| putative sigma factor [Bacillus anthracis str. Ames]
 gi|47505959|gb|AAT34635.1| putative sigma factor [Bacillus anthracis str. 'Ames Ancestor']
 gi|49182015|gb|AAT57391.1| sigma factor, putative [Bacillus anthracis str. Sterne]
          Length = 146

 Score = 41.7 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 16/64 (25%), Positives = 33/64 (51%), Gaps = 2/64 (3%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++        MSVL+ +E+ I   R       T+  ++ E E++  +VR I  +A +K++
Sbjct: 84  EDIEMKAKDFMSVLDEKEKYIIFERFFVG--KTMGEIALETEMTYYQVRWIYRQALEKMR 141

Query: 282 ESIQ 285
            S++
Sbjct: 142 NSLR 145


>gi|228988476|ref|ZP_04148566.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|228771244|gb|EEM19720.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
          Length = 156

 Score = 41.7 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 15/64 (23%), Positives = 34/64 (53%), Gaps = 2/64 (3%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    +   MSVL+ +E+ I   R       T+  ++ E E++  +VR +  +A +K++
Sbjct: 94  EDIEMKVKDFMSVLDEKEKYIIFERFFVG--KTMGEIALETEMTYYQVRWVYRQALEKMR 151

Query: 282 ESIQ 285
            S++
Sbjct: 152 NSLR 155


>gi|220929260|ref|YP_002506169.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           cellulolyticum H10]
 gi|219999588|gb|ACL76189.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           cellulolyticum H10]
          Length = 230

 Score = 41.7 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 15/74 (20%), Positives = 28/74 (37%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + GD  A   L  +++ ++ K+   Y        + + E    L+  VK + PER    
Sbjct: 10  AKQGDKQALQALYDNNIGIMHKLIFRYSVSKQDRDDFLQECYFVLLNCVKAYKPEREILF 69

Query: 102 ATYSMWWIKAAMQE 115
            +Y    I   +  
Sbjct: 70  ISYLGNAIVWMILR 83


>gi|42523210|ref|NP_968590.1| putative RNA polymerase ECF-type sigma factor [Bdellovibrio
           bacteriovorus HD100]
 gi|39575415|emb|CAE79583.1| putative RNA polymerase ECF-type sigma factor [Bdellovibrio
           bacteriovorus HD100]
          Length = 190

 Score = 41.7 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 19/88 (21%), Positives = 39/88 (44%), Gaps = 4/88 (4%)

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D  + + +D+L +D    +    E      +++     +  L PRE+ I   R L E   
Sbjct: 98  DYRNREIKDFLEWDDSLSQTS--ESSPILEQKDEAEALLQDLKPREQEILRLRYLDEMEY 155

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQ 281
               +++  + S   +RQI +R+ K ++
Sbjct: 156 N--EIAALLQESESNIRQIVSRSLKFLR 181


>gi|325264076|ref|ZP_08130808.1| putative RNA polymerase ECF-subfamily sigma factor [Clostridium sp.
           D5]
 gi|324030560|gb|EGB91843.1| putative RNA polymerase ECF-subfamily sigma factor [Clostridium sp.
           D5]
          Length = 179

 Score = 41.7 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 16/60 (26%), Positives = 30/60 (50%), Gaps = 2/60 (3%)

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +   MS+LN +E+ I   R       + E ++S+ + +   +R    RA KK+   +Q+Q
Sbjct: 114 VEALMSILNEKEKPIIFLRYF--EGYSFEEIASKLDKNSSTIRTTHERALKKMLTYLQQQ 171


>gi|313204970|ref|YP_004043627.1| RNA polymerase, sigma-24 subunit, ecf subfamily [Paludibacter
           propionicigenes WB4]
 gi|312444286|gb|ADQ80642.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Paludibacter
           propionicigenes WB4]
          Length = 206

 Score = 41.7 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 21/137 (15%), Positives = 58/137 (42%), Gaps = 10/137 (7%)

Query: 154 LKPEQVVAIAKKLNVSESEVISMNC------RLAGDESLNALINSSDKNSSQWQDWLVYD 207
              + V  +  KL  + + +  +        R+A +++++ L   S +  +   +++  +
Sbjct: 53  RAEDMVQDVFMKLWQNRANIADIENINAFIFRMAQNQAIDELRRFSKETLAHSSEFI--N 110

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            +       E    K  R  +  ++  L P+++RI+      E+    E ++SE  +S  
Sbjct: 111 EEALSPNPAESLLNKEIREKIKEAVDQLPPQQKRIYILH--NEDGYKYEEIASELNLSVS 168

Query: 268 RVRQIEARAFKKVQESI 284
            +R   ++A   +++ +
Sbjct: 169 TIRNHMSQAMGNIRKLL 185


>gi|228999993|ref|ZP_04159565.1| RNA polymerase sigma factor [Bacillus mycoides Rock3-17]
 gi|229008121|ref|ZP_04165652.1| RNA polymerase sigma factor [Bacillus mycoides Rock1-4]
 gi|228753127|gb|EEM02634.1| RNA polymerase sigma factor [Bacillus mycoides Rock1-4]
 gi|228759935|gb|EEM08909.1| RNA polymerase sigma factor [Bacillus mycoides Rock3-17]
          Length = 157

 Score = 41.7 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 14/55 (25%), Positives = 30/55 (54%), Gaps = 2/55 (3%)

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           MS+L+ +E+ I   R      +    ++ E E++  +VR +  +A  K++ SI++
Sbjct: 105 MSLLDEKEKHIIYERFYAGKKI--HEIAEEMEMTYHQVRWVYRQALGKMRSSIRE 157


>gi|223938875|ref|ZP_03630762.1| RNA polymerase, sigma-24 subunit, ECF subfamily [bacterium
           Ellin514]
 gi|223892428|gb|EEF58902.1| RNA polymerase, sigma-24 subunit, ECF subfamily [bacterium
           Ellin514]
          Length = 624

 Score = 41.7 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 26/153 (16%), Positives = 56/153 (36%), Gaps = 21/153 (13%)

Query: 145 HLQAITDNNLKPEQVVAIAKKL-----NVSESEVIS-MNCRLAGDESLNALINSSDKNSS 198
            L+ + D +L  E   A+   L     ++    ++S   CR A   S NAL     +   
Sbjct: 31  ALRQVRDPHLAEEITQAVFIILARKASSLGPRTILSGWLCRTARYVSANALTVQRRRQRR 90

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           + + ++  +    EQ     +   +    L  +++ L  +E      R ++     L+ +
Sbjct: 91  EQEAYMEMESASNEQGF---DAWSHIAPHLEDALNSLREKEHNAIVLRFMEGKD--LKEV 145

Query: 259 SSEFEVS-----RERVRQIEARAFKKVQESIQK 286
                 +     R RV     RA + +++   +
Sbjct: 146 GMALG-TGEDAARMRV----NRALENMRKYFAR 173


>gi|218290353|ref|ZP_03494489.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Alicyclobacillus
           acidocaldarius LAA1]
 gi|218239589|gb|EED06782.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Alicyclobacillus
           acidocaldarius LAA1]
          Length = 191

 Score = 41.7 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 17/95 (17%), Positives = 40/95 (42%), Gaps = 13/95 (13%)

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
            S +    ++ DH      +    E+ + R+ + ++++ L   +R++ E    Q    T 
Sbjct: 97  ESGEDLFPVLPDHGLTPDRV---AEQSDLRSRIRQALAKLPEEQRQVVEWMYFQG--YTQ 151

Query: 256 ENLSSEFEVS----RERVRQIEARAFKKVQESIQK 286
             ++  F  S    + R R     A +K+++ +Q 
Sbjct: 152 NEIAERFGWSLGTVKSRARL----AMQKLRDELQS 182


>gi|229199367|ref|ZP_04326032.1| RNA polymerase sigma factor [Bacillus cereus m1293]
 gi|228584081|gb|EEK42234.1| RNA polymerase sigma factor [Bacillus cereus m1293]
          Length = 156

 Score = 41.7 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 16/64 (25%), Positives = 34/64 (53%), Gaps = 2/64 (3%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +N    +   MSVL+ +E+ I   R       T+  ++ E E++  +VR +  +A +K++
Sbjct: 94  ENIEMKVKDFMSVLDEKEKYIIFERFFVG--KTMGEIALETEMTYYQVRWVYRQALEKMR 151

Query: 282 ESIQ 285
            S++
Sbjct: 152 NSLR 155


>gi|255038438|ref|YP_003089059.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Dyadobacter
           fermentans DSM 18053]
 gi|254951194|gb|ACT95894.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Dyadobacter
           fermentans DSM 18053]
          Length = 184

 Score = 41.7 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 22/104 (21%), Positives = 44/104 (42%), Gaps = 4/104 (3%)

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
             S ++ S    +    +H   E +LIE E    R   +   ++ L  R+      R   
Sbjct: 76  FPSMEEISELDDEDTPANHTHSEAILIEVESSSIRAQRIQELLAQLPERQVEALTLRYFD 135

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           +   ++E +S    V+ + VR    +A   +++S  +++ L SS
Sbjct: 136 D--FSIEEISGIMNVNEKSVRNFIYKALTSLRQS--REILLISS 175


>gi|293370517|ref|ZP_06617069.1| sigma-70, region 4 [Bacteroides ovatus SD CMC 3f]
 gi|292634251|gb|EFF52788.1| sigma-70, region 4 [Bacteroides ovatus SD CMC 3f]
          Length = 204

 Score = 41.7 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 16/93 (17%), Positives = 44/93 (47%), Gaps = 2/93 (2%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
               + ++ +       E + I  E+ K  +  +   MSVL  R+R I   R ++E  ++
Sbjct: 114 DEIGEREETVDESPSTPETIYINNEQEKQVQATVHTMMSVLTDRQREIIYYRYIKE--MS 171

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++ +S   +++ + +     RA  ++++  +++
Sbjct: 172 IDEISKVTDMNNQSISNSIQRALGRIRDLFKRK 204


>gi|325678276|ref|ZP_08157904.1| RNA polymerase sigma factor, sigma-70 family [Ruminococcus albus 8]
 gi|324110039|gb|EGC04227.1| RNA polymerase sigma factor, sigma-70 family [Ruminococcus albus 8]
          Length = 540

 Score = 41.7 bits (97), Expect = 0.12,   Method: Composition-based stats.
 Identities = 18/95 (18%), Positives = 36/95 (37%), Gaps = 22/95 (23%)

Query: 206 YDHDGQEQVLIEK--EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
            D    E  + E   EE    + +L R +  L+ R+R +        + +T+ +++    
Sbjct: 81  EDISNMEIAVPEDNSEEELAMQQLLRREIGYLSQRQRTVIYMHYY--DKLTVADIAKRLG 138

Query: 264 VSR---------ERVRQIEARAFKKVQESIQKQVE 289
           +S           RV         K++E I+  +E
Sbjct: 139 ISAGTVKWHLSDARV---------KLKEGIKMNIE 164


>gi|110804004|ref|YP_699913.1| uviA protein [Clostridium perfringens SM101]
 gi|110684505|gb|ABG87874.1| uviA protein - Clostridium perfringens plasmid pIP404 [Clostridium
           perfringens SM101]
          Length = 188

 Score = 41.7 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 10/57 (17%), Positives = 27/57 (47%), Gaps = 2/57 (3%)

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +   +  L+ +ER++ + + +         +      SR+ V +I+ RA K +++ +
Sbjct: 132 VHDLIDKLSEKERKVIKYKYIYGKSDV--EIGELLNCSRQYVNKIKNRALKNIKKFL 186


>gi|82659646|gb|ABB88904.1| OrbS [Burkholderia cenocepacia]
          Length = 220

 Score = 41.7 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 18/97 (18%), Positives = 39/97 (40%), Gaps = 2/97 (2%)

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             + ++   R+  + S++A    + +N    ++   +D    E         ++    + 
Sbjct: 88  VRQPVAYVTRMVRNASIDACRRQNLENVYHTEEDDGFDVPSPEPTPEAALMTRDTLRRVW 147

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
            ++  L  R R  FE  RL+E   TL+  +    VS+
Sbjct: 148 AALDDLPARSRAAFEMVRLREE--TLQTAARALNVSQ 182


>gi|89096110|ref|ZP_01169003.1| RNA polymerase sigma-70 factor [Bacillus sp. NRRL B-14911]
 gi|89088964|gb|EAR68072.1| RNA polymerase sigma-70 factor [Bacillus sp. NRRL B-14911]
          Length = 213

 Score = 41.7 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 19/68 (27%), Positives = 32/68 (47%), Gaps = 2/68 (2%)

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
            +K +   + + +S L   ER I   R   E P   E ++    +    VR    RA KK
Sbjct: 137 LKKEKNRQVEKLISTLPEDERIIILLRYANELPY--EEIAETTGMPLSMVRNKLHRAKKK 194

Query: 280 VQESIQKQ 287
           ++E+++KQ
Sbjct: 195 MRETVKKQ 202


>gi|256424129|ref|YP_003124782.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Chitinophaga
           pinensis DSM 2588]
 gi|256039037|gb|ACU62581.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Chitinophaga
           pinensis DSM 2588]
          Length = 195

 Score = 41.7 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 34/150 (22%), Positives = 65/150 (43%), Gaps = 14/150 (9%)

Query: 146 LQAITDNNLKPEQVVAIAKKLNVSESEVISM------NCRLAGDESLNAL--INSSDKNS 197
           L  I D +   +       KL  S +   S+         LA + SLN L  +   +K S
Sbjct: 40  LSIIQDQHQAEDIATESLLKLWQSPNRFESIGKLRAYLFTLARNASLNYLKHLRVREKRS 99

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
            +  +    D +    ++ E E       ++ + ++ L    R I E   LQ+ P    +
Sbjct: 100 LEISEQEQGDDNSIASLMAESELM----RLIYQEIARLPDNYREIVELLYLQDMPS--AD 153

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +++  ++S E +RQ +ARA K+++  + K+
Sbjct: 154 VAARLDISMENLRQRKARAIKELKTVLLKK 183


>gi|76803381|ref|YP_327650.1| DNA binding protein [Natronomonas pharaonis DSM 2160]
 gi|76559196|emb|CAI50795.1| predicted DNA binding protein [Natronomonas pharaonis DSM 2160]
          Length = 250

 Score = 41.7 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 22/108 (20%), Positives = 39/108 (36%), Gaps = 12/108 (11%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE-----ARRLQENPVTLENL 258
           +  D         +  +       L R++  L  RER   E              TL+ +
Sbjct: 140 IKSDDSVHIDDFFDILQNVESLGSLLRTLQSLTDRERETLETAVEDGYFATPRGTTLDGI 199

Query: 259 SSEFEVSRERV----RQIEARAFKKVQESI---QKQVELSSSPPLLQK 299
             EF++SR       R+ + +  +KV   +   + Q+EL    P  Q+
Sbjct: 200 GEEFDISRMGASKNLRRSQRKVLRKVIHVLNDVEAQMELQEEGPETQE 247


>gi|302559194|ref|ZP_07311536.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces
           griseoflavus Tu4000]
 gi|302476812|gb|EFL39905.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces
           griseoflavus Tu4000]
          Length = 578

 Score = 41.7 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 22/93 (23%), Positives = 33/93 (35%), Gaps = 10/93 (10%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           E    A+R    GD  A   LV ++L LV  I          + +VV E  +  + A+  
Sbjct: 10  ETVEAAQR----GDTRAQDELVAAYLPLVYNIVGRALNGHPDVDDVVQESMLRALAALGS 65

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
                GFR       W+ A     +   W   +
Sbjct: 66  LRDPDGFR------PWLVAITMNQLRHHWRAHR 92


>gi|206560050|ref|YP_002230814.1| extracytoplasmic-function sigma-70 factor [Burkholderia cenocepacia
           J2315]
 gi|198036091|emb|CAR51986.1| putative RNA polymerase sigma factor [Burkholderia cenocepacia
           J2315]
          Length = 222

 Score = 41.7 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 18/97 (18%), Positives = 39/97 (40%), Gaps = 2/97 (2%)

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             + ++   R+  + S++A    + +N    ++   +D    E         ++    + 
Sbjct: 90  VRQPVAYVTRMVRNASIDACRRQNLENVYHTEEDDGFDVPSPEPTPEAALMTRDTLRRVW 149

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
            ++  L  R R  FE  RL+E   TL+  +    VS+
Sbjct: 150 AALDDLPARSRAAFEMVRLREE--TLQTAARALNVSQ 184


>gi|218289151|ref|ZP_03493387.1| putative signal-transduction protein with CBS domains
           [Alicyclobacillus acidocaldarius LAA1]
 gi|218240734|gb|EED07913.1| putative signal-transduction protein with CBS domains
           [Alicyclobacillus acidocaldarius LAA1]
          Length = 240

 Score = 41.7 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 1/68 (1%)

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
            L+Y+ D +E +  +  E    R +L      L PR++ I    R    P+T + ++   
Sbjct: 3   MLMYNRDTREHIRGQAVEFPPGRLLLGERPIELTPRQKEILRLVR-THQPITGDQIAEML 61

Query: 263 EVSRERVR 270
            VSR  +R
Sbjct: 62  GVSRPTIR 69


>gi|78042626|ref|YP_359015.1| RNA polymerase sigma-70 factor [Carboxydothermus hydrogenoformans
           Z-2901]
 gi|77994741|gb|ABB13640.1| RNA polymerase sigma-70 factor [Carboxydothermus hydrogenoformans
           Z-2901]
          Length = 175

 Score = 41.7 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 18/77 (23%), Positives = 32/77 (41%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
           +          L+     L+ K A  YR   L   +++ EG I ++++V +FDPERG   
Sbjct: 10  KARKSREGMEELLNYLRPLIKKAAQRYRNPYLTEEDLMQEGMIAVIESVYRFDPERGVYF 69

Query: 102 ATYSMWWIKAAMQEYIL 118
             Y    +   +   + 
Sbjct: 70  LKYVREMVYGRIYSLLR 86


>gi|84497862|ref|ZP_00996659.1| putative RNA polymerase ECF-subfamily sigma factor [Janibacter sp.
           HTCC2649]
 gi|84381362|gb|EAP97245.1| putative RNA polymerase ECF-subfamily sigma factor [Janibacter sp.
           HTCC2649]
          Length = 172

 Score = 41.7 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 18/84 (21%), Positives = 32/84 (38%), Gaps = 4/84 (4%)

Query: 200 WQDWLVYDHDGQEQVL--IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           W   +V D    E V    +  +    R+ L  ++S L PR+R     R  ++ P     
Sbjct: 78  WTRDVVSDAAVTELVPSTDDHADDVVDRDALLEALSGLPPRQRTAVTLRYFEDLPDV--E 135

Query: 258 LSSEFEVSRERVRQIEARAFKKVQ 281
           +++    S   VR     A   ++
Sbjct: 136 IAALMGCSVSTVRSSIHHALAALR 159


>gi|325673272|ref|ZP_08152964.1| ecf family RNA polymerase sigma factor [Rhodococcus equi ATCC
           33707]
 gi|325555862|gb|EGD25532.1| ecf family RNA polymerase sigma factor [Rhodococcus equi ATCC
           33707]
          Length = 191

 Score = 41.7 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 14/86 (16%), Positives = 29/86 (33%), Gaps = 2/86 (2%)

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
              +V +   +     E   R +        + VL  RER I   R +++        + 
Sbjct: 107 PVDIVPEVPVEFDTPEEHAMRAHDTQHAWSLIDVLTARERTILRLRIVEQQSA--AETAR 164

Query: 261 EFEVSRERVRQIEARAFKKVQESIQK 286
               +   VR  + RA  +++  +  
Sbjct: 165 VLNTTAGAVRVAQHRALNRLRAQLAS 190


>gi|34763651|ref|ZP_00144579.1| RNA polymerase sigma factor [Fusobacterium nucleatum subsp.
           vincentii ATCC 49256]
 gi|237742310|ref|ZP_04572791.1| RNA polymerase sigma factor [Fusobacterium sp. 4_1_13]
 gi|27886660|gb|EAA23825.1| RNA polymerase sigma factor [Fusobacterium nucleatum subsp.
           vincentii ATCC 49256]
 gi|229429958|gb|EEO40170.1| RNA polymerase sigma factor [Fusobacterium sp. 4_1_13]
          Length = 274

 Score = 41.7 bits (97), Expect = 0.13,   Method: Composition-based stats.
 Identities = 29/127 (22%), Positives = 51/127 (40%), Gaps = 5/127 (3%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V  +L+ V ++A+     G+   ++  EG IGL++A + F+ ++ F+L  Y  ++I   M
Sbjct: 84  VEKNLKKVYEMALYMLREGISYDDLTQEGIIGLIKAHELFEEDKDFKL--YKDYYIAREM 141

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
             YI    +  K       K        LK  L+   D N   E      +       E+
Sbjct: 142 FNYINNYANYRKSAFKDYAKHEIHKNNHLKVSLK---DRNKSEELKKLEKENKEKHIEEI 198

Query: 174 ISMNCRL 180
             +  R 
Sbjct: 199 KQLEKRA 205


>gi|256423183|ref|YP_003123836.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Chitinophaga
           pinensis DSM 2588]
 gi|256038091|gb|ACU61635.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Chitinophaga
           pinensis DSM 2588]
          Length = 193

 Score = 41.7 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 13/92 (14%), Positives = 42/92 (45%), Gaps = 4/92 (4%)

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA-RRLQENPVTLENL 258
             D +  +       L  + + +  + ++  ++S L+ ++R IF   R+   +  T   +
Sbjct: 95  LVDHVWANISATADALDLELDARESQQLINTALSRLSEQQRTIFRLSRQDGLDHAT---I 151

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
           + +  +S+ RV+ ++    + +++ + +  E 
Sbjct: 152 ADKLHLSKSRVKNVQVETLRFIRQFLSQHAEF 183


>gi|238926479|ref|ZP_04658239.1| RNA polymerase, sigma-24 subunit, ECF subfamily protein
           [Selenomonas flueggei ATCC 43531]
 gi|238885673|gb|EEQ49311.1| RNA polymerase, sigma-24 subunit, ECF subfamily protein
           [Selenomonas flueggei ATCC 43531]
          Length = 210

 Score = 41.7 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 14/64 (21%), Positives = 32/64 (50%), Gaps = 2/64 (3%)

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
            +ER    ++LTR+M  L  RE+ + +    ++  +TL  ++     S   + + +A   
Sbjct: 136 ADERLLAEDILTRAMHRLTEREKEVLDLHYFRD--LTLRRIAVLLGTSAGALSKSKANLL 193

Query: 278 KKVQ 281
           +K++
Sbjct: 194 RKLR 197


>gi|223985953|ref|ZP_03635988.1| hypothetical protein HOLDEFILI_03294 [Holdemania filiformis DSM
           12042]
 gi|223962077|gb|EEF66554.1| hypothetical protein HOLDEFILI_03294 [Holdemania filiformis DSM
           12042]
          Length = 177

 Score = 41.7 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 13/68 (19%), Positives = 27/68 (39%), Gaps = 4/68 (5%)

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV-RQIEARAFKKVQESIQK 286
           L  ++S L   E+ I          +T E +   +  +R    R I     ++++E ++ 
Sbjct: 112 LAAALSSLPETEQEIIFLYFF--EHLTHEEIGKRYGRTRSTAGRHIYLD-LRRLREEMEV 168

Query: 287 QVELSSSP 294
                +SP
Sbjct: 169 LAHEQASP 176


>gi|47569356|ref|ZP_00240039.1| RNA polymerase sigma factor [Bacillus cereus G9241]
 gi|47569748|ref|ZP_00240421.1| RNA polymerase sigma factor [Bacillus cereus G9241]
 gi|47570534|ref|ZP_00241160.1| RNA polymerase sigma factor [Bacillus cereus G9241]
 gi|47552795|gb|EAL11220.1| RNA polymerase sigma factor [Bacillus cereus G9241]
 gi|47553599|gb|EAL11977.1| RNA polymerase sigma factor [Bacillus cereus G9241]
 gi|47553944|gb|EAL12312.1| RNA polymerase sigma factor [Bacillus cereus G9241]
          Length = 156

 Score = 41.7 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 15/64 (23%), Positives = 34/64 (53%), Gaps = 2/64 (3%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    +   MSVL+ +E+ I   R       T+  ++ E E++  +VR +  +A +K++
Sbjct: 94  EDIEMKVKDFMSVLDEKEKYIIFERFFVG--KTMGEIALETEMTYYQVRWVYRQALEKMR 151

Query: 282 ESIQ 285
            S++
Sbjct: 152 NSLR 155


>gi|325955452|ref|YP_004239112.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Weeksella virosa
           DSM 16922]
 gi|323438070|gb|ADX68534.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Weeksella virosa
           DSM 16922]
          Length = 189

 Score = 41.7 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 19/99 (19%), Positives = 43/99 (43%), Gaps = 2/99 (2%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
           K      D +       E+ L  +++   +  ++  ++  L+PR + +F   R      T
Sbjct: 82  KEEIAESDKIFSIQSNYEESLEFEQQYSLKLELIEEAVENLSPRRKEVFRLCRF--EGYT 139

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
            + ++   ++S + V     +A + ++E IQK+    SS
Sbjct: 140 KDEVAQMLKISTDSVSDYLKQANQFIREYIQKEYPTYSS 178


>gi|171912594|ref|ZP_02928064.1| sigma-24, ECF subfamily protein [Verrucomicrobium spinosum DSM
           4136]
          Length = 265

 Score = 41.7 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 26/155 (16%), Positives = 57/155 (36%), Gaps = 12/155 (7%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           +E   L  R +E GD+ A  +LV  H R V+              ++  +  + + ++  
Sbjct: 79  EESVRLMLRVKE-GDMRAFEQLVEMHQRAVIGTVARMLNNMDDAHDIAQQVFVRVWRSAA 137

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           +++P    +  T+            I R+    ++     +K +     + + H +  T 
Sbjct: 138 RYEPS--AKFTTWLFT---------IARNLVFNEMRRRGRKKEVSMEEDQEEHHREHATS 186

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL 186
               P+ VVA  +     +  + S+  +     SL
Sbjct: 187 PRQNPDNVVAQGEMETAIDRAIQSLPEKQRLAVSL 221


>gi|167766469|ref|ZP_02438522.1| hypothetical protein CLOSS21_00975 [Clostridium sp. SS2/1]
 gi|167711878|gb|EDS22457.1| hypothetical protein CLOSS21_00975 [Clostridium sp. SS2/1]
          Length = 110

 Score = 41.7 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 8/47 (17%), Positives = 18/47 (38%), Gaps = 2/47 (4%)

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           E+   +  +   M +L  R+R I           T   ++ E  +++
Sbjct: 59  EQLIEKEQILELMGLLTERQRDIVILYFYYGE--TQWEIAKELGITQ 103


>gi|148654246|ref|YP_001274451.1| ECF subfamily RNA polymerase sigma-24 factor [Roseiflexus sp. RS-1]
 gi|148566356|gb|ABQ88501.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Roseiflexus sp.
           RS-1]
          Length = 215

 Score = 41.7 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 18/100 (18%), Positives = 41/100 (41%), Gaps = 9/100 (9%)

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL+A       +       ++   D   +   +  + +  R  L  +++ L   ER++  
Sbjct: 119 SLDAPT----GDDGLPLHRMI--EDKTLEQHADAYQEEQIRARLDAAIARLPVIERQVVT 172

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            R      V   +++ +F +S   V  I  RA K++++ +
Sbjct: 173 LRLDGVASV---DIARQFGMSPANVTHIHHRAVKRLKQIL 209


>gi|271964403|ref|YP_003338599.1| ECF subfamily RNA polymerase sigma-24 subunit [Streptosporangium
           roseum DSM 43021]
 gi|270507578|gb|ACZ85856.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Streptosporangium
           roseum DSM 43021]
          Length = 171

 Score = 41.7 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 15/77 (19%), Positives = 32/77 (41%), Gaps = 2/77 (2%)

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
               L  +E   + R +L  ++  L PR+R +   R  ++   T    +     S   V+
Sbjct: 86  TPPELPVRETDVDLRRVLMDALRALPPRQRAVVVLRYWEDLGETQT--AEILGCSAGTVK 143

Query: 271 QIEARAFKKVQESIQKQ 287
              ++A  K++ +I  +
Sbjct: 144 SQASKALTKLRSAIGAE 160


>gi|163848658|ref|YP_001636702.1| RNA polymerase sigma-70 factor [Chloroflexus aurantiacus J-10-fl]
 gi|222526594|ref|YP_002571065.1| RNA polymerase, sigma 32 subunit, RpoH [Chloroflexus sp. Y-400-fl]
 gi|163669947|gb|ABY36313.1| RNA polymerase sigma-70 factor [Chloroflexus aurantiacus J-10-fl]
 gi|222450473|gb|ACM54739.1| RNA polymerase, sigma 32 subunit, RpoH [Chloroflexus sp. Y-400-fl]
          Length = 180

 Score = 41.7 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 17/86 (19%), Positives = 35/86 (40%), Gaps = 2/86 (2%)

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
             Q  L      +E +  E  E+      L  ++S L P ++ +   R  Q  P+  + +
Sbjct: 91  SPQTSLDEQLMSREPLPSEIAEKAATNEELRLAISQLTPDQQHVLALRFAQNLPI--QEV 148

Query: 259 SSEFEVSRERVRQIEARAFKKVQESI 284
           +     +   V+Q++ARA   +   +
Sbjct: 149 ARILGKTEGAVKQLQARAIAALARQM 174


>gi|193214908|ref|YP_001996107.1| ECF subfamily RNA polymerase, sigma-24 subunit [Chloroherpeton
           thalassium ATCC 35110]
 gi|193088385|gb|ACF13660.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Chloroherpeton
           thalassium ATCC 35110]
          Length = 317

 Score = 41.7 bits (97), Expect = 0.14,   Method: Composition-based stats.
 Identities = 18/92 (19%), Positives = 40/92 (43%), Gaps = 8/92 (8%)

Query: 179 RLAGDESLNAL------INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           R+A + S++ L        S D   +   D    +     +   +   +  R  ++  ++
Sbjct: 201 RIATNSSIDYLRKRRLKTYSLDNPITTKDDEYTIEIPDSSEEPGKNIMQSQRDALVRSAI 260

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             L P+ R++ E R LQE   T E ++++ ++
Sbjct: 261 KNLPPKYRKVIEMRHLQE--RTYEEIAADLDI 290


>gi|312137932|ref|YP_004005268.1| sigma-70 factor [Rhodococcus equi 103S]
 gi|311887271|emb|CBH46582.1| putative sigma-70 factor [Rhodococcus equi 103S]
          Length = 191

 Score = 41.7 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 14/86 (16%), Positives = 29/86 (33%), Gaps = 2/86 (2%)

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
              +V +   +     E   R +        + VL  RER I   R +++        + 
Sbjct: 107 PVDIVPEVPVEFDTPEEHAMRAHDTQHAWSLIDVLTARERTILRLRIVEQQSA--AETAR 164

Query: 261 EFEVSRERVRQIEARAFKKVQESIQK 286
               +   VR  + RA  +++  +  
Sbjct: 165 VLNTTAGAVRVAQHRALNRLRAQLAS 190


>gi|329666767|gb|AEB92715.1| DNA-directed RNA polymerase sigma factor [Lactobacillus johnsonii
           DPC 6026]
          Length = 185

 Score = 41.7 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 27/149 (18%), Positives = 47/149 (31%), Gaps = 2/149 (1%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           E  L +R +E  D+ A H LV  +  L+    + +        +   E  I   Q+   +
Sbjct: 6   EVYLIRRVKEEQDMDALHELVERYRPLINGAKLNFFIRNFDHDDWEQEALIMCYQSCCTY 65

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D +R      Y        ++  +    +  +   T          + L           
Sbjct: 66  DEKRANSFGAYYRTKFYNHLRSLLRYELAQKRTSFTKAISYDNVVHKNLIKEEVEEMHIT 125

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            + E       KL  SE EVI++   L  
Sbjct: 126 PRKEMYQKFINKL--SEKEVIALKVFLGE 152


>gi|119720524|ref|YP_921019.1| bacterio-opsin activator [Thermofilum pendens Hrk 5]
 gi|119525644|gb|ABL79016.1| Bacterio-opsin activator, HTH domain protein [Thermofilum pendens
           Hrk 5]
          Length = 228

 Score = 41.7 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 21/101 (20%), Positives = 42/101 (41%), Gaps = 11/101 (10%)

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML--TRSMSVLNPRERRI---- 242
            I S ++ S        Y    + + ++  +  K+   +L  T  +S L P +R+I    
Sbjct: 117 FIISEEEPSILLDRLKKYGTVTRMEKVLLTDALKDSYALLMRTDLLSKLTPLQRKILSKA 176

Query: 243 -FEARRLQENPVTLENLSSEFEVSR----ERVRQIEARAFK 278
             +         +L +LS E  +S+    E +R+ E++  K
Sbjct: 177 IIKGYFDWPRKYSLSDLSQELGISKATLAEHIRRSESKILK 217


>gi|150017165|ref|YP_001309419.1| ECF subfamily RNA polymerase sigma-24 factor [Clostridium
           beijerinckii NCIMB 8052]
 gi|149903630|gb|ABR34463.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           beijerinckii NCIMB 8052]
          Length = 188

 Score = 41.7 bits (97), Expect = 0.15,   Method: Composition-based stats.
 Identities = 15/78 (19%), Positives = 32/78 (41%), Gaps = 1/78 (1%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           ++ D  A  +L      L+  I+           +++ E    L ++V  ++ ++  R  
Sbjct: 14  KNNDEEAKEKLAYEFKPLIYNISKRTFIDRYNAHDIIQECYHSLFKSVSMYNLKK-HRFV 72

Query: 103 TYSMWWIKAAMQEYILRS 120
            Y+   IK  M + I R+
Sbjct: 73  AYATNAIKNNMNDLIKRT 90


>gi|20451745|emb|CAD30268.1| RNA polymerase sigma-38 factor [Listonella anguillarum]
          Length = 42

 Score = 41.3 bits (96), Expect = 0.15,   Method: Composition-based stats.
 Identities = 11/29 (37%), Positives = 19/29 (65%)

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQ 287
             E  ++RERVRQI+    ++++E + KQ
Sbjct: 1   GREINLTRERVRQIQVEGLRRLREILVKQ 29


>gi|302545273|ref|ZP_07297615.1| putative RNA polymerase ECF-subfamily sigma factor [Streptomyces
           hygroscopicus ATCC 53653]
 gi|302462891|gb|EFL25984.1| putative RNA polymerase ECF-subfamily sigma factor [Streptomyces
           himastatinicus ATCC 53653]
          Length = 199

 Score = 41.3 bits (96), Expect = 0.15,   Method: Composition-based stats.
 Identities = 12/71 (16%), Positives = 29/71 (40%), Gaps = 2/71 (2%)

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
           + E          +  ++  L  R+R +   R   +  +T   ++    VSR  V+   +
Sbjct: 128 VDEPLLLAEEHRQVLDALGQLTARQREVLVLRYWSD--LTEAQIAETLGVSRGTVKSTAS 185

Query: 275 RAFKKVQESIQ 285
           RA   +++ ++
Sbjct: 186 RALATLEKLLE 196


>gi|299147198|ref|ZP_07040263.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 3_1_23]
 gi|298514476|gb|EFI38360.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 3_1_23]
          Length = 190

 Score = 41.3 bits (96), Expect = 0.15,   Method: Composition-based stats.
 Identities = 17/93 (18%), Positives = 44/93 (47%), Gaps = 2/93 (2%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
               + ++ +       E + I  E+ K  +  +   MSVL  R+R I   R ++E  ++
Sbjct: 100 DEIGEREETVDESPSTPETIYINNEQEKQVQATVHTMMSVLTDRQREIIYYRYIKE--MS 157

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++ +S   +++ + V     RA  ++++  +++
Sbjct: 158 IDEISKVTDMNNQSVSNSIQRALGRIRDLFKRK 190


>gi|221635894|ref|YP_002523770.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermomicrobium
           roseum DSM 5159]
 gi|221157747|gb|ACM06865.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermomicrobium
           roseum DSM 5159]
          Length = 247

 Score = 41.3 bits (96), Expect = 0.15,   Method: Composition-based stats.
 Identities = 13/78 (16%), Positives = 34/78 (43%), Gaps = 10/78 (12%)

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS----R 266
           +E      E+    R ++ ++++ L  R+R I   R   E  +  + ++    +S    +
Sbjct: 160 REACPRAAEDWSADRLLVEQALAKLRDRDREILYLRW--EAELGFDEIADLLGISPTAAQ 217

Query: 267 ERVRQIEARAFKKVQESI 284
            R      RA  ++++++
Sbjct: 218 RRA----HRALVRLRQAL 231


>gi|160885338|ref|ZP_02066341.1| hypothetical protein BACOVA_03337 [Bacteroides ovatus ATCC 8483]
 gi|156108960|gb|EDO10705.1| hypothetical protein BACOVA_03337 [Bacteroides ovatus ATCC 8483]
          Length = 190

 Score = 41.3 bits (96), Expect = 0.15,   Method: Composition-based stats.
 Identities = 17/93 (18%), Positives = 44/93 (47%), Gaps = 2/93 (2%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
               + ++ +       E + I  E+ K  +  +   MSVL  R+R I   R ++E  ++
Sbjct: 100 DEIGEREETVDESPSTPETIYINNEQEKQVQATVHTMMSVLTDRQREIIYYRYIKE--MS 157

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++ +S   +++ + V     RA  ++++  +++
Sbjct: 158 IDEISKVTDMNNQSVSNSIQRALGRIRDLFKRK 190


>gi|83815299|ref|YP_446597.1| ECF subfamily RNA polymerase sigma factor [Salinibacter ruber DSM
           13855]
 gi|83756693|gb|ABC44806.1| RNA polymerase sigma-70 factor, ECF subfamily [Salinibacter ruber
           DSM 13855]
          Length = 205

 Score = 41.3 bits (96), Expect = 0.15,   Method: Composition-based stats.
 Identities = 19/103 (18%), Positives = 39/103 (37%), Gaps = 18/103 (17%)

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           +   + +   + D L  D    +    E+  R  +R  L   +  L P ++ +   R  Q
Sbjct: 103 VPQDEDDGRSFWDTLEDDSPYAD----EQLHRAEQREWLDEHIEQLAPEQKEVLLLR--Q 156

Query: 250 ENPVTLENLSSEFEVS------RERVRQIEARAFKKVQESIQK 286
           E  +T   ++   +VS      R R       A K +++ ++ 
Sbjct: 157 ETDLTFREIAELQDVSINTALGRMR------YALKNLRKMMEA 193


>gi|152967344|ref|YP_001363128.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Kineococcus
           radiotolerans SRS30216]
 gi|151361861|gb|ABS04864.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Kineococcus
           radiotolerans SRS30216]
          Length = 176

 Score = 41.3 bits (96), Expect = 0.15,   Method: Composition-based stats.
 Identities = 12/59 (20%), Positives = 24/59 (40%), Gaps = 2/59 (3%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
            D       E   R     M+  ++  L  R+R +   R   E  ++ E++++   +SR
Sbjct: 96  PDPAPDGPEEHAVRAAEHRMVLGALDALPTRQREVLVLRYQGE--MSEEDIAAALGISR 152


>gi|116624796|ref|YP_826952.1| ECF subfamily RNA polymerase sigma-24 factor [Candidatus Solibacter
           usitatus Ellin6076]
 gi|116227958|gb|ABJ86667.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Candidatus
           Solibacter usitatus Ellin6076]
          Length = 203

 Score = 41.3 bits (96), Expect = 0.15,   Method: Composition-based stats.
 Identities = 16/91 (17%), Positives = 35/91 (38%), Gaps = 2/91 (2%)

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           + +         ++ +            +  +N +  ++  L PRER +FE R  Q   +
Sbjct: 111 ETSDGPIDRMDSFEEEAAHADPERSMWNRQLKNRIDNALEDLTPRERMVFELRHYQG--L 168

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L N+      + E  +    RA +K++  +
Sbjct: 169 RLRNIGEMLGTTEEAAKNCLFRATQKMRAVL 199


>gi|320101624|ref|YP_004177215.1| ECF subfamily RNA polymerase sigma-24 factor [Isosphaera pallida
           ATCC 43644]
 gi|319748906|gb|ADV60666.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Isosphaera pallida
           ATCC 43644]
          Length = 329

 Score = 41.3 bits (96), Expect = 0.16,   Method: Composition-based stats.
 Identities = 17/108 (15%), Positives = 34/108 (31%), Gaps = 2/108 (1%)

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
             L  D  +       D         L+      +    E    +    +L  +++ L  
Sbjct: 210 APLPLDVPVTPGGEGGDSAVGGGPARLLDMLALSQTSPSEAASNRELTVLLADALAQLPS 269

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            E  +          ++ E +     +SR+  R I AR  K V+  ++
Sbjct: 270 NEADVLWL--YHVEGLSFEAIGERLGISRKVARGIWARGLKTVKRQLE 315


>gi|237716608|ref|ZP_04547089.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D1]
 gi|262405384|ref|ZP_06081934.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 2_1_22]
 gi|229442591|gb|EEO48382.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D1]
 gi|262356259|gb|EEZ05349.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 2_1_22]
          Length = 190

 Score = 41.3 bits (96), Expect = 0.16,   Method: Composition-based stats.
 Identities = 17/93 (18%), Positives = 44/93 (47%), Gaps = 2/93 (2%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
               + ++ +       E + I  E+ K  +  +   MSVL  R+R I   R ++E  ++
Sbjct: 100 DEIGEREETVDESPSTPETIYINNEQEKQVQATVHTMMSVLTDRQREIIYYRYIKE--MS 157

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++ +S   +++ + V     RA  ++++  +++
Sbjct: 158 IDEISKVTDMNNQSVSNSIQRALGRIRDLFKRK 190


>gi|134096746|ref|YP_001102407.1| RNA polymerase ECF sigma factor [Saccharopolyspora erythraea NRRL
           2338]
 gi|133909369|emb|CAL99481.1| RNA polymerase ECF sigma factor [Saccharopolyspora erythraea NRRL
           2338]
          Length = 193

 Score = 41.3 bits (96), Expect = 0.16,   Method: Composition-based stats.
 Identities = 10/73 (13%), Positives = 29/73 (39%), Gaps = 2/73 (2%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
             V  +    +     + +++  L PR+R +   R      ++   ++    VS   V+ 
Sbjct: 114 PDVPAQPRHDRLEDEPVWQALQTLPPRQRAVVVLRFY--EGLSEAEIADTLGVSCGTVKS 171

Query: 272 IEARAFKKVQESI 284
             ++A   +++ +
Sbjct: 172 QNSKAMATLRKRL 184


>gi|293402445|ref|ZP_06646581.1| hypothetical protein HMPREF0863_02722 [Erysipelotrichaceae
           bacterium 5_2_54FAA]
 gi|291304108|gb|EFE45361.1| hypothetical protein HMPREF0863_02722 [Erysipelotrichaceae
           bacterium 5_2_54FAA]
          Length = 148

 Score = 41.3 bits (96), Expect = 0.16,   Method: Composition-based stats.
 Identities = 10/64 (15%), Positives = 27/64 (42%), Gaps = 2/64 (3%)

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            +L  +++ L  R+R I       +  ++   +     V R  V +    A  K+++ ++
Sbjct: 83  ELLAEALNALPERKRDIILLSYFLD--MSDAEIGELLNVVRTTVFRHRKSALAKIKQYLE 140

Query: 286 KQVE 289
            + +
Sbjct: 141 GKAD 144


>gi|294776971|ref|ZP_06742432.1| RNA polymerase sigma-70 factor [Bacteroides vulgatus PC510]
 gi|294449219|gb|EFG17758.1| RNA polymerase sigma-70 factor [Bacteroides vulgatus PC510]
          Length = 181

 Score = 41.3 bits (96), Expect = 0.16,   Method: Composition-based stats.
 Identities = 12/70 (17%), Positives = 36/70 (51%), Gaps = 2/70 (2%)

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
           + ++    + +  + R +  L PR++ +F+  R  +  +T + +++   +S + V +   
Sbjct: 106 MEDELSAADLKEFIKRMVGELPPRQQEVFKMSR--DEHLTYKEIATRLNISEKTVERHIN 163

Query: 275 RAFKKVQESI 284
            A K ++++I
Sbjct: 164 EAIKFLKKNI 173


>gi|194365795|ref|YP_002028405.1| ECF subfamily RNA polymerase sigma-24 subunit [Stenotrophomonas
           maltophilia R551-3]
 gi|194348599|gb|ACF51722.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Stenotrophomonas
           maltophilia R551-3]
          Length = 228

 Score = 41.3 bits (96), Expect = 0.16,   Method: Composition-based stats.
 Identities = 13/69 (18%), Positives = 32/69 (46%), Gaps = 2/69 (2%)

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           +  +D +      + Q  ++   ++ R   L  +++ L  R+R  F   R   + +T E+
Sbjct: 112 ADAEDAVQAIASDESQCPLQLSAQRQRLERLREALAELPERQREAFVLCRF--DGLTQED 169

Query: 258 LSSEFEVSR 266
           ++   ++SR
Sbjct: 170 VADRMQISR 178


>gi|150389630|ref|YP_001319679.1| ECF subfamily RNA polymerase sigma-24 factor [Alkaliphilus
           metalliredigens QYMF]
 gi|149949492|gb|ABR48020.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Alkaliphilus
           metalliredigens QYMF]
          Length = 170

 Score = 41.3 bits (96), Expect = 0.16,   Method: Composition-based stats.
 Identities = 14/67 (20%), Positives = 27/67 (40%), Gaps = 2/67 (2%)

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
             +    + D    E ++IEK + + +R  L R +  L+P  + I   R      +T E 
Sbjct: 71  PFYPMETLEDKHNTEDMVIEKIDLEEKREKLRRGLQQLDPDAKEILILRYYHN--LTYEE 128

Query: 258 LSSEFEV 264
           +     +
Sbjct: 129 MGKALSL 135


>gi|323692844|ref|ZP_08107071.1| hypothetical protein HMPREF9475_01934 [Clostridium symbiosum
           WAL-14673]
 gi|323503158|gb|EGB18993.1| hypothetical protein HMPREF9475_01934 [Clostridium symbiosum
           WAL-14673]
          Length = 145

 Score = 41.3 bits (96), Expect = 0.16,   Method: Composition-based stats.
 Identities = 10/64 (15%), Positives = 27/64 (42%), Gaps = 2/64 (3%)

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            +L  +++ L  R+R I       +  ++   +     V R  V +    A  K+++ ++
Sbjct: 80  ELLAEALNALPERKRDIILLSYFLD--MSDAEIGELLNVVRTTVFRHRKSALAKIKQYLE 137

Query: 286 KQVE 289
            + +
Sbjct: 138 GKAD 141


>gi|294508529|ref|YP_003572588.1| RNA polymerase sigma-E factor [Salinibacter ruber M8]
 gi|294344858|emb|CBH25636.1| RNA polymerase sigma-E factor [Salinibacter ruber M8]
          Length = 201

 Score = 41.3 bits (96), Expect = 0.16,   Method: Composition-based stats.
 Identities = 19/103 (18%), Positives = 39/103 (37%), Gaps = 18/103 (17%)

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           +   + +   + D L  D    +    E+  R  +R  L   +  L P ++ +   R  Q
Sbjct: 99  VPQDEDDGRSFWDTLEDDSPYAD----EQLHRAEQREWLDEHIEQLAPEQKEVLLLR--Q 152

Query: 250 ENPVTLENLSSEFEVS------RERVRQIEARAFKKVQESIQK 286
           E  +T   ++   +VS      R R       A K +++ ++ 
Sbjct: 153 ETDLTFREIAELQDVSINTALGRMR------YALKNLRKMMEA 189


>gi|194014280|ref|ZP_03052897.1| RNA polymerase sigma-I factor [Bacillus pumilus ATCC 7061]
 gi|194013306|gb|EDW22871.1| RNA polymerase sigma-I factor [Bacillus pumilus ATCC 7061]
          Length = 251

 Score = 41.3 bits (96), Expect = 0.16,   Method: Composition-based stats.
 Identities = 23/135 (17%), Positives = 53/135 (39%), Gaps = 8/135 (5%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMG-YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
           + GD+   + L+  +   V K      + Y     +  S G I   +A++K+  E+G  L
Sbjct: 26  QQGDIELQNALIEQYKPFVAKTVSSVCKRYIDEKDDEFSIGLIAFNEAIEKYSAEKGNSL 85

Query: 102 ATYSMWWIKAAMQEYI---LRSWSLVKIGTTANQKRLFFNLRRLKG----HLQAITDNNL 154
             ++   IK  + +YI    R+   V++    ++   +              + + +   
Sbjct: 86  LAFAELIIKRKVIDYIRKEARNAPTVQMDLQESENGEYSQSMIEAELSANEYRRLIEQEH 145

Query: 155 KPEQVVAIAKKLNVS 169
           + E++    ++L V 
Sbjct: 146 RREEIEHFKERLKVY 160


>gi|329954694|ref|ZP_08295754.1| Sigma-70 region 2 [Bacteroides clarus YIT 12056]
 gi|328527235|gb|EGF54239.1| Sigma-70 region 2 [Bacteroides clarus YIT 12056]
          Length = 182

 Score = 41.3 bits (96), Expect = 0.16,   Method: Composition-based stats.
 Identities = 19/88 (21%), Positives = 39/88 (44%), Gaps = 1/88 (1%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE VLA+R R+ GD  A   L   +   ++ + + Y G      +++ +G + L  +  K
Sbjct: 2   EEQVLAERCRQ-GDNLARKELYEQYAGRMLGVCLRYAGDRETAQDLMHDGFLKLFDSFDK 60

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRS 120
           F       L  +    +   + +Y+ ++
Sbjct: 61  FTWRGEGSLRAWMERVMVNTVLQYLRKN 88


>gi|317123813|ref|YP_004097925.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Intrasporangium
           calvum DSM 43043]
 gi|315587901|gb|ADU47198.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Intrasporangium
           calvum DSM 43043]
          Length = 255

 Score = 41.3 bits (96), Expect = 0.16,   Method: Composition-based stats.
 Identities = 16/79 (20%), Positives = 35/79 (44%), Gaps = 2/79 (2%)

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           D D Q      +   + R   L  ++  L+P +      R LQ   ++L   ++    S 
Sbjct: 175 DADEQVDAPEAEVLARLRDERLVTAIRQLSPEQAECITLRFLQG--LSLAETAAVLGKSE 232

Query: 267 ERVRQIEARAFKKVQESIQ 285
             ++Q++ RA + ++ S++
Sbjct: 233 GAIKQLQLRATRALRASLE 251


>gi|196229076|ref|ZP_03127942.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Chthoniobacter
           flavus Ellin428]
 gi|196227357|gb|EDY21861.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Chthoniobacter
           flavus Ellin428]
          Length = 203

 Score = 41.3 bits (96), Expect = 0.16,   Method: Composition-based stats.
 Identities = 28/223 (12%), Positives = 60/223 (26%), Gaps = 71/223 (31%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A   L+ +H   VV       G      ++  +  I + ++  +++P    +  
Sbjct: 27  KQGDTEALRELIEAHQHRVVGTVAKMLGDDCDAEDIAQQVFIRVWRSAARYEPT--AKFT 84

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           T+                           +  +F  LRR K H                 
Sbjct: 85  TWLF----------------------KITRNLVFNELRRRKRH----------------- 105

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
                       S++     D  + A                    D   +   +    +
Sbjct: 106 ---------PAHSLDAAAEDDRPMQAP-------------------DPSTKAPDDSLLNE 137

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
             +  + +++  L   +R     RR  + P   E++     +S
Sbjct: 138 EMQAAIQKAIEELPEIQRMAIVLRRYDDIPY--EDIGEILGLS 178


>gi|225389640|ref|ZP_03759364.1| hypothetical protein CLOSTASPAR_03388 [Clostridium asparagiforme
           DSM 15981]
 gi|225044306|gb|EEG54552.1| hypothetical protein CLOSTASPAR_03388 [Clostridium asparagiforme
           DSM 15981]
          Length = 191

 Score = 41.3 bits (96), Expect = 0.16,   Method: Composition-based stats.
 Identities = 17/77 (22%), Positives = 33/77 (42%), Gaps = 5/77 (6%)

Query: 48  SAAHRLVTSHLRLVVKIAMGYRG-----YGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
            A  +LV  +L +V  +   Y        GL  S++  EG + L +A   +  +   + +
Sbjct: 6   KAQQKLVAQNLPVVHWVICDYIHVNPTICGLEYSDLFQEGCLWLCKAAATYKDDGRAQFS 65

Query: 103 TYSMWWIKAAMQEYILR 119
           TY+   +K  +  Y  +
Sbjct: 66  TYAKTVVKNGLLSYCRK 82


>gi|116328079|ref|YP_797799.1| RNA polymerase sigma subunit [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116331468|ref|YP_801186.1| RNA polymerase sigma subunit [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
 gi|116120823|gb|ABJ78866.1| RNA polymerase sigma subunit [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116125157|gb|ABJ76428.1| RNA polymerase sigma subunit [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
          Length = 182

 Score = 41.3 bits (96), Expect = 0.16,   Method: Composition-based stats.
 Identities = 17/67 (25%), Positives = 38/67 (56%), Gaps = 2/67 (2%)

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
           +EE +N R +L + ++VL+ R+++I    +L    +++  +S    +S   V+ I  RA 
Sbjct: 114 QEELENVREILKKWLNVLDERQKQILTHLKL--EGMSVREVSERTGLSEFNVKVITHRAI 171

Query: 278 KKVQESI 284
           +K+++  
Sbjct: 172 QKIRKHF 178


>gi|291008444|ref|ZP_06566417.1| RNA polymerase ECF sigma factor [Saccharopolyspora erythraea NRRL
           2338]
          Length = 166

 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 10/73 (13%), Positives = 29/73 (39%), Gaps = 2/73 (2%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
             V  +    +     + +++  L PR+R +   R      ++   ++    VS   V+ 
Sbjct: 87  PDVPAQPRHDRLEDEPVWQALQTLPPRQRAVVVLRFY--EGLSEAEIADTLGVSCGTVKS 144

Query: 272 IEARAFKKVQESI 284
             ++A   +++ +
Sbjct: 145 QNSKAMATLRKRL 157


>gi|268318915|ref|YP_003292571.1| DNA-directed RNA polymerase sigma factor [Lactobacillus johnsonii
           FI9785]
 gi|262397290|emb|CAX66304.1| DNA-directed RNA polymerase sigma factor [Lactobacillus johnsonii
           FI9785]
          Length = 185

 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 27/149 (18%), Positives = 47/149 (31%), Gaps = 2/149 (1%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           E  L +R +E  D+ A H LV  +  L+    + +        +   E  I   Q+   +
Sbjct: 6   EVYLIRRVKEEQDMEALHELVERYRPLINGAKLNFFIRNFDNDDWEQEALIMCYQSCCTY 65

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           D +R      Y        ++  +    +  +   T          + L           
Sbjct: 66  DEKRANSFGAYYRTKFYNHLRSLLRYELAQKRTSFTKAISYDNVVHKNLIKEEVEEMQIT 125

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAG 182
            + E       KL  SE EVI++   L  
Sbjct: 126 PRKEMYQKFINKL--SEKEVIALKIFLGE 152


>gi|187918786|ref|YP_001887817.1| extracytoplasmic-function sigma-70 factor [Burkholderia
           phytofirmans PsJN]
 gi|187717224|gb|ACD18447.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Burkholderia
           phytofirmans PsJN]
          Length = 223

 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 19/97 (19%), Positives = 39/97 (40%), Gaps = 2/97 (2%)

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             + ++   R+  + S++A    S +N+    +         E         ++    + 
Sbjct: 91  VRQPVAYVTRMVRNASIDAFRRQSLENTYHADEDDGLHVPSPEPSPEAALLVRDTLRHVY 150

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
            ++  L  R R  FE  RL+E   TL+N +   +VS+
Sbjct: 151 NALEQLPARSRAAFEMVRLREE--TLQNTARALDVSQ 185


>gi|315301174|ref|ZP_07872439.1| RNA polymerase sigma-H factor [Listeria ivanovii FSL F6-596]
 gi|313630456|gb|EFR98324.1| RNA polymerase sigma-H factor [Listeria ivanovii FSL F6-596]
          Length = 75

 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 13/71 (18%), Positives = 29/71 (40%), Gaps = 2/71 (2%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           ++E  +L       GD  A     + +  +V   +  Y   G    +++ E  IGL +A+
Sbjct: 7   REEMKML--ELARSGDTDALEYFFSKYQSVVYWKSTQYFLQGAERDDLIQEAMIGLFKAI 64

Query: 91  KKFDPERGFRL 101
           + ++  +    
Sbjct: 65  RDYNQTKEASF 75


>gi|298480601|ref|ZP_06998798.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D22]
 gi|298273422|gb|EFI14986.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D22]
          Length = 190

 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 17/93 (18%), Positives = 44/93 (47%), Gaps = 2/93 (2%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
               + ++ +       E + I  E+ K  +  +   MSVL  R+R I   R ++E  ++
Sbjct: 100 DEIGEREETVDESPSTPETIYINNEQEKQVQATVHTMMSVLTDRQREIIYYRYIKE--MS 157

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++ +S   +++ + V     RA  ++++  +++
Sbjct: 158 IDEISKVTDMNNQSVSNSIQRALGRIRDLFKRK 190


>gi|312887286|ref|ZP_07746889.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Mucilaginibacter
           paludis DSM 18603]
 gi|311300244|gb|EFQ77310.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Mucilaginibacter
           paludis DSM 18603]
          Length = 198

 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 15/56 (26%), Positives = 22/56 (39%), Gaps = 2/56 (3%)

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           Q     E    K  R  L R ++ L  R R IF   R  E   + + ++    +SR
Sbjct: 109 QRDSTAENLLDKEYRLFLDRVLASLPERTREIFALCR--EQGKSYDEVADILGISR 162


>gi|254976992|ref|ZP_05273464.1| hypothetical protein CdifQC_16848 [Clostridium difficile QCD-66c26]
 gi|255651910|ref|ZP_05398812.1| hypothetical protein CdifQCD_17128 [Clostridium difficile
           QCD-37x79]
 gi|260687130|ref|YP_003218264.1| hypothetical protein CDR20291_1773 [Clostridium difficile R20291]
 gi|266622738|ref|ZP_06115673.1| conserved hypothetical protein [Clostridium hathewayi DSM 13479]
 gi|306521661|ref|ZP_07408008.1| hypothetical protein CdifQ_19490 [Clostridium difficile QCD-32g58]
 gi|260213147|emb|CBE04582.1| putative uncharacterized protein [Clostridium difficile R20291]
 gi|288865501|gb|EFC97799.1| conserved hypothetical protein [Clostridium hathewayi DSM 13479]
 gi|291541456|emb|CBL14566.1| DNA-directed RNA polymerase specialized sigma subunit [Ruminococcus
           bromii L2-63]
 gi|291557354|emb|CBL34471.1| DNA-directed RNA polymerase specialized sigma subunit [Eubacterium
           siraeum V10Sc8a]
 gi|295092180|emb|CBK78287.1| DNA-directed RNA polymerase specialized sigma subunit [Clostridium
           cf. saccharolyticum K10]
          Length = 145

 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 10/64 (15%), Positives = 27/64 (42%), Gaps = 2/64 (3%)

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            +L  +++ L  R+R I       +  ++   +     V R  V +    A  K+++ ++
Sbjct: 80  ELLAEALNALPERKRDIILLSYFLD--MSDAEIGELLNVVRTTVFRHRKSALAKIKQYLE 137

Query: 286 KQVE 289
            + +
Sbjct: 138 GKAD 141


>gi|289523039|ref|ZP_06439893.1| DNA-directed RNA polymerase specialized sigma subunit
           [Anaerobaculum hydrogeniformans ATCC BAA-1850]
 gi|289503582|gb|EFD24746.1| DNA-directed RNA polymerase specialized sigma subunit
           [Anaerobaculum hydrogeniformans ATCC BAA-1850]
          Length = 153

 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 18/64 (28%), Positives = 34/64 (53%), Gaps = 2/64 (3%)

Query: 58  LRLVVKIAMGYRGYGLPI-SEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEY 116
           + LV+K+A         +  ++V EG IGL  A++K+D  RG     ++   ++ AM  Y
Sbjct: 1   MPLVLKMASMLSNGDPHLKEDLVQEGYIGLYHAIRKYDENRGH-FPAFARTCVRNAMISY 59

Query: 117 ILRS 120
           + ++
Sbjct: 60  LRKN 63


>gi|256379685|ref|YP_003103345.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Actinosynnema
           mirum DSM 43827]
 gi|255923988|gb|ACU39499.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Actinosynnema
           mirum DSM 43827]
          Length = 642

 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 32/144 (22%), Positives = 56/144 (38%), Gaps = 22/144 (15%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + G+  A   LV ++L LV  +     G      +VV E    +++AV      R    
Sbjct: 15  AQRGEDGALDELVAAYLPLVYNVVGHALGGHPDTDDVVQET---MLRAVDSLGELRDP-- 69

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRL---------FFNLRRLKGHLQAITDN 152
           A +  W +  AM +   R     ++    +++ L         F +L   K HL      
Sbjct: 70  AAFRSWLLVIAMNQVRERHRR--RLPLPVDERSLADRADPGADFVDLALTKLHL------ 121

Query: 153 NLKPEQVVAIAKKLNVSESEVISM 176
             +  +VVA  + L   E E++S+
Sbjct: 122 TGQRREVVAATRWLGEEERELLSL 145


>gi|255530218|ref|YP_003090590.1| RNA polymerase sigma-70 factor [Pedobacter heparinus DSM 2366]
 gi|255343202|gb|ACU02528.1| RNA polymerase sigma-70 factor [Pedobacter heparinus DSM 2366]
          Length = 203

 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 12/63 (19%), Positives = 33/63 (52%), Gaps = 2/63 (3%)

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
            E    +  R ++ +++S L  +++++F   R  E  ++ E+++ E  +S+ R++ I   
Sbjct: 118 EEALLMRESRALIDKALSTLPAQKQQVFRMCR--EEGMSHEDIALEMGLSKSRIKNIMVE 175

Query: 276 AFK 278
             +
Sbjct: 176 VLR 178


>gi|167587227|ref|ZP_02379615.1| extracytoplasmic-function sigma-70 factor PvdS [Burkholderia
           ubonensis Bu]
          Length = 187

 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 16/97 (16%), Positives = 40/97 (41%), Gaps = 2/97 (2%)

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             + ++   R+  + S++A    + ++     +   +D    E         ++    ++
Sbjct: 55  VRQPVAYVTRMVRNASIDACRRQNLESLYHADEDDGFDVPSPEPTPEAALMTRDTLRRVS 114

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
            ++  L  R R  FE  RL++   TL++ +    VS+
Sbjct: 115 AALDDLPARSRAAFEMVRLRDE--TLQSAARALNVSQ 149


>gi|271962405|ref|YP_003336601.1| ECF subfamily RNA polymerase sigma-24 subunit [Streptosporangium
           roseum DSM 43021]
 gi|270505580|gb|ACZ83858.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Streptosporangium
           roseum DSM 43021]
          Length = 170

 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 14/70 (20%), Positives = 33/70 (47%), Gaps = 10/70 (14%)

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV----RQIE 273
             E  + R ++  +++ L PR+R +   R  ++   T   ++    V   RV     QI 
Sbjct: 96  HAEVADLRLVMRGALARLTPRQRTVLVLRYFEDLSET--EIARLLGV---RVGSVRSQIY 150

Query: 274 ARAFKKVQES 283
            R+ ++++++
Sbjct: 151 -RSLERLKKA 159


>gi|256424175|ref|YP_003124828.1| LuxR family transcriptional regulator [Chitinophaga pinensis DSM
           2588]
 gi|256039083|gb|ACU62627.1| two component transcriptional regulator, LuxR family [Chitinophaga
           pinensis DSM 2588]
          Length = 234

 Score = 41.3 bits (96), Expect = 0.17,   Method: Composition-based stats.
 Identities = 24/114 (21%), Positives = 54/114 (47%), Gaps = 16/114 (14%)

Query: 190 INSSDKNSSQWQDWLVYDHDG-QEQVLIEKEERKNRRNMLTRSMSV----LNPRERRIFE 244
           I+ +D+     Q  L+  ++      L+ +    NR+N L   +      LN RE++I +
Sbjct: 106 ISKTDEPEELLQAILMASNNKLYCNKLLTEALYWNRQNKLGEHLQTSTVELNDREKKILQ 165

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQ 298
               ++N      ++ E  +S   +R IE     K+++ +++++ + S+  LL+
Sbjct: 166 MLWDEKNNR---EIAEELFLS---IRSIE-----KIRQDMKEKLGVRSTVGLLK 208


>gi|189350466|ref|YP_001946094.1| extracytoplasmic-function sigma-70 factor [Burkholderia multivorans
           ATCC 17616]
 gi|189334488|dbj|BAG43558.1| ECF subfamily RNA polymerase sigma-70 factor [Burkholderia
           multivorans ATCC 17616]
          Length = 213

 Score = 41.3 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 18/97 (18%), Positives = 39/97 (40%), Gaps = 2/97 (2%)

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             + ++   R+  + S++A    + +N     +   +D    E         ++    ++
Sbjct: 81  VRQPVAYVTRMVRNASIDACRRQNLENIHHADEDDGFDVPSPEPTPEAALITRDTLRRVS 140

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
            ++  L  R R  FE  RL+E   TL+  +    VS+
Sbjct: 141 AALDDLPARSRAAFEMVRLREE--TLQTAARALNVSQ 175


>gi|37523010|ref|NP_926387.1| hypothetical protein gll3441 [Gloeobacter violaceus PCC 7421]
 gi|35214013|dbj|BAC91382.1| gll3441 [Gloeobacter violaceus PCC 7421]
          Length = 305

 Score = 41.3 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 42/111 (37%), Gaps = 15/111 (13%)

Query: 174 ISMNCRLAGDESLNALIN--SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
             +  R+A  +SL+  +   +    S+   + +   +   E  LIE    ++ R     +
Sbjct: 177 RQIARRIARPDSLDRPVRLSAGGDESTSQAELVSVSYPCVEDGLIE----EDCRERFVEA 232

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +  L   ++ +     L     T + +++    +  R+ Q       ++++
Sbjct: 233 LEQLGEADKVLLTRLYLLGE--TQKEIAASLGRTPARISQ-------RLRQ 274


>gi|161524779|ref|YP_001579791.1| extracytoplasmic-function sigma-70 factor [Burkholderia multivorans
           ATCC 17616]
 gi|160342208|gb|ABX15294.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Burkholderia
           multivorans ATCC 17616]
          Length = 215

 Score = 41.3 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 18/97 (18%), Positives = 39/97 (40%), Gaps = 2/97 (2%)

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             + ++   R+  + S++A    + +N     +   +D    E         ++    ++
Sbjct: 83  VRQPVAYVTRMVRNASIDACRRQNLENIHHADEDDGFDVPSPEPTPEAALITRDTLRRVS 142

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
            ++  L  R R  FE  RL+E   TL+  +    VS+
Sbjct: 143 AALDDLPARSRAAFEMVRLREE--TLQTAARALNVSQ 177


>gi|119717396|ref|YP_924361.1| sigma-70 region 2 domain-containing protein [Nocardioides sp.
           JS614]
 gi|119538057|gb|ABL82674.1| sigma-70 region 2 domain protein [Nocardioides sp. JS614]
          Length = 292

 Score = 41.3 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 23/107 (21%), Positives = 42/107 (39%), Gaps = 2/107 (1%)

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             +  +   R+    SLN L   +        +WL         V  + E  ++    + 
Sbjct: 49  VRDPRAYLVRIVTRLSLNRLRTLTRLREEYVGEWLPEPLLTSPDVAEDVELAESVSIAML 108

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
             +  L P ER +F  R + + P   + +++  + S   VRQI +RA
Sbjct: 109 AVLETLLPTERAVFVLREVFDVPY--DEIAAALDKSSAAVRQIASRA 153


>gi|186472874|ref|YP_001860216.1| ECF subfamily RNA polymerase sigma-24 factor [Burkholderia phymatum
           STM815]
 gi|184195206|gb|ACC73170.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Burkholderia
           phymatum STM815]
          Length = 244

 Score = 41.3 bits (96), Expect = 0.18,   Method: Composition-based stats.
 Identities = 19/98 (19%), Positives = 38/98 (38%), Gaps = 2/98 (2%)

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              + ++   R+  + S++A    S +N+    +    D    E         ++     
Sbjct: 101 DVRQPLAYVARMVRNASIDACRRQSLENTWHTCEEDGLDVPSPEPTPESALVTRDTLRHA 160

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
             +++ L  R R  FE  RL+E   TL+  +    VS+
Sbjct: 161 FDALAQLPERTRSAFERVRLREE--TLQETARALNVSQ 196


>gi|313202507|ref|YP_004041164.1| RNA polymerase, sigma-24 subunit, ecf subfamily [Paludibacter
           propionicigenes WB4]
 gi|312441823|gb|ADQ78179.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Paludibacter
           propionicigenes WB4]
          Length = 189

 Score = 41.3 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 18/107 (16%), Positives = 43/107 (40%), Gaps = 18/107 (16%)

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL       D     + D +  D    E  +    +    R +  ++++ L  ++R++F 
Sbjct: 86  SLEDFAYEDDDGQMVFPDVIQTDVQEAETTM----DTALLRELFFKALNELPEKQRQVFV 141

Query: 245 ARRLQENPVTLENLSSEFE------VSRERVRQIEARAFKKVQESIQ 285
               +   +TL+ ++ +        +SR+R       A  +++E +Q
Sbjct: 142 L--NEMEEMTLQQIADQTGESIKTIISRKR------YAVTRLREQLQ 180


>gi|167762454|ref|ZP_02434581.1| hypothetical protein BACSTE_00809 [Bacteroides stercoris ATCC
           43183]
 gi|167699560|gb|EDS16139.1| hypothetical protein BACSTE_00809 [Bacteroides stercoris ATCC
           43183]
          Length = 182

 Score = 41.3 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 19/88 (21%), Positives = 39/88 (44%), Gaps = 1/88 (1%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE VLA+R R+ GD  A   L   +   ++ + + Y G      +++ +G + L  +  K
Sbjct: 2   EEQVLAERCRQ-GDNLARKELYEQYAGRMLGVCLRYAGDRETAQDLMHDGFLKLFDSFDK 60

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRS 120
           F       L  +    +   + +Y+ ++
Sbjct: 61  FTWRGEGSLRAWMERVMVNTVLQYLRKN 88


>gi|291461239|ref|ZP_06027789.2| RNA polymerase sigma factor [Fusobacterium periodonticum ATCC
           33693]
 gi|291378120|gb|EFE85638.1| RNA polymerase sigma factor [Fusobacterium periodonticum ATCC
           33693]
          Length = 259

 Score = 41.3 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 22/64 (34%), Positives = 37/64 (57%), Gaps = 2/64 (3%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V  +L+ V +IA+     G+   ++  EG IGLM+A + F+ ++ F+L  Y  ++I  AM
Sbjct: 69  VEKNLKKVYQIALYMLRDGILYQDLTQEGVIGLMKAHELFEDDKDFKL--YKDYYIARAM 126

Query: 114 QEYI 117
             YI
Sbjct: 127 FNYI 130


>gi|256845589|ref|ZP_05551047.1| RNA polymerase sigma factor [Fusobacterium sp. 3_1_36A2]
 gi|256719148|gb|EEU32703.1| RNA polymerase sigma factor [Fusobacterium sp. 3_1_36A2]
          Length = 274

 Score = 41.3 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 29/127 (22%), Positives = 51/127 (40%), Gaps = 5/127 (3%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V  +L+ V ++A+     G+   ++  EG IGL++A + F+ ++ F+L  Y  ++I   M
Sbjct: 84  VEKNLKKVYEMALYMLREGISYDDLTQEGIIGLIKAHELFEEDKDFKL--YKDYYIAREM 141

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
             YI    +  K       K        LK  L+   D N   E      +       E+
Sbjct: 142 FNYINNYANYRKSAFKDYAKHEIHKNNHLKVSLK---DRNKSEELKKLEKENKEKHIKEI 198

Query: 174 ISMNCRL 180
             +  R 
Sbjct: 199 KQLEKRA 205


>gi|317476760|ref|ZP_07936003.1| sigma-70 family RNA polymerase sigma factor [Bacteroides eggerthii
           1_2_48FAA]
 gi|316906935|gb|EFV28646.1| sigma-70 family RNA polymerase sigma factor [Bacteroides eggerthii
           1_2_48FAA]
          Length = 187

 Score = 41.3 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 20/93 (21%), Positives = 42/93 (45%), Gaps = 1/93 (1%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           + E+ EE VLA+R R+ GD  A   L   +   ++ + + Y G      +++ +G + L 
Sbjct: 2   LEERMEEQVLAERCRQ-GDNLARKELYERYAGRMLGVCLRYAGDRETAQDLMHDGFLKLF 60

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
            +  KF       L  +    +   + +Y+ ++
Sbjct: 61  DSFDKFTWRGEGSLRAWMERVMVNTVLQYLRKN 93


>gi|296448676|ref|ZP_06890540.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Methylosinus
           trichosporium OB3b]
 gi|296253823|gb|EFH00986.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Methylosinus
           trichosporium OB3b]
          Length = 167

 Score = 41.3 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 19/86 (22%), Positives = 38/86 (44%), Gaps = 2/86 (2%)

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
            D    D   Q        +   R  +L ++++ L PR R IFE R    + ++   ++ 
Sbjct: 84  DDGEAADAPSQMASAESLVDDARRALLLAQAVATLPPRCREIFELR--VTHNLSQREIAE 141

Query: 261 EFEVSRERVRQIEARAFKKVQESIQK 286
              +SR+ V Q    A ++ + ++Q+
Sbjct: 142 RLGISRKTVEQHFHLAMERCRAALQQ 167


>gi|228907436|ref|ZP_04071294.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus
           thuringiensis IBL 200]
 gi|228852297|gb|EEM97093.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus
           thuringiensis IBL 200]
          Length = 188

 Score = 41.3 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 16/83 (19%), Positives = 35/83 (42%), Gaps = 10/83 (12%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           H   E+   ++      R  L + ++ L P ++++F  + L       E +  +  ++R 
Sbjct: 104 HISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKT--EEIGEKLGLTRA 161

Query: 268 ----RVRQIEARAFKKVQESIQK 286
               RV     R  KK++++  K
Sbjct: 162 AIDNRV----YRGKKKLKQNATK 180


>gi|325003485|ref|ZP_08124597.1| RNA polymerase, sigma-24 subunit, ECF subfamily protein
           [Pseudonocardia sp. P1]
          Length = 293

 Score = 41.3 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 23/130 (17%), Positives = 48/130 (36%), Gaps = 11/130 (8%)

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM- 227
           +     +   R+   ++LN L +++    +    WL            E+  R +   + 
Sbjct: 51  TVQNPRAYLARIVTRQALNRLRSTARTRETYPGPWLPEPLPTDPAGADEQVLRTDDVTVA 110

Query: 228 LTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           +   +  L+P ER +F  R      +      ++       + VRQI  RA    +E ++
Sbjct: 111 MLLVLETLSPDERAVFVLREAFGLGH----AEIAETLGRPEDTVRQIAHRA----REHVR 162

Query: 286 KQVELSSSPP 295
            +    + PP
Sbjct: 163 ARRPRFTVPP 172


>gi|282857702|ref|ZP_06266911.1| RNA polymerase sigma factor [Pyramidobacter piscolens W5455]
 gi|282584372|gb|EFB89731.1| RNA polymerase sigma factor [Pyramidobacter piscolens W5455]
          Length = 168

 Score = 41.3 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 19/77 (24%), Positives = 34/77 (44%), Gaps = 1/77 (1%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF-RLATYS 105
               +      L L  KIA  Y   G    ++V EG I L + V+++D ER   RL+ + 
Sbjct: 10  KEQLNETALRFLPLAKKIAWQYTRRGAEYEDLVQEGMIALFELVRRYDEERPPQRLSLFI 69

Query: 106 MWWIKAAMQEYILRSWS 122
            + ++  +++   R   
Sbjct: 70  WYRLRGRVRDAAARLRR 86


>gi|115351582|ref|YP_773421.1| extracytoplasmic-function sigma-70 factor [Burkholderia ambifaria
           AMMD]
 gi|115281570|gb|ABI87087.1| RNA polymerase, sigma-24 subunit, RpoE [Burkholderia ambifaria
           AMMD]
          Length = 222

 Score = 41.3 bits (96), Expect = 0.19,   Method: Composition-based stats.
 Identities = 19/97 (19%), Positives = 39/97 (40%), Gaps = 2/97 (2%)

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             + ++   R+  + S++A    S +N    ++   +D    E         ++    + 
Sbjct: 90  VRQPVAYVTRMVRNASIDACRRQSLENVYHTEEDDGFDVPSPEPTPEAALMTRDTLRRVW 149

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
            ++  L  R R  FE  RL+E   TL+  +    VS+
Sbjct: 150 AALDDLPARSRAAFEMVRLREE--TLQTAARALNVSQ 184


>gi|152964182|ref|YP_001359966.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Kineococcus
           radiotolerans SRS30216]
 gi|151358699|gb|ABS01702.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Kineococcus
           radiotolerans SRS30216]
          Length = 169

 Score = 41.3 bits (96), Expect = 0.20,   Method: Composition-based stats.
 Identities = 10/59 (16%), Positives = 28/59 (47%), Gaps = 2/59 (3%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
            D  ++ + +    +  R+ +  ++  L PR+R +   R  ++     E ++ + +V+R
Sbjct: 80  EDHHDRAVPDGTAERAERSRVVEALRRLPPRQRAVIVLRYFEDWSE--EQIADQLDVTR 136


>gi|237713849|ref|ZP_04544330.1| conserved hypothetical protein [Bacteroides sp. D1]
 gi|262409242|ref|ZP_06085786.1| conserved hypothetical protein [Bacteroides sp. 2_1_22]
 gi|293371822|ref|ZP_06618232.1| RNA polymerase sigma-70 factor [Bacteroides ovatus SD CMC 3f]
 gi|294645961|ref|ZP_06723629.1| RNA polymerase sigma-70 factor [Bacteroides ovatus SD CC 2a]
 gi|294808243|ref|ZP_06767005.1| RNA polymerase sigma-70 factor [Bacteroides xylanisolvens SD CC 1b]
 gi|298482329|ref|ZP_07000516.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D22]
 gi|229446005|gb|EEO51796.1| conserved hypothetical protein [Bacteroides sp. D1]
 gi|262352989|gb|EEZ02085.1| conserved hypothetical protein [Bacteroides sp. 2_1_22]
 gi|292633274|gb|EFF51845.1| RNA polymerase sigma-70 factor [Bacteroides ovatus SD CMC 3f]
 gi|292638706|gb|EFF57056.1| RNA polymerase sigma-70 factor [Bacteroides ovatus SD CC 2a]
 gi|294444549|gb|EFG13254.1| RNA polymerase sigma-70 factor [Bacteroides xylanisolvens SD CC 1b]
 gi|298271616|gb|EFI13190.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D22]
          Length = 195

 Score = 41.0 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 15/65 (23%), Positives = 32/65 (49%), Gaps = 8/65 (12%)

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE---ARA 276
              +    L  ++  L P+ER +FE  RL+      + +++   +S   VR +E   ++A
Sbjct: 120 LYSDLCRQLKNALEQLPPQEREVFEMSRLENIKY--QEIANRLNIS---VRTVEVRISKA 174

Query: 277 FKKVQ 281
            K+++
Sbjct: 175 LKQLR 179


>gi|218130025|ref|ZP_03458829.1| hypothetical protein BACEGG_01608 [Bacteroides eggerthii DSM 20697]
 gi|217987745|gb|EEC54072.1| hypothetical protein BACEGG_01608 [Bacteroides eggerthii DSM 20697]
          Length = 182

 Score = 41.0 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 19/88 (21%), Positives = 39/88 (44%), Gaps = 1/88 (1%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE VLA+R R+ GD  A   L   +   ++ + + Y G      +++ +G + L  +  K
Sbjct: 2   EEQVLAERCRQ-GDNLARKELYERYAGRMLGVCLRYAGDRETAQDLMHDGFLKLFDSFDK 60

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRS 120
           F       L  +    +   + +Y+ ++
Sbjct: 61  FTWRGEGSLRAWMERVMVNTVLQYLRKN 88


>gi|296327930|ref|ZP_06870465.1| RNA polymerase sigma factor [Fusobacterium nucleatum subsp.
           nucleatum ATCC 23726]
 gi|296154886|gb|EFG95668.1| RNA polymerase sigma factor [Fusobacterium nucleatum subsp.
           nucleatum ATCC 23726]
          Length = 274

 Score = 41.0 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 20/66 (30%), Positives = 36/66 (54%), Gaps = 2/66 (3%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V  +L+ V +IA+     G+   ++  EG IGL++A + F+ ++ F+L  Y  ++I   M
Sbjct: 84  VEKNLKKVYEIALYMLRDGISYEDLTQEGIIGLIKAHELFEDDKDFKL--YKDYYIAKEM 141

Query: 114 QEYILR 119
             YI  
Sbjct: 142 FNYINN 147


>gi|237722784|ref|ZP_04553265.1| conserved hypothetical protein [Bacteroides sp. 2_2_4]
 gi|229447306|gb|EEO53097.1| conserved hypothetical protein [Bacteroides sp. 2_2_4]
          Length = 195

 Score = 41.0 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 15/65 (23%), Positives = 32/65 (49%), Gaps = 8/65 (12%)

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE---ARA 276
              +    L  ++  L P+ER +FE  RL+      + +++   +S   VR +E   ++A
Sbjct: 120 LYSDLCRQLKNALEQLPPQEREVFEMSRLENIKY--QEIANRLNIS---VRTVEVRISKA 174

Query: 277 FKKVQ 281
            K+++
Sbjct: 175 LKQLR 179


>gi|283781804|ref|YP_003372559.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Pirellula staleyi
           DSM 6068]
 gi|283440257|gb|ADB18699.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Pirellula staleyi
           DSM 6068]
          Length = 185

 Score = 41.0 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 18/90 (20%), Positives = 38/90 (42%), Gaps = 17/90 (18%)

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
            +  +   +    V++E +ER     +L  ++  L P E+ IF  R  Q   +T E ++ 
Sbjct: 103 DEMQLTSREQPPDVILENDERM---ALLRDALRALRPEEQEIFLLR--QNGNLTYEEIAK 157

Query: 261 EFEV------SRERVRQIEARAFKKVQESI 284
           E  +      +R R+      A   +++ +
Sbjct: 158 ELNIPPGTVKTRMRL------ALNHLRQVL 181


>gi|251778668|ref|ZP_04821588.1| sigma-70 region 2 domain protein [Clostridium botulinum E1 str.
           'BoNT E Beluga']
 gi|243082983|gb|EES48873.1| sigma-70 region 2 domain protein [Clostridium botulinum E1 str.
           'BoNT E Beluga']
          Length = 195

 Score = 41.0 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 16/85 (18%), Positives = 37/85 (43%), Gaps = 2/85 (2%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           +LAK  + +GD  +   L+      +  ++     +G    ++ +E    L + +  +D 
Sbjct: 8   MLAKEAK-NGDNLSKENLIEEFRPFIRNLSRKTFIHGYDKDDIENECYKNLFKCLNSYDL 66

Query: 96  ERGFRLATYSMWWIKAAMQEYILRS 120
           E+  R   Y+   IK  + + I ++
Sbjct: 67  EK-HRFVAYATNGIKNNLNDLIRKT 90


>gi|238925874|ref|YP_002939392.1| hypothetical protein EUBREC_3532 [Eubacterium rectale ATCC 33656]
 gi|238877551|gb|ACR77258.1| Hypothetical protein EUBREC_3532 [Eubacterium rectale ATCC 33656]
          Length = 191

 Score = 41.0 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 17/130 (13%), Positives = 42/130 (32%), Gaps = 2/130 (1%)

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
            +  E   A+      S+++ + +   L                S   + +++ D     
Sbjct: 57  EITKEVAYAMNNFYRSSKAKKVEIKNELGEVVDKMLREVPYSGQSIDGEGFMIEDFPDLN 116

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
             +      K  +  + + ++ LN  ER I      +    T   ++    +SR+ +   
Sbjct: 117 CDVEHSVLTKMEQQDIHKVINQLNSEERMIIYGIFFEN--KTQTQMAEIMGISRQMLSYK 174

Query: 273 EARAFKKVQE 282
                 K++E
Sbjct: 175 LKSILNKMRE 184


>gi|284033449|ref|YP_003383380.1| ECF subfamily RNA polymerase sigma-24 subunit [Kribbella flavida
           DSM 17836]
 gi|283812742|gb|ADB34581.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Kribbella flavida
           DSM 17836]
          Length = 181

 Score = 41.0 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 16/82 (19%), Positives = 32/82 (39%), Gaps = 12/82 (14%)

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS----RERVRQIEARAFK 278
           + R+ L R+++ L  R R     R  ++ P     ++     S    +  V     R   
Sbjct: 100 DDRDQLLRALATLPRRTRAALVLRFFEDLPD--AEIAKVMGCSVGTVKSTVS----RGLA 153

Query: 279 KVQESIQKQVELSSSPPLLQKP 300
           K++E     +  ++SP    +P
Sbjct: 154 KLREH--HLLTETNSPTPAPRP 173


>gi|157692018|ref|YP_001486480.1| putative RNA polymerase sigma factor SigI [Bacillus pumilus
           SAFR-032]
 gi|157680776|gb|ABV61920.1| DNA-directed RNA polymerase sigma subunit SgiI [Bacillus pumilus
           SAFR-032]
          Length = 251

 Score = 41.0 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 23/135 (17%), Positives = 52/135 (38%), Gaps = 8/135 (5%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMG-YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
           + GD    + L+  +   V K      + Y     +  S G I   +A++K+  E+G  L
Sbjct: 26  QQGDTELQNALIEQYKPFVAKTVSSVCKRYIDEKDDEFSIGLIAFNEAIEKYSAEKGNSL 85

Query: 102 ATYSMWWIKAAMQEYI---LRSWSLVKIGTTANQKRLFFNLRRLKG----HLQAITDNNL 154
             ++   IK  + +YI    R+   V++    ++   +              + + +   
Sbjct: 86  LAFAELIIKRKVIDYIRKEARNAPTVQMDLQESENGEYSQSMIEAELSTNEYRRLIEQEH 145

Query: 155 KPEQVVAIAKKLNVS 169
           + E++    ++L V 
Sbjct: 146 RREEIEHFKERLKVY 160


>gi|260175073|ref|ZP_05761485.1| RNA polymerase, sigma-24 subunit, ECF subfamily protein
           [Bacteroides sp. D2]
 gi|315923301|ref|ZP_07919541.1| RNA polymerase [Bacteroides sp. D2]
 gi|313697176|gb|EFS34011.1| RNA polymerase [Bacteroides sp. D2]
          Length = 195

 Score = 41.0 bits (95), Expect = 0.20,   Method: Composition-based stats.
 Identities = 15/65 (23%), Positives = 32/65 (49%), Gaps = 8/65 (12%)

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE---ARA 276
              +    L  ++  L P+ER +FE  RL+      + +++   +S   VR +E   ++A
Sbjct: 120 LYSDLCRQLKNALEQLPPQEREVFEMSRLENIKY--QEIANRLNIS---VRTVEVRISKA 174

Query: 277 FKKVQ 281
            K+++
Sbjct: 175 LKQLR 179


>gi|196230800|ref|ZP_03129661.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Chthoniobacter
           flavus Ellin428]
 gi|196225141|gb|EDY19650.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Chthoniobacter
           flavus Ellin428]
          Length = 206

 Score = 41.0 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 7/69 (10%), Positives = 27/69 (39%), Gaps = 2/69 (2%)

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           S++ +   + +    + +  E+  R     ++   +  L+ R R +   R      ++ +
Sbjct: 114 STEDESCPIQEASDSQPLPDEQIARWEGIGLVRLVLETLDERSRELIRLRF--NEDLSYK 171

Query: 257 NLSSEFEVS 265
            ++    ++
Sbjct: 172 EIAERTGLT 180


>gi|160884952|ref|ZP_02065955.1| hypothetical protein BACOVA_02944 [Bacteroides ovatus ATCC 8483]
 gi|299147652|ref|ZP_07040716.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 3_1_23]
 gi|156109302|gb|EDO11047.1| hypothetical protein BACOVA_02944 [Bacteroides ovatus ATCC 8483]
 gi|298514439|gb|EFI38324.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 3_1_23]
          Length = 195

 Score = 41.0 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 15/65 (23%), Positives = 32/65 (49%), Gaps = 8/65 (12%)

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE---ARA 276
              +    L  ++  L P+ER +FE  RL+      + +++   +S   VR +E   ++A
Sbjct: 120 LYSDLCRQLKNALEQLPPQEREVFEMSRLENIKY--QEIANRLNIS---VRTVEVRISKA 174

Query: 277 FKKVQ 281
            K+++
Sbjct: 175 LKQLR 179


>gi|78066248|ref|YP_369017.1| extracytoplasmic-function sigma-70 factor PvdS [Burkholderia sp.
           383]
 gi|77966993|gb|ABB08373.1| RNA polymerase, sigma-24 subunit, RpoE [Burkholderia sp. 383]
          Length = 218

 Score = 41.0 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 19/97 (19%), Positives = 39/97 (40%), Gaps = 2/97 (2%)

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             + ++   R+  + S++A    S +N    ++   +D    E         ++    + 
Sbjct: 86  VRQPVAYVTRMVRNASIDACRRQSLENVYHTEEDDGFDVPSPEPTPEAALLTRDTLRRVW 145

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
            ++  L  R R  FE  RL+E   TL+  +    VS+
Sbjct: 146 AALDDLPARSRAAFEMVRLREE--TLQTAARALNVSQ 180


>gi|332983352|ref|YP_004464793.1| Sigma-70 region 4 type 2 [Mahella australiensis 50-1 BON]
 gi|332701030|gb|AEE97971.1| Sigma-70 region 4 type 2 [Mahella australiensis 50-1 BON]
          Length = 164

 Score = 41.0 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 27/139 (19%), Positives = 60/139 (43%), Gaps = 11/139 (7%)

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
           +N +    +  +    +    E    + R+     L+A  +   +++     +L  +   
Sbjct: 31  ENGVTEADIQLLHTMDDNEVDEQRRYDYRVTAH--LDAYHDGEGEDADDRNKYLADETGN 88

Query: 211 QEQVLIEKEERKNRRNMLTR---SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            E ++I+ E     R+ML +   +M  L P+++ +F+   L     T   +++E  V+  
Sbjct: 89  PELLIIQAENEAEHRDMLDKLRIAMECLLPQQKELFKKVYL--EKRTNTEIAAEEGVTEA 146

Query: 268 RVRQIEARAFKKVQESIQK 286
            +R    R  KK+QE ++K
Sbjct: 147 AIR---GR-LKKLQEKLRK 161


>gi|295085358|emb|CBK66881.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase
           sigma-70 factor, Bacteroides expansion family 1
           [Bacteroides xylanisolvens XB1A]
          Length = 195

 Score = 41.0 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 15/65 (23%), Positives = 32/65 (49%), Gaps = 8/65 (12%)

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE---ARA 276
              +    L  ++  L P+ER +FE  RL+      + +++   +S   VR +E   ++A
Sbjct: 120 LYSDLCRQLKNALEQLPPQEREVFEMSRLENIKY--QEIANHLNIS---VRTVEVRISKA 174

Query: 277 FKKVQ 281
            K+++
Sbjct: 175 LKQLR 179


>gi|219114075|ref|XP_002176215.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|219114140|ref|XP_002176244.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217402780|gb|EEC42763.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
 gi|217402817|gb|EEC42793.1| predicted protein [Phaeodactylum tricornutum CCAP 1055/1]
          Length = 472

 Score = 41.0 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 34/207 (16%), Positives = 68/207 (32%), Gaps = 24/207 (11%)

Query: 35  YVLAKRY-------REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS------EVVSE 81
             LA+R        R+  DL      V   LRLV  +                  E+V E
Sbjct: 82  RDLAERIWNWEQQRRQELDLPKIEYSVREGLRLVDCLVHEVLRTRSEAVTRSSRVELVQE 141

Query: 82  GNIGLMQAVKKFDPERGF--RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNL 139
           G + L+ A+  +  E          +   I+  +   +      V++      + +   +
Sbjct: 142 GLVSLLDAMSHYRKEDHTETDFEHTARKQIRKHLIRSLDLDTRPVRLP-----RAVIVMV 196

Query: 140 RRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS-MNCRLAGDESLNALINSSDKNSS 198
           R+ K   + I D   +      +A++L ++   +   +     G  S+ + +   + N  
Sbjct: 197 RKAKELKRTIIDEKGRQPTWNDVAEELQIARERLHDYLIMAQGGTLSMESTV---EINHP 253

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRR 225
             +D      D +E  L +       R
Sbjct: 254 HLEDARPAYEDQEEWELSQGMVLDTGR 280


>gi|242278414|ref|YP_002990543.1| LuxR family transcriptional regulator [Desulfovibrio salexigens DSM
           2638]
 gi|242121308|gb|ACS79004.1| transcriptional regulator, LuxR family [Desulfovibrio salexigens
           DSM 2638]
          Length = 181

 Score = 41.0 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 8/57 (14%), Positives = 24/57 (42%), Gaps = 2/57 (3%)

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
            +L+ R++ +       +       ++ +  ++   VR I+ +A +K++       E
Sbjct: 122 DILSKRQKEVVRMIFWGDLKAV--EVAEQLGITSRTVRCIKHQAIQKLRRHFSAASE 176


>gi|126653115|ref|ZP_01725244.1| possible RNA polymerase sigma-B factor (Sigma-37) (General stress
           protein84) (GSP84) [Bacillus sp. B14905]
 gi|126590120|gb|EAZ84245.1| possible RNA polymerase sigma-B factor (Sigma-37) (General stress
           protein84) (GSP84) [Bacillus sp. B14905]
          Length = 185

 Score = 41.0 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 10/76 (13%), Positives = 39/76 (51%), Gaps = 2/76 (2%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           ++++ E          L +S+  L  ++ +I E   +++   +++ ++   + + + +  
Sbjct: 110 DEIIQEGLLEAVENEELFQSLKGLTDKQLQILEMIYVKD--YSIKAIAETLQTTPQNISN 167

Query: 272 IEARAFKKVQESIQKQ 287
           +  +A +K+Q+ ++K+
Sbjct: 168 LHRKALQKLQQKLRKE 183


>gi|147678469|ref|YP_001212684.1| DNA-directed RNA polymerase specialized sigma subunit, sigma24-like
           protein [Pelotomaculum thermopropionicum SI]
 gi|146274566|dbj|BAF60315.1| DNA-directed RNA polymerase specialized sigma subunit, sigma24
           homolog [Pelotomaculum thermopropionicum SI]
          Length = 204

 Score = 41.0 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 19/80 (23%), Positives = 33/80 (41%), Gaps = 2/80 (2%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           ++GDL A   LV  +   V  +A  + G     S++  E  + L QA+ +F  E      
Sbjct: 13  QNGDLEAFEMLVRRYENKVYTVAYRFLGNHADASDLAQEAFLRLYQALPRFRGE--SSFM 70

Query: 103 TYSMWWIKAAMQEYILRSWS 122
           T+       A ++ + R   
Sbjct: 71  TWLYRITANACRDELRRRQR 90


>gi|302544196|ref|ZP_07296538.1| putative RNA polymerase ECF-subfamily sigma factor [Streptomyces
           hygroscopicus ATCC 53653]
 gi|302461814|gb|EFL24907.1| putative RNA polymerase ECF-subfamily sigma factor [Streptomyces
           himastatinicus ATCC 53653]
          Length = 221

 Score = 41.0 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 11/62 (17%), Positives = 23/62 (37%), Gaps = 2/62 (3%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L+           E    +  R+ L ++M  L  R+R +   R   +  +T   ++    
Sbjct: 139 LLSKPMPDMASAEEGAYDQLERDQLIKAMKGLQRRQREVLVLRYFAD--MTEAQVAETLG 196

Query: 264 VS 265
           +S
Sbjct: 197 IS 198


>gi|172060601|ref|YP_001808253.1| extracytoplasmic-function sigma-70 factor [Burkholderia ambifaria
           MC40-6]
 gi|171993118|gb|ACB64037.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Burkholderia
           ambifaria MC40-6]
          Length = 222

 Score = 41.0 bits (95), Expect = 0.21,   Method: Composition-based stats.
 Identities = 19/97 (19%), Positives = 39/97 (40%), Gaps = 2/97 (2%)

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             + ++   R+  + S++A    S +N    ++   +D    E         ++    + 
Sbjct: 90  VRQPVAYVTRMVRNASIDACRRQSLENVYHTEEDDGFDVPSPEPTPEAALMTRDTLRRVW 149

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
            ++  L  R R  FE  RL+E   TL+  +    VS+
Sbjct: 150 AALDDLPARSRAAFEMVRLREE--TLQTAARALNVSQ 184


>gi|261211561|ref|ZP_05925849.1| RNA polymerase sigma factor RpoE [Vibrio sp. RC341]
 gi|260839516|gb|EEX66142.1| RNA polymerase sigma factor RpoE [Vibrio sp. RC341]
          Length = 190

 Score = 41.0 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 24/144 (16%), Positives = 48/144 (33%), Gaps = 3/144 (2%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
            VL +R + +GD  A + LV  +   V  +   Y      +++V  E  I   +A+  F 
Sbjct: 8   QVLIERVQ-NGDKQAFNLLVLRYQNKVCNLISRYVSNSGDVADVAQEAFIKAYRAIPTFR 66

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNL 154
            E      T+         + +I+             ++  F+        L    +  L
Sbjct: 67  GE--SAFYTWLYRIAVNTAKNHIVAQSRRPPASDVDAEEAEFYEGGDALKELSNPENITL 124

Query: 155 KPEQVVAIAKKLNVSESEVISMNC 178
             E   A+   L+    ++ +   
Sbjct: 125 SKELKQAVFDALDALPDDLRTAMT 148


>gi|147678228|ref|YP_001212443.1| DNA-directed RNA polymerase specialized sigma subunit, sigma24-like
           protein [Pelotomaculum thermopropionicum SI]
 gi|146274325|dbj|BAF60074.1| DNA-directed RNA polymerase specialized sigma subunit, sigma24
           homolog [Pelotomaculum thermopropionicum SI]
          Length = 127

 Score = 41.0 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 17/98 (17%), Positives = 46/98 (46%), Gaps = 10/98 (10%)

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           N L   ++   ++  D +     G + +L E E+       L  ++++L P+++++  A 
Sbjct: 32  NLLSQEAEDEMTEMLDTVA----GTDDILAEVEDSV----FLQEALTMLTPQQQKVITAT 83

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L     T   ++ +  +S+  V +++ RA  ++++  
Sbjct: 84  VL--EGRTEREVAEQLGISQSVVHRLKERALNRLRKHF 119


>gi|134299216|ref|YP_001112712.1| ECF subfamily RNA polymerase sigma-24 factor [Desulfotomaculum
           reducens MI-1]
 gi|134051916|gb|ABO49887.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Desulfotomaculum
           reducens MI-1]
          Length = 179

 Score = 41.0 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 16/88 (18%), Positives = 33/88 (37%), Gaps = 6/88 (6%)

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE--NLS 259
           D ++    G +    E   +      L + +  L+P  R +   R   E    L    ++
Sbjct: 91  DVMLELAAGSDDGPEETVLQGEEITRLRQLLKGLSPDYRDVVSLRYAAE----LRFVQIA 146

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQ 287
                S   VR +  RA K++++   ++
Sbjct: 147 EVLGKSESAVRMLHHRAIKQLRQRYVRE 174


>gi|213619184|ref|ZP_03373010.1| RNA polymerase sigma factor RpoS [Salmonella enterica subsp.
          enterica serovar Typhi str. E98-2068]
          Length = 93

 Score = 41.0 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 12/34 (35%), Positives = 19/34 (55%), Gaps = 1/34 (2%)

Query: 19 YIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHR 52
          Y+ EI   P+L  +EE   A+R    GD+++  R
Sbjct: 61 YLGEIGYSPLLTAEEEVYFARR-ALRGDVASRRR 93


>gi|125973407|ref|YP_001037317.1| ECF subfamily RNA polymerase sigma-24 factor [Clostridium
           thermocellum ATCC 27405]
 gi|125713632|gb|ABN52124.1| RNA polymerase, sigma-24 subunit, RpoE [Clostridium thermocellum
           ATCC 27405]
 gi|316940359|gb|ADU74393.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           thermocellum DSM 1313]
          Length = 220

 Score = 41.0 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 20/89 (22%), Positives = 34/89 (38%), Gaps = 7/89 (7%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           E  L KR ++ GD+ A  +L+    + V  IA+   G     SE+  E  +   +++K F
Sbjct: 27  EKELIKRAKK-GDVEAFEQLIEGCQKKVFNIALRMLGNYDDASELAQEVFLKAYKSIKNF 85

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWS 122
             +      +    WI        L    
Sbjct: 86  KGD------SLFNTWIYKVTTNACLDEIR 108


>gi|229587477|ref|YP_002860515.1| putative sigma K [Clostridium botulinum Ba4 str. 657]
 gi|229260209|gb|ACQ51246.1| putative sigma K [Clostridium botulinum Ba4 str. 657]
          Length = 171

 Score = 41.0 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 19/89 (21%), Positives = 40/89 (44%), Gaps = 3/89 (3%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGL--PISEVVSEGNIGLMQAVKKFDPERGFRL 101
           + D      ++ +   L+  I+  Y        + E+   G I ++++ + F+ ++G  L
Sbjct: 2   NNDKPDIDAILNNFQELIDIISKKYTSKYSFAELDELQQIGRIAILKSYENFNKDKGS-L 60

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
             Y    IK  M++Y+L+S+   KI    
Sbjct: 61  EGYIYVCIKNDMKKYVLKSYRKAKIERPV 89


>gi|168214011|ref|ZP_02639636.1| conserved hypothetical protein [Clostridium perfringens CPE str.
           F4969]
 gi|170714473|gb|EDT26655.1| conserved hypothetical protein [Clostridium perfringens CPE str.
           F4969]
          Length = 137

 Score = 41.0 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 11/50 (22%), Positives = 23/50 (46%)

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
            +   N +  +++ L+  ER+I E R L+    T + + +    S +  R
Sbjct: 67  LEVCINSIDNALNELSDTERKILELRYLEGKKHTWKEIGNIVGYSSDYCR 116


>gi|166032980|ref|ZP_02235809.1| hypothetical protein DORFOR_02701 [Dorea formicigenerans ATCC
           27755]
 gi|166027337|gb|EDR46094.1| hypothetical protein DORFOR_02701 [Dorea formicigenerans ATCC
           27755]
          Length = 219

 Score = 41.0 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 9/71 (12%), Positives = 31/71 (43%), Gaps = 2/71 (2%)

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           +  +    R +L   +  L  R++ +      +E  +  ++++    + ++ V  +  RA
Sbjct: 149 DFVDDVIDREILHALIKELTERQKMVLNLVYFEE--MRQQDVADYLGIKQQSVNDLLNRA 206

Query: 277 FKKVQESIQKQ 287
            K +++  + +
Sbjct: 207 LKTMKKKAENE 217


>gi|19704652|ref|NP_604214.1| RNA polymerase sigma factor [Fusobacterium nucleatum subsp.
           nucleatum ATCC 25586]
 gi|19714956|gb|AAL95513.1| RNA polymerase sigma factor [Fusobacterium nucleatum subsp.
           nucleatum ATCC 25586]
          Length = 270

 Score = 41.0 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 20/66 (30%), Positives = 36/66 (54%), Gaps = 2/66 (3%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V  +L+ V +IA+     G+   ++  EG IGL++A + F+ ++ F+L  Y  ++I   M
Sbjct: 80  VEKNLKKVYEIALYMLRDGISYEDLTQEGIIGLIKAHELFEDDKDFKL--YKDYYIAKEM 137

Query: 114 QEYILR 119
             YI  
Sbjct: 138 FNYINN 143


>gi|317500120|ref|ZP_07958354.1| conjugative transposon protein [Lachnospiraceae bacterium
           8_1_57FAA]
 gi|331087651|ref|ZP_08336579.1| hypothetical protein HMPREF1025_00162 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|316898475|gb|EFV20512.1| conjugative transposon protein [Lachnospiraceae bacterium
           8_1_57FAA]
 gi|330399830|gb|EGG79490.1| hypothetical protein HMPREF1025_00162 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 139

 Score = 41.0 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 11/61 (18%), Positives = 30/61 (49%), Gaps = 2/61 (3%)

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             L  ++  L+ +ER +   R  Q   ++ + ++  + VSR  + +  +   KK++  ++
Sbjct: 79  EKLAVALYKLSNKERDVILLRYFQ--SMSDQEIAELYHVSRSAIYRRRSNGLKKLKTVLK 136

Query: 286 K 286
           +
Sbjct: 137 E 137


>gi|228474825|ref|ZP_04059556.1| pathogenicity island protein [Staphylococcus hominis SK119]
 gi|228271488|gb|EEK12856.1| pathogenicity island protein [Staphylococcus hominis SK119]
          Length = 113

 Score = 41.0 bits (95), Expect = 0.22,   Method: Composition-based stats.
 Identities = 16/95 (16%), Positives = 34/95 (35%), Gaps = 4/95 (4%)

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS-VLNPRERRIFEA 245
           N       ++      +     D +   + +  + +   N L + +  V   +E  +F  
Sbjct: 17  NTTTIEVKESELDIDSFFEISDDVEAVEVNDNIDNQIFFNELEQIVDRVGTDKEYFVF-- 74

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             L     +L  +   F +S ER+RQ+      K+
Sbjct: 75  -YLLCQGKSLNEVGKVFNLSGERIRQMYNGLLDKI 108


>gi|207743817|ref|YP_002260209.1| rna polymerase sigma d (sigma-70) factor (partial sequence n
           terminus) protein [Ralstonia solanacearum IPO1609]
 gi|206595217|emb|CAQ62144.1| probable rna polymerase sigma d (sigma-70) factor (partial sequence
           n terminus) protein [Ralstonia solanacearum IPO1609]
          Length = 39

 Score = 41.0 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 9/29 (31%), Positives = 19/29 (65%)

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              F+V+RE +RQ++A+A +K++   +  
Sbjct: 2   GKHFDVTRESIRQMKAKAVRKLRHPSRSD 30


>gi|256421229|ref|YP_003121882.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Chitinophaga
           pinensis DSM 2588]
 gi|256036137|gb|ACU59681.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Chitinophaga
           pinensis DSM 2588]
          Length = 194

 Score = 41.0 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 18/69 (26%), Positives = 40/69 (57%), Gaps = 2/69 (2%)

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            +++ ++L  ++S L+P+++RI    +L     T + ++ E ++SR  V++  + A  ++
Sbjct: 115 YEDQYHLLEEAISQLSPKKQRIVTLCKL--EGKTYDEVAEEMKISRNTVKEHLSIAMTRI 172

Query: 281 QESIQKQVE 289
            E IQK  E
Sbjct: 173 NEYIQKNKE 181


>gi|169351325|ref|ZP_02868263.1| hypothetical protein CLOSPI_02105 [Clostridium spiroforme DSM 1552]
 gi|169291547|gb|EDS73680.1| hypothetical protein CLOSPI_02105 [Clostridium spiroforme DSM 1552]
          Length = 146

 Score = 41.0 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 11/61 (18%), Positives = 30/61 (49%), Gaps = 2/61 (3%)

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             L  ++  L+ +ER +   R  Q   ++ + ++  + VSR  + +  +   KK++  ++
Sbjct: 86  EKLAVALYKLSSKERDVILLRYFQG--MSDQEIAELYHVSRSAIYRRRSNGLKKLKTVLK 143

Query: 286 K 286
           +
Sbjct: 144 E 144


>gi|298247806|ref|ZP_06971611.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297550465|gb|EFH84331.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 180

 Score = 41.0 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 21/122 (17%), Positives = 50/122 (40%), Gaps = 2/122 (1%)

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           L  SE E ++   R+A +++++    ++   S   +  +V      E+   +   R    
Sbjct: 58  LTWSEGEQLAWLRRIAYNKAIDYYRRNARHPSVALEQIIVTHFSDDERSPEQVALRNEAH 117

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            +L   +S L+  ++ I   R         + ++     S E +R   +RA   +++  +
Sbjct: 118 AVLRAHLSNLSGLQQEIVRLRFGHGLRT--KEIAQRLNKSDEVIRVTLSRALNLLRKLYR 175

Query: 286 KQ 287
           +Q
Sbjct: 176 RQ 177


>gi|284124376|ref|ZP_06386959.1| hypothetical protein POR_1563 [Candidatus Poribacteria sp. WGA-A3]
 gi|283829224|gb|EFC33638.1| hypothetical protein POR_1563 [Candidatus Poribacteria sp. WGA-A3]
          Length = 399

 Score = 41.0 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 15/67 (22%), Positives = 30/67 (44%), Gaps = 4/67 (5%)

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV-RQIEAR 275
           E +  ++R  ++   +  L   ER +     L E  +T + +     VS   +  ++  R
Sbjct: 76  ETDNTEHRHEIVKNLLQRLPESERTVVTLHYLGE--MTAKEIGKFLGVSANTINSRL-RR 132

Query: 276 AFKKVQE 282
           A K++QE
Sbjct: 133 AKKRLQE 139


>gi|153811711|ref|ZP_01964379.1| hypothetical protein RUMOBE_02104 [Ruminococcus obeum ATCC 29174]
 gi|149832114|gb|EDM87199.1| hypothetical protein RUMOBE_02104 [Ruminococcus obeum ATCC 29174]
          Length = 219

 Score = 41.0 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 9/71 (12%), Positives = 31/71 (43%), Gaps = 2/71 (2%)

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           +  +    R +L   +  L  R++ +      +E  +  ++++    + ++ V  +  RA
Sbjct: 149 DFVDDVIDREILHALIKELTERQKMVLNLVYFEE--MRQQDVADYLGIKQQSVNDLLNRA 206

Query: 277 FKKVQESIQKQ 287
            K +++  + +
Sbjct: 207 LKTMKKKAENE 217


>gi|206975007|ref|ZP_03235922.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           H3081.97]
 gi|206747026|gb|EDZ58418.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           H3081.97]
          Length = 188

 Score = 41.0 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 17/83 (20%), Positives = 35/83 (42%), Gaps = 10/83 (12%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           H   E+   ++      R  L + ++ L P ++++F  + L       E +  +  ++R 
Sbjct: 104 HISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKT--EEIGDKLGLTRA 161

Query: 268 ----RVRQIEARAFKKVQESIQK 286
               RV     R  KK+Q++  K
Sbjct: 162 AIDNRV----YRGKKKLQQNATK 180


>gi|89892913|ref|YP_516400.1| hypothetical protein DSY0167 [Desulfitobacterium hafniense Y51]
 gi|89332361|dbj|BAE81956.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 184

 Score = 41.0 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 15/86 (17%), Positives = 36/86 (41%), Gaps = 2/86 (2%)

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           D    D   +E    E  E    ++ L ++++ L+ RE+ I   +   +  ++   ++  
Sbjct: 95  DGYTRDIVAREPEPAEIVELNELQHHLLKAIASLSQREQEIIALKFWSD--LSNREIARL 152

Query: 262 FEVSRERVRQIEARAFKKVQESIQKQ 287
             +S      I  RA ++++  +  Q
Sbjct: 153 VGISESNTGVILFRAMRQLRLILASQ 178


>gi|291522929|emb|CBK81222.1| RNA polymerase sigma factor, sigma-70 family [Coprococcus catus
           GD/7]
          Length = 219

 Score = 41.0 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 9/71 (12%), Positives = 31/71 (43%), Gaps = 2/71 (2%)

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           +  +    R +L   +  L  R++ +      +E  +  ++++    + ++ V  +  RA
Sbjct: 149 DFVDDVIDREILHALIKELTERQKMVLNLVYFEE--MRQQDVADYLGIKQQSVNDLLNRA 206

Query: 277 FKKVQESIQKQ 287
            K +++  + +
Sbjct: 207 LKTMKKKAENE 217


>gi|257894125|ref|ZP_05673778.1| RNA polymerase sigma-70 subunit [Enterococcus faecium 1,231,408]
 gi|257830504|gb|EEV57111.1| RNA polymerase sigma-70 subunit [Enterococcus faecium 1,231,408]
          Length = 185

 Score = 41.0 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 16/86 (18%), Positives = 34/86 (39%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R   +GD  A   L   +  L++++   Y        +   E  I L QA++ ++  +G 
Sbjct: 7   RAARNGDEEAFAALYQKYFPLLLRLKNTYYLRNYVSEDWEQEARIALYQALRTYEKSKGV 66

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVK 125
              +Y    I   +   + +  +L +
Sbjct: 67  SFGSYYKSIISNQIYSLLRKQNALKR 92


>gi|255532615|ref|YP_003092987.1| sigma-70 family RNA polymerase sigma factor [Pedobacter heparinus
           DSM 2366]
 gi|255345599|gb|ACU04925.1| RNA polymerase sigma factor, sigma-70 family [Pedobacter heparinus
           DSM 2366]
          Length = 197

 Score = 41.0 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 14/85 (16%), Positives = 40/85 (47%), Gaps = 2/85 (2%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           ++ ++  +   L E  + K+    L   ++ L P+ R +F   R  +   + E  +    
Sbjct: 102 IILNNYTRPDSLEEDLQTKDYMEYLQSILATLTPQSREVFRLCR--QEYKSYEEAAEILG 159

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           +SR  V++   ++ K + +++++ +
Sbjct: 160 ISRSAVKKHMIKSMKTLGDAVKRDL 184


>gi|15807468|ref|NP_296202.1| hypothetical protein DR_2482 [Deinococcus radiodurans R1]
 gi|6460304|gb|AAF12026.1|AE002077_9 hypothetical protein DR_2482 [Deinococcus radiodurans R1]
          Length = 489

 Score = 41.0 bits (95), Expect = 0.23,   Method: Composition-based stats.
 Identities = 12/40 (30%), Positives = 18/40 (45%), Gaps = 2/40 (5%)

Query: 236 NPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
           + R R +   R       TL+       ++RERVRQ+  R
Sbjct: 42  DERNRALIWGRFGAGQ--TLQEAGDAHGITRERVRQVVNR 79


>gi|295703274|ref|YP_003596349.1| RNA polymerase sigma-70factor [Bacillus megaterium DSM 319]
 gi|294800933|gb|ADF37999.1| RNA polymerase sigma factor, sigma-70 family [Bacillus megaterium
           DSM 319]
          Length = 163

 Score = 41.0 bits (95), Expect = 0.24,   Method: Composition-based stats.
 Identities = 14/67 (20%), Positives = 30/67 (44%), Gaps = 2/67 (2%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            ++ +S   L+V +   +  Y     E      IGL +A +KFD  +G   + Y+   ++
Sbjct: 7   DQIASSFHPLIVSMIKKFHIY-KDYDEYYQIALIGLWRAYQKFDENKGS-FSAYAYTTVR 64

Query: 111 AAMQEYI 117
             +  ++
Sbjct: 65  GTILSHL 71


>gi|228911088|ref|ZP_04074895.1| RNA polymerase sigma factor [Bacillus thuringiensis IBL 200]
 gi|228848592|gb|EEM93439.1| RNA polymerase sigma factor [Bacillus thuringiensis IBL 200]
          Length = 156

 Score = 41.0 bits (95), Expect = 0.24,   Method: Composition-based stats.
 Identities = 15/64 (23%), Positives = 35/64 (54%), Gaps = 2/64 (3%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    +   MSVL+ +E+ I   R       T+  ++ E E++  +VR +  +A +K++
Sbjct: 94  EDVEMKVKDFMSVLDEKEKYIIFERFFVG--KTMGEIALETEMTYYQVRWMYRQALEKMR 151

Query: 282 ESIQ 285
           +S++
Sbjct: 152 DSVR 155


>gi|295109373|emb|CBL23326.1| RNA polymerase sigma factor, sigma-70 family [Ruminococcus obeum
           A2-162]
          Length = 162

 Score = 41.0 bits (95), Expect = 0.24,   Method: Composition-based stats.
 Identities = 15/79 (18%), Positives = 39/79 (49%), Gaps = 2/79 (2%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            +     L+E    +  R +L +S+  L  R+R I + +      ++ + +++   ++ E
Sbjct: 80  EESTNGDLLENILAEESRRLLYQSIQKLEVRKREIIQMQYFGG--MSQKEIAAILYITPE 137

Query: 268 RVRQIEARAFKKVQESIQK 286
            VR +  RA K++++ ++ 
Sbjct: 138 NVRVLAYRAKKELKKYLES 156


>gi|149369745|ref|ZP_01889597.1| hypothetical protein SCB49_07957 [unidentified eubacterium SCB49]
 gi|149357172|gb|EDM45727.1| hypothetical protein SCB49_07957 [unidentified eubacterium SCB49]
          Length = 636

 Score = 41.0 bits (95), Expect = 0.24,   Method: Composition-based stats.
 Identities = 10/26 (38%), Positives = 19/26 (73%)

Query: 247 RLQENPVTLENLSSEFEVSRERVRQI 272
              +  +TL++++ E +++RERVRQI
Sbjct: 232 YQNQKELTLDDIAKEVKLTRERVRQI 257


>gi|325279620|ref|YP_004252162.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Odoribacter
           splanchnicus DSM 20712]
 gi|324311429|gb|ADY31982.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Odoribacter
           splanchnicus DSM 20712]
          Length = 181

 Score = 41.0 bits (95), Expect = 0.24,   Method: Composition-based stats.
 Identities = 16/76 (21%), Positives = 36/76 (47%), Gaps = 6/76 (7%)

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE--NLSSEFEVSRER 268
            E         +  + +L  ++  L  RER+IFE   ++     L+   ++ +  VS   
Sbjct: 99  NEAFFANTVIDQETQLLLFNAIHSLPDRERQIFELSFIEG----LKNIEIAEQLGVSDST 154

Query: 269 VRQIEARAFKKVQESI 284
           V++ +A+A + ++E +
Sbjct: 155 VKKAKAKALEILREKL 170


>gi|300854752|ref|YP_003779736.1| putative sigma 70 subunit of a RNA polymerase [Clostridium
           ljungdahlii DSM 13528]
 gi|300434867|gb|ADK14634.1| predicted sigma 70 subunit of a RNA polymerase [Clostridium
           ljungdahlii DSM 13528]
          Length = 181

 Score = 41.0 bits (95), Expect = 0.24,   Method: Composition-based stats.
 Identities = 13/79 (16%), Positives = 36/79 (45%), Gaps = 2/79 (2%)

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
             E+   +   +    + L +++++LN +ER I   +         + ++    ++   V
Sbjct: 105 STEKNPEDVFVKSETNDELLKALNILNIKERNIIAFKFGANLKN--KEIAEIIGITESNV 162

Query: 270 RQIEARAFKKVQESIQKQV 288
             I  R  KK+++ ++++V
Sbjct: 163 GVILYRTMKKLKKELEREV 181


>gi|299536285|ref|ZP_07049598.1| RNA polymerase sigma-B factor [Lysinibacillus fusiformis ZC1]
 gi|298728271|gb|EFI68833.1| RNA polymerase sigma-B factor [Lysinibacillus fusiformis ZC1]
          Length = 155

 Score = 41.0 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 14/84 (16%), Positives = 38/84 (45%), Gaps = 2/84 (2%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L+ D    E+   E    K     L + +  L  ++ +I E   +++   +++ ++   +
Sbjct: 72  LMDDGKRDEESEEEGLLEKIENEQLFKGLQKLTDKQLQILEMIYVKD--YSIKVIAETLK 129

Query: 264 VSRERVRQIEARAFKKVQESIQKQ 287
            + + +  +  +A KK+   I+K+
Sbjct: 130 TTPQNISNLHRKALKKLHHIIRKE 153


>gi|210613357|ref|ZP_03289677.1| hypothetical protein CLONEX_01884 [Clostridium nexile DSM 1787]
 gi|210151199|gb|EEA82207.1| hypothetical protein CLONEX_01884 [Clostridium nexile DSM 1787]
 gi|295108065|emb|CBL22018.1| DNA-directed RNA polymerase specialized sigma subunit [Ruminococcus
           obeum A2-162]
          Length = 211

 Score = 41.0 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 12/63 (19%), Positives = 28/63 (44%), Gaps = 2/63 (3%)

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           E+      +   M +L  R+R++      Q+   T   +S  F ++   V +  ++A +K
Sbjct: 138 EKLIIEEAIGEFMDLLTDRQRQVIHQIYFQQ--RTQREVSRVFGITEPAVSKCISQAKQK 195

Query: 280 VQE 282
           ++ 
Sbjct: 196 MRR 198


>gi|332519894|ref|ZP_08396358.1| RNA polymerase sigma factor, sigma-70 family [Lacinutrix algicola
           5H-3-7-4]
 gi|332044453|gb|EGI80647.1| RNA polymerase sigma factor, sigma-70 family [Lacinutrix algicola
           5H-3-7-4]
          Length = 170

 Score = 41.0 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 15/80 (18%), Positives = 34/80 (42%), Gaps = 8/80 (10%)

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D   +      E +  +  L  ++++L  ++R +F   R++        ++    VS++ 
Sbjct: 94  DVNNESPEYILEEEQFKKKLQHAIALLTDKQREVFLLNRIEGKKY--REIAEILGVSQKA 151

Query: 269 VRQIEAR---AFKKVQESIQ 285
           V   E R   A   ++E I+
Sbjct: 152 V---EKRMSLALTVLREKIE 168


>gi|237744143|ref|ZP_04574624.1| RNA polymerase sigma factor [Fusobacterium sp. 7_1]
 gi|229431372|gb|EEO41584.1| RNA polymerase sigma factor [Fusobacterium sp. 7_1]
          Length = 274

 Score = 41.0 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 28/127 (22%), Positives = 51/127 (40%), Gaps = 5/127 (3%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V  +L+ V +IA+     G+   ++  EG +GL++A + F+ ++ F+L  Y  ++I   M
Sbjct: 84  VEKNLKKVYEIALYMLREGISYDDLTQEGIVGLIKAHELFEDDKDFKL--YKDYYIAKEM 141

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
             YI    +  K       K        LK  L+   D +   E      +       E+
Sbjct: 142 FNYINNYANYRKAAFKDYAKHEIHKDSHLKVSLK---DRDKSEELKKLEKENKEKHIEEM 198

Query: 174 ISMNCRL 180
             +  R 
Sbjct: 199 KQLEKRA 205


>gi|229087725|ref|ZP_04219848.1| RNA polymerase sigma factor [Bacillus cereus Rock3-44]
 gi|228695560|gb|EEL48422.1| RNA polymerase sigma factor [Bacillus cereus Rock3-44]
          Length = 155

 Score = 41.0 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 15/77 (19%), Positives = 34/77 (44%), Gaps = 2/77 (2%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           H   EQ +++        + +   MSVL+ +E+ +   R      +    ++ E  ++  
Sbjct: 81  HTCVEQEILQNVCEAEVPSEIQDYMSVLDEQEKYVIFERFYAGKKI--HEIAEEMRMTYY 138

Query: 268 RVRQIEARAFKKVQESI 284
           + R I  RA +K++  +
Sbjct: 139 QARWIYRRALEKMRAEV 155


>gi|221197915|ref|ZP_03570961.1| RNA polymerase sigma factor, sigma-70 family [Burkholderia
           multivorans CGD2M]
 gi|221204527|ref|ZP_03577544.1| RNA polymerase sigma factor, sigma-70 family [Burkholderia
           multivorans CGD2]
 gi|221212951|ref|ZP_03585927.1| RNA polymerase sigma factor, sigma-70 family [Burkholderia
           multivorans CGD1]
 gi|221167164|gb|EED99634.1| RNA polymerase sigma factor, sigma-70 family [Burkholderia
           multivorans CGD1]
 gi|221175384|gb|EEE07814.1| RNA polymerase sigma factor, sigma-70 family [Burkholderia
           multivorans CGD2]
 gi|221181847|gb|EEE14248.1| RNA polymerase sigma factor, sigma-70 family [Burkholderia
           multivorans CGD2M]
          Length = 215

 Score = 41.0 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 18/97 (18%), Positives = 39/97 (40%), Gaps = 2/97 (2%)

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             + ++   R+  + S++A    + +N     +   +D    E         ++    ++
Sbjct: 83  VRQPVAYVTRMVRNASIDACRRQNLENIHHADEDDGFDVPSPEPTPEAALITRDTLRRVS 142

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
            ++  L  R R  FE  RL+E   TL+  +    VS+
Sbjct: 143 AALDDLPARSRAAFEMVRLREE--TLQTAARALNVSQ 177


>gi|146313026|ref|YP_001178100.1| ECF subfamily RNA polymerase sigma-24 factor [Enterobacter sp. 638]
 gi|145319902|gb|ABP62049.1| RNA polymerase, sigma subunit, ECF family [Enterobacter sp. 638]
          Length = 191

 Score = 41.0 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 17/76 (22%), Positives = 34/76 (44%), Gaps = 2/76 (2%)

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           D    E    +  E ++ +  L+R +  L  R+R+I +   L+E  +TL   +    +S 
Sbjct: 110 DASLSEYAARDDSEHQDIQEELSRILDRLPSRQRQIVQHIHLEE--MTLAEAAKRHNLSL 167

Query: 267 ERVRQIEARAFKKVQE 282
             V+ +  RA   ++ 
Sbjct: 168 SAVKSLLHRALTNLRR 183


>gi|294782672|ref|ZP_06747998.1| RNA polymerase sigma factor [Fusobacterium sp. 1_1_41FAA]
 gi|294481313|gb|EFG29088.1| RNA polymerase sigma factor [Fusobacterium sp. 1_1_41FAA]
          Length = 274

 Score = 41.0 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 21/64 (32%), Positives = 37/64 (57%), Gaps = 2/64 (3%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V  +L+ V +IA+     G+   ++  EG IGL++A + F+ ++ F+L  Y  ++I  AM
Sbjct: 84  VEKNLKKVYQIALYMLRDGILYEDLTQEGVIGLIKAHELFEDDKDFKL--YKDYYIARAM 141

Query: 114 QEYI 117
             YI
Sbjct: 142 FNYI 145


>gi|228923984|ref|ZP_04087261.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
 gi|228835783|gb|EEM81147.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           huazhongensis BGSC 4BD1]
          Length = 156

 Score = 41.0 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 15/64 (23%), Positives = 35/64 (54%), Gaps = 2/64 (3%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    +   MSVL+ +E+ I   R       T+  ++ E E++  +VR +  +A +K++
Sbjct: 94  EDVEIRVKDFMSVLDEKEKYIIFERFFVG--KTMGEIALETEMTYYQVRWMYRQALEKMR 151

Query: 282 ESIQ 285
           +S++
Sbjct: 152 DSVR 155


>gi|158319212|ref|YP_001511719.1| FliA/WhiG family RNA polymerase sigma 28 subunit [Alkaliphilus
           oremlandii OhILAs]
 gi|158139411|gb|ABW17723.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Alkaliphilus oremlandii OhILAs]
          Length = 175

 Score = 41.0 bits (95), Expect = 0.25,   Method: Composition-based stats.
 Identities = 15/108 (13%), Positives = 43/108 (39%), Gaps = 7/108 (6%)

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR-----SMSVLN 236
            + SLN +  + ++         V D        + KE+  +   +L       +++ L 
Sbjct: 66  EELSLNIIDPNFNEERINLITDTVDDFVENIGESLIKEDCCDYSELLYDRELILAINTLT 125

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            R++ I     +     T   ++ +  ++++ V + +  A  K+++ +
Sbjct: 126 DRQKEILHRCVIIGESDT--VVAKKLGITKQGVNKAKKSALNKIRKKL 171


>gi|315037583|ref|YP_004031151.1| DNA-directed RNA polymerase sigma factor, sigma H [Lactobacillus
           amylovorus GRL 1112]
 gi|312275716|gb|ADQ58356.1| DNA-directed RNA polymerase sigma factor, sigma H [Lactobacillus
           amylovorus GRL 1112]
          Length = 181

 Score = 41.0 bits (95), Expect = 0.26,   Method: Composition-based stats.
 Identities = 16/73 (21%), Positives = 27/73 (36%), Gaps = 1/73 (1%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           E  L K+ +  GD  A  +L   +  LV  +   Y       ++   E  I   +A   +
Sbjct: 5   ERKLIKKVK-AGDDEALEKLFVLYKPLVNSVVKKYYLGHYDSNDWEQEAMIICYEAALVY 63

Query: 94  DPERGFRLATYSM 106
             E+G   + Y  
Sbjct: 64  SSEKGNFGSLYKT 76


>gi|325677644|ref|ZP_08157296.1| sigma-70, region 4 [Ruminococcus albus 8]
 gi|324110612|gb|EGC04776.1| sigma-70, region 4 [Ruminococcus albus 8]
          Length = 184

 Score = 41.0 bits (95), Expect = 0.26,   Method: Composition-based stats.
 Identities = 14/93 (15%), Positives = 40/93 (43%), Gaps = 14/93 (15%)

Query: 202 DWLVYDHDGQEQVLIEKEERKNRR----NMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           ++ + D +   +   + E   + +       ++++  LN  E+ I   R   +  +T + 
Sbjct: 93  EYTIDDENVYTEEQADPEAPTDVQVESGMAFSQALETLNDAEKEIINLRVGFD--MTFKE 150

Query: 258 LSSEFEV---SRE-RVRQIEARAFKKVQESIQK 286
           +S    +   +   R RQ    A  K+++++++
Sbjct: 151 ISEALGIPLGTVAWRYRQ----ALNKLKKTVKE 179


>gi|229017089|ref|ZP_04174007.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           AH1273]
 gi|229023268|ref|ZP_04179778.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           AH1272]
 gi|228738062|gb|EEL88548.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           AH1272]
 gi|228744212|gb|EEL94296.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           AH1273]
          Length = 188

 Score = 41.0 bits (95), Expect = 0.26,   Method: Composition-based stats.
 Identities = 10/59 (16%), Positives = 25/59 (42%), Gaps = 2/59 (3%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           H   E+   ++      R  L + ++ L P ++++F  + L       E +  +  ++R
Sbjct: 104 HISTEKSAEDELILMEDREELLKLINQLEPLDQKVFIMKYLLGMKT--EEIGDKLGLTR 160


>gi|153941551|ref|YP_001393018.1| sigma-70 family RNA polymerase sigma factor [Clostridium botulinum
           F str. Langeland]
 gi|152937431|gb|ABS42928.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           F str. Langeland]
 gi|295320993|gb|ADG01370.1| sigma-70 family RNA polymerase sigma factor [Clostridium botulinum
           F str. 230613]
          Length = 176

 Score = 41.0 bits (95), Expect = 0.26,   Method: Composition-based stats.
 Identities = 16/81 (19%), Positives = 36/81 (44%), Gaps = 2/81 (2%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
            Y L K Y+  G+ +    ++   + +++K A  Y+       ++V  G + +++AV  +
Sbjct: 1   MYQLVKGYK-AGEEALLKDIIDKFVPIILKEAAKYKIKCYDYEDLVQHGYLSVIKAVNMY 59

Query: 94  DPERGFRLATYSMWWIKAAMQ 114
             + G     Y +  IK   +
Sbjct: 60  KGD-GDSFKYYCIKAIKQNYR 79


>gi|153807944|ref|ZP_01960612.1| hypothetical protein BACCAC_02230 [Bacteroides caccae ATCC 43185]
 gi|149129553|gb|EDM20767.1| hypothetical protein BACCAC_02230 [Bacteroides caccae ATCC 43185]
          Length = 205

 Score = 41.0 bits (95), Expect = 0.26,   Method: Composition-based stats.
 Identities = 15/70 (21%), Positives = 33/70 (47%), Gaps = 2/70 (2%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
           + S  +  + + +    E   I +EER+ + N + + + VL PR+R I   R ++E    
Sbjct: 93  EESYAFNFYSMEEQYITENDFINEEERREQINEIKKILHVLTPRQREIIYYRFIEEMEY- 151

Query: 255 LENLSSEFEV 264
            + +    ++
Sbjct: 152 -DEICQIMDI 160


>gi|300853720|ref|YP_003778704.1| putative RNA polymerase sigma factor [Clostridium ljungdahlii DSM
           13528]
 gi|300433835|gb|ADK13602.1| predicted RNA polymerase sigma factor [Clostridium ljungdahlii DSM
           13528]
          Length = 188

 Score = 40.6 bits (94), Expect = 0.26,   Method: Composition-based stats.
 Identities = 23/153 (15%), Positives = 61/153 (39%), Gaps = 2/153 (1%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L +R  + GD +A   +      +V+ +A      G  + +++ EG   +++A+  +D  
Sbjct: 9   LLER-AQSGDKNAVESICIKFNGMVINMAKCTYIKGYDMEDLIQEGRYSVIKAIGMYDIN 67

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
             +  A Y    +K      I  +   V   +  ++         +    + I ++ +K 
Sbjct: 68  SKYPFAAYVKSSVKKNFYNMIRTNIKKVSCCSLYSKNEEGCEFINMIASDENIEEDLIKR 127

Query: 157 EQVVAIAKKLNVSESEVISM-NCRLAGDESLNA 188
           + ++ + K ++    +  ++ +     + SLN 
Sbjct: 128 KLIIQLNKSIDKLSEDKRNLIDWYYIQNRSLNE 160


>gi|237720346|ref|ZP_04550827.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 2_2_4]
 gi|229450097|gb|EEO55888.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 2_2_4]
          Length = 190

 Score = 40.6 bits (94), Expect = 0.26,   Method: Composition-based stats.
 Identities = 17/93 (18%), Positives = 44/93 (47%), Gaps = 2/93 (2%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
               + ++ +       E + I  E+ K  +  +   MSVL  R+R I   R ++E  ++
Sbjct: 100 DEIGEREETVDEFPSTPETIYINNEQEKQVQATVHTMMSVLTDRQREIIYYRYIKE--MS 157

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++ +S   +++ + V     RA  ++++  +++
Sbjct: 158 IDEISKVTDMNNQSVSNSIQRALGRIRDLFKRK 190


>gi|94992644|ref|YP_600743.1| RNA polymerase sigma-B factor [Streptococcus pyogenes MGAS2096]
 gi|94546152|gb|ABF36199.1| RNA polymerase sigma-B factor [Streptococcus pyogenes MGAS2096]
          Length = 191

 Score = 40.6 bits (94), Expect = 0.26,   Method: Composition-based stats.
 Identities = 17/115 (14%), Positives = 47/115 (40%), Gaps = 7/115 (6%)

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            E      +L    SL +L   +D   +   D++  +     + ++         + L  
Sbjct: 83  KERWRYLQKLDTKNSLLSLDGFTDSEGNTL-DFIADEAVDVAETVVNAVMV----DRLKA 137

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           ++ +L+  E+ + +A     N ++   +     +++  V + +AR   K+++ I+
Sbjct: 138 ALPLLSDSEQELIQAIFF--NGLSEREVGKRLGITQSVVNKRKARILIKLRKIIE 190


>gi|29345598|ref|NP_809101.1| RNA polymerase ECF-type sigma factor [Bacteroides thetaiotaomicron
           VPI-5482]
 gi|253567598|ref|ZP_04845009.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 1_1_6]
 gi|29337490|gb|AAO75295.1| RNA polymerase ECF-type sigma factor [Bacteroides thetaiotaomicron
           VPI-5482]
 gi|251841671|gb|EES69751.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 1_1_6]
          Length = 200

 Score = 40.6 bits (94), Expect = 0.26,   Method: Composition-based stats.
 Identities = 13/82 (15%), Positives = 33/82 (40%), Gaps = 6/82 (7%)

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
              N  + ++ ++            K    + +++L+R++  L PR+R +F   R  +  
Sbjct: 92  DMANEDKLKEHILSHAVDSANETNNKILFDDLKDVLSRALEQLTPRQREVFNMSRDLQMS 151

Query: 253 VTLENLSSEFEVS----RERVR 270
              + ++    VS    +E + 
Sbjct: 152 H--KEIAEALGVSVNTVQEHIS 171


>gi|256839396|ref|ZP_05544905.1| RNA polymerase ECF-type sigma factor [Parabacteroides sp. D13]
 gi|262384563|ref|ZP_06077697.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 2_1_33B]
 gi|256738326|gb|EEU51651.1| RNA polymerase ECF-type sigma factor [Parabacteroides sp. D13]
 gi|262293856|gb|EEY81790.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 2_1_33B]
          Length = 204

 Score = 40.6 bits (94), Expect = 0.26,   Method: Composition-based stats.
 Identities = 14/95 (14%), Positives = 37/95 (38%), Gaps = 2/95 (2%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
               + +D +            +     +   +L +++  L P+++R+F+  R       
Sbjct: 105 DRELELRDKIRSASLDSTNETEDSVLDTDLNALLDKALETLTPQQKRVFDMSRKDMKSH- 163

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
            + ++    +S   V+Q  + A K ++  + K  E
Sbjct: 164 -KEIADSLGISVYTVQQHISTALKVIRAFLAKYAE 197


>gi|188590656|ref|YP_001921805.1| sigma-70 region 2 domain protein [Clostridium botulinum E3 str.
           Alaska E43]
 gi|188500937|gb|ACD54073.1| sigma-70 region 2 domain protein [Clostridium botulinum E3 str.
           Alaska E43]
          Length = 195

 Score = 40.6 bits (94), Expect = 0.26,   Method: Composition-based stats.
 Identities = 16/85 (18%), Positives = 38/85 (44%), Gaps = 2/85 (2%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           +LAK+  + GD  +   L+      +  ++     +G   +++ +E    L + +  +D 
Sbjct: 8   MLAKK-SKDGDNLSKENLIEEFRPFIRNLSRKTFIHGYDKNDIENECYKNLFKCLNSYDL 66

Query: 96  ERGFRLATYSMWWIKAAMQEYILRS 120
           E+  R   Y+   IK  + + I ++
Sbjct: 67  EK-HRFVAYATNGIKNNLNDLIRKT 90


>gi|262383132|ref|ZP_06076269.1| conserved hypothetical protein [Bacteroides sp. 2_1_33B]
 gi|301311768|ref|ZP_07217693.1| putative RNA polymerase ECF-type sigma factor [Bacteroides sp.
           20_3]
 gi|262296010|gb|EEY83941.1| conserved hypothetical protein [Bacteroides sp. 2_1_33B]
 gi|300830328|gb|EFK60973.1| putative RNA polymerase ECF-type sigma factor [Bacteroides sp.
           20_3]
          Length = 170

 Score = 40.6 bits (94), Expect = 0.27,   Method: Composition-based stats.
 Identities = 18/92 (19%), Positives = 45/92 (48%), Gaps = 6/92 (6%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
            N    +  L+      E+ L EKE+ ++ + ++ +    L   +R++   R +++   +
Sbjct: 80  DNEEALETVLLTTDSSPEKELEEKEDIRHIQELIEQ----LPENQRQVIRLRGIED--CS 133

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            E++     +S   +R + +RA K ++E ++K
Sbjct: 134 YEDIEQITGLSSSNIRTLLSRARKLIREKLEK 165


>gi|294630418|ref|ZP_06708978.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces sp. e14]
 gi|292833751|gb|EFF92100.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces sp. e14]
          Length = 528

 Score = 40.6 bits (94), Expect = 0.27,   Method: Composition-based stats.
 Identities = 27/144 (18%), Positives = 54/144 (37%), Gaps = 6/144 (4%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E  L    R  GD +A  RLV+++L LV  +          + +VV +    L++A+  
Sbjct: 27  DETALVAAAR-RGDPAARDRLVSAYLPLVYNVVGRALNGHADVDDVVQDT---LLRALSG 82

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
            D  R    A +  W +  AM +   R     +     +                     
Sbjct: 83  LDGLRDP--ARFRAWLVAIAMNQVRRRWSVAQRRPLPLDTAADGPAQGDFAELAILRLGL 140

Query: 153 NLKPEQVVAIAKKLNVSESEVISM 176
           + +  +V    + L+ ++ +V+S+
Sbjct: 141 SGQRREVAEATRWLDPADRQVLSL 164


>gi|257882533|ref|ZP_05662186.1| RNA polymerase sigma-70 subunit [Enterococcus faecium 1,231,502]
 gi|294623064|ref|ZP_06701951.1| ComX [Enterococcus faecium U0317]
 gi|257818191|gb|EEV45519.1| RNA polymerase sigma-70 subunit [Enterococcus faecium 1,231,502]
 gi|291597537|gb|EFF28701.1| ComX [Enterococcus faecium U0317]
          Length = 192

 Score = 40.6 bits (94), Expect = 0.27,   Method: Composition-based stats.
 Identities = 16/86 (18%), Positives = 34/86 (39%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R   +GD  A   L   +  L++++   Y        +   E  I L QA++ ++  +G 
Sbjct: 7   RAARNGDEEAFAALYQKYFPLLLRLKNTYYLRNYVSEDWEQEARIALYQALRTYEKSKGV 66

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVK 125
              +Y    I   +   + +  +L +
Sbjct: 67  SFGSYYKSVISNQIYSLLRKQNALKR 92


>gi|154494299|ref|ZP_02033619.1| hypothetical protein PARMER_03650 [Parabacteroides merdae ATCC
           43184]
 gi|154085983|gb|EDN85028.1| hypothetical protein PARMER_03650 [Parabacteroides merdae ATCC
           43184]
          Length = 172

 Score = 40.6 bits (94), Expect = 0.27,   Method: Composition-based stats.
 Identities = 13/80 (16%), Positives = 38/80 (47%), Gaps = 6/80 (7%)

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
                  E+ ER+++   +   +  L   +R++   R +++   +++ +     +S   +
Sbjct: 90  STASSPDEELERQDKVQQIRHLIDRLPENQRQVLRLRGIED--CSMDEIEQITGLSAVNI 147

Query: 270 RQIEARAFKKVQESIQKQVE 289
           R + +RA    ++ I++Q+E
Sbjct: 148 RVLLSRA----RKIIREQLE 163


>gi|69245489|ref|ZP_00603453.1| Sigma-70 region 2 [Enterococcus faecium DO]
 gi|257879807|ref|ZP_05659460.1| RNA polymerase sigma-70 subunit [Enterococcus faecium 1,230,933]
 gi|257886068|ref|ZP_05665721.1| RNA polymerase sigma-70 subunit [Enterococcus faecium 1,231,501]
 gi|257891648|ref|ZP_05671301.1| RNA polymerase sigma-70 subunit [Enterococcus faecium 1,231,410]
 gi|258614233|ref|ZP_05712003.1| RNA polymerase sigma-70 factor family protein [Enterococcus faecium
           DO]
 gi|260559481|ref|ZP_05831662.1| RNA polymerase sigma-70 subunit [Enterococcus faecium C68]
 gi|261206632|ref|ZP_05921330.1| RNA polymerase sigma-70 subunit [Enterococcus faecium TC 6]
 gi|289564993|ref|ZP_06445447.1| sigma-70 factor family protein [Enterococcus faecium D344SRF]
 gi|293553643|ref|ZP_06674267.1| ComX [Enterococcus faecium E1039]
 gi|293564128|ref|ZP_06678534.1| Sigma-70 region 2 [Enterococcus faecium E1162]
 gi|294614950|ref|ZP_06694841.1| ComX [Enterococcus faecium E1636]
 gi|294618282|ref|ZP_06697864.1| ComX [Enterococcus faecium E1679]
 gi|314940059|ref|ZP_07847242.1| sigma-70 region 2 [Enterococcus faecium TX0133a04]
 gi|314942534|ref|ZP_07849373.1| sigma-70 region 2 [Enterococcus faecium TX0133C]
 gi|314949360|ref|ZP_07852701.1| sigma-70 region 2 [Enterococcus faecium TX0082]
 gi|314952820|ref|ZP_07855792.1| sigma-70 region 2 [Enterococcus faecium TX0133A]
 gi|314993747|ref|ZP_07859092.1| sigma-70 region 2 [Enterococcus faecium TX0133B]
 gi|314994812|ref|ZP_07859944.1| sigma-70 region 2 [Enterococcus faecium TX0133a01]
 gi|68195740|gb|EAN10177.1| Sigma-70 region 2 [Enterococcus faecium DO]
 gi|257814035|gb|EEV42793.1| RNA polymerase sigma-70 subunit [Enterococcus faecium 1,230,933]
 gi|257821924|gb|EEV49054.1| RNA polymerase sigma-70 subunit [Enterococcus faecium 1,231,501]
 gi|257828008|gb|EEV54634.1| RNA polymerase sigma-70 subunit [Enterococcus faecium 1,231,410]
 gi|260074580|gb|EEW62901.1| RNA polymerase sigma-70 subunit [Enterococcus faecium C68]
 gi|260079125|gb|EEW66818.1| RNA polymerase sigma-70 subunit [Enterococcus faecium TC 6]
 gi|289163200|gb|EFD11046.1| sigma-70 factor family protein [Enterococcus faecium D344SRF]
 gi|291592236|gb|EFF23854.1| ComX [Enterococcus faecium E1636]
 gi|291595498|gb|EFF26809.1| ComX [Enterococcus faecium E1679]
 gi|291602218|gb|EFF32446.1| ComX [Enterococcus faecium E1039]
 gi|291604046|gb|EFF33574.1| Sigma-70 region 2 [Enterococcus faecium E1162]
 gi|313590996|gb|EFR69841.1| sigma-70 region 2 [Enterococcus faecium TX0133a01]
 gi|313591847|gb|EFR70692.1| sigma-70 region 2 [Enterococcus faecium TX0133B]
 gi|313595054|gb|EFR73899.1| sigma-70 region 2 [Enterococcus faecium TX0133A]
 gi|313598755|gb|EFR77600.1| sigma-70 region 2 [Enterococcus faecium TX0133C]
 gi|313640659|gb|EFS05239.1| sigma-70 region 2 [Enterococcus faecium TX0133a04]
 gi|313644191|gb|EFS08771.1| sigma-70 region 2 [Enterococcus faecium TX0082]
          Length = 192

 Score = 40.6 bits (94), Expect = 0.27,   Method: Composition-based stats.
 Identities = 16/86 (18%), Positives = 34/86 (39%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R   +GD  A   L   +  L++++   Y        +   E  I L QA++ ++  +G 
Sbjct: 7   RAARNGDEEAFAALYQKYFPLLLRLKNTYYLRNYVSEDWEQEARIALYQALRTYEKSKGV 66

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVK 125
              +Y    I   +   + +  +L +
Sbjct: 67  SFGSYYKSIISNQIYSLLRKQNALKR 92


>gi|225572876|ref|ZP_03781631.1| hypothetical protein RUMHYD_01067 [Blautia hydrogenotrophica DSM
           10507]
 gi|225039741|gb|EEG49987.1| hypothetical protein RUMHYD_01067 [Blautia hydrogenotrophica DSM
           10507]
          Length = 146

 Score = 40.6 bits (94), Expect = 0.27,   Method: Composition-based stats.
 Identities = 11/61 (18%), Positives = 30/61 (49%), Gaps = 2/61 (3%)

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             L  ++  L+ +ER +   R  Q   ++ + ++  + VSR  + +  +   KK++  ++
Sbjct: 86  EKLAVALYKLSNKERDVILLRYFQ--SMSDQEIAELYHVSRSAIYRRRSNGLKKLKTVLK 143

Query: 286 K 286
           +
Sbjct: 144 E 144


>gi|317152824|ref|YP_004120872.1| sigma-70 family RNA polymerase sigma factor [Desulfovibrio
           aespoeensis Aspo-2]
 gi|316943075|gb|ADU62126.1| RNA polymerase sigma factor, sigma-70 family [Desulfovibrio
           aespoeensis Aspo-2]
          Length = 185

 Score = 40.6 bits (94), Expect = 0.27,   Method: Composition-based stats.
 Identities = 9/69 (13%), Positives = 27/69 (39%), Gaps = 2/69 (2%)

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
            VL  R+  +       +       ++++  +S    R I+ +A ++++   +     S+
Sbjct: 112 GVLTDRQEEVIALFFKDDMEAG--EIAAKLGISPMTARSIKFQALERLRRHFKTAARAST 169

Query: 293 SPPLLQKPR 301
              + Q  +
Sbjct: 170 DQGVDQGAK 178


>gi|255015471|ref|ZP_05287597.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 2_1_7]
          Length = 192

 Score = 40.6 bits (94), Expect = 0.27,   Method: Composition-based stats.
 Identities = 14/95 (14%), Positives = 37/95 (38%), Gaps = 2/95 (2%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
               + +D +            +     +   +L +++  L P+++R+F+  R       
Sbjct: 93  DRELELRDKIRSASLDSTNETEDSVLDTDLNALLDKALETLTPQQKRVFDMSRKDMKSH- 151

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
            + ++    +S   V+Q  + A K ++  + K  E
Sbjct: 152 -KEIADSLGISVYTVQQHISTALKVIRAFLAKYAE 185


>gi|229178209|ref|ZP_04305580.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           172560W]
 gi|228605339|gb|EEK62789.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           172560W]
          Length = 188

 Score = 40.6 bits (94), Expect = 0.27,   Method: Composition-based stats.
 Identities = 17/83 (20%), Positives = 35/83 (42%), Gaps = 10/83 (12%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           H   E+   ++      R  L + ++ L P ++++F  + L       E +  +  ++R 
Sbjct: 104 HISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKT--EEIGDKLGLTRA 161

Query: 268 ----RVRQIEARAFKKVQESIQK 286
               RV     R  KK+Q++  K
Sbjct: 162 AIDNRV----YRGKKKLQQNATK 180


>gi|255283596|ref|ZP_05348151.1| DNA-directed RNA polymerase specialized sigma subunit [Bryantella
           formatexigens DSM 14469]
 gi|255265858|gb|EET59063.1| DNA-directed RNA polymerase specialized sigma subunit [Bryantella
           formatexigens DSM 14469]
          Length = 191

 Score = 40.6 bits (94), Expect = 0.27,   Method: Composition-based stats.
 Identities = 30/117 (25%), Positives = 44/117 (37%), Gaps = 16/117 (13%)

Query: 49  AAHRLVTSHLRLVVKIAM----GYRG-YGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           AA+RL+  HL LV KI       Y         E+   G + L QA   +D ER    A 
Sbjct: 7   AANRLIVEHLELVPKIVRSLTFSYSHLPVQEYEELTQIGYLALCQAASGYDWER--PFAP 64

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
           Y+   I+ A+ +Y               QK LF +L  ++            P++  
Sbjct: 65  YARTAIRNAIYDYWRDCAR---------QKNLFCSLDAIQADENGDASELPFPDKEE 112


>gi|331696106|ref|YP_004332345.1| LuxR family ATP-dependent transcriptional regulator [Pseudonocardia
           dioxanivorans CB1190]
 gi|326950795|gb|AEA24492.1| ATP-dependent transcriptional regulator, MalT-like, LuxR family
           [Pseudonocardia dioxanivorans CB1190]
          Length = 446

 Score = 40.6 bits (94), Expect = 0.27,   Method: Composition-based stats.
 Identities = 23/91 (25%), Positives = 38/91 (41%), Gaps = 14/91 (15%)

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM---SVLNPRERRIFEARRLQENPVT 254
               D LV +  G   VL E+  R   R+     +     L+PRE  +  A      P+T
Sbjct: 319 PVLHDVLVREEPGMLPVLAERAHRAAVRDDAGPVLVAGEPLSPRELAVLRA---LAGPLT 375

Query: 255 LENLSSEFEVS----RERVRQIEARAFKKVQ 281
           L  +++E  +S    +  VR      F+K++
Sbjct: 376 LREIAAEMHLSHNTVKTHVR----SVFRKLR 402


>gi|229058451|ref|ZP_04196835.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           AH603]
 gi|228719960|gb|EEL71550.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           AH603]
          Length = 188

 Score = 40.6 bits (94), Expect = 0.27,   Method: Composition-based stats.
 Identities = 16/79 (20%), Positives = 33/79 (41%), Gaps = 10/79 (12%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           H   E+   ++      R  L + ++ L P ++++F  + L       E +  +  ++R 
Sbjct: 104 HISTEKSAEDELILMEDREELLKLINQLEPLDQKVFVMKYLLGMKT--EEIGDKLGLTRA 161

Query: 268 ----RVRQIEARAFKKVQE 282
               RV     R  KK+Q+
Sbjct: 162 AIDNRV----YRGKKKLQQ 176


>gi|225388234|ref|ZP_03757958.1| hypothetical protein CLOSTASPAR_01969 [Clostridium asparagiforme
           DSM 15981]
 gi|323485993|ref|ZP_08091324.1| hypothetical protein HMPREF9474_03075 [Clostridium symbiosum
           WAL-14163]
 gi|225045702|gb|EEG55948.1| hypothetical protein CLOSTASPAR_01969 [Clostridium asparagiforme
           DSM 15981]
 gi|323400560|gb|EGA92927.1| hypothetical protein HMPREF9474_03075 [Clostridium symbiosum
           WAL-14163]
          Length = 145

 Score = 40.6 bits (94), Expect = 0.27,   Method: Composition-based stats.
 Identities = 10/64 (15%), Positives = 28/64 (43%), Gaps = 2/64 (3%)

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            +L  +++ L  R+R I       +  ++   ++    V R  V +    A  K+++ ++
Sbjct: 80  ELLAEALNALPERKRDIILLSYFLD--MSDAEIAELLNVVRTTVFRHRKSALAKIKQYLE 137

Query: 286 KQVE 289
            + +
Sbjct: 138 GKAD 141


>gi|223934985|ref|ZP_03626904.1| RNA polymerase, sigma-24 subunit, ECF subfamily [bacterium
           Ellin514]
 gi|223896438|gb|EEF62880.1| RNA polymerase, sigma-24 subunit, ECF subfamily [bacterium
           Ellin514]
          Length = 468

 Score = 40.6 bits (94), Expect = 0.27,   Method: Composition-based stats.
 Identities = 15/75 (20%), Positives = 29/75 (38%), Gaps = 10/75 (13%)

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE----RVRQIEARAFKKVQE 282
            L  ++  L+  +R I   R  Q        ++    ++ E    RV     RA ++++E
Sbjct: 121 HLDAALGELSETDRDILLFRYFQGKSA--REIAQTLGLTDEAAQKRV----NRAVERLRE 174

Query: 283 SIQKQVELSSSPPLL 297
              K+     +  LL
Sbjct: 175 IFAKRGVTVGAGSLL 189


>gi|332140425|ref|YP_004426163.1| RNA polymerase sigma-70 factor [Alteromonas macleodii str. 'Deep
           ecotype']
 gi|327550447|gb|AEA97165.1| RNA polymerase sigma-70 factor [Alteromonas macleodii str. 'Deep
           ecotype']
          Length = 109

 Score = 40.6 bits (94), Expect = 0.27,   Method: Composition-based stats.
 Identities = 19/99 (19%), Positives = 39/99 (39%), Gaps = 5/99 (5%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD +A + LVT +   V+ +   Y      +++V  E  I   +A+  F  +      
Sbjct: 15  QRGDKNAFNLLVTRYQHKVMHLVSRYVKNTGDVADVTQEAFIKAYRALPNFRGD--SAFY 72

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRR 141
           T+       + + Y++      +    +   +L   LRR
Sbjct: 73  TWLYRIAVNSAKNYLVSQGRKPR-PVMSMPTKLI--LRR 108


>gi|299140287|ref|ZP_07033452.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Acidobacterium sp.
           MP5ACTX8]
 gi|298597744|gb|EFI53917.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Acidobacterium sp.
           MP5ACTX8]
          Length = 256

 Score = 40.6 bits (94), Expect = 0.28,   Method: Composition-based stats.
 Identities = 46/255 (18%), Positives = 78/255 (30%), Gaps = 69/255 (27%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           + E+  L  R  + GD +A   LV  + R V+++A+   G      +V  +  I      
Sbjct: 66  RAEDDELI-RAAQKGDRAAFDTLVRRYDRSVLRLALHVLGNEQDAQDVHQDAFI------ 118

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAIT 150
           K +     FR       W+   +    L                    LRR K   +   
Sbjct: 119 KAYRHLSNFRFECSFYTWLYRIVTNLCLDQ------------------LRRRKSRRE--- 157

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDG 210
                P  V+                                   +S    D L    DG
Sbjct: 158 ----DPSTVL----------------------------------DSSGDEIDLLANLQDG 179

Query: 211 QEQV-LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
           +       + ERK     +  +++ L PRER +FE +  Q     L  +      + E  
Sbjct: 180 RAMANPARELERKGMNEAIQSALAELTPRERTVFELKHYQGLK--LRTIGEMLSTTEETA 237

Query: 270 RQIEARAFKKVQESI 284
           +    RA +K++  +
Sbjct: 238 KNTLFRATRKLRARL 252


>gi|326792948|ref|YP_004310769.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           lentocellum DSM 5427]
 gi|326543712|gb|ADZ85571.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           lentocellum DSM 5427]
          Length = 193

 Score = 40.6 bits (94), Expect = 0.28,   Method: Composition-based stats.
 Identities = 15/83 (18%), Positives = 39/83 (46%), Gaps = 6/83 (7%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           +    G E +++E E++      + +++  LN RER I   +      ++ + +     +
Sbjct: 106 ISKEKGPEHIILEMEQQTE----ILKAIKKLNERERNIIAYKYGGN--LSNKEIGILMNL 159

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           + + V  I  R  KK++  ++++
Sbjct: 160 NEKHVSVILCRTLKKLKTRLEEE 182


>gi|291545575|emb|CBL18683.1| RNA polymerase sigma factor, sigma-70 family [Ruminococcus sp.
           SR1/5]
          Length = 216

 Score = 40.6 bits (94), Expect = 0.28,   Method: Composition-based stats.
 Identities = 17/130 (13%), Positives = 42/130 (32%), Gaps = 2/130 (1%)

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
            +  E   A+      S+++ + +   L                S   + +++ D     
Sbjct: 57  EITKEVAYAMNNFYRSSKAKKVEIKNELGEVVDKMLREVPYSGQSIDGEGFMIEDFPDLN 116

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
             +      K  +  + + ++ LN  ER I      +    T   ++    +SR+ +   
Sbjct: 117 CDVEHSVLTKMEQQDIHKVINQLNSEERMIIYGIFFEN--KTQTQMAEIMGISRQMLSYK 174

Query: 273 EARAFKKVQE 282
                 K++E
Sbjct: 175 LKSILNKMRE 184


>gi|217959293|ref|YP_002337841.1| RNA polymerase factor sigma-70 [Bacillus cereus AH187]
 gi|222095431|ref|YP_002529491.1| RNA polymerase factor sigma-70 [Bacillus cereus Q1]
 gi|229138504|ref|ZP_04267092.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           BDRD-ST26]
 gi|217064092|gb|ACJ78342.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           AH187]
 gi|221239489|gb|ACM12199.1| RNA polymerase, ECF-type sigma factor [Bacillus cereus Q1]
 gi|228644950|gb|EEL01194.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           BDRD-ST26]
          Length = 188

 Score = 40.6 bits (94), Expect = 0.28,   Method: Composition-based stats.
 Identities = 17/83 (20%), Positives = 35/83 (42%), Gaps = 10/83 (12%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           H   E+   ++      R  L + ++ L P ++++F  + L       E +  +  ++R 
Sbjct: 104 HISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKT--EEIGDKLGLTRA 161

Query: 268 ----RVRQIEARAFKKVQESIQK 286
               RV     R  KK+Q++  K
Sbjct: 162 AIDNRV----YRGKKKLQQNATK 180


>gi|149280463|ref|ZP_01886582.1| putative ECF-type RNA polymerase sigma factor [Pedobacter sp.
           BAL39]
 gi|149228775|gb|EDM34175.1| putative ECF-type RNA polymerase sigma factor [Pedobacter sp.
           BAL39]
          Length = 196

 Score = 40.6 bits (94), Expect = 0.28,   Method: Composition-based stats.
 Identities = 20/86 (23%), Positives = 42/86 (48%), Gaps = 6/86 (6%)

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE--NL 258
           QD+      G +Q +I  E  +N R  LT ++  +  R+R I   R  +E    LE   +
Sbjct: 98  QDFPFNIELGHDQQIISTERIENIRRNLTVALDHMTSRQREIIHLRYFEE----LEFPEI 153

Query: 259 SSEFEVSRERVRQIEARAFKKVQESI 284
           +   ++S++   ++  RA   +++++
Sbjct: 154 ADVMQLSQKATYKLLYRAIDTLKKNL 179


>gi|116070572|ref|ZP_01467841.1| possible type 3 alternative RNA polymerase sigma factor
           [Synechococcus sp. BL107]
 gi|116065977|gb|EAU71734.1| possible type 3 alternative RNA polymerase sigma factor
           [Synechococcus sp. BL107]
          Length = 150

 Score = 40.6 bits (94), Expect = 0.28,   Method: Composition-based stats.
 Identities = 21/185 (11%), Positives = 55/185 (29%), Gaps = 41/185 (22%)

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
              ++   I+ A+  Y+  + SL+++     ++ L                         
Sbjct: 2   FHVFAKPHIRGAILHYLRDNASLIRLPRHVEERALL------------------------ 37

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEE 220
                L     + IS    L              ++      +            ++  E
Sbjct: 38  -----LRNKNEQTISAADSLVQQSYRYKTTWVEFEDEFMTGRYYG----------LKNIE 82

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           R  +   +  ++  L+  +++I      + N + L        VS   V++   RA   +
Sbjct: 83  RCEQAAKINSALQKLHKNDQKIIRLVIFEGNSLRLA--GKNIGVSAMTVQRRLKRALATL 140

Query: 281 QESIQ 285
           ++ ++
Sbjct: 141 RDRLK 145


>gi|228964794|ref|ZP_04125900.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus
           thuringiensis serovar sotto str. T04001]
 gi|228794867|gb|EEM42367.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus
           thuringiensis serovar sotto str. T04001]
          Length = 188

 Score = 40.6 bits (94), Expect = 0.28,   Method: Composition-based stats.
 Identities = 17/83 (20%), Positives = 35/83 (42%), Gaps = 10/83 (12%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           H   E+   ++      R  L + ++ L P ++++F  + L       E +  +  ++R 
Sbjct: 104 HISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKT--EEIGDKLGLTRA 161

Query: 268 ----RVRQIEARAFKKVQESIQK 286
               RV     R  KK+Q++  K
Sbjct: 162 AIDNRV----YRGKKKLQQNATK 180


>gi|7021516|gb|AAF35384.1| SpoIIGB [Clostridium butyricum]
          Length = 106

 Score = 40.6 bits (94), Expect = 0.28,   Method: Composition-based stats.
 Identities = 17/86 (19%), Positives = 33/86 (38%), Gaps = 7/86 (8%)

Query: 177 NCRLAGDESLNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
           N ++  + S    +N   D N     D L  ++D     +    E +  + +L  ++  L
Sbjct: 25  NSKIKAEISFYEPLNIDWDGNELLLSDILGTEND----TVYNLIEDEVDKQLLVMALKSL 80

Query: 236 NPRERRIFEARRLQENPV--TLENLS 259
           N RE+ I   R         T + ++
Sbjct: 81  NDREKEIVRLRFGLNGTREKTQKXVA 106


>gi|296329668|ref|ZP_06872153.1| putative RNA polymerase sigma factor SigI [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305674065|ref|YP_003865737.1| putative RNA polymerase sigma factor SigmaI [Bacillus subtilis
           subsp. spizizenii str. W23]
 gi|296153166|gb|EFG94030.1| putative RNA polymerase sigma factor SigI [Bacillus subtilis subsp.
           spizizenii ATCC 6633]
 gi|305412309|gb|ADM37428.1| putative RNA polymerase sigma factor SigmaI [Bacillus subtilis
           subsp. spizizenii str. W23]
          Length = 251

 Score = 40.6 bits (94), Expect = 0.29,   Method: Composition-based stats.
 Identities = 17/84 (20%), Positives = 34/84 (40%), Gaps = 7/84 (8%)

Query: 43  EHGDLSAAHRLVTSHLRL----VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           + G+    + L+  +       V  +   Y        +  S G I   +A++K+ PE+G
Sbjct: 26  QKGNKDLQNELIQQYKPFIAKTVSSVCKRYI---DEKDDEFSIGLIAFNEAIEKYSPEKG 82

Query: 99  FRLATYSMWWIKAAMQEYILRSWS 122
             L  ++   IK  + +YI +   
Sbjct: 83  NSLLAFAELIIKRKVIDYIRKEAR 106


>gi|229189899|ref|ZP_04316909.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus ATCC
           10876]
 gi|228593573|gb|EEK51382.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus ATCC
           10876]
          Length = 188

 Score = 40.6 bits (94), Expect = 0.29,   Method: Composition-based stats.
 Identities = 17/83 (20%), Positives = 35/83 (42%), Gaps = 10/83 (12%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           H   E+   ++      R  L + ++ L P ++++F  + L       E +  +  ++R 
Sbjct: 104 HISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKT--EEIGDKLGLTRA 161

Query: 268 ----RVRQIEARAFKKVQESIQK 286
               RV     R  KK+Q++  K
Sbjct: 162 AIDNRV----YRGKKKLQQNATK 180


>gi|16078409|ref|NP_389228.1| RNA polymerase sigma factor SigI [Bacillus subtilis subsp. subtilis
           str. 168]
 gi|221309207|ref|ZP_03591054.1| putative RNA polymerase sigma factor SigI [Bacillus subtilis subsp.
           subtilis str. 168]
 gi|221313535|ref|ZP_03595340.1| putative RNA polymerase sigma factor SigI [Bacillus subtilis subsp.
           subtilis str. NCIB 3610]
 gi|221318457|ref|ZP_03599751.1| putative RNA polymerase sigma factor SigI [Bacillus subtilis subsp.
           subtilis str. JH642]
 gi|221322730|ref|ZP_03604024.1| putative RNA polymerase sigma factor SigI [Bacillus subtilis subsp.
           subtilis str. SMY]
 gi|321315098|ref|YP_004207385.1| putative RNA polymerase sigma factor SigI [Bacillus subtilis BSn5]
 gi|81555906|sp|O31654|SIGI_BACSU RecName: Full=RNA polymerase sigma factor sigI
 gi|2633716|emb|CAB13218.1| RNA polymerase sigma factor [Bacillus subtilis subsp. subtilis str.
           168]
 gi|291483875|dbj|BAI84950.1| putative RNA polymerase sigma factor SigI [Bacillus subtilis subsp.
           natto BEST195]
 gi|320021372|gb|ADV96358.1| putative RNA polymerase sigma factor SigI [Bacillus subtilis BSn5]
          Length = 251

 Score = 40.6 bits (94), Expect = 0.29,   Method: Composition-based stats.
 Identities = 17/84 (20%), Positives = 34/84 (40%), Gaps = 7/84 (8%)

Query: 43  EHGDLSAAHRLVTSHLRL----VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           + G+    + L+  +       V  +   Y        +  S G I   +A++K+ PE+G
Sbjct: 26  QKGNKDLQNELIQQYKPFIAKTVSSVCKRYI---DEKDDEFSIGLIAFNEAIEKYSPEKG 82

Query: 99  FRLATYSMWWIKAAMQEYILRSWS 122
             L  ++   IK  + +YI +   
Sbjct: 83  NSLLAFAELIIKRKVIDYIRKEAR 106


>gi|257899919|ref|ZP_05679572.1| RNA polymerase sigma-70 subunit [Enterococcus faecium Com15]
 gi|293572684|ref|ZP_06683652.1| ComX [Enterococcus faecium E980]
 gi|257837831|gb|EEV62905.1| RNA polymerase sigma-70 subunit [Enterococcus faecium Com15]
 gi|291607270|gb|EFF36624.1| ComX [Enterococcus faecium E980]
          Length = 192

 Score = 40.6 bits (94), Expect = 0.29,   Method: Composition-based stats.
 Identities = 16/86 (18%), Positives = 34/86 (39%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R   +GD  A   L   +  L++++   Y        +   E  I L QA++ ++  +G 
Sbjct: 7   RAARNGDEEAFAALYQKYFPLLLRLKNTYYLRNYVTEDWEQEARIALYQALRTYEKSKGV 66

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVK 125
              +Y    I   +   + +  +L +
Sbjct: 67  SFGSYYKSIISNQIYSLLRKQNALKR 92


>gi|42780899|ref|NP_978146.1| RNA polymerase factor sigma-70 [Bacillus cereus ATCC 10987]
 gi|42736820|gb|AAS40754.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus ATCC
           10987]
          Length = 188

 Score = 40.6 bits (94), Expect = 0.29,   Method: Composition-based stats.
 Identities = 16/79 (20%), Positives = 33/79 (41%), Gaps = 10/79 (12%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           H   E+   ++      R  L + ++ L P ++++F  + L       E +  +  ++R 
Sbjct: 104 HISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKA--EEIGDKLGLTRA 161

Query: 268 ----RVRQIEARAFKKVQE 282
               RV     R  KK+Q+
Sbjct: 162 AIDNRV----YRGXKKLQQ 176


>gi|168702821|ref|ZP_02735098.1| RNA polymerase sigma-H factor [Gemmata obscuriglobus UQM 2246]
          Length = 223

 Score = 40.6 bits (94), Expect = 0.29,   Method: Composition-based stats.
 Identities = 16/109 (14%), Positives = 47/109 (43%), Gaps = 5/109 (4%)

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             +  S    ++    LV   D      ++++E      ++  ++  LN R+R      +
Sbjct: 107 LEVQESGPLGTRPPGALVPTRDEPPNHNLQQQELA---GVIRDALEGLNERQRMAIVLNK 163

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPL 296
            ++  +   +++    ++ + V+ + +RA  K++E++Q  + +    P 
Sbjct: 164 FED--MNYADIADVMGLTTKAVKSLLSRARGKLREALQGYIYMDGVVPP 210


>gi|126654406|ref|ZP_01726151.1| RNA polymerase sigma-70 factor [Bacillus sp. B14905]
 gi|126589156|gb|EAZ83340.1| RNA polymerase sigma-70 factor [Bacillus sp. B14905]
          Length = 79

 Score = 40.6 bits (94), Expect = 0.29,   Method: Composition-based stats.
 Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 1/59 (1%)

Query: 36 VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           L +   + G+  A   L+T +  LV   A  Y   G    ++V EG IGL +A++ F 
Sbjct: 20 ELIEMVHQ-GNTDALDYLITKYRLLVRAKARSYFLIGADKEDIVQEGMIGLYKAIRDFK 77


>gi|293570064|ref|ZP_06681144.1| sigma-70 factor family protein [Enterococcus faecium E1071]
 gi|291587436|gb|EFF19320.1| sigma-70 factor family protein [Enterococcus faecium E1071]
          Length = 192

 Score = 40.6 bits (94), Expect = 0.30,   Method: Composition-based stats.
 Identities = 16/86 (18%), Positives = 34/86 (39%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R   +GD  A   L   +  L++++   Y        +   E  I L QA++ ++  +G 
Sbjct: 7   RAARNGDEEAFAALYQKYFPLLLRLKNTYYLRNYVSEDWEQEARIALYQALRTYEKSKGV 66

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVK 125
              +Y    I   +   + +  +L +
Sbjct: 67  SFGSYYKSIISNQIYSLLRKQNALKR 92


>gi|295687923|ref|YP_003591616.1| RNA polymerase sigma-24 factor [Caulobacter segnis ATCC 21756]
 gi|295429826|gb|ADG08998.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Caulobacter segnis
           ATCC 21756]
          Length = 199

 Score = 40.6 bits (94), Expect = 0.30,   Method: Composition-based stats.
 Identities = 16/83 (19%), Positives = 36/83 (43%), Gaps = 8/83 (9%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           H   E       + + +   +  +++ L  R RR+F   R +E  ++ + ++    VS  
Sbjct: 107 HPVDEMSPERVLQGREQMARVLAALNTLPERTRRVFILVRFEE--MSYKLVAQRLGVS-- 162

Query: 268 RVRQIEA---RAFKKVQESIQKQ 287
            V  +E    +A + + E ++ Q
Sbjct: 163 -VSAVEKHVMKALRHLHERLRDQ 184


>gi|284048553|ref|YP_003398892.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Acidaminococcus
           fermentans DSM 20731]
 gi|283952774|gb|ADB47577.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Acidaminococcus
           fermentans DSM 20731]
          Length = 187

 Score = 40.6 bits (94), Expect = 0.30,   Method: Composition-based stats.
 Identities = 22/113 (19%), Positives = 44/113 (38%), Gaps = 7/113 (6%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A   +V +   LV K+A G         ++ S+  +GL++A++K+  E   R   +
Sbjct: 19  GDQEAQLAIVIAFRPLVQKLA-GQEKNPSLRMDLASQLVLGLLEAIRKYPGEDPRRFPGF 77

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
               +   +  YI +     K+      K   +   +   + +  T    + E
Sbjct: 78  VNTHLHYLLSHYIRKQIRWNKV------KEKIYAQNQETSYTEDFTMRIRRGE 124


>gi|255305113|ref|ZP_05349285.1| hypothetical protein CdifA_00892 [Clostridium difficile ATCC 43255]
          Length = 155

 Score = 40.6 bits (94), Expect = 0.30,   Method: Composition-based stats.
 Identities = 19/99 (19%), Positives = 37/99 (37%), Gaps = 5/99 (5%)

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEE---RKNRRNMLTRSMSVLNPRERRIFEARR 247
            S D       D + +     E  +I+ E+   ++     L  ++  L P + R    R 
Sbjct: 51  FSLDCEDGIENDAIGWAQPSPEDYMIQAEDEAAQELLLEHLWEAIGQLTPTQARRLHMRY 110

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           + E       ++    +S  +      RA KK+Q+  +K
Sbjct: 111 MLEMKY--REIAEAEGISPTQASDSVRRAVKKLQKYFKK 147


>gi|310824067|ref|YP_003956425.1| DNA-binding regulatory protein [Stigmatella aurantiaca DW4/3-1]
 gi|309397139|gb|ADO74598.1| DNA-binding regulatory protein [Stigmatella aurantiaca DW4/3-1]
          Length = 293

 Score = 40.6 bits (94), Expect = 0.30,   Method: Composition-based stats.
 Identities = 32/167 (19%), Positives = 55/167 (32%), Gaps = 26/167 (15%)

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
           T     R+F      +   + +     +P +++  A K  +     +     +A  E+LN
Sbjct: 106 THLRPDRVFVEEVHQRLRQKLLLSREGRPPKLLEYAGKGPL-----VQWLRAVALREALN 160

Query: 188 ALINSSDK---NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
            L          S      L       E  L++       +  L  ++  L  RER    
Sbjct: 161 LLAQQRAGAPLESGTVLPELAAPGPDPELTLLKHRYAPEFKAALEAALRGLPARERNFLR 220

Query: 245 ARRLQENPVTLENLSSEFE-----VS------RERV-----RQIEAR 275
              L    +T+E ++         VS      RERV     RQ++ R
Sbjct: 221 LFFL--ESLTVEQIARMDGTHKSTVSRRMASARERVLTGMRRQLQER 265


>gi|229147783|ref|ZP_04276126.1| RNA polymerase sigma factor [Bacillus cereus BDRD-ST24]
 gi|296505675|ref|YP_003667375.1| RNA polymerase factor sigma-70 [Bacillus thuringiensis BMB171]
 gi|228635796|gb|EEK92283.1| RNA polymerase sigma factor [Bacillus cereus BDRD-ST24]
 gi|296326727|gb|ADH09655.1| RNA polymerase factor sigma-70 [Bacillus thuringiensis BMB171]
          Length = 156

 Score = 40.6 bits (94), Expect = 0.30,   Method: Composition-based stats.
 Identities = 15/64 (23%), Positives = 35/64 (54%), Gaps = 2/64 (3%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    +   MSVL+ +E+ I   R       T+  ++ E E++  +VR +  +A +K++
Sbjct: 94  EDVEIRVKDFMSVLDEKEKYIIFERFFVG--KTMGEIALETEMTYYQVRWMYRQALEKMR 151

Query: 282 ESIQ 285
           +S++
Sbjct: 152 DSVR 155


>gi|168698427|ref|ZP_02730704.1| RNA polymerase sigma factor SigM [Gemmata obscuriglobus UQM 2246]
          Length = 638

 Score = 40.6 bits (94), Expect = 0.30,   Method: Composition-based stats.
 Identities = 22/151 (14%), Positives = 40/151 (26%), Gaps = 5/151 (3%)

Query: 24  RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGN 83
           RK   L       L  R+   GD +A   LV  H  LV  +            +      
Sbjct: 11  RKAESLTPD--ADLLSRFARDGDQTAFEELVRRHGPLVWAVCRHLLPDHADAEDAFQAVF 68

Query: 84  IGLMQAVKKFDPERG-FRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFF-NLR 140
           + L+++ +     R                ++  I  R     K+      + +      
Sbjct: 69  LALVRSARTVRDGRALPAWLHGVAVRAATRVKRSIARRKAREQKVARPEASRPVSDGTWN 128

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            L         +  + E+V  +   L     
Sbjct: 129 ALLRAAHEEVQHLPEAERVAFVLCDLEGVPQ 159


>gi|75759228|ref|ZP_00739329.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|228903726|ref|ZP_04067846.1| RNA polymerase sigma factor [Bacillus thuringiensis IBL 4222]
 gi|74493291|gb|EAO56406.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           israelensis ATCC 35646]
 gi|228855994|gb|EEN00534.1| RNA polymerase sigma factor [Bacillus thuringiensis IBL 4222]
          Length = 156

 Score = 40.6 bits (94), Expect = 0.30,   Method: Composition-based stats.
 Identities = 15/64 (23%), Positives = 35/64 (54%), Gaps = 2/64 (3%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    +   MSVL+ +E+ I   R       T+  ++ E E++  +VR +  +A +K++
Sbjct: 94  EDVEMKVKDFMSVLDEKEKYIIFERFFVG--KTMGEIALETEMTYYQVRWMYRQALEKMR 151

Query: 282 ESIQ 285
           +S++
Sbjct: 152 DSVR 155


>gi|196038947|ref|ZP_03106254.1| RNA polymerase sigma-70 factor, ECF family [Bacillus cereus
           NVH0597-99]
 gi|225863663|ref|YP_002749041.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           03BB102]
 gi|196030092|gb|EDX68692.1| RNA polymerase sigma-70 factor, ECF family [Bacillus cereus
           NVH0597-99]
 gi|225787009|gb|ACO27226.1| RNA polymerase sigma-70 factor, ECF family [Bacillus cereus
           03BB102]
          Length = 188

 Score = 40.6 bits (94), Expect = 0.31,   Method: Composition-based stats.
 Identities = 16/79 (20%), Positives = 33/79 (41%), Gaps = 10/79 (12%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           H   E+   ++      R  L + ++ L P ++++F  + L       E +  +  ++R 
Sbjct: 104 HISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKT--EEIGDKLGLTRA 161

Query: 268 ----RVRQIEARAFKKVQE 282
               RV     R  KK+Q+
Sbjct: 162 AIDNRV----YRGKKKLQQ 176


>gi|311744858|ref|ZP_07718643.1| RNA polymerase sigma-70 factor, ECF subfamily [Algoriphagus sp.
           PR1]
 gi|126577360|gb|EAZ81580.1| RNA polymerase sigma-70 factor, ECF subfamily [Algoriphagus sp.
           PR1]
          Length = 200

 Score = 40.6 bits (94), Expect = 0.31,   Method: Composition-based stats.
 Identities = 9/80 (11%), Positives = 33/80 (41%), Gaps = 14/80 (17%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS------ 265
           E  + +++ R     ++ + +  L   ++++   R   +  ++ + ++ +  VS      
Sbjct: 116 EDTVEDRQMRDETIELVKKLIDELPENQKQVLIMRHYMD--MSFQEIADKTGVSINTALG 173

Query: 266 RERVRQIEARAFKKVQESIQ 285
           R R       A   +++ ++
Sbjct: 174 RMR------YALIHLRKKMK 187


>gi|229090770|ref|ZP_04222003.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           Rock3-42]
 gi|228692712|gb|EEL46438.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           Rock3-42]
          Length = 188

 Score = 40.6 bits (94), Expect = 0.31,   Method: Composition-based stats.
 Identities = 16/79 (20%), Positives = 33/79 (41%), Gaps = 10/79 (12%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           H   E+   ++      R  L + ++ L P ++++F  + L       E +  +  ++R 
Sbjct: 104 HISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKT--EEIGDKLGLTRA 161

Query: 268 ----RVRQIEARAFKKVQE 282
               RV     R  KK+Q+
Sbjct: 162 AIDNRV----YRGKKKLQQ 176


>gi|227552717|ref|ZP_03982766.1| ECF family DNA-directed RNA polymerase sigma subunit [Enterococcus
           faecium TX1330]
 gi|257888685|ref|ZP_05668338.1| RNA polymerase sigma-70 subunit [Enterococcus faecium 1,141,733]
 gi|293378881|ref|ZP_06625036.1| sigma-70 region 2 [Enterococcus faecium PC4.1]
 gi|227178117|gb|EEI59089.1| ECF family DNA-directed RNA polymerase sigma subunit [Enterococcus
           faecium TX1330]
 gi|257824739|gb|EEV51671.1| RNA polymerase sigma-70 subunit [Enterococcus faecium 1,141,733]
 gi|292642422|gb|EFF60577.1| sigma-70 region 2 [Enterococcus faecium PC4.1]
          Length = 192

 Score = 40.6 bits (94), Expect = 0.31,   Method: Composition-based stats.
 Identities = 16/86 (18%), Positives = 34/86 (39%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R   +GD  A   L   +  L++++   Y        +   E  I L QA++ ++  +G 
Sbjct: 7   RAARNGDEEAFAALYQKYFPLLLRLKNTYYLRNYVTEDWEQEARIALYQALRTYEKSKGV 66

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVK 125
              +Y    I   +   + +  +L +
Sbjct: 67  SFGSYYKSIISNQIYSLLRKQNALKR 92


>gi|206970570|ref|ZP_03231522.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           AH1134]
 gi|206734206|gb|EDZ51376.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           AH1134]
          Length = 188

 Score = 40.6 bits (94), Expect = 0.31,   Method: Composition-based stats.
 Identities = 17/83 (20%), Positives = 35/83 (42%), Gaps = 10/83 (12%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           H   E+   ++      R  L + ++ L P ++++F  + L       E +  +  ++R 
Sbjct: 104 HISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKT--EEIGDKLGLTRA 161

Query: 268 ----RVRQIEARAFKKVQESIQK 286
               RV     R  KK+Q++  K
Sbjct: 162 AIDNRV----YRGKKKLQQNATK 180


>gi|308173317|ref|YP_003920022.1| RNA polymerase sigma factor [Bacillus amyloliquefaciens DSM 7]
 gi|307606181|emb|CBI42552.1| RNA polymerase sigma factor [Bacillus amyloliquefaciens DSM 7]
 gi|328553759|gb|AEB24251.1| putative RNA polymerase sigma factor SigI [Bacillus
           amyloliquefaciens TA208]
 gi|328911390|gb|AEB62986.1| RNA polymerase sigma factor [Bacillus amyloliquefaciens LL3]
          Length = 251

 Score = 40.6 bits (94), Expect = 0.31,   Method: Composition-based stats.
 Identities = 17/85 (20%), Positives = 33/85 (38%), Gaps = 7/85 (8%)

Query: 43  EHGDLSAAHRLVTSHLRL----VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           + GD    + L+  +       V  +   Y        +  S G I   +A++K+  E+G
Sbjct: 26  QKGDKDLQNDLIQQYKPFIAKTVSSVCKRYI---DEKDDEFSIGLIAFNEAIEKYSAEKG 82

Query: 99  FRLATYSMWWIKAAMQEYILRSWSL 123
             L  ++   IK  + +YI +    
Sbjct: 83  NSLLAFAELIIKRKVIDYIRKEART 107


>gi|229183996|ref|ZP_04311211.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus BGSC
           6E1]
 gi|228599521|gb|EEK57126.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus BGSC
           6E1]
          Length = 188

 Score = 40.6 bits (94), Expect = 0.32,   Method: Composition-based stats.
 Identities = 16/79 (20%), Positives = 33/79 (41%), Gaps = 10/79 (12%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           H   E+   ++      R  L + ++ L P ++++F  + L       E +  +  ++R 
Sbjct: 104 HISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKT--EEIGDKLGLTRA 161

Query: 268 ----RVRQIEARAFKKVQE 282
               RV     R  KK+Q+
Sbjct: 162 AIDNRV----YRGKKKLQQ 176


>gi|228926836|ref|ZP_04089904.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus
           thuringiensis serovar pondicheriensis BGSC 4BA1]
 gi|228832949|gb|EEM78518.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus
           thuringiensis serovar pondicheriensis BGSC 4BA1]
          Length = 188

 Score = 40.6 bits (94), Expect = 0.32,   Method: Composition-based stats.
 Identities = 16/79 (20%), Positives = 33/79 (41%), Gaps = 10/79 (12%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           H   E+   ++      R  L + ++ L P ++++F  + L       E +  +  ++R 
Sbjct: 104 HISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKA--EEIGDKLGLTRA 161

Query: 268 ----RVRQIEARAFKKVQE 282
               RV     R  KK+Q+
Sbjct: 162 AIDNRV----YRGKKKLQQ 176


>gi|229072714|ref|ZP_04205916.1| RNA polymerase sigma factor [Bacillus cereus F65185]
 gi|228710690|gb|EEL62663.1| RNA polymerase sigma factor [Bacillus cereus F65185]
          Length = 156

 Score = 40.6 bits (94), Expect = 0.32,   Method: Composition-based stats.
 Identities = 15/64 (23%), Positives = 35/64 (54%), Gaps = 2/64 (3%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    +   MSVL+ +E+ I   R       T+  ++ E E++  +VR +  +A +K++
Sbjct: 94  EDVEIRVKDFMSVLDEKEKYIIFERFFVG--KTMGEIALETEMTYYQVRWMYRQALEKMR 151

Query: 282 ESIQ 285
           +S++
Sbjct: 152 DSVR 155


>gi|196233776|ref|ZP_03132615.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Chthoniobacter
           flavus Ellin428]
 gi|196222138|gb|EDY16669.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Chthoniobacter
           flavus Ellin428]
          Length = 183

 Score = 40.6 bits (94), Expect = 0.32,   Method: Composition-based stats.
 Identities = 17/87 (19%), Positives = 35/87 (40%), Gaps = 2/87 (2%)

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
              L  D    E       ER+     L R +  L+P +R +   +   +N ++   ++ 
Sbjct: 87  PMPLPEDRPCAEPGPAAVLERQESATALFRLLDALSPNQREVIRLKF--QNDLSYREIAE 144

Query: 261 EFEVSRERVRQIEARAFKKVQESIQKQ 287
              +S   V  +     KK++E +++Q
Sbjct: 145 ITRLSVTNVGFLLHSGLKKLRELLREQ 171


>gi|218900375|ref|YP_002448786.1| putative sigma factor [Bacillus cereus G9842]
 gi|218544267|gb|ACK96661.1| putative sigma factor [Bacillus cereus G9842]
          Length = 156

 Score = 40.6 bits (94), Expect = 0.32,   Method: Composition-based stats.
 Identities = 15/64 (23%), Positives = 35/64 (54%), Gaps = 2/64 (3%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    +   MSVL+ +E+ I   R       T+  ++ E E++  +VR +  +A +K++
Sbjct: 94  EDVEIRVKDFMSVLDEKEKYIIFERFFVG--KTMGEIALETEMTYYQVRWMYRQALEKMR 151

Query: 282 ESIQ 285
           +S++
Sbjct: 152 DSVR 155


>gi|163845994|ref|YP_001634038.1| sigma-70 family RNA polymerase sigma factor [Chloroflexus
           aurantiacus J-10-fl]
 gi|222523719|ref|YP_002568189.1| ECF subfamily RNA polymerase sigma-24 subunit [Chloroflexus sp.
           Y-400-fl]
 gi|163667283|gb|ABY33649.1| RNA polymerase sigma factor, sigma-70 family [Chloroflexus
           aurantiacus J-10-fl]
 gi|222447598|gb|ACM51864.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Chloroflexus sp.
           Y-400-fl]
          Length = 224

 Score = 40.6 bits (94), Expect = 0.32,   Method: Composition-based stats.
 Identities = 31/223 (13%), Positives = 62/223 (27%), Gaps = 68/223 (30%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + GD  A   L+      V  IAM         +++  E  I L +A+ ++  E   R 
Sbjct: 12  AQQGDQQALTELIIGQQHYVYSIAMSVLKNADDAADLTQEAFIRLFRALPQYSGE--SRF 69

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
            T+    +    ++ + R      I                                   
Sbjct: 70  TTWLYRLVINLCRDELRRRGRQAPIVP--------------------------------- 96

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
                                DE L+AL   +D +  +W D              +  + 
Sbjct: 97  -----------------PATDDEELDALHTVADND--RWVD------------PAQSLDL 125

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
              R  + R++  L P  R +      ++   T  +++   ++
Sbjct: 126 NQLRLEVRRALEQLEPHYRLVLTLYYFEDLKYT--DIAEILDL 166


>gi|328958757|ref|YP_004376143.1| RNA polymerase factor sigma-70 [Carnobacterium sp. 17-4]
 gi|328675081|gb|AEB31127.1| RNA polymerase factor sigma-70 [Carnobacterium sp. 17-4]
          Length = 199

 Score = 40.6 bits (94), Expect = 0.33,   Method: Composition-based stats.
 Identities = 17/106 (16%), Positives = 40/106 (37%), Gaps = 8/106 (7%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L  +E   + K    +GD      L   +  LV K+   Y      + ++  E  I   +
Sbjct: 11  LSDEELIHMIK----NGDGYPFKILFERYHPLVTKLTKEYFLKSYELEDLWQEARIVFHK 66

Query: 89  AVKKFDPERGFRLATYS----MWWIKAAMQEYILRSWSLVKIGTTA 130
            ++ +D ++G     +        I + +++ + +   + KI  + 
Sbjct: 67  TIQTYDKDKGHTFGNFYKLNFKHHIFSLIRKDMAKKRRIEKIAESL 112


>gi|326387551|ref|ZP_08209157.1| ECF subfamily RNA polymerase sigma-24 factor [Novosphingobium
           nitrogenifigens DSM 19370]
 gi|326207597|gb|EGD58408.1| ECF subfamily RNA polymerase sigma-24 factor [Novosphingobium
           nitrogenifigens DSM 19370]
          Length = 205

 Score = 40.6 bits (94), Expect = 0.33,   Method: Composition-based stats.
 Identities = 18/93 (19%), Positives = 43/93 (46%), Gaps = 6/93 (6%)

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
            +D ++S   +  +   D  E++L+ ++E     + L  +++ L    RR     R++E 
Sbjct: 98  DADGSASLDPEDRLDPADSAEEILLRRQEA----DRLHEAIAALPEGARRALWLYRIEEK 153

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                 +++   +SR  V +  A A K+++  +
Sbjct: 154 G--QGEIAAILGISRSGVEKHLALAMKRLRAHL 184


>gi|218896738|ref|YP_002445149.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           G9842]
 gi|218543870|gb|ACK96264.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           G9842]
          Length = 188

 Score = 40.6 bits (94), Expect = 0.33,   Method: Composition-based stats.
 Identities = 17/83 (20%), Positives = 35/83 (42%), Gaps = 10/83 (12%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           H   E+   ++      R  L + ++ L P ++++F  + L       E +  +  ++R 
Sbjct: 104 HISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKT--EEIGDKLGLTRA 161

Query: 268 ----RVRQIEARAFKKVQESIQK 286
               RV     R  KK+Q++  K
Sbjct: 162 AIDNRV----YRGKKKLQQNATK 180


>gi|229121353|ref|ZP_04250584.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           95/8201]
 gi|228662198|gb|EEL17807.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           95/8201]
          Length = 188

 Score = 40.6 bits (94), Expect = 0.33,   Method: Composition-based stats.
 Identities = 16/79 (20%), Positives = 33/79 (41%), Gaps = 10/79 (12%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           H   E+   ++      R  L + ++ L P ++++F  + L       E +  +  ++R 
Sbjct: 104 HISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKA--EEIGDKLGLTRA 161

Query: 268 ----RVRQIEARAFKKVQE 282
               RV     R  KK+Q+
Sbjct: 162 AIDNRV----YRGKKKLQQ 176


>gi|229193499|ref|ZP_04320446.1| RNA polymerase sigma factor [Bacillus cereus ATCC 10876]
 gi|228590031|gb|EEK47903.1| RNA polymerase sigma factor [Bacillus cereus ATCC 10876]
          Length = 156

 Score = 40.6 bits (94), Expect = 0.33,   Method: Composition-based stats.
 Identities = 15/64 (23%), Positives = 35/64 (54%), Gaps = 2/64 (3%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    +   MSVL+ +E+ I   R       T+  ++ E E++  +VR +  +A +K++
Sbjct: 94  EDVEIRVKDFMSVLDEKEKYIIFERFFVG--KTMGEIALETEMTYYQVRWMYRQALEKMR 151

Query: 282 ESIQ 285
           +S++
Sbjct: 152 DSVK 155


>gi|167757783|ref|ZP_02429910.1| hypothetical protein CLOSCI_00114 [Clostridium scindens ATCC 35704]
 gi|167769823|ref|ZP_02441876.1| hypothetical protein ANACOL_01157 [Anaerotruncus colihominis DSM
           17241]
 gi|323487585|ref|ZP_08092875.1| hypothetical protein HMPREF9474_04626 [Clostridium symbiosum
           WAL-14163]
 gi|167664665|gb|EDS08795.1| hypothetical protein CLOSCI_00114 [Clostridium scindens ATCC 35704]
 gi|167668184|gb|EDS12314.1| hypothetical protein ANACOL_01157 [Anaerotruncus colihominis DSM
           17241]
 gi|323399084|gb|EGA91492.1| hypothetical protein HMPREF9474_04626 [Clostridium symbiosum
           WAL-14163]
          Length = 148

 Score = 40.6 bits (94), Expect = 0.33,   Method: Composition-based stats.
 Identities = 11/63 (17%), Positives = 27/63 (42%), Gaps = 10/63 (15%)

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE----RVRQIEARAFKKVQE 282
           +L  ++S L+ RER +      +  P     +  ++  SR      +R    +  +++Q 
Sbjct: 86  LLAEALSRLDEREREMIYLSFFKRIP--QHEIGRQYGRSRSTAGYHIR----KVLRQLQA 139

Query: 283 SIQ 285
            ++
Sbjct: 140 EME 142


>gi|30261806|ref|NP_844183.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. Ames]
 gi|47527044|ref|YP_018393.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. 'Ames
           Ancestor']
 gi|49184640|ref|YP_027892.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. Sterne]
 gi|165869500|ref|ZP_02214159.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus anthracis
           str. A0488]
 gi|167633331|ref|ZP_02391656.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus anthracis
           str. A0442]
 gi|167638754|ref|ZP_02397029.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus anthracis
           str. A0193]
 gi|170686110|ref|ZP_02877332.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus anthracis
           str. A0465]
 gi|177650443|ref|ZP_02933410.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus anthracis
           str. A0174]
 gi|190566343|ref|ZP_03019261.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus anthracis
           Tsiankovskii-I]
 gi|227815422|ref|YP_002815431.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus anthracis
           str. CDC 684]
 gi|229602244|ref|YP_002866192.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus anthracis
           str. A0248]
 gi|254683304|ref|ZP_05147165.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. CNEVA-9066]
 gi|254734658|ref|ZP_05192370.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. Western
           North America USA6153]
 gi|254741066|ref|ZP_05198754.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. Kruger B]
 gi|254755310|ref|ZP_05207344.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. Vollum]
 gi|254759847|ref|ZP_05211871.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. Australia
           94]
 gi|30256034|gb|AAP25669.1| RNA polymerase sigma-70 factor, ECF family [Bacillus anthracis str.
           Ames]
 gi|47502192|gb|AAT30868.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus anthracis
           str. 'Ames Ancestor']
 gi|49178567|gb|AAT53943.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus anthracis
           str. Sterne]
 gi|164714940|gb|EDR20458.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus anthracis
           str. A0488]
 gi|167513218|gb|EDR88589.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus anthracis
           str. A0193]
 gi|167531369|gb|EDR94047.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus anthracis
           str. A0442]
 gi|170669807|gb|EDT20548.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus anthracis
           str. A0465]
 gi|172083587|gb|EDT68647.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus anthracis
           str. A0174]
 gi|190562478|gb|EDV16445.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus anthracis
           Tsiankovskii-I]
 gi|227004369|gb|ACP14112.1| RNA polymerase sigma-70 factor, ECF family [Bacillus anthracis str.
           CDC 684]
 gi|229266652|gb|ACQ48289.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus anthracis
           str. A0248]
          Length = 188

 Score = 40.6 bits (94), Expect = 0.33,   Method: Composition-based stats.
 Identities = 16/79 (20%), Positives = 33/79 (41%), Gaps = 10/79 (12%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           H   E+   ++      R  L + ++ L P ++++F  + L       E +  +  ++R 
Sbjct: 104 HISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKT--EEIGDKLGLTRA 161

Query: 268 ----RVRQIEARAFKKVQE 282
               RV     R  KK+Q+
Sbjct: 162 AIDNRV----YRGKKKLQQ 176


>gi|325956065|ref|YP_004286675.1| DNA-directed RNA polymerase sigma factor, sigma H [Lactobacillus
           acidophilus 30SC]
 gi|325332630|gb|ADZ06538.1| DNA-directed RNA polymerase sigma factor, sigma H [Lactobacillus
           acidophilus 30SC]
 gi|327182879|gb|AEA31326.1| DNA-directed RNA polymerase sigma factor, sigma H [Lactobacillus
           amylovorus GRL 1118]
          Length = 181

 Score = 40.2 bits (93), Expect = 0.34,   Method: Composition-based stats.
 Identities = 16/73 (21%), Positives = 27/73 (36%), Gaps = 1/73 (1%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           E  L K+ +  GD  A  +L   +  LV  +   Y       ++   E  I   +A   +
Sbjct: 5   ERKLIKKVK-AGDDEALEKLFVLYKPLVNSVVKKYYLGHYDRNDWEQEAMIICYEAALVY 63

Query: 94  DPERGFRLATYSM 106
             E+G   + Y  
Sbjct: 64  SSEKGNFGSLYKT 76


>gi|153811834|ref|ZP_01964502.1| hypothetical protein RUMOBE_02227 [Ruminococcus obeum ATCC 29174]
 gi|149831968|gb|EDM87053.1| hypothetical protein RUMOBE_02227 [Ruminococcus obeum ATCC 29174]
          Length = 119

 Score = 40.2 bits (93), Expect = 0.34,   Method: Composition-based stats.
 Identities = 20/115 (17%), Positives = 47/115 (40%), Gaps = 7/115 (6%)

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
               +  +M  +    E L+  + S + +    QD         E ++I + E       
Sbjct: 7   WQPEDPETMTRKTKWTELLD-CVFSENTDGIGVQDLPDECQRSVEDLVILQAESAE---- 61

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           L ++++ L+  E+ I ++            L+ + E+S+ R+ Q  +   KK+++
Sbjct: 62  LHQNIAKLSEHEQFIIKSIYFDGMK--QVELAKKLEISKVRMSQKVSAILKKMRK 114


>gi|317477881|ref|ZP_07937066.1| sigma-70 family RNA polymerase sigma factor [Bacteroides sp.
           4_1_36]
 gi|316905954|gb|EFV27723.1| sigma-70 family RNA polymerase sigma factor [Bacteroides sp.
           4_1_36]
          Length = 169

 Score = 40.2 bits (93), Expect = 0.34,   Method: Composition-based stats.
 Identities = 17/82 (20%), Positives = 34/82 (41%), Gaps = 2/82 (2%)

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           A+  S  K+S   +  L  +         EK   K R  ++ R M+ L  ++R I   R 
Sbjct: 67  AIDRSERKDSRTVELTLEMEQASDASSPYEKLVNKERMTLIHRLMNKLPEKQRLIMLLR- 125

Query: 248 LQENPVTLENLSSEFEVSRERV 269
                 + + +++   ++ E+V
Sbjct: 126 -DVEGKSYKEIAAVLNLTEEQV 146


>gi|226226603|ref|YP_002760709.1| sigma factor, ECF-like family protein [Gemmatimonas aurantiaca
           T-27]
 gi|226089794|dbj|BAH38239.1| sigma factor, ECF-like family protein [Gemmatimonas aurantiaca
           T-27]
          Length = 193

 Score = 40.2 bits (93), Expect = 0.34,   Method: Composition-based stats.
 Identities = 22/129 (17%), Positives = 40/129 (31%), Gaps = 27/129 (20%)

Query: 143 KGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
           +GH   I    ++   V    +          S+    A   SL+ L     ++     D
Sbjct: 76  RGHFFGIAAQMMRRVLVDHARRATADRRDRQRSVPLEAAETVSLDDLATGGAEDVLAVHD 135

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
            L                           +  L+PR+ RI E R      ++LE ++   
Sbjct: 136 AL-------------------------EQLERLDPRQARIVELRFFVG--LSLEEIAELL 168

Query: 263 EVSRERVRQ 271
           ++S   V +
Sbjct: 169 DISPATVSR 177


>gi|16330063|ref|NP_440791.1| RNA polymerase sigma factor RpoE [Synechocystis sp. PCC 6803]
 gi|1652550|dbj|BAA17471.1| RNA polymerase sigma-E factor [Synechocystis sp. PCC 6803]
          Length = 223

 Score = 40.2 bits (93), Expect = 0.34,   Method: Composition-based stats.
 Identities = 21/111 (18%), Positives = 36/111 (32%), Gaps = 17/111 (15%)

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           R++   SL+A     D         + +D +       E          L  ++  L   
Sbjct: 121 RVSHPISLDAPRRMDDGE-------IDWDIESDYPSPDETLSTAEFYECLRSAIKDLPEA 173

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVS----RERVRQIEARAFKKVQESIQ 285
            R     R +       E ++    VS    + R+    ARA  K+Q  +Q
Sbjct: 174 FRTTIILREIDGLAY--EEIAEITGVSLGTVKSRI----ARARAKLQTFLQ 218


>gi|297242722|ref|ZP_06926660.1| DNA-directed sigma24-like RNA polymerase [Gardnerella vaginalis
           AMD]
 gi|296888933|gb|EFH27667.1| DNA-directed sigma24-like RNA polymerase [Gardnerella vaginalis
           AMD]
          Length = 210

 Score = 40.2 bits (93), Expect = 0.35,   Method: Composition-based stats.
 Identities = 8/61 (13%), Positives = 25/61 (40%), Gaps = 2/61 (3%)

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
                    +S L  ++ ++ +         T   ++S   +S   V++   +A +K+++
Sbjct: 151 EMSERTESMLSALTDKQSQVVKLMFFGG--YTQSEIASMLGISSAGVKKHLDKALEKLRK 208

Query: 283 S 283
           +
Sbjct: 209 T 209


>gi|223935461|ref|ZP_03627378.1| RNA polymerase, sigma-24 subunit, ECF subfamily [bacterium
           Ellin514]
 gi|223895871|gb|EEF62315.1| RNA polymerase, sigma-24 subunit, ECF subfamily [bacterium
           Ellin514]
          Length = 457

 Score = 40.2 bits (93), Expect = 0.35,   Method: Composition-based stats.
 Identities = 17/84 (20%), Positives = 38/84 (45%), Gaps = 10/84 (11%)

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV----SRERVRQIE 273
           + E      +L  +MSVL  ++R +   R  ++ P  L+ +     +    +++R+    
Sbjct: 82  ESEWMQIAPLLDEAMSVLGEKDRNLIVLRFFEQKP--LKEVGIALGIDPDTAQKRIS--- 136

Query: 274 ARAFKKVQESIQKQVELSSSPPLL 297
            RA  K++  + K+    S+  L+
Sbjct: 137 -RAVDKLRHVLLKRGAAVSAVALV 159


>gi|118477234|ref|YP_894385.1| RNA polymerase factor sigma-70 [Bacillus thuringiensis str. Al
           Hakam]
 gi|118416459|gb|ABK84878.1| RNA polymerase, ECF-type sigma factor [Bacillus thuringiensis str.
           Al Hakam]
          Length = 188

 Score = 40.2 bits (93), Expect = 0.35,   Method: Composition-based stats.
 Identities = 16/79 (20%), Positives = 33/79 (41%), Gaps = 10/79 (12%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           H   E+   ++      R  L + ++ L P ++++F  + L       E +  +  ++R 
Sbjct: 104 HISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKT--EEIGDKLGLTRA 161

Query: 268 ----RVRQIEARAFKKVQE 282
               RV     R  KK+Q+
Sbjct: 162 AIDNRV----YRGKKKLQQ 176


>gi|88858210|ref|ZP_01132852.1| sigma E (sigma 24) factor of RNA polymerase [Pseudoalteromonas
           tunicata D2]
 gi|88819827|gb|EAR29640.1| sigma E (sigma 24) factor of RNA polymerase [Pseudoalteromonas
           tunicata D2]
          Length = 193

 Score = 40.2 bits (93), Expect = 0.35,   Method: Composition-based stats.
 Identities = 17/92 (18%), Positives = 35/92 (38%), Gaps = 3/92 (3%)

Query: 32  QEEYVLAKRYR-EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           +++  LA   + + GD +A + LV  +   V  +   Y      +++V  E  I   +A+
Sbjct: 3   EQDLDLALVIKVQQGDKNAFNLLVRKYQNKVASLISRYVSNQSDVADVAQEAFIKAYRAI 62

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
             F  E      T+         + Y++    
Sbjct: 63  PGFRGE--SAFYTWLYRIAVNCAKNYLVAQGR 92


>gi|168206180|ref|ZP_02632185.1| hypothetical protein AC3_0056 [Clostridium perfringens E str.
           JGS1987]
 gi|170662375|gb|EDT15058.1| hypothetical protein AC3_0056 [Clostridium perfringens E str.
           JGS1987]
          Length = 143

 Score = 40.2 bits (93), Expect = 0.35,   Method: Composition-based stats.
 Identities = 20/112 (17%), Positives = 44/112 (39%), Gaps = 1/112 (0%)

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
           +  EQ   I K L+  ++  + + C     E L   I    +        +  + + + +
Sbjct: 1   MTKEQKEKIKKLLSNYKTMKVQIECIDYEIELLKEHIEFLKEFRDSDNYIIESNKEIEHK 60

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
             I K   +   N +  +++ ++  ER+I E R L+    T + + +    S
Sbjct: 61  RAIRK-RLEECINSIDNALNEMSDTERKIVELRYLEGEKHTWKEIGNVIGYS 111


>gi|295109543|emb|CBL23496.1| RNA polymerase sigma factor, sigma-70 family [Ruminococcus obeum
           A2-162]
          Length = 784

 Score = 40.2 bits (93), Expect = 0.36,   Method: Composition-based stats.
 Identities = 16/107 (14%), Positives = 41/107 (38%), Gaps = 16/107 (14%)

Query: 189 LINSSDKNSSQWQDWLVY----DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
            I  S+ ++ +  D L +    +    +       + K  + ++   +  L   +R +  
Sbjct: 113 PILFSEMSNQEGMDGLSFVETRESTDIDVNPEMAADEKEVQRLVMEILDQLPEDQRMVVG 172

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV---QESIQKQV 288
               +E PV  ++++    VS       E     ++   ++ I++QV
Sbjct: 173 MFYYEEMPV--KDIAETLGVS-------ENTVKSRLVYARKKIKEQV 210


>gi|160882485|ref|ZP_02063488.1| hypothetical protein BACOVA_00436 [Bacteroides ovatus ATCC 8483]
 gi|156112066|gb|EDO13811.1| hypothetical protein BACOVA_00436 [Bacteroides ovatus ATCC 8483]
          Length = 195

 Score = 40.2 bits (93), Expect = 0.36,   Method: Composition-based stats.
 Identities = 13/89 (14%), Positives = 35/89 (39%), Gaps = 2/89 (2%)

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           S       +D D      +     +   + +   +  L  R++ I   R + E  ++ E 
Sbjct: 97  SLPDYDFAFDLDYTIDEQLAWMHDQGLSDEVHHILKGLTGRQKEIIYLRFIHE--MSFEE 154

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +S   +++ +  R +  R+ +K+++    
Sbjct: 155 ISEIMKINIQSARNLLFRSMEKIRKESSS 183


>gi|218233984|ref|YP_002370030.1| RNA polymerase factor sigma-70 [Bacillus cereus B4264]
 gi|218161941|gb|ACK61933.1| putative sigma factor [Bacillus cereus B4264]
          Length = 156

 Score = 40.2 bits (93), Expect = 0.36,   Method: Composition-based stats.
 Identities = 15/64 (23%), Positives = 35/64 (54%), Gaps = 2/64 (3%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    +   MSVL+ +E+ I   R       T+  ++ E E++  +VR +  +A +K++
Sbjct: 94  EDVEIRVKDFMSVLDEKEKYIIFERFFAG--KTMGEIALETEMTYYQVRWMYRQALEKMR 151

Query: 282 ESIQ 285
           +S++
Sbjct: 152 DSVK 155


>gi|81429116|ref|YP_396117.1| hypothetical protein LSA1509 [Lactobacillus sakei subsp. sakei 23K]
 gi|78610759|emb|CAI55810.1| Hypothetical protein LCA_1509 [Lactobacillus sakei subsp. sakei
           23K]
          Length = 182

 Score = 40.2 bits (93), Expect = 0.36,   Method: Composition-based stats.
 Identities = 12/66 (18%), Positives = 26/66 (39%), Gaps = 2/66 (3%)

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
            D L+   D       + +      ++  +   V +PRERR    R       +L+ ++ 
Sbjct: 99  DDALMDYLDQISDPHCDPDNAVIYNDLFEKLYQVCDPRERRFLVLRYFAN--ASLKEIAV 156

Query: 261 EFEVSR 266
           +  ++R
Sbjct: 157 DLNITR 162


>gi|332312682|gb|EGJ25777.1| hypothetical protein LMOSA_2190 [Listeria monocytogenes str. Scott
           A]
          Length = 134

 Score = 40.2 bits (93), Expect = 0.36,   Method: Composition-based stats.
 Identities = 21/103 (20%), Positives = 47/103 (45%), Gaps = 9/103 (8%)

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           +SL  ++ SS   S    D++        +   E E        L+R++  LN +E+++ 
Sbjct: 41  DSLEDIMRSSISESYLSLDFISESEIMNLENFAENE-------ALSRAIEQLNFKEKKLL 93

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             + +Q    +   ++  F++SR+ V     R  KK++  +++
Sbjct: 94  YEKYIQCKTDS--EIARIFDISRQGVSIFRKRLLKKLEVFLKR 134


>gi|262200030|ref|YP_003271239.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Haliangium
           ochraceum DSM 14365]
 gi|262083377|gb|ACY19346.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Haliangium
           ochraceum DSM 14365]
          Length = 214

 Score = 40.2 bits (93), Expect = 0.36,   Method: Composition-based stats.
 Identities = 39/273 (14%), Positives = 85/273 (31%), Gaps = 77/273 (28%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
           L ++ +  L  RY+ +G++ A   L+T H R +    + + G      +++ E  + +++
Sbjct: 13  LGEEADEDLMLRYQ-NGEVRAFEILLTRHRRPIFNFILRFVGARDRAEDLMQETFLRVVK 71

Query: 89  AVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQA 148
               +   +  +  T+     +    ++  R                    R+ K     
Sbjct: 72  KADTYK--KQAKFTTWLYTIARNLCVDHSRRQ-----------------KHRKAK----- 107

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDH 208
                                     S++  + G              +S     L+   
Sbjct: 108 --------------------------SLDQPMGG------------AGASDGDRTLLDTV 129

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV---- 264
            G E     K   +     + R++  L   +R +F  R  Q+ P    ++     V    
Sbjct: 130 AGDELASDRKAISRQLHMAMHRAIETLPDEQREVFLLREFQDLP--FRDIGEIVGVPENT 187

Query: 265 --SRERVRQIEARAFKKVQESIQKQVELSSSPP 295
             SR R       A  K++  + +  +L+ S P
Sbjct: 188 VKSRMR------YALDKLRGELAEYKDLAKSLP 214


>gi|256004384|ref|ZP_05429365.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           thermocellum DSM 2360]
 gi|281417609|ref|ZP_06248629.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           thermocellum JW20]
 gi|255991668|gb|EEU01769.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           thermocellum DSM 2360]
 gi|281409011|gb|EFB39269.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           thermocellum JW20]
          Length = 198

 Score = 40.2 bits (93), Expect = 0.36,   Method: Composition-based stats.
 Identities = 20/89 (22%), Positives = 34/89 (38%), Gaps = 7/89 (7%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           E  L KR ++ GD+ A  +L+    + V  IA+   G     SE+  E  +   +++K F
Sbjct: 5   EKELIKRAKK-GDVEAFEQLIEGCQKKVFNIALRMLGNYDDASELAQEVFLKAYKSIKNF 63

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWS 122
             +      +    WI        L    
Sbjct: 64  KGD------SLFNTWIYKVTTNACLDEIR 86


>gi|254723888|ref|ZP_05185674.1| RNA polymerase factor sigma-70 [Bacillus anthracis str. A1055]
          Length = 188

 Score = 40.2 bits (93), Expect = 0.37,   Method: Composition-based stats.
 Identities = 10/59 (16%), Positives = 25/59 (42%), Gaps = 2/59 (3%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           H   E+   ++      R  L + ++ L P ++++F  + L       E +  +  ++R
Sbjct: 104 HISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKT--EEIGDKLGLTR 160


>gi|237740232|ref|ZP_04570713.1| RNA polymerase sigma factor [Fusobacterium sp. 2_1_31]
 gi|229422249|gb|EEO37296.1| RNA polymerase sigma factor [Fusobacterium sp. 2_1_31]
          Length = 274

 Score = 40.2 bits (93), Expect = 0.37,   Method: Composition-based stats.
 Identities = 21/64 (32%), Positives = 37/64 (57%), Gaps = 2/64 (3%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V  +L+ V +IA+     G+   ++  EG IGL++A + F+ ++ F+L  Y  ++I  AM
Sbjct: 84  VEKNLKKVYQIALYMLRDGILYEDLTQEGVIGLIRAHELFEDDKDFKL--YKDYYIARAM 141

Query: 114 QEYI 117
             YI
Sbjct: 142 FNYI 145


>gi|228938917|ref|ZP_04101517.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus
           thuringiensis serovar berliner ATCC 10792]
 gi|228971799|ref|ZP_04132420.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus
           thuringiensis serovar thuringiensis str. T01001]
 gi|228787889|gb|EEM35847.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus
           thuringiensis serovar thuringiensis str. T01001]
 gi|228820766|gb|EEM66791.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus
           thuringiensis serovar berliner ATCC 10792]
          Length = 188

 Score = 40.2 bits (93), Expect = 0.37,   Method: Composition-based stats.
 Identities = 10/59 (16%), Positives = 25/59 (42%), Gaps = 2/59 (3%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           H   E+   ++      R  L + ++ L P ++++F  + L       E +  +  ++R
Sbjct: 104 HISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKT--EEIGDKLGLTR 160


>gi|294497918|ref|YP_003561618.1| sigma-70 family RNA polymerase sigma factor [Bacillus megaterium QM
           B1551]
 gi|294347855|gb|ADE68184.1| RNA polymerase sigma factor, sigma-70 family [Bacillus megaterium
           QM B1551]
          Length = 163

 Score = 40.2 bits (93), Expect = 0.37,   Method: Composition-based stats.
 Identities = 14/67 (20%), Positives = 30/67 (44%), Gaps = 2/67 (2%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
            ++ +S   L+V +   +  Y     E      IGL +A +KFD  +G   + Y+   ++
Sbjct: 7   DQIASSFHPLIVSMIKKFHIY-KDYDEYYQIALIGLWRAYQKFDESKGS-FSAYAYTTVR 64

Query: 111 AAMQEYI 117
             +  ++
Sbjct: 65  GTILSHL 71


>gi|302531504|ref|ZP_07283846.1| RNA polymerase ECF sigma factor [Streptomyces sp. AA4]
 gi|302440399|gb|EFL12215.1| RNA polymerase ECF sigma factor [Streptomyces sp. AA4]
          Length = 187

 Score = 40.2 bits (93), Expect = 0.37,   Method: Composition-based stats.
 Identities = 10/63 (15%), Positives = 29/63 (46%), Gaps = 2/63 (3%)

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              L +++  L PR+R +   R      ++   ++   ++S+  V+   ++A   ++  +
Sbjct: 121 HEPLWQALRDLPPRQRTVMVLRYY--EGLSEVEIAKALDISQGTVKSQASKAIASLRAKL 178

Query: 285 QKQ 287
           + Q
Sbjct: 179 RNQ 181


>gi|228984895|ref|ZP_04145065.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus
           thuringiensis serovar tochigiensis BGSC 4Y1]
 gi|229196018|ref|ZP_04322770.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           m1293]
 gi|300117271|ref|ZP_07055061.1| RNA polymerase factor sigma-70 [Bacillus cereus SJ1]
 gi|228587400|gb|EEK45466.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           m1293]
 gi|228774845|gb|EEM23241.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus
           thuringiensis serovar tochigiensis BGSC 4Y1]
 gi|298725106|gb|EFI65758.1| RNA polymerase factor sigma-70 [Bacillus cereus SJ1]
          Length = 188

 Score = 40.2 bits (93), Expect = 0.37,   Method: Composition-based stats.
 Identities = 10/59 (16%), Positives = 25/59 (42%), Gaps = 2/59 (3%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           H   E+   ++      R  L + ++ L P ++++F  + L       E +  +  ++R
Sbjct: 104 HISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKT--EEIGDKLGLTR 160


>gi|154685755|ref|YP_001420916.1| putative RNA polymerase sigma factor SigI [Bacillus
           amyloliquefaciens FZB42]
 gi|154351606|gb|ABS73685.1| SigI [Bacillus amyloliquefaciens FZB42]
          Length = 248

 Score = 40.2 bits (93), Expect = 0.37,   Method: Composition-based stats.
 Identities = 17/85 (20%), Positives = 33/85 (38%), Gaps = 7/85 (8%)

Query: 43  EHGDLSAAHRLVTSHLRL----VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           + GD    + L+  +       V  +   Y        +  S G I   +A++K+  E+G
Sbjct: 23  QKGDKDLQNDLIQQYKPFIAKTVSSVCKRYI---DEKDDEFSIGLIAFNEAIEKYSAEKG 79

Query: 99  FRLATYSMWWIKAAMQEYILRSWSL 123
             L  ++   IK  + +YI +    
Sbjct: 80  NSLLAFAELIIKRKVIDYIRKEART 104


>gi|322382451|ref|ZP_08056348.1| RNA polymerase sigma factor SigW-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
 gi|321153595|gb|EFX45981.1| RNA polymerase sigma factor SigW-like protein [Paenibacillus larvae
           subsp. larvae B-3650]
          Length = 192

 Score = 40.2 bits (93), Expect = 0.37,   Method: Composition-based stats.
 Identities = 17/80 (21%), Positives = 36/80 (45%), Gaps = 8/80 (10%)

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL+A +  S+ N   +   L    D  E  +I  E +++ R     +++ L  + + I  
Sbjct: 93  SLDAEMPDSEGND--FYAMLPSKEDTPEDQVILSETQEHIRC----AINTLPVKYKTIVV 146

Query: 245 ARRLQENPVTLENLSSEFEV 264
            R L +  ++L+ +S    +
Sbjct: 147 LRYLHD--MSLQEISDVLNI 164


>gi|239826355|ref|YP_002948979.1| RNA polymerase sigma factor SigI [Geobacillus sp. WCH70]
 gi|239806648|gb|ACS23713.1| RNA polymerase, sigma 28 subunit, SigI [Geobacillus sp. WCH70]
          Length = 245

 Score = 40.2 bits (93), Expect = 0.37,   Method: Composition-based stats.
 Identities = 22/145 (15%), Positives = 55/145 (37%), Gaps = 15/145 (10%)

Query: 43  EHGDLSAAHRLVTSHLRLVVK----IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           + G+    ++L+  +   + K    +   +   G    + +S G I   +A++K+ P +G
Sbjct: 22  QQGNKVLHNQLIQQYKPFIAKTVSNVCKRFIHEG---DDELSIGLIAFNEAIEKYAPHKG 78

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHL------QAITDN 152
               +++   IK  + +YI +      I    N+         L   L      + +   
Sbjct: 79  GSFISFAELLIKRRLIDYIRKEAKEKNIILHTNEDEENSAQTYLDTKLSMDEFYKQVEQE 138

Query: 153 NLKPEQV--VAIAKKLNVSESEVIS 175
           + + E +    + K+  +   ++I 
Sbjct: 139 HRREEIIHYQQVLKEFGIHFHDLIE 163


>gi|149278490|ref|ZP_01884627.1| RNA polymerase ECF-type sigma factor [Pedobacter sp. BAL39]
 gi|149230860|gb|EDM36242.1| RNA polymerase ECF-type sigma factor [Pedobacter sp. BAL39]
          Length = 198

 Score = 40.2 bits (93), Expect = 0.37,   Method: Composition-based stats.
 Identities = 14/79 (17%), Positives = 34/79 (43%), Gaps = 2/79 (2%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            +G E  +++         +L   +++L    R +F+           E ++ +  +S +
Sbjct: 104 QEGAEDTILKHIITAEVLAILDEEIAMLPDNYREVFKLIYFDLKKT--EEIADQLGLSEQ 161

Query: 268 RVRQIEARAFKKVQESIQK 286
            VR  +ARA   ++ ++ K
Sbjct: 162 TVRNYKARAVNLLKTAMLK 180


>gi|115375261|ref|ZP_01462526.1| RNA polymerase sigma-70 factor, ECF subfamily [Stigmatella
           aurantiaca DW4/3-1]
 gi|310820215|ref|YP_003952573.1| ECF subfamily RNA polymerase sigma-70 factor [Stigmatella
           aurantiaca DW4/3-1]
 gi|115367728|gb|EAU66698.1| RNA polymerase sigma-70 factor, ECF subfamily [Stigmatella
           aurantiaca DW4/3-1]
 gi|309393287|gb|ADO70746.1| RNA polymerase sigma-70 factor, ECF subfamily [Stigmatella
           aurantiaca DW4/3-1]
          Length = 212

 Score = 40.2 bits (93), Expect = 0.37,   Method: Composition-based stats.
 Identities = 22/122 (18%), Positives = 44/122 (36%), Gaps = 14/122 (11%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GD +A   LV  H  LV  +   +       +++V +  +   +A++      G   + 
Sbjct: 34  DGDEAAFATLVERHRGLVFSLVRRFAHRPEDAADLVQQAFL---RALE----SSGRVFSR 86

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
               W   +   +  RSW LV+I     +  +    R     L  + +  + P +    A
Sbjct: 87  ----WSWGSPTPF--RSW-LVRIALNLAKNHVRQGNRWRPAVLAEVEEAAVDPHESAQDA 139

Query: 164 KK 165
            +
Sbjct: 140 LE 141


>gi|325279219|ref|YP_004251761.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Odoribacter
           splanchnicus DSM 20712]
 gi|324311028|gb|ADY31581.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Odoribacter
           splanchnicus DSM 20712]
          Length = 186

 Score = 40.2 bits (93), Expect = 0.37,   Method: Composition-based stats.
 Identities = 15/79 (18%), Positives = 36/79 (45%), Gaps = 2/79 (2%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            + +++ +I  EE       L+  ++ L  R R++     ++       +++ +  +S  
Sbjct: 110 SEEEQENVIRAEEGPEPEQQLSALLNELPERSRQVMIMSHIENRKS--ADIARKLGISVR 167

Query: 268 RVRQIEARAFKKVQESIQK 286
            V  I  +A KK++  I+K
Sbjct: 168 TVETILYQAMKKLRGKIKK 186


>gi|307244526|ref|ZP_07526631.1| sigma-70 region 2 [Peptostreptococcus stomatis DSM 17678]
 gi|306492053|gb|EFM64101.1| sigma-70 region 2 [Peptostreptococcus stomatis DSM 17678]
          Length = 164

 Score = 40.2 bits (93), Expect = 0.37,   Method: Composition-based stats.
 Identities = 9/56 (16%), Positives = 23/56 (41%), Gaps = 2/56 (3%)

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
             +Q   +  E  +  + L  +++ L+ +ER I   +   +   T  ++     +S
Sbjct: 87  DTDQSPEKIVEMTDINSDLKLALAKLSDKERTIIAYKYGADMKNT--DIGDLLGIS 140


>gi|288870078|ref|ZP_06112832.2| sigma-70, region 4 subfamily [Clostridium hathewayi DSM 13479]
 gi|288868527|gb|EFD00826.1| sigma-70, region 4 subfamily [Clostridium hathewayi DSM 13479]
          Length = 243

 Score = 40.2 bits (93), Expect = 0.37,   Method: Composition-based stats.
 Identities = 21/115 (18%), Positives = 43/115 (37%), Gaps = 16/115 (13%)

Query: 175 SMNCRLAGDESLNALINSSDKNSSQWQDWLVYD---HDGQEQVLIEKEERKNRRNMLTRS 231
            M  R   ++SL+AL        S   D+             +LI+ E       ++  +
Sbjct: 129 EMAHRHEREKSLDALTQEEMDKLSVVDDYPSDSYVFSSYGYDLLIDNE-------LVAEA 181

Query: 232 MSVLNPRERRIFEARRLQENPVTLE--NLSSEFEVSRERVRQIEARAFKKVQESI 284
            + L  +E+ I     + +    L    + S   +SR  V++   R  K+++  +
Sbjct: 182 FASLPEQEQSILILHCVLD----LADGEIGSLMGMSRSAVQRHRTRTLKQLRMKL 232


>gi|269957259|ref|YP_003327048.1| ECF subfamily RNA polymerase sigma-24 subunit [Xylanimonas
           cellulosilytica DSM 15894]
 gi|269305940|gb|ACZ31490.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Xylanimonas
           cellulosilytica DSM 15894]
          Length = 181

 Score = 40.2 bits (93), Expect = 0.37,   Method: Composition-based stats.
 Identities = 28/150 (18%), Positives = 62/150 (41%), Gaps = 17/150 (11%)

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESL-----NALINSSDKNSSQWQDWLV 205
           D +L  E V     +  ++ ++V + +        L     N  +    + S        
Sbjct: 33  DEHLAEELVQEALTRTFLAWNKVRTRDPHAYARRVLVGRRTNDRVKRDREPSYALPALPD 92

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
              +G E+ +IE       R+ L R+++ L PR+RRI   R L    ++ + ++ +  VS
Sbjct: 93  DATEGGERAVIE-------RDRLVRALATLTPRQRRIVVLRHLVG--LSEQEVAHDLGVS 143

Query: 266 RERVRQIEARAFKKVQESIQKQVELSSSPP 295
              ++   +R   ++++ ++       +PP
Sbjct: 144 LGTIKSTASRGLAQLRQVLES---ADDAPP 170


>gi|187933964|ref|YP_001884816.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           B str. Eklund 17B]
 gi|187722117|gb|ACD23338.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           B str. Eklund 17B]
          Length = 195

 Score = 40.2 bits (93), Expect = 0.37,   Method: Composition-based stats.
 Identities = 16/85 (18%), Positives = 37/85 (43%), Gaps = 2/85 (2%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           +LAK+  + GD  +  +L+      +  ++     +G   +++ +E    L + +  +D 
Sbjct: 8   MLAKK-SKDGDNLSKEKLIEEFRPFIRNLSRKTFIHGYDKNDIENECYKNLFKCLNSYDL 66

Query: 96  ERGFRLATYSMWWIKAAMQEYILRS 120
            +  R   Y+   IK  +   I +S
Sbjct: 67  RK-HRFVAYATNGIKNNLNNLIKKS 90


>gi|332983102|ref|YP_004464543.1| ECF subfamily RNA polymerase sigma-24 subunit [Mahella
           australiensis 50-1 BON]
 gi|332700780|gb|AEE97721.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Mahella
           australiensis 50-1 BON]
          Length = 191

 Score = 40.2 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 32/252 (12%), Positives = 82/252 (32%), Gaps = 68/252 (26%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L +R +  GD  A   ++     L++          +   ++  E  I ++ ++K FD E
Sbjct: 8   LVERAK-AGDNDAIEEILKKVKPLILSSISKCHSIAMDDDDLYQEAAIEVIYSIKDFDDE 66

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
           R      +                           +KR+F+ L+ L    Q +       
Sbjct: 67  RNIPFLAFL--------------------------KKRIFYRLKNLTRCEQLLL------ 94

Query: 157 EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
                                       SL+  +   D         +          + 
Sbjct: 95  ----------------------------SLDQPVGDVDS-----ACTMADTIPDAGPSVE 121

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           +  +   +   L  +M+ L P++RR+ +   +Q   +++ +++ +  +  + V +++ RA
Sbjct: 122 DIVQVDQQYWHLRMAMAALTPKQRRVLKMHYMQG--MSMADIARKDGLHYQAVVKLKERA 179

Query: 277 FKKVQESIQKQV 288
              ++  ++  +
Sbjct: 180 LNNMRIFMENDI 191


>gi|42784415|ref|NP_981662.1| RNA polymerase factor sigma-70 [Bacillus cereus ATCC 10987]
 gi|42740347|gb|AAS44270.1| sigma factor, putative [Bacillus cereus ATCC 10987]
          Length = 156

 Score = 40.2 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 16/64 (25%), Positives = 34/64 (53%), Gaps = 2/64 (3%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++ +      MSVL+ +E+ I   R       T+  ++ E E+S  +VR +  +A +K++
Sbjct: 94  EDIKMKAKDFMSVLDEKEKYIIFERFFVG--KTMGEIALETEMSYYQVRWMYRQALEKMR 151

Query: 282 ESIQ 285
            S++
Sbjct: 152 NSLR 155


>gi|315127403|ref|YP_004069406.1| RNA polymerase sigma factor RpoE [Pseudoalteromonas sp. SM9913]
 gi|315015917|gb|ADT69255.1| RNA polymerase sigma factor RpoE [Pseudoalteromonas sp. SM9913]
          Length = 193

 Score = 40.2 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 19/93 (20%), Positives = 37/93 (39%), Gaps = 5/93 (5%)

Query: 32  QEEYVLA--KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           ++E  LA  KR ++ GD +A + LV  +   +  +   Y      I++V  E  I   +A
Sbjct: 3   EQELDLALVKRVQQ-GDKNAFNLLVKKYQNKIAGLISRYVSNQGDIADVAQEAFIKAYRA 61

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           +  F  +      T+         + Y++    
Sbjct: 62  LPNFRGD--SAFYTWLYRIAVNCAKNYLVAQGR 92


>gi|298385812|ref|ZP_06995369.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 1_1_14]
 gi|298261040|gb|EFI03907.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 1_1_14]
          Length = 180

 Score = 40.2 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 14/70 (20%), Positives = 38/70 (54%), Gaps = 2/70 (2%)

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
             +I KE++    N + + + +L  R+R     R +QE  ++ + ++S  +++ +  R +
Sbjct: 96  DQMIVKEDQIEIHNKVEKLLDMLTGRQREAIYLRFIQE--MSYDEIASLLDMTPQATRNL 153

Query: 273 EARAFKKVQE 282
             RA +++++
Sbjct: 154 VFRAIERIRQ 163


>gi|320010137|gb|ADW04987.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 312

 Score = 40.2 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 22/105 (20%), Positives = 38/105 (36%), Gaps = 6/105 (5%)

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             +  +   R+   ++L+ L     +  +    WL         V  + E  ++    + 
Sbjct: 69  VRDRRAYLVRITTRQALSRLRTLGRRKETYVGTWLPEPLLTAPDVAEDVELAESVSMAMM 128

Query: 230 RSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQI 272
             M  L P ER +F  R     +     E +S     SR+ VRQI
Sbjct: 129 LVMETLAPNERAVFVLREVFGLD----YEEISEAVGRSRDAVRQI 169


>gi|229155382|ref|ZP_04283492.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus ATCC
           4342]
 gi|228628097|gb|EEK84814.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus ATCC
           4342]
          Length = 188

 Score = 40.2 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 10/59 (16%), Positives = 25/59 (42%), Gaps = 2/59 (3%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           H   E+   ++      R  L + ++ L P ++++F  + L       E +  +  ++R
Sbjct: 104 HISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKA--EEIGDKLGLTR 160


>gi|167767521|ref|ZP_02439574.1| hypothetical protein CLOSS21_02040 [Clostridium sp. SS2/1]
 gi|167710813|gb|EDS21392.1| hypothetical protein CLOSS21_02040 [Clostridium sp. SS2/1]
          Length = 179

 Score = 40.2 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 10/68 (14%), Positives = 28/68 (41%), Gaps = 2/68 (2%)

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           + +   + L  ++  L+ R R         E   T   ++    +SR  V Q    + + 
Sbjct: 114 DIRICDDELAEALKHLSERNRENLLMYYFLEMSDT--EIAKRQNISRSGVFQNRHNSLEL 171

Query: 280 VQESIQKQ 287
           +++ ++++
Sbjct: 172 MKKILKEK 179


>gi|300855629|ref|YP_003780613.1| hypothetical protein CLJU_c24530 [Clostridium ljungdahlii DSM
           13528]
 gi|300435744|gb|ADK15511.1| hypothetical protein with a sigma 70 domain [Clostridium
           ljungdahlii DSM 13528]
          Length = 228

 Score = 40.2 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 19/133 (14%), Positives = 49/133 (36%), Gaps = 10/133 (7%)

Query: 50  AHRLVTSHLRLVVK----IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
               ++ +   + K    I+  Y  +     + +S   I   +A   +   +G     Y+
Sbjct: 12  RDEFISENKNFIYKCTYTISKRYLQWEND--DELSIALIAFNKACDNYTETKGN-FYAYA 68

Query: 106 MWWIKAAMQEYIL--RSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIA 163
              I+ A+ +Y    ++  L+    +        N   +    Q   +N  + ++++ + 
Sbjct: 69  KIIIRNALIDYFRKNKNSPLLTFDDSDCSMEKLNNANSITS-FQLELENKNRADEIIELN 127

Query: 164 KKLNVSESEVISM 176
           KKL   + +  S+
Sbjct: 128 KKLMEYKIDFSSL 140


>gi|228961509|ref|ZP_04123119.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
 gi|228798127|gb|EEM45130.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           pakistani str. T13001]
          Length = 156

 Score = 40.2 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 15/64 (23%), Positives = 35/64 (54%), Gaps = 2/64 (3%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    +   MSVL+ +E+ I   R       T+  ++ E E++  +VR +  +A +K++
Sbjct: 94  EDVEIRVKDFMSVLDEKEKYIIFERFFVG--KTMGEIALETEMTYYQVRWMYRQALEKMR 151

Query: 282 ESIQ 285
           +S++
Sbjct: 152 DSVK 155


>gi|53715075|ref|YP_101067.1| RNA polymerase ECF-type sigma factor [Bacteroides fragilis YCH46]
 gi|52217940|dbj|BAD50533.1| RNA polymerase ECF-type sigma factor [Bacteroides fragilis YCH46]
          Length = 192

 Score = 40.2 bits (93), Expect = 0.38,   Method: Composition-based stats.
 Identities = 11/39 (28%), Positives = 24/39 (61%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           E+ LIE E+  ++++++   ++ L+PR+R I   R  + 
Sbjct: 113 EEKLIETEDETSQKHIVAHLLNTLSPRQREIIYYRFFEG 151


>gi|317052451|ref|YP_004113567.1| sigma-70 family RNA polymerase sigma factor [Desulfurispirillum
           indicum S5]
 gi|316947535|gb|ADU67011.1| RNA polymerase sigma factor, sigma-70 family [Desulfurispirillum
           indicum S5]
          Length = 171

 Score = 40.2 bits (93), Expect = 0.39,   Method: Composition-based stats.
 Identities = 13/76 (17%), Positives = 32/76 (42%), Gaps = 6/76 (7%)

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           +  S +  +  +      E   + +EE      +L  +++ L PR R +F  +RL    +
Sbjct: 77  EDISPEELESAMGRAPSAEDTALSREELA----ILMDAIAELPPRAREVFRLKRL--EGL 130

Query: 254 TLENLSSEFEVSRERV 269
           +   +  +  ++R  +
Sbjct: 131 SYSEIGQQLGITRSTI 146


>gi|116329745|ref|YP_799464.1| RNA polymerase sigma subunit [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116332627|ref|YP_802344.1| RNA polymerase sigma subunit [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
 gi|116122638|gb|ABJ80531.1| RNA polymerase sigma subunit [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116127494|gb|ABJ77586.1| RNA polymerase sigma subunit [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
          Length = 173

 Score = 40.2 bits (93), Expect = 0.39,   Method: Composition-based stats.
 Identities = 28/123 (22%), Positives = 53/123 (43%), Gaps = 8/123 (6%)

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVL--IEKEERKNR 224
           NV   + I +   +A + S+N     S + S+  ++      D QEQ L  + K E K+ 
Sbjct: 53  NVDREQAIRLLYTIARNRSIN----YSQQFSTVKENGNSEMEDFQEQKLSFVRKAELKDL 108

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              L   +  L   E+     R +++   +L  ++    +S   V ++  +A  KV E  
Sbjct: 109 EERLLICLDELEENEKYALILRFMED--YSLATIAEIMNISVSTVSRLIVKATAKVTEIA 166

Query: 285 QKQ 287
           +K+
Sbjct: 167 EKK 169


>gi|229011094|ref|ZP_04168288.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus mycoides
           DSM 2048]
 gi|229166663|ref|ZP_04294414.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           AH621]
 gi|228616804|gb|EEK73878.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           AH621]
 gi|228750266|gb|EEM00098.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus mycoides
           DSM 2048]
          Length = 188

 Score = 40.2 bits (93), Expect = 0.39,   Method: Composition-based stats.
 Identities = 10/59 (16%), Positives = 25/59 (42%), Gaps = 2/59 (3%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           H   E+   ++      R  L + ++ L P ++++F  + L       E +  +  ++R
Sbjct: 104 HISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKT--EEIGDKLGLTR 160


>gi|152982707|ref|YP_001354060.1| ECF subfamily RNA polymerase sigma factor [Janthinobacterium sp.
           Marseille]
 gi|151282784|gb|ABR91194.1| RNA polymerase sigma-70 factor, ECF subfamily [Janthinobacterium
           sp. Marseille]
          Length = 176

 Score = 40.2 bits (93), Expect = 0.39,   Method: Composition-based stats.
 Identities = 23/134 (17%), Positives = 48/134 (35%), Gaps = 2/134 (1%)

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
           ++RL  +L       +A+ +  L+ E      K+        +S   R+A + +L+ +  
Sbjct: 21  KRRLTVHLGSADLAGEALQETWLRLEGSKDSGKEGAEPVQYPLSYLMRMATNAALDRMRA 80

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
                S    + ++ D            E ++    L   +  +  R R I    R+ E 
Sbjct: 81  EKRFLSGDEVEQVLADLSDPAAGPARTFEARSEAERLAAVIQQMPSRRRNILILIRVDEM 140

Query: 252 PVTLENLSSEFEVS 265
           P   + ++    VS
Sbjct: 141 PR--QEVADRLGVS 152


>gi|30019842|ref|NP_831473.1| RNA polymerase factor sigma-70 [Bacillus cereus ATCC 14579]
 gi|228952185|ref|ZP_04114276.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus
           thuringiensis serovar kurstaki str. T03a001]
 gi|228958082|ref|ZP_04119817.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus
           thuringiensis serovar pakistani str. T13001]
 gi|228978407|ref|ZP_04138784.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus
           thuringiensis Bt407]
 gi|229043558|ref|ZP_04191267.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           AH676]
 gi|229069352|ref|ZP_04202642.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           F65185]
 gi|229078984|ref|ZP_04211536.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           Rock4-2]
 gi|229109258|ref|ZP_04238857.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           Rock1-15]
 gi|229127128|ref|ZP_04256125.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           BDRD-Cer4]
 gi|29895387|gb|AAP08674.1| RNA polymerase ECF-type sigma factor [Bacillus cereus ATCC 14579]
 gi|228656244|gb|EEL12085.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           BDRD-Cer4]
 gi|228674268|gb|EEL29513.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           Rock1-15]
 gi|228704398|gb|EEL56832.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           Rock4-2]
 gi|228713839|gb|EEL65724.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           F65185]
 gi|228725780|gb|EEL77028.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           AH676]
 gi|228781424|gb|EEM29625.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus
           thuringiensis Bt407]
 gi|228801599|gb|EEM48481.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus
           thuringiensis serovar pakistani str. T13001]
 gi|228807456|gb|EEM53984.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus
           thuringiensis serovar kurstaki str. T03a001]
 gi|326939418|gb|AEA15314.1| RNA polymerase factor sigma-70 [Bacillus thuringiensis serovar
           chinensis CT-43]
          Length = 188

 Score = 40.2 bits (93), Expect = 0.39,   Method: Composition-based stats.
 Identities = 10/59 (16%), Positives = 25/59 (42%), Gaps = 2/59 (3%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           H   E+   ++      R  L + ++ L P ++++F  + L       E +  +  ++R
Sbjct: 104 HISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKT--EEIGDKLGLTR 160


>gi|303242095|ref|ZP_07328586.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302590389|gb|EFL60146.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 210

 Score = 40.2 bits (93), Expect = 0.40,   Method: Composition-based stats.
 Identities = 20/88 (22%), Positives = 38/88 (43%), Gaps = 3/88 (3%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           ++E  L ++  + GD+ A  +L+ S  + V  IA    G     +E+  E  I   +++K
Sbjct: 3   EKERNLVEK-SKSGDVEAFEQLIESCQKKVFNIAYRMIGNYDDANELAQEVFIKAFRSIK 61

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILR 119
           KF  +     +T+          + I R
Sbjct: 62  KFKGD--SLFSTWIYKVTANVCLDEIRR 87


>gi|228914379|ref|ZP_04077994.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus
           thuringiensis serovar pulsiensis BGSC 4CC1]
 gi|228845373|gb|EEM90409.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus
           thuringiensis serovar pulsiensis BGSC 4CC1]
          Length = 188

 Score = 40.2 bits (93), Expect = 0.40,   Method: Composition-based stats.
 Identities = 10/59 (16%), Positives = 25/59 (42%), Gaps = 2/59 (3%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           H   E+   ++      R  L + ++ L P ++++F  + L       E +  +  ++R
Sbjct: 104 HISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKA--EEIGDKLGLTR 160


>gi|229164189|ref|ZP_04292124.1| RNA polymerase sigma factor [Bacillus cereus R309803]
 gi|228619306|gb|EEK76197.1| RNA polymerase sigma factor [Bacillus cereus R309803]
          Length = 156

 Score = 40.2 bits (93), Expect = 0.40,   Method: Composition-based stats.
 Identities = 17/64 (26%), Positives = 34/64 (53%), Gaps = 2/64 (3%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++        MSVLN +E+ I   R       T+  ++ E E++  +VR I  +A +K++
Sbjct: 94  EDIEMRAKDLMSVLNEKEKYIIFERFFVG--KTMGKIALETEMTYYQVRWIYRQALEKMR 151

Query: 282 ESIQ 285
           +S++
Sbjct: 152 DSLR 155


>gi|226305419|ref|YP_002765377.1| RNA polymerase ECF-type sigma factor SigD [Rhodococcus erythropolis
           PR4]
 gi|229489598|ref|ZP_04383461.1| RNA polymerase sigma factor SigD [Rhodococcus erythropolis SK121]
 gi|226184534|dbj|BAH32638.1| putative RNA polymerase ECF-type sigma factor SigD [Rhodococcus
           erythropolis PR4]
 gi|229323695|gb|EEN89453.1| RNA polymerase sigma factor SigD [Rhodococcus erythropolis SK121]
          Length = 192

 Score = 40.2 bits (93), Expect = 0.40,   Method: Composition-based stats.
 Identities = 21/95 (22%), Positives = 39/95 (41%), Gaps = 7/95 (7%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
           +  S+  D +  D DG EQ  ++ E  +    +L      L  + R I   R +    ++
Sbjct: 102 EPVSEVPDVIALD-DGPEQRALDSESSRQMHELL----GTLPEKHREILILRLVVG--MS 154

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
            E  +     +   VR  + RA  K+++ + K  E
Sbjct: 155 AEETAVAVGSTAGAVRVAQHRAIAKLKKEVTKAGE 189


>gi|297194302|ref|ZP_06911700.1| sigma-70 [Streptomyces pristinaespiralis ATCC 25486]
 gi|197720596|gb|EDY64504.1| sigma-70 [Streptomyces pristinaespiralis ATCC 25486]
          Length = 172

 Score = 40.2 bits (93), Expect = 0.40,   Method: Composition-based stats.
 Identities = 15/73 (20%), Positives = 32/73 (43%), Gaps = 2/73 (2%)

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
            E    ++ +   +R  +  ++  L P++R +   R L++   +   ++         VR
Sbjct: 88  PETAAPDRTDTVTQRGAVMDALGQLPPKQRAVVVLRYLEDRSES--EVARLLGTGIGTVR 145

Query: 271 QIEARAFKKVQES 283
              ARA KK++E 
Sbjct: 146 SHTARALKKLREH 158


>gi|153811849|ref|ZP_01964517.1| hypothetical protein RUMOBE_02242 [Ruminococcus obeum ATCC 29174]
 gi|149831983|gb|EDM87068.1| hypothetical protein RUMOBE_02242 [Ruminococcus obeum ATCC 29174]
          Length = 216

 Score = 40.2 bits (93), Expect = 0.40,   Method: Composition-based stats.
 Identities = 13/63 (20%), Positives = 31/63 (49%), Gaps = 2/63 (3%)

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           ER      +   M++L  R+R++ +    Q+   T + +S E  ++   V +  ++A +K
Sbjct: 138 ERIIAEETVRELMNLLTERQRQMIQRIYFQQQ--TQKEVSHELGITVPAVSKCISQAMQK 195

Query: 280 VQE 282
           ++ 
Sbjct: 196 MRN 198


>gi|332663539|ref|YP_004446327.1| ECF subfamily RNA polymerase sigma-24 subunit [Haliscomenobacter
           hydrossis DSM 1100]
 gi|332332353|gb|AEE49454.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Haliscomenobacter
           hydrossis DSM 1100]
          Length = 192

 Score = 40.2 bits (93), Expect = 0.40,   Method: Composition-based stats.
 Identities = 17/88 (19%), Positives = 40/88 (45%), Gaps = 2/88 (2%)

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           S + ++       G +Q+LI+ E    R   L  +M+ L+ R+R +   +   +   T  
Sbjct: 92  SEEPEERHFQADFGIDQLLIQGELDAERDAKLKVAMAALSERQREVLYLKYFADMDYT-- 149

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESI 284
            +    E++ +  R +  RA + +++ +
Sbjct: 150 QIGEIMELNYQSARNLSHRALEALRQIL 177


>gi|325675534|ref|ZP_08155218.1| RNA polymerase sigma-70 factor [Rhodococcus equi ATCC 33707]
 gi|325553505|gb|EGD23183.1| RNA polymerase sigma-70 factor [Rhodococcus equi ATCC 33707]
          Length = 192

 Score = 40.2 bits (93), Expect = 0.40,   Method: Composition-based stats.
 Identities = 15/85 (17%), Positives = 31/85 (36%), Gaps = 2/85 (2%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           V D    +    E+         +   +  L  + R I   R +    ++ E  ++    
Sbjct: 107 VPDVVSADDSPEERALNSETSRQVNALLQTLPEKHREILVLRLVVG--LSAEETAAAVGS 164

Query: 265 SRERVRQIEARAFKKVQESIQKQVE 289
           +   VR  + RA  K+++ + K  E
Sbjct: 165 TAGAVRVAQHRALAKLKKEVTKAGE 189


>gi|255526342|ref|ZP_05393257.1| transcriptional regulator, LuxR family [Clostridium carboxidivorans
           P7]
 gi|296187013|ref|ZP_06855413.1| RNA polymerase sigma-70 factor, TIGR02952 family [Clostridium
           carboxidivorans P7]
 gi|255509990|gb|EET86315.1| transcriptional regulator, LuxR family [Clostridium carboxidivorans
           P7]
 gi|296048451|gb|EFG87885.1| RNA polymerase sigma-70 factor, TIGR02952 family [Clostridium
           carboxidivorans P7]
          Length = 181

 Score = 40.2 bits (93), Expect = 0.40,   Method: Composition-based stats.
 Identities = 16/79 (20%), Positives = 35/79 (44%), Gaps = 2/79 (2%)

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
            +E    +        N L++++ VLN +ER I   +         + ++   E++   V
Sbjct: 105 SRENNPEDIVLIAEANNKLSKALKVLNSKERNIVALKFGGNLKN--KEIAEILELTESNV 162

Query: 270 RQIEARAFKKVQESIQKQV 288
             I  R  KK++  ++++V
Sbjct: 163 GVILYRVMKKLKVEMEREV 181


>gi|331271156|ref|YP_004385865.1| RNA polymerase sigma-70 factor family [Clostridium botulinum
          BKT015925]
 gi|329127651|gb|AEB77593.1| RNA polymerase sigma-70 factor family [Clostridium botulinum
          BKT015925]
          Length = 177

 Score = 40.2 bits (93), Expect = 0.41,   Method: Composition-based stats.
 Identities = 12/55 (21%), Positives = 28/55 (50%)

Query: 40 RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
          R  + GD+ + + ++  +   V K A GY   G    ++V  G + +++A++ + 
Sbjct: 6  RKAKGGDVESINSIINKYKNFVFKKAAGYNIPGYDFEDLVQHGYLSIIKAIRMYK 60



 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 14/85 (16%), Positives = 37/85 (43%), Gaps = 2/85 (2%)

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
             D ++   +  E  + ++    ++   L  +M  L P ER I     +     + +N++
Sbjct: 93  PDDNILNKDEEYEFTVEDEVIAYDQVKKLYEAMDKLQPLEREILRRYYINHE--SFKNIA 150

Query: 260 SEFEVSRERVRQIEARAFKKVQESI 284
            +  +  +R   +  RA +K+++ +
Sbjct: 151 KDKNLLYDRTTYLRRRAIRKLKDIL 175


>gi|251778080|ref|ZP_04821000.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           botulinum E1 str. 'BoNT E Beluga']
 gi|243082395|gb|EES48285.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           botulinum E1 str. 'BoNT E Beluga']
          Length = 94

 Score = 40.2 bits (93), Expect = 0.41,   Method: Composition-based stats.
 Identities = 14/91 (15%), Positives = 36/91 (39%), Gaps = 7/91 (7%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           +LAK+  + GD  +  +L+      +  ++     +G    ++ +E    L + +  ++ 
Sbjct: 8   MLAKK-SKDGDNLSKEKLIQEFKPFIKNLSRKTFIHGYDKDDIENECYKNLFKCLNSYNL 66

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           E+  R   Y+   I     ++  R     + 
Sbjct: 67  EK-HRFVAYATNGI-----KFNRRGTRTYRF 91


>gi|52143656|ref|YP_083172.1| RNA polymerase factor sigma-70 [Bacillus cereus E33L]
 gi|51977125|gb|AAU18675.1| RNA polymerase, ECF-type sigma factor [Bacillus cereus E33L]
          Length = 188

 Score = 40.2 bits (93), Expect = 0.41,   Method: Composition-based stats.
 Identities = 10/59 (16%), Positives = 25/59 (42%), Gaps = 2/59 (3%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           H   E+   ++      R  L + ++ L P ++++F  + L       E +  +  ++R
Sbjct: 104 HISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKT--EEIGDKLGLTR 160


>gi|325290113|ref|YP_004266294.1| RNA polymerase, sigma-24 subunit, RpoE [Syntrophobotulus glycolicus
           DSM 8271]
 gi|324965514|gb|ADY56293.1| RNA polymerase, sigma-24 subunit, RpoE [Syntrophobotulus glycolicus
           DSM 8271]
          Length = 181

 Score = 40.2 bits (93), Expect = 0.42,   Method: Composition-based stats.
 Identities = 14/78 (17%), Positives = 36/78 (46%), Gaps = 2/78 (2%)

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
            +E+   +   +    + L RS+++L+ RER +   +         + +S   +++    
Sbjct: 105 SREENPEDLVVKAETNDDLARSLNILSSRERHLIALKFGGNLKN--KEISEILDITESNT 162

Query: 270 RQIEARAFKKVQESIQKQ 287
             I  RA +K++  ++K+
Sbjct: 163 AVILYRAIRKLKNEMEKE 180


>gi|298375105|ref|ZP_06985062.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 3_1_19]
 gi|298267605|gb|EFI09261.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 3_1_19]
          Length = 204

 Score = 40.2 bits (93), Expect = 0.42,   Method: Composition-based stats.
 Identities = 14/95 (14%), Positives = 38/95 (40%), Gaps = 2/95 (2%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
               + +D +            +     +   +L +++  L+P+++R+F+  R       
Sbjct: 105 DRELELRDKIRSASLDSTNETEDSVLDTDLNALLDKALETLSPQQKRVFDMSRKDMKSH- 163

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
            + ++    +S   V+Q  + A K ++  + K  E
Sbjct: 164 -KEIADSLGISVYTVQQHISTALKVIRAFLAKYAE 197


>gi|284031535|ref|YP_003381466.1| ECF subfamily RNA polymerase sigma-24 subunit [Kribbella flavida
           DSM 17836]
 gi|283810828|gb|ADB32667.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Kribbella flavida
           DSM 17836]
          Length = 297

 Score = 40.2 bits (93), Expect = 0.42,   Method: Composition-based stats.
 Identities = 23/125 (18%), Positives = 47/125 (37%), Gaps = 6/125 (4%)

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             +  +   R+   ++LN L     +  +    WL         V  + E  ++    L 
Sbjct: 52  VRDERAYLVRITTRQALNRLRTLKRRKEAYVGPWLPEPLLTSPDVAEDVELAESMSMALL 111

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
             +  L P ER +F  R   +  V+   +++    +   VRQI  RA    +  ++ +  
Sbjct: 112 LVLETLTPTERAVFVLREAFD--VSYAEIAAAVGKTPAAVRQIAHRA----RRHVEARRP 165

Query: 290 LSSSP 294
            ++ P
Sbjct: 166 RAAVP 170


>gi|183179718|ref|ZP_02957929.1| RNA polymerase sigma-H factor [Vibrio cholerae MZO-3]
 gi|183013129|gb|EDT88429.1| RNA polymerase sigma-H factor [Vibrio cholerae MZO-3]
          Length = 123

 Score = 40.2 bits (93), Expect = 0.42,   Method: Composition-based stats.
 Identities = 18/88 (20%), Positives = 33/88 (37%), Gaps = 3/88 (3%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
            VL +R + +GD  A + LV  +   V  +   Y      +++V  E  I   +A+  F 
Sbjct: 8   QVLIERVQ-NGDKQAFNLLVLRYQNKVCNLISRYVSNSGDVADVAQEAFIKAYRAIPTFR 66

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWS 122
            E      T+         + +I+    
Sbjct: 67  GE--SAFYTWLYRIAVNTAKNHIVAQSR 92


>gi|182415970|ref|YP_001821036.1| ECF subfamily RNA polymerase sigma-24 factor [Opitutus terrae
           PB90-1]
 gi|177843184|gb|ACB77436.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Opitutus terrae
           PB90-1]
          Length = 472

 Score = 40.2 bits (93), Expect = 0.42,   Method: Composition-based stats.
 Identities = 13/72 (18%), Positives = 29/72 (40%), Gaps = 10/72 (13%)

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS----RERVRQI 272
           E+ E +  + +L  ++  LN  +R     R       +   L +   ++    R RV   
Sbjct: 109 ERVEWERLQPLLDEALDDLNETDRTAVLLRFF--EGRSFGELGASLGLTENAARMRV--- 163

Query: 273 EARAFKKVQESI 284
             R+ +K++  +
Sbjct: 164 -ERSLEKLRRIL 174


>gi|172055114|ref|YP_001806441.1| putative group 3/4 sigma-70 RNA polymerase sigma factor [Cyanothece
           sp. ATCC 51142]
 gi|171701395|gb|ACB54375.1| putative group 3/4 sigma-70 RNA polymerase sigma factor [Cyanothece
           sp. ATCC 51142]
          Length = 216

 Score = 40.2 bits (93), Expect = 0.42,   Method: Composition-based stats.
 Identities = 23/138 (16%), Positives = 57/138 (41%), Gaps = 14/138 (10%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPIS--EVVSEGNIGLMQAVKKFDPERGFRLATY 104
             A   L+  +  L+  +   Y          ++  E  +   +A+KKFD  R  +L+T+
Sbjct: 49  EKAFRELLKKYYGLIKNLVNLYSQRHKARHQKDLKQEAIVAFYEAIKKFDKSRKVKLSTW 108

Query: 105 SMWWIK---AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
             + IK     + + I +    + +    NQ+ +          L+  +   ++ +QV+ 
Sbjct: 109 VFYRIKTKLKTISQQIKKQEKTIHV-VRINQEPI--------SRLEEESSRRIQLKQVLV 159

Query: 162 IAKKLNVSESEVISMNCR 179
           +  +L   + +V+++  +
Sbjct: 160 LLCQLTKKQQKVVNLQLK 177


>gi|86741569|ref|YP_481969.1| XRE family transcriptional regulator [Frankia sp. CcI3]
 gi|86568431|gb|ABD12240.1| transcriptional regulator, XRE family [Frankia sp. CcI3]
          Length = 109

 Score = 40.2 bits (93), Expect = 0.42,   Method: Composition-based stats.
 Identities = 13/56 (23%), Positives = 23/56 (41%), Gaps = 7/56 (12%)

Query: 226 NMLTRSMSVLNP---RERRIFEARRLQEN----PVTLENLSSEFEVSRERVRQIEA 274
           +++  +   L     R +   +  RL E      +T   ++    VS+ RV QIE 
Sbjct: 13  DLIADAEETLTEARRRNQAYIDGHRLAERRRLLGLTQTEVAEHMGVSKSRVSQIER 68


>gi|56962783|ref|YP_174509.1| hypothetical protein ABC1009 [Bacillus clausii KSM-K16]
 gi|56909021|dbj|BAD63548.1| conserved hypothetical protein [Bacillus clausii KSM-K16]
          Length = 201

 Score = 40.2 bits (93), Expect = 0.42,   Method: Composition-based stats.
 Identities = 16/95 (16%), Positives = 39/95 (41%), Gaps = 6/95 (6%)

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR----NMLTRSMSVLNPRERRIFEARRLQ 249
           D  ++  Q +   D      VL +K+     +      L  +++ L  R+ ++ E   + 
Sbjct: 104 DNVTNTLQSYFAVDFSTDPAVLFDKKCESICQCVGNKQLKNALNSLTKRQLQVLELFYIY 163

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +     ++ +    VS + +  I  RA +K+ + +
Sbjct: 164 DMDN--QSAAKYLNVSNQNISTIHNRALEKLYKKM 196


>gi|331270824|ref|YP_004397261.1| RNA polymerase sigma factor [Clostridium botulinum BKT015925]
 gi|329127542|gb|AEB77485.1| RNA polymerase sigma factor [Clostridium botulinum BKT015925]
          Length = 181

 Score = 40.2 bits (93), Expect = 0.42,   Method: Composition-based stats.
 Identities = 12/55 (21%), Positives = 28/55 (50%)

Query: 40 RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
          R  + GD+ + + ++  +   V K A GY   G    ++V  G + +++A++ + 
Sbjct: 6  RKAKGGDVKSINSIINKYKNFVFKKAAGYNIPGYDFEDLVQHGYLSIIKAIRMYK 60


>gi|300779762|ref|ZP_07089618.1| RNA polymerase sigma-70 factor [Corynebacterium genitalium ATCC
           33030]
 gi|300533872|gb|EFK54931.1| RNA polymerase sigma-70 factor [Corynebacterium genitalium ATCC
           33030]
          Length = 231

 Score = 40.2 bits (93), Expect = 0.42,   Method: Composition-based stats.
 Identities = 13/83 (15%), Positives = 31/83 (37%), Gaps = 2/83 (2%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           V D +       +   +    N     +  L+ + R I   R      ++ E  +     
Sbjct: 148 VPDQEFSGLTPEDAAMQMEGSNAARELLDQLSEKAREIIVLRVFVG--LSAEETAEITGS 205

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +   VR  + RA   ++++++K+
Sbjct: 206 TAGAVRVAQHRALATLRKALEKK 228


>gi|258655169|ref|YP_003204325.1| ECF subfamily RNA polymerase sigma-24 subunit [Nakamurella
           multipartita DSM 44233]
 gi|258558394|gb|ACV81336.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Nakamurella
           multipartita DSM 44233]
          Length = 311

 Score = 40.2 bits (93), Expect = 0.42,   Method: Composition-based stats.
 Identities = 24/131 (18%), Positives = 48/131 (36%), Gaps = 14/131 (10%)

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
            ++ L+ ++ VA A ++        +   R+A  ++LN    ++ +       WL     
Sbjct: 48  QESYLRWQEAVAGATEI----RHPRAYLARIATRQALNRNRGNARRREEYVGPWLPEPLV 103

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR----RLQENPVTLENLSSEFEVS 265
               V  +    ++    +   +  L P ER +F  R       +       +++    S
Sbjct: 104 TVPDVAEDAVLAESVSMAMMVVLDSLTPDERAVFVLREVFAFGHD------EIAAAIGKS 157

Query: 266 RERVRQIEARA 276
              VRQI  RA
Sbjct: 158 PVAVRQIAHRA 168


>gi|163802385|ref|ZP_02196279.1| RNA polymerase sigma-70 factor [Vibrio sp. AND4]
 gi|159173914|gb|EDP58728.1| RNA polymerase sigma-70 factor [Vibrio sp. AND4]
          Length = 193

 Score = 40.2 bits (93), Expect = 0.42,   Method: Composition-based stats.
 Identities = 23/107 (21%), Positives = 49/107 (45%), Gaps = 22/107 (20%)

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           +  I+S D   S +    + DH   EQ ++        ++ + + + +L   +R + +A 
Sbjct: 101 DLHIHSDDIWPSDYYPPDLVDHYSPEQDML--------KDQVVKFLDILPKNQREVLQAV 152

Query: 247 RLQENPVTLENLSSEFEV------SRERVRQIEARAFKKVQESIQKQ 287
            LQE P   + ++  F++      SR R+      A +K++ S+Q +
Sbjct: 153 YLQELPH--QQVAELFDIPLGTVKSRLRL------AVEKLRHSMQTE 191


>gi|302876122|ref|YP_003844755.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           cellulovorans 743B]
 gi|307686847|ref|ZP_07629293.1| RNA polymerase, sigma-24 subunit, ECF subfamily protein
           [Clostridium cellulovorans 743B]
 gi|302578979|gb|ADL52991.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           cellulovorans 743B]
          Length = 186

 Score = 40.2 bits (93), Expect = 0.42,   Method: Composition-based stats.
 Identities = 20/108 (18%), Positives = 39/108 (36%), Gaps = 2/108 (1%)

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D N               E+  +E   R    + + +S+ +L   ER I   R       
Sbjct: 72  DDNEKYKISLDACLDFISEEDFVEDIMRNEDTSEVLKSLEILKEIERIIISQRYYGN--Y 129

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQKPR 301
           T   ++ +  +    V     RA +K++ +  K  + S +   L++ R
Sbjct: 130 TFAEIAEKNGIKLNTVLSHHRRALQKLRPTFAKFFDFSENQTTLKQER 177


>gi|229029489|ref|ZP_04185571.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           AH1271]
 gi|228731842|gb|EEL82742.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           AH1271]
          Length = 188

 Score = 40.2 bits (93), Expect = 0.42,   Method: Composition-based stats.
 Identities = 10/59 (16%), Positives = 25/59 (42%), Gaps = 2/59 (3%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           H   E+   ++      R  L + ++ L P ++++F  + L       E +  +  ++R
Sbjct: 104 HISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKT--EEIGDKLGLTR 160


>gi|57237278|ref|YP_178291.1| hypothetical protein CJE0268 [Campylobacter jejuni RM1221]
 gi|57166082|gb|AAW34861.1| conserved domain protein [Campylobacter jejuni RM1221]
          Length = 67

 Score = 40.2 bits (93), Expect = 0.42,   Method: Composition-based stats.
 Identities = 11/29 (37%), Positives = 17/29 (58%)

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +T E ++ E  +S  RV QI   A KK++
Sbjct: 1   MTFEEIAKELGISLTRVHQIYKHAIKKLR 29


>gi|256390626|ref|YP_003112190.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Catenulispora
           acidiphila DSM 44928]
 gi|256356852|gb|ACU70349.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Catenulispora
           acidiphila DSM 44928]
          Length = 192

 Score = 40.2 bits (93), Expect = 0.43,   Method: Composition-based stats.
 Identities = 12/65 (18%), Positives = 27/65 (41%), Gaps = 2/65 (3%)

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           +  +    R  L  ++  L   +R +   R  ++   T E+++    +S   VR    +A
Sbjct: 97  DPADLVASRRDLIAALRQLPRGQRAVVVLRYFED--RTDEDIAEVLGISTGTVRSQHHKA 154

Query: 277 FKKVQ 281
            K ++
Sbjct: 155 LKALR 159


>gi|227879320|ref|ZP_03997186.1| DNA-directed RNA polymerase sigma factor, sigma H [Lactobacillus
           crispatus JV-V01]
 gi|256849113|ref|ZP_05554546.1| ComX [Lactobacillus crispatus MV-1A-US]
 gi|262047594|ref|ZP_06020549.1| conserved hypothetical protein [Lactobacillus crispatus MV-3A-US]
 gi|227861089|gb|EEJ68742.1| DNA-directed RNA polymerase sigma factor, sigma H [Lactobacillus
           crispatus JV-V01]
 gi|256713889|gb|EEU28877.1| ComX [Lactobacillus crispatus MV-1A-US]
 gi|260572170|gb|EEX28735.1| conserved hypothetical protein [Lactobacillus crispatus MV-3A-US]
          Length = 181

 Score = 40.2 bits (93), Expect = 0.43,   Method: Composition-based stats.
 Identities = 18/73 (24%), Positives = 28/73 (38%), Gaps = 1/73 (1%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           E  L K+ R  GD  A  +L   +  LV  I   +  +     +   E  I   +A   F
Sbjct: 4   EEKLIKKVR-AGDDQALEKLFHLYEPLVNSIVKQFYLHHYDRKDWDQEAMIVCYEAALVF 62

Query: 94  DPERGFRLATYSM 106
            P++G   + Y  
Sbjct: 63  SPQKGKFSSLYKT 75


>gi|255035628|ref|YP_003086249.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Dyadobacter
           fermentans DSM 18053]
 gi|254948384|gb|ACT93084.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Dyadobacter
           fermentans DSM 18053]
          Length = 198

 Score = 40.2 bits (93), Expect = 0.43,   Method: Composition-based stats.
 Identities = 13/56 (23%), Positives = 28/56 (50%), Gaps = 2/56 (3%)

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           +T  ++ L  R++ +   R   +  ++ E ++S  E+  + VR I  RA   ++E 
Sbjct: 128 MTSLLTKLPERQKEVLYLRFFHD--LSPEEIASMLEIKPQSVRNIIQRALTNLREH 181


>gi|160939512|ref|ZP_02086862.1| hypothetical protein CLOBOL_04405 [Clostridium bolteae ATCC
           BAA-613]
 gi|332655044|ref|ZP_08420785.1| HTH DNA binding domain protein [Ruminococcaceae bacterium D16]
 gi|158437722|gb|EDP15484.1| hypothetical protein CLOBOL_04405 [Clostridium bolteae ATCC
           BAA-613]
 gi|332515904|gb|EGJ45513.1| HTH DNA binding domain protein [Ruminococcaceae bacterium D16]
          Length = 182

 Score = 40.2 bits (93), Expect = 0.43,   Method: Composition-based stats.
 Identities = 14/82 (17%), Positives = 30/82 (36%), Gaps = 1/82 (1%)

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           S+    +  D++ ++           +     E+         L R++  L+ +ER    
Sbjct: 81  SIFPASHVGDRDGTEEGYQDTDLFVDESVDTAEQAICNLLMADLHRALQQLSQKERSFIL 140

Query: 245 ARRLQENPVTLENLSSEFEVSR 266
                E P TL  L+  + +S+
Sbjct: 141 DYYSMEKPSTL-QLAKRYGISQ 161


>gi|326802241|ref|YP_004320060.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Sphingobacterium
           sp. 21]
 gi|326553005|gb|ADZ81390.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Sphingobacterium
           sp. 21]
          Length = 173

 Score = 40.2 bits (93), Expect = 0.43,   Method: Composition-based stats.
 Identities = 13/82 (15%), Positives = 32/82 (39%), Gaps = 8/82 (9%)

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           D    +Q       + +    + + +  L  ++++IF          T   ++ +  +S 
Sbjct: 94  DELDFQQSAEYNFLQGDLIKQVHKQVKELPEKQQQIFCLFYGNGLRST--EIAQKLNLS- 150

Query: 267 ERVRQIEA---RAFKKVQESIQ 285
             VR IE    RA   +++ ++
Sbjct: 151 --VRTIENQLYRALLTLRKKVK 170


>gi|319763545|ref|YP_004127482.1| RNA polymerase sigma factor, sigma-70 family [Alicycliphilus
           denitrificans BC]
 gi|317118106|gb|ADV00595.1| RNA polymerase sigma factor, sigma-70 family [Alicycliphilus
           denitrificans BC]
          Length = 184

 Score = 40.2 bits (93), Expect = 0.43,   Method: Composition-based stats.
 Identities = 23/137 (16%), Positives = 53/137 (38%), Gaps = 2/137 (1%)

Query: 128 TTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLN 187
            T NQ R++  L R+    +   +   +    V  A      ++++ +   R+A +++L+
Sbjct: 28  VTRNQDRIYRFLVRMTRSQEDARELTQETFLSVYQALPSWRPQAQLSTWLFRIARNQALD 87

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
            L  +         D L               + + R   L R+++ L+   R I   R 
Sbjct: 88  RLRRARHVEFVALDDALHQQVPADTPTPEAMLQARQRIAELERALARLSVEHREILLLRD 147

Query: 248 LQENPVTLENLSSEFEV 264
           +++ P   E+++    +
Sbjct: 148 IEDMPY--EDIAQVLGI 162


>gi|160886446|ref|ZP_02067449.1| hypothetical protein BACOVA_04457 [Bacteroides ovatus ATCC 8483]
 gi|156108331|gb|EDO10076.1| hypothetical protein BACOVA_04457 [Bacteroides ovatus ATCC 8483]
          Length = 196

 Score = 40.2 bits (93), Expect = 0.43,   Method: Composition-based stats.
 Identities = 14/92 (15%), Positives = 34/92 (36%), Gaps = 2/92 (2%)

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
                 E  +I  E  K +  +L + ++ L  ++R +   +      ++ E ++    ++
Sbjct: 104 DLEIDIETAIIHSELEKEQLEVLQKELNNLTKQQREVLYLKYY--KKMSPEEIAQVMGLT 161

Query: 266 RERVRQIEARAFKKVQESIQKQVELSSSPPLL 297
              V      A   ++E + K   L  +  L 
Sbjct: 162 SRTVYNTTHMAISSLRERMSKSFLLLVAANLW 193


>gi|331088988|ref|ZP_08337895.1| hypothetical protein HMPREF1025_01478 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|330406440|gb|EGG85953.1| hypothetical protein HMPREF1025_01478 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 169

 Score = 39.8 bits (92), Expect = 0.44,   Method: Composition-based stats.
 Identities = 11/91 (12%), Positives = 40/91 (43%), Gaps = 6/91 (6%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
            +     D++  +     + ++         + L  ++ +L+  E+ + +A     + ++
Sbjct: 84  DSEGNPLDFIADEAADIAETVVNAVMV----DRLKAALPLLSDSEQELIQAIFF--DGLS 137

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              + + F +++  V + +AR   K+++ I+
Sbjct: 138 EREVGARFGITQSVVNKRKARILIKLRKIIE 168


>gi|115524661|ref|YP_781572.1| ECF subfamily RNA polymerase sigma-24 factor [Rhodopseudomonas
           palustris BisA53]
 gi|115518608|gb|ABJ06592.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Rhodopseudomonas
           palustris BisA53]
          Length = 174

 Score = 39.8 bits (92), Expect = 0.44,   Method: Composition-based stats.
 Identities = 21/75 (28%), Positives = 36/75 (48%), Gaps = 4/75 (5%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           +YD   +        E ++     +R++S L PR+R I  A RL    ++ E ++    +
Sbjct: 92  LYDLIDENPGPDRSVEGQSEFEAFSRALSQLTPRQRTIILAVRL--EQLSREEIAKRLNI 149

Query: 265 SRERVRQIE-ARAFK 278
           SR  V Q+E  RA +
Sbjct: 150 SRSLV-QLELQRALE 163


>gi|125972924|ref|YP_001036834.1| putative RNA polymerase sigma factor SigI [Clostridium thermocellum
           ATCC 27405]
 gi|125713149|gb|ABN51641.1| DNA-directed RNA polymerase sigma factor [Clostridium thermocellum
           ATCC 27405]
 gi|316940840|gb|ADU74874.1| RNA polymerase, sigma 28 subunit, SigI [Clostridium thermocellum
           DSM 1313]
          Length = 274

 Score = 39.8 bits (92), Expect = 0.44,   Method: Composition-based stats.
 Identities = 18/79 (22%), Positives = 35/79 (44%), Gaps = 4/79 (5%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM---QAVKKFDPERGFRL 101
           GD+    + +  +   ++KI     G  +   EV  E ++GLM   +A+  F+PE     
Sbjct: 53  GDIELKEKFIKKYKPYLLKIISSTLGRYVDP-EVSEEYSVGLMAFNEAIDGFNPEINGNF 111

Query: 102 ATYSMWWIKAAMQEYILRS 120
             Y    +   + +YI ++
Sbjct: 112 TNYCNMVVNHRIIDYIRKN 130


>gi|331700227|ref|YP_004336466.1| ECF subfamily RNA polymerase sigma-24 subunit [Pseudonocardia
           dioxanivorans CB1190]
 gi|326954916|gb|AEA28613.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Pseudonocardia
           dioxanivorans CB1190]
          Length = 244

 Score = 39.8 bits (92), Expect = 0.44,   Method: Composition-based stats.
 Identities = 9/63 (14%), Positives = 21/63 (33%), Gaps = 2/63 (3%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
            V  H    +              +  +++ L PR+R +   R      ++   ++    
Sbjct: 159 YVPPHTVTARSAESLAMLSAEHQAVVDALATLPPRQREVLVLRYYGG--MSEAEIAEATG 216

Query: 264 VSR 266
           +SR
Sbjct: 217 ISR 219


>gi|313158864|gb|EFR58244.1| RNA polymerase sigma-70 factor [Alistipes sp. HGB5]
          Length = 205

 Score = 39.8 bits (92), Expect = 0.44,   Method: Composition-based stats.
 Identities = 14/78 (17%), Positives = 41/78 (52%), Gaps = 8/78 (10%)

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE--- 273
           E+        ++ +S+  L    R +F ARR +E  ++ + ++ ++ ++   VR++E   
Sbjct: 122 EEIFSAEVAAIVRQSLDRLPELTREVFVARRFEE--LSYKEIAEKYGIT---VRRVEFEL 176

Query: 274 ARAFKKVQESIQKQVELS 291
            +A K+++ +++  + + 
Sbjct: 177 EKAVKQLRVALKDYLPVL 194


>gi|301053341|ref|YP_003791552.1| RNA polymerase sigma-70 factor [Bacillus anthracis CI]
 gi|300375510|gb|ADK04414.1| RNA polymerase sigma-70 factor [Bacillus cereus biovar anthracis
           str. CI]
          Length = 188

 Score = 39.8 bits (92), Expect = 0.44,   Method: Composition-based stats.
 Identities = 16/79 (20%), Positives = 33/79 (41%), Gaps = 10/79 (12%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           H   E+   ++      R  L + ++ L P ++++F  + L       E +  +  ++R 
Sbjct: 104 HISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLIGMKT--EEIGDKLGLTRA 161

Query: 268 ----RVRQIEARAFKKVQE 282
               RV     R  KK+Q+
Sbjct: 162 AIDNRV----YRGKKKLQQ 176


>gi|266706197|gb|ACY78403.1| sigma factor [Streptomyces chattanoogensis]
          Length = 269

 Score = 39.8 bits (92), Expect = 0.44,   Method: Composition-based stats.
 Identities = 10/28 (35%), Positives = 16/28 (57%)

Query: 14  IGLSRYIHEIRKIPMLEKQEEYVLAKRY 41
             +  Y+ +I K+P L  ++E  LAKR 
Sbjct: 218 DPVKDYLKQIGKVPFLNAEQEVELAKRI 245


>gi|255691723|ref|ZP_05415398.1| ECF-type sigma factor [Bacteroides finegoldii DSM 17565]
 gi|260622608|gb|EEX45479.1| ECF-type sigma factor [Bacteroides finegoldii DSM 17565]
          Length = 183

 Score = 39.8 bits (92), Expect = 0.44,   Method: Composition-based stats.
 Identities = 18/71 (25%), Positives = 36/71 (50%), Gaps = 2/71 (2%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E    EKE+RKN   ++ R ++ L+PR+R       ++E     E++     ++ + VR 
Sbjct: 112 ENDYAEKEQRKNEFFLIKRLLNQLSPRQREALTLYYIEEKKY--EDICEIMNMNYQSVRN 169

Query: 272 IEARAFKKVQE 282
           +  R   K+++
Sbjct: 170 LMYRGLTKLRD 180


>gi|169343379|ref|ZP_02864383.1| hypothetical protein CPC_0057 [Clostridium perfringens C str.
           JGS1495]
 gi|169298465|gb|EDS80551.1| hypothetical protein CPC_0057 [Clostridium perfringens C str.
           JGS1495]
          Length = 134

 Score = 39.8 bits (92), Expect = 0.44,   Method: Composition-based stats.
 Identities = 21/112 (18%), Positives = 45/112 (40%), Gaps = 1/112 (0%)

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
           +  EQ   I K L+  ++  + + C     E L   I    +        +  + + + +
Sbjct: 1   MTKEQKEKIKKLLSNYKTMKVQIECIDYEIELLKEYIEFLKELRDSDNYIIESNKEIEHK 60

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
             I+K   ++  N + ++++ L   ER+I E R L+    T   + +    S
Sbjct: 61  RAIKK-RLEDCINSIDKALNELGDTERKIVELRYLEGEKHTWREIGNIVGYS 111


>gi|295692214|ref|YP_003600824.1| DNA-directed RNA polymerase sigma factor, sigma h [Lactobacillus
           crispatus ST1]
 gi|295030320|emb|CBL49799.1| DNA-directed RNA polymerase sigma factor, sigma H [Lactobacillus
           crispatus ST1]
          Length = 181

 Score = 39.8 bits (92), Expect = 0.45,   Method: Composition-based stats.
 Identities = 17/74 (22%), Positives = 29/74 (39%), Gaps = 2/74 (2%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           E  L K+ R  GD  A  +L   +  LV  I   +  +     +   E  I   +A   F
Sbjct: 4   EEKLIKKVR-AGDDQALEKLFHLYEPLVNSIVKQFYLHHYDRKDWDQEAMIVCYEAALVF 62

Query: 94  DPERGFRLATYSMW 107
            P++G + ++    
Sbjct: 63  SPQKG-KFSSLYKT 75


>gi|296132703|ref|YP_003639950.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           sp. JR]
 gi|296031281|gb|ADG82049.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Thermincola
           potens JR]
          Length = 252

 Score = 39.8 bits (92), Expect = 0.45,   Method: Composition-based stats.
 Identities = 20/83 (24%), Positives = 39/83 (46%), Gaps = 4/83 (4%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM---QAVKKFDPE 96
           R  ++G+  A  RL+  +   V+KI     G  + + E   E +IGLM   +A+  +D  
Sbjct: 22  REAKNGNHFARERLIKRYSPFVLKITSKVCGRFVHMGED-DEVSIGLMAFNEAIDCYDDN 80

Query: 97  RGFRLATYSMWWIKAAMQEYILR 119
           +     +++   IK  + +Y  +
Sbjct: 81  KNMSFLSFAETVIKRRLVDYFRK 103


>gi|256425323|ref|YP_003125976.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Chitinophaga
           pinensis DSM 2588]
 gi|256040231|gb|ACU63775.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Chitinophaga
           pinensis DSM 2588]
          Length = 180

 Score = 39.8 bits (92), Expect = 0.45,   Method: Composition-based stats.
 Identities = 14/97 (14%), Positives = 35/97 (36%), Gaps = 1/97 (1%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
            ++++  L        +  A  +L        + IAM Y       ++++S   + + ++
Sbjct: 3   SQEQDISLLIEGCLANNRKAQEQLYRLFYSFAMSIAMRYARSEADAADIMSHAFVKIFKS 62

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           +  +D  +G   A +    +     +YI        I
Sbjct: 63  MHTYDATKGTMYA-WIKRIVANEGIDYIKSQNKFNPI 98


>gi|206970306|ref|ZP_03231259.1| putative sigma factor [Bacillus cereus AH1134]
 gi|206734883|gb|EDZ52052.1| putative sigma factor [Bacillus cereus AH1134]
          Length = 156

 Score = 39.8 bits (92), Expect = 0.45,   Method: Composition-based stats.
 Identities = 16/72 (22%), Positives = 36/72 (50%), Gaps = 2/72 (2%)

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
              E    ++    +   MSVL+ +E+ I   R       T+  ++ E E++  +VR + 
Sbjct: 86  EYEEIFHFEDVEIRVKDFMSVLDEKEKYIIFERFFVG--KTMGEIALETEMTYYQVRWMY 143

Query: 274 ARAFKKVQESIQ 285
            +A +K+++S++
Sbjct: 144 RQALEKMRDSVK 155


>gi|312140829|ref|YP_004008165.1| sigma-70 factor [Rhodococcus equi 103S]
 gi|311890168|emb|CBH49486.1| sigma-70 factor [Rhodococcus equi 103S]
          Length = 138

 Score = 39.8 bits (92), Expect = 0.45,   Method: Composition-based stats.
 Identities = 15/85 (17%), Positives = 31/85 (36%), Gaps = 2/85 (2%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           V D    +    E+         +   +  L  + R I   R +    ++ E  ++    
Sbjct: 53  VPDVVSADDSPEERALNSETSRQVNALLQTLPEKHREILVLRLVVG--LSAEETAAAVGS 110

Query: 265 SRERVRQIEARAFKKVQESIQKQVE 289
           +   VR  + RA  K+++ + K  E
Sbjct: 111 TAGAVRVAQHRALAKLKKEVTKAGE 135


>gi|255007756|ref|ZP_05279882.1| RNA polymerase ECF-type sigma factor [Bacteroides fragilis 3_1_12]
          Length = 191

 Score = 39.8 bits (92), Expect = 0.45,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 38/73 (52%), Gaps = 2/73 (2%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E  + ++ +  + +  + + +S L PR++ +F   R  E  ++ + +++   +S + V +
Sbjct: 112 EYDIEDEMDAADLQAYIKKLISELTPRQQEVFHLSR--EEHLSYKEIATRLSISEKTVER 169

Query: 272 IEARAFKKVQESI 284
               A K ++++I
Sbjct: 170 HINEALKFLRKNI 182


>gi|238061940|ref|ZP_04606649.1| sigma-70 region 4 domain-containing protein [Micromonospora sp.
           ATCC 39149]
 gi|237883751|gb|EEP72579.1| sigma-70 region 4 domain-containing protein [Micromonospora sp.
           ATCC 39149]
          Length = 176

 Score = 39.8 bits (92), Expect = 0.45,   Method: Composition-based stats.
 Identities = 14/59 (23%), Positives = 27/59 (45%), Gaps = 4/59 (6%)

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV-RQIEARAFKKVQE 282
           R  L  ++  L PR+R +   R  ++  +T    +    V+   V  Q  A A ++++E
Sbjct: 102 RIALHDALGQLPPRQRAVVVLRYFED--LTEAGTAEVLGVTVGTVKSQCHA-ALRRLRE 157


>gi|47565483|ref|ZP_00236524.1| RNA polymerase sigma-E factor, putative [Bacillus cereus G9241]
 gi|47557473|gb|EAL15800.1| RNA polymerase sigma-E factor, putative [Bacillus cereus G9241]
          Length = 188

 Score = 39.8 bits (92), Expect = 0.45,   Method: Composition-based stats.
 Identities = 10/59 (16%), Positives = 25/59 (42%), Gaps = 2/59 (3%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           H   E+   ++      R  L + ++ L P ++++F  + L       E +  +  ++R
Sbjct: 104 HISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKT--EEIGDKLGLTR 160


>gi|331696056|ref|YP_004332295.1| LuxR family ATP-dependent transcriptional regulator [Pseudonocardia
           dioxanivorans CB1190]
 gi|326950745|gb|AEA24442.1| ATP-dependent transcriptional regulator, MalT-like, LuxR family
           [Pseudonocardia dioxanivorans CB1190]
          Length = 663

 Score = 39.8 bits (92), Expect = 0.46,   Method: Composition-based stats.
 Identities = 20/85 (23%), Positives = 36/85 (42%), Gaps = 13/85 (15%)

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
           + D L        + ++   +R   R    +    L+ RE+R+  A      P+TL  ++
Sbjct: 568 FPDELEQRSRAAARDVLAALDRTAARR--EQRARDLSSREQRVLRA---LCGPLTLREIA 622

Query: 260 SEFEVS----RERVRQIEARAFKKV 280
            E  VS    + +VR I    F+K+
Sbjct: 623 DELFVSHNTVKSQVRSI----FRKL 643


>gi|256844499|ref|ZP_05549985.1| DNA-directed RNA polymerase sigma factor [Lactobacillus crispatus
           125-2-CHN]
 gi|293381068|ref|ZP_06627089.1| RNA polymerase sigma factor, sigma-70 family [Lactobacillus
           crispatus 214-1]
 gi|312977947|ref|ZP_07789693.1| putative sigma factor 30 RNA polymerase [Lactobacillus crispatus
           CTV-05]
 gi|256613577|gb|EEU18780.1| DNA-directed RNA polymerase sigma factor [Lactobacillus crispatus
           125-2-CHN]
 gi|290922368|gb|EFD99349.1| RNA polymerase sigma factor, sigma-70 family [Lactobacillus
           crispatus 214-1]
 gi|310895254|gb|EFQ44322.1| putative sigma factor 30 RNA polymerase [Lactobacillus crispatus
           CTV-05]
          Length = 181

 Score = 39.8 bits (92), Expect = 0.46,   Method: Composition-based stats.
 Identities = 17/74 (22%), Positives = 29/74 (39%), Gaps = 2/74 (2%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           E  L K+ R  GD  A  +L   +  LV  I   +  +     +   E  I   +A   F
Sbjct: 4   EEKLIKKVR-AGDDQALEKLFHLYEPLVNSIVKQFYLHHYDRKDWDQEAMIVCYEAALVF 62

Query: 94  DPERGFRLATYSMW 107
            P++G + ++    
Sbjct: 63  SPKKG-KFSSLYKT 75


>gi|229158815|ref|ZP_04286873.1| RNA polymerase sigma factor [Bacillus cereus ATCC 4342]
 gi|228624799|gb|EEK81568.1| RNA polymerase sigma factor [Bacillus cereus ATCC 4342]
          Length = 156

 Score = 39.8 bits (92), Expect = 0.46,   Method: Composition-based stats.
 Identities = 15/64 (23%), Positives = 33/64 (51%), Gaps = 2/64 (3%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    +   MSVL  +E+ I   R       T+  ++ E E++  +VR +  +A +K++
Sbjct: 94  EDIEMKVKDFMSVLGEKEKYIIFERFFVG--KTMGEIALETEMTYYQVRWVYRQALEKMR 151

Query: 282 ESIQ 285
            S++
Sbjct: 152 NSLR 155


>gi|294631578|ref|ZP_06710138.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces sp. e14]
 gi|292834911|gb|EFF93260.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces sp. e14]
          Length = 560

 Score = 39.8 bits (92), Expect = 0.46,   Method: Composition-based stats.
 Identities = 21/86 (24%), Positives = 36/86 (41%), Gaps = 6/86 (6%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           E   L  R RE GD +A   LV++HL LV  I        + + ++V +    +++A+  
Sbjct: 8   ELAALVNRARE-GDPAAQDALVSAHLPLVYNIVGRALNGSVDVDDIVQDT---MLRALDG 63

Query: 93  FDPERGFRLATYSMWWIKAAMQEYIL 118
               R     ++  W +  AM     
Sbjct: 64  LSGLREP--ESFRSWLVAIAMNRVRA 87


>gi|291528076|emb|CBK93662.1| hypothetical protein ERE_17220 [Eubacterium rectale M104/1]
          Length = 301

 Score = 39.8 bits (92), Expect = 0.46,   Method: Composition-based stats.
 Identities = 21/82 (25%), Positives = 36/82 (43%), Gaps = 1/82 (1%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +   ++        Y+ E+ +IP   K E+  + K+    GD S  H +    L+ V+ +
Sbjct: 118 DEDSLIPDSPMFRMYLEELEEIPDYTKAEQDDMYKKLL-AGDESVIHTISNFWLKSVLAM 176

Query: 65  AMGYRGYGLPISEVVSEGNIGL 86
           A           +VV EGN+GL
Sbjct: 177 AKKLAVTSEGFEDVVQEGNMGL 198


>gi|160882665|ref|ZP_02063668.1| hypothetical protein BACOVA_00619 [Bacteroides ovatus ATCC 8483]
 gi|237718438|ref|ZP_04548919.1| conserved hypothetical protein [Bacteroides sp. 2_2_4]
 gi|260173886|ref|ZP_05760298.1| putative RNA polymerase ECF-type sigma factor [Bacteroides sp. D2]
 gi|293371432|ref|ZP_06617863.1| sigma-70, region 4 [Bacteroides ovatus SD CMC 3f]
 gi|299149084|ref|ZP_07042146.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 3_1_23]
 gi|315922150|ref|ZP_07918390.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D2]
 gi|156111980|gb|EDO13725.1| hypothetical protein BACOVA_00619 [Bacteroides ovatus ATCC 8483]
 gi|229452371|gb|EEO58162.1| conserved hypothetical protein [Bacteroides sp. 2_2_4]
 gi|292633629|gb|EFF52187.1| sigma-70, region 4 [Bacteroides ovatus SD CMC 3f]
 gi|298513845|gb|EFI37732.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 3_1_23]
 gi|313696025|gb|EFS32860.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D2]
          Length = 181

 Score = 39.8 bits (92), Expect = 0.46,   Method: Composition-based stats.
 Identities = 15/76 (19%), Positives = 38/76 (50%), Gaps = 3/76 (3%)

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           +++ E++ER   +  L + +  L  R+R     R  Q   ++ E +     +  +  +++
Sbjct: 99  ELIDEEKERAAMQKQLKKMLDSLTDRQREAVYLRYTQG--LSYEEIGKLMGIQPKAAQKL 156

Query: 273 EARAFKKVQESIQKQV 288
             RA +++++ IQ Q+
Sbjct: 157 VYRAIEQMRK-IQPQI 171


>gi|270308514|ref|YP_003330572.1| RNA polymerase sigma-70 factor, ECF subfamily [Dehalococcoides sp.
           VS]
 gi|270154406|gb|ACZ62244.1| RNA polymerase sigma-70 factor, ECF subfamily [Dehalococcoides sp.
           VS]
          Length = 179

 Score = 39.8 bits (92), Expect = 0.47,   Method: Composition-based stats.
 Identities = 23/144 (15%), Positives = 57/144 (39%), Gaps = 9/144 (6%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVV-KIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           E  L +   +  D  A  RL   +   +   IA+   G  +   ++  +  + +++++  
Sbjct: 4   ERHLVE-LAQQKDEQAFARLYEEYFDKIYRYIALK-IGNKMEAEDLTQQVFMNMLRSISS 61

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F  +     + +        + +Y+ +    + +        L   L      ++  T+ 
Sbjct: 62  FKWQDNTPFSAWLYRIAHNQIVDYLRKKSRQLTV-----DIELVTPLACSDDPVE-TTEV 115

Query: 153 NLKPEQVVAIAKKLNVSESEVISM 176
           N+  E+ V ++ KL  ++ EVIS+
Sbjct: 116 NIDYEKFVEVSGKLTPAQQEVISL 139


>gi|229132633|ref|ZP_04261481.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           BDRD-ST196]
 gi|228650865|gb|EEL06852.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           BDRD-ST196]
          Length = 188

 Score = 39.8 bits (92), Expect = 0.47,   Method: Composition-based stats.
 Identities = 10/59 (16%), Positives = 25/59 (42%), Gaps = 2/59 (3%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           H   E+   ++      R  L + ++ L P ++++F  + L       E +  +  ++R
Sbjct: 104 HISMEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKT--EEIGDKLGLTR 160


>gi|30023283|ref|NP_834914.1| RNA polymerase factor sigma-70 [Bacillus cereus ATCC 14579]
 gi|229130499|ref|ZP_04259455.1| RNA polymerase sigma factor [Bacillus cereus BDRD-Cer4]
 gi|229153411|ref|ZP_04281589.1| RNA polymerase sigma factor [Bacillus cereus m1550]
 gi|29898844|gb|AAP12115.1| RNA polymerase sigma factor [Bacillus cereus ATCC 14579]
 gi|228630015|gb|EEK86666.1| RNA polymerase sigma factor [Bacillus cereus m1550]
 gi|228652838|gb|EEL08720.1| RNA polymerase sigma factor [Bacillus cereus BDRD-Cer4]
          Length = 156

 Score = 39.8 bits (92), Expect = 0.47,   Method: Composition-based stats.
 Identities = 15/64 (23%), Positives = 35/64 (54%), Gaps = 2/64 (3%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    +   MSVL+ +E+ I   R       T+  ++ E E++  +VR +  +A +K++
Sbjct: 94  EDVEIRVKDFMSVLDEKEKYIIFERFFVG--KTMGEIALETEMTYYQVRWMYRQALEKMR 151

Query: 282 ESIQ 285
           +S++
Sbjct: 152 DSVK 155


>gi|54025718|ref|YP_119960.1| RNA polymerase sigma factor SigD [Nocardia farcinica IFM 10152]
 gi|54017226|dbj|BAD58596.1| putative sigma factor [Nocardia farcinica IFM 10152]
          Length = 207

 Score = 39.8 bits (92), Expect = 0.47,   Method: Composition-based stats.
 Identities = 20/90 (22%), Positives = 30/90 (33%), Gaps = 6/90 (6%)

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR--RLQENPVTL 255
             +    V D    E    E      RR      M VL P  R +   R         T 
Sbjct: 119 PAYPMAEVPDAASPEAGPEEWALALERRAATRELMKVLAPAHREVLVMRIVLGWSAAQTA 178

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           E + +   V    VR ++ RA  K++  ++
Sbjct: 179 EAIGTSPGV----VRVMQHRALNKLRAQLE 204


>gi|299149342|ref|ZP_07042399.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 3_1_23]
 gi|298512529|gb|EFI36421.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 3_1_23]
          Length = 196

 Score = 39.8 bits (92), Expect = 0.48,   Method: Composition-based stats.
 Identities = 14/92 (15%), Positives = 34/92 (36%), Gaps = 2/92 (2%)

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
                 E  +I  E  K +  +L + ++ L  ++R +   +      ++ E ++    ++
Sbjct: 104 DLEIDIETAIIHSELEKEQLEVLQKELNNLTKQQREVLYLKYY--KKMSPEEIAQVMGLT 161

Query: 266 RERVRQIEARAFKKVQESIQKQVELSSSPPLL 297
              V      A   ++E + K   L  +  L 
Sbjct: 162 SRTVYNTTHMAISSLRERMSKSFLLLVAANLW 193


>gi|291524597|emb|CBK90184.1| hypothetical protein EUR_10340 [Eubacterium rectale DSM 17629]
          Length = 301

 Score = 39.8 bits (92), Expect = 0.48,   Method: Composition-based stats.
 Identities = 21/82 (25%), Positives = 36/82 (43%), Gaps = 1/82 (1%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +   ++        Y+ E+ +IP   K E+  + K+    GD S  H +    L+ V+ +
Sbjct: 118 DEDSLIPDSPMFRMYLEELEEIPDYTKAEQDDMYKKLL-AGDESVIHTISNFWLKSVLAM 176

Query: 65  AMGYRGYGLPISEVVSEGNIGL 86
           A           +VV EGN+GL
Sbjct: 177 AKKLAVTSEGFEDVVQEGNMGL 198


>gi|260584245|ref|ZP_05851993.1| sigma-70 subfamily protein [Granulicatella elegans ATCC 700633]
 gi|260158871|gb|EEW93939.1| sigma-70 subfamily protein [Granulicatella elegans ATCC 700633]
          Length = 187

 Score = 39.8 bits (92), Expect = 0.48,   Method: Composition-based stats.
 Identities = 17/86 (19%), Positives = 32/86 (37%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L  R +   D  A   L      L+  +   +  Y + + + + E +  L  A +KFD +
Sbjct: 7   LVMRIQNGEDEEAFVLLENKIKPLMHMMYYRHFYYCVELEDFIQEASFLLFYAAQKFDFQ 66

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWS 122
           +G     Y    +K    + + R   
Sbjct: 67  KGKSFLAYYRKSLKNYAIQLVRREHR 92


>gi|284036237|ref|YP_003386167.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Spirosoma linguale
           DSM 74]
 gi|283815530|gb|ADB37368.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Spirosoma linguale
           DSM 74]
          Length = 183

 Score = 39.8 bits (92), Expect = 0.48,   Method: Composition-based stats.
 Identities = 21/114 (18%), Positives = 53/114 (46%), Gaps = 18/114 (15%)

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           R   D+SL+ L+   D +  ++++ L+ D     +   ++  +      L ++++ L   
Sbjct: 74  RKRKDDSLSDLMGDEDDDDFRFREILLAD----AETPEDQFFKDIFWEELMKALNELPEN 129

Query: 239 ERRIFEARRLQENPVTLENLSSEFE------VSRERVRQIEARAFKKVQESIQK 286
           +R +F    L++   TL+ ++ E        +SR+R       A + +++ +Q+
Sbjct: 130 QRIVFVQNELED--RTLQEIADEMGENLKTIISRKR------YAVQHLRKRLQR 175


>gi|153955678|ref|YP_001396443.1| RNA polymerase sigma factor rpoD-related protein [Clostridium
           kluyveri DSM 555]
 gi|146348536|gb|EDK35072.1| RNA polymerase sigma factor rpoD-related protein [Clostridium
           kluyveri DSM 555]
          Length = 218

 Score = 39.8 bits (92), Expect = 0.48,   Method: Composition-based stats.
 Identities = 23/103 (22%), Positives = 44/103 (42%), Gaps = 4/103 (3%)

Query: 21  HEI---RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           HEI   R   +L+  +  VL +R +  GD SAA  +      +VV I       G  + +
Sbjct: 15  HEIEIYRDYDLLKISKLEVLLERAK-IGDSSAAEEICRRFNGMVVNICRSIYINGYTMED 73

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++ EG + L++++  +D    +    Y+   +       I  +
Sbjct: 74  MLQEGRVSLIKSINSYDLNSKYPFPAYAKGAVTKNFYYQIRSN 116


>gi|56419467|ref|YP_146785.1| putative RNA polymerase sigma factor SigI [Geobacillus kaustophilus
           HTA426]
 gi|56379309|dbj|BAD75217.1| DNA-directed RNA polymerase sigma factor [Geobacillus kaustophilus
           HTA426]
          Length = 246

 Score = 39.8 bits (92), Expect = 0.48,   Method: Composition-based stats.
 Identities = 16/88 (18%), Positives = 37/88 (42%), Gaps = 13/88 (14%)

Query: 43  EHGDLSAAHRLVTSHLRL----VVKIAMGYRGYGLPISEVVSEGNIGLM---QAVKKFDP 95
           + G+ +  + L+  +       V  +   +      I E   E +IGL+   +A++K+  
Sbjct: 21  QRGNEALRNELIRQYKPFIVKTVSSVCKRF------IREEDDEASIGLIAFNEAIEKYAL 74

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSL 123
            +G    +++   IK  + +YI +    
Sbjct: 75  HKGGSFLSFAELLIKRRLIDYIRKEVRT 102


>gi|253566174|ref|ZP_04843628.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 3_2_5]
 gi|265766925|ref|ZP_06094754.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 2_1_16]
 gi|251945278|gb|EES85716.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 3_2_5]
 gi|263253302|gb|EEZ24778.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 2_1_16]
 gi|301164501|emb|CBW24060.1| putative RNA polymerase sigma factor [Bacteroides fragilis 638R]
          Length = 192

 Score = 39.8 bits (92), Expect = 0.49,   Method: Composition-based stats.
 Identities = 11/39 (28%), Positives = 23/39 (58%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           E+ LIE E+  ++++ +   ++ L+PR+R I   R  + 
Sbjct: 113 EEKLIETEDETSQKHTVAHLLNTLSPRQREIIYYRFFEG 151


>gi|113867116|ref|YP_725605.1| DNA-directed RNA polymerase sigma subunit (RpoE,sigma24) [Ralstonia
           eutropha H16]
 gi|113525892|emb|CAJ92237.1| DNA-directed RNA polymerase sigma subunit (RpoE,sigma24) [Ralstonia
           eutropha H16]
          Length = 207

 Score = 39.8 bits (92), Expect = 0.49,   Method: Composition-based stats.
 Identities = 15/109 (13%), Positives = 42/109 (38%), Gaps = 4/109 (3%)

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
             + S+D    +  D    +    +     + + +   + + R++  L   +R +   R 
Sbjct: 101 DQVRSADARQREALDDQPAEMPADDLSPEAELQLRQHAHHVQRALLQLPVAQREVVVLRF 160

Query: 248 LQENPVTLENLSSEFEVSRERV-RQIEARAFKKVQESIQKQVELSSSPP 295
             +  +++E ++       E V  ++   AF +++ ++   V  S   P
Sbjct: 161 FSD--MSVEEIAQMLGEKFETVKSRL-RYAFARLRANLAGSVPGSQETP 206


>gi|297478828|ref|XP_002690390.1| PREDICTED: spectrin repeat containing, nuclear envelope 1, partial
           [Bos taurus]
 gi|296483898|gb|DAA26013.1| spectrin repeat containing, nuclear envelope 1 [Bos taurus]
          Length = 3408

 Score = 39.8 bits (92), Expect = 0.49,   Method: Composition-based stats.
 Identities = 28/125 (22%), Positives = 53/125 (42%), Gaps = 5/125 (4%)

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
           A  + + RSW  +K   +  Q+ L+  L R + +  ++   + K E   AI  KL+ S  
Sbjct: 523 AKLDDLQRSWETLKNVISEKQRTLYEALERQQKYQDSLQSISTKME---AIEMKLSESLE 579

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLT 229
           +  S   ++A  ++L   I    +  S+ Q  L  +   +  E    E+   ++   +L 
Sbjct: 580 QGRSPESQMAEHQALMDEILMLQEEISELQSALADELVSESPESEPAEQLALQSTLTVLA 639

Query: 230 RSMSV 234
             MS 
Sbjct: 640 ERMST 644


>gi|256397407|ref|YP_003118971.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Catenulispora
           acidiphila DSM 44928]
 gi|256363633|gb|ACU77130.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Catenulispora
           acidiphila DSM 44928]
          Length = 239

 Score = 39.8 bits (92), Expect = 0.49,   Method: Composition-based stats.
 Identities = 15/67 (22%), Positives = 29/67 (43%), Gaps = 6/67 (8%)

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
           +    + D    E V +  EE    R +L  +M  L PR+R +   R   +  ++  +++
Sbjct: 159 YTPPHIPDAASAESVALLSEE---HREVL-EAMQKLPPRQREVLVLRYWSD--LSEADIA 212

Query: 260 SEFEVSR 266
               +SR
Sbjct: 213 DALGISR 219


>gi|75910298|ref|YP_324594.1| hypothetical protein Ava_4098 [Anabaena variabilis ATCC 29413]
 gi|75704023|gb|ABA23699.1| conserved hypothetical protein [Anabaena variabilis ATCC 29413]
          Length = 402

 Score = 39.8 bits (92), Expect = 0.49,   Method: Composition-based stats.
 Identities = 17/92 (18%), Positives = 42/92 (45%), Gaps = 5/92 (5%)

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           +IS+N  +  + S +  I   D      Q+ L+ +   QE++L  + ++    N+L  ++
Sbjct: 256 MISLNVSVGEENSGDEYI---DIVPQLKQESLMTEILAQEELLDRQSQQAQISNVLVTAL 312

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           + L+P    I +        +T + ++ +  +
Sbjct: 313 TELDPEAHNIIQLYYR--EGLTQQQIAQQLGI 342


>gi|270295869|ref|ZP_06202069.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D20]
 gi|270273273|gb|EFA19135.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D20]
          Length = 181

 Score = 39.8 bits (92), Expect = 0.50,   Method: Composition-based stats.
 Identities = 21/89 (23%), Positives = 41/89 (46%), Gaps = 8/89 (8%)

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           SS+    L    D  E  LI +E          +++  L  R R +F   RL+E   +  
Sbjct: 97  SSEQLPELSDQADSPEDTLISEELFARY----VKALDRLPERCREVFI--RLREEKQSYA 150

Query: 257 NLSSEFEVSRERV-RQIEARAFKKVQESI 284
            ++ E  +S + V  Q++ +A  +++E++
Sbjct: 151 QVAEELNISTKTVDAQLQ-KALTRLKEAL 178


>gi|87125127|ref|ZP_01080974.1| Sigma-70 region 2 [Synechococcus sp. RS9917]
 gi|86167447|gb|EAQ68707.1| Sigma-70 region 2 [Synechococcus sp. RS9917]
          Length = 126

 Score = 39.8 bits (92), Expect = 0.50,   Method: Composition-based stats.
 Identities = 13/64 (20%), Positives = 29/64 (45%), Gaps = 1/64 (1%)

Query: 69  RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGT 128
           R  G P  ++     +G++QA +++  ERG     Y+  +    +  Y+     L+K+  
Sbjct: 16  RRTGHPKEDLEQIAMLGIIQAARRYSQERGS-FRPYARTYANGEVYHYLRDKGFLIKVPA 74

Query: 129 TANQ 132
           +  +
Sbjct: 75  SWRE 78


>gi|284030105|ref|YP_003380036.1| ECF subfamily RNA polymerase sigma-24 subunit [Kribbella flavida
           DSM 17836]
 gi|283809398|gb|ADB31237.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Kribbella flavida
           DSM 17836]
          Length = 169

 Score = 39.8 bits (92), Expect = 0.50,   Method: Composition-based stats.
 Identities = 27/155 (17%), Positives = 58/155 (37%), Gaps = 3/155 (1%)

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           +    R L+       D  L  + V    +KL V   +V++ +   A        +  S+
Sbjct: 14  VARQSRWLRTAYLLCNDRQLAEDVVQQSLEKLYVVWPKVVAADSPDAYVRKTILNVYLSE 73

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
                 +     D      V        + R  L R++S L  R+R +   R  ++  VT
Sbjct: 74  TRRMWRRRERSSDDPTAGAVETVDASLDD-RIDLARALSRLPRRQRMVLILRFAEDLSVT 132

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
               ++    +   V+   A A + ++++I+ +++
Sbjct: 133 --ETAAVMGCAEGTVKAHTAAALRALRKTIEFELQ 165


>gi|111023159|ref|YP_706131.1| RNA polymerase sigma factor SigD [Rhodococcus jostii RHA1]
 gi|226365665|ref|YP_002783448.1| RNA polymerase sigma factor SigD [Rhodococcus opacus B4]
 gi|110822689|gb|ABG97973.1| sigma factor, sigma 70 type, group 4 (ECF) [Rhodococcus jostii
           RHA1]
 gi|226244155|dbj|BAH54503.1| RNA polymerase ECF-type sigma factor SigD [Rhodococcus opacus B4]
          Length = 192

 Score = 39.8 bits (92), Expect = 0.50,   Method: Composition-based stats.
 Identities = 14/85 (16%), Positives = 32/85 (37%), Gaps = 2/85 (2%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           V D    +    ++         +   +S L  + R I   R +    ++ E  ++    
Sbjct: 107 VPDVVANDDGPEQRALDSEASRQMNELLSTLPEKHREILILRLVVG--MSAEETAAAVGS 164

Query: 265 SRERVRQIEARAFKKVQESIQKQVE 289
           +   VR  + RA  K+++ + +  E
Sbjct: 165 TAGAVRVAQHRAIAKLKKEVTRAGE 189


>gi|154244874|ref|YP_001415832.1| response regulator receiver protein [Xanthobacter autotrophicus
           Py2]
 gi|154158959|gb|ABS66175.1| response regulator receiver protein [Xanthobacter autotrophicus
           Py2]
          Length = 359

 Score = 39.8 bits (92), Expect = 0.50,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 25/50 (50%), Gaps = 3/50 (6%)

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           E+EE  +   +L  ++S+  PRE+ I     L  N  T   ++ +  +S+
Sbjct: 280 EREEEGDPDQLLDEALSIFTPREKEIL---LLLMNGQTTGEIAQKLSLSK 326


>gi|163939613|ref|YP_001644497.1| RNA polymerase factor sigma-70 [Bacillus weihenstephanensis KBAB4]
 gi|163861810|gb|ABY42869.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Bacillus
           weihenstephanensis KBAB4]
          Length = 182

 Score = 39.8 bits (92), Expect = 0.50,   Method: Composition-based stats.
 Identities = 10/59 (16%), Positives = 25/59 (42%), Gaps = 2/59 (3%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           H   E+   ++      R  L + ++ L P ++++F  + L       E +  +  ++R
Sbjct: 98  HISMEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKT--EEIGDKLGLTR 154


>gi|238923797|ref|YP_002937313.1| hypothetical protein EUBREC_1420 [Eubacterium rectale ATCC 33656]
 gi|238875472|gb|ACR75179.1| Hypothetical protein EUBREC_1420 [Eubacterium rectale ATCC 33656]
          Length = 301

 Score = 39.8 bits (92), Expect = 0.51,   Method: Composition-based stats.
 Identities = 21/82 (25%), Positives = 36/82 (43%), Gaps = 1/82 (1%)

Query: 5   NMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKI 64
           +   ++        Y+ E+ +IP   K E+  + K+    GD S  H +    L+ V+ +
Sbjct: 118 DEDSLIPDSPMFRMYLEELEEIPDYTKAEQDDMYKKLL-AGDESVIHTISNFWLKSVLAM 176

Query: 65  AMGYRGYGLPISEVVSEGNIGL 86
           A           +VV EGN+GL
Sbjct: 177 AKKLAVTSEGFEDVVQEGNMGL 198


>gi|158312391|ref|YP_001504899.1| two component LuxR family transcriptional regulator [Frankia sp.
           EAN1pec]
 gi|158107796|gb|ABW09993.1| two component transcriptional regulator, LuxR family [Frankia sp.
           EAN1pec]
          Length = 219

 Score = 39.8 bits (92), Expect = 0.51,   Method: Composition-based stats.
 Identities = 14/56 (25%), Positives = 23/56 (41%), Gaps = 4/56 (7%)

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           R +LTR+   L  RE  +  A        +   +++   +S E VR    R   K+
Sbjct: 143 RELLTRA-DQLTDREAEVLRA---LAEGRSNTEIAAVLNLSVETVRTHVKRILSKL 194


>gi|237794961|ref|YP_002862513.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           Ba4 str. 657]
 gi|229262478|gb|ACQ53511.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           Ba4 str. 657]
          Length = 179

 Score = 39.8 bits (92), Expect = 0.51,   Method: Composition-based stats.
 Identities = 23/101 (22%), Positives = 50/101 (49%), Gaps = 5/101 (4%)

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE--ERKNRRNMLTRSMSVLNPRERRIFEA 245
           AL+    K+  +  D  + D   +    IE E    +N +  L +++  L P E+ + ++
Sbjct: 80  ALLKGEIKHHREIPDENISDKGNEYFFTIEDEIIAYENIKE-LYKALDKLTPEEKEVIDS 138

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             ++ N  +L+ ++S    S   VR  + +A KK+Q+ +++
Sbjct: 139 FYIKNN--SLQEIASYTNKSYNSVRYTKEKAIKKLQKILEE 177


>gi|332653065|ref|ZP_08418810.1| RNA polymerase sigma-H factor [Ruminococcaceae bacterium D16]
 gi|332518211|gb|EGJ47814.1| RNA polymerase sigma-H factor [Ruminococcaceae bacterium D16]
          Length = 212

 Score = 39.8 bits (92), Expect = 0.51,   Method: Composition-based stats.
 Identities = 17/66 (25%), Positives = 29/66 (43%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           LV  + RLV   A      G    ++  EG +GL+ A++ FD  R     TY+   ++  
Sbjct: 37  LVRRYGRLVRACARPLFLAGGDSEDLFQEGMLGLLSAIRGFDARRDASFRTYAEVCVRNR 96

Query: 113 MQEYIL 118
           +   + 
Sbjct: 97  LYSAVR 102


>gi|323652353|gb|ADX98434.1| conserved hypothetical protein [Campylobacter jejuni]
          Length = 67

 Score = 39.8 bits (92), Expect = 0.51,   Method: Composition-based stats.
 Identities = 11/29 (37%), Positives = 17/29 (58%)

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +T E ++ E  +S  RV QI   A KK++
Sbjct: 1   MTFEEIAKELGISLTRVYQIYKHAIKKLR 29


>gi|219856052|ref|YP_002473174.1| hypothetical protein CKR_2709 [Clostridium kluyveri NBRC 12016]
 gi|219569776|dbj|BAH07760.1| hypothetical protein [Clostridium kluyveri NBRC 12016]
          Length = 233

 Score = 39.8 bits (92), Expect = 0.51,   Method: Composition-based stats.
 Identities = 23/103 (22%), Positives = 44/103 (42%), Gaps = 4/103 (3%)

Query: 21  HEI---RKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
           HEI   R   +L+  +  VL +R +  GD SAA  +      +VV I       G  + +
Sbjct: 30  HEIEIYRDYDLLKISKLEVLLERAK-IGDSSAAEEICRRFNGMVVNICRSIYINGYTMED 88

Query: 78  VVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
           ++ EG + L++++  +D    +    Y+   +       I  +
Sbjct: 89  MLQEGRVSLIKSINSYDLNSKYPFPAYAKGAVTKNFYYQIRSN 131


>gi|255013139|ref|ZP_05285265.1| putative RNA polymerase ECF-type sigma factor [Bacteroides sp.
           2_1_7]
          Length = 170

 Score = 39.8 bits (92), Expect = 0.52,   Method: Composition-based stats.
 Identities = 18/92 (19%), Positives = 44/92 (47%), Gaps = 6/92 (6%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
            N    +  L+      E+ L EKE+ +  + ++ +    L   +R++   R +++   +
Sbjct: 80  DNEEALETVLLTTDSSPEKELEEKEDIRRIQELIEQ----LPENQRQVIRLRGIED--CS 133

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            E++     +S   +R + +RA K ++E ++K
Sbjct: 134 YEDIEQITGLSSSNIRTLLSRARKLIREKLEK 165


>gi|254524134|ref|ZP_05136189.1| RNA polymerase sigma-70 factor, ECF subfamily [Stenotrophomonas sp.
           SKA14]
 gi|219721725|gb|EED40250.1| RNA polymerase sigma-70 factor, ECF subfamily [Stenotrophomonas sp.
           SKA14]
          Length = 179

 Score = 39.8 bits (92), Expect = 0.52,   Method: Composition-based stats.
 Identities = 29/135 (21%), Positives = 48/135 (35%), Gaps = 6/135 (4%)

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           L      L   +Q I   +   E V+           +  S++   A    L A + +  
Sbjct: 25  LIRERSALLRRVQRILGGDNGAEDVIQAVWFKARGVDDNQSIDNPRAYLYRLAANLATDH 84

Query: 195 KNSSQWQDWLVYDH-DGQEQVLIEKEERKNRRNMLTRSMS---VLNPRERRIFEARRLQE 250
              S  ++ L+ DH       +I  EE+   ++ L R +     L    R IF   RLQ 
Sbjct: 85  GRESTRRNRLLADHYLWGPDEVISTEEQAMAQDELQRVLDAAGHLPEPTRTIFRLNRLQG 144

Query: 251 NPVTLENLSSEFEVS 265
             +T   ++    VS
Sbjct: 145 --LTQAEIARRLGVS 157


>gi|297467738|ref|XP_002705285.1| PREDICTED: spectrin repeat containing, nuclear envelope 1, partial
            [Bos taurus]
          Length = 7197

 Score = 39.8 bits (92), Expect = 0.52,   Method: Composition-based stats.
 Identities = 28/125 (22%), Positives = 53/125 (42%), Gaps = 5/125 (4%)

Query: 112  AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            A  + + RSW  +K   +  Q+ L+  L R + +  ++   + K E   AI  KL+ S  
Sbjct: 4335 AKLDDLQRSWETLKNVISEKQRTLYEALERQQKYQDSLQSISTKME---AIEMKLSESLE 4391

Query: 172  EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLT 229
            +  S   ++A  ++L   I    +  S+ Q  L  +   +  E    E+   ++   +L 
Sbjct: 4392 QGRSPESQMAEHQALMDEILMLQEEISELQSALADELVSESPESEPAEQLALQSTLTVLA 4451

Query: 230  RSMSV 234
              MS 
Sbjct: 4452 ERMST 4456


>gi|293371468|ref|ZP_06617891.1| sigma-70, region 4 [Bacteroides ovatus SD CMC 3f]
 gi|294808804|ref|ZP_06767534.1| sigma-70, region 4 [Bacteroides xylanisolvens SD CC 1b]
 gi|298482896|ref|ZP_07001078.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D22]
 gi|292633571|gb|EFF52131.1| sigma-70, region 4 [Bacteroides ovatus SD CMC 3f]
 gi|294443976|gb|EFG12713.1| sigma-70, region 4 [Bacteroides xylanisolvens SD CC 1b]
 gi|298270868|gb|EFI12447.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D22]
          Length = 196

 Score = 39.8 bits (92), Expect = 0.52,   Method: Composition-based stats.
 Identities = 14/92 (15%), Positives = 34/92 (36%), Gaps = 2/92 (2%)

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
                 E  +I  E  K +  +L + ++ L  ++R +   +      ++ E ++    ++
Sbjct: 104 DLEIDIETAIIHSELEKEQLEVLQKELNNLTKQQREVLYLKYY--KKMSPEEIAQVMGLT 161

Query: 266 RERVRQIEARAFKKVQESIQKQVELSSSPPLL 297
              V      A   ++E + K   L  +  L 
Sbjct: 162 SRTVYNTTHMAISSLRERMSKSFLLLVAANLW 193


>gi|255011218|ref|ZP_05283344.1| RNA polymerase ECF-type sigma factor [Bacteroides fragilis 3_1_12]
 gi|313149030|ref|ZP_07811223.1| RNA polymerase ECF-type sigma factor [Bacteroides fragilis 3_1_12]
 gi|313137797|gb|EFR55157.1| RNA polymerase ECF-type sigma factor [Bacteroides fragilis 3_1_12]
          Length = 192

 Score = 39.8 bits (92), Expect = 0.52,   Method: Composition-based stats.
 Identities = 10/39 (25%), Positives = 23/39 (58%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           E+ +IE E+  ++++ +   ++ L+PR+R I   R  + 
Sbjct: 113 EEKIIETEDETSQKHTVAHLLNTLSPRQREIIYYRFFEG 151


>gi|189219175|ref|YP_001939816.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Methylacidiphilum infernorum V4]
 gi|189186033|gb|ACD83218.1| DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32)
           [Methylacidiphilum infernorum V4]
          Length = 330

 Score = 39.8 bits (92), Expect = 0.52,   Method: Composition-based stats.
 Identities = 19/84 (22%), Positives = 37/84 (44%), Gaps = 3/84 (3%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
             L+   + L+ ++             V+S+G IG  +A++K++P        Y+ +WIK
Sbjct: 127 EPLIVKGVELIKRVVK--TNNPNIKEAVLSDGIIGFYKALEKYNPSLSTPFPPYAQYWIK 184

Query: 111 AAMQEYILRSWSLVKIGTTANQKR 134
             +    LR    V+I +   +K 
Sbjct: 185 NEVATEALR-SKTVQISSYQKKKN 207


>gi|324325824|gb|ADY21084.1| RNA polymerase factor sigma-70 [Bacillus thuringiensis serovar
           finitimus YBT-020]
          Length = 188

 Score = 39.8 bits (92), Expect = 0.53,   Method: Composition-based stats.
 Identities = 10/59 (16%), Positives = 24/59 (40%), Gaps = 2/59 (3%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           H   E+   ++      R  L   ++ L P ++++F  + L       E +  +  ++R
Sbjct: 104 HISTEKSAEDELIVMEDREELLNLINQLEPLDQKVFIMKYLLGMKT--EEIGDKLGLTR 160


>gi|320100525|ref|YP_004176117.1| DNA-binding protein, Tfx family [Desulfurococcus mucosus DSM 2162]
 gi|319752877|gb|ADV64635.1| DNA binding protein, Tfx family [Desulfurococcus mucosus DSM 2162]
          Length = 145

 Score = 39.8 bits (92), Expect = 0.53,   Method: Composition-based stats.
 Identities = 11/46 (23%), Positives = 21/46 (45%), Gaps = 3/46 (6%)

Query: 236 NPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             R+  + + R      +T E ++    V+R  V  IE  A +K++
Sbjct: 16  TERQYLVLKYR---AQGLTQEEVAGILGVARSTVAAIERAALRKLR 58


>gi|302382279|ref|YP_003818102.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Brevundimonas
           subvibrioides ATCC 15264]
 gi|302192907|gb|ADL00479.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Brevundimonas
           subvibrioides ATCC 15264]
          Length = 184

 Score = 39.8 bits (92), Expect = 0.53,   Method: Composition-based stats.
 Identities = 25/164 (15%), Positives = 58/164 (35%), Gaps = 10/164 (6%)

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           V I     Q+       R +       ++ L+   +  ++   + + +E  +   RLA +
Sbjct: 18  VLIPVYLEQRDALARFLRARLGSDTDIEDLLQDLYLKIVSLDPDYAVTEPRAFLYRLASN 77

Query: 184 ESLN-------ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
             L+       A +  +             D +          +R+  R +LT  +  L 
Sbjct: 78  LLLDRARSGRRARVRDTAWRQVAHHSEGAEDVNDSPSAETAVMDRQRLRGLLTT-LDTLP 136

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            R R IF   +   + ++   +++   +SR  V +    A +++
Sbjct: 137 ERTRSIFRMHKF--DGLSYAEVAATLGISRSSVEKHMMEALRRL 178


>gi|188586508|ref|YP_001918053.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|179351195|gb|ACB85465.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 206

 Score = 39.8 bits (92), Expect = 0.53,   Method: Composition-based stats.
 Identities = 27/191 (14%), Positives = 71/191 (37%), Gaps = 8/191 (4%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           ++G L A   LV  + + V  +   + G     +++  E  I +  ++ KF        +
Sbjct: 16  QNGHLDAFEELVHKYHQKVYSLCYRFSGNHDDANDLAQEAFIRVYHSINKFH--FKSAFS 73

Query: 103 TYSMWWIKAAMQEYILRSWSLVKI----GTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ 158
           T+          + + +      +        +   L+FNL   K + + + +     E 
Sbjct: 74  TWLYRVTSNVCLDEMRKRKRKSSVSLDSPMETDDGELYFNLPDQKFNPELMAERKDVQEI 133

Query: 159 VVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           V    ++L   + + +++  R     S + +    + +    +  L    +  +++L++K
Sbjct: 134 VHKAIQEL--PKDQKLTLLLREMEGFSYDEMAEVMNVSVGTVKSRLSRARNNLKEILVQK 191

Query: 219 EERKNRRNMLT 229
            E    ++ L 
Sbjct: 192 TELFPDKSHLK 202


>gi|313145458|ref|ZP_07807651.1| RNA polymerase ECF-type sigma factor [Bacteroides fragilis 3_1_12]
 gi|313134225|gb|EFR51585.1| RNA polymerase ECF-type sigma factor [Bacteroides fragilis 3_1_12]
          Length = 182

 Score = 39.8 bits (92), Expect = 0.53,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 38/73 (52%), Gaps = 2/73 (2%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E  + ++ +  + +  + + +S L PR++ +F   R  E  ++ + +++   +S + V +
Sbjct: 103 EYDIEDEMDAADLQAYIKKLISELTPRQQEVFHLSR--EEHLSYKEIATRLSISEKTVER 160

Query: 272 IEARAFKKVQESI 284
               A K ++++I
Sbjct: 161 HINEALKFLRKNI 173


>gi|297156256|gb|ADI05968.1| ECF subfamily RNA polymerase sigma factor [Streptomyces
           bingchenggensis BCW-1]
          Length = 182

 Score = 39.8 bits (92), Expect = 0.54,   Method: Composition-based stats.
 Identities = 13/61 (21%), Positives = 26/61 (42%), Gaps = 2/61 (3%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              R  + R+++ L  R+R +   R  ++ P     ++     S   VR    RA  K++
Sbjct: 99  AELRIQMRRALARLTARQRSMLVLRYFEDCPEG--EVAELLGCSVGTVRSTTHRALAKLR 156

Query: 282 E 282
           +
Sbjct: 157 K 157


>gi|194366163|ref|YP_002028773.1| ECF subfamily RNA polymerase sigma-24 subunit [Stenotrophomonas
           maltophilia R551-3]
 gi|194348967|gb|ACF52090.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Stenotrophomonas
           maltophilia R551-3]
          Length = 169

 Score = 39.8 bits (92), Expect = 0.54,   Method: Composition-based stats.
 Identities = 11/67 (16%), Positives = 26/67 (38%), Gaps = 2/67 (2%)

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
             D  ++       +  ++     +   L   ++ L PR R++F   R+    + L  + 
Sbjct: 85  LDDAQLHAIADPAPLPEQRLLDAEQLRHLDAIIAALPPRSRQVFLLARV--EQMALAEIG 142

Query: 260 SEFEVSR 266
            +  +SR
Sbjct: 143 RQLGISR 149


>gi|60683036|ref|YP_213180.1| putative RNA polymerase sigma factor [Bacteroides fragilis NCTC
           9343]
 gi|60494470|emb|CAH09266.1| putative RNA polymerase sigma factor [Bacteroides fragilis NCTC
           9343]
          Length = 192

 Score = 39.8 bits (92), Expect = 0.54,   Method: Composition-based stats.
 Identities = 11/39 (28%), Positives = 23/39 (58%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           E+ LIE E+  ++++ +   ++ L+PR+R I   R  + 
Sbjct: 113 EEKLIETEDETSQKHTVAHLLNTLSPRQREIIYYRFFEG 151


>gi|255596701|ref|XP_002536595.1| conserved hypothetical protein [Ricinus communis]
 gi|223519148|gb|EEF25787.1| conserved hypothetical protein [Ricinus communis]
          Length = 271

 Score = 39.8 bits (92), Expect = 0.54,   Method: Composition-based stats.
 Identities = 18/90 (20%), Positives = 37/90 (41%), Gaps = 5/90 (5%)

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRS---MSVLNPRERRIFEARRLQENPVTLEN 257
              + +D D   +   +   R + R  L  +   +  L  R R IF  RR+    +T+  
Sbjct: 183 DQHVPFDPDRHGETDDDPAGRLDARETLRAASAALLTLPERTRTIFVLRRI--EGMTVRE 240

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++    +S   V +  A+A +++   +  Q
Sbjct: 241 IAGRLGISGSAVEKHVAKALERLLAQMGDQ 270


>gi|47564873|ref|ZP_00235917.1| conserved hypothetical protein protein [Bacillus cereus G9241]
 gi|47558246|gb|EAL16570.1| conserved hypothetical protein protein [Bacillus cereus G9241]
          Length = 176

 Score = 39.8 bits (92), Expect = 0.54,   Method: Composition-based stats.
 Identities = 16/103 (15%), Positives = 41/103 (39%), Gaps = 6/103 (5%)

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR----NMLTRSMSVLNPRERR 241
           L+  I +  +N +   D +  D      +  EK++   +      +L   +S+L+ ++  
Sbjct: 72  LDKPITNEGENHTTILDLMSDDLTDITYMQFEKKQTHLKEHITDELLYEGLSLLSKKQLE 131

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           I     + +     + +S    VS + +     +A K ++  +
Sbjct: 132 ILNLYYVHQYNN--KQISRILSVSEQTISYNHKKALKTLKSQL 172


>gi|317970593|ref|ZP_07971983.1| RNA polymerase sigma factor, sigma-70 family protein [Synechococcus
           sp. CB0205]
          Length = 68

 Score = 39.8 bits (92), Expect = 0.55,   Method: Composition-based stats.
 Identities = 12/65 (18%), Positives = 34/65 (52%), Gaps = 2/65 (3%)

Query: 231 SMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            +  L   + R+ + R   +   P++L +++   E+SR+R R +E +A ++++   ++  
Sbjct: 4   LLDQLPDLQGRVLKMRYGIDVEEPMSLSSIARALEMSRDRARSLERKAHEELRRRSEEMH 63

Query: 289 ELSSS 293
              ++
Sbjct: 64  AYLAA 68


>gi|254383055|ref|ZP_04998410.1| hypothetical protein SSAG_02712 [Streptomyces sp. Mg1]
 gi|194341955|gb|EDX22921.1| hypothetical protein SSAG_02712 [Streptomyces sp. Mg1]
          Length = 159

 Score = 39.8 bits (92), Expect = 0.55,   Method: Composition-based stats.
 Identities = 13/76 (17%), Positives = 36/76 (47%), Gaps = 3/76 (3%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E  +    +  ++   +  +++ L  R+R++        +  T+  ++ E E+++E VRQ
Sbjct: 83  ESHVPTNIQLSDQEREVYSALAELPARQRQVMAWFY---DGYTVAEIAEELEITKESVRQ 139

Query: 272 IEARAFKKVQESIQKQ 287
              RA   ++  + ++
Sbjct: 140 NLCRARVTLKARLSRE 155


>gi|266618988|ref|ZP_06111923.1| putative RNA polymerase sigma factor [Clostridium botulinum Bf]
 gi|263529105|gb|EEZ28458.1| putative RNA polymerase sigma factor [Clostridium botulinum Bf]
          Length = 122

 Score = 39.8 bits (92), Expect = 0.55,   Method: Composition-based stats.
 Identities = 23/101 (22%), Positives = 50/101 (49%), Gaps = 5/101 (4%)

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE--ERKNRRNMLTRSMSVLNPRERRIFEA 245
           AL+    K+  +  D  + D   +    IE E    +N +  L +++  L P E+ + ++
Sbjct: 23  ALLKGEIKHHREIPDENISDKGNEYFFTIEDEIIAYENIKE-LYKALDKLTPEEKEVIDS 81

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             ++ N  +L+ ++S    S   VR  + +A KK+Q+ +++
Sbjct: 82  FYIKNN--SLQEIASYTNKSYNSVRYTKEKAIKKLQKILEE 120


>gi|255528209|ref|ZP_05395031.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           carboxidivorans P7]
 gi|255508104|gb|EET84522.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           carboxidivorans P7]
          Length = 181

 Score = 39.8 bits (92), Expect = 0.55,   Method: Composition-based stats.
 Identities = 15/89 (16%), Positives = 37/89 (41%), Gaps = 2/89 (2%)

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           +K  S   +            + E+  +K +   L  ++ +L+   + I   R L+E   
Sbjct: 88  EKRHSNRLELKEDLAYSNCDNVFEEVHKKLQEEALKSNLEMLDEDSKEIIVRRYLKEE-- 145

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +L+ +S+   +++  +     R  KK++ 
Sbjct: 146 SLDEISANLGINKSAISNRLLRIRKKLKH 174


>gi|255035206|ref|YP_003085827.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Dyadobacter
           fermentans DSM 18053]
 gi|254947962|gb|ACT92662.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Dyadobacter
           fermentans DSM 18053]
          Length = 195

 Score = 39.8 bits (92), Expect = 0.55,   Method: Composition-based stats.
 Identities = 12/69 (17%), Positives = 33/69 (47%), Gaps = 2/69 (2%)

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
           LI++E    +   L   ++ L+ R++ +   R  Q   ++ E ++    +SR+ V  +  
Sbjct: 125 LIDEEHEIYQVRKLEGILNSLSGRQKELIYLRFYQ--SLSFEQIAEVMNLSRQSVYNLLQ 182

Query: 275 RAFKKVQES 283
           ++   +++ 
Sbjct: 183 KSLGSLRKH 191


>gi|284989787|ref|YP_003408341.1| ECF subfamily RNA polymerase sigma-24 subunit [Geodermatophilus
           obscurus DSM 43160]
 gi|284063032|gb|ADB73970.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Geodermatophilus
           obscurus DSM 43160]
          Length = 196

 Score = 39.8 bits (92), Expect = 0.55,   Method: Composition-based stats.
 Identities = 22/134 (16%), Positives = 52/134 (38%), Gaps = 21/134 (15%)

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           +   +A  L  +   V     R  G E L       D+       +   D DG E     
Sbjct: 66  EPEHVAGWLKTTAHRVCLQVIRQGGREQLTD--WDEDRGPVSGARYDGPDEDGPEA---- 119

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV-------SRERVR 270
              R+  + ++ R+++ L  R +++ E   +   P++ +++S+   +       +R R+ 
Sbjct: 120 AALRREHQVLVRRALAALPDRHQQLMEL-LIASPPISYQDISARLGMPVGSIGPTRARI- 177

Query: 271 QIEARAFKKVQESI 284
                   +++E++
Sbjct: 178 ------LARLREAL 185


>gi|221370105|ref|YP_002521201.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Rhodobacter
           sphaeroides KD131]
 gi|221163157|gb|ACM04128.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Rhodobacter
           sphaeroides KD131]
          Length = 173

 Score = 39.8 bits (92), Expect = 0.55,   Method: Composition-based stats.
 Identities = 27/143 (18%), Positives = 51/143 (35%), Gaps = 7/143 (4%)

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSS 198
           RL  HL          + V+  A        +V  M+   A  G    N  I+       
Sbjct: 20  RLSRHLTRRPGTLCDAQDVMQDAWLRLAKVQDVEEMSSPAAYVGQVVRNLAIDRLRAQRV 79

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS---MSVLNPRERRIFEARRLQENPVTL 255
           + + +   +   Q   L   E   + R  L R    ++ L PR+R++F   +      + 
Sbjct: 80  RERHFTAAEVHDQPADLPSAERIVDFRQRLARLEEIVAELPPRQRQVFLLHKFDGLSHS- 138

Query: 256 ENLSSEFEVSRERVRQIEARAFK 278
             +++   +SR  V ++  +A  
Sbjct: 139 -EIAARLGISRSAVEKLIMKALA 160


>gi|254507468|ref|ZP_05119602.1| RNA polymerase sigma factor RpoE [Vibrio parahaemolyticus 16]
 gi|219549538|gb|EED26529.1| RNA polymerase sigma factor RpoE [Vibrio parahaemolyticus 16]
          Length = 192

 Score = 39.8 bits (92), Expect = 0.55,   Method: Composition-based stats.
 Identities = 20/88 (22%), Positives = 33/88 (37%), Gaps = 3/88 (3%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
            VL +R + +GD  A + LVT +   V  +   Y      + +V  E  I   +A+  F 
Sbjct: 8   QVLIERVQ-NGDKQAFNLLVTKYQNKVCNLISRYVNNPGDVPDVAQEAFIKAYRAIPSFR 66

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWS 122
            E      T+         + YI+    
Sbjct: 67  GE--SAFYTWLYRIAVNTAKNYIVAQGR 92


>gi|254437051|ref|ZP_05050545.1| conserved hypothetical protein TIGR02302 [Octadecabacter
           antarcticus 307]
 gi|198252497|gb|EDY76811.1| conserved hypothetical protein TIGR02302 [Octadecabacter
           antarcticus 307]
          Length = 865

 Score = 39.8 bits (92), Expect = 0.55,   Method: Composition-based stats.
 Identities = 23/133 (17%), Positives = 46/133 (34%), Gaps = 13/133 (9%)

Query: 138 NLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS 197
            L R +  L+    N    E++  + ++L  + ++ + M  + A           +++ S
Sbjct: 493 RLERAQERLEEAMRNGASDEEIAELMQELREAMNDYMQMLAQNAEPNPNGTDQPDNNQES 552

Query: 198 SQWQDWLVYDHDGQEQVLIEK---EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
           +      +     + Q L+E+    E       L   M  L     R+ E       P T
Sbjct: 553 NNISQDELQAMMDRIQELMEEGRMAEAMELMEQLNELMENL-----RVTEGEGGDGGPQT 607

Query: 255 L-----ENLSSEF 262
           L     E+L+   
Sbjct: 608 LGQQSMEDLAETL 620


>gi|331027981|ref|YP_004421531.1| RNA polymerase sigma factor SigF [Synechococcus phage S-CBS2]
 gi|294805594|gb|ADF42433.1| RNA polymerase sigma factor SigF [Synechococcus phage S-CBS2]
          Length = 206

 Score = 39.8 bits (92), Expect = 0.56,   Method: Composition-based stats.
 Identities = 19/142 (13%), Positives = 47/142 (33%), Gaps = 20/142 (14%)

Query: 50  AHRLVTSHLRLVVKIAMG-YRGYGLPISEVVSEGNIGLMQAVKKFDPE-------RGFRL 101
             +L   +L L  + A    R  G+    + S    GL +A  ++D         +  + 
Sbjct: 14  QQKLAADNLNLARREAWRIQRSTGIDYHTLESVAFEGLCKAAYRYDASRPHPVTGKSMKF 73

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
           ++ ++  I+  +  ++        +  +   +  +   R+L            +    + 
Sbjct: 74  SSLAIPTIRGELLHWVRD--RTYSMRLSHKMRERWVKGRKL----------LYRGSTDIE 121

Query: 162 IAKKLNVSESEVISMNCRLAGD 183
           IA  L +   E   +    +G 
Sbjct: 122 IAASLGILLEEWQEVRKVCSGP 143


>gi|295099034|emb|CBK88123.1| RNA polymerase sigma factor, sigma-70 family [Eubacterium
           cylindroides T2-87]
          Length = 206

 Score = 39.8 bits (92), Expect = 0.56,   Method: Composition-based stats.
 Identities = 9/71 (12%), Positives = 31/71 (43%), Gaps = 2/71 (2%)

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           +  +    R +L   +  L  R++ +      +E  +  ++++    + ++ V  +  RA
Sbjct: 136 DFVDDVIDREILNALIKELTERQKTVLNLVYFEE--MRQQDVADYLGIKQQSVNDLLNRA 193

Query: 277 FKKVQESIQKQ 287
            K +++  + +
Sbjct: 194 LKTMKKKAENE 204


>gi|223935178|ref|ZP_03627096.1| putative RNA polymerase, sigma 70 family subunit [bacterium
           Ellin514]
 gi|223896062|gb|EEF62505.1| putative RNA polymerase, sigma 70 family subunit [bacterium
           Ellin514]
          Length = 504

 Score = 39.8 bits (92), Expect = 0.56,   Method: Composition-based stats.
 Identities = 12/88 (13%), Positives = 35/88 (39%), Gaps = 13/88 (14%)

Query: 207 DHDGQEQVLIEKEERKNRRN---MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           + +   Q ++ + + +       +L  ++  L  +E      R  +     L+ + +   
Sbjct: 96  EQESHMQSILNESDSEVWTQIAPLLDEALDCLGEKEHNAIVLRFFEGKD--LKQVGASLG 153

Query: 264 V----SRERVRQIEARAFKKVQESIQKQ 287
           +    +R RV     RA +K+++   ++
Sbjct: 154 MREDAARMRV----NRAVEKLRKFFARK 177


>gi|303239875|ref|ZP_07326398.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302592585|gb|EFL62310.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 245

 Score = 39.4 bits (91), Expect = 0.57,   Method: Composition-based stats.
 Identities = 15/81 (18%), Positives = 36/81 (44%), Gaps = 3/81 (3%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM---QAVKKFDPERGF 99
           ++GD     R ++ +   ++K             E   E +IGL+   +A++K++ +R  
Sbjct: 24  KNGDKLLKDRFISDYRPFIIKSVSKVLNNKFIDIENSEEYSIGLIAFNEAIEKYNEDRKC 83

Query: 100 RLATYSMWWIKAAMQEYILRS 120
               +S   I+  + +Y  ++
Sbjct: 84  SFKKFSYQVIQRRLIDYRRKN 104


>gi|300726924|ref|ZP_07060349.1| ECF-type sigma factor [Prevotella bryantii B14]
 gi|299775799|gb|EFI72384.1| ECF-type sigma factor [Prevotella bryantii B14]
          Length = 187

 Score = 39.4 bits (91), Expect = 0.57,   Method: Composition-based stats.
 Identities = 15/72 (20%), Positives = 32/72 (44%), Gaps = 2/72 (2%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E   +E+E+  +++N +   M  L PR+R   +   L E     + +     ++   VR 
Sbjct: 116 ETDYLEEEKSLHQKNKVAYLMEALTPRQREALQLYYLDEKKY--DEICQIMNMNYHSVRN 173

Query: 272 IEARAFKKVQES 283
           +  R   K++ +
Sbjct: 174 LVHRGMLKLRAA 185


>gi|167463893|ref|ZP_02328982.1| hypothetical protein Plarl_15249 [Paenibacillus larvae subsp.
           larvae BRL-230010]
 gi|322382042|ref|ZP_08055981.1| alternative sigma factor-like protein [Paenibacillus larvae subsp.
           larvae B-3650]
 gi|321153993|gb|EFX46334.1| alternative sigma factor-like protein [Paenibacillus larvae subsp.
           larvae B-3650]
          Length = 204

 Score = 39.4 bits (91), Expect = 0.57,   Method: Composition-based stats.
 Identities = 11/67 (16%), Positives = 31/67 (46%), Gaps = 2/67 (2%)

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
           + E      +L  ++  L  +E+ +  A  + +   T   ++   +VS++ V +   +A 
Sbjct: 125 QLEDMVTNEVLHEAIQQLTGKEKSVLLASYVWDYSDT--EIARLNKVSQQSVSKTRLKAL 182

Query: 278 KKVQESI 284
            K+++ +
Sbjct: 183 SKLRKYL 189


>gi|152966582|ref|YP_001362366.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Kineococcus
           radiotolerans SRS30216]
 gi|151361099|gb|ABS04102.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Kineococcus
           radiotolerans SRS30216]
          Length = 270

 Score = 39.4 bits (91), Expect = 0.58,   Method: Composition-based stats.
 Identities = 23/161 (14%), Positives = 62/161 (38%), Gaps = 8/161 (4%)

Query: 142 LKGHLQAITDNNLKPEQVVAIAK-KLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
           L+  L+    +  + ++  A A+  +  + ++      R   + +L+ L    ++ S   
Sbjct: 57  LQDTLERTYLHWRRVQEPAAYARTVMVRAVTDRWRRRGRRPREVTLDGL--WPEQGSGHD 114

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
                 +      +  +  ER   ++    ++  L+PR+R +   R  ++   T   ++ 
Sbjct: 115 IAAPGSNRRTSHDISHDTAERYAEQDEAVTALRQLSPRQRAVLVLRYYED--WTEAQIAD 172

Query: 261 EFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQKPR 301
               S   V+   +R   ++++ +       + PP  + PR
Sbjct: 173 ALNCSTGTVKTQASRGLSRLRQLLDTS---RADPPGSEPPR 210


>gi|323344606|ref|ZP_08084830.1| hypothetical protein HMPREF0663_11366 [Prevotella oralis ATCC
           33269]
 gi|323093876|gb|EFZ36453.1| hypothetical protein HMPREF0663_11366 [Prevotella oralis ATCC
           33269]
          Length = 149

 Score = 39.4 bits (91), Expect = 0.58,   Method: Composition-based stats.
 Identities = 16/67 (23%), Positives = 29/67 (43%), Gaps = 4/67 (5%)

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR-QIEA 274
            E  ER      L  ++  L PR R++F   +          +++E  +S   V  QI +
Sbjct: 72  EEAAERSLHEAELWTAIDSLPPRCRQVFIMSKRDNKKY--REIAAELGISERTVEHQI-S 128

Query: 275 RAFKKVQ 281
           +A K ++
Sbjct: 129 KALKVLR 135


>gi|295085717|emb|CBK67240.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase
           sigma-70 factor, Bacteroides expansion family 1
           [Bacteroides xylanisolvens XB1A]
          Length = 210

 Score = 39.4 bits (91), Expect = 0.58,   Method: Composition-based stats.
 Identities = 19/84 (22%), Positives = 38/84 (45%), Gaps = 2/84 (2%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           +Y    +  V  E  E+  R   ++++M  L P  R I E   +Q      + ++ E  +
Sbjct: 120 IYSELTKSYVETEYLEQDERMMHISKAMEKLTPHTRHILEECYIQRKKY--QEVAEELNI 177

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           S   VR+   +A + ++E   K++
Sbjct: 178 SVSAVRKHIVKALQVIREECAKKI 201


>gi|256005415|ref|ZP_05430379.1| RNA polymerase, sigma 28 subunit, SigI [Clostridium thermocellum
           DSM 2360]
 gi|281417119|ref|ZP_06248139.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           thermocellum JW20]
 gi|255990641|gb|EEU00759.1| RNA polymerase, sigma 28 subunit, SigI [Clostridium thermocellum
           DSM 2360]
 gi|281408521|gb|EFB38779.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Clostridium
           thermocellum JW20]
          Length = 253

 Score = 39.4 bits (91), Expect = 0.59,   Method: Composition-based stats.
 Identities = 18/79 (22%), Positives = 35/79 (44%), Gaps = 4/79 (5%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM---QAVKKFDPERGFRL 101
           GD+    + +  +   ++KI     G  +   EV  E ++GLM   +A+  F+PE     
Sbjct: 32  GDIELKEKFIKKYKPYLLKIISSTLGRYVDP-EVSEEYSVGLMAFNEAIDGFNPEINGNF 90

Query: 102 ATYSMWWIKAAMQEYILRS 120
             Y    +   + +YI ++
Sbjct: 91  TNYCNMVVNHRIIDYIRKN 109


>gi|256424500|ref|YP_003125153.1| LuxR family transcriptional regulator [Chitinophaga pinensis DSM
           2588]
 gi|256039408|gb|ACU62952.1| transcriptional regulator, LuxR family [Chitinophaga pinensis DSM
           2588]
          Length = 197

 Score = 39.4 bits (91), Expect = 0.59,   Method: Composition-based stats.
 Identities = 13/75 (17%), Positives = 35/75 (46%), Gaps = 2/75 (2%)

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
             Q   ++ E K     +   ++ L  R ++IF   R  E  +++  ++ +  +S + V+
Sbjct: 106 DSQESTDRLETKELTAKIAAVVAQLPARMQQIFRMSR--EEDLSIAEIARKLNLSEQTVK 163

Query: 271 QIEARAFKKVQESIQ 285
                A ++++ S++
Sbjct: 164 NQLTEALRRMRNSLK 178


>gi|150009581|ref|YP_001304324.1| putative RNA polymerase ECF-type sigma factor [Parabacteroides
           distasonis ATCC 8503]
 gi|298373973|ref|ZP_06983931.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacteroides sp.
           3_1_19]
 gi|149938005|gb|ABR44702.1| putative RNA polymerase ECF-type sigma factor [Parabacteroides
           distasonis ATCC 8503]
 gi|298268341|gb|EFI09996.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacteroides sp.
           3_1_19]
          Length = 170

 Score = 39.4 bits (91), Expect = 0.59,   Method: Composition-based stats.
 Identities = 18/92 (19%), Positives = 44/92 (47%), Gaps = 6/92 (6%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
            N    +  L+      E+ L EKE+ +  + ++ +    L   +R++   R +++   +
Sbjct: 80  DNEEALETVLLTTDSSPEKELEEKEDIRRIQELIEQ----LPENQRQVIRLRGIED--CS 133

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            E++     +S   +R + +RA K ++E ++K
Sbjct: 134 YEDIEQITGLSSSNIRTLLSRARKLIREKLEK 165


>gi|149278638|ref|ZP_01884774.1| RNA polymerase ECF-type sigma factor [Pedobacter sp. BAL39]
 gi|149230633|gb|EDM36016.1| RNA polymerase ECF-type sigma factor [Pedobacter sp. BAL39]
          Length = 196

 Score = 39.4 bits (91), Expect = 0.59,   Method: Composition-based stats.
 Identities = 11/66 (16%), Positives = 31/66 (46%), Gaps = 2/66 (3%)

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
            E   +++ +     ++  L P++++IF   R   + +  + ++ +  +SR  V+     
Sbjct: 112 EESILKEDLQRFTEAALVNLPPQQQQIFRMSRF--DGLNYDEIAEKLNISRNTVKNHLVA 169

Query: 276 AFKKVQ 281
           A K ++
Sbjct: 170 ALKTLR 175


>gi|147678014|ref|YP_001212229.1| putative RNA polymerase sigma factor SigI [Pelotomaculum
           thermopropionicum SI]
 gi|146274111|dbj|BAF59860.1| DNA-directed RNA polymerase specialized sigma subunit
           [Pelotomaculum thermopropionicum SI]
          Length = 244

 Score = 39.4 bits (91), Expect = 0.59,   Method: Composition-based stats.
 Identities = 15/92 (16%), Positives = 33/92 (35%), Gaps = 2/92 (2%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI--SEVVSEGNIGLMQAV 90
           +E     R    G+  A    +      + K+A  + G  L     + ++   I   +A+
Sbjct: 5   QEVEERLREIRKGNSLAREDFLEDCKPFIFKVACRFCGRILDWGRDDELAVALIAFNEAI 64

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +F  + G     Y+   I + + +Y  +   
Sbjct: 65  DRFREDAGVPFPAYARMVINSRLADYRRKEGR 96


>gi|320009954|gb|ADW04804.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Streptomyces
           flavogriseus ATCC 33331]
          Length = 191

 Score = 39.4 bits (91), Expect = 0.60,   Method: Composition-based stats.
 Identities = 11/62 (17%), Positives = 23/62 (37%), Gaps = 2/62 (3%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L+           E    +  R+ L ++M  L  R+R +   R   +  +T   ++    
Sbjct: 109 LLSKPMPDMASAEEGAYDQLERDALIKAMKGLQRRQREVLVLRYFSD--MTEAQVAETLG 166

Query: 264 VS 265
           +S
Sbjct: 167 IS 168


>gi|260771439|ref|ZP_05880364.1| RNA polymerase sigma-70 factor ECF subfamily [Vibrio furnissii CIP
           102972]
 gi|260613565|gb|EEX38759.1| RNA polymerase sigma-70 factor ECF subfamily [Vibrio furnissii CIP
           102972]
          Length = 177

 Score = 39.4 bits (91), Expect = 0.60,   Method: Composition-based stats.
 Identities = 17/99 (17%), Positives = 39/99 (39%), Gaps = 16/99 (16%)

Query: 197 SSQWQDWLVYDHDGQEQVLIE--KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
                   ++  D     L+E    E +  +  + + +  L   ++++  A  L+E P  
Sbjct: 85  EPHVLAEDIWPSDFCPPDLVEHYAPEHEMLKEQVLKFLDTLPEAQQKVVRAVYLEELPH- 143

Query: 255 LENLSSEFEV------SRERVRQIEARAFKKVQESIQKQ 287
            + ++  F +      SR R+      A +K++ SI  +
Sbjct: 144 -QQVAEMFNIPLGTVKSRLRL------AVEKLRTSIDAE 175


>gi|317055548|ref|YP_004104015.1| ECF subfamily RNA polymerase sigma-24 subunit [Ruminococcus albus
           7]
 gi|315447817|gb|ADU21381.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ruminococcus albus
           7]
          Length = 566

 Score = 39.4 bits (91), Expect = 0.61,   Method: Composition-based stats.
 Identities = 19/108 (17%), Positives = 42/108 (38%), Gaps = 8/108 (7%)

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
             +D++     D L  +      V  +     +R   L   +  L P  +         +
Sbjct: 95  FDNDEDMENAMDNLSLNEPIM--VPEDYATDNDRARQLKSMIDSLKPDMKSALVLYYYND 152

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ----KQVELSSSP 294
             +++ +++    ++   V+Q   RA KK++  I+    K + LS+ P
Sbjct: 153 --MSISDVAKTMGITENNVKQKLLRARKKLKSKIEELGGKGIMLSAVP 198


>gi|298251281|ref|ZP_06975084.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297545873|gb|EFH79741.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 422

 Score = 39.4 bits (91), Expect = 0.61,   Method: Composition-based stats.
 Identities = 21/124 (16%), Positives = 44/124 (35%), Gaps = 5/124 (4%)

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           ++        +  K  +    A  L+     V     RL  + +        +  +    
Sbjct: 68  VQETFFEAWRHLEKLREPERFAAWLDGICRNVCKRQARLQANGAHEVPFAGDEDEAGTTD 127

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
              V   D       E+ ER++R+ +L R++  L+   R + E   L E P     ++ +
Sbjct: 128 ---VDTCDPLSIDPEEELERQSRQILLDRALGYLSESARELIELCYLAELP--QREVAQK 182

Query: 262 FEVS 265
            ++S
Sbjct: 183 LDMS 186


>gi|57233909|ref|YP_182059.1| ECF subfamily RNA polymerase sigma factor [Dehalococcoides
           ethenogenes 195]
 gi|57224357|gb|AAW39414.1| RNA polymerase sigma-70 factor, ECF subfamily [Dehalococcoides
           ethenogenes 195]
          Length = 179

 Score = 39.4 bits (91), Expect = 0.61,   Method: Composition-based stats.
 Identities = 22/144 (15%), Positives = 55/144 (38%), Gaps = 9/144 (6%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVV-KIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           E  L +   +  D  A  RL   +   +   IA+   G  +   ++  +  + +++++  
Sbjct: 4   EKRLVE-LAQQKDEHAFARLYEEYFDKIYRYIALK-IGNKMEAEDLTQQVFMNMLRSISS 61

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F  +     + +        + +Y+ +               +   L      ++  T+ 
Sbjct: 62  FKWQDNTPFSAWLYRIAHNQIVDYLRKRSR-----QPVLDIEVVTPLACADDPVE-TTEV 115

Query: 153 NLKPEQVVAIAKKLNVSESEVISM 176
           N+  E+ V ++ KL  ++ EVIS+
Sbjct: 116 NIDYEKFVEVSGKLTPAQQEVISL 139


>gi|302559456|ref|ZP_07311798.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces
           griseoflavus Tu4000]
 gi|302477074|gb|EFL40167.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces
           griseoflavus Tu4000]
          Length = 189

 Score = 39.4 bits (91), Expect = 0.61,   Method: Composition-based stats.
 Identities = 12/62 (19%), Positives = 23/62 (37%), Gaps = 2/62 (3%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L+           E    +  R+ L ++M  L  R+R +   R   +  +T   ++    
Sbjct: 107 LLSKPMPDMASAEEGAYDQLERDSLIKAMKGLQRRQREVLVLRYFAD--MTEAQVAETLG 164

Query: 264 VS 265
           VS
Sbjct: 165 VS 166


>gi|257079621|ref|ZP_05573982.1| predicted protein [Enterococcus faecalis JH1]
 gi|294780901|ref|ZP_06746255.1| sigma-70, region 4 [Enterococcus faecalis PC1.1]
 gi|256987651|gb|EEU74953.1| predicted protein [Enterococcus faecalis JH1]
 gi|294452027|gb|EFG20475.1| sigma-70, region 4 [Enterococcus faecalis PC1.1]
          Length = 134

 Score = 39.4 bits (91), Expect = 0.61,   Method: Composition-based stats.
 Identities = 20/103 (19%), Positives = 46/103 (44%), Gaps = 9/103 (8%)

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           +SL  ++ S    S    D++        +   E E        L+R++  LN +E+++ 
Sbjct: 41  DSLEDIMRSGISESYLSLDFISESEIMNLENFTENE-------ALSRAIEQLNFKEKKLL 93

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             + +Q    +   ++  F++SR+ V     R  KK++  +++
Sbjct: 94  YEKYIQCKTDS--EIARTFDISRQGVSIFRKRLLKKLEVFLKR 134


>gi|309775838|ref|ZP_07670832.1| RNA polymerase sigma factor SigV [Erysipelotrichaceae bacterium
           3_1_53]
 gi|308916376|gb|EFP62122.1| RNA polymerase sigma factor SigV [Erysipelotrichaceae bacterium
           3_1_53]
          Length = 163

 Score = 39.4 bits (91), Expect = 0.62,   Method: Composition-based stats.
 Identities = 11/54 (20%), Positives = 25/54 (46%), Gaps = 2/54 (3%)

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           +E  +++++E       L + +  L+P+ R I   R  ++    LE +S    +
Sbjct: 87  EEDTMLQEQEDILLSEELHQLLFTLDPKTRTIILLRYFEDRK--LEEISDILSL 138


>gi|160934022|ref|ZP_02081409.1| hypothetical protein CLOLEP_02884 [Clostridium leptum DSM 753]
 gi|156866695|gb|EDO60067.1| hypothetical protein CLOLEP_02884 [Clostridium leptum DSM 753]
          Length = 155

 Score = 39.4 bits (91), Expect = 0.62,   Method: Composition-based stats.
 Identities = 17/105 (16%), Positives = 36/105 (34%), Gaps = 3/105 (2%)

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
            + SL  L  S         D     +D     + + E+       L  ++S L  + R 
Sbjct: 40  REVSLEYL-MSETSFEPFTTDTYFEQYDQPTVFVAKGEKTVVASKRLADALSKLTEQRRN 98

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +           T   +  E+  SR      +  A K++++ +++
Sbjct: 99  VLFLYFFFGYTDT--QIGKEYGRSRSTANYWKLAALKQLRKEMER 141


>gi|45594273|gb|AAS68513.1| SigE [Candidatus Pasteuria usgae]
          Length = 88

 Score = 39.4 bits (91), Expect = 0.62,   Method: Composition-based stats.
 Identities = 19/77 (24%), Positives = 35/77 (45%), Gaps = 5/77 (6%)

Query: 177 NCRLAGDESLNALINSS-DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
           N +   + S +  +N   D N     D L  ++D   + + E+ +RK    +L +++  L
Sbjct: 15  NSKTRTEVSFDEPLNIDWDGNELLLSDVLGTENDTIYRNIEEQVDRK----LLHKALDKL 70

Query: 236 NPRERRIFEARRLQENP 252
           + RER I E R    + 
Sbjct: 71  SERERTIMELRFGLSDG 87


>gi|254517800|ref|ZP_05129856.1| predicted protein [Clostridium sp. 7_2_43FAA]
 gi|226911549|gb|EEH96750.1| predicted protein [Clostridium sp. 7_2_43FAA]
          Length = 188

 Score = 39.4 bits (91), Expect = 0.63,   Method: Composition-based stats.
 Identities = 17/78 (21%), Positives = 36/78 (46%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            +HGD  +   ++ +   LV K ++ Y  YG    ++     + ++++V+KF+ +     
Sbjct: 8   AKHGDKKSMEEILKNFEPLVYKTSISYYIYGYSEEDIKQIARLTIIESVEKFNTDLSDSF 67

Query: 102 ATYSMWWIKAAMQEYILR 119
             Y    IK  M + I +
Sbjct: 68  PAYVQKCIKNKMYKEIEK 85


>gi|182437163|ref|YP_001824882.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces griseus
           subsp. griseus NBRC 13350]
 gi|326777789|ref|ZP_08237054.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Streptomyces cf.
           griseus XylebKG-1]
 gi|178465679|dbj|BAG20199.1| putative RNA polymerase ECF-subfamily sigma factor [Streptomyces
           griseus subsp. griseus NBRC 13350]
 gi|326658122|gb|EGE42968.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Streptomyces cf.
           griseus XylebKG-1]
          Length = 191

 Score = 39.4 bits (91), Expect = 0.63,   Method: Composition-based stats.
 Identities = 12/62 (19%), Positives = 23/62 (37%), Gaps = 2/62 (3%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L+           E    +  R+ L ++M  L  R+R +   R   +  +T   ++    
Sbjct: 109 LLSKPMPDMASAEEGAYDQLERDALIKAMKGLQRRQREVLVLRYFAD--MTEAQVAETLG 166

Query: 264 VS 265
           VS
Sbjct: 167 VS 168


>gi|119483330|ref|ZP_01618744.1| hypothetical protein L8106_04736 [Lyngbya sp. PCC 8106]
 gi|119458097|gb|EAW39219.1| hypothetical protein L8106_04736 [Lyngbya sp. PCC 8106]
          Length = 395

 Score = 39.4 bits (91), Expect = 0.63,   Method: Composition-based stats.
 Identities = 21/107 (19%), Positives = 50/107 (46%), Gaps = 11/107 (10%)

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNR-------RNMLTRSMSVLNP 237
           SLN  I  SD ++ +  + L   ++     LI +EE ++R       ++ LT ++  L P
Sbjct: 259 SLN--IAKSDSDTREIVEDLADPNEPMLAELIAEEENQDRQTQQVQLKHTLTTALERLKP 316

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
               I       E  +T ++++ + ++ +  V +   +A + + +++
Sbjct: 317 DVLEILRLYY--EQGLTQQDIAQQLDMKQYTVSRRLTKARETLLKAL 361


>gi|296450888|ref|ZP_06892637.1| region 4 superfamily sigma-70 [Clostridium difficile NAP08]
 gi|296878631|ref|ZP_06902636.1| hypothetical protein HMPREF0219_1159 [Clostridium difficile NAP07]
 gi|296260260|gb|EFH07106.1| region 4 superfamily sigma-70 [Clostridium difficile NAP08]
 gi|296430438|gb|EFH16280.1| hypothetical protein HMPREF0219_1159 [Clostridium difficile NAP07]
          Length = 138

 Score = 39.4 bits (91), Expect = 0.64,   Method: Composition-based stats.
 Identities = 10/68 (14%), Positives = 28/68 (41%), Gaps = 2/68 (2%)

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           + +   + L  ++  L+ R R         E   T   ++    +SR  V Q    + + 
Sbjct: 73  DIRICDDELAEALKHLSERNRENLLMYYFLEMSDT--EIAKRQNISRSGVFQNRHNSLEL 130

Query: 280 VQESIQKQ 287
           +++ ++++
Sbjct: 131 MKKILKEK 138


>gi|296445253|ref|ZP_06887212.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Methylosinus
           trichosporium OB3b]
 gi|296257208|gb|EFH04276.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Methylosinus
           trichosporium OB3b]
          Length = 165

 Score = 39.4 bits (91), Expect = 0.64,   Method: Composition-based stats.
 Identities = 17/74 (22%), Positives = 32/74 (43%), Gaps = 3/74 (4%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           + D    E    E+ E   +  +L  ++  L PR R +FE   L    +++  ++    +
Sbjct: 88  LDDAPSDEAPPEERMEHDRKSRLLDSAVDALPPRCREVFE---LSMEDMSVAEIARRLGI 144

Query: 265 SRERVRQIEARAFK 278
           S   VR+  A A +
Sbjct: 145 SDRMVRKHLAHAMQ 158


>gi|146339253|ref|YP_001204301.1| RNA polymerase ECF-subfamily sigma-70 factor [Bradyrhizobium sp.
           ORS278]
 gi|146192059|emb|CAL76064.1| Putative sigma-70 factor, ECF subfamily [Bradyrhizobium sp. ORS278]
          Length = 250

 Score = 39.4 bits (91), Expect = 0.64,   Method: Composition-based stats.
 Identities = 18/89 (20%), Positives = 43/89 (48%), Gaps = 10/89 (11%)

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           +++  D L+   D +     E EER +   +L R+++ L  R R++    R++  P    
Sbjct: 81  TTEEVDVLLDIPDDRPSPEREIEERSDI-ALLRRALADLPERRRQVLMLSRIEGLPH--R 137

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            ++    V+   VR +E+     ++++++
Sbjct: 138 EIAQRMGVT---VRTVESD----LKQAVE 159


>gi|256838300|ref|ZP_05543810.1| conserved hypothetical protein [Parabacteroides sp. D13]
 gi|256739219|gb|EEU52543.1| conserved hypothetical protein [Parabacteroides sp. D13]
          Length = 171

 Score = 39.4 bits (91), Expect = 0.64,   Method: Composition-based stats.
 Identities = 18/92 (19%), Positives = 44/92 (47%), Gaps = 6/92 (6%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
            N    +  L+      E+ L EKE+ +  + ++ +    L   +R++   R +++   +
Sbjct: 81  DNEEALETVLLTTDSSPEKELEEKEDIRRIQELIEQ----LPENQRQVIRLRGIED--CS 134

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
            E++     +S   +R + +RA K ++E ++K
Sbjct: 135 YEDIEQITGLSSSNIRTLLSRARKLIREKLEK 166


>gi|218281912|ref|ZP_03488244.1| hypothetical protein EUBIFOR_00812 [Eubacterium biforme DSM 3989]
 gi|218217055|gb|EEC90593.1| hypothetical protein EUBIFOR_00812 [Eubacterium biforme DSM 3989]
          Length = 206

 Score = 39.4 bits (91), Expect = 0.64,   Method: Composition-based stats.
 Identities = 9/71 (12%), Positives = 32/71 (45%), Gaps = 2/71 (2%)

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           +  +    R +L   +  L  R++ +      +E  +  ++++    + ++ V  + +RA
Sbjct: 136 DFVDDVIDREILNALIKELTERQKTVLNLVYFEE--MRQQDIADYLGIKQQSVNDLLSRA 193

Query: 277 FKKVQESIQKQ 287
            K +++  + +
Sbjct: 194 LKTMKKKAENE 204


>gi|296444845|ref|ZP_06886808.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Methylosinus
           trichosporium OB3b]
 gi|296257793|gb|EFH04857.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Methylosinus
           trichosporium OB3b]
          Length = 166

 Score = 39.4 bits (91), Expect = 0.65,   Method: Composition-based stats.
 Identities = 19/84 (22%), Positives = 37/84 (44%), Gaps = 6/84 (7%)

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           D L+      E  L  +E     R     ++  L PR R++F  RR +      E ++  
Sbjct: 89  DALLAPSLSPEARLDAEETLARFRA----ALDALPPRCRQVFVMRRFENLH--QEEIARR 142

Query: 262 FEVSRERVRQIEARAFKKVQESIQ 285
             +SR  V +    AF++++ +++
Sbjct: 143 LGISRNMVEKHLRTAFRQLRGALK 166


>gi|37521333|ref|NP_924710.1| RNA polymerase sigma factor [Gloeobacter violaceus PCC 7421]
 gi|35212330|dbj|BAC89705.1| glr1764 [Gloeobacter violaceus PCC 7421]
          Length = 197

 Score = 39.4 bits (91), Expect = 0.65,   Method: Composition-based stats.
 Identities = 13/85 (15%), Positives = 34/85 (40%), Gaps = 12/85 (14%)

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS--- 265
           +      +E          +  ++  L+P  RR+ E    +E  ++   ++ +   +   
Sbjct: 119 ETSPVTPMESASINECSQAVRDALEKLSPNHRRVLEMSYFKE--LSQREIAEKLG-TPLG 175

Query: 266 --RERVRQIEARAFKKVQESIQKQV 288
             +  VR    R   +++E++Q+ V
Sbjct: 176 TVKSWVR----RGLSELKETLQEYV 196


>gi|228968725|ref|ZP_04129692.1| Prophage LambdaBa01, positive control factor Xpf [Bacillus
           thuringiensis serovar sotto str. T04001]
 gi|228790955|gb|EEM38589.1| Prophage LambdaBa01, positive control factor Xpf [Bacillus
           thuringiensis serovar sotto str. T04001]
          Length = 166

 Score = 39.4 bits (91), Expect = 0.65,   Method: Composition-based stats.
 Identities = 17/71 (23%), Positives = 32/71 (45%), Gaps = 2/71 (2%)

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
            +   IE       R  L  ++S L  RE+ I+     + N  ++E +S    V++  V+
Sbjct: 86  WDDKPIENSISHWDRIKLEDALSTLTEREKEIYMM--SKGNCFSMEKVSKILGVTKSTVQ 143

Query: 271 QIEARAFKKVQ 281
               RA +K++
Sbjct: 144 TTLKRADEKIK 154


>gi|167461461|ref|ZP_02326550.1| hypothetical protein Plarl_02683 [Paenibacillus larvae subsp.
           larvae BRL-230010]
          Length = 73

 Score = 39.4 bits (91), Expect = 0.65,   Method: Composition-based stats.
 Identities = 17/68 (25%), Positives = 35/68 (51%), Gaps = 2/68 (2%)

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           E + R ++L ++++ L P+ R+I      QE P   + ++    +S++ + Q   RA KK
Sbjct: 2   EEQIRNDILHQAINQLKPKYRQIIIEFYFQEKPY--KEIAQRLGLSQQALAQTLFRARKK 59

Query: 280 VQESIQKQ 287
           +     K+
Sbjct: 60  LLHYFSKK 67


>gi|323495999|ref|ZP_08101063.1| RNA polymerase sigma factor RpoE [Vibrio sinaloensis DSM 21326]
 gi|323318961|gb|EGA71908.1| RNA polymerase sigma factor RpoE [Vibrio sinaloensis DSM 21326]
          Length = 192

 Score = 39.4 bits (91), Expect = 0.66,   Method: Composition-based stats.
 Identities = 19/88 (21%), Positives = 32/88 (36%), Gaps = 3/88 (3%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
            VL +R + +GD  A + LV  +   V  +   Y      + +V  E  I   +A+  F 
Sbjct: 8   QVLIERVQ-NGDKQAFNLLVMRYQNKVCNLISRYVNNPGDVPDVAQEAFIKAYRAIPSFR 66

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWS 122
            E      T+         + YI+    
Sbjct: 67  GE--SAFYTWLYRIAVNTAKNYIVAQGR 92


>gi|315161696|gb|EFU05713.1| sigma-70, region 4 [Enterococcus faecalis TX0645]
          Length = 134

 Score = 39.4 bits (91), Expect = 0.66,   Method: Composition-based stats.
 Identities = 20/103 (19%), Positives = 47/103 (45%), Gaps = 9/103 (8%)

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           +SL  ++ +S   S    D++        +   E E        L+R++  LN +E+++ 
Sbjct: 41  DSLEDIMRNSISESYLSLDFISESEIMNLENFAENE-------ALSRAIEQLNFKEKKLL 93

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             + +Q    +   ++  F++SR+ V     R  KK++  +++
Sbjct: 94  YEKYIQCKTDS--EIARIFDISRQGVSIFRKRLLKKLEVFLKR 134


>gi|302876749|ref|YP_003845382.1| sigma-70 region 4 domain-containing protein [Clostridium
           cellulovorans 743B]
 gi|307687429|ref|ZP_07629875.1| sigma-70 region 4 domain-containing protein [Clostridium
           cellulovorans 743B]
 gi|302579606|gb|ADL53618.1| sigma-70 region 4 domain protein [Clostridium cellulovorans 743B]
          Length = 201

 Score = 39.4 bits (91), Expect = 0.66,   Method: Composition-based stats.
 Identities = 10/91 (10%), Positives = 39/91 (42%), Gaps = 6/91 (6%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
            +     D++  +     + ++         + L  ++ +L+  E+ + +A     + ++
Sbjct: 85  DSEGNPLDFITDEAVDIAETVVNAVMV----DRLKAALPLLSDSEQELIQAIFF--DGLS 138

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              + +   +++  V + +AR   K+++ I+
Sbjct: 139 EREVGARLGITQSVVNKRKARILIKLRKIIE 169


>gi|329770552|ref|ZP_08261930.1| ATP-dependent protease La [Gemella sanguinis M325]
 gi|328836301|gb|EGF85970.1| ATP-dependent protease La [Gemella sanguinis M325]
          Length = 765

 Score = 39.4 bits (91), Expect = 0.67,   Method: Composition-based stats.
 Identities = 35/209 (16%), Positives = 74/209 (35%), Gaps = 45/209 (21%)

Query: 94  DPERGFRLA--TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITD 151
           D E+       + S + +    +  I        I T   +  L   ++ ++  L+ I+ 
Sbjct: 181 DLEKKASFIDKSISYYLLGHEFKREIDDKVRTN-IDTQQKEYFLREQMKVVQDELKQISP 239

Query: 152 NNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQ 211
                E +     K+N+SE++                            ++ L+ + D  
Sbjct: 240 EEDDIESLRQEILKINLSEND----------------------------KNLLLKEVDRL 271

Query: 212 EQVLIEKEERKNRRNMLTRSMS----VLNPRERRIFEARR-LQENPVTLENLSSEFEVSR 266
           E+  +   E    R  +   ++     L   E  I  A + L ++   LE +       +
Sbjct: 272 EKTPVMSPEHSIIRTYIDTVIALPWNSLTEDEIDIVNAEKVLNDDHYGLEKI-------K 324

Query: 267 ERVRQIEARAFKKVQESIQKQVELSSSPP 295
           ER+  +E  A KK+++ ++  +   S PP
Sbjct: 325 ERI--LEFLAVKKLRDDMKSPILCLSGPP 351


>gi|294673393|ref|YP_003574009.1| RNA polymerase sigma-70 factor family protein [Prevotella
           ruminicola 23]
 gi|294472617|gb|ADE82006.1| RNA polymerase sigma-70 factor family protein [Prevotella
           ruminicola 23]
          Length = 226

 Score = 39.4 bits (91), Expect = 0.67,   Method: Composition-based stats.
 Identities = 16/112 (14%), Positives = 44/112 (39%), Gaps = 6/112 (5%)

Query: 11  NGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRG 70
             +  +  ++ ++     L  ++      R  E G       +V  H+  ++++A  Y  
Sbjct: 13  TADPNVLAFLKDVENKKRLSCKDRQYYLTRLHEPGVDEI---IVNDHIPAIIRVAYSYSQ 69

Query: 71  YGL--PISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS 120
                   ++V EG +G+ + ++++   +G         ++  A+Q  I + 
Sbjct: 70  KTKKLTFLDLVGEGVVGVYKFIERYKHRKGAN-DRLLRRYVIQAIQRVICKQ 120


>gi|116754504|ref|YP_843622.1| putative transcriptional regulator [Methanosaeta thermophila PT]
 gi|116665955|gb|ABK14982.1| sigma-70 region 4 domain protein [Methanosaeta thermophila PT]
          Length = 146

 Score = 39.4 bits (91), Expect = 0.67,   Method: Composition-based stats.
 Identities = 10/51 (19%), Positives = 26/51 (50%), Gaps = 3/51 (5%)

Query: 235 LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           L  R+ ++   RR   + ++ E +++    +R  V  +E RA + +  +++
Sbjct: 7   LTERQIQVLRLRR---SGMSQEEVAALLGTTRANVSILEKRAMQNIDRALE 54


>gi|313204987|ref|YP_004043644.1| RNA polymerase, sigma-24 subunit, ecf subfamily [Paludibacter
           propionicigenes WB4]
 gi|312444303|gb|ADQ80659.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Paludibacter
           propionicigenes WB4]
          Length = 202

 Score = 39.4 bits (91), Expect = 0.67,   Method: Composition-based stats.
 Identities = 9/67 (13%), Positives = 27/67 (40%), Gaps = 2/67 (2%)

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
               D        +E       +  L+ ++  L P++++I+     +E  +  + ++ + 
Sbjct: 107 HFELDSQNNTPEPLELLIDNELKEKLSEAVKQLPPQQQKIYTL--YKEQGIRQDEIAKQL 164

Query: 263 EVSRERV 269
            +SR  +
Sbjct: 165 NLSRSTI 171


>gi|239996158|ref|ZP_04716682.1| RNA polymerase sigma factor RpoE [Alteromonas macleodii ATCC 27126]
 gi|332141905|ref|YP_004427643.1| RNA polymerase sigma factor RpoE [Alteromonas macleodii str. 'Deep
           ecotype']
 gi|327551927|gb|AEA98645.1| RNA polymerase sigma factor RpoE [Alteromonas macleodii str. 'Deep
           ecotype']
          Length = 192

 Score = 39.4 bits (91), Expect = 0.67,   Method: Composition-based stats.
 Identities = 24/145 (16%), Positives = 52/145 (35%), Gaps = 3/145 (2%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD +A + LVT +   V+ +   Y      +++V  E  I   +A+  F  +      
Sbjct: 15  QRGDKNAFNLLVTRYQHKVMHLVSRYVKNTGDVADVTQEAFIKAYRALPNFRGD--SAFY 72

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
           T+       + + Y++         +  +     F         Q+  + +L  E++   
Sbjct: 73  TWLYRIAVNSAKNYLVSQGR-KPPASDVDADEADFYEGSDALKEQSTPERSLLSEEIEET 131

Query: 163 AKKLNVSESEVISMNCRLAGDESLN 187
             K+     + + M   L   E L+
Sbjct: 132 LFKVVEKLPDDLRMAITLREIEGLS 156


>gi|153006814|ref|YP_001381139.1| ECF subfamily RNA polymerase sigma-24 factor [Anaeromyxobacter sp.
           Fw109-5]
 gi|152030387|gb|ABS28155.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Anaeromyxobacter
           sp. Fw109-5]
          Length = 213

 Score = 39.4 bits (91), Expect = 0.67,   Method: Composition-based stats.
 Identities = 30/145 (20%), Positives = 54/145 (37%), Gaps = 18/145 (12%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATY 104
           GD  A   LV  H RLV+ I   Y        ++     +  ++A ++    RG R    
Sbjct: 41  GDDDAFGDLVRRHERLVLSIVRRYARTPEDARDLAQRTFLRALEAARR-TFRRGAR---- 95

Query: 105 SMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPE---QVVA 161
                    + +  R W LV+I     +  L  +LR  +  L A+      P    + + 
Sbjct: 96  ---------EGFPFRRW-LVRIAVNLAKNHLRDDLRVGRVSLDALGAREAHPAVAVEALE 145

Query: 162 IAKKLNVSESEVISMNCRLAGDESL 186
            A++     + V+ +  R+    +L
Sbjct: 146 EAERHAAVRAAVLRLPRRMREVLTL 170


>gi|32141360|gb|AAP74645.1| synaptic nuclear envelope protein [Bos taurus]
          Length = 1594

 Score = 39.4 bits (91), Expect = 0.67,   Method: Composition-based stats.
 Identities = 28/125 (22%), Positives = 53/125 (42%), Gaps = 5/125 (4%)

Query: 112  AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            A  + + RSW  +K   +  Q+ L+  L R + +  ++   + K E   AI  KL+ S  
Sbjct: 977  AKLDDLQRSWETLKNVISEKQRTLYEALERQQKYQDSLQSISTKME---AIEMKLSESLE 1033

Query: 172  EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLT 229
            +  S   ++A  ++L   I    +  S+ Q  L  +   +  E    E+   ++   +L 
Sbjct: 1034 QGRSPESQMAEHQALMDEILMLQEEISELQSALADELVSESPESEPAEQLALQSTLTVLA 1093

Query: 230  RSMSV 234
              MS 
Sbjct: 1094 ERMST 1098


>gi|332830565|gb|EGK03186.1| hypothetical protein HMPREF9455_00756 [Dysgonomonas gadei ATCC
           BAA-286]
          Length = 183

 Score = 39.4 bits (91), Expect = 0.68,   Method: Composition-based stats.
 Identities = 20/86 (23%), Positives = 41/86 (47%), Gaps = 6/86 (6%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L  + D Q+    ++ E K    ++ R++  L  R  +IF   R++      + ++    
Sbjct: 98  LSIEKDEQDATPHQQLEYKELEEVINRTLKQLPDRRLKIFRMHRMEGKKY--KEIAEILS 155

Query: 264 VSRERVRQIEARAFKKVQESIQKQVE 289
           VS   V+ IEA    KV + +++++E
Sbjct: 156 VS---VKTIEAE-MTKVYQLLRQEIE 177


>gi|270294887|ref|ZP_06201088.1| conserved hypothetical protein [Bacteroides sp. D20]
 gi|270274134|gb|EFA19995.1| conserved hypothetical protein [Bacteroides sp. D20]
          Length = 169

 Score = 39.4 bits (91), Expect = 0.68,   Method: Composition-based stats.
 Identities = 16/82 (19%), Positives = 34/82 (41%), Gaps = 2/82 (2%)

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           A+  S  K+S   +     +         EK   K R  ++ R M+ L  ++R I + R 
Sbjct: 67  AIDRSERKDSRTVELTPEMEQASDASGPYEKLVNKERMALIHRLMNRLPEKQRLIMQLR- 125

Query: 248 LQENPVTLENLSSEFEVSRERV 269
                 + + +++   ++ E+V
Sbjct: 126 -DVEGKSYKEIAAVLNLTEEQV 146


>gi|228984107|ref|ZP_04144293.1| RNA polymerase sigma-B factor (Sigma-37) [Bacillus thuringiensis
           serovar tochigiensis BGSC 4Y1]
 gi|228775635|gb|EEM24015.1| RNA polymerase sigma-B factor (Sigma-37) [Bacillus thuringiensis
           serovar tochigiensis BGSC 4Y1]
          Length = 159

 Score = 39.4 bits (91), Expect = 0.68,   Method: Composition-based stats.
 Identities = 16/103 (15%), Positives = 41/103 (39%), Gaps = 6/103 (5%)

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR----NMLTRSMSVLNPRERR 241
           L+  I +  +N +   D +  D      +  EK++   +      +L   +S+L+ ++  
Sbjct: 55  LDKPITNEGENHTTILDLMSDDLTDITYMQFEKKQTHLKEHITDELLYEGLSLLSKKQLE 114

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           I     + +     + +S    VS + +     +A K ++  +
Sbjct: 115 ILNLYYVHQYNN--KQISRILSVSEQTISYNHKKALKTLKSQL 155


>gi|160888522|ref|ZP_02069525.1| hypothetical protein BACUNI_00939 [Bacteroides uniformis ATCC 8492]
 gi|156861836|gb|EDO55267.1| hypothetical protein BACUNI_00939 [Bacteroides uniformis ATCC 8492]
          Length = 169

 Score = 39.4 bits (91), Expect = 0.68,   Method: Composition-based stats.
 Identities = 16/82 (19%), Positives = 34/82 (41%), Gaps = 2/82 (2%)

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           A+  S  K+S   +     +         EK   K R  ++ R M+ L  ++R I + R 
Sbjct: 67  AIDRSERKDSRTVELTPEMEQASDASGPYEKLVNKERMALIHRLMNKLPEKQRLIMQLR- 125

Query: 248 LQENPVTLENLSSEFEVSRERV 269
                 + + +++   ++ E+V
Sbjct: 126 -DVEGKSYKEIAAVLNLTEEQV 146


>gi|312197542|ref|YP_004017603.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Frankia sp. EuI1c]
 gi|311228878|gb|ADP81733.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Frankia sp. EuI1c]
          Length = 206

 Score = 39.4 bits (91), Expect = 0.68,   Method: Composition-based stats.
 Identities = 13/69 (18%), Positives = 35/69 (50%), Gaps = 2/69 (2%)

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
            ++  ++  +R  L ++++ L PR+R +   R + + P    ++++    S   VR   +
Sbjct: 100 AVDHADQLTQRASLIQALATLPPRQRAVVVLRYVDDLPEG--DVAAALGCSVGSVRSQAS 157

Query: 275 RAFKKVQES 283
           R   ++++S
Sbjct: 158 RGLARLRDS 166


>gi|229172449|ref|ZP_04300008.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus MM3]
 gi|228610920|gb|EEK68183.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus MM3]
          Length = 188

 Score = 39.4 bits (91), Expect = 0.68,   Method: Composition-based stats.
 Identities = 16/81 (19%), Positives = 34/81 (41%), Gaps = 10/81 (12%)

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE-- 267
             E+   ++      R  L + ++ L P ++++F  + L       E +  +  ++R   
Sbjct: 106 STEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKT--EEIGDKLGLTRAAI 163

Query: 268 --RVRQIEARAFKKVQESIQK 286
             RV     R  KK+Q++  K
Sbjct: 164 DNRV----YRGKKKLQQNATK 180


>gi|302864576|ref|YP_003833213.1| RNA polymerase sigma-70 factor [Micromonospora aurantiaca ATCC
           27029]
 gi|302567435|gb|ADL43637.1| RNA polymerase sigma-70 factor, sigma-E family [Micromonospora
           aurantiaca ATCC 27029]
          Length = 176

 Score = 39.4 bits (91), Expect = 0.69,   Method: Composition-based stats.
 Identities = 12/68 (17%), Positives = 27/68 (39%), Gaps = 8/68 (11%)

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL--SSEFEVSRERV-RQIEA 274
            +     R  +  ++  L PR+R +   R  ++    L  +  +    V+   V  Q   
Sbjct: 94  ADADAALRLTVRAALDRLPPRQRAVVVLRYFED----LTEVATAEALGVTVGTVKSQCHD 149

Query: 275 RAFKKVQE 282
            A +K+++
Sbjct: 150 -ALRKLRD 156


>gi|293373767|ref|ZP_06620113.1| RNA polymerase sigma-70 factor [Bacteroides ovatus SD CMC 3f]
 gi|292631257|gb|EFF49889.1| RNA polymerase sigma-70 factor [Bacteroides ovatus SD CMC 3f]
          Length = 200

 Score = 39.4 bits (91), Expect = 0.69,   Method: Composition-based stats.
 Identities = 20/90 (22%), Positives = 40/90 (44%), Gaps = 2/90 (2%)

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           +  Q   +Y    +  V  E +E+  R   ++++M  L P  R I E   +Q      + 
Sbjct: 112 THEQYVQIYSELTKSYVETEYQEQDERMMHISKAMEKLTPHTRHILEECYIQRKKY--QE 169

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++ E  +S   VR+   +A + ++E   K+
Sbjct: 170 VAEELNISVSAVRKHIVKALQVIREECAKK 199


>gi|282881075|ref|ZP_06289762.1| sigma-70, region 4 [Prevotella timonensis CRIS 5C-B1]
 gi|281304879|gb|EFA96952.1| sigma-70, region 4 [Prevotella timonensis CRIS 5C-B1]
          Length = 207

 Score = 39.4 bits (91), Expect = 0.69,   Method: Composition-based stats.
 Identities = 14/70 (20%), Positives = 31/70 (44%), Gaps = 2/70 (2%)

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
             LI +E+R++    + + +  L  R+R     R +        +++    +  + VR+I
Sbjct: 119 DTLISEEQRQDVSKTVAKLLEGLTDRQREAIYLRYMHGMDY--HDIALLMNMHPDSVRKI 176

Query: 273 EARAFKKVQE 282
             RA   ++E
Sbjct: 177 VYRAMTTLRE 186


>gi|227537378|ref|ZP_03967427.1| RNA polymerase ECF family sigma factor [Sphingobacterium
           spiritivorum ATCC 33300]
 gi|227242756|gb|EEI92771.1| RNA polymerase ECF family sigma factor [Sphingobacterium
           spiritivorum ATCC 33300]
          Length = 202

 Score = 39.4 bits (91), Expect = 0.69,   Method: Composition-based stats.
 Identities = 16/68 (23%), Positives = 36/68 (52%), Gaps = 5/68 (7%)

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR-QIEARAFK 278
           E K  + +L +++  L  + + I+  R   +     + ++ EF++SR  V+ QI + A K
Sbjct: 135 EYKEYKEILRKAVDNLPEQRKAIYLMR---DEGYNYQEIADEFDISRHTVKNQI-SAAMK 190

Query: 279 KVQESIQK 286
            +++ + K
Sbjct: 191 SIRKVLSK 198


>gi|34540024|ref|NP_904503.1| ECF subfamily RNA polymerase sigma factor [Porphyromonas gingivalis
           W83]
 gi|188994138|ref|YP_001928390.1| putative RNA polymerase sigma-70 factor ECF subfamily
           [Porphyromonas gingivalis ATCC 33277]
 gi|34396335|gb|AAQ65402.1| RNA polymerase sigma-70 factor, ECF subfamily [Porphyromonas
           gingivalis W83]
 gi|188593818|dbj|BAG32793.1| putative RNA polymerase sigma-70 factor ECF subfamily
           [Porphyromonas gingivalis ATCC 33277]
          Length = 193

 Score = 39.4 bits (91), Expect = 0.69,   Method: Composition-based stats.
 Identities = 16/97 (16%), Positives = 40/97 (41%), Gaps = 13/97 (13%)

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           A + S D + +   + +   +   E+ LIE    +     L + +SVL   ++ +   R 
Sbjct: 99  ARLQSFDDDDAAPVEKVADSNLTAEEQLIELATIEE----LEQYLSVLPEVQQEVVRMRY 154

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            ++  ++   ++    VS      I   A  +++ ++
Sbjct: 155 WED--MSFREIADATGVS------I-NTALGRMRYAL 182


>gi|47097643|ref|ZP_00235163.1| RNA polymerase sigma-30 factor [Listeria monocytogenes str. 1/2a
           F6854]
 gi|47013987|gb|EAL05000.1| RNA polymerase sigma-30 factor [Listeria monocytogenes str. 1/2a
           F6854]
          Length = 80

 Score = 39.4 bits (91), Expect = 0.69,   Method: Composition-based stats.
 Identities = 15/74 (20%), Positives = 33/74 (44%), Gaps = 1/74 (1%)

Query: 32  QEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           QEE  + +  R  GD  A     + +  ++   +  Y   G    +++ E  IGL +A++
Sbjct: 7   QEELAMLELAR-SGDTEALEYFFSKYQSVIYWKSTQYFLQGAERDDLIQEAMIGLFKAIR 65

Query: 92  KFDPERGFRLATYS 105
            +D  +     +++
Sbjct: 66  DYDKTKEASFRSFA 79


>gi|315500869|ref|YP_004079756.1| RNA polymerase, sigma-24 subunit, ecf subfamily [Micromonospora sp.
           L5]
 gi|315407488|gb|ADU05605.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Micromonospora sp.
           L5]
          Length = 176

 Score = 39.4 bits (91), Expect = 0.70,   Method: Composition-based stats.
 Identities = 12/68 (17%), Positives = 27/68 (39%), Gaps = 8/68 (11%)

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL--SSEFEVSRERV-RQIEA 274
            +     R  +  ++  L PR+R +   R  ++    L  +  +    V+   V  Q   
Sbjct: 94  ADADAALRLTVRAALDRLPPRQRAVVVLRYFED----LTEVATAEALGVTVGTVKSQCHD 149

Query: 275 RAFKKVQE 282
            A +K+++
Sbjct: 150 -ALRKLRD 156


>gi|237723305|ref|ZP_04553786.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 2_2_4]
 gi|229447827|gb|EEO53618.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 2_2_4]
 gi|295088035|emb|CBK69558.1| RNA polymerase sigma factor, sigma-70 family [Bacteroides
           xylanisolvens XB1A]
          Length = 196

 Score = 39.4 bits (91), Expect = 0.71,   Method: Composition-based stats.
 Identities = 14/92 (15%), Positives = 34/92 (36%), Gaps = 2/92 (2%)

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
                 E  +I  E  K +  +L + ++ L  ++R +   +      ++ E ++    ++
Sbjct: 104 DLEIDIETAIIRSELEKEQLEVLQKELNNLTKQQREVLYLKYY--KKMSPEEIAQVMGLT 161

Query: 266 RERVRQIEARAFKKVQESIQKQVELSSSPPLL 297
              V      A   ++E + K   L  +  L 
Sbjct: 162 SRTVYNTTHMAISSLRERMSKSFLLLVAANLW 193


>gi|160883282|ref|ZP_02064285.1| hypothetical protein BACOVA_01251 [Bacteroides ovatus ATCC 8483]
 gi|156111266|gb|EDO13011.1| hypothetical protein BACOVA_01251 [Bacteroides ovatus ATCC 8483]
          Length = 207

 Score = 39.4 bits (91), Expect = 0.71,   Method: Composition-based stats.
 Identities = 13/82 (15%), Positives = 33/82 (40%), Gaps = 6/82 (7%)

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
              N  Q ++ ++                 + + ++ R++  L PR+R +F+  R  E  
Sbjct: 99  DMANEDQLKEQILSQAIDSANETNNHILLNDLKEIIARALEQLTPRQREVFKMSR--ELQ 156

Query: 253 VTLENLSSEFEVS----RERVR 270
           ++ + ++    VS    +E + 
Sbjct: 157 MSHKEIAEALGVSVHTVQEHIS 178


>gi|160878837|ref|YP_001557805.1| ECF subfamily RNA polymerase sigma-24 factor [Clostridium
           phytofermentans ISDg]
 gi|160427503|gb|ABX41066.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           phytofermentans ISDg]
          Length = 178

 Score = 39.4 bits (91), Expect = 0.71,   Method: Composition-based stats.
 Identities = 28/150 (18%), Positives = 55/150 (36%), Gaps = 5/150 (3%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E +L K+ ++ GD SA   L++ +   V K  +   G      ++  E  + L++ +  
Sbjct: 2   DELILIKQCQK-GDKSAFQALISFYYPFVSKYLLKLTGDEYLSEDLTQETFLRLIRFIDH 60

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL---KGHLQAI 149
           +D       +TY M  I   +    LR    +    T  +     ++ +       +   
Sbjct: 61  YDINGKASFSTYIMT-IAKRLYIDHLRKNKQIFTDFTELEIDSGEDMEQAVIKSMEIDEA 119

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
                   Q  AIA K+   E + +    R
Sbjct: 120 IKRLNSLPQDQAIAIKMKYLEQKTLEEIAR 149


>gi|255038451|ref|YP_003089072.1| transcriptional regulator, LuxR family [Dyadobacter fermentans DSM
           18053]
 gi|254951207|gb|ACT95907.1| transcriptional regulator, LuxR family [Dyadobacter fermentans DSM
           18053]
          Length = 199

 Score = 39.4 bits (91), Expect = 0.71,   Method: Composition-based stats.
 Identities = 16/89 (17%), Positives = 36/89 (40%), Gaps = 2/89 (2%)

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           Q +D         E+  I  E    R   L + ++ L  R++ +   +  QE  ++ E +
Sbjct: 102 QDEDDFFEIEFSVEETYIANEATAVRTRQLQQMLNALPRRQKEVVYLKFFQE--LSREQI 159

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +    VS + V  +   A + ++   + +
Sbjct: 160 AEVMAVSPQTVSNMLQIAIRHLKAHWKAE 188


>gi|229587478|ref|YP_002860516.1| putative RNA polymerase sigma factor [Clostridium botulinum Ba4
           str. 657]
 gi|229260183|gb|ACQ51220.1| putative RNA polymerase sigma factor [Clostridium botulinum Ba4
           str. 657]
          Length = 294

 Score = 39.4 bits (91), Expect = 0.72,   Method: Composition-based stats.
 Identities = 11/70 (15%), Positives = 29/70 (41%), Gaps = 2/70 (2%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
             ++  +  L+ K A  +  YG    ++    ++ + +A   +D  +    +TY+   I 
Sbjct: 18  EEVLKKYSNLITKYAYKWIKYG--FEDIKQIAHLAVWKAFNTYDISKNINFSTYANKIIS 75

Query: 111 AAMQEYILRS 120
             +  +I  +
Sbjct: 76  TEILLHIRDN 85


>gi|170747314|ref|YP_001753574.1| ECF subfamily RNA polymerase sigma-24 factor [Methylobacterium
           radiotolerans JCM 2831]
 gi|170653836|gb|ACB22891.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Methylobacterium
           radiotolerans JCM 2831]
          Length = 223

 Score = 39.4 bits (91), Expect = 0.72,   Method: Composition-based stats.
 Identities = 22/100 (22%), Positives = 37/100 (37%), Gaps = 7/100 (7%)

Query: 34  EYVLAKRY--REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91
           E  LA      + GD +A   L+ + L +V  IA      G  + +VV +  + + +A  
Sbjct: 42  EQELATLMTAAQGGDAAAYRALLKACLPVVSAIARAQGVRGEAVDDVVQDALMTVHRARA 101

Query: 92  KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
            +DP R      +  W      +  I R     +     N
Sbjct: 102 SYDPAR-----PFLPWLRAITQRRAIDRLRRAGRRPQEVN 136


>gi|94971553|ref|YP_593601.1| ECF subfamily RNA polymerase sigma-24 factor [Candidatus Koribacter
           versatilis Ellin345]
 gi|94553603|gb|ABF43527.1| RNA polymerase, sigma subunit, ECF family [Candidatus Koribacter
           versatilis Ellin345]
          Length = 237

 Score = 39.4 bits (91), Expect = 0.72,   Method: Composition-based stats.
 Identities = 34/245 (13%), Positives = 69/245 (28%), Gaps = 66/245 (26%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R  + GD +A   LV  +   V+++A+          ++  E  +   +A +       F
Sbjct: 53  RASQRGDHAAFEELVRQYDSAVLRLALHLTRSESDAQDIYQEAFL---KAYRNIG---NF 106

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           R       WI   +    L                                         
Sbjct: 107 RFECSFYTWIYRIVTNLCLDLLR------------------------------------- 129

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
                     + +V   +  +A D+                 D +  D  G         
Sbjct: 130 ----------KRQVRKEDAPVATDQ---------RGEEYDLLDQVADDRSG--ASPERDL 168

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
            R+   + + +++  L PRER +FE +  Q     L  +      + E  +    R  +K
Sbjct: 169 MRRELGSRIAKALEKLTPRERMVFEMKHYQGLK--LRTIGEILNTTEETAKNTLFRGTQK 226

Query: 280 VQESI 284
           ++ ++
Sbjct: 227 LRAAL 231


>gi|317496631|ref|ZP_07954977.1| hypothetical protein HMPREF0432_01581 [Gemella moribillum M424]
 gi|316913245|gb|EFV34745.1| hypothetical protein HMPREF0432_01581 [Gemella moribillum M424]
          Length = 137

 Score = 39.4 bits (91), Expect = 0.73,   Method: Composition-based stats.
 Identities = 15/94 (15%), Positives = 48/94 (51%), Gaps = 6/94 (6%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
            +   + D ++ +    E+++    E K +   L ++++ L   ER + EA   +E   +
Sbjct: 50  DHDGHFVDNIIDEKTDLEKIV----EVKMQIEELNKALATLTKEERDLIEAIFFREE--S 103

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           L+++  + +V+ + + +   R  +K+++ ++ ++
Sbjct: 104 LKSIGEKEKVTHQAIGKRRDRILEKLRKILEDKI 137


>gi|239929893|ref|ZP_04686846.1| RNA polymerase sigma factor [Streptomyces ghanaensis ATCC 14672]
          Length = 191

 Score = 39.4 bits (91), Expect = 0.73,   Method: Composition-based stats.
 Identities = 11/62 (17%), Positives = 23/62 (37%), Gaps = 2/62 (3%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L+           E    +  R+ L ++M  L  R+R +   R   +  +T   ++    
Sbjct: 109 LLSKPMPDMASAEEGAYDQLERDSLIKAMKGLQRRQREVLVLRYFAD--MTEAQVAETLG 166

Query: 264 VS 265
           +S
Sbjct: 167 IS 168


>gi|229160763|ref|ZP_04288755.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           R309803]
 gi|228622778|gb|EEK79612.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           R309803]
          Length = 188

 Score = 39.4 bits (91), Expect = 0.73,   Method: Composition-based stats.
 Identities = 17/83 (20%), Positives = 35/83 (42%), Gaps = 10/83 (12%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           H   E+   ++      R  L + ++ L P ++++F  + L       E +  +  ++R 
Sbjct: 104 HISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMRT--EEIGEKLGLTRA 161

Query: 268 ----RVRQIEARAFKKVQESIQK 286
               RV     R  KK+Q++  K
Sbjct: 162 AIDNRV----YRGKKKLQQNATK 180


>gi|223939858|ref|ZP_03631727.1| RNA polymerase, sigma-24 subunit, ECF subfamily [bacterium
           Ellin514]
 gi|223891450|gb|EEF57942.1| RNA polymerase, sigma-24 subunit, ECF subfamily [bacterium
           Ellin514]
          Length = 1091

 Score = 39.4 bits (91), Expect = 0.73,   Method: Composition-based stats.
 Identities = 12/55 (21%), Positives = 22/55 (40%), Gaps = 2/55 (3%)

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +L  ++  L   +R     R +QE       +      S E  R+   RA +K++
Sbjct: 116 LLDDALEQLGETDRNAVLLRFMQERNH--REVGEALGFSEEAARKRVDRALEKLR 168


>gi|332757291|gb|EGJ87628.1| RNA polymerase sigma factor for flagellar operon domain protein
           [Shigella flexneri 2747-71]
 gi|332766655|gb|EGJ96859.1| fliA [Shigella flexneri 2930-71]
 gi|333017550|gb|EGK36862.1| RNA polymerase sigma factor for flagellar operon domain protein
           [Shigella flexneri K-304]
          Length = 72

 Score = 39.4 bits (91), Expect = 0.74,   Method: Composition-based stats.
 Identities = 15/60 (25%), Positives = 31/60 (51%), Gaps = 3/60 (5%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 13  KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 72


>gi|269120524|ref|YP_003308701.1| PfkB domain protein [Sebaldella termitidis ATCC 33386]
 gi|268614402|gb|ACZ08770.1| PfkB domain protein [Sebaldella termitidis ATCC 33386]
          Length = 363

 Score = 39.4 bits (91), Expect = 0.74,   Method: Composition-based stats.
 Identities = 10/32 (31%), Positives = 17/32 (53%), Gaps = 3/32 (9%)

Query: 236 NPRERRIFEARRLQENPV-TLENLSSEFEVSR 266
             RER I    R  ENP+ + E ++ +  ++R
Sbjct: 2   TEREREILHLIR--ENPMISQEEIAKKIGITR 31


>gi|255034894|ref|YP_003085515.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Dyadobacter
           fermentans DSM 18053]
 gi|254947650|gb|ACT92350.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Dyadobacter
           fermentans DSM 18053]
          Length = 202

 Score = 39.4 bits (91), Expect = 0.74,   Method: Composition-based stats.
 Identities = 18/75 (24%), Positives = 36/75 (48%), Gaps = 2/75 (2%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
               E  +IE E+ + +   L   +S+L+ R++ I   R  Q      E+++S   + R+
Sbjct: 114 DPSIETNIIEDEQIRFQNGHLKHIISLLSKRQQEIIYLRFYQNLDN--EDIASVMGLGRQ 171

Query: 268 RVRQIEARAFKKVQE 282
            V  +  R  K+++E
Sbjct: 172 SVSNLLYRTLKEIKE 186


>gi|254302833|ref|ZP_04970191.1| DNA-directed RNA polymerase sigma subunit RpoD [Fusobacterium
           nucleatum subsp. polymorphum ATCC 10953]
 gi|148323025|gb|EDK88275.1| DNA-directed RNA polymerase sigma subunit RpoD [Fusobacterium
           nucleatum subsp. polymorphum ATCC 10953]
          Length = 274

 Score = 39.4 bits (91), Expect = 0.74,   Method: Composition-based stats.
 Identities = 19/66 (28%), Positives = 35/66 (53%), Gaps = 2/66 (3%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V  +L+ V ++A+     G+   ++  EG IGL++A + F  ++ F+L  Y  ++I   M
Sbjct: 84  VEKNLKKVYEMALYMLRDGISYEDLTQEGIIGLIKAHELFKDDKDFKL--YKDYYIAKEM 141

Query: 114 QEYILR 119
             YI  
Sbjct: 142 FNYINN 147


>gi|315181020|gb|ADT87934.1| DNA-directed RNA polymerase sigma subunit [Vibrio furnissii NCTC
           11218]
          Length = 177

 Score = 39.4 bits (91), Expect = 0.74,   Method: Composition-based stats.
 Identities = 17/99 (17%), Positives = 39/99 (39%), Gaps = 16/99 (16%)

Query: 197 SSQWQDWLVYDHDGQEQVLIE--KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
                   ++  D     L+E    E +  +  + + +  L   ++++  A  L+E P  
Sbjct: 85  EPHVLAEDIWPSDFCPPDLVEHYAPEHEMLKEQVLKFLDTLPEAQQKVVRAVYLEELPH- 143

Query: 255 LENLSSEFEV------SRERVRQIEARAFKKVQESIQKQ 287
            + ++  F +      SR R+      A +K++ SI  +
Sbjct: 144 -QQVAEMFNIPLGTVKSRLRL------AVEKLRTSIDAE 175


>gi|262038185|ref|ZP_06011579.1| hypothetical protein HMPREF0554_1929 [Leptotrichia goodfellowii
           F0264]
 gi|261747766|gb|EEY35211.1| hypothetical protein HMPREF0554_1929 [Leptotrichia goodfellowii
           F0264]
          Length = 314

 Score = 39.4 bits (91), Expect = 0.74,   Method: Composition-based stats.
 Identities = 36/263 (13%), Positives = 90/263 (34%), Gaps = 50/263 (19%)

Query: 33  EEYVLAKRY-------REHGDLSAAHR---LVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
           EE  + K Y        E  D    +    L+  +L++ V+ ++ Y  +G    + V E 
Sbjct: 66  EEKDIIKAYLEDIKEKYEEFDKKMKNESRELIDEYLKVAVRESLLYSKFGFSFLDTVQEA 125

Query: 83  NIGLMQAVKKFD----PERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFN 138
            +G++  +  +D      +      +   +    + E+       +K    +    L   
Sbjct: 126 TLGVLSGINYYDRIKEISKDPEF--FIKSFAVKYILEFQKNLLKDIKASELSYVLYLKVK 183

Query: 139 LRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSS 198
           + +  GH             +  I+K++NV+   +  +                      
Sbjct: 184 VDKEMGH------------SIDEISKQMNVTPEYIEDLEK-------------------- 211

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP-VTLEN 257
              D +  +   Q + ++EK ++  +  +L      L+  + +I       ++   T + 
Sbjct: 212 -LFDGVEPEELIQNEQILEKADKITQLYILENIPKKLSYLDEKILVMAYGLDDKVYTGKE 270

Query: 258 LSSEFEVSRERVRQIEARAFKKV 280
           ++    +S   V  ++ +A  K+
Sbjct: 271 IAKTLNISLHNVNILKEKAINKL 293


>gi|229082464|ref|ZP_04214927.1| RNA polymerase sigma factor [Bacillus cereus Rock4-2]
 gi|228700896|gb|EEL53419.1| RNA polymerase sigma factor [Bacillus cereus Rock4-2]
          Length = 156

 Score = 39.4 bits (91), Expect = 0.74,   Method: Composition-based stats.
 Identities = 15/64 (23%), Positives = 35/64 (54%), Gaps = 2/64 (3%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    +   MSVL+ +E+ I   R       T+  ++ E E++  +VR +  +A +K++
Sbjct: 94  EDVEIRVKDFMSVLDEKEKYIIFERFFVG--KTMGEIALETEMTYYQVRWMYRQAIEKMR 151

Query: 282 ESIQ 285
           +S++
Sbjct: 152 DSVK 155


>gi|166032936|ref|ZP_02235765.1| hypothetical protein DORFOR_02657 [Dorea formicigenerans ATCC
           27755]
 gi|166027293|gb|EDR46050.1| hypothetical protein DORFOR_02657 [Dorea formicigenerans ATCC
           27755]
          Length = 184

 Score = 39.4 bits (91), Expect = 0.74,   Method: Composition-based stats.
 Identities = 12/80 (15%), Positives = 39/80 (48%), Gaps = 10/80 (12%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE--FEVS--RE 267
           +  LI++     R+  + +++ +L   +R +   R   +  V  +++++     VS  + 
Sbjct: 106 DTSLIDEILHDERKETVQKALDLLPEIQREVVILRYYHDLKV--KDIATITGVGVSTVQS 163

Query: 268 RVRQIEARAFKKVQESIQKQ 287
           R+ Q      +K+++ ++++
Sbjct: 164 RIYQ----GLRKLEKVLERE 179


>gi|330469034|ref|YP_004406777.1| RNA polymerase, sigma-24 subunit, ECF subfamily protein
           [Verrucosispora maris AB-18-032]
 gi|328812005|gb|AEB46177.1| RNA polymerase, sigma-24 subunit, ECF subfamily protein
           [Verrucosispora maris AB-18-032]
          Length = 165

 Score = 39.0 bits (90), Expect = 0.75,   Method: Composition-based stats.
 Identities = 16/82 (19%), Positives = 36/82 (43%), Gaps = 2/82 (2%)

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
           W+  L      + +V  + +   + R+ L R++  L  R+R +   R  +E  ++   ++
Sbjct: 74  WRGELPTAELPEVRVAADPQTGFDDRDQLWRALGRLPRRQRAVLVLRYFEE--LSEHEIA 131

Query: 260 SEFEVSRERVRQIEARAFKKVQ 281
                S   V+   +RA  K++
Sbjct: 132 EALGCSVGTVKSQASRALAKLR 153


>gi|326335937|ref|ZP_08202114.1| hypothetical protein HMPREF9071_1580 [Capnocytophaga sp. oral taxon
           338 str. F0234]
 gi|325691901|gb|EGD33863.1| hypothetical protein HMPREF9071_1580 [Capnocytophaga sp. oral taxon
           338 str. F0234]
          Length = 645

 Score = 39.0 bits (90), Expect = 0.75,   Method: Composition-based stats.
 Identities = 8/31 (25%), Positives = 15/31 (48%)

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAF 277
                 + L+ +  + +V+ ERVRQI  +  
Sbjct: 226 YQDSEKLKLKEVGKQMQVTHERVRQIRNQII 256


>gi|298384519|ref|ZP_06994079.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 1_1_14]
 gi|298262798|gb|EFI05662.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 1_1_14]
          Length = 200

 Score = 39.0 bits (90), Expect = 0.75,   Method: Composition-based stats.
 Identities = 12/82 (14%), Positives = 33/82 (40%), Gaps = 6/82 (7%)

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
              N  + ++ ++            K    + +++++R++  L PR+R +F   R  +  
Sbjct: 92  DMANEDKLKEHILSHAVDSANETNNKILFDDLKDVVSRALEQLTPRQREVFNMSRDLQMS 151

Query: 253 VTLENLSSEFEVS----RERVR 270
              + ++    VS    +E + 
Sbjct: 152 H--KEIAEALGVSVNTVQEHIS 171


>gi|260173435|ref|ZP_05759847.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D2]
 gi|315921707|ref|ZP_07917947.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D2]
 gi|313695582|gb|EFS32417.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D2]
          Length = 196

 Score = 39.0 bits (90), Expect = 0.75,   Method: Composition-based stats.
 Identities = 14/92 (15%), Positives = 34/92 (36%), Gaps = 2/92 (2%)

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
                 E  +I  E  K +  +L + ++ L  ++R +   +      ++ E ++    ++
Sbjct: 104 DLEIDIETAIIRSELEKEQLEVLQKELNNLTKQQREVLYLKYY--KKMSPEEIAQVMGLT 161

Query: 266 RERVRQIEARAFKKVQESIQKQVELSSSPPLL 297
              V      A   ++E + K   L  +  L 
Sbjct: 162 SRTVYNTTHMAISSLRERMSKSFLLLVAANLW 193


>gi|196033388|ref|ZP_03100800.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus W]
 gi|218902920|ref|YP_002450754.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           AH820]
 gi|228933084|ref|ZP_04095947.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus
           thuringiensis serovar andalousiensis BGSC 4AW1]
 gi|228945406|ref|ZP_04107761.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus
           thuringiensis serovar monterrey BGSC 4AJ1]
 gi|195993822|gb|EDX57778.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus W]
 gi|218540071|gb|ACK92469.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           AH820]
 gi|228814378|gb|EEM60644.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus
           thuringiensis serovar monterrey BGSC 4AJ1]
 gi|228826685|gb|EEM72456.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus
           thuringiensis serovar andalousiensis BGSC 4AW1]
          Length = 188

 Score = 39.0 bits (90), Expect = 0.75,   Method: Composition-based stats.
 Identities = 10/59 (16%), Positives = 24/59 (40%), Gaps = 2/59 (3%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           H   E+   ++      R  L   ++ L P ++++F  + L       E +  +  ++R
Sbjct: 104 HISTEKSAEDELIIMEDREELLMLINQLEPLDQKVFIMKYLLGMKT--EEIGDKLGLTR 160


>gi|149192321|ref|ZP_01870529.1| RNA polymerase sigma factor RpoE [Vibrio shilonii AK1]
 gi|148833854|gb|EDL50883.1| RNA polymerase sigma factor RpoE [Vibrio shilonii AK1]
          Length = 131

 Score = 39.0 bits (90), Expect = 0.75,   Method: Composition-based stats.
 Identities = 17/88 (19%), Positives = 32/88 (36%), Gaps = 3/88 (3%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
            VL +R +  GD  A + LV  +   V  +   Y      ++++  E  I   +A+  F 
Sbjct: 8   QVLIERVQ-SGDKQAFNLLVLRYQNKVCNLISRYVSNSGDVADIAQEAFIKAYRAIPTFR 66

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWS 122
            E      T+         + +I+    
Sbjct: 67  GE--SAFYTWLYRIAVNTAKNHIVAQSR 92


>gi|126464352|ref|YP_001045465.1| ECF subfamily RNA polymerase sigma-24 factor [Rhodobacter
           sphaeroides ATCC 17029]
 gi|126106163|gb|ABN78693.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Rhodobacter
           sphaeroides ATCC 17029]
          Length = 173

 Score = 39.0 bits (90), Expect = 0.75,   Method: Composition-based stats.
 Identities = 27/143 (18%), Positives = 51/143 (35%), Gaps = 7/143 (4%)

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSS 198
           RL  HL          + V+  A        +V  M+   A  G    N  I+       
Sbjct: 20  RLSRHLTRRPGTLCDAQDVMQDAWLRLAKVQDVEEMSSPAAYVGQVVRNLAIDRLRAQRV 79

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS---MSVLNPRERRIFEARRLQENPVTL 255
           + + +   +   Q   L   E   + R  L R    ++ L PR+R++F   +      + 
Sbjct: 80  RERHFSAAEVHDQPADLPSAERIVDFRQRLARLEEIVAELPPRQRQVFLLHKFDGLSHS- 138

Query: 256 ENLSSEFEVSRERVRQIEARAFK 278
             +++   +SR  V ++  +A  
Sbjct: 139 -EIAARLGISRSAVEKLIMKALA 160


>gi|307324515|ref|ZP_07603722.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306889759|gb|EFN20738.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 210

 Score = 39.0 bits (90), Expect = 0.76,   Method: Composition-based stats.
 Identities = 13/72 (18%), Positives = 30/72 (41%), Gaps = 2/72 (2%)

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
           + E          +  +++ L  R+R +   R   E  +T   ++    VSR  V+   +
Sbjct: 139 VDEPLLLAEEHRQVLDALAELTARQREVLVLRYWSE--LTEAQIAETLGVSRGTVKSTAS 196

Query: 275 RAFKKVQESIQK 286
           RA   +++ ++ 
Sbjct: 197 RALVTLEKLLEA 208


>gi|311739988|ref|ZP_07713822.1| RNA polymerase sigma-70 factor [Corynebacterium pseudogenitalium
           ATCC 33035]
 gi|311305061|gb|EFQ81130.1| RNA polymerase sigma-70 factor [Corynebacterium pseudogenitalium
           ATCC 33035]
          Length = 196

 Score = 39.0 bits (90), Expect = 0.76,   Method: Composition-based stats.
 Identities = 14/88 (15%), Positives = 34/88 (38%), Gaps = 2/88 (2%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           + +    E    E     +  N +   +  L+ + + I   R    N ++ E  +     
Sbjct: 111 IPEDSANEATPEEWALEADGSNRMRALLDTLSDKAKNIVILRVF--NGLSAEETAEIVGS 168

Query: 265 SRERVRQIEARAFKKVQESIQKQVELSS 292
           +   VR  + RA  ++++++Q   E + 
Sbjct: 169 TPGAVRVAQHRALAQLRKTLQAAQETAR 196


>gi|218458847|ref|ZP_03498938.1| putative RNA polymerase sigma factor [Rhizobium etli Kim 5]
          Length = 174

 Score = 39.0 bits (90), Expect = 0.76,   Method: Composition-based stats.
 Identities = 19/87 (21%), Positives = 33/87 (37%), Gaps = 3/87 (3%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L +R  + GD  A  +LV+ H   V   A  + G      ++  E  + L  A++ F  
Sbjct: 4   ELIER-AQGGDREAFGQLVSRHYDFVHATAWRWSGSSTDADDIAQEVCVKLGAAIRGFRG 62

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWS 122
               R  T+       A +++  R   
Sbjct: 63  A--SRFRTWLYTLTLNAARDHRRRLAR 87


>gi|91216542|ref|ZP_01253508.1| predicted cytoskeletal protein [Psychroflexus torquis ATCC 700755]
 gi|91185336|gb|EAS71713.1| predicted cytoskeletal protein [Psychroflexus torquis ATCC 700755]
          Length = 734

 Score = 39.0 bits (90), Expect = 0.76,   Method: Composition-based stats.
 Identities = 9/25 (36%), Positives = 15/25 (60%)

Query: 247 RLQENPVTLENLSSEFEVSRERVRQ 271
              +  +TL+ ++ E  +S ERVRQ
Sbjct: 233 YKNQKELTLDEIAKEVGLSAERVRQ 257


>gi|300813842|ref|ZP_07094147.1| sigma-70, region 4 [Peptoniphilus sp. oral taxon 836 str. F0141]
 gi|300512029|gb|EFK39224.1| sigma-70, region 4 [Peptoniphilus sp. oral taxon 836 str. F0141]
          Length = 206

 Score = 39.0 bits (90), Expect = 0.77,   Method: Composition-based stats.
 Identities = 17/73 (23%), Positives = 38/73 (52%), Gaps = 3/73 (4%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKE-ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
              S++++        ++ + IEKE ERK     LT+++  L PR+R+I     L+   +
Sbjct: 114 DMDSKYKEGEDILEKIEDNINIEKEYERKLENIALTKAIKELPPRQRQIIVLYYLEN--M 171

Query: 254 TLENLSSEFEVSR 266
           +++ +  +  +S+
Sbjct: 172 SIKEIGQKMAISK 184


>gi|296242134|ref|YP_003649621.1| DNA binding protein, Tfx family [Thermosphaera aggregans DSM 11486]
 gi|296094718|gb|ADG90669.1| DNA binding protein, Tfx family [Thermosphaera aggregans DSM 11486]
          Length = 136

 Score = 39.0 bits (90), Expect = 0.77,   Method: Composition-based stats.
 Identities = 17/71 (23%), Positives = 33/71 (46%), Gaps = 6/71 (8%)

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ---ESIQKQVE 289
            +L  ++ RI E R       T   ++     SR  V  +E  A +K++   E+++   E
Sbjct: 7   GLLTEKQYRILELR---SKGYTQAQIAKILSTSRSNVSMLEKAALEKIRLAKETLKLYQE 63

Query: 290 LSSSPPLLQKP 300
           L+S+  +  +P
Sbjct: 64  LNSAAVVTVEP 74


>gi|228955497|ref|ZP_04117502.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
 gi|228804289|gb|EEM50903.1| RNA polymerase sigma factor [Bacillus thuringiensis serovar
           kurstaki str. T03a001]
          Length = 156

 Score = 39.0 bits (90), Expect = 0.77,   Method: Composition-based stats.
 Identities = 15/64 (23%), Positives = 35/64 (54%), Gaps = 2/64 (3%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    +   MSVL+ +E+ I   R       T+  ++ E E++  +VR +  +A +K++
Sbjct: 94  EDVEIRVKDFMSVLDEKEKYIIFERFFVG--KTMGEIALETEMTYYQVRWMYRQAIEKMR 151

Query: 282 ESIQ 285
           +S++
Sbjct: 152 DSVK 155


>gi|227827085|ref|YP_002828864.1| Bacterio-opsin activator HTH domain protein [Sulfolobus islandicus
           M.14.25]
 gi|229584253|ref|YP_002842754.1| Bacterio-opsin activator HTH domain protein [Sulfolobus islandicus
           M.16.27]
 gi|238619250|ref|YP_002914075.1| Bacterio-opsin activator HTH domain protein [Sulfolobus islandicus
           M.16.4]
 gi|227458880|gb|ACP37566.1| Bacterio-opsin activator HTH domain protein [Sulfolobus islandicus
           M.14.25]
 gi|228019302|gb|ACP54709.1| Bacterio-opsin activator HTH domain protein [Sulfolobus islandicus
           M.16.27]
 gi|238380319|gb|ACR41407.1| Bacterio-opsin activator HTH domain protein [Sulfolobus islandicus
           M.16.4]
          Length = 204

 Score = 39.0 bits (90), Expect = 0.77,   Method: Composition-based stats.
 Identities = 12/52 (23%), Positives = 22/52 (42%), Gaps = 5/52 (9%)

Query: 233 SVLNPRERRIFEA-----RRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           + L  R+  I +          +  VTL  L+ +  +S   + +I  RA +K
Sbjct: 143 NDLTDRQMEILKLAYKMGYFDDDRRVTLTELAKQLGISAPTLEEIMRRALRK 194


>gi|198274368|ref|ZP_03206900.1| hypothetical protein BACPLE_00513 [Bacteroides plebeius DSM 17135]
 gi|198272734|gb|EDY97003.1| hypothetical protein BACPLE_00513 [Bacteroides plebeius DSM 17135]
          Length = 169

 Score = 39.0 bits (90), Expect = 0.77,   Method: Composition-based stats.
 Identities = 10/62 (16%), Positives = 27/62 (43%), Gaps = 2/62 (3%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
                Q    + ER  +  ++ R ++ L  ++R I + R +     + + ++    ++ E
Sbjct: 87  EMPDAQTPESQFERNEQFQLVHRLVNELPEKQRTIVQLRDI--EGKSYKEIADVLGITEE 144

Query: 268 RV 269
           +V
Sbjct: 145 QV 146


>gi|86159310|ref|YP_466095.1| sigma-24 FecI-like protein [Anaeromyxobacter dehalogenans 2CP-C]
 gi|85775821|gb|ABC82658.1| sigma-24 (FecI-like) [Anaeromyxobacter dehalogenans 2CP-C]
          Length = 194

 Score = 39.0 bits (90), Expect = 0.77,   Method: Composition-based stats.
 Identities = 17/62 (27%), Positives = 28/62 (45%), Gaps = 2/62 (3%)

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
             R+ L R +  L  RER +  A    E P   E +S +  +S   VR +  RA + ++ 
Sbjct: 128 LPRDRLARCLEALAARERAVVVATFYAEQPA--EAISRDHALSAAHVRVLRHRALRHLRT 185

Query: 283 SI 284
            +
Sbjct: 186 CL 187


>gi|168698817|ref|ZP_02731094.1| RNA polymerase, sigma-24 subunit, ECF subfamily protein [Gemmata
           obscuriglobus UQM 2246]
          Length = 193

 Score = 39.0 bits (90), Expect = 0.78,   Method: Composition-based stats.
 Identities = 32/182 (17%), Positives = 62/182 (34%), Gaps = 26/182 (14%)

Query: 108 WIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLN 167
           W+ A     +  + SLV+  + A         R L+   +   + +        I   L 
Sbjct: 22  WVTAVGPRAVAYARSLVRDPSRAEDVVQECFYRLLRRANEYDLERDG-------IKLLLK 74

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
              +  I+   R     SL++        S+   D  V   D          + +  ++ 
Sbjct: 75  AISNLCINQATREKALLSLDS--------STDPDDGPVTLSDPAALSPERIAQHRELQDA 126

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE-------RVRQIEARAFK-K 279
           +   +  L P +R   E R L    ++ + ++    VS         R RQ+ ARA +  
Sbjct: 127 VRDGLQTLPPLQRAAVELRALG---MSKDEIADALGVSATNAGVLVYRGRQLLARALEPH 183

Query: 280 VQ 281
           ++
Sbjct: 184 LR 185


>gi|330466147|ref|YP_004403890.1| RNA polymerase ECF-subfamily sigma factor [Verrucosispora maris
           AB-18-032]
 gi|328809118|gb|AEB43290.1| RNA polymerase ECF-subfamily sigma factor [Verrucosispora maris
           AB-18-032]
          Length = 539

 Score = 39.0 bits (90), Expect = 0.79,   Method: Composition-based stats.
 Identities = 20/93 (21%), Positives = 32/93 (34%), Gaps = 18/93 (19%)

Query: 45  GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE------GNIGLMQAVKKFDPERG 98
           GD SA  +L+ +HL L+  I          I +VV E       ++  ++A + F     
Sbjct: 10  GDRSAREQLIAAHLPLLYNIVGRALHGHADIDDVVQETLVRVIRDLPALRAPESFR---- 65

Query: 99  FRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
                    W+ A     I      V+  T   
Sbjct: 66  --------SWLVAIAVRQIASHRQRVRTATHRA 90


>gi|323497933|ref|ZP_08102942.1| RNA polymerase sigma factor [Vibrio sinaloensis DSM 21326]
 gi|323316978|gb|EGA69980.1| RNA polymerase sigma factor [Vibrio sinaloensis DSM 21326]
          Length = 194

 Score = 39.0 bits (90), Expect = 0.79,   Method: Composition-based stats.
 Identities = 15/97 (15%), Positives = 41/97 (42%), Gaps = 16/97 (16%)

Query: 199 QWQDWLVYDHDGQEQVLIE--KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
                 ++ +D     +++    E    +  + + +  L   +R++ +A  L++ P   +
Sbjct: 104 HLHSEDIWPNDYCPPDMVDHYSPETDMLKEQVVKFLDRLPEAQRKVVQAVYLEDLPH--Q 161

Query: 257 NLSSEFEV------SRERVRQIEARAFKKVQESIQKQ 287
            ++  F++      SR R+      A +K++ SI+  
Sbjct: 162 QVADMFDIPLGTVKSRLRL------AVEKLRHSIEAD 192


>gi|256390260|ref|YP_003111824.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Catenulispora
           acidiphila DSM 44928]
 gi|256356486|gb|ACU69983.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Catenulispora
           acidiphila DSM 44928]
          Length = 184

 Score = 39.0 bits (90), Expect = 0.79,   Method: Composition-based stats.
 Identities = 17/69 (24%), Positives = 31/69 (44%), Gaps = 2/69 (2%)

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
            +  E  +RR+ + R++  L PR R I   R L++   T    +     S   V+   +R
Sbjct: 101 ADGTEAVDRRDQVWRAVLTLPPRMRAIIVLRFLEDLKET--ETAEVLGCSVGTVKSQTSR 158

Query: 276 AFKKVQESI 284
           A  K++  +
Sbjct: 159 ALAKLRTHL 167


>gi|229181511|ref|ZP_04308839.1| RNA polymerase sigma factor [Bacillus cereus 172560W]
 gi|228602086|gb|EEK59579.1| RNA polymerase sigma factor [Bacillus cereus 172560W]
          Length = 156

 Score = 39.0 bits (90), Expect = 0.79,   Method: Composition-based stats.
 Identities = 15/64 (23%), Positives = 35/64 (54%), Gaps = 2/64 (3%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++    +   MSVL+ +E+ I   R       T+  ++ E E++  +VR +  +A +K++
Sbjct: 94  EDVEIRVKDFMSVLDEKEKYIIFERFFVG--KTMGEIALETEMTYYQVRWMYRQAIEKMR 151

Query: 282 ESIQ 285
           +S++
Sbjct: 152 DSVK 155


>gi|257386138|ref|YP_003175911.1| hypothetical protein Hmuk_0053 [Halomicrobium mukohataei DSM 12286]
 gi|257168445|gb|ACV46204.1| conserved hypothetical protein [Halomicrobium mukohataei DSM 12286]
          Length = 257

 Score = 39.0 bits (90), Expect = 0.79,   Method: Composition-based stats.
 Identities = 16/110 (14%), Positives = 40/110 (36%), Gaps = 2/110 (1%)

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
             IA +++ +  E++    +  GD +          +     D      D + +  I  E
Sbjct: 43  AEIATEVSGASVELVEQVLQEYGDPAAEDDQPVESDDQDTVDDETSEPEDDEVEPPISAE 102

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
              + +      ++ L+ ++R    A   ++   T   ++   +VSR  +
Sbjct: 103 TGPDEKGE-DVDLTALDEKQRETLRAIH-RQPTATQAEIADTLDVSRATI 150


>gi|223935997|ref|ZP_03627911.1| RNA polymerase, sigma-24 subunit, ECF subfamily [bacterium
           Ellin514]
 gi|223895219|gb|EEF61666.1| RNA polymerase, sigma-24 subunit, ECF subfamily [bacterium
           Ellin514]
          Length = 484

 Score = 39.0 bits (90), Expect = 0.79,   Method: Composition-based stats.
 Identities = 18/94 (19%), Positives = 36/94 (38%), Gaps = 15/94 (15%)

Query: 211 QEQVLIEKEERKNRRNM---LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            E  L +       R +   L  +M  L+ +ER +   R  +         ++   + +E
Sbjct: 102 MESTLNDSNSENVWRQLEPLLEEAMIRLSEKERTLVALRFFENKSA--AETAAVLGI-QE 158

Query: 268 -----RVRQIEARAFKKVQESIQKQVELSSSPPL 296
                R     ARA +K+++   K+   S++  L
Sbjct: 159 WAAHKRA----ARAMEKLRKFFIKRGIASTTATL 188



 Score = 35.6 bits (81), Expect = 9.2,   Method: Composition-based stats.
 Identities = 13/52 (25%), Positives = 21/52 (40%)

Query: 35 YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
            L ++Y +    SA   +V  H+ LV  +A+ Y        +V     I L
Sbjct: 7  IALLRKYADCNSESAFAEIVHRHINLVYSVALRYVDNSPDAQDVAQAVFIIL 58


>gi|299144976|ref|ZP_07038044.1| putative RNA polymerase ECF-type sigma factor [Bacteroides sp.
           3_1_23]
 gi|298515467|gb|EFI39348.1| putative RNA polymerase ECF-type sigma factor [Bacteroides sp.
           3_1_23]
          Length = 201

 Score = 39.0 bits (90), Expect = 0.79,   Method: Composition-based stats.
 Identities = 20/90 (22%), Positives = 40/90 (44%), Gaps = 2/90 (2%)

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           +  Q   +Y    +  V  E +E+  R   ++++M  L P  R I E   +Q      + 
Sbjct: 113 THEQYVQIYSELTKSYVETEYQEQDERMMHISKAMEKLTPHTRHILEECYIQRKKY--QE 170

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++ E  +S   VR+   +A + ++E   K+
Sbjct: 171 VAEELNISVSAVRKHIVKALQVIREECAKK 200


>gi|257057262|ref|YP_003135094.1| response regulator containing a CheY-like receiver
           domain-containing protein and an HTH DNA-binding
           domain-containing protein [Saccharomonospora viridis DSM
           43017]
 gi|256587134|gb|ACU98267.1| response regulator containing a CheY-like receiver domain protein
           and an HTH DNA-binding domain protein [Saccharomonospora
           viridis DSM 43017]
          Length = 223

 Score = 39.0 bits (90), Expect = 0.80,   Method: Composition-based stats.
 Identities = 16/67 (23%), Positives = 29/67 (43%), Gaps = 3/67 (4%)

Query: 235 LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSP 294
           L  RER +     L  N  + + ++ E  +S   VR   +   +K++ S + Q  L +  
Sbjct: 159 LTERERDVLI---LIANGYSNKEIADELVISERTVRTHVSSILRKLRLSSRTQAALVAVR 215

Query: 295 PLLQKPR 301
             L  P+
Sbjct: 216 EGLVPPQ 222


>gi|254521165|ref|ZP_05133220.1| RNA polymerase sigma-70 factor, ECF subfamily [Stenotrophomonas sp.
           SKA14]
 gi|219718756|gb|EED37281.1| RNA polymerase sigma-70 factor, ECF subfamily [Stenotrophomonas sp.
           SKA14]
          Length = 169

 Score = 39.0 bits (90), Expect = 0.80,   Method: Composition-based stats.
 Identities = 11/67 (16%), Positives = 26/67 (38%), Gaps = 2/67 (2%)

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
             D  ++       +  ++     +   L   ++ L PR R++F   R+    + L  + 
Sbjct: 85  LDDTQLHAIADPAPLPDQRLLDAEQLRHLDAIIAALPPRSRQVFLLARV--EQMALAEIG 142

Query: 260 SEFEVSR 266
            +  +SR
Sbjct: 143 RQLGISR 149


>gi|212638503|ref|YP_002315023.1| positive control sigma-like factor [Anoxybacillus flavithermus WK1]
 gi|212559983|gb|ACJ33038.1| DNA-directed RNA polymerase specialized sigma subunit
           [Anoxybacillus flavithermus WK1]
          Length = 166

 Score = 39.0 bits (90), Expect = 0.80,   Method: Composition-based stats.
 Identities = 16/70 (22%), Positives = 34/70 (48%), Gaps = 2/70 (2%)

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           E       R  +  ++SVL  RER ++   R     +T   +++   +S   V+ +  RA
Sbjct: 92  ESVITSWDRERIEDALSVLTEREREVYLMSRGYC--LTYSEIANYLCISSSSVQTMIERA 149

Query: 277 FKKVQESIQK 286
            +K+++ I++
Sbjct: 150 ERKIKKRIKE 159


>gi|332521597|ref|ZP_08398050.1| RNA polymerase sigma factor, sigma-70 family [Lacinutrix algicola
           5H-3-7-4]
 gi|332042686|gb|EGI78886.1| RNA polymerase sigma factor, sigma-70 family [Lacinutrix algicola
           5H-3-7-4]
          Length = 171

 Score = 39.0 bits (90), Expect = 0.81,   Method: Composition-based stats.
 Identities = 18/75 (24%), Positives = 31/75 (41%), Gaps = 8/75 (10%)

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           +      E K     L  ++S L   +R  F   R++      + ++    +SR+ V   
Sbjct: 99  ESPEFVLEEKQYLEKLQIALSKLTDAQRTAFMMNRVEGKKH--KEIADLLGISRKAV--- 153

Query: 273 EAR---AFKKVQESI 284
           E R   A KK++E I
Sbjct: 154 EKRIYGALKKLREDI 168


>gi|291528279|emb|CBK93865.1| DNA-directed RNA polymerase specialized sigma subunit [Eubacterium
           rectale M104/1]
          Length = 181

 Score = 39.0 bits (90), Expect = 0.81,   Method: Composition-based stats.
 Identities = 17/130 (13%), Positives = 41/130 (31%), Gaps = 2/130 (1%)

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
            +  E   A+      S+++ + +   L                S   + +++ D     
Sbjct: 47  EITKEVAYAMNNFYRSSKAKKVEIKNELGEVVDKMLREVPYSGQSIDGEGFMIEDFPDLN 106

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
             +      K  +  +   ++ LN  ER I      +    T   ++    +SR+ +   
Sbjct: 107 CDVEHCVLTKMEQQDIHTVINQLNSEERMIIYGIFFEN--KTQTQMAEIMGISRQMLSYK 164

Query: 273 EARAFKKVQE 282
                 K++E
Sbjct: 165 LKSTLNKMRE 174


>gi|239943053|ref|ZP_04694990.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces roseosporus
           NRRL 15998]
 gi|239989511|ref|ZP_04710175.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces roseosporus
           NRRL 11379]
 gi|291446530|ref|ZP_06585920.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces roseosporus
           NRRL 15998]
 gi|291349477|gb|EFE76381.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces roseosporus
           NRRL 15998]
          Length = 166

 Score = 39.0 bits (90), Expect = 0.81,   Method: Composition-based stats.
 Identities = 12/62 (19%), Positives = 23/62 (37%), Gaps = 2/62 (3%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L+           E    +  R+ L ++M  L  R+R +   R   +  +T   ++    
Sbjct: 84  LLSKPMPDMASAEEGAYDQLERDALIKAMKGLQRRQREVLVLRYFAD--MTEAQVAETLG 141

Query: 264 VS 265
           VS
Sbjct: 142 VS 143


>gi|227540296|ref|ZP_03970345.1| RNA polymerase sigma factor (possible RNA polymerase sigma-24
           factor) [Sphingobacterium spiritivorum ATCC 33300]
 gi|227239832|gb|EEI89847.1| RNA polymerase sigma factor (possible RNA polymerase sigma-24
           factor) [Sphingobacterium spiritivorum ATCC 33300]
          Length = 201

 Score = 39.0 bits (90), Expect = 0.81,   Method: Composition-based stats.
 Identities = 19/80 (23%), Positives = 35/80 (43%), Gaps = 4/80 (5%)

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
                 I+K E +   N L   +S L  R + IF   R +      E ++S  ++S+  V
Sbjct: 117 SNSNTAIDKLESEELDNTLRNILSKLPKRCQEIFIMSRFENLKN--EEIASRLQISQRTV 174

Query: 270 R-QIEARAFKKVQESIQKQV 288
             QI   A + +++ + K +
Sbjct: 175 ENQI-TIALRHIRQHLDKTI 193


>gi|311069839|ref|YP_003974762.1| alternative sigma factor sigmaO [Bacillus atrophaeus 1942]
 gi|310870356|gb|ADP33831.1| alternative sigma factor sigmaO [Bacillus atrophaeus 1942]
          Length = 190

 Score = 39.0 bits (90), Expect = 0.82,   Method: Composition-based stats.
 Identities = 7/97 (7%), Positives = 40/97 (41%), Gaps = 3/97 (3%)

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARR 247
            +      + +       +   +E + +E++  ++ ++  L +++  L  +++ +     
Sbjct: 88  PLTVDHPEAGERLPVQGGNDAYEEFLNLEEDLGQHIQDQNLYQAIQGLTDKQKSVLTKIY 147

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +    +  + ++     SR+ +  I  +  + +++ +
Sbjct: 148 VHGAAM--QEIADSLGESRQNISNIHKKGLENIRKQM 182


>gi|302535941|ref|ZP_07288283.1| sigma factor [Streptomyces sp. C]
 gi|302444836|gb|EFL16652.1| sigma factor [Streptomyces sp. C]
          Length = 315

 Score = 39.0 bits (90), Expect = 0.82,   Method: Composition-based stats.
 Identities = 23/107 (21%), Positives = 43/107 (40%), Gaps = 2/107 (1%)

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             +  +   R+   +SLN L   S +  S   +WL         V  + E  ++    + 
Sbjct: 70  VEDRRAYLVRVTTRQSLNRLRAMSRRKESYVGEWLPEPLLTAPDVAQDVELAESVSMAMM 129

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
             +  L+P ER +F  R   +     + +++  + +   VRQI  RA
Sbjct: 130 LVLETLSPTERAVFVLREAFDVGY--DEIAAAVDKTPAAVRQIAHRA 174


>gi|125973982|ref|YP_001037892.1| ECF subfamily RNA polymerase sigma-24 factor [Clostridium
           thermocellum ATCC 27405]
 gi|256004679|ref|ZP_05429656.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           thermocellum DSM 2360]
 gi|281418137|ref|ZP_06249157.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           thermocellum JW20]
 gi|125714207|gb|ABN52699.1| RNA polymerase, sigma subunit, ECF family [Clostridium thermocellum
           ATCC 27405]
 gi|255991414|gb|EEU01519.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           thermocellum DSM 2360]
 gi|281409539|gb|EFB39797.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           thermocellum JW20]
          Length = 205

 Score = 39.0 bits (90), Expect = 0.82,   Method: Composition-based stats.
 Identities = 8/66 (12%), Positives = 24/66 (36%), Gaps = 2/66 (3%)

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           D  + +    +       E K     +   +  L  +++  F  R +++   + + +   
Sbjct: 115 DDFIEEIPSFDDSPELLIEVKEHYKEIIEIIDSLKEKQKTAFILRYIRD--FSYKEIGKI 172

Query: 262 FEVSRE 267
             +S+E
Sbjct: 173 MGISQE 178


>gi|325281795|ref|YP_004254337.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Odoribacter
           splanchnicus DSM 20712]
 gi|324313604|gb|ADY34157.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Odoribacter
           splanchnicus DSM 20712]
          Length = 197

 Score = 39.0 bits (90), Expect = 0.83,   Method: Composition-based stats.
 Identities = 24/162 (14%), Positives = 61/162 (37%), Gaps = 27/162 (16%)

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK------------- 195
                  PE+   IA++  V+  E       +  D S+ A I +  K             
Sbjct: 35  AQQYLPDPEEAREIAQETFVTLWEKR---TEIRPDLSVQAFILTIAKHKCLNVLRKKIAE 91

Query: 196 ---NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
              + +      + ++        +  + +    ++ +++S L  + R I++  R  +  
Sbjct: 92  QKYSDNLTARETMANYSALSDETFDTVQMQELEQLIGQALSELPEKTRIIYKMSR--DQE 149

Query: 253 VTLENLSSEFEVSRERVRQIE---ARAFKKVQESIQKQVELS 291
           +T E ++ E ++S   V+ +E    +A   ++  ++  + L 
Sbjct: 150 MTYEEIAQEIDLS---VKSVEYHMTKALAHMRYKLKDYLILL 188


>gi|253580876|ref|ZP_04858139.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251847946|gb|EES75913.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 157

 Score = 39.0 bits (90), Expect = 0.83,   Method: Composition-based stats.
 Identities = 17/130 (13%), Positives = 42/130 (32%), Gaps = 2/130 (1%)

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
            +  E   A+      S+++ + +   L                S   + +++ D     
Sbjct: 23  EVTKEVAYAMNNFYRSSKAKKVEIKNELGEVVDKMLREVPYSGQSIDGEVFMIEDFPDLN 82

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
             +      K  +  + + ++ LN  ER I      +    T   ++    +SR+ +   
Sbjct: 83  CDVEHCVLTKMEQQDIHKVINQLNSEERMIIYGIFFEN--KTQTQMAEIMGISRQMLSYK 140

Query: 273 EARAFKKVQE 282
                 K++E
Sbjct: 141 LKSTLNKMRE 150


>gi|300771117|ref|ZP_07080993.1| DNA-directed RNA polymerase sigma subunit RpoE [Sphingobacterium
           spiritivorum ATCC 33861]
 gi|300761787|gb|EFK58607.1| DNA-directed RNA polymerase sigma subunit RpoE [Sphingobacterium
           spiritivorum ATCC 33861]
          Length = 201

 Score = 39.0 bits (90), Expect = 0.83,   Method: Composition-based stats.
 Identities = 20/89 (22%), Positives = 38/89 (42%), Gaps = 4/89 (4%)

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
            D  V  +       I+K E +   + L   +S L  R + IF   R +      E ++S
Sbjct: 108 DDLSVVSNATNSNTAIDKLESEELDSTLRNILSKLPKRCQEIFIMSRFENLKN--EEIAS 165

Query: 261 EFEVSRERVR-QIEARAFKKVQESIQKQV 288
             ++S+  V  QI   A + +++ + K +
Sbjct: 166 RLQISQRTVENQI-TIALRHIRQHLHKTI 193


>gi|237713727|ref|ZP_04544208.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D1]
 gi|262409367|ref|ZP_06085910.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 2_1_22]
 gi|229446174|gb|EEO51965.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D1]
 gi|262352819|gb|EEZ01916.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 2_1_22]
          Length = 196

 Score = 39.0 bits (90), Expect = 0.83,   Method: Composition-based stats.
 Identities = 26/138 (18%), Positives = 54/138 (39%), Gaps = 8/138 (5%)

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
            +I   L VS   +I    +     SL +L    +  +S++Q  L  D    E  +I  E
Sbjct: 64  QSIPAYLCVSLRHMIVNELKKENSGSLKSL---DEVGTSEYQFDLEID---IETAIIRSE 117

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
             K +  +L + ++ L  ++R +   +      ++ E ++    ++   V      A   
Sbjct: 118 LEKEQLEVLQKELNNLTKQQREVLYLKYY--KKMSSEEIAQVMGLTSRTVYNTTHMAISS 175

Query: 280 VQESIQKQVELSSSPPLL 297
           ++E + K   L  +  L 
Sbjct: 176 LRERMSKSFLLLVAANLW 193


>gi|313157021|gb|EFR56453.1| RNA polymerase sigma-70 factor [Alistipes sp. HGB5]
          Length = 196

 Score = 39.0 bits (90), Expect = 0.83,   Method: Composition-based stats.
 Identities = 15/73 (20%), Positives = 34/73 (46%), Gaps = 2/73 (2%)

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
           +I K    + R  L  ++  L P+ R +F+   L++  ++   +S    +S+  V     
Sbjct: 114 IIRKLYSDDLRASLDAAIESLPPKCREVFKLSYLED--LSNREISERLGISQSTVENHMY 171

Query: 275 RAFKKVQESIQKQ 287
            A K+++  + K+
Sbjct: 172 SALKQLRRKLSKE 184


>gi|312877791|ref|ZP_07737741.1| RNA polymerase, sigma-24 subunit, ECF subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
 gi|311795417|gb|EFR11796.1| RNA polymerase, sigma-24 subunit, ECF subfamily
           [Caldicellulosiruptor lactoaceticus 6A]
          Length = 183

 Score = 39.0 bits (90), Expect = 0.83,   Method: Composition-based stats.
 Identities = 14/90 (15%), Positives = 39/90 (43%), Gaps = 3/90 (3%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E  L +  ++ G+  A H L+ ++L ++               +VV E  +  +  + K
Sbjct: 2   DEKRLIEEAKK-GNKEALHTLIENNLNILSGFVTKMTQDYHFAQDVVQETLLRAIMNIDK 60

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           F P+   + +T+ +       ++++ ++  
Sbjct: 61  FSPD--AKFSTWLIKISINVYKDFLRKNKR 88


>gi|291558515|emb|CBL37315.1| DNA-directed RNA polymerase specialized sigma subunit, sigma24
           homolog [butyrate-producing bacterium SSC/2]
          Length = 138

 Score = 39.0 bits (90), Expect = 0.83,   Method: Composition-based stats.
 Identities = 10/68 (14%), Positives = 28/68 (41%), Gaps = 2/68 (2%)

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           + +   + L  ++  L+ R R         E   T   ++    +SR  V Q    + + 
Sbjct: 73  DIRICDDELAEALKHLSERNRENLLMYYFLEMSDT--EIAKRQNISRSGVFQNRHNSLEL 130

Query: 280 VQESIQKQ 287
           +++ ++++
Sbjct: 131 MKKILKEK 138


>gi|225873968|ref|YP_002755427.1| RNA polymerase sigma-70 factor, ECF subfamily [Acidobacterium
           capsulatum ATCC 51196]
 gi|225792742|gb|ACO32832.1| RNA polymerase sigma-70 factor, ECF subfamily [Acidobacterium
           capsulatum ATCC 51196]
          Length = 217

 Score = 39.0 bits (90), Expect = 0.83,   Method: Composition-based stats.
 Identities = 19/91 (20%), Positives = 35/91 (38%), Gaps = 2/91 (2%)

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D    +    +    D        + ERK     +  ++  L PRER +FE +  Q   +
Sbjct: 125 DATGGEMDMLVNVSDDRASANPDRELERKVLSRQIRAALEKLTPRERMVFELKHFQG--L 182

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            L  +      + E  +    RA KK++ ++
Sbjct: 183 RLRTIGEMLNTTEETAKNTLFRATKKLRANL 213


>gi|153805862|ref|ZP_01958530.1| hypothetical protein BACCAC_00101 [Bacteroides caccae ATCC 43185]
 gi|149130539|gb|EDM21745.1| hypothetical protein BACCAC_00101 [Bacteroides caccae ATCC 43185]
          Length = 189

 Score = 39.0 bits (90), Expect = 0.83,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 2/49 (4%)

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
           E+   K  + ++  ++S L  + RR+F  RR +E   +   ++SE  +S
Sbjct: 111 EELFSKEMKQLVEHALSKLPEKTRRVFIMRRFEE--KSYREIASEMNMS 157


>gi|158320239|ref|YP_001512746.1| ECF subfamily RNA polymerase sigma-24 factor [Alkaliphilus
           oremlandii OhILAs]
 gi|158140438|gb|ABW18750.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Alkaliphilus
           oremlandii OhILAs]
          Length = 191

 Score = 39.0 bits (90), Expect = 0.83,   Method: Composition-based stats.
 Identities = 14/92 (15%), Positives = 40/92 (43%), Gaps = 3/92 (3%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E  L ++  + G++ +  +L+ +H +    IA    G     ++V  E  +   + + K
Sbjct: 4   QEASLIEQ-SKAGNIDSFEQLILAHQKKAFNIAYRILGNLEDANDVTQEALLKAYKGISK 62

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           F+ +     +T+    +     ++I ++   +
Sbjct: 63  FNAK--SSFSTWLYTIVTNTSMDFIRKNRKTI 92


>gi|15921893|ref|NP_377562.1| hypothetical protein ST1593 [Sulfolobus tokodaii str. 7]
 gi|15622680|dbj|BAB66671.1| 204aa long conserved hypothetical protein [Sulfolobus tokodaii str.
           7]
          Length = 204

 Score = 39.0 bits (90), Expect = 0.83,   Method: Composition-based stats.
 Identities = 12/52 (23%), Positives = 22/52 (42%), Gaps = 5/52 (9%)

Query: 233 SVLNPRERRIFEA-----RRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           + L  R+  I +          +  +TL  L++   VS   + +I  RA +K
Sbjct: 143 NELTERQMEILKLAYRLGYFDDDRGITLTELANRLNVSAPTLEEILRRALRK 194


>gi|331091368|ref|ZP_08340207.1| hypothetical protein HMPREF9477_00850 [Lachnospiraceae bacterium
           2_1_46FAA]
 gi|330404232|gb|EGG83779.1| hypothetical protein HMPREF9477_00850 [Lachnospiraceae bacterium
           2_1_46FAA]
          Length = 139

 Score = 39.0 bits (90), Expect = 0.84,   Method: Composition-based stats.
 Identities = 15/88 (17%), Positives = 33/88 (37%), Gaps = 3/88 (3%)

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
              W  YD D     +   + R    + L  ++  L+ R R         E   T   ++
Sbjct: 54  LAVWDEYDSDYTFFNVCGNDIR-ICDDELAEALKHLSERNRENLLMYYFLEMSDT--EIA 110

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQ 287
               +SR  V Q    + + +++ ++++
Sbjct: 111 KRQNISRSGVFQNRHNSLELMKKILKEK 138


>gi|312793896|ref|YP_004026819.1| RNA polymerase, sigma-24 subunit, ecf subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
 gi|312181036|gb|ADQ41206.1| RNA polymerase, sigma-24 subunit, ECF subfamily
           [Caldicellulosiruptor kristjanssonii 177R1B]
          Length = 183

 Score = 39.0 bits (90), Expect = 0.84,   Method: Composition-based stats.
 Identities = 14/90 (15%), Positives = 39/90 (43%), Gaps = 3/90 (3%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E  L +  ++ G+  A H L+ ++L ++               +VV E  +  +  + K
Sbjct: 2   DEKRLIEEAKK-GNKEALHTLIENNLNILSGFVTKMTQDYHFAQDVVQETLLRAIMNIDK 60

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           F P+   + +T+ +       ++++ ++  
Sbjct: 61  FSPD--AKFSTWLIKISINVYKDFLRKNKR 88


>gi|237722331|ref|ZP_04552812.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 2_2_4]
 gi|299146361|ref|ZP_07039429.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 3_1_23]
 gi|229448141|gb|EEO53932.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 2_2_4]
 gi|298516852|gb|EFI40733.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 3_1_23]
          Length = 207

 Score = 39.0 bits (90), Expect = 0.84,   Method: Composition-based stats.
 Identities = 13/82 (15%), Positives = 33/82 (40%), Gaps = 6/82 (7%)

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
              N  Q ++ ++                 + + ++ R++  L PR+R +F+  R  E  
Sbjct: 99  DMANEDQLKEQILSQAIDSTNETNNHILLNDLKEIIARALEQLTPRQREVFKMSR--ELQ 156

Query: 253 VTLENLSSEFEVS----RERVR 270
           ++ + ++    VS    +E + 
Sbjct: 157 MSHKEIAEALGVSVHTVQEHIS 178


>gi|154246720|ref|YP_001417678.1| ECF subfamily RNA polymerase sigma-24 factor [Xanthobacter
           autotrophicus Py2]
 gi|154160805|gb|ABS68021.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Xanthobacter
           autotrophicus Py2]
          Length = 260

 Score = 39.0 bits (90), Expect = 0.84,   Method: Composition-based stats.
 Identities = 23/137 (16%), Positives = 50/137 (36%), Gaps = 7/137 (5%)

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKL-----NVSESEVISMNCRLAGDESLNAL 189
           L    R ++   + +   +L  + V  +A KL      ++         RL  + +++  
Sbjct: 43  LAHRARLVRMAFRIVQSRHLAEDVVEDVAVKLCEGEGVIAADHPAPFLYRLVRNLAIDRA 102

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
                + S                  +E+ E++    ++ R++  L PR R  F   R+ 
Sbjct: 103 RRLKRERSLAGSAEEAAHVAMPCACPLERLEQREMLEVVIRALDTLPPRTRLAFLRHRID 162

Query: 250 ENPVTLENLSSEFEVSR 266
             P   ++++    VSR
Sbjct: 163 GMP--QKDIAEHLGVSR 177


>gi|325663230|ref|ZP_08151680.1| hypothetical protein HMPREF0490_02421 [Lachnospiraceae bacterium
           4_1_37FAA]
 gi|325470684|gb|EGC73914.1| hypothetical protein HMPREF0490_02421 [Lachnospiraceae bacterium
           4_1_37FAA]
          Length = 141

 Score = 39.0 bits (90), Expect = 0.85,   Method: Composition-based stats.
 Identities = 10/68 (14%), Positives = 28/68 (41%), Gaps = 2/68 (2%)

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           + +   + L  ++  L+ R R         E   T   ++    +SR  V Q    + + 
Sbjct: 76  DIRICDDELAEALKHLSERNRENLLMYYFLEMSDT--EIAKRQNISRSGVFQNRHNSLEL 133

Query: 280 VQESIQKQ 287
           +++ ++++
Sbjct: 134 MKKILKEK 141


>gi|319783081|ref|YP_004142557.1| RNA polymerase sigma factor, sigma-70 family [Mesorhizobium ciceri
           biovar biserrulae WSM1271]
 gi|317168969|gb|ADV12507.1| RNA polymerase sigma factor, sigma-70 family [Mesorhizobium ciceri
           biovar biserrulae WSM1271]
          Length = 186

 Score = 39.0 bits (90), Expect = 0.85,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 39/97 (40%), Gaps = 5/97 (5%)

Query: 28  MLEKQE--EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           ML++ E  +  L  R +  GD  A   L+  H   V + A  + G      ++  E  + 
Sbjct: 4   MLDESEASDAELIGRAK-GGDRRAFSTLLERHYDFVYRAAYRWCGRKADAEDIAQEVCVR 62

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           L +A++ +    G    T+       A ++ + +S  
Sbjct: 63  LGKAIRDYRG--GGAFTTWLYSVTMNAARDVMRKSAR 97


>gi|297159068|gb|ADI08780.1| RNA polymerase, sigma-24 subunit, ECF subfamily protein
           [Streptomyces bingchenggensis BCW-1]
          Length = 296

 Score = 39.0 bits (90), Expect = 0.85,   Method: Composition-based stats.
 Identities = 23/107 (21%), Positives = 43/107 (40%), Gaps = 2/107 (1%)

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             +  +   R+   +SLN L   + +  +    WL         V  + E  ++    L 
Sbjct: 53  VQDRRAYLVRITTRQSLNRLRTMTRRKEAYVGPWLPEPLLTSPDVARDVELAESVSMALM 112

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
             +  L+P ER +F  R + +     + +++  + S   VRQI  RA
Sbjct: 113 LVLETLSPTERAVFVLREVFDVGY--DEIAAAVDKSPAAVRQIAHRA 157


>gi|168213648|ref|ZP_02639273.1| possible sigma factor [Clostridium perfringens CPE str. F4969]
 gi|170714803|gb|EDT26985.1| possible sigma factor [Clostridium perfringens CPE str. F4969]
          Length = 131

 Score = 39.0 bits (90), Expect = 0.85,   Method: Composition-based stats.
 Identities = 12/50 (24%), Positives = 25/50 (50%)

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
            ++  N +  +++ L+  ER+I E R L+    T + +S+    S +  R
Sbjct: 67  LEDCINSIDNALNELSDTERKIVELRYLEGKKHTWKEISNIVGYSSDYCR 116


>gi|49479940|ref|YP_035919.1| RNA polymerase factor sigma-70 [Bacillus thuringiensis serovar
           konkukian str. 97-27]
 gi|49331496|gb|AAT62142.1| RNA polymerase, ECF-type sigma factor [Bacillus thuringiensis
           serovar konkukian str. 97-27]
          Length = 188

 Score = 39.0 bits (90), Expect = 0.85,   Method: Composition-based stats.
 Identities = 10/59 (16%), Positives = 24/59 (40%), Gaps = 2/59 (3%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           H   E+   ++      R  L   ++ L P ++++F  + L       E +  +  ++R
Sbjct: 104 HISTEKSAEDELIIMEDREELLMLINQLEPLDQKVFIMKYLLGMKT--EEIGDKLGLTR 160


>gi|229144414|ref|ZP_04272819.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           BDRD-ST24]
 gi|296502401|ref|YP_003664101.1| RNA polymerase factor sigma-70 [Bacillus thuringiensis BMB171]
 gi|228639045|gb|EEK95470.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           BDRD-ST24]
 gi|296323453|gb|ADH06381.1| RNA polymerase factor sigma-70 [Bacillus thuringiensis BMB171]
          Length = 188

 Score = 39.0 bits (90), Expect = 0.86,   Method: Composition-based stats.
 Identities = 10/59 (16%), Positives = 24/59 (40%), Gaps = 2/59 (3%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           H   E+   ++      R  L   ++ L P ++++F  + L       E +  +  ++R
Sbjct: 104 HISTEKSAEDELIVMEDREELLMLINQLEPLDQKVFIMKYLLGMKT--EEIGDKLGLTR 160


>gi|229150006|ref|ZP_04278231.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           m1550]
 gi|228633444|gb|EEK90048.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           m1550]
          Length = 188

 Score = 39.0 bits (90), Expect = 0.86,   Method: Composition-based stats.
 Identities = 12/66 (18%), Positives = 28/66 (42%), Gaps = 6/66 (9%)

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
            ++ +      E  LI  E+    R  L + ++ L P ++++F  + L       E +  
Sbjct: 101 DEFYISTEKSAEDELIVMED----REELLKLINQLEPLDQKVFIMKYLLGMKT--EEIGD 154

Query: 261 EFEVSR 266
           +  ++R
Sbjct: 155 KLGLTR 160


>gi|207110856|ref|ZP_03245018.1| flagellar biosynthesis sigma factor [Helicobacter pylori
           HPKX_438_CA4C1]
          Length = 70

 Score = 39.0 bits (90), Expect = 0.86,   Method: Composition-based stats.
 Identities = 9/62 (14%), Positives = 30/62 (48%), Gaps = 2/62 (3%)

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
           ++  + +K E +     + ++++ ++ RE+ + +    +E  + L  +     ++  R+ 
Sbjct: 6   EQDEITKKIEAEELLEHVQKALNQMSEREQILIQLYYFEE--LNLSEIKEILGITESRIS 63

Query: 271 QI 272
           QI
Sbjct: 64  QI 65


>gi|329923297|ref|ZP_08278781.1| sigma-70, region 4 [Paenibacillus sp. HGF5]
 gi|328941389|gb|EGG37681.1| sigma-70, region 4 [Paenibacillus sp. HGF5]
          Length = 191

 Score = 39.0 bits (90), Expect = 0.86,   Method: Composition-based stats.
 Identities = 7/39 (17%), Positives = 21/39 (53%), Gaps = 2/39 (5%)

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
            M+++++  L  ++R +   R   +   TLE +++  ++
Sbjct: 121 QMISQAIHKLTDKQRTVIILRFFHD--YTLEEIATLLDI 157


>gi|77359677|ref|YP_339252.1| RNA polymerase sigma factor RpoE [Pseudoalteromonas haloplanktis
           TAC125]
 gi|76874588|emb|CAI85809.1| sigma E (sigma 24) factor of RNA polymerase, response to
           periplasmic stress (TetR/ArcR family) (partial match)
           [Pseudoalteromonas haloplanktis TAC125]
          Length = 193

 Score = 39.0 bits (90), Expect = 0.86,   Method: Composition-based stats.
 Identities = 19/95 (20%), Positives = 38/95 (40%), Gaps = 3/95 (3%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           M E+ ++  L KR ++ GD +A + LV  +   +  +   Y      I++V  E  I   
Sbjct: 1   MSEQDQDLALVKRVQQ-GDKNAFNLLVKKYQNKIAGLISRYVSNQGDIADVAQEAFIKAY 59

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           +A+  F  +      T+         + Y++    
Sbjct: 60  RALPNFRGD--SAFYTWLYRIAVNCAKNYLVAQGR 92


>gi|271962351|ref|YP_003336547.1| ECF subfamily RNA polymerase sigma-24 subunit [Streptosporangium
           roseum DSM 43021]
 gi|270505526|gb|ACZ83804.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Streptosporangium
           roseum DSM 43021]
          Length = 163

 Score = 39.0 bits (90), Expect = 0.87,   Method: Composition-based stats.
 Identities = 14/58 (24%), Positives = 29/58 (50%), Gaps = 4/58 (6%)

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV-RQIEARAFKKVQ 281
           R++L  ++S L+ R+R +      +E  +TL  ++     S   V  Q+  RA  +++
Sbjct: 96  RDVLWTAISELSGRQRAVVVLHYFEE--MTLAQVADVLGCSLGAVKSQL-GRALARLR 150


>gi|332685575|ref|YP_004455349.1| DNA-directed RNA polymerase, sigma factor 30 [Melissococcus
           plutonius ATCC 35311]
 gi|332369584|dbj|BAK20540.1| DNA-directed RNA polymerase, sigma factor 30 [Melissococcus
           plutonius ATCC 35311]
          Length = 185

 Score = 39.0 bits (90), Expect = 0.88,   Method: Composition-based stats.
 Identities = 13/88 (14%), Positives = 34/88 (38%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            G+    + L   +  +V K++  Y   G    + + EG I    ++K + P+R   +  
Sbjct: 9   EGNEEVFNHLYRQYHPIVYKLSKKYYLKGYDNEDWLQEGRISFYHSLKNYQPDRKVTIGK 68

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           +     +  ++  + +  +  +   T  
Sbjct: 69  FFKLNFENHIRSLVRKQCAYKRTADTMA 96


>gi|304438034|ref|ZP_07397978.1| RNA polymerase sigma factor WhiG [Selenomonas sp. oral taxon 149
           str. 67H29BP]
 gi|304368988|gb|EFM22669.1| RNA polymerase sigma factor WhiG [Selenomonas sp. oral taxon 149
           str. 67H29BP]
          Length = 215

 Score = 39.0 bits (90), Expect = 0.88,   Method: Composition-based stats.
 Identities = 15/72 (20%), Positives = 35/72 (48%), Gaps = 2/72 (2%)

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
             ++ +   EER    ++LTR+M  L  RE+ + +    ++  +TL  ++     S   +
Sbjct: 133 AADRPMERTEERLLAEDILTRAMHRLTAREKEVLDLHYFRD--LTLRRIAVLLGTSAGAL 190

Query: 270 RQIEARAFKKVQ 281
            + +A   +K++
Sbjct: 191 SKSKANLLRKLR 202


>gi|282863694|ref|ZP_06272752.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Streptomyces sp.
           ACTE]
 gi|282561395|gb|EFB66939.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Streptomyces sp.
           ACTE]
          Length = 203

 Score = 39.0 bits (90), Expect = 0.88,   Method: Composition-based stats.
 Identities = 11/62 (17%), Positives = 23/62 (37%), Gaps = 2/62 (3%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L+           E    +  R+ L ++M  L  R+R +   R   +  +T   ++    
Sbjct: 121 LLSKPMPDMASAEEGAYDQLERDALIKAMKGLQRRQREVLVLRYFSD--MTEAQVAETLG 178

Query: 264 VS 265
           +S
Sbjct: 179 IS 180


>gi|227549902|ref|ZP_03979951.1| RNA polymerase sigma factor SigD [Corynebacterium lipophiloflavum
           DSM 44291]
 gi|227077998|gb|EEI15961.1| RNA polymerase sigma factor SigD [Corynebacterium lipophiloflavum
           DSM 44291]
          Length = 192

 Score = 39.0 bits (90), Expect = 0.88,   Method: Composition-based stats.
 Identities = 15/82 (18%), Positives = 33/82 (40%), Gaps = 2/82 (2%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           V D +   +   E     +  N +   + +L+ + R I   R      ++ E  +     
Sbjct: 107 VPDEEISGETPEEFMLVSDGSNRVRELLDLLSDKARDIIILRVFVG--LSAEETAEAVGG 164

Query: 265 SRERVRQIEARAFKKVQESIQK 286
           +   VR  + RA   ++++IQ+
Sbjct: 165 TAGAVRVAQHRALATLRKAIQE 186


>gi|160937776|ref|ZP_02085135.1| hypothetical protein CLOBOL_02668 [Clostridium bolteae ATCC
           BAA-613]
 gi|158439215|gb|EDP16968.1| hypothetical protein CLOBOL_02668 [Clostridium bolteae ATCC
           BAA-613]
          Length = 211

 Score = 39.0 bits (90), Expect = 0.88,   Method: Composition-based stats.
 Identities = 21/115 (18%), Positives = 43/115 (37%), Gaps = 16/115 (13%)

Query: 175 SMNCRLAGDESLNALINSSDKNSSQWQDWLVYD---HDGQEQVLIEKEERKNRRNMLTRS 231
            M  R   ++SL+AL        S   D+             +LI+ E       ++  +
Sbjct: 97  EMAHRREREKSLDALTQEEMDKLSVVDDYPSDSYVFSSYGYDLLIDNE-------LVAEA 149

Query: 232 MSVLNPRERRIFEARRLQENPVTLE--NLSSEFEVSRERVRQIEARAFKKVQESI 284
            + L  +E+ I     + +    L    + S   +SR  V++   R  K+++  +
Sbjct: 150 FASLPEQEQSILILHCVLD----LADGEIGSLMGMSRSAVQRHRTRTLKQLRMKL 200


>gi|111019799|ref|YP_702771.1| transcriptional regulator [Rhodococcus jostii RHA1]
 gi|110819329|gb|ABG94613.1| probable transcriptional regulator [Rhodococcus jostii RHA1]
          Length = 340

 Score = 39.0 bits (90), Expect = 0.88,   Method: Composition-based stats.
 Identities = 10/51 (19%), Positives = 23/51 (45%), Gaps = 12/51 (23%)

Query: 251 NPVTLENLSSEFEVSR-------ERVR-----QIEARAFKKVQESIQKQVE 289
           + +T   +++   VSR        R R     +IE +A   ++++++   E
Sbjct: 38  DGMTQAEVATRLGVSRPTAGRLVARARAQGLVRIEVQAPAHLRDALRSDEE 88


>gi|71908689|ref|YP_286276.1| RNA polymerase factor sigma-70 [Dechloromonas aromatica RCB]
 gi|71848310|gb|AAZ47806.1| RNA polymerase, sigma-24 subunit, RpoE [Dechloromonas aromatica
           RCB]
          Length = 192

 Score = 39.0 bits (90), Expect = 0.88,   Method: Composition-based stats.
 Identities = 18/96 (18%), Positives = 35/96 (36%), Gaps = 7/96 (7%)

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
            S+V SM   L     L+A     D++    +     + D   +    K ++    N++ 
Sbjct: 78  RSKVRSMWTTL-----LSAFTPDDDEDHDPLETLAADEDDAGPKTPESKLQQAQTLNLIE 132

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
             +  L  R+R  F  R  ++  V     ++    S
Sbjct: 133 DEIKKLPARQREAFLMRYWEDMDV--AETAAAMGCS 166


>gi|296450730|ref|ZP_06892483.1| conserved hypothetical protein [Clostridium difficile NAP08]
 gi|296260574|gb|EFH07416.1| conserved hypothetical protein [Clostridium difficile NAP08]
          Length = 157

 Score = 39.0 bits (90), Expect = 0.89,   Method: Composition-based stats.
 Identities = 16/98 (16%), Positives = 35/98 (35%), Gaps = 10/98 (10%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
           + + Q  ++ + D       + +       R  + + ++ L+  ER I      +    T
Sbjct: 65  ETNGQDYEFSIEDFPDYSCDVEDSVISSAERRDIHKVINQLDAEERMIIYGIYFEN--KT 122

Query: 255 LENLSSEFEVSRERVRQIEA----RAFKKVQESIQKQV 288
              L+    VS    RQ+ A        K++   Q+ +
Sbjct: 123 QVQLARIMGVS----RQVLAYKLNTILNKMRRMYQENI 156


>gi|295110737|emb|CBL24690.1| DNA-directed RNA polymerase specialized sigma subunit [Ruminococcus
           obeum A2-162]
          Length = 216

 Score = 39.0 bits (90), Expect = 0.89,   Method: Composition-based stats.
 Identities = 13/63 (20%), Positives = 31/63 (49%), Gaps = 2/63 (3%)

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           ER      +   M++L  R+R++ +    Q+   T + +S E  ++   V +  ++A +K
Sbjct: 138 ERIIAEETVRGLMNLLTERQRQMIQRIYFQQ--KTQKEVSHELGITVPAVSKCISQAMQK 195

Query: 280 VQE 282
           ++ 
Sbjct: 196 MRN 198


>gi|83590534|ref|YP_430543.1| putative RNA polymerase sigma factor SigI [Moorella thermoacetica
           ATCC 39073]
 gi|83573448|gb|ABC20000.1| Sigma-70 region 2 [Moorella thermoacetica ATCC 39073]
          Length = 242

 Score = 39.0 bits (90), Expect = 0.89,   Method: Composition-based stats.
 Identities = 18/85 (21%), Positives = 34/85 (40%), Gaps = 4/85 (4%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM---QAVKKFDPER 97
               GD  A   L+  +   ++ +     G+ + + E   E +IGLM   +A+  +  E 
Sbjct: 13  LARSGDAVAREELIRRYTPFILSVVSRTTGHFIRLGED-DEASIGLMAFNEAIDNYRLEG 71

Query: 98  GFRLATYSMWWIKAAMQEYILRSWS 122
           G    T +   I+  + +Y  R   
Sbjct: 72  GATFLTLAETVIRRRLIDYFRREGR 96


>gi|73946144|ref|XP_541154.2| PREDICTED: similar to nesprin 1 isoform beta [Canis familiaris]
          Length = 8760

 Score = 39.0 bits (90), Expect = 0.90,   Method: Composition-based stats.
 Identities = 28/125 (22%), Positives = 51/125 (40%), Gaps = 5/125 (4%)

Query: 112  AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            A  + + RSW  +K   +  Q+ L+  L R + +  ++   + K E   AI  KL+ S  
Sbjct: 5898 AKLDDLQRSWETLKNVISEKQRTLYEALERQQKYQDSLQSISTKME---AIEMKLSESLE 5954

Query: 172  EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLT 229
               S   ++A  ++L   I       S+ Q  L  +   +  E    E+   ++   +L 
Sbjct: 5955 HGRSPESQMAEHQALMDEILMLQDEISELQSSLAEELVSESPESDPAEQLALQSTLTVLA 6014

Query: 230  RSMSV 234
              MS 
Sbjct: 6015 ERMST 6019


>gi|24214801|ref|NP_712282.1| RNA polymerase ECF-type sigma factor [Leptospira interrogans
           serovar Lai str. 56601]
 gi|45657682|ref|YP_001768.1| RNA polymerase ECF-type sigma factor [Leptospira interrogans
           serovar Copenhageni str. Fiocruz L1-130]
 gi|24195810|gb|AAN49300.1| RNA polymerase ECF-type sigma factor [Leptospira interrogans
           serovar Lai str. 56601]
 gi|45600922|gb|AAS70405.1| RNA polymerase ECF-type sigma factor [Leptospira interrogans
           serovar Copenhageni str. Fiocruz L1-130]
          Length = 184

 Score = 39.0 bits (90), Expect = 0.90,   Method: Composition-based stats.
 Identities = 14/60 (23%), Positives = 34/60 (56%), Gaps = 2/60 (3%)

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R +L + + VL+ R+++I    +L  + +++  +S +  +S   V+ I  RA +K+++  
Sbjct: 123 REILKKWLDVLDERQKQILTHLKL--DGMSVREVSEKTGLSESNVKVITHRAVQKIRKHF 180


>gi|304316935|ref|YP_003852080.1| RNA polymerase, sigma-24 subunit, ECF subfamily
           [Thermoanaerobacterium thermosaccharolyticum DSM 571]
 gi|302778437|gb|ADL68996.1| RNA polymerase, sigma-24 subunit, ECF subfamily
           [Thermoanaerobacterium thermosaccharolyticum DSM 571]
          Length = 170

 Score = 39.0 bits (90), Expect = 0.91,   Method: Composition-based stats.
 Identities = 19/97 (19%), Positives = 46/97 (47%), Gaps = 6/97 (6%)

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
            SD + ++    +  D+   E+ ++  EE    ++ L   +  L  + R + E R +   
Sbjct: 76  ISDIHFNEMNVEMFSDNVMLEEYVVNLEE----KDRLYSCLLSLPEKYRTVTELRII--E 129

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            ++L++ +     S   ++ I+ RA  K++E ++K+ 
Sbjct: 130 GLSLKDCAKILGKSTSSIKNIQYRAIIKLRELMKKEA 166


>gi|255529976|ref|YP_003090348.1| sigma-70 family RNA polymerase sigma factor [Pedobacter heparinus
           DSM 2366]
 gi|255342960|gb|ACU02286.1| RNA polymerase sigma factor, sigma-70 family [Pedobacter heparinus
           DSM 2366]
          Length = 200

 Score = 39.0 bits (90), Expect = 0.91,   Method: Composition-based stats.
 Identities = 15/71 (21%), Positives = 33/71 (46%), Gaps = 2/71 (2%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E   I KE+       L  +++ ++PR++ I   R  +E       ++    +S +   +
Sbjct: 112 ESAYIRKEDLNLLSIQLLDALNQISPRQKEILYLRYFEELDYN--QIAEMMNISVKGAYK 169

Query: 272 IEARAFKKVQE 282
           + ARA + ++E
Sbjct: 170 LSARALEALRE 180


>gi|48477348|ref|YP_023054.1| DNA binding protein [Picrophilus torridus DSM 9790]
 gi|48429996|gb|AAT42861.1| DNA binding protein [Picrophilus torridus DSM 9790]
          Length = 204

 Score = 39.0 bits (90), Expect = 0.91,   Method: Composition-based stats.
 Identities = 18/105 (17%), Positives = 39/105 (37%), Gaps = 10/105 (9%)

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK-----NRRNMLTRSMSVLNPRER 240
            + +I  +   SS+   + +   D  E   +E E R      +  +M       L  RE+
Sbjct: 91  FDDVITGTKSLSSENIIYNIILPDIAELKRLENELRSKNIDYSIIDMSENENDNLTDREK 150

Query: 241 RIF-----EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            I            +   +L  ++ +  +S   + +I  ++ KK+
Sbjct: 151 EIIIEIYKRGYFNNDRNQSLTEIARDLNISTASLSEILRKSLKKI 195


>gi|281422799|ref|ZP_06253798.1| RNA polymerase ECF-type sigma factor [Prevotella copri DSM 18205]
 gi|281403167|gb|EFB33847.1| RNA polymerase ECF-type sigma factor [Prevotella copri DSM 18205]
          Length = 164

 Score = 39.0 bits (90), Expect = 0.91,   Method: Composition-based stats.
 Identities = 14/72 (19%), Positives = 31/72 (43%), Gaps = 2/72 (2%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           +Q   + + +K R+  +   + +L    R + E   L         ++ E  V +E V++
Sbjct: 89  DQCYEDNDIQKERQRQVEEMLDLLPDTTRHVLEECYLNHKKY--REVADEMNVCQETVKR 146

Query: 272 IEARAFKKVQES 283
              +A K ++E 
Sbjct: 147 HIIKALKLLREH 158


>gi|149279931|ref|ZP_01886057.1| RNA polymerase ECF-type sigma factor [Pedobacter sp. BAL39]
 gi|149229311|gb|EDM34704.1| RNA polymerase ECF-type sigma factor [Pedobacter sp. BAL39]
          Length = 208

 Score = 39.0 bits (90), Expect = 0.91,   Method: Composition-based stats.
 Identities = 11/76 (14%), Positives = 27/76 (35%), Gaps = 7/76 (9%)

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            +N        +   + +DH      +I+ E  +  +  +   +  L PR++ I   R  
Sbjct: 98  FVNVEHDADYPFHFEVSFDH-----QIIKTESERVMQEKMKSIILTLPPRQQEIIFLRFY 152

Query: 249 QENPVTLENLSSEFEV 264
               +  E ++    +
Sbjct: 153 --EGMAYEEIADIMNL 166


>gi|29348926|ref|NP_812429.1| RNA polymerase ECF-type sigma factor [Bacteroides thetaiotaomicron
           VPI-5482]
 gi|253571061|ref|ZP_04848468.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 1_1_6]
 gi|298386648|ref|ZP_06996203.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 1_1_14]
 gi|29340833|gb|AAO78623.1| RNA polymerase ECF-type sigma factor [Bacteroides thetaiotaomicron
           VPI-5482]
 gi|251839014|gb|EES67098.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 1_1_6]
 gi|298260322|gb|EFI03191.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 1_1_14]
          Length = 190

 Score = 39.0 bits (90), Expect = 0.91,   Method: Composition-based stats.
 Identities = 19/93 (20%), Positives = 43/93 (46%), Gaps = 2/93 (2%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
             + + +D         E + I KE+ KN    +   MS L  R+R I   R +++  ++
Sbjct: 100 DEADEKEDQSEEHFSTPETIYINKEQEKNTHMKVHAMMSSLTTRQREIVYYRYIKD--MS 157

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++ +S   +++ + V     RA  +V+   +++
Sbjct: 158 IDEISKITDMNYQSVSNSIQRALGRVRNLFKRE 190


>gi|330464852|ref|YP_004377753.1| hypothetical protein VAB18032_30209 [Verrucosispora maris
           AB-18-032]
 gi|328813834|gb|AEB48005.1| hypothetical protein VAB18032_30209 [Verrucosispora maris
           AB-18-032]
          Length = 258

 Score = 39.0 bits (90), Expect = 0.92,   Method: Composition-based stats.
 Identities = 11/41 (26%), Positives = 19/41 (46%), Gaps = 1/41 (2%)

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           RERR      L  + +T   ++    +SR RV Q+ +   +
Sbjct: 14  RERREIFE-GLLHDGMTQLQIAEALGMSRSRVSQLLSAGLR 53


>gi|298483687|ref|ZP_07001861.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D22]
 gi|295087577|emb|CBK69100.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase
           sigma-70 factor, Bacteroides expansion family 1
           [Bacteroides xylanisolvens XB1A]
 gi|298270104|gb|EFI11691.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D22]
          Length = 200

 Score = 39.0 bits (90), Expect = 0.92,   Method: Composition-based stats.
 Identities = 13/82 (15%), Positives = 33/82 (40%), Gaps = 6/82 (7%)

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
              N  Q ++ ++                 + + ++ R++  L PR+R +F+  R  E  
Sbjct: 92  DMANEDQLKEQILSQAIDSTNETNNHILLNDLKEIVARALEQLTPRQREVFKMSR--ELQ 149

Query: 253 VTLENLSSEFEVS----RERVR 270
           ++ + ++    VS    +E + 
Sbjct: 150 MSHKEIAEALGVSVHTVQEHIS 171


>gi|294054970|ref|YP_003548628.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Coraliomargarita
           akajimensis DSM 45221]
 gi|293614303|gb|ADE54458.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Coraliomargarita
           akajimensis DSM 45221]
          Length = 201

 Score = 39.0 bits (90), Expect = 0.92,   Method: Composition-based stats.
 Identities = 21/104 (20%), Positives = 44/104 (42%), Gaps = 15/104 (14%)

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL+  I  ++ + +     L      + +   E    +   + +T  MS LN + R +  
Sbjct: 104 SLDQPIGDAEGDMT-----LENVMPSEGETPAEAAVTQEFVDRVTECMSGLNDKHREVLL 158

Query: 245 ARRLQENPVTLENLSSEFEVS----RERVRQIEARAFKKVQESI 284
            R    + ++ E +S + E+S    + R+    ARA   ++E +
Sbjct: 159 LR--NVHNLSYEEISDQLEISVGTVKSRI----ARARDSLRELM 196


>gi|293372013|ref|ZP_06618412.1| RNA polymerase sigma-70 factor [Bacteroides ovatus SD CMC 3f]
 gi|292633024|gb|EFF51606.1| RNA polymerase sigma-70 factor [Bacteroides ovatus SD CMC 3f]
          Length = 193

 Score = 39.0 bits (90), Expect = 0.92,   Method: Composition-based stats.
 Identities = 13/82 (15%), Positives = 33/82 (40%), Gaps = 6/82 (7%)

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
              N  Q ++ ++                 + + ++ R++  L PR+R +F+  R  E  
Sbjct: 85  DMANEDQLKEQILSQAIDSTNETNNHILLNDLKEIIARALEQLTPRQREVFKMSR--ELQ 142

Query: 253 VTLENLSSEFEVS----RERVR 270
           ++ + ++    VS    +E + 
Sbjct: 143 MSHKEIAEALGVSVHTVQEHIS 164


>gi|302865402|ref|YP_003834039.1| helix-turn-helix domain-containing protein [Micromonospora
           aurantiaca ATCC 27029]
 gi|315501947|ref|YP_004080834.1| helix-turn-helix domain protein [Micromonospora sp. L5]
 gi|302568261|gb|ADL44463.1| helix-turn-helix domain protein [Micromonospora aurantiaca ATCC
           27029]
 gi|315408566|gb|ADU06683.1| helix-turn-helix domain protein [Micromonospora sp. L5]
          Length = 105

 Score = 39.0 bits (90), Expect = 0.92,   Method: Composition-based stats.
 Identities = 13/58 (22%), Positives = 23/58 (39%), Gaps = 8/58 (13%)

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
           E      ++ +L   +     R   +  AR L     T + ++    V++ RV QIE 
Sbjct: 21  EDAVDAGKQELLAEVIGH---RLAEVRRARGL-----TQQQVADRMGVTKGRVSQIEQ 70


>gi|260172922|ref|ZP_05759334.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D2]
          Length = 200

 Score = 39.0 bits (90), Expect = 0.92,   Method: Composition-based stats.
 Identities = 20/90 (22%), Positives = 40/90 (44%), Gaps = 2/90 (2%)

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           +  Q   +Y    +  V  E +E+  R   ++++M  L P  R I E   +Q      + 
Sbjct: 112 THEQYIQIYSELTKSYVETEYQEQDERMMHISKAMEKLTPHTRHILEECYIQRKKY--QE 169

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++ E  +S   VR+   +A + ++E   K+
Sbjct: 170 VAEELNISVSAVRKHIVKALQVIREECAKK 199


>gi|320527883|ref|ZP_08029051.1| sigma-70, region 4 [Solobacterium moorei F0204]
 gi|320131820|gb|EFW24382.1| sigma-70, region 4 [Solobacterium moorei F0204]
          Length = 137

 Score = 39.0 bits (90), Expect = 0.93,   Method: Composition-based stats.
 Identities = 15/94 (15%), Positives = 48/94 (51%), Gaps = 6/94 (6%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
            +   + D ++ +    E+++    E K +   L ++++ L   ER + EA   +E   +
Sbjct: 50  DHDGHFVDNIIDEKIDLEKIV----EVKMQIEELNKALATLTKEERDLIEAIFFREE--S 103

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           L+++  + +V+ + + +   R  +K+++ ++ ++
Sbjct: 104 LKSIGEKEKVTHQAIGKRRDRILEKLRKILEDKI 137


>gi|225026231|ref|ZP_03715423.1| hypothetical protein EUBHAL_00472 [Eubacterium hallii DSM 3353]
 gi|224956482|gb|EEG37691.1| hypothetical protein EUBHAL_00472 [Eubacterium hallii DSM 3353]
          Length = 181

 Score = 39.0 bits (90), Expect = 0.93,   Method: Composition-based stats.
 Identities = 17/130 (13%), Positives = 41/130 (31%), Gaps = 2/130 (1%)

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
            +  E   A+      S+++ + +   L                S   + +++ D     
Sbjct: 47  EITKEVAYAMNNFYRSSKAKKVEIKNELGEVVDKMLREVPYSGQSIDGEGFMIEDFPDLN 106

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
             +      K  +  +   ++ LN  ER I      +    T   ++    +SR+ +   
Sbjct: 107 CDVEHCVLTKMEQQDIHTVINQLNSEERMIIYGIFFEN--KTQTQMAEIMGISRQMLSYK 164

Query: 273 EARAFKKVQE 282
                 K++E
Sbjct: 165 LKSTLNKMRE 174


>gi|159897852|ref|YP_001544099.1| ECF subfamily RNA polymerase sigma-24 factor [Herpetosiphon
           aurantiacus ATCC 23779]
 gi|159890891|gb|ABX03971.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Herpetosiphon
           aurantiacus ATCC 23779]
          Length = 182

 Score = 39.0 bits (90), Expect = 0.93,   Method: Composition-based stats.
 Identities = 17/89 (19%), Positives = 38/89 (42%), Gaps = 5/89 (5%)

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D+   ++ ++    H+      IE+         +   +  L  +ER IF  R + E  +
Sbjct: 97  DRKEPRYDEYSKQYHENTMINPIEEALSMLH---IVEYLHDLTDKERYIFIQRLVHE--L 151

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQE 282
           T + +  +  +S + VR    R+  K+++
Sbjct: 152 TFKEIGLKLGISEDNVRMTFNRSIAKIKK 180


>gi|134300125|ref|YP_001113621.1| ECF subfamily RNA polymerase sigma-24 factor [Desulfotomaculum
           reducens MI-1]
 gi|134052825|gb|ABO50796.1| RNA polymerase, sigma-24 subunit, RpoE [Desulfotomaculum reducens
           MI-1]
          Length = 200

 Score = 39.0 bits (90), Expect = 0.93,   Method: Composition-based stats.
 Identities = 23/98 (23%), Positives = 41/98 (41%), Gaps = 10/98 (10%)

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
           Y+    +    E  +R   + M+   ++ L+   R I   R +QE     E ++     S
Sbjct: 109 YEIRSNDPGPEEMLDRSETQAMIQACLNTLSDDYREIIVMREIQELAY--EEIAEILGCS 166

Query: 266 ----RERVRQIEARAFKKVQESIQKQVELSSSPPLLQK 299
               + R+     RA + ++E I KQ+EL +    L K
Sbjct: 167 LGTVKSRLS----RARQALKEKISKQMELITPAKRLAK 200



 Score = 37.1 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 25/147 (17%), Positives = 48/147 (32%), Gaps = 6/147 (4%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           E  L     + GD  A   LV  +   V  IA    G     S++  +  I + QA+  F
Sbjct: 4   EDQLLVERSKKGDREAFEHLVRLYENKVYTIAYRLMGNHADASDLAQDAFIKIYQALPNF 63

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLF----FNLRRLKGHLQAI 149
             +     +T+         ++ + +      +    N         + +R      + +
Sbjct: 64  RGD--SSFSTWIYHITVNVCRDELRKRQRRPTVSLDDNSSDSNNSNTYEIRSNDPGPEEM 121

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISM 176
            D +     + A    L+    E+I M
Sbjct: 122 LDRSETQAMIQACLNTLSDDYREIIVM 148


>gi|187939875|gb|ACD39013.1| hypothetical protein PACL_0225 [Pseudomonas aeruginosa]
          Length = 260

 Score = 39.0 bits (90), Expect = 0.94,   Method: Composition-based stats.
 Identities = 24/111 (21%), Positives = 51/111 (45%), Gaps = 14/111 (12%)

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
             L+N  D+ S++ +D + +        L +    ++ R +L  ++  L P +RRI E  
Sbjct: 156 EELVNDEDEISAEVEDAVAHYDPFDSGELYQ----EDYRRLLDGAIDALPPLQRRIVEMM 211

Query: 247 RLQ-------ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
           RL+        + +T   +S     S + +R    RAF  ++  ++++ E+
Sbjct: 212 RLEIPIASINPDMLT---ISKALGKSEKTIRNQRDRAFATLRRRLERKEEM 259


>gi|170691126|ref|ZP_02882292.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia graminis
           C4D1M]
 gi|170144375|gb|EDT12537.1| RNA polymerase, sigma 70 subunit, RpoD [Burkholderia graminis
           C4D1M]
          Length = 469

 Score = 39.0 bits (90), Expect = 0.94,   Method: Composition-based stats.
 Identities = 10/31 (32%), Positives = 15/31 (48%)

Query: 47  LSAAHRLVTSHLRLVVKIAMGYRGYGLPISE 77
             A   +  ++LRLV+ IA  Y   GL   +
Sbjct: 439 RQAKREMTEANLRLVISIAKKYTNRGLQFLD 469


>gi|21222029|ref|NP_627808.1| RNA polymerase sigma factor [Streptomyces coelicolor A3(2)]
 gi|256786885|ref|ZP_05525316.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
 gi|289770779|ref|ZP_06530157.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
 gi|5123888|emb|CAB45480.1| putative RNA polymerase sigma factor [Streptomyces coelicolor
           A3(2)]
 gi|289700978|gb|EFD68407.1| RNA polymerase sigma factor [Streptomyces lividans TK24]
          Length = 190

 Score = 39.0 bits (90), Expect = 0.94,   Method: Composition-based stats.
 Identities = 11/62 (17%), Positives = 23/62 (37%), Gaps = 2/62 (3%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L+           E    +  R+ L ++M  L  R+R +   R   +  +T   ++    
Sbjct: 108 LLSKPMPDMASAEEGAYDQLERDSLIKAMKGLQRRQREVLVLRYFAD--MTEAQVAETLG 165

Query: 264 VS 265
           +S
Sbjct: 166 IS 167


>gi|302553022|ref|ZP_07305364.1| RNA polymerase sigma factor [Streptomyces viridochromogenes DSM
           40736]
 gi|302470640|gb|EFL33733.1| RNA polymerase sigma factor [Streptomyces viridochromogenes DSM
           40736]
          Length = 189

 Score = 39.0 bits (90), Expect = 0.95,   Method: Composition-based stats.
 Identities = 11/62 (17%), Positives = 23/62 (37%), Gaps = 2/62 (3%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L+           E    +  R+ L ++M  L  R+R +   R   +  +T   ++    
Sbjct: 107 LLSKPMPDMASAEEGAYDQLERDSLIKAMKGLQRRQREVLVLRYFAD--MTEAQVAESLG 164

Query: 264 VS 265
           +S
Sbjct: 165 IS 166


>gi|226310129|ref|YP_002770023.1| RNA polymerase ECF-type sigma factor [Brevibacillus brevis NBRC
           100599]
 gi|226093077|dbj|BAH41519.1| RNA polymerase ECF-type sigma factor [Brevibacillus brevis NBRC
           100599]
          Length = 171

 Score = 39.0 bits (90), Expect = 0.95,   Method: Composition-based stats.
 Identities = 12/79 (15%), Positives = 30/79 (37%), Gaps = 2/79 (2%)

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
             +++  E    +     L   +  L   +R +   R L +  +    ++     +   V
Sbjct: 95  ATDKLPEECLLNQETTEGLWDKVHTLTKDQRNVIALRYLGDLRMN--EIAEILGKTEASV 152

Query: 270 RQIEARAFKKVQESIQKQV 288
           + +  R  KK+Q+ + +Q 
Sbjct: 153 KILHFRGIKKLQQLMTEQA 171


>gi|196045048|ref|ZP_03112281.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           03BB108]
 gi|196024050|gb|EDX62724.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           03BB108]
          Length = 188

 Score = 39.0 bits (90), Expect = 0.95,   Method: Composition-based stats.
 Identities = 15/79 (18%), Positives = 33/79 (41%), Gaps = 10/79 (12%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           H   E+   ++      R  L + ++ L P ++++F  + +       E +  +  ++R 
Sbjct: 104 HISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYVLGMKT--EEIGDKLGLTRA 161

Query: 268 ----RVRQIEARAFKKVQE 282
               RV     R  KK+Q+
Sbjct: 162 AIDNRV----YRGKKKLQQ 176


>gi|320104378|ref|YP_004179969.1| ECF subfamily RNA polymerase sigma-24 factor [Isosphaera pallida
           ATCC 43644]
 gi|319751660|gb|ADV63420.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Isosphaera pallida
           ATCC 43644]
          Length = 251

 Score = 39.0 bits (90), Expect = 0.95,   Method: Composition-based stats.
 Identities = 19/91 (20%), Positives = 34/91 (37%), Gaps = 5/91 (5%)

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
           I+MN  L+       L    D+  S   D             +E+ E +    ++ R++S
Sbjct: 78  IAMNLALSRRRKRKRLFGWWDREGSAPPDPSDLSATSDPTANLERAELE---ALVQRALS 134

Query: 234 VLNPRERRIFEARRLQENPVTLENLSSEFEV 264
            L P  R +   R L    ++ E ++    V
Sbjct: 135 QLPPEARAVIILRDL--EGLSYEEIAEILGV 163


>gi|297193074|ref|ZP_06910472.1| ECF subfamily RNA polymerase sigma factor [Streptomyces
           pristinaespiralis ATCC 25486]
 gi|297151630|gb|EDY63704.2| ECF subfamily RNA polymerase sigma factor [Streptomyces
           pristinaespiralis ATCC 25486]
          Length = 191

 Score = 39.0 bits (90), Expect = 0.95,   Method: Composition-based stats.
 Identities = 12/62 (19%), Positives = 23/62 (37%), Gaps = 2/62 (3%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L+           E    +  R+ L ++M  L  R+R +   R   +  +T   ++    
Sbjct: 109 LLSKPMPDMASAEEGAYDQLERDALIKAMRGLQRRQREVLVLRYFAD--MTEAQVAETLG 166

Query: 264 VS 265
           VS
Sbjct: 167 VS 168


>gi|85057325|ref|YP_456241.1| hypothetical protein AYWB_045 [Aster yellows witches'-broom
           phytoplasma AYWB]
 gi|84789430|gb|ABC65162.1| conserved hypothetical protein [Aster yellows witches'-broom
           phytoplasma AYWB]
          Length = 60

 Score = 39.0 bits (90), Expect = 0.95,   Method: Composition-based stats.
 Identities = 15/57 (26%), Positives = 29/57 (50%), Gaps = 1/57 (1%)

Query: 67  GYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
            Y    L   ++  EG +GL++A+  ++    +   TY+   IK+ ++E I +S S 
Sbjct: 5   KYYLLVLTKEDLYQEGFLGLIKALNNYE-NLDYDFITYTTPTIKSEIKELIRKSNSP 60


>gi|195867529|ref|ZP_03079532.1| sigma-70, region 4 family [Ureaplasma urealyticum serovar 9 str.
           ATCC 33175]
 gi|195660773|gb|EDX54027.1| sigma-70, region 4 family [Ureaplasma urealyticum serovar 9 str.
           ATCC 33175]
          Length = 136

 Score = 39.0 bits (90), Expect = 0.96,   Method: Composition-based stats.
 Identities = 23/93 (24%), Positives = 45/93 (48%), Gaps = 14/93 (15%)

Query: 203 WLVYDHDGQEQVLIEKEER--------KNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
           +  YDHDG  +  +E  E         K     + R++S LNP ER + E+   +E   T
Sbjct: 46  FCSYDHDGNFEENLEDLEFDVEKIIETKEMIEEVRRAISKLNPVERDLIESLFYKEE--T 103

Query: 255 LENLSSEFEVSRERV--RQIEARAFKKVQESIQ 285
           +  ++++  +S   V  R+   +  +K++E ++
Sbjct: 104 IREVAAKLNISHPAVIKRR--NKVLEKLKEMLE 134


>gi|70607833|ref|YP_256703.1| HTH DNA binding domain-containing protein [Sulfolobus
           acidocaldarius DSM 639]
 gi|68568481|gb|AAY81410.1| conserved Archaeal HTH DNA binding domain protein [Sulfolobus
           acidocaldarius DSM 639]
          Length = 230

 Score = 39.0 bits (90), Expect = 0.96,   Method: Composition-based stats.
 Identities = 19/99 (19%), Positives = 41/99 (41%), Gaps = 15/99 (15%)

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF----EARRLQ 249
           D+  +Q  + L   +   E +  ++ E    ++ +   +S L P ER+I     +     
Sbjct: 128 DQLETQISEELKKINVEVENLDFDRVEMDEVKSEMM-ILSSLTPTERQILYTAYKMGFFD 186

Query: 250 ENPVT-LENLSSEFEVSRERVRQIEARAF-KKVQESIQK 286
               T LE L+  + V++         A  + ++ +I+K
Sbjct: 187 YPKKTKLEELAKMYGVTKV--------ALDRHIRNAIRK 217


>gi|71017671|ref|XP_759066.1| hypothetical protein UM02919.1 [Ustilago maydis 521]
 gi|46098858|gb|EAK84091.1| hypothetical protein UM02919.1 [Ustilago maydis 521]
          Length = 766

 Score = 39.0 bits (90), Expect = 0.96,   Method: Composition-based stats.
 Identities = 12/47 (25%), Positives = 27/47 (57%), Gaps = 2/47 (4%)

Query: 245 ARRLQENPVTLENLSSEFEVSRERV-RQ-IEARAFKKVQESIQKQVE 289
            R    +  T E L++ F +  E+V  Q +E +  K ++E+++++V+
Sbjct: 383 LRMGISHAKTHEELAAVFGIDAEQVKSQSVEKQILKDLREALEERVK 429


>gi|311106126|ref|YP_003978979.1| RNA polymerase sigma factor sigma-70 family protein 4
           [Achromobacter xylosoxidans A8]
 gi|310760815|gb|ADP16264.1| RNA polymerase sigma factor, sigma-70 family protein 4
           [Achromobacter xylosoxidans A8]
          Length = 222

 Score = 39.0 bits (90), Expect = 0.97,   Method: Composition-based stats.
 Identities = 11/57 (19%), Positives = 24/57 (42%), Gaps = 2/57 (3%)

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           G     +     + R   L  ++  L  R+R  F   R   + +T + +++  ++SR
Sbjct: 118 GDASCPMRAAAHQQRLERLGAALQELPERQREAFVLSRF--DGLTQDEVAARMQISR 172


>gi|329939489|ref|ZP_08288825.1| SigE-like sigma factor [Streptomyces griseoaurantiacus M045]
 gi|329301718|gb|EGG45612.1| SigE-like sigma factor [Streptomyces griseoaurantiacus M045]
          Length = 183

 Score = 38.6 bits (89), Expect = 0.98,   Method: Composition-based stats.
 Identities = 15/76 (19%), Positives = 34/76 (44%), Gaps = 2/76 (2%)

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
            +  + +  E+   R +L   + VL P++R +   R      +T E  ++   +S   V+
Sbjct: 92  PDASVDDSAEQHADRALLMDVLKVLAPKQRSVVVLR--HWEQMTTEETAAALGMSAGTVK 149

Query: 271 QIEARAFKKVQESIQK 286
               RA  +++E ++ 
Sbjct: 150 STLHRALARLREELES 165


>gi|320103992|ref|YP_004179583.1| ECF subfamily RNA polymerase sigma-24 factor [Isosphaera pallida
           ATCC 43644]
 gi|319751274|gb|ADV63034.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Isosphaera pallida
           ATCC 43644]
          Length = 191

 Score = 38.6 bits (89), Expect = 0.98,   Method: Composition-based stats.
 Identities = 11/80 (13%), Positives = 34/80 (42%), Gaps = 2/80 (2%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           H    +    + E     + + R + +L+ R+  +     L++  +T   +     +   
Sbjct: 112 HRASIEDFPYEVEPTLPADEVERLLRLLSDRDAEVVRMYHLKQ--MTYRQIGQRLSIPES 169

Query: 268 RVRQIEARAFKKVQESIQKQ 287
            V  I ++A +K++++ ++ 
Sbjct: 170 SVGPILSKARRKLRQAARRD 189


>gi|255531830|ref|YP_003092202.1| RNA polymerase sigma-70 factor [Pedobacter heparinus DSM 2366]
 gi|255344814|gb|ACU04140.1| RNA polymerase sigma-70 factor [Pedobacter heparinus DSM 2366]
          Length = 195

 Score = 38.6 bits (89), Expect = 0.98,   Method: Composition-based stats.
 Identities = 16/87 (18%), Positives = 39/87 (44%), Gaps = 8/87 (9%)

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           +++QD+  Y  +   +    K E       + ++++ L  + R IF+  R +E       
Sbjct: 92  TKYQDFASYTMNSHHEPASSKAEMTELEYQIGKALNELPEQCRTIFQMSRFEELKY--RE 149

Query: 258 LSSEFEVSRERVRQIEA---RAFKKVQ 281
           ++ +  +S   V+ IE    +A + ++
Sbjct: 150 IAEQLGLS---VKTIENQMGKALRIMR 173


>gi|148557629|ref|YP_001265211.1| ECF subfamily RNA polymerase sigma-24 factor [Sphingomonas
           wittichii RW1]
 gi|148502819|gb|ABQ71073.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Sphingomonas
           wittichii RW1]
          Length = 161

 Score = 38.6 bits (89), Expect = 0.98,   Method: Composition-based stats.
 Identities = 15/80 (18%), Positives = 35/80 (43%), Gaps = 2/80 (2%)

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
           ++   +    +   E + R   L  ++  L P   R+F   +L         +++E  +S
Sbjct: 84  HEAVDETPSPLAVAEGRQRIRALAAAIEKLPPGAARVFRRHKLDGLGH--AEIAAELGIS 141

Query: 266 RERVRQIEARAFKKVQESIQ 285
           R  V +  A A + ++E+++
Sbjct: 142 RSAVEKHIAVALRHLREALE 161


>gi|226361918|ref|YP_002779696.1| SorC family transcriptional regulator [Rhodococcus opacus B4]
 gi|226240403|dbj|BAH50751.1| putative SorC family transcriptional regulator [Rhodococcus opacus
           B4]
          Length = 312

 Score = 38.6 bits (89), Expect = 0.99,   Method: Composition-based stats.
 Identities = 10/51 (19%), Positives = 23/51 (45%), Gaps = 12/51 (23%)

Query: 251 NPVTLENLSSEFEVSR-------ERVR-----QIEARAFKKVQESIQKQVE 289
           + +T   +++   VSR        R R     +IE +A   ++++++   E
Sbjct: 10  DGMTQAEVATRLGVSRPTAGRLVARARAQGLVRIEVQAPAHLRDALRSDEE 60


>gi|241554202|ref|YP_002979415.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Rhizobium
           leguminosarum bv. trifolii WSM1325]
 gi|240863508|gb|ACS61170.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Rhizobium
           leguminosarum bv. trifolii WSM1325]
          Length = 174

 Score = 38.6 bits (89), Expect = 0.99,   Method: Composition-based stats.
 Identities = 18/87 (20%), Positives = 33/87 (37%), Gaps = 3/87 (3%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L +R  + GD  A  +LV+ H   V   A  + G      ++  E  + L  A++ F  
Sbjct: 4   ELIER-AQGGDREAFGQLVSRHYDFVHATAWRWSGSSTDADDIAQEVCVKLGAAIRSFRG 62

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWS 122
               R  T+       A +++  +   
Sbjct: 63  A--SRFRTWLYTLTLNAARDHRRKLAR 87


>gi|70731967|ref|YP_261709.1| ECF subfamily RNA polymerase sigma factor [Pseudomonas fluorescens
           Pf-5]
 gi|68346266|gb|AAY93872.1| RNA polymerase sigma-70 factor, ECF subfamily [Pseudomonas
           fluorescens Pf-5]
          Length = 172

 Score = 38.6 bits (89), Expect = 0.99,   Method: Composition-based stats.
 Identities = 13/65 (20%), Positives = 27/65 (41%), Gaps = 2/65 (3%)

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
              +V +         +    +     L  S+  L+PR+++IF   RL  +  + + ++ 
Sbjct: 85  PPEVVENVAAPVSSAEDAAHAEQMLERLNLSLGQLSPRQQQIFILSRL--HGHSYQEIAD 142

Query: 261 EFEVS 265
           E  VS
Sbjct: 143 ELGVS 147


>gi|67920560|ref|ZP_00514080.1| Sigma-70 region 2:Sigma-70 region 4 [Crocosphaera watsonii WH 8501]
 gi|67858044|gb|EAM53283.1| Sigma-70 region 2:Sigma-70 region 4 [Crocosphaera watsonii WH 8501]
          Length = 217

 Score = 38.6 bits (89), Expect = 0.99,   Method: Composition-based stats.
 Identities = 21/115 (18%), Positives = 41/115 (35%), Gaps = 17/115 (14%)

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           R++   SL+A     D         + +D         +    +     L  +++ L   
Sbjct: 116 RVSHPISLDAPRRVDDGE-------IEWDIVSDYPSPDDDLATREFYERLKVAIADLPEA 168

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVS----RERVRQIEARAFKKVQESIQKQVE 289
            R     R +    +  E ++    VS    + R+    ARA  K+Q  ++K V+
Sbjct: 169 FRTTIILREI--EGLAYEEIAEMTGVSLGTVKSRI----ARARGKLQTVLKKYVD 217


>gi|328882961|emb|CCA56200.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Streptomyces
           venezuelae ATCC 10712]
          Length = 217

 Score = 38.6 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 15/82 (18%), Positives = 34/82 (41%), Gaps = 6/82 (7%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           H      + E          +  +++ L  R+R +   R   E  +T   ++    +SR 
Sbjct: 139 HPVAGPPVDEDLLLAEEHRHVLDALAGLTRRQREVLVLRYWSE--LTEAQIAQTLGLSRG 196

Query: 268 RVRQIEARAFKKVQESIQKQVE 289
            V+   +RA     ++++K++E
Sbjct: 197 TVKSTASRAL----DALEKKLE 214


>gi|315919361|ref|ZP_07915601.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D2]
 gi|313693236|gb|EFS30071.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D2]
          Length = 200

 Score = 38.6 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 13/82 (15%), Positives = 33/82 (40%), Gaps = 6/82 (7%)

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
              N  Q ++ ++                 + + ++ R++  L PR+R +F+  R  E  
Sbjct: 92  DMANEDQLKEQILSQAIDSTNETNNHILLNDLKEIIARALEQLTPRQREVFKMSR--ELQ 149

Query: 253 VTLENLSSEFEVS----RERVR 270
           ++ + ++    VS    +E + 
Sbjct: 150 MSHKEIAEALGVSVHTVQEHIS 171


>gi|218265124|ref|ZP_03478706.1| hypothetical protein PRABACTJOHN_04416 [Parabacteroides johnsonii
           DSM 18315]
 gi|218221579|gb|EEC94229.1| hypothetical protein PRABACTJOHN_04416 [Parabacteroides johnsonii
           DSM 18315]
          Length = 191

 Score = 38.6 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 21/112 (18%), Positives = 49/112 (43%), Gaps = 2/112 (1%)

Query: 175 SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV 234
           SM   +A +  ++      ++   +       D +  +   +EK    +  + L  +   
Sbjct: 73  SMLFTIAKNHVIDVFRRQINRPDFEDYIRFCEDENLLDNATVEKIYYDDFIDKLALAKQK 132

Query: 235 LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           L P +R IFE  R  E  ++   +++  ++S + V+   + A K ++E ++K
Sbjct: 133 LTPAQRNIFEMSR--EEGMSNAEIAALSDISEQTVKNHLSAALKSLREELRK 182


>gi|261406734|ref|YP_003242975.1| RNA polymerase sigma factor [Paenibacillus sp. Y412MC10]
 gi|261283197|gb|ACX65168.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Paenibacillus sp.
           Y412MC10]
          Length = 191

 Score = 38.6 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 7/39 (17%), Positives = 21/39 (53%), Gaps = 2/39 (5%)

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
            M+++++  L  ++R +   R   +   TLE +++  ++
Sbjct: 121 QMISQAIHKLTDKQRTVIILRFFHD--YTLEEIATLLDI 157


>gi|256822317|ref|YP_003146280.1| ECF subfamily RNA polymerase sigma-24 subunit [Kangiella koreensis
           DSM 16069]
 gi|256795856|gb|ACV26512.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Kangiella
           koreensis DSM 16069]
          Length = 188

 Score = 38.6 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 16/76 (21%), Positives = 31/76 (40%), Gaps = 4/76 (5%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             DH   +    + +   +    L   +  L+ RER +           T + ++SE  +
Sbjct: 99  EDDHFVNDTFSAQHQSFADYD--LDTLLQALSVRERAVLIL--FSIEEYTHQEIASEMGI 154

Query: 265 SRERVRQIEARAFKKV 280
           S    +QI +R+ KK+
Sbjct: 155 SESNSKQIYSRSLKKL 170


>gi|116329138|ref|YP_798858.1| RNA polymerase sigma subunit [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116330254|ref|YP_799972.1| RNA polymerase sigma subunit [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
 gi|116121882|gb|ABJ79925.1| RNA polymerase sigma subunit [Leptospira borgpetersenii serovar
           Hardjo-bovis L550]
 gi|116123943|gb|ABJ75214.1| RNA polymerase sigma subunit [Leptospira borgpetersenii serovar
           Hardjo-bovis JB197]
          Length = 180

 Score = 38.6 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 26/50 (52%), Gaps = 2/50 (4%)

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
           IE EE K++ ++L  S+  L   E+ I   R L+    T++  + +  +S
Sbjct: 104 IEYEEDKHQLDLLNASLENLPHLEKNIIILRFLRN--YTIKETAEKLGIS 151


>gi|298246590|ref|ZP_06970395.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297549249|gb|EFH83115.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 429

 Score = 38.6 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 21/157 (13%), Positives = 51/157 (32%), Gaps = 7/157 (4%)

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I  A +  + R          +    +   L     HL+ +         +  I + +  
Sbjct: 31  ILTATRLRLARIARARGTEPHSIDDVVQETLLEAWSHLERLHSPAGFHPWIDEICRNICR 90

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
             +    M+  L     L    ++ +      +  L+     +    +E+  R++   +L
Sbjct: 91  RAARRREMD--LLRHVPLLQPSSTMEYEEGSNEIDLLA---AETSDPLEELSRQDLVLLL 145

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            R++  L    R+I E   L   P +   ++    ++
Sbjct: 146 DRALGALPLDTRQIVEMCHLLGLPRS--EVAERLSLT 180


>gi|295689900|ref|YP_003593593.1| RNA polymerase sigma-24 factor [Caulobacter segnis ATCC 21756]
 gi|295431803|gb|ADG10975.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Caulobacter
          segnis ATCC 21756]
          Length = 190

 Score = 38.6 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 19/68 (27%), Positives = 29/68 (42%), Gaps = 1/68 (1%)

Query: 30 EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
            ++E  LA R    GD  A   L+  H   +   A  + G      EVV E  +   +A
Sbjct: 6  SDEDESALAHRVA-RGDERAFSILMRRHKGPLHTFARRHVGDPEAAHEVVQESFVAAWKA 64

Query: 90 VKKFDPER 97
          + ++DP R
Sbjct: 65 LDRYDPAR 72


>gi|226948946|ref|YP_002804037.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           A2 str. Kyoto]
 gi|226843777|gb|ACO86443.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           A2 str. Kyoto]
          Length = 179

 Score = 38.6 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 22/100 (22%), Positives = 48/100 (48%), Gaps = 5/100 (5%)

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE--ERKNRRNMLTRSMSVLNPRERRIFEA 245
           AL+    K+  +  D  + D   +    IE E    +N +  L +++  L P E+ + ++
Sbjct: 83  ALLKGEIKHHREIPDENISDKGNEYFFTIEDEIIAYENIKE-LYKALDKLTPEEKEVIDS 141

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             ++ N  +L+ +++    S   VR  + +A KK+Q  ++
Sbjct: 142 FYIKNN--SLQEIANYTNKSYNSVRYTKEKAIKKLQNMLE 179


>gi|316941231|gb|ADU75265.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           thermocellum DSM 1313]
          Length = 187

 Score = 38.6 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 8/66 (12%), Positives = 24/66 (36%), Gaps = 2/66 (3%)

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           D  + +    +       E K     +   +  L  +++  F  R +++   + + +   
Sbjct: 97  DDFIEEIPSFDDSPELLIEVKEHYKEIIEIIDSLKEKQKTAFILRYIRD--FSYKEIGKI 154

Query: 262 FEVSRE 267
             +S+E
Sbjct: 155 MGISQE 160


>gi|317473915|ref|ZP_07933195.1| RNA polymerase sigma-70 factor [Bacteroides eggerthii 1_2_48FAA]
 gi|316909992|gb|EFV31666.1| RNA polymerase sigma-70 factor [Bacteroides eggerthii 1_2_48FAA]
          Length = 200

 Score = 38.6 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 13/74 (17%), Positives = 35/74 (47%), Gaps = 10/74 (13%)

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS----RERVRQI 272
           ++    + R  ++R++  L PR+R IF+  R  E  ++   ++    +S    +E +   
Sbjct: 116 DEIIANDLRQFISRALQQLTPRQREIFQMSR--ERQMSHREIAEVLGISVNTVQESIS-- 171

Query: 273 EARAFKKVQESIQK 286
              + + ++  ++K
Sbjct: 172 --ISLRTLRTYLEK 183


>gi|294630552|ref|ZP_06709112.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces sp. e14]
 gi|292833885|gb|EFF92234.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces sp. e14]
          Length = 190

 Score = 38.6 bits (89), Expect = 1.0,   Method: Composition-based stats.
 Identities = 11/62 (17%), Positives = 23/62 (37%), Gaps = 2/62 (3%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L+           E    +  R+ L ++M  L  R+R +   R   +  +T   ++    
Sbjct: 108 LLSKPMPDMASAEEGAYDQLERDSLIQAMKGLQRRQREVLVLRYFAD--MTEAQVAETLG 165

Query: 264 VS 265
           +S
Sbjct: 166 IS 167


>gi|271961860|ref|YP_003336056.1| ECF subfamily RNA polymerase sigma-24 subunit [Streptosporangium
           roseum DSM 43021]
 gi|270505035|gb|ACZ83313.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Streptosporangium
           roseum DSM 43021]
          Length = 174

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 10/60 (16%), Positives = 27/60 (45%), Gaps = 2/60 (3%)

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              +  +++ L  ++R +   R  +        +++   +SR  VR   +RA  K++ ++
Sbjct: 98  EQAMWEALAGLPRKQRVVVVLRYYEGFSD--AEIAATLGISRGTVRSQASRALDKLRSAV 155


>gi|23099768|ref|NP_693234.1| RNA polymerase ECF-type sigma factor [Oceanobacillus iheyensis
           HTE831]
 gi|22777998|dbj|BAC14269.1| RNA polymerase ECF-type sigma factor [Oceanobacillus iheyensis
           HTE831]
          Length = 155

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 13/64 (20%), Positives = 29/64 (45%), Gaps = 10/64 (15%)

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV----SRERVRQIEARAFKKVQES 283
           + + +  LN +ER I   R      ++ + +S + ++    ++     +  RA KK++  
Sbjct: 95  VEQLLDRLNEKERTIIVLRFYY--ALSFKEISEQLDIPYGTTKS----LSYRALKKLKYF 148

Query: 284 IQKQ 287
             KQ
Sbjct: 149 ANKQ 152


>gi|315921205|ref|ZP_07917445.1| conserved hypothetical protein [Bacteroides sp. D2]
 gi|313695080|gb|EFS31915.1| conserved hypothetical protein [Bacteroides sp. D2]
          Length = 164

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 20/90 (22%), Positives = 40/90 (44%), Gaps = 2/90 (2%)

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           +  Q   +Y    +  V  E +E+  R   ++++M  L P  R I E   +Q      + 
Sbjct: 76  THEQYIQIYSELTKSYVETEYQEQDERMMHISKAMEKLTPHTRHILEECYIQRKKY--QE 133

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++ E  +S   VR+   +A + ++E   K+
Sbjct: 134 VAEELNISVSAVRKHIVKALQVIREECAKK 163


>gi|225875060|ref|YP_002756519.1| RNA polymerase sigma-70 factor, ECF subfamily [Acidobacterium
           capsulatum ATCC 51196]
 gi|225793328|gb|ACO33418.1| RNA polymerase sigma-70 factor, ECF subfamily [Acidobacterium
           capsulatum ATCC 51196]
          Length = 223

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 18/76 (23%), Positives = 35/76 (46%), Gaps = 5/76 (6%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GD+ A  +LV  + R V +IA           +VV +  +   +A +K D  +G   + 
Sbjct: 39  DGDVQAFEKLVRQYDRQVFRIAQHITQNREDAEDVVQDAFL---KAYEKLDQFQGN--SK 93

Query: 104 YSMWWIKAAMQEYILR 119
           +  W ++  + E ++R
Sbjct: 94  FYTWLVRITVNEALMR 109


>gi|149372803|ref|ZP_01891824.1| RNA polymerase sigma-70 factor [unidentified eubacterium SCB49]
 gi|149354500|gb|EDM43065.1| RNA polymerase sigma-70 factor [unidentified eubacterium SCB49]
          Length = 154

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 15/83 (18%), Positives = 37/83 (44%), Gaps = 6/83 (7%)

Query: 208 HDGQEQVLIEKEERKNRRN----MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
            D  E++       ++ ++     L ++M +LN + R++     ++      E +S    
Sbjct: 73  EDQTEEIASNGISEEDYKSVEAGQLMQAMDLLNDKYRQVISLHYMEGYDY--EEISEILN 130

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           VS    R + +RA + ++  I++
Sbjct: 131 VSYGNARTLLSRAKESLRTKIER 153


>gi|237720489|ref|ZP_04550970.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 2_2_4]
 gi|293372183|ref|ZP_06618571.1| RNA polymerase sigma-70 factor [Bacteroides ovatus SD CMC 3f]
 gi|298480471|ref|ZP_06998668.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D22]
 gi|229450240|gb|EEO56031.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 2_2_4]
 gi|292632850|gb|EFF51440.1| RNA polymerase sigma-70 factor [Bacteroides ovatus SD CMC 3f]
 gi|295086149|emb|CBK67672.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase
           sigma-70 factor, Bacteroides expansion family 1
           [Bacteroides xylanisolvens XB1A]
 gi|298273292|gb|EFI14856.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D22]
          Length = 198

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 16/99 (16%), Positives = 38/99 (38%), Gaps = 14/99 (14%)

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           S     +  D     +  +E  E K   +++ +++  L+P  R++F   R +      E 
Sbjct: 98  SSEDLVIYSDLWSLGENPVEHLEGKELHSIIQKTIDGLSPETRKVFLLSRFENKR--QEE 155

Query: 258 LSSEFEVSRERVRQIE------ARAFKKVQESIQKQVEL 290
           ++    ++      I         A  K++E+ +  + L
Sbjct: 156 IAEIMGIT------IHTVKYHMRSALDKLKEAARSYLAL 188


>gi|160939450|ref|ZP_02086800.1| hypothetical protein CLOBOL_04343 [Clostridium bolteae ATCC
           BAA-613]
 gi|158437660|gb|EDP15422.1| hypothetical protein CLOBOL_04343 [Clostridium bolteae ATCC
           BAA-613]
          Length = 135

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 11/92 (11%), Positives = 39/92 (42%), Gaps = 6/92 (6%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
            +     D++  +     + ++         + L  ++ +L+  E+ +  A     + ++
Sbjct: 50  DSEGNPLDFIADEAADIAETVVNAVMV----DRLKAALPLLSDSEQALIHAIFF--DGLS 103

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              + + F +++  V + +AR   K+++ I+ 
Sbjct: 104 EREVGARFGITQSVVNKRKARILIKLRKIIES 135


>gi|262404780|ref|ZP_06081335.1| RNA polymerase sigma factor RpoE [Vibrio sp. RC586]
 gi|262349812|gb|EEY98950.1| RNA polymerase sigma factor RpoE [Vibrio sp. RC586]
          Length = 190

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 18/88 (20%), Positives = 33/88 (37%), Gaps = 3/88 (3%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
            VL +R + +GD  A + LV  +   V  +   Y      +++V  E  I   +A+  F 
Sbjct: 8   QVLIERVQ-NGDKQAFNLLVLRYQNKVCNLISRYMSNSGDVADVAQEAFIKAYRAIPTFR 66

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWS 122
            E      T+         + +I+    
Sbjct: 67  GE--SAFYTWLYRIAVNTAKNHIVAQSR 92


>gi|257897357|ref|ZP_05677010.1| RNA polymerase sigma-70 subunit [Enterococcus faecium Com12]
 gi|257833922|gb|EEV60343.1| RNA polymerase sigma-70 subunit [Enterococcus faecium Com12]
          Length = 192

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 16/86 (18%), Positives = 33/86 (38%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R   +GD  A   L   +  L++++   Y        +   E  I L QA++  +  +G 
Sbjct: 7   RAARNGDEEAFAALYQKYFPLLLRLKNTYYLRNYVTEDWEQEARIALYQALRTHEKSKGV 66

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVK 125
              +Y    I   +   + +  +L +
Sbjct: 67  SFGSYYKSIISNQIYSLLRKQNALKR 92


>gi|153006462|ref|YP_001380787.1| ECF subfamily RNA polymerase sigma-24 factor [Anaeromyxobacter sp.
           Fw109-5]
 gi|152030035|gb|ABS27803.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Anaeromyxobacter
           sp. Fw109-5]
          Length = 218

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 22/134 (16%), Positives = 53/134 (39%), Gaps = 8/134 (5%)

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERK 222
           AK   + E+  + ++   + +E  +A   S D+   +   W  +  +  E     + E  
Sbjct: 91  AKARGLKEARSVPLSSLASDEE--DAPAVSPDRFRGEEDRWAGHWAEPPEPWPDARVESS 148

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE--RVRQIEARAFKKV 280
               ++  ++  L P +R +   R +     +   +     +S    RV  +  RA  KV
Sbjct: 149 ELVALVAEALETLPPSQRTVMSLRDVDGWEAS--EVCELMGISEVNQRV--LLHRARSKV 204

Query: 281 QESIQKQVELSSSP 294
           +  +++++    +P
Sbjct: 205 RAYVEERLGREGAP 218


>gi|149280030|ref|ZP_01886155.1| RNA polymerase ECF-type sigma factor [Pedobacter sp. BAL39]
 gi|149229227|gb|EDM34621.1| RNA polymerase ECF-type sigma factor [Pedobacter sp. BAL39]
          Length = 203

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 15/84 (17%), Positives = 39/84 (46%), Gaps = 2/84 (2%)

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           +H   +    +  +  +  N+L  ++  L P++R +++     ++ +  E  + +  +S 
Sbjct: 105 NHTEFDDSTGQLLDYNDAVNILNIALQELAPQQRLVYKL--CHQDGLKYEEAALQMNIST 162

Query: 267 ERVRQIEARAFKKVQESIQKQVEL 290
           E VR    +A +K++   +K   L
Sbjct: 163 ETVRAHMKQALRKIRSHFRKHALL 186


>gi|312622090|ref|YP_004023703.1| RNA polymerase, sigma-24 subunit, ecf subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
 gi|312202557|gb|ADQ45884.1| RNA polymerase, sigma-24 subunit, ECF subfamily
           [Caldicellulosiruptor kronotskyensis 2002]
          Length = 183

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 13/92 (14%), Positives = 41/92 (44%), Gaps = 3/92 (3%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E  L +  ++ G+  A ++L+ ++L ++               +VV E  +  +  + K
Sbjct: 2   DEKRLIEEAKK-GNKEALYKLIENNLNILSGFVTKMAQDYHFAQDVVQETLLRAIMNIDK 60

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124
           F P+   + +T+ +       ++++ ++   +
Sbjct: 61  FSPD--AKFSTWLIKISINVYKDFLRKNKRYI 90


>gi|307332249|ref|ZP_07611329.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306882110|gb|EFN13216.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 189

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 11/62 (17%), Positives = 23/62 (37%), Gaps = 2/62 (3%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L+           E    +  R+ L ++M  L  R+R +   R   +  +T   ++    
Sbjct: 107 LLSKPMPDMASAEEGAYEQLERDQLIKAMRGLQRRQREVLVLRYFAD--MTEAQVAETLG 164

Query: 264 VS 265
           +S
Sbjct: 165 IS 166


>gi|301769789|ref|XP_002920318.1| PREDICTED: nesprin-1-like [Ailuropoda melanoleuca]
          Length = 8798

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 28/125 (22%), Positives = 50/125 (40%), Gaps = 5/125 (4%)

Query: 112  AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            A  + + RSW  +K   +  Q+ L+  L R + +  ++   + K E   AI  KL+ S  
Sbjct: 5936 AKLDDLQRSWETLKNVISEKQRTLYEALERQQKYQDSLQSISTKME---AIEMKLSESLE 5992

Query: 172  EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLT 229
               S   ++A  ++L   I       S+ Q  L  +      E    E+   ++   +L 
Sbjct: 5993 HSRSPESQMAEHQALMDEILMLQDEISELQSSLAEELVSASPESDPAEQLALQSTLTVLA 6052

Query: 230  RSMSV 234
              MS 
Sbjct: 6053 ERMST 6057


>gi|294813442|ref|ZP_06772085.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|326441845|ref|ZP_08216579.1| ECF subfamily RNA polymerase sigma factor [Streptomyces
           clavuligerus ATCC 27064]
 gi|294326041|gb|EFG07684.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 245

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 11/62 (17%), Positives = 23/62 (37%), Gaps = 2/62 (3%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L+           E    +  R+ L ++M  L  R+R +   R   +  +T   ++    
Sbjct: 163 LLSKPMPDMASAEEGAYDQLERDDLIKAMRGLQRRQREVLVLRYFAD--MTEAQVAETLG 220

Query: 264 VS 265
           +S
Sbjct: 221 IS 222


>gi|325961996|ref|YP_004239902.1| RNA polymerase sigma factor, sigma-70 family [Arthrobacter
           phenanthrenivorans Sphe3]
 gi|323468083|gb|ADX71768.1| RNA polymerase sigma factor, sigma-70 family [Arthrobacter
           phenanthrenivorans Sphe3]
          Length = 183

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 21/81 (25%), Positives = 38/81 (46%), Gaps = 5/81 (6%)

Query: 207 DHDGQEQVLIEKE--ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           D D +E    EKE  ER + + +L   +  L   +R +   R +    +T+E  +     
Sbjct: 99  DLDQREDSSAEKEALERISPQEVLG-LLDALPQEQREVLGLRLVAG--LTVEQAAEAMGK 155

Query: 265 SRERVRQIEARAFKKVQESIQ 285
           S   V+Q++ RA  K++E  +
Sbjct: 156 SEGAVKQLQRRALLKLREIAE 176


>gi|317499668|ref|ZP_07957927.1| sigma-70 protein [Lachnospiraceae bacterium 5_1_63FAA]
 gi|316893030|gb|EFV15253.1| sigma-70 protein [Lachnospiraceae bacterium 5_1_63FAA]
          Length = 142

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 15/88 (17%), Positives = 33/88 (37%), Gaps = 3/88 (3%)

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
              W  YD D     +   + R    + L  ++  L+ R R         E   T   ++
Sbjct: 57  LAVWDEYDSDYTFFNVCGNDIR-ICDDELAEALKHLSERNRENLLMYYFLEMSDT--EIA 113

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQKQ 287
               +SR  V Q    + + +++ ++++
Sbjct: 114 KRQNISRSGVFQNRHNSLELMKKILKEK 141


>gi|331001940|ref|ZP_08325460.1| hypothetical protein HMPREF0491_00322 [Lachnospiraceae oral taxon
           107 str. F0167]
 gi|330411736|gb|EGG91141.1| hypothetical protein HMPREF0491_00322 [Lachnospiraceae oral taxon
           107 str. F0167]
          Length = 126

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 21/92 (22%), Positives = 37/92 (40%), Gaps = 9/92 (9%)

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           N L  S       + D +V +    E+++    E K +   L +++S L   ER I  A 
Sbjct: 43  NVLPFSVCDYDGHFIDNIVDESIDIEKIV----EVKMQIEELNKALSTLTEEERDIITAI 98

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
             +E    L ++       +E +RQ E    +
Sbjct: 99  FFKEER--LRSIGER---KKEAIRQSEKGGIR 125


>gi|324997908|ref|ZP_08119020.1| ECF subfamily RNA polymerase sigma-24 factor [Pseudonocardia sp.
           P1]
          Length = 200

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 12/63 (19%), Positives = 21/63 (33%), Gaps = 2/63 (3%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
            V  H    +              +  ++S L PR+R +   R      +T   +S    
Sbjct: 128 YVPPHSANARSAESLAMLSAEHQSVVDALSALPPRQREVLVLRYYGG--LTESEISEAAG 185

Query: 264 VSR 266
           +SR
Sbjct: 186 MSR 188


>gi|299144330|ref|ZP_07037410.1| sigma-70, region 4 superfamily [Peptoniphilus sp. oral taxon 386
           str. F0131]
 gi|298518815|gb|EFI42554.1| sigma-70, region 4 superfamily [Peptoniphilus sp. oral taxon 386
           str. F0131]
          Length = 138

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 16/93 (17%), Positives = 47/93 (50%), Gaps = 6/93 (6%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
            N   + D ++ +    E+++    E K +   L ++++ L  +ER + EA   +E   +
Sbjct: 51  DNDGHFVDNIIDERIDLEKIV----EVKMQIEELNKALATLTKKERELIEAIFYKEE--S 104

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L ++  + +VS + + +   +  +K+++ ++ +
Sbjct: 105 LRSIGKKEKVSYQAIGKRRDKILEKLRKLLEDK 137


>gi|297158497|gb|ADI08209.1| ECF subfamily RNA polymerase sigma factor [Streptomyces
           bingchenggensis BCW-1]
          Length = 287

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 23/107 (21%), Positives = 38/107 (35%), Gaps = 2/107 (1%)

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             +  +   R    ++LN L   S        +WL         V  + E  ++    + 
Sbjct: 46  VRDPRAYLVRTVTRQALNRLRTLSRSREDYVGEWLPEPLLTSPDVAEDIELAESVSIAML 105

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
             +  L P ER +F  R + + P     ++     S   VRQI  RA
Sbjct: 106 TVLETLGPAERAVFVLREVFDMPYG--EIAEAIGKSTTAVRQIARRA 150


>gi|328884501|emb|CCA57740.1| ECF sigma factor [Streptomyces venezuelae ATCC 10712]
          Length = 230

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 12/91 (13%), Positives = 30/91 (32%), Gaps = 2/91 (2%)

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
            S+      + +         E+    +      + ++ L   +R +   R      +T 
Sbjct: 142 GSTAVPSDEMPERPDDSLGPEERALLSDDAEWAKKLLANLPENQRELLVLRVAVG--LTA 199

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E       +S   VR  + RA  +++   ++
Sbjct: 200 EETGQMLGMSPGAVRVAQHRALSRLRALAEQ 230


>gi|307067533|ref|YP_003876499.1| hypothetical protein SPAP_0908 [Streptococcus pneumoniae AP200]
 gi|306409070|gb|ADM84497.1| hypothetical protein SPAP_0908 [Streptococcus pneumoniae AP200]
          Length = 136

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 23/93 (24%), Positives = 45/93 (48%), Gaps = 14/93 (15%)

Query: 203 WLVYDHDGQEQVLIEKEER--------KNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
           +  YDHDG  +  +E  E         K     + R++S LNP ER + E+   +E   T
Sbjct: 46  FCSYDHDGNFEENLEDLEFDVEKIIETKEMIEEVRRAISKLNPVERDLIESLFYKEE--T 103

Query: 255 LENLSSEFEVSRERV--RQIEARAFKKVQESIQ 285
           +  ++++  +S   V  R+   +  +K++E ++
Sbjct: 104 IREVAAKLNISHPAVIKRR--NKVLEKLKEMLE 134


>gi|90022052|ref|YP_527879.1| sigma-24 (FecI-like) [Saccharophagus degradans 2-40]
 gi|89951652|gb|ABD81667.1| sigma-70 region 2 [Saccharophagus degradans 2-40]
          Length = 179

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 13/76 (17%), Positives = 26/76 (34%), Gaps = 3/76 (3%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L  R + +GD  A  +LV  H   V   A         +++ +       ++A       
Sbjct: 8   LIARVQANGDQHAFSQLVRKHQSQVRSWARRLCNGDEHLADDL--AQEAFIKAYMALAAF 65

Query: 97  RG-FRLATYSMWWIKA 111
           RG  + + +    +  
Sbjct: 66  RGDAKFSVWLYRIVFN 81


>gi|239929660|ref|ZP_04686613.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces ghanaensis
           ATCC 14672]
 gi|291437982|ref|ZP_06577372.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces ghanaensis
           ATCC 14672]
 gi|291340877|gb|EFE67833.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces ghanaensis
           ATCC 14672]
          Length = 273

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 20/94 (21%), Positives = 36/94 (38%), Gaps = 7/94 (7%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           E    A+R    GD+ A   LV+++L LV  I          + +VV E  +  + A+  
Sbjct: 10  ETVEAARR----GDMRAQDELVSAYLPLVYNIVGRALNGHPDVDDVVQETMLRALGALG- 64

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
                  R  ++ +  I      +  RS    ++
Sbjct: 65  -SLNDPARFRSWLVA-ITMNQLRHHWRSERGDRL 96


>gi|256389895|ref|YP_003111459.1| LuxR family transcriptional regulator [Catenulispora acidiphila DSM
           44928]
 gi|256356121|gb|ACU69618.1| two component transcriptional regulator, LuxR family [Catenulispora
           acidiphila DSM 44928]
          Length = 234

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 18/75 (24%), Positives = 32/75 (42%), Gaps = 3/75 (4%)

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             L + ++ L PRER +     L    ++   L++ F +S   V+   AR   K+    +
Sbjct: 160 EALHKDLATLTPREREVL---GLLGRGLSNAELAARFHLSEATVKTHVARILAKLNLRDR 216

Query: 286 KQVELSSSPPLLQKP 300
            Q  + +    L KP
Sbjct: 217 AQAVVVAYETGLIKP 231


>gi|254444332|ref|ZP_05057808.1| RNA polymerase sigma factor, sigma-70 family [Verrucomicrobiae
           bacterium DG1235]
 gi|198258640|gb|EDY82948.1| RNA polymerase sigma factor, sigma-70 family [Verrucomicrobiae
           bacterium DG1235]
          Length = 200

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 41/268 (15%), Positives = 92/268 (34%), Gaps = 76/268 (28%)

Query: 28  MLEKQEEYVLAKRY---REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNI 84
           M  K +E  L K      + GD SA   +V+ +   +  +            EV  +  I
Sbjct: 1   MSTKAQEVALDKALVARFKAGDESAFEEMVSRYWDRIYAMVHKLLRNTQDAEEVTQDAFI 60

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKG 144
              + ++ F  +     +++S W               L +I T   + R ++  RR + 
Sbjct: 61  RAHRGLENFRGD-----SSFSTW---------------LYQIATNLARNRYWYWWRRKRD 100

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
                                                   S +  I +  ++S+   +  
Sbjct: 101 K-------------------------------------SVSFDQPIAA--ESSTTLAEVF 121

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             D +  E + I  E     ++ +  +M +LN + +     R ++   ++ E ++ E ++
Sbjct: 122 PADVESPEDIAITNE----FKSRVAAAMELLNEKHKEALVLRNVRN--LSYEEIADELQI 175

Query: 265 S----RERVRQIEARAFKKVQESIQKQV 288
           S    + R+    ARA + ++E +  ++
Sbjct: 176 SIGTVKSRI----ARARESLREKMGHEL 199


>gi|108761788|ref|YP_635327.1| ECF subfamily RNA polymerase sigma factor [Myxococcus xanthus DK
           1622]
 gi|108465668|gb|ABF90853.1| RNA polymerase sigma-70 factor, ECF subfamily [Myxococcus xanthus
           DK 1622]
          Length = 176

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 10/62 (16%), Positives = 23/62 (37%), Gaps = 2/62 (3%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           V   D   +  ++       R+ L +    L+ R   +     L  + ++ E ++    +
Sbjct: 89  VAPEDAGSEGAVDALAATECRDFLMKLARELDERALTVATLHYL--DGMSQEEIAQVLGL 146

Query: 265 SR 266
           SR
Sbjct: 147 SR 148


>gi|75675926|ref|YP_318347.1| FecI like protein [Nitrobacter winogradskyi Nb-255]
 gi|74420796|gb|ABA04995.1| FecI like protein [Nitrobacter winogradskyi Nb-255]
          Length = 236

 Score = 38.6 bits (89), Expect = 1.1,   Method: Composition-based stats.
 Identities = 17/73 (23%), Positives = 34/73 (46%), Gaps = 6/73 (8%)

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           S++    +V      E  + ++++    R     +++ L  R R  FE  RL E  +T+ 
Sbjct: 152 SAEDFAAIVDPTPSPESAVYDRQKLALTRA----ALAELPERTRVAFEMHRLDE--MTIA 205

Query: 257 NLSSEFEVSRERV 269
            +++E  +S  RV
Sbjct: 206 EVAAELGLSTSRV 218


>gi|282883028|ref|ZP_06291629.1| putative sigma factor [Peptoniphilus lacrimalis 315-B]
 gi|281297085|gb|EFA89580.1| putative sigma factor [Peptoniphilus lacrimalis 315-B]
          Length = 136

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 23/93 (24%), Positives = 45/93 (48%), Gaps = 14/93 (15%)

Query: 203 WLVYDHDGQEQVLIEKEER--------KNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
           +  YDHDG  +  +E  E         K     + R++S LNP ER + E+   +E   T
Sbjct: 46  FCSYDHDGNFEENLEDLEFDVEKIIETKEMIEEVRRAISKLNPAERDLIESLFYKEE--T 103

Query: 255 LENLSSEFEVSRERV--RQIEARAFKKVQESIQ 285
           +  ++++  +S   V  R+   +  +K++E ++
Sbjct: 104 IREVAAKLNISHPAVIKRR--NKVLEKLKEMLE 134


>gi|319950730|ref|ZP_08024626.1| RNA polymerase sigma factor SigD [Dietzia cinnamea P4]
 gi|319435608|gb|EFV90832.1| RNA polymerase sigma factor SigD [Dietzia cinnamea P4]
          Length = 186

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 16/94 (17%), Positives = 41/94 (43%), Gaps = 6/94 (6%)

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
           +  ++   ++    G E  +++ E        ++R +  L  ++R I   R +    ++ 
Sbjct: 95  DPVEYLPEVLSTDTGPEDHVLDGE----VSRAVSRLLDTLPEKQREIIRLRVVVG--LSA 148

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           E  +   + +   VR  + RA K+++  I++  E
Sbjct: 149 EETAEIVDSTAGAVRVAQHRAMKQLRARIEQDGE 182


>gi|313650140|gb|EFS14553.1| RNA polymerase sigma factor for flagellar operon domain protein
           [Shigella flexneri 2a str. 2457T]
 gi|332757482|gb|EGJ87817.1| RNA polymerase sigma factor for flagellar operon domain protein
           [Shigella flexneri K-671]
          Length = 62

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 15/60 (25%), Positives = 31/60 (51%), Gaps = 3/60 (5%)

Query: 50  AHRLVTSHLRLVVKIAMGYRGY---GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSM 106
            H L   ++ LV   A+  +      + + +++  G IGL+ AV+++D  +G    TY++
Sbjct: 3   KHSLWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAV 62


>gi|291438228|ref|ZP_06577618.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces ghanaensis
           ATCC 14672]
 gi|291341123|gb|EFE68079.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces ghanaensis
           ATCC 14672]
          Length = 166

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 11/62 (17%), Positives = 23/62 (37%), Gaps = 2/62 (3%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L+           E    +  R+ L ++M  L  R+R +   R   +  +T   ++    
Sbjct: 84  LLSKPMPDMASAEEGAYDQLERDSLIKAMKGLQRRQREVLVLRYFAD--MTEAQVAETLG 141

Query: 264 VS 265
           +S
Sbjct: 142 IS 143


>gi|227538187|ref|ZP_03968236.1| RNA polymerase ECF family sigma factor [Sphingobacterium
           spiritivorum ATCC 33300]
 gi|227241956|gb|EEI91971.1| RNA polymerase ECF family sigma factor [Sphingobacterium
           spiritivorum ATCC 33300]
          Length = 185

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 17/75 (22%), Positives = 33/75 (44%), Gaps = 2/75 (2%)

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
             E  LI KE +      + + +  L  R++ +   +   E   + E ++S   VS E  
Sbjct: 98  SHELDLILKENQDINVQKVKQEIDKLPKRQKEVLYLKYYME--FSYEEIASIMNVSVESC 155

Query: 270 RQIEARAFKKVQESI 284
           R +  RAF+ ++  +
Sbjct: 156 RTLSYRAFRVLKSHM 170


>gi|17229685|ref|NP_486233.1| RNA polymerase sigma factor [Nostoc sp. PCC 7120]
 gi|17131284|dbj|BAB73892.1| all2193 [Nostoc sp. PCC 7120]
          Length = 201

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 6/58 (10%), Positives = 24/58 (41%), Gaps = 2/58 (3%)

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           +    E   +E+     R   +  +++ L  ++R++ E        ++   ++ + ++
Sbjct: 117 NEAAPEPTPVEQASFAERSGRIHNALAQLPEKQRQVIELAY--HQGLSQSEIAKQIDI 172


>gi|317056373|ref|YP_004104840.1| ECF subfamily RNA polymerase sigma-24 subunit [Ruminococcus albus
           7]
 gi|315448642|gb|ADU22206.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ruminococcus albus
           7]
          Length = 187

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 15/111 (13%), Positives = 44/111 (39%), Gaps = 12/111 (10%)

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +A + +++ L     +  +   + +  +     +   + +          +++ +LN  E
Sbjct: 80  MARNMAIDFLRKRKHEEYTIDDEGIYTEEQADPEAPTDVQVESGI--AFRQALEILNEAE 137

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERV----RQIEARAFKKVQESIQK 286
           R I   R   +  +T + +S    +    V    RQ    A  K+++++++
Sbjct: 138 REIINLRAGLD--MTFKEISETLGIPLGTVAWKYRQ----ALNKLKKTVKE 182


>gi|148379579|ref|YP_001254120.1| RNA polymerase sigma factor [Clostridium botulinum A str. ATCC
           3502]
 gi|153932151|ref|YP_001383958.1| putative RNA polymerase sigma factor [Clostridium botulinum A str.
           ATCC 19397]
 gi|153936854|ref|YP_001387503.1| putative RNA polymerase sigma factor [Clostridium botulinum A str.
           Hall]
 gi|148289063|emb|CAL83153.1| putative RNA polymerase sigma factor [Clostridium botulinum A str.
           ATCC 3502]
 gi|152928195|gb|ABS33695.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           A str. ATCC 19397]
 gi|152932768|gb|ABS38267.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           A str. Hall]
          Length = 176

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 22/100 (22%), Positives = 48/100 (48%), Gaps = 5/100 (5%)

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE--ERKNRRNMLTRSMSVLNPRERRIFEA 245
           AL+    K+  +  D  + D   +    IE E    +N +  L +++  L P E+ + ++
Sbjct: 80  ALLKGEIKHHREIPDENISDKGNEYFFTIEDEIIAYENIKE-LYKALDKLTPEEKEVIDS 138

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             ++ N  +L+ +++    S   VR  + +A KK+Q  ++
Sbjct: 139 FYIKNN--SLQEIANYTNKSYNSVRYTKEKAIKKLQNMLE 176


>gi|326778745|ref|ZP_08238010.1| putative RNA polymerase, sigma 70 family subunit [Streptomyces cf.
           griseus XylebKG-1]
 gi|326659078|gb|EGE43924.1| putative RNA polymerase, sigma 70 family subunit [Streptomyces cf.
           griseus XylebKG-1]
          Length = 510

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 25/134 (18%), Positives = 49/134 (36%), Gaps = 6/134 (4%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           +GD +A  RL   +L LV  +          + +VV E    +++A+      R    A 
Sbjct: 22  NGDRAAGDRLAAHYLPLVYNVVGRALNGHPDVDDVVQET---MLRALSGLPSLRDP--AR 76

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI-TDNNLKPEQVVAI 162
           +  W +  AM +   R   L              +       L  +  + + +  +    
Sbjct: 77  FRSWLVAIAMNQVRTRWSGLGHRPAPLEAAEEPADPAADFVDLTILRLELSGQRRETAEA 136

Query: 163 AKKLNVSESEVISM 176
            + L+ SE +V+S+
Sbjct: 137 TRWLDDSERDVLSL 150


>gi|319786945|ref|YP_004146420.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Pseudoxanthomonas
           suwonensis 11-1]
 gi|317465457|gb|ADV27189.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Pseudoxanthomonas
           suwonensis 11-1]
          Length = 185

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 15/75 (20%), Positives = 27/75 (36%), Gaps = 4/75 (5%)

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV-RQ 271
                   +      L R++  L P +R     R   E P  LE +     V RE V  +
Sbjct: 114 DDPERHASQVEESARLYRALDELPPEQREAVLLRLHGELP--LEEIGRITGVGRETVKSR 171

Query: 272 IEARAFKKVQESIQK 286
           +   A  +++  ++ 
Sbjct: 172 L-RYAMDRLRGRLEA 185


>gi|308070932|ref|YP_003872537.1| RNA polymerase sigma factor sigW [Paenibacillus polymyxa E681]
 gi|305860211|gb|ADM71999.1| RNA polymerase sigma factor sigW [Paenibacillus polymyxa E681]
          Length = 188

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 22/148 (14%), Positives = 49/148 (33%), Gaps = 3/148 (2%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R  + GD  A   LV  +   +  ++    G      ++V E  + + + ++K+  + G 
Sbjct: 10  RLVQKGDQRAFAELVELYKDRIFHLSYRMLGNRHEAEDLVQETFLRVYRNLEKY--DHGQ 67

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +T+          + + R      +    N +        L         + L  E  
Sbjct: 68  KFSTWIYRIATNLCIDRLRRRKPTYSLDAEMNDQEGVDGYAMLASEELTPEGSTLLSETQ 127

Query: 160 VAIAKKLNVSESEVIS-MNCRLAGDESL 186
             I   ++    +  + M  R   + SL
Sbjct: 128 ALIHDAIDNLPDKYRTIMVLRYLQELSL 155



 Score = 35.6 bits (81), Expect = 8.8,   Method: Composition-based stats.
 Identities = 16/91 (17%), Positives = 31/91 (34%), Gaps = 8/91 (8%)

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
           I    R     SL+A +N  +                +E            + ++  ++ 
Sbjct: 82  IDRLRRRKPTYSLDAEMNDQEGVDGYAM------LASEELTPEGSTLLSETQALIHDAID 135

Query: 234 VLNPRERRIFEARRLQENPVTLENLSSEFEV 264
            L  + R I   R LQE  ++L+ +S    +
Sbjct: 136 NLPDKYRTIMVLRYLQE--LSLQEISDVLNL 164


>gi|284029023|ref|YP_003378954.1| ECF subfamily RNA polymerase sigma-24 subunit [Kribbella flavida
           DSM 17836]
 gi|283808316|gb|ADB30155.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Kribbella flavida
           DSM 17836]
          Length = 176

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 17/95 (17%), Positives = 32/95 (33%), Gaps = 5/95 (5%)

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
           +       L     G      +        + + R  + L  R+R     R  +  P   
Sbjct: 84  DDPAVFVDLGEPAVGGSTTGADHAVLHADADAVWRLCASLPTRQRAAVVLRYYEGLPD-- 141

Query: 256 ENLSSEFEVSRERVR-QIEARAFKKVQESIQKQVE 289
             ++     +   VR QI  RA   ++ ++ K+VE
Sbjct: 142 AEIAEVLGCTAATVRSQIH-RALGSLRATL-KEVE 174


>gi|116491406|ref|YP_810950.1| ComX [Oenococcus oeni PSU-1]
 gi|116092131|gb|ABJ57285.1| ComX [Oenococcus oeni PSU-1]
          Length = 193

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 17/69 (24%), Positives = 26/69 (37%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A +  + GD +    L+      + KI   Y    L   E  SE    LM++V K+    
Sbjct: 6   ALKMIKKGDQTGYLFLMEETEGFLRKIHNRYLKSILDFDEWKSEALDVLMRSVDKYQNNF 65

Query: 98  GFRLATYSM 106
             +  TY  
Sbjct: 66  DSKFTTYYF 74


>gi|301310837|ref|ZP_07216766.1| sigma-70 region 2 subfamily [Bacteroides sp. 20_3]
 gi|300830900|gb|EFK61541.1| sigma-70 region 2 subfamily [Bacteroides sp. 20_3]
          Length = 190

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 20/84 (23%), Positives = 43/84 (51%), Gaps = 2/84 (2%)

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           DG+E  +  K   +   + L  +   L PR+R +FE    +E  +T+  ++++  +S + 
Sbjct: 104 DGEETAIERKLSFEEFNHRLEIAKQKLTPRQRELFEL--NKEQGITITEIAAKALISEQS 161

Query: 269 VRQIEARAFKKVQESIQKQVELSS 292
           VR   ++A + +++ + K   L S
Sbjct: 162 VRNQLSQALRVLRKELGKYALLFS 185


>gi|239629219|ref|ZP_04672250.1| ComX [Lactobacillus paracasei subsp. paracasei 8700:2]
 gi|239528525|gb|EEQ67526.1| ComX [Lactobacillus paracasei subsp. paracasei 8700:2]
          Length = 182

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 25/146 (17%), Positives = 51/146 (34%), Gaps = 4/146 (2%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L   +  LV+ +   Y        + + E  I +++A+ ++D  RG +   Y    
Sbjct: 18  AFSQLFKQYRPLVLTVLRPYHLRDFSHEDWLQEARIAMLKAITRYDGSRGSQFGPY-YRM 76

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFF---NLRRLKGHLQAITDNNLKPEQVVAIAKK 165
           +  +    +LR     K    A    +        + +  L++  D  L   +      +
Sbjct: 77  VLQSHLRSVLRKHFAHKRRIDATAIPVEDSALESLQERLALRSYEDGLLMRIEFAQFLAR 136

Query: 166 LNVSESEVISMNCRLAGDESLNALIN 191
           L+  E E          D S + L+ 
Sbjct: 137 LSPLEYEAFEAAVISQTDSSEDPLLQ 162


>gi|66047955|ref|YP_237796.1| RNA polymerase sigma factor [Pseudomonas syringae pv. syringae
           B728a]
 gi|63258662|gb|AAY39758.1| Sigma-70 region 2:Sigma-70 region 4 [Pseudomonas syringae pv.
           syringae B728a]
          Length = 172

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 16/75 (21%), Positives = 30/75 (40%), Gaps = 2/75 (2%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L+   + ++    E+         + R +  L+ + R  F   RL         ++ +  
Sbjct: 89  LMQVPEAEQPSPEEQLLIVEDLKAIDRMLGTLSSKARAAFLYSRLDGMSH--AEIAEQLG 146

Query: 264 VSRERVRQIEARAFK 278
           VS  RVRQ  A+A +
Sbjct: 147 VSVSRVRQYLAQAMR 161


>gi|300790919|ref|YP_003771210.1| ECF subfamily RNA polymerase sigma-24 factor [Amycolatopsis
           mediterranei U32]
 gi|299800433|gb|ADJ50808.1| ECF subfamily RNA polymerase sigma-24 factor [Amycolatopsis
           mediterranei U32]
          Length = 209

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 15/83 (18%), Positives = 34/83 (40%), Gaps = 2/83 (2%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
            V  H    +         +    +  ++S L PR+R +   R      ++   +S    
Sbjct: 127 YVPPHAVNARSAESLAMLSSEHQAVVSALSKLPPRQREVLVLRYYGG--LSEAEISEAAG 184

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+  V+   +RA + +Q+++Q 
Sbjct: 185 ISKGTVKSTASRALEALQKAMQA 207


>gi|257054178|ref|YP_003132010.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase
           sigma-70 factor, sigma-E family [Saccharomonospora
           viridis DSM 43017]
 gi|256584050|gb|ACU95183.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase
           sigma-70 factor, sigma-E family [Saccharomonospora
           viridis DSM 43017]
          Length = 197

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 8/64 (12%), Positives = 28/64 (43%), Gaps = 2/64 (3%)

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              L +++  L P++R +   R      ++   +++   +S   V+   ++A   ++  +
Sbjct: 128 HEPLWQALRELPPKQRAVIVLRYY--EGLSEAEIAASLGISPGTVKSQASKALTSLRGKL 185

Query: 285 QKQV 288
           ++  
Sbjct: 186 RRDA 189


>gi|255323977|ref|ZP_05365103.1| RNA polymerase sigma factor SigD [Corynebacterium
           tuberculostearicum SK141]
 gi|255299157|gb|EET78448.1| RNA polymerase sigma factor SigD [Corynebacterium
           tuberculostearicum SK141]
          Length = 190

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 14/88 (15%), Positives = 34/88 (38%), Gaps = 2/88 (2%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           + +    E    E     +  N +   +  L+ + + I   R    N ++ E  +     
Sbjct: 105 IPEDSAHEATPEEWALEADGSNRMRALLDTLSDKAKNIVILRVF--NGLSAEETAEIVGS 162

Query: 265 SRERVRQIEARAFKKVQESIQKQVELSS 292
           +   VR  + RA  ++++++Q   E + 
Sbjct: 163 TPGAVRVAQHRALAQLRKTLQAAQETAR 190


>gi|229588587|ref|YP_002870706.1| putative RNA polymerase sigma factor [Pseudomonas fluorescens
           SBW25]
 gi|229360453|emb|CAY47310.1| putative RNA polymerase sigma factor [Pseudomonas fluorescens
           SBW25]
          Length = 191

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 25/137 (18%), Positives = 48/137 (35%), Gaps = 6/137 (4%)

Query: 164 KKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKN 223
           ++  V   E+ +   R AG+ +++  + S        + WL    D Q        E  N
Sbjct: 61  RRPLVQVEELSTYLLRCAGNIAID-HLRSEGARVRSSEGWLPEQQDNQGSEPQAALEAGN 119

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
               +  ++  L  R R+IF   R+         ++    +S+  V   E    + ++  
Sbjct: 120 DLRHVEAALRSLPERTRQIFLLNRIHGRKY--AEIAKAMGLSQSAV---EKHMMRALEAC 174

Query: 284 IQKQVELSSSPPLLQKP 300
                E SS     + P
Sbjct: 175 KASLREPSSPRTPGKAP 191


>gi|229083190|ref|ZP_04215573.1| Prophage LambdaBa01, positive control factor Xpf [Bacillus cereus
           Rock4-2]
 gi|228700108|gb|EEL52711.1| Prophage LambdaBa01, positive control factor Xpf [Bacillus cereus
           Rock4-2]
          Length = 166

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 23/85 (27%), Positives = 41/85 (48%), Gaps = 11/85 (12%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
             +D + +E V+ E E     R  L  ++S L   ER I+   R +   +T E ++    
Sbjct: 84  YEWDDENKESVISEWE-----RIKLEDALSTLTKYEREIYIMSRGRG--ITQEKIAKYLN 136

Query: 264 VSRERVRQI----EARAFKKVQESI 284
           VSR  ++ I    E +  K+V++S+
Sbjct: 137 VSRSTIKTILYRSEIKIAKQVRKSL 161


>gi|297201271|ref|ZP_06918668.1| RNA polymerase sigma factor [Streptomyces sviceus ATCC 29083]
 gi|197712867|gb|EDY56901.1| RNA polymerase sigma factor [Streptomyces sviceus ATCC 29083]
          Length = 188

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 11/62 (17%), Positives = 23/62 (37%), Gaps = 2/62 (3%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L+           E    +  R+ L ++M  L  R+R +   R   +  +T   ++    
Sbjct: 106 LLSKPMPDMASAEEGAYDQLERDSLIKAMKGLQRRQREVLVLRYFAD--MTEAQVADTLG 163

Query: 264 VS 265
           +S
Sbjct: 164 IS 165


>gi|169834924|ref|YP_001715917.1| putative RNA polymerase sigma factor [Clostridium botulinum A3 str.
           Loch Maree]
 gi|169409031|gb|ACA57441.1| putative RNA polymerase sigma factor [Clostridium botulinum A3 str.
           Loch Maree]
          Length = 294

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 11/70 (15%), Positives = 29/70 (41%), Gaps = 2/70 (2%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIK 110
             ++  +  L+ K A  +  YG    ++    ++ + +A   +D  +    +TY+   I 
Sbjct: 18  EEVLKKYSNLITKYAYKWIKYG--FEDIKQIAHLAVWKAFNTYDISKNINFSTYANKIIS 75

Query: 111 AAMQEYILRS 120
             +  +I  +
Sbjct: 76  TEILLHIRDN 85


>gi|133919920|emb|CAM12480.1| hypothetical protein [uncultured bacterium]
          Length = 170

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 10/91 (10%), Positives = 39/91 (42%), Gaps = 6/91 (6%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
            +     D++  +     + ++         + L  ++ +L+  E+ + +A     + ++
Sbjct: 85  DSEGNPLDFITDEAVDFAETVVNAVMV----DRLKAALPLLSDSEQELIQAIFF--DGLS 138

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              + +   +++  V + +AR   K+++ I+
Sbjct: 139 EREVGARLGITQSVVNKRKARILIKLRKIIE 169


>gi|145222517|ref|YP_001133195.1| ECF subfamily RNA polymerase sigma-24 factor [Mycobacterium gilvum
           PYR-GCK]
 gi|315442965|ref|YP_004075844.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase
           sigma-70 factor, TIGR02957 family [Mycobacterium sp.
           Spyr1]
 gi|145215003|gb|ABP44407.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Mycobacterium
           gilvum PYR-GCK]
 gi|315261268|gb|ADT98009.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase
           sigma-70 factor, TIGR02957 family [Mycobacterium sp.
           Spyr1]
          Length = 298

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 23/118 (19%), Positives = 45/118 (38%), Gaps = 6/118 (5%)

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           + ++  +   RL   ++LN L   S +       WL      +     +    ++    +
Sbjct: 52  TVTDTKAYLARLVTRQALNTLRAQSRRREDYVGPWLPEPLLTEADPSADVVLAESVSMAM 111

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              +  L+P ER +F  R +       + +++    S   VRQI  RA    +E +Q 
Sbjct: 112 LVVLETLSPDERAVFVLREVFGFGH--DEIAATLGKSTAAVRQIAHRA----REHVQS 163


>gi|297617579|ref|YP_003702738.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Syntrophothermus
           lipocalidus DSM 12680]
 gi|297145416|gb|ADI02173.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Syntrophothermus
           lipocalidus DSM 12680]
          Length = 199

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 17/93 (18%), Positives = 39/93 (41%), Gaps = 9/93 (9%)

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           + N S   D  +        V+ ++EE K     L  ++  L    R +   R   +  +
Sbjct: 97  EDNISNRADPFLNIDYNDPAVVYDREELKLD---LKEALLQLPESYRAMLILRYQLD--M 151

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           + + ++    ++RE V   E +   + ++S++K
Sbjct: 152 SNQEIADALGITRENV---EVK-MHRARKSLRK 180


>gi|255011429|ref|ZP_05283555.1| putative ECF-type RNA polymerase [Bacteroides fragilis 3_1_12]
 gi|313149245|ref|ZP_07811438.1| RNA polymerase ECF-type sigma factor [Bacteroides fragilis 3_1_12]
 gi|313138012|gb|EFR55372.1| RNA polymerase ECF-type sigma factor [Bacteroides fragilis 3_1_12]
          Length = 183

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 14/71 (19%), Positives = 37/71 (52%), Gaps = 2/71 (2%)

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
           + E+ +  N R  +   +S+L PR++ +F   R  +  ++   ++ + ++S   V    +
Sbjct: 107 IEEELDAANLRTHIESLISMLPPRQQEVFRLSR--DEELSYREIAEKLQISERTVEHHIS 164

Query: 275 RAFKKVQESIQ 285
            A K ++++I+
Sbjct: 165 DALKFLRKNIK 175


>gi|229051412|ref|ZP_04194917.1| Prophage LambdaBa01, positive control factor Xpf [Bacillus cereus
           AH676]
 gi|228721981|gb|EEL73421.1| Prophage LambdaBa01, positive control factor Xpf [Bacillus cereus
           AH676]
          Length = 166

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 2/74 (2%)

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
            +  + E    +  R  L  ++S L  RE+ I+   R   +  T E +S+   V R  V+
Sbjct: 87  WDTEVKESVISEWDRIQLEDALSTLTEREKEIYVMSRG--HGFTQEKISNYLGVKRTTVQ 144

Query: 271 QIEARAFKKVQESI 284
           +   RA KK+ E +
Sbjct: 145 EYLKRADKKIGERL 158


>gi|15642463|ref|NP_232096.1| RNA polymerase sigma factor RpoE [Vibrio cholerae O1 biovar El Tor
           str. N16961]
 gi|121590992|ref|ZP_01678311.1| RNA polymerase sigma-E factor [Vibrio cholerae 2740-80]
 gi|121729904|ref|ZP_01682329.1| RNA polymerase sigma-E factor [Vibrio cholerae V52]
 gi|147675349|ref|YP_001217969.1| RNA polymerase sigma factor RpoE [Vibrio cholerae O395]
 gi|153214506|ref|ZP_01949415.1| RNA polymerase sigma-E factor [Vibrio cholerae 1587]
 gi|153820439|ref|ZP_01973106.1| RNA polymerase sigma-E factor [Vibrio cholerae NCTC 8457]
 gi|153823693|ref|ZP_01976360.1| RNA polymerase sigma-E factor [Vibrio cholerae B33]
 gi|153831098|ref|ZP_01983765.1| RNA polymerase sigma-E factor [Vibrio cholerae 623-39]
 gi|227082588|ref|YP_002811139.1| RNA polymerase sigma-E factor [Vibrio cholerae M66-2]
 gi|254291667|ref|ZP_04962455.1| RNA polymerase sigma-E factor [Vibrio cholerae AM-19226]
 gi|254849592|ref|ZP_05238942.1| RNA polymerase sigma-E factor [Vibrio cholerae MO10]
 gi|255746862|ref|ZP_05420807.1| RNA polymerase sigma factor RpoE [Vibrio cholera CIRS 101]
 gi|262162027|ref|ZP_06031043.1| RNA polymerase sigma factor RpoE [Vibrio cholerae INDRE 91/1]
 gi|262167298|ref|ZP_06035008.1| RNA polymerase sigma factor RpoE [Vibrio cholerae RC27]
 gi|262190703|ref|ZP_06048934.1| RNA polymerase sigma factor RpoE [Vibrio cholerae CT 5369-93]
 gi|297581091|ref|ZP_06943016.1| RNA polymerase sigma-E factor [Vibrio cholerae RC385]
 gi|298500176|ref|ZP_07009981.1| RNA polymerase sigma factor RpoE [Vibrio cholerae MAK 757]
 gi|9657045|gb|AAF95609.1| RNA polymerase sigma-E factor [Vibrio cholerae O1 biovar El Tor
           str. N16961]
 gi|121547169|gb|EAX57298.1| RNA polymerase sigma-E factor [Vibrio cholerae 2740-80]
 gi|121628347|gb|EAX60851.1| RNA polymerase sigma-E factor [Vibrio cholerae V52]
 gi|124115308|gb|EAY34128.1| RNA polymerase sigma-E factor [Vibrio cholerae 1587]
 gi|126509016|gb|EAZ71610.1| RNA polymerase sigma-E factor [Vibrio cholerae NCTC 8457]
 gi|126518781|gb|EAZ76004.1| RNA polymerase sigma-E factor [Vibrio cholerae B33]
 gi|146317232|gb|ABQ21771.1| RNA polymerase sigma-E factor [Vibrio cholerae O395]
 gi|148873419|gb|EDL71554.1| RNA polymerase sigma-E factor [Vibrio cholerae 623-39]
 gi|150422439|gb|EDN14398.1| RNA polymerase sigma-E factor [Vibrio cholerae AM-19226]
 gi|227010476|gb|ACP06688.1| RNA polymerase sigma-E factor [Vibrio cholerae M66-2]
 gi|227014359|gb|ACP10569.1| RNA polymerase sigma-E factor [Vibrio cholerae O395]
 gi|254845297|gb|EET23711.1| RNA polymerase sigma-E factor [Vibrio cholerae MO10]
 gi|255735264|gb|EET90664.1| RNA polymerase sigma factor RpoE [Vibrio cholera CIRS 101]
 gi|262024273|gb|EEY42964.1| RNA polymerase sigma factor RpoE [Vibrio cholerae RC27]
 gi|262028276|gb|EEY46933.1| RNA polymerase sigma factor RpoE [Vibrio cholerae INDRE 91/1]
 gi|262033415|gb|EEY51922.1| RNA polymerase sigma factor RpoE [Vibrio cholerae CT 5369-93]
 gi|297534917|gb|EFH73753.1| RNA polymerase sigma-E factor [Vibrio cholerae RC385]
 gi|297540869|gb|EFH76923.1| RNA polymerase sigma factor RpoE [Vibrio cholerae MAK 757]
 gi|327484959|gb|AEA79366.1| RNA polymerase sigma factor RpoE [Vibrio cholerae LMA3894-4]
          Length = 190

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 18/88 (20%), Positives = 33/88 (37%), Gaps = 3/88 (3%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
            VL +R + +GD  A + LV  +   V  +   Y      +++V  E  I   +A+  F 
Sbjct: 8   QVLIERVQ-NGDKQAFNLLVLRYQNKVCNLISRYVSNSGDVADVAQEAFIKAYRAIPTFR 66

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWS 122
            E      T+         + +I+    
Sbjct: 67  GE--SAFYTWLYRIAVNTAKNHIVAQSR 92


>gi|294644909|ref|ZP_06722645.1| sigma-70, region 4 [Bacteroides ovatus SD CC 2a]
 gi|292639722|gb|EFF58004.1| sigma-70, region 4 [Bacteroides ovatus SD CC 2a]
          Length = 120

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 14/92 (15%), Positives = 34/92 (36%), Gaps = 2/92 (2%)

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
                 E  +I  E  K +  +L + ++ L  ++R +   +      ++ E ++    ++
Sbjct: 28  DLEIDIETAIIHSELEKEQLEVLQKELNNLTKQQREVLYLKYY--KKMSPEEIAQVMGLT 85

Query: 266 RERVRQIEARAFKKVQESIQKQVELSSSPPLL 297
              V      A   ++E + K   L  +  L 
Sbjct: 86  SRTVYNTTHMAISSLRERMSKSFLLLVAANLW 117


>gi|260171041|ref|ZP_05757453.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D2]
          Length = 193

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 13/82 (15%), Positives = 33/82 (40%), Gaps = 6/82 (7%)

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
              N  Q ++ ++                 + + ++ R++  L PR+R +F+  R  E  
Sbjct: 85  DMANEDQLKEQILSQAIDSTNETNNHILLNDLKEIIARALEQLTPRQREVFKMSR--ELQ 142

Query: 253 VTLENLSSEFEVS----RERVR 270
           ++ + ++    VS    +E + 
Sbjct: 143 MSHKEIAEALGVSVHTVQEHIS 164


>gi|167748205|ref|ZP_02420332.1| hypothetical protein ANACAC_02949 [Anaerostipes caccae DSM 14662]
 gi|167652197|gb|EDR96326.1| hypothetical protein ANACAC_02949 [Anaerostipes caccae DSM 14662]
          Length = 182

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 15/72 (20%), Positives = 36/72 (50%), Gaps = 2/72 (2%)

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
           L E   ++   + + R +  L  +++ I       E  +++E +S   ++SR+ VR   +
Sbjct: 108 LEEAVVKQELLDEVNRLIGSLPEKQKIIMNMYYAAE--MSIEEISDNLKISRKTVRSSMS 165

Query: 275 RAFKKVQESIQK 286
           +A  K++ S++ 
Sbjct: 166 KARTKIRSSLEA 177


>gi|330975365|gb|EGH75431.1| RNA polymerase sigma factor RpoS [Pseudomonas syringae pv. aptata
           str. DSM 50252]
          Length = 34

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 12/31 (38%), Positives = 20/31 (64%)

Query: 263 EVSRERVRQIEARAFKKVQESIQKQVELSSS 293
            ++RERVRQI+    K+++E ++K    S S
Sbjct: 1   GLTRERVRQIQVEGLKRLREILEKNGLSSES 31


>gi|112789952|gb|ABI21620.1| Smu20A [uncultured organism]
          Length = 262

 Score = 38.6 bits (89), Expect = 1.2,   Method: Composition-based stats.
 Identities = 41/205 (20%), Positives = 84/205 (40%), Gaps = 22/205 (10%)

Query: 54  VTSHLRLVVKIAMGYRGY----GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
           V  ++R V ++A   R       + + E+ ++G  GL++A+  +DP +G  L  Y     
Sbjct: 16  VEQYMRAVRQVARSLRSRLRTDTVDLEELEADGFEGLVRALHDYDPTKGP-LLQYICLRC 74

Query: 110 KAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVS 169
           + AM + + R     ++ +T  Q+    +   L   L+ +T  +L+ ++V+A    L  +
Sbjct: 75  RGAMIDGLRR-----RMLSTRTQRTNGID-EPLLLPLEQVTAEDLRIDEVIADPDAL--T 126

Query: 170 ESEVISMNCRLAGDESLNALINSSDK-------NSSQWQDWLVYDHDGQEQVLIEKEERK 222
             +VI      +   +L  L  S  +        S   +D        ++ V   + E +
Sbjct: 127 AEDVIERVSSASACSALADLPKSQRRILFARFVESRSQEDVAEGMMFSRKTVAQCETEVR 186

Query: 223 NRRNMLTRSMSV--LNPRERRIFEA 245
            R + L  S     L  +E ++   
Sbjct: 187 RRLHHLAESADEQPLTDKELKVLRL 211


>gi|293345670|ref|XP_001076082.2| PREDICTED: ankyrin 2, neuronal [Rattus norvegicus]
          Length = 3983

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 22/123 (17%), Positives = 44/123 (35%), Gaps = 7/123 (5%)

Query: 157  EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
            E++   A KL    ++        + DES +AL  S  +N            D  +   I
Sbjct: 3456 EEISDEASKLVDRLTQSEREQEPPSDDESSSALEVSVIENLPPVDTEHSAPEDIFDTRPI 3515

Query: 217  EKEERKNRRNML------TRSMSVLNPRERRIFEARRLQEN-PVTLENLSSEFEVSRERV 269
              E  +     +       R+    + +ER       + ++   +   L+ E + + E++
Sbjct: 3516 WDESIETMIERIPDENGHDRAEDPQDEQERMEERLAYIADHLGFSWTELARELDFTEEQI 3575

Query: 270  RQI 272
             QI
Sbjct: 3576 HQI 3578


>gi|300772805|ref|ZP_07082675.1| RNA polymerase ECF-type sigma factor [Sphingobacterium spiritivorum
           ATCC 33861]
 gi|300761108|gb|EFK57934.1| RNA polymerase ECF-type sigma factor [Sphingobacterium spiritivorum
           ATCC 33861]
          Length = 185

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 17/75 (22%), Positives = 33/75 (44%), Gaps = 2/75 (2%)

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
             E  LI KE +      + + +  L  R++ +   +   E   + E ++S   VS E  
Sbjct: 98  SHELDLILKENQDINVQKVKQEIDKLPKRQKEVLYLKYYME--FSYEEIASIMNVSVESC 155

Query: 270 RQIEARAFKKVQESI 284
           R +  RAF+ ++  +
Sbjct: 156 RTLSYRAFRVLKSHM 170


>gi|237721932|ref|ZP_04552413.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 2_2_4]
 gi|229448801|gb|EEO54592.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 2_2_4]
          Length = 164

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 20/90 (22%), Positives = 40/90 (44%), Gaps = 2/90 (2%)

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           +  Q   +Y    +  V  E +E+  R   ++++M  L P  R I E   +Q      + 
Sbjct: 76  THEQYVQIYSELTKSYVETEYQEQDERMIHISKAMEKLTPHTRHILEECYIQRKKY--QE 133

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           ++ E  +S   VR+   +A + ++E   K+
Sbjct: 134 VAEELNISVSAVRKHIVKALQVIREECAKK 163


>gi|29831104|ref|NP_825738.1| ECF subfamily RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
 gi|29608218|dbj|BAC72273.1| putative RNA polymerase ECF-subfamily sigma factor [Streptomyces
           avermitilis MA-4680]
          Length = 191

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 11/62 (17%), Positives = 23/62 (37%), Gaps = 2/62 (3%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L+           E    +  R+ L ++M  L  R+R +   R   +  +T   ++    
Sbjct: 109 LLSKPMPDMASAEEGAYDQLERDSLIKAMKGLQRRQREVLVLRYFAD--MTEAQVAETLG 166

Query: 264 VS 265
           +S
Sbjct: 167 IS 168


>gi|54022859|ref|YP_117101.1| RNA polymerase sigma factor SigD [Nocardia farcinica IFM 10152]
 gi|54014367|dbj|BAD55737.1| putative sigma factor [Nocardia farcinica IFM 10152]
          Length = 203

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 14/86 (16%), Positives = 34/86 (39%), Gaps = 2/86 (2%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           V D    +Q   ++         + R ++ L  + R I   R +    ++ E  ++    
Sbjct: 118 VPDVISTDQGPEQRALESETSRQMNRLLATLPEKHREILVLRLVMG--LSAEETAAAVGS 175

Query: 265 SRERVRQIEARAFKKVQESIQKQVEL 290
           +   +R  + RA  K++  + +  E+
Sbjct: 176 TAGAIRVAQHRALAKLKSQVARAGEM 201


>gi|84390098|ref|ZP_00991360.1| RNA polymerase sigma-70 factor [Vibrio splendidus 12B01]
 gi|86146365|ref|ZP_01064689.1| RNA polymerase sigma-70 factor [Vibrio sp. MED222]
 gi|84376752|gb|EAP93627.1| RNA polymerase sigma-70 factor [Vibrio splendidus 12B01]
 gi|85835844|gb|EAQ53978.1| RNA polymerase sigma-70 factor [Vibrio sp. MED222]
          Length = 192

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 18/88 (20%), Positives = 31/88 (35%), Gaps = 3/88 (3%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
            VL +R +  GD  A + LV  +   V  +   Y      + +V  E  I   +A+  F 
Sbjct: 8   QVLIERVQ-SGDKQAFNLLVVKYQNKVCNLISRYVNNSGDVPDVAQEAFIKAYRAIPNFR 66

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWS 122
            E      T+         + +I+    
Sbjct: 67  GE--SAFYTWLYRIAVNTAKNHIVAQSR 92


>gi|331083273|ref|ZP_08332386.1| hypothetical protein HMPREF0992_01310 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|330404354|gb|EGG83899.1| hypothetical protein HMPREF0992_01310 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 163

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 20/84 (23%), Positives = 42/84 (50%), Gaps = 4/84 (4%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF-EARRLQENPVTLENLSSEF 262
           L+ ++   E+ L+     +  R  L  +++ L  + + I  E+   Q +    E ++   
Sbjct: 81  LICEYSSSEEDLLAGMIEQEERKALFLAIAALPVQMKEILMESIYFQLSD---EAIAKAH 137

Query: 263 EVSRERVRQIEARAFKKVQESIQK 286
            +++E VRQI  RA KK+  S+++
Sbjct: 138 GLTKENVRQIRCRAKKKLISSMKE 161


>gi|218710575|ref|YP_002418196.1| RNA polymerase sigma factor RpoE [Vibrio splendidus LGP32]
 gi|218323594|emb|CAV19840.1| RNA polymerase sigma-E factor [Vibrio splendidus LGP32]
          Length = 205

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 18/88 (20%), Positives = 31/88 (35%), Gaps = 3/88 (3%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
            VL +R +  GD  A + LV  +   V  +   Y      + +V  E  I   +A+  F 
Sbjct: 21  QVLIERVQ-SGDKQAFNLLVVKYQNKVCNLISRYVNNSGDVPDVAQEAFIKAYRAIPNFR 79

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWS 122
            E      T+         + +I+    
Sbjct: 80  GE--SAFYTWLYRIAVNTAKNHIVAQSR 105


>gi|154495089|ref|ZP_02034094.1| hypothetical protein PARMER_04136 [Parabacteroides merdae ATCC
           43184]
 gi|154085639|gb|EDN84684.1| hypothetical protein PARMER_04136 [Parabacteroides merdae ATCC
           43184]
          Length = 192

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 19/93 (20%), Positives = 44/93 (47%), Gaps = 4/93 (4%)

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           ++   L  + D  E         ++  +++ R++  L  + + IF   +L+      E +
Sbjct: 95  EYNMTLRMNLDSLEAFEQHIFSDQDIEDLINRALDSLPTKCKEIFIMNKLEGKK--QEQI 152

Query: 259 SSEFEVSRERVR-QIEARAFKKVQESIQKQVEL 290
           ++E  +S   VR QI + A+KK++  ++  + L
Sbjct: 153 ATELNLSTNTVRNQI-SIAYKKLRNELKDYLPL 184


>gi|153007262|ref|YP_001381587.1| ECF subfamily RNA polymerase sigma-24 factor [Anaeromyxobacter sp.
           Fw109-5]
 gi|152030835|gb|ABS28603.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Anaeromyxobacter
           sp. Fw109-5]
          Length = 205

 Score = 38.6 bits (89), Expect = 1.3,   Method: Composition-based stats.
 Identities = 10/78 (12%), Positives = 30/78 (38%), Gaps = 4/78 (5%)

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           + +    + + S+  + ++    G +    E   R+     +  +++ L  + R I   R
Sbjct: 94  DDVDEVREVDLSEAGEGILATSLGND--PAENALRREMAEKIHAALATLPEKHRTILVLR 151

Query: 247 RLQENPVTLENLSSEFEV 264
             +   ++ E L+    +
Sbjct: 152 --EVEGLSYEELAERLGI 167


>gi|302871542|ref|YP_003840178.1| RNA polymerase, sigma-24 subunit, ECF subfamily
           [Caldicellulosiruptor obsidiansis OB47]
 gi|302574401|gb|ADL42192.1| RNA polymerase, sigma-24 subunit, ECF subfamily
           [Caldicellulosiruptor obsidiansis OB47]
          Length = 183

 Score = 38.3 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 14/90 (15%), Positives = 40/90 (44%), Gaps = 3/90 (3%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E  L +  ++ G+  A + L+ ++L ++    M          +VV E  +  +  + K
Sbjct: 2   DEKSLIEEAKK-GNKEALYTLIENNLNILSGFVMKMTQDYHFAQDVVQETLLKAIMNIDK 60

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           F P+   + +T+ +       ++++ ++  
Sbjct: 61  FSPD--AKFSTWLIKISINVYKDFLKKNKR 88


>gi|153826898|ref|ZP_01979565.1| RNA polymerase sigma-E factor [Vibrio cholerae MZO-2]
 gi|149739261|gb|EDM53523.1| RNA polymerase sigma-E factor [Vibrio cholerae MZO-2]
          Length = 190

 Score = 38.3 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 18/88 (20%), Positives = 33/88 (37%), Gaps = 3/88 (3%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
            VL +R + +GD  A + LV  +   V  +   Y      +++V  E  I   +A+  F 
Sbjct: 8   QVLIERVQ-NGDKQAFNLLVLRYQNKVCNLISRYVSNSGDVADVAQEAFIKAYRAIPTFR 66

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWS 122
            E      T+         + +I+    
Sbjct: 67  GE--SAFYTWLYRIAVNTAKNHIVAQSR 92


>gi|83310810|ref|YP_421074.1| hypothetical protein amb1711 [Magnetospirillum magneticum AMB-1]
 gi|82945651|dbj|BAE50515.1| hypothetical protein [Magnetospirillum magneticum AMB-1]
          Length = 363

 Score = 38.3 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 25/191 (13%), Positives = 61/191 (31%), Gaps = 6/191 (3%)

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
            + + +  +   + ++I R     ++     +            H + I         + 
Sbjct: 161 FSGFVLHAVDRLLIDFIRRHSPRRRLPAAIARLGPLDQAVFRYVHWERIAPQPDAILPMA 220

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW---LVYDHDGQEQVLIE 217
           A       S +++     R+A           +        DW   L  D    EQ ++ 
Sbjct: 221 AREFDPPPSSADIAQALERVAKALPDGYEPGVAGSAPVSLGDWGEALPDDGPTPEQAVLA 280

Query: 218 KEE---RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
            EE        + L  +   L+  ER           P+T  +++       E + +++ 
Sbjct: 281 AEETRLLTLASDALRSASEGLSDTERLYVMIALGHGQPLTARDVAHRMRRPVEEIYKLKQ 340

Query: 275 RAFKKVQESIQ 285
           R   +++++I+
Sbjct: 341 RVMGRLRKAIE 351


>gi|260775214|ref|ZP_05884112.1| RNA polymerase sigma factor RpoE [Vibrio coralliilyticus ATCC
           BAA-450]
 gi|260608915|gb|EEX35077.1| RNA polymerase sigma factor RpoE [Vibrio coralliilyticus ATCC
           BAA-450]
          Length = 192

 Score = 38.3 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 19/88 (21%), Positives = 33/88 (37%), Gaps = 3/88 (3%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
            VL +R + +GD  A + LVT +   V  +   Y      + +V  E  I   +A+  F 
Sbjct: 8   QVLIERVQ-NGDKQAFNLLVTKYQNKVCNLISRYVNNPGDVPDVAQEAFIKAYRAIPSFR 66

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWS 122
            E      T+         + +I+    
Sbjct: 67  GE--SAFYTWLYRIAVNTAKNHIVAQGR 92


>gi|190573361|ref|YP_001971206.1| putative RNA polymerase sigma factor [Stenotrophomonas maltophilia
           K279a]
 gi|190011283|emb|CAQ44896.1| putative RNA polymerase sigma factor [Stenotrophomonas maltophilia
           K279a]
          Length = 220

 Score = 38.3 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 11/79 (13%), Positives = 33/79 (41%), Gaps = 2/79 (2%)

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            +        + + E     ++L +++  L  R R ++   R+     T   ++    ++
Sbjct: 132 DEPTSPSPDPLRQAESGQMLSLLRQALFKLPERAREVYLLNRITGMSYT--QIARHCGIT 189

Query: 266 RERVRQIEARAFKKVQESI 284
            + V +  ARA + +++ +
Sbjct: 190 AKTVEKHIARALQGLRQEL 208


>gi|307153998|ref|YP_003889382.1| ECF subfamily RNA polymerase sigma-24 factor [Cyanothece sp. PCC
           7822]
 gi|306984226|gb|ADN16107.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Cyanothece sp. PCC
           7822]
          Length = 219

 Score = 38.3 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 20/111 (18%), Positives = 38/111 (34%), Gaps = 17/111 (15%)

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           R++   SL+A     D         + +D         +    +     L  +++ L   
Sbjct: 116 RVSNPVSLDAPRRVDDGE-------IDWDIVSDYPSPDDHLATREFYEQLRLAIANLPEA 168

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVS----RERVRQIEARAFKKVQESIQ 285
            R     R +    +  E ++    VS    + R+    ARA  K+Q  +Q
Sbjct: 169 FRTTIVLREI--EGMAYEEIAEITGVSLGTVKSRI----ARARAKLQSVLQ 213


>gi|291397154|ref|XP_002714986.1| PREDICTED: spectrin repeat containing, nuclear envelope 1
            [Oryctolagus cuniculus]
          Length = 8699

 Score = 38.3 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 28/118 (23%), Positives = 49/118 (41%), Gaps = 3/118 (2%)

Query: 117  ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
            + RSW  +K   +  Q+ L+  L R K +  ++   + K E   AI  KL+ S     S 
Sbjct: 5898 LQRSWDTLKNVISEKQRTLYEALERQKKYQDSLPSISTKME---AIEVKLSESLEPGRSP 5954

Query: 177  NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV 234
              ++A  ++L   I       ++ Q  L  +   QE    E+   ++   +L   MS 
Sbjct: 5955 ESQMAEHQALMDEILMLHDEINELQSCLAEELGSQECDPTEQLALQSTLTVLAERMST 6012


>gi|288871625|ref|ZP_06118278.2| RNA polymerase sigma-70 factor, ECF family [Clostridium hathewayi
           DSM 13479]
 gi|288862757|gb|EFC95055.1| RNA polymerase sigma-70 factor, ECF family [Clostridium hathewayi
           DSM 13479]
          Length = 168

 Score = 38.3 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 19/91 (20%), Positives = 42/91 (46%), Gaps = 8/91 (8%)

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF-EARRLQENPVT 254
           +  ++   L+ + D   + LI+ EE    R +L  ++  L    + +  ++     +   
Sbjct: 78  DEGRFDFSLLREEDHTLEGLIQDEE----RRLLLEAIMKLPVHYKEVLLDSIYFHLSD-- 131

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            E +     +++E VRQI +RA K+V   ++
Sbjct: 132 -EEIGKSMGITKENVRQIRSRAKKQVMRLLE 161


>gi|312197470|ref|YP_004017531.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Frankia sp. EuI1c]
 gi|311228806|gb|ADP81661.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Frankia sp. EuI1c]
          Length = 210

 Score = 38.3 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 14/74 (18%), Positives = 39/74 (52%), Gaps = 2/74 (2%)

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
            + +  ++  +R  +R+ L R++  L PR+R +   R +++  ++  ++++    S   V
Sbjct: 95  DEPEAAVDAADRLAQRDGLLRALRALPPRQRAVIVLRYVED--LSEADVAAAMGCSVGSV 152

Query: 270 RQIEARAFKKVQES 283
           R   +R   ++++S
Sbjct: 153 RSQASRGLARLRDS 166


>gi|218230792|ref|YP_002366487.1| RNA polymerase factor sigma-70 [Bacillus cereus B4264]
 gi|218158749|gb|ACK58741.1| RNA polymerase sigma-70 factor, ECF family [Bacillus cereus B4264]
          Length = 188

 Score = 38.3 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 10/59 (16%), Positives = 25/59 (42%), Gaps = 2/59 (3%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           H   E+   ++      R  L + ++ L P ++++F  + L       E +  +  ++R
Sbjct: 104 HISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKT--EEIGGKLGLTR 160


>gi|254446450|ref|ZP_05059926.1| RNA polymerase sigma factor, sigma-70 family [Verrucomicrobiae
           bacterium DG1235]
 gi|198260758|gb|EDY85066.1| RNA polymerase sigma factor, sigma-70 family [Verrucomicrobiae
           bacterium DG1235]
          Length = 146

 Score = 38.3 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 14/78 (17%), Positives = 37/78 (47%), Gaps = 6/78 (7%)

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           A +   D +    +  ++ + DG  + +   +E      +LT+++  L  R R+IF  R+
Sbjct: 47  AKVRCEDTSRDFSEFDILDESDGVHETVARNQEL----EILTKAIQSLPDRCRQIFTLRK 102

Query: 248 LQENPVTLENLSSEFEVS 265
           +    ++  +++ +  +S
Sbjct: 103 VYG--MSQRDIAKKLNIS 118


>gi|251796836|ref|YP_003011567.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Paenibacillus sp.
           JDR-2]
 gi|247544462|gb|ACT01481.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Paenibacillus sp.
           JDR-2]
          Length = 177

 Score = 38.3 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 10/78 (12%), Positives = 32/78 (41%), Gaps = 3/78 (3%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           +       Q   +   +++    +   ++ L  R+R +   R    +  +   ++ E  V
Sbjct: 91  LMTEPQTFQSGEQAVIKQDEEEQVQGWLNSLPERDRDLLLLRY---SGYSYSEIAQELNV 147

Query: 265 SRERVRQIEARAFKKVQE 282
            + +V  +  RA +++++
Sbjct: 148 QQPQVGMLLKRAGERLRK 165


>gi|284028450|ref|YP_003378381.1| ECF subfamily RNA polymerase sigma-24 subunit [Kribbella flavida
           DSM 17836]
 gi|283807743|gb|ADB29582.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Kribbella flavida
           DSM 17836]
          Length = 166

 Score = 38.3 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 12/64 (18%), Positives = 29/64 (45%), Gaps = 2/64 (3%)

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           R+ +R+   R ++ L  R+R +   R  ++ P   + +++    +   VR   AR    +
Sbjct: 99  RQAQRDAAWRLLATLPRRQRAVLVLRYYEDLPD--DEIAAVLNCTASTVRSNAARGLASL 156

Query: 281 QESI 284
           +  +
Sbjct: 157 RAEL 160


>gi|256544837|ref|ZP_05472209.1| conserved hypothetical protein [Anaerococcus vaginalis ATCC 51170]
 gi|256399726|gb|EEU13331.1| conserved hypothetical protein [Anaerococcus vaginalis ATCC 51170]
          Length = 141

 Score = 38.3 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 22/105 (20%), Positives = 43/105 (40%), Gaps = 16/105 (15%)

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           + L  SS  +   ++D L   +   E+V+      +     L  +MS LN  ER I E  
Sbjct: 47  HLLFFSSLNHDGNFEDNLEDKNVDVEKVVA----TQMMIEALRNAMSKLNEDEREIIERL 102

Query: 247 RLQENPVTLENLSSEFEVS-----RERVRQIEARAFKKVQESIQK 286
              +   TL  ++    +S     + R      +  +K+++ I++
Sbjct: 103 YFNDE--TLRAVAKTQNISHPALIKRR-----DKILEKLKKFIEE 140


>gi|284035790|ref|YP_003385720.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Spirosoma linguale
           DSM 74]
 gi|283815083|gb|ADB36921.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Spirosoma linguale
           DSM 74]
          Length = 211

 Score = 38.3 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 16/88 (18%), Positives = 37/88 (42%), Gaps = 2/88 (2%)

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
             S   D +  +    +Q LI  E  + +   L   ++ L+ R+R     +   E  ++ 
Sbjct: 108 EDSILFDDVSSEEITADQALIRTELSEYQTARLNALLATLSDRQREAIHLKFYAE--LSN 165

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQES 283
             ++    V+++ V  +  R   +++ES
Sbjct: 166 HEIADILTVNKQSVANLLHRGLSRLRES 193


>gi|160884003|ref|ZP_02065006.1| hypothetical protein BACOVA_01977 [Bacteroides ovatus ATCC 8483]
 gi|299147020|ref|ZP_07040087.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 3_1_23]
 gi|156110733|gb|EDO12478.1| hypothetical protein BACOVA_01977 [Bacteroides ovatus ATCC 8483]
 gi|298514905|gb|EFI38787.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 3_1_23]
          Length = 198

 Score = 38.3 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 16/99 (16%), Positives = 38/99 (38%), Gaps = 14/99 (14%)

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           S     +  D     +  +E  E K   +++ +++  L+P  R++F   R +      E 
Sbjct: 98  SSEDLVIYSDLWSLGENPVEHLEGKELHSIIQKTIDGLSPETRKVFLLSRFENKR--QEE 155

Query: 258 LSSEFEVSRERVRQIE------ARAFKKVQESIQKQVEL 290
           ++    ++      I         A  K++E+ +  + L
Sbjct: 156 IAEIMGIT------IHTVKYHMRSALDKLKEAAKSYLAL 188


>gi|15898660|ref|NP_343265.1| hypothetical protein SSO1868 [Sulfolobus solfataricus P2]
 gi|284173114|ref|ZP_06387083.1| hypothetical protein Ssol98_00455 [Sulfolobus solfataricus 98/2]
 gi|13815121|gb|AAK42055.1| Conserved hypothetical protein [Sulfolobus solfataricus P2]
 gi|261603118|gb|ACX92721.1| Bacterio-opsin activator HTH domain protein [Sulfolobus
           solfataricus 98/2]
          Length = 204

 Score = 38.3 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 12/52 (23%), Positives = 22/52 (42%), Gaps = 5/52 (9%)

Query: 233 SVLNPRERRIFEA-----RRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           + L  R+  I +          +  VTL  L+ +  +S   + +I  RA +K
Sbjct: 143 NELTDRQMEILKLAYKMGYFDDDRRVTLTELAKQLGISTPTLEEILRRALRK 194


>gi|293357553|ref|XP_342338.4| PREDICTED: ankyrin 2, neuronal [Rattus norvegicus]
          Length = 3998

 Score = 38.3 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 22/123 (17%), Positives = 44/123 (35%), Gaps = 7/123 (5%)

Query: 157  EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
            E++   A KL    ++        + DES +AL  S  +N            D  +   I
Sbjct: 3471 EEISDEASKLVDRLTQSEREQEPPSDDESSSALEVSVIENLPPVDTEHSAPEDIFDTRPI 3530

Query: 217  EKEERKNRRNML------TRSMSVLNPRERRIFEARRLQEN-PVTLENLSSEFEVSRERV 269
              E  +     +       R+    + +ER       + ++   +   L+ E + + E++
Sbjct: 3531 WDESIETMIERIPDENGHDRAEDPQDEQERMEERLAYIADHLGFSWTELARELDFTEEQI 3590

Query: 270  RQI 272
             QI
Sbjct: 3591 HQI 3593


>gi|284040863|ref|YP_003390793.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Spirosoma linguale
           DSM 74]
 gi|283820156|gb|ADB41994.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Spirosoma linguale
           DSM 74]
          Length = 199

 Score = 38.3 bits (88), Expect = 1.3,   Method: Composition-based stats.
 Identities = 13/81 (16%), Positives = 31/81 (38%), Gaps = 14/81 (17%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS------ 265
           E  +   + R+     L   +  L  ++R++   R  +E  ++ + ++    VS      
Sbjct: 115 EDSVESLQIRQETHEHLRELIQRLPEQQRQVLIMRHYEE--MSFQEIADATGVSINTALG 172

Query: 266 RERVRQIEARAFKKVQESIQK 286
           R R       A   +++ + K
Sbjct: 173 RMR------YALINLRKQLSK 187


>gi|307332396|ref|ZP_07611465.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306881957|gb|EFN13074.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 187

 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 16/72 (22%), Positives = 33/72 (45%), Gaps = 3/72 (4%)

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           +  +     K+    +  ++S L PR+R++     L     +   +S E  ++ E VRQ 
Sbjct: 111 ECPLAALVLKDEEQHVCAALSALPPRQRQVMAWH-LDGFSHS--EISDELGITVEAVRQN 167

Query: 273 EARAFKKVQESI 284
            ARA   ++ ++
Sbjct: 168 YARARVSLKRAL 179


>gi|148981087|ref|ZP_01816280.1| RNA polymerase sigma factor RpoE [Vibrionales bacterium SWAT-3]
 gi|145960990|gb|EDK26314.1| RNA polymerase sigma factor RpoE [Vibrionales bacterium SWAT-3]
          Length = 192

 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 18/88 (20%), Positives = 31/88 (35%), Gaps = 3/88 (3%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
            VL +R +  GD  A + LV  +   V  +   Y      + +V  E  I   +A+  F 
Sbjct: 8   QVLIERVQ-SGDKQAFNLLVVKYQNKVCNLISRYVNNSGDVPDVAQEAFIKAYRAIPNFR 66

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWS 122
            E      T+         + +I+    
Sbjct: 67  GE--SAFYTWLYRIAVNTAKNHIVAQSR 92


>gi|258626735|ref|ZP_05721557.1| RNA polymerase sigma-E factor [Vibrio mimicus VM603]
 gi|262170584|ref|ZP_06038262.1| RNA polymerase sigma factor RpoE [Vibrio mimicus MB-451]
 gi|258580991|gb|EEW05918.1| RNA polymerase sigma-E factor [Vibrio mimicus VM603]
 gi|261891660|gb|EEY37646.1| RNA polymerase sigma factor RpoE [Vibrio mimicus MB-451]
          Length = 190

 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 18/88 (20%), Positives = 33/88 (37%), Gaps = 3/88 (3%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
            VL +R + +GD  A + LV  +   V  +   Y      +++V  E  I   +A+  F 
Sbjct: 8   QVLIERVQ-NGDKQAFNLLVLRYQNKVCNLISRYVSNSGDVADVAQEAFIKAYRAIPTFR 66

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWS 122
            E      T+         + +I+    
Sbjct: 67  GE--SAFYTWLYRIAVNTAKNHIVAQSR 92


>gi|257416626|ref|ZP_05593620.1| predicted protein [Enterococcus faecalis AR01/DG]
 gi|257158454|gb|EEU88414.1| predicted protein [Enterococcus faecalis ARO1/DG]
          Length = 134

 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 19/103 (18%), Positives = 47/103 (45%), Gaps = 9/103 (8%)

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
           +SL  ++ +S   +    D++        +   E E        L+R++  LN +E+++ 
Sbjct: 41  DSLEDIMRNSISEAYLSLDFISESEIMNLENFAENE-------ALSRAIEQLNFKEKKLL 93

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             + +Q    +   ++  F++SR+ V     R  KK++  +++
Sbjct: 94  YEKYIQCKTDS--EIARIFDISRQGVSIFRKRLLKKLEVFLKR 134


>gi|323700471|ref|ZP_08112383.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Desulfovibrio sp.
           ND132]
 gi|323460403|gb|EGB16268.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Desulfovibrio
           desulfuricans ND132]
          Length = 194

 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 10/66 (15%), Positives = 25/66 (37%), Gaps = 8/66 (12%)

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
            VL  R+  +               ++ +  ++   VR I+ +A  +++      +   +
Sbjct: 124 GVLTDRQAEVVTLYYRDGLIA--CEIAQKLGITSRTVRSIKFQALDRLR------IHYGA 175

Query: 293 SPPLLQ 298
           S PL +
Sbjct: 176 SAPLAE 181


>gi|322433999|ref|YP_004216211.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Acidobacterium sp.
           MP5ACTX9]
 gi|321161726|gb|ADW67431.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Acidobacterium sp.
           MP5ACTX9]
          Length = 262

 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 17/95 (17%), Positives = 32/95 (33%), Gaps = 2/95 (2%)

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
                  D +  +         D        + +RK     +  ++  L PRER +FE +
Sbjct: 161 EDPATVLDSSGDEMDLMANVTDDRAMANPGRELDRKVMGERIASALEKLTPRERTVFELK 220

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             Q     L  +      + E  +    RA +K++
Sbjct: 221 HYQGLK--LRTIGEMLSTTEETAKNTLFRATRKLR 253


>gi|260494273|ref|ZP_05814404.1| RNA polymerase sigma factor [Fusobacterium sp. 3_1_33]
 gi|260198419|gb|EEW95935.1| RNA polymerase sigma factor [Fusobacterium sp. 3_1_33]
          Length = 274

 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 27/127 (21%), Positives = 51/127 (40%), Gaps = 5/127 (3%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V  +L+ V ++A+     G+   ++  EG +GL++A + F+ ++ F+L  Y  ++I   M
Sbjct: 84  VEKNLKKVYEMALYMLREGISYDDLTQEGIVGLIKAHELFEDDKDFKL--YKDYYIAKEM 141

Query: 114 QEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEV 173
             YI    +  K       K        LK  L+   D +   E      +       E+
Sbjct: 142 FNYINNYANYRKAAFKDYAKHEIHKDSHLKISLK---DRDKSEELKKLEKENKEKHIEEM 198

Query: 174 ISMNCRL 180
             +  R 
Sbjct: 199 KQLEKRA 205


>gi|229507473|ref|ZP_04396978.1| RNA polymerase sigma factor RpoE [Vibrio cholerae BX 330286]
 gi|229512332|ref|ZP_04401811.1| RNA polymerase sigma factor RpoE [Vibrio cholerae B33]
 gi|229514093|ref|ZP_04403555.1| RNA polymerase sigma factor RpoE [Vibrio cholerae TMA 21]
 gi|229519468|ref|ZP_04408911.1| RNA polymerase sigma factor RpoE [Vibrio cholerae RC9]
 gi|229521294|ref|ZP_04410714.1| RNA polymerase sigma factor RpoE [Vibrio cholerae TM 11079-80]
 gi|229524454|ref|ZP_04413859.1| RNA polymerase sigma factor RpoE [Vibrio cholerae bv. albensis
           VL426]
 gi|229527075|ref|ZP_04416470.1| RNA polymerase sigma factor RpoE [Vibrio cholerae 12129(1)]
 gi|229606978|ref|YP_002877626.1| RNA polymerase sigma factor RpoE [Vibrio cholerae MJ-1236]
 gi|229335472|gb|EEO00954.1| RNA polymerase sigma factor RpoE [Vibrio cholerae 12129(1)]
 gi|229338035|gb|EEO03052.1| RNA polymerase sigma factor RpoE [Vibrio cholerae bv. albensis
           VL426]
 gi|229341826|gb|EEO06828.1| RNA polymerase sigma factor RpoE [Vibrio cholerae TM 11079-80]
 gi|229344157|gb|EEO09132.1| RNA polymerase sigma factor RpoE [Vibrio cholerae RC9]
 gi|229349274|gb|EEO14231.1| RNA polymerase sigma factor RpoE [Vibrio cholerae TMA 21]
 gi|229352297|gb|EEO17238.1| RNA polymerase sigma factor RpoE [Vibrio cholerae B33]
 gi|229354978|gb|EEO19899.1| RNA polymerase sigma factor RpoE [Vibrio cholerae BX 330286]
 gi|229369633|gb|ACQ60056.1| RNA polymerase sigma factor RpoE [Vibrio cholerae MJ-1236]
          Length = 194

 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 18/88 (20%), Positives = 33/88 (37%), Gaps = 3/88 (3%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
            VL +R + +GD  A + LV  +   V  +   Y      +++V  E  I   +A+  F 
Sbjct: 12  QVLIERVQ-NGDKQAFNLLVLRYQNKVCNLISRYVSNSGDVADVAQEAFIKAYRAIPTFR 70

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWS 122
            E      T+         + +I+    
Sbjct: 71  GE--SAFYTWLYRIAVNTAKNHIVAQSR 96


>gi|282601432|ref|ZP_05981684.2| RNA polymerase ECF-type sigma factor [Subdoligranulum variabile DSM
           15176]
 gi|282569066|gb|EFB74601.1| RNA polymerase ECF-type sigma factor [Subdoligranulum variabile DSM
           15176]
          Length = 161

 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 15/91 (16%), Positives = 41/91 (45%), Gaps = 3/91 (3%)

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM-LTRSMSVLNPRERRIFEARRLQENPVT 254
           + ++  + L+     QE   +E    ++ +   L   ++ L   ++R  +      + +T
Sbjct: 73  DWTELNEELLSRRSAQEPAPVEDAVYESMQTQALREGVNQLPEVQKRRLQMYFF--DGLT 130

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
            E ++     S + V++  A A KK+++ ++
Sbjct: 131 YEEIAVREGCSYQAVQKSIAAALKKIRKFLK 161


>gi|53715755|ref|YP_101747.1| RNA polymerase ECF-type sigma factor [Bacteroides fragilis YCH46]
 gi|60683687|ref|YP_213831.1| putative ECF-type RNA polymerase [Bacteroides fragilis NCTC 9343]
 gi|253566432|ref|ZP_04843885.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 3_2_5]
 gi|265767303|ref|ZP_06094969.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 2_1_16]
 gi|52218620|dbj|BAD51213.1| RNA polymerase ECF-type sigma factor [Bacteroides fragilis YCH46]
 gi|60495121|emb|CAH09941.1| putative ECF-type RNA polymerase [Bacteroides fragilis NCTC 9343]
 gi|251944604|gb|EES85079.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 3_2_5]
 gi|263252608|gb|EEZ24120.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 2_1_16]
 gi|301165200|emb|CBW24771.1| putative ECF-type RNA polymerase [Bacteroides fragilis 638R]
          Length = 183

 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 14/71 (19%), Positives = 37/71 (52%), Gaps = 2/71 (2%)

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
           + E+ +  N R  ++  +S+L PR++ +F   R  +  ++   ++   ++S   V    +
Sbjct: 107 IEEELDAANLRTHISALISMLPPRQQEVFRLSR--DEELSYREIAERLQISERTVEHHIS 164

Query: 275 RAFKKVQESIQ 285
            A K ++++I+
Sbjct: 165 DALKFLRKNIK 175


>gi|300771764|ref|ZP_07081635.1| conserved hypothetical protein [Sphingobacterium spiritivorum ATCC
           33861]
 gi|300761150|gb|EFK57975.1| conserved hypothetical protein [Sphingobacterium spiritivorum ATCC
           33861]
          Length = 189

 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 16/68 (23%), Positives = 35/68 (51%), Gaps = 5/68 (7%)

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR-QIEARAFK 278
           E K  + +L +++  L  + + I+  R   +     + ++ EF++SR  V+ QI + A K
Sbjct: 122 EYKEYKEILRKAVDNLPEQRKAIYLMR---DEGYNYQEIADEFDISRHTVKNQI-SAAMK 177

Query: 279 KVQESIQK 286
            +++   K
Sbjct: 178 SIRKVFSK 185


>gi|87307170|ref|ZP_01089315.1| probable RNA polymerase sigma-E factor [Blastopirellula marina DSM
           3645]
 gi|87289910|gb|EAQ81799.1| probable RNA polymerase sigma-E factor [Blastopirellula marina DSM
           3645]
          Length = 209

 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 20/83 (24%), Positives = 37/83 (44%), Gaps = 5/83 (6%)

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           D +V         +I +EE       L +++S L   +RR+ E R    + +T E +  E
Sbjct: 124 DEIVDPQQATASSMIRREETDLE---LIQAVSQLQSDQRRLIEMR--HRHGMTYEAIGQE 178

Query: 262 FEVSRERVRQIEARAFKKVQESI 284
             +S   VR   A A  ++++ +
Sbjct: 179 LGISERTVRNRWANAITQLRKEL 201


>gi|307244000|ref|ZP_07526121.1| sigma-70, region 4 [Peptostreptococcus stomatis DSM 17678]
 gi|306492650|gb|EFM64682.1| sigma-70, region 4 [Peptostreptococcus stomatis DSM 17678]
          Length = 137

 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 15/94 (15%), Positives = 47/94 (50%), Gaps = 6/94 (6%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
            +   + D ++ +    E+++    E + +   L R+++ L   ER + EA   +E   +
Sbjct: 50  DHDGHFVDSIIDEKIDLEKIV----EVRMQIEELHRALNTLTKEERELMEAIFYKEE--S 103

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           L ++  + +VS + + +   +  +K+++ ++ ++
Sbjct: 104 LRSIGKKEKVSYQAISKRRDKILEKLRKILKDKI 137


>gi|255532560|ref|YP_003092932.1| sigma-70 family RNA polymerase sigma factor [Pedobacter heparinus
           DSM 2366]
 gi|255345544|gb|ACU04870.1| RNA polymerase sigma factor, sigma-70 family [Pedobacter heparinus
           DSM 2366]
          Length = 189

 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 16/77 (20%), Positives = 32/77 (41%), Gaps = 2/77 (2%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
               E+ +I  E++      L + + +L  R++     R   E     E ++    VS E
Sbjct: 105 SSSIEEQIISDEQQSELLLKLNKQLELLPSRQKEALYLRFNAELDY--EEIAVVMNVSLE 162

Query: 268 RVRQIEARAFKKVQESI 284
             R +  R  K+++E +
Sbjct: 163 TCRTLVYRGVKQLRERM 179


>gi|218264750|ref|ZP_03478462.1| hypothetical protein PRABACTJOHN_04171 [Parabacteroides johnsonii
           DSM 18315]
 gi|218221799|gb|EEC94449.1| hypothetical protein PRABACTJOHN_04171 [Parabacteroides johnsonii
           DSM 18315]
          Length = 188

 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 16/107 (14%), Positives = 46/107 (42%), Gaps = 6/107 (5%)

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLI----EKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           I   +  S   ++   ++ + +   L     E+      + ++ ++++ L  + RRIF  
Sbjct: 78  IQVREDASEHLKNHAEWELNTRISTLEACDPEELFTAEAQEIVNKTLATLPEQTRRIFIM 137

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
            R +  P   + ++    ++ + V     +A KK+  +++  + L +
Sbjct: 138 SRYENKPY--KEIAETLGMTTKGVEYHITQALKKLHINLKDYIPLFA 182


>gi|77920714|ref|YP_358529.1| RNA polymerase, sigma-E factor [Pelobacter carbinolicus DSM 2380]
 gi|77546797|gb|ABA90359.1| RNA polymerase, sigma subunit, ECF family [Pelobacter carbinolicus
           DSM 2380]
          Length = 214

 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 36/231 (15%), Positives = 70/231 (30%), Gaps = 71/231 (30%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           E +L +R R+ GD  A  +LV+ HL  VV +A    G      ++  E  + L +++  F
Sbjct: 27  ESLLLERIRQ-GDEGAFTQLVSGHLSSVVNLAYRMLGDRQEAEDLAQEAFLRLHRSLPSF 85

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
             +   +       W+   +   ++                                   
Sbjct: 86  RGDCRIK------TWLYKVVSRLVIDHIR------------------------------- 108

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
              EQV          E +                 + +    S+   D L+        
Sbjct: 109 --REQVRRRIFFFRKHEDDP--------------DPVANFADPSASPSDQLLG------- 145

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
                   +  R  L ++M  L+ R+R +F  R  +  P  L+ ++    +
Sbjct: 146 --------QETRQKLFKAMEKLSGRQRAVFVLRHQEGLP--LKEIAQVLHL 186


>gi|326801608|ref|YP_004319427.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Sphingobacterium
           sp. 21]
 gi|326552372|gb|ADZ80757.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Sphingobacterium
           sp. 21]
          Length = 192

 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 14/101 (13%), Positives = 39/101 (38%), Gaps = 20/101 (19%)

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D  + +    L+ +       ++  E  K+  + + R    L  ++R+IF    + +  +
Sbjct: 91  DAENIEDYSQLLTEDSDAFTQIVRAELLKSIMDEVQR----LPEKQRKIFHMTFIDD--M 144

Query: 254 TLENLSSEFEVS-------RERVRQIEARAFKKVQESIQKQ 287
           +++ +     +S       R R       A   +++ I+ +
Sbjct: 145 SMDEIGLHLGMSPNAVYTNRSR-------ALATLRDHIKTK 178


>gi|319902724|ref|YP_004162452.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Bacteroides
           helcogenes P 36-108]
 gi|319417755|gb|ADV44866.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Bacteroides
           helcogenes P 36-108]
          Length = 195

 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 15/78 (19%), Positives = 41/78 (52%), Gaps = 8/78 (10%)

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR- 275
           E+   K  + ++ ++++ L  + R++F  RR +E  ++ + ++ +  +S   VR +E   
Sbjct: 115 EELLSKEMQELVAKALNKLPEKTRQVFIMRRFKE--MSFKEIAVQTGMS---VRGVEYHL 169

Query: 276 --AFKKVQESIQKQVELS 291
             A   +++S++  + L 
Sbjct: 170 DIATASLKKSLKDYLPLL 187


>gi|332653717|ref|ZP_08419461.1| RNA polymerase sigma factor SigV [Ruminococcaceae bacterium D16]
 gi|332516803|gb|EGJ46408.1| RNA polymerase sigma factor SigV [Ruminococcaceae bacterium D16]
          Length = 153

 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 18/85 (21%), Positives = 41/85 (48%), Gaps = 6/85 (7%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           ++Y  +  EQ+   +E     R  L +++  L+P+ + +   R  +E  + L  ++    
Sbjct: 72  VIYLAEPPEQIQSSQESALEDREALQQAIDRLSPKLKTVVLLRFYEE--MQLSEIAEITG 129

Query: 264 --VSRERVRQIEARAFKKVQESIQK 286
             +S  + R    +  KK++ES+Q+
Sbjct: 130 TNLSTVKSR--LYKGLKKLRESLQE 152


>gi|262183837|ref|ZP_06043258.1| RNA polymerase sigma factor SigD [Corynebacterium aurimucosum ATCC
           700975]
          Length = 205

 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 26/164 (15%), Positives = 63/164 (38%), Gaps = 6/164 (3%)

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I    + + L +   R+ GH +  T  ++  E  +A+A  +   + +       + G  
Sbjct: 42  RIMRIIHPQVLRYCRARIGGH-RQPTAEDVAQEICLAVATSIGTYKDKGRPFMAYVYGIA 100

Query: 185 S--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
           +  +     +  ++ +   + L  D   Q+    E     +  N +   +  L+ + R I
Sbjct: 101 AHKVTDAHRALSRDHTHPTEDLPEDA-AQDATPEESALEVDGSNRVRAMLDTLSDKARDI 159

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              R      ++ E  +   E +   VR  + RA  ++++S+  
Sbjct: 160 IILRVFVG--LSAEETAEIVESTPGAVRVAQHRALAQLRKSLDS 201


>gi|225873643|ref|YP_002755102.1| RNA polymerase sigma-70 factor [Acidobacterium capsulatum ATCC
           51196]
 gi|225793389|gb|ACO33479.1| RNA polymerase sigma-70 factor [Acidobacterium capsulatum ATCC
           51196]
          Length = 242

 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 18/105 (17%), Positives = 45/105 (42%), Gaps = 10/105 (9%)

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           D    +  G  +   +  E+  +  +LT  +  L+P  R +   R   +  ++LE ++  
Sbjct: 139 DDRPMEIPGNGRSPFDHLEQLEKGQLLTEVLLTLDPLHREVILLRF--QEDLSLEEIAQ- 195

Query: 262 FEVSRERVRQIEARAFKKV-----QESIQKQVELSSSPPLLQKPR 301
             ++R  +  +++R ++ +     + S + Q     + P +  PR
Sbjct: 196 --ITRAPLSTVKSRLYRGLTALKPRLSARTQQPAPVTAPPIHSPR 238


>gi|187736323|ref|YP_001878435.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Akkermansia
           muciniphila ATCC BAA-835]
 gi|187426375|gb|ACD05654.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Akkermansia
           muciniphila ATCC BAA-835]
          Length = 197

 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 21/103 (20%), Positives = 38/103 (36%), Gaps = 3/103 (2%)

Query: 20  IHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVV 79
           + E + +P  E  E+  L  R R +GD SA   LV  H   V          G    ++ 
Sbjct: 1   MDEAQDMPPAEPDEDAKLMLRVR-NGDASAMEMLVRKHQNSVYATVARMLNNGPETEDIA 59

Query: 80  SEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
            +  I + +    ++P    R  T+    ++  +   + R   
Sbjct: 60  QQVFIRIWKGAGNYEPS--ARFTTWMFTILRNLVFNEVRRQKR 100


>gi|261367303|ref|ZP_05980186.1| DNA-binding protein [Subdoligranulum variabile DSM 15176]
 gi|282570906|gb|EFB76441.1| DNA-binding protein [Subdoligranulum variabile DSM 15176]
          Length = 132

 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 9/37 (24%), Positives = 19/37 (51%), Gaps = 2/37 (5%)

Query: 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
           VL  ++R I       +  ++L  ++  F ++R+ VR
Sbjct: 21  VLTEKQRLILTEYY--DEDLSLAEIAENFGITRQGVR 55


>gi|94995112|ref|YP_603210.1| hypothetical protein MGAS10750_Spy1716 [Streptococcus pyogenes
           MGAS10750]
 gi|94548620|gb|ABF38666.1| hypothetical protein MGAS10750_Spy1716 [Streptococcus pyogenes
           MGAS10750]
          Length = 136

 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 23/93 (24%), Positives = 45/93 (48%), Gaps = 14/93 (15%)

Query: 203 WLVYDHDGQEQVLIEKEER--------KNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
           +  YDHDG  +  +E  E         K     + R++S LNP ER + E+   +E   T
Sbjct: 46  FCSYDHDGNFEENLEDLEFDVEKIIETKEMIEEVRRAISKLNPVERDLIESLFYKEE--T 103

Query: 255 LENLSSEFEVSRERV--RQIEARAFKKVQESIQ 285
           +  ++++  +S   V  R+   +  +K++E ++
Sbjct: 104 IREVAAKLNISNPAVIKRR--NKVLEKLKEMLE 134


>gi|13471294|ref|NP_102863.1| RNA polymerase sigma factor [Mesorhizobium loti MAFF303099]
 gi|14022038|dbj|BAB48649.1| probable RNA polymerase sigma factor [Mesorhizobium loti
           MAFF303099]
          Length = 187

 Score = 38.3 bits (88), Expect = 1.4,   Method: Composition-based stats.
 Identities = 19/97 (19%), Positives = 40/97 (41%), Gaps = 5/97 (5%)

Query: 28  MLEKQE--EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           ML++ E  +  L  R +  GD  A  +L+  H   V + A  + G      ++  E  + 
Sbjct: 5   MLDESEASDAELIGRAK-GGDRGAFGKLLERHYDFVYRAAYRWCGKKADAEDIAQEVCVR 63

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           L +A++ +    G    T+       A ++ + ++  
Sbjct: 64  LGKAIRDYRG--GGAFTTWLYSVTMNAARDMMRKTAR 98


>gi|331005224|ref|ZP_08328617.1| RNA polymerase sigma-H factor AlgT [gamma proteobacterium IMCC1989]
 gi|330420967|gb|EGG95240.1| RNA polymerase sigma-H factor AlgT [gamma proteobacterium IMCC1989]
          Length = 196

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 18/91 (19%), Positives = 35/91 (38%), Gaps = 6/91 (6%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L +R ++ GD  A   LV  +   ++ +   Y      +++VV E  I   +A+  F  E
Sbjct: 13  LVERVQQ-GDKRAFDLLVLKYQHKIISVVHRYMRDPADVNDVVQEAFIKAYRALPNFRGE 71

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIG 127
                + +  W  + A+        S  +  
Sbjct: 72  -----SAFYTWMYRIAINTAKNDLISKGRRP 97


>gi|222529687|ref|YP_002573569.1| RNA polymerase sigma factor SigY [Caldicellulosiruptor bescii DSM
           6725]
 gi|222456534|gb|ACM60796.1| RNA polymerase, sigma-24 subunit, ECF subfamily
           [Caldicellulosiruptor bescii DSM 6725]
          Length = 183

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 13/90 (14%), Positives = 40/90 (44%), Gaps = 3/90 (3%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E  L +  ++ G+  A ++L+ ++L ++               +VV E  +  +  + K
Sbjct: 2   DEKRLIEEAKK-GNKEALYKLIENNLNILSGFVTKMTQDYHFAQDVVQETLLRAIMNIDK 60

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           F P+   + +T+ +       ++++ ++  
Sbjct: 61  FSPD--AKFSTWLIKISINVYKDFLRKNKR 88


>gi|114565704|ref|YP_752858.1| ECF subfamily RNA polymerase sigma-24 factor [Syntrophomonas wolfei
           subsp. wolfei str. Goettingen]
 gi|114336639|gb|ABI67487.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Syntrophomonas
           wolfei subsp. wolfei str. Goettingen]
          Length = 194

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 17/102 (16%), Positives = 38/102 (37%), Gaps = 11/102 (10%)

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
            LI S D   +     ++ +    E   +E  ER+     +  ++  L P  R +   R 
Sbjct: 90  LLIFSLDNPVNTSNGEVIRELAAGEDSPLEAVERQELSAAVRTALDRLAPEYRTVLILR- 148

Query: 248 LQENPVTLENLSSEFEVS----RERVRQ----IEARAFKKVQ 281
            +    + E ++   + S    + R+ +    I+     K++
Sbjct: 149 -EMEGYSYEEIARMLDCSLGTVKSRISRGRRDIKKEII-KLR 188


>gi|332672046|ref|YP_004455054.1| ECF subfamily RNA polymerase sigma-24 subunit [Cellulomonas fimi
           ATCC 484]
 gi|332341084|gb|AEE47667.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Cellulomonas fimi
           ATCC 484]
          Length = 194

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 12/57 (21%), Positives = 24/57 (42%), Gaps = 2/57 (3%)

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
            + + + +  L PR+R +   R  +  P     +++    S   VR   ARA   ++
Sbjct: 132 EDAMWQRLGRLPPRQRAVLVLRYYEGLPD--AEIAAVLGTSPATVRAHAARALATLR 186


>gi|288925357|ref|ZP_06419291.1| sigma-70, region 4 family [Prevotella buccae D17]
 gi|315606759|ref|ZP_07881769.1| RNA polymerase ECF family sigma factor [Prevotella buccae ATCC
           33574]
 gi|288337828|gb|EFC76180.1| sigma-70, region 4 family [Prevotella buccae D17]
 gi|315251614|gb|EFU31593.1| RNA polymerase ECF family sigma factor [Prevotella buccae ATCC
           33574]
          Length = 170

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 16/90 (17%), Positives = 39/90 (43%), Gaps = 4/90 (4%)

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
           +A + SL+ +    ++N S   D    +         E+  +K+R  ++ R +  L  ++
Sbjct: 62  IARNLSLDRIRKQDNQNDS--LDDANTERADHSSNPYEQMLQKDRMAIVKRLVDELPEKQ 119

Query: 240 RRIFEARRLQENPVTLENLSSEFEVSRERV 269
           R   + R  +  P   + ++    ++ E+V
Sbjct: 120 RSCMQLRDFEGKPY--KEIADVLGITEEQV 147


>gi|239980289|ref|ZP_04702813.1| ECF subfamily RNA polymerase sigma factor [Streptomyces albus
           J1074]
 gi|291452153|ref|ZP_06591543.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces albus
           J1074]
 gi|291355102|gb|EFE82004.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces albus
           J1074]
          Length = 179

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 17/94 (18%), Positives = 42/94 (44%), Gaps = 2/94 (2%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            +  E  + +  E+   R +L   + VL P++R +   R      ++ E  ++   +S  
Sbjct: 85  EELPEPAITDGTEQHADRALLMDVLKVLAPKQRSVVVLR--HWEQMSTEETAAALGMSAG 142

Query: 268 RVRQIEARAFKKVQESIQKQVELSSSPPLLQKPR 301
            V+    RA  ++++ ++ +   S +P   ++ R
Sbjct: 143 TVKSTLHRALARLRQELESRELESRAPEREEQER 176


>gi|237717080|ref|ZP_04547561.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D1]
 gi|229443063|gb|EEO48854.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D1]
          Length = 187

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 19/83 (22%), Positives = 37/83 (44%), Gaps = 2/83 (2%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           +Y    +  V  E  E+  R   ++++M  L P  R I E   +Q      + ++ E  +
Sbjct: 106 IYSELTKSYVETEYLEQDERMMHISKAMEKLTPHTRHILEECYIQRKKY--QEVAEELNI 163

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           S   VR+   +A + ++E   K+
Sbjct: 164 SVSAVRKHIVKALQVIREECAKK 186


>gi|167763362|ref|ZP_02435489.1| hypothetical protein BACSTE_01736 [Bacteroides stercoris ATCC
           43183]
 gi|167698656|gb|EDS15235.1| hypothetical protein BACSTE_01736 [Bacteroides stercoris ATCC
           43183]
          Length = 200

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 14/74 (18%), Positives = 34/74 (45%), Gaps = 10/74 (13%)

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS----RERVRQI 272
           ++    + R  ++ ++  L PR+R IFE  R  E  ++   ++    +S    +E +   
Sbjct: 116 DEIIANDLRQFISCALQQLTPRQREIFEMSR--EQQMSHREIAEVLGISVNTVQESIS-- 171

Query: 273 EARAFKKVQESIQK 286
              + K ++  ++K
Sbjct: 172 --ISLKTLRAYLEK 183


>gi|313158690|gb|EFR58079.1| RNA polymerase sigma-70 factor [Alistipes sp. HGB5]
          Length = 199

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 14/77 (18%), Positives = 38/77 (49%), Gaps = 2/77 (2%)

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
               ++   M+ +    R++F ARR+  +  +   +++E  ++  RV     +A  K++E
Sbjct: 122 EIEKLVRDCMAEMPELTRQVFTARRI--HGKSYREIAAECGITERRVETELEKALGKLRE 179

Query: 283 SIQKQVELSSSPPLLQK 299
            ++  + L  +  +L++
Sbjct: 180 VLRDYLPLVLAAGVLER 196


>gi|302864714|ref|YP_003833351.1| RNA polymerase sigma-70 factor [Micromonospora aurantiaca ATCC
           27029]
 gi|302567573|gb|ADL43775.1| RNA polymerase sigma-70 factor, sigma-E family [Micromonospora
           aurantiaca ATCC 27029]
          Length = 171

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 20/88 (22%), Positives = 33/88 (37%), Gaps = 2/88 (2%)

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D+    W+     D       L   E     R ML   +  L PR R +   R   +  +
Sbjct: 71  DERRRPWRRERSTDEVPDRADLAAGEPSVGEREMLLELLGRLAPRRRAVVVLRFYCD--L 128

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++E  +    VS   V+   ARA + ++
Sbjct: 129 SVEETAQILGVSTGTVKSQAARALETLR 156


>gi|218673469|ref|ZP_03523138.1| putative RNA polymerase sigma factor [Rhizobium etli GR56]
          Length = 174

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 18/87 (20%), Positives = 33/87 (37%), Gaps = 3/87 (3%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L +R  + GD  A  +LV+ H   V   A  + G      ++  E  + L  A++ F  
Sbjct: 4   ELIER-AQGGDREAFGQLVSRHYDFVHATAWRWSGSSTDADDIAQEVCVKLGAAIRGFRG 62

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWS 122
               R  T+       A +++  +   
Sbjct: 63  A--SRFRTWLYTLTLNAARDHRRKLAR 87


>gi|291295648|ref|YP_003507046.1| two component LuxR family transcriptional regulator [Meiothermus
           ruber DSM 1279]
 gi|290470607|gb|ADD28026.1| two component transcriptional regulator, LuxR family [Meiothermus
           ruber DSM 1279]
          Length = 200

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 13/46 (28%), Positives = 20/46 (43%), Gaps = 3/46 (6%)

Query: 235 LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           L  RERR+     L     T   +++E  +S   VR   + A  K+
Sbjct: 140 LTDRERRVLR---LAGEGRTSAEIAAELGLSEGTVRNYLSEAISKL 182


>gi|332798632|ref|YP_004460131.1| DeoR family transcriptional regulator [Tepidanaerobacter sp. Re1]
 gi|332696367|gb|AEE90824.1| transcriptional regulator, DeoR family [Tepidanaerobacter sp. Re1]
          Length = 314

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 10/42 (23%), Positives = 22/42 (52%), Gaps = 2/42 (4%)

Query: 237 PRERRIFE--ARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
             E+RI    A    +  +T + ++++F +SR  V ++  +A
Sbjct: 4   DNEKRILTKIAHMYYDENMTQQEIANKFGISRPSVSRLLQKA 45


>gi|311693666|gb|ADP96539.1| RNA polymerase sigma-70 RpoE type [marine bacterium HP15]
          Length = 247

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 25/140 (17%), Positives = 53/140 (37%), Gaps = 6/140 (4%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L ++ R +GD +A   LV  +   V  I   Y      + ++  E  +   +A+++F  +
Sbjct: 63  LVRKVR-NGDRAAFDLLVVKYQSRVASIISRYVYDSQEVMDLTQETFVKAFRAIERFRGD 121

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
                 T+         + Y+       +    + +   F +  RL+    A  +  L+ 
Sbjct: 122 --SAFYTWLYRIAVNTAKNYLESRGRRPQGSADSAEAENFDDGSRLRDT--ASPERLLQR 177

Query: 157 EQVV-AIAKKLNVSESEVIS 175
           EQ+   + K +     E+ S
Sbjct: 178 EQLQKELNKAIAQLPEELRS 197


>gi|254393630|ref|ZP_05008759.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
 gi|197707246|gb|EDY53058.1| RNA polymerase sigma factor [Streptomyces clavuligerus ATCC 27064]
          Length = 189

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 11/62 (17%), Positives = 23/62 (37%), Gaps = 2/62 (3%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L+           E    +  R+ L ++M  L  R+R +   R   +  +T   ++    
Sbjct: 107 LLSKPMPDMASAEEGAYDQLERDDLIKAMRGLQRRQREVLVLRYFAD--MTEAQVAETLG 164

Query: 264 VS 265
           +S
Sbjct: 165 IS 166


>gi|301122105|ref|XP_002908779.1| kinesin-like protein [Phytophthora infestans T30-4]
 gi|262099541|gb|EEY57593.1| kinesin-like protein [Phytophthora infestans T30-4]
          Length = 1500

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 30/171 (17%), Positives = 61/171 (35%), Gaps = 19/171 (11%)

Query: 116  YILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVIS 175
             + +      +       ++ F +           +  L  +QV       ++ +    +
Sbjct: 971  ALAKIEKTQSLPEARTLLKMLFGMAVDVKKQDQRKEQELAKQQVEMTELVRHLEQEREKT 1030

Query: 176  MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
            M  + + +ESL  ++N      +   D    D    E+  I     + R ++L +    L
Sbjct: 1031 MQIKQSYEESLQRVVNGG----ASPDDPEPADETMDERSRILLSVSEERNSVLRKRCEEL 1086

Query: 236  ------NPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
                     E+++F  R  QE+         +   SRERVR +E +  KK+
Sbjct: 1087 EMMSRATDEEKQLFRDRLEQEH--------QDLVASRERVRYLETK-LKKL 1128


>gi|229818786|ref|YP_002880312.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Beutenbergia
           cavernae DSM 12333]
 gi|229564699|gb|ACQ78550.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Beutenbergia
           cavernae DSM 12333]
          Length = 292

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 20/107 (18%), Positives = 38/107 (35%), Gaps = 2/107 (1%)

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
                S   R+   ++LN +   + +      +WL         V  + E  ++    + 
Sbjct: 46  VRNPRSYLVRVVTRQALNRMRTLARRREDYVGEWLPEPLLTSPDVADDVELAESVSIAML 105

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
             +  L P ER +F  R + + P   + +      +    RQI  RA
Sbjct: 106 TVLETLGPTERAVFVLREVFDVPY--DEIGEAVGRTPATTRQIARRA 150


>gi|126347694|emb|CAJ89409.1| putative ECF-family RNA polymerase sigma factor [Streptomyces
           ambofaciens ATCC 23877]
          Length = 298

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 20/102 (19%), Positives = 43/102 (42%), Gaps = 2/102 (1%)

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
            +    WL    D  +   +  E  +     +   +  LNP ER  +  R   + P   +
Sbjct: 84  ETYVGPWLPEPVDTAQDPQLGAERAEAVEMAVLLLLEKLNPVERTAYVLREAFDYPY--D 141

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQ 298
            ++     SR   RQ+ +RA + + +  +++V+ ++   LL+
Sbjct: 142 RIAEILGTSRANARQLVSRARRHLADERRERVDPATHRRLLE 183


>gi|85716143|ref|ZP_01047118.1| FecI-like protein [Nitrobacter sp. Nb-311A]
 gi|85696976|gb|EAQ34859.1| FecI-like protein [Nitrobacter sp. Nb-311A]
          Length = 182

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 16/73 (21%), Positives = 34/73 (46%), Gaps = 6/73 (8%)

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           S++    ++      E  + ++++    R     +++ L  R R  FE  RL E  +T+ 
Sbjct: 98  SAEDFAAIIDPTPSAEVAVYDRQKLALTRA----ALAELPERTRIAFEMHRLDE--MTIA 151

Query: 257 NLSSEFEVSRERV 269
            +++E  +S  RV
Sbjct: 152 EVAAELGLSTSRV 164


>gi|330509109|ref|YP_004385537.1| hypothetical protein MCON_3496 [Methanosaeta concilii GP-6]
 gi|328929917|gb|AEB69719.1| conserved hypothetical extracellular protein [Methanosaeta concilii
           GP-6]
          Length = 371

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 21/77 (27%), Positives = 34/77 (44%), Gaps = 3/77 (3%)

Query: 182 GDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
            D++L+AL   SD+  +  +D    +    E+    K+E      M+   M  L PRER 
Sbjct: 249 DDQALDALSTESDQPEASEEDVEPEEMPSLEEGP--KKEIAVSSEMMA-VMDALTPRERS 305

Query: 242 IFEARRLQENPVTLENL 258
           I EA   +   +T   +
Sbjct: 306 IVEALIKRGGRMTQAEI 322


>gi|296447719|ref|ZP_06889635.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Methylosinus
           trichosporium OB3b]
 gi|296254751|gb|EFH01862.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Methylosinus
           trichosporium OB3b]
          Length = 168

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 18/111 (16%), Positives = 36/111 (32%), Gaps = 2/111 (1%)

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
           +V+A+  +             R+A + S++             +                
Sbjct: 39  RVLALGMRSEAVVDNPRGYLLRVARNLSIDLGRREGHSPFVGGEIERFEATPDPAPSQET 98

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           +   + +   +  ++  L  R RR FE  RL E   T+  +  E  +S  R
Sbjct: 99  RLSDRQKLAAVAAALDELPERTRRAFEMHRLGE--RTIAEIGVELGLSTSR 147


>gi|294509106|ref|YP_003566034.1| putative RNA polymerase sigma-70, region 4 [Bacillus megaterium QM
           B1551]
 gi|294352030|gb|ADE72354.1| putative RNA polymerase sigma-70, region 4 [Bacillus megaterium QM
           B1551]
          Length = 178

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 14/96 (14%), Positives = 38/96 (39%), Gaps = 2/96 (2%)

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L+  +  SD  +          +   E+V  +K E       L  S+  L+ ++++I   
Sbjct: 80  LDKPVPESDNGTLIDLLIDSSTNYCTEEVPSKKLEDYIENPSLYLSIKKLSSKQKKILYL 139

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
             +++       ++    VS++ + +   +   K++
Sbjct: 140 AYIKDLKDV--EIARYLNVSQQYITRTRNKTLLKLR 173


>gi|294647809|ref|ZP_06725361.1| RNA polymerase sigma-70 factor [Bacteroides ovatus SD CC 2a]
 gi|294806203|ref|ZP_06765050.1| RNA polymerase sigma-70 factor [Bacteroides xylanisolvens SD CC 1b]
 gi|298482598|ref|ZP_07000783.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D22]
 gi|292636717|gb|EFF55183.1| RNA polymerase sigma-70 factor [Bacteroides ovatus SD CC 2a]
 gi|294446459|gb|EFG15079.1| RNA polymerase sigma-70 factor [Bacteroides xylanisolvens SD CC 1b]
 gi|298271305|gb|EFI12881.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D22]
          Length = 200

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 19/83 (22%), Positives = 37/83 (44%), Gaps = 2/83 (2%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           +Y    +  V  E  E+  R   ++++M  L P  R I E   +Q      + ++ E  +
Sbjct: 119 IYSELTKSYVETEYLEQDERMMHISKAMEKLTPHTRHILEECYIQRKKY--QEVAEELNI 176

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           S   VR+   +A + ++E   K+
Sbjct: 177 SVSAVRKHIVKALQVIREECAKK 199


>gi|157128830|ref|XP_001655214.1| sarcolemmal associated protein-2, putative [Aedes aegypti]
 gi|108882169|gb|EAT46394.1| sarcolemmal associated protein-2, putative [Aedes aegypti]
          Length = 573

 Score = 38.3 bits (88), Expect = 1.5,   Method: Composition-based stats.
 Identities = 29/168 (17%), Positives = 72/168 (42%), Gaps = 9/168 (5%)

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV-AIAKKLNVSESEVIS 175
           + R    +K       K+L      LK   + ++    + E +  AIA+      SE +S
Sbjct: 314 LRRQLEDIKSINLDMYKKLQECEASLKHKTELMSRMETQRESMALAIAQLEKKYNSETVS 373

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
           +N      ++L+  + S ++ +++ +  L  + + +  +   + + K + + L   +  L
Sbjct: 374 LNALQETSQALSLQVVSCEQRATRAEADLRIEREWRTAMQENEVKHKEQISSLQLELRQL 433

Query: 236 NP------RER-RIFEARRL-QENPVTLENLSSEFEVSRERVRQIEAR 275
                   R +  + + R+  +E+  TLE L  +  VS+ ++  ++ +
Sbjct: 434 TDELKQHDRTKAELVQLRKQWEEDQRTLEELGVQLSVSKLQISDLKEK 481


>gi|301166234|emb|CBW25809.1| putative ECF-tyype sigma factor [Bacteriovorax marinus SJ]
          Length = 176

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 15/75 (20%), Positives = 36/75 (48%), Gaps = 2/75 (2%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E + +  E+      +  +    L+ +E+ +   + + +   +   +S    +S+   R+
Sbjct: 101 EYIEMASEDTSVDGELELKDYKNLSEKEKELLSLKFISDLDYS--EISEALNISQSNARK 158

Query: 272 IEARAFKKVQESIQK 286
           I +RA KKV+E++ K
Sbjct: 159 IFSRALKKVKEALIK 173


>gi|296168664|ref|ZP_06850413.1| sigma-70 family RNA polymerase sigma factor [Mycobacterium
           parascrofulaceum ATCC BAA-614]
 gi|295896573|gb|EFG76214.1| sigma-70 family RNA polymerase sigma factor [Mycobacterium
           parascrofulaceum ATCC BAA-614]
          Length = 183

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 2/57 (3%)

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
           D  EQ    +E        + R +  L  R R I E R LQ    ++++ ++E  VS
Sbjct: 105 DDVEQPPDSEEAISTAPQRVARVLDSLPDRYRHILELRFLQG--HSIKDSAAELGVS 159


>gi|167461139|ref|ZP_02326228.1| DNA-directed RNA polymerase sigma subunit SigK carboxy-terminus
          [Paenibacillus larvae subsp. larvae BRL-230010]
          Length = 69

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 13/50 (26%), Positives = 23/50 (46%), Gaps = 1/50 (2%)

Query: 16 LSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIA 65
          L  Y+        L ++EE    ++  E G+  + + L+  +LRLV  I 
Sbjct: 18 LVSYVKNNAFPQPLTEEEEERHLRQMAE-GNSMSRNLLIEHNLRLVAHIV 66


>gi|153813483|ref|ZP_01966151.1| hypothetical protein RUMOBE_03903 [Ruminococcus obeum ATCC 29174]
 gi|149830427|gb|EDM85519.1| hypothetical protein RUMOBE_03903 [Ruminococcus obeum ATCC 29174]
          Length = 88

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 13/79 (16%), Positives = 43/79 (54%), Gaps = 2/79 (2%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
              +++ L+EK   +  R +L +++  L  ++R + + +      ++ + +++   ++ E
Sbjct: 9   EKNRDEDLLEKILEEENRRILYQAIRRLEVKKREVIQMQYFGG--MSQKEIAAVLHITPE 66

Query: 268 RVRQIEARAFKKVQESIQK 286
            VR +  RA K++++ +++
Sbjct: 67  NVRVLAYRAKKELKKDLEE 85


>gi|83593732|ref|YP_427484.1| sigma-24 (FecI) [Rhodospirillum rubrum ATCC 11170]
 gi|83576646|gb|ABC23197.1| Sigma-24 (FecI) [Rhodospirillum rubrum ATCC 11170]
          Length = 179

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 10/68 (14%), Positives = 25/68 (36%), Gaps = 2/68 (2%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
                ++   ++    + ++++ L PR R  F+  R +    T   +     +S+ R   
Sbjct: 103 APSPEQEAIGRDDLRAVAQALASLPPRTRTAFDLHRFEN--CTFAEIGQRLGISQTRAHS 160

Query: 272 IEARAFKK 279
           +   A   
Sbjct: 161 LVHEALAH 168


>gi|332992346|gb|AEF02401.1| RNA polymerase sigma factor RpoE [Alteromonas sp. SN2]
          Length = 192

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 15/80 (18%), Positives = 32/80 (40%), Gaps = 2/80 (2%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD +A + LVT +   V+ +   Y      +++V  E  I   +A+  F  +      
Sbjct: 15  QRGDKNAFNLLVTRYQHKVMHLVSRYVKNSGDVADVTQEAFIKAYRALPNFRGD--SAFY 72

Query: 103 TYSMWWIKAAMQEYILRSWS 122
           T+       + + Y++    
Sbjct: 73  TWLYRIAVNSAKNYLVAQGR 92


>gi|312888274|ref|ZP_07747850.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Mucilaginibacter
           paludis DSM 18603]
 gi|311299108|gb|EFQ76201.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Mucilaginibacter
           paludis DSM 18603]
          Length = 201

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 17/80 (21%), Positives = 39/80 (48%), Gaps = 9/80 (11%)

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           S+N+++   D +  Q Q  +  D    E+V +++E+ +    +L   +  L PR R +  
Sbjct: 103 SINSMV-DEDGDDRQLQ--IKSDALNPEEVSMKREQTQ----LLKLLIDGLPPRYRNLIV 155

Query: 245 ARRLQENPVTLENLSSEFEV 264
            R   E  ++ E ++ + ++
Sbjct: 156 LRYFDE--LSYEEIAEQLDL 173


>gi|300772507|ref|ZP_07082377.1| RNA polymerase ECF-type sigma factor [Sphingobacterium spiritivorum
           ATCC 33861]
 gi|300760810|gb|EFK57636.1| RNA polymerase ECF-type sigma factor [Sphingobacterium spiritivorum
           ATCC 33861]
          Length = 198

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 13/70 (18%), Positives = 29/70 (41%), Gaps = 2/70 (2%)

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
             Q  D +    D     + E    K R   L + ++ L  ++R +F+  +L  +  + E
Sbjct: 95  DKQLYDKVSSFIDSSSDEIYETLFVKQRSEQLHQILAQLPSQQRLVFQMAKL--DGYSYE 152

Query: 257 NLSSEFEVSR 266
            ++    +S+
Sbjct: 153 EIARALGISQ 162


>gi|325279740|ref|YP_004252282.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Odoribacter
           splanchnicus DSM 20712]
 gi|324311549|gb|ADY32102.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Odoribacter
           splanchnicus DSM 20712]
          Length = 174

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 17/89 (19%), Positives = 44/89 (49%), Gaps = 3/89 (3%)

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
           ++    + +EQ  + +   +    +L+ ++S L P+ R I +   L+ N  T   ++   
Sbjct: 82  YISQREEEEEQNCLHEITYQETLRLLSFAISQLPPQTREIIQL-GLEGNNNT--EIADLL 138

Query: 263 EVSRERVRQIEARAFKKVQESIQKQVELS 291
            +S   V+ ++  A+++++E + K+  L 
Sbjct: 139 HISVNTVKSMKKSAYRRLREILGKEYTLL 167


>gi|119509925|ref|ZP_01629067.1| hypothetical protein N9414_05579 [Nodularia spumigena CCY9414]
 gi|119465391|gb|EAW46286.1| hypothetical protein N9414_05579 [Nodularia spumigena CCY9414]
          Length = 184

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 15/81 (18%), Positives = 38/81 (46%), Gaps = 2/81 (2%)

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           +     L++K   K   N +  ++S L  ++R++ E        ++   +S + ++    
Sbjct: 106 EDNRNSLMDKASIKETSNRIREALSELPDQQRQVLEMAYY--EGLSQSEISEDLKMPLGT 163

Query: 269 VRQIEARAFKKVQESIQKQVE 289
           V+  + +A  K+++ +Q  VE
Sbjct: 164 VKTYKRKALLKLRQILQDLVE 184


>gi|323476822|gb|ADX82060.1| Bacterio-opsin activator HTH domain protein [Sulfolobus islandicus
           HVE10/4]
          Length = 204

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 12/52 (23%), Positives = 22/52 (42%), Gaps = 5/52 (9%)

Query: 233 SVLNPRERRIFEA-----RRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           + L  R+  I +          +  VTL  L+ +  +S   + +I  RA +K
Sbjct: 143 NDLTDRQMEILKLAYKMGYFDDDRRVTLTELAKQLGISTPTLEEIMRRALRK 194


>gi|284033596|ref|YP_003383527.1| LuxR family transcriptional regulator [Kribbella flavida DSM 17836]
 gi|283812889|gb|ADB34728.1| transcriptional regulator, LuxR family [Kribbella flavida DSM
           17836]
          Length = 176

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 14/57 (24%), Positives = 27/57 (47%), Gaps = 6/57 (10%)

Query: 227 MLTRSMSVLNPRERRIFEARRLQE--NPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           +++ ++ VL  RER +   R L++     T E L          V+ +  RA +K++
Sbjct: 110 VISTALDVLTRRERSVIVLRYLEDLTEKQTAEELGLAVG----TVKSVTFRALRKLR 162


>gi|157876644|ref|XP_001686667.1| dynein heavy chain [Leishmania major strain Friedlin]
 gi|68129742|emb|CAJ09048.1| putative dynein heavy chain [Leishmania major strain Friedlin]
          Length = 4172

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 26/158 (16%), Positives = 60/158 (37%), Gaps = 15/158 (9%)

Query: 131 NQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALI 190
            +  +      L   L  +T+    PE+VVA    +      V+ +   +   + ++ L+
Sbjct: 732 KEIEVNDRYSELYATLLKLTE---TPEEVVAAKDFIKTIPERVVDLETAIEESKEIHELL 788

Query: 191 NS-----SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN-------PR 238
            S     S++  ++    + +       V    EE +  +  L  SM+           R
Sbjct: 789 KSFKRPLSEEEFNKKWKAIGWPSQLDNAVTERVEELEETKRRLLASMNRAQDLFEQEVER 848

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
            ++I E      N   +  ++ +    +E++RQ+ ++A
Sbjct: 849 VQKIVEHYGQHRNAHRMTEIAEDVVRVQEKIRQLRSQA 886


>gi|326774630|ref|ZP_08233895.1| putative RNA polymerase, sigma 70 family subunit [Streptomyces cf.
           griseus XylebKG-1]
 gi|326654963|gb|EGE39809.1| putative RNA polymerase, sigma 70 family subunit [Streptomyces cf.
           griseus XylebKG-1]
          Length = 534

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 8/82 (9%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV-KKFDPERGFR 100
            + GD  A  +LV+++L L+  +          + +VV E  + +++ + +  DPER   
Sbjct: 13  AQGGDQQAKDQLVSAYLPLLYNVVGRALDGHADVDDVVQETVLRMLRGLPELRDPER--- 69

Query: 101 LATYSMWWIKAAMQEYILRSWS 122
              +  W +  AM E I   W 
Sbjct: 70  ---FRSWLVAIAMNE-IRTHWR 87


>gi|282882534|ref|ZP_06291155.1| DNA-directed RNA polymerase specialized sigma subunit
           [Peptoniphilus lacrimalis 315-B]
 gi|281297676|gb|EFA90151.1| DNA-directed RNA polymerase specialized sigma subunit
           [Peptoniphilus lacrimalis 315-B]
          Length = 206

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 16/76 (21%), Positives = 35/76 (46%), Gaps = 4/76 (5%)

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
              D    + +D L    D     + ++ ERK     LT+++  L PR+R+I     L+ 
Sbjct: 113 PDMDSKDKEGEDILEKIEDNI--NIEKEFERKLENIALTKAIKELPPRQRQIIVLYYLEN 170

Query: 251 NPVTLENLSSEFEVSR 266
             ++++ +  +  +S+
Sbjct: 171 --ISIKEIGQKMAISK 184


>gi|182434106|ref|YP_001821825.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces griseus
           subsp. griseus NBRC 13350]
 gi|178462622|dbj|BAG17142.1| putative RNA polymerase ECF-subfamily sigma factor [Streptomyces
           griseus subsp. griseus NBRC 13350]
          Length = 534

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 8/82 (9%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV-KKFDPERGFR 100
            + GD  A  +LV+++L L+  +          + +VV E  + +++ + +  DPER   
Sbjct: 13  AQGGDQQAKDQLVSAYLPLLYNVVGRALDGHADVDDVVQETVLRMLRGLPELRDPER--- 69

Query: 101 LATYSMWWIKAAMQEYILRSWS 122
              +  W +  AM E I   W 
Sbjct: 70  ---FRSWLVAIAMNE-IRTHWR 87


>gi|294102718|ref|YP_003554576.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Aminobacterium
           colombiense DSM 12261]
 gi|293617698|gb|ADE57852.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Aminobacterium
           colombiense DSM 12261]
          Length = 169

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 15/74 (20%), Positives = 32/74 (43%), Gaps = 2/74 (2%)

Query: 46  DLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
           D     +++  +   + KIA  Y G G  + ++  E ++GL+   +K  P     L+ Y 
Sbjct: 8   DKDPEEKILRDYFDYIKKIAWRYAGRGAEVEDLEQEASMGLITLARKCPP--NEELSNYI 65

Query: 106 MWWIKAAMQEYILR 119
              +   +++   R
Sbjct: 66  RKRLPGQVRDAAHR 79


>gi|227832306|ref|YP_002834013.1| ECF-family sigma factor D [Corynebacterium aurimucosum ATCC 700975]
 gi|227453322|gb|ACP32075.1| ECF-family sigma factor D [Corynebacterium aurimucosum ATCC 700975]
          Length = 203

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 26/164 (15%), Positives = 63/164 (38%), Gaps = 6/164 (3%)

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +I    + + L +   R+ GH +  T  ++  E  +A+A  +   + +       + G  
Sbjct: 40  RIMRIIHPQVLRYCRARIGGH-RQPTAEDVAQEICLAVATSIGTYKDKGRPFMAYVYGIA 98

Query: 185 S--LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
           +  +     +  ++ +   + L  D   Q+    E     +  N +   +  L+ + R I
Sbjct: 99  AHKVTDAHRALSRDHTHPTEDLPEDA-AQDATPEESALEVDGSNRVRAMLDTLSDKARDI 157

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
              R      ++ E  +   E +   VR  + RA  ++++S+  
Sbjct: 158 IILRVFVG--LSAEETAEIVESTPGAVRVAQHRALAQLRKSLDS 199


>gi|225570282|ref|ZP_03779307.1| hypothetical protein CLOHYLEM_06378 [Clostridium hylemonae DSM
           15053]
 gi|225160814|gb|EEG73433.1| hypothetical protein CLOHYLEM_06378 [Clostridium hylemonae DSM
           15053]
          Length = 207

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 19/83 (22%), Positives = 33/83 (39%), Gaps = 6/83 (7%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L     G+     ++  RKN    L   +  L P E ++   +   E    LE ++S  +
Sbjct: 119 LADVQAGESLNPEQEFARKNANEELMEKILSLPPHESQVIIMKYYNEMK--LEEIASAMD 176

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +SR  V     R     + S++K
Sbjct: 177 ISRSTV----KRYLAHGRASLEK 195


>gi|170054419|ref|XP_001863120.1| dystrophin major muscle [Culex quinquefasciatus]
 gi|167874726|gb|EDS38109.1| dystrophin major muscle [Culex quinquefasciatus]
          Length = 3479

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 28/163 (17%), Positives = 56/163 (34%), Gaps = 15/163 (9%)

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
           + R   + K   T   +++      L+   + I+         V +  +L   +     M
Sbjct: 415 LERQAQIHKRLATLQMQKIDELSNFLRMTEERISHMQNIGPTPVELKVQLEEHKRLQHDM 474

Query: 177 NCRLAGDESLNALINSSDKNS-SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
             +    ESL+ L+   D  S S  +D L    +    +L     R ++   L++  + L
Sbjct: 475 EKQEILVESLSNLVIIIDSESFSDLEDKLSALEERWSHLLKWIGNRWDKLQSLSQRWTKL 534

Query: 236 NPRERRIFEARRLQENPVTLE--------NLSSEFEVSRERVR 270
           + R R I   R +      L+         + +      ER+ 
Sbjct: 535 SERYRVI--CRWIDCREQNLKKMESYESAEMGAMM----ERIS 571


>gi|167646610|ref|YP_001684273.1| ECF subfamily RNA polymerase sigma-24 factor [Caulobacter sp. K31]
 gi|167349040|gb|ABZ71775.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Caulobacter sp.
           K31]
          Length = 190

 Score = 38.3 bits (88), Expect = 1.6,   Method: Composition-based stats.
 Identities = 17/86 (19%), Positives = 38/86 (44%), Gaps = 2/86 (2%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           H   E       + + +      +++ L  R RR+F   R +E  ++ + ++    VS  
Sbjct: 98  HPVDEMSPERVLQAREQMARALAALNELPERTRRVFVLVRFEE--MSYKLVAQRLGVSVS 155

Query: 268 RVRQIEARAFKKVQESIQKQVELSSS 293
            V +   +A + + E ++ Q EL ++
Sbjct: 156 AVEKHVMKALRHLGERLRDQDELDAA 181


>gi|320162351|ref|YP_004175576.1| RNA polymerase ECF-type sigma factor [Anaerolinea thermophila
           UNI-1]
 gi|319996205|dbj|BAJ64976.1| RNA polymerase ECF-type sigma factor [Anaerolinea thermophila
           UNI-1]
          Length = 203

 Score = 38.3 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 19/90 (21%), Positives = 35/90 (38%), Gaps = 4/90 (4%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E  L +  R +GDL+A +RLV ++  +   +AM          +V     +    A + 
Sbjct: 2   DELALIQEAR-NGDLNAFNRLVLAYQDMAYHLAMRMLSDPDQAEDVTQTAFL---SAYRH 57

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWS 122
               RG     + M  +  A  + + R   
Sbjct: 58  LSSFRGGSFKAWVMRMVTNACYDELRRRQR 87


>gi|260892018|ref|YP_003238115.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ammonifex degensii
           KC4]
 gi|260864159|gb|ACX51265.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ammonifex degensii
           KC4]
          Length = 215

 Score = 38.3 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 13/80 (16%), Positives = 33/80 (41%), Gaps = 8/80 (10%)

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL+  ++  D    +         DG      E+ E++    ++ R+++ L+   R +  
Sbjct: 93  SLDDPVSVPDGELPRQVA------DGNHLHPEEEAEKREFIRLVRRALNSLSREHRAVLV 146

Query: 245 ARRLQENPVTLENLSSEFEV 264
            R  +   ++ E +++   V
Sbjct: 147 LR--EMEEMSYEEIAAVLGV 164


>gi|218245218|ref|YP_002370589.1| RNA polymerase sigma factor RpoE [Cyanothece sp. PCC 8801]
 gi|257058250|ref|YP_003136138.1| RNA polymerase sigma factor RpoE [Cyanothece sp. PCC 8802]
 gi|218165696|gb|ACK64433.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Cyanothece sp. PCC
           8801]
 gi|256588416|gb|ACU99302.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Cyanothece sp. PCC
           8802]
          Length = 217

 Score = 38.3 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 20/115 (17%), Positives = 42/115 (36%), Gaps = 17/115 (14%)

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           R++   SL+A     D         + +D         +    +   + L  +++ L   
Sbjct: 116 RVSHPVSLDAPRRVDDGE-------IEWDIVSDYPSPDDNLATREFYDRLQVAIADLPEA 168

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVS----RERVRQIEARAFKKVQESIQKQVE 289
            R     R +    +  E ++    VS    + R+    ARA  K+Q  +Q+ ++
Sbjct: 169 FRMTIVLREI--EGMAYEEIAQLTGVSLGTVKSRI----ARARAKLQSVLQQYLD 217


>gi|169834773|ref|YP_001715916.1| putative sigma K [Clostridium botulinum A3 str. Loch Maree]
 gi|169408880|gb|ACA57290.1| putative sigma K [Clostridium botulinum A3 str. Loch Maree]
          Length = 171

 Score = 38.3 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 18/89 (20%), Positives = 40/89 (44%), Gaps = 3/89 (3%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGY--RGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
             D      ++ +   L+  I+  Y  +   + + E+   G I ++++ + F+ ++G  L
Sbjct: 2   DNDKPDIDTILNNFQELINIISKKYTAKYSFVELDELQQIGRIAILKSYENFNKDKGS-L 60

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTA 130
             Y    IK  M++Y L+++   KI    
Sbjct: 61  EGYIYVCIKNDMKKYFLKAYRRAKIERPV 89


>gi|149174443|ref|ZP_01853069.1| RNA polymerase sigma factor sigW [Planctomyces maris DSM 8797]
 gi|148846553|gb|EDL60890.1| RNA polymerase sigma factor sigW [Planctomyces maris DSM 8797]
          Length = 299

 Score = 38.3 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 18/78 (23%), Positives = 35/78 (44%), Gaps = 6/78 (7%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           + Q++  L  +  ++GD SA  +LV  H   +  IA+    +     EV  E    L++A
Sbjct: 16  DDQQDVELVDQ-AQNGDRSALEKLVLRHQAWIYNIAIRMVFHPHDAEEVTQEV---LLKA 71

Query: 90  VKKFDPERGFRLATYSMW 107
           + +    +G   + +  W
Sbjct: 72  ITRLSTFQGT--SQFRTW 87


>gi|118586219|ref|ZP_01543684.1| DNA-dependent RNA polymerase, sigma subunit [Oenococcus oeni ATCC
           BAA-1163]
 gi|118433348|gb|EAV40049.1| DNA-dependent RNA polymerase, sigma subunit [Oenococcus oeni ATCC
           BAA-1163]
          Length = 200

 Score = 38.3 bits (88), Expect = 1.7,   Method: Composition-based stats.
 Identities = 17/69 (24%), Positives = 26/69 (37%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           A +  + GD +    L+      + KI   Y    L   E  SE    LM++V K+    
Sbjct: 13  ALKMIKKGDQTGYLFLMEETEGFLRKIHNRYLKSVLDFDEWKSEALDVLMRSVDKYQNNF 72

Query: 98  GFRLATYSM 106
             +  TY  
Sbjct: 73  DSKFTTYYF 81


>gi|327405367|ref|YP_004346205.1| ECF subfamily RNA polymerase sigma-24 subunit [Fluviicola taffensis
           DSM 16823]
 gi|327320875|gb|AEA45367.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Fluviicola
           taffensis DSM 16823]
          Length = 193

 Score = 37.9 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 12/83 (14%), Positives = 32/83 (38%), Gaps = 16/83 (19%)

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
              + +  E +E +  +++L  +M  L   + ++ E R      ++ + +     ++   
Sbjct: 114 PSFDTLFFENQEFEYNQSLLLAAMQRLKEEQLKLIEMRFF--EQLSFKEIGESIGIT--- 168

Query: 269 VRQIEA-------RAFKKVQESI 284
               E        RA +K++E  
Sbjct: 169 ----ENNAKVKTFRALEKLREYF 187


>gi|260102410|ref|ZP_05752647.1| conserved hypothetical protein [Lactobacillus helveticus DSM 20075]
 gi|260083778|gb|EEW67898.1| conserved hypothetical protein [Lactobacillus helveticus DSM 20075]
          Length = 181

 Score = 37.9 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 26/147 (17%), Positives = 50/147 (34%), Gaps = 14/147 (9%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           E  L K+ ++ GD +A   L   +  LV K+  GY        +   E  I   +A   +
Sbjct: 5   EKKLIKQVKK-GDDAALEELFALYQPLVNKVLKGYYLRHYDQKDWQQEAMIICYEAAMVY 63

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              +G               +  +      +    TA ++R + N       L+ I    
Sbjct: 64  SERKGHF---------AGLYKAKLTNHARTLVRYHTALRRRTYNN----SISLERIDLQG 110

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRL 180
           +   +   +A  +N + +  +    RL
Sbjct: 111 INEPKRSELAIPINDTYNNFVKSLSRL 137


>gi|256379221|ref|YP_003102881.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Actinosynnema
           mirum DSM 43827]
 gi|255923524|gb|ACU39035.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Actinosynnema
           mirum DSM 43827]
          Length = 165

 Score = 37.9 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 12/76 (15%), Positives = 34/76 (44%), Gaps = 2/76 (2%)

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           +  E+ +    E    R  L  ++  L PR+R +   R + +  +++E ++     ++  
Sbjct: 83  EPPERPVPPDTESAEHRQNLIPALQELPPRQRAVIVLRFVHD--LSVEQVAQTMGCTQGT 140

Query: 269 VRQIEARAFKKVQESI 284
           V+   +R  + ++ + 
Sbjct: 141 VKSQTSRGLEALRRAF 156


>gi|153868006|ref|ZP_01998147.1| hypothetical protein BGS_0563 [Beggiatoa sp. SS]
 gi|152144673|gb|EDN71852.1| hypothetical protein BGS_0563 [Beggiatoa sp. SS]
          Length = 37

 Score = 37.9 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 13/33 (39%), Positives = 21/33 (63%)

Query: 261 EFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E  ++RERVRQI+  A K ++E I+++     S
Sbjct: 2   EMGLTRERVRQIQMTAIKHLREIIEREGHSLES 34


>gi|256027744|ref|ZP_05441578.1| RNA polymerase sigma factor [Fusobacterium sp. D11]
 gi|289765701|ref|ZP_06525079.1| RNA polymerase sigma factor [Fusobacterium sp. D11]
 gi|289717256|gb|EFD81268.1| RNA polymerase sigma factor [Fusobacterium sp. D11]
          Length = 274

 Score = 37.9 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 18/66 (27%), Positives = 36/66 (54%), Gaps = 2/66 (3%)

Query: 54  VTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAM 113
           V  +L+ V ++A+     G+   ++  EG +GL++A + F+ ++ F+L  Y  ++I   M
Sbjct: 84  VEKNLKKVYEMALYMLREGISYDDLTQEGIVGLIKAHELFEDDKDFKL--YKDYYIAKEM 141

Query: 114 QEYILR 119
             YI  
Sbjct: 142 FNYINN 147


>gi|257057767|ref|YP_003135599.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase
           sigma-70 factor, sigma-E family [Saccharomonospora
           viridis DSM 43017]
 gi|256587639|gb|ACU98772.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase
           sigma-70 factor, sigma-E family [Saccharomonospora
           viridis DSM 43017]
          Length = 207

 Score = 37.9 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 16/89 (17%), Positives = 35/89 (39%), Gaps = 2/89 (2%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
            V  H    +              + +++S L PR+R +   R      ++   +S    
Sbjct: 120 YVPPHAVNARSAESLAMLSTEHQAVVQALSKLPPRQREVLVLRYYGG--LSEAEISEAAG 177

Query: 264 VSRERVRQIEARAFKKVQESIQKQVELSS 292
           +SR  V+   +RA + +Q ++  +   +S
Sbjct: 178 ISRGTVKSTASRALEALQRAMNNERRSAS 206


>gi|223938310|ref|ZP_03630205.1| RNA polymerase, sigma-24 subunit, ECF subfamily [bacterium
           Ellin514]
 gi|223893024|gb|EEF59490.1| RNA polymerase, sigma-24 subunit, ECF subfamily [bacterium
           Ellin514]
          Length = 450

 Score = 37.9 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 32/163 (19%), Positives = 60/163 (36%), Gaps = 27/163 (16%)

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVIS------MNCRLAGDESLNALINSSDKNSS 198
            LQ + D +L  E   A+   L     ++ S        CR     S NAL         
Sbjct: 36  ALQQVHDQHLAEEITQAVFIILARKAGKLSSKTILSGWLCRTVRYVSANAL-------KI 88

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRN---MLTRSMSVLNPRERRIFEARRLQENPVTL 255
           +W+          + +L E E     +    +L+ +++ L+ ++      R  +   +  
Sbjct: 89  EWRRKRREQEAHMQSILNEPESEGAWKQIAPLLSVALAQLSEKDHDAIVLRFFEGKNMN- 147

Query: 256 ENLSSEFEVSRE----RVRQIEARAFKKVQE-SIQKQVELSSS 293
             +     VS+     RV     RA  K++   +++ V LS+S
Sbjct: 148 -EVGVALGVSKNTAKTRVS----RAVDKLRRFFMKRGVVLSAS 185


>gi|160940020|ref|ZP_02087365.1| hypothetical protein CLOBOL_04909 [Clostridium bolteae ATCC
           BAA-613]
 gi|158436600|gb|EDP14367.1| hypothetical protein CLOBOL_04909 [Clostridium bolteae ATCC
           BAA-613]
          Length = 309

 Score = 37.9 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 10/38 (26%), Positives = 17/38 (44%)

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           ER +  AR   E   T   ++  + +SR  V ++   A
Sbjct: 6   ERLVNVARMYYEQDRTQSEIADRYGISRPMVSKLLKEA 43


>gi|152981850|ref|YP_001353720.1| ECF subfamily RNA polymerase sigma factor [Janthinobacterium sp.
           Marseille]
 gi|151281927|gb|ABR90337.1| RNA polymerase sigma-70 factor, ECF subfamily [Janthinobacterium
           sp. Marseille]
          Length = 173

 Score = 37.9 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 16/78 (20%), Positives = 31/78 (39%), Gaps = 2/78 (2%)

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
           +   L    +       ++         + R +  L+ + R  F   +L  + +T   ++
Sbjct: 88  YLAELAALPEDVAPSPEDQALVLETLLAIDRLLDGLSVKARSAFLMSQL--DGMTYSEIA 145

Query: 260 SEFEVSRERVRQIEARAF 277
           +E  VS  RVRQ  A+A 
Sbjct: 146 AELNVSASRVRQYMAQAL 163


>gi|149922820|ref|ZP_01911243.1| RNA polymerase sigma-70 factor, ECF subfamily protein [Plesiocystis
           pacifica SIR-1]
 gi|149816287|gb|EDM75791.1| RNA polymerase sigma-70 factor, ECF subfamily protein [Plesiocystis
           pacifica SIR-1]
          Length = 211

 Score = 37.9 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 15/84 (17%), Positives = 39/84 (46%), Gaps = 6/84 (7%)

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           ++++  ++++  + L       E +++E E + +    +  +++ L   +R +    +L 
Sbjct: 109 VDTAGDDTARLLEGLADVAPNSEGMVVEHERQLSIAARIRGALASLPKGQREVVTKHKL- 167

Query: 250 ENPVTLENLSSEFEVSRE---RVR 270
               T+  ++ E  V RE   RVR
Sbjct: 168 -EGRTMAEIAEELGV-REGTLRVR 189


>gi|160890875|ref|ZP_02071878.1| hypothetical protein BACUNI_03320 [Bacteroides uniformis ATCC 8492]
 gi|156859874|gb|EDO53305.1| hypothetical protein BACUNI_03320 [Bacteroides uniformis ATCC 8492]
          Length = 181

 Score = 37.9 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 20/89 (22%), Positives = 41/89 (46%), Gaps = 8/89 (8%)

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           SS+    +    D  E  LI +E          +++  L  R R +F   RL+E   +  
Sbjct: 97  SSEQLPEVSGQADSPEDTLISEELFARY----VKALDRLPERCREVFI--RLREEKQSYA 150

Query: 257 NLSSEFEVSRERV-RQIEARAFKKVQESI 284
            ++ E  +S + V  Q++ +A  +++E++
Sbjct: 151 QVAEELNISTKTVDAQLQ-KALTRLKEAL 178


>gi|145221122|ref|YP_001131800.1| RNA polymerase factor sigma-70 [Mycobacterium gilvum PYR-GCK]
 gi|145213608|gb|ABP43012.1| RNA polymerase, sigma subunit, ECF family [Mycobacterium gilvum
           PYR-GCK]
          Length = 340

 Score = 37.9 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 15/85 (17%), Positives = 35/85 (41%), Gaps = 3/85 (3%)

Query: 182 GDESLNALINSSDKNSSQWQDWLVYD-HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           G  S +   + ++++   W + +  D H+      +  E R++ R  L  ++  L+PR+R
Sbjct: 103 GGPSADPYADLTERHEIAWLEPIPDDPHEDPADPSVIAESRESVRLALIAALQHLSPRQR 162

Query: 241 RIFEARRLQENPVTLENLSSEFEVS 265
            +   R + +       +      S
Sbjct: 163 AVLVLREVLQWKA--AEVGEVIGAS 185


>gi|4160469|gb|AAD05254.1| putative protein [Bacillus megaterium]
          Length = 236

 Score = 37.9 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 14/81 (17%), Positives = 34/81 (41%), Gaps = 1/81 (1%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMG-YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
           + GD    + ++  +   + K+     + Y     +  S G I   +A++ +  ++G  L
Sbjct: 19  QQGDKQLHNEMIQQYKPFIAKVVSAVCKRYISEADDEFSIGLIAFNEAIENYTIQKGRSL 78

Query: 102 ATYSMWWIKAAMQEYILRSWS 122
             ++   IK  + +YI +   
Sbjct: 79  LAFAELIIKRRVIDYIRKEKR 99


>gi|317406506|gb|EFV86709.1| hypothetical protein HMPREF0005_04731 [Achromobacter xylosoxidans
           C54]
          Length = 222

 Score = 37.9 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 10/59 (16%), Positives = 22/59 (37%), Gaps = 2/59 (3%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
                   +     + R   L  ++  L  R+R  F   R   + +T + ++   ++SR
Sbjct: 116 EADDASCPMRAAACQQRLERLAEALRELPERQREAFVLSRF--DGLTQDEVAERMQISR 172


>gi|320108468|ref|YP_004184058.1| ECF subfamily RNA polymerase sigma-24 factor [Terriglobus saanensis
           SP1PR4]
 gi|319926989|gb|ADV84064.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Terriglobus
           saanensis SP1PR4]
          Length = 239

 Score = 37.9 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 39/252 (15%), Positives = 69/252 (27%), Gaps = 67/252 (26%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           E+  L ++  + G+  A  +LV  +   V+++AM          +V  E  +      K 
Sbjct: 52  EDDELIRQ-AQAGEREAFDQLVRRYDSSVLRLAMHMLQNEQDAQDVHQEAFL------KA 104

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           +     FR       W+   +    L                     RR      A T  
Sbjct: 105 YRHLSNFRFECSFYTWLYRIVTNLCLDQMR-----------------RRKSRREDAAT-- 145

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQE 212
                                                    +         +  D  G  
Sbjct: 146 -------------------------------------FVDQEGGEMDLMANVQDDRSG-- 166

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
                + ERK     +  ++  L PRER +FE +  Q     L  +      S E  +  
Sbjct: 167 ANPARELERKVLSRKIQAALEKLTPRERMVFELKHYQGLK--LRVIGEMLHTSEETAKNT 224

Query: 273 EARAFKKVQESI 284
             RA +K++ ++
Sbjct: 225 LFRATRKLRSNL 236


>gi|209546583|ref|YP_002278501.1| ECF subfamily RNA polymerase sigma-24 factor [Rhizobium
           leguminosarum bv. trifolii WSM2304]
 gi|209537827|gb|ACI57761.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Rhizobium
           leguminosarum bv. trifolii WSM2304]
          Length = 174

 Score = 37.9 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 18/87 (20%), Positives = 33/87 (37%), Gaps = 3/87 (3%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L +R  + GD  A  +LV+ H   V   A  + G      ++  E  + L  A++ F  
Sbjct: 4   ELIER-AQGGDREAFGQLVSRHYDFVHAAAWRWSGSSADADDIAQEVCVKLGAAIRGFRG 62

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWS 122
               R  T+       A +++  +   
Sbjct: 63  A--SRFRTWLYTLTLNAARDHRRKLAR 87


>gi|331090227|ref|ZP_08339115.1| hypothetical protein HMPREF1025_02698 [Lachnospiraceae bacterium
           3_1_46FAA]
 gi|330402173|gb|EGG81745.1| hypothetical protein HMPREF1025_02698 [Lachnospiraceae bacterium
           3_1_46FAA]
          Length = 147

 Score = 37.9 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 10/59 (16%), Positives = 27/59 (45%), Gaps = 4/59 (6%)

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV-RQIEARAFKKVQESIQ 285
           L  +++ L  + +        Q   +T + +  +   +R  + R I+  A K+++E ++
Sbjct: 87  LAAALAELPEQTQEEIFLYYFQH--LTQKEIGEQSGWTRSTIGRHIQL-ALKRLKEEME 142


>gi|302380820|ref|ZP_07269284.1| RNA polymerase sigma factor, sigma-70 family [Finegoldia magna
           ACS-171-V-Col3]
 gi|302311420|gb|EFK93437.1| RNA polymerase sigma factor, sigma-70 family [Finegoldia magna
           ACS-171-V-Col3]
          Length = 138

 Score = 37.9 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 18/108 (16%), Positives = 50/108 (46%), Gaps = 20/108 (18%)

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           + +  S+      + D ++ +    E+++    E K +   L ++++ L  +ER + EA 
Sbjct: 43  DVIPFSAMDYDGHFVDNIIDERIDLEKIV----EVKMQIEELNKALATLTKKERELIEAI 98

Query: 247 RLQENPVTLENLSSEFEVS-------RERVRQIEARAFKKVQESIQKQ 287
             +E   +L ++  + +VS       R+R+        +K+++ ++ +
Sbjct: 99  FYKEE--SLRSIGKKEKVSYQAIGKRRDRI-------LEKLRKLLEDK 137


>gi|297159385|gb|ADI09097.1| SigE-like sigma factor [Streptomyces bingchenggensis BCW-1]
          Length = 214

 Score = 37.9 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 19/100 (19%), Positives = 42/100 (42%), Gaps = 6/100 (6%)

Query: 198 SQWQDWLVYDHDGQEQVL----IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           ++W      D    EQ+      +  E+   R +L   + VL P++R +   R      +
Sbjct: 72  TEWWRARKLDEVPTEQLPDARVEDSTEQHADRALLMDILGVLAPKQRSVVVLR--HWEQM 129

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           T E  +    +S   V+    RA  ++++ ++ +   +S+
Sbjct: 130 TTEETAEALGMSTGTVKSTLHRALARLRQELESRELDASA 169


>gi|187780186|ref|ZP_02996659.1| hypothetical protein CLOSPO_03782 [Clostridium sporogenes ATCC
           15579]
 gi|187773811|gb|EDU37613.1| hypothetical protein CLOSPO_03782 [Clostridium sporogenes ATCC
           15579]
          Length = 191

 Score = 37.9 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 20/82 (24%), Positives = 39/82 (47%), Gaps = 5/82 (6%)

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           + ++ LVY  D       E+  +K     L  S+ +L+   + I  +R  ++   +LE +
Sbjct: 106 ELKEDLVYTIDDNT---FEQVNKKLEGEALKSSLEMLDKNSKEIIVSRYFKDE--SLEEI 160

Query: 259 SSEFEVSRERVRQIEARAFKKV 280
           SS  ++S+  V    +R  KK+
Sbjct: 161 SSNLKISKSAVSNRLSRVKKKL 182


>gi|169614091|ref|XP_001800462.1| hypothetical protein SNOG_10180 [Phaeosphaeria nodorum SN15]
 gi|160707274|gb|EAT82515.2| hypothetical protein SNOG_10180 [Phaeosphaeria nodorum SN15]
          Length = 308

 Score = 37.9 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 30/162 (18%), Positives = 53/162 (32%), Gaps = 42/162 (25%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           +R+  +     R       L+  I       G         G  G M+ V++   E+G R
Sbjct: 157 WRKQKESDERDRCFIITGSLIAWI----DSPGNWEYTATKYGLHGFMRTVRRSSWEQGIR 212

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVV 160
           +   +  WIK+A+                           R K + Q +TD  ++  +  
Sbjct: 213 INYVAPSWIKSAI---------------------------RTKEYEQWLTDRGIEFGE-- 243

Query: 161 AIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQD 202
                    + +V +   R+A D S+N      DK+     D
Sbjct: 244 ---------QEDVAACMMRIASDRSINEGYKDIDKDDYTEDD 276


>gi|317126935|ref|YP_004093217.1| hypothetical protein Bcell_0197 [Bacillus cellulosilyticus DSM
           2522]
 gi|315471883|gb|ADU28486.1| hypothetical protein Bcell_0197 [Bacillus cellulosilyticus DSM
           2522]
          Length = 194

 Score = 37.9 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 9/57 (15%), Positives = 21/57 (36%), Gaps = 8/57 (14%)

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV--------RQIEARAFKKVQ 281
             L  RE+ I +        ++L+ +     +S  RV        R++     + ++
Sbjct: 52  DNLIDREQNILDLVYRNNGELSLKEIGERIGISSSRVAAIRNLAERRLSLVMLRHLR 108


>gi|260771281|ref|ZP_05880208.1| RNA polymerase sigma factor RpoE [Vibrio furnissii CIP 102972]
 gi|260613878|gb|EEX39070.1| RNA polymerase sigma factor RpoE [Vibrio furnissii CIP 102972]
 gi|315179112|gb|ADT86026.1| RNA polymerase sigma factor RpoE [Vibrio furnissii NCTC 11218]
          Length = 190

 Score = 37.9 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 18/88 (20%), Positives = 33/88 (37%), Gaps = 3/88 (3%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
            VL +R + +GD  A + LV  +   V  +   Y      +++V  E  I   +A+  F 
Sbjct: 8   QVLIERVQ-NGDKQAFNLLVLRYQNKVCNLISRYVSNSGDVADVAQEAFIKAYRAIPTFR 66

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWS 122
            E      T+         + +I+    
Sbjct: 67  GE--SAFYTWLYRIAVNTAKNHIVAQSR 92


>gi|269925463|ref|YP_003322086.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermobaculum
           terrenum ATCC BAA-798]
 gi|269789123|gb|ACZ41264.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermobaculum
           terrenum ATCC BAA-798]
          Length = 196

 Score = 37.9 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 13/88 (14%), Positives = 34/88 (38%), Gaps = 14/88 (15%)

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
           +L+   D   +   E      RRN++  ++  L   +R++ E        +T   ++ + 
Sbjct: 107 YLMNLPDSSLEDPDEIIMGGIRRNIVLEALRELPENQRKVLEMSYFGG--LTQSEIADKV 164

Query: 263 EV------SRERVRQIEARAFKKVQESI 284
                   +R R+      A + ++ ++
Sbjct: 165 GEPLGTIKTRMRL------ALQHLRRNL 186


>gi|158334386|ref|YP_001515558.1| RNA polymerase sigma-24 subunit [Acaryochloris marina MBIC11017]
 gi|158304627|gb|ABW26244.1| RNA polymerase sigma-24 subunit [Acaryochloris marina MBIC11017]
          Length = 204

 Score = 37.9 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 12/97 (12%), Positives = 35/97 (36%), Gaps = 14/97 (14%)

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
              W            ++   +  +R  L ++++ L    R++ E         +   ++
Sbjct: 116 LSQWQQSLSPNPSPTPLDHASQSEKRQALQQALTELPEEYRQVLELSYFGG--YSQSQIA 173

Query: 260 SEFE-----V-SRERVRQIEARAFKKVQESIQKQVEL 290
            +       V +  R      +   ++++S++ Q+EL
Sbjct: 174 EQLNKPLGTVKTWAR------KGLIQLRQSLRTQMEL 204


>gi|149025904|gb|EDL82147.1| rCG28869 [Rattus norvegicus]
          Length = 3024

 Score = 37.9 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 22/123 (17%), Positives = 44/123 (35%), Gaps = 7/123 (5%)

Query: 157  EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
            E++   A KL    ++        + DES +AL  S  +N            D  +   I
Sbjct: 2551 EEISDEASKLVDRLTQSEREQEPPSDDESSSALEVSVIENLPPVDTEHSAPEDIFDTRPI 2610

Query: 217  EKEERKNRRNML------TRSMSVLNPRERRIFEARRLQEN-PVTLENLSSEFEVSRERV 269
              E  +     +       R+    + +ER       + ++   +   L+ E + + E++
Sbjct: 2611 WDESIETMIERIPDENGHDRAEDPQDEQERMEERLAYIADHLGFSWTELARELDFTEEQI 2670

Query: 270  RQI 272
             QI
Sbjct: 2671 HQI 2673


>gi|85814047|emb|CAI05918.1| putative RNA polymerase sigma factor [Micromonospora echinospora]
          Length = 218

 Score = 37.9 bits (87), Expect = 1.7,   Method: Composition-based stats.
 Identities = 14/101 (13%), Positives = 33/101 (32%), Gaps = 19/101 (18%)

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
                D        +L+ D    ++ L+    R  RR  L  + + L+PR R +      
Sbjct: 100 FDPYDDSVDGHVGVFLLVDSAAPDEDLL----RAERRQALRDAFAQLSPRCRELLAL-LT 154

Query: 249 QENPVTLENLSSEFEV-------SRERVRQIEARAFKKVQE 282
            + P +   +     +       ++ R          ++++
Sbjct: 155 GDPPASYREIGERLGMPVGSVGPTQARC-------LARLRD 188


>gi|325859597|ref|ZP_08172730.1| RNA polymerase sigma-70 factor [Prevotella denticola CRIS 18C-A]
 gi|325482877|gb|EGC85877.1| RNA polymerase sigma-70 factor [Prevotella denticola CRIS 18C-A]
          Length = 202

 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 12/72 (16%), Positives = 33/72 (45%), Gaps = 8/72 (11%)

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA---RA 276
           E    R  +  ++S L  + R +F      +     + ++ +  +S   +R +E    +A
Sbjct: 136 EGLEMRRQINDAISELPAKCREVFVLSYQHDRKN--KEIAEQLGIS---IRTVEVHLYKA 190

Query: 277 FKKVQESIQKQV 288
            K +++ ++++V
Sbjct: 191 LKSLRQKLRRRV 202


>gi|311067855|ref|YP_003972778.1| putative RNA polymerase sigma factor SigI [Bacillus atrophaeus
           1942]
 gi|310868372|gb|ADP31847.1| putative RNA polymerase sigma factor SigI [Bacillus atrophaeus
           1942]
          Length = 251

 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 16/84 (19%), Positives = 33/84 (39%), Gaps = 7/84 (8%)

Query: 43  EHGDLSAAHRLVTSHLRL----VVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           + G+    + L+  +       V  +   Y        +  S G I   +A++K+  E+G
Sbjct: 26  QKGNKELQNELIQQYKPFIAKTVSSVCKRYI---DEKDDEFSIGLIAFNEAIEKYSAEKG 82

Query: 99  FRLATYSMWWIKAAMQEYILRSWS 122
             L  ++   IK  + +YI +   
Sbjct: 83  NSLLAFAELIIKRKVIDYIRKEAR 106


>gi|291280766|ref|YP_003497600.1| hypothetical protein DEFDS_P224 [Deferribacter desulfuricans SSM1]
 gi|290755468|dbj|BAI81844.1| hypothetical protein [Deferribacter desulfuricans SSM1]
          Length = 136

 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 14/95 (14%), Positives = 38/95 (40%), Gaps = 16/95 (16%)

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL------- 258
            D     Q+  +   ++ ++ ++  S+  L+ +E  +     + E  +T +++       
Sbjct: 3   SDELITNQLEEDIINKRLKQKIVELSIDTLSAKEFFVLMNLLIFEGVLTEDDILYYYNKK 62

Query: 259 ---------SSEFEVSRERVRQIEARAFKKVQESI 284
                    +    V+  R+RQI   A  K+++ +
Sbjct: 63  TKKDLIACLAHLLNVTEVRIRQINKNAINKLKDRL 97


>gi|256380903|ref|YP_003104563.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Actinosynnema
           mirum DSM 43827]
 gi|255925206|gb|ACU40717.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Actinosynnema
           mirum DSM 43827]
          Length = 192

 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 12/79 (15%), Positives = 30/79 (37%), Gaps = 2/79 (2%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           H    +              +  ++S L PR+R +   R   +  ++   ++    +S+ 
Sbjct: 115 HVANARSAESLAMLTAEHQAVVAALSQLPPRQREVLVLRYYGD--LSEAEIAEATGISKG 172

Query: 268 RVRQIEARAFKKVQESIQK 286
            V+   +RA   +Q+ +  
Sbjct: 173 TVKSTASRALDALQKIMAS 191


>gi|150025511|ref|YP_001296337.1| RNA polymerase ECF-type sigma factor [Flavobacterium psychrophilum
           JIP02/86]
 gi|149772052|emb|CAL43528.1| RNA polymerase ECF-type sigma factor [Flavobacterium psychrophilum
           JIP02/86]
          Length = 169

 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 13/76 (17%), Positives = 39/76 (51%), Gaps = 6/76 (7%)

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
             L +K E  +  N + ++++ L  +++ I + R +++     E ++   E+S   +R  
Sbjct: 91  ASLQQKVEDNDSCNWVEKAINDLPEQQKLIIQMRDVEQYE--FEEIAKILEMSEATIR-- 146

Query: 273 EARAFKKVQESIQKQV 288
              A  + +++I++++
Sbjct: 147 --VALSRARKTIREKL 160


>gi|153810235|ref|ZP_01962903.1| hypothetical protein RUMOBE_00616 [Ruminococcus obeum ATCC 29174]
 gi|153855530|ref|ZP_01996649.1| hypothetical protein DORLON_02665 [Dorea longicatena DSM 13814]
 gi|154506117|ref|ZP_02042855.1| hypothetical protein RUMGNA_03659 [Ruminococcus gnavus ATCC 29149]
 gi|160934980|ref|ZP_02082366.1| hypothetical protein CLOLEP_03856 [Clostridium leptum DSM 753]
 gi|167751528|ref|ZP_02423655.1| hypothetical protein EUBSIR_02529 [Eubacterium siraeum DSM 15702]
 gi|167760878|ref|ZP_02433005.1| hypothetical protein CLOSCI_03266 [Clostridium scindens ATCC 35704]
 gi|210617837|ref|ZP_03291773.1| hypothetical protein CLONEX_04005 [Clostridium nexile DSM 1787]
 gi|223932196|ref|ZP_03624200.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Streptococcus suis 89/1591]
 gi|260589814|ref|ZP_05855727.1| RNA polymerase sigma-B factor [Blautia hansenii DSM 20583]
 gi|298346341|ref|YP_003719028.1| RNA polymerase sigma-B factor [Mobiluncus curtisii ATCC 43063]
 gi|325263030|ref|ZP_08129765.1| RNA polymerase sigma-B factor [Clostridium sp. D5]
 gi|149752052|gb|EDM61983.1| hypothetical protein DORLON_02665 [Dorea longicatena DSM 13814]
 gi|149833414|gb|EDM88495.1| hypothetical protein RUMOBE_00616 [Ruminococcus obeum ATCC 29174]
 gi|153793616|gb|EDN76036.1| hypothetical protein RUMGNA_03659 [Ruminococcus gnavus ATCC 29149]
 gi|156866433|gb|EDO59805.1| hypothetical protein CLOLEP_03856 [Clostridium leptum DSM 753]
 gi|167655336|gb|EDR99465.1| hypothetical protein EUBSIR_02529 [Eubacterium siraeum DSM 15702]
 gi|167661481|gb|EDS05611.1| hypothetical protein CLOSCI_03266 [Clostridium scindens ATCC 35704]
 gi|210149116|gb|EEA80125.1| hypothetical protein CLONEX_04005 [Clostridium nexile DSM 1787]
 gi|223899177|gb|EEF65534.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Streptococcus suis 89/1591]
 gi|260539817|gb|EEX20386.1| RNA polymerase sigma-B factor [Blautia hansenii DSM 20583]
 gi|291540148|emb|CBL13259.1| DNA-directed RNA polymerase specialized sigma subunit [Roseburia
           intestinalis XB6B4]
 gi|295090232|emb|CBK76339.1| DNA-directed RNA polymerase specialized sigma subunit [Clostridium
           cf. saccharolyticum K10]
 gi|298236402|gb|ADI67534.1| RNA polymerase sigma-B factor [Mobiluncus curtisii ATCC 43063]
 gi|324031423|gb|EGB92703.1| RNA polymerase sigma-B factor [Clostridium sp. D5]
          Length = 170

 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 10/91 (10%), Positives = 39/91 (42%), Gaps = 6/91 (6%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
            +     D++  +     + ++         + L  ++ +L+  E+ + +A     + ++
Sbjct: 85  DSEGNPLDFITDEAVDIAETVVNAVMV----DRLKAALPLLSDSEQELIQAIFF--DGLS 138

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              + +   +++  V + +AR   K+++ I+
Sbjct: 139 EREVGARLGITQSVVNKRKARILIKLRKIIE 169


>gi|318040246|ref|ZP_07972202.1| type II alternative sigma-70 family RNA polymerase sigma factor
          [Synechococcus sp. CB0101]
          Length = 107

 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 8/42 (19%), Positives = 24/42 (57%)

Query: 2  NRKNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYRE 43
          + ++ + +  G   +  Y+ +I ++P+L  ++E  L ++ +E
Sbjct: 9  SERDAAALAGGTDLVRSYLRDIGRVPLLTHEQEITLGRQVQE 50


>gi|303228338|ref|ZP_07315173.1| RNA polymerase sigma factor, sigma-70 family [Veillonella atypica
           ACS-134-V-Col7a]
 gi|302516987|gb|EFL58894.1| RNA polymerase sigma factor, sigma-70 family [Veillonella atypica
           ACS-134-V-Col7a]
          Length = 243

 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 18/101 (17%), Positives = 39/101 (38%), Gaps = 3/101 (2%)

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
             L   + + D  S    D    D D +  ++    E +  RN L  +   L  +++++ 
Sbjct: 126 HELTLPLCTGDDVSEPAMDQFPSDVDLERDIVGTVTEDEL-RNRLWSAFRKLPRQQQQLL 184

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            A           ++  E   SR+ V+Q   +A  +++  +
Sbjct: 185 YALYRDGKSCV--DIGCEIHQSRQAVQQRHQKAIDQLRYYM 223


>gi|294497991|ref|YP_003561691.1| RNA polymerase sigma-I factor [Bacillus megaterium QM B1551]
 gi|294347928|gb|ADE68257.1| RNA polymerase sigma-I factor [Bacillus megaterium QM B1551]
          Length = 236

 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 14/81 (17%), Positives = 34/81 (41%), Gaps = 1/81 (1%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMG-YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
           + GD    + ++  +   + K+     + Y     +  S G I   +A++ +  ++G  L
Sbjct: 19  QQGDKQLHNEMIQQYKPFIAKVVSAVCKRYISEADDEFSIGLIAFNEAIENYTIQKGRSL 78

Query: 102 ATYSMWWIKAAMQEYILRSWS 122
             ++   IK  + +YI +   
Sbjct: 79  LAFAELIIKRRVIDYIRKEKR 99


>gi|268610389|ref|ZP_06144116.1| putative RNA polymerase sigma factor (ECF subfamily) protein
           [Ruminococcus flavefaciens FD-1]
          Length = 185

 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 17/74 (22%), Positives = 36/74 (48%), Gaps = 2/74 (2%)

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           E+ E K     + R +  L   ER++F  R    + ++  +++  F  +  +VR +  R 
Sbjct: 114 EQLEAKETSECIDRFLGTLKAYERQVFVCRYWYFDSIS--DIAKRFSFTEGKVRSMLFRT 171

Query: 277 FKKVQESIQKQVEL 290
            KK+ +++ K+  L
Sbjct: 172 RKKLMKALDKEGLL 185


>gi|284033899|ref|YP_003383830.1| ECF subfamily RNA polymerase sigma-24 subunit [Kribbella flavida
           DSM 17836]
 gi|283813192|gb|ADB35031.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Kribbella flavida
           DSM 17836]
          Length = 206

 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 12/88 (13%), Positives = 30/88 (34%), Gaps = 2/88 (2%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           + D   +     E   R +    +   +  L  + R I   R +    ++ E       +
Sbjct: 113 LPDGADESPTPEEHAVRHSEVQHIVGLLERLPEKLREILRLRVVAG--MSAEETGRALGM 170

Query: 265 SRERVRQIEARAFKKVQESIQKQVELSS 292
           +   VR  + RA   ++  +  + ++  
Sbjct: 171 TPGAVRVAQHRALNTLRGFVGHEAKVER 198


>gi|163848961|ref|YP_001637005.1| response regulator receiver [Chloroflexus aurantiacus J-10-fl]
 gi|222526915|ref|YP_002571386.1| LuxR family two component transcriptional regulator [Chloroflexus
           sp. Y-400-fl]
 gi|163670250|gb|ABY36616.1| response regulator receiver [Chloroflexus aurantiacus J-10-fl]
 gi|222450794|gb|ACM55060.1| two component transcriptional regulator, LuxR family [Chloroflexus
           sp. Y-400-fl]
          Length = 209

 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 18/104 (17%), Positives = 39/104 (37%), Gaps = 3/104 (2%)

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
           + R+ G     A+     ++  +     +      + VL     ++      +++   L 
Sbjct: 90  DARVIGALRAGAITYIEKESQPEQLLEAIRGAMAGKAVLAPALMQRILEAQTSKAADTLT 149

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
            RER + +   L    +T   ++S   VS E V+   A   +K+
Sbjct: 150 EREREVLK---LVAEGLTNAEIASRLTVSEETVKTHVASILRKL 190


>gi|295703345|ref|YP_003596420.1| RNA polymerase sigma-I factor [Bacillus megaterium DSM 319]
 gi|294801004|gb|ADF38070.1| RNA polymerase sigma-I factor [Bacillus megaterium DSM 319]
          Length = 236

 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 14/81 (17%), Positives = 34/81 (41%), Gaps = 1/81 (1%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMG-YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
           + GD    + ++  +   + K+     + Y     +  S G I   +A++ +  ++G  L
Sbjct: 19  QQGDKQLHNEMIQQYKPFIAKVVSAVCKRYISEADDEFSIGLIAFNEAIENYTIQKGRSL 78

Query: 102 ATYSMWWIKAAMQEYILRSWS 122
             ++   IK  + +YI +   
Sbjct: 79  LAFAELIIKRRVIDYIRKEKR 99


>gi|227544659|ref|ZP_03974708.1| DNA-directed RNA polymerase specialized sigma subunit
           [Lactobacillus reuteri CF48-3A]
 gi|300909424|ref|ZP_07126885.1| DNA-directed RNA polymerase specialized sigma subunit
           [Lactobacillus reuteri SD2112]
 gi|227185384|gb|EEI65455.1| DNA-directed RNA polymerase specialized sigma subunit
           [Lactobacillus reuteri CF48-3A]
 gi|300893289|gb|EFK86648.1| DNA-directed RNA polymerase specialized sigma subunit
           [Lactobacillus reuteri SD2112]
          Length = 172

 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 13/98 (13%), Positives = 37/98 (37%), Gaps = 3/98 (3%)

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVL-IEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           +N +   +D+ S +       D+   + +   E + R+     L  +++ L  +++    
Sbjct: 71  MNMIDTLADRGSIEVTSIYGKDNLLNQIIQKEEHQSRQMLAEQLPAALATLTDKQKYAVT 130

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
                        ++ E  +S+    +    A KK+++
Sbjct: 131 QYYCHGMKKN--QIAKEMGISKVMAGRHVKAAIKKLRQ 166


>gi|331002089|ref|ZP_08325608.1| hypothetical protein HMPREF0491_00470 [Lachnospiraceae oral taxon
           107 str. F0167]
 gi|330411183|gb|EGG90599.1| hypothetical protein HMPREF0491_00470 [Lachnospiraceae oral taxon
           107 str. F0167]
          Length = 131

 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 19/98 (19%), Positives = 41/98 (41%), Gaps = 16/98 (16%)

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
           + S  +++ + D + +   + +  E     + L ++M  L+  ER I +     +   +L
Sbjct: 43  DFSFAENYSIKDIEDKRINVEKIVETNLLIDQLQKAMETLSDDEREIIKRIYFDDE--SL 100

Query: 256 ENLSSEFEVS-------RERVRQIEARAFKKVQESIQK 286
             ++    VS       R+R+        KK++E I K
Sbjct: 101 RKVAKSRNVSHPSLIKKRDRI-------LKKLREIIGK 131


>gi|253563721|ref|ZP_04841178.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 3_2_5]
 gi|251947497|gb|EES87779.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 3_2_5]
          Length = 191

 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 36/73 (49%), Gaps = 2/73 (2%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E  +  + +  + +  + + +S L PR++ +F   R  E  ++ + ++    +S + V +
Sbjct: 112 EYDIENEMDAADLQGYIKKLISELTPRQQEVFHLSR--EEHLSYKEIAIRLSISEKTVER 169

Query: 272 IEARAFKKVQESI 284
               A K ++++I
Sbjct: 170 HINEALKFLRKNI 182


>gi|256810692|ref|YP_003128061.1| DNA binding protein, Tfx family [Methanocaldococcus fervens AG86]
 gi|256793892|gb|ACV24561.1| DNA binding protein, Tfx family [Methanocaldococcus fervens AG86]
          Length = 135

 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 3/49 (6%)

Query: 235 LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           L   + ++ E R   +  +T E ++  F  SR  +  IE RA + V+++
Sbjct: 6   LTETQIKVLELR---KKGLTQEEIAKMFGTSRANISMIEKRAKENVKKA 51


>gi|325280201|ref|YP_004252743.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Odoribacter
           splanchnicus DSM 20712]
 gi|324312010|gb|ADY32563.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Odoribacter
           splanchnicus DSM 20712]
          Length = 207

 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 18/92 (19%), Positives = 33/92 (35%), Gaps = 6/92 (6%)

Query: 31  KQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
            +E+     R    GD  A   L  S+ RL+    M Y        ++V    I L    
Sbjct: 2   AEEQEKNIIRLLAKGDEEATGILFRSYHRLLCAYCMRYLVSREDAEDIVQAVFISL---- 57

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
             +   RG + +     ++  A+ +  L++  
Sbjct: 58  --WQNWRGRKFSGSLEAYLFGAVNKAALKTMR 87


>gi|323474105|gb|ADX84711.1| Bacterio-opsin activator HTH domain protein [Sulfolobus islandicus
           REY15A]
          Length = 204

 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 12/52 (23%), Positives = 22/52 (42%), Gaps = 5/52 (9%)

Query: 233 SVLNPRERRIFEA-----RRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           + L  R+  I +          +  VTL  L+ +  +S   + +I  RA +K
Sbjct: 143 NDLTDRQMEILKLAYKMGYFDDDRRVTLTELAKQLGISTPTLEEIMRRALRK 194


>gi|260172535|ref|ZP_05758947.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D2]
 gi|315920828|ref|ZP_07917068.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D2]
 gi|313694703|gb|EFS31538.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. D2]
          Length = 198

 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 16/99 (16%), Positives = 38/99 (38%), Gaps = 14/99 (14%)

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           S     +  D     +  +E  E K    ++ ++++ L+P  R++F   R +      E 
Sbjct: 98  SSEDLVIYSDLWSLGENPVEHLEGKELHAIIQKTINGLSPETRKVFLLSRFENKR--QEE 155

Query: 258 LSSEFEVSRERVRQIE------ARAFKKVQESIQKQVEL 290
           ++    ++      I         A  K++E+ +  + L
Sbjct: 156 IAEIMGIT------IHTVKYHMRSALDKLKEAAKSYLAL 188


>gi|154491948|ref|ZP_02031574.1| hypothetical protein PARMER_01578 [Parabacteroides merdae ATCC
           43184]
 gi|154088189|gb|EDN87234.1| hypothetical protein PARMER_01578 [Parabacteroides merdae ATCC
           43184]
          Length = 188

 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 17/106 (16%), Positives = 46/106 (43%), Gaps = 6/106 (5%)

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLI----EKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           I   +  S   ++   ++ + +   L     E+      + ++ ++++ L  + RRIF  
Sbjct: 78  IQVREDASEHLKNHAEWELNTRISTLEACNPEELFTAEAQEIVNKTLASLPEQTRRIFIM 137

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
            R +  P   + ++    ++ + V    A+A KK+  +++  + L 
Sbjct: 138 SRYENKPY--KEIAETLGMTTKGVEYHIAQALKKLHVNLKDYIPLL 181


>gi|121488720|emb|CAJ18246.1| sigma 70-type sigma factor [Pelodictyon luteolum]
          Length = 95

 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 19/101 (18%), Positives = 34/101 (33%), Gaps = 6/101 (5%)

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           +      +     +      +A  L++   +V           S++A     D N  +  
Sbjct: 1   ISKAYSQLEQEFERDPNTKELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDN--RLL 58

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRI 242
           D L  D      +      R +    + RS+SVL PRE  +
Sbjct: 59  DVLQNDG----HLPDHGLNRDSLTLEVERSLSVLAPREADV 95


>gi|318058442|ref|ZP_07977165.1| sigma factor [Streptomyces sp. SA3_actG]
          Length = 224

 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 12/62 (19%), Positives = 22/62 (35%), Gaps = 2/62 (3%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L+           E       R+ L ++M  L  R+R +   R   +  +T   ++    
Sbjct: 142 LLSKPMPDMASAEEGAYDLLERDDLIKAMRGLQRRQREVLVLRYFAD--MTEAQVAETLG 199

Query: 264 VS 265
           VS
Sbjct: 200 VS 201


>gi|283781162|ref|YP_003371917.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Pirellula staleyi
           DSM 6068]
 gi|283439615|gb|ADB18057.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Pirellula staleyi
           DSM 6068]
          Length = 204

 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 16/80 (20%), Positives = 33/80 (41%), Gaps = 2/80 (2%)

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
                  +   R  R   L  +++ L   +R     R ++  P   + ++ +   S   +
Sbjct: 126 ASMTTASQAFSRNVREAKLMDAIATLPEEQREALRLRYIENLPS--KEIAQKLGKSDAAI 183

Query: 270 RQIEARAFKKVQESIQKQVE 289
           R +  R+ KK+QE + K +E
Sbjct: 184 RVMLTRSLKKLQEILDKTLE 203


>gi|167950929|ref|ZP_02538003.1| hypothetical protein Epers_32873 [Endoriftia persephone
          'Hot96_1+Hot96_2']
          Length = 64

 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 2/39 (5%)

Query: 16 LSRYIHEIRKIPMLEKQEEYVLAKRYR--EHGDLSAAHR 52
          L+ Y++EI    +L  +EE   A+  +  EH   SA  R
Sbjct: 3  LALYLNEIGGSKLLTAEEEVYYARLAQKGEHPAPSAHDR 41


>gi|319794971|ref|YP_004156611.1| RNA polymerase, sigma-24 subunit, ecf subfamily [Variovorax
           paradoxus EPS]
 gi|315597434|gb|ADU38500.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Variovorax
           paradoxus EPS]
          Length = 179

 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 11/62 (17%), Positives = 23/62 (37%), Gaps = 2/62 (3%)

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           D  + D              +     + + ++ L+PR R +FE  RL    +T   +++ 
Sbjct: 90  DVELLDMPTTASTPDRMMCERQVITAIDKVLAGLSPRTRLVFELYRL--EGLTQREIAAR 147

Query: 262 FE 263
             
Sbjct: 148 LG 149


>gi|315441915|ref|YP_004074794.1| RNA polymerase sigma-70 factor, TIGR02960 family [Mycobacterium sp.
           Spyr1]
 gi|315260218|gb|ADT96959.1| RNA polymerase sigma-70 factor, TIGR02960 family [Mycobacterium sp.
           Spyr1]
          Length = 336

 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 15/85 (17%), Positives = 35/85 (41%), Gaps = 3/85 (3%)

Query: 182 GDESLNALINSSDKNSSQWQDWLVYD-HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           G  S +   + ++++   W + +  D H+      +  E R++ R  L  ++  L+PR+R
Sbjct: 99  GGPSADPYADLTERHEIAWLEPIPDDPHEDPADPSVIAESRESVRLALIAALQHLSPRQR 158

Query: 241 RIFEARRLQENPVTLENLSSEFEVS 265
            +   R + +       +      S
Sbjct: 159 AVLVLREVLQWKA--AEVGEVIGAS 181


>gi|291449571|ref|ZP_06588961.1| conserved hypothetical protein [Streptomyces roseosporus NRRL
           15998]
 gi|291352518|gb|EFE79422.1| conserved hypothetical protein [Streptomyces roseosporus NRRL
           15998]
          Length = 594

 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 8/82 (9%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV-KKFDPERGFR 100
            + GD  A  +LV+++L L+  +          + +VV E  + +++ + +  DPER   
Sbjct: 73  AQGGDQQAKDQLVSAYLPLLYNVVGRALDGHADVDDVVQETVLRMLRGLPELRDPER--- 129

Query: 101 LATYSMWWIKAAMQEYILRSWS 122
              +  W +  AM E I   W 
Sbjct: 130 ---FRSWLVAIAMNE-IRTHWR 147


>gi|317132767|ref|YP_004092081.1| sigma-70 region 4 domain protein [Ethanoligenens harbinense YUAN-3]
 gi|315470746|gb|ADU27350.1| sigma-70 region 4 domain protein [Ethanoligenens harbinense YUAN-3]
          Length = 137

 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 19/106 (17%), Positives = 41/106 (38%), Gaps = 3/106 (2%)

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
             M+  ++G        N +  + + +   L    + Q  V  +  +    R+ +   + 
Sbjct: 28  REMSTSVSGMRYDGMPRNPNTPSDAHFVTCLHKIDEIQADVEKKVAQLITLRDEINARID 87

Query: 234 VL-NPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           +L +P E+ +   R +     T E ++S   VS   V +I   A +
Sbjct: 88  LLADPEEQLVLRYRYIDN--CTWEEIASMLNVSLRTVHRIHGSALQ 131


>gi|264678690|ref|YP_003278597.1| two component transcriptional regulator, LuxR [Comamonas
           testosteroni CNB-2]
 gi|262209203|gb|ACY33301.1| two component transcriptional regulator, LuxR [Comamonas
           testosteroni CNB-2]
          Length = 201

 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 11/59 (18%), Positives = 22/59 (37%), Gaps = 3/59 (5%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             +  ML      L PRE  +     ++    +L  ++     S + V   +  A +K+
Sbjct: 126 SLQHQMLQERFKSLTPREFEVLR-YYVRGG--SLAEIAERLNRSIKTVSSQKMTAMRKL 181


>gi|239926891|ref|ZP_04683844.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces ghanaensis
           ATCC 14672]
 gi|291435237|ref|ZP_06574627.1| RNA polymerase [Streptomyces ghanaensis ATCC 14672]
 gi|291338132|gb|EFE65088.1| RNA polymerase [Streptomyces ghanaensis ATCC 14672]
          Length = 314

 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 17/83 (20%), Positives = 35/83 (42%), Gaps = 2/83 (2%)

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
            QW    + D D         E+R++    +   M  L+P ER ++  R   ++      
Sbjct: 82  GQWLPEPLLDGDPMLGPADTAEQRESVSYAVLTLMERLSPNERAVYVLREAFDHSH--RE 139

Query: 258 LSSEFEVSRERVRQIEARAFKKV 280
           ++   +++    +QI  RA K++
Sbjct: 140 IAEILDLTEAASQQILHRAKKRL 162


>gi|153939834|ref|YP_001390956.1| putative RNA polymerase sigma factor [Clostridium botulinum F str.
           Langeland]
 gi|152935730|gb|ABS41228.1| putative RNA polymerase sigma factor [Clostridium botulinum F str.
           Langeland]
 gi|295319017|gb|ADF99394.1| putative RNA polymerase sigma factor [Clostridium botulinum F str.
           230613]
          Length = 176

 Score = 37.9 bits (87), Expect = 1.8,   Method: Composition-based stats.
 Identities = 23/100 (23%), Positives = 48/100 (48%), Gaps = 5/100 (5%)

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE--ERKNRRNMLTRSMSVLNPRERRIFEA 245
           AL+    K+  +  D  + D   +    IE E    +N +  L +++  L P E+ + ++
Sbjct: 80  ALLKGEIKHHREIPDENISDKGNEYLFTIEDEIIAYENIKE-LYKALDNLTPEEKEVIDS 138

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             ++ N  +L+ ++S    S   VR  + +A KK+Q  ++
Sbjct: 139 FYIKNN--SLQEIASYTNKSYNSVRYTKEKAIKKLQNMLE 176


>gi|318079578|ref|ZP_07986910.1| sigma factor [Streptomyces sp. SA3_actF]
          Length = 213

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 12/62 (19%), Positives = 22/62 (35%), Gaps = 2/62 (3%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L+           E       R+ L ++M  L  R+R +   R   +  +T   ++    
Sbjct: 131 LLSKPMPDMASAEEGAYDLLERDDLIKAMRGLQRRQREVLVLRYFAD--MTEAQVAETLG 188

Query: 264 VS 265
           VS
Sbjct: 189 VS 190


>gi|317479697|ref|ZP_07938820.1| RNA polymerase sigma-70 factor [Bacteroides sp. 4_1_36]
 gi|316904150|gb|EFV25981.1| RNA polymerase sigma-70 factor [Bacteroides sp. 4_1_36]
          Length = 181

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 20/89 (22%), Positives = 41/89 (46%), Gaps = 8/89 (8%)

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           SS+    +    D  E  LI +E          +++  L  R R +F   RL+E   +  
Sbjct: 97  SSEQLPEVSGQADSPEDTLISEELFARY----VKALDRLPERCREVFI--RLREEKQSYA 150

Query: 257 NLSSEFEVSRERV-RQIEARAFKKVQESI 284
            ++ E  +S + V  Q++ +A  +++E++
Sbjct: 151 QVAEELNISTKTVDAQLQ-KALTRLKEAL 178


>gi|172039055|ref|YP_001805556.1| RNA polymerase sigma factor RpoE [Cyanothece sp. ATCC 51142]
 gi|171700509|gb|ACB53490.1| group 4 sigma-70 RNA polymerase sigma factor G [Cyanothece sp. ATCC
           51142]
          Length = 221

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 21/115 (18%), Positives = 42/115 (36%), Gaps = 17/115 (14%)

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           R++   SL+A     D         + +D         +    +   + L  +++ L   
Sbjct: 120 RVSHPISLDAPRRVDDGE-------IEWDIVSDYPSPDDNLATREFYDRLKVAIADLPEA 172

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVS----RERVRQIEARAFKKVQESIQKQVE 289
            R     R +    +  E ++    VS    + R+    ARA  K+Q  +QK ++
Sbjct: 173 FRTTIVLREI--EGLAYEEIAEMTGVSLGTVKSRI----ARARGKLQTVLQKYID 221


>gi|219850006|ref|YP_002464439.1| ECF subfamily RNA polymerase sigma-24 subunit [Chloroflexus
           aggregans DSM 9485]
 gi|219544265|gb|ACL26003.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Chloroflexus
           aggregans DSM 9485]
          Length = 224

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 16/81 (19%), Positives = 31/81 (38%), Gaps = 2/81 (2%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + GD  A   L+ S    V  IAM         +++  E  I L + + +++ E   R 
Sbjct: 12  AQQGDQQALTDLIISQQHYVYSIAMSVLKNADDAADLTQEAFIRLFRTLPQYNGE--SRF 69

Query: 102 ATYSMWWIKAAMQEYILRSWS 122
            T+    +    ++ + R   
Sbjct: 70  TTWLYRLVVNLCRDELRRRGR 90


>gi|315647772|ref|ZP_07900873.1| RNA polymerase, sigma-24 subunit, ECF subfamily protein
           [Paenibacillus vortex V453]
 gi|315276418|gb|EFU39761.1| RNA polymerase, sigma-24 subunit, ECF subfamily protein
           [Paenibacillus vortex V453]
          Length = 582

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 48/257 (18%), Positives = 93/257 (36%), Gaps = 51/257 (19%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           ++ E+  L K Y + G+  A   LV  H   V   A           +VV +    L++A
Sbjct: 12  DEMEDRELVK-YAQAGEREAFGELVRRHRSKVYGYARAITRESYLAEDVVQDA---LIRA 67

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI 149
                  +   +  +  W     +   +         G++A +++ F  L  +       
Sbjct: 68  F--MHLGKLVDVERFLPW-----VHRIVRNQAYTRLRGSSAVKEQTFTELEGVGRADG-- 118

Query: 150 TDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD 209
           T  +     + +I  +L+ S +E                                     
Sbjct: 119 TGGSHNWGNLDSILGRLHRSANE-----------------------------------AS 143

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
               V  E+  ++    +LT  +  L PRER IFE+    +  ++ + +++ F++S   V
Sbjct: 144 AGSSVPEERILQQETLRVLTGIIQCLKPRERLIFESHFFDQ--LSPQEIANLFQLSSANV 201

Query: 270 RQIEARAFKK-VQESIQ 285
            QI +R+ KK +QE I+
Sbjct: 202 YQIISRSRKKVIQEKIR 218


>gi|126734686|ref|ZP_01750432.1| hypothetical protein RCCS2_12454 [Roseobacter sp. CCS2]
 gi|126715241|gb|EBA12106.1| hypothetical protein RCCS2_12454 [Roseobacter sp. CCS2]
          Length = 883

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 24/138 (17%), Positives = 49/138 (35%), Gaps = 14/138 (10%)

Query: 137 FNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKN 196
             LRR +  L     N    E++  + ++L  +  + + M    A         +S  ++
Sbjct: 492 ERLRRAQERLSEAMRNGASDEEIAELMQELREATDDYLRMLAEEAEPNDGTDQADSGQQS 551

Query: 197 SSQWQDWLVYDHDGQEQVLIE--KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP-- 252
                D L    D  ++++ E    E +     L + M  L     R+ +       P  
Sbjct: 552 EQLGMDELQALMDRIQELMEEGRMAEAQELMEQLNQMMENL-----RVTQGEGGDGPPSP 606

Query: 253 --VTLENLSSEFEVSRER 268
              ++E+L+      RE+
Sbjct: 607 GEQSMEDLADTL---REQ 621


>gi|89894901|ref|YP_518388.1| hypothetical protein DSY2155 [Desulfitobacterium hafniense Y51]
 gi|89334349|dbj|BAE83944.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 185

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 17/84 (20%), Positives = 38/84 (45%), Gaps = 2/84 (2%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           + +     + + E   R+ R   L ++++ L  +E+ +   + + E     E L     +
Sbjct: 99  LAEKIPDYEAVEESIIREERIEELGKAIAKLPEKEKDLLYFKYILEMDN--EQLGQILGI 156

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           +   VRQ   R+ +K ++ I K+V
Sbjct: 157 ASASVRQYLTRSRRKAKKLIDKEV 180


>gi|146297240|ref|YP_001181011.1| RNA polymerase sigma factor SigY [Caldicellulosiruptor
           saccharolyticus DSM 8903]
 gi|145410816|gb|ABP67820.1| RNA polymerase, sigma subunit, SigY [Caldicellulosiruptor
           saccharolyticus DSM 8903]
          Length = 183

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 15/90 (16%), Positives = 38/90 (42%), Gaps = 3/90 (3%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E  L    ++ G+  A  +L+ S+L ++    +          +VV E  +  +  + K
Sbjct: 2   DEKRLIDEAKK-GNKEALCKLIESNLNILSGFVIKMTTDYHLAQDVVQETLLKAIINIDK 60

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           F P+   + +T+ +       + ++ R+  
Sbjct: 61  FSPD--VKFSTWLIKISINVYKSFLRRNKR 88


>gi|333026072|ref|ZP_08454136.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
 gi|332745924|gb|EGJ76365.1| putative RNA polymerase sigma factor [Streptomyces sp. Tu6071]
          Length = 224

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 12/62 (19%), Positives = 22/62 (35%), Gaps = 2/62 (3%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L+           E       R+ L ++M  L  R+R +   R   +  +T   ++    
Sbjct: 142 LLSKPMPDMASAEEGAYDLLERDDLIKAMRGLQRRQREVLVLRYFAD--MTEAQVAETLG 199

Query: 264 VS 265
           VS
Sbjct: 200 VS 201


>gi|332711579|ref|ZP_08431510.1| RNA polymerase, sigma subunit, ECF family [Lyngbya majuscula 3L]
 gi|332349557|gb|EGJ29166.1| RNA polymerase, sigma subunit, ECF family [Lyngbya majuscula 3L]
          Length = 240

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 21/115 (18%), Positives = 43/115 (37%), Gaps = 17/115 (14%)

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           R+A   SL+A  +  D +       + ++    E    E    +     L +++S L   
Sbjct: 138 RVAHPLSLDAPRHMDDGD-------MDWEIASAEPGPEEDMTTREFYEQLHKAISELPEV 190

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVS----RERVRQIEARAFKKVQESIQKQVE 289
            R     R +    +  E ++     S    + R+    ARA  ++Q  +Q  ++
Sbjct: 191 FRTTIILREI--EGMAYEEIAEITGASLGTVKSRI----ARARARLQSHLQAYLD 239


>gi|326315195|ref|YP_004232867.1| ECF subfamily RNA polymerase sigma-24 subunit [Acidovorax avenae
           subsp. avenae ATCC 19860]
 gi|323372031|gb|ADX44300.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Acidovorax avenae
           subsp. avenae ATCC 19860]
          Length = 198

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 22/155 (14%), Positives = 53/155 (34%), Gaps = 13/155 (8%)

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQ------VVAIAKKLNVSESEVISMNCRLAGDESLNA 188
           L  +   L G L+     +  P +      V  + + +       ++    ++ D +++ 
Sbjct: 21  LVQHYEELVGALRQRFGEDCFPREILNEVCVRLLERPVPQHVENPVAFLRAVSRDLAIDR 80

Query: 189 LINSSDKNSSQWQDWLVYDHDGQE-----QVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
               + +  +  +  L+  H                  +  R  L  +++ L    R +F
Sbjct: 81  HRARARRPETVLEPELLETHASPAAPARLSPPELACAAQQCRRALLSAIADLPEACRDVF 140

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
              +L   P   + ++    +SR  V +  ARA +
Sbjct: 141 VMAKLYGLP--QDEVAQRLGISRSMVARHLARALR 173


>gi|313889127|ref|ZP_07822783.1| conserved hypothetical protein [Peptoniphilus harei
           ACS-146-V-Sch2b]
 gi|312844867|gb|EFR32272.1| conserved hypothetical protein [Peptoniphilus harei
           ACS-146-V-Sch2b]
          Length = 138

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 18/102 (17%), Positives = 50/102 (49%), Gaps = 6/102 (5%)

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           N +  S   +   + D ++ +    E+++    E K +   L R+++ L+  ER + EA 
Sbjct: 43  NVIPFSGLDHDGHFIDNIIDEKIDLEKIV----EVKMQIEELHRALNTLSKEERELMEAI 98

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
             +E   +L ++  + +V+ + +     R  +K+++ ++ ++
Sbjct: 99  FYKEE--SLRSIGKKEKVTHQAISGRRDRILEKLRKILEDKI 138


>gi|299533896|ref|ZP_07047262.1| two component transcriptional regulator, LuxR [Comamonas
           testosteroni S44]
 gi|298718123|gb|EFI59114.1| two component transcriptional regulator, LuxR [Comamonas
           testosteroni S44]
          Length = 199

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 11/59 (18%), Positives = 22/59 (37%), Gaps = 3/59 (5%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             +  ML      L PRE  +     ++    +L  ++     S + V   +  A +K+
Sbjct: 124 SLQHQMLQERFKSLTPREFEVLR-YYVRGG--SLAEIAERLNRSIKTVSSQKMTAMRKL 179


>gi|290961366|ref|YP_003492548.1| sigma factor [Streptomyces scabiei 87.22]
 gi|260650892|emb|CBG74009.1| putative sigma factor [Streptomyces scabiei 87.22]
          Length = 184

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 12/74 (16%), Positives = 29/74 (39%), Gaps = 2/74 (2%)

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           +  E    +       R ++  +++ L  R+R +   R  ++ P     ++     S   
Sbjct: 85  EPPESGAADGAAGVELRLVMRGALARLTARQRTVLVLRYFEDLPEG--EVARILGCSVGT 142

Query: 269 VRQIEARAFKKVQE 282
           VR    R+  +++E
Sbjct: 143 VRSTTHRSLARLRE 156


>gi|254446672|ref|ZP_05060148.1| RNA polymerase sigma factor, sigma-70 family [Verrucomicrobiae
           bacterium DG1235]
 gi|198260980|gb|EDY85288.1| RNA polymerase sigma factor, sigma-70 family [Verrucomicrobiae
           bacterium DG1235]
          Length = 186

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 18/89 (20%), Positives = 38/89 (42%), Gaps = 5/89 (5%)

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
            S+  + L YD          +  R++ +N +  +   L P  R     + + +  +++E
Sbjct: 92  DSKPTESLEYDIASSSDTPDVEASREDEKNWVWEAAKNLKPDFREALSLKYVDD--LSIE 149

Query: 257 NLSSEFEVSRERVRQIEARA---FKKVQE 282
            +S     S+  V+ I  RA    KK+++
Sbjct: 150 EISRVMGKSQTNVKIILFRARNHLKKLRK 178


>gi|121488751|emb|CAJ18260.1| sigma 70-type sigma factor [Chlorobaculum parvum]
          Length = 94

 Score = 37.9 bits (87), Expect = 1.9,   Method: Composition-based stats.
 Identities = 20/100 (20%), Positives = 35/100 (35%), Gaps = 6/100 (6%)

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
           ++      +     +      +A  L++   +V           S++A     D N  + 
Sbjct: 1   KISKAYSQLEQEYERDPNTKELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDN--RL 58

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
            D L  D    +  L     R +    + RS+SVL PRE 
Sbjct: 59  LDVLQNDGHMPDHTL----NRDSLTLEVERSLSVLAPREA 94


>gi|194364912|ref|YP_002027522.1| ECF subfamily RNA polymerase sigma-24 subunit [Stenotrophomonas
           maltophilia R551-3]
 gi|194347716|gb|ACF50839.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Stenotrophomonas
           maltophilia R551-3]
          Length = 175

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 12/79 (15%), Positives = 34/79 (43%), Gaps = 2/79 (2%)

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            +   Q    + + E     ++L +++  L  R R ++   R+     T   ++    ++
Sbjct: 87  DEPTSQSPDPLRQAESGQMLSLLRQALFKLPERAREVYLLNRITGMSYT--QIARHCGIT 144

Query: 266 RERVRQIEARAFKKVQESI 284
            + V +  ARA + +++ +
Sbjct: 145 AKTVEKHIARALQGLRQEL 163


>gi|29832883|ref|NP_827517.1| ECF subfamily RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
 gi|29610004|dbj|BAC74052.1| putative RNA polymerase ECF-subfamily sigma factor [Streptomyces
           avermitilis MA-4680]
          Length = 206

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 10/74 (13%), Positives = 28/74 (37%), Gaps = 2/74 (2%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
              +     +       R ++  +++ L  R+R +   R  ++ P    +++     S  
Sbjct: 106 EPPEASTGPDAASAAELRLVMRGALARLTARQRTVLVLRYFEDLPE--ADVARILGCSVG 163

Query: 268 RVRQIEARAFKKVQ 281
            VR    R+  +++
Sbjct: 164 TVRSTTHRSLARLR 177


>gi|328883416|emb|CCA56655.1| putative RNA polymerase ECF-subfamily sigma factor [Streptomyces
           venezuelae ATCC 10712]
          Length = 195

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 11/62 (17%), Positives = 22/62 (35%), Gaps = 2/62 (3%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L+           E    +  R  L ++M  L  R+R +   R   +  +T   ++    
Sbjct: 113 LLSKPMPDMASAEEGAYDQLEREDLIKAMRGLQRRQREVLALRYFSD--MTEVQVAEALG 170

Query: 264 VS 265
           +S
Sbjct: 171 IS 172


>gi|326801783|ref|YP_004319602.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Sphingobacterium
           sp. 21]
 gi|326552547|gb|ADZ80932.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Sphingobacterium
           sp. 21]
          Length = 198

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 18/87 (20%), Positives = 37/87 (42%), Gaps = 2/87 (2%)

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
            ++ L Y  +       E+    + R  +   M  L  ++R +F+  RL    ++ + ++
Sbjct: 100 LKEHLQYVVNDVSNHTEEQLLLHDLRQCIDDGMKHLPHQQRLVFQLNRL--EGLSYDEIA 157

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQK 286
              ++SR  VR     A K ++  I K
Sbjct: 158 KNLKISRNTVRNHLVSALKTMKIFISK 184


>gi|323342770|ref|ZP_08083002.1| LexA repressor [Erysipelothrix rhusiopathiae ATCC 19414]
 gi|322463882|gb|EFY09076.1| LexA repressor [Erysipelothrix rhusiopathiae ATCC 19414]
          Length = 195

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 6/51 (11%)

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
           IF AR    + ++LE +     VS+  V + EA   KK+  S++KQ  LS 
Sbjct: 9   IFRAR----HELSLEEVGDAVGVSKSTVSRWEAGIIKKI--SLEKQERLSD 53


>gi|254521284|ref|ZP_05133339.1| RNA polymerase sigma-70 factor [Stenotrophomonas sp. SKA14]
 gi|219718875|gb|EED37400.1| RNA polymerase sigma-70 factor [Stenotrophomonas sp. SKA14]
          Length = 139

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 13/58 (22%), Positives = 28/58 (48%), Gaps = 2/58 (3%)

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
             + Q  ++   ++ R   L  +M+ L  R+R  F   R   + +T E +++  ++SR
Sbjct: 34  SDESQCPLQLTAQRQRLQRLADAMAELPERQREAFVLCRF--DGLTQEEVAARMQISR 89


>gi|108759301|ref|YP_630615.1| ECF subfamily RNA polymerase sigma factor [Myxococcus xanthus DK
           1622]
 gi|108463181|gb|ABF88366.1| RNA polymerase sigma-70 factor, ECF subfamily [Myxococcus xanthus
           DK 1622]
          Length = 213

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 26/144 (18%), Positives = 49/144 (34%), Gaps = 13/144 (9%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK----KFDP 95
           R    GD +A   LVT H  LV  +   Y       +++V    +  ++A +    +F P
Sbjct: 32  RAFLEGDPAAFEVLVTRHRSLVFSLVRRYVTRPEDAADLVQSAFLRALEASRRVFARFTP 91

Query: 96  ERGFRLATYSMWWIKAAMQEYILRS---WSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
                   + +  I   + +   R    W  V + +  +               Q   + 
Sbjct: 92  SGPAPFRAWLV-RIALNLAKNHARQVQRWRPVLVASGPDDVVEDP-----SESAQDRLER 145

Query: 153 NLKPEQVVAIAKKLNVSESEVISM 176
             +  QV A    L   + EV+++
Sbjct: 146 AERERQVRAEVLALPRRQREVLTL 169


>gi|53712242|ref|YP_098234.1| RNA polymerase ECF-type sigma factor [Bacteroides fragilis YCH46]
 gi|265768449|ref|ZP_06095581.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 2_1_16]
 gi|52215107|dbj|BAD47700.1| RNA polymerase ECF-type sigma factor [Bacteroides fragilis YCH46]
 gi|263252200|gb|EEZ23754.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 2_1_16]
          Length = 191

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 36/73 (49%), Gaps = 2/73 (2%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E  +  + +  + +  + + +S L PR++ +F   R  E  ++ + ++    +S + V +
Sbjct: 112 EYDIENEMDAADLQGYIKKLISELTPRQQEVFHLSR--EEHLSYKEIAIRLSISEKTVER 169

Query: 272 IEARAFKKVQESI 284
               A K ++++I
Sbjct: 170 HINEALKFLRKNI 182


>gi|330970937|gb|EGH71003.1| RNA polymerase sigma factor [Pseudomonas syringae pv. aceris str.
           M302273PT]
          Length = 172

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 16/75 (21%), Positives = 30/75 (40%), Gaps = 2/75 (2%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L+   + ++    E+         + R +  L+ + R  F   RL         ++ +  
Sbjct: 89  LMQVPEAEQPSPEEQLLIVEDLKAIDRMLGTLSSKARAAFLYSRLDGMSH--AEIAEKLG 146

Query: 264 VSRERVRQIEARAFK 278
           VS  RVRQ  A+A +
Sbjct: 147 VSVSRVRQYLAQAMR 161


>gi|303235251|ref|ZP_07321869.1| sigma-70, region 4 [Finegoldia magna BVS033A4]
 gi|302493565|gb|EFL53353.1| sigma-70, region 4 [Finegoldia magna BVS033A4]
          Length = 136

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 23/93 (24%), Positives = 45/93 (48%), Gaps = 14/93 (15%)

Query: 203 WLVYDHDGQEQVLIEKEER--------KNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
           +  YDHDG  +  +E  E         K     + R++S LNP ER + E+   +E   T
Sbjct: 46  FCSYDHDGNFEENLEDLEFDVEKIIETKEMIEEVRRAISKLNPVERDLVESLFYKEE--T 103

Query: 255 LENLSSEFEVSRERV--RQIEARAFKKVQESIQ 285
           +  ++++  +S   V  R+   +  +K++E ++
Sbjct: 104 IREVAAKLNISHPAVIKRR--NKVLEKLKEMLE 134


>gi|224535939|ref|ZP_03676478.1| hypothetical protein BACCELL_00803 [Bacteroides cellulosilyticus
           DSM 14838]
 gi|224522449|gb|EEF91554.1| hypothetical protein BACCELL_00803 [Bacteroides cellulosilyticus
           DSM 14838]
          Length = 179

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 22/141 (15%), Positives = 53/141 (37%), Gaps = 12/141 (8%)

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCR------LAGDESLNALINSSDKNSSQWQDWL 204
                 E V+ +  KL     +++ +         L  + SLN      ++         
Sbjct: 43  HEEWSQEIVLDVFMKLWEHRKQLLEITNIEDYCFILVKNASLN--YIEKEERRPTLSTET 100

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           +++H  Q     +    +   +   +++  L  R R +F   R++E   T   ++ E  +
Sbjct: 101 LHEHSDQAVSPEDTLISEEFFSRYVKALDRLPERCREVFI--RIREEKQTYAQVAEELGI 158

Query: 265 SRERV-RQIEARAFKKVQESI 284
           S + V  Q++    + ++E +
Sbjct: 159 STKTVDAQLQKATIR-LKEIL 178


>gi|219669349|ref|YP_002459784.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Desulfitobacterium
           hafniense DCB-2]
 gi|219539609|gb|ACL21348.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Desulfitobacterium
           hafniense DCB-2]
          Length = 188

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 17/84 (20%), Positives = 38/84 (45%), Gaps = 2/84 (2%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           + +     + + E   R+ R   L ++++ L  +E+ +   + + E     E L     +
Sbjct: 102 LAEKIPDYEAVEESIIREERIEELGKAIAKLPEKEKDLLYFKYILEMDN--EQLGQILGI 159

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           +   VRQ   R+ +K ++ I K+V
Sbjct: 160 ASASVRQYLTRSRRKAKKLIDKEV 183


>gi|294814530|ref|ZP_06773173.1| Putative RNA polymerase ECF-subfamily sigma factor [Streptomyces
           clavuligerus ATCC 27064]
 gi|294327129|gb|EFG08772.1| Putative RNA polymerase ECF-subfamily sigma factor [Streptomyces
           clavuligerus ATCC 27064]
          Length = 221

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 12/91 (13%), Positives = 30/91 (32%), Gaps = 2/91 (2%)

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
            S+      + +         E+    +      + ++ L   +R +   R      +T 
Sbjct: 133 GSTAVPSDEMPERPDDSLGPEERALLSDDAEWARKLLANLPENQRELLVLRVAVG--LTA 190

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E       +S   VR  + RA  +++   ++
Sbjct: 191 EETGQMLGMSPGAVRVAQHRALSRLRALAEQ 221


>gi|254673641|emb|CBA09198.1| hypothetical protein predicted by Glimmer/Critica [Neisseria
           meningitidis alpha275]
          Length = 34

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 10/23 (43%), Positives = 18/23 (78%)

Query: 267 ERVRQIEARAFKKVQESIQKQVE 289
           ER+RQIEA+A +K++  + ++ E
Sbjct: 10  ERIRQIEAKAMQKLRGFLAEKAE 32


>gi|239946120|ref|ZP_04698057.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces roseosporus
           NRRL 15998]
 gi|239985804|ref|ZP_04706468.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces roseosporus
           NRRL 11379]
 gi|239992594|ref|ZP_04713258.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces roseosporus
           NRRL 11379]
          Length = 534

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 20/82 (24%), Positives = 37/82 (45%), Gaps = 8/82 (9%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV-KKFDPERGFR 100
            + GD  A  +LV+++L L+  +          + +VV E  + +++ + +  DPER   
Sbjct: 13  AQGGDQQAKDQLVSAYLPLLYNVVGRALDGHADVDDVVQETVLRMLRGLPELRDPER--- 69

Query: 101 LATYSMWWIKAAMQEYILRSWS 122
              +  W +  AM E I   W 
Sbjct: 70  ---FRSWLVAIAMNE-IRTHWR 87


>gi|154491941|ref|ZP_02031567.1| hypothetical protein PARMER_01571 [Parabacteroides merdae ATCC
           43184]
 gi|154088182|gb|EDN87227.1| hypothetical protein PARMER_01571 [Parabacteroides merdae ATCC
           43184]
          Length = 196

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 12/51 (23%), Positives = 27/51 (52%), Gaps = 2/51 (3%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
               E   +  E+  N++  +   +S+L PR++ I   R +QE  +++E++
Sbjct: 105 EPTVEDEFVNNEQYNNQQKKVKEILSILTPRQKEIIYYRFIQE--MSMEDI 153


>gi|329939358|ref|ZP_08288694.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
 gi|329301587|gb|EGG45481.1| RNA polymerase sigma factor [Streptomyces griseoaurantiacus M045]
          Length = 166

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 11/62 (17%), Positives = 24/62 (38%), Gaps = 2/62 (3%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L+           E    +  R+ L ++M  L  R+R +   R   +  +T   +++   
Sbjct: 84  LLSKPMPDMASAEEGAYDQLERDSLIKAMKGLQRRQREVLVLRYFAD--MTEAQVAATLG 141

Query: 264 VS 265
           +S
Sbjct: 142 LS 143


>gi|302541651|ref|ZP_07293993.1| RNA polymerase sigma-E factor [Streptomyces hygroscopicus ATCC
           53653]
 gi|302459269|gb|EFL22362.1| RNA polymerase sigma-E factor [Streptomyces himastatinicus ATCC
           53653]
          Length = 184

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 12/60 (20%), Positives = 26/60 (43%), Gaps = 2/60 (3%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
              R ++ R+++ L  R+R +   R  ++ P     ++     S   VR    RA  +++
Sbjct: 102 AELRILVRRALARLTIRQRAMLVLRYFEDCPE--REVAELLGCSVGTVRSTTHRALARLR 159


>gi|238062525|ref|ZP_04607234.1| RNA polymerase ECF-subfamily sigma factor [Micromonospora sp. ATCC
           39149]
 gi|237884336|gb|EEP73164.1| RNA polymerase ECF-subfamily sigma factor [Micromonospora sp. ATCC
           39149]
          Length = 281

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 17/88 (19%), Positives = 41/88 (46%), Gaps = 2/88 (2%)

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
            E+  +++ E++  R++L R +  L  R+R +   R  ++  ++    ++  E+S   V+
Sbjct: 90  PERAAVDEIEQQLDRDVLWRQLRALPSRQRAVLVLRFYED--MSEAQTAALLEISPGTVK 147

Query: 271 QIEARAFKKVQESIQKQVELSSSPPLLQ 298
              +RA   ++  +  Q  L  +    Q
Sbjct: 148 SQTSRALATLRRRLGDQAALGLADGRAQ 175


>gi|169333723|ref|ZP_02860916.1| hypothetical protein ANASTE_00107 [Anaerofustis stercorihominis DSM
           17244]
 gi|169259572|gb|EDS73538.1| hypothetical protein ANASTE_00107 [Anaerofustis stercorihominis DSM
           17244]
          Length = 98

 Score = 37.9 bits (87), Expect = 2.0,   Method: Composition-based stats.
 Identities = 14/68 (20%), Positives = 36/68 (52%), Gaps = 2/68 (2%)

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           E+E  +   + + ++M  L   E++I     +  N +T+  +S E +++RE   +++  A
Sbjct: 27  EEENTRKLMDNINKAMECLTDLEKKIITDFYI--NNLTMYEISLEIQLTREYTSKVKTAA 84

Query: 277 FKKVQESI 284
            +K++  +
Sbjct: 85  IRKMEHVL 92


>gi|307330202|ref|ZP_07609350.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306884108|gb|EFN15146.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 176

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 18/83 (21%), Positives = 37/83 (44%), Gaps = 3/83 (3%)

Query: 201 QDWLVYDHDGQEQVLI-EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
            ++   +    E V   +  ER+  R+ L R++  L  R+R +   R  ++  ++    +
Sbjct: 88  DEFACEELPEPETVPAPDPAERQVVRDALWRAVLRLPDRQRAMVVLRYYED--LSEAQTA 145

Query: 260 SEFEVSRERVRQIEARAFKKVQE 282
               VS   V+   +RA  K++E
Sbjct: 146 EVLGVSVGTVKSAVSRALSKLRE 168


>gi|299134501|ref|ZP_07027694.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Afipia sp. 1NLS2]
 gi|298591248|gb|EFI51450.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Afipia sp. 1NLS2]
          Length = 193

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 11/88 (12%), Positives = 27/88 (30%), Gaps = 10/88 (11%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             D         +      R   + ++++ L   +  I       E P     ++ E  +
Sbjct: 112 PSDEPDMPPSGEDITITAEREEGVRKALASLPSDQATIVRLSFFAEKPH--AEIARELGI 169

Query: 265 S----RERVRQIEARAFKKVQESIQKQV 288
                + RVR     A  +++  +   +
Sbjct: 170 PLGTVKSRVRL----ALNRLRTLLDNNI 193


>gi|297158529|gb|ADI08241.1| RNA polymerase sigma factor [Streptomyces bingchenggensis BCW-1]
          Length = 166

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 11/62 (17%), Positives = 23/62 (37%), Gaps = 2/62 (3%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L+           E    +  R+ L ++M  L  R+R +   R   +  +T   ++    
Sbjct: 84  LLSKPMPDMASAEEGAYEQLERDQLIKAMRGLQRRQREVLVLRYFAD--MTEAQVAETLG 141

Query: 264 VS 265
           +S
Sbjct: 142 IS 143


>gi|206895249|ref|YP_002246620.1| RNA polymerase ECF-type sigma factor [Coprothermobacter
           proteolyticus DSM 5265]
 gi|206737866|gb|ACI16944.1| RNA polymerase ECF-type sigma factor [Coprothermobacter
           proteolyticus DSM 5265]
          Length = 190

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 13/61 (21%), Positives = 29/61 (47%), Gaps = 5/61 (8%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR-QIE--ARAFK 278
           ++   ML  ++  L   +R +   R +   P+  + ++   ++S E VR Q+    +A +
Sbjct: 101 EDMHLMLEMAVMDLPENQRTLIVLRDIYNFPM--KEIARMLDISEENVRVQLHRARKALR 158

Query: 279 K 279
           K
Sbjct: 159 K 159


>gi|86138239|ref|ZP_01056814.1| putative RNA polymerase sigma factor [Roseobacter sp. MED193]
 gi|85825266|gb|EAQ45466.1| putative RNA polymerase sigma factor [Roseobacter sp. MED193]
          Length = 292

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 17/84 (20%), Positives = 33/84 (39%), Gaps = 4/84 (4%)

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
             + L+     + +   E    +     L  +M  L  RER  F  R   +   +   ++
Sbjct: 82  LPEPLIQSETLEPRHPFELA--QECELALLWAMERLTERERAAFILREAFD--ASYAEIA 137

Query: 260 SEFEVSRERVRQIEARAFKKVQES 283
                +    RQ+ +R+ KK+Q+S
Sbjct: 138 DTLGATEASCRQLVSRSQKKLQDS 161


>gi|332799561|ref|YP_004461060.1| ECF subfamily RNA polymerase sigma-24 subunit [Tepidanaerobacter
           sp. Re1]
 gi|332697296|gb|AEE91753.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Tepidanaerobacter
           sp. Re1]
          Length = 189

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 23/139 (16%), Positives = 52/139 (37%), Gaps = 6/139 (4%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           E  L +R +  GD+SA   L++ + + V   A  +        +V  E  I +  ++++F
Sbjct: 4   EKDLVRRAK-RGDISAFEDLISGYEKKVYNTAYRFFNNAEDAMDVSQEIFIKIFTSLRRF 62

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
             +     +T+          +++ +    V       ++    +  +L    +   +  
Sbjct: 63  RED--SSFSTWLYRIAVNTCIDFLRKKREDV---FPIKEEIAMDDKIKLGFQTELPEEFV 117

Query: 154 LKPEQVVAIAKKLNVSESE 172
            K E   AI K ++    E
Sbjct: 118 EKQETKQAIMKAISTLPEE 136


>gi|313676274|ref|YP_004054270.1| RNA polymerase, sigma subunit, ecf family [Marivirga tractuosa DSM
           4126]
 gi|312942972|gb|ADR22162.1| RNA polymerase, sigma subunit, ECF family [Marivirga tractuosa DSM
           4126]
          Length = 200

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 13/81 (16%), Positives = 34/81 (41%), Gaps = 14/81 (17%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS------ 265
           E    + + +K+    L + +S L   ++++   R   +  ++ + +S +  VS      
Sbjct: 117 EGTFEDAQMKKDVHKSLRKLISELPEAQKQVLIMRHYMD--MSFKEISDQTGVSINTALG 174

Query: 266 RERVRQIEARAFKKVQESIQK 286
           R R       A   +++ +Q+
Sbjct: 175 RMR------YALINLRKKMQQ 189


>gi|296448797|ref|ZP_06890646.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Methylosinus
           trichosporium OB3b]
 gi|296253696|gb|EFH00874.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Methylosinus
           trichosporium OB3b]
          Length = 166

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 12/72 (16%), Positives = 31/72 (43%), Gaps = 9/72 (12%)

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
             +  E K    +   ++  L P+ R +F  RR  +  ++ + ++    +SR  V     
Sbjct: 98  PSQICEAKESVRLFYAALKSLPPKCREVFILRRFHD--LSPDEIAQRLGISRNMV----- 150

Query: 275 RAFKKVQESIQK 286
              K ++ ++++
Sbjct: 151 --LKHLRLALER 160


>gi|300780659|ref|ZP_07090514.1| ECF family RNA polymerase sigma factor W [Corynebacterium
           genitalium ATCC 33030]
 gi|300533645|gb|EFK54705.1| ECF family RNA polymerase sigma factor W [Corynebacterium
           genitalium ATCC 33030]
          Length = 179

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 21/93 (22%), Positives = 38/93 (40%), Gaps = 4/93 (4%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           ++  E  L  R  ++GD  A   LV    R +  +AM   G      + +    I   + 
Sbjct: 2   DRDTEKQLVAR-AQNGDEKAFAELVRDANRRMWAVAMSVTGNQHDAEDAMQNAMISAWKN 60

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           +++F PE   R +T+  + I +     I+R   
Sbjct: 61  IERFKPE--ARFSTWL-YRITSNAALDIMRKKR 90


>gi|70732685|ref|YP_262448.1| ECF subfamily RNA polymerase sigma factor [Pseudomonas fluorescens
           Pf-5]
 gi|68346984|gb|AAY94590.1| RNA polymerase sigma-70 factor, ECF subfamily [Pseudomonas
           fluorescens Pf-5]
          Length = 170

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 12/65 (18%), Positives = 28/65 (43%), Gaps = 2/65 (3%)

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
              ++ D + +   L  +   + +R  L +++  L PR + IF   R+    +T   ++ 
Sbjct: 79  PHEVLADIEDEAAGLEAQAMAQQQRKALKQAIMELPPRTQEIFRLNRI--EGMTHAEVAR 136

Query: 261 EFEVS 265
              +S
Sbjct: 137 HLNIS 141


>gi|119717097|ref|YP_924062.1| sigma-70 region 4 domain-containing protein [Nocardioides sp.
           JS614]
 gi|119537758|gb|ABL82375.1| sigma-70 region 4 domain protein [Nocardioides sp. JS614]
          Length = 171

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 13/78 (16%), Positives = 34/78 (43%), Gaps = 13/78 (16%)

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS----RERVRQIEARAFKKV 280
           R  L ++++ L PR+R +   R  ++  +T +  ++   +S    + + R     A  ++
Sbjct: 99  RMALRQALATLAPRQRAVIVLRYYED--LTEKETAAVLGISVGTVKSQAR----DALARL 152

Query: 281 QES---IQKQVELSSSPP 295
           + +   +  + E    P 
Sbjct: 153 RATAPHLDDEREALRPPG 170


>gi|332663972|ref|YP_004446760.1| ECF subfamily RNA polymerase sigma-24 subunit [Haliscomenobacter
           hydrossis DSM 1100]
 gi|332332786|gb|AEE49887.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Haliscomenobacter
           hydrossis DSM 1100]
          Length = 205

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 17/88 (19%), Positives = 38/88 (43%), Gaps = 6/88 (6%)

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
           + R     +L+      ++   ++ + +  +    E+ LI  ++R   R M+ +    LN
Sbjct: 96  HQRKRRLHTLSIDTQVHEEFEGRYSENIRSNTMNPEESLISAQKRALIRTMIAQ----LN 151

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEV 264
            R + I E R  +   +T   +++E  V
Sbjct: 152 ERYQVIVEMRYFEN--LTYAEIAAEMHV 177


>gi|119490024|ref|ZP_01622648.1| hypothetical protein L8106_20630 [Lyngbya sp. PCC 8106]
 gi|119454176|gb|EAW35328.1| hypothetical protein L8106_20630 [Lyngbya sp. PCC 8106]
          Length = 40

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 11/21 (52%), Positives = 17/21 (80%)

Query: 266 RERVRQIEARAFKKVQESIQK 286
           RERVRQIEA+A +K+++  + 
Sbjct: 5   RERVRQIEAKALQKLRQPKRS 25


>gi|119471899|ref|ZP_01614207.1| RNA polymerase sigma factor RpoE [Alteromonadales bacterium TW-7]
 gi|119445272|gb|EAW26562.1| RNA polymerase sigma factor RpoE [Alteromonadales bacterium TW-7]
          Length = 193

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 17/92 (18%), Positives = 34/92 (36%), Gaps = 3/92 (3%)

Query: 32  QEEYVL-AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAV 90
           ++E  L   R  + GD +A + LV  +   +  +   Y      I++V  E  I   +A+
Sbjct: 3   EQELDLVLVRRVQQGDKNAFNLLVKKYQNKIAGLISRYVSNQGDIADVAQEAFIKAYRAL 62

Query: 91  KKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
             F  +      T+         + Y++    
Sbjct: 63  PNFRGD--SAFYTWLYRIAVNCAKNYLVAQGR 92


>gi|60680420|ref|YP_210564.1| putative RNA polymerase ECF-type sigma factor [Bacteroides fragilis
           NCTC 9343]
 gi|60491854|emb|CAH06612.1| putative RNA polymerase ECF-type sigma factor [Bacteroides fragilis
           NCTC 9343]
 gi|301161954|emb|CBW21498.1| putative RNA polymerase ECF-type sigma factor [Bacteroides fragilis
           638R]
          Length = 182

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 13/73 (17%), Positives = 36/73 (49%), Gaps = 2/73 (2%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E  +  + +  + +  + + +S L PR++ +F   R  E  ++ + ++    +S + V +
Sbjct: 103 EYDIENEMDAADLQGYIKKLISELTPRQQEVFHLSR--EEHLSYKEIAIRLSISEKTVER 160

Query: 272 IEARAFKKVQESI 284
               A K ++++I
Sbjct: 161 HINEALKFLRKNI 173


>gi|291301319|ref|YP_003512597.1| ECF subfamily RNA polymerase sigma-24 subunit [Stackebrandtia
           nassauensis DSM 44728]
 gi|290570539|gb|ADD43504.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Stackebrandtia
           nassauensis DSM 44728]
          Length = 292

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 23/108 (21%), Positives = 42/108 (38%), Gaps = 2/108 (1%)

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +     +   R+A + +LN L ++  +  S    WL         +  + E   +    +
Sbjct: 47  TVDSPKAYLVRIASNTALNRLKSAQVQRESYVGPWLPEPILTSPDIAEDVEMADSVSMAM 106

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
              +  L P ER +F  R +   P T   ++S  +     VRQ+  RA
Sbjct: 107 LVVLESLTPEERAVFVLREVFGFPHT--EIASALDRPEASVRQLAHRA 152


>gi|198274484|ref|ZP_03207016.1| hypothetical protein BACPLE_00632 [Bacteroides plebeius DSM 17135]
 gi|198272686|gb|EDY96955.1| hypothetical protein BACPLE_00632 [Bacteroides plebeius DSM 17135]
          Length = 187

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 14/81 (17%), Positives = 39/81 (48%), Gaps = 9/81 (11%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           + Y +     V+   E  + ++ +L+ +++ L  + R++F+   L +     + ++    
Sbjct: 95  IAYYNYENSDVMARMENLEMKKEILS-AINDLPDQSRKVFKMSYLYDMKN--KEIADILG 151

Query: 264 VSRERVRQIEA---RAFKKVQ 281
           +S   +R +EA   +A K ++
Sbjct: 152 IS---LRTVEAHMYKALKILR 169


>gi|325287893|ref|YP_004263683.1| ECF subfamily RNA polymerase sigma-24 subunit [Cellulophaga lytica
           DSM 7489]
 gi|324323347|gb|ADY30812.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Cellulophaga
           lytica DSM 7489]
          Length = 192

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 11/80 (13%), Positives = 33/80 (41%), Gaps = 8/80 (10%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
               +       E K  +  +   ++ L  + +++F   R  +  +T   ++ +  +S  
Sbjct: 104 DLPSDSSQENSVEYKELQQEINSVIATLPDKCKKVFIMSRFDD--LTNAEIAEKLNLS-- 159

Query: 268 RVRQIE---ARAFKKVQESI 284
            +R +E   + A K ++ ++
Sbjct: 160 -IRTVETHISNAIKHLKNNL 178


>gi|163814571|ref|ZP_02205960.1| hypothetical protein COPEUT_00722 [Coprococcus eutactus ATCC 27759]
 gi|158450206|gb|EDP27201.1| hypothetical protein COPEUT_00722 [Coprococcus eutactus ATCC 27759]
          Length = 179

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 23/116 (19%), Positives = 45/116 (38%), Gaps = 17/116 (14%)

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
            +     SL+  +N SD N   W D +  +     +VL + E      + L   ++ L+P
Sbjct: 76  AKAGDQLSLDNTVNDSDGNEKSWLDDMPDESAAIAEVLEDAELL----HALYAKLNELDP 131

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSR-----ERVRQIEARAFKKVQESIQKQV 288
             R I +     ++     +   E  +SR      R      + FKK++  ++  +
Sbjct: 132 EGRLICQLIMQGKSER---DCGKEMGLSRNTFVYRR-----DKLFKKLRSELKDYI 179


>gi|160884738|ref|ZP_02065741.1| hypothetical protein BACOVA_02727 [Bacteroides ovatus ATCC 8483]
 gi|156109773|gb|EDO11518.1| hypothetical protein BACOVA_02727 [Bacteroides ovatus ATCC 8483]
          Length = 201

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 18/83 (21%), Positives = 38/83 (45%), Gaps = 2/83 (2%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           +Y    +  V  E +E+  R   ++++M  L P  + I E   +Q      + ++ E  +
Sbjct: 120 IYSELTKSYVETEYQEQDERMMHISKAMEKLTPHTKHILEECYIQRKKY--QEVAEELNI 177

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           S   VR+   +A + ++E   K+
Sbjct: 178 SVSAVRKHIVKALQVIREECAKK 200


>gi|121594756|ref|YP_986652.1| ECF subfamily RNA polymerase sigma-24 factor [Acidovorax sp. JS42]
 gi|120606836|gb|ABM42576.1| RNA polymerase, sigma subunit, ECF family [Acidovorax sp. JS42]
          Length = 222

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 18/134 (13%), Positives = 50/134 (37%), Gaps = 2/134 (1%)

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
           Q R++  L R+    +   +   +       A      ++++ +   R+A +++L+ L  
Sbjct: 70  QDRIYRFLFRMTRSQEDARELAQETFLNAYQALPRWQPDAQLSTWLFRIARNQALDLLRR 129

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           +      +  + L               + + R   L  ++  L+   R I   R +++ 
Sbjct: 130 AQRVAFVELDETLSEQMPADTPTPEAALQARQRIEALEGALQRLSVEHREILLLRDIED- 188

Query: 252 PVTLENLSSEFEVS 265
            +  E+++    +S
Sbjct: 189 -MAYEDIAEVLGIS 201


>gi|17233327|ref|NP_490417.1| hypothetical protein alr7311 [Nostoc sp. PCC 7120]
 gi|17135849|dbj|BAB78395.1| alr7311 [Nostoc sp. PCC 7120]
          Length = 404

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 20/112 (17%), Positives = 54/112 (48%), Gaps = 12/112 (10%)

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
           +S++    G E+   L    D+ ++ +QD ++ +   QE+V            +L+ +++
Sbjct: 255 VSLDIPAPGQETGELL----DRLTNNFQDSVLDEIIIQEEVENIALRSTEINRVLSDALA 310

Query: 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV-RQIEARAFKKVQESI 284
            L+P+ + + +    QE  +T + ++ +  + +  V RQ       K+++++
Sbjct: 311 KLDPQAQVLLQTYYKQE--LTQQQIAQQLGIKQYTVSRQ-----LTKIKKTL 355


>gi|121997240|ref|YP_001002027.1| Fis family transcriptional regulator [Halorhodospira halophila SL1]
 gi|121588645|gb|ABM61225.1| RNA polymerase, sigma-24 subunit, RpoE [Halorhodospira halophila
           SL1]
          Length = 197

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 26/161 (16%), Positives = 59/161 (36%), Gaps = 14/161 (8%)

Query: 117 ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQ-VVAIAKKLNVSESEVIS 175
           +L  W   +   TA +  +  +L  L G  + +  ++ + E+ +  +  +L     E+++
Sbjct: 4   LLNLWR-RRGEQTAFETVIGRHLGSLYGFARRLCGDDAEAEELIQELLSRLYPRSHELLA 62

Query: 176 MNCRLAGDE-SLNALINSSD---------KNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
           ++        SL+ L              ++ SQ      Y          E  E+   R
Sbjct: 63  LDQPYPWLARSLHNLWVDRYRRRRARPPWEDQSQDDPHAPYTVAEPGDGPAELVEQALTR 122

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
             L R++  L   +R +     +     +L+ ++    VS+
Sbjct: 123 ERLQRALDALPEAQRSVVILHYV--EGFSLDEVAEISAVSK 161


>gi|327541214|gb|EGF27758.1| RNA polymerase ECF-type sigma factor [Rhodopirellula baltica WH47]
          Length = 215

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 10/56 (17%), Positives = 28/56 (50%), Gaps = 2/56 (3%)

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           D +   L+++++     + L   ++ L+PR+ R+ E R      +  + +++E  +
Sbjct: 108 DDEVTFLLDQDDDVVALDELLLQLASLSPRQARVVELRFFGGLGM--KEIAAELNL 161


>gi|323698914|ref|ZP_08110826.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Desulfovibrio sp.
           ND132]
 gi|323458846|gb|EGB14711.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Desulfovibrio
           desulfuricans ND132]
          Length = 182

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 16/73 (21%), Positives = 27/73 (36%), Gaps = 2/73 (2%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           +GD  A   LV  H      +A  + G      ++V    I L+ A  ++   R  R  T
Sbjct: 20  NGDRQAFGELVRRHQSWAWGVAYRFLGSKDEAEDIVQAAFIKLLAASHRYR--RTARFKT 77

Query: 104 YSMWWIKAAMQEY 116
           +    I     ++
Sbjct: 78  FFHVIISRLCLDH 90


>gi|256397960|ref|YP_003119524.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Catenulispora
           acidiphila DSM 44928]
 gi|256364186|gb|ACU77683.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Catenulispora
           acidiphila DSM 44928]
          Length = 298

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 23/110 (20%), Positives = 40/110 (36%), Gaps = 6/110 (5%)

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           +  +  +   R+   ++L  L     +  S    WL         V  + E   +    +
Sbjct: 53  TVRDRRAYLVRITTRQALTQLRKLGRRKESYVGPWLPEPLLTTPDVAEDVELADSVSMAM 112

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTL--ENLSSEFEVSRERVRQIEARA 276
              M  L P ER +F  R    +  +L  E ++   + +   VRQI  RA
Sbjct: 113 LLVMETLTPAERAVFVLR----DVFSLEYEEIAEAVDKTPAAVRQIAHRA 158


>gi|162456180|ref|YP_001618547.1| ECF family RNA polymerase sigma factor [Sorangium cellulosum 'So ce
           56']
 gi|161166762|emb|CAN98067.1| ECF-family RNA polymerase sigma factor [Sorangium cellulosum 'So ce
           56']
          Length = 292

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 45/267 (16%), Positives = 91/267 (34%), Gaps = 79/267 (29%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
            LE  E   +A+      D SA + LV  + R V  +     G      +V  E  + + 
Sbjct: 91  PLEAGEAQFIARLVA--RDESAFNELVIMYERRVFALVYRMLGRRDEAEDVSQEVFVQVF 148

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
           +A+ +F  E   +L+T+                    +I     + R  +  RR      
Sbjct: 149 KAIDQFRGE--SKLSTWIY------------------RIAVNLCKNRTKYLSRR------ 182

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
               +    + V A+A+++ +S ++ +S+     GD S                      
Sbjct: 183 ----HAGAQDDVDAMAERVPLSAAKGVSV-----GDVS---------------------- 211

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNP--RERRIFEARRLQENPVTLENLSSEFEVS 265
                    E  E      ++ R++  L+P  RE  I          ++ E ++S   + 
Sbjct: 212 ------RPDELVEGMQLEAVVKRAIGQLDPEFREALILR----DVEDMSYEEIASVTGLP 261

Query: 266 ----RERVRQIEARAFKKVQESIQKQV 288
               + R+     RA  +++  ++K +
Sbjct: 262 DGTVKSRI----HRARGQLRALVEKMM 284


>gi|167645519|ref|YP_001683182.1| ECF subfamily RNA polymerase sigma-24 factor [Caulobacter sp. K31]
 gi|167347949|gb|ABZ70684.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Caulobacter sp.
           K31]
          Length = 209

 Score = 37.9 bits (87), Expect = 2.1,   Method: Composition-based stats.
 Identities = 11/82 (13%), Positives = 30/82 (36%), Gaps = 10/82 (12%)

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS----RERVR 270
             +          +  ++S L+P++  +       E+P +   ++    +     + R+R
Sbjct: 134 PDDVLSMSEDAERVREALSRLDPQQLEVLRHAFFMESPHS--EIARHLNLPLGTVKSRIR 191

Query: 271 QIEARAFKKVQESIQKQVELSS 292
                A  K++  ++   E S 
Sbjct: 192 ----NAMIKLRLILEPSQEASR 209


>gi|311897059|dbj|BAJ29467.1| putative RNA polymerase ECF subfamily sigma factor [Kitasatospora
           setae KM-6054]
          Length = 190

 Score = 37.9 bits (87), Expect = 2.2,   Method: Composition-based stats.
 Identities = 9/56 (16%), Positives = 19/56 (33%), Gaps = 2/56 (3%)

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
                  E       R+ L  ++  L  R+R +   R   +  +T   ++    +S
Sbjct: 113 PDMASAEEGAYDALERDELKAALRGLQRRQREVLVLRYYAD--LTEAQVAEVLGIS 166


>gi|300785416|ref|YP_003765707.1| RNA polymerase sigma-70 factor, ECF subfamily [Amycolatopsis
           mediterranei U32]
 gi|299794930|gb|ADJ45305.1| RNA polymerase sigma-70 factor, ECF subfamily [Amycolatopsis
           mediterranei U32]
          Length = 225

 Score = 37.9 bits (87), Expect = 2.2,   Method: Composition-based stats.
 Identities = 20/111 (18%), Positives = 38/111 (34%), Gaps = 7/111 (6%)

Query: 163 AKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQV--LIEKEE 220
           AKK    E   +     L GDE  +       +       +  +  +  E      +   
Sbjct: 98  AKKRGTHEKRSVPWTSLLPGDED-HGPTVDPSRFQGPGGAYPGHWRETPEPWASPEKTAL 156

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE--RV 269
               R ++T  +  L  R+R +   R + +   T E + +  ++S    RV
Sbjct: 157 ALEIREIITGVLDELPARQRAVISLRDVGD--HTAEEVCAMLQISAANQRV 205


>gi|255035995|ref|YP_003086616.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Dyadobacter
           fermentans DSM 18053]
 gi|254948751|gb|ACT93451.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Dyadobacter
           fermentans DSM 18053]
          Length = 206

 Score = 37.9 bits (87), Expect = 2.2,   Method: Composition-based stats.
 Identities = 17/117 (14%), Positives = 40/117 (34%), Gaps = 15/117 (12%)

Query: 148 AITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD 207
            + +N  +  ++ ++   L  S    +  + R    ESL+              + +   
Sbjct: 69  ELWENREQLPEIRSLRFYLLKSLRYKLVKHLRFEQSESLDD-------------ERMETH 115

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
            D  E   + +E    +   L  +++ L  R++     R   E  +  E ++    V
Sbjct: 116 DDHFENQTVRQETLTRQSKQLETALAQLPKRQQEAIHLRFFHE--LNNEEVARIMGV 170


>gi|121488739|emb|CAJ18253.1| sigma 70-type sigma factor [Chlorobaculum limnaeum]
          Length = 95

 Score = 37.9 bits (87), Expect = 2.2,   Method: Composition-based stats.
 Identities = 20/101 (19%), Positives = 35/101 (34%), Gaps = 6/101 (5%)

Query: 141 RLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW 200
           ++      +     +      +A  L++   +V           S++A     D N  + 
Sbjct: 1   KISKAYSQLEQEYERDPNTKELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDN--RL 58

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
            D L  D    +  L     R +    + RS+SVL PRE  
Sbjct: 59  LDVLQNDGHMPDHGL----NRDSLTLEVERSLSVLAPREAD 95


>gi|167038926|ref|YP_001661911.1| ribokinase-like domain-containing protein [Thermoanaerobacter sp.
           X514]
 gi|166853166|gb|ABY91575.1| PfkB domain protein [Thermoanaerobacter sp. X514]
          Length = 380

 Score = 37.5 bits (86), Expect = 2.2,   Method: Composition-based stats.
 Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 3/36 (8%)

Query: 235 LNPRERRIFEARRLQENPV-TLENLSSEFEVSRERV 269
           L  RE+ I   R +++NP+ + E L+    +SR  V
Sbjct: 16  LTQREKEIL--RFIKKNPMISQEELAQLMGISRSAV 49


>gi|89897260|ref|YP_520747.1| putative RNA polymerase sigma factor SigI [Desulfitobacterium
           hafniense Y51]
 gi|89336708|dbj|BAE86303.1| hypothetical protein [Desulfitobacterium hafniense Y51]
          Length = 245

 Score = 37.5 bits (86), Expect = 2.2,   Method: Composition-based stats.
 Identities = 16/97 (16%), Positives = 38/97 (39%), Gaps = 12/97 (12%)

Query: 29  LEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK----IAMGYRGYGLPISEVVSEGNI 84
           L   +  +LA    ++GD      L+ +H   ++K    I   Y  +G    + +S   +
Sbjct: 17  LTIDQALLLA----QNGDERIREELIENHKAFIIKTSSNICKRYLTWGND--DELSIALV 70

Query: 85  GLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSW 121
              +A+  ++ E      +++   I   + +Y  +  
Sbjct: 71  AFNEAIDSYNGE--ASFYSFAKTVISRRLIDYFRKES 105


>gi|326381881|ref|ZP_08203574.1| RNA polymerase sigma factor SigD [Gordonia neofelifaecis NRRL
           B-59395]
 gi|326199307|gb|EGD56488.1| RNA polymerase sigma factor SigD [Gordonia neofelifaecis NRRL
           B-59395]
          Length = 191

 Score = 37.5 bits (86), Expect = 2.2,   Method: Composition-based stats.
 Identities = 18/89 (20%), Positives = 38/89 (42%), Gaps = 6/89 (6%)

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
           +  +     +   +G EQ  +E +  +  R++L    S L  ++R I   R +    ++ 
Sbjct: 102 DPVEDVPDSLDFGNGPEQAALESDASRQMRDLL----STLPEKQREILVLRLVVG--LSA 155

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESI 284
           E  +     S   VR  + RA  K+++ +
Sbjct: 156 EETAEMVGSSPGAVRVAQHRALTKLKKLM 184


>gi|229096288|ref|ZP_04227261.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           Rock3-29]
 gi|229102401|ref|ZP_04233109.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           Rock3-28]
 gi|229115242|ref|ZP_04244652.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           Rock1-3]
 gi|228668382|gb|EEL23814.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           Rock1-3]
 gi|228681048|gb|EEL35217.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           Rock3-28]
 gi|228687248|gb|EEL41153.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           Rock3-29]
          Length = 188

 Score = 37.5 bits (86), Expect = 2.2,   Method: Composition-based stats.
 Identities = 9/59 (15%), Positives = 24/59 (40%), Gaps = 2/59 (3%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           H   ++   ++      R  L   ++ L P ++++F  + L       E +  +  ++R
Sbjct: 104 HISTKKSAEDELIVMEDREELLNLINQLEPLDQKVFIMKYLLGMKT--EEIGDKLGLTR 160


>gi|107099140|ref|ZP_01363058.1| hypothetical protein PaerPA_01000149 [Pseudomonas aeruginosa PACS2]
          Length = 195

 Score = 37.5 bits (86), Expect = 2.2,   Method: Composition-based stats.
 Identities = 21/112 (18%), Positives = 43/112 (38%), Gaps = 6/112 (5%)

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              E+ S   R A + +++  +        Q  DWL     G+     +  E  ++   +
Sbjct: 70  PVEELGSYLLRSARNLAID-HLRGEGSRQRQLDDWLPEQRQGEPVGPEQALEAGDQWRRV 128

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++  L  R RRIF   R+  +  T   ++   ++S+  V   E    + +
Sbjct: 129 EAALRGLPERTRRIFLLNRI--HGRTYAEIAQAMQLSQSAV---EKHMMRAL 175


>gi|326333947|ref|ZP_08200177.1| RNA polymerase sigma-E factor [Nocardioidaceae bacterium Broad-1]
 gi|325948226|gb|EGD40336.1| RNA polymerase sigma-E factor [Nocardioidaceae bacterium Broad-1]
          Length = 159

 Score = 37.5 bits (86), Expect = 2.2,   Method: Composition-based stats.
 Identities = 12/77 (15%), Positives = 29/77 (37%), Gaps = 2/77 (2%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
                +   +     +  + L  ++  L PR+R++   R   +     E    E  ++R 
Sbjct: 77  ETAVPETPEQLPRDDSSFDDLLEAVRRLPPRQRQVVALRYFLDLDA--ETTGHELGIARG 134

Query: 268 RVRQIEARAFKKVQESI 284
            V     +A K +++ +
Sbjct: 135 TVSATLHQALKTLRQRL 151


>gi|310644156|ref|YP_003948914.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
 gi|309249106|gb|ADO58673.1| RNA polymerase sigma factor [Paenibacillus polymyxa SC2]
          Length = 188

 Score = 37.5 bits (86), Expect = 2.2,   Method: Composition-based stats.
 Identities = 22/148 (14%), Positives = 49/148 (33%), Gaps = 3/148 (2%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R  + GD  A   LV  +   +  ++    G      ++V E  + + + ++K+  + G 
Sbjct: 10  RLVQKGDQRAFAELVELYKDRIFHLSYRMLGNRHEAEDLVQETFLRVYRNLEKY--DHGQ 67

Query: 100 RLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQV 159
           + +T+          + + R      +    N +        L         + L  E  
Sbjct: 68  KFSTWIYRIATNLCIDRLRRRKPTYSLDAEMNDQEGVDGYAMLASEELTPEGSTLLSETQ 127

Query: 160 VAIAKKLNVSESEVIS-MNCRLAGDESL 186
             I   ++    +  + M  R   + SL
Sbjct: 128 ALIHDAIDSLPDKYKTIMVLRYLQELSL 155


>gi|298241360|ref|ZP_06965167.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297554414|gb|EFH88278.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 189

 Score = 37.5 bits (86), Expect = 2.2,   Method: Composition-based stats.
 Identities = 16/87 (18%), Positives = 32/87 (36%), Gaps = 2/87 (2%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
             SS  +   V + D   Q+  +   R      L   +  LN  +R + + R + +    
Sbjct: 90  DQSSIDEIIGVLEEDNIYQLPEQLTLRYEDYARLRTHIRKLNALQREVLQLRFVYDMHSV 149

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQ 281
              +      +   +R I +RA  K++
Sbjct: 150 --EIGKRLNKNASAIRAILSRALNKLR 174


>gi|258622351|ref|ZP_05717376.1| RNA polymerase sigma-E factor [Vibrio mimicus VM573]
 gi|258585367|gb|EEW10091.1| RNA polymerase sigma-E factor [Vibrio mimicus VM573]
          Length = 190

 Score = 37.5 bits (86), Expect = 2.2,   Method: Composition-based stats.
 Identities = 18/88 (20%), Positives = 33/88 (37%), Gaps = 3/88 (3%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
            VL +R + +GD  A + LV  +   V  +   Y      +++V  E  I   +A+  F 
Sbjct: 8   QVLIERVQ-NGDKQAFNLLVLRYKNKVCNLISRYVSNSGDVADVAQEAFIKAYRAIPTFR 66

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWS 122
            E      T+         + +I+    
Sbjct: 67  GE--SAFYTWLYRIAVNTAKNHIVAQSR 92


>gi|258511574|ref|YP_003185008.1| putative signal transduction protein with CBS domains
           [Alicyclobacillus acidocaldarius subsp. acidocaldarius
           DSM 446]
 gi|257478300|gb|ACV58619.1| putative signal transduction protein with CBS domains
           [Alicyclobacillus acidocaldarius subsp. acidocaldarius
           DSM 446]
          Length = 238

 Score = 37.5 bits (86), Expect = 2.2,   Method: Composition-based stats.
 Identities = 15/66 (22%), Positives = 29/66 (43%), Gaps = 1/66 (1%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           +Y+ D ++ +  +  E    R +L      L PR++ I         P+T + ++    V
Sbjct: 1   MYNRDTRDPIRGQAVECPPGRLLLGERPIELTPRQKEILRL-VQAHQPITGDQIAEMLGV 59

Query: 265 SRERVR 270
           SR  +R
Sbjct: 60  SRPTIR 65


>gi|224540336|ref|ZP_03680875.1| hypothetical protein BACCELL_05249 [Bacteroides cellulosilyticus
           DSM 14838]
 gi|224518053|gb|EEF87158.1| hypothetical protein BACCELL_05249 [Bacteroides cellulosilyticus
           DSM 14838]
          Length = 200

 Score = 37.5 bits (86), Expect = 2.2,   Method: Composition-based stats.
 Identities = 12/79 (15%), Positives = 37/79 (46%), Gaps = 6/79 (7%)

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
           N  + ++ ++       +    +    + +++++ ++  L PR+R IFE  R  E  ++ 
Sbjct: 94  NEEKLKESILSQALDYTEDTKREVMLNDLKSLISHALQQLTPRQREIFEMSR--EAQLSH 151

Query: 256 ENLSSEFEVS----RERVR 270
           + ++ +  +S    +E + 
Sbjct: 152 KEIADKLGISINTVQEHIS 170


>gi|170756909|ref|YP_001781250.1| putative RNA polymerase sigma factor [Clostridium botulinum B1 str.
           Okra]
 gi|169122121|gb|ACA45957.1| RNA polymerase sigma factor, sigma-70 family [Clostridium botulinum
           B1 str. Okra]
          Length = 176

 Score = 37.5 bits (86), Expect = 2.2,   Method: Composition-based stats.
 Identities = 23/100 (23%), Positives = 48/100 (48%), Gaps = 5/100 (5%)

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE--ERKNRRNMLTRSMSVLNPRERRIFEA 245
           AL+    K+  +  D  + D   +    IE E    +N +  L +++  L P E+ + ++
Sbjct: 80  ALLKGEIKHHREVPDENILDKGNEYFFTIEDEIIAYENIKE-LYKALDKLTPEEKEVIDS 138

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             ++ N  +L+ ++S    S   VR  + +A KK+Q  ++
Sbjct: 139 FYIKNN--SLQEIASYTNKSYNSVRYTKEKAIKKLQNMLE 176


>gi|188586672|ref|YP_001918217.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Natranaerobius
           thermophilus JW/NM-WN-LF]
 gi|179351359|gb|ACB85629.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Natranaerobius
           thermophilus JW/NM-WN-LF]
          Length = 176

 Score = 37.5 bits (86), Expect = 2.2,   Method: Composition-based stats.
 Identities = 17/78 (21%), Positives = 34/78 (43%), Gaps = 3/78 (3%)

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
               +    +    M+ R++ VL   +R + E R +    +T +  + +   S   VR +
Sbjct: 96  DNPEQLALIEEENEMIKRALGVLPEEQRLVIELRFV--EGLTTKETAIQLLKSPGSVRSL 153

Query: 273 EARAFKKVQESI-QKQVE 289
           + RA K ++  I + Q E
Sbjct: 154 QHRAIKNLKNIITRNQAE 171


>gi|113955532|ref|YP_730699.1| RNA polymerase sigma-70 factor family protein [Synechococcus sp.
           CC9311]
 gi|113882883|gb|ABI47841.1| RNA polymerase sigma-70 factor family protein [Synechococcus sp.
           CC9311]
          Length = 183

 Score = 37.5 bits (86), Expect = 2.2,   Method: Composition-based stats.
 Identities = 16/67 (23%), Positives = 34/67 (50%), Gaps = 2/67 (2%)

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           + R  L R+++ L+ RE++I      Q+  ++  N++    +    V+ I  RA  K++ 
Sbjct: 118 DARYQLERALAQLSSREQQILAMNYHQD--ISQSNIAESLHLPLGTVKTISRRALLKLRN 175

Query: 283 SIQKQVE 289
           ++  Q E
Sbjct: 176 ALSSQEE 182


>gi|167038342|ref|YP_001665920.1| ribokinase-like domain-containing protein [Thermoanaerobacter
           pseudethanolicus ATCC 33223]
 gi|166857176|gb|ABY95584.1| PfkB domain protein [Thermoanaerobacter pseudethanolicus ATCC
           33223]
          Length = 380

 Score = 37.5 bits (86), Expect = 2.2,   Method: Composition-based stats.
 Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 3/36 (8%)

Query: 235 LNPRERRIFEARRLQENPV-TLENLSSEFEVSRERV 269
           L  RE+ I   R +++NP+ + E L+    +SR  V
Sbjct: 16  LTQREKEIL--RFIKKNPMISQEELAQLMGISRSAV 49


>gi|332532641|ref|ZP_08408517.1| RNA polymerase sigma factor RpoE [Pseudoalteromonas haloplanktis
           ANT/505]
 gi|332037857|gb|EGI74306.1| RNA polymerase sigma factor RpoE [Pseudoalteromonas haloplanktis
           ANT/505]
          Length = 193

 Score = 37.5 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 18/93 (19%), Positives = 36/93 (38%), Gaps = 5/93 (5%)

Query: 32  QEEYVLA--KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           ++E  L   KR ++ GD +A + LV  +   +  +   Y      I++V  E  I   +A
Sbjct: 3   EQELDLVLVKRVQQ-GDKNAFNLLVKKYQNKIAGLISRYVSNQGDIADVAQEAFIKAYRA 61

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           +  F  +      T+         + Y++    
Sbjct: 62  LPNFRGD--SAFYTWLYRIAVNCAKNYLVAQGR 92


>gi|240142555|ref|YP_002967068.1| hypothetical protein MexAM1_META2p0912 [Methylobacterium extorquens
           AM1]
 gi|240012502|gb|ACS43727.1| hypothetical protein MexAM1_META2p0912 [Methylobacterium extorquens
           AM1]
          Length = 390

 Score = 37.5 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 20/160 (12%), Positives = 52/160 (32%), Gaps = 13/160 (8%)

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +  T  + +     L       +A       PE   +I  +      +    +  +    
Sbjct: 186 RRPTEFSVRDWLTQLAFETVEAEAQAARRAVPEDAASIEAEPEAPAEDPTEADQAM---- 241

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
                           +D +  D     +  +++ +       L R+++ L P ERR+  
Sbjct: 242 ----FEFYQPDEVLMLEDLIADDGGTDPETEVDRHDIAM---ALHRAIADLAPVERRVLY 294

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              L++   T+   +    ++   V +I   A + ++ ++
Sbjct: 295 RMYLED--ATIAETAHLLGLTEAEVLKIAENAAETLRGTL 332


>gi|220928252|ref|YP_002505161.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           cellulolyticum H10]
 gi|219998580|gb|ACL75181.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           cellulolyticum H10]
          Length = 184

 Score = 37.5 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 18/79 (22%), Positives = 30/79 (37%), Gaps = 6/79 (7%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           +GD SA   +V  + RLV  +          + +V  E  I L +++ K++PE       
Sbjct: 14  NGDSSAFEEIVIRYKRLVYSVVYKMISDKEEVHDVCQEVFIRLYRSLDKYNPEFKM---- 69

Query: 104 YSMWWIKAAMQEYILRSWS 122
               WI        L +  
Sbjct: 70  --STWIVKITSNLCLDTLR 86


>gi|313820246|gb|EFS57960.1| hypothetical protein HMPREF9604_01864 [Propionibacterium acnes
           HL036PA1]
          Length = 38

 Score = 37.5 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 10/34 (29%), Positives = 21/34 (61%)

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +T+  ++ E  +S   VR+IE RA  +++  +Q+
Sbjct: 1   MTITAVAHELGLSASNVRRIEQRALGRLRRHLQQ 34


>gi|300913484|ref|ZP_07130801.1| transcriptional regulator, MarR family [Thermoanaerobacter sp.
           X561]
 gi|307723501|ref|YP_003903252.1| MarR family transcriptional regulator [Thermoanaerobacter sp. X513]
 gi|300890169|gb|EFK85314.1| transcriptional regulator, MarR family [Thermoanaerobacter sp.
           X561]
 gi|307580562|gb|ADN53961.1| transcriptional regulator, MarR family [Thermoanaerobacter sp.
           X513]
          Length = 367

 Score = 37.5 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 3/36 (8%)

Query: 235 LNPRERRIFEARRLQENPV-TLENLSSEFEVSRERV 269
           L  RE+ I   R +++NP+ + E L+    +SR  V
Sbjct: 3   LTQREKEIL--RFIKKNPMISQEELAQLMGISRSAV 36


>gi|257414097|ref|ZP_04745221.2| sigma-70, region 4 subfamily [Roseburia intestinalis L1-82]
 gi|257201243|gb|EEU99527.1| sigma-70, region 4 subfamily [Roseburia intestinalis L1-82]
          Length = 198

 Score = 37.5 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 12/86 (13%), Positives = 36/86 (41%), Gaps = 6/86 (6%)

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
           Y  D + +   +   ++    +L  ++  L    R+I          +T   +  +  +S
Sbjct: 112 YFQDEEAEPSYQMAGKEITPKLLLEAIRALPEERRKIVLMYYF--EGLTDVEIGKQLNIS 169

Query: 266 RERV--RQIEARAFKKVQESIQKQVE 289
           R  V  R+    +F+++++ +++  +
Sbjct: 170 RSTVQYRR--TSSFEQLKKYLEENAD 193


>gi|295837991|ref|ZP_06824924.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces sp. SPB74]
 gi|197699457|gb|EDY46390.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces sp. SPB74]
          Length = 193

 Score = 37.5 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 12/62 (19%), Positives = 22/62 (35%), Gaps = 2/62 (3%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L+           E       R+ L ++M  L  R+R +   R   +  +T   ++    
Sbjct: 111 LLSKPMPDMASAEEGAYDLLERDDLIKAMRGLQRRQREVLVLRYFAD--MTEAQVAETLG 168

Query: 264 VS 265
           VS
Sbjct: 169 VS 170


>gi|254385603|ref|ZP_05000928.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces sp. Mg1]
 gi|194344473|gb|EDX25439.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces sp. Mg1]
          Length = 167

 Score = 37.5 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 12/62 (19%), Positives = 23/62 (37%), Gaps = 2/62 (3%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L+           E    +  R+ L ++M  L  R+R +   R   +  +T   ++    
Sbjct: 84  LLSKPMPDMASAEEGAYDQLERDDLIKAMRGLQRRQREVLVLRYFAD--MTESQVAETLG 141

Query: 264 VS 265
           VS
Sbjct: 142 VS 143


>gi|167759537|ref|ZP_02431664.1| hypothetical protein CLOSCI_01887 [Clostridium scindens ATCC 35704]
 gi|167662847|gb|EDS06977.1| hypothetical protein CLOSCI_01887 [Clostridium scindens ATCC 35704]
          Length = 139

 Score = 37.5 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 12/59 (20%), Positives = 28/59 (47%), Gaps = 2/59 (3%)

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
             L  ++  L+ ++R +   R  Q   ++ + +S  + VSR  + +  +   KK++  I
Sbjct: 79  EKLAVALHKLSEKQRSVILLRYFQG--MSDQEISELYHVSRSAIYRRRSNGLKKLKALI 135


>gi|160914381|ref|ZP_02076596.1| hypothetical protein EUBDOL_00385 [Eubacterium dolichum DSM 3991]
 gi|158433539|gb|EDP11828.1| hypothetical protein EUBDOL_00385 [Eubacterium dolichum DSM 3991]
          Length = 135

 Score = 37.5 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 10/91 (10%), Positives = 39/91 (42%), Gaps = 6/91 (6%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
            +     D++  +     + ++         + L  ++ +L+  E+ + +A     + ++
Sbjct: 50  DSEGNPLDFITDEAVDIAETVVNAVMV----DRLKAALPLLSDSEQELIQAIFF--DGLS 103

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              + +   +++  V + +AR   K+++ I+
Sbjct: 104 EREVGARLGITQSVVNKRKARILIKLRKIIE 134


>gi|154493953|ref|ZP_02033273.1| hypothetical protein PARMER_03297 [Parabacteroides merdae ATCC
           43184]
 gi|154086213|gb|EDN85258.1| hypothetical protein PARMER_03297 [Parabacteroides merdae ATCC
           43184]
          Length = 185

 Score = 37.5 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 10/77 (12%), Positives = 37/77 (48%), Gaps = 6/77 (7%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            + +    +++ +  ++  ML  +++ L P ER I     ++E   T++ +++   ++  
Sbjct: 105 SEQEVAEALDRTDSSDQIQMLDAALAQLPPDERAIILLFYMKE--KTIDEVATITGLTA- 161

Query: 268 RVRQIEARAFKKVQESI 284
               I+ +   ++++ +
Sbjct: 162 --SNIKVK-LHRIRKKL 175


>gi|329961881|ref|ZP_08299895.1| RNA polymerase sigma-70 factor [Bacteroides fluxus YIT 12057]
 gi|328531321|gb|EGF58165.1| RNA polymerase sigma-70 factor [Bacteroides fluxus YIT 12057]
          Length = 186

 Score = 37.5 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 21/104 (20%), Positives = 46/104 (44%), Gaps = 10/104 (9%)

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
            + + ++  SQ   + +   D     + E EE      +L ++M  L  R R IF   R+
Sbjct: 88  PLKADEELESQLNLYALQQFDEAVSSISEVEE------LLKQTMQKLPERCREIFLLSRI 141

Query: 249 QENPVTLENLSSEFEVSRERVR-QIEARAFKKVQESIQKQVELS 291
           +      + ++   ++S   V  QI + A +K++  +++ + L 
Sbjct: 142 EGLKY--KEIAERLDISVNTVENQI-SIALRKLKSELKEYIPLL 182


>gi|219850683|ref|YP_002465116.1| ECF subfamily RNA polymerase sigma-24 subunit [Chloroflexus
           aggregans DSM 9485]
 gi|219544942|gb|ACL26680.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Chloroflexus
           aggregans DSM 9485]
          Length = 185

 Score = 37.5 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 16/90 (17%), Positives = 40/90 (44%), Gaps = 4/90 (4%)

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           D + +     +        +++ R M+ R++  L    R +   R   +  ++ E + + 
Sbjct: 99  DDVAFWLPSTQPGPERSALQQSSREMIQRALQRLPAMYRSVIVLRYWHD--LSYEEIGTI 156

Query: 262 FEVSRERVR-QIEARAFKKVQESIQKQVEL 290
             ++   V+ ++  RA K +QE++  + EL
Sbjct: 157 LGLTEATVKTRLH-RARKMLQEALAMEEEL 185


>gi|302543543|ref|ZP_07295885.1| RNA polymerase sigma-E factor [Streptomyces hygroscopicus ATCC
           53653]
 gi|302461161|gb|EFL24254.1| RNA polymerase sigma-E factor [Streptomyces himastatinicus ATCC
           53653]
          Length = 205

 Score = 37.5 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 15/83 (18%), Positives = 36/83 (43%), Gaps = 2/83 (2%)

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
            E  + +  E+   R +L   + VL P++R +   R      +T E  +    +S   V+
Sbjct: 90  PEASVEDGTEQHADRALLMDILGVLAPKQRSVVVLR--HWEQMTTEETAEALGMSTGTVK 147

Query: 271 QIEARAFKKVQESIQKQVELSSS 293
               RA  ++++ ++ +   + +
Sbjct: 148 STLHRALARLRQELESRELDARA 170


>gi|184154740|ref|YP_001843080.1| RNA polymerase sigma-30 factor [Lactobacillus fermentum IFO 3956]
 gi|227514007|ref|ZP_03944056.1| RNA polymerase sigma-30 factor [Lactobacillus fermentum ATCC 14931]
 gi|260663231|ref|ZP_05864123.1| RNA polymerase sigma-30 factor [Lactobacillus fermentum 28-3-CHN]
 gi|183226084|dbj|BAG26600.1| RNA polymerase sigma-30 factor [Lactobacillus fermentum IFO 3956]
 gi|227087651|gb|EEI22963.1| RNA polymerase sigma-30 factor [Lactobacillus fermentum ATCC 14931]
 gi|260552423|gb|EEX25474.1| RNA polymerase sigma-30 factor [Lactobacillus fermentum 28-3-CHN]
          Length = 192

 Score = 37.5 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 20/105 (19%), Positives = 38/105 (36%), Gaps = 1/105 (0%)

Query: 29  LEKQEEYVLA-KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           L  +E   LA       GD      L   +  LV ++ + Y    L   +   E  + L 
Sbjct: 6   LSDEERVELALINGATKGDNETLGELFDRYQPLVRRLWLNYSIANLDRQDWQQEAFLVLD 65

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQ 132
           +AV  +  E+  R   Y    +   +++   ++ +  +I     Q
Sbjct: 66  RAVHNYRQEQRTRFCWYYRQLLTNRLRDLYRQTRAEKRIPAQLVQ 110


>gi|169824672|ref|YP_001692283.1| hypothetical protein FMG_0975 [Finegoldia magna ATCC 29328]
 gi|167831477|dbj|BAG08393.1| hypothetical protein [Finegoldia magna ATCC 29328]
          Length = 138

 Score = 37.5 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 21/93 (22%), Positives = 49/93 (52%), Gaps = 3/93 (3%)

Query: 197 SSQWQDWLVYDHDGQEQVLIEK-EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
           SS   D    D+   E++ +EK  E K +   L ++++ L   ER + EA   +E   +L
Sbjct: 48  SSLDHDGHFVDNIIDEKIDLEKIVEVKMQIEELHKALATLTKEERELMEAIFYREE--SL 105

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            ++S + +V+ + + Q   +  +K+++ ++ ++
Sbjct: 106 RSISRKEKVTHQAIGQRRDQILEKLRKILEDKI 138


>gi|160940646|ref|ZP_02087989.1| hypothetical protein CLOBOL_05540 [Clostridium bolteae ATCC
           BAA-613]
 gi|158436381|gb|EDP14148.1| hypothetical protein CLOBOL_05540 [Clostridium bolteae ATCC
           BAA-613]
          Length = 187

 Score = 37.5 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 16/69 (23%), Positives = 29/69 (42%), Gaps = 5/69 (7%)

Query: 55  TSHLRLVVKIAMGYRGYGLPISE-----VVSEGNIGLMQAVKKFDPERGFRLATYSMWWI 109
             +L LV  +   Y    + I++     +   G + L  A   +DPER    +TY+   I
Sbjct: 14  EEYLHLVDTVISLYITQRIDIADMEYADLYQTGCLALCHAAATYDPEREASFSTYASVVI 73

Query: 110 KAAMQEYIL 118
           +  + +Y  
Sbjct: 74  RNRLYDYCR 82


>gi|296386637|ref|ZP_06876136.1| ECF subfamily RNA polymerase sigma-70 factor [Pseudomonas
           aeruginosa PAb1]
 gi|313112281|ref|ZP_07798050.1| putative sigma-70 factor, ECF subfamily [Pseudomonas aeruginosa
           39016]
 gi|310884552|gb|EFQ43146.1| putative sigma-70 factor, ECF subfamily [Pseudomonas aeruginosa
           39016]
          Length = 195

 Score = 37.5 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 21/112 (18%), Positives = 43/112 (38%), Gaps = 6/112 (5%)

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              E+ S   R A + +++  +        Q  DWL     G+     +  E  ++   +
Sbjct: 70  PVEELGSYLLRSARNLAID-HLRGEGSRQRQLDDWLPEQRQGEPVGPEQALEAGDQWRRV 128

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++  L  R RRIF   R+  +  T   ++   ++S+  V   E    + +
Sbjct: 129 EAALRGLPERTRRIFLLNRI--HGRTYAEIAQAMQLSQSAV---EKHMMRAL 175


>gi|300776378|ref|ZP_07086236.1| RNA polymerase ECF-type sigma factor [Chryseobacterium gleum ATCC
           35910]
 gi|300501888|gb|EFK33028.1| RNA polymerase ECF-type sigma factor [Chryseobacterium gleum ATCC
           35910]
          Length = 163

 Score = 37.5 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 12/80 (15%), Positives = 37/80 (46%), Gaps = 13/80 (16%)

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
             + + +E++ + ++L   +  L   ER I     L + P   ++++    ++       
Sbjct: 91  DFVEDDDEKQQQVSLLYTVIKTLPNVERAIVMM-YLDDLPY--KDIAENLGIT------- 140

Query: 273 EARA---FKKVQESIQKQVE 289
           E  A     ++++++++Q+E
Sbjct: 141 EVNARVKMNRLKKTLKEQME 160


>gi|226363114|ref|YP_002780896.1| RNA polymerase ECF-type sigma factor [Rhodococcus opacus B4]
 gi|226241603|dbj|BAH51951.1| RNA polymerase ECF-type sigma factor [Rhodococcus opacus B4]
          Length = 212

 Score = 37.5 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 38/249 (15%), Positives = 70/249 (28%), Gaps = 66/249 (26%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           E  L    R   D SA   LV  H  +++++A GY        +VV E  I ++Q + +F
Sbjct: 9   EQRLVDSLRAR-DESAFAELVDRHTPMMLRVARGYVASAEVAEDVVQETWIAVLQGIDRF 67

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
           +                       LR+W L +I     +KR   +               
Sbjct: 68  E-------------------GRSTLRTW-LFRILVNIAKKRGIRD--------------- 92

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQ 213
            + +    +A        +      R A                 +             +
Sbjct: 93  -RHDSDAELAAFTGSPTVDPGRFLPRTA----------------PEDPHHWATPPTSWPE 135

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS-------- 265
                       ++ +R +  L  R+R +   R +         +S+   ++        
Sbjct: 136 SPEGSVLGAEVLDVASRELEHLPDRQRIVVVLRDVLGYDA--AEVSAMLSITAANQRVLL 193

Query: 266 ---RERVRQ 271
              R  VRQ
Sbjct: 194 HRGRAHVRQ 202


>gi|32477676|ref|NP_870670.1| ECF subfamily RNA polymerase sigma-70 factor [Rhodopirellula
           baltica SH 1]
 gi|32448230|emb|CAD77747.1| probable sigma-70 factor (ECF subfamily) [Rhodopirellula baltica SH
           1]
          Length = 193

 Score = 37.5 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 13/96 (13%), Positives = 31/96 (32%), Gaps = 2/96 (2%)

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
              D      +  ++   +          L   M  L  R R     R +   P     +
Sbjct: 99  HLSDSPELLDESWQRWAGKDLTGNETVEALRECMESLTERARDALAMRFVHNTPRV--KI 156

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSP 294
                +S    R +  RA  ++++ +++++   + P
Sbjct: 157 GENLGISDHGARNLMQRAKAQLRDCVEEKLRAITQP 192


>gi|288932795|ref|YP_003436855.1| Bacterio-opsin activator HTH domain protein [Ferroglobus placidus
           DSM 10642]
 gi|288895043|gb|ADC66580.1| Bacterio-opsin activator HTH domain protein [Ferroglobus placidus
           DSM 10642]
          Length = 232

 Score = 37.5 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 9/71 (12%)

Query: 228 LTRSMSVLNPRERRIFEA---RRLQENPV--TLENLSSEFEVSRERV----RQIEARAFK 278
           L + +  L   ERRI +A   R   ENP    +  L+ EF +S+  V    R+ E +  +
Sbjct: 162 LMKEIENLTLTERRILKAAIKRGFYENPRKVNVTQLAKEFGISKAGVSKNIRRAEKKILR 221

Query: 279 KVQESIQKQVE 289
            +++ +  + E
Sbjct: 222 HIEKILSLERE 232


>gi|239939770|ref|ZP_04691707.1| LuxR family transcriptional regulator [Streptomyces roseosporus
           NRRL 15998]
 gi|239986253|ref|ZP_04706917.1| LuxR family transcriptional regulator [Streptomyces roseosporus
           NRRL 11379]
          Length = 887

 Score = 37.5 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 18/64 (28%), Positives = 37/64 (57%), Gaps = 5/64 (7%)

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           +++S L+ +ERR+ E   L     T + ++ +  +++  V Q   R F+K+  ++Q++ E
Sbjct: 828 KALSALSKQERRVAE---LASEGYTNQEIADQLFITKSTVEQHLTRVFRKL--NVQRRQE 882

Query: 290 LSSS 293
           LS S
Sbjct: 883 LSQS 886


>gi|124010047|ref|ZP_01694709.1| RNA polymerase ECF-type sigma factor [Microscilla marina ATCC
           23134]
 gi|123983934|gb|EAY24329.1| RNA polymerase ECF-type sigma factor [Microscilla marina ATCC
           23134]
          Length = 203

 Score = 37.5 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 19/86 (22%), Positives = 44/86 (51%), Gaps = 8/86 (9%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           H  +   + E       +++L+++++ L  R   IF   R+    ++ + ++ +  +S++
Sbjct: 113 HIAENATVEEAMHNAELQHVLSQAIAALPKRCSEIFTLTRI--EGLSYQQVADQLGISKK 170

Query: 268 RVRQIEAR---AFKKVQESIQKQVEL 290
            V   EA+   AFKK++  I++  EL
Sbjct: 171 TV---EAQMGIAFKKLRIFIKQHWEL 193


>gi|52786508|ref|YP_092337.1| hypothetical protein BLi02773 [Bacillus licheniformis ATCC 14580]
 gi|52349010|gb|AAU41644.1| putative protein [Bacillus licheniformis ATCC 14580]
          Length = 44

 Score = 37.5 bits (86), Expect = 2.3,   Method: Composition-based stats.
 Identities = 10/29 (34%), Positives = 15/29 (51%)

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKV 280
             T   ++ E  +SR  V +IE RA  K+
Sbjct: 3   KKTQREIAKELGISRCDVSRIEKRALFKM 31


>gi|297159287|gb|ADI08999.1| two component transcriptional regulator, LuxR family protein
           [Streptomyces bingchenggensis BCW-1]
          Length = 225

 Score = 37.5 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 22/115 (19%), Positives = 45/115 (39%), Gaps = 14/115 (12%)

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
           +    +GDE  +A+ ++++  +      LV       +VL    E        T  +  L
Sbjct: 108 LLKSASGDEIADAIRSAAEGETLIPASTLV-------EVLARHRETARSSAQQTERLESL 160

Query: 236 NPRERRIFEAR-RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
            PRE+ I     +  +N      ++    +S   VR    +  +K+   ++ Q+E
Sbjct: 161 TPREQEILTLMSQGLDNRA----VAERLSISYATVRTHVRKILEKL--EVRSQLE 209


>gi|297192633|ref|ZP_06910031.1| RNA polymerase sigma-70 factor [Streptomyces pristinaespiralis ATCC
           25486]
 gi|197722966|gb|EDY66874.1| RNA polymerase sigma-70 factor [Streptomyces pristinaespiralis ATCC
           25486]
          Length = 195

 Score = 37.5 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 13/91 (14%), Positives = 30/91 (32%), Gaps = 2/91 (2%)

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
            S+      + +         E+    +      R ++ L   +R +   R      +T 
Sbjct: 107 GSTAVPSDEMPERPDDSLGPEERALLSDDAEWAKRLLANLPENQRELLVLRVAVG--LTA 164

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E       +S   VR  + RA  +++   ++
Sbjct: 165 EETGQMLGMSPGAVRVAQHRALSRLRALAEQ 195


>gi|167760404|ref|ZP_02432531.1| hypothetical protein CLOSCI_02778 [Clostridium scindens ATCC 35704]
 gi|167661981|gb|EDS06111.1| hypothetical protein CLOSCI_02778 [Clostridium scindens ATCC 35704]
          Length = 399

 Score = 37.5 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 25/175 (14%), Positives = 58/175 (33%), Gaps = 15/175 (8%)

Query: 75  ISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKR 134
             +      + L++ ++ +DP++G    TY+  +I   + +         +   T + K 
Sbjct: 94  FMDYKLSVVLALLECLQNYDPDKGADFLTYAHHFIGNTLLDCR-------RYEETGSFKS 146

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES---EVISMNCRLAGDESLNALIN 191
           L                     E +   A + N +E    E +++  +        + + 
Sbjct: 147 LDEYKAARGSAWLYNNSGKTTKEVITQYAAEQNCTEETAAEYLTLARQNRSRVPFYSTMQ 206

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
             D   +  +D    D     ++L        R + +  +   LN +E+   E R
Sbjct: 207 DEDGEET-GEDVTRDDSWNYAEILWNGI----RADAVQAAFHKLNYQEQDFLEMR 256


>gi|81429289|ref|YP_396290.1| DNA-directed RNA polymerase sigma factor [Lactobacillus sakei
           subsp. sakei 23K]
 gi|78610932|emb|CAI55984.1| Putative DNA-directed RNA polymerase sigma factor, sigma H family
           [Lactobacillus sakei subsp. sakei 23K]
          Length = 186

 Score = 37.5 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 12/102 (11%), Positives = 31/102 (30%), Gaps = 4/102 (3%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L        D  A   L  ++L +V      Y        + + E  I   +  + +D 
Sbjct: 8   ELLISAVAQNDSQALDVLFKAYLPMVYHTLAPYYIRLFDEDDWLQEARIVCYETCQCYDC 67

Query: 96  ERGFRLATYSMWW----IKAAMQEYILRSWSLVKIGTTANQK 133
           ++G    ++        I   ++  + +     +      ++
Sbjct: 68  QKGKSFGSFYKLRFKNHILNLLRRELAQKRRGDRQAVLIAER 109


>gi|302380084|ref|ZP_07268559.1| sigma-70, region 4 [Finegoldia magna ACS-171-V-Col3]
 gi|302312104|gb|EFK94110.1| sigma-70, region 4 [Finegoldia magna ACS-171-V-Col3]
          Length = 163

 Score = 37.5 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 23/93 (24%), Positives = 46/93 (49%), Gaps = 14/93 (15%)

Query: 203 WLVYDHDGQEQVLIEKEER--------KNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
           +  YDHDG  +  +E  E         K     + R++S LNP ER + E+   +E   T
Sbjct: 73  FCSYDHDGNFEENLEDLEFDVEKIIETKEMIEEVRRAISKLNPAERDLIESLFYKEE--T 130

Query: 255 LENLSSEFEVSRERV--RQIEARAFKKVQESIQ 285
           + +++++  +S   V  R+   +  +K++E ++
Sbjct: 131 IRDVAAKLNISHPAVIKRR--NKVLEKLKEMLE 161


>gi|261879671|ref|ZP_06006098.1| conserved hypothetical protein [Prevotella bergensis DSM 17361]
 gi|270333691|gb|EFA44477.1| conserved hypothetical protein [Prevotella bergensis DSM 17361]
          Length = 170

 Score = 37.5 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 10/71 (14%), Positives = 34/71 (47%), Gaps = 2/71 (2%)

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
           +L +  +   + +++ ++M  ++PR R + E    +        ++    +S++ VR+  
Sbjct: 95  LLDDDTDGNEQMDVIYKTMEKMSPRTRLVVEQCYFENMKY--AEVADLLGLSKDGVRKHI 152

Query: 274 ARAFKKVQESI 284
            +A   ++++ 
Sbjct: 153 IKALAMLRKAF 163


>gi|256751073|ref|ZP_05491955.1| PfkB domain protein [Thermoanaerobacter ethanolicus CCSD1]
 gi|256749979|gb|EEU63001.1| PfkB domain protein [Thermoanaerobacter ethanolicus CCSD1]
          Length = 380

 Score = 37.5 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 3/36 (8%)

Query: 235 LNPRERRIFEARRLQENPV-TLENLSSEFEVSRERV 269
           L  RE+ I   R +++NP+ + E L+    +SR  V
Sbjct: 16  LTQREKEIL--RFIKKNPMISQEELAQLMGISRSAV 49


>gi|159027638|emb|CAO87010.1| unnamed protein product [Microcystis aeruginosa PCC 7806]
          Length = 218

 Score = 37.5 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 21/111 (18%), Positives = 38/111 (34%), Gaps = 17/111 (15%)

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           R+    SL+A     D         + +D +       E        + L  +++ L   
Sbjct: 115 RVNHPISLDAPRRVEDGE-------IDWDIESDYPSPDEHLTTHEFYDQLQAAIADLPEA 167

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVS----RERVRQIEARAFKKVQESIQ 285
            R     R +    +  E ++    VS    + R+    ARA  K+Q  +Q
Sbjct: 168 FRTTIILREI--EGMAYEEIAEMTGVSLGTVKSRI----ARARAKLQSVLQ 212


>gi|196228607|ref|ZP_03127473.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Chthoniobacter
           flavus Ellin428]
 gi|196226888|gb|EDY21392.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Chthoniobacter
           flavus Ellin428]
          Length = 170

 Score = 37.5 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 15/79 (18%), Positives = 31/79 (39%), Gaps = 2/79 (2%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
               ++ + E          L  ++  L+ R+R +      Q   ++L   +   +VS  
Sbjct: 88  QPDAQETVAEPAADDFELQALAAALRELSERQREVLHLTFYQ--RLSLSEAAEVMQVSIG 145

Query: 268 RVRQIEARAFKKVQESIQK 286
             RQ   R  K+++E +Q 
Sbjct: 146 SARQHYDRGKKRLREFLQA 164


>gi|150020670|ref|YP_001306024.1| ECF subfamily RNA polymerase sigma-24 factor [Thermosipho
           melanesiensis BI429]
 gi|149793191|gb|ABR30639.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermosipho
           melanesiensis BI429]
          Length = 203

 Score = 37.5 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 10/75 (13%), Positives = 33/75 (44%), Gaps = 5/75 (6%)

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           + S + + ++  +  + D +   Q  +E E        + +++  L  R+R + + R + 
Sbjct: 108 VFSVETDDTEDIEVDIPDKETDVQKEVESEIL---YEKINKALEKLPERDRVLIKLRDID 164

Query: 250 ENPVTLENLSSEFEV 264
           E  ++ + ++    +
Sbjct: 165 E--LSYQEIADILNI 177


>gi|65319086|ref|ZP_00392045.1| COG1595: DNA-directed RNA polymerase specialized sigma subunit,
           sigma24 homolog [Bacillus anthracis str. A2012]
          Length = 188

 Score = 37.5 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 15/79 (18%), Positives = 31/79 (39%), Gaps = 10/79 (12%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           H   E+   ++      R  L + ++ L P ++ +   + L       E +  +  ++R 
Sbjct: 104 HISTEKSAEDELIVMEDREELLKLINQLEPLDQXVXIMKYLLGMKT--EEIGDKLGLTRA 161

Query: 268 ----RVRQIEARAFKKVQE 282
               RV     R  KK+Q+
Sbjct: 162 AIDNRV----YRGKKKLQQ 176


>gi|313903685|ref|ZP_07837074.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermaerobacter
           subterraneus DSM 13965]
 gi|313465873|gb|EFR61398.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermaerobacter
           subterraneus DSM 13965]
          Length = 277

 Score = 37.5 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 24/93 (25%), Positives = 35/93 (37%), Gaps = 14/93 (15%)

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
           S D+        LV   D  E V    E  +     L  ++  L+P ER +   R   E 
Sbjct: 171 SLDEGLPSGGHALVSPADPAELVAARDEAVR-----LRMALESLSPAERDLLIRRYWMEE 225

Query: 252 PVTLENLSSEFEVSRE-------RVRQIEARAF 277
           P+  E ++ E  +SR        R RQ   +A 
Sbjct: 226 PI--ERMAREAGISRNAMDSRLWRARQALRKAL 256


>gi|260892934|ref|YP_003239031.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Ammonifex
           degensii KC4]
 gi|260865075|gb|ACX52181.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Ammonifex
           degensii KC4]
          Length = 227

 Score = 37.5 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 16/80 (20%), Positives = 35/80 (43%), Gaps = 1/80 (1%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPI-SEVVSEGNIGLMQAVKKFDPERGFRLA 102
            GD  A   L+      V+++A  +    +    E  S   + L +A+ + D +RG    
Sbjct: 12  AGDGEAREELLRLLRPFVLRVASHFFKRPVTWSDEAASVAFLALNEAIDQHDEKRGSPFL 71

Query: 103 TYSMWWIKAAMQEYILRSWS 122
            ++ W I++ + ++  +  S
Sbjct: 72  VFARWVIRSRLIDFCRQENS 91


>gi|239944341|ref|ZP_04696278.1| ECF subfamily RNA polymerase sigma factor [Streptomyces roseosporus
           NRRL 15998]
 gi|239990794|ref|ZP_04711458.1| ECF subfamily RNA polymerase sigma factor [Streptomyces roseosporus
           NRRL 11379]
          Length = 187

 Score = 37.5 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 11/57 (19%), Positives = 26/57 (45%), Gaps = 2/57 (3%)

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R ++  ++S L  R+R +   R  ++ P    +++     S   VR    R+  +++
Sbjct: 104 RLLMREALSRLTARQRTVLVLRFFEDLPE--ADVARLLGCSVGTVRSTTHRSLARLR 158


>gi|172036971|ref|YP_001803472.1| putative group 3/4 sigma-70 RNA polymerase sigma factor [Cyanothece
           sp. ATCC 51142]
 gi|171698425|gb|ACB51406.1| putative group 3/4 sigma-70 RNA polymerase sigma factor [Cyanothece
           sp. ATCC 51142]
          Length = 404

 Score = 37.5 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 17/90 (18%), Positives = 36/90 (40%), Gaps = 6/90 (6%)

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
           V S+N    G ES   +    +  S    + L+ D   QE+      ++      LT  +
Sbjct: 266 VSSINQPTPGQESGELVDILPESES----ESLLGDLITQEEEQQRLSQQAQMNQTLTAIL 321

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEF 262
           + + P  ++I +    Q   +T + ++ + 
Sbjct: 322 TQITPDLQQILDLYYGQG--LTQKEIAQQL 349


>gi|29350044|ref|NP_813547.1| RNA polymerase ECF-type sigma factor [Bacteroides thetaiotaomicron
           VPI-5482]
 gi|253571506|ref|ZP_04848912.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 1_1_6]
 gi|29341956|gb|AAO79741.1| RNA polymerase ECF-type sigma factor [Bacteroides thetaiotaomicron
           VPI-5482]
 gi|251838714|gb|EES66799.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 1_1_6]
          Length = 197

 Score = 37.5 bits (86), Expect = 2.4,   Method: Composition-based stats.
 Identities = 15/70 (21%), Positives = 37/70 (52%), Gaps = 2/70 (2%)

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
             I++E R    N + R M +L PR+R +   R ++E  ++ +++     ++ +    + 
Sbjct: 112 EFIDQEARHEEMNNIKRMMKILTPRQREVIYYRFIEE--LSYDDICQIMGLNYQSAYNLL 169

Query: 274 ARAFKKVQES 283
            R+ +K++E+
Sbjct: 170 QRSLQKIREA 179


>gi|312127271|ref|YP_003992145.1| RNA polymerase, sigma-24 subunit, ecf subfamily
           [Caldicellulosiruptor hydrothermalis 108]
 gi|311777290|gb|ADQ06776.1| RNA polymerase, sigma-24 subunit, ECF subfamily
           [Caldicellulosiruptor hydrothermalis 108]
          Length = 183

 Score = 37.5 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 13/90 (14%), Positives = 39/90 (43%), Gaps = 3/90 (3%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E  L +  ++ G+  A ++L+ ++L ++               +VV E  +  +  + K
Sbjct: 2   DEKRLIEEAKK-GNKEALYKLIENNLNILSGFVTKMTQDYHFAQDVVQETLLRAIMNIDK 60

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           F P+   + +T+ +       + ++ ++  
Sbjct: 61  FSPD--AKFSTWLIKISINVYKNFLRKNKR 88


>gi|298373314|ref|ZP_06983303.1| RNA polymerase ECF-type sigma factor [Bacteroidetes oral taxon 274
           str. F0058]
 gi|298274366|gb|EFI15918.1| RNA polymerase ECF-type sigma factor [Bacteroidetes oral taxon 274
           str. F0058]
          Length = 172

 Score = 37.5 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 13/86 (15%), Positives = 35/86 (40%), Gaps = 2/86 (2%)

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           D    +H  Q     +   +      +  ++  L    R IF       +  T++ ++ +
Sbjct: 89  DIDTMEHTLQSTDNEDDTMQGIDIEEIYAAIKQLPDIARTIFNM--FNLDGYTIQEIADK 146

Query: 262 FEVSRERVRQIEARAFKKVQESIQKQ 287
             +S   VR   +RA +++++ + ++
Sbjct: 147 LNMSNVAVRSQHSRAKERLRQILTRK 172


>gi|297562953|ref|YP_003681927.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
 gi|296847401|gb|ADH69421.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
          Length = 198

 Score = 37.5 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 14/78 (17%), Positives = 32/78 (41%), Gaps = 6/78 (7%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             +  G E+  +   E +  R +L      L  ++R++   R +    +T +       +
Sbjct: 118 PDEGPGPEESAVRVIEAQRARELLDE----LPEQQRKLLVMRVIAG--LTADETGHVLGM 171

Query: 265 SRERVRQIEARAFKKVQE 282
           S   VR  + RA  ++++
Sbjct: 172 SAGAVRVAQHRAIARLRQ 189


>gi|154244926|ref|YP_001415884.1| ECF subfamily RNA polymerase sigma-24 factor [Xanthobacter
           autotrophicus Py2]
 gi|154159011|gb|ABS66227.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Xanthobacter
           autotrophicus Py2]
          Length = 202

 Score = 37.5 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 20/93 (21%), Positives = 37/93 (39%), Gaps = 13/93 (13%)

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           +A +   D  + +    L+ D D  E +L+ + E +  R +L      L    R +   R
Sbjct: 100 SAPLPHGDGEAPEDAASLLVDGDTPESLLLRRTEAEAVRALLEHLPEPL----REVLVLR 155

Query: 247 RLQENPVTLENLSSEFEV------SR-ERVRQI 272
            L E  ++   ++    V      SR  R R++
Sbjct: 156 ELDE--LSYREIAEVAGVPVGTVMSRLSRARRL 186


>gi|326802063|ref|YP_004319882.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Sphingobacterium
           sp. 21]
 gi|326552827|gb|ADZ81212.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Sphingobacterium
           sp. 21]
          Length = 188

 Score = 37.5 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 10/59 (16%), Positives = 28/59 (47%), Gaps = 2/59 (3%)

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
           +   L  ++E  N   +L +++  L P+++R++     +   +    ++    +S+E V
Sbjct: 101 EHSRLFSEDELTNYHLLLDQAIDTLPPQQQRVYLL--SKHEHLKYAEIADRMGISKETV 157


>gi|302520178|ref|ZP_07272520.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces sp. SPB78]
 gi|302429073|gb|EFL00889.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces sp. SPB78]
          Length = 193

 Score = 37.5 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 12/62 (19%), Positives = 22/62 (35%), Gaps = 2/62 (3%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L+           E       R+ L ++M  L  R+R +   R   +  +T   ++    
Sbjct: 111 LLSKPMPDMASAEEGAYDLLERDDLIKAMRGLQRRQREVLVLRYFAD--MTEAQVAETLG 168

Query: 264 VS 265
           VS
Sbjct: 169 VS 170


>gi|299144263|ref|ZP_07037343.1| RNA polymerase sigma factor, sigma-70 family [Peptoniphilus sp.
           oral taxon 386 str. F0131]
 gi|298518748|gb|EFI42487.1| RNA polymerase sigma factor, sigma-70 family [Peptoniphilus sp.
           oral taxon 386 str. F0131]
          Length = 185

 Score = 37.5 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 19/96 (19%), Positives = 44/96 (45%), Gaps = 7/96 (7%)

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ 249
           I S D  + +  ++L  D + +E +L   E  K     L  + SVL  R+R +       
Sbjct: 97  IGSLDDETVKIFEFLESDFNLEESILCSDEVLK-----LRSAFSVLTKRQRDVLIMFYFY 151

Query: 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              +++ +++++  +    V   + RA + ++E ++
Sbjct: 152 N--MSISDIANKLRIKYRTVVNTKTRAIEILREVLR 185


>gi|297161021|gb|ADI10733.1| putative sigma factor [Streptomyces bingchenggensis BCW-1]
          Length = 179

 Score = 37.5 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 15/89 (16%), Positives = 38/89 (42%), Gaps = 2/89 (2%)

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           +       D DG +    ++    + R ML  +++ L PR+R+    R  ++   +   +
Sbjct: 83  ELLTLSPGDTDGWQTPDRDRITLADDREMLRHALAQLPPRQRQAVVLRYWEDLSES--QV 140

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           +     S   V+   A+   K++ ++ ++
Sbjct: 141 AVAMGCSVGTVKSQAAKGLAKLRAALARE 169


>gi|302531122|ref|ZP_07283464.1| RNA polymerase [Streptomyces sp. AA4]
 gi|302440017|gb|EFL11833.1| RNA polymerase [Streptomyces sp. AA4]
          Length = 175

 Score = 37.5 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 15/82 (18%), Positives = 34/82 (41%), Gaps = 2/82 (2%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
            V  H    +         +    +  ++S L PR+R +   R      ++   +S    
Sbjct: 93  YVPPHAVNARSAESLAMLSSEHQAVVSALSKLPPRQREVLVLRYYGG--LSEAEISEAAG 150

Query: 264 VSRERVRQIEARAFKKVQESIQ 285
           +S+  V+   +RA + +Q+++Q
Sbjct: 151 ISKGTVKSTASRALEALQKAMQ 172


>gi|257126627|ref|YP_003164741.1| hypothetical protein Lebu_1885 [Leptotrichia buccalis C-1013-b]
 gi|257050566|gb|ACV39750.1| hypothetical protein Lebu_1885 [Leptotrichia buccalis C-1013-b]
          Length = 314

 Score = 37.5 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 39/282 (13%), Positives = 98/282 (34%), Gaps = 52/282 (18%)

Query: 4   KNMSIIVNGEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVK 63
           ++ +I +  +  +  Y+ +IR       ++   L K+ R          L+  +L++ VK
Sbjct: 59  EDENIFIEEKDTIKSYLEDIR-------EKYKELEKKNRNEN-----EELIDRYLKIAVK 106

Query: 64  IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP----ERGFRLATYSMWWIKAAMQEYILR 119
            ++ Y  YG    + V E  +G++  +  FD      +      +   +    + E+   
Sbjct: 107 ESLLYSKYGFSFLDTVQEATLGIISGISYFDEISRITKEPEF--FVKNFAVKYILEFQKE 164

Query: 120 SWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR 179
               +K    +    L   + +  G              +  I+K++NVS   +  +   
Sbjct: 165 LLKDIKSSELSYILYLKVKVDKSMGF------------SMDEISKQMNVSTEYIEQLEK- 211

Query: 180 LAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE 239
                                 D +  +   +   ++EK ++  +  +L      LN  +
Sbjct: 212 --------------------LFDDINPEELIENTQILEKADKITQMYILENIPKKLNYLD 251

Query: 240 RRIFEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKV 280
            +I       ++   T + ++    ++   V  ++ +A  K+
Sbjct: 252 EQILVMAYGLDDRVYTEKEIAKSLNIASHNVNILKEKALNKL 293


>gi|226329254|ref|ZP_03804772.1| hypothetical protein PROPEN_03157 [Proteus penneri ATCC 35198]
 gi|225202440|gb|EEG84794.1| hypothetical protein PROPEN_03157 [Proteus penneri ATCC 35198]
          Length = 182

 Score = 37.5 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 12/72 (16%), Positives = 31/72 (43%), Gaps = 5/72 (6%)

Query: 197 SSQWQDWLVYDHDGQEQVLIEK---EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
                D+ + D        ++     E + R ++L+ +++ L PR R  F   R   + +
Sbjct: 83  DIYQDDYELDDAAQNYTTELDPGYVLEHQQRLDLLSEAIATLPPRRREAFVLYRF--DGL 140

Query: 254 TLENLSSEFEVS 265
           +   ++ + ++S
Sbjct: 141 SQSEIAEQMDIS 152


>gi|225020528|ref|ZP_03709720.1| hypothetical protein CORMATOL_00535 [Corynebacterium matruchotii
           ATCC 33806]
 gi|305679608|ref|ZP_07402418.1| RNA polymerase sigma factor SigD [Corynebacterium matruchotii ATCC
           14266]
 gi|224946917|gb|EEG28126.1| hypothetical protein CORMATOL_00535 [Corynebacterium matruchotii
           ATCC 33806]
 gi|305660228|gb|EFM49725.1| RNA polymerase sigma factor SigD [Corynebacterium matruchotii ATCC
           14266]
          Length = 187

 Score = 37.5 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 15/85 (17%), Positives = 32/85 (37%), Gaps = 2/85 (2%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           V D     +   E        N +   + +L+ + R I   R      ++ E  +     
Sbjct: 105 VPDETVDHESPEELALVAAGSNRVRELLDLLSEKPREIIILRVFVG--LSAEETAEIVGS 162

Query: 265 SRERVRQIEARAFKKVQESIQKQVE 289
           +   VR  + RA   ++++I ++ E
Sbjct: 163 TPGAVRVAQHRALGTLRKAIAQENE 187


>gi|148680322|gb|EDL12269.1| ankyrin 2, brain, isoform CRA_b [Mus musculus]
          Length = 3955

 Score = 37.5 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 21/123 (17%), Positives = 44/123 (35%), Gaps = 7/123 (5%)

Query: 157  EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
            E++   A KL    ++        + DES +AL  S  ++            D  +   I
Sbjct: 3472 EEISDEASKLVDRLTQSEREQEPPSDDESSSALEVSVIESLPPVDIEHSAPEDIFDTRPI 3531

Query: 217  EKEERKNRRNML------TRSMSVLNPRERRIFEARRLQEN-PVTLENLSSEFEVSRERV 269
              E  +     +       R+    + +ER       + ++   +   L+ E + + E++
Sbjct: 3532 WDESIETMIERIPDENGHDRAEDPQDEQERMEERLAYIADHLGFSWTELARELDFTEEQI 3591

Query: 270  RQI 272
             QI
Sbjct: 3592 HQI 3594


>gi|147669798|ref|YP_001214616.1| ECF subfamily RNA polymerase sigma-24 factor [Dehalococcoides sp.
           BAV1]
 gi|146270746|gb|ABQ17738.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Dehalococcoides
           sp. BAV1]
          Length = 179

 Score = 37.5 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 22/144 (15%), Positives = 54/144 (37%), Gaps = 9/144 (6%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVV-KIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           E  L +   +  D  A  RL   +   +   IA+   G  +   ++  +  +  ++++  
Sbjct: 4   ERHLVE-LAQQKDEQAFARLYEEYFDKIYRYIALK-IGNKMEAEDLTQQVFMNALRSMSS 61

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F  +     + +        + +Y+ +               +   L      ++  T+ 
Sbjct: 62  FKWQDNTPFSAWLYRIAHNQIVDYLRKKSR-----QPTVDIEIIAPLACADDPVE-TTEV 115

Query: 153 NLKPEQVVAIAKKLNVSESEVISM 176
           N+  E+ V ++ KL  ++ EVIS+
Sbjct: 116 NIDYEKFVKVSAKLTPAQQEVISL 139


>gi|255536663|ref|YP_003097034.1| RNA polymerase ECF-type sigma factor [Flavobacteriaceae bacterium
           3519-10]
 gi|255342859|gb|ACU08972.1| RNA polymerase ECF-type sigma factor [Flavobacteriaceae bacterium
           3519-10]
          Length = 185

 Score = 37.5 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 28/147 (19%), Positives = 64/147 (43%), Gaps = 15/147 (10%)

Query: 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGD 183
           V++   A Q RL++++RR+        D                  +S++ +   R+A +
Sbjct: 22  VRMMMDAYQSRLYWHIRRIIVDHSLAQDVLQDSFIKAYQNFHQFKQDSQLYTWLYRIATN 81

Query: 184 ESLNAL-----INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           ESL  L     +  +D++   +   +V D+   E         ++ + +L +++  L  +
Sbjct: 82  ESLQQLNKLKRMQKTDEDPEYYLQNMVADNVSPEA--------EDIQILLQKAIHSLPEK 133

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVS 265
           ++ +F  R  +E P   E++S   ++S
Sbjct: 134 QKLVFTMRYYEELPY--EDMSQILDMS 158


>gi|320116743|ref|YP_004186902.1| PfkB domain-containing protein [Thermoanaerobacter brockii subsp.
           finnii Ako-1]
 gi|319929834|gb|ADV80519.1| PfkB domain protein [Thermoanaerobacter brockii subsp. finnii
           Ako-1]
          Length = 367

 Score = 37.5 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 3/36 (8%)

Query: 235 LNPRERRIFEARRLQENPV-TLENLSSEFEVSRERV 269
           L  RE+ I   R +++NP+ + E L+    +SR  V
Sbjct: 3   LTQREKEIL--RFIKKNPMISQEELAQLMGISRSAV 36


>gi|224026918|ref|ZP_03645284.1| hypothetical protein BACCOPRO_03677 [Bacteroides coprophilus DSM
           18228]
 gi|224020154|gb|EEF78152.1| hypothetical protein BACCOPRO_03677 [Bacteroides coprophilus DSM
           18228]
          Length = 191

 Score = 37.5 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 14/73 (19%), Positives = 38/73 (52%), Gaps = 2/73 (2%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           +  + ++ +    +  L ++ S L+PR+R IFE    +E  +++  ++ +  ++ + VR 
Sbjct: 106 DDEISDEIDYDTFQKALEKAKSHLSPRQREIFEL--NKEYGISIPEIAEKLSITDQVVRN 163

Query: 272 IEARAFKKVQESI 284
             + A K ++  +
Sbjct: 164 QLSAALKTLRNEL 176


>gi|166363023|ref|YP_001655296.1| RNA polymerase sigma factor RpoE [Microcystis aeruginosa NIES-843]
 gi|166085396|dbj|BAG00104.1| RNA polymerase ECF-type sigma-E factor [Microcystis aeruginosa
           NIES-843]
          Length = 218

 Score = 37.5 bits (86), Expect = 2.5,   Method: Composition-based stats.
 Identities = 21/111 (18%), Positives = 38/111 (34%), Gaps = 17/111 (15%)

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           R+    SL+A     D         + +D +       E        + L  +++ L   
Sbjct: 115 RVNHPISLDAPRRVEDGE-------IDWDIESDYPSPDEHLTTHEFYDQLQAAIADLPEA 167

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVS----RERVRQIEARAFKKVQESIQ 285
            R     R +    +  E ++    VS    + R+    ARA  K+Q  +Q
Sbjct: 168 FRTTIILREI--EGMAYEEIAEMTGVSLGTVKSRI----ARARAKLQSVLQ 212


>gi|297563564|ref|YP_003682538.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
 gi|296848012|gb|ADH70032.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Nocardiopsis
           dassonvillei subsp. dassonvillei DSM 43111]
          Length = 172

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 14/74 (18%), Positives = 33/74 (44%), Gaps = 2/74 (2%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            +  EQ + +   R +  +++ R++  L  R+R     R   +  +T   ++    V+  
Sbjct: 89  DEIPEQRVDDPTWRSDLADVVERAIDRLPARQRTTVVLRYYDD--LTEAQIAERMGVTLG 146

Query: 268 RVRQIEARAFKKVQ 281
            V+   +RA  K++
Sbjct: 147 TVKSTLSRAVDKLR 160


>gi|262405848|ref|ZP_06082398.1| conserved hypothetical protein [Bacteroides sp. 2_1_22]
 gi|262356723|gb|EEZ05813.1| conserved hypothetical protein [Bacteroides sp. 2_1_22]
          Length = 164

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 19/83 (22%), Positives = 37/83 (44%), Gaps = 2/83 (2%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           +Y    +  V  E  E+  R   ++++M  L P  R I E   +Q      + ++ E  +
Sbjct: 83  IYSELTKSYVETEYLEQDERMMHISKAMEKLTPHTRHILEECYIQRKKY--QEVAEELNI 140

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           S   VR+   +A + ++E   K+
Sbjct: 141 SVSAVRKHIVKALQVIREECAKK 163


>gi|260459670|ref|ZP_05807924.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Mesorhizobium
           opportunistum WSM2075]
 gi|259034472|gb|EEW35729.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Mesorhizobium
           opportunistum WSM2075]
          Length = 186

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 39/97 (40%), Gaps = 5/97 (5%)

Query: 28  MLEKQE--EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           ML++ E  +  L  R +  GD  A   L+  H   V + A  + G      ++  E  + 
Sbjct: 4   MLDESEASDAELIGRAK-GGDRGAFGTLLERHYDFVYRAAYRWCGKKADAEDIAQEVCVR 62

Query: 86  LMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           L +A++ +    G    T+       A ++ + +S  
Sbjct: 63  LGKAIRDYRG--GGAFTTWLYSVTMNAARDMMRKSAR 97


>gi|302542422|ref|ZP_07294764.1| TIGR02957 family RNA polymerase sigma-70 factor [Streptomyces
           hygroscopicus ATCC 53653]
 gi|302460040|gb|EFL23133.1| TIGR02957 family RNA polymerase sigma-70 factor [Streptomyces
           himastatinicus ATCC 53653]
          Length = 301

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 20/103 (19%), Positives = 38/103 (36%), Gaps = 2/103 (1%)

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             +  +   R+   ++L+ L     +  S    WL         V  + E  ++    + 
Sbjct: 57  VRDRRAYLVRITTRQALSRLRTLGRRKESYVGPWLPEPLLTAPDVAEDIELAESVSMAML 116

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
             +  L P ER +F  R + +     E ++   + S   VRQI
Sbjct: 117 LVLETLTPNERAVFVLREVFDLGY--EEIAEAVDKSPAAVRQI 157


>gi|227829876|ref|YP_002831655.1| Bacterio-opsin activator HTH domain protein [Sulfolobus islandicus
           L.S.2.15]
 gi|229578697|ref|YP_002837095.1| Bacterio-opsin activator HTH domain protein [Sulfolobus islandicus
           Y.G.57.14]
 gi|227456323|gb|ACP35010.1| Bacterio-opsin activator HTH domain protein [Sulfolobus islandicus
           L.S.2.15]
 gi|228009411|gb|ACP45173.1| Bacterio-opsin activator HTH domain protein [Sulfolobus islandicus
           Y.G.57.14]
          Length = 203

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 11/52 (21%), Positives = 22/52 (42%), Gaps = 5/52 (9%)

Query: 233 SVLNPRERRIFEA-----RRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           + L  R+  I +          +  +TL  L+ +  +S   + +I  RA +K
Sbjct: 143 AELTERQMEILQLAYKLGYFNDDRGITLSQLADKLGISAPTLEEILRRALRK 194


>gi|300774520|ref|ZP_07084383.1| DNA-directed RNA polymerase sigma subunit RpoE [Chryseobacterium
           gleum ATCC 35910]
 gi|300506335|gb|EFK37470.1| DNA-directed RNA polymerase sigma subunit RpoE [Chryseobacterium
           gleum ATCC 35910]
          Length = 183

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 28/166 (16%), Positives = 68/166 (40%), Gaps = 19/166 (11%)

Query: 109 IKAAMQEYILRSWSL----VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAK 164
           IK A    ++++       V+    A Q RL++++RR+        D   +         
Sbjct: 3   IKDAEIISLMQNPRTQDKGVRALMDAYQSRLYWHIRRIIVDGDLAQDTLQETFIKAYQNF 62

Query: 165 KLNVSESEVISMNCRLAGDESLNAL-----INSSDKNSSQWQDWLVYDHDGQEQVLIEKE 219
               ++S++ +   R+A +E+L  +     +  +D++       LV D+          +
Sbjct: 63  HQFKNDSQLYTWLYRIATNEALQQVNKMKKMQKTDEDPDYHMQNLVADNT--------DD 114

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
           + +  + +L  ++  L  +++ +F  R   + P   E +S   ++S
Sbjct: 115 DAEEIQILLQNAIQSLPEKQKLVFMMRYYDDLPY--EEISKIVDMS 158


>gi|223634791|sp|Q8C8R3|ANK2_MOUSE RecName: Full=Ankyrin-2; Short=ANK-2; AltName: Full=Brain ankyrin
          Length = 3898

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 21/123 (17%), Positives = 44/123 (35%), Gaps = 7/123 (5%)

Query: 157  EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
            E++   A KL    ++        + DES +AL  S  ++            D  +   I
Sbjct: 3432 EEISDEASKLVDRLTQSEREQEPPSDDESSSALEVSVIESLPPVDIEHSAPEDIFDTRPI 3491

Query: 217  EKEERKNRRNML------TRSMSVLNPRERRIFEARRLQEN-PVTLENLSSEFEVSRERV 269
              E  +     +       R+    + +ER       + ++   +   L+ E + + E++
Sbjct: 3492 WDESIETMIERIPDENGHDRAEDPQDEQERMEERLAYIADHLGFSWTELARELDFTEEQI 3551

Query: 270  RQI 272
             QI
Sbjct: 3552 HQI 3554


>gi|254166608|ref|ZP_04873462.1| transcriptional regulator, AsnC family [Aciduliprofundum boonei
           T469]
 gi|254168472|ref|ZP_04875316.1| transcriptional regulator, AsnC family [Aciduliprofundum boonei
           T469]
 gi|197622527|gb|EDY35098.1| transcriptional regulator, AsnC family [Aciduliprofundum boonei
           T469]
 gi|197624218|gb|EDY36779.1| transcriptional regulator, AsnC family [Aciduliprofundum boonei
           T469]
          Length = 152

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 11/45 (24%), Positives = 23/45 (51%), Gaps = 5/45 (11%)

Query: 235 LNPRERRIFEARRLQENPVTLENLSSEFEVS----RERVRQIEAR 275
           L+ R+R+I E   L+ + +    ++    +S    R+R+R +E  
Sbjct: 12  LDDRDRKIIEL-LLKNSRMNYSEIAKVLGISDTAVRKRIRNMEKN 55


>gi|312135453|ref|YP_004002791.1| RNA polymerase, sigma-24 subunit, ecf subfamily
           [Caldicellulosiruptor owensensis OL]
 gi|311775504|gb|ADQ04991.1| RNA polymerase, sigma-24 subunit, ECF subfamily
           [Caldicellulosiruptor owensensis OL]
          Length = 183

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 13/90 (14%), Positives = 39/90 (43%), Gaps = 3/90 (3%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E  L +  ++ G+  A + L+ ++L ++               +VV E  +  +  + K
Sbjct: 2   DEKRLIEEAKK-GNKEALYTLIENNLNILSGFVTKMTQDYHFAQDVVQETFLRAIMNIDK 60

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           F P+   + +T+ +       ++++ ++  
Sbjct: 61  FSPD--AKFSTWLIKISINVYKDFLKKNKR 88


>gi|284035352|ref|YP_003385282.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Spirosoma linguale
           DSM 74]
 gi|283814645|gb|ADB36483.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Spirosoma linguale
           DSM 74]
          Length = 199

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 17/74 (22%), Positives = 29/74 (39%), Gaps = 2/74 (2%)

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
                N  +  D L       E +LI  EE     + L +++  L  R+R     R  Q 
Sbjct: 101 QDDMINGRRVGDTLPGADPSHENLLIAHEEDSYVNDCLHQALDKLPRRQREAVHLRYFQN 160

Query: 251 NPVTLENLSSEFEV 264
             ++ E +S+  E+
Sbjct: 161 --MSNEEISALMEI 172


>gi|227547486|ref|ZP_03977535.1| possible DNA-directed RNA polymerase sigma subunit RpoE
           [Bifidobacterium longum subsp. infantis ATCC 55813]
 gi|227212001|gb|EEI79897.1| possible DNA-directed RNA polymerase sigma subunit RpoE
           [Bifidobacterium longum subsp. infantis ATCC 55813]
          Length = 147

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 10/59 (16%), Positives = 27/59 (45%), Gaps = 4/59 (6%)

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV-RQIEARAFKKVQESIQ 285
           L  +++ L  + +        Q   +T + +  +   +R  + R I+  A K+++E ++
Sbjct: 87  LAAALAGLPEQTQEEIFLYYFQH--LTQKEIGEQSGWTRSTIGRHIQL-ALKRLKEEME 142


>gi|260589019|ref|ZP_05854932.1| putative RNA polymerase sigma factor SigM [Blautia hansenii DSM
           20583]
 gi|260540798|gb|EEX21367.1| putative RNA polymerase sigma factor SigM [Blautia hansenii DSM
           20583]
          Length = 163

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 20/84 (23%), Positives = 42/84 (50%), Gaps = 4/84 (4%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF-EARRLQENPVTLENLSSEF 262
           L+ ++   E+ L+     +  R  L  +++ L  + + I  E+   Q +    E ++   
Sbjct: 81  LICEYLSSEEDLLAGMIEQEERKALFLAIAALPVQMKEILMESIYFQLSD---EAIAKAH 137

Query: 263 EVSRERVRQIEARAFKKVQESIQK 286
            +++E VRQI  RA KK+  S+++
Sbjct: 138 GLTKENVRQIRCRAKKKLISSMKE 161


>gi|223937471|ref|ZP_03629375.1| RNA polymerase, sigma-24 subunit, ECF subfamily [bacterium
          Ellin514]
 gi|223893822|gb|EEF60279.1| RNA polymerase, sigma-24 subunit, ECF subfamily [bacterium
          Ellin514]
          Length = 621

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 16/56 (28%), Positives = 22/56 (39%)

Query: 33 EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQ 88
          E+  L + Y       A   LV+ HL LV  +A+   G      EV     I L +
Sbjct: 5  EDMELVREYAARQSEEAFAALVSRHLNLVYSVALRQLGDPHLAEEVTQAAFIILAR 60


>gi|312885433|ref|ZP_07745073.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Mucilaginibacter
           paludis DSM 18603]
 gi|311302083|gb|EFQ79112.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Mucilaginibacter
           paludis DSM 18603]
          Length = 183

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 15/69 (21%), Positives = 31/69 (44%), Gaps = 10/69 (14%)

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS----RERVRQIE 273
           + E+K     L  +M+ LN  +R +    R QE     + ++    ++    + RV    
Sbjct: 114 QLEKKQAHRELHNAMARLNEDQREVLTLSRFQELKH--QEIAKILNITEGAVKVRV---- 167

Query: 274 ARAFKKVQE 282
            RA ++++E
Sbjct: 168 HRAMQELKE 176


>gi|307330422|ref|ZP_07609566.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306883939|gb|EFN14981.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 202

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 16/76 (21%), Positives = 34/76 (44%), Gaps = 2/76 (2%)

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
            E  + +  E+   R +L   +SVL P++R +   R      +T E  +    +S   V+
Sbjct: 87  PEASVEDSTEQHADRALLMDILSVLAPKQRSVVVLR--HWEQMTTEETAEALGMSTGTVK 144

Query: 271 QIEARAFKKVQESIQK 286
               RA  ++++ ++ 
Sbjct: 145 STLHRALARLRQELES 160


>gi|296283212|ref|ZP_06861210.1| sigma-70 region 2 [Citromicrobium bathyomarinum JL354]
          Length = 350

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 33/242 (13%), Positives = 81/242 (33%), Gaps = 16/242 (6%)

Query: 52  RLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKA 111
           R++      +      Y G      +      I + +A++ +DP +  +  T+  W I+ 
Sbjct: 40  RILKIAAPRIRHFIRQY-GLAAHYEDAEQVCAIAVHRAIEAYDPTK-AKFTTFLNWQIRG 97

Query: 112 AMQEYILRSWSLVKIGTTANQKRLFFNLRR------LKGHLQAITDNNLKPEQVVAIAKK 165
            +Q    R  +  +      +                +  L+A+ ++    E+  + A +
Sbjct: 98  ELQSLRFRLMTDQRPSARKVEAVTIALTTGSISDDGEETSLEALIEDEAALERTESSASE 157

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRR 225
              +++ +  ++  +  +             + +    +                  +  
Sbjct: 158 HLANQACIALVDAYIEAERKTGVEQLRKRARTRRPARDIRESRPDLPASFRAHMAGPDPV 217

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE--VSRERVRQIEARAFKKVQES 283
             L +    L  R+R I E      +      L+   +  ++RER+RQI  RA K + + 
Sbjct: 218 E-LEKLHERL-ERDRAIIERSMFSGDTK----LALSIDNSLTRERIRQIVRRAGKHMAQL 271

Query: 284 IQ 285
           +Q
Sbjct: 272 VQ 273


>gi|284997026|ref|YP_003418793.1| Bacterio-opsin activator, HTH domain protein [Sulfolobus islandicus
           L.D.8.5]
 gi|284444921|gb|ADB86423.1| Bacterio-opsin activator, HTH domain protein [Sulfolobus islandicus
           L.D.8.5]
          Length = 203

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 11/52 (21%), Positives = 22/52 (42%), Gaps = 5/52 (9%)

Query: 233 SVLNPRERRIFEA-----RRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           + L  R+  I +          +  +TL  L+ +  +S   + +I  RA +K
Sbjct: 143 AELTERQMEILQLAYKLGYFNDDRGITLSQLADKLGISAPTLEEILRRALRK 194


>gi|255015689|ref|ZP_05287815.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 2_1_7]
          Length = 190

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 23/99 (23%), Positives = 49/99 (49%), Gaps = 4/99 (4%)

Query: 196 NSSQWQDWLVYDH--DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           NS  + + +V +   DG+E  +  K   +   + L  +   L PR+R +FE    +E  +
Sbjct: 89  NSPLFWEDVVLNESGDGEETAIERKLSFEEFNHRLEIAKQKLTPRQRELFEL--NKEQGI 146

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
           T+  ++++  +S + VR   ++A   +++ + K   L S
Sbjct: 147 TITEIAAKAFISEQSVRNQLSQALHVLRKELGKYALLFS 185


>gi|83999828|emb|CAH60128.1| putative RNA polymerase ECF-subfamily sigma factor [Streptomyces
           tenjimariensis]
          Length = 321

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 13/76 (17%), Positives = 34/76 (44%), Gaps = 2/76 (2%)

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
            +  + +  E+   R +L   + VL P++R +   R      ++ E  ++   +S   V+
Sbjct: 150 PDASVDDATEQHADRALLMDVLKVLAPKQRSVVVLR--HWEQMSTEETAAALGMSTGTVK 207

Query: 271 QIEARAFKKVQESIQK 286
               RA  ++++ ++ 
Sbjct: 208 STLHRALARLRQELES 223


>gi|150387940|ref|YP_001317989.1| putative RNA polymerase sigma factor SigI [Alkaliphilus
           metalliredigens QYMF]
 gi|149947802|gb|ABR46330.1| RNA polymerase, sigma 28 subunit, FliA/WhiG family [Alkaliphilus
           metalliredigens QYMF]
          Length = 247

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 17/100 (17%), Positives = 43/100 (43%), Gaps = 3/100 (3%)

Query: 26  IPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS--EVVSEGN 83
             +L+K++      R  + G+    + ++  H+  + KI     G  + I   ++ S G 
Sbjct: 5   FKILKKRKTIEERIRDIQEGNEEEKNSIIQEHIPFIKKILSQQLGRYIEIENDDMFSIGL 64

Query: 84  IGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123
           +   +A+ K++  RG +  +++   IK    + + +    
Sbjct: 65  MAFNEAIDKYETSRG-KFLSFAAIVIKNRSIDQLRKQSRT 103


>gi|289577543|ref|YP_003476170.1| MarR family transcriptional regulator [Thermoanaerobacter italicus
           Ab9]
 gi|326390263|ref|ZP_08211823.1| transcriptional regulator, MarR family [Thermoanaerobacter
           ethanolicus JW 200]
 gi|289527256|gb|ADD01608.1| transcriptional regulator, MarR family [Thermoanaerobacter italicus
           Ab9]
 gi|325993708|gb|EGD52140.1| transcriptional regulator, MarR family [Thermoanaerobacter
           ethanolicus JW 200]
          Length = 367

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 3/36 (8%)

Query: 235 LNPRERRIFEARRLQENPV-TLENLSSEFEVSRERV 269
           L  RE+ I   R +++NP+ + E L+    +SR  V
Sbjct: 3   LTQREKEIL--RFIKKNPMISQEELAQLMGISRSAV 36


>gi|257067591|ref|YP_003153846.1| transcriptional regulator with sigma factor-related N-terminal
           domain [Brachybacterium faecium DSM 4810]
 gi|256558409|gb|ACU84256.1| transcriptional regulator with sigma factor-related N-terminal
           domain [Brachybacterium faecium DSM 4810]
          Length = 318

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 11/51 (21%), Positives = 22/51 (43%), Gaps = 2/51 (3%)

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPP 295
           AR   E   +   ++ E  +SR  V +I  +A  + +  ++  +     PP
Sbjct: 14  ARLYYEQGHSQTEIAQELGLSRSNVSRILTQA--RDRGIVEITIHDPEGPP 62


>gi|226310347|ref|YP_002770241.1| RNA polymerase ECF-type sigma factor [Brevibacillus brevis NBRC
           100599]
 gi|226093295|dbj|BAH41737.1| RNA polymerase ECF-type sigma factor [Brevibacillus brevis NBRC
           100599]
          Length = 185

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 17/77 (22%), Positives = 36/77 (46%), Gaps = 2/77 (2%)

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
            +  +  E    K +R+ L + M  L+   R I +   LQ   ++   + ++  +S + V
Sbjct: 102 DECPIPEEDYLEKEQRHALRQQMMTLDKNHRAILDLHYLQH--LSYREIGNKLSLSVDTV 159

Query: 270 RQIEARAFKKVQESIQK 286
           R   + A KK+++ + K
Sbjct: 160 RMRLSYARKKLRDQLSK 176


>gi|156740260|ref|YP_001430389.1| ECF subfamily RNA polymerase sigma-24 factor [Roseiflexus
           castenholzii DSM 13941]
 gi|156231588|gb|ABU56371.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Roseiflexus
           castenholzii DSM 13941]
          Length = 197

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 13/82 (15%), Positives = 29/82 (35%), Gaps = 2/82 (2%)

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
            L        +   E    +   + L   M VL   +R +   R   +   TL  ++   
Sbjct: 106 PLDESAPHALEPPDEAVISRIAYHELRSVMRVLTRDQRLVLRLRF--DEDRTLAEIAESL 163

Query: 263 EVSRERVRQIEARAFKKVQESI 284
             +   V+ ++ R   ++ E++
Sbjct: 164 GRTVGSVKALQHRGLTRLAEAL 185


>gi|323491204|ref|ZP_08096390.1| RNA polymerase sigma factor RpoE [Vibrio brasiliensis LMG 20546]
 gi|323314572|gb|EGA67650.1| RNA polymerase sigma factor RpoE [Vibrio brasiliensis LMG 20546]
          Length = 192

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 18/88 (20%), Positives = 33/88 (37%), Gaps = 3/88 (3%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
            VL +R + +GD  A + LVT +   V  +   Y      + +V  E  I   +A+  F 
Sbjct: 8   QVLIERVQ-NGDKQAFNLLVTKYQNKVCNLISRYVNNPGDVPDVAQEAFIKAYRAIPSFR 66

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWS 122
            E      T+         + +++    
Sbjct: 67  GE--SAFYTWLYRIAVNTAKNHLVAQGR 92


>gi|313772342|gb|EFS38308.1| conserved hypothetical protein [Propionibacterium acnes HL074PA1]
 gi|313830776|gb|EFS68490.1| conserved hypothetical protein [Propionibacterium acnes HL007PA1]
 gi|313833994|gb|EFS71708.1| conserved hypothetical protein [Propionibacterium acnes HL056PA1]
 gi|314973201|gb|EFT17297.1| conserved hypothetical protein [Propionibacterium acnes HL053PA1]
 gi|314975873|gb|EFT19968.1| conserved hypothetical protein [Propionibacterium acnes HL045PA1]
 gi|314983592|gb|EFT27684.1| conserved hypothetical protein [Propionibacterium acnes HL005PA1]
 gi|315096111|gb|EFT68087.1| conserved hypothetical protein [Propionibacterium acnes HL038PA1]
 gi|327326030|gb|EGE67820.1| transcriptional regulator, SorC family [Propionibacterium acnes
           HL096PA2]
 gi|327446090|gb|EGE92744.1| hypothetical protein HMPREF9571_01832 [Propionibacterium acnes
           HL043PA2]
 gi|327447931|gb|EGE94585.1| hypothetical protein HMPREF9570_00764 [Propionibacterium acnes
           HL043PA1]
 gi|328760470|gb|EGF74038.1| transcriptional regulator, SorC family [Propionibacterium acnes
           HL099PA1]
          Length = 314

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 15/67 (22%), Positives = 30/67 (44%), Gaps = 9/67 (13%)

Query: 236 NPRE--RRIFE-ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK------VQESIQK 286
             RE  + +   ARR      T   +++E   SR  V ++  +A ++      VQ  +++
Sbjct: 2   TDREHIQTLLTVARRYWLEQATQAEIAAEIGYSRSMVSRLLDKARRRGIITFTVQHPLER 61

Query: 287 QVELSSS 293
            +EL  +
Sbjct: 62  AIELEDA 68


>gi|300853534|ref|YP_003778518.1| hypothetical protein CLJU_c03340 [Clostridium ljungdahlii DSM
           13528]
 gi|300433649|gb|ADK13416.1| putative protein with a sigma-70 r4 domain [Clostridium ljungdahlii
           DSM 13528]
          Length = 162

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 16/109 (14%), Positives = 45/109 (41%), Gaps = 5/109 (4%)

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN---MLTRSMSVL 235
           R      ++A  N ++  ++    +LV       + +I+  E    +     L  ++  L
Sbjct: 56  RYHVPVYMDAYCNENEDVAADRNPYLVDTASDPLESIIQSIEETEHKEKIGRLRAAIGTL 115

Query: 236 NPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            P+++ + +         T  +++ E  V+   +R    + ++K+++ I
Sbjct: 116 KPQQKELIKKVFF--EKRTNVSIADEEGVTEAAIRNRLKKIYEKLRKKI 162


>gi|291447808|ref|ZP_06587198.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces roseosporus
           NRRL 15998]
 gi|291350755|gb|EFE77659.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces roseosporus
           NRRL 15998]
          Length = 185

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 11/57 (19%), Positives = 26/57 (45%), Gaps = 2/57 (3%)

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           R ++  ++S L  R+R +   R  ++ P    +++     S   VR    R+  +++
Sbjct: 102 RLLMREALSRLTARQRTVLVLRFFEDLPE--ADVARLLGCSVGTVRSTTHRSLARLR 156


>gi|312194440|ref|YP_004014501.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Frankia sp. EuI1c]
 gi|311225776|gb|ADP78631.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Frankia sp. EuI1c]
          Length = 194

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 8/39 (20%), Positives = 19/39 (48%), Gaps = 2/39 (5%)

Query: 225 RNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           R+ L  ++  L PR+R +   R   +  +T   ++++  
Sbjct: 114 RHDLLGALRQLPPRQRAVIVLRYFDD--LTEAEIAAQLG 150


>gi|76802039|ref|YP_327047.1| DNA binding protein [Natronomonas pharaonis DSM 2160]
 gi|76557904|emb|CAI49488.1| predicted DNA binding protein [Natronomonas pharaonis DSM 2160]
          Length = 216

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 17/79 (21%), Positives = 31/79 (39%), Gaps = 9/79 (11%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE-----ARRLQENPVTLENLSSEF 262
            D  E + +E E   +    L    ++L  R+R I +              T ++++   
Sbjct: 133 DDIPENLRVELERLSDYDPELQELSAMLTDRQREILDTAAELGYYQVPREATHQDIADHL 192

Query: 263 EVSR----ERVRQIEARAF 277
            +S     E +R+IEAR  
Sbjct: 193 GLSTTTVGEHLRKIEARML 211


>gi|32477269|ref|NP_870263.1| sigma factor [Rhodopirellula baltica SH 1]
 gi|32447820|emb|CAD77338.1| hypothetical protein-putative sigma factor protein [Rhodopirellula
           baltica SH 1]
          Length = 216

 Score = 37.5 bits (86), Expect = 2.6,   Method: Composition-based stats.
 Identities = 10/56 (17%), Positives = 28/56 (50%), Gaps = 2/56 (3%)

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           D +   L+++++     + L   ++ L+PR+ R+ E R      +  + +++E  +
Sbjct: 109 DDEVTFLLDQDDDVVALDELLLQLASLSPRQARVVELRFFGGLGM--KEIAAELNL 162


>gi|317472270|ref|ZP_07931598.1| sigma-70 family RNA polymerase sigma factor [Anaerostipes sp.
           3_2_56FAA]
 gi|316900227|gb|EFV22213.1| sigma-70 family RNA polymerase sigma factor [Anaerostipes sp.
           3_2_56FAA]
          Length = 177

 Score = 37.5 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 15/72 (20%), Positives = 36/72 (50%), Gaps = 2/72 (2%)

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
           L E   ++   + + R +  L  +++ I       E  +++E +S   ++SR+ VR   +
Sbjct: 103 LEEAVVKQELLDEVNRLIGSLPEKQKIIMNMYYAAE--MSIEEISHNLKISRKTVRSSMS 160

Query: 275 RAFKKVQESIQK 286
           +A  K++ S++ 
Sbjct: 161 KARTKIRSSLEA 172


>gi|302346721|ref|YP_003815019.1| RNA polymerase sigma-70 factor [Prevotella melaninogenica ATCC
           25845]
 gi|302151174|gb|ADK97435.1| RNA polymerase sigma-70 factor [Prevotella melaninogenica ATCC
           25845]
          Length = 174

 Score = 37.5 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 12/85 (14%), Positives = 36/85 (42%), Gaps = 8/85 (9%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           +  +D +   ++   E    R  +  ++S L  + R +F      +     + ++ +  +
Sbjct: 93  LDYYDPEANDVMGYIEGLETRKQINDAISELPAKCREVFILSYQHDKKN--KEIAEQLGI 150

Query: 265 SRERVRQIEA---RAFKKVQESIQK 286
           S   +R +E    +A K ++  +++
Sbjct: 151 S---IRTVEVHLYKALKTLRTRLKR 172


>gi|218442035|ref|YP_002380364.1| RNA polymerase sigma factor RpoE [Cyanothece sp. PCC 7424]
 gi|218174763|gb|ACK73496.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Cyanothece sp. PCC
           7424]
          Length = 219

 Score = 37.5 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 20/111 (18%), Positives = 38/111 (34%), Gaps = 17/111 (15%)

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           R++   SL+A     D         + +D         +    +     L  +++ L   
Sbjct: 116 RVSNPVSLDAPRRVDDGE-------IDWDIVSDYPSPDDNLATREFYEQLRLAIADLPEA 168

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVS----RERVRQIEARAFKKVQESIQ 285
            R     R +    +  E ++    VS    + R+    ARA  K+Q  +Q
Sbjct: 169 FRTTIVLREI--EGMAYEEIAEITGVSLGTVKSRI----ARARAKLQSVLQ 213


>gi|319794005|ref|YP_004155645.1| anti-feci sigma factor, fecr [Variovorax paradoxus EPS]
 gi|315596468|gb|ADU37534.1| anti-FecI sigma factor, FecR [Variovorax paradoxus EPS]
          Length = 438

 Score = 37.5 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 14/58 (24%), Positives = 24/58 (41%), Gaps = 2/58 (3%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
           HD     + E+   +   + +  ++  L  R R IF A RL+        L+  + VS
Sbjct: 105 HDHSTHDIAERLSHRQALDAVDAALRQLPQRSRDIFLADRLEGTGH--AELAERYGVS 160


>gi|315150948|gb|EFT94964.1| putative ATP synthase F0, A subunit [Enterococcus faecalis TX0012]
          Length = 683

 Score = 37.5 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 30/149 (20%), Positives = 52/149 (34%), Gaps = 25/149 (16%)

Query: 135 LFFNLRRLKGHLQAITDNNLKPE-QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSS 193
           L   L R     Q    +++ PE ++  + +  NV   E+  +  +   DE  N   ++ 
Sbjct: 475 LNSLLNRSTQEEQQPFKDDMLPEKEIAEVEEPTNVDNEELEEIEDKALTDEVDNFEDSTD 534

Query: 194 D--KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM---LTRSMSVL--------NPRER 240
           D   NS +  D  V D +  +         +N   +   +   +  L        N RE 
Sbjct: 535 DEADNSLEEFDVPVLDENVSDFDTDTSLADENNIELEPIIENELDSLDSSVESSENDREE 594

Query: 241 RIFEARRLQENPVTLENLSSEFEVSRERV 269
            I E   L E     + ++    V   RV
Sbjct: 595 PIQE---LDE-----QEIADNLNV---RV 612


>gi|298242681|ref|ZP_06966488.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297555735|gb|EFH89599.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 177

 Score = 37.5 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 14/73 (19%), Positives = 35/73 (47%), Gaps = 2/73 (2%)

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           + Q+    ++ E + +   L +++  L P +R +   R +QE  +T   ++     S   
Sbjct: 98  EDQDLTPEQQAEEQEKWAWLLQTIEQLTPVQRELIRLRYVQEMHLT--QIAVLLGKSEGT 155

Query: 269 VRQIEARAFKKVQ 281
           VR++ +R  + ++
Sbjct: 156 VRKMLSRTLRHLK 168


>gi|120612380|ref|YP_972058.1| ECF subfamily RNA polymerase sigma-24 factor [Acidovorax citrulli
           AAC00-1]
 gi|120590844|gb|ABM34284.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Acidovorax
           citrulli AAC00-1]
          Length = 177

 Score = 37.5 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 19/135 (14%), Positives = 48/135 (35%), Gaps = 4/135 (2%)

Query: 130 ANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNAL 189
              +   + + R   H + + D ++  +  + +A+         I   C++  + +L+  
Sbjct: 18  VAHRAQLWRVARQIVHTEDLAD-DVVQDAYLKLAEGPGRVAERPIGYCCQVVRNLALDYC 76

Query: 190 INSSDKNSSQWQDWLVYDHD-GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
                + S +  D  V   D    +        +   + +   ++ L PR R +FE  R+
Sbjct: 77  RRHRVEASYRTFDVDVEAIDVPCHRSPDRHMCEQQVIHAIDEVLAQLPPRTRMVFELYRI 136

Query: 249 QENPVTLENLSSEFE 263
               +T   ++    
Sbjct: 137 --EGLTQRQIAERLG 149


>gi|298243306|ref|ZP_06967113.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297556360|gb|EFH90224.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 212

 Score = 37.5 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 11/73 (15%), Positives = 31/73 (42%), Gaps = 2/73 (2%)

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
            S   + + +  L+ +      +  E+ ER + ++ML  ++  L P+ R +   R + + 
Sbjct: 112 ESSGENGESETSLLSEIPDTNPLPEEEIERLDMQDMLQSAIQSLPPKFRSVVLLRYISQ- 170

Query: 252 PVTLENLSSEFEV 264
            ++   +     +
Sbjct: 171 -LSFSEIGQALSM 182


>gi|229099316|ref|ZP_04230247.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Bacillus cereus
           Rock3-29]
 gi|229118327|ref|ZP_04247683.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Bacillus cereus
           Rock1-3]
 gi|228665157|gb|EEL20643.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Bacillus cereus
           Rock1-3]
 gi|228684134|gb|EEL38081.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Bacillus cereus
           Rock3-29]
          Length = 194

 Score = 37.5 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 16/90 (17%), Positives = 32/90 (35%), Gaps = 10/90 (11%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS-- 265
            D    V  +   RK     L   +  L  + R +   R   +   T E ++   ++   
Sbjct: 104 DDPVVDVPEKVLLRKETEEQLLTVIQELPFKFRIVIVYRFYHD--YTYEEIAELLQIPIG 161

Query: 266 --RERVRQIEARAFKKVQESIQKQVELSSS 293
             R R+     RA +K++     +++   S
Sbjct: 162 TVRSRI----HRALEKIRNQSSIEIDEEES 187


>gi|310644791|ref|YP_003949550.1| RNA polymerase ecf-type sigma factor [Paenibacillus polymyxa SC2]
 gi|309249742|gb|ADO59309.1| RNA polymerase ECF-type sigma factor [Paenibacillus polymyxa SC2]
          Length = 196

 Score = 37.5 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 14/77 (18%), Positives = 32/77 (41%), Gaps = 2/77 (2%)

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           +       +  ER+     L+R++  L+  ER +   R  +E   T   +      S E 
Sbjct: 103 NMTSDSAAQVMERQLFSEPLSRALDQLSAEERNLLVLRIFEE--RTFGEIGEIMNKSEEA 160

Query: 269 VRQIEARAFKKVQESIQ 285
           +++   R   K+++ ++
Sbjct: 161 IKKKYGRTKTKLKKIME 177


>gi|284166584|ref|YP_003404863.1| DNA binding protein, Tfx family [Haloterrigena turkmenica DSM 5511]
 gi|284016239|gb|ADB62190.1| DNA binding protein, Tfx family [Haloterrigena turkmenica DSM 5511]
          Length = 155

 Score = 37.5 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 7/68 (10%)

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
           SVL  R+ ++   R   E  V+  +++     SR  V  IE+ A    +E+++K  E  +
Sbjct: 19  SVLTHRQAQVLALR---ERGVSQADIADALGTSRANVSSIESSA----RENLEKAHETVA 71

Query: 293 SPPLLQKP 300
               L+ P
Sbjct: 72  FAEALRAP 79


>gi|153011783|ref|YP_001372996.1| FliA/WhiG family RNA polymerase sigma 28 subunit [Ochrobactrum
           anthropi ATCC 49188]
 gi|151563671|gb|ABS17167.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG family
           [Ochrobactrum anthropi ATCC 49188]
          Length = 390

 Score = 37.5 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 20/160 (12%), Positives = 52/160 (32%), Gaps = 13/160 (8%)

Query: 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDE 184
           +  T  + +     L       +A       PE   +I  +      +    +  +    
Sbjct: 186 RRPTEFSVRDWLTQLAFETVEAEAQAARRAVPEDAASIEAEPEAPAEDPTEADQAM---- 241

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
                           +D +  D     +  +++ +       L R+++ L P ERR+  
Sbjct: 242 ----FEFYQPDEVLMLEDLIADDGGTDPETEVDRHDIAM---ALHRAIADLAPVERRVLY 294

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
              L++   T+   +    ++   V +I   A + ++ ++
Sbjct: 295 RMYLED--ATIAETAHLLGLTEAEVLKIAENAAETLRGTL 332


>gi|311031728|ref|ZP_07709818.1| RNA polymerase, sigma-24 subunit, ECF subfamily protein [Bacillus
           sp. m3-13]
          Length = 202

 Score = 37.5 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 18/80 (22%), Positives = 38/80 (47%), Gaps = 2/80 (2%)

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
            Q+  +IE  ER+  R  +  S+  L+  +++I   R  Q+    L+ ++   ++    V
Sbjct: 104 DQQASVIEIYERQETRKEMLASLKNLSESQQQIVTLRFYQDMK--LKEIADILDLPLGTV 161

Query: 270 RQIEARAFKKVQESIQKQVE 289
           +     A KK++  + K+ E
Sbjct: 162 KSNLFHALKKLKGVLSKEAE 181


>gi|261253906|ref|ZP_05946479.1| RNA polymerase sigma factor RpoE [Vibrio orientalis CIP 102891]
 gi|260937297|gb|EEX93286.1| RNA polymerase sigma factor RpoE [Vibrio orientalis CIP 102891]
          Length = 192

 Score = 37.5 bits (86), Expect = 2.7,   Method: Composition-based stats.
 Identities = 18/88 (20%), Positives = 33/88 (37%), Gaps = 3/88 (3%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
            VL +R + +GD  A + LVT +   V  +   Y      + +V  E  I   +A+  F 
Sbjct: 8   QVLIERVQ-NGDKQAFNLLVTKYQNKVCNLISRYVNNPGDVPDVAQEAFIKAYRAIPSFR 66

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWS 122
            E      T+         + +++    
Sbjct: 67  GE--SAFYTWLYRIAVNTAKNHLVAQGR 92


>gi|291443200|ref|ZP_06582590.1| LuxR-family transcriptional regulator [Streptomyces roseosporus
           NRRL 15998]
 gi|291346147|gb|EFE73051.1| LuxR-family transcriptional regulator [Streptomyces roseosporus
           NRRL 15998]
          Length = 920

 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 18/64 (28%), Positives = 37/64 (57%), Gaps = 5/64 (7%)

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           +++S L+ +ERR+ E   L     T + ++ +  +++  V Q   R F+K+  ++Q++ E
Sbjct: 861 KALSALSKQERRVAE---LASEGYTNQEIADQLFITKSTVEQHLTRVFRKL--NVQRRQE 915

Query: 290 LSSS 293
           LS S
Sbjct: 916 LSQS 919


>gi|290958601|ref|YP_003489783.1| sigma factor [Streptomyces scabiei 87.22]
 gi|260648127|emb|CBG71235.1| putative sigma factor [Streptomyces scabiei 87.22]
          Length = 194

 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 11/62 (17%), Positives = 22/62 (35%), Gaps = 2/62 (3%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L+           E       R+ L ++M  L  R+R +   R   +  +T   ++    
Sbjct: 112 LLSKPMPDMASAEEGAYDLLERDSLIKAMKGLQRRQREVLVLRYFAD--MTEAQVAETLG 169

Query: 264 VS 265
           +S
Sbjct: 170 LS 171


>gi|168705622|ref|ZP_02737899.1| hypothetical protein GobsU_39178 [Gemmata obscuriglobus UQM 2246]
          Length = 198

 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 17/63 (26%), Positives = 34/63 (53%), Gaps = 3/63 (4%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++ R+ + ++   L+PR+RRI E   L  +   +  +++E   + ERV   + +A KK+Q
Sbjct: 136 RDDRDAVAKAAEQLSPRQRRILE---LTADGWPVPEIATELATTVERVSDEKYKAIKKLQ 192

Query: 282 ESI 284
              
Sbjct: 193 HHF 195


>gi|162450150|ref|YP_001612517.1| ECF family RNA polymerase sigma factor [Sorangium cellulosum 'So ce
           56']
 gi|161160732|emb|CAN92037.1| ECF-family RNA polymerase sigma factor [Sorangium cellulosum 'So ce
           56']
          Length = 223

 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 14/75 (18%), Positives = 30/75 (40%), Gaps = 5/75 (6%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVL---NPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           E      +E    R+ L R++  L    P+E+  F    L       E +      S+  
Sbjct: 141 EDERSPLDEVTIARDDLRRALETLGTLPPKEQVAFSMFYLDGKE--QEEIGKILGHSKGY 198

Query: 269 VRQIEARAFKKVQES 283
           V ++  +A  +++++
Sbjct: 199 VCKLIQKAVAQLRDA 213


>gi|150008922|ref|YP_001303665.1| RNA polymerase ECF-type sigma factor [Parabacteroides distasonis
           ATCC 8503]
 gi|298375850|ref|ZP_06985806.1| ECF-type sigma factor [Bacteroides sp. 3_1_19]
 gi|149937346|gb|ABR44043.1| RNA polymerase ECF-type sigma factor [Parabacteroides distasonis
           ATCC 8503]
 gi|298266887|gb|EFI08544.1| ECF-type sigma factor [Bacteroides sp. 3_1_19]
          Length = 241

 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 10/91 (10%), Positives = 33/91 (36%), Gaps = 10/91 (10%)

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
                 +      +   ++ ++  E   R  +L ++++ L+P +R I     +       
Sbjct: 136 EDISLYEDTFQTDELFSRISLDTTEADERVKLLMKALTKLSPHQREIIYLYYVNGLGH-- 193

Query: 256 ENLSSEFEV----SRERVRQIEARAFKKVQE 282
           + ++    +    S+     + +R   K++ 
Sbjct: 194 DEIAEILGINYQSSK----NLLSRTLSKLRR 220


>gi|330809309|ref|YP_004353771.1| Response regulator, NarL family [Pseudomonas brassicacearum subsp.
           brassicacearum NFM421]
 gi|327377417|gb|AEA68767.1| putative Response regulator, NarL family [Pseudomonas
           brassicacearum subsp. brassicacearum NFM421]
          Length = 165

 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 12/53 (22%), Positives = 24/53 (45%), Gaps = 4/53 (7%)

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           +L  ++S L  R+R++     L     T + ++ +  +S   VR I   +  K
Sbjct: 88  ILDDALSQLTARQRQVL---GLIAAGKTNKEIARDLGISPFTVR-IHVSSLLK 136


>gi|226314185|ref|YP_002774081.1| RNA polymerase ECF-type sigma factor [Brevibacillus brevis NBRC
           100599]
 gi|226097135|dbj|BAH45577.1| RNA polymerase ECF-type sigma factor [Brevibacillus brevis NBRC
           100599]
          Length = 189

 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 14/74 (18%), Positives = 29/74 (39%), Gaps = 2/74 (2%)

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
               +   R +    L ++++ L+ +ER I   +           ++    VS   +  +
Sbjct: 111 SSPEDIVIRDDNHQALFQALTKLSDKERNIIAMKYAAGLKN--AEIAELLGVSGSNIGVV 168

Query: 273 EARAFKKVQESIQK 286
             R  KK+Q  +QK
Sbjct: 169 LYRCLKKLQMELQK 182


>gi|189466589|ref|ZP_03015374.1| hypothetical protein BACINT_02964 [Bacteroides intestinalis DSM
           17393]
 gi|189434853|gb|EDV03838.1| hypothetical protein BACINT_02964 [Bacteroides intestinalis DSM
           17393]
          Length = 186

 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 13/70 (18%), Positives = 30/70 (42%), Gaps = 3/70 (4%)

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           +    +    +L  ++  L  + R I   R   E       ++ +  VS E V  ++  A
Sbjct: 110 DAVVEEETYRILAEAIDKLPDQMRAI--MRLAMEGKKN-AEIAEQLNVSVETVHTLKKIA 166

Query: 277 FKKVQESIQK 286
           +KK++  +++
Sbjct: 167 YKKLRIYLKE 176


>gi|169349650|ref|ZP_02866588.1| hypothetical protein CLOSPI_00388 [Clostridium spiroforme DSM 1552]
 gi|169293725|gb|EDS75858.1| hypothetical protein CLOSPI_00388 [Clostridium spiroforme DSM 1552]
          Length = 146

 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 10/61 (16%), Positives = 29/61 (47%), Gaps = 2/61 (3%)

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             L  ++  L+ +ER +   R  Q   ++ + ++  + VS   + +  +   KK++  ++
Sbjct: 86  EKLAVALCKLSCKERDVILLRYFQ--SMSDQEIAELYHVSHSAIYRRRSNGLKKLKTVLK 143

Query: 286 K 286
           +
Sbjct: 144 E 144


>gi|111026455|ref|YP_708738.1| hypothetical protein RHA1_ro10391 [Rhodococcus jostii RHA1]
 gi|110825298|gb|ABH00580.1| conserved hypothetical protein [Rhodococcus jostii RHA1]
          Length = 199

 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 3/35 (8%)

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
            RE+     R+L     T+E  +    VS  R+RQ
Sbjct: 75  EREQ---RMRQLTATAKTVEEAARMLGVSTSRIRQ 106


>gi|86749325|ref|YP_485821.1| sigma-24 (FecI-like) [Rhodopseudomonas palustris HaA2]
 gi|86572353|gb|ABD06910.1| sigma-24 (FecI-like) [Rhodopseudomonas palustris HaA2]
          Length = 193

 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 23/96 (23%), Positives = 42/96 (43%), Gaps = 3/96 (3%)

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
               ++   R A + +LN     + + S+   D L++  D    VL   E R +    L 
Sbjct: 76  VRNPVAYLLRAAFNNALNLRRAETRRLSADEVDALLHIADDAPDVLRIIEGRSDI-ERLK 134

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
           R M+ L PR+R I  A R+  + ++   ++    +S
Sbjct: 135 RIMTELTPRQREILLAARV--DGLSRHEIADRLGIS 168


>gi|49081730|gb|AAT50265.1| PA0149 [synthetic construct]
          Length = 182

 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 21/112 (18%), Positives = 43/112 (38%), Gaps = 6/112 (5%)

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              E+ S   R A + +++  +        Q  DWL     G+     +  E  ++   +
Sbjct: 56  PVEELGSYLLRSARNLAID-HLRGEGSRQRQLDDWLPEQRQGEPVGPEQALEAGDQWRRV 114

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++  L  R RRIF   R+  +  T   ++   ++S+  V   E    + +
Sbjct: 115 EAALRGLPERTRRIFLLNRI--HGRTYAEIAQAMQLSQSAV---EKHMMRAL 161


>gi|158313438|ref|YP_001505946.1| ECF subfamily RNA polymerase sigma-24 factor [Frankia sp. EAN1pec]
 gi|158108843|gb|ABW11040.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Frankia sp.
           EAN1pec]
          Length = 176

 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 10/65 (15%), Positives = 24/65 (36%), Gaps = 2/65 (3%)

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
           +D L            +  +  + R+ L  ++  L PR+R +   R   +   T   +++
Sbjct: 81  EDPLDTATVPIPDSTPDSTDTLSTRDQLFTALRQLPPRQRAVIVLRYFDDLSET--QIAT 138

Query: 261 EFEVS 265
               +
Sbjct: 139 AVGCT 143


>gi|296448525|ref|ZP_06890402.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Methylosinus
           trichosporium OB3b]
 gi|296253964|gb|EFH01114.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Methylosinus
           trichosporium OB3b]
          Length = 170

 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 14/60 (23%), Positives = 25/60 (41%), Gaps = 2/60 (3%)

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           D            E +    +L +++  L PR R I  A R++  P  L  ++ +  +SR
Sbjct: 90  DAADDSPGPARIVEAQQDMELLRQALEELTPRRRLILLASRVEGTP--LRQIADDLGLSR 147


>gi|289581066|ref|YP_003479532.1| DNA binding protein, Tfx family [Natrialba magadii ATCC 43099]
 gi|289530619|gb|ADD04970.1| DNA binding protein, Tfx family [Natrialba magadii ATCC 43099]
          Length = 154

 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 7/68 (10%)

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
           SVL  R+ ++   R   E   +  +++     SR  V  IEA A    +E+++K  E  +
Sbjct: 19  SVLTNRQAQVLALR---ERDTSQADIADALGTSRANVSSIEASA----RENVEKARETVA 71

Query: 293 SPPLLQKP 300
               L+ P
Sbjct: 72  FAEALRAP 79


>gi|126736933|ref|ZP_01752668.1| RNA polymerase sigma-70 factor, ECF family protein [Roseobacter sp.
           SK209-2-6]
 gi|126721518|gb|EBA18221.1| RNA polymerase sigma-70 factor, ECF family protein [Roseobacter sp.
           SK209-2-6]
          Length = 291

 Score = 37.5 bits (86), Expect = 2.8,   Method: Composition-based stats.
 Identities = 20/76 (26%), Positives = 36/76 (47%), Gaps = 2/76 (2%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            DG ++++   E  +     L  +M  LN RER  F  R   +     + ++   E +  
Sbjct: 88  QDGPQEIVPHFELAQECELALLWAMERLNERERAAFILREAFDAGY--DEIAETLETTPA 145

Query: 268 RVRQIEARAFKKVQES 283
             RQ+ +R+ KK+QE+
Sbjct: 146 ACRQLVSRSQKKLQET 161


>gi|325287085|ref|YP_004262875.1| ECF subfamily RNA polymerase sigma-24 subunit [Cellulophaga lytica
           DSM 7489]
 gi|324322539|gb|ADY30004.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Cellulophaga
           lytica DSM 7489]
          Length = 170

 Score = 37.1 bits (85), Expect = 2.8,   Method: Composition-based stats.
 Identities = 19/79 (24%), Positives = 32/79 (40%), Gaps = 8/79 (10%)

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D   +      E K  +  L R+++ L   +R  F   R+ +       ++    VS   
Sbjct: 94  DVSNETPEFLLEEKQFQEKLDRALANLPENQRTTFLLNRIDKKKY--AEIAELEGVS--- 148

Query: 269 VRQIEAR---AFKKVQESI 284
           V+ IE R   A K ++E I
Sbjct: 149 VKAIEKRMHLALKSLREHI 167


>gi|313902029|ref|ZP_07835443.1| sigma-70 region 4 domain protein [Thermaerobacter subterraneus DSM
           13965]
 gi|313467696|gb|EFR63196.1| sigma-70 region 4 domain protein [Thermaerobacter subterraneus DSM
           13965]
          Length = 1070

 Score = 37.1 bits (85), Expect = 2.8,   Method: Composition-based stats.
 Identities = 11/48 (22%), Positives = 21/48 (43%), Gaps = 2/48 (4%)

Query: 225 RNMLTRSMSVLNPRERRIFEARR--LQENPVTLENLSSEFEVSRERVR 270
            + L   +  L  RER +   R   L E    L  +++ ++ +R+ V 
Sbjct: 316 EDWLQELIEPLPDREREVLALRYGLLGEEAHDLSAIAARWQTTRQWVS 363


>gi|303236167|ref|ZP_07322767.1| sigma-70, region 4 [Prevotella disiens FB035-09AN]
 gi|302483626|gb|EFL46621.1| sigma-70, region 4 [Prevotella disiens FB035-09AN]
          Length = 169

 Score = 37.1 bits (85), Expect = 2.8,   Method: Composition-based stats.
 Identities = 16/73 (21%), Positives = 30/73 (41%), Gaps = 2/73 (2%)

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
           +  +  E +     L + +  L   E  I   R  Q    T E ++   ++S   V  + 
Sbjct: 95  LPTDSLESQEMVVWLEQRIKELPETEHTILYMR--QVEKRTNEEIARLLDISVASVSTLL 152

Query: 274 ARAFKKVQESIQK 286
           ARA + + E I++
Sbjct: 153 ARARRHLLEKIKR 165


>gi|302535329|ref|ZP_07287671.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces sp. C]
 gi|302444224|gb|EFL16040.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces sp. C]
          Length = 199

 Score = 37.1 bits (85), Expect = 2.9,   Method: Composition-based stats.
 Identities = 12/62 (19%), Positives = 23/62 (37%), Gaps = 2/62 (3%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L+           E    +  R+ L R+M  L  R+R +   R   +  +T   ++    
Sbjct: 116 LLSKPMPDMASAEEGAYDQLERDDLIRAMRGLQRRQREVLVLRYFAD--MTEVQVAETLG 173

Query: 264 VS 265
           +S
Sbjct: 174 IS 175


>gi|258516492|ref|YP_003192714.1| putative RNA polymerase sigma factor SigI [Desulfotomaculum
           acetoxidans DSM 771]
 gi|257780197|gb|ACV64091.1| RNA polymerase, sigma 28 subunit, SigI [Desulfotomaculum
           acetoxidans DSM 771]
          Length = 294

 Score = 37.1 bits (85), Expect = 2.9,   Method: Composition-based stats.
 Identities = 13/85 (15%), Positives = 32/85 (37%), Gaps = 2/85 (2%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMG--YRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           R    GD  +   ++  +  L+ KI      R       + +S G I   +A+ ++  + 
Sbjct: 61  RIAREGDAKSREDILEMYKPLIGKITSNLCQRRLEWGRDDELSIGLIAFNEAIDRYKEDC 120

Query: 98  GFRLATYSMWWIKAAMQEYILRSWS 122
                 Y+   +++ + +Y  +   
Sbjct: 121 RVPFPAYARIVVRSRLTDYFRKEAR 145


>gi|228996865|ref|ZP_04156499.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus mycoides
           Rock3-17]
 gi|228762926|gb|EEM11839.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus mycoides
           Rock3-17]
          Length = 188

 Score = 37.1 bits (85), Expect = 2.9,   Method: Composition-based stats.
 Identities = 14/62 (22%), Positives = 26/62 (41%), Gaps = 3/62 (4%)

Query: 206 YDHDGQEQVLIEKEER-KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
            D D      IE E      R+ L + ++ L P +++IF  + L       E +  +  +
Sbjct: 101 DDFDVNTGKSIEDELIIMEDRDELIKLINQLEPIDQKIFIMKFLLGLKT--EEIGEKLGL 158

Query: 265 SR 266
           +R
Sbjct: 159 TR 160


>gi|220907060|ref|YP_002482371.1| RNA polymerase sigma factor RpoE [Cyanothece sp. PCC 7425]
 gi|219863671|gb|ACL44010.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Cyanothece sp. PCC
           7425]
          Length = 221

 Score = 37.1 bits (85), Expect = 2.9,   Method: Composition-based stats.
 Identities = 20/111 (18%), Positives = 40/111 (36%), Gaps = 17/111 (15%)

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           R     SL+A +   D         + ++    E    E          L ++++ L   
Sbjct: 119 RNQSPLSLDAPLTMDDGE-------MGWEIASPEPGPEEALSANEFYGQLRQAIACLPQD 171

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVS----RERVRQIEARAFKKVQESIQ 285
            R     R +    ++ E ++    VS    + R+    ARA +++Q  +Q
Sbjct: 172 FRTTIVLREI--EGLSYEEIAEITGVSLGTVKSRI----ARARQRLQTQLQ 216


>gi|167526868|ref|XP_001747767.1| hypothetical protein [Monosiga brevicollis MX1]
 gi|163773871|gb|EDQ87507.1| predicted protein [Monosiga brevicollis MX1]
          Length = 8735

 Score = 37.1 bits (85), Expect = 2.9,   Method: Composition-based stats.
 Identities = 23/155 (14%), Positives = 58/155 (37%), Gaps = 20/155 (12%)

Query: 111  AAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSE 170
              +Q  +       +     ++  +    RR    +Q   D+  + E +  +  +L  ++
Sbjct: 7833 QEVQR-LTEQLDNCRRELRQHEFTIHTAERRAHDLMQVAQDHEERSEILARLEAELKQAQ 7891

Query: 171  SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM--- 227
             +++S+   LA   +  A I+   + + + +  L +DHD      +E  +R+  +     
Sbjct: 7892 LQIVSLEQDLARQSNHEAEIDFLRQANQELKSML-HDHDIALGPQVEALDRQTSQGWTTT 7950

Query: 228  ---------------LTRSMSVLNPRERRIFEARR 247
                           L +++  L+  E++  E  R
Sbjct: 7951 LVDSAVQTEHEYADTLFKALEGLDDAEKQRLELER 7985


>gi|330465617|ref|YP_004403360.1| RNA polymerase sigma-70 factor [Verrucosispora maris AB-18-032]
 gi|328808588|gb|AEB42760.1| RNA polymerase sigma-70 factor [Verrucosispora maris AB-18-032]
          Length = 270

 Score = 37.1 bits (85), Expect = 2.9,   Method: Composition-based stats.
 Identities = 16/94 (17%), Positives = 41/94 (43%), Gaps = 5/94 (5%)

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
            E+  +++ E++  R++L R +  L  R+R +   R  ++   +    ++   +S   V+
Sbjct: 90  PERPGVDEIEQQLDRDVLWRHLRALPARQRAVLVLRFYEDLSESQT--AALLNISTGTVK 147

Query: 271 QIEARAFKKVQESI---QKQVELSSSPPLLQKPR 301
              +RA   ++  I   +      ++   +  PR
Sbjct: 148 SQTSRALATLRRRIGADEAFALPGAASSSVDPPR 181


>gi|83592219|ref|YP_425971.1| sigma-24 (FecI) [Rhodospirillum rubrum ATCC 11170]
 gi|83575133|gb|ABC21684.1| Sigma-24 (FecI) [Rhodospirillum rubrum ATCC 11170]
          Length = 171

 Score = 37.1 bits (85), Expect = 2.9,   Method: Composition-based stats.
 Identities = 18/96 (18%), Positives = 41/96 (42%), Gaps = 2/96 (2%)

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             + ++   R+  + +++ L   S +        ++ D D Q     E    ++   ++ 
Sbjct: 54  VRQPLAYLYRVVRNTAVDCLRRLSAEERRNEAGEILSDPDRQAPSPEEIALGRDHLRLVA 113

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            ++S L  R RR FE +R     ++ + ++   EVS
Sbjct: 114 AALSELPERNRRAFELQRF--EGLSFQQIAQHLEVS 147


>gi|292492142|ref|YP_003527581.1| response regulator receiver [Nitrosococcus halophilus Nc4]
 gi|291580737|gb|ADE15194.1| response regulator receiver [Nitrosococcus halophilus Nc4]
          Length = 205

 Score = 37.1 bits (85), Expect = 2.9,   Method: Composition-based stats.
 Identities = 18/79 (22%), Positives = 42/79 (53%), Gaps = 11/79 (13%)

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE---ARAFKKV 280
           +R+ + + ++ L PRER +     + E  +  + +++E  VS   +R +E   AR   K+
Sbjct: 133 QRDTIEKRLASLTPRERDVLNK--VIEGKLN-KVIAAELGVS---IRTVEIHRARIMSKM 186

Query: 281 QESIQKQVELSSSPPLLQK 299
           +  +++  EL+    +L++
Sbjct: 187 R--VRRATELARLVLMLRR 203


>gi|228990769|ref|ZP_04150734.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus
           pseudomycoides DSM 12442]
 gi|229004542|ref|ZP_04162281.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus mycoides
           Rock1-4]
 gi|228756733|gb|EEM06039.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus mycoides
           Rock1-4]
 gi|228769295|gb|EEM17893.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus
           pseudomycoides DSM 12442]
          Length = 188

 Score = 37.1 bits (85), Expect = 2.9,   Method: Composition-based stats.
 Identities = 14/62 (22%), Positives = 26/62 (41%), Gaps = 3/62 (4%)

Query: 206 YDHDGQEQVLIEKEER-KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
            D D      IE E      R+ L + ++ L P +++IF  + L       E +  +  +
Sbjct: 101 DDFDVNTGKSIEDELIIMEDRDELIKLINQLEPIDQKIFIMKFLLGLKT--EEIGEKLGL 158

Query: 265 SR 266
           +R
Sbjct: 159 TR 160


>gi|190574839|ref|YP_001972684.1| putative ECF family sigma factor [Stenotrophomonas maltophilia
           K279a]
 gi|190012761|emb|CAQ46390.1| putative ECF-family sigma factor [Stenotrophomonas maltophilia
           K279a]
          Length = 169

 Score = 37.1 bits (85), Expect = 2.9,   Method: Composition-based stats.
 Identities = 11/67 (16%), Positives = 25/67 (37%), Gaps = 2/67 (2%)

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
             D  +        +  ++     +   L   ++ L PR R++F   R+    + L  + 
Sbjct: 85  LDDTQLQAIADPAPLPEQRLLDAEQLRHLDAIVAALPPRSRQVFLLARV--EQLALAEIG 142

Query: 260 SEFEVSR 266
            +  +SR
Sbjct: 143 RQLGISR 149


>gi|303238257|ref|ZP_07324793.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Acetivibrio cellulolyticus CD2]
 gi|302594303|gb|EFL64015.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Acetivibrio cellulolyticus CD2]
          Length = 250

 Score = 37.1 bits (85), Expect = 2.9,   Method: Composition-based stats.
 Identities = 18/85 (21%), Positives = 35/85 (41%), Gaps = 5/85 (5%)

Query: 39  KRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM---QAVKKFDP 95
           KR + +GD       ++ +   ++K      G  + I     E +I LM   +A+  FD 
Sbjct: 22  KRIQ-NGDWFLKEEFISDYTPFILKTVARITGKYVDIENS-EEYSIALMAFDEAINCFDI 79

Query: 96  ERGFRLATYSMWWIKAAMQEYILRS 120
            +      +S   I   + +YI ++
Sbjct: 80  GKNKSFLGFSDLVINRRIIDYIRKN 104


>gi|255530866|ref|YP_003091238.1| RNA polymerase sigma-70 factor [Pedobacter heparinus DSM 2366]
 gi|255343850|gb|ACU03176.1| RNA polymerase sigma-70 factor [Pedobacter heparinus DSM 2366]
          Length = 197

 Score = 37.1 bits (85), Expect = 2.9,   Method: Composition-based stats.
 Identities = 17/82 (20%), Positives = 43/82 (52%), Gaps = 2/82 (2%)

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           + ++  LIE+ E +    ++   +  L P+ R +F   R  +  ++ + ++++ ++S   
Sbjct: 107 NAEDHSLIEQIESRELAALINMEIEKLPPKCREVFILSR--KGFLSNKEIAAKLDISENT 164

Query: 269 VRQIEARAFKKVQESIQKQVEL 290
           V Q   +A  K++ S+ + +EL
Sbjct: 165 VEQHIRKAISKLRMSLGQLIEL 186


>gi|163753629|ref|ZP_02160752.1| putative RNA polymerase ECF-type sigma factor [Kordia algicida
           OT-1]
 gi|161325843|gb|EDP97169.1| putative RNA polymerase ECF-type sigma factor [Kordia algicida
           OT-1]
          Length = 169

 Score = 37.1 bits (85), Expect = 2.9,   Method: Composition-based stats.
 Identities = 15/75 (20%), Positives = 34/75 (45%), Gaps = 8/75 (10%)

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           +      E K     L  +++ L+ ++R +F   R+  +  T   ++   ++S++ V   
Sbjct: 97  ESPEFLLEEKEFLTKLENAIAGLSEKQREVFLLNRI--DKKTYAEIAVFLDISKKAV--- 151

Query: 273 EAR---AFKKVQESI 284
           E R   A K +++ I
Sbjct: 152 EKRMRNALKTLRKEI 166


>gi|225018778|ref|ZP_03707970.1| hypothetical protein CLOSTMETH_02728 [Clostridium methylpentosum
           DSM 5476]
 gi|224948506|gb|EEG29715.1| hypothetical protein CLOSTMETH_02728 [Clostridium methylpentosum
           DSM 5476]
          Length = 152

 Score = 37.1 bits (85), Expect = 3.0,   Method: Composition-based stats.
 Identities = 10/59 (16%), Positives = 24/59 (40%), Gaps = 2/59 (3%)

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           L  ++S L  + R +           T   +  E+  SR      +  A K++++ +++
Sbjct: 85  LADALSKLTEQRRNVLFLYFFFGYTDT--QIGKEYGRSRSTANYWKLAALKQLRKEMER 141


>gi|162450688|ref|YP_001613055.1| ECF family RNA polymerase sigma factor [Sorangium cellulosum 'So ce
           56']
 gi|161161270|emb|CAN92575.1| ECF-family RNA polymerase sigma factor [Sorangium cellulosum 'So ce
           56']
          Length = 208

 Score = 37.1 bits (85), Expect = 3.0,   Method: Composition-based stats.
 Identities = 21/104 (20%), Positives = 33/104 (31%), Gaps = 6/104 (5%)

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           I   L V    +     R    E+L       +    +            E  L EK + 
Sbjct: 80  IYPWLRVIALRIALDMLRARRREALFEP----EDLQREIDAAETDLTARGEAELCEKRDL 135

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            + R  +  ++  LNPR       R L E P   + ++    VS
Sbjct: 136 ADARARVEDALGRLNPRYAEAIRLRVLDERPR--DEVALALGVS 177


>gi|332655189|ref|ZP_08420930.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ruminococcaceae
           bacterium D16]
 gi|332516049|gb|EGJ45658.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ruminococcaceae
           bacterium D16]
          Length = 175

 Score = 37.1 bits (85), Expect = 3.0,   Method: Composition-based stats.
 Identities = 17/93 (18%), Positives = 38/93 (40%), Gaps = 5/93 (5%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE    +  +  G   AA +LV ++   + + A    G+     ++     + +++A+  
Sbjct: 3   EEQKWIRDIQRRGSRQAADKLVRAYYDEIYRFAYRQLGHKEDALDLTQNIFLAVLRALPT 62

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVK 125
           FD  +    A++  W  + A  + I      V+
Sbjct: 63  FDGRK----ASFRTWLYRIAAHKAI-DCRRKVR 90


>gi|300311653|ref|YP_003775745.1| ferric regulator sigma-24 subunit [Herbaspirillum seropedicae SmR1]
 gi|300074438|gb|ADJ63837.1| ferric regulator sigma-24 subunit protein [Herbaspirillum
           seropedicae SmR1]
          Length = 178

 Score = 37.1 bits (85), Expect = 3.0,   Method: Composition-based stats.
 Identities = 16/99 (16%), Positives = 40/99 (40%), Gaps = 2/99 (2%)

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           +    + ++   R+  + +++    S+ +     ++    D   +          +   +
Sbjct: 54  DFDIKQPVAYLYRIVRNLAIDRHRRSAFECDVFTEEEDGLDVHQEGDSPEAIAISRQYLS 113

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
           M+ R++  L  R RR FE  RL    +T   +++E  +S
Sbjct: 114 MIGRALEGLPARTRRAFELYRLSG--LTQREIAAELNIS 150


>gi|298251191|ref|ZP_06974995.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297549195|gb|EFH83062.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 189

 Score = 37.1 bits (85), Expect = 3.0,   Method: Composition-based stats.
 Identities = 15/87 (17%), Positives = 32/87 (36%), Gaps = 2/87 (2%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
             SS  +   V + D   Q+  +   R      L   +  LN  ++ + + R + +    
Sbjct: 90  DQSSIDEIIGVLEEDNIYQLPEQLTLRYEDYARLRTHIRKLNALQQEVLQLRFVYDMHSV 149

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQ 281
              +      +   +R I +RA  K++
Sbjct: 150 --EIGKRLNKNASAIRAILSRALNKLR 174


>gi|84496587|ref|ZP_00995441.1| putative RNA polymerase sigma factor [Janibacter sp. HTCC2649]
 gi|84383355|gb|EAP99236.1| putative RNA polymerase sigma factor [Janibacter sp. HTCC2649]
          Length = 174

 Score = 37.1 bits (85), Expect = 3.0,   Method: Composition-based stats.
 Identities = 9/43 (20%), Positives = 22/43 (51%), Gaps = 2/43 (4%)

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
           + R+ +   ++ L+ RER I   R   +  ++   ++ E ++S
Sbjct: 108 DHRDSIVHELAGLSDRERTIVVLRYYLD--LSERQVAEELDIS 148


>gi|323465878|gb|ADX69565.1| Putative DNA-directed RNA polymerase sigma factor, sigma H
           [Lactobacillus helveticus H10]
          Length = 186

 Score = 37.1 bits (85), Expect = 3.0,   Method: Composition-based stats.
 Identities = 26/147 (17%), Positives = 50/147 (34%), Gaps = 14/147 (9%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           E  L K+ ++ GD +A   L   +  LV K+  GY        +   E  I   +A   +
Sbjct: 10  EKKLIKQVKK-GDDAALEELFALYQPLVNKVLKGYYLRHYDQKDWQQEAMIICYEAAMVY 68

Query: 94  DPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNN 153
              +G               +  +      +    TA ++R + N       L+ I    
Sbjct: 69  SERKGNF---------AGLYKAKLTNHARTLVRYHTALRRRTYNN----SISLERIDLQG 115

Query: 154 LKPEQVVAIAKKLNVSESEVISMNCRL 180
           +   +   +A  +N + +  +    RL
Sbjct: 116 INEPKRSELAIPINDTYNNFVKSLSRL 142


>gi|311899919|dbj|BAJ32327.1| putative RNA polymerase ECF subfamily sigma factor [Kitasatospora
           setae KM-6054]
          Length = 172

 Score = 37.1 bits (85), Expect = 3.0,   Method: Composition-based stats.
 Identities = 13/83 (15%), Positives = 34/83 (40%), Gaps = 2/83 (2%)

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           +  V +   +  +   +      R  L  ++  L PR R     R L++   +LE  +  
Sbjct: 82  ELAVDEFPEEPSIGAHEGSAAALRLTLIEALRQLPPRNRAAVVLRYLED--YSLEETAEA 139

Query: 262 FEVSRERVRQIEARAFKKVQESI 284
             ++   V+ + +R+  +++  +
Sbjct: 140 MGITVSAVKSLNSRSMTRLRAIL 162


>gi|259506704|ref|ZP_05749606.1| RNA polymerase sigma-70 factor, ECF subfamily [Corynebacterium
           efficiens YS-314]
 gi|259165722|gb|EEW50276.1| RNA polymerase sigma-70 factor, ECF subfamily [Corynebacterium
           efficiens YS-314]
          Length = 182

 Score = 37.1 bits (85), Expect = 3.0,   Method: Composition-based stats.
 Identities = 13/83 (15%), Positives = 34/83 (40%), Gaps = 2/83 (2%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           + D +       E     +  N +   + +L+ + R I   R +    ++ E  +   + 
Sbjct: 99  IPDTEPDANSPEEFALVADGSNRVRELLDLLSEKARDILILRVMVG--LSAEETAEMVDS 156

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +   VR  + RA   ++ ++++Q
Sbjct: 157 TPGAVRVAQHRALTTLRSALEQQ 179


>gi|325964962|ref|YP_004242868.1| RNA polymerase sigma factor, sigma-70 family [Arthrobacter
           phenanthrenivorans Sphe3]
 gi|323471049|gb|ADX74734.1| RNA polymerase sigma factor, sigma-70 family [Arthrobacter
           phenanthrenivorans Sphe3]
          Length = 191

 Score = 37.1 bits (85), Expect = 3.0,   Method: Composition-based stats.
 Identities = 9/57 (15%), Positives = 30/57 (52%), Gaps = 3/57 (5%)

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQ-ESIQK 286
            +  L+   + +   R + +  ++LE ++     S   ++Q++ RA + ++ +++Q+
Sbjct: 132 LLEGLSEEHQEVLALRVVAD--LSLEQVARIMGKSTGAIKQLQRRALQNLKAQTLQR 186


>gi|297519403|ref|ZP_06937789.1| RNA polymerase sigma factor RpoE [Escherichia coli OP50]
          Length = 104

 Score = 37.1 bits (85), Expect = 3.0,   Method: Composition-based stats.
 Identities = 19/88 (21%), Positives = 34/88 (38%), Gaps = 4/88 (4%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
            VL +R ++ GD  A + LV  +   V  +   Y   G  + +VV E  I   +A+  F 
Sbjct: 8   QVLVERVQK-GDQKAFNLLVVRYQHKVASLVSRYVPSG-DVPDVVQEAFIKAYRALDSFR 65

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWS 122
            +      T+         + Y++    
Sbjct: 66  GD--SAFYTWLYRIAVNTAKNYLVAQGR 91


>gi|326793244|ref|YP_004311065.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           lentocellum DSM 5427]
 gi|326544008|gb|ADZ85867.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           lentocellum DSM 5427]
          Length = 162

 Score = 37.1 bits (85), Expect = 3.0,   Method: Composition-based stats.
 Identities = 22/94 (23%), Positives = 38/94 (40%), Gaps = 9/94 (9%)

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D +SS   +  V D  G EQ  I+KE  K    +L       + R ++I   R       
Sbjct: 75  DIDSSALFEIYVTD--GIEQAFIDKEIIKRINELLGEK----DERTKQIIYMR---AEGY 125

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
               +  +  +S    R IE R  + ++E + ++
Sbjct: 126 AFAEIGKKLGISENSARVIEFRTKRWLKEKLLEE 159


>gi|268318160|ref|YP_003291879.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Rhodothermus
           marinus DSM 4252]
 gi|262335694|gb|ACY49491.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Rhodothermus
           marinus DSM 4252]
          Length = 201

 Score = 37.1 bits (85), Expect = 3.0,   Method: Composition-based stats.
 Identities = 15/75 (20%), Positives = 30/75 (40%), Gaps = 2/75 (2%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E   +++ + +  R  L  +++ L  R R  F   R  E+  T   ++    VS + V  
Sbjct: 125 EPDGLQRLQAEEFRQALEEAIASLPERRRLTFLLHR--EHGFTYAEIARIMGVSPKTVSN 182

Query: 272 IEARAFKKVQESIQK 286
               A K ++  +  
Sbjct: 183 QLTEAVKYLRARLAS 197


>gi|302404836|ref|XP_003000255.1| AdhA [Verticillium albo-atrum VaMs.102]
 gi|261360912|gb|EEY23340.1| AdhA [Verticillium albo-atrum VaMs.102]
          Length = 320

 Score = 37.1 bits (85), Expect = 3.0,   Method: Composition-based stats.
 Identities = 19/102 (18%), Positives = 37/102 (36%), Gaps = 4/102 (3%)

Query: 41  YREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFR 100
           +R+  D     R       +V  I       G         G  G M+  ++   E+G R
Sbjct: 157 FRQQPDSEERDRCFIITGSMVGWI----DSPGNWEYTSTKYGLHGFMRTARRNSWEQGIR 212

Query: 101 LATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRL 142
           +   +  WIK+A++      W + +      Q+ +   + R+
Sbjct: 213 IVYVAPCWIKSAIRTAEYEKWLMDRGVEFGEQEDVGGCMMRV 254


>gi|210613652|ref|ZP_03289811.1| hypothetical protein CLONEX_02018 [Clostridium nexile DSM 1787]
 gi|210151082|gb|EEA82090.1| hypothetical protein CLONEX_02018 [Clostridium nexile DSM 1787]
          Length = 234

 Score = 37.1 bits (85), Expect = 3.0,   Method: Composition-based stats.
 Identities = 22/77 (28%), Positives = 40/77 (51%), Gaps = 2/77 (2%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  D +G E  L++ EER NR+ +    MSVL+ +++++ +      N  T + ++ E  
Sbjct: 149 ISEDFEGMEDELMDVEERVNRQQIAEEMMSVLSDKQKKVVQEFYW--NQKTHKQIAKENG 206

Query: 264 VSRERVRQIEARAFKKV 280
           V R  V +I   A  K+
Sbjct: 207 VKRNAVTEILKYALNKI 223


>gi|288802328|ref|ZP_06407768.1| RNA polymerase sigma-70 factor, ECF subfamily [Prevotella
           melaninogenica D18]
 gi|288335295|gb|EFC73730.1| RNA polymerase sigma-70 factor, ECF subfamily [Prevotella
           melaninogenica D18]
          Length = 174

 Score = 37.1 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 12/85 (14%), Positives = 36/85 (42%), Gaps = 8/85 (9%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           +  +D +   ++   E    R  +  ++S L  + R +F      +     + ++ +  +
Sbjct: 93  LDYYDPEANDVMGYIEGLETRKQINDAISELPAKCREVFILSYQHDKKN--KEIAEQLGI 150

Query: 265 SRERVRQIEA---RAFKKVQESIQK 286
           S   +R +E    +A K ++  +++
Sbjct: 151 S---IRTVEVHLYKALKTLRTRLKR 172


>gi|302526573|ref|ZP_07278915.1| sigma factor [Streptomyces sp. AA4]
 gi|302435468|gb|EFL07284.1| sigma factor [Streptomyces sp. AA4]
          Length = 310

 Score = 37.1 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 22/106 (20%), Positives = 38/106 (35%), Gaps = 2/106 (1%)

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            E  +   R+   ++L  L     +  S    WL         V  + E   +    +  
Sbjct: 69  REHRAYLVRITTRQALTRLRTLGRRKESYVGTWLPEPLLTAPDVAEDVELADHVSMAMLL 128

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
            +  L P ER +F  R + + P   + ++     +   VRQI  RA
Sbjct: 129 VLETLRPTERAVFVLREVFDLPY--DEIAEAVGKTPAAVRQIGHRA 172


>gi|220911446|ref|YP_002486755.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Arthrobacter
           chlorophenolicus A6]
 gi|219858324|gb|ACL38666.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Arthrobacter
           chlorophenolicus A6]
          Length = 183

 Score = 37.1 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 16/86 (18%), Positives = 32/86 (37%), Gaps = 3/86 (3%)

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
            ++       D         E  ER   R ++   +  L   +R +   R +    +T+E
Sbjct: 91  PAKLPFEPGLDGREDPSAEAEALERIAPREIVG-LLESLPDEQREVLSLRLVAG--LTVE 147

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQE 282
             +     S   V+Q++ R   K++E
Sbjct: 148 QTAETMGKSTGAVKQLQRRGILKLRE 173


>gi|94969720|ref|YP_591768.1| ECF subfamily RNA polymerase sigma-24 factor [Candidatus Koribacter
           versatilis Ellin345]
 gi|94551770|gb|ABF41694.1| RNA polymerase, sigma-24 subunit, RpoE [Candidatus Koribacter
           versatilis Ellin345]
          Length = 209

 Score = 37.1 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 21/84 (25%), Positives = 35/84 (41%), Gaps = 6/84 (7%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           EE  L    RE GD+ A   LV  + R V +IA           +VV +  +   +A + 
Sbjct: 14  EEMRLVNAARE-GDVGAFEELVRKYDRNVFRIANHITQNREDAEDVVQDAFL---KAFQN 69

Query: 93  FDPERGFRLATYSMWWIKAAMQEY 116
               +G   + +  W ++ A+ E 
Sbjct: 70  LGQFQGQ--SKFYTWLVRIAVNEA 91


>gi|73749032|ref|YP_308271.1| ECF subfamily RNA polymerase sigma factor [Dehalococcoides sp.
           CBDB1]
 gi|73660748|emb|CAI83355.1| RNA polymerase sigma-70 factor, ECF subfamily [Dehalococcoides sp.
           CBDB1]
          Length = 179

 Score = 37.1 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 22/144 (15%), Positives = 54/144 (37%), Gaps = 9/144 (6%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVV-KIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           E  L +   +  D  A  RL   +   +   IA+   G  +   ++  +  +  ++++  
Sbjct: 4   ERHLVE-LAQQKDEQAFARLYEEYFDKIYRYIALK-IGNKMEAEDLTQQVFMNALRSMSS 61

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           F  +     + +        + +Y+ +               +   L      ++  T+ 
Sbjct: 62  FKWQDNTPFSAWLYRIAHNQIVDYLRKKSR-----QPTVDIEIVAPLACADDPVE-TTEV 115

Query: 153 NLKPEQVVAIAKKLNVSESEVISM 176
           N+  E+ V ++ KL  ++ EVIS+
Sbjct: 116 NIDYEKFVKVSAKLTPAQQEVISL 139


>gi|283781830|ref|YP_003372585.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Pirellula staleyi
           DSM 6068]
 gi|283440283|gb|ADB18725.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Pirellula staleyi
           DSM 6068]
          Length = 186

 Score = 37.1 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 25/140 (17%), Positives = 48/140 (34%), Gaps = 14/140 (10%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  + +  +  LV  +A           + V E  I L +   +FDP+R    AT+    
Sbjct: 16  AVDQCLARYGGLVWSLARRMSPTTSDAEDAVQEIFIDLFRHASRFDPQREPSEATFVAMI 75

Query: 109 IKAAMQEYILRSWSLVK-----------IGTTANQKRLFFNLRRLKGHLQAITDNNLKPE 157
            +  + +   +    VK           +    N   L   + R++  L  +        
Sbjct: 76  ARRRLIDRHRKHTRQVKTIPIDAKGTTPVAIPLNGLELRDEVGRVRELLSQLRCEER--- 132

Query: 158 QVVAIAKKLNVSESEVISMN 177
           QV+ +     +S++E   M 
Sbjct: 133 QVLELIFFHGLSQAETAEML 152


>gi|262198104|ref|YP_003269313.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Haliangium
           ochraceum DSM 14365]
 gi|262081451|gb|ACY17420.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Haliangium
           ochraceum DSM 14365]
          Length = 216

 Score = 37.1 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 37/97 (38%), Gaps = 3/97 (3%)

Query: 30  EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQA 89
           +  +E  L  R R+ GD  A   L   + R V  +A G         +VV EG I   + 
Sbjct: 16  DASDERELVDRARD-GDTEAFRALYQRYHRRVYALAYGVVQNKEDAMDVVQEGFIKAHRY 74

Query: 90  VKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           + +F+        T+    +     ++I +   +  +
Sbjct: 75  LDRFEG--NSSFYTWLYRIVMNLSIDHIRKHKRVRHV 109


>gi|149927528|ref|ZP_01915782.1| RNA polymerase sigma-70 factor [Limnobacter sp. MED105]
 gi|149823801|gb|EDM83027.1| RNA polymerase sigma-70 factor [Limnobacter sp. MED105]
          Length = 186

 Score = 37.1 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 13/80 (16%), Positives = 29/80 (36%), Gaps = 2/80 (2%)

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L +     D+      + L+   + Q     ++ E+      +  +++ L  R+R+ F  
Sbjct: 83  LFSSFQKKDEEDYDVLENLLAQDESQNASAQDEIEQSQNMAAIEEAIANLPERQRQAFIL 142

Query: 246 RRLQENPVTLENLSSEFEVS 265
           R  +E    L   +     S
Sbjct: 143 RYWEEMD--LAETAEIMGCS 160


>gi|126658877|ref|ZP_01730020.1| RNA polymerase sigma factor RpoE [Cyanothece sp. CCY0110]
 gi|126619827|gb|EAZ90553.1| RNA polymerase sigma factor RpoE [Cyanothece sp. CCY0110]
          Length = 217

 Score = 37.1 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 21/115 (18%), Positives = 42/115 (36%), Gaps = 17/115 (14%)

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           R++   SL+A     D         + +D         +    +   + L  +++ L   
Sbjct: 116 RVSHPISLDAPRRVDDGE-------IEWDIVSDYPSPDDTLATREFYDRLKVAIADLPEA 168

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVS----RERVRQIEARAFKKVQESIQKQVE 289
            R     R +    +  E ++    VS    + R+    ARA  K+Q  ++K V+
Sbjct: 169 FRTTIVLREI--EGLAYEEIAEMTGVSLGTVKSRI----ARARGKLQTVLEKYVD 217


>gi|120405756|ref|YP_955585.1| ECF subfamily RNA polymerase sigma-24 factor [Mycobacterium
           vanbaalenii PYR-1]
 gi|119958574|gb|ABM15579.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Mycobacterium
           vanbaalenii PYR-1]
          Length = 293

 Score = 37.1 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 20/95 (21%), Positives = 36/95 (37%), Gaps = 2/95 (2%)

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
             RL   ++LNAL   S +       WL      +     +    ++    +   +  L+
Sbjct: 55  LARLVTRQALNALRAQSRRREDYVGPWLPEPLLTEADPSADVVLAESVSMAMLVVLETLS 114

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           P ER +F  R +       + +++    S E VRQ
Sbjct: 115 PDERAVFVLREVFGFGH--DEIAATLGKSTEAVRQ 147


>gi|328910562|gb|AEB62158.1| positive control sigma-like factor [Bacillus amyloliquefaciens LL3]
          Length = 171

 Score = 37.1 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 13/70 (18%), Positives = 32/70 (45%), Gaps = 5/70 (7%)

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKN---RRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
           +   D  + D   +E  ++++ E +     +  +  ++SVL  RE+ IF    +Q   ++
Sbjct: 76  TILADPRLIDALPEEYAIVQEAEGEVSDWDKERIADALSVLTEREKDIFMMHAVQN--MS 133

Query: 255 LENLSSEFEV 264
            E ++    +
Sbjct: 134 FEEIAQILGI 143


>gi|323344061|ref|ZP_08084287.1| hypothetical protein HMPREF0663_10823 [Prevotella oralis ATCC
           33269]
 gi|323094790|gb|EFZ37365.1| hypothetical protein HMPREF0663_10823 [Prevotella oralis ATCC
           33269]
          Length = 176

 Score = 37.1 bits (85), Expect = 3.1,   Method: Composition-based stats.
 Identities = 12/68 (17%), Positives = 27/68 (39%), Gaps = 2/68 (2%)

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
           V+ + EE +    +L      L P+  RI   R       +   ++    +S   V +  
Sbjct: 93  VVPDDEEDRRIEELLHAIDHDLTPQAGRILRMRYG--EGQSYREIAEALGISVSTVNKHV 150

Query: 274 ARAFKKVQ 281
            +A ++++
Sbjct: 151 VQALRELR 158


>gi|301311960|ref|ZP_07217882.1| sigma-70, region 4 subfamily [Bacteroides sp. 20_3]
 gi|300830062|gb|EFK60710.1| sigma-70, region 4 subfamily [Bacteroides sp. 20_3]
          Length = 230

 Score = 37.1 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 19/125 (15%), Positives = 48/125 (38%), Gaps = 25/125 (20%)

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEER 221
           + K L     + I  N ++  D SL   +   D+  S+              + ++  + 
Sbjct: 121 LLKALRHKLYDTIEKNRKM-EDVSLYEDVFQVDELFSR--------------IALDTTDM 165

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV----SRERVRQIEARAF 277
            +R  +L ++++ L+P +R I     + E       ++    +    S+     + +R  
Sbjct: 166 DDRVKLLMKALTKLSPHQREIIYLYYVNELGHN--EIAGILGINYQSSK----NLLSRTL 219

Query: 278 KKVQE 282
           +K++ 
Sbjct: 220 RKLRR 224


>gi|295103331|emb|CBL00875.1| DNA-directed RNA polymerase specialized sigma subunit, sigma24
           homolog [Faecalibacterium prausnitzii SL3/3]
          Length = 145

 Score = 37.1 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 11/63 (17%), Positives = 23/63 (36%), Gaps = 12/63 (19%)

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR-----QIEARAFKKVQE 282
           L  ++S L  ++R I           T + +   +     R R      I + A + + E
Sbjct: 85  LAEALSSLPEKKREIIYLYFFG--RYTQQEIGELYG----RCRSTAWHHIHS-ALQMLHE 137

Query: 283 SIQ 285
            ++
Sbjct: 138 EME 140


>gi|212696423|ref|ZP_03304551.1| hypothetical protein ANHYDRO_00961 [Anaerococcus hydrogenalis DSM
           7454]
 gi|212676575|gb|EEB36182.1| hypothetical protein ANHYDRO_00961 [Anaerococcus hydrogenalis DSM
           7454]
          Length = 173

 Score = 37.1 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 17/108 (15%), Positives = 44/108 (40%), Gaps = 11/108 (10%)

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
            C+    +SLN L    DKN  +  + +  +   ++    + E  +     L ++++ L 
Sbjct: 71  ECKKERVDSLNDL----DKNGIELIEKIDDEKSIEDDFFKDLEIEE-----LFKAINTLK 121

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +ER I   +  +  P   + ++    +S + +        +K+++  
Sbjct: 122 KQEREILYLKYDKNLPH--KEIARLLNLSTKSITNYHYNIVRKLRKYF 167


>gi|190575746|ref|YP_001973591.1| putative RNA polymerase ECF sigma factor [Stenotrophomonas
           maltophilia K279a]
 gi|190013668|emb|CAQ47303.1| putative RNA polymerase ECF sigma factor [Stenotrophomonas
           maltophilia K279a]
          Length = 166

 Score = 37.1 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 28/135 (20%), Positives = 48/135 (35%), Gaps = 6/135 (4%)

Query: 135 LFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSD 194
           L      L   +Q I   +   E V+           +  +++   A    L A + +  
Sbjct: 12  LIRERPALLRRVQRILGGDNGAEDVIQAVWFKARGVDDSQAIDNPRAYLYRLAANLATDH 71

Query: 195 KNSSQWQDWLVYDH-DGQEQVLIEKEERKNRRNMLTRSMS---VLNPRERRIFEARRLQE 250
              S  ++ L+ DH       +I  EE+   ++ L R +     L    R IF   RLQ 
Sbjct: 72  GRESTRRNRLLADHYLWGADEVISTEEQAMAQDELQRVLDAAGHLPEPTRTIFRLNRLQG 131

Query: 251 NPVTLENLSSEFEVS 265
             +T   ++    VS
Sbjct: 132 --LTQAEIARRLGVS 144


>gi|182411905|ref|YP_001816971.1| ECF subfamily RNA polymerase sigma-24 factor [Opitutus terrae
           PB90-1]
 gi|177839119|gb|ACB73371.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Opitutus terrae
           PB90-1]
          Length = 459

 Score = 37.1 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 17/86 (19%), Positives = 33/86 (38%), Gaps = 10/86 (11%)

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS----RERVR 270
                + +  R +L  +++ LN  +R     R  +       ++ +    S    R RV 
Sbjct: 109 PAANLDWRKVRPVLDEAIAELNDTDREAILLRYFEGCGY--ADVGARLGASENTARMRV- 165

Query: 271 QIEARAFKKVQESIQKQVELSSSPPL 296
               RA  K+Q  + ++   S+S  L
Sbjct: 166 ---ERALDKLQALLVRRGVTSTSGAL 188



 Score = 37.1 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 25/49 (51%)

Query: 33 EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSE 81
          E+  L +RY E  D +A  +LV  H+ LV   A+        ++E V++
Sbjct: 3  EDAALLRRYAEARDQAAFAQLVRRHVNLVHSAALRQVNGDAHLAEDVTQ 51


>gi|302334993|ref|YP_003800200.1| transcriptional regulator, MarR family [Olsenella uli DSM 7084]
 gi|301318833|gb|ADK67320.1| transcriptional regulator, MarR family [Olsenella uli DSM 7084]
          Length = 366

 Score = 37.1 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 15/39 (38%), Positives = 20/39 (51%), Gaps = 3/39 (7%)

Query: 232 MSVLNPRERRIFEARRLQENP-VTLENLSSEFEVSRERV 269
           M  L  RER+I     ++ENP VT   L+    +SR  V
Sbjct: 1   MDSLTERERQILS--WIEENPAVTQSELAGRAGISRSSV 37


>gi|218131817|ref|ZP_03460621.1| hypothetical protein BACEGG_03438 [Bacteroides eggerthii DSM 20697]
 gi|317474566|ref|ZP_07933840.1| sigma-70 family RNA polymerase sigma factor [Bacteroides eggerthii
           1_2_48FAA]
 gi|217986120|gb|EEC52459.1| hypothetical protein BACEGG_03438 [Bacteroides eggerthii DSM 20697]
 gi|316909247|gb|EFV30927.1| sigma-70 family RNA polymerase sigma factor [Bacteroides eggerthii
           1_2_48FAA]
          Length = 169

 Score = 37.1 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 14/82 (17%), Positives = 33/82 (40%), Gaps = 2/82 (2%)

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           A+  S  K++   +     +         E+   K R  ++ R M+ L  ++R I + R 
Sbjct: 67  AIDRSERKDARAVELTPDMEDASDASSPYERLVSKERMALIHRLMNELPEKQRLIMQLR- 125

Query: 248 LQENPVTLENLSSEFEVSRERV 269
                 + + ++    ++ E+V
Sbjct: 126 -DVEGKSYKEIAVVLNLTEEQV 146


>gi|168180275|ref|ZP_02614939.1| putative RNA polymerase sigma factor [Clostridium botulinum NCTC
           2916]
 gi|182668869|gb|EDT80847.1| putative RNA polymerase sigma factor [Clostridium botulinum NCTC
           2916]
          Length = 176

 Score = 37.1 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 23/100 (23%), Positives = 47/100 (47%), Gaps = 5/100 (5%)

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKE--ERKNRRNMLTRSMSVLNPRERRIFEA 245
           AL+    K+  +  D  + D   +    IE E    +N +  L +++  L P E+ + ++
Sbjct: 80  ALLKGEIKHHREVPDENISDKGNEYFFTIEDEIIAYENIKE-LYKALDKLTPEEKEVIDS 138

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             ++ N  +L+ ++S    S   VR  + +A KK+Q   +
Sbjct: 139 FYIKNN--SLQEIASYTNKSYNSVRYTKEKAIKKLQNMFE 176


>gi|160932358|ref|ZP_02079749.1| hypothetical protein CLOLEP_01194 [Clostridium leptum DSM 753]
 gi|156868960|gb|EDO62332.1| hypothetical protein CLOLEP_01194 [Clostridium leptum DSM 753]
          Length = 149

 Score = 37.1 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 16/105 (15%), Positives = 45/105 (42%), Gaps = 3/105 (2%)

Query: 183 DESLNALINSSD-KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERR 241
           + SL+ L++ +  +  S    +  Y ++     +++ +E       L  +++ L+ + R 
Sbjct: 42  EVSLDYLMSETPFEPFSTDNYFEQYVYENPTVFVVKGQEVIVESERLAHALASLSEQRRT 101

Query: 242 IFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           +               + +E+  SR  V   +  A K++++ ++K
Sbjct: 102 VLLMYFFLGYNE--RKIGNEYGRSRSTVNYWKLAALKQLRKELEK 144


>gi|34496192|ref|NP_900407.1| hypothetical protein CV_0737 [Chromobacterium violaceum ATCC 12472]
 gi|34102046|gb|AAQ58413.1| conserved hypothetical protein [Chromobacterium violaceum ATCC
           12472]
          Length = 208

 Score = 37.1 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 11/93 (11%), Positives = 41/93 (44%), Gaps = 16/93 (17%)

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
               ++   + +   L  + + L P ++R+F+ +   E  ++   +++   +        
Sbjct: 100 PTPEQQLSSRQQLAELECAFAALKPDQQRLFQLKF--EQDLSYAQIAARLGI-------- 149

Query: 273 EARAFKK-----VQESIQKQVELSSSPPLLQKP 300
              A  +     +++++++Q++   +PP  ++P
Sbjct: 150 -NEALARKRVELLRKALRRQLDPDFTPPDNRRP 181


>gi|323344773|ref|ZP_08084997.1| hypothetical protein HMPREF0663_11533 [Prevotella oralis ATCC
           33269]
 gi|323094043|gb|EFZ36620.1| hypothetical protein HMPREF0663_11533 [Prevotella oralis ATCC
           33269]
          Length = 176

 Score = 37.1 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 12/68 (17%), Positives = 27/68 (39%), Gaps = 2/68 (2%)

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
           V+ + EE +    +L      L P+  RI   R       +   ++    +S   V +  
Sbjct: 93  VVPDDEEDRRIEELLHAIDHDLTPQAGRILRMRYG--EGQSYREIAEALGISVSTVNKHV 150

Query: 274 ARAFKKVQ 281
            +A ++++
Sbjct: 151 VQALRELR 158


>gi|294498777|ref|YP_003562477.1| RNA polymerase ECF-type sigma factor family protein [Bacillus
           megaterium QM B1551]
 gi|294348714|gb|ADE69043.1| RNA polymerase ECF-type sigma factor family protein [Bacillus
           megaterium QM B1551]
          Length = 188

 Score = 37.1 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 46/97 (47%), Gaps = 14/97 (14%)

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           S +  D++  DH   ++ L  KEE++  R+    ++S L+  +++I ++   +   +T +
Sbjct: 97  SEEIFDFIEDDHPQIDEQLQWKEEQQRVRH----AVSKLSEDQKKIIQSVYFKG--LTQQ 150

Query: 257 NLSSE----FEVSRERVRQIEARAFKKVQESIQKQVE 289
            ++ E        + RVR     A +K++  +    E
Sbjct: 151 KVAEEQQIPLGTVKGRVRL----ALRKLKTYLGTDAE 183


>gi|320009035|gb|ADW03885.1| RNA polymerase, sigma 32 subunit, RpoH [Streptomyces flavogriseus
           ATCC 33331]
          Length = 254

 Score = 37.1 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 13/88 (14%), Positives = 28/88 (31%), Gaps = 6/88 (6%)

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
            S+      + +         E+    +      + ++ L   +R +   R      +T 
Sbjct: 166 GSTAVPSDEMPERPDDSLGPEERALLSSDAAWAKKLLANLPENQRELLVLRVAVG--LTA 223

Query: 256 ENLSSEFEVS--RERVRQIEARAFKKVQ 281
           E       +S    RV Q   RA  +++
Sbjct: 224 EETGQMLGMSPGAVRVAQ--HRALSRLR 249


>gi|300779178|ref|ZP_07089036.1| RNA polymerase sigma-Z factor [Chryseobacterium gleum ATCC 35910]
 gi|300504688|gb|EFK35828.1| RNA polymerase sigma-Z factor [Chryseobacterium gleum ATCC 35910]
          Length = 186

 Score = 37.1 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 8/70 (11%), Positives = 29/70 (41%), Gaps = 2/70 (2%)

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
           ++    + L    +   +   E    +  +  + +++  L+   + I + R  +E   ++
Sbjct: 92  DTEDAVENLDEVKNQYAKSPEELLISEEEQKKIIKTIESLDANYQDIIKLRFFEE--KSI 149

Query: 256 ENLSSEFEVS 265
           + ++ E  +S
Sbjct: 150 KEIAEELGIS 159


>gi|149197523|ref|ZP_01874574.1| probable extracytoplasmic function alternative sigma factor
           [Lentisphaera araneosa HTCC2155]
 gi|149139541|gb|EDM27943.1| probable extracytoplasmic function alternative sigma factor
           [Lentisphaera araneosa HTCC2155]
          Length = 202

 Score = 37.1 bits (85), Expect = 3.2,   Method: Composition-based stats.
 Identities = 17/120 (14%), Positives = 44/120 (36%), Gaps = 1/120 (0%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L +R R   D  +    V  +   +  IA           E+       L   + +FD +
Sbjct: 14  LLERVRLQHDEKSWEEFVFYYRHFIYIIARRLNLRHHDAEEITQAVLFKLWNKLPEFDYD 73

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGH-LQAITDNNLK 155
           +  R  ++     K  ++++  +     ++   A+   L+   +++  H ++ I +   +
Sbjct: 74  KTSRFRSWLYLVTKNTVRDFCRKQSRKTELQDQASHSELWDLGKQISEHQIEEIAEKEWE 133


>gi|291515981|emb|CBK65191.1| RNA polymerase sigma factor, sigma-70 family/RNA polymerase
           sigma-70 factor, Bacteroides expansion family 1
           [Alistipes shahii WAL 8301]
          Length = 184

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 17/79 (21%), Positives = 41/79 (51%), Gaps = 8/79 (10%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
                 +L   E  +  R  L + M  L    ++IF+ARRL     + + ++ +F + ++
Sbjct: 105 ESCDPDILFRNEILEICRAQLEQ-MPELT---QQIFKARRL--EGKSYKEIAEQFGIPQK 158

Query: 268 RV-RQIEARAFKKVQESIQ 285
           +V +Q++ +A  K++ +++
Sbjct: 159 KVDKQLQ-QAVTKLRRALK 176


>gi|217077084|ref|YP_002334800.1| RNA polymerase sigma-E factor [Thermosipho africanus TCF52B]
 gi|217036937|gb|ACJ75459.1| RNA polymerase sigma-E factor [Thermosipho africanus TCF52B]
          Length = 205

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 7/64 (10%), Positives = 29/64 (45%), Gaps = 2/64 (3%)

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
           +D +  D   +E  + ++  ++     + +++  L+ +ER +   R +  + ++   ++ 
Sbjct: 118 EDDVEIDIPDKETDVQKEVTQEILYEKILKALEKLSEKERVLIRMRDI--DGLSYSEIAE 175

Query: 261 EFEV 264
              +
Sbjct: 176 ILGI 179


>gi|149181391|ref|ZP_01859888.1| sigma factor SgiI [Bacillus sp. SG-1]
 gi|148850954|gb|EDL65107.1| sigma factor SgiI [Bacillus sp. SG-1]
          Length = 250

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 23/96 (23%), Positives = 42/96 (43%), Gaps = 2/96 (2%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMG-YRGYGLPISEVVSEGNIGLMQAVKKFDP 95
           LAK  +E G+  A ++++  +   V K      + Y     +  S G I    A+ K++ 
Sbjct: 21  LAKEIQE-GNEEALNQVLVDYKPFVKKTVSSVCKRYIYESDDEFSIGLIAFHDALLKYNS 79

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTAN 131
           +RG  L +++   IK  + +YI  +     I    N
Sbjct: 80  DRGASLLSFAEVIIKRKVIDYIRMNGRHQNISVEVN 115


>gi|126173433|ref|YP_001049582.1| RNA polymerase sigma factor RpoE [Shewanella baltica OS155]
 gi|152999772|ref|YP_001365453.1| RNA polymerase sigma factor RpoE [Shewanella baltica OS185]
 gi|160874391|ref|YP_001553707.1| RNA polymerase sigma factor RpoE [Shewanella baltica OS195]
 gi|217974275|ref|YP_002359026.1| RNA polymerase sigma factor RpoE [Shewanella baltica OS223]
 gi|304409356|ref|ZP_07390976.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Shewanella baltica
           OS183]
 gi|307303714|ref|ZP_07583467.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Shewanella baltica
           BA175]
 gi|125996638|gb|ABN60713.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Shewanella baltica
           OS155]
 gi|151364390|gb|ABS07390.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Shewanella baltica
           OS185]
 gi|160859913|gb|ABX48447.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Shewanella baltica
           OS195]
 gi|217499410|gb|ACK47603.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Shewanella baltica
           OS223]
 gi|304351874|gb|EFM16272.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Shewanella baltica
           OS183]
 gi|306912612|gb|EFN43035.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Shewanella baltica
           BA175]
 gi|315266626|gb|ADT93479.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Shewanella baltica
           OS678]
          Length = 192

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 22/138 (15%), Positives = 44/138 (31%), Gaps = 3/138 (2%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L +R ++ GD +A + LV  +   V+ +   Y      +++V  E  I   +A+  F  E
Sbjct: 10  LVERVQQ-GDKNAFNLLVLKYQSKVISLISRYVRNQADVADVAQEAFIKAYRALPNFRGE 68

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
                 T+         + Y++             +   ++          +     L  
Sbjct: 69  --SAFYTWLYRIAVNTAKNYLVSQGRRTPANDVDAEDAEYYEGSDALKEFASPERLLLSE 126

Query: 157 EQVVAIAKKLNVSESEVI 174
           E    I   L     E+ 
Sbjct: 127 EIKKVIFDTLETLPEELR 144


>gi|326919004|ref|XP_003205774.1| PREDICTED: LOW QUALITY PROTEIN: ankyrin-2-like [Meleagris gallopavo]
          Length = 3909

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 22/123 (17%), Positives = 46/123 (37%), Gaps = 7/123 (5%)

Query: 157  EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
            E++   A KL    ++       ++ DES +AL  S  +N    +       D  +   I
Sbjct: 3293 EEISDEASKLVERLTQSEREQELVSDDESSSALEVSVIENVPSIETQQSVPEDIFDTRPI 3352

Query: 217  EKEERKNRRNML------TRSMSVLNPRERRIFEARRLQEN-PVTLENLSSEFEVSRERV 269
              E  + +   +        +    + RER       + ++   +   L+ E + + E++
Sbjct: 3353 WDESVETQIERIPDDNIHDHAEDQQDDRERTEERLAHIADHLGFSWTELARELDFTEEQI 3412

Query: 270  RQI 272
             QI
Sbjct: 3413 HQI 3415


>gi|313889312|ref|ZP_07822963.1| RNA polymerase sigma factor, sigma-70 family [Streptococcus
           pseudoporcinus SPIN 20026]
 gi|313122360|gb|EFR45448.1| RNA polymerase sigma factor, sigma-70 family [Streptococcus
           pseudoporcinus SPIN 20026]
          Length = 136

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 22/93 (23%), Positives = 44/93 (47%), Gaps = 14/93 (15%)

Query: 203 WLVYDHDGQEQVLIEKEER--------KNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
           +  YD DG  +  +E  E         K     + R++S LNP ER + E+   +E   T
Sbjct: 46  FCSYDRDGNFEENLEDLEFDVEKIIETKEMIEEVRRAISKLNPVERDLIESLFYKEE--T 103

Query: 255 LENLSSEFEVSRERV--RQIEARAFKKVQESIQ 285
           +  ++++  +S   V  R+   +  +K++E ++
Sbjct: 104 IREVAAKLNISHPAVIKRR--NKVLEKLKEMLE 134


>gi|302542901|ref|ZP_07295243.1| putative sigma factor [Streptomyces hygroscopicus ATCC 53653]
 gi|302460519|gb|EFL23612.1| putative sigma factor [Streptomyces himastatinicus ATCC 53653]
          Length = 141

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 19/77 (24%), Positives = 29/77 (37%), Gaps = 2/77 (2%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
            YD   QE   +     +  R      +  L PRER +   R  +      E  ++   +
Sbjct: 46  PYDRTRQELAALYAHRARRYRRPRGGLLDRLTPRERLVLVLRLYEGVAE--EQTAATLGL 103

Query: 265 SRERVRQIEARAFKKVQ 281
             ERVR I  RA   ++
Sbjct: 104 PVERVRAICTRAVTLMR 120


>gi|326790073|ref|YP_004307894.1| Sigma-70 region 4 type 2 [Clostridium lentocellum DSM 5427]
 gi|326540837|gb|ADZ82696.1| Sigma-70 region 4 type 2 [Clostridium lentocellum DSM 5427]
          Length = 134

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 19/133 (14%), Positives = 50/133 (37%), Gaps = 6/133 (4%)

Query: 149 ITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNS-SQWQDWLVYD 207
           I     +   ++  A++L    +E+      ++     N  I   + +  ++    L   
Sbjct: 3   IKQKLQRYANLLDQARELEYRIAEIKEHMTSVSSTNFDNMPICHGNNDKLTEALCKLKDL 62

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
            D   ++  +  E +     +   +S L+ +E+++     +   P  LE +S     +  
Sbjct: 63  RDKYIELWGKVAEEELE---VIDMISKLDYQEQKLIRLHYIDCKP--LEEISCILGYTYR 117

Query: 268 RVRQIEARAFKKV 280
              +I  R ++K+
Sbjct: 118 HTSRIYKRIYEKL 130


>gi|266621860|ref|ZP_06114795.1| RNA polymerase sigma-70 factor, ECF subfamily [Clostridium
           hathewayi DSM 13479]
 gi|288866438|gb|EFC98736.1| RNA polymerase sigma-70 factor, ECF subfamily [Clostridium
           hathewayi DSM 13479]
          Length = 71

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 12/74 (16%), Positives = 32/74 (43%), Gaps = 10/74 (13%)

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS----RERVRQIEARA 276
           R   RN +  ++  L   ++ +   R   +     + +++   V     + R+RQ     
Sbjct: 2   RAEMRNSIQAALDRLPEMQKDVIILRFYYDMK--FKEIAAVVGVGIPTVKSRLRQ----G 55

Query: 277 FKKVQESIQKQVEL 290
            +K+++ + K+ +L
Sbjct: 56  MEKMKQFLGKEGDL 69


>gi|253579033|ref|ZP_04856304.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39B_FAA]
 gi|251849976|gb|EES77935.1| conserved hypothetical protein [Ruminococcus sp. 5_1_39BFAA]
          Length = 147

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 11/63 (17%), Positives = 23/63 (36%), Gaps = 12/63 (19%)

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR-----QIEARAFKKVQE 282
           L  ++S L  ++R I           T + +   +     R R      I + A + + E
Sbjct: 85  LAEALSSLPEKKREIIYLYFFG--RYTQQEIGELYG----RCRSTAWHHIHS-ALQMLHE 137

Query: 283 SIQ 285
            ++
Sbjct: 138 EME 140


>gi|227499332|ref|ZP_03929444.1| sigma-70 family protein [Anaerococcus tetradius ATCC 35098]
 gi|227218616|gb|EEI83852.1| sigma-70 family protein [Anaerococcus tetradius ATCC 35098]
          Length = 136

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 22/93 (23%), Positives = 44/93 (47%), Gaps = 14/93 (15%)

Query: 203 WLVYDHDGQEQVLIEKEER--------KNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
           +  YDHDG  +  +E  E         K     + R++  LNP ER + E+   +E   T
Sbjct: 46  FCSYDHDGNFEENLEDLEFDVEKIIETKEMIEEVRRAIYKLNPAERDLIESLFYKEE--T 103

Query: 255 LENLSSEFEVSRERV--RQIEARAFKKVQESIQ 285
           +  ++++  +S   V  R+   +  +K++E ++
Sbjct: 104 IREVAAKLNISHPAVIKRR--NKVLEKLKEMLE 134


>gi|118090374|ref|XP_420641.2| PREDICTED: similar to ankyrin B (440 kDa) [Gallus gallus]
          Length = 3909

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 22/123 (17%), Positives = 46/123 (37%), Gaps = 7/123 (5%)

Query: 157  EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
            E++   A KL    ++       ++ DES +AL  S  +N    +       D  +   I
Sbjct: 3293 EEISDEASKLVERLTQSEREQELVSDDESSSALEVSVIENVPSIETQQSVPEDIFDTRPI 3352

Query: 217  EKEERKNRRNML------TRSMSVLNPRERRIFEARRLQEN-PVTLENLSSEFEVSRERV 269
              E  + +   +        +    + RER       + ++   +   L+ E + + E++
Sbjct: 3353 WDESVETQIERIPDDNIHDHAEDQQDDRERTEERLAHIADHLGFSWTELARELDFTEEQI 3412

Query: 270  RQI 272
             QI
Sbjct: 3413 HQI 3415


>gi|25027161|ref|NP_737215.1| RNA polymerase sigma factor SigD [Corynebacterium efficiens YS-314]
 gi|23492442|dbj|BAC17415.1| putative RNA polymerase sigma factor [Corynebacterium efficiens
           YS-314]
          Length = 190

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 13/83 (15%), Positives = 34/83 (40%), Gaps = 2/83 (2%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           + D +       E     +  N +   + +L+ + R I   R +    ++ E  +   + 
Sbjct: 107 IPDTEPDANSPEEFALVADGSNRVRELLDLLSEKARDILILRVMVG--LSAEETAEMVDS 164

Query: 265 SRERVRQIEARAFKKVQESIQKQ 287
           +   VR  + RA   ++ ++++Q
Sbjct: 165 TPGAVRVAQHRALTTLRSALEQQ 187


>gi|312902282|ref|ZP_07761490.1| sigma-70, region 4 [Enterococcus faecalis TX0635]
 gi|310634341|gb|EFQ17624.1| sigma-70, region 4 [Enterococcus faecalis TX0635]
          Length = 157

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 15/99 (15%), Positives = 38/99 (38%), Gaps = 9/99 (9%)

Query: 198 SQWQDWLVYDHDGQEQVL-------IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
           S+  D++V      +Q         +E  E   +   L  ++  L  ++R I       E
Sbjct: 61  SELDDYVVEQFASIDQYPSDFSYFELEGAEIAVKSMSLGEALERLPKKKRNIILFYYFIE 120

Query: 251 NPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
                  +++   +SR  V +   +A   +++ +++  +
Sbjct: 121 MND--AEIANLMGLSRSTVNEHRHKALHLIRKFMKEDAQ 157


>gi|312897966|ref|ZP_07757377.1| sigma-70, region 4 [Megasphaera micronuciformis F0359]
 gi|310620949|gb|EFQ04498.1| sigma-70, region 4 [Megasphaera micronuciformis F0359]
          Length = 194

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 10/76 (13%), Positives = 26/76 (34%)

Query: 40  RYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGF 99
           R+   G   +  RL+T +  L++     Y       ++         +  +     +   
Sbjct: 12  RHARRGCTESKERLLTRYTPLILSQVRRYASSFPTHADAYQTAVTAALHCIMACPLDGDK 71

Query: 100 RLATYSMWWIKAAMQE 115
             A Y   +++ A++ 
Sbjct: 72  PFAYYLKAFVRQALRR 87


>gi|118591528|ref|ZP_01548925.1| Sigma-24 (FecI) [Stappia aggregata IAM 12614]
 gi|118435856|gb|EAV42500.1| Sigma-24 (FecI) [Stappia aggregata IAM 12614]
          Length = 304

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 17/93 (18%), Positives = 39/93 (41%), Gaps = 4/93 (4%)

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           D       + L +D     +  +++ +      +L   +  L+P+ER  +  R +   P 
Sbjct: 78  DYVGPWIPEPLQFDSGSDPETDLDRAQSLTTAFLL--LLERLSPKERAAYLLREIFAQPY 135

Query: 254 TLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
             + ++    V+ +  RQ+ +RA + VQ    +
Sbjct: 136 --DEVAQTLGVTEQACRQLVSRASRHVQGPASR 166


>gi|285625|dbj|BAA02557.1| sigma factor H [Bacillus subtilis]
          Length = 105

 Score = 37.1 bits (85), Expect = 3.3,   Method: Composition-based stats.
 Identities = 19/109 (17%), Positives = 44/109 (40%), Gaps = 10/109 (9%)

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SL+  I   + + +             E+++I +EE  +    +   +S L   ER++ 
Sbjct: 4   ASLDKPIFDEESDRTLLDVISGAKTLNPEEMIINQEEFDDIEMKMGELLSDL---ERKVL 60

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSS 292
                  +  + + +S E       V+ I   A ++V+  ++K +E+  
Sbjct: 61  VLYL---DGRSYQEISDELN---RHVKSI-DNALQRVKRKLEKYLEIRE 102


>gi|332672008|ref|YP_004455016.1| DeoR family transcriptional regulator [Cellulomonas fimi ATCC 484]
 gi|332341046|gb|AEE47629.1| transcriptional regulator, DeoR family [Cellulomonas fimi ATCC 484]
          Length = 328

 Score = 37.1 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 10/43 (23%), Positives = 18/43 (41%), Gaps = 5/43 (11%)

Query: 237 PRERRIFE---ARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
            RE+ +        LQ+  +  E ++     SR  V ++  RA
Sbjct: 4   EREQDVLRAASMYYLQDLKM--EVIARHLGTSRSTVSRLIKRA 44


>gi|317471917|ref|ZP_07931252.1| sigma-70 family RNA polymerase sigma factor [Anaerostipes sp.
           3_2_56FAA]
 gi|316900690|gb|EFV22669.1| sigma-70 family RNA polymerase sigma factor [Anaerostipes sp.
           3_2_56FAA]
          Length = 163

 Score = 37.1 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 7/34 (20%), Positives = 18/34 (52%), Gaps = 2/34 (5%)

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
            +++VL+PRE+++   R  ++    L  ++    
Sbjct: 103 DALNVLSPREKQVIVLRFFEDMK--LAEIAEILN 134


>gi|302865200|ref|YP_003833837.1| RNA polymerase sigma-70 factor [Micromonospora aurantiaca ATCC
           27029]
 gi|302568059|gb|ADL44261.1| RNA polymerase sigma-70 factor, sigma-E family [Micromonospora
           aurantiaca ATCC 27029]
          Length = 235

 Score = 37.1 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 16/81 (19%), Positives = 39/81 (48%), Gaps = 2/81 (2%)

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
            E+  +++ E++  R+ L R +  L  R+R +   R  ++  ++    ++  E+S   V+
Sbjct: 93  PERAGVDEIEQQLDRDALWRHLQALPARQRAVLVLRFYED--MSEAQTAALLEISPGTVK 150

Query: 271 QIEARAFKKVQESIQKQVELS 291
              +RA   ++  +  +  LS
Sbjct: 151 SQTSRALNTLRRRLGSEAALS 171


>gi|269958242|ref|YP_003328030.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Xylanimonas cellulosilytica DSM 15894]
 gi|269306923|gb|ACZ32472.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Xylanimonas cellulosilytica DSM 15894]
          Length = 152

 Score = 37.1 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 12/49 (24%), Positives = 21/49 (42%), Gaps = 2/49 (4%)

Query: 226 NMLTRSMSVLNPR--ERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           + L   +  L  R  E      + L E+ +T   ++    +S  RVRQ+
Sbjct: 75  SALQEQLQQLADRAREALALGVQFLLEDGLTQREVALALGLSVARVRQL 123


>gi|239625850|ref|ZP_04668881.1| predicted protein [Clostridiales bacterium 1_7_47_FAA]
 gi|239520080|gb|EEQ59946.1| predicted protein [Clostridiales bacterium 1_7_47FAA]
          Length = 224

 Score = 37.1 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 11/50 (22%), Positives = 25/50 (50%), Gaps = 9/50 (18%)

Query: 252 PVTLENLSSEFEVSRERVRQIEARAFKKVQE-----SIQKQVELSSSPPL 296
            +T + ++    +SR  V    AR   +++E     + +KQ++++  P L
Sbjct: 169 DMTQDEIADILGLSRVHV----ARGLSELRENNIILTQRKQIQVTDLPAL 214


>gi|15595347|ref|NP_248839.1| sigma-70 factor, ECF subfamily [Pseudomonas aeruginosa PAO1]
 gi|116053870|ref|YP_788307.1| RNA polymerase ECF-subfamily sigma-70 factor [Pseudomonas
           aeruginosa UCBPP-PA14]
 gi|218888894|ref|YP_002437758.1| putative sigma-70 factor, ECF subfamily [Pseudomonas aeruginosa
           LESB58]
 gi|254243256|ref|ZP_04936578.1| hypothetical protein PA2G_04063 [Pseudomonas aeruginosa 2192]
 gi|9945980|gb|AAG03539.1|AE004453_2 probable sigma-70 factor, ECF subfamily [Pseudomonas aeruginosa
           PAO1]
 gi|115589091|gb|ABJ15106.1| putative sigma-70 factor, ECF subfamily [Pseudomonas aeruginosa
           UCBPP-PA14]
 gi|126196634|gb|EAZ60697.1| hypothetical protein PA2G_04063 [Pseudomonas aeruginosa 2192]
 gi|218769117|emb|CAW24877.1| probable sigma-70 factor, ECF subfamily [Pseudomonas aeruginosa
           LESB58]
          Length = 181

 Score = 37.1 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 21/112 (18%), Positives = 43/112 (38%), Gaps = 6/112 (5%)

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              E+ S   R A + +++  +        Q  DWL     G+     +  E  ++   +
Sbjct: 56  PVEELGSYLLRSARNLAID-HLRGEGSRQRQLDDWLPEQRQGEPVGPEQALEAGDQWRRV 114

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++  L  R RRIF   R+  +  T   ++   ++S+  V   E    + +
Sbjct: 115 EAALRGLPERTRRIFLLNRI--HGRTYAEIAQAMQLSQSAV---EKHMMRAL 161


>gi|283780845|ref|YP_003371600.1| two component LuxR family transcriptional regulator [Pirellula
           staleyi DSM 6068]
 gi|283439298|gb|ADB17740.1| two component transcriptional regulator, LuxR family [Pirellula
           staleyi DSM 6068]
          Length = 218

 Score = 37.1 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 17/71 (23%), Positives = 30/71 (42%), Gaps = 17/71 (23%)

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS-------RERVR 270
           K +       +   +  L+PRER IFE   + E  VT + ++S   +S       R ++ 
Sbjct: 130 KHQEAIENEEIRARLENLSPREREIFE--WMVEGFVT-KEIASRLGISTKTVDVHRSKIS 186

Query: 271 QIEARAFKKVQ 281
           Q       K++
Sbjct: 187 Q-------KLR 190


>gi|282878816|ref|ZP_06287583.1| sigma-70 region 2 [Prevotella buccalis ATCC 35310]
 gi|281299024|gb|EFA91426.1| sigma-70 region 2 [Prevotella buccalis ATCC 35310]
          Length = 170

 Score = 37.1 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 18/86 (20%), Positives = 40/86 (46%), Gaps = 5/86 (5%)

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
            + L   HD      IE+ E +     L   +S L  ++R+I   R + E  +    +  
Sbjct: 83  PEELQIPHDDDAGRAIEQAEDRQMAWQL---ISGLPEQQRQIVMMRDIGE--MAYREIER 137

Query: 261 EFEVSRERVRQIEARAFKKVQESIQK 286
           +  ++   +R + +RA K+++E +++
Sbjct: 138 QTGLTAVNIRVLLSRARKQMREQLKQ 163


>gi|289191594|ref|YP_003457535.1| transcriptional regulator, XRE family [Methanocaldococcus sp.
           FS406-22]
 gi|288938044|gb|ADC68799.1| transcriptional regulator, XRE family [Methanocaldococcus sp.
           FS406-22]
          Length = 141

 Score = 37.1 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 10/49 (20%), Positives = 24/49 (48%), Gaps = 3/49 (6%)

Query: 235 LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           L   + ++ + R   +  +T E ++     SR  +  IE RA + ++++
Sbjct: 11  LTETQIKVLKLR---KKGLTQEEIAKMLGTSRANISMIEKRAKENIKKA 56


>gi|160941753|ref|ZP_02089080.1| hypothetical protein CLOBOL_06649 [Clostridium bolteae ATCC
           BAA-613]
 gi|158435250|gb|EDP13017.1| hypothetical protein CLOBOL_06649 [Clostridium bolteae ATCC
           BAA-613]
          Length = 167

 Score = 37.1 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 21/124 (16%), Positives = 47/124 (37%), Gaps = 4/124 (3%)

Query: 158 QVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIE 217
            ++ + + + +    VI     L  +     L   S        + L+YD  G    + +
Sbjct: 43  SLMEVTEDMYMKHYRVIRRKKYLTREVPYEILHYQSLDTDEMLGEELLYDDSGL--SIED 100

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAF 277
           K       + L  ++  L   ER +    RL    V+   L+ +  +S+  V + + +  
Sbjct: 101 KAIHNIYTDKLYPALVKLTDEERDLL--YRLYYQGVSERVLAKQLGISQAAVHKRKEKIL 158

Query: 278 KKVQ 281
           K+++
Sbjct: 159 KQLR 162


>gi|330962287|gb|EGH62547.1| extracytoplasmic-function sigma-70 factor [Pseudomonas syringae pv.
           maculicola str. ES4326]
          Length = 178

 Score = 37.1 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 13/40 (32%), Positives = 20/40 (50%), Gaps = 2/40 (5%)

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
             +  ++S L PR R  FE  RL   P   ++++ E  VS
Sbjct: 116 EKIADALSELPPRTRYAFEMYRLHGVP--QKDIAKELGVS 153


>gi|329960237|ref|ZP_08298679.1| RNA polymerase sigma-70 factor [Bacteroides fluxus YIT 12057]
 gi|328532910|gb|EGF59687.1| RNA polymerase sigma-70 factor [Bacteroides fluxus YIT 12057]
          Length = 183

 Score = 37.1 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 6/44 (13%), Positives = 18/44 (40%), Gaps = 2/44 (4%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
              + ++  ++  L  R R +F   R +  P     +++   ++
Sbjct: 110 SEIQKLVDEALESLPERTRLVFVMSRYENKPY--HEIAAVLGIT 151


>gi|291561685|emb|CBL40484.1| DNA-directed RNA polymerase specialized sigma subunit, sigma24
           homolog [butyrate-producing bacterium SS3/4]
          Length = 139

 Score = 37.1 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 10/68 (14%), Positives = 29/68 (42%), Gaps = 2/68 (2%)

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           + +   + L  ++  L+ R R         E  +  E ++ +  +SR  V Q    +   
Sbjct: 73  DIRVYDDELAEALKQLSERNRETLLMYYFLE--MNNEEIAKKQNISRSGVFQNRHNSLAL 130

Query: 280 VQESIQKQ 287
           +++ ++++
Sbjct: 131 MKKLLKEK 138


>gi|268316636|ref|YP_003290355.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Rhodothermus
           marinus DSM 4252]
 gi|262334170|gb|ACY47967.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Rhodothermus
           marinus DSM 4252]
          Length = 187

 Score = 37.1 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 13/90 (14%), Positives = 38/90 (42%), Gaps = 8/90 (8%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             +         ++    +   ++ R +  L  + R IF   R  ++ +T   ++    +
Sbjct: 102 AAEMACDRPHPDQQLVGNDLTELIERLIQELPEQRRLIFTLSR--DHGLTYAEIAQSLGI 159

Query: 265 SRERVRQIEA---RAFKKVQESIQKQVELS 291
           S   ++ +E    RA ++++E +Q  + ++
Sbjct: 160 S---IKTVETQMGRALRQLRERLQAWLNVA 186


>gi|223940674|ref|ZP_03632514.1| RNA polymerase, sigma-24 subunit, ECF subfamily [bacterium
           Ellin514]
 gi|223890644|gb|EEF57165.1| RNA polymerase, sigma-24 subunit, ECF subfamily [bacterium
           Ellin514]
          Length = 252

 Score = 37.1 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 16/118 (13%), Positives = 48/118 (40%), Gaps = 16/118 (13%)

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
            R      L+ L    +  +    + +  ++   ++V+   E     R  + R    L+ 
Sbjct: 136 MREKRPAPLSTLDREEEATARNHIEQITDENCAPDEVVETFERAAQVRLCIER----LSQ 191

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVS----RERVRQIEARAFKKVQ--ESIQKQVE 289
           + +++   R   ++  +LE +++    S    + R+      A +K++  +++  ++E
Sbjct: 192 KHQQVIYLRFYVDD--SLEGIAAALGCSIGTVKSRL----FHALEKLRTMDAMSGEIE 243


>gi|145591836|ref|YP_001153838.1| hypothetical protein Pars_1633 [Pyrobaculum arsenaticum DSM 13514]
 gi|145283604|gb|ABP51186.1| hypothetical protein Pars_1633 [Pyrobaculum arsenaticum DSM 13514]
          Length = 609

 Score = 37.1 bits (85), Expect = 3.4,   Method: Composition-based stats.
 Identities = 30/144 (20%), Positives = 54/144 (37%), Gaps = 24/144 (16%)

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
               RR K  L+ ++      E  V  A++          +        SL  L+   D 
Sbjct: 44  IEQYRRAKERLETVSRRATALEDEVRRARE---------EVQKVGREVASLETLLREKDD 94

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR--LQENPV 253
             +  +  L Y        L E+  R   +  L  ++S L    RR  E  R  L E+ V
Sbjct: 95  EVAALRQALAY-----RDQLEEEALRAVYQEKLEEAISGL----RRTVEKYRALLGEDKV 145

Query: 254 TLE----NLSSEFEVSRERVRQIE 273
             E     +  E+++++E++ ++E
Sbjct: 146 AFESAVVKILEEYKITQEKLARLE 169


>gi|293408383|ref|ZP_06652222.1| conserved hypothetical protein [Escherichia coli B354]
 gi|291471561|gb|EFF14044.1| conserved hypothetical protein [Escherichia coli B354]
          Length = 101

 Score = 37.1 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 18/101 (17%), Positives = 40/101 (39%), Gaps = 22/101 (21%)

Query: 22  EIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMG---YRGYGLPISEV 78
           E    P+L  Q+E    +                ++L LV K+           +   ++
Sbjct: 11  EFAAAPVLTPQQESHYLQ----------------AYLPLVRKVVRQLAPQCNCIIDRQDM 54

Query: 79  VSEGNIGLMQAVKKFD-PERGFRLATYSMWWIKAAMQEYIL 118
                +GL+ A++++  P+ G   A Y++  I+ A+ + + 
Sbjct: 55  EQTALMGLLNAIRRYGLPDEG--FAGYAVHRIRGAILDELR 93


>gi|289596079|ref|YP_003482775.1| transcriptional regulator, AsnC family [Aciduliprofundum boonei
           T469]
 gi|289533866|gb|ADD08213.1| transcriptional regulator, AsnC family [Aciduliprofundum boonei
           T469]
          Length = 143

 Score = 37.1 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 11/45 (24%), Positives = 23/45 (51%), Gaps = 5/45 (11%)

Query: 235 LNPRERRIFEARRLQENPVTLENLSSEFEVS----RERVRQIEAR 275
           L+ R+R+I E   L+ + +    ++    +S    R+R+R +E  
Sbjct: 3   LDDRDRKIIEL-LLKNSRMNYSEIAKVLGISDTAVRKRIRNMEKN 46


>gi|282877083|ref|ZP_06285925.1| sigma-70, region 4 [Prevotella buccalis ATCC 35310]
 gi|281300765|gb|EFA93092.1| sigma-70, region 4 [Prevotella buccalis ATCC 35310]
          Length = 170

 Score = 37.1 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 9/63 (14%), Positives = 26/63 (41%), Gaps = 2/63 (3%)

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           +         E   +++R  ++   ++ L  ++R   + R  +  P   + ++    +S 
Sbjct: 87  ESPDTSSTPFEDTLQQDRIELVRNLVNALPEKQRSCMQLRDFEGKPY--KEIAKILGISE 144

Query: 267 ERV 269
           E+V
Sbjct: 145 EQV 147


>gi|297563266|ref|YP_003682240.1| XRE family transcriptional regulator [Nocardiopsis dassonvillei
           subsp. dassonvillei DSM 43111]
 gi|296847714|gb|ADH69734.1| transcriptional regulator, XRE family [Nocardiopsis dassonvillei
           subsp. dassonvillei DSM 43111]
          Length = 135

 Score = 37.1 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 8/24 (33%), Positives = 14/24 (58%)

Query: 250 ENPVTLENLSSEFEVSRERVRQIE 273
           E+  T + ++    VS+ R+ QIE
Sbjct: 51  ESGRTQKEVAQIMGVSQARISQIE 74


>gi|269926898|ref|YP_003323521.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermobaculum
           terrenum ATCC BAA-798]
 gi|269790558|gb|ACZ42699.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermobaculum
           terrenum ATCC BAA-798]
          Length = 189

 Score = 37.1 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 19/85 (22%), Positives = 35/85 (41%), Gaps = 4/85 (4%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L +R +E GDL A ++LV  +   +  +A+ Y G      +V  E  +   +A+  F  
Sbjct: 8   ELVRRAQE-GDLDAFNKLVERYQVQMYNLAIRYIGDPFLAEDVTQEAFVAAWKALGSF-- 64

Query: 96  ERGFRLATYSMWWIKAAMQEYILRS 120
            RG    ++    +     +   R 
Sbjct: 65  -RGGSFRSWLFRILINEAHDLRRRH 88


>gi|332669297|ref|YP_004452305.1| ECF subfamily RNA polymerase sigma-24 subunit [Cellulomonas fimi
           ATCC 484]
 gi|332338335|gb|AEE44918.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Cellulomonas fimi
           ATCC 484]
          Length = 190

 Score = 37.1 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 10/88 (11%), Positives = 30/88 (34%), Gaps = 14/88 (15%)

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            D         +       R  +   +  L   +R +   R + +  +T+E ++      
Sbjct: 107 DDEGTPVPSAEDGALDTLSRERVLAVLGTLTEEQRDVLTLRVVAD--LTIEQVAEVVG-- 162

Query: 266 RERVRQ------IEARAFKKVQESIQKQ 287
               +Q      ++ R    V+ +++++
Sbjct: 163 ----KQVGAVKALQRRGLAAVRRTLERE 186


>gi|326797535|ref|YP_004315354.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Sphingobacterium
           sp. 21]
 gi|326548299|gb|ADZ76684.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Sphingobacterium
           sp. 21]
          Length = 189

 Score = 37.1 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 21/114 (18%), Positives = 53/114 (46%), Gaps = 5/114 (4%)

Query: 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRS 231
           + +    R+A + +L   I    K  ++  D  ++   G       + E +    ++ ++
Sbjct: 73  KPLEWMMRVAHNIALY-RIREETKRGTEPLDGYIWLAGGSHAD--GELEGRELDRLIRQA 129

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              L P+ER +F    ++ + +T   L     ++ + V+ + A+A KK+++S++
Sbjct: 130 AETLTPKERMVFLL--IKMDGMTNRELMKRHNMAEQTVKNLLAQALKKIRKSLK 181


>gi|315501746|ref|YP_004080633.1| RNA polymerase, sigma-24 subunit, ecf subfamily [Micromonospora sp.
           L5]
 gi|315408365|gb|ADU06482.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Micromonospora sp.
           L5]
          Length = 235

 Score = 37.1 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 16/81 (19%), Positives = 39/81 (48%), Gaps = 2/81 (2%)

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
            E+  +++ E++  R+ L R +  L  R+R +   R  ++  ++    ++  E+S   V+
Sbjct: 93  PERAGVDEIEQQLDRDALWRHLQALPARQRAVLVLRFYED--MSEAQTAALLEISPGTVK 150

Query: 271 QIEARAFKKVQESIQKQVELS 291
              +RA   ++  +  +  LS
Sbjct: 151 SQTSRALNTLRRRLGSEAALS 171


>gi|163802952|ref|ZP_02196839.1| RNA polymerase sigma-70 factor [Vibrio sp. AND4]
 gi|159173242|gb|EDP58070.1| RNA polymerase sigma-70 factor [Vibrio sp. AND4]
          Length = 190

 Score = 37.1 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 19/88 (21%), Positives = 33/88 (37%), Gaps = 3/88 (3%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
            VL +R + +GD  A + LVT +   V  +   Y      + +V  E  I   +A+  F 
Sbjct: 8   QVLIERVQ-NGDKQAFNLLVTKYQNKVCNLISRYVSNPGDVPDVAQEAFIKAYRAIPSFR 66

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWS 122
            E      T+         + +I+    
Sbjct: 67  GE--SAFYTWLYRIAVNTAKNHIVAQGR 92


>gi|320107222|ref|YP_004182812.1| N-acylglucosamine 2-epimerase [Terriglobus saanensis SP1PR4]
 gi|319925743|gb|ADV82818.1| N-acylglucosamine 2-epimerase [Terriglobus saanensis SP1PR4]
          Length = 714

 Score = 37.1 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 25/192 (13%), Positives = 59/192 (30%), Gaps = 32/192 (16%)

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
           I      Y +    +V       +K  + N   LK +++A         +   +A+++  
Sbjct: 260 IGGGFHRYSVDERWVV----PHFEKMAYDNAELLKSYVRAF--RTFLVPEYAEVAREILR 313

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNS------SQWQDWLVYDHDGQEQVLIEKEERK 222
                +S   R     S +A +   D          +    L  +     ++  +  E  
Sbjct: 314 WMDGTLSDRERGGFYSSQDADLTLDDDGDYFTWTRDEAAAVLSPEELAVAEIYYDIGEIG 373

Query: 223 NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282
           +  +         +P  R +   R       TL  +S    ++ E V+ +       ++ 
Sbjct: 374 DMHH---------DP-SRNVLHVRY------TLAEVSRRIGITEEEVQSL----LLSLRG 413

Query: 283 SIQKQVELSSSP 294
            +       ++P
Sbjct: 414 KLASARSERAAP 425


>gi|124484909|ref|YP_001029525.1| putative transcriptional regulator [Methanocorpusculum labreanum Z]
 gi|124362450|gb|ABN06258.1| sigma-70 region 4 domain protein [Methanocorpusculum labreanum Z]
          Length = 134

 Score = 37.1 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 9/54 (16%), Positives = 25/54 (46%), Gaps = 6/54 (11%)

Query: 235 LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA---FKKVQESIQ 285
           L  R++ +   R   +  +T + ++     S+  +  IE  A    ++ +E+++
Sbjct: 6   LTDRQKEVIRFR---KQGMTQQQIADRLGTSKANICTIEKSANENIRRAKETLE 56


>gi|84497434|ref|ZP_00996256.1| putative sigma factor [Janibacter sp. HTCC2649]
 gi|84382322|gb|EAP98204.1| putative sigma factor [Janibacter sp. HTCC2649]
          Length = 297

 Score = 37.1 bits (85), Expect = 3.5,   Method: Composition-based stats.
 Identities = 22/112 (19%), Positives = 37/112 (33%), Gaps = 6/112 (5%)

Query: 167 NVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
                +  +   R+    +L+ L   S +       WL         V  + E   +   
Sbjct: 51  QREVRDPRAFLVRVVSRTALDRLRTVSRRREDYVGPWLPEPLVTARDVAEDVELADSVSI 110

Query: 227 MLTRSMSVLNPRERRIFEAR--RLQENPVTLENLSSEFEVSRERVRQIEARA 276
            +   +  L P ER +F  R     +     + L+   + S   VRQI  RA
Sbjct: 111 AMMLVLETLTPTERAVFVLREVFGLD----YDELAEAVDKSPASVRQIAHRA 158


>gi|15668345|ref|NP_247141.1| putative transcriptional regulator [Methanocaldococcus jannaschii
           DSM 2661]
 gi|1498946|gb|AAB98158.1| conserved hypothetical protein [Methanocaldococcus jannaschii DSM
           2661]
          Length = 157

 Score = 37.1 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 10/49 (20%), Positives = 24/49 (48%), Gaps = 3/49 (6%)

Query: 235 LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           L   + ++ + R   +  +T E ++     SR  +  IE RA + ++++
Sbjct: 27  LTDTQIKVLKLR---KKGLTQEEIAKMLGTSRANISMIEKRAKENIKKA 72


>gi|210617229|ref|ZP_03291473.1| hypothetical protein CLONEX_03695 [Clostridium nexile DSM 1787]
 gi|210149430|gb|EEA80439.1| hypothetical protein CLONEX_03695 [Clostridium nexile DSM 1787]
          Length = 139

 Score = 37.1 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 10/68 (14%), Positives = 29/68 (42%), Gaps = 2/68 (2%)

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           + +   + L  ++  L+ R R         E  +  E ++ +  +SR  V Q    +   
Sbjct: 73  DIRVYDDELAEALKQLSERNRETLLMYYFLE--MNNEEIAKKQNISRSGVFQNRHNSLAL 130

Query: 280 VQESIQKQ 287
           +++ ++++
Sbjct: 131 MKKLLKEK 138


>gi|301065884|ref|YP_003787907.1| comX [Lactobacillus casei str. Zhang]
 gi|300438291|gb|ADK18057.1| ComX [Lactobacillus casei str. Zhang]
          Length = 182

 Score = 37.1 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 25/146 (17%), Positives = 51/146 (34%), Gaps = 4/146 (2%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L   +  LV+ +   Y        + + E  I +++A+ ++D   GF+   Y    
Sbjct: 18  AFSQLFKQYRPLVLTVLRPYHLRDFSHEDWLQEARIAMLKAITRYDGSSGFQFGPY-YRM 76

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFF---NLRRLKGHLQAITDNNLKPEQVVAIAKK 165
           +  +    +LR     K    A    +        + +  L++  D  L   +      +
Sbjct: 77  VLQSHLRSVLRKHFAHKRRIDATAIPVEDSALESLQERLALRSYEDGLLMRIEFAQFLAR 136

Query: 166 LNVSESEVISMNCRLAGDESLNALIN 191
           L+  E E          D S + L+ 
Sbjct: 137 LSPLEYEAFEAAVISQTDSSEDPLLQ 162


>gi|295402541|ref|ZP_06812491.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|312109304|ref|YP_003987620.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Geobacillus sp.
           Y4.1MC1]
 gi|294975435|gb|EFG51063.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Geobacillus
           thermoglucosidasius C56-YS93]
 gi|311214405|gb|ADP73009.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Geobacillus sp.
           Y4.1MC1]
          Length = 187

 Score = 37.1 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 9/72 (12%), Positives = 28/72 (38%), Gaps = 2/72 (2%)

Query: 193 SDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENP 252
            ++ S      +       E    E  E    +  + +++  L  + R +   R +++  
Sbjct: 95  DEEISGTDGLTMYSQLSSSEASPEETLESLELQETVQKAIEKLPEKYRSVIVLRYIED-- 152

Query: 253 VTLENLSSEFEV 264
           ++L+ +S   ++
Sbjct: 153 LSLQEISEILDL 164


>gi|297202034|ref|ZP_06919431.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces sviceus
           ATCC 29083]
 gi|197714331|gb|EDY58365.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces sviceus
           ATCC 29083]
          Length = 167

 Score = 37.1 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 2/49 (4%)

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           +S L P+ER +   R  +      E  ++   +S ERVR I  RA   +
Sbjct: 102 LSRLTPQERLVLVLRLYEGVAE--EQAAALLGLSAERVRAICDRATATL 148


>gi|134099697|ref|YP_001105358.1| large transcriptional regulator [Saccharopolyspora erythraea NRRL
           2338]
 gi|291008299|ref|ZP_06566272.1| large transcriptional regulator [Saccharopolyspora erythraea NRRL
           2338]
 gi|133912320|emb|CAM02433.1| large transcriptional regulator [Saccharopolyspora erythraea NRRL
           2338]
          Length = 946

 Score = 37.1 bits (85), Expect = 3.6,   Method: Composition-based stats.
 Identities = 13/57 (22%), Positives = 27/57 (47%), Gaps = 3/57 (5%)

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
           + L+PRE+ +     L     T   ++    +SR  V Q  AR  +K+  + + +++
Sbjct: 891 NELSPREQDVAR---LLAGGRTNREIAEALFLSRRTVEQHVARVLRKLGAASRTELQ 944


>gi|50120475|ref|YP_049642.1| ECF sigma factor [Pectobacterium atrosepticum SCRI1043]
 gi|49611001|emb|CAG74446.1| ECF sigma factor [Pectobacterium atrosepticum SCRI1043]
          Length = 169

 Score = 37.1 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 19/134 (14%), Positives = 46/134 (34%), Gaps = 3/134 (2%)

Query: 132 QKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALIN 191
           ++ L   LR  +     + ++ L+  Q +     ++  ++ +      L  D   +    
Sbjct: 18  ERYLNHKLRDPQAAADLMQESFLRLAQRLEQQDDVDDKKAYLYKTANNLLLDHIRHQQRW 77

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQEN 251
               +       L Y  D   Q+  +    +     L   ++ L  R ++IF   R    
Sbjct: 78  QMATSVDDVDATLEYLPDAAPQI-DQAAIAQQELEHLANVLATLPERTQQIFHLHRF--E 134

Query: 252 PVTLENLSSEFEVS 265
            +T   ++ +  +S
Sbjct: 135 HMTQAQIAQQLAIS 148


>gi|300088663|ref|YP_003759185.1| hypothetical protein Dehly_1585 [Dehalogenimonas
           lykanthroporepellens BL-DC-9]
 gi|299528396|gb|ADJ26864.1| hypothetical protein Dehly_1585 [Dehalogenimonas
           lykanthroporepellens BL-DC-9]
          Length = 127

 Score = 37.1 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 12/40 (30%), Positives = 21/40 (52%), Gaps = 1/40 (2%)

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
           + L  R R I+E  +      TL  L  +F +S++R+ Q+
Sbjct: 4   NELTKRNRDIYEYHK-ANPDFTLAELGEKFGLSQQRISQL 42


>gi|238764059|ref|ZP_04625014.1| ECF-family sigma factor [Yersinia kristensenii ATCC 33638]
 gi|238697730|gb|EEP90492.1| ECF-family sigma factor [Yersinia kristensenii ATCC 33638]
          Length = 179

 Score = 37.1 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 14/78 (17%), Positives = 32/78 (41%), Gaps = 9/78 (11%)

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
           AL+ S + +  + +     D            E++ R + L  +++ L+PR R  F   R
Sbjct: 82  ALVQSHEDDDVEQEAPAGAD-------PQHLLEQQQRLSRLEEALNSLSPRRREAFLMHR 134

Query: 248 LQENPVTLENLSSEFEVS 265
              + ++   ++    +S
Sbjct: 135 F--DGLSQIEVAERMGIS 150


>gi|149744149|ref|XP_001494325.1| PREDICTED: similar to spectrin repeat containing, nuclear envelope 1
            [Equus caballus]
          Length = 8798

 Score = 37.1 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 27/125 (21%), Positives = 51/125 (40%), Gaps = 5/125 (4%)

Query: 112  AMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171
            A  + + RSW  +K   +  Q+ L+  L R + +  ++   + K E   AI  KL+ S  
Sbjct: 5936 AKLDDLQRSWETLKNVISEKQRTLYEALERQQRYQDSLQSISTKME---AIEMKLSESLE 5992

Query: 172  EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLT 229
               S   ++A  ++L   I    +  ++ Q  L  +      E    E+   ++   +L 
Sbjct: 5993 PGRSPESQMAEHQALMDEILMLQEEITELQSSLAEELVSASPECDPAEQLALQSTLTVLA 6052

Query: 230  RSMSV 234
              MS 
Sbjct: 6053 ERMST 6057


>gi|15808964|gb|AAL08569.1|AF417007_1 DNA-directed RNA polymerase specialized sigma subunit [Pseudomonas
           syringae pv. syringae]
          Length = 48

 Score = 37.1 bits (85), Expect = 3.7,   Method: Composition-based stats.
 Identities = 6/42 (14%), Positives = 17/42 (40%)

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
                  +  + L+ +     VS  RV Q+ ++   +++  +
Sbjct: 1   LVLALYYDEELNLKEIGEVLGVSESRVSQLHSQCAARLRGRL 42


>gi|168705448|ref|ZP_02737725.1| putative lipoprotein [Gemmata obscuriglobus UQM 2246]
          Length = 522

 Score = 36.7 bits (84), Expect = 3.7,   Method: Composition-based stats.
 Identities = 16/63 (25%), Positives = 25/63 (39%), Gaps = 1/63 (1%)

Query: 27 PMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGL 86
          P+L   +  +LA R+ E  D  A  +LV  H RLV  +            +      + L
Sbjct: 10 PLLALDDRTLLA-RFAEQHDEDAFEQLVKRHGRLVFGVCRRAVRDAHLAEDAFQAVFLVL 68

Query: 87 MQA 89
           +A
Sbjct: 69 ARA 71


>gi|166033349|ref|ZP_02236178.1| hypothetical protein DORFOR_03075 [Dorea formicigenerans ATCC
           27755]
 gi|166027706|gb|EDR46463.1| hypothetical protein DORFOR_03075 [Dorea formicigenerans ATCC
           27755]
          Length = 138

 Score = 36.7 bits (84), Expect = 3.7,   Method: Composition-based stats.
 Identities = 14/104 (13%), Positives = 41/104 (39%), Gaps = 4/104 (3%)

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVL--IEKEERKNRRNMLTRSMSVLNPRERRIF 243
           L   +  S+ +  +     VYD    +     +   E +   + L++++  L  R+R I 
Sbjct: 37  LKHEVPFSEISDLELNKAGVYDKYSSDYTAFNVLGMEVQVSDDQLSKALKCLPERKRNII 96

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
                 +  ++   +     V R  V +      +++++ ++++
Sbjct: 97  LLSYFMD--MSDAEIGELMNVVRTTVYRHRTSTLEELRKMMEEE 138


>gi|47564555|ref|ZP_00235600.1| RNA polymerase sigma-I factor [Bacillus cereus G9241]
 gi|228986516|ref|ZP_04146651.1| RNA polymerase sigma-I factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
 gi|229197551|ref|ZP_04324276.1| RNA polymerase sigma-I factor [Bacillus cereus m1293]
 gi|47558707|gb|EAL17030.1| RNA polymerase sigma-I factor [Bacillus cereus G9241]
 gi|228585922|gb|EEK44015.1| RNA polymerase sigma-I factor [Bacillus cereus m1293]
 gi|228773201|gb|EEM21632.1| RNA polymerase sigma-I factor [Bacillus thuringiensis serovar
           tochigiensis BGSC 4Y1]
          Length = 235

 Score = 36.7 bits (84), Expect = 3.7,   Method: Composition-based stats.
 Identities = 15/124 (12%), Positives = 45/124 (36%), Gaps = 1/124 (0%)

Query: 44  HGDLSAAHRLVTSHLRLVV-KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
             +       +  +   +   I+   R Y     +  S G     +A++++  ++G    
Sbjct: 17  QNNEEDKEAFIVQYQPFIRKSISSVCRRYITEQDDEYSIGLFAFNEAIEQYSYKKGKSFL 76

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
            ++   IK  + +YI +     ++    +++     ++          DN+ + E+++  
Sbjct: 77  AFADLLIKRDVIDYIRKESKHNRVFLKEDEQEEMLEMQVSLTEYMKEMDNSNRKEEILHF 136

Query: 163 AKKL 166
              L
Sbjct: 137 QSVL 140


>gi|255034918|ref|YP_003085539.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Dyadobacter
           fermentans DSM 18053]
 gi|254947674|gb|ACT92374.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Dyadobacter
           fermentans DSM 18053]
          Length = 183

 Score = 36.7 bits (84), Expect = 3.7,   Method: Composition-based stats.
 Identities = 18/84 (21%), Positives = 34/84 (40%), Gaps = 10/84 (11%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           V D  G      E  ER+  ++ L  +M  L+P  R +    R QE     + ++    +
Sbjct: 100 VADRLGGGMPADENLERQQDKDFLHEAMGALSPEYREVLILSRFQEMKY--DEIAKVLNI 157

Query: 265 S----RERVRQIEARAFKKVQESI 284
           +    + RV     RA  ++++  
Sbjct: 158 NEGTVKVRV----HRALGELKKRF 177


>gi|298492543|ref|YP_003722720.1| ECF subfamily RNA polymerase sigma 24 subunit ['Nostoc azollae'
           0708]
 gi|298234461|gb|ADI65597.1| RNA polymerase, sigma-24 subunit, ECF subfamily ['Nostoc azollae'
           0708]
          Length = 218

 Score = 36.7 bits (84), Expect = 3.7,   Method: Composition-based stats.
 Identities = 21/115 (18%), Positives = 42/115 (36%), Gaps = 17/115 (14%)

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           R+    SL+A  +  D         + +D  G      E+   +     L  +++ L   
Sbjct: 116 RVVSPLSLDAPRSLEDGE-------MDWDIAGDSPGPEEELTTREFYEQLRDAIADLPEV 168

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVS----RERVRQIEARAFKKVQESIQKQVE 289
            R     R +    +  E ++    VS    + R+    ARA  ++Q  +Q  ++
Sbjct: 169 FRTTIVLREI--EGMAYEEIAEMTGVSLGTVKSRI----ARARSRLQAQLQTYLD 217


>gi|52079892|ref|YP_078683.1| putative RNA polymerase sigma factor SigI [Bacillus licheniformis
           ATCC 14580]
 gi|52785264|ref|YP_091093.1| putative RNA polymerase sigma factor SigI [Bacillus licheniformis
           ATCC 14580]
 gi|319646290|ref|ZP_08000520.1| SigI protein [Bacillus sp. BT1B_CT2]
 gi|52003103|gb|AAU23045.1| RNA polymerase sigma factor [Bacillus licheniformis ATCC 14580]
 gi|52347766|gb|AAU40400.1| SigI [Bacillus licheniformis ATCC 14580]
 gi|317392040|gb|EFV72837.1| SigI protein [Bacillus sp. BT1B_CT2]
          Length = 251

 Score = 36.7 bits (84), Expect = 3.7,   Method: Composition-based stats.
 Identities = 16/81 (19%), Positives = 34/81 (41%), Gaps = 1/81 (1%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMG-YRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
           + G+    + L+  +   V K      + Y     +  S G I   +A++K+  ++G  L
Sbjct: 26  QKGNQQLQNELIDQYKPFVAKTVSSVCKRYIDEKDDEFSIGLIAFNEAIEKYSSDKGNSL 85

Query: 102 ATYSMWWIKAAMQEYILRSWS 122
             ++   IK  + +YI +   
Sbjct: 86  LAFAELIIKRKVIDYIRKEAR 106


>gi|127512405|ref|YP_001093602.1| RNA polymerase sigma factor [Shewanella loihica PV-4]
 gi|126637700|gb|ABO23343.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Shewanella loihica
           PV-4]
          Length = 212

 Score = 36.7 bits (84), Expect = 3.7,   Method: Composition-based stats.
 Identities = 18/91 (19%), Positives = 34/91 (37%), Gaps = 15/91 (16%)

Query: 203 WLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEF 262
            L       E+  +   +    + ML      L   +R + +    QE  ++ E L+ +F
Sbjct: 128 PLEQAQVQSEEEPLHFADHLMEKQMLAYV-DSLPEAQRAVVKGVYYQE--LSQEQLAQQF 184

Query: 263 EV------SRERVRQIEARAFKKVQESIQKQ 287
            V      SR R+      A  K+++ +  Q
Sbjct: 185 GVPIGTIKSRLRL------ALAKLKQQMGDQ 209


>gi|326329527|ref|ZP_08195850.1| RNA polymerase sigma-E factor [Nocardioidaceae bacterium Broad-1]
 gi|325952694|gb|EGD44711.1| RNA polymerase sigma-E factor [Nocardioidaceae bacterium Broad-1]
          Length = 169

 Score = 36.7 bits (84), Expect = 3.8,   Method: Composition-based stats.
 Identities = 11/79 (13%), Positives = 29/79 (36%), Gaps = 22/79 (27%)

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL--SSEFEV------ 264
           +      +  + R  L ++++ L PR+R I   R  ++    L  +  +    +      
Sbjct: 91  EAPSAPAKDSDLRLSLEQALAELTPRQRTILVLRFFED----LTEVQTAHVLGIHSGTVK 146

Query: 265 --SRERVRQIEARAFKKVQ 281
             +R        +A  +++
Sbjct: 147 STTR--------KALDRLR 157


>gi|297157083|gb|ADI06795.1| ECF subfamily RNA polymerase sigma factor [Streptomyces
           bingchenggensis BCW-1]
          Length = 354

 Score = 36.7 bits (84), Expect = 3.8,   Method: Composition-based stats.
 Identities = 17/104 (16%), Positives = 31/104 (29%), Gaps = 6/104 (5%)

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
                 D                   +     L   +  L P ER +F    +     T 
Sbjct: 96  PEPLVTDTAADPPADTVDTADRALRAETVSMALLVVLETLTPLERAVFVLHEVFGYAHT- 154

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQK 299
             ++   + S   VRQ+  RA    +E +  +     + P +Q+
Sbjct: 155 -EIADILDRSPSAVRQLAHRA----REHVHARRPRYQAHPRVQR 193


>gi|300022661|ref|YP_003755272.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Hyphomicrobium
           denitrificans ATCC 51888]
 gi|299524482|gb|ADJ22951.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Hyphomicrobium
           denitrificans ATCC 51888]
          Length = 205

 Score = 36.7 bits (84), Expect = 3.8,   Method: Composition-based stats.
 Identities = 12/82 (14%), Positives = 33/82 (40%), Gaps = 2/82 (2%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
              +    +   E ++ ++ +  +M  L  R+R            ++   + +   VS E
Sbjct: 118 EVPEPAKQLAALESQDVQHRVGDAMQKLPERQR--LALTLFHFEGLSQIEIGNILGVSDE 175

Query: 268 RVRQIEARAFKKVQESIQKQVE 289
            V  + +RA ++++  ++   E
Sbjct: 176 AVESLLSRARRQLKADLKSDWE 197


>gi|209695949|ref|YP_002263879.1| RNA polymerase sigma factor RpoE [Aliivibrio salmonicida LFI1238]
 gi|208009902|emb|CAQ80215.1| RNA polymerase sigma-E factor [Aliivibrio salmonicida LFI1238]
          Length = 192

 Score = 36.7 bits (84), Expect = 3.8,   Method: Composition-based stats.
 Identities = 17/88 (19%), Positives = 31/88 (35%), Gaps = 3/88 (3%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
            VL +R +  GD  A + LV  +   V  +   Y      + +V  E  I   +A+  F 
Sbjct: 8   QVLIERVQ-RGDKQAFNHLVIKYQNKVCNLVARYVKNSGDVPDVAQEAFIKAYRALPTFR 66

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWS 122
            +      T+         + Y++    
Sbjct: 67  GD--SAFYTWLYRIAVNTAKNYLVAQGR 92


>gi|254419614|ref|ZP_05033338.1| RNA polymerase sigma factor, sigma-70 family [Brevundimonas sp.
           BAL3]
 gi|196185791|gb|EDX80767.1| RNA polymerase sigma factor, sigma-70 family [Brevundimonas sp.
           BAL3]
          Length = 183

 Score = 36.7 bits (84), Expect = 3.8,   Method: Composition-based stats.
 Identities = 13/101 (12%), Positives = 38/101 (37%), Gaps = 13/101 (12%)

Query: 188 ALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR 247
            ++    + +   +  L+ +   +   L+   E       L  +M+ L   +  +     
Sbjct: 85  DVLRQDARRTPMPEIELLQEEPERPDQLVLMAEDA---ARLKTAMARLTADQIEVLRLAF 141

Query: 248 LQENPVTLENLSSEFEVS----RERVRQIEARAFKKVQESI 284
            Q+NP +   ++   ++     + R+R    +A  K++  +
Sbjct: 142 FQDNPHS--EIARRLDLPLGTVKSRIR----KAMIKLRTLL 176


>gi|182438100|ref|YP_001825819.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces griseus
           subsp. griseus NBRC 13350]
 gi|178466616|dbj|BAG21136.1| putative RNA polymerase ECF-subfamily sigma factor [Streptomyces
           griseus subsp. griseus NBRC 13350]
          Length = 503

 Score = 36.7 bits (84), Expect = 3.8,   Method: Composition-based stats.
 Identities = 25/134 (18%), Positives = 49/134 (36%), Gaps = 6/134 (4%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
           +GD +A  RL   +L LV  +          + +VV E    +++A+      R    A 
Sbjct: 15  NGDRAAGDRLAAHYLPLVYNVVGRALNGHPDVDDVVQET---MLRALSGLPSLRDP--AR 69

Query: 104 YSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAI-TDNNLKPEQVVAI 162
           +  W +  AM +   R   L              +       L  +  + + +  +    
Sbjct: 70  FRSWLVAIAMNQVRTRWSGLGHRPAPLEATEEPADPAADFVDLTILRLELSGQRRETAEA 129

Query: 163 AKKLNVSESEVISM 176
            + L+ SE +V+S+
Sbjct: 130 TRWLDDSERDVLSL 143


>gi|87312306|ref|ZP_01094403.1| hypothetical protein DSM3645_11631 [Blastopirellula marina DSM
           3645]
 gi|87284978|gb|EAQ76915.1| hypothetical protein DSM3645_11631 [Blastopirellula marina DSM
           3645]
          Length = 196

 Score = 36.7 bits (84), Expect = 3.8,   Method: Composition-based stats.
 Identities = 16/66 (24%), Positives = 28/66 (42%), Gaps = 3/66 (4%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           +  D +        + +     + L R ++ LNPR  RI E R      +T+E  ++  E
Sbjct: 116 IAIDENLTPDAPSREVDLVALDDALER-LAELNPRHARIVELRYFGG--LTVEETAATLE 172

Query: 264 VSRERV 269
           +S   V
Sbjct: 173 ISASTV 178


>gi|260910728|ref|ZP_05917386.1| RNA polymerase ECF-type sigma factor [Prevotella sp. oral taxon 472
           str. F0295]
 gi|260635144|gb|EEX53176.1| RNA polymerase ECF-type sigma factor [Prevotella sp. oral taxon 472
           str. F0295]
          Length = 187

 Score = 36.7 bits (84), Expect = 3.8,   Method: Composition-based stats.
 Identities = 16/81 (19%), Positives = 36/81 (44%), Gaps = 8/81 (9%)

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D   Q        ++    L  ++S L  + R IF   +LQ       +++ +  +S   
Sbjct: 95  DALLQTETNFHNEEDIDRALEEAISRLPEKCREIFVMSKLQGMRH--ADIAQQLGIS--- 149

Query: 269 VRQIEAR---AFKKVQESIQK 286
           V  IE +   A++K+++ +++
Sbjct: 150 VNTIETQMGIAYRKLRQELKQ 170


>gi|192361496|ref|YP_001983140.1| RNA polymerase sigma factor, sigma-70 family [Cellvibrio japonicus
           Ueda107]
 gi|190687661|gb|ACE85339.1| RNA polymerase sigma factor, sigma-70 family [Cellvibrio japonicus
           Ueda107]
          Length = 172

 Score = 36.7 bits (84), Expect = 3.8,   Method: Composition-based stats.
 Identities = 14/95 (14%), Positives = 37/95 (38%), Gaps = 2/95 (2%)

Query: 171 SEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR 230
            +V +   R+A +  ++       + +    + ++ +   +      +   + R   +  
Sbjct: 55  QKVRAYLFRIARNLVIDHFRREQIRCTDSVPEDILDEIPTEVAGPEVRAASQQRLENIRA 114

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
           ++  L PR R +F   R+Q   +TL  +     +S
Sbjct: 115 AVDQLPPRCRDVFIMSRVQG--MTLAEIGLALNIS 147


>gi|52141808|ref|YP_085021.1| positive control sigma-like factor [Bacillus cereus E33L]
 gi|51975277|gb|AAU16827.1| possible positive control factor Xpf [Bacillus cereus E33L]
          Length = 167

 Score = 36.7 bits (84), Expect = 3.8,   Method: Composition-based stats.
 Identities = 14/65 (21%), Positives = 31/65 (47%), Gaps = 2/65 (3%)

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
           +E    +  +  L  ++S+L  RE+ ++   R     +T   ++   +V+   V+ +  R
Sbjct: 92  LEHAIGEWDKIRLEDALSLLTEREKEVYLMSRGYC--LTYREIARYLDVTCSTVQSMVER 149

Query: 276 AFKKV 280
           A KK+
Sbjct: 150 AEKKI 154


>gi|227502737|ref|ZP_03932786.1| RNA polymerase sigma factor SigD [Corynebacterium accolens ATCC
           49725]
 gi|306835318|ref|ZP_07468344.1| RNA polymerase sigma-70 factor [Corynebacterium accolens ATCC
           49726]
 gi|227076467|gb|EEI14430.1| RNA polymerase sigma factor SigD [Corynebacterium accolens ATCC
           49725]
 gi|304568797|gb|EFM44336.1| RNA polymerase sigma-70 factor [Corynebacterium accolens ATCC
           49726]
          Length = 190

 Score = 36.7 bits (84), Expect = 3.8,   Method: Composition-based stats.
 Identities = 12/84 (14%), Positives = 33/84 (39%), Gaps = 2/84 (2%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           + +    E    E     +  N +   +  L+ + + I   R      ++ E  +     
Sbjct: 105 LPESTANEATPEEWALENDGSNRMRALLDTLSDKAKNIVILRVFVG--LSAEETADIVGS 162

Query: 265 SRERVRQIEARAFKKVQESIQKQV 288
           +   VR  + RA  ++++++ +Q+
Sbjct: 163 TPGAVRVAQHRALAQLRKALGQQL 186


>gi|254524052|ref|ZP_05136107.1| sigma-70 factor, ECF subfamily [Stenotrophomonas sp. SKA14]
 gi|219721643|gb|EED40168.1| sigma-70 factor, ECF subfamily [Stenotrophomonas sp. SKA14]
          Length = 175

 Score = 36.7 bits (84), Expect = 3.8,   Method: Composition-based stats.
 Identities = 12/75 (16%), Positives = 33/75 (44%), Gaps = 2/75 (2%)

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
            Q    + + E     ++L +++  L  R R ++   R+     T   ++    ++ + V
Sbjct: 91  SQSPDPLRQAESGQMLSLLRQALFKLPERAREVYLLNRITGMSYT--QIARHCGITAKTV 148

Query: 270 RQIEARAFKKVQESI 284
            +  ARA + +++ +
Sbjct: 149 EKHIARALQGLRQEL 163


>gi|59712700|ref|YP_205476.1| RNA polymerase sigma factor RpoE [Vibrio fischeri ES114]
 gi|197336372|ref|YP_002156892.1| RNA polymerase sigma factor RpoE [Vibrio fischeri MJ11]
 gi|59480801|gb|AAW86588.1| RNA polymerase, sigma-24 (sigma-E) factor [Vibrio fischeri ES114]
 gi|197317862|gb|ACH67309.1| RNA polymerase sigma factor RpoE [Vibrio fischeri MJ11]
          Length = 192

 Score = 36.7 bits (84), Expect = 3.8,   Method: Composition-based stats.
 Identities = 17/88 (19%), Positives = 31/88 (35%), Gaps = 3/88 (3%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
            VL +R +  GD  A + LV  +   V  +   Y      + +V  E  I   +A+  F 
Sbjct: 8   QVLIERVQ-RGDKQAFNHLVVKYQNKVCNLVARYVKNSGDVPDVAQEAFIKAYRALPTFR 66

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWS 122
            +      T+         + Y++    
Sbjct: 67  GD--SAFYTWLYRIAVNTAKNYLVAQGR 92


>gi|330954963|gb|EGH55223.1| RNA polymerase sigma factor [Pseudomonas syringae Cit 7]
          Length = 172

 Score = 36.7 bits (84), Expect = 3.9,   Method: Composition-based stats.
 Identities = 15/75 (20%), Positives = 28/75 (37%), Gaps = 2/75 (2%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L+   + ++    E+         +   +  L+ + R  F   RL         ++    
Sbjct: 89  LMQVPEAEQPSPEEQMLILEDLKAIDSMLGTLSSKARAAFLYSRLDGMSH--AEIAERLG 146

Query: 264 VSRERVRQIEARAFK 278
           VS  RVRQ  A+A +
Sbjct: 147 VSVSRVRQYLAQAMR 161


>gi|256829313|ref|YP_003158041.1| ECF subfamily RNA polymerase sigma-24 subunit [Desulfomicrobium
           baculatum DSM 4028]
 gi|256578489|gb|ACU89625.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Desulfomicrobium
           baculatum DSM 4028]
          Length = 180

 Score = 36.7 bits (84), Expect = 3.9,   Method: Composition-based stats.
 Identities = 11/60 (18%), Positives = 27/60 (45%), Gaps = 10/60 (16%)

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS----RERVRQIEARAFKKVQES 283
           L  ++  L P+ +     R +    ++L  +++   +S    + R+     RA + ++ES
Sbjct: 122 LHDALRDLPPKYKEALALRYI--EGMSLAEVAATLGLSMSGVKMRI----HRALRMLRES 175


>gi|254478502|ref|ZP_05091878.1| kinase, pfkB family [Carboxydibrachium pacificum DSM 12653]
 gi|214035591|gb|EEB76289.1| kinase, pfkB family [Carboxydibrachium pacificum DSM 12653]
          Length = 378

 Score = 36.7 bits (84), Expect = 3.9,   Method: Composition-based stats.
 Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 3/36 (8%)

Query: 235 LNPRERRIFEARRLQENPV-TLENLSSEFEVSRERV 269
           L  RE+ I   R +++NP+ + E L+    +SR  V
Sbjct: 16  LTQREKEIL--RLIKKNPMISQEELAKMLGISRSAV 49


>gi|154504931|ref|ZP_02041669.1| hypothetical protein RUMGNA_02441 [Ruminococcus gnavus ATCC 29149]
 gi|167767736|ref|ZP_02439789.1| hypothetical protein CLOSS21_02271 [Clostridium sp. SS2/1]
 gi|153794814|gb|EDN77234.1| hypothetical protein RUMGNA_02441 [Ruminococcus gnavus ATCC 29149]
 gi|167710475|gb|EDS21054.1| hypothetical protein CLOSS21_02271 [Clostridium sp. SS2/1]
 gi|291558906|emb|CBL37706.1| DNA-directed RNA polymerase specialized sigma subunit
           [butyrate-producing bacterium SSC/2]
          Length = 235

 Score = 36.7 bits (84), Expect = 3.9,   Method: Composition-based stats.
 Identities = 17/113 (15%), Positives = 45/113 (39%), Gaps = 6/113 (5%)

Query: 175 SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV 234
            +N R   + S + L +      + W D   Y+ D     +   + R      L  ++  
Sbjct: 128 ELNRRKNKEISFSELPDVLVDKMAVWDD---YETDYTIFSVCGIDIRVLDDE-LAEALKK 183

Query: 235 LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
           L  R+R         E  +T   +++  ++++  V +    A + +++ ++++
Sbjct: 184 LPERKRNTLLMYYFLE--MTESEIANLQKITQSGVFRNRHHALETMKKILKEE 234


>gi|162447017|ref|YP_001620149.1| ECF subfamily RNA polymerase sigma-70 factor [Acholeplasma
           laidlawii PG-8A]
 gi|161985124|gb|ABX80773.1| RNA polymerase sigma-70 factor, ECF subfamily [Acholeplasma
           laidlawii PG-8A]
          Length = 165

 Score = 36.7 bits (84), Expect = 3.9,   Method: Composition-based stats.
 Identities = 11/70 (15%), Positives = 21/70 (30%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
           Y L   YR          +   +  L++K    +        +   E  + L+  +  FD
Sbjct: 6   YELIYLYRTTKSEEVISIIFQKYKPLILKNIYKFYIPSKDHDDFFQESLMTLLDCIHTFD 65

Query: 95  PERGFRLATY 104
             +      Y
Sbjct: 66  ESKNKTFTKY 75


>gi|53712540|ref|YP_098532.1| RNA polymerase ECF-type sigma factor [Bacteroides fragilis YCH46]
 gi|253563430|ref|ZP_04840887.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 3_2_5]
 gi|265762694|ref|ZP_06091262.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 2_1_16]
 gi|52215405|dbj|BAD47998.1| RNA polymerase ECF-type sigma factor [Bacteroides fragilis YCH46]
 gi|251947206|gb|EES87488.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 3_2_5]
 gi|263255302|gb|EEZ26648.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 2_1_16]
 gi|301162266|emb|CBW21811.1| putative ECF-type RNA polymerase sigma factor [Bacteroides fragilis
           638R]
          Length = 181

 Score = 36.7 bits (84), Expect = 3.9,   Method: Composition-based stats.
 Identities = 18/76 (23%), Positives = 34/76 (44%), Gaps = 4/76 (5%)

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR-QIEAR 275
           ++    +   +L  +++ L  R R IF   RLQ      + ++ +  VS   V  QI   
Sbjct: 105 DRLSDADIEEILNNAINRLPERCREIFIMSRLQNLRY--KEIAEKLNVSPNTVENQI-VI 161

Query: 276 AFKKVQESIQKQVELS 291
           A +K++E ++    L 
Sbjct: 162 ALRKLKEDLKDYFPLF 177


>gi|325848520|ref|ZP_08170180.1| RNA polymerase sigma factor, sigma-70 family [Anaerococcus
           hydrogenalis ACS-025-V-Sch4]
 gi|325480748|gb|EGC83805.1| RNA polymerase sigma factor, sigma-70 family [Anaerococcus
           hydrogenalis ACS-025-V-Sch4]
          Length = 173

 Score = 36.7 bits (84), Expect = 3.9,   Method: Composition-based stats.
 Identities = 17/108 (15%), Positives = 44/108 (40%), Gaps = 11/108 (10%)

Query: 177 NCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLN 236
            C+    +SLN L    DKN  +  + +  ++  ++    + E  +     L +++  L 
Sbjct: 71  ECKKERVDSLNDL----DKNGVELIEKIDDENSLEDDFFKDLEIEE-----LFKAIKTLK 121

Query: 237 PRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
            +ER I   +  +  P   + ++    +S + +        +K+++  
Sbjct: 122 KQEREILYLKYDKNLPH--KEIARLLNLSTKSITNYHYNIVRKLRKYF 167


>gi|303239023|ref|ZP_07325553.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Acetivibrio
           cellulolyticus CD2]
 gi|302593361|gb|EFL63079.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Acetivibrio
           cellulolyticus CD2]
          Length = 184

 Score = 36.7 bits (84), Expect = 3.9,   Method: Composition-based stats.
 Identities = 16/77 (20%), Positives = 36/77 (46%), Gaps = 2/77 (2%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GD  A   L+T + RL+  +          ++++  E  I + +A+ K+DP+  ++ +T
Sbjct: 14  AGDKEAFSELITKYKRLIYNVIYNMINNKEEVNDIAQEVFIRIYRALDKYDPQ--YKFST 71

Query: 104 YSMWWIKAAMQEYILRS 120
           +S+        + I + 
Sbjct: 72  WSVKIATNYCLDVIRKK 88


>gi|220931572|ref|YP_002508480.1| putative helix-turn-helix protein YlxM/p13 family protein
           [Halothermothrix orenii H 168]
 gi|219992882|gb|ACL69485.1| putative helix-turn-helix protein YlxM/p13 family protein
           [Halothermothrix orenii H 168]
          Length = 138

 Score = 36.7 bits (84), Expect = 3.9,   Method: Composition-based stats.
 Identities = 5/34 (14%), Positives = 18/34 (52%), Gaps = 2/34 (5%)

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
            +L  R++ +      ++  ++L  ++ + ++SR
Sbjct: 41  KLLTDRQQEVIYLYYYRD--LSLGEIAEQLDISR 72


>gi|189465248|ref|ZP_03014033.1| hypothetical protein BACINT_01593 [Bacteroides intestinalis DSM
           17393]
 gi|189437522|gb|EDV06507.1| hypothetical protein BACINT_01593 [Bacteroides intestinalis DSM
           17393]
          Length = 201

 Score = 36.7 bits (84), Expect = 3.9,   Method: Composition-based stats.
 Identities = 12/73 (16%), Positives = 37/73 (50%), Gaps = 2/73 (2%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E  +I +EE   +   + + +  L PR++ +   + ++   +T + +    +++ + +  
Sbjct: 110 EDKIIRQEELHYQSRKIRQMLESLTPRQKEVLYYKYMKN--LTYDEIGEIMQMNYQSILN 167

Query: 272 IEARAFKKVQESI 284
           +  R+ KK++E+ 
Sbjct: 168 LIQRSIKKLRETF 180


>gi|168704620|ref|ZP_02736897.1| probable RNA polymerase sigma factor Y [Gemmata obscuriglobus UQM
           2246]
          Length = 193

 Score = 36.7 bits (84), Expect = 3.9,   Method: Composition-based stats.
 Identities = 21/89 (23%), Positives = 33/89 (37%), Gaps = 1/89 (1%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
             L  R R+ GD  A  R V ++  L+   A           ++V +    L+Q + +FD
Sbjct: 6   VTLLARLRQTGDGDAWARFVRTYSPLLYGWARRMALAHDDAVDLVQDVFAVLVQQIPRFD 65

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWSL 123
            +   R   +  W I         R  SL
Sbjct: 66  YDGQQRFRGWL-WTITRRRWADRKRKASL 93


>gi|206973455|ref|ZP_03234376.1| P188 [Bacillus cereus AH1134]
 gi|206731625|gb|EDZ48826.1| P188 [Bacillus cereus AH1134]
          Length = 191

 Score = 36.7 bits (84), Expect = 3.9,   Method: Composition-based stats.
 Identities = 18/101 (17%), Positives = 38/101 (37%), Gaps = 2/101 (1%)

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL       D+ ++  +D L         +       +   + L RS+  L  ++ ++ E
Sbjct: 93  SLTLDKPMIDETTTTIKDNLPDPTVYSNLISNPSLLDEIEDHKLYRSLESLTEKQLQVIE 152

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
              L    +T    +     + + V  I  +A KK++  I+
Sbjct: 153 L--LYAKKLTNNEAAYYLNTTPQNVTNIHTKALKKLKNMIE 191


>gi|167747103|ref|ZP_02419230.1| hypothetical protein ANACAC_01815 [Anaerostipes caccae DSM 14662]
 gi|167654063|gb|EDR98192.1| hypothetical protein ANACAC_01815 [Anaerostipes caccae DSM 14662]
          Length = 164

 Score = 36.7 bits (84), Expect = 3.9,   Method: Composition-based stats.
 Identities = 7/34 (20%), Positives = 18/34 (52%), Gaps = 2/34 (5%)

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
            +++VL+PRE+++   R  ++    L  ++    
Sbjct: 103 DALNVLSPREKQVIVLRFFEDMK--LAEIAEILN 134


>gi|332883990|gb|EGK04270.1| hypothetical protein HMPREF9456_01298 [Dysgonomonas mossii DSM
           22836]
          Length = 196

 Score = 36.7 bits (84), Expect = 4.0,   Method: Composition-based stats.
 Identities = 12/86 (13%), Positives = 37/86 (43%), Gaps = 9/86 (10%)

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           +    L+ +    +  + ++  +    + + + +S L   +R + E R  Q+  ++ + +
Sbjct: 104 EAPVDLLNNPTLCDGTIEDELIKVQITSDIRKLISFLPENQREVLEMRYYQD--LSFKEI 161

Query: 259 SSEFEVSRERVRQIEARAFKKVQESI 284
           + +  VS      I   A  +++ +I
Sbjct: 162 ADQTGVS------I-NTALGRMRYAI 180


>gi|325289574|ref|YP_004265755.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Syntrophobotulus
           glycolicus DSM 8271]
 gi|324964975|gb|ADY55754.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Syntrophobotulus
           glycolicus DSM 8271]
          Length = 177

 Score = 36.7 bits (84), Expect = 4.0,   Method: Composition-based stats.
 Identities = 16/89 (17%), Positives = 42/89 (47%), Gaps = 3/89 (3%)

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
           ++ L YD        +  +  ++  +++  +++ L+     +   +  Q    T   ++ 
Sbjct: 90  ENTLSYDELEIYIADMSSQSNEDTNDVIN-AIAKLSVNYSTVLRLKFSQGYTDT--EIAQ 146

Query: 261 EFEVSRERVRQIEARAFKKVQESIQKQVE 289
             +++ E VRQ  +RA KK+ + ++K+ E
Sbjct: 147 ILDITEENVRQRISRAKKKLSQLLEKEGE 175


>gi|293556495|ref|ZP_06675068.1| putative transcriptional antiterminator [Enterococcus faecium
           E1039]
 gi|291601334|gb|EFF31613.1| putative transcriptional antiterminator [Enterococcus faecium
           E1039]
          Length = 640

 Score = 36.7 bits (84), Expect = 4.0,   Method: Composition-based stats.
 Identities = 14/57 (24%), Positives = 29/57 (50%), Gaps = 7/57 (12%)

Query: 235 LNPRERRIFEARRLQENPVT-LENLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
           L+ R+ RI     L EN  T  + L+ + +VS + +     +A   ++  ++K++ L
Sbjct: 5   LDDRQMRILN--FLLENDHTTYQELAEQLQVSTKTIS----KAIANLKTVVEKEINL 55


>gi|150009070|ref|YP_001303813.1| RNA polymerase ECF-type sigma factor [Parabacteroides distasonis
           ATCC 8503]
 gi|298377175|ref|ZP_06987129.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 3_1_19]
 gi|149937494|gb|ABR44191.1| RNA polymerase ECF-type sigma factor [Parabacteroides distasonis
           ATCC 8503]
 gi|298266159|gb|EFI07818.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 3_1_19]
          Length = 190

 Score = 36.7 bits (84), Expect = 4.0,   Method: Composition-based stats.
 Identities = 20/84 (23%), Positives = 42/84 (50%), Gaps = 2/84 (2%)

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           DG+E  +  K   +   + L  +   L PR+R +FE    +E  +T+  ++++  +S + 
Sbjct: 104 DGEETAIERKLSFEEFNHRLEIAKQKLTPRQRELFEL--NKEQGITITEIAAKAFISEQS 161

Query: 269 VRQIEARAFKKVQESIQKQVELSS 292
           VR   ++A   +++ + K   L S
Sbjct: 162 VRNQLSQALHVLRKELGKYALLFS 185


>gi|295695629|ref|YP_003588867.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
 gi|295411231|gb|ADG05723.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Bacillus
           tusciae DSM 2912]
          Length = 246

 Score = 36.7 bits (84), Expect = 4.0,   Method: Composition-based stats.
 Identities = 26/147 (17%), Positives = 48/147 (32%), Gaps = 23/147 (15%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMG----YRGYGLPISEVVSEGNIGLMQAVKK 92
           LA+   + GD     +L+  ++  V K A      Y   G    +  S       +A+ +
Sbjct: 20  LAR--AKAGDDGVRDQLLRKYIPFVAKSASRASSRYISRGED--DEFSIALAAFNEAIDR 75

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDN 152
           +D  RG     ++   I+  + +Y                +     +R +        D 
Sbjct: 76  YDGNRGASFLGFADTVIRRRLIDYF---------------RSRENRVRDIPMAELETEDE 120

Query: 153 NLKPEQVVAIAKKLNVSESEVISMNCR 179
              P   + I K L V E+  +    R
Sbjct: 121 EDHPYNRIEIRKSLEVYEATQVEAARR 147


>gi|295133452|ref|YP_003584128.1| RNA polymerase ECF-type sigma factor [Zunongwangia profunda SM-A87]
 gi|294981467|gb|ADF51932.1| RNA polymerase ECF-type sigma factor [Zunongwangia profunda SM-A87]
          Length = 163

 Score = 36.7 bits (84), Expect = 4.0,   Method: Composition-based stats.
 Identities = 28/138 (20%), Positives = 53/138 (38%), Gaps = 19/138 (13%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAA 112
           ++  +  L+ K+   Y  Y     +++ E  I L+++ K+FD   G ++ T+        
Sbjct: 11  IIEKNKNLIFKVVNAYCYYPEEQEDLIQEIIIHLLKSYKRFDY--GVQITTWIYKIAFNV 68

Query: 113 MQEYILRSW-----------------SLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLK 155
           +  Y  +                      K+    N K+L   + +LK   +A+    L 
Sbjct: 69  VISYNRKIKTREKYFVPLKEKFVHIQDENKVEDDENLKKLNHFIAQLKPLHKALMIMYLD 128

Query: 156 PEQVVAIAKKLNVSESEV 173
            +    IA  L +SES V
Sbjct: 129 QKSHKEIAMVLGISESNV 146


>gi|226942549|ref|YP_002797622.1| FecI family RNA polymerase sigma factor [Azotobacter vinelandii DJ]
 gi|226717476|gb|ACO76647.1| RNA polymerase sigma factor, FecI family [Azotobacter vinelandii
           DJ]
          Length = 188

 Score = 36.7 bits (84), Expect = 4.0,   Method: Composition-based stats.
 Identities = 18/114 (15%), Positives = 45/114 (39%), Gaps = 4/114 (3%)

Query: 173 VISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM 232
             +   R+A +   + L + +     Q +D  +     Q      + +  +    L   +
Sbjct: 78  PRAYLFRIATNLGTDHLRHQNMGVEIQAEDEEIAQVPAQAVDPAREVQSHDDLERLLEII 137

Query: 233 SVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER-VRQIEARAFKKVQESIQ 285
             L PR R IF   R++        ++    +S+   V Q+  +A  +++++++
Sbjct: 138 DNLPPRCREIFILCRVEGLSH--AQIAERLNISKSTVVSQM-VKALARLEQAME 188


>gi|134103604|ref|YP_001109265.1| ECF subfamily RNA polymerase sigma-24 factor [Saccharopolyspora
           erythraea NRRL 2338]
 gi|291004860|ref|ZP_06562833.1| ECF subfamily RNA polymerase sigma-24 factor [Saccharopolyspora
           erythraea NRRL 2338]
 gi|133916227|emb|CAM06340.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Saccharopolyspora
           erythraea NRRL 2338]
          Length = 193

 Score = 36.7 bits (84), Expect = 4.0,   Method: Composition-based stats.
 Identities = 12/79 (15%), Positives = 30/79 (37%), Gaps = 2/79 (2%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           H    +              +  +++ L PR+R +   R   +  ++   ++    VS+ 
Sbjct: 116 HQADARSAESLAMLTAEHQAVVAALAELPPRQREVLVLRYYGD--LSEAEIAEATGVSKG 173

Query: 268 RVRQIEARAFKKVQESIQK 286
            V+   +RA   +Q  ++ 
Sbjct: 174 TVKSTASRALDALQRIMRS 192


>gi|325287457|ref|YP_004263247.1| ECF subfamily RNA polymerase sigma-24 subunit [Cellulophaga lytica
           DSM 7489]
 gi|324322911|gb|ADY30376.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Cellulophaga
           lytica DSM 7489]
          Length = 179

 Score = 36.7 bits (84), Expect = 4.0,   Method: Composition-based stats.
 Identities = 24/97 (24%), Positives = 44/97 (45%), Gaps = 10/97 (10%)

Query: 170 ESEVISMNCRLAGDESLNAL---INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRN 226
           ES++ S   R+A +ESL+ L          S + QD L+   + Q  V  E +E + +  
Sbjct: 66  ESKLFSWIYRIATNESLSFLKTKSKMLGVTSHELQDLLL--ENLQSDVYFEGDEIQLK-- 121

Query: 227 MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
            L +++S L  +++ +F  +   E     E +S    
Sbjct: 122 -LQKAISTLPEKQKLVFNMKYFDELKY--EEISEILG 155


>gi|291086744|ref|ZP_06344315.2| sigma-70, region 4 superfamily [Clostridium sp. M62/1]
 gi|291076807|gb|EFE14171.1| sigma-70, region 4 superfamily [Clostridium sp. M62/1]
          Length = 215

 Score = 36.7 bits (84), Expect = 4.0,   Method: Composition-based stats.
 Identities = 18/94 (19%), Positives = 41/94 (43%), Gaps = 10/94 (10%)

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           S  + D +  +       L E  ER      L +++S L  ++R+   A  +    +TL 
Sbjct: 126 SLDYGDDIEREAVLFTPTLQEIVERHLEEERLYQAISSLPEKQRQRVYAHYILG--ITLM 183

Query: 257 NLSSEFEVS----RERVRQIEARAFKKVQESIQK 286
           +++    VS     E +R    R  +++++ +++
Sbjct: 184 DIAKMEGVSLHAVHESIR----RGLRRLEKILEE 213


>gi|269960411|ref|ZP_06174784.1| RNA polymerase sigma-E factor [Vibrio harveyi 1DA3]
 gi|269834838|gb|EEZ88924.1| RNA polymerase sigma-E factor [Vibrio harveyi 1DA3]
          Length = 192

 Score = 36.7 bits (84), Expect = 4.0,   Method: Composition-based stats.
 Identities = 19/88 (21%), Positives = 33/88 (37%), Gaps = 3/88 (3%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
            VL +R + +GD  A + LVT +   V  +   Y      + +V  E  I   +A+  F 
Sbjct: 8   QVLIERVQ-NGDKQAFNLLVTKYQNKVCNLISRYVSNPGDVPDVAQEAFIKAYRAIPSFR 66

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWS 122
            E      T+         + +I+    
Sbjct: 67  GE--SAFYTWLYRIAVNTAKNHIVAQGR 92


>gi|45656542|ref|YP_000628.1| RNA polymerase ECF-type sigma factor [Leptospira interrogans
           serovar Copenhageni str. Fiocruz L1-130]
 gi|45599777|gb|AAS69265.1| RNA polymerase ECF-type sigma factor [Leptospira interrogans
           serovar Copenhageni str. Fiocruz L1-130]
          Length = 174

 Score = 36.7 bits (84), Expect = 4.0,   Method: Composition-based stats.
 Identities = 19/85 (22%), Positives = 34/85 (40%), Gaps = 2/85 (2%)

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           D +  +    E   I+  E K     L   +S L   E+ I   + +  N  TLE  S  
Sbjct: 87  DAVFIESLQVEDDFIQNIESKIVEEELREIISSLPEPEKSIILLKEI--NNYTLEKTSQA 144

Query: 262 FEVSRERVRQIEARAFKKVQESIQK 286
             +S   V +   +A   ++E +++
Sbjct: 145 LNISTRTVSRKLLKALDLLREELER 169


>gi|51467745|ref|NP_001003822.1| G2/M phase-specific E3 ubiquitin-protein ligase [Danio rerio]
 gi|26788033|emb|CAD58745.1| novel protein similar to KIAA1333 [Danio rerio]
 gi|27817272|emb|CAD61085.1| novel protein similar to KIAA1333 [Danio rerio]
          Length = 706

 Score = 36.7 bits (84), Expect = 4.0,   Method: Composition-based stats.
 Identities = 12/48 (25%), Positives = 26/48 (54%), Gaps = 5/48 (10%)

Query: 254 TLENLSSE-FEVSRERVRQI-EARAFKKVQESIQKQVELSSSPPLLQK 299
           TLE+L    F     ++RQI EA++ K+++ +++   +   +    +K
Sbjct: 481 TLEDLGDTAFG---HKIRQIAEAKSMKELRHAMKSASQYLEAAGCWRK 525


>gi|75758985|ref|ZP_00739094.1| RNA polymerase ECF-type sigma factor [Bacillus thuringiensis
           serovar israelensis ATCC 35646]
 gi|228900385|ref|ZP_04064614.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus
           thuringiensis IBL 4222]
 gi|74493520|gb|EAO56627.1| RNA polymerase ECF-type sigma factor [Bacillus thuringiensis
           serovar israelensis ATCC 35646]
 gi|228859272|gb|EEN03703.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus
           thuringiensis IBL 4222]
          Length = 188

 Score = 36.7 bits (84), Expect = 4.0,   Method: Composition-based stats.
 Identities = 17/83 (20%), Positives = 35/83 (42%), Gaps = 10/83 (12%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE 267
           H   E+   ++      R  L + ++ L P ++++F  + L       E +  +  ++R 
Sbjct: 104 HISTEKSAEDELIVMEDREELLKLINQLEPLDQKVFIMKYLLGMKT--EEIGEKLRLTRA 161

Query: 268 ----RVRQIEARAFKKVQESIQK 286
               RV Q      KK+Q++  K
Sbjct: 162 AIDNRVYQ----GKKKLQQNATK 180


>gi|260588254|ref|ZP_05854167.1| sigma-70, region 4 subfamily [Blautia hansenii DSM 20583]
 gi|260541392|gb|EEX21961.1| sigma-70, region 4 subfamily [Blautia hansenii DSM 20583]
          Length = 121

 Score = 36.7 bits (84), Expect = 4.1,   Method: Composition-based stats.
 Identities = 10/59 (16%), Positives = 26/59 (44%), Gaps = 4/59 (6%)

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV-RQIEARAFKKVQESIQ 285
           L  ++  L  + +        Q   +T + +  +   +R  + R I+  A K+++E ++
Sbjct: 55  LAAALVELPEQTQEEIFLYYFQH--LTQKEIGEQSGWTRSTIGRHIQL-ALKRLKEEME 110


>gi|225868840|ref|YP_002744788.1| hypothetical protein SZO_12710 [Streptococcus equi subsp.
           zooepidemicus]
 gi|225702116|emb|CAW99779.1| conserved hypothetical protein [Streptococcus equi subsp.
           zooepidemicus]
          Length = 137

 Score = 36.7 bits (84), Expect = 4.1,   Method: Composition-based stats.
 Identities = 19/104 (18%), Positives = 43/104 (41%), Gaps = 15/104 (14%)

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
           + L  SS  +   + D ++ D +     ++E    +     L  ++S LN  ER I E  
Sbjct: 42  HLLFFSSLDHDGHYVDNIIIDENVDVAKIVE---TQMMIESLRYAISKLNDEERDIIERL 98

Query: 247 RLQENPVTLENLSSEFEVS-----RERVRQIEARAFKKVQESIQ 285
              +   TL +++    ++     + R      +  +K+++ I+
Sbjct: 99  YFNDE--TLRSVARLKSITHPALIKRR-----NKILEKLKKFIE 135


>gi|51893666|ref|YP_076357.1| RNA polymerase ECF-type sigma factor [Symbiobacterium thermophilum
           IAM 14863]
 gi|51857355|dbj|BAD41513.1| RNA polymerase ECF-type sigma factor [Symbiobacterium thermophilum
           IAM 14863]
          Length = 183

 Score = 36.7 bits (84), Expect = 4.1,   Method: Composition-based stats.
 Identities = 10/74 (13%), Positives = 32/74 (43%), Gaps = 2/74 (2%)

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
               E     + R  ++R++  L+P ++ +   R   +    L+++++    +   V+ +
Sbjct: 107 PEPEEAALALDDRQAVSRALQALSPDQQDVVLMRFAGDMK--LKDIAAAMGKTEGAVKAL 164

Query: 273 EARAFKKVQESIQK 286
             RA   ++  + +
Sbjct: 165 LFRALNTLRRKLSE 178


>gi|256425420|ref|YP_003126073.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Chitinophaga
           pinensis DSM 2588]
 gi|256040328|gb|ACU63872.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Chitinophaga
           pinensis DSM 2588]
          Length = 206

 Score = 36.7 bits (84), Expect = 4.1,   Method: Composition-based stats.
 Identities = 9/47 (19%), Positives = 22/47 (46%), Gaps = 2/47 (4%)

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           ++E +  RN +   ++ L  R++ I   R      ++ E +S   ++
Sbjct: 115 RQEEQELRNQVIALVNTLPARQQEIIFLRFY--EGMSYEEISVIMDI 159


>gi|152986078|ref|YP_001345623.1| ECF subfamily RNA polymerase sigma-70 factor [Pseudomonas
           aeruginosa PA7]
 gi|150961236|gb|ABR83261.1| probable sigma-70 factor, ECF subfamily [Pseudomonas aeruginosa
           PA7]
          Length = 195

 Score = 36.7 bits (84), Expect = 4.1,   Method: Composition-based stats.
 Identities = 21/112 (18%), Positives = 43/112 (38%), Gaps = 6/112 (5%)

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
              E+ S   R A + +++  +        Q  DWL     G+     +  E  ++   +
Sbjct: 70  PVEELGSYLLRSARNLAID-HLRGEGSRQRQLDDWLPEQRQGEPVGPEQALEAGDQWRRV 128

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             ++  L  R RRIF   R+  +  T   ++   ++S+  V   E    + +
Sbjct: 129 EAALRDLPERTRRIFLLNRI--HGRTYAEIARAMQLSQSAV---EKHMMRAL 175


>gi|119714599|ref|YP_921564.1| sigma-70 region 4 domain-containing protein [Nocardioides sp.
           JS614]
 gi|119535260|gb|ABL79877.1| sigma-70 region 4 domain protein [Nocardioides sp. JS614]
          Length = 268

 Score = 36.7 bits (84), Expect = 4.1,   Method: Composition-based stats.
 Identities = 10/70 (14%), Positives = 29/70 (41%), Gaps = 2/70 (2%)

Query: 215 LIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA 274
               + R  RR  +  ++  L  R R +     +++ P+    ++++   S  R  Q+  
Sbjct: 156 PAHPDRRDERREYVEAALDELPERLRLVVRGYFVEQRPM--AAVAAQVGASEARAVQLLV 213

Query: 275 RAFKKVQESI 284
                +++++
Sbjct: 214 EGLGLLRDAL 223


>gi|302552575|ref|ZP_07304917.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces
           viridochromogenes DSM 40736]
 gi|302470193|gb|EFL33286.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces
           viridochromogenes DSM 40736]
          Length = 186

 Score = 36.7 bits (84), Expect = 4.1,   Method: Composition-based stats.
 Identities = 17/86 (19%), Positives = 38/86 (44%), Gaps = 9/86 (10%)

Query: 202 DWLVYDHDGQEQVLI---EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           D    D   + + ++   +  E++  R+ + R++  L  R+R +   R  ++    L  +
Sbjct: 96  DEFACDELPEPEPVVGADDPAEQQALRDAMWRAIMRLPARQRAMVVLRYYED----LSEV 151

Query: 259 --SSEFEVSRERVRQIEARAFKKVQE 282
             +    VS   V+   +RA  K++E
Sbjct: 152 QTAEVLGVSVGTVKSAVSRALGKLRE 177


>gi|283954057|ref|ZP_06371582.1| hypothetical protein C414_000080045 [Campylobacter jejuni subsp.
           jejuni 414]
 gi|283794336|gb|EFC33080.1| hypothetical protein C414_000080045 [Campylobacter jejuni subsp.
           jejuni 414]
          Length = 63

 Score = 36.7 bits (84), Expect = 4.1,   Method: Composition-based stats.
 Identities = 9/29 (31%), Positives = 18/29 (62%)

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQ 281
           ++ E ++ E ++S  RV QI   A +K++
Sbjct: 1   MSFEEIAKELDLSTARVHQIYTEAIRKLK 29


>gi|134101308|ref|YP_001106969.1| sigma factor, sigma 70 type, group 4 (ECF) [Saccharopolyspora
           erythraea NRRL 2338]
 gi|291008154|ref|ZP_06566127.1| sigma factor, sigma 70 type, group 4 (ECF) [Saccharopolyspora
           erythraea NRRL 2338]
 gi|133913931|emb|CAM04044.1| sigma factor, sigma 70 type, group 4 (ECF) [Saccharopolyspora
           erythraea NRRL 2338]
          Length = 312

 Score = 36.7 bits (84), Expect = 4.1,   Method: Composition-based stats.
 Identities = 21/107 (19%), Positives = 38/107 (35%), Gaps = 2/107 (1%)

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             +  +   R+   ++L  L     +  S    WL         V  + E   +    + 
Sbjct: 68  VRDRRAYLVRITTRQALARLRALGRRKESYVGPWLPEPLLTAPDVAEDVELADSVSMAML 127

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
             +  LNP ER +F  R + +     + ++     +   VRQI  RA
Sbjct: 128 LVLETLNPTERAVFVLREVFDVGY--DEIAEAVGKTPAAVRQIAHRA 172


>gi|47503411|gb|AAT32087.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus anthracis
           str. 'Ames Ancestor']
          Length = 180

 Score = 36.7 bits (84), Expect = 4.1,   Method: Composition-based stats.
 Identities = 30/148 (20%), Positives = 63/148 (42%), Gaps = 10/148 (6%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGY-GLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
           E GD  A   +     + + +  +   G     + ++V+E  I + ++V  +D  R FR 
Sbjct: 2   ESGDQEAFQIIYEYTCKDIYRTVVFLVGSQNQDVDDIVNEVYIKMWKSVTNYDMNRSFRF 61

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
             + +  +   +Q++  +SW   +I     +K+  +   R     +AI     + E V  
Sbjct: 62  WLHGL--VVKQVQDWRRKSWRRFRI----FEKKKMYEQNRSYIMDEAILHKETRSELV-E 114

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNAL 189
           + + L+    EV+ M  R   + SL+ +
Sbjct: 115 VVQNLSYKHREVVIM--RYFHEYSLDEI 140



 Score = 35.9 bits (82), Expect = 6.8,   Method: Composition-based stats.
 Identities = 13/79 (16%), Positives = 34/79 (43%), Gaps = 14/79 (17%)

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV------SRE 267
           ++ E    K  R+ L   +  L+ + R +   R   E   +L+ +++  ++      SR 
Sbjct: 98  IMDEAILHKETRSELVEVVQNLSYKHREVVIMRYFHE--YSLDEIAALLQIPIGTVKSR- 154

Query: 268 RVRQIEARAFKKVQESIQK 286
               +   A K+++  +++
Sbjct: 155 ----LHT-ALKRLRMEMEQ 168


>gi|17547637|ref|NP_521039.1| extracytoplasmic function sigma factor (IRON-regulated)
           transcription regulator protein [Ralstonia solanacearum
           GMI1000]
 gi|17429941|emb|CAD16625.1| putative extracytoplasmic function sigma factor (iron-regulated)
           transcription regulator protein [Ralstonia solanacearum
           GMI1000]
          Length = 174

 Score = 36.7 bits (84), Expect = 4.1,   Method: Composition-based stats.
 Identities = 19/105 (18%), Positives = 41/105 (39%), Gaps = 6/105 (5%)

Query: 166 LNVSESEVISMNCRLAGDESLNALINSSDKNSS--QWQDWLVYDHDGQEQVLIEKEERKN 223
           L     +V++         +LN  I+     S+   W +      D  +++         
Sbjct: 48  LAEPPRQVVAAPAAYVRRAALNLAIDRHRVESTRGAWVESAAELPDCADEMPGHDRHVDA 107

Query: 224 RRNM--LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
            R +  L+ +++ L PR R +F   ++ + P T   ++    +SR
Sbjct: 108 GRELDRLSAAIAQLPPRCREVFVLHKIHDMPQT--EVAVRLGISR 150


>gi|326387865|ref|ZP_08209471.1| ECF subfamily RNA polymerase sigma-24 factor [Novosphingobium
           nitrogenifigens DSM 19370]
 gi|326207911|gb|EGD58722.1| ECF subfamily RNA polymerase sigma-24 factor [Novosphingobium
           nitrogenifigens DSM 19370]
          Length = 202

 Score = 36.7 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 14/78 (17%), Positives = 30/78 (38%), Gaps = 2/78 (2%)

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           D       +    +    M+ R +  L  R RRIF  +R+    ++   ++    VS   
Sbjct: 96  DPDATGPEQAVAARMHLRMVERLIEDLPERCRRIFTMKRV--EGLSQREIARTLGVSESV 153

Query: 269 VRQIEARAFKKVQESIQK 286
           V     +A + +  +++ 
Sbjct: 154 VENDVQKALRLLMAAMRS 171


>gi|323529537|ref|YP_004231689.1| ECF subfamily RNA polymerase sigma-24 subunit [Burkholderia sp.
           CCGE1001]
 gi|323386539|gb|ADX58629.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Burkholderia sp.
           CCGE1001]
          Length = 236

 Score = 36.7 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 19/98 (19%), Positives = 44/98 (44%), Gaps = 2/98 (2%)

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
           +S+     +   H    +       R   R +L R +  L    R +F  R ++E  +++
Sbjct: 111 SSNTADIDIEAMHSSDSEPPDSAVARAEMRALLERKLDELPESFRTVFILRTVEE--LSV 168

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSS 293
           E  +   +++   VR    RA   ++E++ + ++++SS
Sbjct: 169 EETAQCLDIAEATVRSRHFRARSLLREALARDIDIASS 206


>gi|227486252|ref|ZP_03916568.1| ECF subfamily RNA polymerase sigma-24 factor [Anaerococcus
           lactolyticus ATCC 51172]
 gi|227235663|gb|EEI85678.1| ECF subfamily RNA polymerase sigma-24 factor [Anaerococcus
           lactolyticus ATCC 51172]
          Length = 174

 Score = 36.7 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 18/83 (21%), Positives = 36/83 (43%), Gaps = 10/83 (12%)

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE- 267
           D  E       +     +     + VL+ ++R IF    +     + ++L+  +++S+  
Sbjct: 95  DLDEVSPYLSTDDDISIDETEEILKVLDEKDREIFRKLFI--EGYSYDDLAKVYDISKAG 152

Query: 268 ---RVRQIEARAFKKVQESIQKQ 287
              RV    AR  KK++E IQ +
Sbjct: 153 LYNRV----ARGKKKIKEEIQNE 171


>gi|218258616|ref|ZP_03474951.1| hypothetical protein PRABACTJOHN_00606 [Parabacteroides johnsonii
           DSM 18315]
 gi|218225330|gb|EEC97980.1| hypothetical protein PRABACTJOHN_00606 [Parabacteroides johnsonii
           DSM 18315]
          Length = 172

 Score = 36.7 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 12/91 (13%), Positives = 40/91 (43%), Gaps = 6/91 (6%)

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
             +D         +    ++ E +++   +   ++ L   +R++   R +++   +++ +
Sbjct: 79  HDEDVTEAVTLSTDSSPDKELEMQDKVEQVRHLINRLPENQRQVLRLRGIED--CSIDEI 136

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQVE 289
                +S   +R + +RA    ++ I++Q E
Sbjct: 137 EQITGLSAVNIRVLLSRA----RKIIREQFE 163


>gi|162451006|ref|YP_001613373.1| ubiquinone/menaquinone biosynthesis methyltransferase ubiE
           [Sorangium cellulosum 'So ce 56']
 gi|161161588|emb|CAN92893.1| Ubiquinone/menaquinone biosynthesis methyltransferase ubiE
           [Sorangium cellulosum 'So ce 56']
          Length = 499

 Score = 36.7 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 26/130 (20%), Positives = 43/130 (33%), Gaps = 14/130 (10%)

Query: 147 QAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVY 206
           +   D    PE        L+ +  E +    R A   S+  L     K   +  D  V+
Sbjct: 249 EEAEDEKAAPEDRGEARMSLDEARREAVVAALRRAEARSVLDLGCGEGKLLKRLVDERVF 308

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA----------RRLQENPVTLE 256
           +      V +   E    RN L   +  L  ++RR  +           R    + VTL 
Sbjct: 309 ERVAGADVSVRSLEIA--RNRLR--LDDLPDKQRRRIQLFQASVTYRDARFSGYDAVTLV 364

Query: 257 NLSSEFEVSR 266
            +    ++SR
Sbjct: 365 EVIEHVDLSR 374


>gi|60680722|ref|YP_210866.1| putative ECF-type RNA polymerase sigma factor [Bacteroides fragilis
           NCTC 9343]
 gi|60492156|emb|CAH06919.1| putative ECF-type RNA polymerase sigma factor [Bacteroides fragilis
           NCTC 9343]
          Length = 181

 Score = 36.7 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 18/76 (23%), Positives = 34/76 (44%), Gaps = 4/76 (5%)

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR-QIEAR 275
           ++    +   +L  +++ L  R R IF   RLQ      + ++ +  VS   V  QI   
Sbjct: 105 DRLSDADIEEILNNAINRLPERCREIFIMSRLQNLRY--KEIAEKLNVSPNTVENQI-VI 161

Query: 276 AFKKVQESIQKQVELS 291
           A +K++E ++    L 
Sbjct: 162 ALRKLKEDLKDYFPLF 177


>gi|125974313|ref|YP_001038223.1| ECF subfamily RNA polymerase sigma-24 factor [Clostridium
           thermocellum ATCC 27405]
 gi|256003467|ref|ZP_05428457.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           thermocellum DSM 2360]
 gi|281418369|ref|ZP_06249389.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           thermocellum JW20]
 gi|125714538|gb|ABN53030.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           thermocellum ATCC 27405]
 gi|255992491|gb|EEU02583.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           thermocellum DSM 2360]
 gi|281409771|gb|EFB40029.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           thermocellum JW20]
 gi|316941461|gb|ADU75495.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           thermocellum DSM 1313]
          Length = 179

 Score = 36.7 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 15/77 (19%), Positives = 34/77 (44%), Gaps = 2/77 (2%)

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
             +E    +  E   +R ++ +++  L+  +R + E R L+   VT    +   +     
Sbjct: 100 SPEETAAEDTAEISAQRELIRKALGSLSEEQRMVVELRILKGYSVT--ETAKIIDKKETT 157

Query: 269 VRQIEARAFKKVQESIQ 285
           VR ++ RA K +   ++
Sbjct: 158 VRVLQYRALKNLASILK 174


>gi|229829851|ref|ZP_04455920.1| hypothetical protein GCWU000342_01957 [Shuttleworthia satelles DSM
           14600]
 gi|229791149|gb|EEP27263.1| hypothetical protein GCWU000342_01957 [Shuttleworthia satelles DSM
           14600]
          Length = 136

 Score = 36.7 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 18/101 (17%), Positives = 42/101 (41%), Gaps = 16/101 (15%)

Query: 191 NSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE 250
            SS  +   + D +V +     +++    E +     L  ++S LN  ER I E     +
Sbjct: 46  FSSLDHDGHFADNIVDESIDVAKIV----ETQIMIEALRNAISRLNDEERDIIERLYFND 101

Query: 251 NPVTLENLSSEFEVS-----RERVRQIEARAFKKVQESIQK 286
              TL +++    ++     + R      +  +K+++ I++
Sbjct: 102 E--TLRSVAKLKSITHPALIKRR-----NKILEKLKKFIEE 135


>gi|284030774|ref|YP_003380705.1| LuxR family transcriptional regulator [Kribbella flavida DSM 17836]
 gi|283810067|gb|ADB31906.1| transcriptional regulator, LuxR family [Kribbella flavida DSM
           17836]
          Length = 164

 Score = 36.7 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 19/133 (14%), Positives = 46/133 (34%), Gaps = 8/133 (6%)

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRLA--GDESLNALINSSDKNSSQWQDWLVYDH 208
             +L  + V  +  K +     V S +   A      +N  ++   K    W  ++    
Sbjct: 24  GGDLAEDVVQDVLIKAHRHWDRVRSADQPEAYLRRMVVNEFLSWRRK----WSRFVPRPE 79

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
               + + +   ++  R+ L   ++ L  R+R +   R         + ++     +   
Sbjct: 80  ILPAEPVADHARQQADRDQLIGELAKLPRRQRAVLVLRYYGGQSD--QEIADTLGCATST 137

Query: 269 VRQIEARAFKKVQ 281
           VR   +RA   ++
Sbjct: 138 VRAHASRALAALR 150


>gi|225619913|ref|YP_002721170.1| hypothetical protein BHWA1_00983 [Brachyspira hyodysenteriae WA1]
 gi|225214732|gb|ACN83466.1| hypothetical protein BHWA1_00983 [Brachyspira hyodysenteriae WA1]
          Length = 125

 Score = 36.7 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 17/103 (16%), Positives = 39/103 (37%), Gaps = 9/103 (8%)

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           SL     +SD+  S+  + ++ + D    +            +    +++L P+++ I +
Sbjct: 25  SLGTRKINSDRTDSR--ESILTNDDLDNILYANALTESEYSRVSNLIIAILTPKQKMIMK 82

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
                    + E L+    V++  V Q        ++  I KQ
Sbjct: 83  LF---SEGKSQEELAKMLNVTQSAVSQY----LSAIKHEISKQ 118


>gi|126667167|ref|ZP_01738141.1| RNA polymerase sigma factor AlgU [Marinobacter sp. ELB17]
 gi|126628323|gb|EAZ98946.1| RNA polymerase sigma factor AlgU [Marinobacter sp. ELB17]
          Length = 228

 Score = 36.7 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 21/139 (15%), Positives = 51/139 (36%), Gaps = 4/139 (2%)

Query: 37  LAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
           L ++ R +GD +A   LV  +   V  I   Y      + ++  E  +   +A+ +F  +
Sbjct: 43  LVRKVR-NGDRAAFDLLVLKYQSRVASIISRYVFDSHEVMDLTQETFVKAFRAIDRFRGD 101

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKP 156
                 T+         + Y+       +    +     + + +RL+  + +      + 
Sbjct: 102 --SAFYTWLYRIAVNTAKNYLEARSRRPQSSADSADAENYVDGQRLRD-IASPEKLLQRD 158

Query: 157 EQVVAIAKKLNVSESEVIS 175
           +   A+ K ++    E+ S
Sbjct: 159 QLQQALNKAIDALPEELRS 177


>gi|85714974|ref|ZP_01045959.1| Sigma 24, ECF subfamily protein [Nitrobacter sp. Nb-311A]
 gi|85698171|gb|EAQ36043.1| Sigma 24, ECF subfamily protein [Nitrobacter sp. Nb-311A]
          Length = 174

 Score = 36.7 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 13/47 (27%), Positives = 23/47 (48%), Gaps = 2/47 (4%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           +       R+++ L  R R+ FE  RL     T+++++ E  VS  R
Sbjct: 111 RQCLEQTRRALAELPERTRKAFEMHRLGG--RTIQDVADELNVSTSR 155


>gi|284034351|ref|YP_003384282.1| ECF subfamily RNA polymerase sigma-24 subunit [Kribbella flavida
           DSM 17836]
 gi|283813644|gb|ADB35483.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Kribbella flavida
           DSM 17836]
          Length = 332

 Score = 36.7 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 18/96 (18%), Positives = 37/96 (38%), Gaps = 10/96 (10%)

Query: 209 DGQEQVLIEKEERKNRRNMLT----RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           DG   V +  E R  +   ++     ++ VL PR+  +   R +       + ++   + 
Sbjct: 121 DGAVDVPLGPEARYQQTEAISLAFVTALQVLPPRQLAVLVLRDVLGFRA--DEVAELLDC 178

Query: 265 SRERVRQIEARAFKKVQESIQKQVELSSSPPLLQKP 300
           S E V      A K+ +  +++ V  +   P    P
Sbjct: 179 SVESV----KSALKRARAGLRRSVAGAEPAPARDSP 210


>gi|229191520|ref|ZP_04318502.1| RNA polymerase sigma-I factor [Bacillus cereus ATCC 10876]
 gi|228591905|gb|EEK49742.1| RNA polymerase sigma-I factor [Bacillus cereus ATCC 10876]
          Length = 235

 Score = 36.7 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 15/124 (12%), Positives = 43/124 (34%), Gaps = 1/124 (0%)

Query: 44  HGDLSAAHRLVTSHLRLVV-KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
             +       +  +   +   I+   R Y     +  S G     +A++K+   +G    
Sbjct: 17  QNNEEDKEAFIVQYQPFIRKSISSVCRRYITEQDDEYSIGLFAFNEAIEKYSYTKGKSFL 76

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
            ++   IK  + +YI +      +    +++     ++          +N+ + E+++  
Sbjct: 77  AFADLLIKRDVIDYIRKESKHNFVFLKEDEQEEMLEMQVSLTEYMKEMENSNRKEEILHF 136

Query: 163 AKKL 166
              L
Sbjct: 137 QSVL 140


>gi|121488733|emb|CAJ18250.1| sigma 70-type sigma factor [Chlorobium chlorovibrioides]
          Length = 93

 Score = 36.7 bits (84), Expect = 4.2,   Method: Composition-based stats.
 Identities = 20/99 (20%), Positives = 34/99 (34%), Gaps = 6/99 (6%)

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQ 201
           +      +     +      +A  L++   +V           S++A     D N  +  
Sbjct: 1   ISKAYSQLEQEYERDPNTKELANLLDMDSQDVADTLKIAGRHVSVDAPFAQGDDN--RLL 58

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRER 240
           D L  D    +  L     R +    + RS+SVL PRE 
Sbjct: 59  DVLQNDGHMPDHTL----NRDSLTLEVERSLSVLAPREA 93


>gi|326802931|ref|YP_004320749.1| RNA polymerase sigma factor, sigma-70 family [Aerococcus urinae
           ACS-120-V-Col10a]
 gi|326651193|gb|AEA01376.1| RNA polymerase sigma factor, sigma-70 family [Aerococcus urinae
           ACS-120-V-Col10a]
          Length = 206

 Score = 36.7 bits (84), Expect = 4.3,   Method: Composition-based stats.
 Identities = 17/105 (16%), Positives = 36/105 (34%), Gaps = 5/105 (4%)

Query: 28  MLEKQEE--YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIG 85
           ML  +E     L     E  D  A   L   H   V      Y G+   + +      I 
Sbjct: 4   MLSYEEMENQDLIHLLVEGRDDQAFEVLYERHRSTVYFFLRKYYGHIEDVDDYFQLAAIS 63

Query: 86  LMQAVKKFDP-ERGFRLATYS--MWWIKAAMQEYILRSWSLVKIG 127
           L +  + +     G+  + ++     I++ + + + +  S  ++ 
Sbjct: 64  LYEVCQDYQAKTLGYSYSLFTALGRRIESRIIDQMRKQGSKKRLP 108


>gi|254392008|ref|ZP_05007199.1| RNA polymerase sigma factor SigD [Streptomyces clavuligerus ATCC
           27064]
 gi|326442920|ref|ZP_08217654.1| RNA polymerase sigma factor SigD [Streptomyces clavuligerus ATCC
           27064]
 gi|197705686|gb|EDY51498.1| RNA polymerase sigma factor SigD [Streptomyces clavuligerus ATCC
           27064]
          Length = 191

 Score = 36.7 bits (84), Expect = 4.3,   Method: Composition-based stats.
 Identities = 12/91 (13%), Positives = 30/91 (32%), Gaps = 2/91 (2%)

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
            S+      + +         E+    +      + ++ L   +R +   R      +T 
Sbjct: 103 GSTAVPSDEMPERPDDSLGPEERALLSDDAEWARKLLANLPENQRELLVLRVAVG--LTA 160

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E       +S   VR  + RA  +++   ++
Sbjct: 161 EETGQMLGMSPGAVRVAQHRALSRLRALAEQ 191


>gi|223936171|ref|ZP_03628084.1| RNA polymerase, sigma-24 subunit, ECF subfamily [bacterium
           Ellin514]
 gi|223895033|gb|EEF61481.1| RNA polymerase, sigma-24 subunit, ECF subfamily [bacterium
           Ellin514]
          Length = 549

 Score = 36.7 bits (84), Expect = 4.3,   Method: Composition-based stats.
 Identities = 16/73 (21%), Positives = 30/73 (41%), Gaps = 10/73 (13%)

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS----RERVRQIEARAFKKVQES 283
           L  +++ L  ++R     R +      L+ +      S    + RV     RA +K++  
Sbjct: 122 LDAAIAELGEKDRNAIVLRYV--EGKNLKEVGEALGASEDAAKMRV----NRAVEKLRGV 175

Query: 284 IQKQVELSSSPPL 296
            +KQ  + SS  L
Sbjct: 176 FKKQGIVLSSAAL 188


>gi|71679838|gb|AAI00037.1| G2e3 protein [Danio rerio]
          Length = 706

 Score = 36.7 bits (84), Expect = 4.3,   Method: Composition-based stats.
 Identities = 12/48 (25%), Positives = 26/48 (54%), Gaps = 5/48 (10%)

Query: 254 TLENLSSE-FEVSRERVRQI-EARAFKKVQESIQKQVELSSSPPLLQK 299
           TLE+L    F     ++RQI EA++ K+++ +++   +   +    +K
Sbjct: 481 TLEDLGDTAFG---HKIRQIAEAKSMKELRHAMKSASQYLEAAGCWRK 525


>gi|33592739|ref|NP_880383.1| response regulatory protein [Bordetella pertussis Tohama I]
 gi|33572387|emb|CAE41947.1| response regulatory protein [Bordetella pertussis Tohama I]
 gi|332382154|gb|AEE67001.1| response regulatory protein [Bordetella pertussis CS]
          Length = 224

 Score = 36.7 bits (84), Expect = 4.3,   Method: Composition-based stats.
 Identities = 28/115 (24%), Positives = 50/115 (43%), Gaps = 9/115 (7%)

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV----LNPRERRIFE 244
           L+  S+          + D       LI ++     R  L  +       L+PRER++ E
Sbjct: 113 LLKDSEPAGIVRDICALRDGGSPISPLIARQLLDRLREGLPPAEPPAATALSPRERQVLE 172

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSPPLLQK 299
              L     T + ++SE EVSR  V+    R ++K+Q  +  +V+  ++ P L+ 
Sbjct: 173 RITLG---YTYDEIASELEVSRHTVQTFVRRIYRKLQ--VHSKVDAINAAPGLRP 222


>gi|218264707|ref|ZP_03478451.1| hypothetical protein PRABACTJOHN_04160 [Parabacteroides johnsonii
           DSM 18315]
 gi|218221825|gb|EEC94475.1| hypothetical protein PRABACTJOHN_04160 [Parabacteroides johnsonii
           DSM 18315]
          Length = 171

 Score = 36.7 bits (84), Expect = 4.3,   Method: Composition-based stats.
 Identities = 14/71 (19%), Positives = 39/71 (54%), Gaps = 2/71 (2%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQ 271
           E+  +  E+  N++  +   ++VL PR++ I   R +QE  ++ + +    +++ +  + 
Sbjct: 86  EEQYVTDEQYTNQQRKIQEILNVLTPRQKEIIYYRYIQE--LSFDEICIMMDMNYQSAQN 143

Query: 272 IEARAFKKVQE 282
           +  R+ KK+++
Sbjct: 144 LIQRSLKKIRD 154


>gi|182415001|ref|YP_001820067.1| ECF subfamily RNA polymerase sigma-24 factor [Opitutus terrae
           PB90-1]
 gi|177842215|gb|ACB76467.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Opitutus terrae
           PB90-1]
          Length = 200

 Score = 36.7 bits (84), Expect = 4.3,   Method: Composition-based stats.
 Identities = 18/110 (16%), Positives = 48/110 (43%), Gaps = 14/110 (12%)

Query: 179 RLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPR 238
           R   D+S++     S  N++   + +  + +  + + + +E      + + R M  L+ +
Sbjct: 96  RRKRDQSVSIDAPVSSDNATTLAEIIPAEVETPDDIAVTQE----FVSRIGRGMEKLSAK 151

Query: 239 ERRIFEARRLQENPVTLENLSSEFEVS----RERVRQIEARAFKKVQESI 284
            R I   R ++   ++ E ++    +S    + R+    ARA + ++  +
Sbjct: 152 HREILILRNVKN--LSYEEIADILNISVGTVKSRI----ARARESLRSRL 195


>gi|154483084|ref|ZP_02025532.1| hypothetical protein EUBVEN_00782 [Eubacterium ventriosum ATCC
           27560]
 gi|149736169|gb|EDM52055.1| hypothetical protein EUBVEN_00782 [Eubacterium ventriosum ATCC
           27560]
          Length = 139

 Score = 36.7 bits (84), Expect = 4.3,   Method: Composition-based stats.
 Identities = 10/68 (14%), Positives = 29/68 (42%), Gaps = 2/68 (2%)

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKK 279
           + +   + L  ++  L+ R R         E  +  E ++ +  +SR  V Q    +   
Sbjct: 73  DIRVYDDELAEALKQLSERNRETLLMYYFLE--MNNEEIAKKQNISRSGVFQNRHNSLAL 130

Query: 280 VQESIQKQ 287
           +++ ++++
Sbjct: 131 MKKLLKEK 138


>gi|328886792|emb|CCA60031.1| putative RNA polymerase ECF-subfamily sigma factor [Streptomyces
           venezuelae ATCC 10712]
          Length = 516

 Score = 36.7 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 27/164 (16%), Positives = 55/164 (33%), Gaps = 15/164 (9%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + GD  A   L+ ++L LV  I          + +VV E    L++ V+     R    
Sbjct: 15  AQAGDDGAREELIAAYLPLVYNIVGRALSGHADVDDVVQET---LLRVVRDLPAVRAP-- 69

Query: 102 ATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVA 161
            ++  W +   +++          I T  ++K  F     +      I D   +P     
Sbjct: 70  ESFRSWLVSITLRQ----------INTHLHRKYAFAERTTVIDEAHEIPDVGAEPVDTAI 119

Query: 162 IAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLV 205
           +   ++     V+     L  D  +   +   +   S  +D + 
Sbjct: 120 LRLHVSDERRRVVEAGRWLDPDHRVLLSLWWQECAGSLSRDDIA 163


>gi|295687930|ref|YP_003591623.1| RNA polymerase sigma-24 factor [Caulobacter segnis ATCC 21756]
 gi|295429833|gb|ADG09005.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Caulobacter segnis
           ATCC 21756]
          Length = 198

 Score = 36.7 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 15/64 (23%), Positives = 29/64 (45%), Gaps = 5/64 (7%)

Query: 226 NMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
             +   ++ L  R RRIFE R+++  P     ++    V+ E V  +E  A + ++  + 
Sbjct: 113 ERVRGLIADLPERCRRIFEMRKIEGVP--QREIARRLGVT-EHV--VENEAVRGLRAILA 167

Query: 286 KQVE 289
              E
Sbjct: 168 AMTE 171


>gi|260890620|ref|ZP_05901883.1| RNA polymerase sigma factor RpoD [Leptotrichia hofstadii F0254]
 gi|260859665|gb|EEX74165.1| RNA polymerase sigma factor RpoD [Leptotrichia hofstadii F0254]
          Length = 291

 Score = 36.7 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 32/233 (13%), Positives = 80/233 (34%), Gaps = 40/233 (17%)

Query: 53  LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD----PERGFRLATYSMWW 108
           L+  +L++ VK ++ Y  YG    + V E  +G+M  +  ++      +      +   +
Sbjct: 73  LIDKYLKIAVKESLLYSKYGFSFLDTVQEATLGIMSGLNYYNKIMEITKEPEF--FVKNF 130

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNV 168
               + E+       +K    +    L   + R  G              +  I+K++NV
Sbjct: 131 AVKYILEFQKNLLKDIKSSELSYILYLKVKVDRSMGF------------SMDEISKQMNV 178

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
           S   +  +                         D +  +       ++EK ++  +  +L
Sbjct: 179 STEYIEQLEK---------------------LFDEVEPEELIGNTQILEKADKITQMYIL 217

Query: 229 TRSMSVLNPRERRIFEARRLQENP-VTLENLSSEFEVSRERVRQIEARAFKKV 280
                 LN  + +I       ++   T + ++    ++   V+ ++ +A  K+
Sbjct: 218 ENIPKKLNYLDEQILVMAYGLDDKVYTEKEIAKSLNIASHNVKILKEKALNKL 270


>gi|256840890|ref|ZP_05546398.1| RNA polymerase ECF-type sigma factor [Parabacteroides sp. D13]
 gi|256738162|gb|EEU51488.1| RNA polymerase ECF-type sigma factor [Parabacteroides sp. D13]
          Length = 179

 Score = 36.7 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 15/83 (18%), Positives = 39/83 (46%), Gaps = 8/83 (9%)

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            + + +     ++ E K  ++++ R++  L  R  RIF   R +        ++S   +S
Sbjct: 99  ENPESESYTPQDQLEYKELQSLVNRALGKLPERRLRIFRMHRFEGMKY--AEIASSLSLS 156

Query: 266 RERVRQIEA---RAFKKVQESIQ 285
              ++ +EA   +A + +++ I+
Sbjct: 157 ---IKTVEAEMTKALQTLRKEIE 176


>gi|297204867|ref|ZP_06922264.1| sigma-70 region 2 domain-containing protein [Streptomyces sviceus
           ATCC 29083]
 gi|197712588|gb|EDY56622.1| sigma-70 region 2 domain-containing protein [Streptomyces sviceus
           ATCC 29083]
          Length = 290

 Score = 36.7 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 25/107 (23%), Positives = 39/107 (36%), Gaps = 2/107 (1%)

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
            SE  +   R    ++LN L   +        +WL         V  + E  ++    + 
Sbjct: 46  VSEARAYLVRTVTRQALNRLRTLARSREDYVGEWLPEPLLTSPDVAEDVELAESVSIAML 105

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
             +  L P ER +F  R + E P     ++     S   VRQI  RA
Sbjct: 106 TVLETLGPTERAVFVLREVFELPYG--EIAEAIGKSTAAVRQIARRA 150


>gi|299536386|ref|ZP_07049699.1| RNA polymerase sigma factor Y [Lysinibacillus fusiformis ZC1]
 gi|298728372|gb|EFI68934.1| RNA polymerase sigma factor Y [Lysinibacillus fusiformis ZC1]
          Length = 182

 Score = 36.7 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 16/86 (18%), Positives = 31/86 (36%), Gaps = 6/86 (6%)

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
           +D L            E          L R++ VL+ + R         E     E ++ 
Sbjct: 92  EDKLQAQQQKTHSSAEEDVLLFEEDRHLHRAIQVLDEKYRYPLVLYYFHELKY--EEIAE 149

Query: 261 EFEV--SRERVRQIEARAFKKVQESI 284
              +  S  +VR +  RA +K++ ++
Sbjct: 150 VLNISLSTVKVRLL--RAKEKLKAAL 173


>gi|242398440|ref|YP_002993864.1| HTH-type transcriptional regulator lrpA [Thermococcus sibiricus MM
           739]
 gi|242264833|gb|ACS89515.1| HTH-type transcriptional regulator lrpA [Thermococcus sibiricus MM
           739]
          Length = 141

 Score = 36.7 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 7/50 (14%)

Query: 235 LNPRERRIFEARRLQENPVT-LENLSSEFEVS----RERVRQIEARAFKK 279
           L+ R+R I E   L  +  T    ++    +S    R+RVR +E +   K
Sbjct: 2   LDERDRIIIEM--LTRDARTPFTEIAKALGISETAVRKRVRSLEEKGILK 49


>gi|168703273|ref|ZP_02735550.1| sigma-24, ECF subfamily protein [Gemmata obscuriglobus UQM 2246]
          Length = 179

 Score = 36.7 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 13/54 (24%), Positives = 24/54 (44%)

Query: 44 HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPER 97
           GD +A    +  +  LV  +A  + G      + V +  I L +   ++DP+R
Sbjct: 11 AGDPAAVSDCIARYGGLVWSLARRFLGSPSDAEDAVQDVFIELWKNAGRYDPDR 64


>gi|156975798|ref|YP_001446705.1| RNA polymerase sigma factor RpoE [Vibrio harveyi ATCC BAA-1116]
 gi|156527392|gb|ABU72478.1| hypothetical protein VIBHAR_03542 [Vibrio harveyi ATCC BAA-1116]
          Length = 192

 Score = 36.7 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 19/88 (21%), Positives = 33/88 (37%), Gaps = 3/88 (3%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
            VL +R + +GD  A + LVT +   V  +   Y      + +V  E  I   +A+  F 
Sbjct: 8   QVLIERVQ-NGDKQAFNLLVTKYQNKVCNLISRYVSNPGDVPDVAQEAFIKAYRAIPSFR 66

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWS 122
            E      T+         + +I+    
Sbjct: 67  GE--SAFYTWLYRIAVNTAKNHIVAQGR 92


>gi|154503623|ref|ZP_02040683.1| hypothetical protein RUMGNA_01447 [Ruminococcus gnavus ATCC 29149]
 gi|260589870|ref|ZP_05855783.1| putative flagellar protein FliS [Blautia hansenii DSM 20583]
 gi|153795723|gb|EDN78143.1| hypothetical protein RUMGNA_01447 [Ruminococcus gnavus ATCC 29149]
 gi|260539677|gb|EEX20246.1| putative flagellar protein FliS [Blautia hansenii DSM 20583]
          Length = 189

 Score = 36.7 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 16/71 (22%), Positives = 28/71 (39%), Gaps = 7/71 (9%)

Query: 51  HRLVTSHLRLVVKIAMGYRGYG-----LPISEVVSEGNIGLMQAVKKFDPERGFRLATYS 105
            RL   +L LV ++                 +++  GN+ L +A   +D  R    A Y+
Sbjct: 10  RRLTEEYLYLVPEMVKKLTTRCAYVSYDEQQDLLQAGNLALCKAAMNYDNTR--PFAVYA 67

Query: 106 MWWIKAAMQEY 116
              I+ A+  Y
Sbjct: 68  RVAIRNAIYSY 78


>gi|221069264|ref|ZP_03545369.1| Resolvase domain protein [Comamonas testosteroni KF-1]
 gi|220714287|gb|EED69655.1| Resolvase domain protein [Comamonas testosteroni KF-1]
          Length = 203

 Score = 36.7 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 10/33 (30%), Positives = 21/33 (63%)

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           EA RL+++ +T + ++    VSR  + ++E+ A
Sbjct: 150 EALRLRQDGMTQKEVAEVLGVSRSTISRLESPA 182


>gi|305681663|ref|ZP_07404469.1| sigma-70 region 2 [Corynebacterium matruchotii ATCC 14266]
 gi|305658823|gb|EFM48324.1| sigma-70 region 2 [Corynebacterium matruchotii ATCC 14266]
          Length = 212

 Score = 36.7 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 16/77 (20%), Positives = 35/77 (45%), Gaps = 4/77 (5%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG-FRLA 102
            G+ +A   +V+ + RL++ +A  Y    +   +++ E    L++A K     RG   L 
Sbjct: 44  DGNTAAFTVIVSRYYRLMLWVAHKYTDRIIDAEDLLQEA---LLRAAKGLHMYRGECSLG 100

Query: 103 TYSMWWIKAAMQEYILR 119
            +    +  A  +Y+ +
Sbjct: 101 AWLHRLVANAGYDYLQK 117


>gi|258517224|ref|YP_003193446.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Desulfotomaculum
           acetoxidans DSM 771]
 gi|257780929|gb|ACV64823.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Desulfotomaculum
           acetoxidans DSM 771]
          Length = 203

 Score = 36.7 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 13/81 (16%), Positives = 32/81 (39%), Gaps = 2/81 (2%)

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           S + L++  +   S+  D L  +    +   ++  E K   +M+  ++  L+   R +  
Sbjct: 88  SSHQLLSLDEHYQSEDGDSLKREVAAGDGDPLQLLEEKEFSSMVYSALRTLSEEHRAVLV 147

Query: 245 ARRLQENPVTLENLSSEFEVS 265
            R +     + E ++     S
Sbjct: 148 LREI--EGYSYEEVAQMLGCS 166


>gi|28899352|ref|NP_798957.1| RNA polymerase sigma factor RpoE [Vibrio parahaemolyticus RIMD
           2210633]
 gi|153840480|ref|ZP_01993147.1| RNA polymerase sigma factor RpoE [Vibrio parahaemolyticus AQ3810]
 gi|260362195|ref|ZP_05775182.1| RNA polymerase sigma factor RpoE [Vibrio parahaemolyticus K5030]
 gi|260878957|ref|ZP_05891312.1| RNA polymerase sigma factor RpoE [Vibrio parahaemolyticus AN-5034]
 gi|260897482|ref|ZP_05905978.1| RNA polymerase sigma factor RpoE [Vibrio parahaemolyticus Peru-466]
 gi|260899631|ref|ZP_05908026.1| RNA polymerase sigma factor RpoE [Vibrio parahaemolyticus AQ4037]
 gi|28807588|dbj|BAC60841.1| RNA polymerase sigma-E factor [Vibrio parahaemolyticus RIMD
           2210633]
 gi|149745856|gb|EDM56986.1| RNA polymerase sigma factor RpoE [Vibrio parahaemolyticus AQ3810]
 gi|308088019|gb|EFO37714.1| RNA polymerase sigma factor RpoE [Vibrio parahaemolyticus Peru-466]
 gi|308090462|gb|EFO40157.1| RNA polymerase sigma factor RpoE [Vibrio parahaemolyticus AN-5034]
 gi|308108231|gb|EFO45771.1| RNA polymerase sigma factor RpoE [Vibrio parahaemolyticus AQ4037]
 gi|308113964|gb|EFO51504.1| RNA polymerase sigma factor RpoE [Vibrio parahaemolyticus K5030]
          Length = 192

 Score = 36.7 bits (84), Expect = 4.4,   Method: Composition-based stats.
 Identities = 19/88 (21%), Positives = 33/88 (37%), Gaps = 3/88 (3%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
            VL +R + +GD  A + LVT +   V  +   Y      + +V  E  I   +A+  F 
Sbjct: 8   QVLIERVQ-NGDKQAFNLLVTKYQNKVCNLISRYVSNPGDVPDVAQEAFIKAYRAIPSFR 66

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWS 122
            E      T+         + +I+    
Sbjct: 67  GE--SAFYTWLYRIAVNTAKNHIVAQGR 92


>gi|315123466|ref|YP_004065472.1| RNA polymerase sigma factor [Pseudoalteromonas sp. SM9913]
 gi|315017226|gb|ADT70563.1| RNA polymerase sigma factor [Pseudoalteromonas sp. SM9913]
          Length = 207

 Score = 36.7 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 17/100 (17%), Positives = 39/100 (39%), Gaps = 18/100 (18%)

Query: 194 DKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPV 253
           ++N S+    L+ + +       +  E K     + R +  L   +R +      Q+  +
Sbjct: 118 EENISEDIWPLLNESEDTHHEYSDHLEDK----QIKRYLDKLPQAQREVVRGVYFQD--M 171

Query: 254 TLENLSSEFEV------SRERVRQIEARAFKKVQESIQKQ 287
           + E L+ +  +      SR R+      A +K++  +  Q
Sbjct: 172 SQEQLAQQLNIPVGTVKSRLRL------ALQKLRNEMGDQ 205


>gi|268611771|ref|ZP_06145498.1| ECF subfamily RNA polymerase sigma-24 factor [Ruminococcus
           flavefaciens FD-1]
          Length = 184

 Score = 36.7 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 17/93 (18%), Positives = 41/93 (44%), Gaps = 6/93 (6%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
           +     + + V D +  E+  I+ EE    +  L R+M  LN   R++      ++   T
Sbjct: 91  EEYPITEIYNVADQENIERNYIKSEE----KQRLLRAMDKLNNDYRQVLYLTYFEDFSNT 146

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
               +     S  ++R +  R+ + +++ I+++
Sbjct: 147 --ETAKIMGKSERQIRNLLYRSKESLRKIIERE 177


>gi|315646482|ref|ZP_07899600.1| RNA polymerase, sigma-24 subunit, ECF subfamily protein
           [Paenibacillus vortex V453]
 gi|315278125|gb|EFU41445.1| RNA polymerase, sigma-24 subunit, ECF subfamily protein
           [Paenibacillus vortex V453]
          Length = 203

 Score = 36.7 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 14/65 (21%), Positives = 26/65 (40%), Gaps = 2/65 (3%)

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
            D ++     +++ ++     K RR  L   +  L    R I  A  L E     E +++
Sbjct: 116 HDEVLDKLPSRDEDVVSLLIHKERREELREKIEQLPDNHREIITAFYLDEKNY--EQIAT 173

Query: 261 EFEVS 265
           E  V+
Sbjct: 174 ELNVT 178


>gi|255010136|ref|ZP_05282262.1| putative extracytoplasmic function alternative sigma factor
           [Bacteroides fragilis 3_1_12]
 gi|313147934|ref|ZP_07810127.1| RNA polymerase ECF-type sigma factor [Bacteroides fragilis 3_1_12]
 gi|313136701|gb|EFR54061.1| RNA polymerase ECF-type sigma factor [Bacteroides fragilis 3_1_12]
          Length = 169

 Score = 36.7 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 9/65 (13%), Positives = 30/65 (46%), Gaps = 2/65 (3%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
             + + +     ++   K R +++ R ++ L  ++R I + R ++      + ++    +
Sbjct: 84  EMEEESEASGPYDQLINKERMSIIHRLINELPEKQRLIMQLRDIEGESY--KEIAKILNL 141

Query: 265 SRERV 269
           + E+V
Sbjct: 142 TEEQV 146


>gi|302873534|ref|YP_003842167.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           cellulovorans 743B]
 gi|307688286|ref|ZP_07630732.1| RNA polymerase factor sigma-70 [Clostridium cellulovorans 743B]
 gi|302576391|gb|ADL50403.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Clostridium
           cellulovorans 743B]
          Length = 186

 Score = 36.7 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 12/69 (17%), Positives = 28/69 (40%), Gaps = 2/69 (2%)

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
           Q  +       E+VL E+      +  + + ++ L+  ++ IF  +       +L  +  
Sbjct: 97  QCHIDDLMLADERVLEEQILHSESKEEILKVINGLDSPDKDIFIRKYFMGE--SLNEIGE 154

Query: 261 EFEVSRERV 269
           +  +SR  V
Sbjct: 155 KLNLSRSAV 163


>gi|255036030|ref|YP_003086651.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Dyadobacter
           fermentans DSM 18053]
 gi|254948786|gb|ACT93486.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Dyadobacter
           fermentans DSM 18053]
          Length = 191

 Score = 36.7 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 13/68 (19%), Positives = 28/68 (41%), Gaps = 6/68 (8%)

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           +  D++   HD  +   + +E     R      +  L  + R IF  R L    ++   +
Sbjct: 99  EPLDYMALSHDAADSDYLREELLSGIR----LWLETLPEKRREIFRLRYL--EGLSTIEI 152

Query: 259 SSEFEVSR 266
           ++  ++SR
Sbjct: 153 ANLLDISR 160


>gi|160916267|ref|ZP_02078474.1| hypothetical protein EUBDOL_02294 [Eubacterium dolichum DSM 3991]
 gi|158431991|gb|EDP10280.1| hypothetical protein EUBDOL_02294 [Eubacterium dolichum DSM 3991]
          Length = 193

 Score = 36.7 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 25/87 (28%), Positives = 44/87 (50%), Gaps = 9/87 (10%)

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNML--TRSMSVLNPRERRIFEARRLQENPVTLENLS 259
           D L+ D +GQ      K E  ++  +L    +M  LN  E++I E R   +N  T   ++
Sbjct: 112 DNLICDGEGQYTTNSSKNETISKSVLLRIEEAMEHLNAFEKKIVELR---KNGYTYAEIA 168

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQK 286
           ++ +VS E    I AR  +K++ + +K
Sbjct: 169 TDLKVS-EY---IVARTIRKIRNTQKK 191


>gi|77457589|ref|YP_347094.1| RNA polymerase sigma factor AlgU [Pseudomonas fluorescens Pf0-1]
 gi|229588994|ref|YP_002871113.1| RNA polymerase sigma factor AlgU [Pseudomonas fluorescens SBW25]
 gi|312959551|ref|ZP_07774068.1| RNA polymerase sigma-70 factor, ECF subfamily [Pseudomonas
           fluorescens WH6]
 gi|330808069|ref|YP_004352531.1| RNA polymerase sigma factor [Pseudomonas brassicacearum subsp.
           brassicacearum NFM421]
 gi|77381592|gb|ABA73105.1| RNA polymerase, sigma-24 subunit, RpoE [Pseudomonas fluorescens
           Pf0-1]
 gi|229360860|emb|CAY47719.1| alternative ECF subfamily sigma factor [Pseudomonas fluorescens
           SBW25]
 gi|311286268|gb|EFQ64832.1| RNA polymerase sigma-70 factor, ECF subfamily [Pseudomonas
           fluorescens WH6]
 gi|327376177|gb|AEA67527.1| RNA polymerase sigma factor [Pseudomonas brassicacearum subsp.
           brassicacearum NFM421]
          Length = 193

 Score = 36.7 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 17/95 (17%), Positives = 36/95 (37%), Gaps = 3/95 (3%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           ML ++E+  L +R +  GD  A   LV  +   ++ + + +        +V  E  I   
Sbjct: 1   MLTQEEDQQLVERVQ-RGDKRAFDLLVLKYQHKILGLIVRFVHDTHEAQDVAQEAFIKAY 59

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           +A+  F  +      T+         + Y++    
Sbjct: 60  RALGNFRGD--SAFYTWLYRIAINTAKNYLVSRGR 92


>gi|70728827|ref|YP_258576.1| RNA polymerase sigma factor AlgU [Pseudomonas fluorescens Pf-5]
 gi|15277828|gb|AAK94006.1|AF399758_2 alternative sigma factor AlgU [Pseudomonas fluorescens]
 gi|68343126|gb|AAY90732.1| RNA polymerase sigma-H factor AlgT [Pseudomonas fluorescens Pf-5]
          Length = 193

 Score = 36.7 bits (84), Expect = 4.5,   Method: Composition-based stats.
 Identities = 17/95 (17%), Positives = 36/95 (37%), Gaps = 3/95 (3%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           ML ++E+  L +R +  GD  A   LV  +   ++ + + +        +V  E  I   
Sbjct: 1   MLTQEEDQQLVERVQ-RGDKRAFDLLVLKYQHKILGLIVRFVHDTHEAQDVAQEAFIKAY 59

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           +A+  F  +      T+         + Y++    
Sbjct: 60  RALGNFRGD--SAFYTWLYRIAINTAKNYLVSRGR 92


>gi|257792492|ref|YP_003183098.1| ATP-dependent transcriptional regulator, MalT- like, LuxR family
           [Eggerthella lenta DSM 2243]
 gi|257476389|gb|ACV56709.1| ATP-dependent transcriptional regulator, MalT- like, LuxR family
           [Eggerthella lenta DSM 2243]
          Length = 520

 Score = 36.7 bits (84), Expect = 4.6,   Method: Composition-based stats.
 Identities = 16/82 (19%), Positives = 36/82 (43%), Gaps = 9/82 (10%)

Query: 212 EQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS----RE 267
           ++   E    K+   +  ++   L+ RER +     L     T+E ++ E  +S    + 
Sbjct: 438 DRAPREGAWTKSCNALAEQA--GLSLRERDVL---FLLGKGYTIEYIAGELGISFNTAKS 492

Query: 268 RVRQIEARAFKKVQESIQKQVE 289
            +R + A+A    ++ +Q  +E
Sbjct: 493 HIRNVYAKAGVHSKQELQSLIE 514


>gi|257413773|ref|ZP_04744203.2| sigma-70, region 4 superfamily [Roseburia intestinalis L1-82]
 gi|257202418|gb|EEV00703.1| sigma-70, region 4 superfamily [Roseburia intestinalis L1-82]
          Length = 186

 Score = 36.7 bits (84), Expect = 4.6,   Method: Composition-based stats.
 Identities = 9/47 (19%), Positives = 18/47 (38%), Gaps = 2/47 (4%)

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           E +     L  ++  L+ R R +       E P     ++   ++SR
Sbjct: 120 EVRVYDEKLCEAIKKLSERRRNVVLMFYFLELPD--AEIAEILDISR 164


>gi|182413161|ref|YP_001818227.1| ECF subfamily RNA polymerase sigma-24 factor [Opitutus terrae
           PB90-1]
 gi|177840375|gb|ACB74627.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Opitutus terrae
           PB90-1]
          Length = 560

 Score = 36.7 bits (84), Expect = 4.6,   Method: Composition-based stats.
 Identities = 13/56 (23%), Positives = 23/56 (41%), Gaps = 6/56 (10%)

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS----RERV 269
           + E    R +L  ++S L P +R     R      ++L  + +   VS    R R+
Sbjct: 111 EVEWDRVRPVLDDALSELKPADREAVLLRYFMG--ISLAEVGARLSVSENAARMRI 164


>gi|29829139|ref|NP_823773.1| ECF subfamily RNA polymerase sigma factor [Streptomyces avermitilis
           MA-4680]
 gi|29606245|dbj|BAC70308.1| putative RNA polymerase ECF-subfamily sigma factor [Streptomyces
           avermitilis MA-4680]
          Length = 634

 Score = 36.7 bits (84), Expect = 4.6,   Method: Composition-based stats.
 Identities = 18/72 (25%), Positives = 28/72 (38%), Gaps = 5/72 (6%)

Query: 42  REHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRL 101
            + GD  A   LV   L LV  +     G    + +VV E    +++AV      R    
Sbjct: 90  AQAGDREALDELVAGWLPLVYNVVGRALGGHADVDDVVQET---MLRAVDHLGSLRDPD- 145

Query: 102 ATYSMWWIKAAM 113
            ++  W +  AM
Sbjct: 146 -SFRSWLVAIAM 156


>gi|77404544|ref|YP_345120.1| hypothetical protein pREC1_0059 [Rhodococcus erythropolis PR4]
 gi|77019925|dbj|BAE46300.1| hypothetical membrane protein [Rhodococcus erythropolis PR4]
          Length = 455

 Score = 36.7 bits (84), Expect = 4.6,   Method: Composition-based stats.
 Identities = 14/89 (15%), Positives = 29/89 (32%), Gaps = 6/89 (6%)

Query: 192 SSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRE----RRIFEARR 247
              +N ++  +    D +     ++E   R+ +    T     L  R       +   R 
Sbjct: 347 DWSENETETSNGGPMDLETANSTVLEHSRRQWQGLAATMRARQLTTRSTDEVADMLRMRF 406

Query: 248 LQENPVTLENLSSEFEVSRERVRQIEARA 276
             ++   L  +   F V+   V  I  +A
Sbjct: 407 --DDKKALRTIGEHFNVTHSTVSNIVQKA 433


>gi|91227859|ref|ZP_01262032.1| RNA polymerase sigma-70 factor [Vibrio alginolyticus 12G01]
 gi|262393264|ref|YP_003285118.1| RNA polymerase sigma factor RpoE [Vibrio sp. Ex25]
 gi|269965778|ref|ZP_06179875.1| RNA polymerase sigma-E factor [Vibrio alginolyticus 40B]
 gi|91188369|gb|EAS74665.1| RNA polymerase sigma-70 factor [Vibrio alginolyticus 12G01]
 gi|262336858|gb|ACY50653.1| RNA polymerase sigma factor RpoE [Vibrio sp. Ex25]
 gi|269829646|gb|EEZ83883.1| RNA polymerase sigma-E factor [Vibrio alginolyticus 40B]
          Length = 192

 Score = 36.7 bits (84), Expect = 4.6,   Method: Composition-based stats.
 Identities = 19/88 (21%), Positives = 33/88 (37%), Gaps = 3/88 (3%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
            VL +R + +GD  A + LVT +   V  +   Y      + +V  E  I   +A+  F 
Sbjct: 8   QVLIERVQ-NGDKQAFNLLVTKYQNKVCNLISRYVSNPGDVPDVAQEAFIKAYRAIPSFR 66

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWS 122
            E      T+         + +I+    
Sbjct: 67  GE--SAFYTWLYRIAVNTAKNHIVAQGR 92


>gi|299065363|emb|CBJ36532.1| putative two component transcriptional regulator, LuxR family
           [Ralstonia solanacearum CMR15]
          Length = 222

 Score = 36.7 bits (84), Expect = 4.6,   Method: Composition-based stats.
 Identities = 8/56 (14%), Positives = 23/56 (41%), Gaps = 3/56 (5%)

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ++  L  RE  +       E   T+  ++     S + V   + ++ +K++ + + 
Sbjct: 153 ALDRLGKRELEVLRMYVGGE---TVSEIARRLNRSVKTVSAQKQKSMRKLRLATEA 205


>gi|295702347|ref|YP_003595422.1| translation elongation factor G [Bacillus megaterium DSM 319]
 gi|294800006|gb|ADF37072.1| translation elongation factor G (EF-G) [Bacillus megaterium DSM
           319]
          Length = 692

 Score = 36.7 bits (84), Expect = 4.6,   Method: Composition-based stats.
 Identities = 15/83 (18%), Positives = 36/83 (43%), Gaps = 4/83 (4%)

Query: 176 MNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVL 235
           +   +  ++   A+I+  +  +  ++D L    + +E     KE+ +  R  L  +++ L
Sbjct: 162 IQLPIGAEDDFEAIIDLVEMKAYFYEDDLGTRSESREIPEEYKEQAEEYRASLVEAVAEL 221

Query: 236 NPRERRIFEARRLQENPVTLENL 258
           +         + L E  +T+E L
Sbjct: 222 DEE----LMMKYLDEGELTVEEL 240


>gi|300779659|ref|ZP_07089515.1| DNA-directed DNA polymerase III epsilon subunit [Corynebacterium
           genitalium ATCC 33030]
 gi|300533769|gb|EFK54828.1| DNA-directed DNA polymerase III epsilon subunit [Corynebacterium
           genitalium ATCC 33030]
          Length = 959

 Score = 36.7 bits (84), Expect = 4.6,   Method: Composition-based stats.
 Identities = 7/30 (23%), Positives = 16/30 (53%), Gaps = 2/30 (6%)

Query: 243 FEARRLQENPVTLENLSSEFEVSRERVRQI 272
                + +   TLE L   + +S++R++Q+
Sbjct: 535 ISMHYMGD--TTLEELGELYNISQKRIQQL 562


>gi|227505282|ref|ZP_03935331.1| RNA polymerase sigma factor SigD [Corynebacterium striatum ATCC
           6940]
 gi|227198115|gb|EEI78163.1| RNA polymerase sigma factor SigD [Corynebacterium striatum ATCC
           6940]
          Length = 187

 Score = 36.7 bits (84), Expect = 4.6,   Method: Composition-based stats.
 Identities = 14/80 (17%), Positives = 31/80 (38%), Gaps = 2/80 (2%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           V +   +E    E     +  N +   +  L+ + R I   R      ++ E  +     
Sbjct: 105 VPEGATKEANPEETALVADGSNRVRELLDTLSDKARNIIILRVFVG--LSAEETAEIVGS 162

Query: 265 SRERVRQIEARAFKKVQESI 284
           +   VR  + RA  +++++I
Sbjct: 163 TPGAVRVAQHRALSQLRKAI 182


>gi|221195037|ref|ZP_03568093.1| kinase, PfkB family [Atopobium rimae ATCC 49626]
 gi|221184940|gb|EEE17331.1| kinase, PfkB family [Atopobium rimae ATCC 49626]
          Length = 360

 Score = 36.7 bits (84), Expect = 4.6,   Method: Composition-based stats.
 Identities = 11/37 (29%), Positives = 19/37 (51%), Gaps = 3/37 (8%)

Query: 235 LNPRERRIFEARRLQENPV-TLENLSSEFEVSRERVR 270
           L  RE++IF    ++E P  T + ++    +SR  V 
Sbjct: 2   LTEREQQIFN--WIKEQPSITQKEIAERAGISRSSVS 36


>gi|77460598|ref|YP_350105.1| sigma-24 (FecI) [Pseudomonas fluorescens Pf0-1]
 gi|77384601|gb|ABA76114.1| putative ECF sigma factor [Pseudomonas fluorescens Pf0-1]
          Length = 172

 Score = 36.7 bits (84), Expect = 4.6,   Method: Composition-based stats.
 Identities = 16/73 (21%), Positives = 28/73 (38%), Gaps = 6/73 (8%)

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV----LNPRERRIFEARRLQENP 252
           S    D +  D            E       L   ++V    L+PR+++IF   RL  + 
Sbjct: 77  SRTMVDDVPQDVVHSVAAPASSAEDAAHAEQLLERLNVSLGELSPRQQQIFILSRL--HG 134

Query: 253 VTLENLSSEFEVS 265
            + + ++ E  VS
Sbjct: 135 HSYQEIAEELSVS 147


>gi|73662122|ref|YP_300903.1| RNA polymerase sigma-B factor [Staphylococcus saprophyticus
          subsp. saprophyticus ATCC 15305]
 gi|72494637|dbj|BAE17958.1| truncated RNA polymerase sigma-B factor [Staphylococcus
          saprophyticus subsp. saprophyticus ATCC 15305]
          Length = 73

 Score = 36.7 bits (84), Expect = 4.6,   Method: Composition-based stats.
 Identities = 8/53 (15%), Positives = 22/53 (41%)

Query: 30 EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEG 82
            ++      +++ + +  A  +LV  + +L+  +A  Y        ++V  G
Sbjct: 12 SPEQINQWIMQHQNNENTDAQDQLVRHYRKLIESLAYKYSKGQSHHEDLVQVG 64


>gi|325273771|ref|ZP_08139963.1| ECF subfamily RNA polymerase sigma-24 factor [Pseudomonas sp.
           TJI-51]
 gi|324101093|gb|EGB98747.1| ECF subfamily RNA polymerase sigma-24 factor [Pseudomonas sp.
           TJI-51]
          Length = 170

 Score = 36.7 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 14/69 (20%), Positives = 29/69 (42%), Gaps = 2/69 (2%)

Query: 201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSS 260
            D +++          +    +     L+ S++ L+ R++RIF   RL  +  T   ++ 
Sbjct: 85  PDEVLHSVAAPASSSEDAAHAEQLLKHLSISLNQLSERQQRIFILSRL--HGATYLEIAQ 142

Query: 261 EFEVSRERV 269
           +  VS   V
Sbjct: 143 QLNVSASTV 151


>gi|224025222|ref|ZP_03643588.1| hypothetical protein BACCOPRO_01956 [Bacteroides coprophilus DSM
           18228]
 gi|224018458|gb|EEF76456.1| hypothetical protein BACCOPRO_01956 [Bacteroides coprophilus DSM
           18228]
          Length = 169

 Score = 36.7 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 17/110 (15%), Positives = 43/110 (39%), Gaps = 19/110 (17%)

Query: 174 ISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMS 233
           I+ N  +   E L        + +++  D L  D          + E+  +  ++ R ++
Sbjct: 62  IARNLAIDRSEKLETQNIPLMEEATELPDALTPDR---------QIEQDEQLKLIHRLVN 112

Query: 234 VLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV--------RQIEAR 275
            L  ++R + + R       + + ++    ++ E+V        RQI ++
Sbjct: 113 ELPEKQRTVMQLR--DVEGKSYKEIAEIMHLTEEQVKVNLFRARRQIRSK 160


>gi|196232621|ref|ZP_03131473.1| two component transcriptional regulator, LuxR family
           [Chthoniobacter flavus Ellin428]
 gi|196223383|gb|EDY17901.1| two component transcriptional regulator, LuxR family
           [Chthoniobacter flavus Ellin428]
          Length = 220

 Score = 36.7 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 18/80 (22%), Positives = 34/80 (42%), Gaps = 5/80 (6%)

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQI 272
             L EK      R+        L+ RE ++F          +L+  ++E  VS + V   
Sbjct: 127 AALGEKLAADLGRSRNRAHHETLSDREYQVFRLMLGG---KSLKETAAELSVSPKTVSTY 183

Query: 273 EARAFKKVQESIQKQVELSS 292
             R F+K++  ++  +EL+ 
Sbjct: 184 RTRIFEKLR--VKNDIELAR 201


>gi|307324411|ref|ZP_07603619.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306890142|gb|EFN21120.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 237

 Score = 36.7 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 13/53 (24%), Positives = 24/53 (45%), Gaps = 2/53 (3%)

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
            ++ L P+ER +   R  +      E  ++   +  ERVR I  RA   ++ +
Sbjct: 95  LLARLTPQERLVLVLRLYEGVAE--EQTAAALGLPVERVRAICTRAVTAMRSA 145


>gi|251772991|gb|EES53547.1| Resolvase helix-turn-helix domain protein [Leptospirillum
           ferrodiazotrophum]
          Length = 413

 Score = 36.7 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 13/42 (30%), Positives = 25/42 (59%), Gaps = 7/42 (16%)

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQ 285
           EA RL+E  ++L  ++  F VS++ V       FKK+++ ++
Sbjct: 375 EAHRLREEGLSLAEIARRFGVSKQAV-------FKKLKKPME 409


>gi|256396229|ref|YP_003117793.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Catenulispora
           acidiphila DSM 44928]
 gi|256362455|gb|ACU75952.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Catenulispora
           acidiphila DSM 44928]
          Length = 294

 Score = 36.7 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 22/107 (20%), Positives = 38/107 (35%), Gaps = 2/107 (1%)

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             +  +   R+   ++LN L     +  +    WL         V    E  +N    L 
Sbjct: 49  VRDERAYLIRITTRQALNRLRTMKRRREAYVGTWLPEPLLTAPDVAEHVEVAENLSIALM 108

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
             +  L+P ER +F  R   +     + ++     +   VRQI  RA
Sbjct: 109 LVLETLSPTERAVFVLREAFDVGY--DEIAEAVGKTPAAVRQIAHRA 153


>gi|191637711|ref|YP_001986877.1| Competence-specific sigma factor ComX [Lactobacillus casei BL23]
 gi|227535721|ref|ZP_03965770.1| competence-specific sigma factor ComX [Lactobacillus paracasei
           subsp. paracasei ATCC 25302]
 gi|190712013|emb|CAQ66019.1| Competence-specific sigma factor ComX [Lactobacillus casei BL23]
 gi|227186636|gb|EEI66703.1| competence-specific sigma factor ComX [Lactobacillus paracasei
           subsp. paracasei ATCC 25302]
 gi|327381772|gb|AEA53248.1| hypothetical protein LC2W_0914 [Lactobacillus casei LC2W]
 gi|327384935|gb|AEA56409.1| hypothetical protein LCBD_0911 [Lactobacillus casei BD-II]
          Length = 182

 Score = 36.7 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 24/146 (16%), Positives = 50/146 (34%), Gaps = 4/146 (2%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L   +  LV+ +   Y        + + E  I +++A+ ++D   G +   Y    
Sbjct: 18  AFSQLFKQYRPLVLTVLRPYHLRDFSHEDWLQEARIAMLKAITRYDGSSGSQFGPY-YRM 76

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFF---NLRRLKGHLQAITDNNLKPEQVVAIAKK 165
           +  +    +LR     K    A    +        + +  L++  D  L   +      +
Sbjct: 77  VLQSHLRSVLRKHFAHKRRIDATAIPVEDSALESLQERLALRSYEDGLLMRIEFAQFLAR 136

Query: 166 LNVSESEVISMNCRLAGDESLNALIN 191
           L+  E E          D S + L+ 
Sbjct: 137 LSPLEYEAFEAAVISQTDSSEDPLLQ 162


>gi|167765358|ref|ZP_02437471.1| hypothetical protein BACSTE_03746 [Bacteroides stercoris ATCC
           43183]
 gi|167696986|gb|EDS13565.1| hypothetical protein BACSTE_03746 [Bacteroides stercoris ATCC
           43183]
          Length = 162

 Score = 36.7 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 17/71 (23%), Positives = 33/71 (46%), Gaps = 2/71 (2%)

Query: 216 IEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
           +E +E+  R   + + +  + P  R I E   L E     + +++E  +S   VR+   +
Sbjct: 94  VEFKEQDERMMKIQKVLDGMTPHTRHILEECYLHEKKY--KEVAAELNISISAVRKHIVK 151

Query: 276 AFKKVQESIQK 286
           A K ++E   K
Sbjct: 152 ALKAIREEFAK 162


>gi|90416431|ref|ZP_01224362.1| sigma factor AlgU [marine gamma proteobacterium HTCC2207]
 gi|90331630|gb|EAS46858.1| sigma factor AlgU [marine gamma proteobacterium HTCC2207]
          Length = 196

 Score = 36.7 bits (84), Expect = 4.7,   Method: Composition-based stats.
 Identities = 16/80 (20%), Positives = 29/80 (36%), Gaps = 2/80 (2%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A   LV  +   V  I   +      + +VV E  I   +A+ KF  +   +  
Sbjct: 18  QKGDKRAFDLLVLKYQYKVHAIVARFIRDSDEVRDVVQEAFIKAYRALPKFRGD--SQFY 75

Query: 103 TYSMWWIKAAMQEYILRSWS 122
           T+         + Y++    
Sbjct: 76  TWLYRIAVNTAKNYLVARSR 95


>gi|297159677|gb|ADI09389.1| RNA polymerase sigma factor SigD [Streptomyces bingchenggensis
           BCW-1]
          Length = 203

 Score = 36.7 bits (84), Expect = 4.8,   Method: Composition-based stats.
 Identities = 12/91 (13%), Positives = 30/91 (32%), Gaps = 2/91 (2%)

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
            S+      + +         E+    +      + ++ L   +R +   R      +T 
Sbjct: 115 GSTAVPSDEMPEQPDDSLGPEEQALLSSDAEWAKKLLANLPENQRELVLLRVAVG--LTA 172

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E       +S   VR  + RA  +++   ++
Sbjct: 173 EETGQMLGMSPGAVRVAQHRALSRLRALAEQ 203


>gi|326318448|ref|YP_004236120.1| ECF subfamily RNA polymerase sigma-24 subunit [Acidovorax avenae
           subsp. avenae ATCC 19860]
 gi|323375284|gb|ADX47553.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Acidovorax avenae
           subsp. avenae ATCC 19860]
          Length = 177

 Score = 36.7 bits (84), Expect = 4.8,   Method: Composition-based stats.
 Identities = 17/105 (16%), Positives = 37/105 (35%), Gaps = 3/105 (2%)

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHD-GQEQVLIEK 218
           + +A+         I   C++  + +L+       + S +  D  V   D    +     
Sbjct: 47  LKLAEGPGRVAERPIGYCCQVVRNLALDYCRRHRVEASYRTFDVDVEAIDVPCHRSPDRH 106

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
              +   + +   +S L PR R +FE  R+    +T   ++    
Sbjct: 107 MCEQQVIHAIDEVLSQLPPRTRMVFELYRI--EGLTQRQIAERLG 149


>gi|297200818|ref|ZP_06918215.1| RNA polymerase ECF-subfamily sigma factor [Streptomyces sviceus
           ATCC 29083]
 gi|297147740|gb|EDY56429.2| RNA polymerase ECF-subfamily sigma factor [Streptomyces sviceus
           ATCC 29083]
          Length = 185

 Score = 36.7 bits (84), Expect = 4.8,   Method: Composition-based stats.
 Identities = 16/86 (18%), Positives = 37/86 (43%), Gaps = 8/86 (9%)

Query: 201 QDWLVYDHDGQEQVLIEKE--ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
            ++   +    E V  + +  E++   + + R++  L  R+R +   R  ++    L  +
Sbjct: 96  DEFATDEIPEPEPVPGDDDPAEQQALHDAMWRAIMKLPARQRAMVVLRYYED----LSEV 151

Query: 259 --SSEFEVSRERVRQIEARAFKKVQE 282
             +    VS   V+   +RA  K++E
Sbjct: 152 QTAEVLGVSVGTVKSAVSRALGKLRE 177


>gi|160894704|ref|ZP_02075479.1| hypothetical protein CLOL250_02255 [Clostridium sp. L2-50]
 gi|156863638|gb|EDO57069.1| hypothetical protein CLOL250_02255 [Clostridium sp. L2-50]
          Length = 516

 Score = 36.7 bits (84), Expect = 4.8,   Method: Composition-based stats.
 Identities = 20/110 (18%), Positives = 49/110 (44%), Gaps = 5/110 (4%)

Query: 160 VAIAKKLNVSESEVISMNCRLAGDESLNAL-INSSDKNSSQWQDWLVYDHDGQEQVLIEK 218
           ++IA  +  S+  V  +  R    E ++ L +  +   +    D +   HD + + +I+ 
Sbjct: 377 ISIAMFIYSSQLRVNIIEERFERKEDMDGLTVEVASATTGSVFDSVSGKHDIESENVIKG 436

Query: 219 EERKNRRNMLTRSMS--VLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
            +  +  +   R      L  RE+ +   R L E+  ++++++ +  +SR
Sbjct: 437 SDGTDAVDYFARFAEKYRLTDREQEVL--RELLESDESVQDIAGKLYISR 484


>gi|317126708|ref|YP_004100820.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Intrasporangium
           calvum DSM 43043]
 gi|315590796|gb|ADU50093.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Intrasporangium
           calvum DSM 43043]
          Length = 190

 Score = 36.7 bits (84), Expect = 4.8,   Method: Composition-based stats.
 Identities = 11/61 (18%), Positives = 24/61 (39%), Gaps = 2/61 (3%)

Query: 221 RKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
           R + R  L  ++  L  R+R +   R  ++        +     S   V+   ++A  K+
Sbjct: 114 RTDDRTDLWDALGRLPKRQRAVVVLRFYEDQSE--AETAELLGCSVGTVKSQASKALAKL 171

Query: 281 Q 281
           +
Sbjct: 172 R 172


>gi|317152253|ref|YP_004120301.1| sigma-70 family RNA polymerase sigma factor [Desulfovibrio
           aespoeensis Aspo-2]
 gi|316942504|gb|ADU61555.1| RNA polymerase sigma factor, sigma-70 family [Desulfovibrio
           aespoeensis Aspo-2]
          Length = 185

 Score = 36.7 bits (84), Expect = 4.8,   Method: Composition-based stats.
 Identities = 14/77 (18%), Positives = 29/77 (37%), Gaps = 2/77 (2%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GDL A   +V  H     ++A  + G     +++V    + L+ A  ++  E   R   
Sbjct: 17  QGDLHAFGEIVRRHQAWAWRVAHRFLGDEAEAADIVQSAFLRLLDAAGRYRHE--ARFTG 74

Query: 104 YSMWWIKAAMQEYILRS 120
           Y    +     + + + 
Sbjct: 75  YLSRIVTRLCLDRVKKK 91


>gi|17547797|ref|NP_521199.1| response regulator transcription regulator protein [Ralstonia
           solanacearum GMI1000]
 gi|17430102|emb|CAD16787.1| probable response regulator transcription regulator protein
           [Ralstonia solanacearum GMI1000]
          Length = 222

 Score = 36.7 bits (84), Expect = 4.8,   Method: Composition-based stats.
 Identities = 7/56 (12%), Positives = 23/56 (41%), Gaps = 3/56 (5%)

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ++  L  RE  +       E   T+  ++     S + +   + ++ +K++ + + 
Sbjct: 153 ALDRLGKRELEVLRMYVGGE---TVSEIARRLNRSVKTISAQKQKSMRKLRLATEA 205


>gi|315022352|gb|EFT35380.1| RNA polymerase, sigma-24 subunit, ECF subfamily protein [Riemerella
           anatipestifer RA-YM]
          Length = 199

 Score = 36.3 bits (83), Expect = 4.8,   Method: Composition-based stats.
 Identities = 13/97 (13%), Positives = 37/97 (38%), Gaps = 10/97 (10%)

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
            S    +++    +   +   E    +     + +++  L    + I   R  +E   ++
Sbjct: 106 ESETPTEYMEEFRNTLAKSPEELMISEEEDKEIVKAIETLEANYQEIINLRFFEE--KSI 163

Query: 256 ENLSSEFEVS----RERVRQIEARAFKKVQESIQKQV 288
           + +S    +S    + R+     RA K ++E ++  +
Sbjct: 164 KEVSDILNISVSNTKVRI----MRAKKVLKELLKNNI 196


>gi|51891983|ref|YP_074674.1| RNA polymerase ECF-type sigma factor [Symbiobacterium thermophilum
           IAM 14863]
 gi|51855672|dbj|BAD39830.1| RNA polymerase ECF-type sigma factor [Symbiobacterium thermophilum
           IAM 14863]
          Length = 208

 Score = 36.3 bits (83), Expect = 4.8,   Method: Composition-based stats.
 Identities = 18/88 (20%), Positives = 32/88 (36%), Gaps = 4/88 (4%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L     + GD+ A  +L++ H + V  IA    G     S++  E     ++A      
Sbjct: 7   ELLVERAKRGDVEAFEQLISQHEKTVYNIAYRLTGNHEDASDLAQEAF---IRAYSSLAD 63

Query: 96  ERG-FRLATYSMWWIKAAMQEYILRSWS 122
            RG    AT+    +     + + R   
Sbjct: 64  FRGDSSFATWLYRIVNNVCLDELRRRKR 91


>gi|309811963|ref|ZP_07705729.1| Sigma-70 region 2 [Dermacoccus sp. Ellin185]
 gi|308434021|gb|EFP57887.1| Sigma-70 region 2 [Dermacoccus sp. Ellin185]
          Length = 196

 Score = 36.3 bits (83), Expect = 4.9,   Method: Composition-based stats.
 Identities = 16/99 (16%), Positives = 31/99 (31%), Gaps = 9/99 (9%)

Query: 186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEA 245
           L A     D      Q   V D      V       +     L   +  L+ R++ +   
Sbjct: 100 LGAGAAKDDDAGQALQRLFVDDVHPGADV-------EAWDGELWSHVGALSERQQFVVVH 152

Query: 246 RRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           R + +   T   ++ +   S    R+  A A   ++  +
Sbjct: 153 RYVGQ--WTYPEIADKLGCSTAAARRCGADAIAALRHRL 189


>gi|332654654|ref|ZP_08420397.1| RNA polymerase sigma factor AlgU [Ruminococcaceae bacterium D16]
 gi|332516618|gb|EGJ46224.1| RNA polymerase sigma factor AlgU [Ruminococcaceae bacterium D16]
          Length = 203

 Score = 36.3 bits (83), Expect = 4.9,   Method: Composition-based stats.
 Identities = 17/84 (20%), Positives = 32/84 (38%), Gaps = 3/84 (3%)

Query: 34  EYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKF 93
           E  L  R +  GD +A  +LV  +   V  +A+   G      +   E  +   +A+  F
Sbjct: 3   EPELISRAK-AGDPAAFEQLVLDNQNRVYSLALRMLGDPEDAQDAAQEAFLNAWRALPTF 61

Query: 94  DPERGFRLATYSMWWIKAAMQEYI 117
             E     +T+       A  +++
Sbjct: 62  KGE--SSFSTWVYRLTSNACIDHL 83


>gi|302390779|ref|YP_003826600.1| Peptidase M23 [Thermosediminibacter oceani DSM 16646]
 gi|302201407|gb|ADL08977.1| Peptidase M23 [Thermosediminibacter oceani DSM 16646]
          Length = 304

 Score = 36.3 bits (83), Expect = 4.9,   Method: Composition-based stats.
 Identities = 28/123 (22%), Positives = 43/123 (34%), Gaps = 12/123 (9%)

Query: 136 FFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDK 195
           F + R LK   + ++D   K E   AI  ++   E +  SM  ++   E L+A +    K
Sbjct: 54  FLSYRELKARNEELSDKAGKYE---AIQDRIEYFEEKTRSMEEKVKKLEELDASLREMLK 110

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
           N    +  L        Q           R      +  L+         RRL+E    L
Sbjct: 111 NDPALKAQLDRKTSPPSQPAGLASRSGIDRQRALEQLEELD---------RRLEEQENNL 161

Query: 256 ENL 258
           E L
Sbjct: 162 EQL 164


>gi|229822145|ref|YP_002883671.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Beutenbergia
           cavernae DSM 12333]
 gi|229568058|gb|ACQ81909.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Beutenbergia
           cavernae DSM 12333]
          Length = 299

 Score = 36.3 bits (83), Expect = 4.9,   Method: Composition-based stats.
 Identities = 20/107 (18%), Positives = 41/107 (38%), Gaps = 2/107 (1%)

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             +  +   R+   ++L  L + S +  S    WL            + E  ++    + 
Sbjct: 58  VRDPRAYLVRITTRQALTRLRSLSRRKESYVGTWLPEPLLTAPDAAQDVELAESVSMAML 117

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
             +  L P ER +F  R + +  ++ + ++     +   VRQI  RA
Sbjct: 118 LVLETLKPTERAVFVLREVFD--LSYDEVAEAVGKTPAAVRQIAHRA 162


>gi|20806843|ref|NP_622014.1| ribokinase family sugar kinase [Thermoanaerobacter tengcongensis
           MB4]
 gi|20515311|gb|AAM23618.1| Sugar kinases, ribokinase family [Thermoanaerobacter tengcongensis
           MB4]
          Length = 365

 Score = 36.3 bits (83), Expect = 4.9,   Method: Composition-based stats.
 Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 3/36 (8%)

Query: 235 LNPRERRIFEARRLQENPV-TLENLSSEFEVSRERV 269
           L  RE+ I   R +++NP+ + E L+    +SR  V
Sbjct: 3   LTQREKEIL--RLIKKNPMISQEELAKMLGISRSAV 36


>gi|258655255|ref|YP_003204411.1| LuxR family transcriptional regulator [Nakamurella multipartita DSM
           44233]
 gi|258558480|gb|ACV81422.1| transcriptional regulator, LuxR family [Nakamurella multipartita
           DSM 44233]
          Length = 202

 Score = 36.3 bits (83), Expect = 4.9,   Method: Composition-based stats.
 Identities = 12/83 (14%), Positives = 30/83 (36%), Gaps = 2/83 (2%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
            V    G  +              +  ++  L PR+R +   R      ++   ++    
Sbjct: 119 YVPPDPGTARSAESLAMLSAEHQAVVNALGDLAPRQREVLVLRYYGG--LSEAEIAEATG 176

Query: 264 VSRERVRQIEARAFKKVQESIQK 286
           +S+  V+   +RA  K+ + ++ 
Sbjct: 177 LSKGTVKSTASRAVAKLGDIMRS 199


>gi|218263538|ref|ZP_03477619.1| hypothetical protein PRABACTJOHN_03306 [Parabacteroides johnsonii
           DSM 18315]
 gi|218222661|gb|EEC95311.1| hypothetical protein PRABACTJOHN_03306 [Parabacteroides johnsonii
           DSM 18315]
          Length = 95

 Score = 36.3 bits (83), Expect = 4.9,   Method: Composition-based stats.
 Identities = 14/73 (19%), Positives = 33/73 (45%), Gaps = 2/73 (2%)

Query: 219 EERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           +  +  + ++ R++  L  R R +F   R++      + +S E  +S   V      A K
Sbjct: 20  QSEEELQEVIRRALDTLPERCREVFIKSRIEGLKY--KEISDELGISVNTVENQMVTALK 77

Query: 279 KVQESIQKQVELS 291
           K++ +++  + L 
Sbjct: 78  KLRVALKDYLPLL 90


>gi|182414061|ref|YP_001819127.1| ECF subfamily RNA polymerase sigma-24 factor [Opitutus terrae
           PB90-1]
 gi|177841275|gb|ACB75527.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Opitutus terrae
           PB90-1]
          Length = 499

 Score = 36.3 bits (83), Expect = 4.9,   Method: Composition-based stats.
 Identities = 16/79 (20%), Positives = 32/79 (40%), Gaps = 10/79 (12%)

Query: 222 KNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS----RERVRQIEARAF 277
           +    +L  ++S L   +R    AR       +   + +    +    R RV     RA 
Sbjct: 115 EEIETVLDDALSELAEPDRSAILARYFSNQ--SFAEIGTASGRTENAARMRV----ERAL 168

Query: 278 KKVQESIQKQVELSSSPPL 296
            K++E +Q++   S++  L
Sbjct: 169 SKLREQLQRRGFDSTAAVL 187


>gi|328474115|gb|EGF44920.1| RNA polymerase sigma factor RpoE [Vibrio parahaemolyticus 10329]
          Length = 192

 Score = 36.3 bits (83), Expect = 5.0,   Method: Composition-based stats.
 Identities = 19/88 (21%), Positives = 33/88 (37%), Gaps = 3/88 (3%)

Query: 35  YVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFD 94
            VL +R + +GD  A + LVT +   V  +   Y      + +V  E  I   +A+  F 
Sbjct: 8   QVLIERVQ-NGDKQAFNLLVTKYQNKVCNLISRYVSNPGDVPDVAQEAFIKAYRAIPSFR 66

Query: 95  PERGFRLATYSMWWIKAAMQEYILRSWS 122
            E      T+         + +I+    
Sbjct: 67  GE--SAFYTWLYRIAVNTAKNHIVAQGR 92


>gi|327402666|ref|YP_004343504.1| ECF subfamily RNA polymerase sigma-24 subunit [Fluviicola taffensis
           DSM 16823]
 gi|327318174|gb|AEA42666.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Fluviicola
           taffensis DSM 16823]
          Length = 202

 Score = 36.3 bits (83), Expect = 5.0,   Method: Composition-based stats.
 Identities = 13/76 (17%), Positives = 31/76 (40%), Gaps = 2/76 (2%)

Query: 189 LINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRL 248
           L +     +++  + +  D     +   E      +   + + +S L PR R + E R  
Sbjct: 102 LTSMDTGYTNEDGEAVGIDARSDTRDPEEHIIHNQKVKHMRQLVSKLKPRYRELIEKRYF 161

Query: 249 QENPVTLENLSSEFEV 264
           +E  ++ E ++ E  +
Sbjct: 162 EE--LSYEEIAEELNL 175


>gi|312953465|ref|ZP_07772305.1| conserved hypothetical protein [Enterococcus faecalis TX0102]
 gi|310628674|gb|EFQ11957.1| conserved hypothetical protein [Enterococcus faecalis TX0102]
 gi|315152132|gb|EFT96148.1| conserved hypothetical protein [Enterococcus faecalis TX0031]
          Length = 135

 Score = 36.3 bits (83), Expect = 5.0,   Method: Composition-based stats.
 Identities = 16/89 (17%), Positives = 37/89 (41%), Gaps = 2/89 (2%)

Query: 198 SQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLEN 257
           +      V D D    + +   E     N L  S+  LN +E++    + +     T + 
Sbjct: 47  TTPYHDSVLDLDSLSILNVNHLEDYIDNNKLALSLRHLNHKEKQFIYEKYILC--KTDKE 104

Query: 258 LSSEFEVSRERVRQIEARAFKKVQESIQK 286
           ++ +F ++R+ +   + R  KK+    ++
Sbjct: 105 IAIQFNITRQGISIFKKRILKKISHYYKR 133


>gi|108802483|ref|YP_642679.1| hypothetical protein Mmcs_5523 [Mycobacterium sp. MCS]
 gi|119855311|ref|YP_935914.1| hypothetical protein Mkms_5925 [Mycobacterium sp. KMS]
 gi|108772902|gb|ABG11623.1| hypothetical protein Mmcs_5523 [Mycobacterium sp. MCS]
 gi|119698028|gb|ABL95099.1| conserved hypothetical protein [Mycobacterium sp. KMS]
          Length = 561

 Score = 36.3 bits (83), Expect = 5.0,   Method: Composition-based stats.
 Identities = 17/100 (17%), Positives = 38/100 (38%), Gaps = 11/100 (11%)

Query: 145 HLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204
            L+ +T    +    ++I  +L   +  ++S+   +         +  SD   +  ++ L
Sbjct: 425 KLRKLTLAEHRAVNRLSIDPELRFRKRPLLSLEQPVK--------VTDSDTTPTSLRE-L 475

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFE 244
           + D    +     + E  + R  + R    L PRE+ I  
Sbjct: 476 LPDRAAPDPSAAAEPEFSDPR--IVRVWWRLTPREQEILR 513


>gi|23098557|ref|NP_692023.1| putative RNA polymerase sigma factor SigI [Oceanobacillus iheyensis
           HTE831]
 gi|22776783|dbj|BAC13058.1| RNA polymerase sigma factor [Oceanobacillus iheyensis HTE831]
          Length = 242

 Score = 36.3 bits (83), Expect = 5.0,   Method: Composition-based stats.
 Identities = 19/143 (13%), Positives = 52/143 (36%), Gaps = 11/143 (7%)

Query: 43  EHGDLSAAHRLVTSHLRLVVK----IAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG 98
           + G+    + L+ ++   + K    +   Y        +  S G     +A+  + P +G
Sbjct: 19  QQGNKFLQNELLRTYQPFIAKCVSEVCKRYIDPKRD--DEFSIGLSAFNEAIFSYVPNKG 76

Query: 99  FRLATYSMWWIKAAMQEYIL-RSWSLVKIG----TTANQKRLFFNLRRLKGHLQAITDNN 153
               +++   IK  + +YI  +      +         Q      +  ++   Q   D  
Sbjct: 77  SSFLSFAKLVIKRKVIDYIRYQQKRTASLSLDETYDEEQMENSLEIAAVQEKYQMEIDAQ 136

Query: 154 LKPEQVVAIAKKLNVSESEVISM 176
            + E+++   +KL + +  ++ +
Sbjct: 137 NRKEEILEFKEKLKLYKLSLVEL 159


>gi|325917898|ref|ZP_08180071.1| RNA polymerase sigma factor, sigma-70 family [Xanthomonas
           vesicatoria ATCC 35937]
 gi|325535878|gb|EGD07701.1| RNA polymerase sigma factor, sigma-70 family [Xanthomonas
           vesicatoria ATCC 35937]
          Length = 197

 Score = 36.3 bits (83), Expect = 5.0,   Method: Composition-based stats.
 Identities = 13/68 (19%), Positives = 25/68 (36%), Gaps = 6/68 (8%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
              +     +V DH        ++E     R+ L + M  L+P +R + E      +   
Sbjct: 100 DGEAIDDTAMVEDHAPSADDNDDREL----RDWLDKGMERLSPDQRLVIELVYGVGHK-- 153

Query: 255 LENLSSEF 262
           LE ++   
Sbjct: 154 LEEVAEIM 161


>gi|297626399|ref|YP_003688162.1| hypothetical protein PFREUD_12110 [Propionibacterium freudenreichii
           subsp. shermanii CIRM-BIA1]
 gi|296922164|emb|CBL56732.1| Hypothetical protein PFREUD_12110 [Propionibacterium freudenreichii
           subsp. shermanii CIRM-BIA1]
          Length = 477

 Score = 36.3 bits (83), Expect = 5.0,   Method: Composition-based stats.
 Identities = 13/36 (36%), Positives = 19/36 (52%)

Query: 253 VTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
            TL        VSRER+RQ+ AR    +Q  ++ Q+
Sbjct: 45  ATLNQAGDLLGVSRERIRQVMARITPALQGMLRAQL 80


>gi|284041957|ref|YP_003392297.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Conexibacter
           woesei DSM 14684]
 gi|283946178|gb|ADB48922.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Conexibacter
           woesei DSM 14684]
          Length = 290

 Score = 36.3 bits (83), Expect = 5.0,   Method: Composition-based stats.
 Identities = 23/107 (21%), Positives = 42/107 (39%), Gaps = 2/107 (1%)

Query: 170 ESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLT 229
             +  +   R    ++LN L   + +      +WL         V  + E  ++    + 
Sbjct: 46  VHDPRAYLVRTVTRQALNRLRTLARRREEYVGEWLPEPLLTSPDVADDVELAESVSIAML 105

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
             +  L P ER +F  R + + P   + +++  E S   VRQI  RA
Sbjct: 106 TVLETLGPAERAVFVLREVFDAPY--DEIAAALEKSPAAVRQIAHRA 150


>gi|261403776|ref|YP_003248000.1| DNA binding protein, Tfx family [Methanocaldococcus vulcanius M7]
 gi|261370769|gb|ACX73518.1| DNA binding protein, Tfx family [Methanocaldococcus vulcanius M7]
          Length = 137

 Score = 36.3 bits (83), Expect = 5.0,   Method: Composition-based stats.
 Identities = 12/52 (23%), Positives = 25/52 (48%), Gaps = 7/52 (13%)

Query: 235 LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           L   + ++ + R   +  +T E ++     SR  +  IE RA    +E+++K
Sbjct: 7   LTETQIKVLKLR---KKGLTQEEIAKILGTSRANISMIEKRA----RENVKK 51


>gi|256420934|ref|YP_003121587.1| LuxR family transcriptional regulator [Chitinophaga pinensis DSM
           2588]
 gi|256035842|gb|ACU59386.1| transcriptional regulator, LuxR family [Chitinophaga pinensis DSM
           2588]
          Length = 199

 Score = 36.3 bits (83), Expect = 5.0,   Method: Composition-based stats.
 Identities = 19/83 (22%), Positives = 39/83 (46%), Gaps = 4/83 (4%)

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
           +   L+   D Q   + E  + K R   +  +++ L  R + IF   R+     T+E ++
Sbjct: 96  YLQQLIEHFDVQPGGIAELVDSKTRTQDVFETINHLPERMKEIFMLSRV--EHQTVEQIA 153

Query: 260 SEFEVSRERVR-QIEARAFKKVQ 281
               +S++ V+ QI  +A K ++
Sbjct: 154 VRLGLSQQTVKNQI-TKALKILR 175


>gi|269128451|ref|YP_003301821.1| ECF subfamily RNA polymerase sigma-24 subunit [Thermomonospora
           curvata DSM 43183]
 gi|268313409|gb|ACY99783.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Thermomonospora
           curvata DSM 43183]
          Length = 200

 Score = 36.3 bits (83), Expect = 5.1,   Method: Composition-based stats.
 Identities = 16/91 (17%), Positives = 38/91 (41%), Gaps = 6/91 (6%)

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
            ++       D  G E+ ++   E +  R++LTR    L   +R +   R +    ++ E
Sbjct: 113 PTEDLPDGPDDRPGPEETVVRYSEAERARDLLTR----LPEHQRELVLLRVVAG--LSAE 166

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
              +   ++   VR  + RA  +++    ++
Sbjct: 167 ETGNVLGMTAGAVRVAQHRALARLRAMASEE 197


>gi|240170468|ref|ZP_04749127.1| alternative RNA polymerase sigma factor [Mycobacterium kansasii
           ATCC 12478]
          Length = 204

 Score = 36.3 bits (83), Expect = 5.1,   Method: Composition-based stats.
 Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 5/74 (6%)

Query: 219 EERKNRRNMLTR---SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEAR 275
           E+R   R ++ +   ++  L PR+R++   R L       E  S   E+S E  R +  R
Sbjct: 132 EDRTVARELVEQVRAALDTLPPRQRQLIILRDLVGTSA--EEASEILELSAEAQRALLYR 189

Query: 276 AFKKVQESIQKQVE 289
           A   ++  ++K+ +
Sbjct: 190 ARANLRNELEKRYQ 203


>gi|296128422|ref|YP_003635672.1| transcriptional regulator, DeoR family [Cellulomonas flavigena DSM
           20109]
 gi|296020237|gb|ADG73473.1| transcriptional regulator, DeoR family [Cellulomonas flavigena DSM
           20109]
          Length = 322

 Score = 36.3 bits (83), Expect = 5.1,   Method: Composition-based stats.
 Identities = 10/43 (23%), Positives = 18/43 (41%), Gaps = 5/43 (11%)

Query: 237 PRERRIFE---ARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
            RE+ +        LQ+  +  E ++     SR  V ++  RA
Sbjct: 4   EREQDVMRAATMYYLQDLKM--EVIARHLGTSRSTVSRLLRRA 44


>gi|229179704|ref|ZP_04307053.1| RNA polymerase sigma-I factor [Bacillus cereus 172560W]
 gi|228603726|gb|EEK61198.1| RNA polymerase sigma-I factor [Bacillus cereus 172560W]
          Length = 235

 Score = 36.3 bits (83), Expect = 5.1,   Method: Composition-based stats.
 Identities = 15/124 (12%), Positives = 43/124 (34%), Gaps = 1/124 (0%)

Query: 44  HGDLSAAHRLVTSHLRLVV-KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
             +       +  +   +   I+   R Y     +  S G     +A++K+   +G    
Sbjct: 17  QNNEEDKEAFIVQYQPFIRKSISSVCRRYITEQDDEYSIGLFAFNEAIEKYSYTKGKSFL 76

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
            ++   IK  + +YI +      +    +++     ++          +N+ + E+++  
Sbjct: 77  AFADLLIKRDVIDYIRKESKHNFVFLKEDEQEEMLEMQVSLTEYMKEMENSNRKEEILHF 136

Query: 163 AKKL 166
              L
Sbjct: 137 QSVL 140


>gi|206968967|ref|ZP_03229922.1| RNA polymerase sigma-I factor [Bacillus cereus AH1134]
 gi|206736008|gb|EDZ53166.1| RNA polymerase sigma-I factor [Bacillus cereus AH1134]
          Length = 239

 Score = 36.3 bits (83), Expect = 5.1,   Method: Composition-based stats.
 Identities = 15/124 (12%), Positives = 43/124 (34%), Gaps = 1/124 (0%)

Query: 44  HGDLSAAHRLVTSHLRLVV-KIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
             +       +  +   +   I+   R Y     +  S G     +A++K+   +G    
Sbjct: 21  QNNEEDKEAFIVQYQPFIRKSISSVCRRYITEQDDEYSIGLFAFNEAIEKYSYTKGKSFL 80

Query: 103 TYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAI 162
            ++   IK  + +YI +      +    +++     ++          +N+ + E+++  
Sbjct: 81  AFADLLIKRDVIDYIRKESKHNFVFLKEDEQEEMLEMQVSLTEYMKEMENSNRKEEILHF 140

Query: 163 AKKL 166
              L
Sbjct: 141 QSVL 144


>gi|194208508|ref|XP_001503490.2| PREDICTED: ankyrin 2, neuronal [Equus caballus]
          Length = 4012

 Score = 36.3 bits (83), Expect = 5.1,   Method: Composition-based stats.
 Identities = 21/123 (17%), Positives = 45/123 (36%), Gaps = 7/123 (5%)

Query: 157  EQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLI 216
            E++   A KL    ++       ++ DES +AL  S  +N    +       D  +   I
Sbjct: 3476 EEISDEASKLVDRLTQSEREQELVSDDESSSALEVSVIENLPPVETEHSIPEDIFDTRPI 3535

Query: 217  EKEERKNRRNML------TRSMSVLNPRERRIFEARRLQEN-PVTLENLSSEFEVSRERV 269
              E  +     +        +    + +ER       + ++   +   L+ E + + E++
Sbjct: 3536 WDESIETLIERIPDENGHDHAEDQQDEQERTEERLAYIADHLGFSWTELARELDFTEEQI 3595

Query: 270  RQI 272
             QI
Sbjct: 3596 HQI 3598


>gi|168698180|ref|ZP_02730457.1| hypothetical protein GobsU_01572 [Gemmata obscuriglobus UQM 2246]
          Length = 1240

 Score = 36.3 bits (83), Expect = 5.1,   Method: Composition-based stats.
 Identities = 16/99 (16%), Positives = 29/99 (29%), Gaps = 5/99 (5%)

Query: 31  KQEEY---VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
             +E     L  R+    D +A   +V  H   V+  A    G      +V     + L+
Sbjct: 16  ADDERPDAELLDRFCRGRDPAAFEAIVRKHGPRVLSAARHVLGASPDAEDVFQAAFLALV 75

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKI 126
           + V +    R   L  +               +    +I
Sbjct: 76  REVDRIR--RQPALGGWLYSVAHRLALRTRADAARRERI 112


>gi|146295514|ref|YP_001179285.1| ECF subfamily RNA polymerase sigma-24 factor [Caldicellulosiruptor
           saccharolyticus DSM 8903]
 gi|145409090|gb|ABP66094.1| RNA polymerase, sigma-24 subunit, ECF subfamily
           [Caldicellulosiruptor saccharolyticus DSM 8903]
          Length = 180

 Score = 36.3 bits (83), Expect = 5.1,   Method: Composition-based stats.
 Identities = 14/79 (17%), Positives = 32/79 (40%), Gaps = 2/79 (2%)

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
              ++   K  ++ L +++S L   ++ +   R        L  ++     S   +R + 
Sbjct: 104 TPEDEVFDKIEKDTLKKALSKLTKDQQEVVILRYGANMK--LNEIAKMKNKSDVAIRALL 161

Query: 274 ARAFKKVQESIQKQVELSS 292
            RA   ++E + K+V  S 
Sbjct: 162 FRAIHSLKEMLLKEVHESE 180


>gi|83592774|ref|YP_426526.1| sigma-24 (FecI) [Rhodospirillum rubrum ATCC 11170]
 gi|83575688|gb|ABC22239.1| Sigma-24 (FecI) [Rhodospirillum rubrum ATCC 11170]
          Length = 173

 Score = 36.3 bits (83), Expect = 5.1,   Method: Composition-based stats.
 Identities = 19/116 (16%), Positives = 51/116 (43%), Gaps = 2/116 (1%)

Query: 169 SESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNML 228
               V +   R+A + +++ L     +     ++ L+ D    E  +      +    +L
Sbjct: 53  MPDNVRAYLYRMAANLAIDHLRRDGARARGLCEETLLEDIPSAEPAVDRVVAARQELAIL 112

Query: 229 TRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284
           +R+++ L  + R +F   R +   +T++ +++   +S + V +  ARA    ++ +
Sbjct: 113 SRAVAELPEKCRIVFLLYRGRG--LTMKQVAARLGISEKAVEKHIARAMVHCRKRM 166


>gi|328880482|emb|CCA53721.1| hypothetical protein SVEN_0434 [Streptomyces venezuelae ATCC 10712]
          Length = 485

 Score = 36.3 bits (83), Expect = 5.1,   Method: Composition-based stats.
 Identities = 19/79 (24%), Positives = 29/79 (36%), Gaps = 6/79 (7%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GD  A   LV ++L LV  I            ++V E    +++A+      R      
Sbjct: 17  AGDAEARDALVRAYLPLVHNIVGRALDGHADTDDIVQET---MVRALDGLTGLRDPD--R 71

Query: 104 YSMWWIKAAMQEYILRSWS 122
           +  W +  AM   I R W 
Sbjct: 72  FRSWLVAIAMN-GIRRRWR 89


>gi|327539142|gb|EGF25772.1| ECF subfamily RNA polymerase sigma-70 factor [Rhodopirellula
           baltica WH47]
          Length = 173

 Score = 36.3 bits (83), Expect = 5.1,   Method: Composition-based stats.
 Identities = 13/96 (13%), Positives = 31/96 (32%), Gaps = 2/96 (2%)

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
              D      +  ++   +          L   M  L  R R     R +   P     +
Sbjct: 79  HLSDSPELLDESWQRWAGKDLTGNETVEALRECMESLTERARDALAMRFVHNTPRV--KI 136

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQVELSSSP 294
                +S    R +  RA  ++++ +++++   + P
Sbjct: 137 GENLGISDHGARNLMQRAKAQLRDCVEEKLRAITQP 172


>gi|298250628|ref|ZP_06974432.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ktedonobacter
           racemifer DSM 44963]
 gi|297548632|gb|EFH82499.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Ktedonobacter
           racemifer DSM 44963]
          Length = 179

 Score = 36.3 bits (83), Expect = 5.1,   Method: Composition-based stats.
 Identities = 17/73 (23%), Positives = 28/73 (38%), Gaps = 2/73 (2%)

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
            EQ   +   R+     L   M  L   +R I + R   E  ++   ++     S   VR
Sbjct: 99  DEQQPEQVALRREEYAQLYTHMRELPEPQREILQLRFGHE--LSYGEIAQIVSKSEAAVR 156

Query: 271 QIEARAFKKVQES 283
            I  RA K ++ +
Sbjct: 157 MILHRALKVLRGA 169


>gi|295092138|emb|CBK78245.1| Sigma-70, region 4. [Clostridium cf. saccharolyticum K10]
          Length = 153

 Score = 36.3 bits (83), Expect = 5.1,   Method: Composition-based stats.
 Identities = 19/99 (19%), Positives = 42/99 (42%), Gaps = 7/99 (7%)

Query: 190 INSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTR---SMSVLNPRERRIFEAR 246
             S D +       + +     E  L+EKE +     +L R   ++S L P + R   AR
Sbjct: 49  FYSLDCDDGIENAAIGWAQPSPEDYLMEKEAQAEYAELLRRLYEALSSLPPTQARRVHAR 108

Query: 247 RLQENPVTLENLSSEFEVSRERV-RQIEARAFKKVQESI 284
            +    V  +++++   ++  +  + I A A ++++   
Sbjct: 109 YMLGMKV--KDIAAMEGITPSQAGKSIHA-ALRRLRRYF 144


>gi|271961699|ref|YP_003335895.1| ECF subfamily RNA polymerase sigma-24 subunit [Streptosporangium
           roseum DSM 43021]
 gi|270504874|gb|ACZ83152.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Streptosporangium
           roseum DSM 43021]
          Length = 170

 Score = 36.3 bits (83), Expect = 5.1,   Method: Composition-based stats.
 Identities = 13/69 (18%), Positives = 29/69 (42%), Gaps = 2/69 (2%)

Query: 214 VLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIE 273
            L +     + R  + R+++ L  R+R +   R  ++ P     ++     S   VR   
Sbjct: 87  ALADGTHGTDLRIDMRRALARLTARQRAVLVLRYYEDLPE--AEVAGILGCSVGTVRSTA 144

Query: 274 ARAFKKVQE 282
            R+  +++E
Sbjct: 145 HRSLARLRE 153


>gi|146307695|ref|YP_001188160.1| RNA polymerase sigma factor [Pseudomonas mendocina ymp]
 gi|145575896|gb|ABP85428.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Pseudomonas
           mendocina ymp]
          Length = 174

 Score = 36.3 bits (83), Expect = 5.1,   Method: Composition-based stats.
 Identities = 19/111 (17%), Positives = 42/111 (37%), Gaps = 4/111 (3%)

Query: 168 VSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNM 227
            S  E  ++   +A    ++    S+ + +  + + L    +  +    E+     + + 
Sbjct: 57  HSPREPRALLTTIARGLLIDQFRRSALERA--YLEELALAPEALQPSPEEQALALEQLSE 114

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK 278
           + R +  L+ + R  F   RL         ++    VS  RVRQ  A+  +
Sbjct: 115 IDRLLGHLSSKARAAFLYNRLDGLGH--AEIAERLGVSPSRVRQYLAQGLR 163


>gi|104783711|ref|YP_610209.1| ECF subfamily RNA polymerase sigma factor [Pseudomonas entomophila
           L48]
 gi|95112698|emb|CAK17426.1| putative RNA polymerase sigma-70 factor, ECF subfamily [Pseudomonas
           entomophila L48]
          Length = 167

 Score = 36.3 bits (83), Expect = 5.1,   Method: Composition-based stats.
 Identities = 11/53 (20%), Positives = 21/53 (39%), Gaps = 2/53 (3%)

Query: 213 QVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
             L E+  R+     L   +  L  R +++F   RL    +T   ++    +S
Sbjct: 94  PALDEQAAREQHLRRLQAILGELPERTQQVFRLNRL--EGMTHAEVARHLGIS 144


>gi|229169256|ref|ZP_04296968.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           AH621]
 gi|228614197|gb|EEK71310.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacillus cereus
           AH621]
          Length = 181

 Score = 36.3 bits (83), Expect = 5.1,   Method: Composition-based stats.
 Identities = 14/55 (25%), Positives = 33/55 (60%), Gaps = 4/55 (7%)

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV-RQIEARAFKKVQESI 284
            +  LN  +++IF  R L E   +++ ++ EF ++R+ V  ++ +R  KK+++ +
Sbjct: 124 LIKELNEEDKKIFIKRYLDE--YSVQEIALEFGMTRDTVYSRL-SRGRKKLKKML 175


>gi|254518266|ref|ZP_05130322.1| RNA polymerase [Clostridium sp. 7_2_43FAA]
 gi|226912015|gb|EEH97216.1| RNA polymerase [Clostridium sp. 7_2_43FAA]
          Length = 173

 Score = 36.3 bits (83), Expect = 5.1,   Method: Composition-based stats.
 Identities = 14/84 (16%), Positives = 31/84 (36%), Gaps = 11/84 (13%)

Query: 206 YDHDGQEQVLIEKEERK-NRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           Y+    E +  E    +   +  L   +  LN  ++ +   R   +   T E +S   E+
Sbjct: 87  YEEVNLENMTAENAFNESENKIYLKSLIENLNDNQKEVIRLRYYLD--YTYEEISEIMEI 144

Query: 265 S----RERVRQIEARAFKKVQESI 284
                + R+     +   K+++ I
Sbjct: 145 PLGTVKSRI----NKGINKIRKII 164


>gi|226315185|ref|YP_002775081.1| RNA polymerase ECF-type sigma factor [Brevibacillus brevis NBRC
           100599]
 gi|226098135|dbj|BAH46577.1| RNA polymerase ECF-type sigma factor [Brevibacillus brevis NBRC
           100599]
          Length = 190

 Score = 36.3 bits (83), Expect = 5.1,   Method: Composition-based stats.
 Identities = 22/115 (19%), Positives = 43/115 (37%), Gaps = 1/115 (0%)

Query: 33  EEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKK 92
           +E+ L  + +E G+  A  +LV  +L +  + A           + V EG I   Q + +
Sbjct: 2   DEWELIAKCQE-GEPEAFEQLVKPYLAMAYRTAYLIIHDKHLAQDAVQEGLIEAYQHIDR 60

Query: 93  FDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQ 147
            DP+RG     +    I       + +    V+      ++ L      ++   Q
Sbjct: 61  LDPKRGVAFRNWLYRIITFRALNLVRKQKPAVEYEEMIPEEALTPLDNVIQREEQ 115


>gi|154493787|ref|ZP_02033107.1| hypothetical protein PARMER_03130 [Parabacteroides merdae ATCC
           43184]
 gi|154086400|gb|EDN85445.1| hypothetical protein PARMER_03130 [Parabacteroides merdae ATCC
           43184]
          Length = 191

 Score = 36.3 bits (83), Expect = 5.1,   Method: Composition-based stats.
 Identities = 21/112 (18%), Positives = 48/112 (42%), Gaps = 2/112 (1%)

Query: 175 SMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSV 234
           SM   +A +  ++      ++   +       D    +   +EK    +  + L  +   
Sbjct: 73  SMLFTIAKNHVIDVFRQQINRPDFEDYIRFCEDEHLLDNTSVEKIYYDDFIDKLAIAKQK 132

Query: 235 LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           L P +R IFE  R  E  ++   +++  ++S + V+   + A K ++E ++K
Sbjct: 133 LTPAQRNIFEMSR--EEGMSNAEIAALSDISEQTVKNHLSAALKILREELRK 182


>gi|119026382|ref|YP_910227.1| putative transcriptional regulator [Bifidobacterium adolescentis
           ATCC 15703]
 gi|118765966|dbj|BAF40145.1| putative transcriptional regulator [Bifidobacterium adolescentis
           ATCC 15703]
          Length = 164

 Score = 36.3 bits (83), Expect = 5.1,   Method: Composition-based stats.
 Identities = 9/23 (39%), Positives = 13/23 (56%)

Query: 252 PVTLENLSSEFEVSRERVRQIEA 274
            +T E L+ E  VS+  + QIE 
Sbjct: 35  GMTQEQLADEMGVSQSYISQIEN 57


>gi|331270955|ref|YP_004385666.1| putative botulinum neurotoxin regulator protein [Clostridium
           botulinum BKT015925]
 gi|329127347|gb|AEB77291.1| probable botulinum neurotoxin regulator protein [Clostridium
           botulinum BKT015925]
          Length = 179

 Score = 36.3 bits (83), Expect = 5.2,   Method: Composition-based stats.
 Identities = 11/51 (21%), Positives = 26/51 (50%), Gaps = 2/51 (3%)

Query: 230 RSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV 280
             +S+LN +ER+I   +  +        ++    +SR+ + +I  ++ KK+
Sbjct: 121 DLISILNYKERQIIYMKFFECRKDN--EIARRLHLSRQSIYKIRIKSLKKL 169


>gi|302187213|ref|ZP_07263886.1| RNA polymerase sigma factor [Pseudomonas syringae pv. syringae 642]
          Length = 172

 Score = 36.3 bits (83), Expect = 5.2,   Method: Composition-based stats.
 Identities = 16/75 (21%), Positives = 29/75 (38%), Gaps = 2/75 (2%)

Query: 204 LVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE 263
           L+   + ++    E+         + R +  L+ + R  F   RL         ++    
Sbjct: 89  LMQVPEAEQPSPEEQMLILEDLKAIDRMLGTLSSKARAAFLYSRLDAMGH--AEIAERLG 146

Query: 264 VSRERVRQIEARAFK 278
           VS  RVRQ  A+A +
Sbjct: 147 VSVSRVRQYLAQAMR 161


>gi|255009740|ref|ZP_05281866.1| putative RNA polymerase ECF-type sigma factor [Bacteroides fragilis
           3_1_12]
 gi|313147527|ref|ZP_07809720.1| RNA polymerase ECF-type sigma factor [Bacteroides fragilis 3_1_12]
 gi|313136294|gb|EFR53654.1| RNA polymerase ECF-type sigma factor [Bacteroides fragilis 3_1_12]
          Length = 195

 Score = 36.3 bits (83), Expect = 5.2,   Method: Composition-based stats.
 Identities = 16/93 (17%), Positives = 41/93 (44%), Gaps = 2/93 (2%)

Query: 199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENL 258
           +    +    +  +   ++  E K+ R  L  ++  L P+++RI   R   E  ++ + +
Sbjct: 96  EKHYEMAQKDEEADDGFLKDFEDKDFREHLRAAIGKLPPQKQRI--CRLKIEKGLSNQEI 153

Query: 259 SSEFEVSRERVRQIEARAFKKVQESIQKQVELS 291
           + E  ++   V+    +A K ++  I+  + L 
Sbjct: 154 ADEMHITVPTVKSHYTQAIKILRAEIESLIVLL 186


>gi|210612008|ref|ZP_03289124.1| hypothetical protein CLONEX_01323 [Clostridium nexile DSM 1787]
 gi|210151766|gb|EEA82773.1| hypothetical protein CLONEX_01323 [Clostridium nexile DSM 1787]
          Length = 115

 Score = 36.3 bits (83), Expect = 5.2,   Method: Composition-based stats.
 Identities = 10/59 (16%), Positives = 27/59 (45%), Gaps = 4/59 (6%)

Query: 228 LTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV-RQIEARAFKKVQESIQ 285
           L  +++ L  + +        Q   +T + +  +   +R  + R I+  A K+++E ++
Sbjct: 55  LAAALAELPQQTQEEIFLYYFQH--LTQKEIGEQSGWTRSTIGRHIQL-ALKRLKEEME 110


>gi|150007944|ref|YP_001302687.1| RNA polymerase ECF-type sigma factor [Parabacteroides distasonis
           ATCC 8503]
 gi|255013368|ref|ZP_05285494.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 2_1_7]
 gi|262381494|ref|ZP_06074632.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 2_1_33B]
 gi|298376710|ref|ZP_06986665.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacteroides sp.
           3_1_19]
 gi|149936368|gb|ABR43065.1| RNA polymerase ECF-type sigma factor [Parabacteroides distasonis
           ATCC 8503]
 gi|262296671|gb|EEY84601.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 2_1_33B]
 gi|298266588|gb|EFI08246.1| RNA polymerase sigma-70 factor, ECF subfamily [Bacteroides sp.
           3_1_19]
          Length = 179

 Score = 36.3 bits (83), Expect = 5.2,   Method: Composition-based stats.
 Identities = 15/83 (18%), Positives = 39/83 (46%), Gaps = 8/83 (9%)

Query: 206 YDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
            + + +     ++ E K  ++++ R++  L  R  RIF   R +        ++S   +S
Sbjct: 99  ENPESESYTPQDQLEYKELQSLVNRALGKLPERRLRIFRMHRFEGMKY--AEIASSLSLS 156

Query: 266 RERVRQIEA---RAFKKVQESIQ 285
              ++ +EA   +A + +++ I+
Sbjct: 157 ---IKTVEAEMTKALQTLRKEIE 176


>gi|111223538|ref|YP_714332.1| ECF sub family sigma-70 factor [Frankia alni ACN14a]
 gi|111151070|emb|CAJ62779.1| putative ECF sub-family Sigma-70 factor [Frankia alni ACN14a]
          Length = 171

 Score = 36.3 bits (83), Expect = 5.2,   Method: Composition-based stats.
 Identities = 9/34 (26%), Positives = 14/34 (41%), Gaps = 2/34 (5%)

Query: 232 MSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
           ++ L  R  RI   R L     TL   + E  ++
Sbjct: 116 LAALPDRYARILRLRFL--EACTLREAADELGIT 147


>gi|331084582|ref|ZP_08333680.1| hypothetical protein HMPREF0992_02604 [Lachnospiraceae bacterium
           6_1_63FAA]
 gi|330400652|gb|EGG80259.1| hypothetical protein HMPREF0992_02604 [Lachnospiraceae bacterium
           6_1_63FAA]
          Length = 917

 Score = 36.3 bits (83), Expect = 5.2,   Method: Composition-based stats.
 Identities = 18/48 (37%), Positives = 25/48 (52%), Gaps = 8/48 (16%)

Query: 236 NPRERRIFEARRLQENPVTLENL-----SSEFEVSRERVRQIEARAFK 278
           N RE  +F  RR +    TL+ +       E  ++RERVRQ+E   FK
Sbjct: 252 NKREFNVF-LRRAKGE--TLQEIAENPQGDEEPITRERVRQLERSCFK 296


>gi|323343682|ref|ZP_08083909.1| RNA polymerase sigma-70 factor [Prevotella oralis ATCC 33269]
 gi|323095501|gb|EFZ38075.1| RNA polymerase sigma-70 factor [Prevotella oralis ATCC 33269]
          Length = 172

 Score = 36.3 bits (83), Expect = 5.2,   Method: Composition-based stats.
 Identities = 14/83 (16%), Positives = 40/83 (48%), Gaps = 2/83 (2%)

Query: 210 GQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERV 269
             +  + E+ E++     +   ++ L  ++R I   R +++   + + ++++  +    +
Sbjct: 89  AADSNISERLEQREDAAKIMNIIARLPEQQRLIITLRDIED--RSYDEIAAQTGLQAVNI 146

Query: 270 RQIEARAFKKVQESIQKQVELSS 292
           R + +RA K+++E   KQ E   
Sbjct: 147 RVLLSRARKQIREQFNKQTEYER 169


>gi|313207377|ref|YP_004046554.1| RNA polymerase, sigma-24 subunit, ecf subfamily [Riemerella
           anatipestifer DSM 15868]
 gi|312446693|gb|ADQ83048.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Riemerella
           anatipestifer DSM 15868]
 gi|315023272|gb|EFT36282.1| RNA polymerase ECF-type sigma factor [Riemerella anatipestifer
           RA-YM]
 gi|325335167|gb|ADZ11441.1| putative RNA polymerase sigma factor [Riemerella anatipestifer
           RA-GD]
          Length = 164

 Score = 36.3 bits (83), Expect = 5.2,   Method: Composition-based stats.
 Identities = 9/75 (12%), Positives = 32/75 (42%), Gaps = 13/75 (17%)

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA- 276
           + E++ +  +L + +  L   ER I        + ++ + ++    ++       E  A 
Sbjct: 97  QHEQRQQVELLYKVIKKLPEVERAIVMMYL---DELSYKEIAETLGIT-------EVNAR 146

Query: 277 --FKKVQESIQKQVE 289
               +++++++  +E
Sbjct: 147 VKMNRLKKTLKTLME 161


>gi|307331079|ref|ZP_07610208.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Streptomyces
           violaceusniger Tu 4113]
 gi|306883290|gb|EFN14347.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Streptomyces
           violaceusniger Tu 4113]
          Length = 203

 Score = 36.3 bits (83), Expect = 5.2,   Method: Composition-based stats.
 Identities = 12/91 (13%), Positives = 30/91 (32%), Gaps = 2/91 (2%)

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
            S+      + +         E+    +      + ++ L   +R +   R      +T 
Sbjct: 115 GSTAVPSDEMPEQPDDSLGPEERALLSSDAEWAKKLLANLPEHQRELVLLRVAVG--LTA 172

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E       +S   VR  + RA  +++   ++
Sbjct: 173 EETGQMLGMSPGAVRVAQHRALSRLRALAEQ 203


>gi|256841084|ref|ZP_05546591.1| RNA polymerase ECF-type sigma factor [Parabacteroides sp. D13]
 gi|256736927|gb|EEU50254.1| RNA polymerase ECF-type sigma factor [Parabacteroides sp. D13]
          Length = 215

 Score = 36.3 bits (83), Expect = 5.2,   Method: Composition-based stats.
 Identities = 10/91 (10%), Positives = 33/91 (36%), Gaps = 10/91 (10%)

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
                 +      +   ++ ++  E   R  +L ++++ L+P +R I     +       
Sbjct: 110 EDISLYEDTFQTDELFSRISLDTTEADERVKLLMKALTKLSPHQREIIYLYYVNGLGH-- 167

Query: 256 ENLSSEFEV----SRERVRQIEARAFKKVQE 282
           + ++    +    S+     + +R   K++ 
Sbjct: 168 DEIAEILGINYQSSK----NLLSRTLSKLRR 194


>gi|297543657|ref|YP_003675959.1| FliA/WhiG subfamily RNA polymerase sigma-28 subunit
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
 gi|296841432|gb|ADH59948.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Thermoanaerobacter mathranii subsp. mathranii str. A3]
          Length = 218

 Score = 36.3 bits (83), Expect = 5.2,   Method: Composition-based stats.
 Identities = 16/107 (14%), Positives = 41/107 (38%), Gaps = 4/107 (3%)

Query: 38  AKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPIS--EVVSEGNIGLMQAVKKFDP 95
           A+ Y    D S   +L+  +   ++K    +    +     + +S G I   +A+  FD 
Sbjct: 5   ARVYAAKKDPSEREKLIQEYTPFIIKQLSSFTNRYIDERNSDELSIGLIAFNEAIDSFDN 64

Query: 96  ERGFRLATYSMWWIKAAMQEYIL-RSWSLVKIGTTANQKRLFFNLRR 141
            +G    ++S   I+  + +++     + + +     +   +    R
Sbjct: 65  TKGS-FLSFSSMLIRRRLIDFLRQNQQNTIPLELYVEKVTDYEAENR 110


>gi|239626863|ref|ZP_04669894.1| RNA polymerase [Clostridiales bacterium 1_7_47_FAA]
 gi|239517009|gb|EEQ56875.1| RNA polymerase [Clostridiales bacterium 1_7_47FAA]
          Length = 162

 Score = 36.3 bits (83), Expect = 5.2,   Method: Composition-based stats.
 Identities = 22/87 (25%), Positives = 39/87 (44%), Gaps = 5/87 (5%)

Query: 200 WQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLS 259
             D+L+ D     +  I K+ERK     L R++ +L   ER +   R   E  ++   + 
Sbjct: 79  LADYLIDDSAPDGETSILKQERKME---LYRAIHLLPELEREVVLYRITGE--LSFREIG 133

Query: 260 SEFEVSRERVRQIEARAFKKVQESIQK 286
                S    R +  RA +K++E ++K
Sbjct: 134 EILGRSENWGRTVFYRAKQKIREELKK 160


>gi|291303556|ref|YP_003514834.1| ECF subfamily RNA polymerase sigma-24 subunit [Stackebrandtia
           nassauensis DSM 44728]
 gi|290572776|gb|ADD45741.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Stackebrandtia
           nassauensis DSM 44728]
          Length = 170

 Score = 36.3 bits (83), Expect = 5.2,   Method: Composition-based stats.
 Identities = 16/91 (17%), Positives = 32/91 (35%), Gaps = 14/91 (15%)

Query: 208 HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV--- 264
               E    +     + R  L  ++  L PR+R +   R  ++  VT    +        
Sbjct: 84  ETPVETAFADSTHDVDLRLSLRAALFQLAPRQRAVIVLRYFEDRSVTQT--AEILGCAEG 141

Query: 265 ---SRERVRQIEARAFKKVQESIQKQVELSS 292
              ++        RA  K++  +   VEL++
Sbjct: 142 TVKTQA------FRALNKLRSVLPDLVELTN 166


>gi|226943182|ref|YP_002798255.1| FecI family ECF sigma factor [Azotobacter vinelandii DJ]
 gi|226718109|gb|ACO77280.1| ECF sigma factor, FecI family [Azotobacter vinelandii DJ]
          Length = 194

 Score = 36.3 bits (83), Expect = 5.2,   Method: Composition-based stats.
 Identities = 18/94 (19%), Positives = 38/94 (40%), Gaps = 2/94 (2%)

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           D L  +HDG    L    +  +   ++  ++  L  R R IF   R+  +  T   ++  
Sbjct: 98  DSLGPEHDGATASLETALQAGDELRLVEAALRGLPERTRHIFLLNRI--HGRTYGEIARA 155

Query: 262 FEVSRERVRQIEARAFKKVQESIQKQVELSSSPP 295
             +S+  V +   RA    + +++   +   + P
Sbjct: 156 MGLSQSAVEKHMMRALDTCKAALEATPDSRGATP 189


>gi|332883231|gb|EGK03514.1| hypothetical protein HMPREF9456_01581 [Dysgonomonas mossii DSM
           22836]
          Length = 191

 Score = 36.3 bits (83), Expect = 5.3,   Method: Composition-based stats.
 Identities = 20/81 (24%), Positives = 40/81 (49%), Gaps = 4/81 (4%)

Query: 207 DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSR 266
           D       + E    K     +T +++ L PR R +FE  R +   ++ + ++ E  +S 
Sbjct: 97  DEPVGHNEVYEGIVEKELNYKITMAIAQLPPRCREVFELSRFEM--MSYKEIAQELAISP 154

Query: 267 ERVR-QIEARAFKKVQESIQK 286
             V  QI A+A K ++E++++
Sbjct: 155 NTVENQI-AKALKILRENLKE 174


>gi|300022341|ref|YP_003754952.1| LuxR family transcriptional regulator [Hyphomicrobium denitrificans
           ATCC 51888]
 gi|299524162|gb|ADJ22631.1| two component transcriptional regulator, LuxR family
           [Hyphomicrobium denitrificans ATCC 51888]
          Length = 215

 Score = 36.3 bits (83), Expect = 5.3,   Method: Composition-based stats.
 Identities = 8/35 (22%), Positives = 17/35 (48%), Gaps = 3/35 (8%)

Query: 231 SMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
           ++  L+PRE  I     + +   T + ++  F +S
Sbjct: 146 ALETLSPREFEILRM--ILDEKTT-DEIAQAFNLS 177


>gi|220675498|emb|CAX11912.1| spectrin repeat containing, nuclear envelope 1 [Homo sapiens]
 gi|220675589|emb|CAI40730.2| spectrin repeat containing, nuclear envelope 1 [Homo sapiens]
 gi|220732274|emb|CAI42287.2| spectrin repeat containing, nuclear envelope 1 [Homo sapiens]
 gi|220732302|emb|CAX15071.1| spectrin repeat containing, nuclear envelope 1 [Homo sapiens]
 gi|220732319|emb|CAI42787.2| spectrin repeat containing, nuclear envelope 1 [Homo sapiens]
 gi|220732389|emb|CAX14996.1| spectrin repeat containing, nuclear envelope 1 [Homo sapiens]
 gi|220738481|emb|CAX14977.1| spectrin repeat containing, nuclear envelope 1 [Homo sapiens]
 gi|220800504|emb|CAX14914.1| spectrin repeat containing, nuclear envelope 1 [Homo sapiens]
          Length = 8749

 Score = 36.3 bits (83), Expect = 5.3,   Method: Composition-based stats.
 Identities = 26/120 (21%), Positives = 49/120 (40%), Gaps = 5/120 (4%)

Query: 117  ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
            + RSW  +K   +  Q+ L+  L R + +  ++   + K E   AI  KL+ S     S 
Sbjct: 5869 LQRSWETLKNVISEKQRTLYEALERQQKYQDSLQSISTKME---AIELKLSESPEPGRSP 5925

Query: 177  NCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSV 234
              ++A  ++L   I       ++ Q  L  +   +  E    E+   ++   +L   MS 
Sbjct: 5926 ESQMAEHQALMDEILMLQDEINELQSSLAEELVSESCEADPAEQLALQSTLTVLAERMST 5985


>gi|119568122|gb|EAW47737.1| spectrin repeat containing, nuclear envelope 1, isoform CRA_k [Homo
            sapiens]
          Length = 8779

 Score = 36.3 bits (83), Expect = 5.3,   Method: Composition-based stats.
 Identities = 26/120 (21%), Positives = 49/120 (40%), Gaps = 5/120 (4%)

Query: 117  ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
            + RSW  +K   +  Q+ L+  L R + +  ++   + K E   AI  KL+ S     S 
Sbjct: 5885 LQRSWETLKNVISEKQRTLYEALERQQKYQDSLQSISTKME---AIELKLSESPEPGRSP 5941

Query: 177  NCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSV 234
              ++A  ++L   I       ++ Q  L  +   +  E    E+   ++   +L   MS 
Sbjct: 5942 ESQMAEHQALMDEILMLQDEINELQSSLAEELVSESCEADPAEQLALQSTLTVLAERMST 6001


>gi|34849883|tpg|DAA01060.1| TPA_exp: spectrin-like protein of the nuclear envelope and Golgi
            [Homo sapiens]
          Length = 8407

 Score = 36.3 bits (83), Expect = 5.3,   Method: Composition-based stats.
 Identities = 26/120 (21%), Positives = 49/120 (40%), Gaps = 5/120 (4%)

Query: 117  ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
            + RSW  +K   +  Q+ L+  L R + +  ++   + K E   AI  KL+ S     S 
Sbjct: 5550 LQRSWETLKNVISEKQRTLYEALERQQKYQDSLQSISTKME---AIELKLSESPEPGRSP 5606

Query: 177  NCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSV 234
              ++A  ++L   I       ++ Q  L  +   +  E    E+   ++   +L   MS 
Sbjct: 5607 ESQMAEHQALMDEILMLQDEINELQSSLAEELVSESCEADPAEQLALQSTLTVLAERMST 5666


>gi|120599808|ref|YP_964382.1| RNA polymerase sigma factor RpoE [Shewanella sp. W3-18-1]
 gi|146292256|ref|YP_001182680.1| RNA polymerase sigma factor RpoE [Shewanella putrefaciens CN-32]
 gi|120559901|gb|ABM25828.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Shewanella sp.
           W3-18-1]
 gi|145563946|gb|ABP74881.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Shewanella
           putrefaciens CN-32]
 gi|319425555|gb|ADV53629.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Shewanella
           putrefaciens 200]
          Length = 192

 Score = 36.3 bits (83), Expect = 5.3,   Method: Composition-based stats.
 Identities = 15/80 (18%), Positives = 30/80 (37%), Gaps = 2/80 (2%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD +A + LV  +   V+ +   Y      +++V  E  I   +A+  F  E      
Sbjct: 15  QRGDKNAFNLLVLKYQSKVISLISRYVRNQADVADVAQEAFIKAYRALPNFRGE--SAFY 72

Query: 103 TYSMWWIKAAMQEYILRSWS 122
           T+         + Y++    
Sbjct: 73  TWLYRIAVNTAKNYLVSQGR 92


>gi|325849743|ref|ZP_08170890.1| RNA polymerase sigma factor, sigma-70 family [Anaerococcus
           hydrogenalis ACS-025-V-Sch4]
 gi|325479972|gb|EGC83052.1| RNA polymerase sigma factor, sigma-70 family [Anaerococcus
           hydrogenalis ACS-025-V-Sch4]
          Length = 136

 Score = 36.3 bits (83), Expect = 5.3,   Method: Composition-based stats.
 Identities = 23/93 (24%), Positives = 44/93 (47%), Gaps = 14/93 (15%)

Query: 203 WLVYDHDGQEQVLIEKEER--------KNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
           +  YD DG  +  +E  E         K     + R++S LNP ER + E+   +E   T
Sbjct: 46  FCSYDRDGNFEENLENLEFDVEKIIETKEMIEEVRRAISKLNPVERDLIESLFYKEE--T 103

Query: 255 LENLSSEFEVSRERV--RQIEARAFKKVQESIQ 285
           +  ++S+  +S   V  R+   +  +K++E ++
Sbjct: 104 IREVASKLNISHPAVIKRR--NKVLEKLKEMLE 134


>gi|302207199|gb|ADL11541.1| ECF family sigma factor M [Corynebacterium pseudotuberculosis C231]
          Length = 222

 Score = 36.3 bits (83), Expect = 5.3,   Method: Composition-based stats.
 Identities = 11/76 (14%), Positives = 32/76 (42%), Gaps = 2/76 (2%)

Query: 44  HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLAT 103
            GD  A + +   H R +  +A  +        +++ E  +  +++++++  +    L T
Sbjct: 51  EGDNQAFNEIAKRHYRSLWWLARRHSYCDSDADDIMQEAMLKAVRSLERYRGD--SSLNT 108

Query: 104 YSMWWIKAAMQEYILR 119
           +    +     ++I R
Sbjct: 109 WLYRIVFNTAYDHIYR 124


>gi|295704098|ref|YP_003597173.1| RNA polymerase ECF-type sigma factor family protein [Bacillus
           megaterium DSM 319]
 gi|294801757|gb|ADF38823.1| RNA polymerase ECF-type sigma factor family protein [Bacillus
           megaterium DSM 319]
          Length = 188

 Score = 36.3 bits (83), Expect = 5.3,   Method: Composition-based stats.
 Identities = 20/97 (20%), Positives = 46/97 (47%), Gaps = 14/97 (14%)

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
           S +  D++  DH   ++ L  KEE++  R+    ++S L+  +++I ++   +   +T +
Sbjct: 97  SEEIFDFIEDDHPQIDEQLQWKEEQQRVRH----AVSKLSEDQKKIIQSVYFKG--LTQQ 150

Query: 257 NLSSE----FEVSRERVRQIEARAFKKVQESIQKQVE 289
            ++ E        + RVR     A +K++  +    E
Sbjct: 151 KVAEEQQIPLGTVKGRVRL----ALRKLKTYLGTDAE 183


>gi|296125672|ref|YP_003632924.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily [Brachyspira
           murdochii DSM 12563]
 gi|296017488|gb|ADG70725.1| putative RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Brachyspira murdochii DSM 12563]
          Length = 125

 Score = 36.3 bits (83), Expect = 5.3,   Method: Composition-based stats.
 Identities = 17/88 (19%), Positives = 37/88 (42%), Gaps = 7/88 (7%)

Query: 185 SLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSM-SVLNPRERRIF 243
           SL     +SD+  S+       D D    +L      ++  + ++  + ++L P++++I 
Sbjct: 25  SLGTRKVNSDRTDSRETVLTNDDLDN---ILYSNALTESEYSRVSNLIIAILTPKQKKIM 81

Query: 244 EARRLQENPVTLENLSSEFEVSRERVRQ 271
           +         T E L+    V++  V Q
Sbjct: 82  KLF---SEGRTQEELAVMLNVTQSAVSQ 106


>gi|170782794|ref|YP_001711128.1| hypothetical protein CMS_2471 [Clavibacter michiganensis subsp.
           sepedonicus]
 gi|169157364|emb|CAQ02551.1| hypothetical protein CMS2471 [Clavibacter michiganensis subsp.
           sepedonicus]
          Length = 463

 Score = 36.3 bits (83), Expect = 5.3,   Method: Composition-based stats.
 Identities = 12/62 (19%), Positives = 27/62 (43%), Gaps = 14/62 (22%)

Query: 245 ARRLQENPVTLENLSSEFEVSRERVRQIEARA-------------FKKVQESIQKQVELS 291
            R  +E+ +TL+ +     V+RE +R+   RA              ++++   +K   ++
Sbjct: 17  LRLYREDLLTLDEVGLVEGVTREAIRR-RLRALGISPRSLGETLDLRRLRAVSEKATAMT 75

Query: 292 SS 293
            S
Sbjct: 76  ES 77


>gi|23097308|ref|NP_149062.1| nesprin-1 isoform 2 [Homo sapiens]
 gi|22597198|gb|AAN03486.1| enaptin [Homo sapiens]
          Length = 8749

 Score = 36.3 bits (83), Expect = 5.3,   Method: Composition-based stats.
 Identities = 26/120 (21%), Positives = 49/120 (40%), Gaps = 5/120 (4%)

Query: 117  ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
            + RSW  +K   +  Q+ L+  L R + +  ++   + K E   AI  KL+ S     S 
Sbjct: 5869 LQRSWETLKNVISEKQRTLYEALERQQKYQDSLQSISTKME---AIELKLSESPEPGRSP 5925

Query: 177  NCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSV 234
              ++A  ++L   I       ++ Q  L  +   +  E    E+   ++   +L   MS 
Sbjct: 5926 ESQMAEHQALMDEILMLQDEINELQSSLAEELVSESCEADPAEQLALQSTLTVLAERMST 5985


>gi|325280380|ref|YP_004252922.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Odoribacter
           splanchnicus DSM 20712]
 gi|324312189|gb|ADY32742.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Odoribacter
           splanchnicus DSM 20712]
          Length = 166

 Score = 36.3 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 17/85 (20%), Positives = 35/85 (41%), Gaps = 5/85 (5%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARR-LQENPVTLENLSSEFE 263
           + + + +E  +      +    ML  ++  L  +  RI        EN      +S   +
Sbjct: 85  LENPESEEPQIFNLFIEEETNQMLLTAIGQLPEQSARIIRLALSGLENK----EISRLLD 140

Query: 264 VSRERVRQIEARAFKKVQESIQKQV 288
           VS   V+ ++  A +K++E  QK+ 
Sbjct: 141 VSVNTVKTLKYSAIRKLREHFQKKA 165


>gi|313677404|ref|YP_004055400.1| RNA polymerase, sigma-24 subunit, ecf subfamily [Marivirga
           tractuosa DSM 4126]
 gi|312944102|gb|ADR23292.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Marivirga
           tractuosa DSM 4126]
          Length = 181

 Score = 36.3 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 12/71 (16%), Positives = 27/71 (38%), Gaps = 14/71 (19%)

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV------SRERVRQIE 273
           E+      L + +  L+   R + +    +    T   +S EF++      +R R     
Sbjct: 118 EQSIDSIGLEKVLDKLSDELRFVIDQMYFKG--YTQTEISEEFDIPLGTVKTRAR----- 170

Query: 274 ARAFKKVQESI 284
             A + ++E +
Sbjct: 171 -TAMRTLRELL 180


>gi|283769176|ref|ZP_06342080.1| RNA polymerase sigma factor, sigma-70 family [Bulleidia extructa
           W1219]
 gi|283104152|gb|EFC05531.1| RNA polymerase sigma factor, sigma-70 family [Bulleidia extructa
           W1219]
          Length = 137

 Score = 36.3 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 15/94 (15%), Positives = 47/94 (50%), Gaps = 6/94 (6%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
            +   + D ++ +    E+++    E K +   L ++++ L   ER + EA   +E   +
Sbjct: 50  DHDGHFVDNIIDEKIDLEKIV----EVKMQIEELNKALATLTKEERELMEAIFYREE--S 103

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
           L ++  + +VS + + +   +  +K+++ ++ ++
Sbjct: 104 LRSIGKKEKVSYQTIGKRRDKILEKLRKILEDKI 137


>gi|228909093|ref|ZP_04072922.1| Prophage LambdaBa01, positive control factor Xpf [Bacillus
           thuringiensis IBL 200]
 gi|228850601|gb|EEM95426.1| Prophage LambdaBa01, positive control factor Xpf [Bacillus
           thuringiensis IBL 200]
          Length = 135

 Score = 36.3 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 13/64 (20%), Positives = 29/64 (45%), Gaps = 2/64 (3%)

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARA 276
           E    +  +  L  ++S+L  RE+ ++   R     +T   ++    ++   V+ +  RA
Sbjct: 61  EHAIGEWDKIRLEDALSLLTEREKEVYLMSRGYC--LTYREIARYLNITCSTVQSMIERA 118

Query: 277 FKKV 280
            KK+
Sbjct: 119 EKKI 122


>gi|296138633|ref|YP_003645876.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Tsukamurella
           paurometabola DSM 20162]
 gi|296026767|gb|ADG77537.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Tsukamurella
           paurometabola DSM 20162]
          Length = 190

 Score = 36.3 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 18/96 (18%), Positives = 36/96 (37%), Gaps = 7/96 (7%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
              S+  +    D   +   L  +  R+  R      +  L  ++R I   R +    ++
Sbjct: 102 DPVSEMPERASLDSGPEVTALESEANRRMNR-----LLGTLPEKQREILILRVVVG--LS 154

Query: 255 LENLSSEFEVSRERVRQIEARAFKKVQESIQKQVEL 290
            E  +     +   VR  + RA  K++  I K+ E+
Sbjct: 155 AEETAEAVGGTAGAVRVAQHRALAKLKNQIAKEGEM 190


>gi|262194840|ref|YP_003266049.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Haliangium
           ochraceum DSM 14365]
 gi|262078187|gb|ACY14156.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Haliangium
           ochraceum DSM 14365]
          Length = 161

 Score = 36.3 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 28/151 (18%), Positives = 57/151 (37%), Gaps = 16/151 (10%)

Query: 142 LKGHLQAITDNNLKPEQVVAIAKKLNVSESE-----VISMNCRLAGDESLNALINSSDKN 196
           ++   Q + D     + +  +  KL V E +       S+  R+A +  LN +   + + 
Sbjct: 17  MRRCRQLLGDEEAARDAMQDVFVKLLVREQQLDDRAPSSLLYRIATNHCLNQIRTRARRP 76

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
            S   + L      +    ++   R   R  L R     +   R I        + +TLE
Sbjct: 77  ESPEAELLE-----RIAHAVDAVSRSRARLSLARLFRDQSESTRTIAVLH--LHDGMTLE 129

Query: 257 NLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287
            ++ E  +S   VR    +  +K++  ++ Q
Sbjct: 130 EVAGEVGLSVSGVR----KRLRKLRAHLEAQ 156


>gi|168700422|ref|ZP_02732699.1| WD-40 repeat [Gemmata obscuriglobus UQM 2246]
          Length = 940

 Score = 36.3 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 23/136 (16%), Positives = 39/136 (28%), Gaps = 6/136 (4%)

Query: 36  VLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDP 95
            L +R+    D  A   L   H R+V+ +A           +V     + L +  K    
Sbjct: 24  DLVERFALSRDGDAFAELTRRHGRMVLAVARRAVQDQHLADDVAQAAFLVLAR--KAHAL 81

Query: 96  ERGFRLATYSMWWIKAAMQEYILRSWS----LVKIGTTANQKRLFFNLRRLKGHLQAITD 151
            R  RLA +     +   +   +         V +               L   L    D
Sbjct: 82  SRPDRLAGWLFGVTRRIARRAAVHQRREAEQTVPLTAGIAAPERLPMGGDLPQMLDEELD 141

Query: 152 NNLKPEQVVAIAKKLN 167
              + E+V  +   L 
Sbjct: 142 RLPEGERVPLVLCYLE 157


>gi|119568116|gb|EAW47731.1| spectrin repeat containing, nuclear envelope 1, isoform CRA_e [Homo
            sapiens]
          Length = 8749

 Score = 36.3 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 26/120 (21%), Positives = 49/120 (40%), Gaps = 5/120 (4%)

Query: 117  ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
            + RSW  +K   +  Q+ L+  L R + +  ++   + K E   AI  KL+ S     S 
Sbjct: 5869 LQRSWETLKNVISEKQRTLYEALERQQKYQDSLQSISTKME---AIELKLSESPEPGRSP 5925

Query: 177  NCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSV 234
              ++A  ++L   I       ++ Q  L  +   +  E    E+   ++   +L   MS 
Sbjct: 5926 ESQMAEHQALMDEILMLQDEINELQSSLAEELVSESCEADPAEQLALQSTLTVLAERMST 5985


>gi|78047274|ref|YP_363449.1| RNA polymerase ECF-type sigma factor [Xanthomonas campestris pv.
           vesicatoria str. 85-10]
 gi|294625176|ref|ZP_06703819.1| RNA polymerase ECF-type sigma factor [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 11122]
 gi|78035704|emb|CAJ23395.1| RNA polymerase ECF-type sigma factor [Xanthomonas campestris pv.
           vesicatoria str. 85-10]
 gi|292600548|gb|EFF44642.1| RNA polymerase ECF-type sigma factor [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 11122]
          Length = 197

 Score = 36.3 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 14/68 (20%), Positives = 25/68 (36%), Gaps = 6/68 (8%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
              +     LV DH        ++E     R+ L + M  L+P +R + E      +   
Sbjct: 100 DGEAIDDTALVEDHAPSADDNDDREL----RDWLDKGMERLSPDQRLVVELVYGVGHK-- 153

Query: 255 LENLSSEF 262
           LE ++   
Sbjct: 154 LEEVADIM 161


>gi|38503404|sp|Q57637|Y173_METJA RecName: Full=Putative transcriptional regulatory protein MJ0173
          Length = 137

 Score = 36.3 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 10/49 (20%), Positives = 24/49 (48%), Gaps = 3/49 (6%)

Query: 235 LNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQES 283
           L   + ++ + R   +  +T E ++     SR  +  IE RA + ++++
Sbjct: 7   LTDTQIKVLKLR---KKGLTQEEIAKMLGTSRANISMIEKRAKENIKKA 52


>gi|109899460|ref|YP_662715.1| RNA polymerase sigma factor RpoE [Pseudoalteromonas atlantica T6c]
 gi|332305555|ref|YP_004433406.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Glaciecola
           agarilytica 4H-3-7+YE-5]
 gi|109701741|gb|ABG41661.1| RNA polymerase, sigma-24 subunit, RpoE [Pseudoalteromonas atlantica
           T6c]
 gi|332172884|gb|AEE22138.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Glaciecola
           agarilytica 4H-3-7+YE-5]
          Length = 192

 Score = 36.3 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 14/80 (17%), Positives = 28/80 (35%), Gaps = 2/80 (2%)

Query: 43  EHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLA 102
           + GD  A   LV  +   V  +   Y      +++V  E  I   +A+  F  +      
Sbjct: 15  QRGDKDAFGLLVVKYQHKVSYLVSRYVKNSGDVADVAQEAFIKAYRALPNFRGD--SAFY 72

Query: 103 TYSMWWIKAAMQEYILRSWS 122
           T+       + + Y++    
Sbjct: 73  TWLYRIAVNSAKNYLVSQGR 92


>gi|116494375|ref|YP_806109.1| ComX [Lactobacillus casei ATCC 334]
 gi|116104525|gb|ABJ69667.1| ComX [Lactobacillus casei ATCC 334]
          Length = 182

 Score = 36.3 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 23/146 (15%), Positives = 49/146 (33%), Gaps = 4/146 (2%)

Query: 49  AAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWW 108
           A  +L   +  LV+ +   Y        + + E  I +++A+ ++D   G +   Y    
Sbjct: 18  AFSQLFKQYRPLVLTVLRPYHLRDFSHEDWLQEARIAMLKAITRYDGSSGSQFGPY-YRM 76

Query: 109 IKAAMQEYILRSWSLVKIGTTANQKRLFF---NLRRLKGHLQAITDNNLKPEQVVAIAKK 165
           +  +    +LR     K    A    +        + +  L++  D      +      +
Sbjct: 77  VLQSHLRSVLRKHFAHKRRIDAAAIPVEDSALESLQERLALRSYEDGLFMRIEFAQFLAR 136

Query: 166 LNVSESEVISMNCRLAGDESLNALIN 191
           L+  E E          D S + L+ 
Sbjct: 137 LSPLEYEAFEAAVISQTDSSEDPLLQ 162


>gi|26988160|ref|NP_743585.1| RNA polymerase sigma factor AlgU [Pseudomonas putida KT2440]
 gi|148549500|ref|YP_001269602.1| RNA polymerase sigma factor AlgU [Pseudomonas putida F1]
 gi|167035373|ref|YP_001670604.1| RNA polymerase sigma factor AlgU [Pseudomonas putida GB-1]
 gi|170720253|ref|YP_001747941.1| RNA polymerase sigma factor AlgU [Pseudomonas putida W619]
 gi|325275450|ref|ZP_08141381.1| RNA polymerase sigma factor AlgU [Pseudomonas sp. TJI-51]
 gi|24982893|gb|AAN67049.1|AE016333_10 RNA polymerase sigma-H factor AlgT [Pseudomonas putida KT2440]
 gi|148513558|gb|ABQ80418.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Pseudomonas putida
           F1]
 gi|166861861|gb|ABZ00269.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Pseudomonas putida
           GB-1]
 gi|169758256|gb|ACA71572.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Pseudomonas putida
           W619]
 gi|313500345|gb|ADR61711.1| AlgU [Pseudomonas putida BIRD-1]
 gi|324099426|gb|EGB97341.1| RNA polymerase sigma factor AlgU [Pseudomonas sp. TJI-51]
          Length = 193

 Score = 36.3 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 17/95 (17%), Positives = 36/95 (37%), Gaps = 3/95 (3%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           ML ++E+  L +R +  GD  A   LV  +   ++ + + +        +V  E  I   
Sbjct: 1   MLTQEEDQQLVERVQ-RGDRRAFDLLVLKYQHKILGLIVRFVHDTHEAQDVAQEAFIKAY 59

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           +A+  F  +      T+         + Y++    
Sbjct: 60  RALGNFRGD--SAFYTWLYRIAINTAKNYLVSRGR 92


>gi|332665293|ref|YP_004448081.1| ECF subfamily RNA polymerase sigma-24 subunit [Haliscomenobacter
           hydrossis DSM 1100]
 gi|332334107|gb|AEE51208.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Haliscomenobacter
           hydrossis DSM 1100]
          Length = 183

 Score = 36.3 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 9/46 (19%), Positives = 23/46 (50%), Gaps = 2/46 (4%)

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
           +    +  L +++  L  R++ +F  R  +E  ++ E++S    +S
Sbjct: 119 DGDEAQIRLQQALQTLPERQKEVFNLRYYEE--MSYEDMSKLLNIS 162


>gi|331659914|ref|ZP_08360852.1| sigma-70, region 4 superfamily [Escherichia coli TA206]
 gi|315300129|gb|EFU59367.1| sigma-70, region 4 [Escherichia coli MS 16-3]
 gi|331053129|gb|EGI25162.1| sigma-70, region 4 superfamily [Escherichia coli TA206]
          Length = 168

 Score = 36.3 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 10/56 (17%), Positives = 25/56 (44%), Gaps = 6/56 (10%)

Query: 224 RRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRE----RVRQIEAR 275
            +  ++ +++ LN  E  I        +  ++  +S    +S+E    RV +I+ +
Sbjct: 90  NKESVSEAINSLNNIEMEILYLFYF--HGKSVREISKMTNLSKEKIYYRVSRIKVK 143


>gi|313898041|ref|ZP_07831580.1| conserved hypothetical protein [Clostridium sp. HGF2]
 gi|312957069|gb|EFR38698.1| conserved hypothetical protein [Clostridium sp. HGF2]
          Length = 172

 Score = 36.3 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 20/116 (17%), Positives = 43/116 (37%), Gaps = 17/116 (14%)

Query: 178 CRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNP 237
            +     SL+  ++  + N   W D +  +     +VL + E      N L   ++ L+P
Sbjct: 69  AKAGDQLSLDNTVSDGEGNEKSWLDDIPDESAAIAEVLEDAELL----NALYAKLNELDP 124

Query: 238 RERRIFEARRLQENPVTLENLSSEFEVSR-----ERVRQIEARAFKKVQESIQKQV 288
             R I +   L     +  +   E  +SR      R      +  +K++  ++  +
Sbjct: 125 EGRLICQ---LIMEGKSERDCGKEMGLSRNTFVYRR-----DKLLQKLRSDLKDYI 172


>gi|312887393|ref|ZP_07746993.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Mucilaginibacter
           paludis DSM 18603]
 gi|311300121|gb|EFQ77190.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Mucilaginibacter
           paludis DSM 18603]
          Length = 199

 Score = 36.3 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 11/69 (15%), Positives = 27/69 (39%), Gaps = 2/69 (2%)

Query: 197 SSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLE 256
             + Q+ +V           E    K  R +L +++  L P+ + +F   ++     + E
Sbjct: 95  DRRLQEHIVATFAESYSHTEEDIYLKESRELLDKAIDQLTPQRKEVFTLCKI--EGRSYE 152

Query: 257 NLSSEFEVS 265
            ++    +S
Sbjct: 153 EVAQLLGIS 161


>gi|326778554|ref|ZP_08237819.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Streptomyces cf.
           griseus XylebKG-1]
 gi|326658887|gb|EGE43733.1| RNA polymerase, sigma-24 subunit, ECF subfamily [Streptomyces cf.
           griseus XylebKG-1]
          Length = 223

 Score = 36.3 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 12/76 (15%), Positives = 35/76 (46%), Gaps = 2/76 (2%)

Query: 211 QEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVR 270
            +  + +  E++  R +L   + +L P++R +   R      ++ E  ++   +S   V+
Sbjct: 88  PDASVDDGSEQRADRALLMDVLGILAPKQRSVVVLR--HWEQMSTEETAAALGMSAGTVK 145

Query: 271 QIEARAFKKVQESIQK 286
               RA  ++++ ++ 
Sbjct: 146 STLHRALARLRQELES 161


>gi|291286472|ref|YP_003503288.1| hypothetical protein Dacet_0534 [Denitrovibrio acetiphilus DSM
           12809]
 gi|290883632|gb|ADD67332.1| hypothetical protein Dacet_0534 [Denitrovibrio acetiphilus DSM
           12809]
          Length = 791

 Score = 36.3 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 11/66 (16%), Positives = 26/66 (39%), Gaps = 2/66 (3%)

Query: 217 EKEERKNRRNMLTRSMSVLNPRERRIFE--ARRLQENPVTLENLSSEFEVSRERVRQIEA 274
           E E R+    ++   + +L  RE  + +          ++    +     +R+ V  I+ 
Sbjct: 676 EPENRRLNEEIIKTLLGILTVREEEVLDYVLGFTGRGKLSQSEAAELMGTTRDNVAVIQK 735

Query: 275 RAFKKV 280
           +A  K+
Sbjct: 736 KAVDKI 741


>gi|192359235|ref|YP_001982354.1| PsbS [Cellvibrio japonicus Ueda107]
 gi|190685400|gb|ACE83078.1| PsbS [Cellvibrio japonicus Ueda107]
          Length = 206

 Score = 36.3 bits (83), Expect = 5.4,   Method: Composition-based stats.
 Identities = 16/64 (25%), Positives = 25/64 (39%), Gaps = 2/64 (3%)

Query: 202 DWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSE 261
           D    D +  E    +  E +     L+  +S L  R R  FE  R+   P   + ++ E
Sbjct: 126 DAEEDDINPYEISPQKIYEDQRLLEQLSTLLSELPDRTRYAFERHRIFGIP--QKEIAEE 183

Query: 262 FEVS 265
             VS
Sbjct: 184 LGVS 187


>gi|323485905|ref|ZP_08091240.1| hypothetical protein HMPREF9474_02991 [Clostridium symbiosum
           WAL-14163]
 gi|323400893|gb|EGA93256.1| hypothetical protein HMPREF9474_02991 [Clostridium symbiosum
           WAL-14163]
          Length = 184

 Score = 36.3 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 4/60 (6%)

Query: 208 HDGQEQVLIEKEERKNRRN--MLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS 265
               E+V+++K    +      L  ++  LN RER+IF AR L+E     E L  +F +S
Sbjct: 102 EPSSEEVVLDKLPLMDVIENGALLEALQKLNERERQIFLARTLEEED--FETLGLKFGLS 159


>gi|293606814|ref|ZP_06689165.1| sigma-70 family RNA polymerase sigma factor [Achromobacter
           piechaudii ATCC 43553]
 gi|292814818|gb|EFF73948.1| sigma-70 family RNA polymerase sigma factor [Achromobacter
           piechaudii ATCC 43553]
          Length = 166

 Score = 36.3 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 15/74 (20%), Positives = 30/74 (40%), Gaps = 3/74 (4%)

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
           + +   D    +H        +    +   + LTR++  L P+ R ++   RL+    T 
Sbjct: 75  DITSLDDMPGGEHPATPPA-DDGVRFQQLADELTRALQDLPPKCRHVYLRCRLEGWTHT- 132

Query: 256 ENLSSEFEVSRERV 269
             ++ E  +SR  V
Sbjct: 133 -EIAQEMGLSRSMV 145


>gi|294664679|ref|ZP_06730013.1| RNA polymerase ECF-type sigma factor [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 10535]
 gi|292605563|gb|EFF48880.1| RNA polymerase ECF-type sigma factor [Xanthomonas fuscans subsp.
           aurantifolii str. ICPB 10535]
          Length = 197

 Score = 36.3 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 14/68 (20%), Positives = 25/68 (36%), Gaps = 6/68 (8%)

Query: 195 KNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVT 254
              +     LV DH        ++E     R+ L + M  L+P +R + E      +   
Sbjct: 100 DGEAIDDTALVEDHAPSADDNDDREL----RDWLDKGMERLSPDQRLVVELVYGVGHK-- 153

Query: 255 LENLSSEF 262
           LE ++   
Sbjct: 154 LEEVADIM 161


>gi|220675499|emb|CAX11913.1| spectrin repeat containing, nuclear envelope 1 [Homo sapiens]
 gi|220675590|emb|CAX11977.1| spectrin repeat containing, nuclear envelope 1 [Homo sapiens]
 gi|220732275|emb|CAX15014.1| spectrin repeat containing, nuclear envelope 1 [Homo sapiens]
 gi|220732303|emb|CAX15072.1| spectrin repeat containing, nuclear envelope 1 [Homo sapiens]
 gi|220732320|emb|CAX15221.1| spectrin repeat containing, nuclear envelope 1 [Homo sapiens]
 gi|220732390|emb|CAX14997.1| spectrin repeat containing, nuclear envelope 1 [Homo sapiens]
 gi|220738482|emb|CAX14978.1| spectrin repeat containing, nuclear envelope 1 [Homo sapiens]
 gi|220800505|emb|CAX14915.1| spectrin repeat containing, nuclear envelope 1 [Homo sapiens]
          Length = 8797

 Score = 36.3 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 26/120 (21%), Positives = 49/120 (40%), Gaps = 5/120 (4%)

Query: 117  ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
            + RSW  +K   +  Q+ L+  L R + +  ++   + K E   AI  KL+ S     S 
Sbjct: 5940 LQRSWETLKNVISEKQRTLYEALERQQKYQDSLQSISTKME---AIELKLSESPEPGRSP 5996

Query: 177  NCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSV 234
              ++A  ++L   I       ++ Q  L  +   +  E    E+   ++   +L   MS 
Sbjct: 5997 ESQMAEHQALMDEILMLQDEINELQSSLAEELVSESCEADPAEQLALQSTLTVLAERMST 6056


>gi|166368164|ref|YP_001660437.1| hypothetical protein MAE_54230 [Microcystis aeruginosa NIES-843]
 gi|166090537|dbj|BAG05245.1| unknown protein [Microcystis aeruginosa NIES-843]
          Length = 162

 Score = 36.3 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 8/22 (36%), Positives = 15/22 (68%)

Query: 251 NPVTLENLSSEFEVSRERVRQI 272
             ++ + +  ++ +SRERVRQI
Sbjct: 121 QGLSYQQIGDKYGISRERVRQI 142


>gi|160936654|ref|ZP_02084021.1| hypothetical protein CLOBOL_01545 [Clostridium bolteae ATCC
           BAA-613]
 gi|158440445|gb|EDP18190.1| hypothetical protein CLOBOL_01545 [Clostridium bolteae ATCC
           BAA-613]
          Length = 140

 Score = 36.3 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 10/102 (9%), Positives = 35/102 (34%), Gaps = 2/102 (1%)

Query: 187 NALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEAR 246
             L    D  +                  ++    +   ++L  ++  L+ ++R +    
Sbjct: 41  ETLFCDMDDYTVNLFSSEDTYPSHFHTFEMDGFTVRIENSLLAEALEHLDEKKRDVILRY 100

Query: 247 RLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQV 288
                  T   +S   EV+R  +++      + +++ ++++ 
Sbjct: 101 YFLGFDDT--EISKILEVNRSTIQRRRHAGLEFIKKFMEEEA 140


>gi|126736235|ref|ZP_01751978.1| RpoE [Roseobacter sp. CCS2]
 gi|126714401|gb|EBA11269.1| RpoE [Roseobacter sp. CCS2]
          Length = 218

 Score = 36.3 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 10/81 (12%), Positives = 32/81 (39%), Gaps = 10/81 (12%)

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS--- 265
              E    +    +     L ++++ L   +R++ E     E   +   +++E  +    
Sbjct: 144 PEAEPDQADAIGLQQETEQLGQALATLPEEQRKLIERAYFGELSHS--QIAAETGLPLGT 201

Query: 266 -RERVRQIEARAFKKVQESIQ 285
            + R+R     A  +++ +++
Sbjct: 202 IKSRIRL----ALDRLRHAMK 218


>gi|104783269|ref|YP_609767.1| RNA polymerase sigma factor AlgU [Pseudomonas entomophila L48]
 gi|95112256|emb|CAK16983.1| sigma factor AlgU [Pseudomonas entomophila L48]
          Length = 193

 Score = 36.3 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 17/95 (17%), Positives = 36/95 (37%), Gaps = 3/95 (3%)

Query: 28  MLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLM 87
           ML ++E+  L +R +  GD  A   LV  +   ++ + + +        +V  E  I   
Sbjct: 1   MLTQEEDQQLVERVQ-RGDRRAFDLLVLKYQHKILGLIVRFVHDTHEAQDVAQEAFIKAY 59

Query: 88  QAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWS 122
           +A+  F  +      T+         + Y++    
Sbjct: 60  RALGNFRGD--SAFYTWLYRIAINTAKNYLVSRGR 92


>gi|256841630|ref|ZP_05547136.1| RNA polymerase ECF-type sigma factor [Parabacteroides sp. D13]
 gi|262383969|ref|ZP_06077105.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 2_1_33B]
 gi|256736524|gb|EEU49852.1| RNA polymerase ECF-type sigma factor [Parabacteroides sp. D13]
 gi|262294867|gb|EEY82799.1| RNA polymerase ECF-type sigma factor [Bacteroides sp. 2_1_33B]
          Length = 190

 Score = 36.3 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 20/84 (23%), Positives = 42/84 (50%), Gaps = 2/84 (2%)

Query: 209 DGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRER 268
           DG+E  +  K   +   + L  +   L PR+R +FE    +E  +T+  ++++  +S + 
Sbjct: 104 DGEETAIERKLSFEEFNHRLEIAKQKLTPRQRELFEL--NKEQGITITEIAAKALISEQS 161

Query: 269 VRQIEARAFKKVQESIQKQVELSS 292
           VR   ++A   +++ + K   L S
Sbjct: 162 VRNQLSQALHVLRKELGKYALLFS 185


>gi|238567425|ref|XP_002386238.1| hypothetical protein MPER_15593 [Moniliophthora perniciosa FA553]
 gi|215437600|gb|EEB87168.1| hypothetical protein MPER_15593 [Moniliophthora perniciosa FA553]
          Length = 82

 Score = 36.3 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 19/69 (27%), Positives = 30/69 (43%), Gaps = 3/69 (4%)

Query: 151 DNNLKPEQVVAIAKKLNVSESEVISMNCRL-AGDESLNALINSSDKNSSQWQDWLVYDHD 209
            N L   +V  +A++LNV   +V+ M  R+  GD +L     S D   S      + D  
Sbjct: 16  RNTLTEGEVAHVARELNVKREDVLEMETRMSGGDVALEP--QSDDDGESFAPIAYLADDS 73

Query: 210 GQEQVLIEK 218
            +   +IE 
Sbjct: 74  QEPTRVIEA 82


>gi|257051067|sp|Q8NF91|SYNE1_HUMAN RecName: Full=Nesprin-1; AltName: Full=Enaptin; AltName: Full=Myocyte
            nuclear envelope protein 1; Short=Myne-1; AltName:
            Full=Nuclear envelope spectrin repeat protein 1; AltName:
            Full=Synaptic nuclear envelope protein 1; Short=Syne-1
          Length = 8797

 Score = 36.3 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 26/120 (21%), Positives = 49/120 (40%), Gaps = 5/120 (4%)

Query: 117  ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
            + RSW  +K   +  Q+ L+  L R + +  ++   + K E   AI  KL+ S     S 
Sbjct: 5940 LQRSWETLKNVISEKQRTLYEALERQQKYQDSLQSISTKME---AIELKLSESPEPGRSP 5996

Query: 177  NCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSV 234
              ++A  ++L   I       ++ Q  L  +   +  E    E+   ++   +L   MS 
Sbjct: 5997 ESQMAEHQALMDEILMLQDEINELQSSLAEELVSESCEADPAEQLALQSTLTVLAERMST 6056


>gi|149177642|ref|ZP_01856243.1| probable RNA polymerase sigma factor rfaY [Planctomyces maris DSM
           8797]
 gi|148843460|gb|EDL57822.1| probable RNA polymerase sigma factor rfaY [Planctomyces maris DSM
           8797]
          Length = 187

 Score = 36.3 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 11/60 (18%), Positives = 23/60 (38%), Gaps = 9/60 (15%)

Query: 218 KEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFE-------VSRERVR 270
           ++     R++L   +  L  R RR+   R   +     + ++ E         V+  R+R
Sbjct: 111 QQLMTEERDLLEYCLDQLTERSRRLLGLRYTDDLKP--KQIADELGTSMGSVRVTLSRIR 168


>gi|119568112|gb|EAW47727.1| spectrin repeat containing, nuclear envelope 1, isoform CRA_a [Homo
            sapiens]
          Length = 8757

 Score = 36.3 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 26/120 (21%), Positives = 49/120 (40%), Gaps = 5/120 (4%)

Query: 117  ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
            + RSW  +K   +  Q+ L+  L R + +  ++   + K E   AI  KL+ S     S 
Sbjct: 5900 LQRSWETLKNVISEKQRTLYEALERQQKYQDSLQSISTKME---AIELKLSESPEPGRSP 5956

Query: 177  NCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSV 234
              ++A  ++L   I       ++ Q  L  +   +  E    E+   ++   +L   MS 
Sbjct: 5957 ESQMAEHQALMDEILMLQDEINELQSSLAEELVSESCEADPAEQLALQSTLTVLAERMST 6016


>gi|333026589|ref|ZP_08454653.1| putative RNA polymerase sigma-70 factor, ECF subfamily
           [Streptomyces sp. Tu6071]
 gi|332746441|gb|EGJ76882.1| putative RNA polymerase sigma-70 factor, ECF subfamily
           [Streptomyces sp. Tu6071]
          Length = 399

 Score = 36.3 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 12/91 (13%), Positives = 30/91 (32%), Gaps = 2/91 (2%)

Query: 196 NSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTL 255
            S+      + +         E+    +      + ++ L   +R +   R      +T 
Sbjct: 310 GSTAVPSDEMPERPDDSLGPEERALLSSDAAWAKKLLASLPENQRELLLLRIAVG--LTA 367

Query: 256 ENLSSEFEVSRERVRQIEARAFKKVQESIQK 286
           E       +S   VR  + RA  +++   ++
Sbjct: 368 EETGQMLGMSPGAVRVAQHRALSRLRALAEQ 398


>gi|330688408|ref|NP_892006.3| nesprin-1 isoform 1 [Homo sapiens]
          Length = 8797

 Score = 36.3 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 26/120 (21%), Positives = 49/120 (40%), Gaps = 5/120 (4%)

Query: 117  ILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISM 176
            + RSW  +K   +  Q+ L+  L R + +  ++   + K E   AI  KL+ S     S 
Sbjct: 5940 LQRSWETLKNVISEKQRTLYEALERQQKYQDSLQSISTKME---AIELKLSESPEPGRSP 5996

Query: 177  NCRLAGDESLNALINSSDKNSSQWQDWLVYD--HDGQEQVLIEKEERKNRRNMLTRSMSV 234
              ++A  ++L   I       ++ Q  L  +   +  E    E+   ++   +L   MS 
Sbjct: 5997 ESQMAEHQALMDEILMLQDEINELQSSLAEELVSESCEADPAEQLALQSTLTVLAERMST 6056


>gi|327314397|ref|YP_004329834.1| RNA polymerase sigma-70 factor [Prevotella denticola F0289]
 gi|326944262|gb|AEA20147.1| RNA polymerase sigma-70 factor [Prevotella denticola F0289]
          Length = 174

 Score = 36.3 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 12/72 (16%), Positives = 32/72 (44%), Gaps = 8/72 (11%)

Query: 220 ERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEA---RA 276
           E    R  +  ++S L  + R +F      +     + ++ +  +S   +R +E    +A
Sbjct: 108 EGLEMRRQINDAISELPAKCREVFVLSYQHDRKN--KEIAEQLGIS---IRTVEVHLYKA 162

Query: 277 FKKVQESIQKQV 288
            K +++ ++ +V
Sbjct: 163 LKSLRQKLRHRV 174


>gi|325478347|gb|EGC81463.1| RNA polymerase sigma factor, sigma-70 family [Anaerococcus prevotii
           ACS-065-V-Col13]
          Length = 136

 Score = 36.3 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 19/83 (22%), Positives = 42/83 (50%), Gaps = 6/83 (7%)

Query: 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEV 264
           V + +  E  + +  E K     + R++S LNP ER + E+   +E   T+  ++++  +
Sbjct: 56  VENLEDLEFDVEKIIETKEMIEEVRRAISRLNPAERDLIESLFYKEE--TIREVAAKLNI 113

Query: 265 SRERV--RQIEARAFKKVQESIQ 285
           S   V  R+   +  +K++E ++
Sbjct: 114 SNPAVIKRR--NKVLEKLKEMLE 134


>gi|323701178|ref|ZP_08112853.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
 gi|323533780|gb|EGB23644.1| RNA polymerase, sigma 28 subunit, FliA/WhiG subfamily
           [Desulfotomaculum nigrificans DSM 574]
          Length = 236

 Score = 36.3 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 15/136 (11%), Positives = 41/136 (30%), Gaps = 17/136 (12%)

Query: 41  YREHGDLSAAHRLVTSHLRLV----VKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPE 96
             + GD      L+      +      I            + +S   +   +A+  +  E
Sbjct: 11  LAQQGDDQVREELIYQCKPFIQKVCFHICKR--NLTWENDDELSIALLAFNEAINSYSSE 68

Query: 97  RGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLR-----------RLKGH 145
           +     T++   I   + ++  R      +  ++  +     L            +LK  
Sbjct: 69  KTASFQTFARQIIHQRLVDFFRREGRHQHLPFSSFSEEEETELSLAECSQSLENYKLKTE 128

Query: 146 LQAITDNNLKPEQVVA 161
            + + +  ++ EQ + 
Sbjct: 129 QEELAEMMIEFEQRLQ 144


>gi|317132754|ref|YP_004092068.1| Bacterio-opsin activator HTH domain protein [Ethanoligenens
           harbinense YUAN-3]
 gi|315470733|gb|ADU27337.1| Bacterio-opsin activator HTH domain protein [Ethanoligenens
           harbinense YUAN-3]
          Length = 166

 Score = 36.3 bits (83), Expect = 5.5,   Method: Composition-based stats.
 Identities = 20/83 (24%), Positives = 34/83 (40%), Gaps = 10/83 (12%)

Query: 184 ESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIF 243
            SL+  +   +       D++  D    E+VL EK E     + L   +  L P  +RI 
Sbjct: 72  VSLDDPLPDGEG---TLADYVPDDAPLIEEVLSEKAEL----DQLFERLQELMPEAKRIG 124

Query: 244 EARRLQENPVTLENLSSEFEVSR 266
           E R   E  ++ E ++    + R
Sbjct: 125 ELR---EEGLSDEAIADTIGIKR 144


  Database: nr
    Posted date:  May 22, 2011 12:22 AM
  Number of letters in database: 999,999,966
  Number of sequences in database:  2,987,313
  
  Database: /data/usr2/db/fasta/nr.01
    Posted date:  May 22, 2011 12:30 AM
  Number of letters in database: 999,999,796
  Number of sequences in database:  2,903,041
  
  Database: /data/usr2/db/fasta/nr.02
    Posted date:  May 22, 2011 12:36 AM
  Number of letters in database: 999,999,281
  Number of sequences in database:  2,904,016
  
  Database: /data/usr2/db/fasta/nr.03
    Posted date:  May 22, 2011 12:41 AM
  Number of letters in database: 999,999,960
  Number of sequences in database:  2,935,328
  
  Database: /data/usr2/db/fasta/nr.04
    Posted date:  May 22, 2011 12:46 AM
  Number of letters in database: 842,794,627
  Number of sequences in database:  2,394,679
  
Lambda     K      H
   0.317    0.159    0.462 

Lambda     K      H
   0.267   0.0488    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,952,581,027
Number of Sequences: 14124377
Number of extensions: 298783047
Number of successful extensions: 1267438
Number of sequences better than 10.0: 10000
Number of HSP's better than 10.0 without gapping: 15538
Number of HSP's successfully gapped in prelim test: 8501
Number of HSP's that attempted gapping in prelim test: 1202550
Number of HSP's gapped (non-prelim): 37418
length of query: 302
length of database: 4,842,793,630
effective HSP length: 138
effective length of query: 164
effective length of database: 2,893,629,604
effective search space: 474555255056
effective search space used: 474555255056
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.4 bits)
S2: 81 (35.6 bits)